#assembly ID = 3bdf0edc7985bbabd2a02d1a4028383f
#annotation=76e8fc80a3f3167132a130bb85ed0915
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10362.t1 is derived from g7538.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47382649	47383974	.	+	.	Phchi.S1G752100
Phchi.S1	AUGUSTUS	transcript	47382649	47383957	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	start_codon	47382649	47382651	.	+	0	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47382649	47382729	0.76	+	0	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47382649	47382729	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47382730	47382833	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47382834	47383103	0.93	+	0	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47382834	47383103	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47383104	47383179	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47383180	47383434	1	+	0	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47383180	47383434	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47383435	47383525	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47383526	47383784	1	+	0	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47383526	47383784	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47383785	47383928	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47383929	47383957	1	+	2	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47383929	47383957	.	+	.	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	stop_codon	47383958	47383960	.	+	0	transcript_id "Phchi.S1G752100.t1"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	transcript	47382649	47383974	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	start_codon	47382649	47382651	.	+	0	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47382649	47382729	0.71	+	0	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47382649	47382729	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47382730	47382833	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47382834	47383103	0.89	+	0	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47382834	47383103	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47383104	47383179	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47383180	47383434	1	+	0	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47383180	47383434	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47383435	47383525	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47383526	47383758	0.97	+	0	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47383526	47383758	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	intron	47383759	47383928	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	CDS	47383929	47383974	0.98	+	1	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	exon	47383929	47383974	.	+	.	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
Phchi.S1	AUGUSTUS	stop_codon	47383975	47383977	.	+	0	transcript_id "Phchi.S1G752100.t2"; gene_id "Phchi.S1G752100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15819.t1 is derived from g14289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21550761	21551660	.	+	.	Phchi.S3G313800
Phchi.S3	AUGUSTUS	transcript	21550761	21551660	.	+	.	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	start_codon	21550761	21550763	.	+	0	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	CDS	21550761	21551051	1	+	0	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	exon	21550761	21551051	.	+	.	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	intron	21551052	21551134	.	+	.	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	CDS	21551135	21551407	0.98	+	0	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	exon	21551135	21551407	.	+	.	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	intron	21551408	21551513	.	+	.	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	CDS	21551514	21551660	1	+	0	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	exon	21551514	21551660	.	+	.	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
Phchi.S3	AUGUSTUS	stop_codon	21551661	21551663	.	+	0	transcript_id "Phchi.S3G313800.t1"; gene_id "Phchi.S3G313800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11399.t1 is derived from g15449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6142443	6144063	.	-	.	Phchi.S4G098100
Phchi.S4	AUGUSTUS	transcript	6142443	6144063	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	stop_codon	6142440	6142442	.	-	0	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6142443	6142474	1	-	2	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6142443	6142474	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6142475	6142545	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6142546	6142619	1	-	1	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6142546	6142619	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6142620	6142715	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6142716	6142809	0.51	-	2	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6142716	6142809	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6142810	6142924	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6142925	6143021	1	-	0	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6142925	6143021	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6143022	6143139	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6143140	6143237	1	-	2	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6143140	6143237	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6143238	6143357	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6143358	6143535	1	-	0	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6143358	6143535	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6143536	6143630	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6143631	6143830	0.8	-	2	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6143631	6143830	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	intron	6143831	6143963	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	CDS	6143964	6144063	0.46	-	0	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	exon	6143964	6144063	.	-	.	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
Phchi.S4	AUGUSTUS	start_codon	6144061	6144063	.	-	0	transcript_id "Phchi.S4G098100.t1"; gene_id "Phchi.S4G098100"
# This transcript jg9868.t2 is derived from g7044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9869.t1 is derived from g7045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44160478	44165215	.	-	.	Phchi.S1G702800
Phchi.S1	AUGUSTUS	transcript	44160478	44165215	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	stop_codon	44160475	44160477	.	-	0	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	CDS	44160478	44160760	0.36	-	1	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	exon	44160478	44160760	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	intron	44160761	44160927	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	CDS	44160928	44162063	0.4	-	0	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	exon	44160928	44162063	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	intron	44162064	44162176	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	CDS	44162177	44163555	0.97	-	2	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	exon	44162177	44163555	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	intron	44163556	44163649	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	CDS	44163650	44164478	0.94	-	0	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	exon	44163650	44164478	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	intron	44164479	44164567	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	CDS	44164568	44165215	0.5	-	0	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	exon	44164568	44165215	.	-	.	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
Phchi.S1	AUGUSTUS	start_codon	44165213	44165215	.	-	0	transcript_id "Phchi.S1G702800.t1"; gene_id "Phchi.S1G702800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14440.t1 is derived from g12908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12837925	12838953	.	-	.	Phchi.S3G175900
Phchi.S3	AUGUSTUS	transcript	12837925	12838953	.	-	.	transcript_id "Phchi.S3G175900.t1"; gene_id "Phchi.S3G175900"
Phchi.S3	AUGUSTUS	stop_codon	12837922	12837924	.	-	0	transcript_id "Phchi.S3G175900.t1"; gene_id "Phchi.S3G175900"
Phchi.S3	AUGUSTUS	CDS	12837925	12838953	0.43	-	0	transcript_id "Phchi.S3G175900.t1"; gene_id "Phchi.S3G175900"
Phchi.S3	AUGUSTUS	exon	12837925	12838953	.	-	.	transcript_id "Phchi.S3G175900.t1"; gene_id "Phchi.S3G175900"
Phchi.S3	AUGUSTUS	start_codon	12838951	12838953	.	-	0	transcript_id "Phchi.S3G175900.t1"; gene_id "Phchi.S3G175900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3724.t1 is derived from g893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5405494	5407280	.	-	.	Phchi.S1G088300
Phchi.S1	AUGUSTUS	transcript	5405494	5407280	.	-	.	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	stop_codon	5405491	5405493	.	-	0	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	CDS	5405494	5406330	0.98	-	0	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	exon	5405494	5406330	.	-	.	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	intron	5406331	5406440	.	-	.	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	CDS	5406441	5407280	0.82	-	0	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	exon	5406441	5407280	.	-	.	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
Phchi.S1	AUGUSTUS	start_codon	5407278	5407280	.	-	0	transcript_id "Phchi.S1G088300.t1"; gene_id "Phchi.S1G088300"
# This transcript jg12913.t2 is derived from g11378.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12914.t1 is derived from g11379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3114893	3116015	.	-	.	Phchi.S3G023300
Phchi.S3	AUGUSTUS	transcript	3114893	3116015	.	-	.	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	stop_codon	3114890	3114892	.	-	0	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	CDS	3114893	3115049	0.94	-	1	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	exon	3114893	3115049	.	-	.	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	intron	3115050	3115161	.	-	.	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	CDS	3115162	3116015	0.74	-	0	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	exon	3115162	3116015	.	-	.	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
Phchi.S3	AUGUSTUS	start_codon	3116013	3116015	.	-	0	transcript_id "Phchi.S3G023300.t1"; gene_id "Phchi.S3G023300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9951.t1 is derived from g7127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44635058	44635453	.	-	.	Phchi.S1G711000
Phchi.S1	AUGUSTUS	transcript	44635058	44635453	.	-	.	transcript_id "Phchi.S1G711000.t1"; gene_id "Phchi.S1G711000"
Phchi.S1	AUGUSTUS	stop_codon	44635055	44635057	.	-	0	transcript_id "Phchi.S1G711000.t1"; gene_id "Phchi.S1G711000"
Phchi.S1	AUGUSTUS	CDS	44635058	44635453	0.9	-	0	transcript_id "Phchi.S1G711000.t1"; gene_id "Phchi.S1G711000"
Phchi.S1	AUGUSTUS	exon	44635058	44635453	.	-	.	transcript_id "Phchi.S1G711000.t1"; gene_id "Phchi.S1G711000"
Phchi.S1	AUGUSTUS	start_codon	44635451	44635453	.	-	0	transcript_id "Phchi.S1G711000.t1"; gene_id "Phchi.S1G711000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3648.t1 is derived from g817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4956876	4958321	.	+	.	Phchi.S1G080700
Phchi.S1	AUGUSTUS	transcript	4956876	4958321	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	start_codon	4956876	4956878	.	+	0	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	CDS	4956876	4957053	0.99	+	0	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	exon	4956876	4957053	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	intron	4957054	4957154	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	CDS	4957155	4957391	0.46	+	2	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	exon	4957155	4957391	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	intron	4957392	4957600	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	CDS	4957601	4957713	0.55	+	2	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	exon	4957601	4957713	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	intron	4957714	4957813	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	CDS	4957814	4958038	1	+	0	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	exon	4957814	4958038	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	intron	4958039	4958300	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	CDS	4958301	4958321	1	+	0	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	exon	4958301	4958321	.	+	.	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
Phchi.S1	AUGUSTUS	stop_codon	4958322	4958324	.	+	0	transcript_id "Phchi.S1G080700.t1"; gene_id "Phchi.S1G080700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4416.t1 is derived from g1585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10378846	10379707	.	-	.	Phchi.S1G157500
Phchi.S1	AUGUSTUS	transcript	10378846	10379707	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	stop_codon	10378843	10378845	.	-	0	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	CDS	10378846	10378860	0.95	-	0	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	exon	10378846	10378860	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	intron	10378861	10378992	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	CDS	10378993	10379029	0.94	-	1	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	exon	10378993	10379029	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	intron	10379030	10379110	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	CDS	10379111	10379130	0.94	-	0	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	exon	10379111	10379130	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	intron	10379131	10379220	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	CDS	10379221	10379319	1	-	0	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	exon	10379221	10379319	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	intron	10379320	10379419	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	CDS	10379420	10379520	1	-	2	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	exon	10379420	10379520	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	intron	10379521	10379619	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	CDS	10379620	10379707	1	-	0	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	exon	10379620	10379707	.	-	.	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
Phchi.S1	AUGUSTUS	start_codon	10379705	10379707	.	-	0	transcript_id "Phchi.S1G157500.t1"; gene_id "Phchi.S1G157500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7938.t1 is derived from g5112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32013122	32015744	.	-	.	Phchi.S1G509700
Phchi.S1	AUGUSTUS	transcript	32013122	32015744	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	stop_codon	32013119	32013121	.	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32013122	32013192	1	-	2	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32013122	32013192	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32013193	32013280	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32013281	32013859	0.91	-	2	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32013281	32013859	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32013860	32013965	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32013966	32014035	0.73	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32013966	32014035	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32014036	32014178	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32014179	32014240	1	-	2	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32014179	32014240	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32014241	32014355	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32014356	32014441	0.57	-	1	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32014356	32014441	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32014442	32014570	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32014571	32014610	0.86	-	2	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32014571	32014610	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32014611	32014723	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32014724	32014799	0.45	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32014724	32014799	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32014800	32014903	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32014904	32014984	0.64	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32014904	32014984	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32014985	32015064	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32015065	32015142	0.84	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32015065	32015142	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32015143	32015235	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32015236	32015288	0.5	-	2	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32015236	32015288	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32015289	32015436	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32015437	32015504	0.85	-	1	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32015437	32015504	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	intron	32015505	32015634	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	CDS	32015635	32015744	0.7	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	exon	32015635	32015744	.	-	.	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
Phchi.S1	AUGUSTUS	start_codon	32015742	32015744	.	-	0	transcript_id "Phchi.S1G509700.t1"; gene_id "Phchi.S1G509700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10984.t1 is derived from g15034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3530331	3531104	.	-	.	Phchi.S4G056600
Phchi.S4	AUGUSTUS	transcript	3530331	3531104	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	stop_codon	3530328	3530330	.	-	0	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	CDS	3530331	3530406	1	-	1	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	exon	3530331	3530406	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	intron	3530407	3530501	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	CDS	3530502	3530598	1	-	2	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	exon	3530502	3530598	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	intron	3530599	3530694	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	CDS	3530695	3530755	1	-	0	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	exon	3530695	3530755	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	intron	3530756	3530828	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	CDS	3530829	3531104	0.97	-	0	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	exon	3530829	3531104	.	-	.	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
Phchi.S4	AUGUSTUS	start_codon	3531102	3531104	.	-	0	transcript_id "Phchi.S4G056600.t1"; gene_id "Phchi.S4G056600"
# This transcript jg14278.t2 is derived from g12745.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14279.t1 is derived from g12746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11899483	11900566	.	-	.	Phchi.S3G159800
Phchi.S3	AUGUSTUS	transcript	11899483	11900566	.	-	.	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	stop_codon	11899480	11899482	.	-	0	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	CDS	11899483	11900247	1	-	0	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	exon	11899483	11900247	.	-	.	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	intron	11900248	11900326	.	-	.	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	CDS	11900327	11900566	0.99	-	0	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	exon	11900327	11900566	.	-	.	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
Phchi.S3	AUGUSTUS	start_codon	11900564	11900566	.	-	0	transcript_id "Phchi.S3G159800.t1"; gene_id "Phchi.S3G159800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11005.t1 is derived from g15055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3604156	3606825	.	-	.	Phchi.S4G058700
Phchi.S4	AUGUSTUS	transcript	3604156	3606825	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	stop_codon	3604153	3604155	.	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604156	3604252	1	-	1	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604156	3604252	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604253	3604377	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604378	3604436	1	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604378	3604436	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604437	3604559	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604560	3604661	1	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604560	3604661	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604662	3604788	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604789	3604868	1	-	2	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604789	3604868	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604869	3605017	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605018	3605102	1	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605018	3605102	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605103	3605210	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605211	3605294	0.96	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605211	3605294	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605295	3605370	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605371	3605456	1	-	2	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605371	3605456	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605457	3605570	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605571	3605644	1	-	1	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605571	3605644	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605645	3605765	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605766	3605838	1	-	2	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605766	3605838	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605839	3605993	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605994	3606825	0.79	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605994	3606825	.	-	.	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	start_codon	3606823	3606825	.	-	0	transcript_id "Phchi.S4G058700.t1"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	transcript	3604156	3606825	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	stop_codon	3604153	3604155	.	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604156	3604252	1	-	1	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604156	3604252	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604253	3604377	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604378	3604436	1	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604378	3604436	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604437	3604559	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604560	3604661	1	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604560	3604661	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604662	3604788	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3604789	3604868	1	-	2	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3604789	3604868	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3604869	3605017	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605018	3605102	1	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605018	3605102	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605103	3605210	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605211	3605294	0.98	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605211	3605294	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605295	3605370	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605371	3605456	1	-	2	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605371	3605456	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605457	3605570	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605571	3605644	1	-	1	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605571	3605644	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605645	3605765	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3605766	3605838	1	-	2	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3605766	3605838	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	intron	3605839	3606020	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	CDS	3606021	3606825	0.74	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	exon	3606021	3606825	.	-	.	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
Phchi.S4	AUGUSTUS	start_codon	3606823	3606825	.	-	0	transcript_id "Phchi.S4G058700.t2"; gene_id "Phchi.S4G058700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13395.t1 is derived from g11861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6518788	6519195	.	-	.	Phchi.S3G071400
Phchi.S3	AUGUSTUS	transcript	6518788	6519195	.	-	.	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	stop_codon	6518785	6518787	.	-	0	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	CDS	6518788	6518934	0.99	-	0	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	exon	6518788	6518934	.	-	.	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	intron	6518935	6519014	.	-	.	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	CDS	6519015	6519070	1	-	2	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	exon	6519015	6519070	.	-	.	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	intron	6519071	6519155	.	-	.	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	CDS	6519156	6519195	1	-	0	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	exon	6519156	6519195	.	-	.	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
Phchi.S3	AUGUSTUS	start_codon	6519193	6519195	.	-	0	transcript_id "Phchi.S3G071400.t1"; gene_id "Phchi.S3G071400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13292.t1 is derived from g11758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5225681	5226598	.	-	.	Phchi.S3G061100
Phchi.S3	AUGUSTUS	transcript	5225681	5226598	.	-	.	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	stop_codon	5225678	5225680	.	-	0	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	CDS	5225681	5226232	1	-	0	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	exon	5225681	5226232	.	-	.	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	intron	5226233	5226379	.	-	.	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	CDS	5226380	5226598	0.96	-	0	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	exon	5226380	5226598	.	-	.	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
Phchi.S3	AUGUSTUS	start_codon	5226596	5226598	.	-	0	transcript_id "Phchi.S3G061100.t1"; gene_id "Phchi.S3G061100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15953.t1 is derived from g14449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C99	AUGUSTUS	gene	44816	45019	.	+	.	Phchi.C99G000100
Phchi.C99	AUGUSTUS	transcript	44816	45019	.	+	.	transcript_id "Phchi.C99G000100.t1"; gene_id "Phchi.C99G000100"
Phchi.C99	AUGUSTUS	start_codon	44816	44818	.	+	0	transcript_id "Phchi.C99G000100.t1"; gene_id "Phchi.C99G000100"
Phchi.C99	AUGUSTUS	CDS	44816	45019	0.88	+	0	transcript_id "Phchi.C99G000100.t1"; gene_id "Phchi.C99G000100"
Phchi.C99	AUGUSTUS	exon	44816	45019	.	+	.	transcript_id "Phchi.C99G000100.t1"; gene_id "Phchi.C99G000100"
Phchi.C99	AUGUSTUS	stop_codon	45020	45022	.	+	0	transcript_id "Phchi.C99G000100.t1"; gene_id "Phchi.C99G000100"
# This transcript jg5880.t2 is derived from g3050.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5881.t1 is derived from g3051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19569237	19572574	.	+	.	Phchi.S1G304000
Phchi.S1	AUGUSTUS	transcript	19569237	19572574	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	start_codon	19569237	19569239	.	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19569237	19569360	0.58	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19569237	19569360	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19569361	19569508	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19569509	19569517	0.79	+	2	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19569509	19569517	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19569518	19569663	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19569664	19569785	0.77	+	2	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19569664	19569785	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19569786	19569868	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19569869	19570072	1	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19569869	19570072	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19570073	19570208	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19570209	19570289	1	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19570209	19570289	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19570290	19570388	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19570389	19570475	0.99	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19570389	19570475	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19570476	19570588	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19570589	19570684	1	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19570589	19570684	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19570685	19570772	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19570773	19570826	1	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19570773	19570826	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19570827	19570904	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19570905	19571001	0.98	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19570905	19571001	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19571002	19571072	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19571073	19571997	0.96	+	2	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19571073	19571997	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19571998	19572088	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19572089	19572137	1	+	1	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19572089	19572137	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19572138	19572290	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19572291	19572330	1	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19572291	19572330	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	intron	19572331	19572446	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	CDS	19572447	19572574	0.92	+	2	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	exon	19572447	19572574	.	+	.	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
Phchi.S1	AUGUSTUS	stop_codon	19572575	19572577	.	+	0	transcript_id "Phchi.S1G304000.t1"; gene_id "Phchi.S1G304000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10356.t1 is derived from g7532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47328207	47331072	.	+	.	Phchi.S1G751500
Phchi.S1	AUGUSTUS	transcript	47328207	47331072	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	start_codon	47328207	47328209	.	+	0	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47328207	47328818	0.36	+	0	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47328207	47328818	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47328819	47328901	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47328902	47329051	1	+	0	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47328902	47329051	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47329052	47329201	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47329202	47329472	1	+	0	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47329202	47329472	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47329473	47329731	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47329732	47329842	1	+	2	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47329732	47329842	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47329843	47329938	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47329939	47330095	1	+	2	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47329939	47330095	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47330096	47330242	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47330243	47330500	1	+	1	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47330243	47330500	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47330501	47330589	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47330590	47330712	1	+	1	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47330590	47330712	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47330713	47330829	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47330830	47330906	1	+	1	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47330830	47330906	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	intron	47330907	47331052	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	CDS	47331053	47331072	1	+	2	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	exon	47331053	47331072	.	+	.	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
Phchi.S1	AUGUSTUS	stop_codon	47331073	47331075	.	+	0	transcript_id "Phchi.S1G751500.t1"; gene_id "Phchi.S1G751500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2636.t1 is derived from g9556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7900972	7902741	.	-	.	Phchi.S5G124500
Phchi.S5	AUGUSTUS	transcript	7900972	7902741	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	stop_codon	7900969	7900971	.	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	CDS	7900972	7901187	1	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	exon	7900972	7901187	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	intron	7901188	7901286	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	CDS	7901287	7901499	1	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	exon	7901287	7901499	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	intron	7901500	7901588	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	CDS	7901589	7901759	1	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	exon	7901589	7901759	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	intron	7901760	7901851	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	CDS	7901852	7901968	1	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	exon	7901852	7901968	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	intron	7901969	7902564	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	CDS	7902565	7902741	1	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	exon	7902565	7902741	.	-	.	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
Phchi.S5	AUGUSTUS	start_codon	7902739	7902741	.	-	0	transcript_id "Phchi.S5G124500.t1"; gene_id "Phchi.S5G124500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5322.t1 is derived from g2492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16280555	16281926	.	+	.	Phchi.S1G248100
Phchi.S1	AUGUSTUS	transcript	16280555	16281926	.	+	.	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	start_codon	16280555	16280557	.	+	0	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	CDS	16280555	16280922	0.77	+	0	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	exon	16280555	16280922	.	+	.	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	intron	16280923	16281037	.	+	.	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	CDS	16281038	16281926	0.65	+	1	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	exon	16281038	16281926	.	+	.	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
Phchi.S1	AUGUSTUS	stop_codon	16281927	16281929	.	+	0	transcript_id "Phchi.S1G248100.t1"; gene_id "Phchi.S1G248100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg986.t1 is derived from g10769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6888913	6894599	.	-	.	Phchi.S6G094500
Phchi.S6	AUGUSTUS	transcript	6888913	6894599	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	stop_codon	6888910	6888912	.	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6888913	6889101	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6888913	6889101	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6889102	6889182	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6889183	6889251	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6889183	6889251	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6889252	6889332	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6889333	6889380	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6889333	6889380	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6889381	6889457	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6889458	6889553	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6889458	6889553	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6889554	6889638	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6889639	6889749	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6889639	6889749	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6889750	6889920	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6889921	6890005	1	-	1	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6889921	6890005	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6890006	6890086	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6890087	6890199	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6890087	6890199	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6890200	6890285	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6890286	6890351	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6890286	6890351	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6890352	6890458	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6890459	6890578	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6890459	6890578	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6890579	6890693	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6890694	6890741	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6890694	6890741	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6890742	6890840	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6890841	6890912	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6890841	6890912	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6890913	6890993	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6890994	6891059	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6890994	6891059	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6891060	6891159	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6891160	6891222	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6891160	6891222	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6891223	6891321	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6891322	6891452	1	-	2	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6891322	6891452	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6891453	6891542	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6891543	6891765	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6891543	6891765	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6891766	6891861	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6891862	6891918	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6891862	6891918	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6891919	6892006	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6892007	6892072	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6892007	6892072	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6892073	6892174	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6892175	6892237	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6892175	6892237	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6892238	6892364	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6892365	6892532	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6892365	6892532	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6892533	6892617	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6892618	6892711	1	-	1	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6892618	6892711	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6892712	6892840	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6892841	6892941	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6892841	6892941	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6892942	6893044	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6893045	6893158	0.99	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6893045	6893158	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6893159	6893233	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6893234	6893305	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6893234	6893305	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6893306	6893414	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6893415	6893498	0.99	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6893415	6893498	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6893499	6893571	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6893572	6893691	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6893572	6893691	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6893692	6893777	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6893778	6893952	1	-	1	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6893778	6893952	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6893953	6894039	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6894040	6894128	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6894040	6894128	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6894129	6894218	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6894219	6894302	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6894219	6894302	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	intron	6894303	6894392	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	CDS	6894393	6894599	1	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	exon	6894393	6894599	.	-	.	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
Phchi.S6	AUGUSTUS	start_codon	6894597	6894599	.	-	0	transcript_id "Phchi.S6G094500.t1"; gene_id "Phchi.S6G094500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2128.t1 is derived from g9048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4981783	4982175	.	-	.	Phchi.S5G073700
Phchi.S5	AUGUSTUS	transcript	4981783	4982175	.	-	.	transcript_id "Phchi.S5G073700.t1"; gene_id "Phchi.S5G073700"
Phchi.S5	AUGUSTUS	stop_codon	4981780	4981782	.	-	0	transcript_id "Phchi.S5G073700.t1"; gene_id "Phchi.S5G073700"
Phchi.S5	AUGUSTUS	CDS	4981783	4982175	0.99	-	0	transcript_id "Phchi.S5G073700.t1"; gene_id "Phchi.S5G073700"
Phchi.S5	AUGUSTUS	exon	4981783	4982175	.	-	.	transcript_id "Phchi.S5G073700.t1"; gene_id "Phchi.S5G073700"
Phchi.S5	AUGUSTUS	start_codon	4982173	4982175	.	-	0	transcript_id "Phchi.S5G073700.t1"; gene_id "Phchi.S5G073700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4751.t1 is derived from g1921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12620968	12622348	.	-	.	Phchi.S1G191000
Phchi.S1	AUGUSTUS	transcript	12620968	12622348	.	-	.	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	stop_codon	12620965	12620967	.	-	0	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	CDS	12620968	12621750	0.98	-	0	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	exon	12620968	12621750	.	-	.	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	intron	12621751	12621840	.	-	.	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	CDS	12621841	12622062	0.89	-	0	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	exon	12621841	12622062	.	-	.	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	intron	12622063	12622183	.	-	.	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	CDS	12622184	12622348	0.99	-	0	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	exon	12622184	12622348	.	-	.	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
Phchi.S1	AUGUSTUS	start_codon	12622346	12622348	.	-	0	transcript_id "Phchi.S1G191000.t1"; gene_id "Phchi.S1G191000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7756.t1 is derived from g4930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31152480	31152949	.	+	.	Phchi.S1G491500
Phchi.S1	AUGUSTUS	transcript	31152480	31152949	.	+	.	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	start_codon	31152480	31152482	.	+	0	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	CDS	31152480	31152689	0.64	+	0	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	exon	31152480	31152689	.	+	.	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	intron	31152690	31152808	.	+	.	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	CDS	31152809	31152949	0.55	+	0	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	exon	31152809	31152949	.	+	.	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
Phchi.S1	AUGUSTUS	stop_codon	31152950	31152952	.	+	0	transcript_id "Phchi.S1G491500.t1"; gene_id "Phchi.S1G491500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6817.t1 is derived from g3989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25187461	25189239	.	-	.	Phchi.S1G397600
Phchi.S1	AUGUSTUS	transcript	25187461	25189239	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	stop_codon	25187458	25187460	.	-	0	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	CDS	25187461	25187683	0.93	-	1	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	exon	25187461	25187683	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	intron	25187684	25187774	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	CDS	25187775	25187870	1	-	1	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	exon	25187775	25187870	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	intron	25187871	25187958	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	CDS	25187959	25188083	1	-	0	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	exon	25187959	25188083	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	intron	25188084	25188183	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	CDS	25188184	25188336	1	-	0	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	exon	25188184	25188336	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	intron	25188337	25188465	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	CDS	25188466	25188795	0.99	-	0	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	exon	25188466	25188795	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	intron	25188796	25188894	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	CDS	25188895	25189239	1	-	0	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	exon	25188895	25189239	.	-	.	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
Phchi.S1	AUGUSTUS	start_codon	25189237	25189239	.	-	0	transcript_id "Phchi.S1G397600.t1"; gene_id "Phchi.S1G397600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13748.t1 is derived from g12215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8682678	8684078	.	-	.	Phchi.S3G106700
Phchi.S3	AUGUSTUS	transcript	8682678	8684078	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	stop_codon	8682675	8682677	.	-	0	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	CDS	8682678	8682888	1	-	1	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	exon	8682678	8682888	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	intron	8682889	8682992	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	CDS	8682993	8683054	1	-	0	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	exon	8682993	8683054	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	intron	8683055	8683154	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	CDS	8683155	8683265	0.98	-	0	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	exon	8683155	8683265	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	intron	8683266	8683450	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	CDS	8683451	8683675	0.98	-	0	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	exon	8683451	8683675	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	intron	8683676	8683850	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	CDS	8683851	8684078	0.63	-	0	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	exon	8683851	8684078	.	-	.	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
Phchi.S3	AUGUSTUS	start_codon	8684076	8684078	.	-	0	transcript_id "Phchi.S3G106700.t1"; gene_id "Phchi.S3G106700"
# This transcript jg12518.t2 is derived from g8195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12519.t1 is derived from g8196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32803748	32804425	.	-	.	Phchi.S2G059900
Phchi.S2	AUGUSTUS	transcript	32803748	32804425	.	-	.	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	stop_codon	32803745	32803747	.	-	0	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	CDS	32803748	32803873	0.89	-	0	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	exon	32803748	32803873	.	-	.	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	intron	32803874	32803951	.	-	.	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	CDS	32803952	32804019	0.91	-	2	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	exon	32803952	32804019	.	-	.	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	intron	32804020	32804193	.	-	.	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	CDS	32804194	32804425	1	-	0	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	exon	32804194	32804425	.	-	.	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
Phchi.S2	AUGUSTUS	start_codon	32804423	32804425	.	-	0	transcript_id "Phchi.S2G059900.t1"; gene_id "Phchi.S2G059900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4810.t1 is derived from g1980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12930578	12935157	.	+	.	Phchi.S1G196900
Phchi.S1	AUGUSTUS	transcript	12930578	12935157	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	start_codon	12930578	12930580	.	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12930578	12931266	1	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12930578	12931266	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12931267	12931855	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12931856	12933725	0.99	+	1	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12931856	12933725	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12933726	12933842	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12933843	12933975	1	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12933843	12933975	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12933976	12934184	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12934185	12934282	1	+	2	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12934185	12934282	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12934283	12934434	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12934435	12934500	1	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12934435	12934500	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12934501	12934598	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12934599	12934688	1	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12934599	12934688	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12934689	12934843	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12934844	12935020	0.96	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12934844	12935020	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	intron	12935021	12935121	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	CDS	12935122	12935157	0.93	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	exon	12935122	12935157	.	+	.	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
Phchi.S1	AUGUSTUS	stop_codon	12935158	12935160	.	+	0	transcript_id "Phchi.S1G196900.t1"; gene_id "Phchi.S1G196900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7258.t1 is derived from g4430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27891689	27894724	.	+	.	Phchi.S1G441700
Phchi.S1	AUGUSTUS	transcript	27891689	27894724	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	start_codon	27891689	27891691	.	+	0	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	CDS	27891689	27891745	0.42	+	0	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	exon	27891689	27891745	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	intron	27891746	27892053	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	CDS	27892054	27892935	0.32	+	0	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	exon	27892054	27892935	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	intron	27892936	27893081	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	CDS	27893082	27893667	0.46	+	0	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	exon	27893082	27893667	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	intron	27893668	27893813	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	CDS	27893814	27894724	0.4	+	2	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	exon	27893814	27894724	.	+	.	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
Phchi.S1	AUGUSTUS	stop_codon	27894725	27894727	.	+	0	transcript_id "Phchi.S1G441700.t1"; gene_id "Phchi.S1G441700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15609.t1 is derived from g14078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20257008	20259003	.	-	.	Phchi.S3G292800
Phchi.S3	AUGUSTUS	transcript	20257008	20259003	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	stop_codon	20257005	20257007	.	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20257008	20257073	0.98	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20257008	20257073	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20257074	20257161	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20257162	20257243	1	-	1	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20257162	20257243	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20257244	20257412	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20257413	20257520	1	-	1	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20257413	20257520	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20257521	20257627	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20257628	20257725	1	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20257628	20257725	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20257726	20257818	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20257819	20257917	1	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20257819	20257917	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20257918	20258039	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20258040	20258177	1	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20258040	20258177	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20258178	20258306	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20258307	20258358	1	-	1	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20258307	20258358	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20258359	20258451	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20258452	20258565	0.98	-	1	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20258452	20258565	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20258566	20258668	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20258669	20258746	0.81	-	1	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20258669	20258746	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	intron	20258747	20258947	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	CDS	20258948	20259003	0.55	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	exon	20258948	20259003	.	-	.	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
Phchi.S3	AUGUSTUS	start_codon	20259001	20259003	.	-	0	transcript_id "Phchi.S3G292800.t1"; gene_id "Phchi.S3G292800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15502.t1 is derived from g13971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19561535	19562878	.	+	.	Phchi.S3G282100
Phchi.S3	AUGUSTUS	transcript	19561535	19562878	.	+	.	transcript_id "Phchi.S3G282100.t1"; gene_id "Phchi.S3G282100"
Phchi.S3	AUGUSTUS	start_codon	19561535	19561537	.	+	0	transcript_id "Phchi.S3G282100.t1"; gene_id "Phchi.S3G282100"
Phchi.S3	AUGUSTUS	CDS	19561535	19562878	0.99	+	0	transcript_id "Phchi.S3G282100.t1"; gene_id "Phchi.S3G282100"
Phchi.S3	AUGUSTUS	exon	19561535	19562878	.	+	.	transcript_id "Phchi.S3G282100.t1"; gene_id "Phchi.S3G282100"
Phchi.S3	AUGUSTUS	stop_codon	19562879	19562881	.	+	0	transcript_id "Phchi.S3G282100.t1"; gene_id "Phchi.S3G282100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2431.t1 is derived from g9351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6618257	6618862	.	-	.	Phchi.S5G104000
Phchi.S5	AUGUSTUS	transcript	6618257	6618862	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	stop_codon	6618254	6618256	.	-	0	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	CDS	6618257	6618325	1	-	0	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	exon	6618257	6618325	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	intron	6618326	6618445	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	CDS	6618446	6618569	0.98	-	1	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	exon	6618446	6618569	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	intron	6618570	6618674	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	CDS	6618675	6618760	0.86	-	0	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	exon	6618675	6618760	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	intron	6618761	6618856	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	CDS	6618857	6618862	1	-	0	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	exon	6618857	6618862	.	-	.	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
Phchi.S5	AUGUSTUS	start_codon	6618860	6618862	.	-	0	transcript_id "Phchi.S5G104000.t1"; gene_id "Phchi.S5G104000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3984.t1 is derived from g1153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6870916	6872889	.	-	.	Phchi.S1G114300
Phchi.S1	AUGUSTUS	transcript	6870916	6872889	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	stop_codon	6870913	6870915	.	-	0	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	CDS	6870916	6871085	0.86	-	2	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	exon	6870916	6871085	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	intron	6871086	6871183	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	CDS	6871184	6871367	1	-	0	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	exon	6871184	6871367	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	intron	6871368	6871508	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	CDS	6871509	6871841	1	-	0	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	exon	6871509	6871841	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	intron	6871842	6872011	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	CDS	6872012	6872149	1	-	0	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	exon	6872012	6872149	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	intron	6872150	6872405	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	CDS	6872406	6872535	1	-	1	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	exon	6872406	6872535	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	intron	6872536	6872782	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	CDS	6872783	6872889	1	-	0	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	exon	6872783	6872889	.	-	.	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
Phchi.S1	AUGUSTUS	start_codon	6872887	6872889	.	-	0	transcript_id "Phchi.S1G114300.t1"; gene_id "Phchi.S1G114300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14455.t1 is derived from g12923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12943873	12944547	.	+	.	Phchi.S3G177400
Phchi.S3	AUGUSTUS	transcript	12943873	12944547	.	+	.	transcript_id "Phchi.S3G177400.t1"; gene_id "Phchi.S3G177400"
Phchi.S3	AUGUSTUS	start_codon	12943873	12943875	.	+	0	transcript_id "Phchi.S3G177400.t1"; gene_id "Phchi.S3G177400"
Phchi.S3	AUGUSTUS	CDS	12943873	12944547	0.43	+	0	transcript_id "Phchi.S3G177400.t1"; gene_id "Phchi.S3G177400"
Phchi.S3	AUGUSTUS	exon	12943873	12944547	.	+	.	transcript_id "Phchi.S3G177400.t1"; gene_id "Phchi.S3G177400"
Phchi.S3	AUGUSTUS	stop_codon	12944548	12944550	.	+	0	transcript_id "Phchi.S3G177400.t1"; gene_id "Phchi.S3G177400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3971.t1 is derived from g1140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6798153	6801135	.	+	.	Phchi.S1G113000
Phchi.S1	AUGUSTUS	transcript	6798153	6801135	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	start_codon	6798153	6798155	.	+	0	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6798153	6798702	0.27	+	0	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6798153	6798702	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6798703	6798836	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6798837	6799629	0.46	+	2	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6798837	6799629	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6799630	6799726	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6799727	6799850	0.58	+	1	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6799727	6799850	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6799851	6800008	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6800009	6800116	0.66	+	0	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6800009	6800116	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6800117	6800338	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6800339	6800368	0.62	+	0	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6800339	6800368	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6800369	6800472	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6800473	6800489	0.66	+	0	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6800473	6800489	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6800490	6800725	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6800726	6800791	0.69	+	1	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6800726	6800791	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	intron	6800792	6800978	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	CDS	6800979	6801135	0.4	+	1	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	exon	6800979	6801135	.	+	.	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
Phchi.S1	AUGUSTUS	stop_codon	6801136	6801138	.	+	0	transcript_id "Phchi.S1G113000.t1"; gene_id "Phchi.S1G113000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5350.t1 is derived from g2520.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16428861	16430673	.	+	.	Phchi.S1G250900
Phchi.S1	AUGUSTUS	transcript	16428861	16430160	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	start_codon	16428861	16428863	.	+	0	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16428861	16429159	0.64	+	0	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16428861	16429159	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429160	16429292	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429293	16429382	0.66	+	1	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429293	16429382	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429383	16429458	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429459	16429555	1	+	1	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429459	16429555	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429556	16429641	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429642	16429780	1	+	0	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429642	16429780	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429781	16429900	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429901	16429983	1	+	2	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429901	16429983	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429984	16430157	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430158	16430160	1	+	0	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430158	16430160	.	+	.	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	stop_codon	16430161	16430163	.	+	0	transcript_id "Phchi.S1G250900.t1"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	transcript	16428861	16430673	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	start_codon	16428861	16428863	.	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16428861	16429159	0.52	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16428861	16429159	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429160	16429292	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429293	16429382	0.57	+	1	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429293	16429382	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429383	16429458	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429459	16429555	1	+	1	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429459	16429555	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429556	16429641	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429642	16429780	1	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429642	16429780	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429781	16429900	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16429901	16429983	1	+	2	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16429901	16429983	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16429984	16430137	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430138	16430272	1	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430138	16430272	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16430273	16430347	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430348	16430452	0.57	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430348	16430452	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16430453	16430553	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430554	16430673	0.97	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430554	16430673	.	+	.	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	stop_codon	16430674	16430676	.	+	0	transcript_id "Phchi.S1G250900.t2"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	transcript	16430207	16430673	.	+	.	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	start_codon	16430207	16430209	.	+	0	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430207	16430272	1	+	0	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430207	16430272	.	+	.	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16430273	16430347	.	+	.	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430348	16430452	0.58	+	0	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430348	16430452	.	+	.	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	intron	16430453	16430553	.	+	.	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	CDS	16430554	16430673	0.98	+	0	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	exon	16430554	16430673	.	+	.	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
Phchi.S1	AUGUSTUS	stop_codon	16430674	16430676	.	+	0	transcript_id "Phchi.S1G250900.t3"; gene_id "Phchi.S1G250900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9421.t1 is derived from g6597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41404855	41405625	.	-	.	Phchi.S1G658000
Phchi.S1	AUGUSTUS	transcript	41404855	41405544	.	-	.	transcript_id "Phchi.S1G658000.t1"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	stop_codon	41404852	41404854	.	-	0	transcript_id "Phchi.S1G658000.t1"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	CDS	41404855	41405544	1	-	0	transcript_id "Phchi.S1G658000.t1"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	exon	41404855	41405544	.	-	.	transcript_id "Phchi.S1G658000.t1"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	start_codon	41405542	41405544	.	-	0	transcript_id "Phchi.S1G658000.t1"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	transcript	41404855	41405625	.	-	.	transcript_id "Phchi.S1G658000.t2"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	stop_codon	41404852	41404854	.	-	0	transcript_id "Phchi.S1G658000.t2"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	CDS	41404855	41405625	1	-	0	transcript_id "Phchi.S1G658000.t2"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	exon	41404855	41405625	.	-	.	transcript_id "Phchi.S1G658000.t2"; gene_id "Phchi.S1G658000"
Phchi.S1	AUGUSTUS	start_codon	41405623	41405625	.	-	0	transcript_id "Phchi.S1G658000.t2"; gene_id "Phchi.S1G658000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg847.t1 is derived from g10629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5888946	5889593	.	-	.	Phchi.S6G080600
Phchi.S6	AUGUSTUS	transcript	5888946	5889593	.	-	.	transcript_id "Phchi.S6G080600.t1"; gene_id "Phchi.S6G080600"
Phchi.S6	AUGUSTUS	stop_codon	5888943	5888945	.	-	0	transcript_id "Phchi.S6G080600.t1"; gene_id "Phchi.S6G080600"
Phchi.S6	AUGUSTUS	CDS	5888946	5889593	0.97	-	0	transcript_id "Phchi.S6G080600.t1"; gene_id "Phchi.S6G080600"
Phchi.S6	AUGUSTUS	exon	5888946	5889593	.	-	.	transcript_id "Phchi.S6G080600.t1"; gene_id "Phchi.S6G080600"
Phchi.S6	AUGUSTUS	start_codon	5889591	5889593	.	-	0	transcript_id "Phchi.S6G080600.t1"; gene_id "Phchi.S6G080600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8103.t1 is derived from g5278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33060425	33060881	.	+	.	Phchi.S1G526200
Phchi.S1	AUGUSTUS	transcript	33060425	33060881	.	+	.	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	start_codon	33060425	33060427	.	+	0	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	CDS	33060425	33060516	0.85	+	0	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	exon	33060425	33060516	.	+	.	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	intron	33060517	33060593	.	+	.	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	CDS	33060594	33060702	1	+	1	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	exon	33060594	33060702	.	+	.	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	intron	33060703	33060797	.	+	.	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	CDS	33060798	33060881	1	+	0	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	exon	33060798	33060881	.	+	.	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
Phchi.S1	AUGUSTUS	stop_codon	33060882	33060884	.	+	0	transcript_id "Phchi.S1G526200.t1"; gene_id "Phchi.S1G526200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10453.t1 is derived from g14502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	404784	406271	.	-	.	Phchi.S4G003500
Phchi.S4	AUGUSTUS	transcript	404784	406271	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	stop_codon	404781	404783	.	-	0	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	CDS	404784	404851	0.93	-	2	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	exon	404784	404851	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	intron	404852	404954	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	CDS	404955	405216	1	-	0	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	exon	404955	405216	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	intron	405217	405321	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	CDS	405322	405418	1	-	1	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	exon	405322	405418	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	intron	405419	405506	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	CDS	405507	405679	1	-	0	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	exon	405507	405679	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	intron	405680	405766	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	CDS	405767	405970	1	-	0	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	exon	405767	405970	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	intron	405971	406058	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	CDS	406059	406271	0.94	-	0	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	exon	406059	406271	.	-	.	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
Phchi.S4	AUGUSTUS	start_codon	406269	406271	.	-	0	transcript_id "Phchi.S4G003500.t1"; gene_id "Phchi.S4G003500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3272.t1 is derived from g441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2640469	2642148	.	+	.	Phchi.S1G043100
Phchi.S1	AUGUSTUS	transcript	2640469	2642148	.	+	.	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	start_codon	2640469	2640471	.	+	0	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	CDS	2640469	2640796	1	+	0	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	exon	2640469	2640796	.	+	.	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	intron	2640797	2640886	.	+	.	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	CDS	2640887	2641464	0.71	+	2	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	exon	2640887	2641464	.	+	.	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	intron	2641465	2641566	.	+	.	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	CDS	2641567	2642148	0.98	+	0	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	exon	2641567	2642148	.	+	.	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
Phchi.S1	AUGUSTUS	stop_codon	2642149	2642151	.	+	0	transcript_id "Phchi.S1G043100.t1"; gene_id "Phchi.S1G043100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1282.t1 is derived from g11065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8800377	8801247	.	+	.	Phchi.S6G124100
Phchi.S6	AUGUSTUS	transcript	8800377	8801247	.	+	.	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	start_codon	8800377	8800379	.	+	0	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	CDS	8800377	8800699	0.75	+	0	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	exon	8800377	8800699	.	+	.	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	intron	8800700	8800778	.	+	.	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	CDS	8800779	8800813	0.84	+	1	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	exon	8800779	8800813	.	+	.	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	intron	8800814	8800903	.	+	.	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	CDS	8800904	8801247	0.54	+	2	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	exon	8800904	8801247	.	+	.	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
Phchi.S6	AUGUSTUS	stop_codon	8801248	8801250	.	+	0	transcript_id "Phchi.S6G124100.t1"; gene_id "Phchi.S6G124100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3662.t1 is derived from g831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5036727	5037461	.	-	.	Phchi.S1G082100
Phchi.S1	AUGUSTUS	transcript	5036727	5037461	.	-	.	transcript_id "Phchi.S1G082100.t1"; gene_id "Phchi.S1G082100"
Phchi.S1	AUGUSTUS	stop_codon	5036724	5036726	.	-	0	transcript_id "Phchi.S1G082100.t1"; gene_id "Phchi.S1G082100"
Phchi.S1	AUGUSTUS	CDS	5036727	5037461	1	-	0	transcript_id "Phchi.S1G082100.t1"; gene_id "Phchi.S1G082100"
Phchi.S1	AUGUSTUS	exon	5036727	5037461	.	-	.	transcript_id "Phchi.S1G082100.t1"; gene_id "Phchi.S1G082100"
Phchi.S1	AUGUSTUS	start_codon	5037459	5037461	.	-	0	transcript_id "Phchi.S1G082100.t1"; gene_id "Phchi.S1G082100"
# This transcript jg12479.t2 is derived from g8156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12479.t3 is derived from g8156.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12480.t1 is derived from g8157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28341643	28341882	.	-	.	Phchi.S2G056000
Phchi.S2	AUGUSTUS	transcript	28341643	28341882	.	-	.	transcript_id "Phchi.S2G056000.t1"; gene_id "Phchi.S2G056000"
Phchi.S2	AUGUSTUS	stop_codon	28341640	28341642	.	-	0	transcript_id "Phchi.S2G056000.t1"; gene_id "Phchi.S2G056000"
Phchi.S2	AUGUSTUS	CDS	28341643	28341882	0.57	-	0	transcript_id "Phchi.S2G056000.t1"; gene_id "Phchi.S2G056000"
Phchi.S2	AUGUSTUS	exon	28341643	28341882	.	-	.	transcript_id "Phchi.S2G056000.t1"; gene_id "Phchi.S2G056000"
Phchi.S2	AUGUSTUS	start_codon	28341880	28341882	.	-	0	transcript_id "Phchi.S2G056000.t1"; gene_id "Phchi.S2G056000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15922.t1 is derived from g14392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22242112	22243288	.	+	.	Phchi.S3G324100
Phchi.S3	AUGUSTUS	transcript	22242112	22243288	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	start_codon	22242112	22242114	.	+	0	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	CDS	22242112	22242201	0.85	+	0	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	exon	22242112	22242201	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	intron	22242202	22242279	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	CDS	22242280	22242416	1	+	0	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	exon	22242280	22242416	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	intron	22242417	22242499	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	CDS	22242500	22242629	1	+	1	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	exon	22242500	22242629	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	intron	22242630	22242744	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	CDS	22242745	22242936	1	+	0	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	exon	22242745	22242936	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	intron	22242937	22243027	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	CDS	22243028	22243288	1	+	0	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	exon	22243028	22243288	.	+	.	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
Phchi.S3	AUGUSTUS	stop_codon	22243289	22243291	.	+	0	transcript_id "Phchi.S3G324100.t1"; gene_id "Phchi.S3G324100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2467.t1 is derived from g9387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6807316	6810557	.	+	.	Phchi.S5G107600
Phchi.S5	AUGUSTUS	transcript	6807316	6810557	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	start_codon	6807316	6807318	.	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6807316	6807372	1	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6807316	6807372	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6807373	6807634	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6807635	6807908	0.99	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6807635	6807908	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6807909	6808033	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6808034	6808306	0.69	+	2	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6808034	6808306	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6808307	6808582	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6808583	6808789	0.46	+	2	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6808583	6808789	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6808790	6808923	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6808924	6808991	0.97	+	2	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6808924	6808991	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6808992	6809095	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809096	6809347	0.71	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809096	6809347	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809348	6809424	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809425	6809500	1	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809425	6809500	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809501	6809576	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809577	6809653	1	+	2	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809577	6809653	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809654	6809775	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809776	6809825	1	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809776	6809825	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809826	6809969	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809970	6810054	1	+	1	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809970	6810054	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6810055	6810144	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6810145	6810243	1	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6810145	6810243	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6810244	6810332	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6810333	6810557	0.95	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6810333	6810557	.	+	.	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	stop_codon	6810558	6810560	.	+	0	transcript_id "Phchi.S5G107600.t1"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	transcript	6807316	6810557	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	start_codon	6807316	6807318	.	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6807316	6807372	0.99	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6807316	6807372	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6807373	6807634	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6807635	6807908	1	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6807635	6807908	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6807909	6808033	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6808034	6808306	0.74	+	2	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6808034	6808306	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6808307	6808582	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6808583	6808789	0.46	+	2	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6808583	6808789	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6808790	6808923	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6808924	6808991	0.99	+	2	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6808924	6808991	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6808992	6809084	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809085	6809106	0.48	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809085	6809106	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809107	6809213	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809214	6809347	0.52	+	2	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809214	6809347	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809348	6809424	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809425	6809500	1	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809425	6809500	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809501	6809576	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809577	6809653	1	+	2	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809577	6809653	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809654	6809775	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809776	6809825	1	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809776	6809825	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6809826	6809969	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6809970	6810054	1	+	1	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6809970	6810054	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6810055	6810144	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6810145	6810243	1	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6810145	6810243	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	intron	6810244	6810332	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	CDS	6810333	6810557	0.97	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	exon	6810333	6810557	.	+	.	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
Phchi.S5	AUGUSTUS	stop_codon	6810558	6810560	.	+	0	transcript_id "Phchi.S5G107600.t2"; gene_id "Phchi.S5G107600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1192.t1 is derived from g10975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8358083	8360065	.	-	.	Phchi.S6G115100
Phchi.S6	AUGUSTUS	transcript	8358083	8360065	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	stop_codon	8358080	8358082	.	-	0	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	CDS	8358083	8358229	0.77	-	0	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	exon	8358083	8358229	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	intron	8358230	8358365	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	CDS	8358366	8358797	0.92	-	0	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	exon	8358366	8358797	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	intron	8358798	8358906	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	CDS	8358907	8358984	0.88	-	0	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	exon	8358907	8358984	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	intron	8358985	8359090	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	CDS	8359091	8359172	0.37	-	1	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	exon	8359091	8359172	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	intron	8359173	8359383	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	CDS	8359384	8359719	0.33	-	1	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	exon	8359384	8359719	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	intron	8359720	8359811	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	CDS	8359812	8360065	0.78	-	0	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	exon	8359812	8360065	.	-	.	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
Phchi.S6	AUGUSTUS	start_codon	8360063	8360065	.	-	0	transcript_id "Phchi.S6G115100.t1"; gene_id "Phchi.S6G115100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9699.t1 is derived from g6875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43327298	43330812	.	+	.	Phchi.S1G685800
Phchi.S1	AUGUSTUS	transcript	43327298	43330812	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	start_codon	43327298	43327300	.	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43327298	43327737	0.25	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43327298	43327737	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43327738	43328125	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328126	43328183	0.47	+	1	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328126	43328183	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328184	43328280	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328281	43328431	0.82	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328281	43328431	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328432	43328502	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328503	43328561	0.9	+	2	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328503	43328561	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328562	43328669	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328670	43328799	0.89	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328670	43328799	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328800	43328902	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328903	43328970	0.99	+	2	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328903	43328970	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328971	43329109	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329110	43329326	1	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329110	43329326	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329327	43329446	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329447	43329566	0.99	+	2	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329447	43329566	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329567	43329678	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329679	43329791	1	+	2	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329679	43329791	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329792	43329913	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329914	43329979	1	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329914	43329979	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329980	43330109	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330110	43330200	1	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330110	43330200	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43330201	43330292	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330293	43330360	1	+	2	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330293	43330360	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43330361	43330485	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330486	43330523	1	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330486	43330523	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43330524	43330637	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330638	43330812	0.99	+	1	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330638	43330812	.	+	.	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	stop_codon	43330813	43330815	.	+	0	transcript_id "Phchi.S1G685800.t1"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	transcript	43327298	43330812	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	start_codon	43327298	43327300	.	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43327298	43327737	0.22	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43327298	43327737	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43327738	43328125	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328126	43328183	0.45	+	1	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328126	43328183	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328184	43328280	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328281	43328425	0.82	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328281	43328425	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328426	43328502	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328503	43328561	0.92	+	2	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328503	43328561	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328562	43328669	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328670	43328799	0.9	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328670	43328799	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328800	43328902	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43328903	43328970	0.98	+	2	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43328903	43328970	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43328971	43329109	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329110	43329326	1	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329110	43329326	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329327	43329446	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329447	43329566	0.99	+	2	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329447	43329566	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329567	43329678	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329679	43329791	1	+	2	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329679	43329791	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329792	43329913	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43329914	43329979	1	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43329914	43329979	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43329980	43330109	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330110	43330200	1	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330110	43330200	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43330201	43330292	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330293	43330360	1	+	2	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330293	43330360	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43330361	43330485	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330486	43330523	0.99	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330486	43330523	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	intron	43330524	43330637	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	CDS	43330638	43330812	0.97	+	1	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	exon	43330638	43330812	.	+	.	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
Phchi.S1	AUGUSTUS	stop_codon	43330813	43330815	.	+	0	transcript_id "Phchi.S1G685800.t2"; gene_id "Phchi.S1G685800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7440.t1 is derived from g4612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29127467	29127874	.	-	.	Phchi.S1G459900
Phchi.S1	AUGUSTUS	transcript	29127467	29127874	.	-	.	transcript_id "Phchi.S1G459900.t1"; gene_id "Phchi.S1G459900"
Phchi.S1	AUGUSTUS	stop_codon	29127464	29127466	.	-	0	transcript_id "Phchi.S1G459900.t1"; gene_id "Phchi.S1G459900"
Phchi.S1	AUGUSTUS	CDS	29127467	29127874	0.89	-	0	transcript_id "Phchi.S1G459900.t1"; gene_id "Phchi.S1G459900"
Phchi.S1	AUGUSTUS	exon	29127467	29127874	.	-	.	transcript_id "Phchi.S1G459900.t1"; gene_id "Phchi.S1G459900"
Phchi.S1	AUGUSTUS	start_codon	29127872	29127874	.	-	0	transcript_id "Phchi.S1G459900.t1"; gene_id "Phchi.S1G459900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3597.t1 is derived from g766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4667138	4668499	.	-	.	Phchi.S1G075600
Phchi.S1	AUGUSTUS	transcript	4667138	4668499	.	-	.	transcript_id "Phchi.S1G075600.t1"; gene_id "Phchi.S1G075600"
Phchi.S1	AUGUSTUS	stop_codon	4667135	4667137	.	-	0	transcript_id "Phchi.S1G075600.t1"; gene_id "Phchi.S1G075600"
Phchi.S1	AUGUSTUS	CDS	4667138	4668499	0.79	-	0	transcript_id "Phchi.S1G075600.t1"; gene_id "Phchi.S1G075600"
Phchi.S1	AUGUSTUS	exon	4667138	4668499	.	-	.	transcript_id "Phchi.S1G075600.t1"; gene_id "Phchi.S1G075600"
Phchi.S1	AUGUSTUS	start_codon	4668497	4668499	.	-	0	transcript_id "Phchi.S1G075600.t1"; gene_id "Phchi.S1G075600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8941.t1 is derived from g6116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38770801	38771717	.	+	.	Phchi.S1G610000
Phchi.S1	AUGUSTUS	transcript	38770801	38771717	.	+	.	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	start_codon	38770801	38770803	.	+	0	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	CDS	38770801	38771070	0.35	+	0	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	exon	38770801	38771070	.	+	.	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	intron	38771071	38771181	.	+	.	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	CDS	38771182	38771270	1	+	0	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	exon	38771182	38771270	.	+	.	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	intron	38771271	38771374	.	+	.	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	CDS	38771375	38771717	0.65	+	1	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	exon	38771375	38771717	.	+	.	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
Phchi.S1	AUGUSTUS	stop_codon	38771718	38771720	.	+	0	transcript_id "Phchi.S1G610000.t1"; gene_id "Phchi.S1G610000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1425.t1 is derived from g8344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	793620	794953	.	+	.	Phchi.S5G003400
Phchi.S5	AUGUSTUS	transcript	793620	794953	.	+	.	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	start_codon	793620	793622	.	+	0	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	CDS	793620	794573	0.91	+	0	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	exon	793620	794573	.	+	.	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	intron	794574	794656	.	+	.	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	CDS	794657	794953	0.96	+	0	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	exon	794657	794953	.	+	.	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
Phchi.S5	AUGUSTUS	stop_codon	794954	794956	.	+	0	transcript_id "Phchi.S5G003400.t1"; gene_id "Phchi.S5G003400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15166.t1 is derived from g13634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17344668	17345382	.	+	.	Phchi.S3G248500
Phchi.S3	AUGUSTUS	transcript	17344668	17345382	.	+	.	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	start_codon	17344668	17344670	.	+	0	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	CDS	17344668	17344743	1	+	0	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	exon	17344668	17344743	.	+	.	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	intron	17344744	17344843	.	+	.	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	CDS	17344844	17345382	1	+	2	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	exon	17344844	17345382	.	+	.	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
Phchi.S3	AUGUSTUS	stop_codon	17345383	17345385	.	+	0	transcript_id "Phchi.S3G248500.t1"; gene_id "Phchi.S3G248500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5537.t1 is derived from g2707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17451787	17456150	.	-	.	Phchi.S1G269600
Phchi.S1	AUGUSTUS	transcript	17451787	17456150	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	stop_codon	17451784	17451786	.	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17451787	17451876	0.86	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17451787	17451876	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17451877	17451992	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17451993	17452271	1	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17451993	17452271	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17452272	17452481	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17452482	17452642	1	-	2	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17452482	17452642	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17452643	17452765	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17452766	17453000	1	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17452766	17453000	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17453001	17453097	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17453098	17453178	1	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17453098	17453178	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17453179	17453263	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17453264	17453359	1	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17453264	17453359	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17453360	17453712	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17453713	17454435	0.72	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17453713	17454435	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17454436	17454662	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17454663	17455083	1	-	1	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17454663	17455083	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17455084	17455263	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17455264	17455320	1	-	1	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17455264	17455320	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17455321	17455403	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17455404	17455513	0.89	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17455404	17455513	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17455514	17455719	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17455720	17455779	0.69	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17455720	17455779	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	intron	17455780	17456015	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	CDS	17456016	17456150	0.61	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	exon	17456016	17456150	.	-	.	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
Phchi.S1	AUGUSTUS	start_codon	17456148	17456150	.	-	0	transcript_id "Phchi.S1G269600.t1"; gene_id "Phchi.S1G269600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8456.t1 is derived from g5631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36013239	36013659	.	+	.	Phchi.S1G561500
Phchi.S1	AUGUSTUS	transcript	36013239	36013659	.	+	.	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	start_codon	36013239	36013241	.	+	0	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	CDS	36013239	36013384	0.56	+	0	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	exon	36013239	36013384	.	+	.	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	intron	36013385	36013550	.	+	.	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	CDS	36013551	36013659	0.99	+	1	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	exon	36013551	36013659	.	+	.	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
Phchi.S1	AUGUSTUS	stop_codon	36013660	36013662	.	+	0	transcript_id "Phchi.S1G561500.t1"; gene_id "Phchi.S1G561500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6233.t1 is derived from g3405.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21790526	21793868	.	+	.	Phchi.S1G339200
Phchi.S1	AUGUSTUS	transcript	21790526	21793868	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	start_codon	21790526	21790528	.	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790526	21790634	0.91	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790526	21790634	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21790635	21790716	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790717	21790770	1	+	2	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790717	21790770	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21790771	21790865	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790866	21790918	1	+	2	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790866	21790918	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21790919	21790997	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790998	21791049	0.96	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790998	21791049	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791050	21791168	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791169	21791234	0.81	+	2	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791169	21791234	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791235	21791318	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791319	21791393	1	+	2	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791319	21791393	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791394	21791485	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791486	21791514	0.95	+	2	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791486	21791514	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791515	21791587	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791588	21791604	0.82	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791588	21791604	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791605	21791723	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791724	21791812	0.95	+	1	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791724	21791812	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791813	21792352	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792353	21792489	0.64	+	2	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792353	21792489	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792490	21792605	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792606	21792617	0.85	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792606	21792617	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792618	21792709	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792710	21792786	1	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792710	21792786	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792787	21792876	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792877	21792958	1	+	1	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792877	21792958	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792959	21793044	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21793045	21793323	0.59	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21793045	21793323	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21793324	21793432	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21793433	21793681	0.78	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21793433	21793681	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21793682	21793784	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21793785	21793868	0.88	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21793785	21793868	.	+	.	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	stop_codon	21793869	21793871	.	+	0	transcript_id "Phchi.S1G339200.t1"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	transcript	21790526	21793868	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	start_codon	21790526	21790528	.	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790526	21790634	0.94	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790526	21790634	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21790635	21790716	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790717	21790770	1	+	2	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790717	21790770	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21790771	21790865	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790866	21790918	1	+	2	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790866	21790918	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21790919	21790997	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21790998	21791049	0.99	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21790998	21791049	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791050	21791168	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791169	21791234	0.84	+	2	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791169	21791234	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791235	21791318	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791319	21791393	1	+	2	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791319	21791393	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791394	21791488	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791489	21791514	0.92	+	2	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791489	21791514	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791515	21791587	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791588	21791604	0.63	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791588	21791604	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791605	21791723	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21791724	21791812	0.93	+	1	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21791724	21791812	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21791813	21792352	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792353	21792489	0.57	+	2	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792353	21792489	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792490	21792605	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792606	21792617	0.78	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792606	21792617	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792618	21792709	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792710	21792786	1	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792710	21792786	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792787	21792876	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21792877	21792958	1	+	1	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21792877	21792958	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21792959	21793044	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21793045	21793323	0.56	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21793045	21793323	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21793324	21793432	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21793433	21793681	0.86	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21793433	21793681	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	intron	21793682	21793784	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	CDS	21793785	21793868	0.9	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	exon	21793785	21793868	.	+	.	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
Phchi.S1	AUGUSTUS	stop_codon	21793869	21793871	.	+	0	transcript_id "Phchi.S1G339200.t2"; gene_id "Phchi.S1G339200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7319.t1 is derived from g4491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28479346	28480636	.	+	.	Phchi.S1G447800
Phchi.S1	AUGUSTUS	transcript	28479346	28480636	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	start_codon	28479346	28479348	.	+	0	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	CDS	28479346	28479542	0.91	+	0	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	exon	28479346	28479542	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	intron	28479543	28479882	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	CDS	28479883	28479985	1	+	1	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	exon	28479883	28479985	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	intron	28479986	28480088	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	CDS	28480089	28480377	1	+	0	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	exon	28480089	28480377	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	intron	28480378	28480490	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	CDS	28480491	28480636	1	+	2	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	exon	28480491	28480636	.	+	.	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
Phchi.S1	AUGUSTUS	stop_codon	28480637	28480639	.	+	0	transcript_id "Phchi.S1G447800.t1"; gene_id "Phchi.S1G447800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13482.t1 is derived from g11949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7094675	7096699	.	-	.	Phchi.S3G080100
Phchi.S3	AUGUSTUS	transcript	7094675	7096699	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	stop_codon	7094672	7094674	.	-	0	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7094675	7094828	0.99	-	1	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7094675	7094828	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7094829	7094965	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7094966	7095113	1	-	2	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7094966	7095113	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7095114	7095200	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7095201	7095380	1	-	2	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7095201	7095380	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7095381	7095493	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7095494	7095563	1	-	0	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7095494	7095563	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7095564	7095648	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7095649	7095804	1	-	0	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7095649	7095804	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7095805	7095896	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7095897	7096126	1	-	2	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7095897	7096126	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7096127	7096236	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7096237	7096288	1	-	0	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7096237	7096288	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	intron	7096289	7096375	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	CDS	7096376	7096699	0.76	-	0	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	exon	7096376	7096699	.	-	.	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
Phchi.S3	AUGUSTUS	start_codon	7096697	7096699	.	-	0	transcript_id "Phchi.S3G080100.t1"; gene_id "Phchi.S3G080100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8628.t1 is derived from g5803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37149743	37151056	.	+	.	Phchi.S1G578700
Phchi.S1	AUGUSTUS	transcript	37149743	37151056	.	+	.	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	start_codon	37149743	37149745	.	+	0	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	CDS	37149743	37150276	0.64	+	0	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	exon	37149743	37150276	.	+	.	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	intron	37150277	37150475	.	+	.	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	CDS	37150476	37150551	0.87	+	0	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	exon	37150476	37150551	.	+	.	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	intron	37150552	37151003	.	+	.	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	CDS	37151004	37151056	1	+	2	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	exon	37151004	37151056	.	+	.	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
Phchi.S1	AUGUSTUS	stop_codon	37151057	37151059	.	+	0	transcript_id "Phchi.S1G578700.t1"; gene_id "Phchi.S1G578700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7972.t1 is derived from g5147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32191748	32192954	.	-	.	Phchi.S1G513100
Phchi.S1	AUGUSTUS	transcript	32191748	32192954	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	stop_codon	32191745	32191747	.	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32191748	32191795	1	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32191748	32191795	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32191796	32191877	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32191878	32191935	1	-	1	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32191878	32191935	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32191936	32192048	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32192049	32192092	1	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32192049	32192092	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32192093	32192174	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32192175	32192241	1	-	1	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32192175	32192241	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32192242	32192337	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32192338	32192384	1	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32192338	32192384	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32192385	32192516	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32192517	32192564	1	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32192517	32192564	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32192565	32192726	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32192727	32192842	1	-	2	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32192727	32192842	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	intron	32192843	32192935	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	CDS	32192936	32192954	1	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	exon	32192936	32192954	.	-	.	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
Phchi.S1	AUGUSTUS	start_codon	32192952	32192954	.	-	0	transcript_id "Phchi.S1G513100.t1"; gene_id "Phchi.S1G513100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6039.t1 is derived from g3210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20587103	20587342	.	-	.	Phchi.S1G319800
Phchi.S1	AUGUSTUS	transcript	20587103	20587342	.	-	.	transcript_id "Phchi.S1G319800.t1"; gene_id "Phchi.S1G319800"
Phchi.S1	AUGUSTUS	stop_codon	20587100	20587102	.	-	0	transcript_id "Phchi.S1G319800.t1"; gene_id "Phchi.S1G319800"
Phchi.S1	AUGUSTUS	CDS	20587103	20587342	0.93	-	0	transcript_id "Phchi.S1G319800.t1"; gene_id "Phchi.S1G319800"
Phchi.S1	AUGUSTUS	exon	20587103	20587342	.	-	.	transcript_id "Phchi.S1G319800.t1"; gene_id "Phchi.S1G319800"
Phchi.S1	AUGUSTUS	start_codon	20587340	20587342	.	-	0	transcript_id "Phchi.S1G319800.t1"; gene_id "Phchi.S1G319800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11922.t1 is derived from g7597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14854	16581	.	+	.	Phchi.S2G000200
Phchi.S2	AUGUSTUS	transcript	14854	16581	.	+	.	transcript_id "Phchi.S2G000200.t1"; gene_id "Phchi.S2G000200"
Phchi.S2	AUGUSTUS	start_codon	14854	14856	.	+	0	transcript_id "Phchi.S2G000200.t1"; gene_id "Phchi.S2G000200"
Phchi.S2	AUGUSTUS	CDS	14854	16581	0.01	+	0	transcript_id "Phchi.S2G000200.t1"; gene_id "Phchi.S2G000200"
Phchi.S2	AUGUSTUS	exon	14854	16581	.	+	.	transcript_id "Phchi.S2G000200.t1"; gene_id "Phchi.S2G000200"
Phchi.S2	AUGUSTUS	stop_codon	16582	16584	.	+	0	transcript_id "Phchi.S2G000200.t1"; gene_id "Phchi.S2G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15439.t1 is derived from g13907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19156708	19160057	.	-	.	Phchi.S3G275800
Phchi.S3	AUGUSTUS	transcript	19156708	19160057	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	stop_codon	19156705	19156707	.	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19156708	19156860	0.99	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19156708	19156860	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19156861	19156990	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19156991	19157044	0.99	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19156991	19157044	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19157045	19157121	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19157122	19157184	0.99	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19157122	19157184	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19157185	19157299	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19157300	19157347	0.98	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19157300	19157347	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19157348	19157477	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19157478	19157540	0.99	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19157478	19157540	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19157541	19157643	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19157644	19157664	1	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19157644	19157664	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19157665	19157823	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19157824	19157905	1	-	1	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19157824	19157905	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19157906	19158005	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19158006	19158142	1	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19158006	19158142	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19158143	19158267	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19158268	19158369	1	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19158268	19158369	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19158370	19158462	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19158463	19158561	1	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19158463	19158561	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19158562	19158840	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19158841	19158964	1	-	1	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19158841	19158964	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19158965	19159083	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19159084	19159151	1	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19159084	19159151	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19159152	19159262	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19159263	19159341	0.96	-	1	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19159263	19159341	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19159342	19159444	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19159445	19159518	0.81	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19159445	19159518	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19159519	19159622	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19159623	19159703	0.9	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19159623	19159703	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	intron	19159704	19159814	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	CDS	19159815	19160057	0.89	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	exon	19159815	19160057	.	-	.	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
Phchi.S3	AUGUSTUS	start_codon	19160055	19160057	.	-	0	transcript_id "Phchi.S3G275800.t1"; gene_id "Phchi.S3G275800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11748.t1 is derived from g15800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7987916	7988259	.	-	.	Phchi.S4G133000
Phchi.S4	AUGUSTUS	transcript	7987916	7988259	.	-	.	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	stop_codon	7987913	7987915	.	-	0	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	CDS	7987916	7988108	0.96	-	1	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	exon	7987916	7988108	.	-	.	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	intron	7988109	7988197	.	-	.	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	CDS	7988198	7988259	0.98	-	0	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	exon	7988198	7988259	.	-	.	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
Phchi.S4	AUGUSTUS	start_codon	7988257	7988259	.	-	0	transcript_id "Phchi.S4G133000.t1"; gene_id "Phchi.S4G133000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1072.t1 is derived from g10855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7436806	7438706	.	+	.	Phchi.S6G103100
Phchi.S6	AUGUSTUS	transcript	7436806	7438706	.	+	.	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	start_codon	7436806	7436808	.	+	0	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7436806	7437278	0.99	+	0	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7436806	7437278	.	+	.	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	intron	7437279	7437380	.	+	.	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7437381	7437483	1	+	1	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7437381	7437483	.	+	.	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	intron	7437484	7437590	.	+	.	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7437591	7438706	1	+	0	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7437591	7438706	.	+	.	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	stop_codon	7438707	7438709	.	+	0	transcript_id "Phchi.S6G103100.t1"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	transcript	7436806	7438706	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	start_codon	7436806	7436808	.	+	0	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7436806	7437171	0.79	+	0	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7436806	7437171	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	intron	7437172	7437278	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7437279	7437301	0.92	+	0	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7437279	7437301	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	intron	7437302	7437380	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7437381	7437483	1	+	1	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7437381	7437483	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	intron	7437484	7437590	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	CDS	7437591	7438706	0.99	+	0	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	exon	7437591	7438706	.	+	.	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
Phchi.S6	AUGUSTUS	stop_codon	7438707	7438709	.	+	0	transcript_id "Phchi.S6G103100.t2"; gene_id "Phchi.S6G103100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4660.t1 is derived from g1830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11673561	11674315	.	+	.	Phchi.S1G181900
Phchi.S1	AUGUSTUS	transcript	11673561	11674315	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	start_codon	11673561	11673563	.	+	0	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	CDS	11673561	11673636	0.98	+	0	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	exon	11673561	11673636	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	intron	11673637	11673736	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	CDS	11673737	11673837	1	+	2	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	exon	11673737	11673837	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	intron	11673838	11673936	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	CDS	11673937	11674056	0.9	+	0	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	exon	11673937	11674056	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	intron	11674057	11674288	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	CDS	11674289	11674315	0.77	+	0	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	exon	11674289	11674315	.	+	.	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
Phchi.S1	AUGUSTUS	stop_codon	11674316	11674318	.	+	0	transcript_id "Phchi.S1G181900.t1"; gene_id "Phchi.S1G181900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9278.t1 is derived from g6453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40737899	40738345	.	-	.	Phchi.S1G643700
Phchi.S1	AUGUSTUS	transcript	40737899	40738345	.	-	.	transcript_id "Phchi.S1G643700.t1"; gene_id "Phchi.S1G643700"
Phchi.S1	AUGUSTUS	stop_codon	40737896	40737898	.	-	0	transcript_id "Phchi.S1G643700.t1"; gene_id "Phchi.S1G643700"
Phchi.S1	AUGUSTUS	CDS	40737899	40738345	0.74	-	0	transcript_id "Phchi.S1G643700.t1"; gene_id "Phchi.S1G643700"
Phchi.S1	AUGUSTUS	exon	40737899	40738345	.	-	.	transcript_id "Phchi.S1G643700.t1"; gene_id "Phchi.S1G643700"
Phchi.S1	AUGUSTUS	start_codon	40738343	40738345	.	-	0	transcript_id "Phchi.S1G643700.t1"; gene_id "Phchi.S1G643700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11402.t1 is derived from g15452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6177418	6179673	.	-	.	Phchi.S4G098400
Phchi.S4	AUGUSTUS	transcript	6177418	6179673	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	stop_codon	6177415	6177417	.	-	0	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6177418	6177575	0.23	-	2	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6177418	6177575	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6177576	6177994	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6177995	6178205	0.52	-	0	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6177995	6178205	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6178206	6178445	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6178446	6178533	0.92	-	1	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6178446	6178533	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6178534	6178631	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6178632	6178750	0.92	-	0	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6178632	6178750	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6178751	6179003	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6179004	6179018	0.59	-	0	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6179004	6179018	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6179019	6179161	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6179162	6179178	0.99	-	2	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6179162	6179178	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6179179	6179408	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6179409	6179459	1	-	2	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6179409	6179459	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	intron	6179460	6179621	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	CDS	6179622	6179673	0.92	-	0	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	exon	6179622	6179673	.	-	.	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
Phchi.S4	AUGUSTUS	start_codon	6179671	6179673	.	-	0	transcript_id "Phchi.S4G098400.t1"; gene_id "Phchi.S4G098400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10633.t1 is derived from g14683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1353184	1353588	.	+	.	Phchi.S4G021500
Phchi.S4	AUGUSTUS	transcript	1353184	1353588	.	+	.	transcript_id "Phchi.S4G021500.t1"; gene_id "Phchi.S4G021500"
Phchi.S4	AUGUSTUS	start_codon	1353184	1353186	.	+	0	transcript_id "Phchi.S4G021500.t1"; gene_id "Phchi.S4G021500"
Phchi.S4	AUGUSTUS	CDS	1353184	1353588	0.51	+	0	transcript_id "Phchi.S4G021500.t1"; gene_id "Phchi.S4G021500"
Phchi.S4	AUGUSTUS	exon	1353184	1353588	.	+	.	transcript_id "Phchi.S4G021500.t1"; gene_id "Phchi.S4G021500"
Phchi.S4	AUGUSTUS	stop_codon	1353589	1353591	.	+	0	transcript_id "Phchi.S4G021500.t1"; gene_id "Phchi.S4G021500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12623.t1 is derived from g8300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37610391	37615556	.	-	.	Phchi.S2G070300
Phchi.S2	AUGUSTUS	transcript	37610391	37615556	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	stop_codon	37610388	37610390	.	-	0	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37610391	37610413	1	-	2	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37610391	37610413	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37610414	37611324	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37611325	37613208	0.96	-	2	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37611325	37613208	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37613209	37613337	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37613338	37613426	1	-	1	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37613338	37613426	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37613427	37613543	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37613544	37613612	1	-	1	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37613544	37613612	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37613613	37613759	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37613760	37613855	1	-	1	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37613760	37613855	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37613856	37614019	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37614020	37614133	1	-	1	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37614020	37614133	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37614134	37614266	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37614267	37614376	1	-	0	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37614267	37614376	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37614377	37614632	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37614633	37614704	1	-	0	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37614633	37614704	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37614705	37614787	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37614788	37614882	1	-	2	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37614788	37614882	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37614883	37615208	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37615209	37615287	1	-	0	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37615209	37615287	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	intron	37615288	37615382	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	CDS	37615383	37615556	0.94	-	0	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	exon	37615383	37615556	.	-	.	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
Phchi.S2	AUGUSTUS	start_codon	37615554	37615556	.	-	0	transcript_id "Phchi.S2G070300.t1"; gene_id "Phchi.S2G070300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6410.t1 is derived from g3582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22842445	22843186	.	-	.	Phchi.S1G356900
Phchi.S1	AUGUSTUS	transcript	22842445	22843186	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	stop_codon	22842442	22842444	.	-	0	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	CDS	22842445	22842504	0.96	-	0	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	exon	22842445	22842504	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	intron	22842505	22842619	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	CDS	22842620	22842730	1	-	0	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	exon	22842620	22842730	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	intron	22842731	22842826	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	CDS	22842827	22842933	1	-	2	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	exon	22842827	22842933	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	intron	22842934	22843026	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	CDS	22843027	22843186	0.99	-	0	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	exon	22843027	22843186	.	-	.	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
Phchi.S1	AUGUSTUS	start_codon	22843184	22843186	.	-	0	transcript_id "Phchi.S1G356900.t1"; gene_id "Phchi.S1G356900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14600.t1 is derived from g13068.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13673000	13675043	.	+	.	Phchi.S3G191900
Phchi.S3	AUGUSTUS	transcript	13673166	13675043	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	start_codon	13673166	13673168	.	+	0	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673166	13673284	0.39	+	0	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673166	13673284	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673285	13673382	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673383	13673606	1	+	1	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673383	13673606	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673607	13673704	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673705	13674079	1	+	2	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673705	13674079	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674080	13674169	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674170	13674285	1	+	2	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674170	13674285	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674286	13674407	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674408	13674695	1	+	0	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674408	13674695	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674696	13674773	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674774	13675043	0.97	+	0	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674774	13675043	.	+	.	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	stop_codon	13675044	13675046	.	+	0	transcript_id "Phchi.S3G191900.t1"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	transcript	13673000	13675043	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	start_codon	13673000	13673002	.	+	0	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673000	13673008	0.67	+	0	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673000	13673008	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673009	13673094	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673095	13673284	0.8	+	0	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673095	13673284	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673285	13673447	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673448	13673606	0.99	+	2	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673448	13673606	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673607	13673704	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673705	13674079	1	+	2	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673705	13674079	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674080	13674169	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674170	13674285	1	+	2	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674170	13674285	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674286	13674407	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674408	13674695	1	+	0	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674408	13674695	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674696	13674773	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674774	13675043	0.91	+	0	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674774	13675043	.	+	.	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	stop_codon	13675044	13675046	.	+	0	transcript_id "Phchi.S3G191900.t2"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	transcript	13673000	13675043	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	start_codon	13673000	13673002	.	+	0	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673000	13673008	0.56	+	0	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673000	13673008	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673009	13673094	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673095	13673284	0.66	+	0	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673095	13673284	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673285	13673447	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673448	13673606	0.99	+	2	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673448	13673606	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13673607	13673707	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13673708	13674079	0.96	+	2	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13673708	13674079	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674080	13674169	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674170	13674285	1	+	2	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674170	13674285	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674286	13674407	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674408	13674695	1	+	0	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674408	13674695	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	intron	13674696	13674773	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	CDS	13674774	13675043	0.94	+	0	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	exon	13674774	13675043	.	+	.	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
Phchi.S3	AUGUSTUS	stop_codon	13675044	13675046	.	+	0	transcript_id "Phchi.S3G191900.t3"; gene_id "Phchi.S3G191900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11588.t1 is derived from g15639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7240461	7241420	.	+	.	Phchi.S4G117000
Phchi.S4	AUGUSTUS	transcript	7240461	7241420	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	start_codon	7240461	7240463	.	+	0	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	CDS	7240461	7240497	0.82	+	0	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	exon	7240461	7240497	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	intron	7240498	7240708	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	CDS	7240709	7240796	1	+	2	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	exon	7240709	7240796	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	intron	7240797	7240889	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	CDS	7240890	7240937	0.9	+	1	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	exon	7240890	7240937	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	intron	7240938	7241015	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	CDS	7241016	7241143	0.53	+	1	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	exon	7241016	7241143	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	intron	7241144	7241349	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	CDS	7241350	7241420	0.98	+	2	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	exon	7241350	7241420	.	+	.	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
Phchi.S4	AUGUSTUS	stop_codon	7241421	7241423	.	+	0	transcript_id "Phchi.S4G117000.t1"; gene_id "Phchi.S4G117000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1166.t1 is derived from g10949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8122767	8124083	.	-	.	Phchi.S6G112500
Phchi.S6	AUGUSTUS	transcript	8122767	8124083	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	stop_codon	8122764	8122766	.	-	0	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	CDS	8122767	8122810	1	-	2	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	exon	8122767	8122810	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	intron	8122811	8122974	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	CDS	8122975	8123247	1	-	2	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	exon	8122975	8123247	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	intron	8123248	8123328	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	CDS	8123329	8123730	1	-	2	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	exon	8123329	8123730	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	intron	8123731	8123863	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	CDS	8123864	8124083	0.98	-	0	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	exon	8123864	8124083	.	-	.	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
Phchi.S6	AUGUSTUS	start_codon	8124081	8124083	.	-	0	transcript_id "Phchi.S6G112500.t1"; gene_id "Phchi.S6G112500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1098.t1 is derived from g10881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7596577	7597096	.	-	.	Phchi.S6G105700
Phchi.S6	AUGUSTUS	transcript	7596577	7597096	.	-	.	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	stop_codon	7596574	7596576	.	-	0	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	CDS	7596577	7596671	1	-	2	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	exon	7596577	7596671	.	-	.	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	intron	7596672	7596844	.	-	.	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	CDS	7596845	7596981	1	-	1	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	exon	7596845	7596981	.	-	.	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	intron	7596982	7597061	.	-	.	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	CDS	7597062	7597096	0.99	-	0	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	exon	7597062	7597096	.	-	.	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	start_codon	7597094	7597096	.	-	0	transcript_id "Phchi.S6G105700.t1"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	transcript	7596633	7597096	.	-	.	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	stop_codon	7596630	7596632	.	-	0	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	CDS	7596633	7596688	0.78	-	2	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	exon	7596633	7596688	.	-	.	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	intron	7596689	7596844	.	-	.	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	CDS	7596845	7596981	0.87	-	1	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	exon	7596845	7596981	.	-	.	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	intron	7596982	7597061	.	-	.	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	CDS	7597062	7597096	0.98	-	0	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	exon	7597062	7597096	.	-	.	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
Phchi.S6	AUGUSTUS	start_codon	7597094	7597096	.	-	0	transcript_id "Phchi.S6G105700.t2"; gene_id "Phchi.S6G105700"
# This transcript jg3589.t2 is derived from g758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3590.t1 is derived from g759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4644875	4647023	.	+	.	Phchi.S1G074900
Phchi.S1	AUGUSTUS	transcript	4644875	4647023	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	start_codon	4644875	4644877	.	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4644875	4644973	0.98	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4644875	4644973	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4644974	4645064	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4645065	4645178	1	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4645065	4645178	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4645179	4645260	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4645261	4645353	0.99	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4645261	4645353	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4645354	4645465	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4645466	4645531	0.84	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4645466	4645531	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4645532	4645647	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4645648	4645746	1	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4645648	4645746	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4645747	4645903	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4645904	4645977	1	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4645904	4645977	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4645978	4646055	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4646056	4646168	0.57	+	1	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4646056	4646168	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4646169	4646270	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4646271	4646359	1	+	2	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4646271	4646359	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4646360	4646451	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4646452	4646538	1	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4646452	4646538	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4646539	4646708	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4646709	4646777	1	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4646709	4646777	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	intron	4646778	4646876	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	CDS	4646877	4647023	0.99	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	exon	4646877	4647023	.	+	.	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
Phchi.S1	AUGUSTUS	stop_codon	4647024	4647026	.	+	0	transcript_id "Phchi.S1G074900.t1"; gene_id "Phchi.S1G074900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13551.t1 is derived from g12018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7460623	7461687	.	+	.	Phchi.S3G087000
Phchi.S3	AUGUSTUS	transcript	7460623	7461687	.	+	.	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	start_codon	7460623	7460625	.	+	0	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	CDS	7460623	7460863	1	+	0	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	exon	7460623	7460863	.	+	.	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	intron	7460864	7460988	.	+	.	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	CDS	7460989	7461207	0.8	+	2	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	exon	7460989	7461207	.	+	.	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	intron	7461208	7461397	.	+	.	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	CDS	7461398	7461687	0.99	+	2	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	exon	7461398	7461687	.	+	.	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
Phchi.S3	AUGUSTUS	stop_codon	7461688	7461690	.	+	0	transcript_id "Phchi.S3G087000.t1"; gene_id "Phchi.S3G087000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14230.t1 is derived from g12697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11668355	11670004	.	-	.	Phchi.S3G154900
Phchi.S3	AUGUSTUS	transcript	11668355	11670004	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	stop_codon	11668352	11668354	.	-	0	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11668355	11668483	1	-	0	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11668355	11668483	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	intron	11668484	11668560	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11668561	11668754	1	-	2	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11668561	11668754	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	intron	11668755	11668833	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11668834	11668992	1	-	2	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11668834	11668992	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	intron	11668993	11669090	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11669091	11669216	1	-	2	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11669091	11669216	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	intron	11669217	11669316	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11669317	11669519	1	-	1	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11669317	11669519	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	intron	11669520	11669613	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11669614	11669741	1	-	0	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11669614	11669741	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	intron	11669742	11669851	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	CDS	11669852	11670004	0.68	-	0	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	exon	11669852	11670004	.	-	.	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
Phchi.S3	AUGUSTUS	start_codon	11670002	11670004	.	-	0	transcript_id "Phchi.S3G154900.t1"; gene_id "Phchi.S3G154900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11171.t1 is derived from g15221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4451567	4455782	.	+	.	Phchi.S4G075300
Phchi.S4	AUGUSTUS	transcript	4451567	4455782	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	start_codon	4451567	4451569	.	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4451567	4451692	0.64	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4451567	4451692	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4451693	4451784	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4451785	4451858	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4451785	4451858	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4451859	4451949	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4451950	4451995	1	+	1	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4451950	4451995	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4451996	4452131	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4452132	4452237	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4452132	4452237	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4452238	4452328	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4452329	4452474	1	+	2	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4452329	4452474	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4452475	4452568	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4452569	4452679	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4452569	4452679	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4452680	4452793	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4452794	4452957	0.94	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4452794	4452957	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4452958	4453064	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4453065	4453443	1	+	1	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4453065	4453443	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4453444	4453538	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4453539	4453647	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4453539	4453647	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4453648	4453794	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4453795	4453934	0.98	+	2	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4453795	4453934	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4453935	4454032	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4454033	4454170	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4454033	4454170	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4454171	4454257	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4454258	4454349	0.98	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4454258	4454349	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4454350	4454461	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4454462	4454591	0.98	+	1	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4454462	4454591	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4454592	4454708	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4454709	4454867	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4454709	4454867	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4454868	4454944	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4454945	4455115	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4454945	4455115	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4455116	4455188	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4455189	4455323	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4455189	4455323	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4455324	4455415	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4455416	4455487	1	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4455416	4455487	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	intron	4455488	4455563	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	CDS	4455564	4455782	0.99	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	exon	4455564	4455782	.	+	.	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
Phchi.S4	AUGUSTUS	stop_codon	4455783	4455785	.	+	0	transcript_id "Phchi.S4G075300.t1"; gene_id "Phchi.S4G075300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12571.t1 is derived from g8248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35607484	35608598	.	+	.	Phchi.S2G065100
Phchi.S2	AUGUSTUS	transcript	35607484	35608598	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	start_codon	35607484	35607486	.	+	0	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	CDS	35607484	35607555	1	+	0	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	exon	35607484	35607555	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	intron	35607556	35607759	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	CDS	35607760	35608227	0.87	+	0	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	exon	35607760	35608227	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	intron	35608228	35608315	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	CDS	35608316	35608417	0.7	+	0	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	exon	35608316	35608417	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	intron	35608418	35608574	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	CDS	35608575	35608598	1	+	0	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	exon	35608575	35608598	.	+	.	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
Phchi.S2	AUGUSTUS	stop_codon	35608599	35608601	.	+	0	transcript_id "Phchi.S2G065100.t1"; gene_id "Phchi.S2G065100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5034.t1 is derived from g2204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14189222	14191130	.	+	.	Phchi.S1G219300
Phchi.S1	AUGUSTUS	transcript	14189222	14191130	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	start_codon	14189222	14189224	.	+	0	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	CDS	14189222	14189803	0.98	+	0	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	exon	14189222	14189803	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	intron	14189804	14189896	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	CDS	14189897	14190548	0.94	+	0	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	exon	14189897	14190548	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	intron	14190549	14190658	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	CDS	14190659	14190969	0.95	+	2	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	exon	14190659	14190969	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	intron	14190970	14191064	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	CDS	14191065	14191130	1	+	0	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	exon	14191065	14191130	.	+	.	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
Phchi.S1	AUGUSTUS	stop_codon	14191131	14191133	.	+	0	transcript_id "Phchi.S1G219300.t1"; gene_id "Phchi.S1G219300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14295.t1 is derived from g12762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11975039	11978938	.	+	.	Phchi.S3G161400
Phchi.S3	AUGUSTUS	transcript	11975039	11978938	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	start_codon	11975039	11975041	.	+	0	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11975039	11975286	1	+	0	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11975039	11975286	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11975287	11975614	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11975615	11975676	1	+	1	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11975615	11975676	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11975677	11975833	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11975834	11975909	0.96	+	2	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11975834	11975909	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11975910	11976018	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11976019	11976289	0.94	+	1	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11976019	11976289	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11976290	11976424	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11976425	11978938	0.97	+	0	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11976425	11978938	.	+	.	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	stop_codon	11978939	11978941	.	+	0	transcript_id "Phchi.S3G161400.t1"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	transcript	11975039	11978938	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	start_codon	11975039	11975041	.	+	0	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11975039	11975286	1	+	0	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11975039	11975286	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11975287	11975614	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11975615	11975676	1	+	1	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11975615	11975676	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11975677	11975824	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11975825	11975909	0.96	+	2	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11975825	11975909	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11975910	11976018	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11976019	11976289	0.88	+	1	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11976019	11976289	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	intron	11976290	11976424	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	CDS	11976425	11978938	0.97	+	0	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	exon	11976425	11978938	.	+	.	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
Phchi.S3	AUGUSTUS	stop_codon	11978939	11978941	.	+	0	transcript_id "Phchi.S3G161400.t2"; gene_id "Phchi.S3G161400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12874.t1 is derived from g11339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2850811	2851260	.	+	.	Phchi.S3G019300
Phchi.S3	AUGUSTUS	transcript	2850811	2851260	.	+	.	transcript_id "Phchi.S3G019300.t1"; gene_id "Phchi.S3G019300"
Phchi.S3	AUGUSTUS	start_codon	2850811	2850813	.	+	0	transcript_id "Phchi.S3G019300.t1"; gene_id "Phchi.S3G019300"
Phchi.S3	AUGUSTUS	CDS	2850811	2851260	0.81	+	0	transcript_id "Phchi.S3G019300.t1"; gene_id "Phchi.S3G019300"
Phchi.S3	AUGUSTUS	exon	2850811	2851260	.	+	.	transcript_id "Phchi.S3G019300.t1"; gene_id "Phchi.S3G019300"
Phchi.S3	AUGUSTUS	stop_codon	2851261	2851263	.	+	0	transcript_id "Phchi.S3G019300.t1"; gene_id "Phchi.S3G019300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4978.t1 is derived from g2148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13841870	13843066	.	-	.	Phchi.S1G213700
Phchi.S1	AUGUSTUS	transcript	13841870	13843066	.	-	.	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	stop_codon	13841867	13841869	.	-	0	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	CDS	13841870	13842233	1	-	1	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	exon	13841870	13842233	.	-	.	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	intron	13842234	13842348	.	-	.	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	CDS	13842349	13842502	1	-	2	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	exon	13842349	13842502	.	-	.	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	intron	13842503	13842645	.	-	.	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	CDS	13842646	13843066	1	-	0	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	exon	13842646	13843066	.	-	.	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
Phchi.S1	AUGUSTUS	start_codon	13843064	13843066	.	-	0	transcript_id "Phchi.S1G213700.t1"; gene_id "Phchi.S1G213700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13488.t1 is derived from g11955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7132813	7137147	.	+	.	Phchi.S3G080700
Phchi.S3	AUGUSTUS	transcript	7132813	7137147	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	start_codon	7132813	7132815	.	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7132813	7133140	0.8	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7132813	7133140	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7133141	7133230	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7133231	7133451	1	+	2	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7133231	7133451	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7133452	7133562	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7133563	7133730	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7133563	7133730	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7133731	7133819	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7133820	7133943	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7133820	7133943	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7133944	7134038	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7134039	7134115	1	+	2	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7134039	7134115	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7134116	7134209	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7134210	7134353	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7134210	7134353	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7134354	7134548	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7134549	7134701	0.37	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7134549	7134701	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7134702	7134824	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7134825	7134915	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7134825	7134915	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7134916	7135008	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7135009	7135130	1	+	2	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7135009	7135130	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7135131	7135255	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7135256	7135363	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7135256	7135363	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7135364	7135459	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7135460	7135705	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7135460	7135705	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7135706	7135819	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7135820	7135965	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7135820	7135965	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7135966	7136063	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7136064	7136181	1	+	1	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7136064	7136181	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7136182	7136299	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7136300	7136459	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7136300	7136459	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7136460	7136614	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7136615	7136646	1	+	2	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7136615	7136646	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7136647	7136773	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7136774	7136839	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7136774	7136839	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7136840	7136921	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7136922	7136993	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7136922	7136993	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	intron	7136994	7137069	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	CDS	7137070	7137147	1	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	exon	7137070	7137147	.	+	.	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
Phchi.S3	AUGUSTUS	stop_codon	7137148	7137150	.	+	0	transcript_id "Phchi.S3G080700.t1"; gene_id "Phchi.S3G080700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1360.t1 is derived from g15996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C81	AUGUSTUS	gene	3922	6049	.	+	.	Phchi.C81G000200
Phchi.C81	AUGUSTUS	transcript	3922	6049	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	start_codon	3922	3924	.	+	0	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	CDS	3922	4675	0.4	+	0	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	exon	3922	4675	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	intron	4676	4780	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	CDS	4781	4971	0.68	+	2	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	exon	4781	4971	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	intron	4972	5034	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	CDS	5035	5472	0.8	+	0	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	exon	5035	5472	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	intron	5473	5559	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	CDS	5560	5777	0.98	+	0	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	exon	5560	5777	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	intron	5778	5865	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	CDS	5866	6049	1	+	1	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	exon	5866	6049	.	+	.	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
Phchi.C81	AUGUSTUS	stop_codon	6050	6052	.	+	0	transcript_id "Phchi.C81G000200.t1"; gene_id "Phchi.C81G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4208.t1 is derived from g1377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8909221	8912656	.	-	.	Phchi.S1G136700
Phchi.S1	AUGUSTUS	transcript	8909221	8912656	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	stop_codon	8909218	8909220	.	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8909221	8909815	1	-	1	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8909221	8909815	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8909816	8909913	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8909914	8910188	1	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8909914	8910188	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8910189	8910282	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8910283	8910448	0.98	-	1	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8910283	8910448	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8910449	8910551	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8910552	8911112	0.98	-	1	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8910552	8911112	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8911113	8911216	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8911217	8911485	1	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8911217	8911485	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8911486	8911585	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8911586	8911720	0.96	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8911586	8911720	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8911721	8911823	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8911824	8911982	1	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8911824	8911982	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8911983	8912095	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8912096	8912176	1	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8912096	8912176	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8912177	8912273	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8912274	8912389	1	-	2	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8912274	8912389	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	intron	8912390	8912508	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	CDS	8912509	8912656	0.97	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	exon	8912509	8912656	.	-	.	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
Phchi.S1	AUGUSTUS	start_codon	8912654	8912656	.	-	0	transcript_id "Phchi.S1G136700.t1"; gene_id "Phchi.S1G136700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2974.t1 is derived from g143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	911350	915482	.	+	.	Phchi.S1G013300
Phchi.S1	AUGUSTUS	transcript	911350	914002	.	+	.	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	start_codon	911350	911352	.	+	0	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	CDS	911350	913839	0.45	+	0	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	exon	911350	913839	.	+	.	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	intron	913840	913951	.	+	.	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	CDS	913952	914002	0.96	+	0	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	exon	913952	914002	.	+	.	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	stop_codon	914003	914005	.	+	0	transcript_id "Phchi.S1G013300.t1"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	transcript	911350	915482	.	+	.	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	start_codon	911350	911352	.	+	0	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	CDS	911350	913839	0.35	+	0	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	exon	911350	913839	.	+	.	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	intron	913840	913962	.	+	.	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	CDS	913963	914876	0.48	+	0	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	exon	913963	914876	.	+	.	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	intron	914877	914971	.	+	.	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	CDS	914972	915482	0.58	+	1	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	exon	914972	915482	.	+	.	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
Phchi.S1	AUGUSTUS	stop_codon	915483	915485	.	+	0	transcript_id "Phchi.S1G013300.t2"; gene_id "Phchi.S1G013300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9900.t1 is derived from g7076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44333063	44333713	.	+	.	Phchi.S1G705900
Phchi.S1	AUGUSTUS	transcript	44333063	44333713	.	+	.	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	start_codon	44333063	44333065	.	+	0	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	CDS	44333063	44333093	0.97	+	0	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	exon	44333063	44333093	.	+	.	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	intron	44333094	44333288	.	+	.	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	CDS	44333289	44333398	1	+	2	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	exon	44333289	44333398	.	+	.	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	intron	44333399	44333497	.	+	.	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	CDS	44333498	44333713	0.88	+	0	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	exon	44333498	44333713	.	+	.	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
Phchi.S1	AUGUSTUS	stop_codon	44333714	44333716	.	+	0	transcript_id "Phchi.S1G705900.t1"; gene_id "Phchi.S1G705900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15458.t1 is derived from g13926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19286027	19287546	.	-	.	Phchi.S3G277700
Phchi.S3	AUGUSTUS	transcript	19286027	19287546	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	stop_codon	19286024	19286026	.	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19286027	19286134	1	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19286027	19286134	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	intron	19286135	19286264	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19286265	19286354	1	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19286265	19286354	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	intron	19286355	19286509	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19286510	19286617	1	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19286510	19286617	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	intron	19286618	19286785	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19286786	19286940	1	-	2	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19286786	19286940	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	intron	19286941	19287028	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19287029	19287164	1	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19287029	19287164	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	intron	19287165	19287241	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19287242	19287352	1	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19287242	19287352	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	intron	19287353	19287495	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	CDS	19287496	19287546	1	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	exon	19287496	19287546	.	-	.	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
Phchi.S3	AUGUSTUS	start_codon	19287544	19287546	.	-	0	transcript_id "Phchi.S3G277700.t1"; gene_id "Phchi.S3G277700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12034.t1 is derived from g7709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	757365	757997	.	+	.	Phchi.S2G011400
Phchi.S2	AUGUSTUS	transcript	757365	757997	.	+	.	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	start_codon	757365	757367	.	+	0	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	CDS	757365	757433	0.4	+	0	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	exon	757365	757433	.	+	.	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	intron	757434	757609	.	+	.	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	CDS	757610	757702	0.93	+	0	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	exon	757610	757702	.	+	.	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	intron	757703	757850	.	+	.	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	CDS	757851	757997	0.89	+	0	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	exon	757851	757997	.	+	.	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
Phchi.S2	AUGUSTUS	stop_codon	757998	758000	.	+	0	transcript_id "Phchi.S2G011400.t1"; gene_id "Phchi.S2G011400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2101.t1 is derived from g9021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4873441	4876657	.	-	.	Phchi.S5G071000
Phchi.S5	AUGUSTUS	transcript	4873441	4876657	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	stop_codon	4873438	4873440	.	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4873441	4873510	0.36	-	1	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4873441	4873510	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4873511	4873668	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4873669	4873859	0.53	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4873669	4873859	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4873860	4873956	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4873957	4874071	1	-	1	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4873957	4874071	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4874072	4874152	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4874153	4874241	1	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4874153	4874241	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4874242	4874347	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4874348	4874421	1	-	2	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4874348	4874421	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4874422	4874585	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4874586	4874732	1	-	2	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4874586	4874732	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4874733	4874922	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4874923	4875073	1	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4874923	4875073	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4875074	4875165	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4875166	4875259	1	-	1	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4875166	4875259	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4875260	4875409	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4875410	4875522	1	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4875410	4875522	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4875523	4875607	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4875608	4875707	1	-	1	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4875608	4875707	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4875708	4875925	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4875926	4876126	0.94	-	1	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4875926	4876126	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4876127	4876231	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4876232	4876388	0.87	-	2	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4876232	4876388	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	intron	4876389	4876470	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	CDS	4876471	4876657	0.76	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	exon	4876471	4876657	.	-	.	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
Phchi.S5	AUGUSTUS	start_codon	4876655	4876657	.	-	0	transcript_id "Phchi.S5G071000.t1"; gene_id "Phchi.S5G071000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11906.t1 is derived from g15958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9230505	9231245	.	+	.	Phchi.S4G148800
Phchi.S4	AUGUSTUS	transcript	9230505	9231245	.	+	.	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	start_codon	9230505	9230507	.	+	0	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	CDS	9230505	9230663	0.54	+	0	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	exon	9230505	9230663	.	+	.	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	intron	9230664	9230774	.	+	.	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	CDS	9230775	9231064	0.98	+	0	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	exon	9230775	9231064	.	+	.	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	intron	9231065	9231139	.	+	.	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	CDS	9231140	9231245	0.32	+	1	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	exon	9231140	9231245	.	+	.	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
Phchi.S4	AUGUSTUS	stop_codon	9231246	9231248	.	+	0	transcript_id "Phchi.S4G148800.t1"; gene_id "Phchi.S4G148800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7610.t1 is derived from g4784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30241195	30242596	.	+	.	Phchi.S1G476900
Phchi.S1	AUGUSTUS	transcript	30241195	30242596	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	start_codon	30241195	30241197	.	+	0	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	CDS	30241195	30241498	1	+	0	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	exon	30241195	30241498	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	intron	30241499	30241658	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	CDS	30241659	30241853	1	+	2	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	exon	30241659	30241853	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	intron	30241854	30241952	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	CDS	30241953	30242146	1	+	2	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	exon	30241953	30242146	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	intron	30242147	30242272	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	CDS	30242273	30242596	1	+	0	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	exon	30242273	30242596	.	+	.	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
Phchi.S1	AUGUSTUS	stop_codon	30242597	30242599	.	+	0	transcript_id "Phchi.S1G476900.t1"; gene_id "Phchi.S1G476900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg751.t1 is derived from g10533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5336165	5336859	.	-	.	Phchi.S6G071000
Phchi.S6	AUGUSTUS	transcript	5336165	5336859	.	-	.	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	stop_codon	5336162	5336164	.	-	0	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	CDS	5336165	5336291	0.91	-	1	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	exon	5336165	5336291	.	-	.	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	intron	5336292	5336597	.	-	.	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	CDS	5336598	5336728	0.9	-	0	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	exon	5336598	5336728	.	-	.	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	intron	5336729	5336823	.	-	.	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	CDS	5336824	5336859	1	-	0	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	exon	5336824	5336859	.	-	.	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
Phchi.S6	AUGUSTUS	start_codon	5336857	5336859	.	-	0	transcript_id "Phchi.S6G071000.t1"; gene_id "Phchi.S6G071000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15882.t1 is derived from g14352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22021780	22023369	.	+	.	Phchi.S3G320100
Phchi.S3	AUGUSTUS	transcript	22021780	22023369	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	start_codon	22021780	22021782	.	+	0	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	CDS	22021780	22021914	0.64	+	0	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	exon	22021780	22021914	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	intron	22021915	22022021	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	CDS	22022022	22022186	0.96	+	0	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	exon	22022022	22022186	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	intron	22022187	22022447	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	CDS	22022448	22022555	1	+	0	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	exon	22022448	22022555	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	intron	22022556	22022679	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	CDS	22022680	22022786	0.97	+	0	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	exon	22022680	22022786	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	intron	22022787	22022887	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	CDS	22022888	22022980	0.92	+	1	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	exon	22022888	22022980	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	intron	22022981	22023089	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	CDS	22023090	22023369	0.75	+	1	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	exon	22023090	22023369	.	+	.	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
Phchi.S3	AUGUSTUS	stop_codon	22023370	22023372	.	+	0	transcript_id "Phchi.S3G320100.t1"; gene_id "Phchi.S3G320100"
# This transcript jg6279.t2 is derived from g3451.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6279.t3 is derived from g3451.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6279.t4 is derived from g3451.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6280.t1 is derived from g3452.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22064965	22065624	.	+	.	Phchi.S1G343900
Phchi.S1	AUGUSTUS	transcript	22064965	22065619	.	+	.	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	start_codon	22064965	22064967	.	+	0	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22064965	22065105	1	+	0	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22064965	22065105	.	+	.	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	intron	22065106	22065165	.	+	.	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22065166	22065275	1	+	0	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22065166	22065275	.	+	.	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	intron	22065276	22065615	.	+	.	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22065616	22065619	1	+	1	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22065616	22065619	.	+	.	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	stop_codon	22065620	22065622	.	+	0	transcript_id "Phchi.S1G343900.t1"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	transcript	22064965	22065458	.	+	.	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	start_codon	22064965	22064967	.	+	0	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22064965	22065105	0.99	+	0	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22064965	22065105	.	+	.	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	intron	22065106	22065165	.	+	.	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22065166	22065275	1	+	0	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22065166	22065275	.	+	.	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	intron	22065276	22065439	.	+	.	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22065440	22065458	1	+	1	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22065440	22065458	.	+	.	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	stop_codon	22065459	22065461	.	+	0	transcript_id "Phchi.S1G343900.t2"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	transcript	22064965	22065624	.	+	.	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	start_codon	22064965	22064967	.	+	0	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22064965	22065105	0.99	+	0	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22064965	22065105	.	+	.	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	intron	22065106	22065176	.	+	.	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22065177	22065275	1	+	0	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22065177	22065275	.	+	.	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	intron	22065276	22065615	.	+	.	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	CDS	22065616	22065624	0.96	+	0	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	exon	22065616	22065624	.	+	.	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
Phchi.S1	AUGUSTUS	stop_codon	22065625	22065627	.	+	0	transcript_id "Phchi.S1G343900.t3"; gene_id "Phchi.S1G343900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12515.t1 is derived from g8192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32506784	32507546	.	+	.	Phchi.S2G059500
Phchi.S2	AUGUSTUS	transcript	32506784	32507546	.	+	.	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	start_codon	32506784	32506786	.	+	0	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	CDS	32506784	32506970	0.32	+	0	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	exon	32506784	32506970	.	+	.	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	intron	32506971	32507147	.	+	.	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	CDS	32507148	32507320	0.34	+	2	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	exon	32507148	32507320	.	+	.	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	intron	32507321	32507399	.	+	.	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	CDS	32507400	32507546	0.61	+	0	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	exon	32507400	32507546	.	+	.	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
Phchi.S2	AUGUSTUS	stop_codon	32507547	32507549	.	+	0	transcript_id "Phchi.S2G059500.t1"; gene_id "Phchi.S2G059500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3032.t1 is derived from g201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1253142	1253907	.	-	.	Phchi.S1G019100
Phchi.S1	AUGUSTUS	transcript	1253142	1253907	.	-	.	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	stop_codon	1253139	1253141	.	-	0	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	CDS	1253142	1253365	0.96	-	2	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	exon	1253142	1253365	.	-	.	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	intron	1253366	1253459	.	-	.	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	CDS	1253460	1253538	0.66	-	0	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	exon	1253460	1253538	.	-	.	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	intron	1253539	1253691	.	-	.	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	CDS	1253692	1253907	0.7	-	0	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	exon	1253692	1253907	.	-	.	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
Phchi.S1	AUGUSTUS	start_codon	1253905	1253907	.	-	0	transcript_id "Phchi.S1G019100.t1"; gene_id "Phchi.S1G019100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3751.t1 is derived from g920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5496081	5499101	.	-	.	Phchi.S1G091000
Phchi.S1	AUGUSTUS	transcript	5496081	5499101	.	-	.	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	stop_codon	5496078	5496080	.	-	0	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	CDS	5496081	5496084	0.32	-	1	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	exon	5496081	5496084	.	-	.	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	intron	5496085	5496223	.	-	.	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	CDS	5496224	5497610	0.42	-	2	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	exon	5496224	5497610	.	-	.	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	intron	5497611	5497723	.	-	.	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	CDS	5497724	5499101	0.45	-	0	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	exon	5497724	5499101	.	-	.	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
Phchi.S1	AUGUSTUS	start_codon	5499099	5499101	.	-	0	transcript_id "Phchi.S1G091000.t1"; gene_id "Phchi.S1G091000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6138.t1 is derived from g3309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21112153	21114684	.	+	.	Phchi.S1G329700
Phchi.S1	AUGUSTUS	transcript	21112396	21114684	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	start_codon	21112396	21112398	.	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21112396	21112586	0.31	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21112396	21112586	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21112587	21112838	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21112839	21113128	0.99	+	1	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21112839	21113128	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21113129	21113286	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21113287	21113510	1	+	2	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21113287	21113510	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21113511	21113644	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21113645	21113763	1	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21113645	21113763	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21113764	21113919	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21113920	21114076	1	+	1	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21113920	21114076	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21114077	21114187	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21114188	21114289	1	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21114188	21114289	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21114290	21114389	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21114390	21114509	1	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21114390	21114509	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21114510	21114642	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21114643	21114684	1	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21114643	21114684	.	+	.	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	stop_codon	21114685	21114687	.	+	0	transcript_id "Phchi.S1G329700.t1"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	transcript	21112153	21114684	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	start_codon	21112153	21112155	.	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21112153	21112192	0.56	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21112153	21112192	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21112193	21112295	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21112296	21112428	0.78	+	2	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21112296	21112428	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21112429	21112838	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21112839	21113128	0.95	+	1	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21112839	21113128	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21113129	21113286	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21113287	21113510	1	+	2	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21113287	21113510	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21113511	21113644	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21113645	21113763	1	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21113645	21113763	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21113764	21113919	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21113920	21114076	1	+	1	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21113920	21114076	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21114077	21114187	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21114188	21114289	1	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21114188	21114289	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21114290	21114389	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21114390	21114509	1	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21114390	21114509	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	intron	21114510	21114642	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	CDS	21114643	21114684	1	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	exon	21114643	21114684	.	+	.	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
Phchi.S1	AUGUSTUS	stop_codon	21114685	21114687	.	+	0	transcript_id "Phchi.S1G329700.t2"; gene_id "Phchi.S1G329700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13610.t1 is derived from g12077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7683328	7683633	.	+	.	Phchi.S3G092900
Phchi.S3	AUGUSTUS	transcript	7683328	7683633	.	+	.	transcript_id "Phchi.S3G092900.t1"; gene_id "Phchi.S3G092900"
Phchi.S3	AUGUSTUS	start_codon	7683328	7683330	.	+	0	transcript_id "Phchi.S3G092900.t1"; gene_id "Phchi.S3G092900"
Phchi.S3	AUGUSTUS	CDS	7683328	7683633	0.79	+	0	transcript_id "Phchi.S3G092900.t1"; gene_id "Phchi.S3G092900"
Phchi.S3	AUGUSTUS	exon	7683328	7683633	.	+	.	transcript_id "Phchi.S3G092900.t1"; gene_id "Phchi.S3G092900"
Phchi.S3	AUGUSTUS	stop_codon	7683634	7683636	.	+	0	transcript_id "Phchi.S3G092900.t1"; gene_id "Phchi.S3G092900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10338.t1 is derived from g7514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47239517	47242735	.	+	.	Phchi.S1G749700
Phchi.S1	AUGUSTUS	transcript	47239517	47242735	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	start_codon	47239517	47239519	.	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47239517	47239640	1	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47239517	47239640	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47239641	47239876	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47239877	47239952	1	+	2	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47239877	47239952	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47239953	47240071	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47240072	47240136	1	+	1	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47240072	47240136	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47240137	47240221	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47240222	47240307	1	+	2	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47240222	47240307	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47240308	47240434	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47240435	47240519	1	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47240435	47240519	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47240520	47240607	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47240608	47240678	1	+	2	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47240608	47240678	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47240679	47240790	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47240791	47240922	1	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47240791	47240922	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47240923	47241021	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47241022	47241137	1	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47241022	47241137	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47241138	47241358	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47241359	47241482	1	+	1	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47241359	47241482	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47241483	47241574	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47241575	47241643	1	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47241575	47241643	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47241644	47241806	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47241807	47241924	1	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47241807	47241924	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47241925	47242032	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47242033	47242145	0.17	+	2	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47242033	47242145	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47242146	47242478	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47242479	47242496	0.17	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47242479	47242496	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	intron	47242497	47242645	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	CDS	47242646	47242735	0.22	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	exon	47242646	47242735	.	+	.	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
Phchi.S1	AUGUSTUS	stop_codon	47242736	47242738	.	+	0	transcript_id "Phchi.S1G749700.t1"; gene_id "Phchi.S1G749700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8195.t1 is derived from g5370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34374842	34375536	.	+	.	Phchi.S1G535400
Phchi.S1	AUGUSTUS	transcript	34374842	34375536	.	+	.	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	start_codon	34374842	34374844	.	+	0	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	CDS	34374842	34375273	0.84	+	0	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	exon	34374842	34375273	.	+	.	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	intron	34375274	34375488	.	+	.	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	CDS	34375489	34375536	0.98	+	0	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	exon	34375489	34375536	.	+	.	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
Phchi.S1	AUGUSTUS	stop_codon	34375537	34375539	.	+	0	transcript_id "Phchi.S1G535400.t1"; gene_id "Phchi.S1G535400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1724.t1 is derived from g8644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2720636	2722307	.	+	.	Phchi.S5G033300
Phchi.S5	AUGUSTUS	transcript	2720636	2722307	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	start_codon	2720636	2720638	.	+	0	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	CDS	2720636	2720903	0.39	+	0	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	exon	2720636	2720903	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	intron	2720904	2721219	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	CDS	2721220	2721390	0.39	+	2	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	exon	2721220	2721390	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	intron	2721391	2721510	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	CDS	2721511	2721534	0.54	+	2	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	exon	2721511	2721534	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	intron	2721535	2721603	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	CDS	2721604	2722307	0.61	+	2	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	exon	2721604	2722307	.	+	.	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
Phchi.S5	AUGUSTUS	stop_codon	2722308	2722310	.	+	0	transcript_id "Phchi.S5G033300.t1"; gene_id "Phchi.S5G033300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg634.t1 is derived from g10416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4486622	4487104	.	-	.	Phchi.S6G059300
Phchi.S6	AUGUSTUS	transcript	4486622	4487104	.	-	.	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	stop_codon	4486619	4486621	.	-	0	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	CDS	4486622	4486761	0.5	-	2	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	exon	4486622	4486761	.	-	.	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	intron	4486762	4486941	.	-	.	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	CDS	4486942	4487104	0.55	-	0	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	exon	4486942	4487104	.	-	.	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
Phchi.S6	AUGUSTUS	start_codon	4487102	4487104	.	-	0	transcript_id "Phchi.S6G059300.t1"; gene_id "Phchi.S6G059300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5918.t1 is derived from g3089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19870103	19870813	.	+	.	Phchi.S1G307700
Phchi.S1	AUGUSTUS	transcript	19870103	19870813	.	+	.	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	start_codon	19870103	19870105	.	+	0	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	CDS	19870103	19870160	0.2	+	0	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	exon	19870103	19870160	.	+	.	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	intron	19870161	19870242	.	+	.	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	CDS	19870243	19870453	0.42	+	2	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	exon	19870243	19870453	.	+	.	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	intron	19870454	19870617	.	+	.	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	CDS	19870618	19870813	0.68	+	1	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	exon	19870618	19870813	.	+	.	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
Phchi.S1	AUGUSTUS	stop_codon	19870814	19870816	.	+	0	transcript_id "Phchi.S1G307700.t1"; gene_id "Phchi.S1G307700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2863.t1 is derived from g32.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	145803	149187	.	+	.	Phchi.S1G002200
Phchi.S1	AUGUSTUS	transcript	145803	149187	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	start_codon	145803	145805	.	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	145803	145812	0.9	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	145803	145812	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	145813	146144	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146145	146226	0.82	+	2	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146145	146226	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146227	146411	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146412	146442	0.83	+	1	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146412	146442	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146443	146549	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146550	146614	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146550	146614	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146615	146709	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146710	146797	0.61	+	1	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146710	146797	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146798	146904	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146905	147015	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146905	147015	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147016	147097	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147098	147235	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147098	147235	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147236	147656	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147657	147726	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147657	147726	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147727	147824	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147825	147880	1	+	2	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147825	147880	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147881	147977	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147978	148103	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147978	148103	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148104	148214	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148215	148354	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148215	148354	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148355	148462	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148463	148535	1	+	1	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148463	148535	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148536	148622	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148623	148697	1	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148623	148697	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148698	148787	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148788	148907	0.59	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148788	148907	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148908	149115	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	149116	149187	0.51	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	149116	149187	.	+	.	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	stop_codon	149188	149190	.	+	0	transcript_id "Phchi.S1G002200.t1"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	transcript	145803	149187	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	start_codon	145803	145805	.	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	145803	145812	0.91	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	145803	145812	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	145813	146144	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146145	146226	0.85	+	2	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146145	146226	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146227	146549	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146550	146614	0.49	+	1	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146550	146614	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146615	146756	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146757	146797	0.48	+	2	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146757	146797	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	146798	146904	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	146905	147015	0.5	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	146905	147015	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147016	147097	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147098	147235	1	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147098	147235	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147236	147656	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147657	147726	1	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147657	147726	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147727	147824	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147825	147880	1	+	2	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147825	147880	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	147881	147977	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	147978	148103	0.99	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	147978	148103	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148104	148214	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148215	148354	1	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148215	148354	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148355	148462	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148463	148535	1	+	1	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148463	148535	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148536	148622	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148623	148697	1	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148623	148697	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148698	148787	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	148788	148907	0.45	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	148788	148907	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	intron	148908	149115	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	CDS	149116	149187	0.43	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	exon	149116	149187	.	+	.	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
Phchi.S1	AUGUSTUS	stop_codon	149188	149190	.	+	0	transcript_id "Phchi.S1G002200.t2"; gene_id "Phchi.S1G002200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9366.t1 is derived from g6542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41170744	41171310	.	+	.	Phchi.S1G652500
Phchi.S1	AUGUSTUS	transcript	41170744	41171310	.	+	.	transcript_id "Phchi.S1G652500.t1"; gene_id "Phchi.S1G652500"
Phchi.S1	AUGUSTUS	start_codon	41170744	41170746	.	+	0	transcript_id "Phchi.S1G652500.t1"; gene_id "Phchi.S1G652500"
Phchi.S1	AUGUSTUS	CDS	41170744	41171310	0.85	+	0	transcript_id "Phchi.S1G652500.t1"; gene_id "Phchi.S1G652500"
Phchi.S1	AUGUSTUS	exon	41170744	41171310	.	+	.	transcript_id "Phchi.S1G652500.t1"; gene_id "Phchi.S1G652500"
Phchi.S1	AUGUSTUS	stop_codon	41171311	41171313	.	+	0	transcript_id "Phchi.S1G652500.t1"; gene_id "Phchi.S1G652500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14002.t1 is derived from g12469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10225869	10226183	.	+	.	Phchi.S3G132100
Phchi.S3	AUGUSTUS	transcript	10225869	10226183	.	+	.	transcript_id "Phchi.S3G132100.t1"; gene_id "Phchi.S3G132100"
Phchi.S3	AUGUSTUS	start_codon	10225869	10225871	.	+	0	transcript_id "Phchi.S3G132100.t1"; gene_id "Phchi.S3G132100"
Phchi.S3	AUGUSTUS	CDS	10225869	10226183	0.42	+	0	transcript_id "Phchi.S3G132100.t1"; gene_id "Phchi.S3G132100"
Phchi.S3	AUGUSTUS	exon	10225869	10226183	.	+	.	transcript_id "Phchi.S3G132100.t1"; gene_id "Phchi.S3G132100"
Phchi.S3	AUGUSTUS	stop_codon	10226184	10226186	.	+	0	transcript_id "Phchi.S3G132100.t1"; gene_id "Phchi.S3G132100"
# This transcript jg899.t2 is derived from g10681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg900.t1 is derived from g10682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6355998	6357814	.	-	.	Phchi.S6G085900
Phchi.S6	AUGUSTUS	transcript	6355998	6357814	.	-	.	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	stop_codon	6355995	6355997	.	-	0	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	CDS	6355998	6357556	0.96	-	2	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	exon	6355998	6357556	.	-	.	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	intron	6357557	6357708	.	-	.	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	CDS	6357709	6357814	0.99	-	0	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	exon	6357709	6357814	.	-	.	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	start_codon	6357812	6357814	.	-	0	transcript_id "Phchi.S6G085900.t1"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	transcript	6355998	6356390	.	-	.	transcript_id "Phchi.S6G085900.t2"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	stop_codon	6355995	6355997	.	-	0	transcript_id "Phchi.S6G085900.t2"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	CDS	6355998	6356390	0.89	-	0	transcript_id "Phchi.S6G085900.t2"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	exon	6355998	6356390	.	-	.	transcript_id "Phchi.S6G085900.t2"; gene_id "Phchi.S6G085900"
Phchi.S6	AUGUSTUS	start_codon	6356388	6356390	.	-	0	transcript_id "Phchi.S6G085900.t2"; gene_id "Phchi.S6G085900"
# This transcript jg13194.t2 is derived from g11659.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13194.t3 is derived from g11659.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13195.t1 is derived from g11660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4634589	4636605	.	+	.	Phchi.S3G051400
Phchi.S3	AUGUSTUS	transcript	4634589	4636605	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	start_codon	4634589	4634591	.	+	0	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4634589	4634991	0.92	+	0	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4634589	4634991	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	intron	4634992	4635129	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4635130	4635264	1	+	2	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4635130	4635264	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	intron	4635265	4635454	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4635455	4635630	1	+	2	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4635455	4635630	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	intron	4635631	4635717	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4635718	4636149	0.89	+	0	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4635718	4636149	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	intron	4636150	4636244	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4636245	4636316	0.95	+	0	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4636245	4636316	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	intron	4636317	4636397	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4636398	4636402	0.95	+	0	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4636398	4636402	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	intron	4636403	4636589	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	CDS	4636590	4636605	0.96	+	1	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	exon	4636590	4636605	.	+	.	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
Phchi.S3	AUGUSTUS	stop_codon	4636606	4636608	.	+	0	transcript_id "Phchi.S3G051400.t1"; gene_id "Phchi.S3G051400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8947.t1 is derived from g6122.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38801330	38803797	.	-	.	Phchi.S1G610600
Phchi.S1	AUGUSTUS	transcript	38802614	38803797	.	-	.	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	stop_codon	38802611	38802613	.	-	0	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	CDS	38802614	38802667	0.48	-	0	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	exon	38802614	38802667	.	-	.	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	intron	38802668	38802771	.	-	.	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	CDS	38802772	38803797	0.31	-	0	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	exon	38802772	38803797	.	-	.	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	start_codon	38803795	38803797	.	-	0	transcript_id "Phchi.S1G610600.t1"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	transcript	38801330	38803797	.	-	.	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	stop_codon	38801327	38801329	.	-	0	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	CDS	38801330	38802083	0.4	-	1	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	exon	38801330	38802083	.	-	.	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	intron	38802084	38802310	.	-	.	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	CDS	38802311	38802397	0.44	-	1	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	exon	38802311	38802397	.	-	.	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	intron	38802398	38802610	.	-	.	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	CDS	38802611	38803797	0.36	-	0	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	exon	38802611	38803797	.	-	.	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	start_codon	38803795	38803797	.	-	0	transcript_id "Phchi.S1G610600.t2"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	transcript	38801330	38802097	.	-	.	transcript_id "Phchi.S1G610600.t3"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	stop_codon	38801327	38801329	.	-	0	transcript_id "Phchi.S1G610600.t3"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	CDS	38801330	38802097	0.42	-	0	transcript_id "Phchi.S1G610600.t3"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	exon	38801330	38802097	.	-	.	transcript_id "Phchi.S1G610600.t3"; gene_id "Phchi.S1G610600"
Phchi.S1	AUGUSTUS	start_codon	38802095	38802097	.	-	0	transcript_id "Phchi.S1G610600.t3"; gene_id "Phchi.S1G610600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13181.t1 is derived from g11646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4562683	4564312	.	+	.	Phchi.S3G050000
Phchi.S3	AUGUSTUS	transcript	4562683	4564312	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	start_codon	4562683	4562685	.	+	0	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4562683	4562882	0.28	+	0	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4562683	4562882	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	intron	4562883	4563097	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4563098	4563194	0.99	+	1	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4563098	4563194	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	intron	4563195	4563305	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4563306	4563362	0.45	+	0	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4563306	4563362	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	intron	4563363	4563495	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4563496	4563617	0.99	+	0	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4563496	4563617	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	intron	4563618	4563729	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4563730	4563920	1	+	1	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4563730	4563920	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	intron	4563921	4564003	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4564004	4564060	0.96	+	2	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4564004	4564060	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	intron	4564061	4564163	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	CDS	4564164	4564312	0.96	+	2	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	exon	4564164	4564312	.	+	.	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
Phchi.S3	AUGUSTUS	stop_codon	4564313	4564315	.	+	0	transcript_id "Phchi.S3G050000.t1"; gene_id "Phchi.S3G050000"
# This transcript jg3015.t2 is derived from g184.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3016.t1 is derived from g185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1163020	1164276	.	-	.	Phchi.S1G017500
Phchi.S1	AUGUSTUS	transcript	1163020	1164276	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	stop_codon	1163017	1163019	.	-	0	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	CDS	1163020	1163163	0.9	-	0	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	exon	1163020	1163163	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	intron	1163164	1163271	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	CDS	1163272	1163500	1	-	1	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	exon	1163272	1163500	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	intron	1163501	1163597	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	CDS	1163598	1163701	1	-	0	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	exon	1163598	1163701	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	intron	1163702	1164015	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	CDS	1164016	1164276	0.36	-	0	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	exon	1164016	1164276	.	-	.	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
Phchi.S1	AUGUSTUS	start_codon	1164274	1164276	.	-	0	transcript_id "Phchi.S1G017500.t1"; gene_id "Phchi.S1G017500"
# This transcript jg1103.t2 is derived from g10886.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1103.t3 is derived from g10886.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1103.t4 is derived from g10886.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1104.t1 is derived from g10887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7623747	7625733	.	-	.	Phchi.S6G106300
Phchi.S6	AUGUSTUS	transcript	7623747	7625733	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	stop_codon	7623744	7623746	.	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7623747	7623971	0.76	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7623747	7623971	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7623972	7624045	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7624046	7624162	0.48	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7624046	7624162	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7624163	7624267	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7624268	7624376	1	-	1	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7624268	7624376	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7624377	7624469	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7624470	7624551	1	-	2	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7624470	7624551	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7624552	7624636	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7624637	7624844	1	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7624637	7624844	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7624845	7625036	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7625037	7625213	0.63	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7625037	7625213	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7625214	7625332	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7625333	7625449	0.95	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7625333	7625449	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	intron	7625450	7625562	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	CDS	7625563	7625733	0.48	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	exon	7625563	7625733	.	-	.	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
Phchi.S6	AUGUSTUS	start_codon	7625731	7625733	.	-	0	transcript_id "Phchi.S6G106300.t1"; gene_id "Phchi.S6G106300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3691.t1 is derived from g860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5211999	5212672	.	+	.	Phchi.S1G085000
Phchi.S1	AUGUSTUS	transcript	5211999	5212672	.	+	.	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	start_codon	5211999	5212001	.	+	0	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	CDS	5211999	5212230	0.84	+	0	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	exon	5211999	5212230	.	+	.	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	intron	5212231	5212310	.	+	.	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	CDS	5212311	5212672	0.51	+	2	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	exon	5212311	5212672	.	+	.	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
Phchi.S1	AUGUSTUS	stop_codon	5212673	5212675	.	+	0	transcript_id "Phchi.S1G085000.t1"; gene_id "Phchi.S1G085000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10972.t1 is derived from g15022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3417875	3423432	.	-	.	Phchi.S4G055400
Phchi.S4	AUGUSTUS	transcript	3417875	3423432	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	stop_codon	3417872	3417874	.	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3417875	3418037	0.22	-	1	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3417875	3418037	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3418038	3418136	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3418137	3418336	0.95	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3418137	3418336	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3418337	3418447	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3418448	3418525	0.95	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3418448	3418525	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3418526	3418600	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3418601	3418662	1	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3418601	3418662	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3418663	3418746	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3418747	3419058	1	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3418747	3419058	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3419059	3419139	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3419140	3419281	1	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3419140	3419281	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3419282	3419364	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3419365	3419433	1	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3419365	3419433	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3419434	3419539	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3419540	3419596	0.62	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3419540	3419596	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3419597	3419707	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3419708	3419769	1	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3419708	3419769	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3419770	3419860	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3419861	3419926	1	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3419861	3419926	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3419927	3420017	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3420018	3420135	1	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3420018	3420135	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3420136	3420248	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3420249	3420296	0.99	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3420249	3420296	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3420297	3420375	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3420376	3420525	1	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3420376	3420525	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3420526	3420606	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3420607	3420768	1	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3420607	3420768	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3420769	3420865	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3420866	3420963	1	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3420866	3420963	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3420964	3421045	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3421046	3421138	1	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3421046	3421138	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3421139	3421228	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3421229	3421425	1	-	1	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3421229	3421425	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3421426	3421539	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3421540	3421644	1	-	1	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3421540	3421644	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3421645	3421726	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3421727	3421847	0.95	-	2	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3421727	3421847	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3421848	3421955	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3421956	3422214	0.95	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3421956	3422214	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3422215	3422342	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3422343	3422417	1	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3422343	3422417	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3422418	3422507	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3422508	3422559	1	-	1	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3422508	3422559	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	intron	3422560	3422680	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	CDS	3422681	3423432	0.98	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	exon	3422681	3423432	.	-	.	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
Phchi.S4	AUGUSTUS	start_codon	3423430	3423432	.	-	0	transcript_id "Phchi.S4G055400.t1"; gene_id "Phchi.S4G055400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2192.t1 is derived from g9112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5322553	5323095	.	+	.	Phchi.S5G080100
Phchi.S5	AUGUSTUS	transcript	5322553	5323095	.	+	.	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	start_codon	5322553	5322555	.	+	0	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	CDS	5322553	5322642	0.58	+	0	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	exon	5322553	5322642	.	+	.	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	intron	5322643	5322754	.	+	.	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	CDS	5322755	5322824	0.99	+	0	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	exon	5322755	5322824	.	+	.	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	intron	5322825	5323057	.	+	.	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	CDS	5323058	5323095	1	+	2	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	exon	5323058	5323095	.	+	.	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
Phchi.S5	AUGUSTUS	stop_codon	5323096	5323098	.	+	0	transcript_id "Phchi.S5G080100.t1"; gene_id "Phchi.S5G080100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9142.t1 is derived from g6317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40061942	40062897	.	-	.	Phchi.S1G630100
Phchi.S1	AUGUSTUS	transcript	40061942	40062897	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	stop_codon	40061939	40061941	.	-	0	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	CDS	40061942	40062087	0.92	-	2	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	exon	40061942	40062087	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	intron	40062088	40062178	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	CDS	40062179	40062254	1	-	0	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	exon	40062179	40062254	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	intron	40062255	40062332	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	CDS	40062333	40062381	0.75	-	1	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	exon	40062333	40062381	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	intron	40062382	40062521	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	CDS	40062522	40062533	0.73	-	1	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	exon	40062522	40062533	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	intron	40062534	40062627	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	CDS	40062628	40062663	1	-	1	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	exon	40062628	40062663	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	intron	40062664	40062748	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	CDS	40062749	40062897	0.34	-	0	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	exon	40062749	40062897	.	-	.	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
Phchi.S1	AUGUSTUS	start_codon	40062895	40062897	.	-	0	transcript_id "Phchi.S1G630100.t1"; gene_id "Phchi.S1G630100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13923.t1 is derived from g12390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9685106	9686422	.	+	.	Phchi.S3G124200
Phchi.S3	AUGUSTUS	transcript	9685106	9686422	.	+	.	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	start_codon	9685106	9685108	.	+	0	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	CDS	9685106	9685254	0.32	+	0	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	exon	9685106	9685254	.	+	.	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	intron	9685255	9685434	.	+	.	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	CDS	9685435	9686422	0.45	+	1	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	exon	9685435	9686422	.	+	.	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
Phchi.S3	AUGUSTUS	stop_codon	9686423	9686425	.	+	0	transcript_id "Phchi.S3G124200.t1"; gene_id "Phchi.S3G124200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11255.t1 is derived from g15305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5027723	5032018	.	-	.	Phchi.S4G083700
Phchi.S4	AUGUSTUS	transcript	5027723	5032018	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	stop_codon	5027720	5027722	.	-	0	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	CDS	5027723	5028051	0.41	-	2	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	exon	5027723	5028051	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	intron	5028052	5028134	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	CDS	5028135	5028855	0.44	-	0	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	exon	5028135	5028855	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	intron	5028856	5028977	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	CDS	5028978	5030359	0.79	-	2	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	exon	5028978	5030359	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	intron	5030360	5030437	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	CDS	5030438	5030671	0.54	-	2	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	exon	5030438	5030671	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	intron	5030672	5030769	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	CDS	5030770	5032018	0.91	-	0	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	exon	5030770	5032018	.	-	.	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
Phchi.S4	AUGUSTUS	start_codon	5032016	5032018	.	-	0	transcript_id "Phchi.S4G083700.t1"; gene_id "Phchi.S4G083700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10539.t1 is derived from g14589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	876270	877593	.	-	.	Phchi.S4G012100
Phchi.S4	AUGUSTUS	transcript	876270	877593	.	-	.	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	stop_codon	876267	876269	.	-	0	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	CDS	876270	876343	0.95	-	2	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	exon	876270	876343	.	-	.	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	intron	876344	876746	.	-	.	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	CDS	876747	876876	0.9	-	0	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	exon	876747	876876	.	-	.	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	intron	876877	877437	.	-	.	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	CDS	877438	877593	0.48	-	0	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	exon	877438	877593	.	-	.	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
Phchi.S4	AUGUSTUS	start_codon	877591	877593	.	-	0	transcript_id "Phchi.S4G012100.t1"; gene_id "Phchi.S4G012100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6734.t1 is derived from g3906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24790091	24792076	.	-	.	Phchi.S1G389300
Phchi.S1	AUGUSTUS	transcript	24790091	24792076	.	-	.	transcript_id "Phchi.S1G389300.t1"; gene_id "Phchi.S1G389300"
Phchi.S1	AUGUSTUS	stop_codon	24790088	24790090	.	-	0	transcript_id "Phchi.S1G389300.t1"; gene_id "Phchi.S1G389300"
Phchi.S1	AUGUSTUS	CDS	24790091	24792076	0.8	-	0	transcript_id "Phchi.S1G389300.t1"; gene_id "Phchi.S1G389300"
Phchi.S1	AUGUSTUS	exon	24790091	24792076	.	-	.	transcript_id "Phchi.S1G389300.t1"; gene_id "Phchi.S1G389300"
Phchi.S1	AUGUSTUS	start_codon	24792074	24792076	.	-	0	transcript_id "Phchi.S1G389300.t1"; gene_id "Phchi.S1G389300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8179.t1 is derived from g5354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34308678	34309881	.	-	.	Phchi.S1G533800
Phchi.S1	AUGUSTUS	transcript	34308678	34309881	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	stop_codon	34308675	34308677	.	-	0	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	CDS	34308678	34308791	1	-	0	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	exon	34308678	34308791	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	intron	34308792	34308882	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	CDS	34308883	34309023	1	-	0	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	exon	34308883	34309023	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	intron	34309024	34309136	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	CDS	34309137	34309432	1	-	2	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	exon	34309137	34309432	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	intron	34309433	34309574	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	CDS	34309575	34309881	1	-	0	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	exon	34309575	34309881	.	-	.	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
Phchi.S1	AUGUSTUS	start_codon	34309879	34309881	.	-	0	transcript_id "Phchi.S1G533800.t1"; gene_id "Phchi.S1G533800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1168.t1 is derived from g10951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8238297	8238926	.	+	.	Phchi.S6G112700
Phchi.S6	AUGUSTUS	transcript	8238297	8238926	.	+	.	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	start_codon	8238297	8238299	.	+	0	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	CDS	8238297	8238677	0.73	+	0	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	exon	8238297	8238677	.	+	.	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	intron	8238678	8238785	.	+	.	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	CDS	8238786	8238926	1	+	0	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	exon	8238786	8238926	.	+	.	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
Phchi.S6	AUGUSTUS	stop_codon	8238927	8238929	.	+	0	transcript_id "Phchi.S6G112700.t1"; gene_id "Phchi.S6G112700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3342.t1 is derived from g511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3040230	3043480	.	+	.	Phchi.S1G050100
Phchi.S1	AUGUSTUS	transcript	3040230	3043480	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	start_codon	3040230	3040232	.	+	0	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	CDS	3040230	3040904	0.37	+	0	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	exon	3040230	3040904	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	intron	3040905	3041153	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	CDS	3041154	3042388	0.36	+	0	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	exon	3041154	3042388	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	intron	3042389	3042575	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	CDS	3042576	3042631	0.26	+	1	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	exon	3042576	3042631	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	intron	3042632	3042964	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	CDS	3042965	3043066	0.55	+	2	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	exon	3042965	3043066	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	intron	3043067	3043193	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	CDS	3043194	3043480	0.99	+	2	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	exon	3043194	3043480	.	+	.	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
Phchi.S1	AUGUSTUS	stop_codon	3043481	3043483	.	+	0	transcript_id "Phchi.S1G050100.t1"; gene_id "Phchi.S1G050100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13216.t1 is derived from g11681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4729971	4732956	.	+	.	Phchi.S3G053500
Phchi.S3	AUGUSTUS	transcript	4729971	4732956	.	+	.	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	start_codon	4729971	4729973	.	+	0	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	CDS	4729971	4730623	0.32	+	0	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	exon	4729971	4730623	.	+	.	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	intron	4730624	4730718	.	+	.	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	CDS	4730719	4732168	0.67	+	1	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	exon	4730719	4732168	.	+	.	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	intron	4732169	4732263	.	+	.	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	CDS	4732264	4732956	0.9	+	0	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	exon	4732264	4732956	.	+	.	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
Phchi.S3	AUGUSTUS	stop_codon	4732957	4732959	.	+	0	transcript_id "Phchi.S3G053500.t1"; gene_id "Phchi.S3G053500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9874.t1 is derived from g7050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44202634	44203574	.	-	.	Phchi.S1G703300
Phchi.S1	AUGUSTUS	transcript	44202634	44203574	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	stop_codon	44202631	44202633	.	-	0	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	CDS	44202634	44202827	1	-	2	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	exon	44202634	44202827	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	intron	44202828	44202909	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	CDS	44202910	44203140	1	-	2	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	exon	44202910	44203140	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	intron	44203141	44203226	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	CDS	44203227	44203308	1	-	0	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	exon	44203227	44203308	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	intron	44203309	44203394	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	CDS	44203395	44203574	0.83	-	0	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	exon	44203395	44203574	.	-	.	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
Phchi.S1	AUGUSTUS	start_codon	44203572	44203574	.	-	0	transcript_id "Phchi.S1G703300.t1"; gene_id "Phchi.S1G703300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6921.t1 is derived from g4093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26008877	26009238	.	+	.	Phchi.S1G408000
Phchi.S1	AUGUSTUS	transcript	26008877	26009238	.	+	.	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	start_codon	26008877	26008879	.	+	0	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	CDS	26008877	26009050	0.31	+	0	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	exon	26008877	26009050	.	+	.	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	intron	26009051	26009139	.	+	.	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	CDS	26009140	26009238	0.96	+	0	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	exon	26009140	26009238	.	+	.	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
Phchi.S1	AUGUSTUS	stop_codon	26009239	26009241	.	+	0	transcript_id "Phchi.S1G408000.t1"; gene_id "Phchi.S1G408000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5545.t1 is derived from g2715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17474886	17476914	.	-	.	Phchi.S1G270400
Phchi.S1	AUGUSTUS	transcript	17474886	17476914	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	stop_codon	17474883	17474885	.	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17474886	17474997	1	-	1	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17474886	17474997	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17474998	17475084	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17475085	17475131	1	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17475085	17475131	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17475132	17475246	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17475247	17475285	0.93	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17475247	17475285	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17475286	17475395	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17475396	17475479	0.6	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17475396	17475479	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17475480	17475706	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17475707	17475776	0.77	-	1	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17475707	17475776	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17475777	17475858	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17475859	17475928	1	-	2	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17475859	17475928	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17475929	17476106	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17476107	17476267	1	-	1	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17476107	17476267	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17476268	17476383	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17476384	17476505	1	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17476384	17476505	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17476506	17476600	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17476601	17476672	1	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17476601	17476672	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	intron	17476673	17476809	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	CDS	17476810	17476914	1	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	exon	17476810	17476914	.	-	.	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
Phchi.S1	AUGUSTUS	start_codon	17476912	17476914	.	-	0	transcript_id "Phchi.S1G270400.t1"; gene_id "Phchi.S1G270400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4267.t1 is derived from g1436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9310640	9315228	.	+	.	Phchi.S1G142600
Phchi.S1	AUGUSTUS	transcript	9310640	9315228	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	start_codon	9310640	9310642	.	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9310640	9310836	0.31	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9310640	9310836	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9310837	9310992	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9310993	9311010	0.25	+	1	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9310993	9311010	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9311011	9311069	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9311070	9311167	0.85	+	1	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9311070	9311167	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9311168	9311306	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9311307	9311525	0.96	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9311307	9311525	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9311526	9311634	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9311635	9312200	1	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9311635	9312200	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9312201	9312279	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9312280	9312640	1	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9312280	9312640	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9312641	9312727	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9312728	9312804	0.76	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9312728	9312804	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9312805	9312881	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9312882	9312962	0.74	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9312882	9312962	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9312963	9313050	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9313051	9313330	0.99	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9313051	9313330	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9313331	9313428	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9313429	9313788	0.75	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9313429	9313788	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9313789	9313894	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9313895	9314011	0.97	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9313895	9314011	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9314012	9314122	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9314123	9314830	0.88	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9314123	9314830	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9314831	9314944	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9314945	9315078	0.8	+	2	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9314945	9315078	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	intron	9315079	9315156	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	CDS	9315157	9315228	1	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	exon	9315157	9315228	.	+	.	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
Phchi.S1	AUGUSTUS	stop_codon	9315229	9315231	.	+	0	transcript_id "Phchi.S1G142600.t1"; gene_id "Phchi.S1G142600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4988.t1 is derived from g2158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13897332	13899532	.	-	.	Phchi.S1G214700
Phchi.S1	AUGUSTUS	transcript	13897332	13899532	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	stop_codon	13897329	13897331	.	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13897332	13897606	1	-	2	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13897332	13897606	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13897607	13897685	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13897686	13897728	0.82	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13897686	13897728	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13897729	13897823	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13897824	13897850	0.82	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13897824	13897850	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13897851	13897941	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13897942	13898265	1	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13897942	13898265	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13898266	13898338	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13898339	13898636	1	-	1	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13898339	13898636	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13898637	13898760	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13898761	13898938	1	-	2	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13898761	13898938	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13898939	13899067	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13899068	13899329	1	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13899068	13899329	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	intron	13899330	13899478	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	CDS	13899479	13899532	0.52	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	exon	13899479	13899532	.	-	.	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
Phchi.S1	AUGUSTUS	start_codon	13899530	13899532	.	-	0	transcript_id "Phchi.S1G214700.t1"; gene_id "Phchi.S1G214700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6531.t1 is derived from g3703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23519407	23520025	.	-	.	Phchi.S1G369000
Phchi.S1	AUGUSTUS	transcript	23519407	23520025	.	-	.	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	stop_codon	23519404	23519406	.	-	0	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	CDS	23519407	23519634	0.99	-	0	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	exon	23519407	23519634	.	-	.	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	intron	23519635	23519830	.	-	.	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	CDS	23519831	23520025	0.99	-	0	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	exon	23519831	23520025	.	-	.	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
Phchi.S1	AUGUSTUS	start_codon	23520023	23520025	.	-	0	transcript_id "Phchi.S1G369000.t1"; gene_id "Phchi.S1G369000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7432.t1 is derived from g4604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29095246	29096716	.	+	.	Phchi.S1G459100
Phchi.S1	AUGUSTUS	transcript	29095246	29096716	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	start_codon	29095246	29095248	.	+	0	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29095246	29095313	0.6	+	0	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29095246	29095313	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	intron	29095314	29095533	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29095534	29095641	1	+	1	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29095534	29095641	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	intron	29095642	29095738	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29095739	29095820	1	+	1	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29095739	29095820	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	intron	29095821	29095910	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29095911	29096040	1	+	0	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29095911	29096040	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	intron	29096041	29096155	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29096156	29096298	1	+	2	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29096156	29096298	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	intron	29096299	29096445	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29096446	29096532	0.91	+	0	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29096446	29096532	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	intron	29096533	29096644	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	CDS	29096645	29096716	0.91	+	0	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	exon	29096645	29096716	.	+	.	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
Phchi.S1	AUGUSTUS	stop_codon	29096717	29096719	.	+	0	transcript_id "Phchi.S1G459100.t1"; gene_id "Phchi.S1G459100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1824.t1 is derived from g8744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3349625	3350513	.	+	.	Phchi.S5G043300
Phchi.S5	AUGUSTUS	transcript	3349625	3350513	.	+	.	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	start_codon	3349625	3349627	.	+	0	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	CDS	3349625	3349914	0.49	+	0	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	exon	3349625	3349914	.	+	.	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	intron	3349915	3349984	.	+	.	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	CDS	3349985	3350513	0.81	+	1	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	exon	3349985	3350513	.	+	.	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
Phchi.S5	AUGUSTUS	stop_codon	3350514	3350516	.	+	0	transcript_id "Phchi.S5G043300.t1"; gene_id "Phchi.S5G043300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10508.t1 is derived from g14557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	756118	757631	.	+	.	Phchi.S4G009000
Phchi.S4	AUGUSTUS	transcript	756118	757631	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	start_codon	756118	756120	.	+	0	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	CDS	756118	756811	0.33	+	0	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	exon	756118	756811	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	intron	756812	756979	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	CDS	756980	757039	0.98	+	2	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	exon	756980	757039	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	intron	757040	757330	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	CDS	757331	757471	0.33	+	2	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	exon	757331	757471	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	intron	757472	757608	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	CDS	757609	757631	0.31	+	2	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	exon	757609	757631	.	+	.	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	stop_codon	757632	757634	.	+	0	transcript_id "Phchi.S4G009000.t1"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	transcript	756118	756899	.	+	.	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	start_codon	756118	756120	.	+	0	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	CDS	756118	756764	0.34	+	0	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	exon	756118	756764	.	+	.	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	intron	756765	756880	.	+	.	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	CDS	756881	756899	0.51	+	1	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	exon	756881	756899	.	+	.	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
Phchi.S4	AUGUSTUS	stop_codon	756900	756902	.	+	0	transcript_id "Phchi.S4G009000.t2"; gene_id "Phchi.S4G009000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg243.t1 is derived from g10025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1679367	1682162	.	+	.	Phchi.S6G020200
Phchi.S6	AUGUSTUS	transcript	1679367	1682162	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	start_codon	1679367	1679369	.	+	0	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1679367	1679792	0.8	+	0	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1679367	1679792	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1679793	1679945	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1679946	1680098	1	+	0	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1679946	1680098	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1680099	1680187	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1680188	1680296	1	+	0	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1680188	1680296	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1680297	1680391	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1680392	1680454	1	+	2	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1680392	1680454	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1680455	1680542	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1680543	1680575	1	+	2	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1680543	1680575	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1680576	1680763	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1680764	1680898	0.8	+	2	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1680764	1680898	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1680899	1680977	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1680978	1681128	0.77	+	2	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1680978	1681128	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1681129	1681218	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1681219	1681435	1	+	1	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1681219	1681435	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1681436	1681527	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1681528	1681777	1	+	0	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1681528	1681777	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	intron	1681778	1681869	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	CDS	1681870	1682162	0.6	+	2	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	exon	1681870	1682162	.	+	.	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
Phchi.S6	AUGUSTUS	stop_codon	1682163	1682165	.	+	0	transcript_id "Phchi.S6G020200.t1"; gene_id "Phchi.S6G020200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12664.t1 is derived from g9771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C309	AUGUSTUS	gene	2624	3049	.	-	.	Phchi.C309G000200
Phchi.C309	AUGUSTUS	transcript	2624	3049	.	-	.	transcript_id "Phchi.C309G000200.t1"; gene_id "Phchi.C309G000200"
Phchi.C309	AUGUSTUS	stop_codon	2621	2623	.	-	0	transcript_id "Phchi.C309G000200.t1"; gene_id "Phchi.C309G000200"
Phchi.C309	AUGUSTUS	CDS	2624	3049	0.99	-	0	transcript_id "Phchi.C309G000200.t1"; gene_id "Phchi.C309G000200"
Phchi.C309	AUGUSTUS	exon	2624	3049	.	-	.	transcript_id "Phchi.C309G000200.t1"; gene_id "Phchi.C309G000200"
Phchi.C309	AUGUSTUS	start_codon	3047	3049	.	-	0	transcript_id "Phchi.C309G000200.t1"; gene_id "Phchi.C309G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11689.t1 is derived from g15740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7689132	7691292	.	+	.	Phchi.S4G127100
Phchi.S4	AUGUSTUS	transcript	7689132	7691292	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	start_codon	7689132	7689134	.	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	CDS	7689132	7689410	0.61	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	exon	7689132	7689410	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	intron	7689411	7689478	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	CDS	7689479	7690075	0.63	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	exon	7689479	7690075	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	intron	7690076	7690152	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	CDS	7690153	7690440	1	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	exon	7690153	7690440	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	intron	7690441	7690526	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	CDS	7690527	7690727	0.99	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	exon	7690527	7690727	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	intron	7690728	7690816	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	CDS	7690817	7690873	0.96	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	exon	7690817	7690873	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	intron	7690874	7690986	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	CDS	7690987	7691292	0.73	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	exon	7690987	7691292	.	+	.	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
Phchi.S4	AUGUSTUS	stop_codon	7691293	7691295	.	+	0	transcript_id "Phchi.S4G127100.t1"; gene_id "Phchi.S4G127100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg123.t1 is derived from g9905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	694058	696151	.	+	.	Phchi.S6G008200
Phchi.S6	AUGUSTUS	transcript	694058	696151	.	+	.	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	start_codon	694058	694060	.	+	0	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	CDS	694058	694088	0.72	+	0	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	exon	694058	694088	.	+	.	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	intron	694089	694166	.	+	.	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	CDS	694167	696151	0.81	+	2	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	exon	694167	696151	.	+	.	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
Phchi.S6	AUGUSTUS	stop_codon	696152	696154	.	+	0	transcript_id "Phchi.S6G008200.t1"; gene_id "Phchi.S6G008200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11724.t1 is derived from g15776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7847421	7849292	.	-	.	Phchi.S4G130600
Phchi.S4	AUGUSTUS	transcript	7847421	7849292	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	stop_codon	7847418	7847420	.	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7847421	7847588	1	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7847421	7847588	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	intron	7847589	7847728	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7847729	7847821	1	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7847729	7847821	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	intron	7847822	7847943	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7847944	7848171	1	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7847944	7848171	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	intron	7848172	7848294	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7848295	7848426	0.8	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7848295	7848426	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	intron	7848427	7848536	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7848537	7848617	0.8	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7848537	7848617	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	intron	7848618	7848738	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7848739	7848828	1	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7848739	7848828	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	intron	7848829	7848980	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	CDS	7848981	7849292	0.43	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	exon	7848981	7849292	.	-	.	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
Phchi.S4	AUGUSTUS	start_codon	7849290	7849292	.	-	0	transcript_id "Phchi.S4G130600.t1"; gene_id "Phchi.S4G130600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5128.t1 is derived from g2298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15046768	15050431	.	-	.	Phchi.S1G228700
Phchi.S1	AUGUSTUS	transcript	15046768	15050431	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	stop_codon	15046765	15046767	.	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15046768	15046932	0.79	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15046768	15046932	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15046933	15047019	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15047020	15047130	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15047020	15047130	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15047131	15047220	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15047221	15047400	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15047221	15047400	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15047401	15047561	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15047562	15047666	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15047562	15047666	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15047667	15047855	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15047856	15047954	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15047856	15047954	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15047955	15048077	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15048078	15048233	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15048078	15048233	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15048234	15048395	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15048396	15048474	1	-	1	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15048396	15048474	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15048475	15048564	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15048565	15048630	1	-	1	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15048565	15048630	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15048631	15048830	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15048831	15049009	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15048831	15049009	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15049010	15049158	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15049159	15049506	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15049159	15049506	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15049507	15049612	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15049613	15049768	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15049613	15049768	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15049769	15049887	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15049888	15049965	1	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15049888	15049965	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	intron	15049966	15050110	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	CDS	15050111	15050431	0.95	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	exon	15050111	15050431	.	-	.	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
Phchi.S1	AUGUSTUS	start_codon	15050429	15050431	.	-	0	transcript_id "Phchi.S1G228700.t1"; gene_id "Phchi.S1G228700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2277.t1 is derived from g9197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5836213	5837629	.	+	.	Phchi.S5G088600
Phchi.S5	AUGUSTUS	transcript	5836213	5837629	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	start_codon	5836213	5836215	.	+	0	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	CDS	5836213	5836260	1	+	0	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	exon	5836213	5836260	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	intron	5836261	5836359	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	CDS	5836360	5836478	0.96	+	0	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	exon	5836360	5836478	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	intron	5836479	5836604	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	CDS	5836605	5837334	0.85	+	1	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	exon	5836605	5837334	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	intron	5837335	5837548	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	CDS	5837549	5837629	0.99	+	0	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	exon	5837549	5837629	.	+	.	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
Phchi.S5	AUGUSTUS	stop_codon	5837630	5837632	.	+	0	transcript_id "Phchi.S5G088600.t1"; gene_id "Phchi.S5G088600"
# This transcript jg7302.t2 is derived from g4474.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7303.t1 is derived from g4475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28399937	28403898	.	+	.	Phchi.S1G446200
Phchi.S1	AUGUSTUS	transcript	28399937	28403898	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	start_codon	28399937	28399939	.	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28399937	28400133	0.98	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28399937	28400133	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28400134	28400321	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28400322	28400436	1	+	1	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28400322	28400436	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28400437	28400598	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28400599	28400702	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28400599	28400702	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28400703	28400844	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28400845	28400949	1	+	1	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28400845	28400949	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28400950	28401089	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28401090	28401162	1	+	1	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28401090	28401162	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28401163	28401327	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28401328	28401438	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28401328	28401438	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28401439	28401566	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28401567	28401617	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28401567	28401617	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28401618	28401851	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28401852	28402018	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28401852	28402018	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28402019	28402105	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28402106	28402213	1	+	1	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28402106	28402213	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28402214	28402477	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28402478	28402551	1	+	1	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28402478	28402551	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28402552	28402642	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28402643	28402818	1	+	2	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28402643	28402818	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28402819	28402915	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28402916	28403011	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28402916	28403011	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28403012	28403213	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28403214	28403294	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28403214	28403294	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28403295	28403408	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28403409	28403462	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28403409	28403462	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28403463	28403561	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28403562	28403696	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28403562	28403696	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	intron	28403697	28403823	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	CDS	28403824	28403898	1	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	exon	28403824	28403898	.	+	.	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
Phchi.S1	AUGUSTUS	stop_codon	28403899	28403901	.	+	0	transcript_id "Phchi.S1G446200.t1"; gene_id "Phchi.S1G446200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8984.t1 is derived from g6159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38973664	38974863	.	-	.	Phchi.S1G614300
Phchi.S1	AUGUSTUS	transcript	38973664	38974560	.	-	.	transcript_id "Phchi.S1G614300.t1"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	stop_codon	38973661	38973663	.	-	0	transcript_id "Phchi.S1G614300.t1"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	CDS	38973664	38974560	1	-	0	transcript_id "Phchi.S1G614300.t1"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	exon	38973664	38974560	.	-	.	transcript_id "Phchi.S1G614300.t1"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	start_codon	38974558	38974560	.	-	0	transcript_id "Phchi.S1G614300.t1"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	transcript	38973664	38974863	.	-	.	transcript_id "Phchi.S1G614300.t2"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	stop_codon	38973661	38973663	.	-	0	transcript_id "Phchi.S1G614300.t2"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	CDS	38973664	38974863	0.54	-	0	transcript_id "Phchi.S1G614300.t2"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	exon	38973664	38974863	.	-	.	transcript_id "Phchi.S1G614300.t2"; gene_id "Phchi.S1G614300"
Phchi.S1	AUGUSTUS	start_codon	38974861	38974863	.	-	0	transcript_id "Phchi.S1G614300.t2"; gene_id "Phchi.S1G614300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1630.t1 is derived from g8549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2097685	2097891	.	-	.	Phchi.S5G023900
Phchi.S5	AUGUSTUS	transcript	2097685	2097891	.	-	.	transcript_id "Phchi.S5G023900.t1"; gene_id "Phchi.S5G023900"
Phchi.S5	AUGUSTUS	stop_codon	2097682	2097684	.	-	0	transcript_id "Phchi.S5G023900.t1"; gene_id "Phchi.S5G023900"
Phchi.S5	AUGUSTUS	CDS	2097685	2097891	0.75	-	0	transcript_id "Phchi.S5G023900.t1"; gene_id "Phchi.S5G023900"
Phchi.S5	AUGUSTUS	exon	2097685	2097891	.	-	.	transcript_id "Phchi.S5G023900.t1"; gene_id "Phchi.S5G023900"
Phchi.S5	AUGUSTUS	start_codon	2097889	2097891	.	-	0	transcript_id "Phchi.S5G023900.t1"; gene_id "Phchi.S5G023900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11362.t1 is derived from g15412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5768993	5770255	.	-	.	Phchi.S4G094400
Phchi.S4	AUGUSTUS	transcript	5768993	5770255	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	stop_codon	5768990	5768992	.	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	CDS	5768993	5769220	0.98	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	exon	5768993	5769220	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	intron	5769221	5769316	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	CDS	5769317	5769376	0.87	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	exon	5769317	5769376	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	intron	5769377	5769446	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	CDS	5769447	5769653	0.53	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	exon	5769447	5769653	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	intron	5769654	5769829	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	CDS	5769830	5769931	1	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	exon	5769830	5769931	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	intron	5769932	5770162	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	CDS	5770163	5770255	0.61	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	exon	5770163	5770255	.	-	.	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
Phchi.S4	AUGUSTUS	start_codon	5770253	5770255	.	-	0	transcript_id "Phchi.S4G094400.t1"; gene_id "Phchi.S4G094400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2922.t1 is derived from g91.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	570264	570743	.	-	.	Phchi.S1G008100
Phchi.S1	AUGUSTUS	transcript	570264	570743	.	-	.	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	stop_codon	570261	570263	.	-	0	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	CDS	570264	570485	0.34	-	0	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	exon	570264	570485	.	-	.	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	intron	570486	570638	.	-	.	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	CDS	570639	570743	0.24	-	0	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	exon	570639	570743	.	-	.	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
Phchi.S1	AUGUSTUS	start_codon	570741	570743	.	-	0	transcript_id "Phchi.S1G008100.t1"; gene_id "Phchi.S1G008100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5268.t1 is derived from g2438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15967935	15968422	.	-	.	Phchi.S1G242700
Phchi.S1	AUGUSTUS	transcript	15967935	15968422	.	-	.	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	stop_codon	15967932	15967934	.	-	0	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	CDS	15967935	15968064	0.59	-	1	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	exon	15967935	15968064	.	-	.	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	intron	15968065	15968195	.	-	.	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	CDS	15968196	15968422	0.59	-	0	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	exon	15968196	15968422	.	-	.	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
Phchi.S1	AUGUSTUS	start_codon	15968420	15968422	.	-	0	transcript_id "Phchi.S1G242700.t1"; gene_id "Phchi.S1G242700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4566.t1 is derived from g1736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11146028	11146696	.	-	.	Phchi.S1G172500
Phchi.S1	AUGUSTUS	transcript	11146028	11146696	.	-	.	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	stop_codon	11146025	11146027	.	-	0	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	CDS	11146028	11146393	1	-	0	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	exon	11146028	11146393	.	-	.	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	intron	11146394	11146474	.	-	.	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	CDS	11146475	11146696	0.71	-	0	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	exon	11146475	11146696	.	-	.	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
Phchi.S1	AUGUSTUS	start_codon	11146694	11146696	.	-	0	transcript_id "Phchi.S1G172500.t1"; gene_id "Phchi.S1G172500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8756.t1 is derived from g5931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37832559	37835649	.	-	.	Phchi.S1G591500
Phchi.S1	AUGUSTUS	transcript	37832559	37835649	.	-	.	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	stop_codon	37832556	37832558	.	-	0	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	CDS	37832559	37834600	1	-	2	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	exon	37832559	37834600	.	-	.	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	intron	37834601	37834682	.	-	.	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	CDS	37834683	37835156	1	-	2	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	exon	37834683	37835156	.	-	.	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	intron	37835157	37835267	.	-	.	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	CDS	37835268	37835649	0.64	-	0	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	exon	37835268	37835649	.	-	.	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
Phchi.S1	AUGUSTUS	start_codon	37835647	37835649	.	-	0	transcript_id "Phchi.S1G591500.t1"; gene_id "Phchi.S1G591500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11145.t1 is derived from g15195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4376821	4378163	.	-	.	Phchi.S4G072700
Phchi.S4	AUGUSTUS	transcript	4376821	4378163	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	stop_codon	4376818	4376820	.	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4376821	4376982	1	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4376821	4376982	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4376983	4377061	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4377062	4377103	1	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4377062	4377103	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4377104	4377184	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4377185	4377271	1	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4377185	4377271	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4377272	4377362	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4377363	4377460	1	-	2	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4377363	4377460	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4377461	4377545	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4377546	4377652	1	-	1	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4377546	4377652	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4377653	4377732	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4377733	4377795	1	-	1	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4377733	4377795	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4377796	4377922	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4377923	4377927	1	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4377923	4377927	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	intron	4377928	4378019	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	CDS	4378020	4378163	0.96	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	exon	4378020	4378163	.	-	.	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
Phchi.S4	AUGUSTUS	start_codon	4378161	4378163	.	-	0	transcript_id "Phchi.S4G072700.t1"; gene_id "Phchi.S4G072700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9770.t1 is derived from g6946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43607466	43608229	.	-	.	Phchi.S1G692900
Phchi.S1	AUGUSTUS	transcript	43607466	43608229	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	stop_codon	43607463	43607465	.	-	0	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	CDS	43607466	43607496	1	-	1	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	exon	43607466	43607496	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	intron	43607497	43607581	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	CDS	43607582	43607805	0.87	-	0	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	exon	43607582	43607805	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	intron	43607806	43607971	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	CDS	43607972	43608011	0.77	-	1	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	exon	43607972	43608011	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	intron	43608012	43608086	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	CDS	43608087	43608229	0.98	-	0	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	exon	43608087	43608229	.	-	.	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
Phchi.S1	AUGUSTUS	start_codon	43608227	43608229	.	-	0	transcript_id "Phchi.S1G692900.t1"; gene_id "Phchi.S1G692900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9514.t1 is derived from g6690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42166291	42167017	.	+	.	Phchi.S1G667300
Phchi.S1	AUGUSTUS	transcript	42166291	42167017	.	+	.	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	start_codon	42166291	42166293	.	+	0	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	CDS	42166291	42166625	1	+	0	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	exon	42166291	42166625	.	+	.	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	intron	42166626	42166697	.	+	.	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	CDS	42166698	42166797	1	+	1	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	exon	42166698	42166797	.	+	.	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	intron	42166798	42166882	.	+	.	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	CDS	42166883	42167017	1	+	0	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	exon	42166883	42167017	.	+	.	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
Phchi.S1	AUGUSTUS	stop_codon	42167018	42167020	.	+	0	transcript_id "Phchi.S1G667300.t1"; gene_id "Phchi.S1G667300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13992.t1 is derived from g12459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10140113	10140459	.	+	.	Phchi.S3G131100
Phchi.S3	AUGUSTUS	transcript	10140113	10140459	.	+	.	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	start_codon	10140113	10140115	.	+	0	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	CDS	10140113	10140266	1	+	0	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	exon	10140113	10140266	.	+	.	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	intron	10140267	10140355	.	+	.	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	CDS	10140356	10140459	0.96	+	2	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	exon	10140356	10140459	.	+	.	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
Phchi.S3	AUGUSTUS	stop_codon	10140460	10140462	.	+	0	transcript_id "Phchi.S3G131100.t1"; gene_id "Phchi.S3G131100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6615.t1 is derived from g3787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24013506	24014258	.	-	.	Phchi.S1G377400
Phchi.S1	AUGUSTUS	transcript	24013506	24014258	.	-	.	transcript_id "Phchi.S1G377400.t1"; gene_id "Phchi.S1G377400"
Phchi.S1	AUGUSTUS	stop_codon	24013503	24013505	.	-	0	transcript_id "Phchi.S1G377400.t1"; gene_id "Phchi.S1G377400"
Phchi.S1	AUGUSTUS	CDS	24013506	24014258	0.99	-	0	transcript_id "Phchi.S1G377400.t1"; gene_id "Phchi.S1G377400"
Phchi.S1	AUGUSTUS	exon	24013506	24014258	.	-	.	transcript_id "Phchi.S1G377400.t1"; gene_id "Phchi.S1G377400"
Phchi.S1	AUGUSTUS	start_codon	24014256	24014258	.	-	0	transcript_id "Phchi.S1G377400.t1"; gene_id "Phchi.S1G377400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7188.t1 is derived from g4360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27464597	27466962	.	+	.	Phchi.S1G434700
Phchi.S1	AUGUSTUS	transcript	27464597	27466962	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	start_codon	27464597	27464599	.	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27464597	27464860	1	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27464597	27464860	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27464861	27465001	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27465002	27465232	1	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27465002	27465232	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27465233	27465304	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27465305	27465475	1	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27465305	27465475	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27465476	27465607	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27465608	27465754	1	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27465608	27465754	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27465755	27465857	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27465858	27466037	1	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27465858	27466037	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27466038	27466143	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27466144	27466369	0.76	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27466144	27466369	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27466370	27466474	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27466475	27466588	1	+	2	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27466475	27466588	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27466589	27466743	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27466744	27466830	1	+	2	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27466744	27466830	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	intron	27466831	27466921	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	CDS	27466922	27466962	1	+	2	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	exon	27466922	27466962	.	+	.	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
Phchi.S1	AUGUSTUS	stop_codon	27466963	27466965	.	+	0	transcript_id "Phchi.S1G434700.t1"; gene_id "Phchi.S1G434700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15696.t1 is derived from g14165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20735113	20741035	.	+	.	Phchi.S3G301500
Phchi.S3	AUGUSTUS	transcript	20735113	20741035	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	start_codon	20735113	20735115	.	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20735113	20735426	0.99	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20735113	20735426	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20735427	20735547	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20735548	20735608	1	+	1	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20735548	20735608	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20735609	20735709	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20735710	20735832	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20735710	20735832	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20735833	20735919	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20735920	20736013	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20735920	20736013	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20736014	20736129	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20736130	20736166	1	+	2	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20736130	20736166	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20736167	20736254	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20736255	20736363	1	+	1	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20736255	20736363	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20736364	20736466	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20736467	20736524	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20736467	20736524	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20736525	20736620	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20736621	20736718	1	+	2	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20736621	20736718	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20736719	20736832	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20736833	20736952	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20736833	20736952	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20736953	20737052	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20737053	20737119	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20737053	20737119	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20737120	20737231	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20737232	20737350	1	+	2	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20737232	20737350	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20737351	20737441	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20737442	20737569	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20737442	20737569	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20737570	20737647	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20737648	20738239	0.98	+	1	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20737648	20738239	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20738240	20738344	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20738345	20738437	0.99	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20738345	20738437	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20738438	20738573	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20738574	20738759	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20738574	20738759	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20738760	20738876	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20738877	20739096	0.99	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20738877	20739096	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20739097	20739210	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20739211	20739302	0.98	+	2	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20739211	20739302	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20739303	20739512	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20739513	20739575	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20739513	20739575	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20739576	20739774	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20739775	20739930	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20739775	20739930	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20739931	20740016	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20740017	20740067	1	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20740017	20740067	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20740068	20740168	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20740169	20740502	0.94	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20740169	20740502	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20740503	20740605	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20740606	20740844	0.95	+	2	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20740606	20740844	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	intron	20740845	20740948	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	CDS	20740949	20741035	0.91	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	exon	20740949	20741035	.	+	.	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
Phchi.S3	AUGUSTUS	stop_codon	20741036	20741038	.	+	0	transcript_id "Phchi.S3G301500.t1"; gene_id "Phchi.S3G301500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14734.t1 is derived from g13202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14439873	14440376	.	-	.	Phchi.S3G205300
Phchi.S3	AUGUSTUS	transcript	14439873	14440376	.	-	.	transcript_id "Phchi.S3G205300.t1"; gene_id "Phchi.S3G205300"
Phchi.S3	AUGUSTUS	stop_codon	14439870	14439872	.	-	0	transcript_id "Phchi.S3G205300.t1"; gene_id "Phchi.S3G205300"
Phchi.S3	AUGUSTUS	CDS	14439873	14440376	0.56	-	0	transcript_id "Phchi.S3G205300.t1"; gene_id "Phchi.S3G205300"
Phchi.S3	AUGUSTUS	exon	14439873	14440376	.	-	.	transcript_id "Phchi.S3G205300.t1"; gene_id "Phchi.S3G205300"
Phchi.S3	AUGUSTUS	start_codon	14440374	14440376	.	-	0	transcript_id "Phchi.S3G205300.t1"; gene_id "Phchi.S3G205300"
# This transcript jg6946.t2 is derived from g4118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6947.t1 is derived from g4119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26102738	26103349	.	-	.	Phchi.S1G410600
Phchi.S1	AUGUSTUS	transcript	26102738	26103349	.	-	.	transcript_id "Phchi.S1G410600.t1"; gene_id "Phchi.S1G410600"
Phchi.S1	AUGUSTUS	stop_codon	26102735	26102737	.	-	0	transcript_id "Phchi.S1G410600.t1"; gene_id "Phchi.S1G410600"
Phchi.S1	AUGUSTUS	CDS	26102738	26103349	0.81	-	0	transcript_id "Phchi.S1G410600.t1"; gene_id "Phchi.S1G410600"
Phchi.S1	AUGUSTUS	exon	26102738	26103349	.	-	.	transcript_id "Phchi.S1G410600.t1"; gene_id "Phchi.S1G410600"
Phchi.S1	AUGUSTUS	start_codon	26103347	26103349	.	-	0	transcript_id "Phchi.S1G410600.t1"; gene_id "Phchi.S1G410600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6917.t1 is derived from g4089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25983430	25985046	.	+	.	Phchi.S1G407600
Phchi.S1	AUGUSTUS	transcript	25983430	25985046	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	start_codon	25983430	25983432	.	+	0	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	CDS	25983430	25984111	0.99	+	0	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	exon	25983430	25984111	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	intron	25984112	25984240	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	CDS	25984241	25984373	1	+	2	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	exon	25984241	25984373	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	intron	25984374	25984548	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	CDS	25984549	25984758	1	+	1	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	exon	25984549	25984758	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	intron	25984759	25984853	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	CDS	25984854	25985046	0.99	+	1	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	exon	25984854	25985046	.	+	.	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
Phchi.S1	AUGUSTUS	stop_codon	25985047	25985049	.	+	0	transcript_id "Phchi.S1G407600.t1"; gene_id "Phchi.S1G407600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15148.t1 is derived from g13616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17265269	17266995	.	-	.	Phchi.S3G246700
Phchi.S3	AUGUSTUS	transcript	17265269	17266995	.	-	.	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	stop_codon	17265266	17265268	.	-	0	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	CDS	17265269	17265290	0.38	-	1	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	exon	17265269	17265290	.	-	.	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	intron	17265291	17265382	.	-	.	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	CDS	17265383	17266995	0.41	-	0	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	exon	17265383	17266995	.	-	.	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
Phchi.S3	AUGUSTUS	start_codon	17266993	17266995	.	-	0	transcript_id "Phchi.S3G246700.t1"; gene_id "Phchi.S3G246700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10906.t1 is derived from g14956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2857876	2860497	.	+	.	Phchi.S4G048800
Phchi.S4	AUGUSTUS	transcript	2857876	2860497	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	start_codon	2857876	2857878	.	+	0	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	CDS	2857876	2858504	0.67	+	0	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	exon	2857876	2858504	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	intron	2858505	2858611	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	CDS	2858612	2858752	0.98	+	1	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	exon	2858612	2858752	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	intron	2858753	2858904	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	CDS	2858905	2859062	1	+	1	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	exon	2858905	2859062	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	intron	2859063	2859503	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	CDS	2859504	2859583	0.55	+	2	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	exon	2859504	2859583	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	intron	2859584	2859762	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	CDS	2859763	2860497	0.54	+	0	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	exon	2859763	2860497	.	+	.	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
Phchi.S4	AUGUSTUS	stop_codon	2860498	2860500	.	+	0	transcript_id "Phchi.S4G048800.t1"; gene_id "Phchi.S4G048800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13497.t1 is derived from g11964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7165170	7167466	.	+	.	Phchi.S3G081600
Phchi.S3	AUGUSTUS	transcript	7165170	7167466	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	start_codon	7165170	7165172	.	+	0	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7165170	7166330	0.44	+	0	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7165170	7166330	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7166331	7166607	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7166608	7166679	1	+	0	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7166608	7166679	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7166680	7166859	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7166860	7166886	1	+	0	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7166860	7166886	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7166887	7166985	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7166986	7167074	1	+	0	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7166986	7167074	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7167075	7167435	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7167436	7167466	1	+	1	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7167436	7167466	.	+	.	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	stop_codon	7167467	7167469	.	+	0	transcript_id "Phchi.S3G081600.t1"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	transcript	7165170	7167466	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	start_codon	7165170	7165172	.	+	0	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7165170	7166330	0.39	+	0	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7165170	7166330	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7166331	7166607	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7166608	7166679	1	+	0	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7166608	7166679	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7166680	7166862	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7166863	7166886	1	+	0	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7166863	7166886	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7166887	7166985	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7166986	7167074	1	+	0	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7166986	7167074	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	intron	7167075	7167435	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	CDS	7167436	7167466	1	+	1	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	exon	7167436	7167466	.	+	.	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
Phchi.S3	AUGUSTUS	stop_codon	7167467	7167469	.	+	0	transcript_id "Phchi.S3G081600.t2"; gene_id "Phchi.S3G081600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11538.t1 is derived from g15588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6959819	6961171	.	-	.	Phchi.S4G112000
Phchi.S4	AUGUSTUS	transcript	6959819	6961171	.	-	.	transcript_id "Phchi.S4G112000.t1"; gene_id "Phchi.S4G112000"
Phchi.S4	AUGUSTUS	stop_codon	6959816	6959818	.	-	0	transcript_id "Phchi.S4G112000.t1"; gene_id "Phchi.S4G112000"
Phchi.S4	AUGUSTUS	CDS	6959819	6961171	0.98	-	0	transcript_id "Phchi.S4G112000.t1"; gene_id "Phchi.S4G112000"
Phchi.S4	AUGUSTUS	exon	6959819	6961171	.	-	.	transcript_id "Phchi.S4G112000.t1"; gene_id "Phchi.S4G112000"
Phchi.S4	AUGUSTUS	start_codon	6961169	6961171	.	-	0	transcript_id "Phchi.S4G112000.t1"; gene_id "Phchi.S4G112000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14996.t1 is derived from g13464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16175930	16177711	.	+	.	Phchi.S3G231500
Phchi.S3	AUGUSTUS	transcript	16175930	16177711	.	+	.	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	start_codon	16175930	16175932	.	+	0	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	CDS	16175930	16177426	0.72	+	0	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	exon	16175930	16177426	.	+	.	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	intron	16177427	16177528	.	+	.	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	CDS	16177529	16177711	1	+	0	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	exon	16177529	16177711	.	+	.	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
Phchi.S3	AUGUSTUS	stop_codon	16177712	16177714	.	+	0	transcript_id "Phchi.S3G231500.t1"; gene_id "Phchi.S3G231500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12669.t1 is derived from g14467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C42	AUGUSTUS	gene	51937	52449	.	-	.	Phchi.C42G000400
Phchi.C42	AUGUSTUS	transcript	51937	52449	.	-	.	transcript_id "Phchi.C42G000400.t1"; gene_id "Phchi.C42G000400"
Phchi.C42	AUGUSTUS	stop_codon	51934	51936	.	-	0	transcript_id "Phchi.C42G000400.t1"; gene_id "Phchi.C42G000400"
Phchi.C42	AUGUSTUS	CDS	51937	52449	0.86	-	0	transcript_id "Phchi.C42G000400.t1"; gene_id "Phchi.C42G000400"
Phchi.C42	AUGUSTUS	exon	51937	52449	.	-	.	transcript_id "Phchi.C42G000400.t1"; gene_id "Phchi.C42G000400"
Phchi.C42	AUGUSTUS	start_codon	52447	52449	.	-	0	transcript_id "Phchi.C42G000400.t1"; gene_id "Phchi.C42G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3301.t1 is derived from g470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2745491	2746498	.	+	.	Phchi.S1G046000
Phchi.S1	AUGUSTUS	transcript	2745491	2746498	.	+	.	transcript_id "Phchi.S1G046000.t1"; gene_id "Phchi.S1G046000"
Phchi.S1	AUGUSTUS	start_codon	2745491	2745493	.	+	0	transcript_id "Phchi.S1G046000.t1"; gene_id "Phchi.S1G046000"
Phchi.S1	AUGUSTUS	CDS	2745491	2746498	0.45	+	0	transcript_id "Phchi.S1G046000.t1"; gene_id "Phchi.S1G046000"
Phchi.S1	AUGUSTUS	exon	2745491	2746498	.	+	.	transcript_id "Phchi.S1G046000.t1"; gene_id "Phchi.S1G046000"
Phchi.S1	AUGUSTUS	stop_codon	2746499	2746501	.	+	0	transcript_id "Phchi.S1G046000.t1"; gene_id "Phchi.S1G046000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10276.t1 is derived from g7452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46790856	46791690	.	+	.	Phchi.S1G743500
Phchi.S1	AUGUSTUS	transcript	46790856	46791690	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	start_codon	46790856	46790858	.	+	0	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	CDS	46790856	46791231	0.99	+	0	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	exon	46790856	46791231	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	intron	46791232	46791334	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	CDS	46791335	46791368	0.96	+	2	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	exon	46791335	46791368	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	intron	46791369	46791446	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	CDS	46791447	46791524	1	+	1	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	exon	46791447	46791524	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	intron	46791525	46791620	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	CDS	46791621	46791690	1	+	1	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	exon	46791621	46791690	.	+	.	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
Phchi.S1	AUGUSTUS	stop_codon	46791691	46791693	.	+	0	transcript_id "Phchi.S1G743500.t1"; gene_id "Phchi.S1G743500"
# This transcript jg4045.t2 is derived from g1214.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4046.t1 is derived from g1215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7461016	7461420	.	+	.	Phchi.S1G120500
Phchi.S1	AUGUSTUS	transcript	7461016	7461420	.	+	.	transcript_id "Phchi.S1G120500.t1"; gene_id "Phchi.S1G120500"
Phchi.S1	AUGUSTUS	start_codon	7461016	7461018	.	+	0	transcript_id "Phchi.S1G120500.t1"; gene_id "Phchi.S1G120500"
Phchi.S1	AUGUSTUS	CDS	7461016	7461420	0.91	+	0	transcript_id "Phchi.S1G120500.t1"; gene_id "Phchi.S1G120500"
Phchi.S1	AUGUSTUS	exon	7461016	7461420	.	+	.	transcript_id "Phchi.S1G120500.t1"; gene_id "Phchi.S1G120500"
Phchi.S1	AUGUSTUS	stop_codon	7461421	7461423	.	+	0	transcript_id "Phchi.S1G120500.t1"; gene_id "Phchi.S1G120500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13505.t1 is derived from g11972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7221790	7223773	.	+	.	Phchi.S3G082400
Phchi.S3	AUGUSTUS	transcript	7221790	7223773	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	start_codon	7221790	7221792	.	+	0	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	CDS	7221790	7221915	0.76	+	0	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	exon	7221790	7221915	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	intron	7221916	7222034	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	CDS	7222035	7222275	0.91	+	0	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	exon	7222035	7222275	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	intron	7222276	7222366	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	CDS	7222367	7222550	0.54	+	2	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	exon	7222367	7222550	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	intron	7222551	7222631	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	CDS	7222632	7223223	0.69	+	1	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	exon	7222632	7223223	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	intron	7223224	7223323	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	CDS	7223324	7223773	1	+	0	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	exon	7223324	7223773	.	+	.	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
Phchi.S3	AUGUSTUS	stop_codon	7223774	7223776	.	+	0	transcript_id "Phchi.S3G082400.t1"; gene_id "Phchi.S3G082400"
# This transcript jg15817.t2 is derived from g14287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15817.t3 is derived from g14287.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15818.t1 is derived from g14288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21549097	21550090	.	+	.	Phchi.S3G313700
Phchi.S3	AUGUSTUS	transcript	21549097	21550090	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	start_codon	21549097	21549099	.	+	0	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	CDS	21549097	21549153	0.97	+	0	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	exon	21549097	21549153	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	intron	21549154	21549235	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	CDS	21549236	21549334	1	+	0	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	exon	21549236	21549334	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	intron	21549335	21549477	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	CDS	21549478	21549723	1	+	0	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	exon	21549478	21549723	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	intron	21549724	21549802	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	CDS	21549803	21550090	0.95	+	0	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	exon	21549803	21550090	.	+	.	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
Phchi.S3	AUGUSTUS	stop_codon	21550091	21550093	.	+	0	transcript_id "Phchi.S3G313700.t1"; gene_id "Phchi.S3G313700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8677.t1 is derived from g5852.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37387647	37392217	.	+	.	Phchi.S1G583600
Phchi.S1	AUGUSTUS	transcript	37387647	37392217	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	start_codon	37387647	37387649	.	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387647	37387720	0.47	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387647	37387720	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37387721	37387867	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387868	37387879	0.95	+	1	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387868	37387879	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37387880	37387966	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387967	37388020	0.93	+	1	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387967	37388020	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388021	37388496	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388497	37388637	0.68	+	1	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388497	37388637	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388638	37388717	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388718	37388903	0.99	+	1	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388718	37388903	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388904	37388980	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388981	37389158	1	+	1	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388981	37389158	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389159	37389237	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389238	37389301	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389238	37389301	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389302	37389618	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389619	37389743	0.99	+	2	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389619	37389743	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389744	37389969	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389970	37390059	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389970	37390059	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390060	37390232	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390233	37390418	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390233	37390418	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390419	37390531	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390532	37390606	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390532	37390606	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390607	37390725	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390726	37390827	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390726	37390827	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390828	37390936	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390937	37391033	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390937	37391033	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391034	37391149	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391150	37391290	1	+	2	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391150	37391290	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391291	37391375	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391376	37391482	1	+	2	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391376	37391482	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391483	37391646	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391647	37391760	0.97	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391647	37391760	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391761	37391863	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391864	37392217	1	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391864	37392217	.	+	.	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	stop_codon	37392218	37392220	.	+	0	transcript_id "Phchi.S1G583600.t1"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	transcript	37387647	37392217	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	start_codon	37387647	37387649	.	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387647	37387720	0.47	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387647	37387720	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37387721	37387867	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387868	37387879	0.96	+	1	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387868	37387879	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37387880	37387966	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387967	37388020	0.93	+	1	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387967	37388020	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388021	37388496	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388497	37388637	0.6	+	1	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388497	37388637	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388638	37388717	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388718	37388903	1	+	1	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388718	37388903	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388904	37388980	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388981	37389158	1	+	1	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388981	37389158	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389159	37389237	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389238	37389301	1	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389238	37389301	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389302	37389445	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389446	37389570	1	+	2	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389446	37389570	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389571	37389969	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389970	37390059	1	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389970	37390059	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390060	37390232	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390233	37390418	0.99	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390233	37390418	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390419	37390531	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390532	37390606	0.99	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390532	37390606	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390607	37390725	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390726	37390827	1	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390726	37390827	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390828	37390936	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390937	37391033	1	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390937	37391033	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391034	37391149	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391150	37391290	1	+	2	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391150	37391290	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391291	37391375	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391376	37391482	1	+	2	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391376	37391482	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391483	37391646	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391647	37391760	0.98	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391647	37391760	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391761	37391863	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391864	37392217	0.99	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391864	37392217	.	+	.	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	stop_codon	37392218	37392220	.	+	0	transcript_id "Phchi.S1G583600.t2"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	transcript	37387647	37392217	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	start_codon	37387647	37387649	.	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387647	37387720	0.46	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387647	37387720	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37387721	37387867	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387868	37387879	0.95	+	1	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387868	37387879	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37387880	37387966	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37387967	37388020	0.93	+	1	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37387967	37388020	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388021	37388496	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388497	37388637	0.7	+	1	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388497	37388637	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388638	37388717	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388718	37388903	0.99	+	1	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388718	37388903	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37388904	37388980	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37388981	37389158	1	+	1	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37388981	37389158	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389159	37389237	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389238	37389301	1	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389238	37389301	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389302	37389445	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389446	37389557	0.74	+	2	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389446	37389557	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389558	37389631	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389632	37389743	0.74	+	1	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389632	37389743	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37389744	37389969	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37389970	37390059	1	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37389970	37390059	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390060	37390232	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390233	37390418	0.99	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390233	37390418	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390419	37390531	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390532	37390606	0.99	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390532	37390606	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390607	37390725	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390726	37390827	1	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390726	37390827	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37390828	37390936	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37390937	37391033	1	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37390937	37391033	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391034	37391149	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391150	37391290	1	+	2	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391150	37391290	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391291	37391375	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391376	37391482	1	+	2	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391376	37391482	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391483	37391646	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391647	37391760	0.98	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391647	37391760	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	intron	37391761	37391863	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	CDS	37391864	37392217	0.99	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	exon	37391864	37392217	.	+	.	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
Phchi.S1	AUGUSTUS	stop_codon	37392218	37392220	.	+	0	transcript_id "Phchi.S1G583600.t3"; gene_id "Phchi.S1G583600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1878.t1 is derived from g8798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3679097	3679802	.	-	.	Phchi.S5G048700
Phchi.S5	AUGUSTUS	transcript	3679097	3679802	.	-	.	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	stop_codon	3679094	3679096	.	-	0	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	CDS	3679097	3679602	1	-	2	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	exon	3679097	3679602	.	-	.	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	intron	3679603	3679714	.	-	.	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	CDS	3679715	3679802	0.99	-	0	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	exon	3679715	3679802	.	-	.	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
Phchi.S5	AUGUSTUS	start_codon	3679800	3679802	.	-	0	transcript_id "Phchi.S5G048700.t1"; gene_id "Phchi.S5G048700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5288.t1 is derived from g2458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16031828	16032929	.	-	.	Phchi.S1G244700
Phchi.S1	AUGUSTUS	transcript	16031828	16032929	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	stop_codon	16031737	16031739	.	-	0	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	CDS	16031828	16031926	0.93	-	0	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	exon	16031828	16031926	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	intron	16031927	16032012	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	CDS	16032013	16032149	1	-	2	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	exon	16032013	16032149	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	intron	16032150	16032270	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	CDS	16032271	16032576	1	-	2	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	exon	16032271	16032576	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	intron	16032577	16032817	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	CDS	16032818	16032929	0.54	-	0	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	exon	16032818	16032929	.	-	.	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
Phchi.S1	AUGUSTUS	start_codon	16032927	16032929	.	-	0	transcript_id "Phchi.S1G244700.t1"; gene_id "Phchi.S1G244700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1849.t1 is derived from g8769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3546706	3549741	.	-	.	Phchi.S5G045800
Phchi.S5	AUGUSTUS	transcript	3546706	3549741	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	stop_codon	3546703	3546705	.	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3546706	3547269	1	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3546706	3547269	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3547270	3547343	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3547344	3547580	1	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3547344	3547580	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3547581	3547705	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3547706	3547979	1	-	1	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3547706	3547979	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3547980	3548061	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3548062	3548290	0.74	-	2	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3548062	3548290	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3548291	3548462	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3548463	3548520	0.73	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3548463	3548520	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3548521	3548620	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3548621	3548711	1	-	1	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3548621	3548711	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3548712	3548876	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3548877	3548974	1	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3548877	3548974	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3548975	3549209	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3549210	3549337	1	-	2	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3549210	3549337	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3549338	3549485	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3549486	3549560	1	-	2	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3549486	3549560	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	intron	3549561	3549653	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	CDS	3549654	3549741	0.36	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	exon	3549654	3549741	.	-	.	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
Phchi.S5	AUGUSTUS	start_codon	3549739	3549741	.	-	0	transcript_id "Phchi.S5G045800.t1"; gene_id "Phchi.S5G045800"
# This transcript jg6633.t2 is derived from g3805.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6634.t1 is derived from g3806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24180101	24183426	.	-	.	Phchi.S1G379300
Phchi.S1	AUGUSTUS	transcript	24180101	24183426	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	stop_codon	24180098	24180100	.	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24180101	24180544	0.4	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24180101	24180544	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24180545	24180752	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24180753	24180878	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24180753	24180878	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24180879	24181004	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181005	24181211	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181005	24181211	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181212	24181301	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181302	24181409	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181302	24181409	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181410	24181495	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181496	24181585	0.98	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181496	24181585	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181586	24181688	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181689	24181803	0.84	-	1	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181689	24181803	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181804	24181921	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181922	24182048	0.89	-	2	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181922	24182048	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182049	24182153	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182154	24182334	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182154	24182334	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182335	24182509	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182510	24182644	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182510	24182644	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182645	24182761	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182762	24182892	0.99	-	2	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182762	24182892	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182893	24182981	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182982	24183057	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182982	24183057	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24183058	24183147	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24183148	24183155	1	-	2	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24183148	24183155	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24183156	24183239	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24183240	24183426	1	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24183240	24183426	.	-	.	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	start_codon	24183424	24183426	.	-	0	transcript_id "Phchi.S1G379300.t1"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	transcript	24180101	24183426	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	stop_codon	24180098	24180100	.	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24180101	24180544	0.32	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24180101	24180544	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24180545	24180752	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24180753	24180878	1	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24180753	24180878	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24180879	24181004	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181005	24181211	1	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181005	24181211	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181212	24181301	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181302	24181409	1	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181302	24181409	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181410	24181495	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181496	24181585	0.97	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181496	24181585	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181586	24181688	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181689	24181803	0.84	-	1	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181689	24181803	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24181804	24181921	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24181922	24182048	0.87	-	2	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24181922	24182048	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182049	24182153	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182154	24182334	1	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182154	24182334	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182335	24182509	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182510	24182644	0.99	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182510	24182644	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182645	24182761	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182762	24182892	0.99	-	2	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182762	24182892	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24182893	24182981	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24182982	24183065	0.77	-	2	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24182982	24183065	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	intron	24183066	24183239	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	CDS	24183240	24183426	0.99	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	exon	24183240	24183426	.	-	.	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
Phchi.S1	AUGUSTUS	start_codon	24183424	24183426	.	-	0	transcript_id "Phchi.S1G379300.t2"; gene_id "Phchi.S1G379300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15399.t1 is derived from g13867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18820781	18822444	.	-	.	Phchi.S3G271800
Phchi.S3	AUGUSTUS	transcript	18820781	18822444	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	stop_codon	18820778	18820780	.	-	0	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18820781	18820904	0.48	-	1	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18820781	18820904	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	intron	18820905	18820984	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18820985	18821156	1	-	2	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18820985	18821156	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	intron	18821157	18821272	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18821273	18821313	0.7	-	1	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18821273	18821313	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	intron	18821314	18821415	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18821416	18821489	0.7	-	0	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18821416	18821489	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	intron	18821490	18821580	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18821581	18821702	1	-	2	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18821581	18821702	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	intron	18821703	18822007	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18822008	18822263	0.99	-	0	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18822008	18822263	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	intron	18822264	18822360	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	CDS	18822361	18822444	1	-	0	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	exon	18822361	18822444	.	-	.	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
Phchi.S3	AUGUSTUS	start_codon	18822442	18822444	.	-	0	transcript_id "Phchi.S3G271800.t1"; gene_id "Phchi.S3G271800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1062.t1 is derived from g10845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7398481	7401132	.	+	.	Phchi.S6G102100
Phchi.S6	AUGUSTUS	transcript	7398481	7401132	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	start_codon	7398481	7398483	.	+	0	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7398481	7398496	0.99	+	0	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7398481	7398496	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7398497	7398896	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7398897	7399121	1	+	2	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7398897	7399121	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7399122	7399319	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7399320	7399515	1	+	2	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7399320	7399515	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7399516	7399627	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7399628	7399852	1	+	1	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7399628	7399852	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7399853	7399967	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7399968	7400199	1	+	1	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7399968	7400199	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7400200	7400273	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7400274	7400381	0.98	+	0	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7400274	7400381	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7400382	7400485	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7400486	7400758	0.98	+	0	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7400486	7400758	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	intron	7400759	7400853	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	CDS	7400854	7401132	1	+	0	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	exon	7400854	7401132	.	+	.	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
Phchi.S6	AUGUSTUS	stop_codon	7401133	7401135	.	+	0	transcript_id "Phchi.S6G102100.t1"; gene_id "Phchi.S6G102100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1626.t1 is derived from g8545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2083435	2084413	.	-	.	Phchi.S5G023500
Phchi.S5	AUGUSTUS	transcript	2083435	2084413	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	stop_codon	2083432	2083434	.	-	0	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	CDS	2083435	2083665	1	-	0	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	exon	2083435	2083665	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	intron	2083666	2083761	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	CDS	2083762	2083815	1	-	0	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	exon	2083762	2083815	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	intron	2083816	2083909	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	CDS	2083910	2084000	1	-	1	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	exon	2083910	2084000	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	intron	2084001	2084080	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	CDS	2084081	2084088	1	-	0	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	exon	2084081	2084088	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	intron	2084089	2084179	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	CDS	2084180	2084413	0.99	-	0	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	exon	2084180	2084413	.	-	.	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
Phchi.S5	AUGUSTUS	start_codon	2084411	2084413	.	-	0	transcript_id "Phchi.S5G023500.t1"; gene_id "Phchi.S5G023500"
# This transcript jg1693.t2 is derived from g8612.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1694.t1 is derived from g8613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2549672	2551446	.	-	.	Phchi.S5G030300
Phchi.S5	AUGUSTUS	transcript	2549672	2551446	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	stop_codon	2549669	2549671	.	-	0	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2549672	2549742	0.41	-	2	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2549672	2549742	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2549743	2549922	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2549923	2550023	0.43	-	1	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2549923	2550023	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2550024	2550129	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2550130	2550201	0.66	-	1	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2550130	2550201	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2550202	2550289	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2550290	2550416	0.29	-	2	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2550290	2550416	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2550417	2550539	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2550540	2550637	0.52	-	1	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2550540	2550637	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2550638	2550807	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2550808	2550879	1	-	1	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2550808	2550879	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2550880	2550976	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2550977	2551109	0.97	-	2	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2550977	2551109	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	intron	2551110	2551337	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	CDS	2551338	2551446	0.85	-	0	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	exon	2551338	2551446	.	-	.	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
Phchi.S5	AUGUSTUS	start_codon	2551444	2551446	.	-	0	transcript_id "Phchi.S5G030300.t1"; gene_id "Phchi.S5G030300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg738.t1 is derived from g10520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5257106	5257312	.	+	.	Phchi.S6G069700
Phchi.S6	AUGUSTUS	transcript	5257106	5257312	.	+	.	transcript_id "Phchi.S6G069700.t1"; gene_id "Phchi.S6G069700"
Phchi.S6	AUGUSTUS	start_codon	5257106	5257108	.	+	0	transcript_id "Phchi.S6G069700.t1"; gene_id "Phchi.S6G069700"
Phchi.S6	AUGUSTUS	CDS	5257106	5257312	0.56	+	0	transcript_id "Phchi.S6G069700.t1"; gene_id "Phchi.S6G069700"
Phchi.S6	AUGUSTUS	exon	5257106	5257312	.	+	.	transcript_id "Phchi.S6G069700.t1"; gene_id "Phchi.S6G069700"
Phchi.S6	AUGUSTUS	stop_codon	5257313	5257315	.	+	0	transcript_id "Phchi.S6G069700.t1"; gene_id "Phchi.S6G069700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg278.t1 is derived from g10060.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2003770	2004810	.	+	.	Phchi.S6G023700
Phchi.S6	AUGUSTUS	transcript	2003770	2004794	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	start_codon	2003770	2003772	.	+	0	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2003770	2003772	0.99	+	0	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2003770	2003772	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2003773	2003863	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2003864	2003922	1	+	0	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2003864	2003922	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2003923	2004037	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004038	2004143	1	+	1	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004038	2004143	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2004144	2004233	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004234	2004292	0.99	+	0	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004234	2004292	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2004293	2004517	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004518	2004574	0.92	+	1	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004518	2004574	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2004575	2004775	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004776	2004794	0.91	+	1	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004776	2004794	.	+	.	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	stop_codon	2004795	2004797	.	+	0	transcript_id "Phchi.S6G023700.t1"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	transcript	2003770	2004810	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	start_codon	2003770	2003772	.	+	0	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2003770	2003772	1	+	0	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2003770	2003772	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2003773	2003863	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2003864	2003922	1	+	0	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2003864	2003922	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2003923	2004037	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004038	2004143	1	+	1	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004038	2004143	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2004144	2004233	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004234	2004357	1	+	0	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004234	2004357	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2004358	2004517	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004518	2004574	0.67	+	2	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004518	2004574	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	intron	2004575	2004775	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	CDS	2004776	2004810	0.65	+	2	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	exon	2004776	2004810	.	+	.	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
Phchi.S6	AUGUSTUS	stop_codon	2004811	2004813	.	+	0	transcript_id "Phchi.S6G023700.t2"; gene_id "Phchi.S6G023700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11989.t1 is derived from g7664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	401121	402449	.	+	.	Phchi.S2G006900
Phchi.S2	AUGUSTUS	transcript	401121	402449	.	+	.	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	start_codon	401121	401123	.	+	0	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	CDS	401121	401372	0.54	+	0	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	exon	401121	401372	.	+	.	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	intron	401373	401465	.	+	.	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	CDS	401466	402449	0.91	+	0	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	exon	401466	402449	.	+	.	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
Phchi.S2	AUGUSTUS	stop_codon	402450	402452	.	+	0	transcript_id "Phchi.S2G006900.t1"; gene_id "Phchi.S2G006900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2902.t1 is derived from g71.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	398219	398791	.	-	.	Phchi.S1G006100
Phchi.S1	AUGUSTUS	transcript	398219	398791	.	-	.	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	stop_codon	398116	398118	.	-	0	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	CDS	398219	398289	0.59	-	2	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	exon	398219	398289	.	-	.	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	intron	398290	398377	.	-	.	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	CDS	398378	398602	0.99	-	2	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	exon	398378	398602	.	-	.	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	intron	398603	398670	.	-	.	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	CDS	398671	398791	0.92	-	0	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	exon	398671	398791	.	-	.	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
Phchi.S1	AUGUSTUS	start_codon	398789	398791	.	-	0	transcript_id "Phchi.S1G006100.t1"; gene_id "Phchi.S1G006100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2668.t1 is derived from g9588.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8119119	8120696	.	-	.	Phchi.S5G127700
Phchi.S5	AUGUSTUS	transcript	8119119	8120696	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	stop_codon	8119116	8119118	.	-	0	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	CDS	8119119	8119496	0.77	-	0	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	exon	8119119	8119496	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	intron	8119497	8119625	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	CDS	8119626	8119881	1	-	1	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	exon	8119626	8119881	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	intron	8119882	8120011	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	CDS	8120012	8120087	1	-	2	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	exon	8120012	8120087	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	intron	8120088	8120265	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	CDS	8120266	8120460	0.97	-	2	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	exon	8120266	8120460	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	intron	8120461	8120537	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	CDS	8120538	8120552	0.92	-	2	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	exon	8120538	8120552	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	intron	8120553	8120665	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	CDS	8120666	8120696	0.92	-	0	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	exon	8120666	8120696	.	-	.	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
Phchi.S5	AUGUSTUS	start_codon	8120694	8120696	.	-	0	transcript_id "Phchi.S5G127700.t1"; gene_id "Phchi.S5G127700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12692.t1 is derived from g11157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	575011	575408	.	+	.	Phchi.S3G001100
Phchi.S3	AUGUSTUS	transcript	575011	575408	.	+	.	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	start_codon	575011	575013	.	+	0	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	CDS	575011	575077	0.98	+	0	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	exon	575011	575077	.	+	.	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	intron	575078	575232	.	+	.	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	CDS	575233	575408	0.81	+	2	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	exon	575233	575408	.	+	.	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
Phchi.S3	AUGUSTUS	stop_codon	575409	575411	.	+	0	transcript_id "Phchi.S3G001100.t1"; gene_id "Phchi.S3G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14304.t1 is derived from g12771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12022069	12024530	.	-	.	Phchi.S3G162300
Phchi.S3	AUGUSTUS	transcript	12022069	12024530	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	stop_codon	12022066	12022068	.	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12022069	12022140	0.98	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12022069	12022140	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12022141	12022231	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12022232	12022330	0.98	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12022232	12022330	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12022331	12022411	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12022412	12022453	0.98	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12022412	12022453	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12022454	12022558	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12022559	12022600	0.84	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12022559	12022600	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12022601	12022701	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12022702	12022797	1	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12022702	12022797	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12022798	12022964	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12022965	12023088	1	-	1	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12022965	12023088	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12023089	12023256	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12023257	12023583	1	-	1	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12023257	12023583	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12023584	12023769	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12023770	12023920	1	-	2	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12023770	12023920	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12023921	12024078	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12024079	12024113	1	-	1	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12024079	12024113	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	intron	12024114	12024348	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	CDS	12024349	12024530	0.49	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	exon	12024349	12024530	.	-	.	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
Phchi.S3	AUGUSTUS	start_codon	12024528	12024530	.	-	0	transcript_id "Phchi.S3G162300.t1"; gene_id "Phchi.S3G162300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7260.t1 is derived from g4432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27903320	27906008	.	-	.	Phchi.S1G441900
Phchi.S1	AUGUSTUS	transcript	27903320	27906008	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	stop_codon	27903317	27903319	.	-	0	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	CDS	27903320	27903419	0.91	-	1	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	exon	27903320	27903419	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	intron	27903420	27903490	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	CDS	27903491	27903512	0.67	-	2	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	exon	27903491	27903512	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	intron	27903513	27903866	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	CDS	27903867	27904390	0.62	-	1	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	exon	27903867	27904390	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	intron	27904391	27904485	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	CDS	27904486	27905432	0.99	-	0	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	exon	27904486	27905432	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	intron	27905433	27905681	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	CDS	27905682	27906008	0.71	-	0	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	exon	27905682	27906008	.	-	.	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
Phchi.S1	AUGUSTUS	start_codon	27906006	27906008	.	-	0	transcript_id "Phchi.S1G441900.t1"; gene_id "Phchi.S1G441900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9367.t1 is derived from g6543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41187259	41188035	.	-	.	Phchi.S1G652600
Phchi.S1	AUGUSTUS	transcript	41187259	41188035	.	-	.	transcript_id "Phchi.S1G652600.t1"; gene_id "Phchi.S1G652600"
Phchi.S1	AUGUSTUS	stop_codon	41187256	41187258	.	-	0	transcript_id "Phchi.S1G652600.t1"; gene_id "Phchi.S1G652600"
Phchi.S1	AUGUSTUS	CDS	41187259	41188035	0.65	-	0	transcript_id "Phchi.S1G652600.t1"; gene_id "Phchi.S1G652600"
Phchi.S1	AUGUSTUS	exon	41187259	41188035	.	-	.	transcript_id "Phchi.S1G652600.t1"; gene_id "Phchi.S1G652600"
Phchi.S1	AUGUSTUS	start_codon	41188033	41188035	.	-	0	transcript_id "Phchi.S1G652600.t1"; gene_id "Phchi.S1G652600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7663.t1 is derived from g4837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30492450	30493231	.	+	.	Phchi.S1G482200
Phchi.S1	AUGUSTUS	transcript	30492450	30493231	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	start_codon	30492450	30492452	.	+	0	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	CDS	30492450	30492625	0.58	+	0	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	exon	30492450	30492625	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	intron	30492626	30492708	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	CDS	30492709	30492758	1	+	1	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	exon	30492709	30492758	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	intron	30492759	30492886	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	CDS	30492887	30492939	1	+	2	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	exon	30492887	30492939	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	intron	30492940	30493060	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	CDS	30493061	30493231	0.96	+	0	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	exon	30493061	30493231	.	+	.	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
Phchi.S1	AUGUSTUS	stop_codon	30493232	30493234	.	+	0	transcript_id "Phchi.S1G482200.t1"; gene_id "Phchi.S1G482200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7598.t1 is derived from g4772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30199150	30199688	.	+	.	Phchi.S1G475700
Phchi.S1	AUGUSTUS	transcript	30199150	30199688	.	+	.	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	start_codon	30199150	30199152	.	+	0	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	CDS	30199150	30199359	0.45	+	0	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	exon	30199150	30199359	.	+	.	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	intron	30199360	30199457	.	+	.	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	CDS	30199458	30199688	0.88	+	0	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	exon	30199458	30199688	.	+	.	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
Phchi.S1	AUGUSTUS	stop_codon	30199689	30199691	.	+	0	transcript_id "Phchi.S1G475700.t1"; gene_id "Phchi.S1G475700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7767.t1 is derived from g4941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31166322	31168188	.	+	.	Phchi.S1G492600
Phchi.S1	AUGUSTUS	transcript	31166322	31168188	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	start_codon	31166322	31166324	.	+	0	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	CDS	31166322	31166537	0.27	+	0	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	exon	31166322	31166537	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	intron	31166538	31166617	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	CDS	31166618	31166869	0.38	+	0	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	exon	31166618	31166869	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	intron	31166870	31166982	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	CDS	31166983	31167162	0.18	+	0	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	exon	31166983	31167162	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	intron	31167163	31167242	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	CDS	31167243	31167582	0.38	+	0	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	exon	31167243	31167582	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	intron	31167583	31167673	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	CDS	31167674	31168188	0.5	+	2	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	exon	31167674	31168188	.	+	.	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
Phchi.S1	AUGUSTUS	stop_codon	31168189	31168191	.	+	0	transcript_id "Phchi.S1G492600.t1"; gene_id "Phchi.S1G492600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4161.t1 is derived from g1330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8686325	8686747	.	-	.	Phchi.S1G132000
Phchi.S1	AUGUSTUS	transcript	8686325	8686747	.	-	.	transcript_id "Phchi.S1G132000.t1"; gene_id "Phchi.S1G132000"
Phchi.S1	AUGUSTUS	stop_codon	8686322	8686324	.	-	0	transcript_id "Phchi.S1G132000.t1"; gene_id "Phchi.S1G132000"
Phchi.S1	AUGUSTUS	CDS	8686325	8686747	0.5	-	0	transcript_id "Phchi.S1G132000.t1"; gene_id "Phchi.S1G132000"
Phchi.S1	AUGUSTUS	exon	8686325	8686747	.	-	.	transcript_id "Phchi.S1G132000.t1"; gene_id "Phchi.S1G132000"
Phchi.S1	AUGUSTUS	start_codon	8686745	8686747	.	-	0	transcript_id "Phchi.S1G132000.t1"; gene_id "Phchi.S1G132000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8714.t1 is derived from g5889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37620122	37621063	.	+	.	Phchi.S1G587300
Phchi.S1	AUGUSTUS	transcript	37620122	37621063	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	start_codon	37620122	37620124	.	+	0	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	CDS	37620122	37620294	0.81	+	0	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	exon	37620122	37620294	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	intron	37620295	37620440	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	CDS	37620441	37620606	0.52	+	1	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	exon	37620441	37620606	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	intron	37620607	37620714	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	CDS	37620715	37620840	0.99	+	0	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	exon	37620715	37620840	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	intron	37620841	37620940	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	CDS	37620941	37621063	1	+	0	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	exon	37620941	37621063	.	+	.	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
Phchi.S1	AUGUSTUS	stop_codon	37621064	37621066	.	+	0	transcript_id "Phchi.S1G587300.t1"; gene_id "Phchi.S1G587300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5257.t1 is derived from g2427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15892514	15897812	.	-	.	Phchi.S1G241600
Phchi.S1	AUGUSTUS	transcript	15892514	15897812	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	stop_codon	15892511	15892513	.	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15892514	15892607	1	-	1	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15892514	15892607	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15892608	15892703	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15892704	15892885	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15892704	15892885	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15892886	15893011	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15893012	15893194	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15893012	15893194	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15893195	15893271	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15893272	15893445	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15893272	15893445	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15893446	15893547	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15893548	15893708	0.97	-	2	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15893548	15893708	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15893709	15893817	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15893818	15893899	0.99	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15893818	15893899	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15893900	15894000	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15894001	15894033	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15894001	15894033	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15894034	15894114	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15894115	15894353	1	-	2	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15894115	15894353	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15894354	15894436	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15894437	15894601	1	-	2	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15894437	15894601	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15894602	15894680	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15894681	15894825	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15894681	15894825	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15894826	15894897	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15894898	15895002	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15894898	15895002	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15895003	15895098	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15895099	15895221	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15895099	15895221	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15895222	15895300	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15895301	15895420	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15895301	15895420	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15895421	15895524	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15895525	15895644	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15895525	15895644	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15895645	15895727	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15895728	15895934	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15895728	15895934	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15895935	15896026	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15896027	15896206	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15896027	15896206	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15896207	15896293	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15896294	15896428	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15896294	15896428	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15896429	15896504	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15896505	15896642	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15896505	15896642	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15896643	15896819	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15896820	15896918	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15896820	15896918	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15896919	15897006	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15897007	15897126	1	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15897007	15897126	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15897127	15897226	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15897227	15897347	0.64	-	1	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15897227	15897347	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15897348	15897520	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15897521	15897587	0.64	-	2	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15897521	15897587	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	intron	15897588	15897805	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	CDS	15897806	15897812	0.86	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	exon	15897806	15897812	.	-	.	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
Phchi.S1	AUGUSTUS	start_codon	15897810	15897812	.	-	0	transcript_id "Phchi.S1G241600.t1"; gene_id "Phchi.S1G241600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6572.t1 is derived from g3744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23774492	23775821	.	-	.	Phchi.S1G373100
Phchi.S1	AUGUSTUS	transcript	23774492	23775821	.	-	.	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	stop_codon	23774489	23774491	.	-	0	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	CDS	23774492	23775420	0.7	-	2	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	exon	23774492	23775420	.	-	.	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	intron	23775421	23775547	.	-	.	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	CDS	23775548	23775821	0.55	-	0	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	exon	23775548	23775821	.	-	.	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
Phchi.S1	AUGUSTUS	start_codon	23775819	23775821	.	-	0	transcript_id "Phchi.S1G373100.t1"; gene_id "Phchi.S1G373100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5571.t1 is derived from g2741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17633982	17638196	.	-	.	Phchi.S1G273000
Phchi.S1	AUGUSTUS	transcript	17633982	17638196	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	stop_codon	17633979	17633981	.	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17633982	17634115	1	-	2	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17633982	17634115	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17634116	17634319	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17634320	17634419	1	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17634320	17634419	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17634420	17634509	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17634510	17634605	1	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17634510	17634605	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17634606	17634701	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17634702	17634881	1	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17634702	17634881	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17634882	17635052	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17635053	17635139	1	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17635053	17635139	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17635140	17635251	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17635252	17635308	1	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17635252	17635308	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17635309	17635416	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17635417	17635482	0.99	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17635417	17635482	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17635483	17635650	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17635651	17636165	0.54	-	2	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17635651	17636165	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17636166	17636405	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17636406	17636867	0.36	-	2	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17636406	17636867	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17636868	17636960	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17636961	17637063	0.78	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17636961	17637063	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17637064	17637221	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17637222	17637450	1	-	1	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17637222	17637450	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17637451	17637544	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17637545	17637975	1	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17637545	17637975	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	intron	17637976	17638121	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	CDS	17638122	17638196	0.75	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	exon	17638122	17638196	.	-	.	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
Phchi.S1	AUGUSTUS	start_codon	17638194	17638196	.	-	0	transcript_id "Phchi.S1G273000.t1"; gene_id "Phchi.S1G273000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3849.t1 is derived from g1018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6026229	6029833	.	+	.	Phchi.S1G100800
Phchi.S1	AUGUSTUS	transcript	6026229	6029833	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	start_codon	6026229	6026231	.	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6026229	6026401	0.51	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6026229	6026401	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6026402	6026536	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6026537	6026768	1	+	1	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6026537	6026768	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6026769	6027032	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6027033	6027128	1	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6027033	6027128	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6027129	6027298	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6027299	6027468	0.98	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6027299	6027468	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6027469	6027580	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6027581	6027723	0.97	+	1	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6027581	6027723	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6027724	6027832	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6027833	6028010	0.98	+	2	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6027833	6028010	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6028011	6028096	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6028097	6028155	0.96	+	1	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6028097	6028155	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6028156	6028340	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6028341	6028693	0.71	+	2	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6028341	6028693	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6028694	6028824	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6028825	6028937	1	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6028825	6028937	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6028938	6029030	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6029031	6029271	0.91	+	1	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6029031	6029271	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6029272	6029378	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6029379	6029443	0.68	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6029379	6029443	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6029444	6029579	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6029580	6029628	0.67	+	1	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6029580	6029628	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	intron	6029629	6029815	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	CDS	6029816	6029833	0.83	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	exon	6029816	6029833	.	+	.	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
Phchi.S1	AUGUSTUS	stop_codon	6029834	6029836	.	+	0	transcript_id "Phchi.S1G100800.t1"; gene_id "Phchi.S1G100800"
# This transcript jg14407.t2 is derived from g12875.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14408.t1 is derived from g12876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12685426	12686271	.	+	.	Phchi.S3G172700
Phchi.S3	AUGUSTUS	transcript	12685426	12686271	.	+	.	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	start_codon	12685426	12685428	.	+	0	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	CDS	12685426	12685680	0.88	+	0	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	exon	12685426	12685680	.	+	.	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	intron	12685681	12685847	.	+	.	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	CDS	12685848	12685915	1	+	0	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	exon	12685848	12685915	.	+	.	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	intron	12685916	12686114	.	+	.	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	CDS	12686115	12686271	0.93	+	1	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	exon	12686115	12686271	.	+	.	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
Phchi.S3	AUGUSTUS	stop_codon	12686272	12686274	.	+	0	transcript_id "Phchi.S3G172700.t1"; gene_id "Phchi.S3G172700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10705.t1 is derived from g14755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1679939	1680572	.	-	.	Phchi.S4G028700
Phchi.S4	AUGUSTUS	transcript	1679939	1680572	.	-	.	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	stop_codon	1679936	1679938	.	-	0	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	CDS	1679939	1679995	1	-	0	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	exon	1679939	1679995	.	-	.	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	intron	1679996	1680416	.	-	.	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	CDS	1680417	1680572	0.94	-	0	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	exon	1680417	1680572	.	-	.	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
Phchi.S4	AUGUSTUS	start_codon	1680570	1680572	.	-	0	transcript_id "Phchi.S4G028700.t1"; gene_id "Phchi.S4G028700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1897.t1 is derived from g8817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3772330	3773595	.	+	.	Phchi.S5G050600
Phchi.S5	AUGUSTUS	transcript	3772330	3773595	.	+	.	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	start_codon	3772330	3772332	.	+	0	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	CDS	3772330	3772886	0.56	+	0	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	exon	3772330	3772886	.	+	.	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	intron	3772887	3773087	.	+	.	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	CDS	3773088	3773595	0.55	+	1	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	exon	3773088	3773595	.	+	.	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
Phchi.S5	AUGUSTUS	stop_codon	3773596	3773598	.	+	0	transcript_id "Phchi.S5G050600.t1"; gene_id "Phchi.S5G050600"
# This transcript jg7961.t2 is derived from g5136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7962.t1 is derived from g5137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32114683	32117175	.	+	.	Phchi.S1G512100
Phchi.S1	AUGUSTUS	transcript	32114683	32117175	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	start_codon	32114683	32114685	.	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32114683	32114769	0.97	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32114683	32114769	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32114770	32114923	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32114924	32115100	1	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32114924	32115100	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32115101	32115220	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32115221	32115274	1	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32115221	32115274	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32115275	32115368	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32115369	32115431	1	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32115369	32115431	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32115432	32115516	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32115517	32116298	0.89	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32115517	32116298	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32116299	32116372	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32116373	32116529	0.96	+	1	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32116373	32116529	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32116530	32116632	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32116633	32116760	1	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32116633	32116760	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	intron	32116761	32116904	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	CDS	32116905	32117175	1	+	1	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	exon	32116905	32117175	.	+	.	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
Phchi.S1	AUGUSTUS	stop_codon	32117176	32117178	.	+	0	transcript_id "Phchi.S1G512100.t1"; gene_id "Phchi.S1G512100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10085.t1 is derived from g7261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45667249	45667730	.	+	.	Phchi.S1G724400
Phchi.S1	AUGUSTUS	transcript	45667249	45667730	.	+	.	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	start_codon	45667249	45667251	.	+	0	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	CDS	45667249	45667543	0.71	+	0	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	exon	45667249	45667543	.	+	.	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	intron	45667544	45667704	.	+	.	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	CDS	45667705	45667730	0.44	+	2	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	exon	45667705	45667730	.	+	.	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
Phchi.S1	AUGUSTUS	stop_codon	45667731	45667733	.	+	0	transcript_id "Phchi.S1G724400.t1"; gene_id "Phchi.S1G724400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8840.t1 is derived from g6015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38228291	38229354	.	+	.	Phchi.S1G599900
Phchi.S1	AUGUSTUS	transcript	38228291	38229354	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	start_codon	38228291	38228293	.	+	0	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	CDS	38228291	38228571	1	+	0	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	exon	38228291	38228571	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	intron	38228572	38228655	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	CDS	38228656	38228830	1	+	1	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	exon	38228656	38228830	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	intron	38228831	38228951	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	CDS	38228952	38229221	0.48	+	0	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	exon	38228952	38229221	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	intron	38229222	38229303	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	CDS	38229304	38229354	0.48	+	0	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	exon	38229304	38229354	.	+	.	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
Phchi.S1	AUGUSTUS	stop_codon	38229355	38229357	.	+	0	transcript_id "Phchi.S1G599900.t1"; gene_id "Phchi.S1G599900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9310.t1 is derived from g6485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40896797	40898049	.	-	.	Phchi.S1G646900
Phchi.S1	AUGUSTUS	transcript	40896797	40898049	.	-	.	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	stop_codon	40896794	40896796	.	-	0	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	CDS	40896797	40897177	1	-	0	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	exon	40896797	40897177	.	-	.	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	intron	40897178	40897376	.	-	.	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	CDS	40897377	40897608	1	-	1	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	exon	40897377	40897608	.	-	.	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	intron	40897609	40897738	.	-	.	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	CDS	40897739	40898049	0.52	-	0	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	exon	40897739	40898049	.	-	.	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
Phchi.S1	AUGUSTUS	start_codon	40898047	40898049	.	-	0	transcript_id "Phchi.S1G646900.t1"; gene_id "Phchi.S1G646900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6672.t1 is derived from g3844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24436956	24438832	.	+	.	Phchi.S1G383100
Phchi.S1	AUGUSTUS	transcript	24436956	24438832	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	start_codon	24436956	24436958	.	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24436956	24437004	1	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24436956	24437004	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24437005	24437104	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24437105	24437259	1	+	2	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24437105	24437259	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24437260	24437337	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24437338	24437529	1	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24437338	24437529	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24437530	24437625	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24437626	24437841	1	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24437626	24437841	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24437842	24437936	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24437937	24438093	1	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24437937	24438093	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24438094	24438162	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24438163	24438211	1	+	2	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24438163	24438211	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24438212	24438301	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24438302	24438370	1	+	1	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24438302	24438370	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24438371	24438445	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24438446	24438659	1	+	1	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24438446	24438659	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	intron	24438660	24438754	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	CDS	24438755	24438832	1	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	exon	24438755	24438832	.	+	.	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
Phchi.S1	AUGUSTUS	stop_codon	24438833	24438835	.	+	0	transcript_id "Phchi.S1G383100.t1"; gene_id "Phchi.S1G383100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7782.t1 is derived from g4956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31188050	31188526	.	+	.	Phchi.S1G494100
Phchi.S1	AUGUSTUS	transcript	31188050	31188526	.	+	.	transcript_id "Phchi.S1G494100.t1"; gene_id "Phchi.S1G494100"
Phchi.S1	AUGUSTUS	start_codon	31188050	31188052	.	+	0	transcript_id "Phchi.S1G494100.t1"; gene_id "Phchi.S1G494100"
Phchi.S1	AUGUSTUS	CDS	31188050	31188526	1	+	0	transcript_id "Phchi.S1G494100.t1"; gene_id "Phchi.S1G494100"
Phchi.S1	AUGUSTUS	exon	31188050	31188526	.	+	.	transcript_id "Phchi.S1G494100.t1"; gene_id "Phchi.S1G494100"
Phchi.S1	AUGUSTUS	stop_codon	31188527	31188529	.	+	0	transcript_id "Phchi.S1G494100.t1"; gene_id "Phchi.S1G494100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14967.t1 is derived from g13435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15786121	15787933	.	-	.	Phchi.S3G228600
Phchi.S3	AUGUSTUS	transcript	15786121	15787933	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	stop_codon	15786118	15786120	.	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	CDS	15786121	15786636	1	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	exon	15786121	15786636	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	intron	15786637	15786717	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	CDS	15786718	15786894	1	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	exon	15786718	15786894	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	intron	15786895	15786985	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	CDS	15786986	15787192	1	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	exon	15786986	15787192	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	intron	15787193	15787270	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	CDS	15787271	15787405	0.74	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	exon	15787271	15787405	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	intron	15787406	15787513	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	CDS	15787514	15787933	0.67	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	exon	15787514	15787933	.	-	.	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
Phchi.S3	AUGUSTUS	start_codon	15787931	15787933	.	-	0	transcript_id "Phchi.S3G228600.t1"; gene_id "Phchi.S3G228600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4645.t1 is derived from g1815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11622029	11622466	.	-	.	Phchi.S1G180400
Phchi.S1	AUGUSTUS	transcript	11622029	11622466	.	-	.	transcript_id "Phchi.S1G180400.t1"; gene_id "Phchi.S1G180400"
Phchi.S1	AUGUSTUS	stop_codon	11622026	11622028	.	-	0	transcript_id "Phchi.S1G180400.t1"; gene_id "Phchi.S1G180400"
Phchi.S1	AUGUSTUS	CDS	11622029	11622466	0.69	-	0	transcript_id "Phchi.S1G180400.t1"; gene_id "Phchi.S1G180400"
Phchi.S1	AUGUSTUS	exon	11622029	11622466	.	-	.	transcript_id "Phchi.S1G180400.t1"; gene_id "Phchi.S1G180400"
Phchi.S1	AUGUSTUS	start_codon	11622464	11622466	.	-	0	transcript_id "Phchi.S1G180400.t1"; gene_id "Phchi.S1G180400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13879.t1 is derived from g12346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9435180	9436445	.	+	.	Phchi.S3G119800
Phchi.S3	AUGUSTUS	transcript	9435180	9436445	.	+	.	transcript_id "Phchi.S3G119800.t1"; gene_id "Phchi.S3G119800"
Phchi.S3	AUGUSTUS	start_codon	9435180	9435182	.	+	0	transcript_id "Phchi.S3G119800.t1"; gene_id "Phchi.S3G119800"
Phchi.S3	AUGUSTUS	CDS	9435180	9436445	0.76	+	0	transcript_id "Phchi.S3G119800.t1"; gene_id "Phchi.S3G119800"
Phchi.S3	AUGUSTUS	exon	9435180	9436445	.	+	.	transcript_id "Phchi.S3G119800.t1"; gene_id "Phchi.S3G119800"
Phchi.S3	AUGUSTUS	stop_codon	9436446	9436448	.	+	0	transcript_id "Phchi.S3G119800.t1"; gene_id "Phchi.S3G119800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2997.t1 is derived from g166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1060182	1061329	.	+	.	Phchi.S1G015600
Phchi.S1	AUGUSTUS	transcript	1060182	1061329	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	start_codon	1060182	1060184	.	+	0	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	CDS	1060182	1060460	0.99	+	0	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	exon	1060182	1060460	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	intron	1060461	1060580	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	CDS	1060581	1060712	1	+	0	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	exon	1060581	1060712	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	intron	1060713	1060791	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	CDS	1060792	1060908	1	+	0	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	exon	1060792	1060908	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	intron	1060909	1060993	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	CDS	1060994	1061329	1	+	0	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	exon	1060994	1061329	.	+	.	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
Phchi.S1	AUGUSTUS	stop_codon	1061330	1061332	.	+	0	transcript_id "Phchi.S1G015600.t1"; gene_id "Phchi.S1G015600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15835.t1 is derived from g14305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21657226	21658802	.	-	.	Phchi.S3G315400
Phchi.S3	AUGUSTUS	transcript	21657226	21658802	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	stop_codon	21657223	21657225	.	-	0	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	CDS	21657226	21657261	1	-	0	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	exon	21657226	21657261	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	intron	21657262	21657401	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	CDS	21657402	21657446	0.82	-	0	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	exon	21657402	21657446	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	intron	21657447	21657899	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	CDS	21657900	21658060	0.92	-	2	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	exon	21657900	21658060	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	intron	21658061	21658155	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	CDS	21658156	21658386	0.99	-	2	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	exon	21658156	21658386	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	intron	21658387	21658588	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	CDS	21658589	21658676	1	-	0	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	exon	21658589	21658676	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	intron	21658677	21658775	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	CDS	21658776	21658802	0.78	-	0	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	exon	21658776	21658802	.	-	.	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
Phchi.S3	AUGUSTUS	start_codon	21658800	21658802	.	-	0	transcript_id "Phchi.S3G315400.t1"; gene_id "Phchi.S3G315400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3389.t1 is derived from g558.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3313124	3314922	.	-	.	Phchi.S1G054800
Phchi.S1	AUGUSTUS	transcript	3313124	3313964	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	stop_codon	3313121	3313123	.	-	0	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313124	3313134	1	-	2	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313124	3313134	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313135	3313349	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313350	3313461	1	-	0	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313350	3313461	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313462	3313575	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313576	3313643	1	-	2	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313576	3313643	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313644	3313766	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313767	3313800	1	-	0	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313767	3313800	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313801	3313946	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313947	3313964	0.92	-	0	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313947	3313964	.	-	.	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	start_codon	3313962	3313964	.	-	0	transcript_id "Phchi.S1G054800.t1"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	transcript	3313124	3314922	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	stop_codon	3313121	3313123	.	-	0	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313124	3313134	1	-	2	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313124	3313134	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313135	3313349	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313350	3313461	1	-	0	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313350	3313461	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313462	3313575	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313576	3313643	1	-	2	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313576	3313643	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313644	3313766	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3313767	3313800	1	-	0	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3313767	3313800	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3313801	3314010	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3314011	3314042	1	-	2	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3314011	3314042	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3314043	3314235	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3314236	3314287	1	-	0	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3314236	3314287	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	intron	3314288	3314826	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	CDS	3314827	3314922	0.64	-	0	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	exon	3314827	3314922	.	-	.	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
Phchi.S1	AUGUSTUS	start_codon	3314920	3314922	.	-	0	transcript_id "Phchi.S1G054800.t2"; gene_id "Phchi.S1G054800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15087.t1 is derived from g13555.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16955272	16958559	.	-	.	Phchi.S3G240600
Phchi.S3	AUGUSTUS	transcript	16955272	16958559	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	stop_codon	16955269	16955271	.	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955272	16955349	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955272	16955349	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955350	16955420	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955421	16955481	1	-	1	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955421	16955481	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955482	16955624	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955625	16955701	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955625	16955701	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955702	16955794	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955795	16955932	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955795	16955932	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955933	16956016	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956017	16956097	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956017	16956097	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956098	16956198	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956199	16956348	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956199	16956348	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956349	16956513	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956514	16956615	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956514	16956615	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956616	16956705	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956706	16956825	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956706	16956825	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956826	16956904	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956905	16957073	1	-	1	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956905	16957073	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957074	16957149	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957150	16957223	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957150	16957223	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957224	16957319	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957320	16957377	1	-	1	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957320	16957377	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957378	16957468	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957469	16957560	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957469	16957560	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957561	16957637	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957638	16957673	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957638	16957673	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957674	16957747	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957748	16957841	1	-	1	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957748	16957841	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957842	16957933	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957934	16957986	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957934	16957986	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957987	16958117	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16958118	16958179	1	-	2	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16958118	16958179	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16958180	16958381	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16958382	16958559	1	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16958382	16958559	.	-	.	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	start_codon	16958557	16958559	.	-	0	transcript_id "Phchi.S3G240600.t1"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	transcript	16955272	16958559	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	stop_codon	16955269	16955271	.	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955272	16955349	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955272	16955349	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955350	16955420	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955421	16955481	1	-	1	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955421	16955481	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955482	16955624	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955625	16955701	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955625	16955701	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955702	16955794	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16955795	16955932	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16955795	16955932	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16955933	16956016	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956017	16956097	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956017	16956097	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956098	16956198	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956199	16956348	0.98	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956199	16956348	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956349	16956513	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956514	16956615	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956514	16956615	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956616	16956705	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956706	16956825	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956706	16956825	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16956826	16956904	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16956905	16957073	1	-	1	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16956905	16957073	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957074	16957149	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957150	16957223	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957150	16957223	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957224	16957319	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957320	16957377	1	-	1	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957320	16957377	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957378	16957468	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957469	16957560	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957469	16957560	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957561	16957637	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957638	16957808	0.84	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957638	16957808	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16957809	16957933	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16957934	16958002	0.81	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16957934	16958002	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16958003	16958117	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16958118	16958179	1	-	2	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16958118	16958179	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	intron	16958180	16958381	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	CDS	16958382	16958559	1	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	exon	16958382	16958559	.	-	.	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
Phchi.S3	AUGUSTUS	start_codon	16958557	16958559	.	-	0	transcript_id "Phchi.S3G240600.t2"; gene_id "Phchi.S3G240600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7669.t1 is derived from g4843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30538807	30541739	.	-	.	Phchi.S1G482800
Phchi.S1	AUGUSTUS	transcript	30538807	30541739	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	stop_codon	30538804	30538806	.	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30538807	30538950	0.96	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30538807	30538950	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30538951	30539057	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30539058	30539373	1	-	1	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30539058	30539373	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30539374	30539462	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30539463	30539948	1	-	1	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30539463	30539948	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30539949	30540067	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30540068	30540144	1	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30540068	30540144	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30540145	30540238	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30540239	30540354	0.99	-	2	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30540239	30540354	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30540355	30540461	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30540462	30540533	1	-	2	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30540462	30540533	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30540534	30540618	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30540619	30540747	1	-	2	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30540619	30540747	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30540748	30541005	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30541006	30541117	1	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30541006	30541117	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30541118	30541257	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30541258	30541323	1	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30541258	30541323	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30541324	30541526	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30541527	30541583	1	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30541527	30541583	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	intron	30541584	30541730	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	CDS	30541731	30541739	0.99	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	exon	30541731	30541739	.	-	.	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
Phchi.S1	AUGUSTUS	start_codon	30541737	30541739	.	-	0	transcript_id "Phchi.S1G482800.t1"; gene_id "Phchi.S1G482800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5900.t1 is derived from g3070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19663974	19665176	.	+	.	Phchi.S1G305900
Phchi.S1	AUGUSTUS	transcript	19663974	19665176	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	start_codon	19663974	19663976	.	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	CDS	19663974	19664172	0.98	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	exon	19663974	19664172	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	intron	19664173	19664289	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	CDS	19664290	19664387	1	+	2	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	exon	19664290	19664387	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	intron	19664388	19664525	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	CDS	19664526	19664630	1	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	exon	19664526	19664630	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	intron	19664631	19664784	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	CDS	19664785	19664850	1	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	exon	19664785	19664850	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	intron	19664851	19664927	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	CDS	19664928	19665014	0.91	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	exon	19664928	19665014	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	intron	19665015	19665128	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	CDS	19665129	19665176	0.9	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	exon	19665129	19665176	.	+	.	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
Phchi.S1	AUGUSTUS	stop_codon	19665177	19665179	.	+	0	transcript_id "Phchi.S1G305900.t1"; gene_id "Phchi.S1G305900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5709.t1 is derived from g2879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18473837	18479496	.	+	.	Phchi.S1G286800
Phchi.S1	AUGUSTUS	transcript	18473837	18479496	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	start_codon	18473837	18473839	.	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18473837	18474472	0.9	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18473837	18474472	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18474473	18474626	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18474627	18474692	0.98	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18474627	18474692	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18474693	18474800	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18474801	18474995	0.98	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18474801	18474995	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18474996	18475112	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18475113	18475202	0.99	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18475113	18475202	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18475203	18475296	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18475297	18475338	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18475297	18475338	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18475339	18475432	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18475433	18475555	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18475433	18475555	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18475556	18475809	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18475810	18475908	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18475810	18475908	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18475909	18476010	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18476011	18476076	0.98	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18476011	18476076	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18476077	18476189	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18476190	18476276	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18476190	18476276	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18476277	18476367	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18476368	18476407	0.98	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18476368	18476407	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18476408	18476520	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18476521	18476692	0.98	+	2	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18476521	18476692	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18476693	18476783	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18476784	18476908	1	+	1	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18476784	18476908	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18476909	18476997	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18476998	18477128	1	+	2	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18476998	18477128	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18477129	18477239	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18477240	18477344	0.99	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18477240	18477344	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18477345	18477424	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18477425	18477538	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18477425	18477538	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18477539	18477644	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18477645	18477812	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18477645	18477812	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18477813	18477907	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18477908	18478009	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18477908	18478009	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18478010	18478094	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18478095	18478350	0.98	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18478095	18478350	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18478351	18478481	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18478482	18478606	0.67	+	2	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18478482	18478606	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18478607	18478691	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18478692	18479186	1	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18478692	18479186	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	intron	18479187	18479283	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	CDS	18479284	18479496	0.79	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	exon	18479284	18479496	.	+	.	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
Phchi.S1	AUGUSTUS	stop_codon	18479497	18479499	.	+	0	transcript_id "Phchi.S1G286800.t1"; gene_id "Phchi.S1G286800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8862.t1 is derived from g6037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38336456	38336962	.	-	.	Phchi.S1G602100
Phchi.S1	AUGUSTUS	transcript	38336456	38336962	.	-	.	transcript_id "Phchi.S1G602100.t1"; gene_id "Phchi.S1G602100"
Phchi.S1	AUGUSTUS	stop_codon	38336453	38336455	.	-	0	transcript_id "Phchi.S1G602100.t1"; gene_id "Phchi.S1G602100"
Phchi.S1	AUGUSTUS	CDS	38336456	38336962	0.66	-	0	transcript_id "Phchi.S1G602100.t1"; gene_id "Phchi.S1G602100"
Phchi.S1	AUGUSTUS	exon	38336456	38336962	.	-	.	transcript_id "Phchi.S1G602100.t1"; gene_id "Phchi.S1G602100"
Phchi.S1	AUGUSTUS	start_codon	38336960	38336962	.	-	0	transcript_id "Phchi.S1G602100.t1"; gene_id "Phchi.S1G602100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5310.t1 is derived from g2480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16221759	16229983	.	-	.	Phchi.S1G246900
Phchi.S1	AUGUSTUS	transcript	16221759	16229983	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	stop_codon	16221756	16221758	.	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16221759	16222017	0.99	-	1	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16221759	16222017	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16222018	16222095	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16222096	16222192	0.99	-	2	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16222096	16222192	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16222193	16222300	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16222301	16222646	0.9	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16222301	16222646	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16222647	16222726	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16222727	16223124	0.41	-	2	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16222727	16223124	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16223125	16223238	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16223239	16223530	0.32	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16223239	16223530	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16223531	16224455	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16224456	16224599	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16224456	16224599	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16224600	16224714	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16224715	16224859	1	-	1	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16224715	16224859	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16224860	16224961	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16224962	16225201	0.94	-	1	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16224962	16225201	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16225202	16225314	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16225315	16225434	0.99	-	1	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16225315	16225434	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16225435	16225556	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16225557	16225654	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16225557	16225654	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16225655	16225739	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16225740	16225771	1	-	2	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16225740	16225771	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16225772	16225859	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16225860	16225959	0.96	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16225860	16225959	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16225960	16226060	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16226061	16226132	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16226061	16226132	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16226133	16226259	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16226260	16226340	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16226260	16226340	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16226341	16226487	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16226488	16226604	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16226488	16226604	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16226605	16226690	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16226691	16226804	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16226691	16226804	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16226805	16226945	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16226946	16227044	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16226946	16227044	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16227045	16227142	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16227143	16227249	1	-	2	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16227143	16227249	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16227250	16227341	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16227342	16227555	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16227342	16227555	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16227556	16227657	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16227658	16227732	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16227658	16227732	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16227733	16227860	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16227861	16227974	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16227861	16227974	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16227975	16228071	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16228072	16228185	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16228072	16228185	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16228186	16228288	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16228289	16228380	1	-	2	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16228289	16228380	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16228381	16228529	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16228530	16228566	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16228530	16228566	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16228567	16228693	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16228694	16228818	1	-	2	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16228694	16228818	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16228819	16228898	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16228899	16229086	1	-	1	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16228899	16229086	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16229087	16229411	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16229412	16229686	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16229412	16229686	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	intron	16229687	16229929	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	CDS	16229930	16229983	1	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	exon	16229930	16229983	.	-	.	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
Phchi.S1	AUGUSTUS	start_codon	16229981	16229983	.	-	0	transcript_id "Phchi.S1G246900.t1"; gene_id "Phchi.S1G246900"
# This transcript jg3642.t2 is derived from g811.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg3643.t1 is derived from g812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4911432	4922344	.	-	.	Phchi.S1G080200
Phchi.S1	AUGUSTUS	transcript	4920720	4922344	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	stop_codon	4920717	4920719	.	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920720	4920737	0.93	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920720	4920737	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920738	4920935	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920936	4921023	1	-	1	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920936	4921023	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921024	4921145	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921146	4921243	1	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921146	4921243	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921244	4921354	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921355	4921405	1	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921355	4921405	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921406	4921507	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921508	4921618	0.97	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921508	4921618	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921619	4921714	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921715	4921852	1	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921715	4921852	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921853	4921972	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921973	4922053	1	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921973	4922053	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4922054	4922179	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4922180	4922344	1	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4922180	4922344	.	-	.	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	start_codon	4922342	4922344	.	-	0	transcript_id "Phchi.S1G080200.t1"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	transcript	4911432	4922344	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	stop_codon	4911429	4911431	.	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911432	4911475	0.92	-	2	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911432	4911475	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911476	4911688	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911689	4911693	0.98	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911689	4911693	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911694	4911834	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911835	4911885	0.93	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911835	4911885	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911886	4912055	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912056	4912309	0.65	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912056	4912309	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912310	4912419	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912420	4912549	0.66	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912420	4912549	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912550	4912688	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912689	4912774	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912689	4912774	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912775	4912908	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912909	4913026	1	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912909	4913026	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913027	4913114	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913115	4913243	1	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913115	4913243	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913244	4913427	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913428	4913485	1	-	2	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913428	4913485	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913486	4913599	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913600	4913696	0.98	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913600	4913696	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913697	4913787	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913788	4913859	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913788	4913859	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913860	4914033	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914034	4914111	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914034	4914111	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4914112	4914244	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914245	4914324	1	-	2	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914245	4914324	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4914325	4914471	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914472	4915180	0.93	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914472	4915180	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4915181	4915366	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4915367	4918103	0.97	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4915367	4918103	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918104	4918183	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918184	4918413	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918184	4918413	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918414	4918523	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918524	4918616	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918524	4918616	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918617	4918714	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918715	4918762	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918715	4918762	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918763	4918866	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918867	4918941	0.84	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918867	4918941	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918942	4919072	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919073	4919156	0.84	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919073	4919156	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919157	4919281	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919282	4919373	1	-	2	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919282	4919373	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919374	4919536	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919537	4919615	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919537	4919615	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919616	4919761	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919762	4920058	0.99	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919762	4920058	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920059	4920158	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920159	4920296	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920159	4920296	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920297	4920935	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920936	4921023	1	-	1	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920936	4921023	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921024	4921145	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921146	4921243	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921146	4921243	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921244	4921354	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921355	4921405	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921355	4921405	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921406	4921507	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921508	4921618	0.96	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921508	4921618	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921619	4921714	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921715	4921852	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921715	4921852	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4921853	4921972	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4921973	4922053	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4921973	4922053	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4922054	4922179	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4922180	4922344	1	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4922180	4922344	.	-	.	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	start_codon	4922342	4922344	.	-	0	transcript_id "Phchi.S1G080200.t2"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	transcript	4911432	4920580	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	stop_codon	4911429	4911431	.	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911432	4911475	0.94	-	2	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911432	4911475	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911476	4911688	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911689	4911693	0.96	-	1	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911689	4911693	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911694	4911834	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911835	4911885	0.9	-	1	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911835	4911885	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911886	4912055	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912056	4912309	0.65	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912056	4912309	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912310	4912419	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912420	4912549	0.72	-	1	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912420	4912549	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912550	4912688	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912689	4912774	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912689	4912774	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912775	4912908	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912909	4913026	1	-	1	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912909	4913026	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913027	4913114	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913115	4913243	1	-	1	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913115	4913243	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913244	4913427	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913428	4913485	1	-	2	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913428	4913485	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913486	4913599	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913600	4913696	0.95	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913600	4913696	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913697	4913787	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913788	4913859	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913788	4913859	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913860	4914033	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914034	4914111	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914034	4914111	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4914112	4914244	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914245	4914324	1	-	2	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914245	4914324	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4914325	4914471	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914472	4915180	0.89	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914472	4915180	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4915181	4915366	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4915367	4918103	1	-	1	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4915367	4918103	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918104	4918183	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918184	4918413	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918184	4918413	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918414	4918523	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918524	4918616	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918524	4918616	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918617	4918714	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918715	4918762	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918715	4918762	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918763	4918866	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918867	4918941	0.84	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918867	4918941	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918942	4919072	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919073	4919156	0.84	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919073	4919156	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919157	4919281	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919282	4919373	1	-	2	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919282	4919373	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919374	4919536	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919537	4919615	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919537	4919615	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919616	4919761	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919762	4920058	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919762	4920058	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920059	4920158	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920159	4920296	1	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920159	4920296	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920297	4920484	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920485	4920580	0.68	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920485	4920580	.	-	.	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	start_codon	4920578	4920580	.	-	0	transcript_id "Phchi.S1G080200.t3"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	transcript	4911432	4920481	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	stop_codon	4911429	4911431	.	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911432	4911475	0.88	-	2	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911432	4911475	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911476	4911688	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911689	4911693	0.97	-	1	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911689	4911693	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911694	4911834	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4911835	4911885	0.83	-	1	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4911835	4911885	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4911886	4912055	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912056	4912309	0.63	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912056	4912309	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912310	4912419	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912420	4912549	0.66	-	1	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912420	4912549	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912550	4912688	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912689	4912774	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912689	4912774	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4912775	4912908	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4912909	4913026	1	-	1	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4912909	4913026	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913027	4913114	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913115	4913243	1	-	1	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913115	4913243	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913244	4913427	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913428	4913485	1	-	2	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913428	4913485	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913486	4913599	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913600	4913696	0.96	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913600	4913696	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913697	4913787	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4913788	4913859	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4913788	4913859	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4913860	4914033	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914034	4914111	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914034	4914111	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4914112	4914244	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914245	4914324	1	-	2	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914245	4914324	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4914325	4914471	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4914472	4915180	0.86	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4914472	4915180	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4915181	4915366	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4915367	4918103	0.99	-	1	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4915367	4918103	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918104	4918183	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918184	4918413	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918184	4918413	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918414	4918523	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918524	4918616	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918524	4918616	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918617	4918714	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918715	4918762	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918715	4918762	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918763	4918866	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4918867	4918941	0.86	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4918867	4918941	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4918942	4919072	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919073	4919156	0.86	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919073	4919156	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919157	4919281	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919282	4919373	1	-	2	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919282	4919373	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919374	4919536	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919537	4919615	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919537	4919615	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4919616	4919761	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4919762	4920058	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4919762	4920058	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920059	4920158	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920159	4920296	1	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920159	4920296	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	intron	4920297	4920382	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	CDS	4920383	4920481	0.54	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	exon	4920383	4920481	.	-	.	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
Phchi.S1	AUGUSTUS	start_codon	4920479	4920481	.	-	0	transcript_id "Phchi.S1G080200.t4"; gene_id "Phchi.S1G080200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7218.t1 is derived from g4390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27682589	27685860	.	+	.	Phchi.S1G437700
Phchi.S1	AUGUSTUS	transcript	27682589	27685860	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	start_codon	27682589	27682591	.	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27682589	27682632	1	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27682589	27682632	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27682633	27682752	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27682753	27682924	1	+	1	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27682753	27682924	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27682925	27683057	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27683058	27683286	1	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27683058	27683286	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27683287	27683370	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27683371	27684137	1	+	2	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27683371	27684137	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27684138	27684225	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27684226	27684447	0.99	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27684226	27684447	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27684448	27684548	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27684549	27684620	1	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27684549	27684620	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27684621	27684707	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27684708	27684989	1	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27684708	27684989	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27684990	27685118	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27685119	27685478	1	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27685119	27685478	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	intron	27685479	27685566	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	CDS	27685567	27685860	1	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	exon	27685567	27685860	.	+	.	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
Phchi.S1	AUGUSTUS	stop_codon	27685861	27685863	.	+	0	transcript_id "Phchi.S1G437700.t1"; gene_id "Phchi.S1G437700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1183.t1 is derived from g10966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8332799	8333568	.	-	.	Phchi.S6G114200
Phchi.S6	AUGUSTUS	transcript	8332799	8333568	.	-	.	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	stop_codon	8332796	8332798	.	-	0	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	CDS	8332799	8332927	0.55	-	0	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	exon	8332799	8332927	.	-	.	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	intron	8332928	8333013	.	-	.	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	CDS	8333014	8333101	0.99	-	1	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	exon	8333014	8333101	.	-	.	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	intron	8333102	8333218	.	-	.	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	CDS	8333219	8333568	0.61	-	0	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	exon	8333219	8333568	.	-	.	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
Phchi.S6	AUGUSTUS	start_codon	8333566	8333568	.	-	0	transcript_id "Phchi.S6G114200.t1"; gene_id "Phchi.S6G114200"
# This transcript jg10550.t2 is derived from g14600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10551.t1 is derived from g14601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	950704	952545	.	-	.	Phchi.S4G013300
Phchi.S4	AUGUSTUS	transcript	950704	952545	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	stop_codon	950701	950703	.	-	0	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	CDS	950704	950848	1	-	1	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	exon	950704	950848	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	intron	950849	950938	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	CDS	950939	950995	1	-	1	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	exon	950939	950995	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	intron	950996	951112	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	CDS	951113	951303	1	-	0	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	exon	951113	951303	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	intron	951304	951390	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	CDS	951391	951459	1	-	0	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	exon	951391	951459	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	intron	951460	951907	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	CDS	951908	952057	1	-	0	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	exon	951908	952057	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	intron	952058	952353	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	CDS	952354	952545	1	-	0	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	exon	952354	952545	.	-	.	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
Phchi.S4	AUGUSTUS	start_codon	952543	952545	.	-	0	transcript_id "Phchi.S4G013300.t1"; gene_id "Phchi.S4G013300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4795.t1 is derived from g1965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12833028	12833477	.	+	.	Phchi.S1G195400
Phchi.S1	AUGUSTUS	transcript	12833028	12833477	.	+	.	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	start_codon	12833028	12833030	.	+	0	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	CDS	12833028	12833135	0.68	+	0	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	exon	12833028	12833135	.	+	.	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	intron	12833136	12833222	.	+	.	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	CDS	12833223	12833267	0.94	+	0	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	exon	12833223	12833267	.	+	.	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	intron	12833268	12833351	.	+	.	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	CDS	12833352	12833477	0.91	+	0	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	exon	12833352	12833477	.	+	.	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
Phchi.S1	AUGUSTUS	stop_codon	12833478	12833480	.	+	0	transcript_id "Phchi.S1G195400.t1"; gene_id "Phchi.S1G195400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9099.t1 is derived from g6274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39825961	39828030	.	+	.	Phchi.S1G625800
Phchi.S1	AUGUSTUS	transcript	39825961	39828030	.	+	.	transcript_id "Phchi.S1G625800.t1"; gene_id "Phchi.S1G625800"
Phchi.S1	AUGUSTUS	start_codon	39825961	39825963	.	+	0	transcript_id "Phchi.S1G625800.t1"; gene_id "Phchi.S1G625800"
Phchi.S1	AUGUSTUS	CDS	39825961	39828030	1	+	0	transcript_id "Phchi.S1G625800.t1"; gene_id "Phchi.S1G625800"
Phchi.S1	AUGUSTUS	exon	39825961	39828030	.	+	.	transcript_id "Phchi.S1G625800.t1"; gene_id "Phchi.S1G625800"
Phchi.S1	AUGUSTUS	stop_codon	39828031	39828033	.	+	0	transcript_id "Phchi.S1G625800.t1"; gene_id "Phchi.S1G625800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6912.t1 is derived from g4084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25970250	25970876	.	+	.	Phchi.S1G407100
Phchi.S1	AUGUSTUS	transcript	25970250	25970876	.	+	.	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	start_codon	25970250	25970252	.	+	0	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	CDS	25970250	25970277	0.48	+	0	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	exon	25970250	25970277	.	+	.	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	intron	25970278	25970358	.	+	.	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	CDS	25970359	25970876	1	+	2	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	exon	25970359	25970876	.	+	.	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
Phchi.S1	AUGUSTUS	stop_codon	25970877	25970879	.	+	0	transcript_id "Phchi.S1G407100.t1"; gene_id "Phchi.S1G407100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7709.t1 is derived from g4883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30736036	30736510	.	-	.	Phchi.S1G486800
Phchi.S1	AUGUSTUS	transcript	30736036	30736510	.	-	.	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	stop_codon	30736033	30736035	.	-	0	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	CDS	30736036	30736177	0.84	-	1	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	exon	30736036	30736177	.	-	.	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	intron	30736178	30736295	.	-	.	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	CDS	30736296	30736387	0.91	-	0	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	exon	30736296	30736387	.	-	.	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	intron	30736388	30736459	.	-	.	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	CDS	30736460	30736510	0.78	-	0	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	exon	30736460	30736510	.	-	.	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
Phchi.S1	AUGUSTUS	start_codon	30736508	30736510	.	-	0	transcript_id "Phchi.S1G486800.t1"; gene_id "Phchi.S1G486800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14379.t1 is derived from g12846.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12461160	12462959	.	-	.	Phchi.S3G169800
Phchi.S3	AUGUSTUS	transcript	12461917	12462959	.	-	.	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	stop_codon	12461914	12461916	.	-	0	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	CDS	12461917	12461988	0.55	-	0	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	exon	12461917	12461988	.	-	.	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	intron	12461989	12462083	.	-	.	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	CDS	12462084	12462959	0.46	-	0	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	exon	12462084	12462959	.	-	.	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	start_codon	12462957	12462959	.	-	0	transcript_id "Phchi.S3G169800.t1"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	transcript	12461160	12462959	.	-	.	transcript_id "Phchi.S3G169800.t2"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	stop_codon	12461157	12461159	.	-	0	transcript_id "Phchi.S3G169800.t2"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	CDS	12461160	12462959	0.97	-	0	transcript_id "Phchi.S3G169800.t2"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	exon	12461160	12462959	.	-	.	transcript_id "Phchi.S3G169800.t2"; gene_id "Phchi.S3G169800"
Phchi.S3	AUGUSTUS	start_codon	12462957	12462959	.	-	0	transcript_id "Phchi.S3G169800.t2"; gene_id "Phchi.S3G169800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3139.t1 is derived from g308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1955849	1957822	.	-	.	Phchi.S1G029800
Phchi.S1	AUGUSTUS	transcript	1955849	1957822	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	stop_codon	1955846	1955848	.	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1955849	1956133	0.8	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1955849	1956133	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1956134	1956241	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1956242	1956355	0.8	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1956242	1956355	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1956356	1956442	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1956443	1956519	1	-	2	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1956443	1956519	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1956520	1956612	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1956613	1956782	1	-	1	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1956613	1956782	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1956783	1956872	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1956873	1956979	1	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1956873	1956979	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1956980	1957099	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1957100	1957186	0.91	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1957100	1957186	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1957187	1957296	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1957297	1957365	0.89	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1957297	1957365	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	intron	1957366	1957771	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	CDS	1957772	1957822	0.46	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	exon	1957772	1957822	.	-	.	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
Phchi.S1	AUGUSTUS	start_codon	1957820	1957822	.	-	0	transcript_id "Phchi.S1G029800.t1"; gene_id "Phchi.S1G029800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10019.t1 is derived from g7195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45078752	45079596	.	+	.	Phchi.S1G717800
Phchi.S1	AUGUSTUS	transcript	45078752	45079596	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	start_codon	45078752	45078754	.	+	0	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	CDS	45078752	45078825	0.68	+	0	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	exon	45078752	45078825	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	intron	45078826	45078949	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	CDS	45078950	45078954	0.73	+	1	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	exon	45078950	45078954	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	intron	45078955	45079036	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	CDS	45079037	45079044	0.73	+	2	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	exon	45079037	45079044	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	intron	45079045	45079187	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	CDS	45079188	45079238	0.64	+	0	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	exon	45079188	45079238	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	intron	45079239	45079322	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	CDS	45079323	45079353	0.64	+	0	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	exon	45079323	45079353	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	intron	45079354	45079528	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	CDS	45079529	45079596	0.64	+	2	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	exon	45079529	45079596	.	+	.	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
Phchi.S1	AUGUSTUS	stop_codon	45079597	45079599	.	+	0	transcript_id "Phchi.S1G717800.t1"; gene_id "Phchi.S1G717800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14899.t1 is derived from g13367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15433377	15433745	.	-	.	Phchi.S3G221800
Phchi.S3	AUGUSTUS	transcript	15433377	15433745	.	-	.	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	stop_codon	15433374	15433376	.	-	0	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	CDS	15433377	15433580	0.93	-	0	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	exon	15433377	15433580	.	-	.	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	intron	15433581	15433667	.	-	.	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	CDS	15433668	15433745	0.93	-	0	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	exon	15433668	15433745	.	-	.	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
Phchi.S3	AUGUSTUS	start_codon	15433743	15433745	.	-	0	transcript_id "Phchi.S3G221800.t1"; gene_id "Phchi.S3G221800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6221.t1 is derived from g3393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21511929	21517006	.	+	.	Phchi.S1G338000
Phchi.S1	AUGUSTUS	transcript	21511929	21514943	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	start_codon	21511929	21511931	.	+	0	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21511929	21512381	0.9	+	0	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21511929	21512381	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21512382	21512477	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21512478	21512532	0.94	+	0	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21512478	21512532	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21512533	21512651	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21512652	21513288	0.62	+	2	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21512652	21513288	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21513289	21513436	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21513437	21513750	0.98	+	1	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21513437	21513750	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21513751	21513830	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21513831	21514054	1	+	2	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21513831	21514054	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21514055	21514146	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21514147	21514489	0.88	+	0	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21514147	21514489	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21514490	21514592	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21514593	21514669	0.89	+	2	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21514593	21514669	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21514670	21514865	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21514866	21514943	0.94	+	0	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21514866	21514943	.	+	.	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	stop_codon	21514944	21514946	.	+	0	transcript_id "Phchi.S1G338000.t1"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	transcript	21511929	21517006	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	start_codon	21511929	21511931	.	+	0	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21511929	21512381	0.9	+	0	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21511929	21512381	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21512382	21512477	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21512478	21512532	0.96	+	0	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21512478	21512532	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21512533	21512651	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21512652	21513288	0.7	+	2	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21512652	21513288	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21513289	21513436	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21513437	21513750	0.99	+	1	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21513437	21513750	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21513751	21513830	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21513831	21514054	1	+	2	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21513831	21514054	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21514055	21514146	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21514147	21514489	0.35	+	0	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21514147	21514489	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21514490	21514592	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21514593	21514683	0.35	+	2	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21514593	21514683	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21514684	21514865	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21514866	21515296	0.78	+	1	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21514866	21515296	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21515297	21515442	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21515443	21515684	0.99	+	2	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21515443	21515684	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	intron	21515685	21515797	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	CDS	21515798	21517006	0.99	+	0	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	exon	21515798	21517006	.	+	.	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
Phchi.S1	AUGUSTUS	stop_codon	21517007	21517009	.	+	0	transcript_id "Phchi.S1G338000.t2"; gene_id "Phchi.S1G338000"
# This transcript jg6402.t2 is derived from g3574.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6403.t1 is derived from g3575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22777125	22777992	.	+	.	Phchi.S1G356200
Phchi.S1	AUGUSTUS	transcript	22777125	22777992	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	start_codon	22777125	22777127	.	+	0	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	CDS	22777125	22777182	1	+	0	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	exon	22777125	22777182	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	intron	22777183	22777256	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	CDS	22777257	22777475	1	+	2	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	exon	22777257	22777475	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	intron	22777476	22777797	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	CDS	22777798	22777840	1	+	2	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	exon	22777798	22777840	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	intron	22777841	22777922	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	CDS	22777923	22777992	1	+	1	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	exon	22777923	22777992	.	+	.	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
Phchi.S1	AUGUSTUS	stop_codon	22777993	22777995	.	+	0	transcript_id "Phchi.S1G356200.t1"; gene_id "Phchi.S1G356200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg754.t1 is derived from g10536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5341400	5343879	.	+	.	Phchi.S6G071300
Phchi.S6	AUGUSTUS	transcript	5341400	5343879	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	start_codon	5341400	5341402	.	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5341400	5341419	0.76	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5341400	5341419	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5341420	5341580	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5341581	5341654	1	+	1	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5341581	5341654	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5341655	5341727	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5341728	5342062	1	+	2	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5341728	5342062	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5342063	5342186	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5342187	5342283	0.55	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5342187	5342283	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5342284	5342363	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5342364	5342491	1	+	2	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5342364	5342491	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5342492	5342575	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5342576	5342768	1	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5342576	5342768	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5342769	5342900	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5342901	5342974	1	+	2	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5342901	5342974	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5342975	5343075	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5343076	5343165	1	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5343076	5343165	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5343166	5343274	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5343275	5343334	1	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5343275	5343334	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5343335	5343433	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5343434	5343565	1	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5343434	5343565	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	intron	5343566	5343714	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	CDS	5343715	5343879	1	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	exon	5343715	5343879	.	+	.	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
Phchi.S6	AUGUSTUS	stop_codon	5343880	5343882	.	+	0	transcript_id "Phchi.S6G071300.t1"; gene_id "Phchi.S6G071300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1109.t1 is derived from g10892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7666202	7666713	.	-	.	Phchi.S6G106800
Phchi.S6	AUGUSTUS	transcript	7666202	7666713	.	-	.	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	stop_codon	7666199	7666201	.	-	0	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	CDS	7666202	7666343	1	-	1	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	exon	7666202	7666343	.	-	.	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	intron	7666344	7666485	.	-	.	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	CDS	7666486	7666580	1	-	0	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	exon	7666486	7666580	.	-	.	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	intron	7666581	7666668	.	-	.	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	CDS	7666669	7666713	0.68	-	0	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	exon	7666669	7666713	.	-	.	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
Phchi.S6	AUGUSTUS	start_codon	7666711	7666713	.	-	0	transcript_id "Phchi.S6G106800.t1"; gene_id "Phchi.S6G106800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5440.t1 is derived from g2610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16881137	16882403	.	+	.	Phchi.S1G259900
Phchi.S1	AUGUSTUS	transcript	16881137	16882403	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	start_codon	16881137	16881139	.	+	0	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	CDS	16881137	16881481	0.83	+	0	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	exon	16881137	16881481	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	intron	16881482	16881620	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	CDS	16881621	16881857	1	+	0	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	exon	16881621	16881857	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	intron	16881858	16881943	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	CDS	16881944	16882114	1	+	0	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	exon	16881944	16882114	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	intron	16882115	16882235	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	CDS	16882236	16882403	0.93	+	0	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	exon	16882236	16882403	.	+	.	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
Phchi.S1	AUGUSTUS	stop_codon	16882404	16882406	.	+	0	transcript_id "Phchi.S1G259900.t1"; gene_id "Phchi.S1G259900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6229.t1 is derived from g3401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21777554	21778403	.	+	.	Phchi.S1G338800
Phchi.S1	AUGUSTUS	transcript	21777554	21778403	.	+	.	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	start_codon	21777554	21777556	.	+	0	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	CDS	21777554	21778129	0.88	+	0	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	exon	21777554	21778129	.	+	.	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	intron	21778130	21778214	.	+	.	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	CDS	21778215	21778403	1	+	0	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	exon	21778215	21778403	.	+	.	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
Phchi.S1	AUGUSTUS	stop_codon	21778404	21778406	.	+	0	transcript_id "Phchi.S1G338800.t1"; gene_id "Phchi.S1G338800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5516.t1 is derived from g2686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17187459	17195473	.	+	.	Phchi.S1G267500
Phchi.S1	AUGUSTUS	transcript	17187459	17195473	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	start_codon	17187459	17187461	.	+	0	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	CDS	17187459	17187480	0.05	+	0	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	exon	17187459	17187480	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	intron	17187481	17187782	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	CDS	17187783	17187904	0.04	+	2	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	exon	17187783	17187904	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	intron	17187905	17188209	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	CDS	17188210	17188341	0.98	+	0	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	exon	17188210	17188341	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	intron	17188342	17191912	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	CDS	17191913	17191974	1	+	0	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	exon	17191913	17191974	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	intron	17191975	17195436	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	CDS	17195437	17195473	0.01	+	1	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	exon	17195437	17195473	.	+	.	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
Phchi.S1	AUGUSTUS	stop_codon	17195474	17195476	.	+	0	transcript_id "Phchi.S1G267500.t1"; gene_id "Phchi.S1G267500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12933.t1 is derived from g11398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3207432	3209600	.	+	.	Phchi.S3G025200
Phchi.S3	AUGUSTUS	transcript	3207432	3209600	.	+	.	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	start_codon	3207432	3207434	.	+	0	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	CDS	3207432	3207715	0.4	+	0	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	exon	3207432	3207715	.	+	.	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	intron	3207716	3207813	.	+	.	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	CDS	3207814	3208723	0.4	+	1	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	exon	3207814	3208723	.	+	.	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	intron	3208724	3208805	.	+	.	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	CDS	3208806	3209600	0.59	+	0	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	exon	3208806	3209600	.	+	.	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
Phchi.S3	AUGUSTUS	stop_codon	3209601	3209603	.	+	0	transcript_id "Phchi.S3G025200.t1"; gene_id "Phchi.S3G025200"
# This transcript jg4393.t2 is derived from g1562.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4394.t1 is derived from g1563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10219468	10221716	.	-	.	Phchi.S1G155300
Phchi.S1	AUGUSTUS	transcript	10219468	10221716	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	stop_codon	10219465	10219467	.	-	0	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	CDS	10219468	10219481	0.69	-	2	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	exon	10219468	10219481	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	intron	10219482	10219761	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	CDS	10219762	10220251	0.6	-	0	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	exon	10219762	10220251	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	intron	10220252	10220577	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	CDS	10220578	10220626	0.82	-	1	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	exon	10220578	10220626	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	intron	10220627	10220774	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	CDS	10220775	10221445	0.97	-	0	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	exon	10220775	10221445	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	intron	10221446	10221530	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	CDS	10221531	10221716	0.81	-	0	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	exon	10221531	10221716	.	-	.	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
Phchi.S1	AUGUSTUS	start_codon	10221714	10221716	.	-	0	transcript_id "Phchi.S1G155300.t1"; gene_id "Phchi.S1G155300"
# This transcript jg723.t2 is derived from g10505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg724.t1 is derived from g10506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5136549	5138549	.	-	.	Phchi.S6G068300
Phchi.S6	AUGUSTUS	transcript	5136549	5138549	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	stop_codon	5136546	5136548	.	-	0	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	CDS	5136549	5136628	0.99	-	2	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	exon	5136549	5136628	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	intron	5136629	5136776	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	CDS	5136777	5136866	0.56	-	2	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	exon	5136777	5136866	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	intron	5136867	5136963	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	CDS	5136964	5137399	0.68	-	0	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	exon	5136964	5137399	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	intron	5137400	5137507	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	CDS	5137508	5138011	0.7	-	0	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	exon	5137508	5138011	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	intron	5138012	5138255	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	CDS	5138256	5138357	0.78	-	0	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	exon	5138256	5138357	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	intron	5138358	5138519	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	CDS	5138520	5138549	0.89	-	0	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	exon	5138520	5138549	.	-	.	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
Phchi.S6	AUGUSTUS	start_codon	5138547	5138549	.	-	0	transcript_id "Phchi.S6G068300.t1"; gene_id "Phchi.S6G068300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13400.t1 is derived from g11866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6526057	6526894	.	-	.	Phchi.S3G071900
Phchi.S3	AUGUSTUS	transcript	6526057	6526894	.	-	.	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	stop_codon	6526054	6526056	.	-	0	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	CDS	6526057	6526320	0.6	-	0	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	exon	6526057	6526320	.	-	.	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	intron	6526321	6526420	.	-	.	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	CDS	6526421	6526510	0.43	-	0	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	exon	6526421	6526510	.	-	.	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	intron	6526511	6526660	.	-	.	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	CDS	6526661	6526894	0.38	-	0	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	exon	6526661	6526894	.	-	.	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
Phchi.S3	AUGUSTUS	start_codon	6526892	6526894	.	-	0	transcript_id "Phchi.S3G071900.t1"; gene_id "Phchi.S3G071900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11203.t1 is derived from g15253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4666958	4669187	.	-	.	Phchi.S4G078500
Phchi.S4	AUGUSTUS	transcript	4666958	4669187	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	stop_codon	4666955	4666957	.	-	0	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4666958	4667050	0.99	-	0	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4666958	4667050	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4667051	4667130	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4667131	4667213	1	-	2	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4667131	4667213	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4667214	4667297	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4667298	4667551	0.9	-	1	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4667298	4667551	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4667552	4667691	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4667692	4667944	0.95	-	2	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4667692	4667944	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4667945	4668025	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4668026	4668219	1	-	1	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4668026	4668219	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4668220	4668370	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4668371	4668501	1	-	0	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4668371	4668501	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4668502	4668673	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4668674	4668753	1	-	2	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4668674	4668753	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4668754	4668874	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4668875	4668931	1	-	2	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4668875	4668931	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	intron	4668932	4669021	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	CDS	4669022	4669187	0.52	-	0	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	exon	4669022	4669187	.	-	.	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
Phchi.S4	AUGUSTUS	start_codon	4669185	4669187	.	-	0	transcript_id "Phchi.S4G078500.t1"; gene_id "Phchi.S4G078500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1157.t1 is derived from g10940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8085999	8087083	.	+	.	Phchi.S6G111600
Phchi.S6	AUGUSTUS	transcript	8085999	8087083	.	+	.	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	start_codon	8085999	8086001	.	+	0	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	CDS	8085999	8086906	0.42	+	0	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	exon	8085999	8086906	.	+	.	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	intron	8086907	8087040	.	+	.	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	CDS	8087041	8087083	1	+	1	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	exon	8087041	8087083	.	+	.	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
Phchi.S6	AUGUSTUS	stop_codon	8087084	8087086	.	+	0	transcript_id "Phchi.S6G111600.t1"; gene_id "Phchi.S6G111600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10664.t1 is derived from g14714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1499498	1502922	.	+	.	Phchi.S4G024600
Phchi.S4	AUGUSTUS	transcript	1499498	1502922	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	start_codon	1499498	1499500	.	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1499498	1499552	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1499498	1499552	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1499553	1499649	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1499650	1500239	0.98	+	2	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1499650	1500239	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1500240	1500486	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1500487	1500594	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1500487	1500594	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1500595	1500733	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1500734	1500889	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1500734	1500889	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1500890	1501031	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1501032	1501247	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1501032	1501247	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1501248	1501347	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1501348	1501557	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1501348	1501557	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1501558	1501739	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1501740	1501877	0.74	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1501740	1501877	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1501878	1501985	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1501986	1502087	0.99	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1501986	1502087	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1502088	1502174	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1502175	1502240	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1502175	1502240	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1502241	1502415	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1502416	1502500	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1502416	1502500	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1502501	1502582	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1502583	1502630	0.96	+	2	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1502583	1502630	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1502631	1502694	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1502695	1502780	0.79	+	2	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1502695	1502780	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	intron	1502781	1502880	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	CDS	1502881	1502922	1	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	exon	1502881	1502922	.	+	.	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
Phchi.S4	AUGUSTUS	stop_codon	1502923	1502925	.	+	0	transcript_id "Phchi.S4G024600.t1"; gene_id "Phchi.S4G024600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg558.t1 is derived from g10340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4041184	4041545	.	-	.	Phchi.S6G051700
Phchi.S6	AUGUSTUS	transcript	4041184	4041545	.	-	.	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	stop_codon	4041181	4041183	.	-	0	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	CDS	4041184	4041204	0.96	-	0	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	exon	4041184	4041204	.	-	.	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	intron	4041205	4041287	.	-	.	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	CDS	4041288	4041545	0.72	-	0	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	exon	4041288	4041545	.	-	.	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
Phchi.S6	AUGUSTUS	start_codon	4041543	4041545	.	-	0	transcript_id "Phchi.S6G051700.t1"; gene_id "Phchi.S6G051700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1554.t1 is derived from g8473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1723999	1725503	.	+	.	Phchi.S5G016300
Phchi.S5	AUGUSTUS	transcript	1723999	1725503	.	+	.	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	start_codon	1723999	1724001	.	+	0	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	CDS	1723999	1724731	0.28	+	0	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	exon	1723999	1724731	.	+	.	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	intron	1724732	1724817	.	+	.	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	CDS	1724818	1725503	0.54	+	2	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	exon	1724818	1725503	.	+	.	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
Phchi.S5	AUGUSTUS	stop_codon	1725504	1725506	.	+	0	transcript_id "Phchi.S5G016300.t1"; gene_id "Phchi.S5G016300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12013.t1 is derived from g7688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	523419	524756	.	-	.	Phchi.S2G009300
Phchi.S2	AUGUSTUS	transcript	523419	524756	.	-	.	transcript_id "Phchi.S2G009300.t1"; gene_id "Phchi.S2G009300"
Phchi.S2	AUGUSTUS	stop_codon	523416	523418	.	-	0	transcript_id "Phchi.S2G009300.t1"; gene_id "Phchi.S2G009300"
Phchi.S2	AUGUSTUS	CDS	523419	524756	0.87	-	0	transcript_id "Phchi.S2G009300.t1"; gene_id "Phchi.S2G009300"
Phchi.S2	AUGUSTUS	exon	523419	524756	.	-	.	transcript_id "Phchi.S2G009300.t1"; gene_id "Phchi.S2G009300"
Phchi.S2	AUGUSTUS	start_codon	524754	524756	.	-	0	transcript_id "Phchi.S2G009300.t1"; gene_id "Phchi.S2G009300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5614.t1 is derived from g2784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17901244	17901804	.	-	.	Phchi.S1G277300
Phchi.S1	AUGUSTUS	transcript	17901244	17901804	.	-	.	transcript_id "Phchi.S1G277300.t1"; gene_id "Phchi.S1G277300"
Phchi.S1	AUGUSTUS	stop_codon	17901241	17901243	.	-	0	transcript_id "Phchi.S1G277300.t1"; gene_id "Phchi.S1G277300"
Phchi.S1	AUGUSTUS	CDS	17901244	17901804	0.96	-	0	transcript_id "Phchi.S1G277300.t1"; gene_id "Phchi.S1G277300"
Phchi.S1	AUGUSTUS	exon	17901244	17901804	.	-	.	transcript_id "Phchi.S1G277300.t1"; gene_id "Phchi.S1G277300"
Phchi.S1	AUGUSTUS	start_codon	17901802	17901804	.	-	0	transcript_id "Phchi.S1G277300.t1"; gene_id "Phchi.S1G277300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7055.t1 is derived from g4227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26647233	26650438	.	-	.	Phchi.S1G421400
Phchi.S1	AUGUSTUS	transcript	26647233	26649031	.	-	.	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	stop_codon	26647230	26647232	.	-	0	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	CDS	26647233	26647617	0.94	-	1	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	exon	26647233	26647617	.	-	.	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	intron	26647618	26647694	.	-	.	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	CDS	26647695	26649031	0.44	-	0	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	exon	26647695	26649031	.	-	.	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	start_codon	26649029	26649031	.	-	0	transcript_id "Phchi.S1G421400.t1"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	transcript	26647233	26650438	.	-	.	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	stop_codon	26647230	26647232	.	-	0	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	CDS	26647233	26647617	0.86	-	1	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	exon	26647233	26647617	.	-	.	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	intron	26647618	26647694	.	-	.	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	CDS	26647695	26650438	0.08	-	0	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	exon	26647695	26650438	.	-	.	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
Phchi.S1	AUGUSTUS	start_codon	26650436	26650438	.	-	0	transcript_id "Phchi.S1G421400.t2"; gene_id "Phchi.S1G421400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10300.t1 is derived from g7476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46997518	47000384	.	+	.	Phchi.S1G745900
Phchi.S1	AUGUSTUS	transcript	46997518	47000384	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	start_codon	46997518	46997520	.	+	0	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	CDS	46997518	46998381	1	+	0	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	exon	46997518	46998381	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	intron	46998382	46998509	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	CDS	46998510	46999040	1	+	0	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	exon	46998510	46999040	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	intron	46999041	46999270	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	CDS	46999271	46999725	0.99	+	0	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	exon	46999271	46999725	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	intron	46999726	46999826	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	CDS	46999827	46999949	1	+	1	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	exon	46999827	46999949	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	intron	46999950	47000097	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	CDS	47000098	47000157	1	+	1	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	exon	47000098	47000157	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	intron	47000158	47000257	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	CDS	47000258	47000384	0.8	+	1	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	exon	47000258	47000384	.	+	.	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
Phchi.S1	AUGUSTUS	stop_codon	47000385	47000387	.	+	0	transcript_id "Phchi.S1G745900.t1"; gene_id "Phchi.S1G745900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15844.t1 is derived from g14314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21790988	21792392	.	+	.	Phchi.S3G316300
Phchi.S3	AUGUSTUS	transcript	21790988	21792392	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	start_codon	21790988	21790990	.	+	0	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	CDS	21790988	21791270	0.94	+	0	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	exon	21790988	21791270	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	intron	21791271	21791412	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	CDS	21791413	21791666	0.97	+	2	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	exon	21791413	21791666	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	intron	21791667	21791799	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	CDS	21791800	21791996	0.87	+	0	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	exon	21791800	21791996	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	intron	21791997	21792111	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	CDS	21792112	21792256	0.87	+	1	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	exon	21792112	21792256	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	intron	21792257	21792350	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	CDS	21792351	21792392	0.45	+	0	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	exon	21792351	21792392	.	+	.	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
Phchi.S3	AUGUSTUS	stop_codon	21792393	21792395	.	+	0	transcript_id "Phchi.S3G316300.t1"; gene_id "Phchi.S3G316300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13838.t1 is derived from g12305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9136988	9138321	.	-	.	Phchi.S3G115700
Phchi.S3	AUGUSTUS	transcript	9136988	9138321	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	stop_codon	9136985	9136987	.	-	0	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9136988	9136999	0.95	-	0	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9136988	9136999	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	intron	9137000	9137084	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9137085	9137162	1	-	0	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9137085	9137162	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	intron	9137163	9137299	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9137300	9137375	0.92	-	1	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9137300	9137375	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	intron	9137376	9137465	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9137466	9137598	0.92	-	2	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9137466	9137598	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	intron	9137599	9137705	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9137706	9137743	1	-	1	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9137706	9137743	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	intron	9137744	9137851	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9137852	9138031	1	-	1	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9137852	9138031	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	intron	9138032	9138259	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	CDS	9138260	9138321	1	-	0	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	exon	9138260	9138321	.	-	.	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
Phchi.S3	AUGUSTUS	start_codon	9138319	9138321	.	-	0	transcript_id "Phchi.S3G115700.t1"; gene_id "Phchi.S3G115700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14675.t1 is derived from g13143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14127121	14128906	.	+	.	Phchi.S3G199400
Phchi.S3	AUGUSTUS	transcript	14127121	14128906	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	start_codon	14127121	14127123	.	+	0	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14127121	14127244	0.63	+	0	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14127121	14127244	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14127245	14127342	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14127343	14127528	0.9	+	2	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14127343	14127528	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14127529	14127634	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14127635	14127744	0.9	+	2	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14127635	14127744	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14127745	14127866	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14127867	14127886	1	+	0	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14127867	14127886	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14127887	14127969	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14127970	14128014	1	+	1	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14127970	14128014	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14128015	14128128	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14128129	14128208	0.96	+	1	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14128129	14128208	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14128209	14128280	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14128281	14128369	1	+	2	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14128281	14128369	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14128370	14128457	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14128458	14128557	0.77	+	0	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14128458	14128557	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14128558	14128682	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14128683	14128759	0.99	+	2	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14128683	14128759	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	intron	14128760	14128849	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	CDS	14128850	14128906	0.48	+	0	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	exon	14128850	14128906	.	+	.	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
Phchi.S3	AUGUSTUS	stop_codon	14128907	14128909	.	+	0	transcript_id "Phchi.S3G199400.t1"; gene_id "Phchi.S3G199400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8938.t1 is derived from g6113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38759099	38760781	.	-	.	Phchi.S1G609700
Phchi.S1	AUGUSTUS	transcript	38759099	38760781	.	-	.	transcript_id "Phchi.S1G609700.t1"; gene_id "Phchi.S1G609700"
Phchi.S1	AUGUSTUS	stop_codon	38759096	38759098	.	-	0	transcript_id "Phchi.S1G609700.t1"; gene_id "Phchi.S1G609700"
Phchi.S1	AUGUSTUS	CDS	38759099	38760781	0.97	-	0	transcript_id "Phchi.S1G609700.t1"; gene_id "Phchi.S1G609700"
Phchi.S1	AUGUSTUS	exon	38759099	38760781	.	-	.	transcript_id "Phchi.S1G609700.t1"; gene_id "Phchi.S1G609700"
Phchi.S1	AUGUSTUS	start_codon	38760779	38760781	.	-	0	transcript_id "Phchi.S1G609700.t1"; gene_id "Phchi.S1G609700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11211.t1 is derived from g15261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4799129	4800947	.	+	.	Phchi.S4G079300
Phchi.S4	AUGUSTUS	transcript	4799129	4800947	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	start_codon	4799129	4799131	.	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	CDS	4799129	4799140	0.99	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	exon	4799129	4799140	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	intron	4799141	4799361	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	CDS	4799362	4799400	1	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	exon	4799362	4799400	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	intron	4799401	4799496	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	CDS	4799497	4799829	1	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	exon	4799497	4799829	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	intron	4799830	4799920	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	CDS	4799921	4800171	1	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	exon	4799921	4800171	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	intron	4800172	4800330	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	CDS	4800331	4800499	1	+	1	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	exon	4800331	4800499	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	intron	4800500	4800578	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	CDS	4800579	4800947	1	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	exon	4800579	4800947	.	+	.	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
Phchi.S4	AUGUSTUS	stop_codon	4800948	4800950	.	+	0	transcript_id "Phchi.S4G079300.t1"; gene_id "Phchi.S4G079300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg592.t1 is derived from g10374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4326581	4327335	.	-	.	Phchi.S6G055100
Phchi.S6	AUGUSTUS	transcript	4326581	4327335	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	stop_codon	4326578	4326580	.	-	0	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	CDS	4326581	4326709	0.49	-	0	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	exon	4326581	4326709	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	intron	4326710	4326797	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	CDS	4326798	4326865	1	-	2	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	exon	4326798	4326865	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	intron	4326866	4326952	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	CDS	4326953	4327169	1	-	0	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	exon	4326953	4327169	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	intron	4327170	4327260	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	CDS	4327261	4327335	1	-	0	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	exon	4327261	4327335	.	-	.	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
Phchi.S6	AUGUSTUS	start_codon	4327333	4327335	.	-	0	transcript_id "Phchi.S6G055100.t1"; gene_id "Phchi.S6G055100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10698.t1 is derived from g14748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1643132	1643463	.	-	.	Phchi.S4G028000
Phchi.S4	AUGUSTUS	transcript	1643132	1643463	.	-	.	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	stop_codon	1643129	1643131	.	-	0	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	CDS	1643132	1643324	0.5	-	1	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	exon	1643132	1643324	.	-	.	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	intron	1643325	1643416	.	-	.	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	CDS	1643417	1643463	0.98	-	0	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	exon	1643417	1643463	.	-	.	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
Phchi.S4	AUGUSTUS	start_codon	1643461	1643463	.	-	0	transcript_id "Phchi.S4G028000.t1"; gene_id "Phchi.S4G028000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10480.t1 is derived from g14529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	579803	580402	.	-	.	Phchi.S4G006200
Phchi.S4	AUGUSTUS	transcript	579803	580402	.	-	.	transcript_id "Phchi.S4G006200.t1"; gene_id "Phchi.S4G006200"
Phchi.S4	AUGUSTUS	stop_codon	579800	579802	.	-	0	transcript_id "Phchi.S4G006200.t1"; gene_id "Phchi.S4G006200"
Phchi.S4	AUGUSTUS	CDS	579803	580402	0.99	-	0	transcript_id "Phchi.S4G006200.t1"; gene_id "Phchi.S4G006200"
Phchi.S4	AUGUSTUS	exon	579803	580402	.	-	.	transcript_id "Phchi.S4G006200.t1"; gene_id "Phchi.S4G006200"
Phchi.S4	AUGUSTUS	start_codon	580400	580402	.	-	0	transcript_id "Phchi.S4G006200.t1"; gene_id "Phchi.S4G006200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1884.t1 is derived from g8804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3704107	3704591	.	+	.	Phchi.S5G049300
Phchi.S5	AUGUSTUS	transcript	3704107	3704591	.	+	.	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	start_codon	3704107	3704109	.	+	0	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	CDS	3704107	3704132	0.8	+	0	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	exon	3704107	3704132	.	+	.	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	intron	3704133	3704257	.	+	.	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	CDS	3704258	3704591	0.89	+	1	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	exon	3704258	3704591	.	+	.	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
Phchi.S5	AUGUSTUS	stop_codon	3704592	3704594	.	+	0	transcript_id "Phchi.S5G049300.t1"; gene_id "Phchi.S5G049300"
# This transcript jg9907.t2 is derived from g7083.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9908.t1 is derived from g7084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44388552	44390883	.	-	.	Phchi.S1G706700
Phchi.S1	AUGUSTUS	transcript	44388552	44390883	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	stop_codon	44388549	44388551	.	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44388552	44388690	0.99	-	1	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44388552	44388690	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44388691	44388780	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44388781	44388884	1	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44388781	44388884	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44388885	44388967	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44388968	44389161	1	-	2	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44388968	44389161	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44389162	44389249	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44389250	44389379	0.97	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44389250	44389379	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44389380	44389489	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44389490	44389630	1	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44389490	44389630	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44389631	44389740	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44389741	44389825	1	-	1	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44389741	44389825	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44389826	44389981	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44389982	44390043	1	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44389982	44390043	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44390044	44390135	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44390136	44390285	1	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44390136	44390285	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44390286	44390361	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44390362	44390640	0.79	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44390362	44390640	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	intron	44390641	44390829	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	CDS	44390830	44390883	0.99	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	exon	44390830	44390883	.	-	.	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
Phchi.S1	AUGUSTUS	start_codon	44390881	44390883	.	-	0	transcript_id "Phchi.S1G706700.t1"; gene_id "Phchi.S1G706700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8904.t1 is derived from g6079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38580214	38581491	.	+	.	Phchi.S1G606300
Phchi.S1	AUGUSTUS	transcript	38580214	38581491	.	+	.	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	start_codon	38580214	38580216	.	+	0	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	CDS	38580214	38580528	0.9	+	0	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	exon	38580214	38580528	.	+	.	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	intron	38580529	38580648	.	+	.	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	CDS	38580649	38581491	0.98	+	0	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	exon	38580649	38581491	.	+	.	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
Phchi.S1	AUGUSTUS	stop_codon	38581492	38581494	.	+	0	transcript_id "Phchi.S1G606300.t1"; gene_id "Phchi.S1G606300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7652.t1 is derived from g4826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30423673	30424680	.	-	.	Phchi.S1G481100
Phchi.S1	AUGUSTUS	transcript	30423673	30424680	.	-	.	transcript_id "Phchi.S1G481100.t1"; gene_id "Phchi.S1G481100"
Phchi.S1	AUGUSTUS	stop_codon	30423670	30423672	.	-	0	transcript_id "Phchi.S1G481100.t1"; gene_id "Phchi.S1G481100"
Phchi.S1	AUGUSTUS	CDS	30423673	30424680	0.97	-	0	transcript_id "Phchi.S1G481100.t1"; gene_id "Phchi.S1G481100"
Phchi.S1	AUGUSTUS	exon	30423673	30424680	.	-	.	transcript_id "Phchi.S1G481100.t1"; gene_id "Phchi.S1G481100"
Phchi.S1	AUGUSTUS	start_codon	30424678	30424680	.	-	0	transcript_id "Phchi.S1G481100.t1"; gene_id "Phchi.S1G481100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5167.t1 is derived from g2337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15270907	15273250	.	-	.	Phchi.S1G232600
Phchi.S1	AUGUSTUS	transcript	15270907	15273250	.	-	.	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	stop_codon	15270904	15270906	.	-	0	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	CDS	15270907	15271397	0.99	-	2	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	exon	15270907	15271397	.	-	.	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	intron	15271398	15271494	.	-	.	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	CDS	15271495	15271915	1	-	0	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	exon	15271495	15271915	.	-	.	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	intron	15271916	15272011	.	-	.	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	CDS	15272012	15273250	0.55	-	0	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	exon	15272012	15273250	.	-	.	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
Phchi.S1	AUGUSTUS	start_codon	15273248	15273250	.	-	0	transcript_id "Phchi.S1G232600.t1"; gene_id "Phchi.S1G232600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2392.t1 is derived from g9312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6465186	6465647	.	+	.	Phchi.S5G100100
Phchi.S5	AUGUSTUS	transcript	6465186	6465647	.	+	.	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	start_codon	6465186	6465188	.	+	0	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	CDS	6465186	6465253	0.7	+	0	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	exon	6465186	6465253	.	+	.	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	intron	6465254	6465331	.	+	.	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	CDS	6465332	6465647	1	+	1	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	exon	6465332	6465647	.	+	.	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
Phchi.S5	AUGUSTUS	stop_codon	6465648	6465650	.	+	0	transcript_id "Phchi.S5G100100.t1"; gene_id "Phchi.S5G100100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8983.t1 is derived from g6158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38972939	38973583	.	-	.	Phchi.S1G614200
Phchi.S1	AUGUSTUS	transcript	38972939	38973583	.	-	.	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	stop_codon	38972936	38972938	.	-	0	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	CDS	38972939	38973132	0.85	-	2	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	exon	38972939	38973132	.	-	.	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	intron	38973133	38973283	.	-	.	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	CDS	38973284	38973397	1	-	2	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	exon	38973284	38973397	.	-	.	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	intron	38973398	38973531	.	-	.	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	CDS	38973532	38973583	0.86	-	0	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	exon	38973532	38973583	.	-	.	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
Phchi.S1	AUGUSTUS	start_codon	38973581	38973583	.	-	0	transcript_id "Phchi.S1G614200.t1"; gene_id "Phchi.S1G614200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7108.t1 is derived from g4280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27028821	27029764	.	-	.	Phchi.S1G426700
Phchi.S1	AUGUSTUS	transcript	27028821	27029764	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	stop_codon	27028818	27028820	.	-	0	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	CDS	27028821	27028837	0.96	-	2	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	exon	27028821	27028837	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	intron	27028838	27029136	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	CDS	27029137	27029214	1	-	2	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	exon	27029137	27029214	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	intron	27029215	27029366	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	CDS	27029367	27029373	1	-	0	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	exon	27029367	27029373	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	intron	27029374	27029453	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	CDS	27029454	27029544	1	-	1	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	exon	27029454	27029544	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	intron	27029545	27029642	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	CDS	27029643	27029764	0.76	-	0	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	exon	27029643	27029764	.	-	.	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
Phchi.S1	AUGUSTUS	start_codon	27029762	27029764	.	-	0	transcript_id "Phchi.S1G426700.t1"; gene_id "Phchi.S1G426700"
# This transcript jg8122.t2 is derived from g5297.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8123.t1 is derived from g5298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33513275	33514940	.	+	.	Phchi.S1G528200
Phchi.S1	AUGUSTUS	transcript	33513275	33514940	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	start_codon	33513275	33513277	.	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33513275	33513442	0.7	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33513275	33513442	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33513443	33513594	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33513595	33513768	0.81	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33513595	33513768	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33513769	33513874	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33513875	33513967	0.96	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33513875	33513967	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33513968	33514043	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33514044	33514112	1	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33514044	33514112	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33514113	33514202	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33514203	33514242	0.99	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33514203	33514242	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33514243	33514325	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33514326	33514408	1	+	2	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33514326	33514408	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33514409	33514555	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33514556	33514681	0.99	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33514556	33514681	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	intron	33514682	33514787	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	CDS	33514788	33514940	1	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	exon	33514788	33514940	.	+	.	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
Phchi.S1	AUGUSTUS	stop_codon	33514941	33514943	.	+	0	transcript_id "Phchi.S1G528200.t1"; gene_id "Phchi.S1G528200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14068.t1 is derived from g12535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10638124	10639001	.	+	.	Phchi.S3G138700
Phchi.S3	AUGUSTUS	transcript	10638124	10639001	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	start_codon	10638124	10638126	.	+	0	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	CDS	10638124	10638235	0.98	+	0	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	exon	10638124	10638235	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	intron	10638236	10638319	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	CDS	10638320	10638381	0.48	+	2	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	exon	10638320	10638381	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	intron	10638382	10638491	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	CDS	10638492	10638602	0.61	+	0	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	exon	10638492	10638602	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	intron	10638603	10638676	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	CDS	10638677	10638769	1	+	0	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	exon	10638677	10638769	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	intron	10638770	10638848	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	CDS	10638849	10639001	0.97	+	0	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	exon	10638849	10639001	.	+	.	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
Phchi.S3	AUGUSTUS	stop_codon	10639002	10639004	.	+	0	transcript_id "Phchi.S3G138700.t1"; gene_id "Phchi.S3G138700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2983.t1 is derived from g152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	971191	974695	.	-	.	Phchi.S1G014200
Phchi.S1	AUGUSTUS	transcript	971191	974695	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	stop_codon	971188	971190	.	-	0	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	971191	971228	0.97	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	971191	971228	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	971229	971307	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	971308	971477	0.44	-	1	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	971308	971477	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	971478	971656	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	971657	971912	0.59	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	971657	971912	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	971913	972043	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	972044	972181	1	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	972044	972181	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	972182	972267	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	972268	972362	1	-	1	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	972268	972362	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	972363	972526	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	972527	972602	0.5	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	972527	972602	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	972603	972728	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	972729	972803	0.89	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	972729	972803	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	972804	972904	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	972905	973051	0.98	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	972905	973051	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	973052	973185	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	973186	973299	1	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	973186	973299	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	973300	973431	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	973432	973489	1	-	0	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	973432	973489	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	973490	973640	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	973641	973687	1	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	973641	973687	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	973688	973786	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	973787	973873	0.96	-	2	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	973787	973873	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	973874	973979	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	973980	974068	1	-	1	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	973980	974068	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	974069	974152	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	974153	974308	1	-	1	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	974153	974308	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	974309	974397	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	974398	974517	0.82	-	1	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	974398	974517	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	intron	974518	974591	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	CDS	974592	974695	0.57	-	0	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	exon	974592	974695	.	-	.	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
Phchi.S1	AUGUSTUS	start_codon	974693	974695	.	-	0	transcript_id "Phchi.S1G014200.t1"; gene_id "Phchi.S1G014200"
# This transcript jg7685.t2 is derived from g4859.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 5 different transcripts
# This transcript jg7686.t1 is derived from g4860.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30617740	30622776	.	+	.	Phchi.S1G484500
Phchi.S1	AUGUSTUS	transcript	30619962	30622776	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	start_codon	30619962	30619964	.	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619962	30619967	0.81	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619962	30619967	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30619968	30620077	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620078	30620094	0.81	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620078	30620094	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620095	30620279	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620280	30620447	0.81	+	1	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620280	30620447	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620448	30620527	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620528	30620903	1	+	1	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620528	30620903	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620904	30621011	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621012	30621155	1	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621012	30621155	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621156	30621302	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621303	30621455	1	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621303	30621455	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621456	30621536	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621537	30621653	1	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621537	30621653	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621654	30621727	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621728	30621808	1	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621728	30621808	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621809	30621902	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621903	30622055	1	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621903	30622055	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622056	30622138	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622139	30622464	0.42	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622139	30622464	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622465	30622561	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622562	30622675	0.55	+	1	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622562	30622675	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622676	30622769	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622770	30622776	0.55	+	1	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622770	30622776	.	+	.	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	stop_codon	30622777	30622779	.	+	0	transcript_id "Phchi.S1G484500.t1"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	transcript	30617740	30622776	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	start_codon	30617740	30617742	.	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30617740	30617869	0.93	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30617740	30617869	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30617870	30618327	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618328	30618415	0.62	+	2	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618328	30618415	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618416	30618519	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618520	30618581	0.71	+	1	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618520	30618581	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618582	30618810	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618811	30618908	0.58	+	2	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618811	30618908	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618909	30619300	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619301	30619530	1	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619301	30619530	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30619531	30620279	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620280	30620447	1	+	1	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620280	30620447	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620448	30620527	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620528	30620903	0.98	+	1	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620528	30620903	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620904	30621011	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621012	30621155	1	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621012	30621155	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621156	30621302	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621303	30621455	1	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621303	30621455	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621456	30621536	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621537	30621653	1	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621537	30621653	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621654	30621727	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621728	30621808	1	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621728	30621808	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621809	30621902	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621903	30622055	1	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621903	30622055	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622056	30622138	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622139	30622464	0.48	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622139	30622464	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622465	30622561	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622562	30622675	0.54	+	1	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622562	30622675	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622676	30622769	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622770	30622776	0.54	+	1	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622770	30622776	.	+	.	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	stop_codon	30622777	30622779	.	+	0	transcript_id "Phchi.S1G484500.t2"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	transcript	30619962	30622776	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	start_codon	30619962	30619964	.	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619962	30619967	0.49	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619962	30619967	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30619968	30620077	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620078	30620094	0.49	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620078	30620094	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620095	30620279	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620280	30620447	0.95	+	1	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620280	30620447	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620448	30620527	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30620528	30620903	0.95	+	1	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30620528	30620903	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30620904	30621011	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621012	30621155	1	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621012	30621155	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621156	30621302	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621303	30621455	1	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621303	30621455	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621456	30621536	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621537	30621653	1	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621537	30621653	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621654	30621727	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621728	30621808	1	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621728	30621808	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30621809	30621902	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30621903	30622055	1	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30621903	30622055	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622056	30622138	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622139	30622464	0.55	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622139	30622464	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622465	30622561	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622562	30622675	0.67	+	1	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622562	30622675	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30622676	30622772	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30622773	30622776	0.67	+	1	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30622773	30622776	.	+	.	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	stop_codon	30622777	30622779	.	+	0	transcript_id "Phchi.S1G484500.t3"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	transcript	30617740	30619688	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	start_codon	30617740	30617742	.	+	0	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30617740	30617869	0.94	+	0	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30617740	30617869	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30617870	30618327	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618328	30618415	0.7	+	2	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618328	30618415	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618416	30618519	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618520	30618581	0.79	+	1	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618520	30618581	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618582	30618810	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618811	30618908	0.53	+	2	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618811	30618908	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618909	30619300	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619301	30619530	1	+	0	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619301	30619530	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30619531	30619681	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619682	30619688	1	+	1	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619682	30619688	.	+	.	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	stop_codon	30619689	30619691	.	+	0	transcript_id "Phchi.S1G484500.t4"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	transcript	30617740	30619688	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	start_codon	30617740	30617742	.	+	0	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30617740	30617869	0.88	+	0	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30617740	30617869	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30617870	30618327	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618328	30618415	0.56	+	2	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618328	30618415	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618416	30618519	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618520	30618581	0.64	+	1	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618520	30618581	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618582	30618822	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30618823	30618908	1	+	2	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30618823	30618908	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30618909	30619300	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619301	30619530	1	+	0	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619301	30619530	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	intron	30619531	30619681	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	CDS	30619682	30619688	0.49	+	1	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	exon	30619682	30619688	.	+	.	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
Phchi.S1	AUGUSTUS	stop_codon	30619689	30619691	.	+	0	transcript_id "Phchi.S1G484500.t5"; gene_id "Phchi.S1G484500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9457.t1 is derived from g6633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41562241	41562918	.	-	.	Phchi.S1G661600
Phchi.S1	AUGUSTUS	transcript	41562241	41562918	.	-	.	transcript_id "Phchi.S1G661600.t1"; gene_id "Phchi.S1G661600"
Phchi.S1	AUGUSTUS	stop_codon	41562238	41562240	.	-	0	transcript_id "Phchi.S1G661600.t1"; gene_id "Phchi.S1G661600"
Phchi.S1	AUGUSTUS	CDS	41562241	41562918	1	-	0	transcript_id "Phchi.S1G661600.t1"; gene_id "Phchi.S1G661600"
Phchi.S1	AUGUSTUS	exon	41562241	41562918	.	-	.	transcript_id "Phchi.S1G661600.t1"; gene_id "Phchi.S1G661600"
Phchi.S1	AUGUSTUS	start_codon	41562916	41562918	.	-	0	transcript_id "Phchi.S1G661600.t1"; gene_id "Phchi.S1G661600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12255.t1 is derived from g7931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7029783	7033192	.	-	.	Phchi.S2G033500
Phchi.S2	AUGUSTUS	transcript	7029783	7030948	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	stop_codon	7029780	7029782	.	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7029783	7029953	0.96	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7029783	7029953	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7029954	7030058	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030059	7030131	0.98	-	1	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030059	7030131	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030132	7030227	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030228	7030310	1	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030228	7030310	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030311	7030452	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030453	7030491	1	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030453	7030491	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030492	7030632	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030633	7030713	1	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030633	7030713	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030714	7030807	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030808	7030948	0.73	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030808	7030948	.	-	.	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	start_codon	7030946	7030948	.	-	0	transcript_id "Phchi.S2G033500.t1"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	transcript	7029783	7033192	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	stop_codon	7029780	7029782	.	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7029783	7029953	0.96	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7029783	7029953	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7029954	7030058	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030059	7030131	0.99	-	1	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030059	7030131	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030132	7030227	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030228	7030310	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030228	7030310	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030311	7030452	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030453	7030491	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030453	7030491	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030492	7030632	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030633	7030713	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030633	7030713	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030714	7030807	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7030808	7030963	0.99	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7030808	7030963	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7030964	7031064	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031065	7031130	0.89	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031065	7031130	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031131	7031244	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031245	7031325	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031245	7031325	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031326	7031445	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031446	7031508	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031446	7031508	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031509	7031714	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031715	7031822	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031715	7031822	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031823	7032100	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032101	7032184	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032101	7032184	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032185	7032278	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032279	7032350	1	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032279	7032350	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032351	7032466	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032467	7032525	1	-	2	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032467	7032525	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032526	7032607	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032608	7032663	1	-	1	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032608	7032663	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032664	7032753	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032754	7032962	0.89	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032754	7032962	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032963	7033042	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7033043	7033192	0.43	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7033043	7033192	.	-	.	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	start_codon	7033190	7033192	.	-	0	transcript_id "Phchi.S2G033500.t2"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	transcript	7031129	7033192	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	stop_codon	7031126	7031128	.	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031129	7031130	1	-	2	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031129	7031130	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031131	7031219	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031220	7031325	1	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031220	7031325	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031326	7031445	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031446	7031508	1	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031446	7031508	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031509	7031714	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7031715	7031822	1	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7031715	7031822	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7031823	7032100	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032101	7032184	1	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032101	7032184	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032185	7032278	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032279	7032350	1	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032279	7032350	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032351	7032466	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032467	7032525	1	-	2	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032467	7032525	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032526	7032607	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032608	7032663	1	-	1	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032608	7032663	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032664	7032753	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7032754	7032962	0.88	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7032754	7032962	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	intron	7032963	7033042	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	CDS	7033043	7033192	0.51	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	exon	7033043	7033192	.	-	.	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
Phchi.S2	AUGUSTUS	start_codon	7033190	7033192	.	-	0	transcript_id "Phchi.S2G033500.t3"; gene_id "Phchi.S2G033500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5941.t1 is derived from g3112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19958009	19959802	.	+	.	Phchi.S1G310000
Phchi.S1	AUGUSTUS	transcript	19958009	19959802	.	+	.	transcript_id "Phchi.S1G310000.t1"; gene_id "Phchi.S1G310000"
Phchi.S1	AUGUSTUS	start_codon	19958009	19958011	.	+	0	transcript_id "Phchi.S1G310000.t1"; gene_id "Phchi.S1G310000"
Phchi.S1	AUGUSTUS	CDS	19958009	19959802	0.78	+	0	transcript_id "Phchi.S1G310000.t1"; gene_id "Phchi.S1G310000"
Phchi.S1	AUGUSTUS	exon	19958009	19959802	.	+	.	transcript_id "Phchi.S1G310000.t1"; gene_id "Phchi.S1G310000"
Phchi.S1	AUGUSTUS	stop_codon	19959803	19959805	.	+	0	transcript_id "Phchi.S1G310000.t1"; gene_id "Phchi.S1G310000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1659.t1 is derived from g8578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2284298	2285528	.	+	.	Phchi.S5G026800
Phchi.S5	AUGUSTUS	transcript	2284298	2285528	.	+	.	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	start_codon	2284298	2284300	.	+	0	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	CDS	2284298	2284684	0.98	+	0	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	exon	2284298	2284684	.	+	.	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	intron	2284685	2284769	.	+	.	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	CDS	2284770	2285528	1	+	0	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	exon	2284770	2285528	.	+	.	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
Phchi.S5	AUGUSTUS	stop_codon	2285529	2285531	.	+	0	transcript_id "Phchi.S5G026800.t1"; gene_id "Phchi.S5G026800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10158.t1 is derived from g7334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46037132	46038503	.	+	.	Phchi.S1G731700
Phchi.S1	AUGUSTUS	transcript	46037132	46038503	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	start_codon	46037132	46037134	.	+	0	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	CDS	46037132	46037149	1	+	0	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	exon	46037132	46037149	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	intron	46037150	46037482	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	CDS	46037483	46037585	1	+	0	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	exon	46037483	46037585	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	intron	46037586	46037689	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	CDS	46037690	46037784	1	+	2	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	exon	46037690	46037784	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	intron	46037785	46037877	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	CDS	46037878	46038117	1	+	0	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	exon	46037878	46038117	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	intron	46038118	46038211	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	CDS	46038212	46038330	1	+	0	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	exon	46038212	46038330	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	intron	46038331	46038439	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	CDS	46038440	46038503	0.99	+	1	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	exon	46038440	46038503	.	+	.	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
Phchi.S1	AUGUSTUS	stop_codon	46038504	46038506	.	+	0	transcript_id "Phchi.S1G731700.t1"; gene_id "Phchi.S1G731700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8106.t1 is derived from g5281.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33143394	33145719	.	+	.	Phchi.S1G526500
Phchi.S1	AUGUSTUS	transcript	33143394	33145719	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	start_codon	33143394	33143396	.	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33143394	33143469	0.93	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33143394	33143469	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33143470	33143631	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33143632	33143747	0.93	+	2	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33143632	33143747	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33143748	33143962	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33143963	33144062	1	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33143963	33144062	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33144063	33144144	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33144145	33144374	1	+	2	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33144145	33144374	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33144375	33144621	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33144622	33144789	1	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33144622	33144789	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33144790	33145025	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33145026	33145259	1	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33145026	33145259	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33145260	33145479	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33145480	33145719	1	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33145480	33145719	.	+	.	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	stop_codon	33145720	33145722	.	+	0	transcript_id "Phchi.S1G526500.t1"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	transcript	33143394	33145719	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	start_codon	33143394	33143396	.	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33143394	33143469	0.83	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33143394	33143469	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33143470	33143631	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33143632	33143684	0.73	+	2	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33143632	33143684	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33143685	33143962	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33143963	33144062	0.99	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33143963	33144062	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33144063	33144144	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33144145	33144374	1	+	2	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33144145	33144374	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33144375	33144621	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33144622	33144789	1	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33144622	33144789	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33144790	33145025	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33145026	33145259	1	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33145026	33145259	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	intron	33145260	33145479	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	CDS	33145480	33145719	0.97	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	exon	33145480	33145719	.	+	.	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
Phchi.S1	AUGUSTUS	stop_codon	33145720	33145722	.	+	0	transcript_id "Phchi.S1G526500.t2"; gene_id "Phchi.S1G526500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7901.t1 is derived from g5075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31812908	31815200	.	-	.	Phchi.S1G506000
Phchi.S1	AUGUSTUS	transcript	31812908	31815200	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	stop_codon	31812905	31812907	.	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31812908	31813263	1	-	2	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31812908	31813263	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	intron	31813264	31813349	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31813350	31813504	1	-	1	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31813350	31813504	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	intron	31813505	31813592	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31813593	31813831	1	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31813593	31813831	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	intron	31813832	31813911	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31813912	31814136	0.98	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31813912	31814136	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	intron	31814137	31814267	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31814268	31814468	1	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31814268	31814468	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	intron	31814469	31814551	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31814552	31814980	1	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31814552	31814980	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	intron	31814981	31815077	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	CDS	31815078	31815200	1	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	exon	31815078	31815200	.	-	.	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
Phchi.S1	AUGUSTUS	start_codon	31815198	31815200	.	-	0	transcript_id "Phchi.S1G506000.t1"; gene_id "Phchi.S1G506000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7620.t1 is derived from g4794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30298934	30301000	.	+	.	Phchi.S1G477900
Phchi.S1	AUGUSTUS	transcript	30298934	30301000	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	start_codon	30298934	30298936	.	+	0	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30298934	30299205	0.9	+	0	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30298934	30299205	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30299206	30299334	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30299335	30299523	0.72	+	1	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30299335	30299523	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30299524	30299613	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30299614	30299728	1	+	1	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30299614	30299728	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30299729	30299826	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30299827	30299945	1	+	0	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30299827	30299945	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30299946	30300031	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30300032	30300185	1	+	1	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30300032	30300185	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30300186	30300273	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30300274	30300382	1	+	0	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30300274	30300382	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30300383	30300450	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30300451	30300575	1	+	2	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30300451	30300575	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30300576	30300669	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30300670	30300788	1	+	0	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30300670	30300788	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	intron	30300789	30300882	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	CDS	30300883	30301000	0.57	+	1	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	exon	30300883	30301000	.	+	.	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
Phchi.S1	AUGUSTUS	stop_codon	30301001	30301003	.	+	0	transcript_id "Phchi.S1G477900.t1"; gene_id "Phchi.S1G477900"
# This transcript jg6978.t2 is derived from g4150.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6979.t1 is derived from g4151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26253471	26255250	.	-	.	Phchi.S1G413800
Phchi.S1	AUGUSTUS	transcript	26253471	26255250	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	stop_codon	26253468	26253470	.	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26253471	26253525	0.99	-	1	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26253471	26253525	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26253526	26253605	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26253606	26253667	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26253606	26253667	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26253668	26253751	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26253752	26253820	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26253752	26253820	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26253821	26253922	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26253923	26253970	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26253923	26253970	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26253971	26254067	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26254068	26254127	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26254068	26254127	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26254128	26254265	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26254266	26254378	1	-	2	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26254266	26254378	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26254379	26254508	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26254509	26254581	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26254509	26254581	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26254582	26254667	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26254668	26254712	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26254668	26254712	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26254713	26254879	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26254880	26254990	1	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26254880	26254990	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	intron	26254991	26255124	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	CDS	26255125	26255250	0.94	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	exon	26255125	26255250	.	-	.	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
Phchi.S1	AUGUSTUS	start_codon	26255248	26255250	.	-	0	transcript_id "Phchi.S1G413800.t1"; gene_id "Phchi.S1G413800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1310.t1 is derived from g11093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8946128	8947189	.	-	.	Phchi.S6G126900
Phchi.S6	AUGUSTUS	transcript	8946128	8947189	.	-	.	transcript_id "Phchi.S6G126900.t1"; gene_id "Phchi.S6G126900"
Phchi.S6	AUGUSTUS	stop_codon	8946125	8946127	.	-	0	transcript_id "Phchi.S6G126900.t1"; gene_id "Phchi.S6G126900"
Phchi.S6	AUGUSTUS	CDS	8946128	8947189	0.79	-	0	transcript_id "Phchi.S6G126900.t1"; gene_id "Phchi.S6G126900"
Phchi.S6	AUGUSTUS	exon	8946128	8947189	.	-	.	transcript_id "Phchi.S6G126900.t1"; gene_id "Phchi.S6G126900"
Phchi.S6	AUGUSTUS	start_codon	8947187	8947189	.	-	0	transcript_id "Phchi.S6G126900.t1"; gene_id "Phchi.S6G126900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13885.t1 is derived from g12352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9457681	9461216	.	+	.	Phchi.S3G120400
Phchi.S3	AUGUSTUS	transcript	9457681	9461216	.	+	.	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	start_codon	9457681	9457683	.	+	0	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	CDS	9457681	9458415	0.89	+	0	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	exon	9457681	9458415	.	+	.	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	intron	9458416	9458504	.	+	.	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	CDS	9458505	9461216	1	+	0	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	exon	9458505	9461216	.	+	.	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	stop_codon	9461217	9461219	.	+	0	transcript_id "Phchi.S3G120400.t1"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	transcript	9459804	9461216	.	+	.	transcript_id "Phchi.S3G120400.t2"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	start_codon	9459804	9459806	.	+	0	transcript_id "Phchi.S3G120400.t2"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	CDS	9459804	9461216	0.3	+	0	transcript_id "Phchi.S3G120400.t2"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	exon	9459804	9461216	.	+	.	transcript_id "Phchi.S3G120400.t2"; gene_id "Phchi.S3G120400"
Phchi.S3	AUGUSTUS	stop_codon	9461217	9461219	.	+	0	transcript_id "Phchi.S3G120400.t2"; gene_id "Phchi.S3G120400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2549.t1 is derived from g9469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7285462	7285818	.	+	.	Phchi.S5G115800
Phchi.S5	AUGUSTUS	transcript	7285462	7285818	.	+	.	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	start_codon	7285462	7285464	.	+	0	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	CDS	7285462	7285677	0.53	+	0	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	exon	7285462	7285677	.	+	.	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	intron	7285678	7285743	.	+	.	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	CDS	7285744	7285818	0.75	+	0	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	exon	7285744	7285818	.	+	.	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
Phchi.S5	AUGUSTUS	stop_codon	7285819	7285821	.	+	0	transcript_id "Phchi.S5G115800.t1"; gene_id "Phchi.S5G115800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14427.t1 is derived from g12895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12758564	12760493	.	+	.	Phchi.S3G174600
Phchi.S3	AUGUSTUS	transcript	12758564	12760493	.	+	.	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	start_codon	12758564	12758566	.	+	0	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	CDS	12758564	12758630	0.03	+	0	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	exon	12758564	12758630	.	+	.	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	intron	12758631	12760437	.	+	.	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	CDS	12760438	12760493	0.02	+	2	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	exon	12760438	12760493	.	+	.	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
Phchi.S3	AUGUSTUS	stop_codon	12760494	12760496	.	+	0	transcript_id "Phchi.S3G174600.t1"; gene_id "Phchi.S3G174600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13225.t1 is derived from g11690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4778542	4780080	.	-	.	Phchi.S3G054400
Phchi.S3	AUGUSTUS	transcript	4778542	4780080	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	stop_codon	4778539	4778541	.	-	0	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	CDS	4778542	4779075	0.99	-	0	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	exon	4778542	4779075	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	intron	4779076	4779155	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	CDS	4779156	4779440	0.95	-	0	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	exon	4779156	4779440	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	intron	4779441	4779542	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	CDS	4779543	4779671	0.95	-	0	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	exon	4779543	4779671	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	intron	4779672	4779765	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	CDS	4779766	4780080	0.89	-	0	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	exon	4779766	4780080	.	-	.	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
Phchi.S3	AUGUSTUS	start_codon	4780078	4780080	.	-	0	transcript_id "Phchi.S3G054400.t1"; gene_id "Phchi.S3G054400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7708.t1 is derived from g4882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30728894	30729361	.	+	.	Phchi.S1G486700
Phchi.S1	AUGUSTUS	transcript	30728894	30729361	.	+	.	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	start_codon	30728894	30728896	.	+	0	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	CDS	30728894	30729043	0.84	+	0	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	exon	30728894	30729043	.	+	.	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	intron	30729044	30729157	.	+	.	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	CDS	30729158	30729361	0.39	+	0	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	exon	30729158	30729361	.	+	.	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
Phchi.S1	AUGUSTUS	stop_codon	30729362	30729364	.	+	0	transcript_id "Phchi.S1G486700.t1"; gene_id "Phchi.S1G486700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13689.t1 is derived from g12156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8209534	8214439	.	-	.	Phchi.S3G100800
Phchi.S3	AUGUSTUS	transcript	8209534	8210731	.	-	.	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	stop_codon	8209531	8209533	.	-	0	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	CDS	8209534	8210237	0.97	-	2	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	exon	8209534	8210237	.	-	.	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	intron	8210238	8210325	.	-	.	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	CDS	8210326	8210731	0.66	-	0	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	exon	8210326	8210731	.	-	.	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	start_codon	8210729	8210731	.	-	0	transcript_id "Phchi.S3G100800.t1"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	transcript	8209534	8214439	.	-	.	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	stop_codon	8209531	8209533	.	-	0	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	CDS	8209534	8210237	0.86	-	2	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	exon	8209534	8210237	.	-	.	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	intron	8210238	8210325	.	-	.	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	CDS	8210326	8214439	0.82	-	0	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	exon	8210326	8214439	.	-	.	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
Phchi.S3	AUGUSTUS	start_codon	8214437	8214439	.	-	0	transcript_id "Phchi.S3G100800.t2"; gene_id "Phchi.S3G100800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9935.t1 is derived from g7111.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44538744	44541147	.	-	.	Phchi.S1G709400
Phchi.S1	AUGUSTUS	transcript	44538744	44541147	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	stop_codon	44538741	44538743	.	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44538744	44538800	0.98	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44538744	44538800	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44538801	44538892	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44538893	44538964	0.97	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44538893	44538964	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44538965	44539068	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539069	44539128	0.97	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539069	44539128	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539129	44539214	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539215	44539245	0.97	-	1	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539215	44539245	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539246	44539328	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539329	44539397	0.97	-	1	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539329	44539397	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539398	44539512	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539513	44539595	0.97	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539513	44539595	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539596	44539682	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539683	44539739	1	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539683	44539739	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539740	44539835	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539836	44539885	1	-	2	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539836	44539885	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539886	44540081	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540082	44540139	1	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540082	44540139	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540140	44540221	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540222	44540268	1	-	2	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540222	44540268	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540269	44540358	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540359	44540527	0.98	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540359	44540527	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540528	44540662	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540663	44540737	1	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540663	44540737	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540738	44540836	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540837	44540902	1	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540837	44540902	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540903	44541060	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44541061	44541147	1	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44541061	44541147	.	-	.	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	start_codon	44541145	44541147	.	-	0	transcript_id "Phchi.S1G709400.t1"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	transcript	44538744	44541147	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	stop_codon	44538741	44538743	.	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44538744	44538800	0.86	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44538744	44538800	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44538801	44538892	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44538893	44538964	0.86	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44538893	44538964	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44538965	44539068	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539069	44539125	0.71	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539069	44539125	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539126	44539214	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539215	44539245	0.82	-	1	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539215	44539245	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539246	44539328	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539329	44539397	0.83	-	1	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539329	44539397	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539398	44539512	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539513	44539595	0.83	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539513	44539595	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539596	44539682	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539683	44539739	1	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539683	44539739	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539740	44539835	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44539836	44539885	1	-	2	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44539836	44539885	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44539886	44540081	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540082	44540139	1	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540082	44540139	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540140	44540221	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540222	44540268	1	-	2	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540222	44540268	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540269	44540358	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540359	44540527	1	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540359	44540527	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540528	44540662	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540663	44540737	1	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540663	44540737	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540738	44540836	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44540837	44540902	1	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44540837	44540902	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	intron	44540903	44541060	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	CDS	44541061	44541147	0.99	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	exon	44541061	44541147	.	-	.	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
Phchi.S1	AUGUSTUS	start_codon	44541145	44541147	.	-	0	transcript_id "Phchi.S1G709400.t2"; gene_id "Phchi.S1G709400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5254.t1 is derived from g2424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15877910	15878578	.	-	.	Phchi.S1G241300
Phchi.S1	AUGUSTUS	transcript	15877910	15878578	.	-	.	transcript_id "Phchi.S1G241300.t1"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	stop_codon	15877907	15877909	.	-	0	transcript_id "Phchi.S1G241300.t1"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	CDS	15877910	15878578	1	-	0	transcript_id "Phchi.S1G241300.t1"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	exon	15877910	15878578	.	-	.	transcript_id "Phchi.S1G241300.t1"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	start_codon	15878576	15878578	.	-	0	transcript_id "Phchi.S1G241300.t1"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	transcript	15877910	15878131	.	-	.	transcript_id "Phchi.S1G241300.t2"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	stop_codon	15877907	15877909	.	-	0	transcript_id "Phchi.S1G241300.t2"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	CDS	15877910	15878131	0.6	-	0	transcript_id "Phchi.S1G241300.t2"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	exon	15877910	15878131	.	-	.	transcript_id "Phchi.S1G241300.t2"; gene_id "Phchi.S1G241300"
Phchi.S1	AUGUSTUS	start_codon	15878129	15878131	.	-	0	transcript_id "Phchi.S1G241300.t2"; gene_id "Phchi.S1G241300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10990.t1 is derived from g15040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3548767	3551038	.	+	.	Phchi.S4G057200
Phchi.S4	AUGUSTUS	transcript	3548767	3551038	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	start_codon	3548767	3548769	.	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3548767	3548926	1	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3548767	3548926	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3548927	3549049	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3549050	3549119	1	+	2	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3549050	3549119	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3549120	3549207	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3549208	3549332	1	+	1	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3549208	3549332	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3549333	3549587	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3549588	3549804	1	+	2	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3549588	3549804	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3549805	3549985	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3549986	3550082	1	+	1	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3549986	3550082	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3550083	3550178	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3550179	3550244	1	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3550179	3550244	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3550245	3550315	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3550316	3550442	1	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3550316	3550442	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3550443	3550558	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3550559	3550638	1	+	2	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3550559	3550638	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3550639	3550750	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3550751	3550855	1	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3550751	3550855	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	intron	3550856	3550933	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	CDS	3550934	3551038	0.98	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	exon	3550934	3551038	.	+	.	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
Phchi.S4	AUGUSTUS	stop_codon	3551039	3551041	.	+	0	transcript_id "Phchi.S4G057200.t1"; gene_id "Phchi.S4G057200"
# This transcript jg883.t2 is derived from g10665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg884.t1 is derived from g10666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6269468	6272143	.	+	.	Phchi.S6G084300
Phchi.S6	AUGUSTUS	transcript	6269468	6272143	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	start_codon	6269468	6269470	.	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6269468	6269618	1	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6269468	6269618	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6269619	6269698	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6269699	6269809	1	+	2	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6269699	6269809	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6269810	6269932	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6269933	6270037	1	+	2	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6269933	6270037	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6270038	6270139	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6270140	6270360	0.91	+	2	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6270140	6270360	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6270361	6270471	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6270472	6270648	0.91	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6270472	6270648	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6270649	6270764	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6270765	6270923	1	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6270765	6270923	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6270924	6271019	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6271020	6271296	1	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6271020	6271296	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6271297	6271388	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6271389	6271570	0.44	+	2	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6271389	6271570	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6271571	6271790	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6271791	6271851	0.62	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6271791	6271851	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	intron	6271852	6271943	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	CDS	6271944	6272143	0.62	+	2	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	exon	6271944	6272143	.	+	.	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
Phchi.S6	AUGUSTUS	stop_codon	6272144	6272146	.	+	0	transcript_id "Phchi.S6G084300.t1"; gene_id "Phchi.S6G084300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11630.t1 is derived from g15681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7388825	7390105	.	+	.	Phchi.S4G121200
Phchi.S4	AUGUSTUS	transcript	7388825	7390105	.	+	.	transcript_id "Phchi.S4G121200.t1"; gene_id "Phchi.S4G121200"
Phchi.S4	AUGUSTUS	start_codon	7388825	7388827	.	+	0	transcript_id "Phchi.S4G121200.t1"; gene_id "Phchi.S4G121200"
Phchi.S4	AUGUSTUS	CDS	7388825	7390105	0.91	+	0	transcript_id "Phchi.S4G121200.t1"; gene_id "Phchi.S4G121200"
Phchi.S4	AUGUSTUS	exon	7388825	7390105	.	+	.	transcript_id "Phchi.S4G121200.t1"; gene_id "Phchi.S4G121200"
Phchi.S4	AUGUSTUS	stop_codon	7390106	7390108	.	+	0	transcript_id "Phchi.S4G121200.t1"; gene_id "Phchi.S4G121200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8529.t1 is derived from g5704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36502768	36503450	.	+	.	Phchi.S1G568800
Phchi.S1	AUGUSTUS	transcript	36502768	36503450	.	+	.	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	start_codon	36502768	36502770	.	+	0	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	CDS	36502768	36503223	0.8	+	0	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	exon	36502768	36503223	.	+	.	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	intron	36503224	36503324	.	+	.	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	CDS	36503325	36503450	0.97	+	0	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	exon	36503325	36503450	.	+	.	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
Phchi.S1	AUGUSTUS	stop_codon	36503451	36503453	.	+	0	transcript_id "Phchi.S1G568800.t1"; gene_id "Phchi.S1G568800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5656.t1 is derived from g2826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18155688	18157303	.	-	.	Phchi.S1G281500
Phchi.S1	AUGUSTUS	transcript	18155688	18157303	.	-	.	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	stop_codon	18155685	18155687	.	-	0	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	CDS	18155688	18156847	0.7	-	2	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	exon	18155688	18156847	.	-	.	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	intron	18156848	18157257	.	-	.	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	CDS	18157258	18157303	0.01	-	0	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	exon	18157258	18157303	.	-	.	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
Phchi.S1	AUGUSTUS	start_codon	18157301	18157303	.	-	0	transcript_id "Phchi.S1G281500.t1"; gene_id "Phchi.S1G281500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6967.t1 is derived from g4139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26164151	26166458	.	+	.	Phchi.S1G412600
Phchi.S1	AUGUSTUS	transcript	26164151	26166458	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	start_codon	26164151	26164153	.	+	0	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	CDS	26164151	26164232	0.5	+	0	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	exon	26164151	26164232	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	intron	26164233	26164577	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	CDS	26164578	26164703	0.61	+	2	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	exon	26164578	26164703	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	intron	26164704	26164756	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	CDS	26164757	26165721	0.83	+	2	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	exon	26164757	26165721	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	intron	26165722	26165800	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	CDS	26165801	26166246	0.9	+	0	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	exon	26165801	26166246	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	intron	26166247	26166370	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	CDS	26166371	26166458	0.9	+	1	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	exon	26166371	26166458	.	+	.	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
Phchi.S1	AUGUSTUS	stop_codon	26166459	26166461	.	+	0	transcript_id "Phchi.S1G412600.t1"; gene_id "Phchi.S1G412600"
# This transcript jg6442.t2 is derived from g3614.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6443.t1 is derived from g3615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23045025	23048130	.	+	.	Phchi.S1G360200
Phchi.S1	AUGUSTUS	transcript	23045025	23048130	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	start_codon	23045025	23045027	.	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23045025	23045189	1	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23045025	23045189	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23045190	23045286	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23045287	23045358	1	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23045287	23045358	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23045359	23045489	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23045490	23045697	1	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23045490	23045697	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23045698	23045794	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23045795	23045897	1	+	2	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23045795	23045897	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23045898	23046034	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23046035	23046165	1	+	1	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23046035	23046165	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23046166	23046328	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23046329	23046407	1	+	2	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23046329	23046407	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23046408	23046484	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23046485	23046626	1	+	1	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23046485	23046626	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23046627	23046717	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23046718	23046875	1	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23046718	23046875	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23046876	23046968	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23046969	23047086	1	+	1	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23046969	23047086	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23047087	23047186	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23047187	23047374	0.88	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23047187	23047374	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23047375	23047558	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23047559	23047641	0.9	+	1	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23047559	23047641	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23047642	23047726	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23047727	23047817	0.76	+	2	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23047727	23047817	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23047818	23047924	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23047925	23047984	0.76	+	1	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23047925	23047984	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	intron	23047985	23048063	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	CDS	23048064	23048130	0.44	+	1	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	exon	23048064	23048130	.	+	.	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
Phchi.S1	AUGUSTUS	stop_codon	23048131	23048133	.	+	0	transcript_id "Phchi.S1G360200.t1"; gene_id "Phchi.S1G360200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14480.t1 is derived from g12948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13056116	13057873	.	+	.	Phchi.S3G179900
Phchi.S3	AUGUSTUS	transcript	13056116	13057873	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	start_codon	13056116	13056118	.	+	0	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	CDS	13056116	13056723	1	+	0	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	exon	13056116	13056723	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	intron	13056724	13056831	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	CDS	13056832	13057221	0.96	+	1	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	exon	13056832	13057221	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	intron	13057222	13057317	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	CDS	13057318	13057476	1	+	1	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	exon	13057318	13057476	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	intron	13057477	13057563	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	CDS	13057564	13057873	0.98	+	1	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	exon	13057564	13057873	.	+	.	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
Phchi.S3	AUGUSTUS	stop_codon	13057874	13057876	.	+	0	transcript_id "Phchi.S3G179900.t1"; gene_id "Phchi.S3G179900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9085.t1 is derived from g6260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39786311	39788446	.	-	.	Phchi.S1G624400
Phchi.S1	AUGUSTUS	transcript	39786311	39788446	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	stop_codon	39786308	39786310	.	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39786311	39786406	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39786311	39786406	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39786407	39786488	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39786489	39786623	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39786489	39786623	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39786624	39786701	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39786702	39786839	0.98	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39786702	39786839	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39786840	39786942	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39786943	39787049	0.99	-	2	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39786943	39787049	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39787050	39787120	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39787121	39787254	1	-	1	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39787121	39787254	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39787255	39787365	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39787366	39787406	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39787366	39787406	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39787407	39787525	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39787526	39787591	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39787526	39787591	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39787592	39787706	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39787707	39787741	1	-	2	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39787707	39787741	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39787742	39787833	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39787834	39787918	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39787834	39787918	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39787919	39788004	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39788005	39788100	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39788005	39788100	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	intron	39788101	39788296	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	CDS	39788297	39788446	1	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	exon	39788297	39788446	.	-	.	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
Phchi.S1	AUGUSTUS	start_codon	39788444	39788446	.	-	0	transcript_id "Phchi.S1G624400.t1"; gene_id "Phchi.S1G624400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4617.t1 is derived from g1787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11424593	11425935	.	-	.	Phchi.S1G177600
Phchi.S1	AUGUSTUS	transcript	11424593	11425935	.	-	.	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	stop_codon	11424590	11424592	.	-	0	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	CDS	11424593	11424617	0.87	-	1	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	exon	11424593	11424617	.	-	.	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	intron	11424618	11424728	.	-	.	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	CDS	11424729	11425513	0.88	-	0	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	exon	11424729	11425513	.	-	.	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	intron	11425514	11425617	.	-	.	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	CDS	11425618	11425935	0.99	-	0	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	exon	11425618	11425935	.	-	.	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
Phchi.S1	AUGUSTUS	start_codon	11425933	11425935	.	-	0	transcript_id "Phchi.S1G177600.t1"; gene_id "Phchi.S1G177600"
# This transcript jg1591.t2 is derived from g8510.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1591.t3 is derived from g8510.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1592.t1 is derived from g8511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1919794	1923681	.	-	.	Phchi.S5G020100
Phchi.S5	AUGUSTUS	transcript	1919794	1923681	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	stop_codon	1919791	1919793	.	-	0	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1919794	1920149	0.98	-	2	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1919794	1920149	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1920150	1920278	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1920279	1920473	1	-	2	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1920279	1920473	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1920474	1920587	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1920588	1920798	0.52	-	0	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1920588	1920798	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1920799	1920935	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1920936	1921266	1	-	1	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1920936	1921266	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1921267	1921417	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1921418	1921515	0.99	-	0	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1921418	1921515	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1921516	1921618	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1921619	1921980	1	-	2	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1921619	1921980	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1921981	1922083	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1922084	1922277	1	-	1	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1922084	1922277	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1922278	1922396	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1922397	1922508	1	-	2	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1922397	1922508	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1922509	1922640	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1922641	1922862	1	-	2	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1922641	1922862	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1922863	1922993	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1922994	1923091	1	-	1	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1922994	1923091	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1923092	1923364	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1923365	1923456	1	-	0	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1923365	1923456	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	intron	1923457	1923585	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	CDS	1923586	1923681	0.94	-	0	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	exon	1923586	1923681	.	-	.	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
Phchi.S5	AUGUSTUS	start_codon	1923679	1923681	.	-	0	transcript_id "Phchi.S5G020100.t1"; gene_id "Phchi.S5G020100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5714.t1 is derived from g2884.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18493545	18495431	.	+	.	Phchi.S1G287300
Phchi.S1	AUGUSTUS	transcript	18493545	18495431	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	start_codon	18493545	18493547	.	+	0	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18493545	18493826	0.89	+	0	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18493545	18493826	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18493827	18493944	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18493945	18494013	1	+	0	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18493945	18494013	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494014	18494192	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494193	18494396	1	+	0	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494193	18494396	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494397	18494522	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494523	18494634	1	+	0	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494523	18494634	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494635	18494761	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494762	18494833	1	+	2	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494762	18494833	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494834	18494929	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494930	18494992	1	+	2	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494930	18494992	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494993	18495067	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18495068	18495157	1	+	2	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18495068	18495157	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18495158	18495291	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18495292	18495431	0.99	+	2	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18495292	18495431	.	+	.	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	stop_codon	18495432	18495434	.	+	0	transcript_id "Phchi.S1G287300.t1"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	transcript	18493545	18495431	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	start_codon	18493545	18493547	.	+	0	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18493545	18493826	0.81	+	0	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18493545	18493826	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18493827	18493944	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18493945	18494013	1	+	0	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18493945	18494013	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494014	18494198	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494199	18494396	1	+	0	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494199	18494396	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494397	18494522	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494523	18494634	1	+	0	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494523	18494634	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494635	18494761	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494762	18494833	1	+	2	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494762	18494833	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494834	18494929	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18494930	18494992	1	+	2	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18494930	18494992	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18494993	18495067	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18495068	18495157	1	+	2	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18495068	18495157	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	intron	18495158	18495291	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	CDS	18495292	18495431	0.98	+	2	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	exon	18495292	18495431	.	+	.	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
Phchi.S1	AUGUSTUS	stop_codon	18495432	18495434	.	+	0	transcript_id "Phchi.S1G287300.t2"; gene_id "Phchi.S1G287300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10951.t1 is derived from g15001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3237213	3238670	.	-	.	Phchi.S4G053300
Phchi.S4	AUGUSTUS	transcript	3237213	3238670	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	stop_codon	3237210	3237212	.	-	0	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	CDS	3237213	3237362	0.31	-	0	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	exon	3237213	3237362	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	intron	3237363	3237548	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	CDS	3237549	3237610	1	-	2	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	exon	3237549	3237610	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	intron	3237611	3237686	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	CDS	3237687	3237774	1	-	0	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	exon	3237687	3237774	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	intron	3237775	3237940	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	CDS	3237941	3238044	1	-	2	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	exon	3237941	3238044	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	intron	3238045	3238285	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	CDS	3238286	3238413	1	-	1	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	exon	3238286	3238413	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	intron	3238414	3238557	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	CDS	3238558	3238670	0.85	-	0	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	exon	3238558	3238670	.	-	.	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
Phchi.S4	AUGUSTUS	start_codon	3238668	3238670	.	-	0	transcript_id "Phchi.S4G053300.t1"; gene_id "Phchi.S4G053300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10965.t1 is derived from g15015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3386113	3386675	.	-	.	Phchi.S4G054700
Phchi.S4	AUGUSTUS	transcript	3386113	3386675	.	-	.	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	stop_codon	3386110	3386112	.	-	0	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	CDS	3386113	3386381	0.99	-	2	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	exon	3386113	3386381	.	-	.	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	intron	3386382	3386470	.	-	.	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	CDS	3386471	3386675	1	-	0	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	exon	3386471	3386675	.	-	.	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
Phchi.S4	AUGUSTUS	start_codon	3386673	3386675	.	-	0	transcript_id "Phchi.S4G054700.t1"; gene_id "Phchi.S4G054700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8319.t1 is derived from g5494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35261852	35262934	.	+	.	Phchi.S1G547800
Phchi.S1	AUGUSTUS	transcript	35261852	35262934	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	start_codon	35261852	35261854	.	+	0	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35261852	35261983	0.88	+	0	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35261852	35261983	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	intron	35261984	35262060	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35262061	35262129	0.92	+	0	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35262061	35262129	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	intron	35262130	35262237	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35262238	35262313	1	+	0	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35262238	35262313	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	intron	35262314	35262454	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35262455	35262519	1	+	2	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35262455	35262519	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	intron	35262520	35262606	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35262607	35262623	0.88	+	0	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35262607	35262623	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	intron	35262624	35262702	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35262703	35262711	0.85	+	1	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35262703	35262711	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	intron	35262712	35262921	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	CDS	35262922	35262934	0.88	+	1	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	exon	35262922	35262934	.	+	.	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
Phchi.S1	AUGUSTUS	stop_codon	35262935	35262937	.	+	0	transcript_id "Phchi.S1G547800.t1"; gene_id "Phchi.S1G547800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13241.t1 is derived from g11706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4883289	4886033	.	+	.	Phchi.S3G056000
Phchi.S3	AUGUSTUS	transcript	4883289	4886033	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	start_codon	4883289	4883291	.	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4883289	4883759	0.97	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4883289	4883759	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4883760	4883903	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4883904	4884158	1	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4883904	4884158	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4884159	4884311	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4884312	4884905	1	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4884312	4884905	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4884906	4885039	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4885040	4885225	0.92	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4885040	4885225	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4885226	4885333	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4885334	4885398	0.98	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4885334	4885398	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4885399	4885488	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4885489	4885618	1	+	1	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4885489	4885618	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4885619	4885712	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4885713	4885771	1	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4885713	4885771	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	intron	4885772	4885852	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	CDS	4885853	4886033	1	+	1	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	exon	4885853	4886033	.	+	.	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
Phchi.S3	AUGUSTUS	stop_codon	4886034	4886036	.	+	0	transcript_id "Phchi.S3G056000.t1"; gene_id "Phchi.S3G056000"
# This transcript jg14740.t2 is derived from g13208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14741.t1 is derived from g13209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14474724	14475386	.	-	.	Phchi.S3G206000
Phchi.S3	AUGUSTUS	transcript	14474724	14475386	.	-	.	transcript_id "Phchi.S3G206000.t1"; gene_id "Phchi.S3G206000"
Phchi.S3	AUGUSTUS	stop_codon	14474721	14474723	.	-	0	transcript_id "Phchi.S3G206000.t1"; gene_id "Phchi.S3G206000"
Phchi.S3	AUGUSTUS	CDS	14474724	14475386	0.91	-	0	transcript_id "Phchi.S3G206000.t1"; gene_id "Phchi.S3G206000"
Phchi.S3	AUGUSTUS	exon	14474724	14475386	.	-	.	transcript_id "Phchi.S3G206000.t1"; gene_id "Phchi.S3G206000"
Phchi.S3	AUGUSTUS	start_codon	14475384	14475386	.	-	0	transcript_id "Phchi.S3G206000.t1"; gene_id "Phchi.S3G206000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3196.t1 is derived from g365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2200556	2202692	.	-	.	Phchi.S1G035500
Phchi.S1	AUGUSTUS	transcript	2200556	2202692	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	stop_codon	2200553	2200555	.	-	0	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	CDS	2200556	2200744	0.55	-	0	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	exon	2200556	2200744	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	intron	2200745	2200849	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	CDS	2200850	2201550	0.95	-	2	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	exon	2200850	2201550	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	intron	2201551	2201640	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	CDS	2201641	2201787	1	-	2	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	exon	2201641	2201787	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	intron	2201788	2201949	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	CDS	2201950	2202516	0.87	-	2	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	exon	2201950	2202516	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	intron	2202517	2202607	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	CDS	2202608	2202692	1	-	0	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	exon	2202608	2202692	.	-	.	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
Phchi.S1	AUGUSTUS	start_codon	2202690	2202692	.	-	0	transcript_id "Phchi.S1G035500.t1"; gene_id "Phchi.S1G035500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1822.t1 is derived from g8742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3319648	3321118	.	-	.	Phchi.S5G043100
Phchi.S5	AUGUSTUS	transcript	3319648	3321118	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	stop_codon	3319645	3319647	.	-	0	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3319648	3319832	0.48	-	2	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3319648	3319832	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3319833	3319933	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3319934	3320056	0.45	-	2	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3319934	3320056	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3320057	3320137	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3320138	3320221	0.66	-	2	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3320138	3320221	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3320222	3320313	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3320314	3320426	0.73	-	1	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3320314	3320426	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3320427	3320519	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3320520	3320561	0.94	-	1	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3320520	3320561	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3320562	3320678	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3320679	3320857	0.58	-	0	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3320679	3320857	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3320858	3320943	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3320944	3321009	0.59	-	0	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3320944	3321009	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	intron	3321010	3321079	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	CDS	3321080	3321118	0.54	-	0	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	exon	3321080	3321118	.	-	.	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
Phchi.S5	AUGUSTUS	start_codon	3321116	3321118	.	-	0	transcript_id "Phchi.S5G043100.t1"; gene_id "Phchi.S5G043100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4859.t1 is derived from g2029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13126109	13126964	.	-	.	Phchi.S1G201800
Phchi.S1	AUGUSTUS	transcript	13126109	13126964	.	-	.	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	stop_codon	13126106	13126108	.	-	0	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	CDS	13126109	13126690	0.86	-	0	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	exon	13126109	13126690	.	-	.	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	intron	13126691	13126796	.	-	.	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	CDS	13126797	13126964	0.49	-	0	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	exon	13126797	13126964	.	-	.	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
Phchi.S1	AUGUSTUS	start_codon	13126962	13126964	.	-	0	transcript_id "Phchi.S1G201800.t1"; gene_id "Phchi.S1G201800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9020.t1 is derived from g6195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39174701	39177658	.	+	.	Phchi.S1G617900
Phchi.S1	AUGUSTUS	transcript	39174701	39177658	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	start_codon	39174701	39174703	.	+	0	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	CDS	39174701	39175254	0.44	+	0	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	exon	39174701	39175254	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	intron	39175255	39175461	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	CDS	39175462	39175798	0.71	+	1	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	exon	39175462	39175798	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	intron	39175799	39176068	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	CDS	39176069	39176542	0.7	+	0	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	exon	39176069	39176542	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	intron	39176543	39176674	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	CDS	39176675	39177267	0.61	+	0	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	exon	39176675	39177267	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	intron	39177268	39177546	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	CDS	39177547	39177658	0.84	+	1	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	exon	39177547	39177658	.	+	.	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
Phchi.S1	AUGUSTUS	stop_codon	39177659	39177661	.	+	0	transcript_id "Phchi.S1G617900.t1"; gene_id "Phchi.S1G617900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13142.t1 is derived from g11607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4367238	4369266	.	-	.	Phchi.S3G046100
Phchi.S3	AUGUSTUS	transcript	4367238	4369266	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	stop_codon	4367235	4367237	.	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4367238	4367318	0.98	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4367238	4367318	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	intron	4367319	4367419	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4367420	4367563	0.97	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4367420	4367563	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	intron	4367564	4367680	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4367681	4367751	1	-	2	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4367681	4367751	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	intron	4367752	4367837	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4367838	4367937	0.99	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4367838	4367937	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	intron	4367938	4368052	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4368053	4368083	0.99	-	1	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4368053	4368083	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	intron	4368084	4368182	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4368183	4368280	1	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4368183	4368280	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	intron	4368281	4369149	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	CDS	4369150	4369266	0.85	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	exon	4369150	4369266	.	-	.	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
Phchi.S3	AUGUSTUS	start_codon	4369264	4369266	.	-	0	transcript_id "Phchi.S3G046100.t1"; gene_id "Phchi.S3G046100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1842.t1 is derived from g8762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3527226	3528105	.	+	.	Phchi.S5G045100
Phchi.S5	AUGUSTUS	transcript	3527226	3528105	.	+	.	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	start_codon	3527226	3527228	.	+	0	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	CDS	3527226	3527396	0.84	+	0	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	exon	3527226	3527396	.	+	.	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	intron	3527397	3527535	.	+	.	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	CDS	3527536	3527562	0.91	+	0	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	exon	3527536	3527562	.	+	.	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	intron	3527563	3528057	.	+	.	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	CDS	3528058	3528105	0.99	+	0	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	exon	3528058	3528105	.	+	.	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
Phchi.S5	AUGUSTUS	stop_codon	3528106	3528108	.	+	0	transcript_id "Phchi.S5G045100.t1"; gene_id "Phchi.S5G045100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5168.t1 is derived from g2338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15273821	15275491	.	-	.	Phchi.S1G232700
Phchi.S1	AUGUSTUS	transcript	15273821	15275491	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	stop_codon	15273818	15273820	.	-	0	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15273821	15274257	0.91	-	2	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15273821	15274257	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	intron	15274258	15274340	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15274341	15274349	0.92	-	2	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15274341	15274349	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	intron	15274350	15274443	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15274444	15274514	0.81	-	1	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15274444	15274514	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	intron	15274515	15274592	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15274593	15274698	0.23	-	2	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15274593	15274698	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	intron	15274699	15274798	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15274799	15274865	0.33	-	0	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15274799	15274865	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	intron	15274866	15274966	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15274967	15275019	0.72	-	2	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15274967	15275019	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	intron	15275020	15275184	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	CDS	15275185	15275491	0.68	-	0	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	exon	15275185	15275491	.	-	.	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
Phchi.S1	AUGUSTUS	start_codon	15275489	15275491	.	-	0	transcript_id "Phchi.S1G232700.t1"; gene_id "Phchi.S1G232700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2363.t1 is derived from g9283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6355345	6356306	.	-	.	Phchi.S5G097200
Phchi.S5	AUGUSTUS	transcript	6355345	6356306	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	stop_codon	6355342	6355344	.	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	CDS	6355345	6355425	0.95	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	exon	6355345	6355425	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	intron	6355426	6355518	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	CDS	6355519	6355617	0.95	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	exon	6355519	6355617	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	intron	6355618	6355729	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	CDS	6355730	6355885	1	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	exon	6355730	6355885	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	intron	6355886	6355971	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	CDS	6355972	6356046	1	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	exon	6355972	6356046	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	intron	6356047	6356213	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	CDS	6356214	6356306	1	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	exon	6356214	6356306	.	-	.	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
Phchi.S5	AUGUSTUS	start_codon	6356304	6356306	.	-	0	transcript_id "Phchi.S5G097200.t1"; gene_id "Phchi.S5G097200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7415.t1 is derived from g4587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29037309	29038245	.	-	.	Phchi.S1G457400
Phchi.S1	AUGUSTUS	transcript	29037309	29038245	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	stop_codon	29037306	29037308	.	-	0	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	CDS	29037309	29037557	1	-	0	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	exon	29037309	29037557	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	intron	29037558	29037644	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	CDS	29037645	29037794	1	-	0	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	exon	29037645	29037794	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	intron	29037795	29037886	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	CDS	29037887	29038035	1	-	2	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	exon	29037887	29038035	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	intron	29038036	29038127	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	CDS	29038128	29038245	1	-	0	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	exon	29038128	29038245	.	-	.	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
Phchi.S1	AUGUSTUS	start_codon	29038243	29038245	.	-	0	transcript_id "Phchi.S1G457400.t1"; gene_id "Phchi.S1G457400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10380.t1 is derived from g7556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47476619	47478801	.	+	.	Phchi.S1G753900
Phchi.S1	AUGUSTUS	transcript	47476619	47478801	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	start_codon	47476619	47476621	.	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47476619	47476699	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47476619	47476699	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47476700	47476799	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47476800	47476946	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47476800	47476946	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47476947	47477042	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47477043	47477110	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47477043	47477110	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47477111	47477360	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47477361	47477418	1	+	1	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47477361	47477418	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47477419	47477639	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47477640	47477750	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47477640	47477750	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47477751	47477952	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47477953	47478003	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47477953	47478003	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47478004	47478093	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47478094	47478237	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47478094	47478237	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47478238	47478352	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47478353	47478448	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47478353	47478448	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47478449	47478565	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47478566	47478637	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47478566	47478637	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	intron	47478638	47478720	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	CDS	47478721	47478801	1	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	exon	47478721	47478801	.	+	.	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
Phchi.S1	AUGUSTUS	stop_codon	47478802	47478804	.	+	0	transcript_id "Phchi.S1G753900.t1"; gene_id "Phchi.S1G753900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5873.t1 is derived from g3043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19511321	19513720	.	+	.	Phchi.S1G303200
Phchi.S1	AUGUSTUS	transcript	19511321	19513720	.	+	.	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	start_codon	19511321	19511323	.	+	0	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	CDS	19511321	19511722	0.96	+	0	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	exon	19511321	19511722	.	+	.	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	intron	19511723	19512130	.	+	.	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	CDS	19512131	19513720	0.66	+	0	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	exon	19512131	19513720	.	+	.	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
Phchi.S1	AUGUSTUS	stop_codon	19513721	19513723	.	+	0	transcript_id "Phchi.S1G303200.t1"; gene_id "Phchi.S1G303200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11851.t1 is derived from g15903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8623580	8623851	.	-	.	Phchi.S4G143300
Phchi.S4	AUGUSTUS	transcript	8623580	8623851	.	-	.	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	stop_codon	8623577	8623579	.	-	0	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	CDS	8623580	8623699	1	-	0	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	exon	8623580	8623699	.	-	.	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	intron	8623700	8623767	.	-	.	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	CDS	8623768	8623851	0.7	-	0	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	exon	8623768	8623851	.	-	.	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
Phchi.S4	AUGUSTUS	start_codon	8623849	8623851	.	-	0	transcript_id "Phchi.S4G143300.t1"; gene_id "Phchi.S4G143300"
# This transcript jg10365.t2 is derived from g7541.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10366.t1 is derived from g7542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47401616	47402210	.	+	.	Phchi.S1G752500
Phchi.S1	AUGUSTUS	transcript	47401616	47402210	.	+	.	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	start_codon	47401616	47401618	.	+	0	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	CDS	47401616	47401826	1	+	0	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	exon	47401616	47401826	.	+	.	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	intron	47401827	47401938	.	+	.	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	CDS	47401939	47402210	1	+	2	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	exon	47401939	47402210	.	+	.	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
Phchi.S1	AUGUSTUS	stop_codon	47402211	47402213	.	+	0	transcript_id "Phchi.S1G752500.t1"; gene_id "Phchi.S1G752500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3541.t1 is derived from g710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4364162	4367675	.	+	.	Phchi.S1G070000
Phchi.S1	AUGUSTUS	transcript	4364162	4367675	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	start_codon	4364162	4364164	.	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364162	4364326	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364162	4364326	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364327	4364403	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364404	4364487	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364404	4364487	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364488	4364578	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364579	4364652	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364579	4364652	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364653	4364752	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364753	4364786	1	+	1	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364753	4364786	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364787	4364876	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364877	4364935	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364877	4364935	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364936	4365207	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365208	4365322	1	+	1	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365208	4365322	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365323	4365545	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365546	4365583	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365546	4365583	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365584	4365717	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365718	4365815	1	+	1	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365718	4365815	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365816	4365942	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365943	4365998	1	+	2	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365943	4365998	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365999	4366189	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4366190	4366493	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4366190	4366493	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4366494	4366563	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4366564	4366700	1	+	2	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4366564	4366700	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4366701	4366947	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4366948	4367004	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4366948	4367004	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367005	4367139	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367140	4367208	1	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367140	4367208	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367209	4367380	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367381	4367393	0.99	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367381	4367393	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367394	4367479	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367480	4367536	0.99	+	2	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367480	4367536	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367537	4367625	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367626	4367675	1	+	2	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367626	4367675	.	+	.	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	stop_codon	4367676	4367678	.	+	0	transcript_id "Phchi.S1G070000.t1"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	transcript	4364162	4367675	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	start_codon	4364162	4364164	.	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364162	4364326	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364162	4364326	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364327	4364403	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364404	4364487	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364404	4364487	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364488	4364578	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364579	4364652	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364579	4364652	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364653	4364752	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364753	4364786	1	+	1	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364753	4364786	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364787	4364876	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4364877	4364935	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4364877	4364935	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4364936	4365207	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365208	4365322	1	+	1	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365208	4365322	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365323	4365545	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365546	4365583	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365546	4365583	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365584	4365717	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365718	4365815	1	+	1	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365718	4365815	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365816	4365942	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4365943	4365998	1	+	2	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4365943	4365998	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4365999	4366189	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4366190	4366409	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4366190	4366409	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4366410	4366563	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4366564	4366700	1	+	2	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4366564	4366700	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4366701	4366947	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4366948	4367004	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4366948	4367004	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367005	4367139	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367140	4367208	1	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367140	4367208	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367209	4367380	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367381	4367393	0.99	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367381	4367393	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367394	4367479	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367480	4367536	0.99	+	2	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367480	4367536	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	intron	4367537	4367625	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	CDS	4367626	4367675	0.99	+	2	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	exon	4367626	4367675	.	+	.	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
Phchi.S1	AUGUSTUS	stop_codon	4367676	4367678	.	+	0	transcript_id "Phchi.S1G070000.t2"; gene_id "Phchi.S1G070000"
# This transcript jg12963.t2 is derived from g11428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12964.t1 is derived from g11429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3356330	3358456	.	+	.	Phchi.S3G028300
Phchi.S3	AUGUSTUS	transcript	3356330	3358456	.	+	.	transcript_id "Phchi.S3G028300.t1"; gene_id "Phchi.S3G028300"
Phchi.S3	AUGUSTUS	start_codon	3356330	3356332	.	+	0	transcript_id "Phchi.S3G028300.t1"; gene_id "Phchi.S3G028300"
Phchi.S3	AUGUSTUS	CDS	3356330	3358456	1	+	0	transcript_id "Phchi.S3G028300.t1"; gene_id "Phchi.S3G028300"
Phchi.S3	AUGUSTUS	exon	3356330	3358456	.	+	.	transcript_id "Phchi.S3G028300.t1"; gene_id "Phchi.S3G028300"
Phchi.S3	AUGUSTUS	stop_codon	3358457	3358459	.	+	0	transcript_id "Phchi.S3G028300.t1"; gene_id "Phchi.S3G028300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8806.t1 is derived from g5981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38072923	38074554	.	+	.	Phchi.S1G596500
Phchi.S1	AUGUSTUS	transcript	38072923	38074554	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	start_codon	38072923	38072925	.	+	0	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38072923	38072950	0.98	+	0	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38072923	38072950	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38072951	38073039	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38073040	38073062	1	+	2	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38073040	38073062	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38073063	38073218	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38073219	38073298	0.79	+	0	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38073219	38073298	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38073299	38073375	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38073376	38073575	0.74	+	1	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38073376	38073575	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38073576	38073659	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38073660	38073755	1	+	2	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38073660	38073755	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38073756	38073852	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38073853	38073989	1	+	2	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38073853	38073989	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38073990	38074074	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38074075	38074181	0.99	+	0	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38074075	38074181	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38074182	38074287	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38074288	38074375	0.75	+	1	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38074288	38074375	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	intron	38074376	38074482	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	CDS	38074483	38074554	0.71	+	0	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	exon	38074483	38074554	.	+	.	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
Phchi.S1	AUGUSTUS	stop_codon	38074555	38074557	.	+	0	transcript_id "Phchi.S1G596500.t1"; gene_id "Phchi.S1G596500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3283.t1 is derived from g452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2685490	2686488	.	-	.	Phchi.S1G044200
Phchi.S1	AUGUSTUS	transcript	2685490	2686488	.	-	.	transcript_id "Phchi.S1G044200.t1"; gene_id "Phchi.S1G044200"
Phchi.S1	AUGUSTUS	stop_codon	2685487	2685489	.	-	0	transcript_id "Phchi.S1G044200.t1"; gene_id "Phchi.S1G044200"
Phchi.S1	AUGUSTUS	CDS	2685490	2686488	0.63	-	0	transcript_id "Phchi.S1G044200.t1"; gene_id "Phchi.S1G044200"
Phchi.S1	AUGUSTUS	exon	2685490	2686488	.	-	.	transcript_id "Phchi.S1G044200.t1"; gene_id "Phchi.S1G044200"
Phchi.S1	AUGUSTUS	start_codon	2686486	2686488	.	-	0	transcript_id "Phchi.S1G044200.t1"; gene_id "Phchi.S1G044200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6372.t1 is derived from g3544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22620783	22622889	.	-	.	Phchi.S1G353100
Phchi.S1	AUGUSTUS	transcript	22620783	22622889	.	-	.	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	stop_codon	22620780	22620782	.	-	0	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	CDS	22620783	22622339	0.36	-	0	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	exon	22620783	22622339	.	-	.	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	intron	22622340	22622454	.	-	.	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	CDS	22622455	22622889	0.6	-	0	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	exon	22622455	22622889	.	-	.	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
Phchi.S1	AUGUSTUS	start_codon	22622887	22622889	.	-	0	transcript_id "Phchi.S1G353100.t1"; gene_id "Phchi.S1G353100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg153.t1 is derived from g9935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	861938	863287	.	-	.	Phchi.S6G011200
Phchi.S6	AUGUSTUS	transcript	861938	863287	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	stop_codon	861935	861937	.	-	0	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	CDS	861938	861987	0.98	-	2	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	exon	861938	861987	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	intron	861988	862187	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	CDS	862188	862274	1	-	2	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	exon	862188	862274	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	intron	862275	862452	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	CDS	862453	862537	1	-	0	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	exon	862453	862537	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	intron	862538	862696	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	CDS	862697	863015	1	-	1	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	exon	862697	863015	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	intron	863016	863096	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	CDS	863097	863287	0.73	-	0	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	exon	863097	863287	.	-	.	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
Phchi.S6	AUGUSTUS	start_codon	863285	863287	.	-	0	transcript_id "Phchi.S6G011200.t1"; gene_id "Phchi.S6G011200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11809.t1 is derived from g15861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8228881	8231187	.	+	.	Phchi.S4G139100
Phchi.S4	AUGUSTUS	transcript	8228881	8231187	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	start_codon	8228881	8228883	.	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8228881	8228991	0.98	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8228881	8228991	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	intron	8228992	8229102	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8229103	8229366	0.95	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8229103	8229366	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	intron	8229367	8229513	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8229514	8229774	0.86	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8229514	8229774	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	intron	8229775	8229877	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8229878	8230006	0.95	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8229878	8230006	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	intron	8230007	8230159	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8230160	8230389	1	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8230160	8230389	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	intron	8230390	8230479	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8230480	8230810	0.72	+	1	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8230480	8230810	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	intron	8230811	8230905	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	CDS	8230906	8231187	0.95	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	exon	8230906	8231187	.	+	.	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
Phchi.S4	AUGUSTUS	stop_codon	8231188	8231190	.	+	0	transcript_id "Phchi.S4G139100.t1"; gene_id "Phchi.S4G139100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5445.t1 is derived from g2615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16895557	16895814	.	+	.	Phchi.S1G260400
Phchi.S1	AUGUSTUS	transcript	16895557	16895814	.	+	.	transcript_id "Phchi.S1G260400.t1"; gene_id "Phchi.S1G260400"
Phchi.S1	AUGUSTUS	start_codon	16895557	16895559	.	+	0	transcript_id "Phchi.S1G260400.t1"; gene_id "Phchi.S1G260400"
Phchi.S1	AUGUSTUS	CDS	16895557	16895814	0.7	+	0	transcript_id "Phchi.S1G260400.t1"; gene_id "Phchi.S1G260400"
Phchi.S1	AUGUSTUS	exon	16895557	16895814	.	+	.	transcript_id "Phchi.S1G260400.t1"; gene_id "Phchi.S1G260400"
Phchi.S1	AUGUSTUS	stop_codon	16895815	16895817	.	+	0	transcript_id "Phchi.S1G260400.t1"; gene_id "Phchi.S1G260400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6961.t1 is derived from g4133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26148182	26149067	.	+	.	Phchi.S1G412000
Phchi.S1	AUGUSTUS	transcript	26148182	26149067	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	start_codon	26148182	26148184	.	+	0	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	CDS	26148182	26148439	0.51	+	0	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	exon	26148182	26148439	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	intron	26148440	26148513	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	CDS	26148514	26148559	0.67	+	0	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	exon	26148514	26148559	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	intron	26148560	26148651	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	CDS	26148652	26148690	0.66	+	2	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	exon	26148652	26148690	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	intron	26148691	26148847	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	CDS	26148848	26148920	0.67	+	2	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	exon	26148848	26148920	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	intron	26148921	26149048	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	CDS	26149049	26149067	0.67	+	1	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	exon	26149049	26149067	.	+	.	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
Phchi.S1	AUGUSTUS	stop_codon	26149068	26149070	.	+	0	transcript_id "Phchi.S1G412000.t1"; gene_id "Phchi.S1G412000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3898.t1 is derived from g1067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6305936	6308776	.	+	.	Phchi.S1G105700
Phchi.S1	AUGUSTUS	transcript	6305936	6308776	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	start_codon	6305936	6305938	.	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6305936	6306040	0.62	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6305936	6306040	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6306041	6306140	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6306141	6306156	0.76	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6306141	6306156	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6306157	6306281	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6306282	6306353	0.48	+	2	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6306282	6306353	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6306354	6306444	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6306445	6306503	0.98	+	2	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6306445	6306503	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6306504	6306577	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6306578	6306664	1	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6306578	6306664	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6306665	6306818	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6306819	6306896	1	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6306819	6306896	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6306897	6306995	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6306996	6307096	0.81	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6306996	6307096	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6307097	6307167	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6307168	6307230	0.82	+	1	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6307168	6307230	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6307231	6307328	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6307329	6307521	1	+	1	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6307329	6307521	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6307522	6307610	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6307611	6307701	1	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6307611	6307701	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6307702	6307792	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6307793	6307857	1	+	2	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6307793	6307857	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6307858	6307997	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6307998	6308152	1	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6307998	6308152	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6308153	6308243	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6308244	6308325	1	+	1	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6308244	6308325	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6308326	6308424	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6308425	6308534	1	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6308425	6308534	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	intron	6308535	6308625	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	CDS	6308626	6308776	1	+	1	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	exon	6308626	6308776	.	+	.	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
Phchi.S1	AUGUSTUS	stop_codon	6308777	6308779	.	+	0	transcript_id "Phchi.S1G105700.t1"; gene_id "Phchi.S1G105700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9594.t1 is derived from g6770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42855644	42858893	.	-	.	Phchi.S1G675300
Phchi.S1	AUGUSTUS	transcript	42855644	42858893	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	stop_codon	42855641	42855643	.	-	0	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42855644	42855646	0.61	-	0	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42855644	42855646	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42855647	42855739	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42855740	42856352	0.56	-	1	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42855740	42856352	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42856353	42856519	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42856520	42856614	1	-	0	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42856520	42856614	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42856615	42856755	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42856756	42856898	1	-	2	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42856756	42856898	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42856899	42857597	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42857598	42857809	0.71	-	1	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42857598	42857809	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42857810	42857879	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42857880	42858021	0.77	-	2	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42857880	42858021	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42858022	42858296	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42858297	42858373	0.67	-	1	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42858297	42858373	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	intron	42858374	42858849	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	CDS	42858850	42858893	0.89	-	0	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	exon	42858850	42858893	.	-	.	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
Phchi.S1	AUGUSTUS	start_codon	42858891	42858893	.	-	0	transcript_id "Phchi.S1G675300.t1"; gene_id "Phchi.S1G675300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg311.t1 is derived from g10093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2219792	2220199	.	-	.	Phchi.S6G027000
Phchi.S6	AUGUSTUS	transcript	2219792	2220199	.	-	.	transcript_id "Phchi.S6G027000.t1"; gene_id "Phchi.S6G027000"
Phchi.S6	AUGUSTUS	stop_codon	2219789	2219791	.	-	0	transcript_id "Phchi.S6G027000.t1"; gene_id "Phchi.S6G027000"
Phchi.S6	AUGUSTUS	CDS	2219792	2220199	0.53	-	0	transcript_id "Phchi.S6G027000.t1"; gene_id "Phchi.S6G027000"
Phchi.S6	AUGUSTUS	exon	2219792	2220199	.	-	.	transcript_id "Phchi.S6G027000.t1"; gene_id "Phchi.S6G027000"
Phchi.S6	AUGUSTUS	start_codon	2220197	2220199	.	-	0	transcript_id "Phchi.S6G027000.t1"; gene_id "Phchi.S6G027000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15486.t1 is derived from g13955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19439114	19440789	.	-	.	Phchi.S3G280500
Phchi.S3	AUGUSTUS	transcript	19439114	19440789	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	stop_codon	19439111	19439113	.	-	0	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19439114	19439177	1	-	1	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19439114	19439177	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	intron	19439178	19439318	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19439319	19439449	0.97	-	0	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19439319	19439449	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	intron	19439450	19439557	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19439558	19439860	0.97	-	0	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19439558	19439860	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	intron	19439861	19439991	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19439992	19440077	1	-	2	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19439992	19440077	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	intron	19440078	19440331	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19440332	19440428	0.83	-	0	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19440332	19440428	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	intron	19440429	19440586	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19440587	19440615	0.41	-	2	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19440587	19440615	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	intron	19440616	19440713	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	CDS	19440714	19440789	0.6	-	0	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	exon	19440714	19440789	.	-	.	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
Phchi.S3	AUGUSTUS	start_codon	19440787	19440789	.	-	0	transcript_id "Phchi.S3G280500.t1"; gene_id "Phchi.S3G280500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11904.t1 is derived from g15956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9216543	9217415	.	-	.	Phchi.S4G148600
Phchi.S4	AUGUSTUS	transcript	9216543	9217415	.	-	.	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	stop_codon	9216540	9216542	.	-	0	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	CDS	9216543	9216824	0.97	-	0	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	exon	9216543	9216824	.	-	.	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	intron	9216825	9216938	.	-	.	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	CDS	9216939	9217072	1	-	2	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	exon	9216939	9217072	.	-	.	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	intron	9217073	9217165	.	-	.	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	CDS	9217166	9217415	0.98	-	0	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	exon	9217166	9217415	.	-	.	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
Phchi.S4	AUGUSTUS	start_codon	9217413	9217415	.	-	0	transcript_id "Phchi.S4G148600.t1"; gene_id "Phchi.S4G148600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg710.t1 is derived from g10492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5017279	5017920	.	+	.	Phchi.S6G066900
Phchi.S6	AUGUSTUS	transcript	5017279	5017920	.	+	.	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	start_codon	5017279	5017281	.	+	0	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	CDS	5017279	5017569	0.97	+	0	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	exon	5017279	5017569	.	+	.	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	intron	5017570	5017716	.	+	.	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	CDS	5017717	5017920	1	+	0	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	exon	5017717	5017920	.	+	.	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
Phchi.S6	AUGUSTUS	stop_codon	5017921	5017923	.	+	0	transcript_id "Phchi.S6G066900.t1"; gene_id "Phchi.S6G066900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6668.t1 is derived from g3840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24406700	24412832	.	+	.	Phchi.S1G382700
Phchi.S1	AUGUSTUS	transcript	24406700	24412832	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	start_codon	24406700	24406702	.	+	0	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	CDS	24406700	24406860	0.98	+	0	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	exon	24406700	24406860	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	intron	24406861	24407116	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	CDS	24407117	24407261	1	+	1	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	exon	24407117	24407261	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	intron	24407262	24409807	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	CDS	24409808	24409900	0.99	+	0	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	exon	24409808	24409900	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	intron	24409901	24412790	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	CDS	24412791	24412832	0.5	+	0	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	exon	24412791	24412832	.	+	.	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
Phchi.S1	AUGUSTUS	stop_codon	24412833	24412835	.	+	0	transcript_id "Phchi.S1G382700.t1"; gene_id "Phchi.S1G382700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3092.t1 is derived from g261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1726174	1726809	.	+	.	Phchi.S1G025100
Phchi.S1	AUGUSTUS	transcript	1726174	1726809	.	+	.	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	start_codon	1726174	1726176	.	+	0	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	CDS	1726174	1726448	0.56	+	0	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	exon	1726174	1726448	.	+	.	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	intron	1726449	1726550	.	+	.	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	CDS	1726551	1726809	0.81	+	1	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	exon	1726551	1726809	.	+	.	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
Phchi.S1	AUGUSTUS	stop_codon	1726810	1726812	.	+	0	transcript_id "Phchi.S1G025100.t1"; gene_id "Phchi.S1G025100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4377.t1 is derived from g1546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10126496	10127126	.	+	.	Phchi.S1G153600
Phchi.S1	AUGUSTUS	transcript	10126496	10127126	.	+	.	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	start_codon	10126496	10126498	.	+	0	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	CDS	10126496	10126706	0.96	+	0	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	exon	10126496	10126706	.	+	.	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	intron	10126707	10126857	.	+	.	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	CDS	10126858	10127126	0.99	+	2	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	exon	10126858	10127126	.	+	.	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
Phchi.S1	AUGUSTUS	stop_codon	10127127	10127129	.	+	0	transcript_id "Phchi.S1G153600.t1"; gene_id "Phchi.S1G153600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13511.t1 is derived from g11978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7243643	7246152	.	-	.	Phchi.S3G083000
Phchi.S3	AUGUSTUS	transcript	7243643	7246152	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	stop_codon	7243640	7243642	.	-	0	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	CDS	7243643	7244633	0.86	-	1	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	exon	7243643	7244633	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	intron	7244634	7244834	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	CDS	7244835	7244942	0.4	-	1	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	exon	7244835	7244942	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	intron	7244943	7245143	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	CDS	7245144	7245691	0.49	-	0	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	exon	7245144	7245691	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	intron	7245692	7245792	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	CDS	7245793	7246152	0.91	-	0	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	exon	7245793	7246152	.	-	.	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
Phchi.S3	AUGUSTUS	start_codon	7246150	7246152	.	-	0	transcript_id "Phchi.S3G083000.t1"; gene_id "Phchi.S3G083000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14000.t1 is derived from g12467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10182820	10184322	.	-	.	Phchi.S3G131900
Phchi.S3	AUGUSTUS	transcript	10182820	10184322	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	stop_codon	10182817	10182819	.	-	0	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	CDS	10182820	10183101	0.98	-	0	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	exon	10182820	10183101	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	intron	10183102	10183194	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	CDS	10183195	10183497	1	-	0	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	exon	10183195	10183497	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	intron	10183498	10183589	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	CDS	10183590	10184180	1	-	0	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	exon	10183590	10184180	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	intron	10184181	10184319	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	CDS	10184320	10184322	0.95	-	0	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	exon	10184320	10184322	.	-	.	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
Phchi.S3	AUGUSTUS	start_codon	10184320	10184322	.	-	0	transcript_id "Phchi.S3G131900.t1"; gene_id "Phchi.S3G131900"
# This transcript jg7141.t2 is derived from g4313.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7142.t1 is derived from g4314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27150967	27154065	.	+	.	Phchi.S1G430100
Phchi.S1	AUGUSTUS	transcript	27150967	27154065	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	start_codon	27150967	27150969	.	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27150967	27151189	0.47	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27150967	27151189	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27151190	27151319	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27151320	27151438	1	+	2	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27151320	27151438	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27151439	27151630	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27151631	27151683	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27151631	27151683	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27151684	27151793	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27151794	27151866	1	+	1	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27151794	27151866	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27151867	27151969	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27151970	27152074	0.94	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27151970	27152074	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27152075	27152166	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27152167	27152268	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27152167	27152268	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27152269	27152462	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27152463	27152519	0.95	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27152463	27152519	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27152520	27152652	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27152653	27152715	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27152653	27152715	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27152716	27152809	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27152810	27152851	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27152810	27152851	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27152852	27152983	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27152984	27153043	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27152984	27153043	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27153044	27153139	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27153140	27153250	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27153140	27153250	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27153251	27153342	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27153343	27153510	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27153343	27153510	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27153511	27153607	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27153608	27153698	1	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27153608	27153698	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	intron	27153699	27153793	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	CDS	27153794	27154065	0.99	+	2	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	exon	27153794	27154065	.	+	.	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
Phchi.S1	AUGUSTUS	stop_codon	27154066	27154068	.	+	0	transcript_id "Phchi.S1G430100.t1"; gene_id "Phchi.S1G430100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7487.t1 is derived from g4660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29620928	29621537	.	-	.	Phchi.S1G464600
Phchi.S1	AUGUSTUS	transcript	29620928	29621537	.	-	.	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	stop_codon	29620925	29620927	.	-	0	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	CDS	29620928	29620948	1	-	0	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	exon	29620928	29620948	.	-	.	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	intron	29620949	29621162	.	-	.	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	CDS	29621163	29621537	0.8	-	0	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	exon	29621163	29621537	.	-	.	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
Phchi.S1	AUGUSTUS	start_codon	29621535	29621537	.	-	0	transcript_id "Phchi.S1G464600.t1"; gene_id "Phchi.S1G464600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2839.t1 is derived from g9759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9128732	9130376	.	+	.	Phchi.S5G144800
Phchi.S5	AUGUSTUS	transcript	9128732	9130376	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	start_codon	9128732	9128734	.	+	0	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	CDS	9128732	9128905	1	+	0	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	exon	9128732	9128905	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	intron	9128906	9129044	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	CDS	9129045	9129240	1	+	0	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	exon	9129045	9129240	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	intron	9129241	9129434	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	CDS	9129435	9129533	1	+	2	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	exon	9129435	9129533	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	intron	9129534	9129609	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	CDS	9129610	9129765	1	+	2	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	exon	9129610	9129765	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	intron	9129766	9129909	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	CDS	9129910	9130130	1	+	2	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	exon	9129910	9130130	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	intron	9130131	9130211	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	CDS	9130212	9130376	1	+	0	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	exon	9130212	9130376	.	+	.	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
Phchi.S5	AUGUSTUS	stop_codon	9130377	9130379	.	+	0	transcript_id "Phchi.S5G144800.t1"; gene_id "Phchi.S5G144800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg154.t1 is derived from g9936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	879511	881195	.	-	.	Phchi.S6G011300
Phchi.S6	AUGUSTUS	transcript	879511	881195	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	stop_codon	879508	879510	.	-	0	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	879511	879600	0.99	-	0	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	879511	879600	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	879601	879732	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	879733	879792	0.81	-	0	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	879733	879792	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	879793	879949	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	879950	879989	0.84	-	1	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	879950	879989	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	879990	880103	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	880104	880191	0.37	-	2	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	880104	880191	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	880192	880349	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	880350	880363	0.89	-	1	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	880350	880363	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	880364	880463	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	880464	880585	0.91	-	0	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	880464	880585	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	880586	880794	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	880795	881093	0.65	-	2	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	880795	881093	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	intron	881094	881185	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	CDS	881186	881195	0.99	-	0	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	exon	881186	881195	.	-	.	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
Phchi.S6	AUGUSTUS	start_codon	881193	881195	.	-	0	transcript_id "Phchi.S6G011300.t1"; gene_id "Phchi.S6G011300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4009.t1 is derived from g1178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7055690	7057287	.	+	.	Phchi.S1G116800
Phchi.S1	AUGUSTUS	transcript	7055690	7057287	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	start_codon	7055690	7055692	.	+	0	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	CDS	7055690	7055930	0.94	+	0	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	exon	7055690	7055930	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	intron	7055931	7056071	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	CDS	7056072	7056218	0.87	+	2	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	exon	7056072	7056218	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	intron	7056219	7056309	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	CDS	7056310	7056434	1	+	2	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	exon	7056310	7056434	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	intron	7056435	7056524	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	CDS	7056525	7056963	0.79	+	0	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	exon	7056525	7056963	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	intron	7056964	7057051	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	CDS	7057052	7057131	0.9	+	2	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	exon	7057052	7057131	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	intron	7057132	7057200	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	CDS	7057201	7057287	0.92	+	0	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	exon	7057201	7057287	.	+	.	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
Phchi.S1	AUGUSTUS	stop_codon	7057288	7057290	.	+	0	transcript_id "Phchi.S1G116800.t1"; gene_id "Phchi.S1G116800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8435.t1 is derived from g5610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35929668	35932590	.	+	.	Phchi.S1G559400
Phchi.S1	AUGUSTUS	transcript	35929668	35932590	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	start_codon	35929668	35929670	.	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35929668	35929777	0.92	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35929668	35929777	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35929778	35929854	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35929855	35929936	1	+	1	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35929855	35929936	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35929937	35930044	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35930045	35930135	1	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35930045	35930135	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35930136	35930241	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35930242	35930417	1	+	2	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35930242	35930417	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35930418	35930521	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35930522	35930594	0.99	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35930522	35930594	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35930595	35930676	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35930677	35930797	1	+	2	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35930677	35930797	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35930798	35930897	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35930898	35931015	1	+	1	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35930898	35931015	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35931016	35931122	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35931123	35931262	0.9	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35931123	35931262	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35931263	35931360	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35931361	35931418	1	+	1	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35931361	35931418	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35931419	35931544	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35931545	35931615	1	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35931545	35931615	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35931616	35931822	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35931823	35932106	0.66	+	1	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35931823	35932106	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35932107	35932207	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35932208	35932315	0.66	+	2	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35932208	35932315	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	intron	35932316	35932399	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	CDS	35932400	35932590	0.83	+	2	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	exon	35932400	35932590	.	+	.	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
Phchi.S1	AUGUSTUS	stop_codon	35932591	35932593	.	+	0	transcript_id "Phchi.S1G559400.t1"; gene_id "Phchi.S1G559400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4610.t1 is derived from g1780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11383366	11383974	.	-	.	Phchi.S1G176900
Phchi.S1	AUGUSTUS	transcript	11383366	11383974	.	-	.	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	stop_codon	11383363	11383365	.	-	0	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	CDS	11383366	11383590	0.99	-	0	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	exon	11383366	11383590	.	-	.	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	intron	11383591	11383699	.	-	.	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	CDS	11383700	11383780	1	-	0	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	exon	11383700	11383780	.	-	.	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	intron	11383781	11383872	.	-	.	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	CDS	11383873	11383974	1	-	0	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	exon	11383873	11383974	.	-	.	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
Phchi.S1	AUGUSTUS	start_codon	11383972	11383974	.	-	0	transcript_id "Phchi.S1G176900.t1"; gene_id "Phchi.S1G176900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12387.t1 is derived from g8064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15423167	15424634	.	-	.	Phchi.S2G046700
Phchi.S2	AUGUSTUS	transcript	15423167	15424634	.	-	.	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	stop_codon	15423164	15423166	.	-	0	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	CDS	15423167	15423691	0.5	-	0	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	exon	15423167	15423691	.	-	.	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	intron	15423692	15423795	.	-	.	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	CDS	15423796	15424162	0.8	-	1	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	exon	15423796	15424162	.	-	.	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	intron	15424163	15424254	.	-	.	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	CDS	15424255	15424634	0.86	-	0	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	exon	15424255	15424634	.	-	.	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
Phchi.S2	AUGUSTUS	start_codon	15424632	15424634	.	-	0	transcript_id "Phchi.S2G046700.t1"; gene_id "Phchi.S2G046700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4294.t1 is derived from g1463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9465150	9466103	.	+	.	Phchi.S1G145300
Phchi.S1	AUGUSTUS	transcript	9465150	9466103	.	+	.	transcript_id "Phchi.S1G145300.t1"; gene_id "Phchi.S1G145300"
Phchi.S1	AUGUSTUS	start_codon	9465150	9465152	.	+	0	transcript_id "Phchi.S1G145300.t1"; gene_id "Phchi.S1G145300"
Phchi.S1	AUGUSTUS	CDS	9465150	9466103	1	+	0	transcript_id "Phchi.S1G145300.t1"; gene_id "Phchi.S1G145300"
Phchi.S1	AUGUSTUS	exon	9465150	9466103	.	+	.	transcript_id "Phchi.S1G145300.t1"; gene_id "Phchi.S1G145300"
Phchi.S1	AUGUSTUS	stop_codon	9466104	9466106	.	+	0	transcript_id "Phchi.S1G145300.t1"; gene_id "Phchi.S1G145300"
# This transcript jg3920.t2 is derived from g1089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3920.t3 is derived from g1089.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3921.t1 is derived from g1090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6434675	6435514	.	+	.	Phchi.S1G108000
Phchi.S1	AUGUSTUS	transcript	6434675	6435514	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	start_codon	6434675	6434677	.	+	0	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	CDS	6434675	6434687	1	+	0	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	exon	6434675	6434687	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	intron	6434688	6434944	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	CDS	6434945	6435008	0.69	+	2	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	exon	6434945	6435008	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	intron	6435009	6435190	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	CDS	6435191	6435284	0.97	+	1	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	exon	6435191	6435284	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	intron	6435285	6435481	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	CDS	6435482	6435514	0.97	+	0	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	exon	6435482	6435514	.	+	.	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
Phchi.S1	AUGUSTUS	stop_codon	6435515	6435517	.	+	0	transcript_id "Phchi.S1G108000.t1"; gene_id "Phchi.S1G108000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15362.t1 is derived from g13830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18585884	18587449	.	-	.	Phchi.S3G268100
Phchi.S3	AUGUSTUS	transcript	18585884	18587449	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	stop_codon	18585881	18585883	.	-	0	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18585884	18586097	0.96	-	1	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18585884	18586097	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18586098	18586187	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18586188	18586240	1	-	0	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18586188	18586240	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18586241	18586329	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18586330	18586420	0.98	-	1	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18586330	18586420	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18586421	18586523	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18586524	18586604	1	-	1	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18586524	18586604	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18586605	18586689	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18586690	18586742	1	-	0	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18586690	18586742	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18586743	18586819	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18586820	18586931	1	-	1	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18586820	18586931	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18586932	18587011	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18587012	18587100	1	-	0	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18587012	18587100	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	intron	18587101	18587269	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	CDS	18587270	18587449	1	-	0	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	exon	18587270	18587449	.	-	.	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
Phchi.S3	AUGUSTUS	start_codon	18587447	18587449	.	-	0	transcript_id "Phchi.S3G268100.t1"; gene_id "Phchi.S3G268100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7843.t1 is derived from g5017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31493652	31500605	.	-	.	Phchi.S1G500200
Phchi.S1	AUGUSTUS	transcript	31493652	31500605	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	stop_codon	31493649	31493651	.	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31493652	31493799	1	-	1	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31493652	31493799	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31493800	31493957	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31493958	31494049	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31493958	31494049	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31494050	31494186	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31494187	31494426	0.97	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31494187	31494426	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31494427	31494529	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31494530	31494737	0.98	-	1	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31494530	31494737	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31494738	31494817	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31494818	31494942	0.57	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31494818	31494942	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31494943	31495066	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31495067	31495086	0.47	-	2	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31495067	31495086	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31495087	31495293	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31495294	31495396	0.5	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31495294	31495396	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31495397	31495521	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31495522	31495756	0.34	-	1	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31495522	31495756	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31495757	31495851	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31495852	31495979	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31495852	31495979	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31495980	31496070	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31496071	31496342	1	-	2	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31496071	31496342	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31496343	31496432	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31496433	31496541	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31496433	31496541	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31496542	31496732	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31496733	31496826	1	-	1	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31496733	31496826	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31496827	31496904	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31496905	31497214	0.96	-	2	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31496905	31497214	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31497215	31497301	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31497302	31497400	0.83	-	2	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31497302	31497400	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31497401	31497486	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31497487	31497510	0.69	-	2	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31497487	31497510	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31497511	31497591	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31497592	31497709	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31497592	31497709	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31497710	31497898	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31497899	31497998	0.99	-	1	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31497899	31497998	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31497999	31498105	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31498106	31498164	0.99	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31498106	31498164	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31498165	31498311	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31498312	31498437	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31498312	31498437	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31498438	31498587	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31498588	31498716	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31498588	31498716	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31498717	31498804	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31498805	31498924	1	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31498805	31498924	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31498925	31499031	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31499032	31499240	0.71	-	2	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31499032	31499240	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31499241	31499414	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31499415	31499527	1	-	1	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31499415	31499527	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31499528	31499794	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31499795	31500054	0.94	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31499795	31500054	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	intron	31500055	31500158	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	CDS	31500159	31500605	0.33	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	exon	31500159	31500605	.	-	.	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
Phchi.S1	AUGUSTUS	start_codon	31500603	31500605	.	-	0	transcript_id "Phchi.S1G500200.t1"; gene_id "Phchi.S1G500200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5205.t1 is derived from g2375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15466619	15469420	.	+	.	Phchi.S1G236400
Phchi.S1	AUGUSTUS	transcript	15466619	15469420	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	start_codon	15466619	15466621	.	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15466619	15466690	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15466619	15466690	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15466691	15466827	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15466828	15466885	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15466828	15466885	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15466886	15466985	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15466986	15467152	1	+	2	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15466986	15467152	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15467153	15467241	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15467242	15467328	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15467242	15467328	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15467329	15467468	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15467469	15467594	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15467469	15467594	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15467595	15467685	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15467686	15467748	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15467686	15467748	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15467749	15467839	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15467840	15467989	0.99	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15467840	15467989	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15467990	15468094	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15468095	15468162	0.99	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15468095	15468162	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15468163	15468258	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15468259	15468370	1	+	1	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15468259	15468370	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15468371	15468522	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15468523	15468627	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15468523	15468627	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15468628	15468790	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15468791	15468912	1	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15468791	15468912	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15468913	15469006	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15469007	15469153	1	+	1	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15469007	15469153	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	intron	15469154	15469257	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	CDS	15469258	15469420	0.98	+	1	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	exon	15469258	15469420	.	+	.	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
Phchi.S1	AUGUSTUS	stop_codon	15469421	15469423	.	+	0	transcript_id "Phchi.S1G236400.t1"; gene_id "Phchi.S1G236400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10775.t1 is derived from g14825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2055967	2058672	.	+	.	Phchi.S4G035700
Phchi.S4	AUGUSTUS	transcript	2055967	2058672	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	start_codon	2055967	2055969	.	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2055967	2056344	0.99	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2055967	2056344	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2056345	2056426	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2056427	2056501	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2056427	2056501	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2056502	2056656	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2056657	2056710	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2056657	2056710	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2056711	2056830	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2056831	2056909	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2056831	2056909	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2056910	2056991	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2056992	2057119	1	+	2	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2056992	2057119	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2057120	2057301	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2057302	2057385	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2057302	2057385	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2057386	2057513	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2057514	2057597	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2057514	2057597	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2057598	2057758	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2057759	2057910	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2057759	2057910	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2057911	2057988	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2057989	2058139	1	+	1	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2057989	2058139	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	intron	2058140	2058246	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	CDS	2058247	2058672	1	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	exon	2058247	2058672	.	+	.	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
Phchi.S4	AUGUSTUS	stop_codon	2058673	2058675	.	+	0	transcript_id "Phchi.S4G035700.t1"; gene_id "Phchi.S4G035700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7742.t1 is derived from g4916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30920430	30921281	.	+	.	Phchi.S1G490100
Phchi.S1	AUGUSTUS	transcript	30920430	30921281	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	start_codon	30920430	30920432	.	+	0	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	CDS	30920430	30920435	0.31	+	0	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	exon	30920430	30920435	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	intron	30920436	30920522	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	CDS	30920523	30920775	0.31	+	0	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	exon	30920523	30920775	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	intron	30920776	30920870	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	CDS	30920871	30920953	1	+	2	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	exon	30920871	30920953	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	intron	30920954	30921033	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	CDS	30921034	30921096	0.98	+	0	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	exon	30921034	30921096	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	intron	30921097	30921164	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	CDS	30921165	30921281	0.49	+	0	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	exon	30921165	30921281	.	+	.	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
Phchi.S1	AUGUSTUS	stop_codon	30921282	30921284	.	+	0	transcript_id "Phchi.S1G490100.t1"; gene_id "Phchi.S1G490100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10954.t1 is derived from g15004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3268797	3271131	.	-	.	Phchi.S4G053600
Phchi.S4	AUGUSTUS	transcript	3268797	3271131	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	stop_codon	3268794	3268796	.	-	0	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3268797	3269553	0.98	-	1	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3268797	3269553	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	intron	3269554	3269654	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3269655	3269825	0.6	-	1	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3269655	3269825	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	intron	3269826	3269929	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3269930	3270188	0.56	-	2	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3269930	3270188	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	intron	3270189	3270311	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3270312	3270450	0.52	-	0	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3270312	3270450	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	intron	3270451	3270551	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3270552	3270769	1	-	2	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3270552	3270769	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	intron	3270770	3270882	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3270883	3271030	0.97	-	0	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3270883	3271030	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	intron	3271031	3271128	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	CDS	3271129	3271131	1	-	0	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	exon	3271129	3271131	.	-	.	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
Phchi.S4	AUGUSTUS	start_codon	3271129	3271131	.	-	0	transcript_id "Phchi.S4G053600.t1"; gene_id "Phchi.S4G053600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14494.t1 is derived from g12962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13134489	13135241	.	+	.	Phchi.S3G181300
Phchi.S3	AUGUSTUS	transcript	13134489	13135241	.	+	.	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	start_codon	13134489	13134491	.	+	0	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	CDS	13134489	13134569	1	+	0	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	exon	13134489	13134569	.	+	.	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	intron	13134570	13134659	.	+	.	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	CDS	13134660	13134749	1	+	0	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	exon	13134660	13134749	.	+	.	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	intron	13134750	13134830	.	+	.	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	CDS	13134831	13135241	0.98	+	0	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	exon	13134831	13135241	.	+	.	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
Phchi.S3	AUGUSTUS	stop_codon	13135242	13135244	.	+	0	transcript_id "Phchi.S3G181300.t1"; gene_id "Phchi.S3G181300"
# This transcript jg15813.t2 is derived from g14283.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15814.t1 is derived from g14284.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21520694	21523285	.	+	.	Phchi.S3G313300
Phchi.S3	AUGUSTUS	transcript	21520914	21523285	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	start_codon	21520914	21520916	.	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21520914	21520931	0.88	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21520914	21520931	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21520932	21521059	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521060	21521153	0.95	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521060	21521153	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521154	21521326	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521327	21521359	1	+	2	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521327	21521359	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521360	21521471	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521472	21521533	1	+	2	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521472	21521533	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521534	21521656	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521657	21521709	1	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521657	21521709	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521710	21521839	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521840	21521876	1	+	1	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521840	21521876	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521877	21522095	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522096	21522167	1	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522096	21522167	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522168	21522288	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522289	21522408	1	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522289	21522408	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522409	21522504	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522505	21522661	1	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522505	21522661	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522662	21522749	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522750	21522826	1	+	2	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522750	21522826	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522827	21522902	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522903	21522954	0.87	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522903	21522954	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522955	21523142	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21523143	21523285	0.69	+	2	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21523143	21523285	.	+	.	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	stop_codon	21523286	21523288	.	+	0	transcript_id "Phchi.S3G313300.t1"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	transcript	21520694	21523285	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	start_codon	21520694	21520696	.	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21520694	21520881	0.78	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21520694	21520881	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21520882	21520973	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21520974	21521153	0.49	+	1	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21520974	21521153	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521154	21521326	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521327	21521349	0.36	+	1	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521327	21521349	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521350	21521471	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521472	21521533	0.85	+	2	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521472	21521533	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521534	21521656	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521657	21521709	1	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521657	21521709	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521710	21521839	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521840	21521876	1	+	1	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521840	21521876	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521877	21522095	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522096	21522167	1	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522096	21522167	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522168	21522288	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522289	21522408	1	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522289	21522408	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522409	21522504	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522505	21522661	1	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522505	21522661	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522662	21522749	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522750	21522826	1	+	2	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522750	21522826	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522827	21522902	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522903	21522954	0.86	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522903	21522954	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522955	21523142	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21523143	21523285	0.74	+	2	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21523143	21523285	.	+	.	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	stop_codon	21523286	21523288	.	+	0	transcript_id "Phchi.S3G313300.t2"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	transcript	21520914	21523285	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	start_codon	21520914	21520916	.	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21520914	21520931	0.53	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21520914	21520931	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21520932	21521059	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521060	21521153	0.69	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521060	21521153	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521154	21521326	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521327	21521359	0.78	+	2	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521327	21521359	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521360	21521471	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521472	21521533	0.9	+	2	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521472	21521533	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521534	21521656	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521657	21521709	0.99	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521657	21521709	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521710	21521839	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21521840	21521876	1	+	1	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21521840	21521876	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21521877	21522095	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522096	21522167	1	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522096	21522167	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522168	21522288	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522289	21522413	0.92	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522289	21522413	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522414	21522504	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522505	21522515	0.78	+	1	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522505	21522515	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522516	21522613	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522614	21522661	0.75	+	2	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522614	21522661	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522662	21522749	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522750	21522826	1	+	2	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522750	21522826	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522827	21522902	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21522903	21522954	0.8	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21522903	21522954	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	intron	21522955	21523142	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	CDS	21523143	21523285	0.68	+	2	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	exon	21523143	21523285	.	+	.	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
Phchi.S3	AUGUSTUS	stop_codon	21523286	21523288	.	+	0	transcript_id "Phchi.S3G313300.t3"; gene_id "Phchi.S3G313300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg56.t1 is derived from g9838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	245607	246209	.	-	.	Phchi.S6G001500
Phchi.S6	AUGUSTUS	transcript	245607	246209	.	-	.	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	stop_codon	245604	245606	.	-	0	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	CDS	245607	245642	1	-	0	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	exon	245607	245642	.	-	.	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	intron	245643	245719	.	-	.	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	CDS	245720	245776	0.75	-	0	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	exon	245720	245776	.	-	.	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	intron	245777	246059	.	-	.	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	CDS	246060	246209	0.38	-	0	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	exon	246060	246209	.	-	.	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
Phchi.S6	AUGUSTUS	start_codon	246207	246209	.	-	0	transcript_id "Phchi.S6G001500.t1"; gene_id "Phchi.S6G001500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1929.t1 is derived from g8849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3881157	3881492	.	+	.	Phchi.S5G053800
Phchi.S5	AUGUSTUS	transcript	3881157	3881492	.	+	.	transcript_id "Phchi.S5G053800.t1"; gene_id "Phchi.S5G053800"
Phchi.S5	AUGUSTUS	start_codon	3881157	3881159	.	+	0	transcript_id "Phchi.S5G053800.t1"; gene_id "Phchi.S5G053800"
Phchi.S5	AUGUSTUS	CDS	3881157	3881492	0.52	+	0	transcript_id "Phchi.S5G053800.t1"; gene_id "Phchi.S5G053800"
Phchi.S5	AUGUSTUS	exon	3881157	3881492	.	+	.	transcript_id "Phchi.S5G053800.t1"; gene_id "Phchi.S5G053800"
Phchi.S5	AUGUSTUS	stop_codon	3881493	3881495	.	+	0	transcript_id "Phchi.S5G053800.t1"; gene_id "Phchi.S5G053800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3291.t1 is derived from g460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2700395	2700873	.	+	.	Phchi.S1G045000
Phchi.S1	AUGUSTUS	transcript	2700395	2700873	.	+	.	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	start_codon	2700395	2700397	.	+	0	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	CDS	2700395	2700639	0.74	+	0	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	exon	2700395	2700639	.	+	.	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	intron	2700640	2700734	.	+	.	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	CDS	2700735	2700873	0.68	+	1	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	exon	2700735	2700873	.	+	.	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
Phchi.S1	AUGUSTUS	stop_codon	2700874	2700876	.	+	0	transcript_id "Phchi.S1G045000.t1"; gene_id "Phchi.S1G045000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg210.t1 is derived from g9992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1199291	1199539	.	+	.	Phchi.S6G016900
Phchi.S6	AUGUSTUS	transcript	1199291	1199539	.	+	.	transcript_id "Phchi.S6G016900.t1"; gene_id "Phchi.S6G016900"
Phchi.S6	AUGUSTUS	start_codon	1199291	1199293	.	+	0	transcript_id "Phchi.S6G016900.t1"; gene_id "Phchi.S6G016900"
Phchi.S6	AUGUSTUS	CDS	1199291	1199539	0.17	+	0	transcript_id "Phchi.S6G016900.t1"; gene_id "Phchi.S6G016900"
Phchi.S6	AUGUSTUS	exon	1199291	1199539	.	+	.	transcript_id "Phchi.S6G016900.t1"; gene_id "Phchi.S6G016900"
Phchi.S6	AUGUSTUS	stop_codon	1199540	1199542	.	+	0	transcript_id "Phchi.S6G016900.t1"; gene_id "Phchi.S6G016900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13940.t1 is derived from g12407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9826386	9826984	.	+	.	Phchi.S3G125900
Phchi.S3	AUGUSTUS	transcript	9826386	9826984	.	+	.	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	start_codon	9826386	9826388	.	+	0	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	CDS	9826386	9826546	0.57	+	0	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	exon	9826386	9826546	.	+	.	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	intron	9826547	9826764	.	+	.	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	CDS	9826765	9826814	0.7	+	1	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	exon	9826765	9826814	.	+	.	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	intron	9826815	9826901	.	+	.	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	CDS	9826902	9826984	0.36	+	2	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	exon	9826902	9826984	.	+	.	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
Phchi.S3	AUGUSTUS	stop_codon	9826985	9826987	.	+	0	transcript_id "Phchi.S3G125900.t1"; gene_id "Phchi.S3G125900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3796.t1 is derived from g965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5786976	5789822	.	-	.	Phchi.S1G095500
Phchi.S1	AUGUSTUS	transcript	5786976	5789822	.	-	.	transcript_id "Phchi.S1G095500.t1"; gene_id "Phchi.S1G095500"
Phchi.S1	AUGUSTUS	stop_codon	5786973	5786975	.	-	0	transcript_id "Phchi.S1G095500.t1"; gene_id "Phchi.S1G095500"
Phchi.S1	AUGUSTUS	CDS	5786976	5789822	0.52	-	0	transcript_id "Phchi.S1G095500.t1"; gene_id "Phchi.S1G095500"
Phchi.S1	AUGUSTUS	exon	5786976	5789822	.	-	.	transcript_id "Phchi.S1G095500.t1"; gene_id "Phchi.S1G095500"
Phchi.S1	AUGUSTUS	start_codon	5789820	5789822	.	-	0	transcript_id "Phchi.S1G095500.t1"; gene_id "Phchi.S1G095500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10226.t1 is derived from g7402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46474049	46474500	.	-	.	Phchi.S1G738500
Phchi.S1	AUGUSTUS	transcript	46474049	46474500	.	-	.	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	stop_codon	46474046	46474048	.	-	0	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	CDS	46474049	46474063	1	-	0	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	exon	46474049	46474063	.	-	.	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	intron	46474064	46474149	.	-	.	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	CDS	46474150	46474265	1	-	2	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	exon	46474150	46474265	.	-	.	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	intron	46474266	46474391	.	-	.	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	CDS	46474392	46474500	1	-	0	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	exon	46474392	46474500	.	-	.	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
Phchi.S1	AUGUSTUS	start_codon	46474498	46474500	.	-	0	transcript_id "Phchi.S1G738500.t1"; gene_id "Phchi.S1G738500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7452.t1 is derived from g4624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29356196	29356825	.	+	.	Phchi.S1G461100
Phchi.S1	AUGUSTUS	transcript	29356196	29356825	.	+	.	transcript_id "Phchi.S1G461100.t1"; gene_id "Phchi.S1G461100"
Phchi.S1	AUGUSTUS	start_codon	29356196	29356198	.	+	0	transcript_id "Phchi.S1G461100.t1"; gene_id "Phchi.S1G461100"
Phchi.S1	AUGUSTUS	CDS	29356196	29356825	0.51	+	0	transcript_id "Phchi.S1G461100.t1"; gene_id "Phchi.S1G461100"
Phchi.S1	AUGUSTUS	exon	29356196	29356825	.	+	.	transcript_id "Phchi.S1G461100.t1"; gene_id "Phchi.S1G461100"
Phchi.S1	AUGUSTUS	stop_codon	29356826	29356828	.	+	0	transcript_id "Phchi.S1G461100.t1"; gene_id "Phchi.S1G461100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15172.t1 is derived from g13640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17357884	17359455	.	+	.	Phchi.S3G249100
Phchi.S3	AUGUSTUS	transcript	17357884	17359455	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	start_codon	17357884	17357886	.	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	CDS	17357884	17358324	0.44	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	exon	17357884	17358324	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	intron	17358325	17358429	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	CDS	17358430	17358636	0.74	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	exon	17358430	17358636	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	intron	17358637	17358766	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	CDS	17358767	17358913	1	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	exon	17358767	17358913	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	intron	17358914	17359039	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	CDS	17359040	17359093	1	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	exon	17359040	17359093	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	intron	17359094	17359185	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	CDS	17359186	17359455	1	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	exon	17359186	17359455	.	+	.	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
Phchi.S3	AUGUSTUS	stop_codon	17359456	17359458	.	+	0	transcript_id "Phchi.S3G249100.t1"; gene_id "Phchi.S3G249100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7697.t1 is derived from g4871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30693808	30695272	.	+	.	Phchi.S1G485600
Phchi.S1	AUGUSTUS	transcript	30693808	30695272	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	start_codon	30693808	30693810	.	+	0	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	CDS	30693808	30693903	0.62	+	0	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	exon	30693808	30693903	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	intron	30693904	30694189	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	CDS	30694190	30694795	0.87	+	0	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	exon	30694190	30694795	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	intron	30694796	30694888	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	CDS	30694889	30694947	1	+	0	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	exon	30694889	30694947	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	intron	30694948	30695067	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	CDS	30695068	30695272	0.91	+	1	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	exon	30695068	30695272	.	+	.	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
Phchi.S1	AUGUSTUS	stop_codon	30695273	30695275	.	+	0	transcript_id "Phchi.S1G485600.t1"; gene_id "Phchi.S1G485600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12399.t1 is derived from g8076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17460557	17467506	.	-	.	Phchi.S2G047900
Phchi.S2	AUGUSTUS	transcript	17460557	17467506	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	stop_codon	17460554	17460556	.	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17460557	17460729	1	-	2	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17460557	17460729	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17460730	17460815	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17460816	17460854	1	-	2	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17460816	17460854	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17460855	17460933	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17460934	17461048	1	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17460934	17461048	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17461049	17461136	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17461137	17461202	1	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17461137	17461202	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17461203	17461309	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17461310	17461401	1	-	2	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17461310	17461401	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17461402	17461529	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17461530	17461587	1	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17461530	17461587	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17461588	17461721	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17461722	17461758	1	-	1	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17461722	17461758	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17461759	17461859	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17461860	17462549	0.65	-	1	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17461860	17462549	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17462550	17462684	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17462685	17462764	1	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17462685	17462764	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17462765	17462879	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17462880	17462916	1	-	1	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17462880	17462916	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17462917	17463019	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17463020	17463088	1	-	1	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17463020	17463088	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17463089	17463245	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17463246	17463337	1	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17463246	17463337	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17463338	17463470	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17463471	17463555	1	-	1	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17463471	17463555	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17463556	17463638	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17463639	17463718	1	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17463639	17463718	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17463719	17463841	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17463842	17464825	0.98	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17463842	17464825	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17464826	17464999	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17465000	17465085	1	-	2	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17465000	17465085	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17465086	17465181	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17465182	17465276	1	-	1	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17465182	17465276	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17465277	17465365	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17465366	17465456	1	-	2	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17465366	17465456	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17465457	17465574	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17465575	17466448	0.82	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17465575	17466448	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17466449	17466529	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17466530	17466960	0.55	-	2	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17466530	17466960	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	intron	17466961	17467103	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	CDS	17467104	17467506	0.34	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	exon	17467104	17467506	.	-	.	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
Phchi.S2	AUGUSTUS	start_codon	17467504	17467506	.	-	0	transcript_id "Phchi.S2G047900.t1"; gene_id "Phchi.S2G047900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8891.t1 is derived from g6066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38499031	38500056	.	-	.	Phchi.S1G605000
Phchi.S1	AUGUSTUS	transcript	38499031	38500056	.	-	.	transcript_id "Phchi.S1G605000.t1"; gene_id "Phchi.S1G605000"
Phchi.S1	AUGUSTUS	stop_codon	38499028	38499030	.	-	0	transcript_id "Phchi.S1G605000.t1"; gene_id "Phchi.S1G605000"
Phchi.S1	AUGUSTUS	CDS	38499031	38500056	0.43	-	0	transcript_id "Phchi.S1G605000.t1"; gene_id "Phchi.S1G605000"
Phchi.S1	AUGUSTUS	exon	38499031	38500056	.	-	.	transcript_id "Phchi.S1G605000.t1"; gene_id "Phchi.S1G605000"
Phchi.S1	AUGUSTUS	start_codon	38500054	38500056	.	-	0	transcript_id "Phchi.S1G605000.t1"; gene_id "Phchi.S1G605000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg893.t1 is derived from g10675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6331623	6332777	.	+	.	Phchi.S6G085200
Phchi.S6	AUGUSTUS	transcript	6331623	6332777	.	+	.	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	start_codon	6331623	6331625	.	+	0	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	CDS	6331623	6332210	0.53	+	0	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	exon	6331623	6332210	.	+	.	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	intron	6332211	6332339	.	+	.	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	CDS	6332340	6332777	1	+	0	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	exon	6332340	6332777	.	+	.	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
Phchi.S6	AUGUSTUS	stop_codon	6332778	6332780	.	+	0	transcript_id "Phchi.S6G085200.t1"; gene_id "Phchi.S6G085200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3654.t1 is derived from g823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4981442	4981879	.	-	.	Phchi.S1G081300
Phchi.S1	AUGUSTUS	transcript	4981442	4981879	.	-	.	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	stop_codon	4981439	4981441	.	-	0	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	CDS	4981442	4981661	0.84	-	1	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	exon	4981442	4981661	.	-	.	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	intron	4981662	4981754	.	-	.	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	CDS	4981755	4981879	0.77	-	0	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	exon	4981755	4981879	.	-	.	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
Phchi.S1	AUGUSTUS	start_codon	4981877	4981879	.	-	0	transcript_id "Phchi.S1G081300.t1"; gene_id "Phchi.S1G081300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10639.t1 is derived from g14689.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1371478	1373946	.	-	.	Phchi.S4G022100
Phchi.S4	AUGUSTUS	transcript	1371478	1373946	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	stop_codon	1371475	1371477	.	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1371478	1371924	0.96	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1371478	1371924	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1371925	1372027	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1372028	1372375	1	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1372028	1372375	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1372376	1372500	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1372501	1372887	0.98	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1372501	1372887	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1372888	1372968	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1372969	1373111	1	-	2	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1372969	1373111	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1373112	1373402	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1373403	1373670	1	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1373403	1373670	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1373671	1373757	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1373758	1373946	0.8	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1373758	1373946	.	-	.	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	start_codon	1373944	1373946	.	-	0	transcript_id "Phchi.S4G022100.t1"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	transcript	1371478	1373946	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	stop_codon	1371475	1371477	.	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1371478	1371924	0.97	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1371478	1371924	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1371925	1372027	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1372028	1372375	1	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1372028	1372375	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1372376	1372500	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1372501	1372860	0.71	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1372501	1372860	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1372861	1372968	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1372969	1373111	0.98	-	2	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1372969	1373111	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1373112	1373402	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1373403	1373670	1	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1373403	1373670	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	intron	1373671	1373757	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	CDS	1373758	1373946	0.64	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	exon	1373758	1373946	.	-	.	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
Phchi.S4	AUGUSTUS	start_codon	1373944	1373946	.	-	0	transcript_id "Phchi.S4G022100.t2"; gene_id "Phchi.S4G022100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12252.t1 is derived from g7928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7018421	7020899	.	-	.	Phchi.S2G033200
Phchi.S2	AUGUSTUS	transcript	7018421	7020899	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	stop_codon	7018418	7018420	.	-	0	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	CDS	7018421	7018610	1	-	1	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	exon	7018421	7018610	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	intron	7018611	7018725	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	CDS	7018726	7018931	1	-	0	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	exon	7018726	7018931	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	intron	7018932	7019118	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	CDS	7019119	7019271	1	-	0	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	exon	7019119	7019271	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	intron	7019272	7020181	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	CDS	7020182	7020597	1	-	2	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	exon	7020182	7020597	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	intron	7020598	7020820	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	CDS	7020821	7020899	0.52	-	0	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	exon	7020821	7020899	.	-	.	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
Phchi.S2	AUGUSTUS	start_codon	7020897	7020899	.	-	0	transcript_id "Phchi.S2G033200.t1"; gene_id "Phchi.S2G033200"
# This transcript jg1502.t2 is derived from g8421.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1503.t1 is derived from g8422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1234234	1236565	.	-	.	Phchi.S5G011200
Phchi.S5	AUGUSTUS	transcript	1234234	1236565	.	-	.	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	stop_codon	1234231	1234233	.	-	0	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	CDS	1234234	1236274	1	-	1	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	exon	1234234	1236274	.	-	.	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	intron	1236275	1236401	.	-	.	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	CDS	1236402	1236565	1	-	0	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	exon	1236402	1236565	.	-	.	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
Phchi.S5	AUGUSTUS	start_codon	1236563	1236565	.	-	0	transcript_id "Phchi.S5G011200.t1"; gene_id "Phchi.S5G011200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11017.t1 is derived from g15067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3650247	3652679	.	+	.	Phchi.S4G059900
Phchi.S4	AUGUSTUS	transcript	3650247	3652679	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	start_codon	3650247	3650249	.	+	0	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3650247	3650611	0.74	+	0	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3650247	3650611	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3650612	3650845	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3650846	3651488	0.65	+	1	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3650846	3651488	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3651489	3651572	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3651573	3651740	0.84	+	0	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3651573	3651740	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3651741	3652157	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3652158	3652163	1	+	0	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3652158	3652163	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3652164	3652283	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3652284	3652320	0.73	+	0	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3652284	3652320	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3652321	3652584	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3652585	3652679	0.83	+	2	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3652585	3652679	.	+	.	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	stop_codon	3652680	3652682	.	+	0	transcript_id "Phchi.S4G059900.t1"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	transcript	3650247	3652679	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	start_codon	3650247	3650249	.	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3650247	3650611	0.78	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3650247	3650611	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3650612	3650845	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3650846	3651488	0.63	+	1	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3650846	3651488	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3651489	3651572	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3651573	3651659	0.69	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3651573	3651659	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3651660	3651795	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3651796	3651864	0.76	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3651796	3651864	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3651865	3652157	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3652158	3652163	0.98	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3652158	3652163	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3652164	3652283	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3652284	3652320	0.83	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3652284	3652320	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	intron	3652321	3652584	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	CDS	3652585	3652679	0.9	+	2	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	exon	3652585	3652679	.	+	.	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
Phchi.S4	AUGUSTUS	stop_codon	3652680	3652682	.	+	0	transcript_id "Phchi.S4G059900.t2"; gene_id "Phchi.S4G059900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14997.t1 is derived from g13465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16178856	16181157	.	+	.	Phchi.S3G231600
Phchi.S3	AUGUSTUS	transcript	16178856	16181157	.	+	.	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	start_codon	16178856	16178858	.	+	0	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	CDS	16178856	16179365	0.98	+	0	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	exon	16178856	16179365	.	+	.	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	intron	16179366	16179517	.	+	.	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	CDS	16179518	16179758	1	+	0	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	exon	16179518	16179758	.	+	.	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	intron	16179759	16180099	.	+	.	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	CDS	16180100	16181157	1	+	2	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	exon	16180100	16181157	.	+	.	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
Phchi.S3	AUGUSTUS	stop_codon	16181158	16181160	.	+	0	transcript_id "Phchi.S3G231600.t1"; gene_id "Phchi.S3G231600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg508.t1 is derived from g10290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3517020	3518078	.	-	.	Phchi.S6G046700
Phchi.S6	AUGUSTUS	transcript	3517020	3518078	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	stop_codon	3517017	3517019	.	-	0	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	CDS	3517020	3517125	0.31	-	1	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	exon	3517020	3517125	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	intron	3517126	3517221	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	CDS	3517222	3517313	1	-	0	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	exon	3517222	3517313	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	intron	3517314	3517390	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	CDS	3517391	3517427	0.99	-	1	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	exon	3517391	3517427	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	intron	3517428	3517995	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	CDS	3517996	3518078	0.34	-	0	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	exon	3517996	3518078	.	-	.	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
Phchi.S6	AUGUSTUS	start_codon	3518076	3518078	.	-	0	transcript_id "Phchi.S6G046700.t1"; gene_id "Phchi.S6G046700"
# This transcript jg2329.t2 is derived from g9249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2330.t1 is derived from g9250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6203129	6205549	.	+	.	Phchi.S5G093900
Phchi.S5	AUGUSTUS	transcript	6203450	6205549	.	+	.	transcript_id "Phchi.S5G093900.t1"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	start_codon	6203450	6203452	.	+	0	transcript_id "Phchi.S5G093900.t1"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	CDS	6203450	6205549	0.92	+	0	transcript_id "Phchi.S5G093900.t1"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	exon	6203450	6205549	.	+	.	transcript_id "Phchi.S5G093900.t1"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	stop_codon	6205550	6205552	.	+	0	transcript_id "Phchi.S5G093900.t1"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	transcript	6203129	6205549	.	+	.	transcript_id "Phchi.S5G093900.t2"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	start_codon	6203129	6203131	.	+	0	transcript_id "Phchi.S5G093900.t2"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	CDS	6203129	6205549	0.84	+	0	transcript_id "Phchi.S5G093900.t2"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	exon	6203129	6205549	.	+	.	transcript_id "Phchi.S5G093900.t2"; gene_id "Phchi.S5G093900"
Phchi.S5	AUGUSTUS	stop_codon	6205550	6205552	.	+	0	transcript_id "Phchi.S5G093900.t2"; gene_id "Phchi.S5G093900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2633.t1 is derived from g9553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7883017	7886223	.	+	.	Phchi.S5G124200
Phchi.S5	AUGUSTUS	transcript	7883017	7886223	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	start_codon	7883017	7883019	.	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883017	7883120	0.98	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883017	7883120	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7883121	7883354	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883355	7883439	0.93	+	1	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883355	7883439	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7883440	7883516	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883517	7883769	0.95	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883517	7883769	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7883770	7883894	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883895	7884030	1	+	2	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883895	7884030	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884031	7884122	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884123	7884262	1	+	1	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884123	7884262	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884263	7884362	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884363	7884459	1	+	2	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884363	7884459	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884460	7884581	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884582	7884651	1	+	1	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884582	7884651	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884652	7884756	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884757	7884864	0.98	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884757	7884864	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884865	7884965	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884966	7885082	1	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884966	7885082	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885083	7885169	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885170	7885346	0.64	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885170	7885346	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885347	7885449	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885450	7885551	0.94	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885450	7885551	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885552	7885696	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885697	7885785	1	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885697	7885785	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885786	7885874	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885875	7885986	0.95	+	1	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885875	7885986	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885987	7886091	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7886092	7886223	0.94	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7886092	7886223	.	+	.	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	stop_codon	7886224	7886226	.	+	0	transcript_id "Phchi.S5G124200.t1"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	transcript	7883017	7886223	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	start_codon	7883017	7883019	.	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883017	7883120	1	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883017	7883120	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7883121	7883354	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883355	7883439	0.88	+	1	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883355	7883439	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7883440	7883516	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883517	7883769	0.87	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883517	7883769	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7883770	7883894	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7883895	7884030	1	+	2	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7883895	7884030	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884031	7884122	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884123	7884262	1	+	1	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884123	7884262	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884263	7884362	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884363	7884459	1	+	2	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884363	7884459	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884460	7884581	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884582	7884651	1	+	1	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884582	7884651	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884652	7884756	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884757	7884864	1	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884757	7884864	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7884865	7884965	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7884966	7885082	1	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7884966	7885082	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885083	7885166	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885167	7885346	0.68	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885167	7885346	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885347	7885449	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885450	7885551	0.97	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885450	7885551	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885552	7885696	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885697	7885785	1	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885697	7885785	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885786	7885874	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7885875	7885986	0.94	+	1	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7885875	7885986	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	intron	7885987	7886091	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	CDS	7886092	7886223	0.93	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	exon	7886092	7886223	.	+	.	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
Phchi.S5	AUGUSTUS	stop_codon	7886224	7886226	.	+	0	transcript_id "Phchi.S5G124200.t2"; gene_id "Phchi.S5G124200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14155.t1 is derived from g12622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11180160	11183257	.	-	.	Phchi.S3G147400
Phchi.S3	AUGUSTUS	transcript	11180160	11183257	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	stop_codon	11180157	11180159	.	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11180160	11180195	0.99	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11180160	11180195	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11180196	11180279	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11180280	11180364	1	-	1	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11180280	11180364	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11180365	11180446	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11180447	11180622	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11180447	11180622	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11180623	11180717	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11180718	11180828	0.68	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11180718	11180828	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11180829	11180936	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11180937	11181012	0.68	-	1	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11180937	11181012	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11181013	11181107	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11181108	11181169	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11181108	11181169	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11181170	11181293	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11181294	11181371	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11181294	11181371	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11181372	11181478	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11181479	11181574	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11181479	11181574	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11181575	11181715	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11181716	11181853	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11181716	11181853	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11181854	11182560	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11182561	11182769	1	-	2	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11182561	11182769	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11182770	11182866	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11182867	11182996	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11182867	11182996	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	intron	11182997	11183137	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	CDS	11183138	11183257	1	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	exon	11183138	11183257	.	-	.	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
Phchi.S3	AUGUSTUS	start_codon	11183255	11183257	.	-	0	transcript_id "Phchi.S3G147400.t1"; gene_id "Phchi.S3G147400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8878.t1 is derived from g6053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38422849	38424806	.	+	.	Phchi.S1G603700
Phchi.S1	AUGUSTUS	transcript	38422849	38424806	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	start_codon	38422849	38422851	.	+	0	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	CDS	38422849	38423237	0.79	+	0	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	exon	38422849	38423237	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	intron	38423238	38423361	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	CDS	38423362	38423629	0.92	+	1	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	exon	38423362	38423629	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	intron	38423630	38423757	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	CDS	38423758	38424045	0.97	+	0	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	exon	38423758	38424045	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	intron	38424046	38424135	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	CDS	38424136	38424503	0.94	+	0	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	exon	38424136	38424503	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	intron	38424504	38424616	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	CDS	38424617	38424806	0.99	+	1	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	exon	38424617	38424806	.	+	.	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
Phchi.S1	AUGUSTUS	stop_codon	38424807	38424809	.	+	0	transcript_id "Phchi.S1G603700.t1"; gene_id "Phchi.S1G603700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9912.t1 is derived from g7088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44399373	44403151	.	+	.	Phchi.S1G707100
Phchi.S1	AUGUSTUS	transcript	44399373	44403151	.	+	.	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	start_codon	44399373	44399375	.	+	0	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	CDS	44399373	44399615	0.68	+	0	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	exon	44399373	44399615	.	+	.	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	intron	44399616	44399690	.	+	.	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	CDS	44399691	44402911	0.88	+	0	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	exon	44399691	44402911	.	+	.	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	intron	44402912	44403123	.	+	.	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	CDS	44403124	44403151	0.42	+	1	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	exon	44403124	44403151	.	+	.	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
Phchi.S1	AUGUSTUS	stop_codon	44403152	44403154	.	+	0	transcript_id "Phchi.S1G707100.t1"; gene_id "Phchi.S1G707100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9586.t1 is derived from g6762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42799299	42801437	.	+	.	Phchi.S1G674500
Phchi.S1	AUGUSTUS	transcript	42799299	42801437	.	+	.	transcript_id "Phchi.S1G674500.t1"; gene_id "Phchi.S1G674500"
Phchi.S1	AUGUSTUS	start_codon	42799299	42799301	.	+	0	transcript_id "Phchi.S1G674500.t1"; gene_id "Phchi.S1G674500"
Phchi.S1	AUGUSTUS	CDS	42799299	42801437	0.9	+	0	transcript_id "Phchi.S1G674500.t1"; gene_id "Phchi.S1G674500"
Phchi.S1	AUGUSTUS	exon	42799299	42801437	.	+	.	transcript_id "Phchi.S1G674500.t1"; gene_id "Phchi.S1G674500"
Phchi.S1	AUGUSTUS	stop_codon	42801438	42801440	.	+	0	transcript_id "Phchi.S1G674500.t1"; gene_id "Phchi.S1G674500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4787.t1 is derived from g1957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12814137	12814754	.	-	.	Phchi.S1G194600
Phchi.S1	AUGUSTUS	transcript	12814137	12814754	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	stop_codon	12814134	12814136	.	-	0	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	CDS	12814137	12814178	1	-	0	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	exon	12814137	12814178	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	intron	12814179	12814267	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	CDS	12814268	12814369	1	-	0	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	exon	12814268	12814369	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	intron	12814370	12814464	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	CDS	12814465	12814622	1	-	2	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	exon	12814465	12814622	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	intron	12814623	12814717	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	CDS	12814718	12814754	0.99	-	0	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	exon	12814718	12814754	.	-	.	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
Phchi.S1	AUGUSTUS	start_codon	12814752	12814754	.	-	0	transcript_id "Phchi.S1G194600.t1"; gene_id "Phchi.S1G194600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9041.t1 is derived from g6216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39260691	39261017	.	-	.	Phchi.S1G620000
Phchi.S1	AUGUSTUS	transcript	39260691	39261017	.	-	.	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	stop_codon	39260688	39260690	.	-	0	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	CDS	39260691	39260807	1	-	0	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	exon	39260691	39260807	.	-	.	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	intron	39260808	39260888	.	-	.	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	CDS	39260889	39261017	0.99	-	0	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	exon	39260889	39261017	.	-	.	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
Phchi.S1	AUGUSTUS	start_codon	39261015	39261017	.	-	0	transcript_id "Phchi.S1G620000.t1"; gene_id "Phchi.S1G620000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4226.t1 is derived from g1395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9007567	9009003	.	+	.	Phchi.S1G138500
Phchi.S1	AUGUSTUS	transcript	9007567	9009003	.	+	.	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	start_codon	9007567	9007569	.	+	0	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	CDS	9007567	9007830	0.81	+	0	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	exon	9007567	9007830	.	+	.	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	intron	9007831	9007919	.	+	.	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	CDS	9007920	9008346	0.97	+	0	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	exon	9007920	9008346	.	+	.	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	intron	9008347	9008443	.	+	.	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	CDS	9008444	9009003	1	+	2	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	exon	9008444	9009003	.	+	.	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
Phchi.S1	AUGUSTUS	stop_codon	9009004	9009006	.	+	0	transcript_id "Phchi.S1G138500.t1"; gene_id "Phchi.S1G138500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9828.t1 is derived from g7004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43992670	43993175	.	-	.	Phchi.S1G698700
Phchi.S1	AUGUSTUS	transcript	43992670	43993175	.	-	.	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	stop_codon	43992667	43992669	.	-	0	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	CDS	43992670	43992925	0.99	-	1	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	exon	43992670	43992925	.	-	.	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	intron	43992926	43993128	.	-	.	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	CDS	43993129	43993175	1	-	0	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	exon	43993129	43993175	.	-	.	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
Phchi.S1	AUGUSTUS	start_codon	43993173	43993175	.	-	0	transcript_id "Phchi.S1G698700.t1"; gene_id "Phchi.S1G698700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2228.t1 is derived from g9148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5553145	5555961	.	+	.	Phchi.S5G083700
Phchi.S5	AUGUSTUS	transcript	5553145	5555961	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	start_codon	5553145	5553147	.	+	0	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5553145	5553225	0.38	+	0	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5553145	5553225	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	intron	5553226	5553314	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5553315	5553357	0.6	+	0	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5553315	5553357	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	intron	5553358	5553447	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5553448	5553885	0.98	+	2	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5553448	5553885	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	intron	5553886	5553992	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5553993	5554196	0.91	+	2	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5553993	5554196	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	intron	5554197	5554309	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5554310	5554372	1	+	2	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5554310	5554372	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	intron	5554373	5554529	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5554530	5555536	1	+	2	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5554530	5555536	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	intron	5555537	5555685	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	CDS	5555686	5555961	1	+	0	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	exon	5555686	5555961	.	+	.	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
Phchi.S5	AUGUSTUS	stop_codon	5555962	5555964	.	+	0	transcript_id "Phchi.S5G083700.t1"; gene_id "Phchi.S5G083700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10306.t1 is derived from g7482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47055848	47058368	.	+	.	Phchi.S1G746500
Phchi.S1	AUGUSTUS	transcript	47055848	47058368	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	start_codon	47055848	47055850	.	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47055848	47056098	0.5	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47055848	47056098	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47056099	47056263	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47056264	47056555	0.78	+	1	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47056264	47056555	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47056556	47056659	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47056660	47056839	0.63	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47056660	47056839	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47056840	47056942	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47056943	47057003	0.99	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47056943	47057003	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47057004	47057089	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47057090	47057280	0.57	+	2	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47057090	47057280	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47057281	47057387	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47057388	47057477	0.88	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47057388	47057477	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47057478	47057553	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47057554	47057632	1	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47057554	47057632	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47057633	47057713	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47057714	47057820	1	+	2	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47057714	47057820	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47057821	47057945	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47057946	47057992	1	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47057946	47057992	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47057993	47058089	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47058090	47058161	0.91	+	1	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47058090	47058161	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	intron	47058162	47058268	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	CDS	47058269	47058368	0.88	+	1	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	exon	47058269	47058368	.	+	.	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
Phchi.S1	AUGUSTUS	stop_codon	47058369	47058371	.	+	0	transcript_id "Phchi.S1G746500.t1"; gene_id "Phchi.S1G746500"
# This transcript jg7410.t2 is derived from g4582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7411.t1 is derived from g4583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29029280	29029657	.	+	.	Phchi.S1G457000
Phchi.S1	AUGUSTUS	transcript	29029280	29029657	.	+	.	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	start_codon	29029280	29029282	.	+	0	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	CDS	29029280	29029315	1	+	0	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	exon	29029280	29029315	.	+	.	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	intron	29029316	29029393	.	+	.	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	CDS	29029394	29029657	1	+	0	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	exon	29029394	29029657	.	+	.	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
Phchi.S1	AUGUSTUS	stop_codon	29029658	29029660	.	+	0	transcript_id "Phchi.S1G457000.t1"; gene_id "Phchi.S1G457000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5847.t1 is derived from g3017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19309943	19313330	.	+	.	Phchi.S1G300600
Phchi.S1	AUGUSTUS	transcript	19309943	19313330	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	start_codon	19309943	19309945	.	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19309943	19310298	0.43	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19309943	19310298	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19310299	19310818	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19310819	19310944	1	+	1	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19310819	19310944	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19310945	19311130	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19311131	19311236	0.99	+	1	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19311131	19311236	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19311237	19311506	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19311507	19311608	1	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19311507	19311608	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19311609	19311694	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19311695	19311828	0.95	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19311695	19311828	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19311829	19311952	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19311953	19312086	0.83	+	1	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19311953	19312086	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19312087	19312180	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19312181	19312332	1	+	2	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19312181	19312332	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19312333	19312410	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19312411	19312452	1	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19312411	19312452	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19312453	19312540	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19312541	19312596	1	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19312541	19312596	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19312597	19312730	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19312731	19312958	1	+	1	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19312731	19312958	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19312959	19313037	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19313038	19313149	1	+	1	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19313038	19313149	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	intron	19313150	19313225	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	CDS	19313226	19313330	1	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	exon	19313226	19313330	.	+	.	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
Phchi.S1	AUGUSTUS	stop_codon	19313331	19313333	.	+	0	transcript_id "Phchi.S1G300600.t1"; gene_id "Phchi.S1G300600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4743.t1 is derived from g1913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12584314	12587881	.	+	.	Phchi.S1G190200
Phchi.S1	AUGUSTUS	transcript	12584314	12587881	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	start_codon	12584314	12584316	.	+	0	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12584314	12584585	0.61	+	0	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12584314	12584585	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12584586	12584667	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12584668	12585204	0.89	+	1	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12584668	12585204	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12585205	12585371	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12585372	12586624	0.49	+	1	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12585372	12586624	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12586625	12586738	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12586739	12586870	0.38	+	2	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12586739	12586870	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12586871	12587144	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12587145	12587295	0.25	+	2	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12587145	12587295	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12587296	12587376	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12587377	12587453	0.99	+	1	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12587377	12587453	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12587454	12587620	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12587621	12587699	0.99	+	2	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12587621	12587699	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	intron	12587700	12587841	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	CDS	12587842	12587881	0.99	+	1	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	exon	12587842	12587881	.	+	.	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
Phchi.S1	AUGUSTUS	stop_codon	12587882	12587884	.	+	0	transcript_id "Phchi.S1G190200.t1"; gene_id "Phchi.S1G190200"
# This transcript jg14016.t2 is derived from g12483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14017.t1 is derived from g12484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10328165	10329244	.	+	.	Phchi.S3G133600
Phchi.S3	AUGUSTUS	transcript	10328165	10329244	.	+	.	transcript_id "Phchi.S3G133600.t1"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	start_codon	10328165	10328167	.	+	0	transcript_id "Phchi.S3G133600.t1"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	CDS	10328165	10329244	0.8	+	0	transcript_id "Phchi.S3G133600.t1"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	exon	10328165	10329244	.	+	.	transcript_id "Phchi.S3G133600.t1"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	stop_codon	10329245	10329247	.	+	0	transcript_id "Phchi.S3G133600.t1"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	transcript	10328441	10329244	.	+	.	transcript_id "Phchi.S3G133600.t2"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	start_codon	10328441	10328443	.	+	0	transcript_id "Phchi.S3G133600.t2"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	CDS	10328441	10329244	0.56	+	0	transcript_id "Phchi.S3G133600.t2"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	exon	10328441	10329244	.	+	.	transcript_id "Phchi.S3G133600.t2"; gene_id "Phchi.S3G133600"
Phchi.S3	AUGUSTUS	stop_codon	10329245	10329247	.	+	0	transcript_id "Phchi.S3G133600.t2"; gene_id "Phchi.S3G133600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7352.t1 is derived from g4524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28711395	28715186	.	-	.	Phchi.S1G451100
Phchi.S1	AUGUSTUS	transcript	28711395	28715186	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	stop_codon	28711392	28711394	.	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28711395	28711499	0.97	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28711395	28711499	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28711500	28711604	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28711605	28711679	0.97	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28711605	28711679	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28711680	28711748	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28711749	28711889	0.99	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28711749	28711889	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28711890	28712001	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28712002	28712053	0.99	-	1	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28712002	28712053	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28712054	28712141	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28712142	28712245	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28712142	28712245	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28712246	28712342	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28712343	28712453	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28712343	28712453	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28712454	28712543	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28712544	28712606	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28712544	28712606	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28712607	28712682	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28712683	28712739	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28712683	28712739	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28712740	28712850	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28712851	28712964	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28712851	28712964	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28712965	28713038	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28713039	28713143	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28713039	28713143	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28713144	28713331	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28713332	28713448	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28713332	28713448	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28713449	28713579	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28713580	28713690	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28713580	28713690	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28713691	28713781	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28713782	28713889	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28713782	28713889	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28713890	28713986	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28713987	28714082	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28713987	28714082	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28714083	28714188	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28714189	28714245	0.97	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28714189	28714245	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28714246	28714374	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28714375	28714449	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28714375	28714449	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28714450	28714672	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28714673	28714819	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28714673	28714819	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28714820	28714911	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28714912	28715088	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28714912	28715088	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	intron	28715089	28715183	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	CDS	28715184	28715186	1	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	exon	28715184	28715186	.	-	.	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
Phchi.S1	AUGUSTUS	start_codon	28715184	28715186	.	-	0	transcript_id "Phchi.S1G451100.t1"; gene_id "Phchi.S1G451100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13336.t1 is derived from g11802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6142666	6144129	.	-	.	Phchi.S3G065500
Phchi.S3	AUGUSTUS	transcript	6142666	6144129	.	-	.	transcript_id "Phchi.S3G065500.t1"; gene_id "Phchi.S3G065500"
Phchi.S3	AUGUSTUS	stop_codon	6142663	6142665	.	-	0	transcript_id "Phchi.S3G065500.t1"; gene_id "Phchi.S3G065500"
Phchi.S3	AUGUSTUS	CDS	6142666	6144129	1	-	0	transcript_id "Phchi.S3G065500.t1"; gene_id "Phchi.S3G065500"
Phchi.S3	AUGUSTUS	exon	6142666	6144129	.	-	.	transcript_id "Phchi.S3G065500.t1"; gene_id "Phchi.S3G065500"
Phchi.S3	AUGUSTUS	start_codon	6144127	6144129	.	-	0	transcript_id "Phchi.S3G065500.t1"; gene_id "Phchi.S3G065500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15465.t1 is derived from g13933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19333663	19334566	.	-	.	Phchi.S3G278400
Phchi.S3	AUGUSTUS	transcript	19333663	19334566	.	-	.	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	stop_codon	19333660	19333662	.	-	0	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	CDS	19333663	19333743	1	-	0	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	exon	19333663	19333743	.	-	.	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	intron	19333744	19333854	.	-	.	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	CDS	19333855	19333981	1	-	1	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	exon	19333855	19333981	.	-	.	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	intron	19333982	19334120	.	-	.	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	CDS	19334121	19334566	0.31	-	0	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	exon	19334121	19334566	.	-	.	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
Phchi.S3	AUGUSTUS	start_codon	19334564	19334566	.	-	0	transcript_id "Phchi.S3G278400.t1"; gene_id "Phchi.S3G278400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1945.t1 is derived from g8865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3941561	3943245	.	+	.	Phchi.S5G055400
Phchi.S5	AUGUSTUS	transcript	3941561	3943245	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	start_codon	3941561	3941563	.	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3941561	3941596	0.91	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3941561	3941596	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	intron	3941597	3941677	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3941678	3941782	0.91	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3941678	3941782	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	intron	3941783	3941923	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3941924	3942065	1	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3941924	3942065	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	intron	3942066	3942136	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3942137	3942228	1	+	2	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3942137	3942228	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	intron	3942229	3942357	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3942358	3942520	1	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3942358	3942520	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	intron	3942521	3942632	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3942633	3942685	1	+	2	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3942633	3942685	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	intron	3942686	3942777	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	CDS	3942778	3943245	1	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	exon	3942778	3943245	.	+	.	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
Phchi.S5	AUGUSTUS	stop_codon	3943246	3943248	.	+	0	transcript_id "Phchi.S5G055400.t1"; gene_id "Phchi.S5G055400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10638.t1 is derived from g14688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1367709	1371212	.	+	.	Phchi.S4G022000
Phchi.S4	AUGUSTUS	transcript	1367709	1371212	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	start_codon	1367709	1367711	.	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1367709	1367920	0.3	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1367709	1367920	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1367921	1368169	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1368170	1368883	0.96	+	1	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1368170	1368883	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1368884	1369038	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1369039	1369126	1	+	1	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1369039	1369126	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1369127	1369251	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1369252	1369314	1	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1369252	1369314	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1369315	1369430	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1369431	1369459	0.89	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1369431	1369459	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1369460	1369572	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1369573	1369590	0.91	+	1	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1369573	1369590	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1369591	1369677	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1369678	1369753	1	+	1	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1369678	1369753	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1369754	1369842	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1369843	1369902	1	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1369843	1369902	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1369903	1370040	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1370041	1370157	1	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1370041	1370157	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1370158	1370294	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1370295	1370549	1	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1370295	1370549	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1370550	1370627	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1370628	1370728	1	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1370628	1370728	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1370729	1370819	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1370820	1370905	0.38	+	1	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1370820	1370905	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	intron	1370906	1370979	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	CDS	1370980	1371212	0.4	+	2	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	exon	1370980	1371212	.	+	.	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
Phchi.S4	AUGUSTUS	stop_codon	1371213	1371215	.	+	0	transcript_id "Phchi.S4G022000.t1"; gene_id "Phchi.S4G022000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11658.t1 is derived from g15709.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7546081	7553054	.	+	.	Phchi.S4G124000
Phchi.S4	AUGUSTUS	transcript	7546081	7553054	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	start_codon	7546081	7546083	.	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7546081	7546919	0.98	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7546081	7546919	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7546920	7547110	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7547111	7547128	1	+	1	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7547111	7547128	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7547129	7547312	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7547313	7548253	0.99	+	1	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7547313	7548253	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548254	7548432	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548433	7548575	1	+	2	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548433	7548575	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548576	7548673	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548674	7548721	1	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548674	7548721	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548722	7548816	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548817	7548864	1	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548817	7548864	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548865	7548965	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548966	7549079	1	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548966	7549079	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7549080	7549261	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7549262	7549462	1	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7549262	7549462	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7549463	7549607	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7549608	7549693	1	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7549608	7549693	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7549694	7549776	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7549777	7551116	0.97	+	1	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7549777	7551116	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7551117	7551205	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7551206	7551460	0.87	+	2	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7551206	7551460	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7551461	7551877	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7551878	7552042	0.95	+	2	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7551878	7552042	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7552043	7552152	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7552153	7552548	0.55	+	2	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7552153	7552548	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7552549	7552672	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7552673	7552743	0.77	+	2	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7552673	7552743	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7552744	7553003	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7553004	7553054	1	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7553004	7553054	.	+	.	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	stop_codon	7553055	7553057	.	+	0	transcript_id "Phchi.S4G124000.t1"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	transcript	7546081	7553054	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	start_codon	7546081	7546083	.	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7546081	7546919	0.96	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7546081	7546919	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7546920	7547312	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7547313	7548325	0.84	+	1	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7547313	7548325	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548326	7548432	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548433	7548575	0.84	+	2	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548433	7548575	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548576	7548673	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548674	7548721	1	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548674	7548721	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548722	7548816	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548817	7548864	1	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548817	7548864	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7548865	7548965	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7548966	7549079	1	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7548966	7549079	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7549080	7549261	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7549262	7549462	1	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7549262	7549462	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7549463	7549607	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7549608	7549693	1	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7549608	7549693	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7549694	7549776	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7549777	7551116	0.98	+	1	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7549777	7551116	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7551117	7551205	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7551206	7551460	0.83	+	2	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7551206	7551460	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7551461	7551877	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7551878	7552042	0.86	+	2	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7551878	7552042	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7552043	7552152	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7552153	7552548	0.5	+	2	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7552153	7552548	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7552549	7552672	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7552673	7552743	0.77	+	2	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7552673	7552743	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	intron	7552744	7553003	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	CDS	7553004	7553054	1	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	exon	7553004	7553054	.	+	.	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
Phchi.S4	AUGUSTUS	stop_codon	7553055	7553057	.	+	0	transcript_id "Phchi.S4G124000.t2"; gene_id "Phchi.S4G124000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7215.t1 is derived from g4387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27669734	27671196	.	+	.	Phchi.S1G437400
Phchi.S1	AUGUSTUS	transcript	27669734	27671196	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	start_codon	27669734	27669736	.	+	0	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27669734	27669848	0.98	+	0	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27669734	27669848	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	intron	27669849	27669926	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27669927	27669998	0.84	+	2	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27669927	27669998	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	intron	27669999	27670080	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27670081	27670170	0.97	+	2	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27670081	27670170	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	intron	27670171	27670247	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27670248	27670408	1	+	2	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27670248	27670408	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	intron	27670409	27670552	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27670553	27670715	1	+	0	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27670553	27670715	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	intron	27670716	27670795	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27670796	27670996	1	+	2	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27670796	27670996	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	intron	27670997	27671083	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	CDS	27671084	27671196	1	+	2	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	exon	27671084	27671196	.	+	.	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
Phchi.S1	AUGUSTUS	stop_codon	27671197	27671199	.	+	0	transcript_id "Phchi.S1G437400.t1"; gene_id "Phchi.S1G437400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13668.t1 is derived from g12135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8073754	8075394	.	+	.	Phchi.S3G098700
Phchi.S3	AUGUSTUS	transcript	8073754	8075394	.	+	.	transcript_id "Phchi.S3G098700.t1"; gene_id "Phchi.S3G098700"
Phchi.S3	AUGUSTUS	start_codon	8073754	8073756	.	+	0	transcript_id "Phchi.S3G098700.t1"; gene_id "Phchi.S3G098700"
Phchi.S3	AUGUSTUS	CDS	8073754	8075394	0.66	+	0	transcript_id "Phchi.S3G098700.t1"; gene_id "Phchi.S3G098700"
Phchi.S3	AUGUSTUS	exon	8073754	8075394	.	+	.	transcript_id "Phchi.S3G098700.t1"; gene_id "Phchi.S3G098700"
Phchi.S3	AUGUSTUS	stop_codon	8075395	8075397	.	+	0	transcript_id "Phchi.S3G098700.t1"; gene_id "Phchi.S3G098700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15101.t1 is derived from g13569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17070110	17071216	.	-	.	Phchi.S3G242000
Phchi.S3	AUGUSTUS	transcript	17070110	17071216	.	-	.	transcript_id "Phchi.S3G242000.t1"; gene_id "Phchi.S3G242000"
Phchi.S3	AUGUSTUS	stop_codon	17070107	17070109	.	-	0	transcript_id "Phchi.S3G242000.t1"; gene_id "Phchi.S3G242000"
Phchi.S3	AUGUSTUS	CDS	17070110	17071216	0.98	-	0	transcript_id "Phchi.S3G242000.t1"; gene_id "Phchi.S3G242000"
Phchi.S3	AUGUSTUS	exon	17070110	17071216	.	-	.	transcript_id "Phchi.S3G242000.t1"; gene_id "Phchi.S3G242000"
Phchi.S3	AUGUSTUS	start_codon	17071214	17071216	.	-	0	transcript_id "Phchi.S3G242000.t1"; gene_id "Phchi.S3G242000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13780.t1 is derived from g12247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8870807	8871900	.	-	.	Phchi.S3G109900
Phchi.S3	AUGUSTUS	transcript	8870807	8871900	.	-	.	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	stop_codon	8870804	8870806	.	-	0	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	CDS	8870807	8871103	0.99	-	0	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	exon	8870807	8871103	.	-	.	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	intron	8871104	8871196	.	-	.	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	CDS	8871197	8871498	0.99	-	2	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	exon	8871197	8871498	.	-	.	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	intron	8871499	8871599	.	-	.	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	CDS	8871600	8871900	0.85	-	0	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	exon	8871600	8871900	.	-	.	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
Phchi.S3	AUGUSTUS	start_codon	8871898	8871900	.	-	0	transcript_id "Phchi.S3G109900.t1"; gene_id "Phchi.S3G109900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15089.t1 is derived from g13557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16966286	16968229	.	+	.	Phchi.S3G240800
Phchi.S3	AUGUSTUS	transcript	16966286	16968229	.	+	.	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	start_codon	16966286	16966288	.	+	0	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	CDS	16966286	16966610	1	+	0	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	exon	16966286	16966610	.	+	.	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	intron	16966611	16966708	.	+	.	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	CDS	16966709	16966950	1	+	2	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	exon	16966709	16966950	.	+	.	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	intron	16966951	16967098	.	+	.	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	CDS	16967099	16968229	0.88	+	0	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	exon	16967099	16968229	.	+	.	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
Phchi.S3	AUGUSTUS	stop_codon	16968230	16968232	.	+	0	transcript_id "Phchi.S3G240800.t1"; gene_id "Phchi.S3G240800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14649.t1 is derived from g13117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13943041	13944422	.	-	.	Phchi.S3G196800
Phchi.S3	AUGUSTUS	transcript	13943041	13944422	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	stop_codon	13943038	13943040	.	-	0	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13943041	13943175	1	-	0	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13943041	13943175	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13943176	13943259	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13943260	13943342	1	-	2	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13943260	13943342	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13943343	13943443	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13943444	13943539	0.99	-	2	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13943444	13943539	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13943540	13943634	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13943635	13943728	1	-	0	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13943635	13943728	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13943729	13943810	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13943811	13943934	1	-	1	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13943811	13943934	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13943935	13944054	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13944055	13944076	1	-	2	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13944055	13944076	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13944077	13944192	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13944193	13944296	1	-	1	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13944193	13944296	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	intron	13944297	13944396	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	CDS	13944397	13944422	0.99	-	0	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	exon	13944397	13944422	.	-	.	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
Phchi.S3	AUGUSTUS	start_codon	13944420	13944422	.	-	0	transcript_id "Phchi.S3G196800.t1"; gene_id "Phchi.S3G196800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6642.t1 is derived from g3814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24220876	24221466	.	+	.	Phchi.S1G380100
Phchi.S1	AUGUSTUS	transcript	24220876	24221466	.	+	.	transcript_id "Phchi.S1G380100.t1"; gene_id "Phchi.S1G380100"
Phchi.S1	AUGUSTUS	start_codon	24220876	24220878	.	+	0	transcript_id "Phchi.S1G380100.t1"; gene_id "Phchi.S1G380100"
Phchi.S1	AUGUSTUS	CDS	24220876	24221466	1	+	0	transcript_id "Phchi.S1G380100.t1"; gene_id "Phchi.S1G380100"
Phchi.S1	AUGUSTUS	exon	24220876	24221466	.	+	.	transcript_id "Phchi.S1G380100.t1"; gene_id "Phchi.S1G380100"
Phchi.S1	AUGUSTUS	stop_codon	24221467	24221469	.	+	0	transcript_id "Phchi.S1G380100.t1"; gene_id "Phchi.S1G380100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8440.t1 is derived from g5615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35944350	35946675	.	-	.	Phchi.S1G559900
Phchi.S1	AUGUSTUS	transcript	35944350	35946675	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	stop_codon	35944347	35944349	.	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35944350	35944433	1	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35944350	35944433	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35944434	35944533	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35944534	35944716	1	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35944534	35944716	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35944717	35944834	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35944835	35944896	1	-	2	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35944835	35944896	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35944897	35945027	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35945028	35945139	1	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35945028	35945139	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35945140	35945343	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35945344	35945406	1	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35945344	35945406	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35945407	35945539	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35945540	35945644	1	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35945540	35945644	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35945645	35945728	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35945729	35945929	1	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35945729	35945929	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35945930	35946018	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35946019	35946134	1	-	2	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35946019	35946134	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	intron	35946135	35946425	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	CDS	35946426	35946675	0.92	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	exon	35946426	35946675	.	-	.	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
Phchi.S1	AUGUSTUS	start_codon	35946673	35946675	.	-	0	transcript_id "Phchi.S1G559900.t1"; gene_id "Phchi.S1G559900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13939.t1 is derived from g12406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9810656	9812139	.	-	.	Phchi.S3G125800
Phchi.S3	AUGUSTUS	transcript	9810656	9812139	.	-	.	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	stop_codon	9810653	9810655	.	-	0	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	CDS	9810656	9811024	0.8	-	0	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	exon	9810656	9811024	.	-	.	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	intron	9811025	9811096	.	-	.	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	CDS	9811097	9811402	1	-	0	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	exon	9811097	9811402	.	-	.	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	intron	9811403	9811491	.	-	.	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	CDS	9811492	9812139	1	-	0	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	exon	9811492	9812139	.	-	.	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
Phchi.S3	AUGUSTUS	start_codon	9812137	9812139	.	-	0	transcript_id "Phchi.S3G125800.t1"; gene_id "Phchi.S3G125800"
# This transcript jg8191.t2 is derived from g5366.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8191.t3 is derived from g5366.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8192.t1 is derived from g5367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34357667	34359383	.	+	.	Phchi.S1G535100
Phchi.S1	AUGUSTUS	transcript	34357667	34359383	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	start_codon	34357667	34357669	.	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34357667	34357705	1	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34357667	34357705	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34357706	34357965	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34357966	34358045	0.86	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34357966	34358045	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34358046	34358152	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34358153	34358275	0.86	+	1	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34358153	34358275	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34358276	34358407	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34358408	34358492	1	+	1	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34358408	34358492	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34358493	34358610	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34358611	34358743	1	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34358611	34358743	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34358744	34358833	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34358834	34358928	1	+	2	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34358834	34358928	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34358929	34359016	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34359017	34359095	1	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34359017	34359095	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34359096	34359186	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34359187	34359269	1	+	2	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34359187	34359269	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	intron	34359270	34359341	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	CDS	34359342	34359383	1	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	exon	34359342	34359383	.	+	.	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
Phchi.S1	AUGUSTUS	stop_codon	34359384	34359386	.	+	0	transcript_id "Phchi.S1G535100.t1"; gene_id "Phchi.S1G535100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10604.t1 is derived from g14654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1159998	1160777	.	+	.	Phchi.S4G018600
Phchi.S4	AUGUSTUS	transcript	1159998	1160777	.	+	.	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	start_codon	1159998	1160000	.	+	0	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	CDS	1159998	1160290	0.39	+	0	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	exon	1159998	1160290	.	+	.	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	intron	1160291	1160380	.	+	.	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	CDS	1160381	1160777	1	+	1	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	exon	1160381	1160777	.	+	.	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
Phchi.S4	AUGUSTUS	stop_codon	1160778	1160780	.	+	0	transcript_id "Phchi.S4G018600.t1"; gene_id "Phchi.S4G018600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9656.t1 is derived from g6832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43096453	43096656	.	-	.	Phchi.S1G681500
Phchi.S1	AUGUSTUS	transcript	43096453	43096656	.	-	.	transcript_id "Phchi.S1G681500.t1"; gene_id "Phchi.S1G681500"
Phchi.S1	AUGUSTUS	stop_codon	43096450	43096452	.	-	0	transcript_id "Phchi.S1G681500.t1"; gene_id "Phchi.S1G681500"
Phchi.S1	AUGUSTUS	CDS	43096453	43096656	0.6	-	0	transcript_id "Phchi.S1G681500.t1"; gene_id "Phchi.S1G681500"
Phchi.S1	AUGUSTUS	exon	43096453	43096656	.	-	.	transcript_id "Phchi.S1G681500.t1"; gene_id "Phchi.S1G681500"
Phchi.S1	AUGUSTUS	start_codon	43096654	43096656	.	-	0	transcript_id "Phchi.S1G681500.t1"; gene_id "Phchi.S1G681500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6017.t1 is derived from g3188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20459202	20459987	.	+	.	Phchi.S1G317600
Phchi.S1	AUGUSTUS	transcript	20459238	20459987	.	+	.	transcript_id "Phchi.S1G317600.t1"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	start_codon	20459238	20459240	.	+	0	transcript_id "Phchi.S1G317600.t1"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	CDS	20459238	20459987	0.88	+	0	transcript_id "Phchi.S1G317600.t1"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	exon	20459238	20459987	.	+	.	transcript_id "Phchi.S1G317600.t1"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	stop_codon	20459988	20459990	.	+	0	transcript_id "Phchi.S1G317600.t1"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	transcript	20459202	20459987	.	+	.	transcript_id "Phchi.S1G317600.t2"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	start_codon	20459202	20459204	.	+	0	transcript_id "Phchi.S1G317600.t2"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	CDS	20459202	20459987	0.74	+	0	transcript_id "Phchi.S1G317600.t2"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	exon	20459202	20459987	.	+	.	transcript_id "Phchi.S1G317600.t2"; gene_id "Phchi.S1G317600"
Phchi.S1	AUGUSTUS	stop_codon	20459988	20459990	.	+	0	transcript_id "Phchi.S1G317600.t2"; gene_id "Phchi.S1G317600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16007.t1 is derived from g14431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	102967	103604	.	+	.	Phchi.C10G000500
Phchi.C10	AUGUSTUS	transcript	102967	103604	.	+	.	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	start_codon	102967	102969	.	+	0	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	CDS	102967	103089	0.44	+	0	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	exon	102967	103089	.	+	.	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	intron	103090	103271	.	+	.	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	CDS	103272	103604	0.72	+	0	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	exon	103272	103604	.	+	.	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
Phchi.C10	AUGUSTUS	stop_codon	103605	103607	.	+	0	transcript_id "Phchi.C10G000500.t1"; gene_id "Phchi.C10G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg52.t1 is derived from g9834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	123698	124397	.	-	.	Phchi.S6G001100
Phchi.S6	AUGUSTUS	transcript	123698	124397	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	stop_codon	123695	123697	.	-	0	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	CDS	123698	123737	0.87	-	1	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	exon	123698	123737	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	intron	123738	124063	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	CDS	124064	124091	0.75	-	2	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	exon	124064	124091	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	intron	124092	124180	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	CDS	124181	124236	0.75	-	1	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	exon	124181	124236	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	intron	124237	124314	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	CDS	124315	124397	0.39	-	0	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	exon	124315	124397	.	-	.	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
Phchi.S6	AUGUSTUS	start_codon	124395	124397	.	-	0	transcript_id "Phchi.S6G001100.t1"; gene_id "Phchi.S6G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8217.t1 is derived from g5392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34461655	34464115	.	-	.	Phchi.S1G537600
Phchi.S1	AUGUSTUS	transcript	34461655	34464115	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	stop_codon	34461652	34461654	.	-	0	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	CDS	34461655	34461848	1	-	2	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	exon	34461655	34461848	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	intron	34461849	34461946	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	CDS	34461947	34463066	1	-	0	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	exon	34461947	34463066	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	intron	34463067	34463171	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	CDS	34463172	34463452	0.99	-	2	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	exon	34463172	34463452	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	intron	34463453	34463547	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	CDS	34463548	34463755	1	-	0	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	exon	34463548	34463755	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	intron	34463756	34463880	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	CDS	34463881	34463954	0.99	-	2	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	exon	34463881	34463954	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	intron	34463955	34464039	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	CDS	34464040	34464115	0.96	-	0	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	exon	34464040	34464115	.	-	.	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
Phchi.S1	AUGUSTUS	start_codon	34464113	34464115	.	-	0	transcript_id "Phchi.S1G537600.t1"; gene_id "Phchi.S1G537600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10180.t1 is derived from g7356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46178098	46178406	.	-	.	Phchi.S1G733900
Phchi.S1	AUGUSTUS	transcript	46178098	46178406	.	-	.	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	stop_codon	46178095	46178097	.	-	0	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	CDS	46178098	46178267	0.97	-	2	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	exon	46178098	46178267	.	-	.	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	intron	46178268	46178360	.	-	.	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	CDS	46178361	46178406	0.96	-	0	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	exon	46178361	46178406	.	-	.	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
Phchi.S1	AUGUSTUS	start_codon	46178404	46178406	.	-	0	transcript_id "Phchi.S1G733900.t1"; gene_id "Phchi.S1G733900"
# This transcript jg357.t1 is derived from g10138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2621301	2622229	.	-	.	Phchi.S6G031500
Phchi.S6	AUGUSTUS	transcript	2621301	2622229	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	stop_codon	2621298	2621300	.	-	0	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621301	2621405	0.54	-	0	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621301	2621405	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2621406	2621503	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621504	2621590	1	-	0	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621504	2621590	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2621591	2621729	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621730	2621849	0.83	-	0	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621730	2621849	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2621850	2621944	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621945	2622038	0.62	-	1	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621945	2622038	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2622039	2622191	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2622192	2622229	0.84	-	0	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2622192	2622229	.	-	.	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	start_codon	2622227	2622229	.	-	0	transcript_id "Phchi.S6G031500.t1"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	transcript	2621301	2622070	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	stop_codon	2621298	2621300	.	-	0	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621301	2621405	0.4	-	0	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621301	2621405	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2621406	2621503	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621504	2621590	0.99	-	0	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621504	2621590	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2621591	2621729	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621730	2621849	0.75	-	0	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621730	2621849	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	intron	2621850	2621944	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	CDS	2621945	2622070	0.45	-	0	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	exon	2621945	2622070	.	-	.	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
Phchi.S6	AUGUSTUS	start_codon	2622068	2622070	.	-	0	transcript_id "Phchi.S6G031500.t2"; gene_id "Phchi.S6G031500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14765.t1 is derived from g13233.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14590448	14592145	.	-	.	Phchi.S3G208400
Phchi.S3	AUGUSTUS	transcript	14590448	14592145	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	stop_codon	14590445	14590447	.	-	0	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14590448	14590593	0.66	-	2	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14590448	14590593	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14590594	14590957	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14590958	14591025	0.97	-	1	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14590958	14591025	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591026	14591197	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591198	14591301	1	-	0	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591198	14591301	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591302	14591375	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591376	14591474	1	-	0	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591376	14591474	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591475	14591574	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591575	14591629	1	-	1	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591575	14591629	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591630	14591721	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591722	14591970	0.99	-	1	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591722	14591970	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591971	14592053	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14592054	14592145	0.96	-	0	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14592054	14592145	.	-	.	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	start_codon	14592143	14592145	.	-	0	transcript_id "Phchi.S3G208400.t1"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	transcript	14591241	14592145	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	stop_codon	14591238	14591240	.	-	0	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591241	14591288	0.69	-	0	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591241	14591288	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591289	14591375	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591376	14591474	0.99	-	0	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591376	14591474	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591475	14591574	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591575	14591629	1	-	1	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591575	14591629	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591630	14591721	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14591722	14591970	0.99	-	1	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14591722	14591970	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	intron	14591971	14592053	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	CDS	14592054	14592145	0.97	-	0	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	exon	14592054	14592145	.	-	.	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
Phchi.S3	AUGUSTUS	start_codon	14592143	14592145	.	-	0	transcript_id "Phchi.S3G208400.t2"; gene_id "Phchi.S3G208400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10560.t1 is derived from g14610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	980875	981852	.	+	.	Phchi.S4G014200
Phchi.S4	AUGUSTUS	transcript	980875	981852	.	+	.	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	start_codon	980875	980877	.	+	0	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	CDS	980875	981060	0.97	+	0	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	exon	980875	981060	.	+	.	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	intron	981061	981223	.	+	.	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	CDS	981224	981293	1	+	0	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	exon	981224	981293	.	+	.	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	intron	981294	981490	.	+	.	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	CDS	981491	981852	1	+	2	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	exon	981491	981852	.	+	.	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
Phchi.S4	AUGUSTUS	stop_codon	981853	981855	.	+	0	transcript_id "Phchi.S4G014200.t1"; gene_id "Phchi.S4G014200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2976.t1 is derived from g145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	932333	934903	.	-	.	Phchi.S1G013500
Phchi.S1	AUGUSTUS	transcript	932333	934903	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	stop_codon	932330	932332	.	-	0	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	CDS	932333	932491	0.87	-	0	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	exon	932333	932491	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	intron	932492	932644	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	CDS	932645	932926	0.86	-	0	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	exon	932645	932926	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	intron	932927	933097	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	CDS	933098	933528	0.96	-	2	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	exon	933098	933528	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	intron	933529	933675	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	CDS	933676	933771	1	-	2	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	exon	933676	933771	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	intron	933772	933933	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	CDS	933934	934903	0.64	-	0	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	exon	933934	934903	.	-	.	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
Phchi.S1	AUGUSTUS	start_codon	934901	934903	.	-	0	transcript_id "Phchi.S1G013500.t1"; gene_id "Phchi.S1G013500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12060.t1 is derived from g7735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1198922	1203254	.	-	.	Phchi.S2G014000
Phchi.S2	AUGUSTUS	transcript	1198922	1203254	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	stop_codon	1198919	1198921	.	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1198922	1198981	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1198922	1198981	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1198982	1199279	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1199280	1199348	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1199280	1199348	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1199349	1199516	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1199517	1199599	1	-	2	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1199517	1199599	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1199600	1199688	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1199689	1199764	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1199689	1199764	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1199765	1199850	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1199851	1199920	1	-	1	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1199851	1199920	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1199921	1200163	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1200164	1200213	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1200164	1200213	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1200214	1200294	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1200295	1200331	1	-	1	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1200295	1200331	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1200332	1200405	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1200406	1200467	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1200406	1200467	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1200468	1200591	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1200592	1200630	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1200592	1200630	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1200631	1200779	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1200780	1200957	1	-	1	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1200780	1200957	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1200958	1201050	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1201051	1201111	1	-	2	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1201051	1201111	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1201112	1201215	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1201216	1201406	1	-	1	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1201216	1201406	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1201407	1201542	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1201543	1201604	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1201543	1201604	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1201605	1201704	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1201705	1201791	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1201705	1201791	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1201792	1201865	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1201866	1201950	1	-	1	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1201866	1201950	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1201951	1202614	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1202615	1202700	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1202615	1202700	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1202701	1202942	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1202943	1203050	1	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1202943	1203050	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	intron	1203051	1203128	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	CDS	1203129	1203254	0.9	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	exon	1203129	1203254	.	-	.	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
Phchi.S2	AUGUSTUS	start_codon	1203252	1203254	.	-	0	transcript_id "Phchi.S2G014000.t1"; gene_id "Phchi.S2G014000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12861.t1 is derived from g11326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2808195	2808773	.	+	.	Phchi.S3G018000
Phchi.S3	AUGUSTUS	transcript	2808195	2808773	.	+	.	transcript_id "Phchi.S3G018000.t1"; gene_id "Phchi.S3G018000"
Phchi.S3	AUGUSTUS	start_codon	2808195	2808197	.	+	0	transcript_id "Phchi.S3G018000.t1"; gene_id "Phchi.S3G018000"
Phchi.S3	AUGUSTUS	CDS	2808195	2808773	0.72	+	0	transcript_id "Phchi.S3G018000.t1"; gene_id "Phchi.S3G018000"
Phchi.S3	AUGUSTUS	exon	2808195	2808773	.	+	.	transcript_id "Phchi.S3G018000.t1"; gene_id "Phchi.S3G018000"
Phchi.S3	AUGUSTUS	stop_codon	2808774	2808776	.	+	0	transcript_id "Phchi.S3G018000.t1"; gene_id "Phchi.S3G018000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5946.t1 is derived from g3117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19966926	19970879	.	+	.	Phchi.S1G310500
Phchi.S1	AUGUSTUS	transcript	19966926	19970879	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	start_codon	19966926	19966928	.	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19966926	19966979	0.98	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19966926	19966979	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19966980	19967084	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19967085	19967924	0.98	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19967085	19967924	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19967925	19968092	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968093	19968162	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968093	19968162	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968163	19968245	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968246	19968427	1	+	2	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968246	19968427	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968428	19968642	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968643	19968714	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968643	19968714	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968715	19968822	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968823	19968864	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968823	19968864	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968865	19968959	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968960	19969022	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968960	19969022	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19969023	19969143	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19969144	19969186	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19969144	19969186	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19969187	19969265	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19969266	19970068	1	+	2	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19969266	19970068	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19970069	19970152	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19970153	19970248	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19970153	19970248	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19970249	19970336	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19970337	19970879	1	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19970337	19970879	.	+	.	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	stop_codon	19970880	19970882	.	+	0	transcript_id "Phchi.S1G310500.t1"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	transcript	19966926	19970879	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	start_codon	19966926	19966928	.	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19966926	19966979	0.99	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19966926	19966979	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19966980	19967084	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19967085	19967924	0.99	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19967085	19967924	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19967925	19968092	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968093	19968162	1	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968093	19968162	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968163	19968245	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968246	19968434	0.8	+	2	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968246	19968434	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968435	19968537	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968538	19968554	0.81	+	2	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968538	19968554	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968555	19968642	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968643	19968714	0.89	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968643	19968714	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968715	19968822	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968823	19968864	1	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968823	19968864	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19968865	19968959	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19968960	19969022	1	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19968960	19969022	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19969023	19969143	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19969144	19969186	1	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19969144	19969186	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19969187	19969265	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19969266	19970068	1	+	2	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19969266	19970068	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19970069	19970152	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19970153	19970248	1	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19970153	19970248	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	intron	19970249	19970336	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	CDS	19970337	19970879	0.97	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	exon	19970337	19970879	.	+	.	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
Phchi.S1	AUGUSTUS	stop_codon	19970880	19970882	.	+	0	transcript_id "Phchi.S1G310500.t2"; gene_id "Phchi.S1G310500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10702.t1 is derived from g14752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1673894	1675807	.	-	.	Phchi.S4G028400
Phchi.S4	AUGUSTUS	transcript	1673894	1675807	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	stop_codon	1673891	1673893	.	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1673894	1674079	1	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1673894	1674079	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	intron	1674080	1674210	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1674211	1674326	1	-	2	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1674211	1674326	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	intron	1674327	1674449	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1674450	1674588	1	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1674450	1674588	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	intron	1674589	1674721	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1674722	1674832	1	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1674722	1674832	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	intron	1674833	1674993	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1674994	1675144	1	-	1	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1674994	1675144	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	intron	1675145	1675286	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1675287	1675411	1	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1675287	1675411	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	intron	1675412	1675543	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	CDS	1675544	1675807	0.99	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	exon	1675544	1675807	.	-	.	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
Phchi.S4	AUGUSTUS	start_codon	1675805	1675807	.	-	0	transcript_id "Phchi.S4G028400.t1"; gene_id "Phchi.S4G028400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3893.t1 is derived from g1062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6275043	6276899	.	-	.	Phchi.S1G105200
Phchi.S1	AUGUSTUS	transcript	6275043	6276899	.	-	.	transcript_id "Phchi.S1G105200.t1"; gene_id "Phchi.S1G105200"
Phchi.S1	AUGUSTUS	stop_codon	6275040	6275042	.	-	0	transcript_id "Phchi.S1G105200.t1"; gene_id "Phchi.S1G105200"
Phchi.S1	AUGUSTUS	CDS	6275043	6276899	0.83	-	0	transcript_id "Phchi.S1G105200.t1"; gene_id "Phchi.S1G105200"
Phchi.S1	AUGUSTUS	exon	6275043	6276899	.	-	.	transcript_id "Phchi.S1G105200.t1"; gene_id "Phchi.S1G105200"
Phchi.S1	AUGUSTUS	start_codon	6276897	6276899	.	-	0	transcript_id "Phchi.S1G105200.t1"; gene_id "Phchi.S1G105200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg211.t1 is derived from g9993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1199578	1200864	.	+	.	Phchi.S6G017000
Phchi.S6	AUGUSTUS	transcript	1199578	1200864	.	+	.	transcript_id "Phchi.S6G017000.t1"; gene_id "Phchi.S6G017000"
Phchi.S6	AUGUSTUS	start_codon	1199578	1199580	.	+	0	transcript_id "Phchi.S6G017000.t1"; gene_id "Phchi.S6G017000"
Phchi.S6	AUGUSTUS	CDS	1199578	1200864	0.45	+	0	transcript_id "Phchi.S6G017000.t1"; gene_id "Phchi.S6G017000"
Phchi.S6	AUGUSTUS	exon	1199578	1200864	.	+	.	transcript_id "Phchi.S6G017000.t1"; gene_id "Phchi.S6G017000"
Phchi.S6	AUGUSTUS	stop_codon	1200865	1200867	.	+	0	transcript_id "Phchi.S6G017000.t1"; gene_id "Phchi.S6G017000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7264.t1 is derived from g4436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27916451	27919960	.	-	.	Phchi.S1G442300
Phchi.S1	AUGUSTUS	transcript	27916451	27919960	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	stop_codon	27916448	27916450	.	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27916451	27916506	0.78	-	2	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27916451	27916506	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27916507	27916628	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27916629	27917499	0.54	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27916629	27917499	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27917500	27917570	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27917571	27917712	0.67	-	1	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27917571	27917712	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27917713	27917809	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27917810	27917940	0.5	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27917810	27917940	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27917941	27918052	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27918053	27918103	0.69	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27918053	27918103	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27918104	27918225	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27918226	27918378	1	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27918226	27918378	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27918379	27918461	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27918462	27918591	1	-	1	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27918462	27918591	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27918592	27918803	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27918804	27919171	1	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27918804	27919171	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27919172	27919253	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27919254	27919358	1	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27919254	27919358	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27919359	27919456	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27919457	27919503	1	-	2	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27919457	27919503	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	intron	27919504	27919812	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	CDS	27919813	27919960	0.99	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	exon	27919813	27919960	.	-	.	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
Phchi.S1	AUGUSTUS	start_codon	27919958	27919960	.	-	0	transcript_id "Phchi.S1G442300.t1"; gene_id "Phchi.S1G442300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6244.t1 is derived from g3416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21831421	21831795	.	-	.	Phchi.S1G340300
Phchi.S1	AUGUSTUS	transcript	21831421	21831795	.	-	.	transcript_id "Phchi.S1G340300.t1"; gene_id "Phchi.S1G340300"
Phchi.S1	AUGUSTUS	stop_codon	21831418	21831420	.	-	0	transcript_id "Phchi.S1G340300.t1"; gene_id "Phchi.S1G340300"
Phchi.S1	AUGUSTUS	CDS	21831421	21831795	0.76	-	0	transcript_id "Phchi.S1G340300.t1"; gene_id "Phchi.S1G340300"
Phchi.S1	AUGUSTUS	exon	21831421	21831795	.	-	.	transcript_id "Phchi.S1G340300.t1"; gene_id "Phchi.S1G340300"
Phchi.S1	AUGUSTUS	start_codon	21831793	21831795	.	-	0	transcript_id "Phchi.S1G340300.t1"; gene_id "Phchi.S1G340300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14918.t1 is derived from g13386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15490033	15493244	.	-	.	Phchi.S3G223700
Phchi.S3	AUGUSTUS	transcript	15490033	15493244	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	stop_codon	15490030	15490032	.	-	0	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15490033	15491249	1	-	2	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15490033	15491249	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15491250	15491377	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15491378	15491492	1	-	0	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15491378	15491492	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15491493	15491578	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15491579	15491631	1	-	2	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15491579	15491631	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15491632	15491762	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15491763	15492023	0.99	-	2	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15491763	15492023	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15492024	15492132	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15492133	15492186	1	-	2	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15492133	15492186	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15492187	15492350	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15492351	15492599	1	-	2	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15492351	15492599	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15492600	15492690	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15492691	15492928	1	-	0	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15492691	15492928	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	intron	15492929	15493040	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	CDS	15493041	15493244	1	-	0	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	exon	15493041	15493244	.	-	.	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
Phchi.S3	AUGUSTUS	start_codon	15493242	15493244	.	-	0	transcript_id "Phchi.S3G223700.t1"; gene_id "Phchi.S3G223700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7968.t1 is derived from g5143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32174542	32176212	.	-	.	Phchi.S1G512700
Phchi.S1	AUGUSTUS	transcript	32174542	32176212	.	-	.	transcript_id "Phchi.S1G512700.t1"; gene_id "Phchi.S1G512700"
Phchi.S1	AUGUSTUS	stop_codon	32174539	32174541	.	-	0	transcript_id "Phchi.S1G512700.t1"; gene_id "Phchi.S1G512700"
Phchi.S1	AUGUSTUS	CDS	32174542	32176212	1	-	0	transcript_id "Phchi.S1G512700.t1"; gene_id "Phchi.S1G512700"
Phchi.S1	AUGUSTUS	exon	32174542	32176212	.	-	.	transcript_id "Phchi.S1G512700.t1"; gene_id "Phchi.S1G512700"
Phchi.S1	AUGUSTUS	start_codon	32176210	32176212	.	-	0	transcript_id "Phchi.S1G512700.t1"; gene_id "Phchi.S1G512700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14212.t1 is derived from g12679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11524720	11525772	.	+	.	Phchi.S3G153100
Phchi.S3	AUGUSTUS	transcript	11524720	11525772	.	+	.	transcript_id "Phchi.S3G153100.t1"; gene_id "Phchi.S3G153100"
Phchi.S3	AUGUSTUS	start_codon	11524720	11524722	.	+	0	transcript_id "Phchi.S3G153100.t1"; gene_id "Phchi.S3G153100"
Phchi.S3	AUGUSTUS	CDS	11524720	11525772	1	+	0	transcript_id "Phchi.S3G153100.t1"; gene_id "Phchi.S3G153100"
Phchi.S3	AUGUSTUS	exon	11524720	11525772	.	+	.	transcript_id "Phchi.S3G153100.t1"; gene_id "Phchi.S3G153100"
Phchi.S3	AUGUSTUS	stop_codon	11525773	11525775	.	+	0	transcript_id "Phchi.S3G153100.t1"; gene_id "Phchi.S3G153100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9522.t1 is derived from g6698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42262988	42263029	.	-	.	Phchi.S1G668100
Phchi.S1	AUGUSTUS	transcript	42262988	42263029	.	-	.	transcript_id "Phchi.S1G668100.t1"; gene_id "Phchi.S1G668100"
Phchi.S1	AUGUSTUS	stop_codon	42258045	42258047	.	-	0	transcript_id "Phchi.S1G668100.t1"; gene_id "Phchi.S1G668100"
Phchi.S1	AUGUSTUS	CDS	42262988	42263029	0.17	-	0	transcript_id "Phchi.S1G668100.t1"; gene_id "Phchi.S1G668100"
Phchi.S1	AUGUSTUS	exon	42262988	42263029	.	-	.	transcript_id "Phchi.S1G668100.t1"; gene_id "Phchi.S1G668100"
Phchi.S1	AUGUSTUS	start_codon	42263027	42263029	.	-	0	transcript_id "Phchi.S1G668100.t1"; gene_id "Phchi.S1G668100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7672.t1 is derived from g4846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30564738	30566944	.	+	.	Phchi.S1G483100
Phchi.S1	AUGUSTUS	transcript	30564738	30566944	.	+	.	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	start_codon	30564738	30564740	.	+	0	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	CDS	30564738	30565174	0.57	+	0	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	exon	30564738	30565174	.	+	.	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	intron	30565175	30565905	.	+	.	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	CDS	30565906	30566944	1	+	1	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	exon	30565906	30566944	.	+	.	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
Phchi.S1	AUGUSTUS	stop_codon	30566945	30566947	.	+	0	transcript_id "Phchi.S1G483100.t1"; gene_id "Phchi.S1G483100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7276.t1 is derived from g4448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28096923	28103473	.	-	.	Phchi.S1G443500
Phchi.S1	AUGUSTUS	transcript	28096923	28103473	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	stop_codon	28096920	28096922	.	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28096923	28097138	0.87	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28096923	28097138	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28097139	28097240	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28097241	28097367	0.9	-	1	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28097241	28097367	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28097368	28097435	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28097436	28097674	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28097436	28097674	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28097675	28097766	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28097767	28097981	1	-	2	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28097767	28097981	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28097982	28098073	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28098074	28098545	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28098074	28098545	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28098546	28098625	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28098626	28098822	0.96	-	2	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28098626	28098822	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28098823	28098987	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28098988	28099009	0.87	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28098988	28099009	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28099010	28099106	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28099107	28099256	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28099107	28099256	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28099257	28099338	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28099339	28099446	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28099339	28099446	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28099447	28099545	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28099546	28099599	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28099546	28099599	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28099600	28099685	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28099686	28099796	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28099686	28099796	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28099797	28099965	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28099966	28100121	0.7	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28099966	28100121	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28100122	28100226	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28100227	28100635	0.7	-	1	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28100227	28100635	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28100636	28100730	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28100731	28100798	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28100731	28100798	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28100799	28100907	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28100908	28101018	0.97	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28100908	28101018	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28101019	28101116	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28101117	28101317	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28101117	28101317	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28101318	28101398	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28101399	28101500	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28101399	28101500	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28101501	28101627	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28101628	28101735	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28101628	28101735	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28101736	28101843	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28101844	28102010	1	-	2	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28101844	28102010	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28102011	28102128	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28102129	28102198	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28102129	28102198	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28102199	28102310	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28102311	28102379	0.98	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28102311	28102379	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28102380	28102492	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28102493	28102750	1	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28102493	28102750	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28102751	28102850	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28102851	28102926	0.95	-	1	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28102851	28102926	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28102927	28103004	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28103005	28103132	0.83	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28103005	28103132	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28103133	28103218	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28103219	28103334	1	-	2	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28103219	28103334	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	intron	28103335	28103454	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	CDS	28103455	28103473	0.99	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	exon	28103455	28103473	.	-	.	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
Phchi.S1	AUGUSTUS	start_codon	28103471	28103473	.	-	0	transcript_id "Phchi.S1G443500.t1"; gene_id "Phchi.S1G443500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6483.t1 is derived from g3655.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23207961	23214819	.	-	.	Phchi.S1G364200
Phchi.S1	AUGUSTUS	transcript	23207961	23214819	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	stop_codon	23207958	23207960	.	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23207961	23208172	0.88	-	2	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23207961	23208172	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208173	23208247	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208248	23208326	0.89	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208248	23208326	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208327	23208421	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208422	23208473	1	-	1	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208422	23208473	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208474	23208671	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208672	23208733	0.97	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208672	23208733	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208734	23208841	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208842	23208912	0.99	-	2	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208842	23208912	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208913	23209013	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23209014	23209065	0.92	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23209014	23209065	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23209066	23209158	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23209159	23209296	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23209159	23209296	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23209297	23209855	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23209856	23209915	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23209856	23209915	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23209916	23210074	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210075	23210116	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210075	23210116	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23210117	23210258	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210259	23210353	1	-	2	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210259	23210353	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23210354	23210482	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210483	23210640	0.99	-	1	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210483	23210640	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23210641	23210742	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210743	23211003	1	-	1	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210743	23211003	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23211004	23211283	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23211284	23211325	1	-	1	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23211284	23211325	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23211326	23211736	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23211737	23211810	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23211737	23211810	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23211811	23211901	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23211902	23212105	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23211902	23212105	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212106	23212199	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212200	23212267	0.9	-	2	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212200	23212267	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212268	23212367	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212368	23212458	0.9	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212368	23212458	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212459	23212544	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212545	23212715	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212545	23212715	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212716	23212866	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212867	23212935	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212867	23212935	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212936	23213126	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213127	23213208	1	-	1	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213127	23213208	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213209	23213314	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213315	23213359	1	-	1	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213315	23213359	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213360	23213496	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213497	23213621	1	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213497	23213621	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213622	23213735	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213736	23213990	0.97	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213736	23213990	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213991	23214657	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23214658	23214819	0.99	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23214658	23214819	.	-	.	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	start_codon	23214817	23214819	.	-	0	transcript_id "Phchi.S1G364200.t1"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	transcript	23207961	23214819	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	stop_codon	23207958	23207960	.	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23207961	23208172	0.78	-	2	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23207961	23208172	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208173	23208247	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208248	23208326	0.78	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208248	23208326	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208327	23208515	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208516	23208567	0.64	-	1	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208516	23208567	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208568	23208671	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208672	23208733	0.74	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208672	23208733	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208734	23208841	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23208842	23208912	1	-	2	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23208842	23208912	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23208913	23209013	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23209014	23209065	0.89	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23209014	23209065	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23209066	23209158	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23209159	23209296	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23209159	23209296	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23209297	23209855	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23209856	23209915	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23209856	23209915	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23209916	23210074	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210075	23210116	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210075	23210116	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23210117	23210258	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210259	23210353	1	-	2	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210259	23210353	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23210354	23210482	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210483	23210640	1	-	1	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210483	23210640	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23210641	23210742	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23210743	23211003	1	-	1	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23210743	23211003	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23211004	23211283	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23211284	23211325	1	-	1	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23211284	23211325	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23211326	23211736	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23211737	23211810	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23211737	23211810	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23211811	23211901	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23211902	23212105	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23211902	23212105	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212106	23212199	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212200	23212267	0.84	-	2	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212200	23212267	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212268	23212367	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212368	23212458	0.84	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212368	23212458	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212459	23212544	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212545	23212715	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212545	23212715	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212716	23212866	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23212867	23212935	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23212867	23212935	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23212936	23213126	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213127	23213208	1	-	1	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213127	23213208	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213209	23213314	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213315	23213359	1	-	1	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213315	23213359	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213360	23213496	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213497	23213621	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213497	23213621	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213622	23213735	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23213736	23213990	1	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23213736	23213990	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	intron	23213991	23214657	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	CDS	23214658	23214819	0.99	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	exon	23214658	23214819	.	-	.	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
Phchi.S1	AUGUSTUS	start_codon	23214817	23214819	.	-	0	transcript_id "Phchi.S1G364200.t2"; gene_id "Phchi.S1G364200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg76.t1 is derived from g9858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	374864	376791	.	+	.	Phchi.S6G003500
Phchi.S6	AUGUSTUS	transcript	374864	376791	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	start_codon	374864	374866	.	+	0	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	CDS	374864	375013	0.83	+	0	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	exon	374864	375013	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	intron	375014	375105	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	CDS	375106	375206	0.96	+	0	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	exon	375106	375206	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	intron	375207	375320	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	CDS	375321	375388	0.98	+	1	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	exon	375321	375388	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	intron	375389	375517	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	CDS	375518	375911	1	+	2	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	exon	375518	375911	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	intron	375912	376064	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	CDS	376065	376392	0.99	+	1	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	exon	376065	376392	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	intron	376393	376482	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	CDS	376483	376791	1	+	0	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	exon	376483	376791	.	+	.	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
Phchi.S6	AUGUSTUS	stop_codon	376792	376794	.	+	0	transcript_id "Phchi.S6G003500.t1"; gene_id "Phchi.S6G003500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5831.t1 is derived from g3001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19155001	19155777	.	-	.	Phchi.S1G299000
Phchi.S1	AUGUSTUS	transcript	19155001	19155651	.	-	.	transcript_id "Phchi.S1G299000.t1"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	stop_codon	19154998	19155000	.	-	0	transcript_id "Phchi.S1G299000.t1"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	CDS	19155001	19155651	0.98	-	0	transcript_id "Phchi.S1G299000.t1"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	exon	19155001	19155651	.	-	.	transcript_id "Phchi.S1G299000.t1"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	start_codon	19155649	19155651	.	-	0	transcript_id "Phchi.S1G299000.t1"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	transcript	19155001	19155777	.	-	.	transcript_id "Phchi.S1G299000.t2"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	stop_codon	19154998	19155000	.	-	0	transcript_id "Phchi.S1G299000.t2"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	CDS	19155001	19155777	0.85	-	0	transcript_id "Phchi.S1G299000.t2"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	exon	19155001	19155777	.	-	.	transcript_id "Phchi.S1G299000.t2"; gene_id "Phchi.S1G299000"
Phchi.S1	AUGUSTUS	start_codon	19155775	19155777	.	-	0	transcript_id "Phchi.S1G299000.t2"; gene_id "Phchi.S1G299000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4548.t1 is derived from g1718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11061631	11065006	.	-	.	Phchi.S1G170700
Phchi.S1	AUGUSTUS	transcript	11061631	11065006	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	stop_codon	11061628	11061630	.	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11061631	11061724	0.4	-	1	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11061631	11061724	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11061725	11061825	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11061826	11061868	0.48	-	2	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11061826	11061868	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11061869	11062061	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11062062	11062148	0.95	-	2	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11062062	11062148	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11062149	11062239	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11062240	11062696	1	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11062240	11062696	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11062697	11062795	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11062796	11062972	0.95	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11062796	11062972	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11062973	11063096	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11063097	11063303	0.67	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11063097	11063303	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11063304	11063385	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11063386	11063432	0.74	-	2	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11063386	11063432	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11063433	11063835	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11063836	11063968	0.88	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11063836	11063968	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11063969	11064059	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11064060	11064637	0.8	-	2	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11064060	11064637	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	intron	11064638	11064747	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	CDS	11064748	11065006	0.77	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	exon	11064748	11065006	.	-	.	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
Phchi.S1	AUGUSTUS	start_codon	11065004	11065006	.	-	0	transcript_id "Phchi.S1G170700.t1"; gene_id "Phchi.S1G170700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11370.t1 is derived from g15420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5923748	5925285	.	+	.	Phchi.S4G095200
Phchi.S4	AUGUSTUS	transcript	5923748	5925285	.	+	.	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	start_codon	5923748	5923750	.	+	0	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	CDS	5923748	5923844	1	+	0	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	exon	5923748	5923844	.	+	.	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	intron	5923845	5923993	.	+	.	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	CDS	5923994	5924363	1	+	2	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	exon	5923994	5924363	.	+	.	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	intron	5924364	5924480	.	+	.	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	CDS	5924481	5925285	0.97	+	1	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	exon	5924481	5925285	.	+	.	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
Phchi.S4	AUGUSTUS	stop_codon	5925286	5925288	.	+	0	transcript_id "Phchi.S4G095200.t1"; gene_id "Phchi.S4G095200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6134.t1 is derived from g3305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21093349	21095168	.	-	.	Phchi.S1G329300
Phchi.S1	AUGUSTUS	transcript	21093349	21095168	.	-	.	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	stop_codon	21093346	21093348	.	-	0	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	CDS	21093349	21094326	1	-	0	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	exon	21093349	21094326	.	-	.	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	intron	21094327	21094493	.	-	.	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	CDS	21094494	21094607	0.98	-	0	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	exon	21094494	21094607	.	-	.	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	intron	21094608	21094916	.	-	.	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	CDS	21094917	21095168	0.84	-	0	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	exon	21094917	21095168	.	-	.	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
Phchi.S1	AUGUSTUS	start_codon	21095166	21095168	.	-	0	transcript_id "Phchi.S1G329300.t1"; gene_id "Phchi.S1G329300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1050.t1 is derived from g10833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7285034	7287188	.	+	.	Phchi.S6G100900
Phchi.S6	AUGUSTUS	transcript	7285034	7287188	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	start_codon	7285034	7285036	.	+	0	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	CDS	7285034	7285060	0.69	+	0	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	exon	7285034	7285060	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	intron	7285061	7285205	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	CDS	7285206	7285267	1	+	0	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	exon	7285206	7285267	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	intron	7285268	7285414	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	CDS	7285415	7285520	0.45	+	1	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	exon	7285415	7285520	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	intron	7285521	7285769	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	CDS	7285770	7287188	0.59	+	0	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	exon	7285770	7287188	.	+	.	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
Phchi.S6	AUGUSTUS	stop_codon	7287189	7287191	.	+	0	transcript_id "Phchi.S6G100900.t1"; gene_id "Phchi.S6G100900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5711.t1 is derived from g2881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18480869	18482239	.	-	.	Phchi.S1G287000
Phchi.S1	AUGUSTUS	transcript	18480869	18482239	.	-	.	transcript_id "Phchi.S1G287000.t1"; gene_id "Phchi.S1G287000"
Phchi.S1	AUGUSTUS	stop_codon	18480866	18480868	.	-	0	transcript_id "Phchi.S1G287000.t1"; gene_id "Phchi.S1G287000"
Phchi.S1	AUGUSTUS	CDS	18480869	18482239	0.97	-	0	transcript_id "Phchi.S1G287000.t1"; gene_id "Phchi.S1G287000"
Phchi.S1	AUGUSTUS	exon	18480869	18482239	.	-	.	transcript_id "Phchi.S1G287000.t1"; gene_id "Phchi.S1G287000"
Phchi.S1	AUGUSTUS	start_codon	18482237	18482239	.	-	0	transcript_id "Phchi.S1G287000.t1"; gene_id "Phchi.S1G287000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11187.t1 is derived from g15237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4545375	4548477	.	+	.	Phchi.S4G076900
Phchi.S4	AUGUSTUS	transcript	4545375	4548477	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	start_codon	4545375	4545377	.	+	0	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	CDS	4545375	4545678	0.59	+	0	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	exon	4545375	4545678	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	intron	4545679	4545748	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	CDS	4545749	4545915	1	+	2	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	exon	4545749	4545915	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	intron	4545916	4546006	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	CDS	4546007	4546100	0.69	+	0	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	exon	4546007	4546100	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	intron	4546101	4546389	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	CDS	4546390	4546459	0.52	+	2	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	exon	4546390	4546459	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	intron	4546460	4546575	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	CDS	4546576	4548125	0.18	+	1	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	exon	4546576	4548125	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	intron	4548126	4548226	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	CDS	4548227	4548477	0.51	+	2	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	exon	4548227	4548477	.	+	.	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
Phchi.S4	AUGUSTUS	stop_codon	4548478	4548480	.	+	0	transcript_id "Phchi.S4G076900.t1"; gene_id "Phchi.S4G076900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8258.t1 is derived from g5433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34755584	34756635	.	+	.	Phchi.S1G541700
Phchi.S1	AUGUSTUS	transcript	34755584	34756635	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	start_codon	34755584	34755586	.	+	0	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	CDS	34755584	34755742	1	+	0	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	exon	34755584	34755742	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	intron	34755743	34755813	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	CDS	34755814	34755934	1	+	0	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	exon	34755814	34755934	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	intron	34755935	34756019	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	CDS	34756020	34756084	0.97	+	2	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	exon	34756020	34756084	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	intron	34756085	34756200	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	CDS	34756201	34756321	0.85	+	0	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	exon	34756201	34756321	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	intron	34756322	34756438	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	CDS	34756439	34756635	0.88	+	2	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	exon	34756439	34756635	.	+	.	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
Phchi.S1	AUGUSTUS	stop_codon	34756636	34756638	.	+	0	transcript_id "Phchi.S1G541700.t1"; gene_id "Phchi.S1G541700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3020.t1 is derived from g189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1173570	1174682	.	-	.	Phchi.S1G017900
Phchi.S1	AUGUSTUS	transcript	1173570	1174682	.	-	.	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	stop_codon	1173567	1173569	.	-	0	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	CDS	1173570	1174564	0.89	-	2	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	exon	1173570	1174564	.	-	.	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	intron	1174565	1174657	.	-	.	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	CDS	1174658	1174682	0.87	-	0	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	exon	1174658	1174682	.	-	.	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
Phchi.S1	AUGUSTUS	start_codon	1174680	1174682	.	-	0	transcript_id "Phchi.S1G017900.t1"; gene_id "Phchi.S1G017900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2168.t1 is derived from g9088.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5149210	5152256	.	-	.	Phchi.S5G077700
Phchi.S5	AUGUSTUS	transcript	5149210	5152256	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	stop_codon	5149207	5149209	.	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5149210	5149383	0.42	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5149210	5149383	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5149384	5149485	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5149486	5149848	0.74	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5149486	5149848	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5149849	5149929	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5149930	5150372	0.98	-	2	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5149930	5150372	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5150373	5150555	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5150556	5150673	0.77	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5150556	5150673	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5150674	5150986	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5150987	5151001	0.79	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5150987	5151001	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5151002	5151181	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5151182	5151248	1	-	1	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5151182	5151248	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5151249	5151375	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5151376	5151448	1	-	2	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5151376	5151448	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5151449	5151568	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5151569	5151593	1	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5151569	5151593	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5151594	5151684	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5151685	5151773	1	-	2	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5151685	5151773	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5151774	5151875	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5151876	5151960	1	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5151876	5151960	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5151961	5152058	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5152059	5152136	1	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5152059	5152136	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	intron	5152137	5152232	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	CDS	5152233	5152256	0.56	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	exon	5152233	5152256	.	-	.	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
Phchi.S5	AUGUSTUS	start_codon	5152254	5152256	.	-	0	transcript_id "Phchi.S5G077700.t1"; gene_id "Phchi.S5G077700"
# This transcript jg14087.t2 is derived from g12554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14088.t1 is derived from g12555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10793509	10794300	.	+	.	Phchi.S3G140700
Phchi.S3	AUGUSTUS	transcript	10793509	10794300	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	start_codon	10793509	10793511	.	+	0	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	CDS	10793509	10793727	1	+	0	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	exon	10793509	10793727	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	intron	10793728	10793812	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	CDS	10793813	10793914	1	+	0	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	exon	10793813	10793914	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	intron	10793915	10794011	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	CDS	10794012	10794152	1	+	0	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	exon	10794012	10794152	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	intron	10794153	10794261	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	CDS	10794262	10794300	1	+	0	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	exon	10794262	10794300	.	+	.	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
Phchi.S3	AUGUSTUS	stop_codon	10794301	10794303	.	+	0	transcript_id "Phchi.S3G140700.t1"; gene_id "Phchi.S3G140700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15444.t1 is derived from g13912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19184756	19187503	.	-	.	Phchi.S3G276300
Phchi.S3	AUGUSTUS	transcript	19184756	19187503	.	-	.	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	stop_codon	19184753	19184755	.	-	0	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	CDS	19184756	19185202	0.61	-	0	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	exon	19184756	19185202	.	-	.	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	intron	19185203	19185648	.	-	.	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	CDS	19185649	19185793	0.72	-	1	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	exon	19185649	19185793	.	-	.	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	intron	19185794	19185890	.	-	.	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	CDS	19185891	19187503	1	-	0	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	exon	19185891	19187503	.	-	.	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
Phchi.S3	AUGUSTUS	start_codon	19187501	19187503	.	-	0	transcript_id "Phchi.S3G276300.t1"; gene_id "Phchi.S3G276300"
# This transcript jg12047.t2 is derived from g7722.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12048.t1 is derived from g7723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1011083	1011711	.	-	.	Phchi.S2G012800
Phchi.S2	AUGUSTUS	transcript	1011083	1011711	.	-	.	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	stop_codon	1011080	1011082	.	-	0	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	CDS	1011083	1011271	0.98	-	0	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	exon	1011083	1011271	.	-	.	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	intron	1011272	1011400	.	-	.	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	CDS	1011401	1011505	1	-	0	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	exon	1011401	1011505	.	-	.	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	intron	1011506	1011630	.	-	.	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	CDS	1011631	1011711	0.94	-	0	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	exon	1011631	1011711	.	-	.	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
Phchi.S2	AUGUSTUS	start_codon	1011709	1011711	.	-	0	transcript_id "Phchi.S2G012800.t1"; gene_id "Phchi.S2G012800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6439.t1 is derived from g3611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23034431	23035378	.	-	.	Phchi.S1G359800
Phchi.S1	AUGUSTUS	transcript	23034431	23035378	.	-	.	transcript_id "Phchi.S1G359800.t1"; gene_id "Phchi.S1G359800"
Phchi.S1	AUGUSTUS	stop_codon	23034428	23034430	.	-	0	transcript_id "Phchi.S1G359800.t1"; gene_id "Phchi.S1G359800"
Phchi.S1	AUGUSTUS	CDS	23034431	23035378	0.91	-	0	transcript_id "Phchi.S1G359800.t1"; gene_id "Phchi.S1G359800"
Phchi.S1	AUGUSTUS	exon	23034431	23035378	.	-	.	transcript_id "Phchi.S1G359800.t1"; gene_id "Phchi.S1G359800"
Phchi.S1	AUGUSTUS	start_codon	23035376	23035378	.	-	0	transcript_id "Phchi.S1G359800.t1"; gene_id "Phchi.S1G359800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2955.t1 is derived from g124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	754854	755404	.	+	.	Phchi.S1G011400
Phchi.S1	AUGUSTUS	transcript	754854	755404	.	+	.	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	start_codon	754854	754856	.	+	0	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	CDS	754854	754977	0.99	+	0	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	exon	754854	754977	.	+	.	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	intron	754978	755123	.	+	.	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	CDS	755124	755404	1	+	2	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	exon	755124	755404	.	+	.	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
Phchi.S1	AUGUSTUS	stop_codon	755405	755407	.	+	0	transcript_id "Phchi.S1G011400.t1"; gene_id "Phchi.S1G011400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8278.t1 is derived from g5453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35071833	35073934	.	-	.	Phchi.S1G543700
Phchi.S1	AUGUSTUS	transcript	35071833	35073934	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	stop_codon	35071830	35071832	.	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35071833	35071997	0.92	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35071833	35071997	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	intron	35071998	35072110	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35072111	35072188	0.96	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35072111	35072188	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	intron	35072189	35072361	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35072362	35072424	1	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35072362	35072424	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	intron	35072425	35072570	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35072571	35072700	1	-	1	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35072571	35072700	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	intron	35072701	35072818	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35072819	35073042	1	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35072819	35073042	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	intron	35073043	35073244	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35073245	35073361	1	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35073245	35073361	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	intron	35073362	35073457	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	CDS	35073458	35073934	0.89	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	exon	35073458	35073934	.	-	.	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
Phchi.S1	AUGUSTUS	start_codon	35073932	35073934	.	-	0	transcript_id "Phchi.S1G543700.t1"; gene_id "Phchi.S1G543700"
# This transcript jg8222.t2 is derived from g5397.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8222.t3 is derived from g5397.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8223.t1 is derived from g5398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34539019	34540550	.	+	.	Phchi.S1G538200
Phchi.S1	AUGUSTUS	transcript	34539019	34540550	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	start_codon	34539019	34539021	.	+	0	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34539019	34539087	0.72	+	0	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34539019	34539087	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	intron	34539088	34539231	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34539232	34539268	0.95	+	0	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34539232	34539268	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	intron	34539269	34539345	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34539346	34539425	1	+	2	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34539346	34539425	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	intron	34539426	34539521	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34539522	34539685	1	+	0	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34539522	34539685	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	intron	34539686	34539785	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34539786	34539794	0.93	+	1	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34539786	34539794	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	intron	34539795	34540058	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34540059	34540294	0.96	+	1	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34540059	34540294	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	intron	34540295	34540542	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	CDS	34540543	34540550	0.99	+	2	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	exon	34540543	34540550	.	+	.	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
Phchi.S1	AUGUSTUS	stop_codon	34540551	34540553	.	+	0	transcript_id "Phchi.S1G538200.t1"; gene_id "Phchi.S1G538200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8611.t1 is derived from g5786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36908130	36910655	.	+	.	Phchi.S1G577000
Phchi.S1	AUGUSTUS	transcript	36908130	36910655	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	start_codon	36908130	36908132	.	+	0	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	CDS	36908130	36909159	0.53	+	0	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	exon	36908130	36909159	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	intron	36909160	36909281	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	CDS	36909282	36910134	1	+	2	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	exon	36909282	36910134	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	intron	36910135	36910211	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	CDS	36910212	36910350	1	+	1	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	exon	36910212	36910350	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	intron	36910351	36910436	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	CDS	36910437	36910655	0.86	+	0	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	exon	36910437	36910655	.	+	.	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
Phchi.S1	AUGUSTUS	stop_codon	36910656	36910658	.	+	0	transcript_id "Phchi.S1G577000.t1"; gene_id "Phchi.S1G577000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12045.t1 is derived from g7720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	952451	953148	.	+	.	Phchi.S2G012500
Phchi.S2	AUGUSTUS	transcript	952451	953148	.	+	.	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	start_codon	952451	952453	.	+	0	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	CDS	952451	952633	0.73	+	0	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	exon	952451	952633	.	+	.	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	intron	952634	952713	.	+	.	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	CDS	952714	953148	0.8	+	0	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	exon	952714	953148	.	+	.	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
Phchi.S2	AUGUSTUS	stop_codon	953149	953151	.	+	0	transcript_id "Phchi.S2G012500.t1"; gene_id "Phchi.S2G012500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12059.t1 is derived from g7734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1194766	1195776	.	-	.	Phchi.S2G013900
Phchi.S2	AUGUSTUS	transcript	1194766	1195776	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	stop_codon	1194763	1194765	.	-	0	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	CDS	1194766	1195067	0.88	-	2	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	exon	1194766	1195067	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	intron	1195068	1195178	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	CDS	1195179	1195252	1	-	1	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	exon	1195179	1195252	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	intron	1195253	1195379	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	CDS	1195380	1195502	1	-	1	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	exon	1195380	1195502	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	intron	1195503	1195588	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	CDS	1195589	1195776	0.89	-	0	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	exon	1195589	1195776	.	-	.	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
Phchi.S2	AUGUSTUS	start_codon	1195774	1195776	.	-	0	transcript_id "Phchi.S2G013900.t1"; gene_id "Phchi.S2G013900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg502.t1 is derived from g10284.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3488173	3489789	.	-	.	Phchi.S6G046100
Phchi.S6	AUGUSTUS	transcript	3488173	3489728	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	stop_codon	3488170	3488172	.	-	0	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488173	3488267	0.97	-	2	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488173	3488267	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3488268	3488354	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488355	3488455	0.62	-	1	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488355	3488455	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3488456	3488767	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488768	3488836	0.99	-	1	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488768	3488836	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3488837	3488932	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488933	3489024	1	-	0	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488933	3489024	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489025	3489101	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489102	3489138	1	-	1	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489102	3489138	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489139	3489379	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489380	3489481	1	-	1	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489380	3489481	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489482	3489565	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489566	3489614	1	-	2	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489566	3489614	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489615	3489706	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489707	3489728	0.99	-	0	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489707	3489728	.	-	.	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	start_codon	3489726	3489728	.	-	0	transcript_id "Phchi.S6G046100.t1"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	transcript	3488173	3489789	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	stop_codon	3488170	3488172	.	-	0	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488173	3488267	1	-	2	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488173	3488267	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3488268	3488354	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488355	3488455	0.71	-	1	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488355	3488455	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3488456	3488767	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488768	3488836	0.98	-	1	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488768	3488836	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3488837	3488932	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3488933	3489024	1	-	0	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3488933	3489024	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489025	3489101	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489102	3489138	0.96	-	1	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489102	3489138	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489139	3489379	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489380	3489481	0.31	-	1	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489380	3489481	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489482	3489565	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489566	3489601	0.27	-	1	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489566	3489601	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	intron	3489602	3489706	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	CDS	3489707	3489789	0.26	-	0	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	exon	3489707	3489789	.	-	.	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
Phchi.S6	AUGUSTUS	start_codon	3489787	3489789	.	-	0	transcript_id "Phchi.S6G046100.t2"; gene_id "Phchi.S6G046100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13671.t1 is derived from g12138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8083923	8085385	.	+	.	Phchi.S3G099000
Phchi.S3	AUGUSTUS	transcript	8083923	8085385	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	start_codon	8083923	8083925	.	+	0	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8083923	8084023	0.86	+	0	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8083923	8084023	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	intron	8084024	8084229	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8084230	8084311	0.81	+	1	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8084230	8084311	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	intron	8084312	8084446	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8084447	8084535	0.87	+	0	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8084447	8084535	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	intron	8084536	8084630	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8084631	8084641	0.73	+	1	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8084631	8084641	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	intron	8084642	8084761	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8084762	8084974	0.58	+	2	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8084762	8084974	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	intron	8084975	8085117	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8085118	8085174	1	+	2	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8085118	8085174	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	intron	8085175	8085308	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	CDS	8085309	8085385	1	+	2	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	exon	8085309	8085385	.	+	.	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
Phchi.S3	AUGUSTUS	stop_codon	8085386	8085388	.	+	0	transcript_id "Phchi.S3G099000.t1"; gene_id "Phchi.S3G099000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14272.t1 is derived from g12739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11876325	11879156	.	-	.	Phchi.S3G159100
Phchi.S3	AUGUSTUS	transcript	11876325	11879156	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	stop_codon	11876322	11876324	.	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11876325	11876410	1	-	2	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11876325	11876410	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11876411	11876489	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11876490	11876556	1	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11876490	11876556	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11876557	11876633	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11876634	11876732	1	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11876634	11876732	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11876733	11876825	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11876826	11876899	1	-	2	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11876826	11876899	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11876900	11876983	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11876984	11877074	1	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11876984	11877074	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877075	11877180	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11877181	11877444	0.75	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11877181	11877444	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877445	11877622	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11877623	11877715	1	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11877623	11877715	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877716	11877827	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11877828	11877891	1	-	1	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11877828	11877891	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877892	11878021	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878022	11878241	1	-	2	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878022	11878241	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11878242	11878466	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878467	11878547	1	-	2	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878467	11878547	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11878548	11878662	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878663	11878780	0.93	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878663	11878780	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11878781	11878909	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878910	11879022	1	-	2	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878910	11879022	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11879023	11879119	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11879120	11879156	0.93	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11879120	11879156	.	-	.	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	start_codon	11879154	11879156	.	-	0	transcript_id "Phchi.S3G159100.t1"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	transcript	11877522	11879156	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	stop_codon	11877519	11877521	.	-	0	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11877522	11877533	0.44	-	0	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11877522	11877533	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877534	11877622	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11877623	11877715	1	-	0	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11877623	11877715	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877716	11877827	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11877828	11877891	0.99	-	1	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11877828	11877891	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11877892	11878021	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878022	11878241	1	-	2	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878022	11878241	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11878242	11878466	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878467	11878547	1	-	2	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878467	11878547	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11878548	11878662	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878663	11878780	0.92	-	0	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878663	11878780	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11878781	11878909	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11878910	11879022	1	-	2	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11878910	11879022	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	intron	11879023	11879119	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	CDS	11879120	11879156	0.91	-	0	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	exon	11879120	11879156	.	-	.	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
Phchi.S3	AUGUSTUS	start_codon	11879154	11879156	.	-	0	transcript_id "Phchi.S3G159100.t2"; gene_id "Phchi.S3G159100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7057.t1 is derived from g4229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26652897	26655298	.	-	.	Phchi.S1G421600
Phchi.S1	AUGUSTUS	transcript	26652897	26655298	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	stop_codon	26652894	26652896	.	-	0	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	CDS	26652897	26653028	0.62	-	0	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	exon	26652897	26653028	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	intron	26653029	26653107	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	CDS	26653108	26653134	0.62	-	0	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	exon	26653108	26653134	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	intron	26653135	26653216	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	CDS	26653217	26653435	0.7	-	0	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	exon	26653217	26653435	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	intron	26653436	26653515	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	CDS	26653516	26653726	1	-	1	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	exon	26653516	26653726	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	intron	26653727	26653810	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	CDS	26653811	26653948	1	-	1	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	exon	26653811	26653948	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	intron	26653949	26654030	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	CDS	26654031	26655298	0.99	-	0	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	exon	26654031	26655298	.	-	.	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
Phchi.S1	AUGUSTUS	start_codon	26655296	26655298	.	-	0	transcript_id "Phchi.S1G421600.t1"; gene_id "Phchi.S1G421600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10660.t1 is derived from g14710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1481963	1483331	.	-	.	Phchi.S4G024200
Phchi.S4	AUGUSTUS	transcript	1481963	1483331	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	stop_codon	1481960	1481962	.	-	0	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	CDS	1481963	1482073	1	-	0	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	exon	1481963	1482073	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	intron	1482074	1482174	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	CDS	1482175	1482282	0.99	-	0	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	exon	1482175	1482282	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	intron	1482283	1482366	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	CDS	1482367	1482440	1	-	2	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	exon	1482367	1482440	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	intron	1482441	1482527	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	CDS	1482528	1482605	1	-	2	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	exon	1482528	1482605	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	intron	1482606	1482688	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	CDS	1482689	1483331	0.99	-	0	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	exon	1482689	1483331	.	-	.	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
Phchi.S4	AUGUSTUS	start_codon	1483329	1483331	.	-	0	transcript_id "Phchi.S4G024200.t1"; gene_id "Phchi.S4G024200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13774.t1 is derived from g12241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8846037	8846717	.	-	.	Phchi.S3G109300
Phchi.S3	AUGUSTUS	transcript	8846037	8846717	.	-	.	transcript_id "Phchi.S3G109300.t1"; gene_id "Phchi.S3G109300"
Phchi.S3	AUGUSTUS	stop_codon	8846034	8846036	.	-	0	transcript_id "Phchi.S3G109300.t1"; gene_id "Phchi.S3G109300"
Phchi.S3	AUGUSTUS	CDS	8846037	8846717	0.65	-	0	transcript_id "Phchi.S3G109300.t1"; gene_id "Phchi.S3G109300"
Phchi.S3	AUGUSTUS	exon	8846037	8846717	.	-	.	transcript_id "Phchi.S3G109300.t1"; gene_id "Phchi.S3G109300"
Phchi.S3	AUGUSTUS	start_codon	8846715	8846717	.	-	0	transcript_id "Phchi.S3G109300.t1"; gene_id "Phchi.S3G109300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4508.t1 is derived from g1678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10882558	10883305	.	+	.	Phchi.S1G166700
Phchi.S1	AUGUSTUS	transcript	10882558	10883305	.	+	.	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	start_codon	10882558	10882560	.	+	0	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	CDS	10882558	10882749	0.68	+	0	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	exon	10882558	10882749	.	+	.	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	intron	10882750	10882833	.	+	.	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	CDS	10882834	10882986	1	+	0	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	exon	10882834	10882986	.	+	.	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	intron	10882987	10883200	.	+	.	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	CDS	10883201	10883305	0.5	+	0	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	exon	10883201	10883305	.	+	.	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
Phchi.S1	AUGUSTUS	stop_codon	10883306	10883308	.	+	0	transcript_id "Phchi.S1G166700.t1"; gene_id "Phchi.S1G166700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9254.t1 is derived from g6429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40606951	40609739	.	+	.	Phchi.S1G641300
Phchi.S1	AUGUSTUS	transcript	40606951	40609739	.	+	.	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	start_codon	40606951	40606953	.	+	0	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	CDS	40606951	40607163	0.97	+	0	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	exon	40606951	40607163	.	+	.	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	intron	40607164	40607256	.	+	.	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	CDS	40607257	40608187	0.37	+	0	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	exon	40607257	40608187	.	+	.	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	intron	40608188	40608741	.	+	.	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	CDS	40608742	40609739	0.56	+	2	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	exon	40608742	40609739	.	+	.	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
Phchi.S1	AUGUSTUS	stop_codon	40609740	40609742	.	+	0	transcript_id "Phchi.S1G641300.t1"; gene_id "Phchi.S1G641300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg728.t1 is derived from g10510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5198110	5198964	.	-	.	Phchi.S6G068700
Phchi.S6	AUGUSTUS	transcript	5198110	5198964	.	-	.	transcript_id "Phchi.S6G068700.t1"; gene_id "Phchi.S6G068700"
Phchi.S6	AUGUSTUS	stop_codon	5198107	5198109	.	-	0	transcript_id "Phchi.S6G068700.t1"; gene_id "Phchi.S6G068700"
Phchi.S6	AUGUSTUS	CDS	5198110	5198964	0.26	-	0	transcript_id "Phchi.S6G068700.t1"; gene_id "Phchi.S6G068700"
Phchi.S6	AUGUSTUS	exon	5198110	5198964	.	-	.	transcript_id "Phchi.S6G068700.t1"; gene_id "Phchi.S6G068700"
Phchi.S6	AUGUSTUS	start_codon	5198962	5198964	.	-	0	transcript_id "Phchi.S6G068700.t1"; gene_id "Phchi.S6G068700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2455.t1 is derived from g9375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6738618	6741377	.	+	.	Phchi.S5G106400
Phchi.S5	AUGUSTUS	transcript	6738618	6741377	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	start_codon	6738618	6738620	.	+	0	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6738618	6739165	0.55	+	0	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6738618	6739165	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6739166	6739287	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6739288	6739382	0.93	+	1	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6739288	6739382	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6739383	6739467	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6739468	6739679	1	+	2	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6739468	6739679	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6739680	6739764	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6739765	6739900	0.98	+	0	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6739765	6739900	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6739901	6739984	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6739985	6740090	0.98	+	2	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6739985	6740090	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6740091	6740180	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6740181	6740399	0.93	+	1	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6740181	6740399	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6740400	6740503	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6740504	6740642	0.99	+	1	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6740504	6740642	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6740643	6740733	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6740734	6740979	1	+	0	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6740734	6740979	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	intron	6740980	6741071	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	CDS	6741072	6741377	0.99	+	0	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	exon	6741072	6741377	.	+	.	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
Phchi.S5	AUGUSTUS	stop_codon	6741378	6741380	.	+	0	transcript_id "Phchi.S5G106400.t1"; gene_id "Phchi.S5G106400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9888.t1 is derived from g7064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44272280	44277252	.	-	.	Phchi.S1G704700
Phchi.S1	AUGUSTUS	transcript	44272280	44277252	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	stop_codon	44272277	44272279	.	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44272280	44272284	0.82	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44272280	44272284	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44272285	44272374	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44272375	44272396	0.82	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44272375	44272396	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44272397	44272617	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44272618	44272686	0.68	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44272618	44272686	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44272687	44272766	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44272767	44272872	1	-	1	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44272767	44272872	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44272873	44272956	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44272957	44273015	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44272957	44273015	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44273016	44273125	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44273126	44273224	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44273126	44273224	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44273225	44273309	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44273310	44273511	1	-	1	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44273310	44273511	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44273512	44273601	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44273602	44273704	0.98	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44273602	44273704	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44273705	44273827	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44273828	44273936	0.97	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44273828	44273936	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44273937	44274019	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44274020	44274167	1	-	1	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44274020	44274167	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44274168	44274298	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44274299	44274486	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44274299	44274486	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44274487	44274651	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44274652	44274885	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44274652	44274885	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44274886	44274991	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44274992	44275311	0.96	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44274992	44275311	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44275312	44275467	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44275468	44275534	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44275468	44275534	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44275535	44275631	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44275632	44275706	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44275632	44275706	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44275707	44275800	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44275801	44276018	1	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44275801	44276018	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44276019	44276166	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44276167	44276460	1	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44276167	44276460	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44276461	44276568	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44276569	44276724	0.96	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44276569	44276724	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44276725	44276798	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44276799	44276990	1	-	2	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44276799	44276990	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	intron	44276991	44277080	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	CDS	44277081	44277252	1	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	exon	44277081	44277252	.	-	.	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
Phchi.S1	AUGUSTUS	start_codon	44277250	44277252	.	-	0	transcript_id "Phchi.S1G704700.t1"; gene_id "Phchi.S1G704700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14282.t1 is derived from g12749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11908229	11908619	.	-	.	Phchi.S3G160100
Phchi.S3	AUGUSTUS	transcript	11908229	11908619	.	-	.	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	stop_codon	11908226	11908228	.	-	0	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	CDS	11908229	11908236	0.75	-	2	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	exon	11908229	11908236	.	-	.	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	intron	11908237	11908408	.	-	.	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	CDS	11908409	11908619	0.68	-	0	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	exon	11908409	11908619	.	-	.	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
Phchi.S3	AUGUSTUS	start_codon	11908617	11908619	.	-	0	transcript_id "Phchi.S3G160100.t1"; gene_id "Phchi.S3G160100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg947.t1 is derived from g10729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6613243	6616092	.	+	.	Phchi.S6G090600
Phchi.S6	AUGUSTUS	transcript	6613243	6616092	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	start_codon	6613243	6613245	.	+	0	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	CDS	6613243	6615462	0.57	+	0	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	exon	6613243	6615462	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	intron	6615463	6615647	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	CDS	6615648	6615696	0.97	+	0	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	exon	6615648	6615696	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	intron	6615697	6615781	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	CDS	6615782	6615899	1	+	2	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	exon	6615782	6615899	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	intron	6615900	6615992	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	CDS	6615993	6616092	0.96	+	1	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	exon	6615993	6616092	.	+	.	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
Phchi.S6	AUGUSTUS	stop_codon	6616093	6616095	.	+	0	transcript_id "Phchi.S6G090600.t1"; gene_id "Phchi.S6G090600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12607.t1 is derived from g8284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37553752	37557453	.	+	.	Phchi.S2G068700
Phchi.S2	AUGUSTUS	transcript	37553752	37557453	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	start_codon	37553752	37553754	.	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37553752	37553790	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37553752	37553790	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37553791	37553884	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37553885	37553933	0.92	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37553885	37553933	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37553934	37554196	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37554197	37554666	0.64	+	2	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37554197	37554666	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37554667	37554753	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37554754	37554939	0.99	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37554754	37554939	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37554940	37555046	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555047	37555124	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555047	37555124	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555125	37555221	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555222	37555446	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555222	37555446	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555447	37555581	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555582	37555671	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555582	37555671	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555672	37555823	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555824	37555882	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555824	37555882	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555883	37555996	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555997	37556060	1	+	1	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555997	37556060	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556061	37556424	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556425	37556481	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556425	37556481	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556482	37556953	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556954	37557060	1	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556954	37557060	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37557061	37557151	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37557152	37557183	0.66	+	1	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37557152	37557183	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37557184	37557286	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37557287	37557453	0.82	+	2	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37557287	37557453	.	+	.	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	stop_codon	37557454	37557456	.	+	0	transcript_id "Phchi.S2G068700.t1"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	transcript	37553752	37557453	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	start_codon	37553752	37553754	.	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37553752	37553790	0.99	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37553752	37553790	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37553791	37553884	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37553885	37553933	0.87	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37553885	37553933	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37553934	37554196	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37554197	37554666	0.58	+	2	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37554197	37554666	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37554667	37554753	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37554754	37554939	1	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37554754	37554939	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37554940	37555046	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555047	37555124	1	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555047	37555124	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555125	37555212	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555213	37555446	0.63	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555213	37555446	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555447	37555581	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555582	37555671	1	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555582	37555671	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555672	37555823	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555824	37555882	1	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555824	37555882	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555883	37555996	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555997	37556060	1	+	1	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555997	37556060	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556061	37556424	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556425	37556481	1	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556425	37556481	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556482	37556953	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556954	37557060	1	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556954	37557060	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37557061	37557151	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37557152	37557183	0.62	+	1	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37557152	37557183	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37557184	37557286	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37557287	37557453	0.84	+	2	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37557287	37557453	.	+	.	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	stop_codon	37557454	37557456	.	+	0	transcript_id "Phchi.S2G068700.t2"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	transcript	37553752	37557453	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	start_codon	37553752	37553754	.	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37553752	37553790	1	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37553752	37553790	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37553791	37553884	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37553885	37553933	0.82	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37553885	37553933	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37553934	37554196	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37554197	37554666	0.57	+	2	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37554197	37554666	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37554667	37554753	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37554754	37554939	0.99	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37554754	37554939	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37554940	37555046	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555047	37555124	1	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555047	37555124	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555125	37555221	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555222	37555446	1	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555222	37555446	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555447	37555581	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555582	37555671	1	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555582	37555671	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555672	37555823	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555824	37555882	1	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555824	37555882	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37555883	37555996	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37555997	37556060	1	+	1	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37555997	37556060	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556061	37556424	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556425	37556489	0.68	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556425	37556489	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556490	37556684	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556685	37556721	0.82	+	1	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556685	37556721	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37556722	37556953	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37556954	37557060	1	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37556954	37557060	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37557061	37557151	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37557152	37557183	0.6	+	1	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37557152	37557183	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	intron	37557184	37557286	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	CDS	37557287	37557453	0.79	+	2	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	exon	37557287	37557453	.	+	.	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
Phchi.S2	AUGUSTUS	stop_codon	37557454	37557456	.	+	0	transcript_id "Phchi.S2G068700.t3"; gene_id "Phchi.S2G068700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9433.t1 is derived from g6609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41442401	41443788	.	-	.	Phchi.S1G659200
Phchi.S1	AUGUSTUS	transcript	41442401	41443788	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	stop_codon	41442398	41442400	.	-	0	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	CDS	41442401	41442523	1	-	0	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	exon	41442401	41442523	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	intron	41442524	41442607	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	CDS	41442608	41442849	1	-	2	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	exon	41442608	41442849	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	intron	41442850	41442930	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	CDS	41442931	41443027	1	-	0	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	exon	41442931	41443027	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	intron	41443028	41443148	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	CDS	41443149	41443291	0.87	-	2	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	exon	41443149	41443291	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	intron	41443292	41443362	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	CDS	41443363	41443483	0.99	-	0	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	exon	41443363	41443483	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	intron	41443484	41443599	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	CDS	41443600	41443788	1	-	0	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	exon	41443600	41443788	.	-	.	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
Phchi.S1	AUGUSTUS	start_codon	41443786	41443788	.	-	0	transcript_id "Phchi.S1G659200.t1"; gene_id "Phchi.S1G659200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14182.t1 is derived from g12649.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11323952	11325536	.	-	.	Phchi.S3G150100
Phchi.S3	AUGUSTUS	transcript	11324056	11325536	.	-	.	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	stop_codon	11324053	11324055	.	-	0	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324056	11324059	1	-	1	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324056	11324059	.	-	.	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	intron	11324060	11324260	.	-	.	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324261	11324865	0.99	-	0	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324261	11324865	.	-	.	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	intron	11324866	11324963	.	-	.	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324964	11325536	0.95	-	0	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324964	11325536	.	-	.	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	start_codon	11325534	11325536	.	-	0	transcript_id "Phchi.S3G150100.t1"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	transcript	11323952	11325536	.	-	.	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	stop_codon	11323949	11323951	.	-	0	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11323952	11323976	0.95	-	1	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11323952	11323976	.	-	.	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	intron	11323977	11324260	.	-	.	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324261	11324865	0.88	-	0	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324261	11324865	.	-	.	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	intron	11324866	11324963	.	-	.	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324964	11325536	0.89	-	0	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324964	11325536	.	-	.	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	start_codon	11325534	11325536	.	-	0	transcript_id "Phchi.S3G150100.t2"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	transcript	11324056	11325536	.	-	.	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	stop_codon	11324053	11324055	.	-	0	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324056	11324101	0.7	-	1	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324056	11324101	.	-	.	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	intron	11324102	11324260	.	-	.	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324261	11324865	0.7	-	0	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324261	11324865	.	-	.	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	intron	11324866	11324963	.	-	.	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	CDS	11324964	11325536	0.94	-	0	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	exon	11324964	11325536	.	-	.	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
Phchi.S3	AUGUSTUS	start_codon	11325534	11325536	.	-	0	transcript_id "Phchi.S3G150100.t3"; gene_id "Phchi.S3G150100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6595.t1 is derived from g3767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23911131	23913699	.	+	.	Phchi.S1G375400
Phchi.S1	AUGUSTUS	transcript	23911131	23913699	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	start_codon	23911131	23911133	.	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23911131	23911261	0.82	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23911131	23911261	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23911262	23911522	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23911523	23911638	1	+	1	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23911523	23911638	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23911639	23911745	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23911746	23911813	0.98	+	2	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23911746	23911813	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23911814	23911900	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23911901	23912017	1	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23911901	23912017	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23912018	23912213	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23912214	23912276	1	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23912214	23912276	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23912277	23912364	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23912365	23912469	1	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23912365	23912469	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23912470	23912562	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23912563	23912613	1	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23912563	23912613	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23912614	23912701	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23912702	23913022	1	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23912702	23913022	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23913023	23913113	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23913114	23913320	1	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23913114	23913320	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	intron	23913321	23913408	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	CDS	23913409	23913699	0.92	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	exon	23913409	23913699	.	+	.	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
Phchi.S1	AUGUSTUS	stop_codon	23913700	23913702	.	+	0	transcript_id "Phchi.S1G375400.t1"; gene_id "Phchi.S1G375400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13858.t1 is derived from g12325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9268455	9269463	.	-	.	Phchi.S3G117700
Phchi.S3	AUGUSTUS	transcript	9268455	9269463	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	stop_codon	9268452	9268454	.	-	0	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	CDS	9268455	9268797	0.63	-	1	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	exon	9268455	9268797	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	intron	9268798	9268877	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	CDS	9268878	9268950	0.99	-	2	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	exon	9268878	9268950	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	intron	9268951	9269023	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	CDS	9269024	9269104	0.99	-	2	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	exon	9269024	9269104	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	intron	9269105	9269192	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	CDS	9269193	9269463	0.46	-	0	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	exon	9269193	9269463	.	-	.	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
Phchi.S3	AUGUSTUS	start_codon	9269461	9269463	.	-	0	transcript_id "Phchi.S3G117700.t1"; gene_id "Phchi.S3G117700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8061.t1 is derived from g5236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32745148	32747025	.	-	.	Phchi.S1G522000
Phchi.S1	AUGUSTUS	transcript	32745148	32747025	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	stop_codon	32745145	32745147	.	-	0	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	CDS	32745148	32745393	0.97	-	0	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	exon	32745148	32745393	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	intron	32745394	32745477	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	CDS	32745478	32746429	0.99	-	1	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	exon	32745478	32746429	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	intron	32746430	32746528	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	CDS	32746529	32746750	1	-	1	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	exon	32746529	32746750	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	intron	32746751	32746894	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	CDS	32746895	32747025	0.99	-	0	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	exon	32746895	32747025	.	-	.	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
Phchi.S1	AUGUSTUS	start_codon	32747023	32747025	.	-	0	transcript_id "Phchi.S1G522000.t1"; gene_id "Phchi.S1G522000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11029.t1 is derived from g15079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3725410	3726840	.	+	.	Phchi.S4G061100
Phchi.S4	AUGUSTUS	transcript	3725410	3726840	.	+	.	transcript_id "Phchi.S4G061100.t1"; gene_id "Phchi.S4G061100"
Phchi.S4	AUGUSTUS	start_codon	3725410	3725412	.	+	0	transcript_id "Phchi.S4G061100.t1"; gene_id "Phchi.S4G061100"
Phchi.S4	AUGUSTUS	CDS	3725410	3726840	0.68	+	0	transcript_id "Phchi.S4G061100.t1"; gene_id "Phchi.S4G061100"
Phchi.S4	AUGUSTUS	exon	3725410	3726840	.	+	.	transcript_id "Phchi.S4G061100.t1"; gene_id "Phchi.S4G061100"
Phchi.S4	AUGUSTUS	stop_codon	3726841	3726843	.	+	0	transcript_id "Phchi.S4G061100.t1"; gene_id "Phchi.S4G061100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8434.t1 is derived from g5609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35925329	35929093	.	+	.	Phchi.S1G559300
Phchi.S1	AUGUSTUS	transcript	35925329	35929093	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	start_codon	35925329	35925331	.	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35925329	35926637	0.28	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35925329	35926637	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35926638	35926939	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35926940	35927002	0.35	+	2	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35926940	35927002	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35927003	35927230	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35927231	35927335	0.44	+	2	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35927231	35927335	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35927336	35927431	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35927432	35927487	0.51	+	2	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35927432	35927487	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35927488	35927687	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35927688	35927939	0.99	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35927688	35927939	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35927940	35928038	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35928039	35928119	1	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35928039	35928119	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35928120	35928225	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35928226	35928855	0.93	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35928226	35928855	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	intron	35928856	35929045	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	CDS	35929046	35929093	1	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	exon	35929046	35929093	.	+	.	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
Phchi.S1	AUGUSTUS	stop_codon	35929094	35929096	.	+	0	transcript_id "Phchi.S1G559300.t1"; gene_id "Phchi.S1G559300"
# This transcript jg10441.t1 is derived from g14489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	349042	349260	.	-	.	Phchi.S4G002200
Phchi.S4	AUGUSTUS	transcript	349042	349260	.	-	.	transcript_id "Phchi.S4G002200.t1"; gene_id "Phchi.S4G002200"
Phchi.S4	AUGUSTUS	stop_codon	349039	349041	.	-	0	transcript_id "Phchi.S4G002200.t1"; gene_id "Phchi.S4G002200"
Phchi.S4	AUGUSTUS	CDS	349042	349260	0.81	-	0	transcript_id "Phchi.S4G002200.t1"; gene_id "Phchi.S4G002200"
Phchi.S4	AUGUSTUS	exon	349042	349260	.	-	.	transcript_id "Phchi.S4G002200.t1"; gene_id "Phchi.S4G002200"
Phchi.S4	AUGUSTUS	start_codon	349258	349260	.	-	0	transcript_id "Phchi.S4G002200.t1"; gene_id "Phchi.S4G002200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15937.t1 is derived from g14400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C58	AUGUSTUS	gene	19113	21106	.	-	.	Phchi.C58G000100
Phchi.C58	AUGUSTUS	transcript	19113	21106	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	stop_codon	19110	19112	.	-	0	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	CDS	19113	19290	1	-	1	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	exon	19113	19290	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	intron	19291	19373	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	CDS	19374	19591	1	-	0	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	exon	19374	19591	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	intron	19592	19705	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	CDS	19706	20153	0.34	-	1	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	exon	19706	20153	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	intron	20154	20340	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	CDS	20341	20395	0.34	-	2	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	exon	20341	20395	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	intron	20396	20481	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	CDS	20482	21106	0.29	-	0	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	exon	20482	21106	.	-	.	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
Phchi.C58	AUGUSTUS	start_codon	21104	21106	.	-	0	transcript_id "Phchi.C58G000100.t1"; gene_id "Phchi.C58G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15032.t1 is derived from g13500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16635367	16637472	.	+	.	Phchi.S3G235100
Phchi.S3	AUGUSTUS	transcript	16635367	16637472	.	+	.	transcript_id "Phchi.S3G235100.t1"; gene_id "Phchi.S3G235100"
Phchi.S3	AUGUSTUS	start_codon	16635367	16635369	.	+	0	transcript_id "Phchi.S3G235100.t1"; gene_id "Phchi.S3G235100"
Phchi.S3	AUGUSTUS	CDS	16635367	16637472	1	+	0	transcript_id "Phchi.S3G235100.t1"; gene_id "Phchi.S3G235100"
Phchi.S3	AUGUSTUS	exon	16635367	16637472	.	+	.	transcript_id "Phchi.S3G235100.t1"; gene_id "Phchi.S3G235100"
Phchi.S3	AUGUSTUS	stop_codon	16637473	16637475	.	+	0	transcript_id "Phchi.S3G235100.t1"; gene_id "Phchi.S3G235100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16012.t1 is derived from g9768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C120	AUGUSTUS	gene	15489	17477	.	-	.	Phchi.C120G000100
Phchi.C120	AUGUSTUS	transcript	15489	17477	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	stop_codon	15486	15488	.	-	0	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	CDS	15489	15965	0.92	-	0	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	exon	15489	15965	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	intron	15966	16079	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	CDS	16080	16524	0.47	-	1	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	exon	16080	16524	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	intron	16525	16711	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	CDS	16712	16766	0.5	-	2	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	exon	16712	16766	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	intron	16767	16852	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	CDS	16853	17477	0.31	-	0	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	exon	16853	17477	.	-	.	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
Phchi.C120	AUGUSTUS	start_codon	17475	17477	.	-	0	transcript_id "Phchi.C120G000100.t1"; gene_id "Phchi.C120G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15016.t1 is derived from g13484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16538626	16539804	.	-	.	Phchi.S3G233500
Phchi.S3	AUGUSTUS	transcript	16538626	16539804	.	-	.	transcript_id "Phchi.S3G233500.t1"; gene_id "Phchi.S3G233500"
Phchi.S3	AUGUSTUS	stop_codon	16538623	16538625	.	-	0	transcript_id "Phchi.S3G233500.t1"; gene_id "Phchi.S3G233500"
Phchi.S3	AUGUSTUS	CDS	16538626	16539804	0.98	-	0	transcript_id "Phchi.S3G233500.t1"; gene_id "Phchi.S3G233500"
Phchi.S3	AUGUSTUS	exon	16538626	16539804	.	-	.	transcript_id "Phchi.S3G233500.t1"; gene_id "Phchi.S3G233500"
Phchi.S3	AUGUSTUS	start_codon	16539802	16539804	.	-	0	transcript_id "Phchi.S3G233500.t1"; gene_id "Phchi.S3G233500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg145.t1 is derived from g9927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	796308	798004	.	-	.	Phchi.S6G010400
Phchi.S6	AUGUSTUS	transcript	797217	798004	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	stop_codon	797214	797216	.	-	0	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797217	797220	0.19	-	1	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797217	797220	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	797221	797313	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797314	797401	0.97	-	2	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797314	797401	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	797402	797604	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797605	797743	0.98	-	0	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797605	797743	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	797744	797830	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797831	798004	0.32	-	0	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797831	798004	.	-	.	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	start_codon	798002	798004	.	-	0	transcript_id "Phchi.S6G010400.t1"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	transcript	796308	798004	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	stop_codon	796305	796307	.	-	0	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	796308	796313	0.15	-	0	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	796308	796313	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	796314	796444	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	796445	797213	0.16	-	1	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	796445	797213	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	797214	797313	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797314	797401	1	-	2	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797314	797401	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	797402	797604	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797605	797743	1	-	0	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797605	797743	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	intron	797744	797830	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	CDS	797831	798004	0.27	-	0	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	exon	797831	798004	.	-	.	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
Phchi.S6	AUGUSTUS	start_codon	798002	798004	.	-	0	transcript_id "Phchi.S6G010400.t2"; gene_id "Phchi.S6G010400"
# This transcript jg8581.t2 is derived from g5756.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8582.t1 is derived from g5757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36735549	36736078	.	+	.	Phchi.S1G574100
Phchi.S1	AUGUSTUS	transcript	36735549	36736078	.	+	.	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	start_codon	36735549	36735551	.	+	0	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	CDS	36735549	36735815	0.68	+	0	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	exon	36735549	36735815	.	+	.	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	intron	36735816	36735898	.	+	.	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	CDS	36735899	36736078	0.93	+	0	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	exon	36735899	36736078	.	+	.	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
Phchi.S1	AUGUSTUS	stop_codon	36736079	36736081	.	+	0	transcript_id "Phchi.S1G574100.t1"; gene_id "Phchi.S1G574100"
# This transcript jg1736.t2 is derived from g8656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1737.t1 is derived from g8657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2781280	2782270	.	-	.	Phchi.S5G034600
Phchi.S5	AUGUSTUS	transcript	2781280	2782270	.	-	.	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	stop_codon	2781277	2781279	.	-	0	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	CDS	2781280	2781372	1	-	0	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	exon	2781280	2781372	.	-	.	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	intron	2781373	2781452	.	-	.	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	CDS	2781453	2781748	1	-	2	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	exon	2781453	2781748	.	-	.	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	intron	2781749	2781960	.	-	.	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	CDS	2781961	2782270	0.99	-	0	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	exon	2781961	2782270	.	-	.	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
Phchi.S5	AUGUSTUS	start_codon	2782268	2782270	.	-	0	transcript_id "Phchi.S5G034600.t1"; gene_id "Phchi.S5G034600"
# This transcript jg11734.t2 is derived from g15786.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11735.t1 is derived from g15787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7908767	7909886	.	+	.	Phchi.S4G131700
Phchi.S4	AUGUSTUS	transcript	7908767	7909886	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	start_codon	7908767	7908769	.	+	0	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	CDS	7908767	7909317	0.86	+	0	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	exon	7908767	7909317	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	intron	7909318	7909402	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	CDS	7909403	7909498	1	+	1	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	exon	7909403	7909498	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	intron	7909499	7909586	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	CDS	7909587	7909721	1	+	1	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	exon	7909587	7909721	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	intron	7909722	7909807	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	CDS	7909808	7909886	0.99	+	1	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	exon	7909808	7909886	.	+	.	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
Phchi.S4	AUGUSTUS	stop_codon	7909887	7909889	.	+	0	transcript_id "Phchi.S4G131700.t1"; gene_id "Phchi.S4G131700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8305.t1 is derived from g5480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35195119	35196326	.	+	.	Phchi.S1G546400
Phchi.S1	AUGUSTUS	transcript	35195119	35196326	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	start_codon	35195119	35195121	.	+	0	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	CDS	35195119	35195188	0.56	+	0	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	exon	35195119	35195188	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	intron	35195189	35195298	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	CDS	35195299	35195471	0.71	+	2	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	exon	35195299	35195471	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	intron	35195472	35195650	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	CDS	35195651	35195744	0.89	+	0	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	exon	35195651	35195744	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	intron	35195745	35195853	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	CDS	35195854	35195936	1	+	2	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	exon	35195854	35195936	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	intron	35195937	35196035	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	CDS	35196036	35196326	1	+	0	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	exon	35196036	35196326	.	+	.	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
Phchi.S1	AUGUSTUS	stop_codon	35196327	35196329	.	+	0	transcript_id "Phchi.S1G546400.t1"; gene_id "Phchi.S1G546400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14910.t1 is derived from g13378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15465024	15467768	.	-	.	Phchi.S3G222900
Phchi.S3	AUGUSTUS	transcript	15465024	15467768	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	stop_codon	15465021	15465023	.	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15465024	15465146	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15465024	15465146	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15465147	15465269	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15465270	15465353	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15465270	15465353	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15465354	15465474	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15465475	15465600	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15465475	15465600	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15465601	15465689	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15465690	15465809	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15465690	15465809	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15465810	15465902	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15465903	15466010	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15465903	15466010	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15466011	15466096	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15466097	15466249	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15466097	15466249	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15466250	15466324	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15466325	15466420	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15466325	15466420	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15466421	15466515	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15466516	15466600	1	-	1	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15466516	15466600	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	intron	15466601	15466716	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	CDS	15466717	15467768	1	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	exon	15466717	15467768	.	-	.	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
Phchi.S3	AUGUSTUS	start_codon	15467766	15467768	.	-	0	transcript_id "Phchi.S3G222900.t1"; gene_id "Phchi.S3G222900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12587.t1 is derived from g8264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36097270	36100403	.	+	.	Phchi.S2G066700
Phchi.S2	AUGUSTUS	transcript	36097270	36100403	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	start_codon	36097270	36097272	.	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36097270	36098421	0.91	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36097270	36098421	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36098422	36098536	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36098537	36098701	1	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36098537	36098701	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36098702	36098867	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36098868	36098945	1	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36098868	36098945	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36098946	36099069	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099070	36099148	1	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099070	36099148	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099149	36099233	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099234	36099378	0.88	+	2	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099234	36099378	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099379	36099641	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099642	36099705	0.82	+	1	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099642	36099705	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099706	36099799	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099800	36099977	1	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099800	36099977	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099978	36100122	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36100123	36100403	1	+	2	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36100123	36100403	.	+	.	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	stop_codon	36100404	36100406	.	+	0	transcript_id "Phchi.S2G066700.t1"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	transcript	36097270	36100403	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	start_codon	36097270	36097272	.	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36097270	36098421	0.89	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36097270	36098421	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36098422	36098536	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36098537	36098701	1	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36098537	36098701	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36098702	36098867	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36098868	36098945	1	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36098868	36098945	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36098946	36099069	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099070	36099148	1	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099070	36099148	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099149	36099341	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099342	36099378	0.75	+	2	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099342	36099378	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099379	36099641	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099642	36099705	0.68	+	1	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099642	36099705	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099706	36099799	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36099800	36099977	1	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36099800	36099977	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	intron	36099978	36100122	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	CDS	36100123	36100403	0.97	+	2	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	exon	36100123	36100403	.	+	.	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
Phchi.S2	AUGUSTUS	stop_codon	36100404	36100406	.	+	0	transcript_id "Phchi.S2G066700.t2"; gene_id "Phchi.S2G066700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6180.t1 is derived from g3351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21331378	21332427	.	+	.	Phchi.S1G333900
Phchi.S1	AUGUSTUS	transcript	21331378	21332427	.	+	.	transcript_id "Phchi.S1G333900.t1"; gene_id "Phchi.S1G333900"
Phchi.S1	AUGUSTUS	start_codon	21331378	21331380	.	+	0	transcript_id "Phchi.S1G333900.t1"; gene_id "Phchi.S1G333900"
Phchi.S1	AUGUSTUS	CDS	21331378	21332427	0.75	+	0	transcript_id "Phchi.S1G333900.t1"; gene_id "Phchi.S1G333900"
Phchi.S1	AUGUSTUS	exon	21331378	21332427	.	+	.	transcript_id "Phchi.S1G333900.t1"; gene_id "Phchi.S1G333900"
Phchi.S1	AUGUSTUS	stop_codon	21332428	21332430	.	+	0	transcript_id "Phchi.S1G333900.t1"; gene_id "Phchi.S1G333900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8256.t1 is derived from g5431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34742205	34743222	.	+	.	Phchi.S1G541500
Phchi.S1	AUGUSTUS	transcript	34742205	34743222	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	start_codon	34742205	34742207	.	+	0	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	CDS	34742205	34742434	1	+	0	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	exon	34742205	34742434	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	intron	34742435	34742555	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	CDS	34742556	34742692	1	+	1	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	exon	34742556	34742692	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	intron	34742693	34742802	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	CDS	34742803	34742939	1	+	2	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	exon	34742803	34742939	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	intron	34742940	34743048	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	CDS	34743049	34743222	1	+	0	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	exon	34743049	34743222	.	+	.	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
Phchi.S1	AUGUSTUS	stop_codon	34743223	34743225	.	+	0	transcript_id "Phchi.S1G541500.t1"; gene_id "Phchi.S1G541500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8135.t1 is derived from g5310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33755160	33755999	.	+	.	Phchi.S1G529400
Phchi.S1	AUGUSTUS	transcript	33755160	33755999	.	+	.	transcript_id "Phchi.S1G529400.t1"; gene_id "Phchi.S1G529400"
Phchi.S1	AUGUSTUS	start_codon	33755160	33755162	.	+	0	transcript_id "Phchi.S1G529400.t1"; gene_id "Phchi.S1G529400"
Phchi.S1	AUGUSTUS	CDS	33755160	33755999	0.9	+	0	transcript_id "Phchi.S1G529400.t1"; gene_id "Phchi.S1G529400"
Phchi.S1	AUGUSTUS	exon	33755160	33755999	.	+	.	transcript_id "Phchi.S1G529400.t1"; gene_id "Phchi.S1G529400"
Phchi.S1	AUGUSTUS	stop_codon	33756000	33756002	.	+	0	transcript_id "Phchi.S1G529400.t1"; gene_id "Phchi.S1G529400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11270.t1 is derived from g15320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5105474	5107137	.	+	.	Phchi.S4G085200
Phchi.S4	AUGUSTUS	transcript	5105474	5107137	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	start_codon	5105474	5105476	.	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5105474	5105494	0.35	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5105474	5105494	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5105495	5105593	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5105594	5105680	1	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5105594	5105680	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5105681	5105811	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5105812	5105933	1	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5105812	5105933	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5105934	5106020	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5106021	5106122	1	+	1	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5106021	5106122	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5106123	5106235	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5106236	5106427	0.99	+	1	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5106236	5106427	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5106428	5106514	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5106515	5106581	1	+	1	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5106515	5106581	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5106582	5106683	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5106684	5106821	1	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5106684	5106821	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5106822	5106901	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5106902	5106937	1	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5106902	5106937	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	intron	5106938	5107035	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	CDS	5107036	5107137	0.99	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	exon	5107036	5107137	.	+	.	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
Phchi.S4	AUGUSTUS	stop_codon	5107138	5107140	.	+	0	transcript_id "Phchi.S4G085200.t1"; gene_id "Phchi.S4G085200"
# This transcript jg13034.t2 is derived from g11499.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13035.t1 is derived from g11500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3820386	3821901	.	-	.	Phchi.S3G035400
Phchi.S3	AUGUSTUS	transcript	3820386	3821901	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	stop_codon	3820383	3820385	.	-	0	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	CDS	3820386	3820660	1	-	2	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	exon	3820386	3820660	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	intron	3820661	3820759	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	CDS	3820760	3821030	1	-	0	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	exon	3820760	3821030	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	intron	3821031	3821115	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	CDS	3821116	3821276	1	-	2	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	exon	3821116	3821276	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	intron	3821277	3821363	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	CDS	3821364	3821564	1	-	2	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	exon	3821364	3821564	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	intron	3821565	3821654	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	CDS	3821655	3821901	0.95	-	0	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	exon	3821655	3821901	.	-	.	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
Phchi.S3	AUGUSTUS	start_codon	3821899	3821901	.	-	0	transcript_id "Phchi.S3G035400.t1"; gene_id "Phchi.S3G035400"
# This transcript jg11742.t2 is derived from g15794.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11743.t1 is derived from g15795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7969642	7971101	.	-	.	Phchi.S4G132500
Phchi.S4	AUGUSTUS	transcript	7969642	7971101	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	stop_codon	7969639	7969641	.	-	0	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	CDS	7969642	7970050	1	-	1	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	exon	7969642	7970050	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	intron	7970051	7970198	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	CDS	7970199	7970346	1	-	2	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	exon	7970199	7970346	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	intron	7970347	7970450	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	CDS	7970451	7970530	0.94	-	1	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	exon	7970451	7970530	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	intron	7970531	7970621	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	CDS	7970622	7970853	0.91	-	2	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	exon	7970622	7970853	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	intron	7970854	7970980	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	CDS	7970981	7971101	0.94	-	0	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	exon	7970981	7971101	.	-	.	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
Phchi.S4	AUGUSTUS	start_codon	7971099	7971101	.	-	0	transcript_id "Phchi.S4G132500.t1"; gene_id "Phchi.S4G132500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11627.t1 is derived from g15678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7379668	7381166	.	+	.	Phchi.S4G120900
Phchi.S4	AUGUSTUS	transcript	7379668	7381166	.	+	.	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	start_codon	7379668	7379670	.	+	0	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	CDS	7379668	7379829	0.99	+	0	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	exon	7379668	7379829	.	+	.	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	intron	7379830	7379987	.	+	.	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	CDS	7379988	7380707	1	+	0	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	exon	7379988	7380707	.	+	.	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	intron	7380708	7380806	.	+	.	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	CDS	7380807	7381166	0.86	+	0	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	exon	7380807	7381166	.	+	.	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
Phchi.S4	AUGUSTUS	stop_codon	7381167	7381169	.	+	0	transcript_id "Phchi.S4G120900.t1"; gene_id "Phchi.S4G120900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3047.t1 is derived from g216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1354949	1355759	.	-	.	Phchi.S1G020600
Phchi.S1	AUGUSTUS	transcript	1354949	1355759	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	stop_codon	1354946	1354948	.	-	0	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	CDS	1354949	1355195	0.5	-	1	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	exon	1354949	1355195	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	intron	1355196	1355300	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	CDS	1355301	1355322	0.53	-	2	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	exon	1355301	1355322	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	intron	1355323	1355417	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	CDS	1355418	1355531	1	-	2	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	exon	1355418	1355531	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	intron	1355532	1355656	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	CDS	1355657	1355759	1	-	0	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	exon	1355657	1355759	.	-	.	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
Phchi.S1	AUGUSTUS	start_codon	1355757	1355759	.	-	0	transcript_id "Phchi.S1G020600.t1"; gene_id "Phchi.S1G020600"
# This transcript jg14380.t2 is derived from g12848.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14381.t1 is derived from g12849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12467639	12468609	.	+	.	Phchi.S3G170000
Phchi.S3	AUGUSTUS	transcript	12467639	12468609	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	start_codon	12467639	12467641	.	+	0	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	CDS	12467639	12467929	1	+	0	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	exon	12467639	12467929	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	intron	12467930	12468017	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	CDS	12468018	12468140	1	+	0	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	exon	12468018	12468140	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	intron	12468141	12468273	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	CDS	12468274	12468343	1	+	0	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	exon	12468274	12468343	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	intron	12468344	12468439	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	CDS	12468440	12468609	1	+	2	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	exon	12468440	12468609	.	+	.	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
Phchi.S3	AUGUSTUS	stop_codon	12468610	12468612	.	+	0	transcript_id "Phchi.S3G170000.t1"; gene_id "Phchi.S3G170000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1530.t1 is derived from g8449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1608500	1610747	.	+	.	Phchi.S5G013900
Phchi.S5	AUGUSTUS	transcript	1608500	1610747	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	start_codon	1608500	1608502	.	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1608500	1608746	0.57	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1608500	1608746	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1608747	1608824	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1608825	1608889	1	+	2	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1608825	1608889	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1608890	1609040	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1609041	1609133	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1609041	1609133	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1609134	1609211	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1609212	1609412	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1609212	1609412	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1609413	1609506	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1609507	1609587	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1609507	1609587	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1609588	1609688	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1609689	1609784	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1609689	1609784	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1609785	1609884	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1609885	1609962	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1609885	1609962	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1609963	1610068	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1610069	1610158	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1610069	1610158	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1610159	1610278	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1610279	1610346	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1610279	1610346	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1610347	1610507	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1610508	1610589	1	+	1	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1610508	1610589	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	intron	1610590	1610684	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	CDS	1610685	1610747	1	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	exon	1610685	1610747	.	+	.	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
Phchi.S5	AUGUSTUS	stop_codon	1610748	1610750	.	+	0	transcript_id "Phchi.S5G013900.t1"; gene_id "Phchi.S5G013900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13934.t1 is derived from g12401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9798451	9800275	.	-	.	Phchi.S3G125300
Phchi.S3	AUGUSTUS	transcript	9798451	9800275	.	-	.	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	stop_codon	9798448	9798450	.	-	0	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	CDS	9798451	9799827	0.86	-	0	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	exon	9798451	9799827	.	-	.	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	intron	9799828	9799948	.	-	.	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	CDS	9799949	9800275	1	-	0	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	exon	9799949	9800275	.	-	.	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
Phchi.S3	AUGUSTUS	start_codon	9800273	9800275	.	-	0	transcript_id "Phchi.S3G125300.t1"; gene_id "Phchi.S3G125300"
# This transcript jg3462.t2 is derived from g631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3463.t1 is derived from g632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3887449	3888036	.	-	.	Phchi.S1G062200
Phchi.S1	AUGUSTUS	transcript	3887449	3888036	.	-	.	transcript_id "Phchi.S1G062200.t1"; gene_id "Phchi.S1G062200"
Phchi.S1	AUGUSTUS	stop_codon	3887446	3887448	.	-	0	transcript_id "Phchi.S1G062200.t1"; gene_id "Phchi.S1G062200"
Phchi.S1	AUGUSTUS	CDS	3887449	3888036	0.4	-	0	transcript_id "Phchi.S1G062200.t1"; gene_id "Phchi.S1G062200"
Phchi.S1	AUGUSTUS	exon	3887449	3888036	.	-	.	transcript_id "Phchi.S1G062200.t1"; gene_id "Phchi.S1G062200"
Phchi.S1	AUGUSTUS	start_codon	3888034	3888036	.	-	0	transcript_id "Phchi.S1G062200.t1"; gene_id "Phchi.S1G062200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8483.t1 is derived from g5658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36145107	36149390	.	+	.	Phchi.S1G564200
Phchi.S1	AUGUSTUS	transcript	36145107	36149390	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	start_codon	36145107	36145109	.	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36145107	36145207	0.36	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36145107	36145207	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36145208	36145423	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36145424	36145920	0.42	+	1	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36145424	36145920	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36145921	36146124	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36146125	36146711	0.98	+	2	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36146125	36146711	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36146712	36146818	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36146819	36146887	0.99	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36146819	36146887	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36146888	36146983	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36146984	36147181	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36146984	36147181	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36147182	36147344	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36147345	36147476	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36147345	36147476	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36147477	36147563	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36147564	36147650	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36147564	36147650	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36147651	36147745	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36147746	36148183	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36147746	36148183	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36148184	36148313	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36148314	36148481	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36148314	36148481	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36148482	36148573	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36148574	36148819	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36148574	36148819	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36148820	36148906	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36148907	36149022	1	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36148907	36149022	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36149023	36149114	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36149115	36149166	0.99	+	1	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36149115	36149166	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	intron	36149167	36149336	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	CDS	36149337	36149390	0.99	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	exon	36149337	36149390	.	+	.	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
Phchi.S1	AUGUSTUS	stop_codon	36149391	36149393	.	+	0	transcript_id "Phchi.S1G564200.t1"; gene_id "Phchi.S1G564200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14005.t1 is derived from g12472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10248779	10250377	.	+	.	Phchi.S3G132400
Phchi.S3	AUGUSTUS	transcript	10248779	10250377	.	+	.	transcript_id "Phchi.S3G132400.t1"; gene_id "Phchi.S3G132400"
Phchi.S3	AUGUSTUS	start_codon	10248779	10248781	.	+	0	transcript_id "Phchi.S3G132400.t1"; gene_id "Phchi.S3G132400"
Phchi.S3	AUGUSTUS	CDS	10248779	10250377	0.5	+	0	transcript_id "Phchi.S3G132400.t1"; gene_id "Phchi.S3G132400"
Phchi.S3	AUGUSTUS	exon	10248779	10250377	.	+	.	transcript_id "Phchi.S3G132400.t1"; gene_id "Phchi.S3G132400"
Phchi.S3	AUGUSTUS	stop_codon	10250378	10250380	.	+	0	transcript_id "Phchi.S3G132400.t1"; gene_id "Phchi.S3G132400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9906.t1 is derived from g7082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44383659	44384277	.	+	.	Phchi.S1G706500
Phchi.S1	AUGUSTUS	transcript	44383659	44384277	.	+	.	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	start_codon	44383659	44383661	.	+	0	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	CDS	44383659	44383721	1	+	0	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	exon	44383659	44383721	.	+	.	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	intron	44383722	44383808	.	+	.	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	CDS	44383809	44383977	1	+	0	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	exon	44383809	44383977	.	+	.	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	intron	44383978	44384083	.	+	.	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	CDS	44384084	44384277	0.75	+	2	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	exon	44384084	44384277	.	+	.	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
Phchi.S1	AUGUSTUS	stop_codon	44384278	44384280	.	+	0	transcript_id "Phchi.S1G706500.t1"; gene_id "Phchi.S1G706500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1202.t1 is derived from g10985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8403671	8405122	.	+	.	Phchi.S6G116100
Phchi.S6	AUGUSTUS	transcript	8403671	8405122	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	start_codon	8403671	8403673	.	+	0	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	CDS	8403671	8403858	0.81	+	0	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	exon	8403671	8403858	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	intron	8403859	8403992	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	CDS	8403993	8404039	0.32	+	1	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	exon	8403993	8404039	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	intron	8404040	8404107	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	CDS	8404108	8404178	1	+	2	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	exon	8404108	8404178	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	intron	8404179	8404266	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	CDS	8404267	8404476	1	+	0	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	exon	8404267	8404476	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	intron	8404477	8404563	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	CDS	8404564	8404774	1	+	0	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	exon	8404564	8404774	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	intron	8404775	8404865	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	CDS	8404866	8405122	1	+	2	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	exon	8404866	8405122	.	+	.	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
Phchi.S6	AUGUSTUS	stop_codon	8405123	8405125	.	+	0	transcript_id "Phchi.S6G116100.t1"; gene_id "Phchi.S6G116100"
# This transcript jg9859.t2 is derived from g7035.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9860.t1 is derived from g7036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44120293	44121630	.	-	.	Phchi.S1G701900
Phchi.S1	AUGUSTUS	transcript	44120293	44121630	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	stop_codon	44120290	44120292	.	-	0	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	CDS	44120293	44120357	0.82	-	2	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	exon	44120293	44120357	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	intron	44120358	44120523	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	CDS	44120524	44121106	0.81	-	0	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	exon	44120524	44121106	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	intron	44121107	44121186	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	CDS	44121187	44121220	0.93	-	1	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	exon	44121187	44121220	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	intron	44121221	44121411	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	CDS	44121412	44121511	0.97	-	2	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	exon	44121412	44121511	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	intron	44121512	44121605	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	CDS	44121606	44121630	0.56	-	0	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	exon	44121606	44121630	.	-	.	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
Phchi.S1	AUGUSTUS	start_codon	44121628	44121630	.	-	0	transcript_id "Phchi.S1G701900.t1"; gene_id "Phchi.S1G701900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11080.t1 is derived from g15130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3993794	3994586	.	-	.	Phchi.S4G066200
Phchi.S4	AUGUSTUS	transcript	3993794	3994586	.	-	.	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	stop_codon	3993791	3993793	.	-	0	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	CDS	3993794	3994089	0.36	-	2	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	exon	3993794	3994089	.	-	.	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	intron	3994090	3994297	.	-	.	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	CDS	3994298	3994586	0.32	-	0	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	exon	3994298	3994586	.	-	.	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
Phchi.S4	AUGUSTUS	start_codon	3994584	3994586	.	-	0	transcript_id "Phchi.S4G066200.t1"; gene_id "Phchi.S4G066200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9921.t1 is derived from g7097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44478836	44483158	.	+	.	Phchi.S1G708000
Phchi.S1	AUGUSTUS	transcript	44478836	44483158	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	start_codon	44478836	44478838	.	+	0	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	CDS	44478836	44480418	0.37	+	0	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	exon	44478836	44480418	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	intron	44480419	44480559	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	CDS	44480560	44481904	0.61	+	1	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	exon	44480560	44481904	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	intron	44481905	44482018	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	CDS	44482019	44482231	0.47	+	0	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	exon	44482019	44482231	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	intron	44482232	44482351	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	CDS	44482352	44483158	0.62	+	0	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	exon	44482352	44483158	.	+	.	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
Phchi.S1	AUGUSTUS	stop_codon	44483159	44483161	.	+	0	transcript_id "Phchi.S1G708000.t1"; gene_id "Phchi.S1G708000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14352.t1 is derived from g12819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12335491	12338027	.	+	.	Phchi.S3G167100
Phchi.S3	AUGUSTUS	transcript	12335491	12338027	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	start_codon	12335491	12335493	.	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12335491	12335955	1	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12335491	12335955	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12335956	12336049	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12336050	12336160	1	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12336050	12336160	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12336161	12336264	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12336265	12336297	1	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12336265	12336297	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12336298	12336435	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12336436	12336619	1	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12336436	12336619	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12336620	12336704	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12336705	12336889	1	+	2	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12336705	12336889	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12336890	12337023	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12337024	12337160	1	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12337024	12337160	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12337161	12337248	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12337249	12337344	1	+	1	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12337249	12337344	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12337345	12337482	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12337483	12337552	1	+	1	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12337483	12337552	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12337553	12337659	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12337660	12337734	0.86	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12337660	12337734	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12337735	12337847	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12337848	12337893	1	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12337848	12337893	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	intron	12337894	12337974	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	CDS	12337975	12338027	1	+	2	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	exon	12337975	12338027	.	+	.	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
Phchi.S3	AUGUSTUS	stop_codon	12338028	12338030	.	+	0	transcript_id "Phchi.S3G167100.t1"; gene_id "Phchi.S3G167100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8661.t1 is derived from g5836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37315690	37316352	.	-	.	Phchi.S1G582000
Phchi.S1	AUGUSTUS	transcript	37315690	37316352	.	-	.	transcript_id "Phchi.S1G582000.t1"; gene_id "Phchi.S1G582000"
Phchi.S1	AUGUSTUS	stop_codon	37315687	37315689	.	-	0	transcript_id "Phchi.S1G582000.t1"; gene_id "Phchi.S1G582000"
Phchi.S1	AUGUSTUS	CDS	37315690	37316352	0.85	-	0	transcript_id "Phchi.S1G582000.t1"; gene_id "Phchi.S1G582000"
Phchi.S1	AUGUSTUS	exon	37315690	37316352	.	-	.	transcript_id "Phchi.S1G582000.t1"; gene_id "Phchi.S1G582000"
Phchi.S1	AUGUSTUS	start_codon	37316350	37316352	.	-	0	transcript_id "Phchi.S1G582000.t1"; gene_id "Phchi.S1G582000"
# This transcript jg13820.t2 is derived from g12287.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13821.t1 is derived from g12288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9071528	9073457	.	+	.	Phchi.S3G114000
Phchi.S3	AUGUSTUS	transcript	9071528	9073457	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	start_codon	9071528	9071530	.	+	0	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	CDS	9071528	9071633	0.84	+	0	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	exon	9071528	9071633	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	intron	9071634	9071753	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	CDS	9071754	9072015	0.92	+	2	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	exon	9071754	9072015	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	intron	9072016	9072112	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	CDS	9072113	9072240	1	+	1	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	exon	9072113	9072240	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	intron	9072241	9072322	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	CDS	9072323	9072450	1	+	2	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	exon	9072323	9072450	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	intron	9072451	9072521	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	CDS	9072522	9073184	0.99	+	0	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	exon	9072522	9073184	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	intron	9073185	9073283	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	CDS	9073284	9073457	0.94	+	0	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	exon	9073284	9073457	.	+	.	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
Phchi.S3	AUGUSTUS	stop_codon	9073458	9073460	.	+	0	transcript_id "Phchi.S3G114000.t1"; gene_id "Phchi.S3G114000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4991.t1 is derived from g2161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13919402	13920763	.	+	.	Phchi.S1G215000
Phchi.S1	AUGUSTUS	transcript	13919402	13920763	.	+	.	transcript_id "Phchi.S1G215000.t1"; gene_id "Phchi.S1G215000"
Phchi.S1	AUGUSTUS	start_codon	13919402	13919404	.	+	0	transcript_id "Phchi.S1G215000.t1"; gene_id "Phchi.S1G215000"
Phchi.S1	AUGUSTUS	CDS	13919402	13920763	0.99	+	0	transcript_id "Phchi.S1G215000.t1"; gene_id "Phchi.S1G215000"
Phchi.S1	AUGUSTUS	exon	13919402	13920763	.	+	.	transcript_id "Phchi.S1G215000.t1"; gene_id "Phchi.S1G215000"
Phchi.S1	AUGUSTUS	stop_codon	13920764	13920766	.	+	0	transcript_id "Phchi.S1G215000.t1"; gene_id "Phchi.S1G215000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11664.t1 is derived from g15715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7583085	7584095	.	+	.	Phchi.S4G124600
Phchi.S4	AUGUSTUS	transcript	7583085	7584095	.	+	.	transcript_id "Phchi.S4G124600.t1"; gene_id "Phchi.S4G124600"
Phchi.S4	AUGUSTUS	start_codon	7583085	7583087	.	+	0	transcript_id "Phchi.S4G124600.t1"; gene_id "Phchi.S4G124600"
Phchi.S4	AUGUSTUS	CDS	7583085	7584095	1	+	0	transcript_id "Phchi.S4G124600.t1"; gene_id "Phchi.S4G124600"
Phchi.S4	AUGUSTUS	exon	7583085	7584095	.	+	.	transcript_id "Phchi.S4G124600.t1"; gene_id "Phchi.S4G124600"
Phchi.S4	AUGUSTUS	stop_codon	7584096	7584098	.	+	0	transcript_id "Phchi.S4G124600.t1"; gene_id "Phchi.S4G124600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2791.t1 is derived from g9711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8891551	8892036	.	+	.	Phchi.S5G140000
Phchi.S5	AUGUSTUS	transcript	8891551	8892036	.	+	.	transcript_id "Phchi.S5G140000.t1"; gene_id "Phchi.S5G140000"
Phchi.S5	AUGUSTUS	start_codon	8891551	8891553	.	+	0	transcript_id "Phchi.S5G140000.t1"; gene_id "Phchi.S5G140000"
Phchi.S5	AUGUSTUS	CDS	8891551	8892036	0.99	+	0	transcript_id "Phchi.S5G140000.t1"; gene_id "Phchi.S5G140000"
Phchi.S5	AUGUSTUS	exon	8891551	8892036	.	+	.	transcript_id "Phchi.S5G140000.t1"; gene_id "Phchi.S5G140000"
Phchi.S5	AUGUSTUS	stop_codon	8892037	8892039	.	+	0	transcript_id "Phchi.S5G140000.t1"; gene_id "Phchi.S5G140000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11650.t1 is derived from g15701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7460369	7463013	.	-	.	Phchi.S4G123200
Phchi.S4	AUGUSTUS	transcript	7460369	7463013	.	-	.	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	stop_codon	7460366	7460368	.	-	0	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	CDS	7460369	7460733	1	-	2	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	exon	7460369	7460733	.	-	.	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	intron	7460734	7461066	.	-	.	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	CDS	7461067	7461996	0.34	-	2	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	exon	7461067	7461996	.	-	.	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	intron	7461997	7462103	.	-	.	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	CDS	7462104	7463013	0.27	-	0	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	exon	7462104	7463013	.	-	.	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
Phchi.S4	AUGUSTUS	start_codon	7463011	7463013	.	-	0	transcript_id "Phchi.S4G123200.t1"; gene_id "Phchi.S4G123200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12746.t1 is derived from g11211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1762273	1762617	.	-	.	Phchi.S3G006500
Phchi.S3	AUGUSTUS	transcript	1762273	1762617	.	-	.	transcript_id "Phchi.S3G006500.t1"; gene_id "Phchi.S3G006500"
Phchi.S3	AUGUSTUS	stop_codon	1762270	1762272	.	-	0	transcript_id "Phchi.S3G006500.t1"; gene_id "Phchi.S3G006500"
Phchi.S3	AUGUSTUS	CDS	1762273	1762617	0.59	-	0	transcript_id "Phchi.S3G006500.t1"; gene_id "Phchi.S3G006500"
Phchi.S3	AUGUSTUS	exon	1762273	1762617	.	-	.	transcript_id "Phchi.S3G006500.t1"; gene_id "Phchi.S3G006500"
Phchi.S3	AUGUSTUS	start_codon	1762615	1762617	.	-	0	transcript_id "Phchi.S3G006500.t1"; gene_id "Phchi.S3G006500"
# This transcript jg1389.t2 is derived from g16022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1390.t1 is derived from g16023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	23166	24816	.	+	.	Phchi.C243G000800
Phchi.C243	AUGUSTUS	transcript	23166	24816	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	start_codon	23166	23168	.	+	0	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	23166	23329	0.99	+	0	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	23166	23329	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	23330	23409	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	23410	23500	1	+	1	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	23410	23500	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	23501	23579	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	23580	23784	1	+	0	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	23580	23784	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	23785	23870	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	23871	23948	0.91	+	2	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	23871	23948	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	23949	24027	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	24028	24139	0.93	+	2	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	24028	24139	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	24140	24230	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	24231	24307	1	+	1	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	24231	24307	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	24308	24402	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	24403	24443	1	+	2	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	24403	24443	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	intron	24444	24551	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	CDS	24552	24816	0.89	+	0	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
Phchi.C243	AUGUSTUS	exon	24552	24816	.	+	.	transcript_id "Phchi.C243G000800.t1"; gene_id "Phchi.C243G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg355.t1 is derived from g10137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2615608	2616151	.	+	.	Phchi.S6G031400
Phchi.S6	AUGUSTUS	transcript	2615608	2616151	.	+	.	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	start_codon	2615608	2615610	.	+	0	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	CDS	2615608	2615705	0.78	+	0	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	exon	2615608	2615705	.	+	.	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	intron	2615706	2615976	.	+	.	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	CDS	2615977	2616151	0.53	+	1	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	exon	2615977	2616151	.	+	.	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
Phchi.S6	AUGUSTUS	stop_codon	2616152	2616154	.	+	0	transcript_id "Phchi.S6G031400.t1"; gene_id "Phchi.S6G031400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11293.t1 is derived from g15343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5267526	5268261	.	-	.	Phchi.S4G087500
Phchi.S4	AUGUSTUS	transcript	5267526	5268261	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	stop_codon	5267523	5267525	.	-	0	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	CDS	5267526	5267571	0.88	-	1	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	exon	5267526	5267571	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	intron	5267572	5267675	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	CDS	5267676	5267735	0.89	-	1	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	exon	5267676	5267735	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	intron	5267736	5267853	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	CDS	5267854	5267978	1	-	0	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	exon	5267854	5267978	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	intron	5267979	5268120	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	CDS	5268121	5268261	0.68	-	0	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	exon	5268121	5268261	.	-	.	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
Phchi.S4	AUGUSTUS	start_codon	5268259	5268261	.	-	0	transcript_id "Phchi.S4G087500.t1"; gene_id "Phchi.S4G087500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15036.t1 is derived from g13504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16645179	16647753	.	+	.	Phchi.S3G235500
Phchi.S3	AUGUSTUS	transcript	16645666	16647753	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	start_codon	16645666	16645668	.	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16645666	16645668	0.83	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16645666	16645668	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16645669	16645919	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16645920	16646242	1	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16645920	16646242	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16646243	16646333	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16646334	16646502	1	+	1	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16646334	16646502	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16646503	16646601	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16646602	16646769	1	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16646602	16646769	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16646770	16646981	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16646982	16647064	1	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16646982	16647064	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16647065	16647137	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16647138	16647207	1	+	1	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16647138	16647207	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16647208	16647382	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16647383	16647457	1	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16647383	16647457	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16647458	16647534	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16647535	16647753	1	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16647535	16647753	.	+	.	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	stop_codon	16647754	16647756	.	+	0	transcript_id "Phchi.S3G235500.t1"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	transcript	16645179	16647753	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	start_codon	16645179	16645181	.	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16645179	16645294	0.35	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16645179	16645294	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16645295	16645549	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16645550	16645668	0.83	+	1	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16645550	16645668	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16645669	16645995	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16645996	16646242	1	+	2	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16645996	16646242	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16646243	16646333	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16646334	16646502	1	+	1	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16646334	16646502	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16646503	16646601	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16646602	16646769	1	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16646602	16646769	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16646770	16646981	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16646982	16647064	1	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16646982	16647064	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16647065	16647137	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16647138	16647207	1	+	1	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16647138	16647207	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16647208	16647382	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16647383	16647457	1	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16647383	16647457	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	intron	16647458	16647534	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	CDS	16647535	16647753	0.97	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	exon	16647535	16647753	.	+	.	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
Phchi.S3	AUGUSTUS	stop_codon	16647754	16647756	.	+	0	transcript_id "Phchi.S3G235500.t2"; gene_id "Phchi.S3G235500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2569.t1 is derived from g9489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7424888	7425804	.	-	.	Phchi.S5G117800
Phchi.S5	AUGUSTUS	transcript	7424888	7425804	.	-	.	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	stop_codon	7424885	7424887	.	-	0	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	CDS	7424888	7425416	1	-	1	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	exon	7424888	7425416	.	-	.	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	intron	7425417	7425502	.	-	.	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	CDS	7425503	7425804	0.99	-	0	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	exon	7425503	7425804	.	-	.	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
Phchi.S5	AUGUSTUS	start_codon	7425802	7425804	.	-	0	transcript_id "Phchi.S5G117800.t1"; gene_id "Phchi.S5G117800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7773.t1 is derived from g4947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31173777	31174250	.	+	.	Phchi.S1G493200
Phchi.S1	AUGUSTUS	transcript	31173777	31174250	.	+	.	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	start_codon	31173777	31173779	.	+	0	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	CDS	31173777	31173875	0.98	+	0	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	exon	31173777	31173875	.	+	.	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	intron	31173876	31174019	.	+	.	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	CDS	31174020	31174250	0.96	+	0	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	exon	31174020	31174250	.	+	.	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
Phchi.S1	AUGUSTUS	stop_codon	31174251	31174253	.	+	0	transcript_id "Phchi.S1G493200.t1"; gene_id "Phchi.S1G493200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14718.t1 is derived from g13186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14352561	14353824	.	+	.	Phchi.S3G203700
Phchi.S3	AUGUSTUS	transcript	14352561	14353824	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	start_codon	14352561	14352563	.	+	0	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	CDS	14352561	14352803	0.73	+	0	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	exon	14352561	14352803	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	intron	14352804	14352874	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	CDS	14352875	14353063	1	+	0	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	exon	14352875	14353063	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	intron	14353064	14353154	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	CDS	14353155	14353323	1	+	0	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	exon	14353155	14353323	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	intron	14353324	14353423	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	CDS	14353424	14353824	1	+	2	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	exon	14353424	14353824	.	+	.	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
Phchi.S3	AUGUSTUS	stop_codon	14353825	14353827	.	+	0	transcript_id "Phchi.S3G203700.t1"; gene_id "Phchi.S3G203700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8028.t1 is derived from g5203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32553715	32554889	.	-	.	Phchi.S1G518700
Phchi.S1	AUGUSTUS	transcript	32553715	32554889	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	stop_codon	32553712	32553714	.	-	0	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32553715	32553834	1	-	0	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32553715	32553834	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	intron	32553835	32553909	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32553910	32553996	1	-	0	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32553910	32553996	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	intron	32553997	32554074	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32554075	32554202	1	-	2	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32554075	32554202	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	intron	32554203	32554299	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32554300	32554341	1	-	2	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32554300	32554341	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	intron	32554342	32554433	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32554434	32554574	1	-	2	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32554434	32554574	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	intron	32554575	32554659	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32554660	32554727	1	-	1	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32554660	32554727	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	intron	32554728	32554806	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	CDS	32554807	32554889	0.9	-	0	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	exon	32554807	32554889	.	-	.	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
Phchi.S1	AUGUSTUS	start_codon	32554887	32554889	.	-	0	transcript_id "Phchi.S1G518700.t1"; gene_id "Phchi.S1G518700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10917.t1 is derived from g14967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2960042	2961390	.	+	.	Phchi.S4G049900
Phchi.S4	AUGUSTUS	transcript	2960042	2961390	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	start_codon	2960042	2960044	.	+	0	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2960042	2960151	0.55	+	0	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2960042	2960151	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	intron	2960152	2960461	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2960462	2960574	1	+	1	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2960462	2960574	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	intron	2960575	2960656	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2960657	2960722	0.95	+	2	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2960657	2960722	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	intron	2960723	2960811	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2960812	2960924	1	+	2	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2960812	2960924	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	intron	2960925	2961002	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2961003	2961068	1	+	0	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2961003	2961068	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	intron	2961069	2961149	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2961150	2961195	0.96	+	0	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2961150	2961195	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	intron	2961196	2961385	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	CDS	2961386	2961390	0.99	+	2	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	exon	2961386	2961390	.	+	.	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
Phchi.S4	AUGUSTUS	stop_codon	2961391	2961393	.	+	0	transcript_id "Phchi.S4G049900.t1"; gene_id "Phchi.S4G049900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10175.t1 is derived from g7351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46136518	46137450	.	-	.	Phchi.S1G733400
Phchi.S1	AUGUSTUS	transcript	46136518	46137450	.	-	.	transcript_id "Phchi.S1G733400.t1"; gene_id "Phchi.S1G733400"
Phchi.S1	AUGUSTUS	stop_codon	46136515	46136517	.	-	0	transcript_id "Phchi.S1G733400.t1"; gene_id "Phchi.S1G733400"
Phchi.S1	AUGUSTUS	CDS	46136518	46137450	0.45	-	0	transcript_id "Phchi.S1G733400.t1"; gene_id "Phchi.S1G733400"
Phchi.S1	AUGUSTUS	exon	46136518	46137450	.	-	.	transcript_id "Phchi.S1G733400.t1"; gene_id "Phchi.S1G733400"
Phchi.S1	AUGUSTUS	start_codon	46137448	46137450	.	-	0	transcript_id "Phchi.S1G733400.t1"; gene_id "Phchi.S1G733400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6778.t1 is derived from g3950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25056407	25056867	.	-	.	Phchi.S1G393700
Phchi.S1	AUGUSTUS	transcript	25056407	25056867	.	-	.	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	stop_codon	25056404	25056406	.	-	0	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	CDS	25056407	25056531	1	-	2	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	exon	25056407	25056531	.	-	.	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	intron	25056532	25056743	.	-	.	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	CDS	25056744	25056867	1	-	0	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	exon	25056744	25056867	.	-	.	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
Phchi.S1	AUGUSTUS	start_codon	25056865	25056867	.	-	0	transcript_id "Phchi.S1G393700.t1"; gene_id "Phchi.S1G393700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10029.t1 is derived from g7205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45160641	45161977	.	-	.	Phchi.S1G718800
Phchi.S1	AUGUSTUS	transcript	45160641	45161977	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	stop_codon	45160638	45160640	.	-	0	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	CDS	45160641	45160812	0.94	-	1	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	exon	45160641	45160812	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	intron	45160813	45160927	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	CDS	45160928	45161444	0.92	-	2	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	exon	45160928	45161444	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	intron	45161445	45161536	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	CDS	45161537	45161766	1	-	1	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	exon	45161537	45161766	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	intron	45161767	45161888	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	CDS	45161889	45161977	1	-	0	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	exon	45161889	45161977	.	-	.	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
Phchi.S1	AUGUSTUS	start_codon	45161975	45161977	.	-	0	transcript_id "Phchi.S1G718800.t1"; gene_id "Phchi.S1G718800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13007.t1 is derived from g11472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3608723	3611341	.	-	.	Phchi.S3G032600
Phchi.S3	AUGUSTUS	transcript	3608723	3611341	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	stop_codon	3608720	3608722	.	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3608723	3608835	1	-	2	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3608723	3608835	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3608836	3608921	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3608922	3609057	1	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3608922	3609057	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3609058	3609139	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3609140	3609232	1	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3609140	3609232	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3609233	3609315	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3609316	3609417	1	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3609316	3609417	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3609418	3609512	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3609513	3609646	1	-	2	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3609513	3609646	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3609647	3609732	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3609733	3609847	1	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3609733	3609847	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3609848	3610004	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3610005	3610112	0.98	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3610005	3610112	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3610113	3610226	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3610227	3610319	0.99	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3610227	3610319	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3610320	3610808	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3610809	3611110	1	-	2	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3610809	3611110	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	intron	3611111	3611250	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	CDS	3611251	3611341	0.98	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	exon	3611251	3611341	.	-	.	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
Phchi.S3	AUGUSTUS	start_codon	3611339	3611341	.	-	0	transcript_id "Phchi.S3G032600.t1"; gene_id "Phchi.S3G032600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12812.t1 is derived from g11277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2477377	2479857	.	+	.	Phchi.S3G013100
Phchi.S3	AUGUSTUS	transcript	2477377	2479857	.	+	.	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	start_codon	2477377	2477379	.	+	0	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	CDS	2477377	2477473	0.02	+	0	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	exon	2477377	2477473	.	+	.	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	intron	2477474	2479609	.	+	.	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	CDS	2479610	2479857	0.01	+	2	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	exon	2479610	2479857	.	+	.	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
Phchi.S3	AUGUSTUS	stop_codon	2479858	2479860	.	+	0	transcript_id "Phchi.S3G013100.t1"; gene_id "Phchi.S3G013100"
# This transcript jg1415.t2 is derived from g8334.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1415.t3 is derived from g8334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1416.t1 is derived from g8335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	648355	651302	.	+	.	Phchi.S5G002500
Phchi.S5	AUGUSTUS	transcript	648355	651302	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	start_codon	648355	648357	.	+	0	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	CDS	648355	649749	0.52	+	0	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	exon	648355	649749	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	intron	649750	649953	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	CDS	649954	650427	0.99	+	0	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	exon	649954	650427	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	intron	650428	650551	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	CDS	650552	650929	1	+	0	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	exon	650552	650929	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	intron	650930	651013	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	CDS	651014	651081	1	+	0	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	exon	651014	651081	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	intron	651082	651178	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	CDS	651179	651302	0.99	+	1	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	exon	651179	651302	.	+	.	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
Phchi.S5	AUGUSTUS	stop_codon	651303	651305	.	+	0	transcript_id "Phchi.S5G002500.t1"; gene_id "Phchi.S5G002500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13388.t1 is derived from g11854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6496276	6497034	.	+	.	Phchi.S3G070700
Phchi.S3	AUGUSTUS	transcript	6496276	6497034	.	+	.	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	start_codon	6496276	6496278	.	+	0	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	CDS	6496276	6496463	0.99	+	0	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	exon	6496276	6496463	.	+	.	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	intron	6496464	6496646	.	+	.	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	CDS	6496647	6497034	1	+	1	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	exon	6496647	6497034	.	+	.	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
Phchi.S3	AUGUSTUS	stop_codon	6497035	6497037	.	+	0	transcript_id "Phchi.S3G070700.t1"; gene_id "Phchi.S3G070700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg114.t1 is derived from g9896.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	601781	604537	.	-	.	Phchi.S6G007300
Phchi.S6	AUGUSTUS	transcript	602640	604537	.	-	.	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	stop_codon	602637	602639	.	-	0	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	CDS	602640	602706	0.86	-	1	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	exon	602640	602706	.	-	.	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	intron	602707	602774	.	-	.	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	CDS	602775	604537	0.93	-	0	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	exon	602775	604537	.	-	.	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	start_codon	604535	604537	.	-	0	transcript_id "Phchi.S6G007300.t1"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	transcript	601781	604537	.	-	.	transcript_id "Phchi.S6G007300.t2"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	stop_codon	601778	601780	.	-	0	transcript_id "Phchi.S6G007300.t2"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	CDS	601781	604537	0.96	-	0	transcript_id "Phchi.S6G007300.t2"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	exon	601781	604537	.	-	.	transcript_id "Phchi.S6G007300.t2"; gene_id "Phchi.S6G007300"
Phchi.S6	AUGUSTUS	start_codon	604535	604537	.	-	0	transcript_id "Phchi.S6G007300.t2"; gene_id "Phchi.S6G007300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5576.t1 is derived from g2746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17678317	17680011	.	-	.	Phchi.S1G273500
Phchi.S1	AUGUSTUS	transcript	17678317	17680011	.	-	.	transcript_id "Phchi.S1G273500.t1"; gene_id "Phchi.S1G273500"
Phchi.S1	AUGUSTUS	stop_codon	17678314	17678316	.	-	0	transcript_id "Phchi.S1G273500.t1"; gene_id "Phchi.S1G273500"
Phchi.S1	AUGUSTUS	CDS	17678317	17680011	1	-	0	transcript_id "Phchi.S1G273500.t1"; gene_id "Phchi.S1G273500"
Phchi.S1	AUGUSTUS	exon	17678317	17680011	.	-	.	transcript_id "Phchi.S1G273500.t1"; gene_id "Phchi.S1G273500"
Phchi.S1	AUGUSTUS	start_codon	17680009	17680011	.	-	0	transcript_id "Phchi.S1G273500.t1"; gene_id "Phchi.S1G273500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5337.t1 is derived from g2507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16363199	16363783	.	-	.	Phchi.S1G249600
Phchi.S1	AUGUSTUS	transcript	16363199	16363783	.	-	.	transcript_id "Phchi.S1G249600.t1"; gene_id "Phchi.S1G249600"
Phchi.S1	AUGUSTUS	stop_codon	16363196	16363198	.	-	0	transcript_id "Phchi.S1G249600.t1"; gene_id "Phchi.S1G249600"
Phchi.S1	AUGUSTUS	CDS	16363199	16363783	0.85	-	0	transcript_id "Phchi.S1G249600.t1"; gene_id "Phchi.S1G249600"
Phchi.S1	AUGUSTUS	exon	16363199	16363783	.	-	.	transcript_id "Phchi.S1G249600.t1"; gene_id "Phchi.S1G249600"
Phchi.S1	AUGUSTUS	start_codon	16363781	16363783	.	-	0	transcript_id "Phchi.S1G249600.t1"; gene_id "Phchi.S1G249600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1156.t1 is derived from g10939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8076165	8078979	.	-	.	Phchi.S6G111500
Phchi.S6	AUGUSTUS	transcript	8076165	8078979	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	stop_codon	8076162	8076164	.	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8076165	8076239	1	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8076165	8076239	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8076240	8076325	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8076326	8076391	1	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8076326	8076391	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8076392	8076492	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8076493	8076598	1	-	1	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8076493	8076598	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8076599	8076694	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8076695	8077026	0.9	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8076695	8077026	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8077027	8077111	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8077112	8077429	1	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8077112	8077429	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8077430	8077519	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8077520	8077605	1	-	2	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8077520	8077605	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8077606	8077706	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8077707	8077799	0.98	-	2	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8077707	8077799	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8077800	8077923	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8077924	8078013	0.99	-	2	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8077924	8078013	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8078014	8078091	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8078092	8078199	0.79	-	2	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8078092	8078199	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8078200	8078297	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8078298	8078553	1	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8078298	8078553	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	intron	8078554	8078853	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	CDS	8078854	8078979	0.93	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	exon	8078854	8078979	.	-	.	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
Phchi.S6	AUGUSTUS	start_codon	8078977	8078979	.	-	0	transcript_id "Phchi.S6G111500.t1"; gene_id "Phchi.S6G111500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4740.t1 is derived from g1910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12553338	12554001	.	-	.	Phchi.S1G189900
Phchi.S1	AUGUSTUS	transcript	12553338	12554001	.	-	.	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	stop_codon	12553335	12553337	.	-	0	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	CDS	12553338	12553518	0.7	-	1	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	exon	12553338	12553518	.	-	.	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	intron	12553519	12553639	.	-	.	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	CDS	12553640	12554001	0.7	-	0	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	exon	12553640	12554001	.	-	.	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
Phchi.S1	AUGUSTUS	start_codon	12553999	12554001	.	-	0	transcript_id "Phchi.S1G189900.t1"; gene_id "Phchi.S1G189900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8583.t1 is derived from g5758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36737680	36737952	.	+	.	Phchi.S1G574200
Phchi.S1	AUGUSTUS	transcript	36737680	36737952	.	+	.	transcript_id "Phchi.S1G574200.t1"; gene_id "Phchi.S1G574200"
Phchi.S1	AUGUSTUS	start_codon	36737680	36737682	.	+	0	transcript_id "Phchi.S1G574200.t1"; gene_id "Phchi.S1G574200"
Phchi.S1	AUGUSTUS	CDS	36737680	36737952	0.74	+	0	transcript_id "Phchi.S1G574200.t1"; gene_id "Phchi.S1G574200"
Phchi.S1	AUGUSTUS	exon	36737680	36737952	.	+	.	transcript_id "Phchi.S1G574200.t1"; gene_id "Phchi.S1G574200"
Phchi.S1	AUGUSTUS	stop_codon	36737953	36737955	.	+	0	transcript_id "Phchi.S1G574200.t1"; gene_id "Phchi.S1G574200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9052.t1 is derived from g6227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39404109	39406421	.	-	.	Phchi.S1G621100
Phchi.S1	AUGUSTUS	transcript	39404109	39406421	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	stop_codon	39404106	39404108	.	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39404109	39404153	0.48	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39404109	39404153	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39404154	39404418	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39404419	39404877	0.47	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39404419	39404877	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39404878	39404963	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39404964	39404984	0.94	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39404964	39404984	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39404985	39405144	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39405145	39405471	0.54	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39405145	39405471	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39405472	39405584	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39405585	39405607	0.98	-	2	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39405585	39405607	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39405608	39405745	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39405746	39405872	0.98	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39405746	39405872	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39405873	39405959	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39405960	39405981	1	-	1	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39405960	39405981	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39405982	39406099	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39406100	39406157	1	-	2	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39406100	39406157	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	intron	39406158	39406243	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	CDS	39406244	39406421	0.8	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	exon	39406244	39406421	.	-	.	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
Phchi.S1	AUGUSTUS	start_codon	39406419	39406421	.	-	0	transcript_id "Phchi.S1G621100.t1"; gene_id "Phchi.S1G621100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6536.t1 is derived from g3708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23527281	23529882	.	-	.	Phchi.S1G369500
Phchi.S1	AUGUSTUS	transcript	23527281	23529882	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	stop_codon	23527278	23527280	.	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23527281	23527281	1	-	1	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23527281	23527281	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23527282	23527375	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23527376	23527575	1	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23527376	23527575	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23527576	23527726	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23527727	23527888	1	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23527727	23527888	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23527889	23528014	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528015	23528163	1	-	2	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528015	23528163	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23528164	23528340	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528341	23528501	1	-	1	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528341	23528501	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23528502	23528738	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528739	23528797	1	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528739	23528797	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23528798	23528964	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528965	23529147	0.92	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528965	23529147	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23529148	23529229	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529230	23529355	1	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529230	23529355	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23529356	23529501	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529502	23529882	0.92	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529502	23529882	.	-	.	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	start_codon	23529880	23529882	.	-	0	transcript_id "Phchi.S1G369500.t1"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	transcript	23527281	23529882	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	stop_codon	23527278	23527280	.	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23527281	23527281	1	-	1	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23527281	23527281	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23527282	23527375	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23527376	23527575	1	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23527376	23527575	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23527576	23527726	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23527727	23527888	1	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23527727	23527888	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23527889	23528014	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528015	23528163	1	-	2	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528015	23528163	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23528164	23528340	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528341	23528501	1	-	1	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528341	23528501	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23528502	23528738	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528739	23528800	1	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528739	23528800	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23528801	23528964	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23528965	23529147	0.84	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23528965	23529147	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23529148	23529229	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529230	23529355	1	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529230	23529355	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23529356	23529501	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529502	23529882	0.96	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529502	23529882	.	-	.	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	start_codon	23529880	23529882	.	-	0	transcript_id "Phchi.S1G369500.t2"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	transcript	23529116	23529882	.	-	.	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	stop_codon	23529113	23529115	.	-	0	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529116	23529133	1	-	0	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529116	23529133	.	-	.	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23529134	23529229	.	-	.	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529230	23529355	1	-	0	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529230	23529355	.	-	.	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	intron	23529356	23529501	.	-	.	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	CDS	23529502	23529882	0.91	-	0	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	exon	23529502	23529882	.	-	.	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
Phchi.S1	AUGUSTUS	start_codon	23529880	23529882	.	-	0	transcript_id "Phchi.S1G369500.t3"; gene_id "Phchi.S1G369500"
# This transcript jg14929.t2 is derived from g13397.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14930.t1 is derived from g13398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15572834	15573775	.	-	.	Phchi.S3G224900
Phchi.S3	AUGUSTUS	transcript	15572834	15573775	.	-	.	transcript_id "Phchi.S3G224900.t1"; gene_id "Phchi.S3G224900"
Phchi.S3	AUGUSTUS	stop_codon	15572831	15572833	.	-	0	transcript_id "Phchi.S3G224900.t1"; gene_id "Phchi.S3G224900"
Phchi.S3	AUGUSTUS	CDS	15572834	15573775	0.97	-	0	transcript_id "Phchi.S3G224900.t1"; gene_id "Phchi.S3G224900"
Phchi.S3	AUGUSTUS	exon	15572834	15573775	.	-	.	transcript_id "Phchi.S3G224900.t1"; gene_id "Phchi.S3G224900"
Phchi.S3	AUGUSTUS	start_codon	15573773	15573775	.	-	0	transcript_id "Phchi.S3G224900.t1"; gene_id "Phchi.S3G224900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5839.t1 is derived from g3009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19280622	19282024	.	-	.	Phchi.S1G299800
Phchi.S1	AUGUSTUS	transcript	19280622	19282024	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	stop_codon	19280619	19280621	.	-	0	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	CDS	19280622	19281284	0.99	-	0	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	exon	19280622	19281284	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	intron	19281285	19281402	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	CDS	19281403	19281495	1	-	0	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	exon	19281403	19281495	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	intron	19281496	19281612	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	CDS	19281613	19281688	1	-	1	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	exon	19281613	19281688	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	intron	19281689	19281772	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	CDS	19281773	19281885	1	-	0	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	exon	19281773	19281885	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	intron	19281886	19282018	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	CDS	19282019	19282024	1	-	0	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	exon	19282019	19282024	.	-	.	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
Phchi.S1	AUGUSTUS	start_codon	19282022	19282024	.	-	0	transcript_id "Phchi.S1G299800.t1"; gene_id "Phchi.S1G299800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14562.t1 is derived from g13030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13476283	13479644	.	+	.	Phchi.S3G188100
Phchi.S3	AUGUSTUS	transcript	13476283	13479644	.	+	.	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	start_codon	13476283	13476285	.	+	0	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	CDS	13476283	13477940	0.98	+	0	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	exon	13476283	13477940	.	+	.	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	intron	13477941	13478017	.	+	.	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	CDS	13478018	13479644	0.99	+	1	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	exon	13478018	13479644	.	+	.	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
Phchi.S3	AUGUSTUS	stop_codon	13479645	13479647	.	+	0	transcript_id "Phchi.S3G188100.t1"; gene_id "Phchi.S3G188100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15757.t1 is derived from g14227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21090142	21090512	.	+	.	Phchi.S3G307600
Phchi.S3	AUGUSTUS	transcript	21090142	21090512	.	+	.	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	start_codon	21090142	21090144	.	+	0	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	CDS	21090142	21090213	0.82	+	0	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	exon	21090142	21090213	.	+	.	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	intron	21090214	21090299	.	+	.	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	CDS	21090300	21090512	0.84	+	0	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	exon	21090300	21090512	.	+	.	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
Phchi.S3	AUGUSTUS	stop_codon	21090513	21090515	.	+	0	transcript_id "Phchi.S3G307600.t1"; gene_id "Phchi.S3G307600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12797.t1 is derived from g11262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2435112	2436212	.	-	.	Phchi.S3G011600
Phchi.S3	AUGUSTUS	transcript	2435112	2436212	.	-	.	transcript_id "Phchi.S3G011600.t1"; gene_id "Phchi.S3G011600"
Phchi.S3	AUGUSTUS	stop_codon	2435109	2435111	.	-	0	transcript_id "Phchi.S3G011600.t1"; gene_id "Phchi.S3G011600"
Phchi.S3	AUGUSTUS	CDS	2435112	2436212	0.54	-	0	transcript_id "Phchi.S3G011600.t1"; gene_id "Phchi.S3G011600"
Phchi.S3	AUGUSTUS	exon	2435112	2436212	.	-	.	transcript_id "Phchi.S3G011600.t1"; gene_id "Phchi.S3G011600"
Phchi.S3	AUGUSTUS	start_codon	2436210	2436212	.	-	0	transcript_id "Phchi.S3G011600.t1"; gene_id "Phchi.S3G011600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5067.t1 is derived from g2237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14508692	14509214	.	+	.	Phchi.S1G222600
Phchi.S1	AUGUSTUS	transcript	14508692	14509214	.	+	.	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	start_codon	14508692	14508694	.	+	0	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	CDS	14508692	14508806	0.45	+	0	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	exon	14508692	14508806	.	+	.	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	intron	14508807	14508891	.	+	.	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	CDS	14508892	14509214	0.83	+	2	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	exon	14508892	14509214	.	+	.	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
Phchi.S1	AUGUSTUS	stop_codon	14509215	14509217	.	+	0	transcript_id "Phchi.S1G222600.t1"; gene_id "Phchi.S1G222600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12976.t1 is derived from g11441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3408647	3408982	.	+	.	Phchi.S3G029500
Phchi.S3	AUGUSTUS	transcript	3408647	3408982	.	+	.	transcript_id "Phchi.S3G029500.t1"; gene_id "Phchi.S3G029500"
Phchi.S3	AUGUSTUS	start_codon	3408647	3408649	.	+	0	transcript_id "Phchi.S3G029500.t1"; gene_id "Phchi.S3G029500"
Phchi.S3	AUGUSTUS	CDS	3408647	3408982	0.57	+	0	transcript_id "Phchi.S3G029500.t1"; gene_id "Phchi.S3G029500"
Phchi.S3	AUGUSTUS	exon	3408647	3408982	.	+	.	transcript_id "Phchi.S3G029500.t1"; gene_id "Phchi.S3G029500"
Phchi.S3	AUGUSTUS	stop_codon	3408983	3408985	.	+	0	transcript_id "Phchi.S3G029500.t1"; gene_id "Phchi.S3G029500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4043.t1 is derived from g1212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7363610	7364209	.	+	.	Phchi.S1G120200
Phchi.S1	AUGUSTUS	transcript	7363610	7364209	.	+	.	transcript_id "Phchi.S1G120200.t1"; gene_id "Phchi.S1G120200"
Phchi.S1	AUGUSTUS	start_codon	7363610	7363612	.	+	0	transcript_id "Phchi.S1G120200.t1"; gene_id "Phchi.S1G120200"
Phchi.S1	AUGUSTUS	CDS	7363610	7364209	1	+	0	transcript_id "Phchi.S1G120200.t1"; gene_id "Phchi.S1G120200"
Phchi.S1	AUGUSTUS	exon	7363610	7364209	.	+	.	transcript_id "Phchi.S1G120200.t1"; gene_id "Phchi.S1G120200"
Phchi.S1	AUGUSTUS	stop_codon	7364210	7364212	.	+	0	transcript_id "Phchi.S1G120200.t1"; gene_id "Phchi.S1G120200"
# This transcript jg5751.t2 is derived from g2921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5752.t1 is derived from g2922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18725456	18726283	.	-	.	Phchi.S1G291100
Phchi.S1	AUGUSTUS	transcript	18725456	18726283	.	-	.	transcript_id "Phchi.S1G291100.t1"; gene_id "Phchi.S1G291100"
Phchi.S1	AUGUSTUS	stop_codon	18725453	18725455	.	-	0	transcript_id "Phchi.S1G291100.t1"; gene_id "Phchi.S1G291100"
Phchi.S1	AUGUSTUS	CDS	18725456	18726283	0.99	-	0	transcript_id "Phchi.S1G291100.t1"; gene_id "Phchi.S1G291100"
Phchi.S1	AUGUSTUS	exon	18725456	18726283	.	-	.	transcript_id "Phchi.S1G291100.t1"; gene_id "Phchi.S1G291100"
Phchi.S1	AUGUSTUS	start_codon	18726281	18726283	.	-	0	transcript_id "Phchi.S1G291100.t1"; gene_id "Phchi.S1G291100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9100.t1 is derived from g6275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39828419	39829600	.	-	.	Phchi.S1G625900
Phchi.S1	AUGUSTUS	transcript	39828419	39829600	.	-	.	transcript_id "Phchi.S1G625900.t1"; gene_id "Phchi.S1G625900"
Phchi.S1	AUGUSTUS	stop_codon	39828416	39828418	.	-	0	transcript_id "Phchi.S1G625900.t1"; gene_id "Phchi.S1G625900"
Phchi.S1	AUGUSTUS	CDS	39828419	39829600	0.72	-	0	transcript_id "Phchi.S1G625900.t1"; gene_id "Phchi.S1G625900"
Phchi.S1	AUGUSTUS	exon	39828419	39829600	.	-	.	transcript_id "Phchi.S1G625900.t1"; gene_id "Phchi.S1G625900"
Phchi.S1	AUGUSTUS	start_codon	39829598	39829600	.	-	0	transcript_id "Phchi.S1G625900.t1"; gene_id "Phchi.S1G625900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8265.t1 is derived from g5440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35019518	35023038	.	+	.	Phchi.S1G542400
Phchi.S1	AUGUSTUS	transcript	35019518	35023038	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	start_codon	35019518	35019520	.	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35019518	35019574	0.94	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35019518	35019574	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35019575	35019682	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35019683	35019862	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35019683	35019862	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35019863	35019950	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35019951	35020100	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35019951	35020100	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35020101	35020178	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35020179	35020248	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35020179	35020248	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35020249	35020355	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35020356	35020624	0.54	+	2	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35020356	35020624	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35020625	35020722	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35020723	35020782	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35020723	35020782	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35020783	35020953	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35020954	35021107	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35020954	35021107	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35021108	35021191	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35021192	35021227	1	+	2	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35021192	35021227	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35021228	35021323	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35021324	35021383	1	+	2	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35021324	35021383	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35021384	35021558	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35021559	35021830	1	+	2	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35021559	35021830	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35021831	35022003	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35022004	35022075	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35022004	35022075	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35022076	35022159	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35022160	35022240	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35022160	35022240	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35022241	35022356	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35022357	35022551	0.97	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35022357	35022551	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35022552	35022682	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35022683	35022734	1	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35022683	35022734	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	intron	35022735	35022814	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	CDS	35022815	35023038	1	+	2	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	exon	35022815	35023038	.	+	.	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
Phchi.S1	AUGUSTUS	stop_codon	35023039	35023041	.	+	0	transcript_id "Phchi.S1G542400.t1"; gene_id "Phchi.S1G542400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13117.t1 is derived from g11582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4208286	4209815	.	-	.	Phchi.S3G043600
Phchi.S3	AUGUSTUS	transcript	4208286	4209815	.	-	.	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	stop_codon	4208283	4208285	.	-	0	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	CDS	4208286	4208486	0.22	-	0	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	exon	4208286	4208486	.	-	.	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	intron	4208487	4208570	.	-	.	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	CDS	4208571	4208766	1	-	1	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	exon	4208571	4208766	.	-	.	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	intron	4208767	4208859	.	-	.	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	CDS	4208860	4209815	0.93	-	0	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	exon	4208860	4209815	.	-	.	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
Phchi.S3	AUGUSTUS	start_codon	4209813	4209815	.	-	0	transcript_id "Phchi.S3G043600.t1"; gene_id "Phchi.S3G043600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9895.t1 is derived from g7071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44318154	44324394	.	-	.	Phchi.S1G705400
Phchi.S1	AUGUSTUS	transcript	44318154	44324394	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	stop_codon	44318151	44318153	.	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44318154	44318289	1	-	1	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44318154	44318289	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44318290	44318361	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44318362	44318434	1	-	2	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44318362	44318434	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44318435	44318520	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44318521	44318608	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44318521	44318608	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44318609	44318686	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44318687	44318821	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44318687	44318821	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44318822	44318906	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44318907	44318967	1	-	1	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44318907	44318967	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44318968	44319042	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44319043	44319150	1	-	1	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44319043	44319150	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44319151	44319233	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44319234	44319380	1	-	1	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44319234	44319380	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44319381	44319474	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44319475	44319596	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44319475	44319596	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44319597	44319683	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44319684	44319773	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44319684	44319773	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44319774	44319857	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44319858	44320067	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44319858	44320067	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44320068	44320156	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44320157	44320240	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44320157	44320240	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44320241	44320324	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44320325	44320501	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44320325	44320501	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44320502	44320631	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44320632	44320940	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44320632	44320940	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44320941	44321020	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44321021	44321179	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44321021	44321179	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44321180	44321321	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44321322	44321455	1	-	2	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44321322	44321455	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44321456	44321542	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44321543	44321732	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44321543	44321732	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44321733	44321822	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44321823	44321975	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44321823	44321975	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44321976	44322076	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44322077	44322207	0.99	-	2	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44322077	44322207	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44322208	44322315	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44322316	44322460	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44322316	44322460	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44322461	44322549	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44322550	44322678	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44322550	44322678	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44322679	44322765	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44322766	44322841	1	-	1	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44322766	44322841	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44322842	44322952	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44322953	44323110	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44322953	44323110	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44323111	44323186	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44323187	44323265	1	-	1	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44323187	44323265	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44323266	44323353	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44323354	44323484	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44323354	44323484	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44323485	44323617	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44323618	44323794	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44323618	44323794	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44323795	44323904	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44323905	44324006	0.71	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44323905	44324006	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44324007	44324086	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44324087	44324176	1	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44324087	44324176	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	intron	44324177	44324259	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	CDS	44324260	44324394	0.99	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	exon	44324260	44324394	.	-	.	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
Phchi.S1	AUGUSTUS	start_codon	44324392	44324394	.	-	0	transcript_id "Phchi.S1G705400.t1"; gene_id "Phchi.S1G705400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13040.t1 is derived from g11505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3837725	3840944	.	-	.	Phchi.S3G035900
Phchi.S3	AUGUSTUS	transcript	3837725	3840944	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	stop_codon	3837722	3837724	.	-	0	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	CDS	3837725	3838292	0.79	-	1	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	exon	3837725	3838292	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	intron	3838293	3838366	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	CDS	3838367	3840477	0.71	-	0	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	exon	3838367	3840477	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	intron	3840478	3840557	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	CDS	3840558	3840689	0.91	-	0	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	exon	3840558	3840689	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	intron	3840690	3840767	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	CDS	3840768	3840944	1	-	0	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	exon	3840768	3840944	.	-	.	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
Phchi.S3	AUGUSTUS	start_codon	3840942	3840944	.	-	0	transcript_id "Phchi.S3G035900.t1"; gene_id "Phchi.S3G035900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7582.t1 is derived from g4756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30144418	30146551	.	+	.	Phchi.S1G474100
Phchi.S1	AUGUSTUS	transcript	30144418	30146551	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	start_codon	30144418	30144420	.	+	0	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30144418	30144495	0.54	+	0	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30144418	30144495	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	intron	30144496	30144580	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30144581	30144854	1	+	0	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30144581	30144854	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	intron	30144855	30144930	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30144931	30145108	1	+	2	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30144931	30145108	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	intron	30145109	30145208	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30145209	30145515	1	+	1	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30145209	30145515	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	intron	30145516	30145602	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30145603	30145938	1	+	0	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30145603	30145938	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	intron	30145939	30146014	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30146015	30146180	1	+	0	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30146015	30146180	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	intron	30146181	30146264	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	CDS	30146265	30146551	0.76	+	2	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	exon	30146265	30146551	.	+	.	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
Phchi.S1	AUGUSTUS	stop_codon	30146552	30146554	.	+	0	transcript_id "Phchi.S1G474100.t1"; gene_id "Phchi.S1G474100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg296.t1 is derived from g10078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2106911	2107441	.	+	.	Phchi.S6G025500
Phchi.S6	AUGUSTUS	transcript	2106911	2107441	.	+	.	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	start_codon	2106911	2106913	.	+	0	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	CDS	2106911	2106932	0.84	+	0	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	exon	2106911	2106932	.	+	.	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	intron	2106933	2107092	.	+	.	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	CDS	2107093	2107157	0.93	+	2	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	exon	2107093	2107157	.	+	.	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	intron	2107158	2107309	.	+	.	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	CDS	2107310	2107441	0.68	+	0	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	exon	2107310	2107441	.	+	.	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
Phchi.S6	AUGUSTUS	stop_codon	2107442	2107444	.	+	0	transcript_id "Phchi.S6G025500.t1"; gene_id "Phchi.S6G025500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg32.t1 is derived from g9810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C246	AUGUSTUS	gene	21439	21999	.	+	.	Phchi.C246G000500
Phchi.C246	AUGUSTUS	transcript	21439	21999	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	start_codon	21439	21441	.	+	0	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	CDS	21439	21521	0.61	+	0	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	exon	21439	21521	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	intron	21522	21643	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	CDS	21644	21695	0.66	+	1	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	exon	21644	21695	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	intron	21696	21785	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	CDS	21786	21853	1	+	0	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	exon	21786	21853	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	intron	21854	21959	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	CDS	21960	21999	1	+	1	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	exon	21960	21999	.	+	.	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
Phchi.C246	AUGUSTUS	stop_codon	22000	22002	.	+	0	transcript_id "Phchi.C246G000500.t1"; gene_id "Phchi.C246G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13960.t1 is derived from g12427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9936991	9937990	.	+	.	Phchi.S3G127900
Phchi.S3	AUGUSTUS	transcript	9936991	9937990	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	start_codon	9936991	9936993	.	+	0	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	CDS	9936991	9937382	1	+	0	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	exon	9936991	9937382	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	intron	9937383	9937471	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	CDS	9937472	9937559	1	+	1	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	exon	9937472	9937559	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	intron	9937560	9937684	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	CDS	9937685	9937781	1	+	0	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	exon	9937685	9937781	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	intron	9937782	9937865	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	CDS	9937866	9937990	1	+	2	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	exon	9937866	9937990	.	+	.	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
Phchi.S3	AUGUSTUS	stop_codon	9937991	9937993	.	+	0	transcript_id "Phchi.S3G127900.t1"; gene_id "Phchi.S3G127900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15674.t1 is derived from g14143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20611485	20613431	.	+	.	Phchi.S3G299300
Phchi.S3	AUGUSTUS	transcript	20611485	20613431	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	start_codon	20611485	20611487	.	+	0	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	CDS	20611485	20611767	0.95	+	0	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	exon	20611485	20611767	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	intron	20611768	20611857	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	CDS	20611858	20612084	1	+	2	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	exon	20611858	20612084	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	intron	20612085	20612235	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	CDS	20612236	20612504	1	+	0	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	exon	20612236	20612504	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	intron	20612505	20612599	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	CDS	20612600	20613431	1	+	1	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	exon	20612600	20613431	.	+	.	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
Phchi.S3	AUGUSTUS	stop_codon	20613432	20613434	.	+	0	transcript_id "Phchi.S3G299300.t1"; gene_id "Phchi.S3G299300"
# This transcript jg13346.t2 is derived from g11812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13347.t1 is derived from g11813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6220252	6221767	.	+	.	Phchi.S3G066600
Phchi.S3	AUGUSTUS	transcript	6220252	6221767	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	start_codon	6220252	6220254	.	+	0	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	CDS	6220252	6220289	0.95	+	0	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	exon	6220252	6220289	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	intron	6220290	6220585	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	CDS	6220586	6220728	0.99	+	1	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	exon	6220586	6220728	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	intron	6220729	6220862	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	CDS	6220863	6221022	1	+	2	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	exon	6220863	6221022	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	intron	6221023	6221133	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	CDS	6221134	6221290	0.75	+	1	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	exon	6221134	6221290	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	intron	6221291	6221476	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	CDS	6221477	6221767	0.5	+	0	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	exon	6221477	6221767	.	+	.	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
Phchi.S3	AUGUSTUS	stop_codon	6221768	6221770	.	+	0	transcript_id "Phchi.S3G066600.t1"; gene_id "Phchi.S3G066600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9540.t1 is derived from g6716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42392733	42396131	.	+	.	Phchi.S1G669900
Phchi.S1	AUGUSTUS	transcript	42392733	42396131	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	start_codon	42392733	42392735	.	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42392733	42392926	0.82	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42392733	42392926	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42392927	42393054	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42393055	42393360	0.99	+	1	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42393055	42393360	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42393361	42393447	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42393448	42393892	0.79	+	1	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42393448	42393892	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42393893	42393994	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42393995	42394129	0.82	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42393995	42394129	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42394130	42394216	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42394217	42394385	0.98	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42394217	42394385	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42394386	42394473	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42394474	42394609	1	+	2	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42394474	42394609	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42394610	42394699	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42394700	42394838	1	+	1	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42394700	42394838	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42394839	42394936	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42394937	42395113	1	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42394937	42395113	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42395114	42395207	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42395208	42395375	1	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42395208	42395375	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42395376	42395451	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42395452	42395547	1	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42395452	42395547	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42395548	42395643	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42395644	42395772	1	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42395644	42395772	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	intron	42395773	42395894	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	CDS	42395895	42396131	1	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	exon	42395895	42396131	.	+	.	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
Phchi.S1	AUGUSTUS	stop_codon	42396132	42396134	.	+	0	transcript_id "Phchi.S1G669900.t1"; gene_id "Phchi.S1G669900"
# This transcript jg15492.t2 is derived from g13961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15493.t1 is derived from g13962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19486958	19487787	.	+	.	Phchi.S3G281200
Phchi.S3	AUGUSTUS	transcript	19486958	19487787	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	start_codon	19486958	19486960	.	+	0	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	CDS	19486958	19487005	0.85	+	0	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	exon	19486958	19487005	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	intron	19487006	19487095	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	CDS	19487096	19487112	0.88	+	0	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	exon	19487096	19487112	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	intron	19487113	19487262	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	CDS	19487263	19487534	0.88	+	1	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	exon	19487263	19487534	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	intron	19487535	19487710	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	CDS	19487711	19487787	1	+	2	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	exon	19487711	19487787	.	+	.	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
Phchi.S3	AUGUSTUS	stop_codon	19487788	19487790	.	+	0	transcript_id "Phchi.S3G281200.t1"; gene_id "Phchi.S3G281200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11944.t1 is derived from g7619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	144802	150132	.	+	.	Phchi.S2G002400
Phchi.S2	AUGUSTUS	transcript	144802	150132	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	start_codon	144802	144804	.	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	144802	144879	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	144802	144879	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	144880	145028	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	145029	145208	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	145029	145208	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	145209	145292	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	145293	145450	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	145293	145450	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	145451	145553	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	145554	145622	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	145554	145622	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	145623	145717	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	145718	145952	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	145718	145952	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	145953	146087	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	146088	146240	0.96	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	146088	146240	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	146241	146525	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	146526	146648	0.98	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	146526	146648	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	146649	146749	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	146750	146859	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	146750	146859	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	146860	146947	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	146948	147079	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	146948	147079	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	147080	147227	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	147228	147330	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	147228	147330	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	147331	147423	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	147424	147542	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	147424	147542	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	147543	147622	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	147623	147682	0.83	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	147623	147682	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	147683	147821	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	147822	147879	0.46	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	147822	147879	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	147880	148035	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	148036	148178	0.51	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	148036	148178	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	148179	148253	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	148254	148351	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	148254	148351	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	148352	148444	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	148445	148579	1	+	2	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	148445	148579	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	148580	148672	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	148673	148816	0.86	+	2	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	148673	148816	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	148817	148917	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	148918	149009	0.87	+	2	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	148918	149009	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	149010	149116	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	149117	149221	0.9	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	149117	149221	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	149222	149309	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	149310	149383	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	149310	149383	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	149384	149508	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	149509	149587	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	149509	149587	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	149588	149663	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	149664	149782	1	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	149664	149782	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	149783	149861	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	149862	149914	1	+	1	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	149862	149914	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	intron	149915	150052	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	CDS	150053	150132	1	+	2	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	exon	150053	150132	.	+	.	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
Phchi.S2	AUGUSTUS	stop_codon	150133	150135	.	+	0	transcript_id "Phchi.S2G002400.t1"; gene_id "Phchi.S2G002400"
# This transcript jg15550.t2 is derived from g14019.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15551.t1 is derived from g14020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19885159	19886719	.	+	.	Phchi.S3G287000
Phchi.S3	AUGUSTUS	transcript	19885159	19886719	.	+	.	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	start_codon	19885159	19885161	.	+	0	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	CDS	19885159	19886411	0.61	+	0	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	exon	19885159	19886411	.	+	.	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	intron	19886412	19886529	.	+	.	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	CDS	19886530	19886719	0.66	+	1	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	exon	19886530	19886719	.	+	.	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
Phchi.S3	AUGUSTUS	stop_codon	19886720	19886722	.	+	0	transcript_id "Phchi.S3G287000.t1"; gene_id "Phchi.S3G287000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6671.t1 is derived from g3843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24418272	24419363	.	+	.	Phchi.S1G383000
Phchi.S1	AUGUSTUS	transcript	24418272	24419363	.	+	.	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	start_codon	24418272	24418274	.	+	0	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	CDS	24418272	24418529	0.99	+	0	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	exon	24418272	24418529	.	+	.	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	intron	24418530	24418601	.	+	.	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	CDS	24418602	24418856	1	+	0	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	exon	24418602	24418856	.	+	.	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	intron	24418857	24418949	.	+	.	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	CDS	24418950	24419363	0.48	+	0	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	exon	24418950	24419363	.	+	.	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
Phchi.S1	AUGUSTUS	stop_codon	24419364	24419366	.	+	0	transcript_id "Phchi.S1G383000.t1"; gene_id "Phchi.S1G383000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3730.t1 is derived from g899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5427763	5429650	.	-	.	Phchi.S1G088900
Phchi.S1	AUGUSTUS	transcript	5427763	5429650	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	stop_codon	5427760	5427762	.	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5427763	5427936	1	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5427763	5427936	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5427937	5428020	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5428021	5428107	1	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5428021	5428107	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5428108	5428196	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5428197	5428247	1	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5428197	5428247	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5428248	5428387	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5428388	5428503	1	-	2	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5428388	5428503	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5428504	5428660	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5428661	5428746	1	-	1	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5428661	5428746	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5428747	5428889	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5428890	5428975	0.96	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5428890	5428975	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5428976	5429080	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5429081	5429137	0.72	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5429081	5429137	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5429138	5429266	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5429267	5429370	0.73	-	2	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5429267	5429370	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	intron	5429371	5429502	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	CDS	5429503	5429650	0.93	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	exon	5429503	5429650	.	-	.	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
Phchi.S1	AUGUSTUS	start_codon	5429648	5429650	.	-	0	transcript_id "Phchi.S1G088900.t1"; gene_id "Phchi.S1G088900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15531.t1 is derived from g14000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19740562	19742466	.	+	.	Phchi.S3G285000
Phchi.S3	AUGUSTUS	transcript	19740562	19742466	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	start_codon	19740562	19740564	.	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19740562	19740650	1	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19740562	19740650	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19740651	19740744	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19740745	19740796	0.67	+	1	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19740745	19740796	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19740797	19740903	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19740904	19741096	0.67	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19740904	19741096	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19741097	19741222	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19741223	19741302	1	+	2	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19741223	19741302	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19741303	19741406	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19741407	19741526	0.97	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19741407	19741526	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19741527	19741619	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19741620	19741673	1	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19741620	19741673	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19741674	19741808	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19741809	19741875	1	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19741809	19741875	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19741876	19741967	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19741968	19742068	0.99	+	2	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19741968	19742068	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19742069	19742171	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19742172	19742279	0.99	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19742172	19742279	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	intron	19742280	19742355	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	CDS	19742356	19742466	0.99	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	exon	19742356	19742466	.	+	.	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
Phchi.S3	AUGUSTUS	stop_codon	19742467	19742469	.	+	0	transcript_id "Phchi.S3G285000.t1"; gene_id "Phchi.S3G285000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4785.t1 is derived from g1955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12807047	12810069	.	+	.	Phchi.S1G194400
Phchi.S1	AUGUSTUS	transcript	12807047	12810069	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	start_codon	12807047	12807049	.	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12807047	12807057	0.47	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12807047	12807057	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12807058	12807147	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12807148	12807210	1	+	1	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12807148	12807210	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12807211	12807448	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12807449	12807492	0.76	+	1	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12807449	12807492	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12807493	12807868	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12807869	12807925	0.32	+	2	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12807869	12807925	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12807926	12808016	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12808017	12808090	1	+	2	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12808017	12808090	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12808091	12808274	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12808275	12808434	0.94	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12808275	12808434	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12808435	12808535	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12808536	12808560	0.94	+	2	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12808536	12808560	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12808561	12808649	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12808650	12808739	1	+	1	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12808650	12808739	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12808740	12808840	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12808841	12809012	0.98	+	1	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12808841	12809012	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12809013	12809113	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12809114	12809187	1	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12809114	12809187	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12809188	12809273	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12809274	12809343	0.99	+	1	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12809274	12809343	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12809344	12809452	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12809453	12809524	1	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12809453	12809524	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12809525	12809613	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12809614	12809747	1	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12809614	12809747	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12809748	12809838	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12809839	12809912	1	+	1	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12809839	12809912	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	intron	12809913	12810022	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	CDS	12810023	12810069	0.98	+	2	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	exon	12810023	12810069	.	+	.	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
Phchi.S1	AUGUSTUS	stop_codon	12810070	12810072	.	+	0	transcript_id "Phchi.S1G194400.t1"; gene_id "Phchi.S1G194400"
# This transcript jg4733.t2 is derived from g1903.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4734.t1 is derived from g1904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12520743	12523462	.	+	.	Phchi.S1G189300
Phchi.S1	AUGUSTUS	transcript	12520743	12523212	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	start_codon	12520743	12520745	.	+	0	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12520743	12520813	0.55	+	0	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12520743	12520813	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12520814	12520891	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12520892	12520950	0.52	+	1	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12520892	12520950	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12520951	12521060	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521061	12521097	0.52	+	2	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521061	12521097	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521098	12521184	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521185	12521259	0.99	+	1	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521185	12521259	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521260	12521374	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521375	12521564	0.98	+	1	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521375	12521564	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521565	12521688	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521689	12521719	1	+	0	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521689	12521719	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521720	12521869	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521870	12521928	1	+	2	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521870	12521928	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521929	12522208	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12522209	12522282	1	+	0	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12522209	12522282	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12522283	12522537	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12522538	12522624	1	+	1	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12522538	12522624	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12522625	12522833	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12522834	12522895	1	+	1	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12522834	12522895	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12522896	12523001	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12523002	12523030	1	+	2	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12523002	12523030	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12523031	12523119	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12523120	12523212	1	+	0	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12523120	12523212	.	+	.	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	stop_codon	12523213	12523215	.	+	0	transcript_id "Phchi.S1G189300.t1"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	transcript	12520743	12523462	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	start_codon	12520743	12520745	.	+	0	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12520743	12520813	0.54	+	0	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12520743	12520813	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12520814	12520891	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12520892	12520950	0.54	+	1	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12520892	12520950	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12520951	12521060	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521061	12521097	0.53	+	2	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521061	12521097	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521098	12521184	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521185	12521259	0.99	+	1	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521185	12521259	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521260	12521374	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521375	12521564	0.99	+	1	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521375	12521564	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521565	12521688	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521689	12521719	1	+	0	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521689	12521719	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521720	12521869	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12521870	12521928	1	+	2	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12521870	12521928	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12521929	12522208	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12522209	12522282	1	+	0	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12522209	12522282	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12522283	12522537	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12522538	12522624	1	+	1	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12522538	12522624	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12522625	12522833	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12522834	12522870	0.73	+	1	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12522834	12522870	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12522871	12523001	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12523002	12523030	0.99	+	0	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12523002	12523030	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12523031	12523177	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12523178	12523233	0.99	+	1	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12523178	12523233	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	intron	12523234	12523379	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	CDS	12523380	12523462	0.81	+	2	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	exon	12523380	12523462	.	+	.	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
Phchi.S1	AUGUSTUS	stop_codon	12523463	12523465	.	+	0	transcript_id "Phchi.S1G189300.t2"; gene_id "Phchi.S1G189300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5815.t1 is derived from g2985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19081355	19082923	.	+	.	Phchi.S1G297400
Phchi.S1	AUGUSTUS	transcript	19081355	19082923	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	start_codon	19081355	19081357	.	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19081355	19081396	1	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19081355	19081396	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19081397	19081470	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19081471	19081500	1	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19081471	19081500	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19081501	19081574	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19081575	19081660	1	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19081575	19081660	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19081661	19081748	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19081749	19081824	1	+	1	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19081749	19081824	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19081825	19081908	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19081909	19082028	1	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19081909	19082028	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19082029	19082108	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19082109	19082153	0.39	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19082109	19082153	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19082154	19082485	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19082486	19082526	0.58	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19082486	19082526	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19082527	19082622	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19082623	19082663	0.96	+	1	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19082623	19082663	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19082664	19082797	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19082798	19082821	1	+	2	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19082798	19082821	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	intron	19082822	19082909	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	CDS	19082910	19082923	1	+	2	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	exon	19082910	19082923	.	+	.	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
Phchi.S1	AUGUSTUS	stop_codon	19082924	19082926	.	+	0	transcript_id "Phchi.S1G297400.t1"; gene_id "Phchi.S1G297400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4092.t1 is derived from g1261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7767330	7768490	.	-	.	Phchi.S1G125100
Phchi.S1	AUGUSTUS	transcript	7767330	7768490	.	-	.	transcript_id "Phchi.S1G125100.t1"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	stop_codon	7767327	7767329	.	-	0	transcript_id "Phchi.S1G125100.t1"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	CDS	7767330	7768490	0.94	-	0	transcript_id "Phchi.S1G125100.t1"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	exon	7767330	7768490	.	-	.	transcript_id "Phchi.S1G125100.t1"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	start_codon	7768488	7768490	.	-	0	transcript_id "Phchi.S1G125100.t1"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	transcript	7767330	7768118	.	-	.	transcript_id "Phchi.S1G125100.t2"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	stop_codon	7767327	7767329	.	-	0	transcript_id "Phchi.S1G125100.t2"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	CDS	7767330	7768118	0.91	-	0	transcript_id "Phchi.S1G125100.t2"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	exon	7767330	7768118	.	-	.	transcript_id "Phchi.S1G125100.t2"; gene_id "Phchi.S1G125100"
Phchi.S1	AUGUSTUS	start_codon	7768116	7768118	.	-	0	transcript_id "Phchi.S1G125100.t2"; gene_id "Phchi.S1G125100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7806.t1 is derived from g4980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31269993	31270769	.	-	.	Phchi.S1G496500
Phchi.S1	AUGUSTUS	transcript	31269993	31270769	.	-	.	transcript_id "Phchi.S1G496500.t1"; gene_id "Phchi.S1G496500"
Phchi.S1	AUGUSTUS	stop_codon	31269990	31269992	.	-	0	transcript_id "Phchi.S1G496500.t1"; gene_id "Phchi.S1G496500"
Phchi.S1	AUGUSTUS	CDS	31269993	31270769	1	-	0	transcript_id "Phchi.S1G496500.t1"; gene_id "Phchi.S1G496500"
Phchi.S1	AUGUSTUS	exon	31269993	31270769	.	-	.	transcript_id "Phchi.S1G496500.t1"; gene_id "Phchi.S1G496500"
Phchi.S1	AUGUSTUS	start_codon	31270767	31270769	.	-	0	transcript_id "Phchi.S1G496500.t1"; gene_id "Phchi.S1G496500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6409.t1 is derived from g3581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22841251	22841931	.	-	.	Phchi.S1G356800
Phchi.S1	AUGUSTUS	transcript	22841251	22841931	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	stop_codon	22841248	22841250	.	-	0	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	CDS	22841251	22841287	1	-	1	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	exon	22841251	22841287	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	intron	22841288	22841429	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	CDS	22841430	22841498	1	-	1	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	exon	22841430	22841498	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	intron	22841499	22841596	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	CDS	22841597	22841667	1	-	0	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	exon	22841597	22841667	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	intron	22841668	22841760	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	CDS	22841761	22841819	1	-	2	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	exon	22841761	22841819	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	intron	22841820	22841918	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	CDS	22841919	22841931	0.97	-	0	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	exon	22841919	22841931	.	-	.	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
Phchi.S1	AUGUSTUS	start_codon	22841929	22841931	.	-	0	transcript_id "Phchi.S1G356800.t1"; gene_id "Phchi.S1G356800"
# This transcript jg12179.t2 is derived from g7855.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12180.t1 is derived from g7856.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6111563	6114533	.	-	.	Phchi.S2G026000
Phchi.S2	AUGUSTUS	transcript	6111563	6114533	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	stop_codon	6111560	6111562	.	-	0	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6111563	6111566	0.98	-	1	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6111563	6111566	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6111567	6111899	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6111900	6112081	0.99	-	0	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6111900	6112081	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112082	6112415	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112416	6112521	1	-	1	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112416	6112521	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112522	6112664	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112665	6112806	1	-	2	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112665	6112806	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112807	6112902	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112903	6112962	0.87	-	2	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112903	6112962	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112963	6113068	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113069	6113118	0.83	-	1	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113069	6113118	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113119	6113267	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113268	6113315	0.98	-	1	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113268	6113315	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113316	6113518	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113519	6113539	0.59	-	1	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113519	6113539	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113540	6113628	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113629	6113805	0.64	-	1	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113629	6113805	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113806	6114201	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6114202	6114266	0.66	-	0	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6114202	6114266	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6114267	6114437	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6114438	6114533	0.63	-	0	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6114438	6114533	.	-	.	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	start_codon	6114531	6114533	.	-	0	transcript_id "Phchi.S2G026000.t1"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	transcript	6111997	6114533	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	stop_codon	6111994	6111996	.	-	0	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6111997	6112081	0.99	-	1	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6111997	6112081	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112082	6112247	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112248	6112330	1	-	0	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112248	6112330	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112331	6112415	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112416	6112521	1	-	1	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112416	6112521	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112522	6112664	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112665	6112806	0.98	-	2	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112665	6112806	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112807	6112902	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6112903	6112962	0.93	-	2	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6112903	6112962	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6112963	6113068	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113069	6113118	0.93	-	1	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113069	6113118	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113119	6113267	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113268	6113315	1	-	1	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113268	6113315	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113316	6113518	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113519	6113539	0.55	-	1	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113519	6113539	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113540	6113628	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6113629	6113805	0.56	-	1	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6113629	6113805	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6113806	6114201	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6114202	6114266	0.56	-	0	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6114202	6114266	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	intron	6114267	6114437	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	CDS	6114438	6114533	0.69	-	0	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	exon	6114438	6114533	.	-	.	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
Phchi.S2	AUGUSTUS	start_codon	6114531	6114533	.	-	0	transcript_id "Phchi.S2G026000.t2"; gene_id "Phchi.S2G026000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13406.t1 is derived from g11872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6551960	6553112	.	+	.	Phchi.S3G072500
Phchi.S3	AUGUSTUS	transcript	6551960	6553112	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	start_codon	6551960	6551962	.	+	0	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	CDS	6551960	6552147	0.97	+	0	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	exon	6551960	6552147	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	intron	6552148	6552243	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	CDS	6552244	6552404	1	+	1	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	exon	6552244	6552404	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	intron	6552405	6552572	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	CDS	6552573	6552719	1	+	2	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	exon	6552573	6552719	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	intron	6552720	6552874	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	CDS	6552875	6552951	1	+	2	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	exon	6552875	6552951	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	intron	6552952	6553028	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	CDS	6553029	6553112	1	+	0	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	exon	6553029	6553112	.	+	.	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
Phchi.S3	AUGUSTUS	stop_codon	6553113	6553115	.	+	0	transcript_id "Phchi.S3G072500.t1"; gene_id "Phchi.S3G072500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4771.t1 is derived from g1941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12752898	12753194	.	+	.	Phchi.S1G193000
Phchi.S1	AUGUSTUS	transcript	12752898	12753194	.	+	.	transcript_id "Phchi.S1G193000.t1"; gene_id "Phchi.S1G193000"
Phchi.S1	AUGUSTUS	start_codon	12752898	12752900	.	+	0	transcript_id "Phchi.S1G193000.t1"; gene_id "Phchi.S1G193000"
Phchi.S1	AUGUSTUS	CDS	12752898	12753194	0.99	+	0	transcript_id "Phchi.S1G193000.t1"; gene_id "Phchi.S1G193000"
Phchi.S1	AUGUSTUS	exon	12752898	12753194	.	+	.	transcript_id "Phchi.S1G193000.t1"; gene_id "Phchi.S1G193000"
Phchi.S1	AUGUSTUS	stop_codon	12753195	12753197	.	+	0	transcript_id "Phchi.S1G193000.t1"; gene_id "Phchi.S1G193000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg299.t1 is derived from g10081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2117304	2118775	.	+	.	Phchi.S6G025800
Phchi.S6	AUGUSTUS	transcript	2117304	2118775	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	start_codon	2117304	2117306	.	+	0	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	CDS	2117304	2117625	0.52	+	0	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	exon	2117304	2117625	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	intron	2117626	2117717	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	CDS	2117718	2118078	1	+	2	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	exon	2117718	2118078	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	intron	2118079	2118158	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	CDS	2118159	2118369	1	+	1	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	exon	2118159	2118369	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	intron	2118370	2118487	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	CDS	2118488	2118775	0.99	+	0	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	exon	2118488	2118775	.	+	.	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
Phchi.S6	AUGUSTUS	stop_codon	2118776	2118778	.	+	0	transcript_id "Phchi.S6G025800.t1"; gene_id "Phchi.S6G025800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13462.t1 is derived from g11929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7014758	7016637	.	-	.	Phchi.S3G078100
Phchi.S3	AUGUSTUS	transcript	7014758	7016637	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	stop_codon	7014755	7014757	.	-	0	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7014758	7014912	0.38	-	2	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7014758	7014912	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7014913	7015001	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7015002	7015081	1	-	1	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7015002	7015081	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7015082	7015169	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7015170	7015189	1	-	0	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7015170	7015189	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7015190	7015367	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7015368	7015446	1	-	1	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7015368	7015446	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7015447	7015532	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7015533	7015624	1	-	0	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7015533	7015624	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7015625	7015743	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7015744	7015810	0.54	-	1	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7015744	7015810	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7015811	7015902	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7015903	7016233	0.79	-	2	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7015903	7016233	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	intron	7016234	7016513	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	CDS	7016514	7016637	0.45	-	0	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	exon	7016514	7016637	.	-	.	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
Phchi.S3	AUGUSTUS	start_codon	7016635	7016637	.	-	0	transcript_id "Phchi.S3G078100.t1"; gene_id "Phchi.S3G078100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6041.t1 is derived from g3212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20597272	20597852	.	+	.	Phchi.S1G320000
Phchi.S1	AUGUSTUS	transcript	20597272	20597852	.	+	.	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	start_codon	20597272	20597274	.	+	0	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	CDS	20597272	20597402	0.92	+	0	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	exon	20597272	20597402	.	+	.	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	intron	20597403	20597498	.	+	.	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	CDS	20597499	20597544	0.97	+	1	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	exon	20597499	20597544	.	+	.	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	intron	20597545	20597795	.	+	.	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	CDS	20597796	20597852	0.94	+	0	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	exon	20597796	20597852	.	+	.	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
Phchi.S1	AUGUSTUS	stop_codon	20597853	20597855	.	+	0	transcript_id "Phchi.S1G320000.t1"; gene_id "Phchi.S1G320000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9731.t1 is derived from g6907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43438623	43441133	.	+	.	Phchi.S1G689000
Phchi.S1	AUGUSTUS	transcript	43438623	43441133	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	start_codon	43438623	43438625	.	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43438623	43438778	0.85	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43438623	43438778	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43438779	43438857	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43438858	43438944	0.87	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43438858	43438944	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43438945	43439044	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43439045	43439167	1	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43439045	43439167	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43439168	43439247	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43439248	43439430	1	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43439248	43439430	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43439431	43439547	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43439548	43439733	0.97	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43439548	43439733	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43439734	43439935	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43439936	43440154	0.85	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43439936	43440154	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43440155	43440269	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43440270	43440461	0.91	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43440270	43440461	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43440462	43440567	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43440568	43440747	0.73	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43440568	43440747	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	intron	43440748	43440824	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	CDS	43440825	43441133	0.93	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	exon	43440825	43441133	.	+	.	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
Phchi.S1	AUGUSTUS	stop_codon	43441134	43441136	.	+	0	transcript_id "Phchi.S1G689000.t1"; gene_id "Phchi.S1G689000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5490.t1 is derived from g2660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17103643	17105340	.	-	.	Phchi.S1G264900
Phchi.S1	AUGUSTUS	transcript	17103643	17105340	.	-	.	transcript_id "Phchi.S1G264900.t1"; gene_id "Phchi.S1G264900"
Phchi.S1	AUGUSTUS	stop_codon	17103640	17103642	.	-	0	transcript_id "Phchi.S1G264900.t1"; gene_id "Phchi.S1G264900"
Phchi.S1	AUGUSTUS	CDS	17103643	17105340	0.98	-	0	transcript_id "Phchi.S1G264900.t1"; gene_id "Phchi.S1G264900"
Phchi.S1	AUGUSTUS	exon	17103643	17105340	.	-	.	transcript_id "Phchi.S1G264900.t1"; gene_id "Phchi.S1G264900"
Phchi.S1	AUGUSTUS	start_codon	17105338	17105340	.	-	0	transcript_id "Phchi.S1G264900.t1"; gene_id "Phchi.S1G264900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4873.t1 is derived from g2043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13181479	13182185	.	+	.	Phchi.S1G203200
Phchi.S1	AUGUSTUS	transcript	13181479	13182185	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	start_codon	13181479	13181481	.	+	0	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	CDS	13181479	13181520	1	+	0	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	exon	13181479	13181520	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	intron	13181521	13181606	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	CDS	13181607	13181659	1	+	0	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	exon	13181607	13181659	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	intron	13181660	13181821	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	CDS	13181822	13181860	1	+	1	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	exon	13181822	13181860	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	intron	13181861	13181980	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	CDS	13181981	13182050	1	+	1	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	exon	13181981	13182050	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	intron	13182051	13182137	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	CDS	13182138	13182185	0.99	+	0	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	exon	13182138	13182185	.	+	.	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
Phchi.S1	AUGUSTUS	stop_codon	13182186	13182188	.	+	0	transcript_id "Phchi.S1G203200.t1"; gene_id "Phchi.S1G203200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9446.t1 is derived from g6622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41503567	41504864	.	-	.	Phchi.S1G660500
Phchi.S1	AUGUSTUS	transcript	41503567	41504864	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	stop_codon	41503564	41503566	.	-	0	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	CDS	41503567	41503766	0.97	-	2	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	exon	41503567	41503766	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	intron	41503767	41503867	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	CDS	41503868	41504152	0.77	-	2	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	exon	41503868	41504152	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	intron	41504153	41504220	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	CDS	41504221	41504637	0.87	-	2	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	exon	41504221	41504637	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	intron	41504638	41504776	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	CDS	41504777	41504864	0.43	-	0	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	exon	41504777	41504864	.	-	.	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
Phchi.S1	AUGUSTUS	start_codon	41504862	41504864	.	-	0	transcript_id "Phchi.S1G660500.t1"; gene_id "Phchi.S1G660500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10592.t1 is derived from g14642.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1095867	1097703	.	+	.	Phchi.S4G017400
Phchi.S4	AUGUSTUS	transcript	1095867	1097703	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	start_codon	1095867	1095869	.	+	0	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1095867	1096127	0.85	+	0	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1095867	1096127	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096128	1096234	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1096235	1096356	0.99	+	0	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1096235	1096356	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096357	1096504	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1096505	1096588	1	+	1	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1096505	1096588	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096589	1096727	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1096728	1096824	1	+	1	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1096728	1096824	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096825	1097134	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1097135	1097351	1	+	0	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1097135	1097351	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1097352	1097468	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1097469	1097521	1	+	2	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1097469	1097521	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1097522	1097619	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1097620	1097703	1	+	0	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1097620	1097703	.	+	.	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	stop_codon	1097704	1097706	.	+	0	transcript_id "Phchi.S4G017400.t1"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	transcript	1095867	1097703	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	start_codon	1095867	1095869	.	+	0	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1095867	1096127	0.81	+	0	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1095867	1096127	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096128	1096234	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1096235	1096356	1	+	0	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1096235	1096356	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096357	1096504	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1096505	1096588	1	+	1	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1096505	1096588	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096589	1096730	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1096731	1096824	1	+	1	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1096731	1096824	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1096825	1097134	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1097135	1097351	1	+	0	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1097135	1097351	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1097352	1097468	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1097469	1097521	1	+	2	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1097469	1097521	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	intron	1097522	1097619	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	CDS	1097620	1097703	1	+	0	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	exon	1097620	1097703	.	+	.	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
Phchi.S4	AUGUSTUS	stop_codon	1097704	1097706	.	+	0	transcript_id "Phchi.S4G017400.t2"; gene_id "Phchi.S4G017400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2116.t1 is derived from g9036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4927494	4928663	.	-	.	Phchi.S5G072500
Phchi.S5	AUGUSTUS	transcript	4927494	4928663	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	stop_codon	4927491	4927493	.	-	0	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	CDS	4927494	4927878	0.97	-	1	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	exon	4927494	4927878	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	intron	4927879	4927980	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	CDS	4927981	4928039	1	-	0	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	exon	4927981	4928039	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	intron	4928040	4928129	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	CDS	4928130	4928208	1	-	1	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	exon	4928130	4928208	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	intron	4928209	4928284	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	CDS	4928285	4928423	1	-	2	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	exon	4928285	4928423	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	intron	4928424	4928566	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	CDS	4928567	4928663	1	-	0	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	exon	4928567	4928663	.	-	.	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
Phchi.S5	AUGUSTUS	start_codon	4928661	4928663	.	-	0	transcript_id "Phchi.S5G072500.t1"; gene_id "Phchi.S5G072500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1988.t1 is derived from g8908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4331712	4332133	.	+	.	Phchi.S5G059700
Phchi.S5	AUGUSTUS	transcript	4331712	4332133	.	+	.	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	start_codon	4331712	4331714	.	+	0	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	CDS	4331712	4331999	0.43	+	0	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	exon	4331712	4331999	.	+	.	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	intron	4332000	4332085	.	+	.	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	CDS	4332086	4332133	0.61	+	0	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	exon	4332086	4332133	.	+	.	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
Phchi.S5	AUGUSTUS	stop_codon	4332134	4332136	.	+	0	transcript_id "Phchi.S5G059700.t1"; gene_id "Phchi.S5G059700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5017.t1 is derived from g2187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14081992	14083234	.	+	.	Phchi.S1G217600
Phchi.S1	AUGUSTUS	transcript	14081992	14083234	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	start_codon	14081992	14081994	.	+	0	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	CDS	14081992	14082124	0.99	+	0	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	exon	14081992	14082124	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	intron	14082125	14082230	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	CDS	14082231	14082469	1	+	2	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	exon	14082231	14082469	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	intron	14082470	14082550	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	CDS	14082551	14082717	1	+	0	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	exon	14082551	14082717	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	intron	14082718	14082804	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	CDS	14082805	14083234	0.93	+	1	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	exon	14082805	14083234	.	+	.	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
Phchi.S1	AUGUSTUS	stop_codon	14083235	14083237	.	+	0	transcript_id "Phchi.S1G217600.t1"; gene_id "Phchi.S1G217600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2892.t1 is derived from g61.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	343377	344107	.	-	.	Phchi.S1G005100
Phchi.S1	AUGUSTUS	transcript	343377	344107	.	-	.	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	stop_codon	343374	343376	.	-	0	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	CDS	343377	343533	1	-	1	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	exon	343377	343533	.	-	.	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	intron	343534	343800	.	-	.	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	CDS	343801	343865	1	-	0	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	exon	343801	343865	.	-	.	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	intron	343866	344059	.	-	.	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	CDS	344060	344107	0.99	-	0	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	exon	344060	344107	.	-	.	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
Phchi.S1	AUGUSTUS	start_codon	344105	344107	.	-	0	transcript_id "Phchi.S1G005100.t1"; gene_id "Phchi.S1G005100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4913.t1 is derived from g2083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13446688	13448350	.	+	.	Phchi.S1G207200
Phchi.S1	AUGUSTUS	transcript	13446688	13448350	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	start_codon	13446688	13446690	.	+	0	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	CDS	13446688	13447126	0.31	+	0	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	exon	13446688	13447126	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	intron	13447127	13447412	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	CDS	13447413	13447499	0.75	+	2	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	exon	13447413	13447499	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	intron	13447500	13447785	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	CDS	13447786	13447869	0.8	+	2	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	exon	13447786	13447869	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	intron	13447870	13447985	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	CDS	13447986	13448350	0.7	+	2	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	exon	13447986	13448350	.	+	.	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
Phchi.S1	AUGUSTUS	stop_codon	13448351	13448353	.	+	0	transcript_id "Phchi.S1G207200.t1"; gene_id "Phchi.S1G207200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14169.t1 is derived from g12636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11250229	11251498	.	+	.	Phchi.S3G148800
Phchi.S3	AUGUSTUS	transcript	11250229	11251498	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	start_codon	11250229	11250231	.	+	0	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11250229	11250249	0.66	+	0	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11250229	11250249	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	intron	11250250	11250426	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11250427	11250436	0.68	+	0	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11250427	11250436	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	intron	11250437	11250532	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11250533	11250726	1	+	2	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11250533	11250726	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	intron	11250727	11250827	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11250828	11250953	1	+	0	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11250828	11250953	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	intron	11250954	11251157	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11251158	11251257	0.9	+	0	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11251158	11251257	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	intron	11251258	11251355	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11251356	11251386	1	+	2	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11251356	11251386	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	intron	11251387	11251485	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	CDS	11251486	11251498	0.98	+	1	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	exon	11251486	11251498	.	+	.	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
Phchi.S3	AUGUSTUS	stop_codon	11251499	11251501	.	+	0	transcript_id "Phchi.S3G148800.t1"; gene_id "Phchi.S3G148800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8365.t1 is derived from g5540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35524752	35525789	.	-	.	Phchi.S1G552400
Phchi.S1	AUGUSTUS	transcript	35524752	35525789	.	-	.	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	stop_codon	35524749	35524751	.	-	0	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	CDS	35524752	35524925	0.98	-	0	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	exon	35524752	35524925	.	-	.	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	intron	35524926	35525011	.	-	.	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	CDS	35525012	35525150	1	-	1	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	exon	35525012	35525150	.	-	.	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	intron	35525151	35525712	.	-	.	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	CDS	35525713	35525789	0.49	-	0	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	exon	35525713	35525789	.	-	.	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
Phchi.S1	AUGUSTUS	start_codon	35525787	35525789	.	-	0	transcript_id "Phchi.S1G552400.t1"; gene_id "Phchi.S1G552400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10880.t1 is derived from g14930.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2733959	2735000	.	+	.	Phchi.S4G046200
Phchi.S4	AUGUSTUS	transcript	2733959	2734950	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	start_codon	2733959	2733961	.	+	0	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2733959	2734001	0.65	+	0	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2733959	2734001	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734002	2734181	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734182	2734258	0.97	+	2	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734182	2734258	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734259	2734355	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734356	2734402	0.96	+	0	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734356	2734402	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734403	2734561	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734562	2734627	1	+	1	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734562	2734627	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734628	2734710	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734711	2734848	1	+	1	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734711	2734848	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734849	2734946	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734947	2734950	1	+	1	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734947	2734950	.	+	.	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	stop_codon	2734951	2734953	.	+	0	transcript_id "Phchi.S4G046200.t1"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	transcript	2733959	2735000	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	start_codon	2733959	2733961	.	+	0	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2733959	2734001	0.7	+	0	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2733959	2734001	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734002	2734181	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734182	2734258	0.96	+	2	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734182	2734258	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734259	2734355	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734356	2734402	0.94	+	0	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734356	2734402	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734403	2734561	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734562	2734627	1	+	1	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734562	2734627	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734628	2734775	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734776	2734848	1	+	1	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734776	2734848	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734849	2734946	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734947	2735000	0.99	+	0	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734947	2735000	.	+	.	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	stop_codon	2735001	2735003	.	+	0	transcript_id "Phchi.S4G046200.t2"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	transcript	2733999	2735000	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	start_codon	2733999	2734001	.	+	0	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2733999	2734001	0.56	+	0	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2733999	2734001	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734002	2734181	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734182	2734258	0.6	+	0	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734182	2734258	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734259	2734561	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734562	2734627	1	+	1	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734562	2734627	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734628	2734775	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734776	2734848	1	+	1	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734776	2734848	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	intron	2734849	2734946	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	CDS	2734947	2735000	0.97	+	0	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	exon	2734947	2735000	.	+	.	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
Phchi.S4	AUGUSTUS	stop_codon	2735001	2735003	.	+	0	transcript_id "Phchi.S4G046200.t3"; gene_id "Phchi.S4G046200"
# This transcript jg11241.t2 is derived from g15291.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11242.t1 is derived from g15292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4969779	4972017	.	+	.	Phchi.S4G082400
Phchi.S4	AUGUSTUS	transcript	4969779	4972017	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	start_codon	4969779	4969781	.	+	0	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	CDS	4969779	4970189	0.85	+	0	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	exon	4969779	4970189	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	intron	4970190	4970295	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	CDS	4970296	4970617	0.73	+	0	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	exon	4970296	4970617	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	intron	4970618	4970708	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	CDS	4970709	4970792	0.8	+	2	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	exon	4970709	4970792	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	intron	4970793	4970893	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	CDS	4970894	4972017	0.44	+	2	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	exon	4970894	4972017	.	+	.	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
Phchi.S4	AUGUSTUS	stop_codon	4972018	4972020	.	+	0	transcript_id "Phchi.S4G082400.t1"; gene_id "Phchi.S4G082400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5914.t1 is derived from g3085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19855594	19857786	.	+	.	Phchi.S1G307300
Phchi.S1	AUGUSTUS	transcript	19855594	19857786	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	start_codon	19855594	19855596	.	+	0	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19855594	19855996	0.95	+	0	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19855594	19855996	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19855997	19856203	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19856204	19856330	1	+	2	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19856204	19856330	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19856331	19856576	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19856577	19856674	1	+	1	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19856577	19856674	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19856675	19856855	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19856856	19857005	1	+	2	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19856856	19857005	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19857006	19857118	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19857119	19857271	0.84	+	2	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19857119	19857271	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19857272	19857378	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19857379	19857429	0.83	+	2	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19857379	19857429	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19857430	19857562	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19857563	19857612	0.83	+	2	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19857563	19857612	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	intron	19857613	19857780	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	CDS	19857781	19857786	0.83	+	0	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	exon	19857781	19857786	.	+	.	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
Phchi.S1	AUGUSTUS	stop_codon	19857787	19857789	.	+	0	transcript_id "Phchi.S1G307300.t1"; gene_id "Phchi.S1G307300"
# This transcript jg9674.t2 is derived from g6850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9675.t1 is derived from g6851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43232888	43234197	.	+	.	Phchi.S1G683400
Phchi.S1	AUGUSTUS	transcript	43232888	43234197	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	start_codon	43232888	43232890	.	+	0	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	CDS	43232888	43232893	0.64	+	0	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	exon	43232888	43232893	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	intron	43232894	43232973	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	CDS	43232974	43233177	0.54	+	0	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	exon	43232974	43233177	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	intron	43233178	43233260	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	CDS	43233261	43233946	0.86	+	0	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	exon	43233261	43233946	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	intron	43233947	43234142	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	CDS	43234143	43234197	0.8	+	1	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	exon	43234143	43234197	.	+	.	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
Phchi.S1	AUGUSTUS	stop_codon	43234198	43234200	.	+	0	transcript_id "Phchi.S1G683400.t1"; gene_id "Phchi.S1G683400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg442.t1 is derived from g10224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3095086	3095912	.	+	.	Phchi.S6G040100
Phchi.S6	AUGUSTUS	transcript	3095086	3095912	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	start_codon	3095086	3095088	.	+	0	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	CDS	3095086	3095199	0.64	+	0	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	exon	3095086	3095199	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	intron	3095200	3095292	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	CDS	3095293	3095457	0.73	+	0	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	exon	3095293	3095457	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	intron	3095458	3095584	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	CDS	3095585	3095631	1	+	0	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	exon	3095585	3095631	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	intron	3095632	3095794	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	CDS	3095795	3095912	0.32	+	1	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	exon	3095795	3095912	.	+	.	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
Phchi.S6	AUGUSTUS	stop_codon	3095913	3095915	.	+	0	transcript_id "Phchi.S6G040100.t1"; gene_id "Phchi.S6G040100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7787.t1 is derived from g4961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31192412	31192894	.	+	.	Phchi.S1G494600
Phchi.S1	AUGUSTUS	transcript	31192412	31192894	.	+	.	transcript_id "Phchi.S1G494600.t1"; gene_id "Phchi.S1G494600"
Phchi.S1	AUGUSTUS	start_codon	31192412	31192414	.	+	0	transcript_id "Phchi.S1G494600.t1"; gene_id "Phchi.S1G494600"
Phchi.S1	AUGUSTUS	CDS	31192412	31192894	0.97	+	0	transcript_id "Phchi.S1G494600.t1"; gene_id "Phchi.S1G494600"
Phchi.S1	AUGUSTUS	exon	31192412	31192894	.	+	.	transcript_id "Phchi.S1G494600.t1"; gene_id "Phchi.S1G494600"
Phchi.S1	AUGUSTUS	stop_codon	31192895	31192897	.	+	0	transcript_id "Phchi.S1G494600.t1"; gene_id "Phchi.S1G494600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7999.t1 is derived from g5174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32368945	32369923	.	+	.	Phchi.S1G515800
Phchi.S1	AUGUSTUS	transcript	32368945	32369923	.	+	.	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	start_codon	32368945	32368947	.	+	0	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	CDS	32368945	32369331	0.82	+	0	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	exon	32368945	32369331	.	+	.	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	intron	32369332	32369448	.	+	.	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	CDS	32369449	32369596	0.98	+	0	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	exon	32369449	32369596	.	+	.	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	intron	32369597	32369816	.	+	.	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	CDS	32369817	32369923	1	+	2	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	exon	32369817	32369923	.	+	.	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
Phchi.S1	AUGUSTUS	stop_codon	32369924	32369926	.	+	0	transcript_id "Phchi.S1G515800.t1"; gene_id "Phchi.S1G515800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9450.t1 is derived from g6626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41533431	41533946	.	-	.	Phchi.S1G660900
Phchi.S1	AUGUSTUS	transcript	41533431	41533946	.	-	.	transcript_id "Phchi.S1G660900.t1"; gene_id "Phchi.S1G660900"
Phchi.S1	AUGUSTUS	stop_codon	41533428	41533430	.	-	0	transcript_id "Phchi.S1G660900.t1"; gene_id "Phchi.S1G660900"
Phchi.S1	AUGUSTUS	CDS	41533431	41533946	0.39	-	0	transcript_id "Phchi.S1G660900.t1"; gene_id "Phchi.S1G660900"
Phchi.S1	AUGUSTUS	exon	41533431	41533946	.	-	.	transcript_id "Phchi.S1G660900.t1"; gene_id "Phchi.S1G660900"
Phchi.S1	AUGUSTUS	start_codon	41533944	41533946	.	-	0	transcript_id "Phchi.S1G660900.t1"; gene_id "Phchi.S1G660900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1482.t1 is derived from g8401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1138421	1141323	.	+	.	Phchi.S5G009100
Phchi.S5	AUGUSTUS	transcript	1138421	1141323	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	start_codon	1138421	1138423	.	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1138421	1138616	0.97	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1138421	1138616	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1138617	1138962	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1138963	1139056	1	+	2	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1138963	1139056	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1139057	1139320	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1139321	1139363	1	+	1	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1139321	1139363	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1139364	1139457	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1139458	1139580	1	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1139458	1139580	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1139581	1139673	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1139674	1139793	1	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1139674	1139793	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1139794	1139929	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1139930	1140008	1	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1139930	1140008	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1140009	1140095	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1140096	1140209	1	+	2	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1140096	1140209	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1140210	1140305	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1140306	1140403	1	+	2	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1140306	1140403	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1140404	1140573	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1140574	1140664	1	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1140574	1140664	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1140665	1140756	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1140757	1140876	1	+	2	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1140757	1140876	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1140877	1140961	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1140962	1141032	1	+	2	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1140962	1141032	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	intron	1141033	1141125	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	CDS	1141126	1141323	0.79	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	exon	1141126	1141323	.	+	.	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
Phchi.S5	AUGUSTUS	stop_codon	1141324	1141326	.	+	0	transcript_id "Phchi.S5G009100.t1"; gene_id "Phchi.S5G009100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12160.t1 is derived from g7836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5073508	5075462	.	-	.	Phchi.S2G024000
Phchi.S2	AUGUSTUS	transcript	5073508	5075462	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	stop_codon	5073505	5073507	.	-	0	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	CDS	5073508	5073582	0.82	-	0	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	exon	5073508	5073582	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	intron	5073583	5073733	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	CDS	5073734	5073815	0.82	-	1	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	exon	5073734	5073815	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	intron	5073816	5073967	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	CDS	5073968	5074070	0.82	-	2	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	exon	5073968	5074070	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	intron	5074071	5074232	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	CDS	5074233	5074395	0.82	-	0	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	exon	5074233	5074395	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	intron	5074396	5074755	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	CDS	5074756	5074950	1	-	0	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	exon	5074756	5074950	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	intron	5074951	5075213	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	CDS	5075214	5075462	0.87	-	0	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	exon	5075214	5075462	.	-	.	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
Phchi.S2	AUGUSTUS	start_codon	5075460	5075462	.	-	0	transcript_id "Phchi.S2G024000.t1"; gene_id "Phchi.S2G024000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11579.t1 is derived from g15630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7188314	7189966	.	+	.	Phchi.S4G116100
Phchi.S4	AUGUSTUS	transcript	7188314	7189966	.	+	.	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	start_codon	7188314	7188316	.	+	0	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	CDS	7188314	7188957	1	+	0	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	exon	7188314	7188957	.	+	.	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	intron	7188958	7189060	.	+	.	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	CDS	7189061	7189567	0.68	+	1	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	exon	7189061	7189567	.	+	.	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	intron	7189568	7189686	.	+	.	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	CDS	7189687	7189966	0.78	+	1	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	exon	7189687	7189966	.	+	.	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
Phchi.S4	AUGUSTUS	stop_codon	7189967	7189969	.	+	0	transcript_id "Phchi.S4G116100.t1"; gene_id "Phchi.S4G116100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4587.t1 is derived from g1757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11215286	11218044	.	+	.	Phchi.S1G174600
Phchi.S1	AUGUSTUS	transcript	11215286	11218044	.	+	.	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	start_codon	11215286	11215288	.	+	0	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	CDS	11215286	11217059	0.63	+	0	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	exon	11215286	11217059	.	+	.	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	intron	11217060	11217150	.	+	.	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	CDS	11217151	11217270	1	+	2	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	exon	11217151	11217270	.	+	.	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	intron	11217271	11217361	.	+	.	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	CDS	11217362	11218044	0.31	+	2	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	exon	11217362	11218044	.	+	.	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
Phchi.S1	AUGUSTUS	stop_codon	11218045	11218047	.	+	0	transcript_id "Phchi.S1G174600.t1"; gene_id "Phchi.S1G174600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12539.t1 is derived from g8216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33931913	33938576	.	+	.	Phchi.S2G061900
Phchi.S2	AUGUSTUS	transcript	33931913	33938576	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	start_codon	33931913	33931915	.	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33931913	33932338	0.48	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33931913	33932338	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33932339	33932669	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33932670	33932936	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33932670	33932936	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33932937	33933036	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33933037	33933227	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33933037	33933227	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33933228	33933360	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33933361	33933538	0.97	+	1	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33933361	33933538	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33933539	33933674	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33933675	33933812	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33933675	33933812	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33933813	33933893	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33933894	33934035	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33933894	33934035	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33934036	33934157	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33934158	33934408	1	+	2	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33934158	33934408	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33934409	33934792	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33934793	33934975	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33934793	33934975	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33934976	33935114	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33935115	33935225	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33935115	33935225	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33935226	33935319	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33935320	33935439	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33935320	33935439	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33935440	33935531	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33935532	33935673	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33935532	33935673	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33935674	33935893	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33935894	33936054	1	+	2	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33935894	33936054	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33936055	33936286	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33936287	33936373	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33936287	33936373	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33936374	33936520	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33936521	33936849	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33936521	33936849	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33936850	33936957	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33936958	33937039	0.99	+	1	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33936958	33937039	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33937040	33937165	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33937166	33937296	1	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33937166	33937296	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33937297	33937415	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33937416	33937653	1	+	1	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33937416	33937653	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33937654	33937747	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33937748	33937994	0.96	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33937748	33937994	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33937995	33938338	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33938339	33938399	0.95	+	2	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33938339	33938399	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	intron	33938400	33938539	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	CDS	33938540	33938576	0.95	+	1	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	exon	33938540	33938576	.	+	.	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
Phchi.S2	AUGUSTUS	stop_codon	33938577	33938579	.	+	0	transcript_id "Phchi.S2G061900.t1"; gene_id "Phchi.S2G061900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15519.t1 is derived from g13988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19679296	19681079	.	+	.	Phchi.S3G283800
Phchi.S3	AUGUSTUS	transcript	19679296	19681079	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	start_codon	19679296	19679298	.	+	0	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	CDS	19679296	19679628	0.9	+	0	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	exon	19679296	19679628	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	intron	19679629	19679887	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	CDS	19679888	19679975	1	+	0	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	exon	19679888	19679975	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	intron	19679976	19680161	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	CDS	19680162	19680291	1	+	2	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	exon	19680162	19680291	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	intron	19680292	19680416	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	CDS	19680417	19680692	0.77	+	1	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	exon	19680417	19680692	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	intron	19680693	19680787	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	CDS	19680788	19681079	0.77	+	1	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	exon	19680788	19681079	.	+	.	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
Phchi.S3	AUGUSTUS	stop_codon	19681080	19681082	.	+	0	transcript_id "Phchi.S3G283800.t1"; gene_id "Phchi.S3G283800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11053.t1 is derived from g15103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3841104	3843504	.	-	.	Phchi.S4G063500
Phchi.S4	AUGUSTUS	transcript	3841104	3843504	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	stop_codon	3841101	3841103	.	-	0	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	CDS	3841104	3841476	1	-	1	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	exon	3841104	3841476	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	intron	3841477	3841569	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	CDS	3841570	3841727	0.54	-	0	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	exon	3841570	3841727	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	intron	3841728	3841882	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	CDS	3841883	3842253	0.75	-	2	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	exon	3841883	3842253	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	intron	3842254	3842436	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	CDS	3842437	3842602	1	-	0	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	exon	3842437	3842602	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	intron	3842603	3842853	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	CDS	3842854	3843504	0.42	-	0	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	exon	3842854	3843504	.	-	.	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
Phchi.S4	AUGUSTUS	start_codon	3843502	3843504	.	-	0	transcript_id "Phchi.S4G063500.t1"; gene_id "Phchi.S4G063500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg528.t1 is derived from g10310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3785231	3788636	.	-	.	Phchi.S6G048700
Phchi.S6	AUGUSTUS	transcript	3785231	3788636	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	stop_codon	3785228	3785230	.	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785231	3785265	0.52	-	2	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785231	3785265	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785266	3785419	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785420	3785479	0.49	-	2	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785420	3785479	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785480	3785571	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785572	3785612	0.89	-	1	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785572	3785612	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785613	3785705	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785706	3785785	0.53	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785706	3785785	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785786	3785895	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785896	3785940	0.64	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785896	3785940	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785941	3786060	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786061	3786168	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786061	3786168	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786169	3786267	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786268	3786353	1	-	2	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786268	3786353	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786354	3786471	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786472	3786559	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786472	3786559	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786560	3786671	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786672	3786950	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786672	3786950	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786951	3787037	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787038	3787113	1	-	1	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787038	3787113	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787114	3787225	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787226	3787275	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787226	3787275	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787276	3787402	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787403	3787465	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787403	3787465	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787466	3787607	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787608	3787661	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787608	3787661	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787662	3787759	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787760	3787862	0.94	-	1	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787760	3787862	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787863	3787969	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787970	3788072	1	-	2	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787970	3788072	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3788073	3788159	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3788160	3788220	1	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3788160	3788220	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3788221	3788332	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3788333	3788373	1	-	2	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3788333	3788373	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3788374	3788485	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3788486	3788636	0.94	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3788486	3788636	.	-	.	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	start_codon	3788634	3788636	.	-	0	transcript_id "Phchi.S6G048700.t1"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	transcript	3785231	3788636	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	stop_codon	3785228	3785230	.	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785231	3785265	0.59	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785231	3785265	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785266	3785419	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785420	3785479	0.58	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785420	3785479	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785480	3785571	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785572	3785612	0.92	-	1	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785572	3785612	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785613	3785705	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785706	3785785	0.57	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785706	3785785	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785786	3785895	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3785896	3785940	0.65	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3785896	3785940	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3785941	3786060	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786061	3786168	1	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786061	3786168	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786169	3786267	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786268	3786353	1	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786268	3786353	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786354	3786471	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786472	3786559	1	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786472	3786559	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786560	3786671	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3786672	3786943	0.99	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3786672	3786943	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3786944	3787037	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787038	3787113	0.99	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787038	3787113	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787114	3787264	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787265	3787275	0.72	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787265	3787275	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787276	3787371	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787372	3787465	0.99	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787372	3787465	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787466	3787607	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787608	3787661	1	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787608	3787661	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787662	3787759	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787760	3787862	0.96	-	1	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787760	3787862	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3787863	3787969	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3787970	3788072	1	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3787970	3788072	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3788073	3788159	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3788160	3788220	1	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3788160	3788220	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3788221	3788332	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3788333	3788373	1	-	2	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3788333	3788373	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	intron	3788374	3788485	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	CDS	3788486	3788636	0.97	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	exon	3788486	3788636	.	-	.	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
Phchi.S6	AUGUSTUS	start_codon	3788634	3788636	.	-	0	transcript_id "Phchi.S6G048700.t2"; gene_id "Phchi.S6G048700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14815.t1 is derived from g13283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14828964	14830974	.	+	.	Phchi.S3G213400
Phchi.S3	AUGUSTUS	transcript	14828964	14830974	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	start_codon	14828964	14828966	.	+	0	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	CDS	14828964	14829114	0.57	+	0	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	exon	14828964	14829114	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	intron	14829115	14829411	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	CDS	14829412	14830274	0.99	+	2	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	exon	14829412	14830274	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	intron	14830275	14830398	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	CDS	14830399	14830563	1	+	0	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	exon	14830399	14830563	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	intron	14830564	14830680	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	CDS	14830681	14830974	0.99	+	0	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	exon	14830681	14830974	.	+	.	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
Phchi.S3	AUGUSTUS	stop_codon	14830975	14830977	.	+	0	transcript_id "Phchi.S3G213400.t1"; gene_id "Phchi.S3G213400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9708.t1 is derived from g6884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43362352	43363301	.	+	.	Phchi.S1G686700
Phchi.S1	AUGUSTUS	transcript	43362352	43363301	.	+	.	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	start_codon	43362352	43362354	.	+	0	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	CDS	43362352	43362442	1	+	0	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	exon	43362352	43362442	.	+	.	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	intron	43362443	43362616	.	+	.	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	CDS	43362617	43362853	0.76	+	2	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	exon	43362617	43362853	.	+	.	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	intron	43362854	43362960	.	+	.	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	CDS	43362961	43363301	0.98	+	2	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	exon	43362961	43363301	.	+	.	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
Phchi.S1	AUGUSTUS	stop_codon	43363302	43363304	.	+	0	transcript_id "Phchi.S1G686700.t1"; gene_id "Phchi.S1G686700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9271.t1 is derived from g6446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40688143	40692051	.	-	.	Phchi.S1G643000
Phchi.S1	AUGUSTUS	transcript	40688143	40692051	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	stop_codon	40688140	40688142	.	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40688143	40688322	0.99	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40688143	40688322	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40688323	40688445	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40688446	40688560	1	-	1	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40688446	40688560	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40688561	40688641	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40688642	40688730	1	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40688642	40688730	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40688731	40688814	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40688815	40688888	0.86	-	2	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40688815	40688888	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40688889	40689058	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40689059	40689136	0.71	-	2	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40689059	40689136	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40689137	40689290	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40689291	40689444	0.96	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40689291	40689444	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40689445	40689587	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40689588	40689681	1	-	1	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40689588	40689681	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40689682	40689810	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40689811	40689923	1	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40689811	40689923	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40689924	40690010	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40690011	40690110	1	-	1	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40690011	40690110	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40690111	40690374	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40690375	40690507	0.94	-	2	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40690375	40690507	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40690508	40690608	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40690609	40690676	1	-	1	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40690609	40690676	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40690677	40690916	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40690917	40691025	1	-	2	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40690917	40691025	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40691026	40691510	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40691511	40691593	0.64	-	1	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40691511	40691593	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40691594	40691739	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40691740	40691834	0.57	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40691740	40691834	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	intron	40691835	40692027	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	CDS	40692028	40692051	0.63	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	exon	40692028	40692051	.	-	.	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
Phchi.S1	AUGUSTUS	start_codon	40692049	40692051	.	-	0	transcript_id "Phchi.S1G643000.t1"; gene_id "Phchi.S1G643000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg103.t1 is derived from g9885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	520175	520707	.	-	.	Phchi.S6G006200
Phchi.S6	AUGUSTUS	transcript	520175	520707	.	-	.	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	stop_codon	520172	520174	.	-	0	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	CDS	520175	520258	1	-	0	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	exon	520175	520258	.	-	.	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	intron	520259	520503	.	-	.	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	CDS	520504	520707	0.89	-	0	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	exon	520504	520707	.	-	.	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
Phchi.S6	AUGUSTUS	start_codon	520705	520707	.	-	0	transcript_id "Phchi.S6G006200.t1"; gene_id "Phchi.S6G006200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5989.t1 is derived from g3160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20271319	20272951	.	-	.	Phchi.S1G314800
Phchi.S1	AUGUSTUS	transcript	20271319	20272951	.	-	.	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	stop_codon	20271316	20271318	.	-	0	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	CDS	20271319	20272736	0.99	-	2	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	exon	20271319	20272736	.	-	.	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	intron	20272737	20272836	.	-	.	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	CDS	20272837	20272951	1	-	0	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	exon	20272837	20272951	.	-	.	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
Phchi.S1	AUGUSTUS	start_codon	20272949	20272951	.	-	0	transcript_id "Phchi.S1G314800.t1"; gene_id "Phchi.S1G314800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8225.t1 is derived from g5400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34542575	34543950	.	+	.	Phchi.S1G538400
Phchi.S1	AUGUSTUS	transcript	34542575	34543950	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	start_codon	34542575	34542577	.	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34542575	34542646	0.92	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34542575	34542646	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	intron	34542647	34542789	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34542790	34542872	1	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34542790	34542872	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	intron	34542873	34542957	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34542958	34543143	1	+	1	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34542958	34543143	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	intron	34543144	34543239	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34543240	34543324	1	+	1	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34543240	34543324	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	intron	34543325	34543456	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34543457	34543519	1	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34543457	34543519	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	intron	34543520	34543643	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34543644	34543715	1	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34543644	34543715	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	intron	34543716	34543929	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	CDS	34543930	34543950	1	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	exon	34543930	34543950	.	+	.	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
Phchi.S1	AUGUSTUS	stop_codon	34543951	34543953	.	+	0	transcript_id "Phchi.S1G538400.t1"; gene_id "Phchi.S1G538400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5959.t1 is derived from g3130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20086243	20087466	.	+	.	Phchi.S1G311800
Phchi.S1	AUGUSTUS	transcript	20086243	20087466	.	+	.	transcript_id "Phchi.S1G311800.t1"; gene_id "Phchi.S1G311800"
Phchi.S1	AUGUSTUS	start_codon	20086243	20086245	.	+	0	transcript_id "Phchi.S1G311800.t1"; gene_id "Phchi.S1G311800"
Phchi.S1	AUGUSTUS	CDS	20086243	20087466	1	+	0	transcript_id "Phchi.S1G311800.t1"; gene_id "Phchi.S1G311800"
Phchi.S1	AUGUSTUS	exon	20086243	20087466	.	+	.	transcript_id "Phchi.S1G311800.t1"; gene_id "Phchi.S1G311800"
Phchi.S1	AUGUSTUS	stop_codon	20087467	20087469	.	+	0	transcript_id "Phchi.S1G311800.t1"; gene_id "Phchi.S1G311800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13544.t1 is derived from g12011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7435738	7437288	.	-	.	Phchi.S3G086300
Phchi.S3	AUGUSTUS	transcript	7435738	7437288	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	stop_codon	7435735	7435737	.	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7435738	7435857	1	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7435738	7435857	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7435858	7435964	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7435965	7436055	0.99	-	1	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7435965	7436055	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7436056	7436176	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7436177	7436252	1	-	2	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7436177	7436252	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7436253	7436349	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7436350	7436422	0.96	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7436350	7436422	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7436423	7436544	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7436545	7436637	0.7	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7436545	7436637	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7436638	7436722	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7436723	7436779	1	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7436723	7436779	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7436780	7436872	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7436873	7436959	1	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7436873	7436959	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7436960	7437038	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7437039	7437110	1	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7437039	7437110	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	intron	7437111	7437210	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	CDS	7437211	7437288	1	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	exon	7437211	7437288	.	-	.	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
Phchi.S3	AUGUSTUS	start_codon	7437286	7437288	.	-	0	transcript_id "Phchi.S3G086300.t1"; gene_id "Phchi.S3G086300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8886.t1 is derived from g6061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38485120	38487210	.	-	.	Phchi.S1G604500
Phchi.S1	AUGUSTUS	transcript	38485120	38487210	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	stop_codon	38485117	38485119	.	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38485120	38485147	0.87	-	1	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38485120	38485147	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38485148	38485408	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38485409	38485465	0.44	-	1	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38485409	38485465	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38485466	38485567	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38485568	38485620	0.83	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38485568	38485620	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38485621	38485709	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38485710	38485823	1	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38485710	38485823	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38485824	38485919	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38485920	38486084	1	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38485920	38486084	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38486085	38486173	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38486174	38486229	1	-	2	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38486174	38486229	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38486230	38486379	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38486380	38486467	1	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38486380	38486467	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	intron	38486468	38486670	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	CDS	38486671	38487210	0.44	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	exon	38486671	38487210	.	-	.	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
Phchi.S1	AUGUSTUS	start_codon	38487208	38487210	.	-	0	transcript_id "Phchi.S1G604500.t1"; gene_id "Phchi.S1G604500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7265.t1 is derived from g4437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27920006	27922681	.	-	.	Phchi.S1G442400
Phchi.S1	AUGUSTUS	transcript	27920006	27922681	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	stop_codon	27920003	27920005	.	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27920006	27920011	0.99	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27920006	27920011	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27920012	27920101	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27920102	27920152	0.99	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27920102	27920152	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27920153	27920379	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27920380	27920408	0.43	-	2	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27920380	27920408	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27920409	27920598	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27920599	27920692	1	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27920599	27920692	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27920693	27920836	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27920837	27921040	1	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27920837	27921040	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27921041	27921225	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27921226	27921396	1	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27921226	27921396	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27921397	27921653	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27921654	27922163	0.72	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27921654	27922163	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	intron	27922164	27922357	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	CDS	27922358	27922681	0.66	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	exon	27922358	27922681	.	-	.	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
Phchi.S1	AUGUSTUS	start_codon	27922679	27922681	.	-	0	transcript_id "Phchi.S1G442400.t1"; gene_id "Phchi.S1G442400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12076.t1 is derived from g7751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2138671	2140098	.	-	.	Phchi.S2G015600
Phchi.S2	AUGUSTUS	transcript	2138671	2140098	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	stop_codon	2138668	2138670	.	-	0	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	CDS	2138671	2139049	1	-	1	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	exon	2138671	2139049	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	intron	2139050	2139176	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	CDS	2139177	2139359	1	-	1	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	exon	2139177	2139359	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	intron	2139360	2139456	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	CDS	2139457	2139666	0.94	-	1	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	exon	2139457	2139666	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	intron	2139667	2139739	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	CDS	2139740	2139919	1	-	1	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	exon	2139740	2139919	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	intron	2139920	2139994	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	CDS	2139995	2140098	0.97	-	0	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	exon	2139995	2140098	.	-	.	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
Phchi.S2	AUGUSTUS	start_codon	2140096	2140098	.	-	0	transcript_id "Phchi.S2G015600.t1"; gene_id "Phchi.S2G015600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5360.t1 is derived from g2530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16469434	16469793	.	+	.	Phchi.S1G251900
Phchi.S1	AUGUSTUS	transcript	16469434	16469793	.	+	.	transcript_id "Phchi.S1G251900.t1"; gene_id "Phchi.S1G251900"
Phchi.S1	AUGUSTUS	start_codon	16469434	16469436	.	+	0	transcript_id "Phchi.S1G251900.t1"; gene_id "Phchi.S1G251900"
Phchi.S1	AUGUSTUS	CDS	16469434	16469793	1	+	0	transcript_id "Phchi.S1G251900.t1"; gene_id "Phchi.S1G251900"
Phchi.S1	AUGUSTUS	exon	16469434	16469793	.	+	.	transcript_id "Phchi.S1G251900.t1"; gene_id "Phchi.S1G251900"
Phchi.S1	AUGUSTUS	stop_codon	16469794	16469796	.	+	0	transcript_id "Phchi.S1G251900.t1"; gene_id "Phchi.S1G251900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8063.t1 is derived from g5238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32755911	32758672	.	-	.	Phchi.S1G522200
Phchi.S1	AUGUSTUS	transcript	32755911	32758672	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	stop_codon	32755908	32755910	.	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32755911	32756105	0.97	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32755911	32756105	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32756106	32756244	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32756245	32756367	1	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32756245	32756367	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32756368	32756472	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32756473	32756646	1	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32756473	32756646	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32756647	32756793	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32756794	32756925	1	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32756794	32756925	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32756926	32757024	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32757025	32757147	1	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32757025	32757147	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32757148	32757263	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32757264	32757932	1	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32757264	32757932	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32757933	32758015	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32758016	32758080	1	-	2	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32758016	32758080	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32758081	32758174	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32758175	32758286	1	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32758175	32758286	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32758287	32758377	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32758378	32758464	0.91	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32758378	32758464	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	intron	32758465	32758573	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	CDS	32758574	32758672	0.91	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	exon	32758574	32758672	.	-	.	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
Phchi.S1	AUGUSTUS	start_codon	32758670	32758672	.	-	0	transcript_id "Phchi.S1G522200.t1"; gene_id "Phchi.S1G522200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1255.t1 is derived from g11038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8657958	8658751	.	+	.	Phchi.S6G121400
Phchi.S6	AUGUSTUS	transcript	8657958	8658751	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	start_codon	8657958	8657960	.	+	0	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	CDS	8657958	8657960	1	+	0	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	exon	8657958	8657960	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	intron	8657961	8658050	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	CDS	8658051	8658158	1	+	0	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	exon	8658051	8658158	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	intron	8658159	8658239	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	CDS	8658240	8658308	1	+	0	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	exon	8658240	8658308	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	intron	8658309	8658396	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	CDS	8658397	8658451	0.95	+	0	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	exon	8658397	8658451	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	intron	8658452	8658560	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	CDS	8658561	8658751	0.99	+	2	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	exon	8658561	8658751	.	+	.	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
Phchi.S6	AUGUSTUS	stop_codon	8658752	8658754	.	+	0	transcript_id "Phchi.S6G121400.t1"; gene_id "Phchi.S6G121400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg133.t1 is derived from g9915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	721046	724657	.	+	.	Phchi.S6G009200
Phchi.S6	AUGUSTUS	transcript	721046	724657	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	start_codon	721046	721048	.	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	721046	721169	0.95	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	721046	721169	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	721170	721259	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	721260	721358	1	+	2	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	721260	721358	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	721359	721445	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	721446	721537	1	+	2	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	721446	721537	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	721538	721627	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	721628	721728	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	721628	721728	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	721729	721825	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	721826	721916	1	+	1	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	721826	721916	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	721917	722001	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	722002	722060	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	722002	722060	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	722061	722148	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	722149	722269	1	+	1	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	722149	722269	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	722270	722405	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	722406	722474	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	722406	722474	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	722475	722566	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	722567	722619	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	722567	722619	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	722620	722777	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	722778	722886	1	+	1	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	722778	722886	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	722887	722984	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	722985	723155	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	722985	723155	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	723156	723244	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	723245	723403	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	723245	723403	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	723404	723511	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	723512	723604	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	723512	723604	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	723605	723742	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	723743	723821	0.8	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	723743	723821	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	723822	723895	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	723896	723900	1	+	2	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	723896	723900	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	723901	724023	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	724024	724232	1	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	724024	724232	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	intron	724233	724323	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	CDS	724324	724657	0.94	+	1	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	exon	724324	724657	.	+	.	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
Phchi.S6	AUGUSTUS	stop_codon	724658	724660	.	+	0	transcript_id "Phchi.S6G009200.t1"; gene_id "Phchi.S6G009200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14378.t1 is derived from g12845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12458752	12459690	.	+	.	Phchi.S3G169700
Phchi.S3	AUGUSTUS	transcript	12458752	12459690	.	+	.	transcript_id "Phchi.S3G169700.t1"; gene_id "Phchi.S3G169700"
Phchi.S3	AUGUSTUS	start_codon	12458752	12458754	.	+	0	transcript_id "Phchi.S3G169700.t1"; gene_id "Phchi.S3G169700"
Phchi.S3	AUGUSTUS	CDS	12458752	12459690	0.79	+	0	transcript_id "Phchi.S3G169700.t1"; gene_id "Phchi.S3G169700"
Phchi.S3	AUGUSTUS	exon	12458752	12459690	.	+	.	transcript_id "Phchi.S3G169700.t1"; gene_id "Phchi.S3G169700"
Phchi.S3	AUGUSTUS	stop_codon	12459691	12459693	.	+	0	transcript_id "Phchi.S3G169700.t1"; gene_id "Phchi.S3G169700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9454.t1 is derived from g6630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41541462	41545765	.	-	.	Phchi.S1G661300
Phchi.S1	AUGUSTUS	transcript	41541462	41545765	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	stop_codon	41541459	41541461	.	-	0	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41541462	41541589	0.94	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41541462	41541589	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41541590	41541742	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41541743	41541870	0.9	-	1	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41541743	41541870	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41541871	41542044	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542045	41542063	0.64	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542045	41542063	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41542064	41542188	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542189	41542289	0.76	-	1	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542189	41542289	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41542290	41542422	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542423	41542458	0.75	-	1	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542423	41542458	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41542459	41542538	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542539	41542596	0.84	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542539	41542596	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41542597	41542693	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542694	41542699	0.84	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542694	41542699	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41542700	41542797	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542798	41542813	0.84	-	0	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542798	41542813	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41542814	41542898	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41542899	41543045	1	-	0	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41542899	41543045	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41543046	41543139	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41543140	41543594	0.7	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41543140	41543594	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41543595	41543678	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41543679	41543990	1	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41543679	41543990	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41543991	41544144	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41544145	41544345	1	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41544145	41544345	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41544346	41544448	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41544449	41544607	1	-	2	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41544449	41544607	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41544608	41544805	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41544806	41545049	0.86	-	0	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41544806	41545049	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	intron	41545050	41545252	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	CDS	41545253	41545765	0.71	-	0	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	exon	41545253	41545765	.	-	.	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
Phchi.S1	AUGUSTUS	start_codon	41545763	41545765	.	-	0	transcript_id "Phchi.S1G661300.t1"; gene_id "Phchi.S1G661300"
# This transcript jg11131.t2 is derived from g15181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11132.t1 is derived from g15182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4318130	4321289	.	+	.	Phchi.S4G071400
Phchi.S4	AUGUSTUS	transcript	4318130	4321289	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	start_codon	4318130	4318132	.	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318130	4318224	0.72	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318130	4318224	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318225	4318330	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318331	4318387	0.71	+	1	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318331	4318387	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318388	4318481	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318482	4318663	0.97	+	1	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318482	4318663	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318664	4318760	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318761	4318807	1	+	2	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318761	4318807	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318808	4318950	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318951	4319091	1	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318951	4319091	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319092	4319218	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319219	4319302	1	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319219	4319302	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319303	4319409	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319410	4319525	0.99	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319410	4319525	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319526	4319629	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319630	4319731	1	+	1	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319630	4319731	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319732	4319855	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319856	4319969	1	+	1	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319856	4319969	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319970	4320115	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320116	4320172	1	+	1	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320116	4320172	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320173	4320404	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320405	4320471	1	+	1	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320405	4320471	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320472	4320592	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320593	4320646	1	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320593	4320646	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320647	4320895	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320896	4320970	0.91	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320896	4320970	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320971	4321080	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4321081	4321116	1	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4321081	4321116	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4321117	4321202	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4321203	4321289	0.97	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4321203	4321289	.	+	.	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	stop_codon	4321290	4321292	.	+	0	transcript_id "Phchi.S4G071400.t1"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	transcript	4318130	4321289	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	start_codon	4318130	4318132	.	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318130	4318387	0.93	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318130	4318387	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318388	4318481	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318482	4318558	0.74	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318482	4318558	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318559	4318653	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318654	4318663	0.58	+	1	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318654	4318663	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318664	4318774	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318775	4318807	0.83	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318775	4318807	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4318808	4318950	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4318951	4319091	1	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4318951	4319091	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319092	4319218	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319219	4319302	0.99	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319219	4319302	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319303	4319409	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319410	4319525	1	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319410	4319525	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319526	4319629	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319630	4319731	1	+	1	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319630	4319731	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319732	4319855	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4319856	4319969	1	+	1	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4319856	4319969	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4319970	4320115	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320116	4320172	1	+	1	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320116	4320172	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320173	4320404	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320405	4320471	1	+	1	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320405	4320471	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320472	4320592	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320593	4320646	1	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320593	4320646	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320647	4320895	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4320896	4320970	0.94	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4320896	4320970	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4320971	4321080	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4321081	4321116	0.99	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4321081	4321116	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	intron	4321117	4321202	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	CDS	4321203	4321289	0.97	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	exon	4321203	4321289	.	+	.	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
Phchi.S4	AUGUSTUS	stop_codon	4321290	4321292	.	+	0	transcript_id "Phchi.S4G071400.t2"; gene_id "Phchi.S4G071400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4474.t1 is derived from g1644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10685552	10686735	.	-	.	Phchi.S1G163300
Phchi.S1	AUGUSTUS	transcript	10685552	10686735	.	-	.	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	stop_codon	10685549	10685551	.	-	0	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	CDS	10685552	10685586	0.91	-	2	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	exon	10685552	10685586	.	-	.	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	intron	10685587	10685794	.	-	.	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	CDS	10685795	10685894	0.91	-	0	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	exon	10685795	10685894	.	-	.	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	intron	10685895	10685979	.	-	.	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	CDS	10685980	10686735	0.9	-	0	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	exon	10685980	10686735	.	-	.	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
Phchi.S1	AUGUSTUS	start_codon	10686733	10686735	.	-	0	transcript_id "Phchi.S1G163300.t1"; gene_id "Phchi.S1G163300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6999.t1 is derived from g4171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26324895	26331200	.	+	.	Phchi.S1G415800
Phchi.S1	AUGUSTUS	transcript	26324895	26331200	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	start_codon	26324895	26324897	.	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26324895	26324988	1	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26324895	26324988	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26324989	26325957	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26325958	26326248	1	+	2	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26325958	26326248	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26326249	26326323	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26326324	26326407	0.64	+	2	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26326324	26326407	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26326408	26326526	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26326527	26326654	1	+	2	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26326527	26326654	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26326655	26326747	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26326748	26326789	1	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26326748	26326789	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26326790	26326923	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26326924	26327266	0.95	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26326924	26327266	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26327267	26327356	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26327357	26327888	1	+	2	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26327357	26327888	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26327889	26327975	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26327976	26328036	1	+	1	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26327976	26328036	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26328037	26328140	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26328141	26328185	1	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26328141	26328185	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26328186	26328274	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26328275	26328319	0.94	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26328275	26328319	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26328320	26328508	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26328509	26328566	0.45	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26328509	26328566	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26328567	26328662	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26328663	26328801	1	+	2	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26328663	26328801	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26328802	26328900	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26328901	26329003	1	+	1	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26328901	26329003	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26329004	26329098	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26329099	26329545	0.95	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26329099	26329545	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26329546	26329634	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26329635	26330614	0.68	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26329635	26330614	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	intron	26330615	26331172	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	CDS	26331173	26331200	0.53	+	1	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	exon	26331173	26331200	.	+	.	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
Phchi.S1	AUGUSTUS	stop_codon	26331201	26331203	.	+	0	transcript_id "Phchi.S1G415800.t1"; gene_id "Phchi.S1G415800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1569.t1 is derived from g8488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1798226	1800710	.	+	.	Phchi.S5G017800
Phchi.S5	AUGUSTUS	transcript	1798226	1800710	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	start_codon	1798226	1798228	.	+	0	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	CDS	1798226	1798661	0.71	+	0	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	exon	1798226	1798661	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	intron	1798662	1798799	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	CDS	1798800	1800344	0.77	+	2	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	exon	1798800	1800344	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	intron	1800345	1800480	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	CDS	1800481	1800563	1	+	2	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	exon	1800481	1800563	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	intron	1800564	1800644	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	CDS	1800645	1800710	0.98	+	0	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	exon	1800645	1800710	.	+	.	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
Phchi.S5	AUGUSTUS	stop_codon	1800711	1800713	.	+	0	transcript_id "Phchi.S5G017800.t1"; gene_id "Phchi.S5G017800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5021.t1 is derived from g2191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14090647	14091889	.	+	.	Phchi.S1G218000
Phchi.S1	AUGUSTUS	transcript	14090647	14091889	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	start_codon	14090647	14090649	.	+	0	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	CDS	14090647	14090779	0.99	+	0	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	exon	14090647	14090779	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	intron	14090780	14090885	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	CDS	14090886	14091124	1	+	2	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	exon	14090886	14091124	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	intron	14091125	14091205	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	CDS	14091206	14091372	1	+	0	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	exon	14091206	14091372	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	intron	14091373	14091459	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	CDS	14091460	14091889	0.98	+	1	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	exon	14091460	14091889	.	+	.	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
Phchi.S1	AUGUSTUS	stop_codon	14091890	14091892	.	+	0	transcript_id "Phchi.S1G218000.t1"; gene_id "Phchi.S1G218000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9976.t1 is derived from g7152.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44729057	44734177	.	-	.	Phchi.S1G713500
Phchi.S1	AUGUSTUS	transcript	44729057	44734177	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	stop_codon	44729054	44729056	.	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729057	44729398	0.8	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729057	44729398	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44729399	44729478	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729479	44729597	1	-	2	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729479	44729597	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44729598	44729678	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729679	44729844	1	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729679	44729844	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44729845	44729925	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729926	44730043	1	-	1	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729926	44730043	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730044	44730126	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730127	44730296	1	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730127	44730296	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730297	44730370	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730371	44730557	1	-	1	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730371	44730557	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730558	44730638	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730639	44730739	1	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730639	44730739	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730740	44730815	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730816	44731510	0.94	-	2	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730816	44731510	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44731511	44731765	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44731766	44731874	0.99	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44731766	44731874	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44731875	44731970	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44731971	44732081	0.98	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44731971	44732081	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44732082	44732205	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44732206	44733491	0.94	-	2	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44732206	44733491	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44733492	44733607	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44733608	44733822	0.41	-	1	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44733608	44733822	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44733823	44733970	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44733971	44734027	0.39	-	1	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44733971	44734027	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44734028	44734130	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44734131	44734177	0.35	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44734131	44734177	.	-	.	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	start_codon	44734175	44734177	.	-	0	transcript_id "Phchi.S1G713500.t1"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	transcript	44729057	44734177	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	stop_codon	44729054	44729056	.	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729057	44729398	0.81	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729057	44729398	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44729399	44729478	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729479	44729597	1	-	2	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729479	44729597	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44729598	44729678	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729679	44729844	1	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729679	44729844	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44729845	44729925	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44729926	44730043	1	-	1	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44729926	44730043	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730044	44730126	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730127	44730296	1	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730127	44730296	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730297	44730370	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730371	44730557	1	-	1	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730371	44730557	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730558	44730638	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730639	44730739	1	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730639	44730739	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44730740	44730815	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44730816	44731510	0.95	-	2	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44730816	44731510	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44731511	44731765	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44731766	44731874	0.99	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44731766	44731874	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44731875	44731964	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44731965	44732081	0.99	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44731965	44732081	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44732082	44732205	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44732206	44733491	0.94	-	2	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44732206	44733491	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44733492	44733607	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44733608	44733822	0.34	-	1	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44733608	44733822	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44733823	44733970	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44733971	44734027	0.35	-	1	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44733971	44734027	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	intron	44734028	44734130	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	CDS	44734131	44734177	0.31	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	exon	44734131	44734177	.	-	.	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
Phchi.S1	AUGUSTUS	start_codon	44734175	44734177	.	-	0	transcript_id "Phchi.S1G713500.t2"; gene_id "Phchi.S1G713500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1826.t1 is derived from g8746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3366280	3366953	.	+	.	Phchi.S5G043500
Phchi.S5	AUGUSTUS	transcript	3366280	3366953	.	+	.	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	start_codon	3366280	3366282	.	+	0	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	CDS	3366280	3366742	0.43	+	0	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	exon	3366280	3366742	.	+	.	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	intron	3366743	3366855	.	+	.	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	CDS	3366856	3366953	0.48	+	2	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	exon	3366856	3366953	.	+	.	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
Phchi.S5	AUGUSTUS	stop_codon	3366954	3366956	.	+	0	transcript_id "Phchi.S5G043500.t1"; gene_id "Phchi.S5G043500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4975.t1 is derived from g2145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13834908	13835318	.	-	.	Phchi.S1G213400
Phchi.S1	AUGUSTUS	transcript	13834908	13835318	.	-	.	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	stop_codon	13834905	13834907	.	-	0	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	CDS	13834908	13835053	0.48	-	2	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	exon	13834908	13835053	.	-	.	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	intron	13835054	13835200	.	-	.	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	CDS	13835201	13835318	1	-	0	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	exon	13835201	13835318	.	-	.	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
Phchi.S1	AUGUSTUS	start_codon	13835316	13835318	.	-	0	transcript_id "Phchi.S1G213400.t1"; gene_id "Phchi.S1G213400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6663.t1 is derived from g3835.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24366304	24369239	.	+	.	Phchi.S1G382200
Phchi.S1	AUGUSTUS	transcript	24366304	24369239	.	+	.	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	start_codon	24366304	24366306	.	+	0	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	CDS	24366304	24368115	0.34	+	0	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	exon	24366304	24368115	.	+	.	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	intron	24368116	24368219	.	+	.	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	CDS	24368220	24369239	0.61	+	0	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	exon	24368220	24369239	.	+	.	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	stop_codon	24369240	24369242	.	+	0	transcript_id "Phchi.S1G382200.t1"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	transcript	24368850	24369239	.	+	.	transcript_id "Phchi.S1G382200.t2"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	start_codon	24368850	24368852	.	+	0	transcript_id "Phchi.S1G382200.t2"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	CDS	24368850	24369239	0.55	+	0	transcript_id "Phchi.S1G382200.t2"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	exon	24368850	24369239	.	+	.	transcript_id "Phchi.S1G382200.t2"; gene_id "Phchi.S1G382200"
Phchi.S1	AUGUSTUS	stop_codon	24369240	24369242	.	+	0	transcript_id "Phchi.S1G382200.t2"; gene_id "Phchi.S1G382200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6935.t1 is derived from g4107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26052251	26053036	.	-	.	Phchi.S1G409400
Phchi.S1	AUGUSTUS	transcript	26052251	26053036	.	-	.	transcript_id "Phchi.S1G409400.t1"; gene_id "Phchi.S1G409400"
Phchi.S1	AUGUSTUS	stop_codon	26052248	26052250	.	-	0	transcript_id "Phchi.S1G409400.t1"; gene_id "Phchi.S1G409400"
Phchi.S1	AUGUSTUS	CDS	26052251	26053036	0.66	-	0	transcript_id "Phchi.S1G409400.t1"; gene_id "Phchi.S1G409400"
Phchi.S1	AUGUSTUS	exon	26052251	26053036	.	-	.	transcript_id "Phchi.S1G409400.t1"; gene_id "Phchi.S1G409400"
Phchi.S1	AUGUSTUS	start_codon	26053034	26053036	.	-	0	transcript_id "Phchi.S1G409400.t1"; gene_id "Phchi.S1G409400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3999.t1 is derived from g1168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6913158	6915517	.	+	.	Phchi.S1G115800
Phchi.S1	AUGUSTUS	transcript	6913158	6915517	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	start_codon	6913158	6913160	.	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6913158	6913222	0.57	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6913158	6913222	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6913223	6913330	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6913331	6913504	0.56	+	1	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6913331	6913504	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6913505	6913631	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6913632	6913692	0.93	+	1	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6913632	6913692	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6913693	6913800	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6913801	6913854	0.84	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6913801	6913854	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6913855	6913963	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6913964	6914027	0.76	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6913964	6914027	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6914028	6914123	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6914124	6914180	1	+	2	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6914124	6914180	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6914181	6914279	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6914280	6914386	1	+	2	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6914280	6914386	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6914387	6914586	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6914587	6914631	0.78	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6914587	6914631	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6914632	6914760	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6914761	6914825	0.96	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6914761	6914825	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6914826	6914910	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6914911	6914989	1	+	1	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6914911	6914989	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6914990	6915238	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6915239	6915286	1	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6915239	6915286	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	intron	6915287	6915436	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	CDS	6915437	6915517	1	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	exon	6915437	6915517	.	+	.	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
Phchi.S1	AUGUSTUS	stop_codon	6915518	6915520	.	+	0	transcript_id "Phchi.S1G115800.t1"; gene_id "Phchi.S1G115800"
# This transcript jg7549.t2 is derived from g4723.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7550.t1 is derived from g4724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30002154	30002684	.	+	.	Phchi.S1G470900
Phchi.S1	AUGUSTUS	transcript	30002154	30002684	.	+	.	transcript_id "Phchi.S1G470900.t1"; gene_id "Phchi.S1G470900"
Phchi.S1	AUGUSTUS	start_codon	30002154	30002156	.	+	0	transcript_id "Phchi.S1G470900.t1"; gene_id "Phchi.S1G470900"
Phchi.S1	AUGUSTUS	CDS	30002154	30002684	0.97	+	0	transcript_id "Phchi.S1G470900.t1"; gene_id "Phchi.S1G470900"
Phchi.S1	AUGUSTUS	exon	30002154	30002684	.	+	.	transcript_id "Phchi.S1G470900.t1"; gene_id "Phchi.S1G470900"
Phchi.S1	AUGUSTUS	stop_codon	30002685	30002687	.	+	0	transcript_id "Phchi.S1G470900.t1"; gene_id "Phchi.S1G470900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3539.t1 is derived from g708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4357791	4359686	.	-	.	Phchi.S1G069800
Phchi.S1	AUGUSTUS	transcript	4357791	4359686	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	stop_codon	4357788	4357790	.	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4357791	4357965	1	-	1	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4357791	4357965	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	intron	4357966	4358047	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4358048	4358133	1	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4358048	4358133	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	intron	4358134	4358335	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4358336	4358536	1	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4358336	4358536	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	intron	4358537	4358730	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4358731	4358844	1	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4358731	4358844	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	intron	4358845	4358957	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4358958	4359005	1	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4358958	4359005	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	intron	4359006	4359115	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4359116	4359163	1	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4359116	4359163	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	intron	4359164	4359299	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	CDS	4359300	4359686	0.98	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	exon	4359300	4359686	.	-	.	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
Phchi.S1	AUGUSTUS	start_codon	4359684	4359686	.	-	0	transcript_id "Phchi.S1G069800.t1"; gene_id "Phchi.S1G069800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8042.t1 is derived from g5217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32641823	32648873	.	+	.	Phchi.S1G520100
Phchi.S1	AUGUSTUS	transcript	32641823	32648873	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	start_codon	32641823	32641825	.	+	0	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	CDS	32641823	32641856	0.66	+	0	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	exon	32641823	32641856	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	intron	32641857	32642046	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	CDS	32642047	32642138	0.87	+	2	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	exon	32642047	32642138	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	intron	32642139	32642234	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	CDS	32642235	32642410	0.63	+	0	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	exon	32642235	32642410	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	intron	32642411	32642490	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	CDS	32642491	32642593	0.26	+	1	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	exon	32642491	32642593	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	intron	32642594	32642679	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	CDS	32642680	32643823	0.47	+	0	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	exon	32642680	32643823	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	intron	32643824	32643906	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	CDS	32643907	32648873	1	+	2	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	exon	32643907	32648873	.	+	.	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
Phchi.S1	AUGUSTUS	stop_codon	32648874	32648876	.	+	0	transcript_id "Phchi.S1G520100.t1"; gene_id "Phchi.S1G520100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10190.t1 is derived from g7366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46233777	46246105	.	+	.	Phchi.S1G734900
Phchi.S1	AUGUSTUS	transcript	46233777	46246105	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	start_codon	46233777	46233779	.	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46233777	46234375	0.16	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46233777	46234375	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46234376	46234561	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46234562	46235804	0.32	+	1	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46234562	46235804	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46235805	46235942	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46235943	46236100	1	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46235943	46236100	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46236101	46236232	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46236233	46236940	0.94	+	1	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46236233	46236940	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46236941	46237062	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46237063	46237283	0.97	+	1	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46237063	46237283	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46237284	46237488	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46237489	46237715	1	+	2	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46237489	46237715	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46237716	46237865	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46237866	46238153	0.99	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46237866	46238153	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46238154	46238236	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46238237	46238392	1	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46238237	46238392	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46238393	46238598	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46238599	46238853	1	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46238599	46238853	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46238854	46239021	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46239022	46239162	1	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46239022	46239162	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46239163	46239296	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46239297	46239593	1	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46239297	46239593	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46239594	46239714	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46239715	46239885	0.79	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46239715	46239885	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46239886	46239993	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46239994	46240852	0.86	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46239994	46240852	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46240853	46240974	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46240975	46240988	0.91	+	2	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46240975	46240988	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46240989	46241818	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46241819	46243229	0.84	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46241819	46243229	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46243230	46243469	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46243470	46244368	0.75	+	2	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46243470	46244368	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46244369	46244455	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46244456	46244684	0.99	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46244456	46244684	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46244685	46244795	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46244796	46244930	1	+	2	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46244796	46244930	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46244931	46245144	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46245145	46245245	1	+	2	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46245145	46245245	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	intron	46245246	46245328	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	CDS	46245329	46246105	1	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	exon	46245329	46246105	.	+	.	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
Phchi.S1	AUGUSTUS	stop_codon	46246106	46246108	.	+	0	transcript_id "Phchi.S1G734900.t1"; gene_id "Phchi.S1G734900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9212.t1 is derived from g6387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40439489	40439758	.	+	.	Phchi.S1G637100
Phchi.S1	AUGUSTUS	transcript	40439489	40439758	.	+	.	transcript_id "Phchi.S1G637100.t1"; gene_id "Phchi.S1G637100"
Phchi.S1	AUGUSTUS	start_codon	40439489	40439491	.	+	0	transcript_id "Phchi.S1G637100.t1"; gene_id "Phchi.S1G637100"
Phchi.S1	AUGUSTUS	CDS	40439489	40439758	0.62	+	0	transcript_id "Phchi.S1G637100.t1"; gene_id "Phchi.S1G637100"
Phchi.S1	AUGUSTUS	exon	40439489	40439758	.	+	.	transcript_id "Phchi.S1G637100.t1"; gene_id "Phchi.S1G637100"
Phchi.S1	AUGUSTUS	stop_codon	40439759	40439761	.	+	0	transcript_id "Phchi.S1G637100.t1"; gene_id "Phchi.S1G637100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5859.t1 is derived from g3029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19399446	19402132	.	+	.	Phchi.S1G301800
Phchi.S1	AUGUSTUS	transcript	19399446	19402132	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	start_codon	19399446	19399448	.	+	0	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19399446	19399539	0.9	+	0	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19399446	19399539	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19399540	19399692	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19399693	19400266	0.99	+	2	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19399693	19400266	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19400267	19400407	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19400408	19400494	0.53	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19400408	19400494	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19400495	19400584	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19400585	19400827	0.54	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19400585	19400827	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19400828	19400919	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19400920	19401158	0.96	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19400920	19401158	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19401159	19401284	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19401285	19401399	0.96	+	2	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19401285	19401399	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19401400	19401478	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19401479	19401550	1	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19401479	19401550	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19401551	19401648	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19401649	19401720	1	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19401649	19401720	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19401721	19401955	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19401956	19402024	1	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19401956	19402024	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	intron	19402025	19402122	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	CDS	19402123	19402132	0.97	+	1	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	exon	19402123	19402132	.	+	.	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
Phchi.S1	AUGUSTUS	stop_codon	19402133	19402135	.	+	0	transcript_id "Phchi.S1G301800.t1"; gene_id "Phchi.S1G301800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3454.t1 is derived from g623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3854754	3855431	.	+	.	Phchi.S1G061300
Phchi.S1	AUGUSTUS	transcript	3854754	3855431	.	+	.	transcript_id "Phchi.S1G061300.t1"; gene_id "Phchi.S1G061300"
Phchi.S1	AUGUSTUS	start_codon	3854754	3854756	.	+	0	transcript_id "Phchi.S1G061300.t1"; gene_id "Phchi.S1G061300"
Phchi.S1	AUGUSTUS	CDS	3854754	3855431	0.99	+	0	transcript_id "Phchi.S1G061300.t1"; gene_id "Phchi.S1G061300"
Phchi.S1	AUGUSTUS	exon	3854754	3855431	.	+	.	transcript_id "Phchi.S1G061300.t1"; gene_id "Phchi.S1G061300"
Phchi.S1	AUGUSTUS	stop_codon	3855432	3855434	.	+	0	transcript_id "Phchi.S1G061300.t1"; gene_id "Phchi.S1G061300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14827.t1 is derived from g13295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14908538	14908780	.	+	.	Phchi.S3G214600
Phchi.S3	AUGUSTUS	transcript	14908538	14908780	.	+	.	transcript_id "Phchi.S3G214600.t1"; gene_id "Phchi.S3G214600"
Phchi.S3	AUGUSTUS	start_codon	14908538	14908540	.	+	0	transcript_id "Phchi.S3G214600.t1"; gene_id "Phchi.S3G214600"
Phchi.S3	AUGUSTUS	CDS	14908538	14908780	0.74	+	0	transcript_id "Phchi.S3G214600.t1"; gene_id "Phchi.S3G214600"
Phchi.S3	AUGUSTUS	exon	14908538	14908780	.	+	.	transcript_id "Phchi.S3G214600.t1"; gene_id "Phchi.S3G214600"
Phchi.S3	AUGUSTUS	stop_codon	14908781	14908783	.	+	0	transcript_id "Phchi.S3G214600.t1"; gene_id "Phchi.S3G214600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6630.t1 is derived from g3802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24170661	24172013	.	+	.	Phchi.S1G378900
Phchi.S1	AUGUSTUS	transcript	24170661	24172013	.	+	.	transcript_id "Phchi.S1G378900.t1"; gene_id "Phchi.S1G378900"
Phchi.S1	AUGUSTUS	start_codon	24170661	24170663	.	+	0	transcript_id "Phchi.S1G378900.t1"; gene_id "Phchi.S1G378900"
Phchi.S1	AUGUSTUS	CDS	24170661	24172013	0.51	+	0	transcript_id "Phchi.S1G378900.t1"; gene_id "Phchi.S1G378900"
Phchi.S1	AUGUSTUS	exon	24170661	24172013	.	+	.	transcript_id "Phchi.S1G378900.t1"; gene_id "Phchi.S1G378900"
Phchi.S1	AUGUSTUS	stop_codon	24172014	24172016	.	+	0	transcript_id "Phchi.S1G378900.t1"; gene_id "Phchi.S1G378900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2667.t1 is derived from g9587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8115509	8118899	.	-	.	Phchi.S5G127600
Phchi.S5	AUGUSTUS	transcript	8115509	8118899	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	stop_codon	8115506	8115508	.	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8115509	8115760	1	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8115509	8115760	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8115761	8115836	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8115837	8116178	1	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8115837	8116178	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8116179	8116253	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8116254	8116364	1	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8116254	8116364	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8116365	8116511	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8116512	8116601	1	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8116512	8116601	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8116602	8116750	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8116751	8116807	1	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8116751	8116807	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8116808	8116881	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8116882	8116955	1	-	2	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8116882	8116955	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8116956	8117093	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8117094	8117252	0.54	-	2	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8117094	8117252	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8117253	8117360	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8117361	8117935	0.33	-	1	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8117361	8117935	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8117936	8118132	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8118133	8118270	0.99	-	1	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8118133	8118270	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8118271	8118385	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8118386	8118507	0.99	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8118386	8118507	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8118508	8118610	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8118611	8118697	0.99	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8118611	8118697	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	intron	8118698	8118809	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	CDS	8118810	8118899	0.37	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	exon	8118810	8118899	.	-	.	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
Phchi.S5	AUGUSTUS	start_codon	8118897	8118899	.	-	0	transcript_id "Phchi.S5G127600.t1"; gene_id "Phchi.S5G127600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12847.t1 is derived from g11312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2682160	2683532	.	-	.	Phchi.S3G016600
Phchi.S3	AUGUSTUS	transcript	2682160	2683532	.	-	.	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	stop_codon	2682157	2682159	.	-	0	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	CDS	2682160	2682456	0.83	-	0	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	exon	2682160	2682456	.	-	.	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	intron	2682457	2682524	.	-	.	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	CDS	2682525	2682887	0.95	-	0	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	exon	2682525	2682887	.	-	.	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	intron	2682888	2682980	.	-	.	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	CDS	2682981	2683532	0.93	-	0	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	exon	2682981	2683532	.	-	.	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
Phchi.S3	AUGUSTUS	start_codon	2683530	2683532	.	-	0	transcript_id "Phchi.S3G016600.t1"; gene_id "Phchi.S3G016600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7248.t1 is derived from g4420.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27833716	27836797	.	-	.	Phchi.S1G440700
Phchi.S1	AUGUSTUS	transcript	27833716	27836797	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	stop_codon	27833713	27833715	.	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27833716	27833803	0.77	-	1	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27833716	27833803	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27833804	27833890	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27833891	27833997	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27833891	27833997	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27833998	27834071	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834072	27834132	1	-	1	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834072	27834132	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834133	27834227	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834228	27834379	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834228	27834379	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834380	27834467	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834468	27834545	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834468	27834545	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834546	27834645	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834646	27834759	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834646	27834759	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834760	27834846	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834847	27834923	1	-	2	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834847	27834923	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834924	27835065	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835066	27835132	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835066	27835132	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835133	27835266	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835267	27835332	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835267	27835332	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835333	27835438	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835439	27835562	1	-	1	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835439	27835562	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835563	27835649	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835650	27835742	1	-	1	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835650	27835742	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835743	27835867	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835868	27836016	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835868	27836016	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27836017	27836161	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27836162	27836242	1	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27836162	27836242	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27836243	27836358	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27836359	27836501	1	-	2	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27836359	27836501	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27836502	27836688	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27836689	27836797	0.75	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27836689	27836797	.	-	.	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	start_codon	27836795	27836797	.	-	0	transcript_id "Phchi.S1G440700.t1"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	transcript	27833716	27836753	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	stop_codon	27833713	27833715	.	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27833716	27833803	0.78	-	1	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27833716	27833803	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27833804	27833890	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27833891	27833997	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27833891	27833997	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27833998	27834071	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834072	27834132	1	-	1	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834072	27834132	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834133	27834227	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834228	27834379	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834228	27834379	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834380	27834467	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834468	27834545	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834468	27834545	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834546	27834645	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834646	27834759	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834646	27834759	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834760	27834846	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27834847	27834923	1	-	2	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27834847	27834923	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27834924	27835065	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835066	27835132	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835066	27835132	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835133	27835266	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835267	27835332	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835267	27835332	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835333	27835438	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835439	27835562	1	-	1	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835439	27835562	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835563	27835649	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835650	27835742	1	-	1	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835650	27835742	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27835743	27835867	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27835868	27836016	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27835868	27836016	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27836017	27836161	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27836162	27836242	1	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27836162	27836242	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27836243	27836358	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27836359	27836501	1	-	2	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27836359	27836501	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	intron	27836502	27836695	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	CDS	27836696	27836753	0.83	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	exon	27836696	27836753	.	-	.	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
Phchi.S1	AUGUSTUS	start_codon	27836751	27836753	.	-	0	transcript_id "Phchi.S1G440700.t2"; gene_id "Phchi.S1G440700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7611.t1 is derived from g4785.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30244787	30249536	.	-	.	Phchi.S1G477000
Phchi.S1	AUGUSTUS	transcript	30244787	30249536	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	stop_codon	30244784	30244786	.	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30244787	30245245	0.94	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30244787	30245245	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30245246	30245663	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30245664	30245765	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30245664	30245765	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30245766	30245947	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30245948	30245995	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30245948	30245995	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30245996	30246098	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246099	30246236	0.99	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246099	30246236	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246237	30246336	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246337	30246462	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246337	30246462	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246463	30246584	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246585	30246668	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246585	30246668	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246669	30246836	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246837	30246952	1	-	2	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246837	30246952	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246953	30247089	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30247090	30247171	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30247090	30247171	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30247172	30247566	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30247567	30247900	0.96	-	1	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30247567	30247900	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30247901	30248004	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248005	30248089	0.98	-	2	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248005	30248089	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248090	30248221	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248222	30248297	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248222	30248297	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248298	30248507	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248508	30248591	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248508	30248591	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248592	30248743	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248744	30248839	1	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248744	30248839	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248840	30249242	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30249243	30249536	0.96	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30249243	30249536	.	-	.	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	start_codon	30249534	30249536	.	-	0	transcript_id "Phchi.S1G477000.t1"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	transcript	30245476	30249536	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	stop_codon	30245473	30245475	.	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30245476	30245478	0.99	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30245476	30245478	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30245479	30245663	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30245664	30245765	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30245664	30245765	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30245766	30245947	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30245948	30245995	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30245948	30245995	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30245996	30246098	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246099	30246236	0.99	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246099	30246236	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246237	30246336	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246337	30246462	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246337	30246462	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246463	30246584	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246585	30246668	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246585	30246668	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246669	30246836	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30246837	30246952	1	-	2	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30246837	30246952	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30246953	30247089	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30247090	30247171	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30247090	30247171	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30247172	30247566	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30247567	30247900	0.96	-	1	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30247567	30247900	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30247901	30248004	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248005	30248089	0.96	-	2	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248005	30248089	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248090	30248221	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248222	30248297	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248222	30248297	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248298	30248507	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248508	30248591	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248508	30248591	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248592	30248743	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30248744	30248839	1	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30248744	30248839	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	intron	30248840	30249242	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	CDS	30249243	30249536	0.94	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	exon	30249243	30249536	.	-	.	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
Phchi.S1	AUGUSTUS	start_codon	30249534	30249536	.	-	0	transcript_id "Phchi.S1G477000.t2"; gene_id "Phchi.S1G477000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15719.t1 is derived from g14189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20878666	20881326	.	+	.	Phchi.S3G303800
Phchi.S3	AUGUSTUS	transcript	20878666	20881326	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	start_codon	20878666	20878668	.	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20878666	20879090	0.95	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20878666	20879090	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20879091	20879217	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20879218	20879359	1	+	1	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20879218	20879359	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20879360	20879483	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20879484	20879575	1	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20879484	20879575	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20879576	20879692	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20879693	20879765	0.91	+	1	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20879693	20879765	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20879766	20879868	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20879869	20879958	0.92	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20879869	20879958	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20879959	20880146	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20880147	20880214	1	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20880147	20880214	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20880215	20880341	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20880342	20880462	1	+	1	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20880342	20880462	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20880463	20880562	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20880563	20880727	1	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20880563	20880727	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20880728	20880980	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20880981	20881048	1	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20880981	20881048	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	intron	20881049	20881172	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	CDS	20881173	20881326	0.84	+	1	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	exon	20881173	20881326	.	+	.	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
Phchi.S3	AUGUSTUS	stop_codon	20881327	20881329	.	+	0	transcript_id "Phchi.S3G303800.t1"; gene_id "Phchi.S3G303800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6000.t1 is derived from g3171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20328530	20332043	.	+	.	Phchi.S1G315900
Phchi.S1	AUGUSTUS	transcript	20328530	20332043	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	start_codon	20328530	20328532	.	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20328530	20329399	0.76	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20328530	20329399	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20329400	20329501	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20329502	20329542	0.91	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20329502	20329542	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20329543	20329636	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20329637	20329745	0.8	+	1	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20329637	20329745	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20329746	20330112	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20330113	20330352	0.7	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20330113	20330352	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20330353	20330432	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20330433	20330546	0.61	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20330433	20330546	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20330547	20330638	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20330639	20330785	1	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20330639	20330785	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20330786	20330877	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20330878	20330915	1	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20330878	20330915	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20330916	20331015	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20331016	20331095	1	+	1	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20331016	20331095	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20331096	20331178	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20331179	20331277	1	+	2	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20331179	20331277	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20331278	20331390	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20331391	20331508	1	+	2	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20331391	20331508	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20331509	20331613	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20331614	20331801	1	+	1	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20331614	20331801	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	intron	20331802	20331900	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	CDS	20331901	20332043	0.99	+	2	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	exon	20331901	20332043	.	+	.	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
Phchi.S1	AUGUSTUS	stop_codon	20332044	20332046	.	+	0	transcript_id "Phchi.S1G315900.t1"; gene_id "Phchi.S1G315900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2726.t1 is derived from g9646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8455947	8456819	.	+	.	Phchi.S5G133500
Phchi.S5	AUGUSTUS	transcript	8455947	8456819	.	+	.	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	start_codon	8455947	8455949	.	+	0	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	CDS	8455947	8456197	1	+	0	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	exon	8455947	8456197	.	+	.	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	intron	8456198	8456476	.	+	.	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	CDS	8456477	8456819	1	+	1	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	exon	8456477	8456819	.	+	.	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
Phchi.S5	AUGUSTUS	stop_codon	8456820	8456822	.	+	0	transcript_id "Phchi.S5G133500.t1"; gene_id "Phchi.S5G133500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9378.t1 is derived from g6554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41229185	41232617	.	-	.	Phchi.S1G653700
Phchi.S1	AUGUSTUS	transcript	41229185	41232617	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	stop_codon	41229182	41229184	.	-	0	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	CDS	41229185	41230948	0.99	-	0	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	exon	41229185	41230948	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	intron	41230949	41231067	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	CDS	41231068	41231208	0.94	-	0	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	exon	41231068	41231208	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	intron	41231209	41231287	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	CDS	41231288	41232118	0.96	-	0	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	exon	41231288	41232118	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	intron	41232119	41232211	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	CDS	41232212	41232281	0.96	-	1	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	exon	41232212	41232281	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	intron	41232282	41232419	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	CDS	41232420	41232428	0.96	-	1	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	exon	41232420	41232428	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	intron	41232429	41232603	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	CDS	41232604	41232617	0.73	-	0	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	exon	41232604	41232617	.	-	.	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
Phchi.S1	AUGUSTUS	start_codon	41232615	41232617	.	-	0	transcript_id "Phchi.S1G653700.t1"; gene_id "Phchi.S1G653700"
# This transcript jg9976.t2 is derived from g7152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9977.t1 is derived from g7153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44745001	44746930	.	+	.	Phchi.S1G713600
Phchi.S1	AUGUSTUS	transcript	44745001	44746930	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	start_codon	44745001	44745003	.	+	0	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	CDS	44745001	44745419	0.71	+	0	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	exon	44745001	44745419	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	intron	44745420	44745516	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	CDS	44745517	44745769	1	+	1	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	exon	44745517	44745769	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	intron	44745770	44745886	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	CDS	44745887	44746201	1	+	0	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	exon	44745887	44746201	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	intron	44746202	44746300	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	CDS	44746301	44746930	1	+	0	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	exon	44746301	44746930	.	+	.	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
Phchi.S1	AUGUSTUS	stop_codon	44746931	44746933	.	+	0	transcript_id "Phchi.S1G713600.t1"; gene_id "Phchi.S1G713600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12568.t1 is derived from g8245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35539837	35542120	.	-	.	Phchi.S2G064800
Phchi.S2	AUGUSTUS	transcript	35539837	35542120	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	stop_codon	35539834	35539836	.	-	0	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35539837	35539915	0.95	-	1	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35539837	35539915	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35539916	35540053	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35540054	35540132	0.79	-	2	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35540054	35540132	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35540133	35540217	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35540218	35540257	0.92	-	0	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35540218	35540257	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35540258	35540401	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35540402	35540499	1	-	2	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35540402	35540499	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35540500	35540623	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35540624	35540715	1	-	1	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35540624	35540715	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35540716	35540938	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35540939	35541057	1	-	0	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35540939	35541057	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35541058	35541136	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35541137	35541242	1	-	1	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35541137	35541242	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	intron	35541243	35541470	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	CDS	35541471	35542120	0.93	-	0	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	exon	35541471	35542120	.	-	.	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
Phchi.S2	AUGUSTUS	start_codon	35542118	35542120	.	-	0	transcript_id "Phchi.S2G064800.t1"; gene_id "Phchi.S2G064800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7511.t1 is derived from g4685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29757575	29759777	.	-	.	Phchi.S1G467000
Phchi.S1	AUGUSTUS	transcript	29757575	29759777	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	stop_codon	29757572	29757574	.	-	0	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29757575	29757646	0.81	-	0	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29757575	29757646	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29757647	29757720	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29757721	29757731	0.85	-	2	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29757721	29757731	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29757732	29757777	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29757778	29757816	0.99	-	2	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29757778	29757816	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29757817	29757915	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29757916	29757987	1	-	2	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29757916	29757987	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29757988	29758076	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29758077	29758199	1	-	2	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29758077	29758199	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29758200	29758335	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29758336	29758394	1	-	1	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29758336	29758394	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29758395	29758546	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29758547	29758615	1	-	1	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29758547	29758615	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29758616	29758850	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29758851	29758946	1	-	1	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29758851	29758946	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29758947	29759031	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29759032	29759122	1	-	2	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29759032	29759122	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29759123	29759250	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29759251	29759276	1	-	1	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29759251	29759276	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29759277	29759400	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29759401	29759468	1	-	0	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29759401	29759468	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	intron	29759469	29759693	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	CDS	29759694	29759777	1	-	0	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	exon	29759694	29759777	.	-	.	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
Phchi.S1	AUGUSTUS	start_codon	29759775	29759777	.	-	0	transcript_id "Phchi.S1G467000.t1"; gene_id "Phchi.S1G467000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12172.t1 is derived from g7848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5851025	5852521	.	-	.	Phchi.S2G025200
Phchi.S2	AUGUSTUS	transcript	5851025	5852521	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	stop_codon	5851022	5851024	.	-	0	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5851025	5851088	1	-	1	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5851025	5851088	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	intron	5851089	5851177	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5851178	5851229	1	-	2	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5851178	5851229	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	intron	5851230	5851326	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5851327	5851367	1	-	1	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5851327	5851367	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	intron	5851368	5851469	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5851470	5851531	1	-	0	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5851470	5851531	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	intron	5851532	5851759	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5851760	5851999	0.73	-	0	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5851760	5851999	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	intron	5852000	5852177	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5852178	5852252	0.75	-	0	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5852178	5852252	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	intron	5852253	5852335	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	CDS	5852336	5852521	0.64	-	0	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	exon	5852336	5852521	.	-	.	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
Phchi.S2	AUGUSTUS	start_codon	5852519	5852521	.	-	0	transcript_id "Phchi.S2G025200.t1"; gene_id "Phchi.S2G025200"
# This transcript jg11945.t2 is derived from g7620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11946.t1 is derived from g7621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	153870	154758	.	+	.	Phchi.S2G002600
Phchi.S2	AUGUSTUS	transcript	153870	154758	.	+	.	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	start_codon	153870	153872	.	+	0	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	CDS	153870	153983	0.21	+	0	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	exon	153870	153983	.	+	.	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	intron	153984	154398	.	+	.	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	CDS	154399	154758	0.56	+	0	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	exon	154399	154758	.	+	.	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
Phchi.S2	AUGUSTUS	stop_codon	154759	154761	.	+	0	transcript_id "Phchi.S2G002600.t1"; gene_id "Phchi.S2G002600"
# This transcript jg9497.t2 is derived from g6673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9498.t1 is derived from g6674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42062212	42062919	.	-	.	Phchi.S1G665700
Phchi.S1	AUGUSTUS	transcript	42062212	42062919	.	-	.	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	stop_codon	42062209	42062211	.	-	0	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	CDS	42062212	42062463	0.95	-	0	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	exon	42062212	42062463	.	-	.	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	intron	42062464	42062556	.	-	.	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	CDS	42062557	42062656	1	-	1	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	exon	42062557	42062656	.	-	.	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	intron	42062657	42062749	.	-	.	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	CDS	42062750	42062919	0.99	-	0	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	exon	42062750	42062919	.	-	.	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
Phchi.S1	AUGUSTUS	start_codon	42062917	42062919	.	-	0	transcript_id "Phchi.S1G665700.t1"; gene_id "Phchi.S1G665700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13014.t1 is derived from g11479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3635323	3635998	.	-	.	Phchi.S3G033300
Phchi.S3	AUGUSTUS	transcript	3635323	3635998	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	stop_codon	3635320	3635322	.	-	0	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	CDS	3635323	3635363	0.45	-	2	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	exon	3635323	3635363	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	intron	3635364	3635535	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	CDS	3635536	3635675	0.23	-	1	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	exon	3635536	3635675	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	intron	3635676	3635771	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	CDS	3635772	3635910	0.23	-	2	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	exon	3635772	3635910	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	intron	3635911	3635991	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	CDS	3635992	3635998	0.23	-	0	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	exon	3635992	3635998	.	-	.	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
Phchi.S3	AUGUSTUS	start_codon	3635996	3635998	.	-	0	transcript_id "Phchi.S3G033300.t1"; gene_id "Phchi.S3G033300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9424.t1 is derived from g6600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41411559	41413019	.	+	.	Phchi.S1G658300
Phchi.S1	AUGUSTUS	transcript	41411559	41413019	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	start_codon	41411559	41411561	.	+	0	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	CDS	41411559	41411786	1	+	0	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	exon	41411559	41411786	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	intron	41411787	41411878	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	CDS	41411879	41412202	0.99	+	0	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	exon	41411879	41412202	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	intron	41412203	41412333	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	CDS	41412334	41412493	1	+	0	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	exon	41412334	41412493	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	intron	41412494	41412732	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	CDS	41412733	41413019	1	+	2	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	exon	41412733	41413019	.	+	.	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
Phchi.S1	AUGUSTUS	stop_codon	41413020	41413022	.	+	0	transcript_id "Phchi.S1G658300.t1"; gene_id "Phchi.S1G658300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg876.t1 is derived from g10658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6080970	6082227	.	+	.	Phchi.S6G083500
Phchi.S6	AUGUSTUS	transcript	6080970	6082227	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	start_codon	6080970	6080972	.	+	0	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	CDS	6080970	6081114	0.69	+	0	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	exon	6080970	6081114	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	intron	6081115	6081250	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	CDS	6081251	6081465	0.33	+	2	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	exon	6081251	6081465	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	intron	6081466	6081813	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	CDS	6081814	6081954	1	+	0	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	exon	6081814	6081954	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	intron	6081955	6082143	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	CDS	6082144	6082227	1	+	0	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	exon	6082144	6082227	.	+	.	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
Phchi.S6	AUGUSTUS	stop_codon	6082228	6082230	.	+	0	transcript_id "Phchi.S6G083500.t1"; gene_id "Phchi.S6G083500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12343.t1 is derived from g8019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12009746	12016221	.	+	.	Phchi.S2G042300
Phchi.S2	AUGUSTUS	transcript	12009746	12016221	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	start_codon	12009746	12009748	.	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12009746	12009823	0.68	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12009746	12009823	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12009824	12009889	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12009890	12010033	0.96	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12009890	12010033	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12010034	12010112	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12010113	12010196	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12010113	12010196	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12010197	12010294	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12010295	12010383	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12010295	12010383	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12010384	12010482	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12010483	12010657	1	+	1	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12010483	12010657	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12010658	12010958	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12010959	12010986	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12010959	12010986	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12010987	12011057	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12011058	12011078	0.95	+	2	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12011058	12011078	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12011079	12011231	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12011232	12011314	1	+	2	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12011232	12011314	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12011315	12011400	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12011401	12011472	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12011401	12011472	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12011473	12011612	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12011613	12011726	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12011613	12011726	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12011727	12011816	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12011817	12011917	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12011817	12011917	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12011918	12012062	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12012063	12012156	1	+	1	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12012063	12012156	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12012157	12012254	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12012255	12012422	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12012255	12012422	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12012423	12012577	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12012578	12012718	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12012578	12012718	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12012719	12012787	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12012788	12012853	0.71	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12012788	12012853	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12012854	12012955	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12012956	12013012	0.79	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12012956	12013012	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12013013	12013119	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12013120	12013348	0.8	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12013120	12013348	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12013349	12013445	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12013446	12013576	1	+	2	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12013446	12013576	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12013577	12013839	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12013840	12013914	0.99	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12013840	12013914	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12013915	12014019	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12014020	12014085	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12014020	12014085	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12014086	12014208	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12014209	12014280	0.93	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12014209	12014280	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12014281	12014387	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12014388	12014435	0.99	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12014388	12014435	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12014436	12014534	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12014535	12014654	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12014535	12014654	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12014655	12014750	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12014751	12014816	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12014751	12014816	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12014817	12014921	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12014922	12015034	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12014922	12015034	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12015035	12015168	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12015169	12015256	0.78	+	1	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12015169	12015256	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12015257	12015361	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12015362	12015475	0.98	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12015362	12015475	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12015476	12015558	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12015559	12015651	0.94	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12015559	12015651	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12015652	12015755	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12015756	12015803	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12015756	12015803	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12015804	12015880	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12015881	12015946	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12015881	12015946	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	intron	12015947	12016029	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	CDS	12016030	12016221	1	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	exon	12016030	12016221	.	+	.	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
Phchi.S2	AUGUSTUS	stop_codon	12016222	12016224	.	+	0	transcript_id "Phchi.S2G042300.t1"; gene_id "Phchi.S2G042300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8191.t1 is derived from g5366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34354275	34356867	.	+	.	Phchi.S1G535000
Phchi.S1	AUGUSTUS	transcript	34354275	34355553	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	start_codon	34354275	34354277	.	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354275	34354352	0.54	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354275	34354352	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354353	34354435	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354436	34354616	1	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354436	34354616	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354617	34354696	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354697	34354749	1	+	2	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354697	34354749	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354750	34354832	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354833	34354931	0.98	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354833	34354931	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354932	34355032	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355033	34355141	1	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355033	34355141	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355142	34355222	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355223	34355320	1	+	2	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355223	34355320	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355321	34355493	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355494	34355553	0.93	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355494	34355553	.	+	.	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	stop_codon	34355554	34355556	.	+	0	transcript_id "Phchi.S1G535000.t1"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	transcript	34354275	34356867	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	start_codon	34354275	34354277	.	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354275	34354352	0.61	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354275	34354352	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354353	34354435	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354436	34354616	1	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354436	34354616	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354617	34354696	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354697	34354749	1	+	2	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354697	34354749	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354750	34354832	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354833	34354931	1	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354833	34354931	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354932	34355032	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355033	34355141	1	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355033	34355141	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355142	34355222	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355223	34355301	1	+	2	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355223	34355301	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355302	34355493	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355494	34355659	1	+	1	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355494	34355659	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355660	34355751	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355752	34355877	1	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355752	34355877	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355878	34356032	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34356033	34356207	0.99	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34356033	34356207	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34356208	34356354	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34356355	34356362	0.97	+	2	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34356355	34356362	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34356363	34356570	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34356571	34356867	0.48	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34356571	34356867	.	+	.	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	stop_codon	34356868	34356870	.	+	0	transcript_id "Phchi.S1G535000.t2"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	transcript	34354275	34356867	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	start_codon	34354275	34354277	.	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354275	34354352	0.56	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354275	34354352	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354353	34354435	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354436	34354616	1	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354436	34354616	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354617	34354696	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354697	34354749	1	+	2	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354697	34354749	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354750	34354832	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34354833	34354931	0.99	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34354833	34354931	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34354932	34355032	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355033	34355141	1	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355033	34355141	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355142	34355222	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355223	34355301	1	+	2	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355223	34355301	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355302	34355493	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355494	34355659	1	+	1	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355494	34355659	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355660	34355751	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34355752	34355877	1	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34355752	34355877	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34355878	34356032	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34356033	34356207	0.99	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34356033	34356207	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34356208	34356295	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34356296	34356362	0.93	+	2	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34356296	34356362	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	intron	34356363	34356566	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	CDS	34356567	34356867	0.35	+	1	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	exon	34356567	34356867	.	+	.	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
Phchi.S1	AUGUSTUS	stop_codon	34356868	34356870	.	+	0	transcript_id "Phchi.S1G535000.t3"; gene_id "Phchi.S1G535000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg288.t1 is derived from g10070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2065791	2066280	.	-	.	Phchi.S6G024700
Phchi.S6	AUGUSTUS	transcript	2065791	2066280	.	-	.	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	stop_codon	2065788	2065790	.	-	0	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	CDS	2065791	2066107	0.52	-	2	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	exon	2065791	2066107	.	-	.	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	intron	2066108	2066201	.	-	.	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	CDS	2066202	2066280	0.49	-	0	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	exon	2066202	2066280	.	-	.	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
Phchi.S6	AUGUSTUS	start_codon	2066278	2066280	.	-	0	transcript_id "Phchi.S6G024700.t1"; gene_id "Phchi.S6G024700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14845.t1 is derived from g13313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15007362	15008554	.	+	.	Phchi.S3G216400
Phchi.S3	AUGUSTUS	transcript	15007362	15008554	.	+	.	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	start_codon	15007362	15007364	.	+	0	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	CDS	15007362	15007595	0.97	+	0	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	exon	15007362	15007595	.	+	.	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	intron	15007596	15007704	.	+	.	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	CDS	15007705	15007896	1	+	0	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	exon	15007705	15007896	.	+	.	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	intron	15007897	15007993	.	+	.	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	CDS	15007994	15008554	1	+	0	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	exon	15007994	15008554	.	+	.	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
Phchi.S3	AUGUSTUS	stop_codon	15008555	15008557	.	+	0	transcript_id "Phchi.S3G216400.t1"; gene_id "Phchi.S3G216400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9629.t1 is derived from g6805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42989372	42990151	.	+	.	Phchi.S1G678800
Phchi.S1	AUGUSTUS	transcript	42989372	42990151	.	+	.	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	start_codon	42989372	42989374	.	+	0	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	CDS	42989372	42989459	1	+	0	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	exon	42989372	42989459	.	+	.	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	intron	42989460	42989543	.	+	.	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	CDS	42989544	42989677	1	+	2	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	exon	42989544	42989677	.	+	.	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	intron	42989678	42989905	.	+	.	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	CDS	42989906	42990151	1	+	0	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	exon	42989906	42990151	.	+	.	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
Phchi.S1	AUGUSTUS	stop_codon	42990152	42990154	.	+	0	transcript_id "Phchi.S1G678800.t1"; gene_id "Phchi.S1G678800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1249.t1 is derived from g11032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8637385	8639660	.	+	.	Phchi.S6G120800
Phchi.S6	AUGUSTUS	transcript	8637385	8639660	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	start_codon	8637385	8637387	.	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8637385	8637602	1	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8637385	8637602	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8637603	8637793	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8637794	8638115	1	+	1	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8637794	8638115	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8638116	8638210	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8638211	8638360	1	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8638211	8638360	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8638361	8638440	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8638441	8638692	1	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8638441	8638692	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8638693	8638787	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8638788	8638874	1	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8638788	8638874	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8638875	8638983	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8638984	8639062	1	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8638984	8639062	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8639063	8639147	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8639148	8639254	0.86	+	2	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8639148	8639254	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8639255	8639356	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8639357	8639472	1	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8639357	8639472	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	intron	8639473	8639572	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	CDS	8639573	8639660	0.92	+	1	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	exon	8639573	8639660	.	+	.	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
Phchi.S6	AUGUSTUS	stop_codon	8639661	8639663	.	+	0	transcript_id "Phchi.S6G120800.t1"; gene_id "Phchi.S6G120800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12457.t1 is derived from g8134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23770877	23773442	.	+	.	Phchi.S2G053700
Phchi.S2	AUGUSTUS	transcript	23770877	23773442	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	start_codon	23770877	23770879	.	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23770877	23770881	0.9	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23770877	23770881	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23770882	23771056	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23771057	23771148	0.99	+	1	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23771057	23771148	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23771149	23771316	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23771317	23771387	0.99	+	2	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23771317	23771387	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23771388	23771491	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23771492	23771590	1	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23771492	23771590	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23771591	23771712	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23771713	23772228	1	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23771713	23772228	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23772229	23772414	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23772415	23772507	1	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23772415	23772507	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23772508	23772583	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23772584	23772772	1	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23772584	23772772	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23772773	23772973	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23772974	23773070	1	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23772974	23773070	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23773071	23773156	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23773157	23773235	1	+	2	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23773157	23773235	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	intron	23773236	23773354	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	CDS	23773355	23773442	1	+	1	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	exon	23773355	23773442	.	+	.	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
Phchi.S2	AUGUSTUS	stop_codon	23773443	23773445	.	+	0	transcript_id "Phchi.S2G053700.t1"; gene_id "Phchi.S2G053700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4744.t1 is derived from g1914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12588526	12589134	.	-	.	Phchi.S1G190300
Phchi.S1	AUGUSTUS	transcript	12588526	12589134	.	-	.	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	stop_codon	12588523	12588525	.	-	0	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	CDS	12588526	12588591	0.99	-	0	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	exon	12588526	12588591	.	-	.	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	intron	12588592	12588689	.	-	.	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	CDS	12588690	12588793	0.5	-	2	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	exon	12588690	12588793	.	-	.	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	intron	12588794	12588971	.	-	.	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	CDS	12588972	12589134	0.9	-	0	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	exon	12588972	12589134	.	-	.	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
Phchi.S1	AUGUSTUS	start_codon	12589132	12589134	.	-	0	transcript_id "Phchi.S1G190300.t1"; gene_id "Phchi.S1G190300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15653.t1 is derived from g14122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20497374	20498191	.	-	.	Phchi.S3G297200
Phchi.S3	AUGUSTUS	transcript	20497374	20498191	.	-	.	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	stop_codon	20497371	20497373	.	-	0	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	CDS	20497374	20497541	1	-	0	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	exon	20497374	20497541	.	-	.	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	intron	20497542	20497781	.	-	.	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	CDS	20497782	20497993	1	-	2	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	exon	20497782	20497993	.	-	.	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	intron	20497994	20498157	.	-	.	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	CDS	20498158	20498191	1	-	0	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	exon	20498158	20498191	.	-	.	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
Phchi.S3	AUGUSTUS	start_codon	20498189	20498191	.	-	0	transcript_id "Phchi.S3G297200.t1"; gene_id "Phchi.S3G297200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10295.t1 is derived from g7471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46978706	46980493	.	-	.	Phchi.S1G745400
Phchi.S1	AUGUSTUS	transcript	46978706	46980493	.	-	.	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	stop_codon	46978703	46978705	.	-	0	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	CDS	46978706	46979694	0.73	-	2	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	exon	46978706	46979694	.	-	.	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	intron	46979695	46980111	.	-	.	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	CDS	46980112	46980493	0.92	-	0	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	exon	46980112	46980493	.	-	.	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
Phchi.S1	AUGUSTUS	start_codon	46980491	46980493	.	-	0	transcript_id "Phchi.S1G745400.t1"; gene_id "Phchi.S1G745400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13048.t1 is derived from g11513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3902277	3905306	.	+	.	Phchi.S3G036700
Phchi.S3	AUGUSTUS	transcript	3902277	3905306	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	start_codon	3902277	3902279	.	+	0	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	CDS	3902277	3902904	0.98	+	0	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	exon	3902277	3902904	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	intron	3902905	3903089	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	CDS	3903090	3903703	0.97	+	2	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	exon	3903090	3903703	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	intron	3903704	3903817	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	CDS	3903818	3904147	0.49	+	0	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	exon	3903818	3904147	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	intron	3904148	3904295	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	CDS	3904296	3905306	0.92	+	0	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	exon	3904296	3905306	.	+	.	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
Phchi.S3	AUGUSTUS	stop_codon	3905307	3905309	.	+	0	transcript_id "Phchi.S3G036700.t1"; gene_id "Phchi.S3G036700"
# This transcript jg3403.t2 is derived from g572.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3404.t1 is derived from g573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3366459	3367771	.	-	.	Phchi.S1G056300
Phchi.S1	AUGUSTUS	transcript	3366459	3367771	.	-	.	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	stop_codon	3366456	3366458	.	-	0	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	CDS	3366459	3366886	0.89	-	2	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	exon	3366459	3366886	.	-	.	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	intron	3366887	3366990	.	-	.	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	CDS	3366991	3367771	0.57	-	0	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	exon	3366991	3367771	.	-	.	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
Phchi.S1	AUGUSTUS	start_codon	3367769	3367771	.	-	0	transcript_id "Phchi.S1G056300.t1"; gene_id "Phchi.S1G056300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4101.t1 is derived from g1270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7820607	7823423	.	+	.	Phchi.S1G126000
Phchi.S1	AUGUSTUS	transcript	7820607	7821964	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	start_codon	7820607	7820609	.	+	0	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7820607	7820698	0.52	+	0	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7820607	7820698	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7820699	7820779	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7820780	7820840	0.61	+	1	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7820780	7820840	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7820841	7820930	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7820931	7821156	0.74	+	0	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7820931	7821156	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821157	7821250	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821251	7821490	0.97	+	2	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821251	7821490	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821491	7821568	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821569	7821619	0.97	+	2	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821569	7821619	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821620	7821701	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821702	7821964	0.45	+	2	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821702	7821964	.	+	.	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	stop_codon	7821965	7821967	.	+	0	transcript_id "Phchi.S1G126000.t1"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	transcript	7820607	7822661	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	start_codon	7820607	7820609	.	+	0	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7820607	7820698	0.44	+	0	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7820607	7820698	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7820699	7820779	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7820780	7820840	0.51	+	1	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7820780	7820840	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7820841	7820930	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7820931	7821156	0.77	+	0	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7820931	7821156	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821157	7821250	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821251	7821490	1	+	2	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821251	7821490	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821491	7821568	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821569	7821619	0.94	+	2	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821569	7821619	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821620	7821701	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821702	7821962	0.62	+	2	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821702	7821962	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7821963	7822036	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7822037	7822397	0.14	+	2	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7822037	7822397	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7822398	7822501	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7822502	7822661	0.42	+	1	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7822502	7822661	.	+	.	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	stop_codon	7822662	7822664	.	+	0	transcript_id "Phchi.S1G126000.t2"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	transcript	7821997	7823423	.	+	.	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	start_codon	7821997	7821999	.	+	0	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7821997	7822961	0.31	+	0	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7821997	7822961	.	+	.	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	intron	7822962	7823071	.	+	.	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	CDS	7823072	7823423	0.73	+	1	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	exon	7823072	7823423	.	+	.	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
Phchi.S1	AUGUSTUS	stop_codon	7823424	7823426	.	+	0	transcript_id "Phchi.S1G126000.t3"; gene_id "Phchi.S1G126000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13207.t1 is derived from g11672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4667537	4669293	.	-	.	Phchi.S3G052600
Phchi.S3	AUGUSTUS	transcript	4667537	4669293	.	-	.	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	stop_codon	4667534	4667536	.	-	0	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	CDS	4667537	4668048	1	-	2	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	exon	4667537	4668048	.	-	.	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	intron	4668049	4668152	.	-	.	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	CDS	4668153	4669293	0.97	-	0	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	exon	4668153	4669293	.	-	.	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
Phchi.S3	AUGUSTUS	start_codon	4669291	4669293	.	-	0	transcript_id "Phchi.S3G052600.t1"; gene_id "Phchi.S3G052600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10214.t1 is derived from g7390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46401247	46403113	.	+	.	Phchi.S1G737300
Phchi.S1	AUGUSTUS	transcript	46401247	46403113	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	start_codon	46401247	46401249	.	+	0	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	CDS	46401247	46401421	0.97	+	0	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	exon	46401247	46401421	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	intron	46401422	46401564	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	CDS	46401565	46401739	1	+	2	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	exon	46401565	46401739	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	intron	46401740	46401850	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	CDS	46401851	46402034	0.96	+	1	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	exon	46401851	46402034	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	intron	46402035	46402167	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	CDS	46402168	46402432	0.79	+	0	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	exon	46402168	46402432	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	intron	46402433	46402612	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	CDS	46402613	46402779	0.98	+	2	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	exon	46402613	46402779	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	intron	46402780	46402987	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	CDS	46402988	46403113	0.99	+	0	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	exon	46402988	46403113	.	+	.	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
Phchi.S1	AUGUSTUS	stop_codon	46403114	46403116	.	+	0	transcript_id "Phchi.S1G737300.t1"; gene_id "Phchi.S1G737300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3894.t1 is derived from g1063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6277814	6281592	.	-	.	Phchi.S1G105300
Phchi.S1	AUGUSTUS	transcript	6277814	6281592	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	stop_codon	6277811	6277813	.	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6277814	6277916	1	-	1	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6277814	6277916	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6277917	6278155	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6278156	6278478	0.94	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6278156	6278478	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6278479	6278587	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6278588	6278806	0.97	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6278588	6278806	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6278807	6279016	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6279017	6279383	1	-	1	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6279017	6279383	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6279384	6279498	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6279499	6279704	1	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6279499	6279704	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6279705	6279781	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6279782	6280205	1	-	1	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6279782	6280205	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6280206	6280321	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6280322	6280569	1	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6280322	6280569	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6280570	6280653	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6280654	6280866	1	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6280654	6280866	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	intron	6280867	6280959	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	CDS	6280960	6281592	0.48	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	exon	6280960	6281592	.	-	.	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
Phchi.S1	AUGUSTUS	start_codon	6281590	6281592	.	-	0	transcript_id "Phchi.S1G105300.t1"; gene_id "Phchi.S1G105300"
# This transcript jg10246.t2 is derived from g7422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10247.t1 is derived from g7423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46587655	46590774	.	-	.	Phchi.S1G740600
Phchi.S1	AUGUSTUS	transcript	46587655	46590774	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	stop_codon	46587652	46587654	.	-	0	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	CDS	46587655	46587810	0.91	-	0	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	exon	46587655	46587810	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	intron	46587811	46587936	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	CDS	46587937	46589356	0.96	-	1	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	exon	46587937	46589356	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	intron	46589357	46589442	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	CDS	46589443	46590380	1	-	0	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	exon	46589443	46590380	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	intron	46590381	46590738	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	CDS	46590739	46590774	0.98	-	0	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	exon	46590739	46590774	.	-	.	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
Phchi.S1	AUGUSTUS	start_codon	46590772	46590774	.	-	0	transcript_id "Phchi.S1G740600.t1"; gene_id "Phchi.S1G740600"
# This transcript jg13177.t2 is derived from g11642.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13178.t1 is derived from g11643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4537693	4539451	.	-	.	Phchi.S3G049700
Phchi.S3	AUGUSTUS	transcript	4537693	4539451	.	-	.	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	stop_codon	4537690	4537692	.	-	0	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	CDS	4537693	4538334	1	-	0	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	exon	4537693	4538334	.	-	.	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	intron	4538335	4538449	.	-	.	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	CDS	4538450	4538878	1	-	0	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	exon	4538450	4538878	.	-	.	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	intron	4538879	4538995	.	-	.	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	CDS	4538996	4539451	0.95	-	0	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	exon	4538996	4539451	.	-	.	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
Phchi.S3	AUGUSTUS	start_codon	4539449	4539451	.	-	0	transcript_id "Phchi.S3G049700.t1"; gene_id "Phchi.S3G049700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15802.t1 is derived from g14272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21431803	21432945	.	+	.	Phchi.S3G312100
Phchi.S3	AUGUSTUS	transcript	21431840	21432945	.	+	.	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	start_codon	21431840	21431842	.	+	0	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	CDS	21431840	21431912	0.98	+	0	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	exon	21431840	21431912	.	+	.	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	intron	21431913	21432163	.	+	.	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	CDS	21432164	21432246	0.99	+	2	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	exon	21432164	21432246	.	+	.	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	intron	21432247	21432903	.	+	.	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	CDS	21432904	21432945	0.99	+	0	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	exon	21432904	21432945	.	+	.	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	stop_codon	21432946	21432948	.	+	0	transcript_id "Phchi.S3G312100.t1"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	transcript	21431803	21432945	.	+	.	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	start_codon	21431803	21431805	.	+	0	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	CDS	21431803	21431938	0.73	+	0	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	exon	21431803	21431938	.	+	.	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	intron	21431939	21432163	.	+	.	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	CDS	21432164	21432246	1	+	2	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	exon	21432164	21432246	.	+	.	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	intron	21432247	21432903	.	+	.	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	CDS	21432904	21432945	1	+	0	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	exon	21432904	21432945	.	+	.	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
Phchi.S3	AUGUSTUS	stop_codon	21432946	21432948	.	+	0	transcript_id "Phchi.S3G312100.t2"; gene_id "Phchi.S3G312100"
# This transcript jg5115.t2 is derived from g2285.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5116.t1 is derived from g2286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14803776	14806767	.	+	.	Phchi.S1G227500
Phchi.S1	AUGUSTUS	transcript	14803776	14806767	.	+	.	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	start_codon	14803776	14803778	.	+	0	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	CDS	14803776	14805782	1	+	0	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	exon	14803776	14805782	.	+	.	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	intron	14805783	14806026	.	+	.	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	CDS	14806027	14806448	1	+	0	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	exon	14806027	14806448	.	+	.	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	intron	14806449	14806571	.	+	.	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	CDS	14806572	14806767	1	+	1	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	exon	14806572	14806767	.	+	.	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
Phchi.S1	AUGUSTUS	stop_codon	14806768	14806770	.	+	0	transcript_id "Phchi.S1G227500.t1"; gene_id "Phchi.S1G227500"
# This transcript jg9155.t2 is derived from g6330.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9156.t1 is derived from g6331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40135674	40137085	.	+	.	Phchi.S1G631500
Phchi.S1	AUGUSTUS	transcript	40135674	40137085	.	+	.	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	start_codon	40135674	40135676	.	+	0	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	CDS	40135674	40136439	0.42	+	0	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	exon	40135674	40136439	.	+	.	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	intron	40136440	40136561	.	+	.	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	CDS	40136562	40137085	0.47	+	2	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	exon	40136562	40137085	.	+	.	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
Phchi.S1	AUGUSTUS	stop_codon	40137086	40137088	.	+	0	transcript_id "Phchi.S1G631500.t1"; gene_id "Phchi.S1G631500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg867.t1 is derived from g10649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5994388	5996776	.	-	.	Phchi.S6G082600
Phchi.S6	AUGUSTUS	transcript	5994388	5996776	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	stop_codon	5994385	5994387	.	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5994388	5994411	1	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5994388	5994411	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	intron	5994412	5994504	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5994505	5994611	0.79	-	2	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5994505	5994611	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	intron	5994612	5994705	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5994706	5995654	0.22	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5994706	5995654	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	intron	5995655	5995776	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5995777	5995893	0.58	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5995777	5995893	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	intron	5995894	5995988	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5995989	5996153	1	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5995989	5996153	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	intron	5996154	5996300	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5996301	5996418	1	-	1	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5996301	5996418	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	intron	5996419	5996588	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	CDS	5996589	5996776	1	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	exon	5996589	5996776	.	-	.	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
Phchi.S6	AUGUSTUS	start_codon	5996774	5996776	.	-	0	transcript_id "Phchi.S6G082600.t1"; gene_id "Phchi.S6G082600"
# This transcript jg14723.t2 is derived from g13191.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14723.t3 is derived from g13191.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14723.t4 is derived from g13191.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14724.t1 is derived from g13192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14373475	14377230	.	-	.	Phchi.S3G204300
Phchi.S3	AUGUSTUS	transcript	14373475	14377230	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	stop_codon	14373472	14373474	.	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14373475	14373648	1	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14373475	14373648	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14373649	14373730	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14373731	14373823	1	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14373731	14373823	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14373824	14373929	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14373930	14374144	1	-	2	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14373930	14374144	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14374145	14374229	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14374230	14374396	1	-	1	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14374230	14374396	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14374397	14374515	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14374516	14374658	0.99	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14374516	14374658	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14374659	14374774	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14374775	14374993	1	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14374775	14374993	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14374994	14375139	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14375140	14375220	1	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14375140	14375220	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14375221	14375303	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14375304	14375483	0.99	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14375304	14375483	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14375484	14375590	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14375591	14375921	0.88	-	1	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14375591	14375921	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14375922	14376036	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14376037	14376150	0.96	-	1	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14376037	14376150	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14376151	14376272	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14376273	14376364	1	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14376273	14376364	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14376365	14376519	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14376520	14376532	0.97	-	1	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14376520	14376532	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14376533	14376636	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14376637	14376652	0.97	-	2	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14376637	14376652	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14376653	14376743	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14376744	14376899	0.9	-	2	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14376744	14376899	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	intron	14376900	14377076	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	CDS	14377077	14377230	0.54	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	exon	14377077	14377230	.	-	.	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
Phchi.S3	AUGUSTUS	start_codon	14377228	14377230	.	-	0	transcript_id "Phchi.S3G204300.t1"; gene_id "Phchi.S3G204300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4296.t1 is derived from g1465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9490519	9493404	.	+	.	Phchi.S1G145500
Phchi.S1	AUGUSTUS	transcript	9490519	9493404	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	start_codon	9490519	9490521	.	+	0	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	CDS	9490519	9490762	0.51	+	0	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	exon	9490519	9490762	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	intron	9490763	9490886	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	CDS	9490887	9491099	0.59	+	2	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	exon	9490887	9491099	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	intron	9491100	9491201	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	CDS	9491202	9491296	0.99	+	2	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	exon	9491202	9491296	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	intron	9491297	9491381	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	CDS	9491382	9493223	0.69	+	0	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	exon	9491382	9493223	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	intron	9493224	9493398	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	CDS	9493399	9493404	0.78	+	0	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	exon	9493399	9493404	.	+	.	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
Phchi.S1	AUGUSTUS	stop_codon	9493405	9493407	.	+	0	transcript_id "Phchi.S1G145500.t1"; gene_id "Phchi.S1G145500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3980.t1 is derived from g1149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6847001	6853703	.	+	.	Phchi.S1G113900
Phchi.S1	AUGUSTUS	transcript	6847001	6853703	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	start_codon	6847001	6847003	.	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6847001	6847012	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6847001	6847012	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6847013	6847161	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6847162	6847260	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6847162	6847260	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6847261	6847432	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6847433	6847497	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6847433	6847497	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6847498	6847601	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6847602	6847660	0.94	+	1	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6847602	6847660	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6847661	6847769	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6847770	6847940	0.87	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6847770	6847940	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6847941	6848121	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6848122	6848257	1	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6848122	6848257	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6848258	6848368	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6848369	6848483	1	+	1	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6848369	6848483	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6848484	6848558	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6848559	6848845	0.99	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6848559	6848845	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6848846	6848929	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6848930	6849134	1	+	1	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6848930	6849134	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6849135	6849217	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6849218	6849448	0.99	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6849218	6849448	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6849449	6849616	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6849617	6849690	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6849617	6849690	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6849691	6849764	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6849765	6849832	0.88	+	1	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6849765	6849832	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6849833	6849913	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6849914	6850000	0.83	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6849914	6850000	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6850001	6850161	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6850162	6850202	0.83	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6850162	6850202	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6850203	6850427	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6850428	6850716	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6850428	6850716	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6850717	6850816	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6850817	6851280	0.99	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6850817	6851280	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6851281	6851414	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6851415	6851654	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6851415	6851654	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6851655	6851812	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6851813	6851896	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6851813	6851896	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6851897	6851983	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6851984	6851995	0.87	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6851984	6851995	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6851996	6852095	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6852096	6852270	0.56	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6852096	6852270	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6852271	6852359	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6852360	6852552	1	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6852360	6852552	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6852553	6852650	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6852651	6852993	1	+	1	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6852651	6852993	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6852994	6853108	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6853109	6853346	1	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6853109	6853346	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	intron	6853347	6853440	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	CDS	6853441	6853703	0.99	+	2	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	exon	6853441	6853703	.	+	.	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
Phchi.S1	AUGUSTUS	stop_codon	6853704	6853706	.	+	0	transcript_id "Phchi.S1G113900.t1"; gene_id "Phchi.S1G113900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3285.t1 is derived from g454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2691387	2692644	.	-	.	Phchi.S1G044400
Phchi.S1	AUGUSTUS	transcript	2691387	2692644	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	stop_codon	2691384	2691386	.	-	0	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	CDS	2691387	2691442	0.7	-	2	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	exon	2691387	2691442	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	intron	2691443	2691625	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	CDS	2691626	2691704	0.67	-	0	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	exon	2691626	2691704	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	intron	2691705	2691882	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	CDS	2691883	2692134	0.77	-	0	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	exon	2691883	2692134	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	intron	2692135	2692255	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	CDS	2692256	2692393	1	-	0	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	exon	2692256	2692393	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	intron	2692394	2692512	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	CDS	2692513	2692644	0.93	-	0	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	exon	2692513	2692644	.	-	.	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
Phchi.S1	AUGUSTUS	start_codon	2692642	2692644	.	-	0	transcript_id "Phchi.S1G044400.t1"; gene_id "Phchi.S1G044400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg631.t1 is derived from g10413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4475021	4476565	.	+	.	Phchi.S6G059000
Phchi.S6	AUGUSTUS	transcript	4475021	4476565	.	+	.	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	start_codon	4475021	4475023	.	+	0	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	CDS	4475021	4475376	0.54	+	0	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	exon	4475021	4475376	.	+	.	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	intron	4475377	4475460	.	+	.	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	CDS	4475461	4475605	0.99	+	1	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	exon	4475461	4475605	.	+	.	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	intron	4475606	4475689	.	+	.	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	CDS	4475690	4476565	0.95	+	0	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	exon	4475690	4476565	.	+	.	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
Phchi.S6	AUGUSTUS	stop_codon	4476566	4476568	.	+	0	transcript_id "Phchi.S6G059000.t1"; gene_id "Phchi.S6G059000"
# This transcript jg10505.t2 is derived from g14554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10506.t1 is derived from g14555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	751922	754111	.	-	.	Phchi.S4G008800
Phchi.S4	AUGUSTUS	transcript	751922	754111	.	-	.	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	stop_codon	751919	751921	.	-	0	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	CDS	751922	752287	0.91	-	0	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	exon	751922	752287	.	-	.	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	intron	752288	752386	.	-	.	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	CDS	752387	752526	1	-	2	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	exon	752387	752526	.	-	.	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	intron	752527	752691	.	-	.	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	CDS	752692	754111	1	-	0	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	exon	752692	754111	.	-	.	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
Phchi.S4	AUGUSTUS	start_codon	754109	754111	.	-	0	transcript_id "Phchi.S4G008800.t1"; gene_id "Phchi.S4G008800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14099.t1 is derived from g12566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10835025	10837961	.	+	.	Phchi.S3G141800
Phchi.S3	AUGUSTUS	transcript	10835025	10837961	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	start_codon	10835025	10835027	.	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10835025	10835151	0.47	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10835025	10835151	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10835152	10835263	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10835264	10835421	0.45	+	2	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10835264	10835421	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10835422	10835501	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10835502	10835873	0.87	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10835502	10835873	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10835874	10836056	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10836057	10836228	1	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10836057	10836228	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10836229	10836306	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10836307	10837052	0.94	+	2	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10836307	10837052	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837053	10837174	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837175	10837314	1	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837175	10837314	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837315	10837427	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837428	10837578	1	+	1	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837428	10837578	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837579	10837725	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837726	10837794	1	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837726	10837794	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837795	10837868	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837869	10837961	0.99	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837869	10837961	.	+	.	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	stop_codon	10837962	10837964	.	+	0	transcript_id "Phchi.S3G141800.t1"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	transcript	10835025	10837961	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	start_codon	10835025	10835027	.	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10835025	10835151	0.46	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10835025	10835151	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10835152	10835263	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10835264	10835421	0.38	+	2	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10835264	10835421	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10835422	10835501	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10835502	10835873	0.84	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10835502	10835873	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10835874	10836021	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10836022	10836046	0.64	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10836022	10836046	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10836047	10836132	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10836133	10836228	0.85	+	2	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10836133	10836228	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10836229	10836306	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10836307	10837052	0.95	+	2	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10836307	10837052	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837053	10837174	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837175	10837314	0.99	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837175	10837314	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837315	10837427	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837428	10837578	1	+	1	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837428	10837578	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837579	10837725	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837726	10837794	1	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837726	10837794	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	intron	10837795	10837868	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	CDS	10837869	10837961	0.98	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	exon	10837869	10837961	.	+	.	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
Phchi.S3	AUGUSTUS	stop_codon	10837962	10837964	.	+	0	transcript_id "Phchi.S3G141800.t2"; gene_id "Phchi.S3G141800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1211.t1 is derived from g10994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8429888	8431804	.	+	.	Phchi.S6G117000
Phchi.S6	AUGUSTUS	transcript	8429888	8431804	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	start_codon	8429888	8429890	.	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8429888	8429939	0.39	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8429888	8429939	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	intron	8429940	8430422	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8430423	8430451	0.5	+	2	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8430423	8430451	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	intron	8430452	8430623	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8430624	8430674	0.48	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8430624	8430674	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	intron	8430675	8430840	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8430841	8430991	1	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8430841	8430991	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	intron	8430992	8431158	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8431159	8431358	1	+	2	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8431159	8431358	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	intron	8431359	8431450	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8431451	8431627	1	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8431451	8431627	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	intron	8431628	8431714	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	CDS	8431715	8431804	1	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	exon	8431715	8431804	.	+	.	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
Phchi.S6	AUGUSTUS	stop_codon	8431805	8431807	.	+	0	transcript_id "Phchi.S6G117000.t1"; gene_id "Phchi.S6G117000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15615.t1 is derived from g14084.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20299735	20302338	.	-	.	Phchi.S3G293400
Phchi.S3	AUGUSTUS	transcript	20299735	20302338	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	stop_codon	20299732	20299734	.	-	0	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20299735	20299783	1	-	1	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20299735	20299783	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20299784	20299882	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20299883	20299951	1	-	1	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20299883	20299951	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20299952	20300057	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300058	20300124	0.86	-	2	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300058	20300124	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300125	20300577	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300578	20300615	1	-	1	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300578	20300615	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300616	20300702	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300703	20300777	1	-	1	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300703	20300777	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300778	20300856	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300857	20300967	0.93	-	1	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300857	20300967	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300968	20301039	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301040	20301171	1	-	1	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301040	20301171	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301172	20301271	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301272	20301314	0.95	-	2	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301272	20301314	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301315	20301480	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301481	20301552	0.94	-	2	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301481	20301552	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301553	20301782	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301783	20301983	1	-	2	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301783	20301983	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301984	20302220	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20302221	20302338	0.97	-	0	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20302221	20302338	.	-	.	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	start_codon	20302336	20302338	.	-	0	transcript_id "Phchi.S3G293400.t1"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	transcript	20299735	20302338	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	stop_codon	20299732	20299734	.	-	0	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20299735	20299783	1	-	1	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20299735	20299783	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20299784	20299882	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20299883	20299951	1	-	1	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20299883	20299951	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20299952	20300057	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300058	20300124	0.87	-	2	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300058	20300124	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300125	20300577	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300578	20300615	1	-	1	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300578	20300615	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300616	20300702	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300703	20300777	1	-	1	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300703	20300777	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300778	20300856	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20300857	20300967	0.79	-	1	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20300857	20300967	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20300968	20301039	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301040	20301171	0.99	-	1	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301040	20301171	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301172	20301347	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301348	20301552	1	-	2	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301348	20301552	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301553	20301782	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20301783	20301983	1	-	2	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20301783	20301983	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	intron	20301984	20302220	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	CDS	20302221	20302338	0.97	-	0	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	exon	20302221	20302338	.	-	.	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
Phchi.S3	AUGUSTUS	start_codon	20302336	20302338	.	-	0	transcript_id "Phchi.S3G293400.t2"; gene_id "Phchi.S3G293400"
# This transcript jg9402.t2 is derived from g6578.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9403.t1 is derived from g6579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41351452	41352468	.	-	.	Phchi.S1G656200
Phchi.S1	AUGUSTUS	transcript	41351452	41352468	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	stop_codon	41351449	41351451	.	-	0	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	CDS	41351452	41351480	0.64	-	2	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	exon	41351452	41351480	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	intron	41351481	41351579	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	CDS	41351580	41351663	0.64	-	2	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	exon	41351580	41351663	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	intron	41351664	41351751	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	CDS	41351752	41351827	0.65	-	0	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	exon	41351752	41351827	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	intron	41351828	41351972	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	CDS	41351973	41352079	1	-	2	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	exon	41351973	41352079	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	intron	41352080	41352155	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	CDS	41352156	41352224	1	-	2	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	exon	41352156	41352224	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	intron	41352225	41352332	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	CDS	41352333	41352468	0.9	-	0	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	exon	41352333	41352468	.	-	.	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
Phchi.S1	AUGUSTUS	start_codon	41352466	41352468	.	-	0	transcript_id "Phchi.S1G656200.t1"; gene_id "Phchi.S1G656200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9635.t1 is derived from g6811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43003700	43004890	.	+	.	Phchi.S1G679400
Phchi.S1	AUGUSTUS	transcript	43003700	43004890	.	+	.	transcript_id "Phchi.S1G679400.t1"; gene_id "Phchi.S1G679400"
Phchi.S1	AUGUSTUS	start_codon	43003700	43003702	.	+	0	transcript_id "Phchi.S1G679400.t1"; gene_id "Phchi.S1G679400"
Phchi.S1	AUGUSTUS	CDS	43003700	43004890	1	+	0	transcript_id "Phchi.S1G679400.t1"; gene_id "Phchi.S1G679400"
Phchi.S1	AUGUSTUS	exon	43003700	43004890	.	+	.	transcript_id "Phchi.S1G679400.t1"; gene_id "Phchi.S1G679400"
Phchi.S1	AUGUSTUS	stop_codon	43004891	43004893	.	+	0	transcript_id "Phchi.S1G679400.t1"; gene_id "Phchi.S1G679400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4088.t1 is derived from g1257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7750582	7751133	.	-	.	Phchi.S1G124700
Phchi.S1	AUGUSTUS	transcript	7750582	7751133	.	-	.	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	stop_codon	7750579	7750581	.	-	0	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	CDS	7750582	7750611	0.84	-	0	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	exon	7750582	7750611	.	-	.	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	intron	7750612	7750833	.	-	.	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	CDS	7750834	7751133	0.31	-	0	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	exon	7750834	7751133	.	-	.	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
Phchi.S1	AUGUSTUS	start_codon	7751131	7751133	.	-	0	transcript_id "Phchi.S1G124700.t1"; gene_id "Phchi.S1G124700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2904.t1 is derived from g73.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	402939	405143	.	+	.	Phchi.S1G006300
Phchi.S1	AUGUSTUS	transcript	402939	405111	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	start_codon	402939	402941	.	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	402939	403001	0.98	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	402939	403001	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403002	403087	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403088	403174	1	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403088	403174	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403175	403261	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403262	403332	1	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403262	403332	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403333	403435	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403436	403500	1	+	1	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403436	403500	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403501	403631	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403632	403747	1	+	2	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403632	403747	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403748	403866	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403867	403926	0.49	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403867	403926	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403927	404123	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404124	404210	0.97	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404124	404210	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404211	404299	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404300	404380	1	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404300	404380	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404381	404459	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404460	404529	0.82	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404460	404529	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404530	404662	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404663	404736	1	+	2	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404663	404736	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404737	405051	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	405052	405111	1	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	405052	405111	.	+	.	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	stop_codon	405112	405114	.	+	0	transcript_id "Phchi.S1G006300.t1"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	transcript	402939	405143	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	start_codon	402939	402941	.	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	402939	403001	0.99	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	402939	403001	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403002	403087	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403088	403174	1	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403088	403174	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403175	403261	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403262	403332	1	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403262	403332	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403333	403435	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403436	403500	1	+	1	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403436	403500	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403501	403631	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403632	403747	0.99	+	2	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403632	403747	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403748	403866	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	403867	403926	0.42	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	403867	403926	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	403927	404123	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404124	404210	0.94	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404124	404210	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404211	404299	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404300	404380	1	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404300	404380	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404381	404459	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404460	404540	1	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404460	404540	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404541	404662	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404663	404684	0.48	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404663	404684	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404685	404770	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	404771	404794	0.48	+	2	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	404771	404794	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	intron	404795	405051	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	CDS	405052	405143	0.48	+	2	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	exon	405052	405143	.	+	.	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
Phchi.S1	AUGUSTUS	stop_codon	405144	405146	.	+	0	transcript_id "Phchi.S1G006300.t2"; gene_id "Phchi.S1G006300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11905.t1 is derived from g15957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9227902	9229742	.	+	.	Phchi.S4G148700
Phchi.S4	AUGUSTUS	transcript	9227902	9229742	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	start_codon	9227902	9227904	.	+	0	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	CDS	9227902	9227957	1	+	0	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	exon	9227902	9227957	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	intron	9227958	9228391	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	CDS	9228392	9228519	1	+	1	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	exon	9228392	9228519	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	intron	9228520	9228660	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	CDS	9228661	9229088	0.99	+	2	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	exon	9228661	9229088	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	intron	9229089	9229205	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	CDS	9229206	9229742	1	+	0	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	exon	9229206	9229742	.	+	.	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
Phchi.S4	AUGUSTUS	stop_codon	9229743	9229745	.	+	0	transcript_id "Phchi.S4G148700.t1"; gene_id "Phchi.S4G148700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7949.t1 is derived from g5123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32061622	32064543	.	-	.	Phchi.S1G510800
Phchi.S1	AUGUSTUS	transcript	32061622	32064543	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	stop_codon	32061619	32061621	.	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32061622	32061894	0.91	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32061622	32061894	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32061895	32062048	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32062049	32062633	1	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32062049	32062633	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32062634	32062713	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32062714	32063071	1	-	1	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32062714	32063071	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32063072	32063195	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32063196	32063494	1	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32063196	32063494	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32063495	32063647	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32063648	32063703	1	-	2	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32063648	32063703	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32063704	32063822	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32063823	32063901	0.84	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32063823	32063901	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32063902	32063980	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32063981	32064037	1	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32063981	32064037	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32064038	32064145	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32064146	32064177	1	-	2	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32064146	32064177	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	intron	32064178	32064401	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	CDS	32064402	32064543	1	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	exon	32064402	32064543	.	-	.	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
Phchi.S1	AUGUSTUS	start_codon	32064541	32064543	.	-	0	transcript_id "Phchi.S1G510800.t1"; gene_id "Phchi.S1G510800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1462.t1 is derived from g8381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1016105	1016653	.	-	.	Phchi.S5G007100
Phchi.S5	AUGUSTUS	transcript	1016105	1016653	.	-	.	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	stop_codon	1016102	1016104	.	-	0	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	CDS	1016105	1016335	0.64	-	0	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	exon	1016105	1016335	.	-	.	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	intron	1016336	1016434	.	-	.	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	CDS	1016435	1016509	0.41	-	0	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	exon	1016435	1016509	.	-	.	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	intron	1016510	1016590	.	-	.	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	CDS	1016591	1016653	0.4	-	0	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	exon	1016591	1016653	.	-	.	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
Phchi.S5	AUGUSTUS	start_codon	1016651	1016653	.	-	0	transcript_id "Phchi.S5G007100.t1"; gene_id "Phchi.S5G007100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5203.t1 is derived from g2373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15444211	15446229	.	+	.	Phchi.S1G236200
Phchi.S1	AUGUSTUS	transcript	15444211	15446229	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	start_codon	15444211	15444213	.	+	0	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	CDS	15444211	15444502	0.96	+	0	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	exon	15444211	15444502	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	intron	15444503	15444597	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	CDS	15444598	15444640	0.62	+	2	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	exon	15444598	15444640	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	intron	15444641	15444717	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	CDS	15444718	15444823	0.67	+	1	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	exon	15444718	15444823	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	intron	15444824	15444911	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	CDS	15444912	15445168	0.99	+	0	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	exon	15444912	15445168	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	intron	15445169	15445272	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	CDS	15445273	15445666	0.88	+	1	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	exon	15445273	15445666	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	intron	15445667	15445782	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	CDS	15445783	15446229	0.99	+	0	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	exon	15445783	15446229	.	+	.	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
Phchi.S1	AUGUSTUS	stop_codon	15446230	15446232	.	+	0	transcript_id "Phchi.S1G236200.t1"; gene_id "Phchi.S1G236200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg575.t1 is derived from g10357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4248235	4249548	.	-	.	Phchi.S6G053400
Phchi.S6	AUGUSTUS	transcript	4248235	4249548	.	-	.	transcript_id "Phchi.S6G053400.t1"; gene_id "Phchi.S6G053400"
Phchi.S6	AUGUSTUS	stop_codon	4248232	4248234	.	-	0	transcript_id "Phchi.S6G053400.t1"; gene_id "Phchi.S6G053400"
Phchi.S6	AUGUSTUS	CDS	4248235	4249548	0.79	-	0	transcript_id "Phchi.S6G053400.t1"; gene_id "Phchi.S6G053400"
Phchi.S6	AUGUSTUS	exon	4248235	4249548	.	-	.	transcript_id "Phchi.S6G053400.t1"; gene_id "Phchi.S6G053400"
Phchi.S6	AUGUSTUS	start_codon	4249546	4249548	.	-	0	transcript_id "Phchi.S6G053400.t1"; gene_id "Phchi.S6G053400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10778.t1 is derived from g14828.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2065412	2067478	.	-	.	Phchi.S4G036000
Phchi.S4	AUGUSTUS	transcript	2065412	2067478	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	stop_codon	2065409	2065411	.	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065412	2065483	1	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065412	2065483	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065484	2065561	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065562	2065648	0.59	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065562	2065648	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065649	2065755	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065756	2065837	0.99	-	1	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065756	2065837	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065838	2065922	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065923	2065993	1	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065923	2065993	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065994	2066106	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2066107	2066473	0.76	-	1	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2066107	2066473	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2066474	2066563	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2066564	2066703	0.7	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2066564	2066703	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2066704	2066802	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2066803	2066992	0.97	-	1	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2066803	2066992	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2066993	2067083	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2067084	2067478	1	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2067084	2067478	.	-	.	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	start_codon	2067476	2067478	.	-	0	transcript_id "Phchi.S4G036000.t1"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	transcript	2065412	2067478	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	stop_codon	2065409	2065411	.	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065412	2065483	1	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065412	2065483	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065484	2065561	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065562	2065648	0.5	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065562	2065648	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065649	2065755	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065756	2065837	1	-	1	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065756	2065837	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065838	2065922	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2065923	2065993	0.99	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2065923	2065993	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2065994	2066106	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2066107	2066473	0.67	-	1	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2066107	2066473	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2066474	2066563	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2066564	2066703	0.62	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2066564	2066703	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2066704	2066802	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2066803	2066935	1	-	1	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2066803	2066935	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	intron	2066936	2067083	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	CDS	2067084	2067478	1	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	exon	2067084	2067478	.	-	.	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
Phchi.S4	AUGUSTUS	start_codon	2067476	2067478	.	-	0	transcript_id "Phchi.S4G036000.t2"; gene_id "Phchi.S4G036000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6453.t1 is derived from g3625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23102117	23103724	.	-	.	Phchi.S1G361200
Phchi.S1	AUGUSTUS	transcript	23102117	23103724	.	-	.	transcript_id "Phchi.S1G361200.t1"; gene_id "Phchi.S1G361200"
Phchi.S1	AUGUSTUS	stop_codon	23102114	23102116	.	-	0	transcript_id "Phchi.S1G361200.t1"; gene_id "Phchi.S1G361200"
Phchi.S1	AUGUSTUS	CDS	23102117	23103724	0.59	-	0	transcript_id "Phchi.S1G361200.t1"; gene_id "Phchi.S1G361200"
Phchi.S1	AUGUSTUS	exon	23102117	23103724	.	-	.	transcript_id "Phchi.S1G361200.t1"; gene_id "Phchi.S1G361200"
Phchi.S1	AUGUSTUS	start_codon	23103722	23103724	.	-	0	transcript_id "Phchi.S1G361200.t1"; gene_id "Phchi.S1G361200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5655.t1 is derived from g2825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18155203	18155622	.	-	.	Phchi.S1G281400
Phchi.S1	AUGUSTUS	transcript	18155203	18155622	.	-	.	transcript_id "Phchi.S1G281400.t1"; gene_id "Phchi.S1G281400"
Phchi.S1	AUGUSTUS	stop_codon	18155200	18155202	.	-	0	transcript_id "Phchi.S1G281400.t1"; gene_id "Phchi.S1G281400"
Phchi.S1	AUGUSTUS	CDS	18155203	18155622	0.97	-	0	transcript_id "Phchi.S1G281400.t1"; gene_id "Phchi.S1G281400"
Phchi.S1	AUGUSTUS	exon	18155203	18155622	.	-	.	transcript_id "Phchi.S1G281400.t1"; gene_id "Phchi.S1G281400"
Phchi.S1	AUGUSTUS	start_codon	18155620	18155622	.	-	0	transcript_id "Phchi.S1G281400.t1"; gene_id "Phchi.S1G281400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5976.t1 is derived from g3147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20188473	20192388	.	+	.	Phchi.S1G313500
Phchi.S1	AUGUSTUS	transcript	20188473	20192388	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	start_codon	20188473	20188475	.	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20188473	20188727	0.96	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20188473	20188727	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20188728	20188826	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20188827	20188894	1	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20188827	20188894	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20188895	20189021	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20189022	20189155	1	+	1	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20189022	20189155	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20189156	20189309	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20189310	20189398	1	+	2	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20189310	20189398	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20189399	20189501	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20189502	20189559	1	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20189502	20189559	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20189560	20189739	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20189740	20189792	1	+	2	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20189740	20189792	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20189793	20189899	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20189900	20189998	0.99	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20189900	20189998	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20189999	20190080	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20190081	20190194	0.99	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20190081	20190194	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20190195	20190302	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20190303	20190404	0.99	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20190303	20190404	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20190405	20190481	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20190482	20190572	0.98	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20190482	20190572	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	intron	20190573	20191009	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	CDS	20191010	20192388	0.98	+	2	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	exon	20191010	20192388	.	+	.	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
Phchi.S1	AUGUSTUS	stop_codon	20192389	20192391	.	+	0	transcript_id "Phchi.S1G313500.t1"; gene_id "Phchi.S1G313500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15068.t1 is derived from g13536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16862687	16864761	.	-	.	Phchi.S3G238700
Phchi.S3	AUGUSTUS	transcript	16862687	16864761	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	stop_codon	16862684	16862686	.	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16862687	16862830	0.85	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16862687	16862830	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16862831	16862939	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16862940	16863057	1	-	1	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16862940	16863057	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863058	16863172	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863173	16863294	1	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863173	16863294	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863295	16863442	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863443	16863504	0.96	-	2	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863443	16863504	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863505	16863614	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863615	16863783	0.99	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863615	16863783	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863784	16863888	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863889	16864062	0.99	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863889	16864062	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16864063	16864539	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16864540	16864761	1	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16864540	16864761	.	-	.	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	start_codon	16864759	16864761	.	-	0	transcript_id "Phchi.S3G238700.t1"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	transcript	16862687	16864761	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	stop_codon	16862684	16862686	.	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16862687	16862830	0.85	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16862687	16862830	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16862831	16862939	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16862940	16863057	1	-	1	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16862940	16863057	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863058	16863172	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863173	16863294	1	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863173	16863294	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863295	16863442	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863443	16863504	0.98	-	2	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863443	16863504	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863505	16863614	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863615	16863783	1	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863615	16863783	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16863784	16863888	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16863889	16864062	0.98	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16863889	16864062	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16864063	16864397	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16864398	16864431	0.92	-	1	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16864398	16864431	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	intron	16864432	16864534	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	CDS	16864535	16864761	0.93	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	exon	16864535	16864761	.	-	.	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
Phchi.S3	AUGUSTUS	start_codon	16864759	16864761	.	-	0	transcript_id "Phchi.S3G238700.t2"; gene_id "Phchi.S3G238700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13475.t1 is derived from g11942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7076700	7077125	.	+	.	Phchi.S3G079400
Phchi.S3	AUGUSTUS	transcript	7076700	7077125	.	+	.	transcript_id "Phchi.S3G079400.t1"; gene_id "Phchi.S3G079400"
Phchi.S3	AUGUSTUS	start_codon	7076700	7076702	.	+	0	transcript_id "Phchi.S3G079400.t1"; gene_id "Phchi.S3G079400"
Phchi.S3	AUGUSTUS	CDS	7076700	7077125	0.88	+	0	transcript_id "Phchi.S3G079400.t1"; gene_id "Phchi.S3G079400"
Phchi.S3	AUGUSTUS	exon	7076700	7077125	.	+	.	transcript_id "Phchi.S3G079400.t1"; gene_id "Phchi.S3G079400"
Phchi.S3	AUGUSTUS	stop_codon	7077126	7077128	.	+	0	transcript_id "Phchi.S3G079400.t1"; gene_id "Phchi.S3G079400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9980.t1 is derived from g7156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44768834	44770180	.	+	.	Phchi.S1G713900
Phchi.S1	AUGUSTUS	transcript	44768834	44770180	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	start_codon	44768834	44768836	.	+	0	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44768834	44769227	0.69	+	0	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44768834	44769227	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	intron	44769228	44769351	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44769352	44769401	0.98	+	2	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44769352	44769401	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	intron	44769402	44769469	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44769470	44769497	0.88	+	0	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44769470	44769497	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	intron	44769498	44769588	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44769589	44769603	0.99	+	2	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44769589	44769603	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	intron	44769604	44769738	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44769739	44769765	1	+	2	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44769739	44769765	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	intron	44769766	44769915	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44769916	44769986	1	+	2	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44769916	44769986	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	intron	44769987	44770084	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	CDS	44770085	44770180	0.86	+	0	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	exon	44770085	44770180	.	+	.	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
Phchi.S1	AUGUSTUS	stop_codon	44770181	44770183	.	+	0	transcript_id "Phchi.S1G713900.t1"; gene_id "Phchi.S1G713900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2223.t1 is derived from g9143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5514116	5515752	.	+	.	Phchi.S5G083200
Phchi.S5	AUGUSTUS	transcript	5514116	5515752	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	start_codon	5514116	5514118	.	+	0	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5514116	5514406	0.4	+	0	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5514116	5514406	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	intron	5514407	5514511	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5514512	5514638	1	+	0	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5514512	5514638	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	intron	5514639	5514738	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5514739	5514807	1	+	2	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5514739	5514807	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	intron	5514808	5514907	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5514908	5515103	1	+	2	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5514908	5515103	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	intron	5515104	5515250	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5515251	5515368	1	+	1	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5515251	5515368	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	intron	5515369	5515456	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5515457	5515563	0.9	+	0	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5515457	5515563	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	intron	5515564	5515751	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	CDS	5515752	5515752	0.64	+	1	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	exon	5515752	5515752	.	+	.	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
Phchi.S5	AUGUSTUS	stop_codon	5515753	5515755	.	+	0	transcript_id "Phchi.S5G083200.t1"; gene_id "Phchi.S5G083200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12222.t1 is derived from g7898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6824693	6827465	.	-	.	Phchi.S2G030200
Phchi.S2	AUGUSTUS	transcript	6824693	6827465	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	stop_codon	6824690	6824692	.	-	0	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	CDS	6824693	6825348	1	-	2	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	exon	6824693	6825348	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	intron	6825349	6825486	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	CDS	6825487	6825833	0.98	-	1	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	exon	6825487	6825833	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	intron	6825834	6825990	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	CDS	6825991	6826097	0.99	-	0	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	exon	6825991	6826097	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	intron	6826098	6826201	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	CDS	6826202	6826375	0.99	-	0	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	exon	6826202	6826375	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	intron	6826376	6826479	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	CDS	6826480	6826869	0.99	-	0	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	exon	6826480	6826869	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	intron	6826870	6827177	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	CDS	6827178	6827465	0.68	-	0	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	exon	6827178	6827465	.	-	.	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
Phchi.S2	AUGUSTUS	start_codon	6827463	6827465	.	-	0	transcript_id "Phchi.S2G030200.t1"; gene_id "Phchi.S2G030200"
# This transcript jg8873.t2 is derived from g6048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8874.t1 is derived from g6049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38402375	38403247	.	-	.	Phchi.S1G603300
Phchi.S1	AUGUSTUS	transcript	38402375	38403247	.	-	.	transcript_id "Phchi.S1G603300.t1"; gene_id "Phchi.S1G603300"
Phchi.S1	AUGUSTUS	stop_codon	38402372	38402374	.	-	0	transcript_id "Phchi.S1G603300.t1"; gene_id "Phchi.S1G603300"
Phchi.S1	AUGUSTUS	CDS	38402375	38403247	0.47	-	0	transcript_id "Phchi.S1G603300.t1"; gene_id "Phchi.S1G603300"
Phchi.S1	AUGUSTUS	exon	38402375	38403247	.	-	.	transcript_id "Phchi.S1G603300.t1"; gene_id "Phchi.S1G603300"
Phchi.S1	AUGUSTUS	start_codon	38403245	38403247	.	-	0	transcript_id "Phchi.S1G603300.t1"; gene_id "Phchi.S1G603300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13977.t1 is derived from g12444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10016711	10017509	.	+	.	Phchi.S3G129600
Phchi.S3	AUGUSTUS	transcript	10016711	10017509	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	start_codon	10016711	10016713	.	+	0	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	CDS	10016711	10016836	0.77	+	0	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	exon	10016711	10016836	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	intron	10016837	10016935	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	CDS	10016936	10016990	0.68	+	0	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	exon	10016936	10016990	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	intron	10016991	10017078	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	CDS	10017079	10017092	0.68	+	2	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	exon	10017079	10017092	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	intron	10017093	10017182	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	CDS	10017183	10017267	1	+	0	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	exon	10017183	10017267	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	intron	10017268	10017354	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	CDS	10017355	10017509	0.91	+	2	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	exon	10017355	10017509	.	+	.	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
Phchi.S3	AUGUSTUS	stop_codon	10017510	10017512	.	+	0	transcript_id "Phchi.S3G129600.t1"; gene_id "Phchi.S3G129600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12844.t1 is derived from g11309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2665697	2666329	.	-	.	Phchi.S3G016300
Phchi.S3	AUGUSTUS	transcript	2665697	2666329	.	-	.	transcript_id "Phchi.S3G016300.t1"; gene_id "Phchi.S3G016300"
Phchi.S3	AUGUSTUS	stop_codon	2665694	2665696	.	-	0	transcript_id "Phchi.S3G016300.t1"; gene_id "Phchi.S3G016300"
Phchi.S3	AUGUSTUS	CDS	2665697	2666329	0.99	-	0	transcript_id "Phchi.S3G016300.t1"; gene_id "Phchi.S3G016300"
Phchi.S3	AUGUSTUS	exon	2665697	2666329	.	-	.	transcript_id "Phchi.S3G016300.t1"; gene_id "Phchi.S3G016300"
Phchi.S3	AUGUSTUS	start_codon	2666327	2666329	.	-	0	transcript_id "Phchi.S3G016300.t1"; gene_id "Phchi.S3G016300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3324.t1 is derived from g493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2915877	2916160	.	-	.	Phchi.S1G048300
Phchi.S1	AUGUSTUS	transcript	2915877	2916160	.	-	.	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	stop_codon	2915874	2915876	.	-	0	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	CDS	2915877	2916037	0.93	-	2	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	exon	2915877	2916037	.	-	.	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	intron	2916038	2916114	.	-	.	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	CDS	2916115	2916160	0.52	-	0	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	exon	2916115	2916160	.	-	.	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
Phchi.S1	AUGUSTUS	start_codon	2916158	2916160	.	-	0	transcript_id "Phchi.S1G048300.t1"; gene_id "Phchi.S1G048300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2698.t1 is derived from g9618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8246852	8247194	.	+	.	Phchi.S5G130700
Phchi.S5	AUGUSTUS	transcript	8246852	8247194	.	+	.	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	start_codon	8246852	8246854	.	+	0	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	CDS	8246852	8246986	0.84	+	0	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	exon	8246852	8246986	.	+	.	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	intron	8246987	8247119	.	+	.	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	CDS	8247120	8247194	0.92	+	0	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	exon	8247120	8247194	.	+	.	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
Phchi.S5	AUGUSTUS	stop_codon	8247195	8247197	.	+	0	transcript_id "Phchi.S5G130700.t1"; gene_id "Phchi.S5G130700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11113.t1 is derived from g15163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4219750	4221242	.	-	.	Phchi.S4G069500
Phchi.S4	AUGUSTUS	transcript	4219750	4221242	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	stop_codon	4219747	4219749	.	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4219750	4219842	0.98	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4219750	4219842	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4219843	4219919	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4219920	4220001	1	-	1	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4219920	4220001	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4220002	4220084	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4220085	4220237	1	-	1	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4220085	4220237	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4220238	4220315	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4220316	4220407	1	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4220316	4220407	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4220408	4220520	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4220521	4220627	1	-	2	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4220521	4220627	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4220628	4220720	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4220721	4220796	1	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4220721	4220796	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4220797	4220872	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4220873	4220965	1	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4220873	4220965	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	intron	4220966	4221041	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	CDS	4221042	4221242	1	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	exon	4221042	4221242	.	-	.	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
Phchi.S4	AUGUSTUS	start_codon	4221240	4221242	.	-	0	transcript_id "Phchi.S4G069500.t1"; gene_id "Phchi.S4G069500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7106.t1 is derived from g4278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27019532	27025337	.	-	.	Phchi.S1G426500
Phchi.S1	AUGUSTUS	transcript	27019532	27025337	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	stop_codon	27019529	27019531	.	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27019532	27019549	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27019532	27019549	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27019550	27019634	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27019635	27019999	1	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27019635	27019999	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020000	27020080	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020081	27020214	1	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020081	27020214	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020215	27020295	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020296	27020322	0.44	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020296	27020322	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020323	27020393	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020394	27020449	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020394	27020449	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020450	27020539	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020540	27020664	1	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020540	27020664	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020665	27020749	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020750	27020797	1	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020750	27020797	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020798	27020889	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020890	27021011	1	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020890	27021011	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021012	27021095	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021096	27021124	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021096	27021124	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021125	27021323	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021324	27021368	0.98	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021324	27021368	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021369	27021484	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021485	27021678	0.98	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021485	27021678	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021679	27021828	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021829	27021985	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021829	27021985	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021986	27022063	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022064	27022147	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022064	27022147	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022148	27022266	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022267	27022387	0.61	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022267	27022387	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022388	27022475	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022476	27022578	0.97	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022476	27022578	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022579	27022673	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022674	27022766	1	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022674	27022766	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022767	27022944	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022945	27023017	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022945	27023017	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023018	27023096	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023097	27023184	0.98	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023097	27023184	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023185	27023295	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023296	27023366	0.98	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023296	27023366	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023367	27023446	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023447	27023535	0.99	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023447	27023535	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023536	27023638	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023639	27023700	1	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023639	27023700	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023701	27023844	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023845	27023986	1	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023845	27023986	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023987	27024080	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024081	27024181	1	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024081	27024181	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024182	27024294	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024295	27024396	0.99	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024295	27024396	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024397	27024499	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024500	27024564	1	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024500	27024564	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024565	27024656	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024657	27024732	1	-	1	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024657	27024732	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024733	27024826	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024827	27024911	1	-	2	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024827	27024911	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024912	27024991	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024992	27025337	0.51	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024992	27025337	.	-	.	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	start_codon	27025335	27025337	.	-	0	transcript_id "Phchi.S1G426500.t1"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	transcript	27019532	27025337	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	stop_codon	27019529	27019531	.	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27019532	27019549	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27019532	27019549	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27019550	27019634	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27019635	27019999	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27019635	27019999	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020000	27020080	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020081	27020199	0.87	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020081	27020199	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020200	27020295	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020296	27020322	0.45	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020296	27020322	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020323	27020393	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020394	27020449	0.96	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020394	27020449	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020450	27020539	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020540	27020664	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020540	27020664	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020665	27020749	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020750	27020797	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020750	27020797	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27020798	27020889	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27020890	27021011	1	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27020890	27021011	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021012	27021095	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021096	27021124	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021096	27021124	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021125	27021323	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021324	27021368	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021324	27021368	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021369	27021484	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021485	27021678	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021485	27021678	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021679	27021828	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27021829	27021985	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27021829	27021985	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27021986	27022063	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022064	27022147	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022064	27022147	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022148	27022266	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022267	27022387	0.63	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022267	27022387	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022388	27022475	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022476	27022578	0.96	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022476	27022578	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022579	27022673	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022674	27022766	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022674	27022766	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27022767	27022944	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27022945	27023017	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27022945	27023017	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023018	27023096	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023097	27023184	0.98	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023097	27023184	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023185	27023295	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023296	27023366	0.98	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023296	27023366	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023367	27023446	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023447	27023535	0.97	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023447	27023535	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023536	27023638	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023639	27023700	1	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023639	27023700	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023701	27023844	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27023845	27023986	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27023845	27023986	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27023987	27024080	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024081	27024181	1	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024081	27024181	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024182	27024294	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024295	27024396	1	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024295	27024396	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024397	27024499	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024500	27024564	1	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024500	27024564	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024565	27024656	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024657	27024732	1	-	1	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024657	27024732	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024733	27024826	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024827	27024911	1	-	2	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024827	27024911	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	intron	27024912	27024991	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	CDS	27024992	27025337	0.56	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	exon	27024992	27025337	.	-	.	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
Phchi.S1	AUGUSTUS	start_codon	27025335	27025337	.	-	0	transcript_id "Phchi.S1G426500.t2"; gene_id "Phchi.S1G426500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4393.t1 is derived from g1562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10216530	10218148	.	+	.	Phchi.S1G155200
Phchi.S1	AUGUSTUS	transcript	10216530	10218137	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	start_codon	10216530	10216532	.	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10216530	10216551	0.99	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10216530	10216551	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10216552	10216735	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10216736	10216831	1	+	2	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10216736	10216831	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10216832	10216987	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10216988	10217046	1	+	2	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10216988	10217046	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217047	10217131	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10217132	10217317	1	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10217132	10217317	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217318	10217454	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10217455	10217625	0.97	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10217455	10217625	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217626	10217963	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10217964	10218020	0.95	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10217964	10218020	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10218021	10218116	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10218117	10218137	0.97	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10218117	10218137	.	+	.	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	stop_codon	10218138	10218140	.	+	0	transcript_id "Phchi.S1G155200.t1"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	transcript	10216530	10218148	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	start_codon	10216530	10216532	.	+	0	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10216530	10216551	0.99	+	0	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10216530	10216551	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10216552	10216735	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10216736	10216831	1	+	2	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10216736	10216831	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10216832	10216987	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10216988	10217046	1	+	2	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10216988	10217046	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217047	10217131	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10217132	10217317	1	+	0	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10217132	10217317	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217318	10217401	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10217402	10217436	0.82	+	0	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10217402	10217436	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217437	10217580	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10217581	10217625	0.81	+	1	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10217581	10217625	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10217626	10218006	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10218007	10218020	0.75	+	1	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10218007	10218020	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	intron	10218021	10218116	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	CDS	10218117	10218148	0.76	+	2	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	exon	10218117	10218148	.	+	.	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
Phchi.S1	AUGUSTUS	stop_codon	10218149	10218151	.	+	0	transcript_id "Phchi.S1G155200.t2"; gene_id "Phchi.S1G155200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14283.t1 is derived from g12750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11909039	11911561	.	+	.	Phchi.S3G160200
Phchi.S3	AUGUSTUS	transcript	11909039	11911561	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	start_codon	11909039	11909041	.	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11909039	11909341	0.45	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11909039	11909341	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11909342	11909550	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11909551	11909616	1	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11909551	11909616	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11909617	11909718	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11909719	11909908	1	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11909719	11909908	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11909909	11910000	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11910001	11910197	1	+	2	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11910001	11910197	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11910198	11910295	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11910296	11910346	1	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11910296	11910346	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11910347	11910535	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11910536	11910627	1	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11910536	11910627	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11910628	11910739	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11910740	11910834	1	+	1	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11910740	11910834	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11910835	11910924	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11910925	11911040	1	+	2	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11910925	11911040	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11911041	11911194	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11911195	11911299	1	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11911195	11911299	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	intron	11911300	11911411	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	CDS	11911412	11911561	1	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	exon	11911412	11911561	.	+	.	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
Phchi.S3	AUGUSTUS	stop_codon	11911562	11911564	.	+	0	transcript_id "Phchi.S3G160200.t1"; gene_id "Phchi.S3G160200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7035.t1 is derived from g4207.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26518576	26520960	.	-	.	Phchi.S1G419400
Phchi.S1	AUGUSTUS	transcript	26518576	26520960	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	stop_codon	26518573	26518575	.	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26518576	26518863	1	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26518576	26518863	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26518864	26518958	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26518959	26519180	1	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26518959	26519180	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519181	26519249	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519250	26519366	0.99	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519250	26519366	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519367	26519477	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519478	26519580	0.77	-	1	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519478	26519580	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519581	26519696	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519697	26519868	0.79	-	2	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519697	26519868	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519869	26519946	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519947	26520196	0.97	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519947	26520196	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26520197	26520282	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26520283	26520659	0.96	-	2	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26520283	26520659	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26520660	26520740	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26520741	26520960	0.54	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26520741	26520960	.	-	.	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	start_codon	26520958	26520960	.	-	0	transcript_id "Phchi.S1G419400.t1"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	transcript	26518576	26520960	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	stop_codon	26518573	26518575	.	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26518576	26518863	1	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26518576	26518863	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26518864	26518958	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26518959	26519180	1	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26518959	26519180	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519181	26519249	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519250	26519366	0.99	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519250	26519366	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519367	26519477	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519478	26519580	0.78	-	1	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519478	26519580	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519581	26519696	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26519697	26519868	0.79	-	2	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26519697	26519868	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26519869	26520051	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26520052	26520196	0.93	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26520052	26520196	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26520197	26520282	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26520283	26520659	0.92	-	2	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26520283	26520659	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	intron	26520660	26520740	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	CDS	26520741	26520960	0.41	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	exon	26520741	26520960	.	-	.	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
Phchi.S1	AUGUSTUS	start_codon	26520958	26520960	.	-	0	transcript_id "Phchi.S1G419400.t2"; gene_id "Phchi.S1G419400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15595.t1 is derived from g14064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20187743	20189829	.	+	.	Phchi.S3G291400
Phchi.S3	AUGUSTUS	transcript	20187743	20189829	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	start_codon	20187743	20187745	.	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20187743	20188402	0.85	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20187743	20188402	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	intron	20188403	20188488	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20188489	20188638	1	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20188489	20188638	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	intron	20188639	20188732	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20188733	20188990	1	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20188733	20188990	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	intron	20188991	20189077	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20189078	20189243	1	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20189078	20189243	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	intron	20189244	20189328	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20189329	20189435	1	+	2	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20189329	20189435	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	intron	20189436	20189528	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20189529	20189650	1	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20189529	20189650	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	intron	20189651	20189732	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	CDS	20189733	20189829	1	+	1	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	exon	20189733	20189829	.	+	.	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
Phchi.S3	AUGUSTUS	stop_codon	20189830	20189832	.	+	0	transcript_id "Phchi.S3G291400.t1"; gene_id "Phchi.S3G291400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1573.t1 is derived from g8492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1825707	1827232	.	-	.	Phchi.S5G018200
Phchi.S5	AUGUSTUS	transcript	1825707	1827232	.	-	.	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	stop_codon	1825704	1825706	.	-	0	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	CDS	1825707	1826127	1	-	1	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	exon	1825707	1826127	.	-	.	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	intron	1826128	1826291	.	-	.	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	CDS	1826292	1827232	0.76	-	0	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	exon	1826292	1827232	.	-	.	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
Phchi.S5	AUGUSTUS	start_codon	1827230	1827232	.	-	0	transcript_id "Phchi.S5G018200.t1"; gene_id "Phchi.S5G018200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8942.t1 is derived from g6117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38779873	38782568	.	-	.	Phchi.S1G610100
Phchi.S1	AUGUSTUS	transcript	38779873	38782211	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	stop_codon	38779870	38779872	.	-	0	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38779873	38780231	1	-	2	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38779873	38780231	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38780232	38780343	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38780344	38780557	1	-	0	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38780344	38780557	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38780558	38780702	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38780703	38780820	0.99	-	1	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38780703	38780820	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38780821	38780933	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38780934	38781191	1	-	1	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38780934	38781191	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781192	38781307	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781308	38781417	1	-	0	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781308	38781417	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781418	38781536	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781537	38781595	0.92	-	2	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781537	38781595	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781596	38781702	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781703	38781844	0.95	-	0	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781703	38781844	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781845	38781944	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781945	38782211	0.95	-	0	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781945	38782211	.	-	.	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	start_codon	38782209	38782211	.	-	0	transcript_id "Phchi.S1G610100.t1"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	transcript	38779873	38782568	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	stop_codon	38779870	38779872	.	-	0	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38779873	38780231	1	-	2	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38779873	38780231	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38780232	38780343	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38780344	38780557	1	-	0	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38780344	38780557	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38780558	38780702	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38780703	38780820	0.99	-	1	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38780703	38780820	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38780821	38780933	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38780934	38781191	1	-	1	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38780934	38781191	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781192	38781307	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781308	38781417	1	-	0	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781308	38781417	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781418	38781536	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781537	38781595	0.92	-	2	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781537	38781595	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781596	38781702	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781703	38781844	0.98	-	0	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781703	38781844	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38781845	38781944	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38781945	38782161	0.98	-	1	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38781945	38782161	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	intron	38782162	38782272	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	CDS	38782273	38782568	0.62	-	0	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	exon	38782273	38782568	.	-	.	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
Phchi.S1	AUGUSTUS	start_codon	38782566	38782568	.	-	0	transcript_id "Phchi.S1G610100.t2"; gene_id "Phchi.S1G610100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4033.t1 is derived from g1202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7279044	7280166	.	-	.	Phchi.S1G119200
Phchi.S1	AUGUSTUS	transcript	7279044	7280166	.	-	.	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	stop_codon	7279041	7279043	.	-	0	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	CDS	7279044	7279339	1	-	2	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	exon	7279044	7279339	.	-	.	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	intron	7279340	7279707	.	-	.	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	CDS	7279708	7279975	1	-	0	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	exon	7279708	7279975	.	-	.	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	intron	7279976	7280055	.	-	.	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	CDS	7280056	7280166	1	-	0	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	exon	7280056	7280166	.	-	.	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	start_codon	7280164	7280166	.	-	0	transcript_id "Phchi.S1G119200.t1"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	transcript	7279604	7280166	.	-	.	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	stop_codon	7279601	7279603	.	-	0	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	CDS	7279604	7279611	1	-	2	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	exon	7279604	7279611	.	-	.	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	intron	7279612	7279707	.	-	.	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	CDS	7279708	7279975	1	-	0	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	exon	7279708	7279975	.	-	.	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	intron	7279976	7280055	.	-	.	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	CDS	7280056	7280166	1	-	0	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	exon	7280056	7280166	.	-	.	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
Phchi.S1	AUGUSTUS	start_codon	7280164	7280166	.	-	0	transcript_id "Phchi.S1G119200.t2"; gene_id "Phchi.S1G119200"
# This transcript jg5254.t2 is derived from g2424.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5255.t1 is derived from g2425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15879383	15881811	.	-	.	Phchi.S1G241400
Phchi.S1	AUGUSTUS	transcript	15879383	15881811	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	stop_codon	15879380	15879382	.	-	0	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	CDS	15879383	15880387	0.88	-	0	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	exon	15879383	15880387	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	intron	15880388	15880500	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	CDS	15880501	15881238	0.72	-	0	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	exon	15880501	15881238	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	intron	15881239	15881332	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	CDS	15881333	15881432	0.39	-	1	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	exon	15881333	15881432	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	intron	15881433	15881524	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	CDS	15881525	15881610	0.48	-	0	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	exon	15881525	15881610	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	intron	15881611	15881703	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	CDS	15881704	15881811	0.39	-	0	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	exon	15881704	15881811	.	-	.	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
Phchi.S1	AUGUSTUS	start_codon	15881809	15881811	.	-	0	transcript_id "Phchi.S1G241400.t1"; gene_id "Phchi.S1G241400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5471.t1 is derived from g2641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16998945	16999613	.	-	.	Phchi.S1G263000
Phchi.S1	AUGUSTUS	transcript	16998945	16999613	.	-	.	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	stop_codon	16998942	16998944	.	-	0	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	CDS	16998945	16999037	1	-	0	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	exon	16998945	16999037	.	-	.	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	intron	16999038	16999122	.	-	.	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	CDS	16999123	16999212	1	-	0	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	exon	16999123	16999212	.	-	.	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	intron	16999213	16999292	.	-	.	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	CDS	16999293	16999613	1	-	0	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	exon	16999293	16999613	.	-	.	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
Phchi.S1	AUGUSTUS	start_codon	16999611	16999613	.	-	0	transcript_id "Phchi.S1G263000.t1"; gene_id "Phchi.S1G263000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8570.t1 is derived from g5745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36692847	36694039	.	-	.	Phchi.S1G572900
Phchi.S1	AUGUSTUS	transcript	36692847	36694039	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	stop_codon	36692844	36692846	.	-	0	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	CDS	36692847	36692879	1	-	0	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	exon	36692847	36692879	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	intron	36692880	36692952	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	CDS	36692953	36693081	1	-	0	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	exon	36692953	36693081	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	intron	36693082	36693216	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	CDS	36693217	36693352	1	-	1	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	exon	36693217	36693352	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	intron	36693353	36693504	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	CDS	36693505	36693635	1	-	0	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	exon	36693505	36693635	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	intron	36693636	36693722	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	CDS	36693723	36693778	1	-	2	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	exon	36693723	36693778	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	intron	36693779	36693921	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	CDS	36693922	36694039	1	-	0	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	exon	36693922	36694039	.	-	.	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
Phchi.S1	AUGUSTUS	start_codon	36694037	36694039	.	-	0	transcript_id "Phchi.S1G572900.t1"; gene_id "Phchi.S1G572900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2971.t1 is derived from g140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	898492	900120	.	+	.	Phchi.S1G013000
Phchi.S1	AUGUSTUS	transcript	898492	900120	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	start_codon	898492	898494	.	+	0	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	CDS	898492	899133	0.82	+	0	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	exon	898492	899133	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	intron	899134	899242	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	CDS	899243	899500	1	+	0	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	exon	899243	899500	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	intron	899501	899690	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	CDS	899691	899861	1	+	0	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	exon	899691	899861	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	intron	899862	900036	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	CDS	900037	900120	0.99	+	0	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	exon	900037	900120	.	+	.	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
Phchi.S1	AUGUSTUS	stop_codon	900121	900123	.	+	0	transcript_id "Phchi.S1G013000.t1"; gene_id "Phchi.S1G013000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14365.t1 is derived from g12832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12373134	12376130	.	-	.	Phchi.S3G168400
Phchi.S3	AUGUSTUS	transcript	12373134	12376130	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	stop_codon	12373131	12373133	.	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12373134	12373202	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12373134	12373202	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12373203	12373316	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12373317	12373391	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12373317	12373391	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12373392	12373477	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12373478	12373534	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12373478	12373534	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12373535	12373623	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12373624	12373740	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12373624	12373740	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12373741	12373859	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12373860	12373970	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12373860	12373970	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12373971	12374053	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12374054	12374176	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12374054	12374176	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12374177	12374315	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12374316	12374405	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12374316	12374405	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12374406	12374530	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12374531	12374656	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12374531	12374656	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12374657	12374787	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12374788	12374841	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12374788	12374841	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12374842	12374926	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12374927	12375007	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12374927	12375007	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12375008	12375102	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12375103	12375210	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12375103	12375210	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12375211	12375423	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12375424	12375495	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12375424	12375495	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12375496	12375632	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12375633	12375695	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12375633	12375695	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	intron	12375696	12375959	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	CDS	12375960	12376130	1	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	exon	12375960	12376130	.	-	.	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
Phchi.S3	AUGUSTUS	start_codon	12376128	12376130	.	-	0	transcript_id "Phchi.S3G168400.t1"; gene_id "Phchi.S3G168400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7113.t1 is derived from g4285.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27040075	27042333	.	+	.	Phchi.S1G427200
Phchi.S1	AUGUSTUS	transcript	27040075	27042333	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	start_codon	27040075	27040077	.	+	0	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27040075	27040461	0.82	+	0	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27040075	27040461	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27040462	27040702	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27040703	27040777	1	+	0	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27040703	27040777	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27040778	27041268	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27041269	27041457	1	+	0	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27041269	27041457	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27041458	27041650	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27041651	27041775	1	+	0	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27041651	27041775	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27041776	27041871	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27041872	27041991	1	+	1	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27041872	27041991	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27041992	27042070	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27042071	27042171	0.9	+	1	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27042071	27042171	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27042172	27042250	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27042251	27042333	0.88	+	2	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27042251	27042333	.	+	.	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	stop_codon	27042334	27042336	.	+	0	transcript_id "Phchi.S1G427200.t1"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	transcript	27040075	27042333	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	start_codon	27040075	27040077	.	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27040075	27040461	0.8	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27040075	27040461	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27040462	27040702	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27040703	27040756	0.67	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27040703	27040756	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27040757	27040840	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27040841	27040942	1	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27040841	27040942	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27040943	27041268	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27041269	27041457	0.99	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27041269	27041457	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27041458	27041650	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27041651	27041775	1	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27041651	27041775	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27041776	27041871	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27041872	27041991	1	+	1	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27041872	27041991	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27041992	27042070	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27042071	27042171	0.9	+	1	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27042071	27042171	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	intron	27042172	27042250	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	CDS	27042251	27042333	0.88	+	2	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	exon	27042251	27042333	.	+	.	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
Phchi.S1	AUGUSTUS	stop_codon	27042334	27042336	.	+	0	transcript_id "Phchi.S1G427200.t2"; gene_id "Phchi.S1G427200"
# This transcript jg8523.t2 is derived from g5698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8524.t1 is derived from g5699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36432972	36434922	.	-	.	Phchi.S1G568300
Phchi.S1	AUGUSTUS	transcript	36432972	36434922	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	stop_codon	36432969	36432971	.	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36432972	36433223	0.89	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36432972	36433223	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36433224	36433314	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36433315	36433333	1	-	1	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36433315	36433333	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36433334	36433407	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36433408	36433414	1	-	2	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36433408	36433414	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36433415	36433494	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36433495	36433544	1	-	1	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36433495	36433544	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36433545	36433686	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36433687	36433739	1	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36433687	36433739	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36433740	36433890	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36433891	36434013	1	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36433891	36434013	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36434014	36434100	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36434101	36434184	1	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36434101	36434184	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36434185	36434462	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36434463	36434528	1	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36434463	36434528	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36434529	36434805	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36434806	36434922	1	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36434806	36434922	.	-	.	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	start_codon	36434920	36434922	.	-	0	transcript_id "Phchi.S1G568300.t1"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	transcript	36434224	36434922	.	-	.	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	stop_codon	36434221	36434223	.	-	0	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36434224	36434253	0.7	-	0	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36434224	36434253	.	-	.	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36434254	36434462	.	-	.	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36434463	36434528	1	-	0	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36434463	36434528	.	-	.	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	intron	36434529	36434805	.	-	.	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	CDS	36434806	36434922	1	-	0	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	exon	36434806	36434922	.	-	.	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
Phchi.S1	AUGUSTUS	start_codon	36434920	36434922	.	-	0	transcript_id "Phchi.S1G568300.t2"; gene_id "Phchi.S1G568300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3976.t1 is derived from g1145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6827066	6830926	.	-	.	Phchi.S1G113500
Phchi.S1	AUGUSTUS	transcript	6827066	6830926	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	stop_codon	6827063	6827065	.	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6827066	6827302	0.97	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6827066	6827302	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6827303	6827486	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6827487	6827726	1	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6827487	6827726	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6827727	6827814	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6827815	6828043	1	-	1	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6827815	6828043	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6828044	6828124	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6828125	6828222	1	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6828125	6828222	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6828223	6828321	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6828322	6828519	1	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6828322	6828519	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6828520	6828621	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6828622	6828861	0.72	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6828622	6828861	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6828862	6829089	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6829090	6829404	0.69	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6829090	6829404	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6829405	6829525	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6829526	6829773	0.78	-	2	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6829526	6829773	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6829774	6829899	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6829900	6830038	0.94	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6829900	6830038	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6830039	6830211	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6830212	6830436	1	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6830212	6830436	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6830437	6830550	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6830551	6830721	1	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6830551	6830721	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	intron	6830722	6830863	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	CDS	6830864	6830926	0.94	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	exon	6830864	6830926	.	-	.	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
Phchi.S1	AUGUSTUS	start_codon	6830924	6830926	.	-	0	transcript_id "Phchi.S1G113500.t1"; gene_id "Phchi.S1G113500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1313.t1 is derived from g11096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8950207	8954088	.	+	.	Phchi.S6G127200
Phchi.S6	AUGUSTUS	transcript	8950207	8954088	.	+	.	transcript_id "Phchi.S6G127200.t1"; gene_id "Phchi.S6G127200"
Phchi.S6	AUGUSTUS	start_codon	8950207	8950209	.	+	0	transcript_id "Phchi.S6G127200.t1"; gene_id "Phchi.S6G127200"
Phchi.S6	AUGUSTUS	CDS	8950207	8954088	0.62	+	0	transcript_id "Phchi.S6G127200.t1"; gene_id "Phchi.S6G127200"
Phchi.S6	AUGUSTUS	exon	8950207	8954088	.	+	.	transcript_id "Phchi.S6G127200.t1"; gene_id "Phchi.S6G127200"
Phchi.S6	AUGUSTUS	stop_codon	8954089	8954091	.	+	0	transcript_id "Phchi.S6G127200.t1"; gene_id "Phchi.S6G127200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7090.t1 is derived from g4262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26861872	26863685	.	+	.	Phchi.S1G424900
Phchi.S1	AUGUSTUS	transcript	26861872	26863685	.	+	.	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	start_codon	26861872	26861874	.	+	0	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	CDS	26861872	26862260	1	+	0	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	exon	26861872	26862260	.	+	.	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	intron	26862261	26862348	.	+	.	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	CDS	26862349	26862601	1	+	1	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	exon	26862349	26862601	.	+	.	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	intron	26862602	26862701	.	+	.	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	CDS	26862702	26863685	1	+	0	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	exon	26862702	26863685	.	+	.	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
Phchi.S1	AUGUSTUS	stop_codon	26863686	26863688	.	+	0	transcript_id "Phchi.S1G424900.t1"; gene_id "Phchi.S1G424900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13804.t1 is derived from g12271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8964121	8964540	.	-	.	Phchi.S3G112300
Phchi.S3	AUGUSTUS	transcript	8964121	8964540	.	-	.	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	stop_codon	8964118	8964120	.	-	0	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	CDS	8964121	8964331	0.95	-	1	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	exon	8964121	8964331	.	-	.	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	intron	8964332	8964418	.	-	.	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	CDS	8964419	8964540	0.6	-	0	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	exon	8964419	8964540	.	-	.	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
Phchi.S3	AUGUSTUS	start_codon	8964538	8964540	.	-	0	transcript_id "Phchi.S3G112300.t1"; gene_id "Phchi.S3G112300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1855.t1 is derived from g8775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3565616	3567796	.	-	.	Phchi.S5G046400
Phchi.S5	AUGUSTUS	transcript	3565616	3567796	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	stop_codon	3565613	3565615	.	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3565616	3565677	1	-	2	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3565616	3565677	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3565678	3565767	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3565768	3565887	1	-	2	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3565768	3565887	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3565888	3565995	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3565996	3566104	0.82	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3565996	3566104	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3566105	3566231	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3566232	3566378	1	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3566232	3566378	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3566379	3566512	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3566513	3566596	1	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3566513	3566596	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3566597	3566677	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3566678	3566787	1	-	2	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3566678	3566787	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3566788	3566901	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3566902	3566971	1	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3566902	3566971	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3566972	3567098	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3567099	3567166	1	-	2	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3567099	3567166	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3567167	3567245	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3567246	3567321	1	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3567246	3567321	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3567322	3567421	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3567422	3567504	1	-	2	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3567422	3567504	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	intron	3567505	3567705	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	CDS	3567706	3567796	1	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	exon	3567706	3567796	.	-	.	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
Phchi.S5	AUGUSTUS	start_codon	3567794	3567796	.	-	0	transcript_id "Phchi.S5G046400.t1"; gene_id "Phchi.S5G046400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11999.t1 is derived from g7674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	451762	453569	.	-	.	Phchi.S2G007900
Phchi.S2	AUGUSTUS	transcript	451762	453569	.	-	.	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	stop_codon	451759	451761	.	-	0	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	CDS	451762	451834	0.96	-	1	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	exon	451762	451834	.	-	.	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	intron	451835	452064	.	-	.	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	CDS	452065	453569	0.96	-	0	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	exon	452065	453569	.	-	.	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
Phchi.S2	AUGUSTUS	start_codon	453567	453569	.	-	0	transcript_id "Phchi.S2G007900.t1"; gene_id "Phchi.S2G007900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12380.t1 is derived from g8056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14460239	14462000	.	-	.	Phchi.S2G046000
Phchi.S2	AUGUSTUS	transcript	14460239	14462000	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	stop_codon	14460236	14460238	.	-	0	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	CDS	14460239	14460588	0.86	-	2	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	exon	14460239	14460588	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	intron	14460589	14460942	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	CDS	14460943	14461015	0.62	-	0	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	exon	14460943	14461015	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	intron	14461016	14461311	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	CDS	14461312	14461323	0.43	-	0	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	exon	14461312	14461323	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	intron	14461324	14461409	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	CDS	14461410	14461416	0.3	-	1	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	exon	14461410	14461416	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	intron	14461417	14461767	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	CDS	14461768	14462000	0.41	-	0	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	exon	14461768	14462000	.	-	.	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
Phchi.S2	AUGUSTUS	start_codon	14461998	14462000	.	-	0	transcript_id "Phchi.S2G046000.t1"; gene_id "Phchi.S2G046000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10811.t1 is derived from g14861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2206071	2207831	.	-	.	Phchi.S4G039300
Phchi.S4	AUGUSTUS	transcript	2206071	2207831	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	stop_codon	2206068	2206070	.	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2206071	2206194	1	-	1	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2206071	2206194	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2206195	2206271	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2206272	2206396	1	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2206272	2206396	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2206397	2206471	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2206472	2206534	1	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2206472	2206534	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2206535	2206626	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2206627	2206751	1	-	2	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2206627	2206751	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2206752	2206966	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2206967	2207027	1	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2206967	2207027	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2207028	2207132	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2207133	2207423	1	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2207133	2207423	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2207424	2207624	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2207625	2207665	1	-	2	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2207625	2207665	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	intron	2207666	2207749	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	CDS	2207750	2207831	1	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	exon	2207750	2207831	.	-	.	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
Phchi.S4	AUGUSTUS	start_codon	2207829	2207831	.	-	0	transcript_id "Phchi.S4G039300.t1"; gene_id "Phchi.S4G039300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13564.t1 is derived from g12031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7515906	7517738	.	-	.	Phchi.S3G088300
Phchi.S3	AUGUSTUS	transcript	7516000	7517738	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	stop_codon	7515997	7515999	.	-	0	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516000	7516055	0.97	-	2	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516000	7516055	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516056	7516172	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516173	7516269	1	-	0	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516173	7516269	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516270	7516433	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516434	7516511	1	-	0	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516434	7516511	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516512	7516609	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516610	7516710	1	-	2	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516610	7516710	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516711	7516837	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516838	7516911	1	-	1	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516838	7516911	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516912	7517039	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7517040	7517116	1	-	0	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7517040	7517116	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7517117	7517615	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7517616	7517738	1	-	0	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7517616	7517738	.	-	.	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	start_codon	7517736	7517738	.	-	0	transcript_id "Phchi.S3G088300.t1"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	transcript	7515906	7517738	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	stop_codon	7515903	7515905	.	-	0	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7515906	7515961	0.93	-	2	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7515906	7515961	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7515962	7516172	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516173	7516269	1	-	0	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516173	7516269	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516270	7516433	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516434	7516511	1	-	0	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516434	7516511	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516512	7516609	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516610	7516710	1	-	2	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516610	7516710	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516711	7516837	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7516838	7516911	1	-	1	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7516838	7516911	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7516912	7517039	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7517040	7517116	1	-	0	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7517040	7517116	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	intron	7517117	7517615	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	CDS	7517616	7517738	1	-	0	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	exon	7517616	7517738	.	-	.	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
Phchi.S3	AUGUSTUS	start_codon	7517736	7517738	.	-	0	transcript_id "Phchi.S3G088300.t2"; gene_id "Phchi.S3G088300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9190.t1 is derived from g6365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40271739	40272809	.	-	.	Phchi.S1G634900
Phchi.S1	AUGUSTUS	transcript	40271739	40272809	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	stop_codon	40271736	40271738	.	-	0	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	CDS	40271739	40271746	1	-	2	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	exon	40271739	40271746	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	intron	40271747	40271895	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	CDS	40271896	40272000	1	-	2	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	exon	40271896	40272000	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	intron	40272001	40272128	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	CDS	40272129	40272275	0.79	-	2	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	exon	40272129	40272275	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	intron	40272276	40272504	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	CDS	40272505	40272522	0.72	-	2	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	exon	40272505	40272522	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	intron	40272523	40272576	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	CDS	40272577	40272635	0.66	-	1	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	exon	40272577	40272635	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	intron	40272636	40272729	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	CDS	40272730	40272809	0.96	-	0	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	exon	40272730	40272809	.	-	.	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
Phchi.S1	AUGUSTUS	start_codon	40272807	40272809	.	-	0	transcript_id "Phchi.S1G634900.t1"; gene_id "Phchi.S1G634900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8950.t1 is derived from g6125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38811076	38812744	.	-	.	Phchi.S1G610900
Phchi.S1	AUGUSTUS	transcript	38811076	38812744	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	stop_codon	38811073	38811075	.	-	0	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	CDS	38811076	38811429	0.94	-	0	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	exon	38811076	38811429	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	intron	38811430	38811518	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	CDS	38811519	38811687	1	-	1	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	exon	38811519	38811687	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	intron	38811688	38811777	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	CDS	38811778	38812028	1	-	0	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	exon	38811778	38812028	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	intron	38812029	38812175	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	CDS	38812176	38812507	0.55	-	2	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	exon	38812176	38812507	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	intron	38812508	38812737	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	CDS	38812738	38812744	0.53	-	0	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	exon	38812738	38812744	.	-	.	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
Phchi.S1	AUGUSTUS	start_codon	38812742	38812744	.	-	0	transcript_id "Phchi.S1G610900.t1"; gene_id "Phchi.S1G610900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3477.t1 is derived from g646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3982597	3983841	.	+	.	Phchi.S1G063600
Phchi.S1	AUGUSTUS	transcript	3982597	3983841	.	+	.	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	start_codon	3982597	3982599	.	+	0	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	CDS	3982597	3982721	0.38	+	0	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	exon	3982597	3982721	.	+	.	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	intron	3982722	3982834	.	+	.	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	CDS	3982835	3983224	0.11	+	1	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	exon	3982835	3983224	.	+	.	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	intron	3983225	3983291	.	+	.	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	CDS	3983292	3983841	0.45	+	1	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	exon	3983292	3983841	.	+	.	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
Phchi.S1	AUGUSTUS	stop_codon	3983842	3983844	.	+	0	transcript_id "Phchi.S1G063600.t1"; gene_id "Phchi.S1G063600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6887.t1 is derived from g4059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25828785	25829715	.	+	.	Phchi.S1G404600
Phchi.S1	AUGUSTUS	transcript	25828785	25829715	.	+	.	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	start_codon	25828785	25828787	.	+	0	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	CDS	25828785	25828871	0.32	+	0	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	exon	25828785	25828871	.	+	.	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	intron	25828872	25828998	.	+	.	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	CDS	25828999	25829715	0.67	+	0	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	exon	25828999	25829715	.	+	.	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
Phchi.S1	AUGUSTUS	stop_codon	25829716	25829718	.	+	0	transcript_id "Phchi.S1G404600.t1"; gene_id "Phchi.S1G404600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg814.t1 is derived from g10596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5702251	5703088	.	+	.	Phchi.S6G077300
Phchi.S6	AUGUSTUS	transcript	5702251	5703088	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	start_codon	5702251	5702253	.	+	0	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	CDS	5702251	5702255	0.64	+	0	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	exon	5702251	5702255	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	intron	5702256	5702541	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	CDS	5702542	5702762	1	+	1	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	exon	5702542	5702762	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	intron	5702763	5702838	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	CDS	5702839	5702943	0.93	+	2	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	exon	5702839	5702943	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	intron	5702944	5703023	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	CDS	5703024	5703088	0.77	+	2	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	exon	5703024	5703088	.	+	.	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
Phchi.S6	AUGUSTUS	stop_codon	5703089	5703091	.	+	0	transcript_id "Phchi.S6G077300.t1"; gene_id "Phchi.S6G077300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg438.t1 is derived from g10220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3086493	3088259	.	-	.	Phchi.S6G039700
Phchi.S6	AUGUSTUS	transcript	3086493	3088259	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	stop_codon	3086490	3086492	.	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3086493	3086675	0.98	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3086493	3086675	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	intron	3086676	3086772	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3086773	3086931	1	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3086773	3086931	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	intron	3086932	3087019	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3087020	3087128	0.91	-	1	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3087020	3087128	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	intron	3087129	3087230	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3087231	3087403	0.84	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3087231	3087403	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	intron	3087404	3087506	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3087507	3087668	0.97	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3087507	3087668	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	intron	3087669	3087750	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3087751	3087845	1	-	2	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3087751	3087845	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	intron	3087846	3087943	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	CDS	3087944	3088259	1	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	exon	3087944	3088259	.	-	.	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
Phchi.S6	AUGUSTUS	start_codon	3088257	3088259	.	-	0	transcript_id "Phchi.S6G039700.t1"; gene_id "Phchi.S6G039700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6944.t1 is derived from g4116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26087029	26089019	.	-	.	Phchi.S1G410300
Phchi.S1	AUGUSTUS	transcript	26087029	26089019	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	stop_codon	26087026	26087028	.	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	CDS	26087029	26087130	1	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	exon	26087029	26087130	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	intron	26087131	26087215	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	CDS	26087216	26087299	1	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	exon	26087216	26087299	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	intron	26087300	26087392	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	CDS	26087393	26087463	1	-	2	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	exon	26087393	26087463	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	intron	26087464	26087555	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	CDS	26087556	26087643	1	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	exon	26087556	26087643	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	intron	26087644	26087730	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	CDS	26087731	26087922	1	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	exon	26087731	26087922	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	intron	26087923	26088023	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	CDS	26088024	26089019	0.99	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	exon	26088024	26089019	.	-	.	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
Phchi.S1	AUGUSTUS	start_codon	26089017	26089019	.	-	0	transcript_id "Phchi.S1G410300.t1"; gene_id "Phchi.S1G410300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5969.t1 is derived from g3140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20143912	20145919	.	+	.	Phchi.S1G312800
Phchi.S1	AUGUSTUS	transcript	20143912	20145919	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	start_codon	20143912	20143914	.	+	0	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	CDS	20143912	20143978	0.56	+	0	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	exon	20143912	20143978	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	intron	20143979	20144099	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	CDS	20144100	20144506	0.98	+	2	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	exon	20144100	20144506	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	intron	20144507	20144603	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	CDS	20144604	20144804	0.5	+	0	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	exon	20144604	20144804	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	intron	20144805	20144881	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	CDS	20144882	20145370	0.56	+	0	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	exon	20144882	20145370	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	intron	20145371	20145469	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	CDS	20145470	20145919	0.98	+	0	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	exon	20145470	20145919	.	+	.	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
Phchi.S1	AUGUSTUS	stop_codon	20145920	20145922	.	+	0	transcript_id "Phchi.S1G312800.t1"; gene_id "Phchi.S1G312800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8074.t1 is derived from g5249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32826769	32828760	.	-	.	Phchi.S1G523300
Phchi.S1	AUGUSTUS	transcript	32826769	32828760	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	stop_codon	32826766	32826768	.	-	0	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	CDS	32826769	32826906	0.86	-	0	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	exon	32826769	32826906	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	intron	32826907	32827021	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	CDS	32827022	32827120	0.97	-	0	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	exon	32827022	32827120	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	intron	32827121	32827227	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	CDS	32827228	32827309	0.86	-	1	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	exon	32827228	32827309	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	intron	32827310	32827386	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	CDS	32827387	32827590	1	-	1	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	exon	32827387	32827590	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	intron	32827591	32827727	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	CDS	32827728	32828050	1	-	0	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	exon	32827728	32828050	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	intron	32828051	32828142	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	CDS	32828143	32828760	1	-	0	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	exon	32828143	32828760	.	-	.	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
Phchi.S1	AUGUSTUS	start_codon	32828758	32828760	.	-	0	transcript_id "Phchi.S1G523300.t1"; gene_id "Phchi.S1G523300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12550.t1 is derived from g8227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34450722	34453664	.	-	.	Phchi.S2G063000
Phchi.S2	AUGUSTUS	transcript	34450722	34453664	.	-	.	transcript_id "Phchi.S2G063000.t1"; gene_id "Phchi.S2G063000"
Phchi.S2	AUGUSTUS	stop_codon	34450719	34450721	.	-	0	transcript_id "Phchi.S2G063000.t1"; gene_id "Phchi.S2G063000"
Phchi.S2	AUGUSTUS	CDS	34450722	34453664	0.77	-	0	transcript_id "Phchi.S2G063000.t1"; gene_id "Phchi.S2G063000"
Phchi.S2	AUGUSTUS	exon	34450722	34453664	.	-	.	transcript_id "Phchi.S2G063000.t1"; gene_id "Phchi.S2G063000"
Phchi.S2	AUGUSTUS	start_codon	34453662	34453664	.	-	0	transcript_id "Phchi.S2G063000.t1"; gene_id "Phchi.S2G063000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11433.t1 is derived from g15483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6359205	6359882	.	+	.	Phchi.S4G101500
Phchi.S4	AUGUSTUS	transcript	6359205	6359882	.	+	.	transcript_id "Phchi.S4G101500.t1"; gene_id "Phchi.S4G101500"
Phchi.S4	AUGUSTUS	start_codon	6359205	6359207	.	+	0	transcript_id "Phchi.S4G101500.t1"; gene_id "Phchi.S4G101500"
Phchi.S4	AUGUSTUS	CDS	6359205	6359882	0.77	+	0	transcript_id "Phchi.S4G101500.t1"; gene_id "Phchi.S4G101500"
Phchi.S4	AUGUSTUS	exon	6359205	6359882	.	+	.	transcript_id "Phchi.S4G101500.t1"; gene_id "Phchi.S4G101500"
Phchi.S4	AUGUSTUS	stop_codon	6359883	6359885	.	+	0	transcript_id "Phchi.S4G101500.t1"; gene_id "Phchi.S4G101500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4846.t1 is derived from g2016.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13080000	13083029	.	-	.	Phchi.S1G200500
Phchi.S1	AUGUSTUS	transcript	13080000	13083029	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	stop_codon	13079997	13079999	.	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13080000	13080239	0.91	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13080000	13080239	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13080240	13080414	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13080415	13080549	1	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13080415	13080549	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13080550	13080735	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13080736	13080825	0.83	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13080736	13080825	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13080826	13081000	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13081001	13081080	0.86	-	2	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13081001	13081080	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13081081	13081201	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13081202	13081331	1	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13081202	13081331	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13081332	13081608	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13081609	13081747	1	-	1	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13081609	13081747	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13081748	13081828	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13081829	13081947	1	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13081829	13081947	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13081948	13082152	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13082153	13082293	1	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13082153	13082293	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13082294	13082407	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13082408	13082569	1	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13082408	13082569	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13082570	13082803	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13082804	13082941	1	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13082804	13082941	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	intron	13082942	13083026	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	CDS	13083027	13083029	0.91	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	exon	13083027	13083029	.	-	.	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
Phchi.S1	AUGUSTUS	start_codon	13083027	13083029	.	-	0	transcript_id "Phchi.S1G200500.t1"; gene_id "Phchi.S1G200500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6824.t1 is derived from g3996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25225786	25227357	.	-	.	Phchi.S1G398300
Phchi.S1	AUGUSTUS	transcript	25225786	25227357	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	stop_codon	25225783	25225785	.	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	CDS	25225786	25226118	1	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	exon	25225786	25226118	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	intron	25226119	25226196	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	CDS	25226197	25226406	1	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	exon	25226197	25226406	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	intron	25226407	25226496	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	CDS	25226497	25226643	1	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	exon	25226497	25226643	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	intron	25226644	25226728	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	CDS	25226729	25227073	1	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	exon	25226729	25227073	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	intron	25227074	25227150	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	CDS	25227151	25227357	1	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	exon	25227151	25227357	.	-	.	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
Phchi.S1	AUGUSTUS	start_codon	25227355	25227357	.	-	0	transcript_id "Phchi.S1G398300.t1"; gene_id "Phchi.S1G398300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8102.t1 is derived from g5277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33058699	33060368	.	+	.	Phchi.S1G526100
Phchi.S1	AUGUSTUS	transcript	33058699	33060368	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	start_codon	33058699	33058701	.	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33058699	33058800	1	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33058699	33058800	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	intron	33058801	33059100	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33059101	33059218	1	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33059101	33059218	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	intron	33059219	33059428	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33059429	33059496	1	+	2	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33059429	33059496	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	intron	33059497	33059613	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33059614	33059673	1	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33059614	33059673	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	intron	33059674	33059781	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33059782	33059940	1	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33059782	33059940	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	intron	33059941	33060058	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33060059	33060205	1	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33060059	33060205	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	intron	33060206	33060302	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	CDS	33060303	33060368	0.98	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	exon	33060303	33060368	.	+	.	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
Phchi.S1	AUGUSTUS	stop_codon	33060369	33060371	.	+	0	transcript_id "Phchi.S1G526100.t1"; gene_id "Phchi.S1G526100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15928.t1 is derived from g14398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22258358	22258651	.	-	.	Phchi.S3G324700
Phchi.S3	AUGUSTUS	transcript	22258358	22258651	.	-	.	transcript_id "Phchi.S3G324700.t1"; gene_id "Phchi.S3G324700"
Phchi.S3	AUGUSTUS	stop_codon	22258355	22258357	.	-	0	transcript_id "Phchi.S3G324700.t1"; gene_id "Phchi.S3G324700"
Phchi.S3	AUGUSTUS	CDS	22258358	22258651	0.34	-	0	transcript_id "Phchi.S3G324700.t1"; gene_id "Phchi.S3G324700"
Phchi.S3	AUGUSTUS	exon	22258358	22258651	.	-	.	transcript_id "Phchi.S3G324700.t1"; gene_id "Phchi.S3G324700"
Phchi.S3	AUGUSTUS	start_codon	22258649	22258651	.	-	0	transcript_id "Phchi.S3G324700.t1"; gene_id "Phchi.S3G324700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4559.t1 is derived from g1729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11115884	11116654	.	-	.	Phchi.S1G171800
Phchi.S1	AUGUSTUS	transcript	11115884	11116654	.	-	.	transcript_id "Phchi.S1G171800.t1"; gene_id "Phchi.S1G171800"
Phchi.S1	AUGUSTUS	stop_codon	11115881	11115883	.	-	0	transcript_id "Phchi.S1G171800.t1"; gene_id "Phchi.S1G171800"
Phchi.S1	AUGUSTUS	CDS	11115884	11116654	0.73	-	0	transcript_id "Phchi.S1G171800.t1"; gene_id "Phchi.S1G171800"
Phchi.S1	AUGUSTUS	exon	11115884	11116654	.	-	.	transcript_id "Phchi.S1G171800.t1"; gene_id "Phchi.S1G171800"
Phchi.S1	AUGUSTUS	start_codon	11116652	11116654	.	-	0	transcript_id "Phchi.S1G171800.t1"; gene_id "Phchi.S1G171800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10862.t1 is derived from g14912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2602092	2603232	.	+	.	Phchi.S4G044400
Phchi.S4	AUGUSTUS	transcript	2602092	2603232	.	+	.	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	start_codon	2602092	2602094	.	+	0	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	CDS	2602092	2602237	1	+	0	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	exon	2602092	2602237	.	+	.	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	intron	2602238	2602583	.	+	.	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	CDS	2602584	2603232	1	+	1	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	exon	2602584	2603232	.	+	.	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
Phchi.S4	AUGUSTUS	stop_codon	2603233	2603235	.	+	0	transcript_id "Phchi.S4G044400.t1"; gene_id "Phchi.S4G044400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8843.t1 is derived from g6018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38249466	38250666	.	+	.	Phchi.S1G600200
Phchi.S1	AUGUSTUS	transcript	38249466	38250666	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	start_codon	38249466	38249468	.	+	0	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38249466	38249692	0.81	+	0	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38249466	38249692	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	intron	38249693	38249785	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38249786	38249820	1	+	1	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38249786	38249820	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	intron	38249821	38249905	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38249906	38249999	1	+	2	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38249906	38249999	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	intron	38250000	38250139	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38250140	38250200	1	+	1	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38250140	38250200	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	intron	38250201	38250304	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38250305	38250350	1	+	0	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38250305	38250350	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	intron	38250351	38250445	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38250446	38250519	1	+	2	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38250446	38250519	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	intron	38250520	38250591	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	CDS	38250592	38250666	1	+	0	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	exon	38250592	38250666	.	+	.	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
Phchi.S1	AUGUSTUS	stop_codon	38250667	38250669	.	+	0	transcript_id "Phchi.S1G600200.t1"; gene_id "Phchi.S1G600200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12934.t1 is derived from g11399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3210281	3213423	.	-	.	Phchi.S3G025300
Phchi.S3	AUGUSTUS	transcript	3210281	3213423	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	stop_codon	3210278	3210280	.	-	0	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3210281	3210517	1	-	0	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3210281	3210517	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	intron	3210518	3210650	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3210651	3211059	0.94	-	1	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3210651	3211059	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	intron	3211060	3211148	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3211149	3211310	1	-	1	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3211149	3211310	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	intron	3211311	3211452	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3211453	3211457	1	-	0	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3211453	3211457	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	intron	3211458	3211648	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3211649	3211842	1	-	2	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3211649	3211842	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	intron	3211843	3211925	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3211926	3212063	1	-	2	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3211926	3212063	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	intron	3212064	3212156	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	CDS	3212157	3213423	0.84	-	0	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	exon	3212157	3213423	.	-	.	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
Phchi.S3	AUGUSTUS	start_codon	3213421	3213423	.	-	0	transcript_id "Phchi.S3G025300.t1"; gene_id "Phchi.S3G025300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10359.t1 is derived from g7535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47335932	47337872	.	-	.	Phchi.S1G751800
Phchi.S1	AUGUSTUS	transcript	47335932	47337872	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	stop_codon	47335929	47335931	.	-	0	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47335932	47336061	1	-	1	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47335932	47336061	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	intron	47336062	47336248	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47336249	47336329	1	-	1	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47336249	47336329	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	intron	47336330	47336494	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47336495	47336707	1	-	1	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47336495	47336707	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	intron	47336708	47336829	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47336830	47336949	1	-	1	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47336830	47336949	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	intron	47336950	47337062	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47337063	47337208	0.96	-	0	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47337063	47337208	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	intron	47337209	47337466	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47337467	47337601	1	-	0	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47337467	47337601	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	intron	47337602	47337842	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	CDS	47337843	47337872	0.91	-	0	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	exon	47337843	47337872	.	-	.	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
Phchi.S1	AUGUSTUS	start_codon	47337870	47337872	.	-	0	transcript_id "Phchi.S1G751800.t1"; gene_id "Phchi.S1G751800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3448.t1 is derived from g617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3797761	3799858	.	-	.	Phchi.S1G060700
Phchi.S1	AUGUSTUS	transcript	3797761	3799858	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	stop_codon	3797758	3797760	.	-	0	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	CDS	3797761	3798186	0.94	-	0	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	exon	3797761	3798186	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	intron	3798187	3798281	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	CDS	3798282	3798678	1	-	1	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	exon	3798282	3798678	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	intron	3798679	3798800	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	CDS	3798801	3799072	1	-	0	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	exon	3798801	3799072	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	intron	3799073	3799191	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	CDS	3799192	3799451	0.71	-	2	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	exon	3799192	3799451	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	intron	3799452	3799539	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	CDS	3799540	3799858	0.84	-	0	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	exon	3799540	3799858	.	-	.	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
Phchi.S1	AUGUSTUS	start_codon	3799856	3799858	.	-	0	transcript_id "Phchi.S1G060700.t1"; gene_id "Phchi.S1G060700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10619.t1 is derived from g14669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1270545	1270879	.	+	.	Phchi.S4G020100
Phchi.S4	AUGUSTUS	transcript	1270545	1270879	.	+	.	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	start_codon	1270545	1270547	.	+	0	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	CDS	1270545	1270584	0.53	+	0	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	exon	1270545	1270584	.	+	.	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	intron	1270585	1270712	.	+	.	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	CDS	1270713	1270879	0.95	+	2	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	exon	1270713	1270879	.	+	.	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
Phchi.S4	AUGUSTUS	stop_codon	1270880	1270882	.	+	0	transcript_id "Phchi.S4G020100.t1"; gene_id "Phchi.S4G020100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6937.t1 is derived from g4109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26062770	26067096	.	-	.	Phchi.S1G409600
Phchi.S1	AUGUSTUS	transcript	26062770	26067096	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	stop_codon	26062767	26062769	.	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26062770	26062941	0.53	-	1	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26062770	26062941	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26062942	26063263	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26063264	26063422	0.42	-	1	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26063264	26063422	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26063423	26063508	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26063509	26063593	0.48	-	2	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26063509	26063593	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26063594	26063872	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26063873	26064020	0.48	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26063873	26064020	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26064021	26064135	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26064136	26064181	1	-	1	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26064136	26064181	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26064182	26064337	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26064338	26064420	0.96	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26064338	26064420	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26064421	26064534	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26064535	26064614	0.96	-	2	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26064535	26064614	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26064615	26064707	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26064708	26064816	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26064708	26064816	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26064817	26064904	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26064905	26064973	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26064905	26064973	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26064974	26065050	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26065051	26065101	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26065051	26065101	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26065102	26065221	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26065222	26065347	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26065222	26065347	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26065348	26065442	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26065443	26065566	1	-	1	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26065443	26065566	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26065567	26065711	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26065712	26065767	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26065712	26065767	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26065768	26065892	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26065893	26065957	1	-	2	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26065893	26065957	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26065958	26066174	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26066175	26066250	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26066175	26066250	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26066251	26066394	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26066395	26066498	1	-	2	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26066395	26066498	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26066499	26066572	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26066573	26066693	1	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26066573	26066693	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	intron	26066694	26066850	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	CDS	26066851	26067096	0.66	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	exon	26066851	26067096	.	-	.	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
Phchi.S1	AUGUSTUS	start_codon	26067094	26067096	.	-	0	transcript_id "Phchi.S1G409600.t1"; gene_id "Phchi.S1G409600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10903.t1 is derived from g14953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2818036	2827086	.	-	.	Phchi.S4G048500
Phchi.S4	AUGUSTUS	transcript	2818036	2827086	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	stop_codon	2818033	2818035	.	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818036	2818037	1	-	2	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818036	2818037	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818038	2818182	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818183	2818300	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818183	2818300	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818301	2818490	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818491	2818554	1	-	1	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818491	2818554	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818555	2818684	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818685	2818814	1	-	2	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818685	2818814	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818815	2818914	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818915	2819390	1	-	1	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818915	2819390	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2819391	2819530	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2819531	2819766	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2819531	2819766	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2819767	2819881	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2819882	2820062	1	-	1	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2819882	2820062	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2820063	2820330	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2820331	2820740	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2820331	2820740	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2820741	2820824	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2820825	2821017	1	-	1	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2820825	2821017	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2821018	2821131	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2821132	2821289	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2821132	2821289	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2821290	2821930	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2821931	2822086	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2821931	2822086	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2822087	2822185	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2822186	2822764	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2822186	2822764	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2822765	2822953	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2822954	2823520	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2822954	2823520	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823521	2823600	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2823601	2823816	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2823601	2823816	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823817	2823891	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2823892	2823993	0.69	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2823892	2823993	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823994	2824136	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2824137	2825998	0.6	-	2	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2824137	2825998	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2825999	2826177	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826178	2826389	1	-	1	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826178	2826389	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2826390	2826584	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826585	2826625	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826585	2826625	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2826626	2826711	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826712	2826831	1	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826712	2826831	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2826832	2826915	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826916	2827086	0.82	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826916	2827086	.	-	.	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	start_codon	2827084	2827086	.	-	0	transcript_id "Phchi.S4G048500.t1"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	transcript	2818036	2827086	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	stop_codon	2818033	2818035	.	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818036	2818037	1	-	2	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818036	2818037	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818038	2818182	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818183	2818300	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818183	2818300	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818301	2818490	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818491	2818554	1	-	1	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818491	2818554	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818555	2818684	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818685	2818814	1	-	2	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818685	2818814	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2818815	2818914	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2818915	2819390	0.97	-	1	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2818915	2819390	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2819391	2819530	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2819531	2819766	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2819531	2819766	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2819767	2819881	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2819882	2820062	1	-	1	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2819882	2820062	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2820063	2820330	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2820331	2820740	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2820331	2820740	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2820741	2820824	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2820825	2821017	1	-	1	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2820825	2821017	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2821018	2821131	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2821132	2821289	0.99	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2821132	2821289	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2821290	2821930	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2821931	2822086	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2821931	2822086	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2822087	2822185	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2822186	2822764	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2822186	2822764	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2822765	2822953	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2822954	2823456	0.76	-	2	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2822954	2823456	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823457	2823600	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2823601	2823640	0.76	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2823601	2823640	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823641	2823717	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2823718	2823816	0.73	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2823718	2823816	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823817	2823891	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2823892	2823993	0.72	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2823892	2823993	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2823994	2824136	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2824137	2825998	0.57	-	2	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2824137	2825998	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2825999	2826177	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826178	2826389	1	-	1	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826178	2826389	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2826390	2826584	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826585	2826625	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826585	2826625	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2826626	2826711	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826712	2826831	1	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826712	2826831	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	intron	2826832	2826915	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	CDS	2826916	2827086	0.79	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	exon	2826916	2827086	.	-	.	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
Phchi.S4	AUGUSTUS	start_codon	2827084	2827086	.	-	0	transcript_id "Phchi.S4G048500.t2"; gene_id "Phchi.S4G048500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6570.t1 is derived from g3742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23755979	23759630	.	+	.	Phchi.S1G372900
Phchi.S1	AUGUSTUS	transcript	23755979	23759630	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	start_codon	23755979	23755981	.	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23755979	23756204	0.94	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23755979	23756204	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23756205	23756305	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23756306	23756448	1	+	2	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23756306	23756448	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23756449	23756585	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23756586	23756723	1	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23756586	23756723	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23756724	23756826	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23756827	23756937	1	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23756827	23756937	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23756938	23757037	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23757038	23757304	1	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23757038	23757304	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23757305	23757438	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23757439	23757644	1	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23757439	23757644	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23757645	23757735	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23757736	23758063	1	+	1	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23757736	23758063	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23758064	23758221	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23758222	23758338	1	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23758222	23758338	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23758339	23758435	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23758436	23758612	1	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23758436	23758612	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23758613	23758707	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23758708	23758826	0.78	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23758708	23758826	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23758827	23758951	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23758952	23759243	0.52	+	1	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23758952	23759243	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	intron	23759244	23759324	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	CDS	23759325	23759630	0.99	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	exon	23759325	23759630	.	+	.	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
Phchi.S1	AUGUSTUS	stop_codon	23759631	23759633	.	+	0	transcript_id "Phchi.S1G372900.t1"; gene_id "Phchi.S1G372900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15594.t1 is derived from g14063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20170200	20171491	.	-	.	Phchi.S3G291300
Phchi.S3	AUGUSTUS	transcript	20170200	20171491	.	-	.	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	stop_codon	20170197	20170199	.	-	0	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	CDS	20170200	20170839	1	-	1	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	exon	20170200	20170839	.	-	.	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	intron	20170840	20171066	.	-	.	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	CDS	20171067	20171491	0.88	-	0	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	exon	20171067	20171491	.	-	.	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
Phchi.S3	AUGUSTUS	start_codon	20171489	20171491	.	-	0	transcript_id "Phchi.S3G291300.t1"; gene_id "Phchi.S3G291300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15792.t1 is derived from g14262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21360746	21367019	.	-	.	Phchi.S3G311100
Phchi.S3	AUGUSTUS	transcript	21360746	21367019	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	stop_codon	21360743	21360745	.	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21360746	21361261	0.54	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21360746	21361261	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21361262	21361373	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21361374	21361496	1	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21361374	21361496	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21361497	21361613	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21361614	21361687	1	-	2	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21361614	21361687	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21361688	21361789	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21361790	21362117	1	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21361790	21362117	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21362118	21362208	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21362209	21362388	1	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21362209	21362388	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21362389	21362584	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21362585	21363586	0.43	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21362585	21363586	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21363587	21363738	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21363739	21364602	0.69	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21363739	21364602	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21364603	21364698	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21364699	21365108	1	-	2	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21364699	21365108	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	intron	21365109	21365716	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	CDS	21365717	21367019	0.41	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	exon	21365717	21367019	.	-	.	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
Phchi.S3	AUGUSTUS	start_codon	21367017	21367019	.	-	0	transcript_id "Phchi.S3G311100.t1"; gene_id "Phchi.S3G311100"
# This transcript jg12465.t2 is derived from g8142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12466.t1 is derived from g8143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	25422100	25427342	.	+	.	Phchi.S2G054600
Phchi.S2	AUGUSTUS	transcript	25423066	25427342	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	start_codon	25423066	25423068	.	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25423066	25423086	0.66	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25423066	25423086	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25423087	25423235	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25423236	25423472	1	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25423236	25423472	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25423473	25423613	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25423614	25423780	1	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25423614	25423780	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25423781	25424028	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424029	25424238	0.99	+	1	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424029	25424238	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25424239	25424319	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424320	25424506	1	+	1	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424320	25424506	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25424507	25424670	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424671	25424722	1	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424671	25424722	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25424723	25424843	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424844	25425073	1	+	2	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424844	25425073	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25425074	25425304	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25425305	25425403	1	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25425305	25425403	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25425404	25425591	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25425592	25425648	0.6	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25425592	25425648	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25425649	25425854	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25425855	25426297	0.57	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25425855	25426297	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25426298	25426457	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25426458	25426958	0.99	+	1	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25426458	25426958	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25426959	25427095	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25427096	25427342	1	+	1	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25427096	25427342	.	+	.	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	stop_codon	25427343	25427345	.	+	0	transcript_id "Phchi.S2G054600.t1"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	transcript	25422100	25427342	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	start_codon	25422100	25422102	.	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25422100	25422130	0.73	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25422100	25422130	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25422131	25422538	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25422539	25422607	0.61	+	2	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25422539	25422607	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25422608	25422798	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25422799	25423001	0.73	+	2	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25422799	25423001	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25423002	25423235	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25423236	25423472	1	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25423236	25423472	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25423473	25423613	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25423614	25423780	1	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25423614	25423780	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25423781	25424028	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424029	25424238	0.99	+	1	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424029	25424238	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25424239	25424319	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424320	25424506	1	+	1	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424320	25424506	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25424507	25424670	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424671	25424722	1	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424671	25424722	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25424723	25424843	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25424844	25425073	1	+	2	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25424844	25425073	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25425074	25425304	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25425305	25425403	1	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25425305	25425403	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25425404	25425591	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25425592	25425648	0.46	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25425592	25425648	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25425649	25425854	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25425855	25426297	0.5	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25425855	25426297	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25426298	25426457	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25426458	25426958	0.99	+	1	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25426458	25426958	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	intron	25426959	25427095	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	CDS	25427096	25427342	1	+	1	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	exon	25427096	25427342	.	+	.	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
Phchi.S2	AUGUSTUS	stop_codon	25427343	25427345	.	+	0	transcript_id "Phchi.S2G054600.t2"; gene_id "Phchi.S2G054600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2993.t1 is derived from g162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1046066	1047047	.	+	.	Phchi.S1G015200
Phchi.S1	AUGUSTUS	transcript	1046066	1047047	.	+	.	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	start_codon	1046066	1046068	.	+	0	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	CDS	1046066	1046662	0.96	+	0	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	exon	1046066	1046662	.	+	.	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	intron	1046663	1046777	.	+	.	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	CDS	1046778	1047047	0.67	+	0	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	exon	1046778	1047047	.	+	.	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
Phchi.S1	AUGUSTUS	stop_codon	1047048	1047050	.	+	0	transcript_id "Phchi.S1G015200.t1"; gene_id "Phchi.S1G015200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg618.t1 is derived from g10400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4439303	4441619	.	-	.	Phchi.S6G057700
Phchi.S6	AUGUSTUS	transcript	4439303	4441619	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	stop_codon	4439300	4439302	.	-	0	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	CDS	4439303	4439720	1	-	1	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	exon	4439303	4439720	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	intron	4439721	4439797	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	CDS	4439798	4439869	1	-	1	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	exon	4439798	4439869	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	intron	4439870	4439978	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	CDS	4439979	4440058	1	-	0	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	exon	4439979	4440058	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	intron	4440059	4440135	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	CDS	4440136	4441095	0.96	-	0	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	exon	4440136	4441095	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	intron	4441096	4441187	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	CDS	4441188	4441475	0.57	-	0	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	exon	4441188	4441475	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	intron	4441476	4441577	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	CDS	4441578	4441619	0.56	-	0	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	exon	4441578	4441619	.	-	.	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
Phchi.S6	AUGUSTUS	start_codon	4441617	4441619	.	-	0	transcript_id "Phchi.S6G057700.t1"; gene_id "Phchi.S6G057700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6348.t1 is derived from g3520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22438352	22439661	.	+	.	Phchi.S1G350700
Phchi.S1	AUGUSTUS	transcript	22438352	22439661	.	+	.	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	start_codon	22438352	22438354	.	+	0	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	CDS	22438352	22439425	0.71	+	0	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	exon	22438352	22439425	.	+	.	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	intron	22439426	22439529	.	+	.	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	CDS	22439530	22439661	0.91	+	0	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	exon	22439530	22439661	.	+	.	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
Phchi.S1	AUGUSTUS	stop_codon	22439662	22439664	.	+	0	transcript_id "Phchi.S1G350700.t1"; gene_id "Phchi.S1G350700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7104.t1 is derived from g4276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26962481	26964248	.	+	.	Phchi.S1G426300
Phchi.S1	AUGUSTUS	transcript	26962481	26964248	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	start_codon	26962481	26962483	.	+	0	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26962481	26962553	0.98	+	0	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26962481	26962553	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26962554	26962669	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26962670	26962781	0.44	+	2	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26962670	26962781	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26962782	26962869	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26962870	26963010	0.27	+	1	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26962870	26963010	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26963011	26963158	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26963159	26963227	1	+	1	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26963159	26963227	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26963228	26963445	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26963446	26963583	1	+	1	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26963446	26963583	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26963584	26964118	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26964119	26964248	0.98	+	1	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26964119	26964248	.	+	.	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	stop_codon	26964249	26964251	.	+	0	transcript_id "Phchi.S1G426300.t1"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	transcript	26962481	26963865	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	start_codon	26962481	26962483	.	+	0	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26962481	26962553	0.98	+	0	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26962481	26962553	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26962554	26962669	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26962670	26962781	0.42	+	2	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26962670	26962781	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26962782	26962869	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26962870	26963010	0.3	+	1	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26962870	26963010	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26963011	26963158	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26963159	26963227	1	+	1	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26963159	26963227	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26963228	26963445	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26963446	26963583	1	+	1	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26963446	26963583	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	intron	26963584	26963675	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	CDS	26963676	26963865	0.92	+	1	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	exon	26963676	26963865	.	+	.	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
Phchi.S1	AUGUSTUS	stop_codon	26963866	26963868	.	+	0	transcript_id "Phchi.S1G426300.t2"; gene_id "Phchi.S1G426300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13968.t1 is derived from g12435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9980253	9980558	.	+	.	Phchi.S3G128700
Phchi.S3	AUGUSTUS	transcript	9980253	9980558	.	+	.	transcript_id "Phchi.S3G128700.t1"; gene_id "Phchi.S3G128700"
Phchi.S3	AUGUSTUS	start_codon	9980253	9980255	.	+	0	transcript_id "Phchi.S3G128700.t1"; gene_id "Phchi.S3G128700"
Phchi.S3	AUGUSTUS	CDS	9980253	9980558	0.99	+	0	transcript_id "Phchi.S3G128700.t1"; gene_id "Phchi.S3G128700"
Phchi.S3	AUGUSTUS	exon	9980253	9980558	.	+	.	transcript_id "Phchi.S3G128700.t1"; gene_id "Phchi.S3G128700"
Phchi.S3	AUGUSTUS	stop_codon	9980559	9980561	.	+	0	transcript_id "Phchi.S3G128700.t1"; gene_id "Phchi.S3G128700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15345.t1 is derived from g13813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18482271	18483154	.	-	.	Phchi.S3G266400
Phchi.S3	AUGUSTUS	transcript	18482271	18483154	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	stop_codon	18482268	18482270	.	-	0	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	CDS	18482271	18482387	0.44	-	0	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	exon	18482271	18482387	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	intron	18482388	18482508	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	CDS	18482509	18482795	0.94	-	2	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	exon	18482509	18482795	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	intron	18482796	18482874	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	CDS	18482875	18483016	1	-	0	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	exon	18482875	18483016	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	intron	18483017	18483100	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	CDS	18483101	18483154	0.77	-	0	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	exon	18483101	18483154	.	-	.	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
Phchi.S3	AUGUSTUS	start_codon	18483152	18483154	.	-	0	transcript_id "Phchi.S3G266400.t1"; gene_id "Phchi.S3G266400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11247.t1 is derived from g15297.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4991465	4994123	.	-	.	Phchi.S4G082900
Phchi.S4	AUGUSTUS	transcript	4991465	4994123	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	stop_codon	4991462	4991464	.	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4991465	4991602	0.98	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4991465	4991602	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4991603	4991693	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4991694	4991847	0.86	-	1	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4991694	4991847	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4991848	4991932	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4991933	4991942	0.86	-	2	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4991933	4991942	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4991943	4992096	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992097	4992140	0.86	-	1	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992097	4992140	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992141	4992268	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992269	4992320	1	-	2	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992269	4992320	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992321	4992409	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992410	4992423	0.67	-	1	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992410	4992423	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992424	4992503	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992504	4992640	0.65	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992504	4992640	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992641	4992711	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992712	4992853	1	-	1	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992712	4992853	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992854	4992973	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992974	4993080	1	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992974	4993080	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993081	4993295	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4993296	4993394	1	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4993296	4993394	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993395	4993486	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4993487	4993665	0.77	-	2	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4993487	4993665	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993666	4993773	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4993774	4993885	1	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4993774	4993885	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993886	4994015	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4994016	4994123	1	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4994016	4994123	.	-	.	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	start_codon	4994121	4994123	.	-	0	transcript_id "Phchi.S4G082900.t1"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	transcript	4992627	4994123	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	stop_codon	4992624	4992626	.	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992627	4992632	0.38	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992627	4992632	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992633	4992711	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992712	4992853	0.93	-	1	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992712	4992853	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4992854	4992973	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4992974	4993080	1	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4992974	4993080	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993081	4993295	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4993296	4993394	1	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4993296	4993394	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993395	4993486	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4993487	4993665	0.88	-	2	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4993487	4993665	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993666	4993773	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4993774	4993885	1	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4993774	4993885	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	intron	4993886	4994015	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	CDS	4994016	4994123	1	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	exon	4994016	4994123	.	-	.	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
Phchi.S4	AUGUSTUS	start_codon	4994121	4994123	.	-	0	transcript_id "Phchi.S4G082900.t2"; gene_id "Phchi.S4G082900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4079.t1 is derived from g1248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7668531	7668875	.	-	.	Phchi.S1G123800
Phchi.S1	AUGUSTUS	transcript	7668531	7668875	.	-	.	transcript_id "Phchi.S1G123800.t1"; gene_id "Phchi.S1G123800"
Phchi.S1	AUGUSTUS	stop_codon	7668528	7668530	.	-	0	transcript_id "Phchi.S1G123800.t1"; gene_id "Phchi.S1G123800"
Phchi.S1	AUGUSTUS	CDS	7668531	7668875	0.74	-	0	transcript_id "Phchi.S1G123800.t1"; gene_id "Phchi.S1G123800"
Phchi.S1	AUGUSTUS	exon	7668531	7668875	.	-	.	transcript_id "Phchi.S1G123800.t1"; gene_id "Phchi.S1G123800"
Phchi.S1	AUGUSTUS	start_codon	7668873	7668875	.	-	0	transcript_id "Phchi.S1G123800.t1"; gene_id "Phchi.S1G123800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1014.t1 is derived from g10797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7121688	7122672	.	+	.	Phchi.S6G097300
Phchi.S6	AUGUSTUS	transcript	7121688	7122672	.	+	.	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	start_codon	7121688	7121690	.	+	0	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	CDS	7121688	7121947	0.71	+	0	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	exon	7121688	7121947	.	+	.	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	intron	7121948	7122398	.	+	.	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	CDS	7122399	7122672	0.85	+	1	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	exon	7122399	7122672	.	+	.	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
Phchi.S6	AUGUSTUS	stop_codon	7122673	7122675	.	+	0	transcript_id "Phchi.S6G097300.t1"; gene_id "Phchi.S6G097300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8136.t1 is derived from g5311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33816621	33820380	.	-	.	Phchi.S1G529500
Phchi.S1	AUGUSTUS	transcript	33816621	33820380	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	stop_codon	33816618	33816620	.	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33816621	33816882	0.72	-	1	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33816621	33816882	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33816883	33817023	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33817024	33817486	0.79	-	2	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33817024	33817486	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33817487	33817627	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33817628	33817712	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33817628	33817712	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33817713	33817800	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33817801	33817817	1	-	2	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33817801	33817817	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33817818	33817882	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33817883	33817949	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33817883	33817949	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33817950	33818087	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33818088	33818165	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33818088	33818165	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33818166	33818313	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33818314	33818433	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33818314	33818433	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33818434	33818525	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33818526	33818597	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33818526	33818597	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33818598	33818775	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33818776	33818905	1	-	1	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33818776	33818905	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33818906	33819063	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33819064	33819137	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33819064	33819137	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33819138	33819270	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33819271	33819339	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33819271	33819339	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33819340	33819426	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33819427	33819504	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33819427	33819504	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33819505	33819587	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33819588	33819661	1	-	2	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33819588	33819661	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33819662	33819740	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33819741	33819826	1	-	1	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33819741	33819826	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33819827	33819912	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33819913	33820030	1	-	2	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33819913	33820030	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33820031	33820115	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33820116	33820229	1	-	2	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33820116	33820229	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	intron	33820230	33820316	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	CDS	33820317	33820380	1	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	exon	33820317	33820380	.	-	.	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
Phchi.S1	AUGUSTUS	start_codon	33820378	33820380	.	-	0	transcript_id "Phchi.S1G529500.t1"; gene_id "Phchi.S1G529500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14451.t1 is derived from g12919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12902564	12907060	.	-	.	Phchi.S3G177000
Phchi.S3	AUGUSTUS	transcript	12902564	12907060	.	-	.	transcript_id "Phchi.S3G177000.t1"; gene_id "Phchi.S3G177000"
Phchi.S3	AUGUSTUS	stop_codon	12902561	12902563	.	-	0	transcript_id "Phchi.S3G177000.t1"; gene_id "Phchi.S3G177000"
Phchi.S3	AUGUSTUS	CDS	12902564	12907060	0.41	-	0	transcript_id "Phchi.S3G177000.t1"; gene_id "Phchi.S3G177000"
Phchi.S3	AUGUSTUS	exon	12902564	12907060	.	-	.	transcript_id "Phchi.S3G177000.t1"; gene_id "Phchi.S3G177000"
Phchi.S3	AUGUSTUS	start_codon	12907058	12907060	.	-	0	transcript_id "Phchi.S3G177000.t1"; gene_id "Phchi.S3G177000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1476.t1 is derived from g8395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1112766	1115564	.	-	.	Phchi.S5G008500
Phchi.S5	AUGUSTUS	transcript	1112766	1115564	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	stop_codon	1112763	1112765	.	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1112766	1112861	0.85	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1112766	1112861	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1112862	1112942	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1112943	1113016	1	-	2	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1112943	1113016	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113017	1113110	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113111	1113170	1	-	2	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113111	1113170	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113171	1113268	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113269	1113312	1	-	1	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113269	1113312	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113313	1113471	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113472	1113566	0.89	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113472	1113566	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113567	1113700	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113701	1113805	1	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113701	1113805	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113806	1113979	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113980	1114089	1	-	2	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113980	1114089	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114090	1114247	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1114248	1114374	1	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1114248	1114374	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114375	1114487	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1114488	1114616	0.97	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1114488	1114616	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114617	1114796	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1114797	1114913	1	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1114797	1114913	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114914	1115010	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1115011	1115214	0.92	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1115011	1115214	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1115215	1115315	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1115316	1115410	0.87	-	2	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1115316	1115410	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1115411	1115506	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1115507	1115564	1	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1115507	1115564	.	-	.	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	start_codon	1115562	1115564	.	-	0	transcript_id "Phchi.S5G008500.t1"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	transcript	1112766	1115564	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	stop_codon	1112763	1112765	.	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1112766	1112861	0.83	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1112766	1112861	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1112862	1112942	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1112943	1113016	1	-	2	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1112943	1113016	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113017	1113110	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113111	1113170	1	-	2	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113111	1113170	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113171	1113268	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113269	1113312	1	-	1	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113269	1113312	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113313	1113471	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113472	1113566	0.93	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113472	1113566	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113567	1113700	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113701	1113805	1	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113701	1113805	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1113806	1113979	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1113980	1114092	1	-	2	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1113980	1114092	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114093	1114247	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1114248	1114374	0.99	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1114248	1114374	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114375	1114487	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1114488	1114616	0.99	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1114488	1114616	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114617	1114796	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1114797	1114913	1	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1114797	1114913	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1114914	1115010	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1115011	1115214	0.86	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1115011	1115214	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1115215	1115315	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1115316	1115410	0.84	-	2	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1115316	1115410	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	intron	1115411	1115506	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	CDS	1115507	1115564	1	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	exon	1115507	1115564	.	-	.	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
Phchi.S5	AUGUSTUS	start_codon	1115562	1115564	.	-	0	transcript_id "Phchi.S5G008500.t2"; gene_id "Phchi.S5G008500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10057.t1 is derived from g7233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45566731	45569492	.	-	.	Phchi.S1G721600
Phchi.S1	AUGUSTUS	transcript	45566731	45569492	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	stop_codon	45566728	45566730	.	-	0	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45566731	45566995	0.99	-	1	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45566731	45566995	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45566996	45567245	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45567246	45567285	0.99	-	2	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45567246	45567285	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45567286	45567537	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45567538	45567748	0.97	-	0	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45567538	45567748	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45567749	45567839	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45567840	45567898	0.97	-	2	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45567840	45567898	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45567899	45567969	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45567970	45568078	0.98	-	0	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45567970	45568078	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45568079	45568185	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45568186	45568374	1	-	0	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45568186	45568374	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45568375	45568477	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45568478	45569241	0.48	-	2	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45568478	45569241	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45569242	45569368	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45569369	45569492	0.51	-	0	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45569369	45569492	.	-	.	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	start_codon	45569490	45569492	.	-	0	transcript_id "Phchi.S1G721600.t1"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	transcript	45568594	45569492	.	-	.	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	stop_codon	45568591	45568593	.	-	0	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45568594	45568683	0.92	-	0	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45568594	45568683	.	-	.	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45568684	45568828	.	-	.	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45568829	45569241	0.42	-	2	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45568829	45569241	.	-	.	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	intron	45569242	45569368	.	-	.	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	CDS	45569369	45569492	0.46	-	0	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	exon	45569369	45569492	.	-	.	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
Phchi.S1	AUGUSTUS	start_codon	45569490	45569492	.	-	0	transcript_id "Phchi.S1G721600.t2"; gene_id "Phchi.S1G721600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15109.t1 is derived from g13577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17115347	17116834	.	+	.	Phchi.S3G242800
Phchi.S3	AUGUSTUS	transcript	17115347	17116834	.	+	.	transcript_id "Phchi.S3G242800.t1"; gene_id "Phchi.S3G242800"
Phchi.S3	AUGUSTUS	start_codon	17115347	17115349	.	+	0	transcript_id "Phchi.S3G242800.t1"; gene_id "Phchi.S3G242800"
Phchi.S3	AUGUSTUS	CDS	17115347	17116834	0.8	+	0	transcript_id "Phchi.S3G242800.t1"; gene_id "Phchi.S3G242800"
Phchi.S3	AUGUSTUS	exon	17115347	17116834	.	+	.	transcript_id "Phchi.S3G242800.t1"; gene_id "Phchi.S3G242800"
Phchi.S3	AUGUSTUS	stop_codon	17116835	17116837	.	+	0	transcript_id "Phchi.S3G242800.t1"; gene_id "Phchi.S3G242800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4989.t1 is derived from g2159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13912376	13914118	.	-	.	Phchi.S1G214800
Phchi.S1	AUGUSTUS	transcript	13912376	13914118	.	-	.	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	stop_codon	13912373	13912375	.	-	0	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	CDS	13912376	13913446	1	-	0	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	exon	13912376	13913446	.	-	.	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	intron	13913447	13913536	.	-	.	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	CDS	13913537	13914118	1	-	0	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	exon	13913537	13914118	.	-	.	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
Phchi.S1	AUGUSTUS	start_codon	13914116	13914118	.	-	0	transcript_id "Phchi.S1G214800.t1"; gene_id "Phchi.S1G214800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4839.t1 is derived from g2009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13054516	13055706	.	-	.	Phchi.S1G199800
Phchi.S1	AUGUSTUS	transcript	13054516	13055706	.	-	.	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	stop_codon	13054513	13054515	.	-	0	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	CDS	13054516	13054664	0.32	-	2	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	exon	13054516	13054664	.	-	.	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	intron	13054665	13054883	.	-	.	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	CDS	13054884	13055430	0.3	-	0	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	exon	13054884	13055430	.	-	.	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	intron	13055431	13055538	.	-	.	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	CDS	13055539	13055706	0.64	-	0	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	exon	13055539	13055706	.	-	.	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
Phchi.S1	AUGUSTUS	start_codon	13055704	13055706	.	-	0	transcript_id "Phchi.S1G199800.t1"; gene_id "Phchi.S1G199800"
# This transcript jg2371.t2 is derived from g9291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2372.t1 is derived from g9292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6395105	6396631	.	-	.	Phchi.S5G098100
Phchi.S5	AUGUSTUS	transcript	6395105	6396631	.	-	.	transcript_id "Phchi.S5G098100.t1"; gene_id "Phchi.S5G098100"
Phchi.S5	AUGUSTUS	stop_codon	6395102	6395104	.	-	0	transcript_id "Phchi.S5G098100.t1"; gene_id "Phchi.S5G098100"
Phchi.S5	AUGUSTUS	CDS	6395105	6396631	0.99	-	0	transcript_id "Phchi.S5G098100.t1"; gene_id "Phchi.S5G098100"
Phchi.S5	AUGUSTUS	exon	6395105	6396631	.	-	.	transcript_id "Phchi.S5G098100.t1"; gene_id "Phchi.S5G098100"
Phchi.S5	AUGUSTUS	start_codon	6396629	6396631	.	-	0	transcript_id "Phchi.S5G098100.t1"; gene_id "Phchi.S5G098100"
# This transcript jg11713.t2 is derived from g15764.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11714.t1 is derived from g15765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7799196	7801469	.	-	.	Phchi.S4G129600
Phchi.S4	AUGUSTUS	transcript	7799196	7801469	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	stop_codon	7799193	7799195	.	-	0	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7799196	7799437	1	-	2	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7799196	7799437	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7799438	7799554	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7799555	7800002	1	-	0	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7799555	7800002	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7800003	7800085	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7800086	7800173	1	-	1	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7800086	7800173	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7800174	7800286	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7800287	7800387	1	-	0	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7800287	7800387	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7800388	7800591	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7800592	7800682	1	-	1	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7800592	7800682	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7800683	7800803	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7800804	7800884	1	-	1	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7800804	7800884	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7800885	7801072	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7801073	7801146	1	-	0	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7801073	7801146	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	intron	7801147	7801238	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	CDS	7801239	7801469	1	-	0	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	exon	7801239	7801469	.	-	.	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
Phchi.S4	AUGUSTUS	start_codon	7801467	7801469	.	-	0	transcript_id "Phchi.S4G129600.t1"; gene_id "Phchi.S4G129600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1998.t1 is derived from g8918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4367607	4370658	.	+	.	Phchi.S5G060700
Phchi.S5	AUGUSTUS	transcript	4367607	4370658	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	start_codon	4367607	4367609	.	+	0	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	CDS	4367607	4370057	0.14	+	0	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	exon	4367607	4370057	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	intron	4370058	4370211	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	CDS	4370212	4370243	0.33	+	0	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	exon	4370212	4370243	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	intron	4370244	4370319	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	CDS	4370320	4370423	0.33	+	1	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	exon	4370320	4370423	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	intron	4370424	4370653	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	CDS	4370654	4370658	0.33	+	2	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	exon	4370654	4370658	.	+	.	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
Phchi.S5	AUGUSTUS	stop_codon	4370659	4370661	.	+	0	transcript_id "Phchi.S5G060700.t1"; gene_id "Phchi.S5G060700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5570.t1 is derived from g2740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17630511	17633009	.	+	.	Phchi.S1G272900
Phchi.S1	AUGUSTUS	transcript	17630511	17633009	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	start_codon	17630511	17630513	.	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17630511	17630821	0.48	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17630511	17630821	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17630822	17630934	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17630935	17631106	1	+	1	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17630935	17631106	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17631107	17631214	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17631215	17631364	0.97	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17631215	17631364	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17631365	17631476	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17631477	17631680	0.98	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17631477	17631680	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17631681	17631966	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17631967	17632117	1	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17631967	17632117	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17632118	17632201	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17632202	17632292	1	+	2	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17632202	17632292	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17632293	17632407	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17632408	17632477	0.86	+	1	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17632408	17632477	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17632478	17632580	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17632581	17632709	1	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17632581	17632709	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17632710	17632797	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17632798	17632836	1	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17632798	17632836	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	intron	17632837	17632922	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	CDS	17632923	17633009	0.99	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	exon	17632923	17633009	.	+	.	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
Phchi.S1	AUGUSTUS	stop_codon	17633010	17633012	.	+	0	transcript_id "Phchi.S1G272900.t1"; gene_id "Phchi.S1G272900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13266.t1 is derived from g11731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4983819	4985007	.	-	.	Phchi.S3G058500
Phchi.S3	AUGUSTUS	transcript	4983819	4985007	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	stop_codon	4983816	4983818	.	-	0	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	CDS	4983819	4983886	1	-	2	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	exon	4983819	4983886	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	intron	4983887	4984089	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	CDS	4984090	4984225	1	-	0	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	exon	4984090	4984225	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	intron	4984226	4984309	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	CDS	4984310	4984674	0.51	-	2	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	exon	4984310	4984674	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	intron	4984675	4984817	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	CDS	4984818	4985007	0.52	-	0	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	exon	4984818	4985007	.	-	.	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
Phchi.S3	AUGUSTUS	start_codon	4985005	4985007	.	-	0	transcript_id "Phchi.S3G058500.t1"; gene_id "Phchi.S3G058500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1572.t1 is derived from g8491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1823622	1825148	.	-	.	Phchi.S5G018100
Phchi.S5	AUGUSTUS	transcript	1823622	1825148	.	-	.	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	stop_codon	1823619	1823621	.	-	0	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	CDS	1823622	1824048	1	-	1	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	exon	1823622	1824048	.	-	.	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	intron	1824049	1824249	.	-	.	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	CDS	1824250	1825148	1	-	0	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	exon	1824250	1825148	.	-	.	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
Phchi.S5	AUGUSTUS	start_codon	1825146	1825148	.	-	0	transcript_id "Phchi.S5G018100.t1"; gene_id "Phchi.S5G018100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2608.t1 is derived from g9528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7776011	7776448	.	+	.	Phchi.S5G121700
Phchi.S5	AUGUSTUS	transcript	7776011	7776448	.	+	.	transcript_id "Phchi.S5G121700.t1"; gene_id "Phchi.S5G121700"
Phchi.S5	AUGUSTUS	start_codon	7776011	7776013	.	+	0	transcript_id "Phchi.S5G121700.t1"; gene_id "Phchi.S5G121700"
Phchi.S5	AUGUSTUS	CDS	7776011	7776448	0.64	+	0	transcript_id "Phchi.S5G121700.t1"; gene_id "Phchi.S5G121700"
Phchi.S5	AUGUSTUS	exon	7776011	7776448	.	+	.	transcript_id "Phchi.S5G121700.t1"; gene_id "Phchi.S5G121700"
Phchi.S5	AUGUSTUS	stop_codon	7776449	7776451	.	+	0	transcript_id "Phchi.S5G121700.t1"; gene_id "Phchi.S5G121700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15034.t1 is derived from g13502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16641341	16643617	.	-	.	Phchi.S3G235300
Phchi.S3	AUGUSTUS	transcript	16641341	16643617	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	stop_codon	16641338	16641340	.	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16641341	16641353	1	-	1	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16641341	16641353	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16641354	16641440	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16641441	16641499	1	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16641441	16641499	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16641500	16641585	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16641586	16641688	1	-	1	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16641586	16641688	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16641689	16641782	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16641783	16641862	1	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16641783	16641862	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16641863	16641944	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16641945	16642027	1	-	2	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16641945	16642027	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16642028	16642110	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16642111	16642159	1	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16642111	16642159	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16642160	16642301	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16642302	16642367	1	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16642302	16642367	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16642368	16642490	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16642491	16642665	1	-	1	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16642491	16642665	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16642666	16642776	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16642777	16642810	1	-	2	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16642777	16642810	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16642811	16642921	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16642922	16643022	1	-	1	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16642922	16643022	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16643023	16643346	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16643347	16643378	1	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16643347	16643378	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	intron	16643379	16643596	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	CDS	16643597	16643617	0.75	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	exon	16643597	16643617	.	-	.	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
Phchi.S3	AUGUSTUS	start_codon	16643615	16643617	.	-	0	transcript_id "Phchi.S3G235300.t1"; gene_id "Phchi.S3G235300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12374.t1 is derived from g8050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14072382	14072838	.	+	.	Phchi.S2G045400
Phchi.S2	AUGUSTUS	transcript	14072382	14072838	.	+	.	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	start_codon	14072382	14072384	.	+	0	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	CDS	14072382	14072528	0.78	+	0	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	exon	14072382	14072528	.	+	.	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	intron	14072529	14072668	.	+	.	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	CDS	14072669	14072736	0.88	+	0	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	exon	14072669	14072736	.	+	.	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	intron	14072737	14072834	.	+	.	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	CDS	14072835	14072838	0.88	+	1	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	exon	14072835	14072838	.	+	.	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
Phchi.S2	AUGUSTUS	stop_codon	14072839	14072841	.	+	0	transcript_id "Phchi.S2G045400.t1"; gene_id "Phchi.S2G045400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11973.t1 is derived from g7648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	253717	256370	.	+	.	Phchi.S2G005300
Phchi.S2	AUGUSTUS	transcript	253717	256370	.	+	.	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	start_codon	253717	253719	.	+	0	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	CDS	253717	254008	0.93	+	0	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	exon	253717	254008	.	+	.	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	intron	254009	254244	.	+	.	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	CDS	254245	256370	0.98	+	2	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	exon	254245	256370	.	+	.	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
Phchi.S2	AUGUSTUS	stop_codon	256371	256373	.	+	0	transcript_id "Phchi.S2G005300.t1"; gene_id "Phchi.S2G005300"
# This transcript jg15064.t2 is derived from g13532.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15065.t1 is derived from g13533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16843845	16844720	.	+	.	Phchi.S3G238400
Phchi.S3	AUGUSTUS	transcript	16843845	16844720	.	+	.	transcript_id "Phchi.S3G238400.t1"; gene_id "Phchi.S3G238400"
Phchi.S3	AUGUSTUS	start_codon	16843845	16843847	.	+	0	transcript_id "Phchi.S3G238400.t1"; gene_id "Phchi.S3G238400"
Phchi.S3	AUGUSTUS	CDS	16843845	16844720	0.98	+	0	transcript_id "Phchi.S3G238400.t1"; gene_id "Phchi.S3G238400"
Phchi.S3	AUGUSTUS	exon	16843845	16844720	.	+	.	transcript_id "Phchi.S3G238400.t1"; gene_id "Phchi.S3G238400"
Phchi.S3	AUGUSTUS	stop_codon	16844721	16844723	.	+	0	transcript_id "Phchi.S3G238400.t1"; gene_id "Phchi.S3G238400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2338.t1 is derived from g9258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6225824	6227407	.	-	.	Phchi.S5G094700
Phchi.S5	AUGUSTUS	transcript	6225824	6227407	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	stop_codon	6225821	6225823	.	-	0	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	CDS	6225824	6225985	0.99	-	0	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	exon	6225824	6225985	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	intron	6225986	6226081	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	CDS	6226082	6226384	0.61	-	0	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	exon	6226082	6226384	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	intron	6226385	6226473	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	CDS	6226474	6226479	0.61	-	0	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	exon	6226474	6226479	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	intron	6226480	6226554	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	CDS	6226555	6226855	1	-	1	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	exon	6226555	6226855	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	intron	6226856	6226940	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	CDS	6226941	6227407	0.59	-	0	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	exon	6226941	6227407	.	-	.	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
Phchi.S5	AUGUSTUS	start_codon	6227405	6227407	.	-	0	transcript_id "Phchi.S5G094700.t1"; gene_id "Phchi.S5G094700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14971.t1 is derived from g13439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15796088	15799104	.	+	.	Phchi.S3G229000
Phchi.S3	AUGUSTUS	transcript	15796088	15799104	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	start_codon	15796088	15796090	.	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796088	15796123	0.99	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796088	15796123	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796124	15796215	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796216	15796378	0.93	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796216	15796378	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796379	15796464	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796465	15796640	0.98	+	2	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796465	15796640	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796641	15796868	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796869	15797081	0.99	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796869	15797081	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15797082	15797370	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15797371	15797571	1	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15797371	15797571	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15797572	15797746	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15797747	15797854	1	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15797747	15797854	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15797855	15797986	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15797987	15798130	1	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15797987	15798130	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15798131	15798211	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15798212	15798463	1	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15798212	15798463	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15798464	15798544	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15798545	15798865	0.98	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15798545	15798865	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15798866	15798951	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15798952	15799104	1	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15798952	15799104	.	+	.	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	stop_codon	15799105	15799107	.	+	0	transcript_id "Phchi.S3G229000.t1"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	transcript	15796088	15799104	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	start_codon	15796088	15796090	.	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796088	15796123	0.99	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796088	15796123	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796124	15796215	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796216	15796378	0.88	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796216	15796378	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796379	15796464	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796465	15796671	0.93	+	2	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796465	15796671	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796672	15796868	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796869	15796899	0.95	+	2	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796869	15796899	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15796900	15796984	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15796985	15797081	0.95	+	1	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15796985	15797081	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15797082	15797370	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15797371	15797571	1	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15797371	15797571	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15797572	15797746	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15797747	15797854	1	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15797747	15797854	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15797855	15797986	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15797987	15798130	1	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15797987	15798130	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15798131	15798211	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15798212	15798463	1	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15798212	15798463	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15798464	15798544	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15798545	15798865	0.99	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15798545	15798865	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	intron	15798866	15798951	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	CDS	15798952	15799104	1	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	exon	15798952	15799104	.	+	.	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
Phchi.S3	AUGUSTUS	stop_codon	15799105	15799107	.	+	0	transcript_id "Phchi.S3G229000.t2"; gene_id "Phchi.S3G229000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2272.t1 is derived from g9192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5801975	5804480	.	-	.	Phchi.S5G088100
Phchi.S5	AUGUSTUS	transcript	5801975	5804480	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	stop_codon	5801972	5801974	.	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5801975	5802303	0.92	-	2	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5801975	5802303	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802304	5802407	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5802408	5802539	1	-	2	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5802408	5802539	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802540	5802655	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5802656	5802787	0.96	-	2	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5802656	5802787	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802788	5802890	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5802891	5802990	1	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5802891	5802990	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802991	5803103	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803104	5803313	0.99	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803104	5803313	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803314	5803458	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803459	5803470	0.78	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803459	5803470	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803471	5803550	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803551	5803619	0.78	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803551	5803619	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803620	5803694	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803695	5803757	1	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803695	5803757	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803758	5803853	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803854	5804004	1	-	1	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803854	5804004	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5804005	5804101	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5804102	5804199	1	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5804102	5804199	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5804200	5804288	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5804289	5804480	0.67	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5804289	5804480	.	-	.	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	start_codon	5804478	5804480	.	-	0	transcript_id "Phchi.S5G088100.t1"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	transcript	5801975	5804480	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	stop_codon	5801972	5801974	.	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5801975	5802303	0.93	-	2	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5801975	5802303	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802304	5802407	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5802408	5802539	1	-	2	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5802408	5802539	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802540	5802655	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5802656	5802787	0.97	-	2	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5802656	5802787	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802788	5802890	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5802891	5802990	1	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5802891	5802990	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5802991	5803103	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803104	5803313	0.98	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803104	5803313	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803314	5803458	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803459	5803470	0.77	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803459	5803470	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803471	5803550	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803551	5803619	0.77	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803551	5803619	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803620	5803694	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803695	5803757	1	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803695	5803757	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803758	5803843	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803844	5803873	0.94	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803844	5803873	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5803874	5803943	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5803944	5804004	0.77	-	1	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5803944	5804004	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5804005	5804101	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5804102	5804199	1	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5804102	5804199	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	intron	5804200	5804288	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	CDS	5804289	5804480	0.68	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	exon	5804289	5804480	.	-	.	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
Phchi.S5	AUGUSTUS	start_codon	5804478	5804480	.	-	0	transcript_id "Phchi.S5G088100.t2"; gene_id "Phchi.S5G088100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3296.t1 is derived from g465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2719352	2725573	.	+	.	Phchi.S1G045500
Phchi.S1	AUGUSTUS	transcript	2719352	2725573	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	start_codon	2719352	2719354	.	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2719352	2719744	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2719352	2719744	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2719745	2719945	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2719946	2720023	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2719946	2720023	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2720024	2720140	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2720141	2720203	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2720141	2720203	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2720204	2720392	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2720393	2720502	0.96	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2720393	2720502	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2720503	2720616	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2720617	2720717	0.97	+	1	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2720617	2720717	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2720718	2720804	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2720805	2720866	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2720805	2720866	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2720867	2721006	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2721007	2721147	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2721007	2721147	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2721148	2721553	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2721554	2721682	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2721554	2721682	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2721683	2722004	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2722005	2722051	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2722005	2722051	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2722052	2722152	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2722153	2722216	1	+	1	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2722153	2722216	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2722217	2722330	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2722331	2722451	0.91	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2722331	2722451	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2722452	2722537	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2722538	2722596	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2722538	2722596	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2722597	2722726	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2722727	2722795	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2722727	2722795	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2722796	2722924	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2722925	2723065	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2722925	2723065	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2723066	2723209	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2723210	2723274	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2723210	2723274	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2723275	2723431	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2723432	2723528	0.99	+	1	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2723432	2723528	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2723529	2723634	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2723635	2723694	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2723635	2723694	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2723695	2723799	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2723800	2723952	1	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2723800	2723952	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2723953	2724052	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2724053	2724110	0.99	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2724053	2724110	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2724111	2724231	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2724232	2724345	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2724232	2724345	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2724346	2724441	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2724442	2724609	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2724442	2724609	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2724610	2724776	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2724777	2724977	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2724777	2724977	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2724978	2725088	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2725089	2725316	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2725089	2725316	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	intron	2725317	2725397	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	CDS	2725398	2725573	1	+	2	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	exon	2725398	2725573	.	+	.	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
Phchi.S1	AUGUSTUS	stop_codon	2725574	2725576	.	+	0	transcript_id "Phchi.S1G045500.t1"; gene_id "Phchi.S1G045500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5354.t1 is derived from g2524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16444897	16447092	.	-	.	Phchi.S1G251300
Phchi.S1	AUGUSTUS	transcript	16444897	16446660	.	-	.	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	stop_codon	16444894	16444896	.	-	0	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	CDS	16444897	16445560	0.85	-	1	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	exon	16444897	16445560	.	-	.	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	intron	16445561	16445689	.	-	.	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	CDS	16445690	16446660	0.96	-	0	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	exon	16445690	16446660	.	-	.	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	start_codon	16446658	16446660	.	-	0	transcript_id "Phchi.S1G251300.t1"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	transcript	16444897	16447092	.	-	.	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	stop_codon	16444894	16444896	.	-	0	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	CDS	16444897	16445560	0.7	-	1	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	exon	16444897	16445560	.	-	.	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	intron	16445561	16445689	.	-	.	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	CDS	16445690	16447092	0.83	-	0	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	exon	16445690	16447092	.	-	.	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	start_codon	16447090	16447092	.	-	0	transcript_id "Phchi.S1G251300.t2"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	transcript	16445656	16447092	.	-	.	transcript_id "Phchi.S1G251300.t3"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	stop_codon	16445653	16445655	.	-	0	transcript_id "Phchi.S1G251300.t3"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	CDS	16445656	16447092	0.82	-	0	transcript_id "Phchi.S1G251300.t3"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	exon	16445656	16447092	.	-	.	transcript_id "Phchi.S1G251300.t3"; gene_id "Phchi.S1G251300"
Phchi.S1	AUGUSTUS	start_codon	16447090	16447092	.	-	0	transcript_id "Phchi.S1G251300.t3"; gene_id "Phchi.S1G251300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7857.t1 is derived from g5031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31545731	31548672	.	+	.	Phchi.S1G501600
Phchi.S1	AUGUSTUS	transcript	31545731	31548672	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	start_codon	31545731	31545733	.	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31545731	31545790	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31545731	31545790	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31545791	31545961	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31545962	31546018	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31545962	31546018	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31546019	31546108	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31546109	31546206	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31546109	31546206	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31546207	31546331	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31546332	31546401	1	+	1	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31546332	31546401	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31546402	31546514	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31546515	31546563	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31546515	31546563	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31546564	31546655	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31546656	31546709	0.97	+	2	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31546656	31546709	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31546710	31546860	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31546861	31546901	0.94	+	2	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31546861	31546901	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31546902	31546988	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31546989	31547048	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31546989	31547048	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31547049	31547177	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31547178	31547263	0.96	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31547178	31547263	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31547264	31547385	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31547386	31547479	0.42	+	1	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31547386	31547479	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31547480	31547547	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31547548	31547637	0.87	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31547548	31547637	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31547638	31547761	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31547762	31547977	0.99	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31547762	31547977	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31547978	31548058	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31548059	31548120	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31548059	31548120	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31548121	31548189	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31548190	31548274	1	+	1	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31548190	31548274	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31548275	31548367	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31548368	31548526	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31548368	31548526	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	intron	31548527	31548621	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	CDS	31548622	31548672	1	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	exon	31548622	31548672	.	+	.	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
Phchi.S1	AUGUSTUS	stop_codon	31548673	31548675	.	+	0	transcript_id "Phchi.S1G501600.t1"; gene_id "Phchi.S1G501600"
# This transcript jg3099.t2 is derived from g268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3100.t1 is derived from g269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1755182	1756823	.	-	.	Phchi.S1G025900
Phchi.S1	AUGUSTUS	transcript	1755182	1756823	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	stop_codon	1755179	1755181	.	-	0	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	CDS	1755182	1755342	0.96	-	2	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	exon	1755182	1755342	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	intron	1755343	1755456	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	CDS	1755457	1755576	0.88	-	2	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	exon	1755457	1755576	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	intron	1755577	1755672	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	CDS	1755673	1755778	0.54	-	0	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	exon	1755673	1755778	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	intron	1755779	1755900	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	CDS	1755901	1756193	0.53	-	2	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	exon	1755901	1756193	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	intron	1756194	1756351	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	CDS	1756352	1756823	0.83	-	0	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	exon	1756352	1756823	.	-	.	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
Phchi.S1	AUGUSTUS	start_codon	1756821	1756823	.	-	0	transcript_id "Phchi.S1G025900.t1"; gene_id "Phchi.S1G025900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1001.t1 is derived from g10784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6983286	6984746	.	+	.	Phchi.S6G096000
Phchi.S6	AUGUSTUS	transcript	6983286	6984746	.	+	.	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	start_codon	6983286	6983288	.	+	0	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	CDS	6983286	6984333	1	+	0	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	exon	6983286	6984333	.	+	.	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	intron	6984334	6984507	.	+	.	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	CDS	6984508	6984746	1	+	2	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	exon	6984508	6984746	.	+	.	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
Phchi.S6	AUGUSTUS	stop_codon	6984747	6984749	.	+	0	transcript_id "Phchi.S6G096000.t1"; gene_id "Phchi.S6G096000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7739.t1 is derived from g4913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30912716	30914891	.	+	.	Phchi.S1G489800
Phchi.S1	AUGUSTUS	transcript	30912716	30914891	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	start_codon	30912716	30912718	.	+	0	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	CDS	30912716	30913204	0.14	+	0	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	exon	30912716	30913204	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	intron	30913205	30913333	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	CDS	30913334	30914225	0.41	+	0	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	exon	30913334	30914225	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	intron	30914226	30914447	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	CDS	30914448	30914640	0.48	+	2	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	exon	30914448	30914640	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	intron	30914641	30914836	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	CDS	30914837	30914891	0.83	+	1	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	exon	30914837	30914891	.	+	.	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
Phchi.S1	AUGUSTUS	stop_codon	30914892	30914894	.	+	0	transcript_id "Phchi.S1G489800.t1"; gene_id "Phchi.S1G489800"
# This transcript jg6360.t2 is derived from g3532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6361.t1 is derived from g3533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22557677	22559560	.	+	.	Phchi.S1G352000
Phchi.S1	AUGUSTUS	transcript	22557677	22559560	.	+	.	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	start_codon	22557677	22557679	.	+	0	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	CDS	22557677	22557763	0.92	+	0	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	exon	22557677	22557763	.	+	.	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	intron	22557764	22558442	.	+	.	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	CDS	22558443	22558878	0.37	+	0	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	exon	22558443	22558878	.	+	.	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	intron	22558879	22558985	.	+	.	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	CDS	22558986	22559560	0.66	+	2	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	exon	22558986	22559560	.	+	.	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
Phchi.S1	AUGUSTUS	stop_codon	22559561	22559563	.	+	0	transcript_id "Phchi.S1G352000.t1"; gene_id "Phchi.S1G352000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1543.t1 is derived from g8462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1686540	1688849	.	-	.	Phchi.S5G015200
Phchi.S5	AUGUSTUS	transcript	1686540	1688849	.	-	.	transcript_id "Phchi.S5G015200.t1"; gene_id "Phchi.S5G015200"
Phchi.S5	AUGUSTUS	stop_codon	1686537	1686539	.	-	0	transcript_id "Phchi.S5G015200.t1"; gene_id "Phchi.S5G015200"
Phchi.S5	AUGUSTUS	CDS	1686540	1688849	0.77	-	0	transcript_id "Phchi.S5G015200.t1"; gene_id "Phchi.S5G015200"
Phchi.S5	AUGUSTUS	exon	1686540	1688849	.	-	.	transcript_id "Phchi.S5G015200.t1"; gene_id "Phchi.S5G015200"
Phchi.S5	AUGUSTUS	start_codon	1688847	1688849	.	-	0	transcript_id "Phchi.S5G015200.t1"; gene_id "Phchi.S5G015200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9668.t1 is derived from g6844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43183698	43186019	.	+	.	Phchi.S1G682700
Phchi.S1	AUGUSTUS	transcript	43183698	43186019	.	+	.	transcript_id "Phchi.S1G682700.t1"; gene_id "Phchi.S1G682700"
Phchi.S1	AUGUSTUS	start_codon	43183698	43183700	.	+	0	transcript_id "Phchi.S1G682700.t1"; gene_id "Phchi.S1G682700"
Phchi.S1	AUGUSTUS	CDS	43183698	43186019	0.93	+	0	transcript_id "Phchi.S1G682700.t1"; gene_id "Phchi.S1G682700"
Phchi.S1	AUGUSTUS	exon	43183698	43186019	.	+	.	transcript_id "Phchi.S1G682700.t1"; gene_id "Phchi.S1G682700"
Phchi.S1	AUGUSTUS	stop_codon	43186020	43186022	.	+	0	transcript_id "Phchi.S1G682700.t1"; gene_id "Phchi.S1G682700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14532.t1 is derived from g13000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13330241	13332070	.	-	.	Phchi.S3G185100
Phchi.S3	AUGUSTUS	transcript	13330241	13332070	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	stop_codon	13330238	13330240	.	-	0	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	CDS	13330241	13331262	0.89	-	2	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	exon	13330241	13331262	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	intron	13331263	13331435	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	CDS	13331436	13331567	1	-	2	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	exon	13331436	13331567	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	intron	13331568	13331654	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	CDS	13331655	13331825	1	-	2	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	exon	13331655	13331825	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	intron	13331826	13331937	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	CDS	13331938	13332070	0.85	-	0	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	exon	13331938	13332070	.	-	.	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
Phchi.S3	AUGUSTUS	start_codon	13332068	13332070	.	-	0	transcript_id "Phchi.S3G185100.t1"; gene_id "Phchi.S3G185100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12954.t1 is derived from g11419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3294028	3296099	.	-	.	Phchi.S3G027300
Phchi.S3	AUGUSTUS	transcript	3294028	3296099	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	stop_codon	3294025	3294027	.	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3294028	3294105	0.96	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3294028	3294105	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3294106	3294195	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3294196	3294240	0.96	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3294196	3294240	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3294241	3294364	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3294365	3294487	0.96	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3294365	3294487	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3294488	3294573	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3294574	3294759	1	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3294574	3294759	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3294760	3294843	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3294844	3295005	1	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3294844	3295005	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3295006	3295088	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3295089	3295238	1	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3295089	3295238	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3295239	3295402	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3295403	3295427	0.62	-	1	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3295403	3295427	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	intron	3295428	3295527	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	CDS	3295528	3296099	0.38	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	exon	3295528	3296099	.	-	.	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
Phchi.S3	AUGUSTUS	start_codon	3296097	3296099	.	-	0	transcript_id "Phchi.S3G027300.t1"; gene_id "Phchi.S3G027300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4323.t1 is derived from g1492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9783253	9784072	.	+	.	Phchi.S1G148200
Phchi.S1	AUGUSTUS	transcript	9783253	9784072	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	start_codon	9783253	9783255	.	+	0	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783253	9783308	0.71	+	0	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783253	9783308	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783309	9783393	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783394	9783439	0.82	+	1	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783394	9783439	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783440	9783627	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783628	9783719	0.82	+	0	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783628	9783719	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783720	9783817	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783818	9783878	1	+	1	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783818	9783878	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783879	9784063	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9784064	9784072	1	+	0	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9784064	9784072	.	+	.	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	stop_codon	9784073	9784075	.	+	0	transcript_id "Phchi.S1G148200.t1"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	transcript	9783253	9784072	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	start_codon	9783253	9783255	.	+	0	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783253	9783308	0.7	+	0	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783253	9783308	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783309	9783393	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783394	9783439	0.81	+	1	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783394	9783439	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783440	9783627	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783628	9783719	0.81	+	0	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783628	9783719	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783720	9783817	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783818	9783878	1	+	1	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783818	9783878	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783879	9784069	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9784070	9784072	1	+	0	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9784070	9784072	.	+	.	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	stop_codon	9784073	9784075	.	+	0	transcript_id "Phchi.S1G148200.t2"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	transcript	9783253	9784072	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	start_codon	9783253	9783255	.	+	0	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783253	9783308	0.73	+	0	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783253	9783308	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783309	9783393	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783394	9783439	0.82	+	1	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783394	9783439	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783440	9783627	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783628	9783719	0.82	+	0	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783628	9783719	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783720	9783802	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9783803	9783878	1	+	1	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9783803	9783878	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	intron	9783879	9784063	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	CDS	9784064	9784072	0.8	+	0	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	exon	9784064	9784072	.	+	.	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
Phchi.S1	AUGUSTUS	stop_codon	9784073	9784075	.	+	0	transcript_id "Phchi.S1G148200.t3"; gene_id "Phchi.S1G148200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15962.t1 is derived from g16001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	126	2007	.	+	.	Phchi.C133G000100
Phchi.C133	AUGUSTUS	transcript	126	2007	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	126	179	0.83	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	126	179	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	180	282	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	283	357	0.65	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	283	357	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	358	463	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	464	586	0.91	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	464	586	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	587	760	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	761	952	1	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	761	952	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	953	1046	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	1047	1130	0.99	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	1047	1130	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	1131	1227	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	1228	1314	1	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	1228	1314	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	1315	1397	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	1398	1451	1	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	1398	1451	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	1452	1577	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	1578	1660	1	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	1578	1660	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	1661	1754	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	1755	1864	1	+	1	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	1755	1864	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	intron	1865	1945	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	CDS	1946	2007	0.97	+	2	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	exon	1946	2007	.	+	.	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
Phchi.C133	AUGUSTUS	stop_codon	2008	2010	.	+	0	transcript_id "Phchi.C133G000100.t1"; gene_id "Phchi.C133G000100"
# This transcript jg12413.t2 is derived from g8090.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12413.t3 is derived from g8090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12414.t1 is derived from g8091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18824192	18824650	.	+	.	Phchi.S2G049400
Phchi.S2	AUGUSTUS	transcript	18824192	18824650	.	+	.	transcript_id "Phchi.S2G049400.t1"; gene_id "Phchi.S2G049400"
Phchi.S2	AUGUSTUS	start_codon	18824192	18824194	.	+	0	transcript_id "Phchi.S2G049400.t1"; gene_id "Phchi.S2G049400"
Phchi.S2	AUGUSTUS	CDS	18824192	18824650	0.26	+	0	transcript_id "Phchi.S2G049400.t1"; gene_id "Phchi.S2G049400"
Phchi.S2	AUGUSTUS	exon	18824192	18824650	.	+	.	transcript_id "Phchi.S2G049400.t1"; gene_id "Phchi.S2G049400"
Phchi.S2	AUGUSTUS	stop_codon	18824651	18824653	.	+	0	transcript_id "Phchi.S2G049400.t1"; gene_id "Phchi.S2G049400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12415.t1 is derived from g8092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18881190	18883328	.	-	.	Phchi.S2G049500
Phchi.S2	AUGUSTUS	transcript	18881190	18883328	.	-	.	transcript_id "Phchi.S2G049500.t1"; gene_id "Phchi.S2G049500"
Phchi.S2	AUGUSTUS	stop_codon	18881187	18881189	.	-	0	transcript_id "Phchi.S2G049500.t1"; gene_id "Phchi.S2G049500"
Phchi.S2	AUGUSTUS	CDS	18881190	18883328	0.63	-	0	transcript_id "Phchi.S2G049500.t1"; gene_id "Phchi.S2G049500"
Phchi.S2	AUGUSTUS	exon	18881190	18883328	.	-	.	transcript_id "Phchi.S2G049500.t1"; gene_id "Phchi.S2G049500"
Phchi.S2	AUGUSTUS	start_codon	18883326	18883328	.	-	0	transcript_id "Phchi.S2G049500.t1"; gene_id "Phchi.S2G049500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15847.t1 is derived from g14317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21800652	21802267	.	+	.	Phchi.S3G316600
Phchi.S3	AUGUSTUS	transcript	21800652	21802267	.	+	.	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	start_codon	21800652	21800654	.	+	0	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	CDS	21800652	21800744	0.55	+	0	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	exon	21800652	21800744	.	+	.	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	intron	21800745	21800860	.	+	.	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	CDS	21800861	21800888	0.91	+	0	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	exon	21800861	21800888	.	+	.	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	intron	21800889	21801014	.	+	.	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	CDS	21801015	21802267	0.8	+	2	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	exon	21801015	21802267	.	+	.	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
Phchi.S3	AUGUSTUS	stop_codon	21802268	21802270	.	+	0	transcript_id "Phchi.S3G316600.t1"; gene_id "Phchi.S3G316600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6179.t1 is derived from g3350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21330148	21331023	.	-	.	Phchi.S1G333800
Phchi.S1	AUGUSTUS	transcript	21330148	21331023	.	-	.	transcript_id "Phchi.S1G333800.t1"; gene_id "Phchi.S1G333800"
Phchi.S1	AUGUSTUS	stop_codon	21330145	21330147	.	-	0	transcript_id "Phchi.S1G333800.t1"; gene_id "Phchi.S1G333800"
Phchi.S1	AUGUSTUS	CDS	21330148	21331023	0.99	-	0	transcript_id "Phchi.S1G333800.t1"; gene_id "Phchi.S1G333800"
Phchi.S1	AUGUSTUS	exon	21330148	21331023	.	-	.	transcript_id "Phchi.S1G333800.t1"; gene_id "Phchi.S1G333800"
Phchi.S1	AUGUSTUS	start_codon	21331021	21331023	.	-	0	transcript_id "Phchi.S1G333800.t1"; gene_id "Phchi.S1G333800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11366.t1 is derived from g15416.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5792673	5794338	.	+	.	Phchi.S4G094800
Phchi.S4	AUGUSTUS	transcript	5792673	5794338	.	+	.	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	start_codon	5792673	5792675	.	+	0	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	CDS	5792673	5793200	0.92	+	0	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	exon	5792673	5793200	.	+	.	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	intron	5793201	5793327	.	+	.	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	CDS	5793328	5793700	0.99	+	0	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	exon	5793328	5793700	.	+	.	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	intron	5793701	5794165	.	+	.	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	CDS	5794166	5794338	0.7	+	2	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	exon	5794166	5794338	.	+	.	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	stop_codon	5794339	5794341	.	+	0	transcript_id "Phchi.S4G094800.t1"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	transcript	5792673	5794338	.	+	.	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	start_codon	5792673	5792675	.	+	0	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	CDS	5792673	5793191	0.87	+	0	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	exon	5792673	5793191	.	+	.	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	intron	5793192	5793327	.	+	.	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	CDS	5793328	5793700	1	+	0	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	exon	5793328	5793700	.	+	.	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	intron	5793701	5794165	.	+	.	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	CDS	5794166	5794338	0.7	+	2	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	exon	5794166	5794338	.	+	.	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
Phchi.S4	AUGUSTUS	stop_codon	5794339	5794341	.	+	0	transcript_id "Phchi.S4G094800.t2"; gene_id "Phchi.S4G094800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5174.t1 is derived from g2344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15321568	15321935	.	+	.	Phchi.S1G233300
Phchi.S1	AUGUSTUS	transcript	15321568	15321935	.	+	.	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	start_codon	15321568	15321570	.	+	0	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	CDS	15321568	15321768	0.5	+	0	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	exon	15321568	15321768	.	+	.	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	intron	15321769	15321917	.	+	.	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	CDS	15321918	15321935	0.5	+	0	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	exon	15321918	15321935	.	+	.	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
Phchi.S1	AUGUSTUS	stop_codon	15321936	15321938	.	+	0	transcript_id "Phchi.S1G233300.t1"; gene_id "Phchi.S1G233300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14672.t1 is derived from g13140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14119574	14120333	.	+	.	Phchi.S3G199100
Phchi.S3	AUGUSTUS	transcript	14119574	14120333	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	start_codon	14119574	14119576	.	+	0	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	CDS	14119574	14119646	0.98	+	0	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	exon	14119574	14119646	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	intron	14119647	14119735	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	CDS	14119736	14119806	1	+	2	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	exon	14119736	14119806	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	intron	14119807	14119924	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	CDS	14119925	14120049	1	+	0	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	exon	14119925	14120049	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	intron	14120050	14120129	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	CDS	14120130	14120190	1	+	1	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	exon	14120130	14120190	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	intron	14120191	14120279	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	CDS	14120280	14120333	1	+	0	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	exon	14120280	14120333	.	+	.	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
Phchi.S3	AUGUSTUS	stop_codon	14120334	14120336	.	+	0	transcript_id "Phchi.S3G199100.t1"; gene_id "Phchi.S3G199100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8960.t1 is derived from g6135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38848756	38850771	.	-	.	Phchi.S1G611900
Phchi.S1	AUGUSTUS	transcript	38848756	38850771	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	stop_codon	38848753	38848755	.	-	0	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38848756	38849270	1	-	2	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38848756	38849270	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38849271	38849353	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38849354	38849509	1	-	2	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38849354	38849509	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38849510	38849598	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38849599	38849718	1	-	2	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38849599	38849718	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38849719	38849875	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38849876	38849963	1	-	0	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38849876	38849963	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38849964	38850088	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38850089	38850178	1	-	0	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38850089	38850178	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38850179	38850275	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38850276	38850342	1	-	1	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38850276	38850342	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38850343	38850428	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38850429	38850553	1	-	0	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38850429	38850553	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	intron	38850554	38850627	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	CDS	38850628	38850771	0.55	-	0	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	exon	38850628	38850771	.	-	.	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
Phchi.S1	AUGUSTUS	start_codon	38850769	38850771	.	-	0	transcript_id "Phchi.S1G611900.t1"; gene_id "Phchi.S1G611900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14844.t1 is derived from g13312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14964957	14966149	.	+	.	Phchi.S3G216300
Phchi.S3	AUGUSTUS	transcript	14964957	14966149	.	+	.	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	start_codon	14964957	14964959	.	+	0	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	CDS	14964957	14965190	0.91	+	0	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	exon	14964957	14965190	.	+	.	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	intron	14965191	14965299	.	+	.	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	CDS	14965300	14965491	1	+	0	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	exon	14965300	14965491	.	+	.	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	intron	14965492	14965588	.	+	.	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	CDS	14965589	14966149	1	+	0	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	exon	14965589	14966149	.	+	.	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
Phchi.S3	AUGUSTUS	stop_codon	14966150	14966152	.	+	0	transcript_id "Phchi.S3G216300.t1"; gene_id "Phchi.S3G216300"
# This transcript jg12587.t2 is derived from g8264.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12588.t1 is derived from g8265.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36135230	36138777	.	-	.	Phchi.S2G066800
Phchi.S2	AUGUSTUS	transcript	36135230	36138777	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	stop_codon	36135227	36135229	.	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135230	36135496	0.92	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135230	36135496	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135497	36135597	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135598	36135710	0.99	-	2	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135598	36135710	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135711	36135836	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135837	36135900	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135837	36135900	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135901	36136052	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136053	36136133	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136053	36136133	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136134	36136222	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136223	36136285	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136223	36136285	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136286	36136383	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136384	36136401	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136384	36136401	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136402	36136487	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136488	36136551	1	-	1	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136488	36136551	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136552	36136638	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136639	36136767	0.98	-	1	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136639	36136767	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136768	36136976	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136977	36137023	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136977	36137023	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137024	36137130	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137131	36137235	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137131	36137235	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137236	36137412	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137413	36137535	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137413	36137535	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137536	36137756	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137757	36137852	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137757	36137852	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137853	36137979	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137980	36138036	1	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137980	36138036	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138037	36138186	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138187	36138232	1	-	1	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138187	36138232	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138233	36138316	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138317	36138418	1	-	1	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138317	36138418	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138419	36138498	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138499	36138571	1	-	2	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138499	36138571	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138572	36138719	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138720	36138777	0.65	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138720	36138777	.	-	.	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	start_codon	36138775	36138777	.	-	0	transcript_id "Phchi.S2G066800.t1"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	transcript	36135230	36138777	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	stop_codon	36135227	36135229	.	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135230	36135496	0.89	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135230	36135496	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135497	36135597	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135598	36135710	0.97	-	2	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135598	36135710	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135711	36135836	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135837	36135900	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135837	36135900	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135901	36136052	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136053	36136133	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136053	36136133	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136134	36136222	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136223	36136285	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136223	36136285	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136286	36136383	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136384	36136401	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136384	36136401	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136402	36136487	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136488	36136551	1	-	1	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136488	36136551	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136552	36136638	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136639	36136767	0.99	-	1	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136639	36136767	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136768	36136976	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136977	36137023	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136977	36137023	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137024	36137130	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137131	36137235	0.99	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137131	36137235	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137236	36137412	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137413	36137535	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137413	36137535	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137536	36137756	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137757	36137852	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137757	36137852	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137853	36137979	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137980	36138036	1	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137980	36138036	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138037	36138201	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138202	36138232	1	-	1	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138202	36138232	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138233	36138316	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138317	36138418	1	-	1	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138317	36138418	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138419	36138498	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138499	36138571	1	-	2	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138499	36138571	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138572	36138719	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138720	36138777	0.56	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138720	36138777	.	-	.	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	start_codon	36138775	36138777	.	-	0	transcript_id "Phchi.S2G066800.t2"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	transcript	36135230	36138777	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	stop_codon	36135227	36135229	.	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135230	36135496	0.87	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135230	36135496	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135497	36135597	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135598	36135710	0.94	-	2	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135598	36135710	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135711	36135836	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36135837	36135900	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36135837	36135900	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36135901	36136052	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136053	36136133	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136053	36136133	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136134	36136222	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136223	36136285	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136223	36136285	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136286	36136383	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136384	36136406	1	-	2	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136384	36136406	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136407	36136487	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136488	36136571	0.98	-	2	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136488	36136571	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136572	36136660	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136661	36136767	0.98	-	1	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136661	36136767	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36136768	36136976	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36136977	36137023	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36136977	36137023	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137024	36137130	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137131	36137235	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137131	36137235	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137236	36137412	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137413	36137535	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137413	36137535	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137536	36137756	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137757	36137852	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137757	36137852	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36137853	36137979	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36137980	36138036	1	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36137980	36138036	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138037	36138201	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138202	36138232	1	-	1	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138202	36138232	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138233	36138316	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138317	36138418	1	-	1	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138317	36138418	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138419	36138498	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138499	36138571	1	-	2	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138499	36138571	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	intron	36138572	36138719	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	CDS	36138720	36138777	0.56	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	exon	36138720	36138777	.	-	.	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
Phchi.S2	AUGUSTUS	start_codon	36138775	36138777	.	-	0	transcript_id "Phchi.S2G066800.t3"; gene_id "Phchi.S2G066800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1161.t1 is derived from g10944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8096669	8098683	.	+	.	Phchi.S6G112000
Phchi.S6	AUGUSTUS	transcript	8096669	8098683	.	+	.	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	start_codon	8096669	8096671	.	+	0	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	CDS	8096669	8097358	0.41	+	0	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	exon	8096669	8097358	.	+	.	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	intron	8097359	8097468	.	+	.	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	CDS	8097469	8098683	0.46	+	0	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	exon	8097469	8098683	.	+	.	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
Phchi.S6	AUGUSTUS	stop_codon	8098684	8098686	.	+	0	transcript_id "Phchi.S6G112000.t1"; gene_id "Phchi.S6G112000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7777.t1 is derived from g4951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31179231	31179909	.	+	.	Phchi.S1G493600
Phchi.S1	AUGUSTUS	transcript	31179231	31179909	.	+	.	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	start_codon	31179231	31179233	.	+	0	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	CDS	31179231	31179482	0.58	+	0	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	exon	31179231	31179482	.	+	.	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	intron	31179483	31179564	.	+	.	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	CDS	31179565	31179909	0.91	+	0	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	exon	31179565	31179909	.	+	.	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
Phchi.S1	AUGUSTUS	stop_codon	31179910	31179912	.	+	0	transcript_id "Phchi.S1G493600.t1"; gene_id "Phchi.S1G493600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8820.t1 is derived from g5995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38133150	38133591	.	+	.	Phchi.S1G597900
Phchi.S1	AUGUSTUS	transcript	38133150	38133591	.	+	.	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	start_codon	38133150	38133152	.	+	0	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	CDS	38133150	38133371	0.59	+	0	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	exon	38133150	38133371	.	+	.	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	intron	38133372	38133453	.	+	.	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	CDS	38133454	38133591	0.43	+	0	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	exon	38133454	38133591	.	+	.	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
Phchi.S1	AUGUSTUS	stop_codon	38133592	38133594	.	+	0	transcript_id "Phchi.S1G597900.t1"; gene_id "Phchi.S1G597900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11647.t1 is derived from g15698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7447544	7448840	.	-	.	Phchi.S4G122900
Phchi.S4	AUGUSTUS	transcript	7447544	7448840	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	stop_codon	7447541	7447543	.	-	0	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7447544	7447607	1	-	1	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7447544	7447607	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7447608	7447824	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7447825	7448054	1	-	0	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7447825	7448054	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7448055	7448138	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7448139	7448269	1	-	2	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7448139	7448269	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7448270	7448364	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7448365	7448618	1	-	1	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7448365	7448618	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7448619	7448715	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7448716	7448840	0.75	-	0	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7448716	7448840	.	-	.	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	start_codon	7448838	7448840	.	-	0	transcript_id "Phchi.S4G122900.t1"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	transcript	7447575	7448840	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	stop_codon	7447572	7447574	.	-	0	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7447575	7447607	0.94	-	0	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7447575	7447607	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7447608	7447886	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7447887	7448054	0.94	-	0	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7447887	7448054	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7448055	7448138	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7448139	7448269	1	-	2	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7448139	7448269	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7448270	7448364	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7448365	7448618	1	-	1	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7448365	7448618	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	intron	7448619	7448715	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	CDS	7448716	7448840	0.74	-	0	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	exon	7448716	7448840	.	-	.	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
Phchi.S4	AUGUSTUS	start_codon	7448838	7448840	.	-	0	transcript_id "Phchi.S4G122900.t2"; gene_id "Phchi.S4G122900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6288.t1 is derived from g3460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22095649	22096538	.	-	.	Phchi.S1G344700
Phchi.S1	AUGUSTUS	transcript	22095649	22096538	.	-	.	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	stop_codon	22095646	22095648	.	-	0	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	CDS	22095649	22096116	0.45	-	0	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	exon	22095649	22096116	.	-	.	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	intron	22096117	22096238	.	-	.	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	CDS	22096239	22096538	0.49	-	0	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	exon	22096239	22096538	.	-	.	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
Phchi.S1	AUGUSTUS	start_codon	22096536	22096538	.	-	0	transcript_id "Phchi.S1G344700.t1"; gene_id "Phchi.S1G344700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14867.t1 is derived from g13335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15102662	15104100	.	-	.	Phchi.S3G218600
Phchi.S3	AUGUSTUS	transcript	15102662	15104100	.	-	.	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	stop_codon	15102659	15102661	.	-	0	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	CDS	15102662	15102667	0.75	-	0	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	exon	15102662	15102667	.	-	.	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	intron	15102668	15102741	.	-	.	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	CDS	15102742	15104100	0.55	-	0	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	exon	15102742	15104100	.	-	.	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
Phchi.S3	AUGUSTUS	start_codon	15104098	15104100	.	-	0	transcript_id "Phchi.S3G218600.t1"; gene_id "Phchi.S3G218600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12323.t1 is derived from g7999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10873167	10879376	.	+	.	Phchi.S2G040300
Phchi.S2	AUGUSTUS	transcript	10873167	10879376	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	start_codon	10873167	10873169	.	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10873167	10873262	0.58	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10873167	10873262	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10873263	10873421	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10873422	10873830	1	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10873422	10873830	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10873831	10874163	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10874164	10874291	1	+	2	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10874164	10874291	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10874292	10874754	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10874755	10874814	1	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10874755	10874814	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10874815	10875626	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10875627	10875776	0.99	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10875627	10875776	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10875777	10875988	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10875989	10876144	1	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10875989	10876144	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10876145	10877424	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10877425	10877562	1	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10877425	10877562	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10877563	10877677	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10877678	10877751	1	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10877678	10877751	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10877752	10878526	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10878527	10878628	0.94	+	1	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10878527	10878628	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10878629	10878732	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10878733	10878848	1	+	1	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10878733	10878848	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10878849	10878973	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10878974	10879210	0.52	+	2	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10878974	10879210	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	intron	10879211	10879311	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	CDS	10879312	10879376	0.77	+	2	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	exon	10879312	10879376	.	+	.	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
Phchi.S2	AUGUSTUS	stop_codon	10879377	10879379	.	+	0	transcript_id "Phchi.S2G040300.t1"; gene_id "Phchi.S2G040300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14927.t1 is derived from g13395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15551008	15554103	.	+	.	Phchi.S3G224600
Phchi.S3	AUGUSTUS	transcript	15551008	15554103	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	start_codon	15551008	15551010	.	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15551008	15551085	1	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15551008	15551085	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15551086	15551558	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15551559	15551738	1	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15551559	15551738	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15551739	15551839	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15551840	15551915	1	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15551840	15551915	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15551916	15552046	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15552047	15552185	1	+	2	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15552047	15552185	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15552186	15552455	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15552456	15552549	1	+	1	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15552456	15552549	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15552550	15552670	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15552671	15552762	1	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15552671	15552762	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15552763	15552911	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15552912	15552981	1	+	1	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15552912	15552981	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15552982	15553108	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15553109	15553191	1	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15553109	15553191	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15553192	15553291	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15553292	15553368	0.96	+	1	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15553292	15553368	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15553369	15553470	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15553471	15553541	0.99	+	2	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15553471	15553541	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	intron	15553542	15554058	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	CDS	15554059	15554103	0.99	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	exon	15554059	15554103	.	+	.	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
Phchi.S3	AUGUSTUS	stop_codon	15554104	15554106	.	+	0	transcript_id "Phchi.S3G224600.t1"; gene_id "Phchi.S3G224600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7691.t1 is derived from g4865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30641792	30642991	.	-	.	Phchi.S1G485000
Phchi.S1	AUGUSTUS	transcript	30641792	30642991	.	-	.	transcript_id "Phchi.S1G485000.t1"; gene_id "Phchi.S1G485000"
Phchi.S1	AUGUSTUS	stop_codon	30641789	30641791	.	-	0	transcript_id "Phchi.S1G485000.t1"; gene_id "Phchi.S1G485000"
Phchi.S1	AUGUSTUS	CDS	30641792	30642991	0.94	-	0	transcript_id "Phchi.S1G485000.t1"; gene_id "Phchi.S1G485000"
Phchi.S1	AUGUSTUS	exon	30641792	30642991	.	-	.	transcript_id "Phchi.S1G485000.t1"; gene_id "Phchi.S1G485000"
Phchi.S1	AUGUSTUS	start_codon	30642989	30642991	.	-	0	transcript_id "Phchi.S1G485000.t1"; gene_id "Phchi.S1G485000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15591.t1 is derived from g14060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20160994	20163434	.	-	.	Phchi.S3G291000
Phchi.S3	AUGUSTUS	transcript	20160994	20163434	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	stop_codon	20160991	20160993	.	-	0	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	CDS	20160994	20161383	0.97	-	0	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	exon	20160994	20161383	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	intron	20161384	20161493	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	CDS	20161494	20161783	1	-	2	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	exon	20161494	20161783	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	intron	20161784	20162267	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	CDS	20162268	20162832	0.99	-	0	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	exon	20162268	20162832	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	intron	20162833	20163105	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	CDS	20163106	20163260	0.43	-	2	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	exon	20163106	20163260	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	intron	20163261	20163364	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	CDS	20163365	20163434	0.51	-	0	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	exon	20163365	20163434	.	-	.	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
Phchi.S3	AUGUSTUS	start_codon	20163432	20163434	.	-	0	transcript_id "Phchi.S3G291000.t1"; gene_id "Phchi.S3G291000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12638.t1 is derived from g9790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C183	AUGUSTUS	gene	11253	11597	.	+	.	Phchi.C183G000200
Phchi.C183	AUGUSTUS	transcript	11253	11597	.	+	.	transcript_id "Phchi.C183G000200.t1"; gene_id "Phchi.C183G000200"
Phchi.C183	AUGUSTUS	start_codon	11253	11255	.	+	0	transcript_id "Phchi.C183G000200.t1"; gene_id "Phchi.C183G000200"
Phchi.C183	AUGUSTUS	CDS	11253	11597	0.38	+	0	transcript_id "Phchi.C183G000200.t1"; gene_id "Phchi.C183G000200"
Phchi.C183	AUGUSTUS	exon	11253	11597	.	+	.	transcript_id "Phchi.C183G000200.t1"; gene_id "Phchi.C183G000200"
Phchi.C183	AUGUSTUS	stop_codon	11598	11600	.	+	0	transcript_id "Phchi.C183G000200.t1"; gene_id "Phchi.C183G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15542.t1 is derived from g14011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19785422	19787107	.	+	.	Phchi.S3G286100
Phchi.S3	AUGUSTUS	transcript	19785422	19787107	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	start_codon	19785422	19785424	.	+	0	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	CDS	19785422	19785455	1	+	0	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	exon	19785422	19785455	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	intron	19785456	19785544	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	CDS	19785545	19785715	1	+	2	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	exon	19785545	19785715	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	intron	19785716	19785789	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	CDS	19785790	19786128	1	+	2	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	exon	19785790	19786128	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	intron	19786129	19786225	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	CDS	19786226	19786480	1	+	2	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	exon	19786226	19786480	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	intron	19786481	19786611	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	CDS	19786612	19786745	1	+	2	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	exon	19786612	19786745	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	intron	19786746	19786864	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	CDS	19786865	19787107	0.82	+	0	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	exon	19786865	19787107	.	+	.	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
Phchi.S3	AUGUSTUS	stop_codon	19787108	19787110	.	+	0	transcript_id "Phchi.S3G286100.t1"; gene_id "Phchi.S3G286100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1084.t1 is derived from g10867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7514458	7516869	.	+	.	Phchi.S6G104300
Phchi.S6	AUGUSTUS	transcript	7514458	7516869	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	start_codon	7514458	7514460	.	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7514458	7514778	0.64	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7514458	7514778	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7514779	7514997	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7514998	7515077	0.83	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7514998	7515077	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7515078	7515185	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7515186	7515237	0.98	+	1	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7515186	7515237	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7515238	7515335	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7515336	7515469	1	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7515336	7515469	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7515470	7515555	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7515556	7515670	1	+	1	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7515556	7515670	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7515671	7515764	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7515765	7515851	1	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7515765	7515851	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7515852	7516013	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7516014	7516062	1	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7516014	7516062	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7516063	7516215	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7516216	7516283	0.77	+	2	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7516216	7516283	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7516284	7516587	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7516588	7516620	0.84	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7516588	7516620	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	intron	7516621	7516773	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	CDS	7516774	7516869	0.83	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	exon	7516774	7516869	.	+	.	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
Phchi.S6	AUGUSTUS	stop_codon	7516870	7516872	.	+	0	transcript_id "Phchi.S6G104300.t1"; gene_id "Phchi.S6G104300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13163.t1 is derived from g11628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4452616	4453479	.	-	.	Phchi.S3G048200
Phchi.S3	AUGUSTUS	transcript	4452616	4453479	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	stop_codon	4452613	4452615	.	-	0	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	CDS	4452616	4452746	1	-	2	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	exon	4452616	4452746	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	intron	4452747	4452830	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	CDS	4452831	4452891	1	-	0	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	exon	4452831	4452891	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	intron	4452892	4452966	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	CDS	4452967	4453059	1	-	0	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	exon	4452967	4453059	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	intron	4453060	4453137	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	CDS	4453138	4453479	0.99	-	0	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	exon	4453138	4453479	.	-	.	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
Phchi.S3	AUGUSTUS	start_codon	4453477	4453479	.	-	0	transcript_id "Phchi.S3G048200.t1"; gene_id "Phchi.S3G048200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5385.t1 is derived from g2555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16625584	16630163	.	+	.	Phchi.S1G254400
Phchi.S1	AUGUSTUS	transcript	16625584	16630163	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	start_codon	16625584	16625586	.	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16625584	16625961	0.52	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16625584	16625961	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16625962	16626059	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16626060	16626125	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16626060	16626125	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16626126	16626216	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16626217	16626303	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16626217	16626303	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16626304	16626459	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16626460	16626795	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16626460	16626795	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16626796	16626885	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16626886	16626983	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16626886	16626983	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16626984	16627456	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16627457	16627492	1	+	1	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16627457	16627492	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16627493	16627618	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16627619	16627739	1	+	1	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16627619	16627739	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16627740	16627837	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16627838	16628077	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16627838	16628077	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16628078	16628202	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16628203	16628298	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16628203	16628298	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16628299	16628410	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16628411	16628476	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16628411	16628476	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16628477	16628610	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16628611	16628649	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16628611	16628649	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16628650	16628733	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16628734	16628868	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16628734	16628868	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16628869	16628967	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16628968	16629341	0.99	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16628968	16629341	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16629342	16629480	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16629481	16629574	0.94	+	1	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16629481	16629574	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16629575	16629678	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16629679	16629867	1	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16629679	16629867	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	intron	16629868	16630064	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	CDS	16630065	16630163	0.99	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	exon	16630065	16630163	.	+	.	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
Phchi.S1	AUGUSTUS	stop_codon	16630164	16630166	.	+	0	transcript_id "Phchi.S1G254400.t1"; gene_id "Phchi.S1G254400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4169.t1 is derived from g1338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8726364	8728509	.	+	.	Phchi.S1G132800
Phchi.S1	AUGUSTUS	transcript	8726364	8728509	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	start_codon	8726364	8726366	.	+	0	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	CDS	8726364	8726508	0.97	+	0	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	exon	8726364	8726508	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	intron	8726509	8726604	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	CDS	8726605	8728004	0.91	+	2	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	exon	8726605	8728004	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	intron	8728005	8728273	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	CDS	8728274	8728322	0.45	+	0	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	exon	8728274	8728322	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	intron	8728323	8728468	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	CDS	8728469	8728509	0.67	+	2	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	exon	8728469	8728509	.	+	.	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
Phchi.S1	AUGUSTUS	stop_codon	8728510	8728512	.	+	0	transcript_id "Phchi.S1G132800.t1"; gene_id "Phchi.S1G132800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8623.t1 is derived from g5798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37056857	37059147	.	+	.	Phchi.S1G578200
Phchi.S1	AUGUSTUS	transcript	37056857	37059147	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	start_codon	37056857	37056859	.	+	0	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37056857	37056967	0.93	+	0	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37056857	37056967	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	intron	37056968	37057047	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37057048	37057321	1	+	0	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37057048	37057321	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	intron	37057322	37057410	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37057411	37057591	0.84	+	2	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37057411	37057591	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	intron	37057592	37057745	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37057746	37057992	0.22	+	1	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37057746	37057992	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	intron	37057993	37058103	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37058104	37058424	1	+	0	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37058104	37058424	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	intron	37058425	37058544	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37058545	37058710	1	+	0	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37058545	37058710	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	intron	37058711	37058848	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	CDS	37058849	37059147	0.97	+	2	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	exon	37058849	37059147	.	+	.	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
Phchi.S1	AUGUSTUS	stop_codon	37059148	37059150	.	+	0	transcript_id "Phchi.S1G578200.t1"; gene_id "Phchi.S1G578200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3091.t1 is derived from g260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1723846	1724615	.	+	.	Phchi.S1G025000
Phchi.S1	AUGUSTUS	transcript	1723846	1724615	.	+	.	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	start_codon	1723846	1723848	.	+	0	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	CDS	1723846	1724290	0.45	+	0	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	exon	1723846	1724290	.	+	.	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	intron	1724291	1724400	.	+	.	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	CDS	1724401	1724615	0.53	+	2	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	exon	1724401	1724615	.	+	.	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
Phchi.S1	AUGUSTUS	stop_codon	1724616	1724618	.	+	0	transcript_id "Phchi.S1G025000.t1"; gene_id "Phchi.S1G025000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9677.t1 is derived from g6853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43242121	43243375	.	-	.	Phchi.S1G683600
Phchi.S1	AUGUSTUS	transcript	43242121	43243375	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	stop_codon	43242118	43242120	.	-	0	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	CDS	43242121	43242346	0.47	-	1	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	exon	43242121	43242346	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	intron	43242347	43242471	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	CDS	43242472	43242624	0.84	-	1	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	exon	43242472	43242624	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	intron	43242625	43242711	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	CDS	43242712	43242828	0.43	-	1	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	exon	43242712	43242828	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	intron	43242829	43242941	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	CDS	43242942	43243375	0.31	-	0	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	exon	43242942	43243375	.	-	.	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
Phchi.S1	AUGUSTUS	start_codon	43243373	43243375	.	-	0	transcript_id "Phchi.S1G683600.t1"; gene_id "Phchi.S1G683600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10554.t1 is derived from g14604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	965147	967109	.	-	.	Phchi.S4G013600
Phchi.S4	AUGUSTUS	transcript	965147	967109	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	stop_codon	965144	965146	.	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	965147	965164	1	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	965147	965164	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	965165	965253	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	965254	965313	1	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	965254	965313	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	965314	965406	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	965407	965512	1	-	1	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	965407	965512	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	965513	965602	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	965603	965748	1	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	965603	965748	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	965749	965862	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	965863	965945	1	-	2	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	965863	965945	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	965946	966045	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	966046	966151	0.98	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	966046	966151	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	966152	966263	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	966264	966360	1	-	1	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	966264	966360	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	966361	966443	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	966444	966727	0.97	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	966444	966727	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	966728	966821	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	966822	966969	1	-	1	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	966822	966969	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	intron	966970	967047	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	CDS	967048	967109	1	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	exon	967048	967109	.	-	.	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
Phchi.S4	AUGUSTUS	start_codon	967107	967109	.	-	0	transcript_id "Phchi.S4G013600.t1"; gene_id "Phchi.S4G013600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14507.t1 is derived from g12975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13226273	13227792	.	-	.	Phchi.S3G182600
Phchi.S3	AUGUSTUS	transcript	13226273	13227792	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	stop_codon	13226270	13226272	.	-	0	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	CDS	13226273	13226924	0.99	-	1	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	exon	13226273	13226924	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	intron	13226925	13227008	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	CDS	13227009	13227334	1	-	0	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	exon	13227009	13227334	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	intron	13227335	13227403	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	CDS	13227404	13227593	1	-	1	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	exon	13227404	13227593	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	intron	13227594	13227694	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	CDS	13227695	13227792	1	-	0	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	exon	13227695	13227792	.	-	.	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
Phchi.S3	AUGUSTUS	start_codon	13227790	13227792	.	-	0	transcript_id "Phchi.S3G182600.t1"; gene_id "Phchi.S3G182600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15933.t1 is derived from g16034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C71	AUGUSTUS	gene	45711	46241	.	-	.	Phchi.C71G000400
Phchi.C71	AUGUSTUS	transcript	45711	46241	.	-	.	transcript_id "Phchi.C71G000400.t1"; gene_id "Phchi.C71G000400"
Phchi.C71	AUGUSTUS	stop_codon	45708	45710	.	-	0	transcript_id "Phchi.C71G000400.t1"; gene_id "Phchi.C71G000400"
Phchi.C71	AUGUSTUS	CDS	45711	46241	0.72	-	0	transcript_id "Phchi.C71G000400.t1"; gene_id "Phchi.C71G000400"
Phchi.C71	AUGUSTUS	exon	45711	46241	.	-	.	transcript_id "Phchi.C71G000400.t1"; gene_id "Phchi.C71G000400"
Phchi.C71	AUGUSTUS	start_codon	46239	46241	.	-	0	transcript_id "Phchi.C71G000400.t1"; gene_id "Phchi.C71G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10488.t1 is derived from g14537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	671913	672665	.	+	.	Phchi.S4G007000
Phchi.S4	AUGUSTUS	transcript	671913	672665	.	+	.	transcript_id "Phchi.S4G007000.t1"; gene_id "Phchi.S4G007000"
Phchi.S4	AUGUSTUS	start_codon	671913	671915	.	+	0	transcript_id "Phchi.S4G007000.t1"; gene_id "Phchi.S4G007000"
Phchi.S4	AUGUSTUS	CDS	671913	672665	0.56	+	0	transcript_id "Phchi.S4G007000.t1"; gene_id "Phchi.S4G007000"
Phchi.S4	AUGUSTUS	exon	671913	672665	.	+	.	transcript_id "Phchi.S4G007000.t1"; gene_id "Phchi.S4G007000"
Phchi.S4	AUGUSTUS	stop_codon	672666	672668	.	+	0	transcript_id "Phchi.S4G007000.t1"; gene_id "Phchi.S4G007000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11044.t1 is derived from g15094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3796062	3796555	.	-	.	Phchi.S4G062600
Phchi.S4	AUGUSTUS	transcript	3796062	3796555	.	-	.	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	stop_codon	3796059	3796061	.	-	0	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	CDS	3796062	3796119	1	-	1	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	exon	3796062	3796119	.	-	.	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	intron	3796120	3796289	.	-	.	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	CDS	3796290	3796376	1	-	1	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	exon	3796290	3796376	.	-	.	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	intron	3796377	3796475	.	-	.	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	CDS	3796476	3796555	1	-	0	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	exon	3796476	3796555	.	-	.	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
Phchi.S4	AUGUSTUS	start_codon	3796553	3796555	.	-	0	transcript_id "Phchi.S4G062600.t1"; gene_id "Phchi.S4G062600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7223.t1 is derived from g4395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27705181	27705972	.	+	.	Phchi.S1G438200
Phchi.S1	AUGUSTUS	transcript	27705181	27705972	.	+	.	transcript_id "Phchi.S1G438200.t1"; gene_id "Phchi.S1G438200"
Phchi.S1	AUGUSTUS	start_codon	27705181	27705183	.	+	0	transcript_id "Phchi.S1G438200.t1"; gene_id "Phchi.S1G438200"
Phchi.S1	AUGUSTUS	CDS	27705181	27705972	0.95	+	0	transcript_id "Phchi.S1G438200.t1"; gene_id "Phchi.S1G438200"
Phchi.S1	AUGUSTUS	exon	27705181	27705972	.	+	.	transcript_id "Phchi.S1G438200.t1"; gene_id "Phchi.S1G438200"
Phchi.S1	AUGUSTUS	stop_codon	27705973	27705975	.	+	0	transcript_id "Phchi.S1G438200.t1"; gene_id "Phchi.S1G438200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10426.t1 is derived from g14475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	203932	206262	.	+	.	Phchi.S4G000800
Phchi.S4	AUGUSTUS	transcript	203932	206262	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	start_codon	203932	203934	.	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	203932	204135	0.73	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	203932	204135	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	204136	204307	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	204308	204367	1	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	204308	204367	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	204368	204455	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	204456	204545	0.71	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	204456	204545	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	204546	204650	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	204651	204785	0.55	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	204651	204785	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	204786	204888	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	204889	205024	0.98	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	204889	205024	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	205025	205122	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	205123	205308	0.84	+	2	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	205123	205308	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	205309	205415	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	205416	205479	1	+	2	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	205416	205479	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	205480	205661	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	205662	205731	1	+	1	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	205662	205731	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	205732	205968	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	205969	206083	1	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	205969	206083	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	intron	206084	206170	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	CDS	206171	206262	1	+	2	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	exon	206171	206262	.	+	.	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
Phchi.S4	AUGUSTUS	stop_codon	206263	206265	.	+	0	transcript_id "Phchi.S4G000800.t1"; gene_id "Phchi.S4G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15360.t1 is derived from g13828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18584325	18585047	.	-	.	Phchi.S3G267900
Phchi.S3	AUGUSTUS	transcript	18584325	18585047	.	-	.	transcript_id "Phchi.S3G267900.t1"; gene_id "Phchi.S3G267900"
Phchi.S3	AUGUSTUS	stop_codon	18584322	18584324	.	-	0	transcript_id "Phchi.S3G267900.t1"; gene_id "Phchi.S3G267900"
Phchi.S3	AUGUSTUS	CDS	18584325	18585047	0.76	-	0	transcript_id "Phchi.S3G267900.t1"; gene_id "Phchi.S3G267900"
Phchi.S3	AUGUSTUS	exon	18584325	18585047	.	-	.	transcript_id "Phchi.S3G267900.t1"; gene_id "Phchi.S3G267900"
Phchi.S3	AUGUSTUS	start_codon	18585045	18585047	.	-	0	transcript_id "Phchi.S3G267900.t1"; gene_id "Phchi.S3G267900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11256.t1 is derived from g15306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5040370	5041749	.	-	.	Phchi.S4G083800
Phchi.S4	AUGUSTUS	transcript	5040370	5041749	.	-	.	transcript_id "Phchi.S4G083800.t1"; gene_id "Phchi.S4G083800"
Phchi.S4	AUGUSTUS	stop_codon	5040367	5040369	.	-	0	transcript_id "Phchi.S4G083800.t1"; gene_id "Phchi.S4G083800"
Phchi.S4	AUGUSTUS	CDS	5040370	5041749	0.79	-	0	transcript_id "Phchi.S4G083800.t1"; gene_id "Phchi.S4G083800"
Phchi.S4	AUGUSTUS	exon	5040370	5041749	.	-	.	transcript_id "Phchi.S4G083800.t1"; gene_id "Phchi.S4G083800"
Phchi.S4	AUGUSTUS	start_codon	5041747	5041749	.	-	0	transcript_id "Phchi.S4G083800.t1"; gene_id "Phchi.S4G083800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3934.t1 is derived from g1103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6557755	6563002	.	+	.	Phchi.S1G109300
Phchi.S1	AUGUSTUS	transcript	6557755	6563002	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	start_codon	6557755	6557757	.	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6557755	6557961	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6557755	6557961	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6557962	6558048	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558049	6558282	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558049	6558282	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558283	6558379	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558380	6558454	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558380	6558454	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558455	6558648	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558649	6558750	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558649	6558750	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558751	6558839	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558840	6558890	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558840	6558890	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558891	6559017	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559018	6559195	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559018	6559195	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559196	6559321	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559322	6559447	1	+	2	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559322	6559447	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559448	6559547	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559548	6559639	1	+	2	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559548	6559639	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559640	6559790	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559791	6559971	0.91	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559791	6559971	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559972	6560080	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560081	6560157	0.91	+	2	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560081	6560157	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560158	6560241	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560242	6560340	0.99	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560242	6560340	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560341	6560427	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560428	6560539	0.57	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560428	6560539	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560540	6560646	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560647	6560732	1	+	2	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560647	6560732	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560733	6560822	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560823	6560987	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560823	6560987	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560988	6561178	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561179	6561232	0.99	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561179	6561232	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561233	6561338	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561339	6561467	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561339	6561467	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561468	6561560	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561561	6561653	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561561	6561653	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561654	6561782	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561783	6561929	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561783	6561929	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561930	6562013	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562014	6562108	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562014	6562108	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562109	6562198	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562199	6562283	1	+	1	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562199	6562283	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562284	6562412	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562413	6562471	1	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562413	6562471	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562472	6562562	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562563	6562661	1	+	1	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562563	6562661	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562662	6562754	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562755	6562841	1	+	1	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562755	6562841	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562842	6562929	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562930	6563002	1	+	1	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562930	6563002	.	+	.	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	stop_codon	6563003	6563005	.	+	0	transcript_id "Phchi.S1G109300.t1"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	transcript	6557755	6563002	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	start_codon	6557755	6557757	.	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6557755	6557961	0.97	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6557755	6557961	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6557962	6558048	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558049	6558282	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558049	6558282	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558283	6558379	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558380	6558454	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558380	6558454	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558455	6558648	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558649	6558750	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558649	6558750	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558751	6558839	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558840	6558890	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558840	6558890	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558891	6559017	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559018	6559195	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559018	6559195	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559196	6559321	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559322	6559447	1	+	2	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559322	6559447	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559448	6559547	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559548	6559639	1	+	2	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559548	6559639	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559640	6559790	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559791	6559971	0.89	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559791	6559971	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559972	6560080	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560081	6560157	0.87	+	2	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560081	6560157	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560158	6560241	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560242	6560340	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560242	6560340	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560341	6560427	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560428	6560539	0.6	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560428	6560539	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560540	6560646	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560647	6560732	1	+	2	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560647	6560732	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560733	6560822	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560823	6560987	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560823	6560987	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560988	6561065	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561066	6561072	0.87	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561066	6561072	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561073	6561146	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561147	6561232	0.87	+	2	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561147	6561232	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561233	6561338	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561339	6561467	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561339	6561467	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561468	6561560	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561561	6561653	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561561	6561653	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561654	6561782	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561783	6561929	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561783	6561929	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561930	6562013	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562014	6562108	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562014	6562108	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562109	6562198	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562199	6562283	1	+	1	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562199	6562283	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562284	6562412	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562413	6562471	1	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562413	6562471	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562472	6562562	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562563	6562661	1	+	1	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562563	6562661	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562662	6562754	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562755	6562841	1	+	1	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562755	6562841	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562842	6562929	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562930	6563002	1	+	1	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562930	6563002	.	+	.	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	stop_codon	6563003	6563005	.	+	0	transcript_id "Phchi.S1G109300.t2"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	transcript	6557755	6563002	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	start_codon	6557755	6557757	.	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6557755	6557961	0.99	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6557755	6557961	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6557962	6558048	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558049	6558282	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558049	6558282	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558283	6558379	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558380	6558454	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558380	6558454	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558455	6558648	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558649	6558750	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558649	6558750	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558751	6558839	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6558840	6558890	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6558840	6558890	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6558891	6559017	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559018	6559195	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559018	6559195	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559196	6559321	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559322	6559447	1	+	2	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559322	6559447	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559448	6559547	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559548	6559639	1	+	2	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559548	6559639	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559640	6559790	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6559791	6559971	0.91	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6559791	6559971	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6559972	6560080	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560081	6560157	0.87	+	2	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560081	6560157	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560158	6560241	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560242	6560340	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560242	6560340	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560341	6560427	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560428	6560539	0.63	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560428	6560539	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560540	6560646	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560647	6560732	1	+	2	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560647	6560732	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560733	6560822	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6560823	6560987	0.92	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6560823	6560987	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6560988	6561072	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561073	6561115	0.48	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561073	6561115	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561116	6561232	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561233	6561288	0.48	+	2	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561233	6561288	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561289	6561338	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561339	6561467	0.99	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561339	6561467	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561468	6561560	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561561	6561653	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561561	6561653	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561654	6561782	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6561783	6561929	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6561783	6561929	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6561930	6562013	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562014	6562108	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562014	6562108	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562109	6562198	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562199	6562283	1	+	1	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562199	6562283	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562284	6562412	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562413	6562471	1	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562413	6562471	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562472	6562562	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562563	6562661	1	+	1	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562563	6562661	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562662	6562754	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562755	6562841	1	+	1	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562755	6562841	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	intron	6562842	6562929	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	CDS	6562930	6563002	1	+	1	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	exon	6562930	6563002	.	+	.	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
Phchi.S1	AUGUSTUS	stop_codon	6563003	6563005	.	+	0	transcript_id "Phchi.S1G109300.t3"; gene_id "Phchi.S1G109300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4878.t1 is derived from g2048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13189579	13190208	.	-	.	Phchi.S1G203700
Phchi.S1	AUGUSTUS	transcript	13189579	13190208	.	-	.	transcript_id "Phchi.S1G203700.t1"; gene_id "Phchi.S1G203700"
Phchi.S1	AUGUSTUS	stop_codon	13189576	13189578	.	-	0	transcript_id "Phchi.S1G203700.t1"; gene_id "Phchi.S1G203700"
Phchi.S1	AUGUSTUS	CDS	13189579	13190208	0.96	-	0	transcript_id "Phchi.S1G203700.t1"; gene_id "Phchi.S1G203700"
Phchi.S1	AUGUSTUS	exon	13189579	13190208	.	-	.	transcript_id "Phchi.S1G203700.t1"; gene_id "Phchi.S1G203700"
Phchi.S1	AUGUSTUS	start_codon	13190206	13190208	.	-	0	transcript_id "Phchi.S1G203700.t1"; gene_id "Phchi.S1G203700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg431.t1 is derived from g10213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3059136	3059453	.	-	.	Phchi.S6G039000
Phchi.S6	AUGUSTUS	transcript	3059136	3059453	.	-	.	transcript_id "Phchi.S6G039000.t1"; gene_id "Phchi.S6G039000"
Phchi.S6	AUGUSTUS	stop_codon	3059133	3059135	.	-	0	transcript_id "Phchi.S6G039000.t1"; gene_id "Phchi.S6G039000"
Phchi.S6	AUGUSTUS	CDS	3059136	3059453	0.73	-	0	transcript_id "Phchi.S6G039000.t1"; gene_id "Phchi.S6G039000"
Phchi.S6	AUGUSTUS	exon	3059136	3059453	.	-	.	transcript_id "Phchi.S6G039000.t1"; gene_id "Phchi.S6G039000"
Phchi.S6	AUGUSTUS	start_codon	3059451	3059453	.	-	0	transcript_id "Phchi.S6G039000.t1"; gene_id "Phchi.S6G039000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10377.t1 is derived from g7553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47450625	47452480	.	+	.	Phchi.S1G753600
Phchi.S1	AUGUSTUS	transcript	47450625	47452480	.	+	.	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	start_codon	47450625	47450627	.	+	0	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	CDS	47450625	47452329	0.64	+	0	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	exon	47450625	47452329	.	+	.	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	intron	47452330	47452409	.	+	.	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	CDS	47452410	47452480	0.74	+	2	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	exon	47452410	47452480	.	+	.	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
Phchi.S1	AUGUSTUS	stop_codon	47452481	47452483	.	+	0	transcript_id "Phchi.S1G753600.t1"; gene_id "Phchi.S1G753600"
# This transcript jg2863.t2 is derived from g32.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2864.t1 is derived from g33.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	149310	158840	.	-	.	Phchi.S1G002300
Phchi.S1	AUGUSTUS	transcript	149310	158840	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	stop_codon	149307	149309	.	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	149310	149413	1	-	2	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	149310	149413	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	149414	149520	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	149521	149636	0.99	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	149521	149636	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	149637	149728	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	149729	149910	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	149729	149910	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	149911	150043	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150044	150258	0.58	-	2	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150044	150258	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150259	150377	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150378	150399	0.54	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150378	150399	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150400	150619	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150620	150688	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150620	150688	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150689	150767	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150768	150844	1	-	2	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150768	150844	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150845	150920	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150921	151002	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150921	151002	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	151003	151102	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	151103	151325	1	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	151103	151325	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	151326	151559	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	151560	151798	0.91	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	151560	151798	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	151799	151921	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	151922	152224	0.93	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	151922	152224	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	152225	152308	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	152309	153019	0.77	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	152309	153019	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153020	153184	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153185	153329	0.81	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153185	153329	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153330	153419	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153420	153533	1	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153420	153533	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153534	153634	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153635	153746	1	-	2	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153635	153746	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153747	153958	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153959	154164	0.96	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153959	154164	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	154165	154380	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	154381	154538	0.89	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	154381	154538	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	154539	154624	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	154625	155044	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	154625	155044	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155045	155189	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	155190	155273	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	155190	155273	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155274	155429	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	155430	155745	1	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	155430	155745	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155746	155837	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	155838	155983	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	155838	155983	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155984	156081	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156082	156147	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156082	156147	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156148	156277	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156278	156388	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156278	156388	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156389	156571	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156572	156691	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156572	156691	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156692	156880	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156881	156991	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156881	156991	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156992	157070	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157071	157259	0.84	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157071	157259	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157260	157377	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157378	157495	0.99	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157378	157495	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157496	157615	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157616	157668	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157616	157668	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157669	157789	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157790	157909	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157790	157909	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157910	157989	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157990	158076	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157990	158076	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158077	158216	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158217	158427	1	-	1	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158217	158427	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158428	158509	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158510	158634	1	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158510	158634	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158635	158798	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158799	158840	0.67	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158799	158840	.	-	.	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	start_codon	158838	158840	.	-	0	transcript_id "Phchi.S1G002300.t1"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	transcript	149310	158840	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	stop_codon	149307	149309	.	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	149310	149413	1	-	2	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	149310	149413	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	149414	149520	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	149521	149636	0.98	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	149521	149636	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	149637	149728	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	149729	149910	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	149729	149910	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	149911	150043	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150044	150258	0.62	-	2	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150044	150258	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150259	150377	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150378	150399	0.54	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150378	150399	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150400	150619	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150620	150688	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150620	150688	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150689	150767	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150768	150844	1	-	2	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150768	150844	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	150845	150920	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	150921	151002	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	150921	151002	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	151003	151102	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	151103	151325	1	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	151103	151325	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	151326	151559	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	151560	151798	0.9	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	151560	151798	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	151799	151921	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	151922	152224	0.97	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	151922	152224	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	152225	152308	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	152309	153019	0.66	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	152309	153019	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153020	153184	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153185	153329	0.66	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153185	153329	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153330	153419	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153420	153533	1	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153420	153533	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153534	153634	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153635	153746	1	-	2	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153635	153746	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	153747	153958	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	153959	154164	0.97	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	153959	154164	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	154165	154380	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	154381	154538	0.9	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	154381	154538	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	154539	154624	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	154625	155044	0.99	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	154625	155044	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155045	155189	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	155190	155273	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	155190	155273	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155274	155429	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	155430	155745	1	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	155430	155745	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155746	155837	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	155838	155983	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	155838	155983	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	155984	156081	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156082	156147	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156082	156147	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156148	156277	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156278	156388	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156278	156388	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156389	156571	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156572	156691	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156572	156691	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156692	156880	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	156881	156991	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	156881	156991	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	156992	157070	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157071	157259	0.86	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157071	157259	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157260	157377	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157378	157495	0.99	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157378	157495	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157496	157615	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157616	157668	0.69	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157616	157668	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157669	157789	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157790	157893	0.49	-	2	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157790	157893	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	157894	157989	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	157990	158076	0.49	-	2	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	157990	158076	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158077	158216	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158217	158251	0.45	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158217	158251	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158252	158373	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158374	158427	0.47	-	1	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158374	158427	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158428	158509	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158510	158634	1	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158510	158634	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	intron	158635	158798	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	CDS	158799	158840	0.77	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	exon	158799	158840	.	-	.	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
Phchi.S1	AUGUSTUS	start_codon	158838	158840	.	-	0	transcript_id "Phchi.S1G002300.t2"; gene_id "Phchi.S1G002300"
# This transcript jg7227.t2 is derived from g4399.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7228.t1 is derived from g4400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27722434	27727126	.	-	.	Phchi.S1G438700
Phchi.S1	AUGUSTUS	transcript	27722434	27727126	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	stop_codon	27722431	27722433	.	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27722434	27722769	1	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27722434	27722769	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27722770	27722856	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27722857	27723424	0.97	-	1	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27722857	27723424	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27723425	27723527	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27723528	27723760	0.97	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27723528	27723760	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27723761	27723935	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27723936	27724194	1	-	1	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27723936	27724194	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27724195	27724362	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27724363	27724583	1	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27724363	27724583	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27724584	27724681	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27724682	27724778	0.54	-	1	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27724682	27724778	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27724779	27724897	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27724898	27724929	0.67	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27724898	27724929	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27724930	27725047	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27725048	27725183	1	-	1	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27725048	27725183	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27725184	27725271	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27725272	27725639	1	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27725272	27725639	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27725640	27725725	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27725726	27725860	1	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27725726	27725860	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27725861	27725982	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27725983	27726151	1	-	1	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27725983	27726151	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27726152	27726341	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27726342	27726453	1	-	2	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27726342	27726453	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27726454	27726598	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27726599	27726704	1	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27726599	27726704	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27726705	27726800	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27726801	27726864	1	-	1	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27726801	27726864	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	intron	27726865	27727022	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	CDS	27727023	27727126	0.99	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	exon	27727023	27727126	.	-	.	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
Phchi.S1	AUGUSTUS	start_codon	27727124	27727126	.	-	0	transcript_id "Phchi.S1G438700.t1"; gene_id "Phchi.S1G438700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5598.t1 is derived from g2768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17823477	17825188	.	+	.	Phchi.S1G275700
Phchi.S1	AUGUSTUS	transcript	17823477	17825188	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	start_codon	17823477	17823479	.	+	0	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	CDS	17823477	17823481	0.7	+	0	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	exon	17823477	17823481	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	intron	17823482	17823949	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	CDS	17823950	17823973	1	+	1	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	exon	17823950	17823973	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	intron	17823974	17824093	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	CDS	17824094	17824199	1	+	1	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	exon	17824094	17824199	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	intron	17824200	17824319	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	CDS	17824320	17824388	1	+	0	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	exon	17824320	17824388	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	intron	17824389	17824731	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	CDS	17824732	17824932	1	+	0	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	exon	17824732	17824932	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	intron	17824933	17825050	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	CDS	17825051	17825188	0.55	+	0	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	exon	17825051	17825188	.	+	.	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
Phchi.S1	AUGUSTUS	stop_codon	17825189	17825191	.	+	0	transcript_id "Phchi.S1G275700.t1"; gene_id "Phchi.S1G275700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7296.t1 is derived from g4468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28373770	28374764	.	+	.	Phchi.S1G445500
Phchi.S1	AUGUSTUS	transcript	28373770	28374764	.	+	.	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	start_codon	28373770	28373772	.	+	0	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	CDS	28373770	28374233	1	+	0	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	exon	28373770	28374233	.	+	.	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	intron	28374234	28374325	.	+	.	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	CDS	28374326	28374764	0.97	+	1	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	exon	28374326	28374764	.	+	.	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
Phchi.S1	AUGUSTUS	stop_codon	28374765	28374767	.	+	0	transcript_id "Phchi.S1G445500.t1"; gene_id "Phchi.S1G445500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10269.t1 is derived from g7445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46761457	46765241	.	+	.	Phchi.S1G742800
Phchi.S1	AUGUSTUS	transcript	46761457	46765241	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	start_codon	46761457	46761459	.	+	0	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	CDS	46761457	46761896	0.53	+	0	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	exon	46761457	46761896	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	intron	46761897	46761989	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	CDS	46761990	46762512	0.98	+	1	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	exon	46761990	46762512	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	intron	46762513	46762631	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	CDS	46762632	46762833	0.68	+	0	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	exon	46762632	46762833	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	intron	46762834	46762931	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	CDS	46762932	46764301	1	+	2	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	exon	46762932	46764301	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	intron	46764302	46764422	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	CDS	46764423	46765241	1	+	0	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	exon	46764423	46765241	.	+	.	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
Phchi.S1	AUGUSTUS	stop_codon	46765242	46765244	.	+	0	transcript_id "Phchi.S1G742800.t1"; gene_id "Phchi.S1G742800"
# This transcript jg8399.t2 is derived from g5574.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8400.t1 is derived from g5575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35750579	35753374	.	-	.	Phchi.S1G555900
Phchi.S1	AUGUSTUS	transcript	35750579	35753374	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	stop_codon	35750576	35750578	.	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35750579	35750751	1	-	2	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35750579	35750751	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35750752	35750895	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35750896	35750944	1	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35750896	35750944	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35750945	35751035	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35751036	35751123	1	-	1	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35751036	35751123	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35751124	35751211	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35751212	35751336	1	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35751212	35751336	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35751337	35751573	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35751574	35751633	1	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35751574	35751633	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35751634	35751783	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35751784	35751909	1	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35751784	35751909	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35751910	35752010	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35752011	35752104	1	-	1	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35752011	35752104	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35752105	35752228	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35752229	35752319	0.99	-	2	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35752229	35752319	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35752320	35752412	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35752413	35752489	1	-	1	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35752413	35752489	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35752490	35752661	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35752662	35752740	0.95	-	2	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35752662	35752740	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35752741	35752887	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35752888	35752922	0.93	-	1	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35752888	35752922	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	intron	35752923	35753267	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	CDS	35753268	35753374	0.93	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	exon	35753268	35753374	.	-	.	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
Phchi.S1	AUGUSTUS	start_codon	35753372	35753374	.	-	0	transcript_id "Phchi.S1G555900.t1"; gene_id "Phchi.S1G555900"
# This transcript jg13924.t2 is derived from g12391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13925.t1 is derived from g12392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9692385	9693857	.	-	.	Phchi.S3G124400
Phchi.S3	AUGUSTUS	transcript	9692385	9693857	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	stop_codon	9692382	9692384	.	-	0	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	CDS	9692385	9692456	1	-	0	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	exon	9692385	9692456	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	intron	9692457	9692545	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	CDS	9692546	9692635	1	-	0	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	exon	9692546	9692635	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	intron	9692636	9692725	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	CDS	9692726	9692828	1	-	1	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	exon	9692726	9692828	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	intron	9692829	9693032	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	CDS	9693033	9693113	1	-	1	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	exon	9693033	9693113	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	intron	9693114	9693198	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	CDS	9693199	9693857	1	-	0	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	exon	9693199	9693857	.	-	.	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
Phchi.S3	AUGUSTUS	start_codon	9693855	9693857	.	-	0	transcript_id "Phchi.S3G124400.t1"; gene_id "Phchi.S3G124400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15909.t1 is derived from g14379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22161852	22162249	.	-	.	Phchi.S3G322800
Phchi.S3	AUGUSTUS	transcript	22161852	22162249	.	-	.	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	stop_codon	22161849	22161851	.	-	0	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	CDS	22161852	22162114	0.63	-	2	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	exon	22161852	22162114	.	-	.	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	intron	22162115	22162224	.	-	.	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	CDS	22162225	22162249	0.59	-	0	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	exon	22162225	22162249	.	-	.	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
Phchi.S3	AUGUSTUS	start_codon	22162247	22162249	.	-	0	transcript_id "Phchi.S3G322800.t1"; gene_id "Phchi.S3G322800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7179.t1 is derived from g4351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27424464	27425527	.	-	.	Phchi.S1G433800
Phchi.S1	AUGUSTUS	transcript	27424464	27425527	.	-	.	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	stop_codon	27424461	27424463	.	-	0	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	CDS	27424464	27425101	0.61	-	2	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	exon	27424464	27425101	.	-	.	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	intron	27425102	27425213	.	-	.	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	CDS	27425214	27425335	0.82	-	1	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	exon	27425214	27425335	.	-	.	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	intron	27425336	27425474	.	-	.	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	CDS	27425475	27425527	0.85	-	0	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	exon	27425475	27425527	.	-	.	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
Phchi.S1	AUGUSTUS	start_codon	27425525	27425527	.	-	0	transcript_id "Phchi.S1G433800.t1"; gene_id "Phchi.S1G433800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6550.t1 is derived from g3722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23588415	23589399	.	-	.	Phchi.S1G370900
Phchi.S1	AUGUSTUS	transcript	23588415	23589399	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	stop_codon	23588412	23588414	.	-	0	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	CDS	23588415	23588644	1	-	2	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	exon	23588415	23588644	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	intron	23588645	23588764	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	CDS	23588765	23588840	1	-	0	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	exon	23588765	23588840	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	intron	23588841	23588929	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	CDS	23588930	23589019	1	-	0	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	exon	23588930	23589019	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	intron	23589020	23589116	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	CDS	23589117	23589181	0.79	-	2	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	exon	23589117	23589181	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	intron	23589182	23589344	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	CDS	23589345	23589399	0.79	-	0	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	exon	23589345	23589399	.	-	.	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
Phchi.S1	AUGUSTUS	start_codon	23589397	23589399	.	-	0	transcript_id "Phchi.S1G370900.t1"; gene_id "Phchi.S1G370900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8393.t1 is derived from g5568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35681603	35682398	.	-	.	Phchi.S1G555200
Phchi.S1	AUGUSTUS	transcript	35681603	35682398	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	stop_codon	35681600	35681602	.	-	0	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	CDS	35681603	35681732	0.87	-	1	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	exon	35681603	35681732	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	intron	35681733	35681907	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	CDS	35681908	35681989	0.97	-	2	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	exon	35681908	35681989	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	intron	35681990	35682152	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	CDS	35682153	35682166	0.87	-	1	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	exon	35682153	35682166	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	intron	35682167	35682381	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	CDS	35682382	35682398	0.58	-	0	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	exon	35682382	35682398	.	-	.	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
Phchi.S1	AUGUSTUS	start_codon	35682396	35682398	.	-	0	transcript_id "Phchi.S1G555200.t1"; gene_id "Phchi.S1G555200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14666.t1 is derived from g13134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14048518	14052520	.	-	.	Phchi.S3G198500
Phchi.S3	AUGUSTUS	transcript	14048518	14052520	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	stop_codon	14048515	14048517	.	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14048518	14048574	0.94	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14048518	14048574	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14048575	14048655	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14048656	14048844	1	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14048656	14048844	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14048845	14048937	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14048938	14049095	1	-	2	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14048938	14049095	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14049096	14049180	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14049181	14049271	0.98	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14049181	14049271	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14049272	14049374	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14049375	14049549	0.96	-	1	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14049375	14049549	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14049550	14049659	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14049660	14049790	1	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14049660	14049790	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14049791	14049913	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14049914	14050132	1	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14049914	14050132	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14050133	14050252	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14050253	14050382	1	-	1	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14050253	14050382	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14050383	14050485	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14050486	14050552	1	-	2	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14050486	14050552	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14050553	14050722	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14050723	14050817	1	-	1	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14050723	14050817	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14050818	14050903	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14050904	14050975	1	-	1	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14050904	14050975	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14050976	14051078	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14051079	14051134	1	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14051079	14051134	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14051135	14051251	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14051252	14051321	1	-	1	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14051252	14051321	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14051322	14051416	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14051417	14051490	1	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14051417	14051490	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14051491	14051623	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14051624	14051749	1	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14051624	14051749	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	intron	14051750	14051941	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	CDS	14051942	14052520	0.89	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	exon	14051942	14052520	.	-	.	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
Phchi.S3	AUGUSTUS	start_codon	14052518	14052520	.	-	0	transcript_id "Phchi.S3G198500.t1"; gene_id "Phchi.S3G198500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5871.t1 is derived from g3041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19488904	19491353	.	+	.	Phchi.S1G303000
Phchi.S1	AUGUSTUS	transcript	19488904	19491353	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	start_codon	19488904	19488906	.	+	0	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19488904	19488973	1	+	0	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19488904	19488973	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19488974	19489456	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19489457	19489698	1	+	2	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19489457	19489698	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19489699	19489817	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19489818	19489921	1	+	0	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19489818	19489921	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19489922	19490054	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19490055	19490248	1	+	1	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19490055	19490248	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19490249	19490339	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19490340	19490470	1	+	2	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19490340	19490470	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19490471	19490638	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19490639	19490800	1	+	0	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19490639	19490800	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19490801	19490963	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19490964	19491025	1	+	0	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19490964	19491025	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19491026	19491141	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19491142	19491237	1	+	1	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19491142	19491237	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	intron	19491238	19491319	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	CDS	19491320	19491353	1	+	1	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	exon	19491320	19491353	.	+	.	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
Phchi.S1	AUGUSTUS	stop_codon	19491354	19491356	.	+	0	transcript_id "Phchi.S1G303000.t1"; gene_id "Phchi.S1G303000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13189.t1 is derived from g11654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4596668	4598374	.	+	.	Phchi.S3G050800
Phchi.S3	AUGUSTUS	transcript	4596668	4598374	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	start_codon	4596668	4596670	.	+	0	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4596668	4596842	1	+	0	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4596668	4596842	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	intron	4596843	4597081	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4597082	4597198	1	+	2	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4597082	4597198	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	intron	4597199	4597274	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4597275	4597551	1	+	2	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4597275	4597551	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	intron	4597552	4597636	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4597637	4597687	1	+	1	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4597637	4597687	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	intron	4597688	4597775	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4597776	4597872	1	+	1	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4597776	4597872	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	intron	4597873	4597956	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4597957	4598056	1	+	0	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4597957	4598056	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	intron	4598057	4598135	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	CDS	4598136	4598374	0.99	+	2	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	exon	4598136	4598374	.	+	.	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
Phchi.S3	AUGUSTUS	stop_codon	4598375	4598377	.	+	0	transcript_id "Phchi.S3G050800.t1"; gene_id "Phchi.S3G050800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14404.t1 is derived from g12872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12673861	12678751	.	-	.	Phchi.S3G172300
Phchi.S3	AUGUSTUS	transcript	12673861	12678751	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	stop_codon	12673858	12673860	.	-	0	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12673861	12674984	0.8	-	2	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12673861	12674984	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12674985	12675065	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12675066	12675558	0.94	-	0	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12675066	12675558	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12675559	12675753	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12675754	12676161	0.99	-	0	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12675754	12676161	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12676162	12676276	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12676277	12676425	0.97	-	2	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12676277	12676425	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12676426	12676758	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12676759	12678751	0.81	-	0	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12676759	12678751	.	-	.	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	start_codon	12678749	12678751	.	-	0	transcript_id "Phchi.S3G172300.t1"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	transcript	12673861	12676689	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	stop_codon	12673858	12673860	.	-	0	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12673861	12674984	0.82	-	2	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12673861	12674984	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12674985	12675065	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12675066	12675558	0.93	-	0	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12675066	12675558	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12675559	12675753	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12675754	12676161	0.97	-	0	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12675754	12676161	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12676162	12676276	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12676277	12676425	0.99	-	2	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12676277	12676425	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	intron	12676426	12676652	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	CDS	12676653	12676689	0.7	-	0	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	exon	12676653	12676689	.	-	.	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
Phchi.S3	AUGUSTUS	start_codon	12676687	12676689	.	-	0	transcript_id "Phchi.S3G172300.t2"; gene_id "Phchi.S3G172300"
# This transcript jg3813.t2 is derived from g982.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3814.t1 is derived from g983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5854513	5856421	.	+	.	Phchi.S1G097300
Phchi.S1	AUGUSTUS	transcript	5854513	5856421	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	start_codon	5854513	5854515	.	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	CDS	5854513	5854989	0.41	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	exon	5854513	5854989	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	intron	5854990	5855101	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	CDS	5855102	5855269	1	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	exon	5855102	5855269	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	intron	5855270	5855404	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	CDS	5855405	5855506	0.87	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	exon	5855405	5855506	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	intron	5855507	5855634	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	CDS	5855635	5855769	0.81	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	exon	5855635	5855769	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	intron	5855770	5855875	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	CDS	5855876	5856051	0.97	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	exon	5855876	5856051	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	intron	5856052	5856153	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	CDS	5856154	5856421	1	+	1	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	exon	5856154	5856421	.	+	.	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
Phchi.S1	AUGUSTUS	stop_codon	5856422	5856424	.	+	0	transcript_id "Phchi.S1G097300.t1"; gene_id "Phchi.S1G097300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6249.t1 is derived from g3421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21868962	21871495	.	-	.	Phchi.S1G340800
Phchi.S1	AUGUSTUS	transcript	21868962	21871495	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	stop_codon	21868959	21868961	.	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21868962	21869207	1	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21868962	21869207	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21869208	21869361	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21869362	21869580	0.94	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21869362	21869580	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21869581	21869685	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21869686	21869868	0.89	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21869686	21869868	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21869869	21869991	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21869992	21870126	1	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21869992	21870126	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21870127	21870220	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21870221	21870354	1	-	2	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21870221	21870354	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21870355	21870447	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21870448	21870769	1	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21870448	21870769	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21870770	21870894	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21870895	21871019	1	-	2	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21870895	21871019	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21871020	21871115	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21871116	21871248	1	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21871116	21871248	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	intron	21871249	21871390	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	CDS	21871391	21871495	1	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	exon	21871391	21871495	.	-	.	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
Phchi.S1	AUGUSTUS	start_codon	21871493	21871495	.	-	0	transcript_id "Phchi.S1G340800.t1"; gene_id "Phchi.S1G340800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13239.t1 is derived from g11704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4880932	4881723	.	+	.	Phchi.S3G055800
Phchi.S3	AUGUSTUS	transcript	4880932	4881723	.	+	.	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	start_codon	4880932	4880934	.	+	0	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	CDS	4880932	4881204	0.6	+	0	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	exon	4880932	4881204	.	+	.	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	intron	4881205	4881384	.	+	.	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	CDS	4881385	4881723	0.24	+	0	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	exon	4881385	4881723	.	+	.	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
Phchi.S3	AUGUSTUS	stop_codon	4881724	4881726	.	+	0	transcript_id "Phchi.S3G055800.t1"; gene_id "Phchi.S3G055800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13046.t1 is derived from g11511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3865466	3870980	.	+	.	Phchi.S3G036500
Phchi.S3	AUGUSTUS	transcript	3865466	3870980	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	start_codon	3865466	3865468	.	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3865466	3866048	0.75	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3865466	3866048	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3866049	3866233	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3866234	3866847	0.96	+	2	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3866234	3866847	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3866848	3866965	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3866966	3867295	0.49	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3866966	3867295	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3867296	3867443	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3867444	3868466	1	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3867444	3868466	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3868467	3868565	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3868566	3868830	1	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3868566	3868830	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3868831	3868923	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3868924	3869789	1	+	2	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3868924	3869789	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3869790	3869906	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3869907	3870129	0.79	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3869907	3870129	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3870130	3870207	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3870208	3870272	0.79	+	2	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3870208	3870272	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3870273	3870432	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3870433	3870475	0.95	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3870433	3870475	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3870476	3870628	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3870629	3870831	0.94	+	2	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3870629	3870831	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	intron	3870832	3870935	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	CDS	3870936	3870980	0.92	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	exon	3870936	3870980	.	+	.	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
Phchi.S3	AUGUSTUS	stop_codon	3870981	3870983	.	+	0	transcript_id "Phchi.S3G036500.t1"; gene_id "Phchi.S3G036500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12840.t1 is derived from g11305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2646842	2647749	.	-	.	Phchi.S3G015900
Phchi.S3	AUGUSTUS	transcript	2646842	2647749	.	-	.	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	stop_codon	2646839	2646841	.	-	0	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	CDS	2646842	2647279	0.47	-	0	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	exon	2646842	2647279	.	-	.	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	intron	2647280	2647401	.	-	.	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	CDS	2647402	2647749	0.81	-	0	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	exon	2647402	2647749	.	-	.	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
Phchi.S3	AUGUSTUS	start_codon	2647747	2647749	.	-	0	transcript_id "Phchi.S3G015900.t1"; gene_id "Phchi.S3G015900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg98.t1 is derived from g9880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	504504	505763	.	-	.	Phchi.S6G005700
Phchi.S6	AUGUSTUS	transcript	504504	505763	.	-	.	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	stop_codon	504501	504503	.	-	0	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	CDS	504504	504656	0.43	-	0	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	exon	504504	504656	.	-	.	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	intron	504657	504887	.	-	.	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	CDS	504888	505763	0.38	-	0	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	exon	504888	505763	.	-	.	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
Phchi.S6	AUGUSTUS	start_codon	505761	505763	.	-	0	transcript_id "Phchi.S6G005700.t1"; gene_id "Phchi.S6G005700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6147.t1 is derived from g3318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21154508	21155522	.	+	.	Phchi.S1G330600
Phchi.S1	AUGUSTUS	transcript	21154508	21155522	.	+	.	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	start_codon	21154508	21154510	.	+	0	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	CDS	21154508	21154590	0.56	+	0	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	exon	21154508	21154590	.	+	.	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	intron	21154591	21154679	.	+	.	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	CDS	21154680	21154721	0.36	+	1	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	exon	21154680	21154721	.	+	.	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	intron	21154722	21155377	.	+	.	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	CDS	21155378	21155522	0.74	+	1	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	exon	21155378	21155522	.	+	.	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
Phchi.S1	AUGUSTUS	stop_codon	21155523	21155525	.	+	0	transcript_id "Phchi.S1G330600.t1"; gene_id "Phchi.S1G330600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9305.t1 is derived from g6480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40866571	40872007	.	-	.	Phchi.S1G646400
Phchi.S1	AUGUSTUS	transcript	40866571	40872007	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	stop_codon	40866568	40866570	.	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40866571	40866633	0.89	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40866571	40866633	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40866634	40866959	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40866960	40867028	0.52	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40866960	40867028	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40867029	40867573	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40867574	40867753	0.44	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40867574	40867753	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40867754	40867854	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40867855	40867987	0.9	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40867855	40867987	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40867988	40868074	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40868075	40868270	1	-	2	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40868075	40868270	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40868271	40868350	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40868351	40868419	1	-	2	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40868351	40868419	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40868420	40868517	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40868518	40868644	1	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40868518	40868644	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40868645	40868733	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40868734	40868966	1	-	2	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40868734	40868966	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40868967	40869053	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40869054	40869232	0.47	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40869054	40869232	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40869233	40869320	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40869321	40869395	0.99	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40869321	40869395	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40869396	40869501	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40869502	40869576	0.95	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40869502	40869576	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40869577	40869662	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40869663	40869734	0.8	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40869663	40869734	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40869735	40869839	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40869840	40869911	1	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40869840	40869911	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40869912	40870001	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40870002	40870119	1	-	2	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40870002	40870119	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40870120	40870265	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40870266	40870537	0.97	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40870266	40870537	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40870538	40870643	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40870644	40870913	0.94	-	1	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40870644	40870913	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40870914	40871033	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40871034	40871314	0.63	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40871034	40871314	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40871315	40871446	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40871447	40871736	0.52	-	2	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40871447	40871736	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	intron	40871737	40871865	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	CDS	40871866	40872007	0.5	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	exon	40871866	40872007	.	-	.	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
Phchi.S1	AUGUSTUS	start_codon	40872005	40872007	.	-	0	transcript_id "Phchi.S1G646400.t1"; gene_id "Phchi.S1G646400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4750.t1 is derived from g1920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12614065	12614412	.	+	.	Phchi.S1G190900
Phchi.S1	AUGUSTUS	transcript	12614065	12614412	.	+	.	transcript_id "Phchi.S1G190900.t1"; gene_id "Phchi.S1G190900"
Phchi.S1	AUGUSTUS	start_codon	12614065	12614067	.	+	0	transcript_id "Phchi.S1G190900.t1"; gene_id "Phchi.S1G190900"
Phchi.S1	AUGUSTUS	CDS	12614065	12614412	0.35	+	0	transcript_id "Phchi.S1G190900.t1"; gene_id "Phchi.S1G190900"
Phchi.S1	AUGUSTUS	exon	12614065	12614412	.	+	.	transcript_id "Phchi.S1G190900.t1"; gene_id "Phchi.S1G190900"
Phchi.S1	AUGUSTUS	stop_codon	12614413	12614415	.	+	0	transcript_id "Phchi.S1G190900.t1"; gene_id "Phchi.S1G190900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12992.t1 is derived from g11457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3503730	3504896	.	+	.	Phchi.S3G031100
Phchi.S3	AUGUSTUS	transcript	3503730	3504896	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	start_codon	3503730	3503732	.	+	0	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3503730	3503732	1	+	0	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3503730	3503732	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	intron	3503733	3503871	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3503872	3503989	1	+	0	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3503872	3503989	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	intron	3503990	3504105	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3504106	3504142	1	+	2	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3504106	3504142	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	intron	3504143	3504256	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3504257	3504284	1	+	1	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3504257	3504284	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	intron	3504285	3504373	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3504374	3504526	1	+	0	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3504374	3504526	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	intron	3504527	3504624	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3504625	3504727	1	+	0	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3504625	3504727	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	intron	3504728	3504834	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	CDS	3504835	3504896	1	+	2	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	exon	3504835	3504896	.	+	.	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
Phchi.S3	AUGUSTUS	stop_codon	3504897	3504899	.	+	0	transcript_id "Phchi.S3G031100.t1"; gene_id "Phchi.S3G031100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2587.t1 is derived from g9507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7497518	7499350	.	+	.	Phchi.S5G119600
Phchi.S5	AUGUSTUS	transcript	7497518	7499350	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	start_codon	7497518	7497520	.	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7497518	7497548	0.99	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7497518	7497548	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7497549	7497631	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7497632	7497750	1	+	2	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7497632	7497750	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7497751	7497843	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7497844	7497975	1	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7497844	7497975	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7497976	7498104	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7498105	7498209	0.98	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7498105	7498209	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7498210	7498323	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7498324	7498428	0.97	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7498324	7498428	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7498429	7498537	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7498538	7498676	1	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7498538	7498676	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7498677	7498926	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7498927	7499048	0.98	+	2	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7498927	7499048	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7499049	7499155	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7499156	7499218	1	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7499156	7499218	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	intron	7499219	7499284	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	CDS	7499285	7499350	1	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	exon	7499285	7499350	.	+	.	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
Phchi.S5	AUGUSTUS	stop_codon	7499351	7499353	.	+	0	transcript_id "Phchi.S5G119600.t1"; gene_id "Phchi.S5G119600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6919.t1 is derived from g4091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25987900	25989404	.	+	.	Phchi.S1G407800
Phchi.S1	AUGUSTUS	transcript	25987900	25989404	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	start_codon	25987900	25987902	.	+	0	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25987900	25987905	1	+	0	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25987900	25987905	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	intron	25987906	25988030	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25988031	25988095	1	+	0	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25988031	25988095	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	intron	25988096	25988297	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25988298	25988355	1	+	1	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25988298	25988355	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	intron	25988356	25988454	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25988455	25988563	1	+	0	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25988455	25988563	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	intron	25988564	25988677	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25988678	25988794	1	+	2	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25988678	25988794	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	intron	25988795	25988923	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25988924	25989079	1	+	2	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25988924	25989079	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	intron	25989080	25989162	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	CDS	25989163	25989404	1	+	2	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	exon	25989163	25989404	.	+	.	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
Phchi.S1	AUGUSTUS	stop_codon	25989405	25989407	.	+	0	transcript_id "Phchi.S1G407800.t1"; gene_id "Phchi.S1G407800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13765.t1 is derived from g12232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8781948	8782867	.	+	.	Phchi.S3G108400
Phchi.S3	AUGUSTUS	transcript	8781948	8782867	.	+	.	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	start_codon	8781948	8781950	.	+	0	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	CDS	8781948	8782142	0.66	+	0	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	exon	8781948	8782142	.	+	.	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	intron	8782143	8782255	.	+	.	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	CDS	8782256	8782867	0.97	+	0	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	exon	8782256	8782867	.	+	.	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
Phchi.S3	AUGUSTUS	stop_codon	8782868	8782870	.	+	0	transcript_id "Phchi.S3G108400.t1"; gene_id "Phchi.S3G108400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2654.t1 is derived from g9574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8047658	8048254	.	+	.	Phchi.S5G126300
Phchi.S5	AUGUSTUS	transcript	8047658	8048254	.	+	.	transcript_id "Phchi.S5G126300.t1"; gene_id "Phchi.S5G126300"
Phchi.S5	AUGUSTUS	start_codon	8047658	8047660	.	+	0	transcript_id "Phchi.S5G126300.t1"; gene_id "Phchi.S5G126300"
Phchi.S5	AUGUSTUS	CDS	8047658	8048254	0.47	+	0	transcript_id "Phchi.S5G126300.t1"; gene_id "Phchi.S5G126300"
Phchi.S5	AUGUSTUS	exon	8047658	8048254	.	+	.	transcript_id "Phchi.S5G126300.t1"; gene_id "Phchi.S5G126300"
Phchi.S5	AUGUSTUS	stop_codon	8048255	8048257	.	+	0	transcript_id "Phchi.S5G126300.t1"; gene_id "Phchi.S5G126300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12474.t1 is derived from g8151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	26457416	26458403	.	-	.	Phchi.S2G055400
Phchi.S2	AUGUSTUS	transcript	26457416	26458403	.	-	.	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	stop_codon	26457413	26457415	.	-	0	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	CDS	26457416	26458041	0.96	-	2	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	exon	26457416	26458041	.	-	.	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	intron	26458042	26458387	.	-	.	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	CDS	26458388	26458403	0.95	-	0	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	exon	26458388	26458403	.	-	.	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
Phchi.S2	AUGUSTUS	start_codon	26458401	26458403	.	-	0	transcript_id "Phchi.S2G055400.t1"; gene_id "Phchi.S2G055400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6913.t1 is derived from g4085.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25971709	25974630	.	-	.	Phchi.S1G407200
Phchi.S1	AUGUSTUS	transcript	25971709	25974630	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	stop_codon	25971706	25971708	.	-	0	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25971709	25971947	0.84	-	2	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25971709	25971947	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25971948	25972057	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25972058	25972474	0.95	-	2	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25972058	25972474	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25972475	25972647	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25972648	25972742	1	-	1	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25972648	25972742	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25972743	25972850	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25972851	25972963	0.74	-	0	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25972851	25972963	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25972964	25973085	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25973086	25973451	0.54	-	0	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25973086	25973451	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25973452	25973554	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25973555	25973732	0.91	-	1	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25973555	25973732	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25973733	25973908	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25973909	25974052	1	-	1	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25973909	25974052	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25974053	25974421	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25974422	25974630	0.75	-	0	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25974422	25974630	.	-	.	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	start_codon	25974628	25974630	.	-	0	transcript_id "Phchi.S1G407200.t1"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	transcript	25971709	25974630	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	stop_codon	25971706	25971708	.	-	0	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25971709	25971947	0.81	-	2	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25971709	25971947	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25971948	25972057	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25972058	25972474	0.96	-	2	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25972058	25972474	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25972475	25972647	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25972648	25972742	1	-	1	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25972648	25972742	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25972743	25972850	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25972851	25972963	0.56	-	0	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25972851	25972963	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25972964	25973085	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25973086	25973451	0.46	-	0	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25973086	25973451	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25973452	25973554	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25973555	25973732	0.94	-	1	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25973555	25973732	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25973733	25973908	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25973909	25974052	1	-	1	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25973909	25974052	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	intron	25974053	25974463	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	CDS	25974464	25974630	0.68	-	0	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	exon	25974464	25974630	.	-	.	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
Phchi.S1	AUGUSTUS	start_codon	25974628	25974630	.	-	0	transcript_id "Phchi.S1G407200.t2"; gene_id "Phchi.S1G407200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9001.t1 is derived from g6176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39109366	39111660	.	+	.	Phchi.S1G616000
Phchi.S1	AUGUSTUS	transcript	39109366	39111660	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	start_codon	39109366	39109368	.	+	0	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39109366	39109489	0.95	+	0	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39109366	39109489	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39109490	39109603	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39109604	39109660	0.99	+	2	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39109604	39109660	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39109661	39109777	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39109778	39109868	1	+	2	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39109778	39109868	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39109869	39110045	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39110046	39110206	1	+	1	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39110046	39110206	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39110207	39110465	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39110466	39110593	1	+	2	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39110466	39110593	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39110594	39110781	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39110782	39110919	1	+	0	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39110782	39110919	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39110920	39111046	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39111047	39111139	1	+	0	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39111047	39111139	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39111140	39111232	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39111233	39111353	1	+	0	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39111233	39111353	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	intron	39111354	39111523	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	CDS	39111524	39111660	0.83	+	2	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	exon	39111524	39111660	.	+	.	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
Phchi.S1	AUGUSTUS	stop_codon	39111661	39111663	.	+	0	transcript_id "Phchi.S1G616000.t1"; gene_id "Phchi.S1G616000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5025.t1 is derived from g2195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14101366	14102839	.	-	.	Phchi.S1G218400
Phchi.S1	AUGUSTUS	transcript	14101366	14102839	.	-	.	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	stop_codon	14101363	14101365	.	-	0	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	CDS	14101366	14101548	1	-	0	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	exon	14101366	14101548	.	-	.	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	intron	14101549	14101747	.	-	.	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	CDS	14101748	14102839	1	-	0	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	exon	14101748	14102839	.	-	.	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
Phchi.S1	AUGUSTUS	start_codon	14102837	14102839	.	-	0	transcript_id "Phchi.S1G218400.t1"; gene_id "Phchi.S1G218400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6574.t1 is derived from g3746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23818847	23819540	.	-	.	Phchi.S1G373300
Phchi.S1	AUGUSTUS	transcript	23818847	23819540	.	-	.	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	stop_codon	23818844	23818846	.	-	0	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	CDS	23818847	23818859	0.96	-	1	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	exon	23818847	23818859	.	-	.	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	intron	23818860	23818948	.	-	.	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	CDS	23818949	23819199	0.87	-	0	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	exon	23818949	23819199	.	-	.	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	intron	23819200	23819279	.	-	.	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	CDS	23819280	23819540	0.51	-	0	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	exon	23819280	23819540	.	-	.	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
Phchi.S1	AUGUSTUS	start_codon	23819538	23819540	.	-	0	transcript_id "Phchi.S1G373300.t1"; gene_id "Phchi.S1G373300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4529.t1 is derived from g1699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10978509	10981172	.	-	.	Phchi.S1G168800
Phchi.S1	AUGUSTUS	transcript	10978509	10981172	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	stop_codon	10978506	10978508	.	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10978509	10978655	0.92	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10978509	10978655	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10978656	10978731	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10978732	10978848	1	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10978732	10978848	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10978849	10978938	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10978939	10978983	0.52	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10978939	10978983	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10978984	10979093	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10979094	10979204	0.52	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10979094	10979204	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10979205	10979279	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10979280	10979367	1	-	1	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10979280	10979367	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10979368	10979479	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10979480	10979574	1	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10979480	10979574	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10979575	10979691	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10979692	10979853	0.97	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10979692	10979853	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10979854	10980129	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10980130	10980257	1	-	2	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10980130	10980257	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10980258	10980342	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10980343	10980458	1	-	1	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10980343	10980458	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10980459	10980547	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10980548	10980657	0.58	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10980548	10980657	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10980658	10980744	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10980745	10980806	0.34	-	2	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10980745	10980806	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	intron	10980807	10980919	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	CDS	10980920	10981172	0.6	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	exon	10980920	10981172	.	-	.	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
Phchi.S1	AUGUSTUS	start_codon	10981170	10981172	.	-	0	transcript_id "Phchi.S1G168800.t1"; gene_id "Phchi.S1G168800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg539.t1 is derived from g10321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3942306	3943178	.	+	.	Phchi.S6G049800
Phchi.S6	AUGUSTUS	transcript	3942306	3943178	.	+	.	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	start_codon	3942306	3942308	.	+	0	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	CDS	3942306	3942365	0.98	+	0	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	exon	3942306	3942365	.	+	.	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	intron	3942366	3942563	.	+	.	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	CDS	3942564	3942656	0.4	+	0	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	exon	3942564	3942656	.	+	.	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	intron	3942657	3942899	.	+	.	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	CDS	3942900	3943178	0.7	+	0	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	exon	3942900	3943178	.	+	.	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
Phchi.S6	AUGUSTUS	stop_codon	3943179	3943181	.	+	0	transcript_id "Phchi.S6G049800.t1"; gene_id "Phchi.S6G049800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4923.t1 is derived from g2093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13589971	13592402	.	+	.	Phchi.S1G208200
Phchi.S1	AUGUSTUS	transcript	13589971	13592402	.	+	.	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	start_codon	13589971	13589973	.	+	0	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	CDS	13589971	13591102	0.39	+	0	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	exon	13589971	13591102	.	+	.	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	intron	13591103	13591203	.	+	.	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	CDS	13591204	13592402	0.49	+	2	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	exon	13591204	13592402	.	+	.	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
Phchi.S1	AUGUSTUS	stop_codon	13592403	13592405	.	+	0	transcript_id "Phchi.S1G208200.t1"; gene_id "Phchi.S1G208200"
# This transcript jg5252.t2 is derived from g2422.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5252.t3 is derived from g2422.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5252.t4 is derived from g2422.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5253.t1 is derived from g2423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15875716	15877077	.	+	.	Phchi.S1G241200
Phchi.S1	AUGUSTUS	transcript	15875716	15877077	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	start_codon	15875716	15875718	.	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15875716	15875733	0.37	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15875716	15875733	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	intron	15875734	15875887	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15875888	15875947	0.58	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15875888	15875947	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	intron	15875948	15876062	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15876063	15876205	0.44	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15876063	15876205	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	intron	15876206	15876285	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15876286	15876457	1	+	1	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15876286	15876457	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	intron	15876458	15876584	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15876585	15876710	1	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15876585	15876710	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	intron	15876711	15876857	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15876858	15876923	0.97	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15876858	15876923	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	intron	15876924	15877029	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	CDS	15877030	15877077	0.81	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	exon	15877030	15877077	.	+	.	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
Phchi.S1	AUGUSTUS	stop_codon	15877078	15877080	.	+	0	transcript_id "Phchi.S1G241200.t1"; gene_id "Phchi.S1G241200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3244.t1 is derived from g413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2420139	2420666	.	+	.	Phchi.S1G040300
Phchi.S1	AUGUSTUS	transcript	2420139	2420666	.	+	.	transcript_id "Phchi.S1G040300.t1"; gene_id "Phchi.S1G040300"
Phchi.S1	AUGUSTUS	start_codon	2420139	2420141	.	+	0	transcript_id "Phchi.S1G040300.t1"; gene_id "Phchi.S1G040300"
Phchi.S1	AUGUSTUS	CDS	2420139	2420666	0.78	+	0	transcript_id "Phchi.S1G040300.t1"; gene_id "Phchi.S1G040300"
Phchi.S1	AUGUSTUS	exon	2420139	2420666	.	+	.	transcript_id "Phchi.S1G040300.t1"; gene_id "Phchi.S1G040300"
Phchi.S1	AUGUSTUS	stop_codon	2420667	2420669	.	+	0	transcript_id "Phchi.S1G040300.t1"; gene_id "Phchi.S1G040300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10323.t1 is derived from g7499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47110571	47111752	.	+	.	Phchi.S1G748200
Phchi.S1	AUGUSTUS	transcript	47110571	47111752	.	+	.	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	start_codon	47110571	47110573	.	+	0	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	CDS	47110571	47111362	0.63	+	0	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	exon	47110571	47111362	.	+	.	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	intron	47111363	47111491	.	+	.	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	CDS	47111492	47111633	0.86	+	0	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	exon	47111492	47111633	.	+	.	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	intron	47111634	47111726	.	+	.	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	CDS	47111727	47111752	0.88	+	2	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	exon	47111727	47111752	.	+	.	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
Phchi.S1	AUGUSTUS	stop_codon	47111753	47111755	.	+	0	transcript_id "Phchi.S1G748200.t1"; gene_id "Phchi.S1G748200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12678.t1 is derived from g14412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	20605	22177	.	-	.	Phchi.C62G000900
Phchi.C62	AUGUSTUS	transcript	20605	22177	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	stop_codon	20602	20604	.	-	0	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	CDS	20605	20816	1	-	2	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	exon	20605	20816	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	intron	20817	20903	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	CDS	20904	21168	1	-	0	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	exon	20904	21168	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	intron	21169	21238	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	CDS	21239	21475	0.4	-	0	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	exon	21239	21475	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	intron	21476	21605	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	CDS	21606	21634	0.42	-	2	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	exon	21606	21634	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	intron	21635	21808	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	CDS	21809	21935	1	-	0	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	exon	21809	21935	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	intron	21936	22018	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	CDS	22019	22177	1	-	0	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	exon	22019	22177	.	-	.	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
Phchi.C62	AUGUSTUS	start_codon	22175	22177	.	-	0	transcript_id "Phchi.C62G000900.t1"; gene_id "Phchi.C62G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3608.t1 is derived from g777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4728480	4730071	.	+	.	Phchi.S1G076700
Phchi.S1	AUGUSTUS	transcript	4728480	4730071	.	+	.	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	start_codon	4728480	4728482	.	+	0	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	CDS	4728480	4729604	0.74	+	0	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	exon	4728480	4729604	.	+	.	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	intron	4729605	4729696	.	+	.	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	CDS	4729697	4730071	0.72	+	0	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	exon	4729697	4730071	.	+	.	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
Phchi.S1	AUGUSTUS	stop_codon	4730072	4730074	.	+	0	transcript_id "Phchi.S1G076700.t1"; gene_id "Phchi.S1G076700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15734.t1 is derived from g14204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20958653	20960817	.	+	.	Phchi.S3G305300
Phchi.S3	AUGUSTUS	transcript	20958653	20960817	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	start_codon	20958653	20958655	.	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20958653	20958738	0.98	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20958653	20958738	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20958739	20958827	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20958828	20958917	1	+	1	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20958828	20958917	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20958918	20959037	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20959038	20959130	1	+	1	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20959038	20959130	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20959131	20959249	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20959250	20959322	1	+	1	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20959250	20959322	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20959323	20959417	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20959418	20959482	1	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20959418	20959482	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20959483	20959557	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20959558	20959651	1	+	1	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20959558	20959651	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20959652	20959813	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20959814	20959906	1	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20959814	20959906	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20959907	20959982	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20959983	20960018	1	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20959983	20960018	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20960019	20960201	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20960202	20960242	1	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20960202	20960242	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20960243	20960336	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20960337	20960425	1	+	1	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20960337	20960425	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20960426	20960516	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20960517	20960605	1	+	2	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20960517	20960605	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	intron	20960606	20960691	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	CDS	20960692	20960817	1	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	exon	20960692	20960817	.	+	.	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
Phchi.S3	AUGUSTUS	stop_codon	20960818	20960820	.	+	0	transcript_id "Phchi.S3G305300.t1"; gene_id "Phchi.S3G305300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg610.t1 is derived from g10392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4393139	4393828	.	+	.	Phchi.S6G056900
Phchi.S6	AUGUSTUS	transcript	4393139	4393828	.	+	.	transcript_id "Phchi.S6G056900.t1"; gene_id "Phchi.S6G056900"
Phchi.S6	AUGUSTUS	start_codon	4393139	4393141	.	+	0	transcript_id "Phchi.S6G056900.t1"; gene_id "Phchi.S6G056900"
Phchi.S6	AUGUSTUS	CDS	4393139	4393828	0.96	+	0	transcript_id "Phchi.S6G056900.t1"; gene_id "Phchi.S6G056900"
Phchi.S6	AUGUSTUS	exon	4393139	4393828	.	+	.	transcript_id "Phchi.S6G056900.t1"; gene_id "Phchi.S6G056900"
Phchi.S6	AUGUSTUS	stop_codon	4393829	4393831	.	+	0	transcript_id "Phchi.S6G056900.t1"; gene_id "Phchi.S6G056900"
# This transcript jg5911.t2 is derived from g3082.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5912.t1 is derived from g3083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19752796	19758508	.	+	.	Phchi.S1G307100
Phchi.S1	AUGUSTUS	transcript	19752796	19758508	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	start_codon	19752796	19752798	.	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19752796	19753566	0.99	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19752796	19753566	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19753567	19753736	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19753737	19753851	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19753737	19753851	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19753852	19753944	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19753945	19754045	1	+	2	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19753945	19754045	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19754046	19754201	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19754202	19754293	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19754202	19754293	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19754294	19754406	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19754407	19754542	1	+	1	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19754407	19754542	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19754543	19754669	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19754670	19754741	0.98	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19754670	19754741	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19754742	19754843	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19754844	19754945	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19754844	19754945	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19754946	19755100	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19755101	19755199	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19755101	19755199	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19755200	19755396	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19755397	19755507	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19755397	19755507	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19755508	19755621	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19755622	19755828	0.98	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19755622	19755828	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19755829	19756006	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19756007	19756114	0.97	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19756007	19756114	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19756115	19756215	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19756216	19756311	0.8	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19756216	19756311	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19756312	19756480	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19756481	19756537	0.95	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19756481	19756537	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19756538	19756644	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19756645	19756791	0.72	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19756645	19756791	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19756792	19756894	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19756895	19756954	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19756895	19756954	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19756955	19757096	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19757097	19757201	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19757097	19757201	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19757202	19757330	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19757331	19757492	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19757331	19757492	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19757493	19757586	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19757587	19757660	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19757587	19757660	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19757661	19757774	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19757775	19757898	1	+	1	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19757775	19757898	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19757899	19757971	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19757972	19758063	1	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19757972	19758063	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19758064	19758150	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19758151	19758274	1	+	1	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19758151	19758274	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	intron	19758275	19758358	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	CDS	19758359	19758508	0.9	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	exon	19758359	19758508	.	+	.	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
Phchi.S1	AUGUSTUS	stop_codon	19758509	19758511	.	+	0	transcript_id "Phchi.S1G307100.t1"; gene_id "Phchi.S1G307100"
# This transcript jg12930.t2 is derived from g11395.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12931.t1 is derived from g11396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3200626	3200907	.	+	.	Phchi.S3G025000
Phchi.S3	AUGUSTUS	transcript	3200626	3200907	.	+	.	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	start_codon	3200626	3200628	.	+	0	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	CDS	3200626	3200682	0.91	+	0	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	exon	3200626	3200682	.	+	.	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	intron	3200683	3200766	.	+	.	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	CDS	3200767	3200907	0.92	+	0	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	exon	3200767	3200907	.	+	.	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
Phchi.S3	AUGUSTUS	stop_codon	3200908	3200910	.	+	0	transcript_id "Phchi.S3G025000.t1"; gene_id "Phchi.S3G025000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15268.t1 is derived from g13736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18035898	18036183	.	-	.	Phchi.S3G258700
Phchi.S3	AUGUSTUS	transcript	18035898	18036183	.	-	.	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	stop_codon	18035895	18035897	.	-	0	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	CDS	18035898	18036063	0.98	-	1	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	exon	18035898	18036063	.	-	.	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	intron	18036064	18036148	.	-	.	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	CDS	18036149	18036183	0.94	-	0	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	exon	18036149	18036183	.	-	.	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
Phchi.S3	AUGUSTUS	start_codon	18036181	18036183	.	-	0	transcript_id "Phchi.S3G258700.t1"; gene_id "Phchi.S3G258700"
# This transcript jg9135.t2 is derived from g6310.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9135.t3 is derived from g6310.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9136.t1 is derived from g6311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40034395	40034923	.	-	.	Phchi.S1G629500
Phchi.S1	AUGUSTUS	transcript	40034395	40034923	.	-	.	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	stop_codon	40034392	40034394	.	-	0	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	CDS	40034395	40034646	1	-	0	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	exon	40034395	40034646	.	-	.	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	intron	40034647	40034770	.	-	.	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	CDS	40034771	40034923	1	-	0	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	exon	40034771	40034923	.	-	.	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
Phchi.S1	AUGUSTUS	start_codon	40034921	40034923	.	-	0	transcript_id "Phchi.S1G629500.t1"; gene_id "Phchi.S1G629500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13296.t1 is derived from g11762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5403362	5405427	.	-	.	Phchi.S3G061500
Phchi.S3	AUGUSTUS	transcript	5403362	5405427	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	stop_codon	5403359	5403361	.	-	0	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	CDS	5403362	5403614	1	-	1	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	exon	5403362	5403614	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	intron	5403615	5403723	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	CDS	5403724	5404091	1	-	0	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	exon	5403724	5404091	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	intron	5404092	5404231	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	CDS	5404232	5404525	0.97	-	0	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	exon	5404232	5404525	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	intron	5404526	5404639	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	CDS	5404640	5404928	1	-	1	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	exon	5404640	5404928	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	intron	5404929	5405038	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	CDS	5405039	5405427	1	-	0	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	exon	5405039	5405427	.	-	.	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
Phchi.S3	AUGUSTUS	start_codon	5405425	5405427	.	-	0	transcript_id "Phchi.S3G061500.t1"; gene_id "Phchi.S3G061500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8977.t1 is derived from g6152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38939950	38941591	.	+	.	Phchi.S1G613600
Phchi.S1	AUGUSTUS	transcript	38939950	38941591	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	start_codon	38939950	38939952	.	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38939950	38940025	1	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38939950	38940025	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38940026	38940102	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38940103	38940197	1	+	2	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38940103	38940197	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38940198	38940346	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38940347	38940428	1	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38940347	38940428	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38940429	38940569	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38940570	38940666	1	+	2	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38940570	38940666	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38940667	38940762	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38940763	38940821	1	+	1	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38940763	38940821	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38940822	38940930	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38940931	38941013	0.29	+	2	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38940931	38941013	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38941014	38941135	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38941136	38941222	0.44	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38941136	38941222	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38941223	38941313	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38941314	38941373	1	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38941314	38941373	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	intron	38941374	38941501	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	CDS	38941502	38941591	1	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	exon	38941502	38941591	.	+	.	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
Phchi.S1	AUGUSTUS	stop_codon	38941592	38941594	.	+	0	transcript_id "Phchi.S1G613600.t1"; gene_id "Phchi.S1G613600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3380.t1 is derived from g549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3255912	3260250	.	+	.	Phchi.S1G053900
Phchi.S1	AUGUSTUS	transcript	3255912	3260250	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	start_codon	3255912	3255914	.	+	0	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3255912	3256259	0.98	+	0	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3255912	3256259	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3256260	3256343	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3256344	3256503	1	+	0	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3256344	3256503	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3256504	3256610	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3256611	3256741	0.98	+	2	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3256611	3256741	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3256742	3256866	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3256867	3257351	0.8	+	0	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3256867	3257351	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3257352	3257448	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3257449	3258371	0.96	+	1	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3257449	3258371	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3258372	3258456	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3258457	3258768	1	+	2	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3258457	3258768	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3258769	3258868	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3258869	3258973	1	+	2	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3258869	3258973	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3258974	3259136	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3259137	3259224	0.97	+	2	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3259137	3259224	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3259225	3259340	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3259341	3259462	1	+	1	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3259341	3259462	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3259463	3259587	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3259588	3259652	1	+	2	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3259588	3259652	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	intron	3259653	3259737	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	CDS	3259738	3260250	0.98	+	0	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	exon	3259738	3260250	.	+	.	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
Phchi.S1	AUGUSTUS	stop_codon	3260251	3260253	.	+	0	transcript_id "Phchi.S1G053900.t1"; gene_id "Phchi.S1G053900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9167.t1 is derived from g6342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40189497	40190496	.	-	.	Phchi.S1G632600
Phchi.S1	AUGUSTUS	transcript	40189497	40190496	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	stop_codon	40189494	40189496	.	-	0	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	CDS	40189497	40189652	0.97	-	0	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	exon	40189497	40189652	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	intron	40189653	40189763	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	CDS	40189764	40189948	1	-	2	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	exon	40189764	40189948	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	intron	40189949	40190045	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	CDS	40190046	40190152	1	-	1	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	exon	40190046	40190152	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	intron	40190153	40190245	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	CDS	40190246	40190496	0.99	-	0	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	exon	40190246	40190496	.	-	.	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
Phchi.S1	AUGUSTUS	start_codon	40190494	40190496	.	-	0	transcript_id "Phchi.S1G632600.t1"; gene_id "Phchi.S1G632600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8636.t1 is derived from g5811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37173798	37178484	.	-	.	Phchi.S1G579500
Phchi.S1	AUGUSTUS	transcript	37173798	37178484	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	stop_codon	37173795	37173797	.	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37173798	37174409	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37173798	37174409	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37174410	37174522	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37174523	37174832	0.55	-	1	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37174523	37174832	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37174833	37174915	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37174916	37174980	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37174916	37174980	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37174981	37175095	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37175096	37175155	0.99	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37175096	37175155	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37175156	37175290	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37175291	37175521	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37175291	37175521	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37175522	37175625	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37175626	37175710	0.9	-	1	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37175626	37175710	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37175711	37175821	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37175822	37175991	0.88	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37175822	37175991	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37175992	37176105	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37176106	37176219	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37176106	37176219	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37176220	37176311	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37176312	37176411	0.97	-	1	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37176312	37176411	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37176412	37176521	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37176522	37176587	1	-	1	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37176522	37176587	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37176588	37176674	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37176675	37176738	1	-	2	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37176675	37176738	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37176739	37176824	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37176825	37176898	1	-	1	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37176825	37176898	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37176899	37177060	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37177061	37177377	0.87	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37177061	37177377	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37177378	37177500	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37177501	37177550	1	-	2	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37177501	37177550	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37177551	37177763	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37177764	37177836	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37177764	37177836	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37177837	37177984	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37177985	37178056	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37177985	37178056	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37178057	37178212	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37178213	37178287	1	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37178213	37178287	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	intron	37178288	37178442	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	CDS	37178443	37178484	0.95	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	exon	37178443	37178484	.	-	.	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
Phchi.S1	AUGUSTUS	start_codon	37178482	37178484	.	-	0	transcript_id "Phchi.S1G579500.t1"; gene_id "Phchi.S1G579500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4589.t1 is derived from g1759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11221777	11225063	.	+	.	Phchi.S1G174800
Phchi.S1	AUGUSTUS	transcript	11221777	11225063	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	start_codon	11221777	11221779	.	+	0	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11221777	11222017	0.91	+	0	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11221777	11222017	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11222018	11222145	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11222146	11222723	0.67	+	2	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11222146	11222723	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11222724	11222814	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11222815	11222947	0.79	+	0	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11222815	11222947	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11222948	11223076	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11223077	11223106	0.38	+	2	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11223077	11223106	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11223107	11223429	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11223430	11223692	0.49	+	2	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11223430	11223692	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11223693	11223816	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11223817	11223993	0.98	+	0	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11223817	11223993	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11223994	11224092	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11224093	11224546	1	+	0	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11224093	11224546	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11224547	11224637	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11224638	11224724	0.94	+	2	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11224638	11224724	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	intron	11224725	11225061	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	CDS	11225062	11225063	0.98	+	2	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	exon	11225062	11225063	.	+	.	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
Phchi.S1	AUGUSTUS	stop_codon	11225064	11225066	.	+	0	transcript_id "Phchi.S1G174800.t1"; gene_id "Phchi.S1G174800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4234.t1 is derived from g1403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9040974	9042884	.	+	.	Phchi.S1G139300
Phchi.S1	AUGUSTUS	transcript	9040974	9042884	.	+	.	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	start_codon	9040974	9040976	.	+	0	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	CDS	9040974	9042450	0.89	+	0	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	exon	9040974	9042450	.	+	.	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	intron	9042451	9042534	.	+	.	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	CDS	9042535	9042884	1	+	2	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	exon	9042535	9042884	.	+	.	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
Phchi.S1	AUGUSTUS	stop_codon	9042885	9042887	.	+	0	transcript_id "Phchi.S1G139300.t1"; gene_id "Phchi.S1G139300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12093.t1 is derived from g7768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2507247	2507980	.	+	.	Phchi.S2G017300
Phchi.S2	AUGUSTUS	transcript	2507247	2507980	.	+	.	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	start_codon	2507247	2507249	.	+	0	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	CDS	2507247	2507490	0.85	+	0	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	exon	2507247	2507490	.	+	.	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	intron	2507491	2507582	.	+	.	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	CDS	2507583	2507670	0.21	+	2	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	exon	2507583	2507670	.	+	.	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	intron	2507671	2507811	.	+	.	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	CDS	2507812	2507980	0.4	+	1	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	exon	2507812	2507980	.	+	.	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
Phchi.S2	AUGUSTUS	stop_codon	2507981	2507983	.	+	0	transcript_id "Phchi.S2G017300.t1"; gene_id "Phchi.S2G017300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9256.t1 is derived from g6431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40613062	40614237	.	-	.	Phchi.S1G641500
Phchi.S1	AUGUSTUS	transcript	40613062	40614237	.	-	.	transcript_id "Phchi.S1G641500.t1"; gene_id "Phchi.S1G641500"
Phchi.S1	AUGUSTUS	stop_codon	40613059	40613061	.	-	0	transcript_id "Phchi.S1G641500.t1"; gene_id "Phchi.S1G641500"
Phchi.S1	AUGUSTUS	CDS	40613062	40614237	1	-	0	transcript_id "Phchi.S1G641500.t1"; gene_id "Phchi.S1G641500"
Phchi.S1	AUGUSTUS	exon	40613062	40614237	.	-	.	transcript_id "Phchi.S1G641500.t1"; gene_id "Phchi.S1G641500"
Phchi.S1	AUGUSTUS	start_codon	40614235	40614237	.	-	0	transcript_id "Phchi.S1G641500.t1"; gene_id "Phchi.S1G641500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7588.t1 is derived from g4762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30169688	30171165	.	+	.	Phchi.S1G474700
Phchi.S1	AUGUSTUS	transcript	30169688	30171165	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	start_codon	30169688	30169690	.	+	0	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	CDS	30169688	30170194	0.5	+	0	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	exon	30169688	30170194	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	intron	30170195	30170264	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	CDS	30170265	30170437	1	+	0	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	exon	30170265	30170437	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	intron	30170438	30170520	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	CDS	30170521	30170681	1	+	1	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	exon	30170521	30170681	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	intron	30170682	30170777	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	CDS	30170778	30170914	1	+	2	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	exon	30170778	30170914	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	intron	30170915	30171000	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	CDS	30171001	30171165	1	+	0	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	exon	30171001	30171165	.	+	.	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
Phchi.S1	AUGUSTUS	stop_codon	30171166	30171168	.	+	0	transcript_id "Phchi.S1G474700.t1"; gene_id "Phchi.S1G474700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4777.t1 is derived from g1947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12777666	12778027	.	-	.	Phchi.S1G193600
Phchi.S1	AUGUSTUS	transcript	12777666	12778027	.	-	.	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	stop_codon	12777663	12777665	.	-	0	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	CDS	12777666	12777699	0.69	-	1	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	exon	12777666	12777699	.	-	.	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	intron	12777700	12777854	.	-	.	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	CDS	12777855	12778027	0.66	-	0	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	exon	12777855	12778027	.	-	.	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
Phchi.S1	AUGUSTUS	start_codon	12778025	12778027	.	-	0	transcript_id "Phchi.S1G193600.t1"; gene_id "Phchi.S1G193600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13001.t1 is derived from g11466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3588285	3592002	.	+	.	Phchi.S3G032000
Phchi.S3	AUGUSTUS	transcript	3588285	3592002	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	start_codon	3588285	3588287	.	+	0	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	CDS	3588285	3589028	0.96	+	0	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	exon	3588285	3589028	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	intron	3589029	3589144	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	CDS	3589145	3589274	1	+	0	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	exon	3589145	3589274	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	intron	3589275	3589358	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	CDS	3589359	3591277	0.98	+	2	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	exon	3589359	3591277	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	intron	3591278	3591390	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	CDS	3591391	3592002	1	+	0	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	exon	3591391	3592002	.	+	.	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
Phchi.S3	AUGUSTUS	stop_codon	3592003	3592005	.	+	0	transcript_id "Phchi.S3G032000.t1"; gene_id "Phchi.S3G032000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3194.t1 is derived from g363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2158482	2160333	.	-	.	Phchi.S1G035300
Phchi.S1	AUGUSTUS	transcript	2158482	2160333	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	stop_codon	2158479	2158481	.	-	0	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2158482	2158592	0.91	-	0	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2158482	2158592	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	intron	2158593	2158740	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2158741	2158920	0.89	-	0	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2158741	2158920	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	intron	2158921	2159244	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2159245	2159359	0.47	-	1	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2159245	2159359	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	intron	2159360	2159436	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2159437	2159588	0.65	-	0	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2159437	2159588	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	intron	2159589	2159668	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2159669	2159720	0.79	-	1	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2159669	2159720	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	intron	2159721	2159875	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2159876	2160083	0.89	-	2	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2159876	2160083	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	intron	2160084	2160281	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	CDS	2160282	2160333	0.97	-	0	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	exon	2160282	2160333	.	-	.	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
Phchi.S1	AUGUSTUS	start_codon	2160331	2160333	.	-	0	transcript_id "Phchi.S1G035300.t1"; gene_id "Phchi.S1G035300"
# This transcript jg1463.t2 is derived from g8382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1464.t1 is derived from g8383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1054173	1065798	.	-	.	Phchi.S5G007300
Phchi.S5	AUGUSTUS	transcript	1054173	1065798	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	stop_codon	1054170	1054172	.	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1054173	1054400	0.96	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1054173	1054400	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1054401	1054500	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1054501	1054671	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1054501	1054671	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1054672	1054762	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1054763	1054994	0.98	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1054763	1054994	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1054995	1055187	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1055188	1055597	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1055188	1055597	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1055598	1055714	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1055715	1056380	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1055715	1056380	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1056381	1056473	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1056474	1056521	0.51	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1056474	1056521	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1056522	1056634	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1056635	1056688	0.47	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1056635	1056688	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1056689	1056863	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1056864	1057224	0.99	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1056864	1057224	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1057225	1057386	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1057387	1057454	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1057387	1057454	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1057455	1057539	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1057540	1057635	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1057540	1057635	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1057636	1057734	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1057735	1057923	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1057735	1057923	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1057924	1058017	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1058018	1058237	1	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1058018	1058237	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1058238	1058448	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1058449	1058645	0.99	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1058449	1058645	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1058646	1058725	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1058726	1058815	0.98	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1058726	1058815	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1058816	1058918	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1058919	1059023	0.92	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1058919	1059023	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1059024	1059110	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1059111	1059200	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1059111	1059200	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1059201	1059299	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1059300	1059479	0.98	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1059300	1059479	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1059480	1059588	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1059589	1059664	0.98	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1059589	1059664	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1059665	1059920	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1059921	1060101	1	-	2	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1059921	1060101	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1060102	1060237	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1060238	1060322	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1060238	1060322	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1060323	1060443	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1060444	1060625	1	-	2	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1060444	1060625	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1060626	1060740	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1060741	1060897	0.98	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1060741	1060897	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1060898	1061028	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1061029	1061172	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1061029	1061172	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1061173	1061262	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1061263	1061372	0.68	-	2	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1061263	1061372	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1061373	1061592	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1061593	1062022	0.53	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1061593	1062022	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1062023	1062111	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1062112	1062254	1	-	2	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1062112	1062254	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1062255	1062384	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1062385	1062532	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1062385	1062532	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1062533	1062766	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1062767	1062835	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1062767	1062835	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1062836	1062918	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1062919	1063044	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1062919	1063044	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1063045	1063132	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1063133	1063215	1	-	2	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1063133	1063215	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1063216	1063444	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1063445	1063506	0.59	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1063445	1063506	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1063507	1063610	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1063611	1063700	1	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1063611	1063700	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1063701	1063892	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1063893	1063948	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1063893	1063948	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1063949	1064183	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1064184	1064348	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1064184	1064348	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1064349	1064531	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1064532	1064699	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1064532	1064699	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1064700	1064807	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1064808	1064925	0.98	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1064808	1064925	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1064926	1065135	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1065136	1065231	1	-	1	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1065136	1065231	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1065232	1065347	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1065348	1065561	0.92	-	2	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1065348	1065561	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	intron	1065562	1065644	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	CDS	1065645	1065798	1	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	exon	1065645	1065798	.	-	.	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
Phchi.S5	AUGUSTUS	start_codon	1065796	1065798	.	-	0	transcript_id "Phchi.S5G007300.t1"; gene_id "Phchi.S5G007300"
# This transcript jg8825.t2 is derived from g6000.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8826.t1 is derived from g6001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38152141	38154258	.	+	.	Phchi.S1G598500
Phchi.S1	AUGUSTUS	transcript	38152141	38154258	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	start_codon	38152141	38152143	.	+	0	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	CDS	38152141	38152253	0.99	+	0	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	exon	38152141	38152253	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	intron	38152254	38152358	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	CDS	38152359	38152564	0.96	+	1	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	exon	38152359	38152564	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	intron	38152565	38153064	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	CDS	38153065	38153264	1	+	2	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	exon	38153065	38153264	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	intron	38153265	38153344	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	CDS	38153345	38153853	0.88	+	0	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	exon	38153345	38153853	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	intron	38153854	38153948	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	CDS	38153949	38154258	1	+	1	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	exon	38153949	38154258	.	+	.	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
Phchi.S1	AUGUSTUS	stop_codon	38154259	38154261	.	+	0	transcript_id "Phchi.S1G598500.t1"; gene_id "Phchi.S1G598500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg360.t1 is derived from g10142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2645134	2645955	.	-	.	Phchi.S6G031900
Phchi.S6	AUGUSTUS	transcript	2645134	2645955	.	-	.	transcript_id "Phchi.S6G031900.t1"; gene_id "Phchi.S6G031900"
Phchi.S6	AUGUSTUS	stop_codon	2645131	2645133	.	-	0	transcript_id "Phchi.S6G031900.t1"; gene_id "Phchi.S6G031900"
Phchi.S6	AUGUSTUS	CDS	2645134	2645955	0.59	-	0	transcript_id "Phchi.S6G031900.t1"; gene_id "Phchi.S6G031900"
Phchi.S6	AUGUSTUS	exon	2645134	2645955	.	-	.	transcript_id "Phchi.S6G031900.t1"; gene_id "Phchi.S6G031900"
Phchi.S6	AUGUSTUS	start_codon	2645953	2645955	.	-	0	transcript_id "Phchi.S6G031900.t1"; gene_id "Phchi.S6G031900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14700.t1 is derived from g13168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14245259	14247311	.	-	.	Phchi.S3G201900
Phchi.S3	AUGUSTUS	transcript	14245259	14247311	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	stop_codon	14245256	14245258	.	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14245259	14245273	0.74	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14245259	14245273	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14245274	14245359	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14245360	14245395	0.42	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14245360	14245395	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14245396	14245483	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14245484	14245579	0.57	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14245484	14245579	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14245580	14245664	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14245665	14245804	1	-	2	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14245665	14245804	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14245805	14245885	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14245886	14246094	1	-	1	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14245886	14246094	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14246095	14246223	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14246224	14246432	1	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14246224	14246432	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14246433	14246497	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14246498	14246676	1	-	2	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14246498	14246676	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14246677	14246769	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14246770	14246982	1	-	2	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14246770	14246982	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	intron	14246983	14247067	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	CDS	14247068	14247311	0.99	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	exon	14247068	14247311	.	-	.	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
Phchi.S3	AUGUSTUS	start_codon	14247309	14247311	.	-	0	transcript_id "Phchi.S3G201900.t1"; gene_id "Phchi.S3G201900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8601.t1 is derived from g5776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36846691	36848519	.	-	.	Phchi.S1G576000
Phchi.S1	AUGUSTUS	transcript	36846691	36848519	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	stop_codon	36846688	36846690	.	-	0	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	CDS	36846691	36846734	0.81	-	2	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	exon	36846691	36846734	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	intron	36846735	36846822	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	CDS	36846823	36846979	0.81	-	0	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	exon	36846823	36846979	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	intron	36846980	36847152	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	CDS	36847153	36847334	0.94	-	2	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	exon	36847153	36847334	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	intron	36847335	36847467	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	CDS	36847468	36847671	1	-	2	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	exon	36847468	36847671	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	intron	36847672	36847765	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	CDS	36847766	36848241	0.91	-	1	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	exon	36847766	36848241	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	intron	36848242	36848514	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	CDS	36848515	36848519	0.91	-	0	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	exon	36848515	36848519	.	-	.	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
Phchi.S1	AUGUSTUS	start_codon	36848517	36848519	.	-	0	transcript_id "Phchi.S1G576000.t1"; gene_id "Phchi.S1G576000"
# This transcript jg11303.t2 is derived from g15353.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11304.t1 is derived from g15354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5303859	5305260	.	+	.	Phchi.S4G088600
Phchi.S4	AUGUSTUS	transcript	5303859	5305260	.	+	.	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	start_codon	5303859	5303861	.	+	0	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	CDS	5303859	5304135	0.35	+	0	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	exon	5303859	5304135	.	+	.	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	intron	5304136	5304209	.	+	.	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	CDS	5304210	5304502	0.89	+	2	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	exon	5304210	5304502	.	+	.	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	intron	5304503	5304621	.	+	.	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	CDS	5304622	5305260	1	+	0	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	exon	5304622	5305260	.	+	.	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
Phchi.S4	AUGUSTUS	stop_codon	5305261	5305263	.	+	0	transcript_id "Phchi.S4G088600.t1"; gene_id "Phchi.S4G088600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8536.t1 is derived from g5711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36531821	36536069	.	-	.	Phchi.S1G569500
Phchi.S1	AUGUSTUS	transcript	36531821	36536069	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	stop_codon	36531818	36531820	.	-	0	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	CDS	36531821	36533575	0.18	-	0	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	exon	36531821	36533575	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	intron	36533576	36533884	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	CDS	36533885	36533949	0.16	-	2	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	exon	36533885	36533949	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	intron	36533950	36534222	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	CDS	36534223	36535060	0.92	-	0	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	exon	36534223	36535060	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	intron	36535061	36535205	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	CDS	36535206	36536069	0.74	-	0	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	exon	36535206	36536069	.	-	.	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
Phchi.S1	AUGUSTUS	start_codon	36536067	36536069	.	-	0	transcript_id "Phchi.S1G569500.t1"; gene_id "Phchi.S1G569500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13513.t1 is derived from g11980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7263483	7263920	.	-	.	Phchi.S3G083200
Phchi.S3	AUGUSTUS	transcript	7263483	7263920	.	-	.	transcript_id "Phchi.S3G083200.t1"; gene_id "Phchi.S3G083200"
Phchi.S3	AUGUSTUS	stop_codon	7263480	7263482	.	-	0	transcript_id "Phchi.S3G083200.t1"; gene_id "Phchi.S3G083200"
Phchi.S3	AUGUSTUS	CDS	7263483	7263920	0.22	-	0	transcript_id "Phchi.S3G083200.t1"; gene_id "Phchi.S3G083200"
Phchi.S3	AUGUSTUS	exon	7263483	7263920	.	-	.	transcript_id "Phchi.S3G083200.t1"; gene_id "Phchi.S3G083200"
Phchi.S3	AUGUSTUS	start_codon	7263918	7263920	.	-	0	transcript_id "Phchi.S3G083200.t1"; gene_id "Phchi.S3G083200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15070.t1 is derived from g13538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16906959	16909815	.	-	.	Phchi.S3G238900
Phchi.S3	AUGUSTUS	transcript	16906959	16909815	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	stop_codon	16906956	16906958	.	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16906959	16907060	1	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16906959	16907060	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16907061	16907170	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16907171	16907227	1	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16907171	16907227	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16907228	16907315	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16907316	16907401	1	-	2	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16907316	16907401	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16907402	16907490	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16907491	16907548	1	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16907491	16907548	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16907549	16907810	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16907811	16907979	0.99	-	1	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16907811	16907979	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16907980	16908067	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16908068	16908124	1	-	1	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16908068	16908124	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16908125	16908299	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16908300	16908547	0.54	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16908300	16908547	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16908548	16908654	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16908655	16908731	0.59	-	2	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16908655	16908731	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16908732	16908819	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16908820	16908954	1	-	2	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16908820	16908954	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16908955	16909113	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16909114	16909241	0.78	-	1	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16909114	16909241	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16909242	16909343	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16909344	16909404	0.79	-	2	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16909344	16909404	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16909405	16909493	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16909494	16909541	1	-	2	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16909494	16909541	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	intron	16909542	16909664	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	CDS	16909665	16909815	0.97	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	exon	16909665	16909815	.	-	.	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
Phchi.S3	AUGUSTUS	start_codon	16909813	16909815	.	-	0	transcript_id "Phchi.S3G238900.t1"; gene_id "Phchi.S3G238900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13167.t1 is derived from g11632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4467646	4468108	.	-	.	Phchi.S3G048600
Phchi.S3	AUGUSTUS	transcript	4467646	4468108	.	-	.	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	stop_codon	4467643	4467645	.	-	0	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	CDS	4467646	4467691	0.8	-	1	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	exon	4467646	4467691	.	-	.	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	intron	4467692	4467860	.	-	.	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	CDS	4467861	4468108	0.5	-	0	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	exon	4467861	4468108	.	-	.	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
Phchi.S3	AUGUSTUS	start_codon	4468106	4468108	.	-	0	transcript_id "Phchi.S3G048600.t1"; gene_id "Phchi.S3G048600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4196.t1 is derived from g1365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8869123	8871139	.	-	.	Phchi.S1G135500
Phchi.S1	AUGUSTUS	transcript	8869123	8871139	.	-	.	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	stop_codon	8869120	8869122	.	-	0	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	CDS	8869123	8869180	0.51	-	1	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	exon	8869123	8869180	.	-	.	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	intron	8869181	8869267	.	-	.	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	CDS	8869268	8869302	0.35	-	0	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	exon	8869268	8869302	.	-	.	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	intron	8869303	8869573	.	-	.	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	CDS	8869574	8871139	0.26	-	0	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	exon	8869574	8871139	.	-	.	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
Phchi.S1	AUGUSTUS	start_codon	8871137	8871139	.	-	0	transcript_id "Phchi.S1G135500.t1"; gene_id "Phchi.S1G135500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3064.t1 is derived from g233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1404880	1405956	.	-	.	Phchi.S1G022300
Phchi.S1	AUGUSTUS	transcript	1404880	1405956	.	-	.	transcript_id "Phchi.S1G022300.t1"; gene_id "Phchi.S1G022300"
Phchi.S1	AUGUSTUS	stop_codon	1404877	1404879	.	-	0	transcript_id "Phchi.S1G022300.t1"; gene_id "Phchi.S1G022300"
Phchi.S1	AUGUSTUS	CDS	1404880	1405956	0.99	-	0	transcript_id "Phchi.S1G022300.t1"; gene_id "Phchi.S1G022300"
Phchi.S1	AUGUSTUS	exon	1404880	1405956	.	-	.	transcript_id "Phchi.S1G022300.t1"; gene_id "Phchi.S1G022300"
Phchi.S1	AUGUSTUS	start_codon	1405954	1405956	.	-	0	transcript_id "Phchi.S1G022300.t1"; gene_id "Phchi.S1G022300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5028.t1 is derived from g2198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14143031	14144422	.	-	.	Phchi.S1G218700
Phchi.S1	AUGUSTUS	transcript	14143031	14144422	.	-	.	transcript_id "Phchi.S1G218700.t1"; gene_id "Phchi.S1G218700"
Phchi.S1	AUGUSTUS	stop_codon	14143028	14143030	.	-	0	transcript_id "Phchi.S1G218700.t1"; gene_id "Phchi.S1G218700"
Phchi.S1	AUGUSTUS	CDS	14143031	14144422	0.26	-	0	transcript_id "Phchi.S1G218700.t1"; gene_id "Phchi.S1G218700"
Phchi.S1	AUGUSTUS	exon	14143031	14144422	.	-	.	transcript_id "Phchi.S1G218700.t1"; gene_id "Phchi.S1G218700"
Phchi.S1	AUGUSTUS	start_codon	14144420	14144422	.	-	0	transcript_id "Phchi.S1G218700.t1"; gene_id "Phchi.S1G218700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7269.t1 is derived from g4441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27993719	27995050	.	+	.	Phchi.S1G442800
Phchi.S1	AUGUSTUS	transcript	27993719	27995050	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	start_codon	27993719	27993721	.	+	0	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	CDS	27993719	27994039	0.75	+	0	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	exon	27993719	27994039	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	intron	27994040	27994136	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	CDS	27994137	27994389	1	+	0	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	exon	27994137	27994389	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	intron	27994390	27994492	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	CDS	27994493	27994722	1	+	2	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	exon	27994493	27994722	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	intron	27994723	27994807	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	CDS	27994808	27995050	1	+	0	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	exon	27994808	27995050	.	+	.	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
Phchi.S1	AUGUSTUS	stop_codon	27995051	27995053	.	+	0	transcript_id "Phchi.S1G442800.t1"; gene_id "Phchi.S1G442800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4654.t1 is derived from g1824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11650107	11651937	.	+	.	Phchi.S1G181300
Phchi.S1	AUGUSTUS	transcript	11650107	11651937	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	start_codon	11650107	11650109	.	+	0	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	CDS	11650107	11650185	0.9	+	0	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	exon	11650107	11650185	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	intron	11650186	11650293	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	CDS	11650294	11650350	1	+	2	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	exon	11650294	11650350	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	intron	11650351	11650429	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	CDS	11650430	11650643	0.97	+	2	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	exon	11650430	11650643	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	intron	11650644	11650765	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	CDS	11650766	11650939	0.82	+	1	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	exon	11650766	11650939	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	intron	11650940	11651120	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	CDS	11651121	11651937	0.99	+	1	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	exon	11651121	11651937	.	+	.	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
Phchi.S1	AUGUSTUS	stop_codon	11651938	11651940	.	+	0	transcript_id "Phchi.S1G181300.t1"; gene_id "Phchi.S1G181300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6271.t1 is derived from g3443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21946900	21950024	.	+	.	Phchi.S1G343000
Phchi.S1	AUGUSTUS	transcript	21946900	21950024	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	start_codon	21946900	21946902	.	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21946900	21946986	0.99	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21946900	21946986	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21946987	21947174	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21947175	21947230	1	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21947175	21947230	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21947231	21947409	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21947410	21947584	0.99	+	1	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21947410	21947584	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21947585	21947704	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21947705	21947830	0.76	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21947705	21947830	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21947831	21947917	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21947918	21947989	0.75	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21947918	21947989	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21947990	21948105	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21948106	21948222	0.9	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21948106	21948222	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21948223	21948305	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21948306	21948383	1	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21948306	21948383	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21948384	21948570	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21948571	21948633	1	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21948571	21948633	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21948634	21948732	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21948733	21948829	1	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21948733	21948829	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21948830	21948942	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21948943	21949021	1	+	2	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21948943	21949021	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21949022	21949205	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21949206	21949417	1	+	1	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21949206	21949417	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21949418	21949502	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21949503	21949648	1	+	2	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21949503	21949648	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21949649	21949711	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21949712	21949834	1	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21949712	21949834	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	intron	21949835	21949907	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	CDS	21949908	21950024	1	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	exon	21949908	21950024	.	+	.	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
Phchi.S1	AUGUSTUS	stop_codon	21950025	21950027	.	+	0	transcript_id "Phchi.S1G343000.t1"; gene_id "Phchi.S1G343000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13950.t1 is derived from g12417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9882527	9884153	.	-	.	Phchi.S3G126900
Phchi.S3	AUGUSTUS	transcript	9882527	9884153	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	stop_codon	9882524	9882526	.	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9882527	9882631	0.87	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9882527	9882631	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9882632	9882739	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9882740	9882832	0.89	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9882740	9882832	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9882833	9882931	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9882932	9883014	1	-	2	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9882932	9883014	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9883015	9883133	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9883134	9883200	1	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9883134	9883200	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9883201	9883300	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9883301	9883351	1	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9883301	9883351	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9883352	9883500	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9883501	9883563	1	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9883501	9883563	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9883564	9883660	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9883661	9883711	1	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9883661	9883711	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9883712	9883807	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9883808	9883864	1	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9883808	9883864	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	intron	9883865	9884051	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	CDS	9884052	9884153	0.86	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	exon	9884052	9884153	.	-	.	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
Phchi.S3	AUGUSTUS	start_codon	9884151	9884153	.	-	0	transcript_id "Phchi.S3G126900.t1"; gene_id "Phchi.S3G126900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2265.t1 is derived from g9185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5733721	5735879	.	-	.	Phchi.S5G087400
Phchi.S5	AUGUSTUS	transcript	5733721	5735879	.	-	.	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	stop_codon	5733718	5733720	.	-	0	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	CDS	5733721	5734374	0.98	-	0	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	exon	5733721	5734374	.	-	.	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	intron	5734375	5734571	.	-	.	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	CDS	5734572	5735879	0.88	-	0	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	exon	5734572	5735879	.	-	.	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
Phchi.S5	AUGUSTUS	start_codon	5735877	5735879	.	-	0	transcript_id "Phchi.S5G087400.t1"; gene_id "Phchi.S5G087400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13041.t1 is derived from g11506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3843754	3844201	.	-	.	Phchi.S3G036000
Phchi.S3	AUGUSTUS	transcript	3843754	3844201	.	-	.	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	stop_codon	3843751	3843753	.	-	0	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	CDS	3843754	3843908	0.81	-	2	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	exon	3843754	3843908	.	-	.	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	intron	3843909	3844113	.	-	.	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	CDS	3844114	3844201	0.98	-	0	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	exon	3844114	3844201	.	-	.	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
Phchi.S3	AUGUSTUS	start_codon	3844199	3844201	.	-	0	transcript_id "Phchi.S3G036000.t1"; gene_id "Phchi.S3G036000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15958.t1 is derived from g11141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	26603	29989	.	+	.	Phchi.C91G000500
Phchi.C91	AUGUSTUS	transcript	26603	29989	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	start_codon	26603	26605	.	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	26603	26958	0.38	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	26603	26958	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	26959	27478	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	27479	27604	0.98	+	1	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	27479	27604	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	27605	27755	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	27756	27784	0.61	+	1	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	27756	27784	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	27785	27867	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	27868	27896	0.81	+	2	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	27868	27896	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	27897	28166	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	28167	28268	1	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	28167	28268	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	28269	28354	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	28355	28488	0.92	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	28355	28488	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	28489	28612	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	28613	28746	0.85	+	1	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	28613	28746	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	28747	28840	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	28841	28992	1	+	2	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	28841	28992	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	28993	29070	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	29071	29112	1	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	29071	29112	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	29113	29200	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	29201	29256	1	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	29201	29256	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	29257	29390	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	29391	29618	1	+	1	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	29391	29618	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	29619	29697	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	29698	29731	0.67	+	1	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	29698	29731	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	intron	29732	29884	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	CDS	29885	29989	1	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	exon	29885	29989	.	+	.	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
Phchi.C91	AUGUSTUS	stop_codon	29990	29992	.	+	0	transcript_id "Phchi.C91G000500.t1"; gene_id "Phchi.C91G000500"
# This transcript jg3027.t2 is derived from g196.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3028.t1 is derived from g197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1231283	1233595	.	+	.	Phchi.S1G018700
Phchi.S1	AUGUSTUS	transcript	1231283	1233595	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	start_codon	1231283	1231285	.	+	0	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	CDS	1231283	1231297	0.61	+	0	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	exon	1231283	1231297	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	intron	1231298	1231405	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	CDS	1231406	1231568	0.75	+	0	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	exon	1231406	1231568	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	intron	1231569	1231656	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	CDS	1231657	1231874	0.57	+	2	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	exon	1231657	1231874	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	intron	1231875	1231948	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	CDS	1231949	1232242	0.81	+	0	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	exon	1231949	1232242	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	intron	1232243	1232320	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	CDS	1232321	1232589	1	+	0	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	exon	1232321	1232589	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	intron	1232590	1232697	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	CDS	1232698	1233595	0.96	+	1	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	exon	1232698	1233595	.	+	.	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
Phchi.S1	AUGUSTUS	stop_codon	1233596	1233598	.	+	0	transcript_id "Phchi.S1G018700.t1"; gene_id "Phchi.S1G018700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9224.t1 is derived from g6399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40476821	40480202	.	+	.	Phchi.S1G638300
Phchi.S1	AUGUSTUS	transcript	40476821	40480202	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	start_codon	40476821	40476823	.	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40476821	40476842	0.74	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40476821	40476842	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40476843	40476928	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40476929	40477026	1	+	2	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40476929	40477026	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40477027	40477108	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40477109	40477227	1	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40477109	40477227	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40477228	40477310	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40477311	40477429	1	+	1	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40477311	40477429	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40477430	40477508	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40477509	40478576	0.78	+	2	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40477509	40478576	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40478577	40478666	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40478667	40478918	1	+	2	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40478667	40478918	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40478919	40479011	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40479012	40479172	1	+	2	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40479012	40479172	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40479173	40479266	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40479267	40479346	1	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40479267	40479346	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40479347	40479436	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40479437	40479584	1	+	1	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40479437	40479584	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40479585	40479699	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40479700	40479849	1	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40479700	40479849	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	intron	40479850	40479950	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	CDS	40479951	40480202	0.97	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	exon	40479951	40480202	.	+	.	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
Phchi.S1	AUGUSTUS	stop_codon	40480203	40480205	.	+	0	transcript_id "Phchi.S1G638300.t1"; gene_id "Phchi.S1G638300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11744.t1 is derived from g15796.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7971540	7977570	.	+	.	Phchi.S4G132600
Phchi.S4	AUGUSTUS	transcript	7971540	7977570	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	start_codon	7971540	7971542	.	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7971540	7971697	0.75	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7971540	7971697	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7971698	7971862	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7971863	7971959	0.51	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7971863	7971959	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7971960	7972281	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7972282	7972384	0.53	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7972282	7972384	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7972385	7972481	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7972482	7972825	1	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7972482	7972825	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7972826	7972942	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7972943	7973028	1	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7972943	7973028	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973029	7973111	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973112	7973213	1	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973112	7973213	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973214	7973362	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973363	7973469	1	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973363	7973469	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973470	7973602	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973603	7973703	1	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973603	7973703	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973704	7973798	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973799	7973886	1	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973799	7973886	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973887	7974032	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974033	7974121	1	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974033	7974121	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974122	7974243	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974244	7974383	1	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974244	7974383	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974384	7974463	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974464	7974623	1	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974464	7974623	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974624	7974717	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974718	7974826	0.57	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974718	7974826	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974827	7974958	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974959	7975055	0.83	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974959	7975055	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975056	7975181	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975182	7975293	1	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975182	7975293	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975294	7975471	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975472	7975531	1	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975472	7975531	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975532	7975713	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975714	7975832	1	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975714	7975832	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975833	7975925	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975926	7976050	1	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975926	7976050	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7976051	7976167	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7976168	7976392	1	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7976168	7976392	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7976393	7976570	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7976571	7976728	1	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7976571	7976728	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7976729	7976842	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7976843	7977006	1	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7976843	7977006	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7977007	7977101	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7977102	7977184	1	+	1	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7977102	7977184	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7977185	7977263	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7977264	7977352	1	+	2	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7977264	7977352	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7977353	7977429	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7977430	7977570	0.76	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7977430	7977570	.	+	.	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	stop_codon	7977571	7977573	.	+	0	transcript_id "Phchi.S4G132600.t1"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	transcript	7971540	7977570	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	start_codon	7971540	7971542	.	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7971540	7971697	0.66	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7971540	7971697	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7971698	7971862	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7971863	7971959	0.76	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7971863	7971959	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7971960	7972183	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7972184	7972229	0.61	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7972184	7972229	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7972230	7972481	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7972482	7972825	1	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7972482	7972825	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7972826	7972942	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7972943	7973028	1	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7972943	7973028	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973029	7973111	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973112	7973213	1	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973112	7973213	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973214	7973362	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973363	7973469	1	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973363	7973469	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973470	7973602	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973603	7973703	1	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973603	7973703	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973704	7973798	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7973799	7973886	1	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7973799	7973886	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7973887	7974032	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974033	7974121	1	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974033	7974121	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974122	7974243	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974244	7974383	1	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974244	7974383	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974384	7974463	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974464	7974623	1	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974464	7974623	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974624	7974717	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974718	7974826	0.44	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974718	7974826	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7974827	7974958	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7974959	7975055	0.74	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7974959	7975055	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975056	7975181	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975182	7975293	1	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975182	7975293	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975294	7975471	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975472	7975531	1	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975472	7975531	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975532	7975713	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975714	7975832	1	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975714	7975832	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7975833	7975925	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7975926	7976050	1	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7975926	7976050	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7976051	7976167	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7976168	7976392	0.97	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7976168	7976392	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7976393	7976570	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7976571	7976728	1	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7976571	7976728	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7976729	7976842	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7976843	7977006	1	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7976843	7977006	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7977007	7977101	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7977102	7977184	1	+	1	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7977102	7977184	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7977185	7977263	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7977264	7977352	1	+	2	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7977264	7977352	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	intron	7977353	7977429	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	CDS	7977430	7977570	0.73	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	exon	7977430	7977570	.	+	.	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
Phchi.S4	AUGUSTUS	stop_codon	7977571	7977573	.	+	0	transcript_id "Phchi.S4G132600.t2"; gene_id "Phchi.S4G132600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg490.t1 is derived from g10272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3417843	3419681	.	-	.	Phchi.S6G044900
Phchi.S6	AUGUSTUS	transcript	3417843	3419681	.	-	.	transcript_id "Phchi.S6G044900.t1"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	stop_codon	3417840	3417842	.	-	0	transcript_id "Phchi.S6G044900.t1"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	CDS	3417843	3419681	1	-	0	transcript_id "Phchi.S6G044900.t1"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	exon	3417843	3419681	.	-	.	transcript_id "Phchi.S6G044900.t1"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	start_codon	3419679	3419681	.	-	0	transcript_id "Phchi.S6G044900.t1"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	transcript	3417843	3419375	.	-	.	transcript_id "Phchi.S6G044900.t2"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	stop_codon	3417840	3417842	.	-	0	transcript_id "Phchi.S6G044900.t2"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	CDS	3417843	3419375	0.85	-	0	transcript_id "Phchi.S6G044900.t2"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	exon	3417843	3419375	.	-	.	transcript_id "Phchi.S6G044900.t2"; gene_id "Phchi.S6G044900"
Phchi.S6	AUGUSTUS	start_codon	3419373	3419375	.	-	0	transcript_id "Phchi.S6G044900.t2"; gene_id "Phchi.S6G044900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4264.t1 is derived from g1433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9253584	9257533	.	-	.	Phchi.S1G142300
Phchi.S1	AUGUSTUS	transcript	9253584	9257533	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	stop_codon	9253581	9253583	.	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9253584	9253667	0.53	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9253584	9253667	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9253668	9253747	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9253748	9253831	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9253748	9253831	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9253832	9253953	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9253954	9254101	1	-	1	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9253954	9254101	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9254102	9254187	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9254188	9254337	1	-	1	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9254188	9254337	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9254338	9254423	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9254424	9254626	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9254424	9254626	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9254627	9254739	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9254740	9254859	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9254740	9254859	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9254860	9254985	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9254986	9255150	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9254986	9255150	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9255151	9255231	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9255232	9255318	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9255232	9255318	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9255319	9255395	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9255396	9255545	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9255396	9255545	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9255546	9255621	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9255622	9255714	0.99	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9255622	9255714	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9255715	9255816	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9255817	9255987	0.99	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9255817	9255987	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9255988	9256091	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9256092	9256168	0.99	-	2	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9256092	9256168	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9256169	9256271	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9256272	9256512	0.95	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9256272	9256512	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9256513	9256611	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9256612	9256875	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9256612	9256875	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9256876	9256958	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9256959	9257046	1	-	1	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9256959	9257046	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9257047	9257130	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9257131	9257192	1	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9257131	9257192	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	intron	9257193	9257305	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	CDS	9257306	9257533	0.94	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	exon	9257306	9257533	.	-	.	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
Phchi.S1	AUGUSTUS	start_codon	9257531	9257533	.	-	0	transcript_id "Phchi.S1G142300.t1"; gene_id "Phchi.S1G142300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2957.t1 is derived from g126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	785261	786634	.	+	.	Phchi.S1G011600
Phchi.S1	AUGUSTUS	transcript	785261	786634	.	+	.	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	start_codon	785261	785263	.	+	0	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	CDS	785261	786426	0.44	+	0	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	exon	785261	786426	.	+	.	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	intron	786427	786627	.	+	.	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	CDS	786628	786634	0.69	+	1	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	exon	786628	786634	.	+	.	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
Phchi.S1	AUGUSTUS	stop_codon	786635	786637	.	+	0	transcript_id "Phchi.S1G011600.t1"; gene_id "Phchi.S1G011600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6080.t1 is derived from g3251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20858787	20860050	.	-	.	Phchi.S1G323900
Phchi.S1	AUGUSTUS	transcript	20858787	20860050	.	-	.	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	stop_codon	20858784	20858786	.	-	0	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	CDS	20858787	20858855	0.3	-	0	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	exon	20858787	20858855	.	-	.	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	intron	20858856	20858962	.	-	.	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	CDS	20858963	20859060	0.28	-	2	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	exon	20858963	20859060	.	-	.	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	intron	20859061	20859152	.	-	.	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	CDS	20859153	20860050	0.66	-	0	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	exon	20859153	20860050	.	-	.	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
Phchi.S1	AUGUSTUS	start_codon	20860048	20860050	.	-	0	transcript_id "Phchi.S1G323900.t1"; gene_id "Phchi.S1G323900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15714.t1 is derived from g14184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20814563	20818618	.	-	.	Phchi.S3G303300
Phchi.S3	AUGUSTUS	transcript	20814563	20818618	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	stop_codon	20814560	20814562	.	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20814563	20814582	0.99	-	2	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20814563	20814582	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20814583	20814749	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20814750	20815053	1	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20814750	20815053	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20815054	20815140	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20815141	20815396	1	-	1	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20815141	20815396	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20815397	20815486	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20815487	20815599	1	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20815487	20815599	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20815600	20815678	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20815679	20815766	0.78	-	1	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20815679	20815766	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20815767	20815917	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20815918	20816358	0.37	-	1	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20815918	20816358	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20816359	20816474	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20816475	20816611	1	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20816475	20816611	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20816612	20816729	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20816730	20816904	1	-	1	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20816730	20816904	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20816905	20816992	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20816993	20817153	0.73	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20816993	20817153	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20817154	20817256	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20817257	20817352	1	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20817257	20817352	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20817353	20817528	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20817529	20817676	1	-	1	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20817529	20817676	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20817677	20817943	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20817944	20818196	1	-	2	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20817944	20818196	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	intron	20818197	20818332	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	CDS	20818333	20818618	0.53	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	exon	20818333	20818618	.	-	.	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
Phchi.S3	AUGUSTUS	start_codon	20818616	20818618	.	-	0	transcript_id "Phchi.S3G303300.t1"; gene_id "Phchi.S3G303300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5563.t1 is derived from g2733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17603728	17605504	.	+	.	Phchi.S1G272200
Phchi.S1	AUGUSTUS	transcript	17603728	17605504	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	start_codon	17603728	17603730	.	+	0	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	CDS	17603728	17603743	0.37	+	0	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	exon	17603728	17603743	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	intron	17603744	17603892	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	CDS	17603893	17603927	0.98	+	2	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	exon	17603893	17603927	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	intron	17603928	17604109	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	CDS	17604110	17604223	1	+	0	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	exon	17604110	17604223	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	intron	17604224	17604315	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	CDS	17604316	17604467	1	+	0	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	exon	17604316	17604467	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	intron	17604468	17604609	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	CDS	17604610	17605504	0.43	+	1	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	exon	17604610	17605504	.	+	.	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
Phchi.S1	AUGUSTUS	stop_codon	17605505	17605507	.	+	0	transcript_id "Phchi.S1G272200.t1"; gene_id "Phchi.S1G272200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3307.t1 is derived from g476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2770856	2772796	.	+	.	Phchi.S1G046600
Phchi.S1	AUGUSTUS	transcript	2771172	2772796	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	start_codon	2771172	2771174	.	+	0	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2771172	2771198	0.92	+	0	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2771172	2771198	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2771199	2771320	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2771321	2771466	0.91	+	0	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2771321	2771466	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2771467	2771569	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2771570	2771977	0.99	+	1	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2771570	2771977	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2771978	2772242	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2772243	2772334	0.58	+	1	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2772243	2772334	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2772335	2772415	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2772416	2772657	0.52	+	2	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2772416	2772657	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2772658	2772748	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2772749	2772796	0.73	+	0	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2772749	2772796	.	+	.	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	stop_codon	2772797	2772799	.	+	0	transcript_id "Phchi.S1G046600.t1"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	transcript	2770856	2772796	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	start_codon	2770856	2770858	.	+	0	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2770856	2771014	0.64	+	0	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2770856	2771014	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2771015	2771320	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2771321	2771466	0.87	+	0	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2771321	2771466	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2771467	2771569	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2771570	2771977	0.99	+	1	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2771570	2771977	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2771978	2772242	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2772243	2772334	0.59	+	1	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2772243	2772334	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2772335	2772415	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2772416	2772657	0.5	+	2	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2772416	2772657	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	intron	2772658	2772748	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	CDS	2772749	2772796	0.68	+	0	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	exon	2772749	2772796	.	+	.	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
Phchi.S1	AUGUSTUS	stop_codon	2772797	2772799	.	+	0	transcript_id "Phchi.S1G046600.t2"; gene_id "Phchi.S1G046600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13896.t1 is derived from g12363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9529147	9530565	.	+	.	Phchi.S3G121500
Phchi.S3	AUGUSTUS	transcript	9529147	9530565	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	start_codon	9529147	9529149	.	+	0	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	CDS	9529147	9529336	0.67	+	0	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	exon	9529147	9529336	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	intron	9529337	9529636	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	CDS	9529637	9529737	1	+	2	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	exon	9529637	9529737	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	intron	9529738	9529828	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	CDS	9529829	9530022	1	+	0	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	exon	9529829	9530022	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	intron	9530023	9530147	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	CDS	9530148	9530565	1	+	1	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	exon	9530148	9530565	.	+	.	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
Phchi.S3	AUGUSTUS	stop_codon	9530566	9530568	.	+	0	transcript_id "Phchi.S3G121500.t1"; gene_id "Phchi.S3G121500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7399.t1 is derived from g4571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28951884	28952597	.	+	.	Phchi.S1G455800
Phchi.S1	AUGUSTUS	transcript	28951884	28952597	.	+	.	transcript_id "Phchi.S1G455800.t1"; gene_id "Phchi.S1G455800"
Phchi.S1	AUGUSTUS	start_codon	28951884	28951886	.	+	0	transcript_id "Phchi.S1G455800.t1"; gene_id "Phchi.S1G455800"
Phchi.S1	AUGUSTUS	CDS	28951884	28952597	0.78	+	0	transcript_id "Phchi.S1G455800.t1"; gene_id "Phchi.S1G455800"
Phchi.S1	AUGUSTUS	exon	28951884	28952597	.	+	.	transcript_id "Phchi.S1G455800.t1"; gene_id "Phchi.S1G455800"
Phchi.S1	AUGUSTUS	stop_codon	28952598	28952600	.	+	0	transcript_id "Phchi.S1G455800.t1"; gene_id "Phchi.S1G455800"
# This transcript jg5479.t2 is derived from g2649.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5480.t1 is derived from g2650.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17052640	17054541	.	-	.	Phchi.S1G263900
Phchi.S1	AUGUSTUS	transcript	17052640	17054541	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	stop_codon	17052637	17052639	.	-	0	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17052640	17052807	1	-	0	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17052640	17052807	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	intron	17052808	17052935	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17052936	17053340	0.98	-	0	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17052936	17053340	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	intron	17053341	17053443	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17053444	17053566	0.99	-	0	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17053444	17053566	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	intron	17053567	17053695	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17053696	17054541	0.88	-	0	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17053696	17054541	.	-	.	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	start_codon	17054539	17054541	.	-	0	transcript_id "Phchi.S1G263900.t1"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	transcript	17052640	17054541	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	stop_codon	17052637	17052639	.	-	0	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17052640	17052807	1	-	0	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17052640	17052807	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	intron	17052808	17052935	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17052936	17053340	0.99	-	0	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17052936	17053340	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	intron	17053341	17053443	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17053444	17053569	0.8	-	0	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17053444	17053569	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	intron	17053570	17053695	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	CDS	17053696	17054541	0.83	-	0	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	exon	17053696	17054541	.	-	.	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
Phchi.S1	AUGUSTUS	start_codon	17054539	17054541	.	-	0	transcript_id "Phchi.S1G263900.t2"; gene_id "Phchi.S1G263900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6211.t1 is derived from g3382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21480346	21485447	.	+	.	Phchi.S1G337000
Phchi.S1	AUGUSTUS	transcript	21480346	21485447	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	start_codon	21480346	21480348	.	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21480346	21480352	0.97	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21480346	21480352	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21480353	21480517	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21480518	21480630	0.93	+	2	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21480518	21480630	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21480631	21480744	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21480745	21480819	0.92	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21480745	21480819	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21480820	21480904	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21480905	21481047	0.98	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21480905	21481047	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21481048	21481164	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21481165	21481251	0.99	+	1	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21481165	21481251	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21481252	21481356	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21481357	21481440	1	+	1	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21481357	21481440	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21481441	21481515	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21481516	21481723	1	+	1	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21481516	21481723	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21481724	21481894	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21481895	21481980	1	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21481895	21481980	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21481981	21482061	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21482062	21482293	1	+	1	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21482062	21482293	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21482294	21482406	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21482407	21482530	1	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21482407	21482530	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21482531	21482626	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21482627	21482769	1	+	2	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21482627	21482769	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21482770	21482960	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21482961	21483069	1	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21482961	21483069	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21483070	21483166	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21483167	21483209	1	+	2	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21483167	21483209	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21483210	21483332	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21483333	21483513	1	+	1	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21483333	21483513	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21483514	21483658	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21483659	21483729	1	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21483659	21483729	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21483730	21483819	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21483820	21483913	1	+	1	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21483820	21483913	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21483914	21484006	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21484007	21484240	0.96	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21484007	21484240	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21484241	21484358	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21484359	21484568	1	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21484359	21484568	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21484569	21484646	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21484647	21484931	0.96	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21484647	21484931	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21484932	21485009	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21485010	21485126	0.79	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21485010	21485126	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21485127	21485338	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21485339	21485359	0.73	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21485339	21485359	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	intron	21485360	21485444	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	CDS	21485445	21485447	0.73	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	exon	21485445	21485447	.	+	.	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
Phchi.S1	AUGUSTUS	stop_codon	21485448	21485450	.	+	0	transcript_id "Phchi.S1G337000.t1"; gene_id "Phchi.S1G337000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg780.t1 is derived from g10562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5469935	5471918	.	+	.	Phchi.S6G073900
Phchi.S6	AUGUSTUS	transcript	5469935	5471918	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	start_codon	5469935	5469937	.	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5469935	5469946	0.4	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5469935	5469946	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5469947	5470115	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5470116	5470208	0.99	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5470116	5470208	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5470209	5470290	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5470291	5470355	1	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5470291	5470355	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5470356	5470473	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5470474	5470528	1	+	1	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5470474	5470528	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5470529	5470634	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5470635	5470724	1	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5470635	5470724	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5470725	5470840	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5470841	5470925	1	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5470841	5470925	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5470926	5471005	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5471006	5471098	1	+	2	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5471006	5471098	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5471099	5471256	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5471257	5471441	1	+	2	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5471257	5471441	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5471442	5471523	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5471524	5471612	1	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5471524	5471612	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5471613	5471698	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5471699	5471798	1	+	1	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5471699	5471798	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	intron	5471799	5471879	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	CDS	5471880	5471918	1	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	exon	5471880	5471918	.	+	.	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
Phchi.S6	AUGUSTUS	stop_codon	5471919	5471921	.	+	0	transcript_id "Phchi.S6G073900.t1"; gene_id "Phchi.S6G073900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4638.t1 is derived from g1808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11554943	11555485	.	+	.	Phchi.S1G179700
Phchi.S1	AUGUSTUS	transcript	11554943	11555485	.	+	.	transcript_id "Phchi.S1G179700.t1"; gene_id "Phchi.S1G179700"
Phchi.S1	AUGUSTUS	start_codon	11554943	11554945	.	+	0	transcript_id "Phchi.S1G179700.t1"; gene_id "Phchi.S1G179700"
Phchi.S1	AUGUSTUS	CDS	11554943	11555485	0.99	+	0	transcript_id "Phchi.S1G179700.t1"; gene_id "Phchi.S1G179700"
Phchi.S1	AUGUSTUS	exon	11554943	11555485	.	+	.	transcript_id "Phchi.S1G179700.t1"; gene_id "Phchi.S1G179700"
Phchi.S1	AUGUSTUS	stop_codon	11555486	11555488	.	+	0	transcript_id "Phchi.S1G179700.t1"; gene_id "Phchi.S1G179700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4538.t1 is derived from g1708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11009743	11011145	.	-	.	Phchi.S1G169700
Phchi.S1	AUGUSTUS	transcript	11009743	11011145	.	-	.	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	stop_codon	11009740	11009742	.	-	0	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	CDS	11009743	11010489	0.99	-	0	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	exon	11009743	11010489	.	-	.	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	intron	11010490	11010588	.	-	.	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	CDS	11010589	11010765	0.96	-	0	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	exon	11010589	11010765	.	-	.	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	intron	11010766	11010890	.	-	.	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	CDS	11010891	11011145	0.5	-	0	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	exon	11010891	11011145	.	-	.	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
Phchi.S1	AUGUSTUS	start_codon	11011143	11011145	.	-	0	transcript_id "Phchi.S1G169700.t1"; gene_id "Phchi.S1G169700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3586.t1 is derived from g755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4617202	4618299	.	+	.	Phchi.S1G074500
Phchi.S1	AUGUSTUS	transcript	4617202	4618299	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	start_codon	4617202	4617204	.	+	0	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	CDS	4617202	4617218	0.55	+	0	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	exon	4617202	4617218	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	intron	4617219	4617305	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	CDS	4617306	4617312	0.76	+	1	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	exon	4617306	4617312	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	intron	4617313	4617407	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	CDS	4617408	4617425	0.63	+	0	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	exon	4617408	4617425	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	intron	4617426	4617565	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	CDS	4617566	4617729	0.74	+	0	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	exon	4617566	4617729	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	intron	4617730	4618040	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	CDS	4618041	4618299	1	+	1	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	exon	4618041	4618299	.	+	.	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
Phchi.S1	AUGUSTUS	stop_codon	4618300	4618302	.	+	0	transcript_id "Phchi.S1G074500.t1"; gene_id "Phchi.S1G074500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1190.t1 is derived from g10973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8353482	8354009	.	-	.	Phchi.S6G114900
Phchi.S6	AUGUSTUS	transcript	8353482	8354009	.	-	.	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	stop_codon	8353479	8353481	.	-	0	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	CDS	8353482	8353689	1	-	1	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	exon	8353482	8353689	.	-	.	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	intron	8353690	8353830	.	-	.	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	CDS	8353831	8354009	0.95	-	0	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	exon	8353831	8354009	.	-	.	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
Phchi.S6	AUGUSTUS	start_codon	8354007	8354009	.	-	0	transcript_id "Phchi.S6G114900.t1"; gene_id "Phchi.S6G114900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11890.t1 is derived from g15942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9040692	9041465	.	+	.	Phchi.S4G147200
Phchi.S4	AUGUSTUS	transcript	9040692	9041465	.	+	.	transcript_id "Phchi.S4G147200.t1"; gene_id "Phchi.S4G147200"
Phchi.S4	AUGUSTUS	start_codon	9040692	9040694	.	+	0	transcript_id "Phchi.S4G147200.t1"; gene_id "Phchi.S4G147200"
Phchi.S4	AUGUSTUS	CDS	9040692	9041465	0.97	+	0	transcript_id "Phchi.S4G147200.t1"; gene_id "Phchi.S4G147200"
Phchi.S4	AUGUSTUS	exon	9040692	9041465	.	+	.	transcript_id "Phchi.S4G147200.t1"; gene_id "Phchi.S4G147200"
Phchi.S4	AUGUSTUS	stop_codon	9041466	9041468	.	+	0	transcript_id "Phchi.S4G147200.t1"; gene_id "Phchi.S4G147200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9121.t1 is derived from g6296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39933915	39934583	.	-	.	Phchi.S1G628000
Phchi.S1	AUGUSTUS	transcript	39933915	39934583	.	-	.	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	stop_codon	39933912	39933914	.	-	0	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	CDS	39933915	39934062	1	-	1	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	exon	39933915	39934062	.	-	.	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	intron	39934063	39934176	.	-	.	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	CDS	39934177	39934583	0.95	-	0	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	exon	39934177	39934583	.	-	.	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
Phchi.S1	AUGUSTUS	start_codon	39934581	39934583	.	-	0	transcript_id "Phchi.S1G628000.t1"; gene_id "Phchi.S1G628000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14495.t1 is derived from g12963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13153424	13156125	.	+	.	Phchi.S3G181400
Phchi.S3	AUGUSTUS	transcript	13153424	13156125	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	start_codon	13153424	13153426	.	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13153424	13153535	0.25	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13153424	13153535	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13153536	13153618	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13153619	13153763	0.5	+	2	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13153619	13153763	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13153764	13153905	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13153906	13154206	1	+	1	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13153906	13154206	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13154207	13154418	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13154419	13154521	1	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13154419	13154521	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13154522	13154622	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13154623	13154732	1	+	2	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13154623	13154732	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13154733	13154821	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13154822	13154890	1	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13154822	13154890	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13154891	13155010	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13155011	13155126	1	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13155011	13155126	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13155127	13155219	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13155220	13155274	1	+	1	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13155220	13155274	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13155275	13155383	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13155384	13155504	0.98	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13155384	13155504	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13155505	13155626	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13155627	13155674	1	+	2	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13155627	13155674	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13155675	13155810	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13155811	13155905	1	+	2	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13155811	13155905	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	intron	13155906	13156026	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	CDS	13156027	13156125	0.97	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	exon	13156027	13156125	.	+	.	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
Phchi.S3	AUGUSTUS	stop_codon	13156126	13156128	.	+	0	transcript_id "Phchi.S3G181400.t1"; gene_id "Phchi.S3G181400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg7703.t1 is derived from g4877.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30708687	30712465	.	-	.	Phchi.S1G486200
Phchi.S1	AUGUSTUS	transcript	30708687	30712465	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	stop_codon	30708684	30708686	.	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30708687	30708915	0.89	-	1	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30708687	30708915	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30708916	30709008	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709009	30709181	1	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709009	30709181	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709182	30709282	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709283	30709414	0.97	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709283	30709414	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709415	30709524	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709525	30709738	0.98	-	1	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709525	30709738	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709739	30709868	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709869	30710056	1	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709869	30710056	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710057	30710155	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30710156	30710347	1	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30710156	30710347	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710348	30710487	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30710488	30710870	1	-	2	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30710488	30710870	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710871	30711024	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30711025	30711741	1	-	2	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30711025	30711741	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30711742	30711988	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30711989	30712207	0.62	-	2	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30711989	30712207	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30712208	30712323	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30712324	30712465	0.5	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30712324	30712465	.	-	.	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	start_codon	30712463	30712465	.	-	0	transcript_id "Phchi.S1G486200.t1"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	transcript	30708687	30712465	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	stop_codon	30708684	30708686	.	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30708687	30708915	0.9	-	1	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30708687	30708915	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30708916	30709008	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709009	30709181	1	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709009	30709181	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709182	30709282	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709283	30709414	0.93	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709283	30709414	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709415	30709524	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709525	30709738	0.97	-	1	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709525	30709738	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709739	30709868	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709869	30710056	1	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709869	30710056	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710057	30710155	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30710156	30710347	1	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30710156	30710347	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710348	30710487	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30710488	30710870	0.99	-	2	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30710488	30710870	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710871	30711024	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30711025	30711741	0.99	-	2	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30711025	30711741	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30711742	30711979	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30711980	30712207	0.64	-	2	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30711980	30712207	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30712208	30712323	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30712324	30712465	0.47	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30712324	30712465	.	-	.	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	start_codon	30712463	30712465	.	-	0	transcript_id "Phchi.S1G486200.t2"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	transcript	30708687	30712465	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	stop_codon	30708684	30708686	.	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30708687	30708915	0.91	-	1	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30708687	30708915	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30708916	30709008	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709009	30709181	0.99	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709009	30709181	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709182	30709282	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709283	30709414	1	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709283	30709414	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709415	30709524	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709525	30709738	1	-	1	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709525	30709738	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30709739	30709868	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30709869	30710056	1	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30709869	30710056	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710057	30710155	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30710156	30710347	1	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30710156	30710347	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710348	30710487	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30710488	30710870	1	-	2	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30710488	30710870	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30710871	30711024	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30711025	30711741	0.98	-	2	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30711025	30711741	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30711742	30711923	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30711924	30711958	0.8	-	1	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30711924	30711958	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30711959	30712059	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30712060	30712207	0.48	-	2	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30712060	30712207	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	intron	30712208	30712323	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	CDS	30712324	30712465	0.47	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	exon	30712324	30712465	.	-	.	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
Phchi.S1	AUGUSTUS	start_codon	30712463	30712465	.	-	0	transcript_id "Phchi.S1G486200.t3"; gene_id "Phchi.S1G486200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10092.t1 is derived from g7268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45707832	45709583	.	-	.	Phchi.S1G725100
Phchi.S1	AUGUSTUS	transcript	45707832	45709583	.	-	.	transcript_id "Phchi.S1G725100.t1"; gene_id "Phchi.S1G725100"
Phchi.S1	AUGUSTUS	stop_codon	45707829	45707831	.	-	0	transcript_id "Phchi.S1G725100.t1"; gene_id "Phchi.S1G725100"
Phchi.S1	AUGUSTUS	CDS	45707832	45709583	0.83	-	0	transcript_id "Phchi.S1G725100.t1"; gene_id "Phchi.S1G725100"
Phchi.S1	AUGUSTUS	exon	45707832	45709583	.	-	.	transcript_id "Phchi.S1G725100.t1"; gene_id "Phchi.S1G725100"
Phchi.S1	AUGUSTUS	start_codon	45709581	45709583	.	-	0	transcript_id "Phchi.S1G725100.t1"; gene_id "Phchi.S1G725100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5287.t1 is derived from g2457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16029310	16031668	.	-	.	Phchi.S1G244600
Phchi.S1	AUGUSTUS	transcript	16029310	16031668	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	stop_codon	16029307	16029309	.	-	0	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16029310	16029344	0.87	-	2	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16029310	16029344	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16029345	16029487	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16029488	16029499	0.87	-	2	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16029488	16029499	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16029500	16029598	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16029599	16029829	0.8	-	2	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16029599	16029829	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16029830	16029942	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16029943	16030462	0.99	-	0	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16029943	16030462	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16030463	16030553	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16030554	16030702	1	-	2	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16030554	16030702	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16030703	16030827	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16030828	16031142	1	-	2	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16030828	16031142	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16031143	16031252	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16031253	16031294	1	-	2	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16031253	16031294	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	intron	16031295	16031412	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	CDS	16031413	16031668	0.88	-	0	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	exon	16031413	16031668	.	-	.	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
Phchi.S1	AUGUSTUS	start_codon	16031666	16031668	.	-	0	transcript_id "Phchi.S1G244600.t1"; gene_id "Phchi.S1G244600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7076.t1 is derived from g4248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26784119	26786714	.	+	.	Phchi.S1G423500
Phchi.S1	AUGUSTUS	transcript	26784119	26786714	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	start_codon	26784119	26784121	.	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26784119	26784300	0.27	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26784119	26784300	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26784301	26784399	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26784400	26784772	0.89	+	1	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26784400	26784772	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26784773	26784893	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26784894	26785487	0.98	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26784894	26785487	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26785488	26785609	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26785610	26785795	1	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26785610	26785795	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26785796	26785928	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26785929	26785993	1	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26785929	26785993	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26785994	26786088	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26786089	26786245	0.48	+	1	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26786089	26786245	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26786246	26786328	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26786329	26786387	1	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26786329	26786387	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	intron	26786388	26786533	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	CDS	26786534	26786714	1	+	1	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	exon	26786534	26786714	.	+	.	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
Phchi.S1	AUGUSTUS	stop_codon	26786715	26786717	.	+	0	transcript_id "Phchi.S1G423500.t1"; gene_id "Phchi.S1G423500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9940.t1 is derived from g7116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44582549	44586834	.	-	.	Phchi.S1G709900
Phchi.S1	AUGUSTUS	transcript	44582549	44586834	.	-	.	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	stop_codon	44582546	44582548	.	-	0	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	CDS	44582549	44583682	0.66	-	0	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	exon	44582549	44583682	.	-	.	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	intron	44583683	44583795	.	-	.	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	CDS	44583796	44585168	0.99	-	2	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	exon	44583796	44585168	.	-	.	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	intron	44585169	44585273	.	-	.	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	CDS	44585274	44586834	0.94	-	0	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	exon	44585274	44586834	.	-	.	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
Phchi.S1	AUGUSTUS	start_codon	44586832	44586834	.	-	0	transcript_id "Phchi.S1G709900.t1"; gene_id "Phchi.S1G709900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9130.t1 is derived from g6305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40006816	40013240	.	-	.	Phchi.S1G628900
Phchi.S1	AUGUSTUS	transcript	40006816	40013240	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	stop_codon	40006813	40006815	.	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40006816	40007395	0.98	-	1	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40006816	40007395	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007396	40007483	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007484	40007588	1	-	1	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007484	40007588	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007589	40007675	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007676	40007845	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007676	40007845	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007846	40007918	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007919	40008026	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007919	40008026	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008027	40008114	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008115	40008246	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008115	40008246	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008247	40008350	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008351	40008465	0.78	-	1	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008351	40008465	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008466	40008607	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008608	40008837	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008608	40008837	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008838	40008993	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008994	40009086	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008994	40009086	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009087	40009190	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009191	40009284	0.96	-	1	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009191	40009284	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009285	40009368	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009369	40009446	1	-	1	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009369	40009446	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009447	40009590	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009591	40009661	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009591	40009661	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009662	40009808	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009809	40009904	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009809	40009904	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009905	40010110	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010111	40010188	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010111	40010188	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010189	40010292	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010293	40010361	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010293	40010361	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010362	40010521	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010522	40010589	1	-	2	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010522	40010589	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010590	40010798	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010799	40010876	1	-	2	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010799	40010876	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010877	40010999	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011000	40011099	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011000	40011099	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011100	40011244	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011245	40011304	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011245	40011304	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011305	40011777	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011778	40011842	1	-	2	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011778	40011842	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011843	40012088	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012089	40012154	1	-	2	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012089	40012154	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012155	40012237	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012238	40012287	1	-	1	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012238	40012287	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012288	40012400	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012401	40012485	1	-	2	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012401	40012485	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012486	40012596	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012597	40012699	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012597	40012699	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012700	40012833	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012834	40012914	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012834	40012914	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012915	40013222	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40013223	40013240	1	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40013223	40013240	.	-	.	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	start_codon	40013238	40013240	.	-	0	transcript_id "Phchi.S1G628900.t1"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	transcript	40006816	40013240	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	stop_codon	40006813	40006815	.	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40006816	40007395	1	-	1	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40006816	40007395	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007396	40007483	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007484	40007588	1	-	1	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007484	40007588	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007589	40007675	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007676	40007845	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007676	40007845	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007846	40007918	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007919	40008026	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007919	40008026	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008027	40008114	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008115	40008246	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008115	40008246	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008247	40008350	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008351	40008465	0.75	-	1	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008351	40008465	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008466	40008607	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008608	40008834	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008608	40008834	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008835	40008993	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008994	40009086	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008994	40009086	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009087	40009190	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009191	40009284	0.97	-	1	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009191	40009284	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009285	40009368	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009369	40009446	1	-	1	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009369	40009446	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009447	40009590	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009591	40009661	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009591	40009661	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009662	40009808	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009809	40009904	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009809	40009904	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009905	40010110	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010111	40010188	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010111	40010188	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010189	40010292	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010293	40010361	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010293	40010361	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010362	40010521	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010522	40010589	1	-	2	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010522	40010589	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010590	40010798	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010799	40010876	1	-	2	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010799	40010876	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010877	40010999	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011000	40011099	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011000	40011099	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011100	40011244	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011245	40011304	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011245	40011304	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011305	40011777	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011778	40011842	1	-	2	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011778	40011842	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011843	40012088	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012089	40012154	1	-	2	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012089	40012154	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012155	40012237	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012238	40012287	1	-	1	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012238	40012287	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012288	40012400	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012401	40012485	1	-	2	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012401	40012485	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012486	40012596	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012597	40012699	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012597	40012699	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012700	40012833	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012834	40012914	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012834	40012914	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012915	40013222	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40013223	40013240	1	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40013223	40013240	.	-	.	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	start_codon	40013238	40013240	.	-	0	transcript_id "Phchi.S1G628900.t2"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	transcript	40006816	40013240	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	stop_codon	40006813	40006815	.	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40006816	40007395	0.92	-	1	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40006816	40007395	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007396	40007483	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007484	40007588	1	-	1	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007484	40007588	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007589	40007675	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007676	40007845	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007676	40007845	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40007846	40007918	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40007919	40008026	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40007919	40008026	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008027	40008114	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008115	40008246	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008115	40008246	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008247	40008350	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008351	40008465	0.74	-	1	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008351	40008465	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008466	40008607	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008608	40008834	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008608	40008834	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40008835	40008993	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40008994	40009086	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40008994	40009086	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009087	40009190	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009191	40009284	0.95	-	1	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009191	40009284	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009285	40009368	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009369	40009446	1	-	1	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009369	40009446	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009447	40009590	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009591	40009661	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009591	40009661	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009662	40009808	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40009809	40009904	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40009809	40009904	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40009905	40010110	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010111	40010188	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010111	40010188	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010189	40010292	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010293	40010361	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010293	40010361	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010362	40010521	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010522	40010589	1	-	2	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010522	40010589	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010590	40010798	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40010799	40010876	1	-	2	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40010799	40010876	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40010877	40010999	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011000	40011099	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011000	40011099	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011100	40011244	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011245	40011304	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011245	40011304	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011305	40011777	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40011778	40011860	1	-	2	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40011778	40011860	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40011861	40012088	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012089	40012154	1	-	2	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012089	40012154	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012155	40012237	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012238	40012287	1	-	1	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012238	40012287	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012288	40012400	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012401	40012485	1	-	2	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012401	40012485	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012486	40012596	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012597	40012699	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012597	40012699	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012700	40012833	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40012834	40012914	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40012834	40012914	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	intron	40012915	40013222	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	CDS	40013223	40013240	1	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	exon	40013223	40013240	.	-	.	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
Phchi.S1	AUGUSTUS	start_codon	40013238	40013240	.	-	0	transcript_id "Phchi.S1G628900.t3"; gene_id "Phchi.S1G628900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7647.t1 is derived from g4821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30389167	30390486	.	+	.	Phchi.S1G480600
Phchi.S1	AUGUSTUS	transcript	30389167	30390486	.	+	.	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	start_codon	30389167	30389169	.	+	0	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	CDS	30389167	30389413	0.52	+	0	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	exon	30389167	30389413	.	+	.	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	intron	30389414	30389495	.	+	.	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	CDS	30389496	30390076	1	+	2	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	exon	30389496	30390076	.	+	.	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	intron	30390077	30390159	.	+	.	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	CDS	30390160	30390486	1	+	0	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	exon	30390160	30390486	.	+	.	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
Phchi.S1	AUGUSTUS	stop_codon	30390487	30390489	.	+	0	transcript_id "Phchi.S1G480600.t1"; gene_id "Phchi.S1G480600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg860.t1 is derived from g10642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5970638	5971338	.	+	.	Phchi.S6G081900
Phchi.S6	AUGUSTUS	transcript	5970638	5971338	.	+	.	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	start_codon	5970638	5970640	.	+	0	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	CDS	5970638	5970941	0.83	+	0	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	exon	5970638	5970941	.	+	.	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	intron	5970942	5971033	.	+	.	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	CDS	5971034	5971338	0.97	+	2	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	exon	5971034	5971338	.	+	.	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	stop_codon	5971339	5971341	.	+	0	transcript_id "Phchi.S6G081900.t1"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	transcript	5970638	5970976	.	+	.	transcript_id "Phchi.S6G081900.t2"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	start_codon	5970638	5970640	.	+	0	transcript_id "Phchi.S6G081900.t2"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	CDS	5970638	5970976	0.56	+	0	transcript_id "Phchi.S6G081900.t2"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	exon	5970638	5970976	.	+	.	transcript_id "Phchi.S6G081900.t2"; gene_id "Phchi.S6G081900"
Phchi.S6	AUGUSTUS	stop_codon	5970977	5970979	.	+	0	transcript_id "Phchi.S6G081900.t2"; gene_id "Phchi.S6G081900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13523.t1 is derived from g11990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7342788	7344691	.	-	.	Phchi.S3G084200
Phchi.S3	AUGUSTUS	transcript	7342788	7344691	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	stop_codon	7342785	7342787	.	-	0	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7342788	7342915	1	-	2	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7342788	7342915	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7342916	7343090	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7343091	7343302	0.79	-	1	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7343091	7343302	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7343303	7343392	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7343393	7343657	0.79	-	2	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7343393	7343657	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7343658	7343749	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7343750	7343901	0.78	-	1	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7343750	7343901	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7343902	7343986	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7343987	7344176	1	-	2	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7343987	7344176	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7344177	7344263	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7344264	7344332	0.76	-	2	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7344264	7344332	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7344333	7344442	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7344443	7344569	0.72	-	0	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7344443	7344569	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	intron	7344570	7344670	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	CDS	7344671	7344691	0.52	-	0	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	exon	7344671	7344691	.	-	.	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
Phchi.S3	AUGUSTUS	start_codon	7344689	7344691	.	-	0	transcript_id "Phchi.S3G084200.t1"; gene_id "Phchi.S3G084200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13750.t1 is derived from g12217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8689988	8690718	.	-	.	Phchi.S3G106900
Phchi.S3	AUGUSTUS	transcript	8689988	8690718	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	stop_codon	8689985	8689987	.	-	0	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	CDS	8689988	8690066	1	-	1	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	exon	8689988	8690066	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	intron	8690067	8690161	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	CDS	8690162	8690268	0.99	-	0	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	exon	8690162	8690268	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	intron	8690269	8690404	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	CDS	8690405	8690485	0.66	-	0	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	exon	8690405	8690485	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	intron	8690486	8690587	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	CDS	8690588	8690599	0.63	-	0	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	exon	8690588	8690599	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	intron	8690600	8690691	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	CDS	8690692	8690718	0.77	-	0	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	exon	8690692	8690718	.	-	.	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
Phchi.S3	AUGUSTUS	start_codon	8690716	8690718	.	-	0	transcript_id "Phchi.S3G106900.t1"; gene_id "Phchi.S3G106900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10544.t1 is derived from g14594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	887206	890053	.	-	.	Phchi.S4G012600
Phchi.S4	AUGUSTUS	transcript	887206	890053	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	stop_codon	887203	887205	.	-	0	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	CDS	887206	887727	1	-	0	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	exon	887206	887727	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	intron	887728	887828	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	CDS	887829	889034	1	-	0	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	exon	887829	889034	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	intron	889035	889119	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	CDS	889120	889189	1	-	1	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	exon	889120	889189	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	intron	889190	889964	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	CDS	889965	890053	0.99	-	0	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	exon	889965	890053	.	-	.	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
Phchi.S4	AUGUSTUS	start_codon	890051	890053	.	-	0	transcript_id "Phchi.S4G012600.t1"; gene_id "Phchi.S4G012600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11938.t1 is derived from g7613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	120884	124299	.	+	.	Phchi.S2G001800
Phchi.S2	AUGUSTUS	transcript	120884	124299	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	start_codon	120884	120886	.	+	0	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	CDS	120884	121063	0.99	+	0	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	exon	120884	121063	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	intron	121064	121159	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	CDS	121160	121479	1	+	0	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	exon	121160	121479	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	intron	121480	121574	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	CDS	121575	122880	1	+	1	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	exon	121575	122880	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	intron	122881	122970	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	CDS	122971	123240	1	+	0	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	exon	122971	123240	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	intron	123241	123321	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	CDS	123322	124299	0.96	+	0	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	exon	123322	124299	.	+	.	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
Phchi.S2	AUGUSTUS	stop_codon	124300	124302	.	+	0	transcript_id "Phchi.S2G001800.t1"; gene_id "Phchi.S2G001800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2972.t1 is derived from g141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	901248	905987	.	+	.	Phchi.S1G013100
Phchi.S1	AUGUSTUS	transcript	901248	905987	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	start_codon	901248	901250	.	+	0	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	CDS	901248	902817	0.52	+	0	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	exon	901248	902817	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	intron	902818	902937	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	CDS	902938	904253	0.99	+	2	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	exon	902938	904253	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	intron	904254	904348	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	CDS	904349	905755	0.46	+	0	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	exon	904349	905755	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	intron	905756	905840	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	CDS	905841	905899	0.75	+	0	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	exon	905841	905899	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	intron	905900	905986	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	CDS	905987	905987	1	+	1	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	exon	905987	905987	.	+	.	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
Phchi.S1	AUGUSTUS	stop_codon	905988	905990	.	+	0	transcript_id "Phchi.S1G013100.t1"; gene_id "Phchi.S1G013100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5269.t1 is derived from g2439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15968599	15969606	.	+	.	Phchi.S1G242800
Phchi.S1	AUGUSTUS	transcript	15968599	15969606	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	start_codon	15968599	15968601	.	+	0	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15968599	15968753	0.84	+	0	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15968599	15968753	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15968754	15968842	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15968843	15968870	1	+	1	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15968843	15968870	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15968871	15968966	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15968967	15969040	1	+	0	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15968967	15969040	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15969041	15969177	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15969178	15969222	1	+	1	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15969178	15969222	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15969223	15969327	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15969328	15969409	1	+	1	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15969328	15969409	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15969410	15969495	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15969496	15969606	0.99	+	0	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15969496	15969606	.	+	.	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	stop_codon	15969607	15969609	.	+	0	transcript_id "Phchi.S1G242800.t1"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	transcript	15968599	15969606	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	start_codon	15968599	15968601	.	+	0	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15968599	15968753	0.78	+	0	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15968599	15968753	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15968754	15968842	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15968843	15968870	1	+	1	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15968843	15968870	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15968871	15968954	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15968955	15969040	1	+	0	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15968955	15969040	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15969041	15969177	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15969178	15969222	1	+	1	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15969178	15969222	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15969223	15969327	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15969328	15969409	1	+	1	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15969328	15969409	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	intron	15969410	15969495	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	CDS	15969496	15969606	0.99	+	0	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	exon	15969496	15969606	.	+	.	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
Phchi.S1	AUGUSTUS	stop_codon	15969607	15969609	.	+	0	transcript_id "Phchi.S1G242800.t2"; gene_id "Phchi.S1G242800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg922.t1 is derived from g10704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6458980	6459549	.	+	.	Phchi.S6G088100
Phchi.S6	AUGUSTUS	transcript	6458980	6459549	.	+	.	transcript_id "Phchi.S6G088100.t1"; gene_id "Phchi.S6G088100"
Phchi.S6	AUGUSTUS	start_codon	6458980	6458982	.	+	0	transcript_id "Phchi.S6G088100.t1"; gene_id "Phchi.S6G088100"
Phchi.S6	AUGUSTUS	CDS	6458980	6459549	0.66	+	0	transcript_id "Phchi.S6G088100.t1"; gene_id "Phchi.S6G088100"
Phchi.S6	AUGUSTUS	exon	6458980	6459549	.	+	.	transcript_id "Phchi.S6G088100.t1"; gene_id "Phchi.S6G088100"
Phchi.S6	AUGUSTUS	stop_codon	6459550	6459552	.	+	0	transcript_id "Phchi.S6G088100.t1"; gene_id "Phchi.S6G088100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5908.t1 is derived from g3078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19743124	19743846	.	-	.	Phchi.S1G306700
Phchi.S1	AUGUSTUS	transcript	19743124	19743846	.	-	.	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	stop_codon	19743121	19743123	.	-	0	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	CDS	19743124	19743284	0.85	-	2	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	exon	19743124	19743284	.	-	.	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	intron	19743285	19743374	.	-	.	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	CDS	19743375	19743455	0.59	-	2	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	exon	19743375	19743455	.	-	.	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	intron	19743456	19743599	.	-	.	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	CDS	19743600	19743846	0.28	-	0	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	exon	19743600	19743846	.	-	.	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
Phchi.S1	AUGUSTUS	start_codon	19743844	19743846	.	-	0	transcript_id "Phchi.S1G306700.t1"; gene_id "Phchi.S1G306700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9669.t1 is derived from g6845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43194542	43201449	.	+	.	Phchi.S1G682800
Phchi.S1	AUGUSTUS	transcript	43194542	43201449	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	start_codon	43194542	43194544	.	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43194542	43194614	0.49	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43194542	43194614	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43194615	43194696	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43194697	43194854	1	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43194697	43194854	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43194855	43194970	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43194971	43195108	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43194971	43195108	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43195109	43195192	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43195193	43195607	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43195193	43195607	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43195608	43195762	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43195763	43195893	1	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43195763	43195893	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43195894	43196045	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43196046	43196120	0.99	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43196046	43196120	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43196121	43196236	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43196237	43196314	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43196237	43196314	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43196315	43196435	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43196436	43196537	0.94	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43196436	43196537	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43196538	43196646	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43196647	43196676	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43196647	43196676	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43196677	43197319	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43197320	43197661	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43197320	43197661	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43197662	43197797	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43197798	43197879	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43197798	43197879	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43197880	43197995	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43197996	43198091	0.98	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43197996	43198091	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43198092	43198188	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43198189	43198368	1	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43198189	43198368	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43198369	43198451	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43198452	43198558	0.97	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43198452	43198558	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43198559	43198680	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43198681	43198859	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43198681	43198859	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43198860	43198944	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43198945	43199109	1	+	1	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43198945	43199109	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43199110	43199194	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43199195	43199448	1	+	1	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43199195	43199448	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43199449	43199524	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43199525	43199688	1	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43199525	43199688	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43199689	43199766	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43199767	43200039	1	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43199767	43200039	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43200040	43200214	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43200215	43200969	0.96	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43200215	43200969	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43200970	43201101	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43201102	43201271	1	+	1	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43201102	43201271	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	intron	43201272	43201369	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	CDS	43201370	43201449	1	+	2	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	exon	43201370	43201449	.	+	.	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
Phchi.S1	AUGUSTUS	stop_codon	43201450	43201452	.	+	0	transcript_id "Phchi.S1G682800.t1"; gene_id "Phchi.S1G682800"
# This transcript jg15605.t2 is derived from g14074.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15606.t1 is derived from g14075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20254269	20254813	.	-	.	Phchi.S3G292500
Phchi.S3	AUGUSTUS	transcript	20254269	20254813	.	-	.	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	stop_codon	20254266	20254268	.	-	0	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	CDS	20254269	20254558	1	-	2	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	exon	20254269	20254558	.	-	.	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	intron	20254559	20254650	.	-	.	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	CDS	20254651	20254813	0.98	-	0	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	exon	20254651	20254813	.	-	.	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
Phchi.S3	AUGUSTUS	start_codon	20254811	20254813	.	-	0	transcript_id "Phchi.S3G292500.t1"; gene_id "Phchi.S3G292500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11356.t1 is derived from g15406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5717798	5718673	.	-	.	Phchi.S4G093800
Phchi.S4	AUGUSTUS	transcript	5717798	5718673	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	stop_codon	5717795	5717797	.	-	0	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	CDS	5717798	5717810	0.97	-	1	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	exon	5717798	5717810	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	intron	5717811	5718043	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	CDS	5718044	5718086	0.89	-	2	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	exon	5718044	5718086	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	intron	5718087	5718367	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	CDS	5718368	5718587	0.79	-	0	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	exon	5718368	5718587	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	intron	5718588	5718670	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	CDS	5718671	5718673	0.75	-	0	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	exon	5718671	5718673	.	-	.	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
Phchi.S4	AUGUSTUS	start_codon	5718671	5718673	.	-	0	transcript_id "Phchi.S4G093800.t1"; gene_id "Phchi.S4G093800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3629.t1 is derived from g798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4843511	4843858	.	+	.	Phchi.S1G078800
Phchi.S1	AUGUSTUS	transcript	4843511	4843858	.	+	.	transcript_id "Phchi.S1G078800.t1"; gene_id "Phchi.S1G078800"
Phchi.S1	AUGUSTUS	start_codon	4843511	4843513	.	+	0	transcript_id "Phchi.S1G078800.t1"; gene_id "Phchi.S1G078800"
Phchi.S1	AUGUSTUS	CDS	4843511	4843858	0.31	+	0	transcript_id "Phchi.S1G078800.t1"; gene_id "Phchi.S1G078800"
Phchi.S1	AUGUSTUS	exon	4843511	4843858	.	+	.	transcript_id "Phchi.S1G078800.t1"; gene_id "Phchi.S1G078800"
Phchi.S1	AUGUSTUS	stop_codon	4843859	4843861	.	+	0	transcript_id "Phchi.S1G078800.t1"; gene_id "Phchi.S1G078800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4612.t1 is derived from g1782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11387764	11389080	.	-	.	Phchi.S1G177100
Phchi.S1	AUGUSTUS	transcript	11387764	11389080	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	stop_codon	11387761	11387763	.	-	0	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	CDS	11387764	11388082	0.58	-	1	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	exon	11387764	11388082	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	intron	11388083	11388174	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	CDS	11388175	11388430	0.27	-	2	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	exon	11388175	11388430	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	intron	11388431	11388697	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	CDS	11388698	11388819	0.52	-	1	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	exon	11388698	11388819	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	intron	11388820	11388895	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	CDS	11388896	11389080	1	-	0	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	exon	11388896	11389080	.	-	.	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
Phchi.S1	AUGUSTUS	start_codon	11389078	11389080	.	-	0	transcript_id "Phchi.S1G177100.t1"; gene_id "Phchi.S1G177100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13134.t1 is derived from g11599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4314655	4316822	.	-	.	Phchi.S3G045300
Phchi.S3	AUGUSTUS	transcript	4314655	4316822	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	stop_codon	4314652	4314654	.	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4314655	4314664	0.89	-	1	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4314655	4314664	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4314665	4314881	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4314882	4314889	0.89	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4314882	4314889	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4314890	4314981	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4314982	4315003	0.87	-	1	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4314982	4315003	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4315004	4315172	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4315173	4315228	1	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4315173	4315228	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4315229	4315319	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4315320	4315413	1	-	1	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4315320	4315413	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4315414	4315505	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4315506	4315642	1	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4315506	4315642	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4315643	4315761	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4315762	4315865	1	-	2	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4315762	4315865	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4315866	4315968	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4315969	4316054	1	-	1	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4315969	4316054	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4316055	4316234	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4316235	4316316	1	-	2	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4316235	4316316	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4316317	4316478	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4316479	4316587	1	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4316479	4316587	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	intron	4316588	4316774	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	CDS	4316775	4316822	1	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	exon	4316775	4316822	.	-	.	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
Phchi.S3	AUGUSTUS	start_codon	4316820	4316822	.	-	0	transcript_id "Phchi.S3G045300.t1"; gene_id "Phchi.S3G045300"
# This transcript jg8656.t2 is derived from g5831.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8657.t1 is derived from g5832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37295318	37297468	.	+	.	Phchi.S1G581600
Phchi.S1	AUGUSTUS	transcript	37295318	37297468	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	start_codon	37295318	37295320	.	+	0	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	CDS	37295318	37295706	1	+	0	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	exon	37295318	37295706	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	intron	37295707	37295830	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	CDS	37295831	37296089	1	+	1	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	exon	37295831	37296089	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	intron	37296090	37296224	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	CDS	37296225	37296518	1	+	0	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	exon	37296225	37296518	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	intron	37296519	37296688	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	CDS	37296689	37297056	0.98	+	0	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	exon	37296689	37297056	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	intron	37297057	37297158	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	CDS	37297159	37297468	1	+	1	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	exon	37297159	37297468	.	+	.	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
Phchi.S1	AUGUSTUS	stop_codon	37297469	37297471	.	+	0	transcript_id "Phchi.S1G581600.t1"; gene_id "Phchi.S1G581600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8166.t1 is derived from g5341.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34247977	34251377	.	-	.	Phchi.S1G532500
Phchi.S1	AUGUSTUS	transcript	34247977	34251377	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	stop_codon	34247974	34247976	.	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34247977	34248015	1	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34247977	34248015	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34248016	34248092	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34248093	34248410	1	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34248093	34248410	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34248411	34248510	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34248511	34248577	1	-	1	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34248511	34248577	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34248578	34248711	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34248712	34248798	1	-	1	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34248712	34248798	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34248799	34248997	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34248998	34249126	0.99	-	1	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34248998	34249126	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34249127	34249365	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34249366	34249502	1	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34249366	34249502	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34249503	34249688	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34249689	34249899	0.97	-	1	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34249689	34249899	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34249900	34250025	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34250026	34250030	0.58	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34250026	34250030	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34250031	34250125	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34250126	34250255	0.35	-	1	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34250126	34250255	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34250256	34250356	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34250357	34250509	1	-	1	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34250357	34250509	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	intron	34250510	34250649	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	CDS	34250650	34251377	0.74	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	exon	34250650	34251377	.	-	.	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
Phchi.S1	AUGUSTUS	start_codon	34251375	34251377	.	-	0	transcript_id "Phchi.S1G532500.t1"; gene_id "Phchi.S1G532500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3780.t1 is derived from g949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5660057	5660343	.	-	.	Phchi.S1G093900
Phchi.S1	AUGUSTUS	transcript	5660057	5660343	.	-	.	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	stop_codon	5660054	5660056	.	-	0	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	CDS	5660057	5660149	0.86	-	0	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	exon	5660057	5660149	.	-	.	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	intron	5660150	5660220	.	-	.	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	CDS	5660221	5660343	0.95	-	0	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	exon	5660221	5660343	.	-	.	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
Phchi.S1	AUGUSTUS	start_codon	5660341	5660343	.	-	0	transcript_id "Phchi.S1G093900.t1"; gene_id "Phchi.S1G093900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6312.t1 is derived from g3484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22212742	22217081	.	+	.	Phchi.S1G347100
Phchi.S1	AUGUSTUS	transcript	22212742	22217081	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	start_codon	22212742	22212744	.	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22212742	22213713	0.48	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22212742	22213713	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22213714	22213972	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22213973	22214125	0.25	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22213973	22214125	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22214126	22214196	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22214197	22214254	0.98	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22214197	22214254	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22214255	22214619	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22214620	22214760	1	+	2	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22214620	22214760	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22214761	22214960	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22214961	22215048	1	+	2	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22214961	22215048	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215049	22215156	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215157	22215233	1	+	1	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215157	22215233	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215234	22215428	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215429	22215468	1	+	2	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215429	22215468	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215469	22215631	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215632	22215698	1	+	1	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215632	22215698	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215699	22215830	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215831	22215916	1	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215831	22215916	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215917	22216124	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216125	22216212	0.99	+	1	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216125	22216212	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216213	22216320	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216321	22216377	1	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216321	22216377	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216378	22216458	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216459	22216497	1	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216459	22216497	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216498	22216606	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216607	22216677	0.99	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216607	22216677	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216678	22216838	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216839	22216892	0.96	+	1	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216839	22216892	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216893	22217002	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22217003	22217081	0.94	+	1	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22217003	22217081	.	+	.	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	stop_codon	22217082	22217084	.	+	0	transcript_id "Phchi.S1G347100.t1"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	transcript	22212742	22217081	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	start_codon	22212742	22212744	.	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22212742	22213713	0.45	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22212742	22213713	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22213714	22213972	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22213973	22214125	0.23	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22213973	22214125	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22214126	22214196	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22214197	22214254	0.96	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22214197	22214254	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22214255	22214637	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22214638	22214760	1	+	2	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22214638	22214760	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22214761	22214960	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22214961	22215048	1	+	2	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22214961	22215048	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215049	22215156	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215157	22215233	1	+	1	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215157	22215233	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215234	22215428	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215429	22215468	1	+	2	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215429	22215468	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215469	22215631	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215632	22215698	1	+	1	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215632	22215698	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215699	22215830	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22215831	22215916	1	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22215831	22215916	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22215917	22216124	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216125	22216212	1	+	1	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216125	22216212	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216213	22216320	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216321	22216377	1	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216321	22216377	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216378	22216458	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216459	22216497	1	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216459	22216497	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216498	22216606	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216607	22216677	1	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216607	22216677	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216678	22216838	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22216839	22216892	0.98	+	1	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22216839	22216892	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	intron	22216893	22217002	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	CDS	22217003	22217081	0.96	+	1	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	exon	22217003	22217081	.	+	.	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
Phchi.S1	AUGUSTUS	stop_codon	22217082	22217084	.	+	0	transcript_id "Phchi.S1G347100.t2"; gene_id "Phchi.S1G347100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3575.t1 is derived from g744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4589525	4590914	.	+	.	Phchi.S1G073400
Phchi.S1	AUGUSTUS	transcript	4589525	4590914	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	start_codon	4589525	4589527	.	+	0	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4589525	4589616	0.61	+	0	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4589525	4589616	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	intron	4589617	4589745	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4589746	4590022	1	+	1	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4589746	4590022	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	intron	4590023	4590141	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4590142	4590210	1	+	0	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4590142	4590210	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	intron	4590211	4590302	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4590303	4590444	1	+	0	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4590303	4590444	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	intron	4590445	4590522	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4590523	4590603	1	+	2	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4590523	4590603	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	intron	4590604	4590695	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4590696	4590739	1	+	2	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4590696	4590739	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	intron	4590740	4590836	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	CDS	4590837	4590914	1	+	0	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	exon	4590837	4590914	.	+	.	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
Phchi.S1	AUGUSTUS	stop_codon	4590915	4590917	.	+	0	transcript_id "Phchi.S1G073400.t1"; gene_id "Phchi.S1G073400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10439.t1 is derived from g14488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	346303	348499	.	+	.	Phchi.S4G002100
Phchi.S4	AUGUSTUS	transcript	346303	348499	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	start_codon	346303	346305	.	+	0	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	346303	346362	0.64	+	0	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	346303	346362	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	intron	346363	346495	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	346496	346502	1	+	0	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	346496	346502	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	intron	346503	346894	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	346895	346983	1	+	2	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	346895	346983	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	intron	346984	347085	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	347086	347206	1	+	0	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	347086	347206	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	intron	347207	347288	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	347289	347637	1	+	2	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	347289	347637	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	intron	347638	347725	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	347726	348258	0.76	+	1	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	347726	348258	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	intron	348259	348380	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	CDS	348381	348499	0.72	+	2	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	exon	348381	348499	.	+	.	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
Phchi.S4	AUGUSTUS	stop_codon	348500	348502	.	+	0	transcript_id "Phchi.S4G002100.t1"; gene_id "Phchi.S4G002100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5004.t1 is derived from g2174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13964705	13965302	.	+	.	Phchi.S1G216300
Phchi.S1	AUGUSTUS	transcript	13964705	13965302	.	+	.	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	start_codon	13964705	13964707	.	+	0	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	CDS	13964705	13964781	1	+	0	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	exon	13964705	13964781	.	+	.	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	intron	13964782	13964875	.	+	.	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	CDS	13964876	13965302	0.72	+	1	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	exon	13964876	13965302	.	+	.	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
Phchi.S1	AUGUSTUS	stop_codon	13965303	13965305	.	+	0	transcript_id "Phchi.S1G216300.t1"; gene_id "Phchi.S1G216300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2638.t1 is derived from g9558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7905092	7908839	.	+	.	Phchi.S5G124700
Phchi.S5	AUGUSTUS	transcript	7905092	7908839	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	start_codon	7905092	7905094	.	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7905092	7905179	0.73	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7905092	7905179	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7905180	7905278	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7905279	7905451	1	+	2	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7905279	7905451	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7905452	7905563	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7905564	7905737	1	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7905564	7905737	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7905738	7905836	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7905837	7905960	1	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7905837	7905960	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7905961	7906102	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7906103	7906203	1	+	2	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7906103	7906203	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7906204	7906299	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7906300	7906386	1	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7906300	7906386	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7906387	7906495	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7906496	7906591	1	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7906496	7906591	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7906592	7906689	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7906690	7906838	0.59	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7906690	7906838	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7906839	7906964	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7906965	7907092	0.59	+	1	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7906965	7907092	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7907093	7907197	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7907198	7907289	0.76	+	2	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7907198	7907289	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7907290	7907422	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7907423	7907523	0.94	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7907423	7907523	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7907524	7907664	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7907665	7907688	1	+	1	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7907665	7907688	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7907689	7907770	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7907771	7908445	0.96	+	1	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7907771	7908445	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7908446	7908530	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7908531	7908654	0.87	+	1	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7908531	7908654	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	intron	7908655	7908734	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	CDS	7908735	7908839	0.82	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	exon	7908735	7908839	.	+	.	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
Phchi.S5	AUGUSTUS	stop_codon	7908840	7908842	.	+	0	transcript_id "Phchi.S5G124700.t1"; gene_id "Phchi.S5G124700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14452.t1 is derived from g12920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12913894	12916036	.	-	.	Phchi.S3G177100
Phchi.S3	AUGUSTUS	transcript	12913894	12916036	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	stop_codon	12913891	12913893	.	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12913894	12914145	1	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12913894	12914145	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12914146	12914230	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12914231	12914320	1	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12914231	12914320	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12914321	12914402	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12914403	12914467	1	-	2	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12914403	12914467	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12914468	12914543	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12914544	12914631	1	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12914544	12914631	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12914632	12914731	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12914732	12914778	0.52	-	2	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12914732	12914778	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12914779	12914904	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12914905	12914956	0.92	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12914905	12914956	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12914957	12915056	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12915057	12915126	1	-	1	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12915057	12915126	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12915127	12915261	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12915262	12915418	1	-	2	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12915262	12915418	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12915419	12915507	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12915508	12915586	0.99	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12915508	12915586	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12915587	12915691	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12915692	12915772	0.83	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12915692	12915772	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	intron	12915773	12915883	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	CDS	12915884	12916036	0.93	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	exon	12915884	12916036	.	-	.	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
Phchi.S3	AUGUSTUS	start_codon	12916034	12916036	.	-	0	transcript_id "Phchi.S3G177100.t1"; gene_id "Phchi.S3G177100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12966.t1 is derived from g11431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3360614	3363577	.	-	.	Phchi.S3G028500
Phchi.S3	AUGUSTUS	transcript	3360614	3363577	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	stop_codon	3360611	3360613	.	-	0	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3360614	3361487	1	-	1	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3360614	3361487	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	intron	3361488	3361581	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3361582	3361782	1	-	1	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3361582	3361782	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	intron	3361783	3361872	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3361873	3362079	1	-	1	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3361873	3362079	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	intron	3362080	3362159	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3362160	3362321	1	-	1	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3362160	3362321	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	intron	3362322	3362404	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3362405	3362825	0.57	-	2	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3362405	3362825	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	intron	3362826	3362905	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3362906	3363308	0.47	-	0	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3362906	3363308	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	intron	3363309	3363433	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	CDS	3363434	3363577	0.55	-	0	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	exon	3363434	3363577	.	-	.	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
Phchi.S3	AUGUSTUS	start_codon	3363575	3363577	.	-	0	transcript_id "Phchi.S3G028500.t1"; gene_id "Phchi.S3G028500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1526.t1 is derived from g8445.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1585866	1590386	.	+	.	Phchi.S5G013500
Phchi.S5	AUGUSTUS	transcript	1585866	1590386	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	start_codon	1585866	1585868	.	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1585866	1586002	0.58	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1585866	1586002	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1586003	1586140	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1586141	1586582	1	+	1	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1586141	1586582	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1586583	1586728	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1586729	1586861	0.9	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1586729	1586861	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1586862	1586977	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1586978	1587030	0.54	+	2	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1586978	1587030	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1587031	1587276	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1587277	1588481	0.85	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1587277	1588481	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1588482	1588623	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1588624	1588735	1	+	1	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1588624	1588735	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1588736	1588855	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1588856	1589398	0.99	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1588856	1589398	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1589399	1589500	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1589501	1589599	1	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1589501	1589599	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1589600	1589684	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1589685	1590386	0.88	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1589685	1590386	.	+	.	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	stop_codon	1590387	1590389	.	+	0	transcript_id "Phchi.S5G013500.t1"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	transcript	1585866	1590386	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	start_codon	1585866	1585868	.	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1585866	1586002	0.62	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1585866	1586002	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1586003	1586140	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1586141	1586582	0.77	+	1	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1586141	1586582	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1586583	1586724	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1586725	1586767	0.62	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1586725	1586767	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1586768	1586977	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1586978	1587030	0.52	+	2	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1586978	1587030	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1587031	1587276	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1587277	1588481	0.79	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1587277	1588481	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1588482	1588623	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1588624	1588735	1	+	1	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1588624	1588735	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1588736	1588855	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1588856	1589398	0.99	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1588856	1589398	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1589399	1589500	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1589501	1589599	1	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1589501	1589599	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	intron	1589600	1589684	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	CDS	1589685	1590386	0.92	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	exon	1589685	1590386	.	+	.	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
Phchi.S5	AUGUSTUS	stop_codon	1590387	1590389	.	+	0	transcript_id "Phchi.S5G013500.t2"; gene_id "Phchi.S5G013500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5122.t1 is derived from g2292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14828518	14829646	.	+	.	Phchi.S1G228100
Phchi.S1	AUGUSTUS	transcript	14828518	14829646	.	+	.	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	start_codon	14828518	14828520	.	+	0	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	CDS	14828518	14829380	0.47	+	0	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	exon	14828518	14829380	.	+	.	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	intron	14829381	14829576	.	+	.	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	CDS	14829577	14829646	0.5	+	1	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	exon	14829577	14829646	.	+	.	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
Phchi.S1	AUGUSTUS	stop_codon	14829647	14829649	.	+	0	transcript_id "Phchi.S1G228100.t1"; gene_id "Phchi.S1G228100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13527.t1 is derived from g11994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7383367	7385011	.	+	.	Phchi.S3G084600
Phchi.S3	AUGUSTUS	transcript	7383367	7385011	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	start_codon	7383367	7383369	.	+	0	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	CDS	7383367	7383483	0.51	+	0	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	exon	7383367	7383483	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	intron	7383484	7383628	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	CDS	7383629	7383696	0.78	+	0	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	exon	7383629	7383696	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	intron	7383697	7383782	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	CDS	7383783	7383887	1	+	1	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	exon	7383783	7383887	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	intron	7383888	7384036	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	CDS	7384037	7384257	1	+	1	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	exon	7384037	7384257	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	intron	7384258	7384388	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	CDS	7384389	7384493	1	+	2	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	exon	7384389	7384493	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	intron	7384494	7384589	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	CDS	7384590	7385011	0.96	+	2	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	exon	7384590	7385011	.	+	.	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
Phchi.S3	AUGUSTUS	stop_codon	7385012	7385014	.	+	0	transcript_id "Phchi.S3G084600.t1"; gene_id "Phchi.S3G084600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13192.t1 is derived from g11657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4624093	4626406	.	+	.	Phchi.S3G051100
Phchi.S3	AUGUSTUS	transcript	4624093	4626406	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	start_codon	4624093	4624095	.	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4624093	4624121	0.55	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4624093	4624121	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4624122	4624254	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4624255	4624327	0.33	+	1	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4624255	4624327	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4624328	4624437	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4624438	4624480	0.5	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4624438	4624480	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4624481	4624567	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4624568	4624627	0.82	+	2	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4624568	4624627	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4624628	4624751	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4624752	4624770	0.79	+	2	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4624752	4624770	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4624771	4624962	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4624963	4624989	0.48	+	1	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4624963	4624989	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4624990	4625076	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4625077	4625095	0.89	+	1	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4625077	4625095	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4625096	4625199	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4625200	4625259	1	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4625200	4625259	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4625260	4625405	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4625406	4625536	1	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4625406	4625536	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4625537	4625620	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4625621	4625728	0.67	+	1	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4625621	4625728	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4625729	4625814	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4625815	4625887	0.22	+	1	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4625815	4625887	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4625888	4625960	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4625961	4625999	0.71	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4625961	4625999	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	intron	4626000	4626190	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	CDS	4626191	4626406	0.44	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	exon	4626191	4626406	.	+	.	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
Phchi.S3	AUGUSTUS	stop_codon	4626407	4626409	.	+	0	transcript_id "Phchi.S3G051100.t1"; gene_id "Phchi.S3G051100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3907.t1 is derived from g1076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6392619	6394356	.	+	.	Phchi.S1G106600
Phchi.S1	AUGUSTUS	transcript	6392619	6394356	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	start_codon	6392619	6392621	.	+	0	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	CDS	6392619	6393599	0.94	+	0	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	exon	6392619	6393599	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	intron	6393600	6393713	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	CDS	6393714	6393809	0.98	+	0	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	exon	6393714	6393809	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	intron	6393810	6393929	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	CDS	6393930	6394049	0.97	+	0	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	exon	6393930	6394049	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	intron	6394050	6394188	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	CDS	6394189	6394356	0.85	+	0	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	exon	6394189	6394356	.	+	.	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
Phchi.S1	AUGUSTUS	stop_codon	6394357	6394359	.	+	0	transcript_id "Phchi.S1G106600.t1"; gene_id "Phchi.S1G106600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9595.t1 is derived from g6771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42862494	42868456	.	-	.	Phchi.S1G675400
Phchi.S1	AUGUSTUS	transcript	42862494	42868456	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	stop_codon	42862491	42862493	.	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42862494	42862545	0.95	-	1	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42862494	42862545	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42862546	42862722	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42862723	42862793	0.67	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42862723	42862793	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42862794	42862898	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42862899	42862985	0.69	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42862899	42862985	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42862986	42863077	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42863078	42863335	0.65	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42863078	42863335	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42863336	42863443	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42863444	42863567	0.93	-	1	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42863444	42863567	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42863568	42863668	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42863669	42863883	0.95	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42863669	42863883	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42863884	42863959	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42863960	42864676	1	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42863960	42864676	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42864677	42864811	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42864812	42864881	1	-	1	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42864812	42864881	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42864882	42864991	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42864992	42865095	0.74	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42864992	42865095	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42865096	42865197	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42865198	42868134	0.63	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42865198	42868134	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	intron	42868135	42868312	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	CDS	42868313	42868456	0.83	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	exon	42868313	42868456	.	-	.	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
Phchi.S1	AUGUSTUS	start_codon	42868454	42868456	.	-	0	transcript_id "Phchi.S1G675400.t1"; gene_id "Phchi.S1G675400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3560.t1 is derived from g729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4491956	4493659	.	-	.	Phchi.S1G071900
Phchi.S1	AUGUSTUS	transcript	4491956	4493659	.	-	.	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	stop_codon	4491953	4491955	.	-	0	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	CDS	4491956	4491970	0.92	-	0	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	exon	4491956	4491970	.	-	.	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	intron	4491971	4492117	.	-	.	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	CDS	4492118	4493659	0.99	-	0	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	exon	4492118	4493659	.	-	.	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
Phchi.S1	AUGUSTUS	start_codon	4493657	4493659	.	-	0	transcript_id "Phchi.S1G071900.t1"; gene_id "Phchi.S1G071900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5029.t1 is derived from g2199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14145575	14147026	.	-	.	Phchi.S1G218800
Phchi.S1	AUGUSTUS	transcript	14145575	14147026	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	stop_codon	14145572	14145574	.	-	0	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	CDS	14145575	14145644	0.61	-	1	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	exon	14145575	14145644	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	intron	14145645	14145747	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	CDS	14145748	14146052	0.44	-	0	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	exon	14145748	14146052	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	intron	14146053	14146144	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	CDS	14146145	14146213	0.88	-	0	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	exon	14146145	14146213	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	intron	14146214	14146294	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	CDS	14146295	14147026	1	-	0	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	exon	14146295	14147026	.	-	.	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
Phchi.S1	AUGUSTUS	start_codon	14147024	14147026	.	-	0	transcript_id "Phchi.S1G218800.t1"; gene_id "Phchi.S1G218800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9992.t1 is derived from g7168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44845295	44846172	.	-	.	Phchi.S1G715100
Phchi.S1	AUGUSTUS	transcript	44845295	44846172	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	stop_codon	44845292	44845294	.	-	0	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	CDS	44845295	44845621	0.97	-	0	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	exon	44845295	44845621	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	intron	44845622	44845704	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	CDS	44845705	44845745	0.97	-	2	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	exon	44845705	44845745	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	intron	44845746	44845835	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	CDS	44845836	44845911	1	-	0	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	exon	44845836	44845911	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	intron	44845912	44846046	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	CDS	44846047	44846172	0.98	-	0	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	exon	44846047	44846172	.	-	.	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
Phchi.S1	AUGUSTUS	start_codon	44846170	44846172	.	-	0	transcript_id "Phchi.S1G715100.t1"; gene_id "Phchi.S1G715100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7984.t1 is derived from g5159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32235141	32241177	.	-	.	Phchi.S1G514300
Phchi.S1	AUGUSTUS	transcript	32235141	32241177	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	stop_codon	32235138	32235140	.	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32235141	32235578	0.99	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32235141	32235578	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32235579	32235764	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32235765	32235854	1	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32235765	32235854	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32235855	32235946	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32235947	32236166	1	-	1	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32235947	32236166	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32236167	32236254	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32236255	32236732	0.93	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32236255	32236732	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32236733	32236836	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32236837	32237037	1	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32236837	32237037	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32237038	32237170	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32237171	32237312	1	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32237171	32237312	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32237313	32237469	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32237470	32237606	1	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32237470	32237606	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32237607	32237758	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32237759	32237863	0.83	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32237759	32237863	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32237864	32237952	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32237953	32237962	0.85	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32237953	32237962	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32237963	32238073	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32238074	32238235	0.93	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32238074	32238235	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32238236	32238333	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32238334	32238455	1	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32238334	32238455	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32238456	32238560	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32238561	32238821	0.97	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32238561	32238821	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32238822	32238895	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32238896	32238927	0.85	-	1	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32238896	32238927	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32238928	32239058	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32239059	32239066	0.68	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32239059	32239066	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32239067	32239166	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32239167	32239412	0.98	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32239167	32239412	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32239413	32239549	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32239550	32239759	1	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32239550	32239759	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32239760	32239866	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32239867	32240020	1	-	1	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32239867	32240020	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32240021	32240156	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32240157	32240235	1	-	2	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32240157	32240235	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32240236	32240321	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32240322	32240469	1	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32240322	32240469	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	intron	32240470	32240583	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	CDS	32240584	32241177	0.92	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	exon	32240584	32241177	.	-	.	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
Phchi.S1	AUGUSTUS	start_codon	32241175	32241177	.	-	0	transcript_id "Phchi.S1G514300.t1"; gene_id "Phchi.S1G514300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14993.t1 is derived from g13461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16148102	16149886	.	+	.	Phchi.S3G231200
Phchi.S3	AUGUSTUS	transcript	16148102	16149886	.	+	.	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	start_codon	16148102	16148104	.	+	0	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	CDS	16148102	16149598	0.74	+	0	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	exon	16148102	16149598	.	+	.	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	intron	16149599	16149700	.	+	.	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	CDS	16149701	16149886	0.98	+	0	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	exon	16149701	16149886	.	+	.	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
Phchi.S3	AUGUSTUS	stop_codon	16149887	16149889	.	+	0	transcript_id "Phchi.S3G231200.t1"; gene_id "Phchi.S3G231200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg573.t1 is derived from g10355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4155659	4156631	.	-	.	Phchi.S6G053200
Phchi.S6	AUGUSTUS	transcript	4155659	4156631	.	-	.	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	stop_codon	4155656	4155658	.	-	0	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	CDS	4155659	4156307	0.63	-	1	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	exon	4155659	4156307	.	-	.	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	intron	4156308	4156410	.	-	.	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	CDS	4156411	4156631	0.93	-	0	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	exon	4156411	4156631	.	-	.	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
Phchi.S6	AUGUSTUS	start_codon	4156629	4156631	.	-	0	transcript_id "Phchi.S6G053200.t1"; gene_id "Phchi.S6G053200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5136.t1 is derived from g2306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15105035	15106366	.	-	.	Phchi.S1G229500
Phchi.S1	AUGUSTUS	transcript	15105035	15106366	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	stop_codon	15105032	15105034	.	-	0	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	CDS	15105035	15105237	0.55	-	2	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	exon	15105035	15105237	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	intron	15105238	15105361	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	CDS	15105362	15105497	0.79	-	0	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	exon	15105362	15105497	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	intron	15105498	15105633	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	CDS	15105634	15105909	0.94	-	0	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	exon	15105634	15105909	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	intron	15105910	15106003	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	CDS	15106004	15106366	0.81	-	0	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	exon	15106004	15106366	.	-	.	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
Phchi.S1	AUGUSTUS	start_codon	15106364	15106366	.	-	0	transcript_id "Phchi.S1G229500.t1"; gene_id "Phchi.S1G229500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4021.t1 is derived from g1190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7203090	7206069	.	-	.	Phchi.S1G118000
Phchi.S1	AUGUSTUS	transcript	7203090	7206069	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	stop_codon	7203087	7203089	.	-	0	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7203090	7203144	0.97	-	1	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7203090	7203144	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7203145	7203241	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7203242	7203361	0.97	-	1	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7203242	7203361	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7203362	7203451	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7203452	7203501	0.55	-	0	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7203452	7203501	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7203502	7203620	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7203621	7203675	1	-	1	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7203621	7203675	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7203676	7203811	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7203812	7203908	1	-	2	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7203812	7203908	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7203909	7204040	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7204041	7204785	0.99	-	0	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7204041	7204785	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7204786	7204884	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7204885	7205234	1	-	2	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7204885	7205234	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7205235	7205319	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7205320	7205415	1	-	2	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7205320	7205415	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7205416	7205496	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7205497	7205718	0.96	-	2	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7205497	7205718	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	intron	7205719	7205831	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	CDS	7205832	7206069	0.97	-	0	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	exon	7205832	7206069	.	-	.	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
Phchi.S1	AUGUSTUS	start_codon	7206067	7206069	.	-	0	transcript_id "Phchi.S1G118000.t1"; gene_id "Phchi.S1G118000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1515.t1 is derived from g8434.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1488690	1493079	.	-	.	Phchi.S5G012400
Phchi.S5	AUGUSTUS	transcript	1488690	1493079	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	stop_codon	1488687	1488689	.	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1488690	1488823	0.99	-	2	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1488690	1488823	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1488824	1488981	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1488982	1489052	1	-	1	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1488982	1489052	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489053	1489183	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489184	1489261	1	-	1	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489184	1489261	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489262	1489355	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489356	1489447	1	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489356	1489447	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489448	1489630	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489631	1489699	1	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489631	1489699	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489700	1489911	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489912	1490035	1	-	1	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489912	1490035	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1490036	1490342	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1490343	1490466	1	-	2	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1490343	1490466	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1490467	1491409	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491410	1491528	1	-	1	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491410	1491528	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1491529	1491620	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491621	1491715	1	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491621	1491715	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1491716	1491848	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491849	1492061	0.86	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491849	1492061	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492062	1492160	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492161	1492280	1	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492161	1492280	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492281	1492399	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492400	1492495	1	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492400	1492495	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492496	1492584	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492585	1492688	1	-	2	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492585	1492688	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492689	1492958	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492959	1493079	1	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492959	1493079	.	-	.	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	start_codon	1493077	1493079	.	-	0	transcript_id "Phchi.S5G012400.t1"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	transcript	1488690	1493079	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	stop_codon	1488687	1488689	.	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1488690	1488823	0.98	-	2	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1488690	1488823	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1488824	1488981	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1488982	1489052	1	-	1	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1488982	1489052	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489053	1489183	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489184	1489261	1	-	1	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489184	1489261	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489262	1489355	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489356	1489447	1	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489356	1489447	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489448	1489630	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489631	1489699	1	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489631	1489699	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489700	1489911	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489912	1490035	1	-	1	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489912	1490035	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1490036	1490342	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1490343	1490466	1	-	2	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1490343	1490466	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1490467	1491409	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491410	1491528	1	-	1	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491410	1491528	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1491529	1491620	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491621	1491712	1	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491621	1491712	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1491713	1491848	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491849	1492061	0.8	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491849	1492061	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492062	1492160	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492161	1492280	1	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492161	1492280	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492281	1492399	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492400	1492495	1	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492400	1492495	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492496	1492584	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492585	1492688	1	-	2	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492585	1492688	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492689	1492958	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492959	1493079	1	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492959	1493079	.	-	.	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	start_codon	1493077	1493079	.	-	0	transcript_id "Phchi.S5G012400.t2"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	transcript	1488690	1493079	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	stop_codon	1488687	1488689	.	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1488690	1488823	1	-	2	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1488690	1488823	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1488824	1488981	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1488982	1489049	0.89	-	1	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1488982	1489049	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489050	1489183	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489184	1489261	1	-	1	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489184	1489261	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489262	1489355	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489356	1489447	1	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489356	1489447	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489448	1489630	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489631	1489699	1	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489631	1489699	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1489700	1489911	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1489912	1490035	1	-	1	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1489912	1490035	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1490036	1490342	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1490343	1490466	1	-	2	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1490343	1490466	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1490467	1491409	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491410	1491528	1	-	1	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491410	1491528	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1491529	1491620	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491621	1491715	1	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491621	1491715	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1491716	1491848	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1491849	1492061	0.73	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1491849	1492061	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492062	1492160	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492161	1492280	1	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492161	1492280	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492281	1492399	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492400	1492495	1	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492400	1492495	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492496	1492584	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492585	1492688	1	-	2	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492585	1492688	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	intron	1492689	1492958	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	CDS	1492959	1493079	1	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	exon	1492959	1493079	.	-	.	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
Phchi.S5	AUGUSTUS	start_codon	1493077	1493079	.	-	0	transcript_id "Phchi.S5G012400.t3"; gene_id "Phchi.S5G012400"
# This transcript jg4033.t2 is derived from g1202.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4034.t1 is derived from g1203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7288092	7290995	.	+	.	Phchi.S1G119300
Phchi.S1	AUGUSTUS	transcript	7288092	7290995	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	start_codon	7288092	7288094	.	+	0	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	CDS	7288092	7288359	0.92	+	0	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	exon	7288092	7288359	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	intron	7288360	7288538	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	CDS	7288539	7288615	1	+	2	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	exon	7288539	7288615	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	intron	7288616	7288696	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	CDS	7288697	7288781	1	+	0	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	exon	7288697	7288781	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	intron	7288782	7289016	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	CDS	7289017	7289183	1	+	2	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	exon	7289017	7289183	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	intron	7289184	7289330	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	CDS	7289331	7290995	0.89	+	0	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	exon	7289331	7290995	.	+	.	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
Phchi.S1	AUGUSTUS	stop_codon	7290996	7290998	.	+	0	transcript_id "Phchi.S1G119300.t1"; gene_id "Phchi.S1G119300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8664.t1 is derived from g5839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37346518	37347159	.	+	.	Phchi.S1G582300
Phchi.S1	AUGUSTUS	transcript	37346518	37347159	.	+	.	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	start_codon	37346518	37346520	.	+	0	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	CDS	37346518	37346607	0.99	+	0	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	exon	37346518	37346607	.	+	.	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	intron	37346608	37346826	.	+	.	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	CDS	37346827	37347159	0.97	+	0	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	exon	37346827	37347159	.	+	.	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
Phchi.S1	AUGUSTUS	stop_codon	37347160	37347162	.	+	0	transcript_id "Phchi.S1G582300.t1"; gene_id "Phchi.S1G582300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13013.t1 is derived from g11478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3631334	3633738	.	-	.	Phchi.S3G033200
Phchi.S3	AUGUSTUS	transcript	3631334	3633738	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	stop_codon	3631331	3631333	.	-	0	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	CDS	3631334	3631597	0.93	-	0	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	exon	3631334	3631597	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	intron	3631598	3631696	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	CDS	3631697	3631955	1	-	1	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	exon	3631697	3631955	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	intron	3631956	3632067	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	CDS	3632068	3632351	1	-	0	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	exon	3632068	3632351	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	intron	3632352	3632498	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	CDS	3632499	3632588	1	-	0	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	exon	3632499	3632588	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	intron	3632589	3632708	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	CDS	3632709	3632877	1	-	1	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	exon	3632709	3632877	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	intron	3632878	3633139	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	CDS	3633140	3633738	0.94	-	0	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	exon	3633140	3633738	.	-	.	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
Phchi.S3	AUGUSTUS	start_codon	3633736	3633738	.	-	0	transcript_id "Phchi.S3G033200.t1"; gene_id "Phchi.S3G033200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1877.t1 is derived from g8797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3658342	3664089	.	+	.	Phchi.S5G048600
Phchi.S5	AUGUSTUS	transcript	3658342	3664089	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	start_codon	3658342	3658344	.	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3658342	3658479	0.91	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3658342	3658479	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3658480	3658622	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3658623	3658672	0.88	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3658623	3658672	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3658673	3658758	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3658759	3658772	0.89	+	1	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3658759	3658772	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3658773	3658848	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3658849	3659119	0.89	+	2	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3658849	3659119	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3659120	3659202	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3659203	3659367	1	+	1	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3659203	3659367	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3659368	3659465	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3659466	3659653	1	+	1	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3659466	3659653	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3659654	3659759	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3659760	3659922	0.32	+	2	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3659760	3659922	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3659923	3660198	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3660199	3660235	0.65	+	1	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3660199	3660235	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3660236	3660330	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3660331	3660443	0.66	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3660331	3660443	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3660444	3660724	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3660725	3660848	1	+	1	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3660725	3660848	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3660849	3660955	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3660956	3661012	0.98	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3660956	3661012	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3661013	3661110	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3661111	3661206	0.56	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3661111	3661206	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3661207	3661623	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3661624	3662980	0.36	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3661624	3662980	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3662981	3663478	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3663479	3663542	0.18	+	2	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3663479	3663542	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3663543	3663627	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3663628	3663977	0.27	+	1	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3663628	3663977	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	intron	3663978	3664084	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	CDS	3664085	3664089	0.33	+	2	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	exon	3664085	3664089	.	+	.	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
Phchi.S5	AUGUSTUS	stop_codon	3664090	3664092	.	+	0	transcript_id "Phchi.S5G048600.t1"; gene_id "Phchi.S5G048600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6676.t1 is derived from g3848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24452239	24454140	.	+	.	Phchi.S1G383500
Phchi.S1	AUGUSTUS	transcript	24452239	24454140	.	+	.	transcript_id "Phchi.S1G383500.t1"; gene_id "Phchi.S1G383500"
Phchi.S1	AUGUSTUS	start_codon	24452239	24452241	.	+	0	transcript_id "Phchi.S1G383500.t1"; gene_id "Phchi.S1G383500"
Phchi.S1	AUGUSTUS	CDS	24452239	24454140	0.58	+	0	transcript_id "Phchi.S1G383500.t1"; gene_id "Phchi.S1G383500"
Phchi.S1	AUGUSTUS	exon	24452239	24454140	.	+	.	transcript_id "Phchi.S1G383500.t1"; gene_id "Phchi.S1G383500"
Phchi.S1	AUGUSTUS	stop_codon	24454141	24454143	.	+	0	transcript_id "Phchi.S1G383500.t1"; gene_id "Phchi.S1G383500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1039.t1 is derived from g10822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7257139	7260460	.	+	.	Phchi.S6G099800
Phchi.S6	AUGUSTUS	transcript	7257139	7260460	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	start_codon	7257139	7257141	.	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7257139	7257298	0.99	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7257139	7257298	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7257299	7257413	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7257414	7257538	0.99	+	2	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7257414	7257538	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7257539	7257673	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7257674	7257806	1	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7257674	7257806	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7257807	7257909	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7257910	7258066	1	+	2	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7257910	7258066	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7258067	7258203	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7258204	7258282	1	+	1	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7258204	7258282	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7258283	7258387	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7258388	7258428	1	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7258388	7258428	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7258429	7258599	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7258600	7258716	1	+	1	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7258600	7258716	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7258717	7258860	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7258861	7258944	1	+	1	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7258861	7258944	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7258945	7259093	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7259094	7259156	1	+	1	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7259094	7259156	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7259157	7259263	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7259264	7259312	1	+	1	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7259264	7259312	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7259313	7259419	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7259420	7259485	1	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7259420	7259485	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7259486	7259601	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7259602	7259649	1	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7259602	7259649	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7259650	7259767	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7259768	7259803	1	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7259768	7259803	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7259804	7259907	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7259908	7259982	1	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7259908	7259982	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7259983	7260076	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7260077	7260145	0.41	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7260077	7260145	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7260146	7260211	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7260212	7260252	0.92	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7260212	7260252	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	intron	7260253	7260435	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	CDS	7260436	7260460	0.97	+	1	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	exon	7260436	7260460	.	+	.	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
Phchi.S6	AUGUSTUS	stop_codon	7260461	7260463	.	+	0	transcript_id "Phchi.S6G099800.t1"; gene_id "Phchi.S6G099800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13479.t1 is derived from g11946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7087283	7090130	.	-	.	Phchi.S3G079800
Phchi.S3	AUGUSTUS	transcript	7087283	7090130	.	-	.	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	stop_codon	7087280	7087282	.	-	0	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	CDS	7087283	7089720	1	-	2	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	exon	7087283	7089720	.	-	.	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	intron	7089721	7089819	.	-	.	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	CDS	7089820	7089907	1	-	0	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	exon	7089820	7089907	.	-	.	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	intron	7089908	7090127	.	-	.	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	CDS	7090128	7090130	0.96	-	0	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	exon	7090128	7090130	.	-	.	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
Phchi.S3	AUGUSTUS	start_codon	7090128	7090130	.	-	0	transcript_id "Phchi.S3G079800.t1"; gene_id "Phchi.S3G079800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9306.t1 is derived from g6481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40888756	40889028	.	-	.	Phchi.S1G646500
Phchi.S1	AUGUSTUS	transcript	40888756	40889028	.	-	.	transcript_id "Phchi.S1G646500.t1"; gene_id "Phchi.S1G646500"
Phchi.S1	AUGUSTUS	stop_codon	40888753	40888755	.	-	0	transcript_id "Phchi.S1G646500.t1"; gene_id "Phchi.S1G646500"
Phchi.S1	AUGUSTUS	CDS	40888756	40889028	0.57	-	0	transcript_id "Phchi.S1G646500.t1"; gene_id "Phchi.S1G646500"
Phchi.S1	AUGUSTUS	exon	40888756	40889028	.	-	.	transcript_id "Phchi.S1G646500.t1"; gene_id "Phchi.S1G646500"
Phchi.S1	AUGUSTUS	start_codon	40889026	40889028	.	-	0	transcript_id "Phchi.S1G646500.t1"; gene_id "Phchi.S1G646500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1043.t1 is derived from g10826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7271200	7273072	.	-	.	Phchi.S6G100200
Phchi.S6	AUGUSTUS	transcript	7271200	7273072	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	stop_codon	7271197	7271199	.	-	0	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7271200	7271420	0.98	-	2	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7271200	7271420	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	intron	7271421	7271546	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7271547	7271778	0.99	-	0	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7271547	7271778	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	intron	7271779	7271891	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7271892	7272022	0.99	-	2	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7271892	7272022	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	intron	7272023	7272138	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7272139	7272336	1	-	2	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7272139	7272336	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	intron	7272337	7272449	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7272450	7272572	0.98	-	2	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7272450	7272572	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	intron	7272573	7272744	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7272745	7272775	0.99	-	0	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7272745	7272775	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	intron	7272776	7273012	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	CDS	7273013	7273072	0.94	-	0	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	exon	7273013	7273072	.	-	.	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
Phchi.S6	AUGUSTUS	start_codon	7273070	7273072	.	-	0	transcript_id "Phchi.S6G100200.t1"; gene_id "Phchi.S6G100200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5648.t1 is derived from g2818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18052896	18053955	.	+	.	Phchi.S1G280700
Phchi.S1	AUGUSTUS	transcript	18052896	18053955	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	start_codon	18052896	18052898	.	+	0	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	CDS	18052896	18052993	0.94	+	0	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	exon	18052896	18052993	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	intron	18052994	18053145	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	CDS	18053146	18053193	0.95	+	1	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	exon	18053146	18053193	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	intron	18053194	18053288	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	CDS	18053289	18053350	0.76	+	1	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	exon	18053289	18053350	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	intron	18053351	18053430	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	CDS	18053431	18053437	0.76	+	2	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	exon	18053431	18053437	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	intron	18053438	18053517	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	CDS	18053518	18053564	1	+	1	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	exon	18053518	18053564	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	intron	18053565	18053800	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	CDS	18053801	18053955	1	+	2	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	exon	18053801	18053955	.	+	.	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
Phchi.S1	AUGUSTUS	stop_codon	18053956	18053958	.	+	0	transcript_id "Phchi.S1G280700.t1"; gene_id "Phchi.S1G280700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7821.t1 is derived from g4995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31360659	31361532	.	-	.	Phchi.S1G498000
Phchi.S1	AUGUSTUS	transcript	31360659	31361532	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	stop_codon	31360656	31360658	.	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	CDS	31360659	31360760	1	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	exon	31360659	31360760	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	intron	31360761	31360851	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	CDS	31360852	31360926	1	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	exon	31360852	31360926	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	intron	31360927	31361040	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	CDS	31361041	31361097	1	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	exon	31361041	31361097	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	intron	31361098	31361197	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	CDS	31361198	31361320	1	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	exon	31361198	31361320	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	intron	31361321	31361409	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	CDS	31361410	31361532	1	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	exon	31361410	31361532	.	-	.	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
Phchi.S1	AUGUSTUS	start_codon	31361530	31361532	.	-	0	transcript_id "Phchi.S1G498000.t1"; gene_id "Phchi.S1G498000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8974.t1 is derived from g6149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38932820	38933748	.	-	.	Phchi.S1G613300
Phchi.S1	AUGUSTUS	transcript	38932820	38933748	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	stop_codon	38932817	38932819	.	-	0	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	CDS	38932820	38932866	0.49	-	2	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	exon	38932820	38932866	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	intron	38932867	38932957	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	CDS	38932958	38933052	0.79	-	1	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	exon	38932958	38933052	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	intron	38933053	38933280	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	CDS	38933281	38933453	0.91	-	0	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	exon	38933281	38933453	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	intron	38933454	38933541	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	CDS	38933542	38933748	0.84	-	0	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	exon	38933542	38933748	.	-	.	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
Phchi.S1	AUGUSTUS	start_codon	38933746	38933748	.	-	0	transcript_id "Phchi.S1G613300.t1"; gene_id "Phchi.S1G613300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10584.t1 is derived from g14634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1063888	1065723	.	-	.	Phchi.S4G016600
Phchi.S4	AUGUSTUS	transcript	1063888	1065723	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	stop_codon	1063885	1063887	.	-	0	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	CDS	1063888	1064496	1	-	0	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	exon	1063888	1064496	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	intron	1064497	1064585	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	CDS	1064586	1064891	1	-	0	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	exon	1064586	1064891	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	intron	1064892	1064983	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	CDS	1064984	1065218	1	-	1	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	exon	1064984	1065218	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	intron	1065219	1065319	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	CDS	1065320	1065723	0.78	-	0	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	exon	1065320	1065723	.	-	.	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
Phchi.S4	AUGUSTUS	start_codon	1065721	1065723	.	-	0	transcript_id "Phchi.S4G016600.t1"; gene_id "Phchi.S4G016600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16009.t1 is derived from g14433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	141758	142195	.	-	.	Phchi.C10G000700
Phchi.C10	AUGUSTUS	transcript	141758	142195	.	-	.	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	stop_codon	141755	141757	.	-	0	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	CDS	141758	141977	0.65	-	1	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	exon	141758	141977	.	-	.	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	intron	141978	142070	.	-	.	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	CDS	142071	142195	0.63	-	0	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	exon	142071	142195	.	-	.	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
Phchi.C10	AUGUSTUS	start_codon	142193	142195	.	-	0	transcript_id "Phchi.C10G000700.t1"; gene_id "Phchi.C10G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7599.t1 is derived from g4773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30203017	30204896	.	-	.	Phchi.S1G475800
Phchi.S1	AUGUSTUS	transcript	30203017	30204896	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	stop_codon	30203014	30203016	.	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30203017	30203130	0.67	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30203017	30203130	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30203131	30203253	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30203254	30203413	0.98	-	1	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30203254	30203413	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30203414	30203526	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30203527	30203616	0.99	-	1	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30203527	30203616	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30203617	30203708	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30203709	30203743	1	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30203709	30203743	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30203744	30203920	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30203921	30204001	1	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30203921	30204001	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30204002	30204147	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30204148	30204204	1	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30204148	30204204	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30204205	30204283	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30204284	30204388	0.98	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30204284	30204388	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30204389	30204507	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30204508	30204674	0.97	-	2	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30204508	30204674	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	intron	30204675	30204763	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	CDS	30204764	30204896	0.92	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	exon	30204764	30204896	.	-	.	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
Phchi.S1	AUGUSTUS	start_codon	30204894	30204896	.	-	0	transcript_id "Phchi.S1G475800.t1"; gene_id "Phchi.S1G475800"
# This transcript jg5298.t2 is derived from g2468.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5298.t3 is derived from g2468.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5299.t1 is derived from g2469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16089229	16092720	.	+	.	Phchi.S1G245800
Phchi.S1	AUGUSTUS	transcript	16089229	16092720	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	start_codon	16089229	16089231	.	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16089229	16090068	0.57	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16089229	16090068	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16090069	16090211	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16090212	16090364	0.66	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16090212	16090364	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16090365	16090513	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16090514	16090687	0.66	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16090514	16090687	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16090688	16090870	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16090871	16090897	1	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16090871	16090897	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16090898	16091114	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16091115	16091235	1	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16091115	16091235	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16091236	16091331	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16091332	16091434	1	+	2	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16091332	16091434	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16091435	16091614	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16091615	16091708	1	+	1	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16091615	16091708	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16091709	16091805	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16091806	16091884	1	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16091806	16091884	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16091885	16091988	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16091989	16092160	1	+	2	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16091989	16092160	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16092161	16092291	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16092292	16092372	1	+	1	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16092292	16092372	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	intron	16092373	16092494	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	CDS	16092495	16092720	0.71	+	1	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	exon	16092495	16092720	.	+	.	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
Phchi.S1	AUGUSTUS	stop_codon	16092721	16092723	.	+	0	transcript_id "Phchi.S1G245800.t1"; gene_id "Phchi.S1G245800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10206.t1 is derived from g7382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46380059	46381719	.	-	.	Phchi.S1G736500
Phchi.S1	AUGUSTUS	transcript	46380059	46381719	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	stop_codon	46380056	46380058	.	-	0	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	CDS	46380059	46380144	0.69	-	2	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	exon	46380059	46380144	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	intron	46380145	46380295	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	CDS	46380296	46380355	0.55	-	2	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	exon	46380296	46380355	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	intron	46380356	46380441	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	CDS	46380442	46380669	0.74	-	2	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	exon	46380442	46380669	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	intron	46380670	46380960	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	CDS	46380961	46381007	0.55	-	1	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	exon	46380961	46381007	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	intron	46381008	46381410	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	CDS	46381411	46381460	0.6	-	0	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	exon	46381411	46381460	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	intron	46381461	46381536	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	CDS	46381537	46381719	0.42	-	0	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	exon	46381537	46381719	.	-	.	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
Phchi.S1	AUGUSTUS	start_codon	46381717	46381719	.	-	0	transcript_id "Phchi.S1G736500.t1"; gene_id "Phchi.S1G736500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3484.t1 is derived from g653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4008899	4009984	.	+	.	Phchi.S1G064300
Phchi.S1	AUGUSTUS	transcript	4008899	4009984	.	+	.	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	start_codon	4008899	4008901	.	+	0	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	CDS	4008899	4008992	0.5	+	0	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	exon	4008899	4008992	.	+	.	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	intron	4008993	4009161	.	+	.	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	CDS	4009162	4009761	0.48	+	2	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	exon	4009162	4009761	.	+	.	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	intron	4009762	4009865	.	+	.	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	CDS	4009866	4009984	0.39	+	2	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	exon	4009866	4009984	.	+	.	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
Phchi.S1	AUGUSTUS	stop_codon	4009985	4009987	.	+	0	transcript_id "Phchi.S1G064300.t1"; gene_id "Phchi.S1G064300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5052.t1 is derived from g2222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14387565	14387972	.	+	.	Phchi.S1G221100
Phchi.S1	AUGUSTUS	transcript	14387565	14387972	.	+	.	transcript_id "Phchi.S1G221100.t1"; gene_id "Phchi.S1G221100"
Phchi.S1	AUGUSTUS	start_codon	14387565	14387567	.	+	0	transcript_id "Phchi.S1G221100.t1"; gene_id "Phchi.S1G221100"
Phchi.S1	AUGUSTUS	CDS	14387565	14387972	0.89	+	0	transcript_id "Phchi.S1G221100.t1"; gene_id "Phchi.S1G221100"
Phchi.S1	AUGUSTUS	exon	14387565	14387972	.	+	.	transcript_id "Phchi.S1G221100.t1"; gene_id "Phchi.S1G221100"
Phchi.S1	AUGUSTUS	stop_codon	14387973	14387975	.	+	0	transcript_id "Phchi.S1G221100.t1"; gene_id "Phchi.S1G221100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11323.t1 is derived from g15373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5367557	5368952	.	+	.	Phchi.S4G090500
Phchi.S4	AUGUSTUS	transcript	5367557	5368952	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	start_codon	5367557	5367559	.	+	0	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	CDS	5367557	5367877	0.98	+	0	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	exon	5367557	5367877	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	intron	5367878	5367988	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	CDS	5367989	5368200	0.98	+	0	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	exon	5367989	5368200	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	intron	5368201	5368295	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	CDS	5368296	5368351	0.99	+	1	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	exon	5368296	5368351	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	intron	5368352	5368442	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	CDS	5368443	5368513	1	+	2	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	exon	5368443	5368513	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	intron	5368514	5368653	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	CDS	5368654	5368752	1	+	0	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	exon	5368654	5368752	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	intron	5368753	5368844	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	CDS	5368845	5368952	1	+	0	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	exon	5368845	5368952	.	+	.	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
Phchi.S4	AUGUSTUS	stop_codon	5368953	5368955	.	+	0	transcript_id "Phchi.S4G090500.t1"; gene_id "Phchi.S4G090500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2945.t1 is derived from g114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	709463	710747	.	-	.	Phchi.S1G010400
Phchi.S1	AUGUSTUS	transcript	709463	710747	.	-	.	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	stop_codon	709460	709462	.	-	0	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	CDS	709463	709651	1	-	0	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	exon	709463	709651	.	-	.	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	intron	709652	709801	.	-	.	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	CDS	709802	709908	1	-	2	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	exon	709802	709908	.	-	.	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	intron	709909	710068	.	-	.	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	CDS	710069	710747	1	-	0	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	exon	710069	710747	.	-	.	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
Phchi.S1	AUGUSTUS	start_codon	710745	710747	.	-	0	transcript_id "Phchi.S1G010400.t1"; gene_id "Phchi.S1G010400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg918.t1 is derived from g10700.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6423773	6425655	.	-	.	Phchi.S6G087700
Phchi.S6	AUGUSTUS	transcript	6423773	6425289	.	-	.	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	stop_codon	6423770	6423772	.	-	0	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	CDS	6423773	6424815	0.36	-	2	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	exon	6423773	6424815	.	-	.	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	intron	6424816	6424988	.	-	.	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	CDS	6424989	6425289	0.41	-	0	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	exon	6424989	6425289	.	-	.	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	start_codon	6425287	6425289	.	-	0	transcript_id "Phchi.S6G087700.t1"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	transcript	6423773	6425655	.	-	.	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	stop_codon	6423770	6423772	.	-	0	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	CDS	6423773	6424815	0.29	-	2	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	exon	6423773	6424815	.	-	.	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	intron	6424816	6424988	.	-	.	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	CDS	6424989	6425347	0.43	-	1	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	exon	6424989	6425347	.	-	.	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	intron	6425348	6425545	.	-	.	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	CDS	6425546	6425655	0.31	-	0	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	exon	6425546	6425655	.	-	.	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	start_codon	6425653	6425655	.	-	0	transcript_id "Phchi.S6G087700.t2"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	transcript	6423773	6424687	.	-	.	transcript_id "Phchi.S6G087700.t3"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	stop_codon	6423770	6423772	.	-	0	transcript_id "Phchi.S6G087700.t3"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	CDS	6423773	6424687	0.7	-	0	transcript_id "Phchi.S6G087700.t3"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	exon	6423773	6424687	.	-	.	transcript_id "Phchi.S6G087700.t3"; gene_id "Phchi.S6G087700"
Phchi.S6	AUGUSTUS	start_codon	6424685	6424687	.	-	0	transcript_id "Phchi.S6G087700.t3"; gene_id "Phchi.S6G087700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10826.t1 is derived from g14876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2309910	2312214	.	+	.	Phchi.S4G040800
Phchi.S4	AUGUSTUS	transcript	2309910	2312214	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	start_codon	2309910	2309912	.	+	0	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2309910	2310310	1	+	0	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2309910	2310310	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2310311	2310411	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2310412	2310507	1	+	1	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2310412	2310507	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2310508	2310584	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2310585	2310990	1	+	1	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2310585	2310990	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2310991	2311087	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2311088	2311199	0.91	+	0	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2311088	2311199	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2311200	2311391	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2311392	2311529	1	+	2	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2311392	2311529	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2311530	2311603	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2311604	2312214	1	+	2	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2311604	2312214	.	+	.	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	stop_codon	2312215	2312217	.	+	0	transcript_id "Phchi.S4G040800.t1"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	transcript	2309910	2312214	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	start_codon	2309910	2309912	.	+	0	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2309910	2310310	0.99	+	0	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2309910	2310310	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2310311	2310411	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2310412	2310507	1	+	1	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2310412	2310507	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2310508	2310584	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2310585	2310990	1	+	1	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2310585	2310990	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2310991	2311087	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2311088	2311259	0.85	+	0	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2311088	2311259	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2311260	2311391	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2311392	2311529	0.85	+	2	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2311392	2311529	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	intron	2311530	2311603	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	CDS	2311604	2312214	0.99	+	2	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	exon	2311604	2312214	.	+	.	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
Phchi.S4	AUGUSTUS	stop_codon	2312215	2312217	.	+	0	transcript_id "Phchi.S4G040800.t2"; gene_id "Phchi.S4G040800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2149.t1 is derived from g9069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5076819	5077364	.	+	.	Phchi.S5G075800
Phchi.S5	AUGUSTUS	transcript	5076819	5077364	.	+	.	transcript_id "Phchi.S5G075800.t1"; gene_id "Phchi.S5G075800"
Phchi.S5	AUGUSTUS	start_codon	5076819	5076821	.	+	0	transcript_id "Phchi.S5G075800.t1"; gene_id "Phchi.S5G075800"
Phchi.S5	AUGUSTUS	CDS	5076819	5077364	1	+	0	transcript_id "Phchi.S5G075800.t1"; gene_id "Phchi.S5G075800"
Phchi.S5	AUGUSTUS	exon	5076819	5077364	.	+	.	transcript_id "Phchi.S5G075800.t1"; gene_id "Phchi.S5G075800"
Phchi.S5	AUGUSTUS	stop_codon	5077365	5077367	.	+	0	transcript_id "Phchi.S5G075800.t1"; gene_id "Phchi.S5G075800"
# This transcript jg9968.t2 is derived from g7144.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9968.t3 is derived from g7144.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9968.t4 is derived from g7144.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9969.t1 is derived from g7145.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44703241	44704955	.	-	.	Phchi.S1G712800
Phchi.S1	AUGUSTUS	transcript	44703241	44704955	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	stop_codon	44703238	44703240	.	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44703241	44703273	1	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44703241	44703273	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44703274	44703368	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44703369	44703431	1	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44703369	44703431	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44703432	44703512	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44703513	44703605	1	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44703513	44703605	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44703606	44703726	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44703727	44703774	1	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44703727	44703774	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44703775	44703888	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44703889	44703951	0.95	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44703889	44703951	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44703952	44704044	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704045	44704073	0.95	-	2	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704045	44704073	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44704074	44704128	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704129	44704160	0.69	-	1	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704129	44704160	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44704161	44704252	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704253	44704331	0.98	-	2	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704253	44704331	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44704332	44704452	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704453	44704535	0.96	-	1	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704453	44704535	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44704536	44704616	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704617	44704640	0.95	-	1	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704617	44704640	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44704641	44704743	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704744	44704862	0.94	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704744	44704862	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	intron	44704863	44704946	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	CDS	44704947	44704955	0.94	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	exon	44704947	44704955	.	-	.	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
Phchi.S1	AUGUSTUS	start_codon	44704953	44704955	.	-	0	transcript_id "Phchi.S1G712800.t1"; gene_id "Phchi.S1G712800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13274.t1 is derived from g11739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5086995	5088231	.	+	.	Phchi.S3G059300
Phchi.S3	AUGUSTUS	transcript	5086995	5088231	.	+	.	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	start_codon	5086995	5086997	.	+	0	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	CDS	5086995	5087085	0.78	+	0	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	exon	5086995	5087085	.	+	.	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	intron	5087086	5087185	.	+	.	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	CDS	5087186	5088231	0.98	+	2	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	exon	5087186	5088231	.	+	.	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
Phchi.S3	AUGUSTUS	stop_codon	5088232	5088234	.	+	0	transcript_id "Phchi.S3G059300.t1"; gene_id "Phchi.S3G059300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9643.t1 is derived from g6819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43034264	43037702	.	-	.	Phchi.S1G680200
Phchi.S1	AUGUSTUS	transcript	43034264	43037702	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	stop_codon	43034261	43034263	.	-	0	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43034264	43034419	0.99	-	0	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43034264	43034419	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43034420	43034515	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43034516	43034644	1	-	0	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43034516	43034644	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43034645	43034742	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43034743	43034954	1	-	2	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43034743	43034954	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43034955	43035060	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43035061	43036199	0.99	-	1	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43035061	43036199	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43036200	43036277	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43036278	43036404	1	-	2	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43036278	43036404	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43036405	43036554	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43036555	43036712	1	-	1	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43036555	43036712	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43036713	43036876	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43036877	43037328	0.57	-	0	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43036877	43037328	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	intron	43037329	43037435	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	CDS	43037436	43037702	0.73	-	0	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	exon	43037436	43037702	.	-	.	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
Phchi.S1	AUGUSTUS	start_codon	43037700	43037702	.	-	0	transcript_id "Phchi.S1G680200.t1"; gene_id "Phchi.S1G680200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6032.t1 is derived from g3203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20518534	20520388	.	-	.	Phchi.S1G319100
Phchi.S1	AUGUSTUS	transcript	20518534	20520388	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	stop_codon	20518531	20518533	.	-	0	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	CDS	20518534	20518632	1	-	0	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	exon	20518534	20518632	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	intron	20518633	20518728	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	CDS	20518729	20518968	1	-	0	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	exon	20518729	20518968	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	intron	20518969	20519061	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	CDS	20519062	20519199	1	-	0	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	exon	20519062	20519199	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	intron	20519200	20519294	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	CDS	20519295	20520145	1	-	2	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	exon	20519295	20520145	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	intron	20520146	20520330	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	CDS	20520331	20520388	0.97	-	0	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	exon	20520331	20520388	.	-	.	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
Phchi.S1	AUGUSTUS	start_codon	20520386	20520388	.	-	0	transcript_id "Phchi.S1G319100.t1"; gene_id "Phchi.S1G319100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1979.t1 is derived from g8899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4175428	4177647	.	+	.	Phchi.S5G058800
Phchi.S5	AUGUSTUS	transcript	4175428	4177647	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	start_codon	4175428	4175430	.	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4175428	4175434	0.98	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4175428	4175434	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4175435	4175608	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4175609	4175628	0.96	+	2	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4175609	4175628	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4175629	4175726	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4175727	4175765	0.99	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4175727	4175765	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4175766	4175862	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4175863	4176019	1	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4175863	4176019	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4176020	4176101	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4176102	4176233	1	+	2	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4176102	4176233	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4176234	4176326	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4176327	4176441	1	+	2	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4176327	4176441	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4176442	4176535	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4176536	4176638	1	+	1	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4176536	4176638	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4176639	4176772	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4176773	4176841	1	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4176773	4176841	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4176842	4176926	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4176927	4177046	1	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4176927	4177046	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4177047	4177142	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4177143	4177284	1	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4177143	4177284	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	intron	4177285	4177375	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	CDS	4177376	4177647	0.37	+	2	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	exon	4177376	4177647	.	+	.	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
Phchi.S5	AUGUSTUS	stop_codon	4177648	4177650	.	+	0	transcript_id "Phchi.S5G058800.t1"; gene_id "Phchi.S5G058800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7969.t1 is derived from g5144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32176396	32177917	.	+	.	Phchi.S1G512800
Phchi.S1	AUGUSTUS	transcript	32176396	32177917	.	+	.	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	start_codon	32176396	32176398	.	+	0	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	CDS	32176396	32176722	1	+	0	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	exon	32176396	32176722	.	+	.	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	intron	32176723	32176793	.	+	.	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	CDS	32176794	32177365	0.32	+	0	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	exon	32176794	32177365	.	+	.	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	intron	32177366	32177451	.	+	.	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	CDS	32177452	32177917	0.57	+	1	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	exon	32177452	32177917	.	+	.	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
Phchi.S1	AUGUSTUS	stop_codon	32177918	32177920	.	+	0	transcript_id "Phchi.S1G512800.t1"; gene_id "Phchi.S1G512800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14669.t1 is derived from g13137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14108540	14109994	.	-	.	Phchi.S3G198800
Phchi.S3	AUGUSTUS	transcript	14108540	14109994	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	stop_codon	14108537	14108539	.	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14108540	14108662	1	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14108540	14108662	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	intron	14108663	14108754	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14108755	14108910	1	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14108755	14108910	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	intron	14108911	14108997	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14108998	14109069	1	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14108998	14109069	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	intron	14109070	14109163	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14109164	14109294	1	-	2	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14109164	14109294	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	intron	14109295	14109379	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14109380	14109488	1	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14109380	14109488	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	intron	14109489	14109767	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14109768	14109881	0.98	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14109768	14109881	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	intron	14109882	14109991	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	CDS	14109992	14109994	0.95	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	exon	14109992	14109994	.	-	.	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
Phchi.S3	AUGUSTUS	start_codon	14109992	14109994	.	-	0	transcript_id "Phchi.S3G198800.t1"; gene_id "Phchi.S3G198800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg306.t1 is derived from g10088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2202329	2203666	.	-	.	Phchi.S6G026500
Phchi.S6	AUGUSTUS	transcript	2202329	2203666	.	-	.	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	stop_codon	2202326	2202328	.	-	0	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	CDS	2202329	2202441	0.83	-	2	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	exon	2202329	2202441	.	-	.	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	intron	2202442	2202675	.	-	.	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	CDS	2202676	2202845	0.77	-	1	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	exon	2202676	2202845	.	-	.	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	intron	2202846	2203049	.	-	.	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	CDS	2203050	2203666	0.43	-	0	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	exon	2203050	2203666	.	-	.	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
Phchi.S6	AUGUSTUS	start_codon	2203664	2203666	.	-	0	transcript_id "Phchi.S6G026500.t1"; gene_id "Phchi.S6G026500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9516.t1 is derived from g6692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42230024	42231925	.	-	.	Phchi.S1G667500
Phchi.S1	AUGUSTUS	transcript	42230024	42231925	.	-	.	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	stop_codon	42230021	42230023	.	-	0	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	CDS	42230024	42230496	0.71	-	2	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	exon	42230024	42230496	.	-	.	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	intron	42230497	42230739	.	-	.	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	CDS	42230740	42231925	0.46	-	0	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	exon	42230740	42231925	.	-	.	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
Phchi.S1	AUGUSTUS	start_codon	42231923	42231925	.	-	0	transcript_id "Phchi.S1G667500.t1"; gene_id "Phchi.S1G667500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10561.t1 is derived from g14611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	986935	992828	.	-	.	Phchi.S4G014300
Phchi.S4	AUGUSTUS	transcript	986935	992828	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	stop_codon	986932	986934	.	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	986935	989385	0.3	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	986935	989385	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	989386	989541	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	989542	989763	0.92	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	989542	989763	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	989764	989853	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	989854	990083	0.92	-	2	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	989854	990083	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	990084	990176	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	990177	990199	1	-	1	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	990177	990199	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	990200	990403	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	990404	991824	1	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	990404	991824	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	991825	991912	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	991913	992007	1	-	2	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	991913	992007	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	992008	992086	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	992087	992219	1	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	992087	992219	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	992220	992302	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	992303	992407	0.98	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	992303	992407	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	intron	992408	992702	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	CDS	992703	992828	0.98	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	exon	992703	992828	.	-	.	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
Phchi.S4	AUGUSTUS	start_codon	992826	992828	.	-	0	transcript_id "Phchi.S4G014300.t1"; gene_id "Phchi.S4G014300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4706.t1 is derived from g1876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12412357	12415488	.	+	.	Phchi.S1G186500
Phchi.S1	AUGUSTUS	transcript	12412357	12415488	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	start_codon	12412357	12412359	.	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12412357	12412407	0.49	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12412357	12412407	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12412408	12412516	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12412517	12412591	1	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12412517	12412591	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12412592	12412713	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12412714	12412798	1	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12412714	12412798	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12412799	12412933	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12412934	12413043	0.69	+	2	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12412934	12413043	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12413044	12413189	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12413190	12413260	1	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12413190	12413260	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12413261	12413415	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12413416	12413497	0.9	+	1	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12413416	12413497	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12413498	12413604	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12413605	12413703	0.9	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12413605	12413703	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12413704	12413798	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12413799	12413854	0.9	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12413799	12413854	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12413855	12413964	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12413965	12413999	0.91	+	1	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12413965	12413999	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12414000	12414151	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12414152	12414383	0.81	+	2	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12414152	12414383	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12414384	12414498	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12414499	12414735	0.95	+	1	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12414499	12414735	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12414736	12414861	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12414862	12414921	1	+	1	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12414862	12414921	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12414922	12415006	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12415007	12415046	1	+	1	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12415007	12415046	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12415047	12415147	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12415148	12415366	1	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12415148	12415366	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	intron	12415367	12415443	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	CDS	12415444	12415488	1	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	exon	12415444	12415488	.	+	.	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
Phchi.S1	AUGUSTUS	stop_codon	12415489	12415491	.	+	0	transcript_id "Phchi.S1G186500.t1"; gene_id "Phchi.S1G186500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6557.t1 is derived from g3729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23708783	23712372	.	+	.	Phchi.S1G371600
Phchi.S1	AUGUSTUS	transcript	23708783	23712372	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	start_codon	23708783	23708785	.	+	0	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23708783	23708872	1	+	0	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23708783	23708872	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23708873	23708988	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23708989	23709080	1	+	0	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23708989	23709080	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23709081	23709211	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23709212	23709303	1	+	1	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23709212	23709303	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23709304	23709401	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23709402	23709569	1	+	2	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23709402	23709569	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23709570	23709732	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23709733	23709844	1	+	2	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23709733	23709844	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23709845	23709957	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23709958	23710507	1	+	1	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23709958	23710507	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23710508	23710600	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23710601	23710701	1	+	0	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23710601	23710701	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23710702	23710839	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23710840	23711061	1	+	1	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23710840	23711061	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23711062	23711180	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23711181	23711295	1	+	1	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23711181	23711295	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23711296	23711423	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23711424	23711628	0.9	+	0	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23711424	23711628	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23711629	23711726	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23711727	23711927	1	+	2	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23711727	23711927	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	intron	23711928	23712016	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	CDS	23712017	23712372	0.46	+	2	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	exon	23712017	23712372	.	+	.	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
Phchi.S1	AUGUSTUS	stop_codon	23712373	23712375	.	+	0	transcript_id "Phchi.S1G371600.t1"; gene_id "Phchi.S1G371600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3698.t1 is derived from g867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5229900	5230337	.	+	.	Phchi.S1G085700
Phchi.S1	AUGUSTUS	transcript	5229900	5230337	.	+	.	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	start_codon	5229900	5229902	.	+	0	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	CDS	5229900	5230024	0.83	+	0	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	exon	5229900	5230024	.	+	.	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	intron	5230025	5230117	.	+	.	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	CDS	5230118	5230337	0.87	+	1	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	exon	5230118	5230337	.	+	.	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
Phchi.S1	AUGUSTUS	stop_codon	5230338	5230340	.	+	0	transcript_id "Phchi.S1G085700.t1"; gene_id "Phchi.S1G085700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5761.t1 is derived from g2931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18837087	18838880	.	+	.	Phchi.S1G292000
Phchi.S1	AUGUSTUS	transcript	18837087	18838880	.	+	.	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	start_codon	18837087	18837089	.	+	0	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	CDS	18837087	18838571	0.96	+	0	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	exon	18837087	18838571	.	+	.	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	intron	18838572	18838694	.	+	.	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	CDS	18838695	18838880	0.69	+	0	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	exon	18838695	18838880	.	+	.	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
Phchi.S1	AUGUSTUS	stop_codon	18838881	18838883	.	+	0	transcript_id "Phchi.S1G292000.t1"; gene_id "Phchi.S1G292000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12709.t1 is derived from g11174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	685080	687068	.	+	.	Phchi.S3G002800
Phchi.S3	AUGUSTUS	transcript	685080	687068	.	+	.	transcript_id "Phchi.S3G002800.t1"; gene_id "Phchi.S3G002800"
Phchi.S3	AUGUSTUS	start_codon	685080	685082	.	+	0	transcript_id "Phchi.S3G002800.t1"; gene_id "Phchi.S3G002800"
Phchi.S3	AUGUSTUS	CDS	685080	687068	0.96	+	0	transcript_id "Phchi.S3G002800.t1"; gene_id "Phchi.S3G002800"
Phchi.S3	AUGUSTUS	exon	685080	687068	.	+	.	transcript_id "Phchi.S3G002800.t1"; gene_id "Phchi.S3G002800"
Phchi.S3	AUGUSTUS	stop_codon	687069	687071	.	+	0	transcript_id "Phchi.S3G002800.t1"; gene_id "Phchi.S3G002800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7283.t1 is derived from g4455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28133875	28136128	.	+	.	Phchi.S1G444200
Phchi.S1	AUGUSTUS	transcript	28133875	28136128	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	start_codon	28133875	28133877	.	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28133875	28134189	0.58	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28133875	28134189	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28134190	28134364	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28134365	28134511	0.9	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28134365	28134511	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28134512	28134620	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28134621	28134839	1	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28134621	28134839	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28134840	28134935	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28134936	28135000	1	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28134936	28135000	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28135001	28135091	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28135092	28135157	1	+	1	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28135092	28135157	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28135158	28135324	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28135325	28135399	1	+	1	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28135325	28135399	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28135400	28135484	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28135485	28135547	1	+	1	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28135485	28135547	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28135548	28135644	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28135645	28135717	1	+	1	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28135645	28135717	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28135718	28135864	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28135865	28135948	1	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28135865	28135948	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	intron	28135949	28136032	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	CDS	28136033	28136128	1	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	exon	28136033	28136128	.	+	.	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
Phchi.S1	AUGUSTUS	stop_codon	28136129	28136131	.	+	0	transcript_id "Phchi.S1G444200.t1"; gene_id "Phchi.S1G444200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11506.t1 is derived from g15556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6763804	6765664	.	-	.	Phchi.S4G108800
Phchi.S4	AUGUSTUS	transcript	6763804	6765664	.	-	.	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	stop_codon	6763801	6763803	.	-	0	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	CDS	6763804	6764019	1	-	0	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	exon	6763804	6764019	.	-	.	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	intron	6764020	6764200	.	-	.	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	CDS	6764201	6765664	0.91	-	0	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	exon	6764201	6765664	.	-	.	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
Phchi.S4	AUGUSTUS	start_codon	6765662	6765664	.	-	0	transcript_id "Phchi.S4G108800.t1"; gene_id "Phchi.S4G108800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1505.t1 is derived from g8424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1270366	1272945	.	-	.	Phchi.S5G011400
Phchi.S5	AUGUSTUS	transcript	1270366	1272945	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	stop_codon	1270363	1270365	.	-	0	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	CDS	1270366	1270778	0.39	-	2	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	exon	1270366	1270778	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	intron	1270779	1270939	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	CDS	1270940	1272276	0.43	-	1	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	exon	1270940	1272276	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	intron	1272277	1272410	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	CDS	1272411	1272540	0.94	-	2	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	exon	1272411	1272540	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	intron	1272541	1272806	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	CDS	1272807	1272945	0.93	-	0	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	exon	1272807	1272945	.	-	.	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
Phchi.S5	AUGUSTUS	start_codon	1272943	1272945	.	-	0	transcript_id "Phchi.S5G011400.t1"; gene_id "Phchi.S5G011400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10481.t1 is derived from g14530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	580438	580878	.	-	.	Phchi.S4G006300
Phchi.S4	AUGUSTUS	transcript	580438	580878	.	-	.	transcript_id "Phchi.S4G006300.t1"; gene_id "Phchi.S4G006300"
Phchi.S4	AUGUSTUS	stop_codon	580435	580437	.	-	0	transcript_id "Phchi.S4G006300.t1"; gene_id "Phchi.S4G006300"
Phchi.S4	AUGUSTUS	CDS	580438	580878	0.56	-	0	transcript_id "Phchi.S4G006300.t1"; gene_id "Phchi.S4G006300"
Phchi.S4	AUGUSTUS	exon	580438	580878	.	-	.	transcript_id "Phchi.S4G006300.t1"; gene_id "Phchi.S4G006300"
Phchi.S4	AUGUSTUS	start_codon	580876	580878	.	-	0	transcript_id "Phchi.S4G006300.t1"; gene_id "Phchi.S4G006300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5967.t1 is derived from g3138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20114596	20118704	.	-	.	Phchi.S1G312600
Phchi.S1	AUGUSTUS	transcript	20114596	20118704	.	-	.	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	stop_codon	20114593	20114595	.	-	0	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	CDS	20114596	20115970	0.92	-	1	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	exon	20114596	20115970	.	-	.	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	intron	20115971	20116061	.	-	.	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	CDS	20116062	20117125	0.99	-	0	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	exon	20116062	20117125	.	-	.	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	intron	20117126	20117219	.	-	.	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	CDS	20117220	20118704	0.54	-	0	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	exon	20117220	20118704	.	-	.	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
Phchi.S1	AUGUSTUS	start_codon	20118702	20118704	.	-	0	transcript_id "Phchi.S1G312600.t1"; gene_id "Phchi.S1G312600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11583.t1 is derived from g15634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7196190	7199794	.	-	.	Phchi.S4G116500
Phchi.S4	AUGUSTUS	transcript	7196190	7199794	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	stop_codon	7196187	7196189	.	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7196190	7196519	0.97	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7196190	7196519	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7196520	7196615	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7196616	7196789	1	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7196616	7196789	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7196790	7196880	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7196881	7196993	1	-	2	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7196881	7196993	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7196994	7197075	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7197076	7197084	1	-	2	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7197076	7197084	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7197085	7197134	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7197135	7197224	0.87	-	2	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7197135	7197224	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7197225	7197310	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7197311	7197341	1	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7197311	7197341	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7197342	7197439	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7197440	7197515	1	-	1	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7197440	7197515	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7197516	7197675	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7197676	7197763	1	-	2	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7197676	7197763	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7197764	7197866	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7197867	7197928	1	-	1	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7197867	7197928	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7197929	7198015	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7198016	7198092	1	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7198016	7198092	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7198093	7198219	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7198220	7198322	0.98	-	1	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7198220	7198322	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7198323	7198770	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7198771	7198832	1	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7198771	7198832	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7198833	7199371	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7199372	7199446	0.72	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7199372	7199446	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7199447	7199549	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7199550	7199595	0.89	-	1	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7199550	7199595	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	intron	7199596	7199768	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	CDS	7199769	7199794	0.46	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	exon	7199769	7199794	.	-	.	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
Phchi.S4	AUGUSTUS	start_codon	7199792	7199794	.	-	0	transcript_id "Phchi.S4G116500.t1"; gene_id "Phchi.S4G116500"
# This transcript jg6477.t2 is derived from g3649.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6478.t1 is derived from g3650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23193244	23193704	.	-	.	Phchi.S1G363700
Phchi.S1	AUGUSTUS	transcript	23193244	23193704	.	-	.	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	stop_codon	23193241	23193243	.	-	0	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	CDS	23193244	23193412	0.58	-	1	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	exon	23193244	23193412	.	-	.	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	intron	23193413	23193633	.	-	.	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	CDS	23193634	23193704	0.68	-	0	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	exon	23193634	23193704	.	-	.	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
Phchi.S1	AUGUSTUS	start_codon	23193702	23193704	.	-	0	transcript_id "Phchi.S1G363700.t1"; gene_id "Phchi.S1G363700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14372.t1 is derived from g12839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12414438	12415570	.	-	.	Phchi.S3G169100
Phchi.S3	AUGUSTUS	transcript	12414438	12415570	.	-	.	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	stop_codon	12414435	12414437	.	-	0	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	CDS	12414438	12415238	0.71	-	0	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	exon	12414438	12415238	.	-	.	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	intron	12415239	12415360	.	-	.	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	CDS	12415361	12415570	0.71	-	0	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	exon	12415361	12415570	.	-	.	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
Phchi.S3	AUGUSTUS	start_codon	12415568	12415570	.	-	0	transcript_id "Phchi.S3G169100.t1"; gene_id "Phchi.S3G169100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13090.t1 is derived from g11555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4104218	4105576	.	-	.	Phchi.S3G040900
Phchi.S3	AUGUSTUS	transcript	4104218	4105576	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	stop_codon	4104215	4104217	.	-	0	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	CDS	4104218	4104520	0.99	-	0	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	exon	4104218	4104520	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	intron	4104521	4104618	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	CDS	4104619	4104734	0.97	-	2	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	exon	4104619	4104734	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	intron	4104735	4104818	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	CDS	4104819	4105056	0.28	-	0	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	exon	4104819	4105056	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	intron	4105057	4105135	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	CDS	4105136	4105255	0.26	-	0	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	exon	4105136	4105255	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	intron	4105256	4105360	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	CDS	4105361	4105576	0.65	-	0	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	exon	4105361	4105576	.	-	.	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
Phchi.S3	AUGUSTUS	start_codon	4105574	4105576	.	-	0	transcript_id "Phchi.S3G040900.t1"; gene_id "Phchi.S3G040900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15235.t1 is derived from g13703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17863012	17865286	.	+	.	Phchi.S3G255400
Phchi.S3	AUGUSTUS	transcript	17863012	17865286	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	start_codon	17863012	17863014	.	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17863012	17863132	0.76	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17863012	17863132	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17863133	17863237	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17863238	17863465	1	+	2	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17863238	17863465	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17863466	17863555	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17863556	17863601	1	+	2	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17863556	17863601	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17863602	17863685	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17863686	17863821	0.98	+	1	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17863686	17863821	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17863822	17863936	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17863937	17864011	1	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17863937	17864011	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17864012	17864094	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17864095	17864313	1	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17864095	17864313	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17864314	17864405	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17864406	17864501	1	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17864406	17864501	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17864502	17864589	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17864590	17864708	1	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17864590	17864708	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17864709	17864785	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17864786	17864879	0.86	+	1	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17864786	17864879	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17864880	17864993	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17864994	17865044	1	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17864994	17865044	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	intron	17865045	17865142	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	CDS	17865143	17865286	0.76	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	exon	17865143	17865286	.	+	.	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
Phchi.S3	AUGUSTUS	stop_codon	17865287	17865289	.	+	0	transcript_id "Phchi.S3G255400.t1"; gene_id "Phchi.S3G255400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13373.t1 is derived from g11839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6397686	6398831	.	-	.	Phchi.S3G069200
Phchi.S3	AUGUSTUS	transcript	6397686	6398831	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	stop_codon	6397683	6397685	.	-	0	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	CDS	6397686	6397827	0.94	-	1	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	exon	6397686	6397827	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	intron	6397828	6398048	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	CDS	6398049	6398191	1	-	0	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	exon	6398049	6398191	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	intron	6398192	6398272	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	CDS	6398273	6398331	1	-	2	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	exon	6398273	6398331	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	intron	6398332	6398415	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	CDS	6398416	6398527	1	-	0	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	exon	6398416	6398527	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	intron	6398528	6398648	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	CDS	6398649	6398831	1	-	0	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	exon	6398649	6398831	.	-	.	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
Phchi.S3	AUGUSTUS	start_codon	6398829	6398831	.	-	0	transcript_id "Phchi.S3G069200.t1"; gene_id "Phchi.S3G069200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4578.t1 is derived from g1748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11184465	11185448	.	-	.	Phchi.S1G173700
Phchi.S1	AUGUSTUS	transcript	11184465	11185448	.	-	.	transcript_id "Phchi.S1G173700.t1"; gene_id "Phchi.S1G173700"
Phchi.S1	AUGUSTUS	stop_codon	11184462	11184464	.	-	0	transcript_id "Phchi.S1G173700.t1"; gene_id "Phchi.S1G173700"
Phchi.S1	AUGUSTUS	CDS	11184465	11185448	0.97	-	0	transcript_id "Phchi.S1G173700.t1"; gene_id "Phchi.S1G173700"
Phchi.S1	AUGUSTUS	exon	11184465	11185448	.	-	.	transcript_id "Phchi.S1G173700.t1"; gene_id "Phchi.S1G173700"
Phchi.S1	AUGUSTUS	start_codon	11185446	11185448	.	-	0	transcript_id "Phchi.S1G173700.t1"; gene_id "Phchi.S1G173700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12134.t1 is derived from g7810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4261523	4267300	.	-	.	Phchi.S2G021400
Phchi.S2	AUGUSTUS	transcript	4261523	4267300	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	stop_codon	4261520	4261522	.	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4261523	4261604	0.98	-	1	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4261523	4261604	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4261605	4261736	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4261737	4261861	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4261737	4261861	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4261862	4261941	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4261942	4262059	0.99	-	1	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4261942	4262059	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4262060	4262170	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4262171	4262235	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4262171	4262235	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4262236	4262519	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4262520	4262599	1	-	2	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4262520	4262599	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4262600	4262680	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4262681	4262744	0.95	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4262681	4262744	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4262745	4262848	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4262849	4262991	1	-	2	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4262849	4262991	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4262992	4263292	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4263293	4263416	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4263293	4263416	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4263417	4263500	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4263501	4263560	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4263501	4263560	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4263561	4263638	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4263639	4263707	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4263639	4263707	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4263708	4263835	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4263836	4263964	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4263836	4263964	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4263965	4264056	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4264057	4264164	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4264057	4264164	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4264165	4264606	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4264607	4264682	1	-	1	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4264607	4264682	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4264683	4264893	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4264894	4264988	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4264894	4264988	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4264989	4265510	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4265511	4265585	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4265511	4265585	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4265586	4265757	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4265758	4265878	1	-	1	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4265758	4265878	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4265879	4266148	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4266149	4266321	1	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4266149	4266321	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4266322	4266398	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4266399	4266553	1	-	2	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4266399	4266553	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	intron	4266554	4267077	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	CDS	4267078	4267300	0.82	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	exon	4267078	4267300	.	-	.	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
Phchi.S2	AUGUSTUS	start_codon	4267298	4267300	.	-	0	transcript_id "Phchi.S2G021400.t1"; gene_id "Phchi.S2G021400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10492.t1 is derived from g14541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	685492	685853	.	-	.	Phchi.S4G007400
Phchi.S4	AUGUSTUS	transcript	685492	685853	.	-	.	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	stop_codon	685489	685491	.	-	0	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	CDS	685492	685494	0.75	-	0	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	exon	685492	685494	.	-	.	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	intron	685495	685592	.	-	.	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	CDS	685593	685853	0.59	-	0	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	exon	685593	685853	.	-	.	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
Phchi.S4	AUGUSTUS	start_codon	685851	685853	.	-	0	transcript_id "Phchi.S4G007400.t1"; gene_id "Phchi.S4G007400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10807.t1 is derived from g14857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2194359	2196934	.	+	.	Phchi.S4G038900
Phchi.S4	AUGUSTUS	transcript	2194359	2196934	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	start_codon	2194359	2194361	.	+	0	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2194359	2194506	0.95	+	0	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2194359	2194506	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2194507	2194728	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2194729	2196135	1	+	2	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2194729	2196135	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2196136	2196250	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2196251	2196339	1	+	2	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2196251	2196339	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2196340	2196504	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2196505	2196606	1	+	0	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2196505	2196606	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2196607	2196787	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2196788	2196934	1	+	0	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2196788	2196934	.	+	.	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	stop_codon	2196935	2196937	.	+	0	transcript_id "Phchi.S4G038900.t1"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	transcript	2194359	2196934	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	start_codon	2194359	2194361	.	+	0	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2194359	2194506	0.91	+	0	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2194359	2194506	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2194507	2194719	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2194720	2196135	1	+	2	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2194720	2196135	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2196136	2196250	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2196251	2196339	1	+	2	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2196251	2196339	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2196340	2196504	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2196505	2196606	1	+	0	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2196505	2196606	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	intron	2196607	2196787	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	CDS	2196788	2196934	0.98	+	0	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	exon	2196788	2196934	.	+	.	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
Phchi.S4	AUGUSTUS	stop_codon	2196935	2196937	.	+	0	transcript_id "Phchi.S4G038900.t2"; gene_id "Phchi.S4G038900"
# This transcript jg12061.t2 is derived from g7736.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12062.t1 is derived from g7737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1430514	1435336	.	-	.	Phchi.S2G014200
Phchi.S2	AUGUSTUS	transcript	1430514	1435336	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	stop_codon	1430511	1430513	.	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1430514	1430618	0.94	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1430514	1430618	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1430619	1430723	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1430724	1430780	0.94	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1430724	1430780	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1430781	1430938	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1430939	1431082	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1430939	1431082	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1431083	1431377	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1431378	1431542	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1431378	1431542	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1431543	1431623	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1431624	1431833	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1431624	1431833	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1431834	1432867	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1432868	1433117	1	-	1	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1432868	1433117	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1433118	1433386	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1433387	1433514	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1433387	1433514	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1433515	1433660	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1433661	1433756	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1433661	1433756	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1433757	1433915	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1433916	1434459	1	-	1	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1433916	1434459	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1434460	1434737	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1434738	1434799	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1434738	1434799	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1434800	1435086	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1435087	1435152	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1435087	1435152	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	intron	1435153	1435321	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	CDS	1435322	1435336	1	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	exon	1435322	1435336	.	-	.	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
Phchi.S2	AUGUSTUS	start_codon	1435334	1435336	.	-	0	transcript_id "Phchi.S2G014200.t1"; gene_id "Phchi.S2G014200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6116.t1 is derived from g3287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21009766	21010605	.	+	.	Phchi.S1G327500
Phchi.S1	AUGUSTUS	transcript	21009766	21010605	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	start_codon	21009766	21009768	.	+	0	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	CDS	21009766	21009923	0.5	+	0	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	exon	21009766	21009923	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	intron	21009924	21010010	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	CDS	21010011	21010103	0.57	+	1	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	exon	21010011	21010103	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	intron	21010104	21010211	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	CDS	21010212	21010333	0.68	+	1	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	exon	21010212	21010333	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	intron	21010334	21010462	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	CDS	21010463	21010605	0.71	+	2	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	exon	21010463	21010605	.	+	.	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
Phchi.S1	AUGUSTUS	stop_codon	21010606	21010608	.	+	0	transcript_id "Phchi.S1G327500.t1"; gene_id "Phchi.S1G327500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8323.t1 is derived from g5498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35293372	35293749	.	+	.	Phchi.S1G548200
Phchi.S1	AUGUSTUS	transcript	35293372	35293749	.	+	.	transcript_id "Phchi.S1G548200.t1"; gene_id "Phchi.S1G548200"
Phchi.S1	AUGUSTUS	start_codon	35293372	35293374	.	+	0	transcript_id "Phchi.S1G548200.t1"; gene_id "Phchi.S1G548200"
Phchi.S1	AUGUSTUS	CDS	35293372	35293749	0.72	+	0	transcript_id "Phchi.S1G548200.t1"; gene_id "Phchi.S1G548200"
Phchi.S1	AUGUSTUS	exon	35293372	35293749	.	+	.	transcript_id "Phchi.S1G548200.t1"; gene_id "Phchi.S1G548200"
Phchi.S1	AUGUSTUS	stop_codon	35293750	35293752	.	+	0	transcript_id "Phchi.S1G548200.t1"; gene_id "Phchi.S1G548200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2406.t1 is derived from g9326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6500399	6502972	.	-	.	Phchi.S5G101500
Phchi.S5	AUGUSTUS	transcript	6500399	6502972	.	-	.	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	stop_codon	6500396	6500398	.	-	0	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	CDS	6500399	6501776	0.4	-	1	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	exon	6500399	6501776	.	-	.	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	intron	6501777	6501971	.	-	.	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	CDS	6501972	6502039	0.16	-	0	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	exon	6501972	6502039	.	-	.	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	intron	6502040	6502258	.	-	.	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	CDS	6502259	6502972	0.24	-	0	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	exon	6502259	6502972	.	-	.	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
Phchi.S5	AUGUSTUS	start_codon	6502970	6502972	.	-	0	transcript_id "Phchi.S5G101500.t1"; gene_id "Phchi.S5G101500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2081.t1 is derived from g9001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4761501	4764035	.	-	.	Phchi.S5G069000
Phchi.S5	AUGUSTUS	transcript	4761501	4764035	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	stop_codon	4761498	4761500	.	-	0	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	CDS	4761501	4762404	0.92	-	1	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	exon	4761501	4762404	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	intron	4762405	4762491	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	CDS	4762492	4763057	0.99	-	0	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	exon	4762492	4763057	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	intron	4763058	4763167	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	CDS	4763168	4763385	0.99	-	2	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	exon	4763168	4763385	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	intron	4763386	4763483	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	CDS	4763484	4763592	0.98	-	0	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	exon	4763484	4763592	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	intron	4763593	4763702	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	CDS	4763703	4764035	0.68	-	0	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	exon	4763703	4764035	.	-	.	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
Phchi.S5	AUGUSTUS	start_codon	4764033	4764035	.	-	0	transcript_id "Phchi.S5G069000.t1"; gene_id "Phchi.S5G069000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg317.t1 is derived from g10099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2239907	2240926	.	-	.	Phchi.S6G027600
Phchi.S6	AUGUSTUS	transcript	2239907	2240926	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	stop_codon	2239904	2239906	.	-	0	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	CDS	2239907	2240018	0.67	-	1	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	exon	2239907	2240018	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	intron	2240019	2240127	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	CDS	2240128	2240303	0.71	-	0	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	exon	2240128	2240303	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	intron	2240304	2240398	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	CDS	2240399	2240446	0.86	-	0	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	exon	2240399	2240446	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	intron	2240447	2240591	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	CDS	2240592	2240627	0.55	-	0	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	exon	2240592	2240627	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	intron	2240628	2240737	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	CDS	2240738	2240926	0.4	-	0	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	exon	2240738	2240926	.	-	.	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
Phchi.S6	AUGUSTUS	start_codon	2240924	2240926	.	-	0	transcript_id "Phchi.S6G027600.t1"; gene_id "Phchi.S6G027600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14403.t1 is derived from g12871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12672109	12673495	.	-	.	Phchi.S3G172200
Phchi.S3	AUGUSTUS	transcript	12672109	12673495	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	stop_codon	12672106	12672108	.	-	0	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	CDS	12672109	12672562	1	-	1	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	exon	12672109	12672562	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	intron	12672563	12672640	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	CDS	12672641	12672761	1	-	2	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	exon	12672641	12672761	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	intron	12672762	12672854	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	CDS	12672855	12673178	1	-	2	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	exon	12672855	12673178	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	intron	12673179	12673272	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	CDS	12673273	12673495	0.94	-	0	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	exon	12673273	12673495	.	-	.	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
Phchi.S3	AUGUSTUS	start_codon	12673493	12673495	.	-	0	transcript_id "Phchi.S3G172200.t1"; gene_id "Phchi.S3G172200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10265.t1 is derived from g7441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46745730	46747618	.	+	.	Phchi.S1G742400
Phchi.S1	AUGUSTUS	transcript	46745730	46747618	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	start_codon	46745730	46745732	.	+	0	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	CDS	46745730	46745743	1	+	0	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	exon	46745730	46745743	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	intron	46745744	46745904	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	CDS	46745905	46745975	1	+	1	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	exon	46745905	46745975	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	intron	46745976	46746081	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	CDS	46746082	46747072	0.57	+	2	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	exon	46746082	46747072	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	intron	46747073	46747287	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	CDS	46747288	46747299	0.7	+	1	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	exon	46747288	46747299	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	intron	46747300	46747396	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	CDS	46747397	46747415	0.71	+	1	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	exon	46747397	46747415	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	intron	46747416	46747603	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	CDS	46747604	46747618	0.67	+	0	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	exon	46747604	46747618	.	+	.	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
Phchi.S1	AUGUSTUS	stop_codon	46747619	46747621	.	+	0	transcript_id "Phchi.S1G742400.t1"; gene_id "Phchi.S1G742400"
# This transcript jg6760.t2 is derived from g3932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6761.t1 is derived from g3933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24918851	24920266	.	-	.	Phchi.S1G392000
Phchi.S1	AUGUSTUS	transcript	24918851	24920266	.	-	.	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	stop_codon	24918848	24918850	.	-	0	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	CDS	24918851	24919330	1	-	0	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	exon	24918851	24919330	.	-	.	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	intron	24919331	24919468	.	-	.	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	CDS	24919469	24919887	1	-	2	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	exon	24919469	24919887	.	-	.	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	intron	24919888	24919983	.	-	.	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	CDS	24919984	24920266	0.64	-	0	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	exon	24919984	24920266	.	-	.	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
Phchi.S1	AUGUSTUS	start_codon	24920264	24920266	.	-	0	transcript_id "Phchi.S1G392000.t1"; gene_id "Phchi.S1G392000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11631.t1 is derived from g15682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7398034	7398352	.	-	.	Phchi.S4G121300
Phchi.S4	AUGUSTUS	transcript	7398034	7398352	.	-	.	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	stop_codon	7398031	7398033	.	-	0	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	CDS	7398034	7398211	0.4	-	1	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	exon	7398034	7398211	.	-	.	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	intron	7398212	7398308	.	-	.	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	CDS	7398309	7398352	0.91	-	0	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	exon	7398309	7398352	.	-	.	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
Phchi.S4	AUGUSTUS	start_codon	7398350	7398352	.	-	0	transcript_id "Phchi.S4G121300.t1"; gene_id "Phchi.S4G121300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8209.t1 is derived from g5384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34438135	34438958	.	-	.	Phchi.S1G536800
Phchi.S1	AUGUSTUS	transcript	34438135	34438958	.	-	.	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	stop_codon	34438132	34438134	.	-	0	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	CDS	34438135	34438647	1	-	0	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	exon	34438135	34438647	.	-	.	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	intron	34438648	34438730	.	-	.	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	CDS	34438731	34438958	0.93	-	0	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	exon	34438731	34438958	.	-	.	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
Phchi.S1	AUGUSTUS	start_codon	34438956	34438958	.	-	0	transcript_id "Phchi.S1G536800.t1"; gene_id "Phchi.S1G536800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12586.t1 is derived from g8263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36017710	36018530	.	-	.	Phchi.S2G066600
Phchi.S2	AUGUSTUS	transcript	36017710	36018530	.	-	.	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	stop_codon	36017707	36017709	.	-	0	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	CDS	36017710	36018004	0.74	-	1	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	exon	36017710	36018004	.	-	.	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	intron	36018005	36018276	.	-	.	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	CDS	36018277	36018530	0.51	-	0	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	exon	36018277	36018530	.	-	.	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
Phchi.S2	AUGUSTUS	start_codon	36018528	36018530	.	-	0	transcript_id "Phchi.S2G066600.t1"; gene_id "Phchi.S2G066600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3199.t1 is derived from g368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2208605	2210147	.	-	.	Phchi.S1G035800
Phchi.S1	AUGUSTUS	transcript	2208605	2210147	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	stop_codon	2208602	2208604	.	-	0	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	CDS	2208605	2208686	0.66	-	1	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	exon	2208605	2208686	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	intron	2208687	2208876	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	CDS	2208877	2208937	0.56	-	2	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	exon	2208877	2208937	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	intron	2208938	2209005	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	CDS	2209006	2209210	0.66	-	0	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	exon	2209006	2209210	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	intron	2209211	2209304	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	CDS	2209305	2209924	0.91	-	2	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	exon	2209305	2209924	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	intron	2209925	2210008	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	CDS	2210009	2210147	0.68	-	0	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	exon	2210009	2210147	.	-	.	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
Phchi.S1	AUGUSTUS	start_codon	2210145	2210147	.	-	0	transcript_id "Phchi.S1G035800.t1"; gene_id "Phchi.S1G035800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13730.t1 is derived from g12197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8576306	8578472	.	+	.	Phchi.S3G104900
Phchi.S3	AUGUSTUS	transcript	8576306	8578472	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	start_codon	8576306	8576308	.	+	0	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	CDS	8576306	8576329	0.59	+	0	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	exon	8576306	8576329	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	intron	8576330	8576802	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	CDS	8576803	8576866	0.98	+	0	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	exon	8576803	8576866	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	intron	8576867	8576939	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	CDS	8576940	8577115	0.94	+	2	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	exon	8576940	8577115	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	intron	8577116	8577318	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	CDS	8577319	8577381	0.63	+	0	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	exon	8577319	8577381	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	intron	8577382	8577490	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	CDS	8577491	8577896	0.7	+	0	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	exon	8577491	8577896	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	intron	8577897	8578002	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	CDS	8578003	8578472	1	+	2	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	exon	8578003	8578472	.	+	.	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
Phchi.S3	AUGUSTUS	stop_codon	8578473	8578475	.	+	0	transcript_id "Phchi.S3G104900.t1"; gene_id "Phchi.S3G104900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5642.t1 is derived from g2812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18027655	18028429	.	-	.	Phchi.S1G280100
Phchi.S1	AUGUSTUS	transcript	18027655	18028429	.	-	.	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	stop_codon	18027652	18027654	.	-	0	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	CDS	18027655	18027816	1	-	0	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	exon	18027655	18027816	.	-	.	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	intron	18027817	18028093	.	-	.	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	CDS	18028094	18028429	1	-	0	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	exon	18028094	18028429	.	-	.	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
Phchi.S1	AUGUSTUS	start_codon	18028427	18028429	.	-	0	transcript_id "Phchi.S1G280100.t1"; gene_id "Phchi.S1G280100"
# This transcript jg11604.t2 is derived from g15655.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11605.t1 is derived from g15656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7300141	7302303	.	-	.	Phchi.S4G118700
Phchi.S4	AUGUSTUS	transcript	7300141	7302303	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	stop_codon	7300138	7300140	.	-	0	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	CDS	7300141	7300302	1	-	0	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	exon	7300141	7300302	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	intron	7300303	7300390	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	CDS	7300391	7300546	1	-	0	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	exon	7300391	7300546	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	intron	7300547	7300638	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	CDS	7300639	7300924	1	-	1	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	exon	7300639	7300924	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	intron	7300925	7301012	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	CDS	7301013	7301440	1	-	0	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	exon	7301013	7301440	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	intron	7301441	7301518	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	CDS	7301519	7301876	1	-	1	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	exon	7301519	7301876	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	intron	7301877	7302016	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	CDS	7302017	7302303	0.95	-	0	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	exon	7302017	7302303	.	-	.	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
Phchi.S4	AUGUSTUS	start_codon	7302301	7302303	.	-	0	transcript_id "Phchi.S4G118700.t1"; gene_id "Phchi.S4G118700"
# This transcript jg11012.t2 is derived from g15062.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11013.t1 is derived from g15063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3638259	3639584	.	-	.	Phchi.S4G059500
Phchi.S4	AUGUSTUS	transcript	3638259	3639584	.	-	.	transcript_id "Phchi.S4G059500.t1"; gene_id "Phchi.S4G059500"
Phchi.S4	AUGUSTUS	stop_codon	3638256	3638258	.	-	0	transcript_id "Phchi.S4G059500.t1"; gene_id "Phchi.S4G059500"
Phchi.S4	AUGUSTUS	CDS	3638259	3639584	0.89	-	0	transcript_id "Phchi.S4G059500.t1"; gene_id "Phchi.S4G059500"
Phchi.S4	AUGUSTUS	exon	3638259	3639584	.	-	.	transcript_id "Phchi.S4G059500.t1"; gene_id "Phchi.S4G059500"
Phchi.S4	AUGUSTUS	start_codon	3639582	3639584	.	-	0	transcript_id "Phchi.S4G059500.t1"; gene_id "Phchi.S4G059500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15736.t1 is derived from g14206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20962176	20963140	.	+	.	Phchi.S3G305500
Phchi.S3	AUGUSTUS	transcript	20962176	20963140	.	+	.	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	start_codon	20962176	20962178	.	+	0	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	CDS	20962176	20962562	0.94	+	0	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	exon	20962176	20962562	.	+	.	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	intron	20962563	20962650	.	+	.	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	CDS	20962651	20962778	1	+	0	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	exon	20962651	20962778	.	+	.	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	intron	20962779	20963109	.	+	.	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	CDS	20963110	20963140	0.96	+	1	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	exon	20963110	20963140	.	+	.	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
Phchi.S3	AUGUSTUS	stop_codon	20963141	20963143	.	+	0	transcript_id "Phchi.S3G305500.t1"; gene_id "Phchi.S3G305500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg768.t1 is derived from g10550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5427429	5427866	.	-	.	Phchi.S6G072700
Phchi.S6	AUGUSTUS	transcript	5427429	5427866	.	-	.	transcript_id "Phchi.S6G072700.t1"; gene_id "Phchi.S6G072700"
Phchi.S6	AUGUSTUS	stop_codon	5427426	5427428	.	-	0	transcript_id "Phchi.S6G072700.t1"; gene_id "Phchi.S6G072700"
Phchi.S6	AUGUSTUS	CDS	5427429	5427866	0.82	-	0	transcript_id "Phchi.S6G072700.t1"; gene_id "Phchi.S6G072700"
Phchi.S6	AUGUSTUS	exon	5427429	5427866	.	-	.	transcript_id "Phchi.S6G072700.t1"; gene_id "Phchi.S6G072700"
Phchi.S6	AUGUSTUS	start_codon	5427864	5427866	.	-	0	transcript_id "Phchi.S6G072700.t1"; gene_id "Phchi.S6G072700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3613.t1 is derived from g782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4746266	4750167	.	+	.	Phchi.S1G077200
Phchi.S1	AUGUSTUS	transcript	4746266	4750167	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	start_codon	4746266	4746268	.	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4746266	4746343	0.93	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4746266	4746343	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4746344	4746536	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4746537	4746684	0.98	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4746537	4746684	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4746685	4746796	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4746797	4746948	0.99	+	2	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4746797	4746948	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4746949	4747118	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4747119	4747202	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4747119	4747202	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4747203	4747384	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4747385	4747447	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4747385	4747447	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4747448	4747554	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4747555	4747695	0.93	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4747555	4747695	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4747696	4747793	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4747794	4747997	0.99	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4747794	4747997	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4747998	4748096	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4748097	4748207	0.96	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4748097	4748207	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4748208	4748313	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4748314	4748369	0.94	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4748314	4748369	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4748370	4748448	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4748449	4748599	0.97	+	1	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4748449	4748599	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4748600	4748713	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4748714	4748860	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4748714	4748860	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4748861	4748979	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4748980	4749087	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4748980	4749087	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4749088	4749195	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4749196	4749294	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4749196	4749294	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4749295	4749377	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4749378	4749467	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4749378	4749467	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4749468	4749625	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4749626	4749716	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4749626	4749716	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4749717	4749793	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4749794	4749924	1	+	2	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4749794	4749924	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	intron	4749925	4750011	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	CDS	4750012	4750167	1	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	exon	4750012	4750167	.	+	.	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
Phchi.S1	AUGUSTUS	stop_codon	4750168	4750170	.	+	0	transcript_id "Phchi.S1G077200.t1"; gene_id "Phchi.S1G077200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10956.t1 is derived from g15006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3274285	3274809	.	-	.	Phchi.S4G053800
Phchi.S4	AUGUSTUS	transcript	3274285	3274809	.	-	.	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	stop_codon	3274282	3274284	.	-	0	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	CDS	3274285	3274409	1	-	2	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	exon	3274285	3274409	.	-	.	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	intron	3274410	3274688	.	-	.	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	CDS	3274689	3274809	1	-	0	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	exon	3274689	3274809	.	-	.	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
Phchi.S4	AUGUSTUS	start_codon	3274807	3274809	.	-	0	transcript_id "Phchi.S4G053800.t1"; gene_id "Phchi.S4G053800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8117.t1 is derived from g5292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33437679	33438125	.	+	.	Phchi.S1G527600
Phchi.S1	AUGUSTUS	transcript	33437679	33438125	.	+	.	transcript_id "Phchi.S1G527600.t1"; gene_id "Phchi.S1G527600"
Phchi.S1	AUGUSTUS	start_codon	33437679	33437681	.	+	0	transcript_id "Phchi.S1G527600.t1"; gene_id "Phchi.S1G527600"
Phchi.S1	AUGUSTUS	CDS	33437679	33438125	0.71	+	0	transcript_id "Phchi.S1G527600.t1"; gene_id "Phchi.S1G527600"
Phchi.S1	AUGUSTUS	exon	33437679	33438125	.	+	.	transcript_id "Phchi.S1G527600.t1"; gene_id "Phchi.S1G527600"
Phchi.S1	AUGUSTUS	stop_codon	33438126	33438128	.	+	0	transcript_id "Phchi.S1G527600.t1"; gene_id "Phchi.S1G527600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1869.t1 is derived from g8789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3627331	3628567	.	+	.	Phchi.S5G047800
Phchi.S5	AUGUSTUS	transcript	3627331	3628567	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	start_codon	3627331	3627333	.	+	0	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	CDS	3627331	3627960	1	+	0	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	exon	3627331	3627960	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	intron	3627961	3628046	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	CDS	3628047	3628142	1	+	0	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	exon	3628047	3628142	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	intron	3628143	3628237	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	CDS	3628238	3628305	1	+	0	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	exon	3628238	3628305	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	intron	3628306	3628446	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	CDS	3628447	3628567	1	+	1	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	exon	3628447	3628567	.	+	.	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
Phchi.S5	AUGUSTUS	stop_codon	3628568	3628570	.	+	0	transcript_id "Phchi.S5G047800.t1"; gene_id "Phchi.S5G047800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14559.t1 is derived from g13027.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13463986	13469890	.	+	.	Phchi.S3G187800
Phchi.S3	AUGUSTUS	transcript	13463986	13469890	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	start_codon	13463986	13463988	.	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13463986	13464135	0.57	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13463986	13464135	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464136	13464342	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13464343	13464567	0.99	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13464343	13464567	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464568	13464670	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13464671	13464701	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13464671	13464701	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464702	13464788	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13464789	13464973	1	+	2	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13464789	13464973	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464974	13465089	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13465090	13465249	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13465090	13465249	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13465250	13465424	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13465425	13465521	1	+	2	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13465425	13465521	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13465522	13465665	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13465666	13465838	1	+	1	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13465666	13465838	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13465839	13466263	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466264	13466424	1	+	2	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466264	13466424	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13466425	13466514	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466515	13466715	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466515	13466715	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13466716	13466959	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466960	13467049	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466960	13467049	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467050	13467139	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467140	13467220	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467140	13467220	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467221	13467320	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467321	13467464	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467321	13467464	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467465	13467596	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467597	13467679	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467597	13467679	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467680	13467822	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467823	13467964	0.94	+	1	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467823	13467964	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467965	13468073	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468074	13468157	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468074	13468157	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468158	13468328	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468329	13468505	0.99	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468329	13468505	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468506	13468599	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468600	13468687	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468600	13468687	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468688	13468847	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468848	13468925	1	+	2	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468848	13468925	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468926	13469021	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469022	13469088	1	+	2	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469022	13469088	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469089	13469172	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469173	13469275	1	+	1	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469173	13469275	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469276	13469418	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469419	13469535	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469419	13469535	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469536	13469620	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469621	13469677	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469621	13469677	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469678	13469764	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469765	13469890	1	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469765	13469890	.	+	.	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	stop_codon	13469891	13469893	.	+	0	transcript_id "Phchi.S3G187800.t1"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	transcript	13463986	13469890	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	start_codon	13463986	13463988	.	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13463986	13464135	0.56	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13463986	13464135	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464136	13464339	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13464340	13464567	0.96	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13464340	13464567	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464568	13464670	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13464671	13464701	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13464671	13464701	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464702	13464788	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13464789	13464973	0.99	+	2	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13464789	13464973	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13464974	13465089	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13465090	13465249	0.99	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13465090	13465249	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13465250	13465424	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13465425	13465521	1	+	2	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13465425	13465521	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13465522	13465665	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13465666	13465838	1	+	1	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13465666	13465838	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13465839	13466051	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466052	13466138	0.99	+	2	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466052	13466138	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13466139	13466263	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466264	13466424	1	+	2	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466264	13466424	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13466425	13466514	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466515	13466715	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466515	13466715	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13466716	13466959	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13466960	13467049	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13466960	13467049	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467050	13467139	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467140	13467220	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467140	13467220	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467221	13467320	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467321	13467464	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467321	13467464	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467465	13467596	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467597	13467679	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467597	13467679	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467680	13467822	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13467823	13467964	0.89	+	1	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13467823	13467964	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13467965	13468073	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468074	13468157	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468074	13468157	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468158	13468328	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468329	13468505	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468329	13468505	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468506	13468599	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468600	13468687	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468600	13468687	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468688	13468847	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13468848	13468925	1	+	2	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13468848	13468925	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13468926	13469021	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469022	13469088	1	+	2	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469022	13469088	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469089	13469172	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469173	13469275	1	+	1	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469173	13469275	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469276	13469418	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469419	13469535	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469419	13469535	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469536	13469620	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469621	13469677	1	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469621	13469677	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	intron	13469678	13469764	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	CDS	13469765	13469890	0.98	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	exon	13469765	13469890	.	+	.	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
Phchi.S3	AUGUSTUS	stop_codon	13469891	13469893	.	+	0	transcript_id "Phchi.S3G187800.t2"; gene_id "Phchi.S3G187800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13124.t1 is derived from g11589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4240686	4240940	.	+	.	Phchi.S3G044300
Phchi.S3	AUGUSTUS	transcript	4240686	4240940	.	+	.	transcript_id "Phchi.S3G044300.t1"; gene_id "Phchi.S3G044300"
Phchi.S3	AUGUSTUS	start_codon	4240686	4240688	.	+	0	transcript_id "Phchi.S3G044300.t1"; gene_id "Phchi.S3G044300"
Phchi.S3	AUGUSTUS	CDS	4240686	4240940	0.83	+	0	transcript_id "Phchi.S3G044300.t1"; gene_id "Phchi.S3G044300"
Phchi.S3	AUGUSTUS	exon	4240686	4240940	.	+	.	transcript_id "Phchi.S3G044300.t1"; gene_id "Phchi.S3G044300"
Phchi.S3	AUGUSTUS	stop_codon	4240941	4240943	.	+	0	transcript_id "Phchi.S3G044300.t1"; gene_id "Phchi.S3G044300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3624.t1 is derived from g793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4819105	4825651	.	-	.	Phchi.S1G078300
Phchi.S1	AUGUSTUS	transcript	4819105	4825651	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	stop_codon	4819102	4819104	.	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4819105	4819391	1	-	2	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4819105	4819391	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4819392	4819479	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4819480	4819537	1	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4819480	4819537	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4819538	4819640	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4819641	4819816	0.98	-	2	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4819641	4819816	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4819817	4819934	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4819935	4819992	1	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4819935	4819992	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4819993	4820119	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4820120	4820224	1	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4820120	4820224	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4820225	4820320	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4820321	4820378	1	-	1	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4820321	4820378	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4820379	4820521	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4820522	4820605	1	-	1	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4820522	4820605	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4820606	4820811	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4820812	4821000	1	-	1	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4820812	4821000	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4821001	4821154	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4821155	4821208	0.95	-	1	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4821155	4821208	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4821209	4821295	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4821296	4821432	0.42	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4821296	4821432	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4821433	4821683	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4821684	4823215	0.41	-	2	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4821684	4823215	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	intron	4823216	4823304	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	CDS	4823305	4825651	0.54	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	exon	4823305	4825651	.	-	.	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
Phchi.S1	AUGUSTUS	start_codon	4825649	4825651	.	-	0	transcript_id "Phchi.S1G078300.t1"; gene_id "Phchi.S1G078300"
# This transcript jg3711.t2 is derived from g880.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3712.t1 is derived from g881.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5285133	5294023	.	+	.	Phchi.S1G087100
Phchi.S1	AUGUSTUS	transcript	5292572	5294023	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	start_codon	5292572	5292574	.	+	0	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5292572	5292576	1	+	0	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5292572	5292576	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5292577	5292729	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5292730	5293195	1	+	1	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5292730	5293195	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5293196	5293272	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5293273	5293579	1	+	0	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5293273	5293579	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5293580	5293663	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5293664	5293802	0.99	+	2	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5293664	5293802	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5293803	5293911	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5293912	5294023	0.99	+	1	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5293912	5294023	.	+	.	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	stop_codon	5294024	5294026	.	+	0	transcript_id "Phchi.S1G087100.t1"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	transcript	5285133	5294023	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	start_codon	5285133	5285135	.	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285133	5285184	0.32	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285133	5285184	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5285185	5285355	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285356	5285547	0.37	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285356	5285547	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5285548	5285673	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285674	5285696	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285674	5285696	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5285697	5285900	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285901	5286248	0.82	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285901	5286248	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286249	5286368	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286369	5286447	0.91	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286369	5286447	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286448	5286559	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286560	5286595	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286560	5286595	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286596	5286683	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286684	5286820	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286684	5286820	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286821	5286907	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286908	5286952	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286908	5286952	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286953	5287044	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287045	5287096	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287045	5287096	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287097	5287207	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287208	5287392	0.96	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287208	5287392	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287393	5287499	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287500	5287661	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287500	5287661	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287662	5287820	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287821	5287895	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287821	5287895	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287896	5288013	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288014	5288224	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288014	5288224	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288225	5288314	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288315	5288377	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288315	5288377	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288378	5288451	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288452	5288606	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288452	5288606	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288607	5288727	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288728	5288902	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288728	5288902	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288903	5289055	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289056	5289258	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289056	5289258	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289259	5289360	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289361	5289474	0.95	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289361	5289474	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289475	5289562	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289563	5289682	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289563	5289682	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289683	5289795	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289796	5289843	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289796	5289843	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289844	5289926	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289927	5290055	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289927	5290055	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5290056	5290558	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5290559	5291413	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5290559	5291413	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5291414	5291781	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5291782	5292440	0.9	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5291782	5292440	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5292441	5292729	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5292730	5293195	1	+	1	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5292730	5293195	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5293196	5293272	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5293273	5293579	1	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5293273	5293579	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5293580	5293663	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5293664	5293802	1	+	2	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5293664	5293802	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5293803	5293911	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5293912	5294023	0.98	+	1	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5293912	5294023	.	+	.	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	stop_codon	5294024	5294026	.	+	0	transcript_id "Phchi.S1G087100.t2"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	transcript	5285133	5292453	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	start_codon	5285133	5285135	.	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285133	5285184	0.33	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285133	5285184	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5285185	5285355	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285356	5285547	0.34	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285356	5285547	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5285548	5285673	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285674	5285696	0.96	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285674	5285696	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5285697	5285900	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5285901	5286248	0.71	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5285901	5286248	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286249	5286368	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286369	5286447	0.93	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286369	5286447	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286448	5286559	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286560	5286595	1	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286560	5286595	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286596	5286683	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286684	5286820	1	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286684	5286820	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286821	5286907	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5286908	5286952	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5286908	5286952	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5286953	5287044	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287045	5287096	0.99	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287045	5287096	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287097	5287207	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287208	5287392	0.97	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287208	5287392	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287393	5287499	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287500	5287661	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287500	5287661	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287662	5287820	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5287821	5287895	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5287821	5287895	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5287896	5288013	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288014	5288224	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288014	5288224	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288225	5288314	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288315	5288377	1	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288315	5288377	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288378	5288451	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288452	5288606	1	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288452	5288606	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288607	5288727	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5288728	5288902	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5288728	5288902	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5288903	5289055	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289056	5289258	0.99	+	2	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289056	5289258	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289259	5289360	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289361	5289474	0.87	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289361	5289474	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289475	5289562	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289563	5289682	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289563	5289682	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289683	5289795	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289796	5289843	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289796	5289843	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5289844	5289926	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5289927	5290055	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5289927	5290055	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5290056	5290558	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5290559	5291413	1	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5290559	5291413	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	intron	5291414	5291781	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	CDS	5291782	5292453	0.94	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	exon	5291782	5292453	.	+	.	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
Phchi.S1	AUGUSTUS	stop_codon	5292454	5292456	.	+	0	transcript_id "Phchi.S1G087100.t3"; gene_id "Phchi.S1G087100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11954.t1 is derived from g7629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	181702	183291	.	-	.	Phchi.S2G003400
Phchi.S2	AUGUSTUS	transcript	181702	183291	.	-	.	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	stop_codon	181699	181701	.	-	0	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	CDS	181702	181819	0.8	-	1	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	exon	181702	181819	.	-	.	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	intron	181820	181922	.	-	.	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	CDS	181923	182919	0.8	-	2	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	exon	181923	182919	.	-	.	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	intron	182920	182993	.	-	.	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	CDS	182994	183291	1	-	0	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	exon	182994	183291	.	-	.	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
Phchi.S2	AUGUSTUS	start_codon	183289	183291	.	-	0	transcript_id "Phchi.S2G003400.t1"; gene_id "Phchi.S2G003400"
# This transcript jg10764.t2 is derived from g14814.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10765.t1 is derived from g14815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2001565	2005737	.	+	.	Phchi.S4G034700
Phchi.S4	AUGUSTUS	transcript	2001565	2005737	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	start_codon	2001565	2001567	.	+	0	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	CDS	2001565	2001772	0.92	+	0	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	exon	2001565	2001772	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	intron	2001773	2002118	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	CDS	2002119	2002613	0.99	+	2	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	exon	2002119	2002613	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	intron	2002614	2002796	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	CDS	2002797	2003110	0.64	+	2	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	exon	2002797	2003110	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	intron	2003111	2003190	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	CDS	2003191	2005737	0.76	+	0	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	exon	2003191	2005737	.	+	.	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
Phchi.S4	AUGUSTUS	stop_codon	2005738	2005740	.	+	0	transcript_id "Phchi.S4G034700.t1"; gene_id "Phchi.S4G034700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6047.t1 is derived from g3218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20616837	20617064	.	-	.	Phchi.S1G320600
Phchi.S1	AUGUSTUS	transcript	20616837	20617064	.	-	.	transcript_id "Phchi.S1G320600.t1"; gene_id "Phchi.S1G320600"
Phchi.S1	AUGUSTUS	stop_codon	20616834	20616836	.	-	0	transcript_id "Phchi.S1G320600.t1"; gene_id "Phchi.S1G320600"
Phchi.S1	AUGUSTUS	CDS	20616837	20617064	0.41	-	0	transcript_id "Phchi.S1G320600.t1"; gene_id "Phchi.S1G320600"
Phchi.S1	AUGUSTUS	exon	20616837	20617064	.	-	.	transcript_id "Phchi.S1G320600.t1"; gene_id "Phchi.S1G320600"
Phchi.S1	AUGUSTUS	start_codon	20617062	20617064	.	-	0	transcript_id "Phchi.S1G320600.t1"; gene_id "Phchi.S1G320600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13125.t1 is derived from g11590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4249419	4254429	.	-	.	Phchi.S3G044400
Phchi.S3	AUGUSTUS	transcript	4249419	4254429	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	stop_codon	4249416	4249418	.	-	0	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4249419	4249454	0.83	-	0	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4249419	4249454	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	intron	4249455	4249571	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4249572	4249602	0.48	-	1	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4249572	4249602	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	intron	4249603	4249852	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4249853	4251043	0.82	-	1	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4249853	4251043	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	intron	4251044	4251195	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4251196	4253014	0.99	-	2	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4251196	4253014	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	intron	4253015	4253103	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4253104	4253993	0.59	-	1	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4253104	4253993	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	intron	4253994	4254165	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4254166	4254257	0.38	-	0	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4254166	4254257	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	intron	4254258	4254360	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	CDS	4254361	4254429	0.52	-	0	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	exon	4254361	4254429	.	-	.	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
Phchi.S3	AUGUSTUS	start_codon	4254427	4254429	.	-	0	transcript_id "Phchi.S3G044400.t1"; gene_id "Phchi.S3G044400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8018.t1 is derived from g5193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32488779	32489342	.	+	.	Phchi.S1G517700
Phchi.S1	AUGUSTUS	transcript	32488779	32489342	.	+	.	transcript_id "Phchi.S1G517700.t1"; gene_id "Phchi.S1G517700"
Phchi.S1	AUGUSTUS	start_codon	32488779	32488781	.	+	0	transcript_id "Phchi.S1G517700.t1"; gene_id "Phchi.S1G517700"
Phchi.S1	AUGUSTUS	CDS	32488779	32489342	0.79	+	0	transcript_id "Phchi.S1G517700.t1"; gene_id "Phchi.S1G517700"
Phchi.S1	AUGUSTUS	exon	32488779	32489342	.	+	.	transcript_id "Phchi.S1G517700.t1"; gene_id "Phchi.S1G517700"
Phchi.S1	AUGUSTUS	stop_codon	32489343	32489345	.	+	0	transcript_id "Phchi.S1G517700.t1"; gene_id "Phchi.S1G517700"
# This transcript jg11403.t2 is derived from g15454.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11404.t1 is derived from g15453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6180588	6181487	.	+	.	Phchi.S4G098500
Phchi.S4	AUGUSTUS	transcript	6180588	6181487	.	+	.	transcript_id "Phchi.S4G098500.t1"; gene_id "Phchi.S4G098500"
Phchi.S4	AUGUSTUS	start_codon	6180588	6180590	.	+	0	transcript_id "Phchi.S4G098500.t1"; gene_id "Phchi.S4G098500"
Phchi.S4	AUGUSTUS	CDS	6180588	6181487	0.73	+	0	transcript_id "Phchi.S4G098500.t1"; gene_id "Phchi.S4G098500"
Phchi.S4	AUGUSTUS	exon	6180588	6181487	.	+	.	transcript_id "Phchi.S4G098500.t1"; gene_id "Phchi.S4G098500"
Phchi.S4	AUGUSTUS	stop_codon	6181488	6181490	.	+	0	transcript_id "Phchi.S4G098500.t1"; gene_id "Phchi.S4G098500"
# This transcript jg4423.t2 is derived from g1592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4424.t1 is derived from g1593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10432740	10436820	.	+	.	Phchi.S1G158300
Phchi.S1	AUGUSTUS	transcript	10432740	10436820	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	start_codon	10432740	10432742	.	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10432740	10432825	0.87	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10432740	10432825	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10432826	10433320	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10433321	10433602	0.97	+	1	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10433321	10433602	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10433603	10433694	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10433695	10433815	0.99	+	1	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10433695	10433815	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10433816	10433925	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10433926	10434000	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10433926	10434000	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10434001	10434085	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10434086	10434343	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10434086	10434343	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10434344	10434427	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10434428	10434493	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10434428	10434493	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10434494	10434628	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10434629	10434724	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10434629	10434724	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10434725	10434807	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10434808	10434879	0.97	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10434808	10434879	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10434880	10435005	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10435006	10435089	0.98	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10435006	10435089	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10435090	10435185	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10435186	10435284	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10435186	10435284	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10435285	10435391	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10435392	10435439	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10435392	10435439	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10435440	10435521	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10435522	10435575	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10435522	10435575	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10435576	10435654	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10435655	10435753	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10435655	10435753	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10435754	10435836	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10435837	10435926	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10435837	10435926	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10435927	10435999	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10436000	10436077	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10436000	10436077	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10436078	10436156	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10436157	10436231	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10436157	10436231	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10436232	10436315	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10436316	10436406	1	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10436316	10436406	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10436407	10436499	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10436500	10436628	1	+	2	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10436500	10436628	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	intron	10436629	10436734	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	CDS	10436735	10436820	1	+	2	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	exon	10436735	10436820	.	+	.	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
Phchi.S1	AUGUSTUS	stop_codon	10436821	10436823	.	+	0	transcript_id "Phchi.S1G158300.t1"; gene_id "Phchi.S1G158300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1772.t1 is derived from g8692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2947101	2947940	.	+	.	Phchi.S5G038100
Phchi.S5	AUGUSTUS	transcript	2947101	2947940	.	+	.	transcript_id "Phchi.S5G038100.t1"; gene_id "Phchi.S5G038100"
Phchi.S5	AUGUSTUS	start_codon	2947101	2947103	.	+	0	transcript_id "Phchi.S5G038100.t1"; gene_id "Phchi.S5G038100"
Phchi.S5	AUGUSTUS	CDS	2947101	2947940	0.61	+	0	transcript_id "Phchi.S5G038100.t1"; gene_id "Phchi.S5G038100"
Phchi.S5	AUGUSTUS	exon	2947101	2947940	.	+	.	transcript_id "Phchi.S5G038100.t1"; gene_id "Phchi.S5G038100"
Phchi.S5	AUGUSTUS	stop_codon	2947941	2947943	.	+	0	transcript_id "Phchi.S5G038100.t1"; gene_id "Phchi.S5G038100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15682.t1 is derived from g14151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20637241	20638620	.	+	.	Phchi.S3G300100
Phchi.S3	AUGUSTUS	transcript	20637241	20638620	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	start_codon	20637241	20637243	.	+	0	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	CDS	20637241	20637547	0.9	+	0	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	exon	20637241	20637547	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	intron	20637548	20637717	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	CDS	20637718	20637947	0.99	+	2	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	exon	20637718	20637947	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	intron	20637948	20638086	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	CDS	20638087	20638364	0.87	+	0	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	exon	20638087	20638364	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	intron	20638365	20638475	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	CDS	20638476	20638620	0.74	+	1	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	exon	20638476	20638620	.	+	.	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
Phchi.S3	AUGUSTUS	stop_codon	20638621	20638623	.	+	0	transcript_id "Phchi.S3G300100.t1"; gene_id "Phchi.S3G300100"
# This transcript jg2272.t2 is derived from g9192.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2273.t1 is derived from g9193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5807384	5808841	.	-	.	Phchi.S5G088200
Phchi.S5	AUGUSTUS	transcript	5807384	5808841	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	stop_codon	5807381	5807383	.	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5807384	5807743	0.42	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5807384	5807743	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5807744	5807823	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5807824	5807964	1	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5807824	5807964	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5807965	5808064	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5808065	5808139	1	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5808065	5808139	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5808140	5808464	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5808465	5808656	1	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5808465	5808656	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5808657	5808838	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5808839	5808841	0.82	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5808839	5808841	.	-	.	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	start_codon	5808839	5808841	.	-	0	transcript_id "Phchi.S5G088200.t1"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	transcript	5807384	5808756	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	stop_codon	5807381	5807383	.	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5807384	5807743	0.44	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5807384	5807743	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5807744	5807823	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5807824	5807964	1	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5807824	5807964	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5807965	5808064	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5808065	5808139	1	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5808065	5808139	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5808140	5808464	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5808465	5808656	1	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5808465	5808656	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	intron	5808657	5808741	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	CDS	5808742	5808756	0.74	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	exon	5808742	5808756	.	-	.	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
Phchi.S5	AUGUSTUS	start_codon	5808754	5808756	.	-	0	transcript_id "Phchi.S5G088200.t2"; gene_id "Phchi.S5G088200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8517.t1 is derived from g5692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36407345	36408722	.	+	.	Phchi.S1G567600
Phchi.S1	AUGUSTUS	transcript	36407345	36408722	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	start_codon	36407345	36407347	.	+	0	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	CDS	36407345	36407680	0.99	+	0	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	exon	36407345	36407680	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	intron	36407681	36407763	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	CDS	36407764	36407985	0.41	+	0	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	exon	36407764	36407985	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	intron	36407986	36408065	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	CDS	36408066	36408234	1	+	0	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	exon	36408066	36408234	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	intron	36408235	36408324	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	CDS	36408325	36408722	1	+	2	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	exon	36408325	36408722	.	+	.	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
Phchi.S1	AUGUSTUS	stop_codon	36408723	36408725	.	+	0	transcript_id "Phchi.S1G567600.t1"; gene_id "Phchi.S1G567600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9580.t1 is derived from g6756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42751010	42752996	.	+	.	Phchi.S1G673900
Phchi.S1	AUGUSTUS	transcript	42751010	42752996	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	start_codon	42751010	42751012	.	+	0	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42751010	42751104	0.6	+	0	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42751010	42751104	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42751105	42751220	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42751221	42751272	0.98	+	1	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42751221	42751272	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42751273	42751356	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42751357	42751661	0.99	+	0	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42751357	42751661	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42751662	42751774	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42751775	42751869	0.81	+	1	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42751775	42751869	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42751870	42751967	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42751968	42752037	1	+	2	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42751968	42752037	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42752038	42752119	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42752120	42752205	1	+	1	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42752120	42752205	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42752206	42752296	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42752297	42752339	1	+	2	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42752297	42752339	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42752340	42752414	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42752415	42752430	0.36	+	1	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42752415	42752430	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42752431	42752627	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42752628	42752723	1	+	0	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42752628	42752723	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	intron	42752724	42752804	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	CDS	42752805	42752996	0.99	+	0	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	exon	42752805	42752996	.	+	.	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
Phchi.S1	AUGUSTUS	stop_codon	42752997	42752999	.	+	0	transcript_id "Phchi.S1G673900.t1"; gene_id "Phchi.S1G673900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7531.t1 is derived from g4705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29917342	29920184	.	+	.	Phchi.S1G469000
Phchi.S1	AUGUSTUS	transcript	29917342	29919940	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	start_codon	29917342	29917344	.	+	0	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29917342	29918514	0.38	+	0	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29917342	29918514	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	intron	29918515	29918654	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29918655	29918952	0.82	+	0	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29918655	29918952	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	intron	29918953	29919132	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29919133	29919734	0.92	+	2	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29919133	29919734	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	intron	29919735	29919901	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29919902	29919940	0.61	+	0	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29919902	29919940	.	+	.	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	stop_codon	29919941	29919943	.	+	0	transcript_id "Phchi.S1G469000.t1"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	transcript	29917342	29920184	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	start_codon	29917342	29917344	.	+	0	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29917342	29918514	0.31	+	0	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29917342	29918514	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	intron	29918515	29918654	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29918655	29918952	0.84	+	0	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29918655	29918952	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	intron	29918953	29919132	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29919133	29919988	0.34	+	2	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29919133	29919988	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	intron	29919989	29920135	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	CDS	29920136	29920184	0.25	+	1	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	exon	29920136	29920184	.	+	.	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
Phchi.S1	AUGUSTUS	stop_codon	29920185	29920187	.	+	0	transcript_id "Phchi.S1G469000.t2"; gene_id "Phchi.S1G469000"
# This transcript jg3632.t2 is derived from g801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3633.t1 is derived from g802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4864549	4866592	.	-	.	Phchi.S1G079200
Phchi.S1	AUGUSTUS	transcript	4864549	4866592	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	stop_codon	4864546	4864548	.	-	0	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	CDS	4864549	4864858	1	-	1	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	exon	4864549	4864858	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	intron	4864859	4864958	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	CDS	4864959	4865164	0.76	-	0	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	exon	4864959	4865164	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	intron	4865165	4865283	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	CDS	4865284	4865793	0.7	-	0	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	exon	4865284	4865793	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	intron	4865794	4865941	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	CDS	4865942	4866592	0.93	-	0	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	exon	4865942	4866592	.	-	.	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
Phchi.S1	AUGUSTUS	start_codon	4866590	4866592	.	-	0	transcript_id "Phchi.S1G079200.t1"; gene_id "Phchi.S1G079200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12090.t1 is derived from g7765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2188255	2188930	.	-	.	Phchi.S2G017000
Phchi.S2	AUGUSTUS	transcript	2188255	2188930	.	-	.	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	stop_codon	2188252	2188254	.	-	0	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	CDS	2188255	2188291	0.46	-	1	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	exon	2188255	2188291	.	-	.	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	intron	2188292	2188385	.	-	.	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	CDS	2188386	2188397	0.46	-	1	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	exon	2188386	2188397	.	-	.	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	intron	2188398	2188523	.	-	.	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	CDS	2188524	2188930	0.33	-	0	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	exon	2188524	2188930	.	-	.	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
Phchi.S2	AUGUSTUS	start_codon	2188928	2188930	.	-	0	transcript_id "Phchi.S2G017000.t1"; gene_id "Phchi.S2G017000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11485.t1 is derived from g15535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6599140	6600537	.	+	.	Phchi.S4G106700
Phchi.S4	AUGUSTUS	transcript	6599140	6600537	.	+	.	transcript_id "Phchi.S4G106700.t1"; gene_id "Phchi.S4G106700"
Phchi.S4	AUGUSTUS	start_codon	6599140	6599142	.	+	0	transcript_id "Phchi.S4G106700.t1"; gene_id "Phchi.S4G106700"
Phchi.S4	AUGUSTUS	CDS	6599140	6600537	0.74	+	0	transcript_id "Phchi.S4G106700.t1"; gene_id "Phchi.S4G106700"
Phchi.S4	AUGUSTUS	exon	6599140	6600537	.	+	.	transcript_id "Phchi.S4G106700.t1"; gene_id "Phchi.S4G106700"
Phchi.S4	AUGUSTUS	stop_codon	6600538	6600540	.	+	0	transcript_id "Phchi.S4G106700.t1"; gene_id "Phchi.S4G106700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7355.t1 is derived from g4527.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28746342	28748587	.	-	.	Phchi.S1G451400
Phchi.S1	AUGUSTUS	transcript	28746342	28748587	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	stop_codon	28746339	28746341	.	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746342	28746467	0.97	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746342	28746467	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28746468	28746547	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746548	28746667	1	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746548	28746667	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28746668	28746797	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746798	28746863	1	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746798	28746863	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28746864	28746957	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746958	28747006	1	-	1	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746958	28747006	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747007	28747107	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747108	28747245	1	-	1	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747108	28747245	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747246	28747395	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747396	28747496	1	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747396	28747496	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747497	28747701	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747702	28747727	0.63	-	2	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747702	28747727	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747728	28747817	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747818	28747836	0.63	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747818	28747836	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747837	28747930	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747931	28748068	1	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747931	28748068	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28748069	28748200	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28748201	28748295	1	-	2	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28748201	28748295	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28748296	28748424	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28748425	28748587	0.78	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28748425	28748587	.	-	.	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	start_codon	28748585	28748587	.	-	0	transcript_id "Phchi.S1G451400.t1"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	transcript	28746342	28748587	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	stop_codon	28746339	28746341	.	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746342	28746467	0.96	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746342	28746467	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28746468	28746547	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746548	28746667	1	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746548	28746667	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28746668	28746797	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746798	28746863	1	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746798	28746863	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28746864	28746957	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28746958	28747006	1	-	1	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28746958	28747006	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747007	28747107	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747108	28747245	1	-	1	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747108	28747245	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747246	28747395	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747396	28747496	1	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747396	28747496	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747497	28747701	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747702	28747812	0.61	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747702	28747812	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28747813	28747930	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28747931	28748068	0.78	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28747931	28748068	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28748069	28748200	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28748201	28748295	1	-	2	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28748201	28748295	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	intron	28748296	28748424	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	CDS	28748425	28748587	0.78	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	exon	28748425	28748587	.	-	.	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
Phchi.S1	AUGUSTUS	start_codon	28748585	28748587	.	-	0	transcript_id "Phchi.S1G451400.t2"; gene_id "Phchi.S1G451400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15045.t1 is derived from g13513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16734211	16737572	.	+	.	Phchi.S3G236400
Phchi.S3	AUGUSTUS	transcript	16734211	16737572	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	start_codon	16734211	16734213	.	+	0	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16734211	16734364	0.5	+	0	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16734211	16734364	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	intron	16734365	16734445	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16734446	16734525	1	+	2	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16734446	16734525	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	intron	16734526	16734614	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16734615	16734747	1	+	0	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16734615	16734747	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	intron	16734748	16734822	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16734823	16734917	1	+	2	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16734823	16734917	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	intron	16734918	16735006	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16735007	16735693	0.28	+	0	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16735007	16735693	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	intron	16735694	16735872	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16735873	16737128	0.71	+	0	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16735873	16737128	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	intron	16737129	16737448	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	CDS	16737449	16737572	0.87	+	1	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	exon	16737449	16737572	.	+	.	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
Phchi.S3	AUGUSTUS	stop_codon	16737573	16737575	.	+	0	transcript_id "Phchi.S3G236400.t1"; gene_id "Phchi.S3G236400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11532.t1 is derived from g15582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6943914	6946136	.	-	.	Phchi.S4G111400
Phchi.S4	AUGUSTUS	transcript	6943914	6946136	.	-	.	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	stop_codon	6943911	6943913	.	-	0	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	CDS	6943914	6944293	1	-	2	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	exon	6943914	6944293	.	-	.	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	intron	6944294	6944382	.	-	.	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	CDS	6944383	6945395	0.97	-	1	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	exon	6944383	6945395	.	-	.	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	intron	6945396	6945507	.	-	.	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	CDS	6945508	6946136	0.82	-	0	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	exon	6945508	6946136	.	-	.	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
Phchi.S4	AUGUSTUS	start_codon	6946134	6946136	.	-	0	transcript_id "Phchi.S4G111400.t1"; gene_id "Phchi.S4G111400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7437.t1 is derived from g4609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29115407	29115914	.	+	.	Phchi.S1G459600
Phchi.S1	AUGUSTUS	transcript	29115407	29115914	.	+	.	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	start_codon	29115407	29115409	.	+	0	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	CDS	29115407	29115526	0.95	+	0	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	exon	29115407	29115526	.	+	.	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	intron	29115527	29115680	.	+	.	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	CDS	29115681	29115914	1	+	0	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	exon	29115681	29115914	.	+	.	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
Phchi.S1	AUGUSTUS	stop_codon	29115915	29115917	.	+	0	transcript_id "Phchi.S1G459600.t1"; gene_id "Phchi.S1G459600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7083.t1 is derived from g4255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26803721	26806106	.	-	.	Phchi.S1G424200
Phchi.S1	AUGUSTUS	transcript	26803721	26806106	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	stop_codon	26803718	26803720	.	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26803721	26803734	1	-	2	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26803721	26803734	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26803735	26803921	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26803922	26803976	0.95	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26803922	26803976	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26803977	26804165	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26804166	26804242	0.81	-	2	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26804166	26804242	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26804243	26804364	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26804365	26804449	0.53	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26804365	26804449	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26804450	26804594	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26804595	26804663	1	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26804595	26804663	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26804664	26804743	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26804744	26804948	1	-	1	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26804744	26804948	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26804949	26805041	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26805042	26805124	1	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26805042	26805124	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26805125	26805249	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26805250	26805389	1	-	2	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26805250	26805389	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26805390	26805768	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26805769	26805855	0.87	-	2	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26805769	26805855	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	intron	26805856	26806030	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	CDS	26806031	26806106	0.59	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	exon	26806031	26806106	.	-	.	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
Phchi.S1	AUGUSTUS	start_codon	26806104	26806106	.	-	0	transcript_id "Phchi.S1G424200.t1"; gene_id "Phchi.S1G424200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3210.t1 is derived from g379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2260825	2263201	.	+	.	Phchi.S1G036900
Phchi.S1	AUGUSTUS	transcript	2260825	2263201	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	start_codon	2260825	2260827	.	+	0	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	CDS	2260825	2261232	0.8	+	0	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	exon	2260825	2261232	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	intron	2261233	2261321	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	CDS	2261322	2261596	0.28	+	0	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	exon	2261322	2261596	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	intron	2261597	2261712	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	CDS	2261713	2262004	0.29	+	1	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	exon	2261713	2262004	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	intron	2262005	2262123	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	CDS	2262124	2262439	0.3	+	0	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	exon	2262124	2262439	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	intron	2262440	2262577	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	CDS	2262578	2262818	0.98	+	2	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	exon	2262578	2262818	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	intron	2262819	2262906	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	CDS	2262907	2263201	0.89	+	1	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	exon	2262907	2263201	.	+	.	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
Phchi.S1	AUGUSTUS	stop_codon	2263202	2263204	.	+	0	transcript_id "Phchi.S1G036900.t1"; gene_id "Phchi.S1G036900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9030.t1 is derived from g6205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39220044	39221396	.	-	.	Phchi.S1G618900
Phchi.S1	AUGUSTUS	transcript	39220044	39221396	.	-	.	transcript_id "Phchi.S1G618900.t1"; gene_id "Phchi.S1G618900"
Phchi.S1	AUGUSTUS	stop_codon	39220041	39220043	.	-	0	transcript_id "Phchi.S1G618900.t1"; gene_id "Phchi.S1G618900"
Phchi.S1	AUGUSTUS	CDS	39220044	39221396	0.7	-	0	transcript_id "Phchi.S1G618900.t1"; gene_id "Phchi.S1G618900"
Phchi.S1	AUGUSTUS	exon	39220044	39221396	.	-	.	transcript_id "Phchi.S1G618900.t1"; gene_id "Phchi.S1G618900"
Phchi.S1	AUGUSTUS	start_codon	39221394	39221396	.	-	0	transcript_id "Phchi.S1G618900.t1"; gene_id "Phchi.S1G618900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13313.t1 is derived from g11779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5939310	5942409	.	+	.	Phchi.S3G063200
Phchi.S3	AUGUSTUS	transcript	5939310	5942409	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	start_codon	5939310	5939312	.	+	0	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5939310	5940423	0.32	+	0	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5939310	5940423	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	intron	5940424	5940522	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5940523	5940871	0.99	+	2	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5940523	5940871	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	intron	5940872	5941008	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5941009	5941107	1	+	1	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5941009	5941107	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	intron	5941108	5941208	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5941209	5941436	1	+	1	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5941209	5941436	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	intron	5941437	5941525	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5941526	5941664	0.98	+	1	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5941526	5941664	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	intron	5941665	5941778	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5941779	5942024	1	+	0	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5941779	5942024	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	intron	5942025	5942127	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	CDS	5942128	5942409	1	+	0	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	exon	5942128	5942409	.	+	.	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
Phchi.S3	AUGUSTUS	stop_codon	5942410	5942412	.	+	0	transcript_id "Phchi.S3G063200.t1"; gene_id "Phchi.S3G063200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1567.t1 is derived from g8486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1793382	1795046	.	+	.	Phchi.S5G017600
Phchi.S5	AUGUSTUS	transcript	1793382	1795046	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	start_codon	1793382	1793384	.	+	0	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1793382	1793657	0.99	+	0	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1793382	1793657	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	intron	1793658	1793829	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1793830	1793908	1	+	0	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1793830	1793908	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	intron	1793909	1793992	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1793993	1794106	1	+	2	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1793993	1794106	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	intron	1794107	1794204	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1794205	1794317	1	+	2	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1794205	1794317	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	intron	1794318	1794425	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1794426	1794533	1	+	0	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1794426	1794533	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	intron	1794534	1794630	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1794631	1794755	1	+	0	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1794631	1794755	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	intron	1794756	1794991	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	CDS	1794992	1795046	1	+	1	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	exon	1794992	1795046	.	+	.	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
Phchi.S5	AUGUSTUS	stop_codon	1795047	1795049	.	+	0	transcript_id "Phchi.S5G017600.t1"; gene_id "Phchi.S5G017600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13030.t1 is derived from g11495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3746354	3747175	.	+	.	Phchi.S3G034900
Phchi.S3	AUGUSTUS	transcript	3746354	3747175	.	+	.	transcript_id "Phchi.S3G034900.t1"; gene_id "Phchi.S3G034900"
Phchi.S3	AUGUSTUS	start_codon	3746354	3746356	.	+	0	transcript_id "Phchi.S3G034900.t1"; gene_id "Phchi.S3G034900"
Phchi.S3	AUGUSTUS	CDS	3746354	3747175	0.95	+	0	transcript_id "Phchi.S3G034900.t1"; gene_id "Phchi.S3G034900"
Phchi.S3	AUGUSTUS	exon	3746354	3747175	.	+	.	transcript_id "Phchi.S3G034900.t1"; gene_id "Phchi.S3G034900"
Phchi.S3	AUGUSTUS	stop_codon	3747176	3747178	.	+	0	transcript_id "Phchi.S3G034900.t1"; gene_id "Phchi.S3G034900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3249.t1 is derived from g418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2511504	2514058	.	+	.	Phchi.S1G040800
Phchi.S1	AUGUSTUS	transcript	2511504	2514058	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	start_codon	2511504	2511506	.	+	0	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	CDS	2511504	2511742	0.76	+	0	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	exon	2511504	2511742	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	intron	2511743	2512140	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	CDS	2512141	2512313	1	+	1	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	exon	2512141	2512313	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	intron	2512314	2512585	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	CDS	2512586	2512688	1	+	2	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	exon	2512586	2512688	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	intron	2512689	2512827	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	CDS	2512828	2513136	1	+	1	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	exon	2512828	2513136	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	intron	2513137	2513221	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	CDS	2513222	2513697	1	+	1	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	exon	2513222	2513697	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	intron	2513698	2513840	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	CDS	2513841	2514058	1	+	2	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	exon	2513841	2514058	.	+	.	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
Phchi.S1	AUGUSTUS	stop_codon	2514059	2514061	.	+	0	transcript_id "Phchi.S1G040800.t1"; gene_id "Phchi.S1G040800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg354.t1 is derived from g10136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2583806	2584546	.	+	.	Phchi.S6G031300
Phchi.S6	AUGUSTUS	transcript	2583806	2584546	.	+	.	transcript_id "Phchi.S6G031300.t1"; gene_id "Phchi.S6G031300"
Phchi.S6	AUGUSTUS	start_codon	2583806	2583808	.	+	0	transcript_id "Phchi.S6G031300.t1"; gene_id "Phchi.S6G031300"
Phchi.S6	AUGUSTUS	CDS	2583806	2584546	1	+	0	transcript_id "Phchi.S6G031300.t1"; gene_id "Phchi.S6G031300"
Phchi.S6	AUGUSTUS	exon	2583806	2584546	.	+	.	transcript_id "Phchi.S6G031300.t1"; gene_id "Phchi.S6G031300"
Phchi.S6	AUGUSTUS	stop_codon	2584547	2584549	.	+	0	transcript_id "Phchi.S6G031300.t1"; gene_id "Phchi.S6G031300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12291.t1 is derived from g7967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8856385	8862214	.	+	.	Phchi.S2G037100
Phchi.S2	AUGUSTUS	transcript	8856385	8862214	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	start_codon	8856385	8856387	.	+	0	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8856385	8856646	0.38	+	0	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8856385	8856646	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8856647	8856862	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8856863	8857421	1	+	2	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8856863	8857421	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8857422	8857763	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8857764	8858314	0.99	+	1	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8857764	8858314	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858315	8858427	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8858428	8858619	0.99	+	2	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8858428	8858619	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858620	8858769	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8858770	8858828	0.95	+	2	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8858770	8858828	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858829	8859004	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859005	8859150	0.58	+	0	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859005	8859150	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8859151	8859235	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859236	8859353	1	+	1	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859236	8859353	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8859354	8859534	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859535	8861337	0.97	+	0	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859535	8861337	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8861338	8861499	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8861500	8861770	0.59	+	0	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8861500	8861770	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8861771	8861954	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8861955	8862214	0.38	+	2	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8861955	8862214	.	+	.	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	stop_codon	8862215	8862217	.	+	0	transcript_id "Phchi.S2G037100.t1"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	transcript	8856385	8862214	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	start_codon	8856385	8856387	.	+	0	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8856385	8856646	0.46	+	0	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8856385	8856646	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8856647	8856862	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8856863	8857421	1	+	2	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8856863	8857421	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8857422	8857763	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8857764	8858314	0.99	+	1	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8857764	8858314	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858315	8858427	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8858428	8858616	1	+	2	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8858428	8858616	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858617	8858769	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8858770	8858828	0.99	+	2	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8858770	8858828	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858829	8859004	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859005	8859150	0.53	+	0	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859005	8859150	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8859151	8859235	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859236	8859353	1	+	1	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859236	8859353	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8859354	8859534	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859535	8861337	0.98	+	0	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859535	8861337	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8861338	8861499	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8861500	8861770	0.52	+	0	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8861500	8861770	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8861771	8861954	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8861955	8862214	0.31	+	2	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8861955	8862214	.	+	.	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	stop_codon	8862215	8862217	.	+	0	transcript_id "Phchi.S2G037100.t2"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	transcript	8856385	8862214	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	start_codon	8856385	8856387	.	+	0	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8856385	8856646	0.35	+	0	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8856385	8856646	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8856647	8856862	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8856863	8857421	0.98	+	2	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8856863	8857421	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8857422	8857760	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8857761	8858314	0.75	+	1	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8857761	8858314	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858315	8858427	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8858428	8858619	0.97	+	2	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8858428	8858619	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858620	8858769	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8858770	8858828	0.96	+	2	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8858770	8858828	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8858829	8859004	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859005	8859150	0.6	+	0	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859005	8859150	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8859151	8859235	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859236	8859353	1	+	1	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859236	8859353	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8859354	8859534	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8859535	8861337	0.97	+	0	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8859535	8861337	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8861338	8861499	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8861500	8861770	0.43	+	0	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8861500	8861770	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	intron	8861771	8861954	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	CDS	8861955	8862214	0.25	+	2	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	exon	8861955	8862214	.	+	.	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
Phchi.S2	AUGUSTUS	stop_codon	8862215	8862217	.	+	0	transcript_id "Phchi.S2G037100.t3"; gene_id "Phchi.S2G037100"
# This transcript jg9448.t2 is derived from g6624.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9449.t1 is derived from g6625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41532094	41533132	.	-	.	Phchi.S1G660800
Phchi.S1	AUGUSTUS	transcript	41532094	41533132	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	stop_codon	41532091	41532093	.	-	0	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	CDS	41532094	41532213	1	-	0	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	exon	41532094	41532213	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	intron	41532214	41532328	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	CDS	41532329	41532511	1	-	0	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	exon	41532329	41532511	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	intron	41532512	41532644	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	CDS	41532645	41532744	1	-	1	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	exon	41532645	41532744	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	intron	41532745	41532841	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	CDS	41532842	41532939	1	-	0	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	exon	41532842	41532939	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	intron	41532940	41533078	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	CDS	41533079	41533132	0.95	-	0	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	exon	41533079	41533132	.	-	.	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
Phchi.S1	AUGUSTUS	start_codon	41533130	41533132	.	-	0	transcript_id "Phchi.S1G660800.t1"; gene_id "Phchi.S1G660800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11986.t1 is derived from g7661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	366689	367999	.	+	.	Phchi.S2G006600
Phchi.S2	AUGUSTUS	transcript	366689	367999	.	+	.	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	start_codon	366689	366691	.	+	0	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	CDS	366689	366940	0.58	+	0	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	exon	366689	366940	.	+	.	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	intron	366941	367033	.	+	.	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	CDS	367034	367999	0.94	+	0	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	exon	367034	367999	.	+	.	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
Phchi.S2	AUGUSTUS	stop_codon	368000	368002	.	+	0	transcript_id "Phchi.S2G006600.t1"; gene_id "Phchi.S2G006600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15712.t1 is derived from g14182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20810309	20811526	.	+	.	Phchi.S3G303100
Phchi.S3	AUGUSTUS	transcript	20810309	20811526	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	start_codon	20810309	20810311	.	+	0	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20810309	20810404	0.38	+	0	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20810309	20810404	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	intron	20810405	20810507	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20810508	20810699	0.69	+	0	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20810508	20810699	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	intron	20810700	20810795	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20810796	20810967	0.57	+	0	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20810796	20810967	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	intron	20810968	20811098	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20811099	20811319	0.98	+	2	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20811099	20811319	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	intron	20811320	20811421	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20811422	20811526	1	+	0	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20811422	20811526	.	+	.	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	stop_codon	20811527	20811529	.	+	0	transcript_id "Phchi.S3G303100.t1"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	transcript	20810309	20811071	.	+	.	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	start_codon	20810309	20810311	.	+	0	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20810309	20810404	0.34	+	0	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20810309	20810404	.	+	.	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	intron	20810405	20810507	.	+	.	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20810508	20810699	0.65	+	0	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20810508	20810699	.	+	.	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	intron	20810700	20810795	.	+	.	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	CDS	20810796	20811071	0.72	+	0	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	exon	20810796	20811071	.	+	.	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
Phchi.S3	AUGUSTUS	stop_codon	20811072	20811074	.	+	0	transcript_id "Phchi.S3G303100.t2"; gene_id "Phchi.S3G303100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11480.t1 is derived from g15530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6582957	6584480	.	-	.	Phchi.S4G106200
Phchi.S4	AUGUSTUS	transcript	6582957	6584480	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	stop_codon	6582954	6582956	.	-	0	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	CDS	6582957	6583142	1	-	0	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	exon	6582957	6583142	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	intron	6583143	6583232	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	CDS	6583233	6583508	1	-	0	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	exon	6583233	6583508	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	intron	6583509	6583612	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	CDS	6583613	6583744	1	-	0	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	exon	6583613	6583744	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	intron	6583745	6583872	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	CDS	6583873	6584207	1	-	2	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	exon	6583873	6584207	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	intron	6584208	6584284	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	CDS	6584285	6584480	0.59	-	0	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	exon	6584285	6584480	.	-	.	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
Phchi.S4	AUGUSTUS	start_codon	6584478	6584480	.	-	0	transcript_id "Phchi.S4G106200.t1"; gene_id "Phchi.S4G106200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4970.t1 is derived from g2140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13811977	13813154	.	-	.	Phchi.S1G212900
Phchi.S1	AUGUSTUS	transcript	13811977	13813154	.	-	.	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	stop_codon	13811974	13811976	.	-	0	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	CDS	13811977	13812340	1	-	1	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	exon	13811977	13812340	.	-	.	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	intron	13812341	13812456	.	-	.	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	CDS	13812457	13813154	0.67	-	0	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	exon	13812457	13813154	.	-	.	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
Phchi.S1	AUGUSTUS	start_codon	13813152	13813154	.	-	0	transcript_id "Phchi.S1G212900.t1"; gene_id "Phchi.S1G212900"
# This transcript jg1774.t2 is derived from g8694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1775.t1 is derived from g8695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2965758	2966624	.	+	.	Phchi.S5G038400
Phchi.S5	AUGUSTUS	transcript	2965758	2966624	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	start_codon	2965758	2965760	.	+	0	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	CDS	2965758	2965856	1	+	0	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	exon	2965758	2965856	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	intron	2965857	2966044	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	CDS	2966045	2966094	1	+	0	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	exon	2966045	2966094	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	intron	2966095	2966219	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	CDS	2966220	2966325	1	+	1	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	exon	2966220	2966325	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	intron	2966326	2966421	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	CDS	2966422	2966480	0.95	+	0	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	exon	2966422	2966480	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	intron	2966481	2966581	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	CDS	2966582	2966624	0.94	+	1	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	exon	2966582	2966624	.	+	.	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
Phchi.S5	AUGUSTUS	stop_codon	2966625	2966627	.	+	0	transcript_id "Phchi.S5G038400.t1"; gene_id "Phchi.S5G038400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5110.t1 is derived from g2280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14777465	14778102	.	-	.	Phchi.S1G226900
Phchi.S1	AUGUSTUS	transcript	14777465	14778102	.	-	.	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	stop_codon	14777462	14777464	.	-	0	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	CDS	14777465	14777535	0.88	-	2	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	exon	14777465	14777535	.	-	.	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	intron	14777536	14777601	.	-	.	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	CDS	14777602	14777899	0.88	-	0	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	exon	14777602	14777899	.	-	.	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	intron	14777900	14778021	.	-	.	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	CDS	14778022	14778102	0.53	-	0	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	exon	14778022	14778102	.	-	.	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
Phchi.S1	AUGUSTUS	start_codon	14778100	14778102	.	-	0	transcript_id "Phchi.S1G226900.t1"; gene_id "Phchi.S1G226900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14116.t1 is derived from g12583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10940952	10945115	.	-	.	Phchi.S3G143500
Phchi.S3	AUGUSTUS	transcript	10940952	10945115	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	stop_codon	10940949	10940951	.	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10940952	10941131	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10940952	10941131	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10941132	10941231	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10941232	10941316	1	-	1	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10941232	10941316	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10941317	10941395	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10941396	10941617	1	-	1	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10941396	10941617	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10941618	10941752	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10941753	10941928	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10941753	10941928	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10941929	10942050	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10942051	10942114	1	-	1	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10942051	10942114	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10942115	10942303	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10942304	10942398	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10942304	10942398	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10942399	10942559	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10942560	10942609	1	-	2	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10942560	10942609	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10942610	10942689	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10942690	10942816	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10942690	10942816	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10942817	10942972	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10942973	10943104	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10942973	10943104	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10943105	10943202	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10943203	10943283	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10943203	10943283	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10943284	10943370	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10943371	10943529	1	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10943371	10943529	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	intron	10943530	10943693	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	CDS	10943694	10945115	0.95	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	exon	10943694	10945115	.	-	.	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
Phchi.S3	AUGUSTUS	start_codon	10945113	10945115	.	-	0	transcript_id "Phchi.S3G143500.t1"; gene_id "Phchi.S3G143500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8399.t1 is derived from g5574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35748397	35750507	.	+	.	Phchi.S1G555800
Phchi.S1	AUGUSTUS	transcript	35748397	35750507	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	start_codon	35748397	35748399	.	+	0	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35748397	35748671	1	+	0	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35748397	35748671	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35748672	35748782	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35748783	35748825	1	+	1	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35748783	35748825	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35748826	35748904	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35748905	35749069	0.98	+	0	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35748905	35749069	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35749070	35749208	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35749209	35749423	0.98	+	0	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35749209	35749423	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35749424	35749514	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35749515	35749742	1	+	1	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35749515	35749742	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35749743	35749828	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35749829	35750051	1	+	1	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35749829	35750051	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35750052	35750144	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35750145	35750507	1	+	0	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35750145	35750507	.	+	.	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	stop_codon	35750508	35750510	.	+	0	transcript_id "Phchi.S1G555800.t1"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	transcript	35748397	35749424	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	start_codon	35748397	35748399	.	+	0	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35748397	35748671	1	+	0	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35748397	35748671	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35748672	35748782	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35748783	35748825	1	+	1	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35748783	35748825	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35748826	35748904	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35748905	35749069	0.9	+	0	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35748905	35749069	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	intron	35749070	35749208	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	CDS	35749209	35749424	0.9	+	0	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	exon	35749209	35749424	.	+	.	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
Phchi.S1	AUGUSTUS	stop_codon	35749425	35749427	.	+	0	transcript_id "Phchi.S1G555800.t2"; gene_id "Phchi.S1G555800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg982.t1 is derived from g10765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6835960	6836848	.	+	.	Phchi.S6G094100
Phchi.S6	AUGUSTUS	transcript	6835960	6836848	.	+	.	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	start_codon	6835960	6835962	.	+	0	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	CDS	6835960	6836230	0.68	+	0	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	exon	6835960	6836230	.	+	.	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	intron	6836231	6836384	.	+	.	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	CDS	6836385	6836461	0.9	+	2	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	exon	6836385	6836461	.	+	.	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	intron	6836462	6836638	.	+	.	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	CDS	6836639	6836848	0.3	+	0	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	exon	6836639	6836848	.	+	.	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
Phchi.S6	AUGUSTUS	stop_codon	6836849	6836851	.	+	0	transcript_id "Phchi.S6G094100.t1"; gene_id "Phchi.S6G094100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1138.t1 is derived from g10921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7891585	7891854	.	-	.	Phchi.S6G109700
Phchi.S6	AUGUSTUS	transcript	7891585	7891854	.	-	.	transcript_id "Phchi.S6G109700.t1"; gene_id "Phchi.S6G109700"
Phchi.S6	AUGUSTUS	stop_codon	7891582	7891584	.	-	0	transcript_id "Phchi.S6G109700.t1"; gene_id "Phchi.S6G109700"
Phchi.S6	AUGUSTUS	CDS	7891585	7891854	0.93	-	0	transcript_id "Phchi.S6G109700.t1"; gene_id "Phchi.S6G109700"
Phchi.S6	AUGUSTUS	exon	7891585	7891854	.	-	.	transcript_id "Phchi.S6G109700.t1"; gene_id "Phchi.S6G109700"
Phchi.S6	AUGUSTUS	start_codon	7891852	7891854	.	-	0	transcript_id "Phchi.S6G109700.t1"; gene_id "Phchi.S6G109700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6905.t1 is derived from g4077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25925602	25925937	.	-	.	Phchi.S1G406400
Phchi.S1	AUGUSTUS	transcript	25925602	25925937	.	-	.	transcript_id "Phchi.S1G406400.t1"; gene_id "Phchi.S1G406400"
Phchi.S1	AUGUSTUS	stop_codon	25925599	25925601	.	-	0	transcript_id "Phchi.S1G406400.t1"; gene_id "Phchi.S1G406400"
Phchi.S1	AUGUSTUS	CDS	25925602	25925937	0.61	-	0	transcript_id "Phchi.S1G406400.t1"; gene_id "Phchi.S1G406400"
Phchi.S1	AUGUSTUS	exon	25925602	25925937	.	-	.	transcript_id "Phchi.S1G406400.t1"; gene_id "Phchi.S1G406400"
Phchi.S1	AUGUSTUS	start_codon	25925935	25925937	.	-	0	transcript_id "Phchi.S1G406400.t1"; gene_id "Phchi.S1G406400"
# This transcript jg93.t2 is derived from g9875.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg94.t1 is derived from g9876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	480876	483502	.	+	.	Phchi.S6G005300
Phchi.S6	AUGUSTUS	transcript	480876	483502	.	+	.	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	start_codon	480876	480878	.	+	0	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	CDS	480876	481958	0.14	+	0	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	exon	480876	481958	.	+	.	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	intron	481959	482062	.	+	.	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	CDS	482063	482745	0.5	+	0	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	exon	482063	482745	.	+	.	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	intron	482746	482949	.	+	.	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	CDS	482950	483502	0.66	+	1	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	exon	482950	483502	.	+	.	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
Phchi.S6	AUGUSTUS	stop_codon	483503	483505	.	+	0	transcript_id "Phchi.S6G005300.t1"; gene_id "Phchi.S6G005300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2034.t1 is derived from g8954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4539623	4540016	.	-	.	Phchi.S5G064300
Phchi.S5	AUGUSTUS	transcript	4539623	4540016	.	-	.	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	stop_codon	4539620	4539622	.	-	0	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	CDS	4539623	4539652	1	-	0	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	exon	4539623	4539652	.	-	.	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	intron	4539653	4539785	.	-	.	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	CDS	4539786	4540016	0.95	-	0	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	exon	4539786	4540016	.	-	.	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
Phchi.S5	AUGUSTUS	start_codon	4540014	4540016	.	-	0	transcript_id "Phchi.S5G064300.t1"; gene_id "Phchi.S5G064300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6241.t1 is derived from g3413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21820402	21822156	.	+	.	Phchi.S1G340000
Phchi.S1	AUGUSTUS	transcript	21820402	21822156	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	start_codon	21820402	21820404	.	+	0	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	CDS	21820402	21820575	0.89	+	0	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	exon	21820402	21820575	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	intron	21820576	21820664	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	CDS	21820665	21820850	0.99	+	0	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	exon	21820665	21820850	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	intron	21820851	21820944	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	CDS	21820945	21821017	1	+	0	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	exon	21820945	21821017	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	intron	21821018	21821107	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	CDS	21821108	21821586	1	+	2	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	exon	21821108	21821586	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	intron	21821587	21821661	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	CDS	21821662	21822156	1	+	0	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	exon	21821662	21822156	.	+	.	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
Phchi.S1	AUGUSTUS	stop_codon	21822157	21822159	.	+	0	transcript_id "Phchi.S1G340000.t1"; gene_id "Phchi.S1G340000"
# This transcript jg8648.t2 is derived from g5823.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8649.t1 is derived from g5824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37239633	37241136	.	+	.	Phchi.S1G580800
Phchi.S1	AUGUSTUS	transcript	37239633	37241136	.	+	.	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	start_codon	37239633	37239635	.	+	0	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	CDS	37239633	37240811	0.71	+	0	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	exon	37239633	37240811	.	+	.	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	intron	37240812	37240912	.	+	.	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	CDS	37240913	37240955	0.75	+	0	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	exon	37240913	37240955	.	+	.	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	intron	37240956	37241134	.	+	.	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	CDS	37241135	37241136	0.75	+	2	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	exon	37241135	37241136	.	+	.	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
Phchi.S1	AUGUSTUS	stop_codon	37241137	37241139	.	+	0	transcript_id "Phchi.S1G580800.t1"; gene_id "Phchi.S1G580800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10472.t1 is derived from g14521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	550590	551930	.	-	.	Phchi.S4G005400
Phchi.S4	AUGUSTUS	transcript	550590	551930	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	stop_codon	550587	550589	.	-	0	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	CDS	550590	550592	1	-	0	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	exon	550590	550592	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	intron	550593	550797	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	CDS	550798	551142	1	-	0	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	exon	550798	551142	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	intron	551143	551569	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	CDS	551570	551602	0.96	-	0	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	exon	551570	551602	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	intron	551603	551669	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	CDS	551670	551745	0.88	-	1	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	exon	551670	551745	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	intron	551746	551877	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	CDS	551878	551930	0.87	-	0	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	exon	551878	551930	.	-	.	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
Phchi.S4	AUGUSTUS	start_codon	551928	551930	.	-	0	transcript_id "Phchi.S4G005400.t1"; gene_id "Phchi.S4G005400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7401.t1 is derived from g4573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28957073	28959498	.	+	.	Phchi.S1G456000
Phchi.S1	AUGUSTUS	transcript	28957073	28959498	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	start_codon	28957073	28957075	.	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28957073	28957312	0.98	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28957073	28957312	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28957313	28957459	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28957460	28957672	1	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28957460	28957672	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28957673	28957872	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28957873	28958070	1	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28957873	28958070	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28958071	28958195	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28958196	28958291	1	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28958196	28958291	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28958292	28958409	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28958410	28958574	1	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28958410	28958574	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28958575	28958667	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28958668	28958773	1	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28958668	28958773	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28958774	28958879	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28958880	28959043	1	+	2	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28958880	28959043	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	intron	28959044	28959180	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	CDS	28959181	28959498	1	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	exon	28959181	28959498	.	+	.	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
Phchi.S1	AUGUSTUS	stop_codon	28959499	28959501	.	+	0	transcript_id "Phchi.S1G456000.t1"; gene_id "Phchi.S1G456000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9053.t1 is derived from g6228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39408304	39408810	.	+	.	Phchi.S1G621200
Phchi.S1	AUGUSTUS	transcript	39408304	39408810	.	+	.	transcript_id "Phchi.S1G621200.t1"; gene_id "Phchi.S1G621200"
Phchi.S1	AUGUSTUS	start_codon	39408304	39408306	.	+	0	transcript_id "Phchi.S1G621200.t1"; gene_id "Phchi.S1G621200"
Phchi.S1	AUGUSTUS	CDS	39408304	39408810	0.54	+	0	transcript_id "Phchi.S1G621200.t1"; gene_id "Phchi.S1G621200"
Phchi.S1	AUGUSTUS	exon	39408304	39408810	.	+	.	transcript_id "Phchi.S1G621200.t1"; gene_id "Phchi.S1G621200"
Phchi.S1	AUGUSTUS	stop_codon	39408811	39408813	.	+	0	transcript_id "Phchi.S1G621200.t1"; gene_id "Phchi.S1G621200"
# This transcript jg9664.t2 is derived from g6840.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9665.t1 is derived from g6841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43135690	43142224	.	-	.	Phchi.S1G682400
Phchi.S1	AUGUSTUS	transcript	43135690	43142224	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	stop_codon	43135687	43135689	.	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43135690	43135945	0.81	-	1	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43135690	43135945	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43135946	43136082	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43136083	43136129	0.86	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43136083	43136129	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43136130	43136313	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43136314	43136442	0.84	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43136314	43136442	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43136443	43136527	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43136528	43136764	0.71	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43136528	43136764	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43136765	43136871	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43136872	43137034	0.73	-	1	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43136872	43137034	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43137035	43137258	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43137259	43137344	1	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43137259	43137344	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43137345	43137517	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43137518	43137677	0.76	-	1	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43137518	43137677	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43137678	43137899	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43137900	43137976	0.89	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43137900	43137976	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43137977	43138281	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43138282	43138766	0.83	-	2	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43138282	43138766	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43138767	43138935	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43138936	43139179	1	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43138936	43139179	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43139180	43139343	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43139344	43139805	0.99	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43139344	43139805	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43139806	43140003	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43140004	43140707	0.96	-	2	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43140004	43140707	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43140708	43140816	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43140817	43141170	0.74	-	2	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43140817	43141170	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43141171	43141290	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43141291	43141546	0.86	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43141291	43141546	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	intron	43141547	43141675	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	CDS	43141676	43142224	1	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	exon	43141676	43142224	.	-	.	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
Phchi.S1	AUGUSTUS	start_codon	43142222	43142224	.	-	0	transcript_id "Phchi.S1G682400.t1"; gene_id "Phchi.S1G682400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8150.t1 is derived from g5325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34101138	34102468	.	-	.	Phchi.S1G530900
Phchi.S1	AUGUSTUS	transcript	34101138	34102468	.	-	.	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	stop_codon	34101135	34101137	.	-	0	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	CDS	34101138	34101268	0.86	-	2	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	exon	34101138	34101268	.	-	.	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	intron	34101269	34101345	.	-	.	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	CDS	34101346	34102468	0.62	-	0	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	exon	34101346	34102468	.	-	.	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
Phchi.S1	AUGUSTUS	start_codon	34102466	34102468	.	-	0	transcript_id "Phchi.S1G530900.t1"; gene_id "Phchi.S1G530900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13945.t1 is derived from g12412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9851399	9853683	.	-	.	Phchi.S3G126400
Phchi.S3	AUGUSTUS	transcript	9851399	9853683	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	stop_codon	9851396	9851398	.	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9851399	9851507	0.98	-	1	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9851399	9851507	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9851508	9851606	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9851607	9851725	0.98	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9851607	9851725	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9851726	9851856	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9851857	9851963	1	-	2	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9851857	9851963	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9851964	9852053	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852054	9852129	1	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852054	9852129	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852130	9852209	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852210	9852311	0.91	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852210	9852311	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852312	9852409	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852410	9852676	0.98	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852410	9852676	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852677	9852757	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852758	9852913	0.99	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852758	9852913	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852914	9853009	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9853010	9853103	0.77	-	1	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9853010	9853103	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9853104	9853231	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9853232	9853327	0.53	-	1	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9853232	9853327	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9853328	9853429	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9853430	9853683	0.98	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9853430	9853683	.	-	.	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	start_codon	9853681	9853683	.	-	0	transcript_id "Phchi.S3G126400.t1"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	transcript	9851606	9853683	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	stop_codon	9851603	9851605	.	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9851606	9851725	0.98	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9851606	9851725	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9851726	9851856	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9851857	9851963	0.98	-	2	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9851857	9851963	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9851964	9852053	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852054	9852129	1	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852054	9852129	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852130	9852209	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852210	9852311	0.94	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852210	9852311	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852312	9852409	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852410	9852676	0.91	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852410	9852676	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852677	9852757	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9852758	9852913	1	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9852758	9852913	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9852914	9853009	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9853010	9853103	0.74	-	1	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9853010	9853103	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9853104	9853231	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9853232	9853327	0.55	-	1	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9853232	9853327	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	intron	9853328	9853429	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	CDS	9853430	9853683	0.99	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	exon	9853430	9853683	.	-	.	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
Phchi.S3	AUGUSTUS	start_codon	9853681	9853683	.	-	0	transcript_id "Phchi.S3G126400.t2"; gene_id "Phchi.S3G126400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4520.t1 is derived from g1690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10935911	10937350	.	+	.	Phchi.S1G167900
Phchi.S1	AUGUSTUS	transcript	10935911	10937350	.	+	.	transcript_id "Phchi.S1G167900.t1"; gene_id "Phchi.S1G167900"
Phchi.S1	AUGUSTUS	start_codon	10935911	10935913	.	+	0	transcript_id "Phchi.S1G167900.t1"; gene_id "Phchi.S1G167900"
Phchi.S1	AUGUSTUS	CDS	10935911	10937350	1	+	0	transcript_id "Phchi.S1G167900.t1"; gene_id "Phchi.S1G167900"
Phchi.S1	AUGUSTUS	exon	10935911	10937350	.	+	.	transcript_id "Phchi.S1G167900.t1"; gene_id "Phchi.S1G167900"
Phchi.S1	AUGUSTUS	stop_codon	10937351	10937353	.	+	0	transcript_id "Phchi.S1G167900.t1"; gene_id "Phchi.S1G167900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12138.t1 is derived from g7814.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4683953	4687487	.	-	.	Phchi.S2G021800
Phchi.S2	AUGUSTUS	transcript	4683953	4687487	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	stop_codon	4683950	4683952	.	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4683953	4683969	1	-	2	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4683953	4683969	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4683970	4684068	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4684069	4684102	0.94	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4684069	4684102	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4684103	4684178	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4684179	4684199	0.94	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4684179	4684199	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4684200	4684329	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4684330	4684364	0.93	-	2	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4684330	4684364	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4684365	4684469	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4684470	4684539	0.96	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4684470	4684539	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4684540	4685055	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685056	4685135	1	-	2	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685056	4685135	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685136	4685305	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685306	4685375	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685306	4685375	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685376	4685463	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685464	4685556	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685464	4685556	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685557	4685682	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685683	4685776	1	-	1	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685683	4685776	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685777	4685861	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685862	4685923	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685862	4685923	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685924	4686084	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686085	4686297	0.91	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686085	4686297	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686298	4686373	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686374	4686439	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686374	4686439	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686440	4686539	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686540	4686656	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686540	4686656	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686657	4686803	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686804	4686931	0.94	-	2	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686804	4686931	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686932	4687035	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4687036	4687177	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4687036	4687177	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4687178	4687252	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4687253	4687285	1	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4687253	4687285	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4687286	4687421	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4687422	4687487	0.91	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4687422	4687487	.	-	.	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	start_codon	4687485	4687487	.	-	0	transcript_id "Phchi.S2G021800.t1"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	transcript	4684825	4687487	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	stop_codon	4684822	4684824	.	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4684825	4684857	0.63	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4684825	4684857	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4684858	4685055	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685056	4685135	0.88	-	2	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685056	4685135	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685136	4685305	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685306	4685375	1	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685306	4685375	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685376	4685463	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685464	4685556	1	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685464	4685556	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685557	4685682	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685683	4685776	1	-	1	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685683	4685776	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685777	4685861	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4685862	4685923	1	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4685862	4685923	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4685924	4686084	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686085	4686297	0.86	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686085	4686297	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686298	4686373	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686374	4686439	1	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686374	4686439	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686440	4686539	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686540	4686656	1	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686540	4686656	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686657	4686803	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4686804	4686931	0.85	-	2	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4686804	4686931	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4686932	4687035	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4687036	4687177	0.98	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4687036	4687177	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4687178	4687252	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4687253	4687285	1	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4687253	4687285	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	intron	4687286	4687421	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	CDS	4687422	4687487	0.93	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	exon	4687422	4687487	.	-	.	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
Phchi.S2	AUGUSTUS	start_codon	4687485	4687487	.	-	0	transcript_id "Phchi.S2G021800.t2"; gene_id "Phchi.S2G021800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12092.t1 is derived from g7767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2311603	2312613	.	-	.	Phchi.S2G017200
Phchi.S2	AUGUSTUS	transcript	2311603	2312613	.	-	.	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	stop_codon	2311600	2311602	.	-	0	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	CDS	2311603	2311959	1	-	0	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	exon	2311603	2311959	.	-	.	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	intron	2311960	2312061	.	-	.	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	CDS	2312062	2312613	1	-	0	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	exon	2312062	2312613	.	-	.	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
Phchi.S2	AUGUSTUS	start_codon	2312611	2312613	.	-	0	transcript_id "Phchi.S2G017200.t1"; gene_id "Phchi.S2G017200"
# This transcript jg5290.t2 is derived from g2460.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5291.t1 is derived from g2461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16041017	16043332	.	+	.	Phchi.S1G245000
Phchi.S1	AUGUSTUS	transcript	16041017	16043332	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	start_codon	16041017	16041019	.	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16041017	16041170	0.52	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16041017	16041170	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16041171	16041244	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16041245	16041361	0.78	+	2	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16041245	16041361	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16041362	16041426	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16041427	16041551	0.37	+	2	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16041427	16041551	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16041552	16041629	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16041630	16041699	0.66	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16041630	16041699	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16041700	16041852	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16041853	16042007	1	+	2	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16041853	16042007	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16042008	16042098	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16042099	16042299	1	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16042099	16042299	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16042300	16042523	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16042524	16042617	1	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16042524	16042617	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16042618	16042711	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16042712	16042769	0.99	+	2	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16042712	16042769	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16042770	16042871	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16042872	16042941	0.99	+	1	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16042872	16042941	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16042942	16043017	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16043018	16043153	1	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16043018	16043153	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	intron	16043154	16043249	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	CDS	16043250	16043332	1	+	2	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	exon	16043250	16043332	.	+	.	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
Phchi.S1	AUGUSTUS	stop_codon	16043333	16043335	.	+	0	transcript_id "Phchi.S1G245000.t1"; gene_id "Phchi.S1G245000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10310.t1 is derived from g7486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47075340	47077780	.	-	.	Phchi.S1G746900
Phchi.S1	AUGUSTUS	transcript	47075340	47077780	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	stop_codon	47075337	47075339	.	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47075340	47075474	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47075340	47075474	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47075475	47075554	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47075555	47075605	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47075555	47075605	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47075606	47075690	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47075691	47075807	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47075691	47075807	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47075808	47075907	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47075908	47075982	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47075908	47075982	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47075983	47076131	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47076132	47076334	0.77	-	2	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47076132	47076334	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47076335	47076417	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47076418	47076496	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47076418	47076496	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47076497	47076649	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47076650	47076691	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47076650	47076691	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47076692	47076777	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47076778	47076829	1	-	1	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47076778	47076829	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47076830	47076964	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47076965	47077044	1	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47076965	47077044	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	intron	47077045	47077255	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	CDS	47077256	47077780	0.99	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	exon	47077256	47077780	.	-	.	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
Phchi.S1	AUGUSTUS	start_codon	47077778	47077780	.	-	0	transcript_id "Phchi.S1G746900.t1"; gene_id "Phchi.S1G746900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3995.t1 is derived from g1164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6898518	6901804	.	+	.	Phchi.S1G115400
Phchi.S1	AUGUSTUS	transcript	6898518	6901804	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	start_codon	6898518	6898520	.	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6898518	6898662	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6898518	6898662	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6898663	6898750	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6898751	6898812	1	+	2	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6898751	6898812	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6898813	6898893	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6898894	6898994	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6898894	6898994	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6898995	6899085	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6899086	6899167	1	+	1	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6899086	6899167	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6899168	6899301	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6899302	6899361	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6899302	6899361	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6899362	6899585	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6899586	6899652	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6899586	6899652	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6899653	6899750	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6899751	6899770	1	+	2	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6899751	6899770	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6899771	6899860	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6899861	6899944	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6899861	6899944	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6899945	6900031	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900032	6900096	0.93	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900032	6900096	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6900097	6900200	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900201	6900249	1	+	1	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900201	6900249	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6900250	6900329	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900330	6900377	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900330	6900377	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6900378	6900528	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900529	6900618	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900529	6900618	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6900619	6900701	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900702	6900761	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900702	6900761	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6900762	6900863	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900864	6900923	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900864	6900923	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6900924	6900989	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6900990	6901064	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6900990	6901064	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6901065	6901201	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6901202	6901287	1	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6901202	6901287	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6901288	6901374	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6901375	6901468	1	+	1	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6901375	6901468	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6901469	6901554	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6901555	6901671	0.96	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6901555	6901671	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	intron	6901672	6901771	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	CDS	6901772	6901804	0.95	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	exon	6901772	6901804	.	+	.	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
Phchi.S1	AUGUSTUS	stop_codon	6901805	6901807	.	+	0	transcript_id "Phchi.S1G115400.t1"; gene_id "Phchi.S1G115400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6724.t1 is derived from g3896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24749602	24751206	.	-	.	Phchi.S1G388300
Phchi.S1	AUGUSTUS	transcript	24749602	24751206	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	stop_codon	24749599	24749601	.	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	CDS	24749602	24749703	1	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	exon	24749602	24749703	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	intron	24749704	24749801	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	CDS	24749802	24750467	0.99	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	exon	24749802	24750467	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	intron	24750468	24750558	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	CDS	24750559	24750822	1	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	exon	24750559	24750822	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	intron	24750823	24750920	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	CDS	24750921	24751079	1	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	exon	24750921	24751079	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	intron	24751080	24751179	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	CDS	24751180	24751206	1	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	exon	24751180	24751206	.	-	.	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
Phchi.S1	AUGUSTUS	start_codon	24751204	24751206	.	-	0	transcript_id "Phchi.S1G388300.t1"; gene_id "Phchi.S1G388300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10319.t1 is derived from g7495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47094150	47095722	.	-	.	Phchi.S1G747800
Phchi.S1	AUGUSTUS	transcript	47094150	47095722	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	stop_codon	47094147	47094149	.	-	0	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094150	47094356	1	-	0	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094150	47094356	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47094357	47094453	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094454	47094715	1	-	1	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094454	47094715	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47094716	47094925	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094926	47095034	1	-	2	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094926	47095034	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47095035	47095127	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47095128	47095205	1	-	2	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47095128	47095205	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47095206	47095413	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47095414	47095519	1	-	0	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47095414	47095519	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47095520	47095605	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47095606	47095722	0.97	-	0	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47095606	47095722	.	-	.	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	start_codon	47095720	47095722	.	-	0	transcript_id "Phchi.S1G747800.t1"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	transcript	47094150	47095722	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	stop_codon	47094147	47094149	.	-	0	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094150	47094356	1	-	0	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094150	47094356	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47094357	47094453	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094454	47094715	0.99	-	1	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094454	47094715	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47094716	47094855	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094856	47094898	0.57	-	2	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094856	47094898	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47094899	47094983	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47094984	47095034	0.63	-	2	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47094984	47095034	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47095035	47095127	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47095128	47095205	1	-	2	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47095128	47095205	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47095206	47095413	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47095414	47095519	1	-	0	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47095414	47095519	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	intron	47095520	47095605	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	CDS	47095606	47095722	0.94	-	0	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	exon	47095606	47095722	.	-	.	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
Phchi.S1	AUGUSTUS	start_codon	47095720	47095722	.	-	0	transcript_id "Phchi.S1G747800.t2"; gene_id "Phchi.S1G747800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1427.t1 is derived from g8346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	795484	797139	.	-	.	Phchi.S5G003600
Phchi.S5	AUGUSTUS	transcript	795484	797139	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	stop_codon	795481	795483	.	-	0	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	CDS	795484	795636	1	-	0	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	exon	795484	795636	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	intron	795637	796055	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	CDS	796056	796451	1	-	0	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	exon	796056	796451	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	intron	796452	796584	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	CDS	796585	796751	1	-	2	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	exon	796585	796751	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	intron	796752	796876	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	CDS	796877	796955	1	-	0	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	exon	796877	796955	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	intron	796956	797091	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	CDS	797092	797139	0.57	-	0	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	exon	797092	797139	.	-	.	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
Phchi.S5	AUGUSTUS	start_codon	797137	797139	.	-	0	transcript_id "Phchi.S5G003600.t1"; gene_id "Phchi.S5G003600"
# This transcript jg4855.t2 is derived from g2025.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4855.t3 is derived from g2025.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4856.t1 is derived from g2026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13119487	13120683	.	+	.	Phchi.S1G201500
Phchi.S1	AUGUSTUS	transcript	13119487	13120683	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	start_codon	13119487	13119489	.	+	0	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	CDS	13119487	13119751	1	+	0	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	exon	13119487	13119751	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	intron	13119752	13119842	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	CDS	13119843	13120044	1	+	2	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	exon	13119843	13120044	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	intron	13120045	13120136	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	CDS	13120137	13120209	1	+	1	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	exon	13120137	13120209	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	intron	13120210	13120284	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	CDS	13120285	13120334	1	+	0	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	exon	13120285	13120334	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	intron	13120335	13120410	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	CDS	13120411	13120524	1	+	1	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	exon	13120411	13120524	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	intron	13120525	13120607	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	CDS	13120608	13120683	1	+	1	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	exon	13120608	13120683	.	+	.	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
Phchi.S1	AUGUSTUS	stop_codon	13120684	13120686	.	+	0	transcript_id "Phchi.S1G201500.t1"; gene_id "Phchi.S1G201500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14030.t1 is derived from g12497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10370935	10375693	.	-	.	Phchi.S3G134900
Phchi.S3	AUGUSTUS	transcript	10370935	10375693	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	stop_codon	10370932	10370934	.	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10370935	10370985	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10370935	10370985	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10370986	10371053	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10371054	10371335	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10371054	10371335	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10371336	10371427	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10371428	10371563	1	-	1	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10371428	10371563	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10371564	10371655	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10371656	10371739	1	-	1	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10371656	10371739	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10371740	10371819	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10371820	10371939	1	-	1	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10371820	10371939	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10371940	10372107	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10372108	10372184	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10372108	10372184	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10372185	10372291	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10372292	10372411	0.99	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10372292	10372411	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10372412	10372510	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10372511	10372576	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10372511	10372576	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10372577	10372666	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10372667	10372743	0.54	-	2	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10372667	10372743	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10372744	10372947	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10372948	10373215	0.98	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10372948	10373215	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10373216	10373557	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10373558	10373596	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10373558	10373596	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10373597	10374123	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10374124	10374276	0.98	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10374124	10374276	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10374277	10374386	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10374387	10374724	0.94	-	2	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10374387	10374724	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10374725	10374895	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10374896	10374993	1	-	1	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10374896	10374993	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10374994	10375077	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10375078	10375124	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10375078	10375124	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10375125	10375243	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10375244	10375353	1	-	2	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10375244	10375353	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10375354	10375439	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10375440	10375512	1	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10375440	10375512	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	intron	10375513	10375588	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	CDS	10375589	10375693	0.8	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	exon	10375589	10375693	.	-	.	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
Phchi.S3	AUGUSTUS	start_codon	10375691	10375693	.	-	0	transcript_id "Phchi.S3G134900.t1"; gene_id "Phchi.S3G134900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1511.t1 is derived from g8430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1300733	1307213	.	-	.	Phchi.S5G012000
Phchi.S5	AUGUSTUS	transcript	1300733	1307213	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	stop_codon	1300730	1300732	.	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1300733	1300747	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1300733	1300747	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1300748	1300836	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1300837	1300953	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1300837	1300953	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1300954	1301036	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1301037	1301153	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1301037	1301153	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1301154	1301235	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1301236	1301379	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1301236	1301379	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1301380	1301506	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1301507	1301617	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1301507	1301617	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1301618	1301759	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1301760	1301888	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1301760	1301888	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1301889	1301973	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1301974	1302105	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1301974	1302105	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1302106	1302308	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1302309	1302431	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1302309	1302431	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1302432	1302574	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1302575	1302699	1	-	2	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1302575	1302699	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1302700	1302879	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1302880	1303186	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1302880	1303186	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1303187	1303349	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1303350	1303589	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1303350	1303589	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1303590	1303741	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1303742	1303868	0.75	-	1	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1303742	1303868	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1303869	1304004	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1304005	1305237	0.94	-	1	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1304005	1305237	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1305238	1305338	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1305339	1305427	0.98	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1305339	1305427	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1305428	1305577	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1305578	1305832	1	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1305578	1305832	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1305833	1305986	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1305987	1306080	1	-	1	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1305987	1306080	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1306081	1306261	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1306262	1306370	0.53	-	2	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1306262	1306370	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	intron	1306371	1306558	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	CDS	1306559	1307213	0.53	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	exon	1306559	1307213	.	-	.	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
Phchi.S5	AUGUSTUS	start_codon	1307211	1307213	.	-	0	transcript_id "Phchi.S5G012000.t1"; gene_id "Phchi.S5G012000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3224.t1 is derived from g393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2337559	2338928	.	-	.	Phchi.S1G038300
Phchi.S1	AUGUSTUS	transcript	2337559	2338928	.	-	.	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	stop_codon	2337556	2337558	.	-	0	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	CDS	2337559	2337857	0.99	-	2	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	exon	2337559	2337857	.	-	.	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	intron	2337858	2337964	.	-	.	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	CDS	2337965	2338156	1	-	2	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	exon	2337965	2338156	.	-	.	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	intron	2338157	2338852	.	-	.	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	CDS	2338853	2338928	0.81	-	0	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	exon	2338853	2338928	.	-	.	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
Phchi.S1	AUGUSTUS	start_codon	2338926	2338928	.	-	0	transcript_id "Phchi.S1G038300.t1"; gene_id "Phchi.S1G038300"
# This transcript jg14529.t2 is derived from g12997.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14530.t1 is derived from g12998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13326642	13328954	.	-	.	Phchi.S3G184900
Phchi.S3	AUGUSTUS	transcript	13326642	13328954	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	stop_codon	13326639	13326641	.	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13326642	13326746	1	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13326642	13326746	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13326747	13326820	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13326821	13326916	1	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13326821	13326916	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13326917	13327041	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13327042	13327131	1	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13327042	13327131	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13327132	13327224	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13327225	13327276	1	-	1	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13327225	13327276	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13327277	13327354	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13327355	13327425	1	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13327355	13327425	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13327426	13327536	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13327537	13327611	0.99	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13327537	13327611	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13327612	13327742	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13327743	13327817	1	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13327743	13327817	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13327818	13327938	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13327939	13328004	1	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13327939	13328004	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13328005	13328414	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13328415	13328476	1	-	2	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13328415	13328476	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13328477	13328559	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13328560	13328622	1	-	2	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13328560	13328622	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13328623	13328755	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13328756	13328803	1	-	2	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13328756	13328803	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	intron	13328804	13328932	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	CDS	13328933	13328954	0.49	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	exon	13328933	13328954	.	-	.	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
Phchi.S3	AUGUSTUS	start_codon	13328952	13328954	.	-	0	transcript_id "Phchi.S3G184900.t1"; gene_id "Phchi.S3G184900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2169.t1 is derived from g9089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5152630	5153218	.	+	.	Phchi.S5G077800
Phchi.S5	AUGUSTUS	transcript	5152630	5153218	.	+	.	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	start_codon	5152630	5152632	.	+	0	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	CDS	5152630	5152972	0.93	+	0	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	exon	5152630	5152972	.	+	.	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	intron	5152973	5153192	.	+	.	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	CDS	5153193	5153218	1	+	2	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	exon	5153193	5153218	.	+	.	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
Phchi.S5	AUGUSTUS	stop_codon	5153219	5153221	.	+	0	transcript_id "Phchi.S5G077800.t1"; gene_id "Phchi.S5G077800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2308.t1 is derived from g9228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5990638	5991297	.	-	.	Phchi.S5G091700
Phchi.S5	AUGUSTUS	transcript	5990638	5991297	.	-	.	transcript_id "Phchi.S5G091700.t1"; gene_id "Phchi.S5G091700"
Phchi.S5	AUGUSTUS	stop_codon	5990635	5990637	.	-	0	transcript_id "Phchi.S5G091700.t1"; gene_id "Phchi.S5G091700"
Phchi.S5	AUGUSTUS	CDS	5990638	5991297	0.94	-	0	transcript_id "Phchi.S5G091700.t1"; gene_id "Phchi.S5G091700"
Phchi.S5	AUGUSTUS	exon	5990638	5991297	.	-	.	transcript_id "Phchi.S5G091700.t1"; gene_id "Phchi.S5G091700"
Phchi.S5	AUGUSTUS	start_codon	5991295	5991297	.	-	0	transcript_id "Phchi.S5G091700.t1"; gene_id "Phchi.S5G091700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12646.t1 is derived from g16013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	25711	27299	.	-	.	Phchi.C136G000600
Phchi.C136	AUGUSTUS	transcript	25711	27299	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	stop_codon	25708	25710	.	-	0	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	CDS	25711	25830	0.96	-	0	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	exon	25711	25830	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	intron	25831	25960	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	CDS	25961	26221	0.72	-	0	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	exon	25961	26221	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	intron	26222	26325	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	CDS	26326	26475	0.91	-	0	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	exon	26326	26475	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	intron	26476	26601	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	CDS	26602	26690	0.92	-	2	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	exon	26602	26690	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	intron	26691	26785	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	CDS	26786	26928	0.96	-	1	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	exon	26786	26928	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	intron	26929	27021	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	CDS	27022	27299	0.74	-	0	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	exon	27022	27299	.	-	.	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
Phchi.C136	AUGUSTUS	start_codon	27297	27299	.	-	0	transcript_id "Phchi.C136G000600.t1"; gene_id "Phchi.C136G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9964.t1 is derived from g7140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44691337	44691645	.	-	.	Phchi.S1G712300
Phchi.S1	AUGUSTUS	transcript	44691337	44691645	.	-	.	transcript_id "Phchi.S1G712300.t1"; gene_id "Phchi.S1G712300"
Phchi.S1	AUGUSTUS	stop_codon	44691334	44691336	.	-	0	transcript_id "Phchi.S1G712300.t1"; gene_id "Phchi.S1G712300"
Phchi.S1	AUGUSTUS	CDS	44691337	44691645	1	-	0	transcript_id "Phchi.S1G712300.t1"; gene_id "Phchi.S1G712300"
Phchi.S1	AUGUSTUS	exon	44691337	44691645	.	-	.	transcript_id "Phchi.S1G712300.t1"; gene_id "Phchi.S1G712300"
Phchi.S1	AUGUSTUS	start_codon	44691643	44691645	.	-	0	transcript_id "Phchi.S1G712300.t1"; gene_id "Phchi.S1G712300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6808.t1 is derived from g3980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25145556	25148898	.	-	.	Phchi.S1G396700
Phchi.S1	AUGUSTUS	transcript	25145556	25148898	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	stop_codon	25145553	25145555	.	-	0	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	CDS	25145556	25145754	1	-	1	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	exon	25145556	25145754	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	intron	25145755	25145834	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	CDS	25145835	25145932	1	-	0	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	exon	25145835	25145932	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	intron	25145933	25146072	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	CDS	25146073	25146218	1	-	2	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	exon	25146073	25146218	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	intron	25146219	25146313	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	CDS	25146314	25146437	1	-	0	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	exon	25146314	25146437	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	intron	25146438	25146537	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	CDS	25146538	25148898	0.6	-	0	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	exon	25146538	25148898	.	-	.	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
Phchi.S1	AUGUSTUS	start_codon	25148896	25148898	.	-	0	transcript_id "Phchi.S1G396700.t1"; gene_id "Phchi.S1G396700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5735.t1 is derived from g2905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18612728	18614485	.	+	.	Phchi.S1G289400
Phchi.S1	AUGUSTUS	transcript	18612728	18614485	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	start_codon	18612728	18612730	.	+	0	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	CDS	18612728	18613339	0.97	+	0	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	exon	18612728	18613339	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	intron	18613340	18613611	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	CDS	18613612	18613837	0.97	+	0	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	exon	18613612	18613837	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	intron	18613838	18613921	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	CDS	18613922	18614144	1	+	2	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	exon	18613922	18614144	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	intron	18614145	18614262	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	CDS	18614263	18614485	0.99	+	1	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	exon	18614263	18614485	.	+	.	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
Phchi.S1	AUGUSTUS	stop_codon	18614486	18614488	.	+	0	transcript_id "Phchi.S1G289400.t1"; gene_id "Phchi.S1G289400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9217.t1 is derived from g6392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40458613	40459908	.	-	.	Phchi.S1G637600
Phchi.S1	AUGUSTUS	transcript	40458613	40459908	.	-	.	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	stop_codon	40458610	40458612	.	-	0	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	CDS	40458613	40459337	0.99	-	2	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	exon	40458613	40459337	.	-	.	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	intron	40459338	40459436	.	-	.	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	CDS	40459437	40459908	0.93	-	0	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	exon	40459437	40459908	.	-	.	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
Phchi.S1	AUGUSTUS	start_codon	40459906	40459908	.	-	0	transcript_id "Phchi.S1G637600.t1"; gene_id "Phchi.S1G637600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7141.t1 is derived from g4313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27143101	27150712	.	-	.	Phchi.S1G430000
Phchi.S1	AUGUSTUS	transcript	27143101	27150712	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	stop_codon	27143098	27143100	.	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27143101	27143791	0.76	-	1	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27143101	27143791	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27143792	27143953	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27143954	27144075	0.56	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27143954	27144075	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27144076	27144145	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27144146	27144328	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27144146	27144328	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27144329	27144459	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27144460	27144768	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27144460	27144768	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27144769	27144854	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27144855	27145013	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27144855	27145013	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145014	27145164	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145165	27145347	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145165	27145347	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145348	27145438	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145439	27145549	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145439	27145549	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145550	27145645	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145646	27145828	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145646	27145828	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145829	27145973	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145974	27146055	1	-	1	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145974	27146055	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146056	27146209	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146210	27146270	0.98	-	2	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146210	27146270	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146271	27146406	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146407	27146517	1	-	2	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146407	27146517	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146518	27146603	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146604	27146742	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146604	27146742	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146743	27146824	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146825	27146932	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146825	27146932	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146933	27147025	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147026	27147149	1	-	1	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147026	27147149	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147150	27147256	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147257	27147351	0.99	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147257	27147351	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147352	27147584	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147585	27147716	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147585	27147716	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147717	27147795	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147796	27147915	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147796	27147915	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147916	27147998	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147999	27148085	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147999	27148085	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148086	27148257	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27148258	27148408	1	-	1	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27148258	27148408	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148409	27148530	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27148531	27148625	1	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27148531	27148625	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148626	27148814	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27148815	27148895	0.72	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27148815	27148895	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148896	27149013	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149014	27149070	0.99	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149014	27149070	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27149071	27149267	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149268	27149427	1	-	1	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149268	27149427	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27149428	27149683	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149684	27149846	1	-	2	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149684	27149846	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27149847	27149937	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149938	27150042	1	-	2	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149938	27150042	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27150043	27150162	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27150163	27150262	0.88	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27150163	27150262	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27150263	27150338	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27150339	27150433	0.99	-	2	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27150339	27150433	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27150434	27150543	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27150544	27150712	0.56	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27150544	27150712	.	-	.	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	start_codon	27150710	27150712	.	-	0	transcript_id "Phchi.S1G430000.t1"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	transcript	27143101	27150712	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	stop_codon	27143098	27143100	.	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27143101	27143791	0.65	-	1	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27143101	27143791	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27143792	27143953	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27143954	27144075	0.44	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27143954	27144075	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27144076	27144145	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27144146	27144328	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27144146	27144328	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27144329	27144459	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27144460	27144768	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27144460	27144768	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27144769	27144854	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27144855	27145013	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27144855	27145013	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145014	27145164	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145165	27145347	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145165	27145347	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145348	27145438	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145439	27145549	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145439	27145549	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145550	27145645	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145646	27145828	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145646	27145828	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27145829	27145973	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27145974	27146055	1	-	1	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27145974	27146055	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146056	27146209	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146210	27146273	1	-	2	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146210	27146273	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146274	27146406	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146407	27146517	1	-	2	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146407	27146517	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146518	27146603	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146604	27146742	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146604	27146742	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146743	27146824	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27146825	27146932	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27146825	27146932	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27146933	27147025	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147026	27147149	0.98	-	1	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147026	27147149	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147150	27147256	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147257	27147351	0.99	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147257	27147351	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147352	27147584	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147585	27147716	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147585	27147716	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147717	27147795	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147796	27147915	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147796	27147915	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27147916	27147998	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27147999	27148085	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27147999	27148085	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148086	27148257	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27148258	27148408	1	-	1	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27148258	27148408	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148409	27148530	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27148531	27148625	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27148531	27148625	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148626	27148814	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27148815	27148895	0.61	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27148815	27148895	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27148896	27149013	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149014	27149070	1	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149014	27149070	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27149071	27149267	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149268	27149427	1	-	1	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149268	27149427	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27149428	27149683	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149684	27149846	1	-	2	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149684	27149846	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27149847	27149937	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27149938	27150042	1	-	2	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27149938	27150042	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27150043	27150162	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27150163	27150262	0.91	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27150163	27150262	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27150263	27150338	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27150339	27150433	1	-	2	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27150339	27150433	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	intron	27150434	27150543	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	CDS	27150544	27150712	0.51	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	exon	27150544	27150712	.	-	.	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
Phchi.S1	AUGUSTUS	start_codon	27150710	27150712	.	-	0	transcript_id "Phchi.S1G430000.t2"; gene_id "Phchi.S1G430000"
# This transcript jg12081.t2 is derived from g7756.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12082.t1 is derived from g7757.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2169202	2170721	.	-	.	Phchi.S2G016200
Phchi.S2	AUGUSTUS	transcript	2169202	2170721	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	stop_codon	2169199	2169201	.	-	0	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169202	2169375	0.98	-	0	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169202	2169375	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2169376	2169466	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169467	2169690	1	-	2	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169467	2169690	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2169691	2169833	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169834	2170409	0.73	-	2	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169834	2170409	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2170410	2170561	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2170562	2170721	0.57	-	0	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2170562	2170721	.	-	.	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	start_codon	2170719	2170721	.	-	0	transcript_id "Phchi.S2G016200.t1"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	transcript	2169202	2170721	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	stop_codon	2169199	2169201	.	-	0	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169202	2169375	0.92	-	0	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169202	2169375	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2169376	2169466	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169467	2169600	1	-	2	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169467	2169600	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2169601	2169833	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169834	2170409	0.8	-	2	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169834	2170409	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2170410	2170561	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2170562	2170721	0.55	-	0	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2170562	2170721	.	-	.	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	start_codon	2170719	2170721	.	-	0	transcript_id "Phchi.S2G016200.t2"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	transcript	2169202	2170721	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	stop_codon	2169199	2169201	.	-	0	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169202	2169375	0.98	-	0	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169202	2169375	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2169376	2169466	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169467	2169606	0.77	-	2	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169467	2169606	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2169607	2169833	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2169834	2170409	0.74	-	2	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2169834	2170409	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	intron	2170410	2170561	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	CDS	2170562	2170721	0.56	-	0	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	exon	2170562	2170721	.	-	.	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
Phchi.S2	AUGUSTUS	start_codon	2170719	2170721	.	-	0	transcript_id "Phchi.S2G016200.t3"; gene_id "Phchi.S2G016200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg156.t1 is derived from g9938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	889715	891400	.	-	.	Phchi.S6G011500
Phchi.S6	AUGUSTUS	transcript	889715	891400	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	stop_codon	889712	889714	.	-	0	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	889715	889804	0.97	-	0	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	889715	889804	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	889805	889936	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	889937	889992	0.83	-	2	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	889937	889992	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	889993	890087	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	890088	890194	0.98	-	1	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	890088	890194	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	890195	890308	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	890309	890396	0.43	-	2	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	890309	890396	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	890397	890554	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	890555	890568	0.95	-	1	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	890555	890568	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	890569	890668	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	890669	890790	0.95	-	0	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	890669	890790	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	890791	890999	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	891000	891298	0.7	-	2	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	891000	891298	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	intron	891299	891390	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	CDS	891391	891400	0.97	-	0	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	exon	891391	891400	.	-	.	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
Phchi.S6	AUGUSTUS	start_codon	891398	891400	.	-	0	transcript_id "Phchi.S6G011500.t1"; gene_id "Phchi.S6G011500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9941.t1 is derived from g7117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44593152	44593804	.	+	.	Phchi.S1G710000
Phchi.S1	AUGUSTUS	transcript	44593152	44593804	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	start_codon	44593152	44593154	.	+	0	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	CDS	44593152	44593156	0.87	+	0	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	exon	44593152	44593156	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	intron	44593157	44593320	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	CDS	44593321	44593407	0.89	+	1	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	exon	44593321	44593407	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	intron	44593408	44593535	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	CDS	44593536	44593601	0.64	+	1	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	exon	44593536	44593601	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	intron	44593602	44593710	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	CDS	44593711	44593804	0.59	+	1	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	exon	44593711	44593804	.	+	.	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
Phchi.S1	AUGUSTUS	stop_codon	44593805	44593807	.	+	0	transcript_id "Phchi.S1G710000.t1"; gene_id "Phchi.S1G710000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8452.t1 is derived from g5627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36008274	36010289	.	+	.	Phchi.S1G561100
Phchi.S1	AUGUSTUS	transcript	36008274	36010289	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	start_codon	36008274	36008276	.	+	0	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36008274	36008559	0.86	+	0	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36008274	36008559	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	intron	36008560	36008700	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36008701	36009068	1	+	2	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36008701	36009068	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	intron	36009069	36009200	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36009201	36009731	0.92	+	0	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36009201	36009731	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	intron	36009732	36009839	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36009840	36010289	0.81	+	0	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36009840	36010289	.	+	.	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	stop_codon	36010290	36010292	.	+	0	transcript_id "Phchi.S1G561100.t1"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	transcript	36008274	36010289	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	start_codon	36008274	36008276	.	+	0	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36008274	36008559	0.89	+	0	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36008274	36008559	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	intron	36008560	36008697	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36008698	36009068	0.95	+	2	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36008698	36009068	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	intron	36009069	36009200	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36009201	36009731	0.89	+	0	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36009201	36009731	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	intron	36009732	36009839	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	CDS	36009840	36010289	0.81	+	0	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	exon	36009840	36010289	.	+	.	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
Phchi.S1	AUGUSTUS	stop_codon	36010290	36010292	.	+	0	transcript_id "Phchi.S1G561100.t2"; gene_id "Phchi.S1G561100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg37.t1 is derived from g9797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C67	AUGUSTUS	gene	22151	22649	.	+	.	Phchi.C67G000300
Phchi.C67	AUGUSTUS	transcript	22151	22649	.	+	.	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	start_codon	22151	22153	.	+	0	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	CDS	22151	22351	0.94	+	0	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	exon	22151	22351	.	+	.	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	intron	22352	22550	.	+	.	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	CDS	22551	22649	0.59	+	0	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	exon	22551	22649	.	+	.	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
Phchi.C67	AUGUSTUS	stop_codon	22650	22652	.	+	0	transcript_id "Phchi.C67G000300.t1"; gene_id "Phchi.C67G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9009.t1 is derived from g6184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39130207	39131244	.	-	.	Phchi.S1G616800
Phchi.S1	AUGUSTUS	transcript	39130207	39131244	.	-	.	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	stop_codon	39130204	39130206	.	-	0	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	CDS	39130207	39130237	0.65	-	1	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	exon	39130207	39130237	.	-	.	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	intron	39130238	39130424	.	-	.	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	CDS	39130425	39130707	0.77	-	2	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	exon	39130425	39130707	.	-	.	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	intron	39130708	39130799	.	-	.	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	CDS	39130800	39131244	0.95	-	0	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	exon	39130800	39131244	.	-	.	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
Phchi.S1	AUGUSTUS	start_codon	39131242	39131244	.	-	0	transcript_id "Phchi.S1G616800.t1"; gene_id "Phchi.S1G616800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8791.t1 is derived from g5966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37973439	37973909	.	+	.	Phchi.S1G595000
Phchi.S1	AUGUSTUS	transcript	37973439	37973909	.	+	.	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	start_codon	37973439	37973441	.	+	0	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	CDS	37973439	37973538	0.43	+	0	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	exon	37973439	37973538	.	+	.	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	intron	37973539	37973610	.	+	.	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	CDS	37973611	37973660	0.48	+	2	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	exon	37973611	37973660	.	+	.	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	intron	37973661	37973840	.	+	.	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	CDS	37973841	37973909	0.67	+	0	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	exon	37973841	37973909	.	+	.	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
Phchi.S1	AUGUSTUS	stop_codon	37973910	37973912	.	+	0	transcript_id "Phchi.S1G595000.t1"; gene_id "Phchi.S1G595000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7495.t1 is derived from g4669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29644141	29644911	.	-	.	Phchi.S1G465400
Phchi.S1	AUGUSTUS	transcript	29644141	29644911	.	-	.	transcript_id "Phchi.S1G465400.t1"; gene_id "Phchi.S1G465400"
Phchi.S1	AUGUSTUS	stop_codon	29644138	29644140	.	-	0	transcript_id "Phchi.S1G465400.t1"; gene_id "Phchi.S1G465400"
Phchi.S1	AUGUSTUS	CDS	29644141	29644911	0.49	-	0	transcript_id "Phchi.S1G465400.t1"; gene_id "Phchi.S1G465400"
Phchi.S1	AUGUSTUS	exon	29644141	29644911	.	-	.	transcript_id "Phchi.S1G465400.t1"; gene_id "Phchi.S1G465400"
Phchi.S1	AUGUSTUS	start_codon	29644909	29644911	.	-	0	transcript_id "Phchi.S1G465400.t1"; gene_id "Phchi.S1G465400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg2495.t1 is derived from g9415.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6966066	6968547	.	+	.	Phchi.S5G110400
Phchi.S5	AUGUSTUS	transcript	6966145	6968547	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	start_codon	6966145	6966147	.	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966145	6966159	0.49	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966145	6966159	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966160	6966231	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966232	6966428	0.98	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966232	6966428	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966429	6966586	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966587	6966651	0.68	+	1	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966587	6966651	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966652	6966799	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966800	6966822	0.68	+	2	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966800	6966822	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966823	6966928	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966929	6966983	1	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966929	6966983	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966984	6967115	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967116	6967162	0.83	+	2	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967116	6967162	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967163	6967312	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967313	6967393	0.77	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967313	6967393	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967394	6967862	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967863	6967931	0.77	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967863	6967931	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967932	6968014	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968015	6968028	0.77	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968015	6968028	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968029	6968256	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968257	6968406	1	+	1	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968257	6968406	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968407	6968483	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968484	6968547	1	+	1	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968484	6968547	.	+	.	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	stop_codon	6968548	6968550	.	+	0	transcript_id "Phchi.S5G110400.t1"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	transcript	6966086	6968547	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	start_codon	6966086	6966088	.	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966086	6966142	0.33	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966086	6966142	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966143	6966231	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966232	6966428	0.71	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966232	6966428	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966429	6966586	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966587	6966651	0.66	+	1	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966587	6966651	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966652	6966799	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966800	6966822	0.66	+	2	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966800	6966822	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966823	6966928	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966929	6966983	0.99	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966929	6966983	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966984	6967115	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967116	6967162	0.85	+	2	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967116	6967162	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967163	6967312	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967313	6967393	0.68	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967313	6967393	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967394	6967862	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967863	6967931	0.84	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967863	6967931	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967932	6968014	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968015	6968028	0.84	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968015	6968028	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968029	6968256	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968257	6968406	1	+	1	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968257	6968406	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968407	6968483	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968484	6968547	1	+	1	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968484	6968547	.	+	.	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	stop_codon	6968548	6968550	.	+	0	transcript_id "Phchi.S5G110400.t2"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	transcript	6966066	6968547	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	start_codon	6966066	6966068	.	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966066	6966095	0.59	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966066	6966095	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966096	6966231	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966232	6966428	0.71	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966232	6966428	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966429	6966586	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966587	6966651	0.64	+	1	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966587	6966651	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966652	6966799	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966800	6966822	0.64	+	2	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966800	6966822	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966823	6966928	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966929	6966983	0.99	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966929	6966983	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966984	6967115	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967116	6967162	0.75	+	2	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967116	6967162	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967163	6967312	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967313	6967393	0.62	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967313	6967393	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967394	6967862	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967863	6967931	0.76	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967863	6967931	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967932	6968014	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968015	6968028	0.76	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968015	6968028	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968029	6968256	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968257	6968406	1	+	1	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968257	6968406	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968407	6968483	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968484	6968547	1	+	1	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968484	6968547	.	+	.	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	stop_codon	6968548	6968550	.	+	0	transcript_id "Phchi.S5G110400.t3"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	transcript	6966145	6968547	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	start_codon	6966145	6966147	.	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966145	6966159	0.48	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966145	6966159	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966160	6966231	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966232	6966428	0.98	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966232	6966428	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966429	6966586	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966587	6966651	0.63	+	1	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966587	6966651	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966652	6966799	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966800	6966822	0.63	+	2	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966800	6966822	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966823	6966928	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6966929	6966983	0.96	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6966929	6966983	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6966984	6967115	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967116	6967162	0.58	+	2	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967116	6967162	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967163	6967312	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967313	6967387	0.5	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967313	6967387	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967388	6967862	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6967863	6967931	0.51	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6967863	6967931	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6967932	6968014	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968015	6968028	0.51	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968015	6968028	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968029	6968256	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968257	6968406	1	+	1	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968257	6968406	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	intron	6968407	6968483	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	CDS	6968484	6968547	1	+	1	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	exon	6968484	6968547	.	+	.	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
Phchi.S5	AUGUSTUS	stop_codon	6968548	6968550	.	+	0	transcript_id "Phchi.S5G110400.t4"; gene_id "Phchi.S5G110400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3554.t1 is derived from g723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4458213	4459223	.	-	.	Phchi.S1G071300
Phchi.S1	AUGUSTUS	transcript	4458213	4459223	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	stop_codon	4458210	4458212	.	-	0	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	CDS	4458213	4458354	0.99	-	1	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	exon	4458213	4458354	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	intron	4458355	4458451	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	CDS	4458452	4458538	0.99	-	1	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	exon	4458452	4458538	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	intron	4458539	4458760	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	CDS	4458761	4458920	0.81	-	2	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	exon	4458761	4458920	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	intron	4458921	4459036	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	CDS	4459037	4459223	0.86	-	0	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	exon	4459037	4459223	.	-	.	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
Phchi.S1	AUGUSTUS	start_codon	4459221	4459223	.	-	0	transcript_id "Phchi.S1G071300.t1"; gene_id "Phchi.S1G071300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13867.t1 is derived from g12334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9369567	9370988	.	-	.	Phchi.S3G118600
Phchi.S3	AUGUSTUS	transcript	9369567	9370988	.	-	.	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	stop_codon	9369564	9369566	.	-	0	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	CDS	9369567	9369988	1	-	2	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	exon	9369567	9369988	.	-	.	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	intron	9369989	9370086	.	-	.	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	CDS	9370087	9370754	1	-	1	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	exon	9370087	9370754	.	-	.	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	intron	9370755	9370902	.	-	.	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	CDS	9370903	9370988	0.99	-	0	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	exon	9370903	9370988	.	-	.	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
Phchi.S3	AUGUSTUS	start_codon	9370986	9370988	.	-	0	transcript_id "Phchi.S3G118600.t1"; gene_id "Phchi.S3G118600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7363.t1 is derived from g4535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28779510	28780914	.	+	.	Phchi.S1G452200
Phchi.S1	AUGUSTUS	transcript	28779510	28780914	.	+	.	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	start_codon	28779510	28779512	.	+	0	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	CDS	28779510	28780031	0.85	+	0	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	exon	28779510	28780031	.	+	.	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	intron	28780032	28780302	.	+	.	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	CDS	28780303	28780914	0.88	+	0	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	exon	28780303	28780914	.	+	.	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
Phchi.S1	AUGUSTUS	stop_codon	28780915	28780917	.	+	0	transcript_id "Phchi.S1G452200.t1"; gene_id "Phchi.S1G452200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1888.t1 is derived from g8808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3712029	3713596	.	-	.	Phchi.S5G049700
Phchi.S5	AUGUSTUS	transcript	3712029	3713596	.	-	.	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	stop_codon	3712026	3712028	.	-	0	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	CDS	3712029	3713016	0.7	-	1	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	exon	3712029	3713016	.	-	.	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	intron	3713017	3713156	.	-	.	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	CDS	3713157	3713596	0.67	-	0	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	exon	3713157	3713596	.	-	.	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
Phchi.S5	AUGUSTUS	start_codon	3713594	3713596	.	-	0	transcript_id "Phchi.S5G049700.t1"; gene_id "Phchi.S5G049700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7790.t1 is derived from g4964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31197389	31199121	.	+	.	Phchi.S1G494900
Phchi.S1	AUGUSTUS	transcript	31197389	31199121	.	+	.	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	start_codon	31197389	31197391	.	+	0	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	CDS	31197389	31197604	0.53	+	0	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	exon	31197389	31197604	.	+	.	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	intron	31197605	31198046	.	+	.	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	CDS	31198047	31198492	0.27	+	0	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	exon	31198047	31198492	.	+	.	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	intron	31198493	31198706	.	+	.	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	CDS	31198707	31199121	0.52	+	1	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	exon	31198707	31199121	.	+	.	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
Phchi.S1	AUGUSTUS	stop_codon	31199122	31199124	.	+	0	transcript_id "Phchi.S1G494900.t1"; gene_id "Phchi.S1G494900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7981.t1 is derived from g5156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32212284	32218250	.	-	.	Phchi.S1G514000
Phchi.S1	AUGUSTUS	transcript	32212284	32218250	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	stop_codon	32212281	32212283	.	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32212284	32212432	0.69	-	2	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32212284	32212432	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32212433	32212556	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32212557	32213501	0.66	-	2	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32212557	32213501	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32213502	32213588	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32213589	32213720	1	-	2	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32213589	32213720	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32213721	32213811	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32213812	32213955	0.67	-	2	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32213812	32213955	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32213956	32214157	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32214158	32214239	0.84	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32214158	32214239	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32214240	32214365	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32214366	32214416	1	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32214366	32214416	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32214417	32214525	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32214526	32214585	1	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32214526	32214585	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32214586	32215025	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32215026	32215153	1	-	2	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32215026	32215153	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32215154	32215289	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32215290	32216229	1	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32215290	32216229	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32216230	32216486	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32216487	32216674	1	-	2	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32216487	32216674	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32216675	32216801	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32216802	32216881	1	-	1	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32216802	32216881	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	intron	32216882	32217054	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	CDS	32217055	32218250	1	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	exon	32217055	32218250	.	-	.	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
Phchi.S1	AUGUSTUS	start_codon	32218248	32218250	.	-	0	transcript_id "Phchi.S1G514000.t1"; gene_id "Phchi.S1G514000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13713.t1 is derived from g12180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8331968	8332489	.	-	.	Phchi.S3G103200
Phchi.S3	AUGUSTUS	transcript	8331968	8332489	.	-	.	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	stop_codon	8331965	8331967	.	-	0	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	CDS	8331968	8332076	0.99	-	1	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	exon	8331968	8332076	.	-	.	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	intron	8332077	8332280	.	-	.	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	CDS	8332281	8332489	1	-	0	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	exon	8332281	8332489	.	-	.	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
Phchi.S3	AUGUSTUS	start_codon	8332487	8332489	.	-	0	transcript_id "Phchi.S3G103200.t1"; gene_id "Phchi.S3G103200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8579.t1 is derived from g5754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36719988	36721847	.	+	.	Phchi.S1G573800
Phchi.S1	AUGUSTUS	transcript	36719988	36721847	.	+	.	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	start_codon	36719988	36719990	.	+	0	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	CDS	36719988	36720329	0.44	+	0	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	exon	36719988	36720329	.	+	.	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	intron	36720330	36720590	.	+	.	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	CDS	36720591	36721847	0.66	+	0	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	exon	36720591	36721847	.	+	.	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
Phchi.S1	AUGUSTUS	stop_codon	36721848	36721850	.	+	0	transcript_id "Phchi.S1G573800.t1"; gene_id "Phchi.S1G573800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3959.t1 is derived from g1128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6726026	6726856	.	-	.	Phchi.S1G111800
Phchi.S1	AUGUSTUS	transcript	6726026	6726856	.	-	.	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	stop_codon	6726023	6726025	.	-	0	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	CDS	6726026	6726071	0.98	-	1	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	exon	6726026	6726071	.	-	.	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	intron	6726072	6726203	.	-	.	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	CDS	6726204	6726856	0.88	-	0	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	exon	6726204	6726856	.	-	.	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	start_codon	6726854	6726856	.	-	0	transcript_id "Phchi.S1G111800.t1"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	transcript	6726097	6726856	.	-	.	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	stop_codon	6726094	6726096	.	-	0	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	CDS	6726097	6726124	0.63	-	1	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	exon	6726097	6726124	.	-	.	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	intron	6726125	6726203	.	-	.	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	CDS	6726204	6726856	0.57	-	0	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	exon	6726204	6726856	.	-	.	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
Phchi.S1	AUGUSTUS	start_codon	6726854	6726856	.	-	0	transcript_id "Phchi.S1G111800.t2"; gene_id "Phchi.S1G111800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4884.t1 is derived from g2054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13211129	13211935	.	+	.	Phchi.S1G204300
Phchi.S1	AUGUSTUS	transcript	13211129	13211935	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	start_codon	13211129	13211131	.	+	0	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	CDS	13211129	13211179	0.49	+	0	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	exon	13211129	13211179	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	intron	13211180	13211316	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	CDS	13211317	13211365	0.99	+	0	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	exon	13211317	13211365	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	intron	13211366	13211459	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	CDS	13211460	13211607	1	+	2	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	exon	13211460	13211607	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	intron	13211608	13211793	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	CDS	13211794	13211935	0.77	+	1	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	exon	13211794	13211935	.	+	.	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
Phchi.S1	AUGUSTUS	stop_codon	13211936	13211938	.	+	0	transcript_id "Phchi.S1G204300.t1"; gene_id "Phchi.S1G204300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12127.t1 is derived from g7803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4010515	4012521	.	+	.	Phchi.S2G020700
Phchi.S2	AUGUSTUS	transcript	4010515	4012521	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	start_codon	4010515	4010517	.	+	0	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	CDS	4010515	4010573	0.72	+	0	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	exon	4010515	4010573	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	intron	4010574	4010941	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	CDS	4010942	4011323	1	+	1	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	exon	4010942	4011323	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	intron	4011324	4011460	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	CDS	4011461	4011657	1	+	0	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	exon	4011461	4011657	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	intron	4011658	4011899	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	CDS	4011900	4012044	1	+	1	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	exon	4011900	4012044	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	intron	4012045	4012162	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	CDS	4012163	4012322	1	+	0	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	exon	4012163	4012322	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	intron	4012323	4012486	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	CDS	4012487	4012521	1	+	2	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	exon	4012487	4012521	.	+	.	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
Phchi.S2	AUGUSTUS	stop_codon	4012522	4012524	.	+	0	transcript_id "Phchi.S2G020700.t1"; gene_id "Phchi.S2G020700"
# This transcript jg2385.t2 is derived from g9305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2386.t1 is derived from g9306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6450372	6453162	.	+	.	Phchi.S5G099500
Phchi.S5	AUGUSTUS	transcript	6450372	6453162	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	start_codon	6450372	6450374	.	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6450372	6450494	0.63	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6450372	6450494	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6450495	6450641	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6450642	6450980	0.63	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6450642	6450980	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6450981	6451064	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6451065	6451154	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6451065	6451154	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6451155	6451255	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6451256	6451333	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6451256	6451333	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6451334	6451427	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6451428	6451502	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6451428	6451502	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6451503	6451649	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6451650	6451702	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6451650	6451702	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6451703	6451777	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6451778	6451928	1	+	1	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6451778	6451928	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6451929	6452014	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6452015	6452128	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6452015	6452128	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6452129	6452219	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6452220	6452346	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6452220	6452346	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6452347	6452459	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6452460	6452563	1	+	2	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6452460	6452563	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6452564	6452657	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6452658	6452799	1	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6452658	6452799	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6452800	6452941	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6452942	6452994	1	+	2	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6452942	6452994	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	intron	6452995	6453084	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	CDS	6453085	6453162	0.79	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	exon	6453085	6453162	.	+	.	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
Phchi.S5	AUGUSTUS	stop_codon	6453163	6453165	.	+	0	transcript_id "Phchi.S5G099500.t1"; gene_id "Phchi.S5G099500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8403.t1 is derived from g5578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35794346	35796055	.	+	.	Phchi.S1G556200
Phchi.S1	AUGUSTUS	transcript	35794346	35796055	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	start_codon	35794346	35794348	.	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35794346	35794609	0.68	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35794346	35794609	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35794610	35794786	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35794787	35794874	1	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35794787	35794874	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35794875	35794957	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35794958	35795022	1	+	2	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35794958	35795022	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35795023	35795163	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35795164	35795212	1	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35795164	35795212	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35795213	35795337	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35795338	35795390	1	+	2	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35795338	35795390	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35795391	35795538	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35795539	35795654	1	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35795539	35795654	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35795655	35795751	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35795752	35795809	1	+	1	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35795752	35795809	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	intron	35795810	35795968	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	CDS	35795969	35796055	0.87	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	exon	35795969	35796055	.	+	.	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
Phchi.S1	AUGUSTUS	stop_codon	35796056	35796058	.	+	0	transcript_id "Phchi.S1G556200.t1"; gene_id "Phchi.S1G556200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15478.t1 is derived from g13946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19391690	19394005	.	+	.	Phchi.S3G279700
Phchi.S3	AUGUSTUS	transcript	19391690	19394005	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	start_codon	19391690	19391692	.	+	0	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	CDS	19391690	19391713	0.99	+	0	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	exon	19391690	19391713	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	intron	19391714	19392037	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	CDS	19392038	19393110	0.9	+	0	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	exon	19392038	19393110	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	intron	19393111	19393225	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	CDS	19393226	19393331	1	+	1	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	exon	19393226	19393331	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	intron	19393332	19393434	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	CDS	19393435	19393631	0.72	+	0	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	exon	19393435	19393631	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	intron	19393632	19393743	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	CDS	19393744	19394005	0.64	+	1	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	exon	19393744	19394005	.	+	.	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
Phchi.S3	AUGUSTUS	stop_codon	19394006	19394008	.	+	0	transcript_id "Phchi.S3G279700.t1"; gene_id "Phchi.S3G279700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10193.t1 is derived from g7369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46320286	46324572	.	+	.	Phchi.S1G735200
Phchi.S1	AUGUSTUS	transcript	46320286	46324572	.	+	.	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	start_codon	46320286	46320288	.	+	0	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	CDS	46320286	46321717	0.86	+	0	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	exon	46320286	46321717	.	+	.	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	intron	46321718	46321872	.	+	.	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	CDS	46321873	46323326	0.87	+	2	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	exon	46321873	46323326	.	+	.	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	intron	46323327	46323438	.	+	.	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	CDS	46323439	46324572	0.94	+	0	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	exon	46323439	46324572	.	+	.	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
Phchi.S1	AUGUSTUS	stop_codon	46324573	46324575	.	+	0	transcript_id "Phchi.S1G735200.t1"; gene_id "Phchi.S1G735200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11342.t1 is derived from g15392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5645490	5646574	.	+	.	Phchi.S4G092400
Phchi.S4	AUGUSTUS	transcript	5645490	5646574	.	+	.	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	start_codon	5645490	5645492	.	+	0	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	CDS	5645490	5645807	0.99	+	0	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	exon	5645490	5645807	.	+	.	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	intron	5645808	5645899	.	+	.	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	CDS	5645900	5646574	0.99	+	0	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	exon	5645900	5646574	.	+	.	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
Phchi.S4	AUGUSTUS	stop_codon	5646575	5646577	.	+	0	transcript_id "Phchi.S4G092400.t1"; gene_id "Phchi.S4G092400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3716.t1 is derived from g885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5348724	5351588	.	+	.	Phchi.S1G087500
Phchi.S1	AUGUSTUS	transcript	5348724	5351588	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	start_codon	5348724	5348726	.	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5348724	5348839	1	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5348724	5348839	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5348840	5349121	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5349122	5349222	1	+	1	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5349122	5349222	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5349223	5349542	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5349543	5349715	1	+	2	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5349543	5349715	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5349716	5349821	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5349822	5350053	1	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5349822	5350053	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5350054	5350234	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5350235	5350353	1	+	2	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5350235	5350353	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5350354	5350588	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5350589	5350645	1	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5350589	5350645	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5350646	5350741	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5350742	5350926	1	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5350742	5350926	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5350927	5351018	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5351019	5351163	1	+	1	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5351019	5351163	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5351164	5351258	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5351259	5351342	1	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5351259	5351342	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5351343	5351431	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5351432	5351495	1	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5351432	5351495	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5351496	5351580	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5351581	5351588	1	+	2	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5351581	5351588	.	+	.	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	stop_codon	5351589	5351591	.	+	0	transcript_id "Phchi.S1G087500.t1"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	transcript	5348724	5349429	.	+	.	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	start_codon	5348724	5348726	.	+	0	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5348724	5348839	1	+	0	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5348724	5348839	.	+	.	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5348840	5349121	.	+	.	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5349122	5349222	1	+	1	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5349122	5349222	.	+	.	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	intron	5349223	5349397	.	+	.	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	CDS	5349398	5349429	0.78	+	2	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	exon	5349398	5349429	.	+	.	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
Phchi.S1	AUGUSTUS	stop_codon	5349430	5349432	.	+	0	transcript_id "Phchi.S1G087500.t2"; gene_id "Phchi.S1G087500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13629.t1 is derived from g12096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7828859	7833823	.	+	.	Phchi.S3G094800
Phchi.S3	AUGUSTUS	transcript	7828859	7833823	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	start_codon	7828859	7828861	.	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7828859	7829132	0.89	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7828859	7829132	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7829133	7829691	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7829692	7829888	1	+	2	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7829692	7829888	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7829889	7829971	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7829972	7830178	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7829972	7830178	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7830179	7830276	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7830277	7830372	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7830277	7830372	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7830373	7830475	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7830476	7830664	0.99	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7830476	7830664	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7830665	7830778	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7830779	7830922	0.98	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7830779	7830922	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7830923	7831068	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7831069	7831302	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7831069	7831302	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7831303	7831423	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7831424	7831558	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7831424	7831558	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7831559	7831693	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7831694	7832029	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7831694	7832029	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7832030	7832137	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7832138	7832317	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7832138	7832317	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7832318	7832451	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7832452	7833429	1	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7832452	7833429	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	intron	7833430	7833517	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	CDS	7833518	7833823	0.99	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	exon	7833518	7833823	.	+	.	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
Phchi.S3	AUGUSTUS	stop_codon	7833824	7833826	.	+	0	transcript_id "Phchi.S3G094800.t1"; gene_id "Phchi.S3G094800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2907.t1 is derived from g76.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	417390	419833	.	-	.	Phchi.S1G006600
Phchi.S1	AUGUSTUS	transcript	417390	419833	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	stop_codon	417387	417389	.	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	417390	417431	1	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	417390	417431	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	417432	417522	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	417523	417585	0.96	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	417523	417585	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	417586	417687	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	417688	417776	1	-	2	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	417688	417776	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	417777	417959	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	417960	418083	1	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	417960	418083	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	418084	418163	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	418164	418485	1	-	1	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	418164	418485	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	418486	418647	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	418648	418857	1	-	1	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	418648	418857	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	418858	418932	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	418933	419047	1	-	2	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	418933	419047	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	419048	419145	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	419146	419251	1	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	419146	419251	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	419252	419353	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	419354	419467	1	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	419354	419467	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	intron	419468	419821	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	CDS	419822	419833	1	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	exon	419822	419833	.	-	.	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
Phchi.S1	AUGUSTUS	start_codon	419831	419833	.	-	0	transcript_id "Phchi.S1G006600.t1"; gene_id "Phchi.S1G006600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13050.t1 is derived from g11515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3908175	3909335	.	+	.	Phchi.S3G036900
Phchi.S3	AUGUSTUS	transcript	3908175	3909335	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	start_codon	3908175	3908177	.	+	0	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	CDS	3908175	3908350	0.57	+	0	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	exon	3908175	3908350	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	intron	3908351	3908436	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	CDS	3908437	3908546	0.85	+	1	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	exon	3908437	3908546	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	intron	3908547	3908766	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	CDS	3908767	3908844	0.72	+	2	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	exon	3908767	3908844	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	intron	3908845	3908922	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	CDS	3908923	3909335	0.95	+	2	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	exon	3908923	3909335	.	+	.	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
Phchi.S3	AUGUSTUS	stop_codon	3909336	3909338	.	+	0	transcript_id "Phchi.S3G036900.t1"; gene_id "Phchi.S3G036900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10212.t1 is derived from g7388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46396279	46396857	.	-	.	Phchi.S1G737100
Phchi.S1	AUGUSTUS	transcript	46396279	46396857	.	-	.	transcript_id "Phchi.S1G737100.t1"; gene_id "Phchi.S1G737100"
Phchi.S1	AUGUSTUS	stop_codon	46396276	46396278	.	-	0	transcript_id "Phchi.S1G737100.t1"; gene_id "Phchi.S1G737100"
Phchi.S1	AUGUSTUS	CDS	46396279	46396857	0.21	-	0	transcript_id "Phchi.S1G737100.t1"; gene_id "Phchi.S1G737100"
Phchi.S1	AUGUSTUS	exon	46396279	46396857	.	-	.	transcript_id "Phchi.S1G737100.t1"; gene_id "Phchi.S1G737100"
Phchi.S1	AUGUSTUS	start_codon	46396855	46396857	.	-	0	transcript_id "Phchi.S1G737100.t1"; gene_id "Phchi.S1G737100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8019.t1 is derived from g5194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32489468	32492522	.	-	.	Phchi.S1G517800
Phchi.S1	AUGUSTUS	transcript	32489468	32492522	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	stop_codon	32489465	32489467	.	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32489468	32489541	1	-	2	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32489468	32489541	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32489542	32489636	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32489637	32489695	1	-	1	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32489637	32489695	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32489696	32489790	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32489791	32489885	1	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32489791	32489885	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32489886	32489976	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32489977	32490040	1	-	1	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32489977	32490040	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32490041	32490137	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32490138	32490223	1	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32490138	32490223	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32490224	32490370	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32490371	32490459	1	-	2	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32490371	32490459	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32490460	32490587	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32490588	32490669	1	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32490588	32490669	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32490670	32490825	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32490826	32490868	1	-	1	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32490826	32490868	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32490869	32490981	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32490982	32491055	1	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32490982	32491055	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32491056	32491267	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32491268	32491337	1	-	1	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32491268	32491337	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32491338	32491416	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32491417	32491486	1	-	2	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32491417	32491486	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32491487	32491610	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32491611	32491705	1	-	1	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32491611	32491705	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32491706	32491857	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32491858	32491934	1	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32491858	32491934	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32491935	32492032	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32492033	32492127	1	-	2	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32492033	32492127	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	intron	32492128	32492452	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	CDS	32492453	32492522	0.84	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	exon	32492453	32492522	.	-	.	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
Phchi.S1	AUGUSTUS	start_codon	32492520	32492522	.	-	0	transcript_id "Phchi.S1G517800.t1"; gene_id "Phchi.S1G517800"
# This transcript jg3512.t2 is derived from g681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3513.t1 is derived from g682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4153667	4155058	.	+	.	Phchi.S1G067200
Phchi.S1	AUGUSTUS	transcript	4153667	4155058	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	start_codon	4153667	4153669	.	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4153667	4153699	1	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4153667	4153699	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	intron	4153700	4153906	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4153907	4154034	0.93	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4153907	4154034	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	intron	4154035	4154118	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4154119	4154245	0.93	+	1	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4154119	4154245	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	intron	4154246	4154343	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4154344	4154463	1	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4154344	4154463	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	intron	4154464	4154590	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4154591	4154667	1	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4154591	4154667	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	intron	4154668	4154773	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4154774	4154852	1	+	1	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4154774	4154852	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	intron	4154853	4154944	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	CDS	4154945	4155058	0.69	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	exon	4154945	4155058	.	+	.	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
Phchi.S1	AUGUSTUS	stop_codon	4155059	4155061	.	+	0	transcript_id "Phchi.S1G067200.t1"; gene_id "Phchi.S1G067200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15871.t1 is derived from g14341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21980969	21981937	.	+	.	Phchi.S3G319000
Phchi.S3	AUGUSTUS	transcript	21980969	21981937	.	+	.	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	start_codon	21980969	21980971	.	+	0	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	CDS	21980969	21981238	1	+	0	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	exon	21980969	21981238	.	+	.	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	intron	21981239	21981868	.	+	.	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	CDS	21981869	21981937	0.99	+	0	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	exon	21981869	21981937	.	+	.	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
Phchi.S3	AUGUSTUS	stop_codon	21981938	21981940	.	+	0	transcript_id "Phchi.S3G319000.t1"; gene_id "Phchi.S3G319000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg748.t1 is derived from g10530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5321250	5322023	.	+	.	Phchi.S6G070700
Phchi.S6	AUGUSTUS	transcript	5321250	5322023	.	+	.	transcript_id "Phchi.S6G070700.t1"; gene_id "Phchi.S6G070700"
Phchi.S6	AUGUSTUS	start_codon	5321250	5321252	.	+	0	transcript_id "Phchi.S6G070700.t1"; gene_id "Phchi.S6G070700"
Phchi.S6	AUGUSTUS	CDS	5321250	5322023	0.92	+	0	transcript_id "Phchi.S6G070700.t1"; gene_id "Phchi.S6G070700"
Phchi.S6	AUGUSTUS	exon	5321250	5322023	.	+	.	transcript_id "Phchi.S6G070700.t1"; gene_id "Phchi.S6G070700"
Phchi.S6	AUGUSTUS	stop_codon	5322024	5322026	.	+	0	transcript_id "Phchi.S6G070700.t1"; gene_id "Phchi.S6G070700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3572.t1 is derived from g741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4560129	4560443	.	-	.	Phchi.S1G073100
Phchi.S1	AUGUSTUS	transcript	4560129	4560443	.	-	.	transcript_id "Phchi.S1G073100.t1"; gene_id "Phchi.S1G073100"
Phchi.S1	AUGUSTUS	stop_codon	4560126	4560128	.	-	0	transcript_id "Phchi.S1G073100.t1"; gene_id "Phchi.S1G073100"
Phchi.S1	AUGUSTUS	CDS	4560129	4560443	0.96	-	0	transcript_id "Phchi.S1G073100.t1"; gene_id "Phchi.S1G073100"
Phchi.S1	AUGUSTUS	exon	4560129	4560443	.	-	.	transcript_id "Phchi.S1G073100.t1"; gene_id "Phchi.S1G073100"
Phchi.S1	AUGUSTUS	start_codon	4560441	4560443	.	-	0	transcript_id "Phchi.S1G073100.t1"; gene_id "Phchi.S1G073100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13023.t1 is derived from g11488.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3661550	3663594	.	-	.	Phchi.S3G034200
Phchi.S3	AUGUSTUS	transcript	3661550	3663594	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	stop_codon	3661547	3661549	.	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3661550	3661578	0.99	-	2	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3661550	3661578	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3661579	3661705	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3661706	3661731	0.91	-	1	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3661706	3661731	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3661732	3661940	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3661941	3662008	0.96	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3661941	3662008	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662009	3662088	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662089	3662265	1	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662089	3662265	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662266	3662345	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662346	3662498	1	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662346	3662498	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662499	3662567	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662568	3662651	1	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662568	3662651	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662652	3662723	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662724	3662806	1	-	2	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662724	3662806	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662807	3662907	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662908	3662971	1	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662908	3662971	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662972	3663066	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3663067	3663337	1	-	1	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3663067	3663337	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3663338	3663421	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3663422	3663594	0.98	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3663422	3663594	.	-	.	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	start_codon	3663592	3663594	.	-	0	transcript_id "Phchi.S3G034200.t1"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	transcript	3661550	3663428	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	stop_codon	3661547	3661549	.	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3661550	3661578	1	-	2	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3661550	3661578	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3661579	3661705	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3661706	3661731	0.88	-	1	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3661706	3661731	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3661732	3661940	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3661941	3662008	0.92	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3661941	3662008	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662009	3662088	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662089	3662265	1	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662089	3662265	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662266	3662345	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662346	3662498	1	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662346	3662498	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662499	3662567	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662568	3662651	1	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662568	3662651	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662652	3662723	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662724	3662806	1	-	2	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662724	3662806	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662807	3662907	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3662908	3662971	1	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3662908	3662971	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3662972	3663066	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3663067	3663329	1	-	2	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3663067	3663329	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	intron	3663330	3663421	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	CDS	3663422	3663428	1	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	exon	3663422	3663428	.	-	.	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
Phchi.S3	AUGUSTUS	start_codon	3663426	3663428	.	-	0	transcript_id "Phchi.S3G034200.t2"; gene_id "Phchi.S3G034200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13116.t1 is derived from g11581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4205961	4207733	.	+	.	Phchi.S3G043500
Phchi.S3	AUGUSTUS	transcript	4205961	4207733	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	start_codon	4205961	4205963	.	+	0	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	CDS	4205961	4206181	0.56	+	0	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	exon	4205961	4206181	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	intron	4206182	4206393	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	CDS	4206394	4206553	1	+	1	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	exon	4206394	4206553	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	intron	4206554	4206678	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	CDS	4206679	4206858	1	+	0	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	exon	4206679	4206858	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	intron	4206859	4206948	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	CDS	4206949	4207032	1	+	0	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	exon	4206949	4207032	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	intron	4207033	4207122	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	CDS	4207123	4207204	1	+	0	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	exon	4207123	4207204	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	intron	4207205	4207293	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	CDS	4207294	4207733	0.99	+	2	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	exon	4207294	4207733	.	+	.	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
Phchi.S3	AUGUSTUS	stop_codon	4207734	4207736	.	+	0	transcript_id "Phchi.S3G043500.t1"; gene_id "Phchi.S3G043500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5926.t1 is derived from g3097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19891729	19892750	.	+	.	Phchi.S1G308500
Phchi.S1	AUGUSTUS	transcript	19891729	19892750	.	+	.	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	start_codon	19891729	19891731	.	+	0	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	CDS	19891729	19892252	1	+	0	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	exon	19891729	19892252	.	+	.	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	intron	19892253	19892350	.	+	.	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	CDS	19892351	19892750	1	+	1	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	exon	19892351	19892750	.	+	.	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
Phchi.S1	AUGUSTUS	stop_codon	19892751	19892753	.	+	0	transcript_id "Phchi.S1G308500.t1"; gene_id "Phchi.S1G308500"
# This transcript jg12292.t2 is derived from g7968.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12293.t1 is derived from g7969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8959762	8961257	.	-	.	Phchi.S2G037300
Phchi.S2	AUGUSTUS	transcript	8959762	8961257	.	-	.	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	stop_codon	8959759	8959761	.	-	0	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	CDS	8959762	8959850	1	-	2	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	exon	8959762	8959850	.	-	.	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	intron	8959851	8960014	.	-	.	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	CDS	8960015	8960073	1	-	1	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	exon	8960015	8960073	.	-	.	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	intron	8960074	8961081	.	-	.	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	CDS	8961082	8961257	0.01	-	0	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	exon	8961082	8961257	.	-	.	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
Phchi.S2	AUGUSTUS	start_codon	8961255	8961257	.	-	0	transcript_id "Phchi.S2G037300.t1"; gene_id "Phchi.S2G037300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9824.t1 is derived from g7000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43965844	43966460	.	+	.	Phchi.S1G698300
Phchi.S1	AUGUSTUS	transcript	43965844	43966460	.	+	.	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	start_codon	43965844	43965846	.	+	0	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	CDS	43965844	43966092	0.36	+	0	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	exon	43965844	43966092	.	+	.	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	intron	43966093	43966235	.	+	.	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	CDS	43966236	43966460	0.45	+	0	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	exon	43966236	43966460	.	+	.	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
Phchi.S1	AUGUSTUS	stop_codon	43966461	43966463	.	+	0	transcript_id "Phchi.S1G698300.t1"; gene_id "Phchi.S1G698300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7320.t1 is derived from g4492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28484363	28487669	.	-	.	Phchi.S1G447900
Phchi.S1	AUGUSTUS	transcript	28484363	28487669	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	stop_codon	28484360	28484362	.	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28484363	28484449	1	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28484363	28484449	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28484450	28484558	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28484559	28484650	0.98	-	2	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28484559	28484650	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28484651	28484736	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28484737	28484822	0.85	-	1	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28484737	28484822	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28484823	28484927	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28484928	28485046	0.85	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28484928	28485046	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28485047	28485123	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28485124	28485195	1	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28485124	28485195	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28485196	28485358	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28485359	28485430	1	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28485359	28485430	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28485431	28485519	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28485520	28485693	1	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28485520	28485693	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28485694	28485764	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28485765	28485920	1	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28485765	28485920	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28485921	28486028	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28486029	28486110	1	-	1	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28486029	28486110	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28486111	28486208	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28486209	28486355	1	-	1	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28486209	28486355	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28486356	28486442	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28486443	28486629	0.99	-	2	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28486443	28486629	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28486630	28487169	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28487170	28487311	0.54	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28487170	28487311	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	intron	28487312	28487420	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	CDS	28487421	28487669	0.46	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	exon	28487421	28487669	.	-	.	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
Phchi.S1	AUGUSTUS	start_codon	28487667	28487669	.	-	0	transcript_id "Phchi.S1G447900.t1"; gene_id "Phchi.S1G447900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15421.t1 is derived from g13889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19009330	19010625	.	-	.	Phchi.S3G274000
Phchi.S3	AUGUSTUS	transcript	19009330	19010625	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	stop_codon	19009327	19009329	.	-	0	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	CDS	19009330	19009388	0.99	-	2	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	exon	19009330	19009388	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	intron	19009389	19009636	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	CDS	19009637	19009746	0.87	-	1	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	exon	19009637	19009746	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	intron	19009747	19010081	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	CDS	19010082	19010116	0.91	-	0	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	exon	19010082	19010116	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	intron	19010117	19010598	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	CDS	19010599	19010625	0.92	-	0	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	exon	19010599	19010625	.	-	.	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
Phchi.S3	AUGUSTUS	start_codon	19010623	19010625	.	-	0	transcript_id "Phchi.S3G274000.t1"; gene_id "Phchi.S3G274000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6197.t1 is derived from g3368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21442753	21444214	.	-	.	Phchi.S1G335600
Phchi.S1	AUGUSTUS	transcript	21442753	21444214	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	stop_codon	21442750	21442752	.	-	0	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	CDS	21442753	21443478	0.96	-	0	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	exon	21442753	21443478	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	intron	21443479	21443575	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	CDS	21443576	21443722	1	-	0	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	exon	21443576	21443722	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	intron	21443723	21443855	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	CDS	21443856	21444019	0.83	-	2	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	exon	21443856	21444019	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	intron	21444020	21444129	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	CDS	21444130	21444214	0.63	-	0	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	exon	21444130	21444214	.	-	.	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
Phchi.S1	AUGUSTUS	start_codon	21444212	21444214	.	-	0	transcript_id "Phchi.S1G335600.t1"; gene_id "Phchi.S1G335600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15431.t1 is derived from g13899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19055811	19058851	.	+	.	Phchi.S3G275000
Phchi.S3	AUGUSTUS	transcript	19055811	19058851	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	start_codon	19055811	19055813	.	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19055811	19056148	0.77	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19055811	19056148	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19056149	19056284	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19056285	19056369	0.36	+	1	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19056285	19056369	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19056370	19056468	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19056469	19056559	0.3	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19056469	19056559	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19056560	19056709	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19056710	19056907	0.99	+	2	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19056710	19056907	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19056908	19057011	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19057012	19057103	0.94	+	2	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19057012	19057103	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19057104	19057212	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19057213	19057442	0.94	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19057213	19057442	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19057443	19057641	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19057642	19057766	1	+	1	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19057642	19057766	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19057767	19057868	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19057869	19057990	1	+	2	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19057869	19057990	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19057991	19058101	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19058102	19058437	1	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19058102	19058437	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19058438	19058600	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19058601	19058731	0.71	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19058601	19058731	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	intron	19058732	19058814	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	CDS	19058815	19058851	0.71	+	1	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	exon	19058815	19058851	.	+	.	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
Phchi.S3	AUGUSTUS	stop_codon	19058852	19058854	.	+	0	transcript_id "Phchi.S3G275000.t1"; gene_id "Phchi.S3G275000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9007.t1 is derived from g6182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39123364	39124668	.	+	.	Phchi.S1G616600
Phchi.S1	AUGUSTUS	transcript	39123364	39124668	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	start_codon	39123364	39123366	.	+	0	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	CDS	39123364	39123516	0.97	+	0	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	exon	39123364	39123516	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	intron	39123517	39123599	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	CDS	39123600	39124211	0.96	+	0	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	exon	39123600	39124211	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	intron	39124212	39124330	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	CDS	39124331	39124486	1	+	0	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	exon	39124331	39124486	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	intron	39124487	39124584	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	CDS	39124585	39124668	1	+	0	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	exon	39124585	39124668	.	+	.	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
Phchi.S1	AUGUSTUS	stop_codon	39124669	39124671	.	+	0	transcript_id "Phchi.S1G616600.t1"; gene_id "Phchi.S1G616600"
# This transcript jg8478.t2 is derived from g5653.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8478.t3 is derived from g5653.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8479.t1 is derived from g5654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36138872	36140871	.	+	.	Phchi.S1G563800
Phchi.S1	AUGUSTUS	transcript	36138872	36140871	.	+	.	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	start_codon	36138872	36138874	.	+	0	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	CDS	36138872	36140074	0.42	+	0	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	exon	36138872	36140074	.	+	.	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	intron	36140075	36140154	.	+	.	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	CDS	36140155	36140871	0.64	+	0	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	exon	36140155	36140871	.	+	.	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
Phchi.S1	AUGUSTUS	stop_codon	36140872	36140874	.	+	0	transcript_id "Phchi.S1G563800.t1"; gene_id "Phchi.S1G563800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6528.t1 is derived from g3700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23495432	23498809	.	-	.	Phchi.S1G368700
Phchi.S1	AUGUSTUS	transcript	23495432	23498809	.	-	.	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	stop_codon	23495429	23495431	.	-	0	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	CDS	23495432	23495472	0.49	-	2	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	exon	23495432	23495472	.	-	.	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	intron	23495473	23495567	.	-	.	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	CDS	23495568	23495655	0.38	-	0	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	exon	23495568	23495655	.	-	.	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	intron	23495656	23495965	.	-	.	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	CDS	23495966	23498809	0.64	-	0	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	exon	23495966	23498809	.	-	.	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
Phchi.S1	AUGUSTUS	start_codon	23498807	23498809	.	-	0	transcript_id "Phchi.S1G368700.t1"; gene_id "Phchi.S1G368700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15332.t1 is derived from g13800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18430917	18432452	.	+	.	Phchi.S3G265100
Phchi.S3	AUGUSTUS	transcript	18430917	18432452	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	start_codon	18430917	18430919	.	+	0	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	CDS	18430917	18431372	0.85	+	0	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	exon	18430917	18431372	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	intron	18431373	18431475	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	CDS	18431476	18431703	0.97	+	0	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	exon	18431476	18431703	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	intron	18431704	18431813	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	CDS	18431814	18432069	0.97	+	0	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	exon	18431814	18432069	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	intron	18432070	18432216	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	CDS	18432217	18432452	0.97	+	2	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	exon	18432217	18432452	.	+	.	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
Phchi.S3	AUGUSTUS	stop_codon	18432453	18432455	.	+	0	transcript_id "Phchi.S3G265100.t1"; gene_id "Phchi.S3G265100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5872.t1 is derived from g3042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19491953	19492588	.	-	.	Phchi.S1G303100
Phchi.S1	AUGUSTUS	transcript	19491953	19492588	.	-	.	transcript_id "Phchi.S1G303100.t1"; gene_id "Phchi.S1G303100"
Phchi.S1	AUGUSTUS	stop_codon	19491950	19491952	.	-	0	transcript_id "Phchi.S1G303100.t1"; gene_id "Phchi.S1G303100"
Phchi.S1	AUGUSTUS	CDS	19491953	19492588	0.97	-	0	transcript_id "Phchi.S1G303100.t1"; gene_id "Phchi.S1G303100"
Phchi.S1	AUGUSTUS	exon	19491953	19492588	.	-	.	transcript_id "Phchi.S1G303100.t1"; gene_id "Phchi.S1G303100"
Phchi.S1	AUGUSTUS	start_codon	19492586	19492588	.	-	0	transcript_id "Phchi.S1G303100.t1"; gene_id "Phchi.S1G303100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6770.t1 is derived from g3942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25000048	25004787	.	-	.	Phchi.S1G392900
Phchi.S1	AUGUSTUS	transcript	25000048	25004787	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	stop_codon	25000045	25000047	.	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25000048	25000129	0.51	-	1	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25000048	25000129	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25000130	25000298	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25000299	25000365	0.38	-	2	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25000299	25000365	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25000366	25000628	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25000629	25000743	0.8	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25000629	25000743	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25000744	25000856	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25000857	25000952	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25000857	25000952	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25000953	25001079	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25001080	25001550	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25001080	25001550	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25001551	25001640	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25001641	25001715	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25001641	25001715	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25001716	25001903	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25001904	25002027	1	-	1	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25001904	25002027	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25002028	25002217	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25002218	25002360	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25002218	25002360	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25002361	25002468	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25002469	25002570	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25002469	25002570	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25002571	25002675	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25002676	25002720	0.99	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25002676	25002720	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25002721	25002847	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25002848	25002973	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25002848	25002973	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25002974	25003214	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25003215	25003349	0.98	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25003215	25003349	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25003350	25003464	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25003465	25003740	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25003465	25003740	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25003741	25003829	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25003830	25004045	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25003830	25004045	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25004046	25004140	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25004141	25004198	1	-	1	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25004141	25004198	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25004199	25004373	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25004374	25004507	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25004374	25004507	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	intron	25004508	25004583	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	CDS	25004584	25004787	1	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	exon	25004584	25004787	.	-	.	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
Phchi.S1	AUGUSTUS	start_codon	25004785	25004787	.	-	0	transcript_id "Phchi.S1G392900.t1"; gene_id "Phchi.S1G392900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4172.t1 is derived from g1341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8732854	8738461	.	+	.	Phchi.S1G133100
Phchi.S1	AUGUSTUS	transcript	8732854	8738461	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	start_codon	8732854	8732856	.	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8732854	8733558	0.97	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8732854	8733558	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8733559	8733719	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8733720	8733845	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8733720	8733845	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8733846	8733933	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8733934	8734085	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8733934	8734085	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8734086	8734179	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8734180	8734342	1	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8734180	8734342	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8734343	8734471	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8734472	8734531	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8734472	8734531	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8734532	8734715	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8734716	8734906	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8734716	8734906	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8734907	8735142	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8735143	8735184	1	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8735143	8735184	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8735185	8735271	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8735272	8735346	1	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8735272	8735346	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8735347	8735418	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8735419	8735484	1	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8735419	8735484	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8735485	8735646	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8735647	8735749	1	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8735647	8735749	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8735750	8735842	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8735843	8735907	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8735843	8735907	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8735908	8735994	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8735995	8736079	1	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8735995	8736079	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8736080	8736176	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8736177	8736254	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8736177	8736254	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8736255	8736412	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8736413	8736490	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8736413	8736490	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8736491	8736616	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8736617	8736730	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8736617	8736730	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8736731	8736804	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8736805	8736876	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8736805	8736876	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8736877	8736972	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8736973	8737098	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8736973	8737098	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737099	8737198	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8737199	8737247	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8737199	8737247	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737248	8737324	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8737325	8737383	1	+	2	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8737325	8737383	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737384	8737472	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8737473	8737481	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8737473	8737481	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737482	8737558	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8737559	8737579	1	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8737559	8737579	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737580	8737667	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8737668	8737801	0.7	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8737668	8737801	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737802	8737910	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8737911	8737954	0.67	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8737911	8737954	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8737955	8738067	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8738068	8738185	0.74	+	2	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8738068	8738185	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	intron	8738186	8738274	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	CDS	8738275	8738461	0.95	+	1	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	exon	8738275	8738461	.	+	.	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
Phchi.S1	AUGUSTUS	stop_codon	8738462	8738464	.	+	0	transcript_id "Phchi.S1G133100.t1"; gene_id "Phchi.S1G133100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg614.t1 is derived from g10396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4405790	4406659	.	-	.	Phchi.S6G057300
Phchi.S6	AUGUSTUS	transcript	4405790	4406659	.	-	.	transcript_id "Phchi.S6G057300.t1"; gene_id "Phchi.S6G057300"
Phchi.S6	AUGUSTUS	stop_codon	4405787	4405789	.	-	0	transcript_id "Phchi.S6G057300.t1"; gene_id "Phchi.S6G057300"
Phchi.S6	AUGUSTUS	CDS	4405790	4406659	0.52	-	0	transcript_id "Phchi.S6G057300.t1"; gene_id "Phchi.S6G057300"
Phchi.S6	AUGUSTUS	exon	4405790	4406659	.	-	.	transcript_id "Phchi.S6G057300.t1"; gene_id "Phchi.S6G057300"
Phchi.S6	AUGUSTUS	start_codon	4406657	4406659	.	-	0	transcript_id "Phchi.S6G057300.t1"; gene_id "Phchi.S6G057300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5523.t1 is derived from g2693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17404027	17405324	.	-	.	Phchi.S1G268200
Phchi.S1	AUGUSTUS	transcript	17404027	17405324	.	-	.	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	stop_codon	17404024	17404026	.	-	0	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	CDS	17404027	17404131	0.49	-	0	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	exon	17404027	17404131	.	-	.	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	intron	17404132	17404236	.	-	.	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	CDS	17404237	17405047	0.22	-	1	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	exon	17404237	17405047	.	-	.	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	intron	17405048	17405199	.	-	.	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	CDS	17405200	17405324	0.44	-	0	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	exon	17405200	17405324	.	-	.	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
Phchi.S1	AUGUSTUS	start_codon	17405322	17405324	.	-	0	transcript_id "Phchi.S1G268200.t1"; gene_id "Phchi.S1G268200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6162.t1 is derived from g3333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21254047	21255447	.	-	.	Phchi.S1G332100
Phchi.S1	AUGUSTUS	transcript	21254047	21255447	.	-	.	transcript_id "Phchi.S1G332100.t1"; gene_id "Phchi.S1G332100"
Phchi.S1	AUGUSTUS	stop_codon	21254044	21254046	.	-	0	transcript_id "Phchi.S1G332100.t1"; gene_id "Phchi.S1G332100"
Phchi.S1	AUGUSTUS	CDS	21254047	21255447	0.93	-	0	transcript_id "Phchi.S1G332100.t1"; gene_id "Phchi.S1G332100"
Phchi.S1	AUGUSTUS	exon	21254047	21255447	.	-	.	transcript_id "Phchi.S1G332100.t1"; gene_id "Phchi.S1G332100"
Phchi.S1	AUGUSTUS	start_codon	21255445	21255447	.	-	0	transcript_id "Phchi.S1G332100.t1"; gene_id "Phchi.S1G332100"
# This transcript jg4619.t2 is derived from g1789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4620.t1 is derived from g1790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11444610	11445455	.	+	.	Phchi.S1G177900
Phchi.S1	AUGUSTUS	transcript	11444610	11445455	.	+	.	transcript_id "Phchi.S1G177900.t1"; gene_id "Phchi.S1G177900"
Phchi.S1	AUGUSTUS	start_codon	11444610	11444612	.	+	0	transcript_id "Phchi.S1G177900.t1"; gene_id "Phchi.S1G177900"
Phchi.S1	AUGUSTUS	CDS	11444610	11445455	0.5	+	0	transcript_id "Phchi.S1G177900.t1"; gene_id "Phchi.S1G177900"
Phchi.S1	AUGUSTUS	exon	11444610	11445455	.	+	.	transcript_id "Phchi.S1G177900.t1"; gene_id "Phchi.S1G177900"
Phchi.S1	AUGUSTUS	stop_codon	11445456	11445458	.	+	0	transcript_id "Phchi.S1G177900.t1"; gene_id "Phchi.S1G177900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2571.t1 is derived from g9491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7429430	7430135	.	-	.	Phchi.S5G118000
Phchi.S5	AUGUSTUS	transcript	7429430	7430135	.	-	.	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	stop_codon	7429427	7429429	.	-	0	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	CDS	7429430	7429603	0.9	-	0	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	exon	7429430	7429603	.	-	.	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	intron	7429604	7429931	.	-	.	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	CDS	7429932	7430135	1	-	0	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	exon	7429932	7430135	.	-	.	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
Phchi.S5	AUGUSTUS	start_codon	7430133	7430135	.	-	0	transcript_id "Phchi.S5G118000.t1"; gene_id "Phchi.S5G118000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9809.t1 is derived from g6985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43835854	43838003	.	+	.	Phchi.S1G696800
Phchi.S1	AUGUSTUS	transcript	43835854	43838003	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	start_codon	43835854	43835856	.	+	0	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	CDS	43835854	43836037	0.89	+	0	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	exon	43835854	43836037	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	intron	43836038	43836128	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	CDS	43836129	43836346	1	+	2	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	exon	43836129	43836346	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	intron	43836347	43836431	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	CDS	43836432	43837000	1	+	0	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	exon	43836432	43837000	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	intron	43837001	43837099	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	CDS	43837100	43838003	1	+	1	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	exon	43837100	43838003	.	+	.	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
Phchi.S1	AUGUSTUS	stop_codon	43838004	43838006	.	+	0	transcript_id "Phchi.S1G696800.t1"; gene_id "Phchi.S1G696800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2686.t1 is derived from g9606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8204387	8207963	.	-	.	Phchi.S5G129500
Phchi.S5	AUGUSTUS	transcript	8204387	8207963	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	stop_codon	8204384	8204386	.	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8204387	8204728	0.99	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8204387	8204728	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8204729	8204817	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8204818	8205090	1	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8204818	8205090	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8205091	8205179	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8205180	8205362	1	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8205180	8205362	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8205363	8205465	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8205466	8205692	1	-	2	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8205466	8205692	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8205693	8205985	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8205986	8206166	1	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8205986	8206166	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8206167	8206279	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8206280	8206518	0.97	-	2	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8206280	8206518	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8206519	8206603	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8206604	8206782	1	-	1	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8206604	8206782	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8206783	8206910	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8206911	8206963	0.97	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8206911	8206963	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8206964	8207069	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8207070	8207159	0.9	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8207070	8207159	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8207160	8207275	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8207276	8207386	0.99	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8207276	8207386	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8207387	8207472	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8207473	8207754	1	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8207473	8207754	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	intron	8207755	8207864	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	CDS	8207865	8207963	0.94	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	exon	8207865	8207963	.	-	.	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
Phchi.S5	AUGUSTUS	start_codon	8207961	8207963	.	-	0	transcript_id "Phchi.S5G129500.t1"; gene_id "Phchi.S5G129500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11676.t1 is derived from g15727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7631310	7637143	.	+	.	Phchi.S4G125800
Phchi.S4	AUGUSTUS	transcript	7631310	7637143	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	start_codon	7631310	7631312	.	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7631310	7632421	0.91	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7631310	7632421	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7632422	7632528	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7632529	7632610	0.83	+	1	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7632529	7632610	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7632611	7632713	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7632714	7632905	0.9	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7632714	7632905	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7632906	7633051	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7633052	7633068	0.6	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7633052	7633068	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7633069	7633266	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7633267	7633426	0.68	+	1	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7633267	7633426	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7633427	7633563	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7633564	7633827	0.9	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7633564	7633827	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7633828	7633918	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7633919	7634041	1	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7633919	7634041	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7634042	7634126	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7634127	7634312	0.93	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7634127	7634312	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7634313	7634421	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7634422	7634503	0.59	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7634422	7634503	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7634504	7634611	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7634612	7635552	0.81	+	2	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7634612	7635552	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7635553	7635711	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7635712	7636225	0.86	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7635712	7636225	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7636226	7636307	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7636308	7636498	0.98	+	2	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7636308	7636498	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7636499	7636589	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7636590	7637021	0.48	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7636590	7637021	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	intron	7637022	7637116	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	CDS	7637117	7637143	0.45	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	exon	7637117	7637143	.	+	.	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
Phchi.S4	AUGUSTUS	stop_codon	7637144	7637146	.	+	0	transcript_id "Phchi.S4G125800.t1"; gene_id "Phchi.S4G125800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14232.t1 is derived from g12699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11675875	11678635	.	-	.	Phchi.S3G155100
Phchi.S3	AUGUSTUS	transcript	11675875	11678635	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	stop_codon	11675872	11675874	.	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11675875	11676153	0.42	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11675875	11676153	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11676154	11676256	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11676257	11676464	1	-	1	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11676257	11676464	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11676465	11676562	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11676563	11676807	1	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11676563	11676807	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11676808	11676967	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11676968	11677096	1	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11676968	11677096	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11677097	11677312	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11677313	11677543	1	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11677313	11677543	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11677544	11677706	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11677707	11677976	1	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11677707	11677976	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11677977	11678073	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11678074	11678218	1	-	1	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11678074	11678218	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11678219	11678399	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11678400	11678439	0.61	-	2	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11678400	11678439	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	intron	11678440	11678541	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	CDS	11678542	11678635	0.71	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	exon	11678542	11678635	.	-	.	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
Phchi.S3	AUGUSTUS	start_codon	11678633	11678635	.	-	0	transcript_id "Phchi.S3G155100.t1"; gene_id "Phchi.S3G155100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10078.t1 is derived from g7254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45637700	45641313	.	+	.	Phchi.S1G723700
Phchi.S1	AUGUSTUS	transcript	45637700	45641313	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	start_codon	45637700	45637702	.	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45637700	45638040	0.71	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45637700	45638040	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45638041	45638141	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45638142	45638320	0.96	+	1	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45638142	45638320	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45638321	45638485	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45638486	45638708	1	+	2	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45638486	45638708	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45638709	45638796	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45638797	45638938	1	+	1	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45638797	45638938	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45638939	45639108	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45639109	45639312	0.97	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45639109	45639312	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45639313	45639418	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45639419	45639553	0.99	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45639419	45639553	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45639554	45639666	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45639667	45639792	1	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45639667	45639792	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45639793	45639929	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45639930	45640107	0.92	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45639930	45640107	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45640108	45640188	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45640189	45640338	0.92	+	2	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45640189	45640338	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45640339	45640484	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45640485	45640511	0.97	+	2	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45640485	45640511	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45640512	45640591	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45640592	45640701	0.43	+	2	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45640592	45640701	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45640702	45640807	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45640808	45641001	0.97	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45640808	45641001	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	intron	45641002	45641126	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	CDS	45641127	45641313	1	+	1	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	exon	45641127	45641313	.	+	.	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
Phchi.S1	AUGUSTUS	stop_codon	45641314	45641316	.	+	0	transcript_id "Phchi.S1G723700.t1"; gene_id "Phchi.S1G723700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14229.t1 is derived from g12696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11666391	11668089	.	+	.	Phchi.S3G154800
Phchi.S3	AUGUSTUS	transcript	11666391	11668089	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	start_codon	11666391	11666393	.	+	0	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11666391	11666486	0.99	+	0	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11666391	11666486	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	intron	11666487	11666584	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11666585	11666712	1	+	0	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11666585	11666712	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	intron	11666713	11666889	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11666890	11667092	0.99	+	1	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11666890	11667092	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	intron	11667093	11667195	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11667196	11667321	1	+	2	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11667196	11667321	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	intron	11667322	11667417	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11667418	11667576	1	+	2	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11667418	11667576	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	intron	11667577	11667667	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11667668	11667861	1	+	2	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11667668	11667861	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	intron	11667862	11667957	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	CDS	11667958	11668089	0.99	+	0	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	exon	11667958	11668089	.	+	.	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
Phchi.S3	AUGUSTUS	stop_codon	11668090	11668092	.	+	0	transcript_id "Phchi.S3G154800.t1"; gene_id "Phchi.S3G154800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7492.t1 is derived from g4665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29628368	29632057	.	-	.	Phchi.S1G465100
Phchi.S1	AUGUSTUS	transcript	29628456	29632057	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	stop_codon	29628453	29628455	.	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29628456	29628518	0.99	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29628456	29628518	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29628519	29629195	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629196	29629264	1	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629196	29629264	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629265	29629408	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629409	29629698	1	-	2	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629409	29629698	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629699	29629784	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629785	29629821	1	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629785	29629821	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629822	29629901	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629902	29630068	1	-	2	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629902	29630068	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630069	29630167	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630168	29630252	1	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630168	29630252	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630253	29630340	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630341	29630413	1	-	1	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630341	29630413	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630414	29630503	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630504	29630679	1	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630504	29630679	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630680	29630805	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630806	29631015	1	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630806	29631015	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631016	29631112	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631113	29631250	0.72	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631113	29631250	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631251	29631355	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631356	29631479	0.99	-	1	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631356	29631479	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631480	29631636	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631637	29631756	1	-	1	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631637	29631756	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631757	29631896	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631897	29632057	0.98	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631897	29632057	.	-	.	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	start_codon	29632055	29632057	.	-	0	transcript_id "Phchi.S1G465100.t1"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	transcript	29628368	29632057	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	stop_codon	29628365	29628367	.	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29628368	29628518	0.94	-	1	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29628368	29628518	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29628519	29628683	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29628684	29628881	0.68	-	1	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29628684	29628881	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29628882	29628967	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29628968	29629058	0.44	-	2	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29628968	29629058	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629059	29629185	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629186	29629264	0.62	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629186	29629264	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629265	29629408	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629409	29629698	1	-	2	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629409	29629698	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629699	29629784	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629785	29629821	1	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629785	29629821	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29629822	29629901	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29629902	29630068	1	-	2	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29629902	29630068	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630069	29630167	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630168	29630252	1	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630168	29630252	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630253	29630340	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630341	29630413	1	-	1	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630341	29630413	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630414	29630503	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630504	29630679	1	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630504	29630679	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29630680	29630805	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29630806	29631015	1	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29630806	29631015	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631016	29631112	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631113	29631250	0.78	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631113	29631250	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631251	29631355	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631356	29631479	1	-	1	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631356	29631479	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631480	29631636	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631637	29631756	1	-	1	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631637	29631756	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	intron	29631757	29631896	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	CDS	29631897	29632057	0.94	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	exon	29631897	29632057	.	-	.	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
Phchi.S1	AUGUSTUS	start_codon	29632055	29632057	.	-	0	transcript_id "Phchi.S1G465100.t2"; gene_id "Phchi.S1G465100"
# This transcript jg8016.t2 is derived from g5191.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8017.t1 is derived from g5192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32487730	32488233	.	-	.	Phchi.S1G517600
Phchi.S1	AUGUSTUS	transcript	32487730	32488233	.	-	.	transcript_id "Phchi.S1G517600.t1"; gene_id "Phchi.S1G517600"
Phchi.S1	AUGUSTUS	stop_codon	32487727	32487729	.	-	0	transcript_id "Phchi.S1G517600.t1"; gene_id "Phchi.S1G517600"
Phchi.S1	AUGUSTUS	CDS	32487730	32488233	0.76	-	0	transcript_id "Phchi.S1G517600.t1"; gene_id "Phchi.S1G517600"
Phchi.S1	AUGUSTUS	exon	32487730	32488233	.	-	.	transcript_id "Phchi.S1G517600.t1"; gene_id "Phchi.S1G517600"
Phchi.S1	AUGUSTUS	start_codon	32488231	32488233	.	-	0	transcript_id "Phchi.S1G517600.t1"; gene_id "Phchi.S1G517600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10033.t1 is derived from g7209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45175279	45175554	.	+	.	Phchi.S1G719200
Phchi.S1	AUGUSTUS	transcript	45175279	45175554	.	+	.	transcript_id "Phchi.S1G719200.t1"; gene_id "Phchi.S1G719200"
Phchi.S1	AUGUSTUS	start_codon	45175279	45175281	.	+	0	transcript_id "Phchi.S1G719200.t1"; gene_id "Phchi.S1G719200"
Phchi.S1	AUGUSTUS	CDS	45175279	45175554	0.33	+	0	transcript_id "Phchi.S1G719200.t1"; gene_id "Phchi.S1G719200"
Phchi.S1	AUGUSTUS	exon	45175279	45175554	.	+	.	transcript_id "Phchi.S1G719200.t1"; gene_id "Phchi.S1G719200"
Phchi.S1	AUGUSTUS	stop_codon	45175555	45175557	.	+	0	transcript_id "Phchi.S1G719200.t1"; gene_id "Phchi.S1G719200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11751.t1 is derived from g15803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8004670	8006488	.	-	.	Phchi.S4G133300
Phchi.S4	AUGUSTUS	transcript	8004670	8006488	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	stop_codon	8004667	8004669	.	-	0	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8004670	8004758	0.63	-	2	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8004670	8004758	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	intron	8004759	8004856	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8004857	8005025	0.64	-	0	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8004857	8005025	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	intron	8005026	8005161	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8005162	8005358	1	-	2	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8005162	8005358	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	intron	8005359	8005456	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8005457	8005537	0.91	-	2	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8005457	8005537	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	intron	8005538	8005665	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8005666	8005718	0.79	-	1	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8005666	8005718	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	intron	8005719	8005816	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8005817	8006159	1	-	2	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8005817	8006159	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	intron	8006160	8006295	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	CDS	8006296	8006488	0.99	-	0	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	exon	8006296	8006488	.	-	.	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
Phchi.S4	AUGUSTUS	start_codon	8006486	8006488	.	-	0	transcript_id "Phchi.S4G133300.t1"; gene_id "Phchi.S4G133300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10474.t1 is derived from g14523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	555874	559536	.	-	.	Phchi.S4G005600
Phchi.S4	AUGUSTUS	transcript	555874	559536	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	stop_codon	555871	555873	.	-	0	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	555874	555982	0.78	-	1	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	555874	555982	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	555983	556208	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556209	556238	0.76	-	1	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556209	556238	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	556239	556325	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556326	556332	0.79	-	2	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556326	556332	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	556333	556554	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556555	556661	1	-	1	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556555	556661	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	556662	556913	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556914	557000	0.59	-	1	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556914	557000	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	557001	557244	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	557245	557383	0.61	-	2	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	557245	557383	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	557384	557698	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	557699	558016	0.96	-	2	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	557699	558016	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	558017	558304	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	558305	559191	0.52	-	1	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	558305	559191	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	559192	559345	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	559346	559536	0.66	-	0	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	559346	559536	.	-	.	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	start_codon	559534	559536	.	-	0	transcript_id "Phchi.S4G005600.t1"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	transcript	555874	559536	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	stop_codon	555871	555873	.	-	0	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	555874	555982	0.69	-	1	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	555874	555982	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	555983	556208	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556209	556238	0.7	-	1	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556209	556238	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	556239	556325	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556326	556332	0.73	-	2	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556326	556332	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	556333	556527	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556528	556661	1	-	1	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556528	556661	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	556662	556913	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	556914	557000	0.73	-	1	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	556914	557000	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	557001	557244	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	557245	557383	0.7	-	2	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	557245	557383	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	557384	557698	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	557699	558016	0.92	-	2	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	557699	558016	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	558017	558304	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	558305	559191	0.45	-	1	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	558305	559191	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	intron	559192	559345	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	CDS	559346	559536	0.58	-	0	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	exon	559346	559536	.	-	.	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
Phchi.S4	AUGUSTUS	start_codon	559534	559536	.	-	0	transcript_id "Phchi.S4G005600.t2"; gene_id "Phchi.S4G005600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11871.t1 is derived from g15923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8935836	8938334	.	+	.	Phchi.S4G145300
Phchi.S4	AUGUSTUS	transcript	8935836	8938334	.	+	.	transcript_id "Phchi.S4G145300.t1"; gene_id "Phchi.S4G145300"
Phchi.S4	AUGUSTUS	start_codon	8935836	8935838	.	+	0	transcript_id "Phchi.S4G145300.t1"; gene_id "Phchi.S4G145300"
Phchi.S4	AUGUSTUS	CDS	8935836	8938334	1	+	0	transcript_id "Phchi.S4G145300.t1"; gene_id "Phchi.S4G145300"
Phchi.S4	AUGUSTUS	exon	8935836	8938334	.	+	.	transcript_id "Phchi.S4G145300.t1"; gene_id "Phchi.S4G145300"
Phchi.S4	AUGUSTUS	stop_codon	8938335	8938337	.	+	0	transcript_id "Phchi.S4G145300.t1"; gene_id "Phchi.S4G145300"
# This transcript jg4453.t2 is derived from g1623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4454.t1 is derived from g1624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10578132	10581950	.	-	.	Phchi.S1G161300
Phchi.S1	AUGUSTUS	transcript	10578132	10581950	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	stop_codon	10578129	10578131	.	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10578132	10578173	0.92	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10578132	10578173	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10578174	10578271	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10578272	10578288	1	-	2	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10578272	10578288	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10578289	10578377	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10578378	10579179	0.8	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10578378	10579179	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10579180	10579287	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10579288	10579332	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10579288	10579332	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10579333	10579463	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10579464	10579512	1	-	1	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10579464	10579512	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10579513	10579612	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10579613	10579710	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10579613	10579710	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10579711	10579873	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10579874	10579948	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10579874	10579948	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10579949	10580045	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10580046	10580105	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10580046	10580105	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10580106	10580197	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10580198	10580278	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10580198	10580278	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10580279	10580421	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10580422	10580464	1	-	1	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10580422	10580464	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10580465	10580608	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10580609	10580679	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10580609	10580679	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10580680	10580859	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10580860	10580955	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10580860	10580955	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10580956	10581029	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10581030	10581086	1	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10581030	10581086	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10581087	10581231	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10581232	10581344	1	-	2	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10581232	10581344	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	intron	10581345	10581436	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	CDS	10581437	10581950	0.92	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	exon	10581437	10581950	.	-	.	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
Phchi.S1	AUGUSTUS	start_codon	10581948	10581950	.	-	0	transcript_id "Phchi.S1G161300.t1"; gene_id "Phchi.S1G161300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15993.t1 is derived from g16025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C69	AUGUSTUS	gene	49731	51577	.	+	.	Phchi.C69G000100
Phchi.C69	AUGUSTUS	transcript	49731	51577	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	start_codon	49731	49733	.	+	0	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	CDS	49731	50180	0.6	+	0	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	exon	49731	50180	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	intron	50181	50266	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	CDS	50267	50381	0.39	+	0	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	exon	50267	50381	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	intron	50382	50514	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	CDS	50515	50895	0.38	+	2	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	exon	50515	50895	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	intron	50896	51003	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	CDS	51004	51224	0.74	+	2	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	exon	51004	51224	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	intron	51225	51400	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	CDS	51401	51577	1	+	0	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	exon	51401	51577	.	+	.	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
Phchi.C69	AUGUSTUS	stop_codon	51578	51580	.	+	0	transcript_id "Phchi.C69G000100.t1"; gene_id "Phchi.C69G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4142.t1 is derived from g1311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8614800	8616685	.	+	.	Phchi.S1G130100
Phchi.S1	AUGUSTUS	transcript	8614800	8616685	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	start_codon	8614800	8614802	.	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8614800	8615135	0.77	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8614800	8615135	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8615136	8615230	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8615231	8615392	0.81	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8615231	8615392	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8615393	8615484	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8615485	8615517	0.95	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8615485	8615517	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8615518	8615606	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8615607	8615642	0.95	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8615607	8615642	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8615643	8615741	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8615742	8615915	0.86	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8615742	8615915	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8615916	8616041	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8616042	8616226	0.68	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8616042	8616226	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8616227	8616355	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8616356	8616530	0.71	+	1	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8616356	8616530	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	intron	8616531	8616622	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	CDS	8616623	8616685	1	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	exon	8616623	8616685	.	+	.	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
Phchi.S1	AUGUSTUS	stop_codon	8616686	8616688	.	+	0	transcript_id "Phchi.S1G130100.t1"; gene_id "Phchi.S1G130100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7500.t1 is derived from g4674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29678991	29680064	.	-	.	Phchi.S1G465900
Phchi.S1	AUGUSTUS	transcript	29678991	29680064	.	-	.	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	stop_codon	29678988	29678990	.	-	0	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	CDS	29678991	29679538	0.94	-	2	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	exon	29678991	29679538	.	-	.	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	intron	29679539	29679689	.	-	.	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	CDS	29679690	29679727	0.88	-	1	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	exon	29679690	29679727	.	-	.	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	intron	29679728	29679861	.	-	.	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	CDS	29679862	29680064	0.85	-	0	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	exon	29679862	29680064	.	-	.	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
Phchi.S1	AUGUSTUS	start_codon	29680062	29680064	.	-	0	transcript_id "Phchi.S1G465900.t1"; gene_id "Phchi.S1G465900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1853.t1 is derived from g8773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3559934	3560635	.	-	.	Phchi.S5G046200
Phchi.S5	AUGUSTUS	transcript	3559934	3560635	.	-	.	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	stop_codon	3559931	3559933	.	-	0	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	CDS	3559934	3560310	0.77	-	2	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	exon	3559934	3560310	.	-	.	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	intron	3560311	3560421	.	-	.	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	CDS	3560422	3560635	0.69	-	0	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	exon	3560422	3560635	.	-	.	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
Phchi.S5	AUGUSTUS	start_codon	3560633	3560635	.	-	0	transcript_id "Phchi.S5G046200.t1"; gene_id "Phchi.S5G046200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14990.t1 is derived from g13458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16101103	16103219	.	+	.	Phchi.S3G230900
Phchi.S3	AUGUSTUS	transcript	16101103	16103219	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	start_codon	16101103	16101105	.	+	0	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	CDS	16101103	16101681	1	+	0	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	exon	16101103	16101681	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	intron	16101682	16101794	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	CDS	16101795	16102035	1	+	0	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	exon	16101795	16102035	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	intron	16102036	16102150	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	CDS	16102151	16102822	0.4	+	2	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	exon	16102151	16102822	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	intron	16102823	16102911	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	CDS	16102912	16103219	0.37	+	2	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	exon	16102912	16103219	.	+	.	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
Phchi.S3	AUGUSTUS	stop_codon	16103220	16103222	.	+	0	transcript_id "Phchi.S3G230900.t1"; gene_id "Phchi.S3G230900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3578.t1 is derived from g747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4597414	4599169	.	+	.	Phchi.S1G073700
Phchi.S1	AUGUSTUS	transcript	4597414	4599169	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	start_codon	4597414	4597416	.	+	0	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4597414	4597462	0.3	+	0	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4597414	4597462	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4597463	4597795	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4597796	4597805	0.37	+	2	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4597796	4597805	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4597806	4597904	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4597905	4598076	0.37	+	1	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4597905	4598076	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4598077	4598184	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4598185	4598266	0.99	+	0	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4598185	4598266	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4598267	4598370	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4598371	4598444	0.99	+	2	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4598371	4598444	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4598445	4598541	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4598542	4598602	1	+	0	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4598542	4598602	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4598603	4598697	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4598698	4598829	1	+	2	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4598698	4598829	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	intron	4598830	4598966	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	CDS	4598967	4599169	0.98	+	2	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	exon	4598967	4599169	.	+	.	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
Phchi.S1	AUGUSTUS	stop_codon	4599170	4599172	.	+	0	transcript_id "Phchi.S1G073700.t1"; gene_id "Phchi.S1G073700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6891.t1 is derived from g4063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25857569	25861865	.	-	.	Phchi.S1G405000
Phchi.S1	AUGUSTUS	transcript	25857569	25861865	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	stop_codon	25857566	25857568	.	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25857569	25857676	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25857569	25857676	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25857677	25857760	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25857761	25857864	1	-	2	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25857761	25857864	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25857865	25857996	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25857997	25858111	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25857997	25858111	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25858112	25858203	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25858204	25858254	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25858204	25858254	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25858255	25858345	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25858346	25858435	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25858346	25858435	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25858436	25858513	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25858514	25858588	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25858514	25858588	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25858589	25858753	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25858754	25858906	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25858754	25858906	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25858907	25858993	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25858994	25859078	1	-	1	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25858994	25859078	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25859079	25859168	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25859169	25859239	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25859169	25859239	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25859240	25859326	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25859327	25859377	0.98	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25859327	25859377	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25859378	25859480	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25859481	25859897	0.55	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25859481	25859897	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25859898	25859996	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25859997	25860128	0.99	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25859997	25860128	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25860129	25860242	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25860243	25860356	0.99	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25860243	25860356	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25860357	25860512	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25860513	25860815	0.84	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25860513	25860815	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25860816	25861046	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25861047	25861113	0.99	-	1	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25861047	25861113	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25861114	25861229	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25861230	25861366	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25861230	25861366	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25861367	25861447	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25861448	25861657	1	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25861448	25861657	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	intron	25861658	25861745	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	CDS	25861746	25861865	0.97	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	exon	25861746	25861865	.	-	.	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
Phchi.S1	AUGUSTUS	start_codon	25861863	25861865	.	-	0	transcript_id "Phchi.S1G405000.t1"; gene_id "Phchi.S1G405000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8971.t1 is derived from g6146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38896273	38897370	.	-	.	Phchi.S1G613000
Phchi.S1	AUGUSTUS	transcript	38896273	38897370	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	stop_codon	38896270	38896272	.	-	0	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	CDS	38896273	38896414	0.96	-	1	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	exon	38896273	38896414	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	intron	38896415	38896565	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	CDS	38896566	38896959	1	-	2	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	exon	38896566	38896959	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	intron	38896960	38897126	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	CDS	38897127	38897212	0.97	-	1	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	exon	38897127	38897212	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	intron	38897213	38897326	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	CDS	38897327	38897370	0.45	-	0	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	exon	38897327	38897370	.	-	.	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
Phchi.S1	AUGUSTUS	start_codon	38897368	38897370	.	-	0	transcript_id "Phchi.S1G613000.t1"; gene_id "Phchi.S1G613000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8688.t1 is derived from g5863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37452327	37453188	.	+	.	Phchi.S1G584700
Phchi.S1	AUGUSTUS	transcript	37452327	37453188	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	start_codon	37452327	37452329	.	+	0	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452327	37452495	0.64	+	0	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452327	37452495	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37452496	37452587	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452588	37452643	1	+	2	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452588	37452643	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37452644	37452718	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452719	37452839	1	+	0	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452719	37452839	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37452840	37452978	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452979	37453082	1	+	2	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452979	37453082	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37453083	37453164	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37453165	37453188	1	+	0	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37453165	37453188	.	+	.	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	stop_codon	37453189	37453191	.	+	0	transcript_id "Phchi.S1G584700.t1"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	transcript	37452327	37453188	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	start_codon	37452327	37452329	.	+	0	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452327	37452495	0.6	+	0	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452327	37452495	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37452496	37452587	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452588	37452643	1	+	2	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452588	37452643	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37452644	37452718	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452719	37452839	0.97	+	0	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452719	37452839	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37452840	37452942	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37452943	37453082	0.93	+	2	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37452943	37453082	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	intron	37453083	37453164	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	CDS	37453165	37453188	1	+	0	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	exon	37453165	37453188	.	+	.	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
Phchi.S1	AUGUSTUS	stop_codon	37453189	37453191	.	+	0	transcript_id "Phchi.S1G584700.t2"; gene_id "Phchi.S1G584700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10249.t1 is derived from g7425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46594922	46596420	.	+	.	Phchi.S1G740800
Phchi.S1	AUGUSTUS	transcript	46594922	46596420	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	start_codon	46594922	46594924	.	+	0	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46594922	46594946	0.98	+	0	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46594922	46594946	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46594947	46595089	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595090	46595275	0.97	+	2	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595090	46595275	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46595276	46595420	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595421	46595590	0.62	+	2	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595421	46595590	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46595591	46595749	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595750	46595758	0.87	+	0	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595750	46595758	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46595759	46595923	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595924	46596073	1	+	0	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595924	46596073	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46596074	46596225	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46596226	46596420	0.98	+	0	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46596226	46596420	.	+	.	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	stop_codon	46596421	46596423	.	+	0	transcript_id "Phchi.S1G740800.t1"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	transcript	46594922	46596420	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	start_codon	46594922	46594924	.	+	0	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46594922	46594946	0.99	+	0	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46594922	46594946	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46594947	46595089	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595090	46595275	0.99	+	2	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595090	46595275	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46595276	46595420	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595421	46595618	0.19	+	2	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595421	46595618	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46595619	46595700	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595701	46595714	0.5	+	2	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595701	46595714	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46595715	46595923	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46595924	46596073	1	+	0	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46595924	46596073	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	intron	46596074	46596225	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	CDS	46596226	46596420	0.99	+	0	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	exon	46596226	46596420	.	+	.	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
Phchi.S1	AUGUSTUS	stop_codon	46596421	46596423	.	+	0	transcript_id "Phchi.S1G740800.t2"; gene_id "Phchi.S1G740800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7491.t1 is derived from g4664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29627122	29627960	.	+	.	Phchi.S1G465000
Phchi.S1	AUGUSTUS	transcript	29627122	29627960	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	start_codon	29627122	29627124	.	+	0	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	CDS	29627122	29627149	0.93	+	0	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	exon	29627122	29627149	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	intron	29627150	29627273	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	CDS	29627274	29627323	1	+	2	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	exon	29627274	29627323	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	intron	29627324	29627455	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	CDS	29627456	29627610	1	+	0	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	exon	29627456	29627610	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	intron	29627611	29627743	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	CDS	29627744	29627960	0.97	+	1	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	exon	29627744	29627960	.	+	.	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
Phchi.S1	AUGUSTUS	stop_codon	29627961	29627963	.	+	0	transcript_id "Phchi.S1G465000.t1"; gene_id "Phchi.S1G465000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4569.t1 is derived from g1739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11157923	11159469	.	-	.	Phchi.S1G172800
Phchi.S1	AUGUSTUS	transcript	11157923	11159469	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	stop_codon	11157920	11157922	.	-	0	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	CDS	11157923	11158194	0.58	-	2	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	exon	11157923	11158194	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	intron	11158195	11158326	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	CDS	11158327	11158597	0.79	-	0	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	exon	11158327	11158597	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	intron	11158598	11158672	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	CDS	11158673	11158776	0.7	-	2	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	exon	11158673	11158776	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	intron	11158777	11158918	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	CDS	11158919	11159119	0.78	-	2	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	exon	11158919	11159119	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	intron	11159120	11159210	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	CDS	11159211	11159469	0.59	-	0	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	exon	11159211	11159469	.	-	.	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
Phchi.S1	AUGUSTUS	start_codon	11159467	11159469	.	-	0	transcript_id "Phchi.S1G172800.t1"; gene_id "Phchi.S1G172800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4922.t1 is derived from g2092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13568388	13570885	.	-	.	Phchi.S1G208100
Phchi.S1	AUGUSTUS	transcript	13568388	13570885	.	-	.	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	stop_codon	13568385	13568387	.	-	0	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	CDS	13568388	13569628	0.9	-	2	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	exon	13568388	13569628	.	-	.	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	intron	13569629	13569771	.	-	.	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	CDS	13569772	13570885	0.58	-	0	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	exon	13569772	13570885	.	-	.	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
Phchi.S1	AUGUSTUS	start_codon	13570883	13570885	.	-	0	transcript_id "Phchi.S1G208100.t1"; gene_id "Phchi.S1G208100"
# This transcript jg219.t2 is derived from g10001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg220.t1 is derived from g10002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1452103	1452566	.	+	.	Phchi.S6G017900
Phchi.S6	AUGUSTUS	transcript	1452103	1452566	.	+	.	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	start_codon	1452103	1452105	.	+	0	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	CDS	1452103	1452120	0.97	+	0	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	exon	1452103	1452120	.	+	.	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	intron	1452121	1452353	.	+	.	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	CDS	1452354	1452566	1	+	0	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	exon	1452354	1452566	.	+	.	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
Phchi.S6	AUGUSTUS	stop_codon	1452567	1452569	.	+	0	transcript_id "Phchi.S6G017900.t1"; gene_id "Phchi.S6G017900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11000.t1 is derived from g15050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3584561	3587048	.	+	.	Phchi.S4G058200
Phchi.S4	AUGUSTUS	transcript	3584561	3587048	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	start_codon	3584561	3584563	.	+	0	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	CDS	3584561	3585923	0.9	+	0	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	exon	3584561	3585923	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	intron	3585924	3586054	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	CDS	3586055	3586380	0.77	+	2	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	exon	3586055	3586380	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	intron	3586381	3586457	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	CDS	3586458	3586768	1	+	0	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	exon	3586458	3586768	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	intron	3586769	3586870	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	CDS	3586871	3587048	0.99	+	1	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	exon	3586871	3587048	.	+	.	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
Phchi.S4	AUGUSTUS	stop_codon	3587049	3587051	.	+	0	transcript_id "Phchi.S4G058200.t1"; gene_id "Phchi.S4G058200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg28.t1 is derived from g9806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C246	AUGUSTUS	gene	335	818	.	+	.	Phchi.C246G000100
Phchi.C246	AUGUSTUS	transcript	335	818	.	+	.	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	start_codon	335	337	.	+	0	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	CDS	335	385	0.99	+	0	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	exon	335	385	.	+	.	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	intron	386	480	.	+	.	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	CDS	481	548	1	+	0	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	exon	481	548	.	+	.	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	intron	549	655	.	+	.	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	CDS	656	818	0.83	+	1	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	exon	656	818	.	+	.	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
Phchi.C246	AUGUSTUS	stop_codon	819	821	.	+	0	transcript_id "Phchi.C246G000100.t1"; gene_id "Phchi.C246G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15602.t1 is derived from g14071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20224416	20227676	.	-	.	Phchi.S3G292100
Phchi.S3	AUGUSTUS	transcript	20224416	20227676	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	stop_codon	20224413	20224415	.	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20224416	20224450	1	-	2	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20224416	20224450	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20224451	20224534	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20224535	20224637	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20224535	20224637	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20224638	20224783	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20224784	20224867	0.99	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20224784	20224867	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20224868	20224976	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20224977	20225072	0.99	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20224977	20225072	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20225073	20225150	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20225151	20225201	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20225151	20225201	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20225202	20225310	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20225311	20225451	0.99	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20225311	20225451	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20225452	20225546	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20225547	20225603	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20225547	20225603	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20225604	20225728	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20225729	20225803	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20225729	20225803	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20225804	20225907	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20225908	20226180	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20225908	20226180	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20226181	20226288	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20226289	20226348	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20226289	20226348	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20226349	20226480	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20226481	20226573	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20226481	20226573	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20226574	20226666	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20226667	20226788	0.91	-	2	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20226667	20226788	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20226789	20226877	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20226878	20226897	0.92	-	1	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20226878	20226897	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20226898	20227026	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20227027	20227058	0.99	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20227027	20227058	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20227059	20227184	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20227185	20227208	0.94	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20227185	20227208	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20227209	20227483	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20227484	20227531	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20227484	20227531	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	intron	20227532	20227631	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	CDS	20227632	20227676	1	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	exon	20227632	20227676	.	-	.	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
Phchi.S3	AUGUSTUS	start_codon	20227674	20227676	.	-	0	transcript_id "Phchi.S3G292100.t1"; gene_id "Phchi.S3G292100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1307.t1 is derived from g11090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8930929	8931968	.	+	.	Phchi.S6G126600
Phchi.S6	AUGUSTUS	transcript	8930929	8931968	.	+	.	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	start_codon	8930929	8930931	.	+	0	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	CDS	8930929	8931572	0.8	+	0	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	exon	8930929	8931572	.	+	.	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	intron	8931573	8931685	.	+	.	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	CDS	8931686	8931968	0.84	+	1	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	exon	8931686	8931968	.	+	.	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
Phchi.S6	AUGUSTUS	stop_codon	8931969	8931971	.	+	0	transcript_id "Phchi.S6G126600.t1"; gene_id "Phchi.S6G126600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12481.t1 is derived from g8158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28460238	28465182	.	-	.	Phchi.S2G056100
Phchi.S2	AUGUSTUS	transcript	28460238	28465182	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	stop_codon	28460235	28460237	.	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28460238	28460239	0.98	-	2	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28460238	28460239	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28460240	28460328	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28460329	28460446	0.98	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28460329	28460446	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28460447	28460560	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28460561	28460656	0.99	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28460561	28460656	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28460657	28461007	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28461008	28461279	1	-	2	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28461008	28461279	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28461280	28462056	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28462057	28462231	1	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28462057	28462231	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28462232	28462341	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28462342	28462551	0.49	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28462342	28462551	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28462552	28462652	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28462653	28462754	0.96	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28462653	28462754	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28462755	28462848	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28462849	28462958	0.46	-	2	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28462849	28462958	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28462959	28463038	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28463039	28463143	0.59	-	2	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28463039	28463143	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28463144	28463227	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28463228	28463303	1	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28463228	28463303	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28463304	28463535	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28463536	28463724	1	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28463536	28463724	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28463725	28463885	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28463886	28464003	1	-	1	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28463886	28464003	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28464004	28464353	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28464354	28464553	1	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28464354	28464553	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	intron	28464554	28465008	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	CDS	28465009	28465182	0.74	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	exon	28465009	28465182	.	-	.	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
Phchi.S2	AUGUSTUS	start_codon	28465180	28465182	.	-	0	transcript_id "Phchi.S2G056100.t1"; gene_id "Phchi.S2G056100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1357.t1 is derived from g14424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C23	AUGUSTUS	gene	75501	78358	.	+	.	Phchi.C23G000600
Phchi.C23	AUGUSTUS	transcript	75501	78358	.	+	.	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	start_codon	75501	75503	.	+	0	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	CDS	75501	75599	0.96	+	0	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	exon	75501	75599	.	+	.	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	intron	75600	75911	.	+	.	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	CDS	75912	75948	0.98	+	0	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	exon	75912	75948	.	+	.	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	intron	75949	76223	.	+	.	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	CDS	76224	78358	0.89	+	2	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	exon	76224	78358	.	+	.	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
Phchi.C23	AUGUSTUS	stop_codon	78359	78361	.	+	0	transcript_id "Phchi.C23G000600.t1"; gene_id "Phchi.C23G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2397.t1 is derived from g9317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6476754	6477191	.	-	.	Phchi.S5G100600
Phchi.S5	AUGUSTUS	transcript	6476754	6477191	.	-	.	transcript_id "Phchi.S5G100600.t1"; gene_id "Phchi.S5G100600"
Phchi.S5	AUGUSTUS	stop_codon	6476751	6476753	.	-	0	transcript_id "Phchi.S5G100600.t1"; gene_id "Phchi.S5G100600"
Phchi.S5	AUGUSTUS	CDS	6476754	6477191	0.94	-	0	transcript_id "Phchi.S5G100600.t1"; gene_id "Phchi.S5G100600"
Phchi.S5	AUGUSTUS	exon	6476754	6477191	.	-	.	transcript_id "Phchi.S5G100600.t1"; gene_id "Phchi.S5G100600"
Phchi.S5	AUGUSTUS	start_codon	6477189	6477191	.	-	0	transcript_id "Phchi.S5G100600.t1"; gene_id "Phchi.S5G100600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13554.t1 is derived from g12021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7476263	7477308	.	-	.	Phchi.S3G087300
Phchi.S3	AUGUSTUS	transcript	7476263	7477308	.	-	.	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	stop_codon	7476260	7476262	.	-	0	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	CDS	7476263	7476440	0.99	-	1	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	exon	7476263	7476440	.	-	.	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	intron	7476441	7476527	.	-	.	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	CDS	7476528	7476754	1	-	0	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	exon	7476528	7476754	.	-	.	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	intron	7476755	7477038	.	-	.	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	CDS	7477039	7477308	0.79	-	0	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	exon	7477039	7477308	.	-	.	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
Phchi.S3	AUGUSTUS	start_codon	7477306	7477308	.	-	0	transcript_id "Phchi.S3G087300.t1"; gene_id "Phchi.S3G087300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg65.t1 is derived from g9847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	324408	325186	.	+	.	Phchi.S6G002400
Phchi.S6	AUGUSTUS	transcript	324408	325186	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	start_codon	324408	324410	.	+	0	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	CDS	324408	324412	0.72	+	0	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	exon	324408	324412	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	intron	324413	324571	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	CDS	324572	324727	1	+	1	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	exon	324572	324727	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	intron	324728	324811	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	CDS	324812	324938	1	+	1	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	exon	324812	324938	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	intron	324939	325048	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	CDS	325049	325186	1	+	0	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	exon	325049	325186	.	+	.	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
Phchi.S6	AUGUSTUS	stop_codon	325187	325189	.	+	0	transcript_id "Phchi.S6G002400.t1"; gene_id "Phchi.S6G002400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8288.t1 is derived from g5463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35105387	35106142	.	+	.	Phchi.S1G544700
Phchi.S1	AUGUSTUS	transcript	35105387	35106142	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	start_codon	35105387	35105389	.	+	0	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	CDS	35105387	35105414	0.56	+	0	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	exon	35105387	35105414	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	intron	35105415	35105653	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	CDS	35105654	35105779	0.42	+	2	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	exon	35105654	35105779	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	intron	35105780	35105860	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	CDS	35105861	35105993	0.71	+	2	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	exon	35105861	35105993	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	intron	35105994	35106138	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	CDS	35106139	35106142	0.86	+	1	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	exon	35106139	35106142	.	+	.	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
Phchi.S1	AUGUSTUS	stop_codon	35106143	35106145	.	+	0	transcript_id "Phchi.S1G544700.t1"; gene_id "Phchi.S1G544700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9814.t1 is derived from g6990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43866421	43871408	.	+	.	Phchi.S1G697300
Phchi.S1	AUGUSTUS	transcript	43866421	43871408	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	start_codon	43866421	43866423	.	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43866421	43866436	0.5	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43866421	43866436	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43866437	43866533	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43866534	43866586	0.49	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43866534	43866586	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43866587	43866733	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43866734	43867068	0.98	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43866734	43867068	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43867069	43867239	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43867240	43867343	1	+	1	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43867240	43867343	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43867344	43867515	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43867516	43867584	0.67	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43867516	43867584	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43867585	43867698	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43867699	43867759	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43867699	43867759	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43867760	43867883	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43867884	43868023	1	+	1	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43867884	43868023	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43868024	43868151	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43868152	43868341	0.96	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43868152	43868341	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43868342	43868580	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43868581	43868642	1	+	1	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43868581	43868642	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43868643	43868768	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43868769	43868857	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43868769	43868857	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43868858	43868940	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43868941	43869013	1	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43868941	43869013	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43869014	43869111	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43869112	43869171	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43869112	43869171	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43869172	43869362	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43869363	43869509	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43869363	43869509	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43869510	43869598	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43869599	43869640	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43869599	43869640	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43869641	43869861	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43869862	43869932	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43869862	43869932	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43869933	43870097	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43870098	43870184	0.99	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43870098	43870184	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43870185	43870292	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43870293	43870458	0.99	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43870293	43870458	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43870459	43870562	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43870563	43870640	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43870563	43870640	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43870641	43870754	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43870755	43870891	1	+	2	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43870755	43870891	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43870892	43871011	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43871012	43871088	1	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43871012	43871088	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43871089	43871181	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43871182	43871251	1	+	1	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43871182	43871251	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	intron	43871252	43871336	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	CDS	43871337	43871408	0.75	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	exon	43871337	43871408	.	+	.	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
Phchi.S1	AUGUSTUS	stop_codon	43871409	43871411	.	+	0	transcript_id "Phchi.S1G697300.t1"; gene_id "Phchi.S1G697300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15752.t1 is derived from g14222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21070022	21073720	.	-	.	Phchi.S3G307100
Phchi.S3	AUGUSTUS	transcript	21070022	21073720	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	stop_codon	21070019	21070021	.	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21070022	21070189	0.81	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21070022	21070189	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21070190	21070268	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21070269	21070373	1	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21070269	21070373	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21070374	21070446	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21070447	21070551	1	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21070447	21070551	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21070552	21070642	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21070643	21070724	1	-	1	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21070643	21070724	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21070725	21070812	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21070813	21071009	0.99	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21070813	21071009	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21071010	21071118	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21071119	21071280	0.96	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21071119	21071280	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21071281	21071358	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21071359	21071468	1	-	2	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21071359	21071468	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21071469	21071548	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21071549	21071690	1	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21071549	21071690	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21071691	21071777	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21071778	21071924	1	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21071778	21071924	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21071925	21072012	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21072013	21072087	1	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21072013	21072087	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21072088	21072179	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21072180	21072406	0.55	-	2	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21072180	21072406	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21072407	21072532	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21072533	21072683	0.6	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21072533	21072683	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21072684	21072767	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21072768	21072887	0.97	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21072768	21072887	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21072888	21072965	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21072966	21073075	1	-	2	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21072966	21073075	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21073076	21073185	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21073186	21073330	1	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21073186	21073330	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	intron	21073331	21073426	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	CDS	21073427	21073720	0.75	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	exon	21073427	21073720	.	-	.	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
Phchi.S3	AUGUSTUS	start_codon	21073718	21073720	.	-	0	transcript_id "Phchi.S3G307100.t1"; gene_id "Phchi.S3G307100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15436.t1 is derived from g13904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19088882	19089682	.	+	.	Phchi.S3G275500
Phchi.S3	AUGUSTUS	transcript	19088882	19089682	.	+	.	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	start_codon	19088882	19088884	.	+	0	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	CDS	19088882	19089028	0.6	+	0	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	exon	19088882	19089028	.	+	.	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	intron	19089029	19089136	.	+	.	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	CDS	19089137	19089682	0.5	+	0	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	exon	19089137	19089682	.	+	.	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
Phchi.S3	AUGUSTUS	stop_codon	19089683	19089685	.	+	0	transcript_id "Phchi.S3G275500.t1"; gene_id "Phchi.S3G275500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9425.t1 is derived from g6601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41413159	41417317	.	-	.	Phchi.S1G658400
Phchi.S1	AUGUSTUS	transcript	41413159	41417317	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	stop_codon	41413156	41413158	.	-	0	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41413159	41413228	0.62	-	1	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41413159	41413228	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41413229	41413435	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41413436	41413454	0.62	-	2	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41413436	41413454	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41413455	41413572	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41413573	41413788	0.35	-	2	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41413573	41413788	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41413789	41413874	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41413875	41414142	0.69	-	0	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41413875	41414142	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41414143	41414222	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41414223	41415074	1	-	0	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41414223	41415074	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41415075	41415172	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41415173	41415557	0.81	-	1	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41415173	41415557	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41415558	41415887	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41415888	41416072	1	-	0	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41415888	41416072	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41416073	41416255	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41416256	41416385	1	-	1	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41416256	41416385	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41416386	41416523	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41416524	41416647	1	-	2	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41416524	41416647	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41416648	41416728	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41416729	41417019	1	-	2	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41416729	41417019	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	intron	41417020	41417184	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	CDS	41417185	41417317	0.49	-	0	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	exon	41417185	41417317	.	-	.	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
Phchi.S1	AUGUSTUS	start_codon	41417315	41417317	.	-	0	transcript_id "Phchi.S1G658400.t1"; gene_id "Phchi.S1G658400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8817.t1 is derived from g5992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38120531	38121013	.	-	.	Phchi.S1G597600
Phchi.S1	AUGUSTUS	transcript	38120531	38121013	.	-	.	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	stop_codon	38120528	38120530	.	-	0	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	CDS	38120531	38120665	1	-	0	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	exon	38120531	38120665	.	-	.	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	intron	38120666	38120753	.	-	.	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	CDS	38120754	38120792	1	-	0	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	exon	38120754	38120792	.	-	.	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	intron	38120793	38120890	.	-	.	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	CDS	38120891	38121013	0.54	-	0	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	exon	38120891	38121013	.	-	.	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
Phchi.S1	AUGUSTUS	start_codon	38121011	38121013	.	-	0	transcript_id "Phchi.S1G597600.t1"; gene_id "Phchi.S1G597600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10117.t1 is derived from g7293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45806926	45808651	.	-	.	Phchi.S1G727600
Phchi.S1	AUGUSTUS	transcript	45806926	45808651	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	stop_codon	45806923	45806925	.	-	0	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	CDS	45806926	45806990	0.24	-	2	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	exon	45806926	45806990	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	intron	45806991	45807108	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	CDS	45807109	45807343	0.2	-	0	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	exon	45807109	45807343	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	intron	45807344	45807420	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	CDS	45807421	45808068	0.94	-	0	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	exon	45807421	45808068	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	intron	45808069	45808200	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	CDS	45808201	45808320	0.52	-	0	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	exon	45808201	45808320	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	intron	45808321	45808435	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	CDS	45808436	45808651	0.85	-	0	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	exon	45808436	45808651	.	-	.	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
Phchi.S1	AUGUSTUS	start_codon	45808649	45808651	.	-	0	transcript_id "Phchi.S1G727600.t1"; gene_id "Phchi.S1G727600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5138.t1 is derived from g2308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15117897	15119581	.	-	.	Phchi.S1G229700
Phchi.S1	AUGUSTUS	transcript	15117897	15119581	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	stop_codon	15117894	15117896	.	-	0	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	CDS	15117897	15118109	0.98	-	0	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	exon	15117897	15118109	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	intron	15118110	15118207	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	CDS	15118208	15118372	1	-	0	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	exon	15118208	15118372	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	intron	15118373	15118505	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	CDS	15118506	15118761	1	-	1	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	exon	15118506	15118761	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	intron	15118762	15118873	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	CDS	15118874	15119161	0.98	-	1	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	exon	15118874	15119161	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	intron	15119162	15119267	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	CDS	15119268	15119581	0.67	-	0	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	exon	15119268	15119581	.	-	.	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
Phchi.S1	AUGUSTUS	start_codon	15119579	15119581	.	-	0	transcript_id "Phchi.S1G229700.t1"; gene_id "Phchi.S1G229700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2938.t1 is derived from g107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	667166	670552	.	-	.	Phchi.S1G009700
Phchi.S1	AUGUSTUS	transcript	667166	670552	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	stop_codon	667163	667165	.	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	667166	667555	0.97	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	667166	667555	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	667556	667637	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	667638	667786	0.98	-	2	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	667638	667786	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	667787	667892	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	667893	667993	0.68	-	1	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	667893	667993	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	667994	668077	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	668078	668175	0.69	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	668078	668175	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	668176	668323	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	668324	668401	1	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	668324	668401	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	668402	668490	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	668491	668551	1	-	1	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	668491	668551	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	668552	668645	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	668646	668745	1	-	2	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	668646	668745	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	668746	668873	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	668874	669015	1	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	668874	669015	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	669016	669223	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	669224	669387	0.77	-	2	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	669224	669387	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	669388	669488	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	669489	669568	0.99	-	1	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	669489	669568	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	669569	669683	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	669684	669796	1	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	669684	669796	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	669797	669929	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	669930	670070	1	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	669930	670070	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	intron	670071	670282	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	CDS	670283	670552	0.99	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	exon	670283	670552	.	-	.	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
Phchi.S1	AUGUSTUS	start_codon	670550	670552	.	-	0	transcript_id "Phchi.S1G009700.t1"; gene_id "Phchi.S1G009700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4306.t1 is derived from g1475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9526136	9528280	.	+	.	Phchi.S1G146500
Phchi.S1	AUGUSTUS	transcript	9526136	9528280	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	start_codon	9526136	9526138	.	+	0	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	CDS	9526136	9526373	0.62	+	0	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	exon	9526136	9526373	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	intron	9526374	9526485	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	CDS	9526486	9526703	0.95	+	2	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	exon	9526486	9526703	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	intron	9526704	9526822	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	CDS	9526823	9526989	0.71	+	0	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	exon	9526823	9526989	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	intron	9526990	9527088	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	CDS	9527089	9527409	0.64	+	1	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	exon	9527089	9527409	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	intron	9527410	9527482	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	CDS	9527483	9527546	0.64	+	1	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	exon	9527483	9527546	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	intron	9527547	9527623	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	CDS	9527624	9528280	0.61	+	0	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	exon	9527624	9528280	.	+	.	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
Phchi.S1	AUGUSTUS	stop_codon	9528281	9528283	.	+	0	transcript_id "Phchi.S1G146500.t1"; gene_id "Phchi.S1G146500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg468.t1 is derived from g10250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3284362	3284964	.	+	.	Phchi.S6G042700
Phchi.S6	AUGUSTUS	transcript	3284362	3284964	.	+	.	transcript_id "Phchi.S6G042700.t1"; gene_id "Phchi.S6G042700"
Phchi.S6	AUGUSTUS	start_codon	3284362	3284364	.	+	0	transcript_id "Phchi.S6G042700.t1"; gene_id "Phchi.S6G042700"
Phchi.S6	AUGUSTUS	CDS	3284362	3284964	1	+	0	transcript_id "Phchi.S6G042700.t1"; gene_id "Phchi.S6G042700"
Phchi.S6	AUGUSTUS	exon	3284362	3284964	.	+	.	transcript_id "Phchi.S6G042700.t1"; gene_id "Phchi.S6G042700"
Phchi.S6	AUGUSTUS	stop_codon	3284965	3284967	.	+	0	transcript_id "Phchi.S6G042700.t1"; gene_id "Phchi.S6G042700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15574.t1 is derived from g14043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20082608	20085101	.	+	.	Phchi.S3G289300
Phchi.S3	AUGUSTUS	transcript	20082608	20085101	.	+	.	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	start_codon	20082608	20082610	.	+	0	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	CDS	20082608	20083195	0.11	+	0	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	exon	20082608	20083195	.	+	.	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	intron	20083196	20083569	.	+	.	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	CDS	20083570	20084138	0.76	+	0	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	exon	20083570	20084138	.	+	.	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	intron	20084139	20084419	.	+	.	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	CDS	20084420	20085101	0.76	+	1	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	exon	20084420	20085101	.	+	.	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
Phchi.S3	AUGUSTUS	stop_codon	20085102	20085104	.	+	0	transcript_id "Phchi.S3G289300.t1"; gene_id "Phchi.S3G289300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15569.t1 is derived from g14038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20028252	20029587	.	-	.	Phchi.S3G288800
Phchi.S3	AUGUSTUS	transcript	20028252	20029587	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	stop_codon	20028249	20028251	.	-	0	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	CDS	20028252	20028443	0.65	-	0	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	exon	20028252	20028443	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	intron	20028444	20028542	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	CDS	20028543	20028656	0.98	-	0	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	exon	20028543	20028656	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	intron	20028657	20028782	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	CDS	20028783	20028960	0.25	-	1	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	exon	20028783	20028960	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	intron	20028961	20029053	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	CDS	20029054	20029092	0.43	-	1	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	exon	20029054	20029092	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	intron	20029093	20029393	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	CDS	20029394	20029587	0.71	-	0	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	exon	20029394	20029587	.	-	.	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
Phchi.S3	AUGUSTUS	start_codon	20029585	20029587	.	-	0	transcript_id "Phchi.S3G288800.t1"; gene_id "Phchi.S3G288800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13065.t1 is derived from g11530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3987004	3988270	.	-	.	Phchi.S3G038400
Phchi.S3	AUGUSTUS	transcript	3987004	3988270	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	stop_codon	3987001	3987003	.	-	0	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	CDS	3987004	3987213	1	-	0	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	exon	3987004	3987213	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	intron	3987214	3987311	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	CDS	3987312	3987524	1	-	0	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	exon	3987312	3987524	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	intron	3987525	3987590	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	CDS	3987591	3987761	0.84	-	0	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	exon	3987591	3987761	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	intron	3987762	3987884	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	CDS	3987885	3987912	0.58	-	1	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	exon	3987885	3987912	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	intron	3987913	3988124	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	CDS	3988125	3988270	0.58	-	0	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	exon	3988125	3988270	.	-	.	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
Phchi.S3	AUGUSTUS	start_codon	3988268	3988270	.	-	0	transcript_id "Phchi.S3G038400.t1"; gene_id "Phchi.S3G038400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8922.t1 is derived from g6097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38678546	38682336	.	-	.	Phchi.S1G608100
Phchi.S1	AUGUSTUS	transcript	38678546	38682336	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	stop_codon	38678543	38678545	.	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38678546	38678608	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38678546	38678608	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38678609	38678707	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38678708	38678761	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38678708	38678761	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38678762	38678847	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38678848	38678916	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38678848	38678916	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38678917	38679014	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679015	38679080	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679015	38679080	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679081	38679235	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679236	38679315	0.63	-	2	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679236	38679315	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679316	38679420	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679421	38679494	0.7	-	1	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679421	38679494	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679495	38679609	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679610	38679723	0.75	-	1	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679610	38679723	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679724	38679878	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679879	38679945	1	-	2	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679879	38679945	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679946	38680025	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680026	38680090	1	-	1	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680026	38680090	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680091	38680244	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680245	38680324	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680245	38680324	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680325	38680436	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680437	38680481	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680437	38680481	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680482	38680591	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680592	38680666	0.99	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680592	38680666	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680667	38680786	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680787	38680958	0.93	-	1	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680787	38680958	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680959	38681117	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681118	38681143	0.96	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681118	38681143	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681144	38681220	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681221	38681298	0.97	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681221	38681298	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681299	38681413	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681414	38681456	1	-	1	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681414	38681456	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681457	38681540	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681541	38681584	1	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681541	38681584	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681585	38681724	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681725	38681797	1	-	1	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681725	38681797	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681798	38682235	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38682236	38682336	0.66	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38682236	38682336	.	-	.	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	start_codon	38682334	38682336	.	-	0	transcript_id "Phchi.S1G608100.t1"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	transcript	38678546	38682336	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	stop_codon	38678543	38678545	.	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38678546	38678608	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38678546	38678608	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38678609	38678707	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38678708	38678761	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38678708	38678761	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38678762	38678847	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38678848	38678916	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38678848	38678916	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38678917	38679014	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679015	38679080	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679015	38679080	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679081	38679235	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679236	38679315	0.68	-	2	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679236	38679315	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679316	38679420	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679421	38679494	0.69	-	1	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679421	38679494	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679495	38679609	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679610	38679723	0.72	-	1	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679610	38679723	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679724	38679878	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38679879	38679945	1	-	2	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38679879	38679945	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38679946	38680025	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680026	38680090	1	-	1	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680026	38680090	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680091	38680244	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680245	38680324	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680245	38680324	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680325	38680436	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680437	38680481	0.98	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680437	38680481	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680482	38680591	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680592	38680666	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680592	38680666	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38680667	38680786	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38680787	38681022	0.48	-	2	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38680787	38681022	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681023	38681117	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681118	38681143	0.44	-	1	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681118	38681143	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681144	38681220	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681221	38681298	1	-	1	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681221	38681298	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681299	38681540	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681541	38681584	1	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681541	38681584	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681585	38681724	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38681725	38681797	1	-	1	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38681725	38681797	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	intron	38681798	38682235	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	CDS	38682236	38682336	0.74	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	exon	38682236	38682336	.	-	.	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
Phchi.S1	AUGUSTUS	start_codon	38682334	38682336	.	-	0	transcript_id "Phchi.S1G608100.t2"; gene_id "Phchi.S1G608100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10233.t1 is derived from g7409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46501943	46503425	.	+	.	Phchi.S1G739200
Phchi.S1	AUGUSTUS	transcript	46501943	46503425	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	start_codon	46501943	46501945	.	+	0	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	CDS	46501943	46502139	0.83	+	0	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	exon	46501943	46502139	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	intron	46502140	46502226	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	CDS	46502227	46502665	0.99	+	1	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	exon	46502227	46502665	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	intron	46502666	46502766	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	CDS	46502767	46503072	0.99	+	0	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	exon	46502767	46503072	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	intron	46503073	46503218	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	CDS	46503219	46503425	1	+	0	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	exon	46503219	46503425	.	+	.	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
Phchi.S1	AUGUSTUS	stop_codon	46503426	46503428	.	+	0	transcript_id "Phchi.S1G739200.t1"; gene_id "Phchi.S1G739200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15498.t1 is derived from g13967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19516744	19523546	.	-	.	Phchi.S3G281700
Phchi.S3	AUGUSTUS	transcript	19516744	19523546	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	stop_codon	19516741	19516743	.	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19516744	19516851	0.95	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19516744	19516851	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19516852	19516953	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19516954	19517074	0.78	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19516954	19517074	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517075	19517157	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517158	19517304	1	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517158	19517304	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517305	19517388	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517389	19517494	1	-	2	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517389	19517494	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517495	19517639	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517640	19517722	1	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517640	19517722	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517723	19517822	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517823	19517950	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517823	19517950	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517951	19518105	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518106	19518192	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518106	19518192	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518193	19518283	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518284	19518394	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518284	19518394	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518395	19518481	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518482	19518649	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518482	19518649	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518650	19518886	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518887	19518971	1	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518887	19518971	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518972	19519045	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519046	19519075	0.68	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519046	19519075	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519076	19519155	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519156	19519161	1	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519156	19519161	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519162	19519294	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519295	19519371	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519295	19519371	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519372	19519465	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519466	19519537	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519466	19519537	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519538	19519622	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519623	19519719	1	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519623	19519719	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519720	19519804	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519805	19520007	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519805	19520007	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520008	19520101	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520102	19520204	1	-	1	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520102	19520204	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520205	19520294	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520295	19520362	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520295	19520362	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520363	19520484	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520485	19520538	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520485	19520538	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520539	19520645	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520646	19520755	1	-	2	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520646	19520755	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520756	19521401	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19521402	19521480	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19521402	19521480	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19521481	19521687	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19521688	19521750	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19521688	19521750	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19521751	19522016	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522017	19522136	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522017	19522136	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522137	19522321	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522322	19522378	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522322	19522378	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522379	19522463	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522464	19522580	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522464	19522580	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522581	19522682	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522683	19522733	0.99	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522683	19522733	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522734	19522880	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522881	19522979	1	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522881	19522979	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522980	19523064	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19523065	19523228	1	-	2	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19523065	19523228	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19523229	19523350	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19523351	19523546	0.46	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19523351	19523546	.	-	.	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	start_codon	19523544	19523546	.	-	0	transcript_id "Phchi.S3G281700.t1"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	transcript	19516744	19523546	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	stop_codon	19516741	19516743	.	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19516744	19516851	0.9	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19516744	19516851	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19516852	19516953	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19516954	19517074	0.66	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19516954	19517074	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517075	19517157	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517158	19517304	1	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517158	19517304	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517305	19517388	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517389	19517494	1	-	2	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517389	19517494	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517495	19517639	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517640	19517722	1	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517640	19517722	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517723	19517822	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19517823	19517950	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19517823	19517950	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19517951	19518105	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518106	19518192	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518106	19518192	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518193	19518283	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518284	19518394	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518284	19518394	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518395	19518481	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518482	19518649	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518482	19518649	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518650	19518886	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19518887	19518971	1	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19518887	19518971	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19518972	19519045	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519046	19519075	0.56	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519046	19519075	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519076	19519155	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519156	19519161	1	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519156	19519161	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519162	19519294	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519295	19519371	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519295	19519371	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519372	19519465	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519466	19519537	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519466	19519537	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519538	19519622	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519623	19519719	1	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519623	19519719	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19519720	19519804	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19519805	19520007	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19519805	19520007	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520008	19520101	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520102	19520204	1	-	1	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520102	19520204	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520205	19520294	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520295	19520362	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520295	19520362	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520363	19520484	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520485	19520538	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520485	19520538	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520539	19520645	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19520646	19520726	0.55	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19520646	19520726	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19520727	19521149	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19521150	19521202	0.38	-	2	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19521150	19521202	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19521203	19521401	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19521402	19521480	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19521402	19521480	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19521481	19521687	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19521688	19521750	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19521688	19521750	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19521751	19522016	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522017	19522136	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522017	19522136	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522137	19522321	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522322	19522378	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522322	19522378	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522379	19522463	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522464	19522580	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522464	19522580	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522581	19522682	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522683	19522733	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522683	19522733	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522734	19522880	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19522881	19522979	1	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19522881	19522979	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19522980	19523064	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19523065	19523228	0.99	-	2	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19523065	19523228	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	intron	19523229	19523350	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	CDS	19523351	19523546	0.48	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	exon	19523351	19523546	.	-	.	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
Phchi.S3	AUGUSTUS	start_codon	19523544	19523546	.	-	0	transcript_id "Phchi.S3G281700.t2"; gene_id "Phchi.S3G281700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6923.t1 is derived from g4095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26011999	26012742	.	-	.	Phchi.S1G408200
Phchi.S1	AUGUSTUS	transcript	26011999	26012742	.	-	.	transcript_id "Phchi.S1G408200.t1"; gene_id "Phchi.S1G408200"
Phchi.S1	AUGUSTUS	stop_codon	26011996	26011998	.	-	0	transcript_id "Phchi.S1G408200.t1"; gene_id "Phchi.S1G408200"
Phchi.S1	AUGUSTUS	CDS	26011999	26012742	0.34	-	0	transcript_id "Phchi.S1G408200.t1"; gene_id "Phchi.S1G408200"
Phchi.S1	AUGUSTUS	exon	26011999	26012742	.	-	.	transcript_id "Phchi.S1G408200.t1"; gene_id "Phchi.S1G408200"
Phchi.S1	AUGUSTUS	start_codon	26012740	26012742	.	-	0	transcript_id "Phchi.S1G408200.t1"; gene_id "Phchi.S1G408200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11285.t1 is derived from g15335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5196673	5197765	.	-	.	Phchi.S4G086700
Phchi.S4	AUGUSTUS	transcript	5196673	5197765	.	-	.	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	stop_codon	5196670	5196672	.	-	0	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	CDS	5196673	5197058	0.41	-	2	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	exon	5196673	5197058	.	-	.	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	intron	5197059	5197515	.	-	.	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	CDS	5197516	5197765	0.51	-	0	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	exon	5197516	5197765	.	-	.	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
Phchi.S4	AUGUSTUS	start_codon	5197763	5197765	.	-	0	transcript_id "Phchi.S4G086700.t1"; gene_id "Phchi.S4G086700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5762.t1 is derived from g2932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18839575	18840057	.	+	.	Phchi.S1G292100
Phchi.S1	AUGUSTUS	transcript	18839575	18840057	.	+	.	transcript_id "Phchi.S1G292100.t1"; gene_id "Phchi.S1G292100"
Phchi.S1	AUGUSTUS	start_codon	18839575	18839577	.	+	0	transcript_id "Phchi.S1G292100.t1"; gene_id "Phchi.S1G292100"
Phchi.S1	AUGUSTUS	CDS	18839575	18840057	0.74	+	0	transcript_id "Phchi.S1G292100.t1"; gene_id "Phchi.S1G292100"
Phchi.S1	AUGUSTUS	exon	18839575	18840057	.	+	.	transcript_id "Phchi.S1G292100.t1"; gene_id "Phchi.S1G292100"
Phchi.S1	AUGUSTUS	stop_codon	18840058	18840060	.	+	0	transcript_id "Phchi.S1G292100.t1"; gene_id "Phchi.S1G292100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg566.t1 is derived from g10348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4078314	4079002	.	+	.	Phchi.S6G052500
Phchi.S6	AUGUSTUS	transcript	4078314	4079002	.	+	.	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	start_codon	4078314	4078316	.	+	0	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	CDS	4078314	4078318	0.69	+	0	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	exon	4078314	4078318	.	+	.	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	intron	4078319	4078408	.	+	.	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	CDS	4078409	4078796	0.69	+	1	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	exon	4078409	4078796	.	+	.	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	intron	4078797	4078876	.	+	.	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	CDS	4078877	4079002	1	+	0	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	exon	4078877	4079002	.	+	.	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
Phchi.S6	AUGUSTUS	stop_codon	4079003	4079005	.	+	0	transcript_id "Phchi.S6G052500.t1"; gene_id "Phchi.S6G052500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg298.t1 is derived from g10080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2109942	2111431	.	-	.	Phchi.S6G025700
Phchi.S6	AUGUSTUS	transcript	2109942	2111431	.	-	.	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	stop_codon	2109939	2109941	.	-	0	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	CDS	2109942	2111010	0.65	-	1	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	exon	2109942	2111010	.	-	.	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	intron	2111011	2111162	.	-	.	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	CDS	2111163	2111431	0.42	-	0	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	exon	2111163	2111431	.	-	.	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
Phchi.S6	AUGUSTUS	start_codon	2111429	2111431	.	-	0	transcript_id "Phchi.S6G025700.t1"; gene_id "Phchi.S6G025700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6787.t1 is derived from g3959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25084097	25085068	.	-	.	Phchi.S1G394600
Phchi.S1	AUGUSTUS	transcript	25084097	25085068	.	-	.	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	stop_codon	25084094	25084096	.	-	0	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	CDS	25084097	25084737	0.63	-	2	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	exon	25084097	25084737	.	-	.	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	intron	25084738	25084845	.	-	.	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	CDS	25084846	25085068	0.48	-	0	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	exon	25084846	25085068	.	-	.	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
Phchi.S1	AUGUSTUS	start_codon	25085066	25085068	.	-	0	transcript_id "Phchi.S1G394600.t1"; gene_id "Phchi.S1G394600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3046.t1 is derived from g215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1335226	1336332	.	-	.	Phchi.S1G020500
Phchi.S1	AUGUSTUS	transcript	1335226	1336332	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	stop_codon	1335223	1335225	.	-	0	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	CDS	1335226	1335353	0.62	-	2	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	exon	1335226	1335353	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	intron	1335354	1335468	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	CDS	1335469	1335634	0.73	-	0	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	exon	1335469	1335634	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	intron	1335635	1335734	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	CDS	1335735	1335792	0.61	-	1	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	exon	1335735	1335792	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	intron	1335793	1335991	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	CDS	1335992	1336084	0.4	-	1	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	exon	1335992	1336084	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	intron	1336085	1336318	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	CDS	1336319	1336332	0.4	-	0	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	exon	1336319	1336332	.	-	.	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
Phchi.S1	AUGUSTUS	start_codon	1336330	1336332	.	-	0	transcript_id "Phchi.S1G020500.t1"; gene_id "Phchi.S1G020500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1607.t1 is derived from g8526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2011776	2015211	.	-	.	Phchi.S5G021600
Phchi.S5	AUGUSTUS	transcript	2011776	2015211	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	stop_codon	2011773	2011775	.	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2011776	2012090	1	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2011776	2012090	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2012091	2012316	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2012317	2012445	1	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2012317	2012445	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2012446	2012541	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2012542	2012823	1	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2012542	2012823	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2012824	2012910	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2012911	2013045	1	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2012911	2013045	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2013046	2013124	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2013125	2013382	1	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2013125	2013382	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2013383	2013472	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2013473	2013652	1	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2013473	2013652	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2013653	2013760	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2013761	2014956	0.74	-	2	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2013761	2014956	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	intron	2014957	2015135	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	CDS	2015136	2015211	0.44	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	exon	2015136	2015211	.	-	.	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
Phchi.S5	AUGUSTUS	start_codon	2015209	2015211	.	-	0	transcript_id "Phchi.S5G021600.t1"; gene_id "Phchi.S5G021600"
# This transcript jg15911.t2 is derived from g14381.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15912.t1 is derived from g14382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22190364	22190719	.	+	.	Phchi.S3G323100
Phchi.S3	AUGUSTUS	transcript	22190364	22190719	.	+	.	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	start_codon	22190364	22190366	.	+	0	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	CDS	22190364	22190493	0.99	+	0	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	exon	22190364	22190493	.	+	.	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	intron	22190494	22190606	.	+	.	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	CDS	22190607	22190719	1	+	2	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	exon	22190607	22190719	.	+	.	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
Phchi.S3	AUGUSTUS	stop_codon	22190720	22190722	.	+	0	transcript_id "Phchi.S3G323100.t1"; gene_id "Phchi.S3G323100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15491.t1 is derived from g13960.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19479770	19485243	.	-	.	Phchi.S3G281000
Phchi.S3	AUGUSTUS	transcript	19480482	19485243	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	stop_codon	19480479	19480481	.	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480482	19480573	0.65	-	2	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480482	19480573	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480574	19480715	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480716	19480794	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480716	19480794	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480795	19480870	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480871	19480957	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480871	19480957	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480958	19481091	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481092	19481163	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481092	19481163	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481164	19481245	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481246	19481332	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481246	19481332	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481333	19481429	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481430	19481561	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481430	19481561	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481562	19481712	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481713	19481889	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481713	19481889	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481890	19481976	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481977	19482078	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481977	19482078	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482079	19482203	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482204	19482260	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482204	19482260	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482261	19482408	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482409	19482471	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482409	19482471	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482472	19482562	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482563	19482623	1	-	1	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482563	19482623	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482624	19482827	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482828	19482925	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482828	19482925	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482926	19483028	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483029	19483136	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483029	19483136	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483137	19483229	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483230	19483301	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483230	19483301	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483302	19483430	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483431	19483508	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483431	19483508	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483509	19483711	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483712	19483813	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483712	19483813	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483814	19483907	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483908	19484039	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483908	19484039	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484040	19484320	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19484321	19484413	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19484321	19484413	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484414	19484539	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19484540	19484605	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19484540	19484605	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484606	19484682	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19484683	19484856	1	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19484683	19484856	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484857	19485012	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19485013	19485243	0.91	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19485013	19485243	.	-	.	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	start_codon	19485241	19485243	.	-	0	transcript_id "Phchi.S3G281000.t1"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	transcript	19479770	19485243	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	stop_codon	19479767	19479769	.	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19479770	19479865	0.67	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19479770	19479865	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19479866	19479948	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19479949	19480017	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19479949	19480017	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480018	19480108	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480109	19480170	0.99	-	2	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480109	19480170	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480171	19480283	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480284	19480559	0.93	-	2	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480284	19480559	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480560	19480715	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480716	19480794	0.93	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480716	19480794	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480795	19480870	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480871	19480957	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480871	19480957	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480958	19481091	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481092	19481163	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481092	19481163	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481164	19481245	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481246	19481332	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481246	19481332	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481333	19481429	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481430	19481561	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481430	19481561	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481562	19481712	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481713	19481889	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481713	19481889	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19481890	19481976	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19481977	19482078	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19481977	19482078	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482079	19482203	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482204	19482260	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482204	19482260	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482261	19482408	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482409	19482471	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482409	19482471	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482472	19482562	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482563	19482623	1	-	1	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482563	19482623	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482624	19482827	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19482828	19482925	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19482828	19482925	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19482926	19483028	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483029	19483136	0.99	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483029	19483136	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483137	19483229	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483230	19483301	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483230	19483301	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483302	19483430	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483431	19483508	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483431	19483508	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483509	19483711	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483712	19483813	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483712	19483813	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19483814	19483907	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19483908	19484039	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19483908	19484039	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484040	19484320	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19484321	19484413	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19484321	19484413	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484414	19484539	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19484540	19484605	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19484540	19484605	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484606	19484682	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19484683	19484856	1	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19484683	19484856	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19484857	19485012	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19485013	19485243	0.93	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19485013	19485243	.	-	.	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	start_codon	19485241	19485243	.	-	0	transcript_id "Phchi.S3G281000.t2"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	transcript	19479770	19480431	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	stop_codon	19479767	19479769	.	-	0	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19479770	19479865	0.68	-	0	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19479770	19479865	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19479866	19479948	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19479949	19480017	1	-	0	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19479949	19480017	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480018	19480108	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480109	19480170	1	-	2	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480109	19480170	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	intron	19480171	19480283	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	CDS	19480284	19480431	0.47	-	0	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	exon	19480284	19480431	.	-	.	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
Phchi.S3	AUGUSTUS	start_codon	19480429	19480431	.	-	0	transcript_id "Phchi.S3G281000.t3"; gene_id "Phchi.S3G281000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10732.t1 is derived from g14782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1795265	1798929	.	-	.	Phchi.S4G031400
Phchi.S4	AUGUSTUS	transcript	1795265	1798929	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	stop_codon	1795262	1795264	.	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1795265	1795510	0.99	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1795265	1795510	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1795511	1795615	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1795616	1795699	1	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1795616	1795699	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1795700	1795884	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1795885	1796006	0.94	-	2	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1795885	1796006	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1796007	1796091	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1796092	1796224	0.98	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1796092	1796224	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1796225	1796312	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1796313	1796535	0.95	-	1	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1796313	1796535	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1796536	1796625	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1796626	1796646	0.68	-	1	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1796626	1796646	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1796647	1796728	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1796729	1796797	0.39	-	1	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1796729	1796797	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1796798	1796869	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1796870	1796973	0.43	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1796870	1796973	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1796974	1797046	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1797047	1797122	0.83	-	1	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1797047	1797122	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1797123	1797264	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1797265	1797379	0.89	-	2	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1797265	1797379	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1797380	1797460	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1797461	1797699	0.86	-	1	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1797461	1797699	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1797700	1797982	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1797983	1798246	0.54	-	1	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1797983	1798246	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	intron	1798247	1798318	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	CDS	1798319	1798929	0.9	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	exon	1798319	1798929	.	-	.	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
Phchi.S4	AUGUSTUS	start_codon	1798927	1798929	.	-	0	transcript_id "Phchi.S4G031400.t1"; gene_id "Phchi.S4G031400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2507.t1 is derived from g9427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7057026	7059848	.	-	.	Phchi.S5G111600
Phchi.S5	AUGUSTUS	transcript	7057026	7059848	.	-	.	transcript_id "Phchi.S5G111600.t1"; gene_id "Phchi.S5G111600"
Phchi.S5	AUGUSTUS	stop_codon	7057023	7057025	.	-	0	transcript_id "Phchi.S5G111600.t1"; gene_id "Phchi.S5G111600"
Phchi.S5	AUGUSTUS	CDS	7057026	7059848	0.44	-	0	transcript_id "Phchi.S5G111600.t1"; gene_id "Phchi.S5G111600"
Phchi.S5	AUGUSTUS	exon	7057026	7059848	.	-	.	transcript_id "Phchi.S5G111600.t1"; gene_id "Phchi.S5G111600"
Phchi.S5	AUGUSTUS	start_codon	7059846	7059848	.	-	0	transcript_id "Phchi.S5G111600.t1"; gene_id "Phchi.S5G111600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4596.t1 is derived from g1766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11271787	11273609	.	+	.	Phchi.S1G175500
Phchi.S1	AUGUSTUS	transcript	11271787	11273609	.	+	.	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	start_codon	11271787	11271789	.	+	0	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	CDS	11271787	11272824	0.56	+	0	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	exon	11271787	11272824	.	+	.	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	intron	11272825	11272961	.	+	.	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	CDS	11272962	11273609	0.46	+	0	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	exon	11272962	11273609	.	+	.	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
Phchi.S1	AUGUSTUS	stop_codon	11273610	11273612	.	+	0	transcript_id "Phchi.S1G175500.t1"; gene_id "Phchi.S1G175500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13333.t1 is derived from g11799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6137777	6139789	.	-	.	Phchi.S3G065200
Phchi.S3	AUGUSTUS	transcript	6137777	6139789	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	stop_codon	6137774	6137776	.	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6137777	6137927	0.92	-	1	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6137777	6137927	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6137928	6138021	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6138022	6138086	1	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6138022	6138086	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6138087	6138167	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6138168	6138276	1	-	1	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6138168	6138276	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6138277	6138392	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6138393	6138538	1	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6138393	6138538	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6138539	6138628	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6138629	6138694	0.99	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6138629	6138694	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6138695	6138801	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6138802	6138894	0.77	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6138802	6138894	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6138895	6138992	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6138993	6139098	1	-	1	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6138993	6139098	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6139099	6139242	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6139243	6139319	1	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6139243	6139319	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	intron	6139320	6139549	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	CDS	6139550	6139789	1	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	exon	6139550	6139789	.	-	.	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
Phchi.S3	AUGUSTUS	start_codon	6139787	6139789	.	-	0	transcript_id "Phchi.S3G065200.t1"; gene_id "Phchi.S3G065200"
# This transcript jg1394.t2 is derived from g8313.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1395.t1 is derived from g8314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	26684	32428	.	-	.	Phchi.S5G000400
Phchi.S5	AUGUSTUS	transcript	26684	32428	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	stop_codon	26681	26683	.	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	26684	26773	0.99	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	26684	26773	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	26774	26856	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	26857	26873	0.76	-	2	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	26857	26873	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	26874	27065	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	27066	28104	0.6	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	27066	28104	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	28105	28197	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	28198	28439	1	-	2	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	28198	28439	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	28440	28543	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	28544	28778	0.96	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	28544	28778	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	28779	28876	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	28877	28970	0.98	-	1	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	28877	28970	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	28971	29055	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	29056	29178	0.88	-	1	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	29056	29178	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	29179	29261	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	29262	29302	0.85	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	29262	29302	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	29303	29378	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	29379	29423	0.86	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	29379	29423	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	29424	29522	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	29523	29746	1	-	2	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	29523	29746	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	29747	30026	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	30027	30145	0.45	-	1	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	30027	30145	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	30146	30285	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	30286	30342	0.46	-	1	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	30286	30342	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	30343	30556	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	30557	30816	1	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	30557	30816	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	30817	30947	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	30948	31148	1	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	30948	31148	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	31149	31337	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	31338	31513	0.99	-	2	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	31338	31513	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	31514	31850	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	31851	31905	1	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	31851	31905	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	intron	31906	31984	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	CDS	31985	32428	0.99	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	exon	31985	32428	.	-	.	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
Phchi.S5	AUGUSTUS	start_codon	32426	32428	.	-	0	transcript_id "Phchi.S5G000400.t1"; gene_id "Phchi.S5G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12982.t1 is derived from g11447.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3445790	3446710	.	+	.	Phchi.S3G030100
Phchi.S3	AUGUSTUS	transcript	3445790	3446710	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	start_codon	3445790	3445792	.	+	0	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3445790	3445859	0.79	+	0	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3445790	3445859	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3445860	3446000	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446001	3446052	0.98	+	2	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446001	3446052	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3446053	3446173	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446174	3446207	0.73	+	1	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446174	3446207	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3446208	3446338	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446339	3446470	1	+	0	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446339	3446470	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3446471	3446554	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446555	3446710	0.68	+	0	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446555	3446710	.	+	.	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	stop_codon	3446711	3446713	.	+	0	transcript_id "Phchi.S3G030100.t1"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	transcript	3445790	3446710	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	start_codon	3445790	3445792	.	+	0	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3445790	3445859	0.46	+	0	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3445790	3445859	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3445860	3445958	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3445959	3446052	0.57	+	2	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3445959	3446052	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3446053	3446173	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446174	3446207	0.77	+	1	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446174	3446207	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3446208	3446338	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446339	3446470	1	+	0	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446339	3446470	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	intron	3446471	3446554	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	CDS	3446555	3446710	0.7	+	0	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	exon	3446555	3446710	.	+	.	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
Phchi.S3	AUGUSTUS	stop_codon	3446711	3446713	.	+	0	transcript_id "Phchi.S3G030100.t2"; gene_id "Phchi.S3G030100"
# This transcript jg5338.t2 is derived from g2508.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5339.t1 is derived from g2509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16368458	16369105	.	+	.	Phchi.S1G249800
Phchi.S1	AUGUSTUS	transcript	16368458	16369105	.	+	.	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	start_codon	16368458	16368460	.	+	0	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	CDS	16368458	16368560	0.65	+	0	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	exon	16368458	16368560	.	+	.	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	intron	16368561	16368806	.	+	.	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	CDS	16368807	16369105	0.4	+	2	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	exon	16368807	16369105	.	+	.	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
Phchi.S1	AUGUSTUS	stop_codon	16369106	16369108	.	+	0	transcript_id "Phchi.S1G249800.t1"; gene_id "Phchi.S1G249800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2821.t1 is derived from g9741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9033628	9035823	.	+	.	Phchi.S5G143000
Phchi.S5	AUGUSTUS	transcript	9033628	9035823	.	+	.	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	start_codon	9033628	9033630	.	+	0	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	CDS	9033628	9034544	0.36	+	0	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	exon	9033628	9034544	.	+	.	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	intron	9034545	9034868	.	+	.	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	CDS	9034869	9035823	0.18	+	1	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	exon	9034869	9035823	.	+	.	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
Phchi.S5	AUGUSTUS	stop_codon	9035824	9035826	.	+	0	transcript_id "Phchi.S5G143000.t1"; gene_id "Phchi.S5G143000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2346.t1 is derived from g9266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6273279	6274579	.	+	.	Phchi.S5G095500
Phchi.S5	AUGUSTUS	transcript	6273279	6274579	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	start_codon	6273279	6273281	.	+	0	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	CDS	6273279	6273661	0.4	+	0	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	exon	6273279	6273661	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	intron	6273662	6273849	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	CDS	6273850	6273985	0.66	+	1	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	exon	6273850	6273985	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	intron	6273986	6274161	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	CDS	6274162	6274216	0.56	+	0	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	exon	6274162	6274216	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	intron	6274217	6274376	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	CDS	6274377	6274579	0.39	+	2	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	exon	6274377	6274579	.	+	.	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
Phchi.S5	AUGUSTUS	stop_codon	6274580	6274582	.	+	0	transcript_id "Phchi.S5G095500.t1"; gene_id "Phchi.S5G095500"
# This transcript jg1646.t2 is derived from g8565.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1646.t3 is derived from g8565.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1647.t1 is derived from g8566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2199363	2206267	.	-	.	Phchi.S5G025600
Phchi.S5	AUGUSTUS	transcript	2199363	2206267	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	stop_codon	2199360	2199362	.	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2199363	2199461	0.64	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2199363	2199461	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2199462	2199550	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2199551	2199670	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2199551	2199670	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2199671	2199804	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2199805	2199877	1	-	1	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2199805	2199877	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2199878	2200071	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2200072	2200134	1	-	1	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2200072	2200134	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2200135	2200431	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2200432	2200502	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2200432	2200502	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2200503	2200644	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2200645	2200770	0.95	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2200645	2200770	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2200771	2200895	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2200896	2201104	0.99	-	2	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2200896	2201104	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2201105	2201242	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2201243	2201345	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2201243	2201345	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2201346	2201439	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2201440	2201503	1	-	1	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2201440	2201503	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2201504	2201635	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2201636	2202093	0.84	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2201636	2202093	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2202094	2202216	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2202217	2202558	0.99	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2202217	2202558	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2202559	2203053	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2203054	2203186	1	-	1	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2203054	2203186	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2203187	2203282	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2203283	2203317	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2203283	2203317	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2203318	2203463	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2203464	2203583	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2203464	2203583	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2203584	2203783	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2203784	2203867	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2203784	2203867	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2203868	2204095	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2204096	2204182	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2204096	2204182	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2204183	2204445	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2204446	2204535	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2204446	2204535	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2204536	2204708	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2204709	2204798	0.79	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2204709	2204798	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2204799	2204922	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2204923	2204987	0.42	-	2	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2204923	2204987	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2204988	2205208	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2205209	2205287	0.45	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2205209	2205287	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2205288	2205537	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2205538	2205612	1	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2205538	2205612	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2205613	2205731	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2205732	2205893	0.98	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2205732	2205893	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	intron	2205894	2206174	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	CDS	2206175	2206267	0.81	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	exon	2206175	2206267	.	-	.	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
Phchi.S5	AUGUSTUS	start_codon	2206265	2206267	.	-	0	transcript_id "Phchi.S5G025600.t1"; gene_id "Phchi.S5G025600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2868.t1 is derived from g37.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	187292	188269	.	+	.	Phchi.S1G002700
Phchi.S1	AUGUSTUS	transcript	187292	188269	.	+	.	transcript_id "Phchi.S1G002700.t1"; gene_id "Phchi.S1G002700"
Phchi.S1	AUGUSTUS	start_codon	187292	187294	.	+	0	transcript_id "Phchi.S1G002700.t1"; gene_id "Phchi.S1G002700"
Phchi.S1	AUGUSTUS	CDS	187292	188269	0.87	+	0	transcript_id "Phchi.S1G002700.t1"; gene_id "Phchi.S1G002700"
Phchi.S1	AUGUSTUS	exon	187292	188269	.	+	.	transcript_id "Phchi.S1G002700.t1"; gene_id "Phchi.S1G002700"
Phchi.S1	AUGUSTUS	stop_codon	188270	188272	.	+	0	transcript_id "Phchi.S1G002700.t1"; gene_id "Phchi.S1G002700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14038.t1 is derived from g12505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10404937	10408233	.	-	.	Phchi.S3G135700
Phchi.S3	AUGUSTUS	transcript	10404937	10408233	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	stop_codon	10404934	10404936	.	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10404937	10405215	0.71	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10404937	10405215	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10405216	10405327	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10405328	10405482	1	-	2	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10405328	10405482	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10405483	10405599	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10405600	10405645	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10405600	10405645	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10405646	10405746	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10405747	10405974	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10405747	10405974	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10405975	10406061	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10406062	10406102	1	-	2	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10406062	10406102	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10406103	10406205	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10406206	10406335	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10406206	10406335	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10406336	10406433	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10406434	10406502	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10406434	10406502	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10406503	10406609	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10406610	10406663	0.99	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10406610	10406663	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10406664	10406762	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10406763	10406921	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10406763	10406921	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10406922	10407075	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10407076	10407213	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10407076	10407213	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10407214	10407300	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10407301	10407366	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10407301	10407366	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10407367	10407482	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10407483	10407522	1	-	1	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10407483	10407522	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10407523	10407714	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10407715	10407761	1	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10407715	10407761	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	intron	10407762	10407858	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	CDS	10407859	10408233	0.97	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	exon	10407859	10408233	.	-	.	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
Phchi.S3	AUGUSTUS	start_codon	10408231	10408233	.	-	0	transcript_id "Phchi.S3G135700.t1"; gene_id "Phchi.S3G135700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12129.t1 is derived from g7805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4041811	4043018	.	-	.	Phchi.S2G020900
Phchi.S2	AUGUSTUS	transcript	4041811	4043018	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	stop_codon	4041808	4041810	.	-	0	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	CDS	4041811	4041994	1	-	1	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	exon	4041811	4041994	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	intron	4041995	4042073	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	CDS	4042074	4042241	1	-	1	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	exon	4042074	4042241	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	intron	4042242	4042323	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	CDS	4042324	4042400	1	-	0	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	exon	4042324	4042400	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	intron	4042401	4042484	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	CDS	4042485	4042625	1	-	0	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	exon	4042485	4042625	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	intron	4042626	4042733	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	CDS	4042734	4042811	0.95	-	0	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	exon	4042734	4042811	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	intron	4042812	4042907	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	CDS	4042908	4043018	0.93	-	0	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	exon	4042908	4043018	.	-	.	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
Phchi.S2	AUGUSTUS	start_codon	4043016	4043018	.	-	0	transcript_id "Phchi.S2G020900.t1"; gene_id "Phchi.S2G020900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14703.t1 is derived from g13171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14258879	14259888	.	+	.	Phchi.S3G202200
Phchi.S3	AUGUSTUS	transcript	14258879	14259888	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	start_codon	14258879	14258881	.	+	0	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	CDS	14258879	14259077	0.31	+	0	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	exon	14258879	14259077	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	intron	14259078	14259174	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	CDS	14259175	14259246	0.42	+	2	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	exon	14259175	14259246	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	intron	14259247	14259394	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	CDS	14259395	14259565	0.36	+	2	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	exon	14259395	14259565	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	intron	14259566	14259654	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	CDS	14259655	14259734	0.83	+	2	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	exon	14259655	14259734	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	intron	14259735	14259813	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	CDS	14259814	14259888	0.53	+	0	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	exon	14259814	14259888	.	+	.	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
Phchi.S3	AUGUSTUS	stop_codon	14259889	14259891	.	+	0	transcript_id "Phchi.S3G202200.t1"; gene_id "Phchi.S3G202200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12945.t1 is derived from g11410.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3265818	3268433	.	+	.	Phchi.S3G026400
Phchi.S3	AUGUSTUS	transcript	3265818	3268433	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	start_codon	3265818	3265820	.	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3265818	3266171	0.96	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3265818	3266171	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266172	3266263	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266264	3266324	0.98	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266264	3266324	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266325	3266642	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266643	3266743	0.89	+	2	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266643	3266743	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266744	3266838	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266839	3267033	0.83	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266839	3267033	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267034	3267149	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267150	3267271	0.88	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267150	3267271	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267272	3267415	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267416	3267485	0.91	+	1	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267416	3267485	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267486	3267641	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267642	3267791	0.88	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267642	3267791	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267792	3267904	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267905	3268040	1	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267905	3268040	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3268041	3268186	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3268187	3268283	1	+	2	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3268187	3268283	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3268284	3268366	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3268367	3268433	0.98	+	1	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3268367	3268433	.	+	.	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	stop_codon	3268434	3268436	.	+	0	transcript_id "Phchi.S3G026400.t1"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	transcript	3265818	3268433	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	start_codon	3265818	3265820	.	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3265818	3266171	0.95	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3265818	3266171	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266172	3266263	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266264	3266324	0.75	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266264	3266324	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266325	3266437	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266438	3266523	0.75	+	2	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266438	3266523	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266524	3266642	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266643	3266743	1	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266643	3266743	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3266744	3266897	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3266898	3267033	0.88	+	1	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3266898	3267033	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267034	3267149	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267150	3267271	0.88	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267150	3267271	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267272	3267415	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267416	3267485	0.88	+	1	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267416	3267485	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267486	3267641	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267642	3267791	0.85	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267642	3267791	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3267792	3267904	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3267905	3268040	1	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3267905	3268040	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3268041	3268186	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3268187	3268283	1	+	2	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3268187	3268283	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	intron	3268284	3268366	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	CDS	3268367	3268433	1	+	1	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	exon	3268367	3268433	.	+	.	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
Phchi.S3	AUGUSTUS	stop_codon	3268434	3268436	.	+	0	transcript_id "Phchi.S3G026400.t2"; gene_id "Phchi.S3G026400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13083.t1 is derived from g11548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4079533	4082855	.	-	.	Phchi.S3G040200
Phchi.S3	AUGUSTUS	transcript	4079533	4082855	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	stop_codon	4079530	4079532	.	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4079533	4079778	0.86	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4079533	4079778	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4079779	4079873	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4079874	4079981	0.98	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4079874	4079981	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4079982	4080091	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4080092	4080364	0.97	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4080092	4080364	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4080365	4080451	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4080452	4080538	1	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4080452	4080538	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4080539	4080631	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4080632	4080823	1	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4080632	4080823	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4080824	4080908	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4080909	4081040	1	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4080909	4081040	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4081041	4081118	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4081119	4081232	1	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4081119	4081232	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4081233	4081323	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4081324	4081495	0.99	-	1	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4081324	4081495	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4081496	4081613	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4081614	4081894	1	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4081614	4081894	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4081895	4081965	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4081966	4082045	1	-	2	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4081966	4082045	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	intron	4082046	4082161	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	CDS	4082162	4082855	0.99	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	exon	4082162	4082855	.	-	.	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
Phchi.S3	AUGUSTUS	start_codon	4082853	4082855	.	-	0	transcript_id "Phchi.S3G040200.t1"; gene_id "Phchi.S3G040200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6747.t1 is derived from g3919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24833787	24836083	.	+	.	Phchi.S1G390600
Phchi.S1	AUGUSTUS	transcript	24833787	24836083	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	start_codon	24833787	24833789	.	+	0	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24833787	24834024	0.98	+	0	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24833787	24834024	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24834025	24834130	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24834131	24834238	1	+	2	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24834131	24834238	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24834239	24834314	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24834315	24834404	1	+	2	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24834315	24834404	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24834405	24834510	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24834511	24834603	1	+	2	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24834511	24834603	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24834604	24834687	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24834688	24834770	1	+	2	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24834688	24834770	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24834771	24834878	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24834879	24835175	1	+	0	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24834879	24835175	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24835176	24835265	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24835266	24835396	1	+	0	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24835266	24835396	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24835397	24835538	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24835539	24835640	1	+	1	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24835539	24835640	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24835641	24835737	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24835738	24835843	1	+	1	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24835738	24835843	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	intron	24835844	24835939	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	CDS	24835940	24836083	1	+	0	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	exon	24835940	24836083	.	+	.	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
Phchi.S1	AUGUSTUS	stop_codon	24836084	24836086	.	+	0	transcript_id "Phchi.S1G390600.t1"; gene_id "Phchi.S1G390600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14799.t1 is derived from g13267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14772033	14778357	.	-	.	Phchi.S3G211800
Phchi.S3	AUGUSTUS	transcript	14772033	14778357	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	stop_codon	14772030	14772032	.	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772033	14772374	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772033	14772374	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772375	14772488	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772489	14772557	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772489	14772557	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772558	14772707	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772708	14772797	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772708	14772797	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772798	14772896	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772897	14772980	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772897	14772980	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772981	14773105	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14773106	14773423	0.97	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14773106	14773423	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14773424	14773615	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14773616	14773657	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14773616	14773657	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14773658	14773746	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14773747	14773848	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14773747	14773848	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14773849	14774025	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774026	14774148	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774026	14774148	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774149	14774247	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774248	14774292	0.95	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774248	14774292	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774293	14774396	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774397	14774450	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774397	14774450	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774451	14774552	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774553	14774587	1	-	2	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774553	14774587	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774588	14774676	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774677	14774815	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774677	14774815	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774816	14774914	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774915	14775024	1	-	2	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774915	14775024	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775025	14775169	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775170	14775236	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775170	14775236	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775237	14775368	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775369	14775448	1	-	2	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775369	14775448	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775449	14775601	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775602	14775734	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775602	14775734	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775735	14775908	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775909	14776049	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775909	14776049	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14776050	14776126	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14776127	14776192	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14776127	14776192	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14776193	14776283	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14776284	14776571	1	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14776284	14776571	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14776572	14777520	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14777521	14778357	0.98	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14777521	14778357	.	-	.	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	start_codon	14778355	14778357	.	-	0	transcript_id "Phchi.S3G211800.t1"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	transcript	14772033	14778357	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	stop_codon	14772030	14772032	.	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772033	14772374	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772033	14772374	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772375	14772488	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772489	14772557	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772489	14772557	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772558	14772707	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772708	14772797	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772708	14772797	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772798	14772896	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14772897	14772980	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14772897	14772980	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14772981	14773105	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14773106	14773423	0.98	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14773106	14773423	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14773424	14773615	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14773616	14773657	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14773616	14773657	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14773658	14773746	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14773747	14773869	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14773747	14773869	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14773870	14774025	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774026	14774148	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774026	14774148	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774149	14774247	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774248	14774292	0.9	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774248	14774292	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774293	14774396	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774397	14774450	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774397	14774450	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774451	14774552	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774553	14774587	0.98	-	2	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774553	14774587	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774588	14774676	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774677	14774815	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774677	14774815	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14774816	14774914	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14774915	14775024	1	-	2	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14774915	14775024	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775025	14775169	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775170	14775236	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775170	14775236	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775237	14775368	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775369	14775448	1	-	2	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775369	14775448	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775449	14775601	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775602	14775734	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775602	14775734	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14775735	14775908	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14775909	14776049	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14775909	14776049	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14776050	14776126	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14776127	14776192	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14776127	14776192	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14776193	14776283	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14776284	14776571	1	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14776284	14776571	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	intron	14776572	14777520	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	CDS	14777521	14778357	0.99	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	exon	14777521	14778357	.	-	.	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
Phchi.S3	AUGUSTUS	start_codon	14778355	14778357	.	-	0	transcript_id "Phchi.S3G211800.t2"; gene_id "Phchi.S3G211800"
# This transcript jg12099.t2 is derived from g7774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12100.t1 is derived from g7775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2913620	2915130	.	+	.	Phchi.S2G018000
Phchi.S2	AUGUSTUS	transcript	2913620	2915130	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	start_codon	2913620	2913622	.	+	0	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	CDS	2913620	2914237	0.72	+	0	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	exon	2913620	2914237	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	intron	2914238	2914347	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	CDS	2914348	2914554	1	+	0	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	exon	2914348	2914554	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	intron	2914555	2914670	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	CDS	2914671	2914906	0.99	+	0	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	exon	2914671	2914906	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	intron	2914907	2915021	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	CDS	2915022	2915130	0.99	+	1	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	exon	2915022	2915130	.	+	.	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
Phchi.S2	AUGUSTUS	stop_codon	2915131	2915133	.	+	0	transcript_id "Phchi.S2G018000.t1"; gene_id "Phchi.S2G018000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8220.t1 is derived from g5395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34507566	34509416	.	+	.	Phchi.S1G537900
Phchi.S1	AUGUSTUS	transcript	34507566	34509416	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	start_codon	34507566	34507568	.	+	0	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	CDS	34507566	34507672	0.97	+	0	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	exon	34507566	34507672	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	intron	34507673	34507798	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	CDS	34507799	34508508	1	+	1	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	exon	34507799	34508508	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	intron	34508509	34508583	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	CDS	34508584	34508996	1	+	2	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	exon	34508584	34508996	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	intron	34508997	34509178	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	CDS	34509179	34509221	1	+	0	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	exon	34509179	34509221	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	intron	34509222	34509300	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	CDS	34509301	34509416	1	+	2	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	exon	34509301	34509416	.	+	.	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
Phchi.S1	AUGUSTUS	stop_codon	34509417	34509419	.	+	0	transcript_id "Phchi.S1G537900.t1"; gene_id "Phchi.S1G537900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15772.t1 is derived from g14242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21277251	21277982	.	-	.	Phchi.S3G309100
Phchi.S3	AUGUSTUS	transcript	21277251	21277982	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	stop_codon	21277248	21277250	.	-	0	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	CDS	21277251	21277322	0.75	-	0	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	exon	21277251	21277322	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	intron	21277323	21277414	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	CDS	21277415	21277510	0.78	-	0	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	exon	21277415	21277510	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	intron	21277511	21277620	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	CDS	21277621	21277707	1	-	0	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	exon	21277621	21277707	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	intron	21277708	21277847	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	CDS	21277848	21277982	0.99	-	0	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	exon	21277848	21277982	.	-	.	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
Phchi.S3	AUGUSTUS	start_codon	21277980	21277982	.	-	0	transcript_id "Phchi.S3G309100.t1"; gene_id "Phchi.S3G309100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9742.t1 is derived from g6918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43472709	43476467	.	-	.	Phchi.S1G690100
Phchi.S1	AUGUSTUS	transcript	43472709	43476467	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	stop_codon	43472706	43472708	.	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43472709	43472823	1	-	1	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43472709	43472823	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43472824	43472908	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43472909	43473081	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43472909	43473081	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43473082	43473168	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43473169	43473480	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43473169	43473480	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43473481	43473547	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43473548	43473743	0.99	-	1	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43473548	43473743	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43473744	43473833	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43473834	43474090	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43473834	43474090	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43474091	43474172	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43474173	43474367	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43474173	43474367	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43474368	43474464	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43474465	43474587	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43474465	43474587	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43474588	43474670	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43474671	43474958	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43474671	43474958	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43474959	43475046	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43475047	43475229	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43475047	43475229	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43475230	43475325	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43475326	43475661	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43475326	43475661	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43475662	43475743	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43475744	43475854	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43475744	43475854	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43475855	43475990	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43475991	43476170	1	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43475991	43476170	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	intron	43476171	43476290	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	CDS	43476291	43476467	0.6	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	exon	43476291	43476467	.	-	.	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
Phchi.S1	AUGUSTUS	start_codon	43476465	43476467	.	-	0	transcript_id "Phchi.S1G690100.t1"; gene_id "Phchi.S1G690100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3901.t1 is derived from g1070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6316157	6317638	.	+	.	Phchi.S1G106000
Phchi.S1	AUGUSTUS	transcript	6316157	6317638	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	start_codon	6316157	6316159	.	+	0	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	CDS	6316157	6316413	0.66	+	0	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	exon	6316157	6316413	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	intron	6316414	6316505	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	CDS	6316506	6316742	0.3	+	1	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	exon	6316506	6316742	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	intron	6316743	6316978	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	CDS	6316979	6317346	0.38	+	1	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	exon	6316979	6317346	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	intron	6317347	6317456	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	CDS	6317457	6317638	1	+	2	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	exon	6317457	6317638	.	+	.	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
Phchi.S1	AUGUSTUS	stop_codon	6317639	6317641	.	+	0	transcript_id "Phchi.S1G106000.t1"; gene_id "Phchi.S1G106000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9680.t1 is derived from g6856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43256576	43257750	.	-	.	Phchi.S1G683900
Phchi.S1	AUGUSTUS	transcript	43256576	43257750	.	-	.	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	stop_codon	43256573	43256575	.	-	0	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	CDS	43256576	43257280	0.93	-	0	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	exon	43256576	43257280	.	-	.	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	intron	43257281	43257381	.	-	.	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	CDS	43257382	43257750	0.93	-	0	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	exon	43257382	43257750	.	-	.	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
Phchi.S1	AUGUSTUS	start_codon	43257748	43257750	.	-	0	transcript_id "Phchi.S1G683900.t1"; gene_id "Phchi.S1G683900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6892.t1 is derived from g4064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25862066	25862833	.	-	.	Phchi.S1G405100
Phchi.S1	AUGUSTUS	transcript	25862066	25862833	.	-	.	transcript_id "Phchi.S1G405100.t1"; gene_id "Phchi.S1G405100"
Phchi.S1	AUGUSTUS	stop_codon	25862063	25862065	.	-	0	transcript_id "Phchi.S1G405100.t1"; gene_id "Phchi.S1G405100"
Phchi.S1	AUGUSTUS	CDS	25862066	25862833	0.76	-	0	transcript_id "Phchi.S1G405100.t1"; gene_id "Phchi.S1G405100"
Phchi.S1	AUGUSTUS	exon	25862066	25862833	.	-	.	transcript_id "Phchi.S1G405100.t1"; gene_id "Phchi.S1G405100"
Phchi.S1	AUGUSTUS	start_codon	25862831	25862833	.	-	0	transcript_id "Phchi.S1G405100.t1"; gene_id "Phchi.S1G405100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11081.t1 is derived from g15131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3998687	3998969	.	-	.	Phchi.S4G066300
Phchi.S4	AUGUSTUS	transcript	3998687	3998969	.	-	.	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	stop_codon	3998684	3998686	.	-	0	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	CDS	3998687	3998772	0.97	-	2	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	exon	3998687	3998772	.	-	.	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	intron	3998773	3998851	.	-	.	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	CDS	3998852	3998969	1	-	0	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	exon	3998852	3998969	.	-	.	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
Phchi.S4	AUGUSTUS	start_codon	3998967	3998969	.	-	0	transcript_id "Phchi.S4G066300.t1"; gene_id "Phchi.S4G066300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4747.t1 is derived from g1917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12608285	12609135	.	-	.	Phchi.S1G190600
Phchi.S1	AUGUSTUS	transcript	12608285	12609135	.	-	.	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	stop_codon	12608282	12608284	.	-	0	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	CDS	12608285	12608527	0.43	-	0	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	exon	12608285	12608527	.	-	.	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	intron	12608528	12608668	.	-	.	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	CDS	12608669	12608732	0.52	-	1	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	exon	12608669	12608732	.	-	.	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	intron	12608733	12609043	.	-	.	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	CDS	12609044	12609135	0.31	-	0	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	exon	12609044	12609135	.	-	.	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
Phchi.S1	AUGUSTUS	start_codon	12609133	12609135	.	-	0	transcript_id "Phchi.S1G190600.t1"; gene_id "Phchi.S1G190600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1733.t1 is derived from g8653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2756097	2757524	.	-	.	Phchi.S5G034200
Phchi.S5	AUGUSTUS	transcript	2756097	2757524	.	-	.	transcript_id "Phchi.S5G034200.t1"; gene_id "Phchi.S5G034200"
Phchi.S5	AUGUSTUS	stop_codon	2756094	2756096	.	-	0	transcript_id "Phchi.S5G034200.t1"; gene_id "Phchi.S5G034200"
Phchi.S5	AUGUSTUS	CDS	2756097	2757524	0.71	-	0	transcript_id "Phchi.S5G034200.t1"; gene_id "Phchi.S5G034200"
Phchi.S5	AUGUSTUS	exon	2756097	2757524	.	-	.	transcript_id "Phchi.S5G034200.t1"; gene_id "Phchi.S5G034200"
Phchi.S5	AUGUSTUS	start_codon	2757522	2757524	.	-	0	transcript_id "Phchi.S5G034200.t1"; gene_id "Phchi.S5G034200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2175.t1 is derived from g9095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5221547	5222644	.	-	.	Phchi.S5G078400
Phchi.S5	AUGUSTUS	transcript	5221547	5222644	.	-	.	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	stop_codon	5221544	5221546	.	-	0	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	CDS	5221547	5221804	1	-	0	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	exon	5221547	5221804	.	-	.	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	intron	5221805	5221904	.	-	.	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	CDS	5221905	5222302	0.28	-	2	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	exon	5221905	5222302	.	-	.	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	intron	5222303	5222433	.	-	.	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	CDS	5222434	5222644	0.49	-	0	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	exon	5222434	5222644	.	-	.	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
Phchi.S5	AUGUSTUS	start_codon	5222642	5222644	.	-	0	transcript_id "Phchi.S5G078400.t1"; gene_id "Phchi.S5G078400"
# This transcript jg13023.t2 is derived from g11488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13024.t1 is derived from g11489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3663826	3666844	.	-	.	Phchi.S3G034300
Phchi.S3	AUGUSTUS	transcript	3663826	3666844	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	stop_codon	3663823	3663825	.	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3663826	3663933	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3663826	3663933	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3663934	3664029	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3664030	3664171	1	-	1	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3664030	3664171	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3664172	3664271	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3664272	3664349	1	-	1	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3664272	3664349	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3664350	3664464	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3664465	3664535	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3664465	3664535	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3664536	3664634	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3664635	3664769	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3664635	3664769	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3664770	3664895	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3664896	3665030	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3664896	3665030	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3665031	3665153	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3665154	3665339	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3665154	3665339	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3665340	3665417	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3665418	3665486	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3665418	3665486	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3665487	3665671	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3665672	3665754	0.82	-	2	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3665672	3665754	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3665755	3665858	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3665859	3665953	1	-	1	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3665859	3665953	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3665954	3666050	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3666051	3666097	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3666051	3666097	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3666098	3666237	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3666238	3666425	1	-	2	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3666238	3666425	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	intron	3666426	3666681	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	CDS	3666682	3666844	1	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	exon	3666682	3666844	.	-	.	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
Phchi.S3	AUGUSTUS	start_codon	3666842	3666844	.	-	0	transcript_id "Phchi.S3G034300.t1"; gene_id "Phchi.S3G034300"
# This transcript jg10556.t2 is derived from g14606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10557.t1 is derived from g14607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	975501	976859	.	+	.	Phchi.S4G013900
Phchi.S4	AUGUSTUS	transcript	975501	976859	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	start_codon	975501	975503	.	+	0	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	CDS	975501	975613	0.39	+	0	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	exon	975501	975613	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	intron	975614	975717	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	CDS	975718	975926	1	+	1	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	exon	975718	975926	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	intron	975927	976020	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	CDS	976021	976582	1	+	2	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	exon	976021	976582	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	intron	976583	976726	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	CDS	976727	976859	1	+	1	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	exon	976727	976859	.	+	.	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
Phchi.S4	AUGUSTUS	stop_codon	976860	976862	.	+	0	transcript_id "Phchi.S4G013900.t1"; gene_id "Phchi.S4G013900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15187.t1 is derived from g13655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17470184	17471266	.	-	.	Phchi.S3G250600
Phchi.S3	AUGUSTUS	transcript	17470184	17471266	.	-	.	transcript_id "Phchi.S3G250600.t1"; gene_id "Phchi.S3G250600"
Phchi.S3	AUGUSTUS	stop_codon	17470181	17470183	.	-	0	transcript_id "Phchi.S3G250600.t1"; gene_id "Phchi.S3G250600"
Phchi.S3	AUGUSTUS	CDS	17470184	17471266	0.34	-	0	transcript_id "Phchi.S3G250600.t1"; gene_id "Phchi.S3G250600"
Phchi.S3	AUGUSTUS	exon	17470184	17471266	.	-	.	transcript_id "Phchi.S3G250600.t1"; gene_id "Phchi.S3G250600"
Phchi.S3	AUGUSTUS	start_codon	17471264	17471266	.	-	0	transcript_id "Phchi.S3G250600.t1"; gene_id "Phchi.S3G250600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10829.t1 is derived from g14879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2326901	2327610	.	+	.	Phchi.S4G041100
Phchi.S4	AUGUSTUS	transcript	2326901	2327610	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	start_codon	2326901	2326903	.	+	0	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	CDS	2326901	2326926	0.88	+	0	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	exon	2326901	2326926	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	intron	2326927	2327024	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	CDS	2327025	2327097	0.72	+	1	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	exon	2327025	2327097	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	intron	2327098	2327336	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	CDS	2327337	2327364	0.53	+	0	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	exon	2327337	2327364	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	intron	2327365	2327446	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	CDS	2327447	2327610	0.5	+	2	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	exon	2327447	2327610	.	+	.	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
Phchi.S4	AUGUSTUS	stop_codon	2327611	2327613	.	+	0	transcript_id "Phchi.S4G041100.t1"; gene_id "Phchi.S4G041100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15371.t1 is derived from g13839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18674371	18675460	.	-	.	Phchi.S3G269000
Phchi.S3	AUGUSTUS	transcript	18674371	18675460	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	stop_codon	18674368	18674370	.	-	0	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	CDS	18674371	18674503	0.99	-	1	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	exon	18674371	18674503	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	intron	18674504	18674602	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	CDS	18674603	18674667	1	-	0	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	exon	18674603	18674667	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	intron	18674668	18674870	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	CDS	18674871	18675074	1	-	0	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	exon	18674871	18675074	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	intron	18675075	18675151	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	CDS	18675152	18675261	0.85	-	2	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	exon	18675152	18675261	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	intron	18675262	18675342	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	CDS	18675343	18675460	0.38	-	0	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	exon	18675343	18675460	.	-	.	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
Phchi.S3	AUGUSTUS	start_codon	18675458	18675460	.	-	0	transcript_id "Phchi.S3G269000.t1"; gene_id "Phchi.S3G269000"
# This transcript jg12407.t2 is derived from g8084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12408.t1 is derived from g8085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18398279	18400705	.	-	.	Phchi.S2G048800
Phchi.S2	AUGUSTUS	transcript	18398279	18400705	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	stop_codon	18398276	18398278	.	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18398279	18398416	0.73	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18398279	18398416	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	intron	18398417	18398508	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18398509	18398643	0.95	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18398509	18398643	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	intron	18398644	18398752	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18398753	18398870	0.97	-	1	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18398753	18398870	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	intron	18398871	18398982	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18398983	18399053	1	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18398983	18399053	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	intron	18399054	18399128	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18399129	18399377	1	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18399129	18399377	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	intron	18399378	18399451	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18399452	18399928	1	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18399452	18399928	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	intron	18399929	18400015	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	CDS	18400016	18400705	0.92	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	exon	18400016	18400705	.	-	.	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
Phchi.S2	AUGUSTUS	start_codon	18400703	18400705	.	-	0	transcript_id "Phchi.S2G048800.t1"; gene_id "Phchi.S2G048800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12318.t1 is derived from g7994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10424862	10425458	.	-	.	Phchi.S2G039800
Phchi.S2	AUGUSTUS	transcript	10424862	10425458	.	-	.	transcript_id "Phchi.S2G039800.t1"; gene_id "Phchi.S2G039800"
Phchi.S2	AUGUSTUS	stop_codon	10424859	10424861	.	-	0	transcript_id "Phchi.S2G039800.t1"; gene_id "Phchi.S2G039800"
Phchi.S2	AUGUSTUS	CDS	10424862	10425458	0.42	-	0	transcript_id "Phchi.S2G039800.t1"; gene_id "Phchi.S2G039800"
Phchi.S2	AUGUSTUS	exon	10424862	10425458	.	-	.	transcript_id "Phchi.S2G039800.t1"; gene_id "Phchi.S2G039800"
Phchi.S2	AUGUSTUS	start_codon	10425456	10425458	.	-	0	transcript_id "Phchi.S2G039800.t1"; gene_id "Phchi.S2G039800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10314.t1 is derived from g7490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47084502	47085034	.	-	.	Phchi.S1G747300
Phchi.S1	AUGUSTUS	transcript	47084502	47085034	.	-	.	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	stop_codon	47084499	47084501	.	-	0	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	CDS	47084502	47084704	1	-	2	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	exon	47084502	47084704	.	-	.	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	intron	47084705	47084804	.	-	.	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	CDS	47084805	47084895	1	-	0	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	exon	47084805	47084895	.	-	.	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	intron	47084896	47084974	.	-	.	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	CDS	47084975	47085034	0.65	-	0	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	exon	47084975	47085034	.	-	.	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
Phchi.S1	AUGUSTUS	start_codon	47085032	47085034	.	-	0	transcript_id "Phchi.S1G747300.t1"; gene_id "Phchi.S1G747300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg185.t1 is derived from g9967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1064368	1066031	.	+	.	Phchi.S6G014400
Phchi.S6	AUGUSTUS	transcript	1064368	1066031	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	start_codon	1064368	1064370	.	+	0	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	CDS	1064368	1064484	1	+	0	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	exon	1064368	1064484	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	intron	1064485	1064609	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	CDS	1064610	1064824	1	+	0	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	exon	1064610	1064824	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	intron	1064825	1065011	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	CDS	1065012	1065167	1	+	1	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	exon	1065012	1065167	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	intron	1065168	1065326	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	CDS	1065327	1065512	1	+	1	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	exon	1065327	1065512	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	intron	1065513	1065739	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	CDS	1065740	1065918	1	+	1	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	exon	1065740	1065918	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	intron	1065919	1066014	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	CDS	1066015	1066031	1	+	2	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	exon	1066015	1066031	.	+	.	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
Phchi.S6	AUGUSTUS	stop_codon	1066032	1066034	.	+	0	transcript_id "Phchi.S6G014400.t1"; gene_id "Phchi.S6G014400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4125.t1 is derived from g1294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8377217	8379606	.	+	.	Phchi.S1G128400
Phchi.S1	AUGUSTUS	transcript	8377217	8379606	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	start_codon	8377217	8377219	.	+	0	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8377217	8377239	0.7	+	0	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8377217	8377239	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8377240	8377575	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8377576	8377656	0.76	+	1	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8377576	8377656	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8377657	8377738	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8377739	8377981	1	+	1	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8377739	8377981	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8377982	8378104	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8378105	8378151	1	+	1	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8378105	8378151	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8378152	8378278	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8378279	8378397	0.99	+	2	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8378279	8378397	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8378398	8378503	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8378504	8378652	0.99	+	0	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8378504	8378652	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8378653	8378789	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8378790	8378899	1	+	1	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8378790	8378899	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8378900	8379014	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8379015	8379114	1	+	2	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8379015	8379114	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8379115	8379209	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8379210	8379333	1	+	1	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8379210	8379333	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	intron	8379334	8379432	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	CDS	8379433	8379606	1	+	0	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	exon	8379433	8379606	.	+	.	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
Phchi.S1	AUGUSTUS	stop_codon	8379607	8379609	.	+	0	transcript_id "Phchi.S1G128400.t1"; gene_id "Phchi.S1G128400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9485.t1 is derived from g6661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41972030	41976429	.	-	.	Phchi.S1G664400
Phchi.S1	AUGUSTUS	transcript	41972030	41976429	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	stop_codon	41972027	41972029	.	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41972030	41972805	0.98	-	2	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41972030	41972805	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41972806	41972909	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41972910	41972979	0.99	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41972910	41972979	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41972980	41973080	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41973081	41973174	1	-	1	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41973081	41973174	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41973175	41973282	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41973283	41973368	1	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41973283	41973368	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41973369	41973487	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41973488	41973556	0.88	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41973488	41973556	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41973557	41973662	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41973663	41973710	0.85	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41973663	41973710	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41973711	41973816	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41973817	41973892	0.98	-	1	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41973817	41973892	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41973893	41974024	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41974025	41974115	1	-	2	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41974025	41974115	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41974116	41974297	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41974298	41974346	1	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41974298	41974346	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41974347	41974428	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41974429	41974557	1	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41974429	41974557	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41974558	41974657	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41974658	41975104	0.9	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41974658	41975104	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41975105	41975200	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41975201	41975389	0.65	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41975201	41975389	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41975390	41975491	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41975492	41975659	0.31	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41975492	41975659	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	intron	41975660	41975787	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	CDS	41975788	41976429	0.35	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	exon	41975788	41976429	.	-	.	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
Phchi.S1	AUGUSTUS	start_codon	41976427	41976429	.	-	0	transcript_id "Phchi.S1G664400.t1"; gene_id "Phchi.S1G664400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9716.t1 is derived from g6892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43387907	43389500	.	-	.	Phchi.S1G687500
Phchi.S1	AUGUSTUS	transcript	43387907	43389500	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	stop_codon	43387904	43387906	.	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43387907	43388069	1	-	1	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43387907	43388069	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43388070	43388213	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43388214	43388422	1	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43388214	43388422	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43388423	43388571	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43388572	43388640	0.88	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43388572	43388640	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43388641	43388752	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43388753	43388815	1	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43388753	43388815	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43388816	43389015	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43389016	43389071	1	-	2	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43389016	43389071	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43389072	43389168	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43389169	43389226	1	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43389169	43389226	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43389227	43389315	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43389316	43389372	1	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43389316	43389372	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	intron	43389373	43389461	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	CDS	43389462	43389500	1	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	exon	43389462	43389500	.	-	.	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
Phchi.S1	AUGUSTUS	start_codon	43389498	43389500	.	-	0	transcript_id "Phchi.S1G687500.t1"; gene_id "Phchi.S1G687500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15570.t1 is derived from g14039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20050777	20053143	.	+	.	Phchi.S3G288900
Phchi.S3	AUGUSTUS	transcript	20050777	20053143	.	+	.	transcript_id "Phchi.S3G288900.t1"; gene_id "Phchi.S3G288900"
Phchi.S3	AUGUSTUS	start_codon	20050777	20050779	.	+	0	transcript_id "Phchi.S3G288900.t1"; gene_id "Phchi.S3G288900"
Phchi.S3	AUGUSTUS	CDS	20050777	20053143	0.51	+	0	transcript_id "Phchi.S3G288900.t1"; gene_id "Phchi.S3G288900"
Phchi.S3	AUGUSTUS	exon	20050777	20053143	.	+	.	transcript_id "Phchi.S3G288900.t1"; gene_id "Phchi.S3G288900"
Phchi.S3	AUGUSTUS	stop_codon	20053144	20053146	.	+	0	transcript_id "Phchi.S3G288900.t1"; gene_id "Phchi.S3G288900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13173.t1 is derived from g11638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4498628	4500376	.	+	.	Phchi.S3G049200
Phchi.S3	AUGUSTUS	transcript	4498628	4500376	.	+	.	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	start_codon	4498628	4498630	.	+	0	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	CDS	4498628	4499019	1	+	0	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	exon	4498628	4499019	.	+	.	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	intron	4499020	4499148	.	+	.	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	CDS	4499149	4499398	1	+	1	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	exon	4499149	4499398	.	+	.	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	intron	4499399	4499485	.	+	.	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	CDS	4499486	4500376	1	+	0	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	exon	4499486	4500376	.	+	.	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
Phchi.S3	AUGUSTUS	stop_codon	4500377	4500379	.	+	0	transcript_id "Phchi.S3G049200.t1"; gene_id "Phchi.S3G049200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11713.t1 is derived from g15764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7797426	7798984	.	-	.	Phchi.S4G129500
Phchi.S4	AUGUSTUS	transcript	7797426	7798984	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	stop_codon	7797423	7797425	.	-	0	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7797426	7797513	0.95	-	1	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7797426	7797513	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7797514	7797719	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7797720	7797850	1	-	0	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7797720	7797850	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7797851	7797937	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7797938	7798063	1	-	0	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7797938	7798063	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798064	7798145	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798146	7798255	1	-	2	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798146	7798255	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798256	7798394	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798395	7798709	1	-	2	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798395	7798709	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798710	7798788	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798789	7798824	1	-	2	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798789	7798824	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798825	7798974	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798975	7798984	1	-	0	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798975	7798984	.	-	.	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	start_codon	7798982	7798984	.	-	0	transcript_id "Phchi.S4G129500.t1"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	transcript	7797426	7798984	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	stop_codon	7797423	7797425	.	-	0	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7797426	7797513	0.9	-	1	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7797426	7797513	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7797514	7797719	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7797720	7797850	1	-	0	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7797720	7797850	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7797851	7797937	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7797938	7798063	1	-	0	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7797938	7798063	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798064	7798145	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798146	7798242	1	-	1	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798146	7798242	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798243	7798394	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798395	7798435	1	-	0	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798395	7798435	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798436	7798593	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798594	7798709	1	-	2	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798594	7798709	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798710	7798788	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798789	7798824	1	-	2	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798789	7798824	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	intron	7798825	7798974	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	CDS	7798975	7798984	0.99	-	0	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	exon	7798975	7798984	.	-	.	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
Phchi.S4	AUGUSTUS	start_codon	7798982	7798984	.	-	0	transcript_id "Phchi.S4G129500.t2"; gene_id "Phchi.S4G129500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6606.t1 is derived from g3778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23989171	23991316	.	-	.	Phchi.S1G376500
Phchi.S1	AUGUSTUS	transcript	23989171	23991316	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	stop_codon	23989168	23989170	.	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23989171	23989206	1	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23989171	23989206	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23989207	23989342	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23989343	23989418	1	-	1	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23989343	23989418	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23989419	23989497	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23989498	23989570	1	-	2	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23989498	23989570	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23989571	23989665	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23989666	23989727	1	-	1	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23989666	23989727	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23989728	23990084	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23990085	23990173	1	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23990085	23990173	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23990174	23990256	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23990257	23990331	1	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23990257	23990331	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23990332	23990437	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23990438	23990549	1	-	1	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23990438	23990549	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23990550	23990920	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23990921	23991045	1	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23990921	23991045	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	intron	23991046	23991127	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	CDS	23991128	23991316	0.55	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	exon	23991128	23991316	.	-	.	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
Phchi.S1	AUGUSTUS	start_codon	23991314	23991316	.	-	0	transcript_id "Phchi.S1G376500.t1"; gene_id "Phchi.S1G376500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8751.t1 is derived from g5926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37797150	37798860	.	+	.	Phchi.S1G591000
Phchi.S1	AUGUSTUS	transcript	37797150	37798860	.	+	.	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	start_codon	37797150	37797152	.	+	0	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	CDS	37797150	37798533	0.88	+	0	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	exon	37797150	37798533	.	+	.	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	intron	37798534	37798810	.	+	.	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	CDS	37798811	37798860	0.34	+	2	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	exon	37798811	37798860	.	+	.	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
Phchi.S1	AUGUSTUS	stop_codon	37798861	37798863	.	+	0	transcript_id "Phchi.S1G591000.t1"; gene_id "Phchi.S1G591000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8864.t1 is derived from g6039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38341682	38343361	.	+	.	Phchi.S1G602300
Phchi.S1	AUGUSTUS	transcript	38341682	38343361	.	+	.	transcript_id "Phchi.S1G602300.t1"; gene_id "Phchi.S1G602300"
Phchi.S1	AUGUSTUS	start_codon	38341682	38341684	.	+	0	transcript_id "Phchi.S1G602300.t1"; gene_id "Phchi.S1G602300"
Phchi.S1	AUGUSTUS	CDS	38341682	38343361	0.56	+	0	transcript_id "Phchi.S1G602300.t1"; gene_id "Phchi.S1G602300"
Phchi.S1	AUGUSTUS	exon	38341682	38343361	.	+	.	transcript_id "Phchi.S1G602300.t1"; gene_id "Phchi.S1G602300"
Phchi.S1	AUGUSTUS	stop_codon	38343362	38343364	.	+	0	transcript_id "Phchi.S1G602300.t1"; gene_id "Phchi.S1G602300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15746.t1 is derived from g14216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21035420	21039776	.	+	.	Phchi.S3G306500
Phchi.S3	AUGUSTUS	transcript	21035420	21039776	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	start_codon	21035420	21035422	.	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21035420	21035524	0.73	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21035420	21035524	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21035525	21035661	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21035662	21035753	1	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21035662	21035753	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21035754	21035870	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21035871	21035985	1	+	1	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21035871	21035985	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21035986	21036157	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21036158	21036313	1	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21036158	21036313	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21036314	21036501	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21036502	21036614	1	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21036502	21036614	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21036615	21036815	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21036816	21036954	1	+	1	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21036816	21036954	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21036955	21037080	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21037081	21037248	1	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21037081	21037248	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21037249	21037409	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21037410	21037701	1	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21037410	21037701	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21037702	21037788	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21037789	21038363	0.33	+	2	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21037789	21038363	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21038364	21038533	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21038534	21039511	0.35	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21038534	21039511	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	intron	21039512	21039593	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	CDS	21039594	21039776	1	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	exon	21039594	21039776	.	+	.	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
Phchi.S3	AUGUSTUS	stop_codon	21039777	21039779	.	+	0	transcript_id "Phchi.S3G306500.t1"; gene_id "Phchi.S3G306500"
# This transcript jg6233.t2 is derived from g3405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6234.t1 is derived from g3406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21798215	21803141	.	-	.	Phchi.S1G339300
Phchi.S1	AUGUSTUS	transcript	21798215	21803141	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	stop_codon	21798212	21798214	.	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21798215	21799993	0.4	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21798215	21799993	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	intron	21799994	21800330	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21800331	21800453	1	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21800331	21800453	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	intron	21800454	21800902	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21800903	21800995	1	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21800903	21800995	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	intron	21800996	21801108	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21801109	21801506	0.42	-	2	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21801109	21801506	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	intron	21801507	21801892	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21801893	21802580	0.48	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21801893	21802580	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	intron	21802581	21802697	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21802698	21802816	0.93	-	2	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21802698	21802816	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	intron	21802817	21802930	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	CDS	21802931	21803141	0.77	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	exon	21802931	21803141	.	-	.	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
Phchi.S1	AUGUSTUS	start_codon	21803139	21803141	.	-	0	transcript_id "Phchi.S1G339300.t1"; gene_id "Phchi.S1G339300"
# This transcript jg9314.t2 is derived from g6489.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9314.t3 is derived from g6489.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9315.t1 is derived from g6490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40913841	40915188	.	+	.	Phchi.S1G647400
Phchi.S1	AUGUSTUS	transcript	40913841	40915188	.	+	.	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	start_codon	40913841	40913843	.	+	0	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	CDS	40913841	40914020	0.97	+	0	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	exon	40913841	40914020	.	+	.	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	intron	40914021	40914242	.	+	.	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	CDS	40914243	40914605	1	+	0	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	exon	40914243	40914605	.	+	.	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	intron	40914606	40914693	.	+	.	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	CDS	40914694	40915188	0.55	+	0	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	exon	40914694	40915188	.	+	.	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
Phchi.S1	AUGUSTUS	stop_codon	40915189	40915191	.	+	0	transcript_id "Phchi.S1G647400.t1"; gene_id "Phchi.S1G647400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4137.t1 is derived from g1306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8468711	8470492	.	-	.	Phchi.S1G129600
Phchi.S1	AUGUSTUS	transcript	8468711	8470492	.	-	.	transcript_id "Phchi.S1G129600.t1"; gene_id "Phchi.S1G129600"
Phchi.S1	AUGUSTUS	stop_codon	8468708	8468710	.	-	0	transcript_id "Phchi.S1G129600.t1"; gene_id "Phchi.S1G129600"
Phchi.S1	AUGUSTUS	CDS	8468711	8470492	0.6	-	0	transcript_id "Phchi.S1G129600.t1"; gene_id "Phchi.S1G129600"
Phchi.S1	AUGUSTUS	exon	8468711	8470492	.	-	.	transcript_id "Phchi.S1G129600.t1"; gene_id "Phchi.S1G129600"
Phchi.S1	AUGUSTUS	start_codon	8470490	8470492	.	-	0	transcript_id "Phchi.S1G129600.t1"; gene_id "Phchi.S1G129600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15136.t1 is derived from g13604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17217492	17218343	.	-	.	Phchi.S3G245500
Phchi.S3	AUGUSTUS	transcript	17217492	17218343	.	-	.	transcript_id "Phchi.S3G245500.t1"; gene_id "Phchi.S3G245500"
Phchi.S3	AUGUSTUS	stop_codon	17217489	17217491	.	-	0	transcript_id "Phchi.S3G245500.t1"; gene_id "Phchi.S3G245500"
Phchi.S3	AUGUSTUS	CDS	17217492	17218343	0.99	-	0	transcript_id "Phchi.S3G245500.t1"; gene_id "Phchi.S3G245500"
Phchi.S3	AUGUSTUS	exon	17217492	17218343	.	-	.	transcript_id "Phchi.S3G245500.t1"; gene_id "Phchi.S3G245500"
Phchi.S3	AUGUSTUS	start_codon	17218341	17218343	.	-	0	transcript_id "Phchi.S3G245500.t1"; gene_id "Phchi.S3G245500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13067.t1 is derived from g11532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3991995	3995276	.	-	.	Phchi.S3G038600
Phchi.S3	AUGUSTUS	transcript	3991995	3995276	.	-	.	transcript_id "Phchi.S3G038600.t1"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	stop_codon	3991992	3991994	.	-	0	transcript_id "Phchi.S3G038600.t1"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	CDS	3991995	3995276	0.8	-	0	transcript_id "Phchi.S3G038600.t1"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	exon	3991995	3995276	.	-	.	transcript_id "Phchi.S3G038600.t1"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	start_codon	3995274	3995276	.	-	0	transcript_id "Phchi.S3G038600.t1"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	transcript	3991995	3994202	.	-	.	transcript_id "Phchi.S3G038600.t2"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	stop_codon	3991992	3991994	.	-	0	transcript_id "Phchi.S3G038600.t2"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	CDS	3991995	3994202	0.77	-	0	transcript_id "Phchi.S3G038600.t2"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	exon	3991995	3994202	.	-	.	transcript_id "Phchi.S3G038600.t2"; gene_id "Phchi.S3G038600"
Phchi.S3	AUGUSTUS	start_codon	3994200	3994202	.	-	0	transcript_id "Phchi.S3G038600.t2"; gene_id "Phchi.S3G038600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4149.t1 is derived from g1318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8650939	8651912	.	+	.	Phchi.S1G130800
Phchi.S1	AUGUSTUS	transcript	8650939	8651912	.	+	.	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	start_codon	8650939	8650941	.	+	0	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	CDS	8650939	8651527	0.75	+	0	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	exon	8650939	8651527	.	+	.	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	intron	8651528	8651676	.	+	.	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	CDS	8651677	8651912	0.84	+	2	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	exon	8651677	8651912	.	+	.	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
Phchi.S1	AUGUSTUS	stop_codon	8651913	8651915	.	+	0	transcript_id "Phchi.S1G130800.t1"; gene_id "Phchi.S1G130800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3946.t1 is derived from g1115.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6593035	6593701	.	+	.	Phchi.S1G110500
Phchi.S1	AUGUSTUS	transcript	6593114	6593701	.	+	.	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	start_codon	6593114	6593116	.	+	0	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	CDS	6593114	6593215	1	+	0	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	exon	6593114	6593215	.	+	.	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	intron	6593216	6593398	.	+	.	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	CDS	6593399	6593522	0.99	+	0	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	exon	6593399	6593522	.	+	.	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	intron	6593523	6593696	.	+	.	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	CDS	6593697	6593701	0.94	+	2	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	exon	6593697	6593701	.	+	.	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	stop_codon	6593702	6593704	.	+	0	transcript_id "Phchi.S1G110500.t1"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	transcript	6593035	6593701	.	+	.	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	start_codon	6593035	6593037	.	+	0	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	CDS	6593035	6593208	0.56	+	0	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	exon	6593035	6593208	.	+	.	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	intron	6593209	6593398	.	+	.	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	CDS	6593399	6593522	0.94	+	0	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	exon	6593399	6593522	.	+	.	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	intron	6593523	6593696	.	+	.	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	CDS	6593697	6593701	0.82	+	2	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	exon	6593697	6593701	.	+	.	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
Phchi.S1	AUGUSTUS	stop_codon	6593702	6593704	.	+	0	transcript_id "Phchi.S1G110500.t2"; gene_id "Phchi.S1G110500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11921.t1 is derived from g7596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11492	13100	.	-	.	Phchi.S2G000100
Phchi.S2	AUGUSTUS	transcript	11492	13100	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	stop_codon	11489	11491	.	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	11492	11582	1	-	1	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	11492	11582	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	11583	11656	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	11657	11706	1	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	11657	11706	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	11707	11782	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	11783	11879	1	-	1	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	11783	11879	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	11880	11978	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	11979	12024	1	-	2	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	11979	12024	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	12025	12173	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	12174	12279	1	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	12174	12279	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	12280	12392	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	12393	12554	1	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	12393	12554	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	12555	12683	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	12684	12773	1	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	12684	12773	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	12774	12851	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	12852	12940	1	-	2	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	12852	12940	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	intron	12941	13024	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	CDS	13025	13100	0.73	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	exon	13025	13100	.	-	.	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
Phchi.S2	AUGUSTUS	start_codon	13098	13100	.	-	0	transcript_id "Phchi.S2G000100.t1"; gene_id "Phchi.S2G000100"
# This transcript jg10474.t2 is derived from g14523.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10475.t1 is derived from g14524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	566795	567341	.	-	.	Phchi.S4G005700
Phchi.S4	AUGUSTUS	transcript	566795	567341	.	-	.	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	stop_codon	566792	566794	.	-	0	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	CDS	566795	566819	1	-	1	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	exon	566795	566819	.	-	.	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	intron	566820	566919	.	-	.	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	CDS	566920	567341	0.61	-	0	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	exon	566920	567341	.	-	.	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
Phchi.S4	AUGUSTUS	start_codon	567339	567341	.	-	0	transcript_id "Phchi.S4G005700.t1"; gene_id "Phchi.S4G005700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2570.t1 is derived from g9490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7426596	7428974	.	+	.	Phchi.S5G117900
Phchi.S5	AUGUSTUS	transcript	7426596	7428974	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	start_codon	7426596	7426598	.	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7426596	7426673	0.96	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7426596	7426673	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7426674	7426940	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7426941	7427380	0.35	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7426941	7427380	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7427381	7427556	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7427557	7427710	0.34	+	1	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7427557	7427710	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7427711	7427982	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7427983	7428078	1	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7427983	7428078	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7428079	7428170	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7428171	7428320	1	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7428171	7428320	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7428321	7428423	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7428424	7428658	1	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7428424	7428658	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7428659	7428773	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7428774	7428811	1	+	2	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7428774	7428811	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	intron	7428812	7428896	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	CDS	7428897	7428974	0.97	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	exon	7428897	7428974	.	+	.	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
Phchi.S5	AUGUSTUS	stop_codon	7428975	7428977	.	+	0	transcript_id "Phchi.S5G117900.t1"; gene_id "Phchi.S5G117900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5553.t1 is derived from g2723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17573553	17574791	.	+	.	Phchi.S1G271200
Phchi.S1	AUGUSTUS	transcript	17573553	17574791	.	+	.	transcript_id "Phchi.S1G271200.t1"; gene_id "Phchi.S1G271200"
Phchi.S1	AUGUSTUS	start_codon	17573553	17573555	.	+	0	transcript_id "Phchi.S1G271200.t1"; gene_id "Phchi.S1G271200"
Phchi.S1	AUGUSTUS	CDS	17573553	17574791	0.77	+	0	transcript_id "Phchi.S1G271200.t1"; gene_id "Phchi.S1G271200"
Phchi.S1	AUGUSTUS	exon	17573553	17574791	.	+	.	transcript_id "Phchi.S1G271200.t1"; gene_id "Phchi.S1G271200"
Phchi.S1	AUGUSTUS	stop_codon	17574792	17574794	.	+	0	transcript_id "Phchi.S1G271200.t1"; gene_id "Phchi.S1G271200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8006.t1 is derived from g5181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32416819	32419140	.	+	.	Phchi.S1G516500
Phchi.S1	AUGUSTUS	transcript	32416819	32419140	.	+	.	transcript_id "Phchi.S1G516500.t1"; gene_id "Phchi.S1G516500"
Phchi.S1	AUGUSTUS	start_codon	32416819	32416821	.	+	0	transcript_id "Phchi.S1G516500.t1"; gene_id "Phchi.S1G516500"
Phchi.S1	AUGUSTUS	CDS	32416819	32419140	0.49	+	0	transcript_id "Phchi.S1G516500.t1"; gene_id "Phchi.S1G516500"
Phchi.S1	AUGUSTUS	exon	32416819	32419140	.	+	.	transcript_id "Phchi.S1G516500.t1"; gene_id "Phchi.S1G516500"
Phchi.S1	AUGUSTUS	stop_codon	32419141	32419143	.	+	0	transcript_id "Phchi.S1G516500.t1"; gene_id "Phchi.S1G516500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13081.t1 is derived from g11546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4066362	4067044	.	+	.	Phchi.S3G040000
Phchi.S3	AUGUSTUS	transcript	4066362	4067044	.	+	.	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	start_codon	4066362	4066364	.	+	0	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	CDS	4066362	4066733	0.63	+	0	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	exon	4066362	4066733	.	+	.	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	intron	4066734	4066867	.	+	.	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	CDS	4066868	4067044	1	+	0	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	exon	4066868	4067044	.	+	.	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
Phchi.S3	AUGUSTUS	stop_codon	4067045	4067047	.	+	0	transcript_id "Phchi.S3G040000.t1"; gene_id "Phchi.S3G040000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15581.t1 is derived from g14050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20120756	20123321	.	+	.	Phchi.S3G290000
Phchi.S3	AUGUSTUS	transcript	20120756	20123321	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	start_codon	20120756	20120758	.	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20120756	20121009	0.57	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20120756	20121009	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20121010	20121220	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20121221	20121296	1	+	1	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20121221	20121296	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20121297	20121417	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20121418	20121510	0.99	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20121418	20121510	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20121511	20121660	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20121661	20121705	1	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20121661	20121705	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20121706	20121880	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20121881	20122023	1	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20121881	20122023	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20122024	20122222	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20122223	20122319	1	+	1	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20122223	20122319	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20122320	20122489	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20122490	20122603	1	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20122490	20122603	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20122604	20122699	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20122700	20122726	1	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20122700	20122726	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20122727	20122858	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20122859	20122963	1	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20122859	20122963	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20122964	20123060	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20123061	20123165	1	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20123061	20123165	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	intron	20123166	20123246	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	CDS	20123247	20123321	0.98	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	exon	20123247	20123321	.	+	.	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
Phchi.S3	AUGUSTUS	stop_codon	20123322	20123324	.	+	0	transcript_id "Phchi.S3G290000.t1"; gene_id "Phchi.S3G290000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12439.t1 is derived from g8116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20377191	20378522	.	+	.	Phchi.S2G051900
Phchi.S2	AUGUSTUS	transcript	20377191	20378522	.	+	.	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	start_codon	20377191	20377193	.	+	0	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	CDS	20377191	20377260	0.99	+	0	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	exon	20377191	20377260	.	+	.	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	intron	20377261	20377358	.	+	.	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	CDS	20377359	20377405	0.99	+	2	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	exon	20377359	20377405	.	+	.	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	intron	20377406	20377490	.	+	.	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	CDS	20377491	20378522	1	+	0	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	exon	20377491	20378522	.	+	.	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
Phchi.S2	AUGUSTUS	stop_codon	20378523	20378525	.	+	0	transcript_id "Phchi.S2G051900.t1"; gene_id "Phchi.S2G051900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14015.t1 is derived from g12482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10318705	10321414	.	+	.	Phchi.S3G133400
Phchi.S3	AUGUSTUS	transcript	10318705	10321414	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	start_codon	10318705	10318707	.	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10318705	10318797	0.91	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10318705	10318797	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10318798	10318892	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10318893	10318977	1	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10318893	10318977	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10318978	10319168	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10319169	10319230	1	+	2	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10319169	10319230	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10319231	10319313	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10319314	10319399	1	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10319314	10319399	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10319400	10319499	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10319500	10319573	1	+	1	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10319500	10319573	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10319574	10319715	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10319716	10319818	1	+	2	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10319716	10319818	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10319819	10319964	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10319965	10320093	1	+	1	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10319965	10320093	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10320094	10320204	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10320205	10320304	1	+	1	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10320205	10320304	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10320305	10320458	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10320459	10320578	1	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10320459	10320578	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10320579	10320673	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10320674	10320764	1	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10320674	10320764	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10320765	10320882	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10320883	10320946	1	+	2	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10320883	10320946	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10320947	10321029	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10321030	10321120	1	+	1	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10321030	10321120	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	intron	10321121	10321243	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	CDS	10321244	10321414	1	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	exon	10321244	10321414	.	+	.	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
Phchi.S3	AUGUSTUS	stop_codon	10321415	10321417	.	+	0	transcript_id "Phchi.S3G133400.t1"; gene_id "Phchi.S3G133400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg85.t1 is derived from g9867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	433859	437579	.	+	.	Phchi.S6G004400
Phchi.S6	AUGUSTUS	transcript	433859	437579	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	start_codon	433859	433861	.	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	433859	433927	0.52	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	433859	433927	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	433928	434079	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	434080	434275	0.94	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	434080	434275	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	434276	434418	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	434419	434575	1	+	2	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	434419	434575	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	434576	434726	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	434727	434818	1	+	1	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	434727	434818	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	434819	434916	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	434917	434990	0.98	+	2	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	434917	434990	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	434991	435073	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	435074	435126	1	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	435074	435126	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	435127	435290	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	435291	435393	0.98	+	1	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	435291	435393	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	435394	435501	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	435502	435635	0.98	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	435502	435635	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	435636	435734	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	435735	436033	1	+	1	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	435735	436033	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	436034	436253	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	436254	436317	1	+	2	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	436254	436317	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	436318	436410	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	436411	436474	0.74	+	1	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	436411	436474	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	436475	436588	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	436589	436696	1	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	436589	436696	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	436697	436824	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	436825	437118	0.93	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	436825	437118	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	437119	437226	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	437227	437343	0.57	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	437227	437343	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	intron	437344	437426	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	CDS	437427	437579	0.67	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	exon	437427	437579	.	+	.	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
Phchi.S6	AUGUSTUS	stop_codon	437580	437582	.	+	0	transcript_id "Phchi.S6G004400.t1"; gene_id "Phchi.S6G004400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10790.t1 is derived from g14840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2132975	2136101	.	+	.	Phchi.S4G037200
Phchi.S4	AUGUSTUS	transcript	2132975	2136101	.	+	.	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	start_codon	2132975	2132977	.	+	0	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	CDS	2132975	2135596	0.46	+	0	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	exon	2132975	2135596	.	+	.	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	intron	2135597	2135685	.	+	.	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	CDS	2135686	2135873	0.47	+	0	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	exon	2135686	2135873	.	+	.	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	intron	2135874	2136010	.	+	.	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	CDS	2136011	2136101	0.41	+	1	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	exon	2136011	2136101	.	+	.	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
Phchi.S4	AUGUSTUS	stop_codon	2136102	2136104	.	+	0	transcript_id "Phchi.S4G037200.t1"; gene_id "Phchi.S4G037200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8933.t1 is derived from g6108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38730762	38735478	.	+	.	Phchi.S1G609200
Phchi.S1	AUGUSTUS	transcript	38730762	38735478	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	start_codon	38730762	38730764	.	+	0	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38730762	38731011	0.96	+	0	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38730762	38731011	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38731012	38731083	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38731084	38731385	1	+	2	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38731084	38731385	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38731386	38731472	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38731473	38731741	1	+	0	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38731473	38731741	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38731742	38731832	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38731833	38732102	1	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38731833	38732102	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38732103	38732198	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38732199	38732434	1	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38732199	38732434	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38732435	38732560	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38732561	38732678	1	+	2	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38732561	38732678	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38732679	38732763	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38732764	38732835	0.84	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38732764	38732835	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38732836	38732938	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38732939	38733010	0.69	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38732939	38733010	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38733011	38733113	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38733114	38733182	0.78	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38733114	38733182	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38733183	38733286	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38733287	38733358	0.81	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38733287	38733358	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38733359	38733454	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38733455	38733571	0.81	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38733455	38733571	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38733572	38733651	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38733652	38733695	0.83	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38733652	38733695	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38733696	38733786	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38733787	38733867	0.93	+	2	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38733787	38733867	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38733868	38734156	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38734157	38734213	0.41	+	2	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38734157	38734213	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38734214	38734404	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38734405	38734461	1	+	2	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38734405	38734461	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38734462	38734558	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38734559	38734604	1	+	2	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38734559	38734604	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38734605	38734691	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38734692	38734832	1	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38734692	38734832	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38734833	38734925	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38734926	38735064	1	+	1	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38734926	38735064	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	intron	38735065	38735154	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	CDS	38735155	38735478	0.89	+	0	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	exon	38735155	38735478	.	+	.	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
Phchi.S1	AUGUSTUS	stop_codon	38735479	38735481	.	+	0	transcript_id "Phchi.S1G609200.t1"; gene_id "Phchi.S1G609200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14065.t1 is derived from g12532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10631301	10632379	.	-	.	Phchi.S3G138400
Phchi.S3	AUGUSTUS	transcript	10631301	10632379	.	-	.	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	stop_codon	10631298	10631300	.	-	0	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	CDS	10631301	10631632	0.69	-	2	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	exon	10631301	10631632	.	-	.	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	intron	10631633	10631889	.	-	.	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	CDS	10631890	10632379	0.8	-	0	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	exon	10631890	10632379	.	-	.	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
Phchi.S3	AUGUSTUS	start_codon	10632377	10632379	.	-	0	transcript_id "Phchi.S3G138400.t1"; gene_id "Phchi.S3G138400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10611.t1 is derived from g14661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1201453	1202792	.	-	.	Phchi.S4G019300
Phchi.S4	AUGUSTUS	transcript	1201453	1202792	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	stop_codon	1201450	1201452	.	-	0	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	CDS	1201453	1201755	0.97	-	0	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	exon	1201453	1201755	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	intron	1201756	1201846	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	CDS	1201847	1202092	0.97	-	0	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	exon	1201847	1202092	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	intron	1202093	1202194	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	CDS	1202195	1202440	0.97	-	0	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	exon	1202195	1202440	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	intron	1202441	1202525	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	CDS	1202526	1202792	0.45	-	0	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	exon	1202526	1202792	.	-	.	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
Phchi.S4	AUGUSTUS	start_codon	1202790	1202792	.	-	0	transcript_id "Phchi.S4G019300.t1"; gene_id "Phchi.S4G019300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13369.t1 is derived from g11835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6371821	6373394	.	-	.	Phchi.S3G068800
Phchi.S3	AUGUSTUS	transcript	6371821	6373394	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	stop_codon	6371818	6371820	.	-	0	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	CDS	6371821	6372032	1	-	2	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	exon	6371821	6372032	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	intron	6372033	6372119	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	CDS	6372120	6372384	0.98	-	0	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	exon	6372120	6372384	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	intron	6372385	6372454	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	CDS	6372455	6372691	0.72	-	0	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	exon	6372455	6372691	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	intron	6372692	6372822	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	CDS	6372823	6372851	0.86	-	2	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	exon	6372823	6372851	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	intron	6372852	6373025	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	CDS	6373026	6373152	1	-	0	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	exon	6373026	6373152	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	intron	6373153	6373235	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	CDS	6373236	6373394	1	-	0	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	exon	6373236	6373394	.	-	.	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
Phchi.S3	AUGUSTUS	start_codon	6373392	6373394	.	-	0	transcript_id "Phchi.S3G068800.t1"; gene_id "Phchi.S3G068800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12803.t1 is derived from g11268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2452610	2455354	.	-	.	Phchi.S3G012200
Phchi.S3	AUGUSTUS	transcript	2452610	2455354	.	-	.	transcript_id "Phchi.S3G012200.t1"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	stop_codon	2452607	2452609	.	-	0	transcript_id "Phchi.S3G012200.t1"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	CDS	2452610	2455354	0.79	-	0	transcript_id "Phchi.S3G012200.t1"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	exon	2452610	2455354	.	-	.	transcript_id "Phchi.S3G012200.t1"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	start_codon	2455352	2455354	.	-	0	transcript_id "Phchi.S3G012200.t1"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	transcript	2452610	2452993	.	-	.	transcript_id "Phchi.S3G012200.t2"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	stop_codon	2452607	2452609	.	-	0	transcript_id "Phchi.S3G012200.t2"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	CDS	2452610	2452993	0.65	-	0	transcript_id "Phchi.S3G012200.t2"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	exon	2452610	2452993	.	-	.	transcript_id "Phchi.S3G012200.t2"; gene_id "Phchi.S3G012200"
Phchi.S3	AUGUSTUS	start_codon	2452991	2452993	.	-	0	transcript_id "Phchi.S3G012200.t2"; gene_id "Phchi.S3G012200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8057.t1 is derived from g5232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32733827	32736267	.	+	.	Phchi.S1G521600
Phchi.S1	AUGUSTUS	transcript	32733827	32736267	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	start_codon	32733827	32733829	.	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32733827	32733838	1	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32733827	32733838	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	intron	32733839	32734039	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32734040	32734142	1	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32734040	32734142	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	intron	32734143	32734311	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32734312	32734394	1	+	2	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32734312	32734394	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	intron	32734395	32734509	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32734510	32734668	1	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32734510	32734668	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	intron	32734669	32734753	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32734754	32734870	1	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32734754	32734870	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	intron	32734871	32734999	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32735000	32735223	1	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32735000	32735223	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	intron	32735224	32736170	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	CDS	32736171	32736267	1	+	1	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	exon	32736171	32736267	.	+	.	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
Phchi.S1	AUGUSTUS	stop_codon	32736268	32736270	.	+	0	transcript_id "Phchi.S1G521600.t1"; gene_id "Phchi.S1G521600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13470.t1 is derived from g11937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7060206	7060814	.	-	.	Phchi.S3G078900
Phchi.S3	AUGUSTUS	transcript	7060206	7060814	.	-	.	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	stop_codon	7060203	7060205	.	-	0	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	CDS	7060206	7060303	0.87	-	2	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	exon	7060206	7060303	.	-	.	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	intron	7060304	7060391	.	-	.	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	CDS	7060392	7060401	0.78	-	0	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	exon	7060392	7060401	.	-	.	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	intron	7060402	7060667	.	-	.	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	CDS	7060668	7060814	0.67	-	0	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	exon	7060668	7060814	.	-	.	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
Phchi.S3	AUGUSTUS	start_codon	7060812	7060814	.	-	0	transcript_id "Phchi.S3G078900.t1"; gene_id "Phchi.S3G078900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12693.t1 is derived from g11158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	575964	577624	.	+	.	Phchi.S3G001200
Phchi.S3	AUGUSTUS	transcript	575964	577624	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	start_codon	575964	575966	.	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	575964	575979	0.99	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	575964	575979	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	575980	576152	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576153	576235	1	+	2	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576153	576235	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576236	576338	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576339	576451	1	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576339	576451	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576452	576551	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576552	576633	1	+	1	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576552	576633	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576634	576773	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576774	576911	1	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576774	576911	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576912	577007	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577008	577127	1	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577008	577127	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577128	577211	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577212	577306	0.8	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577212	577306	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577307	577383	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577384	577484	0.77	+	1	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577384	577484	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577485	577571	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577572	577624	0.79	+	2	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577572	577624	.	+	.	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	stop_codon	577625	577627	.	+	0	transcript_id "Phchi.S3G001200.t1"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	transcript	576048	577624	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	start_codon	576048	576050	.	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576048	576062	0.47	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576048	576062	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576063	576152	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576153	576235	1	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576153	576235	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576236	576322	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576323	576451	1	+	1	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576323	576451	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576452	576551	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576552	576633	1	+	1	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576552	576633	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576634	576773	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576774	576911	1	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576774	576911	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576912	577007	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577008	577127	1	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577008	577127	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577128	577211	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577212	577306	0.85	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577212	577306	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577307	577383	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577384	577484	0.75	+	1	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577384	577484	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577485	577571	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577572	577624	0.8	+	2	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577572	577624	.	+	.	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	stop_codon	577625	577627	.	+	0	transcript_id "Phchi.S3G001200.t2"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	transcript	575964	577624	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	start_codon	575964	575966	.	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	575964	575979	1	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	575964	575979	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	575980	576152	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576153	576235	1	+	2	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576153	576235	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576236	576338	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576339	576451	1	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576339	576451	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576452	576551	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576552	576633	1	+	1	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576552	576633	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576634	576773	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	576774	576911	1	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	576774	576911	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	576912	577007	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577008	577127	1	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577008	577127	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577128	577194	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577195	577235	0.6	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577195	577235	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577236	577383	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577384	577484	0.77	+	1	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577384	577484	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	intron	577485	577571	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	CDS	577572	577624	0.82	+	2	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	exon	577572	577624	.	+	.	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
Phchi.S3	AUGUSTUS	stop_codon	577625	577627	.	+	0	transcript_id "Phchi.S3G001200.t3"; gene_id "Phchi.S3G001200"
# This transcript jg3163.t2 is derived from g332.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3164.t1 is derived from g333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2036343	2036783	.	+	.	Phchi.S1G032300
Phchi.S1	AUGUSTUS	transcript	2036343	2036783	.	+	.	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	start_codon	2036343	2036345	.	+	0	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	CDS	2036343	2036574	0.84	+	0	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	exon	2036343	2036574	.	+	.	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	intron	2036575	2036736	.	+	.	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	CDS	2036737	2036783	0.84	+	2	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	exon	2036737	2036783	.	+	.	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
Phchi.S1	AUGUSTUS	stop_codon	2036784	2036786	.	+	0	transcript_id "Phchi.S1G032300.t1"; gene_id "Phchi.S1G032300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15513.t1 is derived from g13982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19627928	19630585	.	+	.	Phchi.S3G283200
Phchi.S3	AUGUSTUS	transcript	19627986	19630585	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	start_codon	19627986	19627988	.	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19627986	19628023	1	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19627986	19628023	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628024	19628185	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628186	19628291	1	+	1	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628186	19628291	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628292	19628404	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628405	19628603	1	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628405	19628603	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628604	19628757	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628758	19628803	0.99	+	2	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628758	19628803	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628804	19628919	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628920	19628989	0.98	+	1	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628920	19628989	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628990	19629086	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19629087	19629245	1	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19629087	19629245	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19629246	19629474	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19629475	19629594	1	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19629475	19629594	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19629595	19629719	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19629720	19629885	1	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19629720	19629885	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19629886	19630016	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19630017	19630129	1	+	2	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19630017	19630129	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19630130	19630321	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19630322	19630398	1	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19630322	19630398	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19630399	19630581	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19630582	19630585	1	+	1	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19630582	19630585	.	+	.	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	stop_codon	19630586	19630588	.	+	0	transcript_id "Phchi.S3G283200.t1"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	transcript	19627928	19630585	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	start_codon	19627928	19627930	.	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19627928	19628023	0.61	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19627928	19628023	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628024	19628198	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628199	19628291	1	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628199	19628291	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628292	19628404	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628405	19628603	1	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628405	19628603	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628604	19628757	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628758	19628803	1	+	2	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628758	19628803	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628804	19628919	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19628920	19628989	1	+	1	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19628920	19628989	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19628990	19629086	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19629087	19629245	1	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19629087	19629245	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19629246	19629474	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19629475	19629594	1	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19629475	19629594	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19629595	19629719	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19629720	19629885	1	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19629720	19629885	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19629886	19630016	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19630017	19630129	1	+	2	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19630017	19630129	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19630130	19630321	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19630322	19630398	1	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19630322	19630398	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	intron	19630399	19630581	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	CDS	19630582	19630585	1	+	1	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	exon	19630582	19630585	.	+	.	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
Phchi.S3	AUGUSTUS	stop_codon	19630586	19630588	.	+	0	transcript_id "Phchi.S3G283200.t2"; gene_id "Phchi.S3G283200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11265.t1 is derived from g15315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5086320	5087919	.	-	.	Phchi.S4G084700
Phchi.S4	AUGUSTUS	transcript	5086320	5087919	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	stop_codon	5086317	5086319	.	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5086320	5086442	0.84	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5086320	5086442	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5086443	5086558	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5086559	5086582	1	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5086559	5086582	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5086583	5086673	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5086674	5086700	1	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5086674	5086700	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5086701	5086791	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5086792	5086859	1	-	2	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5086792	5086859	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5086860	5086956	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5086957	5087128	1	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5086957	5087128	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5087129	5087253	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5087254	5087442	1	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5087254	5087442	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5087443	5087523	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5087524	5087673	0.72	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5087524	5087673	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	intron	5087674	5087862	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	CDS	5087863	5087919	0.7	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	exon	5087863	5087919	.	-	.	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
Phchi.S4	AUGUSTUS	start_codon	5087917	5087919	.	-	0	transcript_id "Phchi.S4G084700.t1"; gene_id "Phchi.S4G084700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8894.t1 is derived from g6069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38524912	38527865	.	+	.	Phchi.S1G605300
Phchi.S1	AUGUSTUS	transcript	38524912	38527865	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	start_codon	38524912	38524914	.	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38524912	38525218	0.31	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38524912	38525218	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38525219	38525367	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38525368	38525387	0.58	+	2	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38525368	38525387	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38525388	38525582	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38525583	38525681	1	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38525583	38525681	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38525682	38525776	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38525777	38525875	1	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38525777	38525875	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38525876	38525957	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38525958	38526116	1	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38525958	38526116	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38526117	38526205	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38526206	38526358	0.98	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38526206	38526358	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38526359	38526465	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38526466	38526582	0.84	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38526466	38526582	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38526583	38526684	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38526685	38526798	0.88	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38526685	38526798	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38526799	38526948	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38526949	38527093	0.42	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38526949	38527093	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38527094	38527352	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38527353	38527382	0.49	+	2	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38527353	38527382	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38527383	38527515	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38527516	38527616	0.89	+	2	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38527516	38527616	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38527617	38527706	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38527707	38527775	0.9	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38527707	38527775	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	intron	38527776	38527844	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	CDS	38527845	38527865	0.9	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	exon	38527845	38527865	.	+	.	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
Phchi.S1	AUGUSTUS	stop_codon	38527866	38527868	.	+	0	transcript_id "Phchi.S1G605300.t1"; gene_id "Phchi.S1G605300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8687.t1 is derived from g5862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37449979	37451845	.	-	.	Phchi.S1G584600
Phchi.S1	AUGUSTUS	transcript	37449979	37451845	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	stop_codon	37449976	37449978	.	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37449979	37450093	0.97	-	1	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37449979	37450093	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37450094	37450168	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37450169	37450281	1	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37450169	37450281	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37450282	37450369	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37450370	37450465	1	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37450370	37450465	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37450466	37450558	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37450559	37450675	1	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37450559	37450675	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37450676	37450752	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37450753	37450851	1	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37450753	37450851	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37450852	37451041	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37451042	37451173	1	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37451042	37451173	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37451174	37451287	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37451288	37451464	1	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37451288	37451464	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	intron	37451465	37451557	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	CDS	37451558	37451845	0.55	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	exon	37451558	37451845	.	-	.	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
Phchi.S1	AUGUSTUS	start_codon	37451843	37451845	.	-	0	transcript_id "Phchi.S1G584600.t1"; gene_id "Phchi.S1G584600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12615.t1 is derived from g8292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37579642	37580694	.	+	.	Phchi.S2G069500
Phchi.S2	AUGUSTUS	transcript	37579642	37580694	.	+	.	transcript_id "Phchi.S2G069500.t1"; gene_id "Phchi.S2G069500"
Phchi.S2	AUGUSTUS	start_codon	37579642	37579644	.	+	0	transcript_id "Phchi.S2G069500.t1"; gene_id "Phchi.S2G069500"
Phchi.S2	AUGUSTUS	CDS	37579642	37580694	0.94	+	0	transcript_id "Phchi.S2G069500.t1"; gene_id "Phchi.S2G069500"
Phchi.S2	AUGUSTUS	exon	37579642	37580694	.	+	.	transcript_id "Phchi.S2G069500.t1"; gene_id "Phchi.S2G069500"
Phchi.S2	AUGUSTUS	stop_codon	37580695	37580697	.	+	0	transcript_id "Phchi.S2G069500.t1"; gene_id "Phchi.S2G069500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5117.t1 is derived from g2287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14810127	14811967	.	-	.	Phchi.S1G227600
Phchi.S1	AUGUSTUS	transcript	14810127	14811967	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	stop_codon	14810124	14810126	.	-	0	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	CDS	14810127	14810691	1	-	1	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	exon	14810127	14810691	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	intron	14810692	14810849	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	CDS	14810850	14811061	1	-	0	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	exon	14810850	14811061	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	intron	14811062	14811603	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	CDS	14811604	14811801	1	-	0	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	exon	14811604	14811801	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	intron	14811802	14811886	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	CDS	14811887	14811967	1	-	0	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	exon	14811887	14811967	.	-	.	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
Phchi.S1	AUGUSTUS	start_codon	14811965	14811967	.	-	0	transcript_id "Phchi.S1G227600.t1"; gene_id "Phchi.S1G227600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6117.t1 is derived from g3288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21016544	21017735	.	+	.	Phchi.S1G327600
Phchi.S1	AUGUSTUS	transcript	21016544	21017735	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	start_codon	21016544	21016546	.	+	0	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	CDS	21016544	21016684	0.99	+	0	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	exon	21016544	21016684	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	intron	21016685	21016840	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	CDS	21016841	21017099	0.98	+	0	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	exon	21016841	21017099	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	intron	21017100	21017270	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	CDS	21017271	21017338	1	+	2	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	exon	21017271	21017338	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	intron	21017339	21017423	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	CDS	21017424	21017735	0.93	+	0	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	exon	21017424	21017735	.	+	.	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
Phchi.S1	AUGUSTUS	stop_codon	21017736	21017738	.	+	0	transcript_id "Phchi.S1G327600.t1"; gene_id "Phchi.S1G327600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5897.t1 is derived from g3067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19642942	19644810	.	+	.	Phchi.S1G305600
Phchi.S1	AUGUSTUS	transcript	19642942	19644810	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	start_codon	19642942	19642944	.	+	0	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19642942	19643212	0.98	+	0	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19642942	19643212	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19643213	19643294	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19643295	19643468	1	+	2	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19643295	19643468	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19643469	19643550	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19643551	19643610	1	+	2	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19643551	19643610	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19643611	19643698	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19643699	19643802	0.75	+	2	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19643699	19643802	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19643803	19643879	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19643880	19643946	0.75	+	0	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19643880	19643946	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19643947	19644034	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19644035	19644111	1	+	2	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19644035	19644111	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19644112	19644238	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19644239	19644315	1	+	0	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19644239	19644315	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19644316	19644428	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19644429	19644561	1	+	1	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19644429	19644561	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	intron	19644562	19644666	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	CDS	19644667	19644810	1	+	0	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	exon	19644667	19644810	.	+	.	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
Phchi.S1	AUGUSTUS	stop_codon	19644811	19644813	.	+	0	transcript_id "Phchi.S1G305600.t1"; gene_id "Phchi.S1G305600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6277.t1 is derived from g3449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22042489	22043977	.	+	.	Phchi.S1G343600
Phchi.S1	AUGUSTUS	transcript	22042489	22043977	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	start_codon	22042489	22042491	.	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	CDS	22042489	22042596	0.82	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	exon	22042489	22042596	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	intron	22042597	22042783	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	CDS	22042784	22042912	0.5	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	exon	22042784	22042912	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	intron	22042913	22043017	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	CDS	22043018	22043114	1	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	exon	22043018	22043114	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	intron	22043115	22043270	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	CDS	22043271	22043386	1	+	2	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	exon	22043271	22043386	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	intron	22043387	22043491	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	CDS	22043492	22043782	0.98	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	exon	22043492	22043782	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	intron	22043783	22043881	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	CDS	22043882	22043977	0.97	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	exon	22043882	22043977	.	+	.	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
Phchi.S1	AUGUSTUS	stop_codon	22043978	22043980	.	+	0	transcript_id "Phchi.S1G343600.t1"; gene_id "Phchi.S1G343600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12350.t1 is derived from g8026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12375015	12376207	.	+	.	Phchi.S2G043000
Phchi.S2	AUGUSTUS	transcript	12375015	12376207	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	start_codon	12375015	12375017	.	+	0	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	CDS	12375015	12375210	0.44	+	0	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	exon	12375015	12375210	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	intron	12375211	12375308	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	CDS	12375309	12375398	0.87	+	2	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	exon	12375309	12375398	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	intron	12375399	12375609	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	CDS	12375610	12375724	0.76	+	2	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	exon	12375610	12375724	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	intron	12375725	12376006	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	CDS	12376007	12376040	0.69	+	1	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	exon	12376007	12376040	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	intron	12376041	12376126	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	CDS	12376127	12376207	0.71	+	0	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	exon	12376127	12376207	.	+	.	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
Phchi.S2	AUGUSTUS	stop_codon	12376208	12376210	.	+	0	transcript_id "Phchi.S2G043000.t1"; gene_id "Phchi.S2G043000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10610.t1 is derived from g14660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1199504	1200286	.	-	.	Phchi.S4G019200
Phchi.S4	AUGUSTUS	transcript	1199504	1200286	.	-	.	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	stop_codon	1199501	1199503	.	-	0	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	CDS	1199504	1199560	0.99	-	0	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	exon	1199504	1199560	.	-	.	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	intron	1199561	1199640	.	-	.	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	CDS	1199641	1200077	1	-	2	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	exon	1199641	1200077	.	-	.	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	intron	1200078	1200174	.	-	.	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	CDS	1200175	1200286	0.99	-	0	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	exon	1200175	1200286	.	-	.	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
Phchi.S4	AUGUSTUS	start_codon	1200284	1200286	.	-	0	transcript_id "Phchi.S4G019200.t1"; gene_id "Phchi.S4G019200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg512.t1 is derived from g10294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3543230	3543992	.	-	.	Phchi.S6G047100
Phchi.S6	AUGUSTUS	transcript	3543230	3543992	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	stop_codon	3543227	3543229	.	-	0	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	CDS	3543230	3543309	0.87	-	2	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	exon	3543230	3543309	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	intron	3543310	3543384	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	CDS	3543385	3543468	0.87	-	2	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	exon	3543385	3543468	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	intron	3543469	3543562	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	CDS	3543563	3543799	0.57	-	2	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	exon	3543563	3543799	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	intron	3543800	3543889	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	CDS	3543890	3543992	0.43	-	0	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	exon	3543890	3543992	.	-	.	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
Phchi.S6	AUGUSTUS	start_codon	3543990	3543992	.	-	0	transcript_id "Phchi.S6G047100.t1"; gene_id "Phchi.S6G047100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3198.t1 is derived from g367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2204134	2206612	.	-	.	Phchi.S1G035700
Phchi.S1	AUGUSTUS	transcript	2204134	2206612	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	stop_codon	2204131	2204133	.	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2204134	2204309	0.73	-	2	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2204134	2204309	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2204310	2204391	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2204392	2204461	0.55	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2204392	2204461	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2204462	2204564	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2204565	2204695	0.62	-	2	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2204565	2204695	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2204696	2204949	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2204950	2205038	0.79	-	1	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2204950	2205038	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2205039	2205128	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2205129	2205209	1	-	1	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2205129	2205209	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2205210	2205342	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2205343	2205389	1	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2205343	2205389	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2205390	2205507	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2205508	2205603	1	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2205508	2205603	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2205604	2205695	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2205696	2205762	1	-	1	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2205696	2205762	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2205763	2205882	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2205883	2206041	1	-	1	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2205883	2206041	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2206042	2206139	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2206140	2206210	1	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2206140	2206210	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	intron	2206211	2206297	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	CDS	2206298	2206612	0.93	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	exon	2206298	2206612	.	-	.	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
Phchi.S1	AUGUSTUS	start_codon	2206610	2206612	.	-	0	transcript_id "Phchi.S1G035700.t1"; gene_id "Phchi.S1G035700"
# This transcript jg5935.t2 is derived from g3106.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5936.t1 is derived from g3107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19943457	19945586	.	+	.	Phchi.S1G309500
Phchi.S1	AUGUSTUS	transcript	19943457	19945586	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	start_codon	19943457	19943459	.	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19943457	19943715	0.9	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19943457	19943715	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19943716	19943839	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19943840	19944045	1	+	2	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19943840	19944045	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19944046	19944143	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19944144	19944204	1	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19944144	19944204	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19944205	19944286	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19944287	19944335	1	+	2	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19944287	19944335	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19944336	19944426	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19944427	19944569	1	+	1	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19944427	19944569	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19944570	19944657	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19944658	19944776	1	+	2	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19944658	19944776	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19944777	19944861	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19944862	19944987	1	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19944862	19944987	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19944988	19945075	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19945076	19945196	0.99	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19945076	19945196	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19945197	19945300	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19945301	19945455	1	+	2	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19945301	19945455	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	intron	19945456	19945529	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	CDS	19945530	19945586	1	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	exon	19945530	19945586	.	+	.	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
Phchi.S1	AUGUSTUS	stop_codon	19945587	19945589	.	+	0	transcript_id "Phchi.S1G309500.t1"; gene_id "Phchi.S1G309500"
# This transcript jg7422.t2 is derived from g4594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7423.t1 is derived from g4595.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29071218	29072221	.	+	.	Phchi.S1G458200
Phchi.S1	AUGUSTUS	transcript	29071218	29072221	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	start_codon	29071218	29071220	.	+	0	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071218	29071287	0.82	+	0	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071218	29071287	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	intron	29071288	29071432	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071433	29071482	0.99	+	2	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071433	29071482	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	intron	29071483	29071635	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071636	29071733	0.72	+	0	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071636	29071733	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	intron	29071734	29071818	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071819	29072221	0.53	+	1	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071819	29072221	.	+	.	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	stop_codon	29072222	29072224	.	+	0	transcript_id "Phchi.S1G458200.t1"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	transcript	29071218	29072221	.	+	.	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	start_codon	29071218	29071220	.	+	0	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071218	29071287	0.88	+	0	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071218	29071287	.	+	.	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	intron	29071288	29071635	.	+	.	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071636	29071733	0.38	+	2	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071636	29071733	.	+	.	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	intron	29071734	29071858	.	+	.	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	CDS	29071859	29072221	0.25	+	0	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	exon	29071859	29072221	.	+	.	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
Phchi.S1	AUGUSTUS	stop_codon	29072222	29072224	.	+	0	transcript_id "Phchi.S1G458200.t2"; gene_id "Phchi.S1G458200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg151.t1 is derived from g9933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	845089	846900	.	-	.	Phchi.S6G011000
Phchi.S6	AUGUSTUS	transcript	845089	846900	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	stop_codon	845086	845088	.	-	0	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845089	845160	1	-	0	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845089	845160	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845161	845237	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845238	845406	1	-	1	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845238	845406	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845407	845501	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845502	845653	1	-	0	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845502	845653	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845654	845731	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845732	845890	1	-	0	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845732	845890	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845891	845992	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845993	846269	1	-	1	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845993	846269	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	846270	846346	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	846347	846463	1	-	1	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	846347	846463	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	846464	846553	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	846554	846616	1	-	1	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	846554	846616	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	846617	846715	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	846716	846900	1	-	0	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	846716	846900	.	-	.	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	start_codon	846898	846900	.	-	0	transcript_id "Phchi.S6G011000.t1"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	transcript	845147	846900	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	stop_codon	845144	845146	.	-	0	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845147	845155	0.99	-	0	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845147	845155	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845156	845237	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845238	845406	0.99	-	1	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845238	845406	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845407	845501	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845502	845653	1	-	0	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845502	845653	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845654	845731	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845732	845890	1	-	0	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845732	845890	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	845891	845992	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	845993	846269	1	-	1	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	845993	846269	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	846270	846346	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	846347	846463	1	-	1	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	846347	846463	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	846464	846553	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	846554	846616	1	-	1	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	846554	846616	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	intron	846617	846715	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	CDS	846716	846900	1	-	0	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	exon	846716	846900	.	-	.	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
Phchi.S6	AUGUSTUS	start_codon	846898	846900	.	-	0	transcript_id "Phchi.S6G011000.t2"; gene_id "Phchi.S6G011000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4431.t1 is derived from g1600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10473613	10474238	.	+	.	Phchi.S1G159000
Phchi.S1	AUGUSTUS	transcript	10473613	10474238	.	+	.	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	start_codon	10473613	10473615	.	+	0	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	CDS	10473613	10473670	0.98	+	0	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	exon	10473613	10473670	.	+	.	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	intron	10473671	10473810	.	+	.	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	CDS	10473811	10473878	0.98	+	2	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	exon	10473811	10473878	.	+	.	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	intron	10473879	10474004	.	+	.	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	CDS	10474005	10474238	0.98	+	0	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	exon	10474005	10474238	.	+	.	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
Phchi.S1	AUGUSTUS	stop_codon	10474239	10474241	.	+	0	transcript_id "Phchi.S1G159000.t1"; gene_id "Phchi.S1G159000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5276.t1 is derived from g2446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16002638	16003597	.	+	.	Phchi.S1G243500
Phchi.S1	AUGUSTUS	transcript	16002638	16003597	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	start_codon	16002638	16002640	.	+	0	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	CDS	16002638	16002686	0.97	+	0	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	exon	16002638	16002686	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	intron	16002687	16002840	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	CDS	16002841	16002850	0.99	+	2	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	exon	16002841	16002850	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	intron	16002851	16002960	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	CDS	16002961	16002983	0.99	+	1	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	exon	16002961	16002983	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	intron	16002984	16003071	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	CDS	16003072	16003133	0.46	+	2	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	exon	16003072	16003133	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	intron	16003134	16003229	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	CDS	16003230	16003246	0.47	+	0	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	exon	16003230	16003246	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	intron	16003247	16003338	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	CDS	16003339	16003597	0.99	+	1	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	exon	16003339	16003597	.	+	.	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
Phchi.S1	AUGUSTUS	stop_codon	16003598	16003600	.	+	0	transcript_id "Phchi.S1G243500.t1"; gene_id "Phchi.S1G243500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15657.t1 is derived from g14126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20519775	20520981	.	-	.	Phchi.S3G297600
Phchi.S3	AUGUSTUS	transcript	20519775	20520981	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	stop_codon	20519772	20519774	.	-	0	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	CDS	20519775	20519796	0.58	-	1	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	exon	20519775	20519796	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	intron	20519797	20519926	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	CDS	20519927	20519988	0.58	-	0	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	exon	20519927	20519988	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	intron	20519989	20520148	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	CDS	20520149	20520205	0.48	-	0	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	exon	20520149	20520205	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	intron	20520206	20520340	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	CDS	20520341	20520396	1	-	2	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	exon	20520341	20520396	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	intron	20520397	20520536	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	CDS	20520537	20520637	1	-	1	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	exon	20520537	20520637	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	intron	20520638	20520898	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	CDS	20520899	20520981	0.7	-	0	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	exon	20520899	20520981	.	-	.	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
Phchi.S3	AUGUSTUS	start_codon	20520979	20520981	.	-	0	transcript_id "Phchi.S3G297600.t1"; gene_id "Phchi.S3G297600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15314.t1 is derived from g13782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18355894	18357673	.	-	.	Phchi.S3G263300
Phchi.S3	AUGUSTUS	transcript	18355894	18357673	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	stop_codon	18355891	18355893	.	-	0	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	CDS	18355894	18356284	1	-	1	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	exon	18355894	18356284	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	intron	18356285	18356402	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	CDS	18356403	18356855	1	-	1	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	exon	18356403	18356855	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	intron	18356856	18356960	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	CDS	18356961	18357256	0.73	-	0	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	exon	18356961	18357256	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	intron	18357257	18357373	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	CDS	18357374	18357673	0.57	-	0	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	exon	18357374	18357673	.	-	.	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
Phchi.S3	AUGUSTUS	start_codon	18357671	18357673	.	-	0	transcript_id "Phchi.S3G263300.t1"; gene_id "Phchi.S3G263300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4356.t1 is derived from g1525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9984467	9985991	.	-	.	Phchi.S1G151500
Phchi.S1	AUGUSTUS	transcript	9984467	9985991	.	-	.	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	stop_codon	9984464	9984466	.	-	0	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	CDS	9984467	9984744	0.55	-	2	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	exon	9984467	9984744	.	-	.	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	intron	9984745	9984913	.	-	.	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	CDS	9984914	9985239	0.63	-	1	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	exon	9984914	9985239	.	-	.	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	intron	9985240	9985326	.	-	.	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	CDS	9985327	9985991	0.96	-	0	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	exon	9985327	9985991	.	-	.	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
Phchi.S1	AUGUSTUS	start_codon	9985989	9985991	.	-	0	transcript_id "Phchi.S1G151500.t1"; gene_id "Phchi.S1G151500"
# This transcript jg9723.t2 is derived from g6899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9724.t1 is derived from g6900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43407131	43407442	.	+	.	Phchi.S1G688300
Phchi.S1	AUGUSTUS	transcript	43407131	43407442	.	+	.	transcript_id "Phchi.S1G688300.t1"; gene_id "Phchi.S1G688300"
Phchi.S1	AUGUSTUS	start_codon	43407131	43407133	.	+	0	transcript_id "Phchi.S1G688300.t1"; gene_id "Phchi.S1G688300"
Phchi.S1	AUGUSTUS	CDS	43407131	43407442	0.82	+	0	transcript_id "Phchi.S1G688300.t1"; gene_id "Phchi.S1G688300"
Phchi.S1	AUGUSTUS	exon	43407131	43407442	.	+	.	transcript_id "Phchi.S1G688300.t1"; gene_id "Phchi.S1G688300"
Phchi.S1	AUGUSTUS	stop_codon	43407443	43407445	.	+	0	transcript_id "Phchi.S1G688300.t1"; gene_id "Phchi.S1G688300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6114.t1 is derived from g3285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21002606	21003558	.	+	.	Phchi.S1G327300
Phchi.S1	AUGUSTUS	transcript	21002606	21003558	.	+	.	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	start_codon	21002606	21002608	.	+	0	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	CDS	21002606	21003401	0.46	+	0	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	exon	21002606	21003401	.	+	.	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	intron	21003402	21003523	.	+	.	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	CDS	21003524	21003558	0.19	+	2	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	exon	21003524	21003558	.	+	.	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
Phchi.S1	AUGUSTUS	stop_codon	21003559	21003561	.	+	0	transcript_id "Phchi.S1G327300.t1"; gene_id "Phchi.S1G327300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7794.t1 is derived from g4968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31203242	31203484	.	+	.	Phchi.S1G495300
Phchi.S1	AUGUSTUS	transcript	31203242	31203484	.	+	.	transcript_id "Phchi.S1G495300.t1"; gene_id "Phchi.S1G495300"
Phchi.S1	AUGUSTUS	start_codon	31203242	31203244	.	+	0	transcript_id "Phchi.S1G495300.t1"; gene_id "Phchi.S1G495300"
Phchi.S1	AUGUSTUS	CDS	31203242	31203484	0.81	+	0	transcript_id "Phchi.S1G495300.t1"; gene_id "Phchi.S1G495300"
Phchi.S1	AUGUSTUS	exon	31203242	31203484	.	+	.	transcript_id "Phchi.S1G495300.t1"; gene_id "Phchi.S1G495300"
Phchi.S1	AUGUSTUS	stop_codon	31203485	31203487	.	+	0	transcript_id "Phchi.S1G495300.t1"; gene_id "Phchi.S1G495300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10974.t1 is derived from g15024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3427693	3429173	.	+	.	Phchi.S4G055600
Phchi.S4	AUGUSTUS	transcript	3427693	3429173	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	start_codon	3427693	3427695	.	+	0	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3427693	3427966	0.59	+	0	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3427693	3427966	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	intron	3427967	3428109	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3428110	3428149	1	+	2	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3428110	3428149	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	intron	3428150	3428290	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3428291	3428361	1	+	1	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3428291	3428361	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	intron	3428362	3428482	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3428483	3428577	1	+	2	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3428483	3428577	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	intron	3428578	3428667	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3428668	3428735	1	+	0	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3428668	3428735	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	intron	3428736	3428847	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3428848	3428955	1	+	1	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3428848	3428955	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	intron	3428956	3429031	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	CDS	3429032	3429173	1	+	1	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	exon	3429032	3429173	.	+	.	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
Phchi.S4	AUGUSTUS	stop_codon	3429174	3429176	.	+	0	transcript_id "Phchi.S4G055600.t1"; gene_id "Phchi.S4G055600"
# This transcript jg3307.t2 is derived from g476.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3308.t1 is derived from g477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2773735	2774787	.	+	.	Phchi.S1G046700
Phchi.S1	AUGUSTUS	transcript	2773735	2774787	.	+	.	transcript_id "Phchi.S1G046700.t1"; gene_id "Phchi.S1G046700"
Phchi.S1	AUGUSTUS	start_codon	2773735	2773737	.	+	0	transcript_id "Phchi.S1G046700.t1"; gene_id "Phchi.S1G046700"
Phchi.S1	AUGUSTUS	CDS	2773735	2774787	0.44	+	0	transcript_id "Phchi.S1G046700.t1"; gene_id "Phchi.S1G046700"
Phchi.S1	AUGUSTUS	exon	2773735	2774787	.	+	.	transcript_id "Phchi.S1G046700.t1"; gene_id "Phchi.S1G046700"
Phchi.S1	AUGUSTUS	stop_codon	2774788	2774790	.	+	0	transcript_id "Phchi.S1G046700.t1"; gene_id "Phchi.S1G046700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9509.t1 is derived from g6685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42118549	42119117	.	-	.	Phchi.S1G666800
Phchi.S1	AUGUSTUS	transcript	42118549	42119117	.	-	.	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	stop_codon	42118546	42118548	.	-	0	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	CDS	42118549	42118713	0.94	-	0	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	exon	42118549	42118713	.	-	.	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	intron	42118714	42118844	.	-	.	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	CDS	42118845	42118935	0.96	-	1	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	exon	42118845	42118935	.	-	.	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	intron	42118936	42119025	.	-	.	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	CDS	42119026	42119117	0.43	-	0	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	exon	42119026	42119117	.	-	.	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
Phchi.S1	AUGUSTUS	start_codon	42119115	42119117	.	-	0	transcript_id "Phchi.S1G666800.t1"; gene_id "Phchi.S1G666800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7502.t1 is derived from g4676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29685922	29687074	.	+	.	Phchi.S1G466100
Phchi.S1	AUGUSTUS	transcript	29685922	29687074	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	start_codon	29685922	29685924	.	+	0	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	CDS	29685922	29685964	0.55	+	0	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	exon	29685922	29685964	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	intron	29685965	29686620	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	CDS	29686621	29686697	0.55	+	2	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	exon	29686621	29686697	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	intron	29686698	29686832	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	CDS	29686833	29686929	0.99	+	0	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	exon	29686833	29686929	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	intron	29686930	29687021	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	CDS	29687022	29687074	1	+	2	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	exon	29687022	29687074	.	+	.	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
Phchi.S1	AUGUSTUS	stop_codon	29687075	29687077	.	+	0	transcript_id "Phchi.S1G466100.t1"; gene_id "Phchi.S1G466100"
# This transcript jg6012.t2 is derived from g3183.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6012.t3 is derived from g3183.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6013.t1 is derived from g3184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20429076	20429576	.	+	.	Phchi.S1G317200
Phchi.S1	AUGUSTUS	transcript	20429076	20429576	.	+	.	transcript_id "Phchi.S1G317200.t1"; gene_id "Phchi.S1G317200"
Phchi.S1	AUGUSTUS	start_codon	20429076	20429078	.	+	0	transcript_id "Phchi.S1G317200.t1"; gene_id "Phchi.S1G317200"
Phchi.S1	AUGUSTUS	CDS	20429076	20429576	0.76	+	0	transcript_id "Phchi.S1G317200.t1"; gene_id "Phchi.S1G317200"
Phchi.S1	AUGUSTUS	exon	20429076	20429576	.	+	.	transcript_id "Phchi.S1G317200.t1"; gene_id "Phchi.S1G317200"
Phchi.S1	AUGUSTUS	stop_codon	20429577	20429579	.	+	0	transcript_id "Phchi.S1G317200.t1"; gene_id "Phchi.S1G317200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14936.t1 is derived from g13404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15610890	15615656	.	+	.	Phchi.S3G225500
Phchi.S3	AUGUSTUS	transcript	15610890	15615656	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	start_codon	15610890	15610892	.	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15610890	15611072	0.94	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15610890	15611072	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611073	15611183	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15611184	15611383	0.94	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15611184	15611383	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611384	15611465	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15611466	15611669	1	+	1	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15611466	15611669	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611670	15611777	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15611778	15611914	0.99	+	1	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15611778	15611914	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611915	15612002	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612003	15612106	1	+	2	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612003	15612106	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612107	15612243	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612244	15612347	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612244	15612347	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612348	15612446	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612447	15612609	1	+	1	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612447	15612609	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612610	15612712	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612713	15612829	0.99	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612713	15612829	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612830	15612923	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612924	15613031	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612924	15613031	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613032	15613217	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613218	15613280	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613218	15613280	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613281	15613378	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613379	15613501	0.99	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613379	15613501	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613502	15613614	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613615	15613783	0.99	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613615	15613783	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613784	15613886	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613887	15614002	0.98	+	2	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613887	15614002	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614003	15614080	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614081	15614218	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614081	15614218	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614219	15614303	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614304	15614431	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614304	15614431	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614432	15614518	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614519	15614596	1	+	1	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614519	15614596	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614597	15614677	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614678	15614741	1	+	1	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614678	15614741	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614742	15614817	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614818	15614923	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614818	15614923	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614924	15615017	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615018	15615091	1	+	2	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615018	15615091	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15615092	15615164	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615165	15615259	1	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615165	15615259	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15615260	15615350	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615351	15615382	1	+	1	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615351	15615382	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15615383	15615468	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615469	15615656	0.97	+	2	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615469	15615656	.	+	.	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	stop_codon	15615657	15615659	.	+	0	transcript_id "Phchi.S3G225500.t1"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	transcript	15610890	15615656	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	start_codon	15610890	15610892	.	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15610890	15611072	0.98	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15610890	15611072	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611073	15611183	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15611184	15611383	0.98	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15611184	15611383	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611384	15611465	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15611466	15611669	1	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15611466	15611669	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611670	15611777	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15611778	15611914	0.98	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15611778	15611914	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15611915	15612002	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612003	15612106	1	+	2	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612003	15612106	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612107	15612243	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612244	15612347	1	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612244	15612347	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612348	15612446	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612447	15612609	1	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612447	15612609	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612610	15612712	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612713	15612829	0.92	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612713	15612829	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15612830	15612923	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15612924	15613117	0.83	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15612924	15613117	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613118	15613217	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613218	15613280	0.83	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613218	15613280	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613281	15613378	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613379	15613457	0.83	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613379	15613457	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613458	15613614	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613615	15613783	0.99	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613615	15613783	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15613784	15613886	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15613887	15614002	1	+	2	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15613887	15614002	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614003	15614080	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614081	15614218	1	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614081	15614218	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614219	15614303	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614304	15614431	1	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614304	15614431	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614432	15614518	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614519	15614596	1	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614519	15614596	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614597	15614677	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614678	15614741	1	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614678	15614741	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614742	15614817	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15614818	15614923	1	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15614818	15614923	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15614924	15615017	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615018	15615091	1	+	2	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615018	15615091	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15615092	15615164	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615165	15615259	1	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615165	15615259	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15615260	15615350	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615351	15615382	1	+	1	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615351	15615382	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	intron	15615383	15615468	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	CDS	15615469	15615656	0.97	+	2	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	exon	15615469	15615656	.	+	.	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
Phchi.S3	AUGUSTUS	stop_codon	15615657	15615659	.	+	0	transcript_id "Phchi.S3G225500.t2"; gene_id "Phchi.S3G225500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1875.t1 is derived from g8795.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3645435	3647192	.	+	.	Phchi.S5G048400
Phchi.S5	AUGUSTUS	transcript	3645435	3647192	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	start_codon	3645435	3645437	.	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3645435	3645524	0.74	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3645435	3645524	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3645525	3645669	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3645670	3645824	1	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3645670	3645824	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3645825	3646122	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646123	3646204	1	+	1	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646123	3646204	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646205	3646304	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646305	3646337	1	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646305	3646337	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646338	3646467	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646468	3646589	1	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646468	3646589	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646590	3646675	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646676	3646837	0.97	+	1	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646676	3646837	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646838	3646941	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646942	3646969	0.7	+	1	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646942	3646969	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646970	3647126	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3647127	3647192	0.79	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3647127	3647192	.	+	.	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	stop_codon	3647193	3647195	.	+	0	transcript_id "Phchi.S5G048400.t1"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	transcript	3645435	3647192	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	start_codon	3645435	3645437	.	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3645435	3645524	0.67	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3645435	3645524	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3645525	3645624	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3645625	3645824	0.98	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3645625	3645824	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3645825	3646122	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646123	3646204	1	+	1	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646123	3646204	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646205	3646304	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646305	3646337	1	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646305	3646337	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646338	3646467	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646468	3646589	1	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646468	3646589	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646590	3646675	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646676	3646837	0.95	+	1	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646676	3646837	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646838	3646941	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3646942	3646969	0.67	+	1	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3646942	3646969	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	intron	3646970	3647126	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	CDS	3647127	3647192	0.77	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	exon	3647127	3647192	.	+	.	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
Phchi.S5	AUGUSTUS	stop_codon	3647193	3647195	.	+	0	transcript_id "Phchi.S5G048400.t2"; gene_id "Phchi.S5G048400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5157.t1 is derived from g2327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15187143	15188035	.	-	.	Phchi.S1G231600
Phchi.S1	AUGUSTUS	transcript	15187143	15188035	.	-	.	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	stop_codon	15187140	15187142	.	-	0	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	CDS	15187143	15187508	0.56	-	0	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	exon	15187143	15187508	.	-	.	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	intron	15187509	15187840	.	-	.	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	CDS	15187841	15188035	0.71	-	0	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	exon	15187841	15188035	.	-	.	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
Phchi.S1	AUGUSTUS	start_codon	15188033	15188035	.	-	0	transcript_id "Phchi.S1G231600.t1"; gene_id "Phchi.S1G231600"
# This transcript jg9399.t2 is derived from g6575.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9400.t1 is derived from g6576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41343244	41343450	.	+	.	Phchi.S1G655900
Phchi.S1	AUGUSTUS	transcript	41343244	41343450	.	+	.	transcript_id "Phchi.S1G655900.t1"; gene_id "Phchi.S1G655900"
Phchi.S1	AUGUSTUS	start_codon	41343244	41343246	.	+	0	transcript_id "Phchi.S1G655900.t1"; gene_id "Phchi.S1G655900"
Phchi.S1	AUGUSTUS	CDS	41343244	41343450	1	+	0	transcript_id "Phchi.S1G655900.t1"; gene_id "Phchi.S1G655900"
Phchi.S1	AUGUSTUS	exon	41343244	41343450	.	+	.	transcript_id "Phchi.S1G655900.t1"; gene_id "Phchi.S1G655900"
Phchi.S1	AUGUSTUS	stop_codon	41343451	41343453	.	+	0	transcript_id "Phchi.S1G655900.t1"; gene_id "Phchi.S1G655900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15490.t1 is derived from g13959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19473629	19479184	.	+	.	Phchi.S3G280900
Phchi.S3	AUGUSTUS	transcript	19473629	19479184	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	start_codon	19473629	19473631	.	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19473629	19473797	0.53	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19473629	19473797	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19473798	19473991	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19473992	19474103	0.6	+	2	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19473992	19474103	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19474104	19474192	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19474193	19474254	0.46	+	1	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19474193	19474254	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19474255	19474523	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19474524	19474665	0.71	+	2	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19474524	19474665	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19474666	19474828	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19474829	19474917	0.99	+	1	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19474829	19474917	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19474918	19474997	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19474998	19475083	0.48	+	2	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19474998	19475083	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19475084	19475164	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19475165	19475814	0.68	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19475165	19475814	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19475815	19475902	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19475903	19476313	0.65	+	1	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19475903	19476313	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19476314	19476481	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19476482	19476566	0.36	+	1	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19476482	19476566	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19476567	19476875	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19476876	19476968	0.24	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19476876	19476968	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19476969	19477050	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19477051	19477122	0.2	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19477051	19477122	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19477123	19477356	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19477357	19477454	0.44	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19477357	19477454	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19477455	19477555	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19477556	19477604	0.76	+	1	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19477556	19477604	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19477605	19477688	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19477689	19477781	0.8	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19477689	19477781	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	intron	19477782	19477876	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	CDS	19477877	19479184	0.79	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	exon	19477877	19479184	.	+	.	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
Phchi.S3	AUGUSTUS	stop_codon	19479185	19479187	.	+	0	transcript_id "Phchi.S3G280900.t1"; gene_id "Phchi.S3G280900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3466.t1 is derived from g635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3892324	3894028	.	+	.	Phchi.S1G062500
Phchi.S1	AUGUSTUS	transcript	3892324	3894028	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	start_codon	3892324	3892326	.	+	0	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	CDS	3892324	3892576	0.4	+	0	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	exon	3892324	3892576	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	intron	3892577	3892793	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	CDS	3892794	3892822	0.52	+	2	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	exon	3892794	3892822	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	intron	3892823	3892993	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	CDS	3892994	3893366	0.65	+	0	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	exon	3892994	3893366	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	intron	3893367	3893462	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	CDS	3893463	3894028	0.97	+	2	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	exon	3893463	3894028	.	+	.	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
Phchi.S1	AUGUSTUS	stop_codon	3894029	3894031	.	+	0	transcript_id "Phchi.S1G062500.t1"; gene_id "Phchi.S1G062500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3235.t1 is derived from g404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2381843	2384888	.	-	.	Phchi.S1G039400
Phchi.S1	AUGUSTUS	transcript	2381843	2384888	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	stop_codon	2381840	2381842	.	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2381843	2382364	0.95	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2381843	2382364	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2382365	2382485	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2382486	2382539	1	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2382486	2382539	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2382540	2382709	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2382710	2382764	1	-	1	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2382710	2382764	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2382765	2382887	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2382888	2383045	1	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2382888	2383045	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2383046	2383183	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2383184	2383363	1	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2383184	2383363	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2383364	2383470	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2383471	2383571	0.99	-	2	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2383471	2383571	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2383572	2383690	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2383691	2383742	1	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2383691	2383742	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2383743	2383833	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2383834	2383969	1	-	1	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2383834	2383969	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2383970	2384121	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2384122	2384240	0.94	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2384122	2384240	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2384241	2384351	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2384352	2384443	1	-	2	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2384352	2384443	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	intron	2384444	2384656	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	CDS	2384657	2384888	1	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	exon	2384657	2384888	.	-	.	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
Phchi.S1	AUGUSTUS	start_codon	2384886	2384888	.	-	0	transcript_id "Phchi.S1G039400.t1"; gene_id "Phchi.S1G039400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6106.t1 is derived from g3277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20970843	20971392	.	+	.	Phchi.S1G326500
Phchi.S1	AUGUSTUS	transcript	20970843	20971392	.	+	.	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	start_codon	20970843	20970845	.	+	0	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	CDS	20970843	20970921	0.99	+	0	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	exon	20970843	20970921	.	+	.	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	intron	20970922	20971007	.	+	.	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	CDS	20971008	20971213	1	+	2	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	exon	20971008	20971213	.	+	.	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	intron	20971214	20971290	.	+	.	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	CDS	20971291	20971392	1	+	0	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	exon	20971291	20971392	.	+	.	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
Phchi.S1	AUGUSTUS	stop_codon	20971393	20971395	.	+	0	transcript_id "Phchi.S1G326500.t1"; gene_id "Phchi.S1G326500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13518.t1 is derived from g11985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7274559	7275537	.	+	.	Phchi.S3G083700
Phchi.S3	AUGUSTUS	transcript	7274559	7275537	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	start_codon	7274559	7274561	.	+	0	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	CDS	7274559	7274657	1	+	0	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	exon	7274559	7274657	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	intron	7274658	7274741	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	CDS	7274742	7275167	1	+	0	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	exon	7274742	7275167	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	intron	7275168	7275264	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	CDS	7275265	7275340	1	+	0	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	exon	7275265	7275340	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	intron	7275341	7275427	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	CDS	7275428	7275537	0.97	+	2	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	exon	7275428	7275537	.	+	.	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
Phchi.S3	AUGUSTUS	stop_codon	7275538	7275540	.	+	0	transcript_id "Phchi.S3G083700.t1"; gene_id "Phchi.S3G083700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12904.t1 is derived from g11369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3083721	3084422	.	+	.	Phchi.S3G022300
Phchi.S3	AUGUSTUS	transcript	3083721	3084422	.	+	.	transcript_id "Phchi.S3G022300.t1"; gene_id "Phchi.S3G022300"
Phchi.S3	AUGUSTUS	start_codon	3083721	3083723	.	+	0	transcript_id "Phchi.S3G022300.t1"; gene_id "Phchi.S3G022300"
Phchi.S3	AUGUSTUS	CDS	3083721	3084422	0.91	+	0	transcript_id "Phchi.S3G022300.t1"; gene_id "Phchi.S3G022300"
Phchi.S3	AUGUSTUS	exon	3083721	3084422	.	+	.	transcript_id "Phchi.S3G022300.t1"; gene_id "Phchi.S3G022300"
Phchi.S3	AUGUSTUS	stop_codon	3084423	3084425	.	+	0	transcript_id "Phchi.S3G022300.t1"; gene_id "Phchi.S3G022300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14257.t1 is derived from g12724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11782785	11785390	.	-	.	Phchi.S3G157600
Phchi.S3	AUGUSTUS	transcript	11782785	11785390	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	stop_codon	11782782	11782784	.	-	0	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11782785	11782976	1	-	0	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11782785	11782976	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	intron	11782977	11783053	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11783054	11783144	1	-	1	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11783054	11783144	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	intron	11783145	11783225	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11783226	11783476	1	-	0	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11783226	11783476	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	intron	11783477	11783579	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11783580	11783741	0.99	-	0	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11783580	11783741	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	intron	11783742	11783848	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11783849	11784729	0.99	-	2	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11783849	11784729	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	intron	11784730	11784828	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11784829	11784837	1	-	2	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11784829	11784837	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	intron	11784838	11784984	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	CDS	11784985	11785390	0.94	-	0	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	exon	11784985	11785390	.	-	.	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
Phchi.S3	AUGUSTUS	start_codon	11785388	11785390	.	-	0	transcript_id "Phchi.S3G157600.t1"; gene_id "Phchi.S3G157600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11912.t1 is derived from g15964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9273594	9274685	.	+	.	Phchi.S4G149400
Phchi.S4	AUGUSTUS	transcript	9273594	9274685	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	start_codon	9273594	9273596	.	+	0	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	CDS	9273594	9273634	0.83	+	0	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	exon	9273594	9273634	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	intron	9273635	9273729	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	CDS	9273730	9273845	0.85	+	1	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	exon	9273730	9273845	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	intron	9273846	9273958	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	CDS	9273959	9274044	1	+	2	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	exon	9273959	9274044	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	intron	9274045	9274143	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	CDS	9274144	9274245	1	+	0	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	exon	9274144	9274245	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	intron	9274246	9274523	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	CDS	9274524	9274582	1	+	0	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	exon	9274524	9274582	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	intron	9274583	9274675	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	CDS	9274676	9274685	1	+	1	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	exon	9274676	9274685	.	+	.	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
Phchi.S4	AUGUSTUS	stop_codon	9274686	9274688	.	+	0	transcript_id "Phchi.S4G149400.t1"; gene_id "Phchi.S4G149400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1382.t1 is derived from g15974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C41	AUGUSTUS	gene	35620	36511	.	-	.	Phchi.C41G000200
Phchi.C41	AUGUSTUS	transcript	35620	36511	.	-	.	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	stop_codon	35617	35619	.	-	0	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	CDS	35620	35739	0.96	-	0	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	exon	35620	35739	.	-	.	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	intron	35740	35895	.	-	.	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	CDS	35896	35980	0.44	-	1	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	exon	35896	35980	.	-	.	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	intron	35981	36320	.	-	.	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	CDS	36321	36511	0.93	-	0	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	exon	36321	36511	.	-	.	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
Phchi.C41	AUGUSTUS	start_codon	36509	36511	.	-	0	transcript_id "Phchi.C41G000200.t1"; gene_id "Phchi.C41G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9884.t1 is derived from g7060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44251173	44252858	.	+	.	Phchi.S1G704300
Phchi.S1	AUGUSTUS	transcript	44251173	44252858	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	start_codon	44251173	44251175	.	+	0	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	CDS	44251173	44251189	1	+	0	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	exon	44251173	44251189	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	intron	44251190	44251498	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	CDS	44251499	44251554	1	+	1	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	exon	44251499	44251554	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	intron	44251555	44251670	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	CDS	44251671	44251877	1	+	2	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	exon	44251671	44251877	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	intron	44251878	44251970	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	CDS	44251971	44252309	0.88	+	2	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	exon	44251971	44252309	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	intron	44252310	44252552	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	CDS	44252553	44252667	0.33	+	2	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	exon	44252553	44252667	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	intron	44252668	44252836	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	CDS	44252837	44252858	0.28	+	1	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	exon	44252837	44252858	.	+	.	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
Phchi.S1	AUGUSTUS	stop_codon	44252859	44252861	.	+	0	transcript_id "Phchi.S1G704300.t1"; gene_id "Phchi.S1G704300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8442.t1 is derived from g5617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35950779	35952251	.	-	.	Phchi.S1G560100
Phchi.S1	AUGUSTUS	transcript	35950779	35952251	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	stop_codon	35950776	35950778	.	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35950779	35950883	0.96	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35950779	35950883	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	intron	35950884	35950966	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35950967	35951032	1	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35950967	35951032	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	intron	35951033	35951117	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35951118	35951208	1	-	1	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35951118	35951208	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	intron	35951209	35951304	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35951305	35951474	1	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35951305	35951474	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	intron	35951475	35951561	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35951562	35951675	1	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35951562	35951675	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	intron	35951676	35951877	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35951878	35951991	1	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35951878	35951991	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	intron	35951992	35952200	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	CDS	35952201	35952251	1	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	exon	35952201	35952251	.	-	.	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
Phchi.S1	AUGUSTUS	start_codon	35952249	35952251	.	-	0	transcript_id "Phchi.S1G560100.t1"; gene_id "Phchi.S1G560100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7979.t1 is derived from g5154.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32205859	32206501	.	+	.	Phchi.S1G513800
Phchi.S1	AUGUSTUS	transcript	32205859	32206501	.	+	.	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	start_codon	32205859	32205861	.	+	0	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	CDS	32205859	32205999	0.92	+	0	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	exon	32205859	32205999	.	+	.	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	intron	32206000	32206303	.	+	.	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	CDS	32206304	32206501	1	+	0	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	exon	32206304	32206501	.	+	.	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	stop_codon	32206502	32206504	.	+	0	transcript_id "Phchi.S1G513800.t1"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	transcript	32205859	32206501	.	+	.	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	start_codon	32205859	32205861	.	+	0	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	CDS	32205859	32205993	0.88	+	0	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	exon	32205859	32205993	.	+	.	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	intron	32205994	32206303	.	+	.	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	CDS	32206304	32206501	1	+	0	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	exon	32206304	32206501	.	+	.	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
Phchi.S1	AUGUSTUS	stop_codon	32206502	32206504	.	+	0	transcript_id "Phchi.S1G513800.t2"; gene_id "Phchi.S1G513800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14092.t1 is derived from g12559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10819157	10820326	.	-	.	Phchi.S3G141100
Phchi.S3	AUGUSTUS	transcript	10819157	10820326	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	stop_codon	10819154	10819156	.	-	0	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	CDS	10819157	10819199	0.96	-	1	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	exon	10819157	10819199	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	intron	10819200	10819333	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	CDS	10819334	10819482	0.73	-	0	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	exon	10819334	10819482	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	intron	10819483	10819794	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	CDS	10819795	10819968	0.87	-	0	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	exon	10819795	10819968	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	intron	10819969	10820056	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	CDS	10820057	10820326	0.56	-	0	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	exon	10820057	10820326	.	-	.	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
Phchi.S3	AUGUSTUS	start_codon	10820324	10820326	.	-	0	transcript_id "Phchi.S3G141100.t1"; gene_id "Phchi.S3G141100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7918.t1 is derived from g5092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31903872	31909062	.	+	.	Phchi.S1G507700
Phchi.S1	AUGUSTUS	transcript	31903872	31909062	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	start_codon	31903872	31903874	.	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31903872	31903946	0.54	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31903872	31903946	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31903947	31904250	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31904251	31904478	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31904251	31904478	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31904479	31904572	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31904573	31904659	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31904573	31904659	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31904660	31904756	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31904757	31904846	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31904757	31904846	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31904847	31904961	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31904962	31905088	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31904962	31905088	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31905089	31905282	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31905283	31905383	1	+	2	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31905283	31905383	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31905384	31905461	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31905462	31905630	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31905462	31905630	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31905631	31905707	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31905708	31905829	1	+	2	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31905708	31905829	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31905830	31905962	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31905963	31906091	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31905963	31906091	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31906092	31906227	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31906228	31906326	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31906228	31906326	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31906327	31906641	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31906642	31906699	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31906642	31906699	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31906700	31906857	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31906858	31906933	1	+	2	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31906858	31906933	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31906934	31907085	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31907086	31907224	1	+	1	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31907086	31907224	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31907225	31907350	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31907351	31907508	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31907351	31907508	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31907509	31907585	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31907586	31907658	1	+	1	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31907586	31907658	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31907659	31907745	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31907746	31907940	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31907746	31907940	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31907941	31908035	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31908036	31908129	1	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31908036	31908129	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	intron	31908130	31908229	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	CDS	31908230	31909062	1	+	2	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	exon	31908230	31909062	.	+	.	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
Phchi.S1	AUGUSTUS	stop_codon	31909063	31909065	.	+	0	transcript_id "Phchi.S1G507700.t1"; gene_id "Phchi.S1G507700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4371.t1 is derived from g1540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10104819	10108067	.	-	.	Phchi.S1G153000
Phchi.S1	AUGUSTUS	transcript	10104819	10108067	.	-	.	transcript_id "Phchi.S1G153000.t1"; gene_id "Phchi.S1G153000"
Phchi.S1	AUGUSTUS	stop_codon	10104816	10104818	.	-	0	transcript_id "Phchi.S1G153000.t1"; gene_id "Phchi.S1G153000"
Phchi.S1	AUGUSTUS	CDS	10104819	10108067	0.63	-	0	transcript_id "Phchi.S1G153000.t1"; gene_id "Phchi.S1G153000"
Phchi.S1	AUGUSTUS	exon	10104819	10108067	.	-	.	transcript_id "Phchi.S1G153000.t1"; gene_id "Phchi.S1G153000"
Phchi.S1	AUGUSTUS	start_codon	10108065	10108067	.	-	0	transcript_id "Phchi.S1G153000.t1"; gene_id "Phchi.S1G153000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3564.t1 is derived from g733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4499833	4501350	.	+	.	Phchi.S1G072300
Phchi.S1	AUGUSTUS	transcript	4499833	4501350	.	+	.	transcript_id "Phchi.S1G072300.t1"; gene_id "Phchi.S1G072300"
Phchi.S1	AUGUSTUS	start_codon	4499833	4499835	.	+	0	transcript_id "Phchi.S1G072300.t1"; gene_id "Phchi.S1G072300"
Phchi.S1	AUGUSTUS	CDS	4499833	4501350	0.66	+	0	transcript_id "Phchi.S1G072300.t1"; gene_id "Phchi.S1G072300"
Phchi.S1	AUGUSTUS	exon	4499833	4501350	.	+	.	transcript_id "Phchi.S1G072300.t1"; gene_id "Phchi.S1G072300"
Phchi.S1	AUGUSTUS	stop_codon	4501351	4501353	.	+	0	transcript_id "Phchi.S1G072300.t1"; gene_id "Phchi.S1G072300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3720.t1 is derived from g889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5369690	5370547	.	+	.	Phchi.S1G087900
Phchi.S1	AUGUSTUS	transcript	5369690	5370547	.	+	.	transcript_id "Phchi.S1G087900.t1"; gene_id "Phchi.S1G087900"
Phchi.S1	AUGUSTUS	start_codon	5369690	5369692	.	+	0	transcript_id "Phchi.S1G087900.t1"; gene_id "Phchi.S1G087900"
Phchi.S1	AUGUSTUS	CDS	5369690	5370547	0.85	+	0	transcript_id "Phchi.S1G087900.t1"; gene_id "Phchi.S1G087900"
Phchi.S1	AUGUSTUS	exon	5369690	5370547	.	+	.	transcript_id "Phchi.S1G087900.t1"; gene_id "Phchi.S1G087900"
Phchi.S1	AUGUSTUS	stop_codon	5370548	5370550	.	+	0	transcript_id "Phchi.S1G087900.t1"; gene_id "Phchi.S1G087900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2563.t1 is derived from g9483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7407351	7407822	.	+	.	Phchi.S5G117200
Phchi.S5	AUGUSTUS	transcript	7407351	7407822	.	+	.	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	start_codon	7407351	7407353	.	+	0	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	CDS	7407351	7407638	0.69	+	0	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	exon	7407351	7407638	.	+	.	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	intron	7407639	7407750	.	+	.	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	CDS	7407751	7407822	0.7	+	0	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	exon	7407751	7407822	.	+	.	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
Phchi.S5	AUGUSTUS	stop_codon	7407823	7407825	.	+	0	transcript_id "Phchi.S5G117200.t1"; gene_id "Phchi.S5G117200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7548.t1 is derived from g4722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29988495	29990556	.	+	.	Phchi.S1G470700
Phchi.S1	AUGUSTUS	transcript	29988495	29990556	.	+	.	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	start_codon	29988495	29988497	.	+	0	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	CDS	29988495	29988792	0.99	+	0	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	exon	29988495	29988792	.	+	.	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	intron	29988793	29989079	.	+	.	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	CDS	29989080	29989321	0.97	+	2	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	exon	29989080	29989321	.	+	.	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	intron	29989322	29989422	.	+	.	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	CDS	29989423	29990556	1	+	0	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	exon	29989423	29990556	.	+	.	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
Phchi.S1	AUGUSTUS	stop_codon	29990557	29990559	.	+	0	transcript_id "Phchi.S1G470700.t1"; gene_id "Phchi.S1G470700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15429.t1 is derived from g13897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19044914	19051691	.	+	.	Phchi.S3G274800
Phchi.S3	AUGUSTUS	transcript	19044914	19051691	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	start_codon	19044914	19044916	.	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19044914	19044926	0.84	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19044914	19044926	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19044927	19045028	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19045029	19045081	1	+	2	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19045029	19045081	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19045082	19045163	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19045164	19045228	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19045164	19045228	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19045229	19045365	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19045366	19045471	1	+	1	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19045366	19045471	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19045472	19045603	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19045604	19045714	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19045604	19045714	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19045715	19045839	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19045840	19045899	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19045840	19045899	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19045900	19046062	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19046063	19046107	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19046063	19046107	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19046108	19046192	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19046193	19046243	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19046193	19046243	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19046244	19046454	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19046455	19046553	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19046455	19046553	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19046554	19046681	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19046682	19046741	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19046682	19046741	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19046742	19046845	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19046846	19046938	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19046846	19046938	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19046939	19047148	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19047149	19047250	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19047149	19047250	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19047251	19047332	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19047333	19047443	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19047333	19047443	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19047444	19047576	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19047577	19047595	0.45	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19047577	19047595	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19047596	19047675	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19047676	19047692	1	+	2	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19047676	19047692	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19047693	19047879	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19047880	19047996	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19047880	19047996	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19047997	19048109	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19048110	19048190	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19048110	19048190	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19048191	19048362	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19048363	19048467	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19048363	19048467	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19048468	19048585	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19048586	19048666	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19048586	19048666	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19048667	19048766	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19048767	19048898	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19048767	19048898	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19048899	19048992	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19048993	19049037	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19048993	19049037	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19049038	19049135	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19049136	19049213	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19049136	19049213	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19049214	19049321	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19049322	19049461	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19049322	19049461	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19049462	19049552	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19049553	19049658	1	+	1	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19049553	19049658	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19049659	19049733	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19049734	19049858	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19049734	19049858	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19049859	19049946	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19049947	19050082	1	+	1	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19049947	19050082	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19050083	19050178	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19050179	19050309	0.99	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19050179	19050309	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19050310	19050421	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19050422	19050547	1	+	1	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19050422	19050547	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19050548	19050641	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19050642	19050697	1	+	1	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19050642	19050697	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19050698	19050832	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19050833	19050903	1	+	2	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19050833	19050903	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19050904	19051012	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19051013	19051097	1	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19051013	19051097	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19051098	19051187	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19051188	19051291	1	+	2	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19051188	19051291	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19051292	19051411	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19051412	19051540	0.98	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19051412	19051540	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	intron	19051541	19051643	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	CDS	19051644	19051691	0.87	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	exon	19051644	19051691	.	+	.	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
Phchi.S3	AUGUSTUS	stop_codon	19051692	19051694	.	+	0	transcript_id "Phchi.S3G274800.t1"; gene_id "Phchi.S3G274800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4826.t1 is derived from g1996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13021984	13024103	.	-	.	Phchi.S1G198500
Phchi.S1	AUGUSTUS	transcript	13021984	13024103	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	stop_codon	13021981	13021983	.	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13021984	13022055	1	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13021984	13022055	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13022056	13022143	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13022144	13022240	1	-	1	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13022144	13022240	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13022241	13022338	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13022339	13022439	1	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13022339	13022439	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13022440	13022567	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13022568	13022759	1	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13022568	13022759	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13022760	13022895	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13022896	13023053	1	-	2	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13022896	13023053	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13023054	13023172	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13023173	13023404	1	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13023173	13023404	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13023405	13023499	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13023500	13023635	1	-	1	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13023500	13023635	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13023636	13023741	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13023742	13023845	1	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13023742	13023845	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	intron	13023846	13023917	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	CDS	13023918	13024103	0.77	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	exon	13023918	13024103	.	-	.	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
Phchi.S1	AUGUSTUS	start_codon	13024101	13024103	.	-	0	transcript_id "Phchi.S1G198500.t1"; gene_id "Phchi.S1G198500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7245.t1 is derived from g4417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27814448	27816086	.	-	.	Phchi.S1G440400
Phchi.S1	AUGUSTUS	transcript	27814448	27816086	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	stop_codon	27814445	27814447	.	-	0	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	CDS	27814448	27814463	0.92	-	1	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	exon	27814448	27814463	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	intron	27814464	27814587	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	CDS	27814588	27814653	0.93	-	1	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	exon	27814588	27814653	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	intron	27814654	27814763	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	CDS	27814764	27814848	0.84	-	2	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	exon	27814764	27814848	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	intron	27814849	27815019	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	CDS	27815020	27815103	0.31	-	2	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	exon	27815020	27815103	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	intron	27815104	27815995	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	CDS	27815996	27816086	0.87	-	0	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	exon	27815996	27816086	.	-	.	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
Phchi.S1	AUGUSTUS	start_codon	27816084	27816086	.	-	0	transcript_id "Phchi.S1G440400.t1"; gene_id "Phchi.S1G440400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2552.t1 is derived from g9472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7306074	7307090	.	+	.	Phchi.S5G116100
Phchi.S5	AUGUSTUS	transcript	7306074	7307090	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	start_codon	7306074	7306076	.	+	0	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	CDS	7306074	7306213	0.61	+	0	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	exon	7306074	7306213	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	intron	7306214	7306689	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	CDS	7306690	7306744	0.79	+	1	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	exon	7306690	7306744	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	intron	7306745	7306835	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	CDS	7306836	7306946	0.7	+	0	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	exon	7306836	7306946	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	intron	7306947	7307069	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	CDS	7307070	7307090	0.4	+	0	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	exon	7307070	7307090	.	+	.	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
Phchi.S5	AUGUSTUS	stop_codon	7307091	7307093	.	+	0	transcript_id "Phchi.S5G116100.t1"; gene_id "Phchi.S5G116100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9413.t1 is derived from g6589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41372572	41373620	.	+	.	Phchi.S1G657200
Phchi.S1	AUGUSTUS	transcript	41372572	41373620	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	start_codon	41372572	41372574	.	+	0	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	CDS	41372572	41372877	0.69	+	0	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	exon	41372572	41372877	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	intron	41372878	41373005	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	CDS	41373006	41373056	1	+	0	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	exon	41373006	41373056	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	intron	41373057	41373132	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	CDS	41373133	41373266	1	+	0	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	exon	41373133	41373266	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	intron	41373267	41373356	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	CDS	41373357	41373448	0.58	+	1	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	exon	41373357	41373448	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	intron	41373449	41373564	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	CDS	41373565	41373620	0.59	+	2	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	exon	41373565	41373620	.	+	.	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
Phchi.S1	AUGUSTUS	stop_codon	41373621	41373623	.	+	0	transcript_id "Phchi.S1G657200.t1"; gene_id "Phchi.S1G657200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13472.t1 is derived from g11939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7067543	7068905	.	+	.	Phchi.S3G079100
Phchi.S3	AUGUSTUS	transcript	7067543	7068905	.	+	.	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	start_codon	7067543	7067545	.	+	0	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	CDS	7067543	7067858	1	+	0	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	exon	7067543	7067858	.	+	.	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	intron	7067859	7068024	.	+	.	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	CDS	7068025	7068905	1	+	2	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	exon	7068025	7068905	.	+	.	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
Phchi.S3	AUGUSTUS	stop_codon	7068906	7068908	.	+	0	transcript_id "Phchi.S3G079100.t1"; gene_id "Phchi.S3G079100"
# This transcript jg15346.t2 is derived from g13814.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15346.t3 is derived from g13814.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15347.t1 is derived from g13815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18490109	18493335	.	-	.	Phchi.S3G266600
Phchi.S3	AUGUSTUS	transcript	18490109	18493335	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	stop_codon	18490106	18490108	.	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18490109	18490348	1	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18490109	18490348	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18490349	18490506	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18490507	18490569	0.92	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18490507	18490569	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18490570	18490690	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18490691	18490722	0.92	-	2	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18490691	18490722	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18490723	18490896	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18490897	18491095	0.92	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18490897	18491095	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18491096	18491181	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18491182	18491319	0.99	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18491182	18491319	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18491320	18491427	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18491428	18491517	1	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18491428	18491517	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18491518	18491635	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18491636	18491713	1	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18491636	18491713	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18491714	18491822	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18491823	18492479	1	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18491823	18492479	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18492480	18492573	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18492574	18492692	1	-	2	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18492574	18492692	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	intron	18492693	18493097	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	CDS	18493098	18493335	1	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	exon	18493098	18493335	.	-	.	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
Phchi.S3	AUGUSTUS	start_codon	18493333	18493335	.	-	0	transcript_id "Phchi.S3G266600.t1"; gene_id "Phchi.S3G266600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2867.t1 is derived from g36.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	184549	185483	.	-	.	Phchi.S1G002600
Phchi.S1	AUGUSTUS	transcript	184549	185483	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	stop_codon	184546	184548	.	-	0	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	CDS	184549	184629	0.99	-	0	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	exon	184549	184629	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	intron	184630	184826	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	CDS	184827	184849	0.99	-	2	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	exon	184827	184849	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	intron	184850	184943	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	CDS	184944	184970	0.94	-	2	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	exon	184944	184970	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	intron	184971	185238	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	CDS	185239	185309	0.57	-	1	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	exon	185239	185309	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	intron	185310	185424	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	CDS	185425	185483	0.24	-	0	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	exon	185425	185483	.	-	.	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
Phchi.S1	AUGUSTUS	start_codon	185481	185483	.	-	0	transcript_id "Phchi.S1G002600.t1"; gene_id "Phchi.S1G002600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg563.t1 is derived from g10345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4061975	4062220	.	-	.	Phchi.S6G052200
Phchi.S6	AUGUSTUS	transcript	4061975	4062220	.	-	.	transcript_id "Phchi.S6G052200.t1"; gene_id "Phchi.S6G052200"
Phchi.S6	AUGUSTUS	stop_codon	4061972	4061974	.	-	0	transcript_id "Phchi.S6G052200.t1"; gene_id "Phchi.S6G052200"
Phchi.S6	AUGUSTUS	CDS	4061975	4062220	0.49	-	0	transcript_id "Phchi.S6G052200.t1"; gene_id "Phchi.S6G052200"
Phchi.S6	AUGUSTUS	exon	4061975	4062220	.	-	.	transcript_id "Phchi.S6G052200.t1"; gene_id "Phchi.S6G052200"
Phchi.S6	AUGUSTUS	start_codon	4062218	4062220	.	-	0	transcript_id "Phchi.S6G052200.t1"; gene_id "Phchi.S6G052200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15642.t1 is derived from g14111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20452272	20454613	.	+	.	Phchi.S3G296100
Phchi.S3	AUGUSTUS	transcript	20452272	20454613	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	start_codon	20452272	20452274	.	+	0	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20452272	20452428	1	+	0	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20452272	20452428	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20452429	20452502	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20452503	20452852	1	+	2	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20452503	20452852	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20452853	20452969	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20452970	20453157	1	+	0	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20452970	20453157	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20453158	20453270	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20453271	20453337	1	+	1	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20453271	20453337	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20453338	20453426	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20453427	20453587	1	+	0	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20453427	20453587	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20453588	20453736	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20453737	20453980	0.99	+	1	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20453737	20453980	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20453981	20454097	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20454098	20454285	1	+	0	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20454098	20454285	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	intron	20454286	20454366	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	CDS	20454367	20454613	1	+	1	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	exon	20454367	20454613	.	+	.	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
Phchi.S3	AUGUSTUS	stop_codon	20454614	20454616	.	+	0	transcript_id "Phchi.S3G296100.t1"; gene_id "Phchi.S3G296100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6540.t1 is derived from g3712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23554313	23556249	.	+	.	Phchi.S1G369900
Phchi.S1	AUGUSTUS	transcript	23554313	23556249	.	+	.	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	start_codon	23554313	23554315	.	+	0	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	CDS	23554313	23554584	0.45	+	0	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	exon	23554313	23554584	.	+	.	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	intron	23554585	23555306	.	+	.	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	CDS	23555307	23556249	0.99	+	1	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	exon	23555307	23556249	.	+	.	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
Phchi.S1	AUGUSTUS	stop_codon	23556250	23556252	.	+	0	transcript_id "Phchi.S1G369900.t1"; gene_id "Phchi.S1G369900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9211.t1 is derived from g6386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40421057	40422918	.	-	.	Phchi.S1G637000
Phchi.S1	AUGUSTUS	transcript	40421057	40422918	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	stop_codon	40421054	40421056	.	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40421057	40421308	0.81	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40421057	40421308	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	intron	40421309	40421398	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40421399	40421497	1	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40421399	40421497	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	intron	40421498	40421596	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40421597	40421707	1	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40421597	40421707	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	intron	40421708	40421804	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40421805	40421972	1	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40421805	40421972	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	intron	40421973	40422063	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40422064	40422224	1	-	2	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40422064	40422224	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	intron	40422225	40422325	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40422326	40422505	1	-	2	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40422326	40422505	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	intron	40422506	40422596	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	CDS	40422597	40422918	0.69	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	exon	40422597	40422918	.	-	.	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
Phchi.S1	AUGUSTUS	start_codon	40422916	40422918	.	-	0	transcript_id "Phchi.S1G637000.t1"; gene_id "Phchi.S1G637000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6798.t1 is derived from g3970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25117133	25117606	.	-	.	Phchi.S1G395700
Phchi.S1	AUGUSTUS	transcript	25117133	25117606	.	-	.	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	stop_codon	25117130	25117132	.	-	0	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	CDS	25117133	25117243	1	-	0	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	exon	25117133	25117243	.	-	.	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	intron	25117244	25117332	.	-	.	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	CDS	25117333	25117440	0.99	-	0	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	exon	25117333	25117440	.	-	.	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	intron	25117441	25117537	.	-	.	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	CDS	25117538	25117606	0.92	-	0	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	exon	25117538	25117606	.	-	.	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
Phchi.S1	AUGUSTUS	start_codon	25117604	25117606	.	-	0	transcript_id "Phchi.S1G395700.t1"; gene_id "Phchi.S1G395700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2649.t1 is derived from g9569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7992864	7996319	.	+	.	Phchi.S5G125800
Phchi.S5	AUGUSTUS	transcript	7992864	7996319	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	start_codon	7992864	7992866	.	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7992864	7992866	0.9	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7992864	7992866	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7992867	7993060	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7993061	7993162	0.9	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7993061	7993162	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7993163	7993275	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7993276	7993494	0.9	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7993276	7993494	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7993495	7993655	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7993656	7993766	0.97	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7993656	7993766	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7993767	7993885	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7993886	7994070	0.69	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7993886	7994070	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7994071	7994144	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7994145	7994768	0.99	+	1	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7994145	7994768	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7994769	7994881	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7994882	7995299	0.97	+	1	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7994882	7995299	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7995300	7995427	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7995428	7995667	1	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7995428	7995667	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7995668	7995763	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7995764	7995887	0.89	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7995764	7995887	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7995888	7995980	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7995981	7996129	0.7	+	2	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7995981	7996129	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	intron	7996130	7996250	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	CDS	7996251	7996319	0.7	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	exon	7996251	7996319	.	+	.	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
Phchi.S5	AUGUSTUS	stop_codon	7996320	7996322	.	+	0	transcript_id "Phchi.S5G125800.t1"; gene_id "Phchi.S5G125800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1825.t1 is derived from g8745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3363997	3366138	.	+	.	Phchi.S5G043400
Phchi.S5	AUGUSTUS	transcript	3363997	3366138	.	+	.	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	start_codon	3363997	3363999	.	+	0	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	CDS	3363997	3364190	0.65	+	0	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	exon	3363997	3364190	.	+	.	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	intron	3364191	3364313	.	+	.	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	CDS	3364314	3364864	0.66	+	1	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	exon	3364314	3364864	.	+	.	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	intron	3364865	3364960	.	+	.	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	CDS	3364961	3366138	0.65	+	2	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	exon	3364961	3366138	.	+	.	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
Phchi.S5	AUGUSTUS	stop_codon	3366139	3366141	.	+	0	transcript_id "Phchi.S5G043400.t1"; gene_id "Phchi.S5G043400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7546.t1 is derived from g4720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29982224	29984301	.	-	.	Phchi.S1G470500
Phchi.S1	AUGUSTUS	transcript	29982224	29984301	.	-	.	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	stop_codon	29982221	29982223	.	-	0	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	CDS	29982224	29982290	0.55	-	1	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	exon	29982224	29982290	.	-	.	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	intron	29982291	29982563	.	-	.	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	CDS	29982564	29983010	0.44	-	1	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	exon	29982564	29983010	.	-	.	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	intron	29983011	29983084	.	-	.	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	CDS	29983085	29984301	0.65	-	0	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	exon	29983085	29984301	.	-	.	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
Phchi.S1	AUGUSTUS	start_codon	29984299	29984301	.	-	0	transcript_id "Phchi.S1G470500.t1"; gene_id "Phchi.S1G470500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6173.t1 is derived from g3344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21293724	21296755	.	+	.	Phchi.S1G333200
Phchi.S1	AUGUSTUS	transcript	21293724	21296755	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	start_codon	21293724	21293726	.	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21293724	21293935	0.74	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21293724	21293935	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21293936	21294695	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21294696	21294870	1	+	1	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21294696	21294870	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21294871	21295035	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21295036	21295096	1	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21295036	21295096	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21295097	21295265	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21295266	21295398	1	+	2	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21295266	21295398	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21295399	21295481	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21295482	21295605	1	+	1	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21295482	21295605	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21295606	21295739	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21295740	21295796	1	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21295740	21295796	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21295797	21295980	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21295981	21296077	1	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21295981	21296077	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21296078	21296175	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21296176	21296389	1	+	2	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21296176	21296389	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21296390	21296475	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21296476	21296536	1	+	1	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21296476	21296536	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	intron	21296537	21296704	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	CDS	21296705	21296755	1	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	exon	21296705	21296755	.	+	.	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
Phchi.S1	AUGUSTUS	stop_codon	21296756	21296758	.	+	0	transcript_id "Phchi.S1G333200.t1"; gene_id "Phchi.S1G333200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5608.t1 is derived from g2778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17862360	17863702	.	-	.	Phchi.S1G276700
Phchi.S1	AUGUSTUS	transcript	17862360	17863702	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	stop_codon	17862357	17862359	.	-	0	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	CDS	17862360	17862494	0.73	-	0	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	exon	17862360	17862494	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	intron	17862495	17862570	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	CDS	17862571	17862699	0.98	-	0	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	exon	17862571	17862699	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	intron	17862700	17862806	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	CDS	17862807	17863106	0.81	-	0	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	exon	17862807	17863106	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	intron	17863107	17863197	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	CDS	17863198	17863429	1	-	1	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	exon	17863198	17863429	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	intron	17863430	17863532	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	CDS	17863533	17863702	0.45	-	0	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	exon	17863533	17863702	.	-	.	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
Phchi.S1	AUGUSTUS	start_codon	17863700	17863702	.	-	0	transcript_id "Phchi.S1G276700.t1"; gene_id "Phchi.S1G276700"
# This transcript jg5148.t2 is derived from g2318.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5149.t1 is derived from g2319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15162435	15166958	.	+	.	Phchi.S1G230800
Phchi.S1	AUGUSTUS	transcript	15162435	15166958	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	start_codon	15162435	15162437	.	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15162435	15163395	1	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15162435	15163395	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15163396	15163550	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15163551	15163783	1	+	2	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15163551	15163783	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15163784	15163925	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15163926	15164052	1	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15163926	15164052	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15164053	15164140	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15164141	15164209	0.99	+	2	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15164141	15164209	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15164210	15164310	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15164311	15164503	1	+	2	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15164311	15164503	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15164504	15164601	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15164602	15164722	0.99	+	1	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15164602	15164722	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15164723	15164826	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15164827	15164908	0.46	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15164827	15164908	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15164909	15165053	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15165054	15165103	0.64	+	2	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15165054	15165103	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15165104	15165503	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15165504	15165575	0.58	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15165504	15165575	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	intron	15165576	15165665	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	CDS	15165666	15166958	0.58	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	exon	15165666	15166958	.	+	.	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
Phchi.S1	AUGUSTUS	stop_codon	15166959	15166961	.	+	0	transcript_id "Phchi.S1G230800.t1"; gene_id "Phchi.S1G230800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3350.t1 is derived from g519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3064524	3066545	.	-	.	Phchi.S1G050900
Phchi.S1	AUGUSTUS	transcript	3064524	3066545	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	stop_codon	3064521	3064523	.	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	CDS	3064524	3064700	1	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	exon	3064524	3064700	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	intron	3064701	3064790	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	CDS	3064791	3065025	1	-	1	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	exon	3064791	3065025	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	intron	3065026	3065228	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	CDS	3065229	3065314	1	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	exon	3065229	3065314	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	intron	3065315	3065434	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	CDS	3065435	3065551	1	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	exon	3065435	3065551	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	intron	3065552	3065657	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	CDS	3065658	3065978	1	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	exon	3065658	3065978	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	intron	3065979	3066257	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	CDS	3066258	3066545	1	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	exon	3066258	3066545	.	-	.	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
Phchi.S1	AUGUSTUS	start_codon	3066543	3066545	.	-	0	transcript_id "Phchi.S1G050900.t1"; gene_id "Phchi.S1G050900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12434.t1 is derived from g8111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19797977	19800902	.	+	.	Phchi.S2G051400
Phchi.S2	AUGUSTUS	transcript	19797977	19800902	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	start_codon	19797977	19797979	.	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	CDS	19797977	19800010	0.57	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	exon	19797977	19800010	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	intron	19800011	19800111	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	CDS	19800112	19800261	1	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	exon	19800112	19800261	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	intron	19800262	19800356	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	CDS	19800357	19800452	0.59	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	exon	19800357	19800452	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	intron	19800453	19800534	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	CDS	19800535	19800600	1	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	exon	19800535	19800600	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	intron	19800601	19800701	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	CDS	19800702	19800902	0.99	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	exon	19800702	19800902	.	+	.	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
Phchi.S2	AUGUSTUS	stop_codon	19800903	19800905	.	+	0	transcript_id "Phchi.S2G051400.t1"; gene_id "Phchi.S2G051400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2301.t1 is derived from g9221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5946157	5947001	.	+	.	Phchi.S5G091000
Phchi.S5	AUGUSTUS	transcript	5946157	5947001	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	start_codon	5946157	5946159	.	+	0	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	CDS	5946157	5946325	0.33	+	0	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	exon	5946157	5946325	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	intron	5946326	5946609	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	CDS	5946610	5946638	0.43	+	2	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	exon	5946610	5946638	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	intron	5946639	5946718	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	CDS	5946719	5946796	1	+	0	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	exon	5946719	5946796	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	intron	5946797	5946878	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	CDS	5946879	5947001	1	+	0	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	exon	5946879	5947001	.	+	.	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
Phchi.S5	AUGUSTUS	stop_codon	5947002	5947004	.	+	0	transcript_id "Phchi.S5G091000.t1"; gene_id "Phchi.S5G091000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11774.t1 is derived from g15826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8114542	8116812	.	+	.	Phchi.S4G135600
Phchi.S4	AUGUSTUS	transcript	8114542	8116812	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	start_codon	8114542	8114544	.	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8114542	8114580	0.6	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8114542	8114580	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8114581	8114734	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8114735	8114850	1	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8114735	8114850	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8114851	8114981	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8114982	8115228	1	+	1	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8114982	8115228	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8115229	8115340	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8115341	8115397	1	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8115341	8115397	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8115398	8115496	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8115497	8115502	1	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8115497	8115502	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8115503	8115587	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8115588	8115647	1	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8115588	8115647	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8115648	8115737	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8115738	8115818	1	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8115738	8115818	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8115819	8115916	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8115917	8116003	1	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8115917	8116003	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8116004	8116083	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8116084	8116325	0.72	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8116084	8116325	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8116326	8116412	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8116413	8116520	0.74	+	1	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8116413	8116520	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	intron	8116521	8116757	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	CDS	8116758	8116812	0.9	+	1	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	exon	8116758	8116812	.	+	.	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
Phchi.S4	AUGUSTUS	stop_codon	8116813	8116815	.	+	0	transcript_id "Phchi.S4G135600.t1"; gene_id "Phchi.S4G135600"
# This transcript jg4109.t2 is derived from g1278.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4110.t1 is derived from g1279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7874908	7875378	.	-	.	Phchi.S1G126900
Phchi.S1	AUGUSTUS	transcript	7874908	7875378	.	-	.	transcript_id "Phchi.S1G126900.t1"; gene_id "Phchi.S1G126900"
Phchi.S1	AUGUSTUS	stop_codon	7874905	7874907	.	-	0	transcript_id "Phchi.S1G126900.t1"; gene_id "Phchi.S1G126900"
Phchi.S1	AUGUSTUS	CDS	7874908	7875378	0.87	-	0	transcript_id "Phchi.S1G126900.t1"; gene_id "Phchi.S1G126900"
Phchi.S1	AUGUSTUS	exon	7874908	7875378	.	-	.	transcript_id "Phchi.S1G126900.t1"; gene_id "Phchi.S1G126900"
Phchi.S1	AUGUSTUS	start_codon	7875376	7875378	.	-	0	transcript_id "Phchi.S1G126900.t1"; gene_id "Phchi.S1G126900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2405.t1 is derived from g9325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6499366	6500160	.	-	.	Phchi.S5G101400
Phchi.S5	AUGUSTUS	transcript	6499366	6500160	.	-	.	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	stop_codon	6499363	6499365	.	-	0	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	CDS	6499366	6499542	1	-	0	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	exon	6499366	6499542	.	-	.	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	intron	6499543	6499651	.	-	.	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	CDS	6499652	6499778	0.99	-	1	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	exon	6499652	6499778	.	-	.	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	intron	6499779	6499900	.	-	.	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	CDS	6499901	6500160	0.98	-	0	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	exon	6499901	6500160	.	-	.	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
Phchi.S5	AUGUSTUS	start_codon	6500158	6500160	.	-	0	transcript_id "Phchi.S5G101400.t1"; gene_id "Phchi.S5G101400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2147.t1 is derived from g9067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5066182	5067298	.	-	.	Phchi.S5G075600
Phchi.S5	AUGUSTUS	transcript	5066182	5067298	.	-	.	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	stop_codon	5066179	5066181	.	-	0	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	CDS	5066182	5066661	0.99	-	0	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	exon	5066182	5066661	.	-	.	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	intron	5066662	5067133	.	-	.	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	CDS	5067134	5067298	1	-	0	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	exon	5067134	5067298	.	-	.	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
Phchi.S5	AUGUSTUS	start_codon	5067296	5067298	.	-	0	transcript_id "Phchi.S5G075600.t1"; gene_id "Phchi.S5G075600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14082.t1 is derived from g12549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10720612	10723045	.	-	.	Phchi.S3G140100
Phchi.S3	AUGUSTUS	transcript	10720612	10723045	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	stop_codon	10720609	10720611	.	-	0	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10720612	10720720	0.93	-	1	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10720612	10720720	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10720721	10721098	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10721099	10721290	0.95	-	1	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10721099	10721290	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10721291	10721454	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10721455	10721483	0.97	-	0	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10721455	10721483	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10721484	10721569	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10721570	10722781	0.75	-	0	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10721570	10722781	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10722782	10722877	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10722878	10723045	0.92	-	0	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10722878	10723045	.	-	.	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	start_codon	10723043	10723045	.	-	0	transcript_id "Phchi.S3G140100.t1"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	transcript	10720647	10723045	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	stop_codon	10720644	10720646	.	-	0	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10720647	10720720	0.91	-	2	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10720647	10720720	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10720721	10720885	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10720886	10720952	0.82	-	0	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10720886	10720952	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10720953	10721187	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10721188	10721290	0.48	-	1	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10721188	10721290	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10721291	10721454	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10721455	10721483	0.72	-	0	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10721455	10721483	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10721484	10721569	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10721570	10722781	0.6	-	0	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10721570	10722781	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	intron	10722782	10722877	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	CDS	10722878	10723045	0.89	-	0	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	exon	10722878	10723045	.	-	.	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
Phchi.S3	AUGUSTUS	start_codon	10723043	10723045	.	-	0	transcript_id "Phchi.S3G140100.t2"; gene_id "Phchi.S3G140100"
# This transcript jg9779.t2 is derived from g6955.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9780.t1 is derived from g6956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43651483	43651686	.	-	.	Phchi.S1G693900
Phchi.S1	AUGUSTUS	transcript	43651483	43651686	.	-	.	transcript_id "Phchi.S1G693900.t1"; gene_id "Phchi.S1G693900"
Phchi.S1	AUGUSTUS	stop_codon	43651480	43651482	.	-	0	transcript_id "Phchi.S1G693900.t1"; gene_id "Phchi.S1G693900"
Phchi.S1	AUGUSTUS	CDS	43651483	43651686	0.64	-	0	transcript_id "Phchi.S1G693900.t1"; gene_id "Phchi.S1G693900"
Phchi.S1	AUGUSTUS	exon	43651483	43651686	.	-	.	transcript_id "Phchi.S1G693900.t1"; gene_id "Phchi.S1G693900"
Phchi.S1	AUGUSTUS	start_codon	43651684	43651686	.	-	0	transcript_id "Phchi.S1G693900.t1"; gene_id "Phchi.S1G693900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5805.t1 is derived from g2975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19030972	19036201	.	+	.	Phchi.S1G296400
Phchi.S1	AUGUSTUS	transcript	19030972	19036201	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	start_codon	19030972	19030974	.	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19030972	19031371	0.93	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19030972	19031371	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19031372	19031734	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19031735	19031970	1	+	2	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19031735	19031970	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19031971	19032048	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19032049	19032259	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19032049	19032259	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19032260	19032386	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19032387	19032565	1	+	2	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19032387	19032565	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19032566	19032709	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19032710	19032761	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19032710	19032761	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19032762	19032949	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19032950	19033077	1	+	2	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19032950	19033077	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19033078	19033206	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19033207	19033386	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19033207	19033386	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19033387	19033536	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19033537	19033604	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19033537	19033604	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19033605	19033694	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19033695	19033837	1	+	1	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19033695	19033837	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19033838	19034112	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19034113	19034174	1	+	2	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19034113	19034174	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19034175	19034384	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19034385	19034498	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19034385	19034498	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19034499	19034586	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19034587	19034727	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19034587	19034727	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19034728	19034850	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19034851	19035003	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19034851	19035003	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19035004	19035123	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19035124	19035177	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19035124	19035177	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19035178	19035282	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19035283	19035393	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19035283	19035393	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19035394	19035530	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19035531	19035704	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19035531	19035704	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19035705	19035783	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19035784	19035864	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19035784	19035864	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19035865	19035945	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19035946	19036044	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19035946	19036044	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	intron	19036045	19036135	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	CDS	19036136	19036201	1	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	exon	19036136	19036201	.	+	.	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
Phchi.S1	AUGUSTUS	stop_codon	19036202	19036204	.	+	0	transcript_id "Phchi.S1G296400.t1"; gene_id "Phchi.S1G296400"
# This transcript jg15943.t2 is derived from g5.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15943.t3 is derived from g5.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15944.t1 is derived from g9801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C14	AUGUSTUS	gene	89092	89796	.	+	.	Phchi.C14G000100
Phchi.C14	AUGUSTUS	transcript	89092	89796	.	+	.	transcript_id "Phchi.C14G000100.t1"; gene_id "Phchi.C14G000100"
Phchi.C14	AUGUSTUS	start_codon	89092	89094	.	+	0	transcript_id "Phchi.C14G000100.t1"; gene_id "Phchi.C14G000100"
Phchi.C14	AUGUSTUS	CDS	89092	89796	0.3	+	0	transcript_id "Phchi.C14G000100.t1"; gene_id "Phchi.C14G000100"
Phchi.C14	AUGUSTUS	exon	89092	89796	.	+	.	transcript_id "Phchi.C14G000100.t1"; gene_id "Phchi.C14G000100"
Phchi.C14	AUGUSTUS	stop_codon	89797	89799	.	+	0	transcript_id "Phchi.C14G000100.t1"; gene_id "Phchi.C14G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12843.t1 is derived from g11308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2661325	2665136	.	+	.	Phchi.S3G016200
Phchi.S3	AUGUSTUS	transcript	2661325	2665136	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	start_codon	2661325	2661327	.	+	0	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	CDS	2661325	2663413	1	+	0	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	exon	2661325	2663413	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	intron	2663414	2663555	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	CDS	2663556	2663628	0.81	+	2	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	exon	2663556	2663628	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	intron	2663629	2663870	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	CDS	2663871	2664409	0.83	+	1	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	exon	2663871	2664409	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	intron	2664410	2664549	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	CDS	2664550	2665136	0.54	+	2	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	exon	2664550	2665136	.	+	.	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
Phchi.S3	AUGUSTUS	stop_codon	2665137	2665139	.	+	0	transcript_id "Phchi.S3G016200.t1"; gene_id "Phchi.S3G016200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1558.t1 is derived from g8477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1760139	1761251	.	-	.	Phchi.S5G016700
Phchi.S5	AUGUSTUS	transcript	1760139	1761251	.	-	.	transcript_id "Phchi.S5G016700.t1"; gene_id "Phchi.S5G016700"
Phchi.S5	AUGUSTUS	stop_codon	1760136	1760138	.	-	0	transcript_id "Phchi.S5G016700.t1"; gene_id "Phchi.S5G016700"
Phchi.S5	AUGUSTUS	CDS	1760139	1761251	1	-	0	transcript_id "Phchi.S5G016700.t1"; gene_id "Phchi.S5G016700"
Phchi.S5	AUGUSTUS	exon	1760139	1761251	.	-	.	transcript_id "Phchi.S5G016700.t1"; gene_id "Phchi.S5G016700"
Phchi.S5	AUGUSTUS	start_codon	1761249	1761251	.	-	0	transcript_id "Phchi.S5G016700.t1"; gene_id "Phchi.S5G016700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10455.t1 is derived from g14504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	409199	409989	.	+	.	Phchi.S4G003700
Phchi.S4	AUGUSTUS	transcript	409199	409989	.	+	.	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	start_codon	409199	409201	.	+	0	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	CDS	409199	409427	0.9	+	0	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	exon	409199	409427	.	+	.	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	intron	409428	409510	.	+	.	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	CDS	409511	409989	0.95	+	2	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	exon	409511	409989	.	+	.	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
Phchi.S4	AUGUSTUS	stop_codon	409990	409992	.	+	0	transcript_id "Phchi.S4G003700.t1"; gene_id "Phchi.S4G003700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6964.t1 is derived from g4136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26157743	26158915	.	-	.	Phchi.S1G412300
Phchi.S1	AUGUSTUS	transcript	26157743	26158915	.	-	.	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	stop_codon	26157740	26157742	.	-	0	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	CDS	26157743	26158576	0.99	-	0	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	exon	26157743	26158576	.	-	.	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	intron	26158577	26158663	.	-	.	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	CDS	26158664	26158915	0.99	-	0	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	exon	26158664	26158915	.	-	.	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
Phchi.S1	AUGUSTUS	start_codon	26158913	26158915	.	-	0	transcript_id "Phchi.S1G412300.t1"; gene_id "Phchi.S1G412300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10166.t1 is derived from g7342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46065502	46070473	.	+	.	Phchi.S1G732500
Phchi.S1	AUGUSTUS	transcript	46065502	46070473	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	start_codon	46065502	46065504	.	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46065502	46066092	0.94	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46065502	46066092	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46066093	46066189	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46066190	46066236	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46066190	46066236	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46066237	46066350	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46066351	46066444	0.99	+	1	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46066351	46066444	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46066445	46066556	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46066557	46066661	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46066557	46066661	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46066662	46066753	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46066754	46066882	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46066754	46066882	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46066883	46066969	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46066970	46067063	0.81	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46066970	46067063	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46067064	46067283	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46067284	46067360	0.79	+	2	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46067284	46067360	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46067361	46067457	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46067458	46067523	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46067458	46067523	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46067524	46067606	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46067607	46067831	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46067607	46067831	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46067832	46067904	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46067905	46067963	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46067905	46067963	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46067964	46068043	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46068044	46068110	0.95	+	1	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46068044	46068110	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46068111	46068252	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46068253	46068456	0.85	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46068253	46068456	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46068457	46068556	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46068557	46068643	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46068557	46068643	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46068644	46068737	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46068738	46068806	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46068738	46068806	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46068807	46068903	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46068904	46068990	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46068904	46068990	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46068991	46069078	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46069079	46069166	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46069079	46069166	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46069167	46069239	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46069240	46069328	1	+	2	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46069240	46069328	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46069329	46069410	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46069411	46069512	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46069411	46069512	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46069513	46069604	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46069605	46069648	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46069605	46069648	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46069649	46069745	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46069746	46069815	1	+	1	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46069746	46069815	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46069816	46069912	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46069913	46070016	1	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46069913	46070016	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	intron	46070017	46070151	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	CDS	46070152	46070473	1	+	1	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	exon	46070152	46070473	.	+	.	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
Phchi.S1	AUGUSTUS	stop_codon	46070474	46070476	.	+	0	transcript_id "Phchi.S1G732500.t1"; gene_id "Phchi.S1G732500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2915.t1 is derived from g84.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	474268	476633	.	+	.	Phchi.S1G007400
Phchi.S1	AUGUSTUS	transcript	474268	476633	.	+	.	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	start_codon	474268	474270	.	+	0	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	CDS	474268	474567	0.99	+	0	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	exon	474268	474567	.	+	.	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	intron	474568	474746	.	+	.	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	CDS	474747	476109	0.58	+	0	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	exon	474747	476109	.	+	.	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	intron	476110	476208	.	+	.	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	CDS	476209	476633	0.52	+	2	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	exon	476209	476633	.	+	.	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
Phchi.S1	AUGUSTUS	stop_codon	476634	476636	.	+	0	transcript_id "Phchi.S1G007400.t1"; gene_id "Phchi.S1G007400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11794.t1 is derived from g15846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8185006	8187021	.	-	.	Phchi.S4G137600
Phchi.S4	AUGUSTUS	transcript	8185006	8187021	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	stop_codon	8185003	8185005	.	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8185006	8185119	0.99	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8185006	8185119	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8185120	8185210	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8185211	8185375	1	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8185211	8185375	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8185376	8185459	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8185460	8185555	1	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8185460	8185555	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8185556	8185689	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8185690	8185751	1	-	2	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8185690	8185751	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8185752	8185830	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8185831	8185906	1	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8185831	8185906	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8185907	8185984	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8185985	8186067	1	-	2	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8185985	8186067	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8186068	8186162	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8186163	8186488	1	-	1	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8186163	8186488	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8186489	8186607	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8186608	8186648	1	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8186608	8186648	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8186649	8186746	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8186747	8186883	1	-	2	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8186747	8186883	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	intron	8186884	8186969	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	CDS	8186970	8187021	1	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	exon	8186970	8187021	.	-	.	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
Phchi.S4	AUGUSTUS	start_codon	8187019	8187021	.	-	0	transcript_id "Phchi.S4G137600.t1"; gene_id "Phchi.S4G137600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14814.t1 is derived from g13282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14825707	14827375	.	+	.	Phchi.S3G213300
Phchi.S3	AUGUSTUS	transcript	14825707	14827375	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	start_codon	14825707	14825709	.	+	0	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	CDS	14825707	14825996	1	+	0	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	exon	14825707	14825996	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	intron	14825997	14826079	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	CDS	14826080	14826461	1	+	1	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	exon	14826080	14826461	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	intron	14826462	14826584	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	CDS	14826585	14826671	1	+	0	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	exon	14826585	14826671	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	intron	14826672	14826765	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	CDS	14826766	14826887	1	+	0	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	exon	14826766	14826887	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	intron	14826888	14827012	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	CDS	14827013	14827103	1	+	1	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	exon	14827013	14827103	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	intron	14827104	14827186	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	CDS	14827187	14827375	0.97	+	0	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	exon	14827187	14827375	.	+	.	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
Phchi.S3	AUGUSTUS	stop_codon	14827376	14827378	.	+	0	transcript_id "Phchi.S3G213300.t1"; gene_id "Phchi.S3G213300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2708.t1 is derived from g9628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8289299	8289610	.	+	.	Phchi.S5G131700
Phchi.S5	AUGUSTUS	transcript	8289299	8289610	.	+	.	transcript_id "Phchi.S5G131700.t1"; gene_id "Phchi.S5G131700"
Phchi.S5	AUGUSTUS	start_codon	8289299	8289301	.	+	0	transcript_id "Phchi.S5G131700.t1"; gene_id "Phchi.S5G131700"
Phchi.S5	AUGUSTUS	CDS	8289299	8289610	0.84	+	0	transcript_id "Phchi.S5G131700.t1"; gene_id "Phchi.S5G131700"
Phchi.S5	AUGUSTUS	exon	8289299	8289610	.	+	.	transcript_id "Phchi.S5G131700.t1"; gene_id "Phchi.S5G131700"
Phchi.S5	AUGUSTUS	stop_codon	8289611	8289613	.	+	0	transcript_id "Phchi.S5G131700.t1"; gene_id "Phchi.S5G131700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11549.t1 is derived from g15599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6995701	6998891	.	-	.	Phchi.S4G113100
Phchi.S4	AUGUSTUS	transcript	6995701	6998891	.	-	.	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	stop_codon	6995698	6995700	.	-	0	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	CDS	6995701	6996080	1	-	2	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	exon	6995701	6996080	.	-	.	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	intron	6996081	6996169	.	-	.	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	CDS	6996170	6998891	0.77	-	0	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	exon	6996170	6998891	.	-	.	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
Phchi.S4	AUGUSTUS	start_codon	6998889	6998891	.	-	0	transcript_id "Phchi.S4G113100.t1"; gene_id "Phchi.S4G113100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6942.t1 is derived from g4114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26080510	26084955	.	+	.	Phchi.S1G410100
Phchi.S1	AUGUSTUS	transcript	26080510	26084955	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	start_codon	26080510	26080512	.	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26080510	26080809	0.66	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26080510	26080809	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26080810	26080891	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26080892	26081050	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26080892	26081050	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081051	26081150	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081151	26081207	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081151	26081207	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081208	26081295	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081296	26081387	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081296	26081387	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081388	26081507	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081508	26081626	1	+	1	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081508	26081626	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081627	26081720	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081721	26081888	1	+	2	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081721	26081888	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081889	26082080	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082081	26082223	0.98	+	2	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082081	26082223	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082224	26082328	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082329	26082415	0.98	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082329	26082415	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082416	26082586	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082587	26082712	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082587	26082712	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082713	26082799	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082800	26082887	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082800	26082887	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082888	26083021	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083022	26083099	1	+	2	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083022	26083099	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083100	26083183	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083184	26083290	1	+	2	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083184	26083290	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083291	26083376	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083377	26083438	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083377	26083438	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083439	26083516	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083517	26083552	1	+	1	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083517	26083552	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083553	26083646	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083647	26083785	1	+	1	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083647	26083785	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083786	26083876	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083877	26083983	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083877	26083983	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083984	26084109	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084110	26084287	1	+	1	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084110	26084287	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26084288	26084361	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084362	26084427	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084362	26084427	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26084428	26084518	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084519	26084697	1	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084519	26084697	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26084698	26084786	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084787	26084955	0.99	+	1	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084787	26084955	.	+	.	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	stop_codon	26084956	26084958	.	+	0	transcript_id "Phchi.S1G410100.t1"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	transcript	26080510	26084955	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	start_codon	26080510	26080512	.	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26080510	26080809	0.58	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26080510	26080809	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26080810	26080891	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26080892	26081050	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26080892	26081050	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081051	26081150	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081151	26081207	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081151	26081207	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081208	26081295	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081296	26081387	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081296	26081387	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081388	26081507	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081508	26081626	1	+	1	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081508	26081626	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081627	26081720	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081721	26081735	0.6	+	2	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081721	26081735	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081736	26081841	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26081842	26081907	0.59	+	2	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26081842	26081907	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26081908	26082080	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082081	26082223	0.93	+	2	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082081	26082223	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082224	26082328	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082329	26082415	0.94	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082329	26082415	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082416	26082586	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082587	26082712	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082587	26082712	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082713	26082799	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26082800	26082887	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26082800	26082887	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26082888	26083021	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083022	26083099	1	+	2	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083022	26083099	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083100	26083183	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083184	26083290	1	+	2	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083184	26083290	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083291	26083376	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083377	26083438	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083377	26083438	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083439	26083516	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083517	26083552	1	+	1	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083517	26083552	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083553	26083646	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083647	26083785	1	+	1	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083647	26083785	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083786	26083876	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26083877	26083983	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26083877	26083983	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26083984	26084109	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084110	26084287	1	+	1	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084110	26084287	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26084288	26084361	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084362	26084427	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084362	26084427	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26084428	26084518	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084519	26084697	1	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084519	26084697	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	intron	26084698	26084786	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	CDS	26084787	26084955	0.99	+	1	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	exon	26084787	26084955	.	+	.	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
Phchi.S1	AUGUSTUS	stop_codon	26084956	26084958	.	+	0	transcript_id "Phchi.S1G410100.t2"; gene_id "Phchi.S1G410100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12780.t1 is derived from g11245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2163256	2163489	.	+	.	Phchi.S3G009900
Phchi.S3	AUGUSTUS	transcript	2163256	2163489	.	+	.	transcript_id "Phchi.S3G009900.t1"; gene_id "Phchi.S3G009900"
Phchi.S3	AUGUSTUS	start_codon	2163256	2163258	.	+	0	transcript_id "Phchi.S3G009900.t1"; gene_id "Phchi.S3G009900"
Phchi.S3	AUGUSTUS	CDS	2163256	2163489	0.96	+	0	transcript_id "Phchi.S3G009900.t1"; gene_id "Phchi.S3G009900"
Phchi.S3	AUGUSTUS	exon	2163256	2163489	.	+	.	transcript_id "Phchi.S3G009900.t1"; gene_id "Phchi.S3G009900"
Phchi.S3	AUGUSTUS	stop_codon	2163490	2163492	.	+	0	transcript_id "Phchi.S3G009900.t1"; gene_id "Phchi.S3G009900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14581.t1 is derived from g13049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13565618	13566448	.	+	.	Phchi.S3G190000
Phchi.S3	AUGUSTUS	transcript	13565618	13566448	.	+	.	transcript_id "Phchi.S3G190000.t1"; gene_id "Phchi.S3G190000"
Phchi.S3	AUGUSTUS	start_codon	13565618	13565620	.	+	0	transcript_id "Phchi.S3G190000.t1"; gene_id "Phchi.S3G190000"
Phchi.S3	AUGUSTUS	CDS	13565618	13566448	0.95	+	0	transcript_id "Phchi.S3G190000.t1"; gene_id "Phchi.S3G190000"
Phchi.S3	AUGUSTUS	exon	13565618	13566448	.	+	.	transcript_id "Phchi.S3G190000.t1"; gene_id "Phchi.S3G190000"
Phchi.S3	AUGUSTUS	stop_codon	13566449	13566451	.	+	0	transcript_id "Phchi.S3G190000.t1"; gene_id "Phchi.S3G190000"
# This transcript jg10045.t2 is derived from g7221.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10046.t1 is derived from g7222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45233893	45234522	.	-	.	Phchi.S1G720500
Phchi.S1	AUGUSTUS	transcript	45233893	45234522	.	-	.	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	stop_codon	45233890	45233892	.	-	0	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	CDS	45233893	45234175	0.84	-	1	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	exon	45233893	45234175	.	-	.	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	intron	45234176	45234298	.	-	.	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	CDS	45234299	45234522	0.91	-	0	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	exon	45234299	45234522	.	-	.	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
Phchi.S1	AUGUSTUS	start_codon	45234520	45234522	.	-	0	transcript_id "Phchi.S1G720500.t1"; gene_id "Phchi.S1G720500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8742.t1 is derived from g5917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37763910	37765374	.	-	.	Phchi.S1G590100
Phchi.S1	AUGUSTUS	transcript	37763910	37765374	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	stop_codon	37763907	37763909	.	-	0	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	CDS	37763910	37764180	0.96	-	1	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	exon	37763910	37764180	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	intron	37764181	37764289	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	CDS	37764290	37764399	0.97	-	0	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	exon	37764290	37764399	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	intron	37764400	37764596	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	CDS	37764597	37764671	1	-	0	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	exon	37764597	37764671	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	intron	37764672	37764762	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	CDS	37764763	37765374	0.98	-	0	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	exon	37764763	37765374	.	-	.	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
Phchi.S1	AUGUSTUS	start_codon	37765372	37765374	.	-	0	transcript_id "Phchi.S1G590100.t1"; gene_id "Phchi.S1G590100"
# This transcript jg7944.t2 is derived from g5118.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7945.t1 is derived from g5119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32043383	32045054	.	-	.	Phchi.S1G510400
Phchi.S1	AUGUSTUS	transcript	32043383	32045054	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	stop_codon	32043380	32043382	.	-	0	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	CDS	32043383	32043535	0.99	-	0	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	exon	32043383	32043535	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	intron	32043536	32043618	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	CDS	32043619	32043760	1	-	1	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	exon	32043619	32043760	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	intron	32043761	32043843	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	CDS	32043844	32043975	1	-	1	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	exon	32043844	32043975	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	intron	32043976	32044073	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	CDS	32044074	32044138	1	-	0	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	exon	32044074	32044138	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	intron	32044139	32044331	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	CDS	32044332	32045054	0.96	-	0	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	exon	32044332	32045054	.	-	.	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
Phchi.S1	AUGUSTUS	start_codon	32045052	32045054	.	-	0	transcript_id "Phchi.S1G510400.t1"; gene_id "Phchi.S1G510400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1907.t1 is derived from g8827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3807603	3814665	.	+	.	Phchi.S5G051600
Phchi.S5	AUGUSTUS	transcript	3807603	3814665	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	start_codon	3807603	3807605	.	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3807603	3807622	1	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3807603	3807622	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3807623	3807770	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3807771	3807851	1	+	1	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3807771	3807851	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3807852	3808097	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3808098	3808142	1	+	1	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3808098	3808142	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3808143	3808235	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3808236	3808743	0.97	+	1	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3808236	3808743	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3808744	3808889	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3808890	3808986	1	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3808890	3808986	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3808987	3809123	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3809124	3809207	1	+	2	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3809124	3809207	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3809208	3809292	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3809293	3809499	1	+	2	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3809293	3809499	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3809500	3809622	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3809623	3810591	0.52	+	2	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3809623	3810591	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3810592	3810704	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3810705	3810814	0.68	+	2	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3810705	3810814	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3810815	3810903	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3810904	3811332	0.78	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3810904	3811332	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3811333	3811686	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3811687	3814032	0.92	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3811687	3814032	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3814033	3814122	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3814123	3814665	0.65	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3814123	3814665	.	+	.	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	stop_codon	3814666	3814668	.	+	0	transcript_id "Phchi.S5G051600.t1"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	transcript	3807603	3814665	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	start_codon	3807603	3807605	.	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3807603	3807622	1	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3807603	3807622	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3807623	3807770	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3807771	3807851	1	+	1	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3807771	3807851	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3807852	3808097	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3808098	3808142	1	+	1	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3808098	3808142	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3808143	3808235	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3808236	3808743	0.98	+	1	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3808236	3808743	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3808744	3808889	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3808890	3808986	1	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3808890	3808986	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3808987	3809123	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3809124	3809207	1	+	2	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3809124	3809207	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3809208	3809283	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3809284	3809499	1	+	2	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3809284	3809499	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3809500	3809622	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3809623	3810591	0.48	+	2	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3809623	3810591	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3810592	3810704	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3810705	3810814	0.71	+	2	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3810705	3810814	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3810815	3810903	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3810904	3811332	0.8	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3810904	3811332	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3811333	3811686	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3811687	3814032	0.88	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3811687	3814032	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	intron	3814033	3814122	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	CDS	3814123	3814665	0.57	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	exon	3814123	3814665	.	+	.	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
Phchi.S5	AUGUSTUS	stop_codon	3814666	3814668	.	+	0	transcript_id "Phchi.S5G051600.t2"; gene_id "Phchi.S5G051600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10419.t1 is derived from g14468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	60025	62026	.	+	.	Phchi.S4G000100
Phchi.S4	AUGUSTUS	transcript	60481	62026	.	+	.	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	start_codon	60481	60483	.	+	0	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	CDS	60481	61703	0.4	+	0	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	exon	60481	61703	.	+	.	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	intron	61704	61797	.	+	.	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	CDS	61798	62026	0.61	+	1	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	exon	61798	62026	.	+	.	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	stop_codon	62027	62029	.	+	0	transcript_id "Phchi.S4G000100.t1"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	transcript	60025	61809	.	+	.	transcript_id "Phchi.S4G000100.t2"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	start_codon	60025	60027	.	+	0	transcript_id "Phchi.S4G000100.t2"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	CDS	60025	61809	0.44	+	0	transcript_id "Phchi.S4G000100.t2"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	exon	60025	61809	.	+	.	transcript_id "Phchi.S4G000100.t2"; gene_id "Phchi.S4G000100"
Phchi.S4	AUGUSTUS	stop_codon	61810	61812	.	+	0	transcript_id "Phchi.S4G000100.t2"; gene_id "Phchi.S4G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13931.t1 is derived from g12398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9786935	9787282	.	+	.	Phchi.S3G125000
Phchi.S3	AUGUSTUS	transcript	9786935	9787282	.	+	.	transcript_id "Phchi.S3G125000.t1"; gene_id "Phchi.S3G125000"
Phchi.S3	AUGUSTUS	start_codon	9786935	9786937	.	+	0	transcript_id "Phchi.S3G125000.t1"; gene_id "Phchi.S3G125000"
Phchi.S3	AUGUSTUS	CDS	9786935	9787282	0.93	+	0	transcript_id "Phchi.S3G125000.t1"; gene_id "Phchi.S3G125000"
Phchi.S3	AUGUSTUS	exon	9786935	9787282	.	+	.	transcript_id "Phchi.S3G125000.t1"; gene_id "Phchi.S3G125000"
Phchi.S3	AUGUSTUS	stop_codon	9787283	9787285	.	+	0	transcript_id "Phchi.S3G125000.t1"; gene_id "Phchi.S3G125000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6420.t1 is derived from g3592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22910379	22913432	.	-	.	Phchi.S1G357900
Phchi.S1	AUGUSTUS	transcript	22910379	22913432	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	stop_codon	22910376	22910378	.	-	0	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	CDS	22910379	22910482	0.92	-	2	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	exon	22910379	22910482	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	intron	22910483	22910716	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	CDS	22910717	22910911	0.95	-	2	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	exon	22910717	22910911	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	intron	22910912	22911346	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	CDS	22911347	22913009	0.5	-	0	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	exon	22911347	22913009	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	intron	22913010	22913093	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	CDS	22913094	22913138	0.98	-	0	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	exon	22913094	22913138	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	intron	22913139	22913230	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	CDS	22913231	22913274	0.61	-	2	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	exon	22913231	22913274	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	intron	22913275	22913422	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	CDS	22913423	22913432	0.99	-	0	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	exon	22913423	22913432	.	-	.	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
Phchi.S1	AUGUSTUS	start_codon	22913430	22913432	.	-	0	transcript_id "Phchi.S1G357900.t1"; gene_id "Phchi.S1G357900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10752.t1 is derived from g14802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1933158	1936433	.	-	.	Phchi.S4G033400
Phchi.S4	AUGUSTUS	transcript	1933158	1936433	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	stop_codon	1933155	1933157	.	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1933158	1933208	0.97	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1933158	1933208	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1933209	1933296	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1933297	1933503	1	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1933297	1933503	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1933504	1933577	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1933578	1933704	1	-	1	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1933578	1933704	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1933705	1933803	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1933804	1933958	1	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1933804	1933958	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1933959	1934047	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1934048	1934220	1	-	2	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1934048	1934220	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1934221	1934339	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1934340	1934419	1	-	1	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1934340	1934419	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1934420	1934523	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1934524	1934594	0.62	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1934524	1934594	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1934595	1934759	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1934760	1934873	1	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1934760	1934873	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1934874	1935002	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1935003	1935140	1	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1935003	1935140	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1935141	1935278	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1935279	1935382	0.66	-	2	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1935279	1935382	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1935383	1935486	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1935487	1935609	0.8	-	2	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1935487	1935609	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1935610	1935699	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1935700	1935894	0.76	-	2	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1935700	1935894	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1935895	1936043	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1936044	1936133	0.91	-	2	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1936044	1936133	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	intron	1936134	1936342	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	CDS	1936343	1936433	1	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	exon	1936343	1936433	.	-	.	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
Phchi.S4	AUGUSTUS	start_codon	1936431	1936433	.	-	0	transcript_id "Phchi.S4G033400.t1"; gene_id "Phchi.S4G033400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15608.t1 is derived from g14077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20256297	20256700	.	-	.	Phchi.S3G292700
Phchi.S3	AUGUSTUS	transcript	20256297	20256700	.	-	.	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	stop_codon	20256294	20256296	.	-	0	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	CDS	20256297	20256316	1	-	2	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	exon	20256297	20256316	.	-	.	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	intron	20256317	20256438	.	-	.	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	CDS	20256439	20256700	1	-	0	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	exon	20256439	20256700	.	-	.	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
Phchi.S3	AUGUSTUS	start_codon	20256698	20256700	.	-	0	transcript_id "Phchi.S3G292700.t1"; gene_id "Phchi.S3G292700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3505.t1 is derived from g674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4121754	4122554	.	+	.	Phchi.S1G066400
Phchi.S1	AUGUSTUS	transcript	4121754	4122554	.	+	.	transcript_id "Phchi.S1G066400.t1"; gene_id "Phchi.S1G066400"
Phchi.S1	AUGUSTUS	start_codon	4121754	4121756	.	+	0	transcript_id "Phchi.S1G066400.t1"; gene_id "Phchi.S1G066400"
Phchi.S1	AUGUSTUS	CDS	4121754	4122554	1	+	0	transcript_id "Phchi.S1G066400.t1"; gene_id "Phchi.S1G066400"
Phchi.S1	AUGUSTUS	exon	4121754	4122554	.	+	.	transcript_id "Phchi.S1G066400.t1"; gene_id "Phchi.S1G066400"
Phchi.S1	AUGUSTUS	stop_codon	4122555	4122557	.	+	0	transcript_id "Phchi.S1G066400.t1"; gene_id "Phchi.S1G066400"
# This transcript jg7827.t2 is derived from g5001.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7828.t1 is derived from g5002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31395068	31395848	.	+	.	Phchi.S1G498700
Phchi.S1	AUGUSTUS	transcript	31395068	31395848	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	start_codon	31395068	31395070	.	+	0	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	CDS	31395068	31395341	0.99	+	0	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	exon	31395068	31395341	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	intron	31395342	31395433	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	CDS	31395434	31395480	1	+	2	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	exon	31395434	31395480	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	intron	31395481	31395598	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	CDS	31395599	31395652	1	+	0	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	exon	31395599	31395652	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	intron	31395653	31395776	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	CDS	31395777	31395848	0.97	+	0	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	exon	31395777	31395848	.	+	.	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
Phchi.S1	AUGUSTUS	stop_codon	31395849	31395851	.	+	0	transcript_id "Phchi.S1G498700.t1"; gene_id "Phchi.S1G498700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3134.t1 is derived from g303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1893735	1894567	.	+	.	Phchi.S1G029300
Phchi.S1	AUGUSTUS	transcript	1893735	1894567	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	start_codon	1893735	1893737	.	+	0	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	CDS	1893735	1893838	0.78	+	0	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	exon	1893735	1893838	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	intron	1893839	1893923	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	CDS	1893924	1894145	0.79	+	1	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	exon	1893924	1894145	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	intron	1894146	1894234	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	CDS	1894235	1894314	1	+	1	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	exon	1894235	1894314	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	intron	1894315	1894412	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	CDS	1894413	1894567	0.66	+	2	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	exon	1894413	1894567	.	+	.	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
Phchi.S1	AUGUSTUS	stop_codon	1894568	1894570	.	+	0	transcript_id "Phchi.S1G029300.t1"; gene_id "Phchi.S1G029300"
# This transcript jg5269.t2 is derived from g2439.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5270.t1 is derived from g2440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15981580	15985323	.	+	.	Phchi.S1G242900
Phchi.S1	AUGUSTUS	transcript	15981580	15985323	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	start_codon	15981580	15981582	.	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15981580	15981819	0.81	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15981580	15981819	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15981820	15981914	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15981915	15982077	0.95	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15981915	15982077	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15982078	15982155	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15982156	15982265	0.99	+	2	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15982156	15982265	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15982266	15982361	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15982362	15982461	0.98	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15982362	15982461	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15982462	15982556	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15982557	15982643	0.99	+	2	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15982557	15982643	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15982644	15982737	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15982738	15982920	0.46	+	2	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15982738	15982920	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15982921	15982997	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15982998	15983282	0.68	+	2	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15982998	15983282	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15983283	15983424	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15983425	15983542	0.76	+	2	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15983425	15983542	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15983543	15983639	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15983640	15983893	0.98	+	1	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15983640	15983893	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15983894	15984000	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15984001	15984164	0.99	+	2	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15984001	15984164	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15984165	15984249	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15984250	15984354	1	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15984250	15984354	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	intron	15984355	15984459	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	CDS	15984460	15985323	0.78	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	exon	15984460	15985323	.	+	.	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
Phchi.S1	AUGUSTUS	stop_codon	15985324	15985326	.	+	0	transcript_id "Phchi.S1G242900.t1"; gene_id "Phchi.S1G242900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3080.t1 is derived from g249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1502382	1503581	.	+	.	Phchi.S1G023900
Phchi.S1	AUGUSTUS	transcript	1502382	1503581	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	start_codon	1502382	1502384	.	+	0	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	CDS	1502382	1502514	1	+	0	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	exon	1502382	1502514	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	intron	1502515	1502599	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	CDS	1502600	1502668	1	+	2	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	exon	1502600	1502668	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	intron	1502669	1502787	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	CDS	1502788	1502853	1	+	2	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	exon	1502788	1502853	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	intron	1502854	1502969	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	CDS	1502970	1503091	1	+	2	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	exon	1502970	1503091	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	intron	1503092	1503217	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	CDS	1503218	1503346	1	+	0	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	exon	1503218	1503346	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	intron	1503347	1503467	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	CDS	1503468	1503581	1	+	0	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	exon	1503468	1503581	.	+	.	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
Phchi.S1	AUGUSTUS	stop_codon	1503582	1503584	.	+	0	transcript_id "Phchi.S1G023900.t1"; gene_id "Phchi.S1G023900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9894.t1 is derived from g7070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44315267	44317799	.	-	.	Phchi.S1G705300
Phchi.S1	AUGUSTUS	transcript	44315267	44317799	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	stop_codon	44315264	44315266	.	-	0	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44315267	44315412	0.96	-	2	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44315267	44315412	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	intron	44315413	44315506	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44315507	44315678	0.98	-	0	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44315507	44315678	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	intron	44315679	44315781	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44315782	44315919	0.99	-	0	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44315782	44315919	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	intron	44315920	44316019	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44316020	44317013	0.96	-	1	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44316020	44317013	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	intron	44317014	44317174	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44317175	44317250	0.99	-	2	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44317175	44317250	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	intron	44317251	44317341	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44317342	44317453	1	-	0	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44317342	44317453	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	intron	44317454	44317556	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	CDS	44317557	44317799	0.88	-	0	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	exon	44317557	44317799	.	-	.	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
Phchi.S1	AUGUSTUS	start_codon	44317797	44317799	.	-	0	transcript_id "Phchi.S1G705300.t1"; gene_id "Phchi.S1G705300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9481.t1 is derived from g6657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41963339	41965097	.	-	.	Phchi.S1G664000
Phchi.S1	AUGUSTUS	transcript	41963339	41965097	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	stop_codon	41963336	41963338	.	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41963339	41963353	1	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41963339	41963353	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41963354	41963438	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41963439	41963495	1	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41963439	41963495	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41963496	41963586	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41963587	41963637	1	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41963587	41963637	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41963638	41963722	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41963723	41963779	1	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41963723	41963779	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41963780	41963884	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41963885	41963926	1	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41963885	41963926	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41963927	41964022	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41964023	41964134	1	-	1	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41964023	41964134	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41964135	41964214	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41964215	41964312	1	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41964215	41964312	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41964313	41964415	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41964416	41964511	0.97	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41964416	41964511	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41964512	41964596	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41964597	41964666	1	-	1	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41964597	41964666	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41964667	41964756	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41964757	41964892	1	-	2	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41964757	41964892	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	intron	41964893	41964979	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	CDS	41964980	41965097	0.68	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	exon	41964980	41965097	.	-	.	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
Phchi.S1	AUGUSTUS	start_codon	41965095	41965097	.	-	0	transcript_id "Phchi.S1G664000.t1"; gene_id "Phchi.S1G664000"
# This transcript jg4893.t2 is derived from g2063.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4894.t1 is derived from g2064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13285751	13288192	.	-	.	Phchi.S1G205300
Phchi.S1	AUGUSTUS	transcript	13285751	13288192	.	-	.	transcript_id "Phchi.S1G205300.t1"; gene_id "Phchi.S1G205300"
Phchi.S1	AUGUSTUS	stop_codon	13285748	13285750	.	-	0	transcript_id "Phchi.S1G205300.t1"; gene_id "Phchi.S1G205300"
Phchi.S1	AUGUSTUS	CDS	13285751	13288192	1	-	0	transcript_id "Phchi.S1G205300.t1"; gene_id "Phchi.S1G205300"
Phchi.S1	AUGUSTUS	exon	13285751	13288192	.	-	.	transcript_id "Phchi.S1G205300.t1"; gene_id "Phchi.S1G205300"
Phchi.S1	AUGUSTUS	start_codon	13288190	13288192	.	-	0	transcript_id "Phchi.S1G205300.t1"; gene_id "Phchi.S1G205300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg609.t1 is derived from g10391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4392280	4392765	.	-	.	Phchi.S6G056800
Phchi.S6	AUGUSTUS	transcript	4392280	4392765	.	-	.	transcript_id "Phchi.S6G056800.t1"; gene_id "Phchi.S6G056800"
Phchi.S6	AUGUSTUS	stop_codon	4392277	4392279	.	-	0	transcript_id "Phchi.S6G056800.t1"; gene_id "Phchi.S6G056800"
Phchi.S6	AUGUSTUS	CDS	4392280	4392765	0.48	-	0	transcript_id "Phchi.S6G056800.t1"; gene_id "Phchi.S6G056800"
Phchi.S6	AUGUSTUS	exon	4392280	4392765	.	-	.	transcript_id "Phchi.S6G056800.t1"; gene_id "Phchi.S6G056800"
Phchi.S6	AUGUSTUS	start_codon	4392763	4392765	.	-	0	transcript_id "Phchi.S6G056800.t1"; gene_id "Phchi.S6G056800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg409.t1 is derived from g10191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2940816	2942432	.	+	.	Phchi.S6G036800
Phchi.S6	AUGUSTUS	transcript	2940816	2942432	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	start_codon	2940816	2940818	.	+	0	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2940816	2940837	0.93	+	0	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2940816	2940837	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	intron	2940838	2941065	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2941066	2941082	1	+	2	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2941066	2941082	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	intron	2941083	2941532	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2941533	2941632	1	+	0	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2941533	2941632	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	intron	2941633	2941725	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2941726	2941788	1	+	2	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2941726	2941788	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	intron	2941789	2941878	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2941879	2941942	1	+	2	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2941879	2941942	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	intron	2941943	2942021	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2942022	2942248	1	+	1	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2942022	2942248	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	intron	2942249	2942349	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	CDS	2942350	2942432	1	+	2	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	exon	2942350	2942432	.	+	.	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
Phchi.S6	AUGUSTUS	stop_codon	2942433	2942435	.	+	0	transcript_id "Phchi.S6G036800.t1"; gene_id "Phchi.S6G036800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13529.t1 is derived from g11996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7386573	7387400	.	-	.	Phchi.S3G084800
Phchi.S3	AUGUSTUS	transcript	7386573	7387400	.	-	.	transcript_id "Phchi.S3G084800.t1"; gene_id "Phchi.S3G084800"
Phchi.S3	AUGUSTUS	stop_codon	7386570	7386572	.	-	0	transcript_id "Phchi.S3G084800.t1"; gene_id "Phchi.S3G084800"
Phchi.S3	AUGUSTUS	CDS	7386573	7387400	0.57	-	0	transcript_id "Phchi.S3G084800.t1"; gene_id "Phchi.S3G084800"
Phchi.S3	AUGUSTUS	exon	7386573	7387400	.	-	.	transcript_id "Phchi.S3G084800.t1"; gene_id "Phchi.S3G084800"
Phchi.S3	AUGUSTUS	start_codon	7387398	7387400	.	-	0	transcript_id "Phchi.S3G084800.t1"; gene_id "Phchi.S3G084800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3213.t1 is derived from g382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2266688	2270278	.	+	.	Phchi.S1G037200
Phchi.S1	AUGUSTUS	transcript	2266688	2270278	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	start_codon	2266688	2266690	.	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2266688	2266830	0.51	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2266688	2266830	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2266831	2266921	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2266922	2267018	1	+	1	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2266922	2267018	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2267019	2267102	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2267103	2267378	1	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2267103	2267378	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2267379	2267461	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2267462	2267938	0.94	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2267462	2267938	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2267939	2268023	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2268024	2268589	0.97	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2268024	2268589	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2268590	2268670	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2268671	2268819	1	+	1	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2268671	2268819	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2268820	2268918	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2268919	2269094	1	+	2	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2268919	2269094	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2269095	2269231	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2269232	2269384	0.94	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2269232	2269384	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2269385	2269492	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2269493	2269643	1	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2269493	2269643	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2269644	2269743	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2269744	2269851	0.41	+	2	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2269744	2269851	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	intron	2269852	2270273	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	CDS	2270274	2270278	0.55	+	2	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	exon	2270274	2270278	.	+	.	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
Phchi.S1	AUGUSTUS	stop_codon	2270279	2270281	.	+	0	transcript_id "Phchi.S1G037200.t1"; gene_id "Phchi.S1G037200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13075.t1 is derived from g11540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4037190	4039158	.	+	.	Phchi.S3G039400
Phchi.S3	AUGUSTUS	transcript	4037190	4039158	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	start_codon	4037190	4037192	.	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4037190	4037279	1	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4037190	4037279	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4037280	4037424	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4037425	4037483	1	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4037425	4037483	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4037484	4037578	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4037579	4037627	1	+	1	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4037579	4037627	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4037628	4037744	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4037745	4037790	1	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4037745	4037790	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4037791	4037880	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4037881	4038102	1	+	2	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4037881	4038102	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4038103	4038191	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4038192	4038250	0.87	+	2	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4038192	4038250	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4038251	4038361	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4038362	4038422	1	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4038362	4038422	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4038423	4038512	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4038513	4038604	1	+	2	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4038513	4038604	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4038605	4038693	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4038694	4038927	1	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4038694	4038927	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	intron	4038928	4039020	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	CDS	4039021	4039158	1	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	exon	4039021	4039158	.	+	.	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
Phchi.S3	AUGUSTUS	stop_codon	4039159	4039161	.	+	0	transcript_id "Phchi.S3G039400.t1"; gene_id "Phchi.S3G039400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1397.t1 is derived from g8316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	38979	39323	.	+	.	Phchi.S5G000600
Phchi.S5	AUGUSTUS	transcript	38979	39323	.	+	.	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	start_codon	38979	38981	.	+	0	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	CDS	38979	39032	0.98	+	0	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	exon	38979	39032	.	+	.	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	intron	39033	39179	.	+	.	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	CDS	39180	39323	0.98	+	0	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	exon	39180	39323	.	+	.	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
Phchi.S5	AUGUSTUS	stop_codon	39324	39326	.	+	0	transcript_id "Phchi.S5G000600.t1"; gene_id "Phchi.S5G000600"
# This transcript jg1633.t2 is derived from g8552.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1633.t3 is derived from g8552.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1634.t1 is derived from g8553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2115535	2117019	.	-	.	Phchi.S5G024300
Phchi.S5	AUGUSTUS	transcript	2115535	2117019	.	-	.	transcript_id "Phchi.S5G024300.t1"; gene_id "Phchi.S5G024300"
Phchi.S5	AUGUSTUS	stop_codon	2115532	2115534	.	-	0	transcript_id "Phchi.S5G024300.t1"; gene_id "Phchi.S5G024300"
Phchi.S5	AUGUSTUS	CDS	2115535	2117019	0.75	-	0	transcript_id "Phchi.S5G024300.t1"; gene_id "Phchi.S5G024300"
Phchi.S5	AUGUSTUS	exon	2115535	2117019	.	-	.	transcript_id "Phchi.S5G024300.t1"; gene_id "Phchi.S5G024300"
Phchi.S5	AUGUSTUS	start_codon	2117017	2117019	.	-	0	transcript_id "Phchi.S5G024300.t1"; gene_id "Phchi.S5G024300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14472.t1 is derived from g12940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13028287	13029620	.	+	.	Phchi.S3G179100
Phchi.S3	AUGUSTUS	transcript	13028287	13029620	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	start_codon	13028287	13028289	.	+	0	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	CDS	13028287	13028340	1	+	0	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	exon	13028287	13028340	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	intron	13028341	13028475	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	CDS	13028476	13028793	1	+	0	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	exon	13028476	13028793	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	intron	13028794	13029187	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	CDS	13029188	13029412	1	+	0	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	exon	13029188	13029412	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	intron	13029413	13029575	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	CDS	13029576	13029620	0.97	+	0	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	exon	13029576	13029620	.	+	.	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
Phchi.S3	AUGUSTUS	stop_codon	13029621	13029623	.	+	0	transcript_id "Phchi.S3G179100.t1"; gene_id "Phchi.S3G179100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5316.t1 is derived from g2486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16257994	16259051	.	+	.	Phchi.S1G247500
Phchi.S1	AUGUSTUS	transcript	16257994	16259051	.	+	.	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	start_codon	16257994	16257996	.	+	0	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	CDS	16257994	16258485	0.55	+	0	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	exon	16257994	16258485	.	+	.	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	intron	16258486	16258707	.	+	.	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	CDS	16258708	16258713	0.48	+	0	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	exon	16258708	16258713	.	+	.	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	intron	16258714	16258793	.	+	.	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	CDS	16258794	16259051	0.72	+	0	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	exon	16258794	16259051	.	+	.	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
Phchi.S1	AUGUSTUS	stop_codon	16259052	16259054	.	+	0	transcript_id "Phchi.S1G247500.t1"; gene_id "Phchi.S1G247500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11069.t1 is derived from g15119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3960423	3961580	.	-	.	Phchi.S4G065100
Phchi.S4	AUGUSTUS	transcript	3960423	3961580	.	-	.	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	stop_codon	3960420	3960422	.	-	0	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	CDS	3960423	3960884	1	-	0	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	exon	3960423	3960884	.	-	.	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	intron	3960885	3961314	.	-	.	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	CDS	3961315	3961320	1	-	0	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	exon	3961315	3961320	.	-	.	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	intron	3961321	3961460	.	-	.	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	CDS	3961461	3961580	0.99	-	0	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	exon	3961461	3961580	.	-	.	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
Phchi.S4	AUGUSTUS	start_codon	3961578	3961580	.	-	0	transcript_id "Phchi.S4G065100.t1"; gene_id "Phchi.S4G065100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1749.t1 is derived from g8669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2871988	2873310	.	+	.	Phchi.S5G035800
Phchi.S5	AUGUSTUS	transcript	2871988	2873310	.	+	.	transcript_id "Phchi.S5G035800.t1"; gene_id "Phchi.S5G035800"
Phchi.S5	AUGUSTUS	start_codon	2871988	2871990	.	+	0	transcript_id "Phchi.S5G035800.t1"; gene_id "Phchi.S5G035800"
Phchi.S5	AUGUSTUS	CDS	2871988	2873310	0.36	+	0	transcript_id "Phchi.S5G035800.t1"; gene_id "Phchi.S5G035800"
Phchi.S5	AUGUSTUS	exon	2871988	2873310	.	+	.	transcript_id "Phchi.S5G035800.t1"; gene_id "Phchi.S5G035800"
Phchi.S5	AUGUSTUS	stop_codon	2873311	2873313	.	+	0	transcript_id "Phchi.S5G035800.t1"; gene_id "Phchi.S5G035800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11100.t1 is derived from g15150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4112607	4132030	.	-	.	Phchi.S4G068200
Phchi.S4	AUGUSTUS	transcript	4112607	4132030	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	stop_codon	4112604	4112606	.	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4112607	4112719	0.96	-	2	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4112607	4112719	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4112720	4112797	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4112798	4113017	0.92	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4112798	4113017	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4113018	4113102	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4113103	4113201	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4113103	4113201	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4113202	4113286	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4113287	4113439	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4113287	4113439	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4113440	4113525	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4113526	4113594	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4113526	4113594	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4113595	4113735	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4113736	4113798	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4113736	4113798	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4113799	4113892	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4113893	4114018	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4113893	4114018	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4114019	4114113	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4114114	4114251	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4114114	4114251	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4114252	4114329	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4114330	4114445	1	-	2	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4114330	4114445	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4114446	4114535	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4114536	4114846	0.85	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4114536	4114846	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4114847	4114991	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4114992	4115104	0.99	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4114992	4115104	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4115105	4115207	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4115208	4115295	1	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4115208	4115295	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4115296	4115387	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4115388	4115546	1	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4115388	4115546	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4115547	4115638	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4115639	4115685	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4115639	4115685	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4115686	4115774	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4115775	4115843	0.98	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4115775	4115843	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4115844	4115951	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4115952	4116104	0.9	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4115952	4116104	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4116105	4116252	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4116253	4116400	1	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4116253	4116400	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4116401	4116534	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4116535	4116696	0.65	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4116535	4116696	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4116697	4116816	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4116817	4117022	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4116817	4117022	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4117023	4117225	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4117226	4117342	0.95	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4117226	4117342	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4117343	4117492	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4117493	4117564	0.87	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4117493	4117564	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4117565	4117705	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4117706	4117830	0.94	-	2	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4117706	4117830	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4117831	4117959	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4117960	4118032	0.99	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4117960	4118032	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4118033	4118141	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4118142	4118871	0.95	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4118142	4118871	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4118872	4118981	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4118982	4119079	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4118982	4119079	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4119080	4119272	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4119273	4119380	0.65	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4119273	4119380	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4119381	4119464	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4119465	4119686	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4119465	4119686	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4119687	4119772	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4119773	4120189	0.77	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4119773	4120189	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4120190	4120298	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4120299	4120553	0.76	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4120299	4120553	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4120554	4120681	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4120682	4120846	0.81	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4120682	4120846	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4120847	4120980	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4120981	4121154	0.97	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4120981	4121154	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4121155	4121233	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4121234	4124596	0.77	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4121234	4124596	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4124597	4124707	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4124708	4125712	0.91	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4124708	4125712	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4125713	4125865	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4125866	4126144	0.98	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4125866	4126144	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4126145	4126233	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4126234	4126491	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4126234	4126491	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4126492	4126631	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4126632	4126853	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4126632	4126853	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4126854	4127076	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4127077	4127166	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4127077	4127166	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4127167	4127320	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4127321	4127656	0.97	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4127321	4127656	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4127657	4127775	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4127776	4128651	0.94	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4127776	4128651	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4128652	4128781	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4128782	4128850	0.91	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4128782	4128850	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4128851	4128965	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4128966	4129182	0.99	-	1	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4128966	4129182	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4129183	4129359	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4129360	4129409	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4129360	4129409	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4129410	4129553	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4129554	4129646	1	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4129554	4129646	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4129647	4129814	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4129815	4130026	1	-	2	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4129815	4130026	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4130027	4130154	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4130155	4130665	0.29	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4130155	4130665	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	intron	4130666	4130800	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	CDS	4130801	4132030	0.72	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	exon	4130801	4132030	.	-	.	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
Phchi.S4	AUGUSTUS	start_codon	4132028	4132030	.	-	0	transcript_id "Phchi.S4G068200.t1"; gene_id "Phchi.S4G068200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10417.t1 is derived from g7593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47757883	47758468	.	-	.	Phchi.S1G757600
Phchi.S1	AUGUSTUS	transcript	47757883	47758468	.	-	.	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	stop_codon	47757880	47757882	.	-	0	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	CDS	47757883	47757906	0.97	-	0	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	exon	47757883	47757906	.	-	.	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	intron	47757907	47758288	.	-	.	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	CDS	47758289	47758468	0.67	-	0	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	exon	47758289	47758468	.	-	.	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
Phchi.S1	AUGUSTUS	start_codon	47758466	47758468	.	-	0	transcript_id "Phchi.S1G757600.t1"; gene_id "Phchi.S1G757600"
# This transcript jg9153.t2 is derived from g6328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9154.t1 is derived from g6329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40122378	40123588	.	-	.	Phchi.S1G631300
Phchi.S1	AUGUSTUS	transcript	40122378	40123588	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	stop_codon	40122375	40122377	.	-	0	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	CDS	40122378	40122641	1	-	0	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	exon	40122378	40122641	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	intron	40122642	40122728	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	CDS	40122729	40122859	1	-	2	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	exon	40122729	40122859	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	intron	40122860	40122948	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	CDS	40122949	40123025	1	-	1	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	exon	40122949	40123025	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	intron	40123026	40123135	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	CDS	40123136	40123198	1	-	1	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	exon	40123136	40123198	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	intron	40123199	40123328	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	CDS	40123329	40123588	0.59	-	0	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	exon	40123329	40123588	.	-	.	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
Phchi.S1	AUGUSTUS	start_codon	40123586	40123588	.	-	0	transcript_id "Phchi.S1G631300.t1"; gene_id "Phchi.S1G631300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11868.t1 is derived from g15920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8891659	8891970	.	+	.	Phchi.S4G145000
Phchi.S4	AUGUSTUS	transcript	8891659	8891970	.	+	.	transcript_id "Phchi.S4G145000.t1"; gene_id "Phchi.S4G145000"
Phchi.S4	AUGUSTUS	start_codon	8891659	8891661	.	+	0	transcript_id "Phchi.S4G145000.t1"; gene_id "Phchi.S4G145000"
Phchi.S4	AUGUSTUS	CDS	8891659	8891970	0.74	+	0	transcript_id "Phchi.S4G145000.t1"; gene_id "Phchi.S4G145000"
Phchi.S4	AUGUSTUS	exon	8891659	8891970	.	+	.	transcript_id "Phchi.S4G145000.t1"; gene_id "Phchi.S4G145000"
Phchi.S4	AUGUSTUS	stop_codon	8891971	8891973	.	+	0	transcript_id "Phchi.S4G145000.t1"; gene_id "Phchi.S4G145000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10036.t1 is derived from g7212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45190959	45193876	.	+	.	Phchi.S1G719500
Phchi.S1	AUGUSTUS	transcript	45190959	45193876	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	start_codon	45190959	45190961	.	+	0	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45190959	45191115	0.98	+	0	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45190959	45191115	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	intron	45191116	45191214	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45191215	45191292	1	+	2	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45191215	45191292	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	intron	45191293	45191855	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45191856	45191876	1	+	2	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45191856	45191876	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	intron	45191877	45191959	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45191960	45191997	1	+	2	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45191960	45191997	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	intron	45191998	45192291	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45192292	45192364	1	+	0	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45192292	45192364	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	intron	45192365	45192459	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45192460	45192737	0.87	+	2	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45192460	45192737	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	intron	45192738	45192853	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	CDS	45192854	45193876	0.72	+	0	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	exon	45192854	45193876	.	+	.	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
Phchi.S1	AUGUSTUS	stop_codon	45193877	45193879	.	+	0	transcript_id "Phchi.S1G719500.t1"; gene_id "Phchi.S1G719500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4036.t1 is derived from g1205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7295905	7297506	.	-	.	Phchi.S1G119500
Phchi.S1	AUGUSTUS	transcript	7295905	7297506	.	-	.	transcript_id "Phchi.S1G119500.t1"; gene_id "Phchi.S1G119500"
Phchi.S1	AUGUSTUS	stop_codon	7295902	7295904	.	-	0	transcript_id "Phchi.S1G119500.t1"; gene_id "Phchi.S1G119500"
Phchi.S1	AUGUSTUS	CDS	7295905	7297506	0.55	-	0	transcript_id "Phchi.S1G119500.t1"; gene_id "Phchi.S1G119500"
Phchi.S1	AUGUSTUS	exon	7295905	7297506	.	-	.	transcript_id "Phchi.S1G119500.t1"; gene_id "Phchi.S1G119500"
Phchi.S1	AUGUSTUS	start_codon	7297504	7297506	.	-	0	transcript_id "Phchi.S1G119500.t1"; gene_id "Phchi.S1G119500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7887.t1 is derived from g5061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31764302	31765180	.	-	.	Phchi.S1G504600
Phchi.S1	AUGUSTUS	transcript	31764302	31765180	.	-	.	transcript_id "Phchi.S1G504600.t1"; gene_id "Phchi.S1G504600"
Phchi.S1	AUGUSTUS	stop_codon	31764299	31764301	.	-	0	transcript_id "Phchi.S1G504600.t1"; gene_id "Phchi.S1G504600"
Phchi.S1	AUGUSTUS	CDS	31764302	31765180	0.98	-	0	transcript_id "Phchi.S1G504600.t1"; gene_id "Phchi.S1G504600"
Phchi.S1	AUGUSTUS	exon	31764302	31765180	.	-	.	transcript_id "Phchi.S1G504600.t1"; gene_id "Phchi.S1G504600"
Phchi.S1	AUGUSTUS	start_codon	31765178	31765180	.	-	0	transcript_id "Phchi.S1G504600.t1"; gene_id "Phchi.S1G504600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10684.t1 is derived from g14734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1570924	1575785	.	-	.	Phchi.S4G026600
Phchi.S4	AUGUSTUS	transcript	1570924	1575785	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	stop_codon	1570921	1570923	.	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1570924	1570998	0.99	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1570924	1570998	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1570999	1571084	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1571085	1571236	1	-	2	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1571085	1571236	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1571237	1571335	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1571336	1571387	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1571336	1571387	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1571388	1571469	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1571470	1571559	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1571470	1571559	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1571560	1571648	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1571649	1571759	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1571649	1571759	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1571760	1571965	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1571966	1572031	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1571966	1572031	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1572032	1572300	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1572301	1572453	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1572301	1572453	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1572454	1572539	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1572540	1572671	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1572540	1572671	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1572672	1572785	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1572786	1572872	1	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1572786	1572872	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1572873	1572988	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1572989	1574272	0.44	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1572989	1574272	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1574273	1574409	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1574410	1575246	0.34	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1574410	1575246	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	intron	1575247	1575515	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	CDS	1575516	1575785	0.74	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	exon	1575516	1575785	.	-	.	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
Phchi.S4	AUGUSTUS	start_codon	1575783	1575785	.	-	0	transcript_id "Phchi.S4G026600.t1"; gene_id "Phchi.S4G026600"
# This transcript jg3218.t2 is derived from g387.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3218.t3 is derived from g387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3219.t1 is derived from g388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2303593	2304805	.	-	.	Phchi.S1G037800
Phchi.S1	AUGUSTUS	transcript	2303593	2304805	.	-	.	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	stop_codon	2303590	2303592	.	-	0	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	CDS	2303593	2303919	1	-	0	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	exon	2303593	2303919	.	-	.	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	intron	2303920	2304057	.	-	.	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	CDS	2304058	2304282	1	-	0	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	exon	2304058	2304282	.	-	.	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	intron	2304283	2304679	.	-	.	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	CDS	2304680	2304805	1	-	0	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	exon	2304680	2304805	.	-	.	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
Phchi.S1	AUGUSTUS	start_codon	2304803	2304805	.	-	0	transcript_id "Phchi.S1G037800.t1"; gene_id "Phchi.S1G037800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12944.t1 is derived from g11409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3263190	3264348	.	+	.	Phchi.S3G026300
Phchi.S3	AUGUSTUS	transcript	3263190	3264348	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	start_codon	3263190	3263192	.	+	0	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	CDS	3263190	3263450	0.86	+	0	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	exon	3263190	3263450	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	intron	3263451	3263697	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	CDS	3263698	3263776	0.99	+	0	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	exon	3263698	3263776	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	intron	3263777	3263917	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	CDS	3263918	3263970	0.38	+	2	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	exon	3263918	3263970	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	intron	3263971	3264249	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	CDS	3264250	3264348	0.49	+	0	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	exon	3264250	3264348	.	+	.	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
Phchi.S3	AUGUSTUS	stop_codon	3264349	3264351	.	+	0	transcript_id "Phchi.S3G026300.t1"; gene_id "Phchi.S3G026300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7198.t1 is derived from g4370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27608911	27611073	.	+	.	Phchi.S1G435700
Phchi.S1	AUGUSTUS	transcript	27608911	27611073	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	start_codon	27608911	27608913	.	+	0	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27608911	27608981	0.97	+	0	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27608911	27608981	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27608982	27609343	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609344	27609563	0.99	+	1	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609344	27609563	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27609564	27609657	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609658	27609797	1	+	0	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609658	27609797	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27609798	27609910	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609911	27610040	0.98	+	1	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609911	27610040	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610041	27610144	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610145	27610243	1	+	0	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610145	27610243	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610244	27610353	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610354	27610508	0.99	+	0	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610354	27610508	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610509	27610633	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610634	27610750	1	+	1	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610634	27610750	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610751	27610839	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610840	27610937	1	+	1	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610840	27610937	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610938	27611029	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27611030	27611073	1	+	2	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27611030	27611073	.	+	.	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	stop_codon	27611074	27611076	.	+	0	transcript_id "Phchi.S1G435700.t1"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	transcript	27609047	27611073	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	start_codon	27609047	27609049	.	+	0	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609047	27609126	0.59	+	0	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609047	27609126	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27609127	27609343	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609344	27609563	1	+	1	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609344	27609563	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27609564	27609657	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609658	27609797	1	+	0	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609658	27609797	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27609798	27609910	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27609911	27610040	0.99	+	1	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27609911	27610040	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610041	27610144	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610145	27610243	0.99	+	0	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610145	27610243	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610244	27610353	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610354	27610508	0.99	+	0	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610354	27610508	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610509	27610633	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610634	27610750	1	+	1	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610634	27610750	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610751	27610839	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27610840	27610937	1	+	1	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27610840	27610937	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	intron	27610938	27611029	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	CDS	27611030	27611073	1	+	2	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	exon	27611030	27611073	.	+	.	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
Phchi.S1	AUGUSTUS	stop_codon	27611074	27611076	.	+	0	transcript_id "Phchi.S1G435700.t2"; gene_id "Phchi.S1G435700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11243.t1 is derived from g15293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4984394	4986001	.	+	.	Phchi.S4G082500
Phchi.S4	AUGUSTUS	transcript	4984394	4986001	.	+	.	transcript_id "Phchi.S4G082500.t1"; gene_id "Phchi.S4G082500"
Phchi.S4	AUGUSTUS	start_codon	4984394	4984396	.	+	0	transcript_id "Phchi.S4G082500.t1"; gene_id "Phchi.S4G082500"
Phchi.S4	AUGUSTUS	CDS	4984394	4986001	1	+	0	transcript_id "Phchi.S4G082500.t1"; gene_id "Phchi.S4G082500"
Phchi.S4	AUGUSTUS	exon	4984394	4986001	.	+	.	transcript_id "Phchi.S4G082500.t1"; gene_id "Phchi.S4G082500"
Phchi.S4	AUGUSTUS	stop_codon	4986002	4986004	.	+	0	transcript_id "Phchi.S4G082500.t1"; gene_id "Phchi.S4G082500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6181.t1 is derived from g3352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21332897	21333973	.	+	.	Phchi.S1G334000
Phchi.S1	AUGUSTUS	transcript	21332897	21333973	.	+	.	transcript_id "Phchi.S1G334000.t1"; gene_id "Phchi.S1G334000"
Phchi.S1	AUGUSTUS	start_codon	21332897	21332899	.	+	0	transcript_id "Phchi.S1G334000.t1"; gene_id "Phchi.S1G334000"
Phchi.S1	AUGUSTUS	CDS	21332897	21333973	0.45	+	0	transcript_id "Phchi.S1G334000.t1"; gene_id "Phchi.S1G334000"
Phchi.S1	AUGUSTUS	exon	21332897	21333973	.	+	.	transcript_id "Phchi.S1G334000.t1"; gene_id "Phchi.S1G334000"
Phchi.S1	AUGUSTUS	stop_codon	21333974	21333976	.	+	0	transcript_id "Phchi.S1G334000.t1"; gene_id "Phchi.S1G334000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg543.t1 is derived from g10325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3990525	3992392	.	-	.	Phchi.S6G050200
Phchi.S6	AUGUSTUS	transcript	3990525	3992392	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	stop_codon	3990522	3990524	.	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3990525	3990650	1	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3990525	3990650	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3990651	3990760	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3990761	3990847	1	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3990761	3990847	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3990848	3990940	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3990941	3991175	1	-	1	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3990941	3991175	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3991176	3991271	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3991272	3991351	1	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3991272	3991351	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3991352	3991423	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3991424	3991582	1	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3991424	3991582	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3991583	3991670	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3991671	3991731	0.96	-	1	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3991671	3991731	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3991732	3991848	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3991849	3991987	0.98	-	2	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3991849	3991987	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3991988	3992083	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3992084	3992164	1	-	2	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3992084	3992164	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	intron	3992165	3992319	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	CDS	3992320	3992392	1	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	exon	3992320	3992392	.	-	.	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
Phchi.S6	AUGUSTUS	start_codon	3992390	3992392	.	-	0	transcript_id "Phchi.S6G050200.t1"; gene_id "Phchi.S6G050200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8958.t1 is derived from g6133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38845713	38846033	.	+	.	Phchi.S1G611700
Phchi.S1	AUGUSTUS	transcript	38845713	38846033	.	+	.	transcript_id "Phchi.S1G611700.t1"; gene_id "Phchi.S1G611700"
Phchi.S1	AUGUSTUS	start_codon	38845713	38845715	.	+	0	transcript_id "Phchi.S1G611700.t1"; gene_id "Phchi.S1G611700"
Phchi.S1	AUGUSTUS	CDS	38845713	38846033	0.7	+	0	transcript_id "Phchi.S1G611700.t1"; gene_id "Phchi.S1G611700"
Phchi.S1	AUGUSTUS	exon	38845713	38846033	.	+	.	transcript_id "Phchi.S1G611700.t1"; gene_id "Phchi.S1G611700"
Phchi.S1	AUGUSTUS	stop_codon	38846034	38846036	.	+	0	transcript_id "Phchi.S1G611700.t1"; gene_id "Phchi.S1G611700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12948.t1 is derived from g11413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3280152	3281776	.	-	.	Phchi.S3G026700
Phchi.S3	AUGUSTUS	transcript	3280152	3281776	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	stop_codon	3280149	3280151	.	-	0	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	CDS	3280152	3280175	0.5	-	0	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	exon	3280152	3280175	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	intron	3280176	3280297	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	CDS	3280298	3280432	0.58	-	0	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	exon	3280298	3280432	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	intron	3280433	3280543	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	CDS	3280544	3281566	0.61	-	0	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	exon	3280544	3281566	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	intron	3281567	3281647	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	CDS	3281648	3281776	0.55	-	0	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	exon	3281648	3281776	.	-	.	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
Phchi.S3	AUGUSTUS	start_codon	3281774	3281776	.	-	0	transcript_id "Phchi.S3G026700.t1"; gene_id "Phchi.S3G026700"
# This transcript jg12299.t2 is derived from g7975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12300.t1 is derived from g7976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9626510	9632215	.	-	.	Phchi.S2G038000
Phchi.S2	AUGUSTUS	transcript	9626510	9632215	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	stop_codon	9626507	9626509	.	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9626510	9626920	0.99	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9626510	9626920	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9626921	9627009	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9627010	9627051	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9627010	9627051	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9627052	9627137	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9627138	9627191	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9627138	9627191	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9627192	9627292	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9627293	9627356	1	-	1	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9627293	9627356	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9627357	9627442	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9627443	9627537	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9627443	9627537	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9627538	9627628	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9627629	9627736	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9627629	9627736	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9627737	9627819	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9627820	9627893	1	-	2	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9627820	9627893	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9627894	9628007	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9628008	9628080	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9628008	9628080	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9628081	9628191	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9628192	9628239	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9628192	9628239	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9628240	9628332	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9628333	9628516	1	-	1	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9628333	9628516	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9628517	9628696	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9628697	9628875	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9628697	9628875	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9628876	9629051	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9629052	9629144	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9629052	9629144	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9629145	9629224	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9629225	9629338	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9629225	9629338	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9629339	9629485	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9629486	9629560	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9629486	9629560	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9629561	9629676	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9629677	9629940	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9629677	9629940	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9629941	9630046	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9630047	9630160	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9630047	9630160	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9630161	9630313	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9630314	9630370	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9630314	9630370	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9630371	9630609	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9630610	9630766	1	-	1	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9630610	9630766	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9630767	9630897	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9630898	9630962	0.99	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9630898	9630962	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9630963	9631065	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9631066	9631149	0.98	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9631066	9631149	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9631150	9631261	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9631262	9631304	1	-	1	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9631262	9631304	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9631305	9631451	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9631452	9631558	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9631452	9631558	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9631559	9631689	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9631690	9631758	1	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9631690	9631758	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	intron	9631759	9632029	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	CDS	9632030	9632215	0.65	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	exon	9632030	9632215	.	-	.	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
Phchi.S2	AUGUSTUS	start_codon	9632213	9632215	.	-	0	transcript_id "Phchi.S2G038000.t1"; gene_id "Phchi.S2G038000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1903.t1 is derived from g8823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3784247	3785805	.	-	.	Phchi.S5G051200
Phchi.S5	AUGUSTUS	transcript	3784247	3785805	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	stop_codon	3784244	3784246	.	-	0	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	CDS	3784247	3785032	0.89	-	0	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	exon	3784247	3785032	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	intron	3785033	3785130	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	CDS	3785131	3785206	1	-	1	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	exon	3785131	3785206	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	intron	3785207	3785332	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	CDS	3785333	3785442	1	-	0	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	exon	3785333	3785442	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	intron	3785443	3785526	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	CDS	3785527	3785627	1	-	2	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	exon	3785527	3785627	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	intron	3785628	3785702	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	CDS	3785703	3785805	0.98	-	0	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	exon	3785703	3785805	.	-	.	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
Phchi.S5	AUGUSTUS	start_codon	3785803	3785805	.	-	0	transcript_id "Phchi.S5G051200.t1"; gene_id "Phchi.S5G051200"
# This transcript jg14042.t2 is derived from g12509.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14043.t1 is derived from g12510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10432344	10436168	.	+	.	Phchi.S3G136200
Phchi.S3	AUGUSTUS	transcript	10432344	10436168	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	start_codon	10432344	10432346	.	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10432344	10432527	0.65	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10432344	10432527	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10432528	10432682	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10432683	10432691	0.72	+	2	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10432683	10432691	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10432692	10432779	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10432780	10434068	0.62	+	2	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10432780	10434068	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10434069	10434186	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10434187	10434354	0.59	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10434187	10434354	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10434355	10434462	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10434463	10434537	0.4	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10434463	10434537	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10434538	10434698	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10434699	10435196	0.6	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10434699	10435196	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10435197	10435308	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10435309	10435506	1	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10435309	10435506	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10435507	10435597	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10435598	10435892	1	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10435598	10435892	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	intron	10435893	10435998	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	CDS	10435999	10436168	0.81	+	2	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	exon	10435999	10436168	.	+	.	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
Phchi.S3	AUGUSTUS	stop_codon	10436169	10436171	.	+	0	transcript_id "Phchi.S3G136200.t1"; gene_id "Phchi.S3G136200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg647.t1 is derived from g10429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4576071	4576373	.	-	.	Phchi.S6G060600
Phchi.S6	AUGUSTUS	transcript	4576071	4576373	.	-	.	transcript_id "Phchi.S6G060600.t1"; gene_id "Phchi.S6G060600"
Phchi.S6	AUGUSTUS	stop_codon	4576068	4576070	.	-	0	transcript_id "Phchi.S6G060600.t1"; gene_id "Phchi.S6G060600"
Phchi.S6	AUGUSTUS	CDS	4576071	4576373	0.75	-	0	transcript_id "Phchi.S6G060600.t1"; gene_id "Phchi.S6G060600"
Phchi.S6	AUGUSTUS	exon	4576071	4576373	.	-	.	transcript_id "Phchi.S6G060600.t1"; gene_id "Phchi.S6G060600"
Phchi.S6	AUGUSTUS	start_codon	4576371	4576373	.	-	0	transcript_id "Phchi.S6G060600.t1"; gene_id "Phchi.S6G060600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11305.t1 is derived from g15355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5305671	5306717	.	+	.	Phchi.S4G088700
Phchi.S4	AUGUSTUS	transcript	5305671	5306717	.	+	.	transcript_id "Phchi.S4G088700.t1"; gene_id "Phchi.S4G088700"
Phchi.S4	AUGUSTUS	start_codon	5305671	5305673	.	+	0	transcript_id "Phchi.S4G088700.t1"; gene_id "Phchi.S4G088700"
Phchi.S4	AUGUSTUS	CDS	5305671	5306717	0.93	+	0	transcript_id "Phchi.S4G088700.t1"; gene_id "Phchi.S4G088700"
Phchi.S4	AUGUSTUS	exon	5305671	5306717	.	+	.	transcript_id "Phchi.S4G088700.t1"; gene_id "Phchi.S4G088700"
Phchi.S4	AUGUSTUS	stop_codon	5306718	5306720	.	+	0	transcript_id "Phchi.S4G088700.t1"; gene_id "Phchi.S4G088700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1230.t1 is derived from g11013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8515863	8516876	.	+	.	Phchi.S6G118900
Phchi.S6	AUGUSTUS	transcript	8515863	8516876	.	+	.	transcript_id "Phchi.S6G118900.t1"; gene_id "Phchi.S6G118900"
Phchi.S6	AUGUSTUS	start_codon	8515863	8515865	.	+	0	transcript_id "Phchi.S6G118900.t1"; gene_id "Phchi.S6G118900"
Phchi.S6	AUGUSTUS	CDS	8515863	8516876	0.66	+	0	transcript_id "Phchi.S6G118900.t1"; gene_id "Phchi.S6G118900"
Phchi.S6	AUGUSTUS	exon	8515863	8516876	.	+	.	transcript_id "Phchi.S6G118900.t1"; gene_id "Phchi.S6G118900"
Phchi.S6	AUGUSTUS	stop_codon	8516877	8516879	.	+	0	transcript_id "Phchi.S6G118900.t1"; gene_id "Phchi.S6G118900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12240.t1 is derived from g7916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6936016	6937716	.	+	.	Phchi.S2G032000
Phchi.S2	AUGUSTUS	transcript	6936016	6937716	.	+	.	transcript_id "Phchi.S2G032000.t1"; gene_id "Phchi.S2G032000"
Phchi.S2	AUGUSTUS	start_codon	6936016	6936018	.	+	0	transcript_id "Phchi.S2G032000.t1"; gene_id "Phchi.S2G032000"
Phchi.S2	AUGUSTUS	CDS	6936016	6937716	0.98	+	0	transcript_id "Phchi.S2G032000.t1"; gene_id "Phchi.S2G032000"
Phchi.S2	AUGUSTUS	exon	6936016	6937716	.	+	.	transcript_id "Phchi.S2G032000.t1"; gene_id "Phchi.S2G032000"
Phchi.S2	AUGUSTUS	stop_codon	6937717	6937719	.	+	0	transcript_id "Phchi.S2G032000.t1"; gene_id "Phchi.S2G032000"
# This transcript jg10243.t2 is derived from g7419.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10244.t1 is derived from g7420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46571902	46573523	.	-	.	Phchi.S1G740300
Phchi.S1	AUGUSTUS	transcript	46571902	46573523	.	-	.	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	stop_codon	46571899	46571901	.	-	0	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	CDS	46571902	46572567	1	-	0	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	exon	46571902	46572567	.	-	.	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	intron	46572568	46572833	.	-	.	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	CDS	46572834	46573523	0.56	-	0	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	exon	46572834	46573523	.	-	.	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
Phchi.S1	AUGUSTUS	start_codon	46573521	46573523	.	-	0	transcript_id "Phchi.S1G740300.t1"; gene_id "Phchi.S1G740300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1914.t1 is derived from g8834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3837430	3838582	.	-	.	Phchi.S5G052300
Phchi.S5	AUGUSTUS	transcript	3837430	3838582	.	-	.	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	stop_codon	3837427	3837429	.	-	0	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	CDS	3837430	3837906	0.62	-	0	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	exon	3837430	3837906	.	-	.	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	intron	3837907	3837992	.	-	.	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	CDS	3837993	3838256	1	-	0	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	exon	3837993	3838256	.	-	.	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	intron	3838257	3838345	.	-	.	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	CDS	3838346	3838582	1	-	0	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	exon	3838346	3838582	.	-	.	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
Phchi.S5	AUGUSTUS	start_codon	3838580	3838582	.	-	0	transcript_id "Phchi.S5G052300.t1"; gene_id "Phchi.S5G052300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7633.t1 is derived from g4807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30330470	30331714	.	-	.	Phchi.S1G479200
Phchi.S1	AUGUSTUS	transcript	30330470	30331714	.	-	.	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	stop_codon	30330467	30330469	.	-	0	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	CDS	30330470	30330802	0.95	-	0	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	exon	30330470	30330802	.	-	.	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	intron	30330803	30330914	.	-	.	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	CDS	30330915	30331190	0.55	-	0	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	exon	30330915	30331190	.	-	.	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	intron	30331191	30331285	.	-	.	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	CDS	30331286	30331714	0.35	-	0	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	exon	30331286	30331714	.	-	.	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
Phchi.S1	AUGUSTUS	start_codon	30331712	30331714	.	-	0	transcript_id "Phchi.S1G479200.t1"; gene_id "Phchi.S1G479200"
# This transcript jg5350.t2 is derived from g2520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5350.t3 is derived from g2520.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5351.t1 is derived from g2521.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16433369	16435489	.	-	.	Phchi.S1G251000
Phchi.S1	AUGUSTUS	transcript	16433369	16435489	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	stop_codon	16433366	16433368	.	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433369	16433376	1	-	2	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433369	16433376	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433377	16433519	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433520	16433608	0.97	-	1	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433520	16433608	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433609	16433682	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433683	16433792	1	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433683	16433792	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433793	16433877	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433878	16433943	1	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433878	16433943	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433944	16434048	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16434049	16434102	1	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16434049	16434102	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16434103	16434696	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16434697	16434771	1	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16434697	16434771	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16434772	16434988	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16434989	16435041	0.94	-	2	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16434989	16435041	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16435042	16435171	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435172	16435231	0.93	-	2	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435172	16435231	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16435232	16435328	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435329	16435359	0.65	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435329	16435359	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16435360	16435435	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435436	16435489	0.35	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435436	16435489	.	-	.	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	start_codon	16435487	16435489	.	-	0	transcript_id "Phchi.S1G251000.t1"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	transcript	16433369	16435489	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	stop_codon	16433366	16433368	.	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433369	16433376	1	-	2	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433369	16433376	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433377	16433519	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433520	16433608	1	-	1	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433520	16433608	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433609	16433682	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433683	16433792	1	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433683	16433792	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433793	16433877	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16433878	16433943	1	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16433878	16433943	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16433944	16434048	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16434049	16434102	1	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16434049	16434102	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16434103	16434696	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16434697	16434771	1	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16434697	16434771	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16434772	16435009	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435010	16435041	0.88	-	2	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435010	16435041	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16435042	16435171	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435172	16435231	0.88	-	2	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435172	16435231	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16435232	16435328	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435329	16435359	0.62	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435329	16435359	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	intron	16435360	16435435	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	CDS	16435436	16435489	0.4	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	exon	16435436	16435489	.	-	.	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
Phchi.S1	AUGUSTUS	start_codon	16435487	16435489	.	-	0	transcript_id "Phchi.S1G251000.t2"; gene_id "Phchi.S1G251000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11523.t1 is derived from g15573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6895143	6896686	.	+	.	Phchi.S4G110500
Phchi.S4	AUGUSTUS	transcript	6895143	6896686	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	start_codon	6895143	6895145	.	+	0	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	CDS	6895143	6895958	1	+	0	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	exon	6895143	6895958	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	intron	6895959	6896088	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	CDS	6896089	6896307	1	+	0	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	exon	6896089	6896307	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	intron	6896308	6896382	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	CDS	6896383	6896470	1	+	0	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	exon	6896383	6896470	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	intron	6896471	6896591	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	CDS	6896592	6896686	1	+	2	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	exon	6896592	6896686	.	+	.	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
Phchi.S4	AUGUSTUS	stop_codon	6896687	6896689	.	+	0	transcript_id "Phchi.S4G110500.t1"; gene_id "Phchi.S4G110500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5799.t1 is derived from g2969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18998533	18999813	.	-	.	Phchi.S1G295800
Phchi.S1	AUGUSTUS	transcript	18998533	18999813	.	-	.	transcript_id "Phchi.S1G295800.t1"; gene_id "Phchi.S1G295800"
Phchi.S1	AUGUSTUS	stop_codon	18998530	18998532	.	-	0	transcript_id "Phchi.S1G295800.t1"; gene_id "Phchi.S1G295800"
Phchi.S1	AUGUSTUS	CDS	18998533	18999813	0.78	-	0	transcript_id "Phchi.S1G295800.t1"; gene_id "Phchi.S1G295800"
Phchi.S1	AUGUSTUS	exon	18998533	18999813	.	-	.	transcript_id "Phchi.S1G295800.t1"; gene_id "Phchi.S1G295800"
Phchi.S1	AUGUSTUS	start_codon	18999811	18999813	.	-	0	transcript_id "Phchi.S1G295800.t1"; gene_id "Phchi.S1G295800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14611.t1 is derived from g13079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13746059	13751596	.	+	.	Phchi.S3G193000
Phchi.S3	AUGUSTUS	transcript	13746059	13751596	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	start_codon	13746059	13746061	.	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13746059	13746308	0.47	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13746059	13746308	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13746309	13746577	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13746578	13746670	0.59	+	2	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13746578	13746670	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13746671	13746758	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13746759	13746850	1	+	2	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13746759	13746850	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13746851	13747093	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13747094	13748910	0.63	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13747094	13748910	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13748911	13749059	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13749060	13749239	0.62	+	1	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13749060	13749239	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13749240	13749323	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13749324	13749501	1	+	1	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13749324	13749501	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13749502	13749593	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13749594	13749719	0.9	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13749594	13749719	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13749720	13749832	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13749833	13750282	0.91	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13749833	13750282	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13750283	13750367	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13750368	13751396	0.96	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13750368	13751396	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	intron	13751397	13751497	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	CDS	13751498	13751596	0.98	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	exon	13751498	13751596	.	+	.	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
Phchi.S3	AUGUSTUS	stop_codon	13751597	13751599	.	+	0	transcript_id "Phchi.S3G193000.t1"; gene_id "Phchi.S3G193000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5679.t1 is derived from g2849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18270564	18277927	.	+	.	Phchi.S1G283800
Phchi.S1	AUGUSTUS	transcript	18270564	18277927	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	start_codon	18270564	18270566	.	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18270564	18270941	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18270564	18270941	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18270942	18271120	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18271121	18271274	0.67	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18271121	18271274	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18271275	18271363	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18271364	18272574	0.31	+	2	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18271364	18272574	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18272575	18272647	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18272648	18272754	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18272648	18272754	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18272755	18272955	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18272956	18273043	1	+	1	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18272956	18273043	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18273044	18273125	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18273126	18273212	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18273126	18273212	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18273213	18273329	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18273330	18273422	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18273330	18273422	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18273423	18273570	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18273571	18273654	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18273571	18273654	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18273655	18273775	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18273776	18273979	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18273776	18273979	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18273980	18274080	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18274081	18274323	0.99	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18274081	18274323	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18274324	18274427	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18274428	18276116	0.91	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18274428	18276116	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18276117	18276247	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18276248	18276793	0.99	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18276248	18276793	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18276794	18276939	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18276940	18277170	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18276940	18277170	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	intron	18277171	18277270	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	CDS	18277271	18277927	1	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	exon	18277271	18277927	.	+	.	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
Phchi.S1	AUGUSTUS	stop_codon	18277928	18277930	.	+	0	transcript_id "Phchi.S1G283800.t1"; gene_id "Phchi.S1G283800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6352.t1 is derived from g3524.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22459694	22460551	.	+	.	Phchi.S1G351100
Phchi.S1	AUGUSTUS	transcript	22459694	22460551	.	+	.	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	start_codon	22459694	22459696	.	+	0	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	CDS	22459694	22459870	1	+	0	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	exon	22459694	22459870	.	+	.	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	intron	22459871	22460066	.	+	.	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	CDS	22460067	22460452	1	+	0	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	exon	22460067	22460452	.	+	.	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	intron	22460453	22460535	.	+	.	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	CDS	22460536	22460551	1	+	1	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	exon	22460536	22460551	.	+	.	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	stop_codon	22460552	22460554	.	+	0	transcript_id "Phchi.S1G351100.t1"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	transcript	22459694	22460551	.	+	.	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	start_codon	22459694	22459696	.	+	0	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	CDS	22459694	22459870	0.81	+	0	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	exon	22459694	22459870	.	+	.	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	intron	22459871	22460069	.	+	.	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	CDS	22460070	22460452	0.81	+	0	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	exon	22460070	22460452	.	+	.	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	intron	22460453	22460535	.	+	.	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	CDS	22460536	22460551	1	+	1	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	exon	22460536	22460551	.	+	.	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
Phchi.S1	AUGUSTUS	stop_codon	22460552	22460554	.	+	0	transcript_id "Phchi.S1G351100.t2"; gene_id "Phchi.S1G351100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5915.t1 is derived from g3086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19857864	19858515	.	+	.	Phchi.S1G307400
Phchi.S1	AUGUSTUS	transcript	19857864	19858515	.	+	.	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	start_codon	19857864	19857866	.	+	0	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	CDS	19857864	19857960	0.83	+	0	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	exon	19857864	19857960	.	+	.	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	intron	19857961	19858108	.	+	.	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	CDS	19858109	19858287	1	+	2	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	exon	19858109	19858287	.	+	.	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	intron	19858288	19858491	.	+	.	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	CDS	19858492	19858515	1	+	0	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	exon	19858492	19858515	.	+	.	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
Phchi.S1	AUGUSTUS	stop_codon	19858516	19858518	.	+	0	transcript_id "Phchi.S1G307400.t1"; gene_id "Phchi.S1G307400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10919.t1 is derived from g14969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2963569	2964690	.	+	.	Phchi.S4G050100
Phchi.S4	AUGUSTUS	transcript	2963569	2964690	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	start_codon	2963569	2963571	.	+	0	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	CDS	2963569	2963699	0.83	+	0	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	exon	2963569	2963699	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	intron	2963700	2963902	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	CDS	2963903	2963978	1	+	1	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	exon	2963903	2963978	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	intron	2963979	2964059	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	CDS	2964060	2964126	1	+	0	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	exon	2964060	2964126	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	intron	2964127	2964264	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	CDS	2964265	2964382	0.99	+	2	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	exon	2964265	2964382	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	intron	2964383	2964467	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	CDS	2964468	2964507	0.92	+	1	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	exon	2964468	2964507	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	intron	2964508	2964678	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	CDS	2964679	2964690	0.71	+	0	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	exon	2964679	2964690	.	+	.	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
Phchi.S4	AUGUSTUS	stop_codon	2964691	2964693	.	+	0	transcript_id "Phchi.S4G050100.t1"; gene_id "Phchi.S4G050100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1992.t1 is derived from g8912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4339559	4339951	.	-	.	Phchi.S5G060100
Phchi.S5	AUGUSTUS	transcript	4339559	4339951	.	-	.	transcript_id "Phchi.S5G060100.t1"; gene_id "Phchi.S5G060100"
Phchi.S5	AUGUSTUS	stop_codon	4339556	4339558	.	-	0	transcript_id "Phchi.S5G060100.t1"; gene_id "Phchi.S5G060100"
Phchi.S5	AUGUSTUS	CDS	4339559	4339951	0.58	-	0	transcript_id "Phchi.S5G060100.t1"; gene_id "Phchi.S5G060100"
Phchi.S5	AUGUSTUS	exon	4339559	4339951	.	-	.	transcript_id "Phchi.S5G060100.t1"; gene_id "Phchi.S5G060100"
Phchi.S5	AUGUSTUS	start_codon	4339949	4339951	.	-	0	transcript_id "Phchi.S5G060100.t1"; gene_id "Phchi.S5G060100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9578.t1 is derived from g6754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42742677	42747317	.	-	.	Phchi.S1G673700
Phchi.S1	AUGUSTUS	transcript	42742677	42747317	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	stop_codon	42742674	42742676	.	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42742677	42742692	1	-	1	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42742677	42742692	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42742693	42742783	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42742784	42743416	0.82	-	1	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42742784	42743416	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42743417	42743553	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42743554	42743560	0.98	-	2	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42743554	42743560	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42743561	42743650	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42743651	42743723	0.98	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42743651	42743723	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42743724	42743811	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42743812	42743828	0.41	-	2	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42743812	42743828	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42743829	42743989	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42743990	42744037	1	-	2	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42743990	42744037	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42744038	42744267	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42744268	42744463	1	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42744268	42744463	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42744464	42744681	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42744682	42744866	1	-	2	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42744682	42744866	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42744867	42744984	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42744985	42745072	1	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42744985	42745072	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42745073	42745164	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42745165	42745302	1	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42745165	42745302	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42745303	42745381	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42745382	42745558	0.42	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42745382	42745558	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42745559	42745788	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42745789	42745860	0.33	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42745789	42745860	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	intron	42745861	42746483	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	CDS	42746484	42747317	0.36	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	exon	42746484	42747317	.	-	.	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
Phchi.S1	AUGUSTUS	start_codon	42747315	42747317	.	-	0	transcript_id "Phchi.S1G673700.t1"; gene_id "Phchi.S1G673700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2093.t1 is derived from g9013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4839690	4840424	.	-	.	Phchi.S5G070200
Phchi.S5	AUGUSTUS	transcript	4839690	4840424	.	-	.	transcript_id "Phchi.S5G070200.t1"; gene_id "Phchi.S5G070200"
Phchi.S5	AUGUSTUS	stop_codon	4839687	4839689	.	-	0	transcript_id "Phchi.S5G070200.t1"; gene_id "Phchi.S5G070200"
Phchi.S5	AUGUSTUS	CDS	4839690	4840424	1	-	0	transcript_id "Phchi.S5G070200.t1"; gene_id "Phchi.S5G070200"
Phchi.S5	AUGUSTUS	exon	4839690	4840424	.	-	.	transcript_id "Phchi.S5G070200.t1"; gene_id "Phchi.S5G070200"
Phchi.S5	AUGUSTUS	start_codon	4840422	4840424	.	-	0	transcript_id "Phchi.S5G070200.t1"; gene_id "Phchi.S5G070200"
# This transcript jg12521.t2 is derived from g8198.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12522.t1 is derived from g8199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32807728	32814862	.	+	.	Phchi.S2G060200
Phchi.S2	AUGUSTUS	transcript	32807728	32814862	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	start_codon	32807728	32807730	.	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32807728	32807829	0.87	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32807728	32807829	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32807830	32807938	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32807939	32808004	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32807939	32808004	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32808005	32808214	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32808215	32808301	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32808215	32808301	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32808302	32808431	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32808432	32808488	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32808432	32808488	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32808489	32808579	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32808580	32808644	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32808580	32808644	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32808645	32808762	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32808763	32808944	1	+	1	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32808763	32808944	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32808945	32809151	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32809152	32809213	1	+	2	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32809152	32809213	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32809214	32809379	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32809380	32809463	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32809380	32809463	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32809464	32809559	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32809560	32809716	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32809560	32809716	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32809717	32809865	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32809866	32809981	1	+	2	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32809866	32809981	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32809982	32810213	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32810214	32810342	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32810214	32810342	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32810343	32810426	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32810427	32810498	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32810427	32810498	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32810499	32810645	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32810646	32810741	0.99	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32810646	32810741	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32810742	32810846	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32810847	32810930	0.83	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32810847	32810930	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32810931	32811065	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32811066	32811194	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32811066	32811194	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32811195	32811393	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32811394	32811585	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32811394	32811585	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32811586	32811713	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32811714	32811920	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32811714	32811920	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32811921	32812012	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32812013	32812126	0.71	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32812013	32812126	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32812127	32812228	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32812229	32812476	0.73	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32812229	32812476	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32812477	32812577	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32812578	32812662	1	+	1	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32812578	32812662	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32812663	32812812	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32812813	32813061	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32812813	32813061	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32813062	32813143	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32813144	32813374	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32813144	32813374	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32813375	32813470	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32813471	32813562	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32813471	32813562	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32813563	32813732	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32813733	32813964	1	+	1	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32813733	32813964	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32813965	32814097	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32814098	32814179	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32814098	32814179	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32814180	32814389	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32814390	32814460	1	+	2	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32814390	32814460	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32814461	32814550	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32814551	32814624	1	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32814551	32814624	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	intron	32814625	32814759	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	CDS	32814760	32814862	1	+	1	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	exon	32814760	32814862	.	+	.	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
Phchi.S2	AUGUSTUS	stop_codon	32814863	32814865	.	+	0	transcript_id "Phchi.S2G060200.t1"; gene_id "Phchi.S2G060200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9750.t1 is derived from g6926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43498700	43499855	.	-	.	Phchi.S1G690900
Phchi.S1	AUGUSTUS	transcript	43498700	43499855	.	-	.	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	stop_codon	43498697	43498699	.	-	0	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	CDS	43498700	43498734	0.66	-	2	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	exon	43498700	43498734	.	-	.	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	intron	43498735	43498816	.	-	.	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	CDS	43498817	43499855	0.79	-	0	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	exon	43498817	43499855	.	-	.	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
Phchi.S1	AUGUSTUS	start_codon	43499853	43499855	.	-	0	transcript_id "Phchi.S1G690900.t1"; gene_id "Phchi.S1G690900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg400.t1 is derived from g10182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2887972	2888749	.	+	.	Phchi.S6G035900
Phchi.S6	AUGUSTUS	transcript	2887972	2888749	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	start_codon	2887972	2887974	.	+	0	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	CDS	2887972	2888038	1	+	0	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	exon	2887972	2888038	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	intron	2888039	2888139	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	CDS	2888140	2888209	1	+	2	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	exon	2888140	2888209	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	intron	2888210	2888291	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	CDS	2888292	2888401	1	+	1	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	exon	2888292	2888401	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	intron	2888402	2888476	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	CDS	2888477	2888591	1	+	2	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	exon	2888477	2888591	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	intron	2888592	2888670	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	CDS	2888671	2888749	0.96	+	1	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	exon	2888671	2888749	.	+	.	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
Phchi.S6	AUGUSTUS	stop_codon	2888750	2888752	.	+	0	transcript_id "Phchi.S6G035900.t1"; gene_id "Phchi.S6G035900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5377.t1 is derived from g2547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16579125	16582368	.	+	.	Phchi.S1G253600
Phchi.S1	AUGUSTUS	transcript	16579125	16582368	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	start_codon	16579125	16579127	.	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16579125	16579408	0.94	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16579125	16579408	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16579409	16579498	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16579499	16579664	1	+	1	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16579499	16579664	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16579665	16579750	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16579751	16579849	0.89	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16579751	16579849	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16579850	16580079	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16580080	16580263	0.98	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16580080	16580263	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16580264	16580350	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16580351	16580556	1	+	2	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16580351	16580556	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16580557	16580637	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16580638	16580912	1	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16580638	16580912	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16580913	16581026	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16581027	16581220	1	+	1	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16581027	16581220	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16581221	16581345	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16581346	16581641	0.96	+	2	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16581346	16581641	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16581642	16581753	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16581754	16581800	0.99	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16581754	16581800	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16581801	16581908	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16581909	16581930	1	+	1	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16581909	16581930	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16581931	16582029	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16582030	16582098	1	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16582030	16582098	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16582099	16582182	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16582183	16582221	1	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16582183	16582221	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	intron	16582222	16582311	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	CDS	16582312	16582368	1	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	exon	16582312	16582368	.	+	.	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
Phchi.S1	AUGUSTUS	stop_codon	16582369	16582371	.	+	0	transcript_id "Phchi.S1G253600.t1"; gene_id "Phchi.S1G253600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2227.t1 is derived from g9147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5539507	5540919	.	+	.	Phchi.S5G083600
Phchi.S5	AUGUSTUS	transcript	5539507	5540919	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	start_codon	5539507	5539509	.	+	0	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5539507	5539694	0.44	+	0	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5539507	5539694	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	intron	5539695	5539791	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5539792	5539944	1	+	1	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5539792	5539944	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	intron	5539945	5540031	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5540032	5540114	1	+	1	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5540032	5540114	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	intron	5540115	5540210	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5540211	5540310	0.97	+	2	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5540211	5540310	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	intron	5540311	5540418	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5540419	5540532	0.97	+	1	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5540419	5540532	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	intron	5540533	5540618	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5540619	5540761	1	+	1	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5540619	5540761	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	intron	5540762	5540836	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	CDS	5540837	5540919	1	+	2	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	exon	5540837	5540919	.	+	.	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
Phchi.S5	AUGUSTUS	stop_codon	5540920	5540922	.	+	0	transcript_id "Phchi.S5G083600.t1"; gene_id "Phchi.S5G083600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6867.t1 is derived from g4039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25671264	25678169	.	-	.	Phchi.S1G402600
Phchi.S1	AUGUSTUS	transcript	25671264	25678169	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	stop_codon	25671261	25671263	.	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25671264	25671530	0.55	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25671264	25671530	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25671531	25671632	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25671633	25671887	0.93	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25671633	25671887	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25671888	25672006	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25672007	25672178	0.98	-	1	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25672007	25672178	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25672179	25672260	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25672261	25672488	1	-	1	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25672261	25672488	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25672489	25672607	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25672608	25672741	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25672608	25672741	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25672742	25672838	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25672839	25672922	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25672839	25672922	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25672923	25673021	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25673022	25673312	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25673022	25673312	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25673313	25673409	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25673410	25673742	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25673410	25673742	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25673743	25673876	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25673877	25674031	1	-	2	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25673877	25674031	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25674032	25674169	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25674170	25674295	1	-	2	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25674170	25674295	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25674296	25674382	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25674383	25674545	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25674383	25674545	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25674546	25674625	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25674626	25674726	1	-	2	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25674626	25674726	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25674727	25674809	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25674810	25674970	1	-	1	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25674810	25674970	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25674971	25675049	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25675050	25675366	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25675050	25675366	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25675367	25675488	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25675489	25675770	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25675489	25675770	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25675771	25675855	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25675856	25676157	1	-	2	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25675856	25676157	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25676158	25676246	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25676247	25676337	0.98	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25676247	25676337	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25676338	25676445	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25676446	25676499	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25676446	25676499	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25676500	25676590	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25676591	25676667	1	-	2	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25676591	25676667	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25676668	25676828	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25676829	25676988	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25676829	25676988	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25676989	25677122	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25677123	25677207	0.99	-	1	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25677123	25677207	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25677208	25677297	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25677298	25677386	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25677298	25677386	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25677387	25677472	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25677473	25677593	1	-	1	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25677473	25677593	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	intron	25677594	25677759	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	CDS	25677760	25678169	1	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	exon	25677760	25678169	.	-	.	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
Phchi.S1	AUGUSTUS	start_codon	25678167	25678169	.	-	0	transcript_id "Phchi.S1G402600.t1"; gene_id "Phchi.S1G402600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5496.t1 is derived from g2666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17123420	17124128	.	-	.	Phchi.S1G265500
Phchi.S1	AUGUSTUS	transcript	17123420	17124128	.	-	.	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	stop_codon	17123417	17123419	.	-	0	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	CDS	17123420	17123495	0.97	-	1	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	exon	17123420	17123495	.	-	.	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	intron	17123496	17123783	.	-	.	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	CDS	17123784	17123812	0.98	-	0	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	exon	17123784	17123812	.	-	.	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	intron	17123813	17123981	.	-	.	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	CDS	17123982	17124128	0.58	-	0	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	exon	17123982	17124128	.	-	.	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
Phchi.S1	AUGUSTUS	start_codon	17124126	17124128	.	-	0	transcript_id "Phchi.S1G265500.t1"; gene_id "Phchi.S1G265500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5940.t1 is derived from g3111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19957604	19957903	.	-	.	Phchi.S1G309900
Phchi.S1	AUGUSTUS	transcript	19957604	19957903	.	-	.	transcript_id "Phchi.S1G309900.t1"; gene_id "Phchi.S1G309900"
Phchi.S1	AUGUSTUS	stop_codon	19957601	19957603	.	-	0	transcript_id "Phchi.S1G309900.t1"; gene_id "Phchi.S1G309900"
Phchi.S1	AUGUSTUS	CDS	19957604	19957903	0.62	-	0	transcript_id "Phchi.S1G309900.t1"; gene_id "Phchi.S1G309900"
Phchi.S1	AUGUSTUS	exon	19957604	19957903	.	-	.	transcript_id "Phchi.S1G309900.t1"; gene_id "Phchi.S1G309900"
Phchi.S1	AUGUSTUS	start_codon	19957901	19957903	.	-	0	transcript_id "Phchi.S1G309900.t1"; gene_id "Phchi.S1G309900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1145.t1 is derived from g10928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7989153	7989647	.	-	.	Phchi.S6G110400
Phchi.S6	AUGUSTUS	transcript	7989153	7989647	.	-	.	transcript_id "Phchi.S6G110400.t1"; gene_id "Phchi.S6G110400"
Phchi.S6	AUGUSTUS	stop_codon	7989150	7989152	.	-	0	transcript_id "Phchi.S6G110400.t1"; gene_id "Phchi.S6G110400"
Phchi.S6	AUGUSTUS	CDS	7989153	7989647	0.74	-	0	transcript_id "Phchi.S6G110400.t1"; gene_id "Phchi.S6G110400"
Phchi.S6	AUGUSTUS	exon	7989153	7989647	.	-	.	transcript_id "Phchi.S6G110400.t1"; gene_id "Phchi.S6G110400"
Phchi.S6	AUGUSTUS	start_codon	7989645	7989647	.	-	0	transcript_id "Phchi.S6G110400.t1"; gene_id "Phchi.S6G110400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10322.t1 is derived from g7498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47108294	47109474	.	+	.	Phchi.S1G748100
Phchi.S1	AUGUSTUS	transcript	47108294	47109474	.	+	.	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	start_codon	47108294	47108296	.	+	0	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	CDS	47108294	47108629	0.89	+	0	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	exon	47108294	47108629	.	+	.	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	intron	47108630	47108953	.	+	.	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	CDS	47108954	47109377	0.46	+	0	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	exon	47108954	47109377	.	+	.	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	intron	47109378	47109466	.	+	.	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	CDS	47109467	47109474	0.48	+	2	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	exon	47109467	47109474	.	+	.	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
Phchi.S1	AUGUSTUS	stop_codon	47109475	47109477	.	+	0	transcript_id "Phchi.S1G748100.t1"; gene_id "Phchi.S1G748100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14407.t1 is derived from g12875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12683180	12684828	.	-	.	Phchi.S3G172600
Phchi.S3	AUGUSTUS	transcript	12683180	12684828	.	-	.	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	stop_codon	12683177	12683179	.	-	0	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	CDS	12683180	12684194	0.86	-	1	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	exon	12683180	12684194	.	-	.	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	intron	12684195	12684289	.	-	.	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	CDS	12684290	12684828	0.75	-	0	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	exon	12684290	12684828	.	-	.	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	start_codon	12684826	12684828	.	-	0	transcript_id "Phchi.S3G172600.t1"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	transcript	12683180	12683944	.	-	.	transcript_id "Phchi.S3G172600.t2"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	stop_codon	12683177	12683179	.	-	0	transcript_id "Phchi.S3G172600.t2"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	CDS	12683180	12683944	0.76	-	0	transcript_id "Phchi.S3G172600.t2"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	exon	12683180	12683944	.	-	.	transcript_id "Phchi.S3G172600.t2"; gene_id "Phchi.S3G172600"
Phchi.S3	AUGUSTUS	start_codon	12683942	12683944	.	-	0	transcript_id "Phchi.S3G172600.t2"; gene_id "Phchi.S3G172600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1149.t1 is derived from g10932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8022142	8022600	.	-	.	Phchi.S6G110800
Phchi.S6	AUGUSTUS	transcript	8022142	8022600	.	-	.	transcript_id "Phchi.S6G110800.t1"; gene_id "Phchi.S6G110800"
Phchi.S6	AUGUSTUS	stop_codon	8022139	8022141	.	-	0	transcript_id "Phchi.S6G110800.t1"; gene_id "Phchi.S6G110800"
Phchi.S6	AUGUSTUS	CDS	8022142	8022600	0.8	-	0	transcript_id "Phchi.S6G110800.t1"; gene_id "Phchi.S6G110800"
Phchi.S6	AUGUSTUS	exon	8022142	8022600	.	-	.	transcript_id "Phchi.S6G110800.t1"; gene_id "Phchi.S6G110800"
Phchi.S6	AUGUSTUS	start_codon	8022598	8022600	.	-	0	transcript_id "Phchi.S6G110800.t1"; gene_id "Phchi.S6G110800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11458.t1 is derived from g15508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6463891	6464381	.	-	.	Phchi.S4G104000
Phchi.S4	AUGUSTUS	transcript	6463891	6464381	.	-	.	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	stop_codon	6463888	6463890	.	-	0	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	CDS	6463891	6464103	0.67	-	0	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	exon	6463891	6464103	.	-	.	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	intron	6464104	6464210	.	-	.	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	CDS	6464211	6464381	0.45	-	0	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	exon	6464211	6464381	.	-	.	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
Phchi.S4	AUGUSTUS	start_codon	6464379	6464381	.	-	0	transcript_id "Phchi.S4G104000.t1"; gene_id "Phchi.S4G104000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6712.t1 is derived from g3884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24666378	24669207	.	-	.	Phchi.S1G387100
Phchi.S1	AUGUSTUS	transcript	24666378	24669207	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	stop_codon	24666375	24666377	.	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24666378	24666518	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24666378	24666518	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24666519	24666610	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24666611	24666632	1	-	1	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24666611	24666632	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24666633	24666759	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24666760	24666839	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24666760	24666839	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24666840	24666923	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24666924	24667017	1	-	1	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24666924	24667017	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24667018	24667097	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24667098	24667213	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24667098	24667213	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24667214	24667320	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24667321	24667548	0.95	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24667321	24667548	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24667549	24667645	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24667646	24667730	1	-	1	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24667646	24667730	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24667731	24667817	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24667818	24667891	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24667818	24667891	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24667892	24667992	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24667993	24668133	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24667993	24668133	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24668134	24668247	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24668248	24668287	1	-	1	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24668248	24668287	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24668288	24668387	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24668388	24668483	1	-	1	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24668388	24668483	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24668484	24668585	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24668586	24668662	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24668586	24668662	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24668663	24668783	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24668784	24668894	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24668784	24668894	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24668895	24668976	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24668977	24669069	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24668977	24669069	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	intron	24669070	24669162	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	CDS	24669163	24669207	1	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	exon	24669163	24669207	.	-	.	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
Phchi.S1	AUGUSTUS	start_codon	24669205	24669207	.	-	0	transcript_id "Phchi.S1G387100.t1"; gene_id "Phchi.S1G387100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11966.t1 is derived from g7641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	237436	239412	.	+	.	Phchi.S2G004600
Phchi.S2	AUGUSTUS	transcript	237436	239412	.	+	.	transcript_id "Phchi.S2G004600.t1"; gene_id "Phchi.S2G004600"
Phchi.S2	AUGUSTUS	start_codon	237436	237438	.	+	0	transcript_id "Phchi.S2G004600.t1"; gene_id "Phchi.S2G004600"
Phchi.S2	AUGUSTUS	CDS	237436	239412	0.29	+	0	transcript_id "Phchi.S2G004600.t1"; gene_id "Phchi.S2G004600"
Phchi.S2	AUGUSTUS	exon	237436	239412	.	+	.	transcript_id "Phchi.S2G004600.t1"; gene_id "Phchi.S2G004600"
Phchi.S2	AUGUSTUS	stop_codon	239413	239415	.	+	0	transcript_id "Phchi.S2G004600.t1"; gene_id "Phchi.S2G004600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12572.t1 is derived from g8249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35609083	35610804	.	+	.	Phchi.S2G065200
Phchi.S2	AUGUSTUS	transcript	35609083	35610804	.	+	.	transcript_id "Phchi.S2G065200.t1"; gene_id "Phchi.S2G065200"
Phchi.S2	AUGUSTUS	start_codon	35609083	35609085	.	+	0	transcript_id "Phchi.S2G065200.t1"; gene_id "Phchi.S2G065200"
Phchi.S2	AUGUSTUS	CDS	35609083	35610804	0.98	+	0	transcript_id "Phchi.S2G065200.t1"; gene_id "Phchi.S2G065200"
Phchi.S2	AUGUSTUS	exon	35609083	35610804	.	+	.	transcript_id "Phchi.S2G065200.t1"; gene_id "Phchi.S2G065200"
Phchi.S2	AUGUSTUS	stop_codon	35610805	35610807	.	+	0	transcript_id "Phchi.S2G065200.t1"; gene_id "Phchi.S2G065200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14798.t1 is derived from g13266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14770658	14771222	.	-	.	Phchi.S3G211700
Phchi.S3	AUGUSTUS	transcript	14770658	14771222	.	-	.	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	stop_codon	14770655	14770657	.	-	0	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	CDS	14770658	14770739	0.98	-	1	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	exon	14770658	14770739	.	-	.	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	intron	14770740	14770927	.	-	.	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	CDS	14770928	14770975	0.98	-	1	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	exon	14770928	14770975	.	-	.	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	intron	14770976	14771136	.	-	.	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	CDS	14771137	14771222	0.98	-	0	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	exon	14771137	14771222	.	-	.	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
Phchi.S3	AUGUSTUS	start_codon	14771220	14771222	.	-	0	transcript_id "Phchi.S3G211700.t1"; gene_id "Phchi.S3G211700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9255.t1 is derived from g6430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40610337	40611600	.	-	.	Phchi.S1G641400
Phchi.S1	AUGUSTUS	transcript	40610337	40611600	.	-	.	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	stop_codon	40610334	40610336	.	-	0	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	CDS	40610337	40611068	1	-	0	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	exon	40610337	40611068	.	-	.	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	intron	40611069	40611257	.	-	.	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	CDS	40611258	40611328	1	-	2	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	exon	40611258	40611328	.	-	.	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	intron	40611329	40611413	.	-	.	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	CDS	40611414	40611600	1	-	0	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	exon	40611414	40611600	.	-	.	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
Phchi.S1	AUGUSTUS	start_codon	40611598	40611600	.	-	0	transcript_id "Phchi.S1G641400.t1"; gene_id "Phchi.S1G641400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3764.t1 is derived from g933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5581469	5585959	.	-	.	Phchi.S1G092300
Phchi.S1	AUGUSTUS	transcript	5581469	5585959	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	stop_codon	5581466	5581468	.	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5581469	5581630	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5581469	5581630	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5581631	5581707	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5581708	5581841	1	-	2	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5581708	5581841	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5581842	5581930	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5581931	5582047	1	-	2	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5581931	5582047	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5582048	5582140	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5582141	5582256	1	-	1	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5582141	5582256	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5582257	5582331	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5582332	5582387	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5582332	5582387	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5582388	5582638	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5582639	5582659	0.9	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5582639	5582659	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5582660	5582750	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5582751	5582954	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5582751	5582954	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5582955	5583058	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5583059	5583199	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5583059	5583199	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5583200	5583309	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5583310	5583384	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5583310	5583384	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5583385	5583632	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5583633	5583747	1	-	1	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5583633	5583747	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5583748	5583841	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5583842	5584071	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5583842	5584071	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5584072	5584251	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5584252	5584323	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5584252	5584323	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5584324	5584396	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5584397	5584592	1	-	1	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5584397	5584592	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5584593	5584678	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5584679	5584872	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5584679	5584872	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5584873	5584964	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5584965	5585127	1	-	1	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5584965	5585127	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5585128	5585250	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5585251	5585376	1	-	1	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5585251	5585376	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5585377	5585497	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5585498	5585683	1	-	1	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5585498	5585683	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	intron	5585684	5585888	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	CDS	5585889	5585959	1	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	exon	5585889	5585959	.	-	.	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
Phchi.S1	AUGUSTUS	start_codon	5585957	5585959	.	-	0	transcript_id "Phchi.S1G092300.t1"; gene_id "Phchi.S1G092300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7313.t1 is derived from g4485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28464803	28467289	.	+	.	Phchi.S1G447200
Phchi.S1	AUGUSTUS	transcript	28464803	28467289	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	start_codon	28464803	28464805	.	+	0	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	CDS	28464803	28465392	1	+	0	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	exon	28464803	28465392	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	intron	28465393	28465482	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	CDS	28465483	28466150	1	+	1	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	exon	28465483	28466150	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	intron	28466151	28466239	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	CDS	28466240	28466856	0.84	+	2	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	exon	28466240	28466856	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	intron	28466857	28466929	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	CDS	28466930	28466941	1	+	0	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	exon	28466930	28466941	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	intron	28466942	28467142	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	CDS	28467143	28467289	1	+	0	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	exon	28467143	28467289	.	+	.	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
Phchi.S1	AUGUSTUS	stop_codon	28467290	28467292	.	+	0	transcript_id "Phchi.S1G447200.t1"; gene_id "Phchi.S1G447200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6832.t1 is derived from g4004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25459823	25460791	.	+	.	Phchi.S1G399100
Phchi.S1	AUGUSTUS	transcript	25459823	25460791	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	start_codon	25459823	25459825	.	+	0	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	CDS	25459823	25459833	1	+	0	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	exon	25459823	25459833	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	intron	25459834	25459990	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	CDS	25459991	25460066	1	+	1	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	exon	25459991	25460066	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	intron	25460067	25460151	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	CDS	25460152	25460253	1	+	0	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	exon	25460152	25460253	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	intron	25460254	25460393	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	CDS	25460394	25460542	1	+	0	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	exon	25460394	25460542	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	intron	25460543	25460637	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	CDS	25460638	25460791	1	+	1	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	exon	25460638	25460791	.	+	.	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
Phchi.S1	AUGUSTUS	stop_codon	25460792	25460794	.	+	0	transcript_id "Phchi.S1G399100.t1"; gene_id "Phchi.S1G399100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11380.t1 is derived from g15430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5979496	5979783	.	-	.	Phchi.S4G096200
Phchi.S4	AUGUSTUS	transcript	5979496	5979783	.	-	.	transcript_id "Phchi.S4G096200.t1"; gene_id "Phchi.S4G096200"
Phchi.S4	AUGUSTUS	stop_codon	5979493	5979495	.	-	0	transcript_id "Phchi.S4G096200.t1"; gene_id "Phchi.S4G096200"
Phchi.S4	AUGUSTUS	CDS	5979496	5979783	0.99	-	0	transcript_id "Phchi.S4G096200.t1"; gene_id "Phchi.S4G096200"
Phchi.S4	AUGUSTUS	exon	5979496	5979783	.	-	.	transcript_id "Phchi.S4G096200.t1"; gene_id "Phchi.S4G096200"
Phchi.S4	AUGUSTUS	start_codon	5979781	5979783	.	-	0	transcript_id "Phchi.S4G096200.t1"; gene_id "Phchi.S4G096200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15006.t1 is derived from g13474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16333839	16334560	.	-	.	Phchi.S3G232500
Phchi.S3	AUGUSTUS	transcript	16333839	16334560	.	-	.	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	stop_codon	16333836	16333838	.	-	0	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	CDS	16333839	16334183	0.76	-	0	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	exon	16333839	16334183	.	-	.	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	intron	16334184	16334290	.	-	.	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	CDS	16334291	16334452	0.14	-	0	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	exon	16334291	16334452	.	-	.	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	intron	16334453	16334551	.	-	.	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	CDS	16334552	16334560	0.64	-	0	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	exon	16334552	16334560	.	-	.	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
Phchi.S3	AUGUSTUS	start_codon	16334558	16334560	.	-	0	transcript_id "Phchi.S3G232500.t1"; gene_id "Phchi.S3G232500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13641.t1 is derived from g12108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7983602	7984551	.	+	.	Phchi.S3G096000
Phchi.S3	AUGUSTUS	transcript	7983602	7984551	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	start_codon	7983602	7983604	.	+	0	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	CDS	7983602	7983929	0.9	+	0	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	exon	7983602	7983929	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	intron	7983930	7984032	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	CDS	7984033	7984148	1	+	2	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	exon	7984033	7984148	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	intron	7984149	7984244	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	CDS	7984245	7984363	1	+	0	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	exon	7984245	7984363	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	intron	7984364	7984427	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	CDS	7984428	7984551	1	+	1	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	exon	7984428	7984551	.	+	.	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
Phchi.S3	AUGUSTUS	stop_codon	7984552	7984554	.	+	0	transcript_id "Phchi.S3G096000.t1"; gene_id "Phchi.S3G096000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10387.t1 is derived from g7563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47498101	47500855	.	-	.	Phchi.S1G754600
Phchi.S1	AUGUSTUS	transcript	47498101	47500855	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	stop_codon	47498098	47498100	.	-	0	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	CDS	47498101	47499182	0.92	-	2	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	exon	47498101	47499182	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	intron	47499183	47499265	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	CDS	47499266	47500485	0.99	-	1	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	exon	47499266	47500485	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	intron	47500486	47500562	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	CDS	47500563	47500657	1	-	0	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	exon	47500563	47500657	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	intron	47500658	47500735	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	CDS	47500736	47500855	0.98	-	0	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	exon	47500736	47500855	.	-	.	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
Phchi.S1	AUGUSTUS	start_codon	47500853	47500855	.	-	0	transcript_id "Phchi.S1G754600.t1"; gene_id "Phchi.S1G754600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7966.t1 is derived from g5141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32148566	32150077	.	-	.	Phchi.S1G512500
Phchi.S1	AUGUSTUS	transcript	32148566	32150077	.	-	.	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	stop_codon	32148563	32148565	.	-	0	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	CDS	32148566	32149193	0.74	-	1	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	exon	32148566	32149193	.	-	.	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	intron	32149194	32149313	.	-	.	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	CDS	32149314	32150077	0.99	-	0	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	exon	32149314	32150077	.	-	.	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
Phchi.S1	AUGUSTUS	start_codon	32150075	32150077	.	-	0	transcript_id "Phchi.S1G512500.t1"; gene_id "Phchi.S1G512500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3338.t1 is derived from g507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2981508	2984356	.	+	.	Phchi.S1G049700
Phchi.S1	AUGUSTUS	transcript	2981508	2984356	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	start_codon	2981508	2981510	.	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2981508	2981912	0.85	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2981508	2981912	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2981913	2982006	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2982007	2982082	1	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2982007	2982082	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2982083	2982180	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2982181	2982248	1	+	2	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2982181	2982248	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2982249	2982350	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2982351	2982439	1	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2982351	2982439	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2982440	2982587	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2982588	2982785	1	+	1	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2982588	2982785	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2982786	2982883	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2982884	2983091	1	+	1	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2982884	2983091	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2983092	2983191	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2983192	2983356	1	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2983192	2983356	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2983357	2983437	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2983438	2983605	1	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2983438	2983605	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2983606	2983700	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2983701	2983754	0.9	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2983701	2983754	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2983755	2983834	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2983835	2983890	0.66	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2983835	2983890	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2983891	2983961	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2983962	2984042	0.73	+	1	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2983962	2984042	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	intron	2984043	2984133	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	CDS	2984134	2984356	0.85	+	1	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	exon	2984134	2984356	.	+	.	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
Phchi.S1	AUGUSTUS	stop_codon	2984357	2984359	.	+	0	transcript_id "Phchi.S1G049700.t1"; gene_id "Phchi.S1G049700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7947.t1 is derived from g5121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32055563	32058153	.	-	.	Phchi.S1G510600
Phchi.S1	AUGUSTUS	transcript	32055563	32058153	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	stop_codon	32055560	32055562	.	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32055563	32055809	1	-	1	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32055563	32055809	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32055810	32055900	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32055901	32055960	1	-	1	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32055901	32055960	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32055961	32056047	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32056048	32056146	1	-	1	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32056048	32056146	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32056147	32056299	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32056300	32056333	1	-	2	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32056300	32056333	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32056334	32056431	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32056432	32056491	1	-	2	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32056432	32056491	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32056492	32056584	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32056585	32056685	1	-	1	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32056585	32056685	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32056686	32056770	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32056771	32056836	0.99	-	1	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32056771	32056836	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32056837	32056944	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32056945	32057075	1	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32056945	32057075	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32057076	32057157	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32057158	32057228	0.95	-	2	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32057158	32057228	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32057229	32057326	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32057327	32057438	1	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32057327	32057438	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32057439	32057535	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32057536	32057571	1	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32057536	32057571	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32057572	32057666	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32057667	32057741	1	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32057667	32057741	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	intron	32057742	32057832	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	CDS	32057833	32058153	0.92	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	exon	32057833	32058153	.	-	.	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
Phchi.S1	AUGUSTUS	start_codon	32058151	32058153	.	-	0	transcript_id "Phchi.S1G510600.t1"; gene_id "Phchi.S1G510600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14241.t1 is derived from g12708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11700018	11703619	.	+	.	Phchi.S3G156000
Phchi.S3	AUGUSTUS	transcript	11700018	11703619	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	start_codon	11700018	11700020	.	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11700018	11700050	0.96	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11700018	11700050	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11700051	11700431	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11700432	11700460	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11700432	11700460	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11700461	11700581	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11700582	11700690	1	+	1	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11700582	11700690	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11700691	11700788	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11700789	11700886	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11700789	11700886	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11700887	11700967	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11700968	11701064	1	+	1	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11700968	11701064	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11701065	11701145	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11701146	11701235	0.95	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11701146	11701235	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11701236	11701343	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11701344	11701406	0.99	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11701344	11701406	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11701407	11701509	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11701510	11701584	0.92	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11701510	11701584	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11701585	11701781	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11701782	11701850	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11701782	11701850	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11701851	11701951	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11701952	11702029	0.99	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11701952	11702029	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11702030	11702108	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11702109	11702201	0.79	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11702109	11702201	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11702202	11702321	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11702322	11702399	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11702322	11702399	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11702400	11702488	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11702489	11702608	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11702489	11702608	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11702609	11702689	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11702690	11702733	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11702690	11702733	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11702734	11702834	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11702835	11702880	0.64	+	1	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11702835	11702880	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11702881	11702995	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11702996	11703118	0.89	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11702996	11703118	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11703119	11703199	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11703200	11703274	1	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11703200	11703274	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11703275	11703364	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11703365	11703466	0.95	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11703365	11703466	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	intron	11703467	11703553	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	CDS	11703554	11703619	0.77	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	exon	11703554	11703619	.	+	.	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
Phchi.S3	AUGUSTUS	stop_codon	11703620	11703622	.	+	0	transcript_id "Phchi.S3G156000.t1"; gene_id "Phchi.S3G156000"
# This transcript jg15970.t2 is derived from g14403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15971.t1 is derived from g14447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C266	AUGUSTUS	gene	14387	15063	.	-	.	Phchi.C266G000100
Phchi.C266	AUGUSTUS	transcript	14387	15063	.	-	.	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	stop_codon	14384	14386	.	-	0	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	CDS	14387	14519	0.46	-	1	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	exon	14387	14519	.	-	.	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	intron	14520	14662	.	-	.	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	CDS	14663	15063	0.45	-	0	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	exon	14663	15063	.	-	.	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
Phchi.C266	AUGUSTUS	start_codon	15061	15063	.	-	0	transcript_id "Phchi.C266G000100.t1"; gene_id "Phchi.C266G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14227.t1 is derived from g12694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11650847	11653768	.	-	.	Phchi.S3G154600
Phchi.S3	AUGUSTUS	transcript	11650847	11653768	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	stop_codon	11650844	11650846	.	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11650847	11650952	0.95	-	1	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11650847	11650952	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11650953	11651063	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11651064	11651167	0.96	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11651064	11651167	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11651168	11651295	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11651296	11651451	1	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11651296	11651451	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11651452	11651601	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11651602	11651722	1	-	1	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11651602	11651722	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11651723	11651817	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11651818	11651879	1	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11651818	11651879	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11651880	11651981	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11651982	11652038	0.95	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11651982	11652038	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11652039	11652177	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11652178	11652243	1	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11652178	11652243	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11652244	11652363	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11652364	11652408	1	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11652364	11652408	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11652409	11652535	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11652536	11652577	1	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11652536	11652577	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11652578	11652684	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11652685	11652771	0.95	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11652685	11652771	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11652772	11652864	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11652865	11653350	1	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11652865	11653350	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	intron	11653351	11653711	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	CDS	11653712	11653768	0.95	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	exon	11653712	11653768	.	-	.	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
Phchi.S3	AUGUSTUS	start_codon	11653766	11653768	.	-	0	transcript_id "Phchi.S3G154600.t1"; gene_id "Phchi.S3G154600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg915.t1 is derived from g10697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6413812	6416619	.	+	.	Phchi.S6G087400
Phchi.S6	AUGUSTUS	transcript	6413812	6416619	.	+	.	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	start_codon	6413812	6413814	.	+	0	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	CDS	6413812	6416445	0.7	+	0	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	exon	6413812	6416445	.	+	.	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	intron	6416446	6416565	.	+	.	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	CDS	6416566	6416619	0.86	+	0	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	exon	6416566	6416619	.	+	.	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
Phchi.S6	AUGUSTUS	stop_codon	6416620	6416622	.	+	0	transcript_id "Phchi.S6G087400.t1"; gene_id "Phchi.S6G087400"
# This transcript jg5533.t2 is derived from g2703.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5534.t1 is derived from g2704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17439609	17440734	.	-	.	Phchi.S1G269300
Phchi.S1	AUGUSTUS	transcript	17439609	17440734	.	-	.	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	stop_codon	17439606	17439608	.	-	0	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	CDS	17439609	17439783	0.99	-	1	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	exon	17439609	17439783	.	-	.	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	intron	17439784	17439914	.	-	.	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	CDS	17439915	17440245	1	-	2	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	exon	17439915	17440245	.	-	.	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	intron	17440246	17440436	.	-	.	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	CDS	17440437	17440734	0.52	-	0	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	exon	17440437	17440734	.	-	.	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
Phchi.S1	AUGUSTUS	start_codon	17440732	17440734	.	-	0	transcript_id "Phchi.S1G269300.t1"; gene_id "Phchi.S1G269300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13465.t1 is derived from g11932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7021999	7022695	.	+	.	Phchi.S3G078400
Phchi.S3	AUGUSTUS	transcript	7021999	7022695	.	+	.	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	start_codon	7021999	7022001	.	+	0	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	CDS	7021999	7022241	0.53	+	0	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	exon	7021999	7022241	.	+	.	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	intron	7022242	7022350	.	+	.	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	CDS	7022351	7022455	0.58	+	0	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	exon	7022351	7022455	.	+	.	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	intron	7022456	7022653	.	+	.	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	CDS	7022654	7022695	0.96	+	0	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	exon	7022654	7022695	.	+	.	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
Phchi.S3	AUGUSTUS	stop_codon	7022696	7022698	.	+	0	transcript_id "Phchi.S3G078400.t1"; gene_id "Phchi.S3G078400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg684.t1 is derived from g10466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4778773	4780758	.	-	.	Phchi.S6G064300
Phchi.S6	AUGUSTUS	transcript	4778773	4780758	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	stop_codon	4778770	4778772	.	-	0	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	CDS	4778773	4779160	1	-	1	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	exon	4778773	4779160	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	intron	4779161	4779235	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	CDS	4779236	4779489	1	-	0	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	exon	4779236	4779489	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	intron	4779490	4779576	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	CDS	4779577	4779924	1	-	0	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	exon	4779577	4779924	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	intron	4779925	4780067	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	CDS	4780068	4780338	0.73	-	1	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	exon	4780068	4780338	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	intron	4780339	4780468	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	CDS	4780469	4780758	0.83	-	0	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	exon	4780469	4780758	.	-	.	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
Phchi.S6	AUGUSTUS	start_codon	4780756	4780758	.	-	0	transcript_id "Phchi.S6G064300.t1"; gene_id "Phchi.S6G064300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6603.t1 is derived from g3775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23944532	23947006	.	+	.	Phchi.S1G376200
Phchi.S1	AUGUSTUS	transcript	23944532	23947006	.	+	.	transcript_id "Phchi.S1G376200.t1"; gene_id "Phchi.S1G376200"
Phchi.S1	AUGUSTUS	start_codon	23944532	23944534	.	+	0	transcript_id "Phchi.S1G376200.t1"; gene_id "Phchi.S1G376200"
Phchi.S1	AUGUSTUS	CDS	23944532	23947006	0.49	+	0	transcript_id "Phchi.S1G376200.t1"; gene_id "Phchi.S1G376200"
Phchi.S1	AUGUSTUS	exon	23944532	23947006	.	+	.	transcript_id "Phchi.S1G376200.t1"; gene_id "Phchi.S1G376200"
Phchi.S1	AUGUSTUS	stop_codon	23947007	23947009	.	+	0	transcript_id "Phchi.S1G376200.t1"; gene_id "Phchi.S1G376200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10017.t1 is derived from g7193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45061908	45063746	.	+	.	Phchi.S1G717600
Phchi.S1	AUGUSTUS	transcript	45061908	45063746	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	start_codon	45061908	45061910	.	+	0	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45061908	45062127	0.95	+	0	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45061908	45062127	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45062128	45062221	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45062222	45062303	1	+	2	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45062222	45062303	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45062304	45062386	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45062387	45062485	1	+	1	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45062387	45062485	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45062486	45062569	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45062570	45062738	1	+	1	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45062570	45062738	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45062739	45062836	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45062837	45062936	1	+	0	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45062837	45062936	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45062937	45063011	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45063012	45063081	0.85	+	2	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45063012	45063081	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45063082	45063185	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45063186	45063240	1	+	1	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45063186	45063240	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45063241	45063340	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45063341	45063460	1	+	0	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45063341	45063460	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	intron	45063461	45063539	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	CDS	45063540	45063746	0.82	+	0	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	exon	45063540	45063746	.	+	.	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
Phchi.S1	AUGUSTUS	stop_codon	45063747	45063749	.	+	0	transcript_id "Phchi.S1G717600.t1"; gene_id "Phchi.S1G717600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12346.t1 is derived from g8022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12255362	12255656	.	+	.	Phchi.S2G042600
Phchi.S2	AUGUSTUS	transcript	12255362	12255656	.	+	.	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	start_codon	12255362	12255364	.	+	0	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	CDS	12255362	12255488	0.56	+	0	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	exon	12255362	12255488	.	+	.	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	intron	12255489	12255579	.	+	.	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	CDS	12255580	12255656	0.45	+	2	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	exon	12255580	12255656	.	+	.	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
Phchi.S2	AUGUSTUS	stop_codon	12255657	12255659	.	+	0	transcript_id "Phchi.S2G042600.t1"; gene_id "Phchi.S2G042600"
# This transcript jg7169.t2 is derived from g4341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7170.t1 is derived from g4342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27382693	27386564	.	-	.	Phchi.S1G432900
Phchi.S1	AUGUSTUS	transcript	27382693	27386564	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	stop_codon	27382690	27382692	.	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27382693	27382833	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27382693	27382833	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27382834	27382927	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27382928	27383044	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27382928	27383044	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27383045	27383111	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27383112	27383253	1	-	1	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27383112	27383253	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27383254	27383336	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27383337	27383446	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27383337	27383446	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27383447	27383537	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27383538	27383675	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27383538	27383675	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27383676	27383770	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27383771	27383869	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27383771	27383869	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27383870	27383970	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27383971	27384039	0.91	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27383971	27384039	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27384040	27384169	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27384170	27384226	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27384170	27384226	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27384227	27384321	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27384322	27384399	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27384322	27384399	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27384400	27384490	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27384491	27384580	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27384491	27384580	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27384581	27384660	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27384661	27384736	1	-	1	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27384661	27384736	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27384737	27384847	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27384848	27384903	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27384848	27384903	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27384904	27384987	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27384988	27385039	0.99	-	1	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27384988	27385039	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27385040	27385145	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27385146	27385345	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27385146	27385345	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27385346	27385462	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27385463	27385528	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27385463	27385528	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27385529	27385672	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27385673	27385751	1	-	1	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27385673	27385751	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27385752	27385844	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27385845	27386000	1	-	1	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27385845	27386000	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27386001	27386184	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27386185	27386340	1	-	1	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27386185	27386340	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	intron	27386341	27386499	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	CDS	27386500	27386564	1	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	exon	27386500	27386564	.	-	.	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
Phchi.S1	AUGUSTUS	start_codon	27386562	27386564	.	-	0	transcript_id "Phchi.S1G432900.t1"; gene_id "Phchi.S1G432900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11887.t1 is derived from g15939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9029461	9031356	.	+	.	Phchi.S4G146900
Phchi.S4	AUGUSTUS	transcript	9029461	9031356	.	+	.	transcript_id "Phchi.S4G146900.t1"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	start_codon	9029461	9029463	.	+	0	transcript_id "Phchi.S4G146900.t1"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	CDS	9029461	9031356	0.99	+	0	transcript_id "Phchi.S4G146900.t1"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	exon	9029461	9031356	.	+	.	transcript_id "Phchi.S4G146900.t1"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	stop_codon	9031357	9031359	.	+	0	transcript_id "Phchi.S4G146900.t1"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	transcript	9030217	9031356	.	+	.	transcript_id "Phchi.S4G146900.t2"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	start_codon	9030217	9030219	.	+	0	transcript_id "Phchi.S4G146900.t2"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	CDS	9030217	9031356	0.79	+	0	transcript_id "Phchi.S4G146900.t2"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	exon	9030217	9031356	.	+	.	transcript_id "Phchi.S4G146900.t2"; gene_id "Phchi.S4G146900"
Phchi.S4	AUGUSTUS	stop_codon	9031357	9031359	.	+	0	transcript_id "Phchi.S4G146900.t2"; gene_id "Phchi.S4G146900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2292.t1 is derived from g9212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5905170	5906224	.	-	.	Phchi.S5G090100
Phchi.S5	AUGUSTUS	transcript	5905170	5906224	.	-	.	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	stop_codon	5905167	5905169	.	-	0	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	CDS	5905170	5905241	0.04	-	0	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	exon	5905170	5905241	.	-	.	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	intron	5905242	5905334	.	-	.	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	CDS	5905335	5905395	0.01	-	1	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	exon	5905335	5905395	.	-	.	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	intron	5905396	5906165	.	-	.	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	CDS	5906166	5906224	0.02	-	0	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	exon	5906166	5906224	.	-	.	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
Phchi.S5	AUGUSTUS	start_codon	5906222	5906224	.	-	0	transcript_id "Phchi.S5G090100.t1"; gene_id "Phchi.S5G090100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2606.t1 is derived from g9526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7770545	7771012	.	-	.	Phchi.S5G121500
Phchi.S5	AUGUSTUS	transcript	7770545	7771012	.	-	.	transcript_id "Phchi.S5G121500.t1"; gene_id "Phchi.S5G121500"
Phchi.S5	AUGUSTUS	stop_codon	7770542	7770544	.	-	0	transcript_id "Phchi.S5G121500.t1"; gene_id "Phchi.S5G121500"
Phchi.S5	AUGUSTUS	CDS	7770545	7771012	0.99	-	0	transcript_id "Phchi.S5G121500.t1"; gene_id "Phchi.S5G121500"
Phchi.S5	AUGUSTUS	exon	7770545	7771012	.	-	.	transcript_id "Phchi.S5G121500.t1"; gene_id "Phchi.S5G121500"
Phchi.S5	AUGUSTUS	start_codon	7771010	7771012	.	-	0	transcript_id "Phchi.S5G121500.t1"; gene_id "Phchi.S5G121500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8009.t1 is derived from g5184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32462955	32463368	.	-	.	Phchi.S1G516800
Phchi.S1	AUGUSTUS	transcript	32462955	32463368	.	-	.	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	stop_codon	32462952	32462954	.	-	0	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	CDS	32462955	32463110	0.58	-	0	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	exon	32462955	32463110	.	-	.	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	intron	32463111	32463260	.	-	.	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	CDS	32463261	32463368	0.63	-	0	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	exon	32463261	32463368	.	-	.	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
Phchi.S1	AUGUSTUS	start_codon	32463366	32463368	.	-	0	transcript_id "Phchi.S1G516800.t1"; gene_id "Phchi.S1G516800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7433.t1 is derived from g4605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29097653	29101148	.	+	.	Phchi.S1G459200
Phchi.S1	AUGUSTUS	transcript	29097653	29101148	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	start_codon	29097653	29097655	.	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29097653	29097866	0.48	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29097653	29097866	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29097867	29097949	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29097950	29098041	0.63	+	2	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29097950	29098041	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29098042	29098201	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29098202	29098308	1	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29098202	29098308	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29098309	29098390	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29098391	29098594	0.73	+	1	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29098391	29098594	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29098595	29098725	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29098726	29098894	0.71	+	1	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29098726	29098894	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29098895	29099078	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29099079	29099150	0.96	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29099079	29099150	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29099151	29099253	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29099254	29099375	0.97	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29099254	29099375	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29099376	29099490	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29099491	29099706	0.93	+	1	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29099491	29099706	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29099707	29099823	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29099824	29099935	1	+	1	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29099824	29099935	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29099936	29100088	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29100089	29100201	1	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29100089	29100201	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29100202	29100320	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29100321	29100471	1	+	1	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29100321	29100471	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29100472	29100637	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29100638	29100713	1	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29100638	29100713	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	intron	29100714	29100897	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	CDS	29100898	29101148	0.9	+	2	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	exon	29100898	29101148	.	+	.	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
Phchi.S1	AUGUSTUS	stop_codon	29101149	29101151	.	+	0	transcript_id "Phchi.S1G459200.t1"; gene_id "Phchi.S1G459200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9101.t1 is derived from g6276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39836444	39836904	.	-	.	Phchi.S1G626000
Phchi.S1	AUGUSTUS	transcript	39836444	39836904	.	-	.	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	stop_codon	39836441	39836443	.	-	0	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	CDS	39836444	39836642	0.42	-	1	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	exon	39836444	39836642	.	-	.	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	intron	39836643	39836722	.	-	.	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	CDS	39836723	39836904	0.61	-	0	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	exon	39836723	39836904	.	-	.	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
Phchi.S1	AUGUSTUS	start_codon	39836902	39836904	.	-	0	transcript_id "Phchi.S1G626000.t1"; gene_id "Phchi.S1G626000"
# This transcript jg4814.t2 is derived from g1984.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4815.t1 is derived from g1985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12965500	12966336	.	+	.	Phchi.S1G197400
Phchi.S1	AUGUSTUS	transcript	12965500	12966336	.	+	.	transcript_id "Phchi.S1G197400.t1"; gene_id "Phchi.S1G197400"
Phchi.S1	AUGUSTUS	start_codon	12965500	12965502	.	+	0	transcript_id "Phchi.S1G197400.t1"; gene_id "Phchi.S1G197400"
Phchi.S1	AUGUSTUS	CDS	12965500	12966336	0.5	+	0	transcript_id "Phchi.S1G197400.t1"; gene_id "Phchi.S1G197400"
Phchi.S1	AUGUSTUS	exon	12965500	12966336	.	+	.	transcript_id "Phchi.S1G197400.t1"; gene_id "Phchi.S1G197400"
Phchi.S1	AUGUSTUS	stop_codon	12966337	12966339	.	+	0	transcript_id "Phchi.S1G197400.t1"; gene_id "Phchi.S1G197400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13764.t1 is derived from g12231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8776104	8776727	.	-	.	Phchi.S3G108300
Phchi.S3	AUGUSTUS	transcript	8776104	8776727	.	-	.	transcript_id "Phchi.S3G108300.t1"; gene_id "Phchi.S3G108300"
Phchi.S3	AUGUSTUS	stop_codon	8776101	8776103	.	-	0	transcript_id "Phchi.S3G108300.t1"; gene_id "Phchi.S3G108300"
Phchi.S3	AUGUSTUS	CDS	8776104	8776727	0.94	-	0	transcript_id "Phchi.S3G108300.t1"; gene_id "Phchi.S3G108300"
Phchi.S3	AUGUSTUS	exon	8776104	8776727	.	-	.	transcript_id "Phchi.S3G108300.t1"; gene_id "Phchi.S3G108300"
Phchi.S3	AUGUSTUS	start_codon	8776725	8776727	.	-	0	transcript_id "Phchi.S3G108300.t1"; gene_id "Phchi.S3G108300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14384.t1 is derived from g12852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12547260	12548855	.	+	.	Phchi.S3G170300
Phchi.S3	AUGUSTUS	transcript	12547260	12548855	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	start_codon	12547260	12547262	.	+	0	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	CDS	12547260	12547985	0.99	+	0	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	exon	12547260	12547985	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	intron	12547986	12548074	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	CDS	12548075	12548209	1	+	0	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	exon	12548075	12548209	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	intron	12548210	12548294	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	CDS	12548295	12548438	0.98	+	0	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	exon	12548295	12548438	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	intron	12548439	12548549	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	CDS	12548550	12548855	0.95	+	0	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	exon	12548550	12548855	.	+	.	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
Phchi.S3	AUGUSTUS	stop_codon	12548856	12548858	.	+	0	transcript_id "Phchi.S3G170300.t1"; gene_id "Phchi.S3G170300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5147.t1 is derived from g2317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15143091	15144110	.	-	.	Phchi.S1G230600
Phchi.S1	AUGUSTUS	transcript	15143091	15144110	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	stop_codon	15143088	15143090	.	-	0	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	CDS	15143091	15143181	1	-	1	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	exon	15143091	15143181	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	intron	15143182	15143263	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	CDS	15143264	15143353	1	-	1	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	exon	15143264	15143353	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	intron	15143354	15143446	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	CDS	15143447	15143591	1	-	2	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	exon	15143447	15143591	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	intron	15143592	15143671	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	CDS	15143672	15143772	1	-	1	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	exon	15143672	15143772	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	intron	15143773	15143884	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	CDS	15143885	15143925	1	-	0	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	exon	15143885	15143925	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	intron	15143926	15144098	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	CDS	15144099	15144110	1	-	0	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	exon	15144099	15144110	.	-	.	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
Phchi.S1	AUGUSTUS	start_codon	15144108	15144110	.	-	0	transcript_id "Phchi.S1G230600.t1"; gene_id "Phchi.S1G230600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8650.t1 is derived from g5825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37241740	37242762	.	+	.	Phchi.S1G580900
Phchi.S1	AUGUSTUS	transcript	37241740	37242762	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	start_codon	37241740	37241742	.	+	0	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	CDS	37241740	37241848	0.33	+	0	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	exon	37241740	37241848	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	intron	37241849	37242171	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	CDS	37242172	37242271	1	+	2	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	exon	37242172	37242271	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	intron	37242272	37242456	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	CDS	37242457	37242563	1	+	1	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	exon	37242457	37242563	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	intron	37242564	37242640	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	CDS	37242641	37242762	0.97	+	2	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	exon	37242641	37242762	.	+	.	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
Phchi.S1	AUGUSTUS	stop_codon	37242763	37242765	.	+	0	transcript_id "Phchi.S1G580900.t1"; gene_id "Phchi.S1G580900"
# This transcript jg15778.t2 is derived from g14248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15778.t3 is derived from g14248.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15779.t1 is derived from g14249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21306008	21306565	.	+	.	Phchi.S3G309800
Phchi.S3	AUGUSTUS	transcript	21306008	21306565	.	+	.	transcript_id "Phchi.S3G309800.t1"; gene_id "Phchi.S3G309800"
Phchi.S3	AUGUSTUS	start_codon	21306008	21306010	.	+	0	transcript_id "Phchi.S3G309800.t1"; gene_id "Phchi.S3G309800"
Phchi.S3	AUGUSTUS	CDS	21306008	21306565	0.88	+	0	transcript_id "Phchi.S3G309800.t1"; gene_id "Phchi.S3G309800"
Phchi.S3	AUGUSTUS	exon	21306008	21306565	.	+	.	transcript_id "Phchi.S3G309800.t1"; gene_id "Phchi.S3G309800"
Phchi.S3	AUGUSTUS	stop_codon	21306566	21306568	.	+	0	transcript_id "Phchi.S3G309800.t1"; gene_id "Phchi.S3G309800"
# This transcript jg1295.t2 is derived from g11078.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1295.t3 is derived from g11078.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1295.t4 is derived from g11078.t6 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1295.t5 is derived from g11078.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1295.t6 is derived from g11078.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1296.t1 is derived from g11079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8893591	8895004	.	-	.	Phchi.S6G125500
Phchi.S6	AUGUSTUS	transcript	8893591	8895004	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	stop_codon	8893588	8893590	.	-	0	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8893591	8893754	0.98	-	2	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8893591	8893754	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	intron	8893755	8893845	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8893846	8893925	1	-	1	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8893846	8893925	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	intron	8893926	8894009	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8894010	8894090	1	-	1	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8894010	8894090	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	intron	8894091	8894219	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8894220	8894293	0.99	-	0	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8894220	8894293	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	intron	8894294	8894406	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8894407	8894521	0.64	-	1	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8894407	8894521	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	intron	8894522	8894624	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8894625	8894822	0.99	-	1	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8894625	8894822	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	intron	8894823	8894918	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	CDS	8894919	8895004	1	-	0	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	exon	8894919	8895004	.	-	.	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
Phchi.S6	AUGUSTUS	start_codon	8895002	8895004	.	-	0	transcript_id "Phchi.S6G125500.t1"; gene_id "Phchi.S6G125500"
# This transcript jg6536.t2 is derived from g3708.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6536.t3 is derived from g3708.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6537.t1 is derived from g3709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23530728	23531896	.	+	.	Phchi.S1G369600
Phchi.S1	AUGUSTUS	transcript	23530728	23531896	.	+	.	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	start_codon	23530728	23530730	.	+	0	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	CDS	23530728	23531171	0.52	+	0	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	exon	23530728	23531171	.	+	.	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	intron	23531172	23531281	.	+	.	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	CDS	23531282	23531896	0.99	+	0	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	exon	23531282	23531896	.	+	.	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
Phchi.S1	AUGUSTUS	stop_codon	23531897	23531899	.	+	0	transcript_id "Phchi.S1G369600.t1"; gene_id "Phchi.S1G369600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg655.t1 is derived from g10437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4607423	4608579	.	+	.	Phchi.S6G061400
Phchi.S6	AUGUSTUS	transcript	4607423	4608579	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	start_codon	4607423	4607425	.	+	0	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	CDS	4607423	4607524	1	+	0	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	exon	4607423	4607524	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	intron	4607525	4607679	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	CDS	4607680	4608258	1	+	0	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	exon	4607680	4608258	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	intron	4608259	4608375	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	CDS	4608376	4608441	0.98	+	0	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	exon	4608376	4608441	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	intron	4608442	4608522	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	CDS	4608523	4608579	1	+	0	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	exon	4608523	4608579	.	+	.	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
Phchi.S6	AUGUSTUS	stop_codon	4608580	4608582	.	+	0	transcript_id "Phchi.S6G061400.t1"; gene_id "Phchi.S6G061400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5974.t1 is derived from g3145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20182021	20182857	.	-	.	Phchi.S1G313300
Phchi.S1	AUGUSTUS	transcript	20182021	20182857	.	-	.	transcript_id "Phchi.S1G313300.t1"; gene_id "Phchi.S1G313300"
Phchi.S1	AUGUSTUS	stop_codon	20182018	20182020	.	-	0	transcript_id "Phchi.S1G313300.t1"; gene_id "Phchi.S1G313300"
Phchi.S1	AUGUSTUS	CDS	20182021	20182857	1	-	0	transcript_id "Phchi.S1G313300.t1"; gene_id "Phchi.S1G313300"
Phchi.S1	AUGUSTUS	exon	20182021	20182857	.	-	.	transcript_id "Phchi.S1G313300.t1"; gene_id "Phchi.S1G313300"
Phchi.S1	AUGUSTUS	start_codon	20182855	20182857	.	-	0	transcript_id "Phchi.S1G313300.t1"; gene_id "Phchi.S1G313300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3636.t1 is derived from g805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4872186	4872772	.	-	.	Phchi.S1G079500
Phchi.S1	AUGUSTUS	transcript	4872186	4872772	.	-	.	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	stop_codon	4872183	4872185	.	-	0	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	CDS	4872186	4872325	1	-	2	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	exon	4872186	4872325	.	-	.	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	intron	4872326	4872669	.	-	.	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	CDS	4872670	4872772	0.94	-	0	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	exon	4872670	4872772	.	-	.	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
Phchi.S1	AUGUSTUS	start_codon	4872770	4872772	.	-	0	transcript_id "Phchi.S1G079500.t1"; gene_id "Phchi.S1G079500"
# This transcript jg1172.t2 is derived from g10955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1173.t1 is derived from g10956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8273679	8276599	.	+	.	Phchi.S6G113200
Phchi.S6	AUGUSTUS	transcript	8273679	8276599	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	start_codon	8273679	8273681	.	+	0	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8273679	8273860	1	+	0	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8273679	8273860	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8273861	8273933	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8273934	8274042	1	+	1	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8273934	8274042	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8274043	8274124	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8274125	8274424	1	+	0	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8274125	8274424	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8274425	8274517	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8274518	8274938	0.89	+	0	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8274518	8274938	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8274939	8275060	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8275061	8275216	0.51	+	2	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8275061	8275216	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8275217	8275430	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8275431	8275692	0.35	+	2	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8275431	8275692	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8275693	8276011	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8276012	8276192	0.34	+	1	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8276012	8276192	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8276193	8276304	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8276305	8276482	1	+	0	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8276305	8276482	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	intron	8276483	8276555	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	CDS	8276556	8276599	1	+	2	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	exon	8276556	8276599	.	+	.	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
Phchi.S6	AUGUSTUS	stop_codon	8276600	8276602	.	+	0	transcript_id "Phchi.S6G113200.t1"; gene_id "Phchi.S6G113200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9412.t1 is derived from g6588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41370429	41372099	.	+	.	Phchi.S1G657100
Phchi.S1	AUGUSTUS	transcript	41370429	41372099	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	start_codon	41370429	41370431	.	+	0	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	CDS	41370429	41370588	0.92	+	0	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	exon	41370429	41370588	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	intron	41370589	41370767	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	CDS	41370768	41370994	1	+	2	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	exon	41370768	41370994	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	intron	41370995	41371168	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	CDS	41371169	41371459	1	+	0	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	exon	41371169	41371459	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	intron	41371460	41371559	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	CDS	41371560	41371765	1	+	0	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	exon	41371560	41371765	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	intron	41371766	41371855	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	CDS	41371856	41372099	1	+	1	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	exon	41371856	41372099	.	+	.	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
Phchi.S1	AUGUSTUS	stop_codon	41372100	41372102	.	+	0	transcript_id "Phchi.S1G657100.t1"; gene_id "Phchi.S1G657100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13878.t1 is derived from g12345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9432593	9434652	.	-	.	Phchi.S3G119700
Phchi.S3	AUGUSTUS	transcript	9432593	9434652	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	stop_codon	9432590	9432592	.	-	0	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9432593	9432687	0.97	-	2	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9432593	9432687	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9432688	9432760	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9432761	9432864	1	-	1	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9432761	9432864	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9432865	9432962	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9432963	9433015	1	-	0	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9432963	9433015	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9433016	9433108	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9433109	9433321	1	-	0	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9433109	9433321	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9433322	9433456	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9433457	9433563	1	-	2	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9433457	9433563	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9433564	9433645	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9433646	9433752	0.97	-	1	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9433646	9433752	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9433753	9433855	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9433856	9433960	0.61	-	1	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9433856	9433960	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9433961	9434085	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9434086	9434199	0.97	-	1	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9434086	9434199	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9434200	9434293	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9434294	9434480	1	-	2	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9434294	9434480	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	intron	9434481	9434570	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	CDS	9434571	9434652	0.88	-	0	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	exon	9434571	9434652	.	-	.	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
Phchi.S3	AUGUSTUS	start_codon	9434650	9434652	.	-	0	transcript_id "Phchi.S3G119700.t1"; gene_id "Phchi.S3G119700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12405.t1 is derived from g8082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18374691	18375263	.	+	.	Phchi.S2G048500
Phchi.S2	AUGUSTUS	transcript	18374691	18375263	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	start_codon	18374691	18374693	.	+	0	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	CDS	18374691	18374695	0.83	+	0	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	exon	18374691	18374695	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	intron	18374696	18374766	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	CDS	18374767	18374842	0.98	+	1	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	exon	18374767	18374842	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	intron	18374843	18374952	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	CDS	18374953	18375111	1	+	0	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	exon	18374953	18375111	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	intron	18375112	18375191	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	CDS	18375192	18375263	1	+	0	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	exon	18375192	18375263	.	+	.	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
Phchi.S2	AUGUSTUS	stop_codon	18375264	18375266	.	+	0	transcript_id "Phchi.S2G048500.t1"; gene_id "Phchi.S2G048500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg943.t1 is derived from g10725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6599522	6602460	.	+	.	Phchi.S6G090200
Phchi.S6	AUGUSTUS	transcript	6599522	6602460	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	start_codon	6599522	6599524	.	+	0	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	CDS	6599522	6599581	0.49	+	0	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	exon	6599522	6599581	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	intron	6599582	6599717	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	CDS	6599718	6599925	0.18	+	0	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	exon	6599718	6599925	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	intron	6599926	6600023	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	CDS	6600024	6600178	0.48	+	2	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	exon	6600024	6600178	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	intron	6600179	6600299	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	CDS	6600300	6601675	0.56	+	0	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	exon	6600300	6601675	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	intron	6601676	6601821	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	CDS	6601822	6602014	1	+	1	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	exon	6601822	6602014	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	intron	6602015	6602172	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	CDS	6602173	6602460	1	+	0	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	exon	6602173	6602460	.	+	.	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
Phchi.S6	AUGUSTUS	stop_codon	6602461	6602463	.	+	0	transcript_id "Phchi.S6G090200.t1"; gene_id "Phchi.S6G090200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11234.t1 is derived from g15284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4928359	4929671	.	+	.	Phchi.S4G081600
Phchi.S4	AUGUSTUS	transcript	4928359	4929671	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	start_codon	4928359	4928361	.	+	0	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928359	4928406	0.98	+	0	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928359	4928406	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4928407	4928568	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928569	4928726	1	+	0	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928569	4928726	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4928727	4928903	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928904	4929006	1	+	1	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928904	4929006	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4929007	4929101	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4929102	4929173	1	+	0	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4929102	4929173	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4929174	4929257	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4929258	4929337	1	+	0	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4929258	4929337	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4929338	4929652	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4929653	4929671	1	+	1	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4929653	4929671	.	+	.	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	stop_codon	4929672	4929674	.	+	0	transcript_id "Phchi.S4G081600.t1"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	transcript	4928387	4929671	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	start_codon	4928387	4928389	.	+	0	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928387	4928406	0.89	+	0	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928387	4928406	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4928407	4928490	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928491	4928520	0.41	+	1	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928491	4928520	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4928521	4928594	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928595	4928726	0.41	+	1	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928595	4928726	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4928727	4928903	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4928904	4929006	1	+	1	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4928904	4929006	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4929007	4929101	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4929102	4929173	1	+	0	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4929102	4929173	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4929174	4929257	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4929258	4929337	1	+	0	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4929258	4929337	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	intron	4929338	4929652	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	CDS	4929653	4929671	1	+	1	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	exon	4929653	4929671	.	+	.	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
Phchi.S4	AUGUSTUS	stop_codon	4929672	4929674	.	+	0	transcript_id "Phchi.S4G081600.t2"; gene_id "Phchi.S4G081600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg670.t1 is derived from g10452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4650620	4651956	.	-	.	Phchi.S6G062900
Phchi.S6	AUGUSTUS	transcript	4650620	4651956	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	stop_codon	4650617	4650619	.	-	0	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	CDS	4650620	4650957	0.28	-	2	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	exon	4650620	4650957	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	intron	4650958	4651070	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	CDS	4651071	4651307	0.5	-	2	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	exon	4651071	4651307	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	intron	4651308	4651393	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	CDS	4651394	4651565	1	-	0	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	exon	4651394	4651565	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	intron	4651566	4651647	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	CDS	4651648	4651956	1	-	0	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	exon	4651648	4651956	.	-	.	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
Phchi.S6	AUGUSTUS	start_codon	4651954	4651956	.	-	0	transcript_id "Phchi.S6G062900.t1"; gene_id "Phchi.S6G062900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13516.t1 is derived from g11983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7268490	7269986	.	-	.	Phchi.S3G083500
Phchi.S3	AUGUSTUS	transcript	7268490	7269986	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	stop_codon	7268487	7268489	.	-	0	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	CDS	7268490	7268707	0.57	-	2	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	exon	7268490	7268707	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	intron	7268708	7268847	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	CDS	7268848	7269100	0.54	-	0	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	exon	7268848	7269100	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	intron	7269101	7269221	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	CDS	7269222	7269461	0.98	-	0	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	exon	7269222	7269461	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	intron	7269462	7269567	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	CDS	7269568	7269695	1	-	2	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	exon	7269568	7269695	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	intron	7269696	7269790	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	CDS	7269791	7269986	0.61	-	0	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	exon	7269791	7269986	.	-	.	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
Phchi.S3	AUGUSTUS	start_codon	7269984	7269986	.	-	0	transcript_id "Phchi.S3G083500.t1"; gene_id "Phchi.S3G083500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12825.t1 is derived from g11290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2581041	2582402	.	-	.	Phchi.S3G014400
Phchi.S3	AUGUSTUS	transcript	2581041	2582402	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	stop_codon	2581038	2581040	.	-	0	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	CDS	2581041	2581244	0.76	-	0	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	exon	2581041	2581244	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	intron	2581245	2581410	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	CDS	2581411	2581679	0.67	-	2	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	exon	2581411	2581679	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	intron	2581680	2581881	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	CDS	2581882	2581996	1	-	0	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	exon	2581882	2581996	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	intron	2581997	2582285	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	CDS	2582286	2582402	1	-	0	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	exon	2582286	2582402	.	-	.	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
Phchi.S3	AUGUSTUS	start_codon	2582400	2582402	.	-	0	transcript_id "Phchi.S3G014400.t1"; gene_id "Phchi.S3G014400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2594.t1 is derived from g9514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7607554	7607826	.	+	.	Phchi.S5G120300
Phchi.S5	AUGUSTUS	transcript	7607554	7607826	.	+	.	transcript_id "Phchi.S5G120300.t1"; gene_id "Phchi.S5G120300"
Phchi.S5	AUGUSTUS	start_codon	7607554	7607556	.	+	0	transcript_id "Phchi.S5G120300.t1"; gene_id "Phchi.S5G120300"
Phchi.S5	AUGUSTUS	CDS	7607554	7607826	0.65	+	0	transcript_id "Phchi.S5G120300.t1"; gene_id "Phchi.S5G120300"
Phchi.S5	AUGUSTUS	exon	7607554	7607826	.	+	.	transcript_id "Phchi.S5G120300.t1"; gene_id "Phchi.S5G120300"
Phchi.S5	AUGUSTUS	stop_codon	7607827	7607829	.	+	0	transcript_id "Phchi.S5G120300.t1"; gene_id "Phchi.S5G120300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg209.t1 is derived from g9991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1192126	1193283	.	+	.	Phchi.S6G016800
Phchi.S6	AUGUSTUS	transcript	1192126	1193283	.	+	.	transcript_id "Phchi.S6G016800.t1"; gene_id "Phchi.S6G016800"
Phchi.S6	AUGUSTUS	start_codon	1192126	1192128	.	+	0	transcript_id "Phchi.S6G016800.t1"; gene_id "Phchi.S6G016800"
Phchi.S6	AUGUSTUS	CDS	1192126	1193283	0.46	+	0	transcript_id "Phchi.S6G016800.t1"; gene_id "Phchi.S6G016800"
Phchi.S6	AUGUSTUS	exon	1192126	1193283	.	+	.	transcript_id "Phchi.S6G016800.t1"; gene_id "Phchi.S6G016800"
Phchi.S6	AUGUSTUS	stop_codon	1193284	1193286	.	+	0	transcript_id "Phchi.S6G016800.t1"; gene_id "Phchi.S6G016800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4671.t1 is derived from g1841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11738875	11740221	.	-	.	Phchi.S1G183000
Phchi.S1	AUGUSTUS	transcript	11738875	11740221	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	stop_codon	11738872	11738874	.	-	0	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	CDS	11738875	11739435	1	-	0	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	exon	11738875	11739435	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	intron	11739436	11739525	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	CDS	11739526	11739717	1	-	0	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	exon	11739526	11739717	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	intron	11739718	11739819	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	CDS	11739820	11740052	0.87	-	2	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	exon	11739820	11740052	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	intron	11740053	11740136	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	CDS	11740137	11740221	0.19	-	0	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	exon	11740137	11740221	.	-	.	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
Phchi.S1	AUGUSTUS	start_codon	11740219	11740221	.	-	0	transcript_id "Phchi.S1G183000.t1"; gene_id "Phchi.S1G183000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3173.t1 is derived from g342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2098695	2100263	.	+	.	Phchi.S1G033200
Phchi.S1	AUGUSTUS	transcript	2098941	2100263	.	+	.	transcript_id "Phchi.S1G033200.t1"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	start_codon	2098941	2098943	.	+	0	transcript_id "Phchi.S1G033200.t1"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	CDS	2098941	2100263	0.94	+	0	transcript_id "Phchi.S1G033200.t1"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	exon	2098941	2100263	.	+	.	transcript_id "Phchi.S1G033200.t1"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	stop_codon	2100264	2100266	.	+	0	transcript_id "Phchi.S1G033200.t1"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	transcript	2098695	2100263	.	+	.	transcript_id "Phchi.S1G033200.t2"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	start_codon	2098695	2098697	.	+	0	transcript_id "Phchi.S1G033200.t2"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	CDS	2098695	2100263	0.59	+	0	transcript_id "Phchi.S1G033200.t2"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	exon	2098695	2100263	.	+	.	transcript_id "Phchi.S1G033200.t2"; gene_id "Phchi.S1G033200"
Phchi.S1	AUGUSTUS	stop_codon	2100264	2100266	.	+	0	transcript_id "Phchi.S1G033200.t2"; gene_id "Phchi.S1G033200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12148.t1 is derived from g7824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4904932	4907244	.	+	.	Phchi.S2G022800
Phchi.S2	AUGUSTUS	transcript	4904932	4907244	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	start_codon	4904932	4904934	.	+	0	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	CDS	4904932	4905043	0.96	+	0	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	exon	4904932	4905043	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	intron	4905044	4905238	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	CDS	4905239	4905264	0.53	+	2	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	exon	4905239	4905264	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	intron	4905265	4905490	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	CDS	4905491	4906469	0.35	+	0	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	exon	4905491	4906469	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	intron	4906470	4906628	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	CDS	4906629	4906873	0.88	+	2	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	exon	4906629	4906873	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	intron	4906874	4906986	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	CDS	4906987	4907244	0.93	+	0	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	exon	4906987	4907244	.	+	.	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
Phchi.S2	AUGUSTUS	stop_codon	4907245	4907247	.	+	0	transcript_id "Phchi.S2G022800.t1"; gene_id "Phchi.S2G022800"
# This transcript jg6631.t2 is derived from g3803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6632.t1 is derived from g3804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24174809	24177051	.	-	.	Phchi.S1G379100
Phchi.S1	AUGUSTUS	transcript	24174809	24177051	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	stop_codon	24174806	24174808	.	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24174809	24175113	0.96	-	2	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24174809	24175113	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24175114	24175185	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24175186	24175281	1	-	2	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24175186	24175281	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24175282	24175376	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24175377	24175453	1	-	1	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24175377	24175453	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24175454	24175586	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24175587	24175627	0.9	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24175587	24175627	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24175628	24175734	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24175735	24175881	0.59	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24175735	24175881	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24175882	24176015	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24176016	24176126	0.87	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24176016	24176126	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24176127	24176264	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24176265	24176405	0.95	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24176265	24176405	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24176406	24176550	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24176551	24176664	0.91	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24176551	24176664	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	intron	24176665	24176814	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	CDS	24176815	24177051	0.68	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	exon	24176815	24177051	.	-	.	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
Phchi.S1	AUGUSTUS	start_codon	24177049	24177051	.	-	0	transcript_id "Phchi.S1G379100.t1"; gene_id "Phchi.S1G379100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9960.t1 is derived from g7136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44668806	44671029	.	+	.	Phchi.S1G711900
Phchi.S1	AUGUSTUS	transcript	44668806	44671029	.	+	.	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	start_codon	44668806	44668808	.	+	0	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	CDS	44668806	44669020	0.46	+	0	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	exon	44668806	44669020	.	+	.	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	intron	44669021	44669168	.	+	.	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	CDS	44669169	44671029	0.36	+	1	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	exon	44669169	44671029	.	+	.	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
Phchi.S1	AUGUSTUS	stop_codon	44671030	44671032	.	+	0	transcript_id "Phchi.S1G711900.t1"; gene_id "Phchi.S1G711900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11943.t1 is derived from g7618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	141986	143248	.	+	.	Phchi.S2G002300
Phchi.S2	AUGUSTUS	transcript	141986	143248	.	+	.	transcript_id "Phchi.S2G002300.t1"; gene_id "Phchi.S2G002300"
Phchi.S2	AUGUSTUS	start_codon	141986	141988	.	+	0	transcript_id "Phchi.S2G002300.t1"; gene_id "Phchi.S2G002300"
Phchi.S2	AUGUSTUS	CDS	141986	143248	0.55	+	0	transcript_id "Phchi.S2G002300.t1"; gene_id "Phchi.S2G002300"
Phchi.S2	AUGUSTUS	exon	141986	143248	.	+	.	transcript_id "Phchi.S2G002300.t1"; gene_id "Phchi.S2G002300"
Phchi.S2	AUGUSTUS	stop_codon	143249	143251	.	+	0	transcript_id "Phchi.S2G002300.t1"; gene_id "Phchi.S2G002300"
# This transcript jg13791.t2 is derived from g12258.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13791.t3 is derived from g12258.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13791.t4 is derived from g12258.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13792.t1 is derived from g12259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8905181	8907064	.	+	.	Phchi.S3G111100
Phchi.S3	AUGUSTUS	transcript	8905181	8907064	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	start_codon	8905181	8905183	.	+	0	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	CDS	8905181	8905547	0.97	+	0	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	exon	8905181	8905547	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	intron	8905548	8905931	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	CDS	8905932	8906032	1	+	2	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	exon	8905932	8906032	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	intron	8906033	8906289	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	CDS	8906290	8906387	1	+	0	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	exon	8906290	8906387	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	intron	8906388	8906472	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	CDS	8906473	8906711	1	+	1	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	exon	8906473	8906711	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	intron	8906712	8906809	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	CDS	8906810	8906850	1	+	2	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	exon	8906810	8906850	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	intron	8906851	8906980	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	CDS	8906981	8907064	0.89	+	0	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	exon	8906981	8907064	.	+	.	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
Phchi.S3	AUGUSTUS	stop_codon	8907065	8907067	.	+	0	transcript_id "Phchi.S3G111100.t1"; gene_id "Phchi.S3G111100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8903.t1 is derived from g6078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38577923	38579248	.	+	.	Phchi.S1G606200
Phchi.S1	AUGUSTUS	transcript	38577923	38579248	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	start_codon	38577923	38577925	.	+	0	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38577923	38578057	1	+	0	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38577923	38578057	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	intron	38578058	38578142	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38578143	38578235	1	+	0	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38578143	38578235	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	intron	38578236	38578330	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38578331	38578475	1	+	0	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38578331	38578475	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	intron	38578476	38578560	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38578561	38578671	1	+	2	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38578561	38578671	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	intron	38578672	38578757	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38578758	38578840	1	+	2	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38578758	38578840	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	intron	38578841	38578973	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38578974	38579031	1	+	0	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38578974	38579031	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	intron	38579032	38579171	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	CDS	38579172	38579248	1	+	2	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	exon	38579172	38579248	.	+	.	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
Phchi.S1	AUGUSTUS	stop_codon	38579249	38579251	.	+	0	transcript_id "Phchi.S1G606200.t1"; gene_id "Phchi.S1G606200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1649.t1 is derived from g8568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2211234	2215138	.	-	.	Phchi.S5G025800
Phchi.S5	AUGUSTUS	transcript	2211234	2215138	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	stop_codon	2211231	2211233	.	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2211234	2211235	0.99	-	2	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2211234	2211235	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2211236	2211356	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2211357	2211705	0.99	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2211357	2211705	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2211706	2211806	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2211807	2212102	1	-	2	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2211807	2212102	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2212103	2212224	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2212225	2212396	0.99	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2212225	2212396	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2212397	2212508	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2212509	2212664	0.97	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2212509	2212664	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2212665	2212764	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2212765	2213178	0.84	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2212765	2213178	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2213179	2213294	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2213295	2213882	0.64	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2213295	2213882	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2213883	2213970	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2213971	2214707	0.63	-	2	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2213971	2214707	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2214708	2214799	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2214800	2214866	1	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2214800	2214866	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	intron	2214867	2214943	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	CDS	2214944	2215138	0.92	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	exon	2214944	2215138	.	-	.	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
Phchi.S5	AUGUSTUS	start_codon	2215136	2215138	.	-	0	transcript_id "Phchi.S5G025800.t1"; gene_id "Phchi.S5G025800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2413.t1 is derived from g9333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6540441	6541144	.	+	.	Phchi.S5G102200
Phchi.S5	AUGUSTUS	transcript	6540441	6541144	.	+	.	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	start_codon	6540441	6540443	.	+	0	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	CDS	6540441	6540714	0.71	+	0	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	exon	6540441	6540714	.	+	.	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	intron	6540715	6540821	.	+	.	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	CDS	6540822	6541040	0.24	+	2	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	exon	6540822	6541040	.	+	.	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	intron	6541041	6541115	.	+	.	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	CDS	6541116	6541144	0.38	+	2	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	exon	6541116	6541144	.	+	.	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
Phchi.S5	AUGUSTUS	stop_codon	6541145	6541147	.	+	0	transcript_id "Phchi.S5G102200.t1"; gene_id "Phchi.S5G102200"
# This transcript jg4899.t2 is derived from g2069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4900.t1 is derived from g2070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13321863	13324984	.	-	.	Phchi.S1G205900
Phchi.S1	AUGUSTUS	transcript	13321863	13324984	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	stop_codon	13321860	13321862	.	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13321863	13321888	1	-	2	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13321863	13321888	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13321889	13322088	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322089	13322497	0.98	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322089	13322497	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322498	13322580	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322581	13322716	1	-	1	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322581	13322716	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322717	13322810	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322811	13322866	1	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322811	13322866	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322867	13323187	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323188	13323268	1	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323188	13323268	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323269	13323367	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323368	13323449	1	-	1	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323368	13323449	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323450	13323543	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323544	13323656	1	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323544	13323656	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323657	13323747	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323748	13323855	1	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323748	13323855	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323856	13323986	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323987	13324098	1	-	1	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323987	13324098	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324099	13324233	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324234	13324343	1	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324234	13324343	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324344	13324431	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324432	13324569	1	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324432	13324569	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324570	13324657	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324658	13324984	0.99	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324658	13324984	.	-	.	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	start_codon	13324982	13324984	.	-	0	transcript_id "Phchi.S1G205900.t1"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	transcript	13321863	13324984	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	stop_codon	13321860	13321862	.	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13321863	13321888	1	-	2	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13321863	13321888	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13321889	13322088	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322089	13322497	0.99	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322089	13322497	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322498	13322580	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322581	13322716	1	-	1	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322581	13322716	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322717	13322810	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322811	13322866	1	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322811	13322866	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322867	13322952	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322953	13322977	0.98	-	1	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322953	13322977	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322978	13323206	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323207	13323268	0.69	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323207	13323268	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323269	13323367	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323368	13323449	1	-	1	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323368	13323449	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323450	13323543	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323544	13323656	1	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323544	13323656	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323657	13323747	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323748	13323855	1	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323748	13323855	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323856	13323986	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323987	13324098	1	-	1	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323987	13324098	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324099	13324233	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324234	13324343	1	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324234	13324343	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324344	13324431	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324432	13324569	1	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324432	13324569	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324570	13324657	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324658	13324984	0.98	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324658	13324984	.	-	.	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	start_codon	13324982	13324984	.	-	0	transcript_id "Phchi.S1G205900.t2"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	transcript	13321863	13324984	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	stop_codon	13321860	13321862	.	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13321863	13321888	1	-	2	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13321863	13321888	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13321889	13322088	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322089	13322497	1	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322089	13322497	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322498	13322580	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322581	13322620	0.59	-	1	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322581	13322620	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322621	13322703	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322704	13322733	0.56	-	1	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322704	13322733	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322734	13322810	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13322811	13322866	0.96	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13322811	13322866	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13322867	13323187	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323188	13323268	1	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323188	13323268	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323269	13323367	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323368	13323449	1	-	1	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323368	13323449	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323450	13323543	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323544	13323656	1	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323544	13323656	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323657	13323747	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323748	13323855	1	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323748	13323855	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13323856	13323986	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13323987	13324098	1	-	1	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13323987	13324098	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324099	13324233	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324234	13324343	1	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324234	13324343	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324344	13324431	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324432	13324569	1	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324432	13324569	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	intron	13324570	13324657	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	CDS	13324658	13324984	0.96	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	exon	13324658	13324984	.	-	.	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
Phchi.S1	AUGUSTUS	start_codon	13324982	13324984	.	-	0	transcript_id "Phchi.S1G205900.t3"; gene_id "Phchi.S1G205900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3152.t1 is derived from g321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1988738	1989409	.	-	.	Phchi.S1G031100
Phchi.S1	AUGUSTUS	transcript	1988738	1989409	.	-	.	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	stop_codon	1988735	1988737	.	-	0	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	CDS	1988738	1989209	0.73	-	1	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	exon	1988738	1989209	.	-	.	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	intron	1989210	1989302	.	-	.	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	CDS	1989303	1989409	0.86	-	0	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	exon	1989303	1989409	.	-	.	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
Phchi.S1	AUGUSTUS	start_codon	1989407	1989409	.	-	0	transcript_id "Phchi.S1G031100.t1"; gene_id "Phchi.S1G031100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8463.t1 is derived from g5638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36054659	36057976	.	-	.	Phchi.S1G562200
Phchi.S1	AUGUSTUS	transcript	36054659	36057976	.	-	.	transcript_id "Phchi.S1G562200.t1"; gene_id "Phchi.S1G562200"
Phchi.S1	AUGUSTUS	stop_codon	36054656	36054658	.	-	0	transcript_id "Phchi.S1G562200.t1"; gene_id "Phchi.S1G562200"
Phchi.S1	AUGUSTUS	CDS	36054659	36057976	0.46	-	0	transcript_id "Phchi.S1G562200.t1"; gene_id "Phchi.S1G562200"
Phchi.S1	AUGUSTUS	exon	36054659	36057976	.	-	.	transcript_id "Phchi.S1G562200.t1"; gene_id "Phchi.S1G562200"
Phchi.S1	AUGUSTUS	start_codon	36057974	36057976	.	-	0	transcript_id "Phchi.S1G562200.t1"; gene_id "Phchi.S1G562200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10931.t1 is derived from g14981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3046615	3049016	.	+	.	Phchi.S4G051300
Phchi.S4	AUGUSTUS	transcript	3046615	3049016	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	start_codon	3046615	3046617	.	+	0	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	CDS	3046615	3046792	0.61	+	0	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	exon	3046615	3046792	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	intron	3046793	3046908	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	CDS	3046909	3047126	1	+	2	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	exon	3046909	3047126	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	intron	3047127	3047259	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	CDS	3047260	3047660	0.99	+	0	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	exon	3047260	3047660	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	intron	3047661	3047863	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	CDS	3047864	3048034	0.99	+	1	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	exon	3047864	3048034	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	intron	3048035	3048169	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	CDS	3048170	3049016	1	+	1	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	exon	3048170	3049016	.	+	.	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
Phchi.S4	AUGUSTUS	stop_codon	3049017	3049019	.	+	0	transcript_id "Phchi.S4G051300.t1"; gene_id "Phchi.S4G051300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12520.t1 is derived from g8197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32804548	32805515	.	+	.	Phchi.S2G060000
Phchi.S2	AUGUSTUS	transcript	32804548	32805515	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	start_codon	32804548	32804550	.	+	0	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	CDS	32804548	32804784	0.98	+	0	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	exon	32804548	32804784	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	intron	32804785	32804868	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	CDS	32804869	32805012	1	+	0	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	exon	32804869	32805012	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	intron	32805013	32805106	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	CDS	32805107	32805239	1	+	0	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	exon	32805107	32805239	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	intron	32805240	32805312	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	CDS	32805313	32805352	1	+	2	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	exon	32805313	32805352	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	intron	32805353	32805430	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	CDS	32805431	32805515	0.98	+	1	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	exon	32805431	32805515	.	+	.	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
Phchi.S2	AUGUSTUS	stop_codon	32805516	32805518	.	+	0	transcript_id "Phchi.S2G060000.t1"; gene_id "Phchi.S2G060000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg857.t1 is derived from g10639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5955877	5957095	.	-	.	Phchi.S6G081600
Phchi.S6	AUGUSTUS	transcript	5955877	5957095	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	stop_codon	5955874	5955876	.	-	0	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	CDS	5955877	5956269	1	-	0	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	exon	5955877	5956269	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	intron	5956270	5956361	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	CDS	5956362	5956580	1	-	0	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	exon	5956362	5956580	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	intron	5956581	5956656	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	CDS	5956657	5956779	1	-	0	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	exon	5956657	5956779	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	intron	5956780	5956918	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	CDS	5956919	5957095	1	-	0	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	exon	5956919	5957095	.	-	.	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
Phchi.S6	AUGUSTUS	start_codon	5957093	5957095	.	-	0	transcript_id "Phchi.S6G081600.t1"; gene_id "Phchi.S6G081600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg909.t1 is derived from g10691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6382460	6383767	.	+	.	Phchi.S6G086800
Phchi.S6	AUGUSTUS	transcript	6382460	6383767	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	start_codon	6382460	6382462	.	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6382460	6382536	0.5	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6382460	6382536	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	intron	6382537	6382630	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6382631	6382769	1	+	1	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6382631	6382769	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	intron	6382770	6382865	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6382866	6382940	1	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6382866	6382940	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	intron	6382941	6383037	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6383038	6383159	1	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6383038	6383159	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	intron	6383160	6383328	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6383329	6383404	1	+	1	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6383329	6383404	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	intron	6383405	6383488	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6383489	6383548	1	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6383489	6383548	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	intron	6383549	6383632	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	CDS	6383633	6383767	0.88	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	exon	6383633	6383767	.	+	.	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
Phchi.S6	AUGUSTUS	stop_codon	6383768	6383770	.	+	0	transcript_id "Phchi.S6G086800.t1"; gene_id "Phchi.S6G086800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8558.t1 is derived from g5733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36616462	36618035	.	+	.	Phchi.S1G571700
Phchi.S1	AUGUSTUS	transcript	36616462	36618035	.	+	.	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	start_codon	36616462	36616464	.	+	0	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	CDS	36616462	36616965	0.7	+	0	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	exon	36616462	36616965	.	+	.	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	intron	36616966	36617096	.	+	.	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	CDS	36617097	36618035	0.35	+	0	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	exon	36617097	36618035	.	+	.	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
Phchi.S1	AUGUSTUS	stop_codon	36618036	36618038	.	+	0	transcript_id "Phchi.S1G571700.t1"; gene_id "Phchi.S1G571700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14056.t1 is derived from g12523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10533366	10534717	.	+	.	Phchi.S3G137500
Phchi.S3	AUGUSTUS	transcript	10533366	10534717	.	+	.	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	start_codon	10533366	10533368	.	+	0	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	CDS	10533366	10533444	0.49	+	0	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	exon	10533366	10533444	.	+	.	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	intron	10533445	10533588	.	+	.	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	CDS	10533589	10534346	0.63	+	2	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	exon	10533589	10534346	.	+	.	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	intron	10534347	10534486	.	+	.	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	CDS	10534487	10534717	0.61	+	0	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	exon	10534487	10534717	.	+	.	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
Phchi.S3	AUGUSTUS	stop_codon	10534718	10534720	.	+	0	transcript_id "Phchi.S3G137500.t1"; gene_id "Phchi.S3G137500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg625.t1 is derived from g10407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4457988	4458903	.	-	.	Phchi.S6G058400
Phchi.S6	AUGUSTUS	transcript	4457988	4458903	.	-	.	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	stop_codon	4457985	4457987	.	-	0	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	CDS	4457988	4458314	0.71	-	0	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	exon	4457988	4458314	.	-	.	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	intron	4458315	4458509	.	-	.	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	CDS	4458510	4458675	0.31	-	1	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	exon	4458510	4458675	.	-	.	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	intron	4458676	4458760	.	-	.	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	CDS	4458761	4458903	0.66	-	0	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	exon	4458761	4458903	.	-	.	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
Phchi.S6	AUGUSTUS	start_codon	4458901	4458903	.	-	0	transcript_id "Phchi.S6G058400.t1"; gene_id "Phchi.S6G058400"
# This transcript jg10467.t2 is derived from g14516.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10468.t1 is derived from g14517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	537694	539075	.	+	.	Phchi.S4G005000
Phchi.S4	AUGUSTUS	transcript	537694	539075	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	start_codon	537694	537696	.	+	0	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	CDS	537694	537909	0.35	+	0	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	exon	537694	537909	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	intron	537910	538001	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	CDS	538002	538209	0.99	+	0	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	exon	538002	538209	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	intron	538210	538295	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	CDS	538296	538467	0.99	+	2	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	exon	538296	538467	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	intron	538468	538548	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	CDS	538549	538645	1	+	1	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	exon	538549	538645	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	intron	538646	538742	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	CDS	538743	539075	1	+	0	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	exon	538743	539075	.	+	.	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
Phchi.S4	AUGUSTUS	stop_codon	539076	539078	.	+	0	transcript_id "Phchi.S4G005000.t1"; gene_id "Phchi.S4G005000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13109.t1 is derived from g11574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4183433	4186386	.	-	.	Phchi.S3G042800
Phchi.S3	AUGUSTUS	transcript	4183433	4186386	.	-	.	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	stop_codon	4183430	4183432	.	-	0	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	CDS	4183433	4186170	0.58	-	2	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	exon	4183433	4186170	.	-	.	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	intron	4186171	4186265	.	-	.	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	CDS	4186266	4186386	1	-	0	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	exon	4186266	4186386	.	-	.	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
Phchi.S3	AUGUSTUS	start_codon	4186384	4186386	.	-	0	transcript_id "Phchi.S3G042800.t1"; gene_id "Phchi.S3G042800"
# This transcript jg976.t2 is derived from g10759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg977.t1 is derived from g10760.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6758613	6759790	.	+	.	Phchi.S6G093600
Phchi.S6	AUGUSTUS	transcript	6758613	6759604	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	start_codon	6758613	6758615	.	+	0	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6758613	6759067	0.17	+	0	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6758613	6759067	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759068	6759214	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759215	6759288	1	+	1	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759215	6759288	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759289	6759427	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759428	6759488	1	+	2	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759428	6759488	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759489	6759582	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759583	6759604	1	+	1	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759583	6759604	.	+	.	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	stop_codon	6759605	6759607	.	+	0	transcript_id "Phchi.S6G093600.t1"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	transcript	6758613	6759790	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	start_codon	6758613	6758615	.	+	0	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6758613	6759067	0.25	+	0	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6758613	6759067	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759068	6759214	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759215	6759288	1	+	1	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759215	6759288	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759289	6759416	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759417	6759488	0.85	+	2	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759417	6759488	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759489	6759582	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759583	6759609	0.84	+	2	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759583	6759609	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	intron	6759610	6759716	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	CDS	6759717	6759790	0.84	+	2	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	exon	6759717	6759790	.	+	.	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
Phchi.S6	AUGUSTUS	stop_codon	6759791	6759793	.	+	0	transcript_id "Phchi.S6G093600.t2"; gene_id "Phchi.S6G093600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13027.t1 is derived from g11492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3736306	3738660	.	+	.	Phchi.S3G034600
Phchi.S3	AUGUSTUS	transcript	3736306	3738660	.	+	.	transcript_id "Phchi.S3G034600.t1"; gene_id "Phchi.S3G034600"
Phchi.S3	AUGUSTUS	start_codon	3736306	3736308	.	+	0	transcript_id "Phchi.S3G034600.t1"; gene_id "Phchi.S3G034600"
Phchi.S3	AUGUSTUS	CDS	3736306	3738660	1	+	0	transcript_id "Phchi.S3G034600.t1"; gene_id "Phchi.S3G034600"
Phchi.S3	AUGUSTUS	exon	3736306	3738660	.	+	.	transcript_id "Phchi.S3G034600.t1"; gene_id "Phchi.S3G034600"
Phchi.S3	AUGUSTUS	stop_codon	3738661	3738663	.	+	0	transcript_id "Phchi.S3G034600.t1"; gene_id "Phchi.S3G034600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8255.t1 is derived from g5430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34734925	34737492	.	-	.	Phchi.S1G541400
Phchi.S1	AUGUSTUS	transcript	34734925	34737492	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	stop_codon	34734922	34734924	.	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34734925	34735554	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34734925	34735554	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34735555	34735636	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34735637	34735717	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34735637	34735717	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34735718	34735810	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34735811	34735870	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34735811	34735870	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34735871	34735965	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34735966	34736190	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34735966	34736190	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34736191	34736307	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34736308	34736502	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34736308	34736502	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34736503	34736586	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34736587	34736704	1	-	1	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34736587	34736704	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34736705	34736795	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34736796	34737175	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34736796	34737175	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	intron	34737176	34737261	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	CDS	34737262	34737492	1	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	exon	34737262	34737492	.	-	.	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
Phchi.S1	AUGUSTUS	start_codon	34737490	34737492	.	-	0	transcript_id "Phchi.S1G541400.t1"; gene_id "Phchi.S1G541400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15102.t1 is derived from g13570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17072037	17072828	.	+	.	Phchi.S3G242100
Phchi.S3	AUGUSTUS	transcript	17072037	17072828	.	+	.	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	start_codon	17072037	17072039	.	+	0	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	CDS	17072037	17072093	0.98	+	0	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	exon	17072037	17072093	.	+	.	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	intron	17072094	17072192	.	+	.	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	CDS	17072193	17072354	0.77	+	0	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	exon	17072193	17072354	.	+	.	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	intron	17072355	17072477	.	+	.	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	CDS	17072478	17072828	0.8	+	0	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	exon	17072478	17072828	.	+	.	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
Phchi.S3	AUGUSTUS	stop_codon	17072829	17072831	.	+	0	transcript_id "Phchi.S3G242100.t1"; gene_id "Phchi.S3G242100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2114.t1 is derived from g9034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4924235	4924772	.	-	.	Phchi.S5G072300
Phchi.S5	AUGUSTUS	transcript	4924235	4924772	.	-	.	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	stop_codon	4924232	4924234	.	-	0	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	CDS	4924235	4924303	1	-	0	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	exon	4924235	4924303	.	-	.	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	intron	4924304	4924384	.	-	.	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	CDS	4924385	4924517	1	-	1	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	exon	4924385	4924517	.	-	.	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	intron	4924518	4924614	.	-	.	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	CDS	4924615	4924772	0.99	-	0	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	exon	4924615	4924772	.	-	.	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
Phchi.S5	AUGUSTUS	start_codon	4924770	4924772	.	-	0	transcript_id "Phchi.S5G072300.t1"; gene_id "Phchi.S5G072300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6624.t1 is derived from g3796.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24139964	24142650	.	-	.	Phchi.S1G378300
Phchi.S1	AUGUSTUS	transcript	24139964	24142650	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	stop_codon	24139961	24139963	.	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24139964	24140113	0.81	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24139964	24140113	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24140114	24140464	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24140465	24140503	1	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24140465	24140503	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24140504	24140598	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24140599	24140777	0.7	-	2	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24140599	24140777	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24140778	24140896	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24140897	24141296	0.74	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24140897	24141296	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24141297	24141376	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24141377	24141505	1	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24141377	24141505	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24141506	24141603	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24141604	24141918	1	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24141604	24141918	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24141919	24142014	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24142015	24142134	1	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24142015	24142134	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24142135	24142213	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24142214	24142289	1	-	1	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24142214	24142289	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24142290	24142399	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24142400	24142650	0.96	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24142400	24142650	.	-	.	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	start_codon	24142648	24142650	.	-	0	transcript_id "Phchi.S1G378300.t1"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	transcript	24139964	24142650	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	stop_codon	24139961	24139963	.	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24139964	24140113	0.93	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24139964	24140113	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24140114	24140464	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24140465	24140503	1	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24140465	24140503	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24140504	24140598	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24140599	24140777	0.66	-	2	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24140599	24140777	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24140778	24140896	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24140897	24141296	0.66	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24140897	24141296	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24141297	24141376	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24141377	24141505	1	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24141377	24141505	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24141506	24141603	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24141604	24141918	1	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24141604	24141918	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24141919	24142014	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24142015	24142134	0.97	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24142015	24142134	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24142135	24142279	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24142280	24142289	0.97	-	1	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24142280	24142289	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	intron	24142290	24142399	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	CDS	24142400	24142650	0.96	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	exon	24142400	24142650	.	-	.	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
Phchi.S1	AUGUSTUS	start_codon	24142648	24142650	.	-	0	transcript_id "Phchi.S1G378300.t2"; gene_id "Phchi.S1G378300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg866.t1 is derived from g10648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5992661	5993854	.	-	.	Phchi.S6G082500
Phchi.S6	AUGUSTUS	transcript	5992661	5993854	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	stop_codon	5992658	5992660	.	-	0	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	CDS	5992661	5992774	1	-	0	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	exon	5992661	5992774	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	intron	5992775	5992867	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	CDS	5992868	5993008	1	-	0	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	exon	5992868	5993008	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	intron	5993009	5993093	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	CDS	5993094	5993148	1	-	1	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	exon	5993094	5993148	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	intron	5993149	5993317	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	CDS	5993318	5993461	1	-	1	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	exon	5993318	5993461	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	intron	5993462	5993585	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	CDS	5993586	5993638	1	-	0	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	exon	5993586	5993638	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	intron	5993639	5993821	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	CDS	5993822	5993854	1	-	0	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	exon	5993822	5993854	.	-	.	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
Phchi.S6	AUGUSTUS	start_codon	5993852	5993854	.	-	0	transcript_id "Phchi.S6G082500.t1"; gene_id "Phchi.S6G082500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12705.t1 is derived from g11170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	651835	653236	.	+	.	Phchi.S3G002400
Phchi.S3	AUGUSTUS	transcript	651835	653236	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	start_codon	651835	651837	.	+	0	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	CDS	651835	651927	1	+	0	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	exon	651835	651927	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	intron	651928	652268	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	CDS	652269	652409	1	+	0	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	exon	652269	652409	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	intron	652410	652530	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	CDS	652531	652639	1	+	0	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	exon	652531	652639	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	intron	652640	652782	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	CDS	652783	652844	0.96	+	2	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	exon	652783	652844	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	intron	652845	652955	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	CDS	652956	653059	1	+	0	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	exon	652956	653059	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	intron	653060	653136	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	CDS	653137	653236	1	+	1	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	exon	653137	653236	.	+	.	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
Phchi.S3	AUGUSTUS	stop_codon	653237	653239	.	+	0	transcript_id "Phchi.S3G002400.t1"; gene_id "Phchi.S3G002400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1193.t1 is derived from g10976.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8362044	8365136	.	-	.	Phchi.S6G115200
Phchi.S6	AUGUSTUS	transcript	8362044	8365136	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	stop_codon	8362041	8362043	.	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8362044	8362790	0.64	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8362044	8362790	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8362791	8362869	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8362870	8362929	0.99	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8362870	8362929	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8362930	8363011	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363012	8363087	1	-	1	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363012	8363087	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363088	8363183	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363184	8363323	1	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363184	8363323	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363324	8363460	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363461	8363551	1	-	1	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363461	8363551	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363552	8363676	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363677	8363819	1	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363677	8363819	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363820	8364034	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8364035	8364475	1	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8364035	8364475	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8364476	8364605	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8364606	8365136	0.95	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8364606	8365136	.	-	.	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	start_codon	8365134	8365136	.	-	0	transcript_id "Phchi.S6G115200.t1"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	transcript	8362044	8365136	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	stop_codon	8362041	8362043	.	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8362044	8362790	0.62	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8362044	8362790	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8362791	8362869	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8362870	8362929	0.99	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8362870	8362929	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8362930	8363011	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363012	8363087	1	-	1	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363012	8363087	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363088	8363201	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363202	8363323	0.65	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363202	8363323	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363324	8363460	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363461	8363551	1	-	1	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363461	8363551	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363552	8363676	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8363677	8363819	1	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8363677	8363819	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8363820	8364034	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8364035	8364475	1	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8364035	8364475	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	intron	8364476	8364605	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	CDS	8364606	8365136	0.98	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	exon	8364606	8365136	.	-	.	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
Phchi.S6	AUGUSTUS	start_codon	8365134	8365136	.	-	0	transcript_id "Phchi.S6G115200.t2"; gene_id "Phchi.S6G115200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5696.t1 is derived from g2866.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18374153	18375385	.	+	.	Phchi.S1G285500
Phchi.S1	AUGUSTUS	transcript	18374153	18375385	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	start_codon	18374153	18374155	.	+	0	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374153	18374363	1	+	0	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374153	18374363	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18374364	18374469	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374470	18374541	0.99	+	2	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374470	18374541	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18374542	18374644	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374645	18374732	0.85	+	2	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374645	18374732	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18374733	18374872	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374873	18375005	1	+	1	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374873	18375005	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18375006	18375120	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18375121	18375159	1	+	0	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18375121	18375159	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18375160	18375283	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18375284	18375385	1	+	0	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18375284	18375385	.	+	.	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	stop_codon	18375386	18375388	.	+	0	transcript_id "Phchi.S1G285500.t1"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	transcript	18374153	18375385	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	start_codon	18374153	18374155	.	+	0	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374153	18374363	1	+	0	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374153	18374363	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18374364	18374469	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374470	18374541	1	+	2	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374470	18374541	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18374542	18374644	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374645	18374732	0.89	+	2	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374645	18374732	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18374733	18374998	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18374999	18375005	0.93	+	1	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18374999	18375005	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18375006	18375120	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18375121	18375159	0.98	+	0	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18375121	18375159	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	intron	18375160	18375283	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	CDS	18375284	18375385	0.98	+	0	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	exon	18375284	18375385	.	+	.	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
Phchi.S1	AUGUSTUS	stop_codon	18375386	18375388	.	+	0	transcript_id "Phchi.S1G285500.t2"; gene_id "Phchi.S1G285500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2857.t1 is derived from g26.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	78355	82147	.	-	.	Phchi.S1G001600
Phchi.S1	AUGUSTUS	transcript	78355	82147	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	stop_codon	78352	78354	.	-	0	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	78355	79661	1	-	2	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	78355	79661	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	79662	79781	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	79782	80233	1	-	1	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	79782	80233	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	80234	80357	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	80358	80455	1	-	0	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	80358	80455	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	80456	80531	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	80532	80600	1	-	0	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	80532	80600	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	80601	80786	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	80787	80900	1	-	0	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	80787	80900	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	80901	81059	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	81060	81154	1	-	2	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	81060	81154	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	81155	81289	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	81290	81351	0.9	-	1	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	81290	81351	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	81352	81452	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	81453	81612	0.97	-	2	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	81453	81612	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	intron	81613	81855	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	CDS	81856	82147	1	-	0	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	exon	81856	82147	.	-	.	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
Phchi.S1	AUGUSTUS	start_codon	82145	82147	.	-	0	transcript_id "Phchi.S1G001600.t1"; gene_id "Phchi.S1G001600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12986.t1 is derived from g11451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3458958	3460243	.	-	.	Phchi.S3G030500
Phchi.S3	AUGUSTUS	transcript	3458958	3460243	.	-	.	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	stop_codon	3458955	3458957	.	-	0	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	CDS	3458958	3459584	0.68	-	0	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	exon	3458958	3459584	.	-	.	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	intron	3459585	3459775	.	-	.	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	CDS	3459776	3460243	1	-	0	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	exon	3459776	3460243	.	-	.	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
Phchi.S3	AUGUSTUS	start_codon	3460241	3460243	.	-	0	transcript_id "Phchi.S3G030500.t1"; gene_id "Phchi.S3G030500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15726.t1 is derived from g14196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20906987	20908295	.	+	.	Phchi.S3G304500
Phchi.S3	AUGUSTUS	transcript	20906987	20908295	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	start_codon	20906987	20906989	.	+	0	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20906987	20907072	0.95	+	0	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20906987	20907072	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	intron	20907073	20907178	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20907179	20907273	0.81	+	1	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20907179	20907273	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	intron	20907274	20907354	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20907355	20907441	0.81	+	2	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20907355	20907441	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	intron	20907442	20907529	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20907530	20907616	1	+	2	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20907530	20907616	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	intron	20907617	20907706	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20907707	20907870	1	+	2	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20907707	20907870	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	intron	20907871	20907953	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20907954	20908070	1	+	0	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20907954	20908070	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	intron	20908071	20908166	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	CDS	20908167	20908295	0.51	+	0	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	exon	20908167	20908295	.	+	.	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
Phchi.S3	AUGUSTUS	stop_codon	20908296	20908298	.	+	0	transcript_id "Phchi.S3G304500.t1"; gene_id "Phchi.S3G304500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7407.t1 is derived from g4579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28983971	28984703	.	+	.	Phchi.S1G456600
Phchi.S1	AUGUSTUS	transcript	28983971	28984703	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	start_codon	28983971	28983973	.	+	0	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	CDS	28983971	28984008	0.82	+	0	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	exon	28983971	28984008	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	intron	28984009	28984105	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	CDS	28984106	28984116	0.82	+	1	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	exon	28984106	28984116	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	intron	28984117	28984221	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	CDS	28984222	28984227	0.83	+	2	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	exon	28984222	28984227	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	intron	28984228	28984425	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	CDS	28984426	28984703	0.83	+	2	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	exon	28984426	28984703	.	+	.	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
Phchi.S1	AUGUSTUS	stop_codon	28984704	28984706	.	+	0	transcript_id "Phchi.S1G456600.t1"; gene_id "Phchi.S1G456600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10549.t1 is derived from g14599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	945537	946393	.	+	.	Phchi.S4G013100
Phchi.S4	AUGUSTUS	transcript	945537	946393	.	+	.	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	start_codon	945537	945539	.	+	0	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	CDS	945537	946100	0.53	+	0	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	exon	945537	946100	.	+	.	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	intron	946101	946291	.	+	.	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	CDS	946292	946393	0.58	+	0	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	exon	946292	946393	.	+	.	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
Phchi.S4	AUGUSTUS	stop_codon	946394	946396	.	+	0	transcript_id "Phchi.S4G013100.t1"; gene_id "Phchi.S4G013100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12237.t1 is derived from g7913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6929824	6931610	.	+	.	Phchi.S2G031700
Phchi.S2	AUGUSTUS	transcript	6929824	6931610	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	start_codon	6929824	6929826	.	+	0	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6929824	6929886	1	+	0	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6929824	6929886	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6929887	6929996	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6929997	6930289	1	+	0	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6929997	6930289	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6930290	6930369	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6930370	6930514	1	+	1	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6930370	6930514	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6930515	6930616	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6930617	6930728	0.96	+	0	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6930617	6930728	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6930729	6930825	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6930826	6930976	0.99	+	2	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6930826	6930976	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6930977	6931079	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6931080	6931265	0.99	+	1	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6931080	6931265	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6931266	6931350	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6931351	6931431	0.96	+	1	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6931351	6931431	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	intron	6931432	6931546	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	CDS	6931547	6931610	0.94	+	1	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	exon	6931547	6931610	.	+	.	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
Phchi.S2	AUGUSTUS	stop_codon	6931611	6931613	.	+	0	transcript_id "Phchi.S2G031700.t1"; gene_id "Phchi.S2G031700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6812.t1 is derived from g3984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25171706	25173095	.	-	.	Phchi.S1G397100
Phchi.S1	AUGUSTUS	transcript	25171706	25173095	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	stop_codon	25171703	25171705	.	-	0	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25171706	25171803	1	-	2	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25171706	25171803	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	intron	25171804	25171890	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25171891	25171987	1	-	0	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25171891	25171987	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	intron	25171988	25172068	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25172069	25172140	1	-	0	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25172069	25172140	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	intron	25172141	25172227	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25172228	25172350	1	-	0	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25172228	25172350	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	intron	25172351	25172442	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25172443	25172516	1	-	2	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25172443	25172516	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	intron	25172517	25172676	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25172677	25172778	1	-	2	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25172677	25172778	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	intron	25172779	25172923	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	CDS	25172924	25173095	0.98	-	0	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	exon	25172924	25173095	.	-	.	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
Phchi.S1	AUGUSTUS	start_codon	25173093	25173095	.	-	0	transcript_id "Phchi.S1G397100.t1"; gene_id "Phchi.S1G397100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2376.t1 is derived from g9296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6410565	6411421	.	+	.	Phchi.S5G098500
Phchi.S5	AUGUSTUS	transcript	6410565	6411421	.	+	.	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	start_codon	6410565	6410567	.	+	0	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	CDS	6410565	6410758	1	+	0	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	exon	6410565	6410758	.	+	.	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	intron	6410759	6411414	.	+	.	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	CDS	6411415	6411421	1	+	1	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	exon	6411415	6411421	.	+	.	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
Phchi.S5	AUGUSTUS	stop_codon	6411422	6411424	.	+	0	transcript_id "Phchi.S5G098500.t1"; gene_id "Phchi.S5G098500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1583.t1 is derived from g8502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1873081	1874704	.	+	.	Phchi.S5G019200
Phchi.S5	AUGUSTUS	transcript	1873081	1874704	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	start_codon	1873081	1873083	.	+	0	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	CDS	1873081	1873349	1	+	0	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	exon	1873081	1873349	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	intron	1873350	1873431	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	CDS	1873432	1873779	0.57	+	1	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	exon	1873432	1873779	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	intron	1873780	1873874	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	CDS	1873875	1874308	0.93	+	1	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	exon	1873875	1874308	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	intron	1874309	1874441	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	CDS	1874442	1874704	0.66	+	2	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	exon	1874442	1874704	.	+	.	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
Phchi.S5	AUGUSTUS	stop_codon	1874705	1874707	.	+	0	transcript_id "Phchi.S5G019200.t1"; gene_id "Phchi.S5G019200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9881.t1 is derived from g7057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44239922	44240170	.	+	.	Phchi.S1G704000
Phchi.S1	AUGUSTUS	transcript	44239922	44240170	.	+	.	transcript_id "Phchi.S1G704000.t1"; gene_id "Phchi.S1G704000"
Phchi.S1	AUGUSTUS	start_codon	44239922	44239924	.	+	0	transcript_id "Phchi.S1G704000.t1"; gene_id "Phchi.S1G704000"
Phchi.S1	AUGUSTUS	CDS	44239922	44240170	0.91	+	0	transcript_id "Phchi.S1G704000.t1"; gene_id "Phchi.S1G704000"
Phchi.S1	AUGUSTUS	exon	44239922	44240170	.	+	.	transcript_id "Phchi.S1G704000.t1"; gene_id "Phchi.S1G704000"
Phchi.S1	AUGUSTUS	stop_codon	44240171	44240173	.	+	0	transcript_id "Phchi.S1G704000.t1"; gene_id "Phchi.S1G704000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12725.t1 is derived from g11190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1413642	1414191	.	-	.	Phchi.S3G004400
Phchi.S3	AUGUSTUS	transcript	1413642	1414191	.	-	.	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	stop_codon	1413639	1413641	.	-	0	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	CDS	1413642	1413838	0.69	-	2	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	exon	1413642	1413838	.	-	.	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	intron	1413839	1414010	.	-	.	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	CDS	1414011	1414191	0.48	-	0	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	exon	1414011	1414191	.	-	.	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
Phchi.S3	AUGUSTUS	start_codon	1414189	1414191	.	-	0	transcript_id "Phchi.S3G004400.t1"; gene_id "Phchi.S3G004400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3752.t1 is derived from g921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5499983	5502100	.	+	.	Phchi.S1G091100
Phchi.S1	AUGUSTUS	transcript	5499983	5502100	.	+	.	transcript_id "Phchi.S1G091100.t1"; gene_id "Phchi.S1G091100"
Phchi.S1	AUGUSTUS	start_codon	5499983	5499985	.	+	0	transcript_id "Phchi.S1G091100.t1"; gene_id "Phchi.S1G091100"
Phchi.S1	AUGUSTUS	CDS	5499983	5502100	0.52	+	0	transcript_id "Phchi.S1G091100.t1"; gene_id "Phchi.S1G091100"
Phchi.S1	AUGUSTUS	exon	5499983	5502100	.	+	.	transcript_id "Phchi.S1G091100.t1"; gene_id "Phchi.S1G091100"
Phchi.S1	AUGUSTUS	stop_codon	5502101	5502103	.	+	0	transcript_id "Phchi.S1G091100.t1"; gene_id "Phchi.S1G091100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6319.t1 is derived from g3491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22242890	22248614	.	-	.	Phchi.S1G347800
Phchi.S1	AUGUSTUS	transcript	22242890	22248614	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	stop_codon	22242887	22242889	.	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22242890	22242905	1	-	1	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22242890	22242905	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22242906	22243066	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22243067	22243134	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22243067	22243134	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22243135	22243265	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22243266	22243568	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22243266	22243568	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22243569	22243699	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22243700	22243924	0.96	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22243700	22243924	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22243925	22244016	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22244017	22244601	0.96	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22244017	22244601	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22244602	22244686	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22244687	22244785	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22244687	22244785	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22244786	22244872	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22244873	22245067	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22244873	22245067	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22245068	22245202	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22245203	22245307	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22245203	22245307	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22245308	22245397	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22245398	22245490	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22245398	22245490	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22245491	22245593	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22245594	22245808	0.97	-	2	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22245594	22245808	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22245809	22245935	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22245936	22246020	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22245936	22246020	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22246021	22246118	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22246119	22246229	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22246119	22246229	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22246230	22246381	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22246382	22246439	1	-	1	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22246382	22246439	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22246440	22246552	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22246553	22246671	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22246553	22246671	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22246672	22246745	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22246746	22246814	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22246746	22246814	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22246815	22246906	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22246907	22246981	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22246907	22246981	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22246982	22247077	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22247078	22247293	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22247078	22247293	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22247294	22247391	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22247392	22247508	1	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22247392	22247508	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22247509	22247599	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22247600	22247717	1	-	1	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22247600	22247717	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22247718	22247817	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22247818	22248053	0.99	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22247818	22248053	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22248054	22248127	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22248128	22248355	0.72	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22248128	22248355	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	intron	22248356	22248479	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	CDS	22248480	22248614	0.71	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	exon	22248480	22248614	.	-	.	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
Phchi.S1	AUGUSTUS	start_codon	22248612	22248614	.	-	0	transcript_id "Phchi.S1G347800.t1"; gene_id "Phchi.S1G347800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5517.t1 is derived from g2687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17196996	17198251	.	-	.	Phchi.S1G267600
Phchi.S1	AUGUSTUS	transcript	17196996	17198251	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	stop_codon	17196993	17196995	.	-	0	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	CDS	17196996	17197081	1	-	2	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	exon	17196996	17197081	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	intron	17197082	17197251	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	CDS	17197252	17197344	1	-	2	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	exon	17197252	17197344	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	intron	17197345	17197429	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	CDS	17197430	17197540	0.55	-	2	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	exon	17197430	17197540	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	intron	17197541	17197673	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	CDS	17197674	17197754	0.97	-	2	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	exon	17197674	17197754	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	intron	17197755	17197842	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	CDS	17197843	17197962	1	-	2	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	exon	17197843	17197962	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	intron	17197963	17198220	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	CDS	17198221	17198251	0.59	-	0	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	exon	17198221	17198251	.	-	.	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
Phchi.S1	AUGUSTUS	start_codon	17198249	17198251	.	-	0	transcript_id "Phchi.S1G267600.t1"; gene_id "Phchi.S1G267600"
# This transcript jg9421.t2 is derived from g6597.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9422.t1 is derived from g6598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41405881	41406919	.	+	.	Phchi.S1G658100
Phchi.S1	AUGUSTUS	transcript	41405881	41406919	.	+	.	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	start_codon	41405881	41405883	.	+	0	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	CDS	41405881	41406522	0.99	+	0	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	exon	41405881	41406522	.	+	.	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	intron	41406523	41406592	.	+	.	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	CDS	41406593	41406919	1	+	0	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	exon	41406593	41406919	.	+	.	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
Phchi.S1	AUGUSTUS	stop_codon	41406920	41406922	.	+	0	transcript_id "Phchi.S1G658100.t1"; gene_id "Phchi.S1G658100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5404.t1 is derived from g2574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16707535	16707765	.	+	.	Phchi.S1G256300
Phchi.S1	AUGUSTUS	transcript	16707535	16707765	.	+	.	transcript_id "Phchi.S1G256300.t1"; gene_id "Phchi.S1G256300"
Phchi.S1	AUGUSTUS	start_codon	16707535	16707537	.	+	0	transcript_id "Phchi.S1G256300.t1"; gene_id "Phchi.S1G256300"
Phchi.S1	AUGUSTUS	CDS	16707535	16707765	0.73	+	0	transcript_id "Phchi.S1G256300.t1"; gene_id "Phchi.S1G256300"
Phchi.S1	AUGUSTUS	exon	16707535	16707765	.	+	.	transcript_id "Phchi.S1G256300.t1"; gene_id "Phchi.S1G256300"
Phchi.S1	AUGUSTUS	stop_codon	16707766	16707768	.	+	0	transcript_id "Phchi.S1G256300.t1"; gene_id "Phchi.S1G256300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15563.t1 is derived from g14032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19927350	19928740	.	-	.	Phchi.S3G288200
Phchi.S3	AUGUSTUS	transcript	19927350	19928740	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	stop_codon	19927347	19927349	.	-	0	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	CDS	19927350	19927496	0.56	-	0	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	exon	19927350	19927496	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	intron	19927497	19927587	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	CDS	19927588	19927878	0.86	-	0	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	exon	19927588	19927878	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	intron	19927879	19927965	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	CDS	19927966	19928128	0.99	-	1	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	exon	19927966	19928128	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	intron	19928129	19928213	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	CDS	19928214	19928330	1	-	1	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	exon	19928214	19928330	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	intron	19928331	19928413	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	CDS	19928414	19928542	1	-	1	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	exon	19928414	19928542	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	intron	19928543	19928618	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	CDS	19928619	19928740	0.85	-	0	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	exon	19928619	19928740	.	-	.	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
Phchi.S3	AUGUSTUS	start_codon	19928738	19928740	.	-	0	transcript_id "Phchi.S3G288200.t1"; gene_id "Phchi.S3G288200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12389.t1 is derived from g8066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15430833	15431180	.	-	.	Phchi.S2G046900
Phchi.S2	AUGUSTUS	transcript	15430833	15431180	.	-	.	transcript_id "Phchi.S2G046900.t1"; gene_id "Phchi.S2G046900"
Phchi.S2	AUGUSTUS	stop_codon	15430830	15430832	.	-	0	transcript_id "Phchi.S2G046900.t1"; gene_id "Phchi.S2G046900"
Phchi.S2	AUGUSTUS	CDS	15430833	15431180	0.82	-	0	transcript_id "Phchi.S2G046900.t1"; gene_id "Phchi.S2G046900"
Phchi.S2	AUGUSTUS	exon	15430833	15431180	.	-	.	transcript_id "Phchi.S2G046900.t1"; gene_id "Phchi.S2G046900"
Phchi.S2	AUGUSTUS	start_codon	15431178	15431180	.	-	0	transcript_id "Phchi.S2G046900.t1"; gene_id "Phchi.S2G046900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13489.t1 is derived from g11956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7137419	7139729	.	-	.	Phchi.S3G080800
Phchi.S3	AUGUSTUS	transcript	7137419	7139729	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	stop_codon	7137416	7137418	.	-	0	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	CDS	7137419	7137996	1	-	2	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	exon	7137419	7137996	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	intron	7137997	7138092	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	CDS	7138093	7138519	0.62	-	0	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	exon	7138093	7138519	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	intron	7138520	7138602	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	CDS	7138603	7139005	1	-	1	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	exon	7138603	7139005	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	intron	7139006	7139169	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	CDS	7139170	7139271	1	-	1	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	exon	7139170	7139271	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	intron	7139272	7139436	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	CDS	7139437	7139729	0.65	-	0	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	exon	7139437	7139729	.	-	.	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
Phchi.S3	AUGUSTUS	start_codon	7139727	7139729	.	-	0	transcript_id "Phchi.S3G080800.t1"; gene_id "Phchi.S3G080800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3927.t1 is derived from g1096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6469364	6471366	.	-	.	Phchi.S1G108600
Phchi.S1	AUGUSTUS	transcript	6469364	6471366	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	stop_codon	6469361	6469363	.	-	0	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	CDS	6469364	6469392	1	-	2	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	exon	6469364	6469392	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	intron	6469393	6469507	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	CDS	6469508	6469646	1	-	0	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	exon	6469508	6469646	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	intron	6469647	6469825	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	CDS	6469826	6470645	0.6	-	1	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	exon	6469826	6470645	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	intron	6470646	6470757	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	CDS	6470758	6471127	1	-	2	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	exon	6470758	6471127	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	intron	6471128	6471269	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	CDS	6471270	6471366	1	-	0	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	exon	6471270	6471366	.	-	.	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
Phchi.S1	AUGUSTUS	start_codon	6471364	6471366	.	-	0	transcript_id "Phchi.S1G108600.t1"; gene_id "Phchi.S1G108600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3341.t1 is derived from g510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3025681	3026025	.	+	.	Phchi.S1G050000
Phchi.S1	AUGUSTUS	transcript	3025681	3026025	.	+	.	transcript_id "Phchi.S1G050000.t1"; gene_id "Phchi.S1G050000"
Phchi.S1	AUGUSTUS	start_codon	3025681	3025683	.	+	0	transcript_id "Phchi.S1G050000.t1"; gene_id "Phchi.S1G050000"
Phchi.S1	AUGUSTUS	CDS	3025681	3026025	0.77	+	0	transcript_id "Phchi.S1G050000.t1"; gene_id "Phchi.S1G050000"
Phchi.S1	AUGUSTUS	exon	3025681	3026025	.	+	.	transcript_id "Phchi.S1G050000.t1"; gene_id "Phchi.S1G050000"
Phchi.S1	AUGUSTUS	stop_codon	3026026	3026028	.	+	0	transcript_id "Phchi.S1G050000.t1"; gene_id "Phchi.S1G050000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13323.t1 is derived from g11789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6099176	6100474	.	+	.	Phchi.S3G064200
Phchi.S3	AUGUSTUS	transcript	6099176	6100474	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	start_codon	6099176	6099178	.	+	0	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	CDS	6099176	6099355	1	+	0	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	exon	6099176	6099355	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	intron	6099356	6099437	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	CDS	6099438	6099572	1	+	0	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	exon	6099438	6099572	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	intron	6099573	6099657	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	CDS	6099658	6099889	1	+	0	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	exon	6099658	6099889	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	intron	6099890	6100005	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	CDS	6100006	6100209	1	+	2	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	exon	6100006	6100209	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	intron	6100210	6100313	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	CDS	6100314	6100474	0.99	+	2	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	exon	6100314	6100474	.	+	.	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
Phchi.S3	AUGUSTUS	stop_codon	6100475	6100477	.	+	0	transcript_id "Phchi.S3G064200.t1"; gene_id "Phchi.S3G064200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13022.t1 is derived from g11487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3658012	3660266	.	-	.	Phchi.S3G034100
Phchi.S3	AUGUSTUS	transcript	3658012	3660266	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	stop_codon	3658009	3658011	.	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3658012	3658179	0.99	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3658012	3658179	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3658180	3658258	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3658259	3658347	1	-	2	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3658259	3658347	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3658348	3658455	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3658456	3658518	0.58	-	2	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3658456	3658518	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3658519	3658606	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3658607	3658709	1	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3658607	3658709	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3658710	3658830	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3658831	3658905	1	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3658831	3658905	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3658906	3659018	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3659019	3659081	1	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3659019	3659081	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3659082	3659224	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3659225	3659320	1	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3659225	3659320	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3659321	3659447	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3659448	3659599	1	-	2	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3659448	3659599	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3659600	3659704	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3659705	3659804	0.99	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3659705	3659804	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	intron	3659805	3659897	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	CDS	3659898	3660266	0.52	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	exon	3659898	3660266	.	-	.	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
Phchi.S3	AUGUSTUS	start_codon	3660264	3660266	.	-	0	transcript_id "Phchi.S3G034100.t1"; gene_id "Phchi.S3G034100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11782.t1 is derived from g15834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8145828	8147294	.	-	.	Phchi.S4G136400
Phchi.S4	AUGUSTUS	transcript	8145828	8147294	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	stop_codon	8145825	8145827	.	-	0	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	CDS	8145828	8146368	1	-	1	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	exon	8145828	8146368	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	intron	8146369	8146462	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	CDS	8146463	8146651	0.81	-	1	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	exon	8146463	8146651	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	intron	8146652	8146738	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	CDS	8146739	8146777	0.57	-	1	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	exon	8146739	8146777	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	intron	8146778	8146853	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	CDS	8146854	8146872	0.89	-	2	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	exon	8146854	8146872	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	intron	8146873	8146955	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	CDS	8146956	8147051	0.24	-	2	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	exon	8146956	8147051	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	intron	8147052	8147167	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	CDS	8147168	8147294	0.19	-	0	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	exon	8147168	8147294	.	-	.	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
Phchi.S4	AUGUSTUS	start_codon	8147292	8147294	.	-	0	transcript_id "Phchi.S4G136400.t1"; gene_id "Phchi.S4G136400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8154.t1 is derived from g5329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34133925	34146255	.	+	.	Phchi.S1G531300
Phchi.S1	AUGUSTUS	transcript	34133925	34146255	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	start_codon	34133925	34133927	.	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34133925	34134858	0.85	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34133925	34134858	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34134859	34134995	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34134996	34135050	0.69	+	2	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34134996	34135050	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34135051	34135184	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34135185	34135335	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34135185	34135335	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34135336	34135471	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34135472	34135738	0.99	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34135472	34135738	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34135739	34135892	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34135893	34136042	0.92	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34135893	34136042	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136043	34136151	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136152	34136379	0.98	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136152	34136379	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136380	34136480	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136481	34136569	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136481	34136569	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136570	34136668	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136669	34136846	0.87	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136669	34136846	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136847	34136954	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136955	34137355	0.92	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136955	34137355	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137356	34137480	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34137481	34137586	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34137481	34137586	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137587	34137722	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34137723	34137821	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34137723	34137821	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137822	34137896	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34137897	34137968	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34137897	34137968	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137969	34138130	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34138131	34138241	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34138131	34138241	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34138242	34138394	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34138395	34138536	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34138395	34138536	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34138537	34138624	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34138625	34138989	0.8	+	2	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34138625	34138989	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34138990	34139122	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139123	34139173	0.49	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139123	34139173	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139174	34139252	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139253	34139314	0.87	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139253	34139314	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139315	34139408	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139409	34139489	0.96	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139409	34139489	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139490	34139624	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139625	34139990	0.95	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139625	34139990	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139991	34140083	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140084	34140311	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140084	34140311	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34140312	34140573	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140574	34140664	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140574	34140664	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34140665	34140739	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140740	34140817	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140740	34140817	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34140818	34140900	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140901	34141185	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140901	34141185	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34141186	34141284	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34141285	34141482	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34141285	34141482	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34141483	34141608	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34141609	34141864	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34141609	34141864	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34141865	34142017	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34142018	34142091	1	+	2	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34142018	34142091	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34142092	34142302	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34142303	34142464	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34142303	34142464	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34142465	34142542	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34142543	34142851	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34142543	34142851	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34142852	34143094	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143095	34143177	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143095	34143177	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143178	34143268	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143269	34143373	0.96	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143269	34143373	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143374	34143488	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143489	34143723	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143489	34143723	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143724	34143836	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143837	34143939	0.95	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143837	34143939	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143940	34144028	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34144029	34144180	0.96	+	2	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34144029	34144180	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34144181	34144409	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34144410	34144511	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34144410	34144511	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34144512	34144742	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34144743	34144883	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34144743	34144883	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34144884	34145137	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145138	34145226	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145138	34145226	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145227	34145350	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145351	34145433	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145351	34145433	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145434	34145508	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145509	34145624	1	+	2	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145509	34145624	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145625	34145698	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145699	34145784	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145699	34145784	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145785	34145899	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145900	34145999	1	+	1	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145900	34145999	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34146000	34146090	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34146091	34146153	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34146091	34146153	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34146154	34146252	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34146253	34146255	1	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34146253	34146255	.	+	.	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	stop_codon	34146256	34146258	.	+	0	transcript_id "Phchi.S1G531300.t1"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	transcript	34133925	34146255	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	start_codon	34133925	34133927	.	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34133925	34134858	0.88	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34133925	34134858	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34134859	34134995	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34134996	34135050	0.8	+	2	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34134996	34135050	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34135051	34135184	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34135185	34135335	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34135185	34135335	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34135336	34135471	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34135472	34135738	0.96	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34135472	34135738	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34135739	34135892	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34135893	34136042	0.96	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34135893	34136042	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136043	34136151	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136152	34136379	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136152	34136379	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136380	34136480	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136481	34136569	0.95	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136481	34136569	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136570	34136668	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136669	34136846	0.78	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136669	34136846	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34136847	34136954	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34136955	34137355	0.81	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34136955	34137355	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137356	34137480	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34137481	34137586	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34137481	34137586	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137587	34137722	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34137723	34137821	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34137723	34137821	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137822	34137896	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34137897	34137968	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34137897	34137968	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34137969	34138130	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34138131	34138241	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34138131	34138241	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34138242	34138394	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34138395	34138536	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34138395	34138536	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34138537	34138624	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34138625	34138989	0.83	+	2	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34138625	34138989	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34138990	34139122	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139123	34139173	0.36	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139123	34139173	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139174	34139252	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139253	34139314	0.54	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139253	34139314	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139315	34139375	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139376	34139489	0.51	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139376	34139489	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139490	34139624	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34139625	34139990	0.94	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34139625	34139990	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34139991	34140083	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140084	34140311	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140084	34140311	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34140312	34140573	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140574	34140664	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140574	34140664	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34140665	34140739	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140740	34140817	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140740	34140817	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34140818	34140900	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34140901	34141185	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34140901	34141185	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34141186	34141284	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34141285	34141482	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34141285	34141482	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34141483	34141608	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34141609	34141864	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34141609	34141864	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34141865	34142017	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34142018	34142091	1	+	2	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34142018	34142091	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34142092	34142302	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34142303	34142464	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34142303	34142464	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34142465	34142542	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34142543	34142851	0.99	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34142543	34142851	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34142852	34143094	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143095	34143177	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143095	34143177	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143178	34143268	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143269	34143373	0.99	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143269	34143373	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143374	34143488	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143489	34143723	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143489	34143723	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143724	34143836	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34143837	34143939	0.96	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34143837	34143939	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34143940	34144028	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34144029	34144180	0.99	+	2	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34144029	34144180	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34144181	34144409	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34144410	34144511	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34144410	34144511	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34144512	34144742	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34144743	34144883	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34144743	34144883	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34144884	34145137	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145138	34145226	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145138	34145226	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145227	34145350	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145351	34145433	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145351	34145433	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145434	34145508	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145509	34145624	1	+	2	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145509	34145624	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145625	34145698	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145699	34145784	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145699	34145784	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34145785	34145899	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34145900	34145999	1	+	1	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34145900	34145999	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34146000	34146090	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34146091	34146153	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34146091	34146153	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	intron	34146154	34146252	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	CDS	34146253	34146255	1	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	exon	34146253	34146255	.	+	.	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
Phchi.S1	AUGUSTUS	stop_codon	34146256	34146258	.	+	0	transcript_id "Phchi.S1G531300.t2"; gene_id "Phchi.S1G531300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9639.t1 is derived from g6815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43019252	43022303	.	+	.	Phchi.S1G679800
Phchi.S1	AUGUSTUS	transcript	43019252	43022303	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	start_codon	43019252	43019254	.	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43019252	43019464	0.95	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43019252	43019464	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43019465	43019554	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43019555	43019610	1	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43019555	43019610	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43019611	43019763	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43019764	43020719	0.99	+	1	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43019764	43020719	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43020720	43020799	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43020800	43021686	0.92	+	2	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43020800	43021686	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43021687	43021774	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43021775	43021816	1	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43021775	43021816	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43021817	43021940	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43021941	43021988	1	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43021941	43021988	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43021989	43022077	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43022078	43022139	1	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43022078	43022139	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	intron	43022140	43022227	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	CDS	43022228	43022303	1	+	1	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	exon	43022228	43022303	.	+	.	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
Phchi.S1	AUGUSTUS	stop_codon	43022304	43022306	.	+	0	transcript_id "Phchi.S1G679800.t1"; gene_id "Phchi.S1G679800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13212.t1 is derived from g11677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4704333	4705283	.	+	.	Phchi.S3G053100
Phchi.S3	AUGUSTUS	transcript	4704333	4705283	.	+	.	transcript_id "Phchi.S3G053100.t1"; gene_id "Phchi.S3G053100"
Phchi.S3	AUGUSTUS	start_codon	4704333	4704335	.	+	0	transcript_id "Phchi.S3G053100.t1"; gene_id "Phchi.S3G053100"
Phchi.S3	AUGUSTUS	CDS	4704333	4705283	0.65	+	0	transcript_id "Phchi.S3G053100.t1"; gene_id "Phchi.S3G053100"
Phchi.S3	AUGUSTUS	exon	4704333	4705283	.	+	.	transcript_id "Phchi.S3G053100.t1"; gene_id "Phchi.S3G053100"
Phchi.S3	AUGUSTUS	stop_codon	4705284	4705286	.	+	0	transcript_id "Phchi.S3G053100.t1"; gene_id "Phchi.S3G053100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2465.t1 is derived from g9385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6793622	6796588	.	-	.	Phchi.S5G107400
Phchi.S5	AUGUSTUS	transcript	6793622	6796588	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	stop_codon	6793619	6793621	.	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6793622	6793747	1	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6793622	6793747	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6793748	6793834	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6793835	6793950	1	-	2	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6793835	6793950	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6793951	6794038	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6794039	6794178	1	-	1	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6794039	6794178	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6794179	6794385	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6794386	6794534	1	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6794386	6794534	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6794535	6794639	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6794640	6794782	1	-	2	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6794640	6794782	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6794783	6794867	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6794868	6794949	1	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6794868	6794949	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6794950	6795128	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6795129	6795226	1	-	2	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6795129	6795226	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6795227	6795398	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6795399	6795460	1	-	1	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6795399	6795460	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6795461	6795545	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6795546	6795613	1	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6795546	6795613	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6795614	6795737	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6795738	6795808	0.98	-	2	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6795738	6795808	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6795809	6796013	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6796014	6796099	1	-	1	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6796014	6796099	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	intron	6796100	6796286	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	CDS	6796287	6796588	0.97	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	exon	6796287	6796588	.	-	.	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
Phchi.S5	AUGUSTUS	start_codon	6796586	6796588	.	-	0	transcript_id "Phchi.S5G107400.t1"; gene_id "Phchi.S5G107400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5434.t1 is derived from g2604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16847184	16850120	.	+	.	Phchi.S1G259300
Phchi.S1	AUGUSTUS	transcript	16847184	16850120	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	start_codon	16847184	16847186	.	+	0	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	CDS	16847184	16847696	0.65	+	0	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	exon	16847184	16847696	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	intron	16847697	16847834	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	CDS	16847835	16848186	0.24	+	0	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	exon	16847835	16848186	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	intron	16848187	16848318	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	CDS	16848319	16848381	0.84	+	2	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	exon	16848319	16848381	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	intron	16848382	16848624	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	CDS	16848625	16850120	0.91	+	2	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	exon	16848625	16850120	.	+	.	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
Phchi.S1	AUGUSTUS	stop_codon	16850121	16850123	.	+	0	transcript_id "Phchi.S1G259300.t1"; gene_id "Phchi.S1G259300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8347.t1 is derived from g5522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35435941	35437291	.	+	.	Phchi.S1G550600
Phchi.S1	AUGUSTUS	transcript	35435941	35437291	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	start_codon	35435941	35435943	.	+	0	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	CDS	35435941	35436537	0.63	+	0	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	exon	35435941	35436537	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	intron	35436538	35436623	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	CDS	35436624	35436826	0.98	+	0	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	exon	35436624	35436826	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	intron	35436827	35436955	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	CDS	35436956	35437015	0.75	+	1	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	exon	35436956	35437015	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	intron	35437016	35437131	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	CDS	35437132	35437291	0.75	+	1	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	exon	35437132	35437291	.	+	.	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
Phchi.S1	AUGUSTUS	stop_codon	35437292	35437294	.	+	0	transcript_id "Phchi.S1G550600.t1"; gene_id "Phchi.S1G550600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15063.t1 is derived from g13531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16835989	16836474	.	-	.	Phchi.S3G238200
Phchi.S3	AUGUSTUS	transcript	16835989	16836474	.	-	.	transcript_id "Phchi.S3G238200.t1"; gene_id "Phchi.S3G238200"
Phchi.S3	AUGUSTUS	stop_codon	16835986	16835988	.	-	0	transcript_id "Phchi.S3G238200.t1"; gene_id "Phchi.S3G238200"
Phchi.S3	AUGUSTUS	CDS	16835989	16836474	0.57	-	0	transcript_id "Phchi.S3G238200.t1"; gene_id "Phchi.S3G238200"
Phchi.S3	AUGUSTUS	exon	16835989	16836474	.	-	.	transcript_id "Phchi.S3G238200.t1"; gene_id "Phchi.S3G238200"
Phchi.S3	AUGUSTUS	start_codon	16836472	16836474	.	-	0	transcript_id "Phchi.S3G238200.t1"; gene_id "Phchi.S3G238200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5064.t1 is derived from g2234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14499319	14501292	.	-	.	Phchi.S1G222300
Phchi.S1	AUGUSTUS	transcript	14499319	14501292	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	stop_codon	14499316	14499318	.	-	0	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	CDS	14499319	14499524	0.85	-	2	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	exon	14499319	14499524	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	intron	14499525	14499612	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	CDS	14499613	14499706	0.93	-	0	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	exon	14499613	14499706	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	intron	14499707	14499867	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	CDS	14499868	14500203	0.31	-	0	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	exon	14499868	14500203	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	intron	14500204	14500353	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	CDS	14500354	14501292	0.16	-	0	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	exon	14500354	14501292	.	-	.	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
Phchi.S1	AUGUSTUS	start_codon	14501290	14501292	.	-	0	transcript_id "Phchi.S1G222300.t1"; gene_id "Phchi.S1G222300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14591.t1 is derived from g13059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13616684	13616947	.	-	.	Phchi.S3G191000
Phchi.S3	AUGUSTUS	transcript	13616684	13616947	.	-	.	transcript_id "Phchi.S3G191000.t1"; gene_id "Phchi.S3G191000"
Phchi.S3	AUGUSTUS	stop_codon	13616681	13616683	.	-	0	transcript_id "Phchi.S3G191000.t1"; gene_id "Phchi.S3G191000"
Phchi.S3	AUGUSTUS	CDS	13616684	13616947	0.43	-	0	transcript_id "Phchi.S3G191000.t1"; gene_id "Phchi.S3G191000"
Phchi.S3	AUGUSTUS	exon	13616684	13616947	.	-	.	transcript_id "Phchi.S3G191000.t1"; gene_id "Phchi.S3G191000"
Phchi.S3	AUGUSTUS	start_codon	13616945	13616947	.	-	0	transcript_id "Phchi.S3G191000.t1"; gene_id "Phchi.S3G191000"
# This transcript jg1048.t2 is derived from g10831.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1049.t1 is derived from g10832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7283904	7284873	.	+	.	Phchi.S6G100800
Phchi.S6	AUGUSTUS	transcript	7283904	7284873	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	start_codon	7283904	7283906	.	+	0	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	CDS	7283904	7283918	0.25	+	0	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	exon	7283904	7283918	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	intron	7283919	7284246	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	CDS	7284247	7284284	0.2	+	0	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	exon	7284247	7284284	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	intron	7284285	7284502	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	CDS	7284503	7284580	0.17	+	1	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	exon	7284503	7284580	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	intron	7284581	7284785	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	CDS	7284786	7284873	0.7	+	1	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	exon	7284786	7284873	.	+	.	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
Phchi.S6	AUGUSTUS	stop_codon	7284874	7284876	.	+	0	transcript_id "Phchi.S6G100800.t1"; gene_id "Phchi.S6G100800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg347.t1 is derived from g10129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2528062	2531497	.	+	.	Phchi.S6G030600
Phchi.S6	AUGUSTUS	transcript	2528062	2531497	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	start_codon	2528062	2528064	.	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2528062	2528102	0.46	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2528062	2528102	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2528103	2528232	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2528233	2528281	1	+	1	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2528233	2528281	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2528282	2528556	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2528557	2528596	1	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2528557	2528596	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2528597	2528679	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2528680	2528771	1	+	2	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2528680	2528771	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2528772	2528946	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2528947	2529015	1	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2528947	2529015	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2529016	2529278	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2529279	2529376	1	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2529279	2529376	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2529377	2529482	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2529483	2529576	1	+	1	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2529483	2529576	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2529577	2529686	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2529687	2529756	1	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2529687	2529756	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2529757	2529879	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2529880	2530065	0.74	+	2	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2529880	2530065	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2530066	2530278	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2530279	2530748	0.47	+	2	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2530279	2530748	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2530749	2530978	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2530979	2531150	0.69	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2530979	2531150	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	intron	2531151	2531474	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	CDS	2531475	2531497	1	+	2	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	exon	2531475	2531497	.	+	.	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
Phchi.S6	AUGUSTUS	stop_codon	2531498	2531500	.	+	0	transcript_id "Phchi.S6G030600.t1"; gene_id "Phchi.S6G030600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15106.t1 is derived from g13574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17103728	17104892	.	+	.	Phchi.S3G242500
Phchi.S3	AUGUSTUS	transcript	17103728	17104892	.	+	.	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	start_codon	17103728	17103730	.	+	0	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	CDS	17103728	17104648	0.56	+	0	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	exon	17103728	17104648	.	+	.	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	intron	17104649	17104871	.	+	.	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	CDS	17104872	17104892	1	+	0	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	exon	17104872	17104892	.	+	.	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	stop_codon	17104893	17104895	.	+	0	transcript_id "Phchi.S3G242500.t1"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	transcript	17104124	17104892	.	+	.	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	start_codon	17104124	17104126	.	+	0	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	CDS	17104124	17104648	0.26	+	0	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	exon	17104124	17104648	.	+	.	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	intron	17104649	17104871	.	+	.	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	CDS	17104872	17104892	0.88	+	0	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	exon	17104872	17104892	.	+	.	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
Phchi.S3	AUGUSTUS	stop_codon	17104893	17104895	.	+	0	transcript_id "Phchi.S3G242500.t2"; gene_id "Phchi.S3G242500"
# This transcript jg10199.t1 is derived from g7374.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46340736	46342400	.	-	.	Phchi.S1G735700
Phchi.S1	AUGUSTUS	transcript	46340736	46342400	.	-	.	transcript_id "Phchi.S1G735700.t1"; gene_id "Phchi.S1G735700"
Phchi.S1	AUGUSTUS	stop_codon	46340733	46340735	.	-	0	transcript_id "Phchi.S1G735700.t1"; gene_id "Phchi.S1G735700"
Phchi.S1	AUGUSTUS	CDS	46340736	46342400	0.54	-	0	transcript_id "Phchi.S1G735700.t1"; gene_id "Phchi.S1G735700"
Phchi.S1	AUGUSTUS	exon	46340736	46342400	.	-	.	transcript_id "Phchi.S1G735700.t1"; gene_id "Phchi.S1G735700"
Phchi.S1	AUGUSTUS	start_codon	46342398	46342400	.	-	0	transcript_id "Phchi.S1G735700.t1"; gene_id "Phchi.S1G735700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15351.t1 is derived from g13819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18521238	18522171	.	-	.	Phchi.S3G267000
Phchi.S3	AUGUSTUS	transcript	18521238	18522171	.	-	.	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	stop_codon	18521235	18521237	.	-	0	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	CDS	18521238	18521455	0.95	-	2	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	exon	18521238	18521455	.	-	.	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	intron	18521456	18521579	.	-	.	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	CDS	18521580	18522171	0.33	-	0	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	exon	18521580	18522171	.	-	.	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
Phchi.S3	AUGUSTUS	start_codon	18522169	18522171	.	-	0	transcript_id "Phchi.S3G267000.t1"; gene_id "Phchi.S3G267000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8540.t1 is derived from g5715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36544118	36544597	.	+	.	Phchi.S1G569900
Phchi.S1	AUGUSTUS	transcript	36544118	36544597	.	+	.	transcript_id "Phchi.S1G569900.t1"; gene_id "Phchi.S1G569900"
Phchi.S1	AUGUSTUS	start_codon	36544118	36544120	.	+	0	transcript_id "Phchi.S1G569900.t1"; gene_id "Phchi.S1G569900"
Phchi.S1	AUGUSTUS	CDS	36544118	36544597	0.91	+	0	transcript_id "Phchi.S1G569900.t1"; gene_id "Phchi.S1G569900"
Phchi.S1	AUGUSTUS	exon	36544118	36544597	.	+	.	transcript_id "Phchi.S1G569900.t1"; gene_id "Phchi.S1G569900"
Phchi.S1	AUGUSTUS	stop_codon	36544598	36544600	.	+	0	transcript_id "Phchi.S1G569900.t1"; gene_id "Phchi.S1G569900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3641.t1 is derived from g810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4907068	4908546	.	-	.	Phchi.S1G080000
Phchi.S1	AUGUSTUS	transcript	4907068	4908383	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	stop_codon	4907065	4907067	.	-	0	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4907068	4907730	1	-	0	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4907068	4907730	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4907731	4907820	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4907821	4907915	0.99	-	2	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4907821	4907915	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4907916	4908045	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4908046	4908152	0.98	-	1	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4908046	4908152	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4908153	4908234	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4908235	4908281	0.99	-	0	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4908235	4908281	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4908282	4908368	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4908369	4908383	0.98	-	0	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4908369	4908383	.	-	.	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	start_codon	4908381	4908383	.	-	0	transcript_id "Phchi.S1G080000.t1"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	transcript	4907068	4908546	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	stop_codon	4907065	4907067	.	-	0	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4907068	4907730	0.99	-	0	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4907068	4907730	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4907731	4907820	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4907821	4907915	1	-	2	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4907821	4907915	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4907916	4908113	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4908114	4908138	0.73	-	0	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4908114	4908138	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4908139	4908234	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4908235	4908281	1	-	2	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4908235	4908281	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	intron	4908282	4908368	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	CDS	4908369	4908546	0.56	-	0	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	exon	4908369	4908546	.	-	.	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
Phchi.S1	AUGUSTUS	start_codon	4908544	4908546	.	-	0	transcript_id "Phchi.S1G080000.t2"; gene_id "Phchi.S1G080000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3076.t1 is derived from g245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1454432	1459613	.	+	.	Phchi.S1G023500
Phchi.S1	AUGUSTUS	transcript	1454432	1459613	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	start_codon	1454432	1454434	.	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1454432	1454962	0.99	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1454432	1454962	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1454963	1455038	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1455039	1455093	0.99	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1455039	1455093	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1455094	1455197	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1455198	1455373	0.99	+	2	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1455198	1455373	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1455374	1455455	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1455456	1455656	0.87	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1455456	1455656	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1455657	1455773	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1455774	1456036	0.98	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1455774	1456036	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1456037	1456119	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1456120	1456436	1	+	1	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1456120	1456436	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1456437	1456522	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1456523	1456746	0.98	+	2	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1456523	1456746	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1456747	1456841	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1456842	1457188	0.99	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1456842	1457188	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1457189	1457284	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1457285	1457907	0.95	+	1	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1457285	1457907	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1457908	1457987	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1457988	1458229	0.98	+	2	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1457988	1458229	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1458230	1458325	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1458326	1458747	0.94	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1458326	1458747	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	intron	1458748	1458826	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	CDS	1458827	1459613	0.95	+	1	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	exon	1458827	1459613	.	+	.	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
Phchi.S1	AUGUSTUS	stop_codon	1459614	1459616	.	+	0	transcript_id "Phchi.S1G023500.t1"; gene_id "Phchi.S1G023500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9658.t1 is derived from g6834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43111413	43112906	.	+	.	Phchi.S1G681700
Phchi.S1	AUGUSTUS	transcript	43111413	43112906	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	start_codon	43111413	43111415	.	+	0	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	CDS	43111413	43111547	0.2	+	0	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	exon	43111413	43111547	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	intron	43111548	43111706	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	CDS	43111707	43111774	1	+	0	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	exon	43111707	43111774	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	intron	43111775	43111923	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	CDS	43111924	43112055	1	+	1	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	exon	43111924	43112055	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	intron	43112056	43112174	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	CDS	43112175	43112290	1	+	1	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	exon	43112175	43112290	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	intron	43112291	43112366	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	CDS	43112367	43112481	1	+	2	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	exon	43112367	43112481	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	intron	43112482	43112701	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	CDS	43112702	43112906	1	+	1	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	exon	43112702	43112906	.	+	.	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
Phchi.S1	AUGUSTUS	stop_codon	43112907	43112909	.	+	0	transcript_id "Phchi.S1G681700.t1"; gene_id "Phchi.S1G681700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15801.t1 is derived from g14271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21430810	21431259	.	-	.	Phchi.S3G312000
Phchi.S3	AUGUSTUS	transcript	21430810	21431259	.	-	.	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	stop_codon	21430807	21430809	.	-	0	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	CDS	21430810	21430889	0.89	-	2	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	exon	21430810	21430889	.	-	.	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	intron	21430890	21431028	.	-	.	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	CDS	21431029	21431137	0.93	-	0	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	exon	21431029	21431137	.	-	.	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	intron	21431138	21431229	.	-	.	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	CDS	21431230	21431259	0.94	-	0	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	exon	21431230	21431259	.	-	.	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
Phchi.S3	AUGUSTUS	start_codon	21431257	21431259	.	-	0	transcript_id "Phchi.S3G312000.t1"; gene_id "Phchi.S3G312000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2688.t1 is derived from g9608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8223457	8224437	.	-	.	Phchi.S5G129700
Phchi.S5	AUGUSTUS	transcript	8223457	8224437	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	stop_codon	8223454	8223456	.	-	0	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	CDS	8223457	8223464	0.46	-	2	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	exon	8223457	8223464	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	intron	8223465	8223711	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	CDS	8223712	8223734	0.46	-	1	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	exon	8223712	8223734	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	intron	8223735	8223842	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	CDS	8223843	8223855	0.69	-	2	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	exon	8223843	8223855	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	intron	8223856	8224001	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	CDS	8224002	8224079	0.7	-	2	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	exon	8224002	8224079	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	intron	8224080	8224171	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	CDS	8224172	8224337	0.7	-	0	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	exon	8224172	8224337	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	intron	8224338	8224416	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	CDS	8224417	8224437	0.7	-	0	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	exon	8224417	8224437	.	-	.	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
Phchi.S5	AUGUSTUS	start_codon	8224435	8224437	.	-	0	transcript_id "Phchi.S5G129700.t1"; gene_id "Phchi.S5G129700"
# This transcript jg14693.t2 is derived from g13161.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14694.t1 is derived from g13162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14198740	14201464	.	+	.	Phchi.S3G201300
Phchi.S3	AUGUSTUS	transcript	14198740	14201464	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	start_codon	14198740	14198742	.	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14198740	14199118	0.65	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14198740	14199118	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14199119	14199287	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14199288	14199556	1	+	2	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14199288	14199556	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14199557	14199713	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14199714	14199803	1	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14199714	14199803	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14199804	14199896	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14199897	14200073	0.99	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14199897	14200073	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200074	14200189	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200190	14200255	1	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200190	14200255	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200256	14200519	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200520	14200585	1	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200520	14200585	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200586	14200668	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200669	14200737	1	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200669	14200737	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200738	14200832	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200833	14201124	0.97	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200833	14201124	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14201125	14201240	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14201241	14201296	1	+	2	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14201241	14201296	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14201297	14201446	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14201447	14201464	1	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14201447	14201464	.	+	.	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	stop_codon	14201465	14201467	.	+	0	transcript_id "Phchi.S3G201300.t1"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	transcript	14198740	14201464	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	start_codon	14198740	14198742	.	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14198740	14199118	0.64	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14198740	14199118	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14199119	14199287	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14199288	14199556	1	+	2	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14199288	14199556	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14199557	14199713	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14199714	14199803	1	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14199714	14199803	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14199804	14199899	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14199900	14200073	0.96	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14199900	14200073	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200074	14200189	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200190	14200255	0.99	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200190	14200255	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200256	14200519	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200520	14200585	1	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200520	14200585	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200586	14200668	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200669	14200737	1	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200669	14200737	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14200738	14200832	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14200833	14201124	0.96	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14200833	14201124	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14201125	14201240	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14201241	14201296	0.99	+	2	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14201241	14201296	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	intron	14201297	14201446	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	CDS	14201447	14201464	1	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	exon	14201447	14201464	.	+	.	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
Phchi.S3	AUGUSTUS	stop_codon	14201465	14201467	.	+	0	transcript_id "Phchi.S3G201300.t2"; gene_id "Phchi.S3G201300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3268.t1 is derived from g437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2629596	2631191	.	+	.	Phchi.S1G042700
Phchi.S1	AUGUSTUS	transcript	2629596	2631191	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	start_codon	2629596	2629598	.	+	0	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2629596	2629598	0.99	+	0	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2629596	2629598	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	intron	2629599	2629694	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2629695	2629855	0.78	+	0	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2629695	2629855	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	intron	2629856	2629982	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2629983	2630101	0.63	+	1	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2629983	2630101	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	intron	2630102	2630197	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2630198	2630342	0.89	+	2	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2630198	2630342	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	intron	2630343	2630422	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2630423	2630674	0.5	+	1	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2630423	2630674	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	intron	2630675	2630904	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2630905	2630946	0.96	+	1	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2630905	2630946	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	intron	2630947	2631094	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	CDS	2631095	2631191	1	+	1	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	exon	2631095	2631191	.	+	.	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
Phchi.S1	AUGUSTUS	stop_codon	2631192	2631194	.	+	0	transcript_id "Phchi.S1G042700.t1"; gene_id "Phchi.S1G042700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2314.t1 is derived from g9234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6037231	6038346	.	-	.	Phchi.S5G092300
Phchi.S5	AUGUSTUS	transcript	6037231	6038346	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	stop_codon	6037228	6037230	.	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	CDS	6037231	6037322	0.4	-	2	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	exon	6037231	6037322	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	intron	6037323	6037419	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	CDS	6037420	6037462	1	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	exon	6037420	6037462	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	intron	6037463	6037544	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	CDS	6037545	6037622	1	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	exon	6037545	6037622	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	intron	6037623	6037702	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	CDS	6037703	6037792	1	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	exon	6037703	6037792	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	intron	6037793	6037894	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	CDS	6037895	6038026	0.48	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	exon	6037895	6038026	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	intron	6038027	6038241	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	CDS	6038242	6038346	0.54	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	exon	6038242	6038346	.	-	.	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
Phchi.S5	AUGUSTUS	start_codon	6038344	6038346	.	-	0	transcript_id "Phchi.S5G092300.t1"; gene_id "Phchi.S5G092300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15666.t1 is derived from g14135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20577147	20579156	.	+	.	Phchi.S3G298500
Phchi.S3	AUGUSTUS	transcript	20577147	20579156	.	+	.	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	start_codon	20577147	20577149	.	+	0	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	CDS	20577147	20578178	1	+	0	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	exon	20577147	20578178	.	+	.	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	intron	20578179	20578269	.	+	.	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	CDS	20578270	20578945	0.54	+	0	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	exon	20578270	20578945	.	+	.	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	intron	20578946	20579103	.	+	.	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	CDS	20579104	20579156	0.4	+	2	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	exon	20579104	20579156	.	+	.	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
Phchi.S3	AUGUSTUS	stop_codon	20579157	20579159	.	+	0	transcript_id "Phchi.S3G298500.t1"; gene_id "Phchi.S3G298500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11117.t1 is derived from g15167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4234780	4236115	.	-	.	Phchi.S4G069900
Phchi.S4	AUGUSTUS	transcript	4234780	4236115	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	stop_codon	4234777	4234779	.	-	0	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	CDS	4234780	4234980	0.98	-	0	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	exon	4234780	4234980	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	intron	4234981	4235060	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	CDS	4235061	4235198	1	-	0	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	exon	4235061	4235198	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	intron	4235199	4235294	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	CDS	4235295	4235434	1	-	2	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	exon	4235295	4235434	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	intron	4235435	4235578	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	CDS	4235579	4235653	1	-	2	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	exon	4235579	4235653	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	intron	4235654	4235817	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	CDS	4235818	4236115	0.56	-	0	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	exon	4235818	4236115	.	-	.	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
Phchi.S4	AUGUSTUS	start_codon	4236113	4236115	.	-	0	transcript_id "Phchi.S4G069900.t1"; gene_id "Phchi.S4G069900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11611.t1 is derived from g15662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7317467	7320295	.	-	.	Phchi.S4G119300
Phchi.S4	AUGUSTUS	transcript	7317467	7320295	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	stop_codon	7317464	7317466	.	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7317467	7317547	1	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7317467	7317547	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7317548	7317651	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7317652	7317702	1	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7317652	7317702	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7317703	7317808	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7317809	7317887	0.98	-	1	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7317809	7317887	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7317888	7318004	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7318005	7318102	1	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7318005	7318102	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7318103	7318191	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7318192	7318282	1	-	1	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7318192	7318282	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7318283	7318411	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7318412	7318532	1	-	2	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7318412	7318532	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7318533	7318634	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7318635	7318794	1	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7318635	7318794	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7318795	7318993	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7318994	7319055	1	-	2	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7318994	7319055	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7319056	7319358	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7319359	7319518	0.9	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7319359	7319518	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	intron	7319519	7319632	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	CDS	7319633	7320295	0.99	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	exon	7319633	7320295	.	-	.	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
Phchi.S4	AUGUSTUS	start_codon	7320293	7320295	.	-	0	transcript_id "Phchi.S4G119300.t1"; gene_id "Phchi.S4G119300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg287.t1 is derived from g10069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2036169	2036658	.	-	.	Phchi.S6G024600
Phchi.S6	AUGUSTUS	transcript	2036169	2036658	.	-	.	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	stop_codon	2036166	2036168	.	-	0	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	CDS	2036169	2036485	1	-	2	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	exon	2036169	2036485	.	-	.	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	intron	2036486	2036579	.	-	.	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	CDS	2036580	2036658	0.87	-	0	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	exon	2036580	2036658	.	-	.	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
Phchi.S6	AUGUSTUS	start_codon	2036656	2036658	.	-	0	transcript_id "Phchi.S6G024600.t1"; gene_id "Phchi.S6G024600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10721.t1 is derived from g14771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1758142	1760499	.	+	.	Phchi.S4G030300
Phchi.S4	AUGUSTUS	transcript	1758142	1760499	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	start_codon	1758142	1758144	.	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1758142	1758494	0.53	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1758142	1758494	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1758495	1758609	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1758610	1758763	1	+	1	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1758610	1758763	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1758764	1758874	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1758875	1758996	0.4	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1758875	1758996	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1758997	1759121	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1759122	1759209	0.72	+	1	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1759122	1759209	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1759210	1759351	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1759352	1759423	1	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1759352	1759423	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1759424	1759508	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1759509	1759718	0.6	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1759509	1759718	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1759719	1759826	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1759827	1760100	0.91	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1759827	1760100	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1760101	1760294	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1760295	1760325	0.99	+	2	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1760295	1760325	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	intron	1760326	1760474	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	CDS	1760475	1760499	0.98	+	1	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	exon	1760475	1760499	.	+	.	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
Phchi.S4	AUGUSTUS	stop_codon	1760500	1760502	.	+	0	transcript_id "Phchi.S4G030300.t1"; gene_id "Phchi.S4G030300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6543.t1 is derived from g3715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23562694	23564467	.	+	.	Phchi.S1G370200
Phchi.S1	AUGUSTUS	transcript	23562694	23564467	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	start_codon	23562694	23562696	.	+	0	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23562694	23562796	1	+	0	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23562694	23562796	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	intron	23562797	23562887	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23562888	23562982	1	+	2	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23562888	23562982	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	intron	23562983	23563064	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23563065	23563133	0.97	+	0	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23563065	23563133	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	intron	23563134	23563275	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23563276	23563308	0.84	+	0	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23563276	23563308	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	intron	23563309	23563391	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23563392	23563737	0.7	+	0	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23563392	23563737	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	intron	23563738	23564070	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23564071	23564326	0.4	+	2	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23564071	23564326	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	intron	23564327	23564409	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	CDS	23564410	23564467	0.49	+	1	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	exon	23564410	23564467	.	+	.	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
Phchi.S1	AUGUSTUS	stop_codon	23564468	23564470	.	+	0	transcript_id "Phchi.S1G370200.t1"; gene_id "Phchi.S1G370200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg11509.t1 is derived from g15559.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6815257	6818818	.	-	.	Phchi.S4G109100
Phchi.S4	AUGUSTUS	transcript	6815257	6818818	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	stop_codon	6815254	6815256	.	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815257	6815397	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815257	6815397	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815398	6815476	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815477	6815614	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815477	6815614	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815615	6815764	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815765	6815863	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815765	6815863	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815864	6815964	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815965	6816045	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815965	6816045	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816046	6816130	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816131	6816193	0.89	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816131	6816193	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816194	6816298	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816299	6816346	0.89	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816299	6816346	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816347	6816477	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816478	6816637	0.89	-	1	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816478	6816637	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816638	6816784	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816785	6816840	0.89	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816785	6816840	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816841	6816940	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816941	6817042	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816941	6817042	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817043	6817159	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817160	6817284	1	-	2	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817160	6817284	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817285	6817437	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817438	6817504	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817438	6817504	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817505	6817619	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817620	6817679	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817620	6817679	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817680	6817839	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817840	6817918	1	-	1	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817840	6817918	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817919	6818047	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818048	6818163	1	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818048	6818163	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818164	6818305	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818306	6818529	0.95	-	2	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818306	6818529	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818530	6818721	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818722	6818818	0.95	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818722	6818818	.	-	.	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	start_codon	6818816	6818818	.	-	0	transcript_id "Phchi.S4G109100.t1"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	transcript	6815257	6818818	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	stop_codon	6815254	6815256	.	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815257	6815397	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815257	6815397	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815398	6815476	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815477	6815614	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815477	6815614	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815615	6815764	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815765	6815863	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815765	6815863	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815864	6815964	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815965	6816045	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815965	6816045	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816046	6816130	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816131	6816193	0.91	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816131	6816193	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816194	6816298	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816299	6816346	0.91	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816299	6816346	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816347	6816477	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816478	6816637	0.92	-	1	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816478	6816637	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816638	6816784	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816785	6816840	0.91	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816785	6816840	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816841	6816940	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816941	6817042	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816941	6817042	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817043	6817159	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817160	6817284	1	-	2	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817160	6817284	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817285	6817437	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817438	6817504	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817438	6817504	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817505	6817619	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817620	6817679	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817620	6817679	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817680	6817839	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817840	6817918	1	-	1	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817840	6817918	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817919	6818047	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818048	6818163	1	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818048	6818163	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818164	6818305	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818306	6818517	0.93	-	2	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818306	6818517	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818518	6818721	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818722	6818818	0.89	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818722	6818818	.	-	.	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	start_codon	6818816	6818818	.	-	0	transcript_id "Phchi.S4G109100.t2"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	transcript	6815257	6818777	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	stop_codon	6815254	6815256	.	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815257	6815397	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815257	6815397	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815398	6815476	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815477	6815614	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815477	6815614	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815615	6815764	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815765	6815863	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815765	6815863	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815864	6815964	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815965	6816045	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815965	6816045	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816046	6816130	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816131	6816193	0.89	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816131	6816193	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816194	6816298	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816299	6816346	0.89	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816299	6816346	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816347	6816477	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816478	6816637	0.91	-	1	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816478	6816637	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816638	6816784	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816785	6816840	0.91	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816785	6816840	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816841	6816940	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816941	6817042	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816941	6817042	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817043	6817159	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817160	6817284	1	-	2	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817160	6817284	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817285	6817437	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817438	6817504	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817438	6817504	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817505	6817619	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817620	6817679	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817620	6817679	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817680	6817839	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817840	6817918	1	-	1	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817840	6817918	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817919	6818047	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818048	6818163	1	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818048	6818163	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818164	6818305	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818306	6818579	0.97	-	1	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818306	6818579	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818580	6818721	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818722	6818777	0.65	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818722	6818777	.	-	.	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	start_codon	6818775	6818777	.	-	0	transcript_id "Phchi.S4G109100.t3"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	transcript	6815257	6818777	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	stop_codon	6815254	6815256	.	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815257	6815397	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815257	6815397	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815398	6815476	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815477	6815614	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815477	6815614	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815615	6815764	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815765	6815863	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815765	6815863	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6815864	6815964	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6815965	6816045	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6815965	6816045	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816046	6816130	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816131	6816193	0.82	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816131	6816193	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816194	6816298	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816299	6816346	0.82	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816299	6816346	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816347	6816477	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816478	6816637	0.9	-	1	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816478	6816637	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816638	6816784	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816785	6816840	0.9	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816785	6816840	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6816841	6816940	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6816941	6817042	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6816941	6817042	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817043	6817159	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817160	6817284	1	-	2	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817160	6817284	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817285	6817437	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817438	6817504	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817438	6817504	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817505	6817619	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817620	6817665	0.74	-	1	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817620	6817665	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817666	6817741	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817742	6817746	0.74	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817742	6817746	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817747	6817839	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6817840	6817918	1	-	1	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6817840	6817918	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6817919	6818047	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818048	6818163	1	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818048	6818163	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818164	6818305	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818306	6818579	0.98	-	1	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818306	6818579	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	intron	6818580	6818721	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	CDS	6818722	6818777	0.64	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	exon	6818722	6818777	.	-	.	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
Phchi.S4	AUGUSTUS	start_codon	6818775	6818777	.	-	0	transcript_id "Phchi.S4G109100.t4"; gene_id "Phchi.S4G109100"
# This transcript jg8158.t2 is derived from g5333.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8159.t1 is derived from g5334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34223469	34224978	.	-	.	Phchi.S1G531800
Phchi.S1	AUGUSTUS	transcript	34223469	34224978	.	-	.	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	stop_codon	34223466	34223468	.	-	0	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	CDS	34223469	34223782	0.81	-	2	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	exon	34223469	34223782	.	-	.	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	intron	34223783	34223913	.	-	.	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	CDS	34223914	34224155	0.01	-	1	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	exon	34223914	34224155	.	-	.	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	intron	34224156	34224358	.	-	.	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	CDS	34224359	34224978	0.13	-	0	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	exon	34224359	34224978	.	-	.	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
Phchi.S1	AUGUSTUS	start_codon	34224976	34224978	.	-	0	transcript_id "Phchi.S1G531800.t1"; gene_id "Phchi.S1G531800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6848.t1 is derived from g4020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25537003	25537656	.	+	.	Phchi.S1G400700
Phchi.S1	AUGUSTUS	transcript	25537003	25537656	.	+	.	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	start_codon	25537003	25537005	.	+	0	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	CDS	25537003	25537110	0.62	+	0	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	exon	25537003	25537110	.	+	.	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	intron	25537111	25537273	.	+	.	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	CDS	25537274	25537309	0.64	+	0	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	exon	25537274	25537309	.	+	.	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	intron	25537310	25537494	.	+	.	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	CDS	25537495	25537656	0.69	+	0	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	exon	25537495	25537656	.	+	.	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
Phchi.S1	AUGUSTUS	stop_codon	25537657	25537659	.	+	0	transcript_id "Phchi.S1G400700.t1"; gene_id "Phchi.S1G400700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15457.t1 is derived from g13925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19284757	19285639	.	+	.	Phchi.S3G277600
Phchi.S3	AUGUSTUS	transcript	19284757	19285639	.	+	.	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	start_codon	19284757	19284759	.	+	0	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	CDS	19284757	19285365	0.67	+	0	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	exon	19284757	19285365	.	+	.	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	intron	19285366	19285459	.	+	.	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	CDS	19285460	19285639	1	+	0	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	exon	19285460	19285639	.	+	.	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
Phchi.S3	AUGUSTUS	stop_codon	19285640	19285642	.	+	0	transcript_id "Phchi.S3G277600.t1"; gene_id "Phchi.S3G277600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg506.t1 is derived from g10288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3507035	3508736	.	-	.	Phchi.S6G046500
Phchi.S6	AUGUSTUS	transcript	3507035	3508736	.	-	.	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	stop_codon	3507032	3507034	.	-	0	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	CDS	3507035	3507129	0.81	-	2	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	exon	3507035	3507129	.	-	.	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	intron	3507130	3508588	.	-	.	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	CDS	3508589	3508736	0.01	-	0	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	exon	3508589	3508736	.	-	.	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
Phchi.S6	AUGUSTUS	start_codon	3508734	3508736	.	-	0	transcript_id "Phchi.S6G046500.t1"; gene_id "Phchi.S6G046500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11520.t1 is derived from g15570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6886429	6888610	.	-	.	Phchi.S4G110200
Phchi.S4	AUGUSTUS	transcript	6886429	6888610	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	stop_codon	6886426	6886428	.	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886429	6886472	0.78	-	2	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886429	6886472	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886473	6886661	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886662	6886700	0.64	-	2	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886662	6886700	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886701	6886787	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886788	6886819	0.64	-	1	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886788	6886819	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886820	6886911	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886912	6886994	0.98	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886912	6886994	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886995	6887107	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887108	6887188	0.97	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887108	6887188	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887189	6887294	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887295	6887310	0.98	-	1	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887295	6887310	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887311	6887435	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887436	6887514	1	-	2	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887436	6887514	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887515	6887599	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887600	6887674	1	-	2	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887600	6887674	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887675	6887763	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887764	6887857	1	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887764	6887857	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887858	6888007	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6888008	6888223	1	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6888008	6888223	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6888224	6888302	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6888303	6888419	0.9	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6888303	6888419	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6888420	6888502	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6888503	6888610	0.3	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6888503	6888610	.	-	.	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	start_codon	6888608	6888610	.	-	0	transcript_id "Phchi.S4G110200.t1"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	transcript	6886464	6888610	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	stop_codon	6886461	6886463	.	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886464	6886472	0.84	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886464	6886472	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886473	6886661	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886662	6886732	0.45	-	2	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886662	6886732	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886733	6886830	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886831	6886838	0.67	-	1	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886831	6886838	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886839	6886911	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6886912	6886994	0.98	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6886912	6886994	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6886995	6887107	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887108	6887188	0.95	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887108	6887188	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887189	6887294	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887295	6887310	0.98	-	1	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887295	6887310	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887311	6887435	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887436	6887514	1	-	2	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887436	6887514	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887515	6887599	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887600	6887674	1	-	2	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887600	6887674	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887675	6887763	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6887764	6887857	1	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6887764	6887857	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6887858	6888007	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6888008	6888223	1	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6888008	6888223	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6888224	6888302	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6888303	6888419	0.85	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6888303	6888419	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	intron	6888420	6888502	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	CDS	6888503	6888610	0.24	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	exon	6888503	6888610	.	-	.	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
Phchi.S4	AUGUSTUS	start_codon	6888608	6888610	.	-	0	transcript_id "Phchi.S4G110200.t2"; gene_id "Phchi.S4G110200"
# This transcript jg5235.t1 is derived from g2405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15786181	15786636	.	+	.	Phchi.S1G239400
Phchi.S1	AUGUSTUS	transcript	15786181	15786636	.	+	.	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	start_codon	15786181	15786183	.	+	0	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	CDS	15786181	15786270	0.53	+	0	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	exon	15786181	15786270	.	+	.	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	intron	15786271	15786405	.	+	.	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	CDS	15786406	15786636	0.41	+	0	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	exon	15786406	15786636	.	+	.	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
Phchi.S1	AUGUSTUS	stop_codon	15786637	15786639	.	+	0	transcript_id "Phchi.S1G239400.t1"; gene_id "Phchi.S1G239400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8621.t1 is derived from g5796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37043272	37043745	.	+	.	Phchi.S1G578000
Phchi.S1	AUGUSTUS	transcript	37043272	37043745	.	+	.	transcript_id "Phchi.S1G578000.t1"; gene_id "Phchi.S1G578000"
Phchi.S1	AUGUSTUS	start_codon	37043272	37043274	.	+	0	transcript_id "Phchi.S1G578000.t1"; gene_id "Phchi.S1G578000"
Phchi.S1	AUGUSTUS	CDS	37043272	37043745	0.51	+	0	transcript_id "Phchi.S1G578000.t1"; gene_id "Phchi.S1G578000"
Phchi.S1	AUGUSTUS	exon	37043272	37043745	.	+	.	transcript_id "Phchi.S1G578000.t1"; gene_id "Phchi.S1G578000"
Phchi.S1	AUGUSTUS	stop_codon	37043746	37043748	.	+	0	transcript_id "Phchi.S1G578000.t1"; gene_id "Phchi.S1G578000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9257.t1 is derived from g6432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40614610	40616492	.	-	.	Phchi.S1G641600
Phchi.S1	AUGUSTUS	transcript	40614610	40616492	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	stop_codon	40614607	40614609	.	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40614610	40614705	1	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40614610	40614705	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40614706	40614803	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40614804	40614853	1	-	2	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40614804	40614853	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40614854	40614943	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40614944	40614998	1	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40614944	40614998	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40614999	40615083	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40615084	40615143	1	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40615084	40615143	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40615144	40615231	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40615232	40615291	1	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40615232	40615291	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40615292	40615372	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40615373	40615471	1	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40615373	40615471	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40615472	40615572	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40615573	40615640	1	-	2	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40615573	40615640	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40615641	40615732	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40615733	40615782	1	-	1	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40615733	40615782	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40615783	40615889	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40615890	40615995	1	-	2	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40615890	40615995	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40615996	40616083	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40616084	40616325	0.99	-	1	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40616084	40616325	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	intron	40616326	40616412	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	CDS	40616413	40616492	1	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	exon	40616413	40616492	.	-	.	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
Phchi.S1	AUGUSTUS	start_codon	40616490	40616492	.	-	0	transcript_id "Phchi.S1G641600.t1"; gene_id "Phchi.S1G641600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg10860.t1 is derived from g14910.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2591738	2594806	.	-	.	Phchi.S4G044200
Phchi.S4	AUGUSTUS	transcript	2591738	2594806	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	stop_codon	2591735	2591737	.	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591738	2591926	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591738	2591926	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2591927	2591996	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591997	2592110	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591997	2592110	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592111	2592216	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592217	2592300	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592217	2592300	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592301	2592480	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592481	2592592	1	-	1	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592481	2592592	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592593	2592745	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592746	2592762	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592746	2592762	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592763	2592920	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592921	2593006	0.99	-	2	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592921	2593006	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593007	2593105	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593106	2593118	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593106	2593118	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593119	2593195	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593196	2593305	1	-	2	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593196	2593305	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593306	2593421	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593422	2593482	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593422	2593482	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593483	2593607	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593608	2593726	1	-	2	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593608	2593726	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593727	2593807	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593808	2593952	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593808	2593952	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593953	2594028	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594029	2594247	1	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594029	2594247	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594248	2594405	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594406	2594478	0.93	-	1	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594406	2594478	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594479	2594631	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594632	2594668	0.88	-	2	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594632	2594668	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594669	2594748	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594749	2594806	0.98	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594749	2594806	.	-	.	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	start_codon	2594804	2594806	.	-	0	transcript_id "Phchi.S4G044200.t1"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	transcript	2591738	2594806	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	stop_codon	2591735	2591737	.	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591738	2591926	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591738	2591926	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2591927	2591996	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591997	2592110	0.99	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591997	2592110	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592111	2592216	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592217	2592300	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592217	2592300	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592301	2592480	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592481	2592592	1	-	1	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592481	2592592	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592593	2592662	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592663	2592817	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592663	2592817	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592818	2592920	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592921	2593006	0.99	-	2	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592921	2593006	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593007	2593105	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593106	2593118	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593106	2593118	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593119	2593195	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593196	2593305	1	-	2	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593196	2593305	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593306	2593421	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593422	2593482	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593422	2593482	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593483	2593607	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593608	2593726	1	-	2	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593608	2593726	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593727	2593807	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593808	2593952	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593808	2593952	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593953	2594028	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594029	2594247	1	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594029	2594247	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594248	2594405	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594406	2594478	0.91	-	1	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594406	2594478	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594479	2594631	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594632	2594668	0.86	-	2	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594632	2594668	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594669	2594748	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594749	2594806	0.95	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594749	2594806	.	-	.	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	start_codon	2594804	2594806	.	-	0	transcript_id "Phchi.S4G044200.t2"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	transcript	2591738	2594806	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	stop_codon	2591735	2591737	.	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591738	2591926	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591738	2591926	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2591927	2591996	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591997	2592110	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591997	2592110	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592111	2592216	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592217	2592300	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592217	2592300	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592301	2592480	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592481	2592592	1	-	1	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592481	2592592	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592593	2592662	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592663	2592817	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592663	2592817	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592818	2592920	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592921	2593010	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592921	2593010	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593011	2593195	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593196	2593305	1	-	2	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593196	2593305	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593306	2593421	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593422	2593482	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593422	2593482	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593483	2593607	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593608	2593726	1	-	2	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593608	2593726	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593727	2593807	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593808	2593952	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593808	2593952	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593953	2594028	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594029	2594247	1	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594029	2594247	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594248	2594405	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594406	2594478	0.89	-	1	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594406	2594478	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594479	2594631	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594632	2594668	0.84	-	2	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594632	2594668	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594669	2594748	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594749	2594806	0.99	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594749	2594806	.	-	.	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	start_codon	2594804	2594806	.	-	0	transcript_id "Phchi.S4G044200.t3"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	transcript	2591738	2594806	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	stop_codon	2591735	2591737	.	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591738	2591926	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591738	2591926	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2591927	2591996	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2591997	2592110	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2591997	2592110	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592111	2592216	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592217	2592300	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592217	2592300	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592301	2592480	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592481	2592592	1	-	1	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592481	2592592	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592593	2592662	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592663	2592817	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592663	2592817	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2592818	2592920	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2592921	2593006	1	-	2	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2592921	2593006	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593007	2593105	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593106	2593118	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593106	2593118	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593119	2593195	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593196	2593305	1	-	2	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593196	2593305	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593306	2593421	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593422	2593482	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593422	2593482	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593483	2593607	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593608	2593726	1	-	2	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593608	2593726	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593727	2593807	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2593808	2593952	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2593808	2593952	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2593953	2594028	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594029	2594247	1	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594029	2594247	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594248	2594336	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594337	2594478	0.69	-	1	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594337	2594478	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594479	2594631	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594632	2594668	0.64	-	2	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594632	2594668	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	intron	2594669	2594748	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	CDS	2594749	2594806	0.83	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	exon	2594749	2594806	.	-	.	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
Phchi.S4	AUGUSTUS	start_codon	2594804	2594806	.	-	0	transcript_id "Phchi.S4G044200.t4"; gene_id "Phchi.S4G044200"
# This transcript jg8928.t2 is derived from g6103.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8929.t1 is derived from g6104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38716683	38718264	.	+	.	Phchi.S1G608800
Phchi.S1	AUGUSTUS	transcript	38716683	38718264	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	start_codon	38716683	38716685	.	+	0	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	CDS	38716683	38716997	0.53	+	0	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	exon	38716683	38716997	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	intron	38716998	38717183	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	CDS	38717184	38717308	0.97	+	0	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	exon	38717184	38717308	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	intron	38717309	38717451	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	CDS	38717452	38717601	1	+	1	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	exon	38717452	38717601	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	intron	38717602	38717690	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	CDS	38717691	38718264	0.96	+	1	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	exon	38717691	38718264	.	+	.	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
Phchi.S1	AUGUSTUS	stop_codon	38718265	38718267	.	+	0	transcript_id "Phchi.S1G608800.t1"; gene_id "Phchi.S1G608800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14312.t1 is derived from g12779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12056784	12058186	.	-	.	Phchi.S3G163100
Phchi.S3	AUGUSTUS	transcript	12056784	12058186	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	stop_codon	12056781	12056783	.	-	0	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	CDS	12056784	12056890	0.99	-	2	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	exon	12056784	12056890	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	intron	12056891	12056981	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	CDS	12056982	12057069	1	-	0	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	exon	12056982	12057069	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	intron	12057070	12057167	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	CDS	12057168	12057259	1	-	2	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	exon	12057168	12057259	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	intron	12057260	12057354	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	CDS	12057355	12057525	1	-	2	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	exon	12057355	12057525	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	intron	12057526	12057611	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	CDS	12057612	12057753	1	-	0	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	exon	12057612	12057753	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	intron	12057754	12057835	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	CDS	12057836	12058186	0.57	-	0	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	exon	12057836	12058186	.	-	.	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
Phchi.S3	AUGUSTUS	start_codon	12058184	12058186	.	-	0	transcript_id "Phchi.S3G163100.t1"; gene_id "Phchi.S3G163100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11165.t1 is derived from g15215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4439467	4440789	.	+	.	Phchi.S4G074700
Phchi.S4	AUGUSTUS	transcript	4439467	4440789	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	start_codon	4439467	4439469	.	+	0	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	CDS	4439467	4439486	0.56	+	0	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	exon	4439467	4439486	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	intron	4439487	4439626	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	CDS	4439627	4439894	0.94	+	1	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	exon	4439627	4439894	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	intron	4439895	4440154	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	CDS	4440155	4440238	0.97	+	0	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	exon	4440155	4440238	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	intron	4440239	4440341	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	CDS	4440342	4440431	1	+	0	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	exon	4440342	4440431	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	intron	4440432	4440543	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	CDS	4440544	4440789	0.4	+	0	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	exon	4440544	4440789	.	+	.	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
Phchi.S4	AUGUSTUS	stop_codon	4440790	4440792	.	+	0	transcript_id "Phchi.S4G074700.t1"; gene_id "Phchi.S4G074700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6895.t1 is derived from g4067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25869201	25871611	.	-	.	Phchi.S1G405400
Phchi.S1	AUGUSTUS	transcript	25869201	25871611	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	stop_codon	25869198	25869200	.	-	0	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25869201	25869282	0.99	-	1	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25869201	25869282	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25869283	25869422	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25869423	25869508	0.99	-	0	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25869423	25869508	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25869509	25869606	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25869607	25869670	0.94	-	1	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25869607	25869670	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25869671	25870018	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25870019	25870178	0.71	-	2	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25870019	25870178	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25870179	25870264	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25870265	25870416	1	-	1	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25870265	25870416	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25870417	25870508	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25870509	25870819	1	-	0	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25870509	25870819	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25870820	25870954	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25870955	25871066	1	-	1	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25870955	25871066	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25871067	25871165	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25871166	25871267	1	-	1	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25871166	25871267	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	intron	25871268	25871381	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	CDS	25871382	25871611	0.62	-	0	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	exon	25871382	25871611	.	-	.	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
Phchi.S1	AUGUSTUS	start_codon	25871609	25871611	.	-	0	transcript_id "Phchi.S1G405400.t1"; gene_id "Phchi.S1G405400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4350.t1 is derived from g1519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9917187	9920316	.	-	.	Phchi.S1G150900
Phchi.S1	AUGUSTUS	transcript	9917187	9920316	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	stop_codon	9917184	9917186	.	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9917187	9917255	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9917187	9917255	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9917256	9917337	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9917338	9917356	1	-	1	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9917338	9917356	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9917357	9917514	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9917515	9917588	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9917515	9917588	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9917589	9917682	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9917683	9917760	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9917683	9917760	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9917761	9917842	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9917843	9917935	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9917843	9917935	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9917936	9918016	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9918017	9918075	1	-	2	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9918017	9918075	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9918076	9918152	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9918153	9918235	0.67	-	1	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9918153	9918235	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9918236	9918474	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9918475	9918480	0.67	-	1	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9918475	9918480	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9918481	9918603	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9918604	9918751	0.38	-	2	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9918604	9918751	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9918752	9918859	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9918860	9918928	0.66	-	2	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9918860	9918928	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9918929	9919034	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9919035	9919149	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9919035	9919149	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9919150	9919256	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9919257	9919371	0.98	-	1	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9919257	9919371	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9919372	9919457	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9919458	9919540	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9919458	9919540	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9919541	9919643	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9919644	9919730	0.89	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9919644	9919730	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9919731	9919928	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9919929	9920012	0.78	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9919929	9920012	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9920013	9920089	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9920090	9920146	1	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9920090	9920146	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	intron	9920147	9920214	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	CDS	9920215	9920316	0.68	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	exon	9920215	9920316	.	-	.	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
Phchi.S1	AUGUSTUS	start_codon	9920314	9920316	.	-	0	transcript_id "Phchi.S1G150900.t1"; gene_id "Phchi.S1G150900"
# This transcript jg1847.t2 is derived from g8767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1848.t1 is derived from g8768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3544131	3545870	.	-	.	Phchi.S5G045700
Phchi.S5	AUGUSTUS	transcript	3544131	3545870	.	-	.	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	stop_codon	3544128	3544130	.	-	0	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	CDS	3544131	3544666	0.97	-	2	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	exon	3544131	3544666	.	-	.	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	intron	3544667	3544759	.	-	.	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	CDS	3544760	3544887	0.99	-	1	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	exon	3544760	3544887	.	-	.	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	intron	3544888	3544998	.	-	.	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	CDS	3544999	3545870	0.97	-	0	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	exon	3544999	3545870	.	-	.	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
Phchi.S5	AUGUSTUS	start_codon	3545868	3545870	.	-	0	transcript_id "Phchi.S5G045700.t1"; gene_id "Phchi.S5G045700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13038.t1 is derived from g11503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3831658	3832008	.	-	.	Phchi.S3G035700
Phchi.S3	AUGUSTUS	transcript	3831658	3832008	.	-	.	transcript_id "Phchi.S3G035700.t1"; gene_id "Phchi.S3G035700"
Phchi.S3	AUGUSTUS	stop_codon	3831655	3831657	.	-	0	transcript_id "Phchi.S3G035700.t1"; gene_id "Phchi.S3G035700"
Phchi.S3	AUGUSTUS	CDS	3831658	3832008	0.84	-	0	transcript_id "Phchi.S3G035700.t1"; gene_id "Phchi.S3G035700"
Phchi.S3	AUGUSTUS	exon	3831658	3832008	.	-	.	transcript_id "Phchi.S3G035700.t1"; gene_id "Phchi.S3G035700"
Phchi.S3	AUGUSTUS	start_codon	3832006	3832008	.	-	0	transcript_id "Phchi.S3G035700.t1"; gene_id "Phchi.S3G035700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10119.t1 is derived from g7295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45823711	45830236	.	-	.	Phchi.S1G727800
Phchi.S1	AUGUSTUS	transcript	45823711	45830236	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	stop_codon	45823708	45823710	.	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45823711	45823824	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45823711	45823824	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45823825	45823910	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45823911	45823970	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45823911	45823970	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45823971	45824063	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824064	45824111	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824064	45824111	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45824112	45824194	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824195	45824275	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824195	45824275	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45824276	45824361	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824362	45824442	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824362	45824442	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45824443	45824518	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824519	45824584	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824519	45824584	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45824585	45824684	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824685	45824741	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824685	45824741	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45824742	45824833	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824834	45824890	0.99	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824834	45824890	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45824891	45824992	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45824993	45825061	0.99	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45824993	45825061	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45825062	45825135	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45825136	45825189	0.88	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45825136	45825189	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45825190	45825527	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45825528	45825671	0.39	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45825528	45825671	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45825672	45825795	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45825796	45825896	0.78	-	2	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45825796	45825896	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45825897	45826010	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45826011	45826074	0.95	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45826011	45826074	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45826075	45826200	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45826201	45826374	0.99	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45826201	45826374	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45826375	45826464	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45826465	45826695	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45826465	45826695	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45826696	45826769	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45826770	45826892	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45826770	45826892	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45826893	45826978	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45826979	45827041	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45826979	45827041	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45827042	45827162	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45827163	45827279	0.98	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45827163	45827279	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45827280	45827374	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45827375	45827563	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45827375	45827563	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45827564	45827655	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45827656	45827784	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45827656	45827784	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45827785	45827869	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45827870	45828097	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45827870	45828097	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45828098	45828188	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45828189	45828470	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45828189	45828470	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45828471	45828556	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45828557	45828700	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45828557	45828700	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45828701	45828791	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45828792	45828965	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45828792	45828965	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45828966	45829065	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45829066	45829160	1	-	2	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45829066	45829160	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45829161	45829383	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45829384	45829516	1	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45829384	45829516	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45829517	45829605	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45829606	45829732	1	-	1	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45829606	45829732	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45829733	45829823	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45829824	45829990	0.98	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45829824	45829990	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	intron	45829991	45830119	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	CDS	45830120	45830236	0.67	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	exon	45830120	45830236	.	-	.	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
Phchi.S1	AUGUSTUS	start_codon	45830234	45830236	.	-	0	transcript_id "Phchi.S1G727800.t1"; gene_id "Phchi.S1G727800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9384.t1 is derived from g6560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41260383	41261942	.	-	.	Phchi.S1G654300
Phchi.S1	AUGUSTUS	transcript	41260383	41261942	.	-	.	transcript_id "Phchi.S1G654300.t1"; gene_id "Phchi.S1G654300"
Phchi.S1	AUGUSTUS	stop_codon	41260380	41260382	.	-	0	transcript_id "Phchi.S1G654300.t1"; gene_id "Phchi.S1G654300"
Phchi.S1	AUGUSTUS	CDS	41260383	41261942	0.92	-	0	transcript_id "Phchi.S1G654300.t1"; gene_id "Phchi.S1G654300"
Phchi.S1	AUGUSTUS	exon	41260383	41261942	.	-	.	transcript_id "Phchi.S1G654300.t1"; gene_id "Phchi.S1G654300"
Phchi.S1	AUGUSTUS	start_codon	41261940	41261942	.	-	0	transcript_id "Phchi.S1G654300.t1"; gene_id "Phchi.S1G654300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6726.t1 is derived from g3898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24753632	24754303	.	-	.	Phchi.S1G388500
Phchi.S1	AUGUSTUS	transcript	24753632	24754303	.	-	.	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	stop_codon	24753629	24753631	.	-	0	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	CDS	24753632	24753730	0.96	-	0	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	exon	24753632	24753730	.	-	.	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	intron	24753731	24753838	.	-	.	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	CDS	24753839	24754096	0.78	-	0	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	exon	24753839	24754096	.	-	.	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	intron	24754097	24754174	.	-	.	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	CDS	24754175	24754303	0.48	-	0	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	exon	24754175	24754303	.	-	.	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
Phchi.S1	AUGUSTUS	start_codon	24754301	24754303	.	-	0	transcript_id "Phchi.S1G388500.t1"; gene_id "Phchi.S1G388500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4408.t1 is derived from g1577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10262714	10266741	.	+	.	Phchi.S1G156700
Phchi.S1	AUGUSTUS	transcript	10262714	10266741	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	start_codon	10262714	10262716	.	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10262714	10262769	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10262714	10262769	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10262770	10262870	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10262871	10262970	1	+	1	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10262871	10262970	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10262971	10263058	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10263059	10263139	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10263059	10263139	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10263140	10263221	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10263222	10263329	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10263222	10263329	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10263330	10263477	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10263478	10263558	0.95	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10263478	10263558	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10263559	10263630	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10263631	10263720	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10263631	10263720	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10263721	10263876	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10263877	10263966	0.65	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10263877	10263966	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10263967	10264076	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10264077	10264126	0.61	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10264077	10264126	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10264127	10264247	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10264248	10264356	0.99	+	1	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10264248	10264356	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10264357	10264463	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10264464	10264532	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10264464	10264532	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10264533	10264631	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10264632	10264698	0.94	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10264632	10264698	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10264699	10264905	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10264906	10264932	0.27	+	2	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10264906	10264932	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10264933	10265021	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10265022	10265086	0.24	+	2	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10265022	10265086	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10265087	10265212	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10265213	10265287	0.58	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10265213	10265287	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10265288	10265393	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10265394	10265443	0.83	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10265394	10265443	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10265444	10265604	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10265605	10265662	0.82	+	1	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10265605	10265662	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10265663	10265764	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10265765	10265902	0.99	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10265765	10265902	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10265903	10265987	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10265988	10266053	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10265988	10266053	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10266054	10266145	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10266146	10266196	0.65	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10266146	10266196	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10266197	10266294	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10266295	10266366	0.65	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10266295	10266366	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10266367	10266455	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10266456	10266485	0.94	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10266456	10266485	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	intron	10266486	10266606	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	CDS	10266607	10266741	1	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	exon	10266607	10266741	.	+	.	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
Phchi.S1	AUGUSTUS	stop_codon	10266742	10266744	.	+	0	transcript_id "Phchi.S1G156700.t1"; gene_id "Phchi.S1G156700"
# This transcript jg15376.t2 is derived from g13844.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15376.t3 is derived from g13844.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15376.t4 is derived from g13844.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15376.t5 is derived from g13844.t6 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15376.t6 is derived from g13844.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15377.t1 is derived from g13845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18687956	18689096	.	-	.	Phchi.S3G269600
Phchi.S3	AUGUSTUS	transcript	18687956	18689096	.	-	.	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	stop_codon	18687953	18687955	.	-	0	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	CDS	18687956	18688114	1	-	0	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	exon	18687956	18688114	.	-	.	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	intron	18688115	18688208	.	-	.	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	CDS	18688209	18689096	1	-	0	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	exon	18688209	18689096	.	-	.	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
Phchi.S3	AUGUSTUS	start_codon	18689094	18689096	.	-	0	transcript_id "Phchi.S3G269600.t1"; gene_id "Phchi.S3G269600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13524.t1 is derived from g11991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7344724	7347837	.	-	.	Phchi.S3G084300
Phchi.S3	AUGUSTUS	transcript	7344724	7347837	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	stop_codon	7344721	7344723	.	-	0	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7344724	7344881	0.74	-	2	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7344724	7344881	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7344882	7344992	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7344993	7345195	0.93	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7344993	7345195	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7345196	7345337	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7345338	7345406	1	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7345338	7345406	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7345407	7345497	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7345498	7345566	1	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7345498	7345566	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7345567	7345752	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7345753	7345818	1	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7345753	7345818	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7345819	7345932	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7345933	7346001	0.97	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7345933	7346001	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7346002	7346087	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7346088	7346159	1	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7346088	7346159	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7346160	7346253	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7346254	7346383	1	-	2	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7346254	7346383	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7346384	7346534	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7346535	7346571	0.48	-	0	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7346535	7346571	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7346572	7346759	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7346760	7346958	0.5	-	1	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7346760	7346958	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7346959	7347073	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7347074	7347602	1	-	2	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7347074	7347602	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	intron	7347603	7347731	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	CDS	7347732	7347837	0.74	-	0	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	exon	7347732	7347837	.	-	.	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
Phchi.S3	AUGUSTUS	start_codon	7347835	7347837	.	-	0	transcript_id "Phchi.S3G084300.t1"; gene_id "Phchi.S3G084300"
# This transcript jg4813.t2 is derived from g1983.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4814.t1 is derived from g1984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12957869	12958705	.	+	.	Phchi.S1G197300
Phchi.S1	AUGUSTUS	transcript	12958400	12958705	.	+	.	transcript_id "Phchi.S1G197300.t1"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	start_codon	12958400	12958402	.	+	0	transcript_id "Phchi.S1G197300.t1"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	CDS	12958400	12958705	0.65	+	0	transcript_id "Phchi.S1G197300.t1"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	exon	12958400	12958705	.	+	.	transcript_id "Phchi.S1G197300.t1"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	stop_codon	12958706	12958708	.	+	0	transcript_id "Phchi.S1G197300.t1"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	transcript	12957869	12958705	.	+	.	transcript_id "Phchi.S1G197300.t2"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	start_codon	12957869	12957871	.	+	0	transcript_id "Phchi.S1G197300.t2"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	CDS	12957869	12958705	0.52	+	0	transcript_id "Phchi.S1G197300.t2"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	exon	12957869	12958705	.	+	.	transcript_id "Phchi.S1G197300.t2"; gene_id "Phchi.S1G197300"
Phchi.S1	AUGUSTUS	stop_codon	12958706	12958708	.	+	0	transcript_id "Phchi.S1G197300.t2"; gene_id "Phchi.S1G197300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3021.t1 is derived from g190.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1175320	1181211	.	+	.	Phchi.S1G018000
Phchi.S1	AUGUSTUS	transcript	1175320	1181211	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	start_codon	1175320	1175322	.	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1175320	1175610	0.88	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1175320	1175610	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1175611	1175803	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1175804	1175935	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1175804	1175935	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1175936	1176035	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176036	1176142	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176036	1176142	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176143	1176228	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176229	1176341	1	+	1	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176229	1176341	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176342	1176450	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176451	1176548	1	+	2	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176451	1176548	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176549	1176638	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176639	1176818	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176639	1176818	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176819	1176901	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176902	1177123	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176902	1177123	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177124	1177226	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177227	1177361	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177227	1177361	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177362	1177457	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177458	1177489	0.69	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177458	1177489	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177490	1177602	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177603	1177733	0.68	+	1	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177603	1177733	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177734	1177839	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177840	1177913	1	+	2	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177840	1177913	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177914	1177990	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177991	1178211	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177991	1178211	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178212	1178351	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1178352	1178439	1	+	1	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1178352	1178439	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178440	1178511	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1178512	1178605	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1178512	1178605	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178606	1178695	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1178696	1178884	1	+	2	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1178696	1178884	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178885	1179041	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179042	1179079	1	+	2	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179042	1179079	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179080	1179190	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179191	1179267	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179191	1179267	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179268	1179382	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179383	1179475	1	+	1	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179383	1179475	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179476	1179571	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179572	1179641	1	+	1	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179572	1179641	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179642	1179739	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179740	1179794	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179740	1179794	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179795	1179913	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179914	1179972	1	+	2	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179914	1179972	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179973	1180099	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180100	1180265	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180100	1180265	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1180266	1180377	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180378	1180556	1	+	2	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180378	1180556	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1180557	1180644	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180645	1180863	0.98	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180645	1180863	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1180864	1180974	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180975	1181094	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180975	1181094	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1181095	1181193	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1181194	1181211	1	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1181194	1181211	.	+	.	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	stop_codon	1181212	1181214	.	+	0	transcript_id "Phchi.S1G018000.t1"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	transcript	1175320	1181211	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	start_codon	1175320	1175322	.	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1175320	1175610	0.85	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1175320	1175610	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1175611	1175803	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1175804	1175935	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1175804	1175935	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1175936	1176035	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176036	1176142	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176036	1176142	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176143	1176228	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176229	1176341	1	+	1	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176229	1176341	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176342	1176450	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176451	1176548	1	+	2	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176451	1176548	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176549	1176638	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176639	1176818	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176639	1176818	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1176819	1176901	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1176902	1177123	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1176902	1177123	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177124	1177226	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177227	1177361	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177227	1177361	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177362	1177457	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177458	1177489	0.61	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177458	1177489	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177490	1177602	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177603	1177733	0.58	+	1	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177603	1177733	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177734	1177839	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177840	1177913	1	+	2	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177840	1177913	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1177914	1177990	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1177991	1178211	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1177991	1178211	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178212	1178351	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1178352	1178439	1	+	1	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1178352	1178439	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178440	1178511	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1178512	1178605	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1178512	1178605	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178606	1178695	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1178696	1178884	1	+	2	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1178696	1178884	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1178885	1179041	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179042	1179079	1	+	2	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179042	1179079	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179080	1179190	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179191	1179267	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179191	1179267	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179268	1179382	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179383	1179475	1	+	1	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179383	1179475	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179476	1179571	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179572	1179641	1	+	1	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179572	1179641	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179642	1179736	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179737	1179794	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179737	1179794	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179795	1179913	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1179914	1179972	1	+	2	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1179914	1179972	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1179973	1180099	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180100	1180265	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180100	1180265	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1180266	1180377	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180378	1180556	1	+	2	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180378	1180556	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1180557	1180644	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180645	1180863	0.96	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180645	1180863	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1180864	1180974	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1180975	1181094	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1180975	1181094	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	intron	1181095	1181193	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	CDS	1181194	1181211	1	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	exon	1181194	1181211	.	+	.	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
Phchi.S1	AUGUSTUS	stop_codon	1181212	1181214	.	+	0	transcript_id "Phchi.S1G018000.t2"; gene_id "Phchi.S1G018000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2356.t1 is derived from g9276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6326877	6327403	.	-	.	Phchi.S5G096500
Phchi.S5	AUGUSTUS	transcript	6326877	6327403	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	stop_codon	6326874	6326876	.	-	0	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	CDS	6326877	6327040	0.79	-	2	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	exon	6326877	6327040	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	intron	6327041	6327122	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	CDS	6327123	6327155	1	-	2	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	exon	6327123	6327155	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	intron	6327156	6327236	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	CDS	6327237	6327281	1	-	2	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	exon	6327237	6327281	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	intron	6327282	6327363	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	CDS	6327364	6327403	0.97	-	0	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	exon	6327364	6327403	.	-	.	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
Phchi.S5	AUGUSTUS	start_codon	6327401	6327403	.	-	0	transcript_id "Phchi.S5G096500.t1"; gene_id "Phchi.S5G096500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg635.t1 is derived from g10417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4488558	4490948	.	-	.	Phchi.S6G059400
Phchi.S6	AUGUSTUS	transcript	4488558	4490948	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	stop_codon	4488555	4488557	.	-	0	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	CDS	4488558	4488926	0.98	-	0	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	exon	4488558	4488926	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	intron	4488927	4489015	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	CDS	4489016	4489222	0.99	-	0	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	exon	4489016	4489222	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	intron	4489223	4489299	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	CDS	4489300	4489581	1	-	0	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	exon	4489300	4489581	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	intron	4489582	4489666	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	CDS	4489667	4489853	0.39	-	1	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	exon	4489667	4489853	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	intron	4489854	4489977	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	CDS	4489978	4490948	0.36	-	0	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	exon	4489978	4490948	.	-	.	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
Phchi.S6	AUGUSTUS	start_codon	4490946	4490948	.	-	0	transcript_id "Phchi.S6G059400.t1"; gene_id "Phchi.S6G059400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9187.t1 is derived from g6362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40263309	40265713	.	-	.	Phchi.S1G634600
Phchi.S1	AUGUSTUS	transcript	40263309	40265713	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	stop_codon	40263306	40263308	.	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40263309	40263673	1	-	2	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40263309	40263673	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40263674	40263788	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40263789	40263992	1	-	2	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40263789	40263992	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40263993	40264083	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40264084	40264273	0.99	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40264084	40264273	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40264274	40264426	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40264427	40264543	1	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40264427	40264543	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40264544	40264641	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40264642	40264876	1	-	1	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40264642	40264876	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40264877	40264966	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40264967	40265106	0.9	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40264967	40265106	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40265107	40265211	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40265212	40265329	0.94	-	1	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40265212	40265329	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40265330	40265412	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40265413	40265435	0.8	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40265413	40265435	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	intron	40265436	40265509	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	CDS	40265510	40265713	1	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	exon	40265510	40265713	.	-	.	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
Phchi.S1	AUGUSTUS	start_codon	40265711	40265713	.	-	0	transcript_id "Phchi.S1G634600.t1"; gene_id "Phchi.S1G634600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6822.t1 is derived from g3994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25220240	25221220	.	-	.	Phchi.S1G398100
Phchi.S1	AUGUSTUS	transcript	25220240	25221220	.	-	.	transcript_id "Phchi.S1G398100.t1"; gene_id "Phchi.S1G398100"
Phchi.S1	AUGUSTUS	stop_codon	25220237	25220239	.	-	0	transcript_id "Phchi.S1G398100.t1"; gene_id "Phchi.S1G398100"
Phchi.S1	AUGUSTUS	CDS	25220240	25221220	0.9	-	0	transcript_id "Phchi.S1G398100.t1"; gene_id "Phchi.S1G398100"
Phchi.S1	AUGUSTUS	exon	25220240	25221220	.	-	.	transcript_id "Phchi.S1G398100.t1"; gene_id "Phchi.S1G398100"
Phchi.S1	AUGUSTUS	start_codon	25221218	25221220	.	-	0	transcript_id "Phchi.S1G398100.t1"; gene_id "Phchi.S1G398100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15265.t1 is derived from g13733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18020702	18025008	.	-	.	Phchi.S3G258400
Phchi.S3	AUGUSTUS	transcript	18020702	18025008	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	stop_codon	18020699	18020701	.	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18020702	18020891	0.89	-	1	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18020702	18020891	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18020892	18021020	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18021021	18021241	1	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18021021	18021241	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18021242	18021332	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18021333	18021517	1	-	2	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18021333	18021517	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18021518	18021608	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18021609	18021741	1	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18021609	18021741	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18021742	18021899	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18021900	18022042	1	-	2	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18021900	18022042	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18022043	18022244	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18022245	18022265	0.47	-	2	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18022245	18022265	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18022266	18022808	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18022809	18022831	0.53	-	1	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18022809	18022831	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18022832	18022920	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18022921	18023024	0.6	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18022921	18023024	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18023025	18023161	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18023162	18023502	0.58	-	2	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18023162	18023502	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18023503	18023601	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18023602	18023814	1	-	2	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18023602	18023814	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18023815	18024428	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18024429	18024535	1	-	1	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18024429	18024535	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18024536	18024628	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18024629	18024636	0.89	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18024629	18024636	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18024637	18024713	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18024714	18024794	0.89	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18024714	18024794	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	intron	18024795	18024957	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	CDS	18024958	18025008	1	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	exon	18024958	18025008	.	-	.	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
Phchi.S3	AUGUSTUS	start_codon	18025006	18025008	.	-	0	transcript_id "Phchi.S3G258400.t1"; gene_id "Phchi.S3G258400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9027.t1 is derived from g6202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39209786	39211728	.	-	.	Phchi.S1G618600
Phchi.S1	AUGUSTUS	transcript	39209786	39211728	.	-	.	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	stop_codon	39209783	39209785	.	-	0	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	CDS	39209786	39211299	0.64	-	2	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	exon	39209786	39211299	.	-	.	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	intron	39211300	39211466	.	-	.	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	CDS	39211467	39211728	0.61	-	0	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	exon	39211467	39211728	.	-	.	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
Phchi.S1	AUGUSTUS	start_codon	39211726	39211728	.	-	0	transcript_id "Phchi.S1G618600.t1"; gene_id "Phchi.S1G618600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1398.t1 is derived from g8317.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	40956	45325	.	-	.	Phchi.S5G000700
Phchi.S5	AUGUSTUS	transcript	40956	45325	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	stop_codon	40953	40955	.	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	40956	40958	1	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	40956	40958	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	40959	41036	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41037	41043	1	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41037	41043	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41044	41143	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41144	41167	1	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41144	41167	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41168	41407	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41408	41451	0.95	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41408	41451	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41452	41763	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41764	41776	1	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41764	41776	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41777	41948	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41949	41984	1	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41949	41984	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41985	42113	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42114	42161	0.64	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42114	42161	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42162	42336	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42337	42397	0.59	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42337	42397	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42398	42564	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42565	42693	0.94	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42565	42693	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42694	42913	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42914	42922	0.92	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42914	42922	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42923	43213	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43214	43298	0.53	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43214	43298	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43299	43396	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43397	43434	0.94	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43397	43434	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43435	43518	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43519	43553	0.94	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43519	43553	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43554	43756	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43757	43778	1	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43757	43778	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43779	43950	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43951	44003	0.96	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43951	44003	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44004	44100	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44101	44307	0.93	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44101	44307	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44308	44474	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44475	44525	0.61	-	1	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44475	44525	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44526	44604	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44605	44611	0.64	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44605	44611	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44612	44710	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44711	44732	0.64	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44711	44732	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44733	45046	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	45047	45078	1	-	2	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	45047	45078	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	45079	45179	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	45180	45216	1	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	45180	45216	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	45217	45283	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	45284	45325	1	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	45284	45325	.	-	.	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	start_codon	45323	45325	.	-	0	transcript_id "Phchi.S5G000700.t1"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	transcript	40956	45325	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	stop_codon	40953	40955	.	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	40956	40958	1	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	40956	40958	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	40959	41036	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41037	41043	1	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41037	41043	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41044	41143	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41144	41167	1	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41144	41167	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41168	41407	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41408	41451	0.94	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41408	41451	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41452	41763	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41764	41776	0.98	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41764	41776	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41777	41948	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	41949	41984	0.99	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	41949	41984	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	41985	42113	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42114	42161	0.64	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42114	42161	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42162	42336	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42337	42397	0.56	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42337	42397	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42398	42564	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42565	42693	0.98	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42565	42693	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42694	42913	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	42914	42922	0.95	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	42914	42922	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	42923	43213	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43214	43298	0.54	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43214	43298	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43299	43396	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43397	43434	0.98	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43397	43434	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43435	43518	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43519	43553	0.98	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43519	43553	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43554	43756	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43757	43778	0.78	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43757	43778	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43779	43854	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	43855	43889	0.76	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	43855	43889	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	43890	44100	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44101	44307	0.94	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44101	44307	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44308	44474	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44475	44525	0.52	-	1	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44475	44525	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44526	44604	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44605	44611	0.53	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44605	44611	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44612	44710	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	44711	44732	0.54	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	44711	44732	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	44733	45046	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	45047	45078	1	-	2	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	45047	45078	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	45079	45179	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	45180	45216	1	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	45180	45216	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	intron	45217	45283	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	CDS	45284	45325	1	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	exon	45284	45325	.	-	.	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
Phchi.S5	AUGUSTUS	start_codon	45323	45325	.	-	0	transcript_id "Phchi.S5G000700.t2"; gene_id "Phchi.S5G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11090.t1 is derived from g15140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4037642	4038777	.	-	.	Phchi.S4G067200
Phchi.S4	AUGUSTUS	transcript	4037642	4038777	.	-	.	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	stop_codon	4037639	4037641	.	-	0	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	CDS	4037642	4037827	0.7	-	0	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	exon	4037642	4037827	.	-	.	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	intron	4037828	4037919	.	-	.	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	CDS	4037920	4038777	0.45	-	0	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	exon	4037920	4038777	.	-	.	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
Phchi.S4	AUGUSTUS	start_codon	4038775	4038777	.	-	0	transcript_id "Phchi.S4G067200.t1"; gene_id "Phchi.S4G067200"
# This transcript jg12005.t2 is derived from g7680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12005.t3 is derived from g7680.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12006.t1 is derived from g7681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	506031	506822	.	+	.	Phchi.S2G008600
Phchi.S2	AUGUSTUS	transcript	506031	506822	.	+	.	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	start_codon	506031	506033	.	+	0	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	CDS	506031	506170	0.59	+	0	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	exon	506031	506170	.	+	.	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	intron	506171	506408	.	+	.	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	CDS	506409	506541	1	+	1	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	exon	506409	506541	.	+	.	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	intron	506542	506639	.	+	.	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	CDS	506640	506822	1	+	0	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	exon	506640	506822	.	+	.	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
Phchi.S2	AUGUSTUS	stop_codon	506823	506825	.	+	0	transcript_id "Phchi.S2G008600.t1"; gene_id "Phchi.S2G008600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10983.t1 is derived from g15033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3522089	3524413	.	+	.	Phchi.S4G056500
Phchi.S4	AUGUSTUS	transcript	3522089	3524413	.	+	.	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	start_codon	3522089	3522091	.	+	0	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	CDS	3522089	3522351	0.75	+	0	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	exon	3522089	3522351	.	+	.	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	intron	3522352	3522450	.	+	.	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	CDS	3522451	3523224	0.78	+	1	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	exon	3522451	3523224	.	+	.	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	intron	3523225	3523455	.	+	.	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	CDS	3523456	3524413	0.63	+	1	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	exon	3523456	3524413	.	+	.	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
Phchi.S4	AUGUSTUS	stop_codon	3524414	3524416	.	+	0	transcript_id "Phchi.S4G056500.t1"; gene_id "Phchi.S4G056500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8512.t1 is derived from g5687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36385546	36386175	.	-	.	Phchi.S1G567100
Phchi.S1	AUGUSTUS	transcript	36385546	36386175	.	-	.	transcript_id "Phchi.S1G567100.t1"; gene_id "Phchi.S1G567100"
Phchi.S1	AUGUSTUS	stop_codon	36385543	36385545	.	-	0	transcript_id "Phchi.S1G567100.t1"; gene_id "Phchi.S1G567100"
Phchi.S1	AUGUSTUS	CDS	36385546	36386175	1	-	0	transcript_id "Phchi.S1G567100.t1"; gene_id "Phchi.S1G567100"
Phchi.S1	AUGUSTUS	exon	36385546	36386175	.	-	.	transcript_id "Phchi.S1G567100.t1"; gene_id "Phchi.S1G567100"
Phchi.S1	AUGUSTUS	start_codon	36386173	36386175	.	-	0	transcript_id "Phchi.S1G567100.t1"; gene_id "Phchi.S1G567100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5412.t1 is derived from g2582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16743831	16746279	.	-	.	Phchi.S1G257100
Phchi.S1	AUGUSTUS	transcript	16743831	16746279	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	stop_codon	16743828	16743830	.	-	0	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	CDS	16743831	16743884	0.68	-	0	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	exon	16743831	16743884	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	intron	16743885	16744199	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	CDS	16744200	16744280	0.67	-	0	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	exon	16744200	16744280	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	intron	16744281	16744372	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	CDS	16744373	16744437	0.42	-	2	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	exon	16744373	16744437	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	intron	16744438	16744528	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	CDS	16744529	16744575	0.6	-	1	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	exon	16744529	16744575	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	intron	16744576	16744895	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	CDS	16744896	16745469	0.32	-	2	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	exon	16744896	16745469	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	intron	16745470	16745543	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	CDS	16745544	16746279	0.54	-	0	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	exon	16745544	16746279	.	-	.	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
Phchi.S1	AUGUSTUS	start_codon	16746277	16746279	.	-	0	transcript_id "Phchi.S1G257100.t1"; gene_id "Phchi.S1G257100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2988.t1 is derived from g157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1022564	1023794	.	+	.	Phchi.S1G014700
Phchi.S1	AUGUSTUS	transcript	1022564	1023794	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	start_codon	1022564	1022566	.	+	0	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	CDS	1022564	1022611	0.97	+	0	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	exon	1022564	1022611	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	intron	1022612	1022715	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	CDS	1022716	1022739	0.98	+	0	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	exon	1022716	1022739	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	intron	1022740	1022968	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	CDS	1022969	1023033	0.98	+	0	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	exon	1022969	1023033	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	intron	1023034	1023141	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	CDS	1023142	1023363	0.62	+	1	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	exon	1023142	1023363	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	intron	1023364	1023463	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	CDS	1023464	1023509	0.42	+	1	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	exon	1023464	1023509	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	intron	1023510	1023656	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	CDS	1023657	1023794	0.48	+	0	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	exon	1023657	1023794	.	+	.	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
Phchi.S1	AUGUSTUS	stop_codon	1023795	1023797	.	+	0	transcript_id "Phchi.S1G014700.t1"; gene_id "Phchi.S1G014700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2991.t1 is derived from g160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1042086	1043790	.	+	.	Phchi.S1G015000
Phchi.S1	AUGUSTUS	transcript	1042086	1043790	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	start_codon	1042086	1042088	.	+	0	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	CDS	1042086	1042189	0.64	+	0	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	exon	1042086	1042189	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	intron	1042190	1042300	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	CDS	1042301	1042391	0.79	+	1	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	exon	1042301	1042391	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	intron	1042392	1042570	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	CDS	1042571	1042597	1	+	0	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	exon	1042571	1042597	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	intron	1042598	1042687	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	CDS	1042688	1042815	1	+	0	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	exon	1042688	1042815	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	intron	1042816	1042908	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	CDS	1042909	1043009	1	+	1	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	exon	1042909	1043009	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	intron	1043010	1043125	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	CDS	1043126	1043790	0.91	+	2	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	exon	1043126	1043790	.	+	.	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
Phchi.S1	AUGUSTUS	stop_codon	1043791	1043793	.	+	0	transcript_id "Phchi.S1G015000.t1"; gene_id "Phchi.S1G015000"
# This transcript jg1519.t2 is derived from g8438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1519.t3 is derived from g8438.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1520.t1 is derived from g8439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1524882	1527473	.	+	.	Phchi.S5G012900
Phchi.S5	AUGUSTUS	transcript	1524882	1527473	.	+	.	transcript_id "Phchi.S5G012900.t1"; gene_id "Phchi.S5G012900"
Phchi.S5	AUGUSTUS	start_codon	1524882	1524884	.	+	0	transcript_id "Phchi.S5G012900.t1"; gene_id "Phchi.S5G012900"
Phchi.S5	AUGUSTUS	CDS	1524882	1527473	0.53	+	0	transcript_id "Phchi.S5G012900.t1"; gene_id "Phchi.S5G012900"
Phchi.S5	AUGUSTUS	exon	1524882	1527473	.	+	.	transcript_id "Phchi.S5G012900.t1"; gene_id "Phchi.S5G012900"
Phchi.S5	AUGUSTUS	stop_codon	1527474	1527476	.	+	0	transcript_id "Phchi.S5G012900.t1"; gene_id "Phchi.S5G012900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9293.t1 is derived from g6468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40803999	40804828	.	-	.	Phchi.S1G645200
Phchi.S1	AUGUSTUS	transcript	40803999	40804828	.	-	.	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	stop_codon	40803996	40803998	.	-	0	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	CDS	40803999	40804097	0.74	-	0	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	exon	40803999	40804097	.	-	.	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	intron	40804098	40804333	.	-	.	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	CDS	40804334	40804828	0.73	-	0	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	exon	40804334	40804828	.	-	.	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
Phchi.S1	AUGUSTUS	start_codon	40804826	40804828	.	-	0	transcript_id "Phchi.S1G645200.t1"; gene_id "Phchi.S1G645200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1672.t1 is derived from g8591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2382794	2383066	.	-	.	Phchi.S5G028100
Phchi.S5	AUGUSTUS	transcript	2382794	2383066	.	-	.	transcript_id "Phchi.S5G028100.t1"; gene_id "Phchi.S5G028100"
Phchi.S5	AUGUSTUS	stop_codon	2382791	2382793	.	-	0	transcript_id "Phchi.S5G028100.t1"; gene_id "Phchi.S5G028100"
Phchi.S5	AUGUSTUS	CDS	2382794	2383066	0.61	-	0	transcript_id "Phchi.S5G028100.t1"; gene_id "Phchi.S5G028100"
Phchi.S5	AUGUSTUS	exon	2382794	2383066	.	-	.	transcript_id "Phchi.S5G028100.t1"; gene_id "Phchi.S5G028100"
Phchi.S5	AUGUSTUS	start_codon	2383064	2383066	.	-	0	transcript_id "Phchi.S5G028100.t1"; gene_id "Phchi.S5G028100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14453.t1 is derived from g12921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12926073	12937083	.	+	.	Phchi.S3G177200
Phchi.S3	AUGUSTUS	transcript	12926073	12937083	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	start_codon	12926073	12926075	.	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12926073	12926178	0.66	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12926073	12926178	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12926179	12926303	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12926304	12926832	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12926304	12926832	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12926833	12926964	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12926965	12927425	0.76	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12926965	12927425	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12927426	12927541	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12927542	12927671	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12927542	12927671	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12927672	12927764	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12927765	12927836	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12927765	12927836	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12927837	12927923	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12927924	12927992	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12927924	12927992	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12927993	12928107	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12928108	12928173	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12928108	12928173	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12928174	12928363	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12928364	12928432	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12928364	12928432	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12928433	12928523	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12928524	12928592	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12928524	12928592	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12928593	12928733	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12928734	12928961	0.79	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12928734	12928961	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12928962	12929186	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12929187	12929256	0.99	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12929187	12929256	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12929257	12929336	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12929337	12929463	1	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12929337	12929463	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12929464	12929572	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12929573	12929641	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12929573	12929641	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12929642	12929720	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12929721	12929910	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12929721	12929910	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12929911	12929995	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12929996	12930128	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12929996	12930128	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12930129	12930239	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12930240	12930341	0.99	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12930240	12930341	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12930342	12930426	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12930427	12930505	0.96	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12930427	12930505	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12930506	12930602	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12930603	12930652	0.99	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12930603	12930652	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12930653	12930764	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12930765	12930831	0.99	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12930765	12930831	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12930832	12931001	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12931002	12931117	0.97	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12931002	12931117	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12931118	12931238	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12931239	12931338	0.95	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12931239	12931338	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12931339	12931977	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12931978	12932595	0.91	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12931978	12932595	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12932596	12932765	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12932766	12933061	0.99	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12932766	12933061	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12933062	12933165	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12933166	12933325	1	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12933166	12933325	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12933326	12933449	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12933450	12933589	0.98	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12933450	12933589	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12933590	12933703	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12933704	12933866	0.99	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12933704	12933866	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12933867	12933947	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12933948	12934057	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12933948	12934057	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12934058	12934154	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12934155	12934254	1	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12934155	12934254	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12934255	12934346	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12934347	12934433	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12934347	12934433	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12934434	12934516	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12934517	12934699	1	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12934517	12934699	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12934700	12934790	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12934791	12934904	0.42	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12934791	12934904	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12934905	12934996	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12934997	12935075	0.55	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12934997	12935075	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12935076	12935167	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12935168	12935329	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12935168	12935329	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12935330	12935413	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12935414	12935454	1	+	1	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12935414	12935454	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12935455	12935528	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12935529	12935585	0.6	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12935529	12935585	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12935586	12935768	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12935769	12935932	0.67	+	2	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12935769	12935932	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12935933	12936037	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12936038	12936142	1	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12936038	12936142	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	intron	12936143	12936219	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	CDS	12936220	12937083	0.98	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	exon	12936220	12937083	.	+	.	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
Phchi.S3	AUGUSTUS	stop_codon	12937084	12937086	.	+	0	transcript_id "Phchi.S3G177200.t1"; gene_id "Phchi.S3G177200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12046.t1 is derived from g7721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	987534	987872	.	+	.	Phchi.S2G012600
Phchi.S2	AUGUSTUS	transcript	987534	987872	.	+	.	transcript_id "Phchi.S2G012600.t1"; gene_id "Phchi.S2G012600"
Phchi.S2	AUGUSTUS	start_codon	987534	987536	.	+	0	transcript_id "Phchi.S2G012600.t1"; gene_id "Phchi.S2G012600"
Phchi.S2	AUGUSTUS	CDS	987534	987872	0.63	+	0	transcript_id "Phchi.S2G012600.t1"; gene_id "Phchi.S2G012600"
Phchi.S2	AUGUSTUS	exon	987534	987872	.	+	.	transcript_id "Phchi.S2G012600.t1"; gene_id "Phchi.S2G012600"
Phchi.S2	AUGUSTUS	stop_codon	987873	987875	.	+	0	transcript_id "Phchi.S2G012600.t1"; gene_id "Phchi.S2G012600"
# This transcript jg14071.t2 is derived from g12538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14072.t1 is derived from g12539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10659241	10661051	.	-	.	Phchi.S3G139100
Phchi.S3	AUGUSTUS	transcript	10659241	10661051	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	stop_codon	10659238	10659240	.	-	0	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10659241	10659503	0.76	-	2	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10659241	10659503	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	intron	10659504	10659628	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10659629	10660073	1	-	0	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10659629	10660073	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	intron	10660074	10660158	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10660159	10660268	0.97	-	2	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10660159	10660268	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	intron	10660269	10660380	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10660381	10660525	1	-	0	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10660381	10660525	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	intron	10660526	10660664	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10660665	10660824	0.93	-	1	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10660665	10660824	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	intron	10660825	10660907	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10660908	10660925	0.95	-	1	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10660908	10660925	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	intron	10660926	10660998	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	CDS	10660999	10661051	0.42	-	0	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	exon	10660999	10661051	.	-	.	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
Phchi.S3	AUGUSTUS	start_codon	10661049	10661051	.	-	0	transcript_id "Phchi.S3G139100.t1"; gene_id "Phchi.S3G139100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9728.t1 is derived from g6904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43416264	43422021	.	-	.	Phchi.S1G688700
Phchi.S1	AUGUSTUS	transcript	43416264	43422021	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	stop_codon	43416261	43416263	.	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43416264	43416463	1	-	2	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43416264	43416463	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43416464	43416555	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43416556	43416638	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43416556	43416638	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43416639	43416727	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43416728	43416776	1	-	2	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43416728	43416776	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43416777	43416896	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43416897	43416969	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43416897	43416969	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43416970	43417057	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43417058	43417120	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43417058	43417120	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43417121	43417225	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43417226	43417326	0.83	-	2	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43417226	43417326	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43417327	43417427	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43417428	43417614	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43417428	43417614	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43417615	43417699	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43417700	43418740	0.97	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43417700	43418740	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43418741	43418859	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43418860	43418926	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43418860	43418926	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43418927	43419006	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43419007	43419012	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43419007	43419012	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43419013	43419104	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43419105	43419121	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43419105	43419121	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43419122	43419312	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43419313	43419399	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43419313	43419399	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43419400	43419564	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43419565	43419654	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43419565	43419654	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43419655	43419782	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43419783	43419851	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43419783	43419851	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43419852	43419941	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43419942	43420013	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43419942	43420013	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43420014	43420140	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43420141	43420198	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43420141	43420198	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43420199	43420274	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43420275	43420329	1	-	2	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43420275	43420329	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43420330	43420514	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43420515	43420582	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43420515	43420582	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43420583	43420696	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43420697	43420779	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43420697	43420779	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43420780	43420867	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43420868	43420931	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43420868	43420931	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43420932	43421068	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43421069	43421140	1	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43421069	43421140	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43421141	43421264	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43421265	43421324	0.99	-	1	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43421265	43421324	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43421325	43421408	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43421409	43421499	0.74	-	2	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43421409	43421499	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43421500	43421602	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43421603	43421636	0.99	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43421603	43421636	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	intron	43421637	43421721	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	CDS	43421722	43422021	1	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	exon	43421722	43422021	.	-	.	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
Phchi.S1	AUGUSTUS	start_codon	43422019	43422021	.	-	0	transcript_id "Phchi.S1G688700.t1"; gene_id "Phchi.S1G688700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11672.t1 is derived from g15723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7601401	7601762	.	+	.	Phchi.S4G125400
Phchi.S4	AUGUSTUS	transcript	7601401	7601762	.	+	.	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	start_codon	7601401	7601403	.	+	0	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	CDS	7601401	7601573	0.68	+	0	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	exon	7601401	7601573	.	+	.	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	intron	7601574	7601689	.	+	.	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	CDS	7601690	7601762	0.94	+	1	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	exon	7601690	7601762	.	+	.	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
Phchi.S4	AUGUSTUS	stop_codon	7601763	7601765	.	+	0	transcript_id "Phchi.S4G125400.t1"; gene_id "Phchi.S4G125400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4464.t1 is derived from g1634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10630445	10633161	.	-	.	Phchi.S1G162300
Phchi.S1	AUGUSTUS	transcript	10630445	10633161	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	stop_codon	10630442	10630444	.	-	0	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	CDS	10630445	10631659	0.87	-	0	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	exon	10630445	10631659	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	intron	10631660	10631904	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	CDS	10631905	10632117	0.75	-	0	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	exon	10631905	10632117	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	intron	10632118	10632427	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	CDS	10632428	10632600	0.37	-	2	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	exon	10632428	10632600	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	intron	10632601	10632671	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	CDS	10632672	10633161	0.57	-	0	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	exon	10632672	10633161	.	-	.	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
Phchi.S1	AUGUSTUS	start_codon	10633159	10633161	.	-	0	transcript_id "Phchi.S1G162300.t1"; gene_id "Phchi.S1G162300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3582.t1 is derived from g751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4604265	4606983	.	+	.	Phchi.S1G074100
Phchi.S1	AUGUSTUS	transcript	4604265	4606983	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	start_codon	4604265	4604267	.	+	0	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	CDS	4604265	4604370	0.99	+	0	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	exon	4604265	4604370	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	intron	4604371	4604542	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	CDS	4604543	4604625	0.89	+	2	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	exon	4604543	4604625	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	intron	4604626	4604748	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	CDS	4604749	4604796	0.98	+	0	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	exon	4604749	4604796	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	intron	4604797	4605735	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	CDS	4605736	4606983	0.96	+	0	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	exon	4605736	4606983	.	+	.	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
Phchi.S1	AUGUSTUS	stop_codon	4606984	4606986	.	+	0	transcript_id "Phchi.S1G074100.t1"; gene_id "Phchi.S1G074100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10981.t1 is derived from g15031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3504986	3519100	.	+	.	Phchi.S4G056300
Phchi.S4	AUGUSTUS	transcript	3504986	3519100	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	start_codon	3504986	3504988	.	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3504986	3504988	1	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3504986	3504988	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3504989	3505065	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3505066	3505135	1	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3505066	3505135	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3505136	3505210	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3505211	3505589	1	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3505211	3505589	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3505590	3505665	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3505666	3506046	0.73	+	1	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3505666	3506046	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3506047	3506308	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3506309	3506631	0.43	+	1	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3506309	3506631	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3506632	3506757	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3506758	3507275	0.94	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3506758	3507275	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3507276	3507410	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3507411	3508251	0.59	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3507411	3508251	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3508252	3508333	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3508334	3509080	0.95	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3508334	3509080	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3509081	3509372	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3509373	3510248	0.91	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3509373	3510248	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3510249	3510406	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3510407	3510793	0.98	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3510407	3510793	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3510794	3510885	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3510886	3512258	0.7	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3510886	3512258	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3512259	3512432	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3512433	3512724	0.84	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3512433	3512724	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3512725	3512842	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3512843	3512955	0.98	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3512843	3512955	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3512956	3513072	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3513073	3513446	0.97	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3513073	3513446	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3513447	3513623	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3513624	3513864	1	+	1	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3513624	3513864	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3513865	3514076	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3514077	3515114	0.91	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3514077	3515114	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3515115	3515218	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3515219	3515445	1	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3515219	3515445	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3515446	3515531	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3515532	3516363	1	+	1	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3515532	3516363	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3516364	3516515	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3516516	3516858	0.84	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3516516	3516858	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3516859	3517008	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3517009	3517152	0.54	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3517009	3517152	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3517153	3517276	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3517277	3517495	1	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3517277	3517495	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3517496	3517607	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3517608	3518008	0.94	+	2	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3517608	3518008	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3518009	3518100	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3518101	3518670	0.93	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3518101	3518670	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	intron	3518671	3518752	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	CDS	3518753	3519100	0.32	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	exon	3518753	3519100	.	+	.	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
Phchi.S4	AUGUSTUS	stop_codon	3519101	3519103	.	+	0	transcript_id "Phchi.S4G056300.t1"; gene_id "Phchi.S4G056300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9423.t1 is derived from g6599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41406943	41411236	.	-	.	Phchi.S1G658200
Phchi.S1	AUGUSTUS	transcript	41406943	41411236	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	stop_codon	41406940	41406942	.	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41406943	41407070	1	-	2	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41406943	41407070	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41407071	41407159	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41407160	41407437	0.73	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41407160	41407437	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41407438	41407534	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41407535	41407594	1	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41407535	41407594	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41407595	41407684	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41407685	41407878	1	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41407685	41407878	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41407879	41408016	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41408017	41408161	0.99	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41408017	41408161	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41408162	41408286	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41408287	41408522	0.99	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41408287	41408522	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41408523	41408593	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41408594	41408817	0.55	-	2	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41408594	41408817	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41408818	41408942	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41408943	41409052	0.81	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41408943	41409052	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41409053	41409147	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41409148	41409228	0.93	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41409148	41409228	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41409229	41409332	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41409333	41409457	0.99	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41409333	41409457	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41409458	41409814	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41409815	41409833	1	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41409815	41409833	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41409834	41409932	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41409933	41409960	1	-	2	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41409933	41409960	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41409961	41410046	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41410047	41410057	0.58	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41410047	41410057	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41410058	41410172	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41410173	41410216	0.57	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41410173	41410216	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41410217	41410311	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41410312	41410432	1	-	1	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41410312	41410432	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	intron	41410433	41410514	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	CDS	41410515	41411236	0.99	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	exon	41410515	41411236	.	-	.	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
Phchi.S1	AUGUSTUS	start_codon	41411234	41411236	.	-	0	transcript_id "Phchi.S1G658200.t1"; gene_id "Phchi.S1G658200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14500.t1 is derived from g12968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13203346	13203810	.	-	.	Phchi.S3G181900
Phchi.S3	AUGUSTUS	transcript	13203346	13203810	.	-	.	transcript_id "Phchi.S3G181900.t1"; gene_id "Phchi.S3G181900"
Phchi.S3	AUGUSTUS	stop_codon	13203343	13203345	.	-	0	transcript_id "Phchi.S3G181900.t1"; gene_id "Phchi.S3G181900"
Phchi.S3	AUGUSTUS	CDS	13203346	13203810	0.99	-	0	transcript_id "Phchi.S3G181900.t1"; gene_id "Phchi.S3G181900"
Phchi.S3	AUGUSTUS	exon	13203346	13203810	.	-	.	transcript_id "Phchi.S3G181900.t1"; gene_id "Phchi.S3G181900"
Phchi.S3	AUGUSTUS	start_codon	13203808	13203810	.	-	0	transcript_id "Phchi.S3G181900.t1"; gene_id "Phchi.S3G181900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5180.t1 is derived from g2350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15349058	15350426	.	-	.	Phchi.S1G233900
Phchi.S1	AUGUSTUS	transcript	15349058	15350426	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	stop_codon	15349055	15349057	.	-	0	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	CDS	15349058	15349362	0.98	-	2	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	exon	15349058	15349362	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	intron	15349363	15349476	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	CDS	15349477	15349552	0.99	-	0	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	exon	15349477	15349552	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	intron	15349553	15349673	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	CDS	15349674	15349958	1	-	0	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	exon	15349674	15349958	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	intron	15349959	15350387	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	CDS	15350388	15350426	0.95	-	0	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	exon	15350388	15350426	.	-	.	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
Phchi.S1	AUGUSTUS	start_codon	15350424	15350426	.	-	0	transcript_id "Phchi.S1G233900.t1"; gene_id "Phchi.S1G233900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1740.t1 is derived from g8660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2795441	2797127	.	+	.	Phchi.S5G034900
Phchi.S5	AUGUSTUS	transcript	2795441	2797127	.	+	.	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	start_codon	2795441	2795443	.	+	0	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	CDS	2795441	2796406	1	+	0	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	exon	2795441	2796406	.	+	.	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	intron	2796407	2796620	.	+	.	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	CDS	2796621	2796893	1	+	0	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	exon	2796621	2796893	.	+	.	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	intron	2796894	2796974	.	+	.	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	CDS	2796975	2797127	1	+	0	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	exon	2796975	2797127	.	+	.	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
Phchi.S5	AUGUSTUS	stop_codon	2797128	2797130	.	+	0	transcript_id "Phchi.S5G034900.t1"; gene_id "Phchi.S5G034900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3803.t1 is derived from g972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5810797	5814441	.	+	.	Phchi.S1G096200
Phchi.S1	AUGUSTUS	transcript	5810797	5814441	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	start_codon	5810797	5810799	.	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5810797	5810898	0.36	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5810797	5810898	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5810899	5811000	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5811001	5811303	0.35	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5811001	5811303	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5811304	5811534	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5811535	5811585	0.47	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5811535	5811585	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5811586	5811713	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5811714	5811841	1	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5811714	5811841	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5811842	5811961	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5811962	5812102	1	+	1	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5811962	5812102	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5812103	5812200	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5812201	5812287	1	+	1	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5812201	5812287	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5812288	5812373	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5812374	5812527	1	+	1	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5812374	5812527	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5812528	5812618	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5812619	5812678	0.99	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5812619	5812678	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5812679	5812791	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5812792	5813220	0.95	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5812792	5813220	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5813221	5813312	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5813313	5813608	1	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5813313	5813608	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5813609	5813708	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5813709	5813838	1	+	1	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5813709	5813838	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	intron	5813839	5813949	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	CDS	5813950	5814441	0.99	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	exon	5813950	5814441	.	+	.	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
Phchi.S1	AUGUSTUS	stop_codon	5814442	5814444	.	+	0	transcript_id "Phchi.S1G096200.t1"; gene_id "Phchi.S1G096200"
# This transcript jg8154.t2 is derived from g5329.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8155.t1 is derived from g5330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34154184	34155876	.	-	.	Phchi.S1G531400
Phchi.S1	AUGUSTUS	transcript	34154184	34155876	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	stop_codon	34154181	34154183	.	-	0	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	CDS	34154184	34154640	0.43	-	1	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	exon	34154184	34154640	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	intron	34154641	34154749	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	CDS	34154750	34155406	0.99	-	1	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	exon	34154750	34155406	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	intron	34155407	34155564	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	CDS	34155565	34155638	1	-	0	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	exon	34155565	34155638	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	intron	34155639	34155834	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	CDS	34155835	34155876	0.7	-	0	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	exon	34155835	34155876	.	-	.	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
Phchi.S1	AUGUSTUS	start_codon	34155874	34155876	.	-	0	transcript_id "Phchi.S1G531400.t1"; gene_id "Phchi.S1G531400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11883.t1 is derived from g15935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8985480	8988576	.	+	.	Phchi.S4G146500
Phchi.S4	AUGUSTUS	transcript	8985480	8988576	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	start_codon	8985480	8985482	.	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8985480	8985550	0.62	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8985480	8985550	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8985551	8985655	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8985656	8985792	0.91	+	1	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8985656	8985792	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8985793	8985882	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8985883	8986610	0.85	+	2	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8985883	8986610	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8986611	8986720	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8986721	8986966	0.85	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8986721	8986966	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8986967	8987079	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8987080	8987488	0.4	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8987080	8987488	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8987489	8987839	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8987840	8988008	0.39	+	2	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8987840	8988008	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8988009	8988106	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8988107	8988185	0.84	+	1	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8988107	8988185	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8988186	8988259	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8988260	8988373	0.77	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8988260	8988373	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	intron	8988374	8988483	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	CDS	8988484	8988576	0.75	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	exon	8988484	8988576	.	+	.	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
Phchi.S4	AUGUSTUS	stop_codon	8988577	8988579	.	+	0	transcript_id "Phchi.S4G146500.t1"; gene_id "Phchi.S4G146500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6135.t1 is derived from g3306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21099475	21102086	.	-	.	Phchi.S1G329400
Phchi.S1	AUGUSTUS	transcript	21099475	21102086	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	stop_codon	21099472	21099474	.	-	0	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21099475	21099554	1	-	2	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21099475	21099554	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21099555	21099647	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21099648	21099705	1	-	0	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21099648	21099705	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21099706	21099792	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21099793	21099913	1	-	1	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21099793	21099913	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21099914	21099995	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21099996	21100090	1	-	0	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21099996	21100090	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21100091	21100213	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21100214	21100352	0.99	-	1	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21100214	21100352	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21100353	21100468	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21100469	21100699	0.64	-	1	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21100469	21100699	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21100700	21100984	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21100985	21101049	0.53	-	0	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21100985	21101049	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21101050	21101161	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21101162	21101279	0.92	-	1	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21101162	21101279	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	intron	21101280	21101499	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	CDS	21101500	21102086	0.93	-	0	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	exon	21101500	21102086	.	-	.	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
Phchi.S1	AUGUSTUS	start_codon	21102084	21102086	.	-	0	transcript_id "Phchi.S1G329400.t1"; gene_id "Phchi.S1G329400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4893.t1 is derived from g2063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13270063	13273820	.	+	.	Phchi.S1G205200
Phchi.S1	AUGUSTUS	transcript	13270063	13273820	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	start_codon	13270063	13270065	.	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270063	13270334	0.82	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270063	13270334	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270335	13270439	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270440	13270658	0.97	+	1	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270440	13270658	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270659	13270736	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270737	13270848	1	+	1	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270737	13270848	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270849	13270924	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270925	13270987	0.99	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270925	13270987	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270988	13271101	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271102	13271240	1	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271102	13271240	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271241	13271371	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271372	13271427	1	+	2	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271372	13271427	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271428	13271534	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271535	13271608	0.99	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271535	13271608	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271609	13271772	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271773	13271920	0.99	+	1	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271773	13271920	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271921	13272052	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272053	13272226	1	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272053	13272226	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272227	13272327	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272328	13272415	1	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272328	13272415	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272416	13272600	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272601	13272762	1	+	2	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272601	13272762	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272763	13272892	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272893	13272990	1	+	2	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272893	13272990	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272991	13273091	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273092	13273209	1	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273092	13273209	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13273210	13273349	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273350	13273444	1	+	2	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273350	13273444	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13273445	13273533	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273534	13273640	1	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273534	13273640	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13273641	13273723	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273724	13273820	1	+	1	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273724	13273820	.	+	.	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	stop_codon	13273821	13273823	.	+	0	transcript_id "Phchi.S1G205200.t1"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	transcript	13270063	13273820	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	start_codon	13270063	13270065	.	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270063	13270334	0.73	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270063	13270334	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270335	13270439	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270440	13270658	0.94	+	1	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270440	13270658	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270659	13270736	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270737	13270848	1	+	1	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270737	13270848	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270849	13270924	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13270925	13270987	0.98	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13270925	13270987	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13270988	13271101	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271102	13271240	1	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271102	13271240	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271241	13271371	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271372	13271427	1	+	2	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271372	13271427	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271428	13271595	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271596	13271608	0.7	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271596	13271608	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271609	13271772	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13271773	13271915	0.7	+	2	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13271773	13271915	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13271916	13272052	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272053	13272226	0.82	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272053	13272226	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272227	13272327	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272328	13272415	1	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272328	13272415	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272416	13272600	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272601	13272762	1	+	2	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272601	13272762	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272763	13272892	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13272893	13272990	1	+	2	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13272893	13272990	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13272991	13273091	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273092	13273209	1	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273092	13273209	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13273210	13273349	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273350	13273444	1	+	2	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273350	13273444	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13273445	13273533	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273534	13273640	1	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273534	13273640	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	intron	13273641	13273723	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	CDS	13273724	13273820	1	+	1	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	exon	13273724	13273820	.	+	.	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
Phchi.S1	AUGUSTUS	stop_codon	13273821	13273823	.	+	0	transcript_id "Phchi.S1G205200.t2"; gene_id "Phchi.S1G205200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8370.t1 is derived from g5545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35547622	35552255	.	-	.	Phchi.S1G552900
Phchi.S1	AUGUSTUS	transcript	35547622	35552255	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	stop_codon	35547619	35547621	.	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35547622	35547714	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35547622	35547714	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35547715	35547802	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35547803	35547872	1	-	1	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35547803	35547872	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35547873	35547956	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35547957	35548400	1	-	1	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35547957	35548400	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35548401	35548531	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35548532	35548695	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35548532	35548695	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35548696	35548783	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35548784	35548822	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35548784	35548822	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35548823	35548899	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35548900	35549781	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35548900	35549781	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35549782	35549858	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35549859	35550227	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35549859	35550227	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35550228	35550354	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35550355	35550511	1	-	1	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35550355	35550511	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35550512	35550588	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35550589	35550671	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35550589	35550671	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35550672	35550748	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35550749	35550799	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35550749	35550799	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35550800	35550889	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35550890	35550952	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35550890	35550952	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35550953	35551041	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35551042	35551107	0.96	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35551042	35551107	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35551108	35551210	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35551211	35551310	0.96	-	1	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35551211	35551310	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35551311	35551397	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35551398	35551492	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35551398	35551492	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35551493	35551586	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35551587	35551701	1	-	1	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35551587	35551701	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35551702	35551777	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35551778	35551974	1	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35551778	35551974	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	intron	35551975	35552048	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	CDS	35552049	35552255	0.54	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	exon	35552049	35552255	.	-	.	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
Phchi.S1	AUGUSTUS	start_codon	35552253	35552255	.	-	0	transcript_id "Phchi.S1G552900.t1"; gene_id "Phchi.S1G552900"
# This transcript jg13885.t2 is derived from g12352.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13886.t1 is derived from g12353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9461651	9462410	.	-	.	Phchi.S3G120500
Phchi.S3	AUGUSTUS	transcript	9461651	9462410	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	stop_codon	9461648	9461650	.	-	0	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	CDS	9461651	9461771	0.97	-	1	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	exon	9461651	9461771	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	intron	9461772	9461851	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	CDS	9461852	9461896	1	-	1	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	exon	9461852	9461896	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	intron	9461897	9461977	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	CDS	9461978	9462108	1	-	0	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	exon	9461978	9462108	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	intron	9462109	9462197	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	CDS	9462198	9462239	1	-	0	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	exon	9462198	9462239	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	intron	9462240	9462323	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	CDS	9462324	9462410	0.87	-	0	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	exon	9462324	9462410	.	-	.	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
Phchi.S3	AUGUSTUS	start_codon	9462408	9462410	.	-	0	transcript_id "Phchi.S3G120500.t1"; gene_id "Phchi.S3G120500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13179.t1 is derived from g11644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4540008	4541761	.	-	.	Phchi.S3G049800
Phchi.S3	AUGUSTUS	transcript	4540008	4541761	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	stop_codon	4540005	4540007	.	-	0	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540008	4540074	1	-	1	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540008	4540074	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4540075	4540151	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540152	4540231	1	-	0	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540152	4540231	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4540232	4540363	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540364	4540409	1	-	1	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540364	4540409	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4540410	4540504	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540505	4540561	1	-	1	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540505	4540561	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4540562	4540654	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540655	4540713	1	-	0	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540655	4540713	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4540714	4540792	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540793	4540893	1	-	2	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540793	4540893	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4540894	4540986	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4540987	4541108	1	-	1	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4540987	4541108	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4541109	4541324	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4541325	4541376	1	-	2	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4541325	4541376	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4541377	4541458	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4541459	4541554	1	-	2	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4541459	4541554	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	intron	4541555	4541631	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	CDS	4541632	4541761	0.74	-	0	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	exon	4541632	4541761	.	-	.	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
Phchi.S3	AUGUSTUS	start_codon	4541759	4541761	.	-	0	transcript_id "Phchi.S3G049800.t1"; gene_id "Phchi.S3G049800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1778.t1 is derived from g8698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2970321	2971091	.	-	.	Phchi.S5G038700
Phchi.S5	AUGUSTUS	transcript	2970321	2971091	.	-	.	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	stop_codon	2970318	2970320	.	-	0	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	CDS	2970321	2970503	0.99	-	0	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	exon	2970321	2970503	.	-	.	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	intron	2970504	2970599	.	-	.	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	CDS	2970600	2971091	0.6	-	0	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	exon	2970600	2971091	.	-	.	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
Phchi.S5	AUGUSTUS	start_codon	2971089	2971091	.	-	0	transcript_id "Phchi.S5G038700.t1"; gene_id "Phchi.S5G038700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1532.t1 is derived from g8451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1615194	1615529	.	+	.	Phchi.S5G014100
Phchi.S5	AUGUSTUS	transcript	1615194	1615529	.	+	.	transcript_id "Phchi.S5G014100.t1"; gene_id "Phchi.S5G014100"
Phchi.S5	AUGUSTUS	start_codon	1615194	1615196	.	+	0	transcript_id "Phchi.S5G014100.t1"; gene_id "Phchi.S5G014100"
Phchi.S5	AUGUSTUS	CDS	1615194	1615529	1	+	0	transcript_id "Phchi.S5G014100.t1"; gene_id "Phchi.S5G014100"
Phchi.S5	AUGUSTUS	exon	1615194	1615529	.	+	.	transcript_id "Phchi.S5G014100.t1"; gene_id "Phchi.S5G014100"
Phchi.S5	AUGUSTUS	stop_codon	1615530	1615532	.	+	0	transcript_id "Phchi.S5G014100.t1"; gene_id "Phchi.S5G014100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12848.t1 is derived from g11313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2686774	2688856	.	-	.	Phchi.S3G016700
Phchi.S3	AUGUSTUS	transcript	2686774	2688856	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	stop_codon	2686771	2686773	.	-	0	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2686774	2686818	0.92	-	0	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2686774	2686818	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2686819	2686914	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2686915	2686963	0.88	-	1	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2686915	2686963	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2686964	2687086	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2687087	2687218	0.88	-	1	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2687087	2687218	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2687219	2687336	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2687337	2687496	1	-	2	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2687337	2687496	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2687497	2687676	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2687677	2687798	1	-	1	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2687677	2687798	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2687799	2687920	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2687921	2688042	1	-	0	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2687921	2688042	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2688043	2688225	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2688226	2688346	1	-	1	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2688226	2688346	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2688347	2688429	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2688430	2688526	1	-	2	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2688430	2688526	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	intron	2688527	2688747	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	CDS	2688748	2688856	0.76	-	0	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	exon	2688748	2688856	.	-	.	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
Phchi.S3	AUGUSTUS	start_codon	2688854	2688856	.	-	0	transcript_id "Phchi.S3G016700.t1"; gene_id "Phchi.S3G016700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12427.t1 is derived from g8104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19581291	19582169	.	+	.	Phchi.S2G050700
Phchi.S2	AUGUSTUS	transcript	19581291	19582169	.	+	.	transcript_id "Phchi.S2G050700.t1"; gene_id "Phchi.S2G050700"
Phchi.S2	AUGUSTUS	start_codon	19581291	19581293	.	+	0	transcript_id "Phchi.S2G050700.t1"; gene_id "Phchi.S2G050700"
Phchi.S2	AUGUSTUS	CDS	19581291	19582169	0.91	+	0	transcript_id "Phchi.S2G050700.t1"; gene_id "Phchi.S2G050700"
Phchi.S2	AUGUSTUS	exon	19581291	19582169	.	+	.	transcript_id "Phchi.S2G050700.t1"; gene_id "Phchi.S2G050700"
Phchi.S2	AUGUSTUS	stop_codon	19582170	19582172	.	+	0	transcript_id "Phchi.S2G050700.t1"; gene_id "Phchi.S2G050700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8183.t1 is derived from g5358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34329613	34331644	.	+	.	Phchi.S1G534200
Phchi.S1	AUGUSTUS	transcript	34329613	34331644	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	start_codon	34329613	34329615	.	+	0	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34329613	34329618	1	+	0	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34329613	34329618	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	intron	34329619	34329714	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34329715	34329843	1	+	0	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34329715	34329843	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	intron	34329844	34329977	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34329978	34330870	1	+	0	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34329978	34330870	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	intron	34330871	34330972	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34330973	34331043	1	+	1	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34330973	34331043	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	intron	34331044	34331183	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34331184	34331286	1	+	2	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34331184	34331286	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	intron	34331287	34331370	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34331371	34331446	1	+	1	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34331371	34331446	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	intron	34331447	34331539	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	CDS	34331540	34331644	1	+	0	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	exon	34331540	34331644	.	+	.	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
Phchi.S1	AUGUSTUS	stop_codon	34331645	34331647	.	+	0	transcript_id "Phchi.S1G534200.t1"; gene_id "Phchi.S1G534200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12975.t1 is derived from g11440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3398868	3400427	.	+	.	Phchi.S3G029400
Phchi.S3	AUGUSTUS	transcript	3398868	3400427	.	+	.	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	start_codon	3398868	3398870	.	+	0	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	CDS	3398868	3398981	0.89	+	0	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	exon	3398868	3398981	.	+	.	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	intron	3398982	3399099	.	+	.	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	CDS	3399100	3399903	0.48	+	0	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	exon	3399100	3399903	.	+	.	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	intron	3399904	3400013	.	+	.	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	CDS	3400014	3400427	0.56	+	0	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	exon	3400014	3400427	.	+	.	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
Phchi.S3	AUGUSTUS	stop_codon	3400428	3400430	.	+	0	transcript_id "Phchi.S3G029400.t1"; gene_id "Phchi.S3G029400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8773.t1 is derived from g5948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37894877	37895725	.	+	.	Phchi.S1G593200
Phchi.S1	AUGUSTUS	transcript	37894877	37895725	.	+	.	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	start_codon	37894877	37894879	.	+	0	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	CDS	37894877	37895140	0.39	+	0	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	exon	37894877	37895140	.	+	.	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	intron	37895141	37895374	.	+	.	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	CDS	37895375	37895725	0.65	+	0	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	exon	37895375	37895725	.	+	.	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
Phchi.S1	AUGUSTUS	stop_codon	37895726	37895728	.	+	0	transcript_id "Phchi.S1G593200.t1"; gene_id "Phchi.S1G593200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8247.t1 is derived from g5422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34681108	34682568	.	+	.	Phchi.S1G540600
Phchi.S1	AUGUSTUS	transcript	34681108	34682568	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	start_codon	34681108	34681110	.	+	0	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	CDS	34681108	34681463	1	+	0	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	exon	34681108	34681463	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	intron	34681464	34681545	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	CDS	34681546	34681688	0.36	+	1	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	exon	34681546	34681688	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	intron	34681689	34681851	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	CDS	34681852	34682098	0.38	+	2	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	exon	34681852	34682098	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	intron	34682099	34682174	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	CDS	34682175	34682568	0.95	+	1	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	exon	34682175	34682568	.	+	.	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
Phchi.S1	AUGUSTUS	stop_codon	34682569	34682571	.	+	0	transcript_id "Phchi.S1G540600.t1"; gene_id "Phchi.S1G540600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3559.t1 is derived from g728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4487503	4491732	.	-	.	Phchi.S1G071800
Phchi.S1	AUGUSTUS	transcript	4487503	4491732	.	-	.	transcript_id "Phchi.S1G071800.t1"; gene_id "Phchi.S1G071800"
Phchi.S1	AUGUSTUS	stop_codon	4487500	4487502	.	-	0	transcript_id "Phchi.S1G071800.t1"; gene_id "Phchi.S1G071800"
Phchi.S1	AUGUSTUS	CDS	4487503	4491732	0.64	-	0	transcript_id "Phchi.S1G071800.t1"; gene_id "Phchi.S1G071800"
Phchi.S1	AUGUSTUS	exon	4487503	4491732	.	-	.	transcript_id "Phchi.S1G071800.t1"; gene_id "Phchi.S1G071800"
Phchi.S1	AUGUSTUS	start_codon	4491730	4491732	.	-	0	transcript_id "Phchi.S1G071800.t1"; gene_id "Phchi.S1G071800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12443.t1 is derived from g8120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20619984	20620307	.	+	.	Phchi.S2G052300
Phchi.S2	AUGUSTUS	transcript	20619984	20620307	.	+	.	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	start_codon	20619984	20619986	.	+	0	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	CDS	20619984	20620171	0.94	+	0	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	exon	20619984	20620171	.	+	.	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	intron	20620172	20620252	.	+	.	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	CDS	20620253	20620307	0.55	+	1	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	exon	20620253	20620307	.	+	.	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
Phchi.S2	AUGUSTUS	stop_codon	20620308	20620310	.	+	0	transcript_id "Phchi.S2G052300.t1"; gene_id "Phchi.S2G052300"
# This transcript jg3903.t2 is derived from g1072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3903.t3 is derived from g1072.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3904.t1 is derived from g1073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6322314	6323301	.	+	.	Phchi.S1G106300
Phchi.S1	AUGUSTUS	transcript	6322314	6323301	.	+	.	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	start_codon	6322314	6322316	.	+	0	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	CDS	6322314	6322443	1	+	0	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	exon	6322314	6322443	.	+	.	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	intron	6322444	6322534	.	+	.	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	CDS	6322535	6323301	1	+	2	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	exon	6322535	6323301	.	+	.	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
Phchi.S1	AUGUSTUS	stop_codon	6323302	6323304	.	+	0	transcript_id "Phchi.S1G106300.t1"; gene_id "Phchi.S1G106300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9512.t1 is derived from g6688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42157841	42158945	.	+	.	Phchi.S1G667100
Phchi.S1	AUGUSTUS	transcript	42157841	42158945	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	start_codon	42157841	42157843	.	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42157841	42157906	0.7	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42157841	42157906	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	intron	42157907	42158051	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42158052	42158129	1	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42158052	42158129	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	intron	42158130	42158222	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42158223	42158313	1	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42158223	42158313	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	intron	42158314	42158392	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42158393	42158446	1	+	2	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42158393	42158446	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	intron	42158447	42158537	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42158538	42158578	1	+	2	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42158538	42158578	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	intron	42158579	42158704	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42158705	42158764	1	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42158705	42158764	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	intron	42158765	42158879	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	CDS	42158880	42158945	1	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	exon	42158880	42158945	.	+	.	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
Phchi.S1	AUGUSTUS	stop_codon	42158946	42158948	.	+	0	transcript_id "Phchi.S1G667100.t1"; gene_id "Phchi.S1G667100"
# This transcript jg5669.t2 is derived from g2839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5670.t1 is derived from g2840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18211333	18213501	.	-	.	Phchi.S1G282900
Phchi.S1	AUGUSTUS	transcript	18211333	18213501	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	stop_codon	18211330	18211332	.	-	0	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18211333	18211473	1	-	0	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18211333	18211473	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	intron	18211474	18211556	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18211557	18211648	1	-	2	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18211557	18211648	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	intron	18211649	18211746	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18211747	18212740	0.88	-	0	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18211747	18212740	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	intron	18212741	18212822	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18212823	18212925	0.99	-	1	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18212823	18212925	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	intron	18212926	18213023	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18213024	18213140	0.75	-	1	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18213024	18213140	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	intron	18213141	18213219	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18213220	18213302	0.65	-	0	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18213220	18213302	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	intron	18213303	18213390	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	CDS	18213391	18213501	0.52	-	0	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	exon	18213391	18213501	.	-	.	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
Phchi.S1	AUGUSTUS	start_codon	18213499	18213501	.	-	0	transcript_id "Phchi.S1G282900.t1"; gene_id "Phchi.S1G282900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15158.t1 is derived from g13626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17312518	17314910	.	+	.	Phchi.S3G247700
Phchi.S3	AUGUSTUS	transcript	17312518	17314910	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	start_codon	17312518	17312520	.	+	0	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	CDS	17312518	17312565	0.59	+	0	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	exon	17312518	17312565	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	intron	17312566	17312743	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	CDS	17312744	17312797	0.9	+	0	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	exon	17312744	17312797	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	intron	17312798	17312955	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	CDS	17312956	17314554	0.87	+	0	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	exon	17312956	17314554	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	intron	17314555	17314775	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	CDS	17314776	17314910	1	+	0	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	exon	17314776	17314910	.	+	.	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
Phchi.S3	AUGUSTUS	stop_codon	17314911	17314913	.	+	0	transcript_id "Phchi.S3G247700.t1"; gene_id "Phchi.S3G247700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12663.t1 is derived from g9770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C309	AUGUSTUS	gene	2053	2556	.	+	.	Phchi.C309G000100
Phchi.C309	AUGUSTUS	transcript	2053	2556	.	+	.	transcript_id "Phchi.C309G000100.t1"; gene_id "Phchi.C309G000100"
Phchi.C309	AUGUSTUS	start_codon	2053	2055	.	+	0	transcript_id "Phchi.C309G000100.t1"; gene_id "Phchi.C309G000100"
Phchi.C309	AUGUSTUS	CDS	2053	2556	0.97	+	0	transcript_id "Phchi.C309G000100.t1"; gene_id "Phchi.C309G000100"
Phchi.C309	AUGUSTUS	exon	2053	2556	.	+	.	transcript_id "Phchi.C309G000100.t1"; gene_id "Phchi.C309G000100"
Phchi.C309	AUGUSTUS	stop_codon	2557	2559	.	+	0	transcript_id "Phchi.C309G000100.t1"; gene_id "Phchi.C309G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7814.t1 is derived from g4988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31335094	31338061	.	+	.	Phchi.S1G497300
Phchi.S1	AUGUSTUS	transcript	31335094	31338061	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	start_codon	31335094	31335096	.	+	0	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31335094	31335175	0.99	+	0	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31335094	31335175	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31335176	31335301	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31335302	31335440	0.99	+	2	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31335302	31335440	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31335441	31335556	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31335557	31335628	0.99	+	1	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31335557	31335628	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31335629	31335734	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31335735	31335806	1	+	1	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31335735	31335806	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31335807	31335962	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31335963	31336034	0.98	+	1	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31335963	31336034	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31336035	31336147	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31336148	31336219	0.97	+	1	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31336148	31336219	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31336220	31336303	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31336304	31336413	1	+	1	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31336304	31336413	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31336414	31336551	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31336552	31336680	1	+	2	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31336552	31336680	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31336681	31336823	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31336824	31337156	0.98	+	2	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31336824	31337156	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31337157	31337256	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31337257	31337511	0.96	+	2	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31337257	31337511	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31337512	31337618	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31337619	31337752	0.98	+	2	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31337619	31337752	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	intron	31337753	31337845	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	CDS	31337846	31338061	1	+	0	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	exon	31337846	31338061	.	+	.	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
Phchi.S1	AUGUSTUS	stop_codon	31338062	31338064	.	+	0	transcript_id "Phchi.S1G497300.t1"; gene_id "Phchi.S1G497300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14320.t1 is derived from g12787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12081864	12083504	.	-	.	Phchi.S3G163900
Phchi.S3	AUGUSTUS	transcript	12081864	12083504	.	-	.	transcript_id "Phchi.S3G163900.t1"; gene_id "Phchi.S3G163900"
Phchi.S3	AUGUSTUS	stop_codon	12081861	12081863	.	-	0	transcript_id "Phchi.S3G163900.t1"; gene_id "Phchi.S3G163900"
Phchi.S3	AUGUSTUS	CDS	12081864	12083504	0.39	-	0	transcript_id "Phchi.S3G163900.t1"; gene_id "Phchi.S3G163900"
Phchi.S3	AUGUSTUS	exon	12081864	12083504	.	-	.	transcript_id "Phchi.S3G163900.t1"; gene_id "Phchi.S3G163900"
Phchi.S3	AUGUSTUS	start_codon	12083502	12083504	.	-	0	transcript_id "Phchi.S3G163900.t1"; gene_id "Phchi.S3G163900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4648.t1 is derived from g1818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11628476	11630486	.	-	.	Phchi.S1G180700
Phchi.S1	AUGUSTUS	transcript	11628476	11630486	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	stop_codon	11628473	11628475	.	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11628476	11628547	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11628476	11628547	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11628548	11628674	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11628675	11628765	1	-	1	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11628675	11628765	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11628766	11628872	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11628873	11628919	0.96	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11628873	11628919	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11628920	11628999	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11629000	11629068	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11629000	11629068	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11629069	11629170	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11629171	11629239	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11629171	11629239	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11629240	11629361	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11629362	11629439	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11629362	11629439	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11629440	11629524	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11629525	11629607	0.99	-	2	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11629525	11629607	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11629608	11629708	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11629709	11629788	0.99	-	1	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11629709	11629788	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11629789	11629861	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11629862	11629917	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11629862	11629917	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11629918	11630016	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11630017	11630079	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11630017	11630079	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11630080	11630176	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11630177	11630289	1	-	2	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11630177	11630289	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	intron	11630290	11630368	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	CDS	11630369	11630486	1	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	exon	11630369	11630486	.	-	.	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
Phchi.S1	AUGUSTUS	start_codon	11630484	11630486	.	-	0	transcript_id "Phchi.S1G180700.t1"; gene_id "Phchi.S1G180700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7517.t1 is derived from g4691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29802665	29804227	.	+	.	Phchi.S1G467600
Phchi.S1	AUGUSTUS	transcript	29802665	29804227	.	+	.	transcript_id "Phchi.S1G467600.t1"; gene_id "Phchi.S1G467600"
Phchi.S1	AUGUSTUS	start_codon	29802665	29802667	.	+	0	transcript_id "Phchi.S1G467600.t1"; gene_id "Phchi.S1G467600"
Phchi.S1	AUGUSTUS	CDS	29802665	29804227	0.88	+	0	transcript_id "Phchi.S1G467600.t1"; gene_id "Phchi.S1G467600"
Phchi.S1	AUGUSTUS	exon	29802665	29804227	.	+	.	transcript_id "Phchi.S1G467600.t1"; gene_id "Phchi.S1G467600"
Phchi.S1	AUGUSTUS	stop_codon	29804228	29804230	.	+	0	transcript_id "Phchi.S1G467600.t1"; gene_id "Phchi.S1G467600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10800.t1 is derived from g14850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2169057	2170603	.	+	.	Phchi.S4G038200
Phchi.S4	AUGUSTUS	transcript	2169057	2170603	.	+	.	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	start_codon	2169057	2169059	.	+	0	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	CDS	2169057	2169357	0.59	+	0	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	exon	2169057	2169357	.	+	.	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	intron	2169358	2169428	.	+	.	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	CDS	2169429	2170603	0.79	+	2	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	exon	2169429	2170603	.	+	.	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
Phchi.S4	AUGUSTUS	stop_codon	2170604	2170606	.	+	0	transcript_id "Phchi.S4G038200.t1"; gene_id "Phchi.S4G038200"
# This transcript jg6263.t2 is derived from g3435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6264.t1 is derived from g3436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21927815	21928536	.	-	.	Phchi.S1G342300
Phchi.S1	AUGUSTUS	transcript	21927815	21928536	.	-	.	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	stop_codon	21927812	21927814	.	-	0	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	CDS	21927815	21927887	1	-	1	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	exon	21927815	21927887	.	-	.	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	intron	21927888	21928213	.	-	.	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	CDS	21928214	21928536	0.28	-	0	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	exon	21928214	21928536	.	-	.	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
Phchi.S1	AUGUSTUS	start_codon	21928534	21928536	.	-	0	transcript_id "Phchi.S1G342300.t1"; gene_id "Phchi.S1G342300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2823.t1 is derived from g9743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9042096	9048916	.	+	.	Phchi.S5G143200
Phchi.S5	AUGUSTUS	transcript	9042096	9048916	.	+	.	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	start_codon	9042096	9042098	.	+	0	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	CDS	9042096	9042333	0.65	+	0	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	exon	9042096	9042333	.	+	.	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	intron	9042334	9042548	.	+	.	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	CDS	9042549	9042744	0.05	+	2	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	exon	9042549	9042744	.	+	.	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	intron	9042745	9047034	.	+	.	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	CDS	9047035	9048916	0.01	+	1	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	exon	9047035	9048916	.	+	.	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
Phchi.S5	AUGUSTUS	stop_codon	9048917	9048919	.	+	0	transcript_id "Phchi.S5G143200.t1"; gene_id "Phchi.S5G143200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2170.t1 is derived from g9090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5153803	5157144	.	+	.	Phchi.S5G077900
Phchi.S5	AUGUSTUS	transcript	5153803	5157144	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	start_codon	5153803	5153805	.	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5153803	5154377	0.9	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5153803	5154377	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5154378	5154484	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5154485	5154575	1	+	1	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5154485	5154575	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5154576	5154705	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5154706	5154909	0.95	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5154706	5154909	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5154910	5154984	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5154985	5155179	1	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5154985	5155179	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5155180	5155264	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5155265	5155320	1	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5155265	5155320	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5155321	5155460	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5155461	5155587	1	+	1	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5155461	5155587	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5155588	5155671	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5155672	5155905	0.62	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5155672	5155905	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5155906	5156046	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5156047	5156232	1	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5156047	5156232	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5156233	5156314	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5156315	5156626	1	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5156315	5156626	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5156627	5156725	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5156726	5156787	1	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5156726	5156787	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5156788	5156858	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5156859	5156927	1	+	1	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5156859	5156927	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	intron	5156928	5157011	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	CDS	5157012	5157144	0.55	+	1	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	exon	5157012	5157144	.	+	.	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
Phchi.S5	AUGUSTUS	stop_codon	5157145	5157147	.	+	0	transcript_id "Phchi.S5G077900.t1"; gene_id "Phchi.S5G077900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8427.t1 is derived from g5602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35890438	35891830	.	-	.	Phchi.S1G558600
Phchi.S1	AUGUSTUS	transcript	35890438	35891830	.	-	.	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	stop_codon	35890435	35890437	.	-	0	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	CDS	35890438	35890505	0.97	-	2	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	exon	35890438	35890505	.	-	.	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	intron	35890506	35890605	.	-	.	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	CDS	35890606	35891830	0.99	-	0	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	exon	35890606	35891830	.	-	.	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
Phchi.S1	AUGUSTUS	start_codon	35891828	35891830	.	-	0	transcript_id "Phchi.S1G558600.t1"; gene_id "Phchi.S1G558600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6239.t1 is derived from g3411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21814406	21815254	.	+	.	Phchi.S1G339800
Phchi.S1	AUGUSTUS	transcript	21814406	21815254	.	+	.	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	start_codon	21814406	21814408	.	+	0	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	CDS	21814406	21814635	0.72	+	0	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	exon	21814406	21814635	.	+	.	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	intron	21814636	21814791	.	+	.	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	CDS	21814792	21815254	0.84	+	1	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	exon	21814792	21815254	.	+	.	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
Phchi.S1	AUGUSTUS	stop_codon	21815255	21815257	.	+	0	transcript_id "Phchi.S1G339800.t1"; gene_id "Phchi.S1G339800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg433.t1 is derived from g10215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3062246	3063837	.	-	.	Phchi.S6G039200
Phchi.S6	AUGUSTUS	transcript	3062919	3063837	.	-	.	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	stop_codon	3062916	3062918	.	-	0	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3062919	3062944	0.77	-	2	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3062919	3062944	.	-	.	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3062945	3063148	.	-	.	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3063149	3063192	1	-	1	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3063149	3063192	.	-	.	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3063193	3063424	.	-	.	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3063425	3063837	1	-	0	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3063425	3063837	.	-	.	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	start_codon	3063835	3063837	.	-	0	transcript_id "Phchi.S6G039200.t1"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	transcript	3062246	3063837	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	stop_codon	3062243	3062245	.	-	0	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3062246	3062315	0.89	-	1	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3062246	3062315	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3062316	3062467	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3062468	3062673	0.93	-	0	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3062468	3062673	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3062674	3062764	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3062765	3062810	0.61	-	1	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3062765	3062810	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3062811	3062912	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3062913	3062944	0.52	-	0	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3062913	3062944	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3062945	3063148	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3063149	3063263	0.99	-	1	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3063149	3063263	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	intron	3063264	3063424	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	CDS	3063425	3063837	0.99	-	0	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	exon	3063425	3063837	.	-	.	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
Phchi.S6	AUGUSTUS	start_codon	3063835	3063837	.	-	0	transcript_id "Phchi.S6G039200.t2"; gene_id "Phchi.S6G039200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1936.t1 is derived from g8856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3904306	3909349	.	+	.	Phchi.S5G054500
Phchi.S5	AUGUSTUS	transcript	3904306	3909349	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	start_codon	3904306	3904308	.	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3904306	3904395	0.66	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3904306	3904395	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3904396	3904495	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3904496	3904608	1	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3904496	3904608	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3904609	3904756	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3904757	3904853	1	+	1	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3904757	3904853	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3904854	3904987	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3904988	3905112	1	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3904988	3905112	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3905113	3905288	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3905289	3905766	1	+	1	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3905289	3905766	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3905767	3905846	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3905847	3906032	1	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3905847	3906032	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3906033	3906123	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3906124	3906417	0.99	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3906124	3906417	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3906418	3906523	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3906524	3906676	1	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3906524	3906676	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3906677	3906760	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3906761	3906915	0.99	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3906761	3906915	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3906916	3907020	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3907021	3907126	0.99	+	1	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3907021	3907126	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3907127	3907221	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3907222	3908235	0.9	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3907222	3908235	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3908236	3908344	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3908345	3908447	1	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3908345	3908447	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3908448	3908545	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3908546	3909010	1	+	2	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3908546	3909010	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	intron	3909011	3909167	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	CDS	3909168	3909349	0.96	+	2	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	exon	3909168	3909349	.	+	.	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
Phchi.S5	AUGUSTUS	stop_codon	3909350	3909352	.	+	0	transcript_id "Phchi.S5G054500.t1"; gene_id "Phchi.S5G054500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15331.t1 is derived from g13799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18429308	18430724	.	+	.	Phchi.S3G265000
Phchi.S3	AUGUSTUS	transcript	18429308	18430724	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	start_codon	18429308	18429310	.	+	0	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	CDS	18429308	18429461	0.97	+	0	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	exon	18429308	18429461	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	intron	18429462	18429576	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	CDS	18429577	18429704	0.64	+	2	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	exon	18429577	18429704	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	intron	18429705	18429812	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	CDS	18429813	18430046	0.96	+	0	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	exon	18429813	18430046	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	intron	18430047	18430156	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	CDS	18430157	18430421	0.7	+	0	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	exon	18430157	18430421	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	intron	18430422	18430524	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	CDS	18430525	18430724	0.7	+	2	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	exon	18430525	18430724	.	+	.	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
Phchi.S3	AUGUSTUS	stop_codon	18430725	18430727	.	+	0	transcript_id "Phchi.S3G265000.t1"; gene_id "Phchi.S3G265000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11616.t1 is derived from g15667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7335829	7338595	.	+	.	Phchi.S4G119800
Phchi.S4	AUGUSTUS	transcript	7335829	7338595	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	start_codon	7335829	7335831	.	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7335829	7336088	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7335829	7336088	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336089	7336275	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336276	7336363	1	+	1	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336276	7336363	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336364	7336446	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336447	7336488	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336447	7336488	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336489	7336566	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336567	7336656	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336567	7336656	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336657	7336805	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336806	7336928	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336806	7336928	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336929	7337084	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337085	7337153	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337085	7337153	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337154	7337229	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337230	7337342	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337230	7337342	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337343	7337435	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337436	7337457	1	+	1	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337436	7337457	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337458	7337572	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337573	7337638	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337573	7337638	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337639	7337727	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337728	7337784	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337728	7337784	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337785	7337882	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337883	7337929	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337883	7337929	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337930	7338024	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7338025	7338106	1	+	1	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7338025	7338106	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7338107	7338196	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7338197	7338286	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7338197	7338286	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7338287	7338385	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7338386	7338595	1	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7338386	7338595	.	+	.	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	stop_codon	7338596	7338598	.	+	0	transcript_id "Phchi.S4G119800.t1"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	transcript	7335829	7338595	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	start_codon	7335829	7335831	.	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7335829	7336088	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7335829	7336088	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336089	7336275	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336276	7336363	1	+	1	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336276	7336363	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336364	7336446	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336447	7336488	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336447	7336488	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336489	7336566	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336567	7336656	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336567	7336656	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336657	7336805	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7336806	7336928	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7336806	7336928	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7336929	7337084	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337085	7337153	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337085	7337153	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337154	7337229	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337230	7337338	0.97	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337230	7337338	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337339	7337435	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337436	7337443	0.97	+	2	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337436	7337443	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337444	7337572	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337573	7337638	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337573	7337638	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337639	7337727	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337728	7337784	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337728	7337784	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337785	7337882	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7337883	7337929	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7337883	7337929	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7337930	7338024	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7338025	7338106	1	+	1	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7338025	7338106	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7338107	7338196	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7338197	7338286	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7338197	7338286	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	intron	7338287	7338385	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	CDS	7338386	7338595	1	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	exon	7338386	7338595	.	+	.	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
Phchi.S4	AUGUSTUS	stop_codon	7338596	7338598	.	+	0	transcript_id "Phchi.S4G119800.t2"; gene_id "Phchi.S4G119800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11225.t1 is derived from g15275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4882508	4883068	.	-	.	Phchi.S4G080700
Phchi.S4	AUGUSTUS	transcript	4882508	4883068	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	stop_codon	4882505	4882507	.	-	0	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	CDS	4882508	4882547	1	-	1	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	exon	4882508	4882547	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	intron	4882548	4882653	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	CDS	4882654	4882721	1	-	0	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	exon	4882654	4882721	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	intron	4882722	4882811	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	CDS	4882812	4882863	0.76	-	1	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	exon	4882812	4882863	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	intron	4882864	4882985	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	CDS	4882986	4883068	0.76	-	0	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	exon	4882986	4883068	.	-	.	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
Phchi.S4	AUGUSTUS	start_codon	4883066	4883068	.	-	0	transcript_id "Phchi.S4G080700.t1"; gene_id "Phchi.S4G080700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9565.t1 is derived from g6741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42687494	42688243	.	-	.	Phchi.S1G672400
Phchi.S1	AUGUSTUS	transcript	42687494	42688243	.	-	.	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	stop_codon	42687491	42687493	.	-	0	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	CDS	42687494	42687646	1	-	0	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	exon	42687494	42687646	.	-	.	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	intron	42687647	42687728	.	-	.	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	CDS	42687729	42687847	0.79	-	2	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	exon	42687729	42687847	.	-	.	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	intron	42687848	42687927	.	-	.	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	CDS	42687928	42688243	0.97	-	0	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	exon	42687928	42688243	.	-	.	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
Phchi.S1	AUGUSTUS	start_codon	42688241	42688243	.	-	0	transcript_id "Phchi.S1G672400.t1"; gene_id "Phchi.S1G672400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9830.t1 is derived from g7006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43994599	43996378	.	-	.	Phchi.S1G698900
Phchi.S1	AUGUSTUS	transcript	43994599	43996378	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	stop_codon	43994596	43994598	.	-	0	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	CDS	43994599	43995072	0.97	-	0	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	exon	43994599	43995072	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	intron	43995073	43995164	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	CDS	43995165	43995446	0.93	-	0	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	exon	43995165	43995446	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	intron	43995447	43995524	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	CDS	43995525	43995836	1	-	0	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	exon	43995525	43995836	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	intron	43995837	43995922	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	CDS	43995923	43996378	0.61	-	0	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	exon	43995923	43996378	.	-	.	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
Phchi.S1	AUGUSTUS	start_codon	43996376	43996378	.	-	0	transcript_id "Phchi.S1G698900.t1"; gene_id "Phchi.S1G698900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6166.t1 is derived from g3337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21267629	21269053	.	-	.	Phchi.S1G332500
Phchi.S1	AUGUSTUS	transcript	21267629	21269053	.	-	.	transcript_id "Phchi.S1G332500.t1"; gene_id "Phchi.S1G332500"
Phchi.S1	AUGUSTUS	stop_codon	21267626	21267628	.	-	0	transcript_id "Phchi.S1G332500.t1"; gene_id "Phchi.S1G332500"
Phchi.S1	AUGUSTUS	CDS	21267629	21269053	0.98	-	0	transcript_id "Phchi.S1G332500.t1"; gene_id "Phchi.S1G332500"
Phchi.S1	AUGUSTUS	exon	21267629	21269053	.	-	.	transcript_id "Phchi.S1G332500.t1"; gene_id "Phchi.S1G332500"
Phchi.S1	AUGUSTUS	start_codon	21269051	21269053	.	-	0	transcript_id "Phchi.S1G332500.t1"; gene_id "Phchi.S1G332500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6081.t1 is derived from g3252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20861143	20862360	.	-	.	Phchi.S1G324000
Phchi.S1	AUGUSTUS	transcript	20861143	20862360	.	-	.	transcript_id "Phchi.S1G324000.t1"; gene_id "Phchi.S1G324000"
Phchi.S1	AUGUSTUS	stop_codon	20861140	20861142	.	-	0	transcript_id "Phchi.S1G324000.t1"; gene_id "Phchi.S1G324000"
Phchi.S1	AUGUSTUS	CDS	20861143	20862360	0.9	-	0	transcript_id "Phchi.S1G324000.t1"; gene_id "Phchi.S1G324000"
Phchi.S1	AUGUSTUS	exon	20861143	20862360	.	-	.	transcript_id "Phchi.S1G324000.t1"; gene_id "Phchi.S1G324000"
Phchi.S1	AUGUSTUS	start_codon	20862358	20862360	.	-	0	transcript_id "Phchi.S1G324000.t1"; gene_id "Phchi.S1G324000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5081.t1 is derived from g2251.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14591934	14594461	.	+	.	Phchi.S1G224000
Phchi.S1	AUGUSTUS	transcript	14591934	14594461	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	start_codon	14591934	14591936	.	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14591934	14592011	0.96	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14591934	14592011	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592012	14592161	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592162	14592236	0.91	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592162	14592236	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592237	14592357	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592358	14592453	0.91	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592358	14592453	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592454	14592540	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592541	14592610	1	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592541	14592610	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592611	14592725	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592726	14592843	1	+	2	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592726	14592843	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592844	14592945	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592946	14593102	1	+	1	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592946	14593102	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593103	14593184	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593185	14593265	1	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593185	14593265	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593266	14593346	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593347	14593454	1	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593347	14593454	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593455	14593596	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593597	14593665	1	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593597	14593665	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593666	14593840	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593841	14593955	1	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593841	14593955	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593956	14594168	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14594169	14594461	1	+	2	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14594169	14594461	.	+	.	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	stop_codon	14594462	14594464	.	+	0	transcript_id "Phchi.S1G224000.t1"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	transcript	14591989	14594461	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	start_codon	14591989	14591991	.	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14591989	14592011	0.58	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14591989	14592011	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592012	14592161	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592162	14592236	1	+	1	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592162	14592236	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592237	14592314	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592315	14592453	1	+	1	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592315	14592453	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592454	14592540	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592541	14592610	1	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592541	14592610	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592611	14592725	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592726	14592843	1	+	2	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592726	14592843	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14592844	14592945	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14592946	14593102	1	+	1	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14592946	14593102	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593103	14593184	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593185	14593265	1	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593185	14593265	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593266	14593346	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593347	14593454	1	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593347	14593454	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593455	14593596	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593597	14593665	1	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593597	14593665	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593666	14593840	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14593841	14593955	1	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14593841	14593955	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	intron	14593956	14594168	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	CDS	14594169	14594461	1	+	2	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	exon	14594169	14594461	.	+	.	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
Phchi.S1	AUGUSTUS	stop_codon	14594462	14594464	.	+	0	transcript_id "Phchi.S1G224000.t2"; gene_id "Phchi.S1G224000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14412.t1 is derived from g12880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12696175	12698033	.	+	.	Phchi.S3G173100
Phchi.S3	AUGUSTUS	transcript	12696175	12698033	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	start_codon	12696175	12696177	.	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12696175	12696330	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12696175	12696330	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12696331	12696522	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12696523	12696648	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12696523	12696648	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12696649	12696867	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12696868	12697036	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12696868	12697036	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12697037	12697131	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12697132	12697214	1	+	2	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12697132	12697214	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12697215	12697291	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12697292	12697360	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12697292	12697360	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12697361	12697560	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12697561	12697605	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12697561	12697605	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12697606	12697694	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12697695	12697757	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12697695	12697757	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12697758	12697866	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12697867	12697943	1	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12697867	12697943	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	intron	12697944	12698023	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	CDS	12698024	12698033	0.49	+	1	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	exon	12698024	12698033	.	+	.	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
Phchi.S3	AUGUSTUS	stop_codon	12698034	12698036	.	+	0	transcript_id "Phchi.S3G173100.t1"; gene_id "Phchi.S3G173100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10782.t1 is derived from g14832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2085477	2088293	.	+	.	Phchi.S4G036400
Phchi.S4	AUGUSTUS	transcript	2085477	2088293	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	start_codon	2085477	2085479	.	+	0	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2085477	2085615	0.84	+	0	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2085477	2085615	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	intron	2085616	2085693	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2085694	2085740	1	+	2	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2085694	2085740	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	intron	2085741	2085829	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2085830	2085957	1	+	0	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2085830	2085957	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	intron	2085958	2086054	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2086055	2086070	0.73	+	1	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2086055	2086070	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	intron	2086071	2086190	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2086191	2086554	0.53	+	0	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2086191	2086554	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	intron	2086555	2086815	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2086816	2087046	0.93	+	2	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2086816	2087046	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	intron	2087047	2087259	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	CDS	2087260	2088293	0.91	+	2	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	exon	2087260	2088293	.	+	.	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
Phchi.S4	AUGUSTUS	stop_codon	2088294	2088296	.	+	0	transcript_id "Phchi.S4G036400.t1"; gene_id "Phchi.S4G036400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11131.t1 is derived from g15181.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4312762	4317620	.	+	.	Phchi.S4G071300
Phchi.S4	AUGUSTUS	transcript	4312762	4317620	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	start_codon	4312762	4312764	.	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4312762	4313234	0.99	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4312762	4313234	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313235	4313320	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4313321	4313456	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4313321	4313456	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313457	4313621	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4313622	4313670	0.99	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4313622	4313670	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313671	4313828	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4313829	4313910	1	+	2	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4313829	4313910	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313911	4314000	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314001	4314082	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314001	4314082	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314083	4314186	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314187	4314484	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314187	4314484	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314485	4314629	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314630	4314688	1	+	2	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314630	4314688	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314689	4314814	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314815	4314904	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314815	4314904	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314905	4315063	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315064	4315155	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315064	4315155	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315156	4315294	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315295	4315393	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315295	4315393	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315394	4315484	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315485	4315562	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315485	4315562	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315563	4315673	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315674	4315758	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315674	4315758	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315759	4315848	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315849	4315907	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315849	4315907	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315908	4316001	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316002	4316071	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316002	4316071	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316072	4316154	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316155	4316246	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316155	4316246	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316247	4316329	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316330	4316392	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316330	4316392	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316393	4316475	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316476	4316542	1	+	1	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316476	4316542	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316543	4316684	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316685	4316835	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316685	4316835	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316836	4316924	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316925	4316998	1	+	2	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316925	4316998	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316999	4317085	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4317086	4317205	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4317086	4317205	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4317206	4317290	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4317291	4317443	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4317291	4317443	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4317444	4317527	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4317528	4317620	1	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4317528	4317620	.	+	.	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	stop_codon	4317621	4317623	.	+	0	transcript_id "Phchi.S4G071300.t1"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	transcript	4312762	4317620	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	start_codon	4312762	4312764	.	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4312762	4313234	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4312762	4313234	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313235	4313320	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4313321	4313456	0.98	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4313321	4313456	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313457	4313581	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4313582	4313910	0.95	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4313582	4313910	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4313911	4314000	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314001	4314082	0.99	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314001	4314082	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314083	4314186	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314187	4314484	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314187	4314484	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314485	4314629	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314630	4314688	1	+	2	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314630	4314688	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314689	4314814	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4314815	4314904	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4314815	4314904	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4314905	4315063	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315064	4315155	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315064	4315155	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315156	4315294	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315295	4315393	1	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315295	4315393	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315394	4315484	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315485	4315562	1	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315485	4315562	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315563	4315673	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315674	4315758	1	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315674	4315758	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315759	4315848	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4315849	4315907	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4315849	4315907	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4315908	4316001	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316002	4316071	1	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316002	4316071	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316072	4316154	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316155	4316246	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316155	4316246	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316247	4316329	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316330	4316392	1	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316330	4316392	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316393	4316475	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316476	4316542	1	+	1	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316476	4316542	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316543	4316684	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316685	4316835	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316685	4316835	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316836	4316924	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4316925	4316998	1	+	2	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4316925	4316998	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4316999	4317085	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4317086	4317205	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4317086	4317205	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4317206	4317290	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4317291	4317443	1	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4317291	4317443	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	intron	4317444	4317527	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	CDS	4317528	4317620	0.99	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	exon	4317528	4317620	.	+	.	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
Phchi.S4	AUGUSTUS	stop_codon	4317621	4317623	.	+	0	transcript_id "Phchi.S4G071300.t2"; gene_id "Phchi.S4G071300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6386.t1 is derived from g3558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22668672	22669929	.	-	.	Phchi.S1G354500
Phchi.S1	AUGUSTUS	transcript	22668672	22669929	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	stop_codon	22668669	22668671	.	-	0	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22668672	22668865	1	-	2	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22668672	22668865	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	intron	22668866	22669054	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22669055	22669104	1	-	1	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22669055	22669104	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	intron	22669105	22669156	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22669157	22669181	1	-	2	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22669157	22669181	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	intron	22669182	22669255	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22669256	22669396	1	-	2	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22669256	22669396	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	intron	22669397	22669491	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22669492	22669593	1	-	2	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22669492	22669593	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	intron	22669594	22669686	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22669687	22669804	1	-	0	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22669687	22669804	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	intron	22669805	22669902	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	CDS	22669903	22669929	0.48	-	0	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	exon	22669903	22669929	.	-	.	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
Phchi.S1	AUGUSTUS	start_codon	22669927	22669929	.	-	0	transcript_id "Phchi.S1G354500.t1"; gene_id "Phchi.S1G354500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12275.t1 is derived from g7951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7932854	7933443	.	-	.	Phchi.S2G035500
Phchi.S2	AUGUSTUS	transcript	7932854	7933443	.	-	.	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	stop_codon	7932851	7932853	.	-	0	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	CDS	7932854	7933244	0.68	-	1	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	exon	7932854	7933244	.	-	.	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	intron	7933245	7933333	.	-	.	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	CDS	7933334	7933443	0.58	-	0	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	exon	7933334	7933443	.	-	.	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
Phchi.S2	AUGUSTUS	start_codon	7933441	7933443	.	-	0	transcript_id "Phchi.S2G035500.t1"; gene_id "Phchi.S2G035500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11418.t1 is derived from g15468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6255270	6256019	.	+	.	Phchi.S4G100000
Phchi.S4	AUGUSTUS	transcript	6255270	6256019	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	start_codon	6255270	6255272	.	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	CDS	6255270	6255281	1	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	exon	6255270	6255281	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	intron	6255282	6255379	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	CDS	6255380	6255424	1	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	exon	6255380	6255424	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	intron	6255425	6255500	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	CDS	6255501	6255563	1	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	exon	6255501	6255563	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	intron	6255564	6255676	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	CDS	6255677	6255772	1	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	exon	6255677	6255772	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	intron	6255773	6255899	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	CDS	6255900	6256019	1	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	exon	6255900	6256019	.	+	.	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
Phchi.S4	AUGUSTUS	stop_codon	6256020	6256022	.	+	0	transcript_id "Phchi.S4G100000.t1"; gene_id "Phchi.S4G100000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6412.t1 is derived from g3584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22844541	22845893	.	+	.	Phchi.S1G357100
Phchi.S1	AUGUSTUS	transcript	22844541	22845893	.	+	.	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	start_codon	22844541	22844543	.	+	0	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	CDS	22844541	22844656	0.57	+	0	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	exon	22844541	22844656	.	+	.	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	intron	22844657	22844935	.	+	.	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	CDS	22844936	22845893	0.61	+	1	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	exon	22844936	22845893	.	+	.	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
Phchi.S1	AUGUSTUS	stop_codon	22845894	22845896	.	+	0	transcript_id "Phchi.S1G357100.t1"; gene_id "Phchi.S1G357100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11590.t1 is derived from g15641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7245701	7246725	.	+	.	Phchi.S4G117200
Phchi.S4	AUGUSTUS	transcript	7245701	7246725	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	start_codon	7245701	7245703	.	+	0	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	CDS	7245701	7245797	0.4	+	0	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	exon	7245701	7245797	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	intron	7245798	7245865	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	CDS	7245866	7245930	0.51	+	2	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	exon	7245866	7245930	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	intron	7245931	7246017	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	CDS	7246018	7246160	1	+	0	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	exon	7246018	7246160	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	intron	7246161	7246238	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	CDS	7246239	7246471	1	+	1	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	exon	7246239	7246471	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	intron	7246472	7246549	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	CDS	7246550	7246725	0.99	+	2	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	exon	7246550	7246725	.	+	.	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
Phchi.S4	AUGUSTUS	stop_codon	7246726	7246728	.	+	0	transcript_id "Phchi.S4G117200.t1"; gene_id "Phchi.S4G117200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3626.t1 is derived from g795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4830944	4834191	.	+	.	Phchi.S1G078500
Phchi.S1	AUGUSTUS	transcript	4830944	4834191	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	start_codon	4830944	4830946	.	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4830944	4831220	1	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4830944	4831220	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4831221	4831344	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4831345	4831481	0.98	+	2	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4831345	4831481	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4831482	4831594	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4831595	4831740	0.98	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4831595	4831740	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4831741	4831873	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4831874	4831887	0.58	+	1	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4831874	4831887	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4831888	4832128	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4832129	4832272	0.5	+	2	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4832129	4832272	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4832273	4832709	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4832710	4832750	0.61	+	2	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4832710	4832750	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4832751	4833111	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4833112	4833227	0.47	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4833112	4833227	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4833228	4833403	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4833404	4833539	0.48	+	1	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4833404	4833539	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4833540	4833679	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4833680	4833934	1	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4833680	4833934	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	intron	4833935	4834044	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	CDS	4834045	4834191	1	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	exon	4834045	4834191	.	+	.	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
Phchi.S1	AUGUSTUS	stop_codon	4834192	4834194	.	+	0	transcript_id "Phchi.S1G078500.t1"; gene_id "Phchi.S1G078500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1641.t1 is derived from g8560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2159605	2161531	.	-	.	Phchi.S5G025000
Phchi.S5	AUGUSTUS	transcript	2159605	2161531	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	stop_codon	2159602	2159604	.	-	0	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	CDS	2159605	2159626	0.85	-	1	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	exon	2159605	2159626	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	intron	2159627	2159711	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	CDS	2159712	2159821	0.84	-	0	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	exon	2159712	2159821	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	intron	2159822	2159939	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	CDS	2159940	2160531	0.84	-	1	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	exon	2159940	2160531	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	intron	2160532	2160614	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	CDS	2160615	2160799	0.37	-	0	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	exon	2160615	2160799	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	intron	2160800	2160924	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	CDS	2160925	2160955	0.32	-	1	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	exon	2160925	2160955	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	intron	2160956	2161106	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	CDS	2161107	2161531	0.52	-	0	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	exon	2161107	2161531	.	-	.	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
Phchi.S5	AUGUSTUS	start_codon	2161529	2161531	.	-	0	transcript_id "Phchi.S5G025000.t1"; gene_id "Phchi.S5G025000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2544.t1 is derived from g9464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7256984	7258476	.	-	.	Phchi.S5G115300
Phchi.S5	AUGUSTUS	transcript	7256984	7258476	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	stop_codon	7256981	7256983	.	-	0	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7256984	7257231	0.68	-	2	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7256984	7257231	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	intron	7257232	7257481	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7257482	7257518	0.88	-	0	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7257482	7257518	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	intron	7257519	7257589	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7257590	7257611	0.58	-	1	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7257590	7257611	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	intron	7257612	7257748	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7257749	7257811	0.36	-	1	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7257749	7257811	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	intron	7257812	7257893	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7257894	7257907	0.36	-	0	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7257894	7257907	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	intron	7257908	7258209	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7258210	7258266	0.43	-	0	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7258210	7258266	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	intron	7258267	7258398	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	CDS	7258399	7258476	0.87	-	0	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	exon	7258399	7258476	.	-	.	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
Phchi.S5	AUGUSTUS	start_codon	7258474	7258476	.	-	0	transcript_id "Phchi.S5G115300.t1"; gene_id "Phchi.S5G115300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg803.t1 is derived from g10585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5679826	5681131	.	+	.	Phchi.S6G076200
Phchi.S6	AUGUSTUS	transcript	5679826	5681131	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	start_codon	5679826	5679828	.	+	0	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	CDS	5679826	5680232	0.97	+	0	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	exon	5679826	5680232	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	intron	5680233	5680328	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	CDS	5680329	5680458	1	+	1	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	exon	5680329	5680458	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	intron	5680459	5680576	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	CDS	5680577	5680945	1	+	0	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	exon	5680577	5680945	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	intron	5680946	5681041	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	CDS	5681042	5681131	0.88	+	0	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	exon	5681042	5681131	.	+	.	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
Phchi.S6	AUGUSTUS	stop_codon	5681132	5681134	.	+	0	transcript_id "Phchi.S6G076200.t1"; gene_id "Phchi.S6G076200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg835.t1 is derived from g10617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5797585	5797861	.	+	.	Phchi.S6G079400
Phchi.S6	AUGUSTUS	transcript	5797585	5797861	.	+	.	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	start_codon	5797585	5797587	.	+	0	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	CDS	5797585	5797621	0.48	+	0	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	exon	5797585	5797621	.	+	.	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	intron	5797622	5797700	.	+	.	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	CDS	5797701	5797861	0.48	+	2	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	exon	5797701	5797861	.	+	.	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
Phchi.S6	AUGUSTUS	stop_codon	5797862	5797864	.	+	0	transcript_id "Phchi.S6G079400.t1"; gene_id "Phchi.S6G079400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3102.t1 is derived from g271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1759497	1759976	.	-	.	Phchi.S1G026100
Phchi.S1	AUGUSTUS	transcript	1759497	1759976	.	-	.	transcript_id "Phchi.S1G026100.t1"; gene_id "Phchi.S1G026100"
Phchi.S1	AUGUSTUS	stop_codon	1759494	1759496	.	-	0	transcript_id "Phchi.S1G026100.t1"; gene_id "Phchi.S1G026100"
Phchi.S1	AUGUSTUS	CDS	1759497	1759976	0.95	-	0	transcript_id "Phchi.S1G026100.t1"; gene_id "Phchi.S1G026100"
Phchi.S1	AUGUSTUS	exon	1759497	1759976	.	-	.	transcript_id "Phchi.S1G026100.t1"; gene_id "Phchi.S1G026100"
Phchi.S1	AUGUSTUS	start_codon	1759974	1759976	.	-	0	transcript_id "Phchi.S1G026100.t1"; gene_id "Phchi.S1G026100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg801.t1 is derived from g10583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5674737	5675201	.	+	.	Phchi.S6G076000
Phchi.S6	AUGUSTUS	transcript	5674737	5675201	.	+	.	transcript_id "Phchi.S6G076000.t1"; gene_id "Phchi.S6G076000"
Phchi.S6	AUGUSTUS	start_codon	5674737	5674739	.	+	0	transcript_id "Phchi.S6G076000.t1"; gene_id "Phchi.S6G076000"
Phchi.S6	AUGUSTUS	CDS	5674737	5675201	0.28	+	0	transcript_id "Phchi.S6G076000.t1"; gene_id "Phchi.S6G076000"
Phchi.S6	AUGUSTUS	exon	5674737	5675201	.	+	.	transcript_id "Phchi.S6G076000.t1"; gene_id "Phchi.S6G076000"
Phchi.S6	AUGUSTUS	stop_codon	5675202	5675204	.	+	0	transcript_id "Phchi.S6G076000.t1"; gene_id "Phchi.S6G076000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4039.t1 is derived from g1208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7306371	7307423	.	-	.	Phchi.S1G119800
Phchi.S1	AUGUSTUS	transcript	7306371	7307423	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	stop_codon	7306368	7306370	.	-	0	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7306371	7306441	0.99	-	2	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7306371	7306441	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	intron	7306442	7306533	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7306534	7306591	1	-	0	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7306534	7306591	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	intron	7306592	7306673	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7306674	7306707	1	-	1	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7306674	7306707	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	intron	7306708	7306801	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7306802	7306953	0.79	-	0	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7306802	7306953	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	intron	7306954	7307103	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7307104	7307113	0.99	-	1	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7307104	7307113	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	intron	7307114	7307260	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7307261	7307325	1	-	0	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7307261	7307325	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	intron	7307326	7307420	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	CDS	7307421	7307423	0.8	-	0	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	exon	7307421	7307423	.	-	.	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
Phchi.S1	AUGUSTUS	start_codon	7307421	7307423	.	-	0	transcript_id "Phchi.S1G119800.t1"; gene_id "Phchi.S1G119800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10855.t1 is derived from g14905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2566763	2567446	.	-	.	Phchi.S4G043700
Phchi.S4	AUGUSTUS	transcript	2566763	2567446	.	-	.	transcript_id "Phchi.S4G043700.t1"; gene_id "Phchi.S4G043700"
Phchi.S4	AUGUSTUS	stop_codon	2566760	2566762	.	-	0	transcript_id "Phchi.S4G043700.t1"; gene_id "Phchi.S4G043700"
Phchi.S4	AUGUSTUS	CDS	2566763	2567446	1	-	0	transcript_id "Phchi.S4G043700.t1"; gene_id "Phchi.S4G043700"
Phchi.S4	AUGUSTUS	exon	2566763	2567446	.	-	.	transcript_id "Phchi.S4G043700.t1"; gene_id "Phchi.S4G043700"
Phchi.S4	AUGUSTUS	start_codon	2567444	2567446	.	-	0	transcript_id "Phchi.S4G043700.t1"; gene_id "Phchi.S4G043700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11663.t1 is derived from g15714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7581876	7582332	.	+	.	Phchi.S4G124500
Phchi.S4	AUGUSTUS	transcript	7581876	7582332	.	+	.	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	start_codon	7581876	7581878	.	+	0	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	CDS	7581876	7581948	0.19	+	0	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	exon	7581876	7581948	.	+	.	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	intron	7581949	7582114	.	+	.	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	CDS	7582115	7582332	0.59	+	2	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	exon	7582115	7582332	.	+	.	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
Phchi.S4	AUGUSTUS	stop_codon	7582333	7582335	.	+	0	transcript_id "Phchi.S4G124500.t1"; gene_id "Phchi.S4G124500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12039.t1 is derived from g7714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	848530	852757	.	+	.	Phchi.S2G011900
Phchi.S2	AUGUSTUS	transcript	848530	852757	.	+	.	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	start_codon	848530	848532	.	+	0	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	CDS	848530	848615	1	+	0	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	exon	848530	848615	.	+	.	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	intron	848616	852663	.	+	.	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	CDS	852664	852757	0.01	+	1	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	exon	852664	852757	.	+	.	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
Phchi.S2	AUGUSTUS	stop_codon	852758	852760	.	+	0	transcript_id "Phchi.S2G011900.t1"; gene_id "Phchi.S2G011900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2428.t1 is derived from g9348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6597940	6598482	.	+	.	Phchi.S5G103700
Phchi.S5	AUGUSTUS	transcript	6597940	6598482	.	+	.	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	start_codon	6597940	6597942	.	+	0	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	CDS	6597940	6598064	0.59	+	0	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	exon	6597940	6598064	.	+	.	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	intron	6598065	6598169	.	+	.	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	CDS	6598170	6598293	0.96	+	1	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	exon	6598170	6598293	.	+	.	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	intron	6598294	6598413	.	+	.	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	CDS	6598414	6598482	0.97	+	0	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	exon	6598414	6598482	.	+	.	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
Phchi.S5	AUGUSTUS	stop_codon	6598483	6598485	.	+	0	transcript_id "Phchi.S5G103700.t1"; gene_id "Phchi.S5G103700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7558.t1 is derived from g4732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30027023	30031235	.	+	.	Phchi.S1G471700
Phchi.S1	AUGUSTUS	transcript	30027023	30031235	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	start_codon	30027023	30027025	.	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30027023	30027157	0.93	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30027023	30027157	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30027158	30027263	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30027264	30027366	0.98	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30027264	30027366	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30027367	30027455	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30027456	30027565	1	+	2	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30027456	30027565	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30027566	30027684	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30027685	30027774	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30027685	30027774	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30027775	30027863	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30027864	30027941	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30027864	30027941	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30027942	30028057	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30028058	30028167	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30028058	30028167	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30028168	30028307	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30028308	30028383	0.99	+	1	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30028308	30028383	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30028384	30028488	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30028489	30028575	0.95	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30028489	30028575	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30028576	30028686	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30028687	30028771	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30028687	30028771	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30028772	30028890	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30028891	30028988	1	+	2	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30028891	30028988	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30028989	30029120	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30029121	30029156	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30029121	30029156	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30029157	30029242	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30029243	30029311	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30029243	30029311	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30029312	30029409	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30029410	30029478	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30029410	30029478	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30029479	30029620	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30029621	30029674	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30029621	30029674	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30029675	30029750	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30029751	30029825	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30029751	30029825	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30029826	30029925	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30029926	30030018	0.98	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30029926	30030018	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30030019	30030183	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30030184	30030239	0.58	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30030184	30030239	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30030240	30030337	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30030338	30030386	1	+	1	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30030338	30030386	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30030387	30030471	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30030472	30030558	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30030472	30030558	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30030559	30030640	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30030641	30030746	1	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30030641	30030746	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30030747	30030823	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30030824	30030911	1	+	2	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30030824	30030911	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30030912	30030982	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30030983	30031076	1	+	1	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30030983	30031076	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	intron	30031077	30031154	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	CDS	30031155	30031235	0.99	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	exon	30031155	30031235	.	+	.	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
Phchi.S1	AUGUSTUS	stop_codon	30031236	30031238	.	+	0	transcript_id "Phchi.S1G471700.t1"; gene_id "Phchi.S1G471700"
# This transcript jg14316.t2 is derived from g12783.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14317.t1 is derived from g12784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12069202	12070067	.	+	.	Phchi.S3G163600
Phchi.S3	AUGUSTUS	transcript	12069202	12070067	.	+	.	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	start_codon	12069202	12069204	.	+	0	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	CDS	12069202	12069356	0.72	+	0	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	exon	12069202	12069356	.	+	.	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	intron	12069357	12069445	.	+	.	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	CDS	12069446	12069606	0.97	+	1	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	exon	12069446	12069606	.	+	.	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	intron	12069607	12069675	.	+	.	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	CDS	12069676	12070067	1	+	2	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	exon	12069676	12070067	.	+	.	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
Phchi.S3	AUGUSTUS	stop_codon	12070068	12070070	.	+	0	transcript_id "Phchi.S3G163600.t1"; gene_id "Phchi.S3G163600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14009.t1 is derived from g12476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10290101	10291627	.	-	.	Phchi.S3G132800
Phchi.S3	AUGUSTUS	transcript	10290101	10291627	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	stop_codon	10290098	10290100	.	-	0	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	CDS	10290101	10290699	1	-	2	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	exon	10290101	10290699	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	intron	10290700	10290780	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	CDS	10290781	10290963	1	-	2	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	exon	10290781	10290963	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	intron	10290964	10291051	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	CDS	10291052	10291182	1	-	1	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	exon	10291052	10291182	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	intron	10291183	10291275	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	CDS	10291276	10291419	1	-	1	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	exon	10291276	10291419	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	intron	10291420	10291502	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	CDS	10291503	10291627	1	-	0	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	exon	10291503	10291627	.	-	.	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
Phchi.S3	AUGUSTUS	start_codon	10291625	10291627	.	-	0	transcript_id "Phchi.S3G132800.t1"; gene_id "Phchi.S3G132800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6300.t1 is derived from g3472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22165590	22166879	.	-	.	Phchi.S1G345900
Phchi.S1	AUGUSTUS	transcript	22165590	22166879	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	stop_codon	22165587	22165589	.	-	0	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	CDS	22165590	22166115	0.97	-	1	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	exon	22165590	22166115	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	intron	22166116	22166214	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	CDS	22166215	22166473	1	-	2	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	exon	22166215	22166473	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	intron	22166474	22166593	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	CDS	22166594	22166683	1	-	2	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	exon	22166594	22166683	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	intron	22166684	22166836	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	CDS	22166837	22166879	1	-	0	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	exon	22166837	22166879	.	-	.	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
Phchi.S1	AUGUSTUS	start_codon	22166877	22166879	.	-	0	transcript_id "Phchi.S1G345900.t1"; gene_id "Phchi.S1G345900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15405.t1 is derived from g13873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18830810	18839146	.	-	.	Phchi.S3G272400
Phchi.S3	AUGUSTUS	transcript	18830810	18839146	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	stop_codon	18830807	18830809	.	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18830810	18831097	0.99	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18830810	18831097	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18831098	18831188	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18831189	18831330	0.44	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18831189	18831330	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18831331	18831409	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18831410	18831441	0.41	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18831410	18831441	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18831442	18831548	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18831549	18831782	0.46	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18831549	18831782	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18831783	18831868	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18831869	18831930	1	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18831869	18831930	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18831931	18832044	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18832045	18832144	0.99	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18832045	18832144	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18832145	18832248	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18832249	18832315	0.95	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18832249	18832315	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18832316	18832417	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18832418	18832472	0.99	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18832418	18832472	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18832473	18832631	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18832632	18832718	0.98	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18832632	18832718	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18832719	18832832	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18832833	18832920	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18832833	18832920	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18832921	18833040	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18833041	18833081	1	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18833041	18833081	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18833082	18833231	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18833232	18833425	1	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18833232	18833425	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18833426	18833546	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18833547	18833656	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18833547	18833656	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18833657	18833837	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18833838	18833972	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18833838	18833972	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18833973	18834138	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18834139	18834234	0.88	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18834139	18834234	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18834235	18834348	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18834349	18834414	0.88	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18834349	18834414	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18834415	18834501	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18834502	18834552	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18834502	18834552	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18834553	18834677	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18834678	18834737	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18834678	18834737	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18834738	18835035	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18835036	18835312	0.57	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18835036	18835312	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18835313	18835442	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18835443	18835509	0.67	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18835443	18835509	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18835510	18835709	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18835710	18835815	0.99	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18835710	18835815	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18835816	18835978	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18835979	18836002	0.85	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18835979	18836002	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18836003	18836180	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18836181	18836318	0.5	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18836181	18836318	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18836319	18836431	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18836432	18836503	0.83	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18836432	18836503	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18836504	18836574	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18836575	18836623	1	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18836575	18836623	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18836624	18836713	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18836714	18836781	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18836714	18836781	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18836782	18836867	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18836868	18836936	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18836868	18836936	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18836937	18837003	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18837004	18837088	1	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18837004	18837088	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18837089	18837177	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18837178	18837254	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18837178	18837254	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18837255	18837342	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18837343	18837418	0.99	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18837343	18837418	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18837419	18837527	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18837528	18837604	1	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18837528	18837604	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18837605	18837734	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18837735	18837819	0.77	-	1	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18837735	18837819	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18837820	18837915	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18837916	18837994	1	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18837916	18837994	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18837995	18838085	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18838086	18838182	0.94	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18838086	18838182	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18838183	18838293	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18838294	18838353	0.44	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18838294	18838353	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18838354	18838439	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18838440	18838504	0.94	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18838440	18838504	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18838505	18838593	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18838594	18838702	0.55	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18838594	18838702	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18838703	18838810	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18838811	18838929	0.51	-	2	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18838811	18838929	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	intron	18838930	18839037	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	CDS	18839038	18839146	0.93	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	exon	18839038	18839146	.	-	.	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
Phchi.S3	AUGUSTUS	start_codon	18839144	18839146	.	-	0	transcript_id "Phchi.S3G272400.t1"; gene_id "Phchi.S3G272400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11109.t1 is derived from g15159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4176424	4177280	.	-	.	Phchi.S4G069100
Phchi.S4	AUGUSTUS	transcript	4176424	4177280	.	-	.	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	stop_codon	4176421	4176423	.	-	0	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	CDS	4176424	4176437	1	-	2	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	exon	4176424	4176437	.	-	.	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	intron	4176438	4176820	.	-	.	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	CDS	4176821	4177057	1	-	2	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	exon	4176821	4177057	.	-	.	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	intron	4177058	4177171	.	-	.	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	CDS	4177172	4177280	0.97	-	0	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	exon	4177172	4177280	.	-	.	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
Phchi.S4	AUGUSTUS	start_codon	4177278	4177280	.	-	0	transcript_id "Phchi.S4G069100.t1"; gene_id "Phchi.S4G069100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9897.t1 is derived from g7073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44325342	44326986	.	-	.	Phchi.S1G705600
Phchi.S1	AUGUSTUS	transcript	44325342	44326986	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	stop_codon	44325339	44325341	.	-	0	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44325342	44325427	0.96	-	2	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44325342	44325427	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	intron	44325428	44325512	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44325513	44325576	1	-	0	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44325513	44325576	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	intron	44325577	44325757	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44325758	44325857	1	-	1	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44325758	44325857	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	intron	44325858	44326083	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44326084	44326175	1	-	0	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44326084	44326175	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	intron	44326176	44326317	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44326318	44326453	1	-	1	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44326318	44326453	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	intron	44326454	44326544	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44326545	44326639	1	-	0	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44326545	44326639	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	intron	44326640	44326800	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	CDS	44326801	44326986	0.99	-	0	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	exon	44326801	44326986	.	-	.	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
Phchi.S1	AUGUSTUS	start_codon	44326984	44326986	.	-	0	transcript_id "Phchi.S1G705600.t1"; gene_id "Phchi.S1G705600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4218.t1 is derived from g1387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8983639	8984915	.	-	.	Phchi.S1G137700
Phchi.S1	AUGUSTUS	transcript	8983639	8984915	.	-	.	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	stop_codon	8983636	8983638	.	-	0	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	CDS	8983639	8984299	0.95	-	1	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	exon	8983639	8984299	.	-	.	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	intron	8984300	8984454	.	-	.	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	CDS	8984455	8984915	0.61	-	0	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	exon	8984455	8984915	.	-	.	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
Phchi.S1	AUGUSTUS	start_codon	8984913	8984915	.	-	0	transcript_id "Phchi.S1G137700.t1"; gene_id "Phchi.S1G137700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5356.t1 is derived from g2526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16449649	16452292	.	-	.	Phchi.S1G251500
Phchi.S1	AUGUSTUS	transcript	16449649	16452292	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	stop_codon	16449646	16449648	.	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16449649	16449789	1	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16449649	16449789	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16449790	16449872	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16449873	16449983	1	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16449873	16449983	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16449984	16450074	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16450075	16450189	1	-	1	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16450075	16450189	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16450190	16450292	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16450293	16450392	1	-	2	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16450293	16450392	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16450393	16450469	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16450470	16450564	0.99	-	1	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16450470	16450564	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16450565	16450668	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16450669	16450799	0.99	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16450669	16450799	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16450800	16450905	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16450906	16450986	0.99	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16450906	16450986	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16450987	16451056	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16451057	16451161	1	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16451057	16451161	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16451162	16451237	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16451238	16451312	1	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16451238	16451312	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16451313	16451408	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16451409	16451528	0.93	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16451409	16451528	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16451529	16451624	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16451625	16451778	0.99	-	1	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16451625	16451778	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16451779	16451891	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16451892	16452042	1	-	2	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16451892	16452042	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	intron	16452043	16452123	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	CDS	16452124	16452292	0.72	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	exon	16452124	16452292	.	-	.	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
Phchi.S1	AUGUSTUS	start_codon	16452290	16452292	.	-	0	transcript_id "Phchi.S1G251500.t1"; gene_id "Phchi.S1G251500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2226.t1 is derived from g9146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5534097	5535588	.	+	.	Phchi.S5G083500
Phchi.S5	AUGUSTUS	transcript	5534097	5535588	.	+	.	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	start_codon	5534097	5534099	.	+	0	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	CDS	5534097	5534166	0.52	+	0	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	exon	5534097	5534166	.	+	.	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	intron	5534167	5534336	.	+	.	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	CDS	5534337	5535394	0.55	+	2	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	exon	5534337	5535394	.	+	.	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	intron	5535395	5535471	.	+	.	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	CDS	5535472	5535588	0.88	+	0	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	exon	5535472	5535588	.	+	.	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
Phchi.S5	AUGUSTUS	stop_codon	5535589	5535591	.	+	0	transcript_id "Phchi.S5G083500.t1"; gene_id "Phchi.S5G083500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7573.t1 is derived from g4747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30098044	30099158	.	-	.	Phchi.S1G473200
Phchi.S1	AUGUSTUS	transcript	30098044	30099158	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	stop_codon	30098041	30098043	.	-	0	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	CDS	30098044	30098122	1	-	1	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	exon	30098044	30098122	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	intron	30098123	30098261	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	CDS	30098262	30098431	0.98	-	0	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	exon	30098262	30098431	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	intron	30098432	30098642	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	CDS	30098643	30098970	1	-	1	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	exon	30098643	30098970	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	intron	30098971	30099081	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	CDS	30099082	30099158	0.98	-	0	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	exon	30099082	30099158	.	-	.	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
Phchi.S1	AUGUSTUS	start_codon	30099156	30099158	.	-	0	transcript_id "Phchi.S1G473200.t1"; gene_id "Phchi.S1G473200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6414.t1 is derived from g3586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22857086	22858909	.	+	.	Phchi.S1G357300
Phchi.S1	AUGUSTUS	transcript	22857086	22858909	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	start_codon	22857086	22857088	.	+	0	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	CDS	22857086	22858110	0.38	+	0	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	exon	22857086	22858110	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	intron	22858111	22858285	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	CDS	22858286	22858394	1	+	1	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	exon	22858286	22858394	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	intron	22858395	22858481	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	CDS	22858482	22858617	1	+	0	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	exon	22858482	22858617	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	intron	22858618	22858778	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	CDS	22858779	22858909	0.99	+	2	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	exon	22858779	22858909	.	+	.	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
Phchi.S1	AUGUSTUS	stop_codon	22858910	22858912	.	+	0	transcript_id "Phchi.S1G357300.t1"; gene_id "Phchi.S1G357300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6356.t1 is derived from g3528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22500898	22501662	.	+	.	Phchi.S1G351500
Phchi.S1	AUGUSTUS	transcript	22500898	22501662	.	+	.	transcript_id "Phchi.S1G351500.t1"; gene_id "Phchi.S1G351500"
Phchi.S1	AUGUSTUS	start_codon	22500898	22500900	.	+	0	transcript_id "Phchi.S1G351500.t1"; gene_id "Phchi.S1G351500"
Phchi.S1	AUGUSTUS	CDS	22500898	22501662	0.74	+	0	transcript_id "Phchi.S1G351500.t1"; gene_id "Phchi.S1G351500"
Phchi.S1	AUGUSTUS	exon	22500898	22501662	.	+	.	transcript_id "Phchi.S1G351500.t1"; gene_id "Phchi.S1G351500"
Phchi.S1	AUGUSTUS	stop_codon	22501663	22501665	.	+	0	transcript_id "Phchi.S1G351500.t1"; gene_id "Phchi.S1G351500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9176.t1 is derived from g6351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40230435	40232364	.	-	.	Phchi.S1G633500
Phchi.S1	AUGUSTUS	transcript	40230435	40232364	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	stop_codon	40230432	40230434	.	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40230435	40230470	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40230435	40230470	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40230471	40230551	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40230552	40230641	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40230552	40230641	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40230642	40230752	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40230753	40230861	1	-	1	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40230753	40230861	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40230862	40230939	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40230940	40231038	1	-	1	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40230940	40231038	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40231039	40231120	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40231121	40231200	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40231121	40231200	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40231201	40231293	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40231294	40231376	1	-	2	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40231294	40231376	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40231377	40231469	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40231470	40231539	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40231470	40231539	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40231540	40231619	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40231620	40231703	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40231620	40231703	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40231704	40231803	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40231804	40231899	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40231804	40231899	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40231900	40231979	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40231980	40232060	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40231980	40232060	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	intron	40232061	40232154	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	CDS	40232155	40232364	1	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	exon	40232155	40232364	.	-	.	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
Phchi.S1	AUGUSTUS	start_codon	40232362	40232364	.	-	0	transcript_id "Phchi.S1G633500.t1"; gene_id "Phchi.S1G633500"
# This transcript jg8314.t2 is derived from g5489.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8315.t1 is derived from g5490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35254590	35254963	.	-	.	Phchi.S1G547400
Phchi.S1	AUGUSTUS	transcript	35254590	35254963	.	-	.	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	stop_codon	35254587	35254589	.	-	0	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	CDS	35254590	35254666	0.98	-	2	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	exon	35254590	35254666	.	-	.	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	intron	35254667	35254821	.	-	.	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	CDS	35254822	35254963	0.86	-	0	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	exon	35254822	35254963	.	-	.	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
Phchi.S1	AUGUSTUS	start_codon	35254961	35254963	.	-	0	transcript_id "Phchi.S1G547400.t1"; gene_id "Phchi.S1G547400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10228.t1 is derived from g7404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46483144	46483731	.	-	.	Phchi.S1G738700
Phchi.S1	AUGUSTUS	transcript	46483144	46483731	.	-	.	transcript_id "Phchi.S1G738700.t1"; gene_id "Phchi.S1G738700"
Phchi.S1	AUGUSTUS	stop_codon	46483141	46483143	.	-	0	transcript_id "Phchi.S1G738700.t1"; gene_id "Phchi.S1G738700"
Phchi.S1	AUGUSTUS	CDS	46483144	46483731	0.48	-	0	transcript_id "Phchi.S1G738700.t1"; gene_id "Phchi.S1G738700"
Phchi.S1	AUGUSTUS	exon	46483144	46483731	.	-	.	transcript_id "Phchi.S1G738700.t1"; gene_id "Phchi.S1G738700"
Phchi.S1	AUGUSTUS	start_codon	46483729	46483731	.	-	0	transcript_id "Phchi.S1G738700.t1"; gene_id "Phchi.S1G738700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg601.t1 is derived from g10383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4351897	4354142	.	-	.	Phchi.S6G056000
Phchi.S6	AUGUSTUS	transcript	4351897	4354142	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	stop_codon	4351894	4351896	.	-	0	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	CDS	4351897	4352055	0.92	-	0	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	exon	4351897	4352055	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	intron	4352056	4352143	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	CDS	4352144	4352266	0.61	-	0	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	exon	4352144	4352266	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	intron	4352267	4352385	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	CDS	4352386	4352469	0.36	-	0	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	exon	4352386	4352469	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	intron	4352470	4352657	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	CDS	4352658	4354142	0.12	-	0	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	exon	4352658	4354142	.	-	.	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
Phchi.S6	AUGUSTUS	start_codon	4354140	4354142	.	-	0	transcript_id "Phchi.S6G056000.t1"; gene_id "Phchi.S6G056000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5134.t1 is derived from g2304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15081600	15082539	.	-	.	Phchi.S1G229300
Phchi.S1	AUGUSTUS	transcript	15081600	15082539	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	stop_codon	15081597	15081599	.	-	0	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	CDS	15081600	15081669	0.89	-	1	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	exon	15081600	15081669	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	intron	15081670	15081853	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	CDS	15081854	15081901	0.53	-	1	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	exon	15081854	15081901	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	intron	15081902	15082088	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	CDS	15082089	15082140	0.9	-	2	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	exon	15082089	15082140	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	intron	15082141	15082230	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	CDS	15082231	15082350	0.43	-	2	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	exon	15082231	15082350	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	intron	15082351	15082493	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	CDS	15082494	15082539	0.43	-	0	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	exon	15082494	15082539	.	-	.	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
Phchi.S1	AUGUSTUS	start_codon	15082537	15082539	.	-	0	transcript_id "Phchi.S1G229300.t1"; gene_id "Phchi.S1G229300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10652.t1 is derived from g14702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1433984	1435743	.	+	.	Phchi.S4G023400
Phchi.S4	AUGUSTUS	transcript	1433984	1435743	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	start_codon	1433984	1433986	.	+	0	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1433984	1434000	0.66	+	0	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1433984	1434000	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434001	1434074	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434075	1434225	0.99	+	1	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434075	1434225	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434226	1434308	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434309	1434402	1	+	0	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434309	1434402	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434403	1434502	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434503	1434618	1	+	2	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434503	1434618	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434619	1434795	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434796	1434904	1	+	0	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434796	1434904	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434905	1434989	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434990	1435058	1	+	2	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434990	1435058	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435059	1435135	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435136	1435207	0.92	+	2	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435136	1435207	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435208	1435314	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435315	1435362	1	+	2	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435315	1435362	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435363	1435453	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435454	1435743	0.97	+	2	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435454	1435743	.	+	.	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	stop_codon	1435744	1435746	.	+	0	transcript_id "Phchi.S4G023400.t1"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	transcript	1433984	1435743	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	start_codon	1433984	1433986	.	+	0	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1433984	1434000	0.68	+	0	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1433984	1434000	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434001	1434080	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434081	1434225	1	+	1	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434081	1434225	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434226	1434308	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434309	1434402	1	+	0	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434309	1434402	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434403	1434502	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434503	1434618	1	+	2	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434503	1434618	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434619	1434795	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434796	1434904	1	+	0	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434796	1434904	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434905	1434989	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434990	1435058	1	+	2	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434990	1435058	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435059	1435135	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435136	1435207	0.91	+	2	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435136	1435207	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435208	1435314	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435315	1435362	1	+	2	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435315	1435362	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435363	1435453	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435454	1435743	0.93	+	2	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435454	1435743	.	+	.	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	stop_codon	1435744	1435746	.	+	0	transcript_id "Phchi.S4G023400.t2"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	transcript	1433984	1435743	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	start_codon	1433984	1433986	.	+	0	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1433984	1434000	0.64	+	0	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1433984	1434000	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434001	1434080	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434081	1434225	1	+	1	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434081	1434225	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434226	1434308	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434309	1434402	1	+	0	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434309	1434402	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434403	1434502	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434503	1434524	0.92	+	2	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434503	1434524	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434525	1434618	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434619	1434655	0.98	+	1	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434619	1434655	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434656	1434795	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434796	1434904	1	+	0	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434796	1434904	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1434905	1434989	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1434990	1435058	1	+	2	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1434990	1435058	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435059	1435135	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435136	1435207	0.93	+	2	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435136	1435207	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435208	1435314	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435315	1435362	1	+	2	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435315	1435362	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	intron	1435363	1435453	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	CDS	1435454	1435743	0.95	+	2	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	exon	1435454	1435743	.	+	.	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
Phchi.S4	AUGUSTUS	stop_codon	1435744	1435746	.	+	0	transcript_id "Phchi.S4G023400.t3"; gene_id "Phchi.S4G023400"
# This transcript jg3757.t2 is derived from g926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3758.t1 is derived from g927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5551303	5553648	.	+	.	Phchi.S1G091700
Phchi.S1	AUGUSTUS	transcript	5551303	5553648	.	+	.	transcript_id "Phchi.S1G091700.t1"; gene_id "Phchi.S1G091700"
Phchi.S1	AUGUSTUS	start_codon	5551303	5551305	.	+	0	transcript_id "Phchi.S1G091700.t1"; gene_id "Phchi.S1G091700"
Phchi.S1	AUGUSTUS	CDS	5551303	5553648	1	+	0	transcript_id "Phchi.S1G091700.t1"; gene_id "Phchi.S1G091700"
Phchi.S1	AUGUSTUS	exon	5551303	5553648	.	+	.	transcript_id "Phchi.S1G091700.t1"; gene_id "Phchi.S1G091700"
Phchi.S1	AUGUSTUS	stop_codon	5553649	5553651	.	+	0	transcript_id "Phchi.S1G091700.t1"; gene_id "Phchi.S1G091700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5960.t1 is derived from g3131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20087781	20093031	.	-	.	Phchi.S1G311900
Phchi.S1	AUGUSTUS	transcript	20087781	20093031	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	stop_codon	20087778	20087780	.	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20087781	20088131	0.53	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20087781	20088131	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20088132	20088211	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20088212	20088307	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20088212	20088307	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20088308	20088423	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20088424	20088492	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20088424	20088492	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20088493	20088570	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20088571	20088633	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20088571	20088633	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20088634	20088748	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20088749	20088826	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20088749	20088826	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20088827	20088903	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20088904	20088997	1	-	1	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20088904	20088997	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20088998	20089102	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20089103	20089236	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20089103	20089236	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20089237	20089367	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20089368	20089445	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20089368	20089445	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20089446	20089622	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20089623	20089688	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20089623	20089688	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20089689	20089825	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20089826	20089933	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20089826	20089933	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20089934	20090028	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20090029	20090106	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20090029	20090106	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20090107	20090208	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20090209	20090268	0.97	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20090209	20090268	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20090269	20090411	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20090412	20090528	0.99	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20090412	20090528	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20090529	20090630	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20090631	20090687	0.99	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20090631	20090687	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20090688	20090829	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20090830	20091006	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20090830	20091006	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20091007	20091090	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20091091	20091154	1	-	1	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20091091	20091154	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20091155	20091307	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20091308	20091449	1	-	2	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20091308	20091449	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20091450	20091554	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20091555	20091715	0.87	-	1	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20091555	20091715	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20091716	20091886	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20091887	20092011	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20091887	20092011	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20092012	20092095	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20092096	20092166	1	-	2	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20092096	20092166	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20092167	20092234	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20092235	20092385	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20092235	20092385	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20092386	20092502	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20092503	20092559	1	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20092503	20092559	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20092560	20092741	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20092742	20092836	1	-	2	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20092742	20092836	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	intron	20092837	20092976	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	CDS	20092977	20093031	0.8	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	exon	20092977	20093031	.	-	.	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
Phchi.S1	AUGUSTUS	start_codon	20093029	20093031	.	-	0	transcript_id "Phchi.S1G311900.t1"; gene_id "Phchi.S1G311900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12875.t1 is derived from g11340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2852437	2852811	.	+	.	Phchi.S3G019400
Phchi.S3	AUGUSTUS	transcript	2852437	2852811	.	+	.	transcript_id "Phchi.S3G019400.t1"; gene_id "Phchi.S3G019400"
Phchi.S3	AUGUSTUS	start_codon	2852437	2852439	.	+	0	transcript_id "Phchi.S3G019400.t1"; gene_id "Phchi.S3G019400"
Phchi.S3	AUGUSTUS	CDS	2852437	2852811	0.7	+	0	transcript_id "Phchi.S3G019400.t1"; gene_id "Phchi.S3G019400"
Phchi.S3	AUGUSTUS	exon	2852437	2852811	.	+	.	transcript_id "Phchi.S3G019400.t1"; gene_id "Phchi.S3G019400"
Phchi.S3	AUGUSTUS	stop_codon	2852812	2852814	.	+	0	transcript_id "Phchi.S3G019400.t1"; gene_id "Phchi.S3G019400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6733.t1 is derived from g3905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24787384	24788736	.	-	.	Phchi.S1G389200
Phchi.S1	AUGUSTUS	transcript	24787384	24788736	.	-	.	transcript_id "Phchi.S1G389200.t1"; gene_id "Phchi.S1G389200"
Phchi.S1	AUGUSTUS	stop_codon	24787381	24787383	.	-	0	transcript_id "Phchi.S1G389200.t1"; gene_id "Phchi.S1G389200"
Phchi.S1	AUGUSTUS	CDS	24787384	24788736	0.84	-	0	transcript_id "Phchi.S1G389200.t1"; gene_id "Phchi.S1G389200"
Phchi.S1	AUGUSTUS	exon	24787384	24788736	.	-	.	transcript_id "Phchi.S1G389200.t1"; gene_id "Phchi.S1G389200"
Phchi.S1	AUGUSTUS	start_codon	24788734	24788736	.	-	0	transcript_id "Phchi.S1G389200.t1"; gene_id "Phchi.S1G389200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6815.t1 is derived from g3987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25182101	25185280	.	-	.	Phchi.S1G397400
Phchi.S1	AUGUSTUS	transcript	25182101	25185280	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	stop_codon	25182098	25182100	.	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25182101	25182370	1	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25182101	25182370	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25182371	25182446	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25182447	25182572	1	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25182447	25182572	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25182573	25182669	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25182670	25182897	1	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25182670	25182897	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25182898	25183053	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25183054	25183158	1	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25183054	25183158	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25183159	25183254	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25183255	25183644	0.89	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25183255	25183644	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25183645	25183761	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25183762	25183814	0.89	-	2	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25183762	25183814	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25183815	25183905	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25183906	25184006	1	-	1	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25183906	25184006	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25184007	25184096	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25184097	25184107	0.91	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25184097	25184107	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25184108	25184181	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25184182	25184193	0.86	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25184182	25184193	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25184194	25184287	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25184288	25184495	0.82	-	1	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25184288	25184495	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25184496	25184656	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25184657	25184700	0.51	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25184657	25184700	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25184701	25184940	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25184941	25184969	0.65	-	2	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25184941	25184969	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25184970	25185115	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25185116	25185140	0.65	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25185116	25185140	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	intron	25185141	25185238	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	CDS	25185239	25185280	0.96	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	exon	25185239	25185280	.	-	.	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
Phchi.S1	AUGUSTUS	start_codon	25185278	25185280	.	-	0	transcript_id "Phchi.S1G397400.t1"; gene_id "Phchi.S1G397400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12713.t1 is derived from g11178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	745257	746718	.	+	.	Phchi.S3G003200
Phchi.S3	AUGUSTUS	transcript	745257	746718	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	start_codon	745257	745259	.	+	0	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	745257	745387	0.77	+	0	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	745257	745387	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	intron	745388	745463	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	745464	745506	1	+	1	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	745464	745506	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	intron	745507	745603	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	745604	745730	1	+	0	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	745604	745730	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	intron	745731	745827	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	745828	745956	0.99	+	2	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	745828	745956	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	intron	745957	746054	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	746055	746210	0.76	+	2	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	746055	746210	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	intron	746211	746362	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	746363	746491	0.76	+	2	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	746363	746491	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	intron	746492	746593	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	CDS	746594	746718	0.71	+	2	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	exon	746594	746718	.	+	.	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
Phchi.S3	AUGUSTUS	stop_codon	746719	746721	.	+	0	transcript_id "Phchi.S3G003200.t1"; gene_id "Phchi.S3G003200"
# This transcript jg9965.t2 is derived from g7141.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9966.t1 is derived from g7142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44694936	44696795	.	-	.	Phchi.S1G712500
Phchi.S1	AUGUSTUS	transcript	44694936	44696480	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	stop_codon	44694933	44694935	.	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44694936	44694950	1	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44694936	44694950	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44694951	44695023	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695024	44695109	1	-	2	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695024	44695109	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695110	44695191	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695192	44695303	1	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695192	44695303	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695304	44695386	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695387	44695476	1	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695387	44695476	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695477	44695558	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695559	44695681	1	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695559	44695681	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695682	44695816	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695817	44695909	1	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695817	44695909	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695910	44696050	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44696051	44696275	0.99	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44696051	44696275	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44696276	44696390	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44696391	44696480	0.99	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44696391	44696480	.	-	.	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	start_codon	44696478	44696480	.	-	0	transcript_id "Phchi.S1G712500.t1"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	transcript	44694936	44696795	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	stop_codon	44694933	44694935	.	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44694936	44694950	1	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44694936	44694950	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44694951	44695023	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695024	44695109	1	-	2	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695024	44695109	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695110	44695191	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695192	44695303	1	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695192	44695303	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695304	44695386	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695387	44695476	1	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695387	44695476	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695477	44695558	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695559	44695681	1	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695559	44695681	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695682	44695816	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44695817	44695909	1	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44695817	44695909	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44695910	44696050	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44696051	44696295	0.99	-	2	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44696051	44696295	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44696296	44696390	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44696391	44696650	0.54	-	1	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44696391	44696650	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	intron	44696651	44696760	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	CDS	44696761	44696795	0.54	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	exon	44696761	44696795	.	-	.	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
Phchi.S1	AUGUSTUS	start_codon	44696793	44696795	.	-	0	transcript_id "Phchi.S1G712500.t2"; gene_id "Phchi.S1G712500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5658.t1 is derived from g2828.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18160678	18166109	.	-	.	Phchi.S1G281700
Phchi.S1	AUGUSTUS	transcript	18160678	18166109	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	stop_codon	18160675	18160677	.	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18160678	18160857	0.96	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18160678	18160857	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18160858	18160937	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18160938	18161170	1	-	2	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18160938	18161170	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18161171	18161271	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18161272	18161343	0.95	-	2	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18161272	18161343	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18161344	18161537	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18161538	18162257	0.58	-	2	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18161538	18162257	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162258	18162359	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162360	18162642	0.98	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162360	18162642	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162643	18162749	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162750	18162905	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162750	18162905	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162906	18162994	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162995	18163063	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162995	18163063	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163064	18163140	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163141	18163232	1	-	2	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163141	18163232	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163233	18163317	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163318	18163405	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163318	18163405	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163406	18163616	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163617	18163779	1	-	1	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163617	18163779	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163780	18163910	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163911	18163990	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163911	18163990	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163991	18164099	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164100	18164192	0.98	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164100	18164192	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18164193	18164271	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164272	18164343	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164272	18164343	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18164344	18164527	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164528	18165365	1	-	1	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164528	18165365	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18165366	18165786	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18165787	18165827	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18165787	18165827	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18165828	18166058	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18166059	18166109	1	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18166059	18166109	.	-	.	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	start_codon	18166107	18166109	.	-	0	transcript_id "Phchi.S1G281700.t1"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	transcript	18160678	18166109	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	stop_codon	18160675	18160677	.	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18160678	18160857	0.94	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18160678	18160857	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18160858	18160937	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18160938	18161170	1	-	2	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18160938	18161170	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18161171	18161271	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18161272	18161343	0.95	-	2	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18161272	18161343	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18161344	18161537	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18161538	18162257	0.6	-	2	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18161538	18162257	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162258	18162359	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162360	18162642	0.99	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162360	18162642	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162643	18162749	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162750	18162905	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162750	18162905	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162906	18162994	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162995	18163063	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162995	18163063	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163064	18163140	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163141	18163232	1	-	2	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163141	18163232	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163233	18163317	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163318	18163405	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163318	18163405	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163406	18163616	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163617	18163776	1	-	1	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163617	18163776	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163777	18163910	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163911	18163990	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163911	18163990	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163991	18164099	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164100	18164192	0.95	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164100	18164192	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18164193	18164271	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164272	18164343	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164272	18164343	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18164344	18164527	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164528	18165365	1	-	1	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164528	18165365	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18165366	18165786	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18165787	18165827	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18165787	18165827	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18165828	18166058	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18166059	18166109	1	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18166059	18166109	.	-	.	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	start_codon	18166107	18166109	.	-	0	transcript_id "Phchi.S1G281700.t2"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	transcript	18160678	18166109	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	stop_codon	18160675	18160677	.	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18160678	18160857	0.96	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18160678	18160857	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18160858	18160937	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18160938	18161170	1	-	2	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18160938	18161170	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18161171	18161271	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18161272	18161343	0.95	-	2	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18161272	18161343	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18161344	18161537	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18161538	18162257	0.46	-	2	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18161538	18162257	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162258	18162359	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162360	18162642	0.99	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162360	18162642	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162643	18162749	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162750	18162905	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162750	18162905	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18162906	18162994	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18162995	18163063	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18162995	18163063	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163064	18163140	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163141	18163232	1	-	2	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163141	18163232	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163233	18163317	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163318	18163405	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163318	18163405	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163406	18163709	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163710	18163776	0.99	-	1	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163710	18163776	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163777	18163910	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18163911	18163990	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18163911	18163990	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18163991	18164099	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164100	18164192	0.96	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164100	18164192	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18164193	18164271	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164272	18164343	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164272	18164343	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18164344	18164527	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18164528	18165365	1	-	1	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18164528	18165365	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18165366	18165786	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18165787	18165827	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18165787	18165827	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	intron	18165828	18166058	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	CDS	18166059	18166109	1	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	exon	18166059	18166109	.	-	.	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
Phchi.S1	AUGUSTUS	start_codon	18166107	18166109	.	-	0	transcript_id "Phchi.S1G281700.t3"; gene_id "Phchi.S1G281700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15243.t1 is derived from g13711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17881220	17882081	.	-	.	Phchi.S3G256200
Phchi.S3	AUGUSTUS	transcript	17881220	17882081	.	-	.	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	stop_codon	17881217	17881219	.	-	0	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	CDS	17881220	17881449	1	-	2	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	exon	17881220	17881449	.	-	.	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	intron	17881450	17881561	.	-	.	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	CDS	17881562	17882081	0.84	-	0	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	exon	17881562	17882081	.	-	.	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
Phchi.S3	AUGUSTUS	start_codon	17882079	17882081	.	-	0	transcript_id "Phchi.S3G256200.t1"; gene_id "Phchi.S3G256200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7444.t1 is derived from g4616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29154091	29154699	.	+	.	Phchi.S1G460300
Phchi.S1	AUGUSTUS	transcript	29154091	29154699	.	+	.	transcript_id "Phchi.S1G460300.t1"; gene_id "Phchi.S1G460300"
Phchi.S1	AUGUSTUS	start_codon	29154091	29154093	.	+	0	transcript_id "Phchi.S1G460300.t1"; gene_id "Phchi.S1G460300"
Phchi.S1	AUGUSTUS	CDS	29154091	29154699	0.67	+	0	transcript_id "Phchi.S1G460300.t1"; gene_id "Phchi.S1G460300"
Phchi.S1	AUGUSTUS	exon	29154091	29154699	.	+	.	transcript_id "Phchi.S1G460300.t1"; gene_id "Phchi.S1G460300"
Phchi.S1	AUGUSTUS	stop_codon	29154700	29154702	.	+	0	transcript_id "Phchi.S1G460300.t1"; gene_id "Phchi.S1G460300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9689.t1 is derived from g6865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43291625	43294229	.	-	.	Phchi.S1G684800
Phchi.S1	AUGUSTUS	transcript	43291625	43294229	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	stop_codon	43291622	43291624	.	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43291625	43291717	0.98	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43291625	43291717	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43291718	43291808	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43291809	43291878	0.73	-	1	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43291809	43291878	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43291879	43291981	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43291982	43292079	0.6	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43291982	43292079	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43292080	43292249	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43292250	43292359	1	-	2	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43292250	43292359	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43292360	43292457	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43292458	43292608	1	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43292458	43292608	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43292609	43292707	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43292708	43292740	1	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43292708	43292740	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43292741	43292924	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43292925	43293063	1	-	1	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43292925	43293063	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43293064	43293203	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43293204	43293416	1	-	1	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43293204	43293416	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43293417	43293535	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43293536	43293674	1	-	2	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43293536	43293674	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43293675	43293817	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43293818	43293947	1	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43293818	43293947	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	intron	43293948	43294136	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	CDS	43294137	43294229	1	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	exon	43294137	43294229	.	-	.	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
Phchi.S1	AUGUSTUS	start_codon	43294227	43294229	.	-	0	transcript_id "Phchi.S1G684800.t1"; gene_id "Phchi.S1G684800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13290.t1 is derived from g11756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5204853	5205444	.	+	.	Phchi.S3G060900
Phchi.S3	AUGUSTUS	transcript	5204853	5205444	.	+	.	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	start_codon	5204853	5204855	.	+	0	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	CDS	5204853	5205162	0.5	+	0	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	exon	5204853	5205162	.	+	.	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	intron	5205163	5205259	.	+	.	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	CDS	5205260	5205444	0.41	+	2	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	exon	5205260	5205444	.	+	.	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
Phchi.S3	AUGUSTUS	stop_codon	5205445	5205447	.	+	0	transcript_id "Phchi.S3G060900.t1"; gene_id "Phchi.S3G060900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1796.t1 is derived from g8716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3065984	3067223	.	-	.	Phchi.S5G040500
Phchi.S5	AUGUSTUS	transcript	3065984	3067223	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	stop_codon	3065981	3065983	.	-	0	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	CDS	3065984	3066082	1	-	0	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	exon	3065984	3066082	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	intron	3066083	3066266	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	CDS	3066267	3066356	0.98	-	0	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	exon	3066267	3066356	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	intron	3066357	3066458	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	CDS	3066459	3066618	0.99	-	1	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	exon	3066459	3066618	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	intron	3066619	3066865	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	CDS	3066866	3066914	1	-	2	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	exon	3066866	3066914	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	intron	3066915	3067045	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	CDS	3067046	3067223	0.89	-	0	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	exon	3067046	3067223	.	-	.	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
Phchi.S5	AUGUSTUS	start_codon	3067221	3067223	.	-	0	transcript_id "Phchi.S5G040500.t1"; gene_id "Phchi.S5G040500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8868.t1 is derived from g6043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38384097	38384765	.	-	.	Phchi.S1G602700
Phchi.S1	AUGUSTUS	transcript	38384097	38384765	.	-	.	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	stop_codon	38384094	38384096	.	-	0	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	CDS	38384097	38384226	0.99	-	1	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	exon	38384097	38384226	.	-	.	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	intron	38384227	38384346	.	-	.	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	CDS	38384347	38384420	0.99	-	0	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	exon	38384347	38384420	.	-	.	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	intron	38384421	38384510	.	-	.	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	CDS	38384511	38384765	1	-	0	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	exon	38384511	38384765	.	-	.	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
Phchi.S1	AUGUSTUS	start_codon	38384763	38384765	.	-	0	transcript_id "Phchi.S1G602700.t1"; gene_id "Phchi.S1G602700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3859.t1 is derived from g1028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6076494	6078173	.	-	.	Phchi.S1G101800
Phchi.S1	AUGUSTUS	transcript	6076494	6078173	.	-	.	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	stop_codon	6076491	6076493	.	-	0	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	CDS	6076494	6076573	0.5	-	2	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	exon	6076494	6076573	.	-	.	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	intron	6076574	6076660	.	-	.	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	CDS	6076661	6076687	0.49	-	2	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	exon	6076661	6076687	.	-	.	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	intron	6076688	6077137	.	-	.	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	CDS	6077138	6078173	0.52	-	0	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	exon	6077138	6078173	.	-	.	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
Phchi.S1	AUGUSTUS	start_codon	6078171	6078173	.	-	0	transcript_id "Phchi.S1G101800.t1"; gene_id "Phchi.S1G101800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14188.t1 is derived from g12655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11394726	11396558	.	+	.	Phchi.S3G150700
Phchi.S3	AUGUSTUS	transcript	11394726	11396558	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	start_codon	11394726	11394728	.	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11394726	11394767	0.72	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11394726	11394767	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11394768	11394847	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11394848	11395189	1	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11394848	11395189	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11395190	11395288	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11395289	11395399	1	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11395289	11395399	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11395400	11395580	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11395581	11395721	0.97	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11395581	11395721	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11395722	11395824	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11395825	11395920	1	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11395825	11395920	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11395921	11395996	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11395997	11396086	0.64	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11395997	11396086	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11396087	11396232	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11396233	11396349	1	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11396233	11396349	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	intron	11396350	11396423	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	CDS	11396424	11396558	1	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	exon	11396424	11396558	.	+	.	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
Phchi.S3	AUGUSTUS	stop_codon	11396559	11396561	.	+	0	transcript_id "Phchi.S3G150700.t1"; gene_id "Phchi.S3G150700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg823.t1 is derived from g10605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5721364	5721835	.	-	.	Phchi.S6G078200
Phchi.S6	AUGUSTUS	transcript	5721364	5721835	.	-	.	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	stop_codon	5721361	5721363	.	-	0	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	CDS	5721364	5721576	0.74	-	0	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	exon	5721364	5721576	.	-	.	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	intron	5721577	5721670	.	-	.	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	CDS	5721671	5721835	0.72	-	0	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	exon	5721671	5721835	.	-	.	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
Phchi.S6	AUGUSTUS	start_codon	5721833	5721835	.	-	0	transcript_id "Phchi.S6G078200.t1"; gene_id "Phchi.S6G078200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg849.t1 is derived from g10631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5894614	5898360	.	+	.	Phchi.S6G080800
Phchi.S6	AUGUSTUS	transcript	5894614	5898360	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	start_codon	5894614	5894616	.	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5894614	5894629	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5894614	5894629	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5894630	5894711	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5894712	5895620	1	+	2	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5894712	5895620	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5895621	5895922	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5895923	5895990	1	+	2	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5895923	5895990	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5895991	5896066	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5896067	5896149	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5896067	5896149	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5896150	5896246	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5896247	5896346	1	+	1	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5896247	5896346	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5896347	5896472	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5896473	5896558	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5896473	5896558	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5896559	5896640	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5896641	5896723	1	+	1	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5896641	5896723	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5896724	5896847	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5896848	5896972	1	+	2	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5896848	5896972	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5896973	5897113	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5897114	5897215	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5897114	5897215	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5897216	5897310	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5897311	5897613	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5897311	5897613	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5897614	5897711	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5897712	5897834	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5897712	5897834	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5897835	5897914	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5897915	5898251	1	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5897915	5898251	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	intron	5898252	5898331	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	CDS	5898332	5898360	1	+	2	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	exon	5898332	5898360	.	+	.	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
Phchi.S6	AUGUSTUS	stop_codon	5898361	5898363	.	+	0	transcript_id "Phchi.S6G080800.t1"; gene_id "Phchi.S6G080800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2490.t1 is derived from g9410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6928617	6931302	.	+	.	Phchi.S5G109900
Phchi.S5	AUGUSTUS	transcript	6928617	6931302	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	start_codon	6928617	6928619	.	+	0	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	CDS	6928617	6928731	0.95	+	0	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	exon	6928617	6928731	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	intron	6928732	6928825	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	CDS	6928826	6928905	1	+	2	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	exon	6928826	6928905	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	intron	6928906	6928987	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	CDS	6928988	6929133	1	+	0	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	exon	6928988	6929133	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	intron	6929134	6929250	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	CDS	6929251	6929437	0.97	+	1	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	exon	6929251	6929437	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	intron	6929438	6929542	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	CDS	6929543	6931133	0.3	+	0	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	exon	6929543	6931133	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	intron	6931134	6931234	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	CDS	6931235	6931302	0.56	+	2	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	exon	6931235	6931302	.	+	.	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
Phchi.S5	AUGUSTUS	stop_codon	6931303	6931305	.	+	0	transcript_id "Phchi.S5G109900.t1"; gene_id "Phchi.S5G109900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6371.t1 is derived from g3543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22601776	22601982	.	-	.	Phchi.S1G353000
Phchi.S1	AUGUSTUS	transcript	22601776	22601982	.	-	.	transcript_id "Phchi.S1G353000.t1"; gene_id "Phchi.S1G353000"
Phchi.S1	AUGUSTUS	stop_codon	22601773	22601775	.	-	0	transcript_id "Phchi.S1G353000.t1"; gene_id "Phchi.S1G353000"
Phchi.S1	AUGUSTUS	CDS	22601776	22601982	0.89	-	0	transcript_id "Phchi.S1G353000.t1"; gene_id "Phchi.S1G353000"
Phchi.S1	AUGUSTUS	exon	22601776	22601982	.	-	.	transcript_id "Phchi.S1G353000.t1"; gene_id "Phchi.S1G353000"
Phchi.S1	AUGUSTUS	start_codon	22601980	22601982	.	-	0	transcript_id "Phchi.S1G353000.t1"; gene_id "Phchi.S1G353000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9510.t1 is derived from g6686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42120665	42126798	.	+	.	Phchi.S1G666900
Phchi.S1	AUGUSTUS	transcript	42120665	42126798	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	start_codon	42120665	42120667	.	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42120665	42120863	0.81	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42120665	42120863	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42120864	42120974	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42120975	42121025	1	+	2	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42120975	42121025	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42121026	42121120	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42121121	42121212	1	+	2	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42121121	42121212	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42121213	42121299	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42121300	42121377	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42121300	42121377	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42121378	42121464	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42121465	42121622	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42121465	42121622	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42121623	42121811	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42121812	42121886	0.84	+	1	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42121812	42121886	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42121887	42121949	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42121950	42121964	0.94	+	1	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42121950	42121964	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42121965	42122114	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42122115	42122232	0.96	+	1	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42122115	42122232	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42122233	42122338	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42122339	42122391	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42122339	42122391	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42122392	42122517	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42122518	42122583	1	+	1	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42122518	42122583	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42122584	42122676	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42122677	42122721	1	+	1	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42122677	42122721	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42122722	42122939	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42122940	42122989	1	+	1	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42122940	42122989	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42122990	42123222	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42123223	42123407	1	+	2	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42123223	42123407	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42123408	42123608	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42123609	42123668	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42123609	42123668	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42123669	42123823	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42123824	42123931	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42123824	42123931	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42123932	42124029	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42124030	42124264	0.98	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42124030	42124264	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42124265	42124391	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42124392	42124694	0.95	+	2	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42124392	42124694	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42124695	42124875	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42124876	42124973	1	+	2	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42124876	42124973	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42124974	42125057	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42125058	42125189	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42125058	42125189	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42125190	42125270	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42125271	42125489	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42125271	42125489	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42125490	42125577	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42125578	42125784	0.96	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42125578	42125784	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42125785	42125899	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42125900	42126143	0.99	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42125900	42126143	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42126144	42126226	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42126227	42126492	1	+	2	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42126227	42126492	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	intron	42126493	42126591	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	CDS	42126592	42126798	1	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	exon	42126592	42126798	.	+	.	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
Phchi.S1	AUGUSTUS	stop_codon	42126799	42126801	.	+	0	transcript_id "Phchi.S1G666900.t1"; gene_id "Phchi.S1G666900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15543.t1 is derived from g14012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19787980	19793497	.	+	.	Phchi.S3G286200
Phchi.S3	AUGUSTUS	transcript	19787980	19793497	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	start_codon	19787980	19787982	.	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19787980	19788071	0.51	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19787980	19788071	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19788072	19788278	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19788279	19788427	0.94	+	1	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19788279	19788427	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19788428	19788528	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19788529	19788719	0.52	+	2	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19788529	19788719	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19788720	19788828	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19788829	19789115	0.57	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19788829	19789115	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19789116	19789203	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19789204	19789275	1	+	1	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19789204	19789275	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19789276	19789422	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19789423	19789498	1	+	1	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19789423	19789498	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19789499	19789576	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19789577	19789675	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19789577	19789675	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19789676	19789761	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19789762	19789916	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19789762	19789916	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19789917	19790010	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19790011	19790115	1	+	1	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19790011	19790115	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19790116	19790266	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19790267	19790353	1	+	1	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19790267	19790353	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19790354	19790444	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19790445	19790529	1	+	1	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19790445	19790529	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19790530	19790609	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19790610	19790757	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19790610	19790757	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19790758	19790889	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19790890	19790966	1	+	2	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19790890	19790966	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19790967	19791050	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19791051	19791131	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19791051	19791131	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19791132	19791302	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19791303	19791467	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19791303	19791467	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19791468	19791647	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19791648	19791761	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19791648	19791761	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19791762	19791998	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19791999	19792091	0.92	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19791999	19792091	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19792092	19792202	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19792203	19792335	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19792203	19792335	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19792336	19792455	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19792456	19792532	1	+	2	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19792456	19792532	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19792533	19792656	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19792657	19792722	0.65	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19792657	19792722	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19792723	19792816	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19792817	19792886	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19792817	19792886	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19792887	19792965	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19792966	19793039	1	+	2	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19792966	19793039	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19793040	19793120	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19793121	19793231	1	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19793121	19793231	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	intron	19793232	19793398	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	CDS	19793399	19793497	0.99	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	exon	19793399	19793497	.	+	.	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
Phchi.S3	AUGUSTUS	stop_codon	19793498	19793500	.	+	0	transcript_id "Phchi.S3G286200.t1"; gene_id "Phchi.S3G286200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15857.t1 is derived from g14327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21868831	21870050	.	-	.	Phchi.S3G317600
Phchi.S3	AUGUSTUS	transcript	21868831	21870050	.	-	.	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	stop_codon	21868828	21868830	.	-	0	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	CDS	21868831	21868858	0.86	-	1	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	exon	21868831	21868858	.	-	.	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	intron	21868859	21868944	.	-	.	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	CDS	21868945	21870050	0.9	-	0	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	exon	21868945	21870050	.	-	.	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
Phchi.S3	AUGUSTUS	start_codon	21870048	21870050	.	-	0	transcript_id "Phchi.S3G317600.t1"; gene_id "Phchi.S3G317600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13358.t1 is derived from g11824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6308361	6310378	.	+	.	Phchi.S3G067700
Phchi.S3	AUGUSTUS	transcript	6308361	6310378	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	start_codon	6308361	6308363	.	+	0	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	CDS	6308361	6309245	0.56	+	0	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	exon	6308361	6309245	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	intron	6309246	6309360	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	CDS	6309361	6309591	0.97	+	0	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	exon	6309361	6309591	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	intron	6309592	6309665	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	CDS	6309666	6309975	1	+	0	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	exon	6309666	6309975	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	intron	6309976	6310082	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	CDS	6310083	6310378	1	+	2	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	exon	6310083	6310378	.	+	.	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
Phchi.S3	AUGUSTUS	stop_codon	6310379	6310381	.	+	0	transcript_id "Phchi.S3G067700.t1"; gene_id "Phchi.S3G067700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10351.t1 is derived from g7527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47317159	47319742	.	+	.	Phchi.S1G751000
Phchi.S1	AUGUSTUS	transcript	47317159	47319742	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	start_codon	47317159	47317161	.	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47317159	47317563	0.9	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47317159	47317563	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47317564	47317661	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47317662	47317805	1	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47317662	47317805	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47317806	47317917	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47317918	47318019	1	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47317918	47318019	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47318020	47318225	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47318226	47318329	1	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47318226	47318329	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47318330	47318453	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47318454	47318580	0.99	+	1	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47318454	47318580	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47318581	47318692	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47318693	47318845	0.99	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47318693	47318845	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47318846	47319021	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47319022	47319122	1	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47319022	47319122	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47319123	47319200	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47319201	47319402	1	+	1	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47319201	47319402	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	intron	47319403	47319520	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	CDS	47319521	47319742	0.96	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	exon	47319521	47319742	.	+	.	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
Phchi.S1	AUGUSTUS	stop_codon	47319743	47319745	.	+	0	transcript_id "Phchi.S1G751000.t1"; gene_id "Phchi.S1G751000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8640.t1 is derived from g5815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37192942	37196201	.	-	.	Phchi.S1G579900
Phchi.S1	AUGUSTUS	transcript	37192942	37196201	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	stop_codon	37192939	37192941	.	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37192942	37193224	1	-	1	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37192942	37193224	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37193225	37193387	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37193388	37193485	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37193388	37193485	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37193486	37193571	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37193572	37193754	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37193572	37193754	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37193755	37193839	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37193840	37193936	1	-	1	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37193840	37193936	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37193937	37194099	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37194100	37194329	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37194100	37194329	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37194330	37194424	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37194425	37194874	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37194425	37194874	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37194875	37194964	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37194965	37195066	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37194965	37195066	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37195067	37195296	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37195297	37195515	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37195297	37195515	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37195516	37195701	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37195702	37195785	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37195702	37195785	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37195786	37195950	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37195951	37196040	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37195951	37196040	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	intron	37196041	37196174	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	CDS	37196175	37196201	1	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	exon	37196175	37196201	.	-	.	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
Phchi.S1	AUGUSTUS	start_codon	37196199	37196201	.	-	0	transcript_id "Phchi.S1G579900.t1"; gene_id "Phchi.S1G579900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2316.t1 is derived from g9236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6043790	6047205	.	-	.	Phchi.S5G092500
Phchi.S5	AUGUSTUS	transcript	6043790	6047205	.	-	.	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	stop_codon	6043787	6043789	.	-	0	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	CDS	6043790	6045922	0.4	-	0	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	exon	6043790	6045922	.	-	.	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	intron	6045923	6046011	.	-	.	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	CDS	6046012	6047205	0.67	-	0	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	exon	6046012	6047205	.	-	.	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
Phchi.S5	AUGUSTUS	start_codon	6047203	6047205	.	-	0	transcript_id "Phchi.S5G092500.t1"; gene_id "Phchi.S5G092500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12551.t1 is derived from g8228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34453813	34459423	.	-	.	Phchi.S2G063100
Phchi.S2	AUGUSTUS	transcript	34453813	34459423	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	stop_codon	34453810	34453812	.	-	0	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	CDS	34453813	34457667	0.87	-	0	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	exon	34453813	34457667	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	intron	34457668	34457799	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	CDS	34457800	34458006	0.95	-	0	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	exon	34457800	34458006	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	intron	34458007	34458121	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	CDS	34458122	34458217	0.99	-	0	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	exon	34458122	34458217	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	intron	34458218	34459390	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	CDS	34459391	34459423	0.99	-	0	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	exon	34459391	34459423	.	-	.	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
Phchi.S2	AUGUSTUS	start_codon	34459421	34459423	.	-	0	transcript_id "Phchi.S2G063100.t1"; gene_id "Phchi.S2G063100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6143.t1 is derived from g3314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21139493	21141913	.	-	.	Phchi.S1G330200
Phchi.S1	AUGUSTUS	transcript	21139493	21141913	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	stop_codon	21139490	21139492	.	-	0	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	CDS	21139493	21139654	0.72	-	0	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	exon	21139493	21139654	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	intron	21139655	21140063	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	CDS	21140064	21140142	0.51	-	1	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	exon	21140064	21140142	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	intron	21140143	21140241	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	CDS	21140242	21140584	0.48	-	2	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	exon	21140242	21140584	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	intron	21140585	21140661	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	CDS	21140662	21141913	0.74	-	0	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	exon	21140662	21141913	.	-	.	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
Phchi.S1	AUGUSTUS	start_codon	21141911	21141913	.	-	0	transcript_id "Phchi.S1G330200.t1"; gene_id "Phchi.S1G330200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10346.t1 is derived from g7522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47286409	47288274	.	-	.	Phchi.S1G750500
Phchi.S1	AUGUSTUS	transcript	47286409	47288274	.	-	.	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	stop_codon	47286406	47286408	.	-	0	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	CDS	47286409	47287464	0.7	-	0	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	exon	47286409	47287464	.	-	.	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	intron	47287465	47287626	.	-	.	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	CDS	47287627	47287773	0.71	-	0	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	exon	47287627	47287773	.	-	.	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	intron	47287774	47287935	.	-	.	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	CDS	47287936	47288274	0.49	-	0	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	exon	47287936	47288274	.	-	.	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
Phchi.S1	AUGUSTUS	start_codon	47288272	47288274	.	-	0	transcript_id "Phchi.S1G750500.t1"; gene_id "Phchi.S1G750500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12620.t1 is derived from g8297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37601798	37602678	.	+	.	Phchi.S2G070000
Phchi.S2	AUGUSTUS	transcript	37601798	37602678	.	+	.	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	start_codon	37601798	37601800	.	+	0	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	CDS	37601798	37602153	0.99	+	0	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	exon	37601798	37602153	.	+	.	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	intron	37602154	37602245	.	+	.	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	CDS	37602246	37602348	1	+	1	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	exon	37602246	37602348	.	+	.	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	intron	37602349	37602627	.	+	.	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	CDS	37602628	37602678	1	+	0	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	exon	37602628	37602678	.	+	.	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
Phchi.S2	AUGUSTUS	stop_codon	37602679	37602681	.	+	0	transcript_id "Phchi.S2G070000.t1"; gene_id "Phchi.S2G070000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1393.t1 is derived from g8312.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	12637	17695	.	-	.	Phchi.S5G000200
Phchi.S5	AUGUSTUS	transcript	12637	17695	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	stop_codon	12634	12636	.	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	12637	12972	0.99	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	12637	12972	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	12973	13082	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	13083	13562	0.98	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	13083	13562	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	13563	13703	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	13704	13853	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	13704	13853	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	13854	14020	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	14021	14092	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	14021	14092	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	14093	14229	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	14230	14490	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	14230	14490	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	14491	14594	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	14595	14726	0.99	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	14595	14726	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	14727	15024	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	15025	15300	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	15025	15300	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	15301	15599	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	15600	15866	0.97	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	15600	15866	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	15867	15988	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	15989	16087	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	15989	16087	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16088	16207	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16208	16372	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16208	16372	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16373	16513	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16514	16522	1	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16514	16522	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16523	16623	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16624	16755	0.98	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16624	16755	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16756	16835	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16836	16981	0.55	-	2	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16836	16981	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16982	17109	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	17110	17695	0.31	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	17110	17695	.	-	.	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	start_codon	17693	17695	.	-	0	transcript_id "Phchi.S5G000200.t1"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	transcript	12637	17695	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	stop_codon	12634	12636	.	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	12637	12972	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	12637	12972	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	12973	13082	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	13083	13421	0.98	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	13083	13421	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	13422	13703	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	13704	13853	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	13704	13853	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	13854	14020	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	14021	14092	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	14021	14092	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	14093	14229	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	14230	14490	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	14230	14490	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	14491	14594	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	14595	14726	0.99	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	14595	14726	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	14727	15024	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	15025	15300	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	15025	15300	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	15301	15599	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	15600	15866	0.97	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	15600	15866	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	15867	15988	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	15989	16087	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	15989	16087	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16088	16207	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16208	16372	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16208	16372	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16373	16623	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16624	16755	1	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16624	16755	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16756	16835	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	16836	16981	0.57	-	2	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	16836	16981	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	intron	16982	17109	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	CDS	17110	17695	0.3	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	exon	17110	17695	.	-	.	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
Phchi.S5	AUGUSTUS	start_codon	17693	17695	.	-	0	transcript_id "Phchi.S5G000200.t2"; gene_id "Phchi.S5G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7872.t1 is derived from g5046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31644662	31648805	.	-	.	Phchi.S1G503100
Phchi.S1	AUGUSTUS	transcript	31644662	31648805	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	stop_codon	31644659	31644661	.	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31644662	31644909	0.97	-	2	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31644662	31644909	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31644910	31645014	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31645015	31645180	0.97	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31645015	31645180	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31645181	31645265	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31645266	31645401	1	-	1	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31645266	31645401	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31645402	31645473	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31645474	31645541	0.99	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31645474	31645541	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31645542	31645651	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31645652	31645777	0.99	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31645652	31645777	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31645778	31645904	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31645905	31646021	1	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31645905	31646021	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31646022	31646119	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31646120	31646275	0.76	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31646120	31646275	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31646276	31646393	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31646394	31646519	0.99	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31646394	31646519	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31646520	31646643	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31646644	31646763	1	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31646644	31646763	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31646764	31646889	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31646890	31646985	0.84	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31646890	31646985	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31646986	31647123	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31647124	31647141	0.57	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31647124	31647141	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31647142	31647229	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31647230	31647350	0.57	-	1	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31647230	31647350	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31647351	31647572	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31647573	31647627	1	-	2	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31647573	31647627	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31647628	31647711	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31647712	31647850	1	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31647712	31647850	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31647851	31647935	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31647936	31647990	1	-	1	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31647936	31647990	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31647991	31648107	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31648108	31648160	1	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31648108	31648160	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31648161	31648344	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31648345	31648426	1	-	1	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31648345	31648426	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	intron	31648427	31648518	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	CDS	31648519	31648805	0.48	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	exon	31648519	31648805	.	-	.	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
Phchi.S1	AUGUSTUS	start_codon	31648803	31648805	.	-	0	transcript_id "Phchi.S1G503100.t1"; gene_id "Phchi.S1G503100"
# This transcript jg4583.t2 is derived from g1753.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4584.t1 is derived from g1754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11210997	11212200	.	+	.	Phchi.S1G174300
Phchi.S1	AUGUSTUS	transcript	11210997	11212200	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	start_codon	11210997	11210999	.	+	0	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	CDS	11210997	11211109	0.45	+	0	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	exon	11210997	11211109	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	intron	11211110	11211293	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	CDS	11211294	11211378	0.62	+	1	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	exon	11211294	11211378	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	intron	11211379	11211522	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	CDS	11211523	11211738	1	+	0	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	exon	11211523	11211738	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	intron	11211739	11211833	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	CDS	11211834	11211990	0.86	+	0	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	exon	11211834	11211990	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	intron	11211991	11212189	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	CDS	11212190	11212200	0.4	+	2	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	exon	11212190	11212200	.	+	.	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
Phchi.S1	AUGUSTUS	stop_codon	11212201	11212203	.	+	0	transcript_id "Phchi.S1G174300.t1"; gene_id "Phchi.S1G174300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10648.t1 is derived from g14698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1424083	1425928	.	-	.	Phchi.S4G023000
Phchi.S4	AUGUSTUS	transcript	1424083	1425928	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	stop_codon	1424080	1424082	.	-	0	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	CDS	1424083	1424124	0.93	-	0	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	exon	1424083	1424124	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	intron	1424125	1424201	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	CDS	1424202	1424304	0.5	-	1	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	exon	1424202	1424304	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	intron	1424305	1424452	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	CDS	1424453	1425303	0.25	-	0	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	exon	1424453	1425303	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	intron	1425304	1425391	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	CDS	1425392	1425928	0.99	-	0	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	exon	1425392	1425928	.	-	.	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
Phchi.S4	AUGUSTUS	start_codon	1425926	1425928	.	-	0	transcript_id "Phchi.S4G023000.t1"; gene_id "Phchi.S4G023000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9784.t1 is derived from g6960.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43675253	43678654	.	+	.	Phchi.S1G694300
Phchi.S1	AUGUSTUS	transcript	43675253	43677668	.	+	.	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	start_codon	43675253	43675255	.	+	0	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	CDS	43675253	43677520	0.7	+	0	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	exon	43675253	43677520	.	+	.	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	intron	43677521	43677605	.	+	.	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	CDS	43677606	43677668	0.97	+	0	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	exon	43677606	43677668	.	+	.	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	stop_codon	43677669	43677671	.	+	0	transcript_id "Phchi.S1G694300.t1"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	transcript	43675253	43678654	.	+	.	transcript_id "Phchi.S1G694300.t2"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	start_codon	43675253	43675255	.	+	0	transcript_id "Phchi.S1G694300.t2"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	CDS	43675253	43678654	0.92	+	0	transcript_id "Phchi.S1G694300.t2"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	exon	43675253	43678654	.	+	.	transcript_id "Phchi.S1G694300.t2"; gene_id "Phchi.S1G694300"
Phchi.S1	AUGUSTUS	stop_codon	43678655	43678657	.	+	0	transcript_id "Phchi.S1G694300.t2"; gene_id "Phchi.S1G694300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10315.t1 is derived from g7491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47085435	47087396	.	+	.	Phchi.S1G747400
Phchi.S1	AUGUSTUS	transcript	47085435	47087396	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	start_codon	47085435	47085437	.	+	0	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	CDS	47085435	47085981	0.23	+	0	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	exon	47085435	47085981	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	intron	47085982	47086226	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	CDS	47086227	47086378	0.26	+	2	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	exon	47086227	47086378	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	intron	47086379	47086473	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	CDS	47086474	47086553	0.59	+	0	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	exon	47086474	47086553	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	intron	47086554	47086637	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	CDS	47086638	47086805	0.53	+	1	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	exon	47086638	47086805	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	intron	47086806	47086887	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	CDS	47086888	47087031	1	+	1	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	exon	47086888	47087031	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	intron	47087032	47087260	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	CDS	47087261	47087396	0.99	+	1	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	exon	47087261	47087396	.	+	.	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
Phchi.S1	AUGUSTUS	stop_codon	47087397	47087399	.	+	0	transcript_id "Phchi.S1G747400.t1"; gene_id "Phchi.S1G747400"
# This transcript jg10284.t2 is derived from g7460.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10285.t1 is derived from g7461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46815080	46818799	.	+	.	Phchi.S1G744400
Phchi.S1	AUGUSTUS	transcript	46815080	46818799	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	start_codon	46815080	46815082	.	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46815080	46815117	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46815080	46815117	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46815118	46815498	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46815499	46815523	1	+	1	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46815499	46815523	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46815524	46815633	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46815634	46815765	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46815634	46815765	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46815766	46815848	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46815849	46816008	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46815849	46816008	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46816009	46816097	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46816098	46816273	1	+	2	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46816098	46816273	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46816274	46816411	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46816412	46816507	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46816412	46816507	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46816508	46816673	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46816674	46816778	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46816674	46816778	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46816779	46816872	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46816873	46816959	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46816873	46816959	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46816960	46817047	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46817048	46817137	0.98	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46817048	46817137	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46817138	46817238	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46817239	46817319	0.88	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46817239	46817319	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46817320	46817422	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46817423	46817491	0.94	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46817423	46817491	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46817492	46817607	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46817608	46817685	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46817608	46817685	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46817686	46817781	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46817782	46817877	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46817782	46817877	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46817878	46817968	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46817969	46818068	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46817969	46818068	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46818069	46818142	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46818143	46818246	1	+	2	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46818143	46818246	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46818247	46818324	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46818325	46818430	1	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46818325	46818430	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46818431	46818520	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46818521	46818599	1	+	2	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46818521	46818599	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	intron	46818600	46818687	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	CDS	46818688	46818799	1	+	1	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	exon	46818688	46818799	.	+	.	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
Phchi.S1	AUGUSTUS	stop_codon	46818800	46818802	.	+	0	transcript_id "Phchi.S1G744400.t1"; gene_id "Phchi.S1G744400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14180.t1 is derived from g12647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11319829	11321054	.	-	.	Phchi.S3G149900
Phchi.S3	AUGUSTUS	transcript	11319829	11321054	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	stop_codon	11319826	11319828	.	-	0	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	CDS	11319829	11319955	0.99	-	1	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	exon	11319829	11319955	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	intron	11319956	11320046	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	CDS	11320047	11320242	1	-	2	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	exon	11320047	11320242	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	intron	11320243	11320337	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	CDS	11320338	11320483	1	-	1	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	exon	11320338	11320483	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	intron	11320484	11320565	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	CDS	11320566	11320687	1	-	0	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	exon	11320566	11320687	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	intron	11320688	11320810	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	CDS	11320811	11320880	0.99	-	1	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	exon	11320811	11320880	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	intron	11320881	11320965	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	CDS	11320966	11321054	0.98	-	0	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	exon	11320966	11321054	.	-	.	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
Phchi.S3	AUGUSTUS	start_codon	11321052	11321054	.	-	0	transcript_id "Phchi.S3G149900.t1"; gene_id "Phchi.S3G149900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3891.t1 is derived from g1060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6271027	6272753	.	+	.	Phchi.S1G105000
Phchi.S1	AUGUSTUS	transcript	6271027	6272753	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	start_codon	6271027	6271029	.	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6271027	6271050	0.99	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6271027	6271050	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6271051	6271138	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6271139	6271267	0.99	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6271139	6271267	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6271268	6271355	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6271356	6271541	1	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6271356	6271541	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6271542	6271650	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6271651	6271732	1	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6271651	6271732	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6271733	6271819	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6271820	6272041	1	+	2	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6271820	6272041	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6272042	6272132	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6272133	6272233	1	+	2	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6272133	6272233	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6272234	6272325	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6272326	6272397	1	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6272326	6272397	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	intron	6272398	6272483	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	CDS	6272484	6272753	1	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	exon	6272484	6272753	.	+	.	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
Phchi.S1	AUGUSTUS	stop_codon	6272754	6272756	.	+	0	transcript_id "Phchi.S1G105000.t1"; gene_id "Phchi.S1G105000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13793.t1 is derived from g12260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8910229	8911418	.	-	.	Phchi.S3G111200
Phchi.S3	AUGUSTUS	transcript	8910229	8911418	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	stop_codon	8910226	8910228	.	-	0	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	CDS	8910229	8910456	0.94	-	0	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	exon	8910229	8910456	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	intron	8910457	8910560	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	CDS	8910561	8910894	0.96	-	1	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	exon	8910561	8910894	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	intron	8910895	8910990	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	CDS	8910991	8911250	0.75	-	0	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	exon	8910991	8911250	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	intron	8911251	8911337	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	CDS	8911338	8911418	0.93	-	0	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	exon	8911338	8911418	.	-	.	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	start_codon	8911416	8911418	.	-	0	transcript_id "Phchi.S3G111200.t1"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	transcript	8910229	8910905	.	-	.	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	stop_codon	8910226	8910228	.	-	0	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	CDS	8910229	8910456	0.94	-	0	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	exon	8910229	8910456	.	-	.	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	intron	8910457	8910560	.	-	.	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	CDS	8910561	8910905	0.84	-	0	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	exon	8910561	8910905	.	-	.	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
Phchi.S3	AUGUSTUS	start_codon	8910903	8910905	.	-	0	transcript_id "Phchi.S3G111200.t2"; gene_id "Phchi.S3G111200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7912.t1 is derived from g5086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31882618	31883752	.	-	.	Phchi.S1G507100
Phchi.S1	AUGUSTUS	transcript	31882618	31883752	.	-	.	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	stop_codon	31882615	31882617	.	-	0	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	CDS	31882618	31882923	0.97	-	0	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	exon	31882618	31882923	.	-	.	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	intron	31882924	31883010	.	-	.	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	CDS	31883011	31883206	0.94	-	1	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	exon	31883011	31883206	.	-	.	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	intron	31883207	31883285	.	-	.	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	CDS	31883286	31883752	0.98	-	0	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	exon	31883286	31883752	.	-	.	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
Phchi.S1	AUGUSTUS	start_codon	31883750	31883752	.	-	0	transcript_id "Phchi.S1G507100.t1"; gene_id "Phchi.S1G507100"
# This transcript jg2760.t2 is derived from g9680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2761.t1 is derived from g9681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8708287	8712748	.	+	.	Phchi.S5G137000
Phchi.S5	AUGUSTUS	transcript	8708287	8712748	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	start_codon	8708287	8708289	.	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8708287	8708499	0.99	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8708287	8708499	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8708500	8708576	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8708577	8708678	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8708577	8708678	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8708679	8708910	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8708911	8709136	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8708911	8709136	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8709137	8709241	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8709242	8709705	0.96	+	2	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8709242	8709705	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8709706	8709816	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8709817	8709888	0.99	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8709817	8709888	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8709889	8709969	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8709970	8710208	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8709970	8710208	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8710209	8710301	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8710302	8710721	1	+	1	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8710302	8710721	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8710722	8710882	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8710883	8711084	1	+	1	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8710883	8711084	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8711085	8711175	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8711176	8711508	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8711176	8711508	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8711509	8711620	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8711621	8711740	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8711621	8711740	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8711741	8711827	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8711828	8711916	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8711828	8711916	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8711917	8712023	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8712024	8712105	1	+	1	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8712024	8712105	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8712106	8712182	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8712183	8712386	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8712183	8712386	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8712387	8712469	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8712470	8712538	1	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8712470	8712538	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	intron	8712539	8712628	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	CDS	8712629	8712748	0.96	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	exon	8712629	8712748	.	+	.	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
Phchi.S5	AUGUSTUS	stop_codon	8712749	8712751	.	+	0	transcript_id "Phchi.S5G137000.t1"; gene_id "Phchi.S5G137000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5838.t1 is derived from g3008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19202205	19204008	.	-	.	Phchi.S1G299700
Phchi.S1	AUGUSTUS	transcript	19202205	19204008	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	stop_codon	19202202	19202204	.	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19202205	19202252	1	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19202205	19202252	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19202253	19202393	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19202394	19202504	1	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19202394	19202504	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19202505	19202594	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19202595	19202664	1	-	1	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19202595	19202664	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19202665	19202821	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19202822	19202919	1	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19202822	19202919	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19202920	19203000	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19203001	19203048	1	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19203001	19203048	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19203049	19203276	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19203277	19203332	1	-	2	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19203277	19203332	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19203333	19203419	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19203420	19203576	1	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19203420	19203576	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19203577	19203669	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19203670	19203890	1	-	2	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19203670	19203890	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	intron	19203891	19203989	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	CDS	19203990	19204008	0.99	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	exon	19203990	19204008	.	-	.	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
Phchi.S1	AUGUSTUS	start_codon	19204006	19204008	.	-	0	transcript_id "Phchi.S1G299700.t1"; gene_id "Phchi.S1G299700"
# This transcript jg15098.t2 is derived from g13566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15099.t1 is derived from g13567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17062374	17064424	.	-	.	Phchi.S3G241800
Phchi.S3	AUGUSTUS	transcript	17062374	17064424	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	stop_codon	17062371	17062373	.	-	0	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	CDS	17062374	17062523	0.88	-	0	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	exon	17062374	17062523	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	intron	17062524	17062738	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	CDS	17062739	17063080	1	-	0	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	exon	17062739	17063080	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	intron	17063081	17063342	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	CDS	17063343	17063728	0.92	-	2	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	exon	17063343	17063728	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	intron	17063729	17063925	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	CDS	17063926	17064424	1	-	0	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	exon	17063926	17064424	.	-	.	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
Phchi.S3	AUGUSTUS	start_codon	17064422	17064424	.	-	0	transcript_id "Phchi.S3G241800.t1"; gene_id "Phchi.S3G241800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12161.t1 is derived from g7837.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5075721	5077492	.	+	.	Phchi.S2G024100
Phchi.S2	AUGUSTUS	transcript	5075721	5077431	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	start_codon	5075721	5075723	.	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5075721	5075835	0.81	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5075721	5075835	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5075836	5075913	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5075914	5076084	1	+	2	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5075914	5076084	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076085	5076223	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076224	5076276	1	+	2	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076224	5076276	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076277	5076353	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076354	5076410	1	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076354	5076410	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076411	5076531	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076532	5076597	1	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076532	5076597	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076598	5076671	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076672	5076743	1	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076672	5076743	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076744	5076828	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076829	5076944	1	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076829	5076944	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076945	5077037	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5077038	5077129	1	+	1	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5077038	5077129	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5077130	5077218	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5077219	5077283	1	+	2	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5077219	5077283	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5077284	5077428	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5077429	5077431	1	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5077429	5077431	.	+	.	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	stop_codon	5077432	5077434	.	+	0	transcript_id "Phchi.S2G024100.t1"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	transcript	5075721	5077492	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	start_codon	5075721	5075723	.	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5075721	5075835	0.89	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5075721	5075835	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5075836	5075913	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5075914	5076084	1	+	2	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5075914	5076084	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076085	5076223	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076224	5076276	1	+	2	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076224	5076276	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076277	5076353	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076354	5076410	1	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076354	5076410	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076411	5076531	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076532	5076597	1	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076532	5076597	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076598	5076671	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076672	5076743	1	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076672	5076743	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076744	5076828	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5076829	5076944	1	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5076829	5076944	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5076945	5077037	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5077038	5077129	1	+	1	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5077038	5077129	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5077130	5077228	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5077229	5077283	1	+	2	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5077229	5077283	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	intron	5077284	5077428	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	CDS	5077429	5077492	0.8	+	1	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	exon	5077429	5077492	.	+	.	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
Phchi.S2	AUGUSTUS	stop_codon	5077493	5077495	.	+	0	transcript_id "Phchi.S2G024100.t2"; gene_id "Phchi.S2G024100"
# This transcript jg4134.t2 is derived from g1303.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4135.t1 is derived from g1304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8453578	8455488	.	+	.	Phchi.S1G129400
Phchi.S1	AUGUSTUS	transcript	8453578	8455488	.	+	.	transcript_id "Phchi.S1G129400.t1"; gene_id "Phchi.S1G129400"
Phchi.S1	AUGUSTUS	start_codon	8453578	8453580	.	+	0	transcript_id "Phchi.S1G129400.t1"; gene_id "Phchi.S1G129400"
Phchi.S1	AUGUSTUS	CDS	8453578	8455488	0.6	+	0	transcript_id "Phchi.S1G129400.t1"; gene_id "Phchi.S1G129400"
Phchi.S1	AUGUSTUS	exon	8453578	8455488	.	+	.	transcript_id "Phchi.S1G129400.t1"; gene_id "Phchi.S1G129400"
Phchi.S1	AUGUSTUS	stop_codon	8455489	8455491	.	+	0	transcript_id "Phchi.S1G129400.t1"; gene_id "Phchi.S1G129400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12201.t1 is derived from g7877.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6716413	6717832	.	+	.	Phchi.S2G028100
Phchi.S2	AUGUSTUS	transcript	6716413	6717832	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	start_codon	6716413	6716415	.	+	0	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6716413	6716738	0.66	+	0	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6716413	6716738	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	intron	6716739	6716965	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6716966	6717188	1	+	1	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6716966	6717188	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	intron	6717189	6717304	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6717305	6717404	1	+	0	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6717305	6717404	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	intron	6717405	6717563	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6717564	6717832	1	+	2	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6717564	6717832	.	+	.	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	stop_codon	6717833	6717835	.	+	0	transcript_id "Phchi.S2G028100.t1"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	transcript	6716413	6717832	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	start_codon	6716413	6716415	.	+	0	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6716413	6716738	0.66	+	0	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6716413	6716738	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	intron	6716739	6716965	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6716966	6717188	1	+	1	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6716966	6717188	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	intron	6717189	6717304	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6717305	6717404	1	+	0	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6717305	6717404	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	intron	6717405	6717566	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	CDS	6717567	6717832	0.99	+	2	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	exon	6717567	6717832	.	+	.	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
Phchi.S2	AUGUSTUS	stop_codon	6717833	6717835	.	+	0	transcript_id "Phchi.S2G028100.t2"; gene_id "Phchi.S2G028100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14175.t1 is derived from g12642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11278343	11279184	.	-	.	Phchi.S3G149400
Phchi.S3	AUGUSTUS	transcript	11278343	11279184	.	-	.	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	stop_codon	11278340	11278342	.	-	0	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	CDS	11278343	11278576	0.17	-	0	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	exon	11278343	11278576	.	-	.	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	intron	11278577	11278659	.	-	.	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	CDS	11278660	11278782	1	-	0	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	exon	11278660	11278782	.	-	.	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	intron	11278783	11278890	.	-	.	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	CDS	11278891	11279184	0.92	-	0	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	exon	11278891	11279184	.	-	.	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
Phchi.S3	AUGUSTUS	start_codon	11279182	11279184	.	-	0	transcript_id "Phchi.S3G149400.t1"; gene_id "Phchi.S3G149400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11191.t1 is derived from g15241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4561891	4563366	.	+	.	Phchi.S4G077300
Phchi.S4	AUGUSTUS	transcript	4561891	4563366	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	start_codon	4561891	4561893	.	+	0	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	CDS	4561891	4561978	0.98	+	0	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	exon	4561891	4561978	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	intron	4561979	4562081	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	CDS	4562082	4562267	1	+	2	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	exon	4562082	4562267	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	intron	4562268	4562346	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	CDS	4562347	4562618	1	+	2	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	exon	4562347	4562618	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	intron	4562619	4562713	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	CDS	4562714	4563014	0.96	+	0	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	exon	4562714	4563014	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	intron	4563015	4563142	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	CDS	4563143	4563366	0.97	+	2	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	exon	4563143	4563366	.	+	.	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
Phchi.S4	AUGUSTUS	stop_codon	4563367	4563369	.	+	0	transcript_id "Phchi.S4G077300.t1"; gene_id "Phchi.S4G077300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3178.t1 is derived from g347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2116124	2117480	.	+	.	Phchi.S1G033700
Phchi.S1	AUGUSTUS	transcript	2116124	2117480	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	start_codon	2116124	2116126	.	+	0	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	CDS	2116124	2116202	0.97	+	0	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	exon	2116124	2116202	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	intron	2116203	2116384	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	CDS	2116385	2116570	1	+	2	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	exon	2116385	2116570	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	intron	2116571	2116705	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	CDS	2116706	2116864	0.77	+	2	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	exon	2116706	2116864	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	intron	2116865	2116969	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	CDS	2116970	2117170	0.79	+	2	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	exon	2116970	2117170	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	intron	2117171	2117271	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	CDS	2117272	2117480	0.98	+	2	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	exon	2117272	2117480	.	+	.	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
Phchi.S1	AUGUSTUS	stop_codon	2117481	2117483	.	+	0	transcript_id "Phchi.S1G033700.t1"; gene_id "Phchi.S1G033700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10659.t1 is derived from g14709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1460666	1460956	.	-	.	Phchi.S4G024100
Phchi.S4	AUGUSTUS	transcript	1460666	1460956	.	-	.	transcript_id "Phchi.S4G024100.t1"; gene_id "Phchi.S4G024100"
Phchi.S4	AUGUSTUS	stop_codon	1460663	1460665	.	-	0	transcript_id "Phchi.S4G024100.t1"; gene_id "Phchi.S4G024100"
Phchi.S4	AUGUSTUS	CDS	1460666	1460956	0.46	-	0	transcript_id "Phchi.S4G024100.t1"; gene_id "Phchi.S4G024100"
Phchi.S4	AUGUSTUS	exon	1460666	1460956	.	-	.	transcript_id "Phchi.S4G024100.t1"; gene_id "Phchi.S4G024100"
Phchi.S4	AUGUSTUS	start_codon	1460954	1460956	.	-	0	transcript_id "Phchi.S4G024100.t1"; gene_id "Phchi.S4G024100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11760.t1 is derived from g15812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8039089	8040371	.	+	.	Phchi.S4G134200
Phchi.S4	AUGUSTUS	transcript	8039089	8040371	.	+	.	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	start_codon	8039089	8039091	.	+	0	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	CDS	8039089	8039743	0.58	+	0	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	exon	8039089	8039743	.	+	.	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	intron	8039744	8039814	.	+	.	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	CDS	8039815	8040371	0.75	+	2	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	exon	8039815	8040371	.	+	.	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
Phchi.S4	AUGUSTUS	stop_codon	8040372	8040374	.	+	0	transcript_id "Phchi.S4G134200.t1"; gene_id "Phchi.S4G134200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14428.t1 is derived from g12896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12760716	12762184	.	+	.	Phchi.S3G174700
Phchi.S3	AUGUSTUS	transcript	12760716	12762184	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	start_codon	12760716	12760718	.	+	0	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	CDS	12760716	12760859	0.89	+	0	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	exon	12760716	12760859	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	intron	12760860	12760949	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	CDS	12760950	12761191	1	+	0	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	exon	12760950	12761191	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	intron	12761192	12761318	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	CDS	12761319	12761474	1	+	1	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	exon	12761319	12761474	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	intron	12761475	12761566	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	CDS	12761567	12761752	1	+	1	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	exon	12761567	12761752	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	intron	12761753	12761897	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	CDS	12761898	12762079	1	+	1	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	exon	12761898	12762079	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	intron	12762080	12762158	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	CDS	12762159	12762184	1	+	2	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	exon	12762159	12762184	.	+	.	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
Phchi.S3	AUGUSTUS	stop_codon	12762185	12762187	.	+	0	transcript_id "Phchi.S3G174700.t1"; gene_id "Phchi.S3G174700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14139.t1 is derived from g12606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11106957	11107507	.	+	.	Phchi.S3G145800
Phchi.S3	AUGUSTUS	transcript	11106957	11107507	.	+	.	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	start_codon	11106957	11106959	.	+	0	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	CDS	11106957	11107052	0.57	+	0	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	exon	11106957	11107052	.	+	.	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	intron	11107053	11107132	.	+	.	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	CDS	11107133	11107237	1	+	0	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	exon	11107133	11107237	.	+	.	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	intron	11107238	11107330	.	+	.	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	CDS	11107331	11107507	0.99	+	0	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	exon	11107331	11107507	.	+	.	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
Phchi.S3	AUGUSTUS	stop_codon	11107508	11107510	.	+	0	transcript_id "Phchi.S3G145800.t1"; gene_id "Phchi.S3G145800"
# This transcript jg8730.t2 is derived from g5905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8731.t1 is derived from g5906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37708155	37710597	.	+	.	Phchi.S1G589000
Phchi.S1	AUGUSTUS	transcript	37708155	37710597	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	start_codon	37708155	37708157	.	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37708155	37708277	0.92	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37708155	37708277	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	intron	37708278	37708372	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37708373	37708471	1	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37708373	37708471	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	intron	37708472	37708643	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37708644	37708765	1	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37708644	37708765	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	intron	37708766	37708895	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37708896	37709013	1	+	1	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37708896	37709013	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	intron	37709014	37709091	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37709092	37709271	0.76	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37709092	37709271	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	intron	37709272	37709493	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37709494	37709594	0.73	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37709494	37709594	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	intron	37709595	37709807	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	CDS	37709808	37710597	1	+	1	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	exon	37709808	37710597	.	+	.	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
Phchi.S1	AUGUSTUS	stop_codon	37710598	37710600	.	+	0	transcript_id "Phchi.S1G589000.t1"; gene_id "Phchi.S1G589000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8147.t1 is derived from g5322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34068540	34069011	.	-	.	Phchi.S1G530600
Phchi.S1	AUGUSTUS	transcript	34068540	34069011	.	-	.	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	stop_codon	34068537	34068539	.	-	0	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	CDS	34068540	34068817	0.96	-	2	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	exon	34068540	34068817	.	-	.	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	intron	34068818	34068893	.	-	.	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	CDS	34068894	34069011	0.96	-	0	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	exon	34068894	34069011	.	-	.	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
Phchi.S1	AUGUSTUS	start_codon	34069009	34069011	.	-	0	transcript_id "Phchi.S1G530600.t1"; gene_id "Phchi.S1G530600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6406.t1 is derived from g3578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22810013	22811548	.	-	.	Phchi.S1G356500
Phchi.S1	AUGUSTUS	transcript	22810013	22811548	.	-	.	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	stop_codon	22810010	22810012	.	-	0	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	CDS	22810013	22810116	0.86	-	2	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	exon	22810013	22810116	.	-	.	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	intron	22810117	22810350	.	-	.	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	CDS	22810351	22810545	0.95	-	2	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	exon	22810351	22810545	.	-	.	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	intron	22810546	22810980	.	-	.	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	CDS	22810981	22811548	0.29	-	0	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	exon	22810981	22811548	.	-	.	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
Phchi.S1	AUGUSTUS	start_codon	22811546	22811548	.	-	0	transcript_id "Phchi.S1G356500.t1"; gene_id "Phchi.S1G356500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1465.t1 is derived from g8384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1072359	1078673	.	-	.	Phchi.S5G007400
Phchi.S5	AUGUSTUS	transcript	1072359	1078673	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	stop_codon	1072356	1072358	.	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072359	1072439	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072359	1072439	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072440	1072521	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072522	1072584	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072522	1072584	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072585	1072662	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072663	1072758	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072663	1072758	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072759	1072839	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072840	1072963	1	-	1	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072840	1072963	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072964	1073046	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073047	1073159	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073047	1073159	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073160	1073255	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073256	1073420	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073256	1073420	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073421	1073493	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073494	1073649	0.89	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073494	1073649	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073650	1073756	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073757	1073873	0.99	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073757	1073873	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073874	1074020	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074021	1074200	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074021	1074200	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074201	1074285	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074286	1074445	1	-	1	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074286	1074445	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074446	1074518	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074519	1074655	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074519	1074655	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074656	1074762	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074763	1074838	0.97	-	1	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074763	1074838	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074839	1074938	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074939	1075046	1	-	1	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074939	1075046	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075047	1075190	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075191	1075270	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075191	1075270	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075271	1075379	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075380	1075481	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075380	1075481	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075482	1075598	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075599	1075666	1	-	2	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075599	1075666	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075667	1075808	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075809	1075903	1	-	1	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075809	1075903	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075904	1076039	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076040	1076119	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076040	1076119	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076120	1076293	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076294	1076425	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076294	1076425	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076426	1076511	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076512	1076661	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076512	1076661	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076662	1076809	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076810	1076932	0.97	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076810	1076932	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076933	1077035	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077036	1077104	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077036	1077104	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077105	1077273	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077274	1077429	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077274	1077429	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077430	1077520	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077521	1077618	1	-	2	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077521	1077618	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077619	1077712	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077713	1077881	1	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077713	1077881	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077882	1078025	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1078026	1078673	0.41	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1078026	1078673	.	-	.	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	start_codon	1078671	1078673	.	-	0	transcript_id "Phchi.S5G007400.t1"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	transcript	1072359	1078673	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	stop_codon	1072356	1072358	.	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072359	1072439	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072359	1072439	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072440	1072521	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072522	1072584	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072522	1072584	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072585	1072662	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072663	1072758	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072663	1072758	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072759	1072839	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1072840	1072963	1	-	1	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1072840	1072963	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1072964	1073046	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073047	1073159	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073047	1073159	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073160	1073255	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073256	1073420	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073256	1073420	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073421	1073493	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073494	1073649	0.93	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073494	1073649	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073650	1073756	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1073757	1073873	0.97	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1073757	1073873	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1073874	1074020	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074021	1074200	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074021	1074200	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074201	1074285	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074286	1074435	0.96	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074286	1074435	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074436	1074518	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074519	1074563	0.57	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074519	1074563	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074564	1074762	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074763	1074838	0.6	-	1	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074763	1074838	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1074839	1074938	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1074939	1075046	1	-	1	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1074939	1075046	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075047	1075190	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075191	1075270	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075191	1075270	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075271	1075379	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075380	1075481	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075380	1075481	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075482	1075598	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075599	1075666	1	-	2	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075599	1075666	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075667	1075808	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1075809	1075903	1	-	1	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1075809	1075903	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1075904	1076039	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076040	1076119	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076040	1076119	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076120	1076293	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076294	1076425	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076294	1076425	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076426	1076511	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076512	1076661	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076512	1076661	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076662	1076809	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1076810	1076932	0.95	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1076810	1076932	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1076933	1077035	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077036	1077104	0.99	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077036	1077104	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077105	1077273	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077274	1077429	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077274	1077429	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077430	1077520	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077521	1077618	1	-	2	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077521	1077618	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077619	1077712	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1077713	1077881	1	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1077713	1077881	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	intron	1077882	1078025	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	CDS	1078026	1078673	0.4	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	exon	1078026	1078673	.	-	.	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
Phchi.S5	AUGUSTUS	start_codon	1078671	1078673	.	-	0	transcript_id "Phchi.S5G007400.t2"; gene_id "Phchi.S5G007400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8101.t1 is derived from g5276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33054440	33058519	.	-	.	Phchi.S1G526000
Phchi.S1	AUGUSTUS	transcript	33054440	33058519	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	stop_codon	33054437	33054439	.	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33054440	33054483	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33054440	33054483	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33054484	33054556	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33054557	33054703	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33054557	33054703	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33054704	33054784	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33054785	33054832	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33054785	33054832	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33054833	33054906	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33054907	33055016	1	-	1	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33054907	33055016	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33055017	33055092	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33055093	33055160	1	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33055093	33055160	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33055161	33055282	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33055283	33055413	0.99	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33055283	33055413	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33055414	33055508	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33055509	33055590	0.99	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33055509	33055590	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33055591	33055669	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33055670	33055736	1	-	1	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33055670	33055736	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33055737	33055859	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33055860	33055932	0.61	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33055860	33055932	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33055933	33056033	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33056034	33056150	0.99	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33056034	33056150	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33056151	33056271	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33056272	33056364	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33056272	33056364	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33056365	33056517	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33056518	33056583	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33056518	33056583	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33056584	33056746	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33056747	33056840	1	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33056747	33056840	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33056841	33057010	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33057011	33057114	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33057011	33057114	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33057115	33057201	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33057202	33057376	1	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33057202	33057376	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33057377	33057538	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33057539	33057605	1	-	1	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33057539	33057605	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33057606	33057731	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33057732	33057870	1	-	2	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33057732	33057870	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33057871	33057982	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33057983	33058079	1	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33057983	33058079	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33058080	33058164	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33058165	33058267	1	-	1	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33058165	33058267	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	intron	33058268	33058358	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	CDS	33058359	33058519	1	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	exon	33058359	33058519	.	-	.	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
Phchi.S1	AUGUSTUS	start_codon	33058517	33058519	.	-	0	transcript_id "Phchi.S1G526000.t1"; gene_id "Phchi.S1G526000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg544.t1 is derived from g10326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3992470	3993891	.	-	.	Phchi.S6G050300
Phchi.S6	AUGUSTUS	transcript	3992470	3993891	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	stop_codon	3992467	3992469	.	-	0	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3992470	3992511	1	-	0	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3992470	3992511	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	intron	3992512	3992606	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3992607	3992895	1	-	1	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3992607	3992895	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	intron	3992896	3992978	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3992979	3993104	1	-	1	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3992979	3993104	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	intron	3993105	3993211	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3993212	3993301	1	-	1	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3993212	3993301	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	intron	3993302	3993373	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3993374	3993452	1	-	2	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3993374	3993452	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	intron	3993453	3993536	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3993537	3993625	1	-	1	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3993537	3993625	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	intron	3993626	3993697	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	CDS	3993698	3993891	1	-	0	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	exon	3993698	3993891	.	-	.	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
Phchi.S6	AUGUSTUS	start_codon	3993889	3993891	.	-	0	transcript_id "Phchi.S6G050300.t1"; gene_id "Phchi.S6G050300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3252.t1 is derived from g421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2518577	2520275	.	-	.	Phchi.S1G041100
Phchi.S1	AUGUSTUS	transcript	2518577	2520275	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	stop_codon	2518574	2518576	.	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	CDS	2518577	2519089	0.87	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	exon	2518577	2519089	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	intron	2519090	2519186	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	CDS	2519187	2519312	1	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	exon	2519187	2519312	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	intron	2519313	2519384	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	CDS	2519385	2519573	1	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	exon	2519385	2519573	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	intron	2519574	2519693	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	CDS	2519694	2519804	1	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	exon	2519694	2519804	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	intron	2519805	2519981	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	CDS	2519982	2520275	0.99	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	exon	2519982	2520275	.	-	.	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
Phchi.S1	AUGUSTUS	start_codon	2520273	2520275	.	-	0	transcript_id "Phchi.S1G041100.t1"; gene_id "Phchi.S1G041100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15986.t1 is derived from g9775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C16	AUGUSTUS	gene	68797	69717	.	-	.	Phchi.C16G000400
Phchi.C16	AUGUSTUS	transcript	68797	69717	.	-	.	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	stop_codon	68794	68796	.	-	0	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	CDS	68797	68926	0.77	-	1	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	exon	68797	68926	.	-	.	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	intron	68927	69355	.	-	.	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	CDS	69356	69717	0.77	-	0	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	exon	69356	69717	.	-	.	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
Phchi.C16	AUGUSTUS	start_codon	69715	69717	.	-	0	transcript_id "Phchi.C16G000400.t1"; gene_id "Phchi.C16G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15380.t1 is derived from g13848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18720896	18722597	.	-	.	Phchi.S3G269900
Phchi.S3	AUGUSTUS	transcript	18720896	18722597	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	stop_codon	18720893	18720895	.	-	0	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18720896	18720965	0.99	-	1	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18720896	18720965	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18720966	18721054	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18721055	18721176	1	-	0	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18721055	18721176	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18721177	18721269	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18721270	18721279	0.76	-	1	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18721270	18721279	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18721280	18721347	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18721348	18721388	0.76	-	0	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18721348	18721388	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18721389	18721488	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18721489	18721611	0.96	-	0	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18721489	18721611	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18721612	18721696	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18721697	18721824	0.55	-	2	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18721697	18721824	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18721825	18722167	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18722168	18722281	0.76	-	2	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18722168	18722281	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	intron	18722282	18722488	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	CDS	18722489	18722597	0.54	-	0	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	exon	18722489	18722597	.	-	.	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
Phchi.S3	AUGUSTUS	start_codon	18722595	18722597	.	-	0	transcript_id "Phchi.S3G269900.t1"; gene_id "Phchi.S3G269900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11719.t1 is derived from g15771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7835019	7835366	.	+	.	Phchi.S4G130100
Phchi.S4	AUGUSTUS	transcript	7835019	7835366	.	+	.	transcript_id "Phchi.S4G130100.t1"; gene_id "Phchi.S4G130100"
Phchi.S4	AUGUSTUS	start_codon	7835019	7835021	.	+	0	transcript_id "Phchi.S4G130100.t1"; gene_id "Phchi.S4G130100"
Phchi.S4	AUGUSTUS	CDS	7835019	7835366	0.82	+	0	transcript_id "Phchi.S4G130100.t1"; gene_id "Phchi.S4G130100"
Phchi.S4	AUGUSTUS	exon	7835019	7835366	.	+	.	transcript_id "Phchi.S4G130100.t1"; gene_id "Phchi.S4G130100"
Phchi.S4	AUGUSTUS	stop_codon	7835367	7835369	.	+	0	transcript_id "Phchi.S4G130100.t1"; gene_id "Phchi.S4G130100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4253.t1 is derived from g1422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9177028	9177468	.	-	.	Phchi.S1G141200
Phchi.S1	AUGUSTUS	transcript	9177028	9177468	.	-	.	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	stop_codon	9177025	9177027	.	-	0	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	CDS	9177028	9177140	0.96	-	2	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	exon	9177028	9177140	.	-	.	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	intron	9177141	9177332	.	-	.	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	CDS	9177333	9177468	0.41	-	0	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	exon	9177333	9177468	.	-	.	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
Phchi.S1	AUGUSTUS	start_codon	9177466	9177468	.	-	0	transcript_id "Phchi.S1G141200.t1"; gene_id "Phchi.S1G141200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9653.t1 is derived from g6829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43066203	43068630	.	-	.	Phchi.S1G681200
Phchi.S1	AUGUSTUS	transcript	43066282	43068630	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	stop_codon	43066279	43066281	.	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066282	43066365	0.95	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066282	43066365	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066366	43066454	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066455	43066558	0.93	-	2	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066455	43066558	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066559	43066650	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066651	43066777	0.93	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066651	43066777	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066778	43066863	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066864	43067037	0.95	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066864	43067037	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067038	43067264	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067265	43067377	1	-	2	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067265	43067377	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067378	43067524	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067525	43067595	0.77	-	1	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067525	43067595	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067596	43067724	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067725	43067903	0.82	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067725	43067903	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067904	43068021	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43068022	43068108	1	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43068022	43068108	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43068109	43068273	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43068274	43068403	1	-	1	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43068274	43068403	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43068404	43068496	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43068497	43068630	0.98	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43068497	43068630	.	-	.	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	start_codon	43068628	43068630	.	-	0	transcript_id "Phchi.S1G681200.t1"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	transcript	43066203	43068630	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	stop_codon	43066200	43066202	.	-	0	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066203	43066365	0.59	-	1	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066203	43066365	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066366	43066454	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066455	43066547	0.38	-	1	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066455	43066547	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066548	43066650	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066651	43066777	0.34	-	2	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066651	43066777	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066778	43066863	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43066864	43066884	0.37	-	2	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43066864	43066884	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43066885	43067012	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067013	43067037	0.42	-	0	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067013	43067037	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067038	43067264	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067265	43067377	1	-	2	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067265	43067377	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067378	43067524	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067525	43067595	0.74	-	1	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067525	43067595	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067596	43067724	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43067725	43067903	0.76	-	0	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43067725	43067903	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43067904	43068021	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43068022	43068108	1	-	0	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43068022	43068108	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43068109	43068273	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43068274	43068403	1	-	1	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43068274	43068403	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	intron	43068404	43068496	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	CDS	43068497	43068630	0.99	-	0	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	exon	43068497	43068630	.	-	.	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
Phchi.S1	AUGUSTUS	start_codon	43068628	43068630	.	-	0	transcript_id "Phchi.S1G681200.t2"; gene_id "Phchi.S1G681200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6626.t1 is derived from g3798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24148324	24159443	.	+	.	Phchi.S1G378500
Phchi.S1	AUGUSTUS	transcript	24148324	24159443	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	start_codon	24148324	24148326	.	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24148324	24148366	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24148324	24148366	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24148367	24148451	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24148452	24148542	1	+	2	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24148452	24148542	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24148543	24148623	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24148624	24148678	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24148624	24148678	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24148679	24148852	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24148853	24148996	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24148853	24148996	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24148997	24149084	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24149085	24149156	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24149085	24149156	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24149157	24149291	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24149292	24149382	0.94	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24149292	24149382	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24149383	24149513	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24149514	24149582	0.5	+	2	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24149514	24149582	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24149583	24149750	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24149751	24149829	1	+	2	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24149751	24149829	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24149830	24149921	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24149922	24149985	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24149922	24149985	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24149986	24150133	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24150134	24150237	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24150134	24150237	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24150238	24150332	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24150333	24150438	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24150333	24150438	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24150439	24150567	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24150568	24150657	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24150568	24150657	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24150658	24150753	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24150754	24150831	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24150754	24150831	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24150832	24150967	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24150968	24151035	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24150968	24151035	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24151036	24151113	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24151114	24151213	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24151114	24151213	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24151214	24151291	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24151292	24151468	0.89	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24151292	24151468	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24151469	24151579	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24151580	24151669	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24151580	24151669	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24151670	24151775	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24151776	24151841	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24151776	24151841	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24151842	24151918	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24151919	24152017	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24151919	24152017	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24152018	24152182	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24152183	24152257	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24152183	24152257	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24152258	24152343	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24152344	24152403	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24152344	24152403	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24152404	24152501	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24152502	24152591	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24152502	24152591	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24152592	24152822	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24152823	24152944	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24152823	24152944	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24152945	24153032	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24153033	24153162	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24153033	24153162	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24153163	24153284	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24153285	24153364	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24153285	24153364	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24153365	24153449	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24153450	24153585	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24153450	24153585	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24153586	24153777	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24153778	24153859	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24153778	24153859	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24153860	24153950	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24153951	24154108	1	+	2	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24153951	24154108	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24154109	24154256	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24154257	24154337	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24154257	24154337	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24154338	24154427	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24154428	24154528	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24154428	24154528	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24154529	24154663	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24154664	24154893	0.98	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24154664	24154893	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24154894	24154990	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24154991	24155100	1	+	2	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24154991	24155100	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24155101	24155213	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24155214	24155339	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24155214	24155339	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24155340	24155418	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24155419	24155493	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24155419	24155493	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24155494	24155671	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24155672	24155805	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24155672	24155805	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24155806	24155892	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24155893	24155965	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24155893	24155965	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24155966	24156157	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24156158	24156289	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24156158	24156289	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24156290	24156415	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24156416	24156600	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24156416	24156600	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24156601	24156687	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24156688	24156807	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24156688	24156807	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24156808	24156937	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24156938	24156998	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24156938	24156998	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24156999	24157125	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24157126	24157224	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24157126	24157224	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24157225	24157316	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24157317	24157417	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24157317	24157417	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24157418	24157712	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24157713	24157818	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24157713	24157818	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24157819	24157958	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24157959	24158072	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24157959	24158072	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24158073	24158170	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24158171	24158245	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24158171	24158245	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24158246	24158392	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24158393	24158491	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24158393	24158491	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24158492	24158578	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24158579	24158650	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24158579	24158650	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24158651	24158738	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24158739	24158824	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24158739	24158824	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24158825	24158903	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24158904	24158997	1	+	1	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24158904	24158997	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24158998	24159144	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24159145	24159252	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24159145	24159252	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	intron	24159253	24159332	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	CDS	24159333	24159443	1	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	exon	24159333	24159443	.	+	.	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
Phchi.S1	AUGUSTUS	stop_codon	24159444	24159446	.	+	0	transcript_id "Phchi.S1G378500.t1"; gene_id "Phchi.S1G378500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13595.t1 is derived from g12062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7626906	7627773	.	+	.	Phchi.S3G091400
Phchi.S3	AUGUSTUS	transcript	7626906	7627773	.	+	.	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	start_codon	7626906	7626908	.	+	0	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	CDS	7626906	7627085	1	+	0	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	exon	7626906	7627085	.	+	.	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	intron	7627086	7627189	.	+	.	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	CDS	7627190	7627287	1	+	0	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	exon	7627190	7627287	.	+	.	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	intron	7627288	7627358	.	+	.	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	CDS	7627359	7627773	1	+	1	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	exon	7627359	7627773	.	+	.	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
Phchi.S3	AUGUSTUS	stop_codon	7627774	7627776	.	+	0	transcript_id "Phchi.S3G091400.t1"; gene_id "Phchi.S3G091400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1054.t1 is derived from g10837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7314506	7317847	.	+	.	Phchi.S6G101300
Phchi.S6	AUGUSTUS	transcript	7314506	7317847	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	start_codon	7314506	7314508	.	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7314506	7314589	0.38	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7314506	7314589	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7314590	7314661	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7314662	7314721	0.92	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7314662	7314721	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7314722	7314797	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7314798	7314914	0.99	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7314798	7314914	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7314915	7315040	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7315041	7315052	0.98	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7315041	7315052	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7315053	7315138	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7315139	7315333	0.97	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7315139	7315333	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7315334	7315427	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7315428	7315496	1	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7315428	7315496	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7315497	7315666	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7315667	7315765	1	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7315667	7315765	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7315766	7315939	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7315940	7316034	1	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7315940	7316034	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7316035	7316161	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7316162	7316282	1	+	1	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7316162	7316282	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7316283	7316448	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7316449	7316528	1	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7316449	7316528	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7316529	7316645	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7316646	7316708	1	+	1	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7316646	7316708	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7316709	7316807	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7316808	7316926	1	+	1	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7316808	7316926	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7316927	7317213	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7317214	7317299	1	+	2	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7317214	7317299	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7317300	7317465	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7317466	7317587	1	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7317466	7317587	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	intron	7317588	7317717	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	CDS	7317718	7317847	0.79	+	1	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	exon	7317718	7317847	.	+	.	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
Phchi.S6	AUGUSTUS	stop_codon	7317848	7317850	.	+	0	transcript_id "Phchi.S6G101300.t1"; gene_id "Phchi.S6G101300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11388.t1 is derived from g15438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6081132	6083328	.	-	.	Phchi.S4G097000
Phchi.S4	AUGUSTUS	transcript	6081132	6083328	.	-	.	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	stop_codon	6081129	6081131	.	-	0	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	CDS	6081132	6082612	0.99	-	2	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	exon	6081132	6082612	.	-	.	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	intron	6082613	6082817	.	-	.	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	CDS	6082818	6082853	0.86	-	2	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	exon	6082818	6082853	.	-	.	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	intron	6082854	6083063	.	-	.	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	CDS	6083064	6083328	1	-	0	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	exon	6083064	6083328	.	-	.	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
Phchi.S4	AUGUSTUS	start_codon	6083326	6083328	.	-	0	transcript_id "Phchi.S4G097000.t1"; gene_id "Phchi.S4G097000"
# This transcript jg7796.t2 is derived from g4970.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7797.t1 is derived from g4971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31207897	31208461	.	+	.	Phchi.S1G495600
Phchi.S1	AUGUSTUS	transcript	31207897	31208461	.	+	.	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	start_codon	31207897	31207899	.	+	0	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	CDS	31207897	31208164	0.62	+	0	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	exon	31207897	31208164	.	+	.	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	intron	31208165	31208258	.	+	.	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	CDS	31208259	31208461	0.92	+	2	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	exon	31208259	31208461	.	+	.	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
Phchi.S1	AUGUSTUS	stop_codon	31208462	31208464	.	+	0	transcript_id "Phchi.S1G495600.t1"; gene_id "Phchi.S1G495600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4563.t1 is derived from g1733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11128084	11128797	.	-	.	Phchi.S1G172200
Phchi.S1	AUGUSTUS	transcript	11128084	11128797	.	-	.	transcript_id "Phchi.S1G172200.t1"; gene_id "Phchi.S1G172200"
Phchi.S1	AUGUSTUS	stop_codon	11128081	11128083	.	-	0	transcript_id "Phchi.S1G172200.t1"; gene_id "Phchi.S1G172200"
Phchi.S1	AUGUSTUS	CDS	11128084	11128797	0.74	-	0	transcript_id "Phchi.S1G172200.t1"; gene_id "Phchi.S1G172200"
Phchi.S1	AUGUSTUS	exon	11128084	11128797	.	-	.	transcript_id "Phchi.S1G172200.t1"; gene_id "Phchi.S1G172200"
Phchi.S1	AUGUSTUS	start_codon	11128795	11128797	.	-	0	transcript_id "Phchi.S1G172200.t1"; gene_id "Phchi.S1G172200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12555.t1 is derived from g8232.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34744118	34745112	.	+	.	Phchi.S2G063500
Phchi.S2	AUGUSTUS	transcript	34744409	34745112	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	start_codon	34744409	34744411	.	+	0	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744409	34744489	0.99	+	0	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744409	34744489	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744490	34744569	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744570	34744674	0.99	+	0	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744570	34744674	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744675	34744941	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744942	34744956	1	+	0	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744942	34744956	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744957	34745049	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34745050	34745112	1	+	0	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34745050	34745112	.	+	.	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	stop_codon	34745113	34745115	.	+	0	transcript_id "Phchi.S2G063500.t1"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	transcript	34744118	34745112	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	start_codon	34744118	34744120	.	+	0	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744118	34744248	0.6	+	0	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744118	34744248	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744249	34744569	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744570	34744674	1	+	1	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744570	34744674	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744675	34744768	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744769	34744844	1	+	1	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744769	34744844	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744845	34744941	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34744942	34744956	1	+	0	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34744942	34744956	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	intron	34744957	34745049	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	CDS	34745050	34745112	0.99	+	0	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	exon	34745050	34745112	.	+	.	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
Phchi.S2	AUGUSTUS	stop_codon	34745113	34745115	.	+	0	transcript_id "Phchi.S2G063500.t2"; gene_id "Phchi.S2G063500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13108.t1 is derived from g11573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4182519	4183358	.	-	.	Phchi.S3G042700
Phchi.S3	AUGUSTUS	transcript	4182519	4183358	.	-	.	transcript_id "Phchi.S3G042700.t1"; gene_id "Phchi.S3G042700"
Phchi.S3	AUGUSTUS	stop_codon	4182516	4182518	.	-	0	transcript_id "Phchi.S3G042700.t1"; gene_id "Phchi.S3G042700"
Phchi.S3	AUGUSTUS	CDS	4182519	4183358	0.55	-	0	transcript_id "Phchi.S3G042700.t1"; gene_id "Phchi.S3G042700"
Phchi.S3	AUGUSTUS	exon	4182519	4183358	.	-	.	transcript_id "Phchi.S3G042700.t1"; gene_id "Phchi.S3G042700"
Phchi.S3	AUGUSTUS	start_codon	4183356	4183358	.	-	0	transcript_id "Phchi.S3G042700.t1"; gene_id "Phchi.S3G042700"
# This transcript jg7423.t2 is derived from g4595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7424.t1 is derived from g4596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29074452	29074763	.	+	.	Phchi.S1G458300
Phchi.S1	AUGUSTUS	transcript	29074452	29074763	.	+	.	transcript_id "Phchi.S1G458300.t1"; gene_id "Phchi.S1G458300"
Phchi.S1	AUGUSTUS	start_codon	29074452	29074454	.	+	0	transcript_id "Phchi.S1G458300.t1"; gene_id "Phchi.S1G458300"
Phchi.S1	AUGUSTUS	CDS	29074452	29074763	0.91	+	0	transcript_id "Phchi.S1G458300.t1"; gene_id "Phchi.S1G458300"
Phchi.S1	AUGUSTUS	exon	29074452	29074763	.	+	.	transcript_id "Phchi.S1G458300.t1"; gene_id "Phchi.S1G458300"
Phchi.S1	AUGUSTUS	stop_codon	29074764	29074766	.	+	0	transcript_id "Phchi.S1G458300.t1"; gene_id "Phchi.S1G458300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7237.t1 is derived from g4409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27791607	27793220	.	+	.	Phchi.S1G439600
Phchi.S1	AUGUSTUS	transcript	27791607	27793220	.	+	.	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	start_codon	27791607	27791609	.	+	0	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	CDS	27791607	27792344	0.99	+	0	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	exon	27791607	27792344	.	+	.	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	intron	27792345	27792471	.	+	.	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	CDS	27792472	27792747	1	+	0	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	exon	27792472	27792747	.	+	.	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	intron	27792748	27792836	.	+	.	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	CDS	27792837	27793220	1	+	0	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	exon	27792837	27793220	.	+	.	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
Phchi.S1	AUGUSTUS	stop_codon	27793221	27793223	.	+	0	transcript_id "Phchi.S1G439600.t1"; gene_id "Phchi.S1G439600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5368.t1 is derived from g2538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16530587	16531189	.	+	.	Phchi.S1G252700
Phchi.S1	AUGUSTUS	transcript	16530587	16531189	.	+	.	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	start_codon	16530587	16530589	.	+	0	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	CDS	16530587	16530832	0.57	+	0	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	exon	16530587	16530832	.	+	.	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	intron	16530833	16530931	.	+	.	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	CDS	16530932	16531189	0.98	+	0	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	exon	16530932	16531189	.	+	.	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
Phchi.S1	AUGUSTUS	stop_codon	16531190	16531192	.	+	0	transcript_id "Phchi.S1G252700.t1"; gene_id "Phchi.S1G252700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7068.t1 is derived from g4240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26708302	26710331	.	-	.	Phchi.S1G422700
Phchi.S1	AUGUSTUS	transcript	26708302	26710331	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	stop_codon	26708299	26708301	.	-	0	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	CDS	26708302	26708887	0.96	-	1	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	exon	26708302	26708887	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	intron	26708888	26709003	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	CDS	26709004	26709315	0.97	-	1	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	exon	26709004	26709315	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	intron	26709316	26709398	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	CDS	26709399	26709618	0.96	-	2	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	exon	26709399	26709618	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	intron	26709619	26709712	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	CDS	26709713	26710331	0.64	-	0	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	exon	26709713	26710331	.	-	.	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
Phchi.S1	AUGUSTUS	start_codon	26710329	26710331	.	-	0	transcript_id "Phchi.S1G422700.t1"; gene_id "Phchi.S1G422700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11321.t1 is derived from g15371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5365249	5365860	.	+	.	Phchi.S4G090300
Phchi.S4	AUGUSTUS	transcript	5365249	5365860	.	+	.	transcript_id "Phchi.S4G090300.t1"; gene_id "Phchi.S4G090300"
Phchi.S4	AUGUSTUS	start_codon	5365249	5365251	.	+	0	transcript_id "Phchi.S4G090300.t1"; gene_id "Phchi.S4G090300"
Phchi.S4	AUGUSTUS	CDS	5365249	5365860	0.98	+	0	transcript_id "Phchi.S4G090300.t1"; gene_id "Phchi.S4G090300"
Phchi.S4	AUGUSTUS	exon	5365249	5365860	.	+	.	transcript_id "Phchi.S4G090300.t1"; gene_id "Phchi.S4G090300"
Phchi.S4	AUGUSTUS	stop_codon	5365861	5365863	.	+	0	transcript_id "Phchi.S4G090300.t1"; gene_id "Phchi.S4G090300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8824.t1 is derived from g5999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38146771	38147623	.	+	.	Phchi.S1G598300
Phchi.S1	AUGUSTUS	transcript	38146771	38147623	.	+	.	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	start_codon	38146771	38146773	.	+	0	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	CDS	38146771	38146799	0.8	+	0	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	exon	38146771	38146799	.	+	.	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	intron	38146800	38146884	.	+	.	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	CDS	38146885	38146982	0.74	+	1	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	exon	38146885	38146982	.	+	.	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	intron	38146983	38147096	.	+	.	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	CDS	38147097	38147623	0.9	+	2	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	exon	38147097	38147623	.	+	.	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
Phchi.S1	AUGUSTUS	stop_codon	38147624	38147626	.	+	0	transcript_id "Phchi.S1G598300.t1"; gene_id "Phchi.S1G598300"
# This transcript jg10436.t2 is derived from g14485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10437.t1 is derived from g14486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	335801	338622	.	-	.	Phchi.S4G001900
Phchi.S4	AUGUSTUS	transcript	335801	338622	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	stop_codon	335798	335800	.	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	335801	335809	0.89	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	335801	335809	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	335810	336101	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	336102	336210	0.9	-	1	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	336102	336210	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	336211	336343	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	336344	336430	0.56	-	1	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	336344	336430	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	336431	336650	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	336651	336785	1	-	1	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	336651	336785	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	336786	336877	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	336878	337812	0.98	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	336878	337812	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	337813	337944	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	337945	338031	1	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	337945	338031	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	338032	338151	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	338152	338244	1	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	338152	338244	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	338245	338338	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	338339	338414	0.99	-	1	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	338339	338414	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	intron	338415	338515	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	CDS	338516	338622	0.77	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	exon	338516	338622	.	-	.	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
Phchi.S4	AUGUSTUS	start_codon	338620	338622	.	-	0	transcript_id "Phchi.S4G001900.t1"; gene_id "Phchi.S4G001900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13556.t1 is derived from g12023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7479560	7481886	.	-	.	Phchi.S3G087500
Phchi.S3	AUGUSTUS	transcript	7479560	7481886	.	-	.	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	stop_codon	7479557	7479559	.	-	0	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	CDS	7479560	7480713	1	-	2	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	exon	7479560	7480713	.	-	.	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	intron	7480714	7480836	.	-	.	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	CDS	7480837	7480884	1	-	2	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	exon	7480837	7480884	.	-	.	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	intron	7480885	7481018	.	-	.	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	CDS	7481019	7481886	0.75	-	0	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	exon	7481019	7481886	.	-	.	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
Phchi.S3	AUGUSTUS	start_codon	7481884	7481886	.	-	0	transcript_id "Phchi.S3G087500.t1"; gene_id "Phchi.S3G087500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15880.t1 is derived from g14350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22012364	22016623	.	-	.	Phchi.S3G319900
Phchi.S3	AUGUSTUS	transcript	22012364	22016623	.	-	.	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	stop_codon	22012361	22012363	.	-	0	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	CDS	22012364	22012453	0.08	-	0	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	exon	22012364	22012453	.	-	.	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	intron	22012454	22012541	.	-	.	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	CDS	22012542	22012615	0.09	-	2	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	exon	22012542	22012615	.	-	.	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	intron	22012616	22016343	.	-	.	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	CDS	22016344	22016623	0.18	-	0	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	exon	22016344	22016623	.	-	.	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
Phchi.S3	AUGUSTUS	start_codon	22016621	22016623	.	-	0	transcript_id "Phchi.S3G319900.t1"; gene_id "Phchi.S3G319900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13242.t1 is derived from g11707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4886457	4888603	.	-	.	Phchi.S3G056100
Phchi.S3	AUGUSTUS	transcript	4886457	4888603	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	stop_codon	4886454	4886456	.	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4886457	4886646	1	-	1	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4886457	4886646	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4886647	4886738	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4886739	4886794	1	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4886739	4886794	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4886795	4886864	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4886865	4887037	0.99	-	2	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4886865	4887037	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4887038	4887149	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4887150	4887306	0.88	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4887150	4887306	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4887307	4887430	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4887431	4887574	1	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4887431	4887574	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4887575	4887663	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4887664	4887813	1	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4887664	4887813	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4887814	4887913	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4887914	4888072	1	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4887914	4888072	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4888073	4888152	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4888153	4888325	1	-	2	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4888153	4888325	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	intron	4888326	4888413	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	CDS	4888414	4888603	0.48	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	exon	4888414	4888603	.	-	.	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
Phchi.S3	AUGUSTUS	start_codon	4888601	4888603	.	-	0	transcript_id "Phchi.S3G056100.t1"; gene_id "Phchi.S3G056100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2873.t1 is derived from g42.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	210925	213271	.	+	.	Phchi.S1G003200
Phchi.S1	AUGUSTUS	transcript	210925	213271	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	start_codon	210925	210927	.	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	210925	211116	0.94	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	210925	211116	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	211117	211209	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	211210	211373	0.71	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	211210	211373	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	211374	211485	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	211486	211688	0.82	+	1	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	211486	211688	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	211689	211799	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	211800	212032	1	+	2	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	211800	212032	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	212033	212128	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	212129	212191	1	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	212129	212191	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	212192	212369	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	212370	212426	1	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	212370	212426	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	212427	212515	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	212516	212637	1	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	212516	212637	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	212638	212780	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	212781	212898	0.96	+	1	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	212781	212898	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	intron	212899	213001	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	CDS	213002	213271	0.99	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	exon	213002	213271	.	+	.	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
Phchi.S1	AUGUSTUS	stop_codon	213272	213274	.	+	0	transcript_id "Phchi.S1G003200.t1"; gene_id "Phchi.S1G003200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11567.t1 is derived from g15618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7089499	7090617	.	-	.	Phchi.S4G114900
Phchi.S4	AUGUSTUS	transcript	7089499	7090617	.	-	.	transcript_id "Phchi.S4G114900.t1"; gene_id "Phchi.S4G114900"
Phchi.S4	AUGUSTUS	stop_codon	7089496	7089498	.	-	0	transcript_id "Phchi.S4G114900.t1"; gene_id "Phchi.S4G114900"
Phchi.S4	AUGUSTUS	CDS	7089499	7090617	1	-	0	transcript_id "Phchi.S4G114900.t1"; gene_id "Phchi.S4G114900"
Phchi.S4	AUGUSTUS	exon	7089499	7090617	.	-	.	transcript_id "Phchi.S4G114900.t1"; gene_id "Phchi.S4G114900"
Phchi.S4	AUGUSTUS	start_codon	7090615	7090617	.	-	0	transcript_id "Phchi.S4G114900.t1"; gene_id "Phchi.S4G114900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13604.t1 is derived from g12071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7660072	7664978	.	+	.	Phchi.S3G092300
Phchi.S3	AUGUSTUS	transcript	7660072	7664978	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	start_codon	7660072	7660074	.	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7660072	7660734	0.97	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7660072	7660734	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7660735	7660890	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7660891	7660957	0.58	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7660891	7660957	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7660958	7661049	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7661050	7661167	0.29	+	2	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7661050	7661167	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7661168	7661296	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7661297	7661435	0.49	+	1	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7661297	7661435	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7661436	7661569	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7661570	7661626	0.57	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7661570	7661626	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7661627	7661746	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7661747	7661854	0.96	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7661747	7661854	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7661855	7661943	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7661944	7662042	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7661944	7662042	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7662043	7662140	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7662141	7662257	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7662141	7662257	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7662258	7662332	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7662333	7662440	0.83	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7662333	7662440	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7662441	7662593	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7662594	7662680	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7662594	7662680	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7662681	7662763	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7662764	7662916	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7662764	7662916	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7662917	7663006	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7663007	7663192	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7663007	7663192	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7663193	7663515	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7663516	7663608	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7663516	7663608	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7663609	7663884	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7663885	7663968	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7663885	7663968	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7663969	7664063	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7664064	7664144	1	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7664064	7664144	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7664145	7664262	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7664263	7664475	0.76	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7664263	7664475	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	intron	7664476	7664579	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	CDS	7664580	7664978	0.77	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	exon	7664580	7664978	.	+	.	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
Phchi.S3	AUGUSTUS	stop_codon	7664979	7664981	.	+	0	transcript_id "Phchi.S3G092300.t1"; gene_id "Phchi.S3G092300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12507.t1 is derived from g8184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31470073	31470417	.	+	.	Phchi.S2G058700
Phchi.S2	AUGUSTUS	transcript	31470073	31470417	.	+	.	transcript_id "Phchi.S2G058700.t1"; gene_id "Phchi.S2G058700"
Phchi.S2	AUGUSTUS	start_codon	31470073	31470075	.	+	0	transcript_id "Phchi.S2G058700.t1"; gene_id "Phchi.S2G058700"
Phchi.S2	AUGUSTUS	CDS	31470073	31470417	1	+	0	transcript_id "Phchi.S2G058700.t1"; gene_id "Phchi.S2G058700"
Phchi.S2	AUGUSTUS	exon	31470073	31470417	.	+	.	transcript_id "Phchi.S2G058700.t1"; gene_id "Phchi.S2G058700"
Phchi.S2	AUGUSTUS	stop_codon	31470418	31470420	.	+	0	transcript_id "Phchi.S2G058700.t1"; gene_id "Phchi.S2G058700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12213.t1 is derived from g7889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6768079	6771016	.	-	.	Phchi.S2G029300
Phchi.S2	AUGUSTUS	transcript	6768079	6771016	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	stop_codon	6768076	6768078	.	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6768079	6768321	0.77	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6768079	6768321	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6768322	6768393	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6768394	6768561	1	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6768394	6768561	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6768562	6768698	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6768699	6768767	1	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6768699	6768767	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6768768	6768847	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6768848	6768895	1	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6768848	6768895	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6768896	6769058	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6769059	6769155	1	-	1	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6769059	6769155	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6769156	6769305	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6769306	6769385	1	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6769306	6769385	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6769386	6769503	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6769504	6769575	1	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6769504	6769575	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6769576	6769690	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6769691	6769785	1	-	2	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6769691	6769785	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6769786	6769977	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6769978	6770059	1	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6769978	6770059	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	intron	6770060	6770545	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	CDS	6770546	6771016	0.96	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	exon	6770546	6771016	.	-	.	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
Phchi.S2	AUGUSTUS	start_codon	6771014	6771016	.	-	0	transcript_id "Phchi.S2G029300.t1"; gene_id "Phchi.S2G029300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6398.t1 is derived from g3570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22763329	22764174	.	+	.	Phchi.S1G355700
Phchi.S1	AUGUSTUS	transcript	22763329	22764174	.	+	.	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	start_codon	22763329	22763331	.	+	0	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	CDS	22763329	22763418	1	+	0	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	exon	22763329	22763418	.	+	.	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	intron	22763419	22763737	.	+	.	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	CDS	22763738	22763919	1	+	0	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	exon	22763738	22763919	.	+	.	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	intron	22763920	22764047	.	+	.	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	CDS	22764048	22764174	1	+	1	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	exon	22764048	22764174	.	+	.	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
Phchi.S1	AUGUSTUS	stop_codon	22764175	22764177	.	+	0	transcript_id "Phchi.S1G355700.t1"; gene_id "Phchi.S1G355700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3126.t1 is derived from g295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1856060	1857797	.	+	.	Phchi.S1G028500
Phchi.S1	AUGUSTUS	transcript	1856060	1857797	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	start_codon	1856060	1856062	.	+	0	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	CDS	1856060	1856478	0.28	+	0	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	exon	1856060	1856478	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	intron	1856479	1856564	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	CDS	1856565	1856674	0.95	+	1	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	exon	1856565	1856674	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	intron	1856675	1856841	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	CDS	1856842	1856927	0.59	+	2	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	exon	1856842	1856927	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	intron	1856928	1857021	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	CDS	1857022	1857073	0.23	+	0	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	exon	1857022	1857073	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	intron	1857074	1857293	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	CDS	1857294	1857375	0.21	+	2	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	exon	1857294	1857375	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	intron	1857376	1857598	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	CDS	1857599	1857797	0.79	+	1	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	exon	1857599	1857797	.	+	.	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
Phchi.S1	AUGUSTUS	stop_codon	1857798	1857800	.	+	0	transcript_id "Phchi.S1G028500.t1"; gene_id "Phchi.S1G028500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9328.t1 is derived from g6503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40955728	40959711	.	+	.	Phchi.S1G648700
Phchi.S1	AUGUSTUS	transcript	40955728	40959711	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	start_codon	40955728	40955730	.	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40955728	40955874	0.49	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40955728	40955874	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40955875	40956056	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956057	40956182	0.98	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956057	40956182	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956183	40956292	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956293	40956364	0.98	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956293	40956364	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956365	40956482	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956483	40956613	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956483	40956613	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956614	40956710	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956711	40956827	1	+	1	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956711	40956827	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956828	40956969	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956970	40957081	0.98	+	1	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956970	40957081	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957082	40957183	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957184	40957381	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957184	40957381	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957382	40957511	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957512	40957601	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957512	40957601	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957602	40957696	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957697	40957921	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957697	40957921	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957922	40958100	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958101	40958178	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958101	40958178	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958179	40958338	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958339	40958554	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958339	40958554	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958555	40958794	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958795	40958833	0.84	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958795	40958833	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958834	40958910	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958911	40959112	0.94	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958911	40959112	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959113	40959210	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959211	40959299	1	+	2	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959211	40959299	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959300	40959376	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959377	40959496	1	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959377	40959496	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959497	40959594	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959595	40959711	0.99	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959595	40959711	.	+	.	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	stop_codon	40959712	40959714	.	+	0	transcript_id "Phchi.S1G648700.t1"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	transcript	40955728	40959711	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	start_codon	40955728	40955730	.	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40955728	40955874	0.54	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40955728	40955874	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40955875	40956056	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956057	40956182	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956057	40956182	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956183	40956272	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956273	40956364	0.7	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956273	40956364	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956365	40956496	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956497	40956613	0.5	+	1	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956497	40956613	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956614	40956710	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956711	40956827	1	+	1	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956711	40956827	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956828	40956969	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956970	40957081	1	+	1	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956970	40957081	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957082	40957183	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957184	40957381	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957184	40957381	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957382	40957511	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957512	40957601	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957512	40957601	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957602	40957696	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957697	40957921	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957697	40957921	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957922	40958100	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958101	40958178	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958101	40958178	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958179	40958338	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958339	40958554	0.99	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958339	40958554	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958555	40958661	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958662	40958833	0.98	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958662	40958833	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958834	40959210	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959211	40959299	1	+	2	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959211	40959299	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959300	40959376	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959377	40959496	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959377	40959496	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959497	40959594	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959595	40959711	1	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959595	40959711	.	+	.	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	stop_codon	40959712	40959714	.	+	0	transcript_id "Phchi.S1G648700.t2"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	transcript	40955728	40959711	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	start_codon	40955728	40955730	.	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40955728	40955874	0.57	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40955728	40955874	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40955875	40956056	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956057	40956182	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956057	40956182	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956183	40956272	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956273	40956364	0.7	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956273	40956364	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956365	40956496	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956497	40956613	0.6	+	1	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956497	40956613	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956614	40956710	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956711	40956827	1	+	1	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956711	40956827	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40956828	40956969	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40956970	40957081	1	+	1	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40956970	40957081	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957082	40957183	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957184	40957381	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957184	40957381	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957382	40957511	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957512	40957601	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957512	40957601	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957602	40957696	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40957697	40957921	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40957697	40957921	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40957922	40958100	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958101	40958178	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958101	40958178	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958179	40958338	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958339	40958554	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958339	40958554	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958555	40958794	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958795	40958833	0.83	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958795	40958833	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40958834	40958910	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40958911	40959112	0.9	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40958911	40959112	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959113	40959210	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959211	40959299	1	+	2	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959211	40959299	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959300	40959376	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959377	40959496	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959377	40959496	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	intron	40959497	40959594	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	CDS	40959595	40959711	1	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	exon	40959595	40959711	.	+	.	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
Phchi.S1	AUGUSTUS	stop_codon	40959712	40959714	.	+	0	transcript_id "Phchi.S1G648700.t3"; gene_id "Phchi.S1G648700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13953.t1 is derived from g12420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9887529	9889903	.	-	.	Phchi.S3G127200
Phchi.S3	AUGUSTUS	transcript	9887529	9889903	.	-	.	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	stop_codon	9887526	9887528	.	-	0	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	CDS	9887529	9887644	0.88	-	2	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	exon	9887529	9887644	.	-	.	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	intron	9887645	9887734	.	-	.	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	CDS	9887735	9889736	0.73	-	0	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	exon	9887735	9889736	.	-	.	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	intron	9889737	9889825	.	-	.	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	CDS	9889826	9889903	1	-	0	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	exon	9889826	9889903	.	-	.	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
Phchi.S3	AUGUSTUS	start_codon	9889901	9889903	.	-	0	transcript_id "Phchi.S3G127200.t1"; gene_id "Phchi.S3G127200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9945.t1 is derived from g7121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44613707	44616289	.	-	.	Phchi.S1G710400
Phchi.S1	AUGUSTUS	transcript	44613707	44616289	.	-	.	transcript_id "Phchi.S1G710400.t1"; gene_id "Phchi.S1G710400"
Phchi.S1	AUGUSTUS	stop_codon	44613704	44613706	.	-	0	transcript_id "Phchi.S1G710400.t1"; gene_id "Phchi.S1G710400"
Phchi.S1	AUGUSTUS	CDS	44613707	44616289	0.91	-	0	transcript_id "Phchi.S1G710400.t1"; gene_id "Phchi.S1G710400"
Phchi.S1	AUGUSTUS	exon	44613707	44616289	.	-	.	transcript_id "Phchi.S1G710400.t1"; gene_id "Phchi.S1G710400"
Phchi.S1	AUGUSTUS	start_codon	44616287	44616289	.	-	0	transcript_id "Phchi.S1G710400.t1"; gene_id "Phchi.S1G710400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2015.t1 is derived from g8935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4464528	4467173	.	-	.	Phchi.S5G062400
Phchi.S5	AUGUSTUS	transcript	4464528	4467173	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	stop_codon	4464525	4464527	.	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4464528	4464584	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4464528	4464584	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4464585	4464694	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4464695	4464775	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4464695	4464775	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4464776	4464864	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4464865	4464921	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4464865	4464921	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4464922	4464996	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4464997	4465134	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4464997	4465134	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4465135	4465238	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4465239	4465271	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4465239	4465271	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4465272	4465452	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4465453	4465524	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4465453	4465524	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4465525	4465784	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4465785	4465877	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4465785	4465877	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4465878	4465946	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4465947	4466245	1	-	2	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4465947	4466245	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4466246	4466340	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4466341	4466470	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4466341	4466470	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4466471	4466569	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4466570	4466632	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4466570	4466632	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4466633	4466717	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4466718	4466778	1	-	1	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4466718	4466778	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4466779	4466873	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4466874	4466956	1	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4466874	4466956	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	intron	4466957	4467041	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	CDS	4467042	4467173	0.99	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	exon	4467042	4467173	.	-	.	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
Phchi.S5	AUGUSTUS	start_codon	4467171	4467173	.	-	0	transcript_id "Phchi.S5G062400.t1"; gene_id "Phchi.S5G062400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg193.t1 is derived from g9975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1083489	1084859	.	-	.	Phchi.S6G015200
Phchi.S6	AUGUSTUS	transcript	1083489	1084859	.	-	.	transcript_id "Phchi.S6G015200.t1"; gene_id "Phchi.S6G015200"
Phchi.S6	AUGUSTUS	stop_codon	1083486	1083488	.	-	0	transcript_id "Phchi.S6G015200.t1"; gene_id "Phchi.S6G015200"
Phchi.S6	AUGUSTUS	CDS	1083489	1084859	0.39	-	0	transcript_id "Phchi.S6G015200.t1"; gene_id "Phchi.S6G015200"
Phchi.S6	AUGUSTUS	exon	1083489	1084859	.	-	.	transcript_id "Phchi.S6G015200.t1"; gene_id "Phchi.S6G015200"
Phchi.S6	AUGUSTUS	start_codon	1084857	1084859	.	-	0	transcript_id "Phchi.S6G015200.t1"; gene_id "Phchi.S6G015200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11878.t1 is derived from g15930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8954106	8954502	.	+	.	Phchi.S4G146000
Phchi.S4	AUGUSTUS	transcript	8954106	8954502	.	+	.	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	start_codon	8954106	8954108	.	+	0	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	CDS	8954106	8954294	0.44	+	0	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	exon	8954106	8954294	.	+	.	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	intron	8954295	8954478	.	+	.	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	CDS	8954479	8954502	0.72	+	0	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	exon	8954479	8954502	.	+	.	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
Phchi.S4	AUGUSTUS	stop_codon	8954503	8954505	.	+	0	transcript_id "Phchi.S4G146000.t1"; gene_id "Phchi.S4G146000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3050.t1 is derived from g219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1359073	1359890	.	-	.	Phchi.S1G020900
Phchi.S1	AUGUSTUS	transcript	1359073	1359890	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	stop_codon	1359070	1359072	.	-	0	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	CDS	1359073	1359186	1	-	0	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	exon	1359073	1359186	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	intron	1359187	1359365	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	CDS	1359366	1359499	1	-	2	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	exon	1359366	1359499	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	intron	1359500	1359688	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	CDS	1359689	1359776	0.93	-	0	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	exon	1359689	1359776	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	intron	1359777	1359887	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	CDS	1359888	1359890	0.9	-	0	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	exon	1359888	1359890	.	-	.	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
Phchi.S1	AUGUSTUS	start_codon	1359888	1359890	.	-	0	transcript_id "Phchi.S1G020900.t1"; gene_id "Phchi.S1G020900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg169.t1 is derived from g9951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	974703	975479	.	-	.	Phchi.S6G012800
Phchi.S6	AUGUSTUS	transcript	974703	975479	.	-	.	transcript_id "Phchi.S6G012800.t1"; gene_id "Phchi.S6G012800"
Phchi.S6	AUGUSTUS	stop_codon	974700	974702	.	-	0	transcript_id "Phchi.S6G012800.t1"; gene_id "Phchi.S6G012800"
Phchi.S6	AUGUSTUS	CDS	974703	975479	0.86	-	0	transcript_id "Phchi.S6G012800.t1"; gene_id "Phchi.S6G012800"
Phchi.S6	AUGUSTUS	exon	974703	975479	.	-	.	transcript_id "Phchi.S6G012800.t1"; gene_id "Phchi.S6G012800"
Phchi.S6	AUGUSTUS	start_codon	975477	975479	.	-	0	transcript_id "Phchi.S6G012800.t1"; gene_id "Phchi.S6G012800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8351.t1 is derived from g5526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35452672	35453481	.	-	.	Phchi.S1G551000
Phchi.S1	AUGUSTUS	transcript	35452672	35453481	.	-	.	transcript_id "Phchi.S1G551000.t1"; gene_id "Phchi.S1G551000"
Phchi.S1	AUGUSTUS	stop_codon	35452669	35452671	.	-	0	transcript_id "Phchi.S1G551000.t1"; gene_id "Phchi.S1G551000"
Phchi.S1	AUGUSTUS	CDS	35452672	35453481	0.82	-	0	transcript_id "Phchi.S1G551000.t1"; gene_id "Phchi.S1G551000"
Phchi.S1	AUGUSTUS	exon	35452672	35453481	.	-	.	transcript_id "Phchi.S1G551000.t1"; gene_id "Phchi.S1G551000"
Phchi.S1	AUGUSTUS	start_codon	35453479	35453481	.	-	0	transcript_id "Phchi.S1G551000.t1"; gene_id "Phchi.S1G551000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5348.t1 is derived from g2518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16421727	16422246	.	+	.	Phchi.S1G250700
Phchi.S1	AUGUSTUS	transcript	16421727	16422246	.	+	.	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	start_codon	16421727	16421729	.	+	0	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	CDS	16421727	16421889	0.32	+	0	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	exon	16421727	16421889	.	+	.	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	intron	16421890	16421978	.	+	.	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	CDS	16421979	16422054	0.42	+	2	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	exon	16421979	16422054	.	+	.	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	intron	16422055	16422176	.	+	.	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	CDS	16422177	16422246	0.41	+	1	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	exon	16422177	16422246	.	+	.	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
Phchi.S1	AUGUSTUS	stop_codon	16422247	16422249	.	+	0	transcript_id "Phchi.S1G250700.t1"; gene_id "Phchi.S1G250700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4478.t1 is derived from g1648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10702987	10705809	.	-	.	Phchi.S1G163700
Phchi.S1	AUGUSTUS	transcript	10702987	10705809	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	stop_codon	10702984	10702986	.	-	0	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	CDS	10702987	10703215	0.99	-	1	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	exon	10702987	10703215	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	intron	10703216	10703310	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	CDS	10703311	10703402	1	-	0	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	exon	10703311	10703402	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	intron	10703403	10703511	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	CDS	10703512	10703580	1	-	0	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	exon	10703512	10703580	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	intron	10703581	10703771	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	CDS	10703772	10703980	1	-	2	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	exon	10703772	10703980	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	intron	10703981	10704106	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	CDS	10704107	10704278	1	-	0	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	exon	10704107	10704278	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	intron	10704279	10704372	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	CDS	10704373	10705809	0.81	-	0	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	exon	10704373	10705809	.	-	.	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
Phchi.S1	AUGUSTUS	start_codon	10705807	10705809	.	-	0	transcript_id "Phchi.S1G163700.t1"; gene_id "Phchi.S1G163700"
# This transcript jg4593.t2 is derived from g1763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4594.t1 is derived from g1764.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11246954	11248599	.	+	.	Phchi.S1G175300
Phchi.S1	AUGUSTUS	transcript	11246954	11248599	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	start_codon	11246954	11246956	.	+	0	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11246954	11247208	1	+	0	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11246954	11247208	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247209	11247289	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247290	11247442	1	+	0	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247290	11247442	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247443	11247571	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247572	11247758	1	+	0	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247572	11247758	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247759	11247844	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247845	11248204	1	+	2	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247845	11248204	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11248205	11248289	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11248290	11248377	1	+	2	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11248290	11248377	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11248378	11248469	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11248470	11248599	1	+	1	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11248470	11248599	.	+	.	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	stop_codon	11248600	11248602	.	+	0	transcript_id "Phchi.S1G175300.t1"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	transcript	11246954	11248599	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	start_codon	11246954	11246956	.	+	0	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11246954	11247208	1	+	0	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11246954	11247208	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247209	11247292	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247293	11247442	1	+	0	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247293	11247442	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247443	11247571	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247572	11247758	1	+	0	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247572	11247758	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247759	11247844	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247845	11248204	1	+	2	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247845	11248204	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11248205	11248289	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11248290	11248377	1	+	2	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11248290	11248377	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11248378	11248469	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11248470	11248599	1	+	1	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11248470	11248599	.	+	.	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	stop_codon	11248600	11248602	.	+	0	transcript_id "Phchi.S1G175300.t2"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	transcript	11246954	11248599	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	start_codon	11246954	11246956	.	+	0	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11246954	11247208	1	+	0	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11246954	11247208	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247209	11247292	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247293	11247442	0.99	+	0	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247293	11247442	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247443	11247571	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247572	11247758	1	+	0	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247572	11247758	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11247759	11247844	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11247845	11248204	1	+	2	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11247845	11248204	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11248205	11248295	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11248296	11248377	0.99	+	2	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11248296	11248377	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	intron	11248378	11248469	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	CDS	11248470	11248599	1	+	1	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	exon	11248470	11248599	.	+	.	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
Phchi.S1	AUGUSTUS	stop_codon	11248600	11248602	.	+	0	transcript_id "Phchi.S1G175300.t3"; gene_id "Phchi.S1G175300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9934.t1 is derived from g7110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44536351	44538282	.	+	.	Phchi.S1G709300
Phchi.S1	AUGUSTUS	transcript	44536351	44538282	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	start_codon	44536351	44536353	.	+	0	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44536351	44536390	1	+	0	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44536351	44536390	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	intron	44536391	44536883	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44536884	44537086	1	+	2	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44536884	44537086	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	intron	44537087	44537247	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44537248	44537397	1	+	0	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44537248	44537397	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	intron	44537398	44537483	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44537484	44537625	1	+	0	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44537484	44537625	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	intron	44537626	44537720	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44537721	44537792	0.98	+	2	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44537721	44537792	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	intron	44537793	44537908	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44537909	44537993	0.64	+	2	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44537909	44537993	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	intron	44537994	44538077	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	CDS	44538078	44538282	1	+	1	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	exon	44538078	44538282	.	+	.	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
Phchi.S1	AUGUSTUS	stop_codon	44538283	44538285	.	+	0	transcript_id "Phchi.S1G709300.t1"; gene_id "Phchi.S1G709300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5988.t1 is derived from g3159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20269138	20270559	.	+	.	Phchi.S1G314700
Phchi.S1	AUGUSTUS	transcript	20269138	20270559	.	+	.	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	start_codon	20269138	20269140	.	+	0	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	CDS	20269138	20269596	0.96	+	0	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	exon	20269138	20269596	.	+	.	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	intron	20269597	20269742	.	+	.	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	CDS	20269743	20270095	1	+	0	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	exon	20269743	20270095	.	+	.	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	intron	20270096	20270204	.	+	.	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	CDS	20270205	20270559	1	+	1	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	exon	20270205	20270559	.	+	.	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
Phchi.S1	AUGUSTUS	stop_codon	20270560	20270562	.	+	0	transcript_id "Phchi.S1G314700.t1"; gene_id "Phchi.S1G314700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8777.t1 is derived from g5952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37908071	37909517	.	-	.	Phchi.S1G593600
Phchi.S1	AUGUSTUS	transcript	37908071	37909517	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	stop_codon	37908068	37908070	.	-	0	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	CDS	37908071	37908089	0.54	-	1	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	exon	37908071	37908089	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	intron	37908090	37908195	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	CDS	37908196	37908878	0.68	-	0	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	exon	37908196	37908878	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	intron	37908879	37908968	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	CDS	37908969	37909116	0.56	-	1	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	exon	37908969	37909116	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	intron	37909117	37909248	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	CDS	37909249	37909253	0.52	-	0	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	exon	37909249	37909253	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	intron	37909254	37909424	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	CDS	37909425	37909517	0.78	-	0	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	exon	37909425	37909517	.	-	.	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
Phchi.S1	AUGUSTUS	start_codon	37909515	37909517	.	-	0	transcript_id "Phchi.S1G593600.t1"; gene_id "Phchi.S1G593600"
# This transcript jg12385.t2 is derived from g8062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12385.t3 is derived from g8062.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12386.t1 is derived from g8063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15392232	15392570	.	+	.	Phchi.S2G046600
Phchi.S2	AUGUSTUS	transcript	15392232	15392570	.	+	.	transcript_id "Phchi.S2G046600.t1"; gene_id "Phchi.S2G046600"
Phchi.S2	AUGUSTUS	start_codon	15392232	15392234	.	+	0	transcript_id "Phchi.S2G046600.t1"; gene_id "Phchi.S2G046600"
Phchi.S2	AUGUSTUS	CDS	15392232	15392570	0.93	+	0	transcript_id "Phchi.S2G046600.t1"; gene_id "Phchi.S2G046600"
Phchi.S2	AUGUSTUS	exon	15392232	15392570	.	+	.	transcript_id "Phchi.S2G046600.t1"; gene_id "Phchi.S2G046600"
Phchi.S2	AUGUSTUS	stop_codon	15392571	15392573	.	+	0	transcript_id "Phchi.S2G046600.t1"; gene_id "Phchi.S2G046600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3599.t1 is derived from g768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4671193	4671857	.	+	.	Phchi.S1G075800
Phchi.S1	AUGUSTUS	transcript	4671193	4671857	.	+	.	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	start_codon	4671193	4671195	.	+	0	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	CDS	4671193	4671303	0.38	+	0	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	exon	4671193	4671303	.	+	.	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	intron	4671304	4671543	.	+	.	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	CDS	4671544	4671665	1	+	0	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	exon	4671544	4671665	.	+	.	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	intron	4671666	4671817	.	+	.	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	CDS	4671818	4671857	1	+	1	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	exon	4671818	4671857	.	+	.	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
Phchi.S1	AUGUSTUS	stop_codon	4671858	4671860	.	+	0	transcript_id "Phchi.S1G075800.t1"; gene_id "Phchi.S1G075800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4467.t1 is derived from g1637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10642941	10645012	.	+	.	Phchi.S1G162600
Phchi.S1	AUGUSTUS	transcript	10642941	10645012	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	start_codon	10642941	10642943	.	+	0	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	CDS	10642941	10643236	0.99	+	0	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	exon	10642941	10643236	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	intron	10643237	10643367	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	CDS	10643368	10643469	0.95	+	1	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	exon	10643368	10643469	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	intron	10643470	10643679	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	CDS	10643680	10644207	0.58	+	1	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	exon	10643680	10644207	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	intron	10644208	10644353	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	CDS	10644354	10644532	0.76	+	1	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	exon	10644354	10644532	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	intron	10644533	10644608	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	CDS	10644609	10645012	1	+	2	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	exon	10644609	10645012	.	+	.	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
Phchi.S1	AUGUSTUS	stop_codon	10645013	10645015	.	+	0	transcript_id "Phchi.S1G162600.t1"; gene_id "Phchi.S1G162600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg415.t1 is derived from g10197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2956638	2958926	.	+	.	Phchi.S6G037400
Phchi.S6	AUGUSTUS	transcript	2956638	2958926	.	+	.	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	start_codon	2956638	2956640	.	+	0	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	CDS	2956638	2958506	0.71	+	0	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	exon	2956638	2958506	.	+	.	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	intron	2958507	2958728	.	+	.	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	CDS	2958729	2958782	0.92	+	0	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	exon	2958729	2958782	.	+	.	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	intron	2958783	2958878	.	+	.	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	CDS	2958879	2958926	0.93	+	0	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	exon	2958879	2958926	.	+	.	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
Phchi.S6	AUGUSTUS	stop_codon	2958927	2958929	.	+	0	transcript_id "Phchi.S6G037400.t1"; gene_id "Phchi.S6G037400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12284.t1 is derived from g7960.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8751270	8752882	.	+	.	Phchi.S2G036400
Phchi.S2	AUGUSTUS	transcript	8751270	8752882	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	start_codon	8751270	8751272	.	+	0	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8751270	8751470	0.67	+	0	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8751270	8751470	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8751471	8751624	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8751625	8751746	1	+	0	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8751625	8751746	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8751747	8751835	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8751836	8752012	1	+	1	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8751836	8752012	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8752013	8752155	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8752156	8752300	1	+	1	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8752156	8752300	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8752301	8752381	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8752382	8752560	1	+	0	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8752382	8752560	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8752561	8752635	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8752636	8752882	0.91	+	1	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8752636	8752882	.	+	.	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	stop_codon	8752883	8752885	.	+	0	transcript_id "Phchi.S2G036400.t1"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	transcript	8751270	8752882	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	start_codon	8751270	8751272	.	+	0	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8751270	8751470	0.55	+	0	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8751270	8751470	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8751471	8751624	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8751625	8751746	1	+	0	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8751625	8751746	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8751747	8751841	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8751842	8752012	1	+	1	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8751842	8752012	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8752013	8752155	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8752156	8752300	1	+	1	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8752156	8752300	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8752301	8752381	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8752382	8752560	1	+	0	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8752382	8752560	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	intron	8752561	8752635	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	CDS	8752636	8752882	0.89	+	1	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	exon	8752636	8752882	.	+	.	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
Phchi.S2	AUGUSTUS	stop_codon	8752883	8752885	.	+	0	transcript_id "Phchi.S2G036400.t2"; gene_id "Phchi.S2G036400"
# This transcript jg6242.t2 is derived from g3414.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6242.t3 is derived from g3414.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6243.t1 is derived from g3415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21825481	21826593	.	-	.	Phchi.S1G340200
Phchi.S1	AUGUSTUS	transcript	21825481	21826593	.	-	.	transcript_id "Phchi.S1G340200.t1"; gene_id "Phchi.S1G340200"
Phchi.S1	AUGUSTUS	stop_codon	21825478	21825480	.	-	0	transcript_id "Phchi.S1G340200.t1"; gene_id "Phchi.S1G340200"
Phchi.S1	AUGUSTUS	CDS	21825481	21826593	0.53	-	0	transcript_id "Phchi.S1G340200.t1"; gene_id "Phchi.S1G340200"
Phchi.S1	AUGUSTUS	exon	21825481	21826593	.	-	.	transcript_id "Phchi.S1G340200.t1"; gene_id "Phchi.S1G340200"
Phchi.S1	AUGUSTUS	start_codon	21826591	21826593	.	-	0	transcript_id "Phchi.S1G340200.t1"; gene_id "Phchi.S1G340200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7151.t1 is derived from g4323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27201285	27201893	.	-	.	Phchi.S1G431000
Phchi.S1	AUGUSTUS	transcript	27201285	27201893	.	-	.	transcript_id "Phchi.S1G431000.t1"; gene_id "Phchi.S1G431000"
Phchi.S1	AUGUSTUS	stop_codon	27201282	27201284	.	-	0	transcript_id "Phchi.S1G431000.t1"; gene_id "Phchi.S1G431000"
Phchi.S1	AUGUSTUS	CDS	27201285	27201893	1	-	0	transcript_id "Phchi.S1G431000.t1"; gene_id "Phchi.S1G431000"
Phchi.S1	AUGUSTUS	exon	27201285	27201893	.	-	.	transcript_id "Phchi.S1G431000.t1"; gene_id "Phchi.S1G431000"
Phchi.S1	AUGUSTUS	start_codon	27201891	27201893	.	-	0	transcript_id "Phchi.S1G431000.t1"; gene_id "Phchi.S1G431000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3384.t1 is derived from g553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3271371	3274763	.	+	.	Phchi.S1G054300
Phchi.S1	AUGUSTUS	transcript	3271371	3274763	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	start_codon	3271371	3271373	.	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3271371	3271526	1	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3271371	3271526	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3271527	3271788	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3271789	3271884	1	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3271789	3271884	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3271885	3272067	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3272068	3272273	1	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3272068	3272273	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3272274	3272393	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3272394	3272651	1	+	1	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3272394	3272651	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3272652	3272730	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3272731	3272869	1	+	1	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3272731	3272869	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3272870	3272979	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3272980	3273192	1	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3272980	3273192	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3273193	3273292	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3273293	3273498	1	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3273293	3273498	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3273499	3273693	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3273694	3273894	1	+	1	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3273694	3273894	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3273895	3273973	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3273974	3274073	0.98	+	1	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3273974	3274073	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3274074	3274178	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3274179	3274300	0.98	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3274179	3274300	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3274301	3274414	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3274415	3274561	1	+	1	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3274415	3274561	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	intron	3274562	3274648	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	CDS	3274649	3274763	1	+	1	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	exon	3274649	3274763	.	+	.	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
Phchi.S1	AUGUSTUS	stop_codon	3274764	3274766	.	+	0	transcript_id "Phchi.S1G054300.t1"; gene_id "Phchi.S1G054300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7763.t1 is derived from g4937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31159306	31160401	.	+	.	Phchi.S1G492200
Phchi.S1	AUGUSTUS	transcript	31159306	31160401	.	+	.	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	start_codon	31159306	31159308	.	+	0	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	CDS	31159306	31159702	0.47	+	0	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	exon	31159306	31159702	.	+	.	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	intron	31159703	31159941	.	+	.	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	CDS	31159942	31160060	0.5	+	2	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	exon	31159942	31160060	.	+	.	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	intron	31160061	31160152	.	+	.	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	CDS	31160153	31160401	0.94	+	0	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	exon	31160153	31160401	.	+	.	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
Phchi.S1	AUGUSTUS	stop_codon	31160402	31160404	.	+	0	transcript_id "Phchi.S1G492200.t1"; gene_id "Phchi.S1G492200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15195.t1 is derived from g13663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17509947	17511068	.	-	.	Phchi.S3G251400
Phchi.S3	AUGUSTUS	transcript	17509947	17511068	.	-	.	transcript_id "Phchi.S3G251400.t1"; gene_id "Phchi.S3G251400"
Phchi.S3	AUGUSTUS	stop_codon	17509944	17509946	.	-	0	transcript_id "Phchi.S3G251400.t1"; gene_id "Phchi.S3G251400"
Phchi.S3	AUGUSTUS	CDS	17509947	17511068	0.2	-	0	transcript_id "Phchi.S3G251400.t1"; gene_id "Phchi.S3G251400"
Phchi.S3	AUGUSTUS	exon	17509947	17511068	.	-	.	transcript_id "Phchi.S3G251400.t1"; gene_id "Phchi.S3G251400"
Phchi.S3	AUGUSTUS	start_codon	17511066	17511068	.	-	0	transcript_id "Phchi.S3G251400.t1"; gene_id "Phchi.S3G251400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1904.t1 is derived from g8824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3786489	3792897	.	+	.	Phchi.S5G051300
Phchi.S5	AUGUSTUS	transcript	3786489	3792897	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	start_codon	3786489	3786491	.	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3786489	3786720	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3786489	3786720	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3786721	3786824	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3786825	3786944	1	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3786825	3786944	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3786945	3787206	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3787207	3787313	0.96	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3787207	3787313	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3787314	3787490	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3787491	3787581	0.43	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3787491	3787581	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3787582	3787673	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3787674	3787869	1	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3787674	3787869	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3787870	3787992	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3787993	3788128	1	+	1	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3787993	3788128	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3788129	3788222	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3788223	3788250	0.23	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3788223	3788250	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3788251	3788333	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3788334	3788359	0.23	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3788334	3788359	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3788360	3788457	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3788458	3788535	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3788458	3788535	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3788536	3788669	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3788670	3788761	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3788670	3788761	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3788762	3788880	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3788881	3788947	1	+	1	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3788881	3788947	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3788948	3789060	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3789061	3789132	0.92	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3789061	3789132	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3789133	3789273	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3789274	3789360	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3789274	3789360	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3789361	3789525	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3789526	3789645	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3789526	3789645	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3789646	3789750	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3789751	3789849	0.99	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3789751	3789849	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3789850	3789970	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3789971	3790078	0.99	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3789971	3790078	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3790079	3790169	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3790170	3790265	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3790170	3790265	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3790266	3790378	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3790379	3790444	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3790379	3790444	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3790445	3790536	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3790537	3790593	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3790537	3790593	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3790594	3790673	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3790674	3790761	0.95	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3790674	3790761	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3790762	3790868	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3790869	3790948	1	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3790869	3790948	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3790949	3791051	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3791052	3791165	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3791052	3791165	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3791166	3791265	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3791266	3791380	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3791266	3791380	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3791381	3791483	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3791484	3791656	0.98	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3791484	3791656	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3791657	3791770	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3791771	3791842	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3791771	3791842	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3791843	3791920	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3791921	3791995	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3791921	3791995	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3791996	3792076	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3792077	3792166	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3792077	3792166	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3792167	3792247	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3792248	3792408	1	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3792248	3792408	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3792409	3792506	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3792507	3792580	0.99	+	1	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3792507	3792580	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3792581	3792690	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3792691	3792774	0.67	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3792691	3792774	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	intron	3792775	3792850	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	CDS	3792851	3792897	0.69	+	2	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	exon	3792851	3792897	.	+	.	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
Phchi.S5	AUGUSTUS	stop_codon	3792898	3792900	.	+	0	transcript_id "Phchi.S5G051300.t1"; gene_id "Phchi.S5G051300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10729.t1 is derived from g14779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1791758	1792090	.	+	.	Phchi.S4G031100
Phchi.S4	AUGUSTUS	transcript	1791758	1792090	.	+	.	transcript_id "Phchi.S4G031100.t1"; gene_id "Phchi.S4G031100"
Phchi.S4	AUGUSTUS	start_codon	1791758	1791760	.	+	0	transcript_id "Phchi.S4G031100.t1"; gene_id "Phchi.S4G031100"
Phchi.S4	AUGUSTUS	CDS	1791758	1792090	0.9	+	0	transcript_id "Phchi.S4G031100.t1"; gene_id "Phchi.S4G031100"
Phchi.S4	AUGUSTUS	exon	1791758	1792090	.	+	.	transcript_id "Phchi.S4G031100.t1"; gene_id "Phchi.S4G031100"
Phchi.S4	AUGUSTUS	stop_codon	1792091	1792093	.	+	0	transcript_id "Phchi.S4G031100.t1"; gene_id "Phchi.S4G031100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9265.t1 is derived from g6440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40666381	40668472	.	-	.	Phchi.S1G642400
Phchi.S1	AUGUSTUS	transcript	40666381	40668472	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	stop_codon	40666378	40666380	.	-	0	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	CDS	40666381	40666738	0.99	-	1	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	exon	40666381	40666738	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	intron	40666739	40666816	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	CDS	40666817	40667109	1	-	0	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	exon	40666817	40667109	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	intron	40667110	40667464	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	CDS	40667465	40667630	1	-	1	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	exon	40667465	40667630	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	intron	40667631	40667817	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	CDS	40667818	40667919	1	-	1	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	exon	40667818	40667919	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	intron	40667920	40668017	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	CDS	40668018	40668472	1	-	0	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	exon	40668018	40668472	.	-	.	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
Phchi.S1	AUGUSTUS	start_codon	40668470	40668472	.	-	0	transcript_id "Phchi.S1G642400.t1"; gene_id "Phchi.S1G642400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8620.t1 is derived from g5795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37023000	37023326	.	+	.	Phchi.S1G577900
Phchi.S1	AUGUSTUS	transcript	37023000	37023326	.	+	.	transcript_id "Phchi.S1G577900.t1"; gene_id "Phchi.S1G577900"
Phchi.S1	AUGUSTUS	start_codon	37023000	37023002	.	+	0	transcript_id "Phchi.S1G577900.t1"; gene_id "Phchi.S1G577900"
Phchi.S1	AUGUSTUS	CDS	37023000	37023326	0.67	+	0	transcript_id "Phchi.S1G577900.t1"; gene_id "Phchi.S1G577900"
Phchi.S1	AUGUSTUS	exon	37023000	37023326	.	+	.	transcript_id "Phchi.S1G577900.t1"; gene_id "Phchi.S1G577900"
Phchi.S1	AUGUSTUS	stop_codon	37023327	37023329	.	+	0	transcript_id "Phchi.S1G577900.t1"; gene_id "Phchi.S1G577900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6441.t1 is derived from g3613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23037661	23040862	.	+	.	Phchi.S1G360000
Phchi.S1	AUGUSTUS	transcript	23037661	23040862	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	start_codon	23037661	23037663	.	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23037661	23038137	1	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23037661	23038137	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23038138	23038351	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23038352	23038468	1	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23038352	23038468	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23038469	23038602	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23038603	23038842	1	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23038603	23038842	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23038843	23038933	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23038934	23039479	0.84	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23038934	23039479	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23039480	23039645	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23039646	23039855	0.52	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23039646	23039855	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23039856	23039942	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23039943	23039999	0.93	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23039943	23039999	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23040000	23040118	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23040119	23040226	0.83	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23040119	23040226	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23040227	23040320	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23040321	23040441	1	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23040321	23040441	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23040442	23040517	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23040518	23040687	1	+	2	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23040518	23040687	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	intron	23040688	23040766	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	CDS	23040767	23040862	1	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	exon	23040767	23040862	.	+	.	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
Phchi.S1	AUGUSTUS	stop_codon	23040863	23040865	.	+	0	transcript_id "Phchi.S1G360000.t1"; gene_id "Phchi.S1G360000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2862.t1 is derived from g31.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	142510	144897	.	-	.	Phchi.S1G002100
Phchi.S1	AUGUSTUS	transcript	142510	144897	.	-	.	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	stop_codon	142507	142509	.	-	0	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	CDS	142510	144263	0.99	-	2	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	exon	142510	144263	.	-	.	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	intron	144264	144361	.	-	.	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	CDS	144362	144602	1	-	0	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	exon	144362	144602	.	-	.	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	intron	144603	144684	.	-	.	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	CDS	144685	144897	1	-	0	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	exon	144685	144897	.	-	.	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
Phchi.S1	AUGUSTUS	start_codon	144895	144897	.	-	0	transcript_id "Phchi.S1G002100.t1"; gene_id "Phchi.S1G002100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11140.t1 is derived from g15190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4364832	4366034	.	-	.	Phchi.S4G072200
Phchi.S4	AUGUSTUS	transcript	4364832	4366034	.	-	.	transcript_id "Phchi.S4G072200.t1"; gene_id "Phchi.S4G072200"
Phchi.S4	AUGUSTUS	stop_codon	4364829	4364831	.	-	0	transcript_id "Phchi.S4G072200.t1"; gene_id "Phchi.S4G072200"
Phchi.S4	AUGUSTUS	CDS	4364832	4366034	0.73	-	0	transcript_id "Phchi.S4G072200.t1"; gene_id "Phchi.S4G072200"
Phchi.S4	AUGUSTUS	exon	4364832	4366034	.	-	.	transcript_id "Phchi.S4G072200.t1"; gene_id "Phchi.S4G072200"
Phchi.S4	AUGUSTUS	start_codon	4366032	4366034	.	-	0	transcript_id "Phchi.S4G072200.t1"; gene_id "Phchi.S4G072200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11406.t1 is derived from g15456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6205538	6210458	.	-	.	Phchi.S4G098800
Phchi.S4	AUGUSTUS	transcript	6205538	6210458	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	stop_codon	6205535	6205537	.	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6205538	6205743	0.85	-	2	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6205538	6205743	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6205744	6205850	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6205851	6206363	0.72	-	2	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6205851	6206363	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6206364	6206456	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6206457	6206478	0.65	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6206457	6206478	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6206479	6206603	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6206604	6208400	0.73	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6206604	6208400	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6208401	6208475	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6208476	6208604	1	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6208476	6208604	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6208605	6208870	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6208871	6209002	1	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6208871	6209002	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6209003	6209100	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6209101	6209475	0.97	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6209101	6209475	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6209476	6210028	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6210029	6210170	1	-	1	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6210029	6210170	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	intron	6210171	6210318	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	CDS	6210319	6210458	0.51	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	exon	6210319	6210458	.	-	.	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
Phchi.S4	AUGUSTUS	start_codon	6210456	6210458	.	-	0	transcript_id "Phchi.S4G098800.t1"; gene_id "Phchi.S4G098800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13929.t1 is derived from g12396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9763250	9768388	.	+	.	Phchi.S3G124800
Phchi.S3	AUGUSTUS	transcript	9763250	9768388	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	start_codon	9763250	9763252	.	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9763250	9763587	0.65	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9763250	9763587	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9763588	9763740	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9763741	9764110	0.99	+	1	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9763741	9764110	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9764111	9764206	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9764207	9764761	1	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9764207	9764761	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9764762	9764870	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9764871	9765191	0.99	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9764871	9765191	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9765192	9765329	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9765330	9765419	1	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9765330	9765419	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9765420	9765585	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9765586	9766305	0.91	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9765586	9766305	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9766306	9766412	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9766413	9766577	1	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9766413	9766577	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9766578	9766694	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9766695	9766989	1	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9766695	9766989	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9766990	9767095	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9767096	9767310	0.94	+	2	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9767096	9767310	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9767311	9767414	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9767415	9767720	0.98	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9767415	9767720	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9767721	9767810	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9767811	9767874	1	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9767811	9767874	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9767875	9767950	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9767951	9768190	1	+	2	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9767951	9768190	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	intron	9768191	9768281	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	CDS	9768282	9768388	1	+	2	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	exon	9768282	9768388	.	+	.	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
Phchi.S3	AUGUSTUS	stop_codon	9768389	9768391	.	+	0	transcript_id "Phchi.S3G124800.t1"; gene_id "Phchi.S3G124800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10894.t1 is derived from g14944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2794263	2796352	.	-	.	Phchi.S4G047600
Phchi.S4	AUGUSTUS	transcript	2794263	2796352	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	stop_codon	2794260	2794262	.	-	0	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	CDS	2794263	2794862	0.62	-	0	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	exon	2794263	2794862	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	intron	2794863	2794969	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	CDS	2794970	2795171	0.98	-	1	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	exon	2794970	2795171	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	intron	2795172	2795306	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	CDS	2795307	2795515	0.97	-	0	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	exon	2795307	2795515	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	intron	2795516	2795614	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	CDS	2795615	2795910	0.9	-	2	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	exon	2795615	2795910	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	intron	2795911	2796006	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	CDS	2796007	2796352	0.7	-	0	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	exon	2796007	2796352	.	-	.	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
Phchi.S4	AUGUSTUS	start_codon	2796350	2796352	.	-	0	transcript_id "Phchi.S4G047600.t1"; gene_id "Phchi.S4G047600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15858.t1 is derived from g14328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21893660	21893977	.	-	.	Phchi.S3G317700
Phchi.S3	AUGUSTUS	transcript	21893660	21893977	.	-	.	transcript_id "Phchi.S3G317700.t1"; gene_id "Phchi.S3G317700"
Phchi.S3	AUGUSTUS	stop_codon	21893657	21893659	.	-	0	transcript_id "Phchi.S3G317700.t1"; gene_id "Phchi.S3G317700"
Phchi.S3	AUGUSTUS	CDS	21893660	21893977	0.85	-	0	transcript_id "Phchi.S3G317700.t1"; gene_id "Phchi.S3G317700"
Phchi.S3	AUGUSTUS	exon	21893660	21893977	.	-	.	transcript_id "Phchi.S3G317700.t1"; gene_id "Phchi.S3G317700"
Phchi.S3	AUGUSTUS	start_codon	21893975	21893977	.	-	0	transcript_id "Phchi.S3G317700.t1"; gene_id "Phchi.S3G317700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9748.t1 is derived from g6924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43490461	43490904	.	+	.	Phchi.S1G690700
Phchi.S1	AUGUSTUS	transcript	43490461	43490904	.	+	.	transcript_id "Phchi.S1G690700.t1"; gene_id "Phchi.S1G690700"
Phchi.S1	AUGUSTUS	start_codon	43490461	43490463	.	+	0	transcript_id "Phchi.S1G690700.t1"; gene_id "Phchi.S1G690700"
Phchi.S1	AUGUSTUS	CDS	43490461	43490904	0.93	+	0	transcript_id "Phchi.S1G690700.t1"; gene_id "Phchi.S1G690700"
Phchi.S1	AUGUSTUS	exon	43490461	43490904	.	+	.	transcript_id "Phchi.S1G690700.t1"; gene_id "Phchi.S1G690700"
Phchi.S1	AUGUSTUS	stop_codon	43490905	43490907	.	+	0	transcript_id "Phchi.S1G690700.t1"; gene_id "Phchi.S1G690700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10612.t1 is derived from g14662.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1209452	1215438	.	-	.	Phchi.S4G019400
Phchi.S4	AUGUSTUS	transcript	1209452	1215438	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	stop_codon	1209449	1209451	.	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209452	1209520	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209452	1209520	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209521	1209610	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209611	1209697	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209611	1209697	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209698	1209782	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209783	1209854	0.99	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209783	1209854	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209855	1209937	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209938	1210030	0.97	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209938	1210030	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210031	1210125	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210126	1210242	0.88	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210126	1210242	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210243	1210354	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210355	1210387	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210355	1210387	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210388	1210567	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210568	1210655	1	-	1	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210568	1210655	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210656	1210729	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210730	1210785	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210730	1210785	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210786	1210927	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210928	1211116	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210928	1211116	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211117	1211212	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211213	1211303	1	-	1	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211213	1211303	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211304	1211396	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211397	1211509	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211397	1211509	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211510	1211687	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211688	1211776	0.97	-	2	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211688	1211776	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211777	1211861	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211862	1211886	0.97	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211862	1211886	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211887	1212060	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212061	1212177	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212061	1212177	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212178	1212371	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212372	1212525	1	-	1	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212372	1212525	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212526	1212736	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212737	1212888	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212737	1212888	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212889	1213045	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213046	1213153	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213046	1213153	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213154	1213229	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213230	1213463	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213230	1213463	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213464	1213567	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213568	1213696	0.97	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213568	1213696	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213697	1213791	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213792	1213884	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213792	1213884	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213885	1213956	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213957	1214032	1	-	1	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213957	1214032	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214033	1214134	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214135	1214295	0.72	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214135	1214295	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214296	1214405	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214406	1214486	0.35	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214406	1214486	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214487	1214598	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214599	1214679	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214599	1214679	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214680	1214767	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214768	1214877	1	-	2	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214768	1214877	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214878	1214969	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214970	1215081	1	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214970	1215081	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1215082	1215162	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1215163	1215266	0.99	-	2	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1215163	1215266	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1215267	1215407	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1215408	1215438	0.82	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1215408	1215438	.	-	.	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	start_codon	1215436	1215438	.	-	0	transcript_id "Phchi.S4G019400.t1"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	transcript	1209452	1215438	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	stop_codon	1209449	1209451	.	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209452	1209520	0.98	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209452	1209520	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209521	1209610	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209611	1209697	0.98	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209611	1209697	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209698	1209782	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209783	1209854	0.99	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209783	1209854	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209855	1209937	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209938	1210030	0.94	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209938	1210030	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210031	1210125	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210126	1210242	0.89	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210126	1210242	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210243	1210354	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210355	1210387	0.99	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210355	1210387	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210388	1210567	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210568	1210655	1	-	1	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210568	1210655	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210656	1210729	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210730	1210785	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210730	1210785	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210786	1210927	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210928	1211116	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210928	1211116	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211117	1211212	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211213	1211303	1	-	1	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211213	1211303	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211304	1211396	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211397	1211509	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211397	1211509	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211510	1211687	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211688	1211771	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211688	1211771	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211772	1211861	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211862	1211987	0.84	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211862	1211987	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211988	1212060	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212061	1212177	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212061	1212177	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212178	1212371	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212372	1212525	1	-	1	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212372	1212525	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212526	1212736	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212737	1212888	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212737	1212888	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212889	1213045	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213046	1213153	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213046	1213153	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213154	1213229	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213230	1213463	0.99	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213230	1213463	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213464	1213567	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213568	1213696	0.93	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213568	1213696	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213697	1213791	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213792	1213884	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213792	1213884	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213885	1213956	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213957	1214032	1	-	1	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213957	1214032	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214033	1214134	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214135	1214295	0.77	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214135	1214295	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214296	1214405	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214406	1214486	0.42	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214406	1214486	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214487	1214598	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214599	1214679	0.94	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214599	1214679	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214680	1214767	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214768	1214877	1	-	2	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214768	1214877	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214878	1214969	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214970	1215081	1	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214970	1215081	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1215082	1215162	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1215163	1215266	0.99	-	2	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1215163	1215266	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1215267	1215407	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1215408	1215438	0.82	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1215408	1215438	.	-	.	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	start_codon	1215436	1215438	.	-	0	transcript_id "Phchi.S4G019400.t2"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	transcript	1209452	1215438	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	stop_codon	1209449	1209451	.	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209452	1209520	0.99	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209452	1209520	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209521	1209610	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209611	1209697	0.99	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209611	1209697	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209698	1209782	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209783	1209854	0.99	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209783	1209854	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1209855	1209937	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1209938	1210030	0.9	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1209938	1210030	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210031	1210125	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210126	1210242	0.91	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210126	1210242	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210243	1210354	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210355	1210447	0.66	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210355	1210447	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210448	1210567	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210568	1210655	0.95	-	1	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210568	1210655	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210656	1210729	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210730	1210785	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210730	1210785	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1210786	1210927	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1210928	1211116	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1210928	1211116	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211117	1211212	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211213	1211303	1	-	1	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211213	1211303	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211304	1211396	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211397	1211509	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211397	1211509	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211510	1211687	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211688	1211771	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211688	1211771	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211772	1211861	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1211862	1211987	0.83	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1211862	1211987	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1211988	1212060	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212061	1212177	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212061	1212177	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212178	1212371	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212372	1212525	1	-	1	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212372	1212525	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212526	1212736	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1212737	1212888	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1212737	1212888	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1212889	1213045	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213046	1213153	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213046	1213153	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213154	1213229	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213230	1213463	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213230	1213463	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213464	1213567	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213568	1213696	0.91	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213568	1213696	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213697	1213791	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213792	1213884	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213792	1213884	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1213885	1213956	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1213957	1214032	1	-	1	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1213957	1214032	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214033	1214134	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214135	1214295	0.83	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214135	1214295	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214296	1214405	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214406	1214486	0.37	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214406	1214486	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214487	1214598	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214599	1214679	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214599	1214679	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214680	1214767	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214768	1214877	1	-	2	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214768	1214877	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1214878	1214969	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1214970	1215081	1	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1214970	1215081	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1215082	1215162	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1215163	1215266	1	-	2	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1215163	1215266	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	intron	1215267	1215407	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	CDS	1215408	1215438	0.73	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	exon	1215408	1215438	.	-	.	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
Phchi.S4	AUGUSTUS	start_codon	1215436	1215438	.	-	0	transcript_id "Phchi.S4G019400.t3"; gene_id "Phchi.S4G019400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4725.t1 is derived from g1895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12489475	12489882	.	+	.	Phchi.S1G188400
Phchi.S1	AUGUSTUS	transcript	12489475	12489882	.	+	.	transcript_id "Phchi.S1G188400.t1"; gene_id "Phchi.S1G188400"
Phchi.S1	AUGUSTUS	start_codon	12489475	12489477	.	+	0	transcript_id "Phchi.S1G188400.t1"; gene_id "Phchi.S1G188400"
Phchi.S1	AUGUSTUS	CDS	12489475	12489882	0.99	+	0	transcript_id "Phchi.S1G188400.t1"; gene_id "Phchi.S1G188400"
Phchi.S1	AUGUSTUS	exon	12489475	12489882	.	+	.	transcript_id "Phchi.S1G188400.t1"; gene_id "Phchi.S1G188400"
Phchi.S1	AUGUSTUS	stop_codon	12489883	12489885	.	+	0	transcript_id "Phchi.S1G188400.t1"; gene_id "Phchi.S1G188400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4171.t1 is derived from g1340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8731157	8732324	.	-	.	Phchi.S1G133000
Phchi.S1	AUGUSTUS	transcript	8731157	8732324	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	stop_codon	8731154	8731156	.	-	0	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	CDS	8731157	8731609	0.94	-	0	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	exon	8731157	8731609	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	intron	8731610	8731705	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	CDS	8731706	8731888	1	-	0	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	exon	8731706	8731888	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	intron	8731889	8731963	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	CDS	8731964	8732225	1	-	1	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	exon	8731964	8732225	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	intron	8732226	8732304	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	CDS	8732305	8732324	1	-	0	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	exon	8732305	8732324	.	-	.	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
Phchi.S1	AUGUSTUS	start_codon	8732322	8732324	.	-	0	transcript_id "Phchi.S1G133000.t1"; gene_id "Phchi.S1G133000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4565.t1 is derived from g1735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11144008	11145236	.	+	.	Phchi.S1G172400
Phchi.S1	AUGUSTUS	transcript	11144008	11145236	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	start_codon	11144008	11144010	.	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	CDS	11144008	11144010	1	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	exon	11144008	11144010	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	intron	11144011	11144097	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	CDS	11144098	11144154	1	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	exon	11144098	11144154	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	intron	11144155	11144240	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	CDS	11144241	11144448	0.98	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	exon	11144241	11144448	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	intron	11144449	11144549	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	CDS	11144550	11144719	1	+	2	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	exon	11144550	11144719	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	intron	11144720	11144799	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	CDS	11144800	11145021	1	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	exon	11144800	11145021	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	intron	11145022	11145107	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	CDS	11145108	11145236	0.86	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	exon	11145108	11145236	.	+	.	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
Phchi.S1	AUGUSTUS	stop_codon	11145237	11145239	.	+	0	transcript_id "Phchi.S1G172400.t1"; gene_id "Phchi.S1G172400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11927.t1 is derived from g7602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	52340	52870	.	-	.	Phchi.S2G000700
Phchi.S2	AUGUSTUS	transcript	52340	52870	.	-	.	transcript_id "Phchi.S2G000700.t1"; gene_id "Phchi.S2G000700"
Phchi.S2	AUGUSTUS	stop_codon	52337	52339	.	-	0	transcript_id "Phchi.S2G000700.t1"; gene_id "Phchi.S2G000700"
Phchi.S2	AUGUSTUS	CDS	52340	52870	0.97	-	0	transcript_id "Phchi.S2G000700.t1"; gene_id "Phchi.S2G000700"
Phchi.S2	AUGUSTUS	exon	52340	52870	.	-	.	transcript_id "Phchi.S2G000700.t1"; gene_id "Phchi.S2G000700"
Phchi.S2	AUGUSTUS	start_codon	52868	52870	.	-	0	transcript_id "Phchi.S2G000700.t1"; gene_id "Phchi.S2G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1433.t1 is derived from g8352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	818150	822462	.	-	.	Phchi.S5G004200
Phchi.S5	AUGUSTUS	transcript	818150	822462	.	-	.	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	stop_codon	818147	818149	.	-	0	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	CDS	818150	818262	0.7	-	2	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	exon	818150	818262	.	-	.	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	intron	818263	818446	.	-	.	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	CDS	818447	820062	0.64	-	1	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	exon	818447	820062	.	-	.	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	intron	820063	820198	.	-	.	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	CDS	820199	822462	0.46	-	0	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	exon	820199	822462	.	-	.	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
Phchi.S5	AUGUSTUS	start_codon	822460	822462	.	-	0	transcript_id "Phchi.S5G004200.t1"; gene_id "Phchi.S5G004200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15025.t1 is derived from g13493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16586605	16589628	.	-	.	Phchi.S3G234400
Phchi.S3	AUGUSTUS	transcript	16586605	16589628	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	stop_codon	16586602	16586604	.	-	0	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16586605	16586885	1	-	2	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16586605	16586885	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	intron	16586886	16586967	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16586968	16587238	1	-	0	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16586968	16587238	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	intron	16587239	16587326	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16587327	16587484	1	-	2	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16587327	16587484	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	intron	16587485	16587581	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16587582	16587815	0.99	-	2	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16587582	16587815	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	intron	16587816	16587926	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16587927	16588180	0.71	-	1	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16587927	16588180	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	intron	16588181	16588412	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16588413	16589223	0.59	-	2	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16588413	16589223	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	intron	16589224	16589330	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	CDS	16589331	16589628	0.42	-	0	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	exon	16589331	16589628	.	-	.	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
Phchi.S3	AUGUSTUS	start_codon	16589626	16589628	.	-	0	transcript_id "Phchi.S3G234400.t1"; gene_id "Phchi.S3G234400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9601.t1 is derived from g6777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42885558	42888209	.	-	.	Phchi.S1G676000
Phchi.S1	AUGUSTUS	transcript	42885558	42888209	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	stop_codon	42885555	42885557	.	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42885558	42885634	0.95	-	2	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42885558	42885634	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42885635	42885737	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42885738	42885852	0.94	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42885738	42885852	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42885853	42885959	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42885960	42886015	1	-	2	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42885960	42886015	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42886016	42886105	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42886106	42886179	1	-	1	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42886106	42886179	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42886180	42886289	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42886290	42886336	1	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42886290	42886336	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42886337	42886417	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42886418	42886463	1	-	1	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42886418	42886463	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42886464	42886584	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42886585	42886661	1	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42886585	42886661	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42886662	42886746	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42886747	42886803	1	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42886747	42886803	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42886804	42887062	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42887063	42887167	0.52	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42887063	42887167	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42887168	42887283	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42887284	42887356	0.97	-	1	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42887284	42887356	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42887357	42887450	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42887451	42887538	0.97	-	2	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42887451	42887538	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42887539	42887639	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42887640	42887704	0.9	-	1	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42887640	42887704	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42887705	42887819	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42887820	42887852	1	-	1	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42887820	42887852	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	intron	42887853	42888087	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	CDS	42888088	42888209	0.99	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	exon	42888088	42888209	.	-	.	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
Phchi.S1	AUGUSTUS	start_codon	42888207	42888209	.	-	0	transcript_id "Phchi.S1G676000.t1"; gene_id "Phchi.S1G676000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12165.t1 is derived from g7841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5082418	5083443	.	-	.	Phchi.S2G024500
Phchi.S2	AUGUSTUS	transcript	5082418	5083221	.	-	.	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	stop_codon	5082415	5082417	.	-	0	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	CDS	5082418	5082745	0.93	-	1	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	exon	5082418	5082745	.	-	.	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	intron	5082746	5082886	.	-	.	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	CDS	5082887	5083221	0.99	-	0	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	exon	5082887	5083221	.	-	.	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	start_codon	5083219	5083221	.	-	0	transcript_id "Phchi.S2G024500.t1"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	transcript	5082418	5083443	.	-	.	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	stop_codon	5082415	5082417	.	-	0	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	CDS	5082418	5082745	0.94	-	1	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	exon	5082418	5082745	.	-	.	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	intron	5082746	5082886	.	-	.	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	CDS	5082887	5083443	0.94	-	0	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	exon	5082887	5083443	.	-	.	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
Phchi.S2	AUGUSTUS	start_codon	5083441	5083443	.	-	0	transcript_id "Phchi.S2G024500.t2"; gene_id "Phchi.S2G024500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2720.t1 is derived from g9640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8403578	8404442	.	-	.	Phchi.S5G132900
Phchi.S5	AUGUSTUS	transcript	8403578	8404442	.	-	.	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	stop_codon	8403575	8403577	.	-	0	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	CDS	8403578	8403854	0.81	-	1	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	exon	8403578	8403854	.	-	.	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	intron	8403855	8403994	.	-	.	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	CDS	8403995	8404146	0.95	-	0	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	exon	8403995	8404146	.	-	.	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	intron	8404147	8404256	.	-	.	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	CDS	8404257	8404442	0.95	-	0	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	exon	8404257	8404442	.	-	.	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
Phchi.S5	AUGUSTUS	start_codon	8404440	8404442	.	-	0	transcript_id "Phchi.S5G132900.t1"; gene_id "Phchi.S5G132900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3096.t1 is derived from g265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1734411	1737517	.	+	.	Phchi.S1G025500
Phchi.S1	AUGUSTUS	transcript	1734411	1737517	.	+	.	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	start_codon	1734411	1734413	.	+	0	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	CDS	1734411	1734957	0.64	+	0	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	exon	1734411	1734957	.	+	.	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	intron	1734958	1735118	.	+	.	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	CDS	1735119	1737075	1	+	2	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	exon	1735119	1737075	.	+	.	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	intron	1737076	1737165	.	+	.	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	CDS	1737166	1737517	1	+	1	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	exon	1737166	1737517	.	+	.	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
Phchi.S1	AUGUSTUS	stop_codon	1737518	1737520	.	+	0	transcript_id "Phchi.S1G025500.t1"; gene_id "Phchi.S1G025500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg333.t1 is derived from g10115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2440060	2440607	.	+	.	Phchi.S6G029200
Phchi.S6	AUGUSTUS	transcript	2440060	2440607	.	+	.	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	start_codon	2440060	2440062	.	+	0	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	CDS	2440060	2440209	0.66	+	0	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	exon	2440060	2440209	.	+	.	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	intron	2440210	2440289	.	+	.	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	CDS	2440290	2440607	0.35	+	0	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	exon	2440290	2440607	.	+	.	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
Phchi.S6	AUGUSTUS	stop_codon	2440608	2440610	.	+	0	transcript_id "Phchi.S6G029200.t1"; gene_id "Phchi.S6G029200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10989.t1 is derived from g15039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3542881	3548415	.	-	.	Phchi.S4G057100
Phchi.S4	AUGUSTUS	transcript	3542881	3548415	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	stop_codon	3542878	3542880	.	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3542881	3543489	0.79	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3542881	3543489	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3543490	3543597	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3543598	3544398	0.93	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3543598	3544398	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3544399	3544521	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3544522	3544587	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3544522	3544587	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3544588	3544704	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3544705	3544753	1	-	1	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3544705	3544753	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3544754	3544840	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3544841	3544950	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3544841	3544950	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3544951	3545079	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3545080	3545265	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3545080	3545265	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3545266	3545353	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3545354	3545425	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3545354	3545425	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3545426	3545545	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3545546	3545659	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3545546	3545659	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3545660	3545755	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3545756	3545845	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3545756	3545845	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3545846	3545936	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3545937	3545987	0.98	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3545937	3545987	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3545988	3546102	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3546103	3546198	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3546103	3546198	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3546199	3546320	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3546321	3546374	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3546321	3546374	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3546375	3546579	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3546580	3546649	1	-	1	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3546580	3546649	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3546650	3546740	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3546741	3546814	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3546741	3546814	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3546815	3546908	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3546909	3547055	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3546909	3547055	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3547056	3547532	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3547533	3547585	1	-	2	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3547533	3547585	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3547586	3547939	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3547940	3548067	1	-	1	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3547940	3548067	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3548068	3548198	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3548199	3548254	1	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3548199	3548254	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	intron	3548255	3548364	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	CDS	3548365	3548415	0.57	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	exon	3548365	3548415	.	-	.	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
Phchi.S4	AUGUSTUS	start_codon	3548413	3548415	.	-	0	transcript_id "Phchi.S4G057100.t1"; gene_id "Phchi.S4G057100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13975.t1 is derived from g12442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10007842	10010001	.	-	.	Phchi.S3G129400
Phchi.S3	AUGUSTUS	transcript	10007842	10010001	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	stop_codon	10007839	10007841	.	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10007842	10007915	0.47	-	2	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10007842	10007915	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	intron	10007916	10008004	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10008005	10008101	0.49	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10008005	10008101	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	intron	10008102	10008232	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10008233	10008373	1	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10008233	10008373	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	intron	10008374	10008493	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10008494	10008585	1	-	2	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10008494	10008585	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	intron	10008586	10008725	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10008726	10008876	0.47	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10008726	10008876	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	intron	10008877	10008957	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10008958	10009128	0.85	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10008958	10009128	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	intron	10009129	10009341	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	CDS	10009342	10010001	0.7	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	exon	10009342	10010001	.	-	.	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
Phchi.S3	AUGUSTUS	start_codon	10009999	10010001	.	-	0	transcript_id "Phchi.S3G129400.t1"; gene_id "Phchi.S3G129400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11281.t1 is derived from g15331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5189207	5190097	.	+	.	Phchi.S4G086300
Phchi.S4	AUGUSTUS	transcript	5189207	5190097	.	+	.	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	start_codon	5189207	5189209	.	+	0	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	CDS	5189207	5189427	1	+	0	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	exon	5189207	5189427	.	+	.	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	intron	5189428	5189658	.	+	.	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	CDS	5189659	5190097	0.82	+	1	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	exon	5189659	5190097	.	+	.	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
Phchi.S4	AUGUSTUS	stop_codon	5190098	5190100	.	+	0	transcript_id "Phchi.S4G086300.t1"; gene_id "Phchi.S4G086300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7838.t1 is derived from g5012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31468908	31470399	.	+	.	Phchi.S1G499700
Phchi.S1	AUGUSTUS	transcript	31468908	31470399	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	start_codon	31468908	31468910	.	+	0	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	CDS	31468908	31469052	1	+	0	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	exon	31468908	31469052	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	intron	31469053	31469233	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	CDS	31469234	31469328	1	+	2	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	exon	31469234	31469328	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	intron	31469329	31469422	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	CDS	31469423	31469540	1	+	0	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	exon	31469423	31469540	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	intron	31469541	31469649	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	CDS	31469650	31469782	1	+	2	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	exon	31469650	31469782	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	intron	31469783	31469874	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	CDS	31469875	31470094	1	+	1	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	exon	31469875	31470094	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	intron	31470095	31470171	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	CDS	31470172	31470399	0.5	+	0	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	exon	31470172	31470399	.	+	.	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
Phchi.S1	AUGUSTUS	stop_codon	31470400	31470402	.	+	0	transcript_id "Phchi.S1G499700.t1"; gene_id "Phchi.S1G499700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4611.t1 is derived from g1781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11384716	11386300	.	-	.	Phchi.S1G177000
Phchi.S1	AUGUSTUS	transcript	11384716	11386300	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	stop_codon	11384713	11384715	.	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	CDS	11384716	11385020	0.92	-	2	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	exon	11384716	11385020	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	intron	11385021	11385113	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	CDS	11385114	11385417	0.96	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	exon	11385114	11385417	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	intron	11385418	11385502	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	CDS	11385503	11385601	0.9	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	exon	11385503	11385601	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	intron	11385602	11385708	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	CDS	11385709	11385843	0.95	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	exon	11385709	11385843	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	intron	11385844	11385940	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	CDS	11385941	11386057	0.85	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	exon	11385941	11386057	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	intron	11386058	11386213	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	CDS	11386214	11386300	0.75	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	exon	11386214	11386300	.	-	.	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
Phchi.S1	AUGUSTUS	start_codon	11386298	11386300	.	-	0	transcript_id "Phchi.S1G177000.t1"; gene_id "Phchi.S1G177000"
# This transcript jg5874.t2 is derived from g3044.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5875.t1 is derived from g3045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19526805	19527238	.	-	.	Phchi.S1G303400
Phchi.S1	AUGUSTUS	transcript	19526805	19527238	.	-	.	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	stop_codon	19526802	19526804	.	-	0	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	CDS	19526805	19527047	0.35	-	0	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	exon	19526805	19527047	.	-	.	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	intron	19527048	19527199	.	-	.	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	CDS	19527200	19527238	0.36	-	0	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	exon	19527200	19527238	.	-	.	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
Phchi.S1	AUGUSTUS	start_codon	19527236	19527238	.	-	0	transcript_id "Phchi.S1G303400.t1"; gene_id "Phchi.S1G303400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6725.t1 is derived from g3897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24751252	24751901	.	-	.	Phchi.S1G388400
Phchi.S1	AUGUSTUS	transcript	24751252	24751901	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	stop_codon	24751249	24751251	.	-	0	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	CDS	24751252	24751253	0.98	-	2	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	exon	24751252	24751253	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	intron	24751254	24751330	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	CDS	24751331	24751452	0.61	-	1	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	exon	24751331	24751452	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	intron	24751453	24751530	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	CDS	24751531	24751591	0.44	-	2	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	exon	24751531	24751591	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	intron	24751592	24751843	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	CDS	24751844	24751901	0.6	-	0	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	exon	24751844	24751901	.	-	.	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
Phchi.S1	AUGUSTUS	start_codon	24751899	24751901	.	-	0	transcript_id "Phchi.S1G388400.t1"; gene_id "Phchi.S1G388400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15221.t1 is derived from g13689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17810808	17811171	.	-	.	Phchi.S3G254000
Phchi.S3	AUGUSTUS	transcript	17810808	17811171	.	-	.	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	stop_codon	17810805	17810807	.	-	0	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	CDS	17810808	17810883	0.98	-	1	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	exon	17810808	17810883	.	-	.	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	intron	17810884	17811031	.	-	.	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	CDS	17811032	17811171	0.46	-	0	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	exon	17811032	17811171	.	-	.	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
Phchi.S3	AUGUSTUS	start_codon	17811169	17811171	.	-	0	transcript_id "Phchi.S3G254000.t1"; gene_id "Phchi.S3G254000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15786.t1 is derived from g14256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21342228	21345898	.	+	.	Phchi.S3G310500
Phchi.S3	AUGUSTUS	transcript	21342228	21345898	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	start_codon	21342228	21342230	.	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21342228	21342542	0.7	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21342228	21342542	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	intron	21342543	21342730	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21342731	21343514	0.69	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21342731	21343514	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	intron	21343515	21343672	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21343673	21344124	0.88	+	2	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21343673	21344124	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	intron	21344125	21344296	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21344297	21344551	1	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21344297	21344551	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	intron	21344552	21344651	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21344652	21344774	1	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21344652	21344774	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	intron	21344775	21344894	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21344895	21345380	1	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21344895	21345380	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	intron	21345381	21345493	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	CDS	21345494	21345898	1	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	exon	21345494	21345898	.	+	.	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
Phchi.S3	AUGUSTUS	stop_codon	21345899	21345901	.	+	0	transcript_id "Phchi.S3G310500.t1"; gene_id "Phchi.S3G310500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12905.t1 is derived from g11370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3084987	3085807	.	-	.	Phchi.S3G022400
Phchi.S3	AUGUSTUS	transcript	3084987	3085807	.	-	.	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	stop_codon	3084984	3084986	.	-	0	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	CDS	3084987	3085353	1	-	1	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	exon	3084987	3085353	.	-	.	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	intron	3085354	3085430	.	-	.	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	CDS	3085431	3085552	1	-	0	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	exon	3085431	3085552	.	-	.	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	intron	3085553	3085675	.	-	.	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	CDS	3085676	3085807	0.94	-	0	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	exon	3085676	3085807	.	-	.	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
Phchi.S3	AUGUSTUS	start_codon	3085805	3085807	.	-	0	transcript_id "Phchi.S3G022400.t1"; gene_id "Phchi.S3G022400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3458.t1 is derived from g627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3869913	3870289	.	+	.	Phchi.S1G061700
Phchi.S1	AUGUSTUS	transcript	3869913	3870289	.	+	.	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	start_codon	3869913	3869915	.	+	0	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	CDS	3869913	3870151	0.71	+	0	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	exon	3869913	3870151	.	+	.	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	intron	3870152	3870234	.	+	.	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	CDS	3870235	3870289	0.98	+	1	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	exon	3870235	3870289	.	+	.	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
Phchi.S1	AUGUSTUS	stop_codon	3870290	3870292	.	+	0	transcript_id "Phchi.S1G061700.t1"; gene_id "Phchi.S1G061700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5456.t1 is derived from g2626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16936397	16937347	.	-	.	Phchi.S1G261500
Phchi.S1	AUGUSTUS	transcript	16936397	16937347	.	-	.	transcript_id "Phchi.S1G261500.t1"; gene_id "Phchi.S1G261500"
Phchi.S1	AUGUSTUS	stop_codon	16936394	16936396	.	-	0	transcript_id "Phchi.S1G261500.t1"; gene_id "Phchi.S1G261500"
Phchi.S1	AUGUSTUS	CDS	16936397	16937347	0.95	-	0	transcript_id "Phchi.S1G261500.t1"; gene_id "Phchi.S1G261500"
Phchi.S1	AUGUSTUS	exon	16936397	16937347	.	-	.	transcript_id "Phchi.S1G261500.t1"; gene_id "Phchi.S1G261500"
Phchi.S1	AUGUSTUS	start_codon	16937345	16937347	.	-	0	transcript_id "Phchi.S1G261500.t1"; gene_id "Phchi.S1G261500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8995.t1 is derived from g6170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39030666	39031153	.	+	.	Phchi.S1G615400
Phchi.S1	AUGUSTUS	transcript	39030666	39031153	.	+	.	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	start_codon	39030666	39030668	.	+	0	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	CDS	39030666	39030985	0.72	+	0	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	exon	39030666	39030985	.	+	.	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	intron	39030986	39031071	.	+	.	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	CDS	39031072	39031153	0.68	+	1	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	exon	39031072	39031153	.	+	.	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
Phchi.S1	AUGUSTUS	stop_codon	39031154	39031156	.	+	0	transcript_id "Phchi.S1G615400.t1"; gene_id "Phchi.S1G615400"
# This transcript jg11427.t2 is derived from g15477.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11428.t1 is derived from g15478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6294281	6295201	.	+	.	Phchi.S4G101000
Phchi.S4	AUGUSTUS	transcript	6294281	6295201	.	+	.	transcript_id "Phchi.S4G101000.t1"; gene_id "Phchi.S4G101000"
Phchi.S4	AUGUSTUS	start_codon	6294281	6294283	.	+	0	transcript_id "Phchi.S4G101000.t1"; gene_id "Phchi.S4G101000"
Phchi.S4	AUGUSTUS	CDS	6294281	6295201	0.94	+	0	transcript_id "Phchi.S4G101000.t1"; gene_id "Phchi.S4G101000"
Phchi.S4	AUGUSTUS	exon	6294281	6295201	.	+	.	transcript_id "Phchi.S4G101000.t1"; gene_id "Phchi.S4G101000"
Phchi.S4	AUGUSTUS	stop_codon	6295202	6295204	.	+	0	transcript_id "Phchi.S4G101000.t1"; gene_id "Phchi.S4G101000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3145.t1 is derived from g314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1978849	1980474	.	+	.	Phchi.S1G030400
Phchi.S1	AUGUSTUS	transcript	1978849	1980474	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	start_codon	1978849	1978851	.	+	0	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	CDS	1978849	1978864	0.6	+	0	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	exon	1978849	1978864	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	intron	1978865	1978975	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	CDS	1978976	1979004	0.52	+	2	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	exon	1978976	1979004	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	intron	1979005	1979231	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	CDS	1979232	1979258	0.66	+	0	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	exon	1979232	1979258	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	intron	1979259	1979343	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	CDS	1979344	1980062	0.57	+	0	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	exon	1979344	1980062	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	intron	1980063	1980154	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	CDS	1980155	1980238	0.53	+	1	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	exon	1980155	1980238	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	intron	1980239	1980410	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	CDS	1980411	1980474	1	+	1	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	exon	1980411	1980474	.	+	.	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
Phchi.S1	AUGUSTUS	stop_codon	1980475	1980477	.	+	0	transcript_id "Phchi.S1G030400.t1"; gene_id "Phchi.S1G030400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1069.t1 is derived from g10852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7425291	7427180	.	-	.	Phchi.S6G102800
Phchi.S6	AUGUSTUS	transcript	7425291	7427180	.	-	.	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	stop_codon	7425288	7425290	.	-	0	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	CDS	7425291	7426584	0.26	-	1	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	exon	7425291	7426584	.	-	.	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	intron	7426585	7426875	.	-	.	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	CDS	7426876	7427180	0.88	-	0	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	exon	7426876	7427180	.	-	.	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
Phchi.S6	AUGUSTUS	start_codon	7427178	7427180	.	-	0	transcript_id "Phchi.S6G102800.t1"; gene_id "Phchi.S6G102800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9326.t1 is derived from g6501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40949592	40950345	.	-	.	Phchi.S1G648500
Phchi.S1	AUGUSTUS	transcript	40949592	40950345	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	stop_codon	40949589	40949591	.	-	0	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	CDS	40949592	40949714	1	-	0	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	exon	40949592	40949714	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	intron	40949715	40949821	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	CDS	40949822	40949944	0.9	-	0	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	exon	40949822	40949944	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	intron	40949945	40950046	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	CDS	40950047	40950154	0.74	-	0	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	exon	40950047	40950154	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	intron	40950155	40950279	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	CDS	40950280	40950345	0.72	-	0	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	exon	40950280	40950345	.	-	.	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
Phchi.S1	AUGUSTUS	start_codon	40950343	40950345	.	-	0	transcript_id "Phchi.S1G648500.t1"; gene_id "Phchi.S1G648500"
# This transcript jg10394.t2 is derived from g7570.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10395.t1 is derived from g7571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47532929	47533260	.	-	.	Phchi.S1G755400
Phchi.S1	AUGUSTUS	transcript	47532929	47533260	.	-	.	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	stop_codon	47532926	47532928	.	-	0	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	CDS	47532929	47533148	0.46	-	1	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	exon	47532929	47533148	.	-	.	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	intron	47533149	47533234	.	-	.	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	CDS	47533235	47533260	0.46	-	0	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	exon	47533235	47533260	.	-	.	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
Phchi.S1	AUGUSTUS	start_codon	47533258	47533260	.	-	0	transcript_id "Phchi.S1G755400.t1"; gene_id "Phchi.S1G755400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6043.t1 is derived from g3214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20600461	20600963	.	+	.	Phchi.S1G320200
Phchi.S1	AUGUSTUS	transcript	20600461	20600963	.	+	.	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	start_codon	20600461	20600463	.	+	0	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	CDS	20600461	20600701	1	+	0	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	exon	20600461	20600701	.	+	.	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	intron	20600702	20600961	.	+	.	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	CDS	20600962	20600963	1	+	2	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	exon	20600962	20600963	.	+	.	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
Phchi.S1	AUGUSTUS	stop_codon	20600964	20600966	.	+	0	transcript_id "Phchi.S1G320200.t1"; gene_id "Phchi.S1G320200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10313.t1 is derived from g7489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47082837	47083370	.	+	.	Phchi.S1G747200
Phchi.S1	AUGUSTUS	transcript	47082837	47083370	.	+	.	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	start_codon	47082837	47082839	.	+	0	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	CDS	47082837	47082910	0.24	+	0	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	exon	47082837	47082910	.	+	.	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	intron	47082911	47083113	.	+	.	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	CDS	47083114	47083204	0.64	+	1	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	exon	47083114	47083204	.	+	.	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	intron	47083205	47083289	.	+	.	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	CDS	47083290	47083370	0.63	+	0	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	exon	47083290	47083370	.	+	.	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
Phchi.S1	AUGUSTUS	stop_codon	47083371	47083373	.	+	0	transcript_id "Phchi.S1G747200.t1"; gene_id "Phchi.S1G747200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg248.t1 is derived from g10030.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1703840	1706012	.	+	.	Phchi.S6G020700
Phchi.S6	AUGUSTUS	transcript	1703840	1706012	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	start_codon	1703840	1703842	.	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1703840	1704100	0.38	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1703840	1704100	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704101	1704174	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704175	1704293	1	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704175	1704293	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704294	1704404	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704405	1704484	0.98	+	1	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704405	1704484	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704485	1704670	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704671	1704726	1	+	2	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704671	1704726	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704727	1704903	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704904	1705012	0.4	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704904	1705012	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705013	1705126	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705127	1705182	0.62	+	2	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705127	1705182	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705183	1705315	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705316	1705411	1	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705316	1705411	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705412	1705559	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705560	1705697	1	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705560	1705697	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705698	1705777	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705778	1705840	1	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705778	1705840	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705841	1705922	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705923	1706012	1	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705923	1706012	.	+	.	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	stop_codon	1706013	1706015	.	+	0	transcript_id "Phchi.S6G020700.t1"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	transcript	1703840	1706012	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	start_codon	1703840	1703842	.	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1703840	1704100	0.39	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1703840	1704100	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704101	1704180	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704181	1704293	0.92	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704181	1704293	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704294	1704404	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704405	1704484	1	+	1	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704405	1704484	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704485	1704670	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704671	1704726	1	+	2	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704671	1704726	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1704727	1704903	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1704904	1705012	0.31	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1704904	1705012	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705013	1705126	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705127	1705182	0.5	+	2	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705127	1705182	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705183	1705315	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705316	1705411	1	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705316	1705411	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705412	1705559	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705560	1705697	1	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705560	1705697	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705698	1705777	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705778	1705840	1	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705778	1705840	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	intron	1705841	1705922	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	CDS	1705923	1706012	0.99	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	exon	1705923	1706012	.	+	.	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
Phchi.S6	AUGUSTUS	stop_codon	1706013	1706015	.	+	0	transcript_id "Phchi.S6G020700.t2"; gene_id "Phchi.S6G020700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9528.t1 is derived from g6704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42323107	42324340	.	+	.	Phchi.S1G668700
Phchi.S1	AUGUSTUS	transcript	42323107	42324340	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	start_codon	42323107	42323109	.	+	0	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	CDS	42323107	42323129	1	+	0	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	exon	42323107	42323129	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	intron	42323130	42323295	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	CDS	42323296	42323557	1	+	1	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	exon	42323296	42323557	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	intron	42323558	42323644	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	CDS	42323645	42323809	1	+	0	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	exon	42323645	42323809	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	intron	42323810	42323908	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	CDS	42323909	42324340	1	+	0	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	exon	42323909	42324340	.	+	.	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
Phchi.S1	AUGUSTUS	stop_codon	42324341	42324343	.	+	0	transcript_id "Phchi.S1G668700.t1"; gene_id "Phchi.S1G668700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4582.t1 is derived from g1752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11200619	11202475	.	-	.	Phchi.S1G174100
Phchi.S1	AUGUSTUS	transcript	11200619	11202475	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	stop_codon	11200616	11200618	.	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11200619	11200780	1	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11200619	11200780	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11200781	11200905	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11200906	11200983	1	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11200906	11200983	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11200984	11201071	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11201072	11201152	0.99	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11201072	11201152	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11201153	11201287	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11201288	11201343	0.98	-	2	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11201288	11201343	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11201344	11201596	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11201597	11201660	0.98	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11201597	11201660	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11201661	11201756	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11201757	11201806	0.99	-	2	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11201757	11201806	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11201807	11201896	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11201897	11201974	1	-	2	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11201897	11201974	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	intron	11201975	11202054	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	CDS	11202055	11202475	0.98	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	exon	11202055	11202475	.	-	.	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
Phchi.S1	AUGUSTUS	start_codon	11202473	11202475	.	-	0	transcript_id "Phchi.S1G174100.t1"; gene_id "Phchi.S1G174100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14826.t1 is derived from g13294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14902854	14903641	.	-	.	Phchi.S3G214500
Phchi.S3	AUGUSTUS	transcript	14902854	14903641	.	-	.	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	stop_codon	14902851	14902853	.	-	0	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	CDS	14902854	14903453	0.58	-	0	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	exon	14902854	14903453	.	-	.	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	intron	14903454	14903536	.	-	.	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	CDS	14903537	14903641	0.45	-	0	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	exon	14903537	14903641	.	-	.	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
Phchi.S3	AUGUSTUS	start_codon	14903639	14903641	.	-	0	transcript_id "Phchi.S3G214500.t1"; gene_id "Phchi.S3G214500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5482.t1 is derived from g2652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17058617	17060279	.	-	.	Phchi.S1G264100
Phchi.S1	AUGUSTUS	transcript	17058617	17060279	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	stop_codon	17058614	17058616	.	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17058617	17058711	1	-	2	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17058617	17058711	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17058712	17058793	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17058794	17058867	1	-	1	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17058794	17058867	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17058868	17058958	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17058959	17059026	1	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17058959	17059026	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17059027	17059128	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17059129	17059221	1	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17059129	17059221	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17059222	17059311	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17059312	17059395	1	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17059312	17059395	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17059396	17059513	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17059514	17059569	1	-	2	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17059514	17059569	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17059570	17059655	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17059656	17059802	1	-	2	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17059656	17059802	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17059803	17059901	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17059902	17060082	1	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17059902	17060082	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	intron	17060083	17060180	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	CDS	17060181	17060279	1	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	exon	17060181	17060279	.	-	.	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
Phchi.S1	AUGUSTUS	start_codon	17060277	17060279	.	-	0	transcript_id "Phchi.S1G264100.t1"; gene_id "Phchi.S1G264100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3065.t1 is derived from g234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1410370	1410902	.	+	.	Phchi.S1G022400
Phchi.S1	AUGUSTUS	transcript	1410370	1410902	.	+	.	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	start_codon	1410370	1410372	.	+	0	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	CDS	1410370	1410635	0.75	+	0	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	exon	1410370	1410635	.	+	.	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	intron	1410636	1410832	.	+	.	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	CDS	1410833	1410902	0.94	+	1	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	exon	1410833	1410902	.	+	.	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
Phchi.S1	AUGUSTUS	stop_codon	1410903	1410905	.	+	0	transcript_id "Phchi.S1G022400.t1"; gene_id "Phchi.S1G022400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8554.t1 is derived from g5729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36605012	36605769	.	-	.	Phchi.S1G571300
Phchi.S1	AUGUSTUS	transcript	36605012	36605769	.	-	.	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	stop_codon	36605009	36605011	.	-	0	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	CDS	36605012	36605051	0.67	-	1	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	exon	36605012	36605051	.	-	.	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	intron	36605052	36605248	.	-	.	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	CDS	36605249	36605769	0.58	-	0	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	exon	36605249	36605769	.	-	.	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
Phchi.S1	AUGUSTUS	start_codon	36605767	36605769	.	-	0	transcript_id "Phchi.S1G571300.t1"; gene_id "Phchi.S1G571300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13776.t1 is derived from g12243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8856427	8856949	.	+	.	Phchi.S3G109500
Phchi.S3	AUGUSTUS	transcript	8856427	8856949	.	+	.	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	start_codon	8856427	8856429	.	+	0	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	CDS	8856427	8856445	0.74	+	0	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	exon	8856427	8856445	.	+	.	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	intron	8856446	8856530	.	+	.	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	CDS	8856531	8856949	0.7	+	2	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	exon	8856531	8856949	.	+	.	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
Phchi.S3	AUGUSTUS	stop_codon	8856950	8856952	.	+	0	transcript_id "Phchi.S3G109500.t1"; gene_id "Phchi.S3G109500"
# This transcript jg9039.t2 is derived from g6214.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9040.t1 is derived from g6215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39246741	39247788	.	+	.	Phchi.S1G619900
Phchi.S1	AUGUSTUS	transcript	39246741	39247788	.	+	.	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	start_codon	39246741	39246743	.	+	0	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	CDS	39246741	39247033	0.89	+	0	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	exon	39246741	39247033	.	+	.	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	intron	39247034	39247258	.	+	.	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	CDS	39247259	39247529	0.99	+	1	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	exon	39247259	39247529	.	+	.	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	intron	39247530	39247617	.	+	.	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	CDS	39247618	39247788	0.89	+	0	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	exon	39247618	39247788	.	+	.	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
Phchi.S1	AUGUSTUS	stop_codon	39247789	39247791	.	+	0	transcript_id "Phchi.S1G619900.t1"; gene_id "Phchi.S1G619900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6096.t1 is derived from g3267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20940393	20942661	.	-	.	Phchi.S1G325500
Phchi.S1	AUGUSTUS	transcript	20940393	20942661	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	stop_codon	20940390	20940392	.	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20940393	20940721	1	-	2	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20940393	20940721	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20940722	20940841	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20940842	20940937	1	-	2	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20940842	20940937	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20940938	20941048	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20941049	20941128	0.99	-	1	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20941049	20941128	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20941129	20941223	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20941224	20941264	1	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20941224	20941264	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20941265	20941353	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20941354	20941497	1	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20941354	20941497	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20941498	20941580	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20941581	20941691	1	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20941581	20941691	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20941692	20941847	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20941848	20941988	1	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20941848	20941988	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20941989	20942080	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20942081	20942197	1	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20942081	20942197	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20942198	20942380	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20942381	20942556	1	-	2	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20942381	20942556	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	intron	20942557	20942648	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	CDS	20942649	20942661	0.67	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	exon	20942649	20942661	.	-	.	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
Phchi.S1	AUGUSTUS	start_codon	20942659	20942661	.	-	0	transcript_id "Phchi.S1G325500.t1"; gene_id "Phchi.S1G325500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1946.t1 is derived from g8866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3954457	3955129	.	+	.	Phchi.S5G055500
Phchi.S5	AUGUSTUS	transcript	3954457	3955129	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	start_codon	3954457	3954459	.	+	0	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	CDS	3954457	3954495	1	+	0	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	exon	3954457	3954495	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	intron	3954496	3954581	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	CDS	3954582	3954794	1	+	0	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	exon	3954582	3954794	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	intron	3954795	3954885	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	CDS	3954886	3955018	0.87	+	0	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	exon	3954886	3955018	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	intron	3955019	3955088	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	CDS	3955089	3955129	0.39	+	2	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	exon	3955089	3955129	.	+	.	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
Phchi.S5	AUGUSTUS	stop_codon	3955130	3955132	.	+	0	transcript_id "Phchi.S5G055500.t1"; gene_id "Phchi.S5G055500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7675.t1 is derived from g4849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30572193	30573269	.	-	.	Phchi.S1G483400
Phchi.S1	AUGUSTUS	transcript	30572193	30573269	.	-	.	transcript_id "Phchi.S1G483400.t1"; gene_id "Phchi.S1G483400"
Phchi.S1	AUGUSTUS	stop_codon	30572190	30572192	.	-	0	transcript_id "Phchi.S1G483400.t1"; gene_id "Phchi.S1G483400"
Phchi.S1	AUGUSTUS	CDS	30572193	30573269	0.68	-	0	transcript_id "Phchi.S1G483400.t1"; gene_id "Phchi.S1G483400"
Phchi.S1	AUGUSTUS	exon	30572193	30573269	.	-	.	transcript_id "Phchi.S1G483400.t1"; gene_id "Phchi.S1G483400"
Phchi.S1	AUGUSTUS	start_codon	30573267	30573269	.	-	0	transcript_id "Phchi.S1G483400.t1"; gene_id "Phchi.S1G483400"
# This transcript jg2916.t2 is derived from g85.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2917.t1 is derived from g86.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	535291	537491	.	-	.	Phchi.S1G007600
Phchi.S1	AUGUSTUS	transcript	535291	537491	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	stop_codon	535288	535290	.	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	535291	535377	1	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	535291	535377	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	535378	535471	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	535472	535530	1	-	2	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	535472	535530	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	535531	535634	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	535635	535699	0.64	-	1	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	535635	535699	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	535700	535865	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	535866	535918	1	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	535866	535918	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	535919	536045	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	536046	536129	1	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	536046	536129	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	536130	536314	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	536315	536367	1	-	2	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	536315	536367	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	536368	536613	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	536614	536691	1	-	2	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	536614	536691	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	536692	536879	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	536880	536946	1	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	536880	536946	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	intron	536947	537422	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	CDS	537423	537491	1	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	exon	537423	537491	.	-	.	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
Phchi.S1	AUGUSTUS	start_codon	537489	537491	.	-	0	transcript_id "Phchi.S1G007600.t1"; gene_id "Phchi.S1G007600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1449.t1 is derived from g8368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	952911	953345	.	-	.	Phchi.S5G005800
Phchi.S5	AUGUSTUS	transcript	952911	953345	.	-	.	transcript_id "Phchi.S5G005800.t1"; gene_id "Phchi.S5G005800"
Phchi.S5	AUGUSTUS	stop_codon	952908	952910	.	-	0	transcript_id "Phchi.S5G005800.t1"; gene_id "Phchi.S5G005800"
Phchi.S5	AUGUSTUS	CDS	952911	953345	0.96	-	0	transcript_id "Phchi.S5G005800.t1"; gene_id "Phchi.S5G005800"
Phchi.S5	AUGUSTUS	exon	952911	953345	.	-	.	transcript_id "Phchi.S5G005800.t1"; gene_id "Phchi.S5G005800"
Phchi.S5	AUGUSTUS	start_codon	953343	953345	.	-	0	transcript_id "Phchi.S5G005800.t1"; gene_id "Phchi.S5G005800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14556.t1 is derived from g13024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13454144	13455190	.	-	.	Phchi.S3G187500
Phchi.S3	AUGUSTUS	transcript	13454144	13455190	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	stop_codon	13454141	13454143	.	-	0	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	CDS	13454144	13454484	0.98	-	2	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	exon	13454144	13454484	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	intron	13454485	13454563	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	CDS	13454564	13454714	0.92	-	0	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	exon	13454564	13454714	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	intron	13454715	13454823	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	CDS	13454824	13455091	1	-	1	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	exon	13454824	13455091	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	intron	13455092	13455170	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	CDS	13455171	13455190	0.91	-	0	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	exon	13455171	13455190	.	-	.	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
Phchi.S3	AUGUSTUS	start_codon	13455188	13455190	.	-	0	transcript_id "Phchi.S3G187500.t1"; gene_id "Phchi.S3G187500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10044.t1 is derived from g7220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45223844	45228085	.	-	.	Phchi.S1G720300
Phchi.S1	AUGUSTUS	transcript	45223844	45228085	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	stop_codon	45223841	45223843	.	-	0	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	CDS	45223844	45224126	0.47	-	1	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	exon	45223844	45224126	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	intron	45224127	45224227	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	CDS	45224228	45224943	0.95	-	0	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	exon	45224228	45224943	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	intron	45224944	45225050	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	CDS	45225051	45226444	0.99	-	2	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	exon	45225051	45226444	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	intron	45226445	45226593	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	CDS	45226594	45228085	0.95	-	0	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	exon	45226594	45228085	.	-	.	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
Phchi.S1	AUGUSTUS	start_codon	45228083	45228085	.	-	0	transcript_id "Phchi.S1G720300.t1"; gene_id "Phchi.S1G720300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4337.t1 is derived from g1506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9841033	9842060	.	+	.	Phchi.S1G149600
Phchi.S1	AUGUSTUS	transcript	9841033	9842060	.	+	.	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	start_codon	9841033	9841035	.	+	0	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	CDS	9841033	9841668	0.54	+	0	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	exon	9841033	9841668	.	+	.	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	intron	9841669	9841769	.	+	.	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	CDS	9841770	9842060	0.73	+	0	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	exon	9841770	9842060	.	+	.	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
Phchi.S1	AUGUSTUS	stop_codon	9842061	9842063	.	+	0	transcript_id "Phchi.S1G149600.t1"; gene_id "Phchi.S1G149600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7454.t1 is derived from g4626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29369301	29371974	.	-	.	Phchi.S1G461300
Phchi.S1	AUGUSTUS	transcript	29369301	29371974	.	-	.	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	stop_codon	29369298	29369300	.	-	0	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	CDS	29369301	29371092	0.82	-	1	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	exon	29369301	29371092	.	-	.	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	intron	29371093	29371435	.	-	.	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	CDS	29371436	29371974	0.34	-	0	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	exon	29371436	29371974	.	-	.	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
Phchi.S1	AUGUSTUS	start_codon	29371972	29371974	.	-	0	transcript_id "Phchi.S1G461300.t1"; gene_id "Phchi.S1G461300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5188.t1 is derived from g2358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15394530	15395473	.	-	.	Phchi.S1G234700
Phchi.S1	AUGUSTUS	transcript	15394530	15395473	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	stop_codon	15394527	15394529	.	-	0	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	CDS	15394530	15394576	1	-	2	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	exon	15394530	15394576	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	intron	15394577	15394669	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	CDS	15394670	15394763	0.94	-	0	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	exon	15394670	15394763	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	intron	15394764	15394871	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	CDS	15394872	15394931	0.95	-	0	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	exon	15394872	15394931	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	intron	15394932	15395061	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	CDS	15395062	15395119	1	-	1	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	exon	15395062	15395119	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	intron	15395120	15395207	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	CDS	15395208	15395473	0.97	-	0	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	exon	15395208	15395473	.	-	.	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
Phchi.S1	AUGUSTUS	start_codon	15395471	15395473	.	-	0	transcript_id "Phchi.S1G234700.t1"; gene_id "Phchi.S1G234700"
# This transcript jg14769.t2 is derived from g13237.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14769.t3 is derived from g13237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14770.t1 is derived from g13238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14635110	14636936	.	+	.	Phchi.S3G208900
Phchi.S3	AUGUSTUS	transcript	14635110	14636936	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	start_codon	14635110	14635112	.	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14635110	14635382	0.98	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14635110	14635382	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14635383	14635508	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14635509	14635539	1	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14635509	14635539	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14635540	14635637	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14635638	14635651	1	+	2	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14635638	14635651	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14635652	14635740	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14635741	14635791	1	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14635741	14635791	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14635792	14635881	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14635882	14635951	1	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14635882	14635951	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14635952	14636036	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14636037	14636103	1	+	2	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14636037	14636103	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14636104	14636231	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14636232	14636299	1	+	1	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14636232	14636299	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14636300	14636379	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14636380	14636503	1	+	2	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14636380	14636503	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14636504	14636589	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14636590	14636629	1	+	1	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14636590	14636629	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14636630	14636759	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14636760	14636827	1	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14636760	14636827	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	intron	14636828	14636926	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	CDS	14636927	14636936	1	+	1	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	exon	14636927	14636936	.	+	.	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
Phchi.S3	AUGUSTUS	stop_codon	14636937	14636939	.	+	0	transcript_id "Phchi.S3G208900.t1"; gene_id "Phchi.S3G208900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5925.t1 is derived from g3096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19887515	19891328	.	-	.	Phchi.S1G308400
Phchi.S1	AUGUSTUS	transcript	19887515	19891328	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	stop_codon	19887512	19887514	.	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19887515	19887769	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19887515	19887769	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19887770	19887855	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19887856	19887927	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19887856	19887927	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19887928	19888010	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19888011	19888112	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19888011	19888112	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19888113	19888186	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19888187	19888264	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19888187	19888264	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19888265	19888345	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19888346	19888414	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19888346	19888414	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19888415	19888508	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19888509	19888565	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19888509	19888565	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19888566	19888688	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19888689	19888748	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19888689	19888748	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19888749	19888844	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19888845	19888914	1	-	1	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19888845	19888914	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19888915	19889009	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19889010	19889107	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19889010	19889107	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19889108	19889274	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19889275	19889420	1	-	2	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19889275	19889420	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19889421	19889506	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19889507	19889564	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19889507	19889564	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19889565	19889651	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19889652	19889813	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19889652	19889813	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19889814	19889916	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19889917	19890001	1	-	1	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19889917	19890001	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19890002	19890120	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19890121	19890179	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19890121	19890179	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19890180	19890311	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19890312	19890344	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19890312	19890344	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19890345	19890518	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19890519	19890569	0.59	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19890519	19890569	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19890570	19890690	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19890691	19890788	1	-	2	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19890691	19890788	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19890789	19890865	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19890866	19890935	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19890866	19890935	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19890936	19891031	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19891032	19891119	1	-	1	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19891032	19891119	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	intron	19891120	19891260	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	CDS	19891261	19891328	1	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	exon	19891261	19891328	.	-	.	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
Phchi.S1	AUGUSTUS	start_codon	19891326	19891328	.	-	0	transcript_id "Phchi.S1G308400.t1"; gene_id "Phchi.S1G308400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9201.t1 is derived from g6376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40341126	40345274	.	-	.	Phchi.S1G636000
Phchi.S1	AUGUSTUS	transcript	40341126	40345274	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	stop_codon	40341123	40341125	.	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40341126	40341206	1	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40341126	40341206	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40341207	40341353	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40341354	40341416	1	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40341354	40341416	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40341417	40341499	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40341500	40341560	1	-	1	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40341500	40341560	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40341561	40341677	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40341678	40341718	1	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40341678	40341718	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40341719	40341804	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40341805	40341852	1	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40341805	40341852	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40341853	40341961	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40341962	40342028	1	-	1	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40341962	40342028	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40342029	40342115	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40342116	40342192	0.99	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40342116	40342192	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40342193	40342305	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40342306	40342379	1	-	2	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40342306	40342379	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40342380	40342540	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40342541	40342632	1	-	1	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40342541	40342632	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40342633	40342770	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40342771	40342803	1	-	1	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40342771	40342803	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40342804	40342892	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40342893	40343196	0.91	-	2	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40342893	40343196	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343197	40343286	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343287	40343452	1	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343287	40343452	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343453	40343576	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343577	40343639	1	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343577	40343639	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343640	40343791	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343792	40343870	1	-	1	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343792	40343870	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343871	40344000	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40344001	40344043	0.89	-	2	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40344001	40344043	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40344044	40344158	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40344159	40344303	0.91	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40344159	40344303	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40344304	40344441	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40344442	40344992	1	-	2	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40344442	40344992	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40344993	40345087	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40345088	40345274	0.98	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40345088	40345274	.	-	.	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	start_codon	40345272	40345274	.	-	0	transcript_id "Phchi.S1G636000.t1"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	transcript	40343158	40345274	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	stop_codon	40343155	40343157	.	-	0	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343158	40343201	0.52	-	2	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343158	40343201	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343202	40343286	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343287	40343452	0.67	-	0	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343287	40343452	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343453	40343576	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343577	40343639	1	-	0	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343577	40343639	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343640	40343791	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40343792	40343870	1	-	1	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40343792	40343870	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40343871	40344000	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40344001	40344043	0.89	-	2	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40344001	40344043	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40344044	40344158	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40344159	40344303	0.85	-	0	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40344159	40344303	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40344304	40344441	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40344442	40344992	1	-	2	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40344442	40344992	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	intron	40344993	40345087	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	CDS	40345088	40345274	0.96	-	0	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	exon	40345088	40345274	.	-	.	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
Phchi.S1	AUGUSTUS	start_codon	40345272	40345274	.	-	0	transcript_id "Phchi.S1G636000.t2"; gene_id "Phchi.S1G636000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg482.t1 is derived from g10264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3375556	3376165	.	+	.	Phchi.S6G044100
Phchi.S6	AUGUSTUS	transcript	3375556	3376165	.	+	.	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	start_codon	3375556	3375558	.	+	0	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	CDS	3375556	3375802	0.97	+	0	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	exon	3375556	3375802	.	+	.	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	intron	3375803	3375908	.	+	.	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	CDS	3375909	3375971	0.96	+	2	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	exon	3375909	3375971	.	+	.	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	intron	3375972	3376055	.	+	.	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	CDS	3376056	3376165	0.8	+	2	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	exon	3376056	3376165	.	+	.	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
Phchi.S6	AUGUSTUS	stop_codon	3376166	3376168	.	+	0	transcript_id "Phchi.S6G044100.t1"; gene_id "Phchi.S6G044100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13562.t1 is derived from g12029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7499532	7501298	.	+	.	Phchi.S3G088100
Phchi.S3	AUGUSTUS	transcript	7499532	7501298	.	+	.	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	start_codon	7499532	7499534	.	+	0	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	CDS	7499532	7501111	0.8	+	0	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	exon	7499532	7501111	.	+	.	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	intron	7501112	7501264	.	+	.	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	CDS	7501265	7501298	0.74	+	1	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	exon	7501265	7501298	.	+	.	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
Phchi.S3	AUGUSTUS	stop_codon	7501299	7501301	.	+	0	transcript_id "Phchi.S3G088100.t1"; gene_id "Phchi.S3G088100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8272.t1 is derived from g5447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35054714	35055907	.	-	.	Phchi.S1G543100
Phchi.S1	AUGUSTUS	transcript	35054714	35055907	.	-	.	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	stop_codon	35054711	35054713	.	-	0	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	CDS	35054714	35054849	0.97	-	1	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	exon	35054714	35054849	.	-	.	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	intron	35054850	35055011	.	-	.	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	CDS	35055012	35055907	0.83	-	0	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	exon	35055012	35055907	.	-	.	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
Phchi.S1	AUGUSTUS	start_codon	35055905	35055907	.	-	0	transcript_id "Phchi.S1G543100.t1"; gene_id "Phchi.S1G543100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5179.t1 is derived from g2349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15347409	15348449	.	+	.	Phchi.S1G233800
Phchi.S1	AUGUSTUS	transcript	15347409	15348449	.	+	.	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	start_codon	15347409	15347411	.	+	0	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	CDS	15347409	15347628	0.96	+	0	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	exon	15347409	15347628	.	+	.	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	intron	15347629	15347880	.	+	.	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	CDS	15347881	15348083	1	+	2	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	exon	15347881	15348083	.	+	.	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	intron	15348084	15348215	.	+	.	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	CDS	15348216	15348449	0.98	+	0	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	exon	15348216	15348449	.	+	.	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
Phchi.S1	AUGUSTUS	stop_codon	15348450	15348452	.	+	0	transcript_id "Phchi.S1G233800.t1"; gene_id "Phchi.S1G233800"
# This transcript jg3110.t2 is derived from g279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3110.t3 is derived from g279.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3111.t1 is derived from g280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1773674	1776533	.	-	.	Phchi.S1G027000
Phchi.S1	AUGUSTUS	transcript	1773674	1776533	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	stop_codon	1773671	1773673	.	-	0	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1773674	1773730	0.84	-	0	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1773674	1773730	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1773731	1773832	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1773833	1773917	0.89	-	1	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1773833	1773917	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1773918	1774069	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1774070	1774147	1	-	1	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1774070	1774147	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1774148	1774228	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1774229	1774376	1	-	2	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1774229	1774376	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1774377	1774500	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1774501	1774660	1	-	0	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1774501	1774660	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1774661	1774949	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1774950	1775026	0.75	-	2	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1774950	1775026	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1775027	1775443	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1775444	1776326	0.66	-	0	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1775444	1776326	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	intron	1776327	1776458	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	CDS	1776459	1776533	1	-	0	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	exon	1776459	1776533	.	-	.	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
Phchi.S1	AUGUSTUS	start_codon	1776531	1776533	.	-	0	transcript_id "Phchi.S1G027000.t1"; gene_id "Phchi.S1G027000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3841.t1 is derived from g1010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5959813	5962754	.	-	.	Phchi.S1G100000
Phchi.S1	AUGUSTUS	transcript	5959813	5962754	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	stop_codon	5959810	5959812	.	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5959813	5959938	0.97	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5959813	5959938	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5959939	5960030	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960031	5960133	0.97	-	1	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960031	5960133	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960134	5960244	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960245	5960288	0.97	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960245	5960288	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960289	5960369	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960370	5960446	0.99	-	2	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960370	5960446	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960447	5960559	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960560	5960604	1	-	2	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960560	5960604	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960605	5960697	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960698	5960806	1	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960698	5960806	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960807	5960884	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960885	5960999	1	-	1	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960885	5960999	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961000	5961081	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961082	5961246	1	-	1	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961082	5961246	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961247	5961332	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961333	5961441	1	-	2	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961333	5961441	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961442	5961536	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961537	5961574	1	-	1	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961537	5961574	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961575	5961718	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961719	5961789	1	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961719	5961789	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961790	5961890	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961891	5962067	0.99	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961891	5962067	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5962068	5962326	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5962327	5962458	0.87	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5962327	5962458	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5962459	5962562	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5962563	5962754	0.91	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5962563	5962754	.	-	.	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	start_codon	5962752	5962754	.	-	0	transcript_id "Phchi.S1G100000.t1"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	transcript	5959813	5962754	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	stop_codon	5959810	5959812	.	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5959813	5959938	0.94	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5959813	5959938	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5959939	5960030	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960031	5960133	0.91	-	1	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960031	5960133	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960134	5960244	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960245	5960288	0.92	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960245	5960288	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960289	5960369	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960370	5960446	0.96	-	2	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960370	5960446	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960447	5960559	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960560	5960604	1	-	2	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960560	5960604	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960605	5960697	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960698	5960706	0.5	-	2	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960698	5960706	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960707	5960777	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960778	5960806	0.55	-	1	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960778	5960806	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960807	5960884	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5960885	5960989	0.55	-	1	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5960885	5960989	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5960990	5961081	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961082	5961246	1	-	1	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961082	5961246	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961247	5961332	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961333	5961441	1	-	2	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961333	5961441	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961442	5961536	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961537	5961574	1	-	1	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961537	5961574	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961575	5961718	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961719	5961789	1	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961719	5961789	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5961790	5961890	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5961891	5962067	0.98	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5961891	5962067	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5962068	5962326	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5962327	5962458	0.9	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5962327	5962458	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	intron	5962459	5962562	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	CDS	5962563	5962754	0.92	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	exon	5962563	5962754	.	-	.	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
Phchi.S1	AUGUSTUS	start_codon	5962752	5962754	.	-	0	transcript_id "Phchi.S1G100000.t2"; gene_id "Phchi.S1G100000"
# This transcript jg1348.t2 is derived from g11131.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1349.t1 is derived from g11132.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9131681	9136265	.	-	.	Phchi.S6G130800
Phchi.S6	AUGUSTUS	transcript	9132234	9136265	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	stop_codon	9132231	9132233	.	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132234	9132266	0.81	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132234	9132266	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9132267	9132627	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132628	9132697	0.96	-	1	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132628	9132697	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9132698	9132872	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132873	9133012	0.57	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132873	9133012	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133013	9133187	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133188	9133265	1	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133188	9133265	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133266	9133344	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133345	9133428	1	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133345	9133428	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133429	9133516	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133517	9133571	0.88	-	1	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133517	9133571	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133572	9133675	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133676	9133772	0.99	-	2	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133676	9133772	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133773	9134112	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134113	9134182	1	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134113	9134182	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9134183	9134732	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134733	9134827	1	-	2	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134733	9134827	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9134828	9134953	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134954	9135061	1	-	2	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134954	9135061	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135062	9135310	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135311	9135463	1	-	2	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135311	9135463	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135464	9135558	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135559	9135664	1	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135559	9135664	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135665	9135836	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135837	9135893	1	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135837	9135893	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135894	9136142	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9136143	9136265	0.98	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9136143	9136265	.	-	.	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	start_codon	9136263	9136265	.	-	0	transcript_id "Phchi.S6G130800.t1"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	transcript	9131681	9136265	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	stop_codon	9131678	9131680	.	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9131681	9131851	0.97	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9131681	9131851	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9131852	9132105	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132106	9132266	1	-	2	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132106	9132266	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9132267	9132627	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132628	9132800	0.59	-	1	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132628	9132800	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9132801	9132908	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132909	9133012	0.66	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132909	9133012	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133013	9133187	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133188	9133265	1	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133188	9133265	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133266	9133344	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133345	9133428	1	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133345	9133428	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133429	9133516	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133517	9133571	0.95	-	1	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133517	9133571	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133572	9133675	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133676	9133772	1	-	2	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133676	9133772	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133773	9134112	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134113	9134182	1	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134113	9134182	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9134183	9134732	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134733	9134827	1	-	2	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134733	9134827	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9134828	9134953	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134954	9135061	1	-	2	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134954	9135061	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135062	9135310	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135311	9135463	1	-	2	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135311	9135463	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135464	9135558	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135559	9135664	1	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135559	9135664	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135665	9135836	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135837	9135885	0.61	-	1	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135837	9135885	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135886	9136218	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9136219	9136265	0.44	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9136219	9136265	.	-	.	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	start_codon	9136263	9136265	.	-	0	transcript_id "Phchi.S6G130800.t2"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	transcript	9131681	9135621	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	stop_codon	9131678	9131680	.	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9131681	9131851	0.96	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9131681	9131851	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9131852	9132105	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132106	9132266	1	-	2	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132106	9132266	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9132267	9132627	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132628	9132800	0.56	-	1	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132628	9132800	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9132801	9132908	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9132909	9133012	0.63	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9132909	9133012	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133013	9133187	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133188	9133265	1	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133188	9133265	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133266	9133344	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133345	9133428	1	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133345	9133428	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133429	9133516	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133517	9133571	0.92	-	1	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133517	9133571	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133572	9133675	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9133676	9133772	1	-	2	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9133676	9133772	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9133773	9134112	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134113	9134182	1	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134113	9134182	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9134183	9134732	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134733	9134827	1	-	2	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134733	9134827	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9134828	9134953	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9134954	9135061	1	-	2	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9134954	9135061	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135062	9135310	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135311	9135463	0.47	-	2	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135311	9135463	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	intron	9135464	9135602	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	CDS	9135603	9135621	0.25	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	exon	9135603	9135621	.	-	.	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
Phchi.S6	AUGUSTUS	start_codon	9135619	9135621	.	-	0	transcript_id "Phchi.S6G130800.t3"; gene_id "Phchi.S6G130800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5260.t1 is derived from g2430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15906560	15906943	.	-	.	Phchi.S1G241900
Phchi.S1	AUGUSTUS	transcript	15906560	15906943	.	-	.	transcript_id "Phchi.S1G241900.t1"; gene_id "Phchi.S1G241900"
Phchi.S1	AUGUSTUS	stop_codon	15906557	15906559	.	-	0	transcript_id "Phchi.S1G241900.t1"; gene_id "Phchi.S1G241900"
Phchi.S1	AUGUSTUS	CDS	15906560	15906943	0.68	-	0	transcript_id "Phchi.S1G241900.t1"; gene_id "Phchi.S1G241900"
Phchi.S1	AUGUSTUS	exon	15906560	15906943	.	-	.	transcript_id "Phchi.S1G241900.t1"; gene_id "Phchi.S1G241900"
Phchi.S1	AUGUSTUS	start_codon	15906941	15906943	.	-	0	transcript_id "Phchi.S1G241900.t1"; gene_id "Phchi.S1G241900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1748.t1 is derived from g8668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2844386	2847764	.	-	.	Phchi.S5G035700
Phchi.S5	AUGUSTUS	transcript	2844386	2847764	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	stop_codon	2844383	2844385	.	-	0	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	CDS	2844386	2844529	1	-	0	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	exon	2844386	2844529	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	intron	2844530	2844626	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	CDS	2844627	2844653	1	-	0	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	exon	2844627	2844653	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	intron	2844654	2845046	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	CDS	2845047	2846429	1	-	0	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	exon	2845047	2846429	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	intron	2846430	2846570	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	CDS	2846571	2847660	1	-	1	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	exon	2846571	2847660	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	intron	2847661	2847753	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	CDS	2847754	2847764	0.37	-	0	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	exon	2847754	2847764	.	-	.	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
Phchi.S5	AUGUSTUS	start_codon	2847762	2847764	.	-	0	transcript_id "Phchi.S5G035700.t1"; gene_id "Phchi.S5G035700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10645.t1 is derived from g14695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1397311	1398252	.	-	.	Phchi.S4G022700
Phchi.S4	AUGUSTUS	transcript	1397311	1398252	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	stop_codon	1397308	1397310	.	-	0	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	CDS	1397311	1397456	0.5	-	2	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	exon	1397311	1397456	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	intron	1397457	1397594	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	CDS	1397595	1397682	1	-	0	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	exon	1397595	1397682	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	intron	1397683	1397759	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	CDS	1397760	1397875	1	-	2	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	exon	1397760	1397875	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	intron	1397876	1397950	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	CDS	1397951	1397972	1	-	0	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	exon	1397951	1397972	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	intron	1397973	1398065	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	CDS	1398066	1398098	1	-	0	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	exon	1398066	1398098	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	intron	1398099	1398183	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	CDS	1398184	1398252	1	-	0	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	exon	1398184	1398252	.	-	.	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
Phchi.S4	AUGUSTUS	start_codon	1398250	1398252	.	-	0	transcript_id "Phchi.S4G022700.t1"; gene_id "Phchi.S4G022700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12651.t1 is derived from g14450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	58	584	.	+	.	Phchi.C12G000100
Phchi.C12	AUGUSTUS	transcript	58	584	.	+	.	transcript_id "Phchi.C12G000100.t1"; gene_id "Phchi.C12G000100"
Phchi.C12	AUGUSTUS	CDS	58	584	0.33	+	2	transcript_id "Phchi.C12G000100.t1"; gene_id "Phchi.C12G000100"
Phchi.C12	AUGUSTUS	exon	58	584	.	+	.	transcript_id "Phchi.C12G000100.t1"; gene_id "Phchi.C12G000100"
Phchi.C12	AUGUSTUS	stop_codon	585	587	.	+	0	transcript_id "Phchi.C12G000100.t1"; gene_id "Phchi.C12G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7178.t1 is derived from g4350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27423286	27423609	.	-	.	Phchi.S1G433700
Phchi.S1	AUGUSTUS	transcript	27423286	27423609	.	-	.	transcript_id "Phchi.S1G433700.t1"; gene_id "Phchi.S1G433700"
Phchi.S1	AUGUSTUS	stop_codon	27423283	27423285	.	-	0	transcript_id "Phchi.S1G433700.t1"; gene_id "Phchi.S1G433700"
Phchi.S1	AUGUSTUS	CDS	27423286	27423609	0.57	-	0	transcript_id "Phchi.S1G433700.t1"; gene_id "Phchi.S1G433700"
Phchi.S1	AUGUSTUS	exon	27423286	27423609	.	-	.	transcript_id "Phchi.S1G433700.t1"; gene_id "Phchi.S1G433700"
Phchi.S1	AUGUSTUS	start_codon	27423607	27423609	.	-	0	transcript_id "Phchi.S1G433700.t1"; gene_id "Phchi.S1G433700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg218.t1 is derived from g10000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1409227	1410879	.	-	.	Phchi.S6G017700
Phchi.S6	AUGUSTUS	transcript	1409227	1410879	.	-	.	transcript_id "Phchi.S6G017700.t1"; gene_id "Phchi.S6G017700"
Phchi.S6	AUGUSTUS	stop_codon	1409224	1409226	.	-	0	transcript_id "Phchi.S6G017700.t1"; gene_id "Phchi.S6G017700"
Phchi.S6	AUGUSTUS	CDS	1409227	1410879	0.49	-	0	transcript_id "Phchi.S6G017700.t1"; gene_id "Phchi.S6G017700"
Phchi.S6	AUGUSTUS	exon	1409227	1410879	.	-	.	transcript_id "Phchi.S6G017700.t1"; gene_id "Phchi.S6G017700"
Phchi.S6	AUGUSTUS	start_codon	1410877	1410879	.	-	0	transcript_id "Phchi.S6G017700.t1"; gene_id "Phchi.S6G017700"
# This transcript jg3420.t2 is derived from g589.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3421.t1 is derived from g590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3532358	3533317	.	-	.	Phchi.S1G058000
Phchi.S1	AUGUSTUS	transcript	3532358	3533317	.	-	.	transcript_id "Phchi.S1G058000.t1"; gene_id "Phchi.S1G058000"
Phchi.S1	AUGUSTUS	stop_codon	3532355	3532357	.	-	0	transcript_id "Phchi.S1G058000.t1"; gene_id "Phchi.S1G058000"
Phchi.S1	AUGUSTUS	CDS	3532358	3533317	1	-	0	transcript_id "Phchi.S1G058000.t1"; gene_id "Phchi.S1G058000"
Phchi.S1	AUGUSTUS	exon	3532358	3533317	.	-	.	transcript_id "Phchi.S1G058000.t1"; gene_id "Phchi.S1G058000"
Phchi.S1	AUGUSTUS	start_codon	3533315	3533317	.	-	0	transcript_id "Phchi.S1G058000.t1"; gene_id "Phchi.S1G058000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13203.t1 is derived from g11668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4654593	4655075	.	-	.	Phchi.S3G052200
Phchi.S3	AUGUSTUS	transcript	4654593	4655075	.	-	.	transcript_id "Phchi.S3G052200.t1"; gene_id "Phchi.S3G052200"
Phchi.S3	AUGUSTUS	stop_codon	4654590	4654592	.	-	0	transcript_id "Phchi.S3G052200.t1"; gene_id "Phchi.S3G052200"
Phchi.S3	AUGUSTUS	CDS	4654593	4655075	0.8	-	0	transcript_id "Phchi.S3G052200.t1"; gene_id "Phchi.S3G052200"
Phchi.S3	AUGUSTUS	exon	4654593	4655075	.	-	.	transcript_id "Phchi.S3G052200.t1"; gene_id "Phchi.S3G052200"
Phchi.S3	AUGUSTUS	start_codon	4655073	4655075	.	-	0	transcript_id "Phchi.S3G052200.t1"; gene_id "Phchi.S3G052200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13678.t1 is derived from g12145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8175251	8178224	.	+	.	Phchi.S3G099700
Phchi.S3	AUGUSTUS	transcript	8175251	8178224	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	start_codon	8175251	8175253	.	+	0	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8175251	8175763	0.94	+	0	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8175251	8175763	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	intron	8175764	8175974	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8175975	8176065	1	+	0	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8175975	8176065	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	intron	8176066	8176194	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8176195	8176300	1	+	2	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8176195	8176300	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	intron	8176301	8176392	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8176393	8176675	1	+	1	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8176393	8176675	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	intron	8176676	8176758	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8176759	8176907	1	+	0	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8176759	8176907	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	intron	8176908	8177008	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8177009	8177162	1	+	1	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8177009	8177162	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	intron	8177163	8177264	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	CDS	8177265	8178224	1	+	0	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	exon	8177265	8178224	.	+	.	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
Phchi.S3	AUGUSTUS	stop_codon	8178225	8178227	.	+	0	transcript_id "Phchi.S3G099700.t1"; gene_id "Phchi.S3G099700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6309.t1 is derived from g3481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22202002	22207819	.	+	.	Phchi.S1G346800
Phchi.S1	AUGUSTUS	transcript	22202002	22207819	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	start_codon	22202002	22202004	.	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22202002	22202091	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22202002	22202091	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22202092	22202761	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22202762	22202875	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22202762	22202875	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22202876	22203043	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22203044	22203109	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22203044	22203109	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22203110	22203193	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22203194	22203283	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22203194	22203283	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22203284	22203369	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22203370	22203489	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22203370	22203489	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22203490	22203619	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22203620	22203648	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22203620	22203648	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22203649	22203838	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22203839	22203981	1	+	1	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22203839	22203981	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22203982	22204148	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22204149	22204243	1	+	2	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22204149	22204243	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22204244	22204344	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22204345	22204431	0.54	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22204345	22204431	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22204432	22204537	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22204538	22204645	0.99	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22204538	22204645	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22204646	22204754	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22204755	22204846	0.95	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22204755	22204846	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22204847	22205019	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22205020	22205101	1	+	1	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22205020	22205101	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22205102	22205351	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22205352	22205417	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22205352	22205417	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22205418	22205516	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22205517	22205632	0.99	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22205517	22205632	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22205633	22205736	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22205737	22205857	1	+	1	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22205737	22205857	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22205858	22206249	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22206250	22206411	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22206250	22206411	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22206412	22206579	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22206580	22206708	0.92	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22206580	22206708	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22206709	22206816	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22206817	22206885	0.92	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22206817	22206885	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22206886	22207108	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22207109	22207140	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22207109	22207140	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22207141	22207224	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22207225	22207453	1	+	1	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22207225	22207453	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22207454	22207670	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22207671	22207722	1	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22207671	22207722	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	intron	22207723	22207808	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	CDS	22207809	22207819	1	+	2	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	exon	22207809	22207819	.	+	.	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
Phchi.S1	AUGUSTUS	stop_codon	22207820	22207822	.	+	0	transcript_id "Phchi.S1G346800.t1"; gene_id "Phchi.S1G346800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7075.t1 is derived from g4247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26772914	26776761	.	+	.	Phchi.S1G423400
Phchi.S1	AUGUSTUS	transcript	26772914	26776761	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	start_codon	26772914	26772916	.	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26772914	26773138	0.5	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26772914	26773138	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26773139	26773258	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26773259	26773305	1	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26773259	26773305	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26773306	26773430	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26773431	26773470	1	+	1	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26773431	26773470	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26773471	26773581	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26773582	26773647	1	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26773582	26773647	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26773648	26773744	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26773745	26773882	0.95	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26773745	26773882	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26773883	26774061	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26774062	26774220	0.99	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26774062	26774220	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26774221	26774327	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26774328	26774381	0.98	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26774328	26774381	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26774382	26774458	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26774459	26774527	1	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26774459	26774527	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26774528	26774637	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26774638	26774767	1	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26774638	26774767	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26774768	26774883	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26774884	26774924	0.61	+	2	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26774884	26774924	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26774925	26775014	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26775015	26775242	0.65	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26775015	26775242	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26775243	26775363	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26775364	26775412	0.98	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26775364	26775412	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26775413	26775513	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26775514	26775668	0.88	+	2	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26775514	26775668	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26775669	26775774	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26775775	26775990	0.94	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26775775	26775990	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26775991	26776074	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26776075	26776271	0.73	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26776075	26776271	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26776272	26776437	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26776438	26776476	0.22	+	1	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26776438	26776476	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	intron	26776477	26776631	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	CDS	26776632	26776761	0.62	+	1	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	exon	26776632	26776761	.	+	.	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
Phchi.S1	AUGUSTUS	stop_codon	26776762	26776764	.	+	0	transcript_id "Phchi.S1G423400.t1"; gene_id "Phchi.S1G423400"
# This transcript jg5640.t2 is derived from g2810.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5641.t1 is derived from g2811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18020333	18024083	.	+	.	Phchi.S1G280000
Phchi.S1	AUGUSTUS	transcript	18020333	18024083	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	start_codon	18020333	18020335	.	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18020333	18020456	0.8	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18020333	18020456	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18020457	18020754	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18020755	18021078	0.99	+	2	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18020755	18021078	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18021079	18021187	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18021188	18021406	0.99	+	2	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18021188	18021406	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18021407	18021497	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18021498	18021590	1	+	2	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18021498	18021590	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18021591	18021676	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18021677	18021876	1	+	2	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18021677	18021876	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18021877	18021957	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18021958	18022037	1	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18021958	18022037	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18022038	18022107	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18022108	18022221	1	+	1	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18022108	18022221	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18022222	18022300	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18022301	18022344	1	+	1	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18022301	18022344	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18022345	18022459	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18022460	18022515	1	+	2	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18022460	18022515	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18022516	18022592	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18022593	18022651	1	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18022593	18022651	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18022652	18022747	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18022748	18022897	1	+	1	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18022748	18022897	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18022898	18022982	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18022983	18023036	1	+	1	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18022983	18023036	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18023037	18023143	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18023144	18023234	1	+	1	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18023144	18023234	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18023235	18023354	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18023355	18023435	1	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18023355	18023435	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18023436	18023559	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18023560	18023640	1	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18023560	18023640	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18023641	18023790	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18023791	18023869	0.98	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18023791	18023869	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	intron	18023870	18023973	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	CDS	18023974	18024083	0.97	+	2	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	exon	18023974	18024083	.	+	.	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
Phchi.S1	AUGUSTUS	stop_codon	18024084	18024086	.	+	0	transcript_id "Phchi.S1G280000.t1"; gene_id "Phchi.S1G280000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4737.t1 is derived from g1907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12544324	12545365	.	-	.	Phchi.S1G189600
Phchi.S1	AUGUSTUS	transcript	12544324	12545365	.	-	.	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	stop_codon	12544321	12544323	.	-	0	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	CDS	12544324	12544389	0.56	-	0	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	exon	12544324	12544389	.	-	.	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	intron	12544390	12544612	.	-	.	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	CDS	12544613	12544695	0.98	-	2	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	exon	12544613	12544695	.	-	.	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	intron	12544696	12545169	.	-	.	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	CDS	12545170	12545365	0.36	-	0	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	exon	12545170	12545365	.	-	.	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
Phchi.S1	AUGUSTUS	start_codon	12545363	12545365	.	-	0	transcript_id "Phchi.S1G189600.t1"; gene_id "Phchi.S1G189600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7471.t1 is derived from g4644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29535759	29536604	.	-	.	Phchi.S1G463000
Phchi.S1	AUGUSTUS	transcript	29535759	29536604	.	-	.	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	stop_codon	29535756	29535758	.	-	0	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	CDS	29535759	29535841	0.33	-	2	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	exon	29535759	29535841	.	-	.	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	intron	29535842	29536207	.	-	.	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	CDS	29536208	29536604	0.61	-	0	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	exon	29536208	29536604	.	-	.	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
Phchi.S1	AUGUSTUS	start_codon	29536602	29536604	.	-	0	transcript_id "Phchi.S1G463000.t1"; gene_id "Phchi.S1G463000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5888.t1 is derived from g3058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19604109	19615644	.	-	.	Phchi.S1G304700
Phchi.S1	AUGUSTUS	transcript	19604109	19615644	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	stop_codon	19604106	19604108	.	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19604109	19604195	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19604109	19604195	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19604196	19604289	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19604290	19604410	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19604290	19604410	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19604411	19604498	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19604499	19604618	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19604499	19604618	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19604619	19604713	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19604714	19604814	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19604714	19604814	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19604815	19604951	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19604952	19605089	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19604952	19605089	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19605090	19605228	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19605229	19605339	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19605229	19605339	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19605340	19605429	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19605430	19605588	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19605430	19605588	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19605589	19605709	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19605710	19605853	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19605710	19605853	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19605854	19605931	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19605932	19606075	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19605932	19606075	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19606076	19606179	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19606180	19606353	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19606180	19606353	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19606354	19606506	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19606507	19606671	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19606507	19606671	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19606672	19606813	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19606814	19606891	0.99	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19606814	19606891	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19606892	19606997	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19606998	19607127	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19606998	19607127	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19607128	19607233	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19607234	19607427	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19607234	19607427	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19607428	19607521	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19607522	19607594	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19607522	19607594	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19607595	19607676	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19607677	19607732	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19607677	19607732	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19607733	19607818	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19607819	19607989	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19607819	19607989	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19607990	19608153	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19608154	19608267	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19608154	19608267	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19608268	19608351	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19608352	19608444	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19608352	19608444	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19608445	19608742	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19608743	19608940	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19608743	19608940	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19608941	19609094	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19609095	19609172	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19609095	19609172	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19609173	19609291	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19609292	19609378	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19609292	19609378	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19609379	19609554	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19609555	19609636	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19609555	19609636	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19609637	19609726	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19609727	19609839	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19609727	19609839	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19609840	19609929	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19609930	19610080	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19609930	19610080	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19610081	19610222	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19610223	19610341	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19610223	19610341	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19610342	19610427	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19610428	19610625	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19610428	19610625	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19610626	19610708	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19610709	19610847	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19610709	19610847	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19610848	19611059	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19611060	19611179	1	-	1	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19611060	19611179	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19611180	19611271	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19611272	19611402	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19611272	19611402	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19611403	19611485	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19611486	19611578	0.89	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19611486	19611578	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19611579	19611705	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19611706	19611807	0.93	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19611706	19611807	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19611808	19611911	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19611912	19612118	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19611912	19612118	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19612119	19612205	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19612206	19612322	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19612206	19612322	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19612323	19612398	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19612399	19612560	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19612399	19612560	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19612561	19612682	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19612683	19612772	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19612683	19612772	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19612773	19612879	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19612880	19613086	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19612880	19613086	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19613087	19613172	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19613173	19613298	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19613173	19613298	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19613299	19613474	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19613475	19613560	1	-	2	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19613475	19613560	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19613561	19613693	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19613694	19613853	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19613694	19613853	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19613854	19614005	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19614006	19614116	0.97	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19614006	19614116	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19614117	19614240	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19614241	19614345	0.98	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19614241	19614345	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19614346	19614470	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19614471	19614545	0.95	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19614471	19614545	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19614546	19614669	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19614670	19614765	0.98	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19614670	19614765	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	intron	19614766	19615506	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	CDS	19615507	19615644	1	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	exon	19615507	19615644	.	-	.	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
Phchi.S1	AUGUSTUS	start_codon	19615642	19615644	.	-	0	transcript_id "Phchi.S1G304700.t1"; gene_id "Phchi.S1G304700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 5 different transcripts
# This transcript jg10099.t1 is derived from g7275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45738722	45744284	.	-	.	Phchi.S1G725800
Phchi.S1	AUGUSTUS	transcript	45740751	45744284	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	stop_codon	45740748	45740750	.	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45740751	45740759	0.64	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45740751	45740759	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45740760	45740861	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45740862	45741025	1	-	2	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45740862	45741025	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741026	45741117	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741118	45741232	1	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741118	45741232	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741233	45741413	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741414	45741505	1	-	2	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741414	45741505	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741506	45741631	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741632	45741705	1	-	1	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741632	45741705	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741706	45741793	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741794	45741950	1	-	2	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741794	45741950	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741951	45742044	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742045	45742117	1	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742045	45742117	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742118	45742252	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742253	45742321	1	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742253	45742321	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742322	45742437	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742438	45742697	1	-	2	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742438	45742697	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742698	45742782	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742783	45742970	1	-	1	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742783	45742970	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742971	45743058	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45743059	45744284	0.8	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45743059	45744284	.	-	.	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	start_codon	45744282	45744284	.	-	0	transcript_id "Phchi.S1G725800.t1"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	transcript	45738722	45744284	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	stop_codon	45738719	45738721	.	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738722	45738803	0.96	-	1	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738722	45738803	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45738804	45738997	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738998	45739097	0.69	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738998	45739097	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739098	45739258	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739259	45739354	0.62	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739259	45739354	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739355	45739427	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739428	45739469	0.83	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739428	45739469	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739470	45739624	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739625	45739811	1	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739625	45739811	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739812	45739928	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739929	45740003	1	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739929	45740003	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45740004	45740861	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45740862	45741025	1	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45740862	45741025	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741026	45741117	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741118	45741232	1	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741118	45741232	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741233	45741413	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741414	45741505	0.97	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741414	45741505	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741506	45741631	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741632	45741705	0.97	-	1	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741632	45741705	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741706	45741793	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741794	45741950	1	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741794	45741950	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741951	45742044	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742045	45742117	1	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742045	45742117	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742118	45742252	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742253	45742321	1	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742253	45742321	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742322	45742437	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742438	45742697	1	-	2	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742438	45742697	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742698	45742782	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742783	45742970	1	-	1	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742783	45742970	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742971	45743058	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45743059	45744284	0.83	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45743059	45744284	.	-	.	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	start_codon	45744282	45744284	.	-	0	transcript_id "Phchi.S1G725800.t2"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	transcript	45738722	45744284	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	stop_codon	45738719	45738721	.	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738722	45738803	0.92	-	1	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738722	45738803	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45738804	45738997	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738998	45739097	0.68	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738998	45739097	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739098	45739258	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739259	45739354	0.6	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739259	45739354	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739355	45739427	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739428	45739469	0.82	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739428	45739469	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739470	45739624	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739625	45739811	1	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739625	45739811	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739812	45739928	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739929	45740003	1	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739929	45740003	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45740004	45740861	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45740862	45741025	1	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45740862	45741025	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741026	45741117	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741118	45741232	1	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741118	45741232	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741233	45741413	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741414	45741505	0.98	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741414	45741505	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741506	45741631	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741632	45741705	0.98	-	1	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741632	45741705	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741706	45741793	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741794	45741950	1	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741794	45741950	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741951	45742044	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742045	45742117	1	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742045	45742117	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742118	45742252	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742253	45742321	1	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742253	45742321	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742322	45742437	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742438	45742694	1	-	2	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742438	45742694	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742695	45742782	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742783	45742970	1	-	1	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742783	45742970	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742971	45743058	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45743059	45744284	0.8	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45743059	45744284	.	-	.	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	start_codon	45744282	45744284	.	-	0	transcript_id "Phchi.S1G725800.t3"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	transcript	45738722	45744284	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	stop_codon	45738719	45738721	.	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738722	45738803	0.97	-	1	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738722	45738803	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45738804	45738997	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738998	45739094	0.64	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738998	45739094	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739095	45739258	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739259	45739354	0.36	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739259	45739354	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739355	45739427	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739428	45739469	0.59	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739428	45739469	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739470	45739624	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739625	45739811	1	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739625	45739811	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739812	45739928	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739929	45740003	1	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739929	45740003	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45740004	45740861	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45740862	45741025	1	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45740862	45741025	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741026	45741117	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741118	45741232	1	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741118	45741232	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741233	45741413	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741414	45741505	1	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741414	45741505	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741506	45741631	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741632	45741705	1	-	1	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741632	45741705	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741706	45741793	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45741794	45741950	1	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45741794	45741950	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45741951	45742044	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742045	45742117	1	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742045	45742117	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742118	45742252	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742253	45742321	1	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742253	45742321	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742322	45742437	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742438	45742697	1	-	2	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742438	45742697	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742698	45742782	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45742783	45742970	1	-	1	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45742783	45742970	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45742971	45743058	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45743059	45744284	0.81	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45743059	45744284	.	-	.	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	start_codon	45744282	45744284	.	-	0	transcript_id "Phchi.S1G725800.t4"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	transcript	45738722	45740689	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	stop_codon	45738719	45738721	.	-	0	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738722	45738803	0.94	-	1	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738722	45738803	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45738804	45738997	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45738998	45739097	0.61	-	2	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45738998	45739097	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739098	45739258	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739259	45739354	0.63	-	2	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739259	45739354	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739355	45739427	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739428	45739469	0.84	-	2	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739428	45739469	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739470	45739624	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739625	45739811	1	-	0	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739625	45739811	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45739812	45739928	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45739929	45740003	0.94	-	0	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45739929	45740003	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	intron	45740004	45740686	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	CDS	45740687	45740689	0.38	-	0	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	exon	45740687	45740689	.	-	.	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
Phchi.S1	AUGUSTUS	start_codon	45740687	45740689	.	-	0	transcript_id "Phchi.S1G725800.t5"; gene_id "Phchi.S1G725800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14432.t1 is derived from g12900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12770344	12770959	.	-	.	Phchi.S3G175100
Phchi.S3	AUGUSTUS	transcript	12770344	12770959	.	-	.	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	stop_codon	12770341	12770343	.	-	0	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	CDS	12770344	12770366	0.9	-	2	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	exon	12770344	12770366	.	-	.	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	intron	12770367	12770503	.	-	.	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	CDS	12770504	12770787	0.89	-	1	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	exon	12770504	12770787	.	-	.	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	intron	12770788	12770873	.	-	.	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	CDS	12770874	12770959	0.47	-	0	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	exon	12770874	12770959	.	-	.	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
Phchi.S3	AUGUSTUS	start_codon	12770957	12770959	.	-	0	transcript_id "Phchi.S3G175100.t1"; gene_id "Phchi.S3G175100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3008.t1 is derived from g177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1113997	1114684	.	+	.	Phchi.S1G016700
Phchi.S1	AUGUSTUS	transcript	1113997	1114684	.	+	.	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	start_codon	1113997	1113999	.	+	0	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	CDS	1113997	1114221	1	+	0	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	exon	1113997	1114221	.	+	.	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	intron	1114222	1114330	.	+	.	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	CDS	1114331	1114684	1	+	0	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	exon	1114331	1114684	.	+	.	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
Phchi.S1	AUGUSTUS	stop_codon	1114685	1114687	.	+	0	transcript_id "Phchi.S1G016700.t1"; gene_id "Phchi.S1G016700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3852.t1 is derived from g1021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6042915	6043745	.	-	.	Phchi.S1G101100
Phchi.S1	AUGUSTUS	transcript	6042915	6043745	.	-	.	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	stop_codon	6042912	6042914	.	-	0	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	CDS	6042915	6043306	0.53	-	2	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	exon	6042915	6043306	.	-	.	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	intron	6043307	6043398	.	-	.	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	CDS	6043399	6043453	1	-	0	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	exon	6043399	6043453	.	-	.	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	intron	6043454	6043658	.	-	.	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	CDS	6043659	6043745	0.89	-	0	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	exon	6043659	6043745	.	-	.	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
Phchi.S1	AUGUSTUS	start_codon	6043743	6043745	.	-	0	transcript_id "Phchi.S1G101100.t1"; gene_id "Phchi.S1G101100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1990.t1 is derived from g8910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4335430	4337094	.	+	.	Phchi.S5G059900
Phchi.S5	AUGUSTUS	transcript	4335430	4337094	.	+	.	transcript_id "Phchi.S5G059900.t1"; gene_id "Phchi.S5G059900"
Phchi.S5	AUGUSTUS	start_codon	4335430	4335432	.	+	0	transcript_id "Phchi.S5G059900.t1"; gene_id "Phchi.S5G059900"
Phchi.S5	AUGUSTUS	CDS	4335430	4337094	0.96	+	0	transcript_id "Phchi.S5G059900.t1"; gene_id "Phchi.S5G059900"
Phchi.S5	AUGUSTUS	exon	4335430	4337094	.	+	.	transcript_id "Phchi.S5G059900.t1"; gene_id "Phchi.S5G059900"
Phchi.S5	AUGUSTUS	stop_codon	4337095	4337097	.	+	0	transcript_id "Phchi.S5G059900.t1"; gene_id "Phchi.S5G059900"
# This transcript jg2830.t2 is derived from g9750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2831.t1 is derived from g9751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9093303	9095213	.	-	.	Phchi.S5G144000
Phchi.S5	AUGUSTUS	transcript	9093303	9095213	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	stop_codon	9093300	9093302	.	-	0	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	CDS	9093303	9093345	1	-	1	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	exon	9093303	9093345	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	intron	9093346	9093471	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	CDS	9093472	9093712	1	-	2	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	exon	9093472	9093712	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	intron	9093713	9093830	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	CDS	9093831	9094145	0.6	-	2	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	exon	9093831	9094145	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	intron	9094146	9094243	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	CDS	9094244	9094254	0.46	-	1	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	exon	9094244	9094254	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	intron	9094255	9094402	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	CDS	9094403	9094476	0.46	-	0	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	exon	9094403	9094476	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	intron	9094477	9094574	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	CDS	9094575	9095213	0.4	-	0	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	exon	9094575	9095213	.	-	.	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
Phchi.S5	AUGUSTUS	start_codon	9095211	9095213	.	-	0	transcript_id "Phchi.S5G144000.t1"; gene_id "Phchi.S5G144000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12015.t1 is derived from g7690.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	527978	531805	.	-	.	Phchi.S2G009500
Phchi.S2	AUGUSTUS	transcript	527978	530964	.	-	.	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	stop_codon	527975	527977	.	-	0	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	CDS	527978	530381	0.75	-	1	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	exon	527978	530381	.	-	.	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	intron	530382	530614	.	-	.	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	CDS	530615	530964	0.67	-	0	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	exon	530615	530964	.	-	.	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	start_codon	530962	530964	.	-	0	transcript_id "Phchi.S2G009500.t1"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	transcript	530614	531805	.	-	.	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	stop_codon	530611	530613	.	-	0	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	CDS	530614	531103	0.66	-	1	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	exon	530614	531103	.	-	.	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	intron	531104	531222	.	-	.	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	CDS	531223	531341	0.26	-	0	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	exon	531223	531341	.	-	.	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	intron	531342	531427	.	-	.	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	CDS	531428	531805	0.58	-	0	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	exon	531428	531805	.	-	.	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	start_codon	531803	531805	.	-	0	transcript_id "Phchi.S2G009500.t2"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	transcript	527978	530101	.	-	.	transcript_id "Phchi.S2G009500.t3"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	stop_codon	527975	527977	.	-	0	transcript_id "Phchi.S2G009500.t3"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	CDS	527978	530101	0.78	-	0	transcript_id "Phchi.S2G009500.t3"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	exon	527978	530101	.	-	.	transcript_id "Phchi.S2G009500.t3"; gene_id "Phchi.S2G009500"
Phchi.S2	AUGUSTUS	start_codon	530099	530101	.	-	0	transcript_id "Phchi.S2G009500.t3"; gene_id "Phchi.S2G009500"
# This transcript jg9966.t2 is derived from g7142.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9967.t1 is derived from g7143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44697162	44698623	.	+	.	Phchi.S1G712600
Phchi.S1	AUGUSTUS	transcript	44697162	44698228	.	+	.	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	start_codon	44697162	44697164	.	+	0	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44697162	44697867	0.31	+	0	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44697162	44697867	.	+	.	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	intron	44697868	44697973	.	+	.	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44697974	44698076	0.38	+	2	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44697974	44698076	.	+	.	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	intron	44698077	44698215	.	+	.	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44698216	44698228	0.88	+	1	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44698216	44698228	.	+	.	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	stop_codon	44698229	44698231	.	+	0	transcript_id "Phchi.S1G712600.t1"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	transcript	44697162	44698623	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	start_codon	44697162	44697164	.	+	0	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44697162	44697867	0.49	+	0	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44697162	44697867	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	intron	44697868	44697973	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44697974	44698044	0.67	+	2	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44697974	44698044	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	intron	44698045	44698215	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44698216	44698269	0.52	+	0	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44698216	44698269	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	intron	44698270	44698572	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	CDS	44698573	44698623	0.35	+	0	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	exon	44698573	44698623	.	+	.	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
Phchi.S1	AUGUSTUS	stop_codon	44698624	44698626	.	+	0	transcript_id "Phchi.S1G712600.t2"; gene_id "Phchi.S1G712600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1575.t1 is derived from g8494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1831807	1833695	.	+	.	Phchi.S5G018400
Phchi.S5	AUGUSTUS	transcript	1831807	1833695	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	start_codon	1831807	1831809	.	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1831807	1831878	0.96	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1831807	1831878	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1831879	1832019	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832020	1832125	1	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832020	1832125	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832126	1832280	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832281	1832357	1	+	2	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832281	1832357	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832358	1832461	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832462	1832525	1	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832462	1832525	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832526	1832631	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832632	1832681	1	+	2	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832632	1832681	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832682	1832781	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832782	1832853	1	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832782	1832853	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832854	1832968	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832969	1833028	1	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832969	1833028	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1833029	1833115	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1833116	1833363	1	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1833116	1833363	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1833364	1833454	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1833455	1833695	0.87	+	1	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1833455	1833695	.	+	.	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	stop_codon	1833696	1833698	.	+	0	transcript_id "Phchi.S5G018400.t1"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	transcript	1831807	1833695	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	start_codon	1831807	1831809	.	+	0	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1831807	1831878	0.92	+	0	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1831807	1831878	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1831879	1832019	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832020	1832125	1	+	0	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832020	1832125	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832126	1832280	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832281	1832357	1	+	2	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832281	1832357	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832358	1832461	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832462	1832525	0.88	+	0	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832462	1832525	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832526	1832631	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832632	1832681	0.94	+	2	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832632	1832681	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832682	1832781	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832782	1832872	0.56	+	0	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832782	1832872	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1832873	1832968	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1832969	1833028	0.81	+	2	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1832969	1833028	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1833029	1833107	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1833108	1833363	0.81	+	2	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1833108	1833363	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	intron	1833364	1833454	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	CDS	1833455	1833695	0.84	+	1	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	exon	1833455	1833695	.	+	.	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
Phchi.S5	AUGUSTUS	stop_codon	1833696	1833698	.	+	0	transcript_id "Phchi.S5G018400.t2"; gene_id "Phchi.S5G018400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13584.t1 is derived from g12051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7578934	7581385	.	+	.	Phchi.S3G090300
Phchi.S3	AUGUSTUS	transcript	7578934	7581385	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	start_codon	7578934	7578936	.	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7578934	7579162	1	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7578934	7579162	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	intron	7579163	7579253	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7579254	7579324	1	+	2	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7579254	7579324	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	intron	7579325	7579410	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7579411	7579746	0.92	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7579411	7579746	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	intron	7579747	7579941	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7579942	7580049	1	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7579942	7580049	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	intron	7580050	7580142	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7580143	7580196	0.38	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7580143	7580196	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	intron	7580197	7580441	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7580442	7580837	0.97	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7580442	7580837	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	intron	7580838	7580935	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	CDS	7580936	7581385	0.94	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	exon	7580936	7581385	.	+	.	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
Phchi.S3	AUGUSTUS	stop_codon	7581386	7581388	.	+	0	transcript_id "Phchi.S3G090300.t1"; gene_id "Phchi.S3G090300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11320.t1 is derived from g15370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5363230	5364855	.	+	.	Phchi.S4G090200
Phchi.S4	AUGUSTUS	transcript	5363230	5364855	.	+	.	transcript_id "Phchi.S4G090200.t1"; gene_id "Phchi.S4G090200"
Phchi.S4	AUGUSTUS	start_codon	5363230	5363232	.	+	0	transcript_id "Phchi.S4G090200.t1"; gene_id "Phchi.S4G090200"
Phchi.S4	AUGUSTUS	CDS	5363230	5364855	0.49	+	0	transcript_id "Phchi.S4G090200.t1"; gene_id "Phchi.S4G090200"
Phchi.S4	AUGUSTUS	exon	5363230	5364855	.	+	.	transcript_id "Phchi.S4G090200.t1"; gene_id "Phchi.S4G090200"
Phchi.S4	AUGUSTUS	stop_codon	5364856	5364858	.	+	0	transcript_id "Phchi.S4G090200.t1"; gene_id "Phchi.S4G090200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5605.t1 is derived from g2775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17843797	17846028	.	-	.	Phchi.S1G276400
Phchi.S1	AUGUSTUS	transcript	17843797	17846028	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	stop_codon	17843794	17843796	.	-	0	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	CDS	17843797	17844271	1	-	1	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	exon	17843797	17844271	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	intron	17844272	17844386	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	CDS	17844387	17844839	0.53	-	1	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	exon	17844387	17844839	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	intron	17844840	17845030	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	CDS	17845031	17845329	1	-	0	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	exon	17845031	17845329	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	intron	17845330	17845419	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	CDS	17845420	17845738	0.48	-	1	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	exon	17845420	17845738	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	intron	17845739	17845936	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	CDS	17845937	17846028	0.58	-	0	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	exon	17845937	17846028	.	-	.	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
Phchi.S1	AUGUSTUS	start_codon	17846026	17846028	.	-	0	transcript_id "Phchi.S1G276400.t1"; gene_id "Phchi.S1G276400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5058.t1 is derived from g2228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14453611	14455224	.	-	.	Phchi.S1G221700
Phchi.S1	AUGUSTUS	transcript	14453611	14455224	.	-	.	transcript_id "Phchi.S1G221700.t1"; gene_id "Phchi.S1G221700"
Phchi.S1	AUGUSTUS	stop_codon	14453608	14453610	.	-	0	transcript_id "Phchi.S1G221700.t1"; gene_id "Phchi.S1G221700"
Phchi.S1	AUGUSTUS	CDS	14453611	14455224	0.99	-	0	transcript_id "Phchi.S1G221700.t1"; gene_id "Phchi.S1G221700"
Phchi.S1	AUGUSTUS	exon	14453611	14455224	.	-	.	transcript_id "Phchi.S1G221700.t1"; gene_id "Phchi.S1G221700"
Phchi.S1	AUGUSTUS	start_codon	14455222	14455224	.	-	0	transcript_id "Phchi.S1G221700.t1"; gene_id "Phchi.S1G221700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9077.t1 is derived from g6252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39736906	39738122	.	+	.	Phchi.S1G623600
Phchi.S1	AUGUSTUS	transcript	39736906	39738122	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	start_codon	39736906	39736908	.	+	0	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	CDS	39736906	39737139	1	+	0	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	exon	39736906	39737139	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	intron	39737140	39737397	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	CDS	39737398	39737528	0.81	+	0	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	exon	39737398	39737528	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	intron	39737529	39737642	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	CDS	39737643	39737827	0.81	+	1	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	exon	39737643	39737827	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	intron	39737828	39738024	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	CDS	39738025	39738122	1	+	2	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	exon	39738025	39738122	.	+	.	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
Phchi.S1	AUGUSTUS	stop_codon	39738123	39738125	.	+	0	transcript_id "Phchi.S1G623600.t1"; gene_id "Phchi.S1G623600"
# This transcript jg7940.t2 is derived from g5114.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7941.t1 is derived from g5115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32025104	32026341	.	+	.	Phchi.S1G510000
Phchi.S1	AUGUSTUS	transcript	32025104	32026341	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	start_codon	32025104	32025106	.	+	0	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	CDS	32025104	32025666	0.4	+	0	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	exon	32025104	32025666	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	intron	32025667	32025781	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	CDS	32025782	32025936	1	+	1	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	exon	32025782	32025936	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	intron	32025937	32026018	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	CDS	32026019	32026116	1	+	2	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	exon	32026019	32026116	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	intron	32026117	32026302	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	CDS	32026303	32026341	0.66	+	0	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	exon	32026303	32026341	.	+	.	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
Phchi.S1	AUGUSTUS	stop_codon	32026342	32026344	.	+	0	transcript_id "Phchi.S1G510000.t1"; gene_id "Phchi.S1G510000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12536.t1 is derived from g8213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33636232	33644242	.	+	.	Phchi.S2G061600
Phchi.S2	AUGUSTUS	transcript	33636232	33644242	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	start_codon	33636232	33636234	.	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636232	33636264	0.98	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636232	33636264	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636265	33636618	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636619	33636668	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636619	33636668	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636669	33636860	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636861	33636894	1	+	1	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636861	33636894	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636895	33637040	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637041	33637058	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637041	33637058	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637059	33637150	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637151	33637166	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637151	33637166	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637167	33637243	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637244	33637287	0.95	+	2	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637244	33637287	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637288	33637385	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637386	33637460	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637386	33637460	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637461	33637650	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637651	33637696	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637651	33637696	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637697	33637832	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637833	33637892	1	+	2	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637833	33637892	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637893	33638002	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638003	33638083	0.78	+	2	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638003	33638083	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638084	33638343	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638344	33638429	1	+	2	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638344	33638429	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638430	33638565	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638566	33638667	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638566	33638667	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638668	33638873	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638874	33638927	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638874	33638927	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638928	33639090	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639091	33639192	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639091	33639192	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639193	33639346	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639347	33639405	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639347	33639405	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639406	33639561	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639562	33639706	1	+	1	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639562	33639706	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639707	33639889	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639890	33639997	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639890	33639997	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639998	33640080	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640081	33640233	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640081	33640233	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640234	33640341	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640342	33640446	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640342	33640446	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640447	33640672	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640673	33640869	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640673	33640869	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640870	33641033	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641034	33641145	1	+	1	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641034	33641145	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641146	33641224	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641225	33641323	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641225	33641323	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641324	33641441	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641442	33641587	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641442	33641587	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641588	33641677	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641678	33641735	0.91	+	1	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641678	33641735	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641736	33641843	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641844	33641936	0.97	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641844	33641936	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641937	33642178	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642179	33642229	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642179	33642229	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642230	33642335	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642336	33642467	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642336	33642467	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642468	33642596	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642597	33642698	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642597	33642698	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642699	33642785	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642786	33642840	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642786	33642840	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642841	33643007	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643008	33643093	1	+	2	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643008	33643093	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643094	33643272	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643273	33643421	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643273	33643421	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643422	33643604	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643605	33643710	1	+	1	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643605	33643710	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643711	33643826	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643827	33643880	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643827	33643880	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643881	33644023	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33644024	33644072	1	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33644024	33644072	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33644073	33644171	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33644172	33644242	1	+	2	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33644172	33644242	.	+	.	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	stop_codon	33644243	33644245	.	+	0	transcript_id "Phchi.S2G061600.t1"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	transcript	33636232	33644242	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	start_codon	33636232	33636234	.	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636232	33636264	0.97	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636232	33636264	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636265	33636618	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636619	33636668	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636619	33636668	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636669	33636860	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636861	33636894	1	+	1	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636861	33636894	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636895	33637040	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637041	33637058	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637041	33637058	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637059	33637150	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637151	33637166	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637151	33637166	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637167	33637243	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637244	33637287	0.95	+	2	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637244	33637287	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637288	33637385	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637386	33637460	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637386	33637460	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637461	33637650	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637651	33637696	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637651	33637696	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637697	33637832	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637833	33637892	1	+	2	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637833	33637892	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637893	33638002	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638003	33638083	0.79	+	2	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638003	33638083	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638084	33638343	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638344	33638429	1	+	2	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638344	33638429	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638430	33638565	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638566	33638667	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638566	33638667	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638668	33638873	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638874	33638927	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638874	33638927	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638928	33639090	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639091	33639192	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639091	33639192	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639193	33639346	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639347	33639405	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639347	33639405	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639406	33639561	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639562	33639706	1	+	1	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639562	33639706	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639707	33639889	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639890	33639997	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639890	33639997	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639998	33640080	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640081	33640233	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640081	33640233	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640234	33640341	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640342	33640446	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640342	33640446	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640447	33640672	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640673	33640869	0.98	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640673	33640869	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640870	33641030	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641031	33641145	0.74	+	1	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641031	33641145	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641146	33641224	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641225	33641323	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641225	33641323	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641324	33641441	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641442	33641587	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641442	33641587	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641588	33641677	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641678	33641735	0.87	+	1	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641678	33641735	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641736	33641843	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641844	33641936	0.98	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641844	33641936	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641937	33642178	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642179	33642229	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642179	33642229	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642230	33642335	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642336	33642467	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642336	33642467	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642468	33642596	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642597	33642698	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642597	33642698	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642699	33642785	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642786	33642840	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642786	33642840	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642841	33643007	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643008	33643093	1	+	2	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643008	33643093	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643094	33643272	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643273	33643421	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643273	33643421	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643422	33643604	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643605	33643710	1	+	1	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643605	33643710	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643711	33643826	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643827	33643880	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643827	33643880	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643881	33644023	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33644024	33644072	1	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33644024	33644072	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33644073	33644171	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33644172	33644242	1	+	2	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33644172	33644242	.	+	.	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	stop_codon	33644243	33644245	.	+	0	transcript_id "Phchi.S2G061600.t2"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	transcript	33636232	33644242	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	start_codon	33636232	33636234	.	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636232	33636264	0.99	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636232	33636264	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636265	33636618	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636619	33636668	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636619	33636668	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636669	33636860	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33636861	33636894	1	+	1	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33636861	33636894	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33636895	33637040	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637041	33637058	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637041	33637058	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637059	33637150	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637151	33637166	0.99	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637151	33637166	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637167	33637243	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637244	33637287	0.94	+	2	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637244	33637287	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637288	33637385	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637386	33637460	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637386	33637460	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637461	33637650	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637651	33637696	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637651	33637696	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637697	33637832	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33637833	33637892	1	+	2	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33637833	33637892	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33637893	33638002	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638003	33638083	0.73	+	2	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638003	33638083	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638084	33638343	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638344	33638429	1	+	2	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638344	33638429	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638430	33638565	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638566	33638667	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638566	33638667	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638668	33638873	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33638874	33638927	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33638874	33638927	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33638928	33639090	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639091	33639192	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639091	33639192	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639193	33639346	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639347	33639405	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639347	33639405	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639406	33639561	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639562	33639706	1	+	1	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639562	33639706	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639707	33639889	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33639890	33639997	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33639890	33639997	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33639998	33640080	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640081	33640233	0.99	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640081	33640233	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640234	33640341	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640342	33640446	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640342	33640446	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640447	33640672	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33640673	33640869	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33640673	33640869	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33640870	33641033	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641034	33641145	1	+	1	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641034	33641145	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641146	33641224	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641225	33641323	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641225	33641323	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641324	33641441	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641442	33641587	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641442	33641587	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641588	33641677	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641678	33641735	0.87	+	1	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641678	33641735	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641736	33641843	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33641844	33641936	0.96	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33641844	33641936	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33641937	33642178	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642179	33642229	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642179	33642229	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642230	33642335	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642336	33642467	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642336	33642467	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642468	33642596	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642597	33642698	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642597	33642698	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642699	33642785	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33642786	33642840	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33642786	33642840	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33642841	33643007	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643008	33643093	1	+	2	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643008	33643093	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643094	33643272	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643273	33643421	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643273	33643421	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643422	33643604	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643605	33643710	1	+	1	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643605	33643710	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643711	33643826	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33643827	33643880	1	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33643827	33643880	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33643881	33644023	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33644024	33644072	0.76	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33644024	33644072	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	intron	33644073	33644180	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	CDS	33644181	33644242	0.72	+	2	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	exon	33644181	33644242	.	+	.	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
Phchi.S2	AUGUSTUS	stop_codon	33644243	33644245	.	+	0	transcript_id "Phchi.S2G061600.t3"; gene_id "Phchi.S2G061600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8736.t1 is derived from g5911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37741250	37747415	.	-	.	Phchi.S1G589500
Phchi.S1	AUGUSTUS	transcript	37741250	37747415	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	stop_codon	37741247	37741249	.	-	0	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	CDS	37741250	37741268	0.98	-	1	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	exon	37741250	37741268	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	intron	37741269	37741494	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	CDS	37741495	37741670	1	-	0	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	exon	37741495	37741670	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	intron	37741671	37744886	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	CDS	37744887	37745049	1	-	1	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	exon	37744887	37745049	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	intron	37745050	37747401	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	CDS	37747402	37747415	0.01	-	0	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	exon	37747402	37747415	.	-	.	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
Phchi.S1	AUGUSTUS	start_codon	37747413	37747415	.	-	0	transcript_id "Phchi.S1G589500.t1"; gene_id "Phchi.S1G589500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11400.t1 is derived from g15450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6144280	6145351	.	+	.	Phchi.S4G098200
Phchi.S4	AUGUSTUS	transcript	6144280	6145351	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	start_codon	6144280	6144282	.	+	0	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	CDS	6144280	6144473	0.95	+	0	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	exon	6144280	6144473	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	intron	6144474	6144563	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	CDS	6144564	6144738	1	+	1	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	exon	6144564	6144738	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	intron	6144739	6144830	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	CDS	6144831	6144900	1	+	0	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	exon	6144831	6144900	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	intron	6144901	6144989	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	CDS	6144990	6145108	1	+	2	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	exon	6144990	6145108	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	intron	6145109	6145192	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	CDS	6145193	6145351	1	+	0	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	exon	6145193	6145351	.	+	.	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
Phchi.S4	AUGUSTUS	stop_codon	6145352	6145354	.	+	0	transcript_id "Phchi.S4G098200.t1"; gene_id "Phchi.S4G098200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15279.t1 is derived from g13747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18134176	18135313	.	+	.	Phchi.S3G259800
Phchi.S3	AUGUSTUS	transcript	18134176	18135313	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	start_codon	18134176	18134178	.	+	0	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	CDS	18134176	18134480	0.7	+	0	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	exon	18134176	18134480	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	intron	18134481	18134652	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	CDS	18134653	18134758	1	+	1	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	exon	18134653	18134758	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	intron	18134759	18134857	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	CDS	18134858	18134995	1	+	0	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	exon	18134858	18134995	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	intron	18134996	18135095	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	CDS	18135096	18135187	1	+	0	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	exon	18135096	18135187	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	intron	18135188	18135276	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	CDS	18135277	18135313	1	+	1	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	exon	18135277	18135313	.	+	.	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
Phchi.S3	AUGUSTUS	stop_codon	18135314	18135316	.	+	0	transcript_id "Phchi.S3G259800.t1"; gene_id "Phchi.S3G259800"
# This transcript jg7035.t2 is derived from g4207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7036.t1 is derived from g4208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26521357	26524251	.	+	.	Phchi.S1G419500
Phchi.S1	AUGUSTUS	transcript	26521357	26524251	.	+	.	transcript_id "Phchi.S1G419500.t1"; gene_id "Phchi.S1G419500"
Phchi.S1	AUGUSTUS	start_codon	26521357	26521359	.	+	0	transcript_id "Phchi.S1G419500.t1"; gene_id "Phchi.S1G419500"
Phchi.S1	AUGUSTUS	CDS	26521357	26524251	0.88	+	0	transcript_id "Phchi.S1G419500.t1"; gene_id "Phchi.S1G419500"
Phchi.S1	AUGUSTUS	exon	26521357	26524251	.	+	.	transcript_id "Phchi.S1G419500.t1"; gene_id "Phchi.S1G419500"
Phchi.S1	AUGUSTUS	stop_codon	26524252	26524254	.	+	0	transcript_id "Phchi.S1G419500.t1"; gene_id "Phchi.S1G419500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7268.t1 is derived from g4440.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27985003	27986979	.	-	.	Phchi.S1G442700
Phchi.S1	AUGUSTUS	transcript	27985003	27986979	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	stop_codon	27985000	27985002	.	-	0	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27985003	27985138	0.6	-	1	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27985003	27985138	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27985139	27985212	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27985213	27985356	0.99	-	1	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27985213	27985356	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27985357	27985499	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27985500	27985575	1	-	2	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27985500	27985575	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27985576	27985718	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27985719	27985901	1	-	2	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27985719	27985901	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27985902	27985992	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27985993	27986016	1	-	2	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27985993	27986016	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27986017	27986142	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27986143	27986190	0.99	-	2	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27986143	27986190	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27986191	27986296	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27986297	27986372	0.8	-	0	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27986297	27986372	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	intron	27986373	27986898	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	CDS	27986899	27986979	0.56	-	0	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	exon	27986899	27986979	.	-	.	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
Phchi.S1	AUGUSTUS	start_codon	27986977	27986979	.	-	0	transcript_id "Phchi.S1G442700.t1"; gene_id "Phchi.S1G442700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10209.t1 is derived from g7385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46390109	46393506	.	+	.	Phchi.S1G736800
Phchi.S1	AUGUSTUS	transcript	46390109	46393506	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	start_codon	46390109	46390111	.	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46390109	46390190	0.93	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46390109	46390190	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46390191	46390271	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46390272	46390286	0.95	+	2	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46390272	46390286	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46390287	46390408	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46390409	46390489	0.54	+	2	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46390409	46390489	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46390490	46390584	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46390585	46390648	1	+	2	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46390585	46390648	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46390649	46390866	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46390867	46391044	0.99	+	1	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46390867	46391044	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46391045	46391161	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46391162	46391223	0.99	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46391162	46391223	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46391224	46391367	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46391368	46391575	1	+	1	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46391368	46391575	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46391576	46391697	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46391698	46391868	1	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46391698	46391868	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46391869	46391951	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46391952	46392267	1	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46391952	46392267	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46392268	46392352	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46392353	46392513	0.96	+	2	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46392353	46392513	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46392514	46392622	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46392623	46392657	0.72	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46392623	46392657	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46392658	46392846	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46392847	46392943	0.52	+	1	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46392847	46392943	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46392944	46393062	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46393063	46393225	0.83	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46393063	46393225	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	intron	46393226	46393378	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	CDS	46393379	46393506	0.83	+	2	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	exon	46393379	46393506	.	+	.	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
Phchi.S1	AUGUSTUS	stop_codon	46393507	46393509	.	+	0	transcript_id "Phchi.S1G736800.t1"; gene_id "Phchi.S1G736800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2673.t1 is derived from g9593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8141315	8142338	.	+	.	Phchi.S5G128200
Phchi.S5	AUGUSTUS	transcript	8141315	8142338	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	start_codon	8141315	8141317	.	+	0	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	CDS	8141315	8141459	1	+	0	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	exon	8141315	8141459	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	intron	8141460	8141594	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	CDS	8141595	8141896	1	+	2	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	exon	8141595	8141896	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	intron	8141897	8141995	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	CDS	8141996	8142184	1	+	0	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	exon	8141996	8142184	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	intron	8142185	8142278	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	CDS	8142279	8142338	1	+	0	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	exon	8142279	8142338	.	+	.	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
Phchi.S5	AUGUSTUS	stop_codon	8142339	8142341	.	+	0	transcript_id "Phchi.S5G128200.t1"; gene_id "Phchi.S5G128200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14184.t1 is derived from g12651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11335852	11338077	.	-	.	Phchi.S3G150300
Phchi.S3	AUGUSTUS	transcript	11335852	11338077	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	stop_codon	11335849	11335851	.	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11335852	11335923	0.92	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11335852	11335923	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11335924	11336019	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11336020	11336076	1	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11336020	11336076	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11336077	11336163	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11336164	11336271	1	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11336164	11336271	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11336272	11336372	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11336373	11336470	1	-	2	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11336373	11336470	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11336471	11336594	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11336595	11336639	1	-	2	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11336595	11336639	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11336640	11336799	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11336800	11336930	1	-	1	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11336800	11336930	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11336931	11337166	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11337167	11337300	1	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11337167	11337300	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11337301	11337410	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11337411	11337569	0.96	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11337411	11337569	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11337570	11337704	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11337705	11337781	1	-	2	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11337705	11337781	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	intron	11337782	11337944	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	CDS	11337945	11338077	0.99	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	exon	11337945	11338077	.	-	.	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
Phchi.S3	AUGUSTUS	start_codon	11338075	11338077	.	-	0	transcript_id "Phchi.S3G150300.t1"; gene_id "Phchi.S3G150300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14210.t1 is derived from g12677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11521111	11522421	.	+	.	Phchi.S3G152900
Phchi.S3	AUGUSTUS	transcript	11521111	11522421	.	+	.	transcript_id "Phchi.S3G152900.t1"; gene_id "Phchi.S3G152900"
Phchi.S3	AUGUSTUS	start_codon	11521111	11521113	.	+	0	transcript_id "Phchi.S3G152900.t1"; gene_id "Phchi.S3G152900"
Phchi.S3	AUGUSTUS	CDS	11521111	11522421	0.81	+	0	transcript_id "Phchi.S3G152900.t1"; gene_id "Phchi.S3G152900"
Phchi.S3	AUGUSTUS	exon	11521111	11522421	.	+	.	transcript_id "Phchi.S3G152900.t1"; gene_id "Phchi.S3G152900"
Phchi.S3	AUGUSTUS	stop_codon	11522422	11522424	.	+	0	transcript_id "Phchi.S3G152900.t1"; gene_id "Phchi.S3G152900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14940.t1 is derived from g13408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15640131	15641249	.	-	.	Phchi.S3G225900
Phchi.S3	AUGUSTUS	transcript	15640131	15641249	.	-	.	transcript_id "Phchi.S3G225900.t1"; gene_id "Phchi.S3G225900"
Phchi.S3	AUGUSTUS	stop_codon	15640128	15640130	.	-	0	transcript_id "Phchi.S3G225900.t1"; gene_id "Phchi.S3G225900"
Phchi.S3	AUGUSTUS	CDS	15640131	15641249	0.72	-	0	transcript_id "Phchi.S3G225900.t1"; gene_id "Phchi.S3G225900"
Phchi.S3	AUGUSTUS	exon	15640131	15641249	.	-	.	transcript_id "Phchi.S3G225900.t1"; gene_id "Phchi.S3G225900"
Phchi.S3	AUGUSTUS	start_codon	15641247	15641249	.	-	0	transcript_id "Phchi.S3G225900.t1"; gene_id "Phchi.S3G225900"
# This transcript jg3173.t2 is derived from g342.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3174.t1 is derived from g343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2106613	2108661	.	+	.	Phchi.S1G033300
Phchi.S1	AUGUSTUS	transcript	2106613	2108661	.	+	.	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	start_codon	2106613	2106615	.	+	0	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	CDS	2106613	2106797	0.99	+	0	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	exon	2106613	2106797	.	+	.	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	intron	2106798	2107088	.	+	.	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	CDS	2107089	2108661	0.99	+	1	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	exon	2107089	2108661	.	+	.	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
Phchi.S1	AUGUSTUS	stop_codon	2108662	2108664	.	+	0	transcript_id "Phchi.S1G033300.t1"; gene_id "Phchi.S1G033300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14049.t1 is derived from g12516.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10483751	10485912	.	+	.	Phchi.S3G136800
Phchi.S3	AUGUSTUS	transcript	10483751	10485912	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	start_codon	10483751	10483753	.	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10483751	10483900	0.92	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10483751	10483900	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10483901	10484025	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10484026	10484136	0.6	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10484026	10484136	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10484137	10484255	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10484256	10484396	1	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10484256	10484396	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10484397	10484568	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10484569	10484679	0.97	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10484569	10484679	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10484680	10484801	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10484802	10484948	1	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10484802	10484948	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10484949	10485069	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10485070	10485110	0.99	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10485070	10485110	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10485111	10485203	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10485204	10485283	1	+	1	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10485204	10485283	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10485284	10485376	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10485377	10485472	1	+	2	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10485377	10485472	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	intron	10485473	10485610	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	CDS	10485611	10485912	0.95	+	2	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	exon	10485611	10485912	.	+	.	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
Phchi.S3	AUGUSTUS	stop_codon	10485913	10485915	.	+	0	transcript_id "Phchi.S3G136800.t1"; gene_id "Phchi.S3G136800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg895.t1 is derived from g10677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6347073	6349617	.	+	.	Phchi.S6G085400
Phchi.S6	AUGUSTUS	transcript	6347073	6349617	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	start_codon	6347073	6347075	.	+	0	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	CDS	6347073	6347114	0.39	+	0	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	exon	6347073	6347114	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	intron	6347115	6347449	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	CDS	6347450	6347518	0.87	+	0	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	exon	6347450	6347518	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	intron	6347519	6347646	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	CDS	6347647	6347726	1	+	0	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	exon	6347647	6347726	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	intron	6347727	6347846	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	CDS	6347847	6348045	0.97	+	1	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	exon	6347847	6348045	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	intron	6348046	6348151	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	CDS	6348152	6349398	0.85	+	0	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	exon	6348152	6349398	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	intron	6349399	6349487	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	CDS	6349488	6349617	0.89	+	1	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	exon	6349488	6349617	.	+	.	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
Phchi.S6	AUGUSTUS	stop_codon	6349618	6349620	.	+	0	transcript_id "Phchi.S6G085400.t1"; gene_id "Phchi.S6G085400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14353.t1 is derived from g12820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12338355	12339688	.	+	.	Phchi.S3G167200
Phchi.S3	AUGUSTUS	transcript	12338355	12339688	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	start_codon	12338355	12338357	.	+	0	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	CDS	12338355	12338504	1	+	0	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	exon	12338355	12338504	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	intron	12338505	12338582	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	CDS	12338583	12338707	1	+	0	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	exon	12338583	12338707	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	intron	12338708	12338787	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	CDS	12338788	12339017	1	+	1	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	exon	12338788	12339017	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	intron	12339018	12339112	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	CDS	12339113	12339152	1	+	2	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	exon	12339113	12339152	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	intron	12339153	12339324	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	CDS	12339325	12339416	1	+	1	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	exon	12339325	12339416	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	intron	12339417	12339506	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	CDS	12339507	12339688	0.95	+	2	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	exon	12339507	12339688	.	+	.	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
Phchi.S3	AUGUSTUS	stop_codon	12339689	12339691	.	+	0	transcript_id "Phchi.S3G167200.t1"; gene_id "Phchi.S3G167200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12452.t1 is derived from g8129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23330377	23330769	.	-	.	Phchi.S2G053200
Phchi.S2	AUGUSTUS	transcript	23330377	23330769	.	-	.	transcript_id "Phchi.S2G053200.t1"; gene_id "Phchi.S2G053200"
Phchi.S2	AUGUSTUS	stop_codon	23330374	23330376	.	-	0	transcript_id "Phchi.S2G053200.t1"; gene_id "Phchi.S2G053200"
Phchi.S2	AUGUSTUS	CDS	23330377	23330769	0.51	-	0	transcript_id "Phchi.S2G053200.t1"; gene_id "Phchi.S2G053200"
Phchi.S2	AUGUSTUS	exon	23330377	23330769	.	-	.	transcript_id "Phchi.S2G053200.t1"; gene_id "Phchi.S2G053200"
Phchi.S2	AUGUSTUS	start_codon	23330767	23330769	.	-	0	transcript_id "Phchi.S2G053200.t1"; gene_id "Phchi.S2G053200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8572.t1 is derived from g5747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36698004	36700004	.	+	.	Phchi.S1G573100
Phchi.S1	AUGUSTUS	transcript	36698004	36700004	.	+	.	transcript_id "Phchi.S1G573100.t1"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	start_codon	36698004	36698006	.	+	0	transcript_id "Phchi.S1G573100.t1"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	CDS	36698004	36700004	1	+	0	transcript_id "Phchi.S1G573100.t1"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	exon	36698004	36700004	.	+	.	transcript_id "Phchi.S1G573100.t1"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	stop_codon	36700005	36700007	.	+	0	transcript_id "Phchi.S1G573100.t1"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	transcript	36698688	36700004	.	+	.	transcript_id "Phchi.S1G573100.t2"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	start_codon	36698688	36698690	.	+	0	transcript_id "Phchi.S1G573100.t2"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	CDS	36698688	36700004	0.96	+	0	transcript_id "Phchi.S1G573100.t2"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	exon	36698688	36700004	.	+	.	transcript_id "Phchi.S1G573100.t2"; gene_id "Phchi.S1G573100"
Phchi.S1	AUGUSTUS	stop_codon	36700005	36700007	.	+	0	transcript_id "Phchi.S1G573100.t2"; gene_id "Phchi.S1G573100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6851.t1 is derived from g4023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25571216	25572530	.	-	.	Phchi.S1G401000
Phchi.S1	AUGUSTUS	transcript	25571216	25572530	.	-	.	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	stop_codon	25571213	25571215	.	-	0	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	CDS	25571216	25571857	0.97	-	0	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	exon	25571216	25571857	.	-	.	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	intron	25571858	25571948	.	-	.	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	CDS	25571949	25572530	0.95	-	0	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	exon	25571949	25572530	.	-	.	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
Phchi.S1	AUGUSTUS	start_codon	25572528	25572530	.	-	0	transcript_id "Phchi.S1G401000.t1"; gene_id "Phchi.S1G401000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5695.t1 is derived from g2865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18372302	18373942	.	-	.	Phchi.S1G285400
Phchi.S1	AUGUSTUS	transcript	18372302	18373942	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	stop_codon	18372299	18372301	.	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18372302	18372387	1	-	2	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18372302	18372387	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18372388	18372648	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18372649	18372745	1	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18372649	18372745	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18372746	18372837	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18372838	18372919	1	-	1	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18372838	18372919	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18372920	18373008	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18373009	18373079	1	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18373009	18373079	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18373080	18373167	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18373168	18373221	1	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18373168	18373221	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18373222	18373309	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18373310	18373398	0.99	-	2	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18373310	18373398	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18373399	18373514	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18373515	18373533	1	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18373515	18373533	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18373534	18373675	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18373676	18373787	1	-	1	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18373676	18373787	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	intron	18373788	18373883	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	CDS	18373884	18373942	1	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	exon	18373884	18373942	.	-	.	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
Phchi.S1	AUGUSTUS	start_codon	18373940	18373942	.	-	0	transcript_id "Phchi.S1G285400.t1"; gene_id "Phchi.S1G285400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15800.t1 is derived from g14270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21427817	21429659	.	+	.	Phchi.S3G311900
Phchi.S3	AUGUSTUS	transcript	21427817	21429659	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	start_codon	21427817	21427819	.	+	0	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	CDS	21427817	21428204	0.69	+	0	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	exon	21427817	21428204	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	intron	21428205	21428327	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	CDS	21428328	21428656	0.99	+	2	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	exon	21428328	21428656	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	intron	21428657	21428757	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	CDS	21428758	21428973	0.99	+	0	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	exon	21428758	21428973	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	intron	21428974	21429044	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	CDS	21429045	21429659	0.99	+	0	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	exon	21429045	21429659	.	+	.	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
Phchi.S3	AUGUSTUS	stop_codon	21429660	21429662	.	+	0	transcript_id "Phchi.S3G311900.t1"; gene_id "Phchi.S3G311900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6322.t1 is derived from g3494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22251580	22252964	.	-	.	Phchi.S1G348100
Phchi.S1	AUGUSTUS	transcript	22251580	22252964	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	stop_codon	22251577	22251579	.	-	0	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	CDS	22251580	22251595	1	-	1	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	exon	22251580	22251595	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	intron	22251596	22251677	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	CDS	22251678	22251749	1	-	1	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	exon	22251678	22251749	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	intron	22251750	22251900	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	CDS	22251901	22252121	0.98	-	0	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	exon	22251901	22252121	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	intron	22252122	22252227	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	CDS	22252228	22252323	0.98	-	0	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	exon	22252228	22252323	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	intron	22252324	22252661	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	CDS	22252662	22252964	0.65	-	0	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	exon	22252662	22252964	.	-	.	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
Phchi.S1	AUGUSTUS	start_codon	22252962	22252964	.	-	0	transcript_id "Phchi.S1G348100.t1"; gene_id "Phchi.S1G348100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10433.t1 is derived from g14482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	316545	318685	.	+	.	Phchi.S4G001500
Phchi.S4	AUGUSTUS	transcript	316545	318570	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	start_codon	316545	316547	.	+	0	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	316545	316565	0.89	+	0	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	316545	316565	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	316566	316770	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	316771	316807	0.92	+	0	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	316771	316807	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	316808	316893	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	316894	317095	0.46	+	2	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	316894	317095	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	317096	317248	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	317249	317560	0.29	+	1	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	317249	317560	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	317561	317731	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	317732	317779	0.72	+	1	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	317732	317779	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	317780	318120	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	318121	318149	0.8	+	1	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	318121	318149	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	318150	318490	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	318491	318570	0.68	+	2	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	318491	318570	.	+	.	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	stop_codon	318571	318573	.	+	0	transcript_id "Phchi.S4G001500.t1"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	transcript	316545	318685	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	start_codon	316545	316547	.	+	0	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	316545	316565	0.94	+	0	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	316545	316565	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	316566	316770	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	316771	316807	0.94	+	0	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	316771	316807	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	316808	316893	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	316894	317095	0.33	+	2	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	316894	317095	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	317096	317248	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	317249	317560	0.09	+	1	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	317249	317560	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	317561	317731	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	317732	317779	0.46	+	1	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	317732	317779	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	317780	318120	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	318121	318128	0.42	+	1	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	318121	318128	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	318129	318348	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	318349	318447	0.38	+	2	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	318349	318447	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	intron	318448	318593	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	CDS	318594	318685	0.37	+	2	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	exon	318594	318685	.	+	.	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
Phchi.S4	AUGUSTUS	stop_codon	318686	318688	.	+	0	transcript_id "Phchi.S4G001500.t2"; gene_id "Phchi.S4G001500"
# This transcript jg5263.t2 is derived from g2433.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5264.t1 is derived from g2434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15941444	15945710	.	+	.	Phchi.S1G242300
Phchi.S1	AUGUSTUS	transcript	15941444	15945710	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	start_codon	15941444	15941446	.	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15941444	15941478	0.66	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15941444	15941478	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15941479	15941730	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15941731	15941761	0.71	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15941731	15941761	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15941762	15941863	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15941864	15941948	0.68	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15941864	15941948	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15941949	15942058	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15942059	15942241	1	+	2	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15942059	15942241	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15942242	15942385	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15942386	15942623	1	+	2	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15942386	15942623	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15942624	15942763	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15942764	15942898	1	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15942764	15942898	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15942899	15942998	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15942999	15943103	1	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15942999	15943103	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15943104	15943198	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15943199	15943297	1	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15943199	15943297	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15943298	15943432	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15943433	15943562	1	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15943433	15943562	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15943563	15943728	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15943729	15943779	1	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15943729	15943779	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15943780	15943875	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15943876	15943986	0.99	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15943876	15943986	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15943987	15944091	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15944092	15944177	0.99	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15944092	15944177	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15944178	15944252	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15944253	15944424	1	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15944253	15944424	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15944425	15944508	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15944509	15944595	1	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15944509	15944595	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15944596	15944683	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15944684	15944755	1	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15944684	15944755	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15944756	15944985	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15944986	15945099	1	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15944986	15945099	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15945100	15945192	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15945193	15945254	1	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15945193	15945254	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15945255	15945378	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15945379	15945493	1	+	1	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15945379	15945493	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	intron	15945494	15945593	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	CDS	15945594	15945710	1	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	exon	15945594	15945710	.	+	.	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
Phchi.S1	AUGUSTUS	stop_codon	15945711	15945713	.	+	0	transcript_id "Phchi.S1G242300.t1"; gene_id "Phchi.S1G242300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2735.t1 is derived from g9655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8498011	8499233	.	-	.	Phchi.S5G134400
Phchi.S5	AUGUSTUS	transcript	8498011	8499233	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	stop_codon	8498008	8498010	.	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8498011	8498037	1	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8498011	8498037	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	intron	8498038	8498165	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8498166	8498225	1	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8498166	8498225	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	intron	8498226	8498334	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8498335	8498376	1	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8498335	8498376	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	intron	8498377	8498488	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8498489	8498554	1	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8498489	8498554	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	intron	8498555	8498656	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8498657	8498712	0.98	-	2	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8498657	8498712	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	intron	8498713	8498808	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8498809	8498899	1	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8498809	8498899	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	intron	8498900	8499098	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	CDS	8499099	8499233	0.84	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	exon	8499099	8499233	.	-	.	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
Phchi.S5	AUGUSTUS	start_codon	8499231	8499233	.	-	0	transcript_id "Phchi.S5G134400.t1"; gene_id "Phchi.S5G134400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9592.t1 is derived from g6768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42818119	42819036	.	-	.	Phchi.S1G675100
Phchi.S1	AUGUSTUS	transcript	42818119	42819036	.	-	.	transcript_id "Phchi.S1G675100.t1"; gene_id "Phchi.S1G675100"
Phchi.S1	AUGUSTUS	stop_codon	42818116	42818118	.	-	0	transcript_id "Phchi.S1G675100.t1"; gene_id "Phchi.S1G675100"
Phchi.S1	AUGUSTUS	CDS	42818119	42819036	0.55	-	0	transcript_id "Phchi.S1G675100.t1"; gene_id "Phchi.S1G675100"
Phchi.S1	AUGUSTUS	exon	42818119	42819036	.	-	.	transcript_id "Phchi.S1G675100.t1"; gene_id "Phchi.S1G675100"
Phchi.S1	AUGUSTUS	start_codon	42819034	42819036	.	-	0	transcript_id "Phchi.S1G675100.t1"; gene_id "Phchi.S1G675100"
# This transcript jg15288.t2 is derived from g13756.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15289.t1 is derived from g13757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18223304	18223687	.	+	.	Phchi.S3G260800
Phchi.S3	AUGUSTUS	transcript	18223304	18223687	.	+	.	transcript_id "Phchi.S3G260800.t1"; gene_id "Phchi.S3G260800"
Phchi.S3	AUGUSTUS	start_codon	18223304	18223306	.	+	0	transcript_id "Phchi.S3G260800.t1"; gene_id "Phchi.S3G260800"
Phchi.S3	AUGUSTUS	CDS	18223304	18223687	0.79	+	0	transcript_id "Phchi.S3G260800.t1"; gene_id "Phchi.S3G260800"
Phchi.S3	AUGUSTUS	exon	18223304	18223687	.	+	.	transcript_id "Phchi.S3G260800.t1"; gene_id "Phchi.S3G260800"
Phchi.S3	AUGUSTUS	stop_codon	18223688	18223690	.	+	0	transcript_id "Phchi.S3G260800.t1"; gene_id "Phchi.S3G260800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8663.t1 is derived from g5838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37345581	37346335	.	-	.	Phchi.S1G582200
Phchi.S1	AUGUSTUS	transcript	37345581	37346335	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	stop_codon	37345578	37345580	.	-	0	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	CDS	37345581	37345721	0.93	-	0	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	exon	37345581	37345721	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	intron	37345722	37345814	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	CDS	37345815	37345883	1	-	0	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	exon	37345815	37345883	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	intron	37345884	37345974	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	CDS	37345975	37346101	1	-	1	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	exon	37345975	37346101	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	intron	37346102	37346189	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	CDS	37346190	37346335	0.99	-	0	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	exon	37346190	37346335	.	-	.	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
Phchi.S1	AUGUSTUS	start_codon	37346333	37346335	.	-	0	transcript_id "Phchi.S1G582200.t1"; gene_id "Phchi.S1G582200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9642.t1 is derived from g6818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43032849	43034126	.	+	.	Phchi.S1G680100
Phchi.S1	AUGUSTUS	transcript	43032849	43034126	.	+	.	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	start_codon	43032849	43032851	.	+	0	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	CDS	43032849	43033325	0.55	+	0	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	exon	43032849	43033325	.	+	.	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	intron	43033326	43033568	.	+	.	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	CDS	43033569	43034126	0.73	+	0	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	exon	43033569	43034126	.	+	.	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
Phchi.S1	AUGUSTUS	stop_codon	43034127	43034129	.	+	0	transcript_id "Phchi.S1G680100.t1"; gene_id "Phchi.S1G680100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11597.t1 is derived from g15648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7271813	7273051	.	+	.	Phchi.S4G117900
Phchi.S4	AUGUSTUS	transcript	7271813	7273051	.	+	.	transcript_id "Phchi.S4G117900.t1"; gene_id "Phchi.S4G117900"
Phchi.S4	AUGUSTUS	start_codon	7271813	7271815	.	+	0	transcript_id "Phchi.S4G117900.t1"; gene_id "Phchi.S4G117900"
Phchi.S4	AUGUSTUS	CDS	7271813	7273051	1	+	0	transcript_id "Phchi.S4G117900.t1"; gene_id "Phchi.S4G117900"
Phchi.S4	AUGUSTUS	exon	7271813	7273051	.	+	.	transcript_id "Phchi.S4G117900.t1"; gene_id "Phchi.S4G117900"
Phchi.S4	AUGUSTUS	stop_codon	7273052	7273054	.	+	0	transcript_id "Phchi.S4G117900.t1"; gene_id "Phchi.S4G117900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9237.t1 is derived from g6412.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40543716	40547645	.	-	.	Phchi.S1G639600
Phchi.S1	AUGUSTUS	transcript	40546244	40547645	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	stop_codon	40546241	40546243	.	-	0	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40546244	40546244	0.98	-	1	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40546244	40546244	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40546245	40546338	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40546339	40546469	0.98	-	0	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40546339	40546469	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40546470	40546573	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40546574	40546926	0.76	-	2	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40546574	40546926	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40546927	40547055	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40547056	40547272	1	-	0	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40547056	40547272	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40547273	40547348	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40547349	40547645	0.48	-	0	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40547349	40547645	.	-	.	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	start_codon	40547643	40547645	.	-	0	transcript_id "Phchi.S1G639600.t1"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	transcript	40543716	40547645	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	stop_codon	40543713	40543715	.	-	0	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40543716	40544114	0.96	-	0	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40543716	40544114	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40544115	40544194	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40544195	40544568	0.49	-	2	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40544195	40544568	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40544569	40544671	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40544672	40545004	0.98	-	2	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40544672	40545004	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40545005	40545080	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40545081	40546244	0.91	-	2	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40545081	40546244	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40546245	40546342	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40546343	40546469	1	-	0	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40546343	40546469	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40546470	40546573	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40546574	40546926	0.76	-	2	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40546574	40546926	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40546927	40547055	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40547056	40547272	1	-	0	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40547056	40547272	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	intron	40547273	40547348	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	CDS	40547349	40547645	0.51	-	0	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	exon	40547349	40547645	.	-	.	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
Phchi.S1	AUGUSTUS	start_codon	40547643	40547645	.	-	0	transcript_id "Phchi.S1G639600.t2"; gene_id "Phchi.S1G639600"
# This transcript jg1193.t2 is derived from g10976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1194.t1 is derived from g10977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8366335	8366877	.	-	.	Phchi.S6G115300
Phchi.S6	AUGUSTUS	transcript	8366335	8366877	.	-	.	transcript_id "Phchi.S6G115300.t1"; gene_id "Phchi.S6G115300"
Phchi.S6	AUGUSTUS	stop_codon	8366332	8366334	.	-	0	transcript_id "Phchi.S6G115300.t1"; gene_id "Phchi.S6G115300"
Phchi.S6	AUGUSTUS	CDS	8366335	8366877	1	-	0	transcript_id "Phchi.S6G115300.t1"; gene_id "Phchi.S6G115300"
Phchi.S6	AUGUSTUS	exon	8366335	8366877	.	-	.	transcript_id "Phchi.S6G115300.t1"; gene_id "Phchi.S6G115300"
Phchi.S6	AUGUSTUS	start_codon	8366875	8366877	.	-	0	transcript_id "Phchi.S6G115300.t1"; gene_id "Phchi.S6G115300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1971.t1 is derived from g8891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4083396	4087561	.	+	.	Phchi.S5G058000
Phchi.S5	AUGUSTUS	transcript	4083396	4087561	.	+	.	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	start_codon	4083396	4083398	.	+	0	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	CDS	4083396	4085926	0.23	+	0	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	exon	4083396	4085926	.	+	.	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	intron	4085927	4086315	.	+	.	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	CDS	4086316	4086581	0.44	+	1	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	exon	4086316	4086581	.	+	.	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	intron	4086582	4086680	.	+	.	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	CDS	4086681	4087561	0.74	+	2	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	exon	4086681	4087561	.	+	.	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
Phchi.S5	AUGUSTUS	stop_codon	4087562	4087564	.	+	0	transcript_id "Phchi.S5G058000.t1"; gene_id "Phchi.S5G058000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2899.t1 is derived from g68.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	384496	385161	.	-	.	Phchi.S1G005800
Phchi.S1	AUGUSTUS	transcript	384496	385161	.	-	.	transcript_id "Phchi.S1G005800.t1"; gene_id "Phchi.S1G005800"
Phchi.S1	AUGUSTUS	stop_codon	384493	384495	.	-	0	transcript_id "Phchi.S1G005800.t1"; gene_id "Phchi.S1G005800"
Phchi.S1	AUGUSTUS	CDS	384496	385161	0.8	-	0	transcript_id "Phchi.S1G005800.t1"; gene_id "Phchi.S1G005800"
Phchi.S1	AUGUSTUS	exon	384496	385161	.	-	.	transcript_id "Phchi.S1G005800.t1"; gene_id "Phchi.S1G005800"
Phchi.S1	AUGUSTUS	start_codon	385159	385161	.	-	0	transcript_id "Phchi.S1G005800.t1"; gene_id "Phchi.S1G005800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1112.t1 is derived from g10895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7674748	7677182	.	-	.	Phchi.S6G107100
Phchi.S6	AUGUSTUS	transcript	7674748	7677182	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	stop_codon	7674745	7674747	.	-	0	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7674748	7674889	1	-	1	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7674748	7674889	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	intron	7674890	7675031	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7675032	7675126	1	-	0	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7675032	7675126	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	intron	7675127	7675214	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7675215	7675379	0.78	-	0	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7675215	7675379	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	intron	7675380	7675469	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7675470	7675576	0.77	-	2	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7675470	7675576	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	intron	7675577	7675629	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7675630	7675651	0.7	-	0	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7675630	7675651	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	intron	7675652	7676031	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7676032	7676062	0.23	-	1	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7676032	7676062	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	intron	7676063	7676169	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	CDS	7676170	7677182	0.32	-	0	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	exon	7676170	7677182	.	-	.	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
Phchi.S6	AUGUSTUS	start_codon	7677180	7677182	.	-	0	transcript_id "Phchi.S6G107100.t1"; gene_id "Phchi.S6G107100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3552.t1 is derived from g721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4441360	4443252	.	+	.	Phchi.S1G071100
Phchi.S1	AUGUSTUS	transcript	4441360	4443252	.	+	.	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	start_codon	4441360	4441362	.	+	0	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	CDS	4441360	4441731	0.54	+	0	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	exon	4441360	4441731	.	+	.	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	intron	4441732	4442169	.	+	.	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	CDS	4442170	4443252	0.9	+	0	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	exon	4442170	4443252	.	+	.	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
Phchi.S1	AUGUSTUS	stop_codon	4443253	4443255	.	+	0	transcript_id "Phchi.S1G071100.t1"; gene_id "Phchi.S1G071100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5245.t1 is derived from g2415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15846736	15847937	.	-	.	Phchi.S1G240400
Phchi.S1	AUGUSTUS	transcript	15846736	15847937	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	stop_codon	15846733	15846735	.	-	0	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	CDS	15846736	15846775	0.76	-	1	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	exon	15846736	15846775	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	intron	15846776	15847010	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	CDS	15847011	15847354	0.38	-	0	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	exon	15847011	15847354	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	intron	15847355	15847455	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	CDS	15847456	15847668	0.49	-	0	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	exon	15847456	15847668	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	intron	15847669	15847757	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	CDS	15847758	15847937	0.98	-	0	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	exon	15847758	15847937	.	-	.	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
Phchi.S1	AUGUSTUS	start_codon	15847935	15847937	.	-	0	transcript_id "Phchi.S1G240400.t1"; gene_id "Phchi.S1G240400"
# This transcript jg11716.t2 is derived from g15767.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11717.t1 is derived from g15769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7823656	7826452	.	-	.	Phchi.S4G129900
Phchi.S4	AUGUSTUS	transcript	7823656	7826452	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	stop_codon	7823653	7823655	.	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7823656	7824754	0.94	-	1	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7823656	7824754	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7824755	7824865	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7824866	7825005	0.95	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7824866	7825005	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7825006	7825096	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7825097	7825195	1	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7825097	7825195	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7825196	7825282	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7825283	7825357	1	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7825283	7825357	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7825358	7825455	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7825456	7825556	1	-	2	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7825456	7825556	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7825557	7825626	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7825627	7825750	0.83	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7825627	7825750	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7825751	7825862	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7825863	7826066	0.9	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7825863	7826066	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7826067	7826151	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7826152	7826319	1	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7826152	7826319	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	intron	7826320	7826401	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	CDS	7826402	7826452	1	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	exon	7826402	7826452	.	-	.	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
Phchi.S4	AUGUSTUS	start_codon	7826450	7826452	.	-	0	transcript_id "Phchi.S4G129900.t1"; gene_id "Phchi.S4G129900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4298.t1 is derived from g1467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9499364	9506881	.	+	.	Phchi.S1G145700
Phchi.S1	AUGUSTUS	transcript	9499364	9506881	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	start_codon	9499364	9499366	.	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9499364	9499526	0.49	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9499364	9499526	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9499527	9499664	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9499665	9500104	0.52	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9499665	9500104	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9500105	9500217	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9500218	9500533	0.95	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9500218	9500533	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9500534	9500674	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9500675	9500919	0.7	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9500675	9500919	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9500920	9501115	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9501116	9501359	0.98	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9501116	9501359	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9501360	9501472	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9501473	9501492	1	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9501473	9501492	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9501493	9501583	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9501584	9501599	1	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9501584	9501599	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9501600	9501706	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9501707	9501740	1	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9501707	9501740	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9501741	9501975	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9501976	9502247	0.99	+	1	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9501976	9502247	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9502248	9502433	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9502434	9502447	1	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9502434	9502447	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9502448	9502530	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9502531	9502633	1	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9502531	9502633	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9502634	9502719	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9502720	9505005	0.97	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9502720	9505005	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	intron	9505006	9505211	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	CDS	9505212	9506881	0.88	+	2	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	exon	9505212	9506881	.	+	.	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
Phchi.S1	AUGUSTUS	stop_codon	9506882	9506884	.	+	0	transcript_id "Phchi.S1G145700.t1"; gene_id "Phchi.S1G145700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3327.t1 is derived from g496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2932693	2934158	.	+	.	Phchi.S1G048600
Phchi.S1	AUGUSTUS	transcript	2932693	2934158	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	start_codon	2932693	2932695	.	+	0	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	CDS	2932693	2933068	1	+	0	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	exon	2932693	2933068	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	intron	2933069	2933288	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	CDS	2933289	2933369	1	+	2	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	exon	2933289	2933369	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	intron	2933370	2933484	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	CDS	2933485	2933618	0.61	+	2	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	exon	2933485	2933618	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	intron	2933619	2933758	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	CDS	2933759	2933931	0.6	+	0	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	exon	2933759	2933931	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	intron	2933932	2934022	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	CDS	2934023	2934158	0.44	+	1	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	exon	2934023	2934158	.	+	.	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
Phchi.S1	AUGUSTUS	stop_codon	2934159	2934161	.	+	0	transcript_id "Phchi.S1G048600.t1"; gene_id "Phchi.S1G048600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1629.t1 is derived from g8548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2094199	2095560	.	+	.	Phchi.S5G023800
Phchi.S5	AUGUSTUS	transcript	2094199	2095560	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	start_codon	2094199	2094201	.	+	0	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	CDS	2094199	2094470	0.26	+	0	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	exon	2094199	2094470	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	intron	2094471	2094589	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	CDS	2094590	2094797	0.17	+	1	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	exon	2094590	2094797	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	intron	2094798	2094892	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	CDS	2094893	2095064	0.73	+	0	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	exon	2094893	2095064	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	intron	2095065	2095195	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	CDS	2095196	2095560	0.21	+	2	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	exon	2095196	2095560	.	+	.	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
Phchi.S5	AUGUSTUS	stop_codon	2095561	2095563	.	+	0	transcript_id "Phchi.S5G023800.t1"; gene_id "Phchi.S5G023800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg688.t1 is derived from g10470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4908614	4909207	.	+	.	Phchi.S6G064700
Phchi.S6	AUGUSTUS	transcript	4908614	4909207	.	+	.	transcript_id "Phchi.S6G064700.t1"; gene_id "Phchi.S6G064700"
Phchi.S6	AUGUSTUS	start_codon	4908614	4908616	.	+	0	transcript_id "Phchi.S6G064700.t1"; gene_id "Phchi.S6G064700"
Phchi.S6	AUGUSTUS	CDS	4908614	4909207	0.74	+	0	transcript_id "Phchi.S6G064700.t1"; gene_id "Phchi.S6G064700"
Phchi.S6	AUGUSTUS	exon	4908614	4909207	.	+	.	transcript_id "Phchi.S6G064700.t1"; gene_id "Phchi.S6G064700"
Phchi.S6	AUGUSTUS	stop_codon	4909208	4909210	.	+	0	transcript_id "Phchi.S6G064700.t1"; gene_id "Phchi.S6G064700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4279.t1 is derived from g1448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9377539	9378318	.	+	.	Phchi.S1G143800
Phchi.S1	AUGUSTUS	transcript	9377539	9378318	.	+	.	transcript_id "Phchi.S1G143800.t1"; gene_id "Phchi.S1G143800"
Phchi.S1	AUGUSTUS	start_codon	9377539	9377541	.	+	0	transcript_id "Phchi.S1G143800.t1"; gene_id "Phchi.S1G143800"
Phchi.S1	AUGUSTUS	CDS	9377539	9378318	0.54	+	0	transcript_id "Phchi.S1G143800.t1"; gene_id "Phchi.S1G143800"
Phchi.S1	AUGUSTUS	exon	9377539	9378318	.	+	.	transcript_id "Phchi.S1G143800.t1"; gene_id "Phchi.S1G143800"
Phchi.S1	AUGUSTUS	stop_codon	9378319	9378321	.	+	0	transcript_id "Phchi.S1G143800.t1"; gene_id "Phchi.S1G143800"
# This transcript jg3726.t2 is derived from g895.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3727.t1 is derived from g896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5419574	5420188	.	+	.	Phchi.S1G088600
Phchi.S1	AUGUSTUS	transcript	5419574	5420188	.	+	.	transcript_id "Phchi.S1G088600.t1"; gene_id "Phchi.S1G088600"
Phchi.S1	AUGUSTUS	start_codon	5419574	5419576	.	+	0	transcript_id "Phchi.S1G088600.t1"; gene_id "Phchi.S1G088600"
Phchi.S1	AUGUSTUS	CDS	5419574	5420188	0.72	+	0	transcript_id "Phchi.S1G088600.t1"; gene_id "Phchi.S1G088600"
Phchi.S1	AUGUSTUS	exon	5419574	5420188	.	+	.	transcript_id "Phchi.S1G088600.t1"; gene_id "Phchi.S1G088600"
Phchi.S1	AUGUSTUS	stop_codon	5420189	5420191	.	+	0	transcript_id "Phchi.S1G088600.t1"; gene_id "Phchi.S1G088600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7426.t1 is derived from g4598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29086081	29086395	.	-	.	Phchi.S1G458500
Phchi.S1	AUGUSTUS	transcript	29086081	29086395	.	-	.	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	stop_codon	29086078	29086080	.	-	0	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	CDS	29086081	29086184	0.96	-	2	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	exon	29086081	29086184	.	-	.	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	intron	29086185	29086268	.	-	.	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	CDS	29086269	29086395	0.7	-	0	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	exon	29086269	29086395	.	-	.	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
Phchi.S1	AUGUSTUS	start_codon	29086393	29086395	.	-	0	transcript_id "Phchi.S1G458500.t1"; gene_id "Phchi.S1G458500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8980.t1 is derived from g6155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38953155	38954952	.	-	.	Phchi.S1G613900
Phchi.S1	AUGUSTUS	transcript	38953155	38954952	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	stop_codon	38953152	38953154	.	-	0	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	CDS	38953155	38953841	0.67	-	0	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	exon	38953155	38953841	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	intron	38953842	38953921	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	CDS	38953922	38954074	0.95	-	0	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	exon	38953922	38954074	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	intron	38954075	38954313	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	CDS	38954314	38954417	0.96	-	2	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	exon	38954314	38954417	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	intron	38954418	38954774	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	CDS	38954775	38954952	0.51	-	0	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	exon	38954775	38954952	.	-	.	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
Phchi.S1	AUGUSTUS	start_codon	38954950	38954952	.	-	0	transcript_id "Phchi.S1G613900.t1"; gene_id "Phchi.S1G613900"
# This transcript jg12466.t2 is derived from g8143.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12467.t1 is derived from g8144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	25810982	25811434	.	+	.	Phchi.S2G054700
Phchi.S2	AUGUSTUS	transcript	25810982	25811434	.	+	.	transcript_id "Phchi.S2G054700.t1"; gene_id "Phchi.S2G054700"
Phchi.S2	AUGUSTUS	start_codon	25810982	25810984	.	+	0	transcript_id "Phchi.S2G054700.t1"; gene_id "Phchi.S2G054700"
Phchi.S2	AUGUSTUS	CDS	25810982	25811434	1	+	0	transcript_id "Phchi.S2G054700.t1"; gene_id "Phchi.S2G054700"
Phchi.S2	AUGUSTUS	exon	25810982	25811434	.	+	.	transcript_id "Phchi.S2G054700.t1"; gene_id "Phchi.S2G054700"
Phchi.S2	AUGUSTUS	stop_codon	25811435	25811437	.	+	0	transcript_id "Phchi.S2G054700.t1"; gene_id "Phchi.S2G054700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7965.t1 is derived from g5140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32142281	32145622	.	-	.	Phchi.S1G512400
Phchi.S1	AUGUSTUS	transcript	32142281	32145622	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	stop_codon	32142278	32142280	.	-	0	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32142281	32142800	0.7	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32142281	32142800	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32142801	32142937	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32142938	32143000	0.65	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32142938	32143000	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32143001	32143174	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32143175	32143276	0.95	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32143175	32143276	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32143277	32143413	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32143414	32143515	0.99	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32143414	32143515	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32143516	32143652	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32143653	32143754	0.7	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32143653	32143754	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32143755	32143891	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32143892	32143993	0.99	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32143892	32143993	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32143994	32144130	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32144131	32144232	0.95	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32144131	32144232	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32144233	32144369	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32144370	32144471	0.98	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32144370	32144471	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32144472	32144607	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32144608	32144709	0.94	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32144608	32144709	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32144710	32144846	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32144847	32144948	0.95	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32144847	32144948	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32144949	32145085	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32145086	32145187	0.96	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32145086	32145187	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32145188	32145324	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32145325	32145426	0.91	-	1	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32145325	32145426	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	intron	32145427	32145563	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	CDS	32145564	32145622	0.89	-	0	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	exon	32145564	32145622	.	-	.	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
Phchi.S1	AUGUSTUS	start_codon	32145620	32145622	.	-	0	transcript_id "Phchi.S1G512400.t1"; gene_id "Phchi.S1G512400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15881.t1 is derived from g14351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22020731	22021732	.	+	.	Phchi.S3G320000
Phchi.S3	AUGUSTUS	transcript	22020731	22021732	.	+	.	transcript_id "Phchi.S3G320000.t1"; gene_id "Phchi.S3G320000"
Phchi.S3	AUGUSTUS	start_codon	22020731	22020733	.	+	0	transcript_id "Phchi.S3G320000.t1"; gene_id "Phchi.S3G320000"
Phchi.S3	AUGUSTUS	CDS	22020731	22021732	0.42	+	0	transcript_id "Phchi.S3G320000.t1"; gene_id "Phchi.S3G320000"
Phchi.S3	AUGUSTUS	exon	22020731	22021732	.	+	.	transcript_id "Phchi.S3G320000.t1"; gene_id "Phchi.S3G320000"
Phchi.S3	AUGUSTUS	stop_codon	22021733	22021735	.	+	0	transcript_id "Phchi.S3G320000.t1"; gene_id "Phchi.S3G320000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6365.t1 is derived from g3537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22584688	22586538	.	+	.	Phchi.S1G352400
Phchi.S1	AUGUSTUS	transcript	22584688	22586538	.	+	.	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	start_codon	22584688	22584690	.	+	0	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	CDS	22584688	22585052	0.51	+	0	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	exon	22584688	22585052	.	+	.	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	intron	22585053	22585253	.	+	.	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	CDS	22585254	22585335	0.88	+	1	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	exon	22585254	22585335	.	+	.	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	intron	22585336	22585497	.	+	.	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	CDS	22585498	22586538	0.37	+	0	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	exon	22585498	22586538	.	+	.	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
Phchi.S1	AUGUSTUS	stop_codon	22586539	22586541	.	+	0	transcript_id "Phchi.S1G352400.t1"; gene_id "Phchi.S1G352400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13494.t1 is derived from g11961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7156365	7157615	.	-	.	Phchi.S3G081300
Phchi.S3	AUGUSTUS	transcript	7156365	7157615	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	stop_codon	7156362	7156364	.	-	0	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	CDS	7156365	7156547	1	-	0	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	exon	7156365	7156547	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	intron	7156548	7156673	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	CDS	7156674	7156780	0.94	-	2	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	exon	7156674	7156780	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	intron	7156781	7156883	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	CDS	7156884	7157100	0.94	-	0	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	exon	7156884	7157100	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	intron	7157101	7157208	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	CDS	7157209	7157416	0.98	-	1	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	exon	7157209	7157416	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	intron	7157417	7157529	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	CDS	7157530	7157615	0.98	-	0	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	exon	7157530	7157615	.	-	.	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
Phchi.S3	AUGUSTUS	start_codon	7157613	7157615	.	-	0	transcript_id "Phchi.S3G081300.t1"; gene_id "Phchi.S3G081300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9667.t1 is derived from g6843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43173659	43175767	.	-	.	Phchi.S1G682600
Phchi.S1	AUGUSTUS	transcript	43173659	43175767	.	-	.	transcript_id "Phchi.S1G682600.t1"; gene_id "Phchi.S1G682600"
Phchi.S1	AUGUSTUS	stop_codon	43173656	43173658	.	-	0	transcript_id "Phchi.S1G682600.t1"; gene_id "Phchi.S1G682600"
Phchi.S1	AUGUSTUS	CDS	43173659	43175767	0.98	-	0	transcript_id "Phchi.S1G682600.t1"; gene_id "Phchi.S1G682600"
Phchi.S1	AUGUSTUS	exon	43173659	43175767	.	-	.	transcript_id "Phchi.S1G682600.t1"; gene_id "Phchi.S1G682600"
Phchi.S1	AUGUSTUS	start_codon	43175765	43175767	.	-	0	transcript_id "Phchi.S1G682600.t1"; gene_id "Phchi.S1G682600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4583.t1 is derived from g1753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11206189	11207787	.	+	.	Phchi.S1G174200
Phchi.S1	AUGUSTUS	transcript	11206189	11207787	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	start_codon	11206189	11206191	.	+	0	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206189	11206242	0.78	+	0	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206189	11206242	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206243	11206317	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206318	11206415	1	+	0	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206318	11206415	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206416	11206505	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206506	11206646	1	+	1	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206506	11206646	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206647	11206718	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206719	11206800	1	+	1	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206719	11206800	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206801	11206890	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206891	11207084	0.99	+	0	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206891	11207084	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11207085	11207196	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11207197	11207308	0.94	+	1	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11207197	11207308	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11207309	11207400	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11207401	11207495	0.99	+	0	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11207401	11207495	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11207496	11207753	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11207754	11207787	0.95	+	1	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11207754	11207787	.	+	.	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	stop_codon	11207788	11207790	.	+	0	transcript_id "Phchi.S1G174200.t1"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	transcript	11206189	11207577	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	start_codon	11206189	11206191	.	+	0	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206189	11206242	0.78	+	0	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206189	11206242	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206243	11206317	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206318	11206415	1	+	0	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206318	11206415	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206416	11206505	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206506	11206646	1	+	1	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206506	11206646	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206647	11206718	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206719	11206800	1	+	1	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206719	11206800	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11206801	11206890	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11206891	11207084	1	+	0	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11206891	11207084	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11207085	11207196	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11207197	11207308	0.96	+	1	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11207197	11207308	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11207309	11207400	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11207401	11207495	0.86	+	0	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11207401	11207495	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	intron	11207496	11207573	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	CDS	11207574	11207577	0.86	+	1	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	exon	11207574	11207577	.	+	.	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
Phchi.S1	AUGUSTUS	stop_codon	11207578	11207580	.	+	0	transcript_id "Phchi.S1G174200.t2"; gene_id "Phchi.S1G174200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14568.t1 is derived from g13036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13507712	13514739	.	+	.	Phchi.S3G188700
Phchi.S3	AUGUSTUS	transcript	13507712	13514739	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	start_codon	13507712	13507714	.	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13507712	13507735	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13507712	13507735	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13507736	13507804	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13507805	13507960	0.95	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13507805	13507960	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13507961	13508053	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508054	13508146	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508054	13508146	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508147	13508235	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508236	13508276	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508236	13508276	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508277	13508390	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508391	13508482	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508391	13508482	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508483	13508566	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508567	13508760	1	+	2	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508567	13508760	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508761	13508880	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508881	13508955	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508881	13508955	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508956	13509045	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509046	13509151	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509046	13509151	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509152	13509281	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509282	13509378	1	+	2	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509282	13509378	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509379	13509489	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509490	13509497	0.67	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509490	13509497	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509498	13509675	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509676	13509925	1	+	2	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509676	13509925	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509926	13510085	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510086	13510131	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510086	13510131	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510132	13510235	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510236	13510429	0.99	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510236	13510429	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510430	13510705	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510706	13510810	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510706	13510810	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510811	13510911	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510912	13510984	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510912	13510984	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510985	13511075	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511076	13511206	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511076	13511206	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511207	13511282	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511283	13511415	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511283	13511415	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511416	13511584	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511585	13511713	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511585	13511713	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511714	13511793	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511794	13511910	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511794	13511910	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511911	13511994	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511995	13512059	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511995	13512059	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512060	13512163	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512164	13512236	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512164	13512236	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512237	13512314	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512315	13512359	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512315	13512359	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512360	13512445	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512446	13512499	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512446	13512499	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512500	13512599	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512600	13512638	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512600	13512638	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512639	13512757	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512758	13512825	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512758	13512825	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512826	13512914	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512915	13513074	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512915	13513074	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513075	13513247	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513248	13513361	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513248	13513361	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513362	13513454	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513455	13513529	0.9	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513455	13513529	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513530	13513636	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513637	13513738	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513637	13513738	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513739	13513833	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513834	13513906	1	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513834	13513906	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513907	13513989	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513990	13514298	1	+	2	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513990	13514298	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13514299	13514387	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13514388	13514459	1	+	2	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13514388	13514459	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13514460	13514553	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13514554	13514605	1	+	2	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13514554	13514605	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13514606	13514702	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13514703	13514739	1	+	1	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13514703	13514739	.	+	.	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	stop_codon	13514740	13514742	.	+	0	transcript_id "Phchi.S3G188700.t1"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	transcript	13507712	13514739	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	start_codon	13507712	13507714	.	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13507712	13507735	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13507712	13507735	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13507736	13507804	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13507805	13507960	0.87	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13507805	13507960	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13507961	13508053	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508054	13508146	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508054	13508146	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508147	13508235	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508236	13508276	0.99	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508236	13508276	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508277	13508390	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508391	13508482	0.98	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508391	13508482	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508483	13508566	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508567	13508760	1	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508567	13508760	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508761	13508880	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13508881	13508955	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13508881	13508955	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13508956	13509045	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509046	13509151	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509046	13509151	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509152	13509281	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509282	13509378	1	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509282	13509378	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509379	13509489	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509490	13509497	0.7	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509490	13509497	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509498	13509675	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13509676	13509925	0.98	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13509676	13509925	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13509926	13510085	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510086	13510131	0.98	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510086	13510131	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510132	13510235	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510236	13510429	0.95	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510236	13510429	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510430	13510705	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510706	13510810	1	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510706	13510810	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510811	13510911	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13510912	13510984	1	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13510912	13510984	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13510985	13511075	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511076	13511206	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511076	13511206	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511207	13511282	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511283	13511415	1	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511283	13511415	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511416	13511584	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511585	13511713	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511585	13511713	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511714	13511793	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511794	13511910	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511794	13511910	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13511911	13511994	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13511995	13512059	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13511995	13512059	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512060	13512213	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512214	13512236	0.6	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512214	13512236	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512237	13512324	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512325	13512359	0.6	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512325	13512359	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512360	13512445	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512446	13512499	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512446	13512499	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512500	13512599	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512600	13512638	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512600	13512638	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512639	13512757	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512758	13512825	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512758	13512825	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13512826	13512914	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13512915	13513074	1	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13512915	13513074	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513075	13513247	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513248	13513361	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513248	13513361	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513362	13513454	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513455	13513529	0.84	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513455	13513529	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513530	13513636	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513637	13513738	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513637	13513738	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513739	13513833	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513834	13513906	1	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513834	13513906	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13513907	13513989	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13513990	13514298	1	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13513990	13514298	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13514299	13514387	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13514388	13514459	1	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13514388	13514459	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13514460	13514553	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13514554	13514605	1	+	2	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13514554	13514605	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	intron	13514606	13514702	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	CDS	13514703	13514739	1	+	1	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	exon	13514703	13514739	.	+	.	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
Phchi.S3	AUGUSTUS	stop_codon	13514740	13514742	.	+	0	transcript_id "Phchi.S3G188700.t2"; gene_id "Phchi.S3G188700"
# This transcript jg7026.t2 is derived from g4198.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7027.t1 is derived from g4199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26480658	26483078	.	-	.	Phchi.S1G418600
Phchi.S1	AUGUSTUS	transcript	26480658	26483078	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	stop_codon	26480655	26480657	.	-	0	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26480658	26481002	0.99	-	0	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26480658	26481002	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26481003	26481115	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26481116	26481245	0.97	-	1	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26481116	26481245	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26481246	26481352	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26481353	26481415	1	-	1	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26481353	26481415	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26481416	26481484	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26481485	26481530	1	-	2	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26481485	26481530	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26481531	26481615	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26481616	26481910	1	-	0	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26481616	26481910	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26481911	26482002	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26482003	26482232	1	-	2	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26482003	26482232	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26482233	26482322	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26482323	26482547	1	-	2	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26482323	26482547	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	intron	26482548	26482627	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	CDS	26482628	26483078	1	-	0	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	exon	26482628	26483078	.	-	.	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
Phchi.S1	AUGUSTUS	start_codon	26483076	26483078	.	-	0	transcript_id "Phchi.S1G418600.t1"; gene_id "Phchi.S1G418600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2184.t1 is derived from g9104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5261436	5262562	.	+	.	Phchi.S5G079300
Phchi.S5	AUGUSTUS	transcript	5261436	5262562	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	start_codon	5261436	5261438	.	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	CDS	5261436	5261572	0.83	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	exon	5261436	5261572	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	intron	5261573	5261654	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	CDS	5261655	5261763	1	+	1	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	exon	5261655	5261763	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	intron	5261764	5261858	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	CDS	5261859	5261930	1	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	exon	5261859	5261930	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	intron	5261931	5262007	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	CDS	5262008	5262088	1	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	exon	5262008	5262088	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	intron	5262089	5262172	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	CDS	5262173	5262247	1	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	exon	5262173	5262247	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	intron	5262248	5262325	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	CDS	5262326	5262562	1	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	exon	5262326	5262562	.	+	.	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
Phchi.S5	AUGUSTUS	stop_codon	5262563	5262565	.	+	0	transcript_id "Phchi.S5G079300.t1"; gene_id "Phchi.S5G079300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13526.t1 is derived from g11993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7377487	7383331	.	+	.	Phchi.S3G084500
Phchi.S3	AUGUSTUS	transcript	7377487	7383331	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	start_codon	7377487	7377489	.	+	0	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7377487	7377517	0.91	+	0	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7377487	7377517	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7377518	7377660	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7377661	7377749	1	+	2	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7377661	7377749	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7377750	7377865	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7377866	7378813	0.92	+	0	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7377866	7378813	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7378814	7379017	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7379018	7379147	1	+	0	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7379018	7379147	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7379148	7379393	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7379394	7379561	1	+	2	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7379394	7379561	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7379562	7379644	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7379645	7379700	0.82	+	2	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7379645	7379700	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7379701	7379828	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7379829	7380591	0.98	+	0	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7379829	7380591	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	intron	7380592	7380677	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	CDS	7380678	7383331	0.66	+	2	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	exon	7380678	7383331	.	+	.	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
Phchi.S3	AUGUSTUS	stop_codon	7383332	7383334	.	+	0	transcript_id "Phchi.S3G084500.t1"; gene_id "Phchi.S3G084500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15361.t1 is derived from g13829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18585211	18585636	.	+	.	Phchi.S3G268000
Phchi.S3	AUGUSTUS	transcript	18585211	18585636	.	+	.	transcript_id "Phchi.S3G268000.t1"; gene_id "Phchi.S3G268000"
Phchi.S3	AUGUSTUS	start_codon	18585211	18585213	.	+	0	transcript_id "Phchi.S3G268000.t1"; gene_id "Phchi.S3G268000"
Phchi.S3	AUGUSTUS	CDS	18585211	18585636	0.97	+	0	transcript_id "Phchi.S3G268000.t1"; gene_id "Phchi.S3G268000"
Phchi.S3	AUGUSTUS	exon	18585211	18585636	.	+	.	transcript_id "Phchi.S3G268000.t1"; gene_id "Phchi.S3G268000"
Phchi.S3	AUGUSTUS	stop_codon	18585637	18585639	.	+	0	transcript_id "Phchi.S3G268000.t1"; gene_id "Phchi.S3G268000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10282.t1 is derived from g7458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46805083	46809830	.	-	.	Phchi.S1G744100
Phchi.S1	AUGUSTUS	transcript	46805083	46809830	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	stop_codon	46805080	46805082	.	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46805083	46805169	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46805083	46805169	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46805170	46805263	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46805264	46805338	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46805264	46805338	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46805339	46805430	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46805431	46805586	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46805431	46805586	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46805587	46805688	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46805689	46805766	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46805689	46805766	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46805767	46805876	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46805877	46805977	0.99	-	2	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46805877	46805977	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46805978	46806065	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46806066	46806213	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46806066	46806213	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46806214	46806303	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46806304	46806448	1	-	1	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46806304	46806448	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46806449	46806548	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46806549	46806655	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46806549	46806655	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46806656	46806775	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46806776	46806904	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46806776	46806904	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46806905	46807034	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46807035	46807145	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46807035	46807145	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46807146	46807249	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46807250	46807379	1	-	1	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46807250	46807379	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46807380	46807470	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46807471	46807590	1	-	1	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46807471	46807590	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46807591	46807876	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46807877	46807998	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46807877	46807998	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46807999	46808095	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46808096	46808179	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46808096	46808179	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46808180	46808291	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46808292	46808408	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46808292	46808408	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46808409	46808503	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46808504	46808584	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46808504	46808584	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46808585	46808669	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46808670	46808729	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46808670	46808729	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46808730	46808837	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46808838	46808880	1	-	1	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46808838	46808880	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46808881	46808978	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46808979	46809077	1	-	1	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46808979	46809077	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46809078	46809166	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46809167	46809312	1	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46809167	46809312	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	intron	46809313	46809485	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	CDS	46809486	46809830	0.95	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	exon	46809486	46809830	.	-	.	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
Phchi.S1	AUGUSTUS	start_codon	46809828	46809830	.	-	0	transcript_id "Phchi.S1G744100.t1"; gene_id "Phchi.S1G744100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10116.t1 is derived from g7292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45805812	45806254	.	-	.	Phchi.S1G727500
Phchi.S1	AUGUSTUS	transcript	45805812	45806254	.	-	.	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	stop_codon	45805809	45805811	.	-	0	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	CDS	45805812	45806146	0.59	-	2	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	exon	45805812	45806146	.	-	.	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	intron	45806147	45806241	.	-	.	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	CDS	45806242	45806254	0.29	-	0	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	exon	45806242	45806254	.	-	.	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
Phchi.S1	AUGUSTUS	start_codon	45806252	45806254	.	-	0	transcript_id "Phchi.S1G727500.t1"; gene_id "Phchi.S1G727500"
# This transcript jg11940.t2 is derived from g7615.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11940.t3 is derived from g7615.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11941.t1 is derived from g7616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	135018	137339	.	+	.	Phchi.S2G002100
Phchi.S2	AUGUSTUS	transcript	135018	137339	.	+	.	transcript_id "Phchi.S2G002100.t1"; gene_id "Phchi.S2G002100"
Phchi.S2	AUGUSTUS	start_codon	135018	135020	.	+	0	transcript_id "Phchi.S2G002100.t1"; gene_id "Phchi.S2G002100"
Phchi.S2	AUGUSTUS	CDS	135018	137339	1	+	0	transcript_id "Phchi.S2G002100.t1"; gene_id "Phchi.S2G002100"
Phchi.S2	AUGUSTUS	exon	135018	137339	.	+	.	transcript_id "Phchi.S2G002100.t1"; gene_id "Phchi.S2G002100"
Phchi.S2	AUGUSTUS	stop_codon	137340	137342	.	+	0	transcript_id "Phchi.S2G002100.t1"; gene_id "Phchi.S2G002100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3863.t1 is derived from g1032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6086641	6087855	.	+	.	Phchi.S1G102200
Phchi.S1	AUGUSTUS	transcript	6086641	6087855	.	+	.	transcript_id "Phchi.S1G102200.t1"; gene_id "Phchi.S1G102200"
Phchi.S1	AUGUSTUS	start_codon	6086641	6086643	.	+	0	transcript_id "Phchi.S1G102200.t1"; gene_id "Phchi.S1G102200"
Phchi.S1	AUGUSTUS	CDS	6086641	6087855	0.97	+	0	transcript_id "Phchi.S1G102200.t1"; gene_id "Phchi.S1G102200"
Phchi.S1	AUGUSTUS	exon	6086641	6087855	.	+	.	transcript_id "Phchi.S1G102200.t1"; gene_id "Phchi.S1G102200"
Phchi.S1	AUGUSTUS	stop_codon	6087856	6087858	.	+	0	transcript_id "Phchi.S1G102200.t1"; gene_id "Phchi.S1G102200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6275.t1 is derived from g3447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22034230	22035244	.	+	.	Phchi.S1G343400
Phchi.S1	AUGUSTUS	transcript	22034230	22035244	.	+	.	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	start_codon	22034230	22034232	.	+	0	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	CDS	22034230	22034524	0.31	+	0	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	exon	22034230	22034524	.	+	.	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	intron	22034525	22034627	.	+	.	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	CDS	22034628	22034844	0.99	+	2	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	exon	22034628	22034844	.	+	.	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	intron	22034845	22034943	.	+	.	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	CDS	22034944	22035244	0.98	+	1	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	exon	22034944	22035244	.	+	.	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
Phchi.S1	AUGUSTUS	stop_codon	22035245	22035247	.	+	0	transcript_id "Phchi.S1G343400.t1"; gene_id "Phchi.S1G343400"
# This transcript jg8457.t2 is derived from g5632.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8458.t1 is derived from g5633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36022907	36024810	.	-	.	Phchi.S1G561700
Phchi.S1	AUGUSTUS	transcript	36022907	36024810	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	stop_codon	36022904	36022906	.	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	CDS	36022907	36023080	1	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	exon	36022907	36023080	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	intron	36023081	36023192	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	CDS	36023193	36023438	1	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	exon	36023193	36023438	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	intron	36023439	36023564	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	CDS	36023565	36023723	1	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	exon	36023565	36023723	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	intron	36023724	36023836	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	CDS	36023837	36023884	1	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	exon	36023837	36023884	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	intron	36023885	36024558	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	CDS	36024559	36024810	0.94	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	exon	36024559	36024810	.	-	.	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
Phchi.S1	AUGUSTUS	start_codon	36024808	36024810	.	-	0	transcript_id "Phchi.S1G561700.t1"; gene_id "Phchi.S1G561700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg5539.t1 is derived from g2709.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17457727	17459735	.	+	.	Phchi.S1G269800
Phchi.S1	AUGUSTUS	transcript	17457727	17459361	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	start_codon	17457727	17457729	.	+	0	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17457727	17457839	0.77	+	0	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17457727	17457839	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17457840	17457985	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17457986	17458076	1	+	1	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17457986	17458076	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458077	17458201	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458202	17458287	0.98	+	0	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458202	17458287	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458288	17458382	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458383	17458499	0.98	+	1	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458383	17458499	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458500	17458591	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458592	17458634	0.46	+	1	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458592	17458634	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458635	17458741	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458742	17458783	0.88	+	0	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458742	17458783	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458784	17459096	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459097	17459160	0.99	+	0	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459097	17459160	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17459161	17459329	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459330	17459361	0.94	+	2	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459330	17459361	.	+	.	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	stop_codon	17459362	17459364	.	+	0	transcript_id "Phchi.S1G269800.t1"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	transcript	17457727	17459361	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	start_codon	17457727	17457729	.	+	0	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17457727	17457839	0.37	+	0	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17457727	17457839	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17457840	17457985	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17457986	17458076	0.51	+	1	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17457986	17458076	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458077	17458214	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458215	17458287	0.5	+	0	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458215	17458287	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458288	17458382	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458383	17458411	0.48	+	2	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458383	17458411	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458412	17458741	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458742	17458783	0.98	+	0	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458742	17458783	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458784	17459096	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459097	17459160	1	+	0	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459097	17459160	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17459161	17459329	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459330	17459361	1	+	2	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459330	17459361	.	+	.	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	stop_codon	17459362	17459364	.	+	0	transcript_id "Phchi.S1G269800.t2"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	transcript	17457727	17459735	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	start_codon	17457727	17457729	.	+	0	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17457727	17457839	0.36	+	0	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17457727	17457839	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17457840	17457985	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17457986	17458076	0.47	+	1	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17457986	17458076	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458077	17458214	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458215	17458287	0.47	+	0	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458215	17458287	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458288	17458382	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458383	17458411	0.46	+	2	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458383	17458411	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458412	17458741	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17458742	17458783	0.86	+	0	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17458742	17458783	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17458784	17459096	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459097	17459160	0.91	+	0	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459097	17459160	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17459161	17459313	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459314	17459427	0.91	+	2	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459314	17459427	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	intron	17459428	17459643	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	CDS	17459644	17459735	0.9	+	2	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	exon	17459644	17459735	.	+	.	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
Phchi.S1	AUGUSTUS	stop_codon	17459736	17459738	.	+	0	transcript_id "Phchi.S1G269800.t3"; gene_id "Phchi.S1G269800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7054.t1 is derived from g4226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26643264	26645317	.	-	.	Phchi.S1G421300
Phchi.S1	AUGUSTUS	transcript	26643264	26645317	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	stop_codon	26643261	26643263	.	-	0	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	CDS	26643264	26643575	1	-	0	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	exon	26643264	26643575	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	intron	26643576	26643698	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	CDS	26643699	26643909	0.97	-	1	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	exon	26643699	26643909	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	intron	26643910	26644013	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	CDS	26644014	26644078	0.98	-	0	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	exon	26644014	26644078	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	intron	26644079	26644171	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	CDS	26644172	26645122	0.87	-	0	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	exon	26644172	26645122	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	intron	26645123	26645212	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	CDS	26645213	26645317	0.99	-	0	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	exon	26645213	26645317	.	-	.	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
Phchi.S1	AUGUSTUS	start_codon	26645315	26645317	.	-	0	transcript_id "Phchi.S1G421300.t1"; gene_id "Phchi.S1G421300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2797.t1 is derived from g9717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8935278	8935797	.	+	.	Phchi.S5G140600
Phchi.S5	AUGUSTUS	transcript	8935278	8935797	.	+	.	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	start_codon	8935278	8935280	.	+	0	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	CDS	8935278	8935324	0.32	+	0	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	exon	8935278	8935324	.	+	.	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	intron	8935325	8935521	.	+	.	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	CDS	8935522	8935595	0.73	+	1	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	exon	8935522	8935595	.	+	.	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	intron	8935596	8935690	.	+	.	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	CDS	8935691	8935797	0.81	+	2	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	exon	8935691	8935797	.	+	.	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
Phchi.S5	AUGUSTUS	stop_codon	8935798	8935800	.	+	0	transcript_id "Phchi.S5G140600.t1"; gene_id "Phchi.S5G140600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1906.t1 is derived from g8826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3802415	3804640	.	-	.	Phchi.S5G051500
Phchi.S5	AUGUSTUS	transcript	3802415	3804640	.	-	.	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	stop_codon	3802412	3802414	.	-	0	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	CDS	3802415	3802894	1	-	0	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	exon	3802415	3802894	.	-	.	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	intron	3802895	3802996	.	-	.	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	CDS	3802997	3803158	0.93	-	0	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	exon	3802997	3803158	.	-	.	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	intron	3803159	3803380	.	-	.	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	CDS	3803381	3804640	1	-	0	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	exon	3803381	3804640	.	-	.	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
Phchi.S5	AUGUSTUS	start_codon	3804638	3804640	.	-	0	transcript_id "Phchi.S5G051500.t1"; gene_id "Phchi.S5G051500"
# This transcript jg14762.t2 is derived from g13230.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14763.t1 is derived from g13231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14585311	14586243	.	+	.	Phchi.S3G208200
Phchi.S3	AUGUSTUS	transcript	14585311	14586243	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	start_codon	14585311	14585313	.	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	CDS	14585311	14585390	0.64	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	exon	14585311	14585390	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	intron	14585391	14585470	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	CDS	14585471	14585636	1	+	1	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	exon	14585471	14585636	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	intron	14585637	14585721	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	CDS	14585722	14585772	0.99	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	exon	14585722	14585772	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	intron	14585773	14585880	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	CDS	14585881	14585946	1	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	exon	14585881	14585946	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	intron	14585947	14586025	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	CDS	14586026	14586094	1	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	exon	14586026	14586094	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	intron	14586095	14586177	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	CDS	14586178	14586243	0.96	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	exon	14586178	14586243	.	+	.	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
Phchi.S3	AUGUSTUS	stop_codon	14586244	14586246	.	+	0	transcript_id "Phchi.S3G208200.t1"; gene_id "Phchi.S3G208200"
# This transcript jg3853.t2 is derived from g1022.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3854.t1 is derived from g1023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6045178	6045696	.	+	.	Phchi.S1G101300
Phchi.S1	AUGUSTUS	transcript	6045178	6045696	.	+	.	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	start_codon	6045178	6045180	.	+	0	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	CDS	6045178	6045250	0.37	+	0	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	exon	6045178	6045250	.	+	.	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	intron	6045251	6045410	.	+	.	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	CDS	6045411	6045491	0.21	+	2	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	exon	6045411	6045491	.	+	.	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	intron	6045492	6045643	.	+	.	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	CDS	6045644	6045696	0.59	+	2	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	exon	6045644	6045696	.	+	.	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
Phchi.S1	AUGUSTUS	stop_codon	6045697	6045699	.	+	0	transcript_id "Phchi.S1G101300.t1"; gene_id "Phchi.S1G101300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8240.t1 is derived from g5415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34633946	34637368	.	-	.	Phchi.S1G539900
Phchi.S1	AUGUSTUS	transcript	34633946	34637368	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	stop_codon	34633943	34633945	.	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34633946	34634017	0.92	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34633946	34634017	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34634018	34634106	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34634107	34634215	1	-	1	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34634107	34634215	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34634216	34634339	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34634340	34634464	1	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34634340	34634464	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34634465	34634542	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34634543	34634587	1	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34634543	34634587	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34634588	34634662	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34634663	34634766	0.6	-	2	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34634663	34634766	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34634767	34634954	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34634955	34635029	0.78	-	2	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34634955	34635029	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34635030	34635107	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34635108	34635153	1	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34635108	34635153	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34635154	34635335	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34635336	34635444	0.86	-	1	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34635336	34635444	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34635445	34635661	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34635662	34635677	0.87	-	2	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34635662	34635677	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34635678	34636508	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34636509	34636561	0.7	-	1	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34636509	34636561	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34636562	34636651	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34636652	34636716	0.66	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34636652	34636716	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34636717	34637007	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34637008	34637046	0.68	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34637008	34637046	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	intron	34637047	34637323	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	CDS	34637324	34637368	0.68	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	exon	34637324	34637368	.	-	.	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
Phchi.S1	AUGUSTUS	start_codon	34637366	34637368	.	-	0	transcript_id "Phchi.S1G539900.t1"; gene_id "Phchi.S1G539900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15558.t1 is derived from g14027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19916845	19917240	.	-	.	Phchi.S3G287700
Phchi.S3	AUGUSTUS	transcript	19916845	19917240	.	-	.	transcript_id "Phchi.S3G287700.t1"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	stop_codon	19916842	19916844	.	-	0	transcript_id "Phchi.S3G287700.t1"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	CDS	19916845	19917240	0.47	-	0	transcript_id "Phchi.S3G287700.t1"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	exon	19916845	19917240	.	-	.	transcript_id "Phchi.S3G287700.t1"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	start_codon	19917238	19917240	.	-	0	transcript_id "Phchi.S3G287700.t1"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	transcript	19916845	19917177	.	-	.	transcript_id "Phchi.S3G287700.t2"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	stop_codon	19916842	19916844	.	-	0	transcript_id "Phchi.S3G287700.t2"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	CDS	19916845	19917177	0.46	-	0	transcript_id "Phchi.S3G287700.t2"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	exon	19916845	19917177	.	-	.	transcript_id "Phchi.S3G287700.t2"; gene_id "Phchi.S3G287700"
Phchi.S3	AUGUSTUS	start_codon	19917175	19917177	.	-	0	transcript_id "Phchi.S3G287700.t2"; gene_id "Phchi.S3G287700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14551.t1 is derived from g13019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13438530	13439639	.	-	.	Phchi.S3G187000
Phchi.S3	AUGUSTUS	transcript	13438530	13439639	.	-	.	transcript_id "Phchi.S3G187000.t1"; gene_id "Phchi.S3G187000"
Phchi.S3	AUGUSTUS	stop_codon	13438527	13438529	.	-	0	transcript_id "Phchi.S3G187000.t1"; gene_id "Phchi.S3G187000"
Phchi.S3	AUGUSTUS	CDS	13438530	13439639	0.67	-	0	transcript_id "Phchi.S3G187000.t1"; gene_id "Phchi.S3G187000"
Phchi.S3	AUGUSTUS	exon	13438530	13439639	.	-	.	transcript_id "Phchi.S3G187000.t1"; gene_id "Phchi.S3G187000"
Phchi.S3	AUGUSTUS	start_codon	13439637	13439639	.	-	0	transcript_id "Phchi.S3G187000.t1"; gene_id "Phchi.S3G187000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7046.t1 is derived from g4218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26581992	26582903	.	+	.	Phchi.S1G420500
Phchi.S1	AUGUSTUS	transcript	26581992	26582903	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	start_codon	26581992	26581994	.	+	0	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	CDS	26581992	26582069	0.79	+	0	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	exon	26581992	26582069	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	intron	26582070	26582203	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	CDS	26582204	26582299	0.79	+	0	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	exon	26582204	26582299	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	intron	26582300	26582388	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	CDS	26582389	26582469	0.76	+	0	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	exon	26582389	26582469	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	intron	26582470	26582636	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	CDS	26582637	26582903	0.47	+	0	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	exon	26582637	26582903	.	+	.	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
Phchi.S1	AUGUSTUS	stop_codon	26582904	26582906	.	+	0	transcript_id "Phchi.S1G420500.t1"; gene_id "Phchi.S1G420500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1045.t1 is derived from g10828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7275448	7276523	.	+	.	Phchi.S6G100400
Phchi.S6	AUGUSTUS	transcript	7275448	7276523	.	+	.	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	start_codon	7275448	7275450	.	+	0	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	CDS	7275448	7275878	0.63	+	0	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	exon	7275448	7275878	.	+	.	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	intron	7275879	7275996	.	+	.	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	CDS	7275997	7276068	0.97	+	1	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	exon	7275997	7276068	.	+	.	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	intron	7276069	7276165	.	+	.	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	CDS	7276166	7276523	0.97	+	1	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	exon	7276166	7276523	.	+	.	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
Phchi.S6	AUGUSTUS	stop_codon	7276524	7276526	.	+	0	transcript_id "Phchi.S6G100400.t1"; gene_id "Phchi.S6G100400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3286.t1 is derived from g455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2692862	2694222	.	+	.	Phchi.S1G044500
Phchi.S1	AUGUSTUS	transcript	2692862	2694222	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	start_codon	2692862	2692864	.	+	0	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	CDS	2692862	2693166	0.77	+	0	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	exon	2692862	2693166	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	intron	2693167	2693548	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	CDS	2693549	2693621	1	+	1	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	exon	2693549	2693621	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	intron	2693622	2693742	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	CDS	2693743	2693790	1	+	0	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	exon	2693743	2693790	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	intron	2693791	2693888	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	CDS	2693889	2693983	0.67	+	0	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	exon	2693889	2693983	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	intron	2693984	2694095	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	CDS	2694096	2694222	0.67	+	1	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	exon	2694096	2694222	.	+	.	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
Phchi.S1	AUGUSTUS	stop_codon	2694223	2694225	.	+	0	transcript_id "Phchi.S1G044500.t1"; gene_id "Phchi.S1G044500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6151.t1 is derived from g3322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21205268	21206299	.	+	.	Phchi.S1G331000
Phchi.S1	AUGUSTUS	transcript	21205268	21206299	.	+	.	transcript_id "Phchi.S1G331000.t1"; gene_id "Phchi.S1G331000"
Phchi.S1	AUGUSTUS	start_codon	21205268	21205270	.	+	0	transcript_id "Phchi.S1G331000.t1"; gene_id "Phchi.S1G331000"
Phchi.S1	AUGUSTUS	CDS	21205268	21206299	0.83	+	0	transcript_id "Phchi.S1G331000.t1"; gene_id "Phchi.S1G331000"
Phchi.S1	AUGUSTUS	exon	21205268	21206299	.	+	.	transcript_id "Phchi.S1G331000.t1"; gene_id "Phchi.S1G331000"
Phchi.S1	AUGUSTUS	stop_codon	21206300	21206302	.	+	0	transcript_id "Phchi.S1G331000.t1"; gene_id "Phchi.S1G331000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2142.t1 is derived from g9062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5037581	5039232	.	+	.	Phchi.S5G075100
Phchi.S5	AUGUSTUS	transcript	5037581	5039232	.	+	.	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	start_codon	5037581	5037583	.	+	0	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	CDS	5037581	5037941	0.57	+	0	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	exon	5037581	5037941	.	+	.	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	intron	5037942	5038342	.	+	.	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	CDS	5038343	5038566	1	+	2	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	exon	5038343	5038566	.	+	.	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	intron	5038567	5038872	.	+	.	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	CDS	5038873	5039232	1	+	0	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	exon	5038873	5039232	.	+	.	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
Phchi.S5	AUGUSTUS	stop_codon	5039233	5039235	.	+	0	transcript_id "Phchi.S5G075100.t1"; gene_id "Phchi.S5G075100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2111.t1 is derived from g9031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4917846	4918283	.	+	.	Phchi.S5G072000
Phchi.S5	AUGUSTUS	transcript	4917846	4918283	.	+	.	transcript_id "Phchi.S5G072000.t1"; gene_id "Phchi.S5G072000"
Phchi.S5	AUGUSTUS	start_codon	4917846	4917848	.	+	0	transcript_id "Phchi.S5G072000.t1"; gene_id "Phchi.S5G072000"
Phchi.S5	AUGUSTUS	CDS	4917846	4918283	1	+	0	transcript_id "Phchi.S5G072000.t1"; gene_id "Phchi.S5G072000"
Phchi.S5	AUGUSTUS	exon	4917846	4918283	.	+	.	transcript_id "Phchi.S5G072000.t1"; gene_id "Phchi.S5G072000"
Phchi.S5	AUGUSTUS	stop_codon	4918284	4918286	.	+	0	transcript_id "Phchi.S5G072000.t1"; gene_id "Phchi.S5G072000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12014.t1 is derived from g7689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	525132	527627	.	-	.	Phchi.S2G009400
Phchi.S2	AUGUSTUS	transcript	525132	527627	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	stop_codon	525129	525131	.	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	525132	525305	1	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	525132	525305	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	525306	525391	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	525392	525519	1	-	2	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	525392	525519	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	525520	525598	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	525599	525682	1	-	2	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	525599	525682	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	525683	525794	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	525795	525960	0.98	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	525795	525960	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	525961	526084	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	526085	526150	1	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	526085	526150	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	526151	526267	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	526268	526355	1	-	1	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	526268	526355	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	526356	526505	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	526506	526570	1	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	526506	526570	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	526571	526769	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	526770	526835	1	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	526770	526835	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	526836	526929	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	526930	527003	1	-	2	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	526930	527003	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	527004	527090	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	527091	527124	1	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	527091	527124	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	527125	527208	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	527209	527310	1	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	527209	527310	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	intron	527311	527396	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	CDS	527397	527627	0.47	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	exon	527397	527627	.	-	.	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
Phchi.S2	AUGUSTUS	start_codon	527625	527627	.	-	0	transcript_id "Phchi.S2G009400.t1"; gene_id "Phchi.S2G009400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8280.t1 is derived from g5455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35076919	35079634	.	+	.	Phchi.S1G543900
Phchi.S1	AUGUSTUS	transcript	35076919	35079634	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	start_codon	35076919	35076921	.	+	0	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35076919	35076983	1	+	0	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35076919	35076983	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35076984	35077188	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35077189	35077329	1	+	1	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35077189	35077329	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35077330	35077457	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35077458	35077760	0.85	+	1	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35077458	35077760	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35077761	35077871	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35077872	35078170	1	+	1	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35077872	35078170	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35078171	35078288	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35078289	35079178	1	+	2	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35078289	35079178	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35079179	35079272	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35079273	35079329	1	+	0	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35079273	35079329	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35079330	35079421	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35079422	35079469	1	+	0	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35079422	35079469	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	intron	35079470	35079565	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	CDS	35079566	35079634	0.98	+	0	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	exon	35079566	35079634	.	+	.	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
Phchi.S1	AUGUSTUS	stop_codon	35079635	35079637	.	+	0	transcript_id "Phchi.S1G543900.t1"; gene_id "Phchi.S1G543900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1475.t1 is derived from g8394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1109133	1112367	.	+	.	Phchi.S5G008400
Phchi.S5	AUGUSTUS	transcript	1109133	1112367	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	start_codon	1109133	1109135	.	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1109133	1109171	0.78	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1109133	1109171	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1109172	1109330	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1109331	1109719	0.99	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1109331	1109719	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1109720	1109874	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1109875	1110016	1	+	1	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1109875	1110016	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110017	1110115	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1110116	1110122	0.94	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1110116	1110122	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110123	1110193	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1110194	1110213	0.99	+	2	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1110194	1110213	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110214	1110285	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1110286	1110342	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1110286	1110342	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110343	1110481	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1110482	1110553	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1110482	1110553	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110554	1110662	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1110663	1110752	0.95	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1110663	1110752	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110753	1110853	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1110854	1110913	0.99	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1110854	1110913	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1110914	1111005	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1111006	1111194	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1111006	1111194	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1111195	1111296	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1111297	1111389	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1111297	1111389	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1111390	1111469	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1111470	1111551	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1111470	1111551	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1111552	1111661	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1111662	1111768	1	+	2	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1111662	1111768	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1111769	1111848	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1111849	1111924	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1111849	1111924	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1111925	1112009	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1112010	1112056	1	+	2	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1112010	1112056	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1112057	1112161	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1112162	1112224	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1112162	1112224	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	intron	1112225	1112307	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	CDS	1112308	1112367	1	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	exon	1112308	1112367	.	+	.	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
Phchi.S5	AUGUSTUS	stop_codon	1112368	1112370	.	+	0	transcript_id "Phchi.S5G008400.t1"; gene_id "Phchi.S5G008400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15793.t1 is derived from g14263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21367427	21368373	.	-	.	Phchi.S3G311200
Phchi.S3	AUGUSTUS	transcript	21367427	21368373	.	-	.	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	stop_codon	21367424	21367426	.	-	0	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	CDS	21367427	21367594	1	-	0	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	exon	21367427	21367594	.	-	.	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	intron	21367595	21367763	.	-	.	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	CDS	21367764	21367824	1	-	1	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	exon	21367764	21367824	.	-	.	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	intron	21367825	21368320	.	-	.	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	CDS	21368321	21368373	0.97	-	0	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	exon	21368321	21368373	.	-	.	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
Phchi.S3	AUGUSTUS	start_codon	21368371	21368373	.	-	0	transcript_id "Phchi.S3G311200.t1"; gene_id "Phchi.S3G311200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14156.t1 is derived from g12623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11183668	11188385	.	+	.	Phchi.S3G147500
Phchi.S3	AUGUSTUS	transcript	11183668	11188385	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	start_codon	11183668	11183670	.	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11183668	11183771	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11183668	11183771	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11183772	11183888	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11183889	11184033	0.82	+	1	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11183889	11184033	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184034	11184242	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184243	11184317	0.82	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184243	11184317	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184318	11184520	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184521	11184610	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184521	11184610	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184611	11184706	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184707	11184786	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184707	11184786	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184787	11184881	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184882	11184950	1	+	1	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184882	11184950	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184951	11185049	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185050	11185135	1	+	1	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185050	11185135	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185136	11185272	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185273	11185337	1	+	2	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185273	11185337	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185338	11185423	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185424	11185519	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185424	11185519	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185520	11185604	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185605	11185710	0.7	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185605	11185710	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185711	11185817	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185818	11185864	1	+	2	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185818	11185864	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185865	11186030	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186031	11186114	0.74	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186031	11186114	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186115	11186219	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186220	11186273	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186220	11186273	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186274	11186406	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186407	11186507	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186407	11186507	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186508	11186645	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186646	11186736	1	+	1	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186646	11186736	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186737	11186826	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186827	11186991	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186827	11186991	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186992	11187114	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187115	11187204	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187115	11187204	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187205	11187294	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187295	11187366	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187295	11187366	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187367	11187459	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187460	11187558	0.93	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187460	11187558	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187559	11187668	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187669	11187755	0.97	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187669	11187755	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187756	11187871	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187872	11187925	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187872	11187925	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187926	11188038	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11188039	11188118	1	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11188039	11188118	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11188119	11188237	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11188238	11188385	1	+	1	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11188238	11188385	.	+	.	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	stop_codon	11188386	11188388	.	+	0	transcript_id "Phchi.S3G147500.t1"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	transcript	11183668	11188385	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	start_codon	11183668	11183670	.	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11183668	11183771	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11183668	11183771	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11183772	11183998	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11183999	11184033	1	+	1	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11183999	11184033	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184034	11184237	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184238	11184317	1	+	2	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184238	11184317	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184318	11184520	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184521	11184610	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184521	11184610	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184611	11184706	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184707	11184786	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184707	11184786	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184787	11184881	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184882	11184915	0.78	+	1	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184882	11184915	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184916	11185049	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185050	11185135	0.91	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185050	11185135	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185136	11185267	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185268	11185337	0.93	+	1	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185268	11185337	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185338	11185423	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185424	11185519	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185424	11185519	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185520	11185604	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185605	11185710	0.64	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185605	11185710	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185711	11185817	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185818	11185864	1	+	2	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185818	11185864	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185865	11186030	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186031	11186114	0.75	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186031	11186114	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186115	11186219	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186220	11186273	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186220	11186273	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186274	11186406	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186407	11186507	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186407	11186507	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186508	11186645	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186646	11186736	1	+	1	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186646	11186736	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186737	11186826	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186827	11186991	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186827	11186991	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186992	11187114	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187115	11187204	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187115	11187204	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187205	11187294	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187295	11187366	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187295	11187366	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187367	11187459	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187460	11187558	0.91	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187460	11187558	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187559	11187668	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187669	11187755	0.98	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187669	11187755	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187756	11187871	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187872	11187925	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187872	11187925	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187926	11188038	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11188039	11188118	1	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11188039	11188118	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11188119	11188237	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11188238	11188385	0.98	+	1	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11188238	11188385	.	+	.	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	stop_codon	11188386	11188388	.	+	0	transcript_id "Phchi.S3G147500.t2"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	transcript	11183668	11188385	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	start_codon	11183668	11183670	.	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11183668	11183771	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11183668	11183771	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11183772	11183888	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11183889	11184033	1	+	1	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11183889	11184033	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184034	11184242	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184243	11184317	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184243	11184317	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184318	11184520	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184521	11184610	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184521	11184610	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184611	11184706	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184707	11184786	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184707	11184786	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184787	11184881	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11184882	11184915	0.67	+	1	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11184882	11184915	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11184916	11185049	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185050	11185135	0.88	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185050	11185135	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185136	11185267	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185268	11185337	0.9	+	1	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185268	11185337	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185338	11185423	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185424	11185519	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185424	11185519	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185520	11185604	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185605	11185710	0.71	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185605	11185710	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185711	11185817	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11185818	11185864	1	+	2	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11185818	11185864	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11185865	11186030	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186031	11186114	0.75	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186031	11186114	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186115	11186219	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186220	11186273	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186220	11186273	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186274	11186406	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186407	11186507	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186407	11186507	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186508	11186645	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186646	11186736	1	+	1	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186646	11186736	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186737	11186826	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11186827	11186991	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11186827	11186991	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11186992	11187114	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187115	11187204	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187115	11187204	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187205	11187294	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187295	11187366	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187295	11187366	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187367	11187459	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187460	11187558	0.96	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187460	11187558	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187559	11187668	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187669	11187755	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187669	11187755	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187756	11187871	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11187872	11187925	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11187872	11187925	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11187926	11188038	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11188039	11188118	1	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11188039	11188118	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	intron	11188119	11188237	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	CDS	11188238	11188385	0.99	+	1	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	exon	11188238	11188385	.	+	.	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
Phchi.S3	AUGUSTUS	stop_codon	11188386	11188388	.	+	0	transcript_id "Phchi.S3G147500.t3"; gene_id "Phchi.S3G147500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12611.t1 is derived from g8288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37573166	37573851	.	+	.	Phchi.S2G069100
Phchi.S2	AUGUSTUS	transcript	37573166	37573851	.	+	.	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	start_codon	37573166	37573168	.	+	0	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	CDS	37573166	37573277	0.61	+	0	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	exon	37573166	37573277	.	+	.	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	intron	37573278	37573446	.	+	.	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	CDS	37573447	37573468	0.69	+	2	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	exon	37573447	37573468	.	+	.	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	intron	37573469	37573646	.	+	.	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	CDS	37573647	37573851	0.68	+	1	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	exon	37573647	37573851	.	+	.	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
Phchi.S2	AUGUSTUS	stop_codon	37573852	37573854	.	+	0	transcript_id "Phchi.S2G069100.t1"; gene_id "Phchi.S2G069100"
# This transcript jg10826.t2 is derived from g14876.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10827.t1 is derived from g14877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2313441	2315670	.	+	.	Phchi.S4G040900
Phchi.S4	AUGUSTUS	transcript	2313441	2315670	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	start_codon	2313441	2313443	.	+	0	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	CDS	2313441	2313742	1	+	0	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	exon	2313441	2313742	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	intron	2313743	2313843	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	CDS	2313844	2313939	1	+	1	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	exon	2313844	2313939	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	intron	2313940	2314025	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	CDS	2314026	2314431	0.98	+	1	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	exon	2314026	2314431	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	intron	2314432	2314562	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	CDS	2314563	2314995	1	+	0	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	exon	2314563	2314995	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	intron	2314996	2315083	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	CDS	2315084	2315670	0.93	+	2	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	exon	2315084	2315670	.	+	.	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
Phchi.S4	AUGUSTUS	stop_codon	2315671	2315673	.	+	0	transcript_id "Phchi.S4G040900.t1"; gene_id "Phchi.S4G040900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10161.t1 is derived from g7337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46045219	46049460	.	+	.	Phchi.S1G732000
Phchi.S1	AUGUSTUS	transcript	46045219	46049460	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	start_codon	46045219	46045221	.	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46045219	46045241	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46045219	46045241	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46045242	46045328	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46045329	46045395	0.82	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46045329	46045395	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46045396	46045474	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46045475	46045619	0.82	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46045475	46045619	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46045620	46045836	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46045837	46046153	0.97	+	2	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46045837	46046153	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46046154	46046267	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46046268	46046345	0.97	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46046268	46046345	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46046346	46046469	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46046470	46046690	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46046470	46046690	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46046691	46046792	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46046793	46046828	1	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46046793	46046828	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46046829	46047028	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46047029	46047121	1	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46047029	46047121	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46047122	46047211	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46047212	46047295	1	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46047212	46047295	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46047296	46047464	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46047465	46047581	1	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46047465	46047581	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46047582	46047724	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46047725	46047830	1	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46047725	46047830	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46047831	46047938	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46047939	46048010	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46047939	46048010	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46048011	46048106	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46048107	46048160	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46048107	46048160	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46048161	46048242	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46048243	46048300	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46048243	46048300	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46048301	46048480	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46048481	46048557	1	+	2	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46048481	46048557	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46048558	46048703	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46048704	46048774	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46048704	46048774	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46048775	46048859	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46048860	46048920	1	+	1	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46048860	46048920	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46048921	46049041	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46049042	46049101	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46049042	46049101	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46049102	46049179	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46049180	46049242	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46049180	46049242	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	intron	46049243	46049340	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	CDS	46049341	46049460	1	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	exon	46049341	46049460	.	+	.	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
Phchi.S1	AUGUSTUS	stop_codon	46049461	46049463	.	+	0	transcript_id "Phchi.S1G732000.t1"; gene_id "Phchi.S1G732000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10218.t1 is derived from g7394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46427391	46429576	.	+	.	Phchi.S1G737700
Phchi.S1	AUGUSTUS	transcript	46427391	46429576	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	start_codon	46427391	46427393	.	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46427391	46427441	0.86	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46427391	46427441	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46427442	46427557	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46427558	46427696	0.87	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46427558	46427696	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46427697	46427790	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46427791	46427950	1	+	2	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46427791	46427950	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46427951	46428035	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46428036	46428198	1	+	1	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46428036	46428198	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46428199	46428295	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46428296	46428556	1	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46428296	46428556	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46428557	46428685	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46428686	46428856	1	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46428686	46428856	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46428857	46428986	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46428987	46429317	1	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46428987	46429317	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	intron	46429318	46429403	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	CDS	46429404	46429576	0.73	+	2	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	exon	46429404	46429576	.	+	.	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
Phchi.S1	AUGUSTUS	stop_codon	46429577	46429579	.	+	0	transcript_id "Phchi.S1G737700.t1"; gene_id "Phchi.S1G737700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13044.t1 is derived from g11509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3855977	3856880	.	+	.	Phchi.S3G036300
Phchi.S3	AUGUSTUS	transcript	3855977	3856880	.	+	.	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	start_codon	3855977	3855979	.	+	0	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	CDS	3855977	3856626	0.62	+	0	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	exon	3855977	3856626	.	+	.	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	intron	3856627	3856822	.	+	.	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	CDS	3856823	3856880	0.8	+	1	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	exon	3856823	3856880	.	+	.	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
Phchi.S3	AUGUSTUS	stop_codon	3856881	3856883	.	+	0	transcript_id "Phchi.S3G036300.t1"; gene_id "Phchi.S3G036300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5956.t1 is derived from g3127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20067609	20068993	.	-	.	Phchi.S1G311500
Phchi.S1	AUGUSTUS	transcript	20067609	20068993	.	-	.	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	stop_codon	20067606	20067608	.	-	0	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	CDS	20067609	20068481	0.88	-	0	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	exon	20067609	20068481	.	-	.	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	intron	20068482	20068603	.	-	.	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	CDS	20068604	20068993	0.79	-	0	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	exon	20068604	20068993	.	-	.	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
Phchi.S1	AUGUSTUS	start_codon	20068991	20068993	.	-	0	transcript_id "Phchi.S1G311500.t1"; gene_id "Phchi.S1G311500"
# This transcript jg9842.t2 is derived from g7018.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9843.t1 is derived from g7019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44035951	44038193	.	+	.	Phchi.S1G700200
Phchi.S1	AUGUSTUS	transcript	44035951	44038193	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	start_codon	44035951	44035953	.	+	0	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	CDS	44035951	44036145	0.95	+	0	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	exon	44035951	44036145	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	intron	44036146	44036236	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	CDS	44036237	44036442	0.64	+	0	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	exon	44036237	44036442	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	intron	44036443	44036544	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	CDS	44036545	44036644	0.92	+	1	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	exon	44036545	44036644	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	intron	44036645	44036795	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	CDS	44036796	44038193	0.88	+	0	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	exon	44036796	44038193	.	+	.	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
Phchi.S1	AUGUSTUS	stop_codon	44038194	44038196	.	+	0	transcript_id "Phchi.S1G700200.t1"; gene_id "Phchi.S1G700200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3701.t1 is derived from g870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5234915	5236131	.	+	.	Phchi.S1G086000
Phchi.S1	AUGUSTUS	transcript	5234915	5236131	.	+	.	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	start_codon	5234915	5234917	.	+	0	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	CDS	5234915	5235175	0.75	+	0	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	exon	5234915	5235175	.	+	.	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	intron	5235176	5235336	.	+	.	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	CDS	5235337	5236131	0.62	+	0	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	exon	5235337	5236131	.	+	.	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
Phchi.S1	AUGUSTUS	stop_codon	5236132	5236134	.	+	0	transcript_id "Phchi.S1G086000.t1"; gene_id "Phchi.S1G086000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15447.t1 is derived from g13915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19212669	19217215	.	+	.	Phchi.S3G276600
Phchi.S3	AUGUSTUS	transcript	19212669	19217215	.	+	.	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	start_codon	19212669	19212671	.	+	0	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	CDS	19212669	19214600	0.71	+	0	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	exon	19212669	19214600	.	+	.	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	intron	19214601	19214716	.	+	.	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	CDS	19214717	19217215	0.98	+	0	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	exon	19214717	19217215	.	+	.	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
Phchi.S3	AUGUSTUS	stop_codon	19217216	19217218	.	+	0	transcript_id "Phchi.S3G276600.t1"; gene_id "Phchi.S3G276600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1469.t1 is derived from g8388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1084495	1089993	.	-	.	Phchi.S5G007800
Phchi.S5	AUGUSTUS	transcript	1084495	1089993	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	stop_codon	1084492	1084494	.	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1084495	1084551	1	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1084495	1084551	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1084552	1084623	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1084624	1084715	1	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1084624	1084715	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1084716	1084863	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1084864	1084998	0.62	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1084864	1084998	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1084999	1085147	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085148	1085206	0.98	-	1	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085148	1085206	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085207	1085296	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085297	1085446	0.72	-	1	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085297	1085446	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085447	1085568	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085569	1085632	1	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085569	1085632	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085633	1085726	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085727	1085828	1	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085727	1085828	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085829	1085916	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085917	1085998	0.73	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085917	1085998	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085999	1086087	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1086088	1087860	0.41	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1086088	1087860	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1087861	1087941	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1087942	1088000	0.39	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1087942	1088000	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088001	1088118	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088119	1088173	0.73	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088119	1088173	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088174	1088336	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088337	1088401	1	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088337	1088401	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088402	1088547	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088548	1088605	1	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088548	1088605	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088606	1088695	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088696	1088795	1	-	1	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088696	1088795	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088796	1088923	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088924	1089157	1	-	1	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088924	1089157	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1089158	1089256	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089257	1089419	1	-	2	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089257	1089419	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1089420	1089516	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089517	1089745	1	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089517	1089745	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1089746	1089879	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089880	1089993	1	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089880	1089993	.	-	.	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	start_codon	1089991	1089993	.	-	0	transcript_id "Phchi.S5G007800.t1"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	transcript	1084495	1089993	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	stop_codon	1084492	1084494	.	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1084495	1084551	1	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1084495	1084551	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1084552	1084623	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1084624	1084715	1	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1084624	1084715	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1084716	1084863	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1084864	1084998	0.61	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1084864	1084998	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1084999	1085147	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085148	1085206	0.99	-	1	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085148	1085206	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085207	1085296	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085297	1085446	0.75	-	1	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085297	1085446	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085447	1085568	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085569	1085632	1	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085569	1085632	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085633	1085726	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085727	1085828	1	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085727	1085828	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085829	1085916	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1085917	1085998	0.79	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1085917	1085998	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1085999	1086087	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1086088	1087860	0.55	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1086088	1087860	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1087861	1087941	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1087942	1088000	0.46	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1087942	1088000	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088001	1088118	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088119	1088173	0.81	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088119	1088173	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088174	1088336	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088337	1088401	1	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088337	1088401	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088402	1088547	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088548	1088605	1	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088548	1088605	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088606	1088695	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088696	1088775	0.81	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088696	1088775	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088776	1088923	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1088924	1088952	0.81	-	1	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1088924	1088952	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1088953	1089064	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089065	1089157	0.75	-	1	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089065	1089157	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1089158	1089256	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089257	1089419	1	-	2	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089257	1089419	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1089420	1089516	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089517	1089745	1	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089517	1089745	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	intron	1089746	1089879	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	CDS	1089880	1089993	1	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	exon	1089880	1089993	.	-	.	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
Phchi.S5	AUGUSTUS	start_codon	1089991	1089993	.	-	0	transcript_id "Phchi.S5G007800.t2"; gene_id "Phchi.S5G007800"
# This transcript jg444.t2 is derived from g10226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg445.t1 is derived from g10227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3113807	3114190	.	-	.	Phchi.S6G040400
Phchi.S6	AUGUSTUS	transcript	3113807	3114190	.	-	.	transcript_id "Phchi.S6G040400.t1"; gene_id "Phchi.S6G040400"
Phchi.S6	AUGUSTUS	stop_codon	3113804	3113806	.	-	0	transcript_id "Phchi.S6G040400.t1"; gene_id "Phchi.S6G040400"
Phchi.S6	AUGUSTUS	CDS	3113807	3114190	0.97	-	0	transcript_id "Phchi.S6G040400.t1"; gene_id "Phchi.S6G040400"
Phchi.S6	AUGUSTUS	exon	3113807	3114190	.	-	.	transcript_id "Phchi.S6G040400.t1"; gene_id "Phchi.S6G040400"
Phchi.S6	AUGUSTUS	start_codon	3114188	3114190	.	-	0	transcript_id "Phchi.S6G040400.t1"; gene_id "Phchi.S6G040400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14565.t1 is derived from g13033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13498565	13501849	.	-	.	Phchi.S3G188400
Phchi.S3	AUGUSTUS	transcript	13498565	13501849	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	stop_codon	13498562	13498564	.	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13498565	13498625	1	-	1	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13498565	13498625	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13498626	13498719	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13498720	13498829	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13498720	13498829	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13498830	13498954	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13498955	13499089	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13498955	13499089	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13499090	13499174	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13499175	13499243	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13499175	13499243	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13499244	13499316	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13499317	13499383	1	-	1	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13499317	13499383	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13499384	13499455	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13499456	13499658	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13499456	13499658	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13499659	13499819	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13499820	13499872	1	-	2	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13499820	13499872	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13499873	13499955	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13499956	13500040	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13499956	13500040	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13500041	13500211	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13500212	13500268	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13500212	13500268	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13500269	13500362	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13500363	13500503	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13500363	13500503	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13500504	13500592	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13500593	13500643	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13500593	13500643	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13500644	13500750	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13500751	13500844	1	-	1	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13500751	13500844	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13500845	13500952	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13500953	13501007	1	-	2	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13500953	13501007	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13501008	13501182	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13501183	13501411	1	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13501183	13501411	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13501412	13501510	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13501511	13501549	0.4	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13501511	13501549	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	intron	13501550	13501789	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	CDS	13501790	13501849	0.66	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	exon	13501790	13501849	.	-	.	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
Phchi.S3	AUGUSTUS	start_codon	13501847	13501849	.	-	0	transcript_id "Phchi.S3G188400.t1"; gene_id "Phchi.S3G188400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1948.t1 is derived from g8868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3956630	3957608	.	+	.	Phchi.S5G055700
Phchi.S5	AUGUSTUS	transcript	3956630	3957608	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	start_codon	3956630	3956632	.	+	0	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	CDS	3956630	3956915	0.45	+	0	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	exon	3956630	3956915	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	intron	3956916	3956996	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	CDS	3956997	3957117	0.71	+	2	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	exon	3956997	3957117	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	intron	3957118	3957350	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	CDS	3957351	3957415	1	+	1	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	exon	3957351	3957415	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	intron	3957416	3957504	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	CDS	3957505	3957608	1	+	2	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	exon	3957505	3957608	.	+	.	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
Phchi.S5	AUGUSTUS	stop_codon	3957609	3957611	.	+	0	transcript_id "Phchi.S5G055700.t1"; gene_id "Phchi.S5G055700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8705.t1 is derived from g5880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37538881	37542072	.	+	.	Phchi.S1G586400
Phchi.S1	AUGUSTUS	transcript	37538881	37542072	.	+	.	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	start_codon	37538881	37538883	.	+	0	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	CDS	37538881	37539456	0.05	+	0	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	exon	37538881	37539456	.	+	.	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	intron	37539457	37541982	.	+	.	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	CDS	37541983	37542072	0.05	+	0	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	exon	37541983	37542072	.	+	.	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
Phchi.S1	AUGUSTUS	stop_codon	37542073	37542075	.	+	0	transcript_id "Phchi.S1G586400.t1"; gene_id "Phchi.S1G586400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5609.t1 is derived from g2779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17864687	17866247	.	+	.	Phchi.S1G276800
Phchi.S1	AUGUSTUS	transcript	17864687	17866247	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	start_codon	17864687	17864689	.	+	0	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	CDS	17864687	17865019	1	+	0	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	exon	17864687	17865019	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	intron	17865020	17865346	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	CDS	17865347	17865461	1	+	0	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	exon	17865347	17865461	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	intron	17865462	17865556	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	CDS	17865557	17865586	0.94	+	2	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	exon	17865557	17865586	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	intron	17865587	17865822	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	CDS	17865823	17866247	0.99	+	2	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	exon	17865823	17866247	.	+	.	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
Phchi.S1	AUGUSTUS	stop_codon	17866248	17866250	.	+	0	transcript_id "Phchi.S1G276800.t1"; gene_id "Phchi.S1G276800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9000.t1 is derived from g6175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39105480	39108417	.	-	.	Phchi.S1G615900
Phchi.S1	AUGUSTUS	transcript	39105480	39108417	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	stop_codon	39105477	39105479	.	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39105480	39105594	1	-	1	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39105480	39105594	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39105595	39105678	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39105679	39105766	1	-	2	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39105679	39105766	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39105767	39105861	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39105862	39105955	1	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39105862	39105955	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39105956	39106046	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39106047	39106094	1	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39106047	39106094	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39106095	39106260	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39106261	39106356	1	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39106261	39106356	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39106357	39106454	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39106455	39106557	1	-	1	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39106455	39106557	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39106558	39106714	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39106715	39106811	1	-	2	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39106715	39106811	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39106812	39106905	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39106906	39106960	1	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39106906	39106960	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39106961	39107074	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39107075	39107182	1	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39107075	39107182	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39107183	39107307	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39107308	39107382	1	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39107308	39107382	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39107383	39107483	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39107484	39107556	0.99	-	1	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39107484	39107556	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39107557	39107674	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39107675	39107754	0.99	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39107675	39107754	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39107755	39107848	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39107849	39108059	1	-	1	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39107849	39108059	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39108060	39108144	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39108145	39108247	0.79	-	2	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39108145	39108247	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	intron	39108248	39108350	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	CDS	39108351	39108417	0.79	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	exon	39108351	39108417	.	-	.	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
Phchi.S1	AUGUSTUS	start_codon	39108415	39108417	.	-	0	transcript_id "Phchi.S1G615900.t1"; gene_id "Phchi.S1G615900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14921.t1 is derived from g13389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15512105	15514548	.	-	.	Phchi.S3G224000
Phchi.S3	AUGUSTUS	transcript	15512105	15514548	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	stop_codon	15512102	15512104	.	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15512105	15512152	0.88	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15512105	15512152	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15512153	15512238	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15512239	15512352	1	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15512239	15512352	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15512353	15512433	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15512434	15512538	1	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15512434	15512538	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15512539	15512690	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15512691	15512735	1	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15512691	15512735	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15512736	15512828	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15512829	15513008	1	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15512829	15513008	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15513009	15513101	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15513102	15513178	1	-	2	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15513102	15513178	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15513179	15513414	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15513415	15513532	1	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15513415	15513532	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15513533	15513641	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15513642	15513848	1	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15513642	15513848	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15513849	15513979	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15513980	15514173	1	-	2	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15513980	15514173	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	intron	15514174	15514256	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	CDS	15514257	15514548	0.47	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	exon	15514257	15514548	.	-	.	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
Phchi.S3	AUGUSTUS	start_codon	15514546	15514548	.	-	0	transcript_id "Phchi.S3G224000.t1"; gene_id "Phchi.S3G224000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg804.t1 is derived from g10586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5682207	5683154	.	+	.	Phchi.S6G076300
Phchi.S6	AUGUSTUS	transcript	5682207	5683154	.	+	.	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	start_codon	5682207	5682209	.	+	0	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	CDS	5682207	5682428	0.96	+	0	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	exon	5682207	5682428	.	+	.	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	intron	5682429	5682609	.	+	.	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	CDS	5682610	5682849	1	+	0	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	exon	5682610	5682849	.	+	.	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	intron	5682850	5683070	.	+	.	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	CDS	5683071	5683154	0.99	+	0	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	exon	5683071	5683154	.	+	.	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
Phchi.S6	AUGUSTUS	stop_codon	5683155	5683157	.	+	0	transcript_id "Phchi.S6G076300.t1"; gene_id "Phchi.S6G076300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11818.t1 is derived from g15870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8390515	8391321	.	-	.	Phchi.S4G140000
Phchi.S4	AUGUSTUS	transcript	8390515	8391321	.	-	.	transcript_id "Phchi.S4G140000.t1"; gene_id "Phchi.S4G140000"
Phchi.S4	AUGUSTUS	stop_codon	8390512	8390514	.	-	0	transcript_id "Phchi.S4G140000.t1"; gene_id "Phchi.S4G140000"
Phchi.S4	AUGUSTUS	CDS	8390515	8391321	1	-	0	transcript_id "Phchi.S4G140000.t1"; gene_id "Phchi.S4G140000"
Phchi.S4	AUGUSTUS	exon	8390515	8391321	.	-	.	transcript_id "Phchi.S4G140000.t1"; gene_id "Phchi.S4G140000"
Phchi.S4	AUGUSTUS	start_codon	8391319	8391321	.	-	0	transcript_id "Phchi.S4G140000.t1"; gene_id "Phchi.S4G140000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12826.t1 is derived from g11291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2582662	2585004	.	+	.	Phchi.S3G014500
Phchi.S3	AUGUSTUS	transcript	2582662	2585004	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	start_codon	2582662	2582664	.	+	0	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2582662	2582746	1	+	0	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2582662	2582746	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2582747	2582840	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2582841	2583077	1	+	2	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2582841	2583077	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2583078	2583199	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2583200	2583232	1	+	2	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2583200	2583232	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2583233	2583318	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2583319	2583431	0.89	+	2	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2583319	2583431	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2583432	2583544	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2583545	2583693	1	+	0	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2583545	2583693	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2583694	2583780	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2583781	2583922	1	+	1	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2583781	2583922	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2583923	2584023	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2584024	2584283	0.58	+	0	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2584024	2584283	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2584284	2584397	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2584398	2584434	0.58	+	1	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2584398	2584434	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	intron	2584435	2584515	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	CDS	2584516	2585004	0.96	+	0	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	exon	2584516	2585004	.	+	.	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
Phchi.S3	AUGUSTUS	stop_codon	2585005	2585007	.	+	0	transcript_id "Phchi.S3G014500.t1"; gene_id "Phchi.S3G014500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13943.t1 is derived from g12410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9833219	9838690	.	+	.	Phchi.S3G126200
Phchi.S3	AUGUSTUS	transcript	9833219	9838690	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	start_codon	9833219	9833221	.	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9833219	9833489	0.37	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9833219	9833489	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9833490	9833580	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9833581	9833702	1	+	2	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9833581	9833702	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9833703	9833842	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9833843	9833925	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9833843	9833925	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9833926	9834035	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9834036	9834192	0.99	+	1	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9834036	9834192	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9834193	9834431	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9834432	9834983	0.99	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9834432	9834983	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9834984	9835065	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9835066	9835178	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9835066	9835178	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9835179	9835313	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9835314	9835551	1	+	1	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9835314	9835551	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9835552	9835638	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9835639	9835832	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9835639	9835832	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9835833	9835911	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9835912	9835993	1	+	1	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9835912	9835993	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9835994	9836094	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9836095	9836184	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9836095	9836184	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9836185	9836375	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9836376	9836603	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9836376	9836603	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9836604	9836766	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9836767	9836838	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9836767	9836838	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9836839	9836986	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9836987	9837136	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9836987	9837136	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9837137	9837221	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9837222	9837365	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9837222	9837365	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9837366	9837454	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9837455	9837634	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9837455	9837634	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9837635	9837783	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9837784	9837867	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9837784	9837867	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9837868	9837951	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9837952	9838521	1	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9837952	9838521	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	intron	9838522	9838606	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	CDS	9838607	9838690	0.54	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	exon	9838607	9838690	.	+	.	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
Phchi.S3	AUGUSTUS	stop_codon	9838691	9838693	.	+	0	transcript_id "Phchi.S3G126200.t1"; gene_id "Phchi.S3G126200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9859.t1 is derived from g7035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44108304	44109919	.	-	.	Phchi.S1G701800
Phchi.S1	AUGUSTUS	transcript	44108398	44109919	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	stop_codon	44108395	44108397	.	-	0	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108398	44108425	0.96	-	1	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108398	44108425	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108426	44108507	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108508	44108584	0.97	-	0	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108508	44108584	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108585	44108722	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108723	44108802	0.92	-	2	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108723	44108802	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108803	44108934	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108935	44108939	0.92	-	1	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108935	44108939	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108940	44109237	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109238	44109335	0.67	-	0	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109238	44109335	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109336	44109417	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109418	44109451	0.67	-	1	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109418	44109451	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109452	44109545	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109546	44109563	0.67	-	1	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109546	44109563	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109564	44109675	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109676	44109701	0.67	-	0	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109676	44109701	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109702	44109787	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109788	44109919	0.89	-	0	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109788	44109919	.	-	.	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	start_codon	44109917	44109919	.	-	0	transcript_id "Phchi.S1G701800.t1"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	transcript	44108304	44109919	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	stop_codon	44108301	44108303	.	-	0	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108304	44108409	0.85	-	1	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108304	44108409	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108410	44108507	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108508	44108584	0.96	-	0	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108508	44108584	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108585	44108722	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108723	44108802	0.95	-	2	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108723	44108802	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108803	44108934	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44108935	44108939	0.95	-	1	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44108935	44108939	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44108940	44109237	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109238	44109335	0.57	-	0	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109238	44109335	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109336	44109417	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109418	44109451	0.59	-	1	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109418	44109451	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109452	44109545	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109546	44109563	0.59	-	1	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109546	44109563	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109564	44109675	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109676	44109701	0.59	-	0	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109676	44109701	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	intron	44109702	44109787	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	CDS	44109788	44109919	0.83	-	0	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	exon	44109788	44109919	.	-	.	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
Phchi.S1	AUGUSTUS	start_codon	44109917	44109919	.	-	0	transcript_id "Phchi.S1G701800.t2"; gene_id "Phchi.S1G701800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4772.t1 is derived from g1942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12764317	12766079	.	+	.	Phchi.S1G193100
Phchi.S1	AUGUSTUS	transcript	12764317	12766079	.	+	.	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	start_codon	12764317	12764319	.	+	0	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	CDS	12764317	12765609	0.8	+	0	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	exon	12764317	12765609	.	+	.	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	intron	12765610	12765839	.	+	.	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	CDS	12765840	12766079	0.53	+	0	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	exon	12765840	12766079	.	+	.	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
Phchi.S1	AUGUSTUS	stop_codon	12766080	12766082	.	+	0	transcript_id "Phchi.S1G193100.t1"; gene_id "Phchi.S1G193100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3782.t1 is derived from g951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5664115	5665629	.	-	.	Phchi.S1G094100
Phchi.S1	AUGUSTUS	transcript	5664115	5665629	.	-	.	transcript_id "Phchi.S1G094100.t1"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	stop_codon	5664112	5664114	.	-	0	transcript_id "Phchi.S1G094100.t1"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	CDS	5664115	5665629	0.97	-	0	transcript_id "Phchi.S1G094100.t1"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	exon	5664115	5665629	.	-	.	transcript_id "Phchi.S1G094100.t1"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	start_codon	5665627	5665629	.	-	0	transcript_id "Phchi.S1G094100.t1"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	transcript	5664115	5664510	.	-	.	transcript_id "Phchi.S1G094100.t2"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	stop_codon	5664112	5664114	.	-	0	transcript_id "Phchi.S1G094100.t2"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	CDS	5664115	5664510	0.54	-	0	transcript_id "Phchi.S1G094100.t2"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	exon	5664115	5664510	.	-	.	transcript_id "Phchi.S1G094100.t2"; gene_id "Phchi.S1G094100"
Phchi.S1	AUGUSTUS	start_codon	5664508	5664510	.	-	0	transcript_id "Phchi.S1G094100.t2"; gene_id "Phchi.S1G094100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6592.t1 is derived from g3764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23906241	23907032	.	+	.	Phchi.S1G375100
Phchi.S1	AUGUSTUS	transcript	23906241	23907032	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	start_codon	23906241	23906243	.	+	0	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	CDS	23906241	23906393	0.4	+	0	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	exon	23906241	23906393	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	intron	23906394	23906482	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	CDS	23906483	23906554	0.57	+	0	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	exon	23906483	23906554	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	intron	23906555	23906635	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	CDS	23906636	23906733	0.56	+	0	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	exon	23906636	23906733	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	intron	23906734	23906815	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	CDS	23906816	23907032	1	+	1	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	exon	23906816	23907032	.	+	.	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
Phchi.S1	AUGUSTUS	stop_codon	23907033	23907035	.	+	0	transcript_id "Phchi.S1G375100.t1"; gene_id "Phchi.S1G375100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8685.t1 is derived from g5860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37444089	37445410	.	+	.	Phchi.S1G584400
Phchi.S1	AUGUSTUS	transcript	37444089	37445410	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	start_codon	37444089	37444091	.	+	0	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	CDS	37444089	37444365	0.82	+	0	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	exon	37444089	37444365	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	intron	37444366	37444498	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	CDS	37444499	37444569	0.83	+	2	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	exon	37444499	37444569	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	intron	37444570	37444662	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	CDS	37444663	37444730	0.96	+	0	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	exon	37444663	37444730	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	intron	37444731	37444832	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	CDS	37444833	37444929	0.9	+	1	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	exon	37444833	37444929	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	intron	37444930	37445037	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	CDS	37445038	37445124	0.88	+	0	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	exon	37445038	37445124	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	intron	37445125	37445233	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	CDS	37445234	37445410	0.89	+	0	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	exon	37445234	37445410	.	+	.	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
Phchi.S1	AUGUSTUS	stop_codon	37445411	37445413	.	+	0	transcript_id "Phchi.S1G584400.t1"; gene_id "Phchi.S1G584400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11518.t1 is derived from g15568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6880401	6881385	.	-	.	Phchi.S4G110000
Phchi.S4	AUGUSTUS	transcript	6880401	6881385	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	stop_codon	6880398	6880400	.	-	0	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	CDS	6880401	6880737	1	-	1	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	exon	6880401	6880737	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	intron	6880738	6880832	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	CDS	6880833	6880986	0.45	-	2	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	exon	6880833	6880986	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	intron	6880987	6881231	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	CDS	6881232	6881283	0.44	-	0	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	exon	6881232	6881283	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	intron	6881284	6881364	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	CDS	6881365	6881385	0.3	-	0	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	exon	6881365	6881385	.	-	.	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
Phchi.S4	AUGUSTUS	start_codon	6881383	6881385	.	-	0	transcript_id "Phchi.S4G110000.t1"; gene_id "Phchi.S4G110000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13920.t1 is derived from g12387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9661141	9661605	.	-	.	Phchi.S3G123900
Phchi.S3	AUGUSTUS	transcript	9661141	9661605	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	stop_codon	9661138	9661140	.	-	0	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	CDS	9661141	9661182	1	-	0	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	exon	9661141	9661182	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	intron	9661183	9661268	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	CDS	9661269	9661313	1	-	0	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	exon	9661269	9661313	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	intron	9661314	9661391	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	CDS	9661392	9661432	1	-	2	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	exon	9661392	9661432	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	intron	9661433	9661508	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	CDS	9661509	9661605	0.61	-	0	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	exon	9661509	9661605	.	-	.	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
Phchi.S3	AUGUSTUS	start_codon	9661603	9661605	.	-	0	transcript_id "Phchi.S3G123900.t1"; gene_id "Phchi.S3G123900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14872.t1 is derived from g13340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15217177	15219768	.	+	.	Phchi.S3G219100
Phchi.S3	AUGUSTUS	transcript	15217177	15219768	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	start_codon	15217177	15217179	.	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15217177	15217275	0.67	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15217177	15217275	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15217276	15217422	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15217423	15217507	1	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15217423	15217507	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15217508	15217813	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15217814	15217952	1	+	2	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15217814	15217952	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15217953	15218031	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15218032	15218080	1	+	1	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15218032	15218080	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15218081	15218274	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15218275	15218457	1	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15218275	15218457	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15218458	15218550	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15218551	15218625	1	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15218551	15218625	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15218626	15218743	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15218744	15218790	0.85	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15218744	15218790	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15218791	15218894	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15218895	15218928	0.82	+	1	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15218895	15218928	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15218929	15219015	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15219016	15219104	1	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15219016	15219104	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	intron	15219105	15219218	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	CDS	15219219	15219768	1	+	1	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	exon	15219219	15219768	.	+	.	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
Phchi.S3	AUGUSTUS	stop_codon	15219769	15219771	.	+	0	transcript_id "Phchi.S3G219100.t1"; gene_id "Phchi.S3G219100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1244.t1 is derived from g11027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8605618	8610343	.	-	.	Phchi.S6G120300
Phchi.S6	AUGUSTUS	transcript	8605618	8610343	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	stop_codon	8605615	8605617	.	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8605618	8606199	0.99	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8605618	8606199	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8606200	8606285	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8606286	8606636	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8606286	8606636	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8606637	8606727	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8606728	8606924	1	-	2	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8606728	8606924	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8606925	8606998	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8606999	8607281	0.98	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8606999	8607281	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8607282	8607409	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8607410	8607622	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8607410	8607622	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8607623	8607722	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8607723	8607848	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8607723	8607848	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8607849	8607924	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8607925	8608062	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8607925	8608062	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8608063	8608142	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8608143	8608485	1	-	1	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8608143	8608485	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8608486	8608568	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8608569	8608835	0.98	-	1	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8608569	8608835	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8608836	8608945	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8608946	8609144	0.88	-	2	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8608946	8609144	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8609145	8609247	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8609248	8609365	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8609248	8609365	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8609366	8609505	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8609506	8609726	1	-	2	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8609506	8609726	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8609727	8609938	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8609939	8610134	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8609939	8610134	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	intron	8610135	8610265	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	CDS	8610266	8610343	1	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	exon	8610266	8610343	.	-	.	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
Phchi.S6	AUGUSTUS	start_codon	8610341	8610343	.	-	0	transcript_id "Phchi.S6G120300.t1"; gene_id "Phchi.S6G120300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12348.t1 is derived from g8024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12369501	12371240	.	+	.	Phchi.S2G042800
Phchi.S2	AUGUSTUS	transcript	12369501	12371240	.	+	.	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	start_codon	12369501	12369503	.	+	0	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	CDS	12369501	12370530	0.74	+	0	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	exon	12369501	12370530	.	+	.	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	intron	12370531	12370608	.	+	.	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	CDS	12370609	12370778	0.99	+	2	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	exon	12370609	12370778	.	+	.	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	intron	12370779	12370871	.	+	.	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	CDS	12370872	12371240	0.94	+	0	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	exon	12370872	12371240	.	+	.	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
Phchi.S2	AUGUSTUS	stop_codon	12371241	12371243	.	+	0	transcript_id "Phchi.S2G042800.t1"; gene_id "Phchi.S2G042800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6535.t1 is derived from g3707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23524870	23525493	.	-	.	Phchi.S1G369400
Phchi.S1	AUGUSTUS	transcript	23524870	23525493	.	-	.	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	stop_codon	23524867	23524869	.	-	0	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	CDS	23524870	23525019	1	-	0	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	exon	23524870	23525019	.	-	.	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	intron	23525020	23525103	.	-	.	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	CDS	23525104	23525163	1	-	0	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	exon	23525104	23525163	.	-	.	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	intron	23525164	23525238	.	-	.	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	CDS	23525239	23525493	0.75	-	0	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	exon	23525239	23525493	.	-	.	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
Phchi.S1	AUGUSTUS	start_codon	23525491	23525493	.	-	0	transcript_id "Phchi.S1G369400.t1"; gene_id "Phchi.S1G369400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7903.t1 is derived from g5077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31818777	31820935	.	-	.	Phchi.S1G506200
Phchi.S1	AUGUSTUS	transcript	31818777	31820935	.	-	.	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	stop_codon	31818774	31818776	.	-	0	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	CDS	31818777	31819586	0.68	-	0	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	exon	31818777	31819586	.	-	.	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	intron	31819587	31819687	.	-	.	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	CDS	31819688	31820935	0.54	-	0	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	exon	31819688	31820935	.	-	.	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
Phchi.S1	AUGUSTUS	start_codon	31820933	31820935	.	-	0	transcript_id "Phchi.S1G506200.t1"; gene_id "Phchi.S1G506200"
# This transcript jg15354.t1 is derived from g13822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18562908	18564232	.	-	.	Phchi.S3G267300
Phchi.S3	AUGUSTUS	transcript	18562908	18564232	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	stop_codon	18562905	18562907	.	-	0	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	CDS	18562908	18562936	0.66	-	2	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	exon	18562908	18562936	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	intron	18562937	18563119	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	CDS	18563120	18563265	0.64	-	1	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	exon	18563120	18563265	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	intron	18563266	18563345	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	CDS	18563346	18563381	0.5	-	1	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	exon	18563346	18563381	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	intron	18563382	18563792	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	CDS	18563793	18563856	0.85	-	2	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	exon	18563793	18563856	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	intron	18563857	18564011	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	CDS	18564012	18564035	0.83	-	2	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	exon	18564012	18564035	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	intron	18564036	18564153	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	CDS	18564154	18564232	0.38	-	0	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	exon	18564154	18564232	.	-	.	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
Phchi.S3	AUGUSTUS	start_codon	18564230	18564232	.	-	0	transcript_id "Phchi.S3G267300.t1"; gene_id "Phchi.S3G267300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7831.t1 is derived from g5005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31409484	31410365	.	-	.	Phchi.S1G499000
Phchi.S1	AUGUSTUS	transcript	31409484	31410365	.	-	.	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	stop_codon	31409481	31409483	.	-	0	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	CDS	31409484	31410089	0.99	-	0	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	exon	31409484	31410089	.	-	.	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	intron	31410090	31410209	.	-	.	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	CDS	31410210	31410365	0.56	-	0	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	exon	31410210	31410365	.	-	.	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
Phchi.S1	AUGUSTUS	start_codon	31410363	31410365	.	-	0	transcript_id "Phchi.S1G499000.t1"; gene_id "Phchi.S1G499000"
# This transcript jg8519.t2 is derived from g5694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8520.t1 is derived from g5695.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36415289	36415765	.	-	.	Phchi.S1G567900
Phchi.S1	AUGUSTUS	transcript	36415289	36415765	.	-	.	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	stop_codon	36415286	36415288	.	-	0	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	CDS	36415289	36415384	0.93	-	0	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	exon	36415289	36415384	.	-	.	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	intron	36415385	36415561	.	-	.	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	CDS	36415562	36415765	0.57	-	0	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	exon	36415562	36415765	.	-	.	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	start_codon	36415763	36415765	.	-	0	transcript_id "Phchi.S1G567900.t1"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	transcript	36415365	36415765	.	-	.	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	stop_codon	36415362	36415364	.	-	0	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	CDS	36415365	36415415	0.76	-	0	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	exon	36415365	36415415	.	-	.	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	intron	36415416	36415561	.	-	.	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	CDS	36415562	36415765	0.39	-	0	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	exon	36415562	36415765	.	-	.	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
Phchi.S1	AUGUSTUS	start_codon	36415763	36415765	.	-	0	transcript_id "Phchi.S1G567900.t2"; gene_id "Phchi.S1G567900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1764.t1 is derived from g8684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2927545	2929694	.	-	.	Phchi.S5G037300
Phchi.S5	AUGUSTUS	transcript	2927545	2929648	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	stop_codon	2927542	2927544	.	-	0	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2927545	2927709	1	-	0	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2927545	2927709	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2927710	2927801	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2927802	2927926	1	-	2	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2927802	2927926	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2927927	2928010	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2928011	2928219	0.83	-	1	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2928011	2928219	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2928220	2928309	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2928310	2928491	1	-	0	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2928310	2928491	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2928492	2928714	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2928715	2928910	1	-	1	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2928715	2928910	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2928911	2929016	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929017	2929109	1	-	1	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929017	2929109	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2929110	2929198	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929199	2929304	1	-	2	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929199	2929304	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2929305	2929386	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929387	2929648	0.84	-	0	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929387	2929648	.	-	.	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	start_codon	2929646	2929648	.	-	0	transcript_id "Phchi.S5G037300.t1"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	transcript	2927545	2929694	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	stop_codon	2927542	2927544	.	-	0	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2927545	2927709	1	-	0	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2927545	2927709	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2927710	2927801	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2927802	2927926	1	-	2	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2927802	2927926	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2927927	2928010	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2928011	2928219	0.82	-	1	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2928011	2928219	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2928220	2928309	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2928310	2928491	1	-	0	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2928310	2928491	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2928492	2928714	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2928715	2928910	1	-	1	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2928715	2928910	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2928911	2929016	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929017	2929109	1	-	1	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929017	2929109	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2929110	2929198	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929199	2929294	0.86	-	1	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929199	2929294	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2929295	2929386	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929387	2929441	0.86	-	2	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929387	2929441	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	intron	2929442	2929618	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	CDS	2929619	2929694	0.36	-	0	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	exon	2929619	2929694	.	-	.	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
Phchi.S5	AUGUSTUS	start_codon	2929692	2929694	.	-	0	transcript_id "Phchi.S5G037300.t2"; gene_id "Phchi.S5G037300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14366.t1 is derived from g12833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12379630	12380682	.	-	.	Phchi.S3G168500
Phchi.S3	AUGUSTUS	transcript	12379630	12380682	.	-	.	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	stop_codon	12379627	12379629	.	-	0	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	CDS	12379630	12379945	0.99	-	1	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	exon	12379630	12379945	.	-	.	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	intron	12379946	12380041	.	-	.	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	CDS	12380042	12380682	0.99	-	0	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	exon	12380042	12380682	.	-	.	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
Phchi.S3	AUGUSTUS	start_codon	12380680	12380682	.	-	0	transcript_id "Phchi.S3G168500.t1"; gene_id "Phchi.S3G168500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10784.t1 is derived from g14834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2093775	2094721	.	+	.	Phchi.S4G036600
Phchi.S4	AUGUSTUS	transcript	2093775	2094721	.	+	.	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	start_codon	2093775	2093777	.	+	0	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	CDS	2093775	2094244	0.26	+	0	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	exon	2093775	2094244	.	+	.	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	intron	2094245	2094409	.	+	.	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	CDS	2094410	2094574	0.48	+	1	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	exon	2094410	2094574	.	+	.	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	intron	2094575	2094714	.	+	.	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	CDS	2094715	2094721	0.59	+	1	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	exon	2094715	2094721	.	+	.	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
Phchi.S4	AUGUSTUS	stop_codon	2094722	2094724	.	+	0	transcript_id "Phchi.S4G036600.t1"; gene_id "Phchi.S4G036600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3282.t1 is derived from g451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2684163	2684867	.	-	.	Phchi.S1G044100
Phchi.S1	AUGUSTUS	transcript	2684163	2684867	.	-	.	transcript_id "Phchi.S1G044100.t1"; gene_id "Phchi.S1G044100"
Phchi.S1	AUGUSTUS	stop_codon	2684160	2684162	.	-	0	transcript_id "Phchi.S1G044100.t1"; gene_id "Phchi.S1G044100"
Phchi.S1	AUGUSTUS	CDS	2684163	2684867	0.52	-	0	transcript_id "Phchi.S1G044100.t1"; gene_id "Phchi.S1G044100"
Phchi.S1	AUGUSTUS	exon	2684163	2684867	.	-	.	transcript_id "Phchi.S1G044100.t1"; gene_id "Phchi.S1G044100"
Phchi.S1	AUGUSTUS	start_codon	2684865	2684867	.	-	0	transcript_id "Phchi.S1G044100.t1"; gene_id "Phchi.S1G044100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7321.t1 is derived from g4493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28496050	28497606	.	-	.	Phchi.S1G448000
Phchi.S1	AUGUSTUS	transcript	28496050	28497606	.	-	.	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	stop_codon	28496047	28496049	.	-	0	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	CDS	28496050	28496310	1	-	0	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	exon	28496050	28496310	.	-	.	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	intron	28496311	28496401	.	-	.	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	CDS	28496402	28496935	1	-	0	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	exon	28496402	28496935	.	-	.	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	intron	28496936	28497021	.	-	.	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	CDS	28497022	28497606	0.82	-	0	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	exon	28497022	28497606	.	-	.	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
Phchi.S1	AUGUSTUS	start_codon	28497604	28497606	.	-	0	transcript_id "Phchi.S1G448000.t1"; gene_id "Phchi.S1G448000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13646.t1 is derived from g12113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7999054	8002777	.	-	.	Phchi.S3G096500
Phchi.S3	AUGUSTUS	transcript	7999054	8002777	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	stop_codon	7999051	7999053	.	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	7999054	7999119	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	7999054	7999119	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	7999120	7999209	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	7999210	7999378	1	-	1	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	7999210	7999378	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	7999379	7999460	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	7999461	7999564	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	7999461	7999564	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	7999565	7999655	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	7999656	7999745	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	7999656	7999745	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	7999746	7999831	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	7999832	7999909	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	7999832	7999909	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	7999910	8000002	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8000003	8000136	1	-	2	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8000003	8000136	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8000137	8000240	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8000241	8000331	0.51	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8000241	8000331	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8000332	8000493	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8000494	8000574	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8000494	8000574	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8000575	8000657	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8000658	8000783	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8000658	8000783	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8000784	8000871	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8000872	8001085	0.9	-	1	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8000872	8001085	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8001086	8001180	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8001181	8001275	0.94	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8001181	8001275	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8001276	8001377	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8001378	8001437	0.99	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8001378	8001437	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8001438	8001585	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8001586	8001666	1	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8001586	8001666	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8001667	8001767	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8001768	8001962	0.99	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8001768	8001962	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	intron	8001963	8002054	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	CDS	8002055	8002777	0.99	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	exon	8002055	8002777	.	-	.	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
Phchi.S3	AUGUSTUS	start_codon	8002775	8002777	.	-	0	transcript_id "Phchi.S3G096500.t1"; gene_id "Phchi.S3G096500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg483.t1 is derived from g10265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3378118	3379526	.	+	.	Phchi.S6G044200
Phchi.S6	AUGUSTUS	transcript	3378118	3379526	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	start_codon	3378118	3378120	.	+	0	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3378118	3378221	0.96	+	0	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3378118	3378221	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	intron	3378222	3378309	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3378310	3378441	1	+	1	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3378310	3378441	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	intron	3378442	3378529	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3378530	3378574	1	+	1	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3378530	3378574	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	intron	3378575	3378676	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3378677	3378846	1	+	1	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3378677	3378846	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	intron	3378847	3379019	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3379020	3379105	0.96	+	2	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3379020	3379105	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	intron	3379106	3379299	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3379300	3379323	0.99	+	0	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3379300	3379323	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	intron	3379324	3379406	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	CDS	3379407	3379526	0.77	+	0	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	exon	3379407	3379526	.	+	.	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
Phchi.S6	AUGUSTUS	stop_codon	3379527	3379529	.	+	0	transcript_id "Phchi.S6G044200.t1"; gene_id "Phchi.S6G044200"
# This transcript jg10778.t2 is derived from g14828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10779.t1 is derived from g14829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2077898	2078624	.	-	.	Phchi.S4G036100
Phchi.S4	AUGUSTUS	transcript	2077898	2078624	.	-	.	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	stop_codon	2077895	2077897	.	-	0	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	CDS	2077898	2078009	0.99	-	1	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	exon	2077898	2078009	.	-	.	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	intron	2078010	2078116	.	-	.	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	CDS	2078117	2078233	0.95	-	1	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	exon	2078117	2078233	.	-	.	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	intron	2078234	2078538	.	-	.	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	CDS	2078539	2078624	1	-	0	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	exon	2078539	2078624	.	-	.	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
Phchi.S4	AUGUSTUS	start_codon	2078622	2078624	.	-	0	transcript_id "Phchi.S4G036100.t1"; gene_id "Phchi.S4G036100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10998.t1 is derived from g15048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3574140	3575512	.	-	.	Phchi.S4G058000
Phchi.S4	AUGUSTUS	transcript	3574140	3575512	.	-	.	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	stop_codon	3574137	3574139	.	-	0	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	CDS	3574140	3574637	0.49	-	0	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	exon	3574140	3574637	.	-	.	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	intron	3574638	3574759	.	-	.	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	CDS	3574760	3575040	0.98	-	2	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	exon	3574760	3575040	.	-	.	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	intron	3575041	3575118	.	-	.	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	CDS	3575119	3575512	0.99	-	0	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	exon	3575119	3575512	.	-	.	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
Phchi.S4	AUGUSTUS	start_codon	3575510	3575512	.	-	0	transcript_id "Phchi.S4G058000.t1"; gene_id "Phchi.S4G058000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1791.t1 is derived from g8711.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3044794	3046524	.	+	.	Phchi.S5G040000
Phchi.S5	AUGUSTUS	transcript	3044794	3046524	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	start_codon	3044794	3044796	.	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3044794	3045174	0.91	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3044794	3045174	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045175	3045325	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045326	3045332	1	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045326	3045332	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045333	3045431	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045432	3045515	1	+	2	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045432	3045515	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045516	3045663	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045664	3045746	1	+	2	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045664	3045746	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045747	3045829	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045830	3045897	1	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045830	3045897	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045898	3046021	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046022	3046091	1	+	1	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046022	3046091	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3046092	3046177	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046178	3046243	1	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046178	3046243	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3046244	3046322	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046323	3046400	1	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046323	3046400	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3046401	3046485	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046486	3046524	0.49	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046486	3046524	.	+	.	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	stop_codon	3046525	3046527	.	+	0	transcript_id "Phchi.S5G040000.t1"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	transcript	3044794	3046524	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	start_codon	3044794	3044796	.	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3044794	3045174	0.89	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3044794	3045174	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045175	3045278	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045279	3045332	1	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045279	3045332	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045333	3045431	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045432	3045515	0.91	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045432	3045515	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045516	3045620	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045621	3045746	0.92	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045621	3045746	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045747	3045829	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3045830	3045897	1	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3045830	3045897	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3045898	3046021	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046022	3046091	1	+	1	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046022	3046091	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3046092	3046177	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046178	3046243	1	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046178	3046243	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3046244	3046322	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046323	3046400	1	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046323	3046400	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	intron	3046401	3046485	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	CDS	3046486	3046524	0.48	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	exon	3046486	3046524	.	+	.	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
Phchi.S5	AUGUSTUS	stop_codon	3046525	3046527	.	+	0	transcript_id "Phchi.S5G040000.t2"; gene_id "Phchi.S5G040000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4466.t1 is derived from g1636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10635744	10636601	.	+	.	Phchi.S1G162500
Phchi.S1	AUGUSTUS	transcript	10635744	10636601	.	+	.	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	start_codon	10635744	10635746	.	+	0	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	CDS	10635744	10636002	0.99	+	0	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	exon	10635744	10636002	.	+	.	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	intron	10636003	10636575	.	+	.	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	CDS	10636576	10636601	0.99	+	2	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	exon	10636576	10636601	.	+	.	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
Phchi.S1	AUGUSTUS	stop_codon	10636602	10636604	.	+	0	transcript_id "Phchi.S1G162500.t1"; gene_id "Phchi.S1G162500"
# This transcript jg7127.t2 is derived from g4299.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7128.t1 is derived from g4300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27093116	27094532	.	+	.	Phchi.S1G428700
Phchi.S1	AUGUSTUS	transcript	27093116	27094532	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	start_codon	27093116	27093118	.	+	0	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27093116	27093163	0.93	+	0	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27093116	27093163	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	intron	27093164	27093240	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27093241	27093306	1	+	0	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27093241	27093306	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	intron	27093307	27093398	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27093399	27093529	1	+	0	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27093399	27093529	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	intron	27093530	27093601	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27093602	27093702	1	+	1	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27093602	27093702	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	intron	27093703	27093787	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27093788	27093930	0.52	+	2	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27093788	27093930	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	intron	27093931	27094032	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27094033	27094142	0.95	+	0	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27094033	27094142	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	intron	27094143	27094231	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	CDS	27094232	27094532	0.99	+	1	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	exon	27094232	27094532	.	+	.	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
Phchi.S1	AUGUSTUS	stop_codon	27094533	27094535	.	+	0	transcript_id "Phchi.S1G428700.t1"; gene_id "Phchi.S1G428700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6193.t1 is derived from g3364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21410786	21412390	.	-	.	Phchi.S1G335200
Phchi.S1	AUGUSTUS	transcript	21410786	21412390	.	-	.	transcript_id "Phchi.S1G335200.t1"; gene_id "Phchi.S1G335200"
Phchi.S1	AUGUSTUS	stop_codon	21410783	21410785	.	-	0	transcript_id "Phchi.S1G335200.t1"; gene_id "Phchi.S1G335200"
Phchi.S1	AUGUSTUS	CDS	21410786	21412390	0.82	-	0	transcript_id "Phchi.S1G335200.t1"; gene_id "Phchi.S1G335200"
Phchi.S1	AUGUSTUS	exon	21410786	21412390	.	-	.	transcript_id "Phchi.S1G335200.t1"; gene_id "Phchi.S1G335200"
Phchi.S1	AUGUSTUS	start_codon	21412388	21412390	.	-	0	transcript_id "Phchi.S1G335200.t1"; gene_id "Phchi.S1G335200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5748.t1 is derived from g2918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18701418	18703649	.	+	.	Phchi.S1G290700
Phchi.S1	AUGUSTUS	transcript	18701418	18703649	.	+	.	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	start_codon	18701418	18701420	.	+	0	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	CDS	18701418	18702575	0.25	+	0	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	exon	18701418	18702575	.	+	.	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	intron	18702576	18703064	.	+	.	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	CDS	18703065	18703170	0.28	+	0	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	exon	18703065	18703170	.	+	.	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	intron	18703171	18703278	.	+	.	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	CDS	18703279	18703649	0.96	+	2	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	exon	18703279	18703649	.	+	.	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
Phchi.S1	AUGUSTUS	stop_codon	18703650	18703652	.	+	0	transcript_id "Phchi.S1G290700.t1"; gene_id "Phchi.S1G290700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15208.t1 is derived from g13676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17659502	17660590	.	+	.	Phchi.S3G252700
Phchi.S3	AUGUSTUS	transcript	17659502	17660590	.	+	.	transcript_id "Phchi.S3G252700.t1"; gene_id "Phchi.S3G252700"
Phchi.S3	AUGUSTUS	start_codon	17659502	17659504	.	+	0	transcript_id "Phchi.S3G252700.t1"; gene_id "Phchi.S3G252700"
Phchi.S3	AUGUSTUS	CDS	17659502	17660590	0.29	+	0	transcript_id "Phchi.S3G252700.t1"; gene_id "Phchi.S3G252700"
Phchi.S3	AUGUSTUS	exon	17659502	17660590	.	+	.	transcript_id "Phchi.S3G252700.t1"; gene_id "Phchi.S3G252700"
Phchi.S3	AUGUSTUS	stop_codon	17660591	17660593	.	+	0	transcript_id "Phchi.S3G252700.t1"; gene_id "Phchi.S3G252700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg650.t1 is derived from g10432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4580171	4581600	.	+	.	Phchi.S6G060900
Phchi.S6	AUGUSTUS	transcript	4580171	4581600	.	+	.	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	start_codon	4580171	4580173	.	+	0	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	CDS	4580171	4580833	0.98	+	0	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	exon	4580171	4580833	.	+	.	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	intron	4580834	4580925	.	+	.	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	CDS	4580926	4581600	1	+	0	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	exon	4580926	4581600	.	+	.	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
Phchi.S6	AUGUSTUS	stop_codon	4581601	4581603	.	+	0	transcript_id "Phchi.S6G060900.t1"; gene_id "Phchi.S6G060900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4451.t1 is derived from g1621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10568882	10570633	.	-	.	Phchi.S1G161000
Phchi.S1	AUGUSTUS	transcript	10568882	10570633	.	-	.	transcript_id "Phchi.S1G161000.t1"; gene_id "Phchi.S1G161000"
Phchi.S1	AUGUSTUS	stop_codon	10568879	10568881	.	-	0	transcript_id "Phchi.S1G161000.t1"; gene_id "Phchi.S1G161000"
Phchi.S1	AUGUSTUS	CDS	10568882	10570633	0.72	-	0	transcript_id "Phchi.S1G161000.t1"; gene_id "Phchi.S1G161000"
Phchi.S1	AUGUSTUS	exon	10568882	10570633	.	-	.	transcript_id "Phchi.S1G161000.t1"; gene_id "Phchi.S1G161000"
Phchi.S1	AUGUSTUS	start_codon	10570631	10570633	.	-	0	transcript_id "Phchi.S1G161000.t1"; gene_id "Phchi.S1G161000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5938.t1 is derived from g3109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19949330	19955211	.	+	.	Phchi.S1G309700
Phchi.S1	AUGUSTUS	transcript	19949330	19955211	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	start_codon	19949330	19949332	.	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19949330	19949455	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19949330	19949455	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19949456	19949589	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19949590	19949685	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19949590	19949685	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19949686	19949816	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19949817	19949879	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19949817	19949879	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19949880	19949975	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19949976	19950053	0.98	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19949976	19950053	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19950054	19950160	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19950161	19950329	0.99	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19950161	19950329	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19950330	19950443	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19950444	19950721	0.99	+	2	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19950444	19950721	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19950722	19950850	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19950851	19951265	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19950851	19951265	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19951266	19951525	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19951526	19951618	1	+	2	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19951526	19951618	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19951619	19951757	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19951758	19951975	1	+	2	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19951758	19951975	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19951976	19952052	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19952053	19952100	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19952053	19952100	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19952101	19952192	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19952193	19952510	0.98	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19952193	19952510	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19952511	19952632	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19952633	19952808	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19952633	19952808	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19952809	19952909	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19952910	19953201	1	+	1	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19952910	19953201	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19953202	19953343	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19953344	19953592	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19953344	19953592	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19953593	19953708	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19953709	19953873	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19953709	19953873	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19953874	19954001	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19954002	19954133	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19954002	19954133	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19954134	19954234	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19954235	19954438	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19954235	19954438	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19954439	19954525	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19954526	19954900	1	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19954526	19954900	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	intron	19954901	19955001	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	CDS	19955002	19955211	0.97	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	exon	19955002	19955211	.	+	.	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
Phchi.S1	AUGUSTUS	stop_codon	19955212	19955214	.	+	0	transcript_id "Phchi.S1G309700.t1"; gene_id "Phchi.S1G309700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5776.t1 is derived from g2946.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18897111	18901061	.	-	.	Phchi.S1G293500
Phchi.S1	AUGUSTUS	transcript	18897111	18901061	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	stop_codon	18897108	18897110	.	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897111	18897249	1	-	1	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897111	18897249	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18897250	18897330	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897331	18897435	1	-	1	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897331	18897435	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18897436	18897519	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897520	18897635	1	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897520	18897635	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18897636	18897796	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897797	18898057	0.65	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897797	18898057	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898058	18898141	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898142	18898213	0.92	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898142	18898213	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898214	18898312	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898313	18898324	0.48	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898313	18898324	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898325	18898606	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898607	18898663	1	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898607	18898663	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898664	18898843	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898844	18898908	0.97	-	2	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898844	18898908	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898909	18899012	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899013	18899096	0.97	-	2	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899013	18899096	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899097	18899308	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899309	18899667	0.97	-	1	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899309	18899667	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899668	18899858	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899859	18899885	0.94	-	1	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899859	18899885	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899886	18899988	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899989	18900071	0.96	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899989	18900071	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900072	18900194	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900195	18900300	0.98	-	1	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900195	18900300	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900301	18900417	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900418	18900595	0.99	-	2	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900418	18900595	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900596	18900693	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900694	18900790	1	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900694	18900790	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900791	18900998	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900999	18901061	0.98	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900999	18901061	.	-	.	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	start_codon	18901059	18901061	.	-	0	transcript_id "Phchi.S1G293500.t1"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	transcript	18897111	18901061	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	stop_codon	18897108	18897110	.	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897111	18897249	0.99	-	1	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897111	18897249	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18897250	18897330	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897331	18897435	1	-	1	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897331	18897435	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18897436	18897519	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897520	18897635	1	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897520	18897635	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18897636	18897796	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18897797	18898057	0.55	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18897797	18898057	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898058	18898141	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898142	18898213	1	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898142	18898213	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898214	18898606	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898607	18898663	1	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898607	18898663	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898664	18898843	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18898844	18898908	0.95	-	2	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18898844	18898908	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18898909	18899012	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899013	18899096	0.89	-	2	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899013	18899096	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899097	18899308	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899309	18899564	0.51	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899309	18899564	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899565	18899649	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899650	18899667	0.52	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899650	18899667	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899668	18899822	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899823	18899850	0.54	-	1	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899823	18899850	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18899851	18899988	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18899989	18900071	0.55	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18899989	18900071	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900072	18900194	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900195	18900300	0.93	-	1	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900195	18900300	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900301	18900417	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900418	18900595	0.98	-	2	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900418	18900595	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900596	18900693	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900694	18900790	1	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900694	18900790	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	intron	18900791	18900998	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	CDS	18900999	18901061	0.97	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	exon	18900999	18901061	.	-	.	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
Phchi.S1	AUGUSTUS	start_codon	18901059	18901061	.	-	0	transcript_id "Phchi.S1G293500.t2"; gene_id "Phchi.S1G293500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4476.t1 is derived from g1646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10688388	10690966	.	-	.	Phchi.S1G163500
Phchi.S1	AUGUSTUS	transcript	10688388	10690966	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	stop_codon	10688385	10688387	.	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10688388	10688422	0.48	-	2	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10688388	10688422	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10688423	10688863	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10688864	10688913	0.36	-	1	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10688864	10688913	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10688914	10689050	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10689051	10689136	0.5	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10689051	10689136	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10689137	10689275	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10689276	10689533	0.61	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10689276	10689533	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10689534	10689626	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10689627	10689767	1	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10689627	10689767	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10689768	10690065	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10690066	10690140	1	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10690066	10690140	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10690141	10690548	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10690549	10690740	1	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10690549	10690740	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	intron	10690741	10690963	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	CDS	10690964	10690966	1	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	exon	10690964	10690966	.	-	.	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
Phchi.S1	AUGUSTUS	start_codon	10690964	10690966	.	-	0	transcript_id "Phchi.S1G163500.t1"; gene_id "Phchi.S1G163500"
# This transcript jg1072.t2 is derived from g10855.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1073.t1 is derived from g10856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7439007	7442983	.	-	.	Phchi.S6G103200
Phchi.S6	AUGUSTUS	transcript	7439007	7442983	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	stop_codon	7439004	7439006	.	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7439007	7439204	0.97	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7439007	7439204	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7439205	7439301	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7439302	7439489	1	-	2	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7439302	7439489	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7439490	7439668	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7439669	7439727	1	-	1	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7439669	7439727	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7439728	7439821	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7439822	7439931	0.97	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7439822	7439931	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7439932	7440045	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7440046	7441055	0.9	-	2	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7440046	7441055	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7441056	7441183	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7441184	7441328	0.57	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7441184	7441328	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7441329	7441474	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7441475	7441822	0.79	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7441475	7441822	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7441823	7441897	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7441898	7442008	0.96	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7441898	7442008	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7442009	7442174	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7442175	7442267	1	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7442175	7442267	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7442268	7442382	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7442383	7442434	1	-	1	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7442383	7442434	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7442435	7442598	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7442599	7442696	1	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7442599	7442696	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7442697	7442783	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7442784	7442851	0.93	-	2	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7442784	7442851	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	intron	7442852	7442976	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	CDS	7442977	7442983	0.61	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	exon	7442977	7442983	.	-	.	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
Phchi.S6	AUGUSTUS	start_codon	7442981	7442983	.	-	0	transcript_id "Phchi.S6G103200.t1"; gene_id "Phchi.S6G103200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13077.t1 is derived from g11542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4054642	4056225	.	-	.	Phchi.S3G039600
Phchi.S3	AUGUSTUS	transcript	4054642	4056225	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	stop_codon	4054639	4054641	.	-	0	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	CDS	4054642	4054690	0.94	-	1	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	exon	4054642	4054690	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	intron	4054691	4054852	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	CDS	4054853	4054920	1	-	0	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	exon	4054853	4054920	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	intron	4054921	4055186	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	CDS	4055187	4055373	1	-	1	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	exon	4055187	4055373	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	intron	4055374	4055508	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	CDS	4055509	4055795	1	-	0	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	exon	4055509	4055795	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	intron	4055796	4055901	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	CDS	4055902	4056225	0.99	-	0	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	exon	4055902	4056225	.	-	.	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
Phchi.S3	AUGUSTUS	start_codon	4056223	4056225	.	-	0	transcript_id "Phchi.S3G039600.t1"; gene_id "Phchi.S3G039600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15306.t1 is derived from g13774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18316874	18319297	.	+	.	Phchi.S3G262500
Phchi.S3	AUGUSTUS	transcript	18316874	18319297	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	start_codon	18316874	18316876	.	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18316874	18317123	0.58	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18316874	18317123	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317124	18317200	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317201	18317271	1	+	2	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317201	18317271	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317272	18317384	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317385	18317473	1	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317385	18317473	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317474	18317562	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317563	18317689	0.95	+	1	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317563	18317689	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317690	18317802	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317803	18318086	0.97	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317803	18318086	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318087	18318161	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18318162	18318291	1	+	1	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18318162	18318291	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318292	18318371	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18318372	18318767	0.73	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18318372	18318767	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318768	18318912	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18318913	18318961	0.65	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18318913	18318961	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318962	18319057	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18319058	18319084	0.75	+	2	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18319058	18319084	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18319085	18319172	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18319173	18319297	0.8	+	2	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18319173	18319297	.	+	.	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	stop_codon	18319298	18319300	.	+	0	transcript_id "Phchi.S3G262500.t1"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	transcript	18316874	18319297	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	start_codon	18316874	18316876	.	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18316874	18317123	0.49	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18316874	18317123	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317124	18317200	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317201	18317271	0.88	+	2	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317201	18317271	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317272	18317439	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317440	18317473	0.97	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317440	18317473	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317474	18317573	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317574	18317689	0.94	+	2	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317574	18317689	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18317690	18317802	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18317803	18318086	0.95	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18317803	18318086	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318087	18318161	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18318162	18318291	1	+	1	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18318162	18318291	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318292	18318371	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18318372	18318767	0.72	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18318372	18318767	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318768	18318912	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18318913	18318961	0.62	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18318913	18318961	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18318962	18319057	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18319058	18319084	0.71	+	2	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18319058	18319084	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	intron	18319085	18319172	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	CDS	18319173	18319297	0.69	+	2	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	exon	18319173	18319297	.	+	.	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
Phchi.S3	AUGUSTUS	stop_codon	18319298	18319300	.	+	0	transcript_id "Phchi.S3G262500.t2"; gene_id "Phchi.S3G262500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1958.t1 is derived from g8878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4023431	4024490	.	-	.	Phchi.S5G056700
Phchi.S5	AUGUSTUS	transcript	4023431	4024490	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	stop_codon	4023428	4023430	.	-	0	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	CDS	4023431	4023706	1	-	0	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	exon	4023431	4023706	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	intron	4023707	4023798	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	CDS	4023799	4023936	1	-	0	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	exon	4023799	4023936	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	intron	4023937	4024046	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	CDS	4024047	4024190	1	-	0	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	exon	4024047	4024190	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	intron	4024191	4024268	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	CDS	4024269	4024490	1	-	0	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	exon	4024269	4024490	.	-	.	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
Phchi.S5	AUGUSTUS	start_codon	4024488	4024490	.	-	0	transcript_id "Phchi.S5G056700.t1"; gene_id "Phchi.S5G056700"
# This transcript jg6893.t2 is derived from g4065.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6894.t1 is derived from g4066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25867305	25868385	.	+	.	Phchi.S1G405300
Phchi.S1	AUGUSTUS	transcript	25867305	25868385	.	+	.	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	start_codon	25867305	25867307	.	+	0	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	CDS	25867305	25867499	0.39	+	0	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	exon	25867305	25867499	.	+	.	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	intron	25867500	25867590	.	+	.	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	CDS	25867591	25867656	0.91	+	0	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	exon	25867591	25867656	.	+	.	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	intron	25867657	25867839	.	+	.	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	CDS	25867840	25868385	0.55	+	0	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	exon	25867840	25868385	.	+	.	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
Phchi.S1	AUGUSTUS	stop_codon	25868386	25868388	.	+	0	transcript_id "Phchi.S1G405300.t1"; gene_id "Phchi.S1G405300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10398.t1 is derived from g7574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47543702	47544272	.	+	.	Phchi.S1G755700
Phchi.S1	AUGUSTUS	transcript	47543702	47544272	.	+	.	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	start_codon	47543702	47543704	.	+	0	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	CDS	47543702	47543855	0.93	+	0	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	exon	47543702	47543855	.	+	.	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	intron	47543856	47543952	.	+	.	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	CDS	47543953	47544020	0.94	+	2	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	exon	47543953	47544020	.	+	.	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	intron	47544021	47544086	.	+	.	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	CDS	47544087	47544272	0.35	+	0	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	exon	47544087	47544272	.	+	.	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
Phchi.S1	AUGUSTUS	stop_codon	47544273	47544275	.	+	0	transcript_id "Phchi.S1G755700.t1"; gene_id "Phchi.S1G755700"
# This transcript jg3822.t2 is derived from g991.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3823.t1 is derived from g992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5894099	5896717	.	+	.	Phchi.S1G098200
Phchi.S1	AUGUSTUS	transcript	5894099	5896717	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	start_codon	5894099	5894101	.	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5894099	5894294	0.48	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5894099	5894294	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5894295	5894632	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5894633	5894718	0.99	+	2	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5894633	5894718	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5894719	5894836	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5894837	5894975	1	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5894837	5894975	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5894976	5895082	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5895083	5895171	1	+	2	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5895083	5895171	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5895172	5895302	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5895303	5895504	1	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5895303	5895504	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5895505	5895828	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5895829	5896091	0.97	+	2	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5895829	5896091	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5896092	5896175	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5896176	5896253	0.94	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5896176	5896253	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5896254	5896418	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5896419	5896580	0.41	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5896419	5896580	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	intron	5896581	5896696	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	CDS	5896697	5896717	0.77	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	exon	5896697	5896717	.	+	.	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
Phchi.S1	AUGUSTUS	stop_codon	5896718	5896720	.	+	0	transcript_id "Phchi.S1G098200.t1"; gene_id "Phchi.S1G098200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10275.t1 is derived from g7451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46788126	46790741	.	-	.	Phchi.S1G743400
Phchi.S1	AUGUSTUS	transcript	46788126	46790741	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	stop_codon	46788123	46788125	.	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46788126	46788263	0.45	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46788126	46788263	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46788264	46788362	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46788363	46788599	0.43	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46788363	46788599	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46788600	46788835	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46788836	46788886	0.67	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46788836	46788886	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46788887	46789012	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46789013	46789123	0.7	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46789013	46789123	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46789124	46789279	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46789280	46789357	1	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46789280	46789357	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46789358	46789437	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46789438	46789506	1	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46789438	46789506	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46789507	46789675	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46789676	46789775	1	-	1	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46789676	46789775	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46789776	46789988	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46789989	46790102	1	-	1	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46789989	46790102	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	intron	46790103	46790196	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	CDS	46790197	46790741	0.99	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	exon	46790197	46790741	.	-	.	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
Phchi.S1	AUGUSTUS	start_codon	46790739	46790741	.	-	0	transcript_id "Phchi.S1G743400.t1"; gene_id "Phchi.S1G743400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12859.t1 is derived from g11324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2758691	2759251	.	+	.	Phchi.S3G017800
Phchi.S3	AUGUSTUS	transcript	2758691	2759251	.	+	.	transcript_id "Phchi.S3G017800.t1"; gene_id "Phchi.S3G017800"
Phchi.S3	AUGUSTUS	start_codon	2758691	2758693	.	+	0	transcript_id "Phchi.S3G017800.t1"; gene_id "Phchi.S3G017800"
Phchi.S3	AUGUSTUS	CDS	2758691	2759251	1	+	0	transcript_id "Phchi.S3G017800.t1"; gene_id "Phchi.S3G017800"
Phchi.S3	AUGUSTUS	exon	2758691	2759251	.	+	.	transcript_id "Phchi.S3G017800.t1"; gene_id "Phchi.S3G017800"
Phchi.S3	AUGUSTUS	stop_codon	2759252	2759254	.	+	0	transcript_id "Phchi.S3G017800.t1"; gene_id "Phchi.S3G017800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2263.t1 is derived from g9183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5724470	5725182	.	-	.	Phchi.S5G087200
Phchi.S5	AUGUSTUS	transcript	5724470	5725182	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	stop_codon	5724467	5724469	.	-	0	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	CDS	5724470	5724533	0.73	-	1	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	exon	5724470	5724533	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	intron	5724534	5724692	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	CDS	5724693	5724769	0.99	-	0	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	exon	5724693	5724769	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	intron	5724770	5724842	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	CDS	5724843	5724997	0.99	-	2	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	exon	5724843	5724997	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	intron	5724998	5725142	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	CDS	5725143	5725182	0.79	-	0	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	exon	5725143	5725182	.	-	.	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
Phchi.S5	AUGUSTUS	start_codon	5725180	5725182	.	-	0	transcript_id "Phchi.S5G087200.t1"; gene_id "Phchi.S5G087200"
# This transcript jg9343.t2 is derived from g6518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9343.t3 is derived from g6518.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9344.t1 is derived from g6519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41064611	41065168	.	+	.	Phchi.S1G650300
Phchi.S1	AUGUSTUS	transcript	41064611	41065168	.	+	.	transcript_id "Phchi.S1G650300.t1"; gene_id "Phchi.S1G650300"
Phchi.S1	AUGUSTUS	start_codon	41064611	41064613	.	+	0	transcript_id "Phchi.S1G650300.t1"; gene_id "Phchi.S1G650300"
Phchi.S1	AUGUSTUS	CDS	41064611	41065168	0.71	+	0	transcript_id "Phchi.S1G650300.t1"; gene_id "Phchi.S1G650300"
Phchi.S1	AUGUSTUS	exon	41064611	41065168	.	+	.	transcript_id "Phchi.S1G650300.t1"; gene_id "Phchi.S1G650300"
Phchi.S1	AUGUSTUS	stop_codon	41065169	41065171	.	+	0	transcript_id "Phchi.S1G650300.t1"; gene_id "Phchi.S1G650300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6720.t1 is derived from g3892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24708752	24710655	.	-	.	Phchi.S1G387900
Phchi.S1	AUGUSTUS	transcript	24708752	24710655	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	stop_codon	24708749	24708751	.	-	0	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	CDS	24708752	24708907	0.84	-	0	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	exon	24708752	24708907	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	intron	24708908	24708987	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	CDS	24708988	24709236	0.7	-	0	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	exon	24708988	24709236	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	intron	24709237	24709319	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	CDS	24709320	24710271	0.78	-	1	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	exon	24709320	24710271	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	intron	24710272	24710422	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	CDS	24710423	24710655	0.35	-	0	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	exon	24710423	24710655	.	-	.	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
Phchi.S1	AUGUSTUS	start_codon	24710653	24710655	.	-	0	transcript_id "Phchi.S1G387900.t1"; gene_id "Phchi.S1G387900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15742.t1 is derived from g14212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21024233	21024919	.	-	.	Phchi.S3G306100
Phchi.S3	AUGUSTUS	transcript	21024233	21024919	.	-	.	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	stop_codon	21024230	21024232	.	-	0	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	CDS	21024233	21024511	1	-	0	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	exon	21024233	21024511	.	-	.	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	intron	21024512	21024676	.	-	.	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	CDS	21024677	21024919	1	-	0	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	exon	21024677	21024919	.	-	.	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
Phchi.S3	AUGUSTUS	start_codon	21024917	21024919	.	-	0	transcript_id "Phchi.S3G306100.t1"; gene_id "Phchi.S3G306100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1993.t1 is derived from g8913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4341253	4341504	.	-	.	Phchi.S5G060200
Phchi.S5	AUGUSTUS	transcript	4341253	4341504	.	-	.	transcript_id "Phchi.S5G060200.t1"; gene_id "Phchi.S5G060200"
Phchi.S5	AUGUSTUS	stop_codon	4341250	4341252	.	-	0	transcript_id "Phchi.S5G060200.t1"; gene_id "Phchi.S5G060200"
Phchi.S5	AUGUSTUS	CDS	4341253	4341504	0.99	-	0	transcript_id "Phchi.S5G060200.t1"; gene_id "Phchi.S5G060200"
Phchi.S5	AUGUSTUS	exon	4341253	4341504	.	-	.	transcript_id "Phchi.S5G060200.t1"; gene_id "Phchi.S5G060200"
Phchi.S5	AUGUSTUS	start_codon	4341502	4341504	.	-	0	transcript_id "Phchi.S5G060200.t1"; gene_id "Phchi.S5G060200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1184.t1 is derived from g10967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8334051	8334578	.	-	.	Phchi.S6G114300
Phchi.S6	AUGUSTUS	transcript	8334051	8334578	.	-	.	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	stop_codon	8334048	8334050	.	-	0	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	CDS	8334051	8334258	0.7	-	1	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	exon	8334051	8334258	.	-	.	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	intron	8334259	8334399	.	-	.	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	CDS	8334400	8334578	0.99	-	0	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	exon	8334400	8334578	.	-	.	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
Phchi.S6	AUGUSTUS	start_codon	8334576	8334578	.	-	0	transcript_id "Phchi.S6G114300.t1"; gene_id "Phchi.S6G114300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4984.t1 is derived from g2154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13884256	13886478	.	+	.	Phchi.S1G214300
Phchi.S1	AUGUSTUS	transcript	13884256	13886478	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	start_codon	13884256	13884258	.	+	0	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	CDS	13884256	13884324	0.99	+	0	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	exon	13884256	13884324	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	intron	13884325	13884408	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	CDS	13884409	13884637	0.79	+	0	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	exon	13884409	13884637	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	intron	13884638	13884877	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	CDS	13884878	13884963	0.76	+	2	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	exon	13884878	13884963	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	intron	13884964	13885125	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	CDS	13885126	13885269	0.46	+	0	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	exon	13885126	13885269	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	intron	13885270	13885431	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	CDS	13885432	13886478	0.39	+	0	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	exon	13885432	13886478	.	+	.	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
Phchi.S1	AUGUSTUS	stop_codon	13886479	13886481	.	+	0	transcript_id "Phchi.S1G214300.t1"; gene_id "Phchi.S1G214300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg937.t1 is derived from g10719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6510358	6513362	.	-	.	Phchi.S6G089600
Phchi.S6	AUGUSTUS	transcript	6510358	6513362	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	stop_codon	6510355	6510357	.	-	0	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	CDS	6510358	6512376	1	-	0	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	exon	6510358	6512376	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	intron	6512377	6512513	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	CDS	6512514	6512765	1	-	0	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	exon	6512514	6512765	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	intron	6512766	6512871	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	CDS	6512872	6513041	0.81	-	2	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	exon	6512872	6513041	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	intron	6513042	6513154	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	CDS	6513155	6513362	0.81	-	0	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	exon	6513155	6513362	.	-	.	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
Phchi.S6	AUGUSTUS	start_codon	6513360	6513362	.	-	0	transcript_id "Phchi.S6G089600.t1"; gene_id "Phchi.S6G089600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2029.t1 is derived from g8949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4521107	4521880	.	-	.	Phchi.S5G063800
Phchi.S5	AUGUSTUS	transcript	4521107	4521880	.	-	.	transcript_id "Phchi.S5G063800.t1"; gene_id "Phchi.S5G063800"
Phchi.S5	AUGUSTUS	stop_codon	4521104	4521106	.	-	0	transcript_id "Phchi.S5G063800.t1"; gene_id "Phchi.S5G063800"
Phchi.S5	AUGUSTUS	CDS	4521107	4521880	1	-	0	transcript_id "Phchi.S5G063800.t1"; gene_id "Phchi.S5G063800"
Phchi.S5	AUGUSTUS	exon	4521107	4521880	.	-	.	transcript_id "Phchi.S5G063800.t1"; gene_id "Phchi.S5G063800"
Phchi.S5	AUGUSTUS	start_codon	4521878	4521880	.	-	0	transcript_id "Phchi.S5G063800.t1"; gene_id "Phchi.S5G063800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15483.t1 is derived from g13951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19418564	19419115	.	+	.	Phchi.S3G280200
Phchi.S3	AUGUSTUS	transcript	19418564	19419115	.	+	.	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	start_codon	19418564	19418566	.	+	0	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	CDS	19418564	19418657	0.97	+	0	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	exon	19418564	19418657	.	+	.	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	intron	19418658	19418798	.	+	.	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	CDS	19418799	19419115	0.81	+	2	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	exon	19418799	19419115	.	+	.	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
Phchi.S3	AUGUSTUS	stop_codon	19419116	19419118	.	+	0	transcript_id "Phchi.S3G280200.t1"; gene_id "Phchi.S3G280200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6660.t1 is derived from g3832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24356273	24356806	.	+	.	Phchi.S1G381900
Phchi.S1	AUGUSTUS	transcript	24356273	24356806	.	+	.	transcript_id "Phchi.S1G381900.t1"; gene_id "Phchi.S1G381900"
Phchi.S1	AUGUSTUS	start_codon	24356273	24356275	.	+	0	transcript_id "Phchi.S1G381900.t1"; gene_id "Phchi.S1G381900"
Phchi.S1	AUGUSTUS	CDS	24356273	24356806	0.94	+	0	transcript_id "Phchi.S1G381900.t1"; gene_id "Phchi.S1G381900"
Phchi.S1	AUGUSTUS	exon	24356273	24356806	.	+	.	transcript_id "Phchi.S1G381900.t1"; gene_id "Phchi.S1G381900"
Phchi.S1	AUGUSTUS	stop_codon	24356807	24356809	.	+	0	transcript_id "Phchi.S1G381900.t1"; gene_id "Phchi.S1G381900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12653.t1 is derived from g14452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	5701	7533	.	-	.	Phchi.C12G000300
Phchi.C12	AUGUSTUS	transcript	5701	7533	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	stop_codon	5698	5700	.	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	5701	5862	0.99	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	5701	5862	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	intron	5863	5977	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	5978	6075	0.47	-	2	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	5978	6075	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	intron	6076	6180	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	6181	6247	0.5	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	6181	6247	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	intron	6248	6341	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	6342	6470	1	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	6342	6470	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	intron	6471	6558	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	6559	6702	0.96	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	6559	6702	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	intron	6703	6788	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	6789	6962	0.95	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	6789	6962	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	intron	6963	7215	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	CDS	7216	7533	0.53	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	exon	7216	7533	.	-	.	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
Phchi.C12	AUGUSTUS	start_codon	7531	7533	.	-	0	transcript_id "Phchi.C12G000300.t1"; gene_id "Phchi.C12G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11572.t1 is derived from g15623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7133706	7134656	.	+	.	Phchi.S4G115400
Phchi.S4	AUGUSTUS	transcript	7133706	7134656	.	+	.	transcript_id "Phchi.S4G115400.t1"; gene_id "Phchi.S4G115400"
Phchi.S4	AUGUSTUS	start_codon	7133706	7133708	.	+	0	transcript_id "Phchi.S4G115400.t1"; gene_id "Phchi.S4G115400"
Phchi.S4	AUGUSTUS	CDS	7133706	7134656	0.92	+	0	transcript_id "Phchi.S4G115400.t1"; gene_id "Phchi.S4G115400"
Phchi.S4	AUGUSTUS	exon	7133706	7134656	.	+	.	transcript_id "Phchi.S4G115400.t1"; gene_id "Phchi.S4G115400"
Phchi.S4	AUGUSTUS	stop_codon	7134657	7134659	.	+	0	transcript_id "Phchi.S4G115400.t1"; gene_id "Phchi.S4G115400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2304.t1 is derived from g9224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5952922	5957209	.	-	.	Phchi.S5G091300
Phchi.S5	AUGUSTUS	transcript	5952922	5957209	.	-	.	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	stop_codon	5952919	5952921	.	-	0	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	CDS	5952922	5953561	0.44	-	1	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	exon	5952922	5953561	.	-	.	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	intron	5953562	5953697	.	-	.	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	CDS	5953698	5953758	0.38	-	2	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	exon	5953698	5953758	.	-	.	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	intron	5953759	5953842	.	-	.	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	CDS	5953843	5957209	0.7	-	0	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	exon	5953843	5957209	.	-	.	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
Phchi.S5	AUGUSTUS	start_codon	5957207	5957209	.	-	0	transcript_id "Phchi.S5G091300.t1"; gene_id "Phchi.S5G091300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6742.t1 is derived from g3914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24808590	24809448	.	+	.	Phchi.S1G390100
Phchi.S1	AUGUSTUS	transcript	24808590	24809448	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	start_codon	24808590	24808592	.	+	0	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	CDS	24808590	24808592	1	+	0	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	exon	24808590	24808592	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	intron	24808593	24808718	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	CDS	24808719	24808820	1	+	0	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	exon	24808719	24808820	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	intron	24808821	24808943	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	CDS	24808944	24809073	1	+	0	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	exon	24808944	24809073	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	intron	24809074	24809192	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	CDS	24809193	24809305	1	+	2	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	exon	24809193	24809305	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	intron	24809306	24809397	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	CDS	24809398	24809448	1	+	0	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	exon	24809398	24809448	.	+	.	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
Phchi.S1	AUGUSTUS	stop_codon	24809449	24809451	.	+	0	transcript_id "Phchi.S1G390100.t1"; gene_id "Phchi.S1G390100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg370.t1 is derived from g10152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2689457	2691560	.	+	.	Phchi.S6G032900
Phchi.S6	AUGUSTUS	transcript	2689457	2691560	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	start_codon	2689457	2689459	.	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2689457	2689606	0.48	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2689457	2689606	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2689607	2689882	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2689883	2689909	1	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2689883	2689909	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2689910	2690100	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2690101	2690186	1	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2690101	2690186	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2690187	2690379	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2690380	2690587	1	+	1	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2690380	2690587	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2690588	2690683	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2690684	2690798	1	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2690684	2690798	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2690799	2690932	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2690933	2691117	1	+	2	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2690933	2691117	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2691118	2691216	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2691217	2691351	1	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2691217	2691351	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	intron	2691352	2691464	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	CDS	2691465	2691560	1	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	exon	2691465	2691560	.	+	.	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
Phchi.S6	AUGUSTUS	stop_codon	2691561	2691563	.	+	0	transcript_id "Phchi.S6G032900.t1"; gene_id "Phchi.S6G032900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14327.t1 is derived from g12794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12106581	12107753	.	+	.	Phchi.S3G164600
Phchi.S3	AUGUSTUS	transcript	12106581	12107753	.	+	.	transcript_id "Phchi.S3G164600.t1"; gene_id "Phchi.S3G164600"
Phchi.S3	AUGUSTUS	start_codon	12106581	12106583	.	+	0	transcript_id "Phchi.S3G164600.t1"; gene_id "Phchi.S3G164600"
Phchi.S3	AUGUSTUS	CDS	12106581	12107753	0.62	+	0	transcript_id "Phchi.S3G164600.t1"; gene_id "Phchi.S3G164600"
Phchi.S3	AUGUSTUS	exon	12106581	12107753	.	+	.	transcript_id "Phchi.S3G164600.t1"; gene_id "Phchi.S3G164600"
Phchi.S3	AUGUSTUS	stop_codon	12107754	12107756	.	+	0	transcript_id "Phchi.S3G164600.t1"; gene_id "Phchi.S3G164600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3038.t1 is derived from g207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1271826	1275049	.	+	.	Phchi.S1G019700
Phchi.S1	AUGUSTUS	transcript	1271826	1275049	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	start_codon	1271826	1271828	.	+	0	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	CDS	1271826	1272069	0.83	+	0	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	exon	1271826	1272069	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	intron	1272070	1272152	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	CDS	1272153	1273086	0.94	+	2	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	exon	1272153	1273086	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	intron	1273087	1273219	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	CDS	1273220	1273307	0.98	+	1	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	exon	1273220	1273307	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	intron	1273308	1273387	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	CDS	1273388	1275049	0.6	+	0	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	exon	1273388	1275049	.	+	.	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
Phchi.S1	AUGUSTUS	stop_codon	1275050	1275052	.	+	0	transcript_id "Phchi.S1G019700.t1"; gene_id "Phchi.S1G019700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12151.t1 is derived from g7827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4958857	4962537	.	+	.	Phchi.S2G023100
Phchi.S2	AUGUSTUS	transcript	4958857	4962537	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	start_codon	4958857	4958859	.	+	0	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4958857	4960080	0.31	+	0	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4958857	4960080	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	intron	4960081	4960190	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4960191	4960551	0.35	+	0	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4960191	4960551	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	intron	4960552	4960781	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4960782	4961416	0.77	+	2	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4960782	4961416	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	intron	4961417	4961509	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4961510	4961640	1	+	0	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4961510	4961640	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	intron	4961641	4961885	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4961886	4962002	1	+	1	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4961886	4962002	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	intron	4962003	4962091	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4962092	4962233	1	+	1	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4962092	4962233	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	intron	4962234	4962330	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	CDS	4962331	4962537	1	+	0	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	exon	4962331	4962537	.	+	.	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
Phchi.S2	AUGUSTUS	stop_codon	4962538	4962540	.	+	0	transcript_id "Phchi.S2G023100.t1"; gene_id "Phchi.S2G023100"
# This transcript jg7164.t2 is derived from g4336.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7165.t1 is derived from g4337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27354322	27356456	.	-	.	Phchi.S1G432400
Phchi.S1	AUGUSTUS	transcript	27354322	27356456	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	stop_codon	27354319	27354321	.	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27354322	27354459	0.86	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27354322	27354459	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27354460	27354546	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27354547	27354657	1	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27354547	27354657	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27354658	27354754	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27354755	27354853	1	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27354755	27354853	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27354854	27354939	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27354940	27355096	1	-	1	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27354940	27355096	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27355097	27355182	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27355183	27355346	1	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27355183	27355346	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27355347	27355481	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27355482	27355544	1	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27355482	27355544	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27355545	27355635	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27355636	27355860	1	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27355636	27355860	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27355861	27356059	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27356060	27356157	1	-	2	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27356060	27356157	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	intron	27356158	27356326	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	CDS	27356327	27356456	1	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	exon	27356327	27356456	.	-	.	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
Phchi.S1	AUGUSTUS	start_codon	27356454	27356456	.	-	0	transcript_id "Phchi.S1G432400.t1"; gene_id "Phchi.S1G432400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7344.t1 is derived from g4516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28629839	28631572	.	-	.	Phchi.S1G450300
Phchi.S1	AUGUSTUS	transcript	28629839	28631572	.	-	.	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	stop_codon	28629836	28629838	.	-	0	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	CDS	28629839	28630303	0.39	-	0	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	exon	28629839	28630303	.	-	.	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	intron	28630304	28630434	.	-	.	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	CDS	28630435	28631054	1	-	2	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	exon	28630435	28631054	.	-	.	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	intron	28631055	28631136	.	-	.	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	CDS	28631137	28631572	1	-	0	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	exon	28631137	28631572	.	-	.	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
Phchi.S1	AUGUSTUS	start_codon	28631570	28631572	.	-	0	transcript_id "Phchi.S1G450300.t1"; gene_id "Phchi.S1G450300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15038.t1 is derived from g13506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16683902	16685552	.	+	.	Phchi.S3G235700
Phchi.S3	AUGUSTUS	transcript	16683902	16685552	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	start_codon	16683902	16683904	.	+	0	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	CDS	16683902	16684106	0.91	+	0	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	exon	16683902	16684106	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	intron	16684107	16684280	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	CDS	16684281	16684565	1	+	2	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	exon	16684281	16684565	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	intron	16684566	16684667	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	CDS	16684668	16685034	0.98	+	2	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	exon	16684668	16685034	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	intron	16685035	16685121	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	CDS	16685122	16685332	1	+	1	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	exon	16685122	16685332	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	intron	16685333	16685417	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	CDS	16685418	16685552	1	+	0	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	exon	16685418	16685552	.	+	.	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
Phchi.S3	AUGUSTUS	stop_codon	16685553	16685555	.	+	0	transcript_id "Phchi.S3G235700.t1"; gene_id "Phchi.S3G235700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13568.t1 is derived from g12035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7534394	7537040	.	-	.	Phchi.S3G088700
Phchi.S3	AUGUSTUS	transcript	7534394	7537040	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	stop_codon	7534391	7534393	.	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7534394	7534478	0.29	-	1	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7534394	7534478	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7534479	7534603	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7534604	7534783	1	-	1	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7534604	7534783	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7534784	7534868	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7534869	7534939	1	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7534869	7534939	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7534940	7535030	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7535031	7535199	1	-	1	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7535031	7535199	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7535200	7535389	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7535390	7535462	1	-	2	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7535390	7535462	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7535463	7535596	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7535597	7535636	1	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7535597	7535636	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7535637	7535742	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7535743	7535815	1	-	1	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7535743	7535815	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7535816	7535930	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7535931	7536001	1	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7535931	7536001	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7536002	7536116	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7536117	7536222	0.99	-	1	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7536117	7536222	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7536223	7536355	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7536356	7536378	1	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7536356	7536378	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7536379	7536480	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7536481	7536567	0.99	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7536481	7536567	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7536568	7536751	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7536752	7536890	1	-	1	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7536752	7536890	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	intron	7536891	7536984	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	CDS	7536985	7537040	0.97	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	exon	7536985	7537040	.	-	.	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
Phchi.S3	AUGUSTUS	start_codon	7537038	7537040	.	-	0	transcript_id "Phchi.S3G088700.t1"; gene_id "Phchi.S3G088700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5181.t1 is derived from g2351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15368390	15368714	.	-	.	Phchi.S1G234000
Phchi.S1	AUGUSTUS	transcript	15368390	15368714	.	-	.	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	stop_codon	15368387	15368389	.	-	0	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	CDS	15368390	15368433	0.37	-	2	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	exon	15368390	15368433	.	-	.	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	intron	15368434	15368542	.	-	.	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	CDS	15368543	15368714	0.44	-	0	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	exon	15368543	15368714	.	-	.	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
Phchi.S1	AUGUSTUS	start_codon	15368712	15368714	.	-	0	transcript_id "Phchi.S1G234000.t1"; gene_id "Phchi.S1G234000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5209.t1 is derived from g2379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15482894	15484749	.	-	.	Phchi.S1G236800
Phchi.S1	AUGUSTUS	transcript	15482894	15484749	.	-	.	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	stop_codon	15482891	15482893	.	-	0	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	CDS	15482894	15482906	0.47	-	1	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	exon	15482894	15482906	.	-	.	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	intron	15482907	15482989	.	-	.	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	CDS	15482990	15483193	0.17	-	1	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	exon	15482990	15483193	.	-	.	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	intron	15483194	15483439	.	-	.	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	CDS	15483440	15484749	0.41	-	0	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	exon	15483440	15484749	.	-	.	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
Phchi.S1	AUGUSTUS	start_codon	15484747	15484749	.	-	0	transcript_id "Phchi.S1G236800.t1"; gene_id "Phchi.S1G236800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2154.t1 is derived from g9074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5090631	5092359	.	+	.	Phchi.S5G076300
Phchi.S5	AUGUSTUS	transcript	5091179	5092359	.	+	.	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	start_codon	5091179	5091181	.	+	0	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5091179	5091247	0.38	+	0	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5091179	5091247	.	+	.	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	intron	5091248	5091402	.	+	.	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5091403	5091552	1	+	0	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5091403	5091552	.	+	.	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	intron	5091553	5091630	.	+	.	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5091631	5092359	1	+	0	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5091631	5092359	.	+	.	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	stop_codon	5092360	5092362	.	+	0	transcript_id "Phchi.S5G076300.t1"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	transcript	5090631	5092359	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	start_codon	5090631	5090633	.	+	0	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5090631	5091076	0.91	+	0	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5090631	5091076	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	intron	5091077	5091199	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5091200	5091247	0.69	+	1	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5091200	5091247	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	intron	5091248	5091407	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5091408	5091552	0.95	+	1	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5091408	5091552	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	intron	5091553	5091630	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	CDS	5091631	5092359	1	+	0	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	exon	5091631	5092359	.	+	.	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
Phchi.S5	AUGUSTUS	stop_codon	5092360	5092362	.	+	0	transcript_id "Phchi.S5G076300.t2"; gene_id "Phchi.S5G076300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13634.t1 is derived from g12101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7845583	7847934	.	-	.	Phchi.S3G095300
Phchi.S3	AUGUSTUS	transcript	7845583	7847934	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	stop_codon	7845580	7845582	.	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7845583	7845657	1	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7845583	7845657	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7845658	7845735	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7845736	7845777	1	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7845736	7845777	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7845778	7845876	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7845877	7846008	1	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7845877	7846008	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846009	7846093	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846094	7846160	1	-	1	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846094	7846160	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846161	7846288	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846289	7846480	1	-	1	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846289	7846480	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846481	7846591	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846592	7846693	1	-	1	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846592	7846693	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846694	7846810	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846811	7846932	1	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846811	7846932	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846933	7847007	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7847008	7847094	1	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7847008	7847094	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7847095	7847186	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7847187	7847726	0.67	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7847187	7847726	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7847727	7847829	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7847830	7847934	0.35	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7847830	7847934	.	-	.	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	start_codon	7847932	7847934	.	-	0	transcript_id "Phchi.S3G095300.t1"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	transcript	7845583	7847934	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	stop_codon	7845580	7845582	.	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7845583	7845657	1	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7845583	7845657	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7845658	7845735	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7845736	7845777	1	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7845736	7845777	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7845778	7845876	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7845877	7846008	1	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7845877	7846008	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846009	7846093	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846094	7846160	1	-	1	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846094	7846160	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846161	7846288	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846289	7846480	1	-	1	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846289	7846480	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846481	7846659	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846660	7846693	0.35	-	2	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846660	7846693	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846694	7846810	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7846811	7846922	0.57	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7846811	7846922	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7846923	7847007	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7847008	7847094	1	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7847008	7847094	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7847095	7847186	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7847187	7847726	0.65	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7847187	7847726	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	intron	7847727	7847829	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	CDS	7847830	7847934	0.32	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	exon	7847830	7847934	.	-	.	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
Phchi.S3	AUGUSTUS	start_codon	7847932	7847934	.	-	0	transcript_id "Phchi.S3G095300.t2"; gene_id "Phchi.S3G095300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12029.t1 is derived from g7704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	645757	647393	.	+	.	Phchi.S2G010900
Phchi.S2	AUGUSTUS	transcript	645757	647393	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	start_codon	645757	645759	.	+	0	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	645757	645820	0.9	+	0	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	645757	645820	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	645821	646293	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646294	646327	1	+	2	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646294	646327	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	646328	646469	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646470	646671	1	+	1	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646470	646671	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	646672	646883	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646884	647243	1	+	0	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646884	647243	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	647244	647318	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	647319	647393	1	+	0	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	647319	647393	.	+	.	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	stop_codon	647394	647396	.	+	0	transcript_id "Phchi.S2G010900.t1"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	transcript	646229	647393	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	start_codon	646229	646231	.	+	0	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646229	646253	0.46	+	0	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646229	646253	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	646254	646350	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646351	646369	0.69	+	2	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646351	646369	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	646370	646469	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646470	646671	1	+	1	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646470	646671	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	646672	646883	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	646884	647243	1	+	0	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	646884	647243	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	intron	647244	647318	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	CDS	647319	647393	1	+	0	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	exon	647319	647393	.	+	.	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
Phchi.S2	AUGUSTUS	stop_codon	647394	647396	.	+	0	transcript_id "Phchi.S2G010900.t2"; gene_id "Phchi.S2G010900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7677.t1 is derived from g4851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30586637	30587005	.	+	.	Phchi.S1G483600
Phchi.S1	AUGUSTUS	transcript	30586637	30587005	.	+	.	transcript_id "Phchi.S1G483600.t1"; gene_id "Phchi.S1G483600"
Phchi.S1	AUGUSTUS	start_codon	30586637	30586639	.	+	0	transcript_id "Phchi.S1G483600.t1"; gene_id "Phchi.S1G483600"
Phchi.S1	AUGUSTUS	CDS	30586637	30587005	1	+	0	transcript_id "Phchi.S1G483600.t1"; gene_id "Phchi.S1G483600"
Phchi.S1	AUGUSTUS	exon	30586637	30587005	.	+	.	transcript_id "Phchi.S1G483600.t1"; gene_id "Phchi.S1G483600"
Phchi.S1	AUGUSTUS	stop_codon	30587006	30587008	.	+	0	transcript_id "Phchi.S1G483600.t1"; gene_id "Phchi.S1G483600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11310.t1 is derived from g15360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5314519	5318040	.	+	.	Phchi.S4G089200
Phchi.S4	AUGUSTUS	transcript	5314519	5318040	.	+	.	transcript_id "Phchi.S4G089200.t1"; gene_id "Phchi.S4G089200"
Phchi.S4	AUGUSTUS	start_codon	5314519	5314521	.	+	0	transcript_id "Phchi.S4G089200.t1"; gene_id "Phchi.S4G089200"
Phchi.S4	AUGUSTUS	CDS	5314519	5318040	0.99	+	0	transcript_id "Phchi.S4G089200.t1"; gene_id "Phchi.S4G089200"
Phchi.S4	AUGUSTUS	exon	5314519	5318040	.	+	.	transcript_id "Phchi.S4G089200.t1"; gene_id "Phchi.S4G089200"
Phchi.S4	AUGUSTUS	stop_codon	5318041	5318043	.	+	0	transcript_id "Phchi.S4G089200.t1"; gene_id "Phchi.S4G089200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5326.t1 is derived from g2496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16302314	16304569	.	-	.	Phchi.S1G248500
Phchi.S1	AUGUSTUS	transcript	16302314	16304569	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	stop_codon	16302311	16302313	.	-	0	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	CDS	16302314	16302843	0.87	-	2	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	exon	16302314	16302843	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	intron	16302844	16302933	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	CDS	16302934	16303052	0.59	-	1	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	exon	16302934	16303052	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	intron	16303053	16303499	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	CDS	16303500	16303723	0.26	-	0	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	exon	16303500	16303723	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	intron	16303724	16304197	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	CDS	16304198	16304569	0.46	-	0	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	exon	16304198	16304569	.	-	.	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
Phchi.S1	AUGUSTUS	start_codon	16304567	16304569	.	-	0	transcript_id "Phchi.S1G248500.t1"; gene_id "Phchi.S1G248500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5818.t1 is derived from g2988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19098102	19099559	.	-	.	Phchi.S1G297700
Phchi.S1	AUGUSTUS	transcript	19098102	19099559	.	-	.	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	stop_codon	19098099	19098101	.	-	0	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	CDS	19098102	19098248	0.84	-	0	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	exon	19098102	19098248	.	-	.	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	intron	19098249	19098328	.	-	.	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	CDS	19098329	19099039	0.77	-	0	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	exon	19098329	19099039	.	-	.	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	intron	19099040	19099184	.	-	.	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	CDS	19099185	19099559	0.98	-	0	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	exon	19099185	19099559	.	-	.	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
Phchi.S1	AUGUSTUS	start_codon	19099557	19099559	.	-	0	transcript_id "Phchi.S1G297700.t1"; gene_id "Phchi.S1G297700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5242.t1 is derived from g2412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15820490	15822616	.	-	.	Phchi.S1G240100
Phchi.S1	AUGUSTUS	transcript	15820490	15822616	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	stop_codon	15820487	15820489	.	-	0	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	CDS	15820490	15821115	0.98	-	2	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	exon	15820490	15821115	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	intron	15821116	15821218	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	CDS	15821219	15821489	0.37	-	0	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	exon	15821219	15821489	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	intron	15821490	15821587	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	CDS	15821588	15822020	0.32	-	1	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	exon	15821588	15822020	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	intron	15822021	15822099	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	CDS	15822100	15822201	1	-	1	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	exon	15822100	15822201	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	intron	15822202	15822290	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	CDS	15822291	15822616	0.98	-	0	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	exon	15822291	15822616	.	-	.	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
Phchi.S1	AUGUSTUS	start_codon	15822614	15822616	.	-	0	transcript_id "Phchi.S1G240100.t1"; gene_id "Phchi.S1G240100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7597.t1 is derived from g4771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30196115	30198032	.	-	.	Phchi.S1G475600
Phchi.S1	AUGUSTUS	transcript	30196115	30198032	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	stop_codon	30196112	30196114	.	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	CDS	30196115	30196519	0.97	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	exon	30196115	30196519	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	intron	30196520	30196621	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	CDS	30196622	30196750	0.9	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	exon	30196622	30196750	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	intron	30196751	30196833	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	CDS	30196834	30196968	1	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	exon	30196834	30196968	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	intron	30196969	30197188	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	CDS	30197189	30197464	1	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	exon	30197189	30197464	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	intron	30197465	30197530	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	CDS	30197531	30197737	1	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	exon	30197531	30197737	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	intron	30197738	30197837	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	CDS	30197838	30198032	0.64	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	exon	30197838	30198032	.	-	.	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
Phchi.S1	AUGUSTUS	start_codon	30198030	30198032	.	-	0	transcript_id "Phchi.S1G475600.t1"; gene_id "Phchi.S1G475600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11900.t1 is derived from g15952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9154177	9156661	.	-	.	Phchi.S4G148200
Phchi.S4	AUGUSTUS	transcript	9154177	9156661	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	stop_codon	9154174	9154176	.	-	0	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9154177	9154639	0.56	-	1	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9154177	9154639	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9154640	9154815	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9154816	9155211	0.3	-	1	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9154816	9155211	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9155212	9155300	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9155301	9155502	0.61	-	2	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9155301	9155502	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9155503	9155600	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9155601	9155830	1	-	1	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9155601	9155830	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9155831	9155972	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9155973	9156115	0.56	-	0	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9155973	9156115	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9156116	9156227	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9156228	9156336	0.56	-	1	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9156228	9156336	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9156337	9156433	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9156434	9156462	0.86	-	0	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9156434	9156462	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	intron	9156463	9156634	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	CDS	9156635	9156661	1	-	0	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	exon	9156635	9156661	.	-	.	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
Phchi.S4	AUGUSTUS	start_codon	9156659	9156661	.	-	0	transcript_id "Phchi.S4G148200.t1"; gene_id "Phchi.S4G148200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13661.t1 is derived from g12128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8048742	8052700	.	-	.	Phchi.S3G098000
Phchi.S3	AUGUSTUS	transcript	8048742	8052700	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	stop_codon	8048739	8048741	.	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8048742	8049128	0.76	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8048742	8049128	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8049129	8049221	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8049222	8049319	1	-	2	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8049222	8049319	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8049320	8049481	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8049482	8049630	0.99	-	1	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8049482	8049630	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8049631	8049744	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8049745	8050089	0.99	-	1	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8049745	8050089	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8050090	8050175	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8050176	8050312	1	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8050176	8050312	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8050313	8050443	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8050444	8050587	1	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8050444	8050587	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8050588	8050703	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8050704	8050842	1	-	1	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8050704	8050842	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8050843	8050980	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8050981	8051144	1	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8050981	8051144	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8051145	8051244	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8051245	8051347	1	-	1	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8051245	8051347	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8051348	8051425	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8051426	8051620	0.44	-	1	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8051426	8051620	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8051621	8051735	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8051736	8052012	0.96	-	2	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8051736	8052012	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8052013	8052121	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8052122	8052321	0.67	-	1	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8052122	8052321	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8052322	8052418	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8052419	8052555	1	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8052419	8052555	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	intron	8052556	8052646	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	CDS	8052647	8052700	0.81	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	exon	8052647	8052700	.	-	.	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
Phchi.S3	AUGUSTUS	start_codon	8052698	8052700	.	-	0	transcript_id "Phchi.S3G098000.t1"; gene_id "Phchi.S3G098000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10969.t1 is derived from g15019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3408028	3410476	.	-	.	Phchi.S4G055100
Phchi.S4	AUGUSTUS	transcript	3408028	3410476	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	stop_codon	3408025	3408027	.	-	0	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3408028	3408350	0.99	-	2	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3408028	3408350	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	intron	3408351	3408471	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3408472	3408706	1	-	0	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3408472	3408706	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	intron	3408707	3408815	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3408816	3409059	1	-	1	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3408816	3409059	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	intron	3409060	3409169	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3409170	3409291	0.97	-	0	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3409170	3409291	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	intron	3409292	3409398	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3409399	3409592	1	-	2	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3409399	3409592	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	intron	3409593	3409712	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3409713	3409800	1	-	0	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3409713	3409800	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	intron	3409801	3409975	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	CDS	3409976	3410476	0.31	-	0	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	exon	3409976	3410476	.	-	.	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
Phchi.S4	AUGUSTUS	start_codon	3410474	3410476	.	-	0	transcript_id "Phchi.S4G055100.t1"; gene_id "Phchi.S4G055100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11249.t1 is derived from g15299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5004351	5005328	.	+	.	Phchi.S4G083100
Phchi.S4	AUGUSTUS	transcript	5004351	5005328	.	+	.	transcript_id "Phchi.S4G083100.t1"; gene_id "Phchi.S4G083100"
Phchi.S4	AUGUSTUS	start_codon	5004351	5004353	.	+	0	transcript_id "Phchi.S4G083100.t1"; gene_id "Phchi.S4G083100"
Phchi.S4	AUGUSTUS	CDS	5004351	5005328	0.6	+	0	transcript_id "Phchi.S4G083100.t1"; gene_id "Phchi.S4G083100"
Phchi.S4	AUGUSTUS	exon	5004351	5005328	.	+	.	transcript_id "Phchi.S4G083100.t1"; gene_id "Phchi.S4G083100"
Phchi.S4	AUGUSTUS	stop_codon	5005329	5005331	.	+	0	transcript_id "Phchi.S4G083100.t1"; gene_id "Phchi.S4G083100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10580.t1 is derived from g14630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1048131	1049440	.	+	.	Phchi.S4G016200
Phchi.S4	AUGUSTUS	transcript	1048131	1049440	.	+	.	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	start_codon	1048131	1048133	.	+	0	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	CDS	1048131	1048880	0.65	+	0	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	exon	1048131	1048880	.	+	.	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	intron	1048881	1048978	.	+	.	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	CDS	1048979	1049440	1	+	0	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	exon	1048979	1049440	.	+	.	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
Phchi.S4	AUGUSTUS	stop_codon	1049441	1049443	.	+	0	transcript_id "Phchi.S4G016200.t1"; gene_id "Phchi.S4G016200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10847.t1 is derived from g14897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2461509	2462756	.	+	.	Phchi.S4G042900
Phchi.S4	AUGUSTUS	transcript	2461509	2462756	.	+	.	transcript_id "Phchi.S4G042900.t1"; gene_id "Phchi.S4G042900"
Phchi.S4	AUGUSTUS	start_codon	2461509	2461511	.	+	0	transcript_id "Phchi.S4G042900.t1"; gene_id "Phchi.S4G042900"
Phchi.S4	AUGUSTUS	CDS	2461509	2462756	1	+	0	transcript_id "Phchi.S4G042900.t1"; gene_id "Phchi.S4G042900"
Phchi.S4	AUGUSTUS	exon	2461509	2462756	.	+	.	transcript_id "Phchi.S4G042900.t1"; gene_id "Phchi.S4G042900"
Phchi.S4	AUGUSTUS	stop_codon	2462757	2462759	.	+	0	transcript_id "Phchi.S4G042900.t1"; gene_id "Phchi.S4G042900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4519.t1 is derived from g1689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10924415	10925584	.	-	.	Phchi.S1G167800
Phchi.S1	AUGUSTUS	transcript	10924415	10925584	.	-	.	transcript_id "Phchi.S1G167800.t1"; gene_id "Phchi.S1G167800"
Phchi.S1	AUGUSTUS	stop_codon	10924412	10924414	.	-	0	transcript_id "Phchi.S1G167800.t1"; gene_id "Phchi.S1G167800"
Phchi.S1	AUGUSTUS	CDS	10924415	10925584	1	-	0	transcript_id "Phchi.S1G167800.t1"; gene_id "Phchi.S1G167800"
Phchi.S1	AUGUSTUS	exon	10924415	10925584	.	-	.	transcript_id "Phchi.S1G167800.t1"; gene_id "Phchi.S1G167800"
Phchi.S1	AUGUSTUS	start_codon	10925582	10925584	.	-	0	transcript_id "Phchi.S1G167800.t1"; gene_id "Phchi.S1G167800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7716.t1 is derived from g4890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30781048	30781961	.	-	.	Phchi.S1G487500
Phchi.S1	AUGUSTUS	transcript	30781048	30781961	.	-	.	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	stop_codon	30781045	30781047	.	-	0	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	CDS	30781048	30781529	0.5	-	2	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	exon	30781048	30781529	.	-	.	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	intron	30781530	30781692	.	-	.	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	CDS	30781693	30781807	1	-	0	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	exon	30781693	30781807	.	-	.	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	intron	30781808	30781940	.	-	.	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	CDS	30781941	30781961	0.97	-	0	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	exon	30781941	30781961	.	-	.	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
Phchi.S1	AUGUSTUS	start_codon	30781959	30781961	.	-	0	transcript_id "Phchi.S1G487500.t1"; gene_id "Phchi.S1G487500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4769.t1 is derived from g1939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12743467	12745566	.	+	.	Phchi.S1G192800
Phchi.S1	AUGUSTUS	transcript	12743467	12745566	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	start_codon	12743467	12743469	.	+	0	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12743467	12743660	0.92	+	0	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12743467	12743660	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12743661	12744110	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12744111	12744232	1	+	1	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12744111	12744232	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12744233	12744326	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12744327	12744439	1	+	2	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12744327	12744439	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12744440	12744524	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12744525	12744598	0.98	+	0	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12744525	12744598	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12744599	12744699	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12744700	12744964	1	+	1	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12744700	12744964	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12744965	12745052	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12745053	12745184	1	+	0	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12745053	12745184	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12745185	12745281	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12745282	12745417	1	+	0	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12745282	12745417	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	intron	12745418	12745516	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	CDS	12745517	12745566	0.85	+	2	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	exon	12745517	12745566	.	+	.	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
Phchi.S1	AUGUSTUS	stop_codon	12745567	12745569	.	+	0	transcript_id "Phchi.S1G192800.t1"; gene_id "Phchi.S1G192800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12503.t1 is derived from g8180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30890336	30896244	.	+	.	Phchi.S2G058300
Phchi.S2	AUGUSTUS	transcript	30890336	30896244	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	start_codon	30890336	30890338	.	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30890336	30890965	0.95	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30890336	30890965	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30890966	30891117	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30891118	30891326	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30891118	30891326	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30891327	30891395	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30891396	30891545	1	+	1	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30891396	30891545	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30891546	30891663	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30891664	30891797	1	+	1	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30891664	30891797	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30891798	30891928	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30891929	30892035	1	+	2	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30891929	30892035	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30892036	30892299	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30892300	30892406	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30892300	30892406	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30892407	30892570	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30892571	30892709	1	+	1	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30892571	30892709	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30892710	30892837	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30892838	30892954	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30892838	30892954	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30892955	30893042	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30893043	30893150	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30893043	30893150	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30893151	30893262	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30893263	30893334	0.99	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30893263	30893334	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30893335	30893446	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30893447	30893569	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30893447	30893569	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30893570	30893691	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30893692	30893851	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30893692	30893851	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30893852	30893992	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30893993	30894114	1	+	2	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30893993	30894114	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30894115	30894251	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30894252	30894389	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30894252	30894389	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30894390	30894628	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30894629	30894771	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30894629	30894771	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30894772	30894906	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30894907	30894969	1	+	1	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30894907	30894969	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30894970	30895102	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30895103	30895166	1	+	1	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30895103	30895166	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30895167	30895260	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30895261	30895396	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30895261	30895396	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30895397	30895488	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30895489	30895562	1	+	2	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30895489	30895562	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30895563	30895651	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30895652	30895746	1	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30895652	30895746	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30895747	30895876	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30895877	30895908	1	+	1	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30895877	30895908	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	intron	30895909	30896020	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	CDS	30896021	30896244	0.99	+	2	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	exon	30896021	30896244	.	+	.	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
Phchi.S2	AUGUSTUS	stop_codon	30896245	30896247	.	+	0	transcript_id "Phchi.S2G058300.t1"; gene_id "Phchi.S2G058300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1453.t1 is derived from g8372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	958888	960342	.	+	.	Phchi.S5G006200
Phchi.S5	AUGUSTUS	transcript	958888	960342	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	start_codon	958888	958890	.	+	0	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	958888	959024	0.94	+	0	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	958888	959024	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	intron	959025	959109	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	959110	959185	1	+	1	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	959110	959185	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	intron	959186	959282	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	959283	959334	1	+	0	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	959283	959334	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	intron	959335	959455	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	959456	959570	1	+	2	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	959456	959570	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	intron	959571	959669	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	959670	959740	1	+	1	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	959670	959740	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	intron	959741	960045	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	960046	960133	0.99	+	2	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	960046	960133	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	intron	960134	960236	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	CDS	960237	960342	0.98	+	1	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	exon	960237	960342	.	+	.	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
Phchi.S5	AUGUSTUS	stop_codon	960343	960345	.	+	0	transcript_id "Phchi.S5G006200.t1"; gene_id "Phchi.S5G006200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg479.t1 is derived from g10261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3351046	3351659	.	-	.	Phchi.S6G043800
Phchi.S6	AUGUSTUS	transcript	3351046	3351659	.	-	.	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	stop_codon	3351043	3351045	.	-	0	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	CDS	3351046	3351158	0.98	-	2	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	exon	3351046	3351158	.	-	.	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	intron	3351159	3351255	.	-	.	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	CDS	3351256	3351431	0.99	-	1	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	exon	3351256	3351431	.	-	.	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	intron	3351432	3351525	.	-	.	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	CDS	3351526	3351659	0.85	-	0	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	exon	3351526	3351659	.	-	.	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
Phchi.S6	AUGUSTUS	start_codon	3351657	3351659	.	-	0	transcript_id "Phchi.S6G043800.t1"; gene_id "Phchi.S6G043800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10061.t1 is derived from g7237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45578938	45579201	.	+	.	Phchi.S1G722000
Phchi.S1	AUGUSTUS	transcript	45578938	45579201	.	+	.	transcript_id "Phchi.S1G722000.t1"; gene_id "Phchi.S1G722000"
Phchi.S1	AUGUSTUS	start_codon	45578938	45578940	.	+	0	transcript_id "Phchi.S1G722000.t1"; gene_id "Phchi.S1G722000"
Phchi.S1	AUGUSTUS	CDS	45578938	45579201	0.64	+	0	transcript_id "Phchi.S1G722000.t1"; gene_id "Phchi.S1G722000"
Phchi.S1	AUGUSTUS	exon	45578938	45579201	.	+	.	transcript_id "Phchi.S1G722000.t1"; gene_id "Phchi.S1G722000"
Phchi.S1	AUGUSTUS	stop_codon	45579202	45579204	.	+	0	transcript_id "Phchi.S1G722000.t1"; gene_id "Phchi.S1G722000"
# This transcript jg6480.t2 is derived from g3652.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6480.t3 is derived from g3652.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6481.t1 is derived from g3653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23204806	23206362	.	+	.	Phchi.S1G364000
Phchi.S1	AUGUSTUS	transcript	23204806	23206362	.	+	.	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	start_codon	23204806	23204808	.	+	0	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	CDS	23204806	23204961	0.79	+	0	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	exon	23204806	23204961	.	+	.	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	intron	23204962	23205099	.	+	.	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	CDS	23205100	23205197	1	+	0	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	exon	23205100	23205197	.	+	.	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	intron	23205198	23205347	.	+	.	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	CDS	23205348	23206362	0.67	+	1	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	exon	23205348	23206362	.	+	.	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
Phchi.S1	AUGUSTUS	stop_codon	23206363	23206365	.	+	0	transcript_id "Phchi.S1G364000.t1"; gene_id "Phchi.S1G364000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5371.t1 is derived from g2541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16535089	16536731	.	+	.	Phchi.S1G253000
Phchi.S1	AUGUSTUS	transcript	16535089	16536731	.	+	.	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	start_codon	16535089	16535091	.	+	0	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	CDS	16535089	16535481	0.67	+	0	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	exon	16535089	16535481	.	+	.	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	intron	16535482	16535567	.	+	.	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	CDS	16535568	16536731	1	+	0	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	exon	16535568	16536731	.	+	.	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
Phchi.S1	AUGUSTUS	stop_codon	16536732	16536734	.	+	0	transcript_id "Phchi.S1G253000.t1"; gene_id "Phchi.S1G253000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2425.t1 is derived from g9345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6583786	6584468	.	+	.	Phchi.S5G103400
Phchi.S5	AUGUSTUS	transcript	6583786	6584468	.	+	.	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	start_codon	6583786	6583788	.	+	0	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	CDS	6583786	6584109	0.22	+	0	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	exon	6583786	6584109	.	+	.	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	intron	6584110	6584225	.	+	.	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	CDS	6584226	6584468	0.62	+	0	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	exon	6584226	6584468	.	+	.	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
Phchi.S5	AUGUSTUS	stop_codon	6584469	6584471	.	+	0	transcript_id "Phchi.S5G103400.t1"; gene_id "Phchi.S5G103400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14078.t1 is derived from g12545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10683502	10685175	.	+	.	Phchi.S3G139700
Phchi.S3	AUGUSTUS	transcript	10683502	10685175	.	+	.	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	start_codon	10683502	10683504	.	+	0	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	CDS	10683502	10685075	0.56	+	0	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	exon	10683502	10685075	.	+	.	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	intron	10685076	10685168	.	+	.	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	CDS	10685169	10685175	0.56	+	1	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	exon	10685169	10685175	.	+	.	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
Phchi.S3	AUGUSTUS	stop_codon	10685176	10685178	.	+	0	transcript_id "Phchi.S3G139700.t1"; gene_id "Phchi.S3G139700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4554.t1 is derived from g1724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11090466	11092657	.	-	.	Phchi.S1G171300
Phchi.S1	AUGUSTUS	transcript	11090466	11092657	.	-	.	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	stop_codon	11090463	11090465	.	-	0	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	CDS	11090466	11090809	0.38	-	2	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	exon	11090466	11090809	.	-	.	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	intron	11090810	11090904	.	-	.	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	CDS	11090905	11092657	0.68	-	0	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	exon	11090905	11092657	.	-	.	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
Phchi.S1	AUGUSTUS	start_codon	11092655	11092657	.	-	0	transcript_id "Phchi.S1G171300.t1"; gene_id "Phchi.S1G171300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg597.t1 is derived from g10379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4340844	4342160	.	-	.	Phchi.S6G055600
Phchi.S6	AUGUSTUS	transcript	4340844	4342160	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	stop_codon	4340841	4340843	.	-	0	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	CDS	4340844	4341026	0.66	-	0	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	exon	4340844	4341026	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	intron	4341027	4341105	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	CDS	4341106	4341160	0.65	-	1	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	exon	4341106	4341160	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	intron	4341161	4341295	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	CDS	4341296	4341369	0.94	-	0	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	exon	4341296	4341369	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	intron	4341370	4341530	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	CDS	4341531	4342160	0.47	-	0	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	exon	4341531	4342160	.	-	.	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
Phchi.S6	AUGUSTUS	start_codon	4342158	4342160	.	-	0	transcript_id "Phchi.S6G055600.t1"; gene_id "Phchi.S6G055600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9844.t1 is derived from g7020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44040792	44043147	.	-	.	Phchi.S1G700300
Phchi.S1	AUGUSTUS	transcript	44040792	44043147	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	stop_codon	44040789	44040791	.	-	0	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44040792	44040847	0.55	-	2	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44040792	44040847	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44040848	44040928	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44040929	44041023	0.56	-	1	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44040929	44041023	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44041024	44041111	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44041112	44041189	0.6	-	1	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44041112	44041189	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44041190	44041335	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44041336	44041384	1	-	2	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44041336	44041384	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44041385	44041579	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44041580	44041756	1	-	2	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44041580	44041756	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44041757	44041877	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44041878	44041919	1	-	2	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44041878	44041919	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44041920	44042019	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44042020	44042149	1	-	0	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44042020	44042149	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44042150	44042283	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44042284	44042442	1	-	0	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44042284	44042442	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44042443	44042538	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44042539	44042664	1	-	0	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44042539	44042664	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44042665	44042767	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44042768	44042990	1	-	1	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44042768	44042990	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	intron	44042991	44043076	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	CDS	44043077	44043147	0.92	-	0	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	exon	44043077	44043147	.	-	.	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
Phchi.S1	AUGUSTUS	start_codon	44043145	44043147	.	-	0	transcript_id "Phchi.S1G700300.t1"; gene_id "Phchi.S1G700300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2393.t1 is derived from g9313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6466019	6468391	.	-	.	Phchi.S5G100200
Phchi.S5	AUGUSTUS	transcript	6466019	6466813	.	-	.	transcript_id "Phchi.S5G100200.t1"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	stop_codon	6466016	6466018	.	-	0	transcript_id "Phchi.S5G100200.t1"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	CDS	6466019	6466813	1	-	0	transcript_id "Phchi.S5G100200.t1"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	exon	6466019	6466813	.	-	.	transcript_id "Phchi.S5G100200.t1"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	start_codon	6466811	6466813	.	-	0	transcript_id "Phchi.S5G100200.t1"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	transcript	6466019	6468391	.	-	.	transcript_id "Phchi.S5G100200.t2"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	stop_codon	6466016	6466018	.	-	0	transcript_id "Phchi.S5G100200.t2"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	CDS	6466019	6468391	0.81	-	0	transcript_id "Phchi.S5G100200.t2"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	exon	6466019	6468391	.	-	.	transcript_id "Phchi.S5G100200.t2"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	start_codon	6468389	6468391	.	-	0	transcript_id "Phchi.S5G100200.t2"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	transcript	6466019	6467821	.	-	.	transcript_id "Phchi.S5G100200.t3"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	stop_codon	6466016	6466018	.	-	0	transcript_id "Phchi.S5G100200.t3"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	CDS	6466019	6467821	0.6	-	0	transcript_id "Phchi.S5G100200.t3"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	exon	6466019	6467821	.	-	.	transcript_id "Phchi.S5G100200.t3"; gene_id "Phchi.S5G100200"
Phchi.S5	AUGUSTUS	start_codon	6467819	6467821	.	-	0	transcript_id "Phchi.S5G100200.t3"; gene_id "Phchi.S5G100200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15820.t1 is derived from g14290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21582851	21583435	.	+	.	Phchi.S3G313900
Phchi.S3	AUGUSTUS	transcript	21582851	21583435	.	+	.	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	start_codon	21582851	21582853	.	+	0	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	CDS	21582851	21583067	0.76	+	0	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	exon	21582851	21583067	.	+	.	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	intron	21583068	21583141	.	+	.	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	CDS	21583142	21583275	0.72	+	2	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	exon	21583142	21583275	.	+	.	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	intron	21583276	21583360	.	+	.	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	CDS	21583361	21583435	0.97	+	0	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	exon	21583361	21583435	.	+	.	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
Phchi.S3	AUGUSTUS	stop_codon	21583436	21583438	.	+	0	transcript_id "Phchi.S3G313900.t1"; gene_id "Phchi.S3G313900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13139.t1 is derived from g11604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4336365	4338971	.	-	.	Phchi.S3G045800
Phchi.S3	AUGUSTUS	transcript	4336365	4338971	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	stop_codon	4336362	4336364	.	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4336365	4336370	0.72	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4336365	4336370	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4336371	4336702	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4336703	4336713	0.65	-	2	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4336703	4336713	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4336714	4336848	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4336849	4337020	0.73	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4336849	4337020	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4337021	4337116	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4337117	4337170	0.79	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4337117	4337170	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4337171	4337241	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4337242	4337283	0.75	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4337242	4337283	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4337284	4337369	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4337370	4337486	1	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4337370	4337486	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4337487	4337666	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4337667	4337806	1	-	2	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4337667	4337806	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4337807	4338002	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4338003	4338314	0.99	-	2	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4338003	4338314	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4338315	4338470	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4338471	4338549	1	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4338471	4338549	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	intron	4338550	4338731	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	CDS	4338732	4338971	0.99	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	exon	4338732	4338971	.	-	.	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
Phchi.S3	AUGUSTUS	start_codon	4338969	4338971	.	-	0	transcript_id "Phchi.S3G045800.t1"; gene_id "Phchi.S3G045800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14459.t1 is derived from g12927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12977253	12984101	.	+	.	Phchi.S3G177800
Phchi.S3	AUGUSTUS	transcript	12977253	12984101	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	start_codon	12977253	12977255	.	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12977253	12978076	0.73	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12977253	12978076	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12978077	12978141	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12978142	12978460	0.98	+	1	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12978142	12978460	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12978461	12978561	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12978562	12978708	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12978562	12978708	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12978709	12978785	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12978786	12978981	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12978786	12978981	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12978982	12979071	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12979072	12979523	0.92	+	2	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12979072	12979523	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12979524	12979656	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12979657	12979731	0.89	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12979657	12979731	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12979732	12979839	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12979840	12979989	0.92	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12979840	12979989	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12979990	12980304	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12980305	12980642	0.99	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12980305	12980642	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12980643	12980783	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12980784	12980925	0.99	+	1	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12980784	12980925	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12980926	12981064	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12981065	12981427	0.69	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12981065	12981427	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12981428	12981517	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12981518	12981771	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12981518	12981771	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12981772	12981854	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12981855	12982112	0.98	+	1	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12981855	12982112	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12982113	12982210	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12982211	12982307	0.66	+	1	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12982211	12982307	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12982308	12982395	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12982396	12982611	0.96	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12982396	12982611	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12982612	12982699	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12982700	12982777	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12982700	12982777	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12982778	12982851	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12982852	12983055	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12982852	12983055	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12983056	12983164	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12983165	12983257	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12983165	12983257	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12983258	12983345	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12983346	12983411	0.99	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12983346	12983411	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12983412	12983516	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12983517	12983780	0.99	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12983517	12983780	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	intron	12983781	12983873	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	CDS	12983874	12984101	1	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	exon	12983874	12984101	.	+	.	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
Phchi.S3	AUGUSTUS	stop_codon	12984102	12984104	.	+	0	transcript_id "Phchi.S3G177800.t1"; gene_id "Phchi.S3G177800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6539.t1 is derived from g3711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23548161	23552024	.	+	.	Phchi.S1G369800
Phchi.S1	AUGUSTUS	transcript	23548161	23552024	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	start_codon	23548161	23548163	.	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23548161	23549370	0.55	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23548161	23549370	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23549371	23549486	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23549487	23550169	1	+	2	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23549487	23550169	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23550170	23550256	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23550257	23550409	1	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23550257	23550409	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23550410	23550492	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23550493	23550609	1	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23550493	23550609	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23550610	23550785	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23550786	23550890	0.98	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23550786	23550890	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23550891	23550992	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23550993	23551058	0.98	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23550993	23551058	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23551059	23551151	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23551152	23551216	1	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23551152	23551216	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23551217	23551376	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23551377	23551572	1	+	1	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23551377	23551572	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23551573	23551653	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23551654	23551794	0.96	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23551654	23551794	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	intron	23551795	23551895	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	CDS	23551896	23552024	0.98	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	exon	23551896	23552024	.	+	.	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
Phchi.S1	AUGUSTUS	stop_codon	23552025	23552027	.	+	0	transcript_id "Phchi.S1G369800.t1"; gene_id "Phchi.S1G369800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15146.t1 is derived from g13614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17260725	17261702	.	-	.	Phchi.S3G246500
Phchi.S3	AUGUSTUS	transcript	17260725	17261702	.	-	.	transcript_id "Phchi.S3G246500.t1"; gene_id "Phchi.S3G246500"
Phchi.S3	AUGUSTUS	stop_codon	17260722	17260724	.	-	0	transcript_id "Phchi.S3G246500.t1"; gene_id "Phchi.S3G246500"
Phchi.S3	AUGUSTUS	CDS	17260725	17261702	0.6	-	0	transcript_id "Phchi.S3G246500.t1"; gene_id "Phchi.S3G246500"
Phchi.S3	AUGUSTUS	exon	17260725	17261702	.	-	.	transcript_id "Phchi.S3G246500.t1"; gene_id "Phchi.S3G246500"
Phchi.S3	AUGUSTUS	start_codon	17261700	17261702	.	-	0	transcript_id "Phchi.S3G246500.t1"; gene_id "Phchi.S3G246500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1279.t1 is derived from g11062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8794542	8795198	.	-	.	Phchi.S6G123800
Phchi.S6	AUGUSTUS	transcript	8794542	8795198	.	-	.	transcript_id "Phchi.S6G123800.t1"; gene_id "Phchi.S6G123800"
Phchi.S6	AUGUSTUS	stop_codon	8794539	8794541	.	-	0	transcript_id "Phchi.S6G123800.t1"; gene_id "Phchi.S6G123800"
Phchi.S6	AUGUSTUS	CDS	8794542	8795198	0.26	-	0	transcript_id "Phchi.S6G123800.t1"; gene_id "Phchi.S6G123800"
Phchi.S6	AUGUSTUS	exon	8794542	8795198	.	-	.	transcript_id "Phchi.S6G123800.t1"; gene_id "Phchi.S6G123800"
Phchi.S6	AUGUSTUS	start_codon	8795196	8795198	.	-	0	transcript_id "Phchi.S6G123800.t1"; gene_id "Phchi.S6G123800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15780.t1 is derived from g14250.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21311847	21314196	.	+	.	Phchi.S3G309900
Phchi.S3	AUGUSTUS	transcript	21311847	21314168	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	start_codon	21311847	21311849	.	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21311847	21311898	0.87	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21311847	21311898	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21311899	21312054	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21312055	21312284	1	+	2	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21312055	21312284	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21312285	21312542	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21312543	21312672	1	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21312543	21312672	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21312673	21312825	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21312826	21313099	1	+	2	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21312826	21313099	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313100	21313223	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313224	21313356	0.97	+	1	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313224	21313356	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313357	21313459	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313460	21313546	1	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313460	21313546	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313547	21313696	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313697	21313754	0.47	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313697	21313754	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313755	21313874	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313875	21313951	0.5	+	2	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313875	21313951	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313952	21314102	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21314103	21314168	0.86	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21314103	21314168	.	+	.	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	stop_codon	21314169	21314171	.	+	0	transcript_id "Phchi.S3G309900.t1"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	transcript	21311847	21314196	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	start_codon	21311847	21311849	.	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21311847	21311898	0.89	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21311847	21311898	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21311899	21312054	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21312055	21312284	1	+	2	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21312055	21312284	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21312285	21312542	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21312543	21312672	1	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21312543	21312672	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21312673	21312825	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21312826	21313099	1	+	2	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21312826	21313099	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313100	21313223	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313224	21313356	0.98	+	1	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313224	21313356	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313357	21313459	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313460	21313546	1	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313460	21313546	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313547	21313696	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313697	21313754	0.42	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313697	21313754	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313755	21313874	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21313875	21313951	0.44	+	2	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21313875	21313951	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	intron	21313952	21314142	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	CDS	21314143	21314196	0.89	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	exon	21314143	21314196	.	+	.	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
Phchi.S3	AUGUSTUS	stop_codon	21314197	21314199	.	+	0	transcript_id "Phchi.S3G309900.t2"; gene_id "Phchi.S3G309900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15280.t1 is derived from g13748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18135534	18136900	.	-	.	Phchi.S3G259900
Phchi.S3	AUGUSTUS	transcript	18135534	18136900	.	-	.	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	stop_codon	18135531	18135533	.	-	0	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	CDS	18135534	18136379	0.99	-	0	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	exon	18135534	18136379	.	-	.	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	intron	18136380	18136504	.	-	.	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	CDS	18136505	18136900	1	-	0	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	exon	18136505	18136900	.	-	.	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
Phchi.S3	AUGUSTUS	start_codon	18136898	18136900	.	-	0	transcript_id "Phchi.S3G259900.t1"; gene_id "Phchi.S3G259900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12185.t1 is derived from g7861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6236217	6239504	.	-	.	Phchi.S2G026500
Phchi.S2	AUGUSTUS	transcript	6236217	6239504	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	stop_codon	6236214	6236216	.	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6236217	6236232	0.7	-	1	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6236217	6236232	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6236233	6236615	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6236616	6236806	0.7	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6236616	6236806	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6236807	6236903	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6236904	6236978	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6236904	6236978	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6236979	6237074	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6237075	6237422	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6237075	6237422	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6237423	6237503	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6237504	6237575	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6237504	6237575	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6237576	6237666	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6237667	6237813	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6237667	6237813	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6237814	6237876	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6237877	6238032	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6237877	6238032	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6238033	6238124	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6238125	6238295	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6238125	6238295	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6238296	6238411	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6238412	6238582	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6238412	6238582	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6238583	6238729	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6238730	6238795	1	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6238730	6238795	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6238796	6239048	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6239049	6239134	1	-	2	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6239049	6239134	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	intron	6239135	6239260	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	CDS	6239261	6239504	0.77	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	exon	6239261	6239504	.	-	.	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
Phchi.S2	AUGUSTUS	start_codon	6239502	6239504	.	-	0	transcript_id "Phchi.S2G026500.t1"; gene_id "Phchi.S2G026500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2332.t1 is derived from g9252.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6208771	6212307	.	-	.	Phchi.S5G094100
Phchi.S5	AUGUSTUS	transcript	6208771	6212307	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	stop_codon	6208768	6208770	.	-	0	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6208771	6209243	0.61	-	2	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6208771	6209243	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6209244	6209370	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6209371	6211214	0.22	-	1	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6209371	6211214	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211215	6211317	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211318	6211459	0.99	-	2	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211318	6211459	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211460	6211613	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211614	6211625	0.78	-	2	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211614	6211625	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211626	6211708	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211709	6211810	1	-	2	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211709	6211810	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211811	6211944	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211945	6212034	1	-	2	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211945	6212034	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6212035	6212249	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6212250	6212307	0.97	-	0	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6212250	6212307	.	-	.	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	start_codon	6212305	6212307	.	-	0	transcript_id "Phchi.S5G094100.t1"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	transcript	6208771	6212307	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	stop_codon	6208768	6208770	.	-	0	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6208771	6209243	0.51	-	2	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6208771	6209243	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6209244	6209370	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6209371	6211214	0.19	-	1	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6209371	6211214	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211215	6211317	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211318	6211459	0.98	-	2	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211318	6211459	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211460	6211613	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211614	6211625	0.74	-	2	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211614	6211625	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211626	6211708	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211709	6211810	0.88	-	2	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211709	6211810	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6211811	6211944	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6211945	6212034	0.79	-	2	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6211945	6212034	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	intron	6212035	6212150	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	CDS	6212151	6212307	0.81	-	0	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	exon	6212151	6212307	.	-	.	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
Phchi.S5	AUGUSTUS	start_codon	6212305	6212307	.	-	0	transcript_id "Phchi.S5G094100.t2"; gene_id "Phchi.S5G094100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13211.t1 is derived from g11676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4700991	4702106	.	-	.	Phchi.S3G053000
Phchi.S3	AUGUSTUS	transcript	4700991	4702106	.	-	.	transcript_id "Phchi.S3G053000.t1"; gene_id "Phchi.S3G053000"
Phchi.S3	AUGUSTUS	stop_codon	4700988	4700990	.	-	0	transcript_id "Phchi.S3G053000.t1"; gene_id "Phchi.S3G053000"
Phchi.S3	AUGUSTUS	CDS	4700991	4702106	0.53	-	0	transcript_id "Phchi.S3G053000.t1"; gene_id "Phchi.S3G053000"
Phchi.S3	AUGUSTUS	exon	4700991	4702106	.	-	.	transcript_id "Phchi.S3G053000.t1"; gene_id "Phchi.S3G053000"
Phchi.S3	AUGUSTUS	start_codon	4702104	4702106	.	-	0	transcript_id "Phchi.S3G053000.t1"; gene_id "Phchi.S3G053000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9562.t1 is derived from g6738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42672174	42673646	.	+	.	Phchi.S1G672100
Phchi.S1	AUGUSTUS	transcript	42672174	42673646	.	+	.	transcript_id "Phchi.S1G672100.t1"; gene_id "Phchi.S1G672100"
Phchi.S1	AUGUSTUS	start_codon	42672174	42672176	.	+	0	transcript_id "Phchi.S1G672100.t1"; gene_id "Phchi.S1G672100"
Phchi.S1	AUGUSTUS	CDS	42672174	42673646	0.64	+	0	transcript_id "Phchi.S1G672100.t1"; gene_id "Phchi.S1G672100"
Phchi.S1	AUGUSTUS	exon	42672174	42673646	.	+	.	transcript_id "Phchi.S1G672100.t1"; gene_id "Phchi.S1G672100"
Phchi.S1	AUGUSTUS	stop_codon	42673647	42673649	.	+	0	transcript_id "Phchi.S1G672100.t1"; gene_id "Phchi.S1G672100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11127.t1 is derived from g15177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4289110	4290439	.	+	.	Phchi.S4G070900
Phchi.S4	AUGUSTUS	transcript	4289110	4290439	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	start_codon	4289110	4289112	.	+	0	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	CDS	4289110	4289328	0.36	+	0	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	exon	4289110	4289328	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	intron	4289329	4289451	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	CDS	4289452	4289521	0.9	+	0	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	exon	4289452	4289521	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	intron	4289522	4289629	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	CDS	4289630	4289680	0.66	+	2	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	exon	4289630	4289680	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	intron	4289681	4289846	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	CDS	4289847	4289966	0.43	+	2	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	exon	4289847	4289966	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	intron	4289967	4290101	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	CDS	4290102	4290287	0.6	+	2	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	exon	4290102	4290287	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	intron	4290288	4290377	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	CDS	4290378	4290439	0.47	+	2	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	exon	4290378	4290439	.	+	.	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
Phchi.S4	AUGUSTUS	stop_codon	4290440	4290442	.	+	0	transcript_id "Phchi.S4G070900.t1"; gene_id "Phchi.S4G070900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5357.t1 is derived from g2527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16454169	16454942	.	-	.	Phchi.S1G251600
Phchi.S1	AUGUSTUS	transcript	16454169	16454942	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	stop_codon	16454166	16454168	.	-	0	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	CDS	16454169	16454295	1	-	1	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	exon	16454169	16454295	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	intron	16454296	16454393	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	CDS	16454394	16454455	1	-	0	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	exon	16454394	16454455	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	intron	16454456	16454538	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	CDS	16454539	16454754	1	-	0	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	exon	16454539	16454754	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	intron	16454755	16454825	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	CDS	16454826	16454942	0.99	-	0	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	exon	16454826	16454942	.	-	.	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
Phchi.S1	AUGUSTUS	start_codon	16454940	16454942	.	-	0	transcript_id "Phchi.S1G251600.t1"; gene_id "Phchi.S1G251600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14696.t1 is derived from g13164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14204856	14206857	.	-	.	Phchi.S3G201500
Phchi.S3	AUGUSTUS	transcript	14204856	14206857	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	stop_codon	14204853	14204855	.	-	0	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	CDS	14204856	14205063	0.93	-	1	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	exon	14204856	14205063	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	intron	14205064	14205186	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	CDS	14205187	14205294	0.95	-	1	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	exon	14205187	14205294	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	intron	14205295	14205387	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	CDS	14205388	14205794	0.96	-	0	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	exon	14205388	14205794	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	intron	14205795	14205894	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	CDS	14205895	14206468	1	-	1	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	exon	14205895	14206468	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	intron	14206469	14206726	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	CDS	14206727	14206857	1	-	0	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	exon	14206727	14206857	.	-	.	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
Phchi.S3	AUGUSTUS	start_codon	14206855	14206857	.	-	0	transcript_id "Phchi.S3G201500.t1"; gene_id "Phchi.S3G201500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2390.t1 is derived from g9310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6462380	6464179	.	+	.	Phchi.S5G099900
Phchi.S5	AUGUSTUS	transcript	6462380	6464179	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	start_codon	6462380	6462382	.	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6462380	6462463	0.81	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6462380	6462463	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6462464	6462551	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6462552	6462737	0.92	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6462552	6462737	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6462738	6462841	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6462842	6463006	1	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6462842	6463006	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6463007	6463093	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6463094	6463285	0.95	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6463094	6463285	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6463286	6463362	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6463363	6463515	0.43	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6463363	6463515	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6463516	6463624	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6463625	6463708	0.8	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6463625	6463708	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6463709	6463820	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6463821	6463927	0.8	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6463821	6463927	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	intron	6463928	6464025	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	CDS	6464026	6464179	0.79	+	1	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	exon	6464026	6464179	.	+	.	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
Phchi.S5	AUGUSTUS	stop_codon	6464180	6464182	.	+	0	transcript_id "Phchi.S5G099900.t1"; gene_id "Phchi.S5G099900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6031.t1 is derived from g3202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20512927	20518307	.	+	.	Phchi.S1G319000
Phchi.S1	AUGUSTUS	transcript	20512927	20518307	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	start_codon	20512927	20512929	.	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20512927	20513636	0.39	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20512927	20513636	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20513637	20513746	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20513747	20514623	0.07	+	1	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20513747	20514623	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20514624	20514772	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20514773	20515186	0.34	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20514773	20515186	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20515187	20515259	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20515260	20515418	0.56	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20515260	20515418	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20515419	20515498	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20515499	20515654	0.64	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20515499	20515654	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20515655	20515896	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20515897	20515906	0.95	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20515897	20515906	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20515907	20516096	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20516097	20516153	0.97	+	2	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20516097	20516153	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20516154	20516283	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20516284	20516335	0.88	+	2	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20516284	20516335	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20516336	20516505	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20516506	20516534	0.46	+	1	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20516506	20516534	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20516535	20516614	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20516615	20516925	0.9	+	2	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20516615	20516925	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	intron	20516926	20517035	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	CDS	20517036	20518307	0.98	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	exon	20517036	20518307	.	+	.	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
Phchi.S1	AUGUSTUS	stop_codon	20518308	20518310	.	+	0	transcript_id "Phchi.S1G319000.t1"; gene_id "Phchi.S1G319000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3095.t1 is derived from g264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1732246	1733167	.	-	.	Phchi.S1G025400
Phchi.S1	AUGUSTUS	transcript	1732246	1733167	.	-	.	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	stop_codon	1732243	1732245	.	-	0	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	CDS	1732246	1732375	0.97	-	1	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	exon	1732246	1732375	.	-	.	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	intron	1732376	1732515	.	-	.	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	CDS	1732516	1732532	0.98	-	0	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	exon	1732516	1732532	.	-	.	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	intron	1732533	1732645	.	-	.	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	CDS	1732646	1733167	0.94	-	0	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	exon	1732646	1733167	.	-	.	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
Phchi.S1	AUGUSTUS	start_codon	1733165	1733167	.	-	0	transcript_id "Phchi.S1G025400.t1"; gene_id "Phchi.S1G025400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8353.t1 is derived from g5528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35465216	35466996	.	+	.	Phchi.S1G551200
Phchi.S1	AUGUSTUS	transcript	35465216	35466996	.	+	.	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	start_codon	35465216	35465218	.	+	0	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	CDS	35465216	35466211	0.4	+	0	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	exon	35465216	35466211	.	+	.	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	intron	35466212	35466321	.	+	.	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	CDS	35466322	35466996	0.41	+	0	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	exon	35466322	35466996	.	+	.	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
Phchi.S1	AUGUSTUS	stop_codon	35466997	35466999	.	+	0	transcript_id "Phchi.S1G551200.t1"; gene_id "Phchi.S1G551200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15335.t1 is derived from g13803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18445222	18447999	.	+	.	Phchi.S3G265400
Phchi.S3	AUGUSTUS	transcript	18445222	18447999	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	start_codon	18445222	18445224	.	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18445222	18445424	0.76	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18445222	18445424	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18445425	18445542	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18445543	18445651	1	+	1	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18445543	18445651	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18445652	18445745	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18445746	18445976	1	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18445746	18445976	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18445977	18446078	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18446079	18446238	1	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18446079	18446238	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18446239	18446357	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18446358	18446413	1	+	2	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18446358	18446413	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18446414	18446485	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18446486	18446638	1	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18446486	18446638	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18446639	18446728	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18446729	18446826	1	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18446729	18446826	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18446827	18446981	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18446982	18447062	1	+	1	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18446982	18447062	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18447063	18447171	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18447172	18447405	1	+	1	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18447172	18447405	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18447406	18447495	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18447496	18447630	1	+	1	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18447496	18447630	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	intron	18447631	18447974	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	CDS	18447975	18447999	1	+	1	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	exon	18447975	18447999	.	+	.	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
Phchi.S3	AUGUSTUS	stop_codon	18448000	18448002	.	+	0	transcript_id "Phchi.S3G265400.t1"; gene_id "Phchi.S3G265400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3399.t1 is derived from g568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3344379	3347305	.	+	.	Phchi.S1G055800
Phchi.S1	AUGUSTUS	transcript	3344379	3347305	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	start_codon	3344379	3344381	.	+	0	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3344379	3345335	0.37	+	0	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3344379	3345335	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3345336	3345436	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3345437	3345584	0.8	+	0	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3345437	3345584	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3345585	3345697	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3345698	3345930	0.93	+	2	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3345698	3345930	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3345931	3346061	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3346062	3346206	1	+	0	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3346062	3346206	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3346207	3346291	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3346292	3346360	1	+	2	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3346292	3346360	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3346361	3346468	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3346469	3346661	1	+	2	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3346469	3346661	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3346662	3346751	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3346752	3346881	0.96	+	1	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3346752	3346881	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	intron	3346882	3346987	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	CDS	3346988	3347305	1	+	0	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	exon	3346988	3347305	.	+	.	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
Phchi.S1	AUGUSTUS	stop_codon	3347306	3347308	.	+	0	transcript_id "Phchi.S1G055800.t1"; gene_id "Phchi.S1G055800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg837.t1 is derived from g10619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5825693	5828395	.	-	.	Phchi.S6G079600
Phchi.S6	AUGUSTUS	transcript	5825693	5828395	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	stop_codon	5825690	5825692	.	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5825693	5825911	1	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5825693	5825911	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5825912	5826002	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5826003	5826149	1	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5826003	5826149	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5826150	5826250	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5826251	5826395	1	-	1	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5826251	5826395	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5826396	5826476	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5826477	5826622	1	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5826477	5826622	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5826623	5826713	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5826714	5826805	1	-	2	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5826714	5826805	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5826806	5826904	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5826905	5826956	1	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5826905	5826956	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5826957	5827040	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5827041	5827324	1	-	2	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5827041	5827324	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5827325	5827415	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5827416	5827574	1	-	2	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5827416	5827574	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5827575	5827669	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5827670	5827887	0.98	-	1	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5827670	5827887	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5827888	5827996	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5827997	5828047	0.99	-	1	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5827997	5828047	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5828048	5828149	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5828150	5828218	1	-	1	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5828150	5828218	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	intron	5828219	5828312	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	CDS	5828313	5828395	0.59	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	exon	5828313	5828395	.	-	.	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
Phchi.S6	AUGUSTUS	start_codon	5828393	5828395	.	-	0	transcript_id "Phchi.S6G079600.t1"; gene_id "Phchi.S6G079600"
# This transcript jg9312.t2 is derived from g6487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9313.t1 is derived from g6488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40905435	40907333	.	+	.	Phchi.S1G647200
Phchi.S1	AUGUSTUS	transcript	40905435	40907333	.	+	.	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	start_codon	40905435	40905437	.	+	0	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	CDS	40905435	40906027	1	+	0	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	exon	40905435	40906027	.	+	.	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	intron	40906028	40906109	.	+	.	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	CDS	40906110	40906341	1	+	1	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	exon	40906110	40906341	.	+	.	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	intron	40906342	40906451	.	+	.	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	CDS	40906452	40907333	1	+	0	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	exon	40906452	40907333	.	+	.	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	stop_codon	40907334	40907336	.	+	0	transcript_id "Phchi.S1G647200.t1"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	transcript	40906126	40907333	.	+	.	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	start_codon	40906126	40906128	.	+	0	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	CDS	40906126	40906341	0.92	+	0	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	exon	40906126	40906341	.	+	.	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	intron	40906342	40906451	.	+	.	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	CDS	40906452	40907333	1	+	0	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	exon	40906452	40907333	.	+	.	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
Phchi.S1	AUGUSTUS	stop_codon	40907334	40907336	.	+	0	transcript_id "Phchi.S1G647200.t2"; gene_id "Phchi.S1G647200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14628.t1 is derived from g13096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13835279	13835938	.	+	.	Phchi.S3G194700
Phchi.S3	AUGUSTUS	transcript	13835279	13835938	.	+	.	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	start_codon	13835279	13835281	.	+	0	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	CDS	13835279	13835455	1	+	0	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	exon	13835279	13835455	.	+	.	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	intron	13835456	13835539	.	+	.	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	CDS	13835540	13835605	1	+	0	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	exon	13835540	13835605	.	+	.	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	intron	13835606	13835683	.	+	.	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	CDS	13835684	13835938	1	+	0	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	exon	13835684	13835938	.	+	.	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
Phchi.S3	AUGUSTUS	stop_codon	13835939	13835941	.	+	0	transcript_id "Phchi.S3G194700.t1"; gene_id "Phchi.S3G194700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15180.t1 is derived from g13648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17429828	17430888	.	+	.	Phchi.S3G249900
Phchi.S3	AUGUSTUS	transcript	17429828	17430888	.	+	.	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	start_codon	17429828	17429830	.	+	0	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	CDS	17429828	17430676	1	+	0	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	exon	17429828	17430676	.	+	.	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	intron	17430677	17430789	.	+	.	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	CDS	17430790	17430888	0.99	+	0	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	exon	17430790	17430888	.	+	.	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
Phchi.S3	AUGUSTUS	stop_codon	17430889	17430891	.	+	0	transcript_id "Phchi.S3G249900.t1"; gene_id "Phchi.S3G249900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6735.t1 is derived from g3907.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24792260	24793848	.	+	.	Phchi.S1G389400
Phchi.S1	AUGUSTUS	transcript	24792260	24793848	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	start_codon	24792260	24792262	.	+	0	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24792260	24792568	0.52	+	0	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24792260	24792568	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24792569	24792647	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24792648	24792846	0.91	+	0	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24792648	24792846	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24792847	24792954	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24792955	24793064	0.99	+	2	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24792955	24793064	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793065	24793171	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793172	24793250	0.99	+	0	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793172	24793250	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793251	24793406	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793407	24793474	1	+	2	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793407	24793474	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793475	24793567	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793568	24793634	0.97	+	0	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793568	24793634	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793635	24793738	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793739	24793848	0.98	+	2	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793739	24793848	.	+	.	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	stop_codon	24793849	24793851	.	+	0	transcript_id "Phchi.S1G389400.t1"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	transcript	24792260	24793848	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	start_codon	24792260	24792262	.	+	0	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24792260	24792568	0.48	+	0	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24792260	24792568	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24792569	24792647	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24792648	24792846	0.92	+	0	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24792648	24792846	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24792847	24792954	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24792955	24793064	1	+	2	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24792955	24793064	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793065	24793171	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793172	24793178	0.86	+	0	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793172	24793178	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793179	24793406	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793407	24793474	1	+	2	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793407	24793474	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793475	24793567	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793568	24793634	0.99	+	0	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793568	24793634	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	intron	24793635	24793738	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	CDS	24793739	24793848	0.99	+	2	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	exon	24793739	24793848	.	+	.	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
Phchi.S1	AUGUSTUS	stop_codon	24793849	24793851	.	+	0	transcript_id "Phchi.S1G389400.t2"; gene_id "Phchi.S1G389400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6836.t1 is derived from g4008.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25476721	25479918	.	+	.	Phchi.S1G399500
Phchi.S1	AUGUSTUS	transcript	25476721	25479918	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	start_codon	25476721	25476723	.	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25476721	25477431	0.99	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25476721	25477431	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25477432	25477567	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25477568	25477600	1	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25477568	25477600	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25477601	25477706	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25477707	25477809	1	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25477707	25477809	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25477810	25477951	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25477952	25478277	0.97	+	2	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25477952	25478277	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25478278	25478364	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25478365	25478442	0.99	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25478365	25478442	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25478443	25478543	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25478544	25478810	0.99	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25478544	25478810	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25478811	25478950	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25478951	25479119	0.93	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25478951	25479119	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25479120	25479218	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25479219	25479300	0.93	+	2	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25479219	25479300	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25479301	25479384	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25479385	25479466	0.99	+	1	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25479385	25479466	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25479467	25479600	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25479601	25479918	0.53	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25479601	25479918	.	+	.	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	stop_codon	25479919	25479921	.	+	0	transcript_id "Phchi.S1G399500.t1"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	transcript	25476721	25479918	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	start_codon	25476721	25476723	.	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25476721	25477431	1	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25476721	25477431	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25477432	25477567	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25477568	25477600	1	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25477568	25477600	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25477601	25477706	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25477707	25477809	1	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25477707	25477809	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25477810	25477951	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25477952	25478277	0.96	+	2	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25477952	25478277	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25478278	25478364	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25478365	25478442	1	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25478365	25478442	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25478443	25478543	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25478544	25478810	0.98	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25478544	25478810	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25478811	25478950	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25478951	25479119	0.8	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25478951	25479119	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25479120	25479209	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25479210	25479300	0.8	+	2	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25479210	25479300	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25479301	25479384	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25479385	25479466	0.99	+	1	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25479385	25479466	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	intron	25479467	25479600	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	CDS	25479601	25479918	0.47	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	exon	25479601	25479918	.	+	.	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
Phchi.S1	AUGUSTUS	stop_codon	25479919	25479921	.	+	0	transcript_id "Phchi.S1G399500.t2"; gene_id "Phchi.S1G399500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13756.t1 is derived from g12223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8726317	8727858	.	+	.	Phchi.S3G107500
Phchi.S3	AUGUSTUS	transcript	8726317	8727858	.	+	.	transcript_id "Phchi.S3G107500.t1"; gene_id "Phchi.S3G107500"
Phchi.S3	AUGUSTUS	start_codon	8726317	8726319	.	+	0	transcript_id "Phchi.S3G107500.t1"; gene_id "Phchi.S3G107500"
Phchi.S3	AUGUSTUS	CDS	8726317	8727858	0.98	+	0	transcript_id "Phchi.S3G107500.t1"; gene_id "Phchi.S3G107500"
Phchi.S3	AUGUSTUS	exon	8726317	8727858	.	+	.	transcript_id "Phchi.S3G107500.t1"; gene_id "Phchi.S3G107500"
Phchi.S3	AUGUSTUS	stop_codon	8727859	8727861	.	+	0	transcript_id "Phchi.S3G107500.t1"; gene_id "Phchi.S3G107500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12357.t1 is derived from g8033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12694450	12695126	.	-	.	Phchi.S2G043700
Phchi.S2	AUGUSTUS	transcript	12694450	12695126	.	-	.	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	stop_codon	12694447	12694449	.	-	0	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	CDS	12694450	12694542	0.6	-	0	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	exon	12694450	12694542	.	-	.	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	intron	12694543	12694686	.	-	.	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	CDS	12694687	12694762	0.6	-	1	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	exon	12694687	12694762	.	-	.	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	intron	12694763	12695067	.	-	.	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	CDS	12695068	12695126	0.44	-	0	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	exon	12695068	12695126	.	-	.	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
Phchi.S2	AUGUSTUS	start_codon	12695124	12695126	.	-	0	transcript_id "Phchi.S2G043700.t1"; gene_id "Phchi.S2G043700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg589.t1 is derived from g10371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4320788	4321845	.	+	.	Phchi.S6G054800
Phchi.S6	AUGUSTUS	transcript	4320788	4321845	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	start_codon	4320788	4320790	.	+	0	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	CDS	4320788	4320929	1	+	0	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	exon	4320788	4320929	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	intron	4320930	4321055	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	CDS	4321056	4321196	1	+	2	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	exon	4321056	4321196	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	intron	4321197	4321344	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	CDS	4321345	4321453	0.99	+	2	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	exon	4321345	4321453	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	intron	4321454	4321565	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	CDS	4321566	4321845	0.99	+	1	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	exon	4321566	4321845	.	+	.	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
Phchi.S6	AUGUSTUS	stop_codon	4321846	4321848	.	+	0	transcript_id "Phchi.S6G054800.t1"; gene_id "Phchi.S6G054800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3634.t1 is derived from g803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4867972	4869207	.	+	.	Phchi.S1G079300
Phchi.S1	AUGUSTUS	transcript	4867972	4869207	.	+	.	transcript_id "Phchi.S1G079300.t1"; gene_id "Phchi.S1G079300"
Phchi.S1	AUGUSTUS	start_codon	4867972	4867974	.	+	0	transcript_id "Phchi.S1G079300.t1"; gene_id "Phchi.S1G079300"
Phchi.S1	AUGUSTUS	CDS	4867972	4869207	0.93	+	0	transcript_id "Phchi.S1G079300.t1"; gene_id "Phchi.S1G079300"
Phchi.S1	AUGUSTUS	exon	4867972	4869207	.	+	.	transcript_id "Phchi.S1G079300.t1"; gene_id "Phchi.S1G079300"
Phchi.S1	AUGUSTUS	stop_codon	4869208	4869210	.	+	0	transcript_id "Phchi.S1G079300.t1"; gene_id "Phchi.S1G079300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12785.t1 is derived from g11250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2190149	2190532	.	+	.	Phchi.S3G010400
Phchi.S3	AUGUSTUS	transcript	2190149	2190532	.	+	.	transcript_id "Phchi.S3G010400.t1"; gene_id "Phchi.S3G010400"
Phchi.S3	AUGUSTUS	start_codon	2190149	2190151	.	+	0	transcript_id "Phchi.S3G010400.t1"; gene_id "Phchi.S3G010400"
Phchi.S3	AUGUSTUS	CDS	2190149	2190532	0.61	+	0	transcript_id "Phchi.S3G010400.t1"; gene_id "Phchi.S3G010400"
Phchi.S3	AUGUSTUS	exon	2190149	2190532	.	+	.	transcript_id "Phchi.S3G010400.t1"; gene_id "Phchi.S3G010400"
Phchi.S3	AUGUSTUS	stop_codon	2190533	2190535	.	+	0	transcript_id "Phchi.S3G010400.t1"; gene_id "Phchi.S3G010400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5503.t1 is derived from g2673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17153498	17154334	.	-	.	Phchi.S1G266200
Phchi.S1	AUGUSTUS	transcript	17153498	17154334	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	stop_codon	17153495	17153497	.	-	0	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	CDS	17153498	17153620	1	-	0	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	exon	17153498	17153620	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	intron	17153621	17153691	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	CDS	17153692	17153755	1	-	1	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	exon	17153692	17153755	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	intron	17153756	17153836	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	CDS	17153837	17153868	1	-	0	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	exon	17153837	17153868	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	intron	17153869	17153950	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	CDS	17153951	17154039	1	-	2	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	exon	17153951	17154039	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	intron	17154040	17154126	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	CDS	17154127	17154334	0.94	-	0	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	exon	17154127	17154334	.	-	.	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
Phchi.S1	AUGUSTUS	start_codon	17154332	17154334	.	-	0	transcript_id "Phchi.S1G266200.t1"; gene_id "Phchi.S1G266200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4850.t1 is derived from g2020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13088145	13089026	.	-	.	Phchi.S1G200900
Phchi.S1	AUGUSTUS	transcript	13088145	13089026	.	-	.	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	stop_codon	13088142	13088144	.	-	0	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	CDS	13088145	13088659	1	-	2	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	exon	13088145	13088659	.	-	.	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	intron	13088660	13088731	.	-	.	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	CDS	13088732	13089026	0.85	-	0	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	exon	13088732	13089026	.	-	.	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
Phchi.S1	AUGUSTUS	start_codon	13089024	13089026	.	-	0	transcript_id "Phchi.S1G200900.t1"; gene_id "Phchi.S1G200900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13420.t1 is derived from g11887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6614895	6617092	.	+	.	Phchi.S3G073900
Phchi.S3	AUGUSTUS	transcript	6614895	6617092	.	+	.	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	start_codon	6614895	6614897	.	+	0	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	CDS	6614895	6616592	0.07	+	0	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	exon	6614895	6616592	.	+	.	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	intron	6616593	6617038	.	+	.	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	CDS	6617039	6617092	0.01	+	0	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	exon	6617039	6617092	.	+	.	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
Phchi.S3	AUGUSTUS	stop_codon	6617093	6617095	.	+	0	transcript_id "Phchi.S3G073900.t1"; gene_id "Phchi.S3G073900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg904.t1 is derived from g10686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6363576	6367137	.	-	.	Phchi.S6G086300
Phchi.S6	AUGUSTUS	transcript	6363576	6367137	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	stop_codon	6363573	6363575	.	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6363576	6365313	0.45	-	1	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6363576	6365313	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6365314	6365422	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6365423	6365607	0.93	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6365423	6365607	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6365608	6365718	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6365719	6365772	0.91	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6365719	6365772	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6365773	6365879	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6365880	6365957	0.86	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6365880	6365957	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6365958	6366062	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6366063	6366168	0.9	-	1	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6366063	6366168	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6366169	6366296	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6366297	6366511	0.99	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6366297	6366511	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6366512	6366636	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6366637	6366887	1	-	2	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6366637	6366887	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6366888	6367049	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6367050	6367137	1	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6367050	6367137	.	-	.	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	start_codon	6367135	6367137	.	-	0	transcript_id "Phchi.S6G086300.t1"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	transcript	6366103	6367137	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	stop_codon	6366100	6366102	.	-	0	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6366103	6366160	0.51	-	1	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6366103	6366160	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6366161	6366296	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6366297	6366511	1	-	0	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6366297	6366511	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6366512	6366636	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6366637	6366887	1	-	2	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6366637	6366887	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	intron	6366888	6367049	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	CDS	6367050	6367137	1	-	0	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	exon	6367050	6367137	.	-	.	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
Phchi.S6	AUGUSTUS	start_codon	6367135	6367137	.	-	0	transcript_id "Phchi.S6G086300.t2"; gene_id "Phchi.S6G086300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1158.t1 is derived from g10941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8090069	8090771	.	+	.	Phchi.S6G111700
Phchi.S6	AUGUSTUS	transcript	8090069	8090771	.	+	.	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	start_codon	8090069	8090071	.	+	0	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	CDS	8090069	8090217	0.68	+	0	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	exon	8090069	8090217	.	+	.	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	intron	8090218	8090701	.	+	.	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	CDS	8090702	8090771	0.93	+	1	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	exon	8090702	8090771	.	+	.	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
Phchi.S6	AUGUSTUS	stop_codon	8090772	8090774	.	+	0	transcript_id "Phchi.S6G111700.t1"; gene_id "Phchi.S6G111700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10301.t1 is derived from g7477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47000870	47001281	.	+	.	Phchi.S1G746000
Phchi.S1	AUGUSTUS	transcript	47000870	47001281	.	+	.	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	start_codon	47000870	47000872	.	+	0	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	CDS	47000870	47001008	0.5	+	0	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	exon	47000870	47001008	.	+	.	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	intron	47001009	47001117	.	+	.	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	CDS	47001118	47001281	0.96	+	2	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	exon	47001118	47001281	.	+	.	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
Phchi.S1	AUGUSTUS	stop_codon	47001282	47001284	.	+	0	transcript_id "Phchi.S1G746000.t1"; gene_id "Phchi.S1G746000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6813.t1 is derived from g3985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25177479	25178788	.	-	.	Phchi.S1G397200
Phchi.S1	AUGUSTUS	transcript	25177479	25178788	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	stop_codon	25177476	25177478	.	-	0	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	CDS	25177479	25177825	0.91	-	2	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	exon	25177479	25177825	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	intron	25177826	25177930	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	CDS	25177931	25178078	0.91	-	0	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	exon	25177931	25178078	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	intron	25178079	25178168	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	CDS	25178169	25178420	0.69	-	0	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	exon	25178169	25178420	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	intron	25178421	25178521	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	CDS	25178522	25178788	0.39	-	0	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	exon	25178522	25178788	.	-	.	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
Phchi.S1	AUGUSTUS	start_codon	25178786	25178788	.	-	0	transcript_id "Phchi.S1G397200.t1"; gene_id "Phchi.S1G397200"
# This transcript jg904.t2 is derived from g10686.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg905.t1 is derived from g10687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6367776	6371142	.	+	.	Phchi.S6G086400
Phchi.S6	AUGUSTUS	transcript	6367776	6371142	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	start_codon	6367776	6367778	.	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6367776	6367829	1	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6367776	6367829	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6367830	6367979	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6367980	6368038	1	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6367980	6368038	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6368039	6368230	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6368231	6368321	1	+	1	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6368231	6368321	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6368322	6368513	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6368514	6368568	1	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6368514	6368568	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6368569	6368660	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6368661	6368769	1	+	2	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6368661	6368769	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6368770	6368883	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6368884	6369232	1	+	1	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6368884	6369232	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6369233	6369314	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6369315	6369495	1	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6369315	6369495	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6369496	6369623	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6369624	6369883	1	+	2	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6369624	6369883	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6369884	6370004	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6370005	6370283	1	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6370005	6370283	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6370284	6370568	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6370569	6370627	1	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6370569	6370627	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	intron	6370628	6370955	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	CDS	6370956	6371142	1	+	1	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	exon	6370956	6371142	.	+	.	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
Phchi.S6	AUGUSTUS	stop_codon	6371143	6371145	.	+	0	transcript_id "Phchi.S6G086400.t1"; gene_id "Phchi.S6G086400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1747.t1 is derived from g8667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2843401	2844208	.	+	.	Phchi.S5G035600
Phchi.S5	AUGUSTUS	transcript	2843401	2844208	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	start_codon	2843401	2843403	.	+	0	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	CDS	2843401	2843586	0.51	+	0	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	exon	2843401	2843586	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	intron	2843587	2843770	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	CDS	2843771	2843950	0.96	+	0	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	exon	2843771	2843950	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	intron	2843951	2844082	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	CDS	2844083	2844098	0.86	+	0	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	exon	2844083	2844098	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	intron	2844099	2844179	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	CDS	2844180	2844208	0.87	+	2	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	exon	2844180	2844208	.	+	.	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
Phchi.S5	AUGUSTUS	stop_codon	2844209	2844211	.	+	0	transcript_id "Phchi.S5G035600.t1"; gene_id "Phchi.S5G035600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg428.t1 is derived from g10210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3042059	3043543	.	-	.	Phchi.S6G038700
Phchi.S6	AUGUSTUS	transcript	3042059	3043543	.	-	.	transcript_id "Phchi.S6G038700.t1"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	stop_codon	3042056	3042058	.	-	0	transcript_id "Phchi.S6G038700.t1"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	CDS	3042059	3043543	0.97	-	0	transcript_id "Phchi.S6G038700.t1"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	exon	3042059	3043543	.	-	.	transcript_id "Phchi.S6G038700.t1"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	start_codon	3043541	3043543	.	-	0	transcript_id "Phchi.S6G038700.t1"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	transcript	3042059	3043096	.	-	.	transcript_id "Phchi.S6G038700.t2"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	stop_codon	3042056	3042058	.	-	0	transcript_id "Phchi.S6G038700.t2"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	CDS	3042059	3043096	0.9	-	0	transcript_id "Phchi.S6G038700.t2"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	exon	3042059	3043096	.	-	.	transcript_id "Phchi.S6G038700.t2"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	start_codon	3043094	3043096	.	-	0	transcript_id "Phchi.S6G038700.t2"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	transcript	3042059	3043255	.	-	.	transcript_id "Phchi.S6G038700.t3"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	stop_codon	3042056	3042058	.	-	0	transcript_id "Phchi.S6G038700.t3"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	CDS	3042059	3043255	0.63	-	0	transcript_id "Phchi.S6G038700.t3"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	exon	3042059	3043255	.	-	.	transcript_id "Phchi.S6G038700.t3"; gene_id "Phchi.S6G038700"
Phchi.S6	AUGUSTUS	start_codon	3043253	3043255	.	-	0	transcript_id "Phchi.S6G038700.t3"; gene_id "Phchi.S6G038700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5603.t1 is derived from g2773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17840101	17841093	.	+	.	Phchi.S1G276200
Phchi.S1	AUGUSTUS	transcript	17840101	17841093	.	+	.	transcript_id "Phchi.S1G276200.t1"; gene_id "Phchi.S1G276200"
Phchi.S1	AUGUSTUS	start_codon	17840101	17840103	.	+	0	transcript_id "Phchi.S1G276200.t1"; gene_id "Phchi.S1G276200"
Phchi.S1	AUGUSTUS	CDS	17840101	17841093	0.65	+	0	transcript_id "Phchi.S1G276200.t1"; gene_id "Phchi.S1G276200"
Phchi.S1	AUGUSTUS	exon	17840101	17841093	.	+	.	transcript_id "Phchi.S1G276200.t1"; gene_id "Phchi.S1G276200"
Phchi.S1	AUGUSTUS	stop_codon	17841094	17841096	.	+	0	transcript_id "Phchi.S1G276200.t1"; gene_id "Phchi.S1G276200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13372.t1 is derived from g11838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6391299	6396552	.	-	.	Phchi.S3G069100
Phchi.S3	AUGUSTUS	transcript	6391299	6396552	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	stop_codon	6391296	6391298	.	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6391299	6391544	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6391299	6391544	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6391545	6391628	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6391629	6391745	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6391629	6391745	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6391746	6391839	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6391840	6391941	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6391840	6391941	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6391942	6392031	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6392032	6392124	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6392032	6392124	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6392125	6392318	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6392319	6392570	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6392319	6392570	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6392571	6392675	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6392676	6394844	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6392676	6394844	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6394845	6395109	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6395110	6395281	1	-	1	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6395110	6395281	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6395282	6395435	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6395436	6395494	0.86	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6395436	6395494	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6395495	6395597	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6395598	6395660	1	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6395598	6395660	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6395661	6395792	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6395793	6395877	1	-	1	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6395793	6395877	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6395878	6396284	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6396285	6396412	0.62	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6396285	6396412	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	intron	6396413	6396528	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	CDS	6396529	6396552	0.55	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	exon	6396529	6396552	.	-	.	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
Phchi.S3	AUGUSTUS	start_codon	6396550	6396552	.	-	0	transcript_id "Phchi.S3G069100.t1"; gene_id "Phchi.S3G069100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4688.t1 is derived from g1858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12104540	12105965	.	+	.	Phchi.S1G184700
Phchi.S1	AUGUSTUS	transcript	12104540	12105965	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	start_codon	12104540	12104542	.	+	0	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	CDS	12104540	12104792	0.86	+	0	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	exon	12104540	12104792	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	intron	12104793	12104954	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	CDS	12104955	12105273	0.2	+	2	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	exon	12104955	12105273	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	intron	12105274	12105397	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	CDS	12105398	12105489	0.89	+	1	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	exon	12105398	12105489	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	intron	12105490	12105664	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	CDS	12105665	12105730	1	+	2	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	exon	12105665	12105730	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	intron	12105731	12105870	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	CDS	12105871	12105965	1	+	2	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	exon	12105871	12105965	.	+	.	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
Phchi.S1	AUGUSTUS	stop_codon	12105966	12105968	.	+	0	transcript_id "Phchi.S1G184700.t1"; gene_id "Phchi.S1G184700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7153.t1 is derived from g4325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27312088	27313931	.	-	.	Phchi.S1G431200
Phchi.S1	AUGUSTUS	transcript	27312088	27313931	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	stop_codon	27312085	27312087	.	-	0	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	CDS	27312088	27312205	0.87	-	1	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	exon	27312088	27312205	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	intron	27312206	27312294	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	CDS	27312295	27312338	0.86	-	0	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	exon	27312295	27312338	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	intron	27312339	27312501	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	CDS	27312502	27312871	0.96	-	1	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	exon	27312502	27312871	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	intron	27312872	27312996	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	CDS	27312997	27313424	0.94	-	0	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	exon	27312997	27313424	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	intron	27313425	27313556	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	CDS	27313557	27313657	1	-	2	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	exon	27313557	27313657	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	intron	27313658	27313825	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	CDS	27313826	27313931	0.99	-	0	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	exon	27313826	27313931	.	-	.	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
Phchi.S1	AUGUSTUS	start_codon	27313929	27313931	.	-	0	transcript_id "Phchi.S1G431200.t1"; gene_id "Phchi.S1G431200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9207.t1 is derived from g6382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40386945	40389138	.	+	.	Phchi.S1G636600
Phchi.S1	AUGUSTUS	transcript	40386945	40389138	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	start_codon	40386945	40386947	.	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40386945	40387124	0.68	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40386945	40387124	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40387125	40387209	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40387210	40387277	0.99	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40387210	40387277	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40387278	40387380	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40387381	40387555	1	+	1	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40387381	40387555	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40387556	40387647	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40387648	40387824	1	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40387648	40387824	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40387825	40387921	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40387922	40388053	1	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40387922	40388053	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40388054	40388154	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40388155	40388253	1	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40388155	40388253	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40388254	40388346	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40388347	40388463	1	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40388347	40388463	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40388464	40388646	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40388647	40388742	1	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40388647	40388742	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40388743	40388827	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40388828	40388940	1	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40388828	40388940	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	intron	40388941	40389026	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	CDS	40389027	40389138	0.99	+	1	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	exon	40389027	40389138	.	+	.	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
Phchi.S1	AUGUSTUS	stop_codon	40389139	40389141	.	+	0	transcript_id "Phchi.S1G636600.t1"; gene_id "Phchi.S1G636600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4581.t1 is derived from g1751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11198773	11200160	.	+	.	Phchi.S1G174000
Phchi.S1	AUGUSTUS	transcript	11198773	11200160	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	start_codon	11198773	11198775	.	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	CDS	11198773	11199039	0.83	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	exon	11198773	11199039	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	intron	11199040	11199156	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	CDS	11199157	11199263	1	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	exon	11199157	11199263	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	intron	11199264	11199361	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	CDS	11199362	11199470	1	+	1	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	exon	11199362	11199470	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	intron	11199471	11199651	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	CDS	11199652	11199822	0.82	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	exon	11199652	11199822	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	intron	11199823	11199924	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	CDS	11199925	11199975	0.82	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	exon	11199925	11199975	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	intron	11199976	11200103	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	CDS	11200104	11200160	0.87	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	exon	11200104	11200160	.	+	.	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
Phchi.S1	AUGUSTUS	stop_codon	11200161	11200163	.	+	0	transcript_id "Phchi.S1G174000.t1"; gene_id "Phchi.S1G174000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1261.t1 is derived from g11044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8700099	8703731	.	-	.	Phchi.S6G122000
Phchi.S6	AUGUSTUS	transcript	8700099	8703731	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	stop_codon	8700096	8700098	.	-	0	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8700099	8700245	1	-	0	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8700099	8700245	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8700246	8700373	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8700374	8700961	0.78	-	0	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8700374	8700961	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8700962	8701055	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8701056	8701894	0.78	-	2	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8701056	8701894	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8701895	8702108	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8702109	8702335	0.35	-	1	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8702109	8702335	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8702336	8702442	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8702443	8702929	0.52	-	2	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8702443	8702929	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8702930	8703032	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8703033	8703209	0.99	-	2	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8703033	8703209	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8703210	8703309	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8703310	8703413	1	-	1	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8703310	8703413	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	intron	8703414	8703510	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	CDS	8703511	8703731	1	-	0	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	exon	8703511	8703731	.	-	.	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
Phchi.S6	AUGUSTUS	start_codon	8703729	8703731	.	-	0	transcript_id "Phchi.S6G122000.t1"; gene_id "Phchi.S6G122000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2127.t1 is derived from g9047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4979316	4981008	.	-	.	Phchi.S5G073600
Phchi.S5	AUGUSTUS	transcript	4979316	4981008	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	stop_codon	4979313	4979315	.	-	0	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	CDS	4979316	4979797	0.85	-	2	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	exon	4979316	4979797	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	intron	4979798	4979882	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	CDS	4979883	4979999	0.88	-	2	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	exon	4979883	4979999	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	intron	4980000	4980232	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	CDS	4980233	4980398	0.9	-	0	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	exon	4980233	4980398	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	intron	4980399	4980486	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	CDS	4980487	4981008	0.97	-	0	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	exon	4980487	4981008	.	-	.	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
Phchi.S5	AUGUSTUS	start_codon	4981006	4981008	.	-	0	transcript_id "Phchi.S5G073600.t1"; gene_id "Phchi.S5G073600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13684.t1 is derived from g12151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8192301	8193257	.	+	.	Phchi.S3G100300
Phchi.S3	AUGUSTUS	transcript	8192301	8193257	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	start_codon	8192301	8192303	.	+	0	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	CDS	8192301	8192365	1	+	0	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	exon	8192301	8192365	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	intron	8192366	8192452	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	CDS	8192453	8192629	1	+	1	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	exon	8192453	8192629	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	intron	8192630	8192734	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	CDS	8192735	8192993	1	+	1	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	exon	8192735	8192993	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	intron	8192994	8193068	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	CDS	8193069	8193257	1	+	0	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	exon	8193069	8193257	.	+	.	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
Phchi.S3	AUGUSTUS	stop_codon	8193258	8193260	.	+	0	transcript_id "Phchi.S3G100300.t1"; gene_id "Phchi.S3G100300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10229.t1 is derived from g7405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46484459	46486138	.	-	.	Phchi.S1G738800
Phchi.S1	AUGUSTUS	transcript	46484459	46486138	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	stop_codon	46484456	46484458	.	-	0	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	CDS	46484459	46484498	1	-	1	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	exon	46484459	46484498	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	intron	46484499	46484648	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	CDS	46484649	46484723	1	-	1	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	exon	46484649	46484723	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	intron	46484724	46484823	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	CDS	46484824	46484926	1	-	2	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	exon	46484824	46484926	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	intron	46484927	46485019	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	CDS	46485020	46485800	1	-	0	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	exon	46485020	46485800	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	intron	46485801	46485883	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	CDS	46485884	46486138	0.89	-	0	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	exon	46485884	46486138	.	-	.	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
Phchi.S1	AUGUSTUS	start_codon	46486136	46486138	.	-	0	transcript_id "Phchi.S1G738800.t1"; gene_id "Phchi.S1G738800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6637.t1 is derived from g3809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24191054	24192495	.	+	.	Phchi.S1G379600
Phchi.S1	AUGUSTUS	transcript	24191054	24192495	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	start_codon	24191054	24191056	.	+	0	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24191054	24191113	0.99	+	0	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24191054	24191113	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	intron	24191114	24191179	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24191180	24191345	1	+	0	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24191180	24191345	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	intron	24191346	24191433	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24191434	24191489	1	+	2	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24191434	24191489	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	intron	24191490	24191571	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24191572	24191690	1	+	0	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24191572	24191690	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	intron	24191691	24191789	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24191790	24192009	1	+	1	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24191790	24192009	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	intron	24192010	24192124	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24192125	24192236	1	+	0	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24192125	24192236	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	intron	24192237	24192406	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	CDS	24192407	24192495	0.77	+	2	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	exon	24192407	24192495	.	+	.	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
Phchi.S1	AUGUSTUS	stop_codon	24192496	24192498	.	+	0	transcript_id "Phchi.S1G379600.t1"; gene_id "Phchi.S1G379600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2956.t1 is derived from g125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	782187	784822	.	+	.	Phchi.S1G011500
Phchi.S1	AUGUSTUS	transcript	782187	784822	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	start_codon	782187	782189	.	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	782187	782240	0.44	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	782187	782240	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	782241	782310	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	782311	782349	0.8	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	782311	782349	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	782350	782473	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	782474	782900	0.38	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	782474	782900	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	782901	783130	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	783131	783635	0.13	+	2	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	783131	783635	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	783636	783742	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	783743	783785	0.5	+	1	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	783743	783785	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	783786	783895	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	783896	783988	0.81	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	783896	783988	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	783989	784152	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	784153	784215	1	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	784153	784215	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	784216	784319	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	784320	784415	1	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	784320	784415	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	784416	784559	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	784560	784637	1	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	784560	784637	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	intron	784638	784738	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	CDS	784739	784822	1	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	exon	784739	784822	.	+	.	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
Phchi.S1	AUGUSTUS	stop_codon	784823	784825	.	+	0	transcript_id "Phchi.S1G011500.t1"; gene_id "Phchi.S1G011500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7047.t1 is derived from g4219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26588454	26588957	.	+	.	Phchi.S1G420600
Phchi.S1	AUGUSTUS	transcript	26588454	26588957	.	+	.	transcript_id "Phchi.S1G420600.t1"; gene_id "Phchi.S1G420600"
Phchi.S1	AUGUSTUS	start_codon	26588454	26588456	.	+	0	transcript_id "Phchi.S1G420600.t1"; gene_id "Phchi.S1G420600"
Phchi.S1	AUGUSTUS	CDS	26588454	26588957	0.73	+	0	transcript_id "Phchi.S1G420600.t1"; gene_id "Phchi.S1G420600"
Phchi.S1	AUGUSTUS	exon	26588454	26588957	.	+	.	transcript_id "Phchi.S1G420600.t1"; gene_id "Phchi.S1G420600"
Phchi.S1	AUGUSTUS	stop_codon	26588958	26588960	.	+	0	transcript_id "Phchi.S1G420600.t1"; gene_id "Phchi.S1G420600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5160.t1 is derived from g2330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15198550	15199305	.	+	.	Phchi.S1G231900
Phchi.S1	AUGUSTUS	transcript	15198550	15199305	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	start_codon	15198550	15198552	.	+	0	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	CDS	15198550	15198759	0.38	+	0	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	exon	15198550	15198759	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	intron	15198760	15198849	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	CDS	15198850	15198993	1	+	0	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	exon	15198850	15198993	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	intron	15198994	15199091	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	CDS	15199092	15199142	1	+	0	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	exon	15199092	15199142	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	intron	15199143	15199221	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	CDS	15199222	15199305	1	+	0	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	exon	15199222	15199305	.	+	.	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
Phchi.S1	AUGUSTUS	stop_codon	15199306	15199308	.	+	0	transcript_id "Phchi.S1G231900.t1"; gene_id "Phchi.S1G231900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1262.t1 is derived from g11045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8704230	8706211	.	-	.	Phchi.S6G122100
Phchi.S6	AUGUSTUS	transcript	8704230	8706211	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	stop_codon	8704227	8704229	.	-	0	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8704230	8704355	1	-	0	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8704230	8704355	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	intron	8704356	8704447	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8704448	8704585	1	-	0	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8704448	8704585	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	intron	8704586	8704683	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8704684	8704868	1	-	2	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8704684	8704868	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	intron	8704869	8704948	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8704949	8705135	1	-	0	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8704949	8705135	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	intron	8705136	8705271	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8705272	8705497	1	-	1	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8705272	8705497	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	intron	8705498	8705594	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8705595	8705729	0.95	-	1	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8705595	8705729	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	intron	8705730	8705834	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	CDS	8705835	8706211	0.89	-	0	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	exon	8705835	8706211	.	-	.	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
Phchi.S6	AUGUSTUS	start_codon	8706209	8706211	.	-	0	transcript_id "Phchi.S6G122100.t1"; gene_id "Phchi.S6G122100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2655.t1 is derived from g9575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8048628	8049539	.	+	.	Phchi.S5G126400
Phchi.S5	AUGUSTUS	transcript	8048628	8049539	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	start_codon	8048628	8048630	.	+	0	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	CDS	8048628	8048888	0.69	+	0	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	exon	8048628	8048888	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	intron	8048889	8048990	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	CDS	8048991	8049060	0.95	+	0	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	exon	8048991	8049060	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	intron	8049061	8049214	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	CDS	8049215	8049305	0.66	+	2	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	exon	8049215	8049305	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	intron	8049306	8049475	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	CDS	8049476	8049539	0.93	+	1	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	exon	8049476	8049539	.	+	.	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
Phchi.S5	AUGUSTUS	stop_codon	8049540	8049542	.	+	0	transcript_id "Phchi.S5G126400.t1"; gene_id "Phchi.S5G126400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7032.t1 is derived from g4204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26497124	26499532	.	+	.	Phchi.S1G419100
Phchi.S1	AUGUSTUS	transcript	26497124	26499532	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	start_codon	26497124	26497126	.	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26497124	26497301	0.98	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26497124	26497301	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26497302	26497426	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26497427	26497809	1	+	2	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26497427	26497809	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26497810	26497899	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26497900	26498149	1	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26497900	26498149	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26498150	26498225	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26498226	26498394	1	+	2	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26498226	26498394	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26498395	26498511	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26498512	26498614	1	+	1	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26498512	26498614	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26498615	26498711	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26498712	26498825	1	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26498712	26498825	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26498826	26498909	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26498910	26499131	1	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26498910	26499131	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	intron	26499132	26499253	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	CDS	26499254	26499532	0.82	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	exon	26499254	26499532	.	+	.	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
Phchi.S1	AUGUSTUS	stop_codon	26499533	26499535	.	+	0	transcript_id "Phchi.S1G419100.t1"; gene_id "Phchi.S1G419100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2414.t1 is derived from g9334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6541645	6542622	.	-	.	Phchi.S5G102300
Phchi.S5	AUGUSTUS	transcript	6541645	6542622	.	-	.	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	stop_codon	6541642	6541644	.	-	0	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	CDS	6541645	6541890	0.97	-	0	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	exon	6541645	6541890	.	-	.	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	intron	6541891	6542048	.	-	.	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	CDS	6542049	6542187	0.98	-	1	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	exon	6542049	6542187	.	-	.	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	intron	6542188	6542314	.	-	.	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	CDS	6542315	6542622	0.95	-	0	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	exon	6542315	6542622	.	-	.	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
Phchi.S5	AUGUSTUS	start_codon	6542620	6542622	.	-	0	transcript_id "Phchi.S5G102300.t1"; gene_id "Phchi.S5G102300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14678.t1 is derived from g13146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14135586	14136758	.	+	.	Phchi.S3G199700
Phchi.S3	AUGUSTUS	transcript	14135586	14136758	.	+	.	transcript_id "Phchi.S3G199700.t1"; gene_id "Phchi.S3G199700"
Phchi.S3	AUGUSTUS	start_codon	14135586	14135588	.	+	0	transcript_id "Phchi.S3G199700.t1"; gene_id "Phchi.S3G199700"
Phchi.S3	AUGUSTUS	CDS	14135586	14136758	0.96	+	0	transcript_id "Phchi.S3G199700.t1"; gene_id "Phchi.S3G199700"
Phchi.S3	AUGUSTUS	exon	14135586	14136758	.	+	.	transcript_id "Phchi.S3G199700.t1"; gene_id "Phchi.S3G199700"
Phchi.S3	AUGUSTUS	stop_codon	14136759	14136761	.	+	0	transcript_id "Phchi.S3G199700.t1"; gene_id "Phchi.S3G199700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15981.t1 is derived from g15989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C20	AUGUSTUS	gene	11763	12908	.	-	.	Phchi.C20G000100
Phchi.C20	AUGUSTUS	transcript	11763	12908	.	-	.	transcript_id "Phchi.C20G000100.t1"; gene_id "Phchi.C20G000100"
Phchi.C20	AUGUSTUS	stop_codon	11760	11762	.	-	0	transcript_id "Phchi.C20G000100.t1"; gene_id "Phchi.C20G000100"
Phchi.C20	AUGUSTUS	CDS	11763	12908	1	-	0	transcript_id "Phchi.C20G000100.t1"; gene_id "Phchi.C20G000100"
Phchi.C20	AUGUSTUS	exon	11763	12908	.	-	.	transcript_id "Phchi.C20G000100.t1"; gene_id "Phchi.C20G000100"
Phchi.C20	AUGUSTUS	start_codon	12906	12908	.	-	0	transcript_id "Phchi.C20G000100.t1"; gene_id "Phchi.C20G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12247.t1 is derived from g7923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7004122	7006244	.	-	.	Phchi.S2G032700
Phchi.S2	AUGUSTUS	transcript	7004122	7006244	.	-	.	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	stop_codon	7004119	7004121	.	-	0	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	CDS	7004122	7004966	1	-	2	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	exon	7004122	7004966	.	-	.	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	intron	7004967	7005172	.	-	.	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	CDS	7005173	7006244	0.96	-	0	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	exon	7005173	7006244	.	-	.	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
Phchi.S2	AUGUSTUS	start_codon	7006242	7006244	.	-	0	transcript_id "Phchi.S2G032700.t1"; gene_id "Phchi.S2G032700"
# This transcript jg3767.t2 is derived from g936.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3768.t1 is derived from g937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5614507	5615835	.	+	.	Phchi.S1G092700
Phchi.S1	AUGUSTUS	transcript	5614507	5615835	.	+	.	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	start_codon	5614507	5614509	.	+	0	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	CDS	5614507	5614640	0.98	+	0	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	exon	5614507	5614640	.	+	.	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	intron	5614641	5614772	.	+	.	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	CDS	5614773	5615835	0.97	+	1	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	exon	5614773	5615835	.	+	.	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
Phchi.S1	AUGUSTUS	stop_codon	5615836	5615838	.	+	0	transcript_id "Phchi.S1G092700.t1"; gene_id "Phchi.S1G092700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14640.t1 is derived from g13108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13888711	13892880	.	+	.	Phchi.S3G195900
Phchi.S3	AUGUSTUS	transcript	13888711	13892880	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	start_codon	13888711	13888713	.	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13888711	13888818	0.5	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13888711	13888818	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13888819	13888965	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13888966	13889053	0.44	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13888966	13889053	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13889054	13889168	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13889169	13889367	0.98	+	2	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13889169	13889367	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13889368	13889485	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13889486	13889564	0.99	+	1	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13889486	13889564	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13889565	13889715	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13889716	13889912	1	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13889716	13889912	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13889913	13890028	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13890029	13890230	0.92	+	1	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13890029	13890230	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13890231	13890357	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13890358	13890501	0.75	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13890358	13890501	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13890502	13890630	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13890631	13890831	0.65	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13890631	13890831	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13890832	13890921	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13890922	13891110	1	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13890922	13891110	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13891111	13891257	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13891258	13891530	1	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13891258	13891530	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13891531	13891626	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13891627	13891827	0.99	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13891627	13891827	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13891828	13891908	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13891909	13892148	0.99	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13891909	13892148	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13892149	13892233	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13892234	13892374	1	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13892234	13892374	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13892375	13892462	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13892463	13892639	1	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13892463	13892639	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	intron	13892640	13892736	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	CDS	13892737	13892880	0.93	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	exon	13892737	13892880	.	+	.	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
Phchi.S3	AUGUSTUS	stop_codon	13892881	13892883	.	+	0	transcript_id "Phchi.S3G195900.t1"; gene_id "Phchi.S3G195900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10294.t1 is derived from g7470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46854776	46855114	.	+	.	Phchi.S1G745300
Phchi.S1	AUGUSTUS	transcript	46854776	46855114	.	+	.	transcript_id "Phchi.S1G745300.t1"; gene_id "Phchi.S1G745300"
Phchi.S1	AUGUSTUS	start_codon	46854776	46854778	.	+	0	transcript_id "Phchi.S1G745300.t1"; gene_id "Phchi.S1G745300"
Phchi.S1	AUGUSTUS	CDS	46854776	46855114	0.83	+	0	transcript_id "Phchi.S1G745300.t1"; gene_id "Phchi.S1G745300"
Phchi.S1	AUGUSTUS	exon	46854776	46855114	.	+	.	transcript_id "Phchi.S1G745300.t1"; gene_id "Phchi.S1G745300"
Phchi.S1	AUGUSTUS	stop_codon	46855115	46855117	.	+	0	transcript_id "Phchi.S1G745300.t1"; gene_id "Phchi.S1G745300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2773.t1 is derived from g9693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8760900	8763620	.	+	.	Phchi.S5G138200
Phchi.S5	AUGUSTUS	transcript	8760900	8763620	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	start_codon	8760900	8760902	.	+	0	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	CDS	8760900	8761053	0.54	+	0	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	exon	8760900	8761053	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	intron	8761054	8761185	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	CDS	8761186	8761249	0.78	+	2	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	exon	8761186	8761249	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	intron	8761250	8761396	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	CDS	8761397	8763188	0.81	+	1	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	exon	8761397	8763188	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	intron	8763189	8763560	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	CDS	8763561	8763620	0.6	+	0	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	exon	8763561	8763620	.	+	.	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
Phchi.S5	AUGUSTUS	stop_codon	8763621	8763623	.	+	0	transcript_id "Phchi.S5G138200.t1"; gene_id "Phchi.S5G138200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7774.t1 is derived from g4948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31174396	31175145	.	+	.	Phchi.S1G493300
Phchi.S1	AUGUSTUS	transcript	31174396	31175145	.	+	.	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	start_codon	31174396	31174398	.	+	0	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	CDS	31174396	31174532	0.73	+	0	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	exon	31174396	31174532	.	+	.	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	intron	31174533	31174835	.	+	.	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	CDS	31174836	31175145	0.21	+	1	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	exon	31174836	31175145	.	+	.	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
Phchi.S1	AUGUSTUS	stop_codon	31175146	31175148	.	+	0	transcript_id "Phchi.S1G493300.t1"; gene_id "Phchi.S1G493300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7329.t1 is derived from g4501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28534144	28535546	.	+	.	Phchi.S1G448800
Phchi.S1	AUGUSTUS	transcript	28534144	28535546	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	start_codon	28534144	28534146	.	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28534144	28534242	0.92	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28534144	28534242	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	intron	28534243	28534463	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28534464	28534551	1	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28534464	28534551	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	intron	28534552	28534676	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28534677	28534786	1	+	2	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28534677	28534786	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	intron	28534787	28534896	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28534897	28534960	1	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28534897	28534960	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	intron	28534961	28535062	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28535063	28535127	1	+	2	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28535063	28535127	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	intron	28535128	28535287	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28535288	28535353	1	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28535288	28535353	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	intron	28535354	28535453	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	CDS	28535454	28535546	0.97	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	exon	28535454	28535546	.	+	.	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
Phchi.S1	AUGUSTUS	stop_codon	28535547	28535549	.	+	0	transcript_id "Phchi.S1G448800.t1"; gene_id "Phchi.S1G448800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5315.t1 is derived from g2485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16254096	16257745	.	-	.	Phchi.S1G247400
Phchi.S1	AUGUSTUS	transcript	16254096	16257745	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	stop_codon	16254093	16254095	.	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16254096	16254178	1	-	2	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16254096	16254178	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16254179	16254268	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16254269	16254447	1	-	1	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16254269	16254447	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16254448	16254570	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16254571	16254655	1	-	2	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16254571	16254655	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16254656	16254753	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16254754	16254981	1	-	2	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16254754	16254981	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16254982	16255128	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16255129	16255189	1	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16255129	16255189	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16255190	16255309	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16255310	16255392	1	-	2	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16255310	16255392	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16255393	16255479	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16255480	16255589	1	-	1	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16255480	16255589	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16255590	16255675	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16255676	16255808	1	-	2	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16255676	16255808	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16255809	16256037	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16256038	16256188	1	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16256038	16256188	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16256189	16256312	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16256313	16256415	1	-	1	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16256313	16256415	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16256416	16256517	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16256518	16256626	1	-	2	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16256518	16256626	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16256627	16256711	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16256712	16256871	1	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16256712	16256871	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16256872	16256952	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16256953	16257054	1	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16256953	16257054	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16257055	16257135	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16257136	16257253	1	-	1	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16257136	16257253	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16257254	16257347	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16257348	16257502	1	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16257348	16257502	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	intron	16257503	16257601	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	CDS	16257602	16257745	1	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	exon	16257602	16257745	.	-	.	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
Phchi.S1	AUGUSTUS	start_codon	16257743	16257745	.	-	0	transcript_id "Phchi.S1G247400.t1"; gene_id "Phchi.S1G247400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11522.t1 is derived from g15572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6890461	6893996	.	-	.	Phchi.S4G110400
Phchi.S4	AUGUSTUS	transcript	6890461	6893996	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	stop_codon	6890458	6890460	.	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6890461	6890827	0.99	-	1	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6890461	6890827	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6890828	6891034	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6891035	6891232	1	-	1	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6891035	6891232	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6891233	6891322	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6891323	6891450	1	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6891323	6891450	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6891451	6891641	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6891642	6891908	1	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6891642	6891908	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6891909	6892050	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6892051	6892419	1	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6892051	6892419	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6892420	6892527	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6892528	6893396	0.76	-	2	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6892528	6893396	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6893397	6893468	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6893469	6893511	0.71	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6893469	6893511	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6893512	6893647	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6893648	6893860	0.49	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6893648	6893860	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	intron	6893861	6893969	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	CDS	6893970	6893996	0.33	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	exon	6893970	6893996	.	-	.	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
Phchi.S4	AUGUSTUS	start_codon	6893994	6893996	.	-	0	transcript_id "Phchi.S4G110400.t1"; gene_id "Phchi.S4G110400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5813.t1 is derived from g2983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19072992	19075764	.	+	.	Phchi.S1G297200
Phchi.S1	AUGUSTUS	transcript	19072992	19075764	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	start_codon	19072992	19072994	.	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19072992	19073585	0.98	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19072992	19073585	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	intron	19073586	19073850	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19073851	19074342	1	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19073851	19074342	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	intron	19074343	19074481	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19074482	19074718	1	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19074482	19074718	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	intron	19074719	19074806	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19074807	19074953	0.59	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19074807	19074953	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	intron	19074954	19075088	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19075089	19075139	0.59	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19075089	19075139	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	intron	19075140	19075244	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19075245	19075487	1	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19075245	19075487	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	intron	19075488	19075584	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	CDS	19075585	19075764	1	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	exon	19075585	19075764	.	+	.	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
Phchi.S1	AUGUSTUS	stop_codon	19075765	19075767	.	+	0	transcript_id "Phchi.S1G297200.t1"; gene_id "Phchi.S1G297200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9885.t1 is derived from g7061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44255152	44256309	.	+	.	Phchi.S1G704400
Phchi.S1	AUGUSTUS	transcript	44255152	44256309	.	+	.	transcript_id "Phchi.S1G704400.t1"; gene_id "Phchi.S1G704400"
Phchi.S1	AUGUSTUS	start_codon	44255152	44255154	.	+	0	transcript_id "Phchi.S1G704400.t1"; gene_id "Phchi.S1G704400"
Phchi.S1	AUGUSTUS	CDS	44255152	44256309	0.63	+	0	transcript_id "Phchi.S1G704400.t1"; gene_id "Phchi.S1G704400"
Phchi.S1	AUGUSTUS	exon	44255152	44256309	.	+	.	transcript_id "Phchi.S1G704400.t1"; gene_id "Phchi.S1G704400"
Phchi.S1	AUGUSTUS	stop_codon	44256310	44256312	.	+	0	transcript_id "Phchi.S1G704400.t1"; gene_id "Phchi.S1G704400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8542.t1 is derived from g5717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36551517	36557440	.	+	.	Phchi.S1G570100
Phchi.S1	AUGUSTUS	transcript	36551517	36557440	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	start_codon	36551517	36551519	.	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36551517	36551790	0.38	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36551517	36551790	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36551791	36551921	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36551922	36551998	0.52	+	2	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36551922	36551998	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36551999	36552167	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36552168	36552319	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36552168	36552319	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36552320	36552410	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36552411	36552498	1	+	1	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36552411	36552498	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36552499	36552602	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36552603	36552845	0.54	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36552603	36552845	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36552846	36552955	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36552956	36553051	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36552956	36553051	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36553052	36553177	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36553178	36553366	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36553178	36553366	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36553367	36553471	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36553472	36553631	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36553472	36553631	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36553632	36553722	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36553723	36553853	1	+	2	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36553723	36553853	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36553854	36554038	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36554039	36554209	0.97	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36554039	36554209	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36554210	36554312	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36554313	36554585	0.97	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36554313	36554585	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36554586	36554719	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36554720	36554914	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36554720	36554914	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36554915	36555100	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36555101	36555304	0.99	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36555101	36555304	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36555305	36555412	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36555413	36555482	0.99	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36555413	36555482	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36555483	36555576	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36555577	36555725	1	+	2	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36555577	36555725	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36555726	36555867	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36555868	36556176	0.95	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36555868	36556176	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36556177	36556279	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36556280	36556339	0.99	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36556280	36556339	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36556340	36556435	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36556436	36556588	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36556436	36556588	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36556589	36556683	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36556684	36556794	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36556684	36556794	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	intron	36556795	36556927	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	CDS	36556928	36557440	1	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	exon	36556928	36557440	.	+	.	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
Phchi.S1	AUGUSTUS	stop_codon	36557441	36557443	.	+	0	transcript_id "Phchi.S1G570100.t1"; gene_id "Phchi.S1G570100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5125.t1 is derived from g2295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15041806	15043091	.	-	.	Phchi.S1G228400
Phchi.S1	AUGUSTUS	transcript	15041806	15043091	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	stop_codon	15041803	15041805	.	-	0	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	CDS	15041806	15042003	0.67	-	0	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	exon	15041806	15042003	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	intron	15042004	15042121	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	CDS	15042122	15042248	1	-	1	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	exon	15042122	15042248	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	intron	15042249	15042363	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	CDS	15042364	15042557	1	-	0	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	exon	15042364	15042557	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	intron	15042558	15042701	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	CDS	15042702	15042811	1	-	2	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	exon	15042702	15042811	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	intron	15042812	15042913	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	CDS	15042914	15043091	0.96	-	0	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	exon	15042914	15043091	.	-	.	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
Phchi.S1	AUGUSTUS	start_codon	15043089	15043091	.	-	0	transcript_id "Phchi.S1G228400.t1"; gene_id "Phchi.S1G228400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2343.t1 is derived from g9263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6260251	6262485	.	+	.	Phchi.S5G095200
Phchi.S5	AUGUSTUS	transcript	6260251	6262485	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	start_codon	6260251	6260253	.	+	0	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	CDS	6260251	6260482	0.67	+	0	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	exon	6260251	6260482	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	intron	6260483	6260568	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	CDS	6260569	6261001	0.28	+	2	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	exon	6260569	6261001	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	intron	6261002	6261248	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	CDS	6261249	6261297	0.41	+	1	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	exon	6261249	6261297	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	intron	6261298	6261462	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	CDS	6261463	6262485	0.82	+	0	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	exon	6261463	6262485	.	+	.	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
Phchi.S5	AUGUSTUS	stop_codon	6262486	6262488	.	+	0	transcript_id "Phchi.S5G095200.t1"; gene_id "Phchi.S5G095200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13061.t1 is derived from g11526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3958512	3960524	.	-	.	Phchi.S3G038000
Phchi.S3	AUGUSTUS	transcript	3958512	3960524	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	stop_codon	3958509	3958511	.	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3958512	3958625	0.86	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3958512	3958625	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3958626	3958752	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3958753	3958803	0.89	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3958753	3958803	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3958804	3958886	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3958887	3958974	0.99	-	1	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3958887	3958974	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3958975	3959250	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3959251	3959444	0.83	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3959251	3959444	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3959445	3959670	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3959671	3959744	0.33	-	2	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3959671	3959744	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3959745	3959850	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3959851	3959919	0.24	-	2	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3959851	3959919	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3959920	3960036	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3960037	3960160	0.56	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3960037	3960160	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	intron	3960161	3960257	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	CDS	3960258	3960524	0.63	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	exon	3960258	3960524	.	-	.	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
Phchi.S3	AUGUSTUS	start_codon	3960522	3960524	.	-	0	transcript_id "Phchi.S3G038000.t1"; gene_id "Phchi.S3G038000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6404.t1 is derived from g3576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22797584	22799341	.	-	.	Phchi.S1G356300
Phchi.S1	AUGUSTUS	transcript	22797584	22799341	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	stop_codon	22797581	22797583	.	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22797584	22797653	0.97	-	1	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22797584	22797653	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22797654	22797751	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22797752	22797822	1	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22797752	22797822	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22797823	22797915	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22797916	22797974	1	-	2	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22797916	22797974	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22797975	22798073	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22798074	22798160	0.99	-	2	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22798074	22798160	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22798161	22798218	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22798219	22798291	0.99	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22798219	22798291	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22798292	22798390	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22798391	22798472	0.84	-	1	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22798391	22798472	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22798473	22798600	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22798601	22798659	0.89	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22798601	22798659	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22798660	22798774	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22798775	22798885	1	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22798775	22798885	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22798886	22798981	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22798982	22799088	1	-	2	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22798982	22799088	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	intron	22799089	22799181	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	CDS	22799182	22799341	0.99	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	exon	22799182	22799341	.	-	.	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
Phchi.S1	AUGUSTUS	start_codon	22799339	22799341	.	-	0	transcript_id "Phchi.S1G356300.t1"; gene_id "Phchi.S1G356300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8557.t1 is derived from g5732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36614257	36615264	.	+	.	Phchi.S1G571600
Phchi.S1	AUGUSTUS	transcript	36614257	36615264	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	start_codon	36614257	36614259	.	+	0	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	CDS	36614257	36614598	0.75	+	0	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	exon	36614257	36614598	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	intron	36614599	36614722	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	CDS	36614723	36614806	0.99	+	0	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	exon	36614723	36614806	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	intron	36614807	36614937	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	CDS	36614938	36615049	1	+	0	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	exon	36614938	36615049	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	intron	36615050	36615181	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	CDS	36615182	36615264	0.94	+	2	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	exon	36615182	36615264	.	+	.	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
Phchi.S1	AUGUSTUS	stop_codon	36615265	36615267	.	+	0	transcript_id "Phchi.S1G571600.t1"; gene_id "Phchi.S1G571600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12465.t1 is derived from g8142.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24853082	24858224	.	-	.	Phchi.S2G054500
Phchi.S2	AUGUSTUS	transcript	24853082	24858224	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	stop_codon	24853079	24853081	.	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853082	24853085	0.39	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853082	24853085	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853086	24853266	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853267	24853355	0.51	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853267	24853355	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853356	24853519	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853520	24853533	0.82	-	2	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853520	24853533	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853534	24853620	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853621	24853664	0.77	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853621	24853664	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853665	24853813	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853814	24853888	0.65	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853814	24853888	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853889	24853977	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853978	24854066	0.76	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853978	24854066	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24854067	24854416	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24854417	24854521	0.57	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24854417	24854521	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24854522	24854650	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24854651	24854655	0.27	-	2	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24854651	24854655	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24854656	24854880	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24854881	24855012	0.29	-	2	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24854881	24855012	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855013	24855309	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855310	24855349	0.34	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855310	24855349	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855350	24855410	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855411	24855453	0.48	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855411	24855453	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855454	24855529	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855530	24855667	0.99	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855530	24855667	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855668	24855868	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855869	24856096	0.96	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855869	24856096	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24856097	24856214	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24856215	24856316	1	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24856215	24856316	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24856317	24856534	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24856535	24856609	1	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24856535	24856609	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24856610	24857016	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24857017	24857083	1	-	2	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24857017	24857083	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24857084	24857402	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24857403	24857482	1	-	1	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24857403	24857482	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24857483	24857574	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24857575	24857653	1	-	2	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24857575	24857653	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24857654	24858056	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24858057	24858074	1	-	2	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24858057	24858074	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24858075	24858166	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24858167	24858224	0.91	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24858167	24858224	.	-	.	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	start_codon	24858222	24858224	.	-	0	transcript_id "Phchi.S2G054500.t1"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	transcript	24853082	24858224	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	stop_codon	24853079	24853081	.	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853082	24853085	0.41	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853082	24853085	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853086	24853266	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853267	24853355	0.54	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853267	24853355	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853356	24853519	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853520	24853533	0.9	-	2	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853520	24853533	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853534	24853620	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853621	24853664	0.88	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853621	24853664	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853665	24853813	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853814	24853888	0.72	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853814	24853888	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24853889	24853977	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24853978	24854066	0.77	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24853978	24854066	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24854067	24854416	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24854417	24854521	0.5	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24854417	24854521	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24854522	24854650	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24854651	24854655	0.19	-	2	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24854651	24854655	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24854656	24854880	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24854881	24855012	0.2	-	2	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24854881	24855012	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855013	24855309	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855310	24855349	0.26	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855310	24855349	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855350	24855410	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855411	24855447	0.44	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855411	24855447	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855448	24855529	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855530	24855667	1	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855530	24855667	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24855668	24855868	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24855869	24856096	0.93	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24855869	24856096	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24856097	24856214	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24856215	24856316	1	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24856215	24856316	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24856317	24856534	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24856535	24856609	1	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24856535	24856609	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24856610	24857016	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24857017	24857083	1	-	2	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24857017	24857083	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24857084	24857402	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24857403	24857482	1	-	1	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24857403	24857482	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24857483	24857574	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24857575	24857653	1	-	2	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24857575	24857653	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24857654	24858056	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24858057	24858074	1	-	2	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24858057	24858074	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	intron	24858075	24858166	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	CDS	24858167	24858224	0.87	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	exon	24858167	24858224	.	-	.	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
Phchi.S2	AUGUSTUS	start_codon	24858222	24858224	.	-	0	transcript_id "Phchi.S2G054500.t2"; gene_id "Phchi.S2G054500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5712.t1 is derived from g2882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18485427	18486810	.	+	.	Phchi.S1G287100
Phchi.S1	AUGUSTUS	transcript	18485427	18486810	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	start_codon	18485427	18485429	.	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18485427	18485565	1	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18485427	18485565	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18485566	18485649	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18485650	18485678	1	+	2	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18485650	18485678	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18485679	18485855	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18485856	18485921	1	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18485856	18485921	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18485922	18486007	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18486008	18486115	1	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18486008	18486115	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18486116	18486212	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18486213	18486278	1	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18486213	18486278	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18486279	18486364	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18486365	18486485	1	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18486365	18486485	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18486486	18486561	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18486562	18486643	1	+	2	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18486562	18486643	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	intron	18486644	18486770	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	CDS	18486771	18486810	1	+	1	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	exon	18486771	18486810	.	+	.	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
Phchi.S1	AUGUSTUS	stop_codon	18486811	18486813	.	+	0	transcript_id "Phchi.S1G287100.t1"; gene_id "Phchi.S1G287100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6728.t1 is derived from g3900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24754961	24757220	.	+	.	Phchi.S1G388700
Phchi.S1	AUGUSTUS	transcript	24754961	24757220	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	start_codon	24754961	24754963	.	+	0	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24754961	24754995	0.93	+	0	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24754961	24754995	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	intron	24754996	24755103	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24755104	24755306	0.94	+	1	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24755104	24755306	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	intron	24755307	24755403	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24755404	24755639	1	+	2	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24755404	24755639	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	intron	24755640	24755726	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24755727	24756407	0.84	+	0	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24755727	24756407	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	intron	24756408	24756551	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24756552	24756573	0.85	+	0	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24756552	24756573	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	intron	24756574	24757024	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24757025	24757080	1	+	2	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24757025	24757080	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	intron	24757081	24757169	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	CDS	24757170	24757220	0.48	+	0	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	exon	24757170	24757220	.	+	.	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
Phchi.S1	AUGUSTUS	stop_codon	24757221	24757223	.	+	0	transcript_id "Phchi.S1G388700.t1"; gene_id "Phchi.S1G388700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10195.t1 is derived from g7371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46333900	46334178	.	-	.	Phchi.S1G735400
Phchi.S1	AUGUSTUS	transcript	46333900	46334178	.	-	.	transcript_id "Phchi.S1G735400.t1"; gene_id "Phchi.S1G735400"
Phchi.S1	AUGUSTUS	stop_codon	46333897	46333899	.	-	0	transcript_id "Phchi.S1G735400.t1"; gene_id "Phchi.S1G735400"
Phchi.S1	AUGUSTUS	CDS	46333900	46334178	0.26	-	0	transcript_id "Phchi.S1G735400.t1"; gene_id "Phchi.S1G735400"
Phchi.S1	AUGUSTUS	exon	46333900	46334178	.	-	.	transcript_id "Phchi.S1G735400.t1"; gene_id "Phchi.S1G735400"
Phchi.S1	AUGUSTUS	start_codon	46334176	46334178	.	-	0	transcript_id "Phchi.S1G735400.t1"; gene_id "Phchi.S1G735400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5672.t1 is derived from g2842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18235519	18237217	.	+	.	Phchi.S1G283100
Phchi.S1	AUGUSTUS	transcript	18235519	18237217	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	start_codon	18235519	18235521	.	+	0	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18235519	18235669	1	+	0	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18235519	18235669	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18235670	18235784	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18235785	18235940	0.85	+	2	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18235785	18235940	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18235941	18236041	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236042	18236200	0.86	+	2	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236042	18236200	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236201	18236362	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236363	18236587	1	+	2	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236363	18236587	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236588	18236727	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236728	18236859	1	+	2	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236728	18236859	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236860	18236951	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236952	18237217	0.71	+	2	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236952	18237217	.	+	.	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	stop_codon	18237218	18237220	.	+	0	transcript_id "Phchi.S1G283100.t1"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	transcript	18235519	18237217	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	start_codon	18235519	18235521	.	+	0	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18235519	18235669	1	+	0	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18235519	18235669	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18235670	18235784	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18235785	18235899	0.86	+	2	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18235785	18235899	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18235900	18236041	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236042	18236050	0.83	+	1	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236042	18236050	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236051	18236149	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236150	18236200	0.84	+	1	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236150	18236200	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236201	18236292	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236293	18236404	0.57	+	1	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236293	18236404	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236405	18236505	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236506	18236587	0.51	+	0	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236506	18236587	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236588	18236727	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236728	18236859	1	+	2	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236728	18236859	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	intron	18236860	18236951	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	CDS	18236952	18237217	0.63	+	2	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	exon	18236952	18237217	.	+	.	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
Phchi.S1	AUGUSTUS	stop_codon	18237218	18237220	.	+	0	transcript_id "Phchi.S1G283100.t2"; gene_id "Phchi.S1G283100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10627.t1 is derived from g14677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1321945	1323138	.	-	.	Phchi.S4G020900
Phchi.S4	AUGUSTUS	transcript	1321945	1323138	.	-	.	transcript_id "Phchi.S4G020900.t1"; gene_id "Phchi.S4G020900"
Phchi.S4	AUGUSTUS	stop_codon	1321942	1321944	.	-	0	transcript_id "Phchi.S4G020900.t1"; gene_id "Phchi.S4G020900"
Phchi.S4	AUGUSTUS	CDS	1321945	1323138	0.97	-	0	transcript_id "Phchi.S4G020900.t1"; gene_id "Phchi.S4G020900"
Phchi.S4	AUGUSTUS	exon	1321945	1323138	.	-	.	transcript_id "Phchi.S4G020900.t1"; gene_id "Phchi.S4G020900"
Phchi.S4	AUGUSTUS	start_codon	1323136	1323138	.	-	0	transcript_id "Phchi.S4G020900.t1"; gene_id "Phchi.S4G020900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9311.t1 is derived from g6486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40898976	40899997	.	-	.	Phchi.S1G647000
Phchi.S1	AUGUSTUS	transcript	40898976	40899997	.	-	.	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	stop_codon	40898973	40898975	.	-	0	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	CDS	40898976	40899353	1	-	0	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	exon	40898976	40899353	.	-	.	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	intron	40899354	40899445	.	-	.	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	CDS	40899446	40899997	1	-	0	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	exon	40899446	40899997	.	-	.	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
Phchi.S1	AUGUSTUS	start_codon	40899995	40899997	.	-	0	transcript_id "Phchi.S1G647000.t1"; gene_id "Phchi.S1G647000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11707.t1 is derived from g15758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7781306	7781780	.	+	.	Phchi.S4G128900
Phchi.S4	AUGUSTUS	transcript	7781306	7781780	.	+	.	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	start_codon	7781306	7781308	.	+	0	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	CDS	7781306	7781384	0.83	+	0	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	exon	7781306	7781384	.	+	.	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	intron	7781385	7781454	.	+	.	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	CDS	7781455	7781567	1	+	2	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	exon	7781455	7781567	.	+	.	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	intron	7781568	7781648	.	+	.	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	CDS	7781649	7781780	0.99	+	0	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	exon	7781649	7781780	.	+	.	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
Phchi.S4	AUGUSTUS	stop_codon	7781781	7781783	.	+	0	transcript_id "Phchi.S4G128900.t1"; gene_id "Phchi.S4G128900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6388.t1 is derived from g3560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22692920	22694502	.	+	.	Phchi.S1G354700
Phchi.S1	AUGUSTUS	transcript	22692920	22694502	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	start_codon	22692920	22692922	.	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	CDS	22692920	22693179	1	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	exon	22692920	22693179	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	intron	22693180	22693337	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	CDS	22693338	22693551	1	+	1	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	exon	22693338	22693551	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	intron	22693552	22693666	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	CDS	22693667	22693753	1	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	exon	22693667	22693753	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	intron	22693754	22693828	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	CDS	22693829	22693972	0.98	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	exon	22693829	22693972	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	intron	22693973	22694078	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	CDS	22694079	22694171	1	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	exon	22694079	22694171	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	intron	22694172	22694274	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	CDS	22694275	22694502	0.96	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	exon	22694275	22694502	.	+	.	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
Phchi.S1	AUGUSTUS	stop_codon	22694503	22694505	.	+	0	transcript_id "Phchi.S1G354700.t1"; gene_id "Phchi.S1G354700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5281.t1 is derived from g2451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16015093	16015823	.	-	.	Phchi.S1G244000
Phchi.S1	AUGUSTUS	transcript	16015093	16015823	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	stop_codon	16015090	16015092	.	-	0	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	CDS	16015093	16015203	0.98	-	0	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	exon	16015093	16015203	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	intron	16015204	16015289	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	CDS	16015290	16015371	0.99	-	1	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	exon	16015290	16015371	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	intron	16015372	16015476	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	CDS	16015477	16015521	0.99	-	1	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	exon	16015477	16015521	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	intron	16015522	16015594	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	CDS	16015595	16015622	0.89	-	2	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	exon	16015595	16015622	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	intron	16015623	16015717	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	CDS	16015718	16015823	0.32	-	0	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	exon	16015718	16015823	.	-	.	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
Phchi.S1	AUGUSTUS	start_codon	16015821	16015823	.	-	0	transcript_id "Phchi.S1G244000.t1"; gene_id "Phchi.S1G244000"
# This transcript jg8748.t2 is derived from g5923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8749.t1 is derived from g5924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37783238	37786584	.	+	.	Phchi.S1G590800
Phchi.S1	AUGUSTUS	transcript	37783238	37786584	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	start_codon	37783238	37783240	.	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37783238	37783614	0.84	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37783238	37783614	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37783615	37783944	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37783945	37784242	0.92	+	1	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37783945	37784242	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37784243	37784351	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37784352	37784504	1	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37784352	37784504	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37784505	37784646	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37784647	37784925	0.97	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37784647	37784925	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37784926	37785118	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37785119	37785304	1	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37785119	37785304	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37785305	37785429	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37785430	37785560	1	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37785430	37785560	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37785561	37785685	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37785686	37785878	1	+	1	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37785686	37785878	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37785879	37785964	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37785965	37786033	1	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37785965	37786033	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37786034	37786148	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37786149	37786236	1	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37786149	37786236	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	intron	37786237	37786378	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	CDS	37786379	37786584	0.99	+	2	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	exon	37786379	37786584	.	+	.	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
Phchi.S1	AUGUSTUS	stop_codon	37786585	37786587	.	+	0	transcript_id "Phchi.S1G590800.t1"; gene_id "Phchi.S1G590800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13028.t1 is derived from g11493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3738918	3745125	.	-	.	Phchi.S3G034700
Phchi.S3	AUGUSTUS	transcript	3738918	3745125	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	stop_codon	3738915	3738917	.	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3738918	3739190	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3738918	3739190	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3739191	3739288	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3739289	3739466	1	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3739289	3739466	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3739467	3739593	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3739594	3739739	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3739594	3739739	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3739740	3739824	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3739825	3739917	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3739825	3739917	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3739918	3740042	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3740043	3740162	0.99	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3740043	3740162	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3740163	3740268	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3740269	3740323	0.99	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3740269	3740323	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3740324	3740407	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3740408	3740482	1	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3740408	3740482	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3740483	3740561	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3740562	3740656	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3740562	3740656	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3740657	3740743	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3740744	3740825	1	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3740744	3740825	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3740826	3740916	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3740917	3741040	1	-	2	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3740917	3741040	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3741041	3741122	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3741123	3741278	1	-	2	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3741123	3741278	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3741279	3741375	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3741376	3741427	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3741376	3741427	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3741428	3741525	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3741526	3741613	0.97	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3741526	3741613	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3741614	3741710	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3741711	3741831	0.89	-	2	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3741711	3741831	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3741832	3741962	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3741963	3742044	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3741963	3742044	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3742045	3742235	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3742236	3742344	1	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3742236	3742344	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3742345	3742487	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3742488	3742608	1	-	2	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3742488	3742608	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3742609	3742725	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3742726	3742801	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3742726	3742801	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3742802	3742905	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3742906	3742974	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3742906	3742974	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3742975	3743092	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3743093	3743220	1	-	2	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3743093	3743220	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3743221	3743653	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3743654	3743745	1	-	1	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3743654	3743745	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3743746	3743844	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3743845	3743885	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3743845	3743885	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3743886	3744012	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3744013	3744150	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3744013	3744150	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3744151	3744247	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3744248	3744391	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3744248	3744391	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3744392	3744505	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3744506	3744553	0.97	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3744506	3744553	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3744554	3744643	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3744644	3744706	1	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3744644	3744706	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3744707	3744807	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3744808	3744885	0.94	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3744808	3744885	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	intron	3744886	3744984	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	CDS	3744985	3745125	0.93	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	exon	3744985	3745125	.	-	.	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
Phchi.S3	AUGUSTUS	start_codon	3745123	3745125	.	-	0	transcript_id "Phchi.S3G034700.t1"; gene_id "Phchi.S3G034700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8178.t1 is derived from g5353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34294864	34296358	.	+	.	Phchi.S1G533700
Phchi.S1	AUGUSTUS	transcript	34294864	34296358	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	start_codon	34294864	34294866	.	+	0	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	CDS	34294864	34295151	0.5	+	0	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	exon	34294864	34295151	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	intron	34295152	34295289	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	CDS	34295290	34295342	0.6	+	0	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	exon	34295290	34295342	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	intron	34295343	34295434	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	CDS	34295435	34295673	0.48	+	1	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	exon	34295435	34295673	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	intron	34295674	34295921	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	CDS	34295922	34296358	0.97	+	2	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	exon	34295922	34296358	.	+	.	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
Phchi.S1	AUGUSTUS	stop_codon	34296359	34296361	.	+	0	transcript_id "Phchi.S1G533700.t1"; gene_id "Phchi.S1G533700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1332.t1 is derived from g11115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9080799	9082109	.	-	.	Phchi.S6G129100
Phchi.S6	AUGUSTUS	transcript	9080799	9082109	.	-	.	transcript_id "Phchi.S6G129100.t1"; gene_id "Phchi.S6G129100"
Phchi.S6	AUGUSTUS	stop_codon	9080796	9080798	.	-	0	transcript_id "Phchi.S6G129100.t1"; gene_id "Phchi.S6G129100"
Phchi.S6	AUGUSTUS	CDS	9080799	9082109	0.64	-	0	transcript_id "Phchi.S6G129100.t1"; gene_id "Phchi.S6G129100"
Phchi.S6	AUGUSTUS	exon	9080799	9082109	.	-	.	transcript_id "Phchi.S6G129100.t1"; gene_id "Phchi.S6G129100"
Phchi.S6	AUGUSTUS	start_codon	9082107	9082109	.	-	0	transcript_id "Phchi.S6G129100.t1"; gene_id "Phchi.S6G129100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9165.t1 is derived from g6340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40182181	40183772	.	+	.	Phchi.S1G632400
Phchi.S1	AUGUSTUS	transcript	40182181	40183772	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	start_codon	40182181	40182183	.	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	CDS	40182181	40182405	0.4	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	exon	40182181	40182405	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	intron	40182406	40182710	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	CDS	40182711	40182812	0.57	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	exon	40182711	40182812	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	intron	40182813	40183003	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	CDS	40183004	40183093	1	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	exon	40183004	40183093	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	intron	40183094	40183188	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	CDS	40183189	40183292	0.99	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	exon	40183189	40183292	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	intron	40183293	40183479	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	CDS	40183480	40183558	0.98	+	1	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	exon	40183480	40183558	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	intron	40183559	40183712	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	CDS	40183713	40183772	1	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	exon	40183713	40183772	.	+	.	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
Phchi.S1	AUGUSTUS	stop_codon	40183773	40183775	.	+	0	transcript_id "Phchi.S1G632400.t1"; gene_id "Phchi.S1G632400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1055.t1 is derived from g10838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7318274	7319374	.	-	.	Phchi.S6G101400
Phchi.S6	AUGUSTUS	transcript	7318274	7319374	.	-	.	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	stop_codon	7318271	7318273	.	-	0	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	CDS	7318274	7319122	0.91	-	0	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	exon	7318274	7319122	.	-	.	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	intron	7319123	7319251	.	-	.	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	CDS	7319252	7319374	0.76	-	0	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	exon	7319252	7319374	.	-	.	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
Phchi.S6	AUGUSTUS	start_codon	7319372	7319374	.	-	0	transcript_id "Phchi.S6G101400.t1"; gene_id "Phchi.S6G101400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15787.t1 is derived from g14257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21346467	21349951	.	+	.	Phchi.S3G310600
Phchi.S3	AUGUSTUS	transcript	21346467	21349951	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	start_codon	21346467	21346469	.	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21346467	21346563	0.64	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21346467	21346563	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21346564	21346736	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21346737	21346844	1	+	2	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21346737	21346844	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21346845	21346933	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21346934	21347126	1	+	2	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21346934	21347126	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21347127	21347211	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21347212	21347470	1	+	1	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21347212	21347470	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21347471	21347555	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21347556	21347615	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21347556	21347615	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21347616	21347730	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21347731	21347778	0.98	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21347731	21347778	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21347779	21347899	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21347900	21347989	0.56	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21347900	21347989	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21347990	21348066	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21348067	21348124	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21348067	21348124	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21348125	21348222	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21348223	21348290	1	+	2	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21348223	21348290	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21348291	21348394	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21348395	21348490	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21348395	21348490	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21348491	21348606	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21348607	21348663	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21348607	21348663	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21348664	21349020	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21349021	21349182	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21349021	21349182	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21349183	21349811	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21349812	21349856	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21349812	21349856	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	intron	21349857	21349942	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	CDS	21349943	21349951	1	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	exon	21349943	21349951	.	+	.	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
Phchi.S3	AUGUSTUS	stop_codon	21349952	21349954	.	+	0	transcript_id "Phchi.S3G310600.t1"; gene_id "Phchi.S3G310600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10822.t1 is derived from g14872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2298251	2300763	.	+	.	Phchi.S4G040400
Phchi.S4	AUGUSTUS	transcript	2298251	2300763	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	start_codon	2298251	2298253	.	+	0	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2298251	2298908	0.76	+	0	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2298251	2298908	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	intron	2298909	2299004	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2299005	2299223	0.99	+	2	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2299005	2299223	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	intron	2299224	2299321	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2299322	2299440	1	+	2	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2299322	2299440	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	intron	2299441	2299535	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2299536	2299746	1	+	0	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2299536	2299746	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	intron	2299747	2299858	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2299859	2300093	0.97	+	2	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2299859	2300093	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	intron	2300094	2300201	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2300202	2300352	1	+	1	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2300202	2300352	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	intron	2300353	2300460	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	CDS	2300461	2300763	0.61	+	0	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	exon	2300461	2300763	.	+	.	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
Phchi.S4	AUGUSTUS	stop_codon	2300764	2300766	.	+	0	transcript_id "Phchi.S4G040400.t1"; gene_id "Phchi.S4G040400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11264.t1 is derived from g15314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5085020	5086143	.	-	.	Phchi.S4G084600
Phchi.S4	AUGUSTUS	transcript	5085020	5086143	.	-	.	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	stop_codon	5085017	5085019	.	-	0	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	CDS	5085020	5085471	1	-	2	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	exon	5085020	5085471	.	-	.	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	intron	5085472	5085590	.	-	.	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	CDS	5085591	5086143	0.83	-	0	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	exon	5085591	5086143	.	-	.	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
Phchi.S4	AUGUSTUS	start_codon	5086141	5086143	.	-	0	transcript_id "Phchi.S4G084600.t1"; gene_id "Phchi.S4G084600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13707.t1 is derived from g12174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8294081	8294528	.	+	.	Phchi.S3G102600
Phchi.S3	AUGUSTUS	transcript	8294081	8294528	.	+	.	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	start_codon	8294081	8294083	.	+	0	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	CDS	8294081	8294130	0.99	+	0	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	exon	8294081	8294130	.	+	.	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	intron	8294131	8294227	.	+	.	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	CDS	8294228	8294360	1	+	1	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	exon	8294228	8294360	.	+	.	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	intron	8294361	8294468	.	+	.	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	CDS	8294469	8294528	1	+	0	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	exon	8294469	8294528	.	+	.	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
Phchi.S3	AUGUSTUS	stop_codon	8294529	8294531	.	+	0	transcript_id "Phchi.S3G102600.t1"; gene_id "Phchi.S3G102600"
# This transcript jg1801.t2 is derived from g8721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1802.t1 is derived from g8722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3114847	3118325	.	-	.	Phchi.S5G041100
Phchi.S5	AUGUSTUS	transcript	3114847	3118325	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	stop_codon	3114844	3114846	.	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3114847	3114885	0.55	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3114847	3114885	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3114886	3115052	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115053	3115060	0.55	-	2	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115053	3115060	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3115061	3115136	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115137	3115161	0.96	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115137	3115161	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3115162	3115257	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115258	3115299	1	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115258	3115299	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3115300	3115452	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115453	3115487	0.97	-	2	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115453	3115487	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3115488	3115607	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115608	3115720	0.7	-	1	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115608	3115720	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3115721	3115845	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115846	3115880	0.7	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115846	3115880	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3115881	3115980	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3115981	3116256	0.7	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3115981	3116256	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3116257	3116472	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3116473	3116566	1	-	1	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3116473	3116566	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3116567	3116810	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3116811	3116829	1	-	2	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3116811	3116829	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3116830	3117034	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3117035	3117450	0.28	-	1	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3117035	3117450	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3117451	3117544	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3117545	3117618	0.54	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3117545	3117618	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3117619	3117761	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3117762	3117820	0.73	-	2	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3117762	3117820	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3117821	3118044	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3118045	3118116	0.98	-	2	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3118045	3118116	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	intron	3118117	3118276	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	CDS	3118277	3118325	0.89	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	exon	3118277	3118325	.	-	.	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
Phchi.S5	AUGUSTUS	start_codon	3118323	3118325	.	-	0	transcript_id "Phchi.S5G041100.t1"; gene_id "Phchi.S5G041100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13757.t1 is derived from g12224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8728431	8731937	.	+	.	Phchi.S3G107600
Phchi.S3	AUGUSTUS	transcript	8728431	8731937	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	start_codon	8728431	8728433	.	+	0	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8728431	8730465	0.17	+	0	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8728431	8730465	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	intron	8730466	8730780	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8730781	8730914	0.23	+	2	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8730781	8730914	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	intron	8730915	8731281	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8731282	8731319	0.5	+	0	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8731282	8731319	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	intron	8731320	8731415	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8731416	8731518	1	+	1	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8731416	8731518	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	intron	8731519	8731612	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8731613	8731643	0.99	+	0	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8731613	8731643	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	intron	8731644	8731749	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8731750	8731792	0.95	+	2	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8731750	8731792	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	intron	8731793	8731879	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	CDS	8731880	8731937	0.96	+	1	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	exon	8731880	8731937	.	+	.	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
Phchi.S3	AUGUSTUS	stop_codon	8731938	8731940	.	+	0	transcript_id "Phchi.S3G107600.t1"; gene_id "Phchi.S3G107600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1962.t1 is derived from g8882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4055714	4057351	.	-	.	Phchi.S5G057100
Phchi.S5	AUGUSTUS	transcript	4055714	4057351	.	-	.	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	stop_codon	4055711	4055713	.	-	0	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	CDS	4055714	4055859	1	-	2	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	exon	4055714	4055859	.	-	.	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	intron	4055860	4056156	.	-	.	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	CDS	4056157	4056621	0.19	-	2	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	exon	4056157	4056621	.	-	.	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	intron	4056622	4056879	.	-	.	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	CDS	4056880	4057351	0.23	-	0	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	exon	4056880	4057351	.	-	.	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
Phchi.S5	AUGUSTUS	start_codon	4057349	4057351	.	-	0	transcript_id "Phchi.S5G057100.t1"; gene_id "Phchi.S5G057100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2119.t1 is derived from g9039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4937804	4938367	.	+	.	Phchi.S5G072800
Phchi.S5	AUGUSTUS	transcript	4937804	4938367	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	start_codon	4937804	4937806	.	+	0	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	CDS	4937804	4937809	1	+	0	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	exon	4937804	4937809	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	intron	4937810	4937909	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	CDS	4937910	4937987	1	+	0	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	exon	4937910	4937987	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	intron	4937988	4938069	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	CDS	4938070	4938157	1	+	0	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	exon	4938070	4938157	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	intron	4938158	4938239	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	CDS	4938240	4938367	0.96	+	2	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	exon	4938240	4938367	.	+	.	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
Phchi.S5	AUGUSTUS	stop_codon	4938368	4938370	.	+	0	transcript_id "Phchi.S5G072800.t1"; gene_id "Phchi.S5G072800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7470.t1 is derived from g4643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29532144	29532536	.	+	.	Phchi.S1G462900
Phchi.S1	AUGUSTUS	transcript	29532144	29532536	.	+	.	transcript_id "Phchi.S1G462900.t1"; gene_id "Phchi.S1G462900"
Phchi.S1	AUGUSTUS	start_codon	29532144	29532146	.	+	0	transcript_id "Phchi.S1G462900.t1"; gene_id "Phchi.S1G462900"
Phchi.S1	AUGUSTUS	CDS	29532144	29532536	0.59	+	0	transcript_id "Phchi.S1G462900.t1"; gene_id "Phchi.S1G462900"
Phchi.S1	AUGUSTUS	exon	29532144	29532536	.	+	.	transcript_id "Phchi.S1G462900.t1"; gene_id "Phchi.S1G462900"
Phchi.S1	AUGUSTUS	stop_codon	29532537	29532539	.	+	0	transcript_id "Phchi.S1G462900.t1"; gene_id "Phchi.S1G462900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9733.t1 is derived from g6909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43443364	43444845	.	+	.	Phchi.S1G689200
Phchi.S1	AUGUSTUS	transcript	43443364	43444845	.	+	.	transcript_id "Phchi.S1G689200.t1"; gene_id "Phchi.S1G689200"
Phchi.S1	AUGUSTUS	start_codon	43443364	43443366	.	+	0	transcript_id "Phchi.S1G689200.t1"; gene_id "Phchi.S1G689200"
Phchi.S1	AUGUSTUS	CDS	43443364	43444845	0.97	+	0	transcript_id "Phchi.S1G689200.t1"; gene_id "Phchi.S1G689200"
Phchi.S1	AUGUSTUS	exon	43443364	43444845	.	+	.	transcript_id "Phchi.S1G689200.t1"; gene_id "Phchi.S1G689200"
Phchi.S1	AUGUSTUS	stop_codon	43444846	43444848	.	+	0	transcript_id "Phchi.S1G689200.t1"; gene_id "Phchi.S1G689200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14895.t1 is derived from g13363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15319384	15321376	.	+	.	Phchi.S3G221400
Phchi.S3	AUGUSTUS	transcript	15319384	15321376	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	start_codon	15319384	15319386	.	+	0	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	CDS	15319384	15320008	0.46	+	0	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	exon	15319384	15320008	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	intron	15320009	15320094	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	CDS	15320095	15320149	0.9	+	2	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	exon	15320095	15320149	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	intron	15320150	15320539	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	CDS	15320540	15320783	0.95	+	1	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	exon	15320540	15320783	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	intron	15320784	15320897	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	CDS	15320898	15321115	0.99	+	0	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	exon	15320898	15321115	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	intron	15321116	15321198	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	CDS	15321199	15321376	1	+	1	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	exon	15321199	15321376	.	+	.	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
Phchi.S3	AUGUSTUS	stop_codon	15321377	15321379	.	+	0	transcript_id "Phchi.S3G221400.t1"; gene_id "Phchi.S3G221400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14897.t1 is derived from g13365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15347486	15349480	.	+	.	Phchi.S3G221600
Phchi.S3	AUGUSTUS	transcript	15347486	15349480	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	start_codon	15347486	15347488	.	+	0	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	CDS	15347486	15348110	0.57	+	0	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	exon	15347486	15348110	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	intron	15348111	15348196	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	CDS	15348197	15348387	1	+	2	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	exon	15348197	15348387	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	intron	15348388	15348479	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	CDS	15348480	15348887	0.99	+	0	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	exon	15348480	15348887	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	intron	15348888	15349001	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	CDS	15349002	15349219	1	+	0	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	exon	15349002	15349219	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	intron	15349220	15349302	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	CDS	15349303	15349480	1	+	1	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	exon	15349303	15349480	.	+	.	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
Phchi.S3	AUGUSTUS	stop_codon	15349481	15349483	.	+	0	transcript_id "Phchi.S3G221600.t1"; gene_id "Phchi.S3G221600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14186.t1 is derived from g12653.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11387740	11388933	.	+	.	Phchi.S3G150500
Phchi.S3	AUGUSTUS	transcript	11387740	11388933	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	start_codon	11387740	11387742	.	+	0	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11387740	11387861	0.93	+	0	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11387740	11387861	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11387862	11388038	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388039	11388101	0.99	+	1	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388039	11388101	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11388102	11388202	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388203	11388280	1	+	1	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388203	11388280	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11388281	11388396	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388397	11388559	1	+	1	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388397	11388559	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11388560	11388654	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388655	11388933	1	+	0	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388655	11388933	.	+	.	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	stop_codon	11388934	11388936	.	+	0	transcript_id "Phchi.S3G150500.t1"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	transcript	11387740	11388933	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	start_codon	11387740	11387742	.	+	0	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11387740	11387873	0.94	+	0	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11387740	11387873	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11387874	11388038	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388039	11388101	0.94	+	1	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388039	11388101	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11388102	11388202	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388203	11388280	1	+	1	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388203	11388280	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11388281	11388396	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388397	11388559	1	+	1	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388397	11388559	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	intron	11388560	11388654	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	CDS	11388655	11388933	1	+	0	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	exon	11388655	11388933	.	+	.	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
Phchi.S3	AUGUSTUS	stop_codon	11388934	11388936	.	+	0	transcript_id "Phchi.S3G150500.t2"; gene_id "Phchi.S3G150500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8181.t1 is derived from g5356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34324917	34328494	.	+	.	Phchi.S1G534000
Phchi.S1	AUGUSTUS	transcript	34324917	34328494	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	start_codon	34324917	34324919	.	+	0	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34324917	34325133	1	+	0	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34324917	34325133	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34325134	34325271	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34325272	34325411	1	+	2	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34325272	34325411	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34325412	34325504	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34325505	34325782	0.5	+	0	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34325505	34325782	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34325783	34325961	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34325962	34326075	0.63	+	1	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34325962	34326075	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34326076	34326215	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34326216	34326233	1	+	1	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34326216	34326233	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34326234	34326329	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34326330	34326368	0.99	+	1	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34326330	34326368	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34326369	34326520	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34326521	34326726	0.99	+	1	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34326521	34326726	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34326727	34326830	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34326831	34326883	1	+	2	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34326831	34326883	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34326884	34327079	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34327080	34327449	1	+	0	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34327080	34327449	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	intron	34327450	34327547	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	CDS	34327548	34328494	0.99	+	2	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	exon	34327548	34328494	.	+	.	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
Phchi.S1	AUGUSTUS	stop_codon	34328495	34328497	.	+	0	transcript_id "Phchi.S1G534000.t1"; gene_id "Phchi.S1G534000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5689.t1 is derived from g2859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18324463	18327905	.	+	.	Phchi.S1G284800
Phchi.S1	AUGUSTUS	transcript	18324463	18327905	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	start_codon	18324463	18324465	.	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18324463	18324576	0.65	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18324463	18324576	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18324577	18324660	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18324661	18324791	0.97	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18324661	18324791	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18324792	18324910	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18324911	18325028	0.99	+	1	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18324911	18325028	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18325029	18325112	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18325113	18325165	1	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18325113	18325165	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18325166	18325379	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18325380	18325429	0.86	+	1	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18325380	18325429	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18325430	18325531	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18325532	18325630	0.86	+	2	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18325532	18325630	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18325631	18325778	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18325779	18325888	1	+	2	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18325779	18325888	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18325889	18325984	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18325985	18326112	1	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18325985	18326112	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18326113	18326197	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18326198	18326264	1	+	1	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18326198	18326264	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18326265	18326421	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18326422	18326505	1	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18326422	18326505	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18326506	18326603	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18326604	18326666	1	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18326604	18326666	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18326667	18326750	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18326751	18326898	1	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18326751	18326898	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18326899	18327044	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18327045	18327215	1	+	2	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18327045	18327215	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18327216	18327307	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18327308	18327409	0.88	+	2	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18327308	18327409	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18327410	18327506	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18327507	18327630	1	+	2	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18327507	18327630	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	intron	18327631	18327817	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	CDS	18327818	18327905	1	+	1	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	exon	18327818	18327905	.	+	.	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
Phchi.S1	AUGUSTUS	stop_codon	18327906	18327908	.	+	0	transcript_id "Phchi.S1G284800.t1"; gene_id "Phchi.S1G284800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15154.t1 is derived from g13622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17292986	17294389	.	-	.	Phchi.S3G247300
Phchi.S3	AUGUSTUS	transcript	17292986	17294389	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	stop_codon	17292983	17292985	.	-	0	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	CDS	17292986	17293160	0.01	-	1	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	exon	17292986	17293160	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	intron	17293161	17293241	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	CDS	17293242	17293449	0.01	-	2	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	exon	17293242	17293449	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	intron	17293450	17293755	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	CDS	17293756	17293924	0.01	-	0	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	exon	17293756	17293924	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	intron	17293925	17294119	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	CDS	17294120	17294389	0.07	-	0	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	exon	17294120	17294389	.	-	.	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
Phchi.S3	AUGUSTUS	start_codon	17294387	17294389	.	-	0	transcript_id "Phchi.S3G247300.t1"; gene_id "Phchi.S3G247300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2694.t1 is derived from g9614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8233498	8235597	.	-	.	Phchi.S5G130300
Phchi.S5	AUGUSTUS	transcript	8233498	8235597	.	-	.	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	stop_codon	8233495	8233497	.	-	0	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	CDS	8233498	8234161	0.9	-	1	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	exon	8233498	8234161	.	-	.	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	intron	8234162	8234312	.	-	.	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	CDS	8234313	8235128	0.58	-	1	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	exon	8234313	8235128	.	-	.	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	intron	8235129	8235262	.	-	.	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	CDS	8235263	8235597	0.57	-	0	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	exon	8235263	8235597	.	-	.	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
Phchi.S5	AUGUSTUS	start_codon	8235595	8235597	.	-	0	transcript_id "Phchi.S5G130300.t1"; gene_id "Phchi.S5G130300"
# This transcript jg5295.t2 is derived from g2465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5296.t1 is derived from g2466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16052367	16053942	.	-	.	Phchi.S1G245500
Phchi.S1	AUGUSTUS	transcript	16052367	16053942	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	stop_codon	16052364	16052366	.	-	0	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	CDS	16052367	16052908	1	-	2	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	exon	16052367	16052908	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	intron	16052909	16052998	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	CDS	16052999	16053190	1	-	2	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	exon	16052999	16053190	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	intron	16053191	16053276	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	CDS	16053277	16053455	1	-	1	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	exon	16053277	16053455	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	intron	16053456	16053558	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	CDS	16053559	16053739	1	-	2	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	exon	16053559	16053739	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	intron	16053740	16053812	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	CDS	16053813	16053942	0.96	-	0	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	exon	16053813	16053942	.	-	.	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
Phchi.S1	AUGUSTUS	start_codon	16053940	16053942	.	-	0	transcript_id "Phchi.S1G245500.t1"; gene_id "Phchi.S1G245500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5542.t1 is derived from g2712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17470982	17472108	.	-	.	Phchi.S1G270100
Phchi.S1	AUGUSTUS	transcript	17470982	17472108	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	stop_codon	17470979	17470981	.	-	0	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	CDS	17470982	17471229	1	-	2	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	exon	17470982	17471229	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	intron	17471230	17471321	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	CDS	17471322	17471459	1	-	2	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	exon	17471322	17471459	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	intron	17471460	17471540	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	CDS	17471541	17471643	1	-	0	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	exon	17471541	17471643	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	intron	17471644	17471723	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	CDS	17471724	17471815	1	-	2	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	exon	17471724	17471815	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	intron	17471816	17471901	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	CDS	17471902	17471957	1	-	1	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	exon	17471902	17471957	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	intron	17471958	17472052	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	CDS	17472053	17472108	0.38	-	0	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	exon	17472053	17472108	.	-	.	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
Phchi.S1	AUGUSTUS	start_codon	17472106	17472108	.	-	0	transcript_id "Phchi.S1G270100.t1"; gene_id "Phchi.S1G270100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15295.t1 is derived from g13763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18261938	18263977	.	+	.	Phchi.S3G261400
Phchi.S3	AUGUSTUS	transcript	18261938	18263977	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	start_codon	18261938	18261940	.	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18261938	18262063	1	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18261938	18262063	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18262064	18262185	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18262186	18262284	1	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18262186	18262284	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18262285	18262381	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18262382	18262564	1	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18262382	18262564	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18262565	18262663	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18262664	18262933	1	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18262664	18262933	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18262934	18263075	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18263076	18263178	1	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18263076	18263178	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18263179	18263268	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18263269	18263530	0.7	+	2	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18263269	18263530	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18263531	18263653	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18263654	18263744	0.7	+	1	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18263654	18263744	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	intron	18263745	18263830	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	CDS	18263831	18263977	0.86	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	exon	18263831	18263977	.	+	.	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
Phchi.S3	AUGUSTUS	stop_codon	18263978	18263980	.	+	0	transcript_id "Phchi.S3G261400.t1"; gene_id "Phchi.S3G261400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9019.t1 is derived from g6194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39171633	39174062	.	+	.	Phchi.S1G617800
Phchi.S1	AUGUSTUS	transcript	39171633	39174062	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	start_codon	39171633	39171635	.	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	CDS	39171633	39171677	0.97	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	exon	39171633	39171677	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	intron	39171678	39171795	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	CDS	39171796	39173178	0.99	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	exon	39171796	39173178	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	intron	39173179	39173362	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	CDS	39173363	39173569	1	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	exon	39173363	39173569	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	intron	39173570	39173652	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	CDS	39173653	39173823	1	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	exon	39173653	39173823	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	intron	39173824	39173984	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	CDS	39173985	39174062	1	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	exon	39173985	39174062	.	+	.	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
Phchi.S1	AUGUSTUS	stop_codon	39174063	39174065	.	+	0	transcript_id "Phchi.S1G617800.t1"; gene_id "Phchi.S1G617800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14410.t1 is derived from g12878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12689734	12690406	.	-	.	Phchi.S3G172900
Phchi.S3	AUGUSTUS	transcript	12689734	12690406	.	-	.	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	stop_codon	12689731	12689733	.	-	0	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	CDS	12689734	12689821	0.99	-	1	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	exon	12689734	12689821	.	-	.	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	intron	12689822	12690155	.	-	.	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	CDS	12690156	12690406	0.72	-	0	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	exon	12690156	12690406	.	-	.	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
Phchi.S3	AUGUSTUS	start_codon	12690404	12690406	.	-	0	transcript_id "Phchi.S3G172900.t1"; gene_id "Phchi.S3G172900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8311.t1 is derived from g5486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35228122	35230681	.	+	.	Phchi.S1G547000
Phchi.S1	AUGUSTUS	transcript	35228122	35230681	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	start_codon	35228122	35228124	.	+	0	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35228122	35228171	1	+	0	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35228122	35228171	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35228172	35228259	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35228260	35228483	1	+	1	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35228260	35228483	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35228484	35228576	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35228577	35228815	1	+	2	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35228577	35228815	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35228816	35228897	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35228898	35229147	1	+	0	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35228898	35229147	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35229148	35229314	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35229315	35229460	1	+	2	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35229315	35229460	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35229461	35229542	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35229543	35229748	1	+	0	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35229543	35229748	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35229749	35229886	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35229887	35230011	1	+	1	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35229887	35230011	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	intron	35230012	35230118	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	CDS	35230119	35230681	1	+	2	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	exon	35230119	35230681	.	+	.	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
Phchi.S1	AUGUSTUS	stop_codon	35230682	35230684	.	+	0	transcript_id "Phchi.S1G547000.t1"; gene_id "Phchi.S1G547000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4004.t1 is derived from g1173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6985310	6985873	.	-	.	Phchi.S1G116300
Phchi.S1	AUGUSTUS	transcript	6985310	6985873	.	-	.	transcript_id "Phchi.S1G116300.t1"; gene_id "Phchi.S1G116300"
Phchi.S1	AUGUSTUS	stop_codon	6985307	6985309	.	-	0	transcript_id "Phchi.S1G116300.t1"; gene_id "Phchi.S1G116300"
Phchi.S1	AUGUSTUS	CDS	6985310	6985873	0.99	-	0	transcript_id "Phchi.S1G116300.t1"; gene_id "Phchi.S1G116300"
Phchi.S1	AUGUSTUS	exon	6985310	6985873	.	-	.	transcript_id "Phchi.S1G116300.t1"; gene_id "Phchi.S1G116300"
Phchi.S1	AUGUSTUS	start_codon	6985871	6985873	.	-	0	transcript_id "Phchi.S1G116300.t1"; gene_id "Phchi.S1G116300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5591.t1 is derived from g2761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17786121	17790590	.	-	.	Phchi.S1G275000
Phchi.S1	AUGUSTUS	transcript	17786121	17790590	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	stop_codon	17786118	17786120	.	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17786121	17786438	0.96	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17786121	17786438	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17786439	17786574	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17786575	17786687	1	-	2	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17786575	17786687	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17786688	17786767	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17786768	17787057	1	-	1	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17786768	17787057	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17787058	17787146	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17787147	17787433	1	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17787147	17787433	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17787434	17787525	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17787526	17787831	0.93	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17787526	17787831	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17787832	17787919	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17787920	17788028	1	-	1	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17787920	17788028	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17788029	17788115	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17788116	17788325	1	-	1	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17788116	17788325	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17788326	17788522	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17788523	17788673	1	-	2	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17788523	17788673	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17788674	17788760	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17788761	17789601	0.98	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17788761	17789601	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17789602	17789719	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17789720	17790178	0.93	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17789720	17790178	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17790179	17790317	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17790318	17790389	1	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17790318	17790389	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	intron	17790390	17790512	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	CDS	17790513	17790590	0.66	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	exon	17790513	17790590	.	-	.	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
Phchi.S1	AUGUSTUS	start_codon	17790588	17790590	.	-	0	transcript_id "Phchi.S1G275000.t1"; gene_id "Phchi.S1G275000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7776.t1 is derived from g4950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31177483	31178734	.	+	.	Phchi.S1G493500
Phchi.S1	AUGUSTUS	transcript	31177483	31178734	.	+	.	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	start_codon	31177483	31177485	.	+	0	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	CDS	31177483	31177888	0.3	+	0	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	exon	31177483	31177888	.	+	.	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	intron	31177889	31178357	.	+	.	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	CDS	31178358	31178734	0.02	+	2	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	exon	31178358	31178734	.	+	.	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
Phchi.S1	AUGUSTUS	stop_codon	31178735	31178737	.	+	0	transcript_id "Phchi.S1G493500.t1"; gene_id "Phchi.S1G493500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8092.t1 is derived from g5267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32901336	32904617	.	+	.	Phchi.S1G525100
Phchi.S1	AUGUSTUS	transcript	32901336	32904617	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	start_codon	32901336	32901338	.	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32901336	32901403	0.96	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32901336	32901403	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32901404	32901482	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32901483	32901549	0.58	+	1	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32901483	32901549	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32901550	32901684	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32901685	32901741	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32901685	32901741	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32901742	32901825	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32901826	32901902	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32901826	32901902	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32901903	32902040	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32902041	32902074	1	+	1	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32902041	32902074	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32902075	32902204	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32902205	32902283	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32902205	32902283	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32902284	32902429	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32902430	32902521	1	+	2	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32902430	32902521	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32902522	32902662	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32902663	32902737	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32902663	32902737	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32902738	32902826	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32902827	32902912	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32902827	32902912	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32902913	32903000	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32903001	32903133	1	+	1	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32903001	32903133	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32903134	32903214	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32903215	32903301	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32903215	32903301	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32903302	32903434	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32903435	32903553	0.95	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32903435	32903553	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32903554	32903817	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32903818	32903883	0.99	+	1	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32903818	32903883	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32903884	32903968	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32903969	32904041	1	+	1	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32903969	32904041	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32904042	32904131	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32904132	32904223	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32904132	32904223	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32904224	32904308	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32904309	32904438	1	+	1	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32904309	32904438	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	intron	32904439	32904533	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	CDS	32904534	32904617	1	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	exon	32904534	32904617	.	+	.	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
Phchi.S1	AUGUSTUS	stop_codon	32904618	32904620	.	+	0	transcript_id "Phchi.S1G525100.t1"; gene_id "Phchi.S1G525100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2770.t1 is derived from g9690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8749596	8751647	.	-	.	Phchi.S5G137900
Phchi.S5	AUGUSTUS	transcript	8749596	8751647	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	stop_codon	8749593	8749595	.	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8749596	8749781	1	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8749596	8749781	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8749782	8749867	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8749868	8749957	1	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8749868	8749957	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8749958	8750063	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8750064	8750099	1	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8750064	8750099	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8750100	8750202	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8750203	8750517	1	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8750203	8750517	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8750518	8750618	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8750619	8750792	1	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8750619	8750792	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8750793	8750880	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8750881	8751353	0.99	-	2	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8750881	8751353	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8751354	8751446	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8751447	8751488	1	-	2	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8751447	8751488	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	intron	8751489	8751568	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	CDS	8751569	8751647	0.85	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	exon	8751569	8751647	.	-	.	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
Phchi.S5	AUGUSTUS	start_codon	8751645	8751647	.	-	0	transcript_id "Phchi.S5G137900.t1"; gene_id "Phchi.S5G137900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5031.t1 is derived from g2201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14155019	14156947	.	-	.	Phchi.S1G219000
Phchi.S1	AUGUSTUS	transcript	14155019	14156947	.	-	.	transcript_id "Phchi.S1G219000.t1"; gene_id "Phchi.S1G219000"
Phchi.S1	AUGUSTUS	stop_codon	14155016	14155018	.	-	0	transcript_id "Phchi.S1G219000.t1"; gene_id "Phchi.S1G219000"
Phchi.S1	AUGUSTUS	CDS	14155019	14156947	0.8	-	0	transcript_id "Phchi.S1G219000.t1"; gene_id "Phchi.S1G219000"
Phchi.S1	AUGUSTUS	exon	14155019	14156947	.	-	.	transcript_id "Phchi.S1G219000.t1"; gene_id "Phchi.S1G219000"
Phchi.S1	AUGUSTUS	start_codon	14156945	14156947	.	-	0	transcript_id "Phchi.S1G219000.t1"; gene_id "Phchi.S1G219000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11945.t1 is derived from g7620.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	151420	152879	.	+	.	Phchi.S2G002500
Phchi.S2	AUGUSTUS	transcript	151420	152879	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	start_codon	151420	151422	.	+	0	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	151420	151653	0.92	+	0	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	151420	151653	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	151654	151857	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	151858	151957	1	+	0	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	151858	151957	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	151958	152167	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	152168	152225	1	+	2	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	152168	152225	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	152226	152338	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	152339	152445	1	+	1	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	152339	152445	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	152446	152568	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	152569	152879	0.97	+	2	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	152569	152879	.	+	.	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	stop_codon	152880	152882	.	+	0	transcript_id "Phchi.S2G002500.t1"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	transcript	151420	152879	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	start_codon	151420	151422	.	+	0	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	151420	151653	0.92	+	0	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	151420	151653	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	151654	151857	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	151858	151957	1	+	0	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	151858	151957	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	151958	152164	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	152165	152225	0.95	+	2	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	152165	152225	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	152226	152338	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	152339	152445	1	+	1	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	152339	152445	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	intron	152446	152568	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	CDS	152569	152879	1	+	2	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	exon	152569	152879	.	+	.	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
Phchi.S2	AUGUSTUS	stop_codon	152880	152882	.	+	0	transcript_id "Phchi.S2G002500.t2"; gene_id "Phchi.S2G002500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14817.t1 is derived from g13285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14833589	14837843	.	-	.	Phchi.S3G213600
Phchi.S3	AUGUSTUS	transcript	14833589	14837843	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	stop_codon	14833586	14833588	.	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14833589	14834087	1	-	1	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14833589	14834087	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14834088	14834172	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14834173	14834254	1	-	2	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14834173	14834254	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14834255	14834327	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14834328	14834436	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14834328	14834436	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14834437	14834519	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14834520	14834672	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14834520	14834672	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14834673	14834755	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14834756	14834872	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14834756	14834872	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14834873	14834959	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14834960	14835007	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14834960	14835007	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14835008	14835082	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14835083	14835202	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14835083	14835202	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14835203	14835718	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14835719	14835818	0.72	-	1	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14835719	14835818	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14835819	14835927	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14835928	14836101	0.7	-	1	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14835928	14836101	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14836102	14836324	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14836325	14836558	1	-	1	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14836325	14836558	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14836559	14836642	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14836643	14836729	0.85	-	1	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14836643	14836729	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14836730	14836834	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14836835	14836881	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14836835	14836881	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14836882	14837159	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14837160	14837297	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14837160	14837297	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14837298	14837394	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14837395	14837706	0.99	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14837395	14837706	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	intron	14837707	14837789	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	CDS	14837790	14837843	1	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	exon	14837790	14837843	.	-	.	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
Phchi.S3	AUGUSTUS	start_codon	14837841	14837843	.	-	0	transcript_id "Phchi.S3G213600.t1"; gene_id "Phchi.S3G213600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14389.t1 is derived from g12857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12567589	12569158	.	+	.	Phchi.S3G170800
Phchi.S3	AUGUSTUS	transcript	12567589	12569158	.	+	.	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	start_codon	12567589	12567591	.	+	0	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	CDS	12567589	12568059	1	+	0	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	exon	12567589	12568059	.	+	.	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	intron	12568060	12568153	.	+	.	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	CDS	12568154	12568543	1	+	0	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	exon	12568154	12568543	.	+	.	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	intron	12568544	12568627	.	+	.	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	CDS	12568628	12569158	0.93	+	0	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	exon	12568628	12569158	.	+	.	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
Phchi.S3	AUGUSTUS	stop_codon	12569159	12569161	.	+	0	transcript_id "Phchi.S3G170800.t1"; gene_id "Phchi.S3G170800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6610.t1 is derived from g3782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23997507	23998716	.	+	.	Phchi.S1G376900
Phchi.S1	AUGUSTUS	transcript	23997507	23998716	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	start_codon	23997507	23997509	.	+	0	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23997507	23997592	0.92	+	0	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23997507	23997592	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	intron	23997593	23997684	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23997685	23997772	0.99	+	1	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23997685	23997772	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	intron	23997773	23997874	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23997875	23997969	1	+	0	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23997875	23997969	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	intron	23997970	23998050	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23998051	23998127	0.68	+	1	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23998051	23998127	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	intron	23998128	23998229	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23998230	23998288	0.64	+	2	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23998230	23998288	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	intron	23998289	23998397	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23998398	23998463	0.96	+	0	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23998398	23998463	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	intron	23998464	23998590	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	CDS	23998591	23998716	0.92	+	0	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	exon	23998591	23998716	.	+	.	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
Phchi.S1	AUGUSTUS	stop_codon	23998717	23998719	.	+	0	transcript_id "Phchi.S1G376900.t1"; gene_id "Phchi.S1G376900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9476.t1 is derived from g6652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41800460	41801466	.	-	.	Phchi.S1G663500
Phchi.S1	AUGUSTUS	transcript	41800460	41801466	.	-	.	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	stop_codon	41800457	41800459	.	-	0	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	CDS	41800460	41800584	0.93	-	2	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	exon	41800460	41800584	.	-	.	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	intron	41800585	41800657	.	-	.	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	CDS	41800658	41800835	0.82	-	0	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	exon	41800658	41800835	.	-	.	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	intron	41800836	41801064	.	-	.	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	CDS	41801065	41801466	0.49	-	0	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	exon	41801065	41801466	.	-	.	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
Phchi.S1	AUGUSTUS	start_codon	41801464	41801466	.	-	0	transcript_id "Phchi.S1G663500.t1"; gene_id "Phchi.S1G663500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14707.t1 is derived from g13175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14320787	14321399	.	+	.	Phchi.S3G202600
Phchi.S3	AUGUSTUS	transcript	14320787	14321399	.	+	.	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	start_codon	14320787	14320789	.	+	0	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	CDS	14320787	14320907	0.8	+	0	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	exon	14320787	14320907	.	+	.	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	intron	14320908	14320995	.	+	.	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	CDS	14320996	14321399	0.79	+	2	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	exon	14320996	14321399	.	+	.	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
Phchi.S3	AUGUSTUS	stop_codon	14321400	14321402	.	+	0	transcript_id "Phchi.S3G202600.t1"; gene_id "Phchi.S3G202600"
# This transcript jg12852.t2 is derived from g11317.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12853.t1 is derived from g11318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2725953	2728146	.	+	.	Phchi.S3G017200
Phchi.S3	AUGUSTUS	transcript	2725953	2728146	.	+	.	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	start_codon	2725953	2725955	.	+	0	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	CDS	2725953	2728013	0.96	+	0	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	exon	2725953	2728013	.	+	.	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	intron	2728014	2728119	.	+	.	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	CDS	2728120	2728146	1	+	0	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	exon	2728120	2728146	.	+	.	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
Phchi.S3	AUGUSTUS	stop_codon	2728147	2728149	.	+	0	transcript_id "Phchi.S3G017200.t1"; gene_id "Phchi.S3G017200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg349.t1 is derived from g10131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2536068	2536681	.	-	.	Phchi.S6G030800
Phchi.S6	AUGUSTUS	transcript	2536068	2536681	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	stop_codon	2536065	2536067	.	-	0	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	CDS	2536068	2536080	0.9	-	1	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	exon	2536068	2536080	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	intron	2536081	2536180	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	CDS	2536181	2536326	1	-	0	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	exon	2536181	2536326	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	intron	2536327	2536399	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	CDS	2536400	2536464	1	-	2	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	exon	2536400	2536464	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	intron	2536465	2536545	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	CDS	2536546	2536681	0.85	-	0	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	exon	2536546	2536681	.	-	.	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
Phchi.S6	AUGUSTUS	start_codon	2536679	2536681	.	-	0	transcript_id "Phchi.S6G030800.t1"; gene_id "Phchi.S6G030800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14289.t1 is derived from g12756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11936525	11938003	.	-	.	Phchi.S3G160800
Phchi.S3	AUGUSTUS	transcript	11936525	11938003	.	-	.	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	stop_codon	11936522	11936524	.	-	0	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	CDS	11936525	11936829	0.89	-	2	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	exon	11936525	11936829	.	-	.	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	intron	11936830	11937033	.	-	.	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	CDS	11937034	11937637	0.63	-	0	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	exon	11937034	11937637	.	-	.	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	intron	11937638	11937805	.	-	.	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	CDS	11937806	11938003	0.77	-	0	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	exon	11937806	11938003	.	-	.	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
Phchi.S3	AUGUSTUS	start_codon	11938001	11938003	.	-	0	transcript_id "Phchi.S3G160800.t1"; gene_id "Phchi.S3G160800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11078.t1 is derived from g15128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3985473	3986074	.	+	.	Phchi.S4G066000
Phchi.S4	AUGUSTUS	transcript	3985473	3986074	.	+	.	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	start_codon	3985473	3985475	.	+	0	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	CDS	3985473	3985761	0.99	+	0	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	exon	3985473	3985761	.	+	.	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	intron	3985762	3985846	.	+	.	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	CDS	3985847	3985906	0.92	+	2	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	exon	3985847	3985906	.	+	.	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	intron	3985907	3985991	.	+	.	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	CDS	3985992	3986074	0.91	+	2	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	exon	3985992	3986074	.	+	.	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
Phchi.S4	AUGUSTUS	stop_codon	3986075	3986077	.	+	0	transcript_id "Phchi.S4G066000.t1"; gene_id "Phchi.S4G066000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6094.t1 is derived from g3265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20930601	20933017	.	-	.	Phchi.S1G325300
Phchi.S1	AUGUSTUS	transcript	20930601	20933017	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	stop_codon	20930598	20930600	.	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20930601	20930822	0.73	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20930601	20930822	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	intron	20930823	20930906	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20930907	20931080	1	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20930907	20931080	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	intron	20931081	20931169	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20931170	20931305	1	-	1	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20931170	20931305	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	intron	20931306	20931422	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20931423	20931505	1	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20931423	20931505	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	intron	20931506	20931600	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20931601	20931759	0.93	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20931601	20931759	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	intron	20931760	20931884	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20931885	20931955	0.91	-	2	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20931885	20931955	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	intron	20931956	20932044	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	CDS	20932045	20933017	0.95	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	exon	20932045	20933017	.	-	.	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
Phchi.S1	AUGUSTUS	start_codon	20933015	20933017	.	-	0	transcript_id "Phchi.S1G325300.t1"; gene_id "Phchi.S1G325300"
# This transcript jg1213.t2 is derived from g10996.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1214.t1 is derived from g10997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8438479	8439004	.	-	.	Phchi.S6G117300
Phchi.S6	AUGUSTUS	transcript	8438479	8439004	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	stop_codon	8438476	8438478	.	-	0	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	CDS	8438479	8438543	1	-	2	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	exon	8438479	8438543	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	intron	8438544	8438700	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	CDS	8438701	8438735	1	-	1	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	exon	8438701	8438735	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	intron	8438736	8438821	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	CDS	8438822	8438928	1	-	0	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	exon	8438822	8438928	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	intron	8438929	8439001	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	CDS	8439002	8439004	1	-	0	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	exon	8439002	8439004	.	-	.	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
Phchi.S6	AUGUSTUS	start_codon	8439002	8439004	.	-	0	transcript_id "Phchi.S6G117300.t1"; gene_id "Phchi.S6G117300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5003.t1 is derived from g2173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13963437	13963910	.	+	.	Phchi.S1G216200
Phchi.S1	AUGUSTUS	transcript	13963437	13963910	.	+	.	transcript_id "Phchi.S1G216200.t1"; gene_id "Phchi.S1G216200"
Phchi.S1	AUGUSTUS	start_codon	13963437	13963439	.	+	0	transcript_id "Phchi.S1G216200.t1"; gene_id "Phchi.S1G216200"
Phchi.S1	AUGUSTUS	CDS	13963437	13963910	0.78	+	0	transcript_id "Phchi.S1G216200.t1"; gene_id "Phchi.S1G216200"
Phchi.S1	AUGUSTUS	exon	13963437	13963910	.	+	.	transcript_id "Phchi.S1G216200.t1"; gene_id "Phchi.S1G216200"
Phchi.S1	AUGUSTUS	stop_codon	13963911	13963913	.	+	0	transcript_id "Phchi.S1G216200.t1"; gene_id "Phchi.S1G216200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4442.t1 is derived from g1611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10541258	10542882	.	-	.	Phchi.S1G160100
Phchi.S1	AUGUSTUS	transcript	10541258	10542882	.	-	.	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	stop_codon	10541255	10541257	.	-	0	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	CDS	10541258	10542076	0.74	-	0	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	exon	10541258	10542076	.	-	.	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	intron	10542077	10542171	.	-	.	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	CDS	10542172	10542642	1	-	0	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	exon	10542172	10542642	.	-	.	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	intron	10542643	10542723	.	-	.	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	CDS	10542724	10542882	0.63	-	0	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	exon	10542724	10542882	.	-	.	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
Phchi.S1	AUGUSTUS	start_codon	10542880	10542882	.	-	0	transcript_id "Phchi.S1G160100.t1"; gene_id "Phchi.S1G160100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg781.t1 is derived from g10563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5472372	5473907	.	+	.	Phchi.S6G074000
Phchi.S6	AUGUSTUS	transcript	5472372	5473907	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	start_codon	5472372	5472374	.	+	0	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	CDS	5472372	5472790	0.51	+	0	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	exon	5472372	5472790	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	intron	5472791	5472869	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	CDS	5472870	5473059	1	+	1	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	exon	5472870	5473059	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	intron	5473060	5473140	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	CDS	5473141	5473347	1	+	0	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	exon	5473141	5473347	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	intron	5473348	5473428	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	CDS	5473429	5473658	0.92	+	0	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	exon	5473429	5473658	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	intron	5473659	5473759	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	CDS	5473760	5473907	0.95	+	1	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	exon	5473760	5473907	.	+	.	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
Phchi.S6	AUGUSTUS	stop_codon	5473908	5473910	.	+	0	transcript_id "Phchi.S6G074000.t1"; gene_id "Phchi.S6G074000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14142.t1 is derived from g12609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11112705	11115608	.	-	.	Phchi.S3G146100
Phchi.S3	AUGUSTUS	transcript	11112705	11115608	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	stop_codon	11112702	11112704	.	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11112705	11112830	0.95	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11112705	11112830	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11112831	11112919	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11112920	11113051	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11112920	11113051	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11113052	11113215	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11113216	11113569	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11113216	11113569	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11113570	11113647	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11113648	11113894	1	-	1	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11113648	11113894	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11113895	11113975	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11113976	11114052	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11113976	11114052	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11114053	11114151	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11114152	11114226	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11114152	11114226	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11114227	11114405	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11114406	11114507	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11114406	11114507	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11114508	11114600	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11114601	11114719	1	-	2	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11114601	11114719	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11114720	11114826	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11114827	11114950	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11114827	11114950	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11114951	11115093	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11115094	11115144	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11115094	11115144	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11115145	11115243	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11115244	11115342	1	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11115244	11115342	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	intron	11115343	11115518	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	CDS	11115519	11115608	0.93	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	exon	11115519	11115608	.	-	.	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
Phchi.S3	AUGUSTUS	start_codon	11115606	11115608	.	-	0	transcript_id "Phchi.S3G146100.t1"; gene_id "Phchi.S3G146100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8231.t1 is derived from g5406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34566192	34567199	.	-	.	Phchi.S1G539000
Phchi.S1	AUGUSTUS	transcript	34566192	34567199	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	stop_codon	34566189	34566191	.	-	0	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	CDS	34566192	34566351	0.98	-	1	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	exon	34566192	34566351	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	intron	34566352	34566435	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	CDS	34566436	34566494	0.92	-	0	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	exon	34566436	34566494	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	intron	34566495	34566589	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	CDS	34566590	34566642	0.72	-	2	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	exon	34566590	34566642	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	intron	34566643	34566751	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	CDS	34566752	34567199	0.68	-	0	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	exon	34566752	34567199	.	-	.	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
Phchi.S1	AUGUSTUS	start_codon	34567197	34567199	.	-	0	transcript_id "Phchi.S1G539000.t1"; gene_id "Phchi.S1G539000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7549.t1 is derived from g4723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29998102	30001059	.	+	.	Phchi.S1G470800
Phchi.S1	AUGUSTUS	transcript	29998102	30001059	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	start_codon	29998102	29998104	.	+	0	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29998102	29998195	0.71	+	0	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29998102	29998195	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29998196	29998345	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29998346	29999380	0.99	+	2	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29998346	29999380	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999381	29999554	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29999555	29999696	1	+	2	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29999555	29999696	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999697	29999901	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29999902	29999973	1	+	1	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29999902	29999973	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999974	30000078	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000079	30000147	1	+	1	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000079	30000147	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000148	30000263	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000264	30000332	1	+	1	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000264	30000332	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000333	30000461	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000462	30000539	1	+	1	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000462	30000539	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000540	30000627	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000628	30000734	0.7	+	1	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000628	30000734	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000735	30000946	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000947	30001059	0.98	+	2	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000947	30001059	.	+	.	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	stop_codon	30001060	30001062	.	+	0	transcript_id "Phchi.S1G470800.t1"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	transcript	29998102	30001059	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	start_codon	29998102	29998104	.	+	0	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29998102	29998195	0.65	+	0	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29998102	29998195	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29998196	29998345	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29998346	29999380	1	+	2	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29998346	29999380	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999381	29999531	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29999532	29999556	1	+	2	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29999532	29999556	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999557	29999612	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29999613	29999696	0.6	+	1	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29999613	29999696	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999697	29999901	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	29999902	29999973	1	+	1	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	29999902	29999973	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	29999974	30000078	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000079	30000147	1	+	1	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000079	30000147	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000148	30000263	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000264	30000332	1	+	1	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000264	30000332	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000333	30000461	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000462	30000539	1	+	1	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000462	30000539	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000540	30000627	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000628	30000734	0.73	+	1	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000628	30000734	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	intron	30000735	30000946	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	CDS	30000947	30001059	0.96	+	2	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	exon	30000947	30001059	.	+	.	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
Phchi.S1	AUGUSTUS	stop_codon	30001060	30001062	.	+	0	transcript_id "Phchi.S1G470800.t2"; gene_id "Phchi.S1G470800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6467.t1 is derived from g3639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23138206	23142662	.	-	.	Phchi.S1G362600
Phchi.S1	AUGUSTUS	transcript	23138206	23142662	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	stop_codon	23138203	23138205	.	-	0	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	CDS	23138206	23138469	1	-	0	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	exon	23138206	23138469	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	intron	23138470	23138625	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	CDS	23138626	23138847	0.99	-	0	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	exon	23138626	23138847	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	intron	23138848	23138976	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	CDS	23138977	23139294	0.99	-	0	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	exon	23138977	23139294	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	intron	23139295	23139437	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	CDS	23139438	23141976	1	-	1	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	exon	23139438	23141976	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	intron	23141977	23142115	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	CDS	23142116	23142284	0.69	-	2	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	exon	23142116	23142284	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	intron	23142285	23142382	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	CDS	23142383	23142662	0.61	-	0	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	exon	23142383	23142662	.	-	.	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
Phchi.S1	AUGUSTUS	start_codon	23142660	23142662	.	-	0	transcript_id "Phchi.S1G362600.t1"; gene_id "Phchi.S1G362600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15656.t1 is derived from g14125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20513849	20518817	.	-	.	Phchi.S3G297500
Phchi.S3	AUGUSTUS	transcript	20513849	20518817	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	stop_codon	20513846	20513848	.	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20513849	20513932	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20513849	20513932	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20513933	20514018	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20514019	20514387	0.54	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20514019	20514387	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20514388	20514491	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20514492	20514678	0.56	-	1	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20514492	20514678	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20514679	20514854	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20514855	20515047	0.99	-	2	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20514855	20515047	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20515048	20515149	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20515150	20515423	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20515150	20515423	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20515424	20515522	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20515523	20515682	1	-	1	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20515523	20515682	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20515683	20515769	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20515770	20515984	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20515770	20515984	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20515985	20516204	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20516205	20516297	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20516205	20516297	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20516298	20516400	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20516401	20516556	0.84	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20516401	20516556	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20516557	20516670	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20516671	20516874	0.98	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20516671	20516874	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20516875	20517005	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20517006	20517281	0.98	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20517006	20517281	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20517282	20517427	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20517428	20517523	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20517428	20517523	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20517524	20517647	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20517648	20517866	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20517648	20517866	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20517867	20518064	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20518065	20518170	1	-	1	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20518065	20518170	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20518171	20518335	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20518336	20518493	1	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20518336	20518493	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	intron	20518494	20518649	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	CDS	20518650	20518817	0.96	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	exon	20518650	20518817	.	-	.	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
Phchi.S3	AUGUSTUS	start_codon	20518815	20518817	.	-	0	transcript_id "Phchi.S3G297500.t1"; gene_id "Phchi.S3G297500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11785.t1 is derived from g15837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8151383	8152141	.	+	.	Phchi.S4G136700
Phchi.S4	AUGUSTUS	transcript	8151383	8152141	.	+	.	transcript_id "Phchi.S4G136700.t1"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	start_codon	8151383	8151385	.	+	0	transcript_id "Phchi.S4G136700.t1"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	CDS	8151383	8152141	0.97	+	0	transcript_id "Phchi.S4G136700.t1"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	exon	8151383	8152141	.	+	.	transcript_id "Phchi.S4G136700.t1"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	stop_codon	8152142	8152144	.	+	0	transcript_id "Phchi.S4G136700.t1"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	transcript	8151446	8152141	.	+	.	transcript_id "Phchi.S4G136700.t2"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	start_codon	8151446	8151448	.	+	0	transcript_id "Phchi.S4G136700.t2"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	CDS	8151446	8152141	0.69	+	0	transcript_id "Phchi.S4G136700.t2"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	exon	8151446	8152141	.	+	.	transcript_id "Phchi.S4G136700.t2"; gene_id "Phchi.S4G136700"
Phchi.S4	AUGUSTUS	stop_codon	8152142	8152144	.	+	0	transcript_id "Phchi.S4G136700.t2"; gene_id "Phchi.S4G136700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4359.t1 is derived from g1528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10006597	10006905	.	-	.	Phchi.S1G151800
Phchi.S1	AUGUSTUS	transcript	10006597	10006905	.	-	.	transcript_id "Phchi.S1G151800.t1"; gene_id "Phchi.S1G151800"
Phchi.S1	AUGUSTUS	stop_codon	10006594	10006596	.	-	0	transcript_id "Phchi.S1G151800.t1"; gene_id "Phchi.S1G151800"
Phchi.S1	AUGUSTUS	CDS	10006597	10006905	0.58	-	0	transcript_id "Phchi.S1G151800.t1"; gene_id "Phchi.S1G151800"
Phchi.S1	AUGUSTUS	exon	10006597	10006905	.	-	.	transcript_id "Phchi.S1G151800.t1"; gene_id "Phchi.S1G151800"
Phchi.S1	AUGUSTUS	start_codon	10006903	10006905	.	-	0	transcript_id "Phchi.S1G151800.t1"; gene_id "Phchi.S1G151800"
# This transcript jg3389.t2 is derived from g558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3390.t1 is derived from g559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3315382	3317069	.	-	.	Phchi.S1G054900
Phchi.S1	AUGUSTUS	transcript	3315382	3317069	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	stop_codon	3315379	3315381	.	-	0	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	CDS	3315382	3315471	1	-	0	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	exon	3315382	3315471	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	intron	3315472	3315588	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	CDS	3315589	3315687	1	-	0	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	exon	3315589	3315687	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	intron	3315688	3315784	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	CDS	3315785	3315966	1	-	2	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	exon	3315785	3315966	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	intron	3315967	3316090	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	CDS	3316091	3316191	1	-	1	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	exon	3316091	3316191	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	intron	3316192	3316366	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	CDS	3316367	3316527	1	-	0	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	exon	3316367	3316527	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	intron	3316528	3316778	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	CDS	3316779	3317069	1	-	0	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	exon	3316779	3317069	.	-	.	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
Phchi.S1	AUGUSTUS	start_codon	3317067	3317069	.	-	0	transcript_id "Phchi.S1G054900.t1"; gene_id "Phchi.S1G054900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1275.t1 is derived from g11058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8778540	8782199	.	-	.	Phchi.S6G123400
Phchi.S6	AUGUSTUS	transcript	8778540	8782199	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	stop_codon	8778537	8778539	.	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8778540	8778602	0.9	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8778540	8778602	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8778603	8778701	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8778702	8778867	1	-	1	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8778702	8778867	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8778868	8778955	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8778956	8779005	1	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8778956	8779005	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8779006	8779097	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8779098	8779199	1	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8779098	8779199	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8779200	8779286	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8779287	8779367	1	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8779287	8779367	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8779368	8779486	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8779487	8779568	1	-	1	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8779487	8779568	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8779569	8779676	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8779677	8779728	0.96	-	2	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8779677	8779728	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8779729	8779846	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8779847	8780329	0.99	-	2	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8779847	8780329	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8780330	8780662	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8780663	8781173	0.96	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8780663	8781173	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8781174	8781290	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8781291	8781372	1	-	1	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8781291	8781372	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8781373	8781467	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8781468	8781574	1	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8781468	8781574	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8781575	8781720	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8781721	8781839	1	-	2	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8781721	8781839	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	intron	8781840	8782072	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	CDS	8782073	8782199	0.94	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	exon	8782073	8782199	.	-	.	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
Phchi.S6	AUGUSTUS	start_codon	8782197	8782199	.	-	0	transcript_id "Phchi.S6G123400.t1"; gene_id "Phchi.S6G123400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11801.t1 is derived from g15853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8212199	8212619	.	+	.	Phchi.S4G138300
Phchi.S4	AUGUSTUS	transcript	8212199	8212619	.	+	.	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	start_codon	8212199	8212201	.	+	0	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	CDS	8212199	8212205	0.75	+	0	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	exon	8212199	8212205	.	+	.	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	intron	8212206	8212296	.	+	.	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	CDS	8212297	8212342	0.8	+	2	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	exon	8212297	8212342	.	+	.	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	intron	8212343	8212435	.	+	.	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	CDS	8212436	8212619	0.93	+	1	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	exon	8212436	8212619	.	+	.	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
Phchi.S4	AUGUSTUS	stop_codon	8212620	8212622	.	+	0	transcript_id "Phchi.S4G138300.t1"; gene_id "Phchi.S4G138300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13425.t1 is derived from g11892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6634454	6636312	.	-	.	Phchi.S3G074400
Phchi.S3	AUGUSTUS	transcript	6634454	6636312	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	stop_codon	6634451	6634453	.	-	0	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	CDS	6634454	6634530	0.51	-	2	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	exon	6634454	6634530	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	intron	6634531	6634631	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	CDS	6634632	6634668	0.53	-	0	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	exon	6634632	6634668	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	intron	6634669	6634747	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	CDS	6634748	6634766	0.52	-	1	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	exon	6634748	6634766	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	intron	6634767	6634886	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	CDS	6634887	6635263	0.62	-	0	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	exon	6634887	6635263	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	intron	6635264	6635352	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	CDS	6635353	6636312	1	-	0	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	exon	6635353	6636312	.	-	.	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
Phchi.S3	AUGUSTUS	start_codon	6636310	6636312	.	-	0	transcript_id "Phchi.S3G074400.t1"; gene_id "Phchi.S3G074400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg611.t1 is derived from g10393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4396524	4400424	.	-	.	Phchi.S6G057000
Phchi.S6	AUGUSTUS	transcript	4396524	4400424	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	stop_codon	4396521	4396523	.	-	0	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4396524	4396607	0.77	-	0	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4396524	4396607	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	intron	4396608	4396690	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4396691	4396739	0.6	-	1	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4396691	4396739	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	intron	4396740	4396898	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4396899	4397912	0.44	-	1	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4396899	4397912	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	intron	4397913	4398025	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4398026	4400014	0.9	-	1	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4398026	4400014	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	intron	4400015	4400087	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4400088	4400203	1	-	0	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4400088	4400203	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	intron	4400204	4400291	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4400292	4400345	1	-	0	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4400292	4400345	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	intron	4400346	4400421	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	CDS	4400422	4400424	0.98	-	0	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	exon	4400422	4400424	.	-	.	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
Phchi.S6	AUGUSTUS	start_codon	4400422	4400424	.	-	0	transcript_id "Phchi.S6G057000.t1"; gene_id "Phchi.S6G057000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6915.t1 is derived from g4087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25977645	25979229	.	-	.	Phchi.S1G407400
Phchi.S1	AUGUSTUS	transcript	25977645	25979229	.	-	.	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	stop_codon	25977642	25977644	.	-	0	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	CDS	25977645	25978994	0.88	-	0	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	exon	25977645	25978994	.	-	.	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	intron	25978995	25979151	.	-	.	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	CDS	25979152	25979229	0.93	-	0	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	exon	25979152	25979229	.	-	.	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
Phchi.S1	AUGUSTUS	start_codon	25979227	25979229	.	-	0	transcript_id "Phchi.S1G407400.t1"; gene_id "Phchi.S1G407400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4367.t1 is derived from g1536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10079646	10083599	.	-	.	Phchi.S1G152600
Phchi.S1	AUGUSTUS	transcript	10079646	10083599	.	-	.	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	stop_codon	10079643	10079645	.	-	0	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	CDS	10079646	10080145	0.99	-	2	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	exon	10079646	10080145	.	-	.	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	intron	10080146	10080232	.	-	.	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	CDS	10080233	10083599	0.5	-	0	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	exon	10080233	10083599	.	-	.	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
Phchi.S1	AUGUSTUS	start_codon	10083597	10083599	.	-	0	transcript_id "Phchi.S1G152600.t1"; gene_id "Phchi.S1G152600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12784.t1 is derived from g11249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2187273	2187554	.	+	.	Phchi.S3G010300
Phchi.S3	AUGUSTUS	transcript	2187273	2187554	.	+	.	transcript_id "Phchi.S3G010300.t1"; gene_id "Phchi.S3G010300"
Phchi.S3	AUGUSTUS	start_codon	2187273	2187275	.	+	0	transcript_id "Phchi.S3G010300.t1"; gene_id "Phchi.S3G010300"
Phchi.S3	AUGUSTUS	CDS	2187273	2187554	0.92	+	0	transcript_id "Phchi.S3G010300.t1"; gene_id "Phchi.S3G010300"
Phchi.S3	AUGUSTUS	exon	2187273	2187554	.	+	.	transcript_id "Phchi.S3G010300.t1"; gene_id "Phchi.S3G010300"
Phchi.S3	AUGUSTUS	stop_codon	2187555	2187557	.	+	0	transcript_id "Phchi.S3G010300.t1"; gene_id "Phchi.S3G010300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8939.t1 is derived from g6114.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38761448	38765155	.	-	.	Phchi.S1G609800
Phchi.S1	AUGUSTUS	transcript	38761448	38765155	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	stop_codon	38761445	38761447	.	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38761448	38761566	1	-	2	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38761448	38761566	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38761567	38761649	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38761650	38762364	0.98	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38761650	38762364	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38762365	38762458	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38762459	38762649	1	-	2	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38762459	38762649	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38762650	38762756	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38762757	38762964	0.98	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38762757	38762964	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38762965	38763060	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38763061	38763165	0.88	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38763061	38763165	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38763166	38763307	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38763308	38763421	0.68	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38763308	38763421	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38763422	38763721	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38763722	38763804	0.85	-	2	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38763722	38763804	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38763805	38764088	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38764089	38764523	1	-	2	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38764089	38764523	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38764524	38764648	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38764649	38764727	1	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38764649	38764727	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38764728	38764803	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38764804	38764851	1	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38764804	38764851	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38764852	38765002	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38765003	38765155	0.57	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38765003	38765155	.	-	.	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	start_codon	38765153	38765155	.	-	0	transcript_id "Phchi.S1G609800.t1"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	transcript	38761448	38765155	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	stop_codon	38761445	38761447	.	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38761448	38761566	1	-	2	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38761448	38761566	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38761567	38761751	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38761752	38762364	0.98	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38761752	38762364	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38762365	38762458	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38762459	38762649	0.97	-	2	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38762459	38762649	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38762650	38762756	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38762757	38762964	0.97	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38762757	38762964	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38762965	38763060	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38763061	38763165	0.86	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38763061	38763165	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38763166	38763307	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38763308	38763421	0.7	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38763308	38763421	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38763422	38763721	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38763722	38763804	0.91	-	2	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38763722	38763804	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38763805	38764088	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38764089	38764523	1	-	2	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38764089	38764523	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38764524	38764648	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38764649	38764727	1	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38764649	38764727	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38764728	38764803	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38764804	38764851	0.99	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38764804	38764851	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	intron	38764852	38765002	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	CDS	38765003	38765155	0.56	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	exon	38765003	38765155	.	-	.	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
Phchi.S1	AUGUSTUS	start_codon	38765153	38765155	.	-	0	transcript_id "Phchi.S1G609800.t2"; gene_id "Phchi.S1G609800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3182.t1 is derived from g351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2125880	2126461	.	-	.	Phchi.S1G034100
Phchi.S1	AUGUSTUS	transcript	2125880	2126461	.	-	.	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	stop_codon	2125877	2125879	.	-	0	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	CDS	2125880	2126288	1	-	1	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	exon	2125880	2126288	.	-	.	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	intron	2126289	2126360	.	-	.	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	CDS	2126361	2126461	1	-	0	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	exon	2126361	2126461	.	-	.	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
Phchi.S1	AUGUSTUS	start_codon	2126459	2126461	.	-	0	transcript_id "Phchi.S1G034100.t1"; gene_id "Phchi.S1G034100"
# This transcript jg188.t2 is derived from g9970.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg189.t1 is derived from g9971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1074222	1075203	.	-	.	Phchi.S6G014800
Phchi.S6	AUGUSTUS	transcript	1074222	1075203	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	stop_codon	1074219	1074221	.	-	0	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	CDS	1074222	1074346	1	-	2	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	exon	1074222	1074346	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	intron	1074347	1074474	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	CDS	1074475	1074550	1	-	0	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	exon	1074475	1074550	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	intron	1074551	1074624	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	CDS	1074625	1074713	1	-	2	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	exon	1074625	1074713	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	intron	1074714	1074784	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	CDS	1074785	1074838	1	-	2	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	exon	1074785	1074838	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	intron	1074839	1074925	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	CDS	1074926	1075065	1	-	1	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	exon	1074926	1075065	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	intron	1075066	1075138	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	CDS	1075139	1075203	1	-	0	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	exon	1075139	1075203	.	-	.	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
Phchi.S6	AUGUSTUS	start_codon	1075201	1075203	.	-	0	transcript_id "Phchi.S6G014800.t1"; gene_id "Phchi.S6G014800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1942.t1 is derived from g8862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3932574	3934353	.	-	.	Phchi.S5G055100
Phchi.S5	AUGUSTUS	transcript	3932574	3934353	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	stop_codon	3932571	3932573	.	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3932574	3933104	0.97	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3932574	3933104	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	intron	3933105	3933230	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3933231	3933283	1	-	2	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3933231	3933283	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	intron	3933284	3933379	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3933380	3933545	1	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3933380	3933545	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	intron	3933546	3933685	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3933686	3933777	1	-	2	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3933686	3933777	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	intron	3933778	3933866	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3933867	3933882	0.95	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3933867	3933882	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	intron	3933883	3933956	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3933957	3934007	0.85	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3933957	3934007	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	intron	3934008	3934284	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	CDS	3934285	3934353	0.8	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	exon	3934285	3934353	.	-	.	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
Phchi.S5	AUGUSTUS	start_codon	3934351	3934353	.	-	0	transcript_id "Phchi.S5G055100.t1"; gene_id "Phchi.S5G055100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1479.t1 is derived from g8398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1132263	1133530	.	+	.	Phchi.S5G008800
Phchi.S5	AUGUSTUS	transcript	1132263	1133530	.	+	.	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	start_codon	1132263	1132265	.	+	0	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	CDS	1132263	1132982	0.55	+	0	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	exon	1132263	1132982	.	+	.	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	intron	1132983	1133185	.	+	.	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	CDS	1133186	1133530	0.45	+	0	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	exon	1133186	1133530	.	+	.	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
Phchi.S5	AUGUSTUS	stop_codon	1133531	1133533	.	+	0	transcript_id "Phchi.S5G008800.t1"; gene_id "Phchi.S5G008800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3372.t1 is derived from g541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3229477	3232463	.	+	.	Phchi.S1G053100
Phchi.S1	AUGUSTUS	transcript	3229477	3232463	.	+	.	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	start_codon	3229477	3229479	.	+	0	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	CDS	3229477	3230533	0.57	+	0	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	exon	3229477	3230533	.	+	.	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	intron	3230534	3230621	.	+	.	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	CDS	3230622	3231362	0.69	+	2	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	exon	3230622	3231362	.	+	.	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	intron	3231363	3231453	.	+	.	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	CDS	3231454	3232463	0.99	+	2	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	exon	3231454	3232463	.	+	.	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
Phchi.S1	AUGUSTUS	stop_codon	3232464	3232466	.	+	0	transcript_id "Phchi.S1G053100.t1"; gene_id "Phchi.S1G053100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1646.t1 is derived from g8565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2183628	2194662	.	-	.	Phchi.S5G025500
Phchi.S5	AUGUSTUS	transcript	2183628	2194662	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	stop_codon	2183625	2183627	.	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183628	2183708	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183628	2183708	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2183709	2183794	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183795	2183854	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183795	2183854	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2183855	2183942	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183943	2184052	0.95	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183943	2184052	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184053	2184164	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184165	2184259	1	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184165	2184259	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184260	2184402	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184403	2184458	0.97	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184403	2184458	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184459	2184748	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184749	2184798	0.98	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184749	2184798	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184799	2184896	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184897	2184980	1	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184897	2184980	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184981	2185142	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185143	2185191	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185143	2185191	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185192	2185308	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185309	2185503	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185309	2185503	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185504	2185585	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185586	2185849	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185586	2185849	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185850	2185930	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185931	2186037	1	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185931	2186037	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186038	2186211	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186212	2186419	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186212	2186419	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186420	2186554	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186555	2186620	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186555	2186620	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186621	2186704	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186705	2186994	1	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186705	2186994	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186995	2187096	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187097	2187169	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187097	2187169	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187170	2187290	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187291	2187539	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187291	2187539	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187540	2187670	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187671	2187869	1	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187671	2187869	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187870	2187971	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187972	2188054	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187972	2188054	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188055	2188142	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188143	2188240	1	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188143	2188240	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188241	2188320	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188321	2188526	0.98	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188321	2188526	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188527	2188632	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188633	2188766	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188633	2188766	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188767	2188845	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188846	2188950	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188846	2188950	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188951	2189072	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189073	2189171	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189073	2189171	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189172	2189283	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189284	2189370	0.89	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189284	2189370	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189371	2189473	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189474	2189536	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189474	2189536	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189537	2189623	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189624	2189659	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189624	2189659	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189660	2189758	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189759	2189863	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189759	2189863	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189864	2189990	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189991	2190087	1	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189991	2190087	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190088	2190221	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190222	2190307	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190222	2190307	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190308	2190461	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190462	2190512	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190462	2190512	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190513	2190624	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190625	2190780	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190625	2190780	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190781	2190960	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190961	2191098	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190961	2191098	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2191099	2192024	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192025	2192102	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192025	2192102	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192103	2192202	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192203	2192325	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192203	2192325	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192326	2192394	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192395	2192440	1	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192395	2192440	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192441	2192651	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192652	2192766	1	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192652	2192766	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192767	2192869	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192870	2193035	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192870	2193035	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193036	2193125	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193126	2193200	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193126	2193200	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193201	2193384	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193385	2193453	1	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193385	2193453	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193454	2193576	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193577	2193704	0.99	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193577	2193704	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193705	2193795	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193796	2193878	1	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193796	2193878	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193879	2194017	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194018	2194084	1	-	2	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194018	2194084	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2194085	2194307	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194308	2194360	1	-	1	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194308	2194360	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2194361	2194453	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194454	2194662	0.66	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194454	2194662	.	-	.	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	start_codon	2194660	2194662	.	-	0	transcript_id "Phchi.S5G025500.t1"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	transcript	2183628	2194662	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	stop_codon	2183625	2183627	.	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183628	2183708	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183628	2183708	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2183709	2183794	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183795	2183854	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183795	2183854	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2183855	2183942	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183943	2184052	0.93	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183943	2184052	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184053	2184164	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184165	2184259	1	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184165	2184259	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184260	2184402	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184403	2184458	0.95	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184403	2184458	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184459	2184748	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184749	2184798	0.96	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184749	2184798	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184799	2184896	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184897	2184980	1	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184897	2184980	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184981	2185142	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185143	2185191	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185143	2185191	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185192	2185308	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185309	2185503	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185309	2185503	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185504	2185585	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185586	2185849	0.96	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185586	2185849	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185850	2185930	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185931	2186037	0.96	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185931	2186037	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186038	2186211	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186212	2186419	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186212	2186419	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186420	2186554	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186555	2186620	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186555	2186620	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186621	2186704	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186705	2186994	1	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186705	2186994	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186995	2187096	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187097	2187169	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187097	2187169	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187170	2187290	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187291	2187539	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187291	2187539	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187540	2187670	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187671	2187869	1	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187671	2187869	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187870	2187971	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187972	2188054	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187972	2188054	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188055	2188142	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188143	2188240	1	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188143	2188240	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188241	2188320	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188321	2188526	0.96	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188321	2188526	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188527	2188632	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188633	2188766	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188633	2188766	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188767	2188845	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188846	2188950	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188846	2188950	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188951	2189072	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189073	2189171	0.98	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189073	2189171	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189172	2189283	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189284	2189370	0.92	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189284	2189370	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189371	2189473	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189474	2189536	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189474	2189536	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189537	2189623	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189624	2189659	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189624	2189659	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189660	2189758	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189759	2189863	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189759	2189863	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189864	2189990	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189991	2190087	1	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189991	2190087	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190088	2190221	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190222	2190307	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190222	2190307	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190308	2190461	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190462	2190512	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190462	2190512	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190513	2190624	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190625	2190780	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190625	2190780	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190781	2190960	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190961	2191098	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190961	2191098	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2191099	2192024	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192025	2192102	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192025	2192102	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192103	2192202	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192203	2192325	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192203	2192325	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192326	2192394	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192395	2192440	1	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192395	2192440	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192441	2192651	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192652	2192766	1	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192652	2192766	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192767	2192869	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192870	2193035	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192870	2193035	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193036	2193125	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193126	2193203	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193126	2193203	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193204	2193384	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193385	2193453	1	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193385	2193453	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193454	2193576	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193577	2193704	0.99	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193577	2193704	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193705	2193795	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193796	2193878	1	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193796	2193878	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193879	2194017	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194018	2194084	1	-	2	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194018	2194084	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2194085	2194307	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194308	2194360	1	-	1	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194308	2194360	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2194361	2194453	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194454	2194662	0.61	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194454	2194662	.	-	.	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	start_codon	2194660	2194662	.	-	0	transcript_id "Phchi.S5G025500.t2"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	transcript	2183628	2194662	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	stop_codon	2183625	2183627	.	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183628	2183708	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183628	2183708	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2183709	2183794	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183795	2183854	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183795	2183854	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2183855	2183942	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2183943	2184052	0.87	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2183943	2184052	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184053	2184164	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184165	2184259	1	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184165	2184259	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184260	2184402	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184403	2184458	0.94	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184403	2184458	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184459	2184748	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184749	2184798	0.94	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184749	2184798	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184799	2184896	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2184897	2184980	1	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2184897	2184980	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2184981	2185160	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185161	2185191	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185161	2185191	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185192	2185308	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185309	2185503	0.99	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185309	2185503	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185504	2185585	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185586	2185849	0.96	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185586	2185849	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2185850	2185930	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2185931	2186037	0.96	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2185931	2186037	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186038	2186211	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186212	2186419	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186212	2186419	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186420	2186554	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186555	2186620	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186555	2186620	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186621	2186704	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2186705	2186994	1	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2186705	2186994	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2186995	2187096	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187097	2187169	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187097	2187169	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187170	2187290	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187291	2187539	0.99	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187291	2187539	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187540	2187670	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187671	2187869	1	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187671	2187869	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2187870	2187971	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2187972	2188054	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2187972	2188054	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188055	2188142	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188143	2188240	1	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188143	2188240	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188241	2188320	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188321	2188526	0.97	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188321	2188526	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188527	2188632	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188633	2188766	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188633	2188766	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188767	2188845	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2188846	2188950	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2188846	2188950	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2188951	2189072	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189073	2189171	0.98	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189073	2189171	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189172	2189283	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189284	2189370	0.93	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189284	2189370	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189371	2189473	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189474	2189536	0.99	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189474	2189536	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189537	2189623	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189624	2189659	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189624	2189659	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189660	2189758	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189759	2189863	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189759	2189863	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2189864	2189990	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2189991	2190087	1	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2189991	2190087	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190088	2190221	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190222	2190307	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190222	2190307	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190308	2190461	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190462	2190512	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190462	2190512	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190513	2190624	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190625	2190780	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190625	2190780	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2190781	2190960	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2190961	2191098	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2190961	2191098	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2191099	2192024	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192025	2192102	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192025	2192102	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192103	2192202	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192203	2192325	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192203	2192325	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192326	2192394	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192395	2192440	1	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192395	2192440	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192441	2192651	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192652	2192766	1	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192652	2192766	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2192767	2192869	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2192870	2193035	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2192870	2193035	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193036	2193125	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193126	2193200	0.87	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193126	2193200	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193201	2193384	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193385	2193453	1	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193385	2193453	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193454	2193576	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193577	2193704	0.99	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193577	2193704	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193705	2193795	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2193796	2193878	1	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2193796	2193878	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2193879	2194017	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194018	2194084	1	-	2	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194018	2194084	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2194085	2194307	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194308	2194360	1	-	1	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194308	2194360	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	intron	2194361	2194453	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	CDS	2194454	2194662	0.52	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	exon	2194454	2194662	.	-	.	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
Phchi.S5	AUGUSTUS	start_codon	2194660	2194662	.	-	0	transcript_id "Phchi.S5G025500.t3"; gene_id "Phchi.S5G025500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7008.t1 is derived from g4180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26371251	26372067	.	-	.	Phchi.S1G416700
Phchi.S1	AUGUSTUS	transcript	26371251	26372067	.	-	.	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	stop_codon	26371248	26371250	.	-	0	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	CDS	26371251	26371681	0.42	-	2	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	exon	26371251	26371681	.	-	.	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	intron	26371682	26371751	.	-	.	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	CDS	26371752	26372067	0.88	-	0	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	exon	26371752	26372067	.	-	.	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
Phchi.S1	AUGUSTUS	start_codon	26372065	26372067	.	-	0	transcript_id "Phchi.S1G416700.t1"; gene_id "Phchi.S1G416700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3370.t1 is derived from g539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3200292	3202160	.	+	.	Phchi.S1G052900
Phchi.S1	AUGUSTUS	transcript	3200292	3202160	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	start_codon	3200292	3200294	.	+	0	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	CDS	3200292	3200498	1	+	0	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	exon	3200292	3200498	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	intron	3200499	3200649	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	CDS	3200650	3200719	1	+	0	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	exon	3200650	3200719	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	intron	3200720	3200795	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	CDS	3200796	3200883	1	+	2	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	exon	3200796	3200883	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	intron	3200884	3200999	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	CDS	3201000	3201099	0.48	+	1	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	exon	3201000	3201099	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	intron	3201100	3201233	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	CDS	3201234	3202160	0.45	+	0	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	exon	3201234	3202160	.	+	.	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
Phchi.S1	AUGUSTUS	stop_codon	3202161	3202163	.	+	0	transcript_id "Phchi.S1G052900.t1"; gene_id "Phchi.S1G052900"
# This transcript jg13432.t2 is derived from g11899.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13432.t3 is derived from g11899.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13432.t4 is derived from g11899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13433.t1 is derived from g11900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6680280	6683496	.	+	.	Phchi.S3G075200
Phchi.S3	AUGUSTUS	transcript	6680280	6683496	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	start_codon	6680280	6680282	.	+	0	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6680280	6680292	0.99	+	0	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6680280	6680292	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6680293	6680550	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6680551	6680640	0.56	+	2	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6680551	6680640	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6680641	6680733	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6680734	6681797	0.69	+	2	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6680734	6681797	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6681798	6682131	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6682132	6682187	1	+	0	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6682132	6682187	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6682188	6682319	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6682320	6682553	1	+	1	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6682320	6682553	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6682554	6682683	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6682684	6682817	0.61	+	1	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6682684	6682817	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6682818	6682891	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6682892	6682977	0.63	+	2	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6682892	6682977	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6682978	6683064	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6683065	6683258	1	+	0	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6683065	6683258	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	intron	6683259	6683345	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	CDS	6683346	6683496	0.97	+	1	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	exon	6683346	6683496	.	+	.	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
Phchi.S3	AUGUSTUS	stop_codon	6683497	6683499	.	+	0	transcript_id "Phchi.S3G075200.t1"; gene_id "Phchi.S3G075200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7404.t1 is derived from g4576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28967380	28969758	.	+	.	Phchi.S1G456300
Phchi.S1	AUGUSTUS	transcript	28967380	28969758	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	start_codon	28967380	28967382	.	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28967380	28967616	0.74	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28967380	28967616	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28967617	28967718	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28967719	28967931	1	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28967719	28967931	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28967932	28968131	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28968132	28968329	1	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28968132	28968329	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28968330	28968454	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28968455	28968550	1	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28968455	28968550	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28968551	28968668	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28968669	28968833	1	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28968669	28968833	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28968834	28968926	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28968927	28969032	1	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28968927	28969032	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28969033	28969138	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28969139	28969302	1	+	2	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28969139	28969302	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	intron	28969303	28969440	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	CDS	28969441	28969758	0.98	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	exon	28969441	28969758	.	+	.	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
Phchi.S1	AUGUSTUS	stop_codon	28969759	28969761	.	+	0	transcript_id "Phchi.S1G456300.t1"; gene_id "Phchi.S1G456300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8754.t1 is derived from g5929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37810966	37811603	.	+	.	Phchi.S1G591300
Phchi.S1	AUGUSTUS	transcript	37810966	37811603	.	+	.	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	start_codon	37810966	37810968	.	+	0	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	CDS	37810966	37811334	0.03	+	0	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	exon	37810966	37811334	.	+	.	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	intron	37811335	37811579	.	+	.	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	CDS	37811580	37811603	0.06	+	0	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	exon	37811580	37811603	.	+	.	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
Phchi.S1	AUGUSTUS	stop_codon	37811604	37811606	.	+	0	transcript_id "Phchi.S1G591300.t1"; gene_id "Phchi.S1G591300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7144.t1 is derived from g4316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27162480	27166529	.	+	.	Phchi.S1G430300
Phchi.S1	AUGUSTUS	transcript	27162480	27166529	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	start_codon	27162480	27162482	.	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27162480	27162554	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27162480	27162554	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27162555	27162753	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27162754	27162828	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27162754	27162828	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27162829	27162992	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27162993	27163124	0.82	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27162993	27163124	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27163125	27163229	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27163230	27163329	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27163230	27163329	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27163330	27163432	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27163433	27163535	1	+	2	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27163433	27163535	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27163536	27163686	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27163687	27163804	1	+	1	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27163687	27163804	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27163805	27163876	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27163877	27163960	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27163877	27163960	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27163961	27164078	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27164079	27164140	0.98	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27164079	27164140	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27164141	27164260	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27164261	27164394	1	+	1	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27164261	27164394	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27164395	27164477	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27164478	27164521	1	+	2	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27164478	27164521	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27164522	27164658	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27164659	27164735	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27164659	27164735	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27164736	27164867	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27164868	27165012	1	+	1	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27164868	27165012	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27165013	27165084	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27165085	27165146	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27165085	27165146	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27165147	27165228	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27165229	27165289	1	+	1	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27165229	27165289	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27165290	27165474	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27165475	27165567	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27165475	27165567	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27165568	27165699	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27165700	27165820	1	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27165700	27165820	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27165821	27165912	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27165913	27166015	1	+	2	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27165913	27166015	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27166016	27166140	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27166141	27166333	1	+	1	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27166141	27166333	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	intron	27166334	27166418	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	CDS	27166419	27166529	0.98	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	exon	27166419	27166529	.	+	.	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
Phchi.S1	AUGUSTUS	stop_codon	27166530	27166532	.	+	0	transcript_id "Phchi.S1G430300.t1"; gene_id "Phchi.S1G430300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10579.t1 is derived from g14629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1047123	1047906	.	-	.	Phchi.S4G016100
Phchi.S4	AUGUSTUS	transcript	1047123	1047906	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	stop_codon	1047120	1047122	.	-	0	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	CDS	1047123	1047219	1	-	1	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	exon	1047123	1047219	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	intron	1047220	1047315	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	CDS	1047316	1047419	1	-	0	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	exon	1047316	1047419	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	intron	1047420	1047602	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	CDS	1047603	1047682	1	-	2	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	exon	1047603	1047682	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	intron	1047683	1047827	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	CDS	1047828	1047906	0.99	-	0	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	exon	1047828	1047906	.	-	.	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
Phchi.S4	AUGUSTUS	start_codon	1047904	1047906	.	-	0	transcript_id "Phchi.S4G016100.t1"; gene_id "Phchi.S4G016100"
# This transcript jg1469.t2 is derived from g8388.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1470.t1 is derived from g8389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1091635	1094034	.	+	.	Phchi.S5G007900
Phchi.S5	AUGUSTUS	transcript	1091635	1094034	.	+	.	transcript_id "Phchi.S5G007900.t1"; gene_id "Phchi.S5G007900"
Phchi.S5	AUGUSTUS	start_codon	1091635	1091637	.	+	0	transcript_id "Phchi.S5G007900.t1"; gene_id "Phchi.S5G007900"
Phchi.S5	AUGUSTUS	CDS	1091635	1094034	0.59	+	0	transcript_id "Phchi.S5G007900.t1"; gene_id "Phchi.S5G007900"
Phchi.S5	AUGUSTUS	exon	1091635	1094034	.	+	.	transcript_id "Phchi.S5G007900.t1"; gene_id "Phchi.S5G007900"
Phchi.S5	AUGUSTUS	stop_codon	1094035	1094037	.	+	0	transcript_id "Phchi.S5G007900.t1"; gene_id "Phchi.S5G007900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9017.t1 is derived from g6192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39158447	39164723	.	+	.	Phchi.S1G617600
Phchi.S1	AUGUSTUS	transcript	39158447	39164723	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	start_codon	39158447	39158449	.	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39158447	39159367	0.4	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39158447	39159367	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39159368	39159649	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39159650	39159737	0.69	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39159650	39159737	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39159738	39159820	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39159821	39159967	0.72	+	2	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39159821	39159967	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39159968	39160065	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39160066	39161682	1	+	2	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39160066	39161682	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39161683	39161766	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39161767	39162026	1	+	2	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39161767	39162026	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39162027	39162115	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39162116	39162331	1	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39162116	39162331	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39162332	39162428	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39162429	39162647	0.95	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39162429	39162647	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39162648	39162755	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39162756	39163730	0.96	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39162756	39163730	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39163731	39163858	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39163859	39163951	1	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39163859	39163951	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39163952	39164050	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39164051	39164149	1	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39164051	39164149	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39164150	39164230	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39164231	39164420	1	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39164231	39164420	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	intron	39164421	39164499	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	CDS	39164500	39164723	0.99	+	2	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	exon	39164500	39164723	.	+	.	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
Phchi.S1	AUGUSTUS	stop_codon	39164724	39164726	.	+	0	transcript_id "Phchi.S1G617600.t1"; gene_id "Phchi.S1G617600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12329.t1 is derived from g8005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10988382	10990440	.	+	.	Phchi.S2G040900
Phchi.S2	AUGUSTUS	transcript	10988382	10990440	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	start_codon	10988382	10988384	.	+	0	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	CDS	10988382	10988743	1	+	0	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	exon	10988382	10988743	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	intron	10988744	10988825	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	CDS	10988826	10989120	0.97	+	1	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	exon	10988826	10989120	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	intron	10989121	10989236	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	CDS	10989237	10989430	1	+	0	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	exon	10989237	10989430	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	intron	10989431	10989530	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	CDS	10989531	10990099	0.9	+	1	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	exon	10989531	10990099	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	intron	10990100	10990222	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	CDS	10990223	10990440	0.93	+	2	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	exon	10990223	10990440	.	+	.	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
Phchi.S2	AUGUSTUS	stop_codon	10990441	10990443	.	+	0	transcript_id "Phchi.S2G040900.t1"; gene_id "Phchi.S2G040900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7077.t1 is derived from g4249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26787271	26789173	.	+	.	Phchi.S1G423600
Phchi.S1	AUGUSTUS	transcript	26787271	26789173	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	start_codon	26787271	26787273	.	+	0	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26787271	26787406	0.87	+	0	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26787271	26787406	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	intron	26787407	26787501	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26787502	26787732	1	+	2	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26787502	26787732	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	intron	26787733	26787810	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26787811	26787908	1	+	2	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26787811	26787908	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	intron	26787909	26787988	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26787989	26788175	1	+	0	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26787989	26788175	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	intron	26788176	26788275	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26788276	26788412	1	+	2	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26788276	26788412	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	intron	26788413	26788503	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26788504	26788725	1	+	0	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26788504	26788725	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	intron	26788726	26788795	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	CDS	26788796	26789173	0.99	+	0	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	exon	26788796	26789173	.	+	.	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
Phchi.S1	AUGUSTUS	stop_codon	26789174	26789176	.	+	0	transcript_id "Phchi.S1G423600.t1"; gene_id "Phchi.S1G423600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6471.t1 is derived from g3643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23170337	23172555	.	-	.	Phchi.S1G363000
Phchi.S1	AUGUSTUS	transcript	23170337	23172555	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	stop_codon	23170334	23170336	.	-	0	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	CDS	23170337	23170896	0.97	-	2	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	exon	23170337	23170896	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	intron	23170897	23171009	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	CDS	23171010	23171241	1	-	0	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	exon	23171010	23171241	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	intron	23171242	23171334	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	CDS	23171335	23171683	1	-	1	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	exon	23171335	23171683	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	intron	23171684	23171864	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	CDS	23171865	23172087	1	-	2	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	exon	23171865	23172087	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	intron	23172088	23172176	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	CDS	23172177	23172555	0.95	-	0	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	exon	23172177	23172555	.	-	.	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
Phchi.S1	AUGUSTUS	start_codon	23172553	23172555	.	-	0	transcript_id "Phchi.S1G363000.t1"; gene_id "Phchi.S1G363000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7745.t1 is derived from g4919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30929859	30933250	.	-	.	Phchi.S1G490400
Phchi.S1	AUGUSTUS	transcript	30929859	30933250	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	stop_codon	30929856	30929858	.	-	0	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30929859	30929898	0.68	-	1	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30929859	30929898	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30929899	30929983	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30929984	30930105	0.66	-	0	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30929984	30930105	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30930106	30930412	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30930413	30930473	0.62	-	1	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30930413	30930473	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30930474	30930626	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30930627	30930726	1	-	2	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30930627	30930726	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30930727	30930816	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30930817	30930875	1	-	1	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30930817	30930875	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30930876	30931000	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30931001	30931197	1	-	0	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30931001	30931197	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30931198	30931281	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30931282	30931378	1	-	1	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30931282	30931378	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30931379	30931475	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30931476	30931551	1	-	2	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30931476	30931551	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30931552	30931983	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30931984	30931997	1	-	1	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30931984	30931997	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30931998	30932086	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30932087	30932403	0.89	-	0	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30932087	30932403	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	intron	30932404	30932755	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	CDS	30932756	30933250	0.56	-	0	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	exon	30932756	30933250	.	-	.	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
Phchi.S1	AUGUSTUS	start_codon	30933248	30933250	.	-	0	transcript_id "Phchi.S1G490400.t1"; gene_id "Phchi.S1G490400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9882.t1 is derived from g7058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44241488	44247142	.	+	.	Phchi.S1G704100
Phchi.S1	AUGUSTUS	transcript	44241488	44247142	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	start_codon	44241488	44241490	.	+	0	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44241488	44242809	0.54	+	0	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44241488	44242809	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44242810	44242940	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44242941	44243068	0.72	+	1	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44242941	44243068	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44243069	44243157	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44243158	44244554	1	+	2	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44243158	44244554	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44244555	44244667	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44244668	44245818	0.96	+	0	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44244668	44245818	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44245819	44245985	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44245986	44246248	0.47	+	1	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44245986	44246248	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44246249	44246337	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44246338	44246454	0.51	+	2	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44246338	44246454	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44246455	44246600	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44246601	44246705	1	+	2	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44246601	44246705	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	intron	44246706	44246960	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	CDS	44246961	44247142	0.79	+	2	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	exon	44246961	44247142	.	+	.	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
Phchi.S1	AUGUSTUS	stop_codon	44247143	44247145	.	+	0	transcript_id "Phchi.S1G704100.t1"; gene_id "Phchi.S1G704100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15482.t1 is derived from g13950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19415926	19418102	.	-	.	Phchi.S3G280100
Phchi.S3	AUGUSTUS	transcript	19415926	19418102	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	stop_codon	19415923	19415925	.	-	0	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19415926	19415980	0.51	-	1	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19415926	19415980	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19415981	19416085	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19416086	19416169	0.89	-	1	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19416086	19416169	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19416170	19416248	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19416249	19416465	1	-	2	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19416249	19416465	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19416466	19416597	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19416598	19416680	1	-	1	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19416598	19416680	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19416681	19416994	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19416995	19417105	1	-	1	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19416995	19417105	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19417106	19417199	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19417200	19417270	1	-	0	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19417200	19417270	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19417271	19417352	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19417353	19417433	1	-	0	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19417353	19417433	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19417434	19417533	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19417534	19417577	1	-	2	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19417534	19417577	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19417578	19417668	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19417669	19417726	1	-	0	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19417669	19417726	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19417727	19417839	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19417840	19417940	0.99	-	2	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19417840	19417940	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	intron	19417941	19418044	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	CDS	19418045	19418102	0.89	-	0	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	exon	19418045	19418102	.	-	.	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
Phchi.S3	AUGUSTUS	start_codon	19418100	19418102	.	-	0	transcript_id "Phchi.S3G280100.t1"; gene_id "Phchi.S3G280100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4811.t1 is derived from g1981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12938027	12938565	.	+	.	Phchi.S1G197000
Phchi.S1	AUGUSTUS	transcript	12938027	12938565	.	+	.	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	start_codon	12938027	12938029	.	+	0	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	CDS	12938027	12938447	0.83	+	0	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	exon	12938027	12938447	.	+	.	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	intron	12938448	12938557	.	+	.	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	CDS	12938558	12938565	0.85	+	2	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	exon	12938558	12938565	.	+	.	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
Phchi.S1	AUGUSTUS	stop_codon	12938566	12938568	.	+	0	transcript_id "Phchi.S1G197000.t1"; gene_id "Phchi.S1G197000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2666.t1 is derived from g9586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8113927	8115249	.	+	.	Phchi.S5G127500
Phchi.S5	AUGUSTUS	transcript	8113927	8115249	.	+	.	transcript_id "Phchi.S5G127500.t1"; gene_id "Phchi.S5G127500"
Phchi.S5	AUGUSTUS	start_codon	8113927	8113929	.	+	0	transcript_id "Phchi.S5G127500.t1"; gene_id "Phchi.S5G127500"
Phchi.S5	AUGUSTUS	CDS	8113927	8115249	0.94	+	0	transcript_id "Phchi.S5G127500.t1"; gene_id "Phchi.S5G127500"
Phchi.S5	AUGUSTUS	exon	8113927	8115249	.	+	.	transcript_id "Phchi.S5G127500.t1"; gene_id "Phchi.S5G127500"
Phchi.S5	AUGUSTUS	stop_codon	8115250	8115252	.	+	0	transcript_id "Phchi.S5G127500.t1"; gene_id "Phchi.S5G127500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1944.t1 is derived from g8864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3940800	3941387	.	-	.	Phchi.S5G055300
Phchi.S5	AUGUSTUS	transcript	3940800	3941387	.	-	.	transcript_id "Phchi.S5G055300.t1"; gene_id "Phchi.S5G055300"
Phchi.S5	AUGUSTUS	stop_codon	3940797	3940799	.	-	0	transcript_id "Phchi.S5G055300.t1"; gene_id "Phchi.S5G055300"
Phchi.S5	AUGUSTUS	CDS	3940800	3941387	0.98	-	0	transcript_id "Phchi.S5G055300.t1"; gene_id "Phchi.S5G055300"
Phchi.S5	AUGUSTUS	exon	3940800	3941387	.	-	.	transcript_id "Phchi.S5G055300.t1"; gene_id "Phchi.S5G055300"
Phchi.S5	AUGUSTUS	start_codon	3941385	3941387	.	-	0	transcript_id "Phchi.S5G055300.t1"; gene_id "Phchi.S5G055300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13979.t1 is derived from g12446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10019990	10023179	.	-	.	Phchi.S3G129800
Phchi.S3	AUGUSTUS	transcript	10019990	10023179	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	stop_codon	10019987	10019989	.	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10019990	10020064	1	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10019990	10020064	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10020065	10020163	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10020164	10020253	0.77	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10020164	10020253	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10020254	10020331	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10020332	10020336	0.38	-	2	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10020332	10020336	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10020337	10020431	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10020432	10020519	0.5	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10020432	10020519	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10020520	10020636	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10020637	10020734	1	-	2	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10020637	10020734	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10020735	10020816	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10020817	10020868	1	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10020817	10020868	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10020869	10021013	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10021014	10021095	1	-	1	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10021014	10021095	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10021096	10021200	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10021201	10021328	1	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10021201	10021328	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10021329	10021456	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10021457	10021519	1	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10021457	10021519	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10021520	10021626	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10021627	10021740	1	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10021627	10021740	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10021741	10021865	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10021866	10021907	1	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10021866	10021907	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10021908	10022048	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10022049	10022169	1	-	1	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10022049	10022169	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10022170	10022330	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10022331	10022435	1	-	1	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10022331	10022435	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10022436	10022787	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10022788	10023005	0.98	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10022788	10023005	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	intron	10023006	10023116	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	CDS	10023117	10023179	0.98	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	exon	10023117	10023179	.	-	.	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
Phchi.S3	AUGUSTUS	start_codon	10023177	10023179	.	-	0	transcript_id "Phchi.S3G129800.t1"; gene_id "Phchi.S3G129800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9409.t1 is derived from g6585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41364310	41366508	.	+	.	Phchi.S1G656800
Phchi.S1	AUGUSTUS	transcript	41364310	41366508	.	+	.	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	start_codon	41364310	41364312	.	+	0	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	CDS	41364310	41364684	0.83	+	0	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	exon	41364310	41364684	.	+	.	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	intron	41364685	41365173	.	+	.	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	CDS	41365174	41366508	0.28	+	0	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	exon	41365174	41366508	.	+	.	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
Phchi.S1	AUGUSTUS	stop_codon	41366509	41366511	.	+	0	transcript_id "Phchi.S1G656800.t1"; gene_id "Phchi.S1G656800"
# This transcript jg1875.t2 is derived from g8795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1876.t1 is derived from g8796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3647956	3657765	.	-	.	Phchi.S5G048500
Phchi.S5	AUGUSTUS	transcript	3647956	3657765	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	stop_codon	3647953	3647955	.	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3647956	3648035	1	-	2	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3647956	3648035	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3648036	3648179	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3648180	3648387	0.63	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3648180	3648387	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3648388	3648491	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3648492	3650126	0.53	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3648492	3650126	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3650127	3650219	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3650220	3650628	0.99	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3650220	3650628	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3650629	3650727	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3650728	3650786	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3650728	3650786	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3650787	3650858	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3650859	3650966	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3650859	3650966	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3650967	3651061	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3651062	3651563	0.96	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3651062	3651563	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3651564	3651689	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3651690	3651871	0.99	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3651690	3651871	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3651872	3651995	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3651996	3652109	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3651996	3652109	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3652110	3652277	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3652278	3652382	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3652278	3652382	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3652383	3652536	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3652537	3652644	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3652537	3652644	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3652645	3652821	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3652822	3652944	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3652822	3652944	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3652945	3653028	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3653029	3653181	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3653029	3653181	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3653182	3653277	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3653278	3653426	0.99	-	2	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3653278	3653426	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3653427	3653552	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3653553	3653641	0.83	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3653553	3653641	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3653642	3653762	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3653763	3653837	1	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3653763	3653837	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3653838	3653955	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3653956	3654066	1	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3653956	3654066	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3654067	3654174	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3654175	3654260	0.98	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3654175	3654260	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3654261	3654370	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3654371	3654493	0.92	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3654371	3654493	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3654494	3654677	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3654678	3654891	1	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3654678	3654891	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3654892	3654980	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3654981	3655138	0.96	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3654981	3655138	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3655139	3655256	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3655257	3655316	0.92	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3655257	3655316	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3655317	3655465	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3655466	3655543	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3655466	3655543	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3655544	3655697	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3655698	3655796	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3655698	3655796	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3655797	3655880	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3655881	3656049	0.99	-	1	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3655881	3656049	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3656050	3656163	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3656164	3656321	0.91	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3656164	3656321	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3656322	3656445	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3656446	3656586	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3656446	3656586	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3656587	3656692	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3656693	3656829	0.99	-	2	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3656693	3656829	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3656830	3656953	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3656954	3657023	0.99	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3656954	3657023	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3657024	3657151	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3657152	3657244	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3657152	3657244	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3657245	3657331	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3657332	3657505	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3657332	3657505	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	intron	3657506	3657579	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	CDS	3657580	3657765	1	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	exon	3657580	3657765	.	-	.	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
Phchi.S5	AUGUSTUS	start_codon	3657763	3657765	.	-	0	transcript_id "Phchi.S5G048500.t1"; gene_id "Phchi.S5G048500"
# This transcript jg7129.t2 is derived from g4301.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7130.t1 is derived from g4302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27096303	27096755	.	-	.	Phchi.S1G428900
Phchi.S1	AUGUSTUS	transcript	27096303	27096755	.	-	.	transcript_id "Phchi.S1G428900.t1"; gene_id "Phchi.S1G428900"
Phchi.S1	AUGUSTUS	stop_codon	27096300	27096302	.	-	0	transcript_id "Phchi.S1G428900.t1"; gene_id "Phchi.S1G428900"
Phchi.S1	AUGUSTUS	CDS	27096303	27096755	0.64	-	0	transcript_id "Phchi.S1G428900.t1"; gene_id "Phchi.S1G428900"
Phchi.S1	AUGUSTUS	exon	27096303	27096755	.	-	.	transcript_id "Phchi.S1G428900.t1"; gene_id "Phchi.S1G428900"
Phchi.S1	AUGUSTUS	start_codon	27096753	27096755	.	-	0	transcript_id "Phchi.S1G428900.t1"; gene_id "Phchi.S1G428900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4406.t1 is derived from g1575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10256559	10257203	.	-	.	Phchi.S1G156500
Phchi.S1	AUGUSTUS	transcript	10256559	10257203	.	-	.	transcript_id "Phchi.S1G156500.t1"; gene_id "Phchi.S1G156500"
Phchi.S1	AUGUSTUS	stop_codon	10256556	10256558	.	-	0	transcript_id "Phchi.S1G156500.t1"; gene_id "Phchi.S1G156500"
Phchi.S1	AUGUSTUS	CDS	10256559	10257203	0.92	-	0	transcript_id "Phchi.S1G156500.t1"; gene_id "Phchi.S1G156500"
Phchi.S1	AUGUSTUS	exon	10256559	10257203	.	-	.	transcript_id "Phchi.S1G156500.t1"; gene_id "Phchi.S1G156500"
Phchi.S1	AUGUSTUS	start_codon	10257201	10257203	.	-	0	transcript_id "Phchi.S1G156500.t1"; gene_id "Phchi.S1G156500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4006.t1 is derived from g1175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6988550	6995196	.	-	.	Phchi.S1G116500
Phchi.S1	AUGUSTUS	transcript	6988550	6995196	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	stop_codon	6988547	6988549	.	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6988550	6991706	0.84	-	1	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6988550	6991706	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6991707	6991992	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6991993	6992099	0.72	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6991993	6992099	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6992100	6992457	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6992458	6992514	0.43	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6992458	6992514	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6992515	6992599	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6992600	6992697	0.91	-	2	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6992600	6992697	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6992698	6992909	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6992910	6993129	0.39	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6992910	6993129	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6993130	6993203	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6993204	6993259	1	-	2	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6993204	6993259	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6993260	6993338	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6993339	6993408	1	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6993339	6993408	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6993409	6993488	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6993489	6993650	1	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6993489	6993650	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6993651	6993828	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6993829	6993882	1	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6993829	6993882	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6993883	6994012	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6994013	6994060	1	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6994013	6994060	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6994061	6994222	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6994223	6994300	1	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6994223	6994300	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6994301	6994430	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6994431	6994495	0.8	-	2	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6994431	6994495	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6994496	6994609	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6994610	6994697	0.8	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6994610	6994697	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6994698	6994793	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6994794	6994830	1	-	1	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6994794	6994830	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6994831	6994916	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6994917	6994984	0.93	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6994917	6994984	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	intron	6994985	6995103	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	CDS	6995104	6995196	0.93	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	exon	6995104	6995196	.	-	.	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
Phchi.S1	AUGUSTUS	start_codon	6995194	6995196	.	-	0	transcript_id "Phchi.S1G116500.t1"; gene_id "Phchi.S1G116500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg777.t1 is derived from g10559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5459531	5462009	.	-	.	Phchi.S6G073600
Phchi.S6	AUGUSTUS	transcript	5459531	5462009	.	-	.	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	stop_codon	5459528	5459530	.	-	0	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	CDS	5459531	5459548	0.25	-	0	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	exon	5459531	5459548	.	-	.	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	intron	5459549	5459831	.	-	.	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	CDS	5459832	5462009	0.26	-	0	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	exon	5459832	5462009	.	-	.	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
Phchi.S6	AUGUSTUS	start_codon	5462007	5462009	.	-	0	transcript_id "Phchi.S6G073600.t1"; gene_id "Phchi.S6G073600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5366.t1 is derived from g2536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16521346	16524156	.	-	.	Phchi.S1G252500
Phchi.S1	AUGUSTUS	transcript	16521346	16524156	.	-	.	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	stop_codon	16521343	16521345	.	-	0	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	CDS	16521346	16523010	0.15	-	0	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	exon	16521346	16523010	.	-	.	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	intron	16523011	16523202	.	-	.	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	CDS	16523203	16523617	0.75	-	1	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	exon	16523203	16523617	.	-	.	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	intron	16523618	16523851	.	-	.	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	CDS	16523852	16524156	0.43	-	0	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	exon	16523852	16524156	.	-	.	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
Phchi.S1	AUGUSTUS	start_codon	16524154	16524156	.	-	0	transcript_id "Phchi.S1G252500.t1"; gene_id "Phchi.S1G252500"
# This transcript jg14386.t2 is derived from g12854.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14387.t1 is derived from g12855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12559092	12560163	.	+	.	Phchi.S3G170600
Phchi.S3	AUGUSTUS	transcript	12559092	12560163	.	+	.	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	start_codon	12559092	12559094	.	+	0	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	CDS	12559092	12559509	0.37	+	0	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	exon	12559092	12559509	.	+	.	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	intron	12559510	12559621	.	+	.	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	CDS	12559622	12560163	0.46	+	2	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	exon	12559622	12560163	.	+	.	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
Phchi.S3	AUGUSTUS	stop_codon	12560164	12560166	.	+	0	transcript_id "Phchi.S3G170600.t1"; gene_id "Phchi.S3G170600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3251.t1 is derived from g420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2515763	2516845	.	-	.	Phchi.S1G041000
Phchi.S1	AUGUSTUS	transcript	2515763	2516845	.	-	.	transcript_id "Phchi.S1G041000.t1"; gene_id "Phchi.S1G041000"
Phchi.S1	AUGUSTUS	stop_codon	2515760	2515762	.	-	0	transcript_id "Phchi.S1G041000.t1"; gene_id "Phchi.S1G041000"
Phchi.S1	AUGUSTUS	CDS	2515763	2516845	0.78	-	0	transcript_id "Phchi.S1G041000.t1"; gene_id "Phchi.S1G041000"
Phchi.S1	AUGUSTUS	exon	2515763	2516845	.	-	.	transcript_id "Phchi.S1G041000.t1"; gene_id "Phchi.S1G041000"
Phchi.S1	AUGUSTUS	start_codon	2516843	2516845	.	-	0	transcript_id "Phchi.S1G041000.t1"; gene_id "Phchi.S1G041000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4749.t1 is derived from g1919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12611427	12613359	.	+	.	Phchi.S1G190800
Phchi.S1	AUGUSTUS	transcript	12611427	12613359	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	start_codon	12611427	12611429	.	+	0	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12611427	12611518	0.97	+	0	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12611427	12611518	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	intron	12611519	12611860	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12611861	12611910	0.98	+	1	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12611861	12611910	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	intron	12611911	12612058	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12612059	12612230	1	+	2	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12612059	12612230	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	intron	12612231	12612716	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12612717	12612820	1	+	1	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12612717	12612820	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	intron	12612821	12612995	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12612996	12613072	0.96	+	2	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12612996	12613072	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	intron	12613073	12613190	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12613191	12613199	0.94	+	0	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12613191	12613199	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	intron	12613200	12613341	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	CDS	12613342	12613359	0.85	+	0	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	exon	12613342	12613359	.	+	.	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
Phchi.S1	AUGUSTUS	stop_codon	12613360	12613362	.	+	0	transcript_id "Phchi.S1G190800.t1"; gene_id "Phchi.S1G190800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3189.t1 is derived from g358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2149212	2151422	.	-	.	Phchi.S1G034800
Phchi.S1	AUGUSTUS	transcript	2149212	2151422	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	stop_codon	2149209	2149211	.	-	0	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2149212	2149340	0.53	-	0	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2149212	2149340	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	intron	2149341	2149431	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2149432	2149569	0.87	-	0	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2149432	2149569	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	intron	2149570	2149677	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2149678	2149849	0.86	-	1	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2149678	2149849	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	intron	2149850	2149941	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2149942	2150433	0.98	-	1	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2149942	2150433	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	intron	2150434	2150512	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2150513	2150709	0.99	-	0	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2150513	2150709	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	intron	2150710	2150801	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2150802	2150952	1	-	1	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2150802	2150952	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	intron	2150953	2151090	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	CDS	2151091	2151422	1	-	0	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	exon	2151091	2151422	.	-	.	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
Phchi.S1	AUGUSTUS	start_codon	2151420	2151422	.	-	0	transcript_id "Phchi.S1G034800.t1"; gene_id "Phchi.S1G034800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg329.t1 is derived from g10111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2283849	2286658	.	-	.	Phchi.S6G028800
Phchi.S6	AUGUSTUS	transcript	2283849	2286658	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	stop_codon	2283846	2283848	.	-	0	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	CDS	2283849	2283902	1	-	0	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	exon	2283849	2283902	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	intron	2283903	2284246	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	CDS	2284247	2284574	1	-	1	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	exon	2284247	2284574	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	intron	2284575	2284733	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	CDS	2284734	2285149	0.11	-	0	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	exon	2284734	2285149	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	intron	2285150	2286649	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	CDS	2286650	2286658	0.01	-	0	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	exon	2286650	2286658	.	-	.	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
Phchi.S6	AUGUSTUS	start_codon	2286656	2286658	.	-	0	transcript_id "Phchi.S6G028800.t1"; gene_id "Phchi.S6G028800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7869.t1 is derived from g5043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31638094	31639205	.	+	.	Phchi.S1G502800
Phchi.S1	AUGUSTUS	transcript	31638094	31639205	.	+	.	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	start_codon	31638094	31638096	.	+	0	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	CDS	31638094	31638579	0.69	+	0	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	exon	31638094	31638579	.	+	.	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	intron	31638580	31638685	.	+	.	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	CDS	31638686	31638878	1	+	0	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	exon	31638686	31638878	.	+	.	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	intron	31638879	31638963	.	+	.	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	CDS	31638964	31639205	1	+	2	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	exon	31638964	31639205	.	+	.	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
Phchi.S1	AUGUSTUS	stop_codon	31639206	31639208	.	+	0	transcript_id "Phchi.S1G502800.t1"; gene_id "Phchi.S1G502800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5784.t1 is derived from g2954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18944681	18948401	.	+	.	Phchi.S1G294300
Phchi.S1	AUGUSTUS	transcript	18944681	18948401	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	start_codon	18944681	18944683	.	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18944681	18944986	0.89	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18944681	18944986	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18944987	18945136	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18945137	18945286	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18945137	18945286	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18945287	18945389	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18945390	18945566	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18945390	18945566	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18945567	18945697	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18945698	18945841	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18945698	18945841	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18945842	18945937	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18945938	18946043	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18945938	18946043	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18946044	18946132	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18946133	18946281	1	+	2	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18946133	18946281	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18946282	18946392	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18946393	18946518	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18946393	18946518	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18946519	18946599	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18946600	18946743	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18946600	18946743	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18946744	18946898	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18946899	18946986	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18946899	18946986	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18946987	18947085	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18947086	18947246	0.89	+	2	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18947086	18947246	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18947247	18947344	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18947345	18947458	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18947345	18947458	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18947459	18947550	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18947551	18947859	1	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18947551	18947859	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18947860	18947956	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18947957	18948072	0.88	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18947957	18948072	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18948073	18948155	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18948156	18948187	0.87	+	1	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18948156	18948187	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	intron	18948188	18948264	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	CDS	18948265	18948401	0.74	+	2	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	exon	18948265	18948401	.	+	.	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
Phchi.S1	AUGUSTUS	stop_codon	18948402	18948404	.	+	0	transcript_id "Phchi.S1G294300.t1"; gene_id "Phchi.S1G294300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9773.t1 is derived from g6949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43617352	43618505	.	+	.	Phchi.S1G693200
Phchi.S1	AUGUSTUS	transcript	43617352	43618505	.	+	.	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	start_codon	43617352	43617354	.	+	0	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	CDS	43617352	43617493	0.78	+	0	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	exon	43617352	43617493	.	+	.	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	intron	43617494	43617703	.	+	.	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	CDS	43617704	43617886	0.58	+	2	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	exon	43617704	43617886	.	+	.	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	intron	43617887	43618125	.	+	.	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	CDS	43618126	43618505	0.76	+	2	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	exon	43618126	43618505	.	+	.	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
Phchi.S1	AUGUSTUS	stop_codon	43618506	43618508	.	+	0	transcript_id "Phchi.S1G693200.t1"; gene_id "Phchi.S1G693200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4600.t1 is derived from g1770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11290685	11291302	.	-	.	Phchi.S1G175900
Phchi.S1	AUGUSTUS	transcript	11290685	11291302	.	-	.	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	stop_codon	11290682	11290684	.	-	0	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	CDS	11290685	11290954	0.7	-	0	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	exon	11290685	11290954	.	-	.	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	intron	11290955	11291050	.	-	.	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	CDS	11291051	11291302	0.35	-	0	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	exon	11291051	11291302	.	-	.	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
Phchi.S1	AUGUSTUS	start_codon	11291300	11291302	.	-	0	transcript_id "Phchi.S1G175900.t1"; gene_id "Phchi.S1G175900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg5252.t1 is derived from g2422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15870764	15873536	.	+	.	Phchi.S1G241100
Phchi.S1	AUGUSTUS	transcript	15872024	15873536	.	+	.	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	start_codon	15872024	15872026	.	+	0	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15872024	15873358	0.73	+	0	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15872024	15873358	.	+	.	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	intron	15873359	15873533	.	+	.	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15873534	15873536	0.46	+	0	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15873534	15873536	.	+	.	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	stop_codon	15873537	15873539	.	+	0	transcript_id "Phchi.S1G241100.t1"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	transcript	15871484	15873536	.	+	.	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	start_codon	15871484	15871486	.	+	0	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15871484	15873358	0.54	+	0	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15871484	15873358	.	+	.	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	intron	15873359	15873533	.	+	.	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15873534	15873536	0.47	+	0	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15873534	15873536	.	+	.	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	stop_codon	15873537	15873539	.	+	0	transcript_id "Phchi.S1G241100.t2"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	transcript	15871961	15873536	.	+	.	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	start_codon	15871961	15871963	.	+	0	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15871961	15873358	0.46	+	0	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15871961	15873358	.	+	.	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	intron	15873359	15873533	.	+	.	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15873534	15873536	0.42	+	0	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15873534	15873536	.	+	.	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	stop_codon	15873537	15873539	.	+	0	transcript_id "Phchi.S1G241100.t3"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	transcript	15870764	15873536	.	+	.	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	start_codon	15870764	15870766	.	+	0	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15870764	15873358	0.52	+	0	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15870764	15873358	.	+	.	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	intron	15873359	15873533	.	+	.	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	CDS	15873534	15873536	0.33	+	0	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	exon	15873534	15873536	.	+	.	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
Phchi.S1	AUGUSTUS	stop_codon	15873537	15873539	.	+	0	transcript_id "Phchi.S1G241100.t4"; gene_id "Phchi.S1G241100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9847.t1 is derived from g7023.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44066792	44067243	.	+	.	Phchi.S1G700600
Phchi.S1	AUGUSTUS	transcript	44066792	44067243	.	+	.	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	start_codon	44066792	44066794	.	+	0	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	CDS	44066792	44067001	1	+	0	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	exon	44066792	44067001	.	+	.	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	intron	44067002	44067096	.	+	.	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	CDS	44067097	44067243	0.63	+	0	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	exon	44067097	44067243	.	+	.	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	stop_codon	44067244	44067246	.	+	0	transcript_id "Phchi.S1G700600.t1"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	transcript	44066792	44067243	.	+	.	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	start_codon	44066792	44066794	.	+	0	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	CDS	44066792	44067001	1	+	0	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	exon	44066792	44067001	.	+	.	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	intron	44067002	44067084	.	+	.	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	CDS	44067085	44067243	0.59	+	0	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	exon	44067085	44067243	.	+	.	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
Phchi.S1	AUGUSTUS	stop_codon	44067244	44067246	.	+	0	transcript_id "Phchi.S1G700600.t2"; gene_id "Phchi.S1G700600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1092.t1 is derived from g10875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7534081	7549040	.	-	.	Phchi.S6G105100
Phchi.S6	AUGUSTUS	transcript	7534081	7549040	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	stop_codon	7534078	7534080	.	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7534081	7534122	0.99	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7534081	7534122	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7534123	7534192	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7534193	7534258	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7534193	7534258	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7534259	7534338	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7534339	7534358	0.55	-	2	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7534339	7534358	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7534359	7534408	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7534409	7534413	0.55	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7534409	7534413	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7534414	7534498	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7534499	7534755	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7534499	7534755	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7534756	7534849	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7534850	7535014	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7534850	7535014	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7535015	7535106	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7535107	7535241	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7535107	7535241	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7535242	7535350	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7535351	7535423	1	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7535351	7535423	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7535424	7535540	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7535541	7535602	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7535541	7535602	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7535603	7535684	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7535685	7535768	0.98	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7535685	7535768	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7535769	7535875	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7535876	7536004	0.99	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7535876	7536004	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7536005	7536086	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7536087	7536260	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7536087	7536260	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7536261	7536344	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7536345	7536502	1	-	2	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7536345	7536502	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7536503	7536588	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7536589	7536655	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7536589	7536655	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7536656	7536740	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7536741	7536815	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7536741	7536815	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7536816	7536948	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7536949	7537029	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7536949	7537029	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7537030	7537181	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7537182	7537376	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7537182	7537376	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7537377	7537522	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7537523	7537636	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7537523	7537636	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7537637	7537714	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7537715	7537921	0.98	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7537715	7537921	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7537922	7538045	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7538046	7538260	0.98	-	2	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7538046	7538260	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7538261	7538361	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7538362	7538533	0.9	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7538362	7538533	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7538534	7538644	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7538645	7538779	0.96	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7538645	7538779	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7538780	7538861	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7538862	7539002	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7538862	7539002	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7539003	7539100	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7539101	7539202	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7539101	7539202	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7539203	7539387	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7539388	7539456	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7539388	7539456	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7539457	7539533	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7539534	7539599	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7539534	7539599	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7539600	7539713	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7539714	7539893	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7539714	7539893	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7539894	7539976	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7539977	7540080	1	-	2	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7539977	7540080	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7540081	7540259	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7540260	7540357	1	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7540260	7540357	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7540358	7540462	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7540463	7540524	0.96	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7540463	7540524	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7540525	7540624	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7540625	7540759	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7540625	7540759	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7540760	7540849	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7540850	7540921	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7540850	7540921	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7540922	7541004	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7541005	7541157	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7541005	7541157	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7541158	7541236	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7541237	7541389	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7541237	7541389	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7541390	7541484	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7541485	7541691	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7541485	7541691	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7541692	7541785	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7541786	7541909	1	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7541786	7541909	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7541910	7542028	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7542029	7542081	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7542029	7542081	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7542082	7542202	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7542203	7542336	1	-	2	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7542203	7542336	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7542337	7542413	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7542414	7542576	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7542414	7542576	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7542577	7542714	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7542715	7542813	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7542715	7542813	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7542814	7542901	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7542902	7543000	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7542902	7543000	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7543001	7543141	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7543142	7543177	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7543142	7543177	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7543178	7543254	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7543255	7543347	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7543255	7543347	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7543348	7543441	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7543442	7543630	0.97	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7543442	7543630	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7543631	7543737	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7543738	7543840	0.97	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7543738	7543840	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7543841	7544016	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7544017	7544147	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7544017	7544147	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7544148	7544282	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7544283	7544378	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7544283	7544378	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7544379	7544480	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7544481	7544580	0.99	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7544481	7544580	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7544581	7544684	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7544685	7544806	0.61	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7544685	7544806	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7544807	7544918	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7544919	7545071	0.92	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7544919	7545071	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7545072	7545209	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7545210	7545428	0.99	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7545210	7545428	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7545429	7545516	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7545517	7545530	1	-	2	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7545517	7545530	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7545531	7545613	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7545614	7545714	1	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7545614	7545714	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7545715	7545861	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7545862	7546031	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7545862	7546031	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7546032	7546129	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7546130	7546273	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7546130	7546273	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7546274	7546440	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7546441	7546600	1	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7546441	7546600	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7546601	7546703	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7546704	7546802	1	-	1	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7546704	7546802	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7546803	7546907	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7546908	7547080	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7546908	7547080	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7547081	7547329	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7547330	7547404	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7547330	7547404	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7547405	7547680	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7547681	7548013	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7547681	7548013	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	intron	7548014	7548800	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	CDS	7548801	7549040	1	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	exon	7548801	7549040	.	-	.	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
Phchi.S6	AUGUSTUS	start_codon	7549038	7549040	.	-	0	transcript_id "Phchi.S6G105100.t1"; gene_id "Phchi.S6G105100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5057.t1 is derived from g2227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14450151	14453104	.	+	.	Phchi.S1G221600
Phchi.S1	AUGUSTUS	transcript	14450151	14453104	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	start_codon	14450151	14450153	.	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14450151	14450242	0.92	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14450151	14450242	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14450243	14450324	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14450325	14450628	0.99	+	1	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14450325	14450628	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14450629	14450729	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14450730	14450879	1	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14450730	14450879	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14450880	14450956	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14450957	14451104	1	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14450957	14451104	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14451105	14451235	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14451236	14451489	1	+	2	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14451236	14451489	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14451490	14451612	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14451613	14451990	0.98	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14451613	14451990	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14451991	14452180	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14452181	14452489	1	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14452181	14452489	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14452490	14452571	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14452572	14452772	1	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14452572	14452772	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	intron	14452773	14452846	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	CDS	14452847	14453104	1	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	exon	14452847	14453104	.	+	.	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
Phchi.S1	AUGUSTUS	stop_codon	14453105	14453107	.	+	0	transcript_id "Phchi.S1G221600.t1"; gene_id "Phchi.S1G221600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7120.t1 is derived from g4292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27063707	27064249	.	-	.	Phchi.S1G427900
Phchi.S1	AUGUSTUS	transcript	27063707	27064249	.	-	.	transcript_id "Phchi.S1G427900.t1"; gene_id "Phchi.S1G427900"
Phchi.S1	AUGUSTUS	stop_codon	27063704	27063706	.	-	0	transcript_id "Phchi.S1G427900.t1"; gene_id "Phchi.S1G427900"
Phchi.S1	AUGUSTUS	CDS	27063707	27064249	0.64	-	0	transcript_id "Phchi.S1G427900.t1"; gene_id "Phchi.S1G427900"
Phchi.S1	AUGUSTUS	exon	27063707	27064249	.	-	.	transcript_id "Phchi.S1G427900.t1"; gene_id "Phchi.S1G427900"
Phchi.S1	AUGUSTUS	start_codon	27064247	27064249	.	-	0	transcript_id "Phchi.S1G427900.t1"; gene_id "Phchi.S1G427900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13845.t1 is derived from g12312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9165987	9167839	.	+	.	Phchi.S3G116400
Phchi.S3	AUGUSTUS	transcript	9165987	9167839	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	start_codon	9165987	9165989	.	+	0	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	CDS	9165987	9166393	0.38	+	0	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	exon	9165987	9166393	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	intron	9166394	9166499	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	CDS	9166500	9166697	0.78	+	1	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	exon	9166500	9166697	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	intron	9166698	9166867	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	CDS	9166868	9166952	1	+	1	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	exon	9166868	9166952	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	intron	9166953	9167070	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	CDS	9167071	9167155	1	+	0	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	exon	9167071	9167155	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	intron	9167156	9167245	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	CDS	9167246	9167490	1	+	2	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	exon	9167246	9167490	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	intron	9167491	9167584	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	CDS	9167585	9167839	1	+	0	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	exon	9167585	9167839	.	+	.	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
Phchi.S3	AUGUSTUS	stop_codon	9167840	9167842	.	+	0	transcript_id "Phchi.S3G116400.t1"; gene_id "Phchi.S3G116400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13082.t1 is derived from g11547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4067668	4070900	.	-	.	Phchi.S3G040100
Phchi.S3	AUGUSTUS	transcript	4067668	4070900	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	stop_codon	4067665	4067667	.	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4067668	4068018	0.97	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4067668	4068018	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4068019	4068106	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4068107	4068214	1	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4068107	4068214	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4068215	4068304	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4068305	4068577	0.96	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4068305	4068577	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4068578	4068657	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4068658	4068744	0.97	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4068658	4068744	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4068745	4068834	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4068835	4069029	1	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4068835	4069029	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4069030	4069126	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4069127	4069264	1	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4069127	4069264	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4069265	4069351	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4069352	4069458	0.81	-	2	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4069352	4069458	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4069459	4069581	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4069582	4069787	0.65	-	1	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4069582	4069787	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4069788	4069869	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4069870	4070159	1	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4069870	4070159	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4070160	4070246	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4070247	4070326	1	-	2	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4070247	4070326	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	intron	4070327	4070470	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	CDS	4070471	4070900	0.69	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	exon	4070471	4070900	.	-	.	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
Phchi.S3	AUGUSTUS	start_codon	4070898	4070900	.	-	0	transcript_id "Phchi.S3G040100.t1"; gene_id "Phchi.S3G040100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7312.t1 is derived from g4484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28460012	28462734	.	+	.	Phchi.S1G447100
Phchi.S1	AUGUSTUS	transcript	28460012	28462734	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	start_codon	28460012	28460014	.	+	0	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	CDS	28460012	28460204	0.7	+	0	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	exon	28460012	28460204	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	intron	28460205	28460324	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	CDS	28460325	28461058	0.5	+	2	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	exon	28460325	28461058	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	intron	28461059	28461159	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	CDS	28461160	28462195	0.17	+	0	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	exon	28461160	28462195	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	intron	28462196	28462397	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	CDS	28462398	28462543	0.23	+	2	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	exon	28462398	28462543	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	intron	28462544	28462704	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	CDS	28462705	28462734	0.96	+	0	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	exon	28462705	28462734	.	+	.	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
Phchi.S1	AUGUSTUS	stop_codon	28462735	28462737	.	+	0	transcript_id "Phchi.S1G447100.t1"; gene_id "Phchi.S1G447100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1206.t1 is derived from g10989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8413825	8415762	.	+	.	Phchi.S6G116500
Phchi.S6	AUGUSTUS	transcript	8413825	8415762	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	start_codon	8413825	8413827	.	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8413825	8414277	0.99	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8413825	8414277	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	intron	8414278	8414395	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8414396	8414653	1	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8414396	8414653	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	intron	8414654	8414791	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8414792	8415034	1	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8414792	8415034	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	intron	8415035	8415118	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8415119	8415289	1	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8415119	8415289	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	intron	8415290	8415411	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8415412	8415491	0.54	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8415412	8415491	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	intron	8415492	8415624	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8415625	8415678	0.54	+	1	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8415625	8415678	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	intron	8415679	8415761	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	CDS	8415762	8415762	0.54	+	1	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	exon	8415762	8415762	.	+	.	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
Phchi.S6	AUGUSTUS	stop_codon	8415763	8415765	.	+	0	transcript_id "Phchi.S6G116500.t1"; gene_id "Phchi.S6G116500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg337.t1 is derived from g10119.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2475559	2476873	.	+	.	Phchi.S6G029600
Phchi.S6	AUGUSTUS	transcript	2475559	2476873	.	+	.	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	start_codon	2475559	2475561	.	+	0	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	CDS	2475559	2475884	0.81	+	0	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	exon	2475559	2475884	.	+	.	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	intron	2475885	2475960	.	+	.	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	CDS	2475961	2476873	0.8	+	1	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	exon	2475961	2476873	.	+	.	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	stop_codon	2476874	2476876	.	+	0	transcript_id "Phchi.S6G029600.t1"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	transcript	2475980	2476873	.	+	.	transcript_id "Phchi.S6G029600.t2"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	start_codon	2475980	2475982	.	+	0	transcript_id "Phchi.S6G029600.t2"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	CDS	2475980	2476873	0.94	+	0	transcript_id "Phchi.S6G029600.t2"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	exon	2475980	2476873	.	+	.	transcript_id "Phchi.S6G029600.t2"; gene_id "Phchi.S6G029600"
Phchi.S6	AUGUSTUS	stop_codon	2476874	2476876	.	+	0	transcript_id "Phchi.S6G029600.t2"; gene_id "Phchi.S6G029600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3063.t1 is derived from g232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1402463	1404557	.	+	.	Phchi.S1G022200
Phchi.S1	AUGUSTUS	transcript	1402463	1404557	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	start_codon	1402463	1402465	.	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1402463	1402670	0.55	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1402463	1402670	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1402671	1402761	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1402762	1402806	0.66	+	2	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1402762	1402806	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1402807	1402858	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1402859	1403044	0.59	+	2	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1402859	1403044	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1403045	1403138	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1403139	1403342	1	+	2	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1403139	1403342	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1403343	1403461	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1403462	1403589	1	+	2	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1403462	1403589	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1403590	1403699	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1403700	1403819	1	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1403700	1403819	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1403820	1403934	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1403935	1404024	0.94	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1403935	1404024	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1404025	1404131	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1404132	1404218	0.99	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1404132	1404218	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1404219	1404326	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1404327	1404406	1	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1404327	1404406	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	intron	1404407	1404484	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	CDS	1404485	1404557	1	+	1	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	exon	1404485	1404557	.	+	.	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
Phchi.S1	AUGUSTUS	stop_codon	1404558	1404560	.	+	0	transcript_id "Phchi.S1G022200.t1"; gene_id "Phchi.S1G022200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5505.t1 is derived from g2675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17156326	17157606	.	-	.	Phchi.S1G266400
Phchi.S1	AUGUSTUS	transcript	17156326	17157606	.	-	.	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	stop_codon	17156323	17156325	.	-	0	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	CDS	17156326	17156961	1	-	0	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	exon	17156326	17156961	.	-	.	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	intron	17156962	17157237	.	-	.	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	CDS	17157238	17157606	0.65	-	0	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	exon	17157238	17157606	.	-	.	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
Phchi.S1	AUGUSTUS	start_codon	17157604	17157606	.	-	0	transcript_id "Phchi.S1G266400.t1"; gene_id "Phchi.S1G266400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7631.t1 is derived from g4805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30326291	30328121	.	-	.	Phchi.S1G479000
Phchi.S1	AUGUSTUS	transcript	30326291	30328121	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	stop_codon	30326288	30326290	.	-	0	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30326291	30326546	0.94	-	1	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30326291	30326546	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	intron	30326547	30326638	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30326639	30326763	1	-	0	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30326639	30326763	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	intron	30326764	30326855	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30326856	30327041	1	-	0	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30326856	30327041	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	intron	30327042	30327126	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30327127	30327270	1	-	0	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30327127	30327270	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	intron	30327271	30327440	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30327441	30327583	1	-	2	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30327441	30327583	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	intron	30327584	30327738	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30327739	30328025	1	-	1	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30327739	30328025	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	intron	30328026	30328107	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	CDS	30328108	30328121	0.99	-	0	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	exon	30328108	30328121	.	-	.	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
Phchi.S1	AUGUSTUS	start_codon	30328119	30328121	.	-	0	transcript_id "Phchi.S1G479000.t1"; gene_id "Phchi.S1G479000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5844.t1 is derived from g3014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19301254	19302656	.	-	.	Phchi.S1G300300
Phchi.S1	AUGUSTUS	transcript	19301254	19302656	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	stop_codon	19301251	19301253	.	-	0	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	CDS	19301254	19301916	1	-	0	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	exon	19301254	19301916	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	intron	19301917	19302034	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	CDS	19302035	19302127	1	-	0	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	exon	19302035	19302127	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	intron	19302128	19302244	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	CDS	19302245	19302320	1	-	1	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	exon	19302245	19302320	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	intron	19302321	19302404	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	CDS	19302405	19302517	1	-	0	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	exon	19302405	19302517	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	intron	19302518	19302650	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	CDS	19302651	19302656	1	-	0	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	exon	19302651	19302656	.	-	.	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
Phchi.S1	AUGUSTUS	start_codon	19302654	19302656	.	-	0	transcript_id "Phchi.S1G300300.t1"; gene_id "Phchi.S1G300300"
# This transcript jg1661.t2 is derived from g8580.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1661.t3 is derived from g8580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1662.t1 is derived from g8581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2288826	2291153	.	+	.	Phchi.S5G027100
Phchi.S5	AUGUSTUS	transcript	2288826	2291153	.	+	.	transcript_id "Phchi.S5G027100.t1"; gene_id "Phchi.S5G027100"
Phchi.S5	AUGUSTUS	start_codon	2288826	2288828	.	+	0	transcript_id "Phchi.S5G027100.t1"; gene_id "Phchi.S5G027100"
Phchi.S5	AUGUSTUS	CDS	2288826	2291153	1	+	0	transcript_id "Phchi.S5G027100.t1"; gene_id "Phchi.S5G027100"
Phchi.S5	AUGUSTUS	exon	2288826	2291153	.	+	.	transcript_id "Phchi.S5G027100.t1"; gene_id "Phchi.S5G027100"
Phchi.S5	AUGUSTUS	stop_codon	2291154	2291156	.	+	0	transcript_id "Phchi.S5G027100.t1"; gene_id "Phchi.S5G027100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3051.t1 is derived from g220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1360317	1361041	.	+	.	Phchi.S1G021000
Phchi.S1	AUGUSTUS	transcript	1360317	1361041	.	+	.	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	start_codon	1360317	1360319	.	+	0	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	CDS	1360317	1360434	0.99	+	0	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	exon	1360317	1360434	.	+	.	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	intron	1360435	1360592	.	+	.	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	CDS	1360593	1360645	1	+	2	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	exon	1360593	1360645	.	+	.	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	intron	1360646	1360867	.	+	.	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	CDS	1360868	1361041	1	+	0	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	exon	1360868	1361041	.	+	.	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
Phchi.S1	AUGUSTUS	stop_codon	1361042	1361044	.	+	0	transcript_id "Phchi.S1G021000.t1"; gene_id "Phchi.S1G021000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10819.t1 is derived from g14869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2268781	2274898	.	-	.	Phchi.S4G040100
Phchi.S4	AUGUSTUS	transcript	2268781	2274898	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	stop_codon	2268778	2268780	.	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2268781	2268821	0.69	-	2	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2268781	2268821	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2268822	2268946	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2268947	2269082	0.77	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2268947	2269082	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2269083	2269180	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2269181	2269243	1	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2269181	2269243	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2269244	2269320	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2269321	2269393	1	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2269321	2269393	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2269394	2269477	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2269478	2269556	0.77	-	2	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2269478	2269556	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2269557	2269890	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2269891	2270117	0.65	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2269891	2270117	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2270118	2270203	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2270204	2270549	1	-	2	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2270204	2270549	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2270550	2270641	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2270642	2271051	0.7	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2270642	2271051	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2271052	2271145	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2271146	2271615	0.84	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2271146	2271615	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2271616	2271730	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2271731	2271899	0.99	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2271731	2271899	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2271900	2272011	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2272012	2272205	0.89	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2272012	2272205	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2272206	2272312	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2272313	2272454	0.99	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2272313	2272454	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2272455	2272563	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2272564	2272615	1	-	2	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2272564	2272615	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2272616	2272744	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2272745	2272872	1	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2272745	2272872	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2272873	2273046	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2273047	2273180	1	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2273047	2273180	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2273181	2273337	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2273338	2273462	1	-	2	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2273338	2273462	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2273463	2273706	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2273707	2273795	1	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2273707	2273795	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2273796	2273933	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2273934	2273993	1	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2273934	2273993	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2273994	2274076	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2274077	2274160	1	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2274077	2274160	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2274161	2274337	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2274338	2274430	1	-	1	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2274338	2274430	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2274431	2274514	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2274515	2274564	1	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2274515	2274564	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	intron	2274565	2274667	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	CDS	2274668	2274898	0.34	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	exon	2274668	2274898	.	-	.	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
Phchi.S4	AUGUSTUS	start_codon	2274896	2274898	.	-	0	transcript_id "Phchi.S4G040100.t1"; gene_id "Phchi.S4G040100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10547.t1 is derived from g14597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	909303	911524	.	-	.	Phchi.S4G012900
Phchi.S4	AUGUSTUS	transcript	909303	911524	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	stop_codon	909300	909302	.	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	909303	909803	1	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	909303	909803	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	intron	909804	909880	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	909881	910063	1	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	909881	910063	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	intron	910064	910192	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	910193	910498	1	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	910193	910498	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	intron	910499	910602	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	910603	910794	0.98	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	910603	910794	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	intron	910795	910879	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	910880	910999	1	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	910880	910999	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	intron	911000	911115	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	911116	911298	0.99	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	911116	911298	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	intron	911299	911419	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	CDS	911420	911524	0.95	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	exon	911420	911524	.	-	.	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
Phchi.S4	AUGUSTUS	start_codon	911522	911524	.	-	0	transcript_id "Phchi.S4G012900.t1"; gene_id "Phchi.S4G012900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4912.t1 is derived from g2082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13358535	13359538	.	+	.	Phchi.S1G207100
Phchi.S1	AUGUSTUS	transcript	13358535	13359538	.	+	.	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	start_codon	13358535	13358537	.	+	0	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	CDS	13358535	13358659	0.98	+	0	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	exon	13358535	13358659	.	+	.	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	intron	13358660	13358798	.	+	.	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	CDS	13358799	13358887	0.82	+	1	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	exon	13358799	13358887	.	+	.	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	intron	13358888	13359287	.	+	.	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	CDS	13359288	13359538	0.6	+	2	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	exon	13359288	13359538	.	+	.	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
Phchi.S1	AUGUSTUS	stop_codon	13359539	13359541	.	+	0	transcript_id "Phchi.S1G207100.t1"; gene_id "Phchi.S1G207100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4956.t1 is derived from g2126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13730108	13731576	.	-	.	Phchi.S1G211500
Phchi.S1	AUGUSTUS	transcript	13730108	13731576	.	-	.	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	stop_codon	13730105	13730107	.	-	0	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	CDS	13730108	13730350	0.65	-	0	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	exon	13730108	13730350	.	-	.	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	intron	13730351	13730466	.	-	.	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	CDS	13730467	13731019	1	-	1	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	exon	13730467	13731019	.	-	.	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	intron	13731020	13731109	.	-	.	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	CDS	13731110	13731576	0.37	-	0	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	exon	13731110	13731576	.	-	.	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
Phchi.S1	AUGUSTUS	start_codon	13731574	13731576	.	-	0	transcript_id "Phchi.S1G211500.t1"; gene_id "Phchi.S1G211500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14888.t1 is derived from g13356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15286430	15287838	.	-	.	Phchi.S3G220700
Phchi.S3	AUGUSTUS	transcript	15286430	15287838	.	-	.	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	stop_codon	15286427	15286429	.	-	0	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	CDS	15286430	15286797	0.99	-	2	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	exon	15286430	15286797	.	-	.	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	intron	15286798	15286949	.	-	.	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	CDS	15286950	15287838	0.97	-	0	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	exon	15286950	15287838	.	-	.	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
Phchi.S3	AUGUSTUS	start_codon	15287836	15287838	.	-	0	transcript_id "Phchi.S3G220700.t1"; gene_id "Phchi.S3G220700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2074.t1 is derived from g8994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4719525	4720697	.	-	.	Phchi.S5G068300
Phchi.S5	AUGUSTUS	transcript	4719525	4720697	.	-	.	transcript_id "Phchi.S5G068300.t1"; gene_id "Phchi.S5G068300"
Phchi.S5	AUGUSTUS	stop_codon	4719522	4719524	.	-	0	transcript_id "Phchi.S5G068300.t1"; gene_id "Phchi.S5G068300"
Phchi.S5	AUGUSTUS	CDS	4719525	4720697	0.82	-	0	transcript_id "Phchi.S5G068300.t1"; gene_id "Phchi.S5G068300"
Phchi.S5	AUGUSTUS	exon	4719525	4720697	.	-	.	transcript_id "Phchi.S5G068300.t1"; gene_id "Phchi.S5G068300"
Phchi.S5	AUGUSTUS	start_codon	4720695	4720697	.	-	0	transcript_id "Phchi.S5G068300.t1"; gene_id "Phchi.S5G068300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12801.t1 is derived from g11266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2443117	2449832	.	-	.	Phchi.S3G012000
Phchi.S3	AUGUSTUS	transcript	2443117	2449832	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	stop_codon	2443114	2443116	.	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2443117	2443708	0.88	-	1	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2443117	2443708	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2443709	2443795	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2443796	2443936	0.99	-	1	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2443796	2443936	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2443937	2444039	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2444040	2444392	0.98	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2444040	2444392	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2444393	2444478	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2444479	2444677	1	-	1	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2444479	2444677	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2444678	2444831	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2444832	2445034	0.8	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2444832	2445034	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2445035	2445138	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2445139	2445344	0.84	-	2	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2445139	2445344	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2445345	2445520	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2445521	2445662	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2445521	2445662	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2445663	2445756	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2445757	2446023	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2445757	2446023	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2446024	2446165	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2446166	2446378	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2446166	2446378	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2446379	2446468	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2446469	2446616	1	-	1	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2446469	2446616	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2446617	2446718	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2446719	2446807	0.99	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2446719	2446807	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2446808	2446919	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2446920	2447210	0.99	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2446920	2447210	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2447211	2447462	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2447463	2447656	1	-	2	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2447463	2447656	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2447657	2447775	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2447776	2447935	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2447776	2447935	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2447936	2448106	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2448107	2448295	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2448107	2448295	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2448296	2448425	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2448426	2448518	0.28	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2448426	2448518	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2448519	2448634	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2448635	2448718	0.29	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2448635	2448718	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2448719	2448864	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2448865	2449188	0.94	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2448865	2449188	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2449189	2449294	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2449295	2449454	0.99	-	1	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2449295	2449454	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2449455	2449552	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2449553	2449722	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2449553	2449722	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	intron	2449723	2449805	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	CDS	2449806	2449832	1	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	exon	2449806	2449832	.	-	.	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
Phchi.S3	AUGUSTUS	start_codon	2449830	2449832	.	-	0	transcript_id "Phchi.S3G012000.t1"; gene_id "Phchi.S3G012000"
# This transcript jg11067.t2 is derived from g15117.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11068.t1 is derived from g15118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3959049	3960138	.	+	.	Phchi.S4G065000
Phchi.S4	AUGUSTUS	transcript	3959049	3960138	.	+	.	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	start_codon	3959049	3959051	.	+	0	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	CDS	3959049	3959421	0.88	+	0	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	exon	3959049	3959421	.	+	.	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	intron	3959422	3959523	.	+	.	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	CDS	3959524	3959753	1	+	2	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	exon	3959524	3959753	.	+	.	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	intron	3959754	3959871	.	+	.	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	CDS	3959872	3960138	1	+	0	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	exon	3959872	3960138	.	+	.	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
Phchi.S4	AUGUSTUS	stop_codon	3960139	3960141	.	+	0	transcript_id "Phchi.S4G065000.t1"; gene_id "Phchi.S4G065000"
# This transcript jg3837.t2 is derived from g1006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3838.t1 is derived from g1007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5951378	5954106	.	-	.	Phchi.S1G099700
Phchi.S1	AUGUSTUS	transcript	5951378	5954106	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	stop_codon	5951375	5951377	.	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5951378	5951389	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5951378	5951389	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5951390	5951484	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5951485	5951590	1	-	1	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5951485	5951590	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5951591	5951674	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5951675	5951769	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5951675	5951769	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5951770	5951895	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5951896	5951934	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5951896	5951934	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5951935	5952009	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5952010	5952082	1	-	1	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5952010	5952082	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5952083	5952167	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5952168	5952274	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5952168	5952274	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5952275	5952384	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5952385	5952453	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5952385	5952453	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5952454	5952542	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5952543	5952575	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5952543	5952575	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5952576	5952704	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5952705	5952780	1	-	1	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5952705	5952780	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5952781	5952954	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5952955	5953030	1	-	2	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5952955	5953030	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5953031	5953156	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5953157	5953202	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5953157	5953202	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5953203	5953284	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5953285	5953341	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5953285	5953341	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5953342	5953525	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5953526	5953600	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5953526	5953600	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5953601	5953732	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5953733	5953808	1	-	1	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5953733	5953808	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5953809	5953876	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5953877	5953959	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5953877	5953959	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	intron	5953960	5954055	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	CDS	5954056	5954106	1	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	exon	5954056	5954106	.	-	.	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
Phchi.S1	AUGUSTUS	start_codon	5954104	5954106	.	-	0	transcript_id "Phchi.S1G099700.t1"; gene_id "Phchi.S1G099700"
# This transcript jg11729.t2 is derived from g15781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11730.t1 is derived from g15782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7896819	7898813	.	-	.	Phchi.S4G131200
Phchi.S4	AUGUSTUS	transcript	7896819	7898813	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	stop_codon	7896816	7896818	.	-	0	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7896819	7896926	1	-	0	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7896819	7896926	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	intron	7896927	7897020	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7897021	7897121	1	-	2	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7897021	7897121	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	intron	7897122	7897360	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7897361	7897417	1	-	2	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7897361	7897417	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	intron	7897418	7897505	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7897506	7897623	1	-	0	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7897506	7897623	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	intron	7897624	7897710	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7897711	7897906	1	-	1	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7897711	7897906	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	intron	7897907	7898027	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7898028	7898149	0.64	-	0	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7898028	7898149	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	intron	7898150	7898255	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	CDS	7898256	7898813	1	-	0	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	exon	7898256	7898813	.	-	.	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
Phchi.S4	AUGUSTUS	start_codon	7898811	7898813	.	-	0	transcript_id "Phchi.S4G131200.t1"; gene_id "Phchi.S4G131200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9050.t1 is derived from g6225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39396922	39398796	.	-	.	Phchi.S1G620900
Phchi.S1	AUGUSTUS	transcript	39396922	39398796	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	stop_codon	39396919	39396921	.	-	0	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39396922	39397005	0.97	-	0	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39396922	39397005	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	intron	39397006	39397158	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39397159	39397283	1	-	2	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39397159	39397283	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	intron	39397284	39397393	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39397394	39397572	0.98	-	1	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39397394	39397572	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	intron	39397573	39397657	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39397658	39397879	1	-	1	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39397658	39397879	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	intron	39397880	39398039	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39398040	39398128	0.96	-	0	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39398040	39398128	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	intron	39398129	39398314	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39398315	39398392	0.63	-	0	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39398315	39398392	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	intron	39398393	39398664	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	CDS	39398665	39398796	1	-	0	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	exon	39398665	39398796	.	-	.	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
Phchi.S1	AUGUSTUS	start_codon	39398794	39398796	.	-	0	transcript_id "Phchi.S1G620900.t1"; gene_id "Phchi.S1G620900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1935.t1 is derived from g8855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3903699	3904230	.	-	.	Phchi.S5G054400
Phchi.S5	AUGUSTUS	transcript	3903699	3904230	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	stop_codon	3903696	3903698	.	-	0	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	CDS	3903699	3903760	0.99	-	2	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	exon	3903699	3903760	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	intron	3903761	3903844	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	CDS	3903845	3903898	1	-	2	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	exon	3903845	3903898	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	intron	3903899	3903985	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	CDS	3903986	3904071	1	-	1	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	exon	3903986	3904071	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	intron	3904072	3904150	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	CDS	3904151	3904230	1	-	0	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	exon	3904151	3904230	.	-	.	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
Phchi.S5	AUGUSTUS	start_codon	3904228	3904230	.	-	0	transcript_id "Phchi.S5G054400.t1"; gene_id "Phchi.S5G054400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10084.t1 is derived from g7260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45665899	45666706	.	-	.	Phchi.S1G724300
Phchi.S1	AUGUSTUS	transcript	45665899	45666706	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	stop_codon	45665896	45665898	.	-	0	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	CDS	45665899	45666101	1	-	2	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	exon	45665899	45666101	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	intron	45666102	45666216	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	CDS	45666217	45666292	1	-	0	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	exon	45666217	45666292	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	intron	45666293	45666435	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	CDS	45666436	45666585	0.82	-	0	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	exon	45666436	45666585	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	intron	45666586	45666688	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	CDS	45666689	45666706	0.82	-	0	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	exon	45666689	45666706	.	-	.	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
Phchi.S1	AUGUSTUS	start_codon	45666704	45666706	.	-	0	transcript_id "Phchi.S1G724300.t1"; gene_id "Phchi.S1G724300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6722.t1 is derived from g3894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24744152	24748085	.	+	.	Phchi.S1G388100
Phchi.S1	AUGUSTUS	transcript	24744152	24748085	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	start_codon	24744152	24744154	.	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24744152	24744652	0.97	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24744152	24744652	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24744653	24744737	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24744738	24744926	0.99	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24744738	24744926	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24744927	24745012	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24745013	24745234	1	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24745013	24745234	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24745235	24745328	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24745329	24745394	0.94	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24745329	24745394	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24745395	24745495	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24745496	24745531	0.78	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24745496	24745531	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24745532	24745643	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24745644	24745760	0.99	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24745644	24745760	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24745761	24745850	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24745851	24747194	0.99	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24745851	24747194	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24747195	24747271	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24747272	24747328	0.97	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24747272	24747328	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	intron	24747329	24747440	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	CDS	24747441	24748085	0.99	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	exon	24747441	24748085	.	+	.	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
Phchi.S1	AUGUSTUS	stop_codon	24748086	24748088	.	+	0	transcript_id "Phchi.S1G388100.t1"; gene_id "Phchi.S1G388100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4327.t1 is derived from g1496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9802341	9804984	.	+	.	Phchi.S1G148600
Phchi.S1	AUGUSTUS	transcript	9802341	9804984	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	start_codon	9802341	9802343	.	+	0	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9802341	9802534	0.74	+	0	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9802341	9802534	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9802535	9802660	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9802661	9802733	1	+	1	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9802661	9802733	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9802734	9802816	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9802817	9802988	0.96	+	0	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9802817	9802988	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9802989	9803070	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9803071	9803169	1	+	2	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9803071	9803169	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9803170	9803257	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9803258	9803355	0.99	+	2	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9803258	9803355	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9803356	9803462	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9803463	9803668	1	+	0	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9803463	9803668	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9803669	9803766	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9803767	9803891	1	+	1	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9803767	9803891	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9803892	9804079	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9804080	9804459	0.97	+	2	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9804080	9804459	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9804460	9804562	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9804563	9804768	1	+	0	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9804563	9804768	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	intron	9804769	9804845	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	CDS	9804846	9804984	1	+	1	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	exon	9804846	9804984	.	+	.	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
Phchi.S1	AUGUSTUS	stop_codon	9804985	9804987	.	+	0	transcript_id "Phchi.S1G148600.t1"; gene_id "Phchi.S1G148600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11852.t1 is derived from g15904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8625348	8626813	.	+	.	Phchi.S4G143400
Phchi.S4	AUGUSTUS	transcript	8625348	8626813	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	start_codon	8625348	8625350	.	+	0	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	CDS	8625348	8625680	0.82	+	0	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	exon	8625348	8625680	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	intron	8625681	8625969	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	CDS	8625970	8626284	1	+	0	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	exon	8625970	8626284	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	intron	8626285	8626381	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	CDS	8626382	8626564	1	+	0	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	exon	8626382	8626564	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	intron	8626565	8626663	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	CDS	8626664	8626813	0.83	+	0	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	exon	8626664	8626813	.	+	.	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
Phchi.S4	AUGUSTUS	stop_codon	8626814	8626816	.	+	0	transcript_id "Phchi.S4G143400.t1"; gene_id "Phchi.S4G143400"
# This transcript jg12378.t2 is derived from g8054.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12379.t1 is derived from g8055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14459364	14460049	.	+	.	Phchi.S2G045900
Phchi.S2	AUGUSTUS	transcript	14459364	14460049	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	start_codon	14459364	14459366	.	+	0	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	CDS	14459364	14459366	1	+	0	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	exon	14459364	14459366	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	intron	14459367	14459457	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	CDS	14459458	14459538	1	+	0	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	exon	14459458	14459538	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	intron	14459539	14459638	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	CDS	14459639	14459679	0.9	+	0	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	exon	14459639	14459679	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	intron	14459680	14459904	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	CDS	14459905	14460049	0.89	+	1	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	exon	14459905	14460049	.	+	.	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
Phchi.S2	AUGUSTUS	stop_codon	14460050	14460052	.	+	0	transcript_id "Phchi.S2G045900.t1"; gene_id "Phchi.S2G045900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3623.t1 is derived from g792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4815418	4818680	.	+	.	Phchi.S1G078200
Phchi.S1	AUGUSTUS	transcript	4815418	4818680	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	start_codon	4815418	4815420	.	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4815418	4815441	0.99	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4815418	4815441	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4815442	4815545	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4815546	4815760	0.99	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4815546	4815760	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4815761	4815866	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4815867	4815986	1	+	1	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4815867	4815986	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4815987	4816081	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4816082	4816207	1	+	1	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4816082	4816207	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4816208	4816367	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4816368	4816452	1	+	1	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4816368	4816452	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4816453	4816568	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4816569	4816679	1	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4816569	4816679	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4816680	4816780	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4816781	4816874	1	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4816781	4816874	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4816875	4816962	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4816963	4817342	1	+	2	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4816963	4817342	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4817343	4817495	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4817496	4817603	1	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4817496	4817603	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4817604	4817740	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4817741	4817862	1	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4817741	4817862	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4817863	4817963	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4817964	4818177	1	+	1	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4817964	4818177	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4818178	4818261	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4818262	4818495	1	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4818262	4818495	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	intron	4818496	4818575	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	CDS	4818576	4818680	0.98	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	exon	4818576	4818680	.	+	.	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
Phchi.S1	AUGUSTUS	stop_codon	4818681	4818683	.	+	0	transcript_id "Phchi.S1G078200.t1"; gene_id "Phchi.S1G078200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12179.t1 is derived from g7855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6105440	6108009	.	+	.	Phchi.S2G025900
Phchi.S2	AUGUSTUS	transcript	6105440	6108009	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	start_codon	6105440	6105442	.	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6105440	6105856	0.66	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6105440	6105856	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6105857	6105979	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6105980	6106323	1	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6105980	6106323	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6106324	6106420	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6106421	6106658	1	+	1	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6106421	6106658	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6106659	6106935	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6106936	6107093	1	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6106936	6107093	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107094	6107203	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107204	6107240	1	+	1	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107204	6107240	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107241	6107374	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107375	6107433	1	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107375	6107433	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107434	6107515	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107516	6107597	1	+	1	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107516	6107597	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107598	6107670	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107671	6107742	1	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107671	6107742	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107743	6107823	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107824	6108009	1	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107824	6108009	.	+	.	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	stop_codon	6108010	6108012	.	+	0	transcript_id "Phchi.S2G025900.t1"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	transcript	6105440	6108009	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	start_codon	6105440	6105442	.	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6105440	6105629	0.41	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6105440	6105629	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6105630	6105826	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6105827	6105890	0.31	+	2	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6105827	6105890	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6105891	6105979	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6105980	6106036	0.99	+	1	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6105980	6106036	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6106037	6106179	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6106180	6106323	0.87	+	1	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6106180	6106323	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6106324	6106420	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6106421	6106658	1	+	1	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6106421	6106658	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6106659	6106935	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6106936	6107093	1	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6106936	6107093	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107094	6107203	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107204	6107240	1	+	1	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107204	6107240	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107241	6107374	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107375	6107433	1	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107375	6107433	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107434	6107515	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107516	6107597	1	+	1	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107516	6107597	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107598	6107670	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107671	6107742	1	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107671	6107742	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	intron	6107743	6107823	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	CDS	6107824	6108009	1	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	exon	6107824	6108009	.	+	.	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
Phchi.S2	AUGUSTUS	stop_codon	6108010	6108012	.	+	0	transcript_id "Phchi.S2G025900.t2"; gene_id "Phchi.S2G025900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3483.t1 is derived from g652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4008321	4008821	.	-	.	Phchi.S1G064200
Phchi.S1	AUGUSTUS	transcript	4008321	4008821	.	-	.	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	stop_codon	4008318	4008320	.	-	0	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	CDS	4008321	4008410	0.72	-	0	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	exon	4008321	4008410	.	-	.	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	intron	4008411	4008504	.	-	.	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	CDS	4008505	4008669	1	-	0	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	exon	4008505	4008669	.	-	.	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	intron	4008670	4008752	.	-	.	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	CDS	4008753	4008821	0.86	-	0	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	exon	4008753	4008821	.	-	.	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
Phchi.S1	AUGUSTUS	start_codon	4008819	4008821	.	-	0	transcript_id "Phchi.S1G064200.t1"; gene_id "Phchi.S1G064200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3470.t1 is derived from g639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3922867	3924571	.	+	.	Phchi.S1G062900
Phchi.S1	AUGUSTUS	transcript	3922867	3924571	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	start_codon	3922867	3922869	.	+	0	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	CDS	3922867	3923119	0.48	+	0	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	exon	3922867	3923119	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	intron	3923120	3923336	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	CDS	3923337	3923365	0.48	+	2	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	exon	3923337	3923365	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	intron	3923366	3923536	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	CDS	3923537	3923909	0.66	+	0	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	exon	3923537	3923909	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	intron	3923910	3924005	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	CDS	3924006	3924571	0.96	+	2	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	exon	3924006	3924571	.	+	.	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
Phchi.S1	AUGUSTUS	stop_codon	3924572	3924574	.	+	0	transcript_id "Phchi.S1G062900.t1"; gene_id "Phchi.S1G062900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg929.t1 is derived from g10711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6486020	6487648	.	+	.	Phchi.S6G088800
Phchi.S6	AUGUSTUS	transcript	6486020	6487648	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	start_codon	6486020	6486022	.	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6486020	6486325	1	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6486020	6486325	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	intron	6486326	6486412	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6486413	6486506	0.94	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6486413	6486506	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	intron	6486507	6486621	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6486622	6486743	0.87	+	2	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6486622	6486743	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	intron	6486744	6486818	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6486819	6486995	1	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6486819	6486995	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	intron	6486996	6487089	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6487090	6487197	1	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6487090	6487197	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	intron	6487198	6487286	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6487287	6487380	0.99	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6487287	6487380	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	intron	6487381	6487643	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	CDS	6487644	6487648	0.99	+	2	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	exon	6487644	6487648	.	+	.	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
Phchi.S6	AUGUSTUS	stop_codon	6487649	6487651	.	+	0	transcript_id "Phchi.S6G088800.t1"; gene_id "Phchi.S6G088800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12177.t1 is derived from g7853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6094845	6096544	.	-	.	Phchi.S2G025700
Phchi.S2	AUGUSTUS	transcript	6094845	6096544	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	stop_codon	6094842	6094844	.	-	0	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	CDS	6094845	6095051	1	-	0	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	exon	6094845	6095051	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	intron	6095052	6095188	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	CDS	6095189	6095390	1	-	1	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	exon	6095189	6095390	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	intron	6095391	6095508	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	CDS	6095509	6095684	1	-	0	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	exon	6095509	6095684	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	intron	6095685	6095776	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	CDS	6095777	6095958	1	-	2	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	exon	6095777	6095958	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	intron	6095959	6096094	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	CDS	6096095	6096244	1	-	2	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	exon	6096095	6096244	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	intron	6096245	6096339	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	CDS	6096340	6096544	1	-	0	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	exon	6096340	6096544	.	-	.	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
Phchi.S2	AUGUSTUS	start_codon	6096542	6096544	.	-	0	transcript_id "Phchi.S2G025700.t1"; gene_id "Phchi.S2G025700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg773.t1 is derived from g10555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5450128	5451714	.	-	.	Phchi.S6G073200
Phchi.S6	AUGUSTUS	transcript	5450128	5451714	.	-	.	transcript_id "Phchi.S6G073200.t1"; gene_id "Phchi.S6G073200"
Phchi.S6	AUGUSTUS	stop_codon	5450125	5450127	.	-	0	transcript_id "Phchi.S6G073200.t1"; gene_id "Phchi.S6G073200"
Phchi.S6	AUGUSTUS	CDS	5450128	5451714	0.8	-	0	transcript_id "Phchi.S6G073200.t1"; gene_id "Phchi.S6G073200"
Phchi.S6	AUGUSTUS	exon	5450128	5451714	.	-	.	transcript_id "Phchi.S6G073200.t1"; gene_id "Phchi.S6G073200"
Phchi.S6	AUGUSTUS	start_codon	5451712	5451714	.	-	0	transcript_id "Phchi.S6G073200.t1"; gene_id "Phchi.S6G073200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4250.t1 is derived from g1419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9169921	9170148	.	-	.	Phchi.S1G140900
Phchi.S1	AUGUSTUS	transcript	9169921	9170148	.	-	.	transcript_id "Phchi.S1G140900.t1"; gene_id "Phchi.S1G140900"
Phchi.S1	AUGUSTUS	stop_codon	9169918	9169920	.	-	0	transcript_id "Phchi.S1G140900.t1"; gene_id "Phchi.S1G140900"
Phchi.S1	AUGUSTUS	CDS	9169921	9170148	0.52	-	0	transcript_id "Phchi.S1G140900.t1"; gene_id "Phchi.S1G140900"
Phchi.S1	AUGUSTUS	exon	9169921	9170148	.	-	.	transcript_id "Phchi.S1G140900.t1"; gene_id "Phchi.S1G140900"
Phchi.S1	AUGUSTUS	start_codon	9170146	9170148	.	-	0	transcript_id "Phchi.S1G140900.t1"; gene_id "Phchi.S1G140900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9722.t1 is derived from g6898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43400251	43401162	.	-	.	Phchi.S1G688100
Phchi.S1	AUGUSTUS	transcript	43400251	43401162	.	-	.	transcript_id "Phchi.S1G688100.t1"; gene_id "Phchi.S1G688100"
Phchi.S1	AUGUSTUS	stop_codon	43400248	43400250	.	-	0	transcript_id "Phchi.S1G688100.t1"; gene_id "Phchi.S1G688100"
Phchi.S1	AUGUSTUS	CDS	43400251	43401162	0.44	-	0	transcript_id "Phchi.S1G688100.t1"; gene_id "Phchi.S1G688100"
Phchi.S1	AUGUSTUS	exon	43400251	43401162	.	-	.	transcript_id "Phchi.S1G688100.t1"; gene_id "Phchi.S1G688100"
Phchi.S1	AUGUSTUS	start_codon	43401160	43401162	.	-	0	transcript_id "Phchi.S1G688100.t1"; gene_id "Phchi.S1G688100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13495.t1 is derived from g11962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7159107	7162007	.	+	.	Phchi.S3G081400
Phchi.S3	AUGUSTUS	transcript	7159107	7162007	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	start_codon	7159107	7159109	.	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7159107	7159183	0.84	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7159107	7159183	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7159184	7159272	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7159273	7159342	1	+	1	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7159273	7159342	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7159343	7159484	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7159485	7159681	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7159485	7159681	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7159682	7159770	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7159771	7159846	1	+	1	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7159771	7159846	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7159847	7159998	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7159999	7160082	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7159999	7160082	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7160083	7160185	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7160186	7160265	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7160186	7160265	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7160266	7160355	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7160356	7160485	1	+	1	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7160356	7160485	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7160486	7160650	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7160651	7160710	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7160651	7160710	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7160711	7160826	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7160827	7160877	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7160827	7160877	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7160878	7160973	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7160974	7161132	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7160974	7161132	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7161133	7161212	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7161213	7161345	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7161213	7161345	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7161346	7161438	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7161439	7161866	1	+	2	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7161439	7161866	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	intron	7161867	7161953	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	CDS	7161954	7162007	1	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	exon	7161954	7162007	.	+	.	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
Phchi.S3	AUGUSTUS	stop_codon	7162008	7162010	.	+	0	transcript_id "Phchi.S3G081400.t1"; gene_id "Phchi.S3G081400"
# This transcript jg10500.t2 is derived from g14549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10500.t3 is derived from g14549.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10501.t1 is derived from g14550.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	725757	728114	.	+	.	Phchi.S4G008300
Phchi.S4	AUGUSTUS	transcript	725757	728114	.	+	.	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	start_codon	725757	725759	.	+	0	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	CDS	725757	727918	1	+	0	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	exon	725757	727918	.	+	.	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	intron	727919	728101	.	+	.	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	CDS	728102	728114	1	+	1	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	exon	728102	728114	.	+	.	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	stop_codon	728115	728117	.	+	0	transcript_id "Phchi.S4G008300.t1"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	transcript	725757	728077	.	+	.	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	start_codon	725757	725759	.	+	0	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	CDS	725757	727918	0.51	+	0	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	exon	725757	727918	.	+	.	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	intron	727919	728058	.	+	.	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	CDS	728059	728077	0.51	+	1	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	exon	728059	728077	.	+	.	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
Phchi.S4	AUGUSTUS	stop_codon	728078	728080	.	+	0	transcript_id "Phchi.S4G008300.t2"; gene_id "Phchi.S4G008300"
# This transcript jg11056.t2 is derived from g15106.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11056.t3 is derived from g15106.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11057.t1 is derived from g15107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3881115	3884305	.	+	.	Phchi.S4G063900
Phchi.S4	AUGUSTUS	transcript	3881115	3884305	.	+	.	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	start_codon	3881115	3881117	.	+	0	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	CDS	3881115	3881222	0.53	+	0	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	exon	3881115	3881222	.	+	.	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	intron	3881223	3881323	.	+	.	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	CDS	3881324	3884305	0.54	+	0	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	exon	3881324	3884305	.	+	.	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
Phchi.S4	AUGUSTUS	stop_codon	3884306	3884308	.	+	0	transcript_id "Phchi.S4G063900.t1"; gene_id "Phchi.S4G063900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2382.t1 is derived from g9302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6432888	6438511	.	+	.	Phchi.S5G099100
Phchi.S5	AUGUSTUS	transcript	6432888	6438511	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	start_codon	6432888	6432890	.	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6432888	6433619	0.55	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6432888	6433619	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6433620	6433702	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6433703	6433828	1	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6433703	6433828	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6433829	6433909	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6433910	6434215	1	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6433910	6434215	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6434216	6434309	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6434310	6434364	1	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6434310	6434364	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6434365	6434467	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6434468	6434643	1	+	2	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6434468	6434643	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6434644	6434740	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6434741	6434905	1	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6434741	6434905	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6434906	6435003	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6435004	6435299	0.98	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6435004	6435299	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6435300	6435425	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6435426	6435742	0.58	+	1	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6435426	6435742	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6435743	6435907	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6435908	6435978	0.59	+	2	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6435908	6435978	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6435979	6436103	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6436104	6436130	0.33	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6436104	6436130	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6436131	6436236	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6436237	6436719	0.96	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6436237	6436719	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6436720	6436834	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6436835	6437842	1	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6436835	6437842	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6437843	6437934	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6437935	6438360	0.99	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6437935	6438360	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	intron	6438361	6438445	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	CDS	6438446	6438511	0.98	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	exon	6438446	6438511	.	+	.	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
Phchi.S5	AUGUSTUS	stop_codon	6438512	6438514	.	+	0	transcript_id "Phchi.S5G099100.t1"; gene_id "Phchi.S5G099100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2777.t1 is derived from g9697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8784683	8787509	.	+	.	Phchi.S5G138600
Phchi.S5	AUGUSTUS	transcript	8784683	8787509	.	+	.	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	start_codon	8784683	8784685	.	+	0	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	CDS	8784683	8784938	0.01	+	0	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	exon	8784683	8784938	.	+	.	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	intron	8784939	8787074	.	+	.	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	CDS	8787075	8787204	0.02	+	2	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	exon	8787075	8787204	.	+	.	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	intron	8787205	8787397	.	+	.	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	CDS	8787398	8787509	0.01	+	1	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	exon	8787398	8787509	.	+	.	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
Phchi.S5	AUGUSTUS	stop_codon	8787510	8787512	.	+	0	transcript_id "Phchi.S5G138600.t1"; gene_id "Phchi.S5G138600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14349.t1 is derived from g12816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12325095	12327352	.	-	.	Phchi.S3G166800
Phchi.S3	AUGUSTUS	transcript	12325095	12327352	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	stop_codon	12325092	12325094	.	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12325095	12325158	1	-	1	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12325095	12325158	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12325159	12325238	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12325239	12325321	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12325239	12325321	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12325322	12325439	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12325440	12325521	1	-	1	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12325440	12325521	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12325522	12325641	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12325642	12325706	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12325642	12325706	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12325707	12325793	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12325794	12325919	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12325794	12325919	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12325920	12326029	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12326030	12326130	0.99	-	2	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12326030	12326130	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12326131	12326223	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12326224	12326350	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12326224	12326350	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12326351	12326474	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12326475	12326588	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12326475	12326588	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12326589	12326684	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12326685	12326750	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12326685	12326750	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12326751	12326848	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12326849	12326951	1	-	1	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12326849	12326951	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12326952	12327026	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12327027	12327082	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12327027	12327082	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	intron	12327083	12327178	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	CDS	12327179	12327352	1	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	exon	12327179	12327352	.	-	.	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
Phchi.S3	AUGUSTUS	start_codon	12327350	12327352	.	-	0	transcript_id "Phchi.S3G166800.t1"; gene_id "Phchi.S3G166800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2487.t1 is derived from g9407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6917190	6918751	.	-	.	Phchi.S5G109600
Phchi.S5	AUGUSTUS	transcript	6917190	6918751	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	stop_codon	6917187	6917189	.	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6917190	6917303	1	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6917190	6917303	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	intron	6917304	6917432	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6917433	6917483	1	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6917433	6917483	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	intron	6917484	6917596	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6917597	6917767	1	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6917597	6917767	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	intron	6917768	6917859	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6917860	6917968	1	-	1	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6917860	6917968	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	intron	6917969	6918062	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6918063	6918169	1	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6918063	6918169	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	intron	6918170	6918314	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6918315	6918529	1	-	2	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6918315	6918529	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	intron	6918530	6918696	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	CDS	6918697	6918751	1	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	exon	6918697	6918751	.	-	.	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
Phchi.S5	AUGUSTUS	start_codon	6918749	6918751	.	-	0	transcript_id "Phchi.S5G109600.t1"; gene_id "Phchi.S5G109600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1391.t1 is derived from g15994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C226	AUGUSTUS	gene	851	1445	.	-	.	Phchi.C226G000100
Phchi.C226	AUGUSTUS	transcript	851	1445	.	-	.	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	stop_codon	848	850	.	-	0	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	CDS	851	968	0.51	-	1	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	exon	851	968	.	-	.	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	intron	969	1182	.	-	.	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	CDS	1183	1445	0.52	-	0	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	exon	1183	1445	.	-	.	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
Phchi.C226	AUGUSTUS	start_codon	1443	1445	.	-	0	transcript_id "Phchi.C226G000100.t1"; gene_id "Phchi.C226G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3410.t1 is derived from g579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3378620	3380022	.	-	.	Phchi.S1G056900
Phchi.S1	AUGUSTUS	transcript	3378620	3380022	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	stop_codon	3378617	3378619	.	-	0	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	CDS	3378620	3378726	0.38	-	2	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	exon	3378620	3378726	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	intron	3378727	3378834	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	CDS	3378835	3379007	0.96	-	1	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	exon	3378835	3379007	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	intron	3379008	3379139	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	CDS	3379140	3379270	1	-	0	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	exon	3379140	3379270	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	intron	3379271	3379406	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	CDS	3379407	3379481	0.83	-	0	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	exon	3379407	3379481	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	intron	3379482	3379600	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	CDS	3379601	3379634	0.82	-	1	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	exon	3379601	3379634	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	intron	3379635	3379816	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	CDS	3379817	3380022	0.49	-	0	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	exon	3379817	3380022	.	-	.	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
Phchi.S1	AUGUSTUS	start_codon	3380020	3380022	.	-	0	transcript_id "Phchi.S1G056900.t1"; gene_id "Phchi.S1G056900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6454.t1 is derived from g3626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23105053	23105748	.	+	.	Phchi.S1G361300
Phchi.S1	AUGUSTUS	transcript	23105053	23105748	.	+	.	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	start_codon	23105053	23105055	.	+	0	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	CDS	23105053	23105130	0.88	+	0	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	exon	23105053	23105130	.	+	.	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	intron	23105131	23105436	.	+	.	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	CDS	23105437	23105748	0.69	+	0	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	exon	23105437	23105748	.	+	.	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
Phchi.S1	AUGUSTUS	stop_codon	23105749	23105751	.	+	0	transcript_id "Phchi.S1G361300.t1"; gene_id "Phchi.S1G361300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4038.t1 is derived from g1207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7301552	7303702	.	-	.	Phchi.S1G119700
Phchi.S1	AUGUSTUS	transcript	7301552	7303702	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	stop_codon	7301549	7301551	.	-	0	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	CDS	7301552	7301602	1	-	0	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	exon	7301552	7301602	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	intron	7301603	7301778	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	CDS	7301779	7301862	1	-	0	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	exon	7301779	7301862	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	intron	7301863	7302131	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	CDS	7302132	7302181	0.93	-	2	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	exon	7302132	7302181	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	intron	7302182	7302390	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	CDS	7302391	7303247	0.89	-	1	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	exon	7302391	7303247	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	intron	7303248	7303448	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	CDS	7303449	7303702	0.66	-	0	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	exon	7303449	7303702	.	-	.	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
Phchi.S1	AUGUSTUS	start_codon	7303700	7303702	.	-	0	transcript_id "Phchi.S1G119700.t1"; gene_id "Phchi.S1G119700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13281.t1 is derived from g11746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5170067	5174236	.	-	.	Phchi.S3G060000
Phchi.S3	AUGUSTUS	transcript	5170067	5174236	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	stop_codon	5170064	5170066	.	-	0	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	CDS	5170067	5170464	0.93	-	2	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	exon	5170067	5170464	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	intron	5170465	5170568	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	CDS	5170569	5171307	0.93	-	0	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	exon	5170569	5171307	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	intron	5171308	5171390	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	CDS	5171391	5172742	1	-	2	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	exon	5171391	5172742	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	intron	5172743	5172858	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	CDS	5172859	5174236	1	-	0	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	exon	5172859	5174236	.	-	.	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
Phchi.S3	AUGUSTUS	start_codon	5174234	5174236	.	-	0	transcript_id "Phchi.S3G060000.t1"; gene_id "Phchi.S3G060000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10876.t1 is derived from g14926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2714386	2717781	.	-	.	Phchi.S4G045800
Phchi.S4	AUGUSTUS	transcript	2714386	2717781	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	stop_codon	2714383	2714385	.	-	0	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	CDS	2714386	2714885	1	-	2	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	exon	2714386	2714885	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	intron	2714886	2715002	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	CDS	2715003	2715887	0.56	-	2	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	exon	2715003	2715887	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	intron	2715888	2715993	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	CDS	2715994	2717396	0.53	-	1	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	exon	2715994	2717396	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	intron	2717397	2717522	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	CDS	2717523	2717585	0.56	-	1	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	exon	2717523	2717585	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	intron	2717586	2717752	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	CDS	2717753	2717781	0.29	-	0	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	exon	2717753	2717781	.	-	.	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
Phchi.S4	AUGUSTUS	start_codon	2717779	2717781	.	-	0	transcript_id "Phchi.S4G045800.t1"; gene_id "Phchi.S4G045800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8865.t1 is derived from g6040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38354346	38354813	.	-	.	Phchi.S1G602400
Phchi.S1	AUGUSTUS	transcript	38354346	38354813	.	-	.	transcript_id "Phchi.S1G602400.t1"; gene_id "Phchi.S1G602400"
Phchi.S1	AUGUSTUS	stop_codon	38354343	38354345	.	-	0	transcript_id "Phchi.S1G602400.t1"; gene_id "Phchi.S1G602400"
Phchi.S1	AUGUSTUS	CDS	38354346	38354813	0.54	-	0	transcript_id "Phchi.S1G602400.t1"; gene_id "Phchi.S1G602400"
Phchi.S1	AUGUSTUS	exon	38354346	38354813	.	-	.	transcript_id "Phchi.S1G602400.t1"; gene_id "Phchi.S1G602400"
Phchi.S1	AUGUSTUS	start_codon	38354811	38354813	.	-	0	transcript_id "Phchi.S1G602400.t1"; gene_id "Phchi.S1G602400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6396.t1 is derived from g3568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22760451	22761771	.	+	.	Phchi.S1G355500
Phchi.S1	AUGUSTUS	transcript	22760451	22761771	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	start_codon	22760451	22760453	.	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	CDS	22760451	22760453	0.99	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	exon	22760451	22760453	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	intron	22760454	22760650	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	CDS	22760651	22760749	1	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	exon	22760651	22760749	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	intron	22760750	22760928	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	CDS	22760929	22761132	1	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	exon	22760929	22761132	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	intron	22761133	22761261	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	CDS	22761262	22761321	1	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	exon	22761262	22761321	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	intron	22761322	22761447	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	CDS	22761448	22761574	0.95	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	exon	22761448	22761574	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	intron	22761575	22761676	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	CDS	22761677	22761771	0.99	+	2	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	exon	22761677	22761771	.	+	.	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
Phchi.S1	AUGUSTUS	stop_codon	22761772	22761774	.	+	0	transcript_id "Phchi.S1G355500.t1"; gene_id "Phchi.S1G355500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15372.t1 is derived from g13840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18675642	18675875	.	-	.	Phchi.S3G269100
Phchi.S3	AUGUSTUS	transcript	18675642	18675875	.	-	.	transcript_id "Phchi.S3G269100.t1"; gene_id "Phchi.S3G269100"
Phchi.S3	AUGUSTUS	stop_codon	18675639	18675641	.	-	0	transcript_id "Phchi.S3G269100.t1"; gene_id "Phchi.S3G269100"
Phchi.S3	AUGUSTUS	CDS	18675642	18675875	0.45	-	0	transcript_id "Phchi.S3G269100.t1"; gene_id "Phchi.S3G269100"
Phchi.S3	AUGUSTUS	exon	18675642	18675875	.	-	.	transcript_id "Phchi.S3G269100.t1"; gene_id "Phchi.S3G269100"
Phchi.S3	AUGUSTUS	start_codon	18675873	18675875	.	-	0	transcript_id "Phchi.S3G269100.t1"; gene_id "Phchi.S3G269100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2712.t1 is derived from g9632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8303186	8304094	.	+	.	Phchi.S5G132100
Phchi.S5	AUGUSTUS	transcript	8303186	8304094	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	start_codon	8303186	8303188	.	+	0	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	CDS	8303186	8303425	0.83	+	0	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	exon	8303186	8303425	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	intron	8303426	8303545	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	CDS	8303546	8303704	1	+	0	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	exon	8303546	8303704	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	intron	8303705	8303780	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	CDS	8303781	8303846	1	+	0	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	exon	8303781	8303846	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	intron	8303847	8303944	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	CDS	8303945	8304094	1	+	0	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	exon	8303945	8304094	.	+	.	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
Phchi.S5	AUGUSTUS	stop_codon	8304095	8304097	.	+	0	transcript_id "Phchi.S5G132100.t1"; gene_id "Phchi.S5G132100"
# This transcript jg8548.t2 is derived from g5723.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8549.t1 is derived from g5724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36578367	36579989	.	-	.	Phchi.S1G570800
Phchi.S1	AUGUSTUS	transcript	36578367	36579989	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	stop_codon	36578364	36578366	.	-	0	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	CDS	36578367	36578777	0.99	-	0	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	exon	36578367	36578777	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	intron	36578778	36578875	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	CDS	36578876	36579020	1	-	1	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	exon	36578876	36579020	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	intron	36579021	36579288	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	CDS	36579289	36579442	1	-	2	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	exon	36579289	36579442	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	intron	36579443	36579544	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	CDS	36579545	36579825	0.68	-	1	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	exon	36579545	36579825	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	intron	36579826	36579945	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	CDS	36579946	36579989	0.56	-	0	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	exon	36579946	36579989	.	-	.	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
Phchi.S1	AUGUSTUS	start_codon	36579987	36579989	.	-	0	transcript_id "Phchi.S1G570800.t1"; gene_id "Phchi.S1G570800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11795.t1 is derived from g15847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8194827	8197179	.	+	.	Phchi.S4G137700
Phchi.S4	AUGUSTUS	transcript	8194827	8197179	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	start_codon	8194827	8194829	.	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8194827	8194869	0.81	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8194827	8194869	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8194870	8195070	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8195071	8195076	1	+	2	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8195071	8195076	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8195077	8195549	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8195550	8195625	1	+	2	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8195550	8195625	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8195626	8195718	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8195719	8195901	1	+	1	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8195719	8195901	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8195902	8195985	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8195986	8196034	1	+	1	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8195986	8196034	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8196035	8196157	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8196158	8196274	1	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8196158	8196274	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8196275	8196361	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8196362	8196415	1	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8196362	8196415	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8196416	8196586	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8196587	8196672	1	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8196587	8196672	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8196673	8196782	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8196783	8196891	1	+	1	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8196783	8196891	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	intron	8196892	8197014	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	CDS	8197015	8197179	1	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	exon	8197015	8197179	.	+	.	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
Phchi.S4	AUGUSTUS	stop_codon	8197180	8197182	.	+	0	transcript_id "Phchi.S4G137700.t1"; gene_id "Phchi.S4G137700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5065.t1 is derived from g2235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14501848	14502309	.	-	.	Phchi.S1G222400
Phchi.S1	AUGUSTUS	transcript	14501848	14502309	.	-	.	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	stop_codon	14501845	14501847	.	-	0	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	CDS	14501848	14501852	0.95	-	2	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	exon	14501848	14501852	.	-	.	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	intron	14501853	14501950	.	-	.	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	CDS	14501951	14502113	0.95	-	0	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	exon	14501951	14502113	.	-	.	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	intron	14502114	14502204	.	-	.	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	CDS	14502205	14502309	1	-	0	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	exon	14502205	14502309	.	-	.	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
Phchi.S1	AUGUSTUS	start_codon	14502307	14502309	.	-	0	transcript_id "Phchi.S1G222400.t1"; gene_id "Phchi.S1G222400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10252.t1 is derived from g7428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46623601	46625343	.	-	.	Phchi.S1G741100
Phchi.S1	AUGUSTUS	transcript	46623601	46625343	.	-	.	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	stop_codon	46623598	46623600	.	-	0	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	CDS	46623601	46624187	1	-	2	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	exon	46623601	46624187	.	-	.	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	intron	46624188	46624279	.	-	.	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	CDS	46624280	46624395	1	-	1	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	exon	46624280	46624395	.	-	.	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	intron	46624396	46624531	.	-	.	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	CDS	46624532	46625343	0.82	-	0	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	exon	46624532	46625343	.	-	.	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
Phchi.S1	AUGUSTUS	start_codon	46625341	46625343	.	-	0	transcript_id "Phchi.S1G741100.t1"; gene_id "Phchi.S1G741100"
# This transcript jg12883.t2 is derived from g11348.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12883.t3 is derived from g11348.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12884.t1 is derived from g11349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2931385	2932227	.	-	.	Phchi.S3G020300
Phchi.S3	AUGUSTUS	transcript	2931385	2932227	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	stop_codon	2931382	2931384	.	-	0	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	CDS	2931385	2931560	0.94	-	2	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	exon	2931385	2931560	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	intron	2931561	2931715	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	CDS	2931716	2931846	0.72	-	1	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	exon	2931716	2931846	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	intron	2931847	2931966	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	CDS	2931967	2931974	0.47	-	0	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	exon	2931967	2931974	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	intron	2931975	2932143	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	CDS	2932144	2932227	0.62	-	0	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	exon	2932144	2932227	.	-	.	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
Phchi.S3	AUGUSTUS	start_codon	2932225	2932227	.	-	0	transcript_id "Phchi.S3G020300.t1"; gene_id "Phchi.S3G020300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1939.t1 is derived from g8859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3920821	3922122	.	+	.	Phchi.S5G054800
Phchi.S5	AUGUSTUS	transcript	3920821	3922122	.	+	.	transcript_id "Phchi.S5G054800.t1"; gene_id "Phchi.S5G054800"
Phchi.S5	AUGUSTUS	start_codon	3920821	3920823	.	+	0	transcript_id "Phchi.S5G054800.t1"; gene_id "Phchi.S5G054800"
Phchi.S5	AUGUSTUS	CDS	3920821	3922122	0.72	+	0	transcript_id "Phchi.S5G054800.t1"; gene_id "Phchi.S5G054800"
Phchi.S5	AUGUSTUS	exon	3920821	3922122	.	+	.	transcript_id "Phchi.S5G054800.t1"; gene_id "Phchi.S5G054800"
Phchi.S5	AUGUSTUS	stop_codon	3922123	3922125	.	+	0	transcript_id "Phchi.S5G054800.t1"; gene_id "Phchi.S5G054800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7830.t1 is derived from g5004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31399252	31402477	.	-	.	Phchi.S1G498900
Phchi.S1	AUGUSTUS	transcript	31399252	31402477	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	stop_codon	31399249	31399251	.	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31399252	31399272	0.8	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31399252	31399272	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31399273	31399375	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31399376	31399459	0.85	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31399376	31399459	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31399460	31399557	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31399558	31399833	1	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31399558	31399833	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31399834	31399975	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31399976	31400073	1	-	2	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31399976	31400073	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31400074	31400299	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31400300	31400405	1	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31400300	31400405	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31400406	31400689	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31400690	31400778	1	-	2	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31400690	31400778	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31400779	31400896	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31400897	31401019	1	-	2	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31400897	31401019	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31401020	31401201	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31401202	31401291	0.93	-	2	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31401202	31401291	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31401292	31401407	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31401408	31401556	0.85	-	1	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31401408	31401556	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31401557	31401694	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31401695	31401798	1	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31401695	31401798	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31401799	31401937	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31401938	31402033	1	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31401938	31402033	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	intron	31402034	31402342	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	CDS	31402343	31402477	1	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	exon	31402343	31402477	.	-	.	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
Phchi.S1	AUGUSTUS	start_codon	31402475	31402477	.	-	0	transcript_id "Phchi.S1G498900.t1"; gene_id "Phchi.S1G498900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9684.t1 is derived from g6860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43275551	43277941	.	-	.	Phchi.S1G684300
Phchi.S1	AUGUSTUS	transcript	43275551	43277941	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	stop_codon	43275548	43275550	.	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43275551	43275821	0.94	-	1	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43275551	43275821	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43275822	43275909	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43275910	43275971	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43275910	43275971	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43275972	43276077	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43276078	43276215	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43276078	43276215	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43276216	43276321	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43276322	43276459	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43276322	43276459	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43276460	43276570	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43276571	43276744	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43276571	43276744	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43276745	43276869	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43276870	43276959	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43276870	43276959	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43276960	43277039	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43277040	43277269	1	-	2	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43277040	43277269	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43277270	43277354	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43277355	43277505	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43277355	43277505	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43277506	43277600	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43277601	43277743	1	-	2	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43277601	43277743	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	intron	43277744	43277835	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	CDS	43277836	43277941	1	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	exon	43277836	43277941	.	-	.	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
Phchi.S1	AUGUSTUS	start_codon	43277939	43277941	.	-	0	transcript_id "Phchi.S1G684300.t1"; gene_id "Phchi.S1G684300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3646.t1 is derived from g815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4929929	4931611	.	+	.	Phchi.S1G080500
Phchi.S1	AUGUSTUS	transcript	4929929	4931611	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	start_codon	4929929	4929931	.	+	0	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	CDS	4929929	4930007	0.25	+	0	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	exon	4929929	4930007	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	intron	4930008	4930089	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	CDS	4930090	4930163	0.53	+	2	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	exon	4930090	4930163	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	intron	4930164	4930245	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	CDS	4930246	4930367	0.52	+	0	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	exon	4930246	4930367	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	intron	4930368	4930473	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	CDS	4930474	4931611	0.59	+	1	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	exon	4930474	4931611	.	+	.	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
Phchi.S1	AUGUSTUS	stop_codon	4931612	4931614	.	+	0	transcript_id "Phchi.S1G080500.t1"; gene_id "Phchi.S1G080500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4641.t1 is derived from g1811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11575508	11577582	.	+	.	Phchi.S1G180000
Phchi.S1	AUGUSTUS	transcript	11575508	11577582	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	start_codon	11575508	11575510	.	+	0	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	CDS	11575508	11576027	0.82	+	0	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	exon	11575508	11576027	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	intron	11576028	11576361	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	CDS	11576362	11576636	0.96	+	2	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	exon	11576362	11576636	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	intron	11576637	11576809	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	CDS	11576810	11577218	0.89	+	0	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	exon	11576810	11577218	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	intron	11577219	11577307	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	CDS	11577308	11577582	1	+	2	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	exon	11577308	11577582	.	+	.	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
Phchi.S1	AUGUSTUS	stop_codon	11577583	11577585	.	+	0	transcript_id "Phchi.S1G180000.t1"; gene_id "Phchi.S1G180000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3497.t1 is derived from g666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4090437	4091129	.	+	.	Phchi.S1G065600
Phchi.S1	AUGUSTUS	transcript	4090437	4091129	.	+	.	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	start_codon	4090437	4090439	.	+	0	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	CDS	4090437	4090620	0.7	+	0	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	exon	4090437	4090620	.	+	.	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	intron	4090621	4090710	.	+	.	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	CDS	4090711	4091129	0.93	+	2	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	exon	4090711	4091129	.	+	.	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
Phchi.S1	AUGUSTUS	stop_codon	4091130	4091132	.	+	0	transcript_id "Phchi.S1G065600.t1"; gene_id "Phchi.S1G065600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2022.t1 is derived from g8942.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4480192	4485268	.	-	.	Phchi.S5G063100
Phchi.S5	AUGUSTUS	transcript	4480192	4485268	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	stop_codon	4480189	4480191	.	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4480192	4481460	0.82	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4480192	4481460	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	intron	4481461	4481534	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4481535	4482446	0.86	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4481535	4482446	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	intron	4482447	4482627	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4482628	4482693	1	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4482628	4482693	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	intron	4482694	4482774	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4482775	4482895	1	-	1	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4482775	4482895	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	intron	4482896	4482991	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4482992	4484769	0.59	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4482992	4484769	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	intron	4484770	4484976	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4484977	4485060	0.17	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4484977	4485060	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	intron	4485061	4485226	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	CDS	4485227	4485268	1	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	exon	4485227	4485268	.	-	.	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
Phchi.S5	AUGUSTUS	start_codon	4485266	4485268	.	-	0	transcript_id "Phchi.S5G063100.t1"; gene_id "Phchi.S5G063100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6296.t1 is derived from g3468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22151264	22152609	.	+	.	Phchi.S1G345500
Phchi.S1	AUGUSTUS	transcript	22151264	22152609	.	+	.	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	start_codon	22151264	22151266	.	+	0	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	CDS	22151264	22151458	0.51	+	0	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	exon	22151264	22151458	.	+	.	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	intron	22151459	22151568	.	+	.	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	CDS	22151569	22152609	0.76	+	0	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	exon	22151569	22152609	.	+	.	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
Phchi.S1	AUGUSTUS	stop_codon	22152610	22152612	.	+	0	transcript_id "Phchi.S1G345500.t1"; gene_id "Phchi.S1G345500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15007.t1 is derived from g13475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16339013	16339831	.	+	.	Phchi.S3G232600
Phchi.S3	AUGUSTUS	transcript	16339013	16339831	.	+	.	transcript_id "Phchi.S3G232600.t1"; gene_id "Phchi.S3G232600"
Phchi.S3	AUGUSTUS	start_codon	16339013	16339015	.	+	0	transcript_id "Phchi.S3G232600.t1"; gene_id "Phchi.S3G232600"
Phchi.S3	AUGUSTUS	CDS	16339013	16339831	1	+	0	transcript_id "Phchi.S3G232600.t1"; gene_id "Phchi.S3G232600"
Phchi.S3	AUGUSTUS	exon	16339013	16339831	.	+	.	transcript_id "Phchi.S3G232600.t1"; gene_id "Phchi.S3G232600"
Phchi.S3	AUGUSTUS	stop_codon	16339832	16339834	.	+	0	transcript_id "Phchi.S3G232600.t1"; gene_id "Phchi.S3G232600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7323.t1 is derived from g4495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28518424	28522414	.	-	.	Phchi.S1G448200
Phchi.S1	AUGUSTUS	transcript	28518424	28522414	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	stop_codon	28518421	28518423	.	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28518424	28518654	0.9	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28518424	28518654	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28518655	28518742	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28518743	28518799	1	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28518743	28518799	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28518800	28518939	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28518940	28519071	1	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28518940	28519071	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28519072	28519250	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28519251	28519329	1	-	1	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28519251	28519329	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28519330	28519437	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28519438	28519523	0.98	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28519438	28519523	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28519524	28519601	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28519602	28519760	1	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28519602	28519760	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28519761	28519882	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28519883	28520290	0.99	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28519883	28520290	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28520291	28520426	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28520427	28520599	1	-	2	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28520427	28520599	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28520600	28520717	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28520718	28522019	0.61	-	2	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28520718	28522019	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28522020	28522236	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28522237	28522270	0.61	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28522237	28522270	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	intron	28522271	28522345	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	CDS	28522346	28522414	0.87	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	exon	28522346	28522414	.	-	.	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
Phchi.S1	AUGUSTUS	start_codon	28522412	28522414	.	-	0	transcript_id "Phchi.S1G448200.t1"; gene_id "Phchi.S1G448200"
# This transcript jg7658.t2 is derived from g4832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7659.t1 is derived from g4833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30457637	30458130	.	+	.	Phchi.S1G481800
Phchi.S1	AUGUSTUS	transcript	30457637	30458130	.	+	.	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	start_codon	30457637	30457639	.	+	0	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	CDS	30457637	30457703	0.74	+	0	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	exon	30457637	30457703	.	+	.	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	intron	30457704	30457999	.	+	.	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	CDS	30458000	30458130	0.94	+	2	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	exon	30458000	30458130	.	+	.	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
Phchi.S1	AUGUSTUS	stop_codon	30458131	30458133	.	+	0	transcript_id "Phchi.S1G481800.t1"; gene_id "Phchi.S1G481800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8171.t1 is derived from g5346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34265790	34269700	.	+	.	Phchi.S1G533000
Phchi.S1	AUGUSTUS	transcript	34265790	34269700	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	start_codon	34265790	34265792	.	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34265790	34266068	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34265790	34266068	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34266069	34266185	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34266186	34266266	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34266186	34266266	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34266267	34266469	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34266470	34266695	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34266470	34266695	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34266696	34266813	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34266814	34266945	1	+	2	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34266814	34266945	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34266946	34267163	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34267164	34267266	1	+	2	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34267164	34267266	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34267267	34267348	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34267349	34267454	1	+	1	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34267349	34267454	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34267455	34267561	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34267562	34267648	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34267562	34267648	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34267649	34267734	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34267735	34267914	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34267735	34267914	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34267915	34268053	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34268054	34268151	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34268054	34268151	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34268152	34268242	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34268243	34268390	0.99	+	1	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34268243	34268390	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34268391	34268491	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34268492	34268653	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34268492	34268653	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34268654	34268724	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34268725	34268853	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34268725	34268853	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34268854	34268971	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34268972	34269094	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34268972	34269094	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34269095	34269193	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34269194	34269382	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34269194	34269382	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34269383	34269460	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34269461	34269550	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34269461	34269550	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	intron	34269551	34269649	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	CDS	34269650	34269700	1	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	exon	34269650	34269700	.	+	.	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
Phchi.S1	AUGUSTUS	stop_codon	34269701	34269703	.	+	0	transcript_id "Phchi.S1G533000.t1"; gene_id "Phchi.S1G533000"
# This transcript jg6757.t2 is derived from g3929.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6758.t1 is derived from g3930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24908840	24909558	.	+	.	Phchi.S1G391700
Phchi.S1	AUGUSTUS	transcript	24908840	24909558	.	+	.	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	start_codon	24908840	24908842	.	+	0	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	CDS	24908840	24909054	0.91	+	0	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	exon	24908840	24909054	.	+	.	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	intron	24909055	24909134	.	+	.	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	CDS	24909135	24909558	1	+	1	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	exon	24909135	24909558	.	+	.	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
Phchi.S1	AUGUSTUS	stop_codon	24909559	24909561	.	+	0	transcript_id "Phchi.S1G391700.t1"; gene_id "Phchi.S1G391700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1770.t1 is derived from g8690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2940599	2943625	.	-	.	Phchi.S5G037900
Phchi.S5	AUGUSTUS	transcript	2940599	2943625	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	stop_codon	2940596	2940598	.	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2940599	2940877	0.98	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2940599	2940877	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2940878	2940975	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2940976	2941152	1	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2940976	2941152	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2941153	2941238	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2941239	2941357	1	-	2	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2941239	2941357	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2941358	2941445	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2941446	2941644	1	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2941446	2941644	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2941645	2941752	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2941753	2941809	1	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2941753	2941809	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2941810	2941904	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2941905	2942161	0.58	-	2	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2941905	2942161	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2942162	2942250	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2942251	2943267	0.55	-	2	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2942251	2943267	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	intron	2943268	2943459	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	CDS	2943460	2943625	0.95	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	exon	2943460	2943625	.	-	.	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
Phchi.S5	AUGUSTUS	start_codon	2943623	2943625	.	-	0	transcript_id "Phchi.S5G037900.t1"; gene_id "Phchi.S5G037900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4381.t1 is derived from g1550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10169261	10170035	.	+	.	Phchi.S1G154000
Phchi.S1	AUGUSTUS	transcript	10169261	10170035	.	+	.	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	start_codon	10169261	10169263	.	+	0	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	CDS	10169261	10169740	0.6	+	0	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	exon	10169261	10169740	.	+	.	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	intron	10169741	10169858	.	+	.	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	CDS	10169859	10170035	0.84	+	0	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	exon	10169859	10170035	.	+	.	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
Phchi.S1	AUGUSTUS	stop_codon	10170036	10170038	.	+	0	transcript_id "Phchi.S1G154000.t1"; gene_id "Phchi.S1G154000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15168.t1 is derived from g13636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17347383	17347837	.	-	.	Phchi.S3G248700
Phchi.S3	AUGUSTUS	transcript	17347383	17347837	.	-	.	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	stop_codon	17347380	17347382	.	-	0	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	CDS	17347383	17347421	0.7	-	0	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	exon	17347383	17347421	.	-	.	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	intron	17347422	17347615	.	-	.	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	CDS	17347616	17347837	0.43	-	0	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	exon	17347616	17347837	.	-	.	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
Phchi.S3	AUGUSTUS	start_codon	17347835	17347837	.	-	0	transcript_id "Phchi.S3G248700.t1"; gene_id "Phchi.S3G248700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4091.t1 is derived from g1260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7755496	7757185	.	-	.	Phchi.S1G125000
Phchi.S1	AUGUSTUS	transcript	7755496	7757185	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	stop_codon	7755493	7755495	.	-	0	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	CDS	7755496	7755551	1	-	2	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	exon	7755496	7755551	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	intron	7755552	7755635	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	CDS	7755636	7755837	1	-	0	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	exon	7755636	7755837	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	intron	7755838	7755911	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	CDS	7755912	7756059	1	-	1	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	exon	7755912	7756059	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	intron	7756060	7756168	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	CDS	7756169	7756349	1	-	2	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	exon	7756169	7756349	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	intron	7756350	7756466	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	CDS	7756467	7756725	1	-	0	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	exon	7756467	7756725	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	intron	7756726	7756936	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	CDS	7756937	7757185	1	-	0	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	exon	7756937	7757185	.	-	.	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
Phchi.S1	AUGUSTUS	start_codon	7757183	7757185	.	-	0	transcript_id "Phchi.S1G125000.t1"; gene_id "Phchi.S1G125000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1781.t1 is derived from g8701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2979272	2984766	.	+	.	Phchi.S5G039000
Phchi.S5	AUGUSTUS	transcript	2979272	2984766	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	start_codon	2979272	2979274	.	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2979272	2979901	0.87	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2979272	2979901	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2979902	2980034	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2980035	2980222	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2980035	2980222	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2980223	2980324	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2980325	2980530	1	+	1	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2980325	2980530	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2980531	2980699	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2980700	2981016	0.63	+	2	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2980700	2981016	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2981017	2981107	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2981108	2981185	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2981108	2981185	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2981186	2981381	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2981382	2981609	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2981382	2981609	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2981610	2981805	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2981806	2981946	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2981806	2981946	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2981947	2982065	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2982066	2982236	0.96	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2982066	2982236	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2982237	2982376	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2982377	2982489	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2982377	2982489	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2982490	2982647	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2982648	2982864	1	+	1	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2982648	2982864	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2982865	2983001	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2983002	2983073	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2983002	2983073	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2983074	2983160	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2983161	2983280	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2983161	2983280	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2983281	2983405	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2983406	2983522	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2983406	2983522	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2983523	2983632	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2983633	2983809	0.98	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2983633	2983809	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2983810	2983920	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2983921	2984040	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2983921	2984040	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2984041	2984136	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2984137	2984211	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2984137	2984211	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2984212	2984307	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2984308	2984415	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2984308	2984415	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2984416	2984514	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2984515	2984598	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2984515	2984598	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	intron	2984599	2984688	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	CDS	2984689	2984766	1	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	exon	2984689	2984766	.	+	.	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
Phchi.S5	AUGUSTUS	stop_codon	2984767	2984769	.	+	0	transcript_id "Phchi.S5G039000.t1"; gene_id "Phchi.S5G039000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5036.t1 is derived from g2206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14195536	14197275	.	+	.	Phchi.S1G219500
Phchi.S1	AUGUSTUS	transcript	14195536	14197275	.	+	.	transcript_id "Phchi.S1G219500.t1"; gene_id "Phchi.S1G219500"
Phchi.S1	AUGUSTUS	start_codon	14195536	14195538	.	+	0	transcript_id "Phchi.S1G219500.t1"; gene_id "Phchi.S1G219500"
Phchi.S1	AUGUSTUS	CDS	14195536	14197275	0.17	+	0	transcript_id "Phchi.S1G219500.t1"; gene_id "Phchi.S1G219500"
Phchi.S1	AUGUSTUS	exon	14195536	14197275	.	+	.	transcript_id "Phchi.S1G219500.t1"; gene_id "Phchi.S1G219500"
Phchi.S1	AUGUSTUS	stop_codon	14197276	14197278	.	+	0	transcript_id "Phchi.S1G219500.t1"; gene_id "Phchi.S1G219500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13486.t1 is derived from g11953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7127240	7129984	.	+	.	Phchi.S3G080500
Phchi.S3	AUGUSTUS	transcript	7127240	7129984	.	+	.	transcript_id "Phchi.S3G080500.t1"; gene_id "Phchi.S3G080500"
Phchi.S3	AUGUSTUS	start_codon	7127240	7127242	.	+	0	transcript_id "Phchi.S3G080500.t1"; gene_id "Phchi.S3G080500"
Phchi.S3	AUGUSTUS	CDS	7127240	7129984	0.99	+	0	transcript_id "Phchi.S3G080500.t1"; gene_id "Phchi.S3G080500"
Phchi.S3	AUGUSTUS	exon	7127240	7129984	.	+	.	transcript_id "Phchi.S3G080500.t1"; gene_id "Phchi.S3G080500"
Phchi.S3	AUGUSTUS	stop_codon	7129985	7129987	.	+	0	transcript_id "Phchi.S3G080500.t1"; gene_id "Phchi.S3G080500"
# This transcript jg5616.t2 is derived from g2786.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5617.t1 is derived from g2787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17913345	17913893	.	+	.	Phchi.S1G277600
Phchi.S1	AUGUSTUS	transcript	17913345	17913893	.	+	.	transcript_id "Phchi.S1G277600.t1"; gene_id "Phchi.S1G277600"
Phchi.S1	AUGUSTUS	start_codon	17913345	17913347	.	+	0	transcript_id "Phchi.S1G277600.t1"; gene_id "Phchi.S1G277600"
Phchi.S1	AUGUSTUS	CDS	17913345	17913893	0.94	+	0	transcript_id "Phchi.S1G277600.t1"; gene_id "Phchi.S1G277600"
Phchi.S1	AUGUSTUS	exon	17913345	17913893	.	+	.	transcript_id "Phchi.S1G277600.t1"; gene_id "Phchi.S1G277600"
Phchi.S1	AUGUSTUS	stop_codon	17913894	17913896	.	+	0	transcript_id "Phchi.S1G277600.t1"; gene_id "Phchi.S1G277600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2738.t1 is derived from g9658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8504967	8505635	.	+	.	Phchi.S5G134700
Phchi.S5	AUGUSTUS	transcript	8504967	8505635	.	+	.	transcript_id "Phchi.S5G134700.t1"; gene_id "Phchi.S5G134700"
Phchi.S5	AUGUSTUS	start_codon	8504967	8504969	.	+	0	transcript_id "Phchi.S5G134700.t1"; gene_id "Phchi.S5G134700"
Phchi.S5	AUGUSTUS	CDS	8504967	8505635	0.99	+	0	transcript_id "Phchi.S5G134700.t1"; gene_id "Phchi.S5G134700"
Phchi.S5	AUGUSTUS	exon	8504967	8505635	.	+	.	transcript_id "Phchi.S5G134700.t1"; gene_id "Phchi.S5G134700"
Phchi.S5	AUGUSTUS	stop_codon	8505636	8505638	.	+	0	transcript_id "Phchi.S5G134700.t1"; gene_id "Phchi.S5G134700"
# This transcript jg4493.t2 is derived from g1663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4494.t1 is derived from g1664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10803668	10807564	.	-	.	Phchi.S1G165300
Phchi.S1	AUGUSTUS	transcript	10803668	10807564	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	stop_codon	10803665	10803667	.	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10803668	10803836	0.9	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10803668	10803836	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10803837	10803935	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10803936	10804039	1	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10803936	10804039	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10804040	10804129	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10804130	10804278	1	-	2	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10804130	10804278	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10804279	10804378	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10804379	10804465	1	-	2	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10804379	10804465	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10804466	10804554	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10804555	10804593	1	-	2	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10804555	10804593	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10804594	10804764	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10804765	10804809	1	-	2	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10804765	10804809	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10804810	10804914	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10804915	10805036	1	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10804915	10805036	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10805037	10805126	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10805127	10805180	1	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10805127	10805180	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10805181	10805290	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10805291	10805365	1	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10805291	10805365	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10805366	10805452	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10805453	10805478	1	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10805453	10805478	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10805479	10805572	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10805573	10805618	1	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10805573	10805618	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10805619	10805743	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10805744	10805883	1	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10805744	10805883	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10805884	10805982	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10805983	10806033	1	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10805983	10806033	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10806034	10806173	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10806174	10806239	1	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10806174	10806239	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10806240	10806354	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10806355	10806424	1	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10806355	10806424	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10806425	10806559	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10806560	10806600	0.59	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10806560	10806600	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10806601	10806701	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10806702	10806771	1	-	1	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10806702	10806771	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	intron	10806772	10807538	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	CDS	10807539	10807564	1	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	exon	10807539	10807564	.	-	.	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
Phchi.S1	AUGUSTUS	start_codon	10807562	10807564	.	-	0	transcript_id "Phchi.S1G165300.t1"; gene_id "Phchi.S1G165300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12526.t1 is derived from g8203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32985442	32987289	.	-	.	Phchi.S2G060600
Phchi.S2	AUGUSTUS	transcript	32985442	32987289	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	stop_codon	32985439	32985441	.	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32985442	32985567	1	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32985442	32985567	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32985568	32985640	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32985641	32985677	1	-	1	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32985641	32985677	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32985678	32985765	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32985766	32985818	1	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32985766	32985818	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32985819	32985897	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32985898	32985976	1	-	1	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32985898	32985976	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32985977	32986052	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32986053	32986125	1	-	2	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32986053	32986125	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32986126	32986216	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32986217	32986319	1	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32986217	32986319	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32986320	32986400	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32986401	32986585	1	-	2	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32986401	32986585	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32986586	32986678	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32986679	32986847	1	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32986679	32986847	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32986848	32987022	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32987023	32987064	1	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32987023	32987064	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	intron	32987065	32987151	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	CDS	32987152	32987289	0.59	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	exon	32987152	32987289	.	-	.	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
Phchi.S2	AUGUSTUS	start_codon	32987287	32987289	.	-	0	transcript_id "Phchi.S2G060600.t1"; gene_id "Phchi.S2G060600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4480.t1 is derived from g1650.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10710531	10713235	.	-	.	Phchi.S1G163900
Phchi.S1	AUGUSTUS	transcript	10710531	10713235	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	stop_codon	10710528	10710530	.	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10710531	10710587	0.41	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10710531	10710587	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10710588	10710700	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10710701	10710788	0.51	-	1	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10710701	10710788	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10710789	10710889	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10710890	10710946	0.82	-	1	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10710890	10710946	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10710947	10711028	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711029	10711107	1	-	2	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711029	10711107	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711108	10711205	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711206	10711339	1	-	1	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711206	10711339	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711340	10711474	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711475	10711591	1	-	1	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711475	10711591	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711592	10711691	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711692	10711780	1	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711692	10711780	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711781	10711875	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711876	10711929	0.94	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711876	10711929	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711930	10712032	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712033	10712104	0.94	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712033	10712104	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712105	10712250	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712251	10712323	1	-	1	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712251	10712323	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712324	10712400	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712401	10712408	1	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712401	10712408	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712409	10712503	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712504	10712572	0.78	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712504	10712572	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712573	10712691	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712692	10712829	0.99	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712692	10712829	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712830	10712965	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712966	10713000	1	-	2	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712966	10713000	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10713001	10713093	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10713094	10713235	0.91	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10713094	10713235	.	-	.	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	start_codon	10713233	10713235	.	-	0	transcript_id "Phchi.S1G163900.t1"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	transcript	10710531	10713235	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	stop_codon	10710528	10710530	.	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10710531	10710587	0.43	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10710531	10710587	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10710588	10710700	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10710701	10710788	0.51	-	1	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10710701	10710788	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10710789	10710889	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10710890	10710946	0.77	-	1	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10710890	10710946	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10710947	10711028	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711029	10711107	1	-	2	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711029	10711107	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711108	10711205	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711206	10711339	1	-	1	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711206	10711339	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711340	10711474	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711475	10711591	1	-	1	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711475	10711591	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711592	10711691	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711692	10711780	1	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711692	10711780	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711781	10711875	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10711876	10711929	0.95	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10711876	10711929	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10711930	10712032	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712033	10712099	0.95	-	1	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712033	10712099	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712100	10712250	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712251	10712408	1	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712251	10712408	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712409	10712503	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712504	10712572	0.77	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712504	10712572	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712573	10712691	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712692	10712829	0.99	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712692	10712829	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10712830	10712965	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10712966	10713000	1	-	2	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10712966	10713000	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	intron	10713001	10713093	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	CDS	10713094	10713235	0.92	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	exon	10713094	10713235	.	-	.	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
Phchi.S1	AUGUSTUS	start_codon	10713233	10713235	.	-	0	transcript_id "Phchi.S1G163900.t2"; gene_id "Phchi.S1G163900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5528.t1 is derived from g2698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17422785	17423987	.	-	.	Phchi.S1G268700
Phchi.S1	AUGUSTUS	transcript	17422785	17423987	.	-	.	transcript_id "Phchi.S1G268700.t1"; gene_id "Phchi.S1G268700"
Phchi.S1	AUGUSTUS	stop_codon	17422782	17422784	.	-	0	transcript_id "Phchi.S1G268700.t1"; gene_id "Phchi.S1G268700"
Phchi.S1	AUGUSTUS	CDS	17422785	17423987	0.71	-	0	transcript_id "Phchi.S1G268700.t1"; gene_id "Phchi.S1G268700"
Phchi.S1	AUGUSTUS	exon	17422785	17423987	.	-	.	transcript_id "Phchi.S1G268700.t1"; gene_id "Phchi.S1G268700"
Phchi.S1	AUGUSTUS	start_codon	17423985	17423987	.	-	0	transcript_id "Phchi.S1G268700.t1"; gene_id "Phchi.S1G268700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8559.t1 is derived from g5734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36619693	36620959	.	-	.	Phchi.S1G571800
Phchi.S1	AUGUSTUS	transcript	36619693	36620959	.	-	.	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	stop_codon	36619690	36619692	.	-	0	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	CDS	36619693	36620843	0.86	-	2	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	exon	36619693	36620843	.	-	.	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	intron	36620844	36620928	.	-	.	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	CDS	36620929	36620959	0.91	-	0	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	exon	36620929	36620959	.	-	.	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
Phchi.S1	AUGUSTUS	start_codon	36620957	36620959	.	-	0	transcript_id "Phchi.S1G571800.t1"; gene_id "Phchi.S1G571800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg698.t1 is derived from g10480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4966714	4967711	.	-	.	Phchi.S6G065700
Phchi.S6	AUGUSTUS	transcript	4966714	4967711	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	stop_codon	4966711	4966713	.	-	0	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	CDS	4966714	4966836	1	-	0	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	exon	4966714	4966836	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	intron	4966837	4966929	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	CDS	4966930	4967036	0.82	-	2	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	exon	4966930	4967036	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	intron	4967037	4967130	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	CDS	4967131	4967225	0.6	-	1	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	exon	4967131	4967225	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	intron	4967226	4967447	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	CDS	4967448	4967602	0.59	-	0	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	exon	4967448	4967602	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	intron	4967603	4967699	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	CDS	4967700	4967711	0.59	-	0	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	exon	4967700	4967711	.	-	.	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
Phchi.S6	AUGUSTUS	start_codon	4967709	4967711	.	-	0	transcript_id "Phchi.S6G065700.t1"; gene_id "Phchi.S6G065700"
# This transcript jg357.t2 is derived from g10138.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg358.t1 is derived from g10140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2624121	2626379	.	+	.	Phchi.S6G031700
Phchi.S6	AUGUSTUS	transcript	2624121	2626379	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	start_codon	2624121	2624123	.	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2624121	2624332	1	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2624121	2624332	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2624333	2624418	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2624419	2624737	1	+	1	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2624419	2624737	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2624738	2624810	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2624811	2624966	1	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2624811	2624966	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2624967	2625117	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2625118	2625372	1	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2625118	2625372	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2625373	2625476	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2625477	2625566	1	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2625477	2625566	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2625567	2625675	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2625676	2625754	1	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2625676	2625754	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2625755	2625846	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2625847	2625953	1	+	2	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2625847	2625953	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2625954	2626057	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2626058	2626176	1	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2626058	2626176	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	intron	2626177	2626270	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	CDS	2626271	2626379	0.99	+	1	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	exon	2626271	2626379	.	+	.	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
Phchi.S6	AUGUSTUS	stop_codon	2626380	2626382	.	+	0	transcript_id "Phchi.S6G031700.t1"; gene_id "Phchi.S6G031700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11959.t1 is derived from g7634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	199239	201328	.	+	.	Phchi.S2G003900
Phchi.S2	AUGUSTUS	transcript	199239	201328	.	+	.	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	start_codon	199239	199241	.	+	0	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	CDS	199239	200200	0.87	+	0	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	exon	199239	200200	.	+	.	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	intron	200201	200345	.	+	.	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	CDS	200346	200780	0.93	+	1	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	exon	200346	200780	.	+	.	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	intron	200781	200859	.	+	.	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	CDS	200860	201328	0.9	+	1	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	exon	200860	201328	.	+	.	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	stop_codon	201329	201331	.	+	0	transcript_id "Phchi.S2G003900.t1"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	transcript	199659	201328	.	+	.	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	start_codon	199659	199661	.	+	0	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	CDS	199659	200200	0.72	+	0	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	exon	199659	200200	.	+	.	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	intron	200201	200345	.	+	.	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	CDS	200346	200780	0.88	+	1	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	exon	200346	200780	.	+	.	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	intron	200781	200859	.	+	.	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	CDS	200860	201328	0.96	+	1	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	exon	200860	201328	.	+	.	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
Phchi.S2	AUGUSTUS	stop_codon	201329	201331	.	+	0	transcript_id "Phchi.S2G003900.t2"; gene_id "Phchi.S2G003900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3131.t1 is derived from g300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1880070	1882406	.	-	.	Phchi.S1G029000
Phchi.S1	AUGUSTUS	transcript	1880070	1882406	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	stop_codon	1880067	1880069	.	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	CDS	1880070	1880387	0.98	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	exon	1880070	1880387	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	intron	1880388	1880458	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	CDS	1880459	1880557	0.94	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	exon	1880459	1880557	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	intron	1880558	1880672	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	CDS	1880673	1881011	1	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	exon	1880673	1881011	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	intron	1881012	1881144	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	CDS	1881145	1881309	1	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	exon	1881145	1881309	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	intron	1881310	1881400	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	CDS	1881401	1881621	1	-	2	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	exon	1881401	1881621	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	intron	1881622	1881745	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	CDS	1881746	1882406	0.99	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	exon	1881746	1882406	.	-	.	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
Phchi.S1	AUGUSTUS	start_codon	1882404	1882406	.	-	0	transcript_id "Phchi.S1G029000.t1"; gene_id "Phchi.S1G029000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2595.t1 is derived from g9515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7608233	7608721	.	+	.	Phchi.S5G120400
Phchi.S5	AUGUSTUS	transcript	7608233	7608721	.	+	.	transcript_id "Phchi.S5G120400.t1"; gene_id "Phchi.S5G120400"
Phchi.S5	AUGUSTUS	start_codon	7608233	7608235	.	+	0	transcript_id "Phchi.S5G120400.t1"; gene_id "Phchi.S5G120400"
Phchi.S5	AUGUSTUS	CDS	7608233	7608721	0.75	+	0	transcript_id "Phchi.S5G120400.t1"; gene_id "Phchi.S5G120400"
Phchi.S5	AUGUSTUS	exon	7608233	7608721	.	+	.	transcript_id "Phchi.S5G120400.t1"; gene_id "Phchi.S5G120400"
Phchi.S5	AUGUSTUS	stop_codon	7608722	7608724	.	+	0	transcript_id "Phchi.S5G120400.t1"; gene_id "Phchi.S5G120400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10484.t1 is derived from g14533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	649021	649699	.	-	.	Phchi.S4G006600
Phchi.S4	AUGUSTUS	transcript	649021	649699	.	-	.	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	stop_codon	649018	649020	.	-	0	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	CDS	649021	649088	0.51	-	2	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	exon	649021	649088	.	-	.	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	intron	649089	649215	.	-	.	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	CDS	649216	649699	0.44	-	0	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	exon	649216	649699	.	-	.	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
Phchi.S4	AUGUSTUS	start_codon	649697	649699	.	-	0	transcript_id "Phchi.S4G006600.t1"; gene_id "Phchi.S4G006600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4452.t1 is derived from g1622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10572045	10574988	.	-	.	Phchi.S1G161100
Phchi.S1	AUGUSTUS	transcript	10572045	10574988	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	stop_codon	10572042	10572044	.	-	0	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10572045	10572204	1	-	1	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10572045	10572204	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10572205	10572300	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10572301	10572360	1	-	1	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10572301	10572360	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10572361	10572455	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10572456	10572596	1	-	1	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10572456	10572596	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10572597	10572715	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10572716	10573018	0.52	-	1	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10572716	10573018	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10573019	10573147	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10573148	10573252	1	-	1	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10573148	10573252	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10573253	10573342	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10573343	10573410	0.94	-	0	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10573343	10573410	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10573411	10573515	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10573516	10573570	0.94	-	1	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10573516	10573570	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10573571	10573666	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10573667	10573823	0.76	-	2	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10573667	10573823	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10573824	10573941	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10573942	10574674	0.98	-	0	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10573942	10574674	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	intron	10574675	10574766	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	CDS	10574767	10574988	0.56	-	0	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	exon	10574767	10574988	.	-	.	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
Phchi.S1	AUGUSTUS	start_codon	10574986	10574988	.	-	0	transcript_id "Phchi.S1G161100.t1"; gene_id "Phchi.S1G161100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11338.t1 is derived from g15388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5633547	5634468	.	+	.	Phchi.S4G092000
Phchi.S4	AUGUSTUS	transcript	5633547	5634468	.	+	.	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	start_codon	5633547	5633549	.	+	0	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	CDS	5633547	5633602	0.03	+	0	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	exon	5633547	5633602	.	+	.	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	intron	5633603	5633966	.	+	.	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	CDS	5633967	5634468	0.01	+	1	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	exon	5633967	5634468	.	+	.	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
Phchi.S4	AUGUSTUS	stop_codon	5634469	5634471	.	+	0	transcript_id "Phchi.S4G092000.t1"; gene_id "Phchi.S4G092000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1210.t1 is derived from g10993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8427040	8429268	.	-	.	Phchi.S6G116900
Phchi.S6	AUGUSTUS	transcript	8427040	8429268	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	stop_codon	8427037	8427039	.	-	0	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8427040	8427127	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8427040	8427127	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8427128	8427243	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8427244	8427315	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8427244	8427315	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8427316	8427390	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8427391	8427462	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8427391	8427462	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8427463	8427559	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8427560	8427631	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8427560	8427631	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8427632	8427709	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8427710	8427790	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8427710	8427790	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8427791	8427980	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8427981	8428124	0.99	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8427981	8428124	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8428125	8428228	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8428229	8428300	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8428229	8428300	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8428301	8428384	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8428385	8428456	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8428385	8428456	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8428457	8428576	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8428577	8428648	1	-	1	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8428577	8428648	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8428649	8428724	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8428725	8428878	1	-	2	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8428725	8428878	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	intron	8428879	8429171	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	CDS	8429172	8429268	1	-	0	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	exon	8429172	8429268	.	-	.	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
Phchi.S6	AUGUSTUS	start_codon	8429266	8429268	.	-	0	transcript_id "Phchi.S6G116900.t1"; gene_id "Phchi.S6G116900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4503.t1 is derived from g1673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10864625	10865096	.	+	.	Phchi.S1G166200
Phchi.S1	AUGUSTUS	transcript	10864625	10865096	.	+	.	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	start_codon	10864625	10864627	.	+	0	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	CDS	10864625	10864641	0.94	+	0	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	exon	10864625	10864641	.	+	.	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	intron	10864642	10864873	.	+	.	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	CDS	10864874	10865096	1	+	1	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	exon	10864874	10865096	.	+	.	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
Phchi.S1	AUGUSTUS	stop_codon	10865097	10865099	.	+	0	transcript_id "Phchi.S1G166200.t1"; gene_id "Phchi.S1G166200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10895.t1 is derived from g14945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2801749	2804465	.	-	.	Phchi.S4G047700
Phchi.S4	AUGUSTUS	transcript	2801749	2804465	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	stop_codon	2801746	2801748	.	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2801749	2801911	0.97	-	1	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2801749	2801911	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2801912	2802108	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2802109	2802702	0.41	-	1	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2802109	2802702	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2802703	2802800	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2802801	2803039	1	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2802801	2803039	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2803040	2803116	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2803117	2803379	1	-	2	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2803117	2803379	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2803380	2803469	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2803470	2803773	1	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2803470	2803773	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2803774	2803858	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2803859	2803954	1	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2803859	2803954	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2803955	2804085	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2804086	2804193	1	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2804086	2804193	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	intron	2804194	2804288	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	CDS	2804289	2804465	1	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	exon	2804289	2804465	.	-	.	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
Phchi.S4	AUGUSTUS	start_codon	2804463	2804465	.	-	0	transcript_id "Phchi.S4G047700.t1"; gene_id "Phchi.S4G047700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12458.t1 is derived from g8135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24177613	24179163	.	-	.	Phchi.S2G053800
Phchi.S2	AUGUSTUS	transcript	24177613	24179163	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	stop_codon	24177610	24177612	.	-	0	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24177613	24177661	1	-	1	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24177613	24177661	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24177662	24177793	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24177794	24177857	1	-	2	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24177794	24177857	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24177858	24177996	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24177997	24178031	0.94	-	1	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24177997	24178031	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24178032	24178105	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24178106	24178167	0.71	-	0	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24178106	24178167	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24178168	24178250	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24178251	24178286	0.99	-	0	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24178251	24178286	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24178287	24178790	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24178791	24178860	0.92	-	1	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24178791	24178860	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24178861	24178969	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24178970	24178988	1	-	2	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24178970	24178988	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	intron	24178989	24179147	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	CDS	24179148	24179163	1	-	0	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	exon	24179148	24179163	.	-	.	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
Phchi.S2	AUGUSTUS	start_codon	24179161	24179163	.	-	0	transcript_id "Phchi.S2G053800.t1"; gene_id "Phchi.S2G053800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11237.t1 is derived from g15287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4934081	4935115	.	-	.	Phchi.S4G081900
Phchi.S4	AUGUSTUS	transcript	4934081	4935115	.	-	.	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	stop_codon	4934078	4934080	.	-	0	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	CDS	4934081	4934567	0.65	-	1	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	exon	4934081	4934567	.	-	.	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	intron	4934568	4934650	.	-	.	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	CDS	4934651	4934706	0.73	-	0	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	exon	4934651	4934706	.	-	.	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	intron	4934707	4934842	.	-	.	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	CDS	4934843	4935115	0.4	-	0	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	exon	4934843	4935115	.	-	.	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
Phchi.S4	AUGUSTUS	start_codon	4935113	4935115	.	-	0	transcript_id "Phchi.S4G081900.t1"; gene_id "Phchi.S4G081900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14750.t1 is derived from g13218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14533659	14536948	.	+	.	Phchi.S3G206900
Phchi.S3	AUGUSTUS	transcript	14533659	14536948	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	start_codon	14533659	14533661	.	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14533659	14533697	0.76	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14533659	14533697	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14533698	14533894	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14533895	14534388	0.99	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14533895	14534388	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14534389	14534694	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14534695	14534824	1	+	1	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14534695	14534824	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14534825	14534978	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14534979	14535144	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14534979	14535144	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14535145	14535288	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14535289	14535407	1	+	2	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14535289	14535407	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14535408	14535491	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14535492	14535572	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14535492	14535572	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14535573	14535675	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14535676	14535765	0.99	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14535676	14535765	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14535766	14535867	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14535868	14535939	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14535868	14535939	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14535940	14536063	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14536064	14536132	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14536064	14536132	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14536133	14536218	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14536219	14536299	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14536219	14536299	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14536300	14536374	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14536375	14536509	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14536375	14536509	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14536510	14536587	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14536588	14536644	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14536588	14536644	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	intron	14536645	14536726	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	CDS	14536727	14536948	1	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	exon	14536727	14536948	.	+	.	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
Phchi.S3	AUGUSTUS	stop_codon	14536949	14536951	.	+	0	transcript_id "Phchi.S3G206900.t1"; gene_id "Phchi.S3G206900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1119.t1 is derived from g10902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7791179	7791689	.	-	.	Phchi.S6G107800
Phchi.S6	AUGUSTUS	transcript	7791179	7791689	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	stop_codon	7791176	7791178	.	-	0	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	CDS	7791179	7791207	0.9	-	2	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	exon	7791179	7791207	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	intron	7791208	7791297	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	CDS	7791298	7791392	1	-	1	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	exon	7791298	7791392	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	intron	7791393	7791489	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	CDS	7791490	7791548	1	-	0	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	exon	7791490	7791548	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	intron	7791549	7791653	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	CDS	7791654	7791689	1	-	0	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	exon	7791654	7791689	.	-	.	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
Phchi.S6	AUGUSTUS	start_codon	7791687	7791689	.	-	0	transcript_id "Phchi.S6G107800.t1"; gene_id "Phchi.S6G107800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4051.t1 is derived from g1220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7539853	7541798	.	-	.	Phchi.S1G121000
Phchi.S1	AUGUSTUS	transcript	7539853	7541798	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	stop_codon	7539850	7539852	.	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7539853	7539943	0.83	-	1	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7539853	7539943	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7539944	7540204	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7540205	7540386	0.56	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7540205	7540386	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7540387	7540476	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7540477	7540574	1	-	2	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7540477	7540574	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7540575	7540701	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7540702	7540762	1	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7540702	7540762	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7540763	7540849	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7540850	7540996	1	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7540850	7540996	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7540997	7541087	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7541088	7541187	1	-	1	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7541088	7541187	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7541188	7541278	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7541279	7541394	1	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7541279	7541394	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7541395	7541479	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7541480	7541580	1	-	2	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7541480	7541580	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7541581	7541658	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7541659	7541691	1	-	2	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7541659	7541691	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	intron	7541692	7541794	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	CDS	7541795	7541798	0.96	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	exon	7541795	7541798	.	-	.	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
Phchi.S1	AUGUSTUS	start_codon	7541796	7541798	.	-	0	transcript_id "Phchi.S1G121000.t1"; gene_id "Phchi.S1G121000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15207.t1 is derived from g13675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17573804	17576238	.	+	.	Phchi.S3G252600
Phchi.S3	AUGUSTUS	transcript	17573804	17576238	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	start_codon	17573804	17573806	.	+	0	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	CDS	17573804	17573871	0.71	+	0	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	exon	17573804	17573871	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	intron	17573872	17574024	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	CDS	17574025	17574109	0.83	+	1	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	exon	17574025	17574109	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	intron	17574110	17574309	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	CDS	17574310	17574519	0.67	+	0	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	exon	17574310	17574519	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	intron	17574520	17574635	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	CDS	17574636	17575919	0.51	+	0	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	exon	17574636	17575919	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	intron	17575920	17576166	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	CDS	17576167	17576238	0.98	+	0	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	exon	17576167	17576238	.	+	.	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
Phchi.S3	AUGUSTUS	stop_codon	17576239	17576241	.	+	0	transcript_id "Phchi.S3G252600.t1"; gene_id "Phchi.S3G252600"
# This transcript jg15667.t2 is derived from g14136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15668.t1 is derived from g14137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20586144	20586435	.	-	.	Phchi.S3G298700
Phchi.S3	AUGUSTUS	transcript	20586144	20586435	.	-	.	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	stop_codon	20586141	20586143	.	-	0	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	CDS	20586144	20586250	0.88	-	2	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	exon	20586144	20586250	.	-	.	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	intron	20586251	20586341	.	-	.	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	CDS	20586342	20586435	0.87	-	0	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	exon	20586342	20586435	.	-	.	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
Phchi.S3	AUGUSTUS	start_codon	20586433	20586435	.	-	0	transcript_id "Phchi.S3G298700.t1"; gene_id "Phchi.S3G298700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10898.t1 is derived from g14948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2809175	2812881	.	-	.	Phchi.S4G048000
Phchi.S4	AUGUSTUS	transcript	2809175	2812881	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	stop_codon	2809172	2809174	.	-	0	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2809175	2810068	1	-	0	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2809175	2810068	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2810069	2810165	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2810166	2810409	1	-	1	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2810166	2810409	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2810410	2810529	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2810530	2810694	1	-	1	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2810530	2810694	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2810695	2810833	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2810834	2811438	0.98	-	0	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2810834	2811438	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2811439	2811536	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2811537	2811737	0.99	-	0	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2811537	2811737	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2811738	2811886	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2811887	2812130	0.98	-	1	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2811887	2812130	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2812131	2812235	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2812236	2812406	0.98	-	1	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2812236	2812406	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2812407	2812507	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2812508	2812881	0.7	-	0	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2812508	2812881	.	-	.	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	start_codon	2812879	2812881	.	-	0	transcript_id "Phchi.S4G048000.t1"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	transcript	2811794	2812881	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	stop_codon	2811791	2811793	.	-	0	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2811794	2811796	1	-	0	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2811794	2811796	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2811797	2811886	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2811887	2812130	0.98	-	1	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2811887	2812130	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2812131	2812235	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2812236	2812406	0.98	-	1	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2812236	2812406	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	intron	2812407	2812507	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	CDS	2812508	2812881	0.63	-	0	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	exon	2812508	2812881	.	-	.	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
Phchi.S4	AUGUSTUS	start_codon	2812879	2812881	.	-	0	transcript_id "Phchi.S4G048000.t2"; gene_id "Phchi.S4G048000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2897.t1 is derived from g66.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	380102	381423	.	-	.	Phchi.S1G005600
Phchi.S1	AUGUSTUS	transcript	380102	381423	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	stop_codon	380099	380101	.	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	CDS	380102	380227	0.97	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	exon	380102	380227	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	intron	380228	380340	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	CDS	380341	380427	0.96	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	exon	380341	380427	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	intron	380428	380513	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	CDS	380514	380587	1	-	2	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	exon	380514	380587	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	intron	380588	380674	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	CDS	380675	380822	1	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	exon	380675	380822	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	intron	380823	380977	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	CDS	380978	381226	1	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	exon	380978	381226	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	intron	381227	381348	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	CDS	381349	381423	0.98	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	exon	381349	381423	.	-	.	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
Phchi.S1	AUGUSTUS	start_codon	381421	381423	.	-	0	transcript_id "Phchi.S1G005600.t1"; gene_id "Phchi.S1G005600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14456.t1 is derived from g12924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12972155	12973636	.	+	.	Phchi.S3G177500
Phchi.S3	AUGUSTUS	transcript	12972155	12973636	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	start_codon	12972155	12972157	.	+	0	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12972155	12972192	0.45	+	0	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12972155	12972192	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	intron	12972193	12972358	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12972359	12972423	0.93	+	1	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12972359	12972423	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	intron	12972424	12972625	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12972626	12972674	0.86	+	2	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12972626	12972674	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	intron	12972675	12972866	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12972867	12972956	0.96	+	1	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12972867	12972956	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	intron	12972957	12973042	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12973043	12973178	1	+	1	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12973043	12973178	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	intron	12973179	12973272	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12973273	12973509	1	+	0	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12973273	12973509	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	intron	12973510	12973585	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	CDS	12973586	12973636	0.99	+	0	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	exon	12973586	12973636	.	+	.	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
Phchi.S3	AUGUSTUS	stop_codon	12973637	12973639	.	+	0	transcript_id "Phchi.S3G177500.t1"; gene_id "Phchi.S3G177500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10273.t1 is derived from g7449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46785698	46786978	.	+	.	Phchi.S1G743200
Phchi.S1	AUGUSTUS	transcript	46785698	46786978	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	start_codon	46785698	46785700	.	+	0	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	CDS	46785698	46785862	0.5	+	0	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	exon	46785698	46785862	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	intron	46785863	46785980	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	CDS	46785981	46786160	0.88	+	0	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	exon	46785981	46786160	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	intron	46786161	46786340	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	CDS	46786341	46786428	0.61	+	0	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	exon	46786341	46786428	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	intron	46786429	46786559	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	CDS	46786560	46786978	0.99	+	2	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	exon	46786560	46786978	.	+	.	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
Phchi.S1	AUGUSTUS	stop_codon	46786979	46786981	.	+	0	transcript_id "Phchi.S1G743200.t1"; gene_id "Phchi.S1G743200"
# This transcript jg13439.t2 is derived from g11906.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13440.t1 is derived from g11907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6710681	6712729	.	+	.	Phchi.S3G075900
Phchi.S3	AUGUSTUS	transcript	6710681	6712729	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	start_codon	6710681	6710683	.	+	0	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6710681	6710765	1	+	0	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6710681	6710765	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6710766	6710864	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6710865	6711001	1	+	2	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6710865	6711001	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6711002	6711086	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6711087	6711229	1	+	0	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6711087	6711229	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6711230	6711316	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6711317	6711514	1	+	1	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6711317	6711514	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6711515	6711599	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6711600	6711771	1	+	1	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6711600	6711771	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6711772	6711889	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6711890	6712043	1	+	0	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6711890	6712043	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6712044	6712129	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6712130	6712219	1	+	2	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6712130	6712219	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6712220	6712296	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6712297	6712352	0.99	+	2	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6712297	6712352	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6712353	6712461	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6712462	6712519	1	+	0	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6712462	6712519	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	intron	6712520	6712610	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	CDS	6712611	6712729	1	+	2	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	exon	6712611	6712729	.	+	.	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
Phchi.S3	AUGUSTUS	stop_codon	6712730	6712732	.	+	0	transcript_id "Phchi.S3G075900.t1"; gene_id "Phchi.S3G075900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9922.t1 is derived from g7098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44484506	44486470	.	-	.	Phchi.S1G708100
Phchi.S1	AUGUSTUS	transcript	44484506	44486470	.	-	.	transcript_id "Phchi.S1G708100.t1"; gene_id "Phchi.S1G708100"
Phchi.S1	AUGUSTUS	stop_codon	44484503	44484505	.	-	0	transcript_id "Phchi.S1G708100.t1"; gene_id "Phchi.S1G708100"
Phchi.S1	AUGUSTUS	CDS	44484506	44486470	0.44	-	0	transcript_id "Phchi.S1G708100.t1"; gene_id "Phchi.S1G708100"
Phchi.S1	AUGUSTUS	exon	44484506	44486470	.	-	.	transcript_id "Phchi.S1G708100.t1"; gene_id "Phchi.S1G708100"
Phchi.S1	AUGUSTUS	start_codon	44486468	44486470	.	-	0	transcript_id "Phchi.S1G708100.t1"; gene_id "Phchi.S1G708100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3772.t1 is derived from g941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5635824	5636792	.	+	.	Phchi.S1G093100
Phchi.S1	AUGUSTUS	transcript	5635824	5636792	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	start_codon	5635824	5635826	.	+	0	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	CDS	5635824	5636093	0.96	+	0	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	exon	5635824	5636093	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	intron	5636094	5636237	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	CDS	5636238	5636396	1	+	0	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	exon	5636238	5636396	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	intron	5636397	5636479	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	CDS	5636480	5636564	0.69	+	0	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	exon	5636480	5636564	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	intron	5636565	5636667	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	CDS	5636668	5636792	0.68	+	2	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	exon	5636668	5636792	.	+	.	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
Phchi.S1	AUGUSTUS	stop_codon	5636793	5636795	.	+	0	transcript_id "Phchi.S1G093100.t1"; gene_id "Phchi.S1G093100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6433.t1 is derived from g3605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23017039	23018637	.	+	.	Phchi.S1G359200
Phchi.S1	AUGUSTUS	transcript	23017039	23018637	.	+	.	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	start_codon	23017039	23017041	.	+	0	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	CDS	23017039	23017116	0.7	+	0	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	exon	23017039	23017116	.	+	.	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	intron	23017117	23017200	.	+	.	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	CDS	23017201	23018637	0.33	+	0	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	exon	23017201	23018637	.	+	.	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
Phchi.S1	AUGUSTUS	stop_codon	23018638	23018640	.	+	0	transcript_id "Phchi.S1G359200.t1"; gene_id "Phchi.S1G359200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4804.t1 is derived from g1974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12902130	12902715	.	+	.	Phchi.S1G196300
Phchi.S1	AUGUSTUS	transcript	12902130	12902715	.	+	.	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	start_codon	12902130	12902132	.	+	0	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	CDS	12902130	12902153	0.76	+	0	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	exon	12902130	12902153	.	+	.	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	intron	12902154	12902263	.	+	.	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	CDS	12902264	12902539	1	+	0	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	exon	12902264	12902539	.	+	.	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	intron	12902540	12902631	.	+	.	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	CDS	12902632	12902715	0.81	+	0	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	exon	12902632	12902715	.	+	.	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
Phchi.S1	AUGUSTUS	stop_codon	12902716	12902718	.	+	0	transcript_id "Phchi.S1G196300.t1"; gene_id "Phchi.S1G196300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg172.t1 is derived from g9954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1013868	1014618	.	-	.	Phchi.S6G013100
Phchi.S6	AUGUSTUS	transcript	1013868	1014618	.	-	.	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	stop_codon	1013865	1013867	.	-	0	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	CDS	1013868	1013874	1	-	1	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	exon	1013868	1013874	.	-	.	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	intron	1013875	1014014	.	-	.	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	CDS	1014015	1014151	1	-	0	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	exon	1014015	1014151	.	-	.	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	intron	1014152	1014489	.	-	.	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	CDS	1014490	1014618	1	-	0	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	exon	1014490	1014618	.	-	.	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
Phchi.S6	AUGUSTUS	start_codon	1014616	1014618	.	-	0	transcript_id "Phchi.S6G013100.t1"; gene_id "Phchi.S6G013100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5935.t1 is derived from g3106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19942589	19943350	.	-	.	Phchi.S1G309400
Phchi.S1	AUGUSTUS	transcript	19942589	19943350	.	-	.	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	stop_codon	19942586	19942588	.	-	0	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	CDS	19942589	19942800	0.99	-	2	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	exon	19942589	19942800	.	-	.	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	intron	19942801	19942914	.	-	.	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	CDS	19942915	19943145	0.99	-	2	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	exon	19942915	19943145	.	-	.	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	intron	19943146	19943214	.	-	.	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	CDS	19943215	19943350	0.79	-	0	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	exon	19943215	19943350	.	-	.	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	start_codon	19943348	19943350	.	-	0	transcript_id "Phchi.S1G309400.t1"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	transcript	19942589	19943350	.	-	.	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	stop_codon	19942586	19942588	.	-	0	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	CDS	19942589	19942800	0.95	-	2	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	exon	19942589	19942800	.	-	.	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	intron	19942801	19942914	.	-	.	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	CDS	19942915	19943133	0.95	-	2	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	exon	19942915	19943133	.	-	.	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	intron	19943134	19943214	.	-	.	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	CDS	19943215	19943350	0.85	-	0	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	exon	19943215	19943350	.	-	.	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
Phchi.S1	AUGUSTUS	start_codon	19943348	19943350	.	-	0	transcript_id "Phchi.S1G309400.t2"; gene_id "Phchi.S1G309400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14202.t1 is derived from g12669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11484223	11485146	.	-	.	Phchi.S3G152100
Phchi.S3	AUGUSTUS	transcript	11484223	11485146	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	stop_codon	11484220	11484222	.	-	0	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	CDS	11484223	11484233	0.67	-	2	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	exon	11484223	11484233	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	intron	11484234	11484331	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	CDS	11484332	11484484	0.61	-	2	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	exon	11484332	11484484	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	intron	11484485	11484673	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	CDS	11484674	11484707	0.57	-	0	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	exon	11484674	11484707	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	intron	11484708	11484912	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	CDS	11484913	11485146	0.35	-	0	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	exon	11484913	11485146	.	-	.	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
Phchi.S3	AUGUSTUS	start_codon	11485144	11485146	.	-	0	transcript_id "Phchi.S3G152100.t1"; gene_id "Phchi.S3G152100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6149.t1 is derived from g3320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21169457	21172366	.	-	.	Phchi.S1G330800
Phchi.S1	AUGUSTUS	transcript	21169457	21172366	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	stop_codon	21169454	21169456	.	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21169457	21169633	0.75	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21169457	21169633	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21169634	21169749	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21169750	21169834	0.87	-	1	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21169750	21169834	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21169835	21170047	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21170048	21170171	0.79	-	2	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21170048	21170171	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21170172	21170260	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21170261	21170399	1	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21170261	21170399	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21170400	21170489	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21170490	21170642	0.99	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21170490	21170642	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21170643	21170748	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21170749	21170924	0.96	-	2	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21170749	21170924	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21170925	21171013	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21171014	21171162	1	-	1	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21171014	21171162	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21171163	21171247	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21171248	21171559	0.63	-	1	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21171248	21171559	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21171560	21171679	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21171680	21171822	0.62	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21171680	21171822	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	intron	21171823	21171898	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	CDS	21171899	21172366	0.97	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	exon	21171899	21172366	.	-	.	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
Phchi.S1	AUGUSTUS	start_codon	21172364	21172366	.	-	0	transcript_id "Phchi.S1G330800.t1"; gene_id "Phchi.S1G330800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9923.t1 is derived from g7099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44487734	44490139	.	-	.	Phchi.S1G708200
Phchi.S1	AUGUSTUS	transcript	44487734	44490139	.	-	.	transcript_id "Phchi.S1G708200.t1"; gene_id "Phchi.S1G708200"
Phchi.S1	AUGUSTUS	stop_codon	44487731	44487733	.	-	0	transcript_id "Phchi.S1G708200.t1"; gene_id "Phchi.S1G708200"
Phchi.S1	AUGUSTUS	CDS	44487734	44490139	1	-	0	transcript_id "Phchi.S1G708200.t1"; gene_id "Phchi.S1G708200"
Phchi.S1	AUGUSTUS	exon	44487734	44490139	.	-	.	transcript_id "Phchi.S1G708200.t1"; gene_id "Phchi.S1G708200"
Phchi.S1	AUGUSTUS	start_codon	44490137	44490139	.	-	0	transcript_id "Phchi.S1G708200.t1"; gene_id "Phchi.S1G708200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12968.t1 is derived from g11433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3385796	3388378	.	-	.	Phchi.S3G028700
Phchi.S3	AUGUSTUS	transcript	3385796	3388378	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	stop_codon	3385793	3385795	.	-	0	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	CDS	3385796	3387163	0.86	-	0	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	exon	3385796	3387163	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	intron	3387164	3387281	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	CDS	3387282	3387577	0.69	-	2	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	exon	3387282	3387577	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	intron	3387578	3387921	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	CDS	3387922	3388047	0.57	-	2	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	exon	3387922	3388047	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	intron	3388048	3388122	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	CDS	3388123	3388199	1	-	1	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	exon	3388123	3388199	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	intron	3388200	3388283	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	CDS	3388284	3388378	0.95	-	0	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	exon	3388284	3388378	.	-	.	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
Phchi.S3	AUGUSTUS	start_codon	3388376	3388378	.	-	0	transcript_id "Phchi.S3G028700.t1"; gene_id "Phchi.S3G028700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5550.t1 is derived from g2720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17496721	17499128	.	+	.	Phchi.S1G270900
Phchi.S1	AUGUSTUS	transcript	17496721	17499128	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	start_codon	17496721	17496723	.	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17496721	17496798	0.96	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17496721	17496798	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17496799	17496916	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17496917	17497122	1	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17496917	17497122	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17497123	17497247	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17497248	17497661	0.87	+	1	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17497248	17497661	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17497662	17497761	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17497762	17498017	1	+	1	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17497762	17498017	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17498018	17498102	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17498103	17498294	1	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17498103	17498294	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17498295	17498402	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17498403	17498538	0.9	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17498403	17498538	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17498539	17498638	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17498639	17498730	0.92	+	2	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17498639	17498730	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17498731	17498811	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17498812	17498880	0.92	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17498812	17498880	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	intron	17498881	17498972	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	CDS	17498973	17499128	0.89	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	exon	17498973	17499128	.	+	.	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
Phchi.S1	AUGUSTUS	stop_codon	17499129	17499131	.	+	0	transcript_id "Phchi.S1G270900.t1"; gene_id "Phchi.S1G270900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15288.t1 is derived from g13756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18219331	18222670	.	+	.	Phchi.S3G260700
Phchi.S3	AUGUSTUS	transcript	18219331	18222670	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	start_codon	18219331	18219333	.	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18219331	18219396	0.96	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18219331	18219396	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18219397	18219484	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18219485	18219691	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18219485	18219691	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18219692	18219827	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18219828	18220076	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18219828	18220076	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220077	18220181	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220182	18220397	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220182	18220397	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220398	18220497	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220498	18220653	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220498	18220653	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220654	18220730	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220731	18220890	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220731	18220890	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220891	18220970	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220971	18221122	1	+	2	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220971	18221122	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221123	18221203	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221204	18221291	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221204	18221291	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221292	18221401	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221402	18221475	1	+	2	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221402	18221475	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221476	18221558	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221559	18221633	1	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221559	18221633	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221634	18221719	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221720	18222053	0.99	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221720	18222053	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18222054	18222341	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18222342	18222670	0.98	+	2	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18222342	18222670	.	+	.	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	stop_codon	18222671	18222673	.	+	0	transcript_id "Phchi.S3G260700.t1"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	transcript	18219331	18222670	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	start_codon	18219331	18219333	.	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18219331	18219396	0.92	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18219331	18219396	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18219397	18219484	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18219485	18219691	1	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18219485	18219691	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18219692	18219827	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18219828	18220076	1	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18219828	18220076	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220077	18220181	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220182	18220397	1	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220182	18220397	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220398	18220497	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220498	18220653	1	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220498	18220653	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220654	18220730	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220731	18220890	1	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220731	18220890	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18220891	18220970	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18220971	18221122	1	+	2	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18220971	18221122	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221123	18221203	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221204	18221291	0.99	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221204	18221291	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221292	18221401	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221402	18221475	1	+	2	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221402	18221475	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221476	18221558	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221559	18221633	1	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221559	18221633	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18221634	18221719	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18221720	18222034	0.41	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18221720	18222034	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18222035	18222109	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18222110	18222116	0.45	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18222110	18222116	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	intron	18222117	18222341	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	CDS	18222342	18222670	0.51	+	2	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	exon	18222342	18222670	.	+	.	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
Phchi.S3	AUGUSTUS	stop_codon	18222671	18222673	.	+	0	transcript_id "Phchi.S3G260700.t2"; gene_id "Phchi.S3G260700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg989.t1 is derived from g10772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6899221	6899559	.	-	.	Phchi.S6G094800
Phchi.S6	AUGUSTUS	transcript	6899221	6899559	.	-	.	transcript_id "Phchi.S6G094800.t1"; gene_id "Phchi.S6G094800"
Phchi.S6	AUGUSTUS	stop_codon	6899218	6899220	.	-	0	transcript_id "Phchi.S6G094800.t1"; gene_id "Phchi.S6G094800"
Phchi.S6	AUGUSTUS	CDS	6899221	6899559	0.17	-	0	transcript_id "Phchi.S6G094800.t1"; gene_id "Phchi.S6G094800"
Phchi.S6	AUGUSTUS	exon	6899221	6899559	.	-	.	transcript_id "Phchi.S6G094800.t1"; gene_id "Phchi.S6G094800"
Phchi.S6	AUGUSTUS	start_codon	6899557	6899559	.	-	0	transcript_id "Phchi.S6G094800.t1"; gene_id "Phchi.S6G094800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15821.t1 is derived from g14291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21587833	21588346	.	+	.	Phchi.S3G314000
Phchi.S3	AUGUSTUS	transcript	21587833	21588346	.	+	.	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	start_codon	21587833	21587835	.	+	0	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	CDS	21587833	21588102	1	+	0	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	exon	21587833	21588102	.	+	.	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	intron	21588103	21588280	.	+	.	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	CDS	21588281	21588346	1	+	0	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	exon	21588281	21588346	.	+	.	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
Phchi.S3	AUGUSTUS	stop_codon	21588347	21588349	.	+	0	transcript_id "Phchi.S3G314000.t1"; gene_id "Phchi.S3G314000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8020.t1 is derived from g5195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32493004	32494069	.	-	.	Phchi.S1G517900
Phchi.S1	AUGUSTUS	transcript	32493004	32494069	.	-	.	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	stop_codon	32493001	32493003	.	-	0	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	CDS	32493004	32493162	0.78	-	0	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	exon	32493004	32493162	.	-	.	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	intron	32493163	32493260	.	-	.	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	CDS	32493261	32493675	0.96	-	1	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	exon	32493261	32493675	.	-	.	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	intron	32493676	32493896	.	-	.	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	CDS	32493897	32494069	1	-	0	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	exon	32493897	32494069	.	-	.	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
Phchi.S1	AUGUSTUS	start_codon	32494067	32494069	.	-	0	transcript_id "Phchi.S1G517900.t1"; gene_id "Phchi.S1G517900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3339.t1 is derived from g508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2985299	2986774	.	+	.	Phchi.S1G049800
Phchi.S1	AUGUSTUS	transcript	2985299	2986774	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	start_codon	2985299	2985301	.	+	0	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	CDS	2985299	2985351	0.43	+	0	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	exon	2985299	2985351	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	intron	2985352	2985545	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	CDS	2985546	2985747	0.76	+	1	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	exon	2985546	2985747	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	intron	2985748	2985835	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	CDS	2985836	2986088	0.51	+	0	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	exon	2985836	2986088	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	intron	2986089	2986292	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	CDS	2986293	2986430	1	+	2	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	exon	2986293	2986430	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	intron	2986431	2986529	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	CDS	2986530	2986774	0.98	+	2	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	exon	2986530	2986774	.	+	.	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
Phchi.S1	AUGUSTUS	stop_codon	2986775	2986777	.	+	0	transcript_id "Phchi.S1G049800.t1"; gene_id "Phchi.S1G049800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15941.t1 is derived from g8.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C143	AUGUSTUS	gene	28758	29918	.	-	.	Phchi.C143G000300
Phchi.C143	AUGUSTUS	transcript	28758	29918	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	stop_codon	28755	28757	.	-	0	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	CDS	28758	28865	0.99	-	0	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	exon	28758	28865	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	intron	28866	29014	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	CDS	29015	29114	0.85	-	1	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	exon	29015	29114	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	intron	29115	29188	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	CDS	29189	29510	0.73	-	2	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	exon	29189	29510	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	intron	29511	29597	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	CDS	29598	29646	1	-	0	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	exon	29598	29646	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	intron	29647	29771	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	CDS	29772	29918	0.98	-	0	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	exon	29772	29918	.	-	.	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
Phchi.C143	AUGUSTUS	start_codon	29916	29918	.	-	0	transcript_id "Phchi.C143G000300.t1"; gene_id "Phchi.C143G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13278.t1 is derived from g11743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5137601	5139156	.	-	.	Phchi.S3G059700
Phchi.S3	AUGUSTUS	transcript	5137601	5139156	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	stop_codon	5137598	5137600	.	-	0	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	CDS	5137601	5138230	1	-	0	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	exon	5137601	5138230	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	intron	5138231	5138313	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	CDS	5138314	5138362	0.98	-	1	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	exon	5138314	5138362	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	intron	5138363	5138487	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	CDS	5138488	5138697	0.85	-	1	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	exon	5138488	5138697	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	intron	5138698	5138788	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	CDS	5138789	5139156	0.58	-	0	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	exon	5138789	5139156	.	-	.	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
Phchi.S3	AUGUSTUS	start_codon	5139154	5139156	.	-	0	transcript_id "Phchi.S3G059700.t1"; gene_id "Phchi.S3G059700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3029.t1 is derived from g198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1236377	1238035	.	+	.	Phchi.S1G018800
Phchi.S1	AUGUSTUS	transcript	1236377	1238035	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	start_codon	1236377	1236379	.	+	0	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	CDS	1236377	1236469	0.92	+	0	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	exon	1236377	1236469	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	intron	1236470	1236561	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	CDS	1236562	1236796	0.92	+	0	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	exon	1236562	1236796	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	intron	1236797	1236930	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	CDS	1236931	1237301	1	+	2	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	exon	1236931	1237301	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	intron	1237302	1237384	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	CDS	1237385	1238035	1	+	0	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	exon	1237385	1238035	.	+	.	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
Phchi.S1	AUGUSTUS	stop_codon	1238036	1238038	.	+	0	transcript_id "Phchi.S1G018800.t1"; gene_id "Phchi.S1G018800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9179.t1 is derived from g6354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40235342	40237001	.	-	.	Phchi.S1G633800
Phchi.S1	AUGUSTUS	transcript	40235342	40237001	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	stop_codon	40235339	40235341	.	-	0	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	CDS	40235342	40235350	0.38	-	0	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	exon	40235342	40235350	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	intron	40235351	40235454	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	CDS	40235455	40235599	0.9	-	1	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	exon	40235455	40235599	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	intron	40235600	40235694	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	CDS	40235695	40235940	1	-	1	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	exon	40235695	40235940	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	intron	40235941	40236025	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	CDS	40236026	40236187	1	-	1	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	exon	40236026	40236187	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	intron	40236188	40236281	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	CDS	40236282	40236648	0.89	-	2	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	exon	40236282	40236648	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	intron	40236649	40236763	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	CDS	40236764	40237001	0.63	-	0	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	exon	40236764	40237001	.	-	.	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
Phchi.S1	AUGUSTUS	start_codon	40236999	40237001	.	-	0	transcript_id "Phchi.S1G633800.t1"; gene_id "Phchi.S1G633800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8783.t1 is derived from g5958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37940321	37942301	.	+	.	Phchi.S1G594200
Phchi.S1	AUGUSTUS	transcript	37940321	37942301	.	+	.	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	start_codon	37940321	37940323	.	+	0	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	CDS	37940321	37941478	0.59	+	0	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	exon	37940321	37941478	.	+	.	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	intron	37941479	37941644	.	+	.	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	CDS	37941645	37942076	0.74	+	0	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	exon	37941645	37942076	.	+	.	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	intron	37942077	37942175	.	+	.	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	CDS	37942176	37942301	0.86	+	0	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	exon	37942176	37942301	.	+	.	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
Phchi.S1	AUGUSTUS	stop_codon	37942302	37942304	.	+	0	transcript_id "Phchi.S1G594200.t1"; gene_id "Phchi.S1G594200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11615.t1 is derived from g15666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7333191	7335251	.	-	.	Phchi.S4G119700
Phchi.S4	AUGUSTUS	transcript	7333191	7335251	.	-	.	transcript_id "Phchi.S4G119700.t1"; gene_id "Phchi.S4G119700"
Phchi.S4	AUGUSTUS	stop_codon	7333188	7333190	.	-	0	transcript_id "Phchi.S4G119700.t1"; gene_id "Phchi.S4G119700"
Phchi.S4	AUGUSTUS	CDS	7333191	7335251	0.63	-	0	transcript_id "Phchi.S4G119700.t1"; gene_id "Phchi.S4G119700"
Phchi.S4	AUGUSTUS	exon	7333191	7335251	.	-	.	transcript_id "Phchi.S4G119700.t1"; gene_id "Phchi.S4G119700"
Phchi.S4	AUGUSTUS	start_codon	7335249	7335251	.	-	0	transcript_id "Phchi.S4G119700.t1"; gene_id "Phchi.S4G119700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1365.t1 is derived from g11145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C72	AUGUSTUS	gene	8992	9823	.	-	.	Phchi.C72G000100
Phchi.C72	AUGUSTUS	transcript	8992	9823	.	-	.	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	stop_codon	8989	8991	.	-	0	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	CDS	8992	9421	0.27	-	1	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	exon	8992	9421	.	-	.	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	intron	9422	9534	.	-	.	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	CDS	9535	9652	0.34	-	2	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	exon	9535	9652	.	-	.	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	intron	9653	9753	.	-	.	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	CDS	9754	9823	0.69	-	0	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	exon	9754	9823	.	-	.	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
Phchi.C72	AUGUSTUS	start_codon	9821	9823	.	-	0	transcript_id "Phchi.C72G000100.t1"; gene_id "Phchi.C72G000100"
# This transcript jg11017.t2 is derived from g15067.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11018.t1 is derived from g15068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3655357	3656106	.	-	.	Phchi.S4G060000
Phchi.S4	AUGUSTUS	transcript	3655357	3656106	.	-	.	transcript_id "Phchi.S4G060000.t1"; gene_id "Phchi.S4G060000"
Phchi.S4	AUGUSTUS	stop_codon	3655354	3655356	.	-	0	transcript_id "Phchi.S4G060000.t1"; gene_id "Phchi.S4G060000"
Phchi.S4	AUGUSTUS	CDS	3655357	3656106	0.99	-	0	transcript_id "Phchi.S4G060000.t1"; gene_id "Phchi.S4G060000"
Phchi.S4	AUGUSTUS	exon	3655357	3656106	.	-	.	transcript_id "Phchi.S4G060000.t1"; gene_id "Phchi.S4G060000"
Phchi.S4	AUGUSTUS	start_codon	3656104	3656106	.	-	0	transcript_id "Phchi.S4G060000.t1"; gene_id "Phchi.S4G060000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4205.t1 is derived from g1374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8902299	8905045	.	+	.	Phchi.S1G136400
Phchi.S1	AUGUSTUS	transcript	8902299	8905045	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	start_codon	8902299	8902301	.	+	0	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8902299	8902334	0.94	+	0	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8902299	8902334	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8902335	8902423	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8902424	8902515	1	+	0	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8902424	8902515	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8902516	8902661	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8902662	8902800	1	+	1	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8902662	8902800	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8902801	8902938	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8902939	8903073	1	+	0	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8902939	8903073	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8903074	8903163	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8903164	8903212	1	+	0	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8903164	8903212	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8903213	8903381	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8903382	8903433	1	+	2	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8903382	8903433	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8903434	8903644	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8903645	8903664	0.95	+	1	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8903645	8903664	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	intron	8903665	8903852	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	CDS	8903853	8905045	0.79	+	2	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	exon	8903853	8905045	.	+	.	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
Phchi.S1	AUGUSTUS	stop_codon	8905046	8905048	.	+	0	transcript_id "Phchi.S1G136400.t1"; gene_id "Phchi.S1G136400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg399.t1 is derived from g10181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2883586	2887826	.	-	.	Phchi.S6G035800
Phchi.S6	AUGUSTUS	transcript	2883586	2887826	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	stop_codon	2883583	2883585	.	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2883586	2883850	1	-	1	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2883586	2883850	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2883851	2883931	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2883932	2884210	1	-	1	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2883932	2884210	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2884211	2884301	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2884302	2884444	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2884302	2884444	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2884445	2884520	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2884521	2884634	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2884521	2884634	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2884635	2884718	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2884719	2884915	1	-	2	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2884719	2884915	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2884916	2885053	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2885054	2885246	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2885054	2885246	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2885247	2885359	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2885360	2886082	0.99	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2885360	2886082	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2886083	2886191	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2886192	2886320	0.99	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2886192	2886320	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2886321	2886456	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2886457	2886669	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2886457	2886669	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2886670	2886783	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2886784	2886843	0.85	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2886784	2886843	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2886844	2886962	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2886963	2887051	1	-	2	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2886963	2887051	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2887052	2887124	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2887125	2887257	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2887125	2887257	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2887258	2887348	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2887349	2887483	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2887349	2887483	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	intron	2887484	2887598	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	CDS	2887599	2887826	1	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	exon	2887599	2887826	.	-	.	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
Phchi.S6	AUGUSTUS	start_codon	2887824	2887826	.	-	0	transcript_id "Phchi.S6G035800.t1"; gene_id "Phchi.S6G035800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14647.t1 is derived from g13115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13939619	13940635	.	-	.	Phchi.S3G196600
Phchi.S3	AUGUSTUS	transcript	13939619	13940635	.	-	.	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	stop_codon	13939616	13939618	.	-	0	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	CDS	13939619	13939653	0.55	-	2	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	exon	13939619	13939653	.	-	.	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	intron	13939654	13939934	.	-	.	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	CDS	13939935	13940397	0.65	-	0	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	exon	13939935	13940397	.	-	.	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	intron	13940398	13940593	.	-	.	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	CDS	13940594	13940635	0.67	-	0	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	exon	13940594	13940635	.	-	.	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
Phchi.S3	AUGUSTUS	start_codon	13940633	13940635	.	-	0	transcript_id "Phchi.S3G196600.t1"; gene_id "Phchi.S3G196600"
# This transcript jg5493.t2 is derived from g2663.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5494.t1 is derived from g2664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17119756	17120697	.	+	.	Phchi.S1G265300
Phchi.S1	AUGUSTUS	transcript	17119756	17120697	.	+	.	transcript_id "Phchi.S1G265300.t1"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	start_codon	17119756	17119758	.	+	0	transcript_id "Phchi.S1G265300.t1"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	CDS	17119756	17120697	1	+	0	transcript_id "Phchi.S1G265300.t1"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	exon	17119756	17120697	.	+	.	transcript_id "Phchi.S1G265300.t1"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	stop_codon	17120698	17120700	.	+	0	transcript_id "Phchi.S1G265300.t1"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	transcript	17119963	17120697	.	+	.	transcript_id "Phchi.S1G265300.t2"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	start_codon	17119963	17119965	.	+	0	transcript_id "Phchi.S1G265300.t2"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	CDS	17119963	17120697	1	+	0	transcript_id "Phchi.S1G265300.t2"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	exon	17119963	17120697	.	+	.	transcript_id "Phchi.S1G265300.t2"; gene_id "Phchi.S1G265300"
Phchi.S1	AUGUSTUS	stop_codon	17120698	17120700	.	+	0	transcript_id "Phchi.S1G265300.t2"; gene_id "Phchi.S1G265300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5622.t1 is derived from g2792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17922032	17922913	.	+	.	Phchi.S1G278100
Phchi.S1	AUGUSTUS	transcript	17922032	17922913	.	+	.	transcript_id "Phchi.S1G278100.t1"; gene_id "Phchi.S1G278100"
Phchi.S1	AUGUSTUS	start_codon	17922032	17922034	.	+	0	transcript_id "Phchi.S1G278100.t1"; gene_id "Phchi.S1G278100"
Phchi.S1	AUGUSTUS	CDS	17922032	17922913	0.98	+	0	transcript_id "Phchi.S1G278100.t1"; gene_id "Phchi.S1G278100"
Phchi.S1	AUGUSTUS	exon	17922032	17922913	.	+	.	transcript_id "Phchi.S1G278100.t1"; gene_id "Phchi.S1G278100"
Phchi.S1	AUGUSTUS	stop_codon	17922914	17922916	.	+	0	transcript_id "Phchi.S1G278100.t1"; gene_id "Phchi.S1G278100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1352.t1 is derived from g14419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C23	AUGUSTUS	gene	45743	47521	.	-	.	Phchi.C23G000100
Phchi.C23	AUGUSTUS	transcript	45743	47521	.	-	.	transcript_id "Phchi.C23G000100.t1"; gene_id "Phchi.C23G000100"
Phchi.C23	AUGUSTUS	stop_codon	45740	45742	.	-	0	transcript_id "Phchi.C23G000100.t1"; gene_id "Phchi.C23G000100"
Phchi.C23	AUGUSTUS	CDS	45743	47521	0.98	-	0	transcript_id "Phchi.C23G000100.t1"; gene_id "Phchi.C23G000100"
Phchi.C23	AUGUSTUS	exon	45743	47521	.	-	.	transcript_id "Phchi.C23G000100.t1"; gene_id "Phchi.C23G000100"
Phchi.C23	AUGUSTUS	start_codon	47519	47521	.	-	0	transcript_id "Phchi.C23G000100.t1"; gene_id "Phchi.C23G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13252.t1 is derived from g11717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4928523	4932035	.	+	.	Phchi.S3G057100
Phchi.S3	AUGUSTUS	transcript	4928523	4932035	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	start_codon	4928523	4928525	.	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4928523	4929263	0.99	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4928523	4929263	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4929264	4929347	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4929348	4929473	1	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4929348	4929473	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4929474	4929570	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4929571	4929674	1	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4929571	4929674	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4929675	4929763	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4929764	4929811	1	+	1	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4929764	4929811	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4929812	4929909	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4929910	4930157	0.96	+	1	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4929910	4930157	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4930158	4930244	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4930245	4930377	1	+	2	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4930245	4930377	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4930378	4930464	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4930465	4930759	0.97	+	1	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4930465	4930759	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4930760	4930866	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4930867	4931098	0.66	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4930867	4931098	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4931099	4931195	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4931196	4931260	0.38	+	2	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4931196	4931260	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4931261	4931533	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4931534	4931622	0.52	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4931534	4931622	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	intron	4931623	4931872	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	CDS	4931873	4932035	0.71	+	1	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	exon	4931873	4932035	.	+	.	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
Phchi.S3	AUGUSTUS	stop_codon	4932036	4932038	.	+	0	transcript_id "Phchi.S3G057100.t1"; gene_id "Phchi.S3G057100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5321.t1 is derived from g2491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16277294	16279776	.	+	.	Phchi.S1G248000
Phchi.S1	AUGUSTUS	transcript	16277294	16279776	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	start_codon	16277294	16277296	.	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	CDS	16277294	16278370	0.83	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	exon	16277294	16278370	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	intron	16278371	16278452	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	CDS	16278453	16278507	1	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	exon	16278453	16278507	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	intron	16278508	16278675	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	CDS	16278676	16278824	1	+	2	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	exon	16278676	16278824	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	intron	16278825	16279246	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	CDS	16279247	16279369	0.73	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	exon	16279247	16279369	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	intron	16279370	16279447	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	CDS	16279448	16279576	1	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	exon	16279448	16279576	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	intron	16279577	16279701	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	CDS	16279702	16279776	0.99	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	exon	16279702	16279776	.	+	.	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
Phchi.S1	AUGUSTUS	stop_codon	16279777	16279779	.	+	0	transcript_id "Phchi.S1G248000.t1"; gene_id "Phchi.S1G248000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6816.t1 is derived from g3988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25186081	25187050	.	-	.	Phchi.S1G397500
Phchi.S1	AUGUSTUS	transcript	25186081	25187050	.	-	.	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	stop_codon	25186078	25186080	.	-	0	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	CDS	25186081	25186729	1	-	1	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	exon	25186081	25186729	.	-	.	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	intron	25186730	25186870	.	-	.	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	CDS	25186871	25186960	0.89	-	1	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	exon	25186871	25186960	.	-	.	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	intron	25186961	25187045	.	-	.	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	CDS	25187046	25187050	0.82	-	0	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	exon	25187046	25187050	.	-	.	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
Phchi.S1	AUGUSTUS	start_codon	25187048	25187050	.	-	0	transcript_id "Phchi.S1G397500.t1"; gene_id "Phchi.S1G397500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1779.t1 is derived from g8699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2971177	2973315	.	-	.	Phchi.S5G038800
Phchi.S5	AUGUSTUS	transcript	2971177	2973315	.	-	.	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	stop_codon	2971174	2971176	.	-	0	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	CDS	2971177	2972482	0.76	-	1	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	exon	2971177	2972482	.	-	.	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	intron	2972483	2972776	.	-	.	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	CDS	2972777	2973315	0.73	-	0	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	exon	2972777	2973315	.	-	.	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
Phchi.S5	AUGUSTUS	start_codon	2973313	2973315	.	-	0	transcript_id "Phchi.S5G038800.t1"; gene_id "Phchi.S5G038800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15186.t1 is derived from g13654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17467167	17468084	.	-	.	Phchi.S3G250500
Phchi.S3	AUGUSTUS	transcript	17467167	17468084	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	stop_codon	17467164	17467166	.	-	0	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	CDS	17467167	17467197	1	-	1	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	exon	17467167	17467197	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	intron	17467198	17467373	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	CDS	17467374	17467457	0.77	-	1	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	exon	17467374	17467457	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	intron	17467458	17467654	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	CDS	17467655	17467679	0.72	-	2	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	exon	17467655	17467679	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	intron	17467680	17467805	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	CDS	17467806	17467812	0.66	-	0	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	exon	17467806	17467812	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	intron	17467813	17467973	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	CDS	17467974	17468084	0.64	-	0	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	exon	17467974	17468084	.	-	.	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
Phchi.S3	AUGUSTUS	start_codon	17468082	17468084	.	-	0	transcript_id "Phchi.S3G250500.t1"; gene_id "Phchi.S3G250500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8991.t1 is derived from g6166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39005899	39008414	.	+	.	Phchi.S1G615000
Phchi.S1	AUGUSTUS	transcript	39005899	39008414	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	start_codon	39005899	39005901	.	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39005899	39006075	1	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39005899	39006075	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39006076	39006163	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39006164	39006248	1	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39006164	39006248	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39006249	39006368	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39006369	39006509	1	+	2	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39006369	39006509	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39006510	39006667	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39006668	39006781	1	+	2	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39006668	39006781	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39006782	39006937	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39006938	39007035	1	+	2	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39006938	39007035	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39007036	39007187	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39007188	39007267	1	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39007188	39007267	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39007268	39007364	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39007365	39007470	1	+	1	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39007365	39007470	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39007471	39007602	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39007603	39007730	1	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39007603	39007730	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39007731	39007826	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39007827	39008052	1	+	1	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39007827	39008052	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39008053	39008138	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39008139	39008195	1	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39008139	39008195	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	intron	39008196	39008336	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	CDS	39008337	39008414	1	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	exon	39008337	39008414	.	+	.	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
Phchi.S1	AUGUSTUS	stop_codon	39008415	39008417	.	+	0	transcript_id "Phchi.S1G615000.t1"; gene_id "Phchi.S1G615000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7012.t1 is derived from g4184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26394465	26400194	.	+	.	Phchi.S1G417100
Phchi.S1	AUGUSTUS	transcript	26394465	26396811	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	start_codon	26394465	26394467	.	+	0	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26394465	26395548	1	+	0	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26394465	26395548	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26395549	26395669	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26395670	26395695	1	+	2	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26395670	26395695	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26395696	26395826	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26395827	26395982	1	+	0	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26395827	26395982	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26395983	26396076	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396077	26396220	1	+	0	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396077	26396220	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396221	26396306	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396307	26396395	1	+	0	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396307	26396395	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396396	26396493	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396494	26396720	1	+	1	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396494	26396720	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396721	26396803	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396804	26396811	0.91	+	2	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396804	26396811	.	+	.	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	stop_codon	26396812	26396814	.	+	0	transcript_id "Phchi.S1G417100.t1"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	transcript	26394465	26400194	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	start_codon	26394465	26394467	.	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26394465	26395548	1	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26394465	26395548	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26395549	26395669	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26395670	26395695	1	+	2	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26395670	26395695	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26395696	26395826	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26395827	26395982	1	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26395827	26395982	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26395983	26396076	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396077	26396220	1	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396077	26396220	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396221	26396306	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396307	26396395	1	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396307	26396395	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396396	26396493	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396494	26396720	1	+	1	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396494	26396720	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396721	26396865	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26396866	26396951	1	+	2	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26396866	26396951	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26396952	26397060	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26397061	26397117	1	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26397061	26397117	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26397118	26397246	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26397247	26397314	1	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26397247	26397314	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26397315	26397420	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26397421	26397527	1	+	1	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26397421	26397527	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26397528	26397605	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26397606	26397667	1	+	2	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26397606	26397667	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26397668	26397762	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26397763	26397840	0.64	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26397763	26397840	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26397841	26398107	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26398108	26399351	0.39	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26398108	26399351	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	intron	26399352	26399425	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	CDS	26399426	26400194	0.87	+	1	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	exon	26399426	26400194	.	+	.	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
Phchi.S1	AUGUSTUS	stop_codon	26400195	26400197	.	+	0	transcript_id "Phchi.S1G417100.t2"; gene_id "Phchi.S1G417100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1064.t1 is derived from g10847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7402413	7404134	.	+	.	Phchi.S6G102300
Phchi.S6	AUGUSTUS	transcript	7402413	7404134	.	+	.	transcript_id "Phchi.S6G102300.t1"; gene_id "Phchi.S6G102300"
Phchi.S6	AUGUSTUS	start_codon	7402413	7402415	.	+	0	transcript_id "Phchi.S6G102300.t1"; gene_id "Phchi.S6G102300"
Phchi.S6	AUGUSTUS	CDS	7402413	7404134	0.92	+	0	transcript_id "Phchi.S6G102300.t1"; gene_id "Phchi.S6G102300"
Phchi.S6	AUGUSTUS	exon	7402413	7404134	.	+	.	transcript_id "Phchi.S6G102300.t1"; gene_id "Phchi.S6G102300"
Phchi.S6	AUGUSTUS	stop_codon	7404135	7404137	.	+	0	transcript_id "Phchi.S6G102300.t1"; gene_id "Phchi.S6G102300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10632.t1 is derived from g14682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1347174	1347767	.	-	.	Phchi.S4G021400
Phchi.S4	AUGUSTUS	transcript	1347174	1347767	.	-	.	transcript_id "Phchi.S4G021400.t1"; gene_id "Phchi.S4G021400"
Phchi.S4	AUGUSTUS	stop_codon	1347171	1347173	.	-	0	transcript_id "Phchi.S4G021400.t1"; gene_id "Phchi.S4G021400"
Phchi.S4	AUGUSTUS	CDS	1347174	1347767	0.68	-	0	transcript_id "Phchi.S4G021400.t1"; gene_id "Phchi.S4G021400"
Phchi.S4	AUGUSTUS	exon	1347174	1347767	.	-	.	transcript_id "Phchi.S4G021400.t1"; gene_id "Phchi.S4G021400"
Phchi.S4	AUGUSTUS	start_codon	1347765	1347767	.	-	0	transcript_id "Phchi.S4G021400.t1"; gene_id "Phchi.S4G021400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13441.t1 is derived from g11908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6720190	6722039	.	-	.	Phchi.S3G076000
Phchi.S3	AUGUSTUS	transcript	6720190	6722039	.	-	.	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	stop_codon	6720187	6720189	.	-	0	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	CDS	6720190	6721362	0.97	-	0	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	exon	6720190	6721362	.	-	.	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	intron	6721363	6721474	.	-	.	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	CDS	6721475	6721812	0.87	-	2	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	exon	6721475	6721812	.	-	.	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	intron	6721813	6721912	.	-	.	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	CDS	6721913	6722039	0.92	-	0	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	exon	6721913	6722039	.	-	.	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
Phchi.S3	AUGUSTUS	start_codon	6722037	6722039	.	-	0	transcript_id "Phchi.S3G076000.t1"; gene_id "Phchi.S3G076000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7780.t1 is derived from g4954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31183943	31184257	.	+	.	Phchi.S1G493900
Phchi.S1	AUGUSTUS	transcript	31183943	31184257	.	+	.	transcript_id "Phchi.S1G493900.t1"; gene_id "Phchi.S1G493900"
Phchi.S1	AUGUSTUS	start_codon	31183943	31183945	.	+	0	transcript_id "Phchi.S1G493900.t1"; gene_id "Phchi.S1G493900"
Phchi.S1	AUGUSTUS	CDS	31183943	31184257	0.63	+	0	transcript_id "Phchi.S1G493900.t1"; gene_id "Phchi.S1G493900"
Phchi.S1	AUGUSTUS	exon	31183943	31184257	.	+	.	transcript_id "Phchi.S1G493900.t1"; gene_id "Phchi.S1G493900"
Phchi.S1	AUGUSTUS	stop_codon	31184258	31184260	.	+	0	transcript_id "Phchi.S1G493900.t1"; gene_id "Phchi.S1G493900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5836.t1 is derived from g3006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19196544	19197285	.	+	.	Phchi.S1G299500
Phchi.S1	AUGUSTUS	transcript	19196544	19197285	.	+	.	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	start_codon	19196544	19196546	.	+	0	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	CDS	19196544	19196553	0.28	+	0	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	exon	19196544	19196553	.	+	.	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	intron	19196554	19196804	.	+	.	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	CDS	19196805	19196904	0.51	+	2	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	exon	19196805	19196904	.	+	.	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	intron	19196905	19197158	.	+	.	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	CDS	19197159	19197285	0.51	+	1	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	exon	19197159	19197285	.	+	.	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
Phchi.S1	AUGUSTUS	stop_codon	19197286	19197288	.	+	0	transcript_id "Phchi.S1G299500.t1"; gene_id "Phchi.S1G299500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8802.t1 is derived from g5977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38056478	38059610	.	-	.	Phchi.S1G596100
Phchi.S1	AUGUSTUS	transcript	38056478	38059610	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	stop_codon	38056475	38056477	.	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38056478	38056534	1	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38056478	38056534	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38056535	38056658	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38056659	38056821	1	-	1	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38056659	38056821	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38056822	38056902	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38056903	38057090	1	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38056903	38057090	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38057091	38057218	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38057219	38057264	1	-	1	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38057219	38057264	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38057265	38057404	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38057405	38057452	1	-	1	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38057405	38057452	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38057453	38057613	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38057614	38057716	1	-	2	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38057614	38057716	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38057717	38057871	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38057872	38058085	1	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38057872	38058085	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38058086	38058176	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38058177	38058296	1	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38058177	38058296	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38058297	38058417	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38058418	38058566	1	-	2	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38058418	38058566	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38058567	38058655	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38058656	38058808	1	-	2	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38058656	38058808	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38058809	38058899	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38058900	38058957	1	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38058900	38058957	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38058958	38059044	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38059045	38059133	1	-	2	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38059045	38059133	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38059134	38059220	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38059221	38059353	1	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38059221	38059353	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	intron	38059354	38059550	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	CDS	38059551	38059610	0.47	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	exon	38059551	38059610	.	-	.	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
Phchi.S1	AUGUSTUS	start_codon	38059608	38059610	.	-	0	transcript_id "Phchi.S1G596100.t1"; gene_id "Phchi.S1G596100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10106.t1 is derived from g7282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45759692	45761510	.	+	.	Phchi.S1G726500
Phchi.S1	AUGUSTUS	transcript	45759692	45761510	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	start_codon	45759692	45759694	.	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45759692	45759892	0.77	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45759692	45759892	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	intron	45759893	45759979	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45759980	45760556	0.95	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45759980	45760556	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	intron	45760557	45760668	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45760669	45760751	1	+	2	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45760669	45760751	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	intron	45760752	45760836	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45760837	45760947	1	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45760837	45760947	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	intron	45760948	45761031	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45761032	45761175	1	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45761032	45761175	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	intron	45761176	45761261	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45761262	45761324	1	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45761262	45761324	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	intron	45761325	45761411	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	CDS	45761412	45761510	1	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	exon	45761412	45761510	.	+	.	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
Phchi.S1	AUGUSTUS	stop_codon	45761511	45761513	.	+	0	transcript_id "Phchi.S1G726500.t1"; gene_id "Phchi.S1G726500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11144.t1 is derived from g15194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4375234	4376626	.	+	.	Phchi.S4G072600
Phchi.S4	AUGUSTUS	transcript	4375234	4376626	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	start_codon	4375234	4375236	.	+	0	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4375234	4375304	0.6	+	0	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4375234	4375304	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4375305	4375392	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4375393	4375458	1	+	1	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4375393	4375458	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4375459	4375569	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4375570	4375675	1	+	1	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4375570	4375675	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4375676	4375764	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4375765	4375807	1	+	0	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4375765	4375807	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4375808	4375905	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4375906	4375978	1	+	2	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4375906	4375978	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4375979	4376120	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4376121	4376208	1	+	1	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4376121	4376208	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4376209	4376286	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4376287	4376343	1	+	0	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4376287	4376343	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4376344	4376438	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4376439	4376517	1	+	0	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4376439	4376517	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	intron	4376518	4376615	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	CDS	4376616	4376626	1	+	2	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	exon	4376616	4376626	.	+	.	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
Phchi.S4	AUGUSTUS	stop_codon	4376627	4376629	.	+	0	transcript_id "Phchi.S4G072600.t1"; gene_id "Phchi.S4G072600"
# This transcript jg62.t2 is derived from g9844.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg62.t3 is derived from g9844.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg63.t1 is derived from g9845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	319295	321084	.	-	.	Phchi.S6G002200
Phchi.S6	AUGUSTUS	transcript	319295	321084	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	stop_codon	319292	319294	.	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	319295	319300	1	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	319295	319300	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	319301	319385	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	319386	319517	1	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	319386	319517	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	319518	319700	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	319701	319777	0.58	-	2	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	319701	319777	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	319778	319917	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	319918	319951	0.61	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	319918	319951	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	319952	320047	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	320048	320139	1	-	2	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	320048	320139	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	320140	320264	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	320265	320364	1	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	320265	320364	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	320365	320453	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	320454	320558	1	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	320454	320558	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	320559	320666	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	320667	320786	1	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	320667	320786	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	intron	320787	320865	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	CDS	320866	321084	0.48	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	exon	320866	321084	.	-	.	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
Phchi.S6	AUGUSTUS	start_codon	321082	321084	.	-	0	transcript_id "Phchi.S6G002200.t1"; gene_id "Phchi.S6G002200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4775.t1 is derived from g1945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12772896	12776478	.	-	.	Phchi.S1G193400
Phchi.S1	AUGUSTUS	transcript	12772896	12776478	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	stop_codon	12772893	12772895	.	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12772896	12772962	1	-	1	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12772896	12772962	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12772963	12773078	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12773079	12773162	0.95	-	1	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12773079	12773162	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12773163	12773269	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12773270	12773346	1	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12773270	12773346	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12773347	12773498	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12773499	12773594	1	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12773499	12773594	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12773595	12773721	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12773722	12773889	1	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12773722	12773889	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12773890	12773993	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12773994	12774172	1	-	2	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12773994	12774172	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12774173	12774299	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12774300	12774357	1	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12774300	12774357	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12774358	12774478	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12774479	12774634	0.83	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12774479	12774634	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12774635	12774736	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12774737	12774750	0.8	-	2	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12774737	12774750	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12774751	12774821	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12774822	12774858	0.81	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12774822	12774858	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12774859	12774941	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12774942	12775044	1	-	1	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12774942	12775044	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12775045	12775128	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12775129	12775346	0.99	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12775129	12775346	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12775347	12775449	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12775450	12775557	1	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12775450	12775557	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12775558	12775824	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12775825	12775992	1	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12775825	12775992	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12775993	12776132	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12776133	12776268	0.94	-	1	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12776133	12776268	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	intron	12776269	12776392	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	CDS	12776393	12776478	0.57	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	exon	12776393	12776478	.	-	.	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
Phchi.S1	AUGUSTUS	start_codon	12776476	12776478	.	-	0	transcript_id "Phchi.S1G193400.t1"; gene_id "Phchi.S1G193400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9587.t1 is derived from g6763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42801591	42803372	.	+	.	Phchi.S1G674600
Phchi.S1	AUGUSTUS	transcript	42801591	42803372	.	+	.	transcript_id "Phchi.S1G674600.t1"; gene_id "Phchi.S1G674600"
Phchi.S1	AUGUSTUS	start_codon	42801591	42801593	.	+	0	transcript_id "Phchi.S1G674600.t1"; gene_id "Phchi.S1G674600"
Phchi.S1	AUGUSTUS	CDS	42801591	42803372	0.5	+	0	transcript_id "Phchi.S1G674600.t1"; gene_id "Phchi.S1G674600"
Phchi.S1	AUGUSTUS	exon	42801591	42803372	.	+	.	transcript_id "Phchi.S1G674600.t1"; gene_id "Phchi.S1G674600"
Phchi.S1	AUGUSTUS	stop_codon	42803373	42803375	.	+	0	transcript_id "Phchi.S1G674600.t1"; gene_id "Phchi.S1G674600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9673.t1 is derived from g6849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43226112	43227260	.	+	.	Phchi.S1G683200
Phchi.S1	AUGUSTUS	transcript	43226112	43227260	.	+	.	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	start_codon	43226112	43226114	.	+	0	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	CDS	43226112	43226287	0.63	+	0	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	exon	43226112	43226287	.	+	.	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	intron	43226288	43226370	.	+	.	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	CDS	43226371	43226399	0.97	+	1	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	exon	43226371	43226399	.	+	.	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	intron	43226400	43226547	.	+	.	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	CDS	43226548	43227260	0.47	+	2	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	exon	43226548	43227260	.	+	.	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
Phchi.S1	AUGUSTUS	stop_codon	43227261	43227263	.	+	0	transcript_id "Phchi.S1G683200.t1"; gene_id "Phchi.S1G683200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6582.t1 is derived from g3754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23848225	23849134	.	-	.	Phchi.S1G374100
Phchi.S1	AUGUSTUS	transcript	23848225	23849134	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	stop_codon	23848222	23848224	.	-	0	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	CDS	23848225	23848323	0.43	-	0	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	exon	23848225	23848323	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	intron	23848324	23848437	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	CDS	23848438	23848503	0.84	-	0	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	exon	23848438	23848503	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	intron	23848504	23848600	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	CDS	23848601	23848641	0.67	-	2	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	exon	23848601	23848641	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	intron	23848642	23849052	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	CDS	23849053	23849134	0.63	-	0	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	exon	23849053	23849134	.	-	.	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
Phchi.S1	AUGUSTUS	start_codon	23849132	23849134	.	-	0	transcript_id "Phchi.S1G374100.t1"; gene_id "Phchi.S1G374100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1364.t1 is derived from g16000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C81	AUGUSTUS	gene	33822	35589	.	-	.	Phchi.C81G000600
Phchi.C81	AUGUSTUS	transcript	33822	35589	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	stop_codon	33819	33821	.	-	0	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	CDS	33822	34077	1	-	1	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	exon	33822	34077	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	intron	34078	34178	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	CDS	34179	34396	0.99	-	0	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	exon	34179	34396	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	intron	34397	34476	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	CDS	34477	34968	1	-	0	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	exon	34477	34968	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	intron	34969	35085	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	CDS	35086	35589	0.98	-	0	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	exon	35086	35589	.	-	.	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
Phchi.C81	AUGUSTUS	start_codon	35587	35589	.	-	0	transcript_id "Phchi.C81G000600.t1"; gene_id "Phchi.C81G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13339.t1 is derived from g11805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6169030	6169596	.	+	.	Phchi.S3G065800
Phchi.S3	AUGUSTUS	transcript	6169030	6169596	.	+	.	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	start_codon	6169030	6169032	.	+	0	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	CDS	6169030	6169146	0.95	+	0	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	exon	6169030	6169146	.	+	.	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	intron	6169147	6169512	.	+	.	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	CDS	6169513	6169596	1	+	0	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	exon	6169513	6169596	.	+	.	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
Phchi.S3	AUGUSTUS	stop_codon	6169597	6169599	.	+	0	transcript_id "Phchi.S3G065800.t1"; gene_id "Phchi.S3G065800"
# This transcript jg10943.t2 is derived from g14993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10944.t1 is derived from g14994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3217700	3218781	.	-	.	Phchi.S4G052600
Phchi.S4	AUGUSTUS	transcript	3217700	3218781	.	-	.	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	stop_codon	3217697	3217699	.	-	0	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	CDS	3217700	3218044	1	-	0	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	exon	3217700	3218044	.	-	.	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	intron	3218045	3218133	.	-	.	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	CDS	3218134	3218781	0.99	-	0	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	exon	3218134	3218781	.	-	.	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
Phchi.S4	AUGUSTUS	start_codon	3218779	3218781	.	-	0	transcript_id "Phchi.S4G052600.t1"; gene_id "Phchi.S4G052600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3212.t1 is derived from g381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2264548	2265797	.	-	.	Phchi.S1G037100
Phchi.S1	AUGUSTUS	transcript	2264548	2265797	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	stop_codon	2264545	2264547	.	-	0	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	CDS	2264548	2264628	0.98	-	0	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	exon	2264548	2264628	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	intron	2264629	2264719	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	CDS	2264720	2264920	1	-	0	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	exon	2264720	2264920	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	intron	2264921	2265015	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	CDS	2265016	2265137	1	-	2	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	exon	2265016	2265137	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	intron	2265138	2265222	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	CDS	2265223	2265325	1	-	0	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	exon	2265223	2265325	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	intron	2265326	2265435	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	CDS	2265436	2265512	1	-	2	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	exon	2265436	2265512	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	intron	2265513	2265685	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	CDS	2265686	2265797	1	-	0	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	exon	2265686	2265797	.	-	.	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
Phchi.S1	AUGUSTUS	start_codon	2265795	2265797	.	-	0	transcript_id "Phchi.S1G037100.t1"; gene_id "Phchi.S1G037100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15384.t1 is derived from g13852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18748310	18751140	.	+	.	Phchi.S3G270300
Phchi.S3	AUGUSTUS	transcript	18748310	18751140	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	start_codon	18748310	18748312	.	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18748310	18748344	0.35	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18748310	18748344	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18748345	18748539	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18748540	18748607	0.39	+	1	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18748540	18748607	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18748608	18748712	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18748713	18750010	0.43	+	2	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18748713	18750010	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18750011	18750163	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18750164	18750340	1	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18750164	18750340	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18750341	18750443	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18750444	18750509	1	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18750444	18750509	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18750510	18750602	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18750603	18750668	1	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18750603	18750668	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18750669	18750785	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18750786	18750836	1	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18750786	18750836	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	intron	18750837	18750975	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	CDS	18750976	18751140	1	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	exon	18750976	18751140	.	+	.	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
Phchi.S3	AUGUSTUS	stop_codon	18751141	18751143	.	+	0	transcript_id "Phchi.S3G270300.t1"; gene_id "Phchi.S3G270300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7348.t1 is derived from g4520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28645830	28646526	.	+	.	Phchi.S1G450700
Phchi.S1	AUGUSTUS	transcript	28645830	28646526	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	start_codon	28645830	28645832	.	+	0	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	CDS	28645830	28645832	0.98	+	0	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	exon	28645830	28645832	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	intron	28645833	28645947	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	CDS	28645948	28646035	1	+	0	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	exon	28645948	28646035	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	intron	28646036	28646157	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	CDS	28646158	28646291	0.96	+	2	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	exon	28646158	28646291	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	intron	28646292	28646406	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	CDS	28646407	28646526	0.64	+	0	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	exon	28646407	28646526	.	+	.	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
Phchi.S1	AUGUSTUS	stop_codon	28646527	28646529	.	+	0	transcript_id "Phchi.S1G450700.t1"; gene_id "Phchi.S1G450700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1909.t1 is derived from g8829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3819790	3821571	.	-	.	Phchi.S5G051800
Phchi.S5	AUGUSTUS	transcript	3819790	3820623	.	-	.	transcript_id "Phchi.S5G051800.t1"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	stop_codon	3819787	3819789	.	-	0	transcript_id "Phchi.S5G051800.t1"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	CDS	3819790	3820623	0.79	-	0	transcript_id "Phchi.S5G051800.t1"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	exon	3819790	3820623	.	-	.	transcript_id "Phchi.S5G051800.t1"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	start_codon	3820621	3820623	.	-	0	transcript_id "Phchi.S5G051800.t1"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	transcript	3819790	3821571	.	-	.	transcript_id "Phchi.S5G051800.t2"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	stop_codon	3819787	3819789	.	-	0	transcript_id "Phchi.S5G051800.t2"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	CDS	3819790	3821571	0.34	-	0	transcript_id "Phchi.S5G051800.t2"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	exon	3819790	3821571	.	-	.	transcript_id "Phchi.S5G051800.t2"; gene_id "Phchi.S5G051800"
Phchi.S5	AUGUSTUS	start_codon	3821569	3821571	.	-	0	transcript_id "Phchi.S5G051800.t2"; gene_id "Phchi.S5G051800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9251.t1 is derived from g6426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40598030	40598787	.	+	.	Phchi.S1G641000
Phchi.S1	AUGUSTUS	transcript	40598030	40598787	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	start_codon	40598030	40598032	.	+	0	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	CDS	40598030	40598080	0.99	+	0	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	exon	40598030	40598080	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	intron	40598081	40598195	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	CDS	40598196	40598337	1	+	0	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	exon	40598196	40598337	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	intron	40598338	40598433	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	CDS	40598434	40598700	0.73	+	2	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	exon	40598434	40598700	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	intron	40598701	40598776	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	CDS	40598777	40598787	0.73	+	2	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	exon	40598777	40598787	.	+	.	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
Phchi.S1	AUGUSTUS	stop_codon	40598788	40598790	.	+	0	transcript_id "Phchi.S1G641000.t1"; gene_id "Phchi.S1G641000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11501.t1 is derived from g15551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6745607	6747080	.	+	.	Phchi.S4G108300
Phchi.S4	AUGUSTUS	transcript	6745607	6747080	.	+	.	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	start_codon	6745607	6745609	.	+	0	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	CDS	6745607	6746304	0.91	+	0	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	exon	6745607	6746304	.	+	.	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	intron	6746305	6746539	.	+	.	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	CDS	6746540	6747080	0.87	+	1	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	exon	6746540	6747080	.	+	.	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
Phchi.S4	AUGUSTUS	stop_codon	6747081	6747083	.	+	0	transcript_id "Phchi.S4G108300.t1"; gene_id "Phchi.S4G108300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg553.t1 is derived from g10335.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4021558	4024077	.	+	.	Phchi.S6G051200
Phchi.S6	AUGUSTUS	transcript	4021558	4024077	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	start_codon	4021558	4021560	.	+	0	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4021558	4021975	1	+	0	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4021558	4021975	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4021976	4022058	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4022059	4023301	1	+	2	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4022059	4023301	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4023302	4023389	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4023390	4023616	0.93	+	1	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4023390	4023616	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4023617	4023710	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4023711	4023759	0.93	+	2	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4023711	4023759	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4023760	4023983	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4023984	4024077	0.99	+	1	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4023984	4024077	.	+	.	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	stop_codon	4024078	4024080	.	+	0	transcript_id "Phchi.S6G051200.t1"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	transcript	4021558	4024077	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	start_codon	4021558	4021560	.	+	0	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4021558	4021975	1	+	0	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4021558	4021975	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4021976	4022058	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4022059	4023301	1	+	2	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4022059	4023301	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4023302	4023389	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4023390	4023563	0.77	+	1	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4023390	4023563	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4023564	4023669	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4023670	4023710	0.75	+	1	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4023670	4023710	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	intron	4023711	4023934	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	CDS	4023935	4024077	0.77	+	2	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	exon	4023935	4024077	.	+	.	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
Phchi.S6	AUGUSTUS	stop_codon	4024078	4024080	.	+	0	transcript_id "Phchi.S6G051200.t2"; gene_id "Phchi.S6G051200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1224.t1 is derived from g11007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8464095	8469915	.	-	.	Phchi.S6G118300
Phchi.S6	AUGUSTUS	transcript	8464095	8469915	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	stop_codon	8464092	8464094	.	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8464095	8464153	1	-	2	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8464095	8464153	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8464154	8464238	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8464239	8464345	0.91	-	1	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8464239	8464345	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8464346	8464595	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8464596	8464681	0.87	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8464596	8464681	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8464682	8464857	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8464858	8464929	1	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8464858	8464929	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8464930	8465057	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8465058	8465455	1	-	2	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8465058	8465455	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8465456	8465551	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8465552	8465659	0.49	-	2	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8465552	8465659	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8465660	8465742	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8465743	8465761	0.39	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8465743	8465761	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8465762	8465866	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8465867	8465920	0.49	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8465867	8465920	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8465921	8466086	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8466087	8466252	1	-	1	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8466087	8466252	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8466253	8466492	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8466493	8466586	1	-	2	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8466493	8466586	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8466587	8466676	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8466677	8466926	1	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8466677	8466926	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8466927	8467103	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8467104	8467382	0.98	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8467104	8467382	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8467383	8467504	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8467505	8467568	1	-	1	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8467505	8467568	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8467569	8467715	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8467716	8467828	1	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8467716	8467828	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8467829	8467932	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8467933	8468127	0.95	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8467933	8468127	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8468128	8468255	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8468256	8468391	1	-	1	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8468256	8468391	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8468392	8468473	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8468474	8468599	1	-	1	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8468474	8468599	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8468600	8468715	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8468716	8468822	1	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8468716	8468822	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8468823	8468948	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8468949	8469025	1	-	2	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8468949	8469025	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8469026	8469113	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8469114	8469258	1	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8469114	8469258	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8469259	8469339	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8469340	8469382	1	-	1	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8469340	8469382	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8469383	8469544	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8469545	8469579	1	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8469545	8469579	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	intron	8469580	8469690	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	CDS	8469691	8469915	0.53	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	exon	8469691	8469915	.	-	.	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
Phchi.S6	AUGUSTUS	start_codon	8469913	8469915	.	-	0	transcript_id "Phchi.S6G118300.t1"; gene_id "Phchi.S6G118300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3011.t1 is derived from g180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1117903	1119963	.	+	.	Phchi.S1G017000
Phchi.S1	AUGUSTUS	transcript	1117903	1119963	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	start_codon	1117903	1117905	.	+	0	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	CDS	1117903	1119079	0.88	+	0	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	exon	1117903	1119079	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	intron	1119080	1119179	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	CDS	1119180	1119223	0.74	+	2	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	exon	1119180	1119223	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	intron	1119224	1119387	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	CDS	1119388	1119771	0.9	+	0	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	exon	1119388	1119771	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	intron	1119772	1119942	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	CDS	1119943	1119963	0.99	+	0	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	exon	1119943	1119963	.	+	.	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
Phchi.S1	AUGUSTUS	stop_codon	1119964	1119966	.	+	0	transcript_id "Phchi.S1G017000.t1"; gene_id "Phchi.S1G017000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10469.t1 is derived from g14518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	542553	543413	.	+	.	Phchi.S4G005100
Phchi.S4	AUGUSTUS	transcript	542553	543413	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	start_codon	542553	542555	.	+	0	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	CDS	542553	542565	0.73	+	0	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	exon	542553	542565	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	intron	542566	542669	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	CDS	542670	542954	0.73	+	2	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	exon	542670	542954	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	intron	542955	543041	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	CDS	543042	543083	1	+	2	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	exon	543042	543083	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	intron	543084	543333	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	CDS	543334	543413	1	+	2	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	exon	543334	543413	.	+	.	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
Phchi.S4	AUGUSTUS	stop_codon	543414	543416	.	+	0	transcript_id "Phchi.S4G005100.t1"; gene_id "Phchi.S4G005100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2498.t1 is derived from g9418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6978186	6980614	.	-	.	Phchi.S5G110700
Phchi.S5	AUGUSTUS	transcript	6978186	6980614	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	stop_codon	6978183	6978185	.	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6978186	6978362	0.99	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6978186	6978362	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6978363	6978541	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6978542	6978644	1	-	1	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6978542	6978644	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6978645	6979224	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6979225	6979341	1	-	1	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6979225	6979341	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6979342	6979453	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6979454	6979575	1	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6979454	6979575	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6979576	6979680	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6979681	6979770	1	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6979681	6979770	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6979771	6979907	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6979908	6979960	1	-	2	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6979908	6979960	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6979961	6980071	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6980072	6980108	0.69	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6980072	6980108	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6980109	6980221	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6980222	6980240	0.65	-	1	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6980222	6980240	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	intron	6980241	6980561	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	CDS	6980562	6980614	0.92	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	exon	6980562	6980614	.	-	.	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
Phchi.S5	AUGUSTUS	start_codon	6980612	6980614	.	-	0	transcript_id "Phchi.S5G110700.t1"; gene_id "Phchi.S5G110700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14254.t1 is derived from g12721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11776851	11777713	.	+	.	Phchi.S3G157300
Phchi.S3	AUGUSTUS	transcript	11776851	11777713	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	start_codon	11776851	11776853	.	+	0	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	CDS	11776851	11777009	0.55	+	0	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	exon	11776851	11777009	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	intron	11777010	11777162	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	CDS	11777163	11777184	0.39	+	0	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	exon	11777163	11777184	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	intron	11777185	11777493	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	CDS	11777494	11777576	0.78	+	2	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	exon	11777494	11777576	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	intron	11777577	11777707	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	CDS	11777708	11777713	0.75	+	0	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	exon	11777708	11777713	.	+	.	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
Phchi.S3	AUGUSTUS	stop_codon	11777714	11777716	.	+	0	transcript_id "Phchi.S3G157300.t1"; gene_id "Phchi.S3G157300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4834.t1 is derived from g2004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13047872	13048327	.	+	.	Phchi.S1G199300
Phchi.S1	AUGUSTUS	transcript	13047872	13048327	.	+	.	transcript_id "Phchi.S1G199300.t1"; gene_id "Phchi.S1G199300"
Phchi.S1	AUGUSTUS	start_codon	13047872	13047874	.	+	0	transcript_id "Phchi.S1G199300.t1"; gene_id "Phchi.S1G199300"
Phchi.S1	AUGUSTUS	CDS	13047872	13048327	0.2	+	0	transcript_id "Phchi.S1G199300.t1"; gene_id "Phchi.S1G199300"
Phchi.S1	AUGUSTUS	exon	13047872	13048327	.	+	.	transcript_id "Phchi.S1G199300.t1"; gene_id "Phchi.S1G199300"
Phchi.S1	AUGUSTUS	stop_codon	13048328	13048330	.	+	0	transcript_id "Phchi.S1G199300.t1"; gene_id "Phchi.S1G199300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11807.t1 is derived from g15859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8224018	8225122	.	+	.	Phchi.S4G138900
Phchi.S4	AUGUSTUS	transcript	8224018	8225122	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	start_codon	8224018	8224020	.	+	0	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	CDS	8224018	8224056	1	+	0	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	exon	8224018	8224056	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	intron	8224057	8224353	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	CDS	8224354	8224665	1	+	0	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	exon	8224354	8224665	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	intron	8224666	8224740	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	CDS	8224741	8224897	1	+	0	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	exon	8224741	8224897	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	intron	8224898	8224994	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	CDS	8224995	8225122	1	+	2	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	exon	8224995	8225122	.	+	.	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
Phchi.S4	AUGUSTUS	stop_codon	8225123	8225125	.	+	0	transcript_id "Phchi.S4G138900.t1"; gene_id "Phchi.S4G138900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1670.t1 is derived from g8589.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2328593	2329669	.	+	.	Phchi.S5G027900
Phchi.S5	AUGUSTUS	transcript	2328593	2329669	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	start_codon	2328593	2328595	.	+	0	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2328593	2328803	0.97	+	0	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2328593	2328803	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2328804	2328900	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2328901	2329052	1	+	2	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2328901	2329052	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2329053	2329148	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2329149	2329180	0.98	+	0	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2329149	2329180	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2329181	2329256	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2329257	2329336	0.98	+	1	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2329257	2329336	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2329337	2329430	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2329431	2329669	1	+	2	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2329431	2329669	.	+	.	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	stop_codon	2329670	2329672	.	+	0	transcript_id "Phchi.S5G027900.t1"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	transcript	2328593	2329669	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	start_codon	2328593	2328595	.	+	0	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2328593	2328803	0.97	+	0	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2328593	2328803	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2328804	2328900	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2328901	2329052	0.91	+	2	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2328901	2329052	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2329053	2329161	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2329162	2329336	0.92	+	0	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2329162	2329336	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	intron	2329337	2329430	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	CDS	2329431	2329669	0.99	+	2	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	exon	2329431	2329669	.	+	.	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
Phchi.S5	AUGUSTUS	stop_codon	2329670	2329672	.	+	0	transcript_id "Phchi.S5G027900.t2"; gene_id "Phchi.S5G027900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15683.t1 is derived from g14152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20638716	20639464	.	+	.	Phchi.S3G300200
Phchi.S3	AUGUSTUS	transcript	20638716	20639464	.	+	.	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	start_codon	20638716	20638718	.	+	0	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	CDS	20638716	20638913	0.34	+	0	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	exon	20638716	20638913	.	+	.	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	intron	20638914	20639035	.	+	.	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	CDS	20639036	20639464	0.95	+	0	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	exon	20639036	20639464	.	+	.	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
Phchi.S3	AUGUSTUS	stop_codon	20639465	20639467	.	+	0	transcript_id "Phchi.S3G300200.t1"; gene_id "Phchi.S3G300200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4489.t1 is derived from g1659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10776623	10779399	.	+	.	Phchi.S1G164800
Phchi.S1	AUGUSTUS	transcript	10776623	10779399	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	start_codon	10776623	10776625	.	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10776623	10776657	0.7	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10776623	10776657	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10776658	10777012	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10777013	10777066	0.7	+	1	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10777013	10777066	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10777067	10777158	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10777159	10777235	0.7	+	1	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10777159	10777235	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10777236	10777323	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10777324	10777382	1	+	2	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10777324	10777382	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10777383	10777475	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10777476	10777568	1	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10777476	10777568	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10777569	10777757	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10777758	10777850	1	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10777758	10777850	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10777851	10778130	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10778131	10778227	1	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10778131	10778227	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10778228	10778362	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10778363	10778586	0.64	+	2	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10778363	10778586	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10778587	10778686	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10778687	10778727	1	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10778687	10778727	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10778728	10778827	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10778828	10778895	1	+	1	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10778828	10778895	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10778896	10778992	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10778993	10779049	1	+	2	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10778993	10779049	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10779050	10779142	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10779143	10779260	1	+	2	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10779143	10779260	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	intron	10779261	10779359	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	CDS	10779360	10779399	1	+	1	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	exon	10779360	10779399	.	+	.	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
Phchi.S1	AUGUSTUS	stop_codon	10779400	10779402	.	+	0	transcript_id "Phchi.S1G164800.t1"; gene_id "Phchi.S1G164800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1304.t1 is derived from g11087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8918106	8918507	.	+	.	Phchi.S6G126300
Phchi.S6	AUGUSTUS	transcript	8918106	8918507	.	+	.	transcript_id "Phchi.S6G126300.t1"; gene_id "Phchi.S6G126300"
Phchi.S6	AUGUSTUS	start_codon	8918106	8918108	.	+	0	transcript_id "Phchi.S6G126300.t1"; gene_id "Phchi.S6G126300"
Phchi.S6	AUGUSTUS	CDS	8918106	8918507	0.63	+	0	transcript_id "Phchi.S6G126300.t1"; gene_id "Phchi.S6G126300"
Phchi.S6	AUGUSTUS	exon	8918106	8918507	.	+	.	transcript_id "Phchi.S6G126300.t1"; gene_id "Phchi.S6G126300"
Phchi.S6	AUGUSTUS	stop_codon	8918508	8918510	.	+	0	transcript_id "Phchi.S6G126300.t1"; gene_id "Phchi.S6G126300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8994.t1 is derived from g6169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39027851	39029251	.	+	.	Phchi.S1G615300
Phchi.S1	AUGUSTUS	transcript	39027851	39029251	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	start_codon	39027851	39027853	.	+	0	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	CDS	39027851	39028102	0.63	+	0	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	exon	39027851	39028102	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	intron	39028103	39028198	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	CDS	39028199	39028439	1	+	0	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	exon	39028199	39028439	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	intron	39028440	39028571	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	CDS	39028572	39028721	1	+	2	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	exon	39028572	39028721	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	intron	39028722	39028832	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	CDS	39028833	39028935	0.98	+	2	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	exon	39028833	39028935	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	intron	39028936	39029015	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	CDS	39029016	39029130	0.98	+	1	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	exon	39029016	39029130	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	intron	39029131	39029233	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	CDS	39029234	39029251	0.94	+	0	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	exon	39029234	39029251	.	+	.	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
Phchi.S1	AUGUSTUS	stop_codon	39029252	39029254	.	+	0	transcript_id "Phchi.S1G615300.t1"; gene_id "Phchi.S1G615300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1323.t1 is derived from g11106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9021083	9023447	.	+	.	Phchi.S6G128200
Phchi.S6	AUGUSTUS	transcript	9021083	9023447	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	start_codon	9021083	9021085	.	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9021083	9021344	0.92	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9021083	9021344	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9021345	9021430	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9021431	9021507	1	+	2	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9021431	9021507	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9021508	9021608	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9021609	9021719	1	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9021609	9021719	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9021720	9021798	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9021799	9021867	0.91	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9021799	9021867	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9021868	9022138	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9022139	9022177	0.89	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9022139	9022177	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9022178	9022272	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9022273	9022374	1	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9022273	9022374	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9022375	9022508	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9022509	9022591	0.94	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9022509	9022591	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9022592	9022703	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9022704	9022785	1	+	1	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9022704	9022785	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9022786	9022906	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9022907	9023050	1	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9022907	9023050	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9023051	9023125	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9023126	9023224	1	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9023126	9023224	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	intron	9023225	9023342	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	CDS	9023343	9023447	1	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	exon	9023343	9023447	.	+	.	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
Phchi.S6	AUGUSTUS	stop_codon	9023448	9023450	.	+	0	transcript_id "Phchi.S6G128200.t1"; gene_id "Phchi.S6G128200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12289.t1 is derived from g7965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8850258	8854999	.	+	.	Phchi.S2G036900
Phchi.S2	AUGUSTUS	transcript	8850258	8854999	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	start_codon	8850258	8850260	.	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8850258	8851521	0.25	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8850258	8851521	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8851522	8851663	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8851664	8851772	0.37	+	2	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8851664	8851772	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8851773	8851858	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8851859	8851993	0.79	+	1	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8851859	8851993	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8851994	8852170	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8852171	8852321	0.47	+	1	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8852171	8852321	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8852322	8852457	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8852458	8852751	1	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8852458	8852751	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8852752	8852843	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8852844	8853126	0.97	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8852844	8853126	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8853127	8853263	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8853264	8853373	1	+	2	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8853264	8853373	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8853374	8853457	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8853458	8853478	1	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8853458	8853478	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8853479	8853561	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8853562	8853682	0.65	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8853562	8853682	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8853683	8853766	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8853767	8853844	0.69	+	2	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8853767	8853844	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8853845	8853931	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8853932	8854047	0.99	+	2	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8853932	8854047	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8854048	8854142	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8854143	8854271	1	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8854143	8854271	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8854272	8854352	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8854353	8854442	1	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8854353	8854442	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	intron	8854443	8854561	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	CDS	8854562	8854999	0.94	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	exon	8854562	8854999	.	+	.	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
Phchi.S2	AUGUSTUS	stop_codon	8855000	8855002	.	+	0	transcript_id "Phchi.S2G036900.t1"; gene_id "Phchi.S2G036900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1257.t1 is derived from g11040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8664160	8664886	.	+	.	Phchi.S6G121600
Phchi.S6	AUGUSTUS	transcript	8664160	8664886	.	+	.	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	start_codon	8664160	8664162	.	+	0	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	CDS	8664160	8664652	0.96	+	0	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	exon	8664160	8664652	.	+	.	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	intron	8664653	8664794	.	+	.	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	CDS	8664795	8664886	0.82	+	2	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	exon	8664795	8664886	.	+	.	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
Phchi.S6	AUGUSTUS	stop_codon	8664887	8664889	.	+	0	transcript_id "Phchi.S6G121600.t1"; gene_id "Phchi.S6G121600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2631.t1 is derived from g9551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7859537	7859935	.	-	.	Phchi.S5G124000
Phchi.S5	AUGUSTUS	transcript	7859537	7859935	.	-	.	transcript_id "Phchi.S5G124000.t1"; gene_id "Phchi.S5G124000"
Phchi.S5	AUGUSTUS	stop_codon	7859534	7859536	.	-	0	transcript_id "Phchi.S5G124000.t1"; gene_id "Phchi.S5G124000"
Phchi.S5	AUGUSTUS	CDS	7859537	7859935	0.44	-	0	transcript_id "Phchi.S5G124000.t1"; gene_id "Phchi.S5G124000"
Phchi.S5	AUGUSTUS	exon	7859537	7859935	.	-	.	transcript_id "Phchi.S5G124000.t1"; gene_id "Phchi.S5G124000"
Phchi.S5	AUGUSTUS	start_codon	7859933	7859935	.	-	0	transcript_id "Phchi.S5G124000.t1"; gene_id "Phchi.S5G124000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8443.t1 is derived from g5618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35952794	35953475	.	+	.	Phchi.S1G560200
Phchi.S1	AUGUSTUS	transcript	35952794	35953475	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	start_codon	35952794	35952796	.	+	0	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	CDS	35952794	35952802	0.33	+	0	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	exon	35952794	35952802	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	intron	35952803	35952983	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	CDS	35952984	35953059	0.79	+	0	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	exon	35952984	35953059	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	intron	35953060	35953266	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	CDS	35953267	35953321	0.85	+	2	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	exon	35953267	35953321	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	intron	35953322	35953414	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	CDS	35953415	35953475	0.99	+	1	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	exon	35953415	35953475	.	+	.	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
Phchi.S1	AUGUSTUS	stop_codon	35953476	35953478	.	+	0	transcript_id "Phchi.S1G560200.t1"; gene_id "Phchi.S1G560200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7547.t1 is derived from g4721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29985956	29987706	.	+	.	Phchi.S1G470600
Phchi.S1	AUGUSTUS	transcript	29985956	29987706	.	+	.	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	start_codon	29985956	29985958	.	+	0	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	CDS	29985956	29986878	0.64	+	0	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	exon	29985956	29986878	.	+	.	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	intron	29986879	29987021	.	+	.	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	CDS	29987022	29987706	0.56	+	1	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	exon	29987022	29987706	.	+	.	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
Phchi.S1	AUGUSTUS	stop_codon	29987707	29987709	.	+	0	transcript_id "Phchi.S1G470600.t1"; gene_id "Phchi.S1G470600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10588.t1 is derived from g14638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1073544	1080453	.	+	.	Phchi.S4G017000
Phchi.S4	AUGUSTUS	transcript	1073544	1080453	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	start_codon	1073544	1073546	.	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1073544	1073878	0.86	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1073544	1073878	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1073879	1074260	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1074261	1074358	1	+	1	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1074261	1074358	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1074359	1074450	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1074451	1074540	1	+	2	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1074451	1074540	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1074541	1074644	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1074645	1074697	1	+	2	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1074645	1074697	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1074698	1074851	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1074852	1074917	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1074852	1074917	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1074918	1074993	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1074994	1075047	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1074994	1075047	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1075048	1075180	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1075181	1075240	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1075181	1075240	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1075241	1075350	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1075351	1075429	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1075351	1075429	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1075430	1075523	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1075524	1075591	1	+	2	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1075524	1075591	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1075592	1075672	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1075673	1075735	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1075673	1075735	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1075736	1075883	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1075884	1075988	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1075884	1075988	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1075989	1076172	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1076173	1076277	0.99	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1076173	1076277	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1076278	1076383	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1076384	1076491	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1076384	1076491	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1076492	1076589	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1076590	1076739	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1076590	1076739	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1076740	1076869	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1076870	1077052	0.96	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1076870	1077052	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1077053	1077153	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1077154	1077336	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1077154	1077336	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1077337	1077432	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1077433	1077672	0.54	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1077433	1077672	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1077673	1077789	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1077790	1077930	0.58	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1077790	1077930	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1077931	1078039	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1078040	1078165	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1078040	1078165	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1078166	1078254	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1078255	1078305	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1078255	1078305	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1078306	1078415	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1078416	1078463	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1078416	1078463	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1078464	1078546	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1078547	1078666	0.98	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1078547	1078666	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1078667	1078806	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1078807	1078824	0.96	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1078807	1078824	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1078825	1078963	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1078964	1079737	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1078964	1079737	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1079738	1079925	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1079926	1080015	1	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1079926	1080015	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1080016	1080104	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1080105	1080233	0.29	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1080105	1080233	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	intron	1080234	1080399	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	CDS	1080400	1080453	0.62	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	exon	1080400	1080453	.	+	.	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
Phchi.S4	AUGUSTUS	stop_codon	1080454	1080456	.	+	0	transcript_id "Phchi.S4G017000.t1"; gene_id "Phchi.S4G017000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3247.t1 is derived from g416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2423659	2425359	.	+	.	Phchi.S1G040600
Phchi.S1	AUGUSTUS	transcript	2423659	2425359	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	start_codon	2423659	2423661	.	+	0	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	CDS	2423659	2424846	0.73	+	0	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	exon	2423659	2424846	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	intron	2424847	2424934	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	CDS	2424935	2425047	0.74	+	0	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	exon	2424935	2425047	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	intron	2425048	2425170	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	CDS	2425171	2425211	0.53	+	1	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	exon	2425171	2425211	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	intron	2425212	2425306	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	CDS	2425307	2425359	0.75	+	2	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	exon	2425307	2425359	.	+	.	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
Phchi.S1	AUGUSTUS	stop_codon	2425360	2425362	.	+	0	transcript_id "Phchi.S1G040600.t1"; gene_id "Phchi.S1G040600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15079.t1 is derived from g13547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16938432	16939673	.	-	.	Phchi.S3G239800
Phchi.S3	AUGUSTUS	transcript	16938432	16939673	.	-	.	transcript_id "Phchi.S3G239800.t1"; gene_id "Phchi.S3G239800"
Phchi.S3	AUGUSTUS	stop_codon	16938429	16938431	.	-	0	transcript_id "Phchi.S3G239800.t1"; gene_id "Phchi.S3G239800"
Phchi.S3	AUGUSTUS	CDS	16938432	16939673	0.99	-	0	transcript_id "Phchi.S3G239800.t1"; gene_id "Phchi.S3G239800"
Phchi.S3	AUGUSTUS	exon	16938432	16939673	.	-	.	transcript_id "Phchi.S3G239800.t1"; gene_id "Phchi.S3G239800"
Phchi.S3	AUGUSTUS	start_codon	16939671	16939673	.	-	0	transcript_id "Phchi.S3G239800.t1"; gene_id "Phchi.S3G239800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6731.t1 is derived from g3903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24775766	24777808	.	-	.	Phchi.S1G389000
Phchi.S1	AUGUSTUS	transcript	24775766	24777808	.	-	.	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	stop_codon	24775763	24775765	.	-	0	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	CDS	24775766	24776638	0.9	-	0	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	exon	24775766	24776638	.	-	.	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	intron	24776639	24776743	.	-	.	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	CDS	24776744	24777318	0.87	-	2	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	exon	24776744	24777318	.	-	.	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	intron	24777319	24777423	.	-	.	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	CDS	24777424	24777808	0.45	-	0	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	exon	24777424	24777808	.	-	.	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
Phchi.S1	AUGUSTUS	start_codon	24777806	24777808	.	-	0	transcript_id "Phchi.S1G389000.t1"; gene_id "Phchi.S1G389000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg561.t1 is derived from g10343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4055235	4058767	.	-	.	Phchi.S6G052000
Phchi.S6	AUGUSTUS	transcript	4055235	4058767	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	stop_codon	4055232	4055234	.	-	0	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4055235	4055259	0.68	-	1	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4055235	4055259	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4055260	4055381	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4055382	4055630	0.51	-	1	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4055382	4055630	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4055631	4055801	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4055802	4056561	0.27	-	2	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4055802	4056561	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4056562	4056659	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4056660	4058022	0.38	-	0	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4056660	4058022	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4058023	4058111	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4058112	4058194	1	-	2	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4058112	4058194	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4058195	4058291	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4058292	4058388	1	-	0	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4058292	4058388	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4058389	4058483	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4058484	4058563	1	-	2	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4058484	4058563	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	intron	4058564	4058652	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	CDS	4058653	4058767	0.96	-	0	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	exon	4058653	4058767	.	-	.	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
Phchi.S6	AUGUSTUS	start_codon	4058765	4058767	.	-	0	transcript_id "Phchi.S6G052000.t1"; gene_id "Phchi.S6G052000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7239.t1 is derived from g4411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27794421	27795801	.	-	.	Phchi.S1G439800
Phchi.S1	AUGUSTUS	transcript	27794421	27795801	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	stop_codon	27794418	27794420	.	-	0	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27794421	27794458	1	-	2	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27794421	27794458	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	intron	27794459	27794558	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27794559	27794607	1	-	0	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27794559	27794607	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	intron	27794608	27794719	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27794720	27794780	1	-	1	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27794720	27794780	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	intron	27794781	27794858	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27794859	27794983	0.99	-	0	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27794859	27794983	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	intron	27794984	27795085	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27795086	27795252	1	-	2	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27795086	27795252	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	intron	27795253	27795346	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27795347	27795563	0.98	-	0	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27795347	27795563	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	intron	27795564	27795672	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	CDS	27795673	27795801	0.99	-	0	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	exon	27795673	27795801	.	-	.	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
Phchi.S1	AUGUSTUS	start_codon	27795799	27795801	.	-	0	transcript_id "Phchi.S1G439800.t1"; gene_id "Phchi.S1G439800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14892.t1 is derived from g13360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15302858	15304442	.	+	.	Phchi.S3G221100
Phchi.S3	AUGUSTUS	transcript	15302858	15304442	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	start_codon	15302858	15302860	.	+	0	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	CDS	15302858	15303668	0.95	+	0	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	exon	15302858	15303668	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	intron	15303669	15303808	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	CDS	15303809	15304040	0.44	+	2	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	exon	15303809	15304040	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	intron	15304041	15304206	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	CDS	15304207	15304236	0.49	+	1	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	exon	15304207	15304236	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	intron	15304237	15304405	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	CDS	15304406	15304442	0.5	+	1	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	exon	15304406	15304442	.	+	.	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
Phchi.S3	AUGUSTUS	stop_codon	15304443	15304445	.	+	0	transcript_id "Phchi.S3G221100.t1"; gene_id "Phchi.S3G221100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13478.t1 is derived from g11945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7085522	7086257	.	-	.	Phchi.S3G079700
Phchi.S3	AUGUSTUS	transcript	7085522	7086257	.	-	.	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	stop_codon	7085519	7085521	.	-	0	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	CDS	7085522	7085628	0.68	-	2	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	exon	7085522	7085628	.	-	.	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	intron	7085629	7085726	.	-	.	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	CDS	7085727	7085882	0.49	-	2	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	exon	7085727	7085882	.	-	.	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	intron	7085883	7086001	.	-	.	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	CDS	7086002	7086257	0.67	-	0	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	exon	7086002	7086257	.	-	.	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
Phchi.S3	AUGUSTUS	start_codon	7086255	7086257	.	-	0	transcript_id "Phchi.S3G079700.t1"; gene_id "Phchi.S3G079700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1252.t1 is derived from g11035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8651074	8652887	.	-	.	Phchi.S6G121100
Phchi.S6	AUGUSTUS	transcript	8651074	8652887	.	-	.	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	stop_codon	8651071	8651073	.	-	0	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	CDS	8651074	8651243	0.96	-	2	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	exon	8651074	8651243	.	-	.	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	intron	8651244	8651320	.	-	.	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	CDS	8651321	8652887	0.96	-	0	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	exon	8651321	8652887	.	-	.	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	start_codon	8652885	8652887	.	-	0	transcript_id "Phchi.S6G121100.t1"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	transcript	8652511	8652887	.	-	.	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	stop_codon	8652508	8652510	.	-	0	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	CDS	8652511	8652515	0.74	-	2	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	exon	8652511	8652515	.	-	.	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	intron	8652516	8652577	.	-	.	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	CDS	8652578	8652887	0.52	-	0	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	exon	8652578	8652887	.	-	.	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
Phchi.S6	AUGUSTUS	start_codon	8652885	8652887	.	-	0	transcript_id "Phchi.S6G121100.t2"; gene_id "Phchi.S6G121100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13147.t1 is derived from g11612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4395184	4395591	.	+	.	Phchi.S3G046600
Phchi.S3	AUGUSTUS	transcript	4395184	4395591	.	+	.	transcript_id "Phchi.S3G046600.t1"; gene_id "Phchi.S3G046600"
Phchi.S3	AUGUSTUS	start_codon	4395184	4395186	.	+	0	transcript_id "Phchi.S3G046600.t1"; gene_id "Phchi.S3G046600"
Phchi.S3	AUGUSTUS	CDS	4395184	4395591	0.75	+	0	transcript_id "Phchi.S3G046600.t1"; gene_id "Phchi.S3G046600"
Phchi.S3	AUGUSTUS	exon	4395184	4395591	.	+	.	transcript_id "Phchi.S3G046600.t1"; gene_id "Phchi.S3G046600"
Phchi.S3	AUGUSTUS	stop_codon	4395592	4395594	.	+	0	transcript_id "Phchi.S3G046600.t1"; gene_id "Phchi.S3G046600"
# This transcript jg3460.t2 is derived from g629.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3461.t1 is derived from g630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3879603	3879922	.	-	.	Phchi.S1G062000
Phchi.S1	AUGUSTUS	transcript	3879603	3879922	.	-	.	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	stop_codon	3879600	3879602	.	-	0	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	CDS	3879603	3879682	0.98	-	2	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	exon	3879603	3879682	.	-	.	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	intron	3879683	3879777	.	-	.	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	CDS	3879778	3879922	0.8	-	0	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	exon	3879778	3879922	.	-	.	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
Phchi.S1	AUGUSTUS	start_codon	3879920	3879922	.	-	0	transcript_id "Phchi.S1G062000.t1"; gene_id "Phchi.S1G062000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12424.t1 is derived from g8101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19551692	19553082	.	+	.	Phchi.S2G050400
Phchi.S2	AUGUSTUS	transcript	19551692	19553082	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	start_codon	19551692	19551694	.	+	0	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	CDS	19551692	19551875	1	+	0	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	exon	19551692	19551875	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	intron	19551876	19552122	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	CDS	19552123	19552156	1	+	2	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	exon	19552123	19552156	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	intron	19552157	19552256	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	CDS	19552257	19552313	0.65	+	1	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	exon	19552257	19552313	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	intron	19552314	19552389	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	CDS	19552390	19552986	0.97	+	1	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	exon	19552390	19552986	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	intron	19552987	19553081	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	CDS	19553082	19553082	0.97	+	1	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	exon	19553082	19553082	.	+	.	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
Phchi.S2	AUGUSTUS	stop_codon	19553083	19553085	.	+	0	transcript_id "Phchi.S2G050400.t1"; gene_id "Phchi.S2G050400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10608.t1 is derived from g14658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1178367	1180041	.	+	.	Phchi.S4G019000
Phchi.S4	AUGUSTUS	transcript	1178367	1180041	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	start_codon	1178367	1178369	.	+	0	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1178367	1178405	0.67	+	0	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1178367	1178405	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	intron	1178406	1178571	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1178572	1178655	0.89	+	0	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1178572	1178655	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	intron	1178656	1178784	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1178785	1178902	0.94	+	0	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1178785	1178902	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	intron	1178903	1179031	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1179032	1179177	0.31	+	2	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1179032	1179177	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	intron	1179178	1179472	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1179473	1179495	0.75	+	0	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1179473	1179495	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	intron	1179496	1179578	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1179579	1179664	0.97	+	1	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1179579	1179664	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	intron	1179665	1179967	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	CDS	1179968	1180041	0.99	+	2	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	exon	1179968	1180041	.	+	.	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
Phchi.S4	AUGUSTUS	stop_codon	1180042	1180044	.	+	0	transcript_id "Phchi.S4G019000.t1"; gene_id "Phchi.S4G019000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5223.t1 is derived from g2393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15609709	15609933	.	-	.	Phchi.S1G238200
Phchi.S1	AUGUSTUS	transcript	15609709	15609933	.	-	.	transcript_id "Phchi.S1G238200.t1"; gene_id "Phchi.S1G238200"
Phchi.S1	AUGUSTUS	stop_codon	15609706	15609708	.	-	0	transcript_id "Phchi.S1G238200.t1"; gene_id "Phchi.S1G238200"
Phchi.S1	AUGUSTUS	CDS	15609709	15609933	0.77	-	0	transcript_id "Phchi.S1G238200.t1"; gene_id "Phchi.S1G238200"
Phchi.S1	AUGUSTUS	exon	15609709	15609933	.	-	.	transcript_id "Phchi.S1G238200.t1"; gene_id "Phchi.S1G238200"
Phchi.S1	AUGUSTUS	start_codon	15609931	15609933	.	-	0	transcript_id "Phchi.S1G238200.t1"; gene_id "Phchi.S1G238200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14633.t1 is derived from g13101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13846440	13847901	.	-	.	Phchi.S3G195200
Phchi.S3	AUGUSTUS	transcript	13846440	13847901	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	stop_codon	13846437	13846439	.	-	0	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	CDS	13846440	13846523	0.99	-	0	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	exon	13846440	13846523	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	intron	13846524	13846617	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	CDS	13846618	13846791	1	-	0	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	exon	13846618	13846791	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	intron	13846792	13846936	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	CDS	13846937	13847148	1	-	2	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	exon	13846937	13847148	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	intron	13847149	13847377	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	CDS	13847378	13847537	1	-	0	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	exon	13847378	13847537	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	intron	13847538	13847652	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	CDS	13847653	13847901	0.97	-	0	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	exon	13847653	13847901	.	-	.	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
Phchi.S3	AUGUSTUS	start_codon	13847899	13847901	.	-	0	transcript_id "Phchi.S3G195200.t1"; gene_id "Phchi.S3G195200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13052.t1 is derived from g11517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3913742	3916076	.	+	.	Phchi.S3G037100
Phchi.S3	AUGUSTUS	transcript	3913742	3916076	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	start_codon	3913742	3913744	.	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3913742	3913950	0.63	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3913742	3913950	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3913951	3914057	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3914058	3914361	0.74	+	1	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3914058	3914361	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3914362	3914459	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3914460	3914609	1	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3914460	3914609	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3914610	3914706	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3914707	3914970	0.99	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3914707	3914970	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3914971	3915062	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3915063	3915149	1	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3915063	3915149	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3915150	3915276	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3915277	3915355	1	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3915277	3915355	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3915356	3915449	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3915450	3915556	0.98	+	2	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3915450	3915556	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3915557	3915686	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3915687	3915808	1	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3915687	3915808	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	intron	3915809	3915973	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	CDS	3915974	3916076	1	+	1	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	exon	3915974	3916076	.	+	.	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
Phchi.S3	AUGUSTUS	stop_codon	3916077	3916079	.	+	0	transcript_id "Phchi.S3G037100.t1"; gene_id "Phchi.S3G037100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3628.t1 is derived from g797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4841647	4842914	.	-	.	Phchi.S1G078700
Phchi.S1	AUGUSTUS	transcript	4841647	4842914	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	stop_codon	4841644	4841646	.	-	0	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	CDS	4841647	4842246	1	-	0	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	exon	4841647	4842246	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	intron	4842247	4842342	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	CDS	4842343	4842450	1	-	0	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	exon	4842343	4842450	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	intron	4842451	4842580	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	CDS	4842581	4842661	1	-	0	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	exon	4842581	4842661	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	intron	4842662	4842761	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	CDS	4842762	4842914	1	-	0	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	exon	4842762	4842914	.	-	.	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
Phchi.S1	AUGUSTUS	start_codon	4842912	4842914	.	-	0	transcript_id "Phchi.S1G078700.t1"; gene_id "Phchi.S1G078700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13543.t1 is derived from g12010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7433092	7435500	.	+	.	Phchi.S3G086200
Phchi.S3	AUGUSTUS	transcript	7433092	7435500	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	start_codon	7433092	7433094	.	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	CDS	7433092	7433247	1	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	exon	7433092	7433247	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	intron	7433248	7433454	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	CDS	7433455	7433604	1	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	exon	7433455	7433604	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	intron	7433605	7433738	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	CDS	7433739	7434914	1	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	exon	7433739	7434914	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	intron	7434915	7435000	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	CDS	7435001	7435147	1	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	exon	7435001	7435147	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	intron	7435148	7435227	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	CDS	7435228	7435500	0.87	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	exon	7435228	7435500	.	+	.	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
Phchi.S3	AUGUSTUS	stop_codon	7435501	7435503	.	+	0	transcript_id "Phchi.S3G086200.t1"; gene_id "Phchi.S3G086200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10325.t1 is derived from g7501.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47120302	47121580	.	-	.	Phchi.S1G748400
Phchi.S1	AUGUSTUS	transcript	47120435	47121580	.	-	.	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	stop_codon	47120432	47120434	.	-	0	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47120435	47120486	1	-	1	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47120435	47120486	.	-	.	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	intron	47120487	47120637	.	-	.	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47120638	47121269	0.99	-	0	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47120638	47121269	.	-	.	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	intron	47121270	47121361	.	-	.	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47121362	47121580	1	-	0	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47121362	47121580	.	-	.	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	start_codon	47121578	47121580	.	-	0	transcript_id "Phchi.S1G748400.t1"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	transcript	47120302	47121580	.	-	.	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	stop_codon	47120299	47120301	.	-	0	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47120302	47120377	1	-	1	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47120302	47120377	.	-	.	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	intron	47120378	47120637	.	-	.	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47120638	47121269	0.94	-	0	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47120638	47121269	.	-	.	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	intron	47121270	47121361	.	-	.	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47121362	47121580	1	-	0	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47121362	47121580	.	-	.	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	start_codon	47121578	47121580	.	-	0	transcript_id "Phchi.S1G748400.t2"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	transcript	47120458	47121580	.	-	.	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	stop_codon	47120455	47120457	.	-	0	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47120458	47120486	0.66	-	2	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47120458	47120486	.	-	.	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	intron	47120487	47120614	.	-	.	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47120615	47121269	0.85	-	0	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47120615	47121269	.	-	.	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	intron	47121270	47121361	.	-	.	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	CDS	47121362	47121580	1	-	0	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	exon	47121362	47121580	.	-	.	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
Phchi.S1	AUGUSTUS	start_codon	47121578	47121580	.	-	0	transcript_id "Phchi.S1G748400.t3"; gene_id "Phchi.S1G748400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15738.t1 is derived from g14208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20978412	20980295	.	+	.	Phchi.S3G305700
Phchi.S3	AUGUSTUS	transcript	20978412	20980295	.	+	.	transcript_id "Phchi.S3G305700.t1"; gene_id "Phchi.S3G305700"
Phchi.S3	AUGUSTUS	start_codon	20978412	20978414	.	+	0	transcript_id "Phchi.S3G305700.t1"; gene_id "Phchi.S3G305700"
Phchi.S3	AUGUSTUS	CDS	20978412	20980295	0.83	+	0	transcript_id "Phchi.S3G305700.t1"; gene_id "Phchi.S3G305700"
Phchi.S3	AUGUSTUS	exon	20978412	20980295	.	+	.	transcript_id "Phchi.S3G305700.t1"; gene_id "Phchi.S3G305700"
Phchi.S3	AUGUSTUS	stop_codon	20980296	20980298	.	+	0	transcript_id "Phchi.S3G305700.t1"; gene_id "Phchi.S3G305700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2008.t1 is derived from g8928.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4422864	4427544	.	+	.	Phchi.S5G061700
Phchi.S5	AUGUSTUS	transcript	4422864	4427544	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	start_codon	4422864	4422866	.	+	0	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4422864	4422892	0.76	+	0	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4422864	4422892	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4422893	4423065	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423066	4423253	1	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423066	4423253	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423254	4423340	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423341	4423422	1	+	2	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423341	4423422	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423423	4423505	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423506	4423593	1	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423506	4423593	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423594	4423862	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423863	4424390	0.89	+	0	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423863	4424390	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424391	4424507	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4424508	4424671	0.92	+	0	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4424508	4424671	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424672	4424752	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4424753	4424884	0.71	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4424753	4424884	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424885	4425038	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425039	4425191	0.85	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425039	4425191	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425192	4425280	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425281	4425504	0.47	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425281	4425504	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425505	4425601	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425602	4425646	1	+	2	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425602	4425646	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425647	4425735	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425736	4425949	1	+	2	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425736	4425949	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425950	4426173	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426174	4426223	1	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426174	4426223	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4426224	4426305	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426306	4426686	0.63	+	2	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426306	4426686	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4426687	4426844	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426845	4427097	0.76	+	2	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426845	4427097	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4427098	4427191	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4427192	4427244	1	+	1	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4427192	4427244	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4427245	4427368	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4427369	4427544	1	+	2	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4427369	4427544	.	+	.	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	stop_codon	4427545	4427547	.	+	0	transcript_id "Phchi.S5G061700.t1"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	transcript	4422864	4427544	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	start_codon	4422864	4422866	.	+	0	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4422864	4422892	0.76	+	0	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4422864	4422892	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4422893	4423065	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423066	4423253	1	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423066	4423253	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423254	4423340	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423341	4423422	1	+	2	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423341	4423422	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423423	4423505	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423506	4423593	1	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423506	4423593	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423594	4423862	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423863	4424390	0.8	+	0	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423863	4424390	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424391	4424507	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4424508	4424671	0.88	+	0	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4424508	4424671	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424672	4424752	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4424753	4424884	0.65	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4424753	4424884	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424885	4425038	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425039	4425191	0.82	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425039	4425191	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425192	4425280	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425281	4425504	0.42	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425281	4425504	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425505	4425601	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425602	4425646	1	+	2	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425602	4425646	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425647	4425738	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425739	4425949	0.98	+	2	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425739	4425949	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425950	4426173	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426174	4426223	1	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426174	4426223	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4426224	4426305	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426306	4426686	0.5	+	2	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426306	4426686	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4426687	4426844	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426845	4427097	0.72	+	2	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426845	4427097	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4427098	4427191	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4427192	4427244	1	+	1	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4427192	4427244	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4427245	4427368	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4427369	4427544	1	+	2	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4427369	4427544	.	+	.	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	stop_codon	4427545	4427547	.	+	0	transcript_id "Phchi.S5G061700.t2"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	transcript	4422864	4427544	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	start_codon	4422864	4422866	.	+	0	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4422864	4422892	0.84	+	0	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4422864	4422892	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4422893	4423065	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423066	4423253	1	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423066	4423253	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423254	4423340	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423341	4423422	1	+	2	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423341	4423422	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423423	4423505	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423506	4423593	1	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423506	4423593	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4423594	4423862	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4423863	4424390	0.84	+	0	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4423863	4424390	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424391	4424507	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4424508	4424671	0.91	+	0	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4424508	4424671	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424672	4424752	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4424753	4424884	0.89	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4424753	4424884	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4424885	4425038	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425039	4425191	1	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425039	4425191	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425192	4425280	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425281	4425333	0.92	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425281	4425333	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425334	4425440	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425441	4425504	0.43	+	2	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425441	4425504	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425505	4425611	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425612	4425646	0.43	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425612	4425646	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425647	4425735	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4425736	4425949	0.98	+	2	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4425736	4425949	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4425950	4426173	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426174	4426223	1	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426174	4426223	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4426224	4426305	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426306	4426686	0.5	+	2	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426306	4426686	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4426687	4426844	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4426845	4427097	0.72	+	2	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4426845	4427097	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4427098	4427191	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4427192	4427244	1	+	1	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4427192	4427244	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	intron	4427245	4427368	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	CDS	4427369	4427544	1	+	2	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	exon	4427369	4427544	.	+	.	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
Phchi.S5	AUGUSTUS	stop_codon	4427545	4427547	.	+	0	transcript_id "Phchi.S5G061700.t3"; gene_id "Phchi.S5G061700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2442.t1 is derived from g9362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6649667	6651304	.	-	.	Phchi.S5G105100
Phchi.S5	AUGUSTUS	transcript	6649667	6651304	.	-	.	transcript_id "Phchi.S5G105100.t1"; gene_id "Phchi.S5G105100"
Phchi.S5	AUGUSTUS	stop_codon	6649664	6649666	.	-	0	transcript_id "Phchi.S5G105100.t1"; gene_id "Phchi.S5G105100"
Phchi.S5	AUGUSTUS	CDS	6649667	6651304	0.75	-	0	transcript_id "Phchi.S5G105100.t1"; gene_id "Phchi.S5G105100"
Phchi.S5	AUGUSTUS	exon	6649667	6651304	.	-	.	transcript_id "Phchi.S5G105100.t1"; gene_id "Phchi.S5G105100"
Phchi.S5	AUGUSTUS	start_codon	6651302	6651304	.	-	0	transcript_id "Phchi.S5G105100.t1"; gene_id "Phchi.S5G105100"
# This transcript jg732.t2 is derived from g10514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg733.t1 is derived from g10515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5216923	5218122	.	-	.	Phchi.S6G069200
Phchi.S6	AUGUSTUS	transcript	5216923	5218122	.	-	.	transcript_id "Phchi.S6G069200.t1"; gene_id "Phchi.S6G069200"
Phchi.S6	AUGUSTUS	stop_codon	5216920	5216922	.	-	0	transcript_id "Phchi.S6G069200.t1"; gene_id "Phchi.S6G069200"
Phchi.S6	AUGUSTUS	CDS	5216923	5218122	0.47	-	0	transcript_id "Phchi.S6G069200.t1"; gene_id "Phchi.S6G069200"
Phchi.S6	AUGUSTUS	exon	5216923	5218122	.	-	.	transcript_id "Phchi.S6G069200.t1"; gene_id "Phchi.S6G069200"
Phchi.S6	AUGUSTUS	start_codon	5218120	5218122	.	-	0	transcript_id "Phchi.S6G069200.t1"; gene_id "Phchi.S6G069200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1898.t1 is derived from g8818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3774353	3774967	.	-	.	Phchi.S5G050700
Phchi.S5	AUGUSTUS	transcript	3774353	3774967	.	-	.	transcript_id "Phchi.S5G050700.t1"; gene_id "Phchi.S5G050700"
Phchi.S5	AUGUSTUS	stop_codon	3774350	3774352	.	-	0	transcript_id "Phchi.S5G050700.t1"; gene_id "Phchi.S5G050700"
Phchi.S5	AUGUSTUS	CDS	3774353	3774967	1	-	0	transcript_id "Phchi.S5G050700.t1"; gene_id "Phchi.S5G050700"
Phchi.S5	AUGUSTUS	exon	3774353	3774967	.	-	.	transcript_id "Phchi.S5G050700.t1"; gene_id "Phchi.S5G050700"
Phchi.S5	AUGUSTUS	start_codon	3774965	3774967	.	-	0	transcript_id "Phchi.S5G050700.t1"; gene_id "Phchi.S5G050700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4708.t1 is derived from g1878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12418445	12418982	.	-	.	Phchi.S1G186700
Phchi.S1	AUGUSTUS	transcript	12418445	12418982	.	-	.	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	stop_codon	12418442	12418444	.	-	0	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	CDS	12418445	12418633	0.77	-	0	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	exon	12418445	12418633	.	-	.	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	intron	12418634	12418829	.	-	.	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	CDS	12418830	12418982	0.86	-	0	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	exon	12418830	12418982	.	-	.	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
Phchi.S1	AUGUSTUS	start_codon	12418980	12418982	.	-	0	transcript_id "Phchi.S1G186700.t1"; gene_id "Phchi.S1G186700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg362.t1 is derived from g10144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2650448	2651298	.	-	.	Phchi.S6G032100
Phchi.S6	AUGUSTUS	transcript	2650448	2651298	.	-	.	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	stop_codon	2650445	2650447	.	-	0	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	CDS	2650448	2650918	0.8	-	0	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	exon	2650448	2650918	.	-	.	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	intron	2650919	2651154	.	-	.	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	CDS	2651155	2651298	0.4	-	0	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	exon	2651155	2651298	.	-	.	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
Phchi.S6	AUGUSTUS	start_codon	2651296	2651298	.	-	0	transcript_id "Phchi.S6G032100.t1"; gene_id "Phchi.S6G032100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14397.t1 is derived from g12865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12610825	12613948	.	+	.	Phchi.S3G171600
Phchi.S3	AUGUSTUS	transcript	12610825	12613948	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	start_codon	12610825	12610827	.	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12610825	12611029	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12610825	12611029	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12611030	12611163	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12611164	12611243	1	+	2	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12611164	12611243	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12611244	12611343	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12611344	12611633	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12611344	12611633	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12611634	12611751	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12611752	12611923	1	+	1	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12611752	12611923	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12611924	12612016	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12612017	12612142	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12612017	12612142	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12612143	12612238	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12612239	12612373	0.99	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12612239	12612373	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12612374	12612486	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12612487	12612681	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12612487	12612681	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12612682	12612791	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12612792	12612878	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12612792	12612878	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12612879	12612963	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12612964	12613236	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12612964	12613236	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12613237	12613442	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12613443	12613550	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12613443	12613550	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	intron	12613551	12613645	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	CDS	12613646	12613948	1	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	exon	12613646	12613948	.	+	.	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
Phchi.S3	AUGUSTUS	stop_codon	12613949	12613951	.	+	0	transcript_id "Phchi.S3G171600.t1"; gene_id "Phchi.S3G171600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6639.t1 is derived from g3811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24201630	24203515	.	-	.	Phchi.S1G379800
Phchi.S1	AUGUSTUS	transcript	24201630	24203515	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	stop_codon	24201627	24201629	.	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24201630	24201677	0.98	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24201630	24201677	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	intron	24201678	24201775	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24201776	24201900	1	-	2	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24201776	24201900	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	intron	24201901	24202107	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24202108	24202171	1	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24202108	24202171	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	intron	24202172	24202257	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24202258	24202398	1	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24202258	24202398	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	intron	24202399	24202524	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24202525	24202656	0.85	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24202525	24202656	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	intron	24202657	24202856	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24202857	24202958	0.83	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24202857	24202958	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	intron	24202959	24203044	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	CDS	24203045	24203515	0.6	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	exon	24203045	24203515	.	-	.	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
Phchi.S1	AUGUSTUS	start_codon	24203513	24203515	.	-	0	transcript_id "Phchi.S1G379800.t1"; gene_id "Phchi.S1G379800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1838.t1 is derived from g8758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3499346	3504031	.	+	.	Phchi.S5G044700
Phchi.S5	AUGUSTUS	transcript	3499346	3504031	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	start_codon	3499346	3499348	.	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499346	3499358	0.31	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499346	3499358	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499359	3499450	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499451	3499469	0.27	+	2	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499451	3499469	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499470	3499639	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499640	3499958	0.41	+	1	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499640	3499958	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499959	3500056	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500057	3500182	1	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500057	3500182	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3500183	3500304	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500305	3500756	1	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500305	3500756	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3500757	3500916	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500917	3501164	1	+	1	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500917	3501164	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501165	3501287	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501288	3501376	1	+	2	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501288	3501376	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501377	3501452	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501453	3501680	0.99	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501453	3501680	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501681	3501790	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501791	3501900	1	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501791	3501900	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501901	3502213	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502214	3502335	0.89	+	1	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502214	3502335	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502336	3502427	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502428	3502489	0.96	+	2	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502428	3502489	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502490	3502641	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502642	3502693	1	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502642	3502693	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502694	3502939	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502940	3502988	0.93	+	2	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502940	3502988	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502989	3503080	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503081	3503108	1	+	1	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503081	3503108	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503109	3503255	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503256	3503453	1	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503256	3503453	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503454	3503541	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503542	3503713	1	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503542	3503713	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503714	3503849	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503850	3504031	0.89	+	2	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503850	3504031	.	+	.	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	stop_codon	3504032	3504034	.	+	0	transcript_id "Phchi.S5G044700.t1"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	transcript	3499346	3504031	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	start_codon	3499346	3499348	.	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499346	3499358	0.33	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499346	3499358	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499359	3499450	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499451	3499469	0.29	+	2	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499451	3499469	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499470	3499639	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499640	3499958	0.36	+	1	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499640	3499958	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499959	3500056	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500057	3500182	1	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500057	3500182	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3500183	3500304	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500305	3500756	1	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500305	3500756	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3500757	3500916	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500917	3501164	0.99	+	1	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500917	3501164	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501165	3501287	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501288	3501376	1	+	2	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501288	3501376	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501377	3501452	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501453	3501680	0.99	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501453	3501680	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501681	3501790	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501791	3501900	0.99	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501791	3501900	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501901	3502213	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502214	3502335	0.99	+	1	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502214	3502335	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502336	3502424	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502425	3502489	0.98	+	2	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502425	3502489	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502490	3502641	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502642	3502693	1	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502642	3502693	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502694	3502939	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502940	3502988	0.74	+	2	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502940	3502988	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502989	3503080	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503081	3503108	0.81	+	1	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503081	3503108	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503109	3503266	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503267	3503292	0.66	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503267	3503292	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503293	3503377	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503378	3503453	0.62	+	1	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503378	3503453	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503454	3503541	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503542	3503713	1	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503542	3503713	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503714	3503849	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503850	3504031	0.83	+	2	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503850	3504031	.	+	.	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	stop_codon	3504032	3504034	.	+	0	transcript_id "Phchi.S5G044700.t2"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	transcript	3499346	3504031	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	start_codon	3499346	3499348	.	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499346	3499358	0.32	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499346	3499358	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499359	3499450	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499451	3499469	0.21	+	2	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499451	3499469	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499470	3499639	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3499640	3499958	0.46	+	1	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3499640	3499958	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3499959	3500056	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500057	3500182	1	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500057	3500182	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3500183	3500304	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500305	3500756	1	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500305	3500756	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3500757	3500916	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3500917	3501164	1	+	1	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3500917	3501164	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501165	3501287	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501288	3501376	1	+	2	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501288	3501376	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501377	3501452	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501453	3501680	0.99	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501453	3501680	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501681	3501790	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3501791	3501900	1	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3501791	3501900	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3501901	3502213	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502214	3502335	0.93	+	1	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502214	3502335	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502336	3502427	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502428	3502489	0.94	+	2	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502428	3502489	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502490	3502641	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502642	3502693	1	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502642	3502693	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502694	3502939	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3502940	3502988	0.8	+	2	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3502940	3502988	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3502989	3503080	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503081	3503108	0.82	+	1	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503081	3503108	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503109	3503266	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503267	3503292	0.66	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503267	3503292	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503293	3503377	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503378	3503453	0.6	+	1	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503378	3503453	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503454	3503541	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503542	3503713	1	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503542	3503713	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	intron	3503714	3503849	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	CDS	3503850	3504031	0.9	+	2	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	exon	3503850	3504031	.	+	.	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
Phchi.S5	AUGUSTUS	stop_codon	3504032	3504034	.	+	0	transcript_id "Phchi.S5G044700.t3"; gene_id "Phchi.S5G044700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14.t1 is derived from g9805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C158	AUGUSTUS	gene	32048	34413	.	-	.	Phchi.C158G000100
Phchi.C158	AUGUSTUS	transcript	32048	34413	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	stop_codon	32045	32047	.	-	0	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	32048	32048	0.65	-	1	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	32048	32048	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	32049	32139	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	32140	32318	0.81	-	0	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	32140	32318	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	32319	32400	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	32401	32482	1	-	1	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	32401	32482	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	32483	32570	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	32571	32732	1	-	1	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	32571	32732	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	32733	32848	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	32849	33059	1	-	2	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	32849	33059	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	33060	33253	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	33254	33354	1	-	1	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	33254	33354	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	33355	33448	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	33449	33648	1	-	0	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	33449	33648	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	33649	33791	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	33792	33895	1	-	2	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	33792	33895	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	intron	33896	33995	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	CDS	33996	34413	0.99	-	0	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	exon	33996	34413	.	-	.	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
Phchi.C158	AUGUSTUS	start_codon	34411	34413	.	-	0	transcript_id "Phchi.C158G000100.t1"; gene_id "Phchi.C158G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3573.t1 is derived from g742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4584782	4586647	.	+	.	Phchi.S1G073200
Phchi.S1	AUGUSTUS	transcript	4584782	4586647	.	+	.	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	start_codon	4584782	4584784	.	+	0	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	CDS	4584782	4584979	1	+	0	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	exon	4584782	4584979	.	+	.	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	intron	4584980	4585070	.	+	.	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	CDS	4585071	4585664	1	+	0	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	exon	4585071	4585664	.	+	.	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	intron	4585665	4585744	.	+	.	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	CDS	4585745	4586647	1	+	0	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	exon	4585745	4586647	.	+	.	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
Phchi.S1	AUGUSTUS	stop_codon	4586648	4586650	.	+	0	transcript_id "Phchi.S1G073200.t1"; gene_id "Phchi.S1G073200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13557.t1 is derived from g12024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7484174	7486366	.	-	.	Phchi.S3G087600
Phchi.S3	AUGUSTUS	transcript	7484174	7486366	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	stop_codon	7484171	7484173	.	-	0	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7484174	7484469	0.52	-	2	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7484174	7484469	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	intron	7484470	7484665	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7484666	7484773	1	-	2	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7484666	7484773	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	intron	7484774	7484885	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7484886	7485074	0.97	-	2	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7484886	7485074	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	intron	7485075	7485167	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7485168	7485618	0.95	-	0	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7485168	7485618	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	intron	7485619	7485717	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7485718	7486008	1	-	0	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7485718	7486008	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	intron	7486009	7486159	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7486160	7486201	0.45	-	0	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7486160	7486201	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	intron	7486202	7486303	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	CDS	7486304	7486366	0.18	-	0	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	exon	7486304	7486366	.	-	.	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
Phchi.S3	AUGUSTUS	start_codon	7486364	7486366	.	-	0	transcript_id "Phchi.S3G087600.t1"; gene_id "Phchi.S3G087600"
# This transcript jg1882.t2 is derived from g8802.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1882.t3 is derived from g8802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1883.t1 is derived from g8803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3700335	3703164	.	+	.	Phchi.S5G049200
Phchi.S5	AUGUSTUS	transcript	3700335	3703164	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	start_codon	3700335	3700337	.	+	0	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3700335	3700384	0.98	+	0	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3700335	3700384	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3700385	3700599	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3700600	3700660	0.83	+	1	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3700600	3700660	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3700661	3700754	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3700755	3700786	0.7	+	0	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3700755	3700786	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3700787	3701086	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3701087	3701515	0.74	+	1	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3701087	3701515	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3701516	3701694	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3701695	3701959	0.99	+	1	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3701695	3701959	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3701960	3702063	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3702064	3702354	1	+	0	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3702064	3702354	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3702355	3702430	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3702431	3702798	1	+	0	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3702431	3702798	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	intron	3702799	3702890	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	CDS	3702891	3703164	0.98	+	1	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	exon	3702891	3703164	.	+	.	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
Phchi.S5	AUGUSTUS	stop_codon	3703165	3703167	.	+	0	transcript_id "Phchi.S5G049200.t1"; gene_id "Phchi.S5G049200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12834.t1 is derived from g11299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2609735	2610172	.	+	.	Phchi.S3G015300
Phchi.S3	AUGUSTUS	transcript	2609735	2610172	.	+	.	transcript_id "Phchi.S3G015300.t1"; gene_id "Phchi.S3G015300"
Phchi.S3	AUGUSTUS	start_codon	2609735	2609737	.	+	0	transcript_id "Phchi.S3G015300.t1"; gene_id "Phchi.S3G015300"
Phchi.S3	AUGUSTUS	CDS	2609735	2610172	0.9	+	0	transcript_id "Phchi.S3G015300.t1"; gene_id "Phchi.S3G015300"
Phchi.S3	AUGUSTUS	exon	2609735	2610172	.	+	.	transcript_id "Phchi.S3G015300.t1"; gene_id "Phchi.S3G015300"
Phchi.S3	AUGUSTUS	stop_codon	2610173	2610175	.	+	0	transcript_id "Phchi.S3G015300.t1"; gene_id "Phchi.S3G015300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4212.t1 is derived from g1381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8925235	8928694	.	+	.	Phchi.S1G137100
Phchi.S1	AUGUSTUS	transcript	8925235	8928694	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	start_codon	8925235	8925237	.	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8925235	8925367	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8925235	8925367	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8925368	8925484	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8925485	8925821	1	+	2	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8925485	8925821	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8925822	8925900	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8925901	8926018	1	+	1	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8925901	8926018	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8926019	8926110	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8926111	8926218	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8926111	8926218	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8926219	8926312	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8926313	8926485	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8926313	8926485	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8926486	8926570	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8926571	8926670	1	+	1	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8926571	8926670	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8926671	8926766	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8926767	8926841	0.91	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8926767	8926841	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8926842	8926983	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8926984	8927090	0.9	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8926984	8927090	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8927091	8927182	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8927183	8927318	1	+	1	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8927183	8927318	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8927319	8927416	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8927417	8927536	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8927417	8927536	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8927537	8927696	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8927697	8927843	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8927697	8927843	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8927844	8927926	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8927927	8928031	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8927927	8928031	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8928032	8928147	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8928148	8928246	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8928148	8928246	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8928247	8928346	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8928347	8928414	1	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8928347	8928414	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	intron	8928415	8928501	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	CDS	8928502	8928694	1	+	1	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	exon	8928502	8928694	.	+	.	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
Phchi.S1	AUGUSTUS	stop_codon	8928695	8928697	.	+	0	transcript_id "Phchi.S1G137100.t1"; gene_id "Phchi.S1G137100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2299.t1 is derived from g9219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5941522	5942895	.	+	.	Phchi.S5G090800
Phchi.S5	AUGUSTUS	transcript	5941522	5942895	.	+	.	transcript_id "Phchi.S5G090800.t1"; gene_id "Phchi.S5G090800"
Phchi.S5	AUGUSTUS	start_codon	5941522	5941524	.	+	0	transcript_id "Phchi.S5G090800.t1"; gene_id "Phchi.S5G090800"
Phchi.S5	AUGUSTUS	CDS	5941522	5942895	1	+	0	transcript_id "Phchi.S5G090800.t1"; gene_id "Phchi.S5G090800"
Phchi.S5	AUGUSTUS	exon	5941522	5942895	.	+	.	transcript_id "Phchi.S5G090800.t1"; gene_id "Phchi.S5G090800"
Phchi.S5	AUGUSTUS	stop_codon	5942896	5942898	.	+	0	transcript_id "Phchi.S5G090800.t1"; gene_id "Phchi.S5G090800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11008.t1 is derived from g15058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3612103	3613868	.	+	.	Phchi.S4G059000
Phchi.S4	AUGUSTUS	transcript	3612103	3613868	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	start_codon	3612103	3612105	.	+	0	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3612103	3612115	0.81	+	0	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3612103	3612115	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3612116	3612207	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3612208	3612285	1	+	2	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3612208	3612285	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3612286	3612385	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3612386	3612483	1	+	2	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3612386	3612483	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3612484	3612575	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3612576	3612629	1	+	0	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3612576	3612629	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3612630	3612723	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3612724	3612947	1	+	0	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3612724	3612947	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3612948	3613228	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3613229	3613374	1	+	1	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3613229	3613374	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3613375	3613507	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3613508	3613626	1	+	2	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3613508	3613626	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	intron	3613627	3613769	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	CDS	3613770	3613868	1	+	0	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	exon	3613770	3613868	.	+	.	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
Phchi.S4	AUGUSTUS	stop_codon	3613869	3613871	.	+	0	transcript_id "Phchi.S4G059000.t1"; gene_id "Phchi.S4G059000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6076.t1 is derived from g3247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20751212	20751630	.	-	.	Phchi.S1G323500
Phchi.S1	AUGUSTUS	transcript	20751212	20751630	.	-	.	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	stop_codon	20751209	20751211	.	-	0	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	CDS	20751212	20751349	0.96	-	0	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	exon	20751212	20751349	.	-	.	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	intron	20751350	20751450	.	-	.	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	CDS	20751451	20751630	0.55	-	0	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	exon	20751451	20751630	.	-	.	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
Phchi.S1	AUGUSTUS	start_codon	20751628	20751630	.	-	0	transcript_id "Phchi.S1G323500.t1"; gene_id "Phchi.S1G323500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12212.t1 is derived from g7888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6765683	6767006	.	-	.	Phchi.S2G029200
Phchi.S2	AUGUSTUS	transcript	6765683	6767006	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	stop_codon	6765680	6765682	.	-	0	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	CDS	6765683	6765729	0.99	-	2	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	exon	6765683	6765729	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	intron	6765730	6765868	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	CDS	6765869	6765928	0.99	-	2	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	exon	6765869	6765928	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	intron	6765929	6766099	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	CDS	6766100	6766163	0.88	-	0	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	exon	6766100	6766163	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	intron	6766164	6766297	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	CDS	6766298	6766525	0.99	-	0	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	exon	6766298	6766525	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	intron	6766526	6766615	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	CDS	6766616	6766643	1	-	1	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	exon	6766616	6766643	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	intron	6766644	6766851	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	CDS	6766852	6767006	0.82	-	0	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	exon	6766852	6767006	.	-	.	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
Phchi.S2	AUGUSTUS	start_codon	6767004	6767006	.	-	0	transcript_id "Phchi.S2G029200.t1"; gene_id "Phchi.S2G029200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15271.t1 is derived from g13739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18041288	18045471	.	-	.	Phchi.S3G259000
Phchi.S3	AUGUSTUS	transcript	18041288	18045471	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	stop_codon	18041285	18041287	.	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18041288	18041362	0.99	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18041288	18041362	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18041363	18041465	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18041466	18041757	0.98	-	1	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18041466	18041757	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18041758	18041845	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18041846	18042027	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18041846	18042027	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18042028	18042162	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18042163	18043065	0.93	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18042163	18043065	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18043066	18043182	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18043183	18043269	0.89	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18043183	18043269	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18043270	18043376	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18043377	18043460	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18043377	18043460	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18043461	18043588	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18043589	18043642	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18043589	18043642	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18043643	18043782	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18043783	18043917	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18043783	18043917	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18043918	18044078	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18044079	18044174	0.98	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18044079	18044174	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18044175	18044276	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18044277	18044540	0.87	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18044277	18044540	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18044541	18044658	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18044659	18044748	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18044659	18044748	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18044749	18044855	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18044856	18044915	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18044856	18044915	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18044916	18044991	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18044992	18045058	1	-	1	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18044992	18045058	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18045059	18045190	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18045191	18045282	1	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18045191	18045282	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	intron	18045283	18045369	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	CDS	18045370	18045471	0.93	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	exon	18045370	18045471	.	-	.	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
Phchi.S3	AUGUSTUS	start_codon	18045469	18045471	.	-	0	transcript_id "Phchi.S3G259000.t1"; gene_id "Phchi.S3G259000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13055.t1 is derived from g11520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3925419	3927206	.	+	.	Phchi.S3G037400
Phchi.S3	AUGUSTUS	transcript	3925419	3927206	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	start_codon	3925419	3925421	.	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	CDS	3925419	3925696	0.73	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	exon	3925419	3925696	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	intron	3925697	3925787	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	CDS	3925788	3926115	1	+	1	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	exon	3925788	3926115	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	intron	3926116	3926241	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	CDS	3926242	3926391	0.93	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	exon	3926242	3926391	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	intron	3926392	3926495	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	CDS	3926496	3926756	0.85	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	exon	3926496	3926756	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	intron	3926757	3926886	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	CDS	3926887	3926970	0.98	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	exon	3926887	3926970	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	intron	3926971	3927083	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	CDS	3927084	3927206	0.68	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	exon	3927084	3927206	.	+	.	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
Phchi.S3	AUGUSTUS	stop_codon	3927207	3927209	.	+	0	transcript_id "Phchi.S3G037400.t1"; gene_id "Phchi.S3G037400"
# This transcript jg3528.t2 is derived from g697.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3529.t1 is derived from g698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4238110	4239531	.	+	.	Phchi.S1G068800
Phchi.S1	AUGUSTUS	transcript	4238110	4239531	.	+	.	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	start_codon	4238110	4238112	.	+	0	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	CDS	4238110	4238916	0.42	+	0	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	exon	4238110	4238916	.	+	.	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	intron	4238917	4238985	.	+	.	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	CDS	4238986	4239531	0.88	+	0	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	exon	4238986	4239531	.	+	.	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
Phchi.S1	AUGUSTUS	stop_codon	4239532	4239534	.	+	0	transcript_id "Phchi.S1G068800.t1"; gene_id "Phchi.S1G068800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15115.t1 is derived from g13583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17155500	17156720	.	-	.	Phchi.S3G243400
Phchi.S3	AUGUSTUS	transcript	17155500	17156720	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	stop_codon	17155497	17155499	.	-	0	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	CDS	17155500	17155840	0.99	-	2	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	exon	17155500	17155840	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	intron	17155841	17155962	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	CDS	17155963	17156125	1	-	0	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	exon	17155963	17156125	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	intron	17156126	17156199	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	CDS	17156200	17156394	1	-	0	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	exon	17156200	17156394	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	intron	17156395	17156486	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	CDS	17156487	17156720	0.98	-	0	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	exon	17156487	17156720	.	-	.	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
Phchi.S3	AUGUSTUS	start_codon	17156718	17156720	.	-	0	transcript_id "Phchi.S3G243400.t1"; gene_id "Phchi.S3G243400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7734.t1 is derived from g4908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30888450	30890909	.	+	.	Phchi.S1G489300
Phchi.S1	AUGUSTUS	transcript	30888450	30890909	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	start_codon	30888450	30888452	.	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30888450	30888578	0.9	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30888450	30888578	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30888579	30888685	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30888686	30888886	0.88	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30888686	30888886	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30888887	30888988	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30888989	30889100	0.9	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30888989	30889100	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30889101	30889239	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30889240	30889640	0.96	+	2	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30889240	30889640	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30889641	30889746	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30889747	30889800	1	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30889747	30889800	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30889801	30889893	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30889894	30889998	1	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30889894	30889998	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30889999	30890089	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30890090	30890164	0.98	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30890090	30890164	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30890165	30890267	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30890268	30890312	0.94	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30890268	30890312	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30890313	30890427	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30890428	30890556	0.98	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30890428	30890556	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30890557	30890657	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30890658	30890762	0.98	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30890658	30890762	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	intron	30890763	30890843	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	CDS	30890844	30890909	1	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	exon	30890844	30890909	.	+	.	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
Phchi.S1	AUGUSTUS	stop_codon	30890910	30890912	.	+	0	transcript_id "Phchi.S1G489300.t1"; gene_id "Phchi.S1G489300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg778.t1 is derived from g10560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5462438	5465533	.	+	.	Phchi.S6G073700
Phchi.S6	AUGUSTUS	transcript	5462438	5465533	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	start_codon	5462438	5462440	.	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5462438	5462971	0.97	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5462438	5462971	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5462972	5463283	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5463284	5463408	1	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5463284	5463408	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5463409	5463507	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5463508	5463706	0.7	+	1	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5463508	5463706	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5463707	5463822	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5463823	5464051	0.98	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5463823	5464051	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5464052	5464166	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5464167	5464333	0.95	+	2	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5464167	5464333	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5464334	5464429	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5464430	5464639	1	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5464430	5464639	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5464640	5464764	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5464765	5464875	1	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5464765	5464875	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5464876	5464975	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5464976	5465152	1	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5464976	5465152	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	intron	5465153	5465269	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	CDS	5465270	5465533	0.31	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	exon	5465270	5465533	.	+	.	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
Phchi.S6	AUGUSTUS	stop_codon	5465534	5465536	.	+	0	transcript_id "Phchi.S6G073700.t1"; gene_id "Phchi.S6G073700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg119.t1 is derived from g9901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	652808	653777	.	-	.	Phchi.S6G007800
Phchi.S6	AUGUSTUS	transcript	652808	653777	.	-	.	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	stop_codon	652805	652807	.	-	0	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	CDS	652808	653502	0.81	-	2	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	exon	652808	653502	.	-	.	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	intron	653503	653686	.	-	.	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	CDS	653687	653777	0.94	-	0	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	exon	653687	653777	.	-	.	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
Phchi.S6	AUGUSTUS	start_codon	653775	653777	.	-	0	transcript_id "Phchi.S6G007800.t1"; gene_id "Phchi.S6G007800"
# This transcript jg2290.t2 is derived from g9210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2291.t1 is derived from g9211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5892990	5894487	.	+	.	Phchi.S5G090000
Phchi.S5	AUGUSTUS	transcript	5892990	5894487	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	start_codon	5892990	5892992	.	+	0	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5892990	5893039	0.92	+	0	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5892990	5893039	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	intron	5893040	5893195	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5893196	5893225	0.96	+	1	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5893196	5893225	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	intron	5893226	5893316	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5893317	5893402	0.9	+	1	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5893317	5893402	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	intron	5893403	5893562	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5893563	5893679	1	+	2	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5893563	5893679	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	intron	5893680	5893873	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5893874	5893893	0.89	+	2	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5893874	5893893	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	intron	5893894	5894165	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5894166	5894211	0.85	+	0	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5894166	5894211	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	intron	5894212	5894464	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	CDS	5894465	5894487	0.85	+	2	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	exon	5894465	5894487	.	+	.	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
Phchi.S5	AUGUSTUS	stop_codon	5894488	5894490	.	+	0	transcript_id "Phchi.S5G090000.t1"; gene_id "Phchi.S5G090000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1689.t1 is derived from g8608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2509050	2511250	.	+	.	Phchi.S5G029800
Phchi.S5	AUGUSTUS	transcript	2509050	2511250	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	start_codon	2509050	2509052	.	+	0	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2509050	2509347	1	+	0	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2509050	2509347	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	intron	2509348	2509426	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2509427	2509733	0.8	+	2	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2509427	2509733	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	intron	2509734	2509961	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2509962	2510452	0.45	+	1	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2509962	2510452	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	intron	2510453	2510598	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2510599	2510740	0.5	+	2	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2510599	2510740	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	intron	2510741	2510887	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2510888	2510894	0.59	+	1	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2510888	2510894	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	intron	2510895	2510958	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2510959	2511047	0.58	+	0	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2510959	2511047	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	intron	2511048	2511231	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	CDS	2511232	2511250	0.84	+	1	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	exon	2511232	2511250	.	+	.	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
Phchi.S5	AUGUSTUS	stop_codon	2511251	2511253	.	+	0	transcript_id "Phchi.S5G029800.t1"; gene_id "Phchi.S5G029800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15840.t1 is derived from g14310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21706267	21708495	.	+	.	Phchi.S3G315900
Phchi.S3	AUGUSTUS	transcript	21706267	21708495	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	start_codon	21706267	21706269	.	+	0	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	CDS	21706267	21706525	0.84	+	0	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	exon	21706267	21706525	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	intron	21706526	21707109	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	CDS	21707110	21707331	1	+	2	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	exon	21707110	21707331	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	intron	21707332	21707611	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	CDS	21707612	21707721	1	+	2	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	exon	21707612	21707721	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	intron	21707722	21707818	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	CDS	21707819	21707984	1	+	0	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	exon	21707819	21707984	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	intron	21707985	21708121	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	CDS	21708122	21708254	0.92	+	2	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	exon	21708122	21708254	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	intron	21708255	21708494	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	CDS	21708495	21708495	0.91	+	1	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	exon	21708495	21708495	.	+	.	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
Phchi.S3	AUGUSTUS	stop_codon	21708496	21708498	.	+	0	transcript_id "Phchi.S3G315900.t1"; gene_id "Phchi.S3G315900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9997.t1 is derived from g7173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44918884	44919231	.	-	.	Phchi.S1G715600
Phchi.S1	AUGUSTUS	transcript	44918884	44919231	.	-	.	transcript_id "Phchi.S1G715600.t1"; gene_id "Phchi.S1G715600"
Phchi.S1	AUGUSTUS	stop_codon	44918881	44918883	.	-	0	transcript_id "Phchi.S1G715600.t1"; gene_id "Phchi.S1G715600"
Phchi.S1	AUGUSTUS	CDS	44918884	44919231	0.88	-	0	transcript_id "Phchi.S1G715600.t1"; gene_id "Phchi.S1G715600"
Phchi.S1	AUGUSTUS	exon	44918884	44919231	.	-	.	transcript_id "Phchi.S1G715600.t1"; gene_id "Phchi.S1G715600"
Phchi.S1	AUGUSTUS	start_codon	44919229	44919231	.	-	0	transcript_id "Phchi.S1G715600.t1"; gene_id "Phchi.S1G715600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12390.t1 is derived from g8067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15499384	15502591	.	-	.	Phchi.S2G047000
Phchi.S2	AUGUSTUS	transcript	15499384	15502591	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	stop_codon	15499381	15499383	.	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15499384	15499558	0.92	-	1	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15499384	15499558	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15499559	15499630	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15499631	15499700	1	-	2	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15499631	15499700	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15499701	15499789	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15499790	15499862	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15499790	15499862	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15499863	15500111	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15500112	15500146	1	-	2	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15500112	15500146	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15500147	15500291	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15500292	15500384	1	-	2	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15500292	15500384	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15500385	15500461	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15500462	15500528	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15500462	15500528	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15500529	15500668	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15500669	15500737	0.87	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15500669	15500737	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15500738	15500840	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15500841	15500906	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15500841	15500906	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15500907	15501021	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15501022	15501130	1	-	1	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15501022	15501130	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15501131	15501210	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15501211	15501277	1	-	2	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15501211	15501277	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15501278	15501377	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15501378	15501430	1	-	1	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15501378	15501430	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15501431	15501524	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15501525	15501627	1	-	2	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15501525	15501627	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15501628	15501756	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15501757	15501895	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15501757	15501895	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15501896	15501989	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15501990	15502079	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15501990	15502079	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15502080	15502180	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15502181	15502249	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15502181	15502249	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15502250	15502381	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15502382	15502460	1	-	1	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15502382	15502460	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	intron	15502461	15502583	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	CDS	15502584	15502591	1	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	exon	15502584	15502591	.	-	.	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
Phchi.S2	AUGUSTUS	start_codon	15502589	15502591	.	-	0	transcript_id "Phchi.S2G047000.t1"; gene_id "Phchi.S2G047000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5991.t1 is derived from g3162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20279946	20280590	.	+	.	Phchi.S1G315000
Phchi.S1	AUGUSTUS	transcript	20279946	20280590	.	+	.	transcript_id "Phchi.S1G315000.t1"; gene_id "Phchi.S1G315000"
Phchi.S1	AUGUSTUS	start_codon	20279946	20279948	.	+	0	transcript_id "Phchi.S1G315000.t1"; gene_id "Phchi.S1G315000"
Phchi.S1	AUGUSTUS	CDS	20279946	20280590	0.86	+	0	transcript_id "Phchi.S1G315000.t1"; gene_id "Phchi.S1G315000"
Phchi.S1	AUGUSTUS	exon	20279946	20280590	.	+	.	transcript_id "Phchi.S1G315000.t1"; gene_id "Phchi.S1G315000"
Phchi.S1	AUGUSTUS	stop_codon	20280591	20280593	.	+	0	transcript_id "Phchi.S1G315000.t1"; gene_id "Phchi.S1G315000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4960.t1 is derived from g2130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13768939	13772591	.	+	.	Phchi.S1G211900
Phchi.S1	AUGUSTUS	transcript	13768939	13772591	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	start_codon	13768939	13768941	.	+	0	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13768939	13769149	0.98	+	0	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13768939	13769149	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13769150	13769279	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13769280	13769324	0.98	+	2	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13769280	13769324	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13769325	13769441	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13769442	13769846	0.99	+	2	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13769442	13769846	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13769847	13769932	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13769933	13770116	1	+	2	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13769933	13770116	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13770117	13770196	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13770197	13770414	1	+	1	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13770197	13770414	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13770415	13770516	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13770517	13771090	0.98	+	2	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13770517	13771090	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13771091	13771189	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13771190	13771288	1	+	1	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13771190	13771288	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13771289	13771386	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13771387	13771602	1	+	1	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13771387	13771602	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13771603	13771728	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13771729	13771867	0.7	+	1	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13771729	13771867	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13771868	13771967	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13771968	13772213	0.92	+	0	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13771968	13772213	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	intron	13772214	13772306	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	CDS	13772307	13772591	0.99	+	0	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	exon	13772307	13772591	.	+	.	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
Phchi.S1	AUGUSTUS	stop_codon	13772592	13772594	.	+	0	transcript_id "Phchi.S1G211900.t1"; gene_id "Phchi.S1G211900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2047.t1 is derived from g8967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4581010	4582467	.	-	.	Phchi.S5G065600
Phchi.S5	AUGUSTUS	transcript	4581010	4582467	.	-	.	transcript_id "Phchi.S5G065600.t1"; gene_id "Phchi.S5G065600"
Phchi.S5	AUGUSTUS	stop_codon	4581007	4581009	.	-	0	transcript_id "Phchi.S5G065600.t1"; gene_id "Phchi.S5G065600"
Phchi.S5	AUGUSTUS	CDS	4581010	4582467	1	-	0	transcript_id "Phchi.S5G065600.t1"; gene_id "Phchi.S5G065600"
Phchi.S5	AUGUSTUS	exon	4581010	4582467	.	-	.	transcript_id "Phchi.S5G065600.t1"; gene_id "Phchi.S5G065600"
Phchi.S5	AUGUSTUS	start_codon	4582465	4582467	.	-	0	transcript_id "Phchi.S5G065600.t1"; gene_id "Phchi.S5G065600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11309.t1 is derived from g15359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5312890	5314149	.	+	.	Phchi.S4G089100
Phchi.S4	AUGUSTUS	transcript	5312890	5314149	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	start_codon	5312890	5312892	.	+	0	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	CDS	5312890	5313492	0.16	+	0	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	exon	5312890	5313492	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	intron	5313493	5313577	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	CDS	5313578	5313776	0.35	+	0	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	exon	5313578	5313776	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	intron	5313777	5313871	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	CDS	5313872	5313978	0.62	+	2	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	exon	5313872	5313978	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	intron	5313979	5314104	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	CDS	5314105	5314149	0.99	+	0	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	exon	5314105	5314149	.	+	.	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
Phchi.S4	AUGUSTUS	stop_codon	5314150	5314152	.	+	0	transcript_id "Phchi.S4G089100.t1"; gene_id "Phchi.S4G089100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4655.t1 is derived from g1825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11655070	11655704	.	+	.	Phchi.S1G181400
Phchi.S1	AUGUSTUS	transcript	11655070	11655704	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	start_codon	11655070	11655072	.	+	0	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	CDS	11655070	11655165	0.79	+	0	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	exon	11655070	11655165	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	intron	11655166	11655251	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	CDS	11655252	11655341	1	+	0	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	exon	11655252	11655341	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	intron	11655342	11655421	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	CDS	11655422	11655499	1	+	0	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	exon	11655422	11655499	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	intron	11655500	11655581	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	CDS	11655582	11655704	0.76	+	0	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	exon	11655582	11655704	.	+	.	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
Phchi.S1	AUGUSTUS	stop_codon	11655705	11655707	.	+	0	transcript_id "Phchi.S1G181400.t1"; gene_id "Phchi.S1G181400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg869.t1 is derived from g10651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5998589	5999384	.	+	.	Phchi.S6G082800
Phchi.S6	AUGUSTUS	transcript	5998589	5999384	.	+	.	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	start_codon	5998589	5998591	.	+	0	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	CDS	5998589	5998727	0.7	+	0	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	exon	5998589	5998727	.	+	.	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	intron	5998728	5998828	.	+	.	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	CDS	5998829	5999012	0.97	+	2	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	exon	5998829	5999012	.	+	.	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	intron	5999013	5999275	.	+	.	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	CDS	5999276	5999384	0.99	+	1	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	exon	5999276	5999384	.	+	.	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
Phchi.S6	AUGUSTUS	stop_codon	5999385	5999387	.	+	0	transcript_id "Phchi.S6G082800.t1"; gene_id "Phchi.S6G082800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14674.t1 is derived from g13142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14126326	14126634	.	-	.	Phchi.S3G199300
Phchi.S3	AUGUSTUS	transcript	14126326	14126634	.	-	.	transcript_id "Phchi.S3G199300.t1"; gene_id "Phchi.S3G199300"
Phchi.S3	AUGUSTUS	stop_codon	14126323	14126325	.	-	0	transcript_id "Phchi.S3G199300.t1"; gene_id "Phchi.S3G199300"
Phchi.S3	AUGUSTUS	CDS	14126326	14126634	1	-	0	transcript_id "Phchi.S3G199300.t1"; gene_id "Phchi.S3G199300"
Phchi.S3	AUGUSTUS	exon	14126326	14126634	.	-	.	transcript_id "Phchi.S3G199300.t1"; gene_id "Phchi.S3G199300"
Phchi.S3	AUGUSTUS	start_codon	14126632	14126634	.	-	0	transcript_id "Phchi.S3G199300.t1"; gene_id "Phchi.S3G199300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7844.t1 is derived from g5018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31503116	31505666	.	-	.	Phchi.S1G500300
Phchi.S1	AUGUSTUS	transcript	31503116	31505666	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	stop_codon	31503113	31503115	.	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31503116	31503246	0.51	-	2	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31503116	31503246	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31503247	31503440	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31503441	31503494	0.79	-	2	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31503441	31503494	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31503495	31503564	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31503565	31503652	1	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31503565	31503652	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31503653	31503734	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31503735	31503852	1	-	1	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31503735	31503852	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31503853	31503934	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31503935	31504083	1	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31503935	31504083	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31504084	31504256	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31504257	31504313	1	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31504257	31504313	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31504314	31504413	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31504414	31504509	1	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31504414	31504509	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31504510	31504674	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31504675	31504775	0.96	-	2	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31504675	31504775	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31504776	31504889	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31504890	31504972	0.97	-	1	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31504890	31504972	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31504973	31505068	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31505069	31505273	1	-	2	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31505069	31505273	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	intron	31505274	31505557	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	CDS	31505558	31505666	1	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	exon	31505558	31505666	.	-	.	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
Phchi.S1	AUGUSTUS	start_codon	31505664	31505666	.	-	0	transcript_id "Phchi.S1G500300.t1"; gene_id "Phchi.S1G500300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14063.t1 is derived from g12530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10618596	10620246	.	+	.	Phchi.S3G138200
Phchi.S3	AUGUSTUS	transcript	10618596	10620246	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	start_codon	10618596	10618598	.	+	0	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	CDS	10618596	10618695	0.95	+	0	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	exon	10618596	10618695	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	intron	10618696	10618782	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	CDS	10618783	10619002	0.69	+	2	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	exon	10618783	10619002	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	intron	10619003	10619373	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	CDS	10619374	10619475	1	+	1	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	exon	10619374	10619475	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	intron	10619476	10619635	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	CDS	10619636	10620091	1	+	1	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	exon	10619636	10620091	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	intron	10620092	10620191	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	CDS	10620192	10620246	1	+	1	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	exon	10620192	10620246	.	+	.	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
Phchi.S3	AUGUSTUS	stop_codon	10620247	10620249	.	+	0	transcript_id "Phchi.S3G138200.t1"; gene_id "Phchi.S3G138200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9710.t1 is derived from g6886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43366264	43368335	.	+	.	Phchi.S1G686900
Phchi.S1	AUGUSTUS	transcript	43366264	43368335	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	start_codon	43366264	43366266	.	+	0	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43366264	43366373	0.92	+	0	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43366264	43366373	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	intron	43366374	43366453	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43366454	43366601	1	+	1	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43366454	43366601	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	intron	43366602	43366786	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43366787	43366957	1	+	0	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43366787	43366957	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	intron	43366958	43367049	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43367050	43367105	0.95	+	0	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43367050	43367105	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	intron	43367106	43367340	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43367341	43367402	0.93	+	1	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43367341	43367402	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	intron	43367403	43367497	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43367498	43367841	0.36	+	2	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43367498	43367841	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	intron	43367842	43367939	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	CDS	43367940	43368335	0.69	+	0	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	exon	43367940	43368335	.	+	.	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
Phchi.S1	AUGUSTUS	stop_codon	43368336	43368338	.	+	0	transcript_id "Phchi.S1G686900.t1"; gene_id "Phchi.S1G686900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9350.t1 is derived from g6526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41087585	41088959	.	+	.	Phchi.S1G650900
Phchi.S1	AUGUSTUS	transcript	41087585	41088959	.	+	.	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	start_codon	41087585	41087587	.	+	0	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	CDS	41087585	41088567	0.39	+	0	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	exon	41087585	41088567	.	+	.	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	intron	41088568	41088703	.	+	.	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	CDS	41088704	41088959	0.36	+	1	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	exon	41088704	41088959	.	+	.	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
Phchi.S1	AUGUSTUS	stop_codon	41088960	41088962	.	+	0	transcript_id "Phchi.S1G650900.t1"; gene_id "Phchi.S1G650900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8376.t1 is derived from g5551.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35581348	35582973	.	-	.	Phchi.S1G553500
Phchi.S1	AUGUSTUS	transcript	35581551	35582973	.	-	.	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	stop_codon	35581548	35581550	.	-	0	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	CDS	35581551	35581556	0.72	-	0	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	exon	35581551	35581556	.	-	.	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	intron	35581557	35581668	.	-	.	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	CDS	35581669	35582973	1	-	0	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	exon	35581669	35582973	.	-	.	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	start_codon	35582971	35582973	.	-	0	transcript_id "Phchi.S1G553500.t1"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	transcript	35581348	35582973	.	-	.	transcript_id "Phchi.S1G553500.t2"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	stop_codon	35581345	35581347	.	-	0	transcript_id "Phchi.S1G553500.t2"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	CDS	35581348	35582973	0.91	-	0	transcript_id "Phchi.S1G553500.t2"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	exon	35581348	35582973	.	-	.	transcript_id "Phchi.S1G553500.t2"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	start_codon	35582971	35582973	.	-	0	transcript_id "Phchi.S1G553500.t2"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	transcript	35581713	35582973	.	-	.	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	stop_codon	35581710	35581712	.	-	0	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	CDS	35581713	35581716	0.4	-	1	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	exon	35581713	35581716	.	-	.	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	intron	35581717	35581801	.	-	.	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	CDS	35581802	35582973	0.57	-	0	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	exon	35581802	35582973	.	-	.	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
Phchi.S1	AUGUSTUS	start_codon	35582971	35582973	.	-	0	transcript_id "Phchi.S1G553500.t3"; gene_id "Phchi.S1G553500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7480.t1 is derived from g4653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29555342	29557765	.	-	.	Phchi.S1G463900
Phchi.S1	AUGUSTUS	transcript	29555342	29557765	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	stop_codon	29555339	29555341	.	-	0	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29555342	29555426	1	-	1	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29555342	29555426	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29555427	29555548	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29555549	29555688	1	-	0	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29555549	29555688	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29555689	29555778	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29555779	29555837	1	-	2	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29555779	29555837	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29555838	29556012	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29556013	29556088	1	-	0	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29556013	29556088	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29556089	29556207	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29556208	29556364	1	-	1	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29556208	29556364	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29556365	29556490	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29556491	29556579	1	-	0	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29556491	29556579	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29556580	29556662	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29556663	29556768	1	-	1	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29556663	29556768	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29556769	29556865	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29556866	29557027	1	-	1	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29556866	29557027	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	intron	29557028	29557478	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	CDS	29557479	29557765	1	-	0	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	exon	29557479	29557765	.	-	.	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
Phchi.S1	AUGUSTUS	start_codon	29557763	29557765	.	-	0	transcript_id "Phchi.S1G463900.t1"; gene_id "Phchi.S1G463900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8083.t1 is derived from g5258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32871553	32872904	.	-	.	Phchi.S1G524200
Phchi.S1	AUGUSTUS	transcript	32871553	32872904	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	stop_codon	32871550	32871552	.	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	CDS	32871553	32871732	1	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	exon	32871553	32871732	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	intron	32871733	32871826	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	CDS	32871827	32871940	1	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	exon	32871827	32871940	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	intron	32871941	32872049	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	CDS	32872050	32872238	1	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	exon	32872050	32872238	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	intron	32872239	32872322	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	CDS	32872323	32872400	1	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	exon	32872323	32872400	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	intron	32872401	32872492	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	CDS	32872493	32872579	1	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	exon	32872493	32872579	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	intron	32872580	32872817	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	CDS	32872818	32872904	0.62	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	exon	32872818	32872904	.	-	.	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
Phchi.S1	AUGUSTUS	start_codon	32872902	32872904	.	-	0	transcript_id "Phchi.S1G524200.t1"; gene_id "Phchi.S1G524200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5625.t1 is derived from g2795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17939825	17942263	.	+	.	Phchi.S1G278400
Phchi.S1	AUGUSTUS	transcript	17939825	17942263	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	start_codon	17939825	17939827	.	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17939825	17940046	1	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17939825	17940046	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	intron	17940047	17940219	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17940220	17940585	0.93	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17940220	17940585	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	intron	17940586	17940766	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17940767	17941312	0.52	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17940767	17941312	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	intron	17941313	17941680	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17941681	17941762	0.97	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17941681	17941762	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	intron	17941763	17941907	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17941908	17941943	0.82	+	2	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17941908	17941943	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	intron	17941944	17941994	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17941995	17942041	0.89	+	2	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17941995	17942041	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	intron	17942042	17942215	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	CDS	17942216	17942263	0.83	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	exon	17942216	17942263	.	+	.	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
Phchi.S1	AUGUSTUS	stop_codon	17942264	17942266	.	+	0	transcript_id "Phchi.S1G278400.t1"; gene_id "Phchi.S1G278400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3866.t1 is derived from g1035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6128720	6129376	.	-	.	Phchi.S1G102500
Phchi.S1	AUGUSTUS	transcript	6128720	6129376	.	-	.	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	stop_codon	6128717	6128719	.	-	0	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	CDS	6128720	6129005	0.54	-	1	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	exon	6128720	6129005	.	-	.	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	intron	6129006	6129314	.	-	.	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	CDS	6129315	6129376	0.8	-	0	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	exon	6129315	6129376	.	-	.	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
Phchi.S1	AUGUSTUS	start_codon	6129374	6129376	.	-	0	transcript_id "Phchi.S1G102500.t1"; gene_id "Phchi.S1G102500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3657.t1 is derived from g826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5001720	5002205	.	-	.	Phchi.S1G081600
Phchi.S1	AUGUSTUS	transcript	5001720	5002205	.	-	.	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	stop_codon	5001717	5001719	.	-	0	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	CDS	5001720	5001981	0.87	-	1	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	exon	5001720	5001981	.	-	.	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	intron	5001982	5002089	.	-	.	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	CDS	5002090	5002205	0.84	-	0	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	exon	5002090	5002205	.	-	.	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
Phchi.S1	AUGUSTUS	start_codon	5002203	5002205	.	-	0	transcript_id "Phchi.S1G081600.t1"; gene_id "Phchi.S1G081600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1033.t1 is derived from g10816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7222844	7224007	.	-	.	Phchi.S6G099200
Phchi.S6	AUGUSTUS	transcript	7222844	7224007	.	-	.	transcript_id "Phchi.S6G099200.t1"; gene_id "Phchi.S6G099200"
Phchi.S6	AUGUSTUS	stop_codon	7222841	7222843	.	-	0	transcript_id "Phchi.S6G099200.t1"; gene_id "Phchi.S6G099200"
Phchi.S6	AUGUSTUS	CDS	7222844	7224007	0.97	-	0	transcript_id "Phchi.S6G099200.t1"; gene_id "Phchi.S6G099200"
Phchi.S6	AUGUSTUS	exon	7222844	7224007	.	-	.	transcript_id "Phchi.S6G099200.t1"; gene_id "Phchi.S6G099200"
Phchi.S6	AUGUSTUS	start_codon	7224005	7224007	.	-	0	transcript_id "Phchi.S6G099200.t1"; gene_id "Phchi.S6G099200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6782.t1 is derived from g3954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25067401	25072653	.	+	.	Phchi.S1G394100
Phchi.S1	AUGUSTUS	transcript	25067401	25072653	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	start_codon	25067401	25067403	.	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25067401	25067419	1	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25067401	25067419	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25067420	25067587	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25067588	25067869	0.98	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25067588	25067869	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25067870	25067978	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25067979	25068395	1	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25067979	25068395	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25068396	25068559	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25068560	25068775	1	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25068560	25068775	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25068776	25068874	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25068875	25069536	1	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25068875	25069536	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25069537	25069810	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25069811	25069901	1	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25069811	25069901	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25069902	25069993	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25069994	25070057	1	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25069994	25070057	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25070058	25070146	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25070147	25070285	1	+	1	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25070147	25070285	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25070286	25070399	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25070400	25070522	1	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25070400	25070522	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25070523	25070617	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25070618	25070801	1	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25070618	25070801	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25070802	25070998	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25070999	25071037	1	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25070999	25071037	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25071038	25071178	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25071179	25071256	1	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25071179	25071256	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25071257	25071333	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25071334	25071584	0.9	+	2	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25071334	25071584	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	intron	25071585	25071690	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	CDS	25071691	25072653	0.94	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	exon	25071691	25072653	.	+	.	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
Phchi.S1	AUGUSTUS	stop_codon	25072654	25072656	.	+	0	transcript_id "Phchi.S1G394100.t1"; gene_id "Phchi.S1G394100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14585.t1 is derived from g13053.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13583120	13585725	.	-	.	Phchi.S3G190400
Phchi.S3	AUGUSTUS	transcript	13583120	13585725	.	-	.	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	stop_codon	13583117	13583119	.	-	0	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	CDS	13583120	13585475	0.79	-	1	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	exon	13583120	13585475	.	-	.	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	intron	13585476	13585600	.	-	.	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	CDS	13585601	13585725	0.4	-	0	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	exon	13585601	13585725	.	-	.	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	start_codon	13585723	13585725	.	-	0	transcript_id "Phchi.S3G190400.t1"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	transcript	13583120	13583413	.	-	.	transcript_id "Phchi.S3G190400.t2"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	stop_codon	13583117	13583119	.	-	0	transcript_id "Phchi.S3G190400.t2"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	CDS	13583120	13583413	0.7	-	0	transcript_id "Phchi.S3G190400.t2"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	exon	13583120	13583413	.	-	.	transcript_id "Phchi.S3G190400.t2"; gene_id "Phchi.S3G190400"
Phchi.S3	AUGUSTUS	start_codon	13583411	13583413	.	-	0	transcript_id "Phchi.S3G190400.t2"; gene_id "Phchi.S3G190400"
# This transcript jg15057.t1 is derived from g13525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16772364	16772636	.	+	.	Phchi.S3G237600
Phchi.S3	AUGUSTUS	transcript	16772364	16772636	.	+	.	transcript_id "Phchi.S3G237600.t1"; gene_id "Phchi.S3G237600"
Phchi.S3	AUGUSTUS	start_codon	16772364	16772366	.	+	0	transcript_id "Phchi.S3G237600.t1"; gene_id "Phchi.S3G237600"
Phchi.S3	AUGUSTUS	CDS	16772364	16772636	0.39	+	0	transcript_id "Phchi.S3G237600.t1"; gene_id "Phchi.S3G237600"
Phchi.S3	AUGUSTUS	exon	16772364	16772636	.	+	.	transcript_id "Phchi.S3G237600.t1"; gene_id "Phchi.S3G237600"
Phchi.S3	AUGUSTUS	stop_codon	16772637	16772639	.	+	0	transcript_id "Phchi.S3G237600.t1"; gene_id "Phchi.S3G237600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1185.t1 is derived from g10968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8338660	8341566	.	-	.	Phchi.S6G114400
Phchi.S6	AUGUSTUS	transcript	8338660	8341566	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	stop_codon	8338657	8338659	.	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8338660	8338806	0.93	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8338660	8338806	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	intron	8338807	8338942	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8338943	8339374	0.95	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8338943	8339374	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	intron	8339375	8339483	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8339484	8339754	0.14	-	1	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8339484	8339754	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	intron	8339755	8339965	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8339966	8340301	0.26	-	1	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8339966	8340301	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	intron	8340302	8340393	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8340394	8340875	0.55	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8340394	8340875	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	intron	8340876	8340994	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8340995	8341444	0.95	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8340995	8341444	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	intron	8341445	8341518	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	CDS	8341519	8341566	0.8	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	exon	8341519	8341566	.	-	.	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
Phchi.S6	AUGUSTUS	start_codon	8341564	8341566	.	-	0	transcript_id "Phchi.S6G114400.t1"; gene_id "Phchi.S6G114400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1439.t1 is derived from g8358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	859445	861189	.	-	.	Phchi.S5G004800
Phchi.S5	AUGUSTUS	transcript	859445	861189	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	stop_codon	859442	859444	.	-	0	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	CDS	859445	860461	0.99	-	0	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	exon	859445	860461	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	intron	860462	860555	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	CDS	860556	860590	0.97	-	2	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	exon	860556	860590	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	intron	860591	860716	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	CDS	860717	860790	0.62	-	1	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	exon	860717	860790	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	intron	860791	860879	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	CDS	860880	860900	0.68	-	1	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	exon	860880	860900	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	intron	860901	861178	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	CDS	861179	861189	0.7	-	0	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	exon	861179	861189	.	-	.	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
Phchi.S5	AUGUSTUS	start_codon	861187	861189	.	-	0	transcript_id "Phchi.S5G004800.t1"; gene_id "Phchi.S5G004800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5380.t1 is derived from g2550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16588852	16590666	.	-	.	Phchi.S1G253900
Phchi.S1	AUGUSTUS	transcript	16588852	16590666	.	-	.	transcript_id "Phchi.S1G253900.t1"; gene_id "Phchi.S1G253900"
Phchi.S1	AUGUSTUS	stop_codon	16588849	16588851	.	-	0	transcript_id "Phchi.S1G253900.t1"; gene_id "Phchi.S1G253900"
Phchi.S1	AUGUSTUS	CDS	16588852	16590666	1	-	0	transcript_id "Phchi.S1G253900.t1"; gene_id "Phchi.S1G253900"
Phchi.S1	AUGUSTUS	exon	16588852	16590666	.	-	.	transcript_id "Phchi.S1G253900.t1"; gene_id "Phchi.S1G253900"
Phchi.S1	AUGUSTUS	start_codon	16590664	16590666	.	-	0	transcript_id "Phchi.S1G253900.t1"; gene_id "Phchi.S1G253900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1347.t1 is derived from g11130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9125608	9127276	.	+	.	Phchi.S6G130600
Phchi.S6	AUGUSTUS	transcript	9125608	9127276	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	start_codon	9125608	9125610	.	+	0	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	CDS	9125608	9125760	0.78	+	0	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	exon	9125608	9125760	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	intron	9125761	9125869	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	CDS	9125870	9126031	0.72	+	0	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	exon	9125870	9126031	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	intron	9126032	9126204	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	CDS	9126205	9126284	0.36	+	0	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	exon	9126205	9126284	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	intron	9126285	9126385	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	CDS	9126386	9126519	0.48	+	1	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	exon	9126386	9126519	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	intron	9126520	9126629	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	CDS	9126630	9127276	0.82	+	2	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	exon	9126630	9127276	.	+	.	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
Phchi.S6	AUGUSTUS	stop_codon	9127277	9127279	.	+	0	transcript_id "Phchi.S6G130600.t1"; gene_id "Phchi.S6G130600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14873.t1 is derived from g13341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15220113	15221607	.	-	.	Phchi.S3G219200
Phchi.S3	AUGUSTUS	transcript	15220113	15221607	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	stop_codon	15220110	15220112	.	-	0	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15220113	15220251	1	-	1	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15220113	15220251	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15220252	15220374	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15220375	15220483	1	-	2	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15220375	15220483	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15220484	15220573	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15220574	15220657	1	-	2	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15220574	15220657	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15220658	15220753	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15220754	15220838	1	-	0	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15220754	15220838	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15220839	15220951	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15220952	15220990	1	-	0	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15220952	15220990	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15220991	15221072	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15221073	15221153	1	-	0	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15221073	15221153	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15221154	15221235	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15221236	15221366	1	-	2	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15221236	15221366	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	intron	15221367	15221453	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	CDS	15221454	15221607	0.78	-	0	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	exon	15221454	15221607	.	-	.	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
Phchi.S3	AUGUSTUS	start_codon	15221605	15221607	.	-	0	transcript_id "Phchi.S3G219200.t1"; gene_id "Phchi.S3G219200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8084.t1 is derived from g5259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32873247	32874988	.	+	.	Phchi.S1G524300
Phchi.S1	AUGUSTUS	transcript	32873247	32874988	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	start_codon	32873247	32873249	.	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	CDS	32873247	32874083	0.79	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	exon	32873247	32874083	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	intron	32874084	32874164	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	CDS	32874165	32874296	1	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	exon	32874165	32874296	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	intron	32874297	32874386	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	CDS	32874387	32874530	1	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	exon	32874387	32874530	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	intron	32874531	32874629	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	CDS	32874630	32874722	1	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	exon	32874630	32874722	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	intron	32874723	32874802	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	CDS	32874803	32874988	0.99	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	exon	32874803	32874988	.	+	.	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
Phchi.S1	AUGUSTUS	stop_codon	32874989	32874991	.	+	0	transcript_id "Phchi.S1G524300.t1"; gene_id "Phchi.S1G524300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4246.t1 is derived from g1415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9154152	9155278	.	+	.	Phchi.S1G140500
Phchi.S1	AUGUSTUS	transcript	9154152	9155278	.	+	.	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	start_codon	9154152	9154154	.	+	0	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	CDS	9154152	9154969	0.61	+	0	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	exon	9154152	9154969	.	+	.	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	intron	9154970	9155226	.	+	.	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	CDS	9155227	9155278	1	+	1	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	exon	9155227	9155278	.	+	.	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
Phchi.S1	AUGUSTUS	stop_codon	9155279	9155281	.	+	0	transcript_id "Phchi.S1G140500.t1"; gene_id "Phchi.S1G140500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1384.t1 is derived from g16017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	521	1006	.	+	.	Phchi.C243G000200
Phchi.C243	AUGUSTUS	transcript	521	1006	.	+	.	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	start_codon	521	523	.	+	0	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	CDS	521	523	1	+	0	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	exon	521	523	.	+	.	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	intron	524	686	.	+	.	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	CDS	687	791	1	+	0	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	exon	687	791	.	+	.	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	intron	792	874	.	+	.	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	CDS	875	1006	0.99	+	0	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	exon	875	1006	.	+	.	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
Phchi.C243	AUGUSTUS	stop_codon	1007	1009	.	+	0	transcript_id "Phchi.C243G000200.t1"; gene_id "Phchi.C243G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11106.t1 is derived from g15156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4158964	4162252	.	-	.	Phchi.S4G068800
Phchi.S4	AUGUSTUS	transcript	4158964	4162252	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	stop_codon	4158961	4158963	.	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4158964	4159327	0.48	-	1	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4158964	4159327	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4159328	4159418	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4159419	4159514	0.55	-	1	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4159419	4159514	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4159515	4159694	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4159695	4159744	0.98	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4159695	4159744	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4159745	4159831	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4159832	4159937	0.76	-	1	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4159832	4159937	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4159938	4160044	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4160045	4160061	0.75	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4160045	4160061	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4160062	4160233	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4160234	4160304	0.54	-	2	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4160234	4160304	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4160305	4160400	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4160401	4160437	0.64	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4160401	4160437	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4160438	4160550	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4160551	4160712	0.77	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4160551	4160712	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4160713	4160838	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4160839	4160918	1	-	2	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4160839	4160918	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4160919	4161014	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4161015	4161116	1	-	2	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4161015	4161116	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4161117	4161223	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4161224	4161275	0.91	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4161224	4161275	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4161276	4161521	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4161522	4161584	0.9	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4161522	4161584	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4161585	4161654	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4161655	4161860	0.51	-	2	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4161655	4161860	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	intron	4161861	4161948	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	CDS	4161949	4162252	0.83	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	exon	4161949	4162252	.	-	.	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
Phchi.S4	AUGUSTUS	start_codon	4162250	4162252	.	-	0	transcript_id "Phchi.S4G068800.t1"; gene_id "Phchi.S4G068800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12349.t1 is derived from g8025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12373902	12374339	.	+	.	Phchi.S2G042900
Phchi.S2	AUGUSTUS	transcript	12373902	12374339	.	+	.	transcript_id "Phchi.S2G042900.t1"; gene_id "Phchi.S2G042900"
Phchi.S2	AUGUSTUS	start_codon	12373902	12373904	.	+	0	transcript_id "Phchi.S2G042900.t1"; gene_id "Phchi.S2G042900"
Phchi.S2	AUGUSTUS	CDS	12373902	12374339	0.43	+	0	transcript_id "Phchi.S2G042900.t1"; gene_id "Phchi.S2G042900"
Phchi.S2	AUGUSTUS	exon	12373902	12374339	.	+	.	transcript_id "Phchi.S2G042900.t1"; gene_id "Phchi.S2G042900"
Phchi.S2	AUGUSTUS	stop_codon	12374340	12374342	.	+	0	transcript_id "Phchi.S2G042900.t1"; gene_id "Phchi.S2G042900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2527.t1 is derived from g9447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7158846	7161091	.	+	.	Phchi.S5G113600
Phchi.S5	AUGUSTUS	transcript	7158846	7161091	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	start_codon	7158846	7158848	.	+	0	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	CDS	7158846	7158914	0.86	+	0	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	exon	7158846	7158914	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	intron	7158915	7159039	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	CDS	7159040	7159780	0.91	+	0	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	exon	7159040	7159780	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	intron	7159781	7159980	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	CDS	7159981	7160647	0.87	+	0	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	exon	7159981	7160647	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	intron	7160648	7160809	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	CDS	7160810	7160922	0.64	+	2	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	exon	7160810	7160922	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	intron	7160923	7161034	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	CDS	7161035	7161091	0.47	+	0	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	exon	7161035	7161091	.	+	.	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
Phchi.S5	AUGUSTUS	stop_codon	7161092	7161094	.	+	0	transcript_id "Phchi.S5G113600.t1"; gene_id "Phchi.S5G113600"
# This transcript jg3827.t2 is derived from g996.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3827.t3 is derived from g996.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3828.t1 is derived from g997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5910641	5914338	.	+	.	Phchi.S1G098700
Phchi.S1	AUGUSTUS	transcript	5910641	5914338	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	start_codon	5910641	5910643	.	+	0	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	CDS	5910641	5910792	1	+	0	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	exon	5910641	5910792	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	intron	5910793	5910875	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	CDS	5910876	5911039	1	+	1	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	exon	5910876	5911039	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	intron	5911040	5911122	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	CDS	5911123	5911246	1	+	2	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	exon	5911123	5911246	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	intron	5911247	5911368	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	CDS	5911369	5911501	1	+	1	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	exon	5911369	5911501	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	intron	5911502	5911617	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	CDS	5911618	5911688	0.99	+	0	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	exon	5911618	5911688	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	intron	5911689	5911805	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	CDS	5911806	5914338	0.96	+	1	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	exon	5911806	5914338	.	+	.	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
Phchi.S1	AUGUSTUS	stop_codon	5914339	5914341	.	+	0	transcript_id "Phchi.S1G098700.t1"; gene_id "Phchi.S1G098700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15885.t1 is derived from g14355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22027644	22028139	.	-	.	Phchi.S3G320400
Phchi.S3	AUGUSTUS	transcript	22027644	22028139	.	-	.	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	stop_codon	22027641	22027643	.	-	0	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	CDS	22027644	22027801	0.97	-	2	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	exon	22027644	22027801	.	-	.	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	intron	22027802	22027898	.	-	.	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	CDS	22027899	22028139	0.94	-	0	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	exon	22027899	22028139	.	-	.	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
Phchi.S3	AUGUSTUS	start_codon	22028137	22028139	.	-	0	transcript_id "Phchi.S3G320400.t1"; gene_id "Phchi.S3G320400"
# This transcript jg7482.t2 is derived from g4655.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7483.t1 is derived from g4656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29577346	29578785	.	+	.	Phchi.S1G464200
Phchi.S1	AUGUSTUS	transcript	29577346	29578785	.	+	.	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	start_codon	29577346	29577348	.	+	0	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	CDS	29577346	29577789	0.43	+	0	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	exon	29577346	29577789	.	+	.	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	intron	29577790	29578402	.	+	.	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	CDS	29578403	29578465	0.31	+	0	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	exon	29578403	29578465	.	+	.	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	intron	29578466	29578752	.	+	.	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	CDS	29578753	29578785	0.48	+	0	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	exon	29578753	29578785	.	+	.	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
Phchi.S1	AUGUSTUS	stop_codon	29578786	29578788	.	+	0	transcript_id "Phchi.S1G464200.t1"; gene_id "Phchi.S1G464200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14485.t1 is derived from g12953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13086135	13088035	.	-	.	Phchi.S3G180400
Phchi.S3	AUGUSTUS	transcript	13086135	13088035	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	stop_codon	13086132	13086134	.	-	0	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13086135	13086263	1	-	0	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13086135	13086263	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13086264	13086339	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13086340	13086416	1	-	2	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13086340	13086416	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13086417	13086516	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13086517	13086657	1	-	2	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13086517	13086657	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13086658	13086745	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13086746	13086864	1	-	1	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13086746	13086864	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13086865	13086986	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13086987	13087075	1	-	0	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13086987	13087075	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13087076	13087175	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13087176	13087247	1	-	0	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13087176	13087247	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13087248	13087458	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13087459	13087549	1	-	1	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13087459	13087549	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13087550	13087648	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13087649	13087805	0.98	-	2	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13087649	13087805	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	intron	13087806	13087917	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	CDS	13087918	13088035	1	-	0	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	exon	13087918	13088035	.	-	.	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
Phchi.S3	AUGUSTUS	start_codon	13088033	13088035	.	-	0	transcript_id "Phchi.S3G180400.t1"; gene_id "Phchi.S3G180400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6860.t1 is derived from g4032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25614324	25615611	.	-	.	Phchi.S1G401900
Phchi.S1	AUGUSTUS	transcript	25614324	25615611	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	stop_codon	25614321	25614323	.	-	0	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	CDS	25614324	25614599	1	-	0	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	exon	25614324	25614599	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	intron	25614600	25614692	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	CDS	25614693	25614930	1	-	1	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	exon	25614693	25614930	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	intron	25614931	25615043	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	CDS	25615044	25615202	0.99	-	1	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	exon	25615044	25615202	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	intron	25615203	25615315	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	CDS	25615316	25615611	1	-	0	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	exon	25615316	25615611	.	-	.	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
Phchi.S1	AUGUSTUS	start_codon	25615609	25615611	.	-	0	transcript_id "Phchi.S1G401900.t1"; gene_id "Phchi.S1G401900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8189.t1 is derived from g5364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34343587	34350809	.	+	.	Phchi.S1G534800
Phchi.S1	AUGUSTUS	transcript	34343587	34350809	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	start_codon	34343587	34343589	.	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34343587	34343769	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34343587	34343769	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34343770	34344218	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34344219	34344264	0.94	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34344219	34344264	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34344265	34344335	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34344336	34344343	0.94	+	2	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34344336	34344343	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34344344	34344482	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34344483	34344556	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34344483	34344556	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34344557	34344701	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34344702	34344803	1	+	1	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34344702	34344803	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34344804	34344937	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34344938	34345610	1	+	1	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34344938	34345610	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34345611	34345696	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34345697	34345777	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34345697	34345777	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34345778	34345919	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34345920	34346117	0.98	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34345920	34346117	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34346118	34346226	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34346227	34346409	0.52	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34346227	34346409	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34346410	34346583	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34346584	34346736	0.64	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34346584	34346736	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34346737	34346901	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34346902	34347051	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34346902	34347051	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34347052	34347150	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34347151	34347216	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34347151	34347216	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34347217	34347306	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34347307	34347336	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34347307	34347336	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34347337	34347742	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34347743	34347781	0.99	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34347743	34347781	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34347782	34347866	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34347867	34347959	0.73	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34347867	34347959	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34347960	34348114	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34348115	34348174	0.99	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34348115	34348174	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34348175	34348277	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34348278	34348463	0.99	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34348278	34348463	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34348464	34348662	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34348663	34348812	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34348663	34348812	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34348813	34348999	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34349000	34349062	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34349000	34349062	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34349063	34349164	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34349165	34349686	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34349165	34349686	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34349687	34349896	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34349897	34350052	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34349897	34350052	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34350053	34350200	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34350201	34350292	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34350201	34350292	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34350293	34350408	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34350409	34350523	1	+	1	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34350409	34350523	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	intron	34350524	34350635	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	CDS	34350636	34350809	1	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	exon	34350636	34350809	.	+	.	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
Phchi.S1	AUGUSTUS	stop_codon	34350810	34350812	.	+	0	transcript_id "Phchi.S1G534800.t1"; gene_id "Phchi.S1G534800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8099.t1 is derived from g5274.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32946798	32952469	.	-	.	Phchi.S1G525800
Phchi.S1	AUGUSTUS	transcript	32946798	32952469	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	stop_codon	32946795	32946797	.	-	0	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32946798	32947219	0.95	-	2	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32946798	32947219	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32947220	32947537	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32947538	32949671	0.66	-	0	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32947538	32949671	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32949672	32949779	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32949780	32951417	0.2	-	0	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32949780	32951417	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32951418	32951565	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32951566	32951683	1	-	1	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32951566	32951683	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32951684	32951917	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32951918	32952023	1	-	2	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32951918	32952023	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32952024	32952288	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32952289	32952469	0.96	-	0	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32952289	32952469	.	-	.	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	start_codon	32952467	32952469	.	-	0	transcript_id "Phchi.S1G525800.t1"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	transcript	32946798	32952469	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	stop_codon	32946795	32946797	.	-	0	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32946798	32947219	0.95	-	2	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32946798	32947219	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32947220	32947445	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32947446	32947451	0.52	-	2	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32947446	32947451	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32947452	32947603	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32947604	32949671	0.79	-	0	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32947604	32949671	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32949672	32949779	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32949780	32951417	0.09	-	0	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32949780	32951417	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32951418	32951565	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32951566	32951683	1	-	1	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32951566	32951683	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32951684	32951917	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32951918	32952023	1	-	2	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32951918	32952023	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	intron	32952024	32952288	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	CDS	32952289	32952469	0.98	-	0	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	exon	32952289	32952469	.	-	.	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
Phchi.S1	AUGUSTUS	start_codon	32952467	32952469	.	-	0	transcript_id "Phchi.S1G525800.t2"; gene_id "Phchi.S1G525800"
# This transcript jg3604.t2 is derived from g773.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3605.t1 is derived from g774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4708977	4710080	.	+	.	Phchi.S1G076400
Phchi.S1	AUGUSTUS	transcript	4708977	4710080	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	start_codon	4708977	4708979	.	+	0	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	CDS	4708977	4708987	0.35	+	0	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	exon	4708977	4708987	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	intron	4708988	4709075	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	CDS	4709076	4709441	0.28	+	1	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	exon	4709076	4709441	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	intron	4709442	4709579	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	CDS	4709580	4709637	1	+	1	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	exon	4709580	4709637	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	intron	4709638	4709748	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	CDS	4709749	4709877	1	+	0	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	exon	4709749	4709877	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	intron	4709878	4710026	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	CDS	4710027	4710080	1	+	0	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	exon	4710027	4710080	.	+	.	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
Phchi.S1	AUGUSTUS	stop_codon	4710081	4710083	.	+	0	transcript_id "Phchi.S1G076400.t1"; gene_id "Phchi.S1G076400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6882.t1 is derived from g4054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25814555	25815389	.	-	.	Phchi.S1G404100
Phchi.S1	AUGUSTUS	transcript	25814555	25815389	.	-	.	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	stop_codon	25814552	25814554	.	-	0	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	CDS	25814555	25814723	0.84	-	1	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	exon	25814555	25814723	.	-	.	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	intron	25814724	25814841	.	-	.	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	CDS	25814842	25815389	0.4	-	0	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	exon	25814842	25815389	.	-	.	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
Phchi.S1	AUGUSTUS	start_codon	25815387	25815389	.	-	0	transcript_id "Phchi.S1G404100.t1"; gene_id "Phchi.S1G404100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg364.t1 is derived from g10146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2658237	2660096	.	+	.	Phchi.S6G032300
Phchi.S6	AUGUSTUS	transcript	2658237	2660096	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	start_codon	2658237	2658239	.	+	0	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	CDS	2658237	2659196	0.49	+	0	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	exon	2658237	2659196	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	intron	2659197	2659304	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	CDS	2659305	2659577	0.98	+	0	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	exon	2659305	2659577	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	intron	2659578	2659709	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	CDS	2659710	2659865	1	+	0	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	exon	2659710	2659865	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	intron	2659866	2659979	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	CDS	2659980	2660096	1	+	0	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	exon	2659980	2660096	.	+	.	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
Phchi.S6	AUGUSTUS	stop_codon	2660097	2660099	.	+	0	transcript_id "Phchi.S6G032300.t1"; gene_id "Phchi.S6G032300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14357.t1 is derived from g12824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12351010	12353181	.	+	.	Phchi.S3G167600
Phchi.S3	AUGUSTUS	transcript	12351010	12353181	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	start_codon	12351010	12351012	.	+	0	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12351010	12351115	1	+	0	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12351010	12351115	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12351116	12351205	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12351206	12351496	0.57	+	2	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12351206	12351496	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12351497	12351616	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12351617	12351735	0.55	+	2	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12351617	12351735	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12351736	12351844	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12351845	12351952	1	+	0	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12351845	12351952	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12351953	12352143	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12352144	12352302	1	+	0	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12352144	12352302	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12352303	12352395	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12352396	12352462	0.71	+	0	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12352396	12352462	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12352463	12352543	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12352544	12352648	0.7	+	2	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12352544	12352648	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	intron	12352649	12352738	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	CDS	12352739	12353181	1	+	2	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	exon	12352739	12353181	.	+	.	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
Phchi.S3	AUGUSTUS	stop_codon	12353182	12353184	.	+	0	transcript_id "Phchi.S3G167600.t1"; gene_id "Phchi.S3G167600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14012.t1 is derived from g12479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10305332	10307067	.	-	.	Phchi.S3G133100
Phchi.S3	AUGUSTUS	transcript	10305332	10307067	.	-	.	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	stop_codon	10305329	10305331	.	-	0	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	CDS	10305332	10305782	0.33	-	1	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	exon	10305332	10305782	.	-	.	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	intron	10305783	10305898	.	-	.	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	CDS	10305899	10307067	0.18	-	0	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	exon	10305899	10307067	.	-	.	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
Phchi.S3	AUGUSTUS	start_codon	10307065	10307067	.	-	0	transcript_id "Phchi.S3G133100.t1"; gene_id "Phchi.S3G133100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8838.t1 is derived from g6013.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38219886	38221622	.	+	.	Phchi.S1G599700
Phchi.S1	AUGUSTUS	transcript	38219886	38221622	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	start_codon	38219886	38219888	.	+	0	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38219886	38219997	0.98	+	0	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38219886	38219997	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38219998	38220160	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220161	38220256	1	+	2	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220161	38220256	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38220257	38220409	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220410	38220458	1	+	2	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220410	38220458	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38220459	38220535	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220536	38220639	0.9	+	1	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220536	38220639	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38220640	38220717	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220718	38221622	0.8	+	2	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220718	38221622	.	+	.	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	stop_codon	38221623	38221625	.	+	0	transcript_id "Phchi.S1G599700.t1"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	transcript	38219886	38221622	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	start_codon	38219886	38219888	.	+	0	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38219886	38219997	1	+	0	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38219886	38219997	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38219998	38220160	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220161	38220256	1	+	2	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220161	38220256	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38220257	38220409	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220410	38220458	0.99	+	2	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220410	38220458	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38220459	38220604	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220605	38220639	0.83	+	1	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220605	38220639	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	intron	38220640	38220717	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	CDS	38220718	38221622	0.68	+	2	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	exon	38220718	38221622	.	+	.	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
Phchi.S1	AUGUSTUS	stop_codon	38221623	38221625	.	+	0	transcript_id "Phchi.S1G599700.t2"; gene_id "Phchi.S1G599700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13297.t1 is derived from g11763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5410727	5413238	.	+	.	Phchi.S3G061600
Phchi.S3	AUGUSTUS	transcript	5410727	5413238	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	start_codon	5410727	5410729	.	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5410727	5410950	1	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5410727	5410950	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5410951	5411099	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5411100	5411424	1	+	1	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5411100	5411424	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5411425	5411542	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5411543	5411692	1	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5411543	5411692	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5411693	5411782	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5411783	5412043	1	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5411783	5412043	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5412044	5412174	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5412175	5412261	1	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5412175	5412261	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5412262	5412382	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5412383	5412461	1	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5412383	5412461	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5412462	5412609	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5412610	5412716	0.98	+	2	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5412610	5412716	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5412717	5412819	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5412820	5412938	0.98	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5412820	5412938	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	intron	5412939	5413099	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	CDS	5413100	5413238	0.98	+	1	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	exon	5413100	5413238	.	+	.	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
Phchi.S3	AUGUSTUS	stop_codon	5413239	5413241	.	+	0	transcript_id "Phchi.S3G061600.t1"; gene_id "Phchi.S3G061600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6115.t1 is derived from g3286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21006656	21008021	.	+	.	Phchi.S1G327400
Phchi.S1	AUGUSTUS	transcript	21006656	21008021	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	start_codon	21006656	21006658	.	+	0	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	CDS	21006656	21006841	0.8	+	0	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	exon	21006656	21006841	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	intron	21006842	21006996	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	CDS	21006997	21007117	1	+	0	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	exon	21006997	21007117	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	intron	21007118	21007217	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	CDS	21007218	21007309	1	+	2	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	exon	21007218	21007309	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	intron	21007310	21007413	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	CDS	21007414	21007510	0.99	+	0	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	exon	21007414	21007510	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	intron	21007511	21007638	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	CDS	21007639	21008021	0.66	+	2	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	exon	21007639	21008021	.	+	.	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
Phchi.S1	AUGUSTUS	stop_codon	21008022	21008024	.	+	0	transcript_id "Phchi.S1G327400.t1"; gene_id "Phchi.S1G327400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4138.t1 is derived from g1307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8471018	8471488	.	+	.	Phchi.S1G129700
Phchi.S1	AUGUSTUS	transcript	8471018	8471488	.	+	.	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	start_codon	8471018	8471020	.	+	0	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	CDS	8471018	8471242	1	+	0	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	exon	8471018	8471242	.	+	.	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	intron	8471243	8471455	.	+	.	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	CDS	8471456	8471488	1	+	0	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	exon	8471456	8471488	.	+	.	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
Phchi.S1	AUGUSTUS	stop_codon	8471489	8471491	.	+	0	transcript_id "Phchi.S1G129700.t1"; gene_id "Phchi.S1G129700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7764.t1 is derived from g4938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31160545	31161028	.	+	.	Phchi.S1G492300
Phchi.S1	AUGUSTUS	transcript	31160545	31161028	.	+	.	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	start_codon	31160545	31160547	.	+	0	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	CDS	31160545	31160760	0.7	+	0	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	exon	31160545	31160760	.	+	.	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	intron	31160761	31160842	.	+	.	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	CDS	31160843	31161028	0.57	+	0	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	exon	31160843	31161028	.	+	.	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
Phchi.S1	AUGUSTUS	stop_codon	31161029	31161031	.	+	0	transcript_id "Phchi.S1G492300.t1"; gene_id "Phchi.S1G492300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13969.t1 is derived from g12436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9981055	9983324	.	+	.	Phchi.S3G128800
Phchi.S3	AUGUSTUS	transcript	9981055	9983324	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	start_codon	9981055	9981057	.	+	0	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9981055	9981502	1	+	0	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9981055	9981502	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9981503	9981587	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9981588	9981825	1	+	2	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9981588	9981825	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9981826	9981919	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9981920	9981981	1	+	1	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9981920	9981981	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9981982	9982066	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9982067	9982215	1	+	2	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9982067	9982215	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9982216	9982306	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9982307	9982427	1	+	0	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9982307	9982427	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9982428	9982511	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9982512	9982667	1	+	2	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9982512	9982667	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9982668	9982810	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9982811	9982856	1	+	2	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9982811	9982856	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9982857	9982947	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9982948	9983023	1	+	1	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9982948	9983023	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9983024	9983105	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9983106	9983182	1	+	0	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9983106	9983182	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	intron	9983183	9983272	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	CDS	9983273	9983324	1	+	1	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	exon	9983273	9983324	.	+	.	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
Phchi.S3	AUGUSTUS	stop_codon	9983325	9983327	.	+	0	transcript_id "Phchi.S3G128800.t1"; gene_id "Phchi.S3G128800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13326.t1 is derived from g11792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6113432	6113767	.	-	.	Phchi.S3G064500
Phchi.S3	AUGUSTUS	transcript	6113432	6113767	.	-	.	transcript_id "Phchi.S3G064500.t1"; gene_id "Phchi.S3G064500"
Phchi.S3	AUGUSTUS	stop_codon	6113429	6113431	.	-	0	transcript_id "Phchi.S3G064500.t1"; gene_id "Phchi.S3G064500"
Phchi.S3	AUGUSTUS	CDS	6113432	6113767	0.87	-	0	transcript_id "Phchi.S3G064500.t1"; gene_id "Phchi.S3G064500"
Phchi.S3	AUGUSTUS	exon	6113432	6113767	.	-	.	transcript_id "Phchi.S3G064500.t1"; gene_id "Phchi.S3G064500"
Phchi.S3	AUGUSTUS	start_codon	6113765	6113767	.	-	0	transcript_id "Phchi.S3G064500.t1"; gene_id "Phchi.S3G064500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15257.t1 is derived from g13725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17947605	17948834	.	+	.	Phchi.S3G257600
Phchi.S3	AUGUSTUS	transcript	17947605	17948834	.	+	.	transcript_id "Phchi.S3G257600.t1"; gene_id "Phchi.S3G257600"
Phchi.S3	AUGUSTUS	start_codon	17947605	17947607	.	+	0	transcript_id "Phchi.S3G257600.t1"; gene_id "Phchi.S3G257600"
Phchi.S3	AUGUSTUS	CDS	17947605	17948834	0.96	+	0	transcript_id "Phchi.S3G257600.t1"; gene_id "Phchi.S3G257600"
Phchi.S3	AUGUSTUS	exon	17947605	17948834	.	+	.	transcript_id "Phchi.S3G257600.t1"; gene_id "Phchi.S3G257600"
Phchi.S3	AUGUSTUS	stop_codon	17948835	17948837	.	+	0	transcript_id "Phchi.S3G257600.t1"; gene_id "Phchi.S3G257600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3276.t1 is derived from g445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2646926	2648849	.	+	.	Phchi.S1G043500
Phchi.S1	AUGUSTUS	transcript	2646926	2648849	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	start_codon	2646926	2646928	.	+	0	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	CDS	2646926	2646961	0.8	+	0	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	exon	2646926	2646961	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	intron	2646962	2647360	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	CDS	2647361	2647419	0.74	+	0	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	exon	2647361	2647419	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	intron	2647420	2647799	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	CDS	2647800	2647888	0.66	+	1	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	exon	2647800	2647888	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	intron	2647889	2647983	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	CDS	2647984	2648849	0.98	+	2	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	exon	2647984	2648849	.	+	.	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
Phchi.S1	AUGUSTUS	stop_codon	2648850	2648852	.	+	0	transcript_id "Phchi.S1G043500.t1"; gene_id "Phchi.S1G043500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14191.t1 is derived from g12658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11402056	11402728	.	-	.	Phchi.S3G151000
Phchi.S3	AUGUSTUS	transcript	11402056	11402728	.	-	.	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	stop_codon	11402053	11402055	.	-	0	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	CDS	11402056	11402170	0.92	-	1	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	exon	11402056	11402170	.	-	.	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	intron	11402171	11402261	.	-	.	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	CDS	11402262	11402455	1	-	0	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	exon	11402262	11402455	.	-	.	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	intron	11402456	11402719	.	-	.	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	CDS	11402720	11402728	1	-	0	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	exon	11402720	11402728	.	-	.	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
Phchi.S3	AUGUSTUS	start_codon	11402726	11402728	.	-	0	transcript_id "Phchi.S3G151000.t1"; gene_id "Phchi.S3G151000"
# This transcript jg11647.t2 is derived from g15698.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11648.t1 is derived from g15699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7449342	7452919	.	+	.	Phchi.S4G123000
Phchi.S4	AUGUSTUS	transcript	7449342	7452919	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	start_codon	7449342	7449344	.	+	0	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7449342	7449344	0.97	+	0	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7449342	7449344	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	intron	7449345	7449494	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7449495	7449633	0.52	+	0	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7449495	7449633	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	intron	7449634	7449760	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7449761	7449895	0.17	+	2	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7449761	7449895	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	intron	7449896	7449991	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7449992	7450086	0.7	+	2	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7449992	7450086	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	intron	7450087	7450169	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7450170	7450230	0.46	+	0	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7450170	7450230	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	intron	7450231	7450343	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7450344	7450384	0.43	+	2	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7450344	7450384	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	intron	7450385	7450477	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	CDS	7450478	7452919	0.78	+	0	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	exon	7450478	7452919	.	+	.	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
Phchi.S4	AUGUSTUS	stop_codon	7452920	7452922	.	+	0	transcript_id "Phchi.S4G123000.t1"; gene_id "Phchi.S4G123000"
# This transcript jg2172.t2 is derived from g9092.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2173.t1 is derived from g9093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5215387	5216858	.	+	.	Phchi.S5G078200
Phchi.S5	AUGUSTUS	transcript	5215387	5216858	.	+	.	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	start_codon	5215387	5215389	.	+	0	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	CDS	5215387	5216220	0.4	+	0	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	exon	5215387	5216220	.	+	.	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	intron	5216221	5216317	.	+	.	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	CDS	5216318	5216555	0.51	+	0	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	exon	5216318	5216555	.	+	.	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	intron	5216556	5216652	.	+	.	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	CDS	5216653	5216858	0.84	+	2	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	exon	5216653	5216858	.	+	.	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
Phchi.S5	AUGUSTUS	stop_codon	5216859	5216861	.	+	0	transcript_id "Phchi.S5G078200.t1"; gene_id "Phchi.S5G078200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14489.t1 is derived from g12957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13113772	13115572	.	+	.	Phchi.S3G180800
Phchi.S3	AUGUSTUS	transcript	13113772	13115572	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	start_codon	13113772	13113774	.	+	0	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13113772	13113841	1	+	0	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13113772	13113841	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13113842	13113927	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13113928	13114031	0.63	+	2	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13113928	13114031	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13114032	13114132	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13114133	13114257	1	+	0	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13114133	13114257	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13114258	13114374	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13114375	13114453	1	+	1	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13114375	13114453	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13114454	13114574	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13114575	13114725	1	+	0	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13114575	13114725	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13114726	13114850	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13114851	13115071	1	+	2	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13114851	13115071	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13115072	13115180	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13115181	13115275	1	+	0	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13115181	13115275	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	intron	13115276	13115355	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	CDS	13115356	13115572	1	+	1	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	exon	13115356	13115572	.	+	.	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
Phchi.S3	AUGUSTUS	stop_codon	13115573	13115575	.	+	0	transcript_id "Phchi.S3G180800.t1"; gene_id "Phchi.S3G180800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4213.t1 is derived from g1382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8949904	8950378	.	+	.	Phchi.S1G137200
Phchi.S1	AUGUSTUS	transcript	8949904	8950378	.	+	.	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	start_codon	8949904	8949906	.	+	0	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	CDS	8949904	8950064	0.68	+	0	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	exon	8949904	8950064	.	+	.	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	intron	8950065	8950206	.	+	.	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	CDS	8950207	8950378	0.96	+	1	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	exon	8950207	8950378	.	+	.	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
Phchi.S1	AUGUSTUS	stop_codon	8950379	8950381	.	+	0	transcript_id "Phchi.S1G137200.t1"; gene_id "Phchi.S1G137200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7167.t1 is derived from g4339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27359626	27361692	.	-	.	Phchi.S1G432600
Phchi.S1	AUGUSTUS	transcript	27359626	27361692	.	-	.	transcript_id "Phchi.S1G432600.t1"; gene_id "Phchi.S1G432600"
Phchi.S1	AUGUSTUS	stop_codon	27359623	27359625	.	-	0	transcript_id "Phchi.S1G432600.t1"; gene_id "Phchi.S1G432600"
Phchi.S1	AUGUSTUS	CDS	27359626	27361692	0.94	-	0	transcript_id "Phchi.S1G432600.t1"; gene_id "Phchi.S1G432600"
Phchi.S1	AUGUSTUS	exon	27359626	27361692	.	-	.	transcript_id "Phchi.S1G432600.t1"; gene_id "Phchi.S1G432600"
Phchi.S1	AUGUSTUS	start_codon	27361690	27361692	.	-	0	transcript_id "Phchi.S1G432600.t1"; gene_id "Phchi.S1G432600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8875.t1 is derived from g6050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38403594	38407272	.	-	.	Phchi.S1G603400
Phchi.S1	AUGUSTUS	transcript	38403594	38407272	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	stop_codon	38403591	38403593	.	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38403594	38403611	0.73	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38403594	38403611	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38403612	38403776	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38403777	38403854	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38403777	38403854	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38403855	38403936	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38403937	38403990	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38403937	38403990	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38403991	38404114	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38404115	38404214	1	-	1	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38404115	38404214	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38404215	38404322	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38404323	38404436	1	-	1	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38404323	38404436	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38404437	38404549	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38404550	38404614	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38404550	38404614	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38404615	38404732	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38404733	38404840	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38404733	38404840	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38404841	38404954	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38404955	38405028	1	-	2	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38404955	38405028	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38405029	38405202	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38405203	38405284	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38405203	38405284	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38405285	38405451	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38405452	38405539	1	-	1	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38405452	38405539	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38405540	38405675	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38405676	38405759	0.98	-	1	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38405676	38405759	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38405760	38405840	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38405841	38405856	0.65	-	2	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38405841	38405856	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38405857	38406012	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38406013	38406085	0.83	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38406013	38406085	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38406086	38406179	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38406180	38406383	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38406180	38406383	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38406384	38406472	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38406473	38406544	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38406473	38406544	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38406545	38406778	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38406779	38406848	1	-	1	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38406779	38406848	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38406849	38406957	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38406958	38407022	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38406958	38407022	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	intron	38407023	38407143	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	CDS	38407144	38407272	1	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	exon	38407144	38407272	.	-	.	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
Phchi.S1	AUGUSTUS	start_codon	38407270	38407272	.	-	0	transcript_id "Phchi.S1G603400.t1"; gene_id "Phchi.S1G603400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14445.t1 is derived from g12913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12867476	12868654	.	+	.	Phchi.S3G176400
Phchi.S3	AUGUSTUS	transcript	12867476	12868654	.	+	.	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	start_codon	12867476	12867478	.	+	0	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	CDS	12867476	12867669	1	+	0	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	exon	12867476	12867669	.	+	.	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	intron	12867670	12868200	.	+	.	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	CDS	12868201	12868654	0.82	+	1	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	exon	12868201	12868654	.	+	.	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
Phchi.S3	AUGUSTUS	stop_codon	12868655	12868657	.	+	0	transcript_id "Phchi.S3G176400.t1"; gene_id "Phchi.S3G176400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11142.t1 is derived from g15192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4372511	4373133	.	-	.	Phchi.S4G072400
Phchi.S4	AUGUSTUS	transcript	4372511	4373133	.	-	.	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	stop_codon	4372508	4372510	.	-	0	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	CDS	4372511	4372753	0.31	-	0	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	exon	4372511	4372753	.	-	.	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	intron	4372754	4372873	.	-	.	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	CDS	4372874	4372929	0.64	-	2	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	exon	4372874	4372929	.	-	.	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	intron	4372930	4373021	.	-	.	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	CDS	4373022	4373133	0.91	-	0	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	exon	4373022	4373133	.	-	.	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
Phchi.S4	AUGUSTUS	start_codon	4373131	4373133	.	-	0	transcript_id "Phchi.S4G072400.t1"; gene_id "Phchi.S4G072400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13566.t1 is derived from g12033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7523020	7530389	.	+	.	Phchi.S3G088500
Phchi.S3	AUGUSTUS	transcript	7523020	7530389	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	start_codon	7523020	7523022	.	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7523020	7523149	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7523020	7523149	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7523150	7523273	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7523274	7523314	0.52	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7523274	7523314	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7523315	7523419	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7523420	7523536	0.78	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7523420	7523536	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7523537	7523699	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7523700	7523871	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7523700	7523871	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7523872	7523952	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7523953	7524065	1	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7523953	7524065	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7524066	7524162	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7524163	7524249	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7524163	7524249	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7524250	7524408	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7524409	7524525	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7524409	7524525	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7524526	7524602	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7524603	7524666	0.98	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7524603	7524666	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7524667	7524778	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7524779	7524921	0.98	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7524779	7524921	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7524922	7525089	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7525090	7525137	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7525090	7525137	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7525138	7525290	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7525291	7525359	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7525291	7525359	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7525360	7525520	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7525521	7525596	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7525521	7525596	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7525597	7525716	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7525717	7525880	0.8	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7525717	7525880	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7525881	7525959	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7525960	7526019	0.99	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7525960	7526019	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7526020	7526106	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7526107	7526176	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7526107	7526176	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7526177	7526418	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7526419	7526483	1	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7526419	7526483	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7526484	7526570	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7526571	7526632	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7526571	7526632	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7526633	7526719	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7526720	7526843	1	+	1	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7526720	7526843	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7526844	7527007	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7527008	7527065	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7527008	7527065	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7527066	7527258	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7527259	7527371	1	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7527259	7527371	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7527372	7527447	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7527448	7527525	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7527448	7527525	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7527526	7527673	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7527674	7527736	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7527674	7527736	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7527737	7527811	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7527812	7527907	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7527812	7527907	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7527908	7528066	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7528067	7528176	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7528067	7528176	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7528177	7528270	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7528271	7528460	1	+	1	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7528271	7528460	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7528461	7528614	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7528615	7528729	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7528615	7528729	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7528730	7528820	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7528821	7528933	1	+	2	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7528821	7528933	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7528934	7529187	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7529188	7529268	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7529188	7529268	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7529269	7529352	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7529353	7529418	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7529353	7529418	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7529419	7529505	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7529506	7529640	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7529506	7529640	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7529641	7529794	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7529795	7529851	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7529795	7529851	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7529852	7530178	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7530179	7530259	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7530179	7530259	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	intron	7530260	7530341	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	CDS	7530342	7530389	1	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	exon	7530342	7530389	.	+	.	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
Phchi.S3	AUGUSTUS	stop_codon	7530390	7530392	.	+	0	transcript_id "Phchi.S3G088500.t1"; gene_id "Phchi.S3G088500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg224.t1 is derived from g10006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1507297	1508349	.	-	.	Phchi.S6G018300
Phchi.S6	AUGUSTUS	transcript	1507297	1508349	.	-	.	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	stop_codon	1507294	1507296	.	-	0	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	CDS	1507297	1507829	0.57	-	2	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	exon	1507297	1507829	.	-	.	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	intron	1507830	1507946	.	-	.	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	CDS	1507947	1508349	0.58	-	0	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	exon	1507947	1508349	.	-	.	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
Phchi.S6	AUGUSTUS	start_codon	1508347	1508349	.	-	0	transcript_id "Phchi.S6G018300.t1"; gene_id "Phchi.S6G018300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7737.t1 is derived from g4911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30899018	30900480	.	+	.	Phchi.S1G489600
Phchi.S1	AUGUSTUS	transcript	30899018	30900480	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	start_codon	30899018	30899020	.	+	0	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	CDS	30899018	30899075	1	+	0	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	exon	30899018	30899075	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	intron	30899076	30899168	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	CDS	30899169	30899468	0.55	+	2	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	exon	30899169	30899468	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	intron	30899469	30899694	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	CDS	30899695	30900299	0.16	+	2	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	exon	30899695	30900299	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	intron	30900300	30900387	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	CDS	30900388	30900480	0.83	+	0	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	exon	30900388	30900480	.	+	.	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
Phchi.S1	AUGUSTUS	stop_codon	30900481	30900483	.	+	0	transcript_id "Phchi.S1G489600.t1"; gene_id "Phchi.S1G489600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1216.t1 is derived from g10999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8442684	8444349	.	-	.	Phchi.S6G117500
Phchi.S6	AUGUSTUS	transcript	8442684	8444349	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	stop_codon	8442681	8442683	.	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8442684	8442899	0.59	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8442684	8442899	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8442900	8443002	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8443003	8443135	1	-	1	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8443003	8443135	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8443136	8443229	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8443230	8443382	1	-	1	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8443230	8443382	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8443383	8443469	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8443470	8443519	1	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8443470	8443519	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8443520	8443618	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8443619	8443675	1	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8443619	8443675	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8443676	8443752	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8443753	8443835	0.61	-	2	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8443753	8443835	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8443836	8443932	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8443933	8444016	1	-	2	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8443933	8444016	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8444017	8444098	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8444099	8444174	1	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8444099	8444174	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	intron	8444175	8444250	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	CDS	8444251	8444349	1	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	exon	8444251	8444349	.	-	.	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
Phchi.S6	AUGUSTUS	start_codon	8444347	8444349	.	-	0	transcript_id "Phchi.S6G117500.t1"; gene_id "Phchi.S6G117500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13275.t1 is derived from g11740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5089203	5090861	.	+	.	Phchi.S3G059400
Phchi.S3	AUGUSTUS	transcript	5089203	5090861	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	start_codon	5089203	5089205	.	+	0	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	CDS	5089203	5089350	1	+	0	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	exon	5089203	5089350	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	intron	5089351	5089471	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	CDS	5089472	5089715	0.99	+	2	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	exon	5089472	5089715	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	intron	5089716	5089821	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	CDS	5089822	5090072	1	+	1	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	exon	5089822	5090072	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	intron	5090073	5090168	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	CDS	5090169	5090636	0.75	+	2	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	exon	5090169	5090636	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	intron	5090637	5090733	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	CDS	5090734	5090861	0.85	+	2	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	exon	5090734	5090861	.	+	.	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
Phchi.S3	AUGUSTUS	stop_codon	5090862	5090864	.	+	0	transcript_id "Phchi.S3G059400.t1"; gene_id "Phchi.S3G059400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14816.t1 is derived from g13284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14832148	14833415	.	+	.	Phchi.S3G213500
Phchi.S3	AUGUSTUS	transcript	14832148	14833415	.	+	.	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	start_codon	14832148	14832150	.	+	0	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	CDS	14832148	14832719	0.46	+	0	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	exon	14832148	14832719	.	+	.	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	intron	14832720	14832814	.	+	.	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	CDS	14832815	14833211	0.37	+	1	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	exon	14832815	14833211	.	+	.	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	intron	14833212	14833316	.	+	.	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	CDS	14833317	14833415	1	+	0	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	exon	14833317	14833415	.	+	.	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
Phchi.S3	AUGUSTUS	stop_codon	14833416	14833418	.	+	0	transcript_id "Phchi.S3G213500.t1"; gene_id "Phchi.S3G213500"
# This transcript jg7240.t2 is derived from g4412.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7241.t1 is derived from g4413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27801658	27803015	.	+	.	Phchi.S1G440000
Phchi.S1	AUGUSTUS	transcript	27801658	27803015	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	start_codon	27801658	27801660	.	+	0	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	CDS	27801658	27802091	0.44	+	0	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	exon	27801658	27802091	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	intron	27802092	27802177	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	CDS	27802178	27802316	1	+	1	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	exon	27802178	27802316	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	intron	27802317	27802416	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	CDS	27802417	27802528	0.71	+	0	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	exon	27802417	27802528	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	intron	27802529	27802631	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	CDS	27802632	27802714	1	+	2	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	exon	27802632	27802714	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	intron	27802715	27802799	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	CDS	27802800	27803015	0.96	+	0	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	exon	27802800	27803015	.	+	.	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
Phchi.S1	AUGUSTUS	stop_codon	27803016	27803018	.	+	0	transcript_id "Phchi.S1G440000.t1"; gene_id "Phchi.S1G440000"
# This transcript jg8130.t2 is derived from g5305.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8130.t3 is derived from g5305.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8131.t1 is derived from g5306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33637805	33642441	.	+	.	Phchi.S1G529000
Phchi.S1	AUGUSTUS	transcript	33637805	33642441	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	start_codon	33637805	33637807	.	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33637805	33637892	0.77	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33637805	33637892	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33637893	33638153	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33638154	33638221	1	+	2	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33638154	33638221	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33638222	33638380	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33638381	33638521	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33638381	33638521	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33638522	33638613	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33638614	33638787	0.65	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33638614	33638787	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33638788	33638891	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33638892	33639039	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33638892	33639039	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33639040	33639167	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33639168	33639247	1	+	2	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33639168	33639247	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33639248	33639335	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33639336	33639417	0.8	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33639336	33639417	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33639418	33639521	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33639522	33639619	0.93	+	2	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33639522	33639619	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33639620	33639793	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33639794	33639937	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33639794	33639937	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33639938	33640087	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33640088	33640222	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33640088	33640222	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33640223	33640367	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33640368	33640469	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33640368	33640469	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33640470	33640596	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33640597	33640653	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33640597	33640653	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33640654	33640761	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33640762	33640889	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33640762	33640889	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33640890	33641009	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33641010	33641113	1	+	1	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33641010	33641113	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33641114	33641265	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33641266	33641381	1	+	2	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33641266	33641381	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33641382	33641495	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33641496	33641564	1	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33641496	33641564	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33641565	33641699	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33641700	33641798	0.99	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33641700	33641798	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33641799	33641901	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33641902	33642045	0.91	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33641902	33642045	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33642046	33642148	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33642149	33642299	0.99	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33642149	33642299	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	intron	33642300	33642397	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	CDS	33642398	33642441	0.99	+	2	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	exon	33642398	33642441	.	+	.	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
Phchi.S1	AUGUSTUS	stop_codon	33642442	33642444	.	+	0	transcript_id "Phchi.S1G529000.t1"; gene_id "Phchi.S1G529000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11696.t1 is derived from g15747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7743399	7743743	.	-	.	Phchi.S4G127800
Phchi.S4	AUGUSTUS	transcript	7743399	7743743	.	-	.	transcript_id "Phchi.S4G127800.t1"; gene_id "Phchi.S4G127800"
Phchi.S4	AUGUSTUS	stop_codon	7743396	7743398	.	-	0	transcript_id "Phchi.S4G127800.t1"; gene_id "Phchi.S4G127800"
Phchi.S4	AUGUSTUS	CDS	7743399	7743743	0.44	-	0	transcript_id "Phchi.S4G127800.t1"; gene_id "Phchi.S4G127800"
Phchi.S4	AUGUSTUS	exon	7743399	7743743	.	-	.	transcript_id "Phchi.S4G127800.t1"; gene_id "Phchi.S4G127800"
Phchi.S4	AUGUSTUS	start_codon	7743741	7743743	.	-	0	transcript_id "Phchi.S4G127800.t1"; gene_id "Phchi.S4G127800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2218.t1 is derived from g9138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5462756	5466187	.	-	.	Phchi.S5G082700
Phchi.S5	AUGUSTUS	transcript	5462756	5466187	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	stop_codon	5462753	5462755	.	-	0	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5462756	5463187	1	-	0	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5462756	5463187	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	intron	5463188	5463267	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5463268	5463530	1	-	2	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5463268	5463530	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	intron	5463531	5463624	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5463625	5463828	1	-	2	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5463625	5463828	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	intron	5463829	5463923	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5463924	5464520	1	-	2	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5463924	5464520	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	intron	5464521	5464613	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5464614	5465666	0.99	-	2	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5464614	5465666	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	intron	5465667	5465756	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5465757	5465885	1	-	2	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5465757	5465885	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	intron	5465886	5466000	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	CDS	5466001	5466187	1	-	0	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	exon	5466001	5466187	.	-	.	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
Phchi.S5	AUGUSTUS	start_codon	5466185	5466187	.	-	0	transcript_id "Phchi.S5G082700.t1"; gene_id "Phchi.S5G082700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11451.t1 is derived from g15501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6432228	6432718	.	+	.	Phchi.S4G103300
Phchi.S4	AUGUSTUS	transcript	6432228	6432718	.	+	.	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	start_codon	6432228	6432230	.	+	0	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	CDS	6432228	6432398	0.49	+	0	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	exon	6432228	6432398	.	+	.	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	intron	6432399	6432505	.	+	.	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	CDS	6432506	6432718	0.56	+	0	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	exon	6432506	6432718	.	+	.	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
Phchi.S4	AUGUSTUS	stop_codon	6432719	6432721	.	+	0	transcript_id "Phchi.S4G103300.t1"; gene_id "Phchi.S4G103300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12193.t1 is derived from g7869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6503854	6507517	.	-	.	Phchi.S2G027300
Phchi.S2	AUGUSTUS	transcript	6503854	6507517	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	stop_codon	6503851	6503853	.	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6503854	6503970	1	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6503854	6503970	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6503971	6504052	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6504053	6504364	1	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6504053	6504364	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6504365	6504454	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6504455	6504679	1	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6504455	6504679	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6504680	6504755	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6504756	6504914	1	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6504756	6504914	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6504915	6505198	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6505199	6505302	1	-	2	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6505199	6505302	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6505303	6505397	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6505398	6505515	1	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6505398	6505515	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6505516	6505697	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6505698	6505786	1	-	2	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6505698	6505786	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6505787	6506069	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6506070	6506145	1	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6506070	6506145	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6506146	6506413	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6506414	6506509	0.97	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6506414	6506509	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6506510	6506601	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6506602	6506616	0.64	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6506602	6506616	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	intron	6506617	6507226	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	CDS	6507227	6507517	0.94	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	exon	6507227	6507517	.	-	.	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
Phchi.S2	AUGUSTUS	start_codon	6507515	6507517	.	-	0	transcript_id "Phchi.S2G027300.t1"; gene_id "Phchi.S2G027300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10163.t1 is derived from g7339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46051950	46052630	.	+	.	Phchi.S1G732200
Phchi.S1	AUGUSTUS	transcript	46051950	46052630	.	+	.	transcript_id "Phchi.S1G732200.t1"; gene_id "Phchi.S1G732200"
Phchi.S1	AUGUSTUS	start_codon	46051950	46051952	.	+	0	transcript_id "Phchi.S1G732200.t1"; gene_id "Phchi.S1G732200"
Phchi.S1	AUGUSTUS	CDS	46051950	46052630	0.99	+	0	transcript_id "Phchi.S1G732200.t1"; gene_id "Phchi.S1G732200"
Phchi.S1	AUGUSTUS	exon	46051950	46052630	.	+	.	transcript_id "Phchi.S1G732200.t1"; gene_id "Phchi.S1G732200"
Phchi.S1	AUGUSTUS	stop_codon	46052631	46052633	.	+	0	transcript_id "Phchi.S1G732200.t1"; gene_id "Phchi.S1G732200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4871.t1 is derived from g2041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13178139	13179554	.	-	.	Phchi.S1G203000
Phchi.S1	AUGUSTUS	transcript	13178139	13179554	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	stop_codon	13178136	13178138	.	-	0	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13178139	13178192	1	-	0	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13178139	13178192	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	intron	13178193	13178402	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13178403	13178485	0.78	-	2	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13178403	13178485	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	intron	13178486	13178571	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13178572	13178609	0.86	-	1	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13178572	13178609	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	intron	13178610	13178727	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13178728	13178831	0.99	-	0	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13178728	13178831	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	intron	13178832	13178939	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13178940	13179030	1	-	1	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13178940	13179030	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	intron	13179031	13179108	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13179109	13179306	1	-	1	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13179109	13179306	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	intron	13179307	13179423	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	CDS	13179424	13179554	0.92	-	0	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	exon	13179424	13179554	.	-	.	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
Phchi.S1	AUGUSTUS	start_codon	13179552	13179554	.	-	0	transcript_id "Phchi.S1G203000.t1"; gene_id "Phchi.S1G203000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6564.t1 is derived from g3736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23737064	23737848	.	-	.	Phchi.S1G372300
Phchi.S1	AUGUSTUS	transcript	23737387	23737848	.	-	.	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	stop_codon	23737384	23737386	.	-	0	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737387	23737402	1	-	1	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737387	23737402	.	-	.	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	intron	23737403	23737481	.	-	.	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737482	23737572	1	-	2	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737482	23737572	.	-	.	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	intron	23737573	23737658	.	-	.	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737659	23737848	1	-	0	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737659	23737848	.	-	.	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	start_codon	23737846	23737848	.	-	0	transcript_id "Phchi.S1G372300.t1"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	transcript	23737064	23737848	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	stop_codon	23737061	23737063	.	-	0	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737064	23737119	1	-	2	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737064	23737119	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	intron	23737120	23737265	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737266	23737306	0.39	-	1	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737266	23737306	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	intron	23737307	23737361	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737362	23737402	0.69	-	0	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737362	23737402	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	intron	23737403	23737481	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737482	23737572	0.69	-	1	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737482	23737572	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	intron	23737573	23737726	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	CDS	23737727	23737848	0.69	-	0	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	exon	23737727	23737848	.	-	.	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
Phchi.S1	AUGUSTUS	start_codon	23737846	23737848	.	-	0	transcript_id "Phchi.S1G372300.t2"; gene_id "Phchi.S1G372300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3270.t1 is derived from g439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2637033	2638472	.	+	.	Phchi.S1G042900
Phchi.S1	AUGUSTUS	transcript	2637033	2638472	.	+	.	transcript_id "Phchi.S1G042900.t1"; gene_id "Phchi.S1G042900"
Phchi.S1	AUGUSTUS	start_codon	2637033	2637035	.	+	0	transcript_id "Phchi.S1G042900.t1"; gene_id "Phchi.S1G042900"
Phchi.S1	AUGUSTUS	CDS	2637033	2638472	0.99	+	0	transcript_id "Phchi.S1G042900.t1"; gene_id "Phchi.S1G042900"
Phchi.S1	AUGUSTUS	exon	2637033	2638472	.	+	.	transcript_id "Phchi.S1G042900.t1"; gene_id "Phchi.S1G042900"
Phchi.S1	AUGUSTUS	stop_codon	2638473	2638475	.	+	0	transcript_id "Phchi.S1G042900.t1"; gene_id "Phchi.S1G042900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10749.t1 is derived from g14799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1914615	1915472	.	+	.	Phchi.S4G033100
Phchi.S4	AUGUSTUS	transcript	1914615	1915472	.	+	.	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	start_codon	1914615	1914617	.	+	0	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	CDS	1914615	1914812	0.27	+	0	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	exon	1914615	1914812	.	+	.	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	intron	1914813	1914952	.	+	.	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	CDS	1914953	1915123	0.26	+	0	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	exon	1914953	1915123	.	+	.	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	intron	1915124	1915205	.	+	.	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	CDS	1915206	1915472	0.87	+	0	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	exon	1915206	1915472	.	+	.	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
Phchi.S4	AUGUSTUS	stop_codon	1915473	1915475	.	+	0	transcript_id "Phchi.S4G033100.t1"; gene_id "Phchi.S4G033100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2075.t1 is derived from g8995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4721099	4721447	.	-	.	Phchi.S5G068400
Phchi.S5	AUGUSTUS	transcript	4721099	4721447	.	-	.	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	stop_codon	4721096	4721098	.	-	0	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	CDS	4721099	4721141	0.7	-	1	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	exon	4721099	4721141	.	-	.	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	intron	4721142	4721289	.	-	.	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	CDS	4721290	4721447	0.26	-	0	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	exon	4721290	4721447	.	-	.	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
Phchi.S5	AUGUSTUS	start_codon	4721445	4721447	.	-	0	transcript_id "Phchi.S5G068400.t1"; gene_id "Phchi.S5G068400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4579.t1 is derived from g1749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11185478	11196134	.	-	.	Phchi.S1G173800
Phchi.S1	AUGUSTUS	transcript	11185478	11196134	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	stop_codon	11185475	11185477	.	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11185478	11190223	0.86	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11185478	11190223	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	intron	11190224	11190354	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11190355	11191233	0.53	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11190355	11191233	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	intron	11191234	11191322	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11191323	11191375	0.51	-	2	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11191323	11191375	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	intron	11191376	11191477	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11191478	11191574	0.65	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11191478	11191574	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	intron	11191575	11191667	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11191668	11193503	0.61	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11191668	11193503	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	intron	11193504	11193595	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11193596	11194496	0.64	-	1	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11193596	11194496	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	intron	11194497	11194584	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	CDS	11194585	11196134	0.49	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	exon	11194585	11196134	.	-	.	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
Phchi.S1	AUGUSTUS	start_codon	11196132	11196134	.	-	0	transcript_id "Phchi.S1G173800.t1"; gene_id "Phchi.S1G173800"
# This transcript jg9503.t2 is derived from g6679.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9504.t1 is derived from g6680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42086476	42091575	.	+	.	Phchi.S1G666300
Phchi.S1	AUGUSTUS	transcript	42086476	42091575	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	start_codon	42086476	42086478	.	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42086476	42086524	0.74	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42086476	42086524	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42086525	42086830	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42086831	42086925	0.5	+	2	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42086831	42086925	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42086926	42087019	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42087020	42087076	0.75	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42087020	42087076	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42087077	42087192	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42087193	42087343	0.78	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42087193	42087343	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42087344	42087425	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42087426	42087496	0.76	+	2	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42087426	42087496	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42087497	42087613	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42087614	42087738	0.76	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42087614	42087738	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42087739	42087890	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42087891	42088051	0.84	+	1	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42087891	42088051	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42088052	42088177	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42088178	42088319	1	+	2	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42088178	42088319	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42088320	42088414	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42088415	42088478	1	+	1	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42088415	42088478	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42088479	42088607	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42088608	42088772	0.83	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42088608	42088772	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42088773	42088857	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42088858	42088911	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42088858	42088911	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42088912	42088994	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42088995	42089111	0.81	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42088995	42089111	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42089112	42089230	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42089231	42089290	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42089231	42089290	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42089291	42089412	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42089413	42089490	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42089413	42089490	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42089491	42089648	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42089649	42089756	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42089649	42089756	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42089757	42089835	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42089836	42089901	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42089836	42089901	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42089902	42089994	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42089995	42090072	0.96	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42089995	42090072	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42090073	42090173	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42090174	42090307	0.94	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42090174	42090307	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42090308	42090425	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42090426	42090519	0.95	+	1	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42090426	42090519	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42090520	42090593	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42090594	42090671	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42090594	42090671	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42090672	42090825	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42090826	42090888	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42090826	42090888	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42090889	42090963	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42090964	42091032	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42090964	42091032	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42091033	42091106	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42091107	42091202	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42091107	42091202	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	intron	42091203	42091281	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	CDS	42091282	42091575	1	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	exon	42091282	42091575	.	+	.	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
Phchi.S1	AUGUSTUS	stop_codon	42091576	42091578	.	+	0	transcript_id "Phchi.S1G666300.t1"; gene_id "Phchi.S1G666300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1700.t1 is derived from g8619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2578389	2581264	.	-	.	Phchi.S5G030900
Phchi.S5	AUGUSTUS	transcript	2578389	2581264	.	-	.	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	stop_codon	2578386	2578388	.	-	0	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	CDS	2578389	2580659	0.87	-	0	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	exon	2578389	2580659	.	-	.	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	intron	2580660	2580718	.	-	.	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	CDS	2580719	2581264	0.79	-	0	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	exon	2580719	2581264	.	-	.	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
Phchi.S5	AUGUSTUS	start_codon	2581262	2581264	.	-	0	transcript_id "Phchi.S5G030900.t1"; gene_id "Phchi.S5G030900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1804.t1 is derived from g8724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3119508	3120486	.	-	.	Phchi.S5G041300
Phchi.S5	AUGUSTUS	transcript	3119508	3120486	.	-	.	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	stop_codon	3119505	3119507	.	-	0	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	CDS	3119508	3119661	0.18	-	1	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	exon	3119508	3119661	.	-	.	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	intron	3119662	3119740	.	-	.	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	CDS	3119741	3119962	0.13	-	1	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	exon	3119741	3119962	.	-	.	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	intron	3119963	3120103	.	-	.	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	CDS	3120104	3120486	0.08	-	0	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	exon	3120104	3120486	.	-	.	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
Phchi.S5	AUGUSTUS	start_codon	3120484	3120486	.	-	0	transcript_id "Phchi.S5G041300.t1"; gene_id "Phchi.S5G041300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15718.t1 is derived from g14188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20855039	20858925	.	-	.	Phchi.S3G303700
Phchi.S3	AUGUSTUS	transcript	20855039	20858925	.	-	.	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	stop_codon	20855036	20855038	.	-	0	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	CDS	20855039	20858508	0.76	-	2	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	exon	20855039	20858508	.	-	.	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	intron	20858509	20858606	.	-	.	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	CDS	20858607	20858925	0.75	-	0	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	exon	20858607	20858925	.	-	.	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
Phchi.S3	AUGUSTUS	start_codon	20858923	20858925	.	-	0	transcript_id "Phchi.S3G303700.t1"; gene_id "Phchi.S3G303700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12779.t1 is derived from g11244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2111207	2111575	.	-	.	Phchi.S3G009800
Phchi.S3	AUGUSTUS	transcript	2111207	2111575	.	-	.	transcript_id "Phchi.S3G009800.t1"; gene_id "Phchi.S3G009800"
Phchi.S3	AUGUSTUS	stop_codon	2111204	2111206	.	-	0	transcript_id "Phchi.S3G009800.t1"; gene_id "Phchi.S3G009800"
Phchi.S3	AUGUSTUS	CDS	2111207	2111575	0.58	-	0	transcript_id "Phchi.S3G009800.t1"; gene_id "Phchi.S3G009800"
Phchi.S3	AUGUSTUS	exon	2111207	2111575	.	-	.	transcript_id "Phchi.S3G009800.t1"; gene_id "Phchi.S3G009800"
Phchi.S3	AUGUSTUS	start_codon	2111573	2111575	.	-	0	transcript_id "Phchi.S3G009800.t1"; gene_id "Phchi.S3G009800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10730.t1 is derived from g14780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1793046	1793952	.	+	.	Phchi.S4G031200
Phchi.S4	AUGUSTUS	transcript	1793046	1793952	.	+	.	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	start_codon	1793046	1793048	.	+	0	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	CDS	1793046	1793335	0.86	+	0	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	exon	1793046	1793335	.	+	.	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	intron	1793336	1793423	.	+	.	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	CDS	1793424	1793562	0.74	+	1	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	exon	1793424	1793562	.	+	.	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	intron	1793563	1793715	.	+	.	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	CDS	1793716	1793952	0.73	+	0	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	exon	1793716	1793952	.	+	.	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
Phchi.S4	AUGUSTUS	stop_codon	1793953	1793955	.	+	0	transcript_id "Phchi.S4G031200.t1"; gene_id "Phchi.S4G031200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3007.t1 is derived from g176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1111580	1113426	.	-	.	Phchi.S1G016600
Phchi.S1	AUGUSTUS	transcript	1111580	1113426	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	stop_codon	1111577	1111579	.	-	0	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1111580	1111620	0.97	-	2	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1111580	1111620	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	intron	1111621	1111718	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1111719	1111818	0.66	-	0	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1111719	1111818	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	intron	1111819	1111972	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1111973	1112032	0.59	-	0	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1111973	1112032	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	intron	1112033	1112263	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1112264	1112498	0.93	-	1	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1112264	1112498	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	intron	1112499	1112610	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1112611	1112757	0.93	-	1	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1112611	1112757	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	intron	1112758	1112891	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1112892	1112931	0.94	-	2	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1112892	1112931	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	intron	1112932	1113257	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	CDS	1113258	1113426	0.99	-	0	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	exon	1113258	1113426	.	-	.	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
Phchi.S1	AUGUSTUS	start_codon	1113424	1113426	.	-	0	transcript_id "Phchi.S1G016600.t1"; gene_id "Phchi.S1G016600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7624.t1 is derived from g4798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30305003	30305380	.	-	.	Phchi.S1G478300
Phchi.S1	AUGUSTUS	transcript	30305003	30305380	.	-	.	transcript_id "Phchi.S1G478300.t1"; gene_id "Phchi.S1G478300"
Phchi.S1	AUGUSTUS	stop_codon	30305000	30305002	.	-	0	transcript_id "Phchi.S1G478300.t1"; gene_id "Phchi.S1G478300"
Phchi.S1	AUGUSTUS	CDS	30305003	30305380	0.87	-	0	transcript_id "Phchi.S1G478300.t1"; gene_id "Phchi.S1G478300"
Phchi.S1	AUGUSTUS	exon	30305003	30305380	.	-	.	transcript_id "Phchi.S1G478300.t1"; gene_id "Phchi.S1G478300"
Phchi.S1	AUGUSTUS	start_codon	30305378	30305380	.	-	0	transcript_id "Phchi.S1G478300.t1"; gene_id "Phchi.S1G478300"
# This transcript jg13785.t2 is derived from g12252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13786.t1 is derived from g12253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8888404	8891205	.	-	.	Phchi.S3G110500
Phchi.S3	AUGUSTUS	transcript	8888404	8891205	.	-	.	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	stop_codon	8888401	8888403	.	-	0	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	CDS	8888404	8888669	0.97	-	2	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	exon	8888404	8888669	.	-	.	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	intron	8888670	8888870	.	-	.	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	CDS	8888871	8891205	0.88	-	0	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	exon	8888871	8891205	.	-	.	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
Phchi.S3	AUGUSTUS	start_codon	8891203	8891205	.	-	0	transcript_id "Phchi.S3G110500.t1"; gene_id "Phchi.S3G110500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1076.t1 is derived from g10859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7453089	7453815	.	+	.	Phchi.S6G103500
Phchi.S6	AUGUSTUS	transcript	7453089	7453815	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	start_codon	7453089	7453091	.	+	0	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	CDS	7453089	7453118	0.92	+	0	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	exon	7453089	7453118	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	intron	7453119	7453269	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	CDS	7453270	7453373	1	+	0	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	exon	7453270	7453373	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	intron	7453374	7453518	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	CDS	7453519	7453616	1	+	1	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	exon	7453519	7453616	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	intron	7453617	7453738	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	CDS	7453739	7453815	0.92	+	2	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	exon	7453739	7453815	.	+	.	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
Phchi.S6	AUGUSTUS	stop_codon	7453816	7453818	.	+	0	transcript_id "Phchi.S6G103500.t1"; gene_id "Phchi.S6G103500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4048.t1 is derived from g1217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7532441	7533040	.	+	.	Phchi.S1G120700
Phchi.S1	AUGUSTUS	transcript	7532441	7533040	.	+	.	transcript_id "Phchi.S1G120700.t1"; gene_id "Phchi.S1G120700"
Phchi.S1	AUGUSTUS	start_codon	7532441	7532443	.	+	0	transcript_id "Phchi.S1G120700.t1"; gene_id "Phchi.S1G120700"
Phchi.S1	AUGUSTUS	CDS	7532441	7533040	1	+	0	transcript_id "Phchi.S1G120700.t1"; gene_id "Phchi.S1G120700"
Phchi.S1	AUGUSTUS	exon	7532441	7533040	.	+	.	transcript_id "Phchi.S1G120700.t1"; gene_id "Phchi.S1G120700"
Phchi.S1	AUGUSTUS	stop_codon	7533041	7533043	.	+	0	transcript_id "Phchi.S1G120700.t1"; gene_id "Phchi.S1G120700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1029.t1 is derived from g10812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7211135	7213371	.	+	.	Phchi.S6G098800
Phchi.S6	AUGUSTUS	transcript	7211135	7213371	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	start_codon	7211135	7211137	.	+	0	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	CDS	7211135	7211343	0.84	+	0	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	exon	7211135	7211343	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	intron	7211344	7211488	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	CDS	7211489	7211655	1	+	1	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	exon	7211489	7211655	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	intron	7211656	7211784	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	CDS	7211785	7212033	1	+	2	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	exon	7211785	7212033	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	intron	7212034	7212142	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	CDS	7212143	7212233	0.69	+	2	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	exon	7212143	7212233	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	intron	7212234	7212431	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	CDS	7212432	7212735	1	+	1	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	exon	7212432	7212735	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	intron	7212736	7212819	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	CDS	7212820	7213371	0.99	+	0	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	exon	7212820	7213371	.	+	.	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
Phchi.S6	AUGUSTUS	stop_codon	7213372	7213374	.	+	0	transcript_id "Phchi.S6G098800.t1"; gene_id "Phchi.S6G098800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3822.t1 is derived from g991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5891531	5893250	.	-	.	Phchi.S1G098100
Phchi.S1	AUGUSTUS	transcript	5891531	5893250	.	-	.	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	stop_codon	5891528	5891530	.	-	0	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	CDS	5891531	5892142	1	-	0	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	exon	5891531	5892142	.	-	.	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	intron	5892143	5892224	.	-	.	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	CDS	5892225	5892393	1	-	1	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	exon	5892225	5892393	.	-	.	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	intron	5892394	5892495	.	-	.	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	CDS	5892496	5893250	0.92	-	0	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	exon	5892496	5893250	.	-	.	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	start_codon	5893248	5893250	.	-	0	transcript_id "Phchi.S1G098100.t1"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	transcript	5891531	5893250	.	-	.	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	stop_codon	5891528	5891530	.	-	0	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	CDS	5891531	5892139	0.99	-	0	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	exon	5891531	5892139	.	-	.	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	intron	5892140	5892224	.	-	.	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	CDS	5892225	5892393	1	-	1	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	exon	5892225	5892393	.	-	.	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	intron	5892394	5892495	.	-	.	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	CDS	5892496	5893250	0.9	-	0	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	exon	5892496	5893250	.	-	.	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
Phchi.S1	AUGUSTUS	start_codon	5893248	5893250	.	-	0	transcript_id "Phchi.S1G098100.t2"; gene_id "Phchi.S1G098100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6457.t1 is derived from g3629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23116981	23118703	.	+	.	Phchi.S1G361600
Phchi.S1	AUGUSTUS	transcript	23116981	23118703	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	start_codon	23116981	23116983	.	+	0	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23116981	23117055	0.8	+	0	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23116981	23117055	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	intron	23117056	23117189	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23117190	23117442	0.61	+	0	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23117190	23117442	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	intron	23117443	23117604	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23117605	23117772	0.7	+	2	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23117605	23117772	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	intron	23117773	23117966	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23117967	23118122	0.48	+	2	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23117967	23118122	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	intron	23118123	23118205	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23118206	23118386	0.37	+	2	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23118206	23118386	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	intron	23118387	23118466	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23118467	23118527	0.58	+	1	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23118467	23118527	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	intron	23118528	23118685	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	CDS	23118686	23118703	0.94	+	0	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	exon	23118686	23118703	.	+	.	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
Phchi.S1	AUGUSTUS	stop_codon	23118704	23118706	.	+	0	transcript_id "Phchi.S1G361600.t1"; gene_id "Phchi.S1G361600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14115.t1 is derived from g12582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10910341	10910679	.	-	.	Phchi.S3G143400
Phchi.S3	AUGUSTUS	transcript	10910341	10910679	.	-	.	transcript_id "Phchi.S3G143400.t1"; gene_id "Phchi.S3G143400"
Phchi.S3	AUGUSTUS	stop_codon	10910338	10910340	.	-	0	transcript_id "Phchi.S3G143400.t1"; gene_id "Phchi.S3G143400"
Phchi.S3	AUGUSTUS	CDS	10910341	10910679	0.92	-	0	transcript_id "Phchi.S3G143400.t1"; gene_id "Phchi.S3G143400"
Phchi.S3	AUGUSTUS	exon	10910341	10910679	.	-	.	transcript_id "Phchi.S3G143400.t1"; gene_id "Phchi.S3G143400"
Phchi.S3	AUGUSTUS	start_codon	10910677	10910679	.	-	0	transcript_id "Phchi.S3G143400.t1"; gene_id "Phchi.S3G143400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2640.t1 is derived from g9560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7911053	7911432	.	+	.	Phchi.S5G124900
Phchi.S5	AUGUSTUS	transcript	7911053	7911432	.	+	.	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	start_codon	7911053	7911055	.	+	0	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	CDS	7911053	7911168	0.59	+	0	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	exon	7911053	7911168	.	+	.	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	intron	7911169	7911317	.	+	.	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	CDS	7911318	7911432	0.4	+	1	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	exon	7911318	7911432	.	+	.	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
Phchi.S5	AUGUSTUS	stop_codon	7911433	7911435	.	+	0	transcript_id "Phchi.S5G124900.t1"; gene_id "Phchi.S5G124900"
# This transcript jg14295.t2 is derived from g12762.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14296.t1 is derived from g12763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11979873	11985299	.	-	.	Phchi.S3G161500
Phchi.S3	AUGUSTUS	transcript	11979873	11985299	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	stop_codon	11979870	11979872	.	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11979873	11979958	0.9	-	2	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11979873	11979958	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11979959	11980043	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11980044	11980247	0.33	-	2	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11980044	11980247	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11980248	11980396	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11980397	11980490	0.49	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11980397	11980490	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11980491	11980574	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11980575	11980805	1	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11980575	11980805	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11980806	11980921	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11980922	11981266	1	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11980922	11981266	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11981267	11981404	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11981405	11981460	0.99	-	2	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11981405	11981460	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11981461	11981584	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11981585	11981684	1	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11981585	11981684	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11981685	11981823	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11981824	11982381	0.91	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11981824	11982381	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11982382	11982504	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11982505	11982570	0.92	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11982505	11982570	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	intron	11982571	11982686	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	CDS	11982687	11985299	0.44	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	exon	11982687	11985299	.	-	.	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
Phchi.S3	AUGUSTUS	start_codon	11985297	11985299	.	-	0	transcript_id "Phchi.S3G161500.t1"; gene_id "Phchi.S3G161500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6619.t1 is derived from g3791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24024712	24025131	.	-	.	Phchi.S1G377800
Phchi.S1	AUGUSTUS	transcript	24024712	24025131	.	-	.	transcript_id "Phchi.S1G377800.t1"; gene_id "Phchi.S1G377800"
Phchi.S1	AUGUSTUS	stop_codon	24024709	24024711	.	-	0	transcript_id "Phchi.S1G377800.t1"; gene_id "Phchi.S1G377800"
Phchi.S1	AUGUSTUS	CDS	24024712	24025131	0.8	-	0	transcript_id "Phchi.S1G377800.t1"; gene_id "Phchi.S1G377800"
Phchi.S1	AUGUSTUS	exon	24024712	24025131	.	-	.	transcript_id "Phchi.S1G377800.t1"; gene_id "Phchi.S1G377800"
Phchi.S1	AUGUSTUS	start_codon	24025129	24025131	.	-	0	transcript_id "Phchi.S1G377800.t1"; gene_id "Phchi.S1G377800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg971.t1 is derived from g10754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6718896	6719676	.	-	.	Phchi.S6G093000
Phchi.S6	AUGUSTUS	transcript	6718896	6719676	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	stop_codon	6718893	6718895	.	-	0	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6718896	6718951	1	-	2	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6718896	6718951	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	intron	6718952	6719098	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6719099	6719202	1	-	1	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6719099	6719202	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	intron	6719203	6719336	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6719337	6719432	1	-	1	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6719337	6719432	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	intron	6719433	6719572	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6719573	6719676	1	-	0	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6719573	6719676	.	-	.	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	start_codon	6719674	6719676	.	-	0	transcript_id "Phchi.S6G093000.t1"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	transcript	6718896	6719668	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	stop_codon	6718893	6718895	.	-	0	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6718896	6718951	1	-	2	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6718896	6718951	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	intron	6718952	6719098	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6719099	6719202	1	-	1	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6719099	6719202	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	intron	6719203	6719336	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6719337	6719432	1	-	1	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6719337	6719432	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	intron	6719433	6719600	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	CDS	6719601	6719668	0.99	-	0	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	exon	6719601	6719668	.	-	.	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
Phchi.S6	AUGUSTUS	start_codon	6719666	6719668	.	-	0	transcript_id "Phchi.S6G093000.t2"; gene_id "Phchi.S6G093000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15810.t1 is derived from g14280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21505298	21507778	.	-	.	Phchi.S3G312900
Phchi.S3	AUGUSTUS	transcript	21505298	21507778	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	stop_codon	21505295	21505297	.	-	0	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	CDS	21505298	21505302	0.96	-	2	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	exon	21505298	21505302	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	intron	21505303	21505386	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	CDS	21505387	21505402	0.96	-	0	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	exon	21505387	21505402	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	intron	21505403	21505568	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	CDS	21505569	21507597	0.67	-	1	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	exon	21505569	21507597	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	intron	21507598	21507683	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	CDS	21507684	21507778	0.3	-	0	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	exon	21507684	21507778	.	-	.	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
Phchi.S3	AUGUSTUS	start_codon	21507776	21507778	.	-	0	transcript_id "Phchi.S3G312900.t1"; gene_id "Phchi.S3G312900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15435.t1 is derived from g13903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19084548	19085436	.	+	.	Phchi.S3G275400
Phchi.S3	AUGUSTUS	transcript	19084548	19085436	.	+	.	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	start_codon	19084548	19084550	.	+	0	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	CDS	19084548	19084583	0.92	+	0	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	exon	19084548	19084583	.	+	.	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	intron	19084584	19084683	.	+	.	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	CDS	19084684	19084881	0.98	+	0	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	exon	19084684	19084881	.	+	.	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	intron	19084882	19084977	.	+	.	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	CDS	19084978	19085436	0.97	+	0	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	exon	19084978	19085436	.	+	.	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
Phchi.S3	AUGUSTUS	stop_codon	19085437	19085439	.	+	0	transcript_id "Phchi.S3G275400.t1"; gene_id "Phchi.S3G275400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7618.t1 is derived from g4792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30296260	30298122	.	+	.	Phchi.S1G477700
Phchi.S1	AUGUSTUS	transcript	30296260	30298122	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	start_codon	30296260	30296262	.	+	0	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	CDS	30296260	30296372	0.98	+	0	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	exon	30296260	30296372	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	intron	30296373	30296627	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	CDS	30296628	30296845	1	+	1	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	exon	30296628	30296845	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	intron	30296846	30296923	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	CDS	30296924	30297123	1	+	2	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	exon	30296924	30297123	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	intron	30297124	30297216	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	CDS	30297217	30297725	1	+	0	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	exon	30297217	30297725	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	intron	30297726	30297815	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	CDS	30297816	30298122	1	+	1	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	exon	30297816	30298122	.	+	.	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
Phchi.S1	AUGUSTUS	stop_codon	30298123	30298125	.	+	0	transcript_id "Phchi.S1G477700.t1"; gene_id "Phchi.S1G477700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8077.t1 is derived from g5252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32841352	32843199	.	-	.	Phchi.S1G523600
Phchi.S1	AUGUSTUS	transcript	32841352	32843199	.	-	.	transcript_id "Phchi.S1G523600.t1"; gene_id "Phchi.S1G523600"
Phchi.S1	AUGUSTUS	stop_codon	32841349	32841351	.	-	0	transcript_id "Phchi.S1G523600.t1"; gene_id "Phchi.S1G523600"
Phchi.S1	AUGUSTUS	CDS	32841352	32843199	0.85	-	0	transcript_id "Phchi.S1G523600.t1"; gene_id "Phchi.S1G523600"
Phchi.S1	AUGUSTUS	exon	32841352	32843199	.	-	.	transcript_id "Phchi.S1G523600.t1"; gene_id "Phchi.S1G523600"
Phchi.S1	AUGUSTUS	start_codon	32843197	32843199	.	-	0	transcript_id "Phchi.S1G523600.t1"; gene_id "Phchi.S1G523600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1499.t1 is derived from g8418.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1208606	1209322	.	-	.	Phchi.S5G010800
Phchi.S5	AUGUSTUS	transcript	1208606	1209322	.	-	.	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	stop_codon	1208603	1208605	.	-	0	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	CDS	1208606	1208649	0.45	-	2	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	exon	1208606	1208649	.	-	.	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	intron	1208650	1208780	.	-	.	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	CDS	1208781	1208988	1	-	0	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	exon	1208781	1208988	.	-	.	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	intron	1208989	1209124	.	-	.	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	CDS	1209125	1209322	0.99	-	0	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	exon	1209125	1209322	.	-	.	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	start_codon	1209320	1209322	.	-	0	transcript_id "Phchi.S5G010800.t1"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	transcript	1208606	1209322	.	-	.	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	stop_codon	1208603	1208605	.	-	0	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	CDS	1208606	1208646	0.26	-	2	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	exon	1208606	1208646	.	-	.	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	intron	1208647	1208780	.	-	.	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	CDS	1208781	1208988	0.54	-	0	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	exon	1208781	1208988	.	-	.	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	intron	1208989	1209124	.	-	.	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	CDS	1209125	1209322	0.98	-	0	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	exon	1209125	1209322	.	-	.	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
Phchi.S5	AUGUSTUS	start_codon	1209320	1209322	.	-	0	transcript_id "Phchi.S5G010800.t2"; gene_id "Phchi.S5G010800"
# This transcript jg9138.t2 is derived from g6313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9139.t1 is derived from g6314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40038776	40039481	.	+	.	Phchi.S1G629800
Phchi.S1	AUGUSTUS	transcript	40038776	40039481	.	+	.	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	start_codon	40038776	40038778	.	+	0	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	CDS	40038776	40038867	0.99	+	0	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	exon	40038776	40038867	.	+	.	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	intron	40038868	40038950	.	+	.	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	CDS	40038951	40039238	0.92	+	1	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	exon	40038951	40039238	.	+	.	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	intron	40039239	40039477	.	+	.	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	CDS	40039478	40039481	0.93	+	1	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	exon	40039478	40039481	.	+	.	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
Phchi.S1	AUGUSTUS	stop_codon	40039482	40039484	.	+	0	transcript_id "Phchi.S1G629800.t1"; gene_id "Phchi.S1G629800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12506.t1 is derived from g8183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31131307	31132048	.	+	.	Phchi.S2G058600
Phchi.S2	AUGUSTUS	transcript	31131307	31132048	.	+	.	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	start_codon	31131307	31131309	.	+	0	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	CDS	31131307	31131382	0.64	+	0	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	exon	31131307	31131382	.	+	.	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	intron	31131383	31131509	.	+	.	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	CDS	31131510	31132048	0.48	+	2	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	exon	31131510	31132048	.	+	.	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
Phchi.S2	AUGUSTUS	stop_codon	31132049	31132051	.	+	0	transcript_id "Phchi.S2G058600.t1"; gene_id "Phchi.S2G058600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg372.t1 is derived from g10154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2694215	2697194	.	-	.	Phchi.S6G033100
Phchi.S6	AUGUSTUS	transcript	2694215	2697194	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	stop_codon	2694212	2694214	.	-	0	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2694215	2694342	1	-	2	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2694215	2694342	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2694343	2694466	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2694467	2694559	1	-	2	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2694467	2694559	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2694560	2694681	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2694682	2694820	1	-	0	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2694682	2694820	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2694821	2695062	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2695063	2695604	1	-	2	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2695063	2695604	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2695605	2695699	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2695700	2695825	1	-	2	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2695700	2695825	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2695826	2695933	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2695934	2696009	1	-	0	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2695934	2696009	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2696010	2696109	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2696110	2696336	0.97	-	2	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2696110	2696336	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2696337	2696430	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2696431	2696527	0.97	-	0	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2696431	2696527	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	intron	2696528	2696723	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	CDS	2696724	2697194	0.54	-	0	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	exon	2696724	2697194	.	-	.	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
Phchi.S6	AUGUSTUS	start_codon	2697192	2697194	.	-	0	transcript_id "Phchi.S6G033100.t1"; gene_id "Phchi.S6G033100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12084.t1 is derived from g7759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2175087	2177436	.	-	.	Phchi.S2G016400
Phchi.S2	AUGUSTUS	transcript	2175087	2177436	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	stop_codon	2175084	2175086	.	-	0	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	CDS	2175087	2175121	1	-	2	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	exon	2175087	2175121	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	intron	2175122	2175215	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	CDS	2175216	2175239	1	-	2	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	exon	2175216	2175239	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	intron	2175240	2175335	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	CDS	2175336	2176769	0.61	-	2	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	exon	2175336	2176769	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	intron	2176770	2176897	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	CDS	2176898	2176916	0.96	-	0	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	exon	2176898	2176916	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	intron	2176917	2177017	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	CDS	2177018	2177024	0.71	-	1	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	exon	2177018	2177024	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	intron	2177025	2177116	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	CDS	2177117	2177436	0.89	-	0	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	exon	2177117	2177436	.	-	.	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
Phchi.S2	AUGUSTUS	start_codon	2177434	2177436	.	-	0	transcript_id "Phchi.S2G016400.t1"; gene_id "Phchi.S2G016400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6100.t1 is derived from g3271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20949614	20953049	.	-	.	Phchi.S1G325900
Phchi.S1	AUGUSTUS	transcript	20949614	20953049	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	stop_codon	20949611	20949613	.	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20949614	20950197	1	-	2	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20949614	20950197	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20950198	20950285	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20950286	20950502	1	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20950286	20950502	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20950503	20950592	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20950593	20950704	1	-	1	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20950593	20950704	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20950705	20950806	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20950807	20951040	1	-	1	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20950807	20951040	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20951041	20951149	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20951150	20951244	1	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20951150	20951244	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20951245	20951333	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20951334	20951657	1	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20951334	20951657	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20951658	20951730	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20951731	20951944	1	-	1	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20951731	20951944	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20951945	20952023	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20952024	20952135	1	-	2	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20952024	20952135	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20952136	20952221	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20952222	20952377	0.98	-	2	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20952222	20952377	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20952378	20952506	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20952507	20952607	0.97	-	1	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20952507	20952607	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20952608	20952748	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20952749	20952843	1	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20952749	20952843	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	intron	20952844	20952932	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	CDS	20952933	20953049	0.96	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	exon	20952933	20953049	.	-	.	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
Phchi.S1	AUGUSTUS	start_codon	20953047	20953049	.	-	0	transcript_id "Phchi.S1G325900.t1"; gene_id "Phchi.S1G325900"
# This transcript jg9126.t2 is derived from g6301.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9127.t1 is derived from g6302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39978922	39991783	.	-	.	Phchi.S1G628600
Phchi.S1	AUGUSTUS	transcript	39978922	39991783	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	stop_codon	39978919	39978921	.	-	0	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	CDS	39978922	39989326	0.56	-	1	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	exon	39978922	39989326	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	intron	39989327	39989415	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	CDS	39989416	39989612	0.58	-	0	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	exon	39989416	39989612	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	intron	39989613	39989784	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	CDS	39989785	39991364	0.95	-	2	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	exon	39989785	39991364	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	intron	39991365	39991512	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	CDS	39991513	39991606	1	-	0	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	exon	39991513	39991606	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	intron	39991607	39991705	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	CDS	39991706	39991783	1	-	0	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	exon	39991706	39991783	.	-	.	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
Phchi.S1	AUGUSTUS	start_codon	39991781	39991783	.	-	0	transcript_id "Phchi.S1G628600.t1"; gene_id "Phchi.S1G628600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13185.t1 is derived from g11650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4586394	4588023	.	+	.	Phchi.S3G050400
Phchi.S3	AUGUSTUS	transcript	4586394	4588023	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	start_codon	4586394	4586396	.	+	0	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4586394	4586593	0.32	+	0	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4586394	4586593	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	intron	4586594	4586808	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4586809	4586905	0.99	+	1	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4586809	4586905	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	intron	4586906	4587016	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4587017	4587073	0.63	+	0	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4587017	4587073	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	intron	4587074	4587206	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4587207	4587328	0.99	+	0	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4587207	4587328	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	intron	4587329	4587440	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4587441	4587631	1	+	1	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4587441	4587631	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	intron	4587632	4587714	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4587715	4587771	0.87	+	2	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4587715	4587771	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	intron	4587772	4587874	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	CDS	4587875	4588023	0.87	+	2	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	exon	4587875	4588023	.	+	.	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
Phchi.S3	AUGUSTUS	stop_codon	4588024	4588026	.	+	0	transcript_id "Phchi.S3G050400.t1"; gene_id "Phchi.S3G050400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14416.t1 is derived from g12884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12718887	12719540	.	-	.	Phchi.S3G173500
Phchi.S3	AUGUSTUS	transcript	12718887	12719540	.	-	.	transcript_id "Phchi.S3G173500.t1"; gene_id "Phchi.S3G173500"
Phchi.S3	AUGUSTUS	stop_codon	12718884	12718886	.	-	0	transcript_id "Phchi.S3G173500.t1"; gene_id "Phchi.S3G173500"
Phchi.S3	AUGUSTUS	CDS	12718887	12719540	0.87	-	0	transcript_id "Phchi.S3G173500.t1"; gene_id "Phchi.S3G173500"
Phchi.S3	AUGUSTUS	exon	12718887	12719540	.	-	.	transcript_id "Phchi.S3G173500.t1"; gene_id "Phchi.S3G173500"
Phchi.S3	AUGUSTUS	start_codon	12719538	12719540	.	-	0	transcript_id "Phchi.S3G173500.t1"; gene_id "Phchi.S3G173500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6843.t1 is derived from g4015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25511457	25512361	.	+	.	Phchi.S1G400200
Phchi.S1	AUGUSTUS	transcript	25511457	25512361	.	+	.	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	start_codon	25511457	25511459	.	+	0	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	CDS	25511457	25511609	0.51	+	0	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	exon	25511457	25511609	.	+	.	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	intron	25511610	25511728	.	+	.	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	CDS	25511729	25512361	1	+	0	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	exon	25511729	25512361	.	+	.	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
Phchi.S1	AUGUSTUS	stop_codon	25512362	25512364	.	+	0	transcript_id "Phchi.S1G400200.t1"; gene_id "Phchi.S1G400200"
# This transcript jg8942.t2 is derived from g6117.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8943.t1 is derived from g6118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38786559	38789971	.	-	.	Phchi.S1G610200
Phchi.S1	AUGUSTUS	transcript	38786559	38789971	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	stop_codon	38786556	38786558	.	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38786559	38786586	0.61	-	1	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38786559	38786586	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38786587	38786702	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38786703	38786775	0.82	-	2	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38786703	38786775	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38786776	38786869	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38786870	38786922	1	-	1	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38786870	38786922	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38786923	38787034	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38787035	38787093	1	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38787035	38787093	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38787094	38787192	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38787193	38787255	1	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38787193	38787255	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38787256	38787361	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38787362	38787446	0.68	-	1	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38787362	38787446	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38787447	38787558	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38787559	38787599	0.66	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38787559	38787599	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38787600	38787701	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38787702	38787765	0.96	-	1	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38787702	38787765	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38787766	38787875	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38787876	38787945	1	-	2	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38787876	38787945	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38787946	38788024	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38788025	38788081	1	-	2	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38788025	38788081	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38788082	38788176	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38788177	38788271	1	-	1	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38788177	38788271	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38788272	38788418	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38788419	38788519	1	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38788419	38788519	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38788520	38788679	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38788680	38788702	1	-	2	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38788680	38788702	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38788703	38788815	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38788816	38788891	1	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38788816	38788891	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38788892	38789039	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38789040	38789117	1	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38789040	38789117	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38789118	38789279	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38789280	38789330	1	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38789280	38789330	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38789331	38789414	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38789415	38789424	1	-	1	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38789415	38789424	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	intron	38789425	38789591	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	CDS	38789592	38789971	0.51	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	exon	38789592	38789971	.	-	.	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
Phchi.S1	AUGUSTUS	start_codon	38789969	38789971	.	-	0	transcript_id "Phchi.S1G610200.t1"; gene_id "Phchi.S1G610200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5790.t1 is derived from g2960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18966752	18967551	.	+	.	Phchi.S1G294900
Phchi.S1	AUGUSTUS	transcript	18966752	18967551	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	start_codon	18966752	18966754	.	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	CDS	18966752	18966862	0.32	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	exon	18966752	18966862	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	intron	18966863	18966946	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	CDS	18966947	18967060	0.53	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	exon	18966947	18967060	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	intron	18967061	18967153	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	CDS	18967154	18967267	1	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	exon	18967154	18967267	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	intron	18967268	18967345	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	CDS	18967346	18967420	1	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	exon	18967346	18967420	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	intron	18967421	18967509	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	CDS	18967510	18967551	1	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	exon	18967510	18967551	.	+	.	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
Phchi.S1	AUGUSTUS	stop_codon	18967552	18967554	.	+	0	transcript_id "Phchi.S1G294900.t1"; gene_id "Phchi.S1G294900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10835.t1 is derived from g14885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2372991	2374238	.	+	.	Phchi.S4G041700
Phchi.S4	AUGUSTUS	transcript	2372991	2374238	.	+	.	transcript_id "Phchi.S4G041700.t1"; gene_id "Phchi.S4G041700"
Phchi.S4	AUGUSTUS	start_codon	2372991	2372993	.	+	0	transcript_id "Phchi.S4G041700.t1"; gene_id "Phchi.S4G041700"
Phchi.S4	AUGUSTUS	CDS	2372991	2374238	1	+	0	transcript_id "Phchi.S4G041700.t1"; gene_id "Phchi.S4G041700"
Phchi.S4	AUGUSTUS	exon	2372991	2374238	.	+	.	transcript_id "Phchi.S4G041700.t1"; gene_id "Phchi.S4G041700"
Phchi.S4	AUGUSTUS	stop_codon	2374239	2374241	.	+	0	transcript_id "Phchi.S4G041700.t1"; gene_id "Phchi.S4G041700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14884.t1 is derived from g13352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15272657	15273171	.	-	.	Phchi.S3G220300
Phchi.S3	AUGUSTUS	transcript	15272657	15273171	.	-	.	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	stop_codon	15272654	15272656	.	-	0	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	CDS	15272657	15272734	1	-	0	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	exon	15272657	15272734	.	-	.	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	intron	15272735	15272863	.	-	.	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	CDS	15272864	15273007	1	-	0	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	exon	15272864	15273007	.	-	.	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	intron	15273008	15273090	.	-	.	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	CDS	15273091	15273171	0.88	-	0	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	exon	15273091	15273171	.	-	.	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
Phchi.S3	AUGUSTUS	start_codon	15273169	15273171	.	-	0	transcript_id "Phchi.S3G220300.t1"; gene_id "Phchi.S3G220300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1667.t1 is derived from g8586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2321967	2323502	.	+	.	Phchi.S5G027600
Phchi.S5	AUGUSTUS	transcript	2321967	2323502	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	start_codon	2321967	2321969	.	+	0	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	CDS	2321967	2322199	0.69	+	0	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	exon	2321967	2322199	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	intron	2322200	2322290	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	CDS	2322291	2322437	1	+	1	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	exon	2322291	2322437	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	intron	2322438	2322567	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	CDS	2322568	2322621	1	+	1	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	exon	2322568	2322621	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	intron	2322622	2322806	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	CDS	2322807	2322942	1	+	1	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	exon	2322807	2322942	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	intron	2322943	2323040	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	CDS	2323041	2323139	0.99	+	0	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	exon	2323041	2323139	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	intron	2323140	2323241	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	CDS	2323242	2323502	0.97	+	0	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	exon	2323242	2323502	.	+	.	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
Phchi.S5	AUGUSTUS	stop_codon	2323503	2323505	.	+	0	transcript_id "Phchi.S5G027600.t1"; gene_id "Phchi.S5G027600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3687.t1 is derived from g856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5183330	5184676	.	-	.	Phchi.S1G084600
Phchi.S1	AUGUSTUS	transcript	5183330	5184676	.	-	.	transcript_id "Phchi.S1G084600.t1"; gene_id "Phchi.S1G084600"
Phchi.S1	AUGUSTUS	stop_codon	5183327	5183329	.	-	0	transcript_id "Phchi.S1G084600.t1"; gene_id "Phchi.S1G084600"
Phchi.S1	AUGUSTUS	CDS	5183330	5184676	0.78	-	0	transcript_id "Phchi.S1G084600.t1"; gene_id "Phchi.S1G084600"
Phchi.S1	AUGUSTUS	exon	5183330	5184676	.	-	.	transcript_id "Phchi.S1G084600.t1"; gene_id "Phchi.S1G084600"
Phchi.S1	AUGUSTUS	start_codon	5184674	5184676	.	-	0	transcript_id "Phchi.S1G084600.t1"; gene_id "Phchi.S1G084600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4802.t1 is derived from g1972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12896454	12899698	.	+	.	Phchi.S1G196100
Phchi.S1	AUGUSTUS	transcript	12896454	12899698	.	+	.	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	start_codon	12896454	12896456	.	+	0	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	CDS	12896454	12896948	1	+	0	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	exon	12896454	12896948	.	+	.	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	intron	12896949	12897046	.	+	.	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	CDS	12897047	12899698	1	+	0	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	exon	12897047	12899698	.	+	.	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
Phchi.S1	AUGUSTUS	stop_codon	12899699	12899701	.	+	0	transcript_id "Phchi.S1G196100.t1"; gene_id "Phchi.S1G196100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7522.t1 is derived from g4696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29831076	29834922	.	+	.	Phchi.S1G468100
Phchi.S1	AUGUSTUS	transcript	29831076	29834922	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	start_codon	29831076	29831078	.	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29831076	29831163	1	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29831076	29831163	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29831164	29831596	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29831597	29831647	1	+	2	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29831597	29831647	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29831648	29831881	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29831882	29832006	1	+	2	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29831882	29832006	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29832007	29832106	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29832107	29832175	1	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29832107	29832175	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29832176	29832352	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29832353	29832394	1	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29832353	29832394	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29832395	29832483	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29832484	29832560	0.98	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29832484	29832560	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29832561	29832678	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29832679	29832781	1	+	1	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29832679	29832781	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29832782	29832899	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29832900	29832981	1	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29832900	29832981	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29832982	29833130	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29833131	29833294	1	+	2	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29833131	29833294	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29833295	29833461	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29833462	29833963	0.7	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29833462	29833963	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29833964	29834112	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29834113	29834246	0.32	+	2	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29834113	29834246	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29834247	29834454	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29834455	29834483	0.43	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29834455	29834483	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29834484	29834598	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29834599	29834679	0.84	+	1	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29834599	29834679	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	intron	29834680	29834870	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	CDS	29834871	29834922	1	+	1	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	exon	29834871	29834922	.	+	.	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
Phchi.S1	AUGUSTUS	stop_codon	29834923	29834925	.	+	0	transcript_id "Phchi.S1G468100.t1"; gene_id "Phchi.S1G468100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6667.t1 is derived from g3839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24404194	24405750	.	-	.	Phchi.S1G382600
Phchi.S1	AUGUSTUS	transcript	24404194	24405750	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	stop_codon	24404191	24404193	.	-	0	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	CDS	24404194	24404475	1	-	0	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	exon	24404194	24404475	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	intron	24404476	24404562	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	CDS	24404563	24404837	1	-	2	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	exon	24404563	24404837	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	intron	24404838	24404964	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	CDS	24404965	24405209	1	-	1	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	exon	24404965	24405209	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	intron	24405210	24405307	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	CDS	24405308	24405750	1	-	0	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	exon	24405308	24405750	.	-	.	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
Phchi.S1	AUGUSTUS	start_codon	24405748	24405750	.	-	0	transcript_id "Phchi.S1G382600.t1"; gene_id "Phchi.S1G382600"
# This transcript jg12336.t2 is derived from g8012.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12337.t1 is derived from g8013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11226111	11227341	.	+	.	Phchi.S2G041700
Phchi.S2	AUGUSTUS	transcript	11226111	11227341	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	start_codon	11226111	11226113	.	+	0	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	CDS	11226111	11226342	0.49	+	0	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	exon	11226111	11226342	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	intron	11226343	11226431	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	CDS	11226432	11226769	1	+	2	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	exon	11226432	11226769	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	intron	11226770	11226876	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	CDS	11226877	11226956	0.99	+	0	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	exon	11226877	11226956	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	intron	11226957	11227061	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	CDS	11227062	11227341	0.98	+	1	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	exon	11227062	11227341	.	+	.	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
Phchi.S2	AUGUSTUS	stop_codon	11227342	11227344	.	+	0	transcript_id "Phchi.S2G041700.t1"; gene_id "Phchi.S2G041700"
# This transcript jg6444.t2 is derived from g3616.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6445.t1 is derived from g3617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23056271	23057664	.	-	.	Phchi.S1G360400
Phchi.S1	AUGUSTUS	transcript	23056271	23057664	.	-	.	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	stop_codon	23056268	23056270	.	-	0	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	CDS	23056271	23056963	0.96	-	0	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	exon	23056271	23056963	.	-	.	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	intron	23056964	23057085	.	-	.	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	CDS	23057086	23057664	0.93	-	0	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	exon	23057086	23057664	.	-	.	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
Phchi.S1	AUGUSTUS	start_codon	23057662	23057664	.	-	0	transcript_id "Phchi.S1G360400.t1"; gene_id "Phchi.S1G360400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13652.t1 is derived from g12119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8019704	8020269	.	-	.	Phchi.S3G097100
Phchi.S3	AUGUSTUS	transcript	8019704	8020269	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	stop_codon	8019701	8019703	.	-	0	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	CDS	8019704	8019815	0.57	-	1	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	exon	8019704	8019815	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	intron	8019816	8019909	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	CDS	8019910	8019984	0.71	-	1	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	exon	8019910	8019984	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	intron	8019985	8020069	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	CDS	8020070	8020172	0.93	-	2	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	exon	8020070	8020172	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	intron	8020173	8020256	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	CDS	8020257	8020269	0.78	-	0	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	exon	8020257	8020269	.	-	.	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
Phchi.S3	AUGUSTUS	start_codon	8020267	8020269	.	-	0	transcript_id "Phchi.S3G097100.t1"; gene_id "Phchi.S3G097100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg331.t1 is derived from g10113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2298375	2299749	.	+	.	Phchi.S6G029000
Phchi.S6	AUGUSTUS	transcript	2298375	2299749	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	start_codon	2298375	2298377	.	+	0	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	CDS	2298375	2298557	1	+	0	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	exon	2298375	2298557	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	intron	2298558	2298645	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	CDS	2298646	2298807	1	+	0	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	exon	2298646	2298807	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	intron	2298808	2298892	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	CDS	2298893	2299124	1	+	0	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	exon	2298893	2299124	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	intron	2299125	2299261	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	CDS	2299262	2299335	1	+	2	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	exon	2299262	2299335	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	intron	2299336	2299415	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	CDS	2299416	2299464	1	+	0	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	exon	2299416	2299464	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	intron	2299465	2299588	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	CDS	2299589	2299749	0.51	+	2	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	exon	2299589	2299749	.	+	.	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
Phchi.S6	AUGUSTUS	stop_codon	2299750	2299752	.	+	0	transcript_id "Phchi.S6G029000.t1"; gene_id "Phchi.S6G029000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10617.t1 is derived from g14667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1258952	1260187	.	+	.	Phchi.S4G019900
Phchi.S4	AUGUSTUS	transcript	1258952	1260187	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	start_codon	1258952	1258954	.	+	0	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	CDS	1258952	1258999	0.84	+	0	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	exon	1258952	1258999	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	intron	1259000	1259080	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	CDS	1259081	1259707	1	+	0	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	exon	1259081	1259707	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	intron	1259708	1259792	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	CDS	1259793	1260078	0.52	+	0	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	exon	1259793	1260078	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	intron	1260079	1260173	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	CDS	1260174	1260187	0.45	+	2	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	exon	1260174	1260187	.	+	.	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
Phchi.S4	AUGUSTUS	stop_codon	1260188	1260190	.	+	0	transcript_id "Phchi.S4G019900.t1"; gene_id "Phchi.S4G019900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10016.t1 is derived from g7192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45060055	45061371	.	+	.	Phchi.S1G717500
Phchi.S1	AUGUSTUS	transcript	45060055	45061371	.	+	.	transcript_id "Phchi.S1G717500.t1"; gene_id "Phchi.S1G717500"
Phchi.S1	AUGUSTUS	start_codon	45060055	45060057	.	+	0	transcript_id "Phchi.S1G717500.t1"; gene_id "Phchi.S1G717500"
Phchi.S1	AUGUSTUS	CDS	45060055	45061371	0.98	+	0	transcript_id "Phchi.S1G717500.t1"; gene_id "Phchi.S1G717500"
Phchi.S1	AUGUSTUS	exon	45060055	45061371	.	+	.	transcript_id "Phchi.S1G717500.t1"; gene_id "Phchi.S1G717500"
Phchi.S1	AUGUSTUS	stop_codon	45061372	45061374	.	+	0	transcript_id "Phchi.S1G717500.t1"; gene_id "Phchi.S1G717500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5644.t1 is derived from g2814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18033826	18036271	.	+	.	Phchi.S1G280300
Phchi.S1	AUGUSTUS	transcript	18033826	18036271	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	start_codon	18033826	18033828	.	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18033826	18034419	0.56	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18033826	18034419	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18034420	18034570	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18034571	18034669	1	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18034571	18034669	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18034670	18034767	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18034768	18034887	1	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18034768	18034887	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18034888	18035029	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18035030	18035196	1	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18035030	18035196	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18035197	18035284	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18035285	18035355	1	+	1	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18035285	18035355	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18035356	18035453	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18035454	18035596	1	+	2	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18035454	18035596	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18035597	18035684	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18035685	18035796	1	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18035685	18035796	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18035797	18035935	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18035936	18036045	1	+	2	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18035936	18036045	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	intron	18036046	18036139	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	CDS	18036140	18036271	1	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	exon	18036140	18036271	.	+	.	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
Phchi.S1	AUGUSTUS	stop_codon	18036272	18036274	.	+	0	transcript_id "Phchi.S1G280300.t1"; gene_id "Phchi.S1G280300"
# This transcript jg920.t2 is derived from g10702.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg921.t1 is derived from g10703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6456975	6458648	.	-	.	Phchi.S6G088000
Phchi.S6	AUGUSTUS	transcript	6456975	6458648	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	stop_codon	6456972	6456974	.	-	0	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	CDS	6456975	6457050	0.93	-	1	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	exon	6456975	6457050	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	intron	6457051	6457257	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	CDS	6457258	6457283	0.88	-	0	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	exon	6457258	6457283	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	intron	6457284	6457435	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	CDS	6457436	6458394	0.33	-	2	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	exon	6457436	6458394	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	intron	6458395	6458554	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	CDS	6458555	6458648	0.79	-	0	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	exon	6458555	6458648	.	-	.	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
Phchi.S6	AUGUSTUS	start_codon	6458646	6458648	.	-	0	transcript_id "Phchi.S6G088000.t1"; gene_id "Phchi.S6G088000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4139.t1 is derived from g1308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8471791	8472069	.	-	.	Phchi.S1G129800
Phchi.S1	AUGUSTUS	transcript	8471791	8472069	.	-	.	transcript_id "Phchi.S1G129800.t1"; gene_id "Phchi.S1G129800"
Phchi.S1	AUGUSTUS	stop_codon	8471788	8471790	.	-	0	transcript_id "Phchi.S1G129800.t1"; gene_id "Phchi.S1G129800"
Phchi.S1	AUGUSTUS	CDS	8471791	8472069	0.79	-	0	transcript_id "Phchi.S1G129800.t1"; gene_id "Phchi.S1G129800"
Phchi.S1	AUGUSTUS	exon	8471791	8472069	.	-	.	transcript_id "Phchi.S1G129800.t1"; gene_id "Phchi.S1G129800"
Phchi.S1	AUGUSTUS	start_codon	8472067	8472069	.	-	0	transcript_id "Phchi.S1G129800.t1"; gene_id "Phchi.S1G129800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12577.t1 is derived from g8254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35817236	35818726	.	-	.	Phchi.S2G065700
Phchi.S2	AUGUSTUS	transcript	35817236	35818726	.	-	.	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	stop_codon	35817233	35817235	.	-	0	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	CDS	35817236	35818022	0.33	-	1	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	exon	35817236	35818022	.	-	.	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	intron	35818023	35818284	.	-	.	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	CDS	35818285	35818377	0.34	-	1	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	exon	35818285	35818377	.	-	.	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	intron	35818378	35818535	.	-	.	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	CDS	35818536	35818726	0.28	-	0	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	exon	35818536	35818726	.	-	.	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
Phchi.S2	AUGUSTUS	start_codon	35818724	35818726	.	-	0	transcript_id "Phchi.S2G065700.t1"; gene_id "Phchi.S2G065700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14721.t1 is derived from g13189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14359200	14362212	.	-	.	Phchi.S3G204000
Phchi.S3	AUGUSTUS	transcript	14359200	14362212	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	stop_codon	14359197	14359199	.	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14359200	14359346	0.98	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14359200	14359346	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14359347	14359529	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14359530	14359845	1	-	1	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14359530	14359845	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14359846	14359999	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14360000	14360485	1	-	1	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14360000	14360485	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14360486	14360627	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14360628	14360704	1	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14360628	14360704	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14360705	14360800	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14360801	14360916	1	-	2	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14360801	14360916	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14360917	14361022	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14361023	14361094	0.98	-	2	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14361023	14361094	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14361095	14361181	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14361182	14361310	1	-	2	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14361182	14361310	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14361311	14361465	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14361466	14361577	1	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14361466	14361577	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14361578	14361708	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14361709	14361774	1	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14361709	14361774	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14361775	14361966	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14361967	14362023	1	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14361967	14362023	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	intron	14362024	14362203	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	CDS	14362204	14362212	1	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	exon	14362204	14362212	.	-	.	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
Phchi.S3	AUGUSTUS	start_codon	14362210	14362212	.	-	0	transcript_id "Phchi.S3G204000.t1"; gene_id "Phchi.S3G204000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8300.t1 is derived from g5475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35147698	35149461	.	-	.	Phchi.S1G545900
Phchi.S1	AUGUSTUS	transcript	35147698	35149461	.	-	.	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	stop_codon	35147695	35147697	.	-	0	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	CDS	35147698	35147759	1	-	2	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	exon	35147698	35147759	.	-	.	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	intron	35147760	35147847	.	-	.	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	CDS	35147848	35148352	0.55	-	0	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	exon	35147848	35148352	.	-	.	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	intron	35148353	35148435	.	-	.	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	CDS	35148436	35149461	0.6	-	0	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	exon	35148436	35149461	.	-	.	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
Phchi.S1	AUGUSTUS	start_codon	35149459	35149461	.	-	0	transcript_id "Phchi.S1G545900.t1"; gene_id "Phchi.S1G545900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1628.t1 is derived from g8547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2086956	2087623	.	-	.	Phchi.S5G023700
Phchi.S5	AUGUSTUS	transcript	2086956	2087623	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	stop_codon	2086953	2086955	.	-	0	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	CDS	2086956	2087038	1	-	2	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	exon	2086956	2087038	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	intron	2087039	2087121	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	CDS	2087122	2087220	1	-	2	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	exon	2087122	2087220	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	intron	2087221	2087306	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	CDS	2087307	2087395	1	-	1	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	exon	2087307	2087395	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	intron	2087396	2087486	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	CDS	2087487	2087623	0.43	-	0	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	exon	2087487	2087623	.	-	.	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
Phchi.S5	AUGUSTUS	start_codon	2087621	2087623	.	-	0	transcript_id "Phchi.S5G023700.t1"; gene_id "Phchi.S5G023700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6015.t1 is derived from g3186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20439996	20442712	.	+	.	Phchi.S1G317400
Phchi.S1	AUGUSTUS	transcript	20439996	20442712	.	+	.	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	start_codon	20439996	20439998	.	+	0	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	CDS	20439996	20440515	0.23	+	0	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	exon	20439996	20440515	.	+	.	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	intron	20440516	20440682	.	+	.	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	CDS	20440683	20442712	0.56	+	2	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	exon	20440683	20442712	.	+	.	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
Phchi.S1	AUGUSTUS	stop_codon	20442713	20442715	.	+	0	transcript_id "Phchi.S1G317400.t1"; gene_id "Phchi.S1G317400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8325.t1 is derived from g5500.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35328345	35329484	.	-	.	Phchi.S1G548400
Phchi.S1	AUGUSTUS	transcript	35328345	35329458	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	stop_codon	35328342	35328344	.	-	0	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328345	35328398	0.99	-	0	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328345	35328398	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328399	35328479	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328480	35328663	0.99	-	1	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328480	35328663	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328664	35328770	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328771	35328921	0.92	-	2	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328771	35328921	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328922	35329133	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35329134	35329266	0.94	-	0	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35329134	35329266	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35329267	35329362	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35329363	35329458	0.93	-	0	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35329363	35329458	.	-	.	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	start_codon	35329456	35329458	.	-	0	transcript_id "Phchi.S1G548400.t1"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	transcript	35328345	35329484	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	stop_codon	35328342	35328344	.	-	0	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328345	35328398	0.98	-	0	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328345	35328398	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328399	35328479	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328480	35328663	0.98	-	1	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328480	35328663	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328664	35328770	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328771	35328921	0.92	-	2	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328771	35328921	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328922	35329147	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35329148	35329266	0.94	-	1	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35329148	35329266	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35329267	35329362	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35329363	35329484	0.61	-	0	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35329363	35329484	.	-	.	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	start_codon	35329482	35329484	.	-	0	transcript_id "Phchi.S1G548400.t2"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	transcript	35328345	35329484	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	stop_codon	35328342	35328344	.	-	0	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328345	35328398	0.97	-	0	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328345	35328398	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328399	35328479	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328480	35328663	0.97	-	1	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328480	35328663	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35328664	35328770	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35328771	35329021	0.87	-	0	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35328771	35329021	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35329022	35329133	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35329134	35329266	0.89	-	1	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35329134	35329266	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	intron	35329267	35329362	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	CDS	35329363	35329484	0.6	-	0	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	exon	35329363	35329484	.	-	.	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
Phchi.S1	AUGUSTUS	start_codon	35329482	35329484	.	-	0	transcript_id "Phchi.S1G548400.t3"; gene_id "Phchi.S1G548400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6150.t1 is derived from g3321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21202217	21204260	.	+	.	Phchi.S1G330900
Phchi.S1	AUGUSTUS	transcript	21202217	21204260	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	start_codon	21202217	21202219	.	+	0	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	CDS	21202217	21202496	0.92	+	0	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	exon	21202217	21202496	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	intron	21202497	21202585	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	CDS	21202586	21202884	0.82	+	2	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	exon	21202586	21202884	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	intron	21202885	21202958	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	CDS	21202959	21203259	1	+	0	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	exon	21202959	21203259	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	intron	21203260	21203361	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	CDS	21203362	21203585	0.52	+	2	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	exon	21203362	21203585	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	intron	21203586	21203666	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	CDS	21203667	21204260	0.48	+	0	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	exon	21203667	21204260	.	+	.	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
Phchi.S1	AUGUSTUS	stop_codon	21204261	21204263	.	+	0	transcript_id "Phchi.S1G330900.t1"; gene_id "Phchi.S1G330900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15448.t1 is derived from g13916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19217566	19218025	.	-	.	Phchi.S3G276700
Phchi.S3	AUGUSTUS	transcript	19217566	19218025	.	-	.	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	stop_codon	19217563	19217565	.	-	0	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	CDS	19217566	19217631	1	-	0	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	exon	19217566	19217631	.	-	.	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	intron	19217632	19217714	.	-	.	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	CDS	19217715	19217780	1	-	0	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	exon	19217715	19217780	.	-	.	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	intron	19217781	19217863	.	-	.	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	CDS	19217864	19218025	0.67	-	0	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	exon	19217864	19218025	.	-	.	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
Phchi.S3	AUGUSTUS	start_codon	19218023	19218025	.	-	0	transcript_id "Phchi.S3G276700.t1"; gene_id "Phchi.S3G276700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8694.t1 is derived from g5869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37463248	37472130	.	-	.	Phchi.S1G585300
Phchi.S1	AUGUSTUS	transcript	37463248	37472130	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	stop_codon	37463245	37463247	.	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37463248	37463310	0.75	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37463248	37463310	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37463311	37463388	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37463389	37463420	0.75	-	2	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37463389	37463420	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37463421	37463491	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37463492	37463504	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37463492	37463504	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37463505	37463657	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37463658	37463706	1	-	1	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37463658	37463706	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37463707	37463874	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37463875	37463997	1	-	1	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37463875	37463997	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37463998	37464081	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37464082	37464128	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37464082	37464128	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37464129	37464227	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37464228	37464377	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37464228	37464377	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37464378	37464529	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37464530	37464613	0.82	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37464530	37464613	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37464614	37464754	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37464755	37464823	0.99	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37464755	37464823	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37464824	37464905	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37464906	37464986	0.84	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37464906	37464986	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37464987	37465128	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37465129	37465179	0.53	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37465129	37465179	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37465180	37465325	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37465326	37465556	0.95	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37465326	37465556	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37465557	37465690	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37465691	37466916	0.66	-	2	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37465691	37466916	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37466917	37467029	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37467030	37467080	0.68	-	2	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37467030	37467080	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37467081	37467185	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37467186	37467354	0.71	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37467186	37467354	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37467355	37467456	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37467457	37467492	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37467457	37467492	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37467493	37467575	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37467576	37467677	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37467576	37467677	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37467678	37467774	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37467775	37469305	0.93	-	1	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37467775	37469305	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37469306	37469457	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37469458	37469579	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37469458	37469579	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37469580	37469666	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37469667	37469924	0.95	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37469667	37469924	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37469925	37470127	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37470128	37470292	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37470128	37470292	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37470293	37470371	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37470372	37470551	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37470372	37470551	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37470552	37470698	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37470699	37470815	0.99	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37470699	37470815	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37470816	37470919	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37470920	37471030	1	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37470920	37471030	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	intron	37471031	37471173	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	CDS	37471174	37472130	0.42	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	exon	37471174	37472130	.	-	.	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
Phchi.S1	AUGUSTUS	start_codon	37472128	37472130	.	-	0	transcript_id "Phchi.S1G585300.t1"; gene_id "Phchi.S1G585300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5921.t1 is derived from g3092.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19879987	19881528	.	-	.	Phchi.S1G308000
Phchi.S1	AUGUSTUS	transcript	19879987	19881528	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	stop_codon	19879984	19879986	.	-	0	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19879987	19880061	0.99	-	0	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19879987	19880061	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880062	19880183	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880184	19880275	0.99	-	2	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880184	19880275	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880276	19880388	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880389	19880448	1	-	2	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880389	19880448	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880449	19880599	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880600	19880693	1	-	0	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880600	19880693	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880694	19880771	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880772	19880832	1	-	1	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880772	19880832	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880833	19880933	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880934	19880993	1	-	1	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880934	19880993	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880994	19881188	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19881189	19881278	1	-	1	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19881189	19881278	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19881279	19881403	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19881404	19881528	0.99	-	0	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19881404	19881528	.	-	.	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	start_codon	19881526	19881528	.	-	0	transcript_id "Phchi.S1G308000.t1"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	transcript	19879987	19881528	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	stop_codon	19879984	19879986	.	-	0	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19879987	19880061	0.94	-	0	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19879987	19880061	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880062	19880183	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880184	19880275	0.94	-	2	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880184	19880275	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880276	19880388	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880389	19880448	0.98	-	2	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880389	19880448	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880449	19880599	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880600	19880693	1	-	0	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880600	19880693	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880694	19880792	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880793	19880832	0.99	-	1	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880793	19880832	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880833	19880933	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19880934	19880993	1	-	1	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19880934	19880993	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19880994	19881188	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19881189	19881278	1	-	1	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19881189	19881278	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	intron	19881279	19881403	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	CDS	19881404	19881528	0.96	-	0	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	exon	19881404	19881528	.	-	.	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
Phchi.S1	AUGUSTUS	start_codon	19881526	19881528	.	-	0	transcript_id "Phchi.S1G308000.t2"; gene_id "Phchi.S1G308000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13264.t1 is derived from g11729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4976009	4976288	.	-	.	Phchi.S3G058300
Phchi.S3	AUGUSTUS	transcript	4976009	4976288	.	-	.	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	stop_codon	4976006	4976008	.	-	0	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	CDS	4976009	4976018	0.94	-	1	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	exon	4976009	4976018	.	-	.	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	intron	4976019	4976100	.	-	.	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	CDS	4976101	4976288	0.89	-	0	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	exon	4976101	4976288	.	-	.	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
Phchi.S3	AUGUSTUS	start_codon	4976286	4976288	.	-	0	transcript_id "Phchi.S3G058300.t1"; gene_id "Phchi.S3G058300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5680.t1 is derived from g2850.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18278244	18282181	.	-	.	Phchi.S1G283900
Phchi.S1	AUGUSTUS	transcript	18278244	18282181	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	stop_codon	18278241	18278243	.	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278244	18278339	0.98	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278244	18278339	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278340	18278418	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278419	18278480	1	-	2	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278419	18278480	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278481	18278566	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278567	18278630	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278567	18278630	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278631	18278730	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278731	18278784	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278731	18278784	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278785	18278896	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278897	18279043	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278897	18279043	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279044	18279156	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279157	18279261	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279157	18279261	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279262	18279410	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279411	18279533	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279411	18279533	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279534	18279636	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279637	18279743	0.97	-	2	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279637	18279743	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279744	18279856	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279857	18279956	0.98	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279857	18279956	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279957	18280074	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280075	18280104	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280075	18280104	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280105	18280224	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280225	18280341	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280225	18280341	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280342	18280524	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280525	18280636	1	-	1	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280525	18280636	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280637	18280765	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280766	18280812	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280766	18280812	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280813	18280936	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280937	18281065	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280937	18281065	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281066	18281174	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281175	18281250	1	-	1	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281175	18281250	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281251	18281360	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281361	18281458	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281361	18281458	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281459	18281600	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281601	18281630	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281601	18281630	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281631	18281959	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281960	18282181	1	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281960	18282181	.	-	.	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	start_codon	18282179	18282181	.	-	0	transcript_id "Phchi.S1G283900.t1"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	transcript	18278244	18282181	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	stop_codon	18278241	18278243	.	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278244	18278339	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278244	18278339	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278340	18278418	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278419	18278480	1	-	2	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278419	18278480	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278481	18278566	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278567	18278630	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278567	18278630	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278631	18278730	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278731	18278784	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278731	18278784	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278785	18278896	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278897	18279043	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278897	18279043	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279044	18279156	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279157	18279261	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279157	18279261	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279262	18279410	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279411	18279533	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279411	18279533	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279534	18279636	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279637	18279743	0.96	-	2	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279637	18279743	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279744	18279856	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279857	18279956	0.95	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279857	18279956	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279957	18280074	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280075	18280104	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280075	18280104	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280105	18280224	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280225	18280341	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280225	18280341	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280342	18280524	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280525	18280636	1	-	1	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280525	18280636	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280637	18280877	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280878	18281065	0.97	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280878	18281065	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281066	18281174	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281175	18281250	1	-	1	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281175	18281250	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281251	18281360	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281361	18281458	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281361	18281458	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281459	18281600	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281601	18281630	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281601	18281630	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281631	18281959	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281960	18282181	1	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281960	18282181	.	-	.	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	start_codon	18282179	18282181	.	-	0	transcript_id "Phchi.S1G283900.t2"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	transcript	18278318	18282181	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	stop_codon	18278315	18278317	.	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278318	18278323	0.97	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278318	18278323	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278324	18278418	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278419	18278480	1	-	2	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278419	18278480	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278481	18278566	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278567	18278630	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278567	18278630	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278631	18278730	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278731	18278784	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278731	18278784	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18278785	18278896	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18278897	18279043	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18278897	18279043	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279044	18279156	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279157	18279261	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279157	18279261	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279262	18279410	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279411	18279533	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279411	18279533	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279534	18279636	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279637	18279743	0.95	-	2	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279637	18279743	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279744	18279856	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18279857	18279956	0.95	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18279857	18279956	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18279957	18280074	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280075	18280104	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280075	18280104	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280105	18280224	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280225	18280341	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280225	18280341	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280342	18280524	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280525	18280636	1	-	1	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280525	18280636	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280637	18280765	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280766	18280812	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280766	18280812	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18280813	18280936	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18280937	18281065	0.98	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18280937	18281065	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281066	18281174	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281175	18281250	1	-	1	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281175	18281250	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281251	18281360	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281361	18281458	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281361	18281458	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281459	18281600	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281601	18281630	1	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281601	18281630	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	intron	18281631	18281959	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	CDS	18281960	18282181	0.98	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	exon	18281960	18282181	.	-	.	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
Phchi.S1	AUGUSTUS	start_codon	18282179	18282181	.	-	0	transcript_id "Phchi.S1G283900.t3"; gene_id "Phchi.S1G283900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10781.t1 is derived from g14831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2084346	2085080	.	-	.	Phchi.S4G036300
Phchi.S4	AUGUSTUS	transcript	2084346	2085080	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	stop_codon	2084343	2084345	.	-	0	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	CDS	2084346	2084468	0.73	-	0	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	exon	2084346	2084468	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	intron	2084469	2084575	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	CDS	2084576	2084686	0.84	-	0	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	exon	2084576	2084686	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	intron	2084687	2084765	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	CDS	2084766	2084929	1	-	2	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	exon	2084766	2084929	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	intron	2084930	2085010	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	CDS	2085011	2085080	0.98	-	0	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	exon	2085011	2085080	.	-	.	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
Phchi.S4	AUGUSTUS	start_codon	2085078	2085080	.	-	0	transcript_id "Phchi.S4G036300.t1"; gene_id "Phchi.S4G036300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4683.t1 is derived from g1853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11856391	11857620	.	+	.	Phchi.S1G184200
Phchi.S1	AUGUSTUS	transcript	11856391	11857620	.	+	.	transcript_id "Phchi.S1G184200.t1"; gene_id "Phchi.S1G184200"
Phchi.S1	AUGUSTUS	start_codon	11856391	11856393	.	+	0	transcript_id "Phchi.S1G184200.t1"; gene_id "Phchi.S1G184200"
Phchi.S1	AUGUSTUS	CDS	11856391	11857620	0.41	+	0	transcript_id "Phchi.S1G184200.t1"; gene_id "Phchi.S1G184200"
Phchi.S1	AUGUSTUS	exon	11856391	11857620	.	+	.	transcript_id "Phchi.S1G184200.t1"; gene_id "Phchi.S1G184200"
Phchi.S1	AUGUSTUS	stop_codon	11857621	11857623	.	+	0	transcript_id "Phchi.S1G184200.t1"; gene_id "Phchi.S1G184200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4397.t1 is derived from g1566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10234224	10234845	.	-	.	Phchi.S1G155600
Phchi.S1	AUGUSTUS	transcript	10234224	10234845	.	-	.	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	stop_codon	10234221	10234223	.	-	0	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	CDS	10234224	10234253	0.44	-	0	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	exon	10234224	10234253	.	-	.	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	intron	10234254	10234504	.	-	.	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	CDS	10234505	10234636	0.79	-	0	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	exon	10234505	10234636	.	-	.	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	intron	10234637	10234785	.	-	.	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	CDS	10234786	10234845	0.83	-	0	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	exon	10234786	10234845	.	-	.	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
Phchi.S1	AUGUSTUS	start_codon	10234843	10234845	.	-	0	transcript_id "Phchi.S1G155600.t1"; gene_id "Phchi.S1G155600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2300.t1 is derived from g9220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5942982	5945788	.	-	.	Phchi.S5G090900
Phchi.S5	AUGUSTUS	transcript	5942982	5945788	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	stop_codon	5942979	5942981	.	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5942982	5943139	1	-	2	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5942982	5943139	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5943140	5943359	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5943360	5943435	0.93	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5943360	5943435	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5943436	5943775	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5943776	5943823	0.97	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5943776	5943823	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5943824	5943991	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5943992	5944038	1	-	2	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5943992	5944038	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5944039	5944138	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5944139	5944325	1	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5944139	5944325	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5944326	5944407	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5944408	5944710	0.97	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5944408	5944710	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5944711	5944814	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5944815	5945009	0.97	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5944815	5945009	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5945010	5945109	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5945110	5945211	1	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5945110	5945211	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5945212	5945296	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5945297	5945596	1	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5945297	5945596	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	intron	5945597	5945731	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	CDS	5945732	5945788	0.77	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	exon	5945732	5945788	.	-	.	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
Phchi.S5	AUGUSTUS	start_codon	5945786	5945788	.	-	0	transcript_id "Phchi.S5G090900.t1"; gene_id "Phchi.S5G090900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13019.t1 is derived from g11484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3650878	3652734	.	-	.	Phchi.S3G033800
Phchi.S3	AUGUSTUS	transcript	3650878	3652734	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	stop_codon	3650875	3650877	.	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3650878	3651000	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3650878	3651000	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3651001	3651126	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3651127	3651162	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3651127	3651162	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3651163	3651268	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3651269	3651331	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3651269	3651331	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3651332	3651444	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3651445	3651525	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3651445	3651525	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3651526	3651619	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3651620	3651708	1	-	2	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3651620	3651708	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3651709	3651871	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3651872	3651989	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3651872	3651989	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3651990	3652092	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3652093	3652224	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3652093	3652224	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3652225	3652305	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3652306	3652386	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3652306	3652386	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3652387	3652461	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3652462	3652503	1	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3652462	3652503	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	intron	3652504	3652590	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	CDS	3652591	3652734	0.56	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	exon	3652591	3652734	.	-	.	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
Phchi.S3	AUGUSTUS	start_codon	3652732	3652734	.	-	0	transcript_id "Phchi.S3G033800.t1"; gene_id "Phchi.S3G033800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14240.t1 is derived from g12707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11698239	11699013	.	+	.	Phchi.S3G155900
Phchi.S3	AUGUSTUS	transcript	11698239	11699013	.	+	.	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	start_codon	11698239	11698241	.	+	0	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	CDS	11698239	11698286	0.38	+	0	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	exon	11698239	11698286	.	+	.	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	intron	11698287	11698361	.	+	.	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	CDS	11698362	11698622	1	+	0	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	exon	11698362	11698622	.	+	.	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	intron	11698623	11698698	.	+	.	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	CDS	11698699	11699013	1	+	0	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	exon	11698699	11699013	.	+	.	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
Phchi.S3	AUGUSTUS	stop_codon	11699014	11699016	.	+	0	transcript_id "Phchi.S3G155900.t1"; gene_id "Phchi.S3G155900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13070.t1 is derived from g11535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4020000	4021200	.	-	.	Phchi.S3G038900
Phchi.S3	AUGUSTUS	transcript	4020000	4021200	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	stop_codon	4019997	4019999	.	-	0	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	CDS	4020000	4020231	1	-	1	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	exon	4020000	4020231	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	intron	4020232	4020358	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	CDS	4020359	4020429	1	-	0	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	exon	4020359	4020429	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	intron	4020430	4020552	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	CDS	4020553	4020630	1	-	0	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	exon	4020553	4020630	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	intron	4020631	4020746	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	CDS	4020747	4020823	1	-	2	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	exon	4020747	4020823	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	intron	4020824	4021034	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	CDS	4021035	4021200	0.99	-	0	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	exon	4021035	4021200	.	-	.	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
Phchi.S3	AUGUSTUS	start_codon	4021198	4021200	.	-	0	transcript_id "Phchi.S3G038900.t1"; gene_id "Phchi.S3G038900"
# This transcript jg13634.t2 is derived from g12101.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13635.t1 is derived from g12102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7854192	7854743	.	-	.	Phchi.S3G095400
Phchi.S3	AUGUSTUS	transcript	7854192	7854743	.	-	.	transcript_id "Phchi.S3G095400.t1"; gene_id "Phchi.S3G095400"
Phchi.S3	AUGUSTUS	stop_codon	7854189	7854191	.	-	0	transcript_id "Phchi.S3G095400.t1"; gene_id "Phchi.S3G095400"
Phchi.S3	AUGUSTUS	CDS	7854192	7854743	0.97	-	0	transcript_id "Phchi.S3G095400.t1"; gene_id "Phchi.S3G095400"
Phchi.S3	AUGUSTUS	exon	7854192	7854743	.	-	.	transcript_id "Phchi.S3G095400.t1"; gene_id "Phchi.S3G095400"
Phchi.S3	AUGUSTUS	start_codon	7854741	7854743	.	-	0	transcript_id "Phchi.S3G095400.t1"; gene_id "Phchi.S3G095400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3075.t1 is derived from g244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1443998	1444598	.	+	.	Phchi.S1G023400
Phchi.S1	AUGUSTUS	transcript	1443998	1444598	.	+	.	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	start_codon	1443998	1444000	.	+	0	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	CDS	1443998	1444166	0.57	+	0	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	exon	1443998	1444166	.	+	.	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	intron	1444167	1444266	.	+	.	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	CDS	1444267	1444401	0.58	+	2	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	exon	1444267	1444401	.	+	.	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	intron	1444402	1444491	.	+	.	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	CDS	1444492	1444598	0.89	+	2	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	exon	1444492	1444598	.	+	.	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
Phchi.S1	AUGUSTUS	stop_codon	1444599	1444601	.	+	0	transcript_id "Phchi.S1G023400.t1"; gene_id "Phchi.S1G023400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11089.t1 is derived from g15139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4035265	4036675	.	-	.	Phchi.S4G067100
Phchi.S4	AUGUSTUS	transcript	4035265	4036675	.	-	.	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	stop_codon	4035262	4035264	.	-	0	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	CDS	4035265	4036455	0.9	-	0	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	exon	4035265	4036455	.	-	.	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	intron	4036456	4036573	.	-	.	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	CDS	4036574	4036675	0.63	-	0	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	exon	4036574	4036675	.	-	.	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
Phchi.S4	AUGUSTUS	start_codon	4036673	4036675	.	-	0	transcript_id "Phchi.S4G067100.t1"; gene_id "Phchi.S4G067100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8163.t1 is derived from g5338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34239226	34241263	.	+	.	Phchi.S1G532200
Phchi.S1	AUGUSTUS	transcript	34239226	34241263	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	start_codon	34239226	34239228	.	+	0	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34239226	34239302	1	+	0	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34239226	34239302	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34239303	34239387	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34239388	34239437	1	+	1	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34239388	34239437	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34239438	34239519	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34239520	34239560	1	+	2	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34239520	34239560	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34239561	34239679	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34239680	34239745	1	+	0	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34239680	34239745	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34239746	34240004	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34240005	34240045	1	+	0	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34240005	34240045	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34240046	34240125	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34240126	34240262	1	+	1	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34240126	34240262	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34240263	34240358	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34240359	34240449	1	+	2	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34240359	34240449	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34240450	34240634	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34240635	34240706	1	+	1	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34240635	34240706	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34240707	34240790	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34240791	34240903	1	+	1	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34240791	34240903	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	intron	34240904	34241048	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	CDS	34241049	34241263	0.97	+	2	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	exon	34241049	34241263	.	+	.	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
Phchi.S1	AUGUSTUS	stop_codon	34241264	34241266	.	+	0	transcript_id "Phchi.S1G532200.t1"; gene_id "Phchi.S1G532200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg580.t1 is derived from g10362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4273076	4274395	.	-	.	Phchi.S6G053900
Phchi.S6	AUGUSTUS	transcript	4273076	4274395	.	-	.	transcript_id "Phchi.S6G053900.t1"; gene_id "Phchi.S6G053900"
Phchi.S6	AUGUSTUS	stop_codon	4273073	4273075	.	-	0	transcript_id "Phchi.S6G053900.t1"; gene_id "Phchi.S6G053900"
Phchi.S6	AUGUSTUS	CDS	4273076	4274395	0.73	-	0	transcript_id "Phchi.S6G053900.t1"; gene_id "Phchi.S6G053900"
Phchi.S6	AUGUSTUS	exon	4273076	4274395	.	-	.	transcript_id "Phchi.S6G053900.t1"; gene_id "Phchi.S6G053900"
Phchi.S6	AUGUSTUS	start_codon	4274393	4274395	.	-	0	transcript_id "Phchi.S6G053900.t1"; gene_id "Phchi.S6G053900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7982.t1 is derived from g5157.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32227638	32232256	.	+	.	Phchi.S1G514100
Phchi.S1	AUGUSTUS	transcript	32227638	32232256	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	start_codon	32227638	32227640	.	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32227638	32227831	0.81	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32227638	32227831	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32227832	32227928	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32227929	32227960	1	+	1	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32227929	32227960	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32227961	32228084	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228085	32228356	1	+	2	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228085	32228356	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228357	32228445	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228446	32228637	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228446	32228637	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228638	32228726	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228727	32228841	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228727	32228841	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228842	32228944	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228945	32228985	1	+	2	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228945	32228985	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228986	32229088	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32229089	32229319	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32229089	32229319	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32229320	32229421	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32229422	32229619	0.91	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32229422	32229619	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32229620	32229751	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32229752	32229846	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32229752	32229846	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32229847	32230148	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230149	32230193	0.99	+	1	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230149	32230193	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32230194	32230335	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230336	32230421	1	+	1	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230336	32230421	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32230422	32230542	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230543	32230817	1	+	2	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230543	32230817	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32230818	32230936	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230937	32231134	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230937	32231134	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231135	32231244	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231245	32231368	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231245	32231368	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231369	32231448	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231449	32231489	1	+	2	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231449	32231489	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231490	32231577	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231578	32231811	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231578	32231811	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231812	32231898	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231899	32232096	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231899	32232096	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32232097	32232181	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32232182	32232256	1	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32232182	32232256	.	+	.	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	stop_codon	32232257	32232259	.	+	0	transcript_id "Phchi.S1G514100.t1"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	transcript	32227638	32232256	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	start_codon	32227638	32227640	.	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32227638	32227831	0.86	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32227638	32227831	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32227832	32227928	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32227929	32227960	1	+	1	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32227929	32227960	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32227961	32228084	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228085	32228356	1	+	2	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228085	32228356	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228357	32228445	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228446	32228637	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228446	32228637	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228638	32228726	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228727	32228841	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228727	32228841	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228842	32228944	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32228945	32228985	1	+	2	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32228945	32228985	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32228986	32229088	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32229089	32229319	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32229089	32229319	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32229320	32229421	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32229422	32229619	0.91	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32229422	32229619	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32229620	32229751	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32229752	32229846	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32229752	32229846	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32229847	32230165	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230166	32230193	0.61	+	1	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230166	32230193	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32230194	32230324	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230325	32230421	0.95	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230325	32230421	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32230422	32230542	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230543	32230817	1	+	2	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230543	32230817	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32230818	32230936	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32230937	32231134	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32230937	32231134	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231135	32231244	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231245	32231368	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231245	32231368	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231369	32231448	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231449	32231489	1	+	2	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231449	32231489	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231490	32231577	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231578	32231811	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231578	32231811	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32231812	32231898	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32231899	32232096	1	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32231899	32232096	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	intron	32232097	32232181	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	CDS	32232182	32232256	0.98	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	exon	32232182	32232256	.	+	.	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
Phchi.S1	AUGUSTUS	stop_codon	32232257	32232259	.	+	0	transcript_id "Phchi.S1G514100.t2"; gene_id "Phchi.S1G514100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15571.t1 is derived from g14040.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20061158	20071086	.	+	.	Phchi.S3G289000
Phchi.S3	AUGUSTUS	transcript	20061158	20071086	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	start_codon	20061158	20061160	.	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20061158	20061289	0.99	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20061158	20061289	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20061290	20061859	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20061860	20062063	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20061860	20062063	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062064	20062244	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20062245	20062429	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20062245	20062429	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062430	20062560	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20062561	20062687	1	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20062561	20062687	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062688	20062762	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20062763	20062984	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20062763	20062984	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062985	20063246	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063247	20063261	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063247	20063261	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063262	20063362	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063363	20063462	0.98	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063363	20063462	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063463	20063591	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063592	20063737	1	+	2	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063592	20063737	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063738	20063824	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063825	20063863	0.99	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063825	20063863	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063864	20063940	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063941	20063981	0.87	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063941	20063981	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063982	20064112	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064113	20064262	1	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064113	20064262	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064263	20064359	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064360	20064408	0.73	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064360	20064408	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064409	20064523	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064524	20064715	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064524	20064715	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064716	20064806	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064807	20064989	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064807	20064989	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064990	20065079	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065080	20065234	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065080	20065234	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065235	20065356	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065357	20065483	1	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065357	20065483	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065484	20065625	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065626	20065775	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065626	20065775	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065776	20065858	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065859	20065909	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065859	20065909	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065910	20066043	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066044	20066186	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066044	20066186	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20066187	20066361	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066362	20066479	1	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066362	20066479	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20066480	20066735	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066736	20066870	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066736	20066870	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20066871	20066979	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066980	20067191	0.99	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066980	20067191	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067192	20067386	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20067387	20067543	1	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20067387	20067543	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067544	20067715	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20067716	20067720	0.76	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20067716	20067720	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067721	20067803	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20067804	20067861	0.76	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20067804	20067861	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067862	20068015	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20068016	20068096	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20068016	20068096	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20068097	20068281	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20068282	20068806	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20068282	20068806	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20068807	20068951	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20068952	20069101	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20068952	20069101	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069102	20069180	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069181	20069269	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069181	20069269	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069270	20069373	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069374	20069425	1	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069374	20069425	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069426	20069528	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069529	20069615	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069529	20069615	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069616	20069700	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069701	20069747	1	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069701	20069747	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069748	20069881	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069882	20069956	0.97	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069882	20069956	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069957	20070080	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20070081	20070346	0.97	+	1	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20070081	20070346	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20070347	20070422	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20070423	20070961	1	+	2	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20070423	20070961	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20070962	20071053	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20071054	20071086	0.9	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20071054	20071086	.	+	.	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	stop_codon	20071087	20071089	.	+	0	transcript_id "Phchi.S3G289000.t1"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	transcript	20061158	20071086	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	start_codon	20061158	20061160	.	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20061158	20061289	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20061158	20061289	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20061290	20061859	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20061860	20062063	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20061860	20062063	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062064	20062244	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20062245	20062429	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20062245	20062429	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062430	20062560	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20062561	20062687	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20062561	20062687	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062688	20062762	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20062763	20062984	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20062763	20062984	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20062985	20063246	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063247	20063261	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063247	20063261	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063262	20063362	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063363	20063462	0.97	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063363	20063462	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063463	20063591	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063592	20063737	1	+	2	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063592	20063737	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063738	20063824	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063825	20063863	0.98	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063825	20063863	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063864	20063940	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20063941	20063981	0.83	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20063941	20063981	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20063982	20064112	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064113	20064262	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064113	20064262	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064263	20064359	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064360	20064408	0.75	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064360	20064408	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064409	20064523	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064524	20064715	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064524	20064715	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064716	20064806	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20064807	20064989	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20064807	20064989	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20064990	20065079	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065080	20065234	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065080	20065234	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065235	20065356	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065357	20065483	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065357	20065483	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065484	20065625	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065626	20065775	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065626	20065775	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065776	20065858	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20065859	20065909	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20065859	20065909	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20065910	20066043	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066044	20066186	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066044	20066186	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20066187	20066361	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066362	20066479	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066362	20066479	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20066480	20066735	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066736	20066870	0.99	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066736	20066870	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20066871	20066979	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20066980	20067191	0.98	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20066980	20067191	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067192	20067386	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20067387	20067543	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20067387	20067543	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067544	20067715	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20067716	20067720	0.83	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20067716	20067720	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067721	20067803	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20067804	20067861	0.83	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20067804	20067861	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20067862	20068015	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20068016	20068096	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20068016	20068096	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20068097	20068281	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20068282	20068806	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20068282	20068806	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20068807	20068951	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20068952	20069101	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20068952	20069101	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069102	20069180	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069181	20069269	1	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069181	20069269	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069270	20069373	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069374	20069425	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069374	20069425	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069426	20069528	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069529	20069615	0.98	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069529	20069615	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069616	20069697	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069698	20069747	0.77	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069698	20069747	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069748	20069881	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20069882	20069956	1	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20069882	20069956	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20069957	20070080	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20070081	20070346	0.94	+	1	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20070081	20070346	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20070347	20070422	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20070423	20070961	1	+	2	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20070423	20070961	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	intron	20070962	20071053	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	CDS	20071054	20071086	0.85	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	exon	20071054	20071086	.	+	.	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
Phchi.S3	AUGUSTUS	stop_codon	20071087	20071089	.	+	0	transcript_id "Phchi.S3G289000.t2"; gene_id "Phchi.S3G289000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10843.t1 is derived from g14893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2435003	2436250	.	+	.	Phchi.S4G042500
Phchi.S4	AUGUSTUS	transcript	2435003	2436250	.	+	.	transcript_id "Phchi.S4G042500.t1"; gene_id "Phchi.S4G042500"
Phchi.S4	AUGUSTUS	start_codon	2435003	2435005	.	+	0	transcript_id "Phchi.S4G042500.t1"; gene_id "Phchi.S4G042500"
Phchi.S4	AUGUSTUS	CDS	2435003	2436250	1	+	0	transcript_id "Phchi.S4G042500.t1"; gene_id "Phchi.S4G042500"
Phchi.S4	AUGUSTUS	exon	2435003	2436250	.	+	.	transcript_id "Phchi.S4G042500.t1"; gene_id "Phchi.S4G042500"
Phchi.S4	AUGUSTUS	stop_codon	2436251	2436253	.	+	0	transcript_id "Phchi.S4G042500.t1"; gene_id "Phchi.S4G042500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2887.t1 is derived from g56.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	290666	292769	.	+	.	Phchi.S1G004600
Phchi.S1	AUGUSTUS	transcript	290666	292769	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	start_codon	290666	290668	.	+	0	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	CDS	290666	291089	0.94	+	0	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	exon	290666	291089	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	intron	291090	291240	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	CDS	291241	291470	0.67	+	2	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	exon	291241	291470	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	intron	291471	291571	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	CDS	291572	291776	0.32	+	0	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	exon	291572	291776	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	intron	291777	291996	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	CDS	291997	292338	0.88	+	2	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	exon	291997	292338	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	intron	292339	292529	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	CDS	292530	292610	0.83	+	2	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	exon	292530	292610	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	intron	292611	292764	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	CDS	292765	292769	0.95	+	2	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	exon	292765	292769	.	+	.	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
Phchi.S1	AUGUSTUS	stop_codon	292770	292772	.	+	0	transcript_id "Phchi.S1G004600.t1"; gene_id "Phchi.S1G004600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15963.t1 is derived from g16002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	4330	5606	.	+	.	Phchi.C133G000200
Phchi.C133	AUGUSTUS	transcript	4330	5606	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	start_codon	4330	4332	.	+	0	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	CDS	4330	4352	1	+	0	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	exon	4330	4352	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	intron	4353	4556	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	CDS	4557	4678	0.95	+	1	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	exon	4557	4678	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	intron	4679	4911	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	CDS	4912	5237	0.7	+	2	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	exon	4912	5237	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	intron	5238	5392	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	CDS	5393	5504	0.97	+	0	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	exon	5393	5504	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	intron	5505	5595	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	CDS	5596	5606	1	+	2	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	exon	5596	5606	.	+	.	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
Phchi.C133	AUGUSTUS	stop_codon	5607	5609	.	+	0	transcript_id "Phchi.C133G000200.t1"; gene_id "Phchi.C133G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7330.t1 is derived from g4502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28542045	28544721	.	+	.	Phchi.S1G448900
Phchi.S1	AUGUSTUS	transcript	28542045	28544721	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	start_codon	28542045	28542047	.	+	0	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28542045	28542208	0.96	+	0	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28542045	28542208	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28542209	28542333	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28542334	28542510	0.99	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28542334	28542510	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28542511	28542594	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28542595	28542661	1	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28542595	28542661	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28542662	28542751	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28542752	28542822	1	+	0	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28542752	28542822	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28542823	28542926	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28542927	28543044	0.98	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28542927	28543044	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28543045	28543137	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28543138	28543211	1	+	0	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28543138	28543211	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28543212	28543321	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28543322	28543377	0.99	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28543322	28543377	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28543378	28543529	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28543530	28543613	1	+	2	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28543530	28543613	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28543614	28543711	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28543712	28543799	1	+	2	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28543712	28543799	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28543800	28543896	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28543897	28543974	1	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28543897	28543974	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28543975	28544101	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28544102	28544158	1	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28544102	28544158	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	intron	28544159	28544258	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	CDS	28544259	28544721	0.93	+	1	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	exon	28544259	28544721	.	+	.	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
Phchi.S1	AUGUSTUS	stop_codon	28544722	28544724	.	+	0	transcript_id "Phchi.S1G448900.t1"; gene_id "Phchi.S1G448900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3400.t1 is derived from g569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3347716	3348024	.	-	.	Phchi.S1G055900
Phchi.S1	AUGUSTUS	transcript	3347716	3348024	.	-	.	transcript_id "Phchi.S1G055900.t1"; gene_id "Phchi.S1G055900"
Phchi.S1	AUGUSTUS	stop_codon	3347713	3347715	.	-	0	transcript_id "Phchi.S1G055900.t1"; gene_id "Phchi.S1G055900"
Phchi.S1	AUGUSTUS	CDS	3347716	3348024	1	-	0	transcript_id "Phchi.S1G055900.t1"; gene_id "Phchi.S1G055900"
Phchi.S1	AUGUSTUS	exon	3347716	3348024	.	-	.	transcript_id "Phchi.S1G055900.t1"; gene_id "Phchi.S1G055900"
Phchi.S1	AUGUSTUS	start_codon	3348022	3348024	.	-	0	transcript_id "Phchi.S1G055900.t1"; gene_id "Phchi.S1G055900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10674.t1 is derived from g14724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1549059	1550606	.	+	.	Phchi.S4G025600
Phchi.S4	AUGUSTUS	transcript	1549059	1550606	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	start_codon	1549059	1549061	.	+	0	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	CDS	1549059	1549348	1	+	0	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	exon	1549059	1549348	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	intron	1549349	1549500	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	CDS	1549501	1549780	0.89	+	1	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	exon	1549501	1549780	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	intron	1549781	1549939	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	CDS	1549940	1549961	1	+	0	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	exon	1549940	1549961	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	intron	1549962	1550094	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	CDS	1550095	1550210	1	+	2	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	exon	1550095	1550210	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	intron	1550211	1550322	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	CDS	1550323	1550388	1	+	0	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	exon	1550323	1550388	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	intron	1550389	1550492	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	CDS	1550493	1550606	0.97	+	0	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	exon	1550493	1550606	.	+	.	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
Phchi.S4	AUGUSTUS	stop_codon	1550607	1550609	.	+	0	transcript_id "Phchi.S4G025600.t1"; gene_id "Phchi.S4G025600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg582.t1 is derived from g10364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4291820	4292262	.	+	.	Phchi.S6G054100
Phchi.S6	AUGUSTUS	transcript	4291820	4292262	.	+	.	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	start_codon	4291820	4291822	.	+	0	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	CDS	4291820	4292124	0.36	+	0	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	exon	4291820	4292124	.	+	.	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	intron	4292125	4292204	.	+	.	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	CDS	4292205	4292262	1	+	1	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	exon	4292205	4292262	.	+	.	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
Phchi.S6	AUGUSTUS	stop_codon	4292263	4292265	.	+	0	transcript_id "Phchi.S6G054100.t1"; gene_id "Phchi.S6G054100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5.t1 is derived from g9793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C102	AUGUSTUS	gene	10225	12589	.	-	.	Phchi.C102G000100
Phchi.C102	AUGUSTUS	transcript	10225	12589	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	stop_codon	10222	10224	.	-	0	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	10225	10225	0.63	-	1	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	10225	10225	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	10226	10316	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	10317	10495	0.84	-	0	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	10317	10495	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	10496	10577	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	10578	10659	1	-	1	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	10578	10659	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	10660	10747	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	10748	10909	1	-	1	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	10748	10909	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	10910	11025	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	11026	11236	1	-	2	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	11026	11236	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	11237	11430	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	11431	11531	1	-	1	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	11431	11531	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	11532	11625	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	11626	11825	1	-	0	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	11626	11825	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	11826	11968	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	11969	12072	0.45	-	2	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	11969	12072	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	intron	12073	12252	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	CDS	12253	12589	0.65	-	0	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	exon	12253	12589	.	-	.	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
Phchi.C102	AUGUSTUS	start_codon	12587	12589	.	-	0	transcript_id "Phchi.C102G000100.t1"; gene_id "Phchi.C102G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14097.t1 is derived from g12564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10832762	10833288	.	+	.	Phchi.S3G141600
Phchi.S3	AUGUSTUS	transcript	10832762	10833288	.	+	.	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	start_codon	10832762	10832764	.	+	0	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	CDS	10832762	10832881	0.99	+	0	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	exon	10832762	10832881	.	+	.	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	intron	10832882	10832982	.	+	.	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	CDS	10832983	10833288	0.92	+	0	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	exon	10832983	10833288	.	+	.	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
Phchi.S3	AUGUSTUS	stop_codon	10833289	10833291	.	+	0	transcript_id "Phchi.S3G141600.t1"; gene_id "Phchi.S3G141600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4608.t1 is derived from g1778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11379359	11381056	.	-	.	Phchi.S1G176700
Phchi.S1	AUGUSTUS	transcript	11379359	11381056	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	stop_codon	11379356	11379358	.	-	0	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11379359	11379549	0.29	-	2	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11379359	11379549	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	intron	11379550	11379679	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11379680	11379712	0.27	-	2	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11379680	11379712	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	intron	11379713	11380027	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11380028	11380214	0.49	-	0	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11380028	11380214	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	intron	11380215	11380428	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11380429	11380433	0.44	-	2	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11380429	11380433	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	intron	11380434	11380641	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11380642	11380708	0.5	-	0	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11380642	11380708	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	intron	11380709	11380912	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11380913	11380956	0.92	-	2	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11380913	11380956	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	intron	11380957	11381043	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	CDS	11381044	11381056	1	-	0	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	exon	11381044	11381056	.	-	.	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
Phchi.S1	AUGUSTUS	start_codon	11381054	11381056	.	-	0	transcript_id "Phchi.S1G176700.t1"; gene_id "Phchi.S1G176700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15165.t1 is derived from g13633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17336466	17337179	.	+	.	Phchi.S3G248400
Phchi.S3	AUGUSTUS	transcript	17336466	17337179	.	+	.	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	start_codon	17336466	17336468	.	+	0	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	CDS	17336466	17336541	1	+	0	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	exon	17336466	17336541	.	+	.	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	intron	17336542	17336641	.	+	.	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	CDS	17336642	17336741	0.5	+	2	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	exon	17336642	17336741	.	+	.	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	intron	17336742	17336818	.	+	.	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	CDS	17336819	17337179	0.51	+	1	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	exon	17336819	17337179	.	+	.	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
Phchi.S3	AUGUSTUS	stop_codon	17337180	17337182	.	+	0	transcript_id "Phchi.S3G248400.t1"; gene_id "Phchi.S3G248400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10697.t1 is derived from g14747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1640025	1642991	.	-	.	Phchi.S4G027900
Phchi.S4	AUGUSTUS	transcript	1640025	1642991	.	-	.	transcript_id "Phchi.S4G027900.t1"; gene_id "Phchi.S4G027900"
Phchi.S4	AUGUSTUS	stop_codon	1640022	1640024	.	-	0	transcript_id "Phchi.S4G027900.t1"; gene_id "Phchi.S4G027900"
Phchi.S4	AUGUSTUS	CDS	1640025	1642991	0.45	-	0	transcript_id "Phchi.S4G027900.t1"; gene_id "Phchi.S4G027900"
Phchi.S4	AUGUSTUS	exon	1640025	1642991	.	-	.	transcript_id "Phchi.S4G027900.t1"; gene_id "Phchi.S4G027900"
Phchi.S4	AUGUSTUS	start_codon	1642989	1642991	.	-	0	transcript_id "Phchi.S4G027900.t1"; gene_id "Phchi.S4G027900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg838.t1 is derived from g10620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5828496	5830436	.	-	.	Phchi.S6G079700
Phchi.S6	AUGUSTUS	transcript	5828496	5830436	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	stop_codon	5828493	5828495	.	-	0	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5828496	5828568	0.6	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5828496	5828568	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5828569	5828650	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5828651	5828722	1	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5828651	5828722	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5828723	5828795	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5828796	5828867	1	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5828796	5828867	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5828868	5828947	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5828948	5829016	1	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5828948	5829016	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5829017	5829095	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5829096	5829167	1	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5829096	5829167	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5829168	5829241	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5829242	5829313	1	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5829242	5829313	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5829314	5829422	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5829423	5829599	1	-	1	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5829423	5829599	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5829600	5829704	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5829705	5829834	1	-	2	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5829705	5829834	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5829835	5829927	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5829928	5830029	1	-	2	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5829928	5830029	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5830030	5830150	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5830151	5830217	0.99	-	0	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5830151	5830217	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	intron	5830218	5830301	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	CDS	5830302	5830436	0.58	-	0	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	exon	5830302	5830436	.	-	.	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
Phchi.S6	AUGUSTUS	start_codon	5830434	5830436	.	-	0	transcript_id "Phchi.S6G079700.t1"; gene_id "Phchi.S6G079700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2572.t1 is derived from g9492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7430596	7432352	.	+	.	Phchi.S5G118100
Phchi.S5	AUGUSTUS	transcript	7430596	7432352	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	start_codon	7430596	7430598	.	+	0	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	CDS	7430596	7430748	1	+	0	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	exon	7430596	7430748	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	intron	7430749	7430935	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	CDS	7430936	7431155	1	+	0	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	exon	7430936	7431155	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	intron	7431156	7431260	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	CDS	7431261	7431502	1	+	2	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	exon	7431261	7431502	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	intron	7431503	7431890	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	CDS	7431891	7432352	0.82	+	0	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	exon	7431891	7432352	.	+	.	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
Phchi.S5	AUGUSTUS	stop_codon	7432353	7432355	.	+	0	transcript_id "Phchi.S5G118100.t1"; gene_id "Phchi.S5G118100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14830.t1 is derived from g13298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14917342	14917987	.	-	.	Phchi.S3G214900
Phchi.S3	AUGUSTUS	transcript	14917342	14917987	.	-	.	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	stop_codon	14917339	14917341	.	-	0	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	CDS	14917342	14917411	0.96	-	1	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	exon	14917342	14917411	.	-	.	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	intron	14917412	14917507	.	-	.	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	CDS	14917508	14917569	0.7	-	0	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	exon	14917508	14917569	.	-	.	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	intron	14917570	14917753	.	-	.	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	CDS	14917754	14917987	0.29	-	0	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	exon	14917754	14917987	.	-	.	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
Phchi.S3	AUGUSTUS	start_codon	14917985	14917987	.	-	0	transcript_id "Phchi.S3G214900.t1"; gene_id "Phchi.S3G214900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5233.t1 is derived from g2403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15778182	15778758	.	-	.	Phchi.S1G239200
Phchi.S1	AUGUSTUS	transcript	15778182	15778758	.	-	.	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	stop_codon	15778179	15778181	.	-	0	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	CDS	15778182	15778433	0.82	-	0	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	exon	15778182	15778433	.	-	.	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	intron	15778434	15778515	.	-	.	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	CDS	15778516	15778758	0.43	-	0	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	exon	15778516	15778758	.	-	.	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
Phchi.S1	AUGUSTUS	start_codon	15778756	15778758	.	-	0	transcript_id "Phchi.S1G239200.t1"; gene_id "Phchi.S1G239200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8669.t1 is derived from g5844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37359652	37360763	.	-	.	Phchi.S1G582800
Phchi.S1	AUGUSTUS	transcript	37359652	37360763	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	stop_codon	37359649	37359651	.	-	0	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	CDS	37359652	37359830	0.87	-	2	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	exon	37359652	37359830	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	intron	37359831	37359914	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	CDS	37359915	37360050	1	-	0	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	exon	37359915	37360050	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	intron	37360051	37360134	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	CDS	37360135	37360218	1	-	0	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	exon	37360135	37360218	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	intron	37360219	37360303	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	CDS	37360304	37360445	1	-	1	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	exon	37360304	37360445	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	intron	37360446	37360590	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	CDS	37360591	37360763	0.74	-	0	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	exon	37360591	37360763	.	-	.	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
Phchi.S1	AUGUSTUS	start_codon	37360761	37360763	.	-	0	transcript_id "Phchi.S1G582800.t1"; gene_id "Phchi.S1G582800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12142.t1 is derived from g7818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4838363	4839086	.	+	.	Phchi.S2G022200
Phchi.S2	AUGUSTUS	transcript	4838363	4839086	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	start_codon	4838363	4838365	.	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	CDS	4838363	4838464	1	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	exon	4838363	4838464	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	intron	4838465	4838554	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	CDS	4838555	4838620	1	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	exon	4838555	4838620	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	intron	4838621	4838711	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	CDS	4838712	4838777	1	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	exon	4838712	4838777	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	intron	4838778	4838904	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	CDS	4838905	4838979	1	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	exon	4838905	4838979	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	intron	4838980	4839071	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	CDS	4839072	4839086	1	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	exon	4839072	4839086	.	+	.	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
Phchi.S2	AUGUSTUS	stop_codon	4839087	4839089	.	+	0	transcript_id "Phchi.S2G022200.t1"; gene_id "Phchi.S2G022200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7413.t1 is derived from g4585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29031682	29032446	.	-	.	Phchi.S1G457200
Phchi.S1	AUGUSTUS	transcript	29031682	29032446	.	-	.	transcript_id "Phchi.S1G457200.t1"; gene_id "Phchi.S1G457200"
Phchi.S1	AUGUSTUS	stop_codon	29031679	29031681	.	-	0	transcript_id "Phchi.S1G457200.t1"; gene_id "Phchi.S1G457200"
Phchi.S1	AUGUSTUS	CDS	29031682	29032446	0.96	-	0	transcript_id "Phchi.S1G457200.t1"; gene_id "Phchi.S1G457200"
Phchi.S1	AUGUSTUS	exon	29031682	29032446	.	-	.	transcript_id "Phchi.S1G457200.t1"; gene_id "Phchi.S1G457200"
Phchi.S1	AUGUSTUS	start_codon	29032444	29032446	.	-	0	transcript_id "Phchi.S1G457200.t1"; gene_id "Phchi.S1G457200"
# This transcript jg8846.t2 is derived from g6021.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8847.t1 is derived from g6022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38263658	38265359	.	-	.	Phchi.S1G600600
Phchi.S1	AUGUSTUS	transcript	38263658	38265359	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	stop_codon	38263655	38263657	.	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38263658	38263680	0.97	-	2	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38263658	38263680	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38263681	38263802	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38263803	38263851	0.97	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38263803	38263851	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38263852	38263962	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38263963	38264013	0.91	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38263963	38264013	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38264014	38264097	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38264098	38264272	1	-	1	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38264098	38264272	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38264273	38264386	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38264387	38264468	1	-	2	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38264387	38264468	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38264469	38264588	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38264589	38264709	1	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38264589	38264709	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38264710	38264804	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38264805	38264930	1	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38264805	38264930	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	intron	38264931	38265071	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	CDS	38265072	38265359	0.96	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	exon	38265072	38265359	.	-	.	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
Phchi.S1	AUGUSTUS	start_codon	38265357	38265359	.	-	0	transcript_id "Phchi.S1G600600.t1"; gene_id "Phchi.S1G600600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5771.t1 is derived from g2941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18879544	18881985	.	-	.	Phchi.S1G293000
Phchi.S1	AUGUSTUS	transcript	18879544	18881985	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	stop_codon	18879541	18879543	.	-	0	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18879544	18879984	0.99	-	0	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18879544	18879984	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18879985	18880087	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18880088	18880370	0.99	-	1	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18880088	18880370	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18880371	18880469	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18880470	18880541	1	-	1	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18880470	18880541	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18880542	18880641	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18880642	18880678	1	-	2	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18880642	18880678	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18880679	18880789	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18880790	18880848	1	-	1	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18880790	18880848	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18880849	18880943	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18880944	18881231	1	-	1	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18880944	18881231	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18881232	18881325	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18881326	18881412	1	-	1	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18881326	18881412	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18881413	18881490	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18881491	18881516	1	-	0	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18881491	18881516	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18881517	18881598	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18881599	18881765	1	-	2	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18881599	18881765	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	intron	18881766	18881843	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	CDS	18881844	18881985	0.55	-	0	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	exon	18881844	18881985	.	-	.	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
Phchi.S1	AUGUSTUS	start_codon	18881983	18881985	.	-	0	transcript_id "Phchi.S1G293000.t1"; gene_id "Phchi.S1G293000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg379.t1 is derived from g10161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2724445	2726846	.	-	.	Phchi.S6G033800
Phchi.S6	AUGUSTUS	transcript	2724445	2726846	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	stop_codon	2724442	2724444	.	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2724445	2724523	1	-	1	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2724445	2724523	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2724524	2724607	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2724608	2724674	0.95	-	2	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2724608	2724674	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2724675	2724761	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2724762	2724840	0.95	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2724762	2724840	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2724841	2724940	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2724941	2725006	1	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2724941	2725006	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2725007	2725113	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2725114	2725181	1	-	2	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2725114	2725181	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2725182	2725280	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2725281	2725371	1	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2725281	2725371	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2725372	2725461	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2725462	2725527	1	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2725462	2725527	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2725528	2725696	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2725697	2725792	1	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2725697	2725792	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2725793	2725932	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2725933	2726031	1	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2725933	2726031	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2726032	2726135	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2726136	2726222	1	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2726136	2726222	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2726223	2726303	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2726304	2726359	1	-	2	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2726304	2726359	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2726360	2726443	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2726444	2726596	0.66	-	2	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2726444	2726596	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	intron	2726597	2726779	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	CDS	2726780	2726846	0.45	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	exon	2726780	2726846	.	-	.	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
Phchi.S6	AUGUSTUS	start_codon	2726844	2726846	.	-	0	transcript_id "Phchi.S6G033800.t1"; gene_id "Phchi.S6G033800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12402.t1 is derived from g8079.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18136030	18136863	.	+	.	Phchi.S2G048200
Phchi.S2	AUGUSTUS	transcript	18136030	18136863	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	start_codon	18136030	18136032	.	+	0	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136030	18136066	0.55	+	0	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136030	18136066	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	intron	18136067	18136254	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136255	18136429	0.57	+	2	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136255	18136429	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	intron	18136430	18136514	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136515	18136552	0.55	+	1	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136515	18136552	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	intron	18136553	18136666	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136667	18136863	0.54	+	2	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136667	18136863	.	+	.	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	stop_codon	18136864	18136866	.	+	0	transcript_id "Phchi.S2G048200.t1"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	transcript	18136297	18136863	.	+	.	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	start_codon	18136297	18136299	.	+	0	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136297	18136429	0.39	+	0	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136297	18136429	.	+	.	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	intron	18136430	18136522	.	+	.	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136523	18136552	0.34	+	2	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136523	18136552	.	+	.	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	intron	18136553	18136666	.	+	.	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	CDS	18136667	18136863	0.34	+	2	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	exon	18136667	18136863	.	+	.	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
Phchi.S2	AUGUSTUS	stop_codon	18136864	18136866	.	+	0	transcript_id "Phchi.S2G048200.t2"; gene_id "Phchi.S2G048200"
# This transcript jg15633.t2 is derived from g14102.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15634.t1 is derived from g14103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20391502	20393058	.	-	.	Phchi.S3G295300
Phchi.S3	AUGUSTUS	transcript	20391502	20393058	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	stop_codon	20391499	20391501	.	-	0	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	CDS	20391502	20391654	1	-	0	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	exon	20391502	20391654	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	intron	20391655	20391739	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	CDS	20391740	20392098	1	-	2	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	exon	20391740	20392098	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	intron	20392099	20392184	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	CDS	20392185	20392704	1	-	0	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	exon	20392185	20392704	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	intron	20392705	20392788	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	CDS	20392789	20392887	1	-	0	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	exon	20392789	20392887	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	intron	20392888	20392995	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	CDS	20392996	20393058	0.98	-	0	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	exon	20392996	20393058	.	-	.	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
Phchi.S3	AUGUSTUS	start_codon	20393056	20393058	.	-	0	transcript_id "Phchi.S3G295300.t1"; gene_id "Phchi.S3G295300"
# This transcript jg11274.t2 is derived from g15324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11275.t1 is derived from g15325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5163687	5165439	.	+	.	Phchi.S4G085700
Phchi.S4	AUGUSTUS	transcript	5163687	5165439	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	start_codon	5163687	5163689	.	+	0	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5163687	5164009	0.99	+	0	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5163687	5164009	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	intron	5164010	5164156	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5164157	5164233	1	+	1	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5164157	5164233	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	intron	5164234	5164647	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5164648	5164785	1	+	2	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5164648	5164785	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	intron	5164786	5164897	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5164898	5164952	0.99	+	2	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5164898	5164952	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	intron	5164953	5165037	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5165038	5165125	1	+	1	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5165038	5165125	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	intron	5165126	5165209	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5165210	5165308	1	+	0	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5165210	5165308	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	intron	5165309	5165394	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	CDS	5165395	5165439	1	+	0	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	exon	5165395	5165439	.	+	.	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
Phchi.S4	AUGUSTUS	stop_codon	5165440	5165442	.	+	0	transcript_id "Phchi.S4G085700.t1"; gene_id "Phchi.S4G085700"
# This transcript jg14936.t2 is derived from g13404.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14937.t1 is derived from g13405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15629845	15630912	.	+	.	Phchi.S3G225600
Phchi.S3	AUGUSTUS	transcript	15629845	15630912	.	+	.	transcript_id "Phchi.S3G225600.t1"; gene_id "Phchi.S3G225600"
Phchi.S3	AUGUSTUS	start_codon	15629845	15629847	.	+	0	transcript_id "Phchi.S3G225600.t1"; gene_id "Phchi.S3G225600"
Phchi.S3	AUGUSTUS	CDS	15629845	15630912	1	+	0	transcript_id "Phchi.S3G225600.t1"; gene_id "Phchi.S3G225600"
Phchi.S3	AUGUSTUS	exon	15629845	15630912	.	+	.	transcript_id "Phchi.S3G225600.t1"; gene_id "Phchi.S3G225600"
Phchi.S3	AUGUSTUS	stop_codon	15630913	15630915	.	+	0	transcript_id "Phchi.S3G225600.t1"; gene_id "Phchi.S3G225600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4453.t1 is derived from g1623.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10576269	10577249	.	+	.	Phchi.S1G161200
Phchi.S1	AUGUSTUS	transcript	10576269	10577089	.	+	.	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	start_codon	10576269	10576271	.	+	0	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	CDS	10576269	10576985	0.46	+	0	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	exon	10576269	10576985	.	+	.	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	intron	10576986	10577077	.	+	.	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	CDS	10577078	10577089	0.6	+	0	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	exon	10577078	10577089	.	+	.	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	stop_codon	10577090	10577092	.	+	0	transcript_id "Phchi.S1G161200.t1"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	transcript	10576269	10577249	.	+	.	transcript_id "Phchi.S1G161200.t2"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	start_codon	10576269	10576271	.	+	0	transcript_id "Phchi.S1G161200.t2"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	CDS	10576269	10577249	0.97	+	0	transcript_id "Phchi.S1G161200.t2"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	exon	10576269	10577249	.	+	.	transcript_id "Phchi.S1G161200.t2"; gene_id "Phchi.S1G161200"
Phchi.S1	AUGUSTUS	stop_codon	10577250	10577252	.	+	0	transcript_id "Phchi.S1G161200.t2"; gene_id "Phchi.S1G161200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14249.t1 is derived from g12716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11753979	11755310	.	+	.	Phchi.S3G156800
Phchi.S3	AUGUSTUS	transcript	11753979	11755310	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	start_codon	11753979	11753981	.	+	0	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	CDS	11753979	11754057	0.76	+	0	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	exon	11753979	11754057	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	intron	11754058	11754132	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	CDS	11754133	11754344	1	+	2	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	exon	11754133	11754344	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	intron	11754345	11754440	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	CDS	11754441	11754611	1	+	0	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	exon	11754441	11754611	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	intron	11754612	11754720	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	CDS	11754721	11754968	1	+	0	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	exon	11754721	11754968	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	intron	11754969	11755063	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	CDS	11755064	11755310	1	+	1	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	exon	11755064	11755310	.	+	.	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
Phchi.S3	AUGUSTUS	stop_codon	11755311	11755313	.	+	0	transcript_id "Phchi.S3G156800.t1"; gene_id "Phchi.S3G156800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2685.t1 is derived from g9605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8189554	8190780	.	+	.	Phchi.S5G129400
Phchi.S5	AUGUSTUS	transcript	8189554	8190780	.	+	.	transcript_id "Phchi.S5G129400.t1"; gene_id "Phchi.S5G129400"
Phchi.S5	AUGUSTUS	start_codon	8189554	8189556	.	+	0	transcript_id "Phchi.S5G129400.t1"; gene_id "Phchi.S5G129400"
Phchi.S5	AUGUSTUS	CDS	8189554	8190780	0.78	+	0	transcript_id "Phchi.S5G129400.t1"; gene_id "Phchi.S5G129400"
Phchi.S5	AUGUSTUS	exon	8189554	8190780	.	+	.	transcript_id "Phchi.S5G129400.t1"; gene_id "Phchi.S5G129400"
Phchi.S5	AUGUSTUS	stop_codon	8190781	8190783	.	+	0	transcript_id "Phchi.S5G129400.t1"; gene_id "Phchi.S5G129400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14745.t1 is derived from g13213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14508181	14510369	.	-	.	Phchi.S3G206400
Phchi.S3	AUGUSTUS	transcript	14508181	14510369	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	stop_codon	14508178	14508180	.	-	0	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	CDS	14508181	14508475	0.98	-	1	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	exon	14508181	14508475	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	intron	14508476	14508572	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	CDS	14508573	14508963	0.9	-	2	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	exon	14508573	14508963	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	intron	14508964	14509053	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	CDS	14509054	14509753	0.88	-	0	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	exon	14509054	14509753	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	intron	14509754	14509826	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	CDS	14509827	14510050	0.39	-	2	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	exon	14509827	14510050	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	intron	14510051	14510164	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	CDS	14510165	14510369	1	-	0	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	exon	14510165	14510369	.	-	.	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
Phchi.S3	AUGUSTUS	start_codon	14510367	14510369	.	-	0	transcript_id "Phchi.S3G206400.t1"; gene_id "Phchi.S3G206400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8202.t1 is derived from g5377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34421666	34422913	.	+	.	Phchi.S1G536100
Phchi.S1	AUGUSTUS	transcript	34421666	34422913	.	+	.	transcript_id "Phchi.S1G536100.t1"; gene_id "Phchi.S1G536100"
Phchi.S1	AUGUSTUS	start_codon	34421666	34421668	.	+	0	transcript_id "Phchi.S1G536100.t1"; gene_id "Phchi.S1G536100"
Phchi.S1	AUGUSTUS	CDS	34421666	34422913	0.83	+	0	transcript_id "Phchi.S1G536100.t1"; gene_id "Phchi.S1G536100"
Phchi.S1	AUGUSTUS	exon	34421666	34422913	.	+	.	transcript_id "Phchi.S1G536100.t1"; gene_id "Phchi.S1G536100"
Phchi.S1	AUGUSTUS	stop_codon	34422914	34422916	.	+	0	transcript_id "Phchi.S1G536100.t1"; gene_id "Phchi.S1G536100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3144.t1 is derived from g313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1973426	1976475	.	-	.	Phchi.S1G030300
Phchi.S1	AUGUSTUS	transcript	1973426	1976475	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	stop_codon	1973423	1973425	.	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1973426	1973743	0.99	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1973426	1973743	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1973744	1973838	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1973839	1974011	0.52	-	2	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1973839	1974011	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1974012	1974148	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1974149	1974275	0.34	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1974149	1974275	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1974276	1974367	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1974368	1974494	1	-	1	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1974368	1974494	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1974495	1974643	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1974644	1974801	1	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1974644	1974801	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1974802	1975020	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1975021	1975041	0.96	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1975021	1975041	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1975042	1975231	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1975232	1975307	0.87	-	1	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1975232	1975307	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1975308	1975418	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1975419	1975529	0.86	-	1	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1975419	1975529	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1975530	1975651	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1975652	1975709	0.9	-	2	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1975652	1975709	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1975710	1975879	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1975880	1975996	0.98	-	2	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1975880	1975996	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1975997	1976092	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1976093	1976210	1	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1976093	1976210	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	intron	1976211	1976304	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	CDS	1976305	1976475	0.99	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	exon	1976305	1976475	.	-	.	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
Phchi.S1	AUGUSTUS	start_codon	1976473	1976475	.	-	0	transcript_id "Phchi.S1G030300.t1"; gene_id "Phchi.S1G030300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7418.t1 is derived from g4590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29043555	29044112	.	-	.	Phchi.S1G457700
Phchi.S1	AUGUSTUS	transcript	29043555	29044112	.	-	.	transcript_id "Phchi.S1G457700.t1"; gene_id "Phchi.S1G457700"
Phchi.S1	AUGUSTUS	stop_codon	29043552	29043554	.	-	0	transcript_id "Phchi.S1G457700.t1"; gene_id "Phchi.S1G457700"
Phchi.S1	AUGUSTUS	CDS	29043555	29044112	0.88	-	0	transcript_id "Phchi.S1G457700.t1"; gene_id "Phchi.S1G457700"
Phchi.S1	AUGUSTUS	exon	29043555	29044112	.	-	.	transcript_id "Phchi.S1G457700.t1"; gene_id "Phchi.S1G457700"
Phchi.S1	AUGUSTUS	start_codon	29044110	29044112	.	-	0	transcript_id "Phchi.S1G457700.t1"; gene_id "Phchi.S1G457700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3405.t1 is derived from g574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3368008	3372442	.	+	.	Phchi.S1G056400
Phchi.S1	AUGUSTUS	transcript	3368008	3372442	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	start_codon	3368008	3368010	.	+	0	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	CDS	3368008	3368166	1	+	0	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	exon	3368008	3368166	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	intron	3368167	3368253	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	CDS	3368254	3368580	0.99	+	0	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	exon	3368254	3368580	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	intron	3368581	3368681	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	CDS	3368682	3371476	0.75	+	0	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	exon	3368682	3371476	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	intron	3371477	3371565	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	CDS	3371566	3371814	0.95	+	1	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	exon	3371566	3371814	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	intron	3371815	3371916	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	CDS	3371917	3372027	1	+	1	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	exon	3371917	3372027	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	intron	3372028	3372114	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	CDS	3372115	3372442	1	+	1	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	exon	3372115	3372442	.	+	.	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
Phchi.S1	AUGUSTUS	stop_codon	3372443	3372445	.	+	0	transcript_id "Phchi.S1G056400.t1"; gene_id "Phchi.S1G056400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14110.t1 is derived from g12577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10892991	10894965	.	+	.	Phchi.S3G142900
Phchi.S3	AUGUSTUS	transcript	10892991	10894965	.	+	.	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	start_codon	10892991	10892993	.	+	0	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	CDS	10892991	10894509	0.36	+	0	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	exon	10892991	10894509	.	+	.	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	intron	10894510	10894963	.	+	.	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	CDS	10894964	10894965	0.54	+	2	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	exon	10894964	10894965	.	+	.	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
Phchi.S3	AUGUSTUS	stop_codon	10894966	10894968	.	+	0	transcript_id "Phchi.S3G142900.t1"; gene_id "Phchi.S3G142900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg13427.t1 is derived from g11894.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6646423	6647609	.	-	.	Phchi.S3G074600
Phchi.S3	AUGUSTUS	transcript	6646423	6647609	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	stop_codon	6646420	6646422	.	-	0	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6646423	6646560	1	-	0	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6646423	6646560	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6646561	6646650	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6646651	6646772	0.99	-	2	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6646651	6646772	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6646773	6647050	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647051	6647125	0.6	-	2	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647051	6647125	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6647126	6647336	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647337	6647420	1	-	2	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647337	6647420	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6647421	6647485	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647486	6647609	0.81	-	0	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647486	6647609	.	-	.	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	start_codon	6647607	6647609	.	-	0	transcript_id "Phchi.S3G074600.t1"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	transcript	6646423	6647593	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	stop_codon	6646420	6646422	.	-	0	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6646423	6646560	1	-	0	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6646423	6646560	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6646561	6646650	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6646651	6646772	0.98	-	2	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6646651	6646772	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6646773	6647050	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647051	6647125	0.49	-	2	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647051	6647125	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6647126	6647336	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647337	6647409	0.97	-	0	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647337	6647409	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6647410	6647485	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647486	6647593	0.61	-	0	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647486	6647593	.	-	.	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	start_codon	6647591	6647593	.	-	0	transcript_id "Phchi.S3G074600.t2"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	transcript	6646423	6647593	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	stop_codon	6646420	6646422	.	-	0	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6646423	6646560	1	-	0	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6646423	6646560	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6646561	6646650	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6646651	6646772	0.95	-	2	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6646651	6646772	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6646773	6647050	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647051	6647098	0.46	-	2	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647051	6647098	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6647099	6647336	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647337	6647409	0.66	-	0	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647337	6647409	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	intron	6647410	6647485	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	CDS	6647486	6647593	0.35	-	0	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	exon	6647486	6647593	.	-	.	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
Phchi.S3	AUGUSTUS	start_codon	6647591	6647593	.	-	0	transcript_id "Phchi.S3G074600.t3"; gene_id "Phchi.S3G074600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9312.t1 is derived from g6487.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40900676	40903601	.	-	.	Phchi.S1G647100
Phchi.S1	AUGUSTUS	transcript	40900676	40903601	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	stop_codon	40900673	40900675	.	-	0	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40900676	40900934	0.92	-	1	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40900676	40900934	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40900935	40901025	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901026	40901226	1	-	1	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901026	40901226	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40901227	40901320	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901321	40901550	1	-	0	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901321	40901550	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40901551	40901677	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901678	40901798	1	-	1	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901678	40901798	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40901799	40901888	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901889	40902038	1	-	1	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901889	40902038	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902039	40902122	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40902123	40902328	1	-	0	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40902123	40902328	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902329	40902564	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40902565	40902679	1	-	1	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40902565	40902679	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902680	40902815	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40902816	40902910	1	-	0	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40902816	40902910	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902911	40903057	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40903058	40903275	1	-	2	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40903058	40903275	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40903276	40903420	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40903421	40903601	0.78	-	0	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40903421	40903601	.	-	.	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	start_codon	40903599	40903601	.	-	0	transcript_id "Phchi.S1G647100.t1"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	transcript	40900676	40903601	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	stop_codon	40900673	40900675	.	-	0	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40900676	40900934	0.92	-	1	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40900676	40900934	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40900935	40901025	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901026	40901226	1	-	1	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901026	40901226	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40901227	40901320	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901321	40901550	1	-	0	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901321	40901550	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40901551	40901677	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901678	40901798	1	-	1	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901678	40901798	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40901799	40901888	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40901889	40902038	1	-	1	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40901889	40902038	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902039	40902122	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40902123	40902328	1	-	0	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40902123	40902328	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902329	40902564	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40902565	40902679	1	-	1	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40902565	40902679	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902680	40902815	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40902816	40902910	1	-	0	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40902816	40902910	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40902911	40903057	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40903058	40903275	1	-	2	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40903058	40903275	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	intron	40903276	40903414	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	CDS	40903415	40903601	0.68	-	0	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	exon	40903415	40903601	.	-	.	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
Phchi.S1	AUGUSTUS	start_codon	40903599	40903601	.	-	0	transcript_id "Phchi.S1G647100.t2"; gene_id "Phchi.S1G647100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6146.t1 is derived from g3317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21149595	21150836	.	-	.	Phchi.S1G330500
Phchi.S1	AUGUSTUS	transcript	21149595	21150836	.	-	.	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	stop_codon	21149592	21149594	.	-	0	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	CDS	21149595	21150280	1	-	2	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	exon	21149595	21150280	.	-	.	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	intron	21150281	21150442	.	-	.	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	CDS	21150443	21150836	0.1	-	0	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	exon	21150443	21150836	.	-	.	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
Phchi.S1	AUGUSTUS	start_codon	21150834	21150836	.	-	0	transcript_id "Phchi.S1G330500.t1"; gene_id "Phchi.S1G330500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14019.t1 is derived from g12486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10332212	10333612	.	-	.	Phchi.S3G133800
Phchi.S3	AUGUSTUS	transcript	10332212	10333612	.	-	.	transcript_id "Phchi.S3G133800.t1"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	stop_codon	10332209	10332211	.	-	0	transcript_id "Phchi.S3G133800.t1"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	CDS	10332212	10333612	0.84	-	0	transcript_id "Phchi.S3G133800.t1"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	exon	10332212	10333612	.	-	.	transcript_id "Phchi.S3G133800.t1"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	start_codon	10333610	10333612	.	-	0	transcript_id "Phchi.S3G133800.t1"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	transcript	10332212	10333222	.	-	.	transcript_id "Phchi.S3G133800.t2"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	stop_codon	10332209	10332211	.	-	0	transcript_id "Phchi.S3G133800.t2"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	CDS	10332212	10333222	0.58	-	0	transcript_id "Phchi.S3G133800.t2"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	exon	10332212	10333222	.	-	.	transcript_id "Phchi.S3G133800.t2"; gene_id "Phchi.S3G133800"
Phchi.S3	AUGUSTUS	start_codon	10333220	10333222	.	-	0	transcript_id "Phchi.S3G133800.t2"; gene_id "Phchi.S3G133800"
# This transcript jg14272.t2 is derived from g12739.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14273.t1 is derived from g12740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11879501	11880076	.	+	.	Phchi.S3G159200
Phchi.S3	AUGUSTUS	transcript	11879501	11880076	.	+	.	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	start_codon	11879501	11879503	.	+	0	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	CDS	11879501	11879898	0.25	+	0	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	exon	11879501	11879898	.	+	.	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	intron	11879899	11879979	.	+	.	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	CDS	11879980	11880076	1	+	1	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	exon	11879980	11880076	.	+	.	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
Phchi.S3	AUGUSTUS	stop_codon	11880077	11880079	.	+	0	transcript_id "Phchi.S3G159200.t1"; gene_id "Phchi.S3G159200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8431.t1 is derived from g5606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35908707	35913809	.	+	.	Phchi.S1G559000
Phchi.S1	AUGUSTUS	transcript	35908707	35913809	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	start_codon	35908707	35908709	.	+	0	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35908707	35909268	0.69	+	0	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35908707	35909268	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35909269	35909387	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35909388	35911544	0.65	+	2	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35909388	35911544	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35911545	35911656	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35911657	35911941	0.98	+	2	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35911657	35911941	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35911942	35912027	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35912028	35912410	0.43	+	2	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35912028	35912410	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35912411	35912513	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35912514	35913809	0.95	+	0	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35912514	35913809	.	+	.	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	stop_codon	35913810	35913812	.	+	0	transcript_id "Phchi.S1G559000.t1"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	transcript	35910155	35913809	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	start_codon	35910155	35910157	.	+	0	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35910155	35911544	0.4	+	0	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35910155	35911544	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35911545	35911656	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35911657	35911941	0.99	+	2	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35911657	35911941	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35911942	35912027	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35912028	35912410	0.51	+	2	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35912028	35912410	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	intron	35912411	35912513	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35912514	35913809	0.95	+	0	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35912514	35913809	.	+	.	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	stop_codon	35913810	35913812	.	+	0	transcript_id "Phchi.S1G559000.t2"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	transcript	35912820	35913809	.	+	.	transcript_id "Phchi.S1G559000.t3"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	start_codon	35912820	35912822	.	+	0	transcript_id "Phchi.S1G559000.t3"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	CDS	35912820	35913809	0.37	+	0	transcript_id "Phchi.S1G559000.t3"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	exon	35912820	35913809	.	+	.	transcript_id "Phchi.S1G559000.t3"; gene_id "Phchi.S1G559000"
Phchi.S1	AUGUSTUS	stop_codon	35913810	35913812	.	+	0	transcript_id "Phchi.S1G559000.t3"; gene_id "Phchi.S1G559000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5577.t1 is derived from g2747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17684554	17686518	.	-	.	Phchi.S1G273600
Phchi.S1	AUGUSTUS	transcript	17684554	17686518	.	-	.	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	stop_codon	17684551	17684553	.	-	0	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	CDS	17684554	17685872	0.9	-	2	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	exon	17684554	17685872	.	-	.	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	intron	17685873	17686220	.	-	.	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	CDS	17686221	17686518	0.66	-	0	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	exon	17686221	17686518	.	-	.	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
Phchi.S1	AUGUSTUS	start_codon	17686516	17686518	.	-	0	transcript_id "Phchi.S1G273600.t1"; gene_id "Phchi.S1G273600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15048.t1 is derived from g13516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16741339	16742953	.	+	.	Phchi.S3G236700
Phchi.S3	AUGUSTUS	transcript	16741339	16742953	.	+	.	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	start_codon	16741339	16741341	.	+	0	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	CDS	16741339	16741574	1	+	0	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	exon	16741339	16741574	.	+	.	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	intron	16741575	16741735	.	+	.	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	CDS	16741736	16741833	1	+	1	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	exon	16741736	16741833	.	+	.	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	intron	16741834	16742939	.	+	.	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	CDS	16742940	16742953	0.85	+	2	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	exon	16742940	16742953	.	+	.	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
Phchi.S3	AUGUSTUS	stop_codon	16742954	16742956	.	+	0	transcript_id "Phchi.S3G236700.t1"; gene_id "Phchi.S3G236700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5626.t1 is derived from g2796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17948728	17951148	.	+	.	Phchi.S1G278500
Phchi.S1	AUGUSTUS	transcript	17948728	17951148	.	+	.	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	start_codon	17948728	17948730	.	+	0	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	CDS	17948728	17949052	0.85	+	0	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	exon	17948728	17949052	.	+	.	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	intron	17949053	17949221	.	+	.	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	CDS	17949222	17949960	1	+	2	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	exon	17949222	17949960	.	+	.	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	intron	17949961	17950631	.	+	.	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	CDS	17950632	17951148	0.89	+	1	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	exon	17950632	17951148	.	+	.	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
Phchi.S1	AUGUSTUS	stop_codon	17951149	17951151	.	+	0	transcript_id "Phchi.S1G278500.t1"; gene_id "Phchi.S1G278500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11095.t1 is derived from g15145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4095324	4099119	.	+	.	Phchi.S4G067700
Phchi.S4	AUGUSTUS	transcript	4095324	4099119	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	start_codon	4095324	4095326	.	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4095324	4095674	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4095324	4095674	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4095675	4095807	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4095808	4095984	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4095808	4095984	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4095985	4096097	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4096098	4096222	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4096098	4096222	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4096223	4096303	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4096304	4096442	0.7	+	1	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4096304	4096442	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4096443	4096550	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4096551	4096700	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4096551	4096700	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4096701	4096779	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4096780	4096833	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4096780	4096833	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4096834	4096952	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4096953	4097048	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4096953	4097048	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4097049	4097130	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4097131	4097190	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4097131	4097190	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4097191	4097279	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4097280	4097354	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4097280	4097354	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4097355	4097474	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4097475	4097528	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4097475	4097528	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4097529	4097612	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4097613	4097714	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4097613	4097714	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4097715	4097806	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4097807	4098460	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4097807	4098460	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4098461	4098553	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4098554	4098685	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4098554	4098685	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4098686	4098787	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4098788	4098895	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4098788	4098895	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	intron	4098896	4098972	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	CDS	4098973	4099119	1	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	exon	4098973	4099119	.	+	.	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
Phchi.S4	AUGUSTUS	stop_codon	4099120	4099122	.	+	0	transcript_id "Phchi.S4G067700.t1"; gene_id "Phchi.S4G067700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1246.t1 is derived from g11029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8623438	8625994	.	-	.	Phchi.S6G120500
Phchi.S6	AUGUSTUS	transcript	8623438	8624673	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	stop_codon	8623435	8623437	.	-	0	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8623438	8623464	0.39	-	0	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8623438	8623464	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	intron	8623465	8623624	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8623625	8624104	0.21	-	0	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8623625	8624104	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	intron	8624105	8624278	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8624279	8624543	0.57	-	1	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8624279	8624543	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	intron	8624544	8624662	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8624663	8624673	0.79	-	0	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8624663	8624673	.	-	.	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	start_codon	8624671	8624673	.	-	0	transcript_id "Phchi.S6G120500.t1"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	transcript	8623438	8625994	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	stop_codon	8623435	8623437	.	-	0	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8623438	8623464	0.37	-	0	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8623438	8623464	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	intron	8623465	8623624	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8623625	8624104	0.27	-	0	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8623625	8624104	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	intron	8624105	8624278	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8624279	8624697	0.57	-	2	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8624279	8624697	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	intron	8624698	8625003	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	CDS	8625004	8625994	0.65	-	0	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	exon	8625004	8625994	.	-	.	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
Phchi.S6	AUGUSTUS	start_codon	8625992	8625994	.	-	0	transcript_id "Phchi.S6G120500.t2"; gene_id "Phchi.S6G120500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10067.t1 is derived from g7243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45614443	45617901	.	+	.	Phchi.S1G722600
Phchi.S1	AUGUSTUS	transcript	45614443	45617901	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	start_codon	45614443	45614445	.	+	0	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	CDS	45614443	45614681	0.99	+	0	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	exon	45614443	45614681	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	intron	45614682	45614770	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	CDS	45614771	45615212	0.97	+	1	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	exon	45614771	45615212	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	intron	45615213	45615354	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	CDS	45615355	45616770	0.82	+	0	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	exon	45615355	45616770	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	intron	45616771	45616890	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	CDS	45616891	45617102	0.97	+	0	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	exon	45616891	45617102	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	intron	45617103	45617198	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	CDS	45617199	45617247	1	+	1	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	exon	45617199	45617247	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	intron	45617248	45617343	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	CDS	45617344	45617901	1	+	0	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	exon	45617344	45617901	.	+	.	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
Phchi.S1	AUGUSTUS	stop_codon	45617902	45617904	.	+	0	transcript_id "Phchi.S1G722600.t1"; gene_id "Phchi.S1G722600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3377.t1 is derived from g546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3241459	3247552	.	+	.	Phchi.S1G053600
Phchi.S1	AUGUSTUS	transcript	3241459	3247552	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	start_codon	3241459	3241461	.	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3241459	3241584	0.67	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3241459	3241584	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3241585	3241953	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3241954	3242049	1	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3241954	3242049	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3242050	3242175	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3242176	3242381	0.87	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3242176	3242381	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3242382	3242499	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3242500	3242757	0.87	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3242500	3242757	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3242758	3242835	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3242836	3242974	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3242836	3242974	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3242975	3243082	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3243083	3243314	0.64	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3243083	3243314	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3243315	3243429	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3243430	3243616	0.69	+	2	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3243430	3243616	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3243617	3243815	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3243816	3244016	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3243816	3244016	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3244017	3244090	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3244091	3244184	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3244091	3244184	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3244185	3244304	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3244305	3244494	1	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3244305	3244494	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3244495	3244720	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3244721	3244853	1	+	2	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3244721	3244853	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3244854	3244934	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3244935	3245006	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3244935	3245006	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3245007	3245115	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3245116	3245259	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3245116	3245259	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3245260	3245486	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3245487	3245558	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3245487	3245558	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3245559	3245656	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3245657	3245716	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3245657	3245716	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3245717	3245811	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3245812	3245897	1	+	1	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3245812	3245897	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3245898	3246027	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3246028	3246174	1	+	2	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3246028	3246174	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3246175	3246274	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3246275	3246613	1	+	2	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3246275	3246613	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3246614	3246735	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3246736	3247130	1	+	2	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3246736	3247130	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	intron	3247131	3247216	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	CDS	3247217	3247552	0.74	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	exon	3247217	3247552	.	+	.	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
Phchi.S1	AUGUSTUS	stop_codon	3247553	3247555	.	+	0	transcript_id "Phchi.S1G053600.t1"; gene_id "Phchi.S1G053600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7526.t1 is derived from g4700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29886089	29886298	.	+	.	Phchi.S1G468500
Phchi.S1	AUGUSTUS	transcript	29886089	29886298	.	+	.	transcript_id "Phchi.S1G468500.t1"; gene_id "Phchi.S1G468500"
Phchi.S1	AUGUSTUS	start_codon	29886089	29886091	.	+	0	transcript_id "Phchi.S1G468500.t1"; gene_id "Phchi.S1G468500"
Phchi.S1	AUGUSTUS	CDS	29886089	29886298	0.7	+	0	transcript_id "Phchi.S1G468500.t1"; gene_id "Phchi.S1G468500"
Phchi.S1	AUGUSTUS	exon	29886089	29886298	.	+	.	transcript_id "Phchi.S1G468500.t1"; gene_id "Phchi.S1G468500"
Phchi.S1	AUGUSTUS	stop_codon	29886299	29886301	.	+	0	transcript_id "Phchi.S1G468500.t1"; gene_id "Phchi.S1G468500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6195.t1 is derived from g3366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21436355	21437940	.	+	.	Phchi.S1G335400
Phchi.S1	AUGUSTUS	transcript	21436355	21437940	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	start_codon	21436355	21436357	.	+	0	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	CDS	21436355	21436897	0.69	+	0	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	exon	21436355	21436897	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	intron	21436898	21437191	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	CDS	21437192	21437720	0.24	+	0	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	exon	21437192	21437720	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	intron	21437721	21437831	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	CDS	21437832	21437837	0.29	+	2	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	exon	21437832	21437837	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	intron	21437838	21437935	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	CDS	21437936	21437940	0.88	+	2	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	exon	21437936	21437940	.	+	.	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
Phchi.S1	AUGUSTUS	stop_codon	21437941	21437943	.	+	0	transcript_id "Phchi.S1G335400.t1"; gene_id "Phchi.S1G335400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8972.t1 is derived from g6147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38897524	38897991	.	-	.	Phchi.S1G613100
Phchi.S1	AUGUSTUS	transcript	38897524	38897991	.	-	.	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	stop_codon	38897521	38897523	.	-	0	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	CDS	38897524	38897756	0.63	-	2	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	exon	38897524	38897756	.	-	.	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	intron	38897757	38897855	.	-	.	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	CDS	38897856	38897991	0.38	-	0	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	exon	38897856	38897991	.	-	.	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
Phchi.S1	AUGUSTUS	start_codon	38897989	38897991	.	-	0	transcript_id "Phchi.S1G613100.t1"; gene_id "Phchi.S1G613100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4243.t1 is derived from g1412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9133879	9134367	.	-	.	Phchi.S1G140200
Phchi.S1	AUGUSTUS	transcript	9133879	9134367	.	-	.	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	stop_codon	9133876	9133878	.	-	0	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	CDS	9133879	9134024	0.69	-	2	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	exon	9133879	9134024	.	-	.	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	intron	9134025	9134171	.	-	.	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	CDS	9134172	9134367	0.98	-	0	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	exon	9134172	9134367	.	-	.	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
Phchi.S1	AUGUSTUS	start_codon	9134365	9134367	.	-	0	transcript_id "Phchi.S1G140200.t1"; gene_id "Phchi.S1G140200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2568.t1 is derived from g9488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7422789	7424377	.	+	.	Phchi.S5G117700
Phchi.S5	AUGUSTUS	transcript	7422789	7424377	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	start_codon	7422789	7422791	.	+	0	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	CDS	7422789	7423685	0.92	+	0	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	exon	7422789	7423685	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	intron	7423686	7423786	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	CDS	7423787	7424000	0.7	+	0	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	exon	7423787	7424000	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	intron	7424001	7424106	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	CDS	7424107	7424166	0.96	+	2	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	exon	7424107	7424166	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	intron	7424167	7424306	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	CDS	7424307	7424377	1	+	2	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	exon	7424307	7424377	.	+	.	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
Phchi.S5	AUGUSTUS	stop_codon	7424378	7424380	.	+	0	transcript_id "Phchi.S5G117700.t1"; gene_id "Phchi.S5G117700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10682.t1 is derived from g14732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1567715	1568379	.	+	.	Phchi.S4G026400
Phchi.S4	AUGUSTUS	transcript	1567715	1568379	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	start_codon	1567715	1567717	.	+	0	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	CDS	1567715	1567762	1	+	0	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	exon	1567715	1567762	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	intron	1567763	1567944	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	CDS	1567945	1568003	1	+	0	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	exon	1567945	1568003	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	intron	1568004	1568082	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	CDS	1568083	1568214	1	+	1	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	exon	1568083	1568214	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	intron	1568215	1568309	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	CDS	1568310	1568379	0.46	+	1	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	exon	1568310	1568379	.	+	.	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
Phchi.S4	AUGUSTUS	stop_codon	1568380	1568382	.	+	0	transcript_id "Phchi.S4G026400.t1"; gene_id "Phchi.S4G026400"
# This transcript jg6663.t2 is derived from g3835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6664.t1 is derived from g3836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24374209	24374758	.	+	.	Phchi.S1G382300
Phchi.S1	AUGUSTUS	transcript	24374209	24374758	.	+	.	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	start_codon	24374209	24374211	.	+	0	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	CDS	24374209	24374340	0.83	+	0	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	exon	24374209	24374340	.	+	.	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	intron	24374341	24374421	.	+	.	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	CDS	24374422	24374638	0.9	+	0	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	exon	24374422	24374638	.	+	.	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	intron	24374639	24374720	.	+	.	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	CDS	24374721	24374758	0.9	+	2	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	exon	24374721	24374758	.	+	.	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
Phchi.S1	AUGUSTUS	stop_codon	24374759	24374761	.	+	0	transcript_id "Phchi.S1G382300.t1"; gene_id "Phchi.S1G382300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg47.t1 is derived from g9829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	67022	68300	.	+	.	Phchi.S6G000600
Phchi.S6	AUGUSTUS	transcript	67022	68300	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	start_codon	67022	67024	.	+	0	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	CDS	67022	67165	0.38	+	0	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	exon	67022	67165	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	intron	67166	67458	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	CDS	67459	67529	0.39	+	0	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	exon	67459	67529	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	intron	67530	67663	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	CDS	67664	67830	0.51	+	1	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	exon	67664	67830	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	intron	67831	68034	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	CDS	68035	68300	0.5	+	2	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	exon	68035	68300	.	+	.	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
Phchi.S6	AUGUSTUS	stop_codon	68301	68303	.	+	0	transcript_id "Phchi.S6G000600.t1"; gene_id "Phchi.S6G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14654.t1 is derived from g13122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13956190	13963318	.	-	.	Phchi.S3G197300
Phchi.S3	AUGUSTUS	transcript	13956190	13963318	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	stop_codon	13956187	13956189	.	-	0	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13956190	13956229	0.85	-	1	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13956190	13956229	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13956230	13956455	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13956456	13956719	0.82	-	1	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13956456	13956719	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13956720	13956840	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13956841	13957226	0.91	-	0	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13956841	13957226	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13957227	13957332	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13957333	13957394	0.58	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13957333	13957394	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13957395	13957499	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13957500	13957862	0.53	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13957500	13957862	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13957863	13958064	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13958065	13958235	0.86	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13958065	13958235	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13958236	13958324	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13958325	13958474	0.63	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13958325	13958474	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13958475	13958753	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13958754	13958879	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13958754	13958879	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13958880	13958975	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13958976	13959053	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13958976	13959053	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13959054	13959133	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13959134	13959280	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13959134	13959280	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13959281	13959515	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13959516	13959644	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13959516	13959644	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13959645	13959832	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13959833	13960372	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13959833	13960372	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13960373	13960459	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13960460	13960519	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13960460	13960519	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13960520	13960612	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13960613	13960753	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13960613	13960753	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13960754	13960859	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13960860	13962059	0.92	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13960860	13962059	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13962060	13962255	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13962256	13962411	1	-	2	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13962256	13962411	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13962412	13962509	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13962510	13962747	0.74	-	0	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13962510	13962747	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13962748	13962829	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13962830	13962958	0.66	-	0	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13962830	13962958	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	intron	13962959	13963102	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	CDS	13963103	13963318	0.88	-	0	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	exon	13963103	13963318	.	-	.	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
Phchi.S3	AUGUSTUS	start_codon	13963316	13963318	.	-	0	transcript_id "Phchi.S3G197300.t1"; gene_id "Phchi.S3G197300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6373.t1 is derived from g3545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22634347	22636664	.	-	.	Phchi.S1G353200
Phchi.S1	AUGUSTUS	transcript	22634347	22636664	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	stop_codon	22634344	22634346	.	-	0	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	CDS	22634347	22634793	0.99	-	0	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	exon	22634347	22634793	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	intron	22634794	22634876	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	CDS	22634877	22635057	0.99	-	1	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	exon	22634877	22635057	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	intron	22635058	22635131	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	CDS	22635132	22635253	0.99	-	0	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	exon	22635132	22635253	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	intron	22635254	22635484	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	CDS	22635485	22635554	1	-	1	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	exon	22635485	22635554	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	intron	22635555	22635678	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	CDS	22635679	22635737	1	-	0	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	exon	22635679	22635737	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	intron	22635738	22635821	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	CDS	22635822	22636664	0.61	-	0	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	exon	22635822	22636664	.	-	.	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
Phchi.S1	AUGUSTUS	start_codon	22636662	22636664	.	-	0	transcript_id "Phchi.S1G353200.t1"; gene_id "Phchi.S1G353200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11516.t1 is derived from g15566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6869168	6872454	.	+	.	Phchi.S4G109800
Phchi.S4	AUGUSTUS	transcript	6869168	6872454	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	start_codon	6869168	6869170	.	+	0	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6869168	6869274	0.31	+	0	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6869168	6869274	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6869275	6869448	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6869449	6869617	0.38	+	1	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6869449	6869617	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6869618	6869693	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6869694	6870039	0.98	+	0	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6869694	6870039	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6870040	6870136	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6870137	6870664	0.99	+	2	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6870137	6870664	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6870665	6870752	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6870753	6871043	0.64	+	2	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6870753	6871043	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6871044	6871158	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6871159	6871519	0.91	+	2	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6871159	6871519	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6871520	6871599	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6871600	6871757	0.96	+	1	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6871600	6871757	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	intron	6871758	6871834	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	CDS	6871835	6872454	1	+	2	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	exon	6871835	6872454	.	+	.	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
Phchi.S4	AUGUSTUS	stop_codon	6872455	6872457	.	+	0	transcript_id "Phchi.S4G109800.t1"; gene_id "Phchi.S4G109800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg725.t1 is derived from g10507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5151767	5152133	.	-	.	Phchi.S6G068400
Phchi.S6	AUGUSTUS	transcript	5151767	5152133	.	-	.	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	stop_codon	5151764	5151766	.	-	0	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	CDS	5151767	5151874	0.71	-	0	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	exon	5151767	5151874	.	-	.	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	intron	5151875	5152040	.	-	.	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	CDS	5152041	5152133	0.74	-	0	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	exon	5152041	5152133	.	-	.	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
Phchi.S6	AUGUSTUS	start_codon	5152131	5152133	.	-	0	transcript_id "Phchi.S6G068400.t1"; gene_id "Phchi.S6G068400"
# This transcript jg12666.t2 is derived from g14464.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12666.t3 is derived from g14464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12667.t1 is derived from g14465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C42	AUGUSTUS	gene	18633	20924	.	+	.	Phchi.C42G000200
Phchi.C42	AUGUSTUS	transcript	18633	20924	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	start_codon	18633	18635	.	+	0	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	18633	18743	0.93	+	0	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	18633	18743	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	intron	18744	18823	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	18824	19097	1	+	0	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	18824	19097	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	intron	19098	19186	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	19187	19367	1	+	2	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	19187	19367	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	intron	19368	19472	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	19473	19769	0.16	+	1	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	19473	19769	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	intron	19770	19837	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	19838	20201	0.21	+	1	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	19838	20201	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	intron	20202	20321	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	20322	20487	1	+	0	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	20322	20487	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	intron	20488	20625	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	CDS	20626	20924	1	+	2	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	exon	20626	20924	.	+	.	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
Phchi.C42	AUGUSTUS	stop_codon	20925	20927	.	+	0	transcript_id "Phchi.C42G000200.t1"; gene_id "Phchi.C42G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8518.t1 is derived from g5693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36408823	36412158	.	-	.	Phchi.S1G567700
Phchi.S1	AUGUSTUS	transcript	36408823	36412158	.	-	.	transcript_id "Phchi.S1G567700.t1"; gene_id "Phchi.S1G567700"
Phchi.S1	AUGUSTUS	stop_codon	36408820	36408822	.	-	0	transcript_id "Phchi.S1G567700.t1"; gene_id "Phchi.S1G567700"
Phchi.S1	AUGUSTUS	CDS	36408823	36412158	0.97	-	0	transcript_id "Phchi.S1G567700.t1"; gene_id "Phchi.S1G567700"
Phchi.S1	AUGUSTUS	exon	36408823	36412158	.	-	.	transcript_id "Phchi.S1G567700.t1"; gene_id "Phchi.S1G567700"
Phchi.S1	AUGUSTUS	start_codon	36412156	36412158	.	-	0	transcript_id "Phchi.S1G567700.t1"; gene_id "Phchi.S1G567700"
# This transcript jg12301.t2 is derived from g7977.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12302.t1 is derived from g7978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9791373	9792328	.	+	.	Phchi.S2G038200
Phchi.S2	AUGUSTUS	transcript	9791373	9792328	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	start_codon	9791373	9791375	.	+	0	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	CDS	9791373	9791386	0.63	+	0	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	exon	9791373	9791386	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	intron	9791387	9791593	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	CDS	9791594	9791758	0.51	+	1	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	exon	9791594	9791758	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	intron	9791759	9791870	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	CDS	9791871	9791907	0.48	+	1	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	exon	9791871	9791907	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	intron	9791908	9792160	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	CDS	9792161	9792328	0.5	+	0	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	exon	9792161	9792328	.	+	.	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
Phchi.S2	AUGUSTUS	stop_codon	9792329	9792331	.	+	0	transcript_id "Phchi.S2G038200.t1"; gene_id "Phchi.S2G038200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5044.t1 is derived from g2214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14230542	14232878	.	+	.	Phchi.S1G220300
Phchi.S1	AUGUSTUS	transcript	14230734	14232878	.	+	.	transcript_id "Phchi.S1G220300.t1"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	start_codon	14230734	14230736	.	+	0	transcript_id "Phchi.S1G220300.t1"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	CDS	14230734	14232878	0.95	+	0	transcript_id "Phchi.S1G220300.t1"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	exon	14230734	14232878	.	+	.	transcript_id "Phchi.S1G220300.t1"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	stop_codon	14232879	14232881	.	+	0	transcript_id "Phchi.S1G220300.t1"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	transcript	14230542	14232878	.	+	.	transcript_id "Phchi.S1G220300.t2"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	start_codon	14230542	14230544	.	+	0	transcript_id "Phchi.S1G220300.t2"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	CDS	14230542	14232878	0.89	+	0	transcript_id "Phchi.S1G220300.t2"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	exon	14230542	14232878	.	+	.	transcript_id "Phchi.S1G220300.t2"; gene_id "Phchi.S1G220300"
Phchi.S1	AUGUSTUS	stop_codon	14232879	14232881	.	+	0	transcript_id "Phchi.S1G220300.t2"; gene_id "Phchi.S1G220300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8858.t1 is derived from g6033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38311626	38313471	.	-	.	Phchi.S1G601700
Phchi.S1	AUGUSTUS	transcript	38311626	38313471	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	stop_codon	38311623	38311625	.	-	0	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38311626	38311749	1	-	1	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38311626	38311749	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	intron	38311750	38311839	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38311840	38311970	1	-	0	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38311840	38311970	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	intron	38311971	38312064	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38312065	38312119	1	-	1	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38312065	38312119	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	intron	38312120	38312209	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38312210	38312309	1	-	2	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38312210	38312309	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	intron	38312310	38312407	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38312408	38312480	1	-	0	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38312408	38312480	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	intron	38312481	38312684	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38312685	38312771	0.94	-	0	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38312685	38312771	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	intron	38312772	38313051	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	CDS	38313052	38313471	0.54	-	0	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	exon	38313052	38313471	.	-	.	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
Phchi.S1	AUGUSTUS	start_codon	38313469	38313471	.	-	0	transcript_id "Phchi.S1G601700.t1"; gene_id "Phchi.S1G601700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5664.t1 is derived from g2834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18181831	18188086	.	+	.	Phchi.S1G282300
Phchi.S1	AUGUSTUS	transcript	18181831	18188086	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	start_codon	18181831	18181833	.	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18181831	18181988	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18181831	18181988	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18181989	18182134	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18182135	18182879	1	+	1	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18182135	18182879	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18182880	18183035	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18183036	18183122	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18183036	18183122	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18183123	18183233	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18183234	18183317	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18183234	18183317	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18183318	18183403	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18183404	18183490	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18183404	18183490	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18183491	18183608	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18183609	18183707	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18183609	18183707	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18183708	18183937	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18183938	18183991	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18183938	18183991	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18183992	18184139	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18184140	18184231	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18184140	18184231	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18184232	18184310	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18184311	18184425	1	+	1	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18184311	18184425	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18184426	18184520	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18184521	18184671	0.96	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18184521	18184671	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18184672	18184773	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18184774	18184896	0.4	+	2	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18184774	18184896	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18184897	18185081	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18185082	18185146	0.23	+	2	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18185082	18185146	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18185147	18185336	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18185337	18185392	0.19	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18185337	18185392	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18185393	18185508	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18185509	18185570	0.13	+	1	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18185509	18185570	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18185571	18185709	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18185710	18185754	1	+	2	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18185710	18185754	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18185755	18185859	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18185860	18185951	1	+	2	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18185860	18185951	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18185952	18186053	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18186054	18186141	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18186054	18186141	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18186142	18186260	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18186261	18186346	1	+	2	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18186261	18186346	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18186347	18186423	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18186424	18186510	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18186424	18186510	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18186511	18186681	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18186682	18186747	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18186682	18186747	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18186748	18186835	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18186836	18186919	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18186836	18186919	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18186920	18187011	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18187012	18187073	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18187012	18187073	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18187074	18187169	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18187170	18187245	1	+	1	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18187170	18187245	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18187246	18187345	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18187346	18187408	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18187346	18187408	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18187409	18187507	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18187508	18187589	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18187508	18187589	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18187590	18187675	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18187676	18187752	1	+	2	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18187676	18187752	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18187753	18187846	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18187847	18187894	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18187847	18187894	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	intron	18187895	18188026	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	CDS	18188027	18188086	1	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	exon	18188027	18188086	.	+	.	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
Phchi.S1	AUGUSTUS	stop_codon	18188087	18188089	.	+	0	transcript_id "Phchi.S1G282300.t1"; gene_id "Phchi.S1G282300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5192.t1 is derived from g2362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15407226	15407885	.	-	.	Phchi.S1G235100
Phchi.S1	AUGUSTUS	transcript	15407226	15407885	.	-	.	transcript_id "Phchi.S1G235100.t1"; gene_id "Phchi.S1G235100"
Phchi.S1	AUGUSTUS	stop_codon	15407223	15407225	.	-	0	transcript_id "Phchi.S1G235100.t1"; gene_id "Phchi.S1G235100"
Phchi.S1	AUGUSTUS	CDS	15407226	15407885	0.66	-	0	transcript_id "Phchi.S1G235100.t1"; gene_id "Phchi.S1G235100"
Phchi.S1	AUGUSTUS	exon	15407226	15407885	.	-	.	transcript_id "Phchi.S1G235100.t1"; gene_id "Phchi.S1G235100"
Phchi.S1	AUGUSTUS	start_codon	15407883	15407885	.	-	0	transcript_id "Phchi.S1G235100.t1"; gene_id "Phchi.S1G235100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2953.t1 is derived from g122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	749651	751859	.	-	.	Phchi.S1G011200
Phchi.S1	AUGUSTUS	transcript	749651	751859	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	stop_codon	749648	749650	.	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	749651	749738	1	-	1	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	749651	749738	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	749739	749835	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	749836	749879	1	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	749836	749879	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	749880	749980	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	749981	750360	1	-	2	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	749981	750360	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	750361	750443	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	750444	750516	1	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	750444	750516	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	750517	750593	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	750594	750659	1	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	750594	750659	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	750660	750738	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	750739	750822	1	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	750739	750822	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	750823	751068	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	751069	751600	1	-	1	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	751069	751600	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	intron	751601	751704	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	CDS	751705	751859	0.4	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	exon	751705	751859	.	-	.	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
Phchi.S1	AUGUSTUS	start_codon	751857	751859	.	-	0	transcript_id "Phchi.S1G011200.t1"; gene_id "Phchi.S1G011200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4229.t1 is derived from g1398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9022477	9022996	.	+	.	Phchi.S1G138800
Phchi.S1	AUGUSTUS	transcript	9022477	9022996	.	+	.	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	start_codon	9022477	9022479	.	+	0	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	CDS	9022477	9022551	0.92	+	0	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	exon	9022477	9022551	.	+	.	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	intron	9022552	9022694	.	+	.	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	CDS	9022695	9022770	0.97	+	0	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	exon	9022695	9022770	.	+	.	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	intron	9022771	9022922	.	+	.	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	CDS	9022923	9022996	0.99	+	2	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	exon	9022923	9022996	.	+	.	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
Phchi.S1	AUGUSTUS	stop_codon	9022997	9022999	.	+	0	transcript_id "Phchi.S1G138800.t1"; gene_id "Phchi.S1G138800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2321.t1 is derived from g9241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6165006	6167201	.	+	.	Phchi.S5G093000
Phchi.S5	AUGUSTUS	transcript	6165006	6167201	.	+	.	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	start_codon	6165006	6165008	.	+	0	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	CDS	6165006	6165377	0.43	+	0	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	exon	6165006	6165377	.	+	.	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	intron	6165378	6165560	.	+	.	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	CDS	6165561	6167201	0.54	+	0	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	exon	6165561	6167201	.	+	.	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
Phchi.S5	AUGUSTUS	stop_codon	6167202	6167204	.	+	0	transcript_id "Phchi.S5G093000.t1"; gene_id "Phchi.S5G093000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13775.t1 is derived from g12242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8847172	8849037	.	-	.	Phchi.S3G109400
Phchi.S3	AUGUSTUS	transcript	8847172	8849037	.	-	.	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	stop_codon	8847169	8847171	.	-	0	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	CDS	8847172	8847827	0.6	-	2	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	exon	8847172	8847827	.	-	.	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	intron	8847828	8847992	.	-	.	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	CDS	8847993	8849037	0.51	-	0	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	exon	8847993	8849037	.	-	.	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
Phchi.S3	AUGUSTUS	start_codon	8849035	8849037	.	-	0	transcript_id "Phchi.S3G109400.t1"; gene_id "Phchi.S3G109400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9918.t1 is derived from g7094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44436763	44438184	.	+	.	Phchi.S1G707700
Phchi.S1	AUGUSTUS	transcript	44436763	44438184	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	start_codon	44436763	44436765	.	+	0	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44436763	44436779	1	+	0	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44436763	44436779	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	intron	44436780	44436966	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44436967	44437102	0.97	+	1	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44436967	44437102	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	intron	44437103	44437208	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44437209	44437282	1	+	0	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44437209	44437282	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	intron	44437283	44437404	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44437405	44437498	1	+	1	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44437405	44437498	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	intron	44437499	44437600	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44437601	44437732	1	+	0	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44437601	44437732	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	intron	44437733	44437815	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44437816	44437976	1	+	0	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44437816	44437976	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	intron	44437977	44438066	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	CDS	44438067	44438184	0.99	+	1	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	exon	44438067	44438184	.	+	.	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
Phchi.S1	AUGUSTUS	stop_codon	44438185	44438187	.	+	0	transcript_id "Phchi.S1G707700.t1"; gene_id "Phchi.S1G707700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9767.t1 is derived from g6943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43593256	43594125	.	-	.	Phchi.S1G692600
Phchi.S1	AUGUSTUS	transcript	43593256	43594125	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	stop_codon	43593253	43593255	.	-	0	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	CDS	43593256	43593279	0.98	-	0	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	exon	43593256	43593279	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	intron	43593280	43593359	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	CDS	43593360	43593442	0.98	-	2	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	exon	43593360	43593442	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	intron	43593443	43593663	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	CDS	43593664	43593762	0.98	-	2	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	exon	43593664	43593762	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	intron	43593763	43594106	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	CDS	43594107	43594125	0.79	-	0	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	exon	43594107	43594125	.	-	.	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
Phchi.S1	AUGUSTUS	start_codon	43594123	43594125	.	-	0	transcript_id "Phchi.S1G692600.t1"; gene_id "Phchi.S1G692600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg61.t1 is derived from g9843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	302720	305631	.	-	.	Phchi.S6G002000
Phchi.S6	AUGUSTUS	transcript	302720	305631	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	stop_codon	302717	302719	.	-	0	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	CDS	302720	302787	0.6	-	2	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	exon	302720	302787	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	intron	302788	302978	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	CDS	302979	303059	0.6	-	2	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	exon	302979	303059	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	intron	303060	303217	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	CDS	303218	303560	0.51	-	0	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	exon	303218	303560	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	intron	303561	303736	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	CDS	303737	304664	0.54	-	1	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	exon	303737	304664	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	intron	304665	304865	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	CDS	304866	305131	0.48	-	0	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	exon	304866	305131	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	intron	305132	305322	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	CDS	305323	305631	0.65	-	0	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	exon	305323	305631	.	-	.	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
Phchi.S6	AUGUSTUS	start_codon	305629	305631	.	-	0	transcript_id "Phchi.S6G002000.t1"; gene_id "Phchi.S6G002000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg225.t1 is derived from g10007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1519242	1520180	.	-	.	Phchi.S6G018400
Phchi.S6	AUGUSTUS	transcript	1519242	1520180	.	-	.	transcript_id "Phchi.S6G018400.t1"; gene_id "Phchi.S6G018400"
Phchi.S6	AUGUSTUS	stop_codon	1519239	1519241	.	-	0	transcript_id "Phchi.S6G018400.t1"; gene_id "Phchi.S6G018400"
Phchi.S6	AUGUSTUS	CDS	1519242	1520180	0.83	-	0	transcript_id "Phchi.S6G018400.t1"; gene_id "Phchi.S6G018400"
Phchi.S6	AUGUSTUS	exon	1519242	1520180	.	-	.	transcript_id "Phchi.S6G018400.t1"; gene_id "Phchi.S6G018400"
Phchi.S6	AUGUSTUS	start_codon	1520178	1520180	.	-	0	transcript_id "Phchi.S6G018400.t1"; gene_id "Phchi.S6G018400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13340.t1 is derived from g11806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6170113	6171545	.	-	.	Phchi.S3G065900
Phchi.S3	AUGUSTUS	transcript	6170113	6171545	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	stop_codon	6170110	6170112	.	-	0	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	CDS	6170113	6170367	0.83	-	0	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	exon	6170113	6170367	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	intron	6170368	6170481	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	CDS	6170482	6170601	0.73	-	0	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	exon	6170482	6170601	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	intron	6170602	6170701	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	CDS	6170702	6170911	0.59	-	0	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	exon	6170702	6170911	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	intron	6170912	6171005	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	CDS	6171006	6171222	0.72	-	1	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	exon	6171006	6171222	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	intron	6171223	6171347	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	CDS	6171348	6171384	0.56	-	2	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	exon	6171348	6171384	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	intron	6171385	6171514	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	CDS	6171515	6171545	0.56	-	0	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	exon	6171515	6171545	.	-	.	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
Phchi.S3	AUGUSTUS	start_codon	6171543	6171545	.	-	0	transcript_id "Phchi.S3G065900.t1"; gene_id "Phchi.S3G065900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12245.t1 is derived from g7921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6994500	6996290	.	+	.	Phchi.S2G032500
Phchi.S2	AUGUSTUS	transcript	6994500	6996290	.	+	.	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	start_codon	6994500	6994502	.	+	0	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	CDS	6994500	6994581	0.41	+	0	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	exon	6994500	6994581	.	+	.	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	intron	6994582	6995004	.	+	.	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	CDS	6995005	6995292	0.99	+	2	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	exon	6995005	6995292	.	+	.	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	intron	6995293	6996102	.	+	.	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	CDS	6996103	6996290	0.99	+	2	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	exon	6996103	6996290	.	+	.	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
Phchi.S2	AUGUSTUS	stop_codon	6996291	6996293	.	+	0	transcript_id "Phchi.S2G032500.t1"; gene_id "Phchi.S2G032500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3737.t1 is derived from g906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5452837	5454394	.	-	.	Phchi.S1G089600
Phchi.S1	AUGUSTUS	transcript	5452837	5454394	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	stop_codon	5452834	5452836	.	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5452837	5452896	1	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5452837	5452896	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5452897	5452977	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5452978	5453067	1	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5452978	5453067	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5453068	5453151	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5453152	5453237	1	-	2	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5453152	5453237	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5453238	5453323	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5453324	5453384	1	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5453324	5453384	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5453385	5453480	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5453481	5453553	1	-	1	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5453481	5453553	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5453554	5453633	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5453634	5453731	1	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5453634	5453731	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5453732	5453874	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5453875	5454021	1	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5453875	5454021	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	intron	5454022	5454160	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	CDS	5454161	5454394	1	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	exon	5454161	5454394	.	-	.	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
Phchi.S1	AUGUSTUS	start_codon	5454392	5454394	.	-	0	transcript_id "Phchi.S1G089600.t1"; gene_id "Phchi.S1G089600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3418.t1 is derived from g587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3400862	3404930	.	+	.	Phchi.S1G057700
Phchi.S1	AUGUSTUS	transcript	3400862	3404930	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	start_codon	3400862	3400864	.	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3400862	3401107	0.61	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3400862	3401107	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3401108	3401292	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3401293	3401385	1	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3401293	3401385	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3401386	3401489	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3401490	3401582	1	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3401490	3401582	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3401583	3401767	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3401768	3401896	1	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3401768	3401896	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3401897	3402048	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3402049	3402098	1	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3402049	3402098	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3402099	3402217	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3402218	3402991	1	+	1	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3402218	3402991	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3402992	3403124	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3403125	3403278	1	+	1	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3403125	3403278	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3403279	3403373	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3403374	3403550	0.81	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3403374	3403550	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3403551	3403652	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3403653	3403847	0.93	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3403653	3403847	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3403848	3403972	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3403973	3404119	1	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3403973	3404119	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3404120	3404241	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3404242	3404451	1	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3404242	3404451	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	intron	3404452	3404537	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	CDS	3404538	3404930	0.99	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	exon	3404538	3404930	.	+	.	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
Phchi.S1	AUGUSTUS	stop_codon	3404931	3404933	.	+	0	transcript_id "Phchi.S1G057700.t1"; gene_id "Phchi.S1G057700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2324.t1 is derived from g9244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6185597	6187587	.	+	.	Phchi.S5G093300
Phchi.S5	AUGUSTUS	transcript	6185597	6187587	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	start_codon	6185597	6185599	.	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6185597	6185614	0.87	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6185597	6185614	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	intron	6185615	6185786	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6185787	6185908	0.89	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6185787	6185908	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	intron	6185909	6186385	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6186386	6186485	1	+	1	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6186386	6186485	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	intron	6186486	6186611	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6186612	6186692	1	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6186612	6186692	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	intron	6186693	6186781	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6186782	6186886	1	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6186782	6186886	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	intron	6186887	6187087	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6187088	6187303	1	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6187088	6187303	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	intron	6187304	6187482	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	CDS	6187483	6187587	0.82	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	exon	6187483	6187587	.	+	.	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
Phchi.S5	AUGUSTUS	stop_codon	6187588	6187590	.	+	0	transcript_id "Phchi.S5G093300.t1"; gene_id "Phchi.S5G093300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7034.t1 is derived from g4206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26515272	26516150	.	-	.	Phchi.S1G419300
Phchi.S1	AUGUSTUS	transcript	26515272	26516150	.	-	.	transcript_id "Phchi.S1G419300.t1"; gene_id "Phchi.S1G419300"
Phchi.S1	AUGUSTUS	stop_codon	26515269	26515271	.	-	0	transcript_id "Phchi.S1G419300.t1"; gene_id "Phchi.S1G419300"
Phchi.S1	AUGUSTUS	CDS	26515272	26516150	1	-	0	transcript_id "Phchi.S1G419300.t1"; gene_id "Phchi.S1G419300"
Phchi.S1	AUGUSTUS	exon	26515272	26516150	.	-	.	transcript_id "Phchi.S1G419300.t1"; gene_id "Phchi.S1G419300"
Phchi.S1	AUGUSTUS	start_codon	26516148	26516150	.	-	0	transcript_id "Phchi.S1G419300.t1"; gene_id "Phchi.S1G419300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14983.t1 is derived from g13451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15885932	15886524	.	+	.	Phchi.S3G230200
Phchi.S3	AUGUSTUS	transcript	15885932	15886524	.	+	.	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	start_codon	15885932	15885934	.	+	0	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	CDS	15885932	15886268	0.47	+	0	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	exon	15885932	15886268	.	+	.	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	intron	15886269	15886387	.	+	.	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	CDS	15886388	15886524	0.69	+	2	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	exon	15886388	15886524	.	+	.	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
Phchi.S3	AUGUSTUS	stop_codon	15886525	15886527	.	+	0	transcript_id "Phchi.S3G230200.t1"; gene_id "Phchi.S3G230200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12455.t1 is derived from g8132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23728965	23734412	.	+	.	Phchi.S2G053500
Phchi.S2	AUGUSTUS	transcript	23728965	23734412	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	start_codon	23728965	23728967	.	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23728965	23729044	0.88	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23728965	23729044	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23729045	23729222	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23729223	23729234	0.82	+	1	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23729223	23729234	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23729235	23729537	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23729538	23729660	0.5	+	1	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23729538	23729660	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23729661	23729737	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23729738	23729896	0.69	+	1	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23729738	23729896	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23729897	23730070	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23730071	23730248	0.67	+	1	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23730071	23730248	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23730249	23730386	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23730387	23730513	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23730387	23730513	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23730514	23730672	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23730673	23730785	1	+	2	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23730673	23730785	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23730786	23730867	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23730868	23731006	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23730868	23731006	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23731007	23731082	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23731083	23731192	0.87	+	2	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23731083	23731192	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23731193	23731294	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23731295	23731364	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23731295	23731364	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23731365	23731458	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23731459	23731532	1	+	2	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23731459	23731532	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23731533	23731774	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23731775	23731876	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23731775	23731876	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23731877	23731960	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23731961	23732056	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23731961	23732056	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23732057	23732151	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23732152	23732279	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23732152	23732279	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23732280	23732410	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23732411	23732645	0.98	+	1	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23732411	23732645	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23732646	23732795	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23732796	23732963	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23732796	23732963	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23732964	23733159	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23733160	23733273	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23733160	23733273	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23733274	23733465	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23733466	23733615	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23733466	23733615	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23733616	23733696	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23733697	23733807	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23733697	23733807	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23733808	23733895	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23733896	23734075	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23733896	23734075	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23734076	23734152	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23734153	23734281	1	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23734153	23734281	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	intron	23734282	23734370	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	CDS	23734371	23734412	0.56	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	exon	23734371	23734412	.	+	.	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
Phchi.S2	AUGUSTUS	stop_codon	23734413	23734415	.	+	0	transcript_id "Phchi.S2G053500.t1"; gene_id "Phchi.S2G053500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12204.t1 is derived from g7880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6723137	6725580	.	+	.	Phchi.S2G028400
Phchi.S2	AUGUSTUS	transcript	6723137	6725580	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	start_codon	6723137	6723139	.	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6723137	6723631	0.56	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6723137	6723631	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6723632	6723726	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6723727	6723913	1	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6723727	6723913	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6723914	6724008	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6724009	6724142	1	+	2	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6724009	6724142	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6724143	6724232	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6724233	6724345	1	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6724233	6724345	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6724346	6724437	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6724438	6724561	1	+	1	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6724438	6724561	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6724562	6724666	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6724667	6724816	1	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6724667	6724816	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6724817	6724894	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6724895	6725050	1	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6724895	6725050	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6725051	6725143	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6725144	6725223	1	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6725144	6725223	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6725224	6725307	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6725308	6725357	1	+	1	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6725308	6725357	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	intron	6725358	6725461	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	CDS	6725462	6725580	0.99	+	2	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	exon	6725462	6725580	.	+	.	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
Phchi.S2	AUGUSTUS	stop_codon	6725581	6725583	.	+	0	transcript_id "Phchi.S2G028400.t1"; gene_id "Phchi.S2G028400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14488.t1 is derived from g12956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13092148	13092581	.	-	.	Phchi.S3G180700
Phchi.S3	AUGUSTUS	transcript	13092148	13092581	.	-	.	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	stop_codon	13092145	13092147	.	-	0	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	CDS	13092148	13092283	0.75	-	1	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	exon	13092148	13092283	.	-	.	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	intron	13092284	13092367	.	-	.	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	CDS	13092368	13092445	0.61	-	1	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	exon	13092368	13092445	.	-	.	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	intron	13092446	13092537	.	-	.	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	CDS	13092538	13092581	0.45	-	0	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	exon	13092538	13092581	.	-	.	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
Phchi.S3	AUGUSTUS	start_codon	13092579	13092581	.	-	0	transcript_id "Phchi.S3G180700.t1"; gene_id "Phchi.S3G180700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg262.t1 is derived from g10044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1766684	1770871	.	+	.	Phchi.S6G022100
Phchi.S6	AUGUSTUS	transcript	1769447	1770871	.	+	.	transcript_id "Phchi.S6G022100.t1"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	start_codon	1769447	1769449	.	+	0	transcript_id "Phchi.S6G022100.t1"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	CDS	1769447	1770871	0.98	+	0	transcript_id "Phchi.S6G022100.t1"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	exon	1769447	1770871	.	+	.	transcript_id "Phchi.S6G022100.t1"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	stop_codon	1770872	1770874	.	+	0	transcript_id "Phchi.S6G022100.t1"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	transcript	1766684	1770871	.	+	.	transcript_id "Phchi.S6G022100.t2"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	start_codon	1766684	1766686	.	+	0	transcript_id "Phchi.S6G022100.t2"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	CDS	1766684	1770871	0.5	+	0	transcript_id "Phchi.S6G022100.t2"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	exon	1766684	1770871	.	+	.	transcript_id "Phchi.S6G022100.t2"; gene_id "Phchi.S6G022100"
Phchi.S6	AUGUSTUS	stop_codon	1770872	1770874	.	+	0	transcript_id "Phchi.S6G022100.t2"; gene_id "Phchi.S6G022100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4528.t1 is derived from g1698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10974663	10978264	.	+	.	Phchi.S1G168700
Phchi.S1	AUGUSTUS	transcript	10974663	10978264	.	+	.	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	start_codon	10974663	10974665	.	+	0	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	CDS	10974663	10975711	0.92	+	0	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	exon	10974663	10975711	.	+	.	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	intron	10975712	10975812	.	+	.	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	CDS	10975813	10978264	0.66	+	1	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	exon	10975813	10978264	.	+	.	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
Phchi.S1	AUGUSTUS	stop_codon	10978265	10978267	.	+	0	transcript_id "Phchi.S1G168700.t1"; gene_id "Phchi.S1G168700"
# This transcript jg7255.t2 is derived from g4427.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7256.t1 is derived from g4428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27886788	27888901	.	+	.	Phchi.S1G441500
Phchi.S1	AUGUSTUS	transcript	27886788	27888901	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	start_codon	27886788	27886790	.	+	0	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	CDS	27886788	27887144	0.96	+	0	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	exon	27886788	27887144	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	intron	27887145	27887248	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	CDS	27887249	27888240	1	+	0	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	exon	27887249	27888240	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	intron	27888241	27888361	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	CDS	27888362	27888421	0.97	+	1	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	exon	27888362	27888421	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	intron	27888422	27888519	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	CDS	27888520	27888901	0.78	+	1	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	exon	27888520	27888901	.	+	.	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
Phchi.S1	AUGUSTUS	stop_codon	27888902	27888904	.	+	0	transcript_id "Phchi.S1G441500.t1"; gene_id "Phchi.S1G441500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14213.t1 is derived from g12680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11526648	11530666	.	+	.	Phchi.S3G153200
Phchi.S3	AUGUSTUS	transcript	11526648	11530666	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	start_codon	11526648	11526650	.	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11526648	11526843	0.99	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11526648	11526843	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11526844	11527001	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11527002	11527167	1	+	2	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11527002	11527167	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11527168	11527331	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11527332	11527566	1	+	1	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11527332	11527566	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11527567	11527655	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11527656	11527727	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11527656	11527727	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11527728	11527887	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11527888	11527998	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11527888	11527998	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11527999	11528124	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11528125	11528316	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11528125	11528316	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11528317	11528411	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11528412	11528573	0.98	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11528412	11528573	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11528574	11528686	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11528687	11528782	0.99	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11528687	11528782	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11528783	11528867	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11528868	11528969	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11528868	11528969	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11528970	11529127	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11529128	11529160	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11529128	11529160	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11529161	11529244	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11529245	11529325	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11529245	11529325	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11529326	11529413	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11529414	11529496	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11529414	11529496	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11529497	11529617	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11529618	11529749	1	+	1	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11529618	11529749	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11529750	11529959	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11529960	11530020	1	+	1	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11529960	11530020	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11530021	11530290	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11530291	11530356	1	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11530291	11530356	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	intron	11530357	11530459	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	CDS	11530460	11530666	0.94	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	exon	11530460	11530666	.	+	.	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
Phchi.S3	AUGUSTUS	stop_codon	11530667	11530669	.	+	0	transcript_id "Phchi.S3G153200.t1"; gene_id "Phchi.S3G153200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3951.t1 is derived from g1120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6637139	6637969	.	-	.	Phchi.S1G111000
Phchi.S1	AUGUSTUS	transcript	6637139	6637969	.	-	.	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	stop_codon	6637136	6637138	.	-	0	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	CDS	6637139	6637184	0.98	-	1	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	exon	6637139	6637184	.	-	.	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	intron	6637185	6637316	.	-	.	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	CDS	6637317	6637969	0.81	-	0	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	exon	6637317	6637969	.	-	.	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
Phchi.S1	AUGUSTUS	start_codon	6637967	6637969	.	-	0	transcript_id "Phchi.S1G111000.t1"; gene_id "Phchi.S1G111000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5504.t1 is derived from g2674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17154826	17156284	.	-	.	Phchi.S1G266300
Phchi.S1	AUGUSTUS	transcript	17154826	17156284	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	stop_codon	17154823	17154825	.	-	0	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	CDS	17154826	17155473	0.71	-	0	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	exon	17154826	17155473	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	intron	17155474	17155558	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	CDS	17155559	17155743	1	-	2	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	exon	17155559	17155743	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	intron	17155744	17155843	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	CDS	17155844	17156035	0.99	-	2	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	exon	17155844	17156035	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	intron	17156036	17156139	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	CDS	17156140	17156284	0.98	-	0	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	exon	17156140	17156284	.	-	.	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
Phchi.S1	AUGUSTUS	start_codon	17156282	17156284	.	-	0	transcript_id "Phchi.S1G266300.t1"; gene_id "Phchi.S1G266300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14310.t1 is derived from g12777.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 2 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12047820	12051675	.	-	.	Phchi.S3G162900
Phchi.S3	AUGUSTUS	transcript	12047820	12051675	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	stop_codon	12047817	12047819	.	-	0	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12047820	12048960	0.95	-	1	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12047820	12048960	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12048961	12049068	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12049069	12049542	0.99	-	1	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12049069	12049542	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12049543	12049805	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12049806	12049897	1	-	0	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12049806	12049897	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12049898	12050082	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12050083	12050519	1	-	2	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12050083	12050519	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12050520	12050728	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12050729	12050798	0.98	-	0	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12050729	12050798	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12050799	12050902	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12050903	12050943	0.94	-	2	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12050903	12050943	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12050944	12051020	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12051021	12051109	0.94	-	1	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12051021	12051109	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12051110	12051419	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12051420	12051467	0.52	-	1	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12051420	12051467	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	intron	12051468	12051586	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	CDS	12051587	12051675	0.79	-	0	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	exon	12051587	12051675	.	-	.	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
Phchi.S3	AUGUSTUS	start_codon	12051673	12051675	.	-	0	transcript_id "Phchi.S3G162900.t1"; gene_id "Phchi.S3G162900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1940.t1 is derived from g8860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3922637	3928829	.	-	.	Phchi.S5G054900
Phchi.S5	AUGUSTUS	transcript	3922637	3928829	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	stop_codon	3922634	3922636	.	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3922637	3922728	0.6	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3922637	3922728	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3922729	3922798	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3922799	3923005	0.52	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3922799	3923005	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3923006	3923327	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3923328	3923551	0.55	-	1	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3923328	3923551	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3923552	3923637	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3923638	3923759	1	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3923638	3923759	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3923760	3923850	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3923851	3924004	1	-	1	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3923851	3924004	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3924005	3924108	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3924109	3924215	0.99	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3924109	3924215	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3924216	3924297	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3924298	3924501	1	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3924298	3924501	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3924502	3924598	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3924599	3924781	1	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3924599	3924781	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3924782	3924910	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3924911	3925060	1	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3924911	3925060	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3925061	3925165	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3925166	3925548	0.99	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3925166	3925548	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3925549	3925671	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3925672	3925827	1	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3925672	3925827	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3925828	3925950	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3925951	3926107	1	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3925951	3926107	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3926108	3926254	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3926255	3926403	1	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3926255	3926403	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3926404	3926498	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3926499	3926732	1	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3926499	3926732	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3926733	3926849	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3926850	3926969	0.79	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3926850	3926969	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3926970	3927090	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3927091	3927186	1	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3927091	3927186	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3927187	3927339	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3927340	3927413	1	-	1	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3927340	3927413	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3927414	3927504	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3927505	3927617	1	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3927505	3927617	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3927618	3927756	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3927757	3927803	1	-	2	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3927757	3927803	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3927804	3927935	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3927936	3928011	0.93	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3927936	3928011	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3928012	3928126	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3928127	3928529	0.93	-	1	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3928127	3928529	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	intron	3928530	3928686	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	CDS	3928687	3928829	0.55	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	exon	3928687	3928829	.	-	.	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
Phchi.S5	AUGUSTUS	start_codon	3928827	3928829	.	-	0	transcript_id "Phchi.S5G054900.t1"; gene_id "Phchi.S5G054900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10179.t1 is derived from g7355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46167556	46171900	.	-	.	Phchi.S1G733800
Phchi.S1	AUGUSTUS	transcript	46167556	46171900	.	-	.	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	stop_codon	46167553	46167555	.	-	0	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	CDS	46167556	46168689	0.92	-	0	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	exon	46167556	46168689	.	-	.	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	intron	46168690	46168802	.	-	.	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	CDS	46168803	46170181	1	-	2	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	exon	46168803	46170181	.	-	.	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	intron	46170182	46170336	.	-	.	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	CDS	46170337	46171900	0.92	-	0	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	exon	46170337	46171900	.	-	.	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
Phchi.S1	AUGUSTUS	start_codon	46171898	46171900	.	-	0	transcript_id "Phchi.S1G733800.t1"; gene_id "Phchi.S1G733800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12121.t1 is derived from g7797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3798223	3812947	.	+	.	Phchi.S2G020100
Phchi.S2	AUGUSTUS	transcript	3798223	3812947	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	start_codon	3798223	3798225	.	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3798223	3798515	0.95	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3798223	3798515	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3798516	3798598	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3798599	3798686	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3798599	3798686	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3798687	3798764	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3798765	3801496	0.88	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3798765	3801496	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3801497	3801663	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3801664	3801778	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3801664	3801778	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3801779	3801858	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3801859	3802160	0.42	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3801859	3802160	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3802161	3802324	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3802325	3802790	0.42	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3802325	3802790	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3802791	3802913	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3802914	3802995	0.96	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3802914	3802995	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3802996	3803080	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3803081	3803278	0.58	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3803081	3803278	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3803279	3803370	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3803371	3803873	0.53	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3803371	3803873	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3803874	3804013	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3804014	3804149	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3804014	3804149	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3804150	3804223	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3804224	3804357	1	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3804224	3804357	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3804358	3804479	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3804480	3805126	0.92	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3804480	3805126	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3805127	3805236	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3805237	3805357	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3805237	3805357	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3805358	3805446	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3805447	3805563	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3805447	3805563	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3805564	3805746	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3805747	3805838	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3805747	3805838	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3805839	3805956	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3805957	3806114	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3805957	3806114	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3806115	3806285	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3806286	3806338	0.86	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3806286	3806338	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3806339	3806452	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3806453	3806663	0.91	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3806453	3806663	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3806664	3806835	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3806836	3807050	0.64	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3806836	3807050	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3807051	3807185	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3807186	3807297	0.6	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3807186	3807297	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3807298	3807370	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3807371	3807666	1	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3807371	3807666	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3807667	3807753	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3807754	3807839	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3807754	3807839	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3807840	3807921	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3807922	3808017	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3807922	3808017	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3808018	3808162	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3808163	3808424	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3808163	3808424	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3808425	3808524	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3808525	3808941	0.58	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3808525	3808941	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3808942	3809051	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3809052	3809148	0.99	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3809052	3809148	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3809149	3809285	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3809286	3809626	0.97	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3809286	3809626	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3809627	3809755	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3809756	3809884	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3809756	3809884	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3809885	3810137	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3810138	3810302	0.96	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3810138	3810302	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3810303	3810405	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3810406	3810534	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3810406	3810534	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3810535	3810608	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3810609	3810698	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3810609	3810698	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3810699	3810825	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3810826	3810932	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3810826	3810932	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3810933	3811024	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3811025	3811173	1	+	1	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3811025	3811173	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3811174	3811338	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3811339	3811421	1	+	2	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3811339	3811421	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3811422	3811661	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3811662	3811757	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3811662	3811757	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3811758	3811874	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3811875	3811997	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3811875	3811997	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3811998	3812126	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3812127	3812210	0.96	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3812127	3812210	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3812211	3812320	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3812321	3812467	1	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3812321	3812467	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	intron	3812468	3812566	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	CDS	3812567	3812947	0.64	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	exon	3812567	3812947	.	+	.	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
Phchi.S2	AUGUSTUS	stop_codon	3812948	3812950	.	+	0	transcript_id "Phchi.S2G020100.t1"; gene_id "Phchi.S2G020100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5660.t1 is derived from g2830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18173434	18175703	.	+	.	Phchi.S1G281900
Phchi.S1	AUGUSTUS	transcript	18173434	18175703	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	start_codon	18173434	18173436	.	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18173434	18174147	1	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18173434	18174147	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	intron	18174148	18174256	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18174257	18174472	0.96	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18174257	18174472	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	intron	18174473	18174564	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18174565	18174630	1	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18174565	18174630	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	intron	18174631	18174773	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18174774	18175195	0.69	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18174774	18175195	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	intron	18175196	18175307	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18175308	18175387	0.32	+	1	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18175308	18175387	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	intron	18175388	18175470	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18175471	18175556	1	+	2	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18175471	18175556	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	intron	18175557	18175646	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	CDS	18175647	18175703	1	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	exon	18175647	18175703	.	+	.	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
Phchi.S1	AUGUSTUS	stop_codon	18175704	18175706	.	+	0	transcript_id "Phchi.S1G281900.t1"; gene_id "Phchi.S1G281900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14736.t1 is derived from g13204.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14449606	14451184	.	+	.	Phchi.S3G205500
Phchi.S3	AUGUSTUS	transcript	14449606	14451184	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	start_codon	14449606	14449608	.	+	0	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14449606	14449748	0.99	+	0	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14449606	14449748	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14449749	14449881	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14449882	14450080	0.93	+	1	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14449882	14450080	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14450081	14450214	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450215	14450358	0.89	+	0	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450215	14450358	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14450359	14450512	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450513	14450697	1	+	0	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450513	14450697	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14450698	14450853	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450854	14451184	0.99	+	1	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450854	14451184	.	+	.	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	stop_codon	14451185	14451187	.	+	0	transcript_id "Phchi.S3G205500.t1"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	transcript	14449606	14451184	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	start_codon	14449606	14449608	.	+	0	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14449606	14449748	0.99	+	0	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14449606	14449748	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14449749	14449838	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14449839	14449984	0.58	+	1	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14449839	14449984	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14449985	14450080	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450081	14450112	0.69	+	2	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450081	14450112	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14450113	14450214	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450215	14450358	0.7	+	0	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450215	14450358	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14450359	14450512	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450513	14450697	1	+	0	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450513	14450697	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	intron	14450698	14450853	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	CDS	14450854	14451184	1	+	1	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	exon	14450854	14451184	.	+	.	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
Phchi.S3	AUGUSTUS	stop_codon	14451185	14451187	.	+	0	transcript_id "Phchi.S3G205500.t2"; gene_id "Phchi.S3G205500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7683.t1 is derived from g4857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30599678	30604712	.	-	.	Phchi.S1G484200
Phchi.S1	AUGUSTUS	transcript	30599678	30604712	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	stop_codon	30599675	30599677	.	-	0	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30599678	30600060	0.6	-	2	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30599678	30600060	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30600061	30600191	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30600192	30600497	0.61	-	2	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30600192	30600497	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30600498	30600592	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30600593	30600782	1	-	0	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30600593	30600782	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30600783	30600872	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30600873	30603075	0.46	-	1	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30600873	30603075	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30603076	30603242	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30603243	30603499	0.37	-	0	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30603243	30603499	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30603500	30603583	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30603584	30603948	1	-	2	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30603584	30603948	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30603949	30604024	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30604025	30604497	0.95	-	1	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30604025	30604497	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	intron	30604498	30604584	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	CDS	30604585	30604712	0.91	-	0	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	exon	30604585	30604712	.	-	.	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
Phchi.S1	AUGUSTUS	start_codon	30604710	30604712	.	-	0	transcript_id "Phchi.S1G484200.t1"; gene_id "Phchi.S1G484200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13623.t1 is derived from g12090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7812936	7813677	.	+	.	Phchi.S3G094200
Phchi.S3	AUGUSTUS	transcript	7812936	7813677	.	+	.	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	start_codon	7812936	7812938	.	+	0	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	CDS	7812936	7813532	0.75	+	0	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	exon	7812936	7813532	.	+	.	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	intron	7813533	7813620	.	+	.	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	CDS	7813621	7813677	0.92	+	0	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	exon	7813621	7813677	.	+	.	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
Phchi.S3	AUGUSTUS	stop_codon	7813678	7813680	.	+	0	transcript_id "Phchi.S3G094200.t1"; gene_id "Phchi.S3G094200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8973.t1 is derived from g6148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38928732	38929508	.	+	.	Phchi.S1G613200
Phchi.S1	AUGUSTUS	transcript	38928732	38929508	.	+	.	transcript_id "Phchi.S1G613200.t1"; gene_id "Phchi.S1G613200"
Phchi.S1	AUGUSTUS	start_codon	38928732	38928734	.	+	0	transcript_id "Phchi.S1G613200.t1"; gene_id "Phchi.S1G613200"
Phchi.S1	AUGUSTUS	CDS	38928732	38929508	0.87	+	0	transcript_id "Phchi.S1G613200.t1"; gene_id "Phchi.S1G613200"
Phchi.S1	AUGUSTUS	exon	38928732	38929508	.	+	.	transcript_id "Phchi.S1G613200.t1"; gene_id "Phchi.S1G613200"
Phchi.S1	AUGUSTUS	stop_codon	38929509	38929511	.	+	0	transcript_id "Phchi.S1G613200.t1"; gene_id "Phchi.S1G613200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12593.t1 is derived from g8270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36501976	36502434	.	+	.	Phchi.S2G067300
Phchi.S2	AUGUSTUS	transcript	36501976	36502434	.	+	.	transcript_id "Phchi.S2G067300.t1"; gene_id "Phchi.S2G067300"
Phchi.S2	AUGUSTUS	start_codon	36501976	36501978	.	+	0	transcript_id "Phchi.S2G067300.t1"; gene_id "Phchi.S2G067300"
Phchi.S2	AUGUSTUS	CDS	36501976	36502434	0.53	+	0	transcript_id "Phchi.S2G067300.t1"; gene_id "Phchi.S2G067300"
Phchi.S2	AUGUSTUS	exon	36501976	36502434	.	+	.	transcript_id "Phchi.S2G067300.t1"; gene_id "Phchi.S2G067300"
Phchi.S2	AUGUSTUS	stop_codon	36502435	36502437	.	+	0	transcript_id "Phchi.S2G067300.t1"; gene_id "Phchi.S2G067300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10243.t1 is derived from g7419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46569785	46571317	.	+	.	Phchi.S1G740200
Phchi.S1	AUGUSTUS	transcript	46569839	46571317	.	+	.	transcript_id "Phchi.S1G740200.t1"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	start_codon	46569839	46569841	.	+	0	transcript_id "Phchi.S1G740200.t1"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	CDS	46569839	46571317	0.71	+	0	transcript_id "Phchi.S1G740200.t1"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	exon	46569839	46571317	.	+	.	transcript_id "Phchi.S1G740200.t1"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	stop_codon	46571318	46571320	.	+	0	transcript_id "Phchi.S1G740200.t1"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	transcript	46569785	46571317	.	+	.	transcript_id "Phchi.S1G740200.t2"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	start_codon	46569785	46569787	.	+	0	transcript_id "Phchi.S1G740200.t2"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	CDS	46569785	46571317	0.6	+	0	transcript_id "Phchi.S1G740200.t2"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	exon	46569785	46571317	.	+	.	transcript_id "Phchi.S1G740200.t2"; gene_id "Phchi.S1G740200"
Phchi.S1	AUGUSTUS	stop_codon	46571318	46571320	.	+	0	transcript_id "Phchi.S1G740200.t2"; gene_id "Phchi.S1G740200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1787.t1 is derived from g8707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2998804	3000248	.	+	.	Phchi.S5G039600
Phchi.S5	AUGUSTUS	transcript	2998804	3000248	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	start_codon	2998804	2998806	.	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	CDS	2998804	2998902	0.65	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	exon	2998804	2998902	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	intron	2998903	2999031	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	CDS	2999032	2999223	1	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	exon	2999032	2999223	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	intron	2999224	2999319	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	CDS	2999320	2999442	1	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	exon	2999320	2999442	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	intron	2999443	2999530	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	CDS	2999531	2999674	1	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	exon	2999531	2999674	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	intron	2999675	2999816	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	CDS	2999817	3000248	0.99	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	exon	2999817	3000248	.	+	.	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
Phchi.S5	AUGUSTUS	stop_codon	3000249	3000251	.	+	0	transcript_id "Phchi.S5G039600.t1"; gene_id "Phchi.S5G039600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13582.t1 is derived from g12049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7572668	7574902	.	-	.	Phchi.S3G090100
Phchi.S3	AUGUSTUS	transcript	7572668	7574902	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	stop_codon	7572665	7572667	.	-	0	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	CDS	7572668	7573084	0.96	-	0	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	exon	7572668	7573084	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	intron	7573085	7573246	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	CDS	7573247	7573429	0.52	-	0	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	exon	7573247	7573429	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	intron	7573430	7573549	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	CDS	7573550	7574093	0.76	-	1	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	exon	7573550	7574093	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	intron	7574094	7574230	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	CDS	7574231	7574400	1	-	0	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	exon	7574231	7574400	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	intron	7574401	7574496	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	CDS	7574497	7574582	1	-	2	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	exon	7574497	7574582	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	intron	7574583	7574667	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	CDS	7574668	7574902	0.81	-	0	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	exon	7574668	7574902	.	-	.	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
Phchi.S3	AUGUSTUS	start_codon	7574900	7574902	.	-	0	transcript_id "Phchi.S3G090100.t1"; gene_id "Phchi.S3G090100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11288.t1 is derived from g15338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5227961	5228369	.	-	.	Phchi.S4G087000
Phchi.S4	AUGUSTUS	transcript	5227961	5228369	.	-	.	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	stop_codon	5227958	5227960	.	-	0	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	CDS	5227961	5228086	0.61	-	0	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	exon	5227961	5228086	.	-	.	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	intron	5228087	5228237	.	-	.	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	CDS	5228238	5228369	0.69	-	0	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	exon	5228238	5228369	.	-	.	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
Phchi.S4	AUGUSTUS	start_codon	5228367	5228369	.	-	0	transcript_id "Phchi.S4G087000.t1"; gene_id "Phchi.S4G087000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3267.t1 is derived from g436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2626684	2628680	.	+	.	Phchi.S1G042600
Phchi.S1	AUGUSTUS	transcript	2626684	2628680	.	+	.	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	start_codon	2626684	2626686	.	+	0	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	CDS	2626684	2627882	0.49	+	0	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	exon	2626684	2627882	.	+	.	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	intron	2627883	2628277	.	+	.	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	CDS	2628278	2628680	0.93	+	1	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	exon	2628278	2628680	.	+	.	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
Phchi.S1	AUGUSTUS	stop_codon	2628681	2628683	.	+	0	transcript_id "Phchi.S1G042600.t1"; gene_id "Phchi.S1G042600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1866.t1 is derived from g8786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3613410	3617647	.	-	.	Phchi.S5G047500
Phchi.S5	AUGUSTUS	transcript	3613410	3617647	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	stop_codon	3613407	3613409	.	-	0	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	CDS	3613410	3616586	0.95	-	0	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	exon	3613410	3616586	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	intron	3616587	3616689	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	CDS	3616690	3616769	0.99	-	2	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	exon	3616690	3616769	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	intron	3616770	3616852	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	CDS	3616853	3616990	0.82	-	2	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	exon	3616853	3616990	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	intron	3616991	3617085	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	CDS	3617086	3617560	0.68	-	0	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	exon	3617086	3617560	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	intron	3617561	3617644	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	CDS	3617645	3617647	0.57	-	0	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	exon	3617645	3617647	.	-	.	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
Phchi.S5	AUGUSTUS	start_codon	3617645	3617647	.	-	0	transcript_id "Phchi.S5G047500.t1"; gene_id "Phchi.S5G047500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13700.t1 is derived from g12167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8259759	8262617	.	-	.	Phchi.S3G101900
Phchi.S3	AUGUSTUS	transcript	8259759	8262617	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	stop_codon	8259756	8259758	.	-	0	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	CDS	8259759	8260341	1	-	1	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	exon	8259759	8260341	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	intron	8260342	8260487	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	CDS	8260488	8260661	1	-	1	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	exon	8260488	8260661	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	intron	8260662	8260797	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	CDS	8260798	8261537	0.98	-	0	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	exon	8260798	8261537	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	intron	8261538	8261703	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	CDS	8261704	8261934	1	-	0	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	exon	8261704	8261934	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	intron	8261935	8262155	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	CDS	8262156	8262617	0.65	-	0	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	exon	8262156	8262617	.	-	.	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
Phchi.S3	AUGUSTUS	start_codon	8262615	8262617	.	-	0	transcript_id "Phchi.S3G101900.t1"; gene_id "Phchi.S3G101900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2219.t1 is derived from g9139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5466351	5466810	.	-	.	Phchi.S5G082800
Phchi.S5	AUGUSTUS	transcript	5466351	5466810	.	-	.	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	stop_codon	5466348	5466350	.	-	0	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	CDS	5466351	5466554	0.88	-	0	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	exon	5466351	5466554	.	-	.	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	intron	5466555	5466708	.	-	.	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	CDS	5466709	5466810	0.29	-	0	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	exon	5466709	5466810	.	-	.	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
Phchi.S5	AUGUSTUS	start_codon	5466808	5466810	.	-	0	transcript_id "Phchi.S5G082800.t1"; gene_id "Phchi.S5G082800"
# This transcript jg9518.t2 is derived from g6694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9519.t1 is derived from g6695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42245022	42245333	.	+	.	Phchi.S1G667800
Phchi.S1	AUGUSTUS	transcript	42245022	42245333	.	+	.	transcript_id "Phchi.S1G667800.t1"; gene_id "Phchi.S1G667800"
Phchi.S1	AUGUSTUS	start_codon	42245022	42245024	.	+	0	transcript_id "Phchi.S1G667800.t1"; gene_id "Phchi.S1G667800"
Phchi.S1	AUGUSTUS	CDS	42245022	42245333	0.85	+	0	transcript_id "Phchi.S1G667800.t1"; gene_id "Phchi.S1G667800"
Phchi.S1	AUGUSTUS	exon	42245022	42245333	.	+	.	transcript_id "Phchi.S1G667800.t1"; gene_id "Phchi.S1G667800"
Phchi.S1	AUGUSTUS	stop_codon	42245334	42245336	.	+	0	transcript_id "Phchi.S1G667800.t1"; gene_id "Phchi.S1G667800"
# This transcript jg12761.t2 is derived from g11226.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12761.t3 is derived from g11226.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12762.t1 is derived from g11227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1941976	1942862	.	-	.	Phchi.S3G008100
Phchi.S3	AUGUSTUS	transcript	1941976	1942862	.	-	.	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	stop_codon	1941973	1941975	.	-	0	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	CDS	1941976	1941997	1	-	1	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	exon	1941976	1941997	.	-	.	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	intron	1941998	1942230	.	-	.	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	CDS	1942231	1942862	1	-	0	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	exon	1942231	1942862	.	-	.	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	start_codon	1942860	1942862	.	-	0	transcript_id "Phchi.S3G008100.t1"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	transcript	1942109	1942862	.	-	.	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	stop_codon	1942106	1942108	.	-	0	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	CDS	1942109	1942130	0.64	-	1	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	exon	1942109	1942130	.	-	.	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	intron	1942131	1942230	.	-	.	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	CDS	1942231	1942862	0.97	-	0	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	exon	1942231	1942862	.	-	.	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
Phchi.S3	AUGUSTUS	start_codon	1942860	1942862	.	-	0	transcript_id "Phchi.S3G008100.t2"; gene_id "Phchi.S3G008100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13615.t1 is derived from g12082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7699300	7699707	.	-	.	Phchi.S3G093400
Phchi.S3	AUGUSTUS	transcript	7699300	7699707	.	-	.	transcript_id "Phchi.S3G093400.t1"; gene_id "Phchi.S3G093400"
Phchi.S3	AUGUSTUS	stop_codon	7699297	7699299	.	-	0	transcript_id "Phchi.S3G093400.t1"; gene_id "Phchi.S3G093400"
Phchi.S3	AUGUSTUS	CDS	7699300	7699707	0.52	-	0	transcript_id "Phchi.S3G093400.t1"; gene_id "Phchi.S3G093400"
Phchi.S3	AUGUSTUS	exon	7699300	7699707	.	-	.	transcript_id "Phchi.S3G093400.t1"; gene_id "Phchi.S3G093400"
Phchi.S3	AUGUSTUS	start_codon	7699705	7699707	.	-	0	transcript_id "Phchi.S3G093400.t1"; gene_id "Phchi.S3G093400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2289.t1 is derived from g9209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5880495	5885490	.	-	.	Phchi.S5G089800
Phchi.S5	AUGUSTUS	transcript	5880495	5885490	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	stop_codon	5880492	5880494	.	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5880495	5880655	0.91	-	2	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5880495	5880655	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5880656	5880887	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5880888	5881062	1	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5880888	5881062	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881063	5881210	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881211	5881303	1	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881211	5881303	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881304	5881471	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881472	5881633	1	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881472	5881633	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881634	5881776	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881777	5881911	1	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881777	5881911	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881912	5882008	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882009	5882247	0.69	-	2	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882009	5882247	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882248	5882412	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882413	5882485	0.78	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882413	5882485	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882486	5882632	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882633	5882738	0.55	-	1	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882633	5882738	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882739	5882827	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882828	5882905	0.9	-	1	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882828	5882905	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882906	5883002	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883003	5883165	0.94	-	2	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883003	5883165	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883166	5883310	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883311	5883461	0.87	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883311	5883461	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883462	5883679	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883680	5883918	1	-	2	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883680	5883918	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883919	5884186	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884187	5884217	1	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884187	5884217	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884218	5884384	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884385	5884531	1	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884385	5884531	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884532	5884869	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884870	5885490	0.78	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884870	5885490	.	-	.	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	start_codon	5885488	5885490	.	-	0	transcript_id "Phchi.S5G089800.t1"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	transcript	5880495	5885490	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	stop_codon	5880492	5880494	.	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5880495	5880655	0.78	-	2	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5880495	5880655	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5880656	5880887	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5880888	5881062	0.97	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5880888	5881062	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881063	5881210	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881211	5881303	1	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881211	5881303	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881304	5881471	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881472	5881633	0.99	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881472	5881633	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881634	5881776	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881777	5881911	0.99	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881777	5881911	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881912	5882008	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882009	5882247	0.73	-	2	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882009	5882247	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882248	5882412	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882413	5882485	0.67	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882413	5882485	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882486	5882632	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882633	5882738	0.48	-	1	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882633	5882738	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882739	5882827	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882828	5882905	0.83	-	1	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882828	5882905	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882906	5883002	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883003	5883165	0.9	-	2	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883003	5883165	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883166	5883310	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883311	5883461	0.84	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883311	5883461	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883462	5883679	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883680	5883918	0.99	-	2	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883680	5883918	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883919	5884012	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884013	5884217	1	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884013	5884217	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884218	5884384	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884385	5884531	1	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884385	5884531	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884532	5884869	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884870	5885490	0.85	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884870	5885490	.	-	.	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	start_codon	5885488	5885490	.	-	0	transcript_id "Phchi.S5G089800.t2"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	transcript	5880495	5885490	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	stop_codon	5880492	5880494	.	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5880495	5880655	0.78	-	2	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5880495	5880655	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5880656	5880887	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5880888	5881062	0.96	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5880888	5881062	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881063	5881210	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881211	5881303	0.99	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881211	5881303	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881304	5881471	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881472	5881633	0.96	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881472	5881633	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881634	5881776	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5881777	5881911	0.97	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5881777	5881911	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5881912	5882008	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882009	5882247	0.71	-	2	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882009	5882247	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882248	5882412	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882413	5882485	0.72	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882413	5882485	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882486	5882632	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882633	5882738	0.54	-	1	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882633	5882738	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882739	5882827	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5882828	5882905	0.87	-	1	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5882828	5882905	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5882906	5883002	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883003	5883165	0.94	-	2	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883003	5883165	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883166	5883310	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883311	5883461	0.83	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883311	5883461	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883462	5883679	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5883680	5883918	1	-	2	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5883680	5883918	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5883919	5884012	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884013	5884217	1	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884013	5884217	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884218	5884384	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884385	5884531	1	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884385	5884531	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884532	5884755	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884756	5884834	0.93	-	1	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884756	5884834	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	intron	5884835	5884930	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	CDS	5884931	5885490	0.64	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	exon	5884931	5885490	.	-	.	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
Phchi.S5	AUGUSTUS	start_codon	5885488	5885490	.	-	0	transcript_id "Phchi.S5G089800.t3"; gene_id "Phchi.S5G089800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11110.t1 is derived from g15160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4204627	4205031	.	-	.	Phchi.S4G069200
Phchi.S4	AUGUSTUS	transcript	4204627	4205031	.	-	.	transcript_id "Phchi.S4G069200.t1"; gene_id "Phchi.S4G069200"
Phchi.S4	AUGUSTUS	stop_codon	4204624	4204626	.	-	0	transcript_id "Phchi.S4G069200.t1"; gene_id "Phchi.S4G069200"
Phchi.S4	AUGUSTUS	CDS	4204627	4205031	0.99	-	0	transcript_id "Phchi.S4G069200.t1"; gene_id "Phchi.S4G069200"
Phchi.S4	AUGUSTUS	exon	4204627	4205031	.	-	.	transcript_id "Phchi.S4G069200.t1"; gene_id "Phchi.S4G069200"
Phchi.S4	AUGUSTUS	start_codon	4205029	4205031	.	-	0	transcript_id "Phchi.S4G069200.t1"; gene_id "Phchi.S4G069200"
# This transcript jg190.t2 is derived from g9972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg190.t3 is derived from g9972.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg191.t1 is derived from g9973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1079275	1081338	.	-	.	Phchi.S6G015000
Phchi.S6	AUGUSTUS	transcript	1079275	1081338	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	stop_codon	1079272	1079274	.	-	0	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	CDS	1079275	1079276	0.63	-	2	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	exon	1079275	1079276	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	intron	1079277	1079370	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	CDS	1079371	1080132	0.54	-	2	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	exon	1079371	1080132	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	intron	1080133	1080552	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	CDS	1080553	1080887	0.82	-	1	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	exon	1080553	1080887	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	intron	1080888	1080976	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	CDS	1080977	1081167	1	-	0	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	exon	1080977	1081167	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	intron	1081168	1081257	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	CDS	1081258	1081338	0.39	-	0	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	exon	1081258	1081338	.	-	.	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
Phchi.S6	AUGUSTUS	start_codon	1081336	1081338	.	-	0	transcript_id "Phchi.S6G015000.t1"; gene_id "Phchi.S6G015000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8921.t1 is derived from g6096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38674421	38675831	.	-	.	Phchi.S1G608000
Phchi.S1	AUGUSTUS	transcript	38674421	38675831	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	stop_codon	38674418	38674420	.	-	0	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	CDS	38674421	38674499	1	-	1	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	exon	38674421	38674499	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	intron	38674500	38674602	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	CDS	38674603	38674862	1	-	0	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	exon	38674603	38674862	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	intron	38674863	38674947	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	CDS	38674948	38675065	1	-	1	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	exon	38674948	38675065	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	intron	38675066	38675155	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	CDS	38675156	38675580	1	-	0	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	exon	38675156	38675580	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	intron	38675581	38675723	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	CDS	38675724	38675831	0.29	-	0	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	exon	38675724	38675831	.	-	.	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
Phchi.S1	AUGUSTUS	start_codon	38675829	38675831	.	-	0	transcript_id "Phchi.S1G608000.t1"; gene_id "Phchi.S1G608000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5508.t1 is derived from g2678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17161781	17164836	.	-	.	Phchi.S1G266700
Phchi.S1	AUGUSTUS	transcript	17161781	17164836	.	-	.	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	stop_codon	17161778	17161780	.	-	0	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	CDS	17161781	17164452	0.96	-	2	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	exon	17161781	17164452	.	-	.	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	intron	17164453	17164538	.	-	.	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	CDS	17164539	17164836	0.79	-	0	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	exon	17164539	17164836	.	-	.	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
Phchi.S1	AUGUSTUS	start_codon	17164834	17164836	.	-	0	transcript_id "Phchi.S1G266700.t1"; gene_id "Phchi.S1G266700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5624.t1 is derived from g2794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17929472	17933597	.	-	.	Phchi.S1G278300
Phchi.S1	AUGUSTUS	transcript	17929472	17933597	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	stop_codon	17929469	17929471	.	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17929472	17929570	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17929472	17929570	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17929571	17929675	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17929676	17929843	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17929676	17929843	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17929844	17929927	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17929928	17930146	0.94	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17929928	17930146	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17930147	17930251	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17930252	17930395	0.94	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17930252	17930395	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17930396	17930489	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17930490	17930657	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17930490	17930657	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17930658	17930757	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17930758	17930878	1	-	1	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17930758	17930878	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17930879	17930965	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17930966	17931021	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17930966	17931021	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17931022	17931113	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17931114	17931263	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17931114	17931263	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17931264	17931380	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17931381	17931467	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17931381	17931467	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17931468	17931566	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17931567	17931602	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17931567	17931602	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17931603	17931725	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17931726	17931788	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17931726	17931788	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17931789	17931872	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17931873	17931953	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17931873	17931953	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17931954	17932082	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17932083	17932172	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17932083	17932172	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17932173	17932254	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17932255	17932332	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17932255	17932332	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17932333	17932410	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17932411	17932614	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17932411	17932614	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17932615	17932701	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17932702	17932749	1	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17932702	17932749	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17932750	17932862	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17932863	17933048	0.9	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17932863	17933048	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17933049	17933214	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17933215	17933314	1	-	1	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17933215	17933314	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	intron	17933315	17933454	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	CDS	17933455	17933597	0.8	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	exon	17933455	17933597	.	-	.	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
Phchi.S1	AUGUSTUS	start_codon	17933595	17933597	.	-	0	transcript_id "Phchi.S1G278300.t1"; gene_id "Phchi.S1G278300"
# This transcript jg11679.t2 is derived from g15730.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11680.t1 is derived from g15731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7644422	7646047	.	-	.	Phchi.S4G126200
Phchi.S4	AUGUSTUS	transcript	7644422	7646047	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	stop_codon	7644419	7644421	.	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7644422	7644649	1	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7644422	7644649	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	intron	7644650	7644748	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7644749	7644841	1	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7644749	7644841	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	intron	7644842	7644919	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7644920	7645055	1	-	1	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7644920	7645055	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	intron	7645056	7645152	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7645153	7645262	1	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7645153	7645262	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	intron	7645263	7645334	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7645335	7645548	1	-	1	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7645335	7645548	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	intron	7645549	7645641	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7645642	7645751	1	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7645642	7645751	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	intron	7645752	7645831	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	CDS	7645832	7646047	0.94	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	exon	7645832	7646047	.	-	.	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
Phchi.S4	AUGUSTUS	start_codon	7646045	7646047	.	-	0	transcript_id "Phchi.S4G126200.t1"; gene_id "Phchi.S4G126200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12721.t1 is derived from g11186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1119758	1120328	.	+	.	Phchi.S3G004000
Phchi.S3	AUGUSTUS	transcript	1119758	1120328	.	+	.	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	start_codon	1119758	1119760	.	+	0	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	CDS	1119758	1119944	0.94	+	0	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	exon	1119758	1119944	.	+	.	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	intron	1119945	1120027	.	+	.	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	CDS	1120028	1120101	0.83	+	2	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	exon	1120028	1120101	.	+	.	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	intron	1120102	1120238	.	+	.	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	CDS	1120239	1120328	0.95	+	0	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	exon	1120239	1120328	.	+	.	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
Phchi.S3	AUGUSTUS	stop_codon	1120329	1120331	.	+	0	transcript_id "Phchi.S3G004000.t1"; gene_id "Phchi.S3G004000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10986.t1 is derived from g15036.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3533721	3535392	.	+	.	Phchi.S4G056800
Phchi.S4	AUGUSTUS	transcript	3533721	3535392	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	start_codon	3533721	3533723	.	+	0	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3533721	3533803	1	+	0	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3533721	3533803	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3533804	3534045	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534046	3534129	1	+	1	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534046	3534129	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534130	3534217	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534218	3534298	0.95	+	1	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534218	3534298	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534299	3534404	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534405	3534550	0.93	+	1	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534405	3534550	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534551	3534654	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534655	3534766	0.98	+	2	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534655	3534766	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534767	3534862	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534863	3534920	1	+	1	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534863	3534920	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534921	3535069	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3535070	3535129	0.86	+	0	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3535070	3535129	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3535130	3535236	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3535237	3535392	0.82	+	0	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3535237	3535392	.	+	.	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	stop_codon	3535393	3535395	.	+	0	transcript_id "Phchi.S4G056800.t1"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	transcript	3533881	3535392	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	start_codon	3533881	3533883	.	+	0	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3533881	3533888	1	+	0	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3533881	3533888	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3533889	3534045	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534046	3534129	1	+	1	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534046	3534129	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534130	3534217	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534218	3534298	0.96	+	1	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534218	3534298	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534299	3534404	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534405	3534550	0.94	+	1	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534405	3534550	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534551	3534654	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534655	3534766	0.97	+	2	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534655	3534766	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534767	3534862	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534863	3534920	0.99	+	1	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534863	3534920	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534921	3535069	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3535070	3535129	0.81	+	0	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3535070	3535129	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3535130	3535236	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3535237	3535392	0.8	+	0	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3535237	3535392	.	+	.	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	stop_codon	3535393	3535395	.	+	0	transcript_id "Phchi.S4G056800.t2"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	transcript	3533721	3535149	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	start_codon	3533721	3533723	.	+	0	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3533721	3533803	1	+	0	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3533721	3533803	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3533804	3534045	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534046	3534129	1	+	1	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534046	3534129	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534130	3534217	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534218	3534298	0.95	+	1	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534218	3534298	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534299	3534404	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534405	3534550	0.9	+	1	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534405	3534550	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534551	3534689	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534690	3534790	0.62	+	2	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534690	3534790	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534791	3534862	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3534863	3534920	0.78	+	0	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3534863	3534920	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	intron	3534921	3535069	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	CDS	3535070	3535149	0.61	+	2	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	exon	3535070	3535149	.	+	.	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
Phchi.S4	AUGUSTUS	stop_codon	3535150	3535152	.	+	0	transcript_id "Phchi.S4G056800.t3"; gene_id "Phchi.S4G056800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10307.t1 is derived from g7483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47061195	47063879	.	+	.	Phchi.S1G746600
Phchi.S1	AUGUSTUS	transcript	47061195	47063879	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	start_codon	47061195	47061197	.	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47061195	47061257	0.94	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47061195	47061257	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47061258	47061372	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47061373	47061430	0.75	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47061373	47061430	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47061431	47061526	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47061527	47061702	1	+	2	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47061527	47061702	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47061703	47061787	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47061788	47061874	1	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47061788	47061874	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47061875	47061998	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47061999	47062124	0.97	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47061999	47062124	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47062125	47062227	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47062228	47062290	1	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47062228	47062290	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47062291	47062374	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47062375	47062524	1	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47062375	47062524	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47062525	47062617	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47062618	47062685	1	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47062618	47062685	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47062686	47062772	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47062773	47062884	1	+	1	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47062773	47062884	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47062885	47063040	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47063041	47063145	0.97	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47063041	47063145	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47063146	47063251	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47063252	47063373	1	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47063252	47063373	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47063374	47063460	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47063461	47063607	1	+	1	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47063461	47063607	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	intron	47063608	47063707	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	CDS	47063708	47063879	0.96	+	1	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	exon	47063708	47063879	.	+	.	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
Phchi.S1	AUGUSTUS	stop_codon	47063880	47063882	.	+	0	transcript_id "Phchi.S1G746600.t1"; gene_id "Phchi.S1G746600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4077.t1 is derived from g1246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7656621	7659107	.	+	.	Phchi.S1G123600
Phchi.S1	AUGUSTUS	transcript	7656621	7659107	.	+	.	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	start_codon	7656621	7656623	.	+	0	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	CDS	7656621	7657721	0.95	+	0	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	exon	7656621	7657721	.	+	.	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	intron	7657722	7657883	.	+	.	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	CDS	7657884	7658911	1	+	0	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	exon	7657884	7658911	.	+	.	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	intron	7658912	7659037	.	+	.	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	CDS	7659038	7659107	0.98	+	1	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	exon	7659038	7659107	.	+	.	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
Phchi.S1	AUGUSTUS	stop_codon	7659108	7659110	.	+	0	transcript_id "Phchi.S1G123600.t1"; gene_id "Phchi.S1G123600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7347.t1 is derived from g4519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28636294	28639786	.	+	.	Phchi.S1G450600
Phchi.S1	AUGUSTUS	transcript	28636294	28639786	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	start_codon	28636294	28636296	.	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28636294	28636400	1	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28636294	28636400	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28636401	28636663	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28636664	28636864	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28636664	28636864	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28636865	28636964	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28636965	28637126	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28636965	28637126	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28637127	28637213	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28637214	28637393	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28637214	28637393	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28637394	28637538	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28637539	28637596	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28637539	28637596	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28637597	28637680	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28637681	28637731	0.98	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28637681	28637731	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28637732	28637834	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28637835	28637917	0.97	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28637835	28637917	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28637918	28638019	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28638020	28638107	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28638020	28638107	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28638108	28638189	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28638190	28638249	1	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28638190	28638249	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28638250	28638411	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28638412	28638486	1	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28638412	28638486	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28638487	28638582	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28638583	28638651	0.78	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28638583	28638651	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28638652	28638752	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28638753	28638868	1	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28638753	28638868	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28638869	28638952	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28638953	28639065	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28638953	28639065	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28639066	28639144	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28639145	28639224	1	+	2	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28639145	28639224	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28639225	28639309	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28639310	28639430	1	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28639310	28639430	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28639431	28639512	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28639513	28639579	1	+	2	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28639513	28639579	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	intron	28639580	28639662	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	CDS	28639663	28639786	1	+	1	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	exon	28639663	28639786	.	+	.	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
Phchi.S1	AUGUSTUS	stop_codon	28639787	28639789	.	+	0	transcript_id "Phchi.S1G450600.t1"; gene_id "Phchi.S1G450600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6176.t1 is derived from g3347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21318467	21318879	.	-	.	Phchi.S1G333500
Phchi.S1	AUGUSTUS	transcript	21318467	21318879	.	-	.	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	stop_codon	21318464	21318466	.	-	0	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	CDS	21318467	21318555	1	-	2	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	exon	21318467	21318555	.	-	.	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	intron	21318556	21318633	.	-	.	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	CDS	21318634	21318729	1	-	2	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	exon	21318634	21318729	.	-	.	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	intron	21318730	21318800	.	-	.	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	CDS	21318801	21318879	0.86	-	0	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	exon	21318801	21318879	.	-	.	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
Phchi.S1	AUGUSTUS	start_codon	21318877	21318879	.	-	0	transcript_id "Phchi.S1G333500.t1"; gene_id "Phchi.S1G333500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12633.t1 is derived from g15982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C86	AUGUSTUS	gene	20494	21158	.	+	.	Phchi.C86G000200
Phchi.C86	AUGUSTUS	transcript	20494	21158	.	+	.	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	start_codon	20494	20496	.	+	0	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	CDS	20494	20620	0.98	+	0	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	exon	20494	20620	.	+	.	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	intron	20621	20738	.	+	.	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	CDS	20739	20870	0.98	+	2	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	exon	20739	20870	.	+	.	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	intron	20871	20970	.	+	.	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	CDS	20971	21158	0.76	+	2	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	exon	20971	21158	.	+	.	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
Phchi.C86	AUGUSTUS	stop_codon	21159	21161	.	+	0	transcript_id "Phchi.C86G000200.t1"; gene_id "Phchi.C86G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9863.t1 is derived from g7039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44130370	44132028	.	+	.	Phchi.S1G702200
Phchi.S1	AUGUSTUS	transcript	44130370	44132028	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	start_codon	44130370	44130372	.	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44130370	44130653	0.89	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44130370	44130653	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	intron	44130654	44130740	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44130741	44130888	1	+	1	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44130741	44130888	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	intron	44130889	44130988	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44130989	44131156	1	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44130989	44131156	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	intron	44131157	44131245	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44131246	44131359	1	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44131246	44131359	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	intron	44131360	44131440	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44131441	44131547	1	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44131441	44131547	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	intron	44131548	44131636	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44131637	44131760	1	+	1	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44131637	44131760	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	intron	44131761	44131857	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	CDS	44131858	44132028	1	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	exon	44131858	44132028	.	+	.	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
Phchi.S1	AUGUSTUS	stop_codon	44132029	44132031	.	+	0	transcript_id "Phchi.S1G702200.t1"; gene_id "Phchi.S1G702200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7402.t1 is derived from g4574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28959681	28960277	.	-	.	Phchi.S1G456100
Phchi.S1	AUGUSTUS	transcript	28959681	28960277	.	-	.	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	stop_codon	28959678	28959680	.	-	0	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	CDS	28959681	28959768	1	-	1	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	exon	28959681	28959768	.	-	.	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	intron	28959769	28959865	.	-	.	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	CDS	28959866	28959972	1	-	0	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	exon	28959866	28959972	.	-	.	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	intron	28959973	28960238	.	-	.	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	CDS	28960239	28960277	1	-	0	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	exon	28960239	28960277	.	-	.	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
Phchi.S1	AUGUSTUS	start_codon	28960275	28960277	.	-	0	transcript_id "Phchi.S1G456100.t1"; gene_id "Phchi.S1G456100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10662.t1 is derived from g14712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1487345	1491203	.	-	.	Phchi.S4G024400
Phchi.S4	AUGUSTUS	transcript	1487345	1491203	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	stop_codon	1487342	1487344	.	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1487345	1488493	0.97	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1487345	1488493	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1488494	1488590	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1488591	1488719	1	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1488591	1488719	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1488720	1488807	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1488808	1488888	0.73	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1488808	1488888	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1488889	1489073	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1489074	1489178	0.95	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1489074	1489178	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1489179	1489255	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1489256	1489372	1	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1489256	1489372	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1489373	1489465	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1489466	1489606	1	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1489466	1489606	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1489607	1489700	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1489701	1489775	1	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1489701	1489775	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1489776	1489880	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1489881	1489982	0.93	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1489881	1489982	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1489983	1490080	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1490081	1490176	1	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1490081	1490176	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1490177	1490267	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1490268	1490330	0.96	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1490268	1490330	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1490331	1490448	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1490449	1490497	1	-	1	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1490449	1490497	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1490498	1490669	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1490670	1490746	1	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1490670	1490746	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1490747	1490829	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1490830	1490899	1	-	1	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1490830	1490899	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	intron	1490900	1491048	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	CDS	1491049	1491203	0.7	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	exon	1491049	1491203	.	-	.	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
Phchi.S4	AUGUSTUS	start_codon	1491201	1491203	.	-	0	transcript_id "Phchi.S4G024400.t1"; gene_id "Phchi.S4G024400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9221.t1 is derived from g6396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40467385	40467926	.	-	.	Phchi.S1G638000
Phchi.S1	AUGUSTUS	transcript	40467385	40467926	.	-	.	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	stop_codon	40467382	40467384	.	-	0	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	CDS	40467385	40467552	0.93	-	0	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	exon	40467385	40467552	.	-	.	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	intron	40467553	40467698	.	-	.	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	CDS	40467699	40467926	0.94	-	0	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	exon	40467699	40467926	.	-	.	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
Phchi.S1	AUGUSTUS	start_codon	40467924	40467926	.	-	0	transcript_id "Phchi.S1G638000.t1"; gene_id "Phchi.S1G638000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10447.t1 is derived from g14496.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	369422	371516	.	-	.	Phchi.S4G002900
Phchi.S4	AUGUSTUS	transcript	369422	371516	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	stop_codon	369419	369421	.	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	369422	369583	0.63	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	369422	369583	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	intron	369584	369736	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	369737	369871	1	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	369737	369871	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	intron	369872	369976	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	369977	370120	0.86	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	369977	370120	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	intron	370121	370201	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	370202	370441	1	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	370202	370441	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	intron	370442	370690	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	370691	370729	0.82	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	370691	370729	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	intron	370730	370850	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	370851	370922	0.49	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	370851	370922	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	intron	370923	371183	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	CDS	371184	371516	0.75	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	exon	371184	371516	.	-	.	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
Phchi.S4	AUGUSTUS	start_codon	371514	371516	.	-	0	transcript_id "Phchi.S4G002900.t1"; gene_id "Phchi.S4G002900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13571.t1 is derived from g12038.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7542947	7546333	.	-	.	Phchi.S3G089000
Phchi.S3	AUGUSTUS	transcript	7542947	7546333	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	stop_codon	7542944	7542946	.	-	0	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7542947	7543459	0.91	-	0	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7542947	7543459	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7543460	7543534	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7543535	7543819	1	-	0	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7543535	7543819	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7543820	7543948	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7543949	7544046	1	-	2	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7543949	7544046	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7544047	7544131	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7544132	7544181	1	-	1	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7544132	7544181	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7544182	7544274	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7544275	7544403	1	-	1	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7544275	7544403	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7544404	7544655	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7544656	7544760	1	-	1	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7544656	7544760	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7544761	7544899	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7544900	7545028	1	-	1	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7544900	7545028	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7545029	7545349	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7545350	7545611	0.96	-	2	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7545350	7545611	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7545612	7545733	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7545734	7545878	0.96	-	0	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7545734	7545878	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7545879	7545994	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7545995	7546086	0.99	-	2	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7545995	7546086	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	intron	7546087	7546308	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	CDS	7546309	7546333	0.96	-	0	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	exon	7546309	7546333	.	-	.	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
Phchi.S3	AUGUSTUS	start_codon	7546331	7546333	.	-	0	transcript_id "Phchi.S3G089000.t1"; gene_id "Phchi.S3G089000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15999.t1 is derived from g15977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C244	AUGUSTUS	gene	11178	11641	.	-	.	Phchi.C244G000300
Phchi.C244	AUGUSTUS	transcript	11178	11641	.	-	.	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	stop_codon	11175	11177	.	-	0	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	CDS	11178	11390	0.98	-	0	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	exon	11178	11390	.	-	.	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	intron	11391	11623	.	-	.	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	CDS	11624	11641	0.98	-	0	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	exon	11624	11641	.	-	.	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
Phchi.C244	AUGUSTUS	start_codon	11639	11641	.	-	0	transcript_id "Phchi.C244G000300.t1"; gene_id "Phchi.C244G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11907.t1 is derived from g15959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9248281	9248718	.	-	.	Phchi.S4G148900
Phchi.S4	AUGUSTUS	transcript	9248281	9248718	.	-	.	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	stop_codon	9248278	9248280	.	-	0	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	CDS	9248281	9248400	0.79	-	0	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	exon	9248281	9248400	.	-	.	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	intron	9248401	9248580	.	-	.	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	CDS	9248581	9248718	1	-	0	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	exon	9248581	9248718	.	-	.	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
Phchi.S4	AUGUSTUS	start_codon	9248716	9248718	.	-	0	transcript_id "Phchi.S4G148900.t1"; gene_id "Phchi.S4G148900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4100.t1 is derived from g1269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7819394	7819795	.	-	.	Phchi.S1G125900
Phchi.S1	AUGUSTUS	transcript	7819394	7819795	.	-	.	transcript_id "Phchi.S1G125900.t1"; gene_id "Phchi.S1G125900"
Phchi.S1	AUGUSTUS	stop_codon	7819391	7819393	.	-	0	transcript_id "Phchi.S1G125900.t1"; gene_id "Phchi.S1G125900"
Phchi.S1	AUGUSTUS	CDS	7819394	7819795	0.95	-	0	transcript_id "Phchi.S1G125900.t1"; gene_id "Phchi.S1G125900"
Phchi.S1	AUGUSTUS	exon	7819394	7819795	.	-	.	transcript_id "Phchi.S1G125900.t1"; gene_id "Phchi.S1G125900"
Phchi.S1	AUGUSTUS	start_codon	7819793	7819795	.	-	0	transcript_id "Phchi.S1G125900.t1"; gene_id "Phchi.S1G125900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5289.t1 is derived from g2459.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16033715	16036317	.	+	.	Phchi.S1G244800
Phchi.S1	AUGUSTUS	transcript	16033715	16036317	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	start_codon	16033715	16033717	.	+	0	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16033715	16033862	0.99	+	0	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16033715	16033862	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16033863	16033961	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16033962	16034073	1	+	2	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16033962	16034073	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16034074	16034285	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16034286	16034294	0.93	+	1	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16034286	16034294	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16034295	16034377	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16034378	16034554	0.99	+	1	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16034378	16034554	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16034555	16034766	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16034767	16034893	1	+	1	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16034767	16034893	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16034894	16035057	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16035058	16035094	0.78	+	0	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16035058	16035094	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16035095	16035378	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16035379	16035429	0.76	+	2	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16035379	16035429	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16035430	16035526	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16035527	16035560	0.51	+	2	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16035527	16035560	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16035561	16035762	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16035763	16035824	0.51	+	1	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16035763	16035824	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	intron	16035825	16035928	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	CDS	16035929	16036317	0.99	+	2	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	exon	16035929	16036317	.	+	.	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
Phchi.S1	AUGUSTUS	stop_codon	16036318	16036320	.	+	0	transcript_id "Phchi.S1G244800.t1"; gene_id "Phchi.S1G244800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15644.t1 is derived from g14113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20462707	20464248	.	-	.	Phchi.S3G296300
Phchi.S3	AUGUSTUS	transcript	20462707	20464248	.	-	.	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	stop_codon	20462704	20462706	.	-	0	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	CDS	20462707	20463515	0.76	-	2	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	exon	20462707	20463515	.	-	.	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	intron	20463516	20463623	.	-	.	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	CDS	20463624	20464248	0.49	-	0	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	exon	20463624	20464248	.	-	.	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
Phchi.S3	AUGUSTUS	start_codon	20464246	20464248	.	-	0	transcript_id "Phchi.S3G296300.t1"; gene_id "Phchi.S3G296300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5966.t1 is derived from g3137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20112848	20114042	.	+	.	Phchi.S1G312500
Phchi.S1	AUGUSTUS	transcript	20112848	20114042	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	start_codon	20112848	20112850	.	+	0	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	CDS	20112848	20112949	0.51	+	0	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	exon	20112848	20112949	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	intron	20112950	20113102	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	CDS	20113103	20113210	0.55	+	0	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	exon	20113103	20113210	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	intron	20113211	20113575	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	CDS	20113576	20113750	1	+	0	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	exon	20113576	20113750	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	intron	20113751	20113848	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	CDS	20113849	20114042	1	+	2	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	exon	20113849	20114042	.	+	.	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
Phchi.S1	AUGUSTUS	stop_codon	20114043	20114045	.	+	0	transcript_id "Phchi.S1G312500.t1"; gene_id "Phchi.S1G312500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13588.t1 is derived from g12055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7604262	7606275	.	-	.	Phchi.S3G090700
Phchi.S3	AUGUSTUS	transcript	7604262	7606275	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	stop_codon	7604259	7604261	.	-	0	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7604262	7604319	0.46	-	1	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7604262	7604319	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7604320	7604417	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7604418	7605181	0.31	-	0	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7604418	7605181	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7605182	7605267	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7605268	7605388	0.39	-	1	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7605268	7605388	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7605389	7605468	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7605469	7605480	0.47	-	1	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7605469	7605480	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7605481	7605580	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7605581	7605611	0.41	-	2	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7605581	7605611	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7605612	7605906	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7605907	7605926	0.53	-	1	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7605907	7605926	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7605927	7606023	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7606024	7606104	0.83	-	1	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7606024	7606104	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	intron	7606105	7606186	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	CDS	7606187	7606275	0.66	-	0	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	exon	7606187	7606275	.	-	.	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
Phchi.S3	AUGUSTUS	start_codon	7606273	7606275	.	-	0	transcript_id "Phchi.S3G090700.t1"; gene_id "Phchi.S3G090700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11052.t1 is derived from g15102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3833700	3834116	.	-	.	Phchi.S4G063400
Phchi.S4	AUGUSTUS	transcript	3833700	3834116	.	-	.	transcript_id "Phchi.S4G063400.t1"; gene_id "Phchi.S4G063400"
Phchi.S4	AUGUSTUS	stop_codon	3833697	3833699	.	-	0	transcript_id "Phchi.S4G063400.t1"; gene_id "Phchi.S4G063400"
Phchi.S4	AUGUSTUS	CDS	3833700	3834116	0.75	-	0	transcript_id "Phchi.S4G063400.t1"; gene_id "Phchi.S4G063400"
Phchi.S4	AUGUSTUS	exon	3833700	3834116	.	-	.	transcript_id "Phchi.S4G063400.t1"; gene_id "Phchi.S4G063400"
Phchi.S4	AUGUSTUS	start_codon	3834114	3834116	.	-	0	transcript_id "Phchi.S4G063400.t1"; gene_id "Phchi.S4G063400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5048.t1 is derived from g2218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14287224	14288037	.	+	.	Phchi.S1G220700
Phchi.S1	AUGUSTUS	transcript	14287224	14288037	.	+	.	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	start_codon	14287224	14287226	.	+	0	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	CDS	14287224	14287916	0.47	+	0	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	exon	14287224	14287916	.	+	.	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	intron	14287917	14288001	.	+	.	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	CDS	14288002	14288037	0.99	+	0	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	exon	14288002	14288037	.	+	.	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
Phchi.S1	AUGUSTUS	stop_codon	14288038	14288040	.	+	0	transcript_id "Phchi.S1G220700.t1"; gene_id "Phchi.S1G220700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10123.t1 is derived from g7299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45844150	45844659	.	-	.	Phchi.S1G728200
Phchi.S1	AUGUSTUS	transcript	45844150	45844659	.	-	.	transcript_id "Phchi.S1G728200.t1"; gene_id "Phchi.S1G728200"
Phchi.S1	AUGUSTUS	stop_codon	45844147	45844149	.	-	0	transcript_id "Phchi.S1G728200.t1"; gene_id "Phchi.S1G728200"
Phchi.S1	AUGUSTUS	CDS	45844150	45844659	0.66	-	0	transcript_id "Phchi.S1G728200.t1"; gene_id "Phchi.S1G728200"
Phchi.S1	AUGUSTUS	exon	45844150	45844659	.	-	.	transcript_id "Phchi.S1G728200.t1"; gene_id "Phchi.S1G728200"
Phchi.S1	AUGUSTUS	start_codon	45844657	45844659	.	-	0	transcript_id "Phchi.S1G728200.t1"; gene_id "Phchi.S1G728200"
# This transcript jg4024.t2 is derived from g1193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4025.t1 is derived from g1194.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7219708	7224328	.	+	.	Phchi.S1G118400
Phchi.S1	AUGUSTUS	transcript	7219708	7224328	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	start_codon	7219708	7219710	.	+	0	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7219708	7220119	0.98	+	0	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7219708	7220119	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7220120	7220200	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7220201	7220391	1	+	2	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7220201	7220391	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7220392	7220534	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7220535	7220949	0.97	+	0	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7220535	7220949	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7220950	7221091	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7221092	7221104	1	+	2	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7221092	7221104	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7221105	7221340	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7221341	7221724	1	+	1	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7221341	7221724	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7221725	7221844	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7221845	7223195	0.95	+	1	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7221845	7223195	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223196	7223303	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7223304	7223539	0.96	+	0	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7223304	7223539	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223540	7223615	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7223616	7223751	1	+	1	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7223616	7223751	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223752	7223854	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7223855	7223931	1	+	0	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7223855	7223931	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223932	7224028	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7224029	7224135	1	+	1	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7224029	7224135	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7224136	7224230	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7224231	7224328	1	+	2	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7224231	7224328	.	+	.	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	stop_codon	7224329	7224331	.	+	0	transcript_id "Phchi.S1G118400.t1"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	transcript	7219708	7224328	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	start_codon	7219708	7219710	.	+	0	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7219708	7220119	1	+	0	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7219708	7220119	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7220120	7220200	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7220201	7220391	1	+	2	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7220201	7220391	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7220392	7220534	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7220535	7220968	0.34	+	0	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7220535	7220968	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7220969	7221039	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7221040	7221104	0.73	+	1	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7221040	7221104	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7221105	7221315	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7221316	7221724	1	+	2	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7221316	7221724	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7221725	7221844	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7221845	7223195	0.94	+	1	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7221845	7223195	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223196	7223303	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7223304	7223539	0.97	+	0	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7223304	7223539	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223540	7223615	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7223616	7223751	0.98	+	1	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7223616	7223751	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223752	7223854	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7223855	7223931	1	+	0	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7223855	7223931	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7223932	7224028	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7224029	7224135	1	+	1	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7224029	7224135	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	intron	7224136	7224230	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	CDS	7224231	7224328	0.98	+	2	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	exon	7224231	7224328	.	+	.	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
Phchi.S1	AUGUSTUS	stop_codon	7224329	7224331	.	+	0	transcript_id "Phchi.S1G118400.t2"; gene_id "Phchi.S1G118400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3918.t1 is derived from g1087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6428998	6430826	.	-	.	Phchi.S1G107700
Phchi.S1	AUGUSTUS	transcript	6428998	6430826	.	-	.	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	stop_codon	6428995	6428997	.	-	0	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	CDS	6428998	6429016	1	-	1	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	exon	6428998	6429016	.	-	.	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	intron	6429017	6429108	.	-	.	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	CDS	6429109	6430826	0.89	-	0	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	exon	6429109	6430826	.	-	.	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
Phchi.S1	AUGUSTUS	start_codon	6430824	6430826	.	-	0	transcript_id "Phchi.S1G107700.t1"; gene_id "Phchi.S1G107700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg914.t1 is derived from g10696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6413260	6413614	.	+	.	Phchi.S6G087300
Phchi.S6	AUGUSTUS	transcript	6413260	6413614	.	+	.	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	start_codon	6413260	6413262	.	+	0	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	CDS	6413260	6413409	1	+	0	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	exon	6413260	6413409	.	+	.	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	intron	6413410	6413491	.	+	.	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	CDS	6413492	6413614	0.71	+	0	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	exon	6413492	6413614	.	+	.	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
Phchi.S6	AUGUSTUS	stop_codon	6413615	6413617	.	+	0	transcript_id "Phchi.S6G087300.t1"; gene_id "Phchi.S6G087300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9482.t1 is derived from g6658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41965290	41966105	.	+	.	Phchi.S1G664100
Phchi.S1	AUGUSTUS	transcript	41965290	41966105	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	start_codon	41965290	41965292	.	+	0	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	CDS	41965290	41965318	1	+	0	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	exon	41965290	41965318	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	intron	41965319	41965594	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	CDS	41965595	41965630	1	+	1	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	exon	41965595	41965630	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	intron	41965631	41965723	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	CDS	41965724	41965952	1	+	1	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	exon	41965724	41965952	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	intron	41965953	41966066	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	CDS	41966067	41966105	1	+	0	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	exon	41966067	41966105	.	+	.	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
Phchi.S1	AUGUSTUS	stop_codon	41966106	41966108	.	+	0	transcript_id "Phchi.S1G664100.t1"; gene_id "Phchi.S1G664100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15024.t1 is derived from g13492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16585270	16586091	.	+	.	Phchi.S3G234300
Phchi.S3	AUGUSTUS	transcript	16585270	16586091	.	+	.	transcript_id "Phchi.S3G234300.t1"; gene_id "Phchi.S3G234300"
Phchi.S3	AUGUSTUS	start_codon	16585270	16585272	.	+	0	transcript_id "Phchi.S3G234300.t1"; gene_id "Phchi.S3G234300"
Phchi.S3	AUGUSTUS	CDS	16585270	16586091	0.95	+	0	transcript_id "Phchi.S3G234300.t1"; gene_id "Phchi.S3G234300"
Phchi.S3	AUGUSTUS	exon	16585270	16586091	.	+	.	transcript_id "Phchi.S3G234300.t1"; gene_id "Phchi.S3G234300"
Phchi.S3	AUGUSTUS	stop_codon	16586092	16586094	.	+	0	transcript_id "Phchi.S3G234300.t1"; gene_id "Phchi.S3G234300"
# This transcript jg3766.t2 is derived from g935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3767.t1 is derived from g936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5610948	5613899	.	-	.	Phchi.S1G092600
Phchi.S1	AUGUSTUS	transcript	5610948	5613899	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	stop_codon	5610945	5610947	.	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5610948	5611215	1	-	1	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5610948	5611215	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611216	5611302	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5611303	5611557	0.65	-	1	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5611303	5611557	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611558	5611653	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5611654	5611811	0.8	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5611654	5611811	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611812	5611900	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5611901	5611975	1	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5611901	5611975	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611976	5612069	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612070	5612127	1	-	1	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612070	5612127	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612128	5612281	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612282	5612319	1	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612282	5612319	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612320	5612441	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612442	5612542	1	-	2	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612442	5612542	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612543	5612620	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612621	5612680	1	-	2	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612621	5612680	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612681	5612855	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612856	5612952	1	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612856	5612952	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612953	5613052	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613053	5613197	1	-	1	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613053	5613197	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5613198	5613327	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613328	5613506	1	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613328	5613506	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5613507	5613602	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613603	5613668	0.73	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613603	5613668	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5613669	5613776	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613777	5613899	0.69	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613777	5613899	.	-	.	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	start_codon	5613897	5613899	.	-	0	transcript_id "Phchi.S1G092600.t1"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	transcript	5610948	5613899	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	stop_codon	5610945	5610947	.	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5610948	5611215	1	-	1	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5610948	5611215	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611216	5611302	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5611303	5611557	0.69	-	1	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5611303	5611557	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611558	5611653	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5611654	5611811	0.79	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5611654	5611811	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611812	5611900	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5611901	5611975	1	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5611901	5611975	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5611976	5612069	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612070	5612127	1	-	1	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612070	5612127	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612128	5612210	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612211	5612227	0.61	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612211	5612227	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612228	5612441	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612442	5612542	0.98	-	2	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612442	5612542	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612543	5612620	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612621	5612680	1	-	2	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612621	5612680	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612681	5612855	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5612856	5612952	1	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5612856	5612952	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5612953	5613052	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613053	5613197	1	-	1	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613053	5613197	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5613198	5613327	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613328	5613506	1	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613328	5613506	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5613507	5613602	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613603	5613668	0.81	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613603	5613668	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	intron	5613669	5613776	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	CDS	5613777	5613899	0.7	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	exon	5613777	5613899	.	-	.	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
Phchi.S1	AUGUSTUS	start_codon	5613897	5613899	.	-	0	transcript_id "Phchi.S1G092600.t2"; gene_id "Phchi.S1G092600"
# This transcript jg15406.t2 is derived from g13874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15407.t1 is derived from g13875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18855724	18860902	.	+	.	Phchi.S3G272600
Phchi.S3	AUGUSTUS	transcript	18855724	18860902	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	start_codon	18855724	18855726	.	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18855724	18856079	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18855724	18856079	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18856080	18856171	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18856172	18856649	1	+	1	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18856172	18856649	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18856650	18856794	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18856795	18857394	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18856795	18857394	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18857395	18857486	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18857487	18857927	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18857487	18857927	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18857928	18858009	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18858010	18858113	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18858010	18858113	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18858114	18858333	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18858334	18858835	1	+	1	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18858334	18858835	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18858836	18858916	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18858917	18859115	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18858917	18859115	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18859116	18859228	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18859229	18859269	1	+	2	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18859229	18859269	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18859270	18859365	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18859366	18859434	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18859366	18859434	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18859435	18859523	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18859524	18859624	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18859524	18859624	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18859625	18859744	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18859745	18859823	1	+	1	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18859745	18859823	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18859824	18859905	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18859906	18860004	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18859906	18860004	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18860005	18860117	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18860118	18860186	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18860118	18860186	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18860187	18860267	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18860268	18860317	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18860268	18860317	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18860318	18860413	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18860414	18860495	1	+	1	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18860414	18860495	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18860496	18860593	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18860594	18860688	1	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18860594	18860688	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	intron	18860689	18860784	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	CDS	18860785	18860902	0.91	+	1	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	exon	18860785	18860902	.	+	.	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
Phchi.S3	AUGUSTUS	stop_codon	18860903	18860905	.	+	0	transcript_id "Phchi.S3G272600.t1"; gene_id "Phchi.S3G272600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2859.t1 is derived from g28.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	106378	110088	.	-	.	Phchi.S1G001800
Phchi.S1	AUGUSTUS	transcript	106378	110088	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	stop_codon	106375	106377	.	-	0	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	CDS	106378	107441	0.82	-	2	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	exon	106378	107441	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	intron	107442	107554	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	CDS	107555	107764	0.93	-	2	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	exon	107555	107764	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	intron	107765	108009	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	CDS	108010	109365	0.43	-	2	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	exon	108010	109365	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	intron	109366	109546	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	CDS	109547	109587	0.65	-	1	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	exon	109547	109587	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	intron	109588	109730	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	CDS	109731	109979	0.58	-	1	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	exon	109731	109979	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	intron	109980	110062	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	CDS	110063	110088	0.93	-	0	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	exon	110063	110088	.	-	.	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
Phchi.S1	AUGUSTUS	start_codon	110086	110088	.	-	0	transcript_id "Phchi.S1G001800.t1"; gene_id "Phchi.S1G001800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6876.t1 is derived from g4048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25760858	25764133	.	-	.	Phchi.S1G403500
Phchi.S1	AUGUSTUS	transcript	25760858	25764133	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	stop_codon	25760855	25760857	.	-	0	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25760858	25761402	1	-	2	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25760858	25761402	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25761403	25761484	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25761485	25761683	1	-	0	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25761485	25761683	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25761684	25761796	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25761797	25761911	0.95	-	1	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25761797	25761911	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25761912	25762036	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25762037	25762255	0.56	-	1	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25762037	25762255	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25762256	25762391	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25762392	25762450	1	-	0	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25762392	25762450	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25762451	25762555	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25762556	25763051	0.95	-	1	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25762556	25763051	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25763052	25763161	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25763162	25763255	0.99	-	2	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25763162	25763255	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25763256	25763357	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25763358	25763513	0.95	-	2	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25763358	25763513	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25763514	25763612	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25763613	25763710	1	-	1	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25763613	25763710	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25763711	25763844	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25763845	25763945	0.86	-	0	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25763845	25763945	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	intron	25763946	25764034	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	CDS	25764035	25764133	0.6	-	0	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	exon	25764035	25764133	.	-	.	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
Phchi.S1	AUGUSTUS	start_codon	25764131	25764133	.	-	0	transcript_id "Phchi.S1G403500.t1"; gene_id "Phchi.S1G403500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2201.t1 is derived from g9121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5405678	5407509	.	-	.	Phchi.S5G081000
Phchi.S5	AUGUSTUS	transcript	5405678	5407509	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	stop_codon	5405675	5405677	.	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5405678	5405752	0.53	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5405678	5405752	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5405753	5405868	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5405869	5405943	0.94	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5405869	5405943	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5405944	5406037	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5406038	5406112	1	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5406038	5406112	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5406113	5406190	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5406191	5406526	0.64	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5406191	5406526	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5406527	5406669	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5406670	5406881	1	-	2	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5406670	5406881	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5406882	5406979	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5406980	5407131	0.92	-	1	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5406980	5407131	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5407132	5407203	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5407204	5407238	0.86	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5407204	5407238	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	intron	5407239	5407320	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	CDS	5407321	5407509	0.4	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	exon	5407321	5407509	.	-	.	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
Phchi.S5	AUGUSTUS	start_codon	5407507	5407509	.	-	0	transcript_id "Phchi.S5G081000.t1"; gene_id "Phchi.S5G081000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4613.t1 is derived from g1783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11417180	11417812	.	+	.	Phchi.S1G177200
Phchi.S1	AUGUSTUS	transcript	11417180	11417812	.	+	.	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	start_codon	11417180	11417182	.	+	0	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	CDS	11417180	11417421	0.81	+	0	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	exon	11417180	11417421	.	+	.	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	intron	11417422	11417634	.	+	.	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	CDS	11417635	11417812	0.89	+	1	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	exon	11417635	11417812	.	+	.	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
Phchi.S1	AUGUSTUS	stop_codon	11417813	11417815	.	+	0	transcript_id "Phchi.S1G177200.t1"; gene_id "Phchi.S1G177200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12970.t1 is derived from g11435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3389017	3392139	.	+	.	Phchi.S3G028900
Phchi.S3	AUGUSTUS	transcript	3389017	3392139	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	start_codon	3389017	3389019	.	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3389017	3389523	0.81	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3389017	3389523	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3389524	3389605	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3389606	3389713	1	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3389606	3389713	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3389714	3389791	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3389792	3389895	1	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3389792	3389895	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3389896	3390114	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3390115	3390207	1	+	1	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3390115	3390207	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3390208	3390337	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3390338	3390404	1	+	1	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3390338	3390404	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3390405	3390502	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3390503	3390568	1	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3390503	3390568	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3390569	3390691	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3390692	3390784	0.98	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3390692	3390784	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3390785	3390893	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3390894	3390959	0.93	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3390894	3390959	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3390960	3391050	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3391051	3391145	1	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3391051	3391145	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3391146	3391331	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3391332	3391418	1	+	1	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3391332	3391418	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3391419	3391559	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3391560	3391635	1	+	1	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3391560	3391635	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3391636	3391731	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3391732	3391875	0.96	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3391732	3391875	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	intron	3391876	3391977	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	CDS	3391978	3392139	0.96	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	exon	3391978	3392139	.	+	.	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
Phchi.S3	AUGUSTUS	stop_codon	3392140	3392142	.	+	0	transcript_id "Phchi.S3G028900.t1"; gene_id "Phchi.S3G028900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1539.t1 is derived from g8458.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1673646	1675571	.	-	.	Phchi.S5G014800
Phchi.S5	AUGUSTUS	transcript	1673646	1675571	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	stop_codon	1673643	1673645	.	-	0	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	CDS	1673646	1674159	0.88	-	1	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	exon	1673646	1674159	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	intron	1674160	1674666	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	CDS	1674667	1674796	0.65	-	2	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	exon	1674667	1674796	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	intron	1674797	1675087	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	CDS	1675088	1675273	0.91	-	2	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	exon	1675088	1675273	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	intron	1675274	1675357	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	CDS	1675358	1675571	0.21	-	0	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	exon	1675358	1675571	.	-	.	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	start_codon	1675569	1675571	.	-	0	transcript_id "Phchi.S5G014800.t1"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	transcript	1673646	1674116	.	-	.	transcript_id "Phchi.S5G014800.t2"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	stop_codon	1673643	1673645	.	-	0	transcript_id "Phchi.S5G014800.t2"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	CDS	1673646	1674116	0.9	-	0	transcript_id "Phchi.S5G014800.t2"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	exon	1673646	1674116	.	-	.	transcript_id "Phchi.S5G014800.t2"; gene_id "Phchi.S5G014800"
Phchi.S5	AUGUSTUS	start_codon	1674114	1674116	.	-	0	transcript_id "Phchi.S5G014800.t2"; gene_id "Phchi.S5G014800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13752.t1 is derived from g12219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8701320	8706030	.	+	.	Phchi.S3G107100
Phchi.S3	AUGUSTUS	transcript	8701320	8706030	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	start_codon	8701320	8701322	.	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8701320	8702033	0.39	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8701320	8702033	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8702034	8702503	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8702504	8703742	0.35	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8702504	8703742	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8703743	8703834	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8703835	8704202	0.17	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8703835	8704202	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8704203	8704304	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8704305	8704446	0.87	+	1	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8704305	8704446	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8704447	8704635	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8704636	8704743	1	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8704636	8704743	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8704744	8704896	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8704897	8705109	0.99	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8704897	8705109	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8705110	8705189	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8705190	8705300	1	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8705190	8705300	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8705301	8705396	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8705397	8705591	1	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8705397	8705591	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8705592	8705670	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8705671	8705845	1	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8705671	8705845	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	intron	8705846	8705992	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	CDS	8705993	8706030	1	+	2	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	exon	8705993	8706030	.	+	.	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
Phchi.S3	AUGUSTUS	stop_codon	8706031	8706033	.	+	0	transcript_id "Phchi.S3G107100.t1"; gene_id "Phchi.S3G107100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11848.t1 is derived from g15900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8575854	8577745	.	-	.	Phchi.S4G143000
Phchi.S4	AUGUSTUS	transcript	8575854	8577745	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	stop_codon	8575851	8575853	.	-	0	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	CDS	8575854	8576152	0.99	-	2	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	exon	8575854	8576152	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	intron	8576153	8576263	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	CDS	8576264	8576378	1	-	0	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	exon	8576264	8576378	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	intron	8576379	8576481	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	CDS	8576482	8577219	0.58	-	0	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	exon	8576482	8577219	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	intron	8577220	8577320	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	CDS	8577321	8577553	0.94	-	2	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	exon	8577321	8577553	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	intron	8577554	8577672	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	CDS	8577673	8577745	0.96	-	0	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	exon	8577673	8577745	.	-	.	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
Phchi.S4	AUGUSTUS	start_codon	8577743	8577745	.	-	0	transcript_id "Phchi.S4G143000.t1"; gene_id "Phchi.S4G143000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12282.t1 is derived from g7958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8479313	8479787	.	-	.	Phchi.S2G036200
Phchi.S2	AUGUSTUS	transcript	8479313	8479787	.	-	.	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	stop_codon	8479310	8479312	.	-	0	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	CDS	8479313	8479462	0.7	-	0	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	exon	8479313	8479462	.	-	.	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	intron	8479463	8479556	.	-	.	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	CDS	8479557	8479633	1	-	2	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	exon	8479557	8479633	.	-	.	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	intron	8479634	8479729	.	-	.	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	CDS	8479730	8479787	0.58	-	0	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	exon	8479730	8479787	.	-	.	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
Phchi.S2	AUGUSTUS	start_codon	8479785	8479787	.	-	0	transcript_id "Phchi.S2G036200.t1"; gene_id "Phchi.S2G036200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5527.t1 is derived from g2697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17419123	17420094	.	+	.	Phchi.S1G268600
Phchi.S1	AUGUSTUS	transcript	17419123	17420094	.	+	.	transcript_id "Phchi.S1G268600.t1"; gene_id "Phchi.S1G268600"
Phchi.S1	AUGUSTUS	start_codon	17419123	17419125	.	+	0	transcript_id "Phchi.S1G268600.t1"; gene_id "Phchi.S1G268600"
Phchi.S1	AUGUSTUS	CDS	17419123	17420094	0.99	+	0	transcript_id "Phchi.S1G268600.t1"; gene_id "Phchi.S1G268600"
Phchi.S1	AUGUSTUS	exon	17419123	17420094	.	+	.	transcript_id "Phchi.S1G268600.t1"; gene_id "Phchi.S1G268600"
Phchi.S1	AUGUSTUS	stop_codon	17420095	17420097	.	+	0	transcript_id "Phchi.S1G268600.t1"; gene_id "Phchi.S1G268600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11059.t1 is derived from g15109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3923711	3924682	.	+	.	Phchi.S4G064100
Phchi.S4	AUGUSTUS	transcript	3923711	3924682	.	+	.	transcript_id "Phchi.S4G064100.t1"; gene_id "Phchi.S4G064100"
Phchi.S4	AUGUSTUS	start_codon	3923711	3923713	.	+	0	transcript_id "Phchi.S4G064100.t1"; gene_id "Phchi.S4G064100"
Phchi.S4	AUGUSTUS	CDS	3923711	3924682	1	+	0	transcript_id "Phchi.S4G064100.t1"; gene_id "Phchi.S4G064100"
Phchi.S4	AUGUSTUS	exon	3923711	3924682	.	+	.	transcript_id "Phchi.S4G064100.t1"; gene_id "Phchi.S4G064100"
Phchi.S4	AUGUSTUS	stop_codon	3924683	3924685	.	+	0	transcript_id "Phchi.S4G064100.t1"; gene_id "Phchi.S4G064100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg170.t1 is derived from g9952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	998249	999022	.	-	.	Phchi.S6G012900
Phchi.S6	AUGUSTUS	transcript	998249	999022	.	-	.	transcript_id "Phchi.S6G012900.t1"; gene_id "Phchi.S6G012900"
Phchi.S6	AUGUSTUS	stop_codon	998246	998248	.	-	0	transcript_id "Phchi.S6G012900.t1"; gene_id "Phchi.S6G012900"
Phchi.S6	AUGUSTUS	CDS	998249	999022	0.48	-	0	transcript_id "Phchi.S6G012900.t1"; gene_id "Phchi.S6G012900"
Phchi.S6	AUGUSTUS	exon	998249	999022	.	-	.	transcript_id "Phchi.S6G012900.t1"; gene_id "Phchi.S6G012900"
Phchi.S6	AUGUSTUS	start_codon	999020	999022	.	-	0	transcript_id "Phchi.S6G012900.t1"; gene_id "Phchi.S6G012900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3970.t1 is derived from g1139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6796821	6797845	.	+	.	Phchi.S1G112900
Phchi.S1	AUGUSTUS	transcript	6796821	6797845	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	start_codon	6796821	6796823	.	+	0	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	CDS	6796821	6796927	0.32	+	0	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	exon	6796821	6796927	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	intron	6796928	6797066	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	CDS	6797067	6797159	0.31	+	1	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	exon	6797067	6797159	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	intron	6797160	6797367	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	CDS	6797368	6797388	0.51	+	1	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	exon	6797368	6797388	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	intron	6797389	6797560	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	CDS	6797561	6797600	0.73	+	1	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	exon	6797561	6797600	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	intron	6797601	6797797	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	CDS	6797798	6797845	0.82	+	0	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	exon	6797798	6797845	.	+	.	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
Phchi.S1	AUGUSTUS	stop_codon	6797846	6797848	.	+	0	transcript_id "Phchi.S1G112900.t1"; gene_id "Phchi.S1G112900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2079.t1 is derived from g8999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4756489	4757136	.	-	.	Phchi.S5G068800
Phchi.S5	AUGUSTUS	transcript	4756489	4757136	.	-	.	transcript_id "Phchi.S5G068800.t1"; gene_id "Phchi.S5G068800"
Phchi.S5	AUGUSTUS	stop_codon	4756486	4756488	.	-	0	transcript_id "Phchi.S5G068800.t1"; gene_id "Phchi.S5G068800"
Phchi.S5	AUGUSTUS	CDS	4756489	4757136	0.7	-	0	transcript_id "Phchi.S5G068800.t1"; gene_id "Phchi.S5G068800"
Phchi.S5	AUGUSTUS	exon	4756489	4757136	.	-	.	transcript_id "Phchi.S5G068800.t1"; gene_id "Phchi.S5G068800"
Phchi.S5	AUGUSTUS	start_codon	4757134	4757136	.	-	0	transcript_id "Phchi.S5G068800.t1"; gene_id "Phchi.S5G068800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3974.t1 is derived from g1143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6817540	6821701	.	+	.	Phchi.S1G113300
Phchi.S1	AUGUSTUS	transcript	6817540	6821701	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	start_codon	6817540	6817542	.	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6817540	6817562	1	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6817540	6817562	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6817563	6817768	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6817769	6817949	1	+	1	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6817769	6817949	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6817950	6818040	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6818041	6818121	1	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6818041	6818121	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6818122	6818213	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6818214	6818411	0.93	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6818214	6818411	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6818412	6818534	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6818535	6818684	0.92	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6818535	6818684	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6818685	6818794	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6818795	6819490	0.99	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6818795	6819490	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6819491	6819587	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6819588	6819682	0.85	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6819588	6819682	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6819683	6819901	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6819902	6820585	0.86	+	1	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6819902	6820585	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6820586	6820718	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6820719	6820860	0.99	+	1	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6820719	6820860	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	intron	6820861	6820960	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	CDS	6820961	6821701	0.46	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	exon	6820961	6821701	.	+	.	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
Phchi.S1	AUGUSTUS	stop_codon	6821702	6821704	.	+	0	transcript_id "Phchi.S1G113300.t1"; gene_id "Phchi.S1G113300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4707.t1 is derived from g1877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12415903	12416781	.	+	.	Phchi.S1G186600
Phchi.S1	AUGUSTUS	transcript	12415903	12416781	.	+	.	transcript_id "Phchi.S1G186600.t1"; gene_id "Phchi.S1G186600"
Phchi.S1	AUGUSTUS	start_codon	12415903	12415905	.	+	0	transcript_id "Phchi.S1G186600.t1"; gene_id "Phchi.S1G186600"
Phchi.S1	AUGUSTUS	CDS	12415903	12416781	0.67	+	0	transcript_id "Phchi.S1G186600.t1"; gene_id "Phchi.S1G186600"
Phchi.S1	AUGUSTUS	exon	12415903	12416781	.	+	.	transcript_id "Phchi.S1G186600.t1"; gene_id "Phchi.S1G186600"
Phchi.S1	AUGUSTUS	stop_codon	12416782	12416784	.	+	0	transcript_id "Phchi.S1G186600.t1"; gene_id "Phchi.S1G186600"
# This transcript jg2273.t2 is derived from g9193.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2274.t1 is derived from g9194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5820714	5823696	.	+	.	Phchi.S5G088300
Phchi.S5	AUGUSTUS	transcript	5820714	5823696	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	start_codon	5820714	5820716	.	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5820714	5820817	0.92	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5820714	5820817	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5820818	5820923	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5820924	5820972	0.84	+	1	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5820924	5820972	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5820973	5821060	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5821061	5821127	0.99	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5821061	5821127	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5821128	5821210	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5821211	5821272	1	+	2	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5821211	5821272	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5821273	5821405	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5821406	5821477	0.57	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5821406	5821477	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5821478	5821679	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5821680	5821778	1	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5821680	5821778	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5821779	5821877	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5821878	5821943	1	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5821878	5821943	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5821944	5822094	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5822095	5822137	0.74	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5822095	5822137	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5822138	5822293	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5822294	5822346	0.81	+	2	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5822294	5822346	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5822347	5822425	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5822426	5822492	1	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5822426	5822492	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	intron	5822493	5822575	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	CDS	5822576	5823696	1	+	2	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	exon	5822576	5823696	.	+	.	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
Phchi.S5	AUGUSTUS	stop_codon	5823697	5823699	.	+	0	transcript_id "Phchi.S5G088300.t1"; gene_id "Phchi.S5G088300"
# This transcript jg12353.t2 is derived from g8029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12354.t1 is derived from g8030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12687308	12688499	.	+	.	Phchi.S2G043400
Phchi.S2	AUGUSTUS	transcript	12687308	12688499	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	start_codon	12687308	12687310	.	+	0	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	CDS	12687308	12687355	0.84	+	0	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	exon	12687308	12687355	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	intron	12687356	12687649	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	CDS	12687650	12687773	1	+	0	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	exon	12687650	12687773	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	intron	12687774	12687981	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	CDS	12687982	12688027	0.94	+	2	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	exon	12687982	12688027	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	intron	12688028	12688108	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	CDS	12688109	12688157	0.64	+	1	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	exon	12688109	12688157	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	intron	12688158	12688289	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	CDS	12688290	12688374	0.96	+	0	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	exon	12688290	12688374	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	intron	12688375	12688464	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	CDS	12688465	12688499	1	+	2	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	exon	12688465	12688499	.	+	.	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
Phchi.S2	AUGUSTUS	stop_codon	12688500	12688502	.	+	0	transcript_id "Phchi.S2G043400.t1"; gene_id "Phchi.S2G043400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8055.t1 is derived from g5230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32725584	32729295	.	+	.	Phchi.S1G521400
Phchi.S1	AUGUSTUS	transcript	32725584	32729295	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	start_codon	32725584	32725586	.	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32725584	32725605	0.51	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32725584	32725605	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32725606	32725736	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32725737	32725861	1	+	2	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32725737	32725861	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32725862	32725954	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32725955	32726020	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32725955	32726020	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32726021	32726117	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32726118	32726178	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32726118	32726178	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32726179	32726302	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32726303	32726472	1	+	2	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32726303	32726472	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32726473	32726558	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32726559	32726768	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32726559	32726768	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32726769	32726869	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32726870	32726944	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32726870	32726944	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32726945	32727041	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32727042	32727214	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32727042	32727214	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32727215	32727339	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32727340	32727423	1	+	1	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32727340	32727423	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32727424	32727499	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32727500	32727607	1	+	1	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32727500	32727607	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32727608	32727705	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32727706	32727796	1	+	1	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32727706	32727796	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32727797	32727889	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32727890	32727992	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32727890	32727992	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32727993	32728090	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32728091	32728179	1	+	2	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32728091	32728179	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32728180	32728267	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32728268	32728391	0.99	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32728268	32728391	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32728392	32728497	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32728498	32728573	0.69	+	2	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32728498	32728573	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32728574	32728670	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32728671	32728758	1	+	1	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32728671	32728758	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32728759	32728840	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32728841	32728927	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32728841	32728927	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32728928	32729008	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32729009	32729059	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32729009	32729059	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	intron	32729060	32729142	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	CDS	32729143	32729295	1	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	exon	32729143	32729295	.	+	.	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
Phchi.S1	AUGUSTUS	stop_codon	32729296	32729298	.	+	0	transcript_id "Phchi.S1G521400.t1"; gene_id "Phchi.S1G521400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3117.t1 is derived from g286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1807544	1812195	.	-	.	Phchi.S1G027600
Phchi.S1	AUGUSTUS	transcript	1807544	1812195	.	-	.	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	stop_codon	1807541	1807543	.	-	0	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	CDS	1807544	1808538	0.91	-	2	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	exon	1807544	1808538	.	-	.	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	intron	1808539	1808631	.	-	.	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	CDS	1808632	1810924	0.57	-	0	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	exon	1808632	1810924	.	-	.	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	intron	1810925	1811058	.	-	.	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	CDS	1811059	1812195	0.62	-	0	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	exon	1811059	1812195	.	-	.	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
Phchi.S1	AUGUSTUS	start_codon	1812193	1812195	.	-	0	transcript_id "Phchi.S1G027600.t1"; gene_id "Phchi.S1G027600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2399.t1 is derived from g9319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6479757	6481711	.	+	.	Phchi.S5G100800
Phchi.S5	AUGUSTUS	transcript	6479757	6481711	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	start_codon	6479757	6479759	.	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6479757	6480050	0.81	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6479757	6480050	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6480051	6480195	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6480196	6480291	1	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6480196	6480291	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6480292	6480434	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6480435	6480509	1	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6480435	6480509	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6480510	6480606	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6480607	6480675	1	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6480607	6480675	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6480676	6480764	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6480765	6480841	1	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6480765	6480841	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6480842	6480917	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6480918	6481006	1	+	1	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6480918	6481006	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6481007	6481085	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6481086	6481215	1	+	2	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6481086	6481215	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6481216	6481295	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6481296	6481386	1	+	1	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6481296	6481386	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6481387	6481455	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6481456	6481521	1	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6481456	6481521	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	intron	6481522	6481594	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	CDS	6481595	6481711	1	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	exon	6481595	6481711	.	+	.	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
Phchi.S5	AUGUSTUS	stop_codon	6481712	6481714	.	+	0	transcript_id "Phchi.S5G100800.t1"; gene_id "Phchi.S5G100800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6755.t1 is derived from g3927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24885690	24896317	.	+	.	Phchi.S1G391400
Phchi.S1	AUGUSTUS	transcript	24885690	24896317	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	start_codon	24885690	24885692	.	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24885690	24889054	0.91	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24885690	24889054	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24889055	24889216	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24889217	24889374	1	+	1	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24889217	24889374	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24889375	24889501	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24889502	24889581	1	+	2	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24889502	24889581	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24889582	24889793	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24889794	24889925	0.82	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24889794	24889925	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24889926	24890103	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24890104	24890142	0.83	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24890104	24890142	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24890143	24890240	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24890241	24890333	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24890241	24890333	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24890334	24890424	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24890425	24890502	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24890425	24890502	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24890503	24890598	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24890599	24890655	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24890599	24890655	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24890656	24890750	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24890751	24891228	0.99	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24890751	24891228	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24891229	24891324	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24891325	24891380	1	+	2	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24891325	24891380	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24891381	24891558	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24891559	24891638	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24891559	24891638	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24891639	24891730	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24891731	24891822	1	+	1	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24891731	24891822	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24891823	24891905	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24891906	24891985	1	+	2	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24891906	24891985	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24891986	24892145	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24892146	24892225	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24892146	24892225	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24892226	24892372	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24892373	24892418	1	+	1	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24892373	24892418	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24892419	24892519	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24892520	24895540	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24892520	24895540	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24895541	24895686	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24895687	24895728	1	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24895687	24895728	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24895729	24895854	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24895855	24895885	0.97	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24895855	24895885	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24895886	24896052	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24896053	24896170	0.98	+	2	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24896053	24896170	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	intron	24896171	24896316	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	CDS	24896317	24896317	0.97	+	1	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	exon	24896317	24896317	.	+	.	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
Phchi.S1	AUGUSTUS	stop_codon	24896318	24896320	.	+	0	transcript_id "Phchi.S1G391400.t1"; gene_id "Phchi.S1G391400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5814.t1 is derived from g2984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19076375	19078580	.	+	.	Phchi.S1G297300
Phchi.S1	AUGUSTUS	transcript	19076375	19078580	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	start_codon	19076375	19076377	.	+	0	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19076375	19076419	1	+	0	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19076375	19076419	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19076420	19076553	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19076554	19076852	1	+	0	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19076554	19076852	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19076853	19076942	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19076943	19077048	1	+	1	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19076943	19077048	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19077049	19077135	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19077136	19077221	1	+	0	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19077136	19077221	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19077222	19077322	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19077323	19077795	1	+	1	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19077323	19077795	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19077796	19077893	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19077894	19078175	1	+	2	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19077894	19078175	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19078176	19078292	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19078293	19078334	1	+	2	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19078293	19078334	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	intron	19078335	19078452	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	CDS	19078453	19078580	1	+	2	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	exon	19078453	19078580	.	+	.	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
Phchi.S1	AUGUSTUS	stop_codon	19078581	19078583	.	+	0	transcript_id "Phchi.S1G297300.t1"; gene_id "Phchi.S1G297300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13767.t1 is derived from g12234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8813718	8818104	.	+	.	Phchi.S3G108600
Phchi.S3	AUGUSTUS	transcript	8813718	8818104	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	start_codon	8813718	8813720	.	+	0	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8813718	8813898	0.61	+	0	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8813718	8813898	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8813899	8813985	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8813986	8814215	0.75	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8813986	8814215	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8814216	8814316	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8814317	8814479	0.76	+	0	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8814317	8814479	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8814480	8814553	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8814554	8814641	1	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8814554	8814641	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8814642	8814738	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8814739	8814986	0.61	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8814739	8814986	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8814987	8815167	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8815168	8815263	0.45	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8815168	8815263	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8815264	8815354	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8815355	8815487	1	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8815355	8815487	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8815488	8815664	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8815665	8815736	1	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8815665	8815736	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8815737	8815890	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8815891	8815965	1	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8815891	8815965	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8815966	8816073	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8816074	8816145	0.99	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8816074	8816145	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8816146	8816247	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8816248	8816417	0.71	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8816248	8816417	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8816418	8816510	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8816511	8816747	0.75	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8816511	8816747	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8816748	8816851	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8816852	8816978	0.45	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8816852	8816978	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8816979	8817074	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8817075	8817142	0.95	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8817075	8817142	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8817143	8817254	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8817255	8817450	0.97	+	2	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8817255	8817450	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8817451	8817545	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8817546	8817678	1	+	1	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8817546	8817678	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	intron	8817679	8817765	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	CDS	8817766	8818104	1	+	0	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	exon	8817766	8818104	.	+	.	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
Phchi.S3	AUGUSTUS	stop_codon	8818105	8818107	.	+	0	transcript_id "Phchi.S3G108600.t1"; gene_id "Phchi.S3G108600"
# This transcript jg3394.t2 is derived from g563.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3395.t1 is derived from g564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3330927	3332373	.	+	.	Phchi.S1G055400
Phchi.S1	AUGUSTUS	transcript	3330927	3332373	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	start_codon	3330927	3330929	.	+	0	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	CDS	3330927	3331456	0.78	+	0	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	exon	3330927	3331456	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	intron	3331457	3331549	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	CDS	3331550	3331610	0.89	+	1	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	exon	3331550	3331610	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	intron	3331611	3331794	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	CDS	3331795	3332039	0.97	+	0	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	exon	3331795	3332039	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	intron	3332040	3332118	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	CDS	3332119	3332263	1	+	1	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	exon	3332119	3332263	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	intron	3332264	3332358	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	CDS	3332359	3332373	1	+	0	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	exon	3332359	3332373	.	+	.	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
Phchi.S1	AUGUSTUS	stop_codon	3332374	3332376	.	+	0	transcript_id "Phchi.S1G055400.t1"; gene_id "Phchi.S1G055400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11120.t1 is derived from g15170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4241319	4242636	.	+	.	Phchi.S4G070200
Phchi.S4	AUGUSTUS	transcript	4241319	4242636	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	start_codon	4241319	4241321	.	+	0	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	CDS	4241319	4241360	0.99	+	0	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	exon	4241319	4241360	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	intron	4241361	4241449	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	CDS	4241450	4241719	0.99	+	0	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	exon	4241450	4241719	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	intron	4241720	4242084	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	CDS	4242085	4242211	1	+	0	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	exon	4242085	4242211	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	intron	4242212	4242304	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	CDS	4242305	4242636	0.99	+	2	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	exon	4242305	4242636	.	+	.	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
Phchi.S4	AUGUSTUS	stop_codon	4242637	4242639	.	+	0	transcript_id "Phchi.S4G070200.t1"; gene_id "Phchi.S4G070200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2573.t1 is derived from g9493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7436784	7437400	.	+	.	Phchi.S5G118200
Phchi.S5	AUGUSTUS	transcript	7436784	7437400	.	+	.	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	start_codon	7436784	7436786	.	+	0	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	CDS	7436784	7437053	0.97	+	0	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	exon	7436784	7437053	.	+	.	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	intron	7437054	7437391	.	+	.	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	CDS	7437392	7437400	1	+	0	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	exon	7437392	7437400	.	+	.	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
Phchi.S5	AUGUSTUS	stop_codon	7437401	7437403	.	+	0	transcript_id "Phchi.S5G118200.t1"; gene_id "Phchi.S5G118200"
# This transcript jg12291.t2 is derived from g7967.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12291.t3 is derived from g7967.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12292.t1 is derived from g7968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8917189	8920033	.	-	.	Phchi.S2G037200
Phchi.S2	AUGUSTUS	transcript	8917189	8920033	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	stop_codon	8917186	8917188	.	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8917189	8917845	0.99	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8917189	8917845	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8917846	8917940	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8917941	8917992	1	-	1	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8917941	8917992	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8917993	8918274	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8918275	8918510	1	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8918275	8918510	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8918511	8918705	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8918706	8918960	0.88	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8918706	8918960	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8918961	8919038	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8919039	8919413	1	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8919039	8919413	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8919414	8919757	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8919758	8920033	0.83	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8919758	8920033	.	-	.	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	start_codon	8920031	8920033	.	-	0	transcript_id "Phchi.S2G037200.t1"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	transcript	8917189	8920033	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	stop_codon	8917186	8917188	.	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8917189	8917845	0.99	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8917189	8917845	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8917846	8917940	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8917941	8917992	1	-	1	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8917941	8917992	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8917993	8918274	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8918275	8918348	0.91	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8918275	8918348	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8918349	8918440	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8918441	8918510	0.9	-	1	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8918441	8918510	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8918511	8918904	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8918905	8918960	0.97	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8918905	8918960	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8918961	8919038	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8919039	8919413	1	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8919039	8919413	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	intron	8919414	8919757	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	CDS	8919758	8920033	0.75	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	exon	8919758	8920033	.	-	.	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
Phchi.S2	AUGUSTUS	start_codon	8920031	8920033	.	-	0	transcript_id "Phchi.S2G037200.t2"; gene_id "Phchi.S2G037200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4152.t1 is derived from g1321.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8655163	8656001	.	-	.	Phchi.S1G131100
Phchi.S1	AUGUSTUS	transcript	8655163	8656001	.	-	.	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	stop_codon	8655160	8655162	.	-	0	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	CDS	8655163	8655577	0.66	-	1	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	exon	8655163	8655577	.	-	.	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	intron	8655578	8655675	.	-	.	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	CDS	8655676	8656001	0.67	-	0	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	exon	8655676	8656001	.	-	.	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	start_codon	8655999	8656001	.	-	0	transcript_id "Phchi.S1G131100.t1"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	transcript	8655576	8656001	.	-	.	transcript_id "Phchi.S1G131100.t2"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	stop_codon	8655573	8655575	.	-	0	transcript_id "Phchi.S1G131100.t2"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	CDS	8655576	8656001	0.94	-	0	transcript_id "Phchi.S1G131100.t2"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	exon	8655576	8656001	.	-	.	transcript_id "Phchi.S1G131100.t2"; gene_id "Phchi.S1G131100"
Phchi.S1	AUGUSTUS	start_codon	8655999	8656001	.	-	0	transcript_id "Phchi.S1G131100.t2"; gene_id "Phchi.S1G131100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2928.t1 is derived from g97.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	592759	594134	.	-	.	Phchi.S1G008700
Phchi.S1	AUGUSTUS	transcript	592759	594134	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	stop_codon	592756	592758	.	-	0	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	CDS	592759	592810	1	-	1	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	exon	592759	592810	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	intron	592811	592923	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	CDS	592924	593012	1	-	0	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	exon	592924	593012	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	intron	593013	593162	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	CDS	593163	593244	1	-	1	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	exon	593163	593244	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	intron	593245	593337	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	CDS	593338	594134	0.7	-	0	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	exon	593338	594134	.	-	.	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
Phchi.S1	AUGUSTUS	start_codon	594132	594134	.	-	0	transcript_id "Phchi.S1G008700.t1"; gene_id "Phchi.S1G008700"
# This transcript jg14928.t2 is derived from g13396.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14928.t3 is derived from g13396.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14929.t1 is derived from g13397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15566018	15572262	.	+	.	Phchi.S3G224800
Phchi.S3	AUGUSTUS	transcript	15566018	15572262	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	start_codon	15566018	15566020	.	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566018	15566098	0.99	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566018	15566098	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566099	15566318	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566319	15566436	0.69	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566319	15566436	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566437	15566542	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566543	15566699	0.49	+	2	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566543	15566699	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566700	15566813	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566814	15566877	0.46	+	1	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566814	15566877	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566878	15567133	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15567134	15567220	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15567134	15567220	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15567221	15567755	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15567756	15567825	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15567756	15567825	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15567826	15567929	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15567930	15568219	0.99	+	2	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15567930	15568219	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15568220	15568367	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15568368	15568532	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15568368	15568532	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15568533	15568614	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15568615	15568686	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15568615	15568686	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15568687	15569110	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15569111	15569825	0.97	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15569111	15569825	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15569826	15569916	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15569917	15570089	1	+	2	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15569917	15570089	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15570090	15570172	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15570173	15570559	0.84	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15570173	15570559	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15570560	15570648	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15570649	15570785	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15570649	15570785	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15570786	15570859	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15570860	15571161	0.67	+	1	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15570860	15571161	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571162	15571254	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15571255	15571337	1	+	2	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15571255	15571337	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571338	15571461	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15571462	15571584	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15571462	15571584	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571585	15571739	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15571740	15571913	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15571740	15571913	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571914	15572121	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15572122	15572262	1	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15572122	15572262	.	+	.	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	stop_codon	15572263	15572265	.	+	0	transcript_id "Phchi.S3G224800.t1"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	transcript	15566018	15572262	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	start_codon	15566018	15566020	.	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566018	15566098	0.99	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566018	15566098	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566099	15566318	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566319	15566436	0.6	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566319	15566436	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566437	15566542	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566543	15566699	0.46	+	2	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566543	15566699	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566700	15566813	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15566814	15566877	0.43	+	1	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15566814	15566877	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15566878	15567133	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15567134	15567220	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15567134	15567220	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15567221	15567755	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15567756	15567825	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15567756	15567825	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15567826	15567929	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15567930	15568219	1	+	2	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15567930	15568219	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15568220	15568367	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15568368	15568532	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15568368	15568532	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15568533	15568614	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15568615	15568686	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15568615	15568686	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15568687	15568930	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15568931	15569825	0.89	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15568931	15569825	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15569826	15569916	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15569917	15570089	1	+	2	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15569917	15570089	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15570090	15570172	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15570173	15570559	0.84	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15570173	15570559	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15570560	15570648	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15570649	15570785	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15570649	15570785	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15570786	15570859	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15570860	15571161	0.64	+	1	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15570860	15571161	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571162	15571254	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15571255	15571337	1	+	2	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15571255	15571337	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571338	15571461	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15571462	15571584	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15571462	15571584	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571585	15571739	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15571740	15571913	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15571740	15571913	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	intron	15571914	15572121	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	CDS	15572122	15572262	1	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	exon	15572122	15572262	.	+	.	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
Phchi.S3	AUGUSTUS	stop_codon	15572263	15572265	.	+	0	transcript_id "Phchi.S3G224800.t2"; gene_id "Phchi.S3G224800"
# This transcript jg6352.t2 is derived from g3524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6353.t1 is derived from g3525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22463881	22464645	.	+	.	Phchi.S1G351200
Phchi.S1	AUGUSTUS	transcript	22463881	22464645	.	+	.	transcript_id "Phchi.S1G351200.t1"; gene_id "Phchi.S1G351200"
Phchi.S1	AUGUSTUS	start_codon	22463881	22463883	.	+	0	transcript_id "Phchi.S1G351200.t1"; gene_id "Phchi.S1G351200"
Phchi.S1	AUGUSTUS	CDS	22463881	22464645	0.71	+	0	transcript_id "Phchi.S1G351200.t1"; gene_id "Phchi.S1G351200"
Phchi.S1	AUGUSTUS	exon	22463881	22464645	.	+	.	transcript_id "Phchi.S1G351200.t1"; gene_id "Phchi.S1G351200"
Phchi.S1	AUGUSTUS	stop_codon	22464646	22464648	.	+	0	transcript_id "Phchi.S1G351200.t1"; gene_id "Phchi.S1G351200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8968.t1 is derived from g6143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38882919	38883961	.	-	.	Phchi.S1G612700
Phchi.S1	AUGUSTUS	transcript	38882919	38883961	.	-	.	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	stop_codon	38882916	38882918	.	-	0	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	CDS	38882919	38882938	0.98	-	2	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	exon	38882919	38882938	.	-	.	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	intron	38882939	38883030	.	-	.	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	CDS	38883031	38883961	1	-	0	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	exon	38883031	38883961	.	-	.	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
Phchi.S1	AUGUSTUS	start_codon	38883959	38883961	.	-	0	transcript_id "Phchi.S1G612700.t1"; gene_id "Phchi.S1G612700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15173.t1 is derived from g13641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17359654	17363473	.	-	.	Phchi.S3G249200
Phchi.S3	AUGUSTUS	transcript	17359654	17363473	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	stop_codon	17359651	17359653	.	-	0	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17359654	17360637	1	-	0	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17359654	17360637	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	intron	17360638	17360750	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17360751	17360878	1	-	2	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17360751	17360878	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	intron	17360879	17360969	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17360970	17361195	1	-	0	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17360970	17361195	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	intron	17361196	17361310	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17361311	17361438	1	-	2	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17361311	17361438	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	intron	17361439	17361593	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17361594	17361921	0.85	-	0	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17361594	17361921	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	intron	17361922	17362019	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17362020	17362501	0.37	-	2	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17362020	17362501	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	intron	17362502	17362626	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	CDS	17362627	17363473	0.49	-	0	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	exon	17362627	17363473	.	-	.	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
Phchi.S3	AUGUSTUS	start_codon	17363471	17363473	.	-	0	transcript_id "Phchi.S3G249200.t1"; gene_id "Phchi.S3G249200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8606.t1 is derived from g5781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36876814	36879262	.	+	.	Phchi.S1G576500
Phchi.S1	AUGUSTUS	transcript	36876814	36879262	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	start_codon	36876814	36876816	.	+	0	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	CDS	36876814	36878322	0.96	+	0	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	exon	36876814	36878322	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	intron	36878323	36878414	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	CDS	36878415	36878554	1	+	0	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	exon	36878415	36878554	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	intron	36878555	36878646	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	CDS	36878647	36878919	1	+	1	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	exon	36878647	36878919	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	intron	36878920	36879000	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	CDS	36879001	36879262	0.99	+	1	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	exon	36879001	36879262	.	+	.	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
Phchi.S1	AUGUSTUS	stop_codon	36879263	36879265	.	+	0	transcript_id "Phchi.S1G576500.t1"; gene_id "Phchi.S1G576500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6524.t1 is derived from g3696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23477478	23480871	.	+	.	Phchi.S1G368300
Phchi.S1	AUGUSTUS	transcript	23477478	23480871	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	start_codon	23477478	23477480	.	+	0	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23477478	23477727	0.86	+	0	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23477478	23477727	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23477728	23477828	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23477829	23478045	1	+	2	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23477829	23478045	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23478046	23478134	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23478135	23478576	1	+	1	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23478135	23478576	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23478577	23478760	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23478761	23478964	1	+	0	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23478761	23478964	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23478965	23479116	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23479117	23479277	1	+	0	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23479117	23479277	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23479278	23479354	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23479355	23479540	1	+	1	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23479355	23479540	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23479541	23479630	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23479631	23479862	1	+	1	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23479631	23479862	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23479863	23479948	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23479949	23480160	1	+	0	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23479949	23480160	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23480161	23480390	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23480391	23480525	1	+	1	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23480391	23480525	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	intron	23480526	23480654	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	CDS	23480655	23480871	1	+	1	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	exon	23480655	23480871	.	+	.	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
Phchi.S1	AUGUSTUS	stop_codon	23480872	23480874	.	+	0	transcript_id "Phchi.S1G368300.t1"; gene_id "Phchi.S1G368300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6938.t1 is derived from g4110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26068073	26069894	.	+	.	Phchi.S1G409700
Phchi.S1	AUGUSTUS	transcript	26068073	26069894	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	start_codon	26068073	26068075	.	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26068073	26068198	0.99	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26068073	26068198	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26068199	26068340	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26068341	26068451	1	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26068341	26068451	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26068452	26068610	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26068611	26068712	1	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26068611	26068712	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26068713	26068937	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26068938	26069039	0.99	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26068938	26069039	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26069040	26069145	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26069146	26069261	0.99	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26069146	26069261	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26069262	26069370	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26069371	26069449	1	+	1	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26069371	26069449	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26069450	26069545	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26069546	26069716	1	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26069546	26069716	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	intron	26069717	26069813	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	CDS	26069814	26069894	1	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	exon	26069814	26069894	.	+	.	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
Phchi.S1	AUGUSTUS	stop_codon	26069895	26069897	.	+	0	transcript_id "Phchi.S1G409700.t1"; gene_id "Phchi.S1G409700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3403.t1 is derived from g572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3363766	3366062	.	-	.	Phchi.S1G056200
Phchi.S1	AUGUSTUS	transcript	3365012	3366062	.	-	.	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	stop_codon	3365009	3365011	.	-	0	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	CDS	3365012	3365037	0.81	-	2	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	exon	3365012	3365037	.	-	.	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	intron	3365038	3365153	.	-	.	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	CDS	3365154	3365520	0.8	-	0	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	exon	3365154	3365520	.	-	.	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	intron	3365521	3365612	.	-	.	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	CDS	3365613	3366062	0.87	-	0	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	exon	3365613	3366062	.	-	.	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	start_codon	3366060	3366062	.	-	0	transcript_id "Phchi.S1G056200.t1"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	transcript	3363766	3366062	.	-	.	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	stop_codon	3363763	3363765	.	-	0	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	CDS	3363766	3365520	0.52	-	0	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	exon	3363766	3365520	.	-	.	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	intron	3365521	3365612	.	-	.	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	CDS	3365613	3366062	0.84	-	0	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	exon	3365613	3366062	.	-	.	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
Phchi.S1	AUGUSTUS	start_codon	3366060	3366062	.	-	0	transcript_id "Phchi.S1G056200.t2"; gene_id "Phchi.S1G056200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15575.t1 is derived from g14044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20086278	20091130	.	+	.	Phchi.S3G289400
Phchi.S3	AUGUSTUS	transcript	20086278	20091130	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	start_codon	20086278	20086280	.	+	0	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20086278	20087637	0.99	+	0	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20086278	20087637	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20087638	20088117	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20088118	20088439	1	+	2	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20088118	20088439	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20088440	20088575	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20088576	20089452	0.85	+	1	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20088576	20089452	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20089453	20089633	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20089634	20089757	1	+	0	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20089634	20089757	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20089758	20089891	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20089892	20090111	1	+	2	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20089892	20090111	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20090112	20090319	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20090320	20090787	0.94	+	1	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20090320	20090787	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20090788	20090919	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20090920	20091130	1	+	1	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20090920	20091130	.	+	.	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	stop_codon	20091131	20091133	.	+	0	transcript_id "Phchi.S3G289400.t1"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	transcript	20086278	20087789	.	+	.	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	start_codon	20086278	20086280	.	+	0	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20086278	20087637	0.94	+	0	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20086278	20087637	.	+	.	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	intron	20087638	20087733	.	+	.	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	CDS	20087734	20087789	0.95	+	2	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	exon	20087734	20087789	.	+	.	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
Phchi.S3	AUGUSTUS	stop_codon	20087790	20087792	.	+	0	transcript_id "Phchi.S3G289400.t2"; gene_id "Phchi.S3G289400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14583.t1 is derived from g13051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13568375	13578613	.	-	.	Phchi.S3G190200
Phchi.S3	AUGUSTUS	transcript	13568375	13578613	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	stop_codon	13568372	13568374	.	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13568375	13568457	1	-	2	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13568375	13568457	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13568458	13568540	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13568541	13568637	0.78	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13568541	13568637	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13568638	13568833	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13568834	13568893	0.75	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13568834	13568893	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13568894	13569040	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13569041	13569149	1	-	1	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13569041	13569149	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13569150	13569306	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13569307	13569659	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13569307	13569659	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13569660	13569755	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13569756	13569872	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13569756	13569872	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13569873	13569975	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13569976	13570186	1	-	1	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13569976	13570186	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13570187	13570264	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13570265	13570524	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13570265	13570524	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13570525	13570608	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13570609	13570806	0.99	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13570609	13570806	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13570807	13570933	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13570934	13572000	0.87	-	2	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13570934	13572000	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13572001	13572100	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13572101	13572218	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13572101	13572218	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13572219	13572408	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13572409	13572627	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13572409	13572627	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13572628	13572764	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13572765	13573019	0.97	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13572765	13573019	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13573020	13573187	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13573188	13573340	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13573188	13573340	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13573341	13573474	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13573475	13573825	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13573475	13573825	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13573826	13573987	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13573988	13574200	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13573988	13574200	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13574201	13574406	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13574407	13574637	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13574407	13574637	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13574638	13574719	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13574720	13574881	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13574720	13574881	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13574882	13575356	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13575357	13575564	1	-	1	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13575357	13575564	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13575565	13575663	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13575664	13575689	0.95	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13575664	13575689	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13575690	13575821	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13575822	13575863	0.7	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13575822	13575863	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13575864	13575972	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13575973	13576078	0.73	-	1	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13575973	13576078	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13576079	13576194	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13576195	13576259	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13576195	13576259	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13576260	13576349	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13576350	13577844	0.95	-	1	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13576350	13577844	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13577845	13577936	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13577937	13578499	1	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13577937	13578499	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	intron	13578500	13578589	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	CDS	13578590	13578613	0.99	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	exon	13578590	13578613	.	-	.	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
Phchi.S3	AUGUSTUS	start_codon	13578611	13578613	.	-	0	transcript_id "Phchi.S3G190200.t1"; gene_id "Phchi.S3G190200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5274.t1 is derived from g2444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15995920	15997220	.	-	.	Phchi.S1G243300
Phchi.S1	AUGUSTUS	transcript	15995920	15997220	.	-	.	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	stop_codon	15995917	15995919	.	-	0	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	CDS	15995920	15995953	1	-	1	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	exon	15995920	15995953	.	-	.	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	intron	15995954	15996045	.	-	.	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	CDS	15996046	15996248	0.67	-	0	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	exon	15996046	15996248	.	-	.	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	intron	15996249	15996428	.	-	.	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	CDS	15996429	15997220	0.38	-	0	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	exon	15996429	15997220	.	-	.	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
Phchi.S1	AUGUSTUS	start_codon	15997218	15997220	.	-	0	transcript_id "Phchi.S1G243300.t1"; gene_id "Phchi.S1G243300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10797.t1 is derived from g14847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2160207	2160515	.	-	.	Phchi.S4G037900
Phchi.S4	AUGUSTUS	transcript	2160207	2160515	.	-	.	transcript_id "Phchi.S4G037900.t1"; gene_id "Phchi.S4G037900"
Phchi.S4	AUGUSTUS	stop_codon	2160204	2160206	.	-	0	transcript_id "Phchi.S4G037900.t1"; gene_id "Phchi.S4G037900"
Phchi.S4	AUGUSTUS	CDS	2160207	2160515	1	-	0	transcript_id "Phchi.S4G037900.t1"; gene_id "Phchi.S4G037900"
Phchi.S4	AUGUSTUS	exon	2160207	2160515	.	-	.	transcript_id "Phchi.S4G037900.t1"; gene_id "Phchi.S4G037900"
Phchi.S4	AUGUSTUS	start_codon	2160513	2160515	.	-	0	transcript_id "Phchi.S4G037900.t1"; gene_id "Phchi.S4G037900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11692.t1 is derived from g15743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7696579	7702761	.	-	.	Phchi.S4G127400
Phchi.S4	AUGUSTUS	transcript	7696579	7702761	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	stop_codon	7696576	7696578	.	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7696579	7696940	1	-	2	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7696579	7696940	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7696941	7697024	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7697025	7697175	0.98	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7697025	7697175	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7697176	7697261	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7697262	7697582	0.87	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7697262	7697582	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7697583	7697698	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7697699	7697994	1	-	2	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7697699	7697994	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7697995	7698110	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7698111	7699491	0.98	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7698111	7699491	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7699492	7699585	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7699586	7699746	1	-	2	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7699586	7699746	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7699747	7699843	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7699844	7699929	1	-	1	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7699844	7699929	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7699930	7700006	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7700007	7700074	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7700007	7700074	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7700075	7700187	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7700188	7700231	1	-	2	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7700188	7700231	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7700232	7700351	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7700352	7700424	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7700352	7700424	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7700425	7700572	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7700573	7700652	1	-	2	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7700573	7700652	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7700653	7700786	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7700787	7700880	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7700787	7700880	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7700881	7701054	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7701055	7701216	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7701055	7701216	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7701217	7701299	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7701300	7701362	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7701300	7701362	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7701363	7701438	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7701439	7701505	1	-	1	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7701439	7701505	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7701506	7701748	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7701749	7701837	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7701749	7701837	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7701838	7701930	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7701931	7701982	1	-	1	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7701931	7701982	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7701983	7702137	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7702138	7702247	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7702138	7702247	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7702248	7702430	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7702431	7702519	1	-	2	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7702431	7702519	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	intron	7702520	7702649	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	CDS	7702650	7702761	1	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	exon	7702650	7702761	.	-	.	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
Phchi.S4	AUGUSTUS	start_codon	7702759	7702761	.	-	0	transcript_id "Phchi.S4G127400.t1"; gene_id "Phchi.S4G127400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2118.t1 is derived from g9038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4932560	4935048	.	-	.	Phchi.S5G072700
Phchi.S5	AUGUSTUS	transcript	4932560	4935048	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	stop_codon	4932557	4932559	.	-	0	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	CDS	4932560	4933456	0.69	-	0	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	exon	4932560	4933456	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	intron	4933457	4933538	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	CDS	4933539	4934320	0.06	-	2	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	exon	4933539	4934320	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	intron	4934321	4934414	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	CDS	4934415	4934487	0.4	-	0	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	exon	4934415	4934487	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	intron	4934488	4934931	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	CDS	4934932	4935048	0.43	-	0	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	exon	4934932	4935048	.	-	.	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
Phchi.S5	AUGUSTUS	start_codon	4935046	4935048	.	-	0	transcript_id "Phchi.S5G072700.t1"; gene_id "Phchi.S5G072700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7803.t1 is derived from g4977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31258395	31259932	.	+	.	Phchi.S1G496200
Phchi.S1	AUGUSTUS	transcript	31258395	31259932	.	+	.	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	start_codon	31258395	31258397	.	+	0	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	CDS	31258395	31259065	0.94	+	0	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	exon	31258395	31259065	.	+	.	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	intron	31259066	31259166	.	+	.	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	CDS	31259167	31259932	0.73	+	1	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	exon	31259167	31259932	.	+	.	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
Phchi.S1	AUGUSTUS	stop_codon	31259933	31259935	.	+	0	transcript_id "Phchi.S1G496200.t1"; gene_id "Phchi.S1G496200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3056.t1 is derived from g225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1374297	1376708	.	+	.	Phchi.S1G021500
Phchi.S1	AUGUSTUS	transcript	1374297	1376708	.	+	.	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	start_codon	1374297	1374299	.	+	0	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	CDS	1374297	1375748	0.54	+	0	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	exon	1374297	1375748	.	+	.	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	intron	1375749	1375833	.	+	.	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	CDS	1375834	1376405	0.87	+	0	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	exon	1375834	1376405	.	+	.	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	intron	1376406	1376494	.	+	.	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	CDS	1376495	1376708	0.96	+	1	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	exon	1376495	1376708	.	+	.	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
Phchi.S1	AUGUSTUS	stop_codon	1376709	1376711	.	+	0	transcript_id "Phchi.S1G021500.t1"; gene_id "Phchi.S1G021500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11282.t1 is derived from g15332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5190542	5191813	.	+	.	Phchi.S4G086400
Phchi.S4	AUGUSTUS	transcript	5190542	5191813	.	+	.	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	start_codon	5190542	5190544	.	+	0	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	CDS	5190542	5190857	0.97	+	0	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	exon	5190542	5190857	.	+	.	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	intron	5190858	5190944	.	+	.	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	CDS	5190945	5191813	1	+	2	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	exon	5190945	5191813	.	+	.	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
Phchi.S4	AUGUSTUS	stop_codon	5191814	5191816	.	+	0	transcript_id "Phchi.S4G086400.t1"; gene_id "Phchi.S4G086400"
# This transcript jg1984.t2 is derived from g8904.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1985.t1 is derived from g8905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4279985	4286871	.	+	.	Phchi.S5G059400
Phchi.S5	AUGUSTUS	transcript	4279985	4286871	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	start_codon	4279985	4279987	.	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4279985	4280112	0.97	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4279985	4280112	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4280113	4280201	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4280202	4280607	0.96	+	1	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4280202	4280607	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4280608	4280682	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4280683	4280769	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4280683	4280769	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4280770	4280854	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4280855	4281029	0.94	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4280855	4281029	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4281030	4281113	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4281114	4281379	0.63	+	2	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4281114	4281379	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4281380	4281488	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4281489	4281638	0.79	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4281489	4281638	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4281639	4281709	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4281710	4281775	0.97	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4281710	4281775	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4281776	4281896	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4281897	4282026	0.99	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4281897	4282026	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4282027	4282121	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4282122	4282155	1	+	2	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4282122	4282155	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4282156	4282315	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4282316	4282484	1	+	1	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4282316	4282484	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4282485	4282569	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4282570	4282686	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4282570	4282686	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4282687	4282825	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4282826	4282972	0.79	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4282826	4282972	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4282973	4283057	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4283058	4283183	0.99	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4283058	4283183	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4283184	4283277	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4283278	4283726	0.84	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4283278	4283726	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4283727	4283811	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4283812	4283998	1	+	1	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4283812	4283998	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4283999	4284083	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4284084	4284149	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4284084	4284149	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4284150	4284234	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4284235	4284288	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4284235	4284288	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4284289	4284383	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4284384	4284467	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4284384	4284467	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4284468	4284603	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4284604	4284723	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4284604	4284723	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4284724	4284842	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4284843	4285084	0.91	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4284843	4285084	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4285085	4285194	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4285195	4285221	0.64	+	1	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4285195	4285221	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4285222	4285361	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4285362	4285455	0.75	+	1	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4285362	4285455	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4285456	4285591	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4285592	4286038	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4285592	4286038	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4286039	4286127	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4286128	4286367	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4286128	4286367	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4286368	4286443	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4286444	4286521	1	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4286444	4286521	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	intron	4286522	4286703	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	CDS	4286704	4286871	0.87	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	exon	4286704	4286871	.	+	.	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
Phchi.S5	AUGUSTUS	stop_codon	4286872	4286874	.	+	0	transcript_id "Phchi.S5G059400.t1"; gene_id "Phchi.S5G059400"
# This transcript jg9954.t2 is derived from g7130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9955.t1 is derived from g7131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44645195	44646796	.	-	.	Phchi.S1G711400
Phchi.S1	AUGUSTUS	transcript	44645195	44646796	.	-	.	transcript_id "Phchi.S1G711400.t1"; gene_id "Phchi.S1G711400"
Phchi.S1	AUGUSTUS	stop_codon	44645192	44645194	.	-	0	transcript_id "Phchi.S1G711400.t1"; gene_id "Phchi.S1G711400"
Phchi.S1	AUGUSTUS	CDS	44645195	44646796	0.57	-	0	transcript_id "Phchi.S1G711400.t1"; gene_id "Phchi.S1G711400"
Phchi.S1	AUGUSTUS	exon	44645195	44646796	.	-	.	transcript_id "Phchi.S1G711400.t1"; gene_id "Phchi.S1G711400"
Phchi.S1	AUGUSTUS	start_codon	44646794	44646796	.	-	0	transcript_id "Phchi.S1G711400.t1"; gene_id "Phchi.S1G711400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11607.t1 is derived from g15658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7307386	7308438	.	-	.	Phchi.S4G118900
Phchi.S4	AUGUSTUS	transcript	7307386	7308438	.	-	.	transcript_id "Phchi.S4G118900.t1"; gene_id "Phchi.S4G118900"
Phchi.S4	AUGUSTUS	stop_codon	7307383	7307385	.	-	0	transcript_id "Phchi.S4G118900.t1"; gene_id "Phchi.S4G118900"
Phchi.S4	AUGUSTUS	CDS	7307386	7308438	0.89	-	0	transcript_id "Phchi.S4G118900.t1"; gene_id "Phchi.S4G118900"
Phchi.S4	AUGUSTUS	exon	7307386	7308438	.	-	.	transcript_id "Phchi.S4G118900.t1"; gene_id "Phchi.S4G118900"
Phchi.S4	AUGUSTUS	start_codon	7308436	7308438	.	-	0	transcript_id "Phchi.S4G118900.t1"; gene_id "Phchi.S4G118900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8368.t1 is derived from g5543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35536511	35539312	.	+	.	Phchi.S1G552700
Phchi.S1	AUGUSTUS	transcript	35536511	35539312	.	+	.	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	start_codon	35536511	35536513	.	+	0	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	CDS	35536511	35538702	0.51	+	0	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	exon	35536511	35538702	.	+	.	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	intron	35538703	35538894	.	+	.	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	CDS	35538895	35539312	1	+	1	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	exon	35538895	35539312	.	+	.	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
Phchi.S1	AUGUSTUS	stop_codon	35539313	35539315	.	+	0	transcript_id "Phchi.S1G552700.t1"; gene_id "Phchi.S1G552700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12807.t1 is derived from g11272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2468468	2470999	.	+	.	Phchi.S3G012600
Phchi.S3	AUGUSTUS	transcript	2468468	2470999	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	start_codon	2468468	2468470	.	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2468468	2468871	0.29	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2468468	2468871	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2468872	2468958	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2468959	2469184	1	+	1	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2468959	2469184	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2469185	2469300	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2469301	2469360	0.75	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2469301	2469360	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2469361	2469458	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2469459	2469578	0.74	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2469459	2469578	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2469579	2469699	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2469700	2469873	1	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2469700	2469873	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2469874	2469954	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2469955	2470008	1	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2469955	2470008	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2470009	2470102	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2470103	2470251	1	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2470103	2470251	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2470252	2470340	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2470341	2470404	1	+	1	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2470341	2470404	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2470405	2470489	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2470490	2470660	1	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2470490	2470660	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2470661	2470751	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2470752	2470895	1	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2470752	2470895	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	intron	2470896	2470969	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	CDS	2470970	2470999	1	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	exon	2470970	2470999	.	+	.	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
Phchi.S3	AUGUSTUS	stop_codon	2471000	2471002	.	+	0	transcript_id "Phchi.S3G012600.t1"; gene_id "Phchi.S3G012600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7101.t1 is derived from g4273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26913961	26915713	.	-	.	Phchi.S1G426000
Phchi.S1	AUGUSTUS	transcript	26913961	26915713	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	stop_codon	26913958	26913960	.	-	0	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26913961	26914093	0.97	-	1	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26913961	26914093	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	intron	26914094	26914194	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26914195	26914356	0.98	-	1	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26914195	26914356	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	intron	26914357	26914436	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26914437	26914525	1	-	0	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26914437	26914525	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	intron	26914526	26914618	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26914619	26914870	1	-	0	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26914619	26914870	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	intron	26914871	26915044	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26915045	26915161	1	-	0	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26915045	26915161	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	intron	26915162	26915253	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26915254	26915410	0.93	-	1	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26915254	26915410	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	intron	26915411	26915534	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	CDS	26915535	26915713	0.34	-	0	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	exon	26915535	26915713	.	-	.	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
Phchi.S1	AUGUSTUS	start_codon	26915711	26915713	.	-	0	transcript_id "Phchi.S1G426000.t1"; gene_id "Phchi.S1G426000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3312.t1 is derived from g481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2793180	2795869	.	-	.	Phchi.S1G047100
Phchi.S1	AUGUSTUS	transcript	2793180	2795869	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	stop_codon	2793177	2793179	.	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2793180	2793485	0.99	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2793180	2793485	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2793486	2793589	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2793590	2793916	0.97	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2793590	2793916	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2793917	2793998	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2793999	2794222	0.92	-	2	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2793999	2794222	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2794223	2794357	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2794358	2794555	0.51	-	2	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2794358	2794555	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2794556	2794681	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2794682	2794955	0.44	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2794682	2794955	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2794956	2795048	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2795049	2795093	0.58	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2795049	2795093	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2795094	2795200	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2795201	2795441	0.72	-	1	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2795201	2795441	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	intron	2795442	2795549	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	CDS	2795550	2795869	0.46	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	exon	2795550	2795869	.	-	.	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
Phchi.S1	AUGUSTUS	start_codon	2795867	2795869	.	-	0	transcript_id "Phchi.S1G047100.t1"; gene_id "Phchi.S1G047100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7006.t1 is derived from g4178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26367895	26368326	.	-	.	Phchi.S1G416500
Phchi.S1	AUGUSTUS	transcript	26367895	26368326	.	-	.	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	stop_codon	26367892	26367894	.	-	0	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	CDS	26367895	26368075	1	-	1	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	exon	26367895	26368075	.	-	.	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	intron	26368076	26368156	.	-	.	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	CDS	26368157	26368215	1	-	0	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	exon	26368157	26368215	.	-	.	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	intron	26368216	26368308	.	-	.	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	CDS	26368309	26368326	0.61	-	0	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	exon	26368309	26368326	.	-	.	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
Phchi.S1	AUGUSTUS	start_codon	26368324	26368326	.	-	0	transcript_id "Phchi.S1G416500.t1"; gene_id "Phchi.S1G416500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6695.t1 is derived from g3867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24565583	24566535	.	+	.	Phchi.S1G385400
Phchi.S1	AUGUSTUS	transcript	24565583	24566535	.	+	.	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	start_codon	24565583	24565585	.	+	0	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	CDS	24565583	24566126	0.42	+	0	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	exon	24565583	24566126	.	+	.	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	intron	24566127	24566293	.	+	.	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	CDS	24566294	24566535	1	+	2	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	exon	24566294	24566535	.	+	.	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
Phchi.S1	AUGUSTUS	stop_codon	24566536	24566538	.	+	0	transcript_id "Phchi.S1G385400.t1"; gene_id "Phchi.S1G385400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7315.t1 is derived from g4487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28468510	28469102	.	-	.	Phchi.S1G447400
Phchi.S1	AUGUSTUS	transcript	28468510	28469102	.	-	.	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	stop_codon	28468507	28468509	.	-	0	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	CDS	28468510	28468510	0.25	-	1	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	exon	28468510	28468510	.	-	.	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	intron	28468511	28468710	.	-	.	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	CDS	28468711	28469102	0.83	-	0	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	exon	28468711	28469102	.	-	.	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
Phchi.S1	AUGUSTUS	start_codon	28469100	28469102	.	-	0	transcript_id "Phchi.S1G447400.t1"; gene_id "Phchi.S1G447400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11654.t1 is derived from g15705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7523786	7524223	.	+	.	Phchi.S4G123600
Phchi.S4	AUGUSTUS	transcript	7523786	7524223	.	+	.	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	start_codon	7523786	7523788	.	+	0	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	CDS	7523786	7523893	0.92	+	0	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	exon	7523786	7523893	.	+	.	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	intron	7523894	7524001	.	+	.	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	CDS	7524002	7524223	1	+	0	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	exon	7524002	7524223	.	+	.	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
Phchi.S4	AUGUSTUS	stop_codon	7524224	7524226	.	+	0	transcript_id "Phchi.S4G123600.t1"; gene_id "Phchi.S4G123600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg15670.t1 is derived from g14139.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20593083	20597601	.	-	.	Phchi.S3G298900
Phchi.S3	AUGUSTUS	transcript	20594625	20597601	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	stop_codon	20594463	20594465	.	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594625	20594630	1	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594625	20594630	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594631	20594700	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594701	20594720	1	-	2	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594701	20594720	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594721	20594902	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594903	20594926	0.99	-	2	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594903	20594926	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594927	20594998	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594999	20595027	1	-	1	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594999	20595027	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595028	20595156	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595157	20595167	1	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595157	20595167	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595168	20595240	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595241	20595357	1	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595241	20595357	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595358	20595465	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595466	20595532	0.91	-	1	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595466	20595532	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595533	20595642	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595643	20595758	0.98	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595643	20595758	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595759	20595845	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595846	20595948	1	-	1	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595846	20595948	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595949	20596109	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596110	20596179	1	-	2	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596110	20596179	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596180	20596337	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596338	20596474	0.99	-	1	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596338	20596474	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596475	20596577	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596578	20596662	0.96	-	2	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596578	20596662	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596663	20596771	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596772	20596868	1	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596772	20596868	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596869	20596959	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596960	20597049	1	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596960	20597049	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20597050	20597145	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20597146	20597311	1	-	1	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20597146	20597311	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20597312	20597404	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20597405	20597601	0.87	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20597405	20597601	.	-	.	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	start_codon	20597599	20597601	.	-	0	transcript_id "Phchi.S3G298900.t1"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	transcript	20593083	20594441	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	stop_codon	20593080	20593082	.	-	0	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593083	20593158	0.99	-	1	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593083	20593158	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593159	20593246	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593247	20593333	1	-	1	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593247	20593333	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593334	20593439	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593440	20593568	1	-	1	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593440	20593568	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593569	20593702	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593703	20593782	1	-	0	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593703	20593782	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593783	20593917	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593918	20594026	1	-	1	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593918	20594026	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594027	20594109	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594110	20594216	1	-	0	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594110	20594216	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594217	20594283	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594284	20594347	1	-	1	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594284	20594347	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594348	20594436	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594437	20594441	1	-	0	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594437	20594441	.	-	.	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	start_codon	20594439	20594441	.	-	0	transcript_id "Phchi.S3G298900.t2"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	transcript	20593083	20594441	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	stop_codon	20593080	20593082	.	-	0	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593083	20593158	0.99	-	1	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593083	20593158	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593159	20593246	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593247	20593333	1	-	1	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593247	20593333	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593334	20593439	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593440	20593568	1	-	1	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593440	20593568	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593569	20593702	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593703	20593776	0.87	-	0	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593703	20593776	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593777	20593917	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593918	20594026	1	-	1	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593918	20594026	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594027	20594109	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594110	20594216	1	-	0	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594110	20594216	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594217	20594283	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594284	20594347	1	-	1	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594284	20594347	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594348	20594436	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594437	20594441	1	-	0	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594437	20594441	.	-	.	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	start_codon	20594439	20594441	.	-	0	transcript_id "Phchi.S3G298900.t3"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	transcript	20593083	20597601	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	stop_codon	20593080	20593082	.	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593083	20593158	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593083	20593158	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593159	20593246	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593247	20593333	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593247	20593333	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593334	20593439	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593440	20593568	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593440	20593568	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593569	20593702	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593703	20593782	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593703	20593782	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20593783	20593917	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20593918	20594026	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20593918	20594026	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594027	20594109	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594110	20594216	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594110	20594216	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594217	20594283	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594284	20594347	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594284	20594347	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594348	20594436	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594437	20594454	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594437	20594454	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594455	20594624	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594625	20594720	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594625	20594720	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594721	20594810	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594811	20594902	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594811	20594902	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20594903	20594996	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20594997	20595027	0.79	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20594997	20595027	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595028	20595156	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595157	20595167	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595157	20595167	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595168	20595240	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595241	20595357	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595241	20595357	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595358	20595465	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595466	20595532	0.92	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595466	20595532	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595533	20595642	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595643	20595758	0.98	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595643	20595758	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595759	20595845	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20595846	20595948	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20595846	20595948	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20595949	20596109	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596110	20596179	1	-	2	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596110	20596179	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596180	20596337	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596338	20596474	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596338	20596474	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596475	20596577	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596578	20596662	0.94	-	2	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596578	20596662	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596663	20596771	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596772	20596868	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596772	20596868	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20596869	20596959	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20596960	20597049	1	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20596960	20597049	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20597050	20597145	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20597146	20597311	1	-	1	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20597146	20597311	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	intron	20597312	20597404	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	CDS	20597405	20597601	0.9	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	exon	20597405	20597601	.	-	.	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
Phchi.S3	AUGUSTUS	start_codon	20597599	20597601	.	-	0	transcript_id "Phchi.S3G298900.t4"; gene_id "Phchi.S3G298900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11245.t1 is derived from g15295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4987557	4989395	.	-	.	Phchi.S4G082700
Phchi.S4	AUGUSTUS	transcript	4987892	4989395	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	stop_codon	4987889	4987891	.	-	0	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4987892	4987975	0.71	-	0	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4987892	4987975	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	intron	4987976	4988048	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4988049	4988340	0.69	-	1	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4988049	4988340	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	intron	4988341	4988462	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4988463	4989240	0.78	-	2	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4988463	4989240	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	intron	4989241	4989316	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4989317	4989395	0.92	-	0	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4989317	4989395	.	-	.	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	start_codon	4989393	4989395	.	-	0	transcript_id "Phchi.S4G082700.t1"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	transcript	4987557	4989395	.	-	.	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	stop_codon	4987554	4987556	.	-	0	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4987557	4988340	0.63	-	1	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4987557	4988340	.	-	.	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	intron	4988341	4988462	.	-	.	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4988463	4989240	0.73	-	2	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4988463	4989240	.	-	.	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	intron	4989241	4989316	.	-	.	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	CDS	4989317	4989395	0.86	-	0	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	exon	4989317	4989395	.	-	.	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
Phchi.S4	AUGUSTUS	start_codon	4989393	4989395	.	-	0	transcript_id "Phchi.S4G082700.t2"; gene_id "Phchi.S4G082700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11154.t1 is derived from g15204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4399516	4403800	.	-	.	Phchi.S4G073600
Phchi.S4	AUGUSTUS	transcript	4399516	4403800	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	stop_codon	4399513	4399515	.	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4399516	4399654	1	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4399516	4399654	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4399655	4399743	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4399744	4399894	1	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4399744	4399894	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4399895	4399976	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4399977	4400049	1	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4399977	4400049	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4400050	4400161	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4400162	4400328	0.99	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4400162	4400328	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4400329	4400423	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4400424	4400522	0.67	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4400424	4400522	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4400523	4400615	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4400616	4400707	0.98	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4400616	4400707	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4400708	4400786	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4400787	4400873	0.71	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4400787	4400873	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4400874	4401034	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4401035	4401102	0.47	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4401035	4401102	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4401103	4401216	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4401217	4401297	0.98	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4401217	4401297	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4401298	4401455	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4401456	4401514	1	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4401456	4401514	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4401515	4401654	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4401655	4401715	1	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4401655	4401715	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4401716	4401798	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4401799	4401865	1	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4401799	4401865	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4401866	4401949	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4401950	4402014	0.99	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4401950	4402014	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402015	4402133	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4402134	4402191	1	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4402134	4402191	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402192	4402326	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4402327	4402339	1	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4402327	4402339	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402340	4402414	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4402415	4402436	0.99	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4402415	4402436	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402437	4402549	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4402550	4402610	0.98	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4402550	4402610	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402611	4402703	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4402704	4402746	1	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4402704	4402746	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402747	4402929	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4402930	4402973	1	-	1	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4402930	4402973	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4402974	4403073	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4403074	4403138	1	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4403074	4403138	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4403139	4403227	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4403228	4403286	1	-	2	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4403228	4403286	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	intron	4403287	4403445	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	CDS	4403446	4403800	0.68	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	exon	4403446	4403800	.	-	.	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
Phchi.S4	AUGUSTUS	start_codon	4403798	4403800	.	-	0	transcript_id "Phchi.S4G073600.t1"; gene_id "Phchi.S4G073600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7148.t1 is derived from g4320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27197776	27198265	.	+	.	Phchi.S1G430700
Phchi.S1	AUGUSTUS	transcript	27197776	27198265	.	+	.	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	start_codon	27197776	27197778	.	+	0	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	CDS	27197776	27198094	0.91	+	0	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	exon	27197776	27198094	.	+	.	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	intron	27198095	27198215	.	+	.	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	CDS	27198216	27198265	0.46	+	2	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	exon	27198216	27198265	.	+	.	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
Phchi.S1	AUGUSTUS	stop_codon	27198266	27198268	.	+	0	transcript_id "Phchi.S1G430700.t1"; gene_id "Phchi.S1G430700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4549.t1 is derived from g1719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11066926	11067972	.	-	.	Phchi.S1G170800
Phchi.S1	AUGUSTUS	transcript	11066926	11067972	.	-	.	transcript_id "Phchi.S1G170800.t1"; gene_id "Phchi.S1G170800"
Phchi.S1	AUGUSTUS	stop_codon	11066923	11066925	.	-	0	transcript_id "Phchi.S1G170800.t1"; gene_id "Phchi.S1G170800"
Phchi.S1	AUGUSTUS	CDS	11066926	11067972	0.95	-	0	transcript_id "Phchi.S1G170800.t1"; gene_id "Phchi.S1G170800"
Phchi.S1	AUGUSTUS	exon	11066926	11067972	.	-	.	transcript_id "Phchi.S1G170800.t1"; gene_id "Phchi.S1G170800"
Phchi.S1	AUGUSTUS	start_codon	11067970	11067972	.	-	0	transcript_id "Phchi.S1G170800.t1"; gene_id "Phchi.S1G170800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10076.t1 is derived from g7252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45634639	45636204	.	+	.	Phchi.S1G723500
Phchi.S1	AUGUSTUS	transcript	45634639	45636204	.	+	.	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	start_codon	45634639	45634641	.	+	0	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	CDS	45634639	45634801	0.51	+	0	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	exon	45634639	45634801	.	+	.	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	intron	45634802	45634893	.	+	.	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	CDS	45634894	45635373	0.99	+	2	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	exon	45634894	45635373	.	+	.	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	intron	45635374	45635458	.	+	.	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	CDS	45635459	45636204	0.97	+	2	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	exon	45635459	45636204	.	+	.	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
Phchi.S1	AUGUSTUS	stop_codon	45636205	45636207	.	+	0	transcript_id "Phchi.S1G723500.t1"; gene_id "Phchi.S1G723500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8119.t1 is derived from g5294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33445783	33448972	.	-	.	Phchi.S1G527800
Phchi.S1	AUGUSTUS	transcript	33445783	33448972	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	stop_codon	33445780	33445782	.	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33445783	33445822	1	-	1	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33445783	33445822	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33445823	33446015	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33446016	33446728	0.81	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33446016	33446728	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33446729	33446874	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33446875	33447025	1	-	1	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33446875	33447025	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33447026	33447283	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33447284	33447396	1	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33447284	33447396	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33447397	33447508	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33447509	33447617	1	-	1	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33447509	33447617	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33447618	33447810	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33447811	33447923	0.95	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33447811	33447923	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33447924	33448030	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33448031	33448195	1	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33448031	33448195	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	intron	33448196	33448837	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	CDS	33448838	33448972	0.64	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	exon	33448838	33448972	.	-	.	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
Phchi.S1	AUGUSTUS	start_codon	33448970	33448972	.	-	0	transcript_id "Phchi.S1G527800.t1"; gene_id "Phchi.S1G527800"
# This transcript jg12428.t2 is derived from g8105.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12429.t1 is derived from g8106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19587579	19588909	.	+	.	Phchi.S2G050900
Phchi.S2	AUGUSTUS	transcript	19587579	19588909	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	start_codon	19587579	19587581	.	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	CDS	19587579	19587626	0.7	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	exon	19587579	19587626	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	intron	19587627	19587754	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	CDS	19587755	19587991	0.3	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	exon	19587755	19587991	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	intron	19587992	19588128	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	CDS	19588129	19588248	0.17	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	exon	19588129	19588248	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	intron	19588249	19588381	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	CDS	19588382	19588594	0.11	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	exon	19588382	19588594	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	intron	19588595	19588720	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	CDS	19588721	19588909	0.21	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	exon	19588721	19588909	.	+	.	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
Phchi.S2	AUGUSTUS	stop_codon	19588910	19588912	.	+	0	transcript_id "Phchi.S2G050900.t1"; gene_id "Phchi.S2G050900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12612.t1 is derived from g8289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37573938	37576037	.	-	.	Phchi.S2G069200
Phchi.S2	AUGUSTUS	transcript	37573938	37576037	.	-	.	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	stop_codon	37573935	37573937	.	-	0	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	CDS	37573938	37575514	0.98	-	2	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	exon	37573938	37575514	.	-	.	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	intron	37575515	37575608	.	-	.	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	CDS	37575609	37575809	0.58	-	2	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	exon	37575609	37575809	.	-	.	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	intron	37575810	37575901	.	-	.	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	CDS	37575902	37576037	0.28	-	0	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	exon	37575902	37576037	.	-	.	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
Phchi.S2	AUGUSTUS	start_codon	37576035	37576037	.	-	0	transcript_id "Phchi.S2G069200.t1"; gene_id "Phchi.S2G069200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13799.t1 is derived from g12266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8948331	8949363	.	+	.	Phchi.S3G111800
Phchi.S3	AUGUSTUS	transcript	8948331	8949363	.	+	.	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	start_codon	8948331	8948333	.	+	0	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	CDS	8948331	8948471	0.91	+	0	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	exon	8948331	8948471	.	+	.	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	intron	8948472	8948643	.	+	.	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	CDS	8948644	8949363	0.93	+	0	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	exon	8948644	8949363	.	+	.	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
Phchi.S3	AUGUSTUS	stop_codon	8949364	8949366	.	+	0	transcript_id "Phchi.S3G111800.t1"; gene_id "Phchi.S3G111800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12626.t1 is derived from g8303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37647587	37648735	.	-	.	Phchi.S2G070600
Phchi.S2	AUGUSTUS	transcript	37647587	37648735	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	stop_codon	37647584	37647586	.	-	0	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	CDS	37647587	37647817	0.88	-	0	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	exon	37647587	37647817	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	intron	37647818	37647895	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	CDS	37647896	37647954	0.92	-	2	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	exon	37647896	37647954	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	intron	37647955	37648147	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	CDS	37648148	37648172	0.92	-	0	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	exon	37648148	37648172	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	intron	37648173	37648289	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	CDS	37648290	37648438	1	-	2	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	exon	37648290	37648438	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	intron	37648439	37648524	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	CDS	37648525	37648586	1	-	1	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	exon	37648525	37648586	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	intron	37648587	37648673	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	CDS	37648674	37648735	1	-	0	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	exon	37648674	37648735	.	-	.	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
Phchi.S2	AUGUSTUS	start_codon	37648733	37648735	.	-	0	transcript_id "Phchi.S2G070600.t1"; gene_id "Phchi.S2G070600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1028.t1 is derived from g10811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7209424	7210457	.	-	.	Phchi.S6G098700
Phchi.S6	AUGUSTUS	transcript	7209424	7210457	.	-	.	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	stop_codon	7209421	7209423	.	-	0	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	CDS	7209424	7209953	0.72	-	2	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	exon	7209424	7209953	.	-	.	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	intron	7209954	7210033	.	-	.	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	CDS	7210034	7210457	0.72	-	0	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	exon	7210034	7210457	.	-	.	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
Phchi.S6	AUGUSTUS	start_codon	7210455	7210457	.	-	0	transcript_id "Phchi.S6G098700.t1"; gene_id "Phchi.S6G098700"
# This transcript jg2330.t2 is derived from g9250.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2331.t1 is derived from g9251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6207108	6208052	.	+	.	Phchi.S5G094000
Phchi.S5	AUGUSTUS	transcript	6207108	6208052	.	+	.	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	start_codon	6207108	6207110	.	+	0	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	CDS	6207108	6207334	1	+	0	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	exon	6207108	6207334	.	+	.	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	intron	6207335	6207619	.	+	.	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	CDS	6207620	6208052	0.99	+	1	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	exon	6207620	6208052	.	+	.	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
Phchi.S5	AUGUSTUS	stop_codon	6208053	6208055	.	+	0	transcript_id "Phchi.S5G094000.t1"; gene_id "Phchi.S5G094000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6152.t1 is derived from g3323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21209569	21211890	.	-	.	Phchi.S1G331100
Phchi.S1	AUGUSTUS	transcript	21209569	21211890	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	stop_codon	21209566	21209568	.	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21209569	21209769	1	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21209569	21209769	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21209770	21209872	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21209873	21210007	0.88	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21209873	21210007	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21210008	21210147	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21210148	21210180	0.79	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21210148	21210180	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21210181	21210264	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21210265	21210392	0.9	-	2	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21210265	21210392	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21210393	21210488	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21210489	21210540	0.91	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21210489	21210540	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21210541	21210637	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21210638	21210703	0.75	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21210638	21210703	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21210704	21210829	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21210830	21210985	0.77	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21210830	21210985	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21210986	21211106	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21211107	21211157	0.77	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21211107	21211157	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21211158	21211240	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21211241	21211254	0.77	-	2	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21211241	21211254	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21211255	21211502	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21211503	21211676	0.76	-	2	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21211503	21211676	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	intron	21211677	21211796	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	CDS	21211797	21211890	0.58	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	exon	21211797	21211890	.	-	.	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
Phchi.S1	AUGUSTUS	start_codon	21211888	21211890	.	-	0	transcript_id "Phchi.S1G331100.t1"; gene_id "Phchi.S1G331100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12939.t1 is derived from g11404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3254193	3255551	.	-	.	Phchi.S3G025800
Phchi.S3	AUGUSTUS	transcript	3254193	3255551	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	stop_codon	3254190	3254192	.	-	0	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	CDS	3254193	3254210	0.75	-	0	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	exon	3254193	3254210	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	intron	3254211	3254293	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	CDS	3254294	3254346	0.42	-	2	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	exon	3254294	3254346	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	intron	3254347	3254467	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	CDS	3254468	3254657	0.37	-	0	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	exon	3254468	3254657	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	intron	3254658	3254734	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	CDS	3254735	3255196	1	-	0	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	exon	3254735	3255196	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	intron	3255197	3255290	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	CDS	3255291	3255551	0.92	-	0	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	exon	3255291	3255551	.	-	.	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
Phchi.S3	AUGUSTUS	start_codon	3255549	3255551	.	-	0	transcript_id "Phchi.S3G025800.t1"; gene_id "Phchi.S3G025800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6145.t1 is derived from g3316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21147359	21148781	.	-	.	Phchi.S1G330400
Phchi.S1	AUGUSTUS	transcript	21147359	21148781	.	-	.	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	stop_codon	21147356	21147358	.	-	0	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	CDS	21147359	21148270	0.63	-	0	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	exon	21147359	21148270	.	-	.	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	intron	21148271	21148356	.	-	.	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	CDS	21148357	21148627	0.67	-	1	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	exon	21148357	21148627	.	-	.	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	intron	21148628	21148722	.	-	.	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	CDS	21148723	21148781	0.87	-	0	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	exon	21148723	21148781	.	-	.	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
Phchi.S1	AUGUSTUS	start_codon	21148779	21148781	.	-	0	transcript_id "Phchi.S1G330400.t1"; gene_id "Phchi.S1G330400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4065.t1 is derived from g1234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7612114	7614547	.	-	.	Phchi.S1G122400
Phchi.S1	AUGUSTUS	transcript	7612114	7614547	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	stop_codon	7612111	7612113	.	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7612114	7612338	0.7	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7612114	7612338	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7612339	7612415	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7612416	7612553	1	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7612416	7612553	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7612554	7612639	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7612640	7612825	1	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7612640	7612825	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7612826	7612951	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7612952	7613077	1	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7612952	7613077	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7613078	7613173	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7613174	7613382	1	-	2	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7613174	7613382	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7613383	7613489	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7613490	7613744	0.68	-	2	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7613490	7613744	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7613745	7613835	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7613836	7614056	1	-	1	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7613836	7614056	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	intron	7614057	7614134	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	CDS	7614135	7614547	0.98	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	exon	7614135	7614547	.	-	.	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
Phchi.S1	AUGUSTUS	start_codon	7614545	7614547	.	-	0	transcript_id "Phchi.S1G122400.t1"; gene_id "Phchi.S1G122400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg679.t1 is derived from g10461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4679473	4679934	.	-	.	Phchi.S6G063800
Phchi.S6	AUGUSTUS	transcript	4679473	4679934	.	-	.	transcript_id "Phchi.S6G063800.t1"; gene_id "Phchi.S6G063800"
Phchi.S6	AUGUSTUS	stop_codon	4679470	4679472	.	-	0	transcript_id "Phchi.S6G063800.t1"; gene_id "Phchi.S6G063800"
Phchi.S6	AUGUSTUS	CDS	4679473	4679934	0.6	-	0	transcript_id "Phchi.S6G063800.t1"; gene_id "Phchi.S6G063800"
Phchi.S6	AUGUSTUS	exon	4679473	4679934	.	-	.	transcript_id "Phchi.S6G063800.t1"; gene_id "Phchi.S6G063800"
Phchi.S6	AUGUSTUS	start_codon	4679932	4679934	.	-	0	transcript_id "Phchi.S6G063800.t1"; gene_id "Phchi.S6G063800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14034.t1 is derived from g12501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10400503	10402211	.	-	.	Phchi.S3G135300
Phchi.S3	AUGUSTUS	transcript	10400503	10402211	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	stop_codon	10400500	10400502	.	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10400503	10400663	0.99	-	2	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10400503	10400663	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10400664	10400747	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10400748	10400783	1	-	2	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10400748	10400783	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10400784	10400947	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10400948	10400999	0.88	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10400948	10400999	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10401000	10401088	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10401089	10401211	1	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10401089	10401211	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10401212	10401355	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10401356	10401481	1	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10401356	10401481	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10401482	10401586	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10401587	10401691	1	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10401587	10401691	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10401692	10401793	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10401794	10401933	1	-	2	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10401794	10401933	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	intron	10401934	10402063	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	CDS	10402064	10402211	0.68	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	exon	10402064	10402211	.	-	.	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
Phchi.S3	AUGUSTUS	start_codon	10402209	10402211	.	-	0	transcript_id "Phchi.S3G135300.t1"; gene_id "Phchi.S3G135300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2365.t1 is derived from g9285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6357782	6361602	.	+	.	Phchi.S5G097400
Phchi.S5	AUGUSTUS	transcript	6357782	6361602	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	start_codon	6357782	6357784	.	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6357782	6358480	0.82	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6357782	6358480	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6358481	6358702	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6358703	6359008	0.53	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6358703	6359008	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6359009	6359111	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6359112	6359237	0.99	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6359112	6359237	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6359238	6359356	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6359357	6359512	1	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6359357	6359512	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6359513	6359608	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6359609	6359788	1	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6359609	6359788	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6359789	6359881	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6359882	6359998	1	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6359882	6359998	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6359999	6360162	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6360163	6360216	1	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6360163	6360216	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6360217	6360345	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6360346	6360417	1	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6360346	6360417	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6360418	6360500	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6360501	6360609	1	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6360501	6360609	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6360610	6360755	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6360756	6360852	1	+	2	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6360756	6360852	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6360853	6360933	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6360934	6361028	1	+	1	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6360934	6361028	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6361029	6361126	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6361127	6361201	1	+	2	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6361127	6361201	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6361202	6361293	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6361294	6361377	1	+	2	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6361294	6361377	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	intron	6361378	6361477	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	CDS	6361478	6361602	1	+	2	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	exon	6361478	6361602	.	+	.	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
Phchi.S5	AUGUSTUS	stop_codon	6361603	6361605	.	+	0	transcript_id "Phchi.S5G097400.t1"; gene_id "Phchi.S5G097400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5290.t1 is derived from g2460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16038245	16040210	.	-	.	Phchi.S1G244900
Phchi.S1	AUGUSTUS	transcript	16038245	16040210	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	stop_codon	16038242	16038244	.	-	0	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	CDS	16038245	16038339	0.62	-	2	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	exon	16038245	16038339	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	intron	16038340	16038586	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	CDS	16038587	16039045	0.8	-	2	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	exon	16038587	16039045	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	intron	16039046	16039216	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	CDS	16039217	16039471	0.77	-	2	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	exon	16039217	16039471	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	intron	16039472	16039582	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	CDS	16039583	16040210	0.81	-	0	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	exon	16039583	16040210	.	-	.	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	start_codon	16040208	16040210	.	-	0	transcript_id "Phchi.S1G244900.t1"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	transcript	16039382	16040210	.	-	.	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	stop_codon	16039379	16039381	.	-	0	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	CDS	16039382	16039457	0.29	-	1	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	exon	16039382	16039457	.	-	.	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	intron	16039458	16039563	.	-	.	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	CDS	16039564	16040210	0.39	-	0	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	exon	16039564	16040210	.	-	.	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
Phchi.S1	AUGUSTUS	start_codon	16040208	16040210	.	-	0	transcript_id "Phchi.S1G244900.t2"; gene_id "Phchi.S1G244900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7335.t1 is derived from g4507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28563700	28565260	.	+	.	Phchi.S1G449400
Phchi.S1	AUGUSTUS	transcript	28563700	28565260	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	start_codon	28563700	28563702	.	+	0	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	CDS	28563700	28563883	0.96	+	0	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	exon	28563700	28563883	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	intron	28563884	28563976	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	CDS	28563977	28564248	1	+	2	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	exon	28563977	28564248	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	intron	28564249	28564349	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	CDS	28564350	28564548	0.92	+	0	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	exon	28564350	28564548	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	intron	28564549	28564651	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	CDS	28564652	28564767	1	+	2	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	exon	28564652	28564767	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	intron	28564768	28564888	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	CDS	28564889	28565024	1	+	0	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	exon	28564889	28565024	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	intron	28565025	28565114	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	CDS	28565115	28565260	1	+	2	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	exon	28565115	28565260	.	+	.	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
Phchi.S1	AUGUSTUS	stop_codon	28565261	28565263	.	+	0	transcript_id "Phchi.S1G449400.t1"; gene_id "Phchi.S1G449400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11915.t1 is derived from g15967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9300247	9301247	.	-	.	Phchi.S4G149700
Phchi.S4	AUGUSTUS	transcript	9300247	9301247	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	stop_codon	9300244	9300246	.	-	0	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	CDS	9300247	9300281	1	-	2	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	exon	9300247	9300281	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	intron	9300282	9300368	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	CDS	9300369	9300433	1	-	1	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	exon	9300369	9300433	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	intron	9300434	9300510	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	CDS	9300511	9300558	1	-	1	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	exon	9300511	9300558	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	intron	9300559	9300665	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	CDS	9300666	9300845	0.99	-	1	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	exon	9300666	9300845	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	intron	9300846	9300916	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	CDS	9300917	9301035	1	-	0	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	exon	9300917	9301035	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	intron	9301036	9301115	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	CDS	9301116	9301247	1	-	0	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	exon	9301116	9301247	.	-	.	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
Phchi.S4	AUGUSTUS	start_codon	9301245	9301247	.	-	0	transcript_id "Phchi.S4G149700.t1"; gene_id "Phchi.S4G149700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13796.t1 is derived from g12263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8930571	8932543	.	-	.	Phchi.S3G111500
Phchi.S3	AUGUSTUS	transcript	8930571	8932543	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	stop_codon	8930568	8930570	.	-	0	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8930571	8930599	0.7	-	2	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8930571	8930599	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8930600	8930945	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8930946	8930953	0.93	-	1	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8930946	8930953	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8930954	8931042	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8931043	8931194	1	-	0	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8931043	8931194	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8931195	8931283	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8931284	8931439	1	-	0	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8931284	8931439	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8931440	8931567	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8931568	8931856	0.99	-	1	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8931568	8931856	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8931857	8931965	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8931966	8932082	0.98	-	1	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8931966	8932082	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8932083	8932188	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8932189	8932278	0.79	-	1	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8932189	8932278	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	intron	8932279	8932358	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	CDS	8932359	8932543	0.82	-	0	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	exon	8932359	8932543	.	-	.	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
Phchi.S3	AUGUSTUS	start_codon	8932541	8932543	.	-	0	transcript_id "Phchi.S3G111500.t1"; gene_id "Phchi.S3G111500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10896.t1 is derived from g14946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2806081	2807592	.	-	.	Phchi.S4G047800
Phchi.S4	AUGUSTUS	transcript	2806081	2807592	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	stop_codon	2806078	2806080	.	-	0	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	CDS	2806081	2806289	0.3	-	2	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	exon	2806081	2806289	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	intron	2806290	2806396	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	CDS	2806397	2806525	0.49	-	2	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	exon	2806397	2806525	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	intron	2806526	2806643	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	CDS	2806644	2806922	1	-	2	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	exon	2806644	2806922	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	intron	2806923	2807006	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	CDS	2807007	2807062	1	-	1	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	exon	2807007	2807062	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	intron	2807063	2807251	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	CDS	2807252	2807342	1	-	2	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	exon	2807252	2807342	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	intron	2807343	2807483	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	CDS	2807484	2807592	0.92	-	0	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	exon	2807484	2807592	.	-	.	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
Phchi.S4	AUGUSTUS	start_codon	2807590	2807592	.	-	0	transcript_id "Phchi.S4G047800.t1"; gene_id "Phchi.S4G047800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1471.t1 is derived from g8390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1094404	1097259	.	-	.	Phchi.S5G008000
Phchi.S5	AUGUSTUS	transcript	1094404	1097259	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	stop_codon	1094401	1094403	.	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1094404	1094494	1	-	1	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1094404	1094494	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1094495	1094587	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1094588	1094700	1	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1094588	1094700	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1094701	1094786	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1094787	1094921	1	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1094787	1094921	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1094922	1095003	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1095004	1095094	1	-	1	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1095004	1095094	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1095095	1095233	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1095234	1095302	1	-	1	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1095234	1095302	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1095303	1095430	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1095431	1095618	1	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1095431	1095618	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1095619	1095905	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1095906	1096040	1	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1095906	1096040	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1096041	1096126	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1096127	1096201	1	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1096127	1096201	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1096202	1096353	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1096354	1096594	1	-	1	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1096354	1096594	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1096595	1096690	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1096691	1096769	1	-	2	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1096691	1096769	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1096770	1096888	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1096889	1096981	1	-	2	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1096889	1096981	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	intron	1096982	1097249	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	CDS	1097250	1097259	1	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	exon	1097250	1097259	.	-	.	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
Phchi.S5	AUGUSTUS	start_codon	1097257	1097259	.	-	0	transcript_id "Phchi.S5G008000.t1"; gene_id "Phchi.S5G008000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9822.t1 is derived from g6998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43951376	43953231	.	-	.	Phchi.S1G698100
Phchi.S1	AUGUSTUS	transcript	43951376	43953030	.	-	.	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	stop_codon	43951373	43951375	.	-	0	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	CDS	43951376	43952590	0.89	-	0	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	exon	43951376	43952590	.	-	.	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	intron	43952591	43952706	.	-	.	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	CDS	43952707	43953030	0.7	-	0	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	exon	43952707	43953030	.	-	.	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	start_codon	43953028	43953030	.	-	0	transcript_id "Phchi.S1G698100.t1"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	transcript	43951376	43953231	.	-	.	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	stop_codon	43951373	43951375	.	-	0	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	CDS	43951376	43952590	0.84	-	0	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	exon	43951376	43952590	.	-	.	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	intron	43952591	43952706	.	-	.	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	CDS	43952707	43953014	0.62	-	2	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	exon	43952707	43953014	.	-	.	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	intron	43953015	43953098	.	-	.	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	CDS	43953099	43953231	0.65	-	0	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	exon	43953099	43953231	.	-	.	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
Phchi.S1	AUGUSTUS	start_codon	43953229	43953231	.	-	0	transcript_id "Phchi.S1G698100.t2"; gene_id "Phchi.S1G698100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13761.t1 is derived from g12228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8749198	8749715	.	-	.	Phchi.S3G108000
Phchi.S3	AUGUSTUS	transcript	8749198	8749715	.	-	.	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	stop_codon	8749195	8749197	.	-	0	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	CDS	8749198	8749312	0.76	-	1	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	exon	8749198	8749312	.	-	.	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	intron	8749313	8749416	.	-	.	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	CDS	8749417	8749715	0.89	-	0	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	exon	8749417	8749715	.	-	.	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
Phchi.S3	AUGUSTUS	start_codon	8749713	8749715	.	-	0	transcript_id "Phchi.S3G108000.t1"; gene_id "Phchi.S3G108000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3217.t1 is derived from g386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2281217	2287282	.	-	.	Phchi.S1G037600
Phchi.S1	AUGUSTUS	transcript	2281217	2287282	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	stop_codon	2281214	2281216	.	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2281217	2281297	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2281217	2281297	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2281298	2281434	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2281435	2281548	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2281435	2281548	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2281549	2281634	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2281635	2281795	1	-	2	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2281635	2281795	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2281796	2282035	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2282036	2282177	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2282036	2282177	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2282178	2282280	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2282281	2282489	0.98	-	2	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2282281	2282489	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2282490	2282623	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2282624	2282780	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2282624	2282780	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2282781	2282931	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2282932	2283106	1	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2282932	2283106	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2283107	2283199	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2283200	2283388	0.99	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2283200	2283388	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2283389	2283503	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2283504	2283602	1	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2283504	2283602	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2283603	2283746	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2283747	2283869	1	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2283747	2283869	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2283870	2284007	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2284008	2284139	1	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2284008	2284139	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2284140	2284258	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2284259	2284344	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2284259	2284344	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2284345	2284441	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2284442	2284499	1	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2284442	2284499	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2284500	2284573	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2284574	2284779	0.99	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2284574	2284779	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2284780	2284913	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2284914	2284997	0.67	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2284914	2284997	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2284998	2285116	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2285117	2285284	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2285117	2285284	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2285285	2285416	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2285417	2285509	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2285417	2285509	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2285510	2285592	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2285593	2285751	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2285593	2285751	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2285752	2285854	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2285855	2285980	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2285855	2285980	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2285981	2286061	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2286062	2286096	1	-	2	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2286062	2286096	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2286097	2286193	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2286194	2286324	0.54	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2286194	2286324	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2286325	2286478	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2286479	2286548	1	-	2	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2286479	2286548	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2286549	2286669	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2286670	2286748	1	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2286670	2286748	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2286749	2286842	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2286843	2286952	0.79	-	2	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2286843	2286952	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2286953	2287071	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2287072	2287136	1	-	1	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2287072	2287136	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	intron	2287137	2287208	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	CDS	2287209	2287282	0.98	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	exon	2287209	2287282	.	-	.	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
Phchi.S1	AUGUSTUS	start_codon	2287280	2287282	.	-	0	transcript_id "Phchi.S1G037600.t1"; gene_id "Phchi.S1G037600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14580.t1 is derived from g13048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13563862	13565204	.	-	.	Phchi.S3G189900
Phchi.S3	AUGUSTUS	transcript	13563862	13565204	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	stop_codon	13563859	13563861	.	-	0	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	CDS	13563862	13564006	0.96	-	1	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	exon	13563862	13564006	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	intron	13564007	13564107	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	CDS	13564108	13564211	0.96	-	0	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	exon	13564108	13564211	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	intron	13564212	13564304	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	CDS	13564305	13564639	0.45	-	2	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	exon	13564305	13564639	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	intron	13564640	13564731	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	CDS	13564732	13564748	0.45	-	1	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	exon	13564732	13564748	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	intron	13564749	13564842	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	CDS	13564843	13565204	0.29	-	0	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	exon	13564843	13565204	.	-	.	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
Phchi.S3	AUGUSTUS	start_codon	13565202	13565204	.	-	0	transcript_id "Phchi.S3G189900.t1"; gene_id "Phchi.S3G189900"
# This transcript jg5886.t2 is derived from g3056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5887.t1 is derived from g3057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19599756	19602985	.	-	.	Phchi.S1G304600
Phchi.S1	AUGUSTUS	transcript	19599756	19602985	.	-	.	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	stop_codon	19599753	19599755	.	-	0	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	CDS	19599756	19600904	0.99	-	0	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	exon	19599756	19600904	.	-	.	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	intron	19600905	19601089	.	-	.	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	CDS	19601090	19602985	0.96	-	0	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	exon	19601090	19602985	.	-	.	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
Phchi.S1	AUGUSTUS	start_codon	19602983	19602985	.	-	0	transcript_id "Phchi.S1G304600.t1"; gene_id "Phchi.S1G304600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11437.t1 is derived from g15487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6372814	6373626	.	-	.	Phchi.S4G101900
Phchi.S4	AUGUSTUS	transcript	6372814	6373626	.	-	.	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	stop_codon	6372811	6372813	.	-	0	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	CDS	6372814	6372882	0.85	-	0	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	exon	6372814	6372882	.	-	.	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	intron	6372883	6372958	.	-	.	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	CDS	6372959	6373128	0.92	-	2	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	exon	6372959	6373128	.	-	.	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	intron	6373129	6373244	.	-	.	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	CDS	6373245	6373626	1	-	0	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	exon	6373245	6373626	.	-	.	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
Phchi.S4	AUGUSTUS	start_codon	6373624	6373626	.	-	0	transcript_id "Phchi.S4G101900.t1"; gene_id "Phchi.S4G101900"
# This transcript jg500.t2 is derived from g10282.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg501.t1 is derived from g10283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3485543	3485999	.	+	.	Phchi.S6G046000
Phchi.S6	AUGUSTUS	transcript	3485543	3485999	.	+	.	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	start_codon	3485543	3485545	.	+	0	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	CDS	3485543	3485689	0.9	+	0	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	exon	3485543	3485689	.	+	.	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	intron	3485690	3485828	.	+	.	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	CDS	3485829	3485999	1	+	0	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	exon	3485829	3485999	.	+	.	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
Phchi.S6	AUGUSTUS	stop_codon	3486000	3486002	.	+	0	transcript_id "Phchi.S6G046000.t1"; gene_id "Phchi.S6G046000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2979.t1 is derived from g148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	946976	947587	.	+	.	Phchi.S1G013800
Phchi.S1	AUGUSTUS	transcript	946976	947587	.	+	.	transcript_id "Phchi.S1G013800.t1"; gene_id "Phchi.S1G013800"
Phchi.S1	AUGUSTUS	start_codon	946976	946978	.	+	0	transcript_id "Phchi.S1G013800.t1"; gene_id "Phchi.S1G013800"
Phchi.S1	AUGUSTUS	CDS	946976	947587	1	+	0	transcript_id "Phchi.S1G013800.t1"; gene_id "Phchi.S1G013800"
Phchi.S1	AUGUSTUS	exon	946976	947587	.	+	.	transcript_id "Phchi.S1G013800.t1"; gene_id "Phchi.S1G013800"
Phchi.S1	AUGUSTUS	stop_codon	947588	947590	.	+	0	transcript_id "Phchi.S1G013800.t1"; gene_id "Phchi.S1G013800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11048.t1 is derived from g15098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3819269	3820828	.	+	.	Phchi.S4G063000
Phchi.S4	AUGUSTUS	transcript	3819269	3820828	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	start_codon	3819269	3819271	.	+	0	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	CDS	3819269	3819302	0.92	+	0	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	exon	3819269	3819302	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	intron	3819303	3819431	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	CDS	3819432	3819468	1	+	2	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	exon	3819432	3819468	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	intron	3819469	3819692	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	CDS	3819693	3819900	0.94	+	1	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	exon	3819693	3819900	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	intron	3819901	3820073	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	CDS	3820074	3820232	0.98	+	0	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	exon	3820074	3820232	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	intron	3820233	3820388	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	CDS	3820389	3820508	0.99	+	0	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	exon	3820389	3820508	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	intron	3820509	3820600	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	CDS	3820601	3820828	1	+	0	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	exon	3820601	3820828	.	+	.	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
Phchi.S4	AUGUSTUS	stop_codon	3820829	3820831	.	+	0	transcript_id "Phchi.S4G063000.t1"; gene_id "Phchi.S4G063000"
# This transcript jg5864.t2 is derived from g3034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5865.t1 is derived from g3035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19477965	19479639	.	-	.	Phchi.S1G302400
Phchi.S1	AUGUSTUS	transcript	19477965	19479639	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	stop_codon	19477962	19477964	.	-	0	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19477965	19478045	1	-	0	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19477965	19478045	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	intron	19478046	19478140	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19478141	19478287	1	-	0	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19478141	19478287	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	intron	19478288	19478406	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19478407	19478479	1	-	1	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19478407	19478479	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	intron	19478480	19478575	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19478576	19478720	1	-	2	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19478576	19478720	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	intron	19478721	19478848	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19478849	19479060	1	-	1	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19478849	19479060	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	intron	19479061	19479142	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19479143	19479235	1	-	1	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19479143	19479235	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	intron	19479236	19479355	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	CDS	19479356	19479639	0.5	-	0	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	exon	19479356	19479639	.	-	.	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
Phchi.S1	AUGUSTUS	start_codon	19479637	19479639	.	-	0	transcript_id "Phchi.S1G302400.t1"; gene_id "Phchi.S1G302400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4340.t1 is derived from g1509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9857055	9857930	.	-	.	Phchi.S1G149900
Phchi.S1	AUGUSTUS	transcript	9857055	9857930	.	-	.	transcript_id "Phchi.S1G149900.t1"; gene_id "Phchi.S1G149900"
Phchi.S1	AUGUSTUS	stop_codon	9857052	9857054	.	-	0	transcript_id "Phchi.S1G149900.t1"; gene_id "Phchi.S1G149900"
Phchi.S1	AUGUSTUS	CDS	9857055	9857930	0.57	-	0	transcript_id "Phchi.S1G149900.t1"; gene_id "Phchi.S1G149900"
Phchi.S1	AUGUSTUS	exon	9857055	9857930	.	-	.	transcript_id "Phchi.S1G149900.t1"; gene_id "Phchi.S1G149900"
Phchi.S1	AUGUSTUS	start_codon	9857928	9857930	.	-	0	transcript_id "Phchi.S1G149900.t1"; gene_id "Phchi.S1G149900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1784.t1 is derived from g8704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2993672	2995511	.	-	.	Phchi.S5G039300
Phchi.S5	AUGUSTUS	transcript	2993672	2995511	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	stop_codon	2993669	2993671	.	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2993672	2993779	0.49	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2993672	2993779	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2993780	2993890	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2993891	2993999	0.47	-	1	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2993891	2993999	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2994000	2994093	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2994094	2994161	1	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2994094	2994161	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2994162	2994371	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2994372	2994420	1	-	1	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2994372	2994420	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2994421	2994514	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2994515	2994569	0.79	-	2	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2994515	2994569	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2994570	2994670	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2994671	2994713	0.68	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2994671	2994713	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2994714	2994816	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2994817	2994882	1	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2994817	2994882	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2994883	2994975	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2994976	2995201	1	-	1	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2994976	2995201	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	intron	2995202	2995473	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	CDS	2995474	2995511	0.63	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	exon	2995474	2995511	.	-	.	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
Phchi.S5	AUGUSTUS	start_codon	2995509	2995511	.	-	0	transcript_id "Phchi.S5G039300.t1"; gene_id "Phchi.S5G039300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11472.t1 is derived from g15522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6515912	6519296	.	+	.	Phchi.S4G105400
Phchi.S4	AUGUSTUS	transcript	6515912	6519296	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	start_codon	6515912	6515914	.	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6515912	6516109	0.98	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6515912	6516109	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516110	6516342	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516343	6516405	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516343	6516405	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516406	6516527	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516528	6516596	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516528	6516596	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516597	6516759	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516760	6516812	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516760	6516812	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516813	6516906	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516907	6517003	0.99	+	1	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516907	6517003	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6517004	6517110	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6517111	6517187	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6517111	6517187	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6517188	6517266	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6517267	6517339	1	+	1	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6517267	6517339	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6517340	6517539	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6517540	6517600	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6517540	6517600	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6517601	6517708	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6517709	6517908	0.98	+	2	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6517709	6517908	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6517909	6518024	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6518025	6518273	0.92	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6518025	6518273	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6518274	6518403	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6518404	6518523	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6518404	6518523	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6518524	6518686	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6518687	6518793	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6518687	6518793	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6518794	6518951	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6518952	6519057	1	+	1	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6518952	6519057	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6519058	6519191	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6519192	6519296	1	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6519192	6519296	.	+	.	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	stop_codon	6519297	6519299	.	+	0	transcript_id "Phchi.S4G105400.t1"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	transcript	6515912	6516764	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	start_codon	6515912	6515914	.	+	0	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6515912	6516109	0.95	+	0	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6515912	6516109	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516110	6516342	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516343	6516405	1	+	0	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516343	6516405	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516406	6516527	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516528	6516596	0.99	+	0	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516528	6516596	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	intron	6516597	6516743	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	CDS	6516744	6516764	0.57	+	0	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	exon	6516744	6516764	.	+	.	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
Phchi.S4	AUGUSTUS	stop_codon	6516765	6516767	.	+	0	transcript_id "Phchi.S4G105400.t2"; gene_id "Phchi.S4G105400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12145.t1 is derived from g7821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4874653	4875171	.	+	.	Phchi.S2G022500
Phchi.S2	AUGUSTUS	transcript	4874653	4875171	.	+	.	transcript_id "Phchi.S2G022500.t1"; gene_id "Phchi.S2G022500"
Phchi.S2	AUGUSTUS	start_codon	4874653	4874655	.	+	0	transcript_id "Phchi.S2G022500.t1"; gene_id "Phchi.S2G022500"
Phchi.S2	AUGUSTUS	CDS	4874653	4875171	0.73	+	0	transcript_id "Phchi.S2G022500.t1"; gene_id "Phchi.S2G022500"
Phchi.S2	AUGUSTUS	exon	4874653	4875171	.	+	.	transcript_id "Phchi.S2G022500.t1"; gene_id "Phchi.S2G022500"
Phchi.S2	AUGUSTUS	stop_codon	4875172	4875174	.	+	0	transcript_id "Phchi.S2G022500.t1"; gene_id "Phchi.S2G022500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15002.t1 is derived from g13470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16200042	16200554	.	+	.	Phchi.S3G232100
Phchi.S3	AUGUSTUS	transcript	16200042	16200554	.	+	.	transcript_id "Phchi.S3G232100.t1"; gene_id "Phchi.S3G232100"
Phchi.S3	AUGUSTUS	start_codon	16200042	16200044	.	+	0	transcript_id "Phchi.S3G232100.t1"; gene_id "Phchi.S3G232100"
Phchi.S3	AUGUSTUS	CDS	16200042	16200554	1	+	0	transcript_id "Phchi.S3G232100.t1"; gene_id "Phchi.S3G232100"
Phchi.S3	AUGUSTUS	exon	16200042	16200554	.	+	.	transcript_id "Phchi.S3G232100.t1"; gene_id "Phchi.S3G232100"
Phchi.S3	AUGUSTUS	stop_codon	16200555	16200557	.	+	0	transcript_id "Phchi.S3G232100.t1"; gene_id "Phchi.S3G232100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3598.t1 is derived from g767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4669556	4670786	.	-	.	Phchi.S1G075700
Phchi.S1	AUGUSTUS	transcript	4669556	4670786	.	-	.	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	stop_codon	4669553	4669555	.	-	0	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	CDS	4669556	4670345	0.65	-	1	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	exon	4669556	4670345	.	-	.	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	intron	4670346	4670475	.	-	.	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	CDS	4670476	4670786	0.58	-	0	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	exon	4670476	4670786	.	-	.	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
Phchi.S1	AUGUSTUS	start_codon	4670784	4670786	.	-	0	transcript_id "Phchi.S1G075700.t1"; gene_id "Phchi.S1G075700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9978.t1 is derived from g7154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44755517	44757434	.	-	.	Phchi.S1G713700
Phchi.S1	AUGUSTUS	transcript	44755517	44757434	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	stop_codon	44755514	44755516	.	-	0	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	CDS	44755517	44756146	0.8	-	0	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	exon	44755517	44756146	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	intron	44756147	44756241	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	CDS	44756242	44756556	1	-	0	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	exon	44756242	44756556	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	intron	44756557	44756660	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	CDS	44756661	44756919	1	-	1	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	exon	44756661	44756919	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	intron	44756920	44757015	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	CDS	44757016	44757434	0.97	-	0	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	exon	44757016	44757434	.	-	.	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
Phchi.S1	AUGUSTUS	start_codon	44757432	44757434	.	-	0	transcript_id "Phchi.S1G713700.t1"; gene_id "Phchi.S1G713700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8506.t1 is derived from g5681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36369933	36371320	.	-	.	Phchi.S1G566500
Phchi.S1	AUGUSTUS	transcript	36369933	36371320	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	stop_codon	36369930	36369932	.	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36369933	36369977	0.98	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36369933	36369977	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36369978	36370071	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36370072	36370200	1	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36370072	36370200	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36370201	36370281	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36370282	36370329	1	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36370282	36370329	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36370330	36370416	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36370417	36370479	1	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36370417	36370479	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36370480	36370604	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36370605	36370643	1	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36370605	36370643	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36370644	36370729	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36370730	36370815	1	-	2	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36370730	36370815	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36370816	36370907	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36370908	36370966	1	-	1	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36370908	36370966	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36370967	36371138	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36371139	36371198	1	-	1	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36371139	36371198	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	intron	36371199	36371276	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	CDS	36371277	36371320	0.64	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	exon	36371277	36371320	.	-	.	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
Phchi.S1	AUGUSTUS	start_codon	36371318	36371320	.	-	0	transcript_id "Phchi.S1G566500.t1"; gene_id "Phchi.S1G566500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6762.t1 is derived from g3934.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24920997	24922213	.	-	.	Phchi.S1G392100
Phchi.S1	AUGUSTUS	transcript	24920997	24922213	.	-	.	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	stop_codon	24920994	24920996	.	-	0	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	CDS	24920997	24921621	0.98	-	1	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	exon	24920997	24921621	.	-	.	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	intron	24921622	24921848	.	-	.	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	CDS	24921849	24921869	0.91	-	1	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	exon	24921849	24921869	.	-	.	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	intron	24921870	24921974	.	-	.	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	CDS	24921975	24922213	0.87	-	0	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	exon	24921975	24922213	.	-	.	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	start_codon	24922211	24922213	.	-	0	transcript_id "Phchi.S1G392100.t1"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	transcript	24920997	24922213	.	-	.	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	stop_codon	24920994	24920996	.	-	0	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	CDS	24920997	24921697	0.77	-	2	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	exon	24920997	24921697	.	-	.	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	intron	24921698	24921848	.	-	.	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	CDS	24921849	24921869	0.69	-	2	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	exon	24921849	24921869	.	-	.	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	intron	24921870	24922032	.	-	.	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	CDS	24922033	24922213	0.4	-	0	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	exon	24922033	24922213	.	-	.	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
Phchi.S1	AUGUSTUS	start_codon	24922211	24922213	.	-	0	transcript_id "Phchi.S1G392100.t2"; gene_id "Phchi.S1G392100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3039.t1 is derived from g208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1301875	1302783	.	-	.	Phchi.S1G019800
Phchi.S1	AUGUSTUS	transcript	1301875	1302783	.	-	.	transcript_id "Phchi.S1G019800.t1"; gene_id "Phchi.S1G019800"
Phchi.S1	AUGUSTUS	stop_codon	1301872	1301874	.	-	0	transcript_id "Phchi.S1G019800.t1"; gene_id "Phchi.S1G019800"
Phchi.S1	AUGUSTUS	CDS	1301875	1302783	0.45	-	0	transcript_id "Phchi.S1G019800.t1"; gene_id "Phchi.S1G019800"
Phchi.S1	AUGUSTUS	exon	1301875	1302783	.	-	.	transcript_id "Phchi.S1G019800.t1"; gene_id "Phchi.S1G019800"
Phchi.S1	AUGUSTUS	start_codon	1302781	1302783	.	-	0	transcript_id "Phchi.S1G019800.t1"; gene_id "Phchi.S1G019800"
# This transcript jg8572.t2 is derived from g5747.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8573.t1 is derived from g5748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36700595	36702228	.	-	.	Phchi.S1G573200
Phchi.S1	AUGUSTUS	transcript	36700595	36702228	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	stop_codon	36700592	36700594	.	-	0	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36700595	36700903	1	-	0	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36700595	36700903	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	intron	36700904	36701043	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701044	36701561	0.95	-	2	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701044	36701561	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	intron	36701562	36701634	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701635	36701817	1	-	2	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701635	36701817	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	intron	36701818	36701957	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701958	36702228	0.71	-	0	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701958	36702228	.	-	.	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	start_codon	36702226	36702228	.	-	0	transcript_id "Phchi.S1G573200.t1"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	transcript	36701849	36702228	.	-	.	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	stop_codon	36701846	36701848	.	-	0	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701849	36701874	0.8	-	2	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701849	36701874	.	-	.	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	intron	36701875	36701957	.	-	.	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701958	36702228	0.79	-	0	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701958	36702228	.	-	.	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	start_codon	36702226	36702228	.	-	0	transcript_id "Phchi.S1G573200.t2"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	transcript	36700595	36701641	.	-	.	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	stop_codon	36700592	36700594	.	-	0	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36700595	36700903	1	-	0	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36700595	36700903	.	-	.	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	intron	36700904	36701043	.	-	.	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701044	36701561	0.91	-	2	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701044	36701561	.	-	.	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	intron	36701562	36701634	.	-	.	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	CDS	36701635	36701641	0.38	-	0	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	exon	36701635	36701641	.	-	.	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
Phchi.S1	AUGUSTUS	start_codon	36701639	36701641	.	-	0	transcript_id "Phchi.S1G573200.t3"; gene_id "Phchi.S1G573200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10688.t1 is derived from g14738.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1585398	1587667	.	-	.	Phchi.S4G027000
Phchi.S4	AUGUSTUS	transcript	1585398	1587667	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	stop_codon	1585395	1585397	.	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1585398	1585562	0.88	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1585398	1585562	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1585563	1585740	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1585741	1585818	1	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1585741	1585818	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1585819	1585986	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1585987	1586028	1	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1585987	1586028	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586029	1586166	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1586167	1586336	1	-	2	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1586167	1586336	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586337	1586668	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1586669	1586750	1	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1586669	1586750	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586751	1586864	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1586865	1586935	1	-	2	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1586865	1586935	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586936	1587298	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1587299	1587400	0.97	-	2	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1587299	1587400	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1587401	1587591	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1587592	1587667	0.94	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1587592	1587667	.	-	.	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	start_codon	1587665	1587667	.	-	0	transcript_id "Phchi.S4G027000.t1"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	transcript	1585398	1587667	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	stop_codon	1585395	1585397	.	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1585398	1585562	0.77	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1585398	1585562	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1585563	1585740	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1585741	1585818	1	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1585741	1585818	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1585819	1585986	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1585987	1586028	1	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1585987	1586028	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586029	1586151	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1586152	1586336	0.56	-	2	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1586152	1586336	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586337	1586668	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1586669	1586750	1	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1586669	1586750	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586751	1586864	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1586865	1586935	1	-	2	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1586865	1586935	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1586936	1587298	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1587299	1587400	0.96	-	2	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1587299	1587400	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	intron	1587401	1587591	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	CDS	1587592	1587667	0.93	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	exon	1587592	1587667	.	-	.	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
Phchi.S4	AUGUSTUS	start_codon	1587665	1587667	.	-	0	transcript_id "Phchi.S4G027000.t2"; gene_id "Phchi.S4G027000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8853.t1 is derived from g6028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38288726	38290658	.	-	.	Phchi.S1G601200
Phchi.S1	AUGUSTUS	transcript	38288726	38290658	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	stop_codon	38288723	38288725	.	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38288726	38288839	1	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38288726	38288839	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38288840	38288963	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38288964	38289063	1	-	1	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38288964	38289063	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38289064	38289150	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38289151	38289268	1	-	2	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38289151	38289268	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38289269	38289427	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38289428	38289542	1	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38289428	38289542	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38289543	38289693	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38289694	38289750	1	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38289694	38289750	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38289751	38289970	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38289971	38290012	1	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38289971	38290012	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38290013	38290200	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38290201	38290301	0.29	-	2	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38290201	38290301	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38290302	38290401	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38290402	38290484	0.3	-	1	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38290402	38290484	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	intron	38290485	38290653	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	CDS	38290654	38290658	0.74	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	exon	38290654	38290658	.	-	.	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
Phchi.S1	AUGUSTUS	start_codon	38290656	38290658	.	-	0	transcript_id "Phchi.S1G601200.t1"; gene_id "Phchi.S1G601200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9369.t1 is derived from g6545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41190461	41191870	.	+	.	Phchi.S1G652800
Phchi.S1	AUGUSTUS	transcript	41190461	41191870	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	start_codon	41190461	41190463	.	+	0	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	CDS	41190461	41190575	0.89	+	0	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	exon	41190461	41190575	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	intron	41190576	41190702	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	CDS	41190703	41190813	1	+	2	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	exon	41190703	41190813	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	intron	41190814	41190984	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	CDS	41190985	41191109	1	+	2	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	exon	41190985	41191109	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	intron	41191110	41191274	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	CDS	41191275	41191375	1	+	0	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	exon	41191275	41191375	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	intron	41191376	41191615	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	CDS	41191616	41191675	1	+	1	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	exon	41191616	41191675	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	intron	41191676	41191779	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	CDS	41191780	41191870	0.93	+	1	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	exon	41191780	41191870	.	+	.	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
Phchi.S1	AUGUSTUS	stop_codon	41191871	41191873	.	+	0	transcript_id "Phchi.S1G652800.t1"; gene_id "Phchi.S1G652800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg660.t1 is derived from g10442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4622210	4623467	.	-	.	Phchi.S6G061900
Phchi.S6	AUGUSTUS	transcript	4622210	4623467	.	-	.	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	stop_codon	4622207	4622209	.	-	0	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	CDS	4622210	4622274	0.47	-	2	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	exon	4622210	4622274	.	-	.	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	intron	4622275	4622554	.	-	.	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	CDS	4622555	4622656	0.16	-	2	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	exon	4622555	4622656	.	-	.	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	intron	4622657	4622827	.	-	.	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	CDS	4622828	4623467	0.5	-	0	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	exon	4622828	4623467	.	-	.	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
Phchi.S6	AUGUSTUS	start_codon	4623465	4623467	.	-	0	transcript_id "Phchi.S6G061900.t1"; gene_id "Phchi.S6G061900"
# This transcript jg14461.t2 is derived from g12929.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14461.t3 is derived from g12929.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14462.t1 is derived from g12930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12993614	12995508	.	-	.	Phchi.S3G178100
Phchi.S3	AUGUSTUS	transcript	12993614	12995508	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	stop_codon	12993611	12993613	.	-	0	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	CDS	12993614	12993816	0.88	-	2	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	exon	12993614	12993816	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	intron	12993817	12993990	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	CDS	12993991	12994186	1	-	0	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	exon	12993991	12994186	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	intron	12994187	12994285	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	CDS	12994286	12994320	0.98	-	2	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	exon	12994286	12994320	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	intron	12994321	12994427	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	CDS	12994428	12994485	1	-	0	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	exon	12994428	12994485	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	intron	12994486	12994587	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	CDS	12994588	12994629	0.98	-	0	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	exon	12994588	12994629	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	intron	12994630	12994725	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	CDS	12994726	12995508	0.51	-	0	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	exon	12994726	12995508	.	-	.	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
Phchi.S3	AUGUSTUS	start_codon	12995506	12995508	.	-	0	transcript_id "Phchi.S3G178100.t1"; gene_id "Phchi.S3G178100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7736.t1 is derived from g4910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30895324	30898349	.	-	.	Phchi.S1G489500
Phchi.S1	AUGUSTUS	transcript	30895324	30898349	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	stop_codon	30895321	30895323	.	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30895324	30895474	1	-	1	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30895324	30895474	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30895475	30895567	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30895568	30895704	1	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30895568	30895704	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30895705	30895904	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30895905	30896093	1	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30895905	30896093	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30896094	30896188	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30896189	30896542	0.7	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30896189	30896542	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30896543	30896625	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30896626	30896739	0.47	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30896626	30896739	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30896740	30896860	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30896861	30897670	0.57	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30896861	30897670	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30897671	30897771	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30897772	30897904	0.56	-	1	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30897772	30897904	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30897905	30897990	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30897991	30898088	1	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30897991	30898088	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	intron	30898089	30898172	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	CDS	30898173	30898349	0.89	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	exon	30898173	30898349	.	-	.	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
Phchi.S1	AUGUSTUS	start_codon	30898347	30898349	.	-	0	transcript_id "Phchi.S1G489500.t1"; gene_id "Phchi.S1G489500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11283.t1 is derived from g15333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5192110	5193162	.	-	.	Phchi.S4G086500
Phchi.S4	AUGUSTUS	transcript	5192110	5193162	.	-	.	transcript_id "Phchi.S4G086500.t1"; gene_id "Phchi.S4G086500"
Phchi.S4	AUGUSTUS	stop_codon	5192107	5192109	.	-	0	transcript_id "Phchi.S4G086500.t1"; gene_id "Phchi.S4G086500"
Phchi.S4	AUGUSTUS	CDS	5192110	5193162	0.7	-	0	transcript_id "Phchi.S4G086500.t1"; gene_id "Phchi.S4G086500"
Phchi.S4	AUGUSTUS	exon	5192110	5193162	.	-	.	transcript_id "Phchi.S4G086500.t1"; gene_id "Phchi.S4G086500"
Phchi.S4	AUGUSTUS	start_codon	5193160	5193162	.	-	0	transcript_id "Phchi.S4G086500.t1"; gene_id "Phchi.S4G086500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12603.t1 is derived from g8280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37451443	37452880	.	+	.	Phchi.S2G068300
Phchi.S2	AUGUSTUS	transcript	37451443	37452880	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	start_codon	37451443	37451445	.	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37451443	37451488	0.59	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37451443	37451488	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37451489	37451596	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37451597	37451699	0.59	+	2	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37451597	37451699	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37451700	37451835	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37451836	37451933	1	+	1	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37451836	37451933	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37451934	37452110	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37452111	37452211	1	+	2	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37452111	37452211	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37452212	37452297	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37452298	37452375	1	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37452298	37452375	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37452376	37452565	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37452566	37452604	1	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37452566	37452604	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37452605	37452695	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37452696	37452704	0.99	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37452696	37452704	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	intron	37452705	37452841	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	CDS	37452842	37452880	0.98	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	exon	37452842	37452880	.	+	.	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
Phchi.S2	AUGUSTUS	stop_codon	37452881	37452883	.	+	0	transcript_id "Phchi.S2G068300.t1"; gene_id "Phchi.S2G068300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7505.t1 is derived from g4679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29706223	29707842	.	+	.	Phchi.S1G466400
Phchi.S1	AUGUSTUS	transcript	29706223	29707842	.	+	.	transcript_id "Phchi.S1G466400.t1"; gene_id "Phchi.S1G466400"
Phchi.S1	AUGUSTUS	start_codon	29706223	29706225	.	+	0	transcript_id "Phchi.S1G466400.t1"; gene_id "Phchi.S1G466400"
Phchi.S1	AUGUSTUS	CDS	29706223	29707842	0.62	+	0	transcript_id "Phchi.S1G466400.t1"; gene_id "Phchi.S1G466400"
Phchi.S1	AUGUSTUS	exon	29706223	29707842	.	+	.	transcript_id "Phchi.S1G466400.t1"; gene_id "Phchi.S1G466400"
Phchi.S1	AUGUSTUS	stop_codon	29707843	29707845	.	+	0	transcript_id "Phchi.S1G466400.t1"; gene_id "Phchi.S1G466400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6641.t1 is derived from g3813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24212417	24212920	.	+	.	Phchi.S1G380000
Phchi.S1	AUGUSTUS	transcript	24212417	24212920	.	+	.	transcript_id "Phchi.S1G380000.t1"; gene_id "Phchi.S1G380000"
Phchi.S1	AUGUSTUS	start_codon	24212417	24212419	.	+	0	transcript_id "Phchi.S1G380000.t1"; gene_id "Phchi.S1G380000"
Phchi.S1	AUGUSTUS	CDS	24212417	24212920	0.5	+	0	transcript_id "Phchi.S1G380000.t1"; gene_id "Phchi.S1G380000"
Phchi.S1	AUGUSTUS	exon	24212417	24212920	.	+	.	transcript_id "Phchi.S1G380000.t1"; gene_id "Phchi.S1G380000"
Phchi.S1	AUGUSTUS	stop_codon	24212921	24212923	.	+	0	transcript_id "Phchi.S1G380000.t1"; gene_id "Phchi.S1G380000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11341.t1 is derived from g15391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5641300	5642436	.	+	.	Phchi.S4G092300
Phchi.S4	AUGUSTUS	transcript	5641300	5642436	.	+	.	transcript_id "Phchi.S4G092300.t1"; gene_id "Phchi.S4G092300"
Phchi.S4	AUGUSTUS	start_codon	5641300	5641302	.	+	0	transcript_id "Phchi.S4G092300.t1"; gene_id "Phchi.S4G092300"
Phchi.S4	AUGUSTUS	CDS	5641300	5642436	0.84	+	0	transcript_id "Phchi.S4G092300.t1"; gene_id "Phchi.S4G092300"
Phchi.S4	AUGUSTUS	exon	5641300	5642436	.	+	.	transcript_id "Phchi.S4G092300.t1"; gene_id "Phchi.S4G092300"
Phchi.S4	AUGUSTUS	stop_codon	5642437	5642439	.	+	0	transcript_id "Phchi.S4G092300.t1"; gene_id "Phchi.S4G092300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg734.t1 is derived from g10516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5241938	5242698	.	-	.	Phchi.S6G069300
Phchi.S6	AUGUSTUS	transcript	5241938	5242698	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	stop_codon	5241935	5241937	.	-	0	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	CDS	5241938	5241988	0.98	-	0	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	exon	5241938	5241988	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	intron	5241989	5242099	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	CDS	5242100	5242188	0.98	-	2	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	exon	5242100	5242188	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	intron	5242189	5242277	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	CDS	5242278	5242401	1	-	0	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	exon	5242278	5242401	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	intron	5242402	5242629	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	CDS	5242630	5242698	0.93	-	0	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	exon	5242630	5242698	.	-	.	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
Phchi.S6	AUGUSTUS	start_codon	5242696	5242698	.	-	0	transcript_id "Phchi.S6G069300.t1"; gene_id "Phchi.S6G069300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8927.t1 is derived from g6102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38708876	38709838	.	+	.	Phchi.S1G608600
Phchi.S1	AUGUSTUS	transcript	38708876	38709838	.	+	.	transcript_id "Phchi.S1G608600.t1"; gene_id "Phchi.S1G608600"
Phchi.S1	AUGUSTUS	start_codon	38708876	38708878	.	+	0	transcript_id "Phchi.S1G608600.t1"; gene_id "Phchi.S1G608600"
Phchi.S1	AUGUSTUS	CDS	38708876	38709838	0.9	+	0	transcript_id "Phchi.S1G608600.t1"; gene_id "Phchi.S1G608600"
Phchi.S1	AUGUSTUS	exon	38708876	38709838	.	+	.	transcript_id "Phchi.S1G608600.t1"; gene_id "Phchi.S1G608600"
Phchi.S1	AUGUSTUS	stop_codon	38709839	38709841	.	+	0	transcript_id "Phchi.S1G608600.t1"; gene_id "Phchi.S1G608600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8665.t1 is derived from g5840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37347714	37349350	.	-	.	Phchi.S1G582400
Phchi.S1	AUGUSTUS	transcript	37347714	37349350	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	stop_codon	37347711	37347713	.	-	0	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	CDS	37347714	37348417	1	-	2	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	exon	37347714	37348417	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	intron	37348418	37348526	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	CDS	37348527	37348689	1	-	0	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	exon	37348527	37348689	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	intron	37348690	37348781	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	CDS	37348782	37348976	1	-	0	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	exon	37348782	37348976	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	intron	37348977	37349128	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	CDS	37349129	37349350	1	-	0	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	exon	37349129	37349350	.	-	.	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
Phchi.S1	AUGUSTUS	start_codon	37349348	37349350	.	-	0	transcript_id "Phchi.S1G582400.t1"; gene_id "Phchi.S1G582400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13197.t1 is derived from g11662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4643306	4644045	.	+	.	Phchi.S3G051600
Phchi.S3	AUGUSTUS	transcript	4643306	4644045	.	+	.	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	start_codon	4643306	4643308	.	+	0	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	CDS	4643306	4643615	0.81	+	0	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	exon	4643306	4643615	.	+	.	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	intron	4643616	4643761	.	+	.	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	CDS	4643762	4643816	1	+	2	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	exon	4643762	4643816	.	+	.	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	intron	4643817	4643894	.	+	.	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	CDS	4643895	4644045	1	+	1	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	exon	4643895	4644045	.	+	.	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
Phchi.S3	AUGUSTUS	stop_codon	4644046	4644048	.	+	0	transcript_id "Phchi.S3G051600.t1"; gene_id "Phchi.S3G051600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11169.t1 is derived from g15219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4449475	4449765	.	+	.	Phchi.S4G075100
Phchi.S4	AUGUSTUS	transcript	4449475	4449765	.	+	.	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	start_codon	4449475	4449477	.	+	0	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	CDS	4449475	4449622	0.3	+	0	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	exon	4449475	4449622	.	+	.	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	intron	4449623	4449715	.	+	.	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	CDS	4449716	4449765	0.77	+	2	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	exon	4449716	4449765	.	+	.	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
Phchi.S4	AUGUSTUS	stop_codon	4449766	4449768	.	+	0	transcript_id "Phchi.S4G075100.t1"; gene_id "Phchi.S4G075100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7152.t1 is derived from g4324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27233778	27234419	.	+	.	Phchi.S1G431100
Phchi.S1	AUGUSTUS	transcript	27233778	27234419	.	+	.	transcript_id "Phchi.S1G431100.t1"; gene_id "Phchi.S1G431100"
Phchi.S1	AUGUSTUS	start_codon	27233778	27233780	.	+	0	transcript_id "Phchi.S1G431100.t1"; gene_id "Phchi.S1G431100"
Phchi.S1	AUGUSTUS	CDS	27233778	27234419	0.35	+	0	transcript_id "Phchi.S1G431100.t1"; gene_id "Phchi.S1G431100"
Phchi.S1	AUGUSTUS	exon	27233778	27234419	.	+	.	transcript_id "Phchi.S1G431100.t1"; gene_id "Phchi.S1G431100"
Phchi.S1	AUGUSTUS	stop_codon	27234420	27234422	.	+	0	transcript_id "Phchi.S1G431100.t1"; gene_id "Phchi.S1G431100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4374.t1 is derived from g1543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10119937	10120770	.	+	.	Phchi.S1G153300
Phchi.S1	AUGUSTUS	transcript	10119937	10120770	.	+	.	transcript_id "Phchi.S1G153300.t1"; gene_id "Phchi.S1G153300"
Phchi.S1	AUGUSTUS	start_codon	10119937	10119939	.	+	0	transcript_id "Phchi.S1G153300.t1"; gene_id "Phchi.S1G153300"
Phchi.S1	AUGUSTUS	CDS	10119937	10120770	0.77	+	0	transcript_id "Phchi.S1G153300.t1"; gene_id "Phchi.S1G153300"
Phchi.S1	AUGUSTUS	exon	10119937	10120770	.	+	.	transcript_id "Phchi.S1G153300.t1"; gene_id "Phchi.S1G153300"
Phchi.S1	AUGUSTUS	stop_codon	10120771	10120773	.	+	0	transcript_id "Phchi.S1G153300.t1"; gene_id "Phchi.S1G153300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13051.t1 is derived from g11516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3911084	3912127	.	+	.	Phchi.S3G037000
Phchi.S3	AUGUSTUS	transcript	3911084	3912127	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	start_codon	3911084	3911086	.	+	0	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	CDS	3911084	3911288	0.94	+	0	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	exon	3911084	3911288	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	intron	3911289	3911370	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	CDS	3911371	3911574	1	+	2	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	exon	3911371	3911574	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	intron	3911575	3911662	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	CDS	3911663	3911812	0.98	+	2	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	exon	3911663	3911812	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	intron	3911813	3911921	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	CDS	3911922	3911980	0.99	+	2	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	exon	3911922	3911980	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	intron	3911981	3912070	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	CDS	3912071	3912127	1	+	0	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	exon	3912071	3912127	.	+	.	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
Phchi.S3	AUGUSTUS	stop_codon	3912128	3912130	.	+	0	transcript_id "Phchi.S3G037000.t1"; gene_id "Phchi.S3G037000"
# This transcript jg15427.t2 is derived from g13895.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15428.t1 is derived from g13896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19044041	19044845	.	+	.	Phchi.S3G274700
Phchi.S3	AUGUSTUS	transcript	19044041	19044845	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	start_codon	19044041	19044043	.	+	0	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	CDS	19044041	19044145	0.89	+	0	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	exon	19044041	19044145	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	intron	19044146	19044226	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	CDS	19044227	19044354	1	+	0	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	exon	19044227	19044354	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	intron	19044355	19044431	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	CDS	19044432	19044524	1	+	1	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	exon	19044432	19044524	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	intron	19044525	19044670	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	CDS	19044671	19044748	1	+	1	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	exon	19044671	19044748	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	intron	19044749	19044835	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	CDS	19044836	19044845	1	+	1	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	exon	19044836	19044845	.	+	.	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
Phchi.S3	AUGUSTUS	stop_codon	19044846	19044848	.	+	0	transcript_id "Phchi.S3G274700.t1"; gene_id "Phchi.S3G274700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6948.t1 is derived from g4120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26103771	26105332	.	+	.	Phchi.S1G410700
Phchi.S1	AUGUSTUS	transcript	26103771	26105332	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	start_codon	26103771	26103773	.	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26103771	26103930	0.84	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26103771	26103930	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	intron	26103931	26104016	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26104017	26104105	0.8	+	2	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26104017	26104105	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	intron	26104106	26104213	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26104214	26104289	1	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26104214	26104289	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	intron	26104290	26104502	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26104503	26104552	1	+	2	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26104503	26104552	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	intron	26104553	26104674	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26104675	26104911	0.99	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26104675	26104911	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	intron	26104912	26105041	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26105042	26105080	1	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26105042	26105080	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	intron	26105081	26105152	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	CDS	26105153	26105332	1	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	exon	26105153	26105332	.	+	.	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
Phchi.S1	AUGUSTUS	stop_codon	26105333	26105335	.	+	0	transcript_id "Phchi.S1G410700.t1"; gene_id "Phchi.S1G410700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6238.t1 is derived from g3410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21814145	21814375	.	+	.	Phchi.S1G339700
Phchi.S1	AUGUSTUS	transcript	21814145	21814375	.	+	.	transcript_id "Phchi.S1G339700.t1"; gene_id "Phchi.S1G339700"
Phchi.S1	AUGUSTUS	start_codon	21814145	21814147	.	+	0	transcript_id "Phchi.S1G339700.t1"; gene_id "Phchi.S1G339700"
Phchi.S1	AUGUSTUS	CDS	21814145	21814375	0.97	+	0	transcript_id "Phchi.S1G339700.t1"; gene_id "Phchi.S1G339700"
Phchi.S1	AUGUSTUS	exon	21814145	21814375	.	+	.	transcript_id "Phchi.S1G339700.t1"; gene_id "Phchi.S1G339700"
Phchi.S1	AUGUSTUS	stop_codon	21814376	21814378	.	+	0	transcript_id "Phchi.S1G339700.t1"; gene_id "Phchi.S1G339700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8561.t1 is derived from g5736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36623441	36626466	.	-	.	Phchi.S1G572000
Phchi.S1	AUGUSTUS	transcript	36623441	36626466	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	stop_codon	36623438	36623440	.	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36623441	36623749	0.96	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36623441	36623749	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36623750	36623841	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36623842	36624159	1	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36623842	36624159	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36624160	36624284	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36624285	36624821	0.84	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36624285	36624821	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36624822	36625001	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36625002	36625022	0.87	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36625002	36625022	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36625023	36625216	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36625217	36625436	1	-	1	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36625217	36625436	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36625437	36625555	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36625556	36625641	1	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36625556	36625641	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36625642	36625816	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36625817	36625933	1	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36625817	36625933	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36625934	36626051	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36626052	36626259	1	-	1	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36626052	36626259	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	intron	36626260	36626353	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	CDS	36626354	36626466	0.59	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	exon	36626354	36626466	.	-	.	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
Phchi.S1	AUGUSTUS	start_codon	36626464	36626466	.	-	0	transcript_id "Phchi.S1G572000.t1"; gene_id "Phchi.S1G572000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15636.t1 is derived from g14105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20412401	20413760	.	+	.	Phchi.S3G295500
Phchi.S3	AUGUSTUS	transcript	20412401	20413760	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	start_codon	20412401	20412403	.	+	0	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	CDS	20412401	20412795	0.67	+	0	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	exon	20412401	20412795	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	intron	20412796	20412867	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	CDS	20412868	20412987	0.99	+	1	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	exon	20412868	20412987	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	intron	20412988	20413088	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	CDS	20413089	20413198	0.58	+	1	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	exon	20413089	20413198	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	intron	20413199	20413281	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	CDS	20413282	20413760	1	+	2	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	exon	20413282	20413760	.	+	.	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
Phchi.S3	AUGUSTUS	stop_codon	20413761	20413763	.	+	0	transcript_id "Phchi.S3G295500.t1"; gene_id "Phchi.S3G295500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10344.t1 is derived from g7520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47268748	47269278	.	-	.	Phchi.S1G750300
Phchi.S1	AUGUSTUS	transcript	47268748	47269278	.	-	.	transcript_id "Phchi.S1G750300.t1"; gene_id "Phchi.S1G750300"
Phchi.S1	AUGUSTUS	stop_codon	47268745	47268747	.	-	0	transcript_id "Phchi.S1G750300.t1"; gene_id "Phchi.S1G750300"
Phchi.S1	AUGUSTUS	CDS	47268748	47269278	0.49	-	0	transcript_id "Phchi.S1G750300.t1"; gene_id "Phchi.S1G750300"
Phchi.S1	AUGUSTUS	exon	47268748	47269278	.	-	.	transcript_id "Phchi.S1G750300.t1"; gene_id "Phchi.S1G750300"
Phchi.S1	AUGUSTUS	start_codon	47269276	47269278	.	-	0	transcript_id "Phchi.S1G750300.t1"; gene_id "Phchi.S1G750300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9611.t1 is derived from g6787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42928687	42929055	.	-	.	Phchi.S1G677000
Phchi.S1	AUGUSTUS	transcript	42928687	42929055	.	-	.	transcript_id "Phchi.S1G677000.t1"; gene_id "Phchi.S1G677000"
Phchi.S1	AUGUSTUS	stop_codon	42928684	42928686	.	-	0	transcript_id "Phchi.S1G677000.t1"; gene_id "Phchi.S1G677000"
Phchi.S1	AUGUSTUS	CDS	42928687	42929055	0.96	-	0	transcript_id "Phchi.S1G677000.t1"; gene_id "Phchi.S1G677000"
Phchi.S1	AUGUSTUS	exon	42928687	42929055	.	-	.	transcript_id "Phchi.S1G677000.t1"; gene_id "Phchi.S1G677000"
Phchi.S1	AUGUSTUS	start_codon	42929053	42929055	.	-	0	transcript_id "Phchi.S1G677000.t1"; gene_id "Phchi.S1G677000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4514.t1 is derived from g1684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10907092	10908371	.	+	.	Phchi.S1G167300
Phchi.S1	AUGUSTUS	transcript	10907092	10908371	.	+	.	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	start_codon	10907092	10907094	.	+	0	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	CDS	10907092	10907574	0.51	+	0	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	exon	10907092	10907574	.	+	.	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	intron	10907575	10907696	.	+	.	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	CDS	10907697	10908371	0.54	+	0	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	exon	10907697	10908371	.	+	.	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
Phchi.S1	AUGUSTUS	stop_codon	10908372	10908374	.	+	0	transcript_id "Phchi.S1G167300.t1"; gene_id "Phchi.S1G167300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5087.t1 is derived from g2257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14676553	14677205	.	-	.	Phchi.S1G224600
Phchi.S1	AUGUSTUS	transcript	14676553	14677205	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	stop_codon	14676550	14676552	.	-	0	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	CDS	14676553	14676555	0.97	-	0	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	exon	14676553	14676555	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	intron	14676556	14676643	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	CDS	14676644	14676665	0.84	-	1	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	exon	14676644	14676665	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	intron	14676666	14676808	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	CDS	14676809	14676836	0.64	-	2	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	exon	14676809	14676836	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	intron	14676837	14676936	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	CDS	14676937	14677030	0.92	-	0	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	exon	14676937	14677030	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	intron	14677031	14677127	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	CDS	14677128	14677205	0.48	-	0	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	exon	14677128	14677205	.	-	.	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
Phchi.S1	AUGUSTUS	start_codon	14677203	14677205	.	-	0	transcript_id "Phchi.S1G224600.t1"; gene_id "Phchi.S1G224600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10654.t1 is derived from g14704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1440424	1445141	.	+	.	Phchi.S4G023600
Phchi.S4	AUGUSTUS	transcript	1440424	1445141	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	start_codon	1440424	1440426	.	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1440424	1440489	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1440424	1440489	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1440490	1440570	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1440571	1440774	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1440571	1440774	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1440775	1440874	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1440875	1440910	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1440875	1440910	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1440911	1441127	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1441128	1441240	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1441128	1441240	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1441241	1441331	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1441332	1441377	1	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1441332	1441377	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1441378	1441505	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1441506	1441552	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1441506	1441552	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1441553	1441641	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1441642	1441749	1	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1441642	1441749	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1441750	1441916	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1441917	1441992	1	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1441917	1441992	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1441993	1442076	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1442077	1442149	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1442077	1442149	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1442150	1442254	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1442255	1442394	0.61	+	2	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1442255	1442394	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1442395	1442487	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1442488	1442570	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1442488	1442570	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1442571	1442662	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1442663	1442802	1	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1442663	1442802	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1442803	1442900	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1442901	1443043	1	+	2	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1442901	1443043	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1443044	1443128	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1443129	1443179	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1443129	1443179	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1443180	1443277	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1443278	1443341	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1443278	1443341	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1443342	1443425	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1443426	1443569	1	+	2	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1443426	1443569	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1443570	1443672	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1443673	1443743	1	+	2	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1443673	1443743	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1443744	1443824	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1443825	1443883	0.98	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1443825	1443883	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1443884	1443986	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1443987	1444143	0.75	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1443987	1444143	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1444144	1444245	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1444246	1444298	0.85	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1444246	1444298	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1444299	1444370	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1444371	1444420	0.97	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1444371	1444420	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1444421	1444517	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1444518	1444572	0.81	+	2	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1444518	1444572	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1444573	1444659	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1444660	1444687	1	+	1	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1444660	1444687	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1444688	1444783	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1444784	1444906	1	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1444784	1444906	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	intron	1444907	1444985	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	CDS	1444986	1445141	0.99	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	exon	1444986	1445141	.	+	.	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
Phchi.S4	AUGUSTUS	stop_codon	1445142	1445144	.	+	0	transcript_id "Phchi.S4G023600.t1"; gene_id "Phchi.S4G023600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4962.t1 is derived from g2132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13777206	13778852	.	-	.	Phchi.S1G212100
Phchi.S1	AUGUSTUS	transcript	13777206	13778852	.	-	.	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	stop_codon	13777203	13777205	.	-	0	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	CDS	13777206	13777861	0.99	-	2	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	exon	13777206	13777861	.	-	.	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	intron	13777862	13778083	.	-	.	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	CDS	13778084	13778196	0.35	-	1	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	exon	13778084	13778196	.	-	.	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	intron	13778197	13778394	.	-	.	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	CDS	13778395	13778852	0.84	-	0	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	exon	13778395	13778852	.	-	.	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
Phchi.S1	AUGUSTUS	start_codon	13778850	13778852	.	-	0	transcript_id "Phchi.S1G212100.t1"; gene_id "Phchi.S1G212100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4188.t1 is derived from g1357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8823141	8823584	.	+	.	Phchi.S1G134700
Phchi.S1	AUGUSTUS	transcript	8823141	8823584	.	+	.	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	start_codon	8823141	8823143	.	+	0	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	CDS	8823141	8823336	0.65	+	0	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	exon	8823141	8823336	.	+	.	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	intron	8823337	8823453	.	+	.	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	CDS	8823454	8823584	0.65	+	2	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	exon	8823454	8823584	.	+	.	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
Phchi.S1	AUGUSTUS	stop_codon	8823585	8823587	.	+	0	transcript_id "Phchi.S1G134700.t1"; gene_id "Phchi.S1G134700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14774.t1 is derived from g13242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14646871	14648528	.	-	.	Phchi.S3G209300
Phchi.S3	AUGUSTUS	transcript	14646871	14648528	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	stop_codon	14646868	14646870	.	-	0	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14646871	14647062	1	-	0	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14646871	14647062	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14647063	14647164	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14647165	14647279	1	-	1	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14647165	14647279	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14647280	14647383	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14647384	14647475	1	-	0	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14647384	14647475	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14647476	14647582	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14647583	14647668	0.99	-	2	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14647583	14647668	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14647669	14647787	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14647788	14647887	1	-	0	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14647788	14647887	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14647888	14647973	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14647974	14648050	1	-	2	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14647974	14648050	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14648051	14648141	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14648142	14648182	0.59	-	1	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14648142	14648182	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14648183	14648353	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14648354	14648398	0.42	-	1	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14648354	14648398	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	intron	14648399	14648478	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	CDS	14648479	14648528	0.92	-	0	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	exon	14648479	14648528	.	-	.	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
Phchi.S3	AUGUSTUS	start_codon	14648526	14648528	.	-	0	transcript_id "Phchi.S3G209300.t1"; gene_id "Phchi.S3G209300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7847.t1 is derived from g5021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31511012	31512645	.	-	.	Phchi.S1G500600
Phchi.S1	AUGUSTUS	transcript	31511201	31512645	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	stop_codon	31511198	31511200	.	-	0	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511201	31511222	0.33	-	1	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511201	31511222	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511223	31511519	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511520	31511567	0.8	-	1	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511520	31511567	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511568	31511721	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511722	31511753	1	-	0	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511722	31511753	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511754	31511844	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511845	31511926	0.82	-	1	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511845	31511926	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511927	31512030	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512031	31512192	0.74	-	1	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512031	31512192	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31512193	31512317	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512318	31512329	0.68	-	1	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512318	31512329	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31512330	31512445	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512446	31512546	0.56	-	0	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512446	31512546	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31512547	31512615	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512616	31512645	0.79	-	0	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512616	31512645	.	-	.	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	start_codon	31512643	31512645	.	-	0	transcript_id "Phchi.S1G500600.t1"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	transcript	31511012	31512645	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	stop_codon	31511009	31511011	.	-	0	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511012	31511082	0.21	-	2	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511012	31511082	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511083	31511272	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511273	31511367	0.56	-	1	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511273	31511367	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511368	31511519	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511520	31511567	0.8	-	1	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511520	31511567	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511568	31511721	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511722	31511753	1	-	0	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511722	31511753	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511754	31511844	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31511845	31511926	0.78	-	1	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31511845	31511926	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31511927	31512030	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512031	31512192	0.69	-	1	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512031	31512192	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31512193	31512317	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512318	31512329	0.67	-	1	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512318	31512329	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31512330	31512445	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512446	31512546	0.54	-	0	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512446	31512546	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	intron	31512547	31512615	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	CDS	31512616	31512645	0.79	-	0	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	exon	31512616	31512645	.	-	.	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
Phchi.S1	AUGUSTUS	start_codon	31512643	31512645	.	-	0	transcript_id "Phchi.S1G500600.t2"; gene_id "Phchi.S1G500600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7536.t1 is derived from g4710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29944810	29945501	.	+	.	Phchi.S1G469500
Phchi.S1	AUGUSTUS	transcript	29944810	29945501	.	+	.	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	start_codon	29944810	29944812	.	+	0	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	CDS	29944810	29944926	0.54	+	0	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	exon	29944810	29944926	.	+	.	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	intron	29944927	29945052	.	+	.	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	CDS	29945053	29945222	0.61	+	0	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	exon	29945053	29945222	.	+	.	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	intron	29945223	29945302	.	+	.	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	CDS	29945303	29945501	0.98	+	1	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	exon	29945303	29945501	.	+	.	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
Phchi.S1	AUGUSTUS	stop_codon	29945502	29945504	.	+	0	transcript_id "Phchi.S1G469500.t1"; gene_id "Phchi.S1G469500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7353.t1 is derived from g4525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28715212	28718309	.	-	.	Phchi.S1G451200
Phchi.S1	AUGUSTUS	transcript	28715212	28718309	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	stop_codon	28715209	28715211	.	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715212	28715332	1	-	1	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715212	28715332	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715333	28715431	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715432	28715536	1	-	1	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715432	28715536	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715537	28715624	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715625	28715683	1	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715625	28715683	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715684	28715804	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715805	28715891	1	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715805	28715891	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715892	28715971	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715972	28716037	1	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715972	28716037	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716038	28716138	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716139	28716246	0.94	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716139	28716246	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716247	28716491	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716492	28716642	0.82	-	1	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716492	28716642	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716643	28716736	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716737	28716801	0.83	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716737	28716801	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716802	28716887	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716888	28716967	1	-	2	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716888	28716967	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716968	28717053	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717054	28717126	1	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717054	28717126	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717127	28717277	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717278	28717371	1	-	1	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717278	28717371	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717372	28717476	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717477	28717534	1	-	2	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717477	28717534	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717535	28717719	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717720	28717767	1	-	2	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717720	28717767	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717768	28717852	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717853	28718309	1	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717853	28718309	.	-	.	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	start_codon	28718307	28718309	.	-	0	transcript_id "Phchi.S1G451200.t1"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	transcript	28715212	28718309	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	stop_codon	28715209	28715211	.	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715212	28715332	0.99	-	1	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715212	28715332	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715333	28715431	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715432	28715536	1	-	1	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715432	28715536	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715537	28715624	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715625	28715683	1	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715625	28715683	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715684	28715804	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715805	28715891	1	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715805	28715891	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28715892	28715971	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28715972	28716037	1	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28715972	28716037	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716038	28716138	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716139	28716231	0.74	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716139	28716231	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716232	28716351	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716352	28716405	1	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716352	28716405	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716406	28716491	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716492	28716642	0.74	-	1	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716492	28716642	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716643	28716736	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716737	28716801	0.89	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716737	28716801	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716802	28716887	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28716888	28716967	1	-	2	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28716888	28716967	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28716968	28717053	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717054	28717126	1	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717054	28717126	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717127	28717277	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717278	28717371	1	-	1	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717278	28717371	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717372	28717476	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717477	28717534	1	-	2	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717477	28717534	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717535	28717719	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717720	28717767	1	-	2	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717720	28717767	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	intron	28717768	28717852	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	CDS	28717853	28718309	0.97	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	exon	28717853	28718309	.	-	.	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
Phchi.S1	AUGUSTUS	start_codon	28718307	28718309	.	-	0	transcript_id "Phchi.S1G451200.t2"; gene_id "Phchi.S1G451200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3933.t1 is derived from g1102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6556545	6557081	.	+	.	Phchi.S1G109200
Phchi.S1	AUGUSTUS	transcript	6556545	6557081	.	+	.	transcript_id "Phchi.S1G109200.t1"; gene_id "Phchi.S1G109200"
Phchi.S1	AUGUSTUS	start_codon	6556545	6556547	.	+	0	transcript_id "Phchi.S1G109200.t1"; gene_id "Phchi.S1G109200"
Phchi.S1	AUGUSTUS	CDS	6556545	6557081	1	+	0	transcript_id "Phchi.S1G109200.t1"; gene_id "Phchi.S1G109200"
Phchi.S1	AUGUSTUS	exon	6556545	6557081	.	+	.	transcript_id "Phchi.S1G109200.t1"; gene_id "Phchi.S1G109200"
Phchi.S1	AUGUSTUS	stop_codon	6557082	6557084	.	+	0	transcript_id "Phchi.S1G109200.t1"; gene_id "Phchi.S1G109200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3165.t1 is derived from g334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2037667	2038763	.	+	.	Phchi.S1G032400
Phchi.S1	AUGUSTUS	transcript	2037667	2038763	.	+	.	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	start_codon	2037667	2037669	.	+	0	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	CDS	2037667	2038314	0.92	+	0	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	exon	2037667	2038314	.	+	.	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	intron	2038315	2038522	.	+	.	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	CDS	2038523	2038618	0.84	+	0	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	exon	2038523	2038618	.	+	.	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	intron	2038619	2038712	.	+	.	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	CDS	2038713	2038763	1	+	0	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	exon	2038713	2038763	.	+	.	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
Phchi.S1	AUGUSTUS	stop_codon	2038764	2038766	.	+	0	transcript_id "Phchi.S1G032400.t1"; gene_id "Phchi.S1G032400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2186.t1 is derived from g9106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5268172	5268519	.	+	.	Phchi.S5G079500
Phchi.S5	AUGUSTUS	transcript	5268172	5268519	.	+	.	transcript_id "Phchi.S5G079500.t1"; gene_id "Phchi.S5G079500"
Phchi.S5	AUGUSTUS	start_codon	5268172	5268174	.	+	0	transcript_id "Phchi.S5G079500.t1"; gene_id "Phchi.S5G079500"
Phchi.S5	AUGUSTUS	CDS	5268172	5268519	0.55	+	0	transcript_id "Phchi.S5G079500.t1"; gene_id "Phchi.S5G079500"
Phchi.S5	AUGUSTUS	exon	5268172	5268519	.	+	.	transcript_id "Phchi.S5G079500.t1"; gene_id "Phchi.S5G079500"
Phchi.S5	AUGUSTUS	stop_codon	5268520	5268522	.	+	0	transcript_id "Phchi.S5G079500.t1"; gene_id "Phchi.S5G079500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15579.t1 is derived from g14048.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20114215	20116162	.	+	.	Phchi.S3G289800
Phchi.S3	AUGUSTUS	transcript	20114215	20116162	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	start_codon	20114215	20114217	.	+	0	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114215	20114296	0.52	+	0	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114215	20114296	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114297	20114420	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114421	20114546	1	+	2	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114421	20114546	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114547	20114676	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114677	20114801	1	+	2	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114677	20114801	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114802	20114895	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114896	20114992	1	+	0	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114896	20114992	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114993	20115104	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115105	20115411	0.98	+	2	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115105	20115411	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20115412	20115514	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115515	20115549	0.98	+	1	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115515	20115549	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20115550	20115657	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115658	20115738	1	+	2	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115658	20115738	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20115739	20115836	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115837	20116162	0.4	+	2	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115837	20116162	.	+	.	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	stop_codon	20116163	20116165	.	+	0	transcript_id "Phchi.S3G289800.t1"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	transcript	20114215	20116162	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	start_codon	20114215	20114217	.	+	0	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114215	20114296	0.45	+	0	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114215	20114296	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114297	20114420	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114421	20114546	1	+	2	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114421	20114546	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114547	20114676	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114677	20114807	1	+	2	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114677	20114807	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114808	20114895	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20114896	20114992	1	+	0	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20114896	20114992	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20114993	20115104	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115105	20115411	0.98	+	2	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115105	20115411	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20115412	20115514	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115515	20115549	0.98	+	1	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115515	20115549	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20115550	20115657	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115658	20115738	0.99	+	2	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115658	20115738	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	intron	20115739	20115836	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	CDS	20115837	20116162	0.35	+	2	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	exon	20115837	20116162	.	+	.	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
Phchi.S3	AUGUSTUS	stop_codon	20116163	20116165	.	+	0	transcript_id "Phchi.S3G289800.t2"; gene_id "Phchi.S3G289800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1563.t1 is derived from g8482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1775380	1776205	.	-	.	Phchi.S5G017200
Phchi.S5	AUGUSTUS	transcript	1775380	1776205	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	stop_codon	1775377	1775379	.	-	0	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	CDS	1775380	1775496	0.85	-	0	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	exon	1775380	1775496	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	intron	1775497	1775598	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	CDS	1775599	1775715	0.89	-	0	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	exon	1775599	1775715	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	intron	1775716	1775824	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	CDS	1775825	1775947	0.97	-	0	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	exon	1775825	1775947	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	intron	1775948	1776037	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	CDS	1776038	1776205	1	-	0	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	exon	1776038	1776205	.	-	.	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
Phchi.S5	AUGUSTUS	start_codon	1776203	1776205	.	-	0	transcript_id "Phchi.S5G017200.t1"; gene_id "Phchi.S5G017200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg956.t1 is derived from g10738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6651245	6652174	.	-	.	Phchi.S6G091500
Phchi.S6	AUGUSTUS	transcript	6651245	6652174	.	-	.	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	stop_codon	6651242	6651244	.	-	0	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	CDS	6651245	6651544	1	-	0	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	exon	6651245	6651544	.	-	.	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	intron	6651545	6651808	.	-	.	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	CDS	6651809	6652174	0.49	-	0	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	exon	6651809	6652174	.	-	.	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
Phchi.S6	AUGUSTUS	start_codon	6652172	6652174	.	-	0	transcript_id "Phchi.S6G091500.t1"; gene_id "Phchi.S6G091500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10518.t1 is derived from g14568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	798152	800828	.	-	.	Phchi.S4G010000
Phchi.S4	AUGUSTUS	transcript	798152	800828	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	stop_codon	798149	798151	.	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	798152	798217	1	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	798152	798217	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	798218	798308	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	798309	798395	1	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	798309	798395	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	798396	798484	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	798485	798603	1	-	2	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	798485	798603	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	798604	798711	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	798712	798950	1	-	1	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	798712	798950	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	798951	799080	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	799081	799137	1	-	1	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	799081	799137	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	799138	799258	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	799259	799345	0.93	-	1	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	799259	799345	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	799346	799470	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	799471	799662	0.77	-	1	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	799471	799662	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	799663	799758	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	799759	800018	0.77	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	799759	800018	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	800019	800115	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	800116	800431	1	-	1	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	800116	800431	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	800432	800569	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	800570	800580	1	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	800570	800580	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	intron	800581	800786	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	CDS	800787	800828	1	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	exon	800787	800828	.	-	.	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
Phchi.S4	AUGUSTUS	start_codon	800826	800828	.	-	0	transcript_id "Phchi.S4G010000.t1"; gene_id "Phchi.S4G010000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8553.t1 is derived from g5728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36600144	36600455	.	+	.	Phchi.S1G571200
Phchi.S1	AUGUSTUS	transcript	36600144	36600455	.	+	.	transcript_id "Phchi.S1G571200.t1"; gene_id "Phchi.S1G571200"
Phchi.S1	AUGUSTUS	start_codon	36600144	36600146	.	+	0	transcript_id "Phchi.S1G571200.t1"; gene_id "Phchi.S1G571200"
Phchi.S1	AUGUSTUS	CDS	36600144	36600455	0.59	+	0	transcript_id "Phchi.S1G571200.t1"; gene_id "Phchi.S1G571200"
Phchi.S1	AUGUSTUS	exon	36600144	36600455	.	+	.	transcript_id "Phchi.S1G571200.t1"; gene_id "Phchi.S1G571200"
Phchi.S1	AUGUSTUS	stop_codon	36600456	36600458	.	+	0	transcript_id "Phchi.S1G571200.t1"; gene_id "Phchi.S1G571200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg149.t1 is derived from g9931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	840851	842196	.	+	.	Phchi.S6G010800
Phchi.S6	AUGUSTUS	transcript	840851	842196	.	+	.	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	start_codon	840851	840853	.	+	0	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	CDS	840851	841196	1	+	0	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	exon	840851	841196	.	+	.	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	intron	841197	841279	.	+	.	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	CDS	841280	842196	0.57	+	2	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	exon	841280	842196	.	+	.	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
Phchi.S6	AUGUSTUS	stop_codon	842197	842199	.	+	0	transcript_id "Phchi.S6G010800.t1"; gene_id "Phchi.S6G010800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14302.t1 is derived from g12769.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12011024	12012505	.	-	.	Phchi.S3G162100
Phchi.S3	AUGUSTUS	transcript	12011024	12011668	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	stop_codon	12011021	12011023	.	-	0	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011024	12011087	0.82	-	1	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011024	12011087	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011088	12011157	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011158	12011275	0.84	-	2	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011158	12011275	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011276	12011419	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011420	12011482	1	-	2	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011420	12011482	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011483	12011661	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011662	12011668	0.75	-	0	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011662	12011668	.	-	.	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	start_codon	12011666	12011668	.	-	0	transcript_id "Phchi.S3G162100.t1"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	transcript	12011024	12012505	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	stop_codon	12011021	12011023	.	-	0	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011024	12011087	0.7	-	1	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011024	12011087	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011088	12011157	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011158	12011275	0.74	-	2	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011158	12011275	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011276	12011419	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011420	12011482	0.91	-	2	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011420	12011482	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011483	12011603	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12011604	12011661	0.53	-	0	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12011604	12011661	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12011662	12012000	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12012001	12012030	0.89	-	0	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12012001	12012030	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12012031	12012229	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12012230	12012288	0.87	-	2	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12012230	12012288	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	intron	12012289	12012474	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	CDS	12012475	12012505	0.96	-	0	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	exon	12012475	12012505	.	-	.	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
Phchi.S3	AUGUSTUS	start_codon	12012503	12012505	.	-	0	transcript_id "Phchi.S3G162100.t2"; gene_id "Phchi.S3G162100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4624.t1 is derived from g1794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11450010	11450955	.	-	.	Phchi.S1G178300
Phchi.S1	AUGUSTUS	transcript	11450010	11450955	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	stop_codon	11450007	11450009	.	-	0	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	CDS	11450010	11450032	0.87	-	2	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	exon	11450010	11450032	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	intron	11450033	11450112	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	CDS	11450113	11450151	0.87	-	2	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	exon	11450113	11450151	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	intron	11450152	11450249	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	CDS	11450250	11450317	0.87	-	1	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	exon	11450250	11450317	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	intron	11450318	11450566	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	CDS	11450567	11450591	0.31	-	2	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	exon	11450567	11450591	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	intron	11450592	11450739	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	CDS	11450740	11450771	0.61	-	1	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	exon	11450740	11450771	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	intron	11450772	11450938	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	CDS	11450939	11450955	1	-	0	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	exon	11450939	11450955	.	-	.	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
Phchi.S1	AUGUSTUS	start_codon	11450953	11450955	.	-	0	transcript_id "Phchi.S1G178300.t1"; gene_id "Phchi.S1G178300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7758.t1 is derived from g4932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31153719	31154809	.	+	.	Phchi.S1G491700
Phchi.S1	AUGUSTUS	transcript	31153719	31154809	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	start_codon	31153719	31153721	.	+	0	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	CDS	31153719	31153880	0.44	+	0	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	exon	31153719	31153880	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	intron	31153881	31153985	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	CDS	31153986	31154109	0.75	+	0	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	exon	31153986	31154109	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	intron	31154110	31154211	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	CDS	31154212	31154471	0.89	+	2	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	exon	31154212	31154471	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	intron	31154472	31154563	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	CDS	31154564	31154809	0.93	+	0	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	exon	31154564	31154809	.	+	.	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
Phchi.S1	AUGUSTUS	stop_codon	31154810	31154812	.	+	0	transcript_id "Phchi.S1G491700.t1"; gene_id "Phchi.S1G491700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7553.t1 is derived from g4727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30009556	30011794	.	-	.	Phchi.S1G471200
Phchi.S1	AUGUSTUS	transcript	30009556	30011794	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	stop_codon	30009553	30009555	.	-	0	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	CDS	30009556	30009871	0.97	-	1	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	exon	30009556	30009871	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	intron	30009872	30009964	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	CDS	30009965	30010227	1	-	0	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	exon	30009965	30010227	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	intron	30010228	30010325	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	CDS	30010326	30010607	0.49	-	0	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	exon	30010326	30010607	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	intron	30010608	30010832	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	CDS	30010833	30010960	1	-	2	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	exon	30010833	30010960	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	intron	30010961	30011078	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	CDS	30011079	30011217	0.99	-	0	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	exon	30011079	30011217	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	intron	30011218	30011302	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	CDS	30011303	30011794	0.48	-	0	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	exon	30011303	30011794	.	-	.	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
Phchi.S1	AUGUSTUS	start_codon	30011792	30011794	.	-	0	transcript_id "Phchi.S1G471200.t1"; gene_id "Phchi.S1G471200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9876.t1 is derived from g7052.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44206737	44207557	.	-	.	Phchi.S1G703500
Phchi.S1	AUGUSTUS	transcript	44206737	44207557	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	stop_codon	44206734	44206736	.	-	0	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44206737	44206808	0.97	-	0	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44206737	44206808	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44206809	44206957	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44206958	44206972	0.97	-	0	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44206958	44206972	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44206973	44207070	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207071	44207155	0.75	-	1	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207071	44207155	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44207156	44207276	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207277	44207349	0.48	-	2	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207277	44207349	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44207350	44207424	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207425	44207453	0.49	-	1	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207425	44207453	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44207454	44207552	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207553	44207557	1	-	0	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207553	44207557	.	-	.	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	start_codon	44207555	44207557	.	-	0	transcript_id "Phchi.S1G703500.t1"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	transcript	44206812	44207557	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	stop_codon	44206809	44206811	.	-	0	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44206812	44206870	0.49	-	2	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44206812	44206870	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44206871	44206957	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44206958	44206972	0.5	-	2	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44206958	44206972	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44206973	44207070	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207071	44207167	0.3	-	0	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207071	44207167	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44207168	44207428	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207429	44207453	0.29	-	1	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207429	44207453	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	intron	44207454	44207552	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	CDS	44207553	44207557	1	-	0	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	exon	44207553	44207557	.	-	.	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
Phchi.S1	AUGUSTUS	start_codon	44207555	44207557	.	-	0	transcript_id "Phchi.S1G703500.t2"; gene_id "Phchi.S1G703500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8029.t1 is derived from g5204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32555231	32561333	.	+	.	Phchi.S1G518800
Phchi.S1	AUGUSTUS	transcript	32555231	32561333	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	start_codon	32555231	32555233	.	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32555231	32555666	0.67	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32555231	32555666	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32555667	32555835	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32555836	32555933	1	+	2	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32555836	32555933	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32555934	32556077	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32556078	32556134	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32556078	32556134	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32556135	32556226	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32556227	32556321	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32556227	32556321	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32556322	32556456	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32556457	32556556	1	+	1	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32556457	32556556	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32556557	32556666	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32556667	32556725	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32556667	32556725	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32556726	32556834	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32556835	32556947	1	+	1	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32556835	32556947	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32556948	32557026	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32557027	32557150	0.95	+	2	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32557027	32557150	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32557151	32557260	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32557261	32557348	0.99	+	1	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32557261	32557348	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32557349	32557496	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32557497	32557566	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32557497	32557566	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32557567	32557653	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32557654	32557714	1	+	2	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32557654	32557714	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32557715	32557836	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32557837	32557912	1	+	1	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32557837	32557912	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32557913	32557990	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32557991	32558101	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32557991	32558101	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32558102	32558195	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32558196	32558291	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32558196	32558291	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32558292	32558413	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32558414	32558536	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32558414	32558536	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32558537	32558613	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32558614	32558811	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32558614	32558811	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32558812	32558907	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32558908	32559009	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32558908	32559009	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32559010	32559099	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32559100	32559164	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32559100	32559164	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32559165	32559276	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32559277	32559370	1	+	1	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32559277	32559370	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32559371	32559451	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32559452	32559609	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32559452	32559609	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32559610	32559715	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32559716	32559765	1	+	1	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32559716	32559765	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32559766	32559837	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32559838	32559959	1	+	2	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32559838	32559959	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32559960	32560053	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32560054	32560161	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32560054	32560161	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32560162	32560240	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32560241	32560333	0.98	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32560241	32560333	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32560334	32560445	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32560446	32560482	1	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32560446	32560482	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32560483	32560568	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32560569	32560825	1	+	2	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32560569	32560825	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32560826	32560915	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32560916	32561071	0.99	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32560916	32561071	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	intron	32561072	32561183	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	CDS	32561184	32561333	0.99	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	exon	32561184	32561333	.	+	.	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
Phchi.S1	AUGUSTUS	stop_codon	32561334	32561336	.	+	0	transcript_id "Phchi.S1G518800.t1"; gene_id "Phchi.S1G518800"
# This transcript jg5910.t2 is derived from g3081.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5911.t1 is derived from g3082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19749191	19752000	.	+	.	Phchi.S1G307000
Phchi.S1	AUGUSTUS	transcript	19749191	19752000	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	start_codon	19749191	19749193	.	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749191	19749330	0.96	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749191	19749330	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749331	19749580	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749581	19749627	0.92	+	1	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749581	19749627	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749628	19749731	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749732	19749760	0.98	+	2	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749732	19749760	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749761	19749929	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749930	19749972	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749930	19749972	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749973	19750071	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750072	19750089	0.97	+	2	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750072	19750089	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750090	19750176	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750177	19750352	0.97	+	2	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750177	19750352	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750353	19750528	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750529	19750606	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750529	19750606	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750607	19750701	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750702	19750740	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750702	19750740	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750741	19750869	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750870	19751064	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750870	19751064	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19751065	19751139	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19751140	19751232	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19751140	19751232	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19751233	19751344	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19751345	19751788	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19751345	19751788	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19751789	19751868	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19751869	19752000	1	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19751869	19752000	.	+	.	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	stop_codon	19752001	19752003	.	+	0	transcript_id "Phchi.S1G307000.t1"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	transcript	19749191	19752000	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	start_codon	19749191	19749193	.	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749191	19749330	0.89	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749191	19749330	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749331	19749580	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749581	19749627	0.91	+	1	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749581	19749627	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749628	19749731	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749732	19749760	0.94	+	2	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749732	19749760	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749761	19749929	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19749930	19749972	1	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19749930	19749972	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19749973	19750071	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750072	19750089	1	+	2	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750072	19750089	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750090	19750176	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750177	19750352	1	+	2	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750177	19750352	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750353	19750528	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750529	19750606	1	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750529	19750606	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750607	19750701	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750702	19750740	1	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750702	19750740	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19750741	19750869	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19750870	19751064	1	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19750870	19751064	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19751065	19751139	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19751140	19751232	1	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19751140	19751232	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19751233	19751344	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19751345	19751788	0.98	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19751345	19751788	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	intron	19751789	19751874	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	CDS	19751875	19752000	1	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	exon	19751875	19752000	.	+	.	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
Phchi.S1	AUGUSTUS	stop_codon	19752001	19752003	.	+	0	transcript_id "Phchi.S1G307000.t2"; gene_id "Phchi.S1G307000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6748.t1 is derived from g3920.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24836416	24841022	.	-	.	Phchi.S1G390700
Phchi.S1	AUGUSTUS	transcript	24836416	24841022	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	stop_codon	24836413	24836415	.	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24836416	24836518	0.82	-	1	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24836416	24836518	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24836519	24836636	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24836637	24836757	0.96	-	2	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24836637	24836757	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24836758	24836831	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24836832	24836947	1	-	1	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24836832	24836947	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24836948	24837027	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837028	24837107	1	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837028	24837107	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837108	24837204	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837205	24837330	1	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837205	24837330	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837331	24837431	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837432	24837512	0.99	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837432	24837512	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837513	24837629	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837630	24837822	0.98	-	1	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837630	24837822	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837823	24837945	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837946	24838010	1	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837946	24838010	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24838011	24838095	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24838096	24838384	0.59	-	1	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24838096	24838384	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24838385	24838599	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24838600	24838771	0.65	-	2	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24838600	24838771	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24838772	24838862	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24838863	24839055	1	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24838863	24839055	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839056	24839173	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24839174	24839410	0.93	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24839174	24839410	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839411	24839516	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24839517	24839681	0.99	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24839517	24839681	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839682	24839762	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24839763	24839982	0.99	-	1	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24839763	24839982	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839983	24840077	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840078	24840088	0.9	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840078	24840088	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24840089	24840331	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840332	24840444	0.82	-	2	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840332	24840444	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24840445	24840593	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840594	24840826	0.96	-	1	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840594	24840826	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24840827	24840930	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840931	24841022	0.99	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840931	24841022	.	-	.	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	start_codon	24841020	24841022	.	-	0	transcript_id "Phchi.S1G390700.t1"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	transcript	24836474	24841022	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	stop_codon	24836471	24836473	.	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24836474	24836540	0.88	-	1	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24836474	24836540	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24836541	24836636	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24836637	24836757	1	-	2	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24836637	24836757	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24836758	24836831	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24836832	24836947	1	-	1	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24836832	24836947	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24836948	24837027	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837028	24837107	1	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837028	24837107	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837108	24837204	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837205	24837330	1	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837205	24837330	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837331	24837431	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837432	24837512	0.99	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837432	24837512	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837513	24837629	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837630	24837822	0.98	-	1	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837630	24837822	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24837823	24837945	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24837946	24838010	1	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24837946	24838010	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24838011	24838095	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24838096	24838384	0.55	-	1	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24838096	24838384	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24838385	24838599	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24838600	24838771	0.64	-	2	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24838600	24838771	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24838772	24838862	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24838863	24839055	1	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24838863	24839055	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839056	24839173	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24839174	24839410	0.92	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24839174	24839410	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839411	24839516	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24839517	24839681	1	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24839517	24839681	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839682	24839762	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24839763	24839982	0.98	-	1	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24839763	24839982	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24839983	24840077	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840078	24840088	0.84	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840078	24840088	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24840089	24840331	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840332	24840444	0.8	-	2	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840332	24840444	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24840445	24840593	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840594	24840826	0.93	-	1	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840594	24840826	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	intron	24840827	24840930	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	CDS	24840931	24841022	0.93	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	exon	24840931	24841022	.	-	.	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
Phchi.S1	AUGUSTUS	start_codon	24841020	24841022	.	-	0	transcript_id "Phchi.S1G390700.t2"; gene_id "Phchi.S1G390700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6374.t1 is derived from g3546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22636862	22637413	.	+	.	Phchi.S1G353300
Phchi.S1	AUGUSTUS	transcript	22636862	22637413	.	+	.	transcript_id "Phchi.S1G353300.t1"; gene_id "Phchi.S1G353300"
Phchi.S1	AUGUSTUS	start_codon	22636862	22636864	.	+	0	transcript_id "Phchi.S1G353300.t1"; gene_id "Phchi.S1G353300"
Phchi.S1	AUGUSTUS	CDS	22636862	22637413	0.67	+	0	transcript_id "Phchi.S1G353300.t1"; gene_id "Phchi.S1G353300"
Phchi.S1	AUGUSTUS	exon	22636862	22637413	.	+	.	transcript_id "Phchi.S1G353300.t1"; gene_id "Phchi.S1G353300"
Phchi.S1	AUGUSTUS	stop_codon	22637414	22637416	.	+	0	transcript_id "Phchi.S1G353300.t1"; gene_id "Phchi.S1G353300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15485.t1 is derived from g13954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19434191	19437027	.	+	.	Phchi.S3G280400
Phchi.S3	AUGUSTUS	transcript	19434191	19437027	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	start_codon	19434191	19434193	.	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19434191	19434817	1	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19434191	19434817	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	intron	19434818	19434950	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19434951	19435268	1	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19434951	19435268	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	intron	19435269	19435465	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19435466	19435543	1	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19435466	19435543	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	intron	19435544	19435729	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19435730	19435795	1	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19435730	19435795	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	intron	19435796	19435907	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19435908	19435973	1	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19435908	19435973	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	intron	19435974	19436118	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19436119	19436167	0.84	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19436119	19436167	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	intron	19436168	19436344	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	CDS	19436345	19437027	0.81	+	2	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	exon	19436345	19437027	.	+	.	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
Phchi.S3	AUGUSTUS	stop_codon	19437028	19437030	.	+	0	transcript_id "Phchi.S3G280400.t1"; gene_id "Phchi.S3G280400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14698.t1 is derived from g13166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14210847	14211567	.	+	.	Phchi.S3G201700
Phchi.S3	AUGUSTUS	transcript	14210847	14211567	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	start_codon	14210847	14210849	.	+	0	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	CDS	14210847	14210943	0.79	+	0	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	exon	14210847	14210943	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	intron	14210944	14211151	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	CDS	14211152	14211234	0.98	+	2	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	exon	14211152	14211234	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	intron	14211235	14211406	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	CDS	14211407	14211421	0.66	+	0	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	exon	14211407	14211421	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	intron	14211422	14211510	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	CDS	14211511	14211567	0.44	+	0	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	exon	14211511	14211567	.	+	.	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
Phchi.S3	AUGUSTUS	stop_codon	14211568	14211570	.	+	0	transcript_id "Phchi.S3G201700.t1"; gene_id "Phchi.S3G201700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1858.t1 is derived from g8778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3573949	3574680	.	-	.	Phchi.S5G046700
Phchi.S5	AUGUSTUS	transcript	3573949	3574680	.	-	.	transcript_id "Phchi.S5G046700.t1"; gene_id "Phchi.S5G046700"
Phchi.S5	AUGUSTUS	stop_codon	3573946	3573948	.	-	0	transcript_id "Phchi.S5G046700.t1"; gene_id "Phchi.S5G046700"
Phchi.S5	AUGUSTUS	CDS	3573949	3574680	1	-	0	transcript_id "Phchi.S5G046700.t1"; gene_id "Phchi.S5G046700"
Phchi.S5	AUGUSTUS	exon	3573949	3574680	.	-	.	transcript_id "Phchi.S5G046700.t1"; gene_id "Phchi.S5G046700"
Phchi.S5	AUGUSTUS	start_codon	3574678	3574680	.	-	0	transcript_id "Phchi.S5G046700.t1"; gene_id "Phchi.S5G046700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1209.t1 is derived from g10992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8425858	8426671	.	+	.	Phchi.S6G116800
Phchi.S6	AUGUSTUS	transcript	8425858	8426671	.	+	.	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	start_codon	8425858	8425860	.	+	0	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	CDS	8425858	8426017	0.99	+	0	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	exon	8425858	8426017	.	+	.	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	intron	8426018	8426138	.	+	.	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	CDS	8426139	8426180	0.97	+	2	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	exon	8426139	8426180	.	+	.	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	intron	8426181	8426273	.	+	.	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	CDS	8426274	8426671	0.97	+	2	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	exon	8426274	8426671	.	+	.	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
Phchi.S6	AUGUSTUS	stop_codon	8426672	8426674	.	+	0	transcript_id "Phchi.S6G116800.t1"; gene_id "Phchi.S6G116800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11535.t1 is derived from g15585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6954250	6956471	.	-	.	Phchi.S4G111700
Phchi.S4	AUGUSTUS	transcript	6954250	6956471	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	stop_codon	6954247	6954249	.	-	0	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	CDS	6954250	6954629	1	-	2	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	exon	6954250	6954629	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	intron	6954630	6954718	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	CDS	6954719	6955731	0.99	-	1	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	exon	6954719	6955731	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	intron	6955732	6955843	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	CDS	6955844	6956106	0.4	-	0	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	exon	6955844	6956106	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	intron	6956107	6956264	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	CDS	6956265	6956471	0.26	-	0	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	exon	6956265	6956471	.	-	.	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
Phchi.S4	AUGUSTUS	start_codon	6956469	6956471	.	-	0	transcript_id "Phchi.S4G111700.t1"; gene_id "Phchi.S4G111700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6517.t1 is derived from g3689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23426622	23427473	.	+	.	Phchi.S1G367600
Phchi.S1	AUGUSTUS	transcript	23426622	23427473	.	+	.	transcript_id "Phchi.S1G367600.t1"; gene_id "Phchi.S1G367600"
Phchi.S1	AUGUSTUS	start_codon	23426622	23426624	.	+	0	transcript_id "Phchi.S1G367600.t1"; gene_id "Phchi.S1G367600"
Phchi.S1	AUGUSTUS	CDS	23426622	23427473	0.6	+	0	transcript_id "Phchi.S1G367600.t1"; gene_id "Phchi.S1G367600"
Phchi.S1	AUGUSTUS	exon	23426622	23427473	.	+	.	transcript_id "Phchi.S1G367600.t1"; gene_id "Phchi.S1G367600"
Phchi.S1	AUGUSTUS	stop_codon	23427474	23427476	.	+	0	transcript_id "Phchi.S1G367600.t1"; gene_id "Phchi.S1G367600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12742.t1 is derived from g11207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1548319	1548915	.	-	.	Phchi.S3G006100
Phchi.S3	AUGUSTUS	transcript	1548319	1548915	.	-	.	transcript_id "Phchi.S3G006100.t1"; gene_id "Phchi.S3G006100"
Phchi.S3	AUGUSTUS	stop_codon	1548316	1548318	.	-	0	transcript_id "Phchi.S3G006100.t1"; gene_id "Phchi.S3G006100"
Phchi.S3	AUGUSTUS	CDS	1548319	1548915	0.97	-	0	transcript_id "Phchi.S3G006100.t1"; gene_id "Phchi.S3G006100"
Phchi.S3	AUGUSTUS	exon	1548319	1548915	.	-	.	transcript_id "Phchi.S3G006100.t1"; gene_id "Phchi.S3G006100"
Phchi.S3	AUGUSTUS	start_codon	1548913	1548915	.	-	0	transcript_id "Phchi.S3G006100.t1"; gene_id "Phchi.S3G006100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4918.t1 is derived from g2088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13555510	13557941	.	+	.	Phchi.S1G207700
Phchi.S1	AUGUSTUS	transcript	13555510	13557941	.	+	.	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	start_codon	13555510	13555512	.	+	0	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	CDS	13555510	13556641	0.55	+	0	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	exon	13555510	13556641	.	+	.	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	intron	13556642	13556742	.	+	.	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	CDS	13556743	13557941	0.5	+	2	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	exon	13556743	13557941	.	+	.	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
Phchi.S1	AUGUSTUS	stop_codon	13557942	13557944	.	+	0	transcript_id "Phchi.S1G207700.t1"; gene_id "Phchi.S1G207700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7858.t1 is derived from g5032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31552053	31554297	.	-	.	Phchi.S1G501700
Phchi.S1	AUGUSTUS	transcript	31552053	31554297	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	stop_codon	31552050	31552052	.	-	0	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	CDS	31552053	31552286	0.93	-	0	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	exon	31552053	31552286	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	intron	31552287	31552385	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	CDS	31552386	31552794	1	-	1	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	exon	31552386	31552794	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	intron	31552795	31552976	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	CDS	31552977	31553378	0.94	-	1	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	exon	31552977	31553378	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	intron	31553379	31553564	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	CDS	31553565	31553914	1	-	0	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	exon	31553565	31553914	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	intron	31553915	31554069	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	CDS	31554070	31554297	0.99	-	0	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	exon	31554070	31554297	.	-	.	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
Phchi.S1	AUGUSTUS	start_codon	31554295	31554297	.	-	0	transcript_id "Phchi.S1G501700.t1"; gene_id "Phchi.S1G501700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2177.t1 is derived from g9097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5232794	5234591	.	-	.	Phchi.S5G078600
Phchi.S5	AUGUSTUS	transcript	5232794	5234591	.	-	.	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	stop_codon	5232791	5232793	.	-	0	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	CDS	5232794	5233270	0.99	-	0	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	exon	5232794	5233270	.	-	.	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	intron	5233271	5233375	.	-	.	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	CDS	5233376	5233480	1	-	0	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	exon	5233376	5233480	.	-	.	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	intron	5233481	5233604	.	-	.	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	CDS	5233605	5234591	0.72	-	0	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	exon	5233605	5234591	.	-	.	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
Phchi.S5	AUGUSTUS	start_codon	5234589	5234591	.	-	0	transcript_id "Phchi.S5G078600.t1"; gene_id "Phchi.S5G078600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14719.t1 is derived from g13187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14354023	14356234	.	-	.	Phchi.S3G203800
Phchi.S3	AUGUSTUS	transcript	14354023	14356234	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	stop_codon	14354020	14354022	.	-	0	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	CDS	14354023	14354766	1	-	0	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	exon	14354023	14354766	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	intron	14354767	14354871	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	CDS	14354872	14355160	1	-	1	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	exon	14354872	14355160	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	intron	14355161	14355247	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	CDS	14355248	14355602	0.98	-	2	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	exon	14355248	14355602	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	intron	14355603	14355689	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	CDS	14355690	14355849	1	-	0	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	exon	14355690	14355849	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	intron	14355850	14355955	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	CDS	14355956	14356234	0.49	-	0	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	exon	14355956	14356234	.	-	.	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
Phchi.S3	AUGUSTUS	start_codon	14356232	14356234	.	-	0	transcript_id "Phchi.S3G203800.t1"; gene_id "Phchi.S3G203800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8210.t1 is derived from g5385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34439467	34440882	.	-	.	Phchi.S1G536900
Phchi.S1	AUGUSTUS	transcript	34439467	34440882	.	-	.	transcript_id "Phchi.S1G536900.t1"; gene_id "Phchi.S1G536900"
Phchi.S1	AUGUSTUS	stop_codon	34439464	34439466	.	-	0	transcript_id "Phchi.S1G536900.t1"; gene_id "Phchi.S1G536900"
Phchi.S1	AUGUSTUS	CDS	34439467	34440882	0.99	-	0	transcript_id "Phchi.S1G536900.t1"; gene_id "Phchi.S1G536900"
Phchi.S1	AUGUSTUS	exon	34439467	34440882	.	-	.	transcript_id "Phchi.S1G536900.t1"; gene_id "Phchi.S1G536900"
Phchi.S1	AUGUSTUS	start_codon	34440880	34440882	.	-	0	transcript_id "Phchi.S1G536900.t1"; gene_id "Phchi.S1G536900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8925.t1 is derived from g6100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38688075	38688696	.	-	.	Phchi.S1G608400
Phchi.S1	AUGUSTUS	transcript	38688075	38688696	.	-	.	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	stop_codon	38688072	38688074	.	-	0	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	CDS	38688075	38688122	1	-	0	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	exon	38688075	38688122	.	-	.	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	intron	38688123	38688312	.	-	.	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	CDS	38688313	38688423	1	-	0	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	exon	38688313	38688423	.	-	.	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	intron	38688424	38688588	.	-	.	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	CDS	38688589	38688696	1	-	0	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	exon	38688589	38688696	.	-	.	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
Phchi.S1	AUGUSTUS	start_codon	38688694	38688696	.	-	0	transcript_id "Phchi.S1G608400.t1"; gene_id "Phchi.S1G608400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13034.t1 is derived from g11499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3803943	3806175	.	+	.	Phchi.S3G035300
Phchi.S3	AUGUSTUS	transcript	3803943	3806175	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	start_codon	3803943	3803945	.	+	0	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3803943	3804544	0.64	+	0	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3803943	3804544	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3804545	3804741	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3804742	3804881	1	+	1	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3804742	3804881	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3804882	3804978	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3804979	3805088	0.83	+	2	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3804979	3805088	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805089	3805273	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805274	3805302	0.51	+	0	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805274	3805302	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805303	3805519	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805520	3805561	0.85	+	1	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805520	3805561	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805562	3805696	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805697	3805763	1	+	1	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805697	3805763	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805764	3805843	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805844	3805927	1	+	0	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805844	3805927	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805928	3806016	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3806017	3806175	0.64	+	0	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3806017	3806175	.	+	.	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	stop_codon	3806176	3806178	.	+	0	transcript_id "Phchi.S3G035300.t1"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	transcript	3803943	3806175	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	start_codon	3803943	3803945	.	+	0	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3803943	3804544	0.61	+	0	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3803943	3804544	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3804545	3804741	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3804742	3804804	0.71	+	1	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3804742	3804804	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3804805	3804881	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3804882	3804901	0.71	+	1	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3804882	3804901	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3804902	3804978	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3804979	3805088	0.83	+	2	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3804979	3805088	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805089	3805273	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805274	3805302	0.37	+	0	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805274	3805302	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805303	3805519	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805520	3805561	0.82	+	1	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805520	3805561	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805562	3805696	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805697	3805763	1	+	1	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805697	3805763	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805764	3805843	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3805844	3805927	1	+	0	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3805844	3805927	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	intron	3805928	3806016	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	CDS	3806017	3806175	0.59	+	0	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	exon	3806017	3806175	.	+	.	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
Phchi.S3	AUGUSTUS	stop_codon	3806176	3806178	.	+	0	transcript_id "Phchi.S3G035300.t2"; gene_id "Phchi.S3G035300"
# This transcript jg12765.t2 is derived from g11230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12766.t1 is derived from g11231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1952304	1953028	.	+	.	Phchi.S3G008500
Phchi.S3	AUGUSTUS	transcript	1952304	1953028	.	+	.	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	start_codon	1952304	1952306	.	+	0	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	CDS	1952304	1952917	0.54	+	0	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	exon	1952304	1952917	.	+	.	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	intron	1952918	1953009	.	+	.	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	CDS	1953010	1953028	0.75	+	1	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	exon	1953010	1953028	.	+	.	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
Phchi.S3	AUGUSTUS	stop_codon	1953029	1953031	.	+	0	transcript_id "Phchi.S3G008500.t1"; gene_id "Phchi.S3G008500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg425.t1 is derived from g10207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3031279	3032764	.	-	.	Phchi.S6G038400
Phchi.S6	AUGUSTUS	transcript	3031279	3032764	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	stop_codon	3031276	3031278	.	-	0	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3031279	3031406	1	-	2	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3031279	3031406	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3031407	3031631	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3031632	3031671	0.99	-	0	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3031632	3031671	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3031672	3031789	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3031790	3031839	0.99	-	2	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3031790	3031839	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3031840	3031981	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3031982	3032051	1	-	0	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3031982	3032051	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3032052	3032141	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3032142	3032211	0.99	-	1	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3032142	3032211	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3032212	3032317	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3032318	3032377	0.92	-	1	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3032318	3032377	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3032378	3032480	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3032481	3032539	1	-	0	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3032481	3032539	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	intron	3032540	3032761	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	CDS	3032762	3032764	0.94	-	0	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	exon	3032762	3032764	.	-	.	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
Phchi.S6	AUGUSTUS	start_codon	3032762	3032764	.	-	0	transcript_id "Phchi.S6G038400.t1"; gene_id "Phchi.S6G038400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11682.t1 is derived from g15733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7650891	7651112	.	+	.	Phchi.S4G126400
Phchi.S4	AUGUSTUS	transcript	7650891	7651112	.	+	.	transcript_id "Phchi.S4G126400.t1"; gene_id "Phchi.S4G126400"
Phchi.S4	AUGUSTUS	start_codon	7650891	7650893	.	+	0	transcript_id "Phchi.S4G126400.t1"; gene_id "Phchi.S4G126400"
Phchi.S4	AUGUSTUS	CDS	7650891	7651112	0.6	+	0	transcript_id "Phchi.S4G126400.t1"; gene_id "Phchi.S4G126400"
Phchi.S4	AUGUSTUS	exon	7650891	7651112	.	+	.	transcript_id "Phchi.S4G126400.t1"; gene_id "Phchi.S4G126400"
Phchi.S4	AUGUSTUS	stop_codon	7651113	7651115	.	+	0	transcript_id "Phchi.S4G126400.t1"; gene_id "Phchi.S4G126400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5000.t1 is derived from g2170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13954035	13956914	.	+	.	Phchi.S1G215900
Phchi.S1	AUGUSTUS	transcript	13954035	13956914	.	+	.	transcript_id "Phchi.S1G215900.t1"; gene_id "Phchi.S1G215900"
Phchi.S1	AUGUSTUS	start_codon	13954035	13954037	.	+	0	transcript_id "Phchi.S1G215900.t1"; gene_id "Phchi.S1G215900"
Phchi.S1	AUGUSTUS	CDS	13954035	13956914	0.46	+	0	transcript_id "Phchi.S1G215900.t1"; gene_id "Phchi.S1G215900"
Phchi.S1	AUGUSTUS	exon	13954035	13956914	.	+	.	transcript_id "Phchi.S1G215900.t1"; gene_id "Phchi.S1G215900"
Phchi.S1	AUGUSTUS	stop_codon	13956915	13956917	.	+	0	transcript_id "Phchi.S1G215900.t1"; gene_id "Phchi.S1G215900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1623.t1 is derived from g8542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2071262	2074303	.	-	.	Phchi.S5G023200
Phchi.S5	AUGUSTUS	transcript	2071262	2074303	.	-	.	transcript_id "Phchi.S5G023200.t1"; gene_id "Phchi.S5G023200"
Phchi.S5	AUGUSTUS	stop_codon	2071259	2071261	.	-	0	transcript_id "Phchi.S5G023200.t1"; gene_id "Phchi.S5G023200"
Phchi.S5	AUGUSTUS	CDS	2071262	2074303	0.97	-	0	transcript_id "Phchi.S5G023200.t1"; gene_id "Phchi.S5G023200"
Phchi.S5	AUGUSTUS	exon	2071262	2074303	.	-	.	transcript_id "Phchi.S5G023200.t1"; gene_id "Phchi.S5G023200"
Phchi.S5	AUGUSTUS	start_codon	2074301	2074303	.	-	0	transcript_id "Phchi.S5G023200.t1"; gene_id "Phchi.S5G023200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3668.t1 is derived from g837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5107016	5107309	.	-	.	Phchi.S1G082700
Phchi.S1	AUGUSTUS	transcript	5107016	5107309	.	-	.	transcript_id "Phchi.S1G082700.t1"; gene_id "Phchi.S1G082700"
Phchi.S1	AUGUSTUS	stop_codon	5107013	5107015	.	-	0	transcript_id "Phchi.S1G082700.t1"; gene_id "Phchi.S1G082700"
Phchi.S1	AUGUSTUS	CDS	5107016	5107309	0.55	-	0	transcript_id "Phchi.S1G082700.t1"; gene_id "Phchi.S1G082700"
Phchi.S1	AUGUSTUS	exon	5107016	5107309	.	-	.	transcript_id "Phchi.S1G082700.t1"; gene_id "Phchi.S1G082700"
Phchi.S1	AUGUSTUS	start_codon	5107307	5107309	.	-	0	transcript_id "Phchi.S1G082700.t1"; gene_id "Phchi.S1G082700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1995.t1 is derived from g8915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4349740	4352932	.	-	.	Phchi.S5G060400
Phchi.S5	AUGUSTUS	transcript	4349740	4352932	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	stop_codon	4349737	4349739	.	-	0	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	CDS	4349740	4352176	0.87	-	1	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	exon	4349740	4352176	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	intron	4352177	4352303	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	CDS	4352304	4352355	0.99	-	2	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	exon	4352304	4352355	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	intron	4352356	4352434	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	CDS	4352435	4352488	1	-	2	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	exon	4352435	4352488	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	intron	4352489	4352625	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	CDS	4352626	4352721	1	-	2	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	exon	4352626	4352721	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	intron	4352722	4352844	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	CDS	4352845	4352932	0.48	-	0	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	exon	4352845	4352932	.	-	.	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
Phchi.S5	AUGUSTUS	start_codon	4352930	4352932	.	-	0	transcript_id "Phchi.S5G060400.t1"; gene_id "Phchi.S5G060400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4694.t1 is derived from g1864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12239484	12240769	.	+	.	Phchi.S1G185300
Phchi.S1	AUGUSTUS	transcript	12239484	12240769	.	+	.	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	start_codon	12239484	12239486	.	+	0	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	CDS	12239484	12239751	0.39	+	0	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	exon	12239484	12239751	.	+	.	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	intron	12239752	12239870	.	+	.	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	CDS	12239871	12240769	0.4	+	2	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	exon	12239871	12240769	.	+	.	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
Phchi.S1	AUGUSTUS	stop_codon	12240770	12240772	.	+	0	transcript_id "Phchi.S1G185300.t1"; gene_id "Phchi.S1G185300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2737.t1 is derived from g9657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8502031	8503321	.	-	.	Phchi.S5G134600
Phchi.S5	AUGUSTUS	transcript	8502031	8503321	.	-	.	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	stop_codon	8502028	8502030	.	-	0	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	CDS	8502031	8502681	1	-	0	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	exon	8502031	8502681	.	-	.	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	intron	8502682	8502763	.	-	.	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	CDS	8502764	8503321	1	-	0	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	exon	8502764	8503321	.	-	.	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
Phchi.S5	AUGUSTUS	start_codon	8503319	8503321	.	-	0	transcript_id "Phchi.S5G134600.t1"; gene_id "Phchi.S5G134600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7998.t1 is derived from g5173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32357539	32359462	.	+	.	Phchi.S1G515700
Phchi.S1	AUGUSTUS	transcript	32357539	32359462	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	start_codon	32357539	32357541	.	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32357539	32357658	0.7	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32357539	32357658	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32357659	32357754	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32357755	32358048	0.75	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32357755	32358048	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32358049	32358131	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32358132	32358248	0.96	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32358132	32358248	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32358249	32358344	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32358345	32358593	0.96	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32358345	32358593	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32358594	32358684	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32358685	32358832	0.99	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32358685	32358832	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32358833	32358918	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32358919	32358988	0.99	+	2	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32358919	32358988	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32358989	32359061	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32359062	32359134	1	+	1	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32359062	32359134	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	intron	32359135	32359204	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	CDS	32359205	32359462	1	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	exon	32359205	32359462	.	+	.	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
Phchi.S1	AUGUSTUS	stop_codon	32359463	32359465	.	+	0	transcript_id "Phchi.S1G515700.t1"; gene_id "Phchi.S1G515700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12870.t1 is derived from g11335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2838556	2840082	.	-	.	Phchi.S3G018900
Phchi.S3	AUGUSTUS	transcript	2838556	2840082	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	stop_codon	2838553	2838555	.	-	0	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	CDS	2838556	2838831	0.59	-	0	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	exon	2838556	2838831	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	intron	2838832	2838920	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	CDS	2838921	2839205	1	-	0	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	exon	2838921	2839205	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	intron	2839206	2839365	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	CDS	2839366	2839745	0.88	-	2	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	exon	2839366	2839745	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	intron	2839746	2839901	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	CDS	2839902	2840082	0.54	-	0	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	exon	2839902	2840082	.	-	.	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
Phchi.S3	AUGUSTUS	start_codon	2840080	2840082	.	-	0	transcript_id "Phchi.S3G018900.t1"; gene_id "Phchi.S3G018900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7540.t1 is derived from g4714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29958213	29958836	.	-	.	Phchi.S1G469900
Phchi.S1	AUGUSTUS	transcript	29958213	29958836	.	-	.	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	stop_codon	29958210	29958212	.	-	0	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	CDS	29958213	29958261	0.54	-	1	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	exon	29958213	29958261	.	-	.	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	intron	29958262	29958404	.	-	.	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	CDS	29958405	29958500	0.38	-	1	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	exon	29958405	29958500	.	-	.	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	intron	29958501	29958774	.	-	.	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	CDS	29958775	29958836	0.37	-	0	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	exon	29958775	29958836	.	-	.	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
Phchi.S1	AUGUSTUS	start_codon	29958834	29958836	.	-	0	transcript_id "Phchi.S1G469900.t1"; gene_id "Phchi.S1G469900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15080.t1 is derived from g13548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16940178	16940486	.	-	.	Phchi.S3G239900
Phchi.S3	AUGUSTUS	transcript	16940178	16940486	.	-	.	transcript_id "Phchi.S3G239900.t1"; gene_id "Phchi.S3G239900"
Phchi.S3	AUGUSTUS	stop_codon	16940175	16940177	.	-	0	transcript_id "Phchi.S3G239900.t1"; gene_id "Phchi.S3G239900"
Phchi.S3	AUGUSTUS	CDS	16940178	16940486	0.59	-	0	transcript_id "Phchi.S3G239900.t1"; gene_id "Phchi.S3G239900"
Phchi.S3	AUGUSTUS	exon	16940178	16940486	.	-	.	transcript_id "Phchi.S3G239900.t1"; gene_id "Phchi.S3G239900"
Phchi.S3	AUGUSTUS	start_codon	16940484	16940486	.	-	0	transcript_id "Phchi.S3G239900.t1"; gene_id "Phchi.S3G239900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8986.t1 is derived from g6161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38983171	38984327	.	+	.	Phchi.S1G614500
Phchi.S1	AUGUSTUS	transcript	38983171	38984327	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	start_codon	38983171	38983173	.	+	0	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	CDS	38983171	38983248	1	+	0	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	exon	38983171	38983248	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	intron	38983249	38983424	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	CDS	38983425	38983515	1	+	0	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	exon	38983425	38983515	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	intron	38983516	38983670	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	CDS	38983671	38983803	1	+	2	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	exon	38983671	38983803	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	intron	38983804	38983928	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	CDS	38983929	38983998	1	+	1	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	exon	38983929	38983998	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	intron	38983999	38984085	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	CDS	38984086	38984146	1	+	0	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	exon	38984086	38984146	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	intron	38984147	38984238	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	CDS	38984239	38984327	1	+	2	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	exon	38984239	38984327	.	+	.	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
Phchi.S1	AUGUSTUS	stop_codon	38984328	38984330	.	+	0	transcript_id "Phchi.S1G614500.t1"; gene_id "Phchi.S1G614500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13708.t1 is derived from g12175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8296297	8297040	.	+	.	Phchi.S3G102700
Phchi.S3	AUGUSTUS	transcript	8296297	8297040	.	+	.	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	start_codon	8296297	8296299	.	+	0	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	CDS	8296297	8296375	0.66	+	0	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	exon	8296297	8296375	.	+	.	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	intron	8296376	8296633	.	+	.	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	CDS	8296634	8296716	0.94	+	2	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	exon	8296634	8296716	.	+	.	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	intron	8296717	8296848	.	+	.	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	CDS	8296849	8297040	0.89	+	0	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	exon	8296849	8297040	.	+	.	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
Phchi.S3	AUGUSTUS	stop_codon	8297041	8297043	.	+	0	transcript_id "Phchi.S3G102700.t1"; gene_id "Phchi.S3G102700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9414.t1 is derived from g6590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41374186	41376044	.	-	.	Phchi.S1G657300
Phchi.S1	AUGUSTUS	transcript	41374186	41376044	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	stop_codon	41374183	41374185	.	-	0	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41374186	41374262	0.99	-	2	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41374186	41374262	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	intron	41374263	41374423	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41374424	41374566	0.6	-	1	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41374424	41374566	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	intron	41374567	41374670	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41374671	41374784	1	-	1	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41374671	41374784	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	intron	41374785	41374865	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41374866	41374965	0.99	-	2	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41374866	41374965	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	intron	41374966	41375069	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41375070	41375152	1	-	1	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41375070	41375152	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	intron	41375153	41375310	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41375311	41375463	1	-	1	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41375311	41375463	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	intron	41375464	41375634	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	CDS	41375635	41376044	1	-	0	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	exon	41375635	41376044	.	-	.	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
Phchi.S1	AUGUSTUS	start_codon	41376042	41376044	.	-	0	transcript_id "Phchi.S1G657300.t1"; gene_id "Phchi.S1G657300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10486.t1 is derived from g14535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	656820	661989	.	-	.	Phchi.S4G006800
Phchi.S4	AUGUSTUS	transcript	656820	661989	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	stop_codon	656817	656819	.	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	656820	657173	0.94	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	656820	657173	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	657174	657266	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	657267	657377	1	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	657267	657377	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	657378	657497	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	657498	658134	0.61	-	1	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	657498	658134	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	658135	658526	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	658527	658772	0.7	-	1	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	658527	658772	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	658773	658869	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	658870	658983	0.99	-	1	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	658870	658983	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	658984	659126	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	659127	659177	0.78	-	1	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	659127	659177	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	659178	659265	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	659266	659366	1	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	659266	659366	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	659367	659541	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	659542	659721	1	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	659542	659721	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	659722	659855	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	659856	659924	1	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	659856	659924	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	659925	660033	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	660034	660160	0.97	-	1	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	660034	660160	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	660161	660256	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	660257	660344	0.5	-	2	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	660257	660344	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	660345	660439	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	660440	660500	0.79	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	660440	660500	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	intron	660501	660966	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	CDS	660967	661989	1	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	exon	660967	661989	.	-	.	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
Phchi.S4	AUGUSTUS	start_codon	661987	661989	.	-	0	transcript_id "Phchi.S4G006800.t1"; gene_id "Phchi.S4G006800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6307.t1 is derived from g3479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22194927	22196788	.	+	.	Phchi.S1G346600
Phchi.S1	AUGUSTUS	transcript	22194927	22196788	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	start_codon	22194927	22194929	.	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22194927	22195049	0.93	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22194927	22195049	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22195050	22195327	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22195328	22195395	1	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22195328	22195395	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22195396	22195490	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22195491	22195554	1	+	1	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22195491	22195554	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22195555	22195649	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22195650	22195721	1	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22195650	22195721	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22195722	22195842	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22195843	22195976	1	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22195843	22195976	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22195977	22196124	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22196125	22196371	1	+	1	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22196125	22196371	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22196372	22196467	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22196468	22196578	1	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22196468	22196578	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	intron	22196579	22196668	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	CDS	22196669	22196788	0.78	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	exon	22196669	22196788	.	+	.	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
Phchi.S1	AUGUSTUS	stop_codon	22196789	22196791	.	+	0	transcript_id "Phchi.S1G346600.t1"; gene_id "Phchi.S1G346600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13071.t1 is derived from g11536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4023491	4024657	.	+	.	Phchi.S3G039000
Phchi.S3	AUGUSTUS	transcript	4023491	4024657	.	+	.	transcript_id "Phchi.S3G039000.t1"; gene_id "Phchi.S3G039000"
Phchi.S3	AUGUSTUS	start_codon	4023491	4023493	.	+	0	transcript_id "Phchi.S3G039000.t1"; gene_id "Phchi.S3G039000"
Phchi.S3	AUGUSTUS	CDS	4023491	4024657	1	+	0	transcript_id "Phchi.S3G039000.t1"; gene_id "Phchi.S3G039000"
Phchi.S3	AUGUSTUS	exon	4023491	4024657	.	+	.	transcript_id "Phchi.S3G039000.t1"; gene_id "Phchi.S3G039000"
Phchi.S3	AUGUSTUS	stop_codon	4024658	4024660	.	+	0	transcript_id "Phchi.S3G039000.t1"; gene_id "Phchi.S3G039000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14871.t1 is derived from g13339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15212969	15215466	.	-	.	Phchi.S3G219000
Phchi.S3	AUGUSTUS	transcript	15212969	15215466	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	stop_codon	15212966	15212968	.	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15212969	15212972	1	-	1	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15212969	15212972	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15212973	15213107	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15213108	15213129	0.8	-	2	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15213108	15213129	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15213130	15213413	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15213414	15213495	0.88	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15213414	15213495	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15213496	15213591	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15213592	15213699	1	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15213592	15213699	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15213700	15213881	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15213882	15213945	1	-	1	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15213882	15213945	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15213946	15214060	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15214061	15214122	1	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15214061	15214122	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15214123	15214209	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15214210	15214313	1	-	2	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15214210	15214313	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15214314	15214399	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15214400	15214451	1	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15214400	15214451	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15214452	15214539	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15214540	15214631	1	-	2	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15214540	15214631	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15214632	15214760	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15214761	15214986	1	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15214761	15214986	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	intron	15214987	15215079	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	CDS	15215080	15215466	0.93	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	exon	15215080	15215466	.	-	.	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
Phchi.S3	AUGUSTUS	start_codon	15215464	15215466	.	-	0	transcript_id "Phchi.S3G219000.t1"; gene_id "Phchi.S3G219000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3489.t1 is derived from g658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4026822	4028066	.	+	.	Phchi.S1G064800
Phchi.S1	AUGUSTUS	transcript	4026822	4028066	.	+	.	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	start_codon	4026822	4026824	.	+	0	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	CDS	4026822	4026946	0.35	+	0	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	exon	4026822	4026946	.	+	.	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	intron	4026947	4027059	.	+	.	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	CDS	4027060	4027449	0.13	+	1	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	exon	4027060	4027449	.	+	.	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	intron	4027450	4027516	.	+	.	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	CDS	4027517	4028066	0.4	+	1	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	exon	4027517	4028066	.	+	.	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
Phchi.S1	AUGUSTUS	stop_codon	4028067	4028069	.	+	0	transcript_id "Phchi.S1G064800.t1"; gene_id "Phchi.S1G064800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2024.t1 is derived from g8944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4494816	4495718	.	-	.	Phchi.S5G063300
Phchi.S5	AUGUSTUS	transcript	4494816	4495718	.	-	.	transcript_id "Phchi.S5G063300.t1"; gene_id "Phchi.S5G063300"
Phchi.S5	AUGUSTUS	stop_codon	4494813	4494815	.	-	0	transcript_id "Phchi.S5G063300.t1"; gene_id "Phchi.S5G063300"
Phchi.S5	AUGUSTUS	CDS	4494816	4495718	1	-	0	transcript_id "Phchi.S5G063300.t1"; gene_id "Phchi.S5G063300"
Phchi.S5	AUGUSTUS	exon	4494816	4495718	.	-	.	transcript_id "Phchi.S5G063300.t1"; gene_id "Phchi.S5G063300"
Phchi.S5	AUGUSTUS	start_codon	4495716	4495718	.	-	0	transcript_id "Phchi.S5G063300.t1"; gene_id "Phchi.S5G063300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4985.t1 is derived from g2155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13887872	13888833	.	-	.	Phchi.S1G214400
Phchi.S1	AUGUSTUS	transcript	13887872	13888833	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	stop_codon	13887869	13887871	.	-	0	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	CDS	13887872	13887877	0.96	-	0	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	exon	13887872	13887877	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	intron	13887878	13887975	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	CDS	13887976	13888051	0.94	-	1	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	exon	13887976	13888051	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	intron	13888052	13888245	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	CDS	13888246	13888256	0.94	-	0	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	exon	13888246	13888256	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	intron	13888257	13888341	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	CDS	13888342	13888381	0.94	-	1	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	exon	13888342	13888381	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	intron	13888382	13888516	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	CDS	13888517	13888591	0.75	-	1	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	exon	13888517	13888591	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	intron	13888592	13888720	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	CDS	13888721	13888833	0.87	-	0	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	exon	13888721	13888833	.	-	.	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
Phchi.S1	AUGUSTUS	start_codon	13888831	13888833	.	-	0	transcript_id "Phchi.S1G214400.t1"; gene_id "Phchi.S1G214400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12081.t1 is derived from g7756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2166090	2168854	.	-	.	Phchi.S2G016100
Phchi.S2	AUGUSTUS	transcript	2166090	2168854	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	stop_codon	2166087	2166089	.	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166090	2166320	0.92	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166090	2166320	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2166321	2166400	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166401	2166470	1	-	1	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166401	2166470	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2166471	2166756	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166757	2166763	0.83	-	2	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166757	2166763	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2166764	2166887	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166888	2167050	0.99	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166888	2167050	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167051	2167160	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167161	2167208	1	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167161	2167208	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167209	2167335	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167336	2167389	1	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167336	2167389	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167390	2167536	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167537	2167650	1	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167537	2167650	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167651	2167788	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167789	2167887	0.99	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167789	2167887	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167888	2167995	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167996	2168112	0.99	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167996	2168112	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168113	2168202	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168203	2168295	1	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168203	2168295	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168296	2168390	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168391	2168429	1	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168391	2168429	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168430	2168526	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168527	2168681	1	-	2	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168527	2168681	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168682	2168766	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168767	2168854	0.97	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168767	2168854	.	-	.	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	start_codon	2168852	2168854	.	-	0	transcript_id "Phchi.S2G016100.t1"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	transcript	2166090	2168854	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	stop_codon	2166087	2166089	.	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166090	2166320	0.92	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166090	2166320	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2166321	2166400	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166401	2166470	1	-	1	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166401	2166470	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2166471	2166756	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166757	2166763	0.84	-	2	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166757	2166763	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2166764	2166887	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2166888	2167050	0.9	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2166888	2167050	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167051	2167152	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167153	2167208	0.66	-	2	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167153	2167208	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167209	2167335	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167336	2167389	1	-	2	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167336	2167389	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167390	2167484	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167485	2167536	0.99	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167485	2167536	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167537	2167635	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167636	2167650	0.84	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167636	2167650	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167651	2167788	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167789	2167887	0.96	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167789	2167887	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2167888	2167995	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2167996	2168112	0.96	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2167996	2168112	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168113	2168202	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168203	2168295	1	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168203	2168295	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168296	2168390	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168391	2168429	1	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168391	2168429	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168430	2168526	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168527	2168681	1	-	2	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168527	2168681	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	intron	2168682	2168766	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	CDS	2168767	2168854	0.93	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	exon	2168767	2168854	.	-	.	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
Phchi.S2	AUGUSTUS	start_codon	2168852	2168854	.	-	0	transcript_id "Phchi.S2G016100.t2"; gene_id "Phchi.S2G016100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3362.t1 is derived from g531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3149120	3151503	.	-	.	Phchi.S1G052100
Phchi.S1	AUGUSTUS	transcript	3149120	3151503	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	stop_codon	3149117	3149119	.	-	0	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3149120	3149295	0.46	-	2	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3149120	3149295	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3149296	3149475	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3149476	3149639	0.51	-	1	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3149476	3149639	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3149640	3149725	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3149726	3150191	0.9	-	2	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3149726	3150191	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3150192	3150454	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3150455	3150623	1	-	0	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3150455	3150623	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3150624	3150718	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3150719	3150787	1	-	0	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3150719	3150787	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3150788	3150897	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3150898	3151155	0.81	-	0	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3150898	3151155	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3151156	3151299	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3151300	3151503	0.5	-	0	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3151300	3151503	.	-	.	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	start_codon	3151501	3151503	.	-	0	transcript_id "Phchi.S1G052100.t1"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	transcript	3149120	3151503	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	stop_codon	3149117	3149119	.	-	0	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3149120	3149295	0.54	-	2	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3149120	3149295	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3149296	3149475	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3149476	3149639	0.54	-	1	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3149476	3149639	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3149640	3149725	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3149726	3150191	0.92	-	2	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3149726	3150191	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3150192	3150454	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3150455	3150619	1	-	2	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3150455	3150619	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3150620	3150718	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3150719	3150761	0.72	-	0	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3150719	3150761	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3150762	3150897	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3150898	3151155	0.88	-	0	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3150898	3151155	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	intron	3151156	3151299	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	CDS	3151300	3151503	0.52	-	0	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	exon	3151300	3151503	.	-	.	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
Phchi.S1	AUGUSTUS	start_codon	3151501	3151503	.	-	0	transcript_id "Phchi.S1G052100.t2"; gene_id "Phchi.S1G052100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10788.t1 is derived from g14838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2119104	2119511	.	+	.	Phchi.S4G037000
Phchi.S4	AUGUSTUS	transcript	2119104	2119511	.	+	.	transcript_id "Phchi.S4G037000.t1"; gene_id "Phchi.S4G037000"
Phchi.S4	AUGUSTUS	start_codon	2119104	2119106	.	+	0	transcript_id "Phchi.S4G037000.t1"; gene_id "Phchi.S4G037000"
Phchi.S4	AUGUSTUS	CDS	2119104	2119511	1	+	0	transcript_id "Phchi.S4G037000.t1"; gene_id "Phchi.S4G037000"
Phchi.S4	AUGUSTUS	exon	2119104	2119511	.	+	.	transcript_id "Phchi.S4G037000.t1"; gene_id "Phchi.S4G037000"
Phchi.S4	AUGUSTUS	stop_codon	2119512	2119514	.	+	0	transcript_id "Phchi.S4G037000.t1"; gene_id "Phchi.S4G037000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5663.t1 is derived from g2833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18180892	18181422	.	+	.	Phchi.S1G282200
Phchi.S1	AUGUSTUS	transcript	18180892	18181422	.	+	.	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	start_codon	18180892	18180894	.	+	0	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	CDS	18180892	18181173	0.49	+	0	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	exon	18180892	18181173	.	+	.	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	intron	18181174	18181383	.	+	.	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	CDS	18181384	18181422	0.99	+	0	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	exon	18181384	18181422	.	+	.	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
Phchi.S1	AUGUSTUS	stop_codon	18181423	18181425	.	+	0	transcript_id "Phchi.S1G282200.t1"; gene_id "Phchi.S1G282200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5984.t1 is derived from g3155.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20239863	20244042	.	+	.	Phchi.S1G314300
Phchi.S1	AUGUSTUS	transcript	20239863	20244042	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	start_codon	20239863	20239865	.	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20239863	20240030	0.72	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20239863	20240030	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240031	20240173	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240174	20240242	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240174	20240242	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240243	20240334	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240335	20240379	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240335	20240379	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240380	20240469	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240470	20240571	0.99	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240470	20240571	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240572	20240674	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240675	20240803	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240675	20240803	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240804	20240896	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240897	20240947	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240897	20240947	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240948	20241077	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241078	20241173	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241078	20241173	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241174	20241274	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241275	20241451	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241275	20241451	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241452	20241578	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241579	20241653	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241579	20241653	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241654	20241749	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241750	20241866	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241750	20241866	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241867	20242080	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242081	20242292	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242081	20242292	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242293	20242378	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242379	20242514	1	+	1	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242379	20242514	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242515	20242594	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242595	20242822	0.98	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242595	20242822	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242823	20242930	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242931	20242998	1	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242931	20242998	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242999	20243090	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243091	20243196	0.96	+	1	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243091	20243196	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243197	20243463	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243464	20243520	0.94	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243464	20243520	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243521	20243610	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243611	20243640	0.89	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243611	20243640	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243641	20243737	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243738	20243793	0.65	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243738	20243793	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243794	20243945	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243946	20244042	0.89	+	1	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243946	20244042	.	+	.	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	stop_codon	20244043	20244045	.	+	0	transcript_id "Phchi.S1G314300.t1"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	transcript	20239863	20244042	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	start_codon	20239863	20239865	.	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20239863	20240030	0.74	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20239863	20240030	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240031	20240173	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240174	20240242	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240174	20240242	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240243	20240334	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240335	20240379	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240335	20240379	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240380	20240469	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240470	20240571	0.99	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240470	20240571	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240572	20240674	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240675	20240803	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240675	20240803	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240804	20240896	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240897	20240947	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240897	20240947	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240948	20241077	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241078	20241173	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241078	20241173	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241174	20241274	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241275	20241451	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241275	20241451	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241452	20241578	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241579	20241653	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241579	20241653	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241654	20241749	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241750	20241866	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241750	20241866	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241867	20242080	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242081	20242292	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242081	20242292	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242293	20242378	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242379	20242514	1	+	1	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242379	20242514	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242515	20242594	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242595	20242822	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242595	20242822	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242823	20242930	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242931	20242998	1	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242931	20242998	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242999	20243090	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243091	20243196	0.46	+	1	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243091	20243196	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243197	20243463	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243464	20243599	0.46	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243464	20243599	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243600	20243699	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243700	20243793	1	+	2	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243700	20243793	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243794	20243945	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243946	20244042	0.84	+	1	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243946	20244042	.	+	.	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	stop_codon	20244043	20244045	.	+	0	transcript_id "Phchi.S1G314300.t2"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	transcript	20239863	20244042	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	start_codon	20239863	20239865	.	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20239863	20240030	0.81	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20239863	20240030	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240031	20240173	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240174	20240242	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240174	20240242	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240243	20240334	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240335	20240379	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240335	20240379	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240380	20240469	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240470	20240571	0.98	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240470	20240571	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240572	20240674	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240675	20240803	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240675	20240803	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240804	20240896	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20240897	20240947	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20240897	20240947	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20240948	20241077	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241078	20241173	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241078	20241173	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241174	20241274	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241275	20241451	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241275	20241451	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241452	20241578	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241579	20241653	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241579	20241653	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241654	20241749	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20241750	20241866	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20241750	20241866	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20241867	20242080	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242081	20242292	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242081	20242292	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242293	20242378	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242379	20242514	1	+	1	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242379	20242514	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242515	20242594	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242595	20242822	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242595	20242822	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242823	20242930	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20242931	20242998	1	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20242931	20242998	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20242999	20243090	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243091	20243183	0.52	+	1	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243091	20243183	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243184	20243485	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243486	20243520	0.52	+	1	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243486	20243520	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243521	20243699	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243700	20243793	0.78	+	2	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243700	20243793	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	intron	20243794	20243945	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	CDS	20243946	20244042	0.87	+	1	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	exon	20243946	20244042	.	+	.	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
Phchi.S1	AUGUSTUS	stop_codon	20244043	20244045	.	+	0	transcript_id "Phchi.S1G314300.t3"; gene_id "Phchi.S1G314300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12521.t1 is derived from g8198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32805966	32807351	.	-	.	Phchi.S2G060100
Phchi.S2	AUGUSTUS	transcript	32805966	32807000	.	-	.	transcript_id "Phchi.S2G060100.t1"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	stop_codon	32805963	32805965	.	-	0	transcript_id "Phchi.S2G060100.t1"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	CDS	32805966	32807000	1	-	0	transcript_id "Phchi.S2G060100.t1"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	exon	32805966	32807000	.	-	.	transcript_id "Phchi.S2G060100.t1"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	start_codon	32806998	32807000	.	-	0	transcript_id "Phchi.S2G060100.t1"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	transcript	32805966	32807351	.	-	.	transcript_id "Phchi.S2G060100.t2"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	stop_codon	32805963	32805965	.	-	0	transcript_id "Phchi.S2G060100.t2"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	CDS	32805966	32807351	0.78	-	0	transcript_id "Phchi.S2G060100.t2"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	exon	32805966	32807351	.	-	.	transcript_id "Phchi.S2G060100.t2"; gene_id "Phchi.S2G060100"
Phchi.S2	AUGUSTUS	start_codon	32807349	32807351	.	-	0	transcript_id "Phchi.S2G060100.t2"; gene_id "Phchi.S2G060100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13341.t1 is derived from g11807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6179875	6180679	.	-	.	Phchi.S3G066000
Phchi.S3	AUGUSTUS	transcript	6179875	6180679	.	-	.	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	stop_codon	6179872	6179874	.	-	0	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	CDS	6179875	6180084	1	-	0	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	exon	6179875	6180084	.	-	.	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	intron	6180085	6180247	.	-	.	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	CDS	6180248	6180679	0.23	-	0	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	exon	6180248	6180679	.	-	.	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
Phchi.S3	AUGUSTUS	start_codon	6180677	6180679	.	-	0	transcript_id "Phchi.S3G066000.t1"; gene_id "Phchi.S3G066000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11263.t1 is derived from g15313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5082022	5084613	.	+	.	Phchi.S4G084500
Phchi.S4	AUGUSTUS	transcript	5082022	5084613	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	start_codon	5082022	5082024	.	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5082022	5082098	0.95	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5082022	5082098	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5082099	5082305	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5082306	5082453	1	+	1	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5082306	5082453	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5082454	5082569	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5082570	5082728	1	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5082570	5082728	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5082729	5082952	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5082953	5083066	1	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5082953	5083066	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5083067	5083156	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5083157	5083314	1	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5083157	5083314	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5083315	5083409	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5083410	5083509	1	+	1	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5083410	5083509	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5083510	5083631	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5083632	5083808	1	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5083632	5083808	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5083809	5083960	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5083961	5084106	1	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5083961	5084106	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5084107	5084197	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5084198	5084344	1	+	1	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5084198	5084344	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	intron	5084345	5084438	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	CDS	5084439	5084613	1	+	1	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	exon	5084439	5084613	.	+	.	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
Phchi.S4	AUGUSTUS	stop_codon	5084614	5084616	.	+	0	transcript_id "Phchi.S4G084500.t1"; gene_id "Phchi.S4G084500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15663.t1 is derived from g14132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20568223	20570522	.	-	.	Phchi.S3G298200
Phchi.S3	AUGUSTUS	transcript	20568223	20570470	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	stop_codon	20568220	20568222	.	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568223	20568279	1	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568223	20568279	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20568280	20568419	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568420	20568621	1	-	1	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568420	20568621	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20568622	20568742	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568743	20568801	0.65	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568743	20568801	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20568802	20568938	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568939	20569040	1	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568939	20569040	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569041	20569181	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569182	20569235	1	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569182	20569235	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569236	20569344	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569345	20569397	0.87	-	2	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569345	20569397	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569398	20569500	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569501	20569597	0.99	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569501	20569597	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569598	20569722	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569723	20569839	1	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569723	20569839	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569840	20570018	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570019	20570131	0.9	-	2	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570019	20570131	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20570132	20570234	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570235	20570304	0.8	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570235	20570304	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20570305	20570467	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570468	20570470	0.99	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570468	20570470	.	-	.	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	start_codon	20570468	20570470	.	-	0	transcript_id "Phchi.S3G298200.t1"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	transcript	20569827	20570470	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	stop_codon	20569824	20569826	.	-	0	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569827	20569847	1	-	0	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569827	20569847	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569848	20570018	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570019	20570131	0.85	-	2	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570019	20570131	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20570132	20570234	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570235	20570304	0.78	-	0	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570235	20570304	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20570305	20570467	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570468	20570470	0.99	-	0	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570468	20570470	.	-	.	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	start_codon	20570468	20570470	.	-	0	transcript_id "Phchi.S3G298200.t2"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	transcript	20568223	20570522	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	stop_codon	20568220	20568222	.	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568223	20568279	1	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568223	20568279	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20568280	20568419	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568420	20568621	1	-	1	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568420	20568621	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20568622	20568742	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568743	20568801	0.62	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568743	20568801	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20568802	20568938	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20568939	20569040	1	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20568939	20569040	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569041	20569181	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569182	20569235	0.97	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569182	20569235	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569236	20569344	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569345	20569397	0.83	-	2	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569345	20569397	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569398	20569500	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569501	20569597	0.96	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569501	20569597	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569598	20569722	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20569723	20569839	1	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20569723	20569839	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20569840	20570018	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570019	20570131	0.96	-	2	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570019	20570131	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	intron	20570132	20570467	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	CDS	20570468	20570522	0.18	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	exon	20570468	20570522	.	-	.	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
Phchi.S3	AUGUSTUS	start_codon	20570520	20570522	.	-	0	transcript_id "Phchi.S3G298200.t3"; gene_id "Phchi.S3G298200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12610.t1 is derived from g8287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37567790	37572626	.	+	.	Phchi.S2G069000
Phchi.S2	AUGUSTUS	transcript	37567790	37572626	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	start_codon	37567790	37567792	.	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37567790	37568192	0.76	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37567790	37568192	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37568193	37568466	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37568467	37568820	0.7	+	2	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37568467	37568820	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37568821	37568929	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37568930	37568993	0.94	+	2	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37568930	37568993	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37568994	37569085	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37569086	37569140	0.66	+	1	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37569086	37569140	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37569141	37569383	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37569384	37569437	1	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37569384	37569437	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37569438	37569522	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37569523	37569591	1	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37569523	37569591	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37569592	37569667	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37569668	37571929	0.99	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37569668	37571929	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37571930	37572007	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37572008	37572085	1	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37572008	37572085	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	intron	37572086	37572176	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	CDS	37572177	37572626	0.99	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	exon	37572177	37572626	.	+	.	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
Phchi.S2	AUGUSTUS	stop_codon	37572627	37572629	.	+	0	transcript_id "Phchi.S2G069000.t1"; gene_id "Phchi.S2G069000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13801.t1 is derived from g12268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8954117	8958423	.	-	.	Phchi.S3G112000
Phchi.S3	AUGUSTUS	transcript	8954117	8958423	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	stop_codon	8954114	8954116	.	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8954117	8954689	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8954117	8954689	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8954690	8954771	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8954772	8954847	1	-	1	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8954772	8954847	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8954848	8954931	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8954932	8955047	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8954932	8955047	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955048	8955117	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955118	8955225	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955118	8955225	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955226	8955306	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955307	8955363	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955307	8955363	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955364	8955448	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955449	8955484	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955449	8955484	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955485	8955580	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955581	8955727	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955581	8955727	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955728	8955811	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955812	8955877	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955812	8955877	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955878	8956013	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956014	8956118	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956014	8956118	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956119	8956246	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956247	8956318	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956247	8956318	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956319	8956460	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956461	8956511	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956461	8956511	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956512	8956590	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956591	8956644	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956591	8956644	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956645	8956775	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956776	8957072	0.62	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956776	8957072	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957073	8957240	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957241	8957288	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957241	8957288	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957289	8957379	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957380	8957478	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957380	8957478	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957479	8957567	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957568	8957627	1	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957568	8957627	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957628	8957700	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957701	8958423	0.54	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957701	8958423	.	-	.	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	start_codon	8958421	8958423	.	-	0	transcript_id "Phchi.S3G112000.t1"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	transcript	8954117	8958423	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	stop_codon	8954114	8954116	.	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8954117	8954689	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8954117	8954689	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8954690	8954771	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8954772	8954847	1	-	1	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8954772	8954847	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8954848	8954931	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8954932	8955047	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8954932	8955047	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955048	8955117	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955118	8955225	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955118	8955225	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955226	8955306	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955307	8955363	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955307	8955363	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955364	8955448	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955449	8955484	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955449	8955484	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955485	8955580	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955581	8955727	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955581	8955727	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955728	8955811	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8955812	8955877	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8955812	8955877	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8955878	8956013	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956014	8956118	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956014	8956118	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956119	8956246	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956247	8956318	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956247	8956318	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956319	8956460	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956461	8956511	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956461	8956511	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956512	8956590	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956591	8956644	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956591	8956644	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956645	8956775	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956776	8956848	0.39	-	1	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956776	8956848	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8956849	8956985	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8956986	8957072	0.39	-	1	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8956986	8957072	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957073	8957157	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957158	8957288	0.99	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957158	8957288	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957289	8957379	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957380	8957478	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957380	8957478	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957479	8957567	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957568	8957627	1	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957568	8957627	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	intron	8957628	8957700	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	CDS	8957701	8958423	0.56	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	exon	8957701	8958423	.	-	.	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
Phchi.S3	AUGUSTUS	start_codon	8958421	8958423	.	-	0	transcript_id "Phchi.S3G112000.t2"; gene_id "Phchi.S3G112000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11543.t1 is derived from g15593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6974922	6977143	.	-	.	Phchi.S4G112500
Phchi.S4	AUGUSTUS	transcript	6974922	6977143	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	stop_codon	6974919	6974921	.	-	0	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	CDS	6974922	6975301	1	-	2	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	exon	6974922	6975301	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	intron	6975302	6975390	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	CDS	6975391	6976403	0.99	-	1	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	exon	6975391	6976403	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	intron	6976404	6976515	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	CDS	6976516	6976778	0.44	-	0	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	exon	6976516	6976778	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	intron	6976779	6976936	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	CDS	6976937	6977143	0.26	-	0	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	exon	6976937	6977143	.	-	.	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
Phchi.S4	AUGUSTUS	start_codon	6977141	6977143	.	-	0	transcript_id "Phchi.S4G112500.t1"; gene_id "Phchi.S4G112500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12488.t1 is derived from g8165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28920819	28921257	.	+	.	Phchi.S2G056800
Phchi.S2	AUGUSTUS	transcript	28920819	28921257	.	+	.	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	start_codon	28920819	28920821	.	+	0	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	CDS	28920819	28921006	0.94	+	0	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	exon	28920819	28921006	.	+	.	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	intron	28921007	28921151	.	+	.	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	CDS	28921152	28921257	0.99	+	1	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	exon	28921152	28921257	.	+	.	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
Phchi.S2	AUGUSTUS	stop_codon	28921258	28921260	.	+	0	transcript_id "Phchi.S2G056800.t1"; gene_id "Phchi.S2G056800"
# This transcript jg9619.t2 is derived from g6795.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9620.t1 is derived from g6796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42951434	42952222	.	-	.	Phchi.S1G677900
Phchi.S1	AUGUSTUS	transcript	42951434	42952222	.	-	.	transcript_id "Phchi.S1G677900.t1"; gene_id "Phchi.S1G677900"
Phchi.S1	AUGUSTUS	stop_codon	42951431	42951433	.	-	0	transcript_id "Phchi.S1G677900.t1"; gene_id "Phchi.S1G677900"
Phchi.S1	AUGUSTUS	CDS	42951434	42952222	0.4	-	0	transcript_id "Phchi.S1G677900.t1"; gene_id "Phchi.S1G677900"
Phchi.S1	AUGUSTUS	exon	42951434	42952222	.	-	.	transcript_id "Phchi.S1G677900.t1"; gene_id "Phchi.S1G677900"
Phchi.S1	AUGUSTUS	start_codon	42952220	42952222	.	-	0	transcript_id "Phchi.S1G677900.t1"; gene_id "Phchi.S1G677900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11099.t1 is derived from g15149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4106342	4107116	.	-	.	Phchi.S4G068100
Phchi.S4	AUGUSTUS	transcript	4106342	4107116	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	stop_codon	4106339	4106341	.	-	0	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	CDS	4106342	4106358	0.51	-	2	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	exon	4106342	4106358	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	intron	4106359	4106500	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	CDS	4106501	4106516	0.51	-	0	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	exon	4106501	4106516	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	intron	4106517	4106662	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	CDS	4106663	4106761	0.56	-	0	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	exon	4106663	4106761	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	intron	4106762	4106848	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	CDS	4106849	4106967	0.94	-	2	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	exon	4106849	4106967	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	intron	4106968	4107082	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	CDS	4107083	4107116	0.9	-	0	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	exon	4107083	4107116	.	-	.	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
Phchi.S4	AUGUSTUS	start_codon	4107114	4107116	.	-	0	transcript_id "Phchi.S4G068100.t1"; gene_id "Phchi.S4G068100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15403.t1 is derived from g13871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18827972	18829218	.	+	.	Phchi.S3G272200
Phchi.S3	AUGUSTUS	transcript	18827972	18829218	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	start_codon	18827972	18827974	.	+	0	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	CDS	18827972	18828151	1	+	0	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	exon	18827972	18828151	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	intron	18828152	18828218	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	CDS	18828219	18828474	1	+	0	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	exon	18828219	18828474	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	intron	18828475	18828554	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	CDS	18828555	18828591	1	+	2	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	exon	18828555	18828591	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	intron	18828592	18828681	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	CDS	18828682	18828787	1	+	1	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	exon	18828682	18828787	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	intron	18828788	18828872	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	CDS	18828873	18828983	1	+	0	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	exon	18828873	18828983	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	intron	18828984	18829059	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	CDS	18829060	18829218	0.97	+	0	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	exon	18829060	18829218	.	+	.	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
Phchi.S3	AUGUSTUS	stop_codon	18829219	18829221	.	+	0	transcript_id "Phchi.S3G272200.t1"; gene_id "Phchi.S3G272200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1418.t1 is derived from g8337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	735047	736708	.	+	.	Phchi.S5G002700
Phchi.S5	AUGUSTUS	transcript	735047	736708	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	start_codon	735047	735049	.	+	0	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	CDS	735047	735720	0.37	+	0	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	exon	735047	735720	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	intron	735721	735846	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	CDS	735847	735937	0.95	+	1	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	exon	735847	735937	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	intron	735938	736050	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	CDS	736051	736177	0.99	+	0	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	exon	736051	736177	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	intron	736178	736349	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	CDS	736350	736708	0.95	+	2	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	exon	736350	736708	.	+	.	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
Phchi.S5	AUGUSTUS	stop_codon	736709	736711	.	+	0	transcript_id "Phchi.S5G002700.t1"; gene_id "Phchi.S5G002700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14190.t1 is derived from g12657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11399351	11400741	.	-	.	Phchi.S3G150900
Phchi.S3	AUGUSTUS	transcript	11399351	11400741	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	stop_codon	11399348	11399350	.	-	0	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	CDS	11399351	11399560	0.99	-	0	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	exon	11399351	11399560	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	intron	11399561	11399668	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	CDS	11399669	11399900	1	-	1	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	exon	11399669	11399900	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	intron	11399901	11400033	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	CDS	11400034	11400160	1	-	2	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	exon	11400034	11400160	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	intron	11400161	11400284	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	CDS	11400285	11400741	0.92	-	0	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	exon	11400285	11400741	.	-	.	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
Phchi.S3	AUGUSTUS	start_codon	11400739	11400741	.	-	0	transcript_id "Phchi.S3G150900.t1"; gene_id "Phchi.S3G150900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14122.t1 is derived from g12589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10982902	10984436	.	-	.	Phchi.S3G144100
Phchi.S3	AUGUSTUS	transcript	10982902	10984436	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	stop_codon	10982899	10982901	.	-	0	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	CDS	10982902	10983243	1	-	0	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	exon	10982902	10983243	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	intron	10983244	10983357	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	CDS	10983358	10983604	1	-	1	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	exon	10983358	10983604	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	intron	10983605	10983692	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	CDS	10983693	10984167	0.98	-	2	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	exon	10983693	10984167	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	intron	10984168	10984363	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	CDS	10984364	10984436	0.85	-	0	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	exon	10984364	10984436	.	-	.	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
Phchi.S3	AUGUSTUS	start_codon	10984434	10984436	.	-	0	transcript_id "Phchi.S3G144100.t1"; gene_id "Phchi.S3G144100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15740.t1 is derived from g14210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21016832	21018803	.	+	.	Phchi.S3G305900
Phchi.S3	AUGUSTUS	transcript	21016832	21018803	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	start_codon	21016832	21016834	.	+	0	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21016832	21017083	1	+	0	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21016832	21017083	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	intron	21017084	21017199	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21017200	21017342	1	+	0	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21017200	21017342	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	intron	21017343	21017478	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21017479	21017735	1	+	1	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21017479	21017735	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	intron	21017736	21017821	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21017822	21017921	1	+	2	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21017822	21017921	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	intron	21017922	21018060	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21018061	21018199	1	+	1	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21018061	21018199	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	intron	21018200	21018336	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21018337	21018464	1	+	0	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21018337	21018464	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	intron	21018465	21018550	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	CDS	21018551	21018803	1	+	1	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	exon	21018551	21018803	.	+	.	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
Phchi.S3	AUGUSTUS	stop_codon	21018804	21018806	.	+	0	transcript_id "Phchi.S3G305900.t1"; gene_id "Phchi.S3G305900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6073.t1 is derived from g3244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20739316	20741664	.	-	.	Phchi.S1G323200
Phchi.S1	AUGUSTUS	transcript	20739316	20741664	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	stop_codon	20739313	20739315	.	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20739316	20739417	1	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20739316	20739417	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20739418	20739503	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20739504	20739625	1	-	2	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20739504	20739625	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20739626	20739745	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20739746	20739793	1	-	2	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20739746	20739793	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20739794	20739878	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20739879	20740002	0.6	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20739879	20740002	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20740003	20740090	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20740091	20740165	0.99	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20740091	20740165	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20740166	20740351	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20740352	20740468	1	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20740352	20740468	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20740469	20740573	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20740574	20740639	0.91	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20740574	20740639	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20740640	20740744	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20740745	20740843	0.98	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20740745	20740843	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20740844	20740935	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20740936	20741041	1	-	1	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20740936	20741041	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20741042	20741154	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20741155	20741228	0.85	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20741155	20741228	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	intron	20741229	20741391	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	CDS	20741392	20741664	0.73	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	exon	20741392	20741664	.	-	.	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
Phchi.S1	AUGUSTUS	start_codon	20741662	20741664	.	-	0	transcript_id "Phchi.S1G323200.t1"; gene_id "Phchi.S1G323200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14819.t1 is derived from g13287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14843694	14845659	.	+	.	Phchi.S3G213800
Phchi.S3	AUGUSTUS	transcript	14843694	14845659	.	+	.	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	start_codon	14843694	14843696	.	+	0	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	CDS	14843694	14843790	0.03	+	0	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	exon	14843694	14843790	.	+	.	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	intron	14843791	14843878	.	+	.	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	CDS	14843879	14843966	0.02	+	2	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	exon	14843879	14843966	.	+	.	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	intron	14843967	14845559	.	+	.	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	CDS	14845560	14845659	0.01	+	1	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	exon	14845560	14845659	.	+	.	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
Phchi.S3	AUGUSTUS	stop_codon	14845660	14845662	.	+	0	transcript_id "Phchi.S3G213800.t1"; gene_id "Phchi.S3G213800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14943.t1 is derived from g13411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15650282	15652298	.	+	.	Phchi.S3G226200
Phchi.S3	AUGUSTUS	transcript	15650282	15652298	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	start_codon	15650282	15650284	.	+	0	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15650282	15650636	0.8	+	0	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15650282	15650636	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15650637	15650732	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15650733	15650817	1	+	2	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15650733	15650817	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15650818	15650903	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15650904	15651020	1	+	1	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15650904	15651020	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15651021	15651118	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15651119	15651183	1	+	1	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15651119	15651183	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15651184	15651293	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15651294	15651382	1	+	2	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15651294	15651382	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15651383	15651518	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15651519	15651598	1	+	0	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15651519	15651598	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15651599	15651682	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15651683	15651784	0.97	+	1	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15651683	15651784	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15651785	15651880	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15651881	15652025	0.8	+	1	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15651881	15652025	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	intron	15652026	15652118	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	CDS	15652119	15652298	1	+	0	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	exon	15652119	15652298	.	+	.	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
Phchi.S3	AUGUSTUS	stop_codon	15652299	15652301	.	+	0	transcript_id "Phchi.S3G226200.t1"; gene_id "Phchi.S3G226200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg83.t1 is derived from g9865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	430795	431630	.	-	.	Phchi.S6G004200
Phchi.S6	AUGUSTUS	transcript	430795	431630	.	-	.	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	stop_codon	430792	430794	.	-	0	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	CDS	430795	430800	1	-	0	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	exon	430795	430800	.	-	.	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	intron	430801	430954	.	-	.	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	CDS	430955	431326	1	-	0	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	exon	430955	431326	.	-	.	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	intron	431327	431414	.	-	.	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	CDS	431415	431630	1	-	0	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	exon	431415	431630	.	-	.	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
Phchi.S6	AUGUSTUS	start_codon	431628	431630	.	-	0	transcript_id "Phchi.S6G004200.t1"; gene_id "Phchi.S6G004200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4336.t1 is derived from g1505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9836413	9838887	.	-	.	Phchi.S1G149500
Phchi.S1	AUGUSTUS	transcript	9836413	9838887	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	stop_codon	9836410	9836412	.	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9836413	9836436	1	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9836413	9836436	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9836437	9836528	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9836529	9836573	1	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9836529	9836573	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9836574	9836809	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9836810	9836858	0.99	-	1	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9836810	9836858	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9836859	9836936	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9836937	9837064	0.21	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9836937	9837064	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9837065	9837397	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9837398	9837627	0.17	-	2	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9837398	9837627	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9837628	9837732	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9837733	9837970	0.97	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9837733	9837970	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9837971	9838124	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9838125	9838458	0.9	-	1	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9838125	9838458	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9838459	9838578	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9838579	9838673	1	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9838579	9838673	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	intron	9838674	9838806	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	CDS	9838807	9838887	0.62	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	exon	9838807	9838887	.	-	.	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
Phchi.S1	AUGUSTUS	start_codon	9838885	9838887	.	-	0	transcript_id "Phchi.S1G149500.t1"; gene_id "Phchi.S1G149500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14235.t1 is derived from g12702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11681900	11684738	.	-	.	Phchi.S3G155400
Phchi.S3	AUGUSTUS	transcript	11681900	11684738	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	stop_codon	11681897	11681899	.	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11681900	11682625	0.99	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11681900	11682625	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11682626	11682711	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11682712	11682777	0.75	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11682712	11682777	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11682778	11682899	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11682900	11683148	1	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11682900	11683148	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11683149	11683288	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11683289	11683473	0.82	-	2	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11683289	11683473	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11683474	11683587	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11683588	11683638	0.92	-	2	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11683588	11683638	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11683639	11683807	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11683808	11683925	1	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11683808	11683925	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11683926	11683999	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11684000	11684197	0.96	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11684000	11684197	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11684198	11684321	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11684322	11684557	0.88	-	2	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11684322	11684557	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	intron	11684558	11684659	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	CDS	11684660	11684738	0.99	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	exon	11684660	11684738	.	-	.	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
Phchi.S3	AUGUSTUS	start_codon	11684736	11684738	.	-	0	transcript_id "Phchi.S3G155400.t1"; gene_id "Phchi.S3G155400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14992.t1 is derived from g13460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16143683	16144543	.	-	.	Phchi.S3G231100
Phchi.S3	AUGUSTUS	transcript	16143683	16144543	.	-	.	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	stop_codon	16143680	16143682	.	-	0	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	CDS	16143683	16143722	0.83	-	1	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	exon	16143683	16143722	.	-	.	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	intron	16143723	16143974	.	-	.	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	CDS	16143975	16144543	0.55	-	0	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	exon	16143975	16144543	.	-	.	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
Phchi.S3	AUGUSTUS	start_codon	16144541	16144543	.	-	0	transcript_id "Phchi.S3G231100.t1"; gene_id "Phchi.S3G231100"
# This transcript jg11234.t2 is derived from g15284.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11235.t1 is derived from g15285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4929854	4931443	.	-	.	Phchi.S4G081700
Phchi.S4	AUGUSTUS	transcript	4929854	4931443	.	-	.	transcript_id "Phchi.S4G081700.t1"; gene_id "Phchi.S4G081700"
Phchi.S4	AUGUSTUS	stop_codon	4929851	4929853	.	-	0	transcript_id "Phchi.S4G081700.t1"; gene_id "Phchi.S4G081700"
Phchi.S4	AUGUSTUS	CDS	4929854	4931443	0.99	-	0	transcript_id "Phchi.S4G081700.t1"; gene_id "Phchi.S4G081700"
Phchi.S4	AUGUSTUS	exon	4929854	4931443	.	-	.	transcript_id "Phchi.S4G081700.t1"; gene_id "Phchi.S4G081700"
Phchi.S4	AUGUSTUS	start_codon	4931441	4931443	.	-	0	transcript_id "Phchi.S4G081700.t1"; gene_id "Phchi.S4G081700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13625.t1 is derived from g12092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7815930	7820603	.	+	.	Phchi.S3G094400
Phchi.S3	AUGUSTUS	transcript	7815930	7820603	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	start_codon	7815930	7815932	.	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7815930	7816175	0.99	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7815930	7816175	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7816176	7816362	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7816363	7816794	1	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7816363	7816794	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7816795	7816926	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7816927	7817152	1	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7816927	7817152	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7817153	7817240	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7817241	7817485	1	+	2	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7817241	7817485	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7817486	7817616	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7817617	7817698	1	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7817617	7817698	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7817699	7817784	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7817785	7818730	0.99	+	2	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7817785	7818730	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7818731	7818836	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7818837	7818889	0.66	+	1	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7818837	7818889	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7818890	7819032	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7819033	7819482	0.57	+	2	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7819033	7819482	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7819483	7819585	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7819586	7819791	0.99	+	2	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7819586	7819791	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	intron	7819792	7819883	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	CDS	7819884	7820603	1	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	exon	7819884	7820603	.	+	.	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
Phchi.S3	AUGUSTUS	stop_codon	7820604	7820606	.	+	0	transcript_id "Phchi.S3G094400.t1"; gene_id "Phchi.S3G094400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg308.t1 is derived from g10090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2207377	2208657	.	+	.	Phchi.S6G026700
Phchi.S6	AUGUSTUS	transcript	2207377	2208657	.	+	.	transcript_id "Phchi.S6G026700.t1"; gene_id "Phchi.S6G026700"
Phchi.S6	AUGUSTUS	start_codon	2207377	2207379	.	+	0	transcript_id "Phchi.S6G026700.t1"; gene_id "Phchi.S6G026700"
Phchi.S6	AUGUSTUS	CDS	2207377	2208657	0.68	+	0	transcript_id "Phchi.S6G026700.t1"; gene_id "Phchi.S6G026700"
Phchi.S6	AUGUSTUS	exon	2207377	2208657	.	+	.	transcript_id "Phchi.S6G026700.t1"; gene_id "Phchi.S6G026700"
Phchi.S6	AUGUSTUS	stop_codon	2208658	2208660	.	+	0	transcript_id "Phchi.S6G026700.t1"; gene_id "Phchi.S6G026700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12776.t1 is derived from g11241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2005682	2006347	.	+	.	Phchi.S3G009500
Phchi.S3	AUGUSTUS	transcript	2005682	2006347	.	+	.	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	start_codon	2005682	2005684	.	+	0	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	CDS	2005682	2006130	0.95	+	0	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	exon	2005682	2006130	.	+	.	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	intron	2006131	2006241	.	+	.	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	CDS	2006242	2006347	0.94	+	1	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	exon	2006242	2006347	.	+	.	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
Phchi.S3	AUGUSTUS	stop_codon	2006348	2006350	.	+	0	transcript_id "Phchi.S3G009500.t1"; gene_id "Phchi.S3G009500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5866.t1 is derived from g3036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19480174	19481028	.	+	.	Phchi.S1G302500
Phchi.S1	AUGUSTUS	transcript	19480174	19481028	.	+	.	transcript_id "Phchi.S1G302500.t1"; gene_id "Phchi.S1G302500"
Phchi.S1	AUGUSTUS	start_codon	19480174	19480176	.	+	0	transcript_id "Phchi.S1G302500.t1"; gene_id "Phchi.S1G302500"
Phchi.S1	AUGUSTUS	CDS	19480174	19481028	1	+	0	transcript_id "Phchi.S1G302500.t1"; gene_id "Phchi.S1G302500"
Phchi.S1	AUGUSTUS	exon	19480174	19481028	.	+	.	transcript_id "Phchi.S1G302500.t1"; gene_id "Phchi.S1G302500"
Phchi.S1	AUGUSTUS	stop_codon	19481029	19481031	.	+	0	transcript_id "Phchi.S1G302500.t1"; gene_id "Phchi.S1G302500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2469.t1 is derived from g9389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6814163	6815681	.	-	.	Phchi.S5G107800
Phchi.S5	AUGUSTUS	transcript	6814163	6815681	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	stop_codon	6814160	6814162	.	-	0	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6814163	6814267	0.73	-	0	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6814163	6814267	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6814268	6814342	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6814343	6814417	1	-	0	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6814343	6814417	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6814418	6814512	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6814513	6814604	0.97	-	2	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6814513	6814604	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6814605	6814711	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6814712	6814798	0.92	-	2	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6814712	6814798	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6814799	6814906	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6814907	6815065	1	-	2	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6814907	6815065	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6815066	6815173	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6815174	6815272	1	-	2	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6815174	6815272	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6815273	6815370	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6815371	6815498	1	-	1	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6815371	6815498	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	intron	6815499	6815625	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	CDS	6815626	6815681	0.78	-	0	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	exon	6815626	6815681	.	-	.	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
Phchi.S5	AUGUSTUS	start_codon	6815679	6815681	.	-	0	transcript_id "Phchi.S5G107800.t1"; gene_id "Phchi.S5G107800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9095.t1 is derived from g6270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39817841	39820486	.	+	.	Phchi.S1G625400
Phchi.S1	AUGUSTUS	transcript	39817841	39820486	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	start_codon	39817841	39817843	.	+	0	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39817841	39818502	0.56	+	0	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39817841	39818502	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	intron	39818503	39818648	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39818649	39818686	0.71	+	1	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39818649	39818686	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	intron	39818687	39818790	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39818791	39819176	0.7	+	2	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39818791	39819176	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	intron	39819177	39819494	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39819495	39819792	0.91	+	0	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39819495	39819792	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	intron	39819793	39819936	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39819937	39820221	0.5	+	2	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39819937	39820221	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	intron	39820222	39820313	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39820314	39820336	1	+	2	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39820314	39820336	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	intron	39820337	39820429	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	CDS	39820430	39820486	0.98	+	0	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	exon	39820430	39820486	.	+	.	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
Phchi.S1	AUGUSTUS	stop_codon	39820487	39820489	.	+	0	transcript_id "Phchi.S1G625400.t1"; gene_id "Phchi.S1G625400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10929.t1 is derived from g14979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3023392	3025676	.	+	.	Phchi.S4G051100
Phchi.S4	AUGUSTUS	transcript	3023392	3025676	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	start_codon	3023392	3023394	.	+	0	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	CDS	3023392	3023499	0.28	+	0	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	exon	3023392	3023499	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	intron	3023500	3023631	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	CDS	3023632	3023877	0.58	+	0	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	exon	3023632	3023877	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	intron	3023878	3024014	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	CDS	3024015	3024431	0.83	+	0	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	exon	3024015	3024431	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	intron	3024432	3024528	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	CDS	3024529	3024698	0.82	+	0	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	exon	3024529	3024698	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	intron	3024699	3024841	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	CDS	3024842	3025676	1	+	1	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	exon	3024842	3025676	.	+	.	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
Phchi.S4	AUGUSTUS	stop_codon	3025677	3025679	.	+	0	transcript_id "Phchi.S4G051100.t1"; gene_id "Phchi.S4G051100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6251.t1 is derived from g3423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21874536	21878898	.	-	.	Phchi.S1G341000
Phchi.S1	AUGUSTUS	transcript	21874536	21878898	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	stop_codon	21874533	21874535	.	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21874536	21874544	0.49	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21874536	21874544	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21874545	21874692	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21874693	21874874	0.49	-	2	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21874693	21874874	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21874875	21874959	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21874960	21875101	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21874960	21875101	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21875102	21875201	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21875202	21875996	0.87	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21875202	21875996	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21875997	21876141	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21876142	21876258	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21876142	21876258	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21876259	21876411	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21876412	21876780	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21876412	21876780	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21876781	21876937	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21876938	21877063	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21876938	21877063	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21877064	21877161	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21877162	21877362	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21877162	21877362	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21877363	21877501	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21877502	21877778	0.39	-	1	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21877502	21877778	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21877779	21877898	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21877899	21878031	0.58	-	2	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21877899	21878031	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21878032	21878197	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21878198	21878351	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21878198	21878351	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21878352	21878449	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21878450	21878540	1	-	1	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21878450	21878540	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21878541	21878619	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21878620	21878749	1	-	2	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21878620	21878749	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	intron	21878750	21878831	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	CDS	21878832	21878898	1	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	exon	21878832	21878898	.	-	.	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
Phchi.S1	AUGUSTUS	start_codon	21878896	21878898	.	-	0	transcript_id "Phchi.S1G341000.t1"; gene_id "Phchi.S1G341000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15133.t1 is derived from g13601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17206291	17207139	.	-	.	Phchi.S3G245200
Phchi.S3	AUGUSTUS	transcript	17206291	17207139	.	-	.	transcript_id "Phchi.S3G245200.t1"; gene_id "Phchi.S3G245200"
Phchi.S3	AUGUSTUS	stop_codon	17206288	17206290	.	-	0	transcript_id "Phchi.S3G245200.t1"; gene_id "Phchi.S3G245200"
Phchi.S3	AUGUSTUS	CDS	17206291	17207139	0.74	-	0	transcript_id "Phchi.S3G245200.t1"; gene_id "Phchi.S3G245200"
Phchi.S3	AUGUSTUS	exon	17206291	17207139	.	-	.	transcript_id "Phchi.S3G245200.t1"; gene_id "Phchi.S3G245200"
Phchi.S3	AUGUSTUS	start_codon	17207137	17207139	.	-	0	transcript_id "Phchi.S3G245200.t1"; gene_id "Phchi.S3G245200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12617.t1 is derived from g8294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37586949	37588049	.	+	.	Phchi.S2G069700
Phchi.S2	AUGUSTUS	transcript	37586949	37588049	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	start_codon	37586949	37586951	.	+	0	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	CDS	37586949	37587094	0.78	+	0	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	exon	37586949	37587094	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	intron	37587095	37587181	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	CDS	37587182	37587247	1	+	1	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	exon	37587182	37587247	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	intron	37587248	37587443	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	CDS	37587444	37587481	0.83	+	1	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	exon	37587444	37587481	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	intron	37587482	37587694	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	CDS	37587695	37587715	0.68	+	2	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	exon	37587695	37587715	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	intron	37587716	37587984	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	CDS	37587985	37588049	0.9	+	2	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	exon	37587985	37588049	.	+	.	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
Phchi.S2	AUGUSTUS	stop_codon	37588050	37588052	.	+	0	transcript_id "Phchi.S2G069700.t1"; gene_id "Phchi.S2G069700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg125.t1 is derived from g9907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	698002	699588	.	+	.	Phchi.S6G008400
Phchi.S6	AUGUSTUS	transcript	698002	699588	.	+	.	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	start_codon	698002	698004	.	+	0	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	CDS	698002	698058	1	+	0	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	exon	698002	698058	.	+	.	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	intron	698059	698150	.	+	.	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	CDS	698151	699410	0.44	+	0	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	exon	698151	699410	.	+	.	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	intron	699411	699585	.	+	.	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	CDS	699586	699588	0.42	+	0	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	exon	699586	699588	.	+	.	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
Phchi.S6	AUGUSTUS	stop_codon	699589	699591	.	+	0	transcript_id "Phchi.S6G008400.t1"; gene_id "Phchi.S6G008400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6739.t1 is derived from g3911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24801620	24803919	.	+	.	Phchi.S1G389800
Phchi.S1	AUGUSTUS	transcript	24801620	24803919	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	start_codon	24801620	24801622	.	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24801620	24801935	0.96	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24801620	24801935	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24801936	24802013	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802014	24802088	1	+	2	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802014	24802088	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24802089	24802188	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802189	24802205	1	+	2	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802189	24802205	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24802206	24802301	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802302	24802339	1	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802302	24802339	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24802340	24802427	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802428	24802589	1	+	1	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802428	24802589	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24802590	24802700	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802701	24802723	1	+	1	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802701	24802723	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24802724	24802812	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802813	24802884	1	+	2	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802813	24802884	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24802885	24802996	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24802997	24803167	1	+	2	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24802997	24803167	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24803168	24803239	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24803240	24803322	1	+	2	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24803240	24803322	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24803323	24803417	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24803418	24803480	1	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24803418	24803480	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24803481	24803620	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24803621	24803689	0.84	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24803621	24803689	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	intron	24803690	24803805	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	CDS	24803806	24803919	0.99	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	exon	24803806	24803919	.	+	.	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
Phchi.S1	AUGUSTUS	stop_codon	24803920	24803922	.	+	0	transcript_id "Phchi.S1G389800.t1"; gene_id "Phchi.S1G389800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12581.t1 is derived from g8258.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35940399	35948923	.	-	.	Phchi.S2G066100
Phchi.S2	AUGUSTUS	transcript	35940399	35948923	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	stop_codon	35940396	35940398	.	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35940399	35940626	0.8	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35940399	35940626	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35940627	35940764	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35940765	35940881	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35940765	35940881	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35940882	35941040	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35941041	35941192	1	-	2	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35941041	35941192	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35941193	35941591	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35941592	35941703	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35941592	35941703	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35941704	35942287	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35942288	35942475	1	-	2	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35942288	35942475	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35942476	35942616	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35942617	35942709	1	-	2	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35942617	35942709	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35942710	35942933	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35942934	35943118	0.89	-	1	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35942934	35943118	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943119	35943222	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35943223	35943308	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35943223	35943308	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943309	35943486	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35943487	35943636	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35943487	35943636	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943637	35943839	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35943840	35943975	1	-	1	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35943840	35943975	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943976	35944394	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35944395	35944474	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35944395	35944474	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35944475	35944622	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35944623	35944736	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35944623	35944736	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35944737	35945423	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35945424	35945510	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35945424	35945510	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35945511	35945652	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35945653	35945793	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35945653	35945793	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35945794	35945877	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35945878	35946004	1	-	1	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35945878	35946004	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946005	35946078	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35946079	35946162	0.7	-	1	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35946079	35946162	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946163	35946567	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35946568	35946629	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35946568	35946629	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946630	35946819	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35946820	35946948	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35946820	35946948	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946949	35947121	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35947122	35947181	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35947122	35947181	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35947182	35947419	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35947420	35947503	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35947420	35947503	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35947504	35947764	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35947765	35947884	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35947765	35947884	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35947885	35948073	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948074	35948295	1	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948074	35948295	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35948296	35948511	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948512	35948610	0.95	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948512	35948610	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35948611	35948713	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948714	35948923	0.86	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948714	35948923	.	-	.	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	start_codon	35948921	35948923	.	-	0	transcript_id "Phchi.S2G066100.t1"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	transcript	35940399	35948923	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	stop_codon	35940396	35940398	.	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35940399	35940626	0.94	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35940399	35940626	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35940627	35940764	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35940765	35940881	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35940765	35940881	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35940882	35941040	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35941041	35941192	1	-	2	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35941041	35941192	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35941193	35941591	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35941592	35941703	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35941592	35941703	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35941704	35942287	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35942288	35942475	1	-	2	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35942288	35942475	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35942476	35942616	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35942617	35942709	1	-	2	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35942617	35942709	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35942710	35942933	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35942934	35943118	0.83	-	1	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35942934	35943118	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943119	35943222	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35943223	35943308	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35943223	35943308	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943309	35943486	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35943487	35943636	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35943487	35943636	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943637	35943839	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35943840	35943975	1	-	1	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35943840	35943975	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35943976	35944394	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35944395	35944474	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35944395	35944474	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35944475	35944622	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35944623	35944736	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35944623	35944736	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35944737	35945423	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35945424	35945510	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35945424	35945510	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35945511	35945652	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35945653	35945793	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35945653	35945793	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35945794	35945877	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35945878	35946004	1	-	1	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35945878	35946004	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946005	35946078	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35946079	35946162	0.63	-	1	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35946079	35946162	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946163	35946567	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35946568	35946629	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35946568	35946629	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946630	35946819	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35946820	35946948	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35946820	35946948	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35946949	35947121	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35947122	35947181	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35947122	35947181	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35947182	35947419	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35947420	35947503	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35947420	35947503	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35947504	35947764	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35947765	35947884	1	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35947765	35947884	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35947885	35948073	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948074	35948195	1	-	2	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948074	35948195	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35948196	35948283	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948284	35948295	0.99	-	2	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948284	35948295	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35948296	35948522	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948523	35948610	0.93	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948523	35948610	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	intron	35948611	35948713	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	CDS	35948714	35948923	0.86	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	exon	35948714	35948923	.	-	.	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
Phchi.S2	AUGUSTUS	start_codon	35948921	35948923	.	-	0	transcript_id "Phchi.S2G066100.t2"; gene_id "Phchi.S2G066100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11032.t1 is derived from g15082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3731690	3734853	.	+	.	Phchi.S4G061400
Phchi.S4	AUGUSTUS	transcript	3731690	3734853	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	start_codon	3731690	3731692	.	+	0	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3731690	3732472	0.41	+	0	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3731690	3732472	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	intron	3732473	3732716	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3732717	3732796	0.88	+	0	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3732717	3732796	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	intron	3732797	3733019	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3733020	3733082	0.64	+	1	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3733020	3733082	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	intron	3733083	3733256	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3733257	3734853	0.59	+	1	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3733257	3734853	.	+	.	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	stop_codon	3734854	3734856	.	+	0	transcript_id "Phchi.S4G061400.t1"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	transcript	3732782	3734853	.	+	.	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	start_codon	3732782	3732784	.	+	0	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3732782	3732927	0.26	+	0	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3732782	3732927	.	+	.	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	intron	3732928	3733019	.	+	.	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3733020	3733082	0.53	+	1	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3733020	3733082	.	+	.	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	intron	3733083	3733256	.	+	.	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	CDS	3733257	3734853	0.46	+	1	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	exon	3733257	3734853	.	+	.	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
Phchi.S4	AUGUSTUS	stop_codon	3734854	3734856	.	+	0	transcript_id "Phchi.S4G061400.t2"; gene_id "Phchi.S4G061400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10548.t1 is derived from g14598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	924656	929234	.	-	.	Phchi.S4G013000
Phchi.S4	AUGUSTUS	transcript	924656	929234	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	stop_codon	924653	924655	.	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	924656	924750	1	-	2	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	924656	924750	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	924751	924838	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	924839	925031	1	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	924839	925031	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	925032	925188	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	925189	925878	0.31	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	925189	925878	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	925879	925966	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	925967	926490	0.18	-	2	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	925967	926490	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	926491	926618	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	926619	926720	0.73	-	2	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	926619	926720	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	926721	926803	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	926804	927143	0.5	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	926804	927143	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	927144	927258	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	927259	927416	0.54	-	2	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	927259	927416	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	927417	927512	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	927513	927736	1	-	1	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	927513	927736	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	927737	927863	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	927864	928091	1	-	1	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	927864	928091	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	928092	928343	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	928344	928381	1	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	928344	928381	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	928382	928843	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	928844	928920	0.99	-	2	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	928844	928920	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	intron	928921	929113	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	CDS	929114	929234	0.97	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	exon	929114	929234	.	-	.	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
Phchi.S4	AUGUSTUS	start_codon	929232	929234	.	-	0	transcript_id "Phchi.S4G013000.t1"; gene_id "Phchi.S4G013000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10883.t1 is derived from g14933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2744519	2752268	.	+	.	Phchi.S4G046500
Phchi.S4	AUGUSTUS	transcript	2744519	2752268	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	start_codon	2744519	2744521	.	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2744519	2744574	1	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2744519	2744574	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2744575	2744654	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2744655	2744769	1	+	1	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2744655	2744769	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2744770	2744921	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2744922	2744984	1	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2744922	2744984	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2744985	2745073	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745074	2745151	1	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745074	2745151	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745152	2745232	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745233	2745324	0.9	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745233	2745324	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745325	2745442	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745443	2745545	1	+	1	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745443	2745545	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745546	2745670	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745671	2745823	0.98	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745671	2745823	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745824	2745937	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745938	2746623	0.75	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745938	2746623	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2746624	2746722	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2746723	2747236	0.99	+	1	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2746723	2747236	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2747237	2747392	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2747393	2747619	0.75	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2747393	2747619	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2747620	2747732	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2747733	2747897	0.77	+	1	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2747733	2747897	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2747898	2748049	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2748050	2748581	0.31	+	1	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2748050	2748581	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2748582	2748763	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2748764	2748894	0.31	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2748764	2748894	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2748895	2749086	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2749087	2749174	0.32	+	1	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2749087	2749174	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2749175	2749277	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2749278	2749827	0.88	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2749278	2749827	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2749828	2749918	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2749919	2750361	0.28	+	2	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2749919	2750361	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2750362	2750432	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2750433	2751014	0.36	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2750433	2751014	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2751015	2751165	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2751166	2751621	0.95	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2751166	2751621	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2751622	2751732	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2751733	2751963	1	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2751733	2751963	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2751964	2752043	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2752044	2752268	0.89	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2752044	2752268	.	+	.	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	stop_codon	2752269	2752271	.	+	0	transcript_id "Phchi.S4G046500.t1"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	transcript	2744519	2752268	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	start_codon	2744519	2744521	.	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2744519	2744574	1	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2744519	2744574	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2744575	2744654	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2744655	2744769	1	+	1	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2744655	2744769	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2744770	2744921	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2744922	2744984	1	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2744922	2744984	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2744985	2745073	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745074	2745151	1	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745074	2745151	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745152	2745232	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745233	2745350	0.94	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745233	2745350	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745351	2745442	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745443	2745465	0.35	+	2	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745443	2745465	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745466	2745670	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745671	2745823	0.99	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745671	2745823	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2745824	2745937	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2745938	2746623	0.77	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2745938	2746623	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2746624	2746722	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2746723	2747236	1	+	1	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2746723	2747236	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2747237	2747392	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2747393	2747619	0.86	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2747393	2747619	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2747620	2747732	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2747733	2747897	0.89	+	1	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2747733	2747897	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2747898	2748049	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2748050	2748581	0.27	+	1	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2748050	2748581	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2748582	2748763	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2748764	2748894	0.28	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2748764	2748894	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2748895	2749086	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2749087	2749174	0.3	+	1	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2749087	2749174	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2749175	2749277	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2749278	2749827	0.83	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2749278	2749827	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2749828	2749918	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2749919	2750361	0.29	+	2	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2749919	2750361	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2750362	2750432	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2750433	2751014	0.34	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2750433	2751014	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2751015	2751165	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2751166	2751621	0.94	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2751166	2751621	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2751622	2751732	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2751733	2751963	1	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2751733	2751963	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	intron	2751964	2752043	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	CDS	2752044	2752268	0.92	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	exon	2752044	2752268	.	+	.	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
Phchi.S4	AUGUSTUS	stop_codon	2752269	2752271	.	+	0	transcript_id "Phchi.S4G046500.t2"; gene_id "Phchi.S4G046500"
# This transcript jg14182.t2 is derived from g12649.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14182.t3 is derived from g12649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14183.t1 is derived from g12650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11325958	11329985	.	-	.	Phchi.S3G150200
Phchi.S3	AUGUSTUS	transcript	11325958	11329985	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	stop_codon	11325955	11325957	.	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11325958	11326105	1	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11325958	11326105	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11326106	11326194	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11326195	11326270	1	-	2	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11326195	11326270	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11326271	11326362	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11326363	11326475	1	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11326363	11326475	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11326476	11326563	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11326564	11326672	1	-	2	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11326564	11326672	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11326673	11326752	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11326753	11326871	1	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11326753	11326871	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11326872	11327012	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11327013	11327158	1	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11327013	11327158	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11327159	11327296	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11327297	11327455	1	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11327297	11327455	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11327456	11327590	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11327591	11327657	1	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11327591	11327657	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11327658	11327750	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11327751	11327923	1	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11327751	11327923	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11327924	11328067	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11328068	11328164	1	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11328068	11328164	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11328165	11328290	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11328291	11328409	1	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11328291	11328409	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11328410	11328505	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11328506	11328643	1	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11328506	11328643	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11328644	11328835	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11328836	11328920	1	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11328836	11328920	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11328921	11329006	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11329007	11329208	1	-	2	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11329007	11329208	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11329209	11329294	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11329295	11329373	0.91	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11329295	11329373	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11329374	11329508	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11329509	11329680	0.63	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11329509	11329680	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11329681	11329752	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11329753	11329782	0.81	-	1	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11329753	11329782	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	intron	11329783	11329869	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	CDS	11329870	11329985	0.4	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	exon	11329870	11329985	.	-	.	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
Phchi.S3	AUGUSTUS	start_codon	11329983	11329985	.	-	0	transcript_id "Phchi.S3G150200.t1"; gene_id "Phchi.S3G150200"
# This transcript jg12138.t2 is derived from g7814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12139.t1 is derived from g7815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4834135	4834771	.	+	.	Phchi.S2G021900
Phchi.S2	AUGUSTUS	transcript	4834135	4834771	.	+	.	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	start_codon	4834135	4834137	.	+	0	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	CDS	4834135	4834611	1	+	0	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	exon	4834135	4834611	.	+	.	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	intron	4834612	4834702	.	+	.	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	CDS	4834703	4834771	1	+	0	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	exon	4834703	4834771	.	+	.	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
Phchi.S2	AUGUSTUS	stop_codon	4834772	4834774	.	+	0	transcript_id "Phchi.S2G021900.t1"; gene_id "Phchi.S2G021900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11214.t1 is derived from g15264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4808500	4809540	.	-	.	Phchi.S4G079600
Phchi.S4	AUGUSTUS	transcript	4808500	4809540	.	-	.	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	stop_codon	4808497	4808499	.	-	0	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	CDS	4808500	4808955	0.99	-	0	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	exon	4808500	4808955	.	-	.	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	intron	4808956	4809129	.	-	.	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	CDS	4809130	4809540	0.64	-	0	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	exon	4809130	4809540	.	-	.	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
Phchi.S4	AUGUSTUS	start_codon	4809538	4809540	.	-	0	transcript_id "Phchi.S4G079600.t1"; gene_id "Phchi.S4G079600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1.t1 is derived from g9767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C85	AUGUSTUS	gene	1200	2360	.	+	.	Phchi.C85G000100
Phchi.C85	AUGUSTUS	transcript	1200	2360	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	start_codon	1200	1202	.	+	0	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	CDS	1200	1378	0.98	+	0	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	exon	1200	1378	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	intron	1379	1543	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	CDS	1544	1640	0.45	+	1	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	exon	1544	1640	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	intron	1641	1735	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	CDS	1736	1959	0.55	+	0	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	exon	1736	1959	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	intron	1960	2233	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	CDS	2234	2360	0.81	+	1	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	exon	2234	2360	.	+	.	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
Phchi.C85	AUGUSTUS	stop_codon	2361	2363	.	+	0	transcript_id "Phchi.C85G000100.t1"; gene_id "Phchi.C85G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12929.t1 is derived from g11394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3194595	3197258	.	-	.	Phchi.S3G024800
Phchi.S3	AUGUSTUS	transcript	3194595	3197258	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	stop_codon	3194592	3194594	.	-	0	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	CDS	3194595	3194719	0.89	-	2	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	exon	3194595	3194719	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	intron	3194720	3194839	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	CDS	3194840	3194900	0.98	-	0	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	exon	3194840	3194900	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	intron	3194901	3194999	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	CDS	3195000	3195167	0.77	-	0	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	exon	3195000	3195167	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	intron	3195168	3195366	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	CDS	3195367	3196628	0.95	-	2	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	exon	3195367	3196628	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	intron	3196629	3196754	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	CDS	3196755	3196962	0.87	-	0	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	exon	3196755	3196962	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	intron	3196963	3197057	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	CDS	3197058	3197258	0.71	-	0	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	exon	3197058	3197258	.	-	.	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
Phchi.S3	AUGUSTUS	start_codon	3197256	3197258	.	-	0	transcript_id "Phchi.S3G024800.t1"; gene_id "Phchi.S3G024800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11279.t1 is derived from g15329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5182958	5185818	.	-	.	Phchi.S4G086100
Phchi.S4	AUGUSTUS	transcript	5182958	5185818	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	stop_codon	5182955	5182957	.	-	0	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5182958	5182997	0.66	-	1	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5182958	5182997	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5182998	5183092	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5183093	5183120	0.37	-	2	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5183093	5183120	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5183121	5183248	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5183249	5183598	0.62	-	1	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5183249	5183598	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5183599	5183755	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5183756	5184009	1	-	0	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5183756	5184009	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5184010	5184154	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5184155	5184197	1	-	1	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5184155	5184197	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5184198	5184337	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5184338	5184549	0.59	-	0	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5184338	5184549	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5184550	5184654	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5184655	5184760	0.58	-	1	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5184655	5184760	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5184761	5184852	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5184853	5184950	1	-	0	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5184853	5184950	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5184951	5185080	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5185081	5185270	1	-	1	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5185081	5185270	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	intron	5185271	5185363	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	CDS	5185364	5185818	0.4	-	0	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	exon	5185364	5185818	.	-	.	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
Phchi.S4	AUGUSTUS	start_codon	5185816	5185818	.	-	0	transcript_id "Phchi.S4G086100.t1"; gene_id "Phchi.S4G086100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3077.t1 is derived from g246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1481521	1483527	.	-	.	Phchi.S1G023600
Phchi.S1	AUGUSTUS	transcript	1481521	1483527	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	stop_codon	1481518	1481520	.	-	0	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	CDS	1481521	1481593	0.84	-	1	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	exon	1481521	1481593	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	intron	1481594	1481783	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	CDS	1481784	1481959	0.5	-	0	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	exon	1481784	1481959	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	intron	1481960	1482064	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	CDS	1482065	1482305	0.19	-	1	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	exon	1482065	1482305	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	intron	1482306	1482481	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	CDS	1482482	1483527	0.18	-	0	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	exon	1482482	1483527	.	-	.	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
Phchi.S1	AUGUSTUS	start_codon	1483525	1483527	.	-	0	transcript_id "Phchi.S1G023600.t1"; gene_id "Phchi.S1G023600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1144.t1 is derived from g10927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7981686	7982180	.	-	.	Phchi.S6G110300
Phchi.S6	AUGUSTUS	transcript	7981686	7982180	.	-	.	transcript_id "Phchi.S6G110300.t1"; gene_id "Phchi.S6G110300"
Phchi.S6	AUGUSTUS	stop_codon	7981683	7981685	.	-	0	transcript_id "Phchi.S6G110300.t1"; gene_id "Phchi.S6G110300"
Phchi.S6	AUGUSTUS	CDS	7981686	7982180	0.69	-	0	transcript_id "Phchi.S6G110300.t1"; gene_id "Phchi.S6G110300"
Phchi.S6	AUGUSTUS	exon	7981686	7982180	.	-	.	transcript_id "Phchi.S6G110300.t1"; gene_id "Phchi.S6G110300"
Phchi.S6	AUGUSTUS	start_codon	7982178	7982180	.	-	0	transcript_id "Phchi.S6G110300.t1"; gene_id "Phchi.S6G110300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2205.t1 is derived from g9125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5412656	5414884	.	-	.	Phchi.S5G081400
Phchi.S5	AUGUSTUS	transcript	5412656	5414884	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	stop_codon	5412653	5412655	.	-	0	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	CDS	5412656	5412672	1	-	2	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	exon	5412656	5412672	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	intron	5412673	5412756	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	CDS	5412757	5412958	1	-	0	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	exon	5412757	5412958	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	intron	5412959	5413035	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	CDS	5413036	5414276	1	-	2	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	exon	5413036	5414276	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	intron	5414277	5414381	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	CDS	5414382	5414448	1	-	0	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	exon	5414382	5414448	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	intron	5414449	5414629	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	CDS	5414630	5414884	0.47	-	0	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	exon	5414630	5414884	.	-	.	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
Phchi.S5	AUGUSTUS	start_codon	5414882	5414884	.	-	0	transcript_id "Phchi.S5G081400.t1"; gene_id "Phchi.S5G081400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5929.t1 is derived from g3100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19897207	19897911	.	+	.	Phchi.S1G308800
Phchi.S1	AUGUSTUS	transcript	19897207	19897911	.	+	.	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	start_codon	19897207	19897209	.	+	0	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	CDS	19897207	19897674	0.93	+	0	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	exon	19897207	19897674	.	+	.	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	intron	19897675	19897824	.	+	.	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	CDS	19897825	19897911	1	+	0	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	exon	19897825	19897911	.	+	.	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
Phchi.S1	AUGUSTUS	stop_codon	19897912	19897914	.	+	0	transcript_id "Phchi.S1G308800.t1"; gene_id "Phchi.S1G308800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8599.t1 is derived from g5774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36843472	36845710	.	+	.	Phchi.S1G575800
Phchi.S1	AUGUSTUS	transcript	36843472	36845710	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	start_codon	36843472	36843474	.	+	0	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36843472	36843791	0.6	+	0	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36843472	36843791	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36843792	36843888	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36843889	36843938	0.66	+	1	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36843889	36843938	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36843939	36844064	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36844065	36844326	0.93	+	2	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36844065	36844326	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36844327	36844486	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36844487	36844551	0.77	+	1	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36844487	36844551	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36844552	36844632	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36844633	36844742	1	+	2	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36844633	36844742	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36844743	36844829	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36844830	36845007	1	+	0	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36844830	36845007	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36845008	36845092	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36845093	36845219	1	+	2	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36845093	36845219	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36845220	36845311	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36845312	36845346	0.49	+	1	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36845312	36845346	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36845347	36845472	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36845473	36845526	0.48	+	2	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36845473	36845526	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	intron	36845527	36845657	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	CDS	36845658	36845710	0.48	+	2	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	exon	36845658	36845710	.	+	.	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
Phchi.S1	AUGUSTUS	stop_codon	36845711	36845713	.	+	0	transcript_id "Phchi.S1G575800.t1"; gene_id "Phchi.S1G575800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5361.t1 is derived from g2531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16472456	16474419	.	+	.	Phchi.S1G252000
Phchi.S1	AUGUSTUS	transcript	16472456	16474419	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	start_codon	16472456	16472458	.	+	0	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16472456	16473165	0.44	+	0	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16472456	16473165	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	intron	16473166	16473305	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16473306	16473323	0.8	+	1	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16473306	16473323	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	intron	16473324	16473412	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16473413	16473547	0.8	+	1	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16473413	16473547	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	intron	16473548	16473729	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16473730	16473748	0.76	+	1	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16473730	16473748	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	intron	16473749	16473845	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16473846	16474074	0.43	+	0	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16473846	16474074	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	intron	16474075	16474165	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16474166	16474274	1	+	2	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16474166	16474274	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	intron	16474275	16474406	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	CDS	16474407	16474419	1	+	1	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	exon	16474407	16474419	.	+	.	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
Phchi.S1	AUGUSTUS	stop_codon	16474420	16474422	.	+	0	transcript_id "Phchi.S1G252000.t1"; gene_id "Phchi.S1G252000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13328.t1 is derived from g11794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6124536	6127236	.	-	.	Phchi.S3G064700
Phchi.S3	AUGUSTUS	transcript	6124536	6127236	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	stop_codon	6124533	6124535	.	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6124536	6124685	0.93	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6124536	6124685	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6124686	6124773	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6124774	6124828	1	-	1	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6124774	6124828	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6124829	6124916	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6124917	6124981	1	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6124917	6124981	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6124982	6125067	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6125068	6125211	1	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6125068	6125211	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6125212	6125389	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6125390	6125443	1	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6125390	6125443	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6125444	6125549	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6125550	6125799	0.8	-	1	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6125550	6125799	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6125800	6125886	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6125887	6125993	1	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6125887	6125993	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6125994	6126073	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6126074	6126171	1	-	2	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6126074	6126171	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6126172	6126296	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6126297	6126411	1	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6126297	6126411	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6126412	6126592	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6126593	6126701	1	-	1	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6126593	6126701	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6126702	6126799	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6126800	6126915	1	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6126800	6126915	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	intron	6126916	6126993	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	CDS	6126994	6127236	0.94	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	exon	6126994	6127236	.	-	.	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
Phchi.S3	AUGUSTUS	start_codon	6127234	6127236	.	-	0	transcript_id "Phchi.S3G064700.t1"; gene_id "Phchi.S3G064700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4086.t1 is derived from g1255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7747705	7748610	.	-	.	Phchi.S1G124500
Phchi.S1	AUGUSTUS	transcript	7747705	7748610	.	-	.	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	stop_codon	7747702	7747704	.	-	0	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	CDS	7747705	7748153	0.71	-	2	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	exon	7747705	7748153	.	-	.	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	intron	7748154	7748272	.	-	.	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	CDS	7748273	7748321	0.68	-	0	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	exon	7748273	7748321	.	-	.	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	intron	7748322	7748427	.	-	.	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	CDS	7748428	7748610	0.56	-	0	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	exon	7748428	7748610	.	-	.	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
Phchi.S1	AUGUSTUS	start_codon	7748608	7748610	.	-	0	transcript_id "Phchi.S1G124500.t1"; gene_id "Phchi.S1G124500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4292.t1 is derived from g1461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9450667	9451461	.	-	.	Phchi.S1G145100
Phchi.S1	AUGUSTUS	transcript	9450667	9451461	.	-	.	transcript_id "Phchi.S1G145100.t1"; gene_id "Phchi.S1G145100"
Phchi.S1	AUGUSTUS	stop_codon	9450664	9450666	.	-	0	transcript_id "Phchi.S1G145100.t1"; gene_id "Phchi.S1G145100"
Phchi.S1	AUGUSTUS	CDS	9450667	9451461	0.55	-	0	transcript_id "Phchi.S1G145100.t1"; gene_id "Phchi.S1G145100"
Phchi.S1	AUGUSTUS	exon	9450667	9451461	.	-	.	transcript_id "Phchi.S1G145100.t1"; gene_id "Phchi.S1G145100"
Phchi.S1	AUGUSTUS	start_codon	9451459	9451461	.	-	0	transcript_id "Phchi.S1G145100.t1"; gene_id "Phchi.S1G145100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13815.t1 is derived from g12282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9041795	9046254	.	+	.	Phchi.S3G113400
Phchi.S3	AUGUSTUS	transcript	9041795	9046254	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	start_codon	9041795	9041797	.	+	0	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	CDS	9041795	9043695	0.12	+	0	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	exon	9041795	9043695	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	intron	9043696	9043799	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	CDS	9043800	9043886	0.45	+	1	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	exon	9043800	9043886	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	intron	9043887	9043965	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	CDS	9043966	9044551	0.42	+	1	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	exon	9043966	9044551	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	intron	9044552	9044664	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	CDS	9044665	9046254	0.86	+	0	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	exon	9044665	9046254	.	+	.	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
Phchi.S3	AUGUSTUS	stop_codon	9046255	9046257	.	+	0	transcript_id "Phchi.S3G113400.t1"; gene_id "Phchi.S3G113400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14577.t1 is derived from g13045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13553344	13557798	.	-	.	Phchi.S3G189600
Phchi.S3	AUGUSTUS	transcript	13553344	13557798	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	stop_codon	13553341	13553343	.	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13553344	13553401	0.43	-	1	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13553344	13553401	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13553402	13553534	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13553535	13553569	0.37	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13553535	13553569	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13553570	13553637	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13553638	13554918	0.58	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13553638	13554918	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13554919	13554993	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13554994	13555205	1	-	2	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13554994	13555205	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13555206	13555362	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13555363	13555477	1	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13555363	13555477	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13555478	13555618	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13555619	13555721	1	-	1	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13555619	13555721	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13555722	13555836	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13555837	13555898	0.98	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13555837	13555898	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13555899	13556094	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13556095	13556194	1	-	1	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13556095	13556194	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13556195	13556328	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13556329	13556451	1	-	1	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13556329	13556451	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13556452	13556690	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13556691	13557211	0.93	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13556691	13557211	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	intron	13557212	13557387	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	CDS	13557388	13557798	0.67	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	exon	13557388	13557798	.	-	.	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
Phchi.S3	AUGUSTUS	start_codon	13557796	13557798	.	-	0	transcript_id "Phchi.S3G189600.t1"; gene_id "Phchi.S3G189600"
# This transcript jg12362.t2 is derived from g8038.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12362.t3 is derived from g8038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12363.t1 is derived from g8039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12742178	12742922	.	+	.	Phchi.S2G044300
Phchi.S2	AUGUSTUS	transcript	12742178	12742922	.	+	.	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	start_codon	12742178	12742180	.	+	0	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	CDS	12742178	12742246	0.02	+	0	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	exon	12742178	12742246	.	+	.	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	intron	12742247	12742742	.	+	.	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	CDS	12742743	12742922	0.01	+	0	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	exon	12742743	12742922	.	+	.	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
Phchi.S2	AUGUSTUS	stop_codon	12742923	12742925	.	+	0	transcript_id "Phchi.S2G044300.t1"; gene_id "Phchi.S2G044300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15892.t1 is derived from g14362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22048014	22051837	.	+	.	Phchi.S3G321100
Phchi.S3	AUGUSTUS	transcript	22048014	22051837	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	start_codon	22048014	22048016	.	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22048014	22048718	0.99	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22048014	22048718	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22048719	22048844	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22048845	22048970	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22048845	22048970	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22048971	22049106	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22049107	22049226	0.99	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22049107	22049226	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22049227	22049327	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22049328	22049603	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22049328	22049603	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22049604	22049732	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22049733	22049905	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22049733	22049905	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22049906	22050021	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22050022	22050294	1	+	1	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22050022	22050294	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22050295	22050421	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22050422	22050767	0.71	+	1	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22050422	22050767	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22050768	22050884	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22050885	22050993	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22050885	22050993	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22050994	22051117	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22051118	22051272	1	+	2	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22051118	22051272	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22051273	22051356	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22051357	22051449	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22051357	22051449	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22051450	22051546	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22051547	22051627	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22051547	22051627	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	intron	22051628	22051723	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	CDS	22051724	22051837	1	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	exon	22051724	22051837	.	+	.	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
Phchi.S3	AUGUSTUS	stop_codon	22051838	22051840	.	+	0	transcript_id "Phchi.S3G321100.t1"; gene_id "Phchi.S3G321100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3375.t1 is derived from g544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3235512	3236228	.	+	.	Phchi.S1G053400
Phchi.S1	AUGUSTUS	transcript	3235512	3236228	.	+	.	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	start_codon	3235512	3235514	.	+	0	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	CDS	3235512	3235550	1	+	0	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	exon	3235512	3235550	.	+	.	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	intron	3235551	3236015	.	+	.	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	CDS	3236016	3236228	0.61	+	0	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	exon	3236016	3236228	.	+	.	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
Phchi.S1	AUGUSTUS	stop_codon	3236229	3236231	.	+	0	transcript_id "Phchi.S1G053400.t1"; gene_id "Phchi.S1G053400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4415.t1 is derived from g1584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10377290	10378136	.	+	.	Phchi.S1G157400
Phchi.S1	AUGUSTUS	transcript	10377290	10378136	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	start_codon	10377290	10377292	.	+	0	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	CDS	10377290	10377382	0.49	+	0	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	exon	10377290	10377382	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	intron	10377383	10377506	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	CDS	10377507	10377572	0.46	+	0	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	exon	10377507	10377572	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	intron	10377573	10377662	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	CDS	10377663	10377705	0.89	+	0	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	exon	10377663	10377705	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	intron	10377706	10377801	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	CDS	10377802	10377957	0.96	+	2	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	exon	10377802	10377957	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	intron	10377958	10378047	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	CDS	10378048	10378136	1	+	2	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	exon	10378048	10378136	.	+	.	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
Phchi.S1	AUGUSTUS	stop_codon	10378137	10378139	.	+	0	transcript_id "Phchi.S1G157400.t1"; gene_id "Phchi.S1G157400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12364.t1 is derived from g8040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12752714	12753820	.	+	.	Phchi.S2G044400
Phchi.S2	AUGUSTUS	transcript	12752714	12753820	.	+	.	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	start_codon	12752714	12752716	.	+	0	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	CDS	12752714	12752796	0.48	+	0	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	exon	12752714	12752796	.	+	.	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	intron	12752797	12752988	.	+	.	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	CDS	12752989	12753820	0.46	+	1	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	exon	12752989	12753820	.	+	.	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
Phchi.S2	AUGUSTUS	stop_codon	12753821	12753823	.	+	0	transcript_id "Phchi.S2G044400.t1"; gene_id "Phchi.S2G044400"
# This transcript jg11247.t2 is derived from g15297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11248.t1 is derived from g15298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4994787	4995390	.	+	.	Phchi.S4G083000
Phchi.S4	AUGUSTUS	transcript	4994787	4995390	.	+	.	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	start_codon	4994787	4994789	.	+	0	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	CDS	4994787	4995236	0.89	+	0	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	exon	4994787	4995236	.	+	.	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	intron	4995237	4995315	.	+	.	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	CDS	4995316	4995390	1	+	0	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	exon	4995316	4995390	.	+	.	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
Phchi.S4	AUGUSTUS	stop_codon	4995391	4995393	.	+	0	transcript_id "Phchi.S4G083000.t1"; gene_id "Phchi.S4G083000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1182.t1 is derived from g10965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8328209	8331848	.	-	.	Phchi.S6G114100
Phchi.S6	AUGUSTUS	transcript	8328209	8331848	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	stop_codon	8328206	8328208	.	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8328209	8328274	0.89	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8328209	8328274	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8328275	8328410	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8328411	8329109	0.97	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8328411	8329109	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8329110	8329316	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8329317	8329442	0.61	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8329317	8329442	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8329443	8329550	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8329551	8329661	0.99	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8329551	8329661	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8329662	8329770	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8329771	8329848	0.96	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8329771	8329848	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8329849	8329954	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8329955	8330036	0.36	-	1	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8329955	8330036	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8330037	8330247	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8330248	8330583	0.3	-	1	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8330248	8330583	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8330584	8330675	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8330676	8331157	0.57	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8330676	8331157	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8331158	8331276	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8331277	8331726	0.97	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8331277	8331726	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	intron	8331727	8331800	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	CDS	8331801	8331848	0.82	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	exon	8331801	8331848	.	-	.	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
Phchi.S6	AUGUSTUS	start_codon	8331846	8331848	.	-	0	transcript_id "Phchi.S6G114100.t1"; gene_id "Phchi.S6G114100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2090.t1 is derived from g9010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4834816	4836092	.	+	.	Phchi.S5G069900
Phchi.S5	AUGUSTUS	transcript	4834816	4836092	.	+	.	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	start_codon	4834816	4834818	.	+	0	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	CDS	4834816	4835539	0.83	+	0	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	exon	4834816	4835539	.	+	.	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	intron	4835540	4835748	.	+	.	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	CDS	4835749	4836092	0.93	+	2	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	exon	4835749	4836092	.	+	.	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
Phchi.S5	AUGUSTUS	stop_codon	4836093	4836095	.	+	0	transcript_id "Phchi.S5G069900.t1"; gene_id "Phchi.S5G069900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg526.t1 is derived from g10308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3780064	3781370	.	-	.	Phchi.S6G048500
Phchi.S6	AUGUSTUS	transcript	3780064	3781370	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	stop_codon	3780061	3780063	.	-	0	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	CDS	3780064	3780244	0.91	-	1	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	exon	3780064	3780244	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	intron	3780245	3780349	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	CDS	3780350	3780456	0.96	-	0	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	exon	3780350	3780456	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	intron	3780457	3780626	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	CDS	3780627	3780691	1	-	2	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	exon	3780627	3780691	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	intron	3780692	3780988	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	CDS	3780989	3781061	1	-	0	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	exon	3780989	3781061	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	intron	3781062	3781268	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	CDS	3781269	3781370	1	-	0	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	exon	3781269	3781370	.	-	.	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
Phchi.S6	AUGUSTUS	start_codon	3781368	3781370	.	-	0	transcript_id "Phchi.S6G048500.t1"; gene_id "Phchi.S6G048500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4308.t1 is derived from g1477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9550697	9552300	.	+	.	Phchi.S1G146700
Phchi.S1	AUGUSTUS	transcript	9550697	9552300	.	+	.	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	start_codon	9550697	9550699	.	+	0	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	CDS	9550697	9550833	0.57	+	0	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	exon	9550697	9550833	.	+	.	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	intron	9550834	9550966	.	+	.	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	CDS	9550967	9551135	0.27	+	1	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	exon	9550967	9551135	.	+	.	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	intron	9551136	9551421	.	+	.	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	CDS	9551422	9552300	0.6	+	0	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	exon	9551422	9552300	.	+	.	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
Phchi.S1	AUGUSTUS	stop_codon	9552301	9552303	.	+	0	transcript_id "Phchi.S1G146700.t1"; gene_id "Phchi.S1G146700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2482.t1 is derived from g9402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6872405	6873529	.	-	.	Phchi.S5G109100
Phchi.S5	AUGUSTUS	transcript	6872405	6873529	.	-	.	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	stop_codon	6872402	6872404	.	-	0	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	CDS	6872405	6872785	0.98	-	0	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	exon	6872405	6872785	.	-	.	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	intron	6872786	6872911	.	-	.	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	CDS	6872912	6873123	1	-	2	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	exon	6872912	6873123	.	-	.	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	intron	6873124	6873249	.	-	.	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	CDS	6873250	6873529	1	-	0	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	exon	6873250	6873529	.	-	.	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
Phchi.S5	AUGUSTUS	start_codon	6873527	6873529	.	-	0	transcript_id "Phchi.S5G109100.t1"; gene_id "Phchi.S5G109100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4320.t1 is derived from g1489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9605877	9607624	.	-	.	Phchi.S1G147900
Phchi.S1	AUGUSTUS	transcript	9605877	9607624	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	stop_codon	9605728	9605730	.	-	0	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	CDS	9605877	9607001	0.61	-	0	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	exon	9605877	9607001	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	intron	9607002	9607071	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	CDS	9607072	9607080	0.61	-	0	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	exon	9607072	9607080	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	intron	9607081	9607236	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	CDS	9607237	9607273	0.61	-	1	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	exon	9607237	9607273	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	intron	9607274	9607469	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	CDS	9607470	9607624	0.31	-	0	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	exon	9607470	9607624	.	-	.	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
Phchi.S1	AUGUSTUS	start_codon	9607622	9607624	.	-	0	transcript_id "Phchi.S1G147900.t1"; gene_id "Phchi.S1G147900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6906.t1 is derived from g4078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25926659	25931644	.	-	.	Phchi.S1G406500
Phchi.S1	AUGUSTUS	transcript	25926659	25931644	.	-	.	transcript_id "Phchi.S1G406500.t1"; gene_id "Phchi.S1G406500"
Phchi.S1	AUGUSTUS	stop_codon	25926656	25926658	.	-	0	transcript_id "Phchi.S1G406500.t1"; gene_id "Phchi.S1G406500"
Phchi.S1	AUGUSTUS	CDS	25926659	25931644	0.64	-	0	transcript_id "Phchi.S1G406500.t1"; gene_id "Phchi.S1G406500"
Phchi.S1	AUGUSTUS	exon	25926659	25931644	.	-	.	transcript_id "Phchi.S1G406500.t1"; gene_id "Phchi.S1G406500"
Phchi.S1	AUGUSTUS	start_codon	25931642	25931644	.	-	0	transcript_id "Phchi.S1G406500.t1"; gene_id "Phchi.S1G406500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12154.t1 is derived from g7830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5002098	5005118	.	+	.	Phchi.S2G023400
Phchi.S2	AUGUSTUS	transcript	5002098	5005118	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	start_codon	5002098	5002100	.	+	0	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	CDS	5002098	5004392	1	+	0	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	exon	5002098	5004392	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	intron	5004393	5004731	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	CDS	5004732	5004845	0.69	+	0	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	exon	5004732	5004845	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	intron	5004846	5004960	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	CDS	5004961	5005009	0.69	+	0	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	exon	5004961	5005009	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	intron	5005010	5005107	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	CDS	5005108	5005118	0.69	+	2	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	exon	5005108	5005118	.	+	.	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
Phchi.S2	AUGUSTUS	stop_codon	5005119	5005121	.	+	0	transcript_id "Phchi.S2G023400.t1"; gene_id "Phchi.S2G023400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10918.t1 is derived from g14968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2962035	2963282	.	-	.	Phchi.S4G050000
Phchi.S4	AUGUSTUS	transcript	2962035	2963282	.	-	.	transcript_id "Phchi.S4G050000.t1"; gene_id "Phchi.S4G050000"
Phchi.S4	AUGUSTUS	stop_codon	2962032	2962034	.	-	0	transcript_id "Phchi.S4G050000.t1"; gene_id "Phchi.S4G050000"
Phchi.S4	AUGUSTUS	CDS	2962035	2963282	1	-	0	transcript_id "Phchi.S4G050000.t1"; gene_id "Phchi.S4G050000"
Phchi.S4	AUGUSTUS	exon	2962035	2963282	.	-	.	transcript_id "Phchi.S4G050000.t1"; gene_id "Phchi.S4G050000"
Phchi.S4	AUGUSTUS	start_codon	2963280	2963282	.	-	0	transcript_id "Phchi.S4G050000.t1"; gene_id "Phchi.S4G050000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10795.t1 is derived from g14845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2148947	2150800	.	-	.	Phchi.S4G037700
Phchi.S4	AUGUSTUS	transcript	2148947	2150800	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	stop_codon	2148944	2148946	.	-	0	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	CDS	2148947	2149374	0.63	-	2	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	exon	2148947	2149374	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	intron	2149375	2149466	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	CDS	2149467	2150139	0.84	-	0	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	exon	2149467	2150139	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	intron	2150140	2150411	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	CDS	2150412	2150490	0.92	-	1	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	exon	2150412	2150490	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	intron	2150491	2150633	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	CDS	2150634	2150800	0.53	-	0	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	exon	2150634	2150800	.	-	.	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
Phchi.S4	AUGUSTUS	start_codon	2150798	2150800	.	-	0	transcript_id "Phchi.S4G037700.t1"; gene_id "Phchi.S4G037700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg20.t1 is derived from g16030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C11	AUGUSTUS	gene	118529	121663	.	+	.	Phchi.C11G000400
Phchi.C11	AUGUSTUS	transcript	118529	121663	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	start_codon	118529	118531	.	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	118529	119680	0.87	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	118529	119680	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	119681	119795	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	119796	119960	0.99	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	119796	119960	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	119961	120126	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	120127	120204	1	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	120127	120204	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	120205	120328	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	120329	120407	1	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	120329	120407	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	120408	120492	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	120493	120638	1	+	2	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	120493	120638	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	120639	120899	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	120900	120965	1	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	120900	120965	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	120966	121059	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	121060	121237	1	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	121060	121237	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	intron	121238	121382	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	CDS	121383	121663	0.99	+	2	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	exon	121383	121663	.	+	.	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
Phchi.C11	AUGUSTUS	stop_codon	121664	121666	.	+	0	transcript_id "Phchi.C11G000400.t1"; gene_id "Phchi.C11G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10988.t1 is derived from g15038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3537113	3538452	.	-	.	Phchi.S4G057000
Phchi.S4	AUGUSTUS	transcript	3537113	3538452	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	stop_codon	3537110	3537112	.	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	CDS	3537113	3537145	1	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	exon	3537113	3537145	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	intron	3537146	3537238	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	CDS	3537239	3537316	1	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	exon	3537239	3537316	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	intron	3537317	3537439	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	CDS	3537440	3537504	1	-	2	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	exon	3537440	3537504	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	intron	3537505	3537623	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	CDS	3537624	3537735	1	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	exon	3537624	3537735	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	intron	3537736	3537901	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	CDS	3537902	3538012	1	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	exon	3537902	3538012	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	intron	3538013	3538299	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	CDS	3538300	3538452	1	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	exon	3538300	3538452	.	-	.	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
Phchi.S4	AUGUSTUS	start_codon	3538450	3538452	.	-	0	transcript_id "Phchi.S4G057000.t1"; gene_id "Phchi.S4G057000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12475.t1 is derived from g8152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	26458581	26459044	.	-	.	Phchi.S2G055500
Phchi.S2	AUGUSTUS	transcript	26458581	26459044	.	-	.	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	stop_codon	26458578	26458580	.	-	0	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	CDS	26458581	26458763	0.67	-	0	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	exon	26458581	26458763	.	-	.	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	intron	26458764	26458861	.	-	.	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	CDS	26458862	26459044	0.66	-	0	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	exon	26458862	26459044	.	-	.	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
Phchi.S2	AUGUSTUS	start_codon	26459042	26459044	.	-	0	transcript_id "Phchi.S2G055500.t1"; gene_id "Phchi.S2G055500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6949.t1 is derived from g4121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26105587	26107282	.	-	.	Phchi.S1G410800
Phchi.S1	AUGUSTUS	transcript	26105587	26107282	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	stop_codon	26105584	26105586	.	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26105587	26105787	0.84	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26105587	26105787	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26105788	26105879	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26105880	26105957	1	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26105880	26105957	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26105958	26106046	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26106047	26106256	1	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26106047	26106256	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26106257	26106358	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26106359	26106500	1	-	1	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26106359	26106500	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26106501	26106577	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26106578	26106771	0.93	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26106578	26106771	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26106772	26106881	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26106882	26106950	0.99	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26106882	26106950	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26106951	26107055	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26107056	26107142	1	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26107056	26107142	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	intron	26107143	26107222	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	CDS	26107223	26107282	1	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	exon	26107223	26107282	.	-	.	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
Phchi.S1	AUGUSTUS	start_codon	26107280	26107282	.	-	0	transcript_id "Phchi.S1G410800.t1"; gene_id "Phchi.S1G410800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg510.t1 is derived from g10292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3525729	3527284	.	-	.	Phchi.S6G046900
Phchi.S6	AUGUSTUS	transcript	3525729	3527284	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	stop_codon	3525726	3525728	.	-	0	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	CDS	3525729	3525823	0.99	-	2	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	exon	3525729	3525823	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	intron	3525824	3525910	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	CDS	3525911	3526011	0.62	-	1	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	exon	3525911	3526011	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	intron	3526012	3526323	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	CDS	3526324	3526392	0.99	-	1	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	exon	3526324	3526392	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	intron	3526393	3526488	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	CDS	3526489	3526580	1	-	0	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	exon	3526489	3526580	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	intron	3526581	3526935	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	CDS	3526936	3526970	0.53	-	2	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	exon	3526936	3526970	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	intron	3526971	3527196	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	CDS	3527197	3527284	0.57	-	0	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	exon	3527197	3527284	.	-	.	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
Phchi.S6	AUGUSTUS	start_codon	3527282	3527284	.	-	0	transcript_id "Phchi.S6G046900.t1"; gene_id "Phchi.S6G046900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15989.t1 is derived from g9761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C297	AUGUSTUS	gene	1834	3195	.	-	.	Phchi.C297G000100
Phchi.C297	AUGUSTUS	transcript	1834	3195	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	stop_codon	1831	1833	.	-	0	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	CDS	1834	2101	0.96	-	1	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	exon	1834	2101	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	intron	2102	2254	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	CDS	2255	2433	0.82	-	0	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	exon	2255	2433	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	intron	2434	2678	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	CDS	2679	2764	0.71	-	2	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	exon	2679	2764	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	intron	2765	2855	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	CDS	2856	3195	0.59	-	0	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	exon	2856	3195	.	-	.	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
Phchi.C297	AUGUSTUS	start_codon	3193	3195	.	-	0	transcript_id "Phchi.C297G000100.t1"; gene_id "Phchi.C297G000100"
# This transcript jg4132.t2 is derived from g1301.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4133.t1 is derived from g1302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8434578	8435321	.	+	.	Phchi.S1G129200
Phchi.S1	AUGUSTUS	transcript	8434578	8435321	.	+	.	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	start_codon	8434578	8434580	.	+	0	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	CDS	8434578	8434971	0.97	+	0	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	exon	8434578	8434971	.	+	.	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	intron	8434972	8435119	.	+	.	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	CDS	8435120	8435197	0.89	+	2	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	exon	8435120	8435197	.	+	.	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	intron	8435198	8435286	.	+	.	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	CDS	8435287	8435321	0.96	+	2	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	exon	8435287	8435321	.	+	.	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
Phchi.S1	AUGUSTUS	stop_codon	8435322	8435324	.	+	0	transcript_id "Phchi.S1G129200.t1"; gene_id "Phchi.S1G129200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3776.t1 is derived from g945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5647248	5649586	.	+	.	Phchi.S1G093500
Phchi.S1	AUGUSTUS	transcript	5647248	5649586	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	start_codon	5647248	5647250	.	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5647248	5647334	1	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5647248	5647334	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5647335	5647478	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5647479	5647538	1	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5647479	5647538	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5647539	5647617	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5647618	5647700	1	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5647618	5647700	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5647701	5647823	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5647824	5647980	1	+	1	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5647824	5647980	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5647981	5648128	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5648129	5648258	1	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5648129	5648258	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5648259	5648618	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5648619	5648774	1	+	2	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5648619	5648774	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5648775	5648854	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5648855	5649033	1	+	2	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5648855	5649033	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5649034	5649132	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5649133	5649213	1	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5649133	5649213	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5649214	5649315	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5649316	5649372	1	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5649316	5649372	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	intron	5649373	5649451	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	CDS	5649452	5649586	0.86	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	exon	5649452	5649586	.	+	.	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
Phchi.S1	AUGUSTUS	stop_codon	5649587	5649589	.	+	0	transcript_id "Phchi.S1G093500.t1"; gene_id "Phchi.S1G093500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg122.t1 is derived from g9904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	690993	693340	.	-	.	Phchi.S6G008100
Phchi.S6	AUGUSTUS	transcript	690993	693340	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	stop_codon	690990	690992	.	-	0	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	CDS	690993	691022	1	-	0	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	exon	690993	691022	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	intron	691023	691226	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	CDS	691227	691325	1	-	0	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	exon	691227	691325	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	intron	691326	691525	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	CDS	691526	691595	0.98	-	1	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	exon	691526	691595	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	intron	691596	691691	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	CDS	691692	691768	0.81	-	0	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	exon	691692	691768	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	intron	691769	691936	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	CDS	691937	693340	0.62	-	0	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	exon	691937	693340	.	-	.	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
Phchi.S6	AUGUSTUS	start_codon	693338	693340	.	-	0	transcript_id "Phchi.S6G008100.t1"; gene_id "Phchi.S6G008100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7791.t1 is derived from g4965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31201051	31201557	.	+	.	Phchi.S1G495000
Phchi.S1	AUGUSTUS	transcript	31201051	31201557	.	+	.	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	start_codon	31201051	31201053	.	+	0	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	CDS	31201051	31201159	0.74	+	0	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	exon	31201051	31201159	.	+	.	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	intron	31201160	31201255	.	+	.	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	CDS	31201256	31201557	0.71	+	2	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	exon	31201256	31201557	.	+	.	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
Phchi.S1	AUGUSTUS	stop_codon	31201558	31201560	.	+	0	transcript_id "Phchi.S1G495000.t1"; gene_id "Phchi.S1G495000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13303.t1 is derived from g11769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5598172	5601386	.	+	.	Phchi.S3G062200
Phchi.S3	AUGUSTUS	transcript	5598172	5601386	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	start_codon	5598172	5598174	.	+	0	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5598172	5599240	0.78	+	0	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5598172	5599240	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	intron	5599241	5599419	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5599420	5599768	1	+	2	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5599420	5599768	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	intron	5599769	5599953	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5599954	5600052	1	+	1	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5599954	5600052	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	intron	5600053	5600152	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5600153	5600380	1	+	1	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5600153	5600380	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	intron	5600381	5600469	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5600470	5600608	0.62	+	1	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5600470	5600608	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	intron	5600609	5600722	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5600723	5600968	0.82	+	0	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5600723	5600968	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	intron	5600969	5601083	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	CDS	5601084	5601386	1	+	0	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	exon	5601084	5601386	.	+	.	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
Phchi.S3	AUGUSTUS	stop_codon	5601387	5601389	.	+	0	transcript_id "Phchi.S3G062200.t1"; gene_id "Phchi.S3G062200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg31.t1 is derived from g9809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C246	AUGUSTUS	gene	17445	18191	.	-	.	Phchi.C246G000400
Phchi.C246	AUGUSTUS	transcript	17445	18191	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	stop_codon	17442	17444	.	-	0	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	CDS	17445	17477	0.48	-	0	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	exon	17445	17477	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	intron	17478	17570	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	CDS	17571	17666	0.48	-	0	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	exon	17571	17666	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	intron	17667	17772	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	CDS	17773	17851	0.99	-	1	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	exon	17773	17851	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	intron	17852	17944	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	CDS	17945	18034	0.98	-	1	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	exon	17945	18034	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	intron	18035	18138	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	CDS	18139	18191	0.76	-	0	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	exon	18139	18191	.	-	.	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
Phchi.C246	AUGUSTUS	start_codon	18189	18191	.	-	0	transcript_id "Phchi.C246G000400.t1"; gene_id "Phchi.C246G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5589.t1 is derived from g2759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17777098	17782960	.	+	.	Phchi.S1G274800
Phchi.S1	AUGUSTUS	transcript	17777098	17782960	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	start_codon	17777098	17777100	.	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17777098	17777820	0.99	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17777098	17777820	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17777821	17777942	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17777943	17778189	0.98	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17777943	17778189	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17778190	17778377	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17778378	17778772	0.21	+	2	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17778378	17778772	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17778773	17778899	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17778900	17779035	0.64	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17778900	17779035	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17779036	17779179	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17779180	17780086	0.58	+	2	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17779180	17780086	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17780087	17780220	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17780221	17780422	0.88	+	1	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17780221	17780422	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17780423	17780499	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17780500	17780824	1	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17780500	17780824	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17780825	17780904	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17780905	17781166	0.92	+	2	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17780905	17781166	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17781167	17781269	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17781270	17781504	1	+	1	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17781270	17781504	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17781505	17781639	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17781640	17781780	1	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17781640	17781780	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17781781	17781866	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17781867	17782063	1	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17781867	17782063	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17782064	17782158	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17782159	17782307	0.83	+	1	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17782159	17782307	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17782308	17782665	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17782666	17782768	0.72	+	2	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17782666	17782768	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	intron	17782769	17782911	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	CDS	17782912	17782960	0.72	+	1	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	exon	17782912	17782960	.	+	.	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
Phchi.S1	AUGUSTUS	stop_codon	17782961	17782963	.	+	0	transcript_id "Phchi.S1G274800.t1"; gene_id "Phchi.S1G274800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3827.t1 is derived from g996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5905076	5908728	.	+	.	Phchi.S1G098600
Phchi.S1	AUGUSTUS	transcript	5905076	5908728	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	start_codon	5905076	5905078	.	+	0	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5905076	5907839	0.68	+	0	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5905076	5907839	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5907840	5907989	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5907990	5908190	0.55	+	2	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5907990	5908190	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5908191	5908269	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5908270	5908410	0.49	+	2	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5908270	5908410	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5908411	5908609	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5908610	5908728	0.74	+	2	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5908610	5908728	.	+	.	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	stop_codon	5908729	5908731	.	+	0	transcript_id "Phchi.S1G098600.t1"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	transcript	5906234	5908728	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	start_codon	5906234	5906236	.	+	0	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5906234	5907839	0.6	+	0	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5906234	5907839	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5907840	5907989	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5907990	5908190	0.54	+	2	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5907990	5908190	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5908191	5908269	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5908270	5908410	0.5	+	2	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5908270	5908410	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5908411	5908609	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5908610	5908728	0.7	+	2	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5908610	5908728	.	+	.	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	stop_codon	5908729	5908731	.	+	0	transcript_id "Phchi.S1G098600.t2"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	transcript	5905541	5908728	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	start_codon	5905541	5905543	.	+	0	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5905541	5907839	0.39	+	0	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5905541	5907839	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5907840	5907989	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5907990	5908190	0.48	+	2	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5907990	5908190	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5908191	5908269	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5908270	5908410	0.42	+	2	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5908270	5908410	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	intron	5908411	5908609	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	CDS	5908610	5908728	0.69	+	2	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	exon	5908610	5908728	.	+	.	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
Phchi.S1	AUGUSTUS	stop_codon	5908729	5908731	.	+	0	transcript_id "Phchi.S1G098600.t3"; gene_id "Phchi.S1G098600"
# This transcript jg3708.t2 is derived from g877.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3709.t1 is derived from g878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5272754	5273261	.	+	.	Phchi.S1G086800
Phchi.S1	AUGUSTUS	transcript	5272754	5273261	.	+	.	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	start_codon	5272754	5272756	.	+	0	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	CDS	5272754	5272768	0.76	+	0	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	exon	5272754	5272768	.	+	.	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	intron	5272769	5273036	.	+	.	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	CDS	5273037	5273261	0.7	+	0	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	exon	5273037	5273261	.	+	.	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
Phchi.S1	AUGUSTUS	stop_codon	5273262	5273264	.	+	0	transcript_id "Phchi.S1G086800.t1"; gene_id "Phchi.S1G086800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3655.t1 is derived from g824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4983902	4984634	.	+	.	Phchi.S1G081400
Phchi.S1	AUGUSTUS	transcript	4983902	4984634	.	+	.	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	start_codon	4983902	4983904	.	+	0	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	CDS	4983902	4984246	0.38	+	0	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	exon	4983902	4984246	.	+	.	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	intron	4984247	4984358	.	+	.	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	CDS	4984359	4984634	0.56	+	0	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	exon	4984359	4984634	.	+	.	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
Phchi.S1	AUGUSTUS	stop_codon	4984635	4984637	.	+	0	transcript_id "Phchi.S1G081400.t1"; gene_id "Phchi.S1G081400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10003.t1 is derived from g7179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45001304	45003525	.	-	.	Phchi.S1G716200
Phchi.S1	AUGUSTUS	transcript	45001304	45003525	.	-	.	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	stop_codon	45001301	45001303	.	-	0	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	CDS	45001304	45001890	0.76	-	2	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	exon	45001304	45001890	.	-	.	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	intron	45001891	45001997	.	-	.	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	CDS	45001998	45003525	0.7	-	0	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	exon	45001998	45003525	.	-	.	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
Phchi.S1	AUGUSTUS	start_codon	45003523	45003525	.	-	0	transcript_id "Phchi.S1G716200.t1"; gene_id "Phchi.S1G716200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4952.t1 is derived from g2122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13705305	13705847	.	-	.	Phchi.S1G211100
Phchi.S1	AUGUSTUS	transcript	13705305	13705847	.	-	.	transcript_id "Phchi.S1G211100.t1"; gene_id "Phchi.S1G211100"
Phchi.S1	AUGUSTUS	stop_codon	13705302	13705304	.	-	0	transcript_id "Phchi.S1G211100.t1"; gene_id "Phchi.S1G211100"
Phchi.S1	AUGUSTUS	CDS	13705305	13705847	0.85	-	0	transcript_id "Phchi.S1G211100.t1"; gene_id "Phchi.S1G211100"
Phchi.S1	AUGUSTUS	exon	13705305	13705847	.	-	.	transcript_id "Phchi.S1G211100.t1"; gene_id "Phchi.S1G211100"
Phchi.S1	AUGUSTUS	start_codon	13705845	13705847	.	-	0	transcript_id "Phchi.S1G211100.t1"; gene_id "Phchi.S1G211100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5130.t1 is derived from g2300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15054035	15054307	.	-	.	Phchi.S1G228900
Phchi.S1	AUGUSTUS	transcript	15054035	15054307	.	-	.	transcript_id "Phchi.S1G228900.t1"; gene_id "Phchi.S1G228900"
Phchi.S1	AUGUSTUS	stop_codon	15054032	15054034	.	-	0	transcript_id "Phchi.S1G228900.t1"; gene_id "Phchi.S1G228900"
Phchi.S1	AUGUSTUS	CDS	15054035	15054307	0.57	-	0	transcript_id "Phchi.S1G228900.t1"; gene_id "Phchi.S1G228900"
Phchi.S1	AUGUSTUS	exon	15054035	15054307	.	-	.	transcript_id "Phchi.S1G228900.t1"; gene_id "Phchi.S1G228900"
Phchi.S1	AUGUSTUS	start_codon	15054305	15054307	.	-	0	transcript_id "Phchi.S1G228900.t1"; gene_id "Phchi.S1G228900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1495.t1 is derived from g8414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1199247	1202861	.	-	.	Phchi.S5G010400
Phchi.S5	AUGUSTUS	transcript	1199247	1202861	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	stop_codon	1199244	1199246	.	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1199247	1199408	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1199247	1199408	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1199409	1199565	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1199566	1199836	1	-	1	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1199566	1199836	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1199837	1199926	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1199927	1199997	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1199927	1199997	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1199998	1200140	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1200141	1200276	1	-	1	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1200141	1200276	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1200277	1200376	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1200377	1200456	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1200377	1200456	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1200457	1200568	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1200569	1200682	0.99	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1200569	1200682	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1200683	1200808	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1200809	1200890	1	-	1	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1200809	1200890	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1200891	1201018	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1201019	1201107	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1201019	1201107	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1201108	1201222	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1201223	1201273	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1201223	1201273	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1201274	1201394	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1201395	1201504	1	-	2	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1201395	1201504	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1201505	1201577	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1201578	1201650	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1201578	1201650	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1201651	1201749	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1201750	1201805	1	-	2	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1201750	1201805	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1201806	1202024	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1202025	1202115	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1202025	1202115	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1202116	1202211	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1202212	1202298	0.99	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1202212	1202298	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1202299	1202410	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1202411	1202503	0.99	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1202411	1202503	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1202504	1202584	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1202585	1202704	1	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1202585	1202704	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	intron	1202705	1202807	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	CDS	1202808	1202861	0.67	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	exon	1202808	1202861	.	-	.	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
Phchi.S5	AUGUSTUS	start_codon	1202859	1202861	.	-	0	transcript_id "Phchi.S5G010400.t1"; gene_id "Phchi.S5G010400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10695.t1 is derived from g14745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1626540	1629546	.	-	.	Phchi.S4G027700
Phchi.S4	AUGUSTUS	transcript	1626540	1629546	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	stop_codon	1626537	1626539	.	-	0	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	CDS	1626540	1627619	0.5	-	0	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	exon	1626540	1627619	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	intron	1627620	1627781	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	CDS	1627782	1628328	0.21	-	1	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	exon	1627782	1628328	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	intron	1628329	1628535	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	CDS	1628536	1628813	0.57	-	0	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	exon	1628536	1628813	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	intron	1628814	1629065	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	CDS	1629066	1629102	0.73	-	1	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	exon	1629066	1629102	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	intron	1629103	1629245	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	CDS	1629246	1629375	0.97	-	2	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	exon	1629246	1629375	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	intron	1629376	1629464	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	CDS	1629465	1629546	0.72	-	0	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	exon	1629465	1629546	.	-	.	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
Phchi.S4	AUGUSTUS	start_codon	1629544	1629546	.	-	0	transcript_id "Phchi.S4G027700.t1"; gene_id "Phchi.S4G027700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4866.t1 is derived from g2036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13158644	13160936	.	-	.	Phchi.S1G202500
Phchi.S1	AUGUSTUS	transcript	13158644	13160936	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	stop_codon	13158641	13158643	.	-	0	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	CDS	13158644	13158825	1	-	2	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	exon	13158644	13158825	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	intron	13158826	13158911	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	CDS	13158912	13159158	1	-	0	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	exon	13158912	13159158	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	intron	13159159	13159252	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	CDS	13159253	13159567	1	-	0	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	exon	13159253	13159567	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	intron	13159568	13159649	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	CDS	13159650	13159730	0.99	-	0	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	exon	13159650	13159730	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	intron	13159731	13159835	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	CDS	13159836	13160017	0.87	-	2	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	exon	13159836	13160017	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	intron	13160018	13160104	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	CDS	13160105	13160936	0.85	-	0	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	exon	13160105	13160936	.	-	.	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
Phchi.S1	AUGUSTUS	start_codon	13160934	13160936	.	-	0	transcript_id "Phchi.S1G202500.t1"; gene_id "Phchi.S1G202500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2657.t1 is derived from g9577.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8056697	8059228	.	-	.	Phchi.S5G126600
Phchi.S5	AUGUSTUS	transcript	8056697	8059228	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	stop_codon	8056694	8056696	.	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8056697	8056861	0.98	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8056697	8056861	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8056862	8056939	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8056940	8057234	1	-	1	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8056940	8057234	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057235	8057312	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8057313	8057425	1	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8057313	8057425	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057426	8057511	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8057512	8057696	1	-	2	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8057512	8057696	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057697	8057842	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8057843	8057990	1	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8057843	8057990	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057991	8058090	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8058091	8058399	1	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8058091	8058399	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8058400	8058566	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8058567	8058671	1	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8058567	8058671	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8058672	8058943	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8058944	8059228	0.94	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8058944	8059228	.	-	.	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	start_codon	8059226	8059228	.	-	0	transcript_id "Phchi.S5G126600.t1"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	transcript	8056697	8059228	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	stop_codon	8056694	8056696	.	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8056697	8056861	0.95	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8056697	8056861	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8056862	8056939	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8056940	8057234	0.98	-	1	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8056940	8057234	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057235	8057312	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8057313	8057425	1	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8057313	8057425	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057426	8057511	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8057512	8057696	1	-	2	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8057512	8057696	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057697	8057842	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8057843	8057990	1	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8057843	8057990	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8057991	8058090	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8058091	8058399	1	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8058091	8058399	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8058400	8058566	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8058567	8058671	1	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8058567	8058671	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	intron	8058672	8058856	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	CDS	8058857	8059228	0.92	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	exon	8058857	8059228	.	-	.	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
Phchi.S5	AUGUSTUS	start_codon	8059226	8059228	.	-	0	transcript_id "Phchi.S5G126600.t2"; gene_id "Phchi.S5G126600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3067.t1 is derived from g236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1417753	1418114	.	-	.	Phchi.S1G022600
Phchi.S1	AUGUSTUS	transcript	1417753	1418114	.	-	.	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	stop_codon	1417750	1417752	.	-	0	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	CDS	1417753	1418009	0.86	-	2	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	exon	1417753	1418009	.	-	.	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	intron	1418010	1418092	.	-	.	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	CDS	1418093	1418114	0.99	-	0	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	exon	1418093	1418114	.	-	.	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
Phchi.S1	AUGUSTUS	start_codon	1418112	1418114	.	-	0	transcript_id "Phchi.S1G022600.t1"; gene_id "Phchi.S1G022600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3240.t1 is derived from g409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2402314	2403229	.	-	.	Phchi.S1G039900
Phchi.S1	AUGUSTUS	transcript	2402314	2403229	.	-	.	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	stop_codon	2402311	2402313	.	-	0	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	CDS	2402314	2402446	0.99	-	1	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	exon	2402314	2402446	.	-	.	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	intron	2402447	2402552	.	-	.	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	CDS	2402553	2402941	1	-	0	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	exon	2402553	2402941	.	-	.	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	intron	2402942	2403145	.	-	.	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	CDS	2403146	2403229	0.94	-	0	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	exon	2403146	2403229	.	-	.	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
Phchi.S1	AUGUSTUS	start_codon	2403227	2403229	.	-	0	transcript_id "Phchi.S1G039900.t1"; gene_id "Phchi.S1G039900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6402.t1 is derived from g3574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22775969	22776710	.	-	.	Phchi.S1G356100
Phchi.S1	AUGUSTUS	transcript	22775969	22776710	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	stop_codon	22775966	22775968	.	-	0	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22775969	22776028	0.94	-	0	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22775969	22776028	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	intron	22776029	22776143	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22776144	22776254	1	-	0	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22776144	22776254	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	intron	22776255	22776350	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22776351	22776457	1	-	2	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22776351	22776457	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	intron	22776458	22776547	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22776548	22776710	0.97	-	0	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22776548	22776710	.	-	.	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	start_codon	22776708	22776710	.	-	0	transcript_id "Phchi.S1G356100.t1"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	transcript	22775969	22776386	.	-	.	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	stop_codon	22775966	22775968	.	-	0	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22775969	22776028	0.91	-	0	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22775969	22776028	.	-	.	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	intron	22776029	22776143	.	-	.	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22776144	22776254	1	-	0	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22776144	22776254	.	-	.	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	intron	22776255	22776350	.	-	.	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	CDS	22776351	22776386	0.77	-	0	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	exon	22776351	22776386	.	-	.	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
Phchi.S1	AUGUSTUS	start_codon	22776384	22776386	.	-	0	transcript_id "Phchi.S1G356100.t2"; gene_id "Phchi.S1G356100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg556.t1 is derived from g10338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4036658	4039582	.	+	.	Phchi.S6G051500
Phchi.S6	AUGUSTUS	transcript	4036658	4039582	.	+	.	transcript_id "Phchi.S6G051500.t1"; gene_id "Phchi.S6G051500"
Phchi.S6	AUGUSTUS	start_codon	4036658	4036660	.	+	0	transcript_id "Phchi.S6G051500.t1"; gene_id "Phchi.S6G051500"
Phchi.S6	AUGUSTUS	CDS	4036658	4039582	0.51	+	0	transcript_id "Phchi.S6G051500.t1"; gene_id "Phchi.S6G051500"
Phchi.S6	AUGUSTUS	exon	4036658	4039582	.	+	.	transcript_id "Phchi.S6G051500.t1"; gene_id "Phchi.S6G051500"
Phchi.S6	AUGUSTUS	stop_codon	4039583	4039585	.	+	0	transcript_id "Phchi.S6G051500.t1"; gene_id "Phchi.S6G051500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3081.t1 is derived from g250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1504004	1505683	.	-	.	Phchi.S1G024000
Phchi.S1	AUGUSTUS	transcript	1504004	1505683	.	-	.	transcript_id "Phchi.S1G024000.t1"; gene_id "Phchi.S1G024000"
Phchi.S1	AUGUSTUS	stop_codon	1504001	1504003	.	-	0	transcript_id "Phchi.S1G024000.t1"; gene_id "Phchi.S1G024000"
Phchi.S1	AUGUSTUS	CDS	1504004	1505683	1	-	0	transcript_id "Phchi.S1G024000.t1"; gene_id "Phchi.S1G024000"
Phchi.S1	AUGUSTUS	exon	1504004	1505683	.	-	.	transcript_id "Phchi.S1G024000.t1"; gene_id "Phchi.S1G024000"
Phchi.S1	AUGUSTUS	start_codon	1505681	1505683	.	-	0	transcript_id "Phchi.S1G024000.t1"; gene_id "Phchi.S1G024000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg197.t1 is derived from g9979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1114753	1116286	.	+	.	Phchi.S6G015600
Phchi.S6	AUGUSTUS	transcript	1114753	1116286	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	start_codon	1114753	1114755	.	+	0	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	CDS	1114753	1114993	0.78	+	0	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	exon	1114753	1114993	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	intron	1114994	1115064	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	CDS	1115065	1115249	0.8	+	2	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	exon	1115065	1115249	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	intron	1115250	1115337	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	CDS	1115338	1115679	1	+	0	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	exon	1115338	1115679	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	intron	1115680	1115803	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	CDS	1115804	1116021	0.97	+	0	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	exon	1115804	1116021	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	intron	1116022	1116135	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	CDS	1116136	1116286	0.97	+	1	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	exon	1116136	1116286	.	+	.	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
Phchi.S6	AUGUSTUS	stop_codon	1116287	1116289	.	+	0	transcript_id "Phchi.S6G015600.t1"; gene_id "Phchi.S6G015600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8951.t1 is derived from g6126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38823325	38828165	.	+	.	Phchi.S1G611000
Phchi.S1	AUGUSTUS	transcript	38823325	38828165	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	start_codon	38823325	38823327	.	+	0	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	CDS	38823325	38823494	0.55	+	0	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	exon	38823325	38823494	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	intron	38823495	38823589	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	CDS	38823590	38823821	0.87	+	1	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	exon	38823590	38823821	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	intron	38823822	38823939	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	CDS	38823940	38824657	0.37	+	0	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	exon	38823940	38824657	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	intron	38824658	38824731	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	CDS	38824732	38828165	0.23	+	2	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	exon	38824732	38828165	.	+	.	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
Phchi.S1	AUGUSTUS	stop_codon	38828166	38828168	.	+	0	transcript_id "Phchi.S1G611000.t1"; gene_id "Phchi.S1G611000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1830.t1 is derived from g8750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3376483	3377954	.	+	.	Phchi.S5G043900
Phchi.S5	AUGUSTUS	transcript	3376483	3377954	.	+	.	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	start_codon	3376483	3376485	.	+	0	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	CDS	3376483	3376537	0.98	+	0	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	exon	3376483	3376537	.	+	.	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	intron	3376538	3376615	.	+	.	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	CDS	3376616	3377600	1	+	2	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	exon	3376616	3377600	.	+	.	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	intron	3377601	3377863	.	+	.	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	CDS	3377864	3377954	1	+	1	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	exon	3377864	3377954	.	+	.	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
Phchi.S5	AUGUSTUS	stop_codon	3377955	3377957	.	+	0	transcript_id "Phchi.S5G043900.t1"; gene_id "Phchi.S5G043900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1240.t1 is derived from g11023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8556409	8558517	.	-	.	Phchi.S6G119900
Phchi.S6	AUGUSTUS	transcript	8556409	8558517	.	-	.	transcript_id "Phchi.S6G119900.t1"; gene_id "Phchi.S6G119900"
Phchi.S6	AUGUSTUS	stop_codon	8556406	8556408	.	-	0	transcript_id "Phchi.S6G119900.t1"; gene_id "Phchi.S6G119900"
Phchi.S6	AUGUSTUS	CDS	8556409	8558517	1	-	0	transcript_id "Phchi.S6G119900.t1"; gene_id "Phchi.S6G119900"
Phchi.S6	AUGUSTUS	exon	8556409	8558517	.	-	.	transcript_id "Phchi.S6G119900.t1"; gene_id "Phchi.S6G119900"
Phchi.S6	AUGUSTUS	start_codon	8558515	8558517	.	-	0	transcript_id "Phchi.S6G119900.t1"; gene_id "Phchi.S6G119900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9583.t1 is derived from g6759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42775700	42780898	.	-	.	Phchi.S1G674200
Phchi.S1	AUGUSTUS	transcript	42775700	42780898	.	-	.	transcript_id "Phchi.S1G674200.t1"; gene_id "Phchi.S1G674200"
Phchi.S1	AUGUSTUS	stop_codon	42775697	42775699	.	-	0	transcript_id "Phchi.S1G674200.t1"; gene_id "Phchi.S1G674200"
Phchi.S1	AUGUSTUS	CDS	42775700	42780898	0.19	-	0	transcript_id "Phchi.S1G674200.t1"; gene_id "Phchi.S1G674200"
Phchi.S1	AUGUSTUS	exon	42775700	42780898	.	-	.	transcript_id "Phchi.S1G674200.t1"; gene_id "Phchi.S1G674200"
Phchi.S1	AUGUSTUS	start_codon	42780896	42780898	.	-	0	transcript_id "Phchi.S1G674200.t1"; gene_id "Phchi.S1G674200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14975.t1 is derived from g13443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15807575	15810504	.	+	.	Phchi.S3G229400
Phchi.S3	AUGUSTUS	transcript	15807575	15810504	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	start_codon	15807575	15807577	.	+	0	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15807575	15807647	0.97	+	0	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15807575	15807647	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15807648	15807846	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15807847	15807912	1	+	2	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15807847	15807912	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15807913	15808082	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15808083	15808517	0.97	+	2	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15808083	15808517	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15808518	15808663	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15808664	15808839	1	+	2	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15808664	15808839	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15808840	15808952	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15808953	15809087	1	+	0	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15808953	15809087	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809088	15809248	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809249	15809369	1	+	0	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809249	15809369	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809370	15809559	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809560	15809603	1	+	2	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809560	15809603	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809604	15809683	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809684	15809882	1	+	0	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809684	15809882	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809883	15809978	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809979	15810108	1	+	2	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809979	15810108	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15810109	15810212	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15810213	15810504	0.99	+	1	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15810213	15810504	.	+	.	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	stop_codon	15810505	15810507	.	+	0	transcript_id "Phchi.S3G229400.t1"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	transcript	15807575	15810504	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	start_codon	15807575	15807577	.	+	0	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15807575	15807647	0.97	+	0	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15807575	15807647	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15807648	15807846	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15807847	15807912	1	+	2	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15807847	15807912	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15807913	15808082	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15808083	15808517	0.96	+	2	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15808083	15808517	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15808518	15808663	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15808664	15808839	1	+	2	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15808664	15808839	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15808840	15808952	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15808953	15808970	0.48	+	0	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15808953	15808970	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15808971	15809073	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809074	15809087	0.59	+	0	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809074	15809087	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809088	15809253	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809254	15809369	0.6	+	1	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809254	15809369	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809370	15809559	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809560	15809603	1	+	2	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809560	15809603	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809604	15809683	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809684	15809882	1	+	0	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809684	15809882	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15809883	15809978	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15809979	15810108	0.99	+	2	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15809979	15810108	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	intron	15810109	15810212	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	CDS	15810213	15810504	0.98	+	1	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	exon	15810213	15810504	.	+	.	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
Phchi.S3	AUGUSTUS	stop_codon	15810505	15810507	.	+	0	transcript_id "Phchi.S3G229400.t2"; gene_id "Phchi.S3G229400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15269.t1 is derived from g13737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18038476	18039296	.	-	.	Phchi.S3G258800
Phchi.S3	AUGUSTUS	transcript	18038476	18039296	.	-	.	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	stop_codon	18038473	18038475	.	-	0	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	CDS	18038476	18038730	1	-	0	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	exon	18038476	18038730	.	-	.	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	intron	18038731	18038814	.	-	.	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	CDS	18038815	18038955	1	-	0	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	exon	18038815	18038955	.	-	.	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	intron	18038956	18039050	.	-	.	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	CDS	18039051	18039296	1	-	0	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	exon	18039051	18039296	.	-	.	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
Phchi.S3	AUGUSTUS	start_codon	18039294	18039296	.	-	0	transcript_id "Phchi.S3G258800.t1"; gene_id "Phchi.S3G258800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5861.t1 is derived from g3031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19464089	19465177	.	-	.	Phchi.S1G302000
Phchi.S1	AUGUSTUS	transcript	19464089	19465177	.	-	.	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	stop_codon	19464086	19464088	.	-	0	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	CDS	19464089	19464218	0.99	-	1	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	exon	19464089	19464218	.	-	.	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	intron	19464219	19464359	.	-	.	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	CDS	19464360	19464933	0.92	-	2	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	exon	19464360	19464933	.	-	.	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	intron	19464934	19465083	.	-	.	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	CDS	19465084	19465177	0.9	-	0	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	exon	19465084	19465177	.	-	.	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
Phchi.S1	AUGUSTUS	start_codon	19465175	19465177	.	-	0	transcript_id "Phchi.S1G302000.t1"; gene_id "Phchi.S1G302000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12313.t1 is derived from g7989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10416851	10417285	.	+	.	Phchi.S2G039300
Phchi.S2	AUGUSTUS	transcript	10416851	10417285	.	+	.	transcript_id "Phchi.S2G039300.t1"; gene_id "Phchi.S2G039300"
Phchi.S2	AUGUSTUS	start_codon	10416851	10416853	.	+	0	transcript_id "Phchi.S2G039300.t1"; gene_id "Phchi.S2G039300"
Phchi.S2	AUGUSTUS	CDS	10416851	10417285	0.97	+	0	transcript_id "Phchi.S2G039300.t1"; gene_id "Phchi.S2G039300"
Phchi.S2	AUGUSTUS	exon	10416851	10417285	.	+	.	transcript_id "Phchi.S2G039300.t1"; gene_id "Phchi.S2G039300"
Phchi.S2	AUGUSTUS	stop_codon	10417286	10417288	.	+	0	transcript_id "Phchi.S2G039300.t1"; gene_id "Phchi.S2G039300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3883.t1 is derived from g1052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6200142	6200883	.	-	.	Phchi.S1G104200
Phchi.S1	AUGUSTUS	transcript	6200142	6200883	.	-	.	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	stop_codon	6200139	6200141	.	-	0	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	CDS	6200142	6200587	1	-	2	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	exon	6200142	6200587	.	-	.	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	intron	6200588	6200679	.	-	.	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	CDS	6200680	6200759	1	-	1	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	exon	6200680	6200759	.	-	.	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	intron	6200760	6200842	.	-	.	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	CDS	6200843	6200883	0.93	-	0	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	exon	6200843	6200883	.	-	.	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
Phchi.S1	AUGUSTUS	start_codon	6200881	6200883	.	-	0	transcript_id "Phchi.S1G104200.t1"; gene_id "Phchi.S1G104200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5126.t1 is derived from g2296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15045003	15045623	.	-	.	Phchi.S1G228500
Phchi.S1	AUGUSTUS	transcript	15045003	15045623	.	-	.	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	stop_codon	15045000	15045002	.	-	0	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	CDS	15045003	15045089	1	-	0	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	exon	15045003	15045089	.	-	.	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	intron	15045090	15045479	.	-	.	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	CDS	15045480	15045623	0.91	-	0	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	exon	15045480	15045623	.	-	.	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
Phchi.S1	AUGUSTUS	start_codon	15045621	15045623	.	-	0	transcript_id "Phchi.S1G228500.t1"; gene_id "Phchi.S1G228500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg75.t1 is derived from g9857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	373550	374592	.	-	.	Phchi.S6G003400
Phchi.S6	AUGUSTUS	transcript	373550	374592	.	-	.	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	stop_codon	373547	373549	.	-	0	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	CDS	373550	373569	0.97	-	2	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	exon	373550	373569	.	-	.	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	intron	373570	373661	.	-	.	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	CDS	373662	374592	0.98	-	0	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	exon	373662	374592	.	-	.	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
Phchi.S6	AUGUSTUS	start_codon	374590	374592	.	-	0	transcript_id "Phchi.S6G003400.t1"; gene_id "Phchi.S6G003400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1969.t1 is derived from g8889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4076062	4077383	.	-	.	Phchi.S5G057800
Phchi.S5	AUGUSTUS	transcript	4076062	4077383	.	-	.	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	stop_codon	4076059	4076061	.	-	0	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	CDS	4076062	4077279	0.55	-	0	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	exon	4076062	4077279	.	-	.	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	intron	4077280	4077356	.	-	.	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	CDS	4077357	4077383	1	-	0	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	exon	4077357	4077383	.	-	.	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
Phchi.S5	AUGUSTUS	start_codon	4077381	4077383	.	-	0	transcript_id "Phchi.S5G057800.t1"; gene_id "Phchi.S5G057800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14984.t1 is derived from g13452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15889176	15889997	.	-	.	Phchi.S3G230300
Phchi.S3	AUGUSTUS	transcript	15889176	15889997	.	-	.	transcript_id "Phchi.S3G230300.t1"; gene_id "Phchi.S3G230300"
Phchi.S3	AUGUSTUS	stop_codon	15889173	15889175	.	-	0	transcript_id "Phchi.S3G230300.t1"; gene_id "Phchi.S3G230300"
Phchi.S3	AUGUSTUS	CDS	15889176	15889997	0.81	-	0	transcript_id "Phchi.S3G230300.t1"; gene_id "Phchi.S3G230300"
Phchi.S3	AUGUSTUS	exon	15889176	15889997	.	-	.	transcript_id "Phchi.S3G230300.t1"; gene_id "Phchi.S3G230300"
Phchi.S3	AUGUSTUS	start_codon	15889995	15889997	.	-	0	transcript_id "Phchi.S3G230300.t1"; gene_id "Phchi.S3G230300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2401.t1 is derived from g9321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6489983	6490695	.	-	.	Phchi.S5G101000
Phchi.S5	AUGUSTUS	transcript	6489983	6490695	.	-	.	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	stop_codon	6489980	6489982	.	-	0	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	CDS	6489983	6490188	0.9	-	2	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	exon	6489983	6490188	.	-	.	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	intron	6490189	6490436	.	-	.	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	CDS	6490437	6490695	0.5	-	0	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	exon	6490437	6490695	.	-	.	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
Phchi.S5	AUGUSTUS	start_codon	6490693	6490695	.	-	0	transcript_id "Phchi.S5G101000.t1"; gene_id "Phchi.S5G101000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11732.t1 is derived from g15784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7901260	7902883	.	+	.	Phchi.S4G131400
Phchi.S4	AUGUSTUS	transcript	7901260	7902883	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	start_codon	7901260	7901262	.	+	0	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	CDS	7901260	7901360	0.85	+	0	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	exon	7901260	7901360	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	intron	7901361	7901454	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	CDS	7901455	7902104	0.8	+	1	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	exon	7901455	7902104	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	intron	7902105	7902199	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	CDS	7902200	7902552	0.98	+	2	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	exon	7902200	7902552	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	intron	7902553	7902646	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	CDS	7902647	7902883	1	+	0	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	exon	7902647	7902883	.	+	.	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
Phchi.S4	AUGUSTUS	stop_codon	7902884	7902886	.	+	0	transcript_id "Phchi.S4G131400.t1"; gene_id "Phchi.S4G131400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14747.t1 is derived from g13215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14524468	14525908	.	-	.	Phchi.S3G206600
Phchi.S3	AUGUSTUS	transcript	14524468	14525908	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	stop_codon	14524465	14524467	.	-	0	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	CDS	14524468	14524518	1	-	0	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	exon	14524468	14524518	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	intron	14524519	14524593	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	CDS	14524594	14524707	1	-	0	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	exon	14524594	14524707	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	intron	14524708	14524790	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	CDS	14524791	14524852	1	-	2	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	exon	14524791	14524852	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	intron	14524853	14524932	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	CDS	14524933	14524981	1	-	0	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	exon	14524933	14524981	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	intron	14524982	14525183	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	CDS	14525184	14525310	1	-	1	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	exon	14525184	14525310	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	intron	14525311	14525399	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	CDS	14525400	14525908	0.97	-	0	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	exon	14525400	14525908	.	-	.	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
Phchi.S3	AUGUSTUS	start_codon	14525906	14525908	.	-	0	transcript_id "Phchi.S3G206600.t1"; gene_id "Phchi.S3G206600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7246.t1 is derived from g4418.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27822504	27828899	.	-	.	Phchi.S1G440500
Phchi.S1	AUGUSTUS	transcript	27822504	27828899	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	stop_codon	27822501	27822503	.	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27822504	27822653	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27822504	27822653	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27822654	27822783	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27822784	27822855	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27822784	27822855	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27822856	27823188	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27823189	27823383	0.97	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27823189	27823383	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823384	27823488	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27823489	27823701	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27823489	27823701	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823702	27823803	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27823804	27823968	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27823804	27823968	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823969	27824056	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824057	27824194	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824057	27824194	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824195	27824287	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824288	27824393	1	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824288	27824393	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824394	27824484	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824485	27824652	1	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824485	27824652	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824653	27824744	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824745	27824935	0.99	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824745	27824935	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824936	27825010	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825011	27825238	0.99	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825011	27825238	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825239	27825354	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825355	27825472	0.84	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825355	27825472	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825473	27825574	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825575	27825738	0.97	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825575	27825738	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825739	27825864	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825865	27825978	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825865	27825978	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825979	27826062	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27826063	27826168	1	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27826063	27826168	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27826169	27826274	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27826275	27826362	1	-	2	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27826275	27826362	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27826363	27826531	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27826532	27826852	0.71	-	2	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27826532	27826852	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27826853	27827048	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827049	27827167	1	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827049	27827167	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827168	27827259	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827260	27827394	1	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827260	27827394	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827395	27827506	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827507	27827647	1	-	1	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827507	27827647	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827648	27827741	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827742	27827950	1	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827742	27827950	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827951	27828049	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27828050	27828507	0.82	-	2	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27828050	27828507	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27828508	27828698	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27828699	27828762	0.67	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27828699	27828762	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27828763	27828851	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27828852	27828899	0.98	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27828852	27828899	.	-	.	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	start_codon	27828897	27828899	.	-	0	transcript_id "Phchi.S1G440500.t1"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	transcript	27822504	27828899	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	stop_codon	27822501	27822503	.	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27822504	27822653	1	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27822504	27822653	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27822654	27822783	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27822784	27822855	0.57	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27822784	27822855	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27822856	27822945	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27822946	27823050	0.5	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27822946	27823050	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823051	27823188	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27823189	27823383	0.92	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27823189	27823383	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823384	27823488	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27823489	27823701	1	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27823489	27823701	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823702	27823803	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27823804	27823968	0.98	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27823804	27823968	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27823969	27824056	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824057	27824194	1	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824057	27824194	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824195	27824287	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824288	27824393	1	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824288	27824393	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824394	27824484	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824485	27824652	1	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824485	27824652	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824653	27824744	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27824745	27824935	1	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27824745	27824935	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27824936	27825010	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825011	27825238	0.99	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825011	27825238	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825239	27825354	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825355	27825472	0.79	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825355	27825472	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825473	27825574	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825575	27825738	0.98	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825575	27825738	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825739	27825864	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27825865	27825978	0.99	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27825865	27825978	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27825979	27826062	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27826063	27826168	1	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27826063	27826168	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27826169	27826274	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27826275	27826362	1	-	2	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27826275	27826362	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27826363	27826531	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27826532	27826693	1	-	2	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27826532	27826693	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27826694	27827048	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827049	27827167	1	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827049	27827167	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827168	27827259	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827260	27827394	1	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827260	27827394	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827395	27827506	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827507	27827647	1	-	1	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827507	27827647	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827648	27827741	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27827742	27827950	1	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27827742	27827950	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27827951	27828049	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27828050	27828507	0.82	-	2	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27828050	27828507	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27828508	27828698	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27828699	27828762	0.67	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27828699	27828762	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	intron	27828763	27828851	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	CDS	27828852	27828899	0.98	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	exon	27828852	27828899	.	-	.	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
Phchi.S1	AUGUSTUS	start_codon	27828897	27828899	.	-	0	transcript_id "Phchi.S1G440500.t2"; gene_id "Phchi.S1G440500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7735.t1 is derived from g4909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30891987	30894354	.	+	.	Phchi.S1G489400
Phchi.S1	AUGUSTUS	transcript	30891987	30894354	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	start_codon	30891987	30891989	.	+	0	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	CDS	30891987	30892923	1	+	0	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	exon	30891987	30892923	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	intron	30892924	30893119	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	CDS	30893120	30893322	1	+	2	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	exon	30893120	30893322	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	intron	30893323	30893415	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	CDS	30893416	30893574	1	+	0	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	exon	30893416	30893574	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	intron	30893575	30893892	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	CDS	30893893	30894354	1	+	0	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	exon	30893893	30894354	.	+	.	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
Phchi.S1	AUGUSTUS	stop_codon	30894355	30894357	.	+	0	transcript_id "Phchi.S1G489400.t1"; gene_id "Phchi.S1G489400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5917.t1 is derived from g3088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19865911	19868507	.	+	.	Phchi.S1G307600
Phchi.S1	AUGUSTUS	transcript	19865911	19868507	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	start_codon	19865911	19865913	.	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19865911	19866066	1	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19865911	19866066	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19866067	19866162	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19866163	19866298	1	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19866163	19866298	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19866299	19866392	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19866393	19866480	1	+	2	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19866393	19866480	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19866481	19866608	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19866609	19866773	1	+	1	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19866609	19866773	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19866774	19867048	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19867049	19867180	1	+	1	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19867049	19867180	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19867181	19867255	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19867256	19867377	0.68	+	1	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19867256	19867377	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19867378	19867491	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19867492	19867589	0.57	+	2	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19867492	19867589	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19867590	19867693	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19867694	19867768	0.99	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19867694	19867768	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19867769	19867955	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19867956	19868015	1	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19867956	19868015	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19868016	19868116	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19868117	19868181	0.71	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19868117	19868181	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19868182	19868284	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19868285	19868375	0.67	+	1	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19868285	19868375	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	intron	19868376	19868462	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	CDS	19868463	19868507	0.69	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	exon	19868463	19868507	.	+	.	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
Phchi.S1	AUGUSTUS	stop_codon	19868508	19868510	.	+	0	transcript_id "Phchi.S1G307600.t1"; gene_id "Phchi.S1G307600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2998.t1 is derived from g167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1076976	1077797	.	+	.	Phchi.S1G015700
Phchi.S1	AUGUSTUS	transcript	1076976	1077797	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	start_codon	1076976	1076978	.	+	0	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	CDS	1076976	1076978	1	+	0	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	exon	1076976	1076978	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	intron	1076979	1077110	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	CDS	1077111	1077271	1	+	0	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	exon	1077111	1077271	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	intron	1077272	1077422	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	CDS	1077423	1077611	1	+	1	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	exon	1077423	1077611	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	intron	1077612	1077694	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	CDS	1077695	1077797	1	+	1	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	exon	1077695	1077797	.	+	.	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
Phchi.S1	AUGUSTUS	stop_codon	1077798	1077800	.	+	0	transcript_id "Phchi.S1G015700.t1"; gene_id "Phchi.S1G015700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9735.t1 is derived from g6911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43450406	43454029	.	-	.	Phchi.S1G689400
Phchi.S1	AUGUSTUS	transcript	43450406	43454029	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	stop_codon	43450403	43450405	.	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43450406	43450554	1	-	2	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43450406	43450554	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43450555	43450639	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43450640	43450718	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43450640	43450718	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43450719	43450855	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43450856	43451041	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43450856	43451041	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43451042	43451122	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43451123	43451239	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43451123	43451239	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43451240	43451348	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43451349	43451508	1	-	1	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43451349	43451508	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43451509	43451607	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43451608	43451762	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43451608	43451762	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43451763	43451856	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43451857	43452054	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43451857	43452054	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43452055	43452148	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43452149	43452241	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43452149	43452241	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43452242	43452339	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43452340	43452429	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43452340	43452429	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43452430	43452573	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43452574	43452679	1	-	1	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43452574	43452679	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43452680	43452798	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43452799	43452893	0.97	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43452799	43452893	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43452894	43452998	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43452999	43453082	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43452999	43453082	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43453083	43453236	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43453237	43453367	1	-	2	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43453237	43453367	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43453368	43453447	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43453448	43453553	1	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43453448	43453553	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	intron	43453554	43453678	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	CDS	43453679	43454029	0.89	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	exon	43453679	43454029	.	-	.	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
Phchi.S1	AUGUSTUS	start_codon	43454027	43454029	.	-	0	transcript_id "Phchi.S1G689400.t1"; gene_id "Phchi.S1G689400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11476.t1 is derived from g15526.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6549678	6559268	.	+	.	Phchi.S4G105800
Phchi.S4	AUGUSTUS	transcript	6549678	6559268	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	start_codon	6549678	6549680	.	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6549678	6549680	0.92	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6549678	6549680	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6549681	6550318	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550319	6550373	0.69	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550319	6550373	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6550374	6550508	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550509	6550546	0.48	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550509	6550546	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6550547	6550625	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550626	6550671	0.96	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550626	6550671	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6550672	6550763	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550764	6552287	0.81	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550764	6552287	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6552288	6552547	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6552548	6552687	0.49	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6552548	6552687	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6552688	6552826	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6552827	6553040	0.54	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6552827	6553040	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6553041	6553268	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6553269	6553787	0.65	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6553269	6553787	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6553788	6553965	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6553966	6554510	0.79	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6553966	6554510	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6554511	6554606	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6554607	6554662	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6554607	6554662	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6554663	6554827	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6554828	6555056	1	+	1	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6554828	6555056	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555057	6555191	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555192	6555320	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555192	6555320	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555321	6555413	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555414	6555482	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555414	6555482	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555483	6555577	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555578	6555646	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555578	6555646	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555647	6555752	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555753	6555829	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555753	6555829	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555830	6555957	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555958	6556050	1	+	1	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555958	6556050	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556051	6556166	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556167	6556308	1	+	1	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556167	6556308	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556309	6556451	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556452	6556557	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556452	6556557	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556558	6556642	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556643	6556742	1	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556643	6556742	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556743	6556856	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556857	6556981	1	+	1	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556857	6556981	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556982	6557057	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557058	6557203	1	+	2	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557058	6557203	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557204	6557321	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557322	6557432	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557322	6557432	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557433	6557520	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557521	6557588	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557521	6557588	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557589	6557686	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557687	6557909	1	+	1	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557687	6557909	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557910	6558024	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558025	6558099	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558025	6558099	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558100	6558211	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558212	6558262	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558212	6558262	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558263	6558374	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558375	6558464	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558375	6558464	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558465	6558567	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558568	6558654	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558568	6558654	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558655	6558827	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558828	6558902	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558828	6558902	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558903	6558984	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558985	6559097	1	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558985	6559097	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6559098	6559189	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6559190	6559268	1	+	1	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6559190	6559268	.	+	.	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	stop_codon	6559269	6559271	.	+	0	transcript_id "Phchi.S4G105800.t1"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	transcript	6549678	6559268	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	start_codon	6549678	6549680	.	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6549678	6549680	0.93	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6549678	6549680	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6549681	6550318	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550319	6550373	0.68	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550319	6550373	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6550374	6550508	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550509	6550546	0.38	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550509	6550546	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6550547	6550625	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550626	6550671	0.96	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550626	6550671	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6550672	6550763	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6550764	6552287	0.92	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6550764	6552287	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6552288	6552547	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6552548	6552687	0.45	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6552548	6552687	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6552688	6552826	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6552827	6553040	0.45	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6552827	6553040	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6553041	6553265	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6553266	6553787	0.61	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6553266	6553787	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6553788	6553965	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6553966	6554510	0.71	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6553966	6554510	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6554511	6554606	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6554607	6554662	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6554607	6554662	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6554663	6554827	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6554828	6555056	1	+	1	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6554828	6555056	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555057	6555191	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555192	6555320	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555192	6555320	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555321	6555413	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555414	6555482	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555414	6555482	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555483	6555577	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555578	6555646	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555578	6555646	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555647	6555752	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555753	6555829	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555753	6555829	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6555830	6555957	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6555958	6556050	1	+	1	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6555958	6556050	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556051	6556166	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556167	6556308	1	+	1	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556167	6556308	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556309	6556451	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556452	6556557	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556452	6556557	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556558	6556642	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556643	6556742	1	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556643	6556742	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556743	6556856	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6556857	6556981	1	+	1	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6556857	6556981	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6556982	6557057	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557058	6557203	1	+	2	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557058	6557203	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557204	6557321	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557322	6557432	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557322	6557432	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557433	6557520	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557521	6557588	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557521	6557588	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557589	6557686	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6557687	6557909	1	+	1	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6557687	6557909	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6557910	6558024	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558025	6558099	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558025	6558099	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558100	6558211	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558212	6558262	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558212	6558262	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558263	6558374	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558375	6558464	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558375	6558464	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558465	6558567	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558568	6558654	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558568	6558654	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558655	6558827	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558828	6558902	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558828	6558902	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6558903	6558984	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6558985	6559097	1	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6558985	6559097	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	intron	6559098	6559189	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	CDS	6559190	6559268	0.99	+	1	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	exon	6559190	6559268	.	+	.	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
Phchi.S4	AUGUSTUS	stop_codon	6559269	6559271	.	+	0	transcript_id "Phchi.S4G105800.t2"; gene_id "Phchi.S4G105800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7615.t1 is derived from g4789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30268036	30269031	.	-	.	Phchi.S1G477400
Phchi.S1	AUGUSTUS	transcript	30268036	30269031	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	stop_codon	30268033	30268035	.	-	0	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	CDS	30268036	30268361	0.99	-	2	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	exon	30268036	30268361	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	intron	30268362	30268444	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	CDS	30268445	30268558	0.93	-	2	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	exon	30268445	30268558	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	intron	30268559	30268665	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	CDS	30268666	30268753	0.81	-	0	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	exon	30268666	30268753	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	intron	30268754	30268872	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	CDS	30268873	30269031	0.2	-	0	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	exon	30268873	30269031	.	-	.	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
Phchi.S1	AUGUSTUS	start_codon	30269029	30269031	.	-	0	transcript_id "Phchi.S1G477400.t1"; gene_id "Phchi.S1G477400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4704.t1 is derived from g1874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12403567	12404884	.	+	.	Phchi.S1G186300
Phchi.S1	AUGUSTUS	transcript	12403567	12404884	.	+	.	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	start_codon	12403567	12403569	.	+	0	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	CDS	12403567	12404119	0.67	+	0	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	exon	12403567	12404119	.	+	.	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	intron	12404120	12404211	.	+	.	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	CDS	12404212	12404378	0.56	+	2	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	exon	12404212	12404378	.	+	.	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	intron	12404379	12404467	.	+	.	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	CDS	12404468	12404884	0.57	+	0	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	exon	12404468	12404884	.	+	.	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
Phchi.S1	AUGUSTUS	stop_codon	12404885	12404887	.	+	0	transcript_id "Phchi.S1G186300.t1"; gene_id "Phchi.S1G186300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10170.t1 is derived from g7346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46087124	46089669	.	+	.	Phchi.S1G732900
Phchi.S1	AUGUSTUS	transcript	46087124	46089669	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	start_codon	46087124	46087126	.	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46087124	46087162	0.99	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46087124	46087162	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46087163	46087248	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46087249	46087330	1	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46087249	46087330	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46087331	46087400	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46087401	46087469	1	+	2	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46087401	46087469	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46087470	46087603	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46087604	46087648	1	+	2	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46087604	46087648	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46087649	46087726	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46087727	46087849	1	+	2	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46087727	46087849	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46087850	46087942	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46087943	46088088	0.69	+	2	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46087943	46088088	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46088089	46088205	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46088206	46088353	0.69	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46088206	46088353	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46088354	46088559	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46088560	46088643	1	+	2	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46088560	46088643	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46088644	46088835	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46088836	46088951	1	+	2	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46088836	46088951	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46088952	46089049	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46089050	46089108	1	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46089050	46089108	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46089109	46089192	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46089193	46089283	1	+	1	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46089193	46089283	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46089284	46089374	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46089375	46089529	1	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46089375	46089529	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	intron	46089530	46089611	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	CDS	46089612	46089669	1	+	1	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	exon	46089612	46089669	.	+	.	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
Phchi.S1	AUGUSTUS	stop_codon	46089670	46089672	.	+	0	transcript_id "Phchi.S1G732900.t1"; gene_id "Phchi.S1G732900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9213.t1 is derived from g6388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40442963	40443631	.	-	.	Phchi.S1G637200
Phchi.S1	AUGUSTUS	transcript	40442963	40443631	.	-	.	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	stop_codon	40442960	40442962	.	-	0	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	CDS	40442963	40443110	0.99	-	1	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	exon	40442963	40443110	.	-	.	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	intron	40443111	40443224	.	-	.	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	CDS	40443225	40443631	0.77	-	0	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	exon	40443225	40443631	.	-	.	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
Phchi.S1	AUGUSTUS	start_codon	40443629	40443631	.	-	0	transcript_id "Phchi.S1G637200.t1"; gene_id "Phchi.S1G637200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7614.t1 is derived from g4788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30265319	30267452	.	-	.	Phchi.S1G477300
Phchi.S1	AUGUSTUS	transcript	30265319	30267452	.	-	.	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	stop_codon	30265316	30265318	.	-	0	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	CDS	30265319	30265728	0.98	-	2	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	exon	30265319	30265728	.	-	.	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	intron	30265729	30265840	.	-	.	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	CDS	30265841	30267452	0.55	-	0	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	exon	30265841	30267452	.	-	.	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
Phchi.S1	AUGUSTUS	start_codon	30267450	30267452	.	-	0	transcript_id "Phchi.S1G477300.t1"; gene_id "Phchi.S1G477300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8025.t1 is derived from g5200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32546939	32547412	.	-	.	Phchi.S1G518400
Phchi.S1	AUGUSTUS	transcript	32546939	32547412	.	-	.	transcript_id "Phchi.S1G518400.t1"; gene_id "Phchi.S1G518400"
Phchi.S1	AUGUSTUS	stop_codon	32546936	32546938	.	-	0	transcript_id "Phchi.S1G518400.t1"; gene_id "Phchi.S1G518400"
Phchi.S1	AUGUSTUS	CDS	32546939	32547412	0.3	-	0	transcript_id "Phchi.S1G518400.t1"; gene_id "Phchi.S1G518400"
Phchi.S1	AUGUSTUS	exon	32546939	32547412	.	-	.	transcript_id "Phchi.S1G518400.t1"; gene_id "Phchi.S1G518400"
Phchi.S1	AUGUSTUS	start_codon	32547410	32547412	.	-	0	transcript_id "Phchi.S1G518400.t1"; gene_id "Phchi.S1G518400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg870.t1 is derived from g10652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6001466	6002091	.	+	.	Phchi.S6G082900
Phchi.S6	AUGUSTUS	transcript	6001466	6002091	.	+	.	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	start_codon	6001466	6001468	.	+	0	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	CDS	6001466	6001792	0.36	+	0	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	exon	6001466	6001792	.	+	.	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	intron	6001793	6002037	.	+	.	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	CDS	6002038	6002091	0.43	+	0	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	exon	6002038	6002091	.	+	.	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
Phchi.S6	AUGUSTUS	stop_codon	6002092	6002094	.	+	0	transcript_id "Phchi.S6G082900.t1"; gene_id "Phchi.S6G082900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7662.t1 is derived from g4836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30489584	30491712	.	-	.	Phchi.S1G482100
Phchi.S1	AUGUSTUS	transcript	30489584	30491712	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	stop_codon	30489581	30489583	.	-	0	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30489584	30489776	0.85	-	1	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30489584	30489776	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30489777	30489860	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30489861	30489943	1	-	0	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30489861	30489943	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30489944	30490088	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30490089	30490242	0.82	-	1	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30490089	30490242	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30490243	30490370	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30490371	30490392	0.72	-	2	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30490371	30490392	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30490393	30490463	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30490464	30490519	0.54	-	1	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30490464	30490519	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30490520	30490651	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30490652	30490773	1	-	0	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30490652	30490773	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30490774	30490924	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30490925	30491029	1	-	0	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30490925	30491029	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	intron	30491030	30491232	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	CDS	30491233	30491712	0.82	-	0	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	exon	30491233	30491712	.	-	.	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
Phchi.S1	AUGUSTUS	start_codon	30491710	30491712	.	-	0	transcript_id "Phchi.S1G482100.t1"; gene_id "Phchi.S1G482100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4428.t1 is derived from g1597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10444588	10446457	.	+	.	Phchi.S1G158700
Phchi.S1	AUGUSTUS	transcript	10444588	10446457	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	start_codon	10444588	10444590	.	+	0	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	CDS	10444588	10444714	0.75	+	0	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	exon	10444588	10444714	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	intron	10444715	10444835	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	CDS	10444836	10444890	1	+	2	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	exon	10444836	10444890	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	intron	10444891	10444980	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	CDS	10444981	10445125	1	+	1	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	exon	10444981	10445125	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	intron	10445126	10445253	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	CDS	10445254	10445584	0.99	+	0	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	exon	10445254	10445584	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	intron	10445585	10445676	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	CDS	10445677	10445811	1	+	2	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	exon	10445677	10445811	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	intron	10445812	10445954	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	CDS	10445955	10446457	0.99	+	2	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	exon	10445955	10446457	.	+	.	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
Phchi.S1	AUGUSTUS	stop_codon	10446458	10446460	.	+	0	transcript_id "Phchi.S1G158700.t1"; gene_id "Phchi.S1G158700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14934.t1 is derived from g13402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15601631	15604278	.	-	.	Phchi.S3G225300
Phchi.S3	AUGUSTUS	transcript	15601631	15604278	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	stop_codon	15601628	15601630	.	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15601631	15601710	0.95	-	2	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15601631	15601710	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15601711	15601831	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15601832	15601910	1	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15601832	15601910	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15601911	15601984	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15601985	15602057	1	-	1	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15601985	15602057	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15602058	15602192	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15602193	15602339	1	-	1	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15602193	15602339	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15602340	15602455	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15602456	15602503	0.96	-	1	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15602456	15602503	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15602504	15602604	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15602605	15602684	0.99	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15602605	15602684	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15602685	15602805	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15602806	15603133	1	-	1	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15602806	15603133	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15603134	15603255	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15603256	15603310	1	-	2	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15603256	15603310	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15603311	15603402	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15603403	15603475	1	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15603403	15603475	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15603476	15603654	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15603655	15603793	1	-	1	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15603655	15603793	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15603794	15603916	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15603917	15603990	1	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15603917	15603990	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	intron	15603991	15604092	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	CDS	15604093	15604278	0.6	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	exon	15604093	15604278	.	-	.	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
Phchi.S3	AUGUSTUS	start_codon	15604276	15604278	.	-	0	transcript_id "Phchi.S3G225300.t1"; gene_id "Phchi.S3G225300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11802.t1 is derived from g15854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8212644	8213206	.	+	.	Phchi.S4G138400
Phchi.S4	AUGUSTUS	transcript	8212644	8213206	.	+	.	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	start_codon	8212644	8212646	.	+	0	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	CDS	8212644	8212675	0.66	+	0	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	exon	8212644	8212675	.	+	.	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	intron	8212676	8213022	.	+	.	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	CDS	8213023	8213206	0.75	+	1	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	exon	8213023	8213206	.	+	.	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
Phchi.S4	AUGUSTUS	stop_codon	8213207	8213209	.	+	0	transcript_id "Phchi.S4G138400.t1"; gene_id "Phchi.S4G138400"
# This transcript jg593.t2 is derived from g10375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg594.t1 is derived from g10376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4331555	4332449	.	+	.	Phchi.S6G055300
Phchi.S6	AUGUSTUS	transcript	4331555	4332449	.	+	.	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	start_codon	4331555	4331557	.	+	0	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	CDS	4331555	4331703	0.98	+	0	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	exon	4331555	4331703	.	+	.	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	intron	4331704	4331801	.	+	.	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	CDS	4331802	4331822	1	+	1	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	exon	4331802	4331822	.	+	.	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	intron	4331823	4331938	.	+	.	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	CDS	4331939	4332449	1	+	1	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	exon	4331939	4332449	.	+	.	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
Phchi.S6	AUGUSTUS	stop_codon	4332450	4332452	.	+	0	transcript_id "Phchi.S6G055300.t1"; gene_id "Phchi.S6G055300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14865.t1 is derived from g13333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15099740	15100397	.	-	.	Phchi.S3G218400
Phchi.S3	AUGUSTUS	transcript	15099740	15100397	.	-	.	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	stop_codon	15099737	15099739	.	-	0	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	CDS	15099740	15099762	0.42	-	2	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	exon	15099740	15099762	.	-	.	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	intron	15099763	15099952	.	-	.	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	CDS	15099953	15100016	0.42	-	0	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	exon	15099953	15100016	.	-	.	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	intron	15100017	15100100	.	-	.	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	CDS	15100101	15100397	0.3	-	0	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	exon	15100101	15100397	.	-	.	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
Phchi.S3	AUGUSTUS	start_codon	15100395	15100397	.	-	0	transcript_id "Phchi.S3G218400.t1"; gene_id "Phchi.S3G218400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15584.t1 is derived from g14053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20130787	20132931	.	-	.	Phchi.S3G290300
Phchi.S3	AUGUSTUS	transcript	20130787	20132931	.	-	.	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	stop_codon	20130784	20130786	.	-	0	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	CDS	20130787	20130816	0.93	-	0	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	exon	20130787	20130816	.	-	.	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	intron	20130817	20130940	.	-	.	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	CDS	20130941	20132031	0.54	-	2	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	exon	20130941	20132031	.	-	.	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	intron	20132032	20132138	.	-	.	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	CDS	20132139	20132931	0.69	-	0	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	exon	20132139	20132931	.	-	.	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
Phchi.S3	AUGUSTUS	start_codon	20132929	20132931	.	-	0	transcript_id "Phchi.S3G290300.t1"; gene_id "Phchi.S3G290300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15762.t1 is derived from g14232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21112070	21114084	.	+	.	Phchi.S3G308100
Phchi.S3	AUGUSTUS	transcript	21112070	21114084	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	start_codon	21112070	21112072	.	+	0	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	CDS	21112070	21112119	0.43	+	0	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	exon	21112070	21112119	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	intron	21112120	21112583	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	CDS	21112584	21112681	0.81	+	1	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	exon	21112584	21112681	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	intron	21112682	21112775	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	CDS	21112776	21112922	0.81	+	2	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	exon	21112776	21112922	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	intron	21112923	21113023	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	CDS	21113024	21113296	1	+	2	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	exon	21113024	21113296	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	intron	21113297	21113503	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	CDS	21113504	21113821	1	+	2	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	exon	21113504	21113821	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	intron	21113822	21113917	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	CDS	21113918	21114084	1	+	2	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	exon	21113918	21114084	.	+	.	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
Phchi.S3	AUGUSTUS	stop_codon	21114085	21114087	.	+	0	transcript_id "Phchi.S3G308100.t1"; gene_id "Phchi.S3G308100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9766.t1 is derived from g6942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43592617	43593053	.	-	.	Phchi.S1G692500
Phchi.S1	AUGUSTUS	transcript	43592617	43593053	.	-	.	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	stop_codon	43592614	43592616	.	-	0	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	CDS	43592617	43592649	1	-	0	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	exon	43592617	43592649	.	-	.	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	intron	43592650	43592733	.	-	.	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	CDS	43592734	43592904	1	-	0	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	exon	43592734	43592904	.	-	.	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	intron	43592905	43592996	.	-	.	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	CDS	43592997	43593053	0.96	-	0	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	exon	43592997	43593053	.	-	.	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
Phchi.S1	AUGUSTUS	start_codon	43593051	43593053	.	-	0	transcript_id "Phchi.S1G692500.t1"; gene_id "Phchi.S1G692500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15381.t1 is derived from g13849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18723267	18725244	.	+	.	Phchi.S3G270000
Phchi.S3	AUGUSTUS	transcript	18723267	18725244	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	start_codon	18723267	18723269	.	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18723267	18723308	1	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18723267	18723308	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18723309	18723678	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18723679	18723804	1	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18723679	18723804	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18723805	18723936	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18723937	18724083	1	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18723937	18724083	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18724084	18724182	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18724183	18724278	1	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18724183	18724278	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18724279	18724358	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18724359	18724454	1	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18724359	18724454	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18724455	18724545	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18724546	18724642	1	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18724546	18724642	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18724643	18724753	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18724754	18724871	1	+	2	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18724754	18724871	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18724872	18724960	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18724961	18725033	1	+	1	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18724961	18725033	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	intron	18725034	18725142	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	CDS	18725143	18725244	0.96	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	exon	18725143	18725244	.	+	.	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
Phchi.S3	AUGUSTUS	stop_codon	18725245	18725247	.	+	0	transcript_id "Phchi.S3G270000.t1"; gene_id "Phchi.S3G270000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4282.t1 is derived from g1451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9393986	9394580	.	-	.	Phchi.S1G144100
Phchi.S1	AUGUSTUS	transcript	9393986	9394580	.	-	.	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	stop_codon	9393983	9393985	.	-	0	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	CDS	9393986	9394356	0.54	-	2	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	exon	9393986	9394356	.	-	.	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	intron	9394357	9394456	.	-	.	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	CDS	9394457	9394580	0.62	-	0	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	exon	9394457	9394580	.	-	.	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
Phchi.S1	AUGUSTUS	start_codon	9394578	9394580	.	-	0	transcript_id "Phchi.S1G144100.t1"; gene_id "Phchi.S1G144100"
# This transcript jg9889.t2 is derived from g7065.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9890.t1 is derived from g7066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44290670	44294495	.	-	.	Phchi.S1G704900
Phchi.S1	AUGUSTUS	transcript	44290670	44294495	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	stop_codon	44290667	44290669	.	-	0	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44290670	44290947	0.89	-	2	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44290670	44290947	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44290948	44291023	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44291024	44291083	0.99	-	2	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44291024	44291083	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44291084	44291191	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44291192	44292968	0.97	-	0	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44291192	44292968	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44292969	44293154	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44293155	44293250	0.98	-	0	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44293155	44293250	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44293251	44293366	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44293367	44293419	0.9	-	2	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44293367	44293419	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44293420	44293562	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44293563	44293724	0.93	-	2	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44293563	44293724	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44293725	44294162	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44294163	44294250	1	-	0	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44294163	44294250	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	intron	44294251	44294462	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	CDS	44294463	44294495	0.98	-	0	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	exon	44294463	44294495	.	-	.	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
Phchi.S1	AUGUSTUS	start_codon	44294493	44294495	.	-	0	transcript_id "Phchi.S1G704900.t1"; gene_id "Phchi.S1G704900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13597.t1 is derived from g12064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7629676	7636967	.	-	.	Phchi.S3G091600
Phchi.S3	AUGUSTUS	transcript	7629676	7636967	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	stop_codon	7629673	7629675	.	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7629676	7630140	0.48	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7629676	7630140	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7630141	7630302	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7630303	7630500	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7630303	7630500	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7630501	7630591	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7630592	7630795	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7630592	7630795	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7630796	7630935	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7630936	7631092	1	-	1	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7630936	7631092	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7631093	7631192	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7631193	7631287	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7631193	7631287	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7631288	7631376	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7631377	7631484	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7631377	7631484	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7631485	7631583	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7631584	7631847	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7631584	7631847	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7631848	7632001	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7632002	7632547	0.88	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7632002	7632547	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7632548	7632668	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7632669	7632815	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7632669	7632815	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7632816	7632967	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7632968	7633192	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7632968	7633192	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7633193	7633294	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7633295	7633352	1	-	1	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7633295	7633352	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7633353	7633428	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7633429	7633590	1	-	1	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7633429	7633590	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7633591	7633732	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7633733	7633858	1	-	1	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7633733	7633858	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7633859	7634018	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7634019	7634191	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7634019	7634191	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7634192	7634287	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7634288	7634368	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7634288	7634368	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7634369	7634507	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7634508	7634616	1	-	1	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7634508	7634616	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7634617	7634765	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7634766	7635205	0.99	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7634766	7635205	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7635206	7635324	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7635325	7635435	0.98	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7635325	7635435	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7635436	7635521	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7635522	7635722	1	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7635522	7635722	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7635723	7635885	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7635886	7636177	0.28	-	1	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7635886	7636177	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	intron	7636178	7636260	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	CDS	7636261	7636967	0.13	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	exon	7636261	7636967	.	-	.	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
Phchi.S3	AUGUSTUS	start_codon	7636965	7636967	.	-	0	transcript_id "Phchi.S3G091600.t1"; gene_id "Phchi.S3G091600"
# This transcript jg11182.t2 is derived from g15232.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11182.t3 is derived from g15232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11182.t4 is derived from g15232.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11182.t5 is derived from g15232.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11183.t1 is derived from g15233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4535690	4537102	.	-	.	Phchi.S4G076500
Phchi.S4	AUGUSTUS	transcript	4535690	4537102	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	stop_codon	4535687	4535689	.	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4535690	4535748	0.9	-	2	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4535690	4535748	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	intron	4535749	4535846	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4535847	4535985	1	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4535847	4535985	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	intron	4535986	4536077	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4536078	4536134	1	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4536078	4536134	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	intron	4536135	4536336	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4536337	4536471	1	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4536337	4536471	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	intron	4536472	4536613	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4536614	4536700	0.89	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4536614	4536700	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	intron	4536701	4536900	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4536901	4536940	0.81	-	1	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4536901	4536940	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	intron	4536941	4537076	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	CDS	4537077	4537102	1	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	exon	4537077	4537102	.	-	.	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
Phchi.S4	AUGUSTUS	start_codon	4537100	4537102	.	-	0	transcript_id "Phchi.S4G076500.t1"; gene_id "Phchi.S4G076500"
# This transcript jg278.t2 is derived from g10060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg279.t1 is derived from g10061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2008032	2008310	.	-	.	Phchi.S6G023800
Phchi.S6	AUGUSTUS	transcript	2008032	2008310	.	-	.	transcript_id "Phchi.S6G023800.t1"; gene_id "Phchi.S6G023800"
Phchi.S6	AUGUSTUS	stop_codon	2008029	2008031	.	-	0	transcript_id "Phchi.S6G023800.t1"; gene_id "Phchi.S6G023800"
Phchi.S6	AUGUSTUS	CDS	2008032	2008310	0.88	-	0	transcript_id "Phchi.S6G023800.t1"; gene_id "Phchi.S6G023800"
Phchi.S6	AUGUSTUS	exon	2008032	2008310	.	-	.	transcript_id "Phchi.S6G023800.t1"; gene_id "Phchi.S6G023800"
Phchi.S6	AUGUSTUS	start_codon	2008308	2008310	.	-	0	transcript_id "Phchi.S6G023800.t1"; gene_id "Phchi.S6G023800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10907.t1 is derived from g14957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2864027	2866538	.	-	.	Phchi.S4G048900
Phchi.S4	AUGUSTUS	transcript	2864027	2866538	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	stop_codon	2864024	2864026	.	-	0	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	CDS	2864027	2864754	0.95	-	2	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	exon	2864027	2864754	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	intron	2864755	2864832	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	CDS	2864833	2864913	1	-	2	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	exon	2864833	2864913	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	intron	2864914	2865013	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	CDS	2865014	2865180	1	-	1	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	exon	2865014	2865180	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	intron	2865181	2865698	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	CDS	2865699	2865812	0.85	-	1	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	exon	2865699	2865812	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	intron	2865813	2865975	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	CDS	2865976	2866538	0.77	-	0	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	exon	2865976	2866538	.	-	.	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
Phchi.S4	AUGUSTUS	start_codon	2866536	2866538	.	-	0	transcript_id "Phchi.S4G048900.t1"; gene_id "Phchi.S4G048900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9631.t1 is derived from g6807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42991196	42993004	.	+	.	Phchi.S1G679000
Phchi.S1	AUGUSTUS	transcript	42991196	42993004	.	+	.	transcript_id "Phchi.S1G679000.t1"; gene_id "Phchi.S1G679000"
Phchi.S1	AUGUSTUS	start_codon	42991196	42991198	.	+	0	transcript_id "Phchi.S1G679000.t1"; gene_id "Phchi.S1G679000"
Phchi.S1	AUGUSTUS	CDS	42991196	42993004	0.52	+	0	transcript_id "Phchi.S1G679000.t1"; gene_id "Phchi.S1G679000"
Phchi.S1	AUGUSTUS	exon	42991196	42993004	.	+	.	transcript_id "Phchi.S1G679000.t1"; gene_id "Phchi.S1G679000"
Phchi.S1	AUGUSTUS	stop_codon	42993005	42993007	.	+	0	transcript_id "Phchi.S1G679000.t1"; gene_id "Phchi.S1G679000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5272.t1 is derived from g2442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15987472	15988098	.	-	.	Phchi.S1G243100
Phchi.S1	AUGUSTUS	transcript	15987472	15988098	.	-	.	transcript_id "Phchi.S1G243100.t1"; gene_id "Phchi.S1G243100"
Phchi.S1	AUGUSTUS	stop_codon	15987469	15987471	.	-	0	transcript_id "Phchi.S1G243100.t1"; gene_id "Phchi.S1G243100"
Phchi.S1	AUGUSTUS	CDS	15987472	15988098	0.46	-	0	transcript_id "Phchi.S1G243100.t1"; gene_id "Phchi.S1G243100"
Phchi.S1	AUGUSTUS	exon	15987472	15988098	.	-	.	transcript_id "Phchi.S1G243100.t1"; gene_id "Phchi.S1G243100"
Phchi.S1	AUGUSTUS	start_codon	15988096	15988098	.	-	0	transcript_id "Phchi.S1G243100.t1"; gene_id "Phchi.S1G243100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8140.t1 is derived from g5315.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33873081	33876998	.	+	.	Phchi.S1G529900
Phchi.S1	AUGUSTUS	transcript	33873081	33876998	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	start_codon	33873081	33873083	.	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873081	33873154	0.95	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873081	33873154	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873155	33873231	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873232	33873329	1	+	1	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873232	33873329	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873330	33873414	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873415	33873550	1	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873415	33873550	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873551	33873709	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873710	33873738	1	+	1	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873710	33873738	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873739	33874019	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874020	33874116	1	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874020	33874116	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874117	33874360	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874361	33874416	1	+	1	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874361	33874416	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874417	33874605	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874606	33874713	1	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874606	33874713	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874714	33874825	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874826	33874882	1	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874826	33874882	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874883	33875045	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875046	33875137	1	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875046	33875137	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875138	33875338	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875339	33875423	1	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875339	33875423	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875424	33875660	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875661	33875813	0.9	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875661	33875813	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875814	33875925	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875926	33876029	0.98	+	2	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875926	33876029	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876030	33876230	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876231	33876398	1	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876231	33876398	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876399	33876515	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876516	33876619	0.96	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876516	33876619	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876620	33876720	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876721	33876778	0.93	+	1	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876721	33876778	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876779	33876869	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876870	33876998	1	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876870	33876998	.	+	.	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	stop_codon	33876999	33877001	.	+	0	transcript_id "Phchi.S1G529900.t1"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	transcript	33873081	33876998	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	start_codon	33873081	33873083	.	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873081	33873154	0.91	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873081	33873154	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873155	33873243	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873244	33873329	1	+	1	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873244	33873329	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873330	33873414	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873415	33873550	1	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873415	33873550	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873551	33873709	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873710	33873738	1	+	1	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873710	33873738	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873739	33874019	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874020	33874116	1	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874020	33874116	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874117	33874360	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874361	33874416	1	+	1	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874361	33874416	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874417	33874605	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874606	33874713	1	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874606	33874713	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874714	33874825	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874826	33874882	1	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874826	33874882	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874883	33875045	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875046	33875137	1	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875046	33875137	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875138	33875338	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875339	33875423	1	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875339	33875423	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875424	33875660	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875661	33875813	0.89	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875661	33875813	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875814	33875925	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875926	33876029	0.99	+	2	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875926	33876029	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876030	33876230	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876231	33876398	1	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876231	33876398	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876399	33876515	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876516	33876619	0.95	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876516	33876619	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876620	33876720	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876721	33876778	0.91	+	1	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876721	33876778	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876779	33876869	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876870	33876998	1	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876870	33876998	.	+	.	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	stop_codon	33876999	33877001	.	+	0	transcript_id "Phchi.S1G529900.t2"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	transcript	33873081	33876998	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	start_codon	33873081	33873083	.	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873081	33873154	0.9	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873081	33873154	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873155	33873231	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873232	33873329	1	+	1	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873232	33873329	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873330	33873414	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873415	33873550	1	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873415	33873550	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873551	33873709	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873710	33873738	1	+	1	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873710	33873738	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873739	33873948	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33873949	33873990	0.5	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33873949	33873990	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33873991	33874067	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874068	33874116	0.47	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874068	33874116	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874117	33874360	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874361	33874416	1	+	1	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874361	33874416	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874417	33874605	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874606	33874713	1	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874606	33874713	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874714	33874825	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33874826	33874882	1	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33874826	33874882	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33874883	33875045	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875046	33875137	1	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875046	33875137	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875138	33875338	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875339	33875423	1	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875339	33875423	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875424	33875660	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875661	33875813	0.85	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875661	33875813	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33875814	33875925	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33875926	33876029	0.97	+	2	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33875926	33876029	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876030	33876230	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876231	33876398	1	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876231	33876398	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876399	33876515	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876516	33876619	0.97	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876516	33876619	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876620	33876720	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876721	33876778	0.93	+	1	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876721	33876778	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	intron	33876779	33876869	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	CDS	33876870	33876998	1	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	exon	33876870	33876998	.	+	.	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
Phchi.S1	AUGUSTUS	stop_codon	33876999	33877001	.	+	0	transcript_id "Phchi.S1G529900.t3"; gene_id "Phchi.S1G529900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11126.t1 is derived from g15176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4284112	4284430	.	+	.	Phchi.S4G070800
Phchi.S4	AUGUSTUS	transcript	4284112	4284430	.	+	.	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	start_codon	4284112	4284114	.	+	0	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	CDS	4284112	4284195	0.89	+	0	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	exon	4284112	4284195	.	+	.	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	intron	4284196	4284298	.	+	.	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	CDS	4284299	4284430	0.9	+	0	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	exon	4284299	4284430	.	+	.	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
Phchi.S4	AUGUSTUS	stop_codon	4284431	4284433	.	+	0	transcript_id "Phchi.S4G070800.t1"; gene_id "Phchi.S4G070800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5740.t1 is derived from g2910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18674507	18678564	.	-	.	Phchi.S1G289900
Phchi.S1	AUGUSTUS	transcript	18674507	18678564	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	stop_codon	18674504	18674506	.	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18674507	18674722	0.62	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18674507	18674722	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18674723	18674818	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18674819	18674887	0.84	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18674819	18674887	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18674888	18674988	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18674989	18675069	0.84	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18674989	18675069	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18675070	18675150	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18675151	18675225	1	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18675151	18675225	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18675226	18675352	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18675353	18675548	1	-	1	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18675353	18675548	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18675549	18675668	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18675669	18675721	1	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18675669	18675721	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18675722	18675809	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18675810	18675857	1	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18675810	18675857	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18675858	18675959	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18675960	18676172	0.99	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18675960	18676172	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18676173	18676280	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18676281	18676445	1	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18676281	18676445	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18676446	18677063	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18677064	18677291	0.97	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18677064	18677291	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18677292	18677402	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18677403	18677735	0.99	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18677403	18677735	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	intron	18677736	18677832	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	CDS	18677833	18678564	1	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	exon	18677833	18678564	.	-	.	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
Phchi.S1	AUGUSTUS	start_codon	18678562	18678564	.	-	0	transcript_id "Phchi.S1G289900.t1"; gene_id "Phchi.S1G289900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg66.t1 is derived from g9848.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	326173	327690	.	+	.	Phchi.S6G002500
Phchi.S6	AUGUSTUS	transcript	326173	327690	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	start_codon	326173	326175	.	+	0	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	CDS	326173	326291	0.79	+	0	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	exon	326173	326291	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	intron	326292	326549	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	CDS	326550	326555	0.92	+	1	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	exon	326550	326555	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	intron	326556	326891	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	CDS	326892	327018	0.94	+	1	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	exon	326892	327018	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	intron	327019	327288	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	CDS	327289	327690	0.83	+	0	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	exon	327289	327690	.	+	.	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
Phchi.S6	AUGUSTUS	stop_codon	327691	327693	.	+	0	transcript_id "Phchi.S6G002500.t1"; gene_id "Phchi.S6G002500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11503.t1 is derived from g15553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6753609	6756236	.	-	.	Phchi.S4G108500
Phchi.S4	AUGUSTUS	transcript	6753609	6756236	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	stop_codon	6753606	6753608	.	-	0	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6753609	6753682	0.96	-	2	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6753609	6753682	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	intron	6753683	6753764	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6753765	6753799	1	-	1	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6753765	6753799	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	intron	6753800	6753960	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6753961	6754026	0.97	-	1	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6753961	6754026	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	intron	6754027	6754287	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6754288	6754325	0.99	-	0	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6754288	6754325	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	intron	6754326	6754471	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6754472	6754488	0.98	-	2	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6754472	6754488	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	intron	6754489	6754600	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6754601	6755196	0.48	-	1	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6754601	6755196	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	intron	6755197	6755418	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	CDS	6755419	6756236	0.4	-	0	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	exon	6755419	6756236	.	-	.	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
Phchi.S4	AUGUSTUS	start_codon	6756234	6756236	.	-	0	transcript_id "Phchi.S4G108500.t1"; gene_id "Phchi.S4G108500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1918.t1 is derived from g8838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3844555	3846359	.	-	.	Phchi.S5G052700
Phchi.S5	AUGUSTUS	transcript	3844555	3846359	.	-	.	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	stop_codon	3844552	3844554	.	-	0	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	CDS	3844555	3844990	0.8	-	1	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	exon	3844555	3844990	.	-	.	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	intron	3844991	3845097	.	-	.	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	CDS	3845098	3846359	0.92	-	0	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	exon	3845098	3846359	.	-	.	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	start_codon	3846357	3846359	.	-	0	transcript_id "Phchi.S5G052700.t1"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	transcript	3844555	3845885	.	-	.	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	stop_codon	3844552	3844554	.	-	0	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	CDS	3844555	3844990	0.75	-	1	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	exon	3844555	3844990	.	-	.	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	intron	3844991	3845097	.	-	.	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	CDS	3845098	3845885	0.55	-	0	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	exon	3845098	3845885	.	-	.	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
Phchi.S5	AUGUSTUS	start_codon	3845883	3845885	.	-	0	transcript_id "Phchi.S5G052700.t2"; gene_id "Phchi.S5G052700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14792.t1 is derived from g13260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14727620	14729599	.	-	.	Phchi.S3G211100
Phchi.S3	AUGUSTUS	transcript	14727620	14729599	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	stop_codon	14727617	14727619	.	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14727620	14727796	0.62	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14727620	14727796	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14727797	14727885	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14727886	14727997	1	-	1	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14727886	14727997	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14727998	14728087	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14728088	14728154	1	-	2	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14728088	14728154	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14728155	14728244	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14728245	14728266	0.9	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14728245	14728266	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14728267	14728380	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14728381	14728468	0.93	-	1	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14728381	14728468	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14728469	14728577	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14728578	14728690	0.93	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14728578	14728690	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14728691	14728846	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14728847	14728966	1	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14728847	14728966	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14728967	14729043	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14729044	14729186	1	-	2	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14729044	14729186	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14729187	14729331	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14729332	14729446	1	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14729332	14729446	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	intron	14729447	14729530	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	CDS	14729531	14729599	1	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	exon	14729531	14729599	.	-	.	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
Phchi.S3	AUGUSTUS	start_codon	14729597	14729599	.	-	0	transcript_id "Phchi.S3G211100.t1"; gene_id "Phchi.S3G211100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3759.t1 is derived from g928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5558787	5563850	.	+	.	Phchi.S1G091800
Phchi.S1	AUGUSTUS	transcript	5558787	5563850	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	start_codon	5558787	5558789	.	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5558787	5558919	0.89	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5558787	5558919	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5558920	5559022	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5559023	5559154	0.56	+	2	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5559023	5559154	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5559155	5559282	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5559283	5560836	0.58	+	2	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5559283	5560836	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5560837	5560937	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5560938	5561197	0.98	+	2	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5560938	5561197	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5561198	5561278	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5561279	5561488	1	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5561279	5561488	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5561489	5561576	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5561577	5561795	1	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5561577	5561795	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5561796	5561921	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5561922	5562899	0.99	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5561922	5562899	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5562900	5562994	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5562995	5563090	1	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5562995	5563090	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5563091	5563171	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5563172	5563270	1	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5563172	5563270	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5563271	5563367	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5563368	5563557	1	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5563368	5563557	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	intron	5563558	5563638	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	CDS	5563639	5563850	1	+	2	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	exon	5563639	5563850	.	+	.	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
Phchi.S1	AUGUSTUS	stop_codon	5563851	5563853	.	+	0	transcript_id "Phchi.S1G091800.t1"; gene_id "Phchi.S1G091800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14080.t1 is derived from g12547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10695249	10697390	.	+	.	Phchi.S3G139900
Phchi.S3	AUGUSTUS	transcript	10695249	10697390	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	start_codon	10695249	10695251	.	+	0	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	CDS	10695249	10695789	0.65	+	0	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	exon	10695249	10695789	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	intron	10695790	10695933	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	CDS	10695934	10696436	1	+	2	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	exon	10695934	10696436	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	intron	10696437	10696510	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	CDS	10696511	10696621	1	+	0	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	exon	10696511	10696621	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	intron	10696622	10696732	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	CDS	10696733	10697109	1	+	0	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	exon	10696733	10697109	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	intron	10697110	10697191	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	CDS	10697192	10697390	0.84	+	1	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	exon	10697192	10697390	.	+	.	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
Phchi.S3	AUGUSTUS	stop_codon	10697391	10697393	.	+	0	transcript_id "Phchi.S3G139900.t1"; gene_id "Phchi.S3G139900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9110.t1 is derived from g6285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39874109	39876096	.	-	.	Phchi.S1G626900
Phchi.S1	AUGUSTUS	transcript	39874109	39876096	.	-	.	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	stop_codon	39874106	39874108	.	-	0	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	CDS	39874109	39874339	0.9	-	0	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	exon	39874109	39874339	.	-	.	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	intron	39874340	39874455	.	-	.	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	CDS	39874456	39876096	0.63	-	0	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	exon	39874456	39876096	.	-	.	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
Phchi.S1	AUGUSTUS	start_codon	39876094	39876096	.	-	0	transcript_id "Phchi.S1G626900.t1"; gene_id "Phchi.S1G626900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12028.t1 is derived from g7703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	642234	643238	.	-	.	Phchi.S2G010800
Phchi.S2	AUGUSTUS	transcript	642234	643238	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	stop_codon	642231	642233	.	-	0	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	CDS	642234	642280	1	-	2	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	exon	642234	642280	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	intron	642281	642373	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	CDS	642374	642551	1	-	0	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	exon	642374	642551	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	intron	642552	642638	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	CDS	642639	642742	1	-	2	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	exon	642639	642742	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	intron	642743	643219	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	CDS	643220	643238	1	-	0	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	exon	643220	643238	.	-	.	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
Phchi.S2	AUGUSTUS	start_codon	643236	643238	.	-	0	transcript_id "Phchi.S2G010800.t1"; gene_id "Phchi.S2G010800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg961.t1 is derived from g10743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6664033	6665317	.	-	.	Phchi.S6G092000
Phchi.S6	AUGUSTUS	transcript	6664033	6665317	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	stop_codon	6664030	6664032	.	-	0	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	CDS	6664033	6664147	0.91	-	1	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	exon	6664033	6664147	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	intron	6664148	6664415	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	CDS	6664416	6664637	0.9	-	1	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	exon	6664416	6664637	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	intron	6664638	6664780	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	CDS	6664781	6664894	0.55	-	1	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	exon	6664781	6664894	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	intron	6664895	6664964	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	CDS	6664965	6665317	0.85	-	0	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	exon	6664965	6665317	.	-	.	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
Phchi.S6	AUGUSTUS	start_codon	6665315	6665317	.	-	0	transcript_id "Phchi.S6G092000.t1"; gene_id "Phchi.S6G092000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8979.t1 is derived from g6154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38950185	38952186	.	-	.	Phchi.S1G613800
Phchi.S1	AUGUSTUS	transcript	38950185	38952186	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	stop_codon	38950182	38950184	.	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38950185	38950428	0.77	-	1	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38950185	38950428	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38950429	38950565	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38950566	38950615	0.77	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38950566	38950615	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38950616	38950715	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38950716	38950862	1	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38950716	38950862	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38950863	38950964	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38950965	38951018	1	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38950965	38951018	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38951019	38951109	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38951110	38951271	1	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38951110	38951271	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38951272	38951352	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38951353	38951616	1	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38951353	38951616	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38951617	38951738	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38951739	38951807	1	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38951739	38951807	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	intron	38951808	38951892	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	CDS	38951893	38952186	0.84	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	exon	38951893	38952186	.	-	.	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
Phchi.S1	AUGUSTUS	start_codon	38952184	38952186	.	-	0	transcript_id "Phchi.S1G613800.t1"; gene_id "Phchi.S1G613800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11229.t1 is derived from g15279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4907042	4907437	.	-	.	Phchi.S4G081100
Phchi.S4	AUGUSTUS	transcript	4907042	4907437	.	-	.	transcript_id "Phchi.S4G081100.t1"; gene_id "Phchi.S4G081100"
Phchi.S4	AUGUSTUS	stop_codon	4907039	4907041	.	-	0	transcript_id "Phchi.S4G081100.t1"; gene_id "Phchi.S4G081100"
Phchi.S4	AUGUSTUS	CDS	4907042	4907437	0.84	-	0	transcript_id "Phchi.S4G081100.t1"; gene_id "Phchi.S4G081100"
Phchi.S4	AUGUSTUS	exon	4907042	4907437	.	-	.	transcript_id "Phchi.S4G081100.t1"; gene_id "Phchi.S4G081100"
Phchi.S4	AUGUSTUS	start_codon	4907435	4907437	.	-	0	transcript_id "Phchi.S4G081100.t1"; gene_id "Phchi.S4G081100"
# This transcript jg12232.t2 is derived from g7908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12233.t1 is derived from g7909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6922346	6923646	.	-	.	Phchi.S2G031300
Phchi.S2	AUGUSTUS	transcript	6922346	6923646	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	stop_codon	6922343	6922345	.	-	0	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	CDS	6922346	6922489	1	-	0	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	exon	6922346	6922489	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	intron	6922490	6922578	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	CDS	6922579	6922686	1	-	0	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	exon	6922579	6922686	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	intron	6922687	6922840	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	CDS	6922841	6923094	1	-	2	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	exon	6922841	6923094	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	intron	6923095	6923438	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	CDS	6923439	6923646	0.96	-	0	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	exon	6923439	6923646	.	-	.	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
Phchi.S2	AUGUSTUS	start_codon	6923644	6923646	.	-	0	transcript_id "Phchi.S2G031300.t1"; gene_id "Phchi.S2G031300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6226.t1 is derived from g3398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21768531	21770259	.	-	.	Phchi.S1G338500
Phchi.S1	AUGUSTUS	transcript	21768531	21770259	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	stop_codon	21768528	21768530	.	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21768531	21768622	1	-	2	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21768531	21768622	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21768623	21768714	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21768715	21768812	1	-	1	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21768715	21768812	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21768813	21768910	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21768911	21768972	1	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21768911	21768972	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21768973	21769054	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21769055	21769127	1	-	1	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21769055	21769127	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21769128	21769263	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21769264	21769349	1	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21769264	21769349	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21769350	21769438	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21769439	21769495	1	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21769439	21769495	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21769496	21769599	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21769600	21769647	1	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21769600	21769647	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21769648	21769736	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21769737	21769808	1	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21769737	21769808	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	intron	21769809	21770175	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	CDS	21770176	21770259	0.54	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	exon	21770176	21770259	.	-	.	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
Phchi.S1	AUGUSTUS	start_codon	21770257	21770259	.	-	0	transcript_id "Phchi.S1G338500.t1"; gene_id "Phchi.S1G338500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg453.t1 is derived from g10235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3175824	3180462	.	-	.	Phchi.S6G041200
Phchi.S6	AUGUSTUS	transcript	3175824	3180462	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	stop_codon	3175821	3175823	.	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3175824	3176137	1	-	2	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3175824	3176137	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3176138	3176285	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3176286	3176343	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3176286	3176343	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3176344	3176439	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3176440	3176514	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3176440	3176514	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3176515	3176598	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3176599	3176733	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3176599	3176733	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3176734	3176825	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3176826	3177005	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3176826	3177005	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3177006	3177121	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3177122	3177172	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3177122	3177172	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3177173	3177357	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3177358	3177458	1	-	2	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3177358	3177458	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3177459	3177654	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3177655	3177713	1	-	1	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3177655	3177713	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3177714	3177994	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3177995	3178110	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3177995	3178110	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3178111	3178227	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3178228	3178413	0.99	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3178228	3178413	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3178414	3178543	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3178544	3178625	1	-	1	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3178544	3178625	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3178626	3178712	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3178713	3178804	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3178713	3178804	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3178805	3178890	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3178891	3179034	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3178891	3179034	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3179035	3179125	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3179126	3179206	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3179126	3179206	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3179207	3179330	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3179331	3179414	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3179331	3179414	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3179415	3179499	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3179500	3179601	0.99	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3179500	3179601	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3179602	3179702	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3179703	3179798	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3179703	3179798	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3179799	3179905	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3179906	3179963	1	-	1	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3179906	3179963	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3179964	3180080	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3180081	3180172	1	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3180081	3180172	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	intron	3180173	3180261	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	CDS	3180262	3180462	0.5	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	exon	3180262	3180462	.	-	.	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
Phchi.S6	AUGUSTUS	start_codon	3180460	3180462	.	-	0	transcript_id "Phchi.S6G041200.t1"; gene_id "Phchi.S6G041200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1456.t1 is derived from g8375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	995884	996389	.	-	.	Phchi.S5G006500
Phchi.S5	AUGUSTUS	transcript	995884	996389	.	-	.	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	stop_codon	995881	995883	.	-	0	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	CDS	995884	996131	0.99	-	2	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	exon	995884	996131	.	-	.	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	intron	996132	996238	.	-	.	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	CDS	996239	996389	0.78	-	0	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	exon	996239	996389	.	-	.	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
Phchi.S5	AUGUSTUS	start_codon	996387	996389	.	-	0	transcript_id "Phchi.S5G006500.t1"; gene_id "Phchi.S5G006500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15304.t1 is derived from g13772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18305670	18306499	.	+	.	Phchi.S3G262300
Phchi.S3	AUGUSTUS	transcript	18305670	18306499	.	+	.	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	start_codon	18305670	18305672	.	+	0	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	CDS	18305670	18306275	0.75	+	0	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	exon	18305670	18306275	.	+	.	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	intron	18306276	18306364	.	+	.	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	CDS	18306365	18306499	0.96	+	0	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	exon	18306365	18306499	.	+	.	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
Phchi.S3	AUGUSTUS	stop_codon	18306500	18306502	.	+	0	transcript_id "Phchi.S3G262300.t1"; gene_id "Phchi.S3G262300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6802.t1 is derived from g3974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25130366	25133504	.	+	.	Phchi.S1G396100
Phchi.S1	AUGUSTUS	transcript	25130366	25133504	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	start_codon	25130366	25130368	.	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25130366	25130443	0.83	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25130366	25130443	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25130444	25130657	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25130658	25130715	1	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25130658	25130715	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25130716	25130839	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25130840	25130934	1	+	2	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25130840	25130934	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25130935	25131031	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25131032	25131135	1	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25131032	25131135	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25131136	25131216	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25131217	25131346	1	+	1	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25131217	25131346	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25131347	25131442	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25131443	25131491	1	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25131443	25131491	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25131492	25131681	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25131682	25132823	0.69	+	2	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25131682	25132823	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25132824	25132960	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25132961	25133203	0.96	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25132961	25133203	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	intron	25133204	25133354	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	CDS	25133355	25133504	0.82	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	exon	25133355	25133504	.	+	.	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
Phchi.S1	AUGUSTUS	stop_codon	25133505	25133507	.	+	0	transcript_id "Phchi.S1G396100.t1"; gene_id "Phchi.S1G396100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6783.t1 is derived from g3955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25075690	25079203	.	+	.	Phchi.S1G394200
Phchi.S1	AUGUSTUS	transcript	25075690	25079203	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	start_codon	25075690	25075692	.	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25075690	25076186	0.72	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25075690	25076186	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25076187	25076272	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25076273	25077266	0.75	+	1	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25076273	25077266	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25077267	25077408	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25077409	25077682	1	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25077409	25077682	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25077683	25077773	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25077774	25077909	1	+	2	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25077774	25077909	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25077910	25078042	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25078043	25078253	0.94	+	1	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25078043	25078253	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25078254	25078359	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25078360	25078566	1	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25078360	25078566	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25078567	25078684	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25078685	25078966	0.71	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25078685	25078966	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	intron	25078967	25079074	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	CDS	25079075	25079203	0.84	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	exon	25079075	25079203	.	+	.	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
Phchi.S1	AUGUSTUS	stop_codon	25079204	25079206	.	+	0	transcript_id "Phchi.S1G394200.t1"; gene_id "Phchi.S1G394200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9276.t1 is derived from g6451.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40728550	40733902	.	+	.	Phchi.S1G643500
Phchi.S1	AUGUSTUS	transcript	40728550	40733902	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	start_codon	40728550	40728552	.	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40728550	40729104	0.79	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40728550	40729104	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40729105	40729209	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40729210	40730555	0.83	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40729210	40730555	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40730556	40730642	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40730643	40730753	1	+	1	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40730643	40730753	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40730754	40730842	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40730843	40731119	1	+	1	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40730843	40731119	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731120	40731221	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731222	40731310	1	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731222	40731310	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731311	40731397	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731398	40731506	1	+	1	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731398	40731506	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731507	40731635	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731636	40731845	1	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731636	40731845	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731846	40731992	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731993	40732118	1	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731993	40732118	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732119	40732238	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40732239	40732337	1	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40732239	40732337	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732338	40732453	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40732454	40732645	1	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40732454	40732645	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732646	40732799	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40732800	40732944	1	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40732800	40732944	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732945	40733034	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40733035	40733544	0.94	+	2	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40733035	40733544	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40733545	40733723	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40733724	40733902	1	+	2	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40733724	40733902	.	+	.	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	stop_codon	40733903	40733905	.	+	0	transcript_id "Phchi.S1G643500.t1"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	transcript	40728550	40733902	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	start_codon	40728550	40728552	.	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40728550	40729104	0.67	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40728550	40729104	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40729105	40729209	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40729210	40730555	0.75	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40729210	40730555	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40730556	40730642	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40730643	40730753	1	+	1	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40730643	40730753	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40730754	40730842	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40730843	40731119	1	+	1	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40730843	40731119	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731120	40731221	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731222	40731310	1	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731222	40731310	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731311	40731397	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731398	40731506	1	+	1	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731398	40731506	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731507	40731635	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731636	40731845	1	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731636	40731845	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40731846	40731992	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40731993	40732118	1	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40731993	40732118	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732119	40732238	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40732239	40732337	1	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40732239	40732337	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732338	40732453	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40732454	40732645	1	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40732454	40732645	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732646	40732799	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40732800	40732944	1	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40732800	40732944	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40732945	40733034	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40733035	40733544	0.95	+	2	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40733035	40733544	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	intron	40733545	40733726	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	CDS	40733727	40733902	1	+	2	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	exon	40733727	40733902	.	+	.	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
Phchi.S1	AUGUSTUS	stop_codon	40733903	40733905	.	+	0	transcript_id "Phchi.S1G643500.t2"; gene_id "Phchi.S1G643500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9520.t1 is derived from g6696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42245736	42249722	.	-	.	Phchi.S1G667900
Phchi.S1	AUGUSTUS	transcript	42245736	42249722	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	stop_codon	42245733	42245735	.	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42245736	42246047	0.85	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42245736	42246047	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42246048	42246148	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42246149	42246274	1	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42246149	42246274	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42246275	42246359	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42246360	42246521	1	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42246360	42246521	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42246522	42246646	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42246647	42246716	0.22	-	1	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42246647	42246716	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42246717	42246899	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42246900	42247008	0.55	-	2	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42246900	42247008	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42247009	42247116	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42247117	42247238	1	-	1	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42247117	42247238	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42247239	42247331	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42247332	42247398	0.83	-	2	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42247332	42247398	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42247399	42247487	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42247488	42247512	0.83	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42247488	42247512	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42247513	42247667	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42247668	42248975	0.95	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42247668	42248975	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42248976	42249126	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42249127	42249171	0.97	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42249127	42249171	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42249172	42249438	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42249439	42249489	0.89	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42249439	42249489	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	intron	42249490	42249704	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	CDS	42249705	42249722	0.92	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	exon	42249705	42249722	.	-	.	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
Phchi.S1	AUGUSTUS	start_codon	42249720	42249722	.	-	0	transcript_id "Phchi.S1G667900.t1"; gene_id "Phchi.S1G667900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3544.t1 is derived from g713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4375841	4376738	.	-	.	Phchi.S1G070300
Phchi.S1	AUGUSTUS	transcript	4375841	4376738	.	-	.	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	stop_codon	4375838	4375840	.	-	0	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	CDS	4375841	4376445	0.76	-	2	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	exon	4375841	4376445	.	-	.	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	intron	4376446	4376530	.	-	.	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	CDS	4376531	4376738	0.47	-	0	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	exon	4376531	4376738	.	-	.	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
Phchi.S1	AUGUSTUS	start_codon	4376736	4376738	.	-	0	transcript_id "Phchi.S1G070300.t1"; gene_id "Phchi.S1G070300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8201.t1 is derived from g5376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34418645	34419523	.	+	.	Phchi.S1G536000
Phchi.S1	AUGUSTUS	transcript	34418645	34419523	.	+	.	transcript_id "Phchi.S1G536000.t1"; gene_id "Phchi.S1G536000"
Phchi.S1	AUGUSTUS	start_codon	34418645	34418647	.	+	0	transcript_id "Phchi.S1G536000.t1"; gene_id "Phchi.S1G536000"
Phchi.S1	AUGUSTUS	CDS	34418645	34419523	0.93	+	0	transcript_id "Phchi.S1G536000.t1"; gene_id "Phchi.S1G536000"
Phchi.S1	AUGUSTUS	exon	34418645	34419523	.	+	.	transcript_id "Phchi.S1G536000.t1"; gene_id "Phchi.S1G536000"
Phchi.S1	AUGUSTUS	stop_codon	34419524	34419526	.	+	0	transcript_id "Phchi.S1G536000.t1"; gene_id "Phchi.S1G536000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9091.t1 is derived from g6266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39808375	39811053	.	-	.	Phchi.S1G625000
Phchi.S1	AUGUSTUS	transcript	39808375	39811053	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	stop_codon	39808372	39808374	.	-	0	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	CDS	39808375	39810502	0.96	-	1	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	exon	39808375	39810502	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	intron	39810503	39810632	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	CDS	39810633	39810771	1	-	2	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	exon	39810633	39810771	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	intron	39810772	39810864	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	CDS	39810865	39810909	1	-	2	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	exon	39810865	39810909	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	intron	39810910	39810995	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	CDS	39810996	39811053	0.57	-	0	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	exon	39810996	39811053	.	-	.	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
Phchi.S1	AUGUSTUS	start_codon	39811051	39811053	.	-	0	transcript_id "Phchi.S1G625000.t1"; gene_id "Phchi.S1G625000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12169.t1 is derived from g7845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5330930	5331303	.	+	.	Phchi.S2G024900
Phchi.S2	AUGUSTUS	transcript	5330930	5331303	.	+	.	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	start_codon	5330930	5330932	.	+	0	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	CDS	5330930	5331001	0.76	+	0	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	exon	5330930	5331001	.	+	.	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	intron	5331002	5331132	.	+	.	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	CDS	5331133	5331303	0.76	+	0	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	exon	5331133	5331303	.	+	.	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
Phchi.S2	AUGUSTUS	stop_codon	5331304	5331306	.	+	0	transcript_id "Phchi.S2G024900.t1"; gene_id "Phchi.S2G024900"
# This transcript jg3021.t2 is derived from g190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3022.t1 is derived from g191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1181763	1183661	.	+	.	Phchi.S1G018100
Phchi.S1	AUGUSTUS	transcript	1181763	1183661	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	start_codon	1181763	1181765	.	+	0	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	CDS	1181763	1182241	0.98	+	0	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	exon	1181763	1182241	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	intron	1182242	1182369	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	CDS	1182370	1182580	1	+	1	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	exon	1182370	1182580	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	intron	1182581	1182657	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	CDS	1182658	1182774	1	+	0	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	exon	1182658	1182774	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	intron	1182775	1182914	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	CDS	1182915	1183661	1	+	0	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	exon	1182915	1183661	.	+	.	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
Phchi.S1	AUGUSTUS	stop_codon	1183662	1183664	.	+	0	transcript_id "Phchi.S1G018100.t1"; gene_id "Phchi.S1G018100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8281.t1 is derived from g5456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35080071	35080753	.	+	.	Phchi.S1G544000
Phchi.S1	AUGUSTUS	transcript	35080071	35080753	.	+	.	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	start_codon	35080071	35080073	.	+	0	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	CDS	35080071	35080413	0.91	+	0	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	exon	35080071	35080413	.	+	.	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	intron	35080414	35080490	.	+	.	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	CDS	35080491	35080753	1	+	2	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	exon	35080491	35080753	.	+	.	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
Phchi.S1	AUGUSTUS	stop_codon	35080754	35080756	.	+	0	transcript_id "Phchi.S1G544000.t1"; gene_id "Phchi.S1G544000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12265.t1 is derived from g7941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7264306	7271180	.	+	.	Phchi.S2G034500
Phchi.S2	AUGUSTUS	transcript	7264306	7271180	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	start_codon	7264306	7264308	.	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7264306	7264431	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7264306	7264431	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7264432	7264519	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7264520	7264547	0.99	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7264520	7264547	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7264548	7264661	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7264662	7264762	0.99	+	2	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7264662	7264762	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7264763	7264865	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7264866	7265078	0.99	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7264866	7265078	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7265079	7265322	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7265323	7265566	0.87	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7265323	7265566	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7265567	7265703	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7265704	7265879	1	+	2	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7265704	7265879	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7265880	7265964	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7265965	7266047	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7265965	7266047	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7266048	7266168	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7266169	7266241	1	+	1	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7266169	7266241	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7266242	7266378	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7266379	7266444	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7266379	7266444	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7266445	7266544	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7266545	7266587	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7266545	7266587	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7266588	7266753	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7266754	7266893	1	+	2	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7266754	7266893	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7266894	7266980	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7266981	7267196	0.99	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7266981	7267196	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7267197	7267298	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7267299	7267383	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7267299	7267383	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7267384	7267525	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7267526	7267820	1	+	2	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7267526	7267820	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7267821	7267984	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7267985	7268270	1	+	1	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7267985	7268270	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7268271	7268399	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7268400	7268637	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7268400	7268637	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7268638	7268717	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7268718	7268902	1	+	2	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7268718	7268902	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7268903	7268998	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7268999	7269069	0.34	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7268999	7269069	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7269070	7269379	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7269380	7270226	0.49	+	1	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7269380	7270226	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7270227	7270377	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7270378	7270727	1	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7270378	7270727	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	intron	7270728	7270807	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	CDS	7270808	7271180	0.92	+	1	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	exon	7270808	7271180	.	+	.	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
Phchi.S2	AUGUSTUS	stop_codon	7271181	7271183	.	+	0	transcript_id "Phchi.S2G034500.t1"; gene_id "Phchi.S2G034500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15884.t1 is derived from g14354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22026053	22027210	.	-	.	Phchi.S3G320300
Phchi.S3	AUGUSTUS	transcript	22026053	22027210	.	-	.	transcript_id "Phchi.S3G320300.t1"; gene_id "Phchi.S3G320300"
Phchi.S3	AUGUSTUS	stop_codon	22026050	22026052	.	-	0	transcript_id "Phchi.S3G320300.t1"; gene_id "Phchi.S3G320300"
Phchi.S3	AUGUSTUS	CDS	22026053	22027210	0.83	-	0	transcript_id "Phchi.S3G320300.t1"; gene_id "Phchi.S3G320300"
Phchi.S3	AUGUSTUS	exon	22026053	22027210	.	-	.	transcript_id "Phchi.S3G320300.t1"; gene_id "Phchi.S3G320300"
Phchi.S3	AUGUSTUS	start_codon	22027208	22027210	.	-	0	transcript_id "Phchi.S3G320300.t1"; gene_id "Phchi.S3G320300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15739.t1 is derived from g14209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21000519	21002402	.	+	.	Phchi.S3G305800
Phchi.S3	AUGUSTUS	transcript	21000519	21002402	.	+	.	transcript_id "Phchi.S3G305800.t1"; gene_id "Phchi.S3G305800"
Phchi.S3	AUGUSTUS	start_codon	21000519	21000521	.	+	0	transcript_id "Phchi.S3G305800.t1"; gene_id "Phchi.S3G305800"
Phchi.S3	AUGUSTUS	CDS	21000519	21002402	0.8	+	0	transcript_id "Phchi.S3G305800.t1"; gene_id "Phchi.S3G305800"
Phchi.S3	AUGUSTUS	exon	21000519	21002402	.	+	.	transcript_id "Phchi.S3G305800.t1"; gene_id "Phchi.S3G305800"
Phchi.S3	AUGUSTUS	stop_codon	21002403	21002405	.	+	0	transcript_id "Phchi.S3G305800.t1"; gene_id "Phchi.S3G305800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4426.t1 is derived from g1595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10440732	10441876	.	+	.	Phchi.S1G158500
Phchi.S1	AUGUSTUS	transcript	10440732	10441876	.	+	.	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	start_codon	10440732	10440734	.	+	0	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	CDS	10440732	10440940	0.89	+	0	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	exon	10440732	10440940	.	+	.	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	intron	10440941	10441047	.	+	.	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	CDS	10441048	10441876	0.9	+	1	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	exon	10441048	10441876	.	+	.	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
Phchi.S1	AUGUSTUS	stop_codon	10441877	10441879	.	+	0	transcript_id "Phchi.S1G158500.t1"; gene_id "Phchi.S1G158500"
# This transcript jg14795.t2 is derived from g13263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14796.t1 is derived from g13264.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14750941	14755724	.	-	.	Phchi.S3G211500
Phchi.S3	AUGUSTUS	transcript	14750941	14755724	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	stop_codon	14750938	14750940	.	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14750941	14751339	1	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14750941	14751339	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14751340	14751434	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14751435	14752045	0.92	-	2	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14751435	14752045	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14752046	14752162	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14752163	14752476	0.98	-	1	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14752163	14752476	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14752477	14752561	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14752562	14752777	0.97	-	1	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14752562	14752777	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14752778	14752886	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14752887	14753020	0.74	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14752887	14753020	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14753021	14753324	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14753325	14753414	0.32	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14753325	14753414	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14753415	14753522	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14753523	14753666	0.76	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14753523	14753666	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14753667	14753784	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14753785	14754023	0.97	-	2	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14753785	14754023	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14754024	14754263	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14754264	14754383	1	-	2	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14754264	14754383	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14754384	14754523	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14754524	14754654	0.77	-	1	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14754524	14754654	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14754655	14754747	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14754748	14755064	1	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14754748	14755064	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14755065	14755167	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14755168	14755391	1	-	2	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14755168	14755391	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14755392	14755603	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14755604	14755724	1	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14755604	14755724	.	-	.	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	start_codon	14755722	14755724	.	-	0	transcript_id "Phchi.S3G211500.t1"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	transcript	14750941	14754332	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	stop_codon	14750938	14750940	.	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14750941	14751339	1	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14750941	14751339	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14751340	14751434	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14751435	14752045	0.98	-	2	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14751435	14752045	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14752046	14752162	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14752163	14752476	0.96	-	1	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14752163	14752476	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14752477	14752561	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14752562	14752777	0.99	-	1	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14752562	14752777	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14752778	14752886	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14752887	14753020	0.82	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14752887	14753020	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14753021	14753324	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14753325	14753414	0.33	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14753325	14753414	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14753415	14753522	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14753523	14753666	0.74	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14753523	14753666	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14753667	14753784	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14753785	14754023	0.69	-	2	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14753785	14754023	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	intron	14754024	14754250	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	CDS	14754251	14754332	0.46	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	exon	14754251	14754332	.	-	.	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
Phchi.S3	AUGUSTUS	start_codon	14754330	14754332	.	-	0	transcript_id "Phchi.S3G211500.t2"; gene_id "Phchi.S3G211500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10900.t1 is derived from g14950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2814627	2816123	.	+	.	Phchi.S4G048200
Phchi.S4	AUGUSTUS	transcript	2814627	2816123	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	start_codon	2814627	2814629	.	+	0	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2814627	2814666	0.94	+	0	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2814627	2814666	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2814667	2814750	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2814751	2814870	0.87	+	2	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2814751	2814870	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2814871	2814978	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2814979	2815012	0.86	+	2	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2814979	2815012	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2815013	2815124	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2815125	2815195	0.86	+	1	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2815125	2815195	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2815196	2815275	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2815276	2815499	0.99	+	2	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2815276	2815499	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2815500	2815610	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2815611	2815742	1	+	0	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2815611	2815742	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2815743	2815827	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2815828	2815894	1	+	0	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2815828	2815894	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	intron	2815895	2815971	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	CDS	2815972	2816123	1	+	2	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	exon	2815972	2816123	.	+	.	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
Phchi.S4	AUGUSTUS	stop_codon	2816124	2816126	.	+	0	transcript_id "Phchi.S4G048200.t1"; gene_id "Phchi.S4G048200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9330.t1 is derived from g6505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40962033	40963379	.	-	.	Phchi.S1G648900
Phchi.S1	AUGUSTUS	transcript	40962033	40963379	.	-	.	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	stop_codon	40962030	40962032	.	-	0	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	CDS	40962033	40963127	0.89	-	0	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	exon	40962033	40963127	.	-	.	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	intron	40963128	40963220	.	-	.	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	CDS	40963221	40963379	0.99	-	0	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	exon	40963221	40963379	.	-	.	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
Phchi.S1	AUGUSTUS	start_codon	40963377	40963379	.	-	0	transcript_id "Phchi.S1G648900.t1"; gene_id "Phchi.S1G648900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6694.t1 is derived from g3866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24564567	24565346	.	+	.	Phchi.S1G385300
Phchi.S1	AUGUSTUS	transcript	24564567	24565346	.	+	.	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	start_codon	24564567	24564569	.	+	0	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	CDS	24564567	24564714	0.65	+	0	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	exon	24564567	24564714	.	+	.	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	intron	24564715	24565212	.	+	.	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	CDS	24565213	24565346	0.81	+	2	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	exon	24565213	24565346	.	+	.	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
Phchi.S1	AUGUSTUS	stop_codon	24565347	24565349	.	+	0	transcript_id "Phchi.S1G385300.t1"; gene_id "Phchi.S1G385300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6797.t1 is derived from g3969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25115591	25116364	.	+	.	Phchi.S1G395600
Phchi.S1	AUGUSTUS	transcript	25115591	25116364	.	+	.	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	start_codon	25115591	25115593	.	+	0	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	CDS	25115591	25115983	0.67	+	0	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	exon	25115591	25115983	.	+	.	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	intron	25115984	25116079	.	+	.	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	CDS	25116080	25116364	1	+	0	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	exon	25116080	25116364	.	+	.	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
Phchi.S1	AUGUSTUS	stop_codon	25116365	25116367	.	+	0	transcript_id "Phchi.S1G395600.t1"; gene_id "Phchi.S1G395600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12833.t1 is derived from g11298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2602378	2604806	.	+	.	Phchi.S3G015200
Phchi.S3	AUGUSTUS	transcript	2602378	2604806	.	+	.	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	start_codon	2602378	2602380	.	+	0	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	CDS	2602378	2602593	0.65	+	0	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	exon	2602378	2602593	.	+	.	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	intron	2602594	2602700	.	+	.	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	CDS	2602701	2602861	0.61	+	0	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	exon	2602701	2602861	.	+	.	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	intron	2602862	2602963	.	+	.	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	CDS	2602964	2604806	0.99	+	1	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	exon	2602964	2604806	.	+	.	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
Phchi.S3	AUGUSTUS	stop_codon	2604807	2604809	.	+	0	transcript_id "Phchi.S3G015200.t1"; gene_id "Phchi.S3G015200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5478.t1 is derived from g2648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17044315	17050230	.	-	.	Phchi.S1G263700
Phchi.S1	AUGUSTUS	transcript	17044315	17050230	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	stop_codon	17044312	17044314	.	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17044315	17044554	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17044315	17044554	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17044555	17044676	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17044677	17044774	1	-	2	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17044677	17044774	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17044775	17044867	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17044868	17045008	1	-	2	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17044868	17045008	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17045009	17045094	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17045095	17045215	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17045095	17045215	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17045216	17045331	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17045332	17045392	0.74	-	1	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17045332	17045392	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17045393	17045494	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17045495	17045573	1	-	2	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17045495	17045573	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17045574	17045653	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17045654	17045754	1	-	1	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17045654	17045754	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17045755	17045846	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17045847	17045904	1	-	2	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17045847	17045904	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17045905	17046032	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17046033	17046203	1	-	2	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17046033	17046203	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17046204	17046285	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17046286	17046385	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17046286	17046385	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17046386	17046469	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17046470	17046613	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17046470	17046613	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17046614	17046750	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17046751	17046906	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17046751	17046906	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17046907	17046997	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17046998	17047046	1	-	1	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17046998	17047046	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17047047	17047129	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17047130	17047227	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17047130	17047227	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17047228	17047325	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17047326	17047481	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17047326	17047481	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17047482	17047573	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17047574	17047928	1	-	1	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17047574	17047928	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17047929	17048016	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17048017	17048090	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17048017	17048090	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17048091	17048211	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17048212	17048298	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17048212	17048298	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17048299	17048393	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17048394	17048552	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17048394	17048552	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17048553	17048649	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17048650	17048805	1	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17048650	17048805	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17048806	17049589	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17049590	17049834	0.99	-	2	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17049590	17049834	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	intron	17049835	17049947	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	CDS	17049948	17050230	0.95	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	exon	17049948	17050230	.	-	.	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
Phchi.S1	AUGUSTUS	start_codon	17050228	17050230	.	-	0	transcript_id "Phchi.S1G263700.t1"; gene_id "Phchi.S1G263700"
# This transcript jg3805.t2 is derived from g974.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3806.t1 is derived from g975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5819942	5820764	.	-	.	Phchi.S1G096500
Phchi.S1	AUGUSTUS	transcript	5819942	5820764	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	stop_codon	5819939	5819941	.	-	0	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	CDS	5819942	5820157	0.68	-	0	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	exon	5819942	5820157	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	intron	5820158	5820352	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	CDS	5820353	5820417	0.67	-	2	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	exon	5820353	5820417	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	intron	5820418	5820525	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	CDS	5820526	5820565	0.93	-	0	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	exon	5820526	5820565	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	intron	5820566	5820725	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	CDS	5820726	5820764	1	-	0	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	exon	5820726	5820764	.	-	.	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
Phchi.S1	AUGUSTUS	start_codon	5820762	5820764	.	-	0	transcript_id "Phchi.S1G096500.t1"; gene_id "Phchi.S1G096500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15813.t1 is derived from g14283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21513385	21513804	.	-	.	Phchi.S3G313200
Phchi.S3	AUGUSTUS	transcript	21513385	21513804	.	-	.	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	stop_codon	21513382	21513384	.	-	0	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	CDS	21513385	21513434	0.99	-	2	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	exon	21513385	21513434	.	-	.	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	intron	21513435	21513590	.	-	.	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	CDS	21513591	21513804	0.84	-	0	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	exon	21513591	21513804	.	-	.	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	start_codon	21513802	21513804	.	-	0	transcript_id "Phchi.S3G313200.t1"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	transcript	21513416	21513804	.	-	.	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	stop_codon	21513413	21513415	.	-	0	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	CDS	21513416	21513434	0.55	-	1	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	exon	21513416	21513434	.	-	.	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	intron	21513435	21513595	.	-	.	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	CDS	21513596	21513804	0.44	-	0	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	exon	21513596	21513804	.	-	.	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
Phchi.S3	AUGUSTUS	start_codon	21513802	21513804	.	-	0	transcript_id "Phchi.S3G313200.t2"; gene_id "Phchi.S3G313200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15900.t1 is derived from g14370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22065855	22067334	.	+	.	Phchi.S3G321900
Phchi.S3	AUGUSTUS	transcript	22065855	22067334	.	+	.	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	start_codon	22065855	22065857	.	+	0	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	CDS	22065855	22066013	1	+	0	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	exon	22065855	22066013	.	+	.	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	intron	22066014	22066476	.	+	.	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	CDS	22066477	22067334	1	+	0	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	exon	22066477	22067334	.	+	.	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
Phchi.S3	AUGUSTUS	stop_codon	22067335	22067337	.	+	0	transcript_id "Phchi.S3G321900.t1"; gene_id "Phchi.S3G321900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8545.t1 is derived from g5720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36570951	36572311	.	+	.	Phchi.S1G570400
Phchi.S1	AUGUSTUS	transcript	36570951	36572311	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	start_codon	36570951	36570953	.	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36570951	36571025	0.43	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36570951	36571025	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	intron	36571026	36571111	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36571112	36571234	1	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36571112	36571234	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	intron	36571235	36571351	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36571352	36571395	1	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36571352	36571395	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	intron	36571396	36571483	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36571484	36571609	1	+	1	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36571484	36571609	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	intron	36571610	36571893	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36571894	36571978	1	+	1	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36571894	36571978	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	intron	36571979	36572089	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36572090	36572146	1	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36572090	36572146	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	intron	36572147	36572242	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	CDS	36572243	36572311	1	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	exon	36572243	36572311	.	+	.	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
Phchi.S1	AUGUSTUS	stop_codon	36572312	36572314	.	+	0	transcript_id "Phchi.S1G570400.t1"; gene_id "Phchi.S1G570400"
# This transcript jg10707.t2 is derived from g14757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10708.t1 is derived from g14758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1685015	1687064	.	-	.	Phchi.S4G029000
Phchi.S4	AUGUSTUS	transcript	1685015	1687064	.	-	.	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	stop_codon	1685012	1685014	.	-	0	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	CDS	1685015	1685824	0.89	-	0	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	exon	1685015	1685824	.	-	.	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	intron	1685825	1685916	.	-	.	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	CDS	1685917	1686427	1	-	1	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	exon	1685917	1686427	.	-	.	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	intron	1686428	1686606	.	-	.	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	CDS	1686607	1687064	0.99	-	0	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	exon	1686607	1687064	.	-	.	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
Phchi.S4	AUGUSTUS	start_codon	1687062	1687064	.	-	0	transcript_id "Phchi.S4G029000.t1"; gene_id "Phchi.S4G029000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14855.t1 is derived from g13323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15074804	15075277	.	-	.	Phchi.S3G217400
Phchi.S3	AUGUSTUS	transcript	15074804	15075277	.	-	.	transcript_id "Phchi.S3G217400.t1"; gene_id "Phchi.S3G217400"
Phchi.S3	AUGUSTUS	stop_codon	15074801	15074803	.	-	0	transcript_id "Phchi.S3G217400.t1"; gene_id "Phchi.S3G217400"
Phchi.S3	AUGUSTUS	CDS	15074804	15075277	0.93	-	0	transcript_id "Phchi.S3G217400.t1"; gene_id "Phchi.S3G217400"
Phchi.S3	AUGUSTUS	exon	15074804	15075277	.	-	.	transcript_id "Phchi.S3G217400.t1"; gene_id "Phchi.S3G217400"
Phchi.S3	AUGUSTUS	start_codon	15075275	15075277	.	-	0	transcript_id "Phchi.S3G217400.t1"; gene_id "Phchi.S3G217400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14952.t1 is derived from g13420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15677545	15679574	.	+	.	Phchi.S3G227100
Phchi.S3	AUGUSTUS	transcript	15677545	15679574	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	start_codon	15677545	15677547	.	+	0	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15677545	15678046	0.57	+	0	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15677545	15678046	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15678047	15678193	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15678194	15678272	1	+	2	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15678194	15678272	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15678273	15678357	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15678358	15678452	1	+	1	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15678358	15678452	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15678453	15678544	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15678545	15678594	1	+	2	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15678545	15678594	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15678595	15678682	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15678683	15678807	0.99	+	0	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15678683	15678807	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15678808	15678924	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15678925	15678991	1	+	1	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15678925	15678991	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15678992	15679073	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15679074	15679163	1	+	0	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15679074	15679163	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15679164	15679268	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15679269	15679380	1	+	0	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15679269	15679380	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	intron	15679381	15679497	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	CDS	15679498	15679574	1	+	2	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	exon	15679498	15679574	.	+	.	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
Phchi.S3	AUGUSTUS	stop_codon	15679575	15679577	.	+	0	transcript_id "Phchi.S3G227100.t1"; gene_id "Phchi.S3G227100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8774.t1 is derived from g5949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37896221	37897781	.	-	.	Phchi.S1G593300
Phchi.S1	AUGUSTUS	transcript	37896221	37897781	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	stop_codon	37896218	37896220	.	-	0	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	CDS	37896221	37896458	0.9	-	1	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	exon	37896221	37896458	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	intron	37896459	37896548	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	CDS	37896549	37896626	1	-	1	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	exon	37896549	37896626	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	intron	37896627	37896738	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	CDS	37896739	37896804	0.99	-	1	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	exon	37896739	37896804	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	intron	37896805	37896952	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	CDS	37896953	37897039	1	-	1	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	exon	37896953	37897039	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	intron	37897040	37897279	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	CDS	37897280	37897325	1	-	2	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	exon	37897280	37897325	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	intron	37897326	37897405	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	CDS	37897406	37897781	1	-	0	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	exon	37897406	37897781	.	-	.	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
Phchi.S1	AUGUSTUS	start_codon	37897779	37897781	.	-	0	transcript_id "Phchi.S1G593300.t1"; gene_id "Phchi.S1G593300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11257.t1 is derived from g15307.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5042097	5043760	.	+	.	Phchi.S4G083900
Phchi.S4	AUGUSTUS	transcript	5042097	5043760	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	start_codon	5042097	5042099	.	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042097	5042144	0.8	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042097	5042144	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042145	5042297	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042298	5042429	1	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042298	5042429	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042430	5042547	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042548	5042605	1	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042548	5042605	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042606	5042681	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042682	5042779	0.97	+	2	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042682	5042779	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042780	5042881	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042882	5042963	0.68	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042882	5042963	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042964	5043201	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043202	5043211	0.56	+	2	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043202	5043211	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5043212	5043296	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043297	5043342	0.38	+	1	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043297	5043342	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5043343	5043524	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043525	5043587	0.73	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043525	5043587	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5043588	5043670	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043671	5043760	0.78	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043671	5043760	.	+	.	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	stop_codon	5043761	5043763	.	+	0	transcript_id "Phchi.S4G083900.t1"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	transcript	5042097	5043760	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	start_codon	5042097	5042099	.	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042097	5042144	0.62	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042097	5042144	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042145	5042297	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042298	5042429	0.81	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042298	5042429	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042430	5042547	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042548	5042605	0.81	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042548	5042605	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042606	5042691	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042692	5042741	0.81	+	2	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042692	5042741	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042742	5042848	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5042849	5042963	0.82	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5042849	5042963	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5042964	5043201	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043202	5043211	0.61	+	2	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043202	5043211	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5043212	5043296	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043297	5043342	0.41	+	1	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043297	5043342	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5043343	5043524	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043525	5043587	0.73	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043525	5043587	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	intron	5043588	5043670	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	CDS	5043671	5043760	0.79	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	exon	5043671	5043760	.	+	.	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
Phchi.S4	AUGUSTUS	stop_codon	5043761	5043763	.	+	0	transcript_id "Phchi.S4G083900.t2"; gene_id "Phchi.S4G083900"
# This transcript jg8342.t2 is derived from g5517.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8342.t3 is derived from g5517.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8343.t1 is derived from g5518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35406697	35407631	.	+	.	Phchi.S1G550200
Phchi.S1	AUGUSTUS	transcript	35406697	35407631	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	start_codon	35406697	35406699	.	+	0	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	CDS	35406697	35406906	1	+	0	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	exon	35406697	35406906	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	intron	35406907	35407044	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	CDS	35407045	35407347	0.99	+	0	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	exon	35407045	35407347	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	intron	35407348	35407432	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	CDS	35407433	35407481	0.96	+	0	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	exon	35407433	35407481	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	intron	35407482	35407566	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	CDS	35407567	35407631	0.96	+	2	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	exon	35407567	35407631	.	+	.	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
Phchi.S1	AUGUSTUS	stop_codon	35407632	35407634	.	+	0	transcript_id "Phchi.S1G550200.t1"; gene_id "Phchi.S1G550200"
# This transcript jg6703.t2 is derived from g3875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6704.t1 is derived from g3876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24635794	24636721	.	-	.	Phchi.S1G386300
Phchi.S1	AUGUSTUS	transcript	24635794	24636721	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	stop_codon	24635791	24635793	.	-	0	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	CDS	24635794	24635952	0.69	-	0	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	exon	24635794	24635952	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	intron	24635953	24636031	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	CDS	24636032	24636187	1	-	0	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	exon	24636032	24636187	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	intron	24636188	24636283	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	CDS	24636284	24636386	1	-	1	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	exon	24636284	24636386	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	intron	24636387	24636461	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	CDS	24636462	24636721	1	-	0	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	exon	24636462	24636721	.	-	.	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
Phchi.S1	AUGUSTUS	start_codon	24636719	24636721	.	-	0	transcript_id "Phchi.S1G386300.t1"; gene_id "Phchi.S1G386300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2384.t1 is derived from g9304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6443515	6446496	.	+	.	Phchi.S5G099300
Phchi.S5	AUGUSTUS	transcript	6443515	6446496	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	start_codon	6443515	6443517	.	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6443515	6443643	0.62	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6443515	6443643	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6443644	6443780	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6443781	6443895	1	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6443781	6443895	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6443896	6443987	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6443988	6444063	0.98	+	2	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6443988	6444063	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6444064	6444143	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6444144	6444255	0.98	+	1	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6444144	6444255	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6444256	6444351	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6444352	6444447	0.86	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6444352	6444447	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6444448	6444555	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6444556	6444718	1	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6444556	6444718	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6444719	6444890	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6444891	6445029	1	+	2	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6444891	6445029	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6445030	6445146	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6445147	6445411	0.78	+	1	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6445147	6445411	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6445412	6445512	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6445513	6445590	1	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6445513	6445590	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6445591	6445714	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6445715	6445801	1	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6445715	6445801	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6445802	6445884	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6445885	6446101	0.99	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6445885	6446101	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6446102	6446192	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6446193	6446371	1	+	2	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6446193	6446371	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	intron	6446372	6446457	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	CDS	6446458	6446496	1	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	exon	6446458	6446496	.	+	.	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
Phchi.S5	AUGUSTUS	stop_codon	6446497	6446499	.	+	0	transcript_id "Phchi.S5G099300.t1"; gene_id "Phchi.S5G099300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg681.t1 is derived from g10463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4727939	4729072	.	-	.	Phchi.S6G064000
Phchi.S6	AUGUSTUS	transcript	4727939	4729072	.	-	.	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	stop_codon	4727936	4727938	.	-	0	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	CDS	4727939	4728783	0.68	-	2	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	exon	4727939	4728783	.	-	.	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	intron	4728784	4729020	.	-	.	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	CDS	4729021	4729072	0.16	-	0	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	exon	4729021	4729072	.	-	.	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
Phchi.S6	AUGUSTUS	start_codon	4729070	4729072	.	-	0	transcript_id "Phchi.S6G064000.t1"; gene_id "Phchi.S6G064000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5700.t1 is derived from g2870.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18426269	18429106	.	-	.	Phchi.S1G285900
Phchi.S1	AUGUSTUS	transcript	18427297	18429106	.	-	.	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	stop_codon	18427294	18427296	.	-	0	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	CDS	18427297	18427302	0.98	-	0	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	exon	18427297	18427302	.	-	.	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	intron	18427303	18427387	.	-	.	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	CDS	18427388	18429106	0.96	-	0	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	exon	18427388	18429106	.	-	.	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	start_codon	18429104	18429106	.	-	0	transcript_id "Phchi.S1G285900.t1"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	transcript	18426269	18429106	.	-	.	transcript_id "Phchi.S1G285900.t2"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	stop_codon	18426266	18426268	.	-	0	transcript_id "Phchi.S1G285900.t2"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	CDS	18426269	18429106	1	-	0	transcript_id "Phchi.S1G285900.t2"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	exon	18426269	18429106	.	-	.	transcript_id "Phchi.S1G285900.t2"; gene_id "Phchi.S1G285900"
Phchi.S1	AUGUSTUS	start_codon	18429104	18429106	.	-	0	transcript_id "Phchi.S1G285900.t2"; gene_id "Phchi.S1G285900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10207.t1 is derived from g7383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46385687	46387485	.	-	.	Phchi.S1G736600
Phchi.S1	AUGUSTUS	transcript	46385687	46387485	.	-	.	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	stop_codon	46385684	46385686	.	-	0	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	CDS	46385687	46386878	0.86	-	1	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	exon	46385687	46386878	.	-	.	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	intron	46386879	46386979	.	-	.	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	CDS	46386980	46387485	0.97	-	0	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	exon	46386980	46387485	.	-	.	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
Phchi.S1	AUGUSTUS	start_codon	46387483	46387485	.	-	0	transcript_id "Phchi.S1G736600.t1"; gene_id "Phchi.S1G736600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14592.t1 is derived from g13060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13618773	13620636	.	+	.	Phchi.S3G191100
Phchi.S3	AUGUSTUS	transcript	13618773	13620636	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	start_codon	13618773	13618775	.	+	0	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	CDS	13618773	13619074	0.99	+	0	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	exon	13618773	13619074	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	intron	13619075	13619150	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	CDS	13619151	13619297	1	+	1	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	exon	13619151	13619297	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	intron	13619298	13619386	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	CDS	13619387	13619452	1	+	1	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	exon	13619387	13619452	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	intron	13619453	13619544	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	CDS	13619545	13619710	1	+	1	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	exon	13619545	13619710	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	intron	13619711	13619794	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	CDS	13619795	13620020	1	+	0	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	exon	13619795	13620020	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	intron	13620021	13620097	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	CDS	13620098	13620636	0.98	+	2	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	exon	13620098	13620636	.	+	.	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
Phchi.S3	AUGUSTUS	stop_codon	13620637	13620639	.	+	0	transcript_id "Phchi.S3G191100.t1"; gene_id "Phchi.S3G191100"
# This transcript jg5786.t2 is derived from g2956.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5787.t1 is derived from g2957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18959760	18960530	.	-	.	Phchi.S1G294600
Phchi.S1	AUGUSTUS	transcript	18959760	18960530	.	-	.	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	stop_codon	18959757	18959759	.	-	0	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	CDS	18959760	18959962	0.97	-	2	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	exon	18959760	18959962	.	-	.	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	intron	18959963	18960055	.	-	.	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	CDS	18960056	18960176	0.89	-	0	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	exon	18960056	18960176	.	-	.	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	intron	18960177	18960299	.	-	.	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	CDS	18960300	18960530	0.61	-	0	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	exon	18960300	18960530	.	-	.	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
Phchi.S1	AUGUSTUS	start_codon	18960528	18960530	.	-	0	transcript_id "Phchi.S1G294600.t1"; gene_id "Phchi.S1G294600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10037.t1 is derived from g7213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45195162	45196843	.	+	.	Phchi.S1G719600
Phchi.S1	AUGUSTUS	transcript	45195162	45196843	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	start_codon	45195162	45195164	.	+	0	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	CDS	45195162	45195389	0.76	+	0	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	exon	45195162	45195389	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	intron	45195390	45195478	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	CDS	45195479	45195500	0.93	+	0	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	exon	45195479	45195500	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	intron	45195501	45195640	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	CDS	45195641	45195780	0.93	+	2	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	exon	45195641	45195780	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	intron	45195781	45196209	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	CDS	45196210	45196284	1	+	0	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	exon	45196210	45196284	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	intron	45196285	45196609	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	CDS	45196610	45196746	0.88	+	0	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	exon	45196610	45196746	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	intron	45196747	45196842	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	CDS	45196843	45196843	0.88	+	1	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	exon	45196843	45196843	.	+	.	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
Phchi.S1	AUGUSTUS	stop_codon	45196844	45196846	.	+	0	transcript_id "Phchi.S1G719600.t1"; gene_id "Phchi.S1G719600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1593.t1 is derived from g8512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1930681	1932772	.	-	.	Phchi.S5G020200
Phchi.S5	AUGUSTUS	transcript	1930681	1932772	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	stop_codon	1930678	1930680	.	-	0	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	CDS	1930681	1930954	1	-	1	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	exon	1930681	1930954	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	intron	1930955	1931051	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	CDS	1931052	1931419	1	-	0	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	exon	1931052	1931419	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	intron	1931420	1931498	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	CDS	1931499	1931801	1	-	0	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	exon	1931499	1931801	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	intron	1931802	1931972	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	CDS	1931973	1932237	1	-	1	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	exon	1931973	1932237	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	intron	1932238	1932380	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	CDS	1932381	1932772	1	-	0	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	exon	1932381	1932772	.	-	.	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
Phchi.S5	AUGUSTUS	start_codon	1932770	1932772	.	-	0	transcript_id "Phchi.S5G020200.t1"; gene_id "Phchi.S5G020200"
# This transcript jg12015.t2 is derived from g7690.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12015.t3 is derived from g7690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12016.t1 is derived from g7691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	532571	533949	.	+	.	Phchi.S2G009600
Phchi.S2	AUGUSTUS	transcript	532571	533949	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	start_codon	532571	532573	.	+	0	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	532571	532626	0.9	+	0	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	532571	532626	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	intron	532627	532718	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	532719	532841	1	+	1	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	532719	532841	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	intron	532842	532932	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	532933	533094	1	+	1	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	532933	533094	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	intron	533095	533220	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	533221	533298	1	+	1	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	533221	533298	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	intron	533299	533381	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	533382	533428	1	+	1	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	533382	533428	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	intron	533429	533605	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	533606	533781	1	+	2	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	533606	533781	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	intron	533782	533877	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	CDS	533878	533949	0.92	+	0	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	exon	533878	533949	.	+	.	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
Phchi.S2	AUGUSTUS	stop_codon	533950	533952	.	+	0	transcript_id "Phchi.S2G009600.t1"; gene_id "Phchi.S2G009600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10098.t1 is derived from g7274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45733654	45736137	.	-	.	Phchi.S1G725700
Phchi.S1	AUGUSTUS	transcript	45733654	45736137	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	stop_codon	45733651	45733653	.	-	0	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	CDS	45733654	45734885	0.96	-	2	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	exon	45733654	45734885	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	intron	45734886	45734982	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	CDS	45734983	45735058	1	-	0	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	exon	45734983	45735058	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	intron	45735059	45735142	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	CDS	45735143	45735756	1	-	2	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	exon	45735143	45735756	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	intron	45735757	45735818	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	CDS	45735819	45735927	1	-	0	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	exon	45735819	45735927	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	intron	45735928	45736014	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	CDS	45736015	45736137	0.87	-	0	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	exon	45736015	45736137	.	-	.	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
Phchi.S1	AUGUSTUS	start_codon	45736135	45736137	.	-	0	transcript_id "Phchi.S1G725700.t1"; gene_id "Phchi.S1G725700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8832.t1 is derived from g6007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38172732	38175458	.	+	.	Phchi.S1G599100
Phchi.S1	AUGUSTUS	transcript	38172732	38175458	.	+	.	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	start_codon	38172732	38172734	.	+	0	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	CDS	38172732	38172867	1	+	0	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	exon	38172732	38172867	.	+	.	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	intron	38172868	38175345	.	+	.	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	CDS	38175346	38175458	0.05	+	2	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	exon	38175346	38175458	.	+	.	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
Phchi.S1	AUGUSTUS	stop_codon	38175459	38175461	.	+	0	transcript_id "Phchi.S1G599100.t1"; gene_id "Phchi.S1G599100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9497.t1 is derived from g6673.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42050121	42053463	.	-	.	Phchi.S1G665600
Phchi.S1	AUGUSTUS	transcript	42050121	42053463	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	stop_codon	42050118	42050120	.	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050121	42050196	0.99	-	1	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050121	42050196	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050197	42050288	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050289	42050368	1	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050289	42050368	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050369	42050455	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050456	42050536	1	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050456	42050536	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050537	42050636	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050637	42050706	1	-	1	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050637	42050706	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050707	42050784	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050785	42050862	1	-	1	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050785	42050862	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050863	42050993	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050994	42051199	0.99	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050994	42051199	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051200	42051325	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42051326	42051575	1	-	1	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42051326	42051575	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051576	42051671	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42051672	42051717	1	-	2	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42051672	42051717	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051718	42051817	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42051818	42051887	1	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42051818	42051887	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051888	42052062	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052063	42052132	1	-	1	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052063	42052132	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42052133	42052302	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052303	42052387	1	-	2	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052303	42052387	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42052388	42052743	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052744	42052828	1	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052744	42052828	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42052829	42052953	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052954	42053044	1	-	1	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052954	42053044	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42053045	42053341	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42053342	42053463	0.54	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42053342	42053463	.	-	.	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	start_codon	42053461	42053463	.	-	0	transcript_id "Phchi.S1G665600.t1"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	transcript	42050121	42053463	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	stop_codon	42050118	42050120	.	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050121	42050196	0.99	-	1	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050121	42050196	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050197	42050288	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050289	42050368	1	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050289	42050368	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050369	42050455	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050456	42050536	1	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050456	42050536	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050537	42050636	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050637	42050706	1	-	1	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050637	42050706	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050707	42050784	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050785	42050862	1	-	1	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050785	42050862	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42050863	42050993	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42050994	42051199	0.98	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42050994	42051199	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051200	42051325	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42051326	42051575	1	-	1	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42051326	42051575	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051576	42051671	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42051672	42051717	1	-	2	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42051672	42051717	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051718	42051811	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42051812	42051887	0.95	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42051812	42051887	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42051888	42052062	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052063	42052132	1	-	1	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052063	42052132	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42052133	42052302	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052303	42052387	1	-	2	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052303	42052387	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42052388	42052743	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052744	42052828	1	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052744	42052828	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42052829	42052953	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42052954	42053044	1	-	1	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42052954	42053044	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	intron	42053045	42053341	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	CDS	42053342	42053463	0.58	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	exon	42053342	42053463	.	-	.	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
Phchi.S1	AUGUSTUS	start_codon	42053461	42053463	.	-	0	transcript_id "Phchi.S1G665600.t2"; gene_id "Phchi.S1G665600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2261.t1 is derived from g9181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5720273	5721073	.	-	.	Phchi.S5G087000
Phchi.S5	AUGUSTUS	transcript	5720273	5721073	.	-	.	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	stop_codon	5720270	5720272	.	-	0	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	CDS	5720273	5720312	1	-	1	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	exon	5720273	5720312	.	-	.	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	intron	5720313	5720500	.	-	.	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	CDS	5720501	5720561	0.98	-	2	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	exon	5720501	5720561	.	-	.	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	intron	5720562	5720757	.	-	.	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	CDS	5720758	5721073	0.85	-	0	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	exon	5720758	5721073	.	-	.	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	start_codon	5721071	5721073	.	-	0	transcript_id "Phchi.S5G087000.t1"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	transcript	5720343	5721073	.	-	.	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	stop_codon	5720340	5720342	.	-	0	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	CDS	5720343	5720343	0.95	-	1	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	exon	5720343	5720343	.	-	.	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	intron	5720344	5720500	.	-	.	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	CDS	5720501	5720561	0.92	-	2	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	exon	5720501	5720561	.	-	.	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	intron	5720562	5720757	.	-	.	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	CDS	5720758	5721073	0.78	-	0	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	exon	5720758	5721073	.	-	.	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
Phchi.S5	AUGUSTUS	start_codon	5721071	5721073	.	-	0	transcript_id "Phchi.S5G087000.t2"; gene_id "Phchi.S5G087000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12715.t1 is derived from g11180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	748535	749096	.	+	.	Phchi.S3G003400
Phchi.S3	AUGUSTUS	transcript	748535	749096	.	+	.	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	start_codon	748535	748537	.	+	0	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	CDS	748535	748799	0.52	+	0	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	exon	748535	748799	.	+	.	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	intron	748800	748881	.	+	.	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	CDS	748882	749096	0.52	+	2	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	exon	748882	749096	.	+	.	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
Phchi.S3	AUGUSTUS	stop_codon	749097	749099	.	+	0	transcript_id "Phchi.S3G003400.t1"; gene_id "Phchi.S3G003400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3503.t1 is derived from g672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4119449	4120291	.	-	.	Phchi.S1G066200
Phchi.S1	AUGUSTUS	transcript	4119449	4120291	.	-	.	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	stop_codon	4119446	4119448	.	-	0	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	CDS	4119449	4119772	1	-	0	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	exon	4119449	4119772	.	-	.	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	intron	4119773	4119862	.	-	.	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	CDS	4119863	4120291	0.6	-	0	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	exon	4119863	4120291	.	-	.	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
Phchi.S1	AUGUSTUS	start_codon	4120289	4120291	.	-	0	transcript_id "Phchi.S1G066200.t1"; gene_id "Phchi.S1G066200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13630.t1 is derived from g12097.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7834096	7836933	.	+	.	Phchi.S3G094900
Phchi.S3	AUGUSTUS	transcript	7834096	7836933	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	start_codon	7834096	7834098	.	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834096	7834119	0.87	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834096	7834119	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834120	7834213	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834214	7834333	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834214	7834333	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834334	7834432	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834433	7834696	0.98	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834433	7834696	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834697	7834798	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834799	7834891	0.97	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834799	7834891	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834892	7835013	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835014	7835220	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835014	7835220	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835221	7835299	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835300	7835403	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835300	7835403	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835404	7835497	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835498	7835564	1	+	1	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835498	7835564	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835565	7835753	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835754	7835861	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835754	7835861	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835862	7836038	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836039	7836131	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836039	7836131	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836132	7836217	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836218	7836317	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836218	7836317	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836318	7836388	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836389	7836459	1	+	2	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836389	7836459	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836460	7836555	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836556	7836614	1	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836556	7836614	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836615	7836702	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836703	7836763	0.95	+	1	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836703	7836763	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836764	7836873	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836874	7836933	0.92	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836874	7836933	.	+	.	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	stop_codon	7836934	7836936	.	+	0	transcript_id "Phchi.S3G094900.t1"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	transcript	7834096	7836933	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	start_codon	7834096	7834098	.	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834096	7834119	0.86	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834096	7834119	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834120	7834213	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834214	7834333	0.98	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834214	7834333	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834334	7834591	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834592	7834696	0.54	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834592	7834696	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834697	7834798	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7834799	7834891	0.99	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7834799	7834891	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7834892	7835013	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835014	7835220	1	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835014	7835220	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835221	7835299	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835300	7835403	1	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835300	7835403	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835404	7835497	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835498	7835564	1	+	1	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835498	7835564	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835565	7835753	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7835754	7835861	1	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7835754	7835861	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7835862	7836038	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836039	7836131	1	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836039	7836131	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836132	7836217	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836218	7836317	1	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836218	7836317	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836318	7836388	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836389	7836459	1	+	2	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836389	7836459	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836460	7836555	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836556	7836614	1	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836556	7836614	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836615	7836702	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836703	7836763	0.95	+	1	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836703	7836763	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	intron	7836764	7836873	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	CDS	7836874	7836933	0.9	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	exon	7836874	7836933	.	+	.	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
Phchi.S3	AUGUSTUS	stop_codon	7836934	7836936	.	+	0	transcript_id "Phchi.S3G094900.t2"; gene_id "Phchi.S3G094900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11118.t1 is derived from g15168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4236797	4239334	.	+	.	Phchi.S4G070000
Phchi.S4	AUGUSTUS	transcript	4236797	4239334	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	start_codon	4236797	4236799	.	+	0	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4236797	4237075	0.57	+	0	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4236797	4237075	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4237076	4237161	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4237162	4237586	1	+	0	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4237162	4237586	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4237587	4237666	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4237667	4237779	1	+	1	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4237667	4237779	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4237780	4237951	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4237952	4238021	0.99	+	2	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4237952	4238021	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4238022	4238133	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4238134	4238233	0.56	+	1	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4238134	4238233	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4238234	4238313	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4238314	4238382	1	+	0	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4238314	4238382	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4238383	4238468	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4238469	4238565	0.79	+	0	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4238469	4238565	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	intron	4238566	4238648	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	CDS	4238649	4239334	0.77	+	2	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	exon	4238649	4239334	.	+	.	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
Phchi.S4	AUGUSTUS	stop_codon	4239335	4239337	.	+	0	transcript_id "Phchi.S4G070000.t1"; gene_id "Phchi.S4G070000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8455.t1 is derived from g5630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36012349	36013121	.	+	.	Phchi.S1G561400
Phchi.S1	AUGUSTUS	transcript	36012349	36013121	.	+	.	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	start_codon	36012349	36012351	.	+	0	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	CDS	36012349	36012376	0.76	+	0	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	exon	36012349	36012376	.	+	.	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	intron	36012377	36012715	.	+	.	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	CDS	36012716	36012827	0.74	+	2	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	exon	36012716	36012827	.	+	.	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	intron	36012828	36013030	.	+	.	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	CDS	36013031	36013121	0.4	+	1	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	exon	36013031	36013121	.	+	.	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
Phchi.S1	AUGUSTUS	stop_codon	36013122	36013124	.	+	0	transcript_id "Phchi.S1G561400.t1"; gene_id "Phchi.S1G561400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1140.t1 is derived from g10923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7929390	7929968	.	-	.	Phchi.S6G109900
Phchi.S6	AUGUSTUS	transcript	7929390	7929968	.	-	.	transcript_id "Phchi.S6G109900.t1"; gene_id "Phchi.S6G109900"
Phchi.S6	AUGUSTUS	stop_codon	7929387	7929389	.	-	0	transcript_id "Phchi.S6G109900.t1"; gene_id "Phchi.S6G109900"
Phchi.S6	AUGUSTUS	CDS	7929390	7929968	0.71	-	0	transcript_id "Phchi.S6G109900.t1"; gene_id "Phchi.S6G109900"
Phchi.S6	AUGUSTUS	exon	7929390	7929968	.	-	.	transcript_id "Phchi.S6G109900.t1"; gene_id "Phchi.S6G109900"
Phchi.S6	AUGUSTUS	start_codon	7929966	7929968	.	-	0	transcript_id "Phchi.S6G109900.t1"; gene_id "Phchi.S6G109900"
# This transcript jg14132.t2 is derived from g12599.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14133.t1 is derived from g12600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11075646	11078198	.	-	.	Phchi.S3G145200
Phchi.S3	AUGUSTUS	transcript	11075646	11078198	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	stop_codon	11075643	11075645	.	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11075646	11075783	1	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11075646	11075783	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11075784	11075872	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11075873	11075948	1	-	1	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11075873	11075948	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11075949	11076022	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11076023	11076126	1	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11076023	11076126	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11076127	11076232	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11076233	11076301	1	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11076233	11076301	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11076302	11076400	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11076401	11076533	1	-	1	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11076401	11076533	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11076534	11076629	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11076630	11076676	1	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11076630	11076676	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11076677	11076802	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11076803	11076871	1	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11076803	11076871	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11076872	11077070	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11077071	11077142	1	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11077071	11077142	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11077143	11077308	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11077309	11077385	1	-	2	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11077309	11077385	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11077386	11077472	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11077473	11077546	1	-	1	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11077473	11077546	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11077547	11077633	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11077634	11077736	0.87	-	2	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11077634	11077736	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11077737	11077847	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11077848	11077863	0.81	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11077848	11077863	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	intron	11077864	11077940	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	CDS	11077941	11078198	0.46	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	exon	11077941	11078198	.	-	.	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
Phchi.S3	AUGUSTUS	start_codon	11078196	11078198	.	-	0	transcript_id "Phchi.S3G145200.t1"; gene_id "Phchi.S3G145200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3710.t1 is derived from g879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5274431	5275777	.	+	.	Phchi.S1G086900
Phchi.S1	AUGUSTUS	transcript	5274431	5275777	.	+	.	transcript_id "Phchi.S1G086900.t1"; gene_id "Phchi.S1G086900"
Phchi.S1	AUGUSTUS	start_codon	5274431	5274433	.	+	0	transcript_id "Phchi.S1G086900.t1"; gene_id "Phchi.S1G086900"
Phchi.S1	AUGUSTUS	CDS	5274431	5275777	0.78	+	0	transcript_id "Phchi.S1G086900.t1"; gene_id "Phchi.S1G086900"
Phchi.S1	AUGUSTUS	exon	5274431	5275777	.	+	.	transcript_id "Phchi.S1G086900.t1"; gene_id "Phchi.S1G086900"
Phchi.S1	AUGUSTUS	stop_codon	5275778	5275780	.	+	0	transcript_id "Phchi.S1G086900.t1"; gene_id "Phchi.S1G086900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2516.t1 is derived from g9436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7104946	7106163	.	+	.	Phchi.S5G112500
Phchi.S5	AUGUSTUS	transcript	7104946	7106163	.	+	.	transcript_id "Phchi.S5G112500.t1"; gene_id "Phchi.S5G112500"
Phchi.S5	AUGUSTUS	start_codon	7104946	7104948	.	+	0	transcript_id "Phchi.S5G112500.t1"; gene_id "Phchi.S5G112500"
Phchi.S5	AUGUSTUS	CDS	7104946	7106163	0.53	+	0	transcript_id "Phchi.S5G112500.t1"; gene_id "Phchi.S5G112500"
Phchi.S5	AUGUSTUS	exon	7104946	7106163	.	+	.	transcript_id "Phchi.S5G112500.t1"; gene_id "Phchi.S5G112500"
Phchi.S5	AUGUSTUS	stop_codon	7106164	7106166	.	+	0	transcript_id "Phchi.S5G112500.t1"; gene_id "Phchi.S5G112500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13747.t1 is derived from g12214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8680245	8681053	.	-	.	Phchi.S3G106600
Phchi.S3	AUGUSTUS	transcript	8680245	8681053	.	-	.	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	stop_codon	8680242	8680244	.	-	0	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	CDS	8680245	8680831	1	-	2	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	exon	8680245	8680831	.	-	.	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	intron	8680832	8681031	.	-	.	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	CDS	8681032	8681053	0.51	-	0	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	exon	8681032	8681053	.	-	.	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
Phchi.S3	AUGUSTUS	start_codon	8681051	8681053	.	-	0	transcript_id "Phchi.S3G106600.t1"; gene_id "Phchi.S3G106600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7194.t1 is derived from g4366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27536154	27538265	.	-	.	Phchi.S1G435300
Phchi.S1	AUGUSTUS	transcript	27536154	27538265	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	stop_codon	27536151	27536153	.	-	0	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	CDS	27536154	27536786	1	-	0	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	exon	27536154	27536786	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	intron	27536787	27536876	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	CDS	27536877	27537076	1	-	2	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	exon	27536877	27537076	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	intron	27537077	27537211	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	CDS	27537212	27537281	1	-	0	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	exon	27537212	27537281	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	intron	27537282	27537366	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	CDS	27537367	27537517	1	-	1	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	exon	27537367	27537517	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	intron	27537518	27537608	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	CDS	27537609	27537842	0.99	-	1	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	exon	27537609	27537842	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	intron	27537843	27537951	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	CDS	27537952	27538265	0.99	-	0	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	exon	27537952	27538265	.	-	.	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
Phchi.S1	AUGUSTUS	start_codon	27538263	27538265	.	-	0	transcript_id "Phchi.S1G435300.t1"; gene_id "Phchi.S1G435300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6.t1 is derived from g9794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C102	AUGUSTUS	gene	26797	27360	.	+	.	Phchi.C102G000200
Phchi.C102	AUGUSTUS	transcript	26797	27360	.	+	.	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	start_codon	26797	26799	.	+	0	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	CDS	26797	26948	0.9	+	0	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	exon	26797	26948	.	+	.	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	intron	26949	27073	.	+	.	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	CDS	27074	27235	0.96	+	1	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	exon	27074	27235	.	+	.	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	intron	27236	27320	.	+	.	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	CDS	27321	27360	0.83	+	1	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	exon	27321	27360	.	+	.	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
Phchi.C102	AUGUSTUS	stop_codon	27361	27363	.	+	0	transcript_id "Phchi.C102G000200.t1"; gene_id "Phchi.C102G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13971.t1 is derived from g12438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9999468	10000561	.	-	.	Phchi.S3G129000
Phchi.S3	AUGUSTUS	transcript	9999468	10000561	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	stop_codon	9999465	9999467	.	-	0	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	CDS	9999468	9999653	1	-	0	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	exon	9999468	9999653	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	intron	9999654	9999750	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	CDS	9999751	9999948	1	-	0	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	exon	9999751	9999948	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	intron	9999949	10000019	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	CDS	10000020	10000156	1	-	2	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	exon	10000020	10000156	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	intron	10000157	10000280	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	CDS	10000281	10000384	1	-	1	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	exon	10000281	10000384	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	intron	10000385	10000475	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	CDS	10000476	10000561	1	-	0	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	exon	10000476	10000561	.	-	.	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
Phchi.S3	AUGUSTUS	start_codon	10000559	10000561	.	-	0	transcript_id "Phchi.S3G129000.t1"; gene_id "Phchi.S3G129000"
# This transcript jg10986.t2 is derived from g15036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10986.t3 is derived from g15036.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10987.t1 is derived from g15037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3535736	3537083	.	-	.	Phchi.S4G056900
Phchi.S4	AUGUSTUS	transcript	3535736	3537083	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	stop_codon	3535733	3535735	.	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3535736	3535807	0.97	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3535736	3535807	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	intron	3535808	3535907	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3535908	3535979	1	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3535908	3535979	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	intron	3535980	3536062	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3536063	3536185	0.82	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3536063	3536185	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	intron	3536186	3536289	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3536290	3536454	1	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3536290	3536454	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	intron	3536455	3536541	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3536542	3536676	1	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3536542	3536676	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	intron	3536677	3536796	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3536797	3536949	1	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3536797	3536949	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	intron	3536950	3537071	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	CDS	3537072	3537083	1	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	exon	3537072	3537083	.	-	.	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
Phchi.S4	AUGUSTUS	start_codon	3537081	3537083	.	-	0	transcript_id "Phchi.S4G056900.t1"; gene_id "Phchi.S4G056900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9730.t1 is derived from g6906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43435769	43436767	.	-	.	Phchi.S1G688900
Phchi.S1	AUGUSTUS	transcript	43435769	43436767	.	-	.	transcript_id "Phchi.S1G688900.t1"; gene_id "Phchi.S1G688900"
Phchi.S1	AUGUSTUS	stop_codon	43435766	43435768	.	-	0	transcript_id "Phchi.S1G688900.t1"; gene_id "Phchi.S1G688900"
Phchi.S1	AUGUSTUS	CDS	43435769	43436767	0.28	-	0	transcript_id "Phchi.S1G688900.t1"; gene_id "Phchi.S1G688900"
Phchi.S1	AUGUSTUS	exon	43435769	43436767	.	-	.	transcript_id "Phchi.S1G688900.t1"; gene_id "Phchi.S1G688900"
Phchi.S1	AUGUSTUS	start_codon	43436765	43436767	.	-	0	transcript_id "Phchi.S1G688900.t1"; gene_id "Phchi.S1G688900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg14120.t1 is derived from g12587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10973217	10978583	.	+	.	Phchi.S3G143900
Phchi.S3	AUGUSTUS	transcript	10973217	10976552	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	start_codon	10973217	10973219	.	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10973217	10973444	1	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10973217	10973444	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10973445	10973622	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10973623	10973865	1	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10973623	10973865	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10973866	10973979	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10973980	10974750	1	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10973980	10974750	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10974751	10974851	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10974852	10975099	1	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10974852	10975099	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975100	10975224	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975225	10975384	1	+	1	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975225	10975384	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975385	10975546	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975547	10975673	1	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975547	10975673	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975674	10975756	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975757	10975846	1	+	2	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975757	10975846	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975847	10975992	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975993	10976136	0.8	+	2	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975993	10976136	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976137	10976239	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976240	10976309	1	+	2	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976240	10976309	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976310	10976395	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976396	10976438	1	+	1	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976396	10976438	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976439	10976531	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976532	10976552	1	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976532	10976552	.	+	.	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	stop_codon	10976553	10976555	.	+	0	transcript_id "Phchi.S3G143900.t1"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	transcript	10976678	10978583	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	start_codon	10976678	10976680	.	+	0	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976678	10976695	0.79	+	0	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976678	10976695	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976696	10976780	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976781	10977033	0.9	+	0	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976781	10977033	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977034	10977125	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977126	10977497	0.57	+	2	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977126	10977497	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977498	10977668	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977669	10977754	1	+	2	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977669	10977754	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977755	10977855	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977856	10978245	0.97	+	0	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977856	10978245	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10978246	10978340	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10978341	10978583	0.74	+	0	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10978341	10978583	.	+	.	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	stop_codon	10978584	10978586	.	+	0	transcript_id "Phchi.S3G143900.t2"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	transcript	10976678	10978583	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	start_codon	10976678	10976680	.	+	0	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976678	10976695	0.84	+	0	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976678	10976695	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976696	10976780	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976781	10977033	0.88	+	0	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976781	10977033	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977034	10977125	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977126	10977497	0.53	+	2	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977126	10977497	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977498	10977671	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977672	10977754	0.97	+	2	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977672	10977754	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977755	10977855	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977856	10978245	1	+	0	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977856	10978245	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10978246	10978340	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10978341	10978583	0.72	+	0	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10978341	10978583	.	+	.	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	stop_codon	10978584	10978586	.	+	0	transcript_id "Phchi.S3G143900.t3"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	transcript	10973217	10978583	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	start_codon	10973217	10973219	.	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10973217	10973444	0.97	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10973217	10973444	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10973445	10973622	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10973623	10973865	1	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10973623	10973865	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10973866	10973979	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10973980	10974750	0.98	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10973980	10974750	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10974751	10974851	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10974852	10975099	1	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10974852	10975099	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975100	10975224	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975225	10975384	1	+	1	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975225	10975384	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975385	10975546	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975547	10975673	1	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975547	10975673	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975674	10975756	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975757	10975846	0.99	+	2	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975757	10975846	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10975847	10975992	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10975993	10976136	0.81	+	2	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10975993	10976136	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976137	10976276	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976277	10976309	0.46	+	2	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976277	10976309	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976310	10976531	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976532	10976695	0.91	+	2	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976532	10976695	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10976696	10976780	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10976781	10977033	0.89	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10976781	10977033	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977034	10977125	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977126	10977497	0.53	+	2	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977126	10977497	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977498	10977668	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977669	10977754	1	+	2	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977669	10977754	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10977755	10977855	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10977856	10978245	0.98	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10977856	10978245	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	intron	10978246	10978340	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	CDS	10978341	10978583	0.61	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	exon	10978341	10978583	.	+	.	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
Phchi.S3	AUGUSTUS	stop_codon	10978584	10978586	.	+	0	transcript_id "Phchi.S3G143900.t4"; gene_id "Phchi.S3G143900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5462.t1 is derived from g2632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16955536	16958106	.	-	.	Phchi.S1G262100
Phchi.S1	AUGUSTUS	transcript	16955536	16958106	.	-	.	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	stop_codon	16955533	16955535	.	-	0	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	CDS	16955536	16956236	1	-	2	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	exon	16955536	16956236	.	-	.	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	intron	16956237	16956342	.	-	.	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	CDS	16956343	16956855	0.94	-	2	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	exon	16956343	16956855	.	-	.	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	intron	16956856	16956980	.	-	.	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	CDS	16956981	16958106	0.64	-	0	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	exon	16956981	16958106	.	-	.	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
Phchi.S1	AUGUSTUS	start_codon	16958104	16958106	.	-	0	transcript_id "Phchi.S1G262100.t1"; gene_id "Phchi.S1G262100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13692.t1 is derived from g12159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8225219	8229462	.	+	.	Phchi.S3G101100
Phchi.S3	AUGUSTUS	transcript	8225219	8229462	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	start_codon	8225219	8225221	.	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8225219	8225299	0.65	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8225219	8225299	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	intron	8225300	8225537	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8225538	8225546	0.89	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8225538	8225546	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	intron	8225547	8225659	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8225660	8228472	0.51	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8225660	8228472	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	intron	8228473	8228651	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8228652	8228781	0.48	+	1	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8228652	8228781	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	intron	8228782	8228912	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8228913	8229145	0.65	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8228913	8229145	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	intron	8229146	8229289	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8229290	8229335	0.74	+	1	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8229290	8229335	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	intron	8229336	8229435	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	CDS	8229436	8229462	0.95	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	exon	8229436	8229462	.	+	.	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
Phchi.S3	AUGUSTUS	stop_codon	8229463	8229465	.	+	0	transcript_id "Phchi.S3G101100.t1"; gene_id "Phchi.S3G101100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8122.t1 is derived from g5297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33451650	33456669	.	-	.	Phchi.S1G528100
Phchi.S1	AUGUSTUS	transcript	33451650	33456669	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	stop_codon	33451647	33451649	.	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33451650	33452068	0.96	-	2	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33451650	33452068	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33452069	33452171	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33452172	33452538	1	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33452172	33452538	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33452539	33453274	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33453275	33453495	1	-	2	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33453275	33453495	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33453496	33453661	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33453662	33453834	1	-	1	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33453662	33453834	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33453835	33454020	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454021	33454113	1	-	1	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454021	33454113	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33454114	33454316	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454317	33454361	1	-	1	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454317	33454361	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33454362	33454490	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454491	33454856	1	-	1	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454491	33454856	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33454857	33454940	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454941	33455086	1	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454941	33455086	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33455087	33455749	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33455750	33455833	1	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33455750	33455833	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33455834	33455911	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33455912	33455990	1	-	1	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33455912	33455990	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33455991	33456129	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33456130	33456209	1	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33456130	33456209	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33456210	33456424	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33456425	33456476	1	-	1	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33456425	33456476	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33456477	33456628	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33456629	33456669	1	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33456629	33456669	.	-	.	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	start_codon	33456667	33456669	.	-	0	transcript_id "Phchi.S1G528100.t1"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	transcript	33451650	33456669	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	stop_codon	33451647	33451649	.	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33451650	33452068	0.97	-	2	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33451650	33452068	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33452069	33452171	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33452172	33452538	1	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33452172	33452538	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33452539	33453274	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33453275	33453495	1	-	2	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33453275	33453495	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33453496	33453661	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33453662	33453834	1	-	1	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33453662	33453834	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33453835	33454020	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454021	33454110	0.95	-	1	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454021	33454110	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33454111	33454316	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454317	33454361	1	-	1	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454317	33454361	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33454362	33454490	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454491	33454856	1	-	1	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454491	33454856	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33454857	33454940	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33454941	33455086	1	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33454941	33455086	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33455087	33455749	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33455750	33455833	1	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33455750	33455833	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33455834	33455911	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33455912	33455990	1	-	1	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33455912	33455990	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33455991	33456129	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33456130	33456209	1	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33456130	33456209	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33456210	33456424	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33456425	33456476	1	-	1	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33456425	33456476	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	intron	33456477	33456628	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	CDS	33456629	33456669	0.99	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	exon	33456629	33456669	.	-	.	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
Phchi.S1	AUGUSTUS	start_codon	33456667	33456669	.	-	0	transcript_id "Phchi.S1G528100.t2"; gene_id "Phchi.S1G528100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6002.t1 is derived from g3173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20342416	20345488	.	+	.	Phchi.S1G316100
Phchi.S1	AUGUSTUS	transcript	20342416	20344364	.	+	.	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	start_codon	20342416	20342418	.	+	0	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	CDS	20342416	20343378	0.88	+	0	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	exon	20342416	20343378	.	+	.	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	intron	20343379	20343473	.	+	.	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	CDS	20343474	20344364	0.84	+	0	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	exon	20343474	20344364	.	+	.	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	stop_codon	20344365	20344367	.	+	0	transcript_id "Phchi.S1G316100.t1"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	transcript	20342416	20345488	.	+	.	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	start_codon	20342416	20342418	.	+	0	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	CDS	20342416	20343378	0.86	+	0	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	exon	20342416	20343378	.	+	.	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	intron	20343379	20343473	.	+	.	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	CDS	20343474	20344271	0.71	+	0	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	exon	20343474	20344271	.	+	.	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	intron	20344272	20344390	.	+	.	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	CDS	20344391	20345488	0.99	+	0	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	exon	20344391	20345488	.	+	.	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
Phchi.S1	AUGUSTUS	stop_codon	20345489	20345491	.	+	0	transcript_id "Phchi.S1G316100.t2"; gene_id "Phchi.S1G316100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7861.t1 is derived from g5035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31571253	31573448	.	+	.	Phchi.S1G502000
Phchi.S1	AUGUSTUS	transcript	31571253	31573448	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	start_codon	31571253	31571255	.	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31571253	31571370	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31571253	31571370	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31571371	31571475	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31571476	31571648	1	+	2	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31571476	31571648	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31571649	31571720	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31571721	31571871	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31571721	31571871	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31571872	31571966	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31571967	31572058	0.99	+	2	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31571967	31572058	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31572059	31572168	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31572169	31572282	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31572169	31572282	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31572283	31572373	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31572374	31572441	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31572374	31572441	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31572442	31572570	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31572571	31572619	1	+	1	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31572571	31572619	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31572620	31572753	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31572754	31572846	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31572754	31572846	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31572847	31572943	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31572944	31573009	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31572944	31573009	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31573010	31573091	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31573092	31573138	1	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31573092	31573138	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31573139	31573238	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31573239	31573306	1	+	1	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31573239	31573306	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	intron	31573307	31573416	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	CDS	31573417	31573448	0.92	+	2	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	exon	31573417	31573448	.	+	.	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
Phchi.S1	AUGUSTUS	stop_codon	31573449	31573451	.	+	0	transcript_id "Phchi.S1G502000.t1"; gene_id "Phchi.S1G502000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13762.t1 is derived from g12229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8770784	8771175	.	-	.	Phchi.S3G108100
Phchi.S3	AUGUSTUS	transcript	8770784	8771175	.	-	.	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	stop_codon	8770781	8770783	.	-	0	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	CDS	8770784	8771001	0.63	-	2	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	exon	8770784	8771001	.	-	.	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	intron	8771002	8771081	.	-	.	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	CDS	8771082	8771175	0.93	-	0	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	exon	8771082	8771175	.	-	.	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
Phchi.S3	AUGUSTUS	start_codon	8771173	8771175	.	-	0	transcript_id "Phchi.S3G108100.t1"; gene_id "Phchi.S3G108100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11344.t1 is derived from g15394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5662427	5665366	.	+	.	Phchi.S4G092600
Phchi.S4	AUGUSTUS	transcript	5662427	5665366	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	start_codon	5662427	5662429	.	+	0	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	CDS	5662427	5662540	0.7	+	0	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	exon	5662427	5662540	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	intron	5662541	5662751	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	CDS	5662752	5662796	0.88	+	0	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	exon	5662752	5662796	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	intron	5662797	5662883	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	CDS	5662884	5663275	0.41	+	0	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	exon	5662884	5663275	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	intron	5663276	5663506	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	CDS	5663507	5664997	0.5	+	1	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	exon	5663507	5664997	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	intron	5664998	5665317	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	CDS	5665318	5665366	0.56	+	1	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	exon	5665318	5665366	.	+	.	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
Phchi.S4	AUGUSTUS	stop_codon	5665367	5665369	.	+	0	transcript_id "Phchi.S4G092600.t1"; gene_id "Phchi.S4G092600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14954.t1 is derived from g13422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15702220	15705393	.	-	.	Phchi.S3G227300
Phchi.S3	AUGUSTUS	transcript	15702220	15705393	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	stop_codon	15702217	15702219	.	-	0	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15702220	15703079	1	-	2	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15702220	15703079	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15703080	15703183	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15703184	15703553	1	-	0	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15703184	15703553	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15703554	15703708	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15703709	15703761	1	-	2	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15703709	15703761	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15703762	15703863	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15703864	15704124	0.99	-	2	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15703864	15704124	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15704125	15704237	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15704238	15704312	1	-	2	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15704238	15704312	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15704313	15704483	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15704484	15704741	1	-	2	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15704484	15704741	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15704742	15704828	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15704829	15705051	1	-	0	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15704829	15705051	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	intron	15705052	15705156	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	CDS	15705157	15705393	0.98	-	0	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	exon	15705157	15705393	.	-	.	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
Phchi.S3	AUGUSTUS	start_codon	15705391	15705393	.	-	0	transcript_id "Phchi.S3G227300.t1"; gene_id "Phchi.S3G227300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6847.t1 is derived from g4019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25534474	25535244	.	-	.	Phchi.S1G400600
Phchi.S1	AUGUSTUS	transcript	25534474	25535244	.	-	.	transcript_id "Phchi.S1G400600.t1"; gene_id "Phchi.S1G400600"
Phchi.S1	AUGUSTUS	stop_codon	25534471	25534473	.	-	0	transcript_id "Phchi.S1G400600.t1"; gene_id "Phchi.S1G400600"
Phchi.S1	AUGUSTUS	CDS	25534474	25535244	1	-	0	transcript_id "Phchi.S1G400600.t1"; gene_id "Phchi.S1G400600"
Phchi.S1	AUGUSTUS	exon	25534474	25535244	.	-	.	transcript_id "Phchi.S1G400600.t1"; gene_id "Phchi.S1G400600"
Phchi.S1	AUGUSTUS	start_codon	25535242	25535244	.	-	0	transcript_id "Phchi.S1G400600.t1"; gene_id "Phchi.S1G400600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4666.t1 is derived from g1836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11707332	11707694	.	-	.	Phchi.S1G182500
Phchi.S1	AUGUSTUS	transcript	11707332	11707694	.	-	.	transcript_id "Phchi.S1G182500.t1"; gene_id "Phchi.S1G182500"
Phchi.S1	AUGUSTUS	stop_codon	11707329	11707331	.	-	0	transcript_id "Phchi.S1G182500.t1"; gene_id "Phchi.S1G182500"
Phchi.S1	AUGUSTUS	CDS	11707332	11707694	0.91	-	0	transcript_id "Phchi.S1G182500.t1"; gene_id "Phchi.S1G182500"
Phchi.S1	AUGUSTUS	exon	11707332	11707694	.	-	.	transcript_id "Phchi.S1G182500.t1"; gene_id "Phchi.S1G182500"
Phchi.S1	AUGUSTUS	start_codon	11707692	11707694	.	-	0	transcript_id "Phchi.S1G182500.t1"; gene_id "Phchi.S1G182500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11502.t1 is derived from g15552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6747464	6748598	.	+	.	Phchi.S4G108400
Phchi.S4	AUGUSTUS	transcript	6747464	6748598	.	+	.	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	start_codon	6747464	6747466	.	+	0	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	CDS	6747464	6747937	0.62	+	0	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	exon	6747464	6747937	.	+	.	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	intron	6747938	6748034	.	+	.	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	CDS	6748035	6748316	1	+	0	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	exon	6748035	6748316	.	+	.	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	intron	6748317	6748397	.	+	.	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	CDS	6748398	6748598	0.91	+	0	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	exon	6748398	6748598	.	+	.	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
Phchi.S4	AUGUSTUS	stop_codon	6748599	6748601	.	+	0	transcript_id "Phchi.S4G108400.t1"; gene_id "Phchi.S4G108400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1782.t1 is derived from g8702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2985511	2989157	.	+	.	Phchi.S5G039100
Phchi.S5	AUGUSTUS	transcript	2985511	2989157	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	start_codon	2985511	2985513	.	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2985511	2985613	0.56	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2985511	2985613	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2985614	2985755	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2985756	2985976	1	+	2	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2985756	2985976	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2985977	2986131	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2986132	2986278	1	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2986132	2986278	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2986279	2986360	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2986361	2986471	1	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2986361	2986471	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2986472	2986605	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2986606	2987313	0.61	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2986606	2987313	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2987314	2987427	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2987428	2987883	0.76	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2987428	2987883	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2987884	2988017	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2988018	2988499	0.82	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2988018	2988499	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2988500	2988588	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2988589	2988661	1	+	1	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2988589	2988661	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2988662	2988748	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2988749	2988776	0.47	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2988749	2988776	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2988777	2988840	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2988841	2988908	0.45	+	2	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2988841	2988908	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2988909	2989004	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2989005	2989075	1	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2989005	2989075	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	intron	2989076	2989156	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	CDS	2989157	2989157	1	+	1	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	exon	2989157	2989157	.	+	.	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
Phchi.S5	AUGUSTUS	stop_codon	2989158	2989160	.	+	0	transcript_id "Phchi.S5G039100.t1"; gene_id "Phchi.S5G039100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5292.t1 is derived from g2462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16043687	16046066	.	-	.	Phchi.S1G245100
Phchi.S1	AUGUSTUS	transcript	16043687	16046066	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	stop_codon	16043684	16043686	.	-	0	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	CDS	16043687	16044629	0.92	-	1	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	exon	16043687	16044629	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	intron	16044630	16044737	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	CDS	16044738	16045000	0.88	-	0	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	exon	16044738	16045000	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	intron	16045001	16045081	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	CDS	16045082	16045378	0.97	-	0	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	exon	16045082	16045378	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	intron	16045379	16045485	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	CDS	16045486	16045703	1	-	2	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	exon	16045486	16045703	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	intron	16045704	16045790	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	CDS	16045791	16045926	0.93	-	0	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	exon	16045791	16045926	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	intron	16045927	16046024	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	CDS	16046025	16046066	0.66	-	0	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	exon	16046025	16046066	.	-	.	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
Phchi.S1	AUGUSTUS	start_codon	16046064	16046066	.	-	0	transcript_id "Phchi.S1G245100.t1"; gene_id "Phchi.S1G245100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg898.t1 is derived from g10680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6353497	6354708	.	-	.	Phchi.S6G085700
Phchi.S6	AUGUSTUS	transcript	6353497	6354708	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	stop_codon	6353494	6353496	.	-	0	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	CDS	6353497	6353597	0.97	-	2	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	exon	6353497	6353597	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	intron	6353598	6353684	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	CDS	6353685	6353877	1	-	0	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	exon	6353685	6353877	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	intron	6353878	6353962	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	CDS	6353963	6354084	1	-	2	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	exon	6353963	6354084	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	intron	6354085	6354165	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	CDS	6354166	6354313	1	-	0	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	exon	6354166	6354313	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	intron	6354314	6354447	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	CDS	6354448	6354569	1	-	2	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	exon	6354448	6354569	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	intron	6354570	6354647	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	CDS	6354648	6354708	0.92	-	0	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	exon	6354648	6354708	.	-	.	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
Phchi.S6	AUGUSTUS	start_codon	6354706	6354708	.	-	0	transcript_id "Phchi.S6G085700.t1"; gene_id "Phchi.S6G085700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11494.t1 is derived from g15544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6640653	6641855	.	+	.	Phchi.S4G107600
Phchi.S4	AUGUSTUS	transcript	6640653	6641855	.	+	.	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	start_codon	6640653	6640655	.	+	0	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	CDS	6640653	6641075	1	+	0	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	exon	6640653	6641075	.	+	.	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	intron	6641076	6641174	.	+	.	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	CDS	6641175	6641855	1	+	0	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	exon	6641175	6641855	.	+	.	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
Phchi.S4	AUGUSTUS	stop_codon	6641856	6641858	.	+	0	transcript_id "Phchi.S4G107600.t1"; gene_id "Phchi.S4G107600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12866.t1 is derived from g11331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2821160	2822307	.	-	.	Phchi.S3G018500
Phchi.S3	AUGUSTUS	transcript	2821160	2822307	.	-	.	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	stop_codon	2821157	2821159	.	-	0	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	CDS	2821160	2821769	0.57	-	1	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	exon	2821160	2821769	.	-	.	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	intron	2821770	2821867	.	-	.	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	CDS	2821868	2822307	0.36	-	0	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	exon	2821868	2822307	.	-	.	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
Phchi.S3	AUGUSTUS	start_codon	2822305	2822307	.	-	0	transcript_id "Phchi.S3G018500.t1"; gene_id "Phchi.S3G018500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15951.t1 is derived from g14444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	29323	30006	.	-	.	Phchi.C116G000700
Phchi.C116	AUGUSTUS	transcript	29323	30006	.	-	.	transcript_id "Phchi.C116G000700.t1"; gene_id "Phchi.C116G000700"
Phchi.C116	AUGUSTUS	stop_codon	29320	29322	.	-	0	transcript_id "Phchi.C116G000700.t1"; gene_id "Phchi.C116G000700"
Phchi.C116	AUGUSTUS	CDS	29323	30006	1	-	0	transcript_id "Phchi.C116G000700.t1"; gene_id "Phchi.C116G000700"
Phchi.C116	AUGUSTUS	exon	29323	30006	.	-	.	transcript_id "Phchi.C116G000700.t1"; gene_id "Phchi.C116G000700"
Phchi.C116	AUGUSTUS	start_codon	30004	30006	.	-	0	transcript_id "Phchi.C116G000700.t1"; gene_id "Phchi.C116G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9210.t1 is derived from g6385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40405390	40405659	.	-	.	Phchi.S1G636900
Phchi.S1	AUGUSTUS	transcript	40405390	40405659	.	-	.	transcript_id "Phchi.S1G636900.t1"; gene_id "Phchi.S1G636900"
Phchi.S1	AUGUSTUS	stop_codon	40405387	40405389	.	-	0	transcript_id "Phchi.S1G636900.t1"; gene_id "Phchi.S1G636900"
Phchi.S1	AUGUSTUS	CDS	40405390	40405659	0.92	-	0	transcript_id "Phchi.S1G636900.t1"; gene_id "Phchi.S1G636900"
Phchi.S1	AUGUSTUS	exon	40405390	40405659	.	-	.	transcript_id "Phchi.S1G636900.t1"; gene_id "Phchi.S1G636900"
Phchi.S1	AUGUSTUS	start_codon	40405657	40405659	.	-	0	transcript_id "Phchi.S1G636900.t1"; gene_id "Phchi.S1G636900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1008.t1 is derived from g10791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7077965	7079153	.	+	.	Phchi.S6G096700
Phchi.S6	AUGUSTUS	transcript	7077965	7079153	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	start_codon	7077965	7077967	.	+	0	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7077965	7078163	1	+	0	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7077965	7078163	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078164	7078252	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7078253	7078510	1	+	2	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7078253	7078510	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078511	7078591	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7078592	7078782	0.56	+	2	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7078592	7078782	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078783	7078907	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7078908	7078932	0.39	+	0	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7078908	7078932	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078933	7079064	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7079065	7079153	0.39	+	2	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7079065	7079153	.	+	.	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	stop_codon	7079154	7079156	.	+	0	transcript_id "Phchi.S6G096700.t1"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	transcript	7077965	7079153	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	start_codon	7077965	7077967	.	+	0	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7077965	7078163	1	+	0	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7077965	7078163	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078164	7078264	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7078265	7078510	0.54	+	2	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7078265	7078510	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078511	7078591	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7078592	7078782	0.62	+	2	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7078592	7078782	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078783	7078907	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7078908	7078932	0.29	+	0	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7078908	7078932	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	intron	7078933	7079064	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	CDS	7079065	7079153	0.34	+	2	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	exon	7079065	7079153	.	+	.	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
Phchi.S6	AUGUSTUS	stop_codon	7079154	7079156	.	+	0	transcript_id "Phchi.S6G096700.t2"; gene_id "Phchi.S6G096700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12117.t1 is derived from g7793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3649431	3650925	.	-	.	Phchi.S2G019700
Phchi.S2	AUGUSTUS	transcript	3649431	3650925	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	stop_codon	3649428	3649430	.	-	0	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3649431	3649624	0.96	-	2	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3649431	3649624	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	intron	3649625	3649707	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3649708	3649846	1	-	0	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3649708	3649846	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	intron	3649847	3649937	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3649938	3650072	1	-	0	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3649938	3650072	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	intron	3650073	3650150	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3650151	3650222	1	-	0	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3650151	3650222	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	intron	3650223	3650323	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3650324	3650436	0.99	-	2	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3650324	3650436	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	intron	3650437	3650521	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3650522	3650578	0.95	-	2	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3650522	3650578	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	intron	3650579	3650726	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	CDS	3650727	3650925	0.83	-	0	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	exon	3650727	3650925	.	-	.	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
Phchi.S2	AUGUSTUS	start_codon	3650923	3650925	.	-	0	transcript_id "Phchi.S2G019700.t1"; gene_id "Phchi.S2G019700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13534.t1 is derived from g12001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7397965	7402943	.	-	.	Phchi.S3G085300
Phchi.S3	AUGUSTUS	transcript	7397965	7402943	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	stop_codon	7397962	7397964	.	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7397965	7398017	0.33	-	2	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7397965	7398017	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7398018	7398145	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7398146	7398272	0.52	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7398146	7398272	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7398273	7398404	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7398405	7398532	1	-	2	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7398405	7398532	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7398533	7398634	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7398635	7398731	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7398635	7398731	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7398732	7398823	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7398824	7398966	0.35	-	2	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7398824	7398966	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7398967	7399064	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7399065	7399218	0.48	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7399065	7399218	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7399219	7399323	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7399324	7399542	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7399324	7399542	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7399543	7399692	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7399693	7399970	0.7	-	2	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7399693	7399970	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7399971	7400081	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7400082	7400211	0.95	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7400082	7400211	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7400212	7400293	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7400294	7400523	1	-	2	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7400294	7400523	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7400524	7400667	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7400668	7400715	1	-	2	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7400668	7400715	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7400716	7400810	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7400811	7400844	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7400811	7400844	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7400845	7400958	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7400959	7401099	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7400959	7401099	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7401100	7401178	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7401179	7401274	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7401179	7401274	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7401275	7401381	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7401382	7401451	1	-	1	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7401382	7401451	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7401452	7401550	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7401551	7401606	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7401551	7401606	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7401607	7401686	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7401687	7401782	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7401687	7401782	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7401783	7401923	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7401924	7402332	1	-	1	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7401924	7402332	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7402333	7402410	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7402411	7402523	1	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7402411	7402523	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7402524	7402596	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7402597	7402759	1	-	1	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7402597	7402759	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	intron	7402760	7402920	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	CDS	7402921	7402943	0.94	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	exon	7402921	7402943	.	-	.	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
Phchi.S3	AUGUSTUS	start_codon	7402941	7402943	.	-	0	transcript_id "Phchi.S3G085300.t1"; gene_id "Phchi.S3G085300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12971.t1 is derived from g11436.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3392406	3394672	.	-	.	Phchi.S3G029000
Phchi.S3	AUGUSTUS	transcript	3392406	3394672	.	-	.	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	stop_codon	3392403	3392405	.	-	0	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	CDS	3392406	3393155	0.71	-	0	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	exon	3392406	3393155	.	-	.	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	intron	3393156	3393226	.	-	.	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	CDS	3393227	3394672	0.67	-	0	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	exon	3393227	3394672	.	-	.	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	start_codon	3394670	3394672	.	-	0	transcript_id "Phchi.S3G029000.t1"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	transcript	3393161	3394672	.	-	.	transcript_id "Phchi.S3G029000.t2"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	stop_codon	3393158	3393160	.	-	0	transcript_id "Phchi.S3G029000.t2"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	CDS	3393161	3394672	0.97	-	0	transcript_id "Phchi.S3G029000.t2"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	exon	3393161	3394672	.	-	.	transcript_id "Phchi.S3G029000.t2"; gene_id "Phchi.S3G029000"
Phchi.S3	AUGUSTUS	start_codon	3394670	3394672	.	-	0	transcript_id "Phchi.S3G029000.t2"; gene_id "Phchi.S3G029000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10532.t1 is derived from g14582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	852888	855654	.	+	.	Phchi.S4G011400
Phchi.S4	AUGUSTUS	transcript	852888	855654	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	start_codon	852888	852890	.	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	852888	853069	0.98	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	852888	853069	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853070	853174	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853175	853231	1	+	1	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853175	853231	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853232	853336	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853337	853355	1	+	1	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853337	853355	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853356	853469	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853470	853531	1	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853470	853531	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853532	853701	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853702	853720	1	+	1	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853702	853720	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853721	853844	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853845	853903	1	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853845	853903	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853904	854064	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854065	854167	0.85	+	1	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854065	854167	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854168	854268	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854269	854310	0.97	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854269	854310	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854311	854417	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854418	854462	0.84	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854418	854462	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854463	854555	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854556	854716	1	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854556	854716	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854717	854892	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854893	855247	0.97	+	1	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854893	855247	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	855248	855345	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	855346	855514	0.72	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	855346	855514	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	855515	855649	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	855650	855654	0.57	+	2	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	855650	855654	.	+	.	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	stop_codon	855655	855657	.	+	0	transcript_id "Phchi.S4G011400.t1"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	transcript	852888	855654	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	start_codon	852888	852890	.	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	852888	853069	0.99	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	852888	853069	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853070	853174	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853175	853231	0.99	+	1	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853175	853231	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853232	853336	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853337	853355	1	+	1	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853337	853355	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853356	853469	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853470	853531	1	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853470	853531	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853532	853701	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853702	853720	1	+	1	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853702	853720	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853721	853844	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	853845	853903	1	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	853845	853903	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	853904	854064	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854065	854167	0.77	+	1	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854065	854167	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854168	854268	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854269	854310	0.96	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854269	854310	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854311	854417	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854418	854462	0.87	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854418	854462	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854463	854555	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854556	854716	1	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854556	854716	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	854717	854907	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	854908	855247	0.99	+	1	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	854908	855247	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	855248	855345	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	855346	855514	0.61	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	855346	855514	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	intron	855515	855649	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	CDS	855650	855654	0.51	+	2	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	exon	855650	855654	.	+	.	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
Phchi.S4	AUGUSTUS	stop_codon	855655	855657	.	+	0	transcript_id "Phchi.S4G011400.t2"; gene_id "Phchi.S4G011400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9740.t1 is derived from g6916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43463370	43467218	.	+	.	Phchi.S1G689900
Phchi.S1	AUGUSTUS	transcript	43463370	43467218	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	start_codon	43463370	43463372	.	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43463370	43463402	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43463370	43463402	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43463403	43463691	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43463692	43463783	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43463692	43463783	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43463784	43463893	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43463894	43464028	1	+	1	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43463894	43464028	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43464029	43464139	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43464140	43464196	1	+	1	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43464140	43464196	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43464197	43464276	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43464277	43464349	1	+	1	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43464277	43464349	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43464350	43464508	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43464509	43464667	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43464509	43464667	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43464668	43464767	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43464768	43464917	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43464768	43464917	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43464918	43465071	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43465072	43465327	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43465072	43465327	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43465328	43465424	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43465425	43465546	0.54	+	2	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43465425	43465546	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43465547	43465648	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43465649	43465735	0.54	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43465649	43465735	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43465736	43465958	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43465959	43466047	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43465959	43466047	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43466048	43466128	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43466129	43466191	1	+	1	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43466129	43466191	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43466192	43466496	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43466497	43466553	1	+	1	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43466497	43466553	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43466554	43466712	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43466713	43466809	1	+	1	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43466713	43466809	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43466810	43466965	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43466966	43467124	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43466966	43467124	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	intron	43467125	43467209	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	CDS	43467210	43467218	1	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	exon	43467210	43467218	.	+	.	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
Phchi.S1	AUGUSTUS	stop_codon	43467219	43467221	.	+	0	transcript_id "Phchi.S1G689900.t1"; gene_id "Phchi.S1G689900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7393.t1 is derived from g4565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28921755	28923691	.	+	.	Phchi.S1G455200
Phchi.S1	AUGUSTUS	transcript	28921755	28923691	.	+	.	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	start_codon	28921755	28921757	.	+	0	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	CDS	28921755	28922235	0.16	+	0	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	exon	28921755	28922235	.	+	.	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	intron	28922236	28922414	.	+	.	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	CDS	28922415	28923691	0.27	+	2	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	exon	28922415	28923691	.	+	.	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
Phchi.S1	AUGUSTUS	stop_codon	28923692	28923694	.	+	0	transcript_id "Phchi.S1G455200.t1"; gene_id "Phchi.S1G455200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15934.t1 is derived from g9785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C18	AUGUSTUS	gene	83078	84886	.	-	.	Phchi.C18G000100
Phchi.C18	AUGUSTUS	transcript	83078	84886	.	-	.	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	stop_codon	83075	83077	.	-	0	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	CDS	83078	83527	0.61	-	0	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	exon	83078	83527	.	-	.	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	intron	83528	83679	.	-	.	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	CDS	83680	84040	0.43	-	1	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	exon	83680	84040	.	-	.	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	intron	84041	84239	.	-	.	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	CDS	84240	84886	0.95	-	0	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	exon	84240	84886	.	-	.	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
Phchi.C18	AUGUSTUS	start_codon	84884	84886	.	-	0	transcript_id "Phchi.C18G000100.t1"; gene_id "Phchi.C18G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6474.t1 is derived from g3646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23180232	23182283	.	-	.	Phchi.S1G363300
Phchi.S1	AUGUSTUS	transcript	23180232	23182283	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	stop_codon	23180229	23180231	.	-	0	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	CDS	23180232	23180421	0.87	-	1	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	exon	23180232	23180421	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	intron	23180422	23180607	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	CDS	23180608	23180819	1	-	0	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	exon	23180608	23180819	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	intron	23180820	23180958	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	CDS	23180959	23181114	1	-	0	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	exon	23180959	23181114	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	intron	23181115	23181248	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	CDS	23181249	23182283	1	-	0	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	exon	23181249	23182283	.	-	.	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
Phchi.S1	AUGUSTUS	start_codon	23182281	23182283	.	-	0	transcript_id "Phchi.S1G363300.t1"; gene_id "Phchi.S1G363300"
# This transcript jg14736.t2 is derived from g13204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14737.t1 is derived from g13205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14452353	14456961	.	+	.	Phchi.S3G205600
Phchi.S3	AUGUSTUS	transcript	14452353	14456961	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	start_codon	14452353	14452355	.	+	0	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	CDS	14452353	14452610	0.47	+	0	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	exon	14452353	14452610	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	intron	14452611	14452991	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	CDS	14452992	14453433	0.36	+	0	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	exon	14452992	14453433	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	intron	14453434	14453534	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	CDS	14453535	14453618	0.31	+	2	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	exon	14453535	14453618	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	intron	14453619	14453774	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	CDS	14453775	14454602	0.53	+	2	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	exon	14453775	14454602	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	intron	14454603	14454700	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	CDS	14454701	14456961	0.49	+	2	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	exon	14454701	14456961	.	+	.	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
Phchi.S3	AUGUSTUS	stop_codon	14456962	14456964	.	+	0	transcript_id "Phchi.S3G205600.t1"; gene_id "Phchi.S3G205600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12112.t1 is derived from g7788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3572060	3573507	.	+	.	Phchi.S2G019200
Phchi.S2	AUGUSTUS	transcript	3572060	3573507	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	start_codon	3572060	3572062	.	+	0	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	CDS	3572060	3572192	0.29	+	0	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	exon	3572060	3572192	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	intron	3572193	3572277	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	CDS	3572278	3572462	0.97	+	2	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	exon	3572278	3572462	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	intron	3572463	3572564	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	CDS	3572565	3572765	0.99	+	0	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	exon	3572565	3572765	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	intron	3572766	3572864	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	CDS	3572865	3573026	1	+	0	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	exon	3572865	3573026	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	intron	3573027	3573159	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	CDS	3573160	3573507	0.97	+	0	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	exon	3573160	3573507	.	+	.	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
Phchi.S2	AUGUSTUS	stop_codon	3573508	3573510	.	+	0	transcript_id "Phchi.S2G019200.t1"; gene_id "Phchi.S2G019200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11301.t1 is derived from g15351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5295615	5295956	.	+	.	Phchi.S4G088300
Phchi.S4	AUGUSTUS	transcript	5295615	5295956	.	+	.	transcript_id "Phchi.S4G088300.t1"; gene_id "Phchi.S4G088300"
Phchi.S4	AUGUSTUS	start_codon	5295615	5295617	.	+	0	transcript_id "Phchi.S4G088300.t1"; gene_id "Phchi.S4G088300"
Phchi.S4	AUGUSTUS	CDS	5295615	5295956	0.78	+	0	transcript_id "Phchi.S4G088300.t1"; gene_id "Phchi.S4G088300"
Phchi.S4	AUGUSTUS	exon	5295615	5295956	.	+	.	transcript_id "Phchi.S4G088300.t1"; gene_id "Phchi.S4G088300"
Phchi.S4	AUGUSTUS	stop_codon	5295957	5295959	.	+	0	transcript_id "Phchi.S4G088300.t1"; gene_id "Phchi.S4G088300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12351.t1 is derived from g8027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12382387	12383082	.	+	.	Phchi.S2G043100
Phchi.S2	AUGUSTUS	transcript	12382387	12383082	.	+	.	transcript_id "Phchi.S2G043100.t1"; gene_id "Phchi.S2G043100"
Phchi.S2	AUGUSTUS	start_codon	12382387	12382389	.	+	0	transcript_id "Phchi.S2G043100.t1"; gene_id "Phchi.S2G043100"
Phchi.S2	AUGUSTUS	CDS	12382387	12383082	0.6	+	0	transcript_id "Phchi.S2G043100.t1"; gene_id "Phchi.S2G043100"
Phchi.S2	AUGUSTUS	exon	12382387	12383082	.	+	.	transcript_id "Phchi.S2G043100.t1"; gene_id "Phchi.S2G043100"
Phchi.S2	AUGUSTUS	stop_codon	12383083	12383085	.	+	0	transcript_id "Phchi.S2G043100.t1"; gene_id "Phchi.S2G043100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10999.t1 is derived from g15049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3577087	3580975	.	-	.	Phchi.S4G058100
Phchi.S4	AUGUSTUS	transcript	3577087	3580975	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	stop_codon	3577084	3577086	.	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3577087	3577164	0.96	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3577087	3577164	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3577165	3577270	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3577271	3577506	0.97	-	2	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3577271	3577506	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3577507	3577641	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3577642	3577882	0.92	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3577642	3577882	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3577883	3577965	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3577966	3578424	0.73	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3577966	3578424	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3578425	3578534	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3578535	3579416	0.5	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3578535	3579416	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3579417	3579543	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3579544	3579738	0.7	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3579544	3579738	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3579739	3580157	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3580158	3580203	0.55	-	1	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3580158	3580203	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3580204	3580291	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3580292	3580486	0.72	-	1	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3580292	3580486	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	intron	3580487	3580886	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	CDS	3580887	3580975	0.95	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	exon	3580887	3580975	.	-	.	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
Phchi.S4	AUGUSTUS	start_codon	3580973	3580975	.	-	0	transcript_id "Phchi.S4G058100.t1"; gene_id "Phchi.S4G058100"
# This transcript jg5153.t2 is derived from g2323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5154.t1 is derived from g2324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15174507	15175679	.	+	.	Phchi.S1G231300
Phchi.S1	AUGUSTUS	transcript	15174507	15175679	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	start_codon	15174507	15174509	.	+	0	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	CDS	15174507	15174626	0.95	+	0	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	exon	15174507	15174626	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	intron	15174627	15174751	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	CDS	15174752	15174972	1	+	0	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	exon	15174752	15174972	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	intron	15174973	15175068	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	CDS	15175069	15175184	1	+	1	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	exon	15175069	15175184	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	intron	15175185	15175269	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	CDS	15175270	15175679	1	+	2	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	exon	15175270	15175679	.	+	.	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
Phchi.S1	AUGUSTUS	stop_codon	15175680	15175682	.	+	0	transcript_id "Phchi.S1G231300.t1"; gene_id "Phchi.S1G231300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10707.t1 is derived from g14757.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1683255	1684522	.	+	.	Phchi.S4G028900
Phchi.S4	AUGUSTUS	transcript	1683255	1684522	.	+	.	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	start_codon	1683255	1683257	.	+	0	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	CDS	1683255	1683709	0.99	+	0	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	exon	1683255	1683709	.	+	.	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	intron	1683710	1683876	.	+	.	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	CDS	1683877	1684124	0.99	+	1	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	exon	1683877	1684124	.	+	.	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	intron	1684125	1684223	.	+	.	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	CDS	1684224	1684522	1	+	2	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	exon	1684224	1684522	.	+	.	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	stop_codon	1684523	1684525	.	+	0	transcript_id "Phchi.S4G028900.t1"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	transcript	1683255	1684236	.	+	.	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	start_codon	1683255	1683257	.	+	0	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	CDS	1683255	1683709	0.98	+	0	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	exon	1683255	1683709	.	+	.	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	intron	1683710	1683980	.	+	.	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	CDS	1683981	1684124	0.56	+	1	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	exon	1683981	1684124	.	+	.	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	intron	1684125	1684223	.	+	.	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	CDS	1684224	1684236	0.56	+	1	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	exon	1684224	1684236	.	+	.	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
Phchi.S4	AUGUSTUS	stop_codon	1684237	1684239	.	+	0	transcript_id "Phchi.S4G028900.t2"; gene_id "Phchi.S4G028900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1865.t1 is derived from g8785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3610993	3611575	.	+	.	Phchi.S5G047400
Phchi.S5	AUGUSTUS	transcript	3610993	3611575	.	+	.	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	start_codon	3610993	3610995	.	+	0	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	CDS	3610993	3611412	0.28	+	0	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	exon	3610993	3611412	.	+	.	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	intron	3611413	3611557	.	+	.	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	CDS	3611558	3611575	0.63	+	0	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	exon	3611558	3611575	.	+	.	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
Phchi.S5	AUGUSTUS	stop_codon	3611576	3611578	.	+	0	transcript_id "Phchi.S5G047400.t1"; gene_id "Phchi.S5G047400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2123.t1 is derived from g9043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4968516	4970668	.	+	.	Phchi.S5G073200
Phchi.S5	AUGUSTUS	transcript	4968516	4970668	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	start_codon	4968516	4968518	.	+	0	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4968516	4968839	0.57	+	0	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4968516	4968839	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4968840	4968912	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4968913	4968980	1	+	0	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4968913	4968980	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4968981	4969073	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4969074	4969162	1	+	1	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4969074	4969162	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4969163	4969300	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4969301	4969484	0.99	+	2	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4969301	4969484	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4969485	4969555	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4969556	4969754	0.99	+	1	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4969556	4969754	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4969755	4969845	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4969846	4970016	1	+	0	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4969846	4970016	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4970017	4970094	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4970095	4970348	0.87	+	0	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4970095	4970348	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	intron	4970349	4970460	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	CDS	4970461	4970668	1	+	1	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	exon	4970461	4970668	.	+	.	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
Phchi.S5	AUGUSTUS	stop_codon	4970669	4970671	.	+	0	transcript_id "Phchi.S5G073200.t1"; gene_id "Phchi.S5G073200"
# This transcript jg6751.t2 is derived from g3923.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6752.t1 is derived from g3924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24849262	24850375	.	-	.	Phchi.S1G391100
Phchi.S1	AUGUSTUS	transcript	24849262	24850375	.	-	.	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	stop_codon	24849259	24849261	.	-	0	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	CDS	24849262	24849795	1	-	0	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	exon	24849262	24849795	.	-	.	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	intron	24849796	24849904	.	-	.	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	CDS	24849905	24850140	1	-	2	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	exon	24849905	24850140	.	-	.	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	intron	24850141	24850233	.	-	.	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	CDS	24850234	24850375	0.93	-	0	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	exon	24850234	24850375	.	-	.	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
Phchi.S1	AUGUSTUS	start_codon	24850373	24850375	.	-	0	transcript_id "Phchi.S1G391100.t1"; gene_id "Phchi.S1G391100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8466.t1 is derived from g5641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36065850	36068235	.	+	.	Phchi.S1G562500
Phchi.S1	AUGUSTUS	transcript	36065850	36068235	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	start_codon	36065850	36065852	.	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36065850	36065927	0.96	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36065850	36065927	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36065928	36066545	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36066546	36066672	1	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36066546	36066672	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36066673	36066863	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36066864	36066919	0.89	+	2	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36066864	36066919	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36066920	36067030	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36067031	36067087	0.94	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36067031	36067087	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36067088	36067260	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36067261	36067372	1	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36067261	36067372	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36067373	36067495	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36067496	36067533	1	+	2	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36067496	36067533	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36067534	36067632	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36067633	36067734	1	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36067633	36067734	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36067735	36068014	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36068015	36068070	1	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36068015	36068070	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	intron	36068071	36068225	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	CDS	36068226	36068235	1	+	1	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	exon	36068226	36068235	.	+	.	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
Phchi.S1	AUGUSTUS	stop_codon	36068236	36068238	.	+	0	transcript_id "Phchi.S1G562500.t1"; gene_id "Phchi.S1G562500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16003.t1 is derived from g14427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	98	666	.	+	.	Phchi.C10G000100
Phchi.C10	AUGUSTUS	transcript	98	666	.	+	.	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
Phchi.C10	AUGUSTUS	CDS	98	382	0.56	+	2	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
Phchi.C10	AUGUSTUS	exon	98	382	.	+	.	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
Phchi.C10	AUGUSTUS	intron	383	505	.	+	.	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
Phchi.C10	AUGUSTUS	CDS	506	666	0.55	+	2	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
Phchi.C10	AUGUSTUS	exon	506	666	.	+	.	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
Phchi.C10	AUGUSTUS	stop_codon	667	669	.	+	0	transcript_id "Phchi.C10G000100.t1"; gene_id "Phchi.C10G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3344.t1 is derived from g513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3047714	3048757	.	+	.	Phchi.S1G050300
Phchi.S1	AUGUSTUS	transcript	3047714	3048757	.	+	.	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	start_codon	3047714	3047716	.	+	0	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	CDS	3047714	3047905	0.98	+	0	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	exon	3047714	3047905	.	+	.	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	intron	3047906	3048397	.	+	.	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	CDS	3048398	3048757	0.99	+	0	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	exon	3048398	3048757	.	+	.	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
Phchi.S1	AUGUSTUS	stop_codon	3048758	3048760	.	+	0	transcript_id "Phchi.S1G050300.t1"; gene_id "Phchi.S1G050300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5023.t1 is derived from g2193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14095323	14097682	.	-	.	Phchi.S1G218200
Phchi.S1	AUGUSTUS	transcript	14095323	14097682	.	-	.	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	stop_codon	14095320	14095322	.	-	0	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	CDS	14095323	14096449	0.99	-	2	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	exon	14095323	14096449	.	-	.	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	intron	14096450	14096612	.	-	.	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	CDS	14096613	14096859	1	-	0	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	exon	14096613	14096859	.	-	.	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	intron	14096860	14097142	.	-	.	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	CDS	14097143	14097682	1	-	0	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	exon	14097143	14097682	.	-	.	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
Phchi.S1	AUGUSTUS	start_codon	14097680	14097682	.	-	0	transcript_id "Phchi.S1G218200.t1"; gene_id "Phchi.S1G218200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6218.t1 is derived from g3390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21499762	21501570	.	-	.	Phchi.S1G337700
Phchi.S1	AUGUSTUS	transcript	21499762	21501570	.	-	.	transcript_id "Phchi.S1G337700.t1"; gene_id "Phchi.S1G337700"
Phchi.S1	AUGUSTUS	stop_codon	21499759	21499761	.	-	0	transcript_id "Phchi.S1G337700.t1"; gene_id "Phchi.S1G337700"
Phchi.S1	AUGUSTUS	CDS	21499762	21501570	0.79	-	0	transcript_id "Phchi.S1G337700.t1"; gene_id "Phchi.S1G337700"
Phchi.S1	AUGUSTUS	exon	21499762	21501570	.	-	.	transcript_id "Phchi.S1G337700.t1"; gene_id "Phchi.S1G337700"
Phchi.S1	AUGUSTUS	start_codon	21501568	21501570	.	-	0	transcript_id "Phchi.S1G337700.t1"; gene_id "Phchi.S1G337700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15868.t1 is derived from g14338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21969914	21972456	.	-	.	Phchi.S3G318700
Phchi.S3	AUGUSTUS	transcript	21969914	21972456	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	stop_codon	21969911	21969913	.	-	0	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21969914	21970156	1	-	0	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21969914	21970156	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21970157	21970232	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21970233	21970371	1	-	1	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21970233	21970371	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21970372	21970455	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21970456	21970639	1	-	2	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21970456	21970639	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21970640	21970756	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21970757	21970828	1	-	2	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21970757	21970828	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21970829	21970916	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21970917	21971043	1	-	0	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21970917	21971043	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21971044	21971137	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21971138	21971376	1	-	2	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21971138	21971376	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21971377	21971452	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21971453	21971545	0.49	-	2	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21971453	21971545	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21971546	21971610	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21971611	21971720	0.32	-	1	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21971611	21971720	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21971721	21971950	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21971951	21972014	1	-	2	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21971951	21972014	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	intron	21972015	21972224	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	CDS	21972225	21972456	0.98	-	0	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	exon	21972225	21972456	.	-	.	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
Phchi.S3	AUGUSTUS	start_codon	21972454	21972456	.	-	0	transcript_id "Phchi.S3G318700.t1"; gene_id "Phchi.S3G318700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9302.t1 is derived from g6477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40858113	40859729	.	+	.	Phchi.S1G646100
Phchi.S1	AUGUSTUS	transcript	40858113	40859729	.	+	.	transcript_id "Phchi.S1G646100.t1"; gene_id "Phchi.S1G646100"
Phchi.S1	AUGUSTUS	start_codon	40858113	40858115	.	+	0	transcript_id "Phchi.S1G646100.t1"; gene_id "Phchi.S1G646100"
Phchi.S1	AUGUSTUS	CDS	40858113	40859729	0.43	+	0	transcript_id "Phchi.S1G646100.t1"; gene_id "Phchi.S1G646100"
Phchi.S1	AUGUSTUS	exon	40858113	40859729	.	+	.	transcript_id "Phchi.S1G646100.t1"; gene_id "Phchi.S1G646100"
Phchi.S1	AUGUSTUS	stop_codon	40859730	40859732	.	+	0	transcript_id "Phchi.S1G646100.t1"; gene_id "Phchi.S1G646100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13754.t1 is derived from g12221.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8713593	8719363	.	-	.	Phchi.S3G107300
Phchi.S3	AUGUSTUS	transcript	8713593	8719363	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	stop_codon	8713590	8713592	.	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8713593	8713616	1	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8713593	8713616	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8713617	8713752	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8713753	8713835	1	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8713753	8713835	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8713836	8713932	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8713933	8714023	1	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8713933	8714023	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714024	8714176	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714177	8714289	0.83	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714177	8714289	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714290	8714386	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714387	8714498	0.83	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714387	8714498	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714499	8714632	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714633	8714677	0.91	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714633	8714677	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714678	8714772	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714773	8714922	0.71	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714773	8714922	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714923	8715023	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715024	8715162	0.98	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715024	8715162	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715163	8715253	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715254	8715409	0.98	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715254	8715409	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715410	8715524	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715525	8715570	1	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715525	8715570	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715571	8715671	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715672	8715743	1	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715672	8715743	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715744	8715836	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715837	8715963	1	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715837	8715963	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715964	8716057	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8716058	8716332	1	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8716058	8716332	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8716333	8716430	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8716431	8716753	0.99	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8716431	8716753	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8716754	8716867	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8716868	8716939	1	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8716868	8716939	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8716940	8717023	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717024	8717095	1	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717024	8717095	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717096	8717205	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717206	8717277	1	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717206	8717277	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717278	8717370	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717371	8717442	1	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717371	8717442	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717443	8717564	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717565	8717694	1	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717565	8717694	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717695	8717797	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717798	8718039	1	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717798	8718039	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8718040	8718148	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8718149	8718415	1	-	1	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8718149	8718415	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8718416	8718513	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8718514	8718791	1	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8718514	8718791	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8718792	8718910	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8718911	8719191	1	-	2	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8718911	8719191	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8719192	8719287	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8719288	8719363	0.54	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8719288	8719363	.	-	.	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	start_codon	8719361	8719363	.	-	0	transcript_id "Phchi.S3G107300.t1"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	transcript	8713593	8719363	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	stop_codon	8713590	8713592	.	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8713593	8713616	1	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8713593	8713616	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8713617	8713752	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8713753	8713835	0.99	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8713753	8713835	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8713836	8713932	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8713933	8714023	0.99	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8713933	8714023	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714024	8714176	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714177	8714289	0.82	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714177	8714289	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714290	8714386	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714387	8714498	0.82	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714387	8714498	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714499	8714632	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714633	8714677	0.86	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714633	8714677	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714678	8714772	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8714773	8714922	0.61	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8714773	8714922	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8714923	8715023	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715024	8715162	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715024	8715162	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715163	8715253	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715254	8715409	0.97	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715254	8715409	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715410	8715524	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715525	8715570	1	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715525	8715570	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715571	8715671	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715672	8715743	1	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715672	8715743	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715744	8715836	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8715837	8715963	1	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8715837	8715963	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8715964	8716057	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8716058	8716338	1	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8716058	8716338	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8716339	8716430	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8716431	8716753	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8716431	8716753	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8716754	8716867	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8716868	8716939	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8716868	8716939	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8716940	8717023	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717024	8717095	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717024	8717095	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717096	8717205	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717206	8717277	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717206	8717277	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717278	8717370	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717371	8717442	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717371	8717442	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717443	8717564	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717565	8717694	0.97	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717565	8717694	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8717695	8717797	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8717798	8718039	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8717798	8718039	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8718040	8718148	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8718149	8718415	1	-	1	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8718149	8718415	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8718416	8718513	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8718514	8718791	1	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8718514	8718791	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8718792	8718910	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8718911	8719191	1	-	2	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8718911	8719191	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	intron	8719192	8719287	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	CDS	8719288	8719363	0.51	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	exon	8719288	8719363	.	-	.	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
Phchi.S3	AUGUSTUS	start_codon	8719361	8719363	.	-	0	transcript_id "Phchi.S3G107300.t2"; gene_id "Phchi.S3G107300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8490.t1 is derived from g5665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36229259	36231231	.	+	.	Phchi.S1G564900
Phchi.S1	AUGUSTUS	transcript	36229259	36231231	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	start_codon	36229259	36229261	.	+	0	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	CDS	36229259	36229337	0.86	+	0	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	exon	36229259	36229337	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	intron	36229338	36229426	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	CDS	36229427	36230099	0.83	+	2	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	exon	36229427	36230099	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	intron	36230100	36230177	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	CDS	36230178	36230370	0.53	+	1	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	exon	36230178	36230370	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	intron	36230371	36230467	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	CDS	36230468	36230532	1	+	0	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	exon	36230468	36230532	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	intron	36230533	36230650	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	CDS	36230651	36230861	0.99	+	1	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	exon	36230651	36230861	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	intron	36230862	36230973	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	CDS	36230974	36231231	0.98	+	0	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	exon	36230974	36231231	.	+	.	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
Phchi.S1	AUGUSTUS	stop_codon	36231232	36231234	.	+	0	transcript_id "Phchi.S1G564900.t1"; gene_id "Phchi.S1G564900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5810.t1 is derived from g2980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19066139	19067430	.	+	.	Phchi.S1G296900
Phchi.S1	AUGUSTUS	transcript	19066139	19067430	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	start_codon	19066139	19066141	.	+	0	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	CDS	19066139	19066545	0.32	+	0	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	exon	19066139	19066545	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	intron	19066546	19066687	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	CDS	19066688	19066820	1	+	1	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	exon	19066688	19066820	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	intron	19066821	19066916	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	CDS	19066917	19067001	1	+	0	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	exon	19066917	19067001	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	intron	19067002	19067098	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	CDS	19067099	19067164	0.99	+	2	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	exon	19067099	19067164	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	intron	19067165	19067347	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	CDS	19067348	19067430	0.95	+	2	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	exon	19067348	19067430	.	+	.	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
Phchi.S1	AUGUSTUS	stop_codon	19067431	19067433	.	+	0	transcript_id "Phchi.S1G296900.t1"; gene_id "Phchi.S1G296900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4629.t1 is derived from g1799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11467015	11467596	.	+	.	Phchi.S1G178800
Phchi.S1	AUGUSTUS	transcript	11467015	11467596	.	+	.	transcript_id "Phchi.S1G178800.t1"; gene_id "Phchi.S1G178800"
Phchi.S1	AUGUSTUS	start_codon	11467015	11467017	.	+	0	transcript_id "Phchi.S1G178800.t1"; gene_id "Phchi.S1G178800"
Phchi.S1	AUGUSTUS	CDS	11467015	11467596	0.96	+	0	transcript_id "Phchi.S1G178800.t1"; gene_id "Phchi.S1G178800"
Phchi.S1	AUGUSTUS	exon	11467015	11467596	.	+	.	transcript_id "Phchi.S1G178800.t1"; gene_id "Phchi.S1G178800"
Phchi.S1	AUGUSTUS	stop_codon	11467597	11467599	.	+	0	transcript_id "Phchi.S1G178800.t1"; gene_id "Phchi.S1G178800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3805.t1 is derived from g974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5816790	5819048	.	-	.	Phchi.S1G096400
Phchi.S1	AUGUSTUS	transcript	5816790	5818718	.	-	.	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	stop_codon	5816787	5816789	.	-	0	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	CDS	5816790	5816882	0.52	-	0	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	exon	5816790	5816882	.	-	.	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	intron	5816883	5817099	.	-	.	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	CDS	5817100	5818388	0.46	-	2	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	exon	5817100	5818388	.	-	.	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	intron	5818389	5818477	.	-	.	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	CDS	5818478	5818718	0.72	-	0	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	exon	5818478	5818718	.	-	.	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	start_codon	5818716	5818718	.	-	0	transcript_id "Phchi.S1G096400.t1"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	transcript	5816790	5819048	.	-	.	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	stop_codon	5816787	5816789	.	-	0	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	CDS	5816790	5816882	0.62	-	0	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	exon	5816790	5816882	.	-	.	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	intron	5816883	5817099	.	-	.	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	CDS	5817100	5818388	0.41	-	2	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	exon	5817100	5818388	.	-	.	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	intron	5818389	5818477	.	-	.	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	CDS	5818478	5819048	0.43	-	0	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	exon	5818478	5819048	.	-	.	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
Phchi.S1	AUGUSTUS	start_codon	5819046	5819048	.	-	0	transcript_id "Phchi.S1G096400.t2"; gene_id "Phchi.S1G096400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4851.t1 is derived from g2021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13089147	13090433	.	+	.	Phchi.S1G201000
Phchi.S1	AUGUSTUS	transcript	13089147	13090433	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	start_codon	13089147	13089149	.	+	0	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	CDS	13089147	13089365	0.85	+	0	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	exon	13089147	13089365	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	intron	13089366	13089454	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	CDS	13089455	13089597	1	+	0	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	exon	13089455	13089597	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	intron	13089598	13089690	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	CDS	13089691	13089872	1	+	1	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	exon	13089691	13089872	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	intron	13089873	13089956	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	CDS	13089957	13090070	1	+	2	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	exon	13089957	13090070	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	intron	13090071	13090141	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	CDS	13090142	13090312	0.59	+	2	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	exon	13090142	13090312	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	intron	13090313	13090419	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	CDS	13090420	13090433	0.66	+	2	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	exon	13090420	13090433	.	+	.	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
Phchi.S1	AUGUSTUS	stop_codon	13090434	13090436	.	+	0	transcript_id "Phchi.S1G201000.t1"; gene_id "Phchi.S1G201000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10087.t1 is derived from g7263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45678385	45679374	.	-	.	Phchi.S1G724600
Phchi.S1	AUGUSTUS	transcript	45678385	45679374	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	stop_codon	45678382	45678384	.	-	0	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	CDS	45678385	45678581	0.94	-	2	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	exon	45678385	45678581	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	intron	45678582	45678731	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	CDS	45678732	45678807	1	-	0	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	exon	45678732	45678807	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	intron	45678808	45678938	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	CDS	45678939	45679247	0.98	-	0	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	exon	45678939	45679247	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	intron	45679248	45679356	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	CDS	45679357	45679374	0.98	-	0	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	exon	45679357	45679374	.	-	.	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
Phchi.S1	AUGUSTUS	start_codon	45679372	45679374	.	-	0	transcript_id "Phchi.S1G724600.t1"; gene_id "Phchi.S1G724600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4920.t1 is derived from g2090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13564330	13567113	.	-	.	Phchi.S1G207900
Phchi.S1	AUGUSTUS	transcript	13564330	13567113	.	-	.	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	stop_codon	13564327	13564329	.	-	0	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	CDS	13564330	13564963	0.89	-	1	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	exon	13564330	13564963	.	-	.	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	intron	13564964	13565506	.	-	.	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	CDS	13565507	13566476	0.43	-	2	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	exon	13565507	13566476	.	-	.	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	intron	13566477	13566758	.	-	.	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	CDS	13566759	13567113	0.41	-	0	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	exon	13566759	13567113	.	-	.	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
Phchi.S1	AUGUSTUS	start_codon	13567111	13567113	.	-	0	transcript_id "Phchi.S1G207900.t1"; gene_id "Phchi.S1G207900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4011.t1 is derived from g1180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7058800	7062504	.	-	.	Phchi.S1G117000
Phchi.S1	AUGUSTUS	transcript	7058800	7062504	.	-	.	transcript_id "Phchi.S1G117000.t1"; gene_id "Phchi.S1G117000"
Phchi.S1	AUGUSTUS	stop_codon	7058797	7058799	.	-	0	transcript_id "Phchi.S1G117000.t1"; gene_id "Phchi.S1G117000"
Phchi.S1	AUGUSTUS	CDS	7058800	7062504	0.94	-	0	transcript_id "Phchi.S1G117000.t1"; gene_id "Phchi.S1G117000"
Phchi.S1	AUGUSTUS	exon	7058800	7062504	.	-	.	transcript_id "Phchi.S1G117000.t1"; gene_id "Phchi.S1G117000"
Phchi.S1	AUGUSTUS	start_codon	7062502	7062504	.	-	0	transcript_id "Phchi.S1G117000.t1"; gene_id "Phchi.S1G117000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3787.t1 is derived from g956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5721537	5723029	.	-	.	Phchi.S1G094600
Phchi.S1	AUGUSTUS	transcript	5721537	5723029	.	-	.	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	stop_codon	5721534	5721536	.	-	0	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	CDS	5721537	5721818	0.53	-	0	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	exon	5721537	5721818	.	-	.	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	intron	5721819	5721985	.	-	.	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	CDS	5721986	5723029	0.4	-	0	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	exon	5721986	5723029	.	-	.	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
Phchi.S1	AUGUSTUS	start_codon	5723027	5723029	.	-	0	transcript_id "Phchi.S1G094600.t1"; gene_id "Phchi.S1G094600"
# This transcript jg9300.t2 is derived from g6475.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9301.t1 is derived from g6476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40849031	40850987	.	-	.	Phchi.S1G646000
Phchi.S1	AUGUSTUS	transcript	40849031	40850987	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	stop_codon	40849028	40849030	.	-	0	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	CDS	40849031	40849067	0.44	-	1	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	exon	40849031	40849067	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	intron	40849068	40849329	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	CDS	40849330	40849608	0.41	-	1	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	exon	40849330	40849608	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	intron	40849609	40849705	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	CDS	40849706	40849720	0.63	-	1	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	exon	40849706	40849720	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	intron	40849721	40849841	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	CDS	40849842	40849922	0.26	-	1	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	exon	40849842	40849922	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	intron	40849923	40850013	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	CDS	40850014	40850103	0.38	-	1	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	exon	40850014	40850103	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	intron	40850104	40850409	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	CDS	40850410	40850987	0.63	-	0	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	exon	40850410	40850987	.	-	.	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
Phchi.S1	AUGUSTUS	start_codon	40850985	40850987	.	-	0	transcript_id "Phchi.S1G646000.t1"; gene_id "Phchi.S1G646000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5868.t1 is derived from g3038.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19482751	19484101	.	-	.	Phchi.S1G302700
Phchi.S1	AUGUSTUS	transcript	19482751	19484101	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	stop_codon	19482748	19482750	.	-	0	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19482751	19483005	0.99	-	0	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19482751	19483005	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483006	19483101	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19483102	19483328	0.99	-	2	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19483102	19483328	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483329	19483435	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19483436	19483574	1	-	0	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19483436	19483574	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483575	19483715	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19483716	19483826	1	-	0	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19483716	19483826	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483827	19484047	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19484048	19484101	1	-	0	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19484048	19484101	.	-	.	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	start_codon	19484099	19484101	.	-	0	transcript_id "Phchi.S1G302700.t1"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	transcript	19482751	19484101	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	stop_codon	19482748	19482750	.	-	0	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19482751	19483005	0.99	-	0	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19482751	19483005	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483006	19483101	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19483102	19483328	0.97	-	2	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19483102	19483328	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483329	19483435	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19483436	19483574	1	-	0	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19483436	19483574	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483575	19483715	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19483716	19483847	0.76	-	0	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19483716	19483847	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	intron	19483848	19484047	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	CDS	19484048	19484101	0.76	-	0	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	exon	19484048	19484101	.	-	.	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
Phchi.S1	AUGUSTUS	start_codon	19484099	19484101	.	-	0	transcript_id "Phchi.S1G302700.t2"; gene_id "Phchi.S1G302700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9304.t1 is derived from g6479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40862783	40865094	.	-	.	Phchi.S1G646300
Phchi.S1	AUGUSTUS	transcript	40862783	40865094	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	stop_codon	40862780	40862782	.	-	0	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	CDS	40862783	40863181	0.99	-	0	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	exon	40862783	40863181	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	intron	40863182	40863272	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	CDS	40863273	40863959	1	-	0	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	exon	40863273	40863959	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	intron	40863960	40864109	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	CDS	40864110	40864492	0.96	-	2	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	exon	40864110	40864492	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	intron	40864493	40865009	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	CDS	40865010	40865094	1	-	0	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	exon	40865010	40865094	.	-	.	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
Phchi.S1	AUGUSTUS	start_codon	40865092	40865094	.	-	0	transcript_id "Phchi.S1G646300.t1"; gene_id "Phchi.S1G646300"
# This transcript jg2068.t2 is derived from g8988.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2069.t1 is derived from g8989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4707513	4709065	.	-	.	Phchi.S5G067800
Phchi.S5	AUGUSTUS	transcript	4707513	4709065	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	stop_codon	4707510	4707512	.	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4707513	4707674	1	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4707513	4707674	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4707675	4707769	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4707770	4707882	1	-	2	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4707770	4707882	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4707883	4707987	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4707988	4708054	0.99	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4707988	4708054	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4708055	4708169	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4708170	4708232	1	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4708170	4708232	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4708233	4708371	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4708372	4708437	1	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4708372	4708437	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4708438	4708523	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4708524	4708532	1	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4708524	4708532	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4708533	4708597	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4708598	4708603	1	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4708598	4708603	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	intron	4708604	4708687	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	CDS	4708688	4709065	0.94	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	exon	4708688	4709065	.	-	.	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
Phchi.S5	AUGUSTUS	start_codon	4709063	4709065	.	-	0	transcript_id "Phchi.S5G067800.t1"; gene_id "Phchi.S5G067800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6805.t1 is derived from g3977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25137221	25139249	.	-	.	Phchi.S1G396400
Phchi.S1	AUGUSTUS	transcript	25137221	25139249	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	stop_codon	25137218	25137220	.	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25137221	25137285	0.79	-	2	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25137221	25137285	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25137286	25137368	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25137369	25137409	1	-	1	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25137369	25137409	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25137410	25137503	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25137504	25137551	1	-	1	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25137504	25137551	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25137552	25137630	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25137631	25137679	0.83	-	2	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25137631	25137679	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25137680	25137737	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25137738	25137773	0.49	-	2	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25137738	25137773	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25137774	25137913	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25137914	25137980	1	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25137914	25137980	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25137981	25138111	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25138112	25138229	0.99	-	1	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25138112	25138229	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25138230	25138373	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25138374	25138399	0.52	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25138374	25138399	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25138400	25138575	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25138576	25138619	1	-	2	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25138576	25138619	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25138620	25138708	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25138709	25138745	0.97	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25138709	25138745	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25138746	25139110	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25139111	25139119	0.44	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25139111	25139119	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	intron	25139120	25139210	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	CDS	25139211	25139249	1	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	exon	25139211	25139249	.	-	.	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
Phchi.S1	AUGUSTUS	start_codon	25139247	25139249	.	-	0	transcript_id "Phchi.S1G396400.t1"; gene_id "Phchi.S1G396400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3555.t1 is derived from g724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4459754	4460216	.	-	.	Phchi.S1G071400
Phchi.S1	AUGUSTUS	transcript	4459754	4460216	.	-	.	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	stop_codon	4459751	4459753	.	-	0	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	CDS	4459754	4460056	1	-	0	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	exon	4459754	4460056	.	-	.	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	intron	4460057	4460141	.	-	.	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	CDS	4460142	4460216	0.76	-	0	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	exon	4460142	4460216	.	-	.	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
Phchi.S1	AUGUSTUS	start_codon	4460214	4460216	.	-	0	transcript_id "Phchi.S1G071400.t1"; gene_id "Phchi.S1G071400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1260.t1 is derived from g11043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8694241	8696768	.	-	.	Phchi.S6G121900
Phchi.S6	AUGUSTUS	transcript	8694241	8696768	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	stop_codon	8694238	8694240	.	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8694241	8694374	0.74	-	2	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8694241	8694374	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8694375	8694516	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8694517	8694568	0.82	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8694517	8694568	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8694569	8694649	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8694650	8694681	0.65	-	2	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8694650	8694681	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8694682	8694892	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8694893	8694926	0.9	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8694893	8694926	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8694927	8695023	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8695024	8695116	1	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8695024	8695116	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8695117	8695274	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8695275	8695337	1	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8695275	8695337	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8695338	8695608	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8695609	8695706	1	-	2	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8695609	8695706	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8695707	8695897	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8695898	8695963	1	-	2	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8695898	8695963	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8695964	8696082	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8696083	8696183	1	-	1	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8696083	8696183	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8696184	8696281	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8696282	8696354	1	-	2	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8696282	8696354	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	intron	8696355	8696695	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	CDS	8696696	8696768	1	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	exon	8696696	8696768	.	-	.	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
Phchi.S6	AUGUSTUS	start_codon	8696766	8696768	.	-	0	transcript_id "Phchi.S6G121900.t1"; gene_id "Phchi.S6G121900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg836.t1 is derived from g10618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5812146	5816725	.	-	.	Phchi.S6G079500
Phchi.S6	AUGUSTUS	transcript	5812146	5816725	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	stop_codon	5812143	5812145	.	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5812146	5812379	0.99	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5812146	5812379	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5812380	5812506	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5812507	5812653	1	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5812507	5812653	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5812654	5812732	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5812733	5812877	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5812733	5812877	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5812878	5812962	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5812963	5813108	1	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5812963	5813108	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5813109	5813203	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5813204	5813295	1	-	2	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5813204	5813295	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5813296	5813445	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5813446	5813497	1	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5813446	5813497	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5813498	5813600	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5813601	5813884	0.8	-	2	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5813601	5813884	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5813885	5814002	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5814003	5814155	0.99	-	2	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5814003	5814155	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5814156	5814231	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5814232	5814310	0.94	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5814232	5814310	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5814311	5814409	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5814410	5814437	0.94	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5814410	5814437	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5814438	5814545	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5814546	5814593	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5814546	5814593	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5814594	5814721	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5814722	5814802	0.97	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5814722	5814802	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5814803	5814907	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5814908	5814982	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5814908	5814982	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5814983	5815080	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5815081	5815152	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5815081	5815152	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5815153	5815272	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5815273	5815344	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5815273	5815344	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5815345	5815443	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5815444	5815515	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5815444	5815515	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5815516	5815602	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5815603	5815674	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5815603	5815674	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5815675	5815760	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5815761	5815832	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5815761	5815832	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5815833	5815930	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5815931	5815999	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5815931	5815999	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5816000	5816101	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5816102	5816275	1	-	1	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5816102	5816275	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5816276	5816413	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5816414	5816543	0.84	-	2	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5816414	5816543	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	intron	5816544	5816646	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	CDS	5816647	5816725	0.81	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	exon	5816647	5816725	.	-	.	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
Phchi.S6	AUGUSTUS	start_codon	5816723	5816725	.	-	0	transcript_id "Phchi.S6G079500.t1"; gene_id "Phchi.S6G079500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4293.t1 is derived from g1462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9464279	9465100	.	-	.	Phchi.S1G145200
Phchi.S1	AUGUSTUS	transcript	9464279	9465100	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	stop_codon	9464276	9464278	.	-	0	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	CDS	9464279	9464313	1	-	2	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	exon	9464279	9464313	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	intron	9464314	9464455	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	CDS	9464456	9464500	1	-	2	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	exon	9464456	9464500	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	intron	9464501	9464585	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	CDS	9464586	9464648	0.92	-	2	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	exon	9464586	9464648	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	intron	9464649	9464763	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	CDS	9464764	9464855	0.96	-	1	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	exon	9464764	9464855	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	intron	9464856	9465095	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	CDS	9465096	9465100	1	-	0	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	exon	9465096	9465100	.	-	.	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
Phchi.S1	AUGUSTUS	start_codon	9465098	9465100	.	-	0	transcript_id "Phchi.S1G145200.t1"; gene_id "Phchi.S1G145200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4223.t1 is derived from g1392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8999353	9001346	.	-	.	Phchi.S1G138200
Phchi.S1	AUGUSTUS	transcript	8999353	9001346	.	-	.	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	stop_codon	8999350	8999352	.	-	0	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	CDS	8999353	9000765	0.97	-	0	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	exon	8999353	9000765	.	-	.	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	intron	9000766	9000869	.	-	.	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	CDS	9000870	9001346	0.74	-	0	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	exon	9000870	9001346	.	-	.	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
Phchi.S1	AUGUSTUS	start_codon	9001344	9001346	.	-	0	transcript_id "Phchi.S1G138200.t1"; gene_id "Phchi.S1G138200"
# This transcript jg14771.t2 is derived from g13239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14771.t3 is derived from g13239.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14772.t1 is derived from g13240.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14643435	14644547	.	+	.	Phchi.S3G209100
Phchi.S3	AUGUSTUS	transcript	14643435	14644547	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	start_codon	14643435	14643437	.	+	0	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14643435	14643689	0.93	+	0	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14643435	14643689	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14643690	14643872	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14643873	14643971	1	+	0	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14643873	14643971	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14643972	14644067	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14644068	14644205	1	+	0	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14644068	14644205	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14644206	14644306	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14644307	14644401	1	+	0	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14644307	14644401	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14644402	14644483	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14644484	14644547	1	+	1	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14644484	14644547	.	+	.	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	stop_codon	14644548	14644550	.	+	0	transcript_id "Phchi.S3G209100.t1"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	transcript	14643435	14644547	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	start_codon	14643435	14643437	.	+	0	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14643435	14643719	0.94	+	0	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14643435	14643719	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14643720	14643872	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14643873	14643971	1	+	0	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14643873	14643971	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14643972	14644067	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14644068	14644205	0.99	+	0	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14644068	14644205	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14644206	14644306	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14644307	14644401	1	+	0	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14644307	14644401	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	intron	14644402	14644483	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	CDS	14644484	14644547	1	+	1	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	exon	14644484	14644547	.	+	.	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
Phchi.S3	AUGUSTUS	stop_codon	14644548	14644550	.	+	0	transcript_id "Phchi.S3G209100.t2"; gene_id "Phchi.S3G209100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10485.t1 is derived from g14534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	653491	655998	.	-	.	Phchi.S4G006700
Phchi.S4	AUGUSTUS	transcript	653491	655998	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	stop_codon	653488	653490	.	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	653491	653532	0.42	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	653491	653532	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	653533	653715	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	653716	653757	0.42	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	653716	653757	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	653758	653842	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	653843	653918	0.42	-	1	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	653843	653918	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	653919	654052	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	654053	654137	1	-	2	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	654053	654137	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	654138	654227	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	654228	654403	1	-	1	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	654228	654403	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	654404	654495	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	654496	654575	1	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	654496	654575	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	654576	654676	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	654677	654787	1	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	654677	654787	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	654788	654910	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	654911	654951	0.81	-	2	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	654911	654951	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	654952	655054	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	655055	655087	1	-	2	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	655055	655087	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	655088	655181	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	655182	655321	1	-	1	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	655182	655321	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	655322	655579	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	655580	655593	1	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	655580	655593	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	655594	655679	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	655680	655733	1	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	655680	655733	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	intron	655734	655842	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	CDS	655843	655998	1	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	exon	655843	655998	.	-	.	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
Phchi.S4	AUGUSTUS	start_codon	655996	655998	.	-	0	transcript_id "Phchi.S4G006700.t1"; gene_id "Phchi.S4G006700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1934.t1 is derived from g8854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3902324	3903154	.	+	.	Phchi.S5G054300
Phchi.S5	AUGUSTUS	transcript	3902324	3903154	.	+	.	transcript_id "Phchi.S5G054300.t1"; gene_id "Phchi.S5G054300"
Phchi.S5	AUGUSTUS	start_codon	3902324	3902326	.	+	0	transcript_id "Phchi.S5G054300.t1"; gene_id "Phchi.S5G054300"
Phchi.S5	AUGUSTUS	CDS	3902324	3903154	0.96	+	0	transcript_id "Phchi.S5G054300.t1"; gene_id "Phchi.S5G054300"
Phchi.S5	AUGUSTUS	exon	3902324	3903154	.	+	.	transcript_id "Phchi.S5G054300.t1"; gene_id "Phchi.S5G054300"
Phchi.S5	AUGUSTUS	stop_codon	3903155	3903157	.	+	0	transcript_id "Phchi.S5G054300.t1"; gene_id "Phchi.S5G054300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8692.t1 is derived from g5867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37458358	37461718	.	-	.	Phchi.S1G585100
Phchi.S1	AUGUSTUS	transcript	37458358	37461718	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	stop_codon	37458355	37458357	.	-	0	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37458358	37458444	1	-	0	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37458358	37458444	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37458445	37458563	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37458564	37458672	1	-	1	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37458564	37458672	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37458673	37458776	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37458777	37458930	1	-	2	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37458777	37458930	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37458931	37459014	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37459015	37459318	1	-	0	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37459015	37459318	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37459319	37459492	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37459493	37459766	1	-	1	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37459493	37459766	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37459767	37459904	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37459905	37460022	0.69	-	2	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37459905	37460022	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37460023	37460125	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37460126	37460843	0.59	-	0	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37460126	37460843	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	intron	37460844	37460950	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	CDS	37460951	37461718	1	-	0	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	exon	37460951	37461718	.	-	.	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
Phchi.S1	AUGUSTUS	start_codon	37461716	37461718	.	-	0	transcript_id "Phchi.S1G585100.t1"; gene_id "Phchi.S1G585100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11757.t1 is derived from g15809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8023406	8024284	.	+	.	Phchi.S4G133900
Phchi.S4	AUGUSTUS	transcript	8023406	8024284	.	+	.	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	start_codon	8023406	8023408	.	+	0	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	CDS	8023406	8023811	0.26	+	0	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	exon	8023406	8023811	.	+	.	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	intron	8023812	8023906	.	+	.	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	CDS	8023907	8024085	0.38	+	2	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	exon	8023907	8024085	.	+	.	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	intron	8024086	8024227	.	+	.	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	CDS	8024228	8024284	0.97	+	0	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	exon	8024228	8024284	.	+	.	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
Phchi.S4	AUGUSTUS	stop_codon	8024285	8024287	.	+	0	transcript_id "Phchi.S4G133900.t1"; gene_id "Phchi.S4G133900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5902.t1 is derived from g3072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19673416	19675731	.	+	.	Phchi.S1G306100
Phchi.S1	AUGUSTUS	transcript	19673416	19675731	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	start_codon	19673416	19673418	.	+	0	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19673416	19673623	0.64	+	0	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19673416	19673623	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19673624	19673769	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19673770	19673904	0.38	+	2	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19673770	19673904	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19673905	19674083	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19674084	19674177	0.87	+	2	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19674084	19674177	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19674178	19674291	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19674292	19674349	0.44	+	1	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19674292	19674349	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19674350	19674449	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19674450	19674552	0.49	+	0	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19674450	19674552	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19674553	19674679	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19674680	19674813	1	+	2	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19674680	19674813	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19674814	19674934	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19674935	19675162	0.64	+	0	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19674935	19675162	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	intron	19675163	19675308	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	CDS	19675309	19675731	0.94	+	0	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	exon	19675309	19675731	.	+	.	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
Phchi.S1	AUGUSTUS	stop_codon	19675732	19675734	.	+	0	transcript_id "Phchi.S1G306100.t1"; gene_id "Phchi.S1G306100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3534.t1 is derived from g703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4334660	4335356	.	+	.	Phchi.S1G069300
Phchi.S1	AUGUSTUS	transcript	4334660	4335356	.	+	.	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	start_codon	4334660	4334662	.	+	0	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	CDS	4334660	4334851	0.97	+	0	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	exon	4334660	4334851	.	+	.	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	intron	4334852	4334966	.	+	.	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	CDS	4334967	4335356	0.96	+	0	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	exon	4334967	4335356	.	+	.	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
Phchi.S1	AUGUSTUS	stop_codon	4335357	4335359	.	+	0	transcript_id "Phchi.S1G069300.t1"; gene_id "Phchi.S1G069300"
# This transcript jg8477.t2 is derived from g5652.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8478.t1 is derived from g5653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36136708	36138150	.	-	.	Phchi.S1G563700
Phchi.S1	AUGUSTUS	transcript	36136708	36137577	.	-	.	transcript_id "Phchi.S1G563700.t1"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	stop_codon	36136705	36136707	.	-	0	transcript_id "Phchi.S1G563700.t1"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	CDS	36136708	36137577	0.79	-	0	transcript_id "Phchi.S1G563700.t1"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	exon	36136708	36137577	.	-	.	transcript_id "Phchi.S1G563700.t1"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	start_codon	36137575	36137577	.	-	0	transcript_id "Phchi.S1G563700.t1"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	transcript	36136708	36137133	.	-	.	transcript_id "Phchi.S1G563700.t2"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	stop_codon	36136705	36136707	.	-	0	transcript_id "Phchi.S1G563700.t2"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	CDS	36136708	36137133	0.52	-	0	transcript_id "Phchi.S1G563700.t2"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	exon	36136708	36137133	.	-	.	transcript_id "Phchi.S1G563700.t2"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	start_codon	36137131	36137133	.	-	0	transcript_id "Phchi.S1G563700.t2"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	transcript	36136708	36138150	.	-	.	transcript_id "Phchi.S1G563700.t3"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	stop_codon	36136705	36136707	.	-	0	transcript_id "Phchi.S1G563700.t3"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	CDS	36136708	36138150	0.46	-	0	transcript_id "Phchi.S1G563700.t3"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	exon	36136708	36138150	.	-	.	transcript_id "Phchi.S1G563700.t3"; gene_id "Phchi.S1G563700"
Phchi.S1	AUGUSTUS	start_codon	36138148	36138150	.	-	0	transcript_id "Phchi.S1G563700.t3"; gene_id "Phchi.S1G563700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4919.t1 is derived from g2089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13559539	13560071	.	+	.	Phchi.S1G207800
Phchi.S1	AUGUSTUS	transcript	13559539	13560071	.	+	.	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	start_codon	13559539	13559541	.	+	0	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	CDS	13559539	13559608	0.87	+	0	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	exon	13559539	13559608	.	+	.	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	intron	13559609	13559705	.	+	.	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	CDS	13559706	13559921	0.87	+	2	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	exon	13559706	13559921	.	+	.	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	intron	13559922	13560018	.	+	.	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	CDS	13560019	13560071	1	+	2	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	exon	13560019	13560071	.	+	.	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
Phchi.S1	AUGUSTUS	stop_codon	13560072	13560074	.	+	0	transcript_id "Phchi.S1G207800.t1"; gene_id "Phchi.S1G207800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3231.t1 is derived from g400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2365885	2368964	.	+	.	Phchi.S1G039000
Phchi.S1	AUGUSTUS	transcript	2365885	2368964	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	start_codon	2365885	2365887	.	+	0	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2365885	2365997	0.69	+	0	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2365885	2365997	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	intron	2365998	2366086	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2366087	2366611	0.75	+	1	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2366087	2366611	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	intron	2366612	2366934	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2366935	2367260	0.7	+	1	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2366935	2367260	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	intron	2367261	2367408	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2367409	2367616	0.99	+	2	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2367409	2367616	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	intron	2367617	2367711	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2367712	2368162	0.97	+	1	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2367712	2368162	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	intron	2368163	2368269	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2368270	2368811	0.91	+	0	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2368270	2368811	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	intron	2368812	2368894	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	CDS	2368895	2368964	1	+	1	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	exon	2368895	2368964	.	+	.	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
Phchi.S1	AUGUSTUS	stop_codon	2368965	2368967	.	+	0	transcript_id "Phchi.S1G039000.t1"; gene_id "Phchi.S1G039000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2234.t1 is derived from g9154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5581544	5582410	.	-	.	Phchi.S5G084300
Phchi.S5	AUGUSTUS	transcript	5581544	5582410	.	-	.	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	stop_codon	5581541	5581543	.	-	0	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	CDS	5581544	5581885	0.91	-	0	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	exon	5581544	5581885	.	-	.	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	intron	5581886	5581965	.	-	.	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	CDS	5581966	5582187	1	-	0	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	exon	5581966	5582187	.	-	.	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	intron	5582188	5582269	.	-	.	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	CDS	5582270	5582410	0.66	-	0	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	exon	5582270	5582410	.	-	.	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
Phchi.S5	AUGUSTUS	start_codon	5582408	5582410	.	-	0	transcript_id "Phchi.S5G084300.t1"; gene_id "Phchi.S5G084300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15310.t1 is derived from g13778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18344821	18345761	.	+	.	Phchi.S3G262900
Phchi.S3	AUGUSTUS	transcript	18344821	18345761	.	+	.	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	start_codon	18344821	18344823	.	+	0	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	CDS	18344821	18344970	1	+	0	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	exon	18344821	18344970	.	+	.	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	intron	18344971	18345126	.	+	.	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	CDS	18345127	18345175	1	+	0	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	exon	18345127	18345175	.	+	.	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	intron	18345176	18345276	.	+	.	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	CDS	18345277	18345761	0.82	+	2	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	exon	18345277	18345761	.	+	.	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
Phchi.S3	AUGUSTUS	stop_codon	18345762	18345764	.	+	0	transcript_id "Phchi.S3G262900.t1"; gene_id "Phchi.S3G262900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10678.t1 is derived from g14728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1556474	1557268	.	-	.	Phchi.S4G026000
Phchi.S4	AUGUSTUS	transcript	1556474	1557268	.	-	.	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	stop_codon	1556471	1556473	.	-	0	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	CDS	1556474	1556812	1	-	0	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	exon	1556474	1556812	.	-	.	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	intron	1556813	1556902	.	-	.	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	CDS	1556903	1557268	1	-	0	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	exon	1556903	1557268	.	-	.	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
Phchi.S4	AUGUSTUS	start_codon	1557266	1557268	.	-	0	transcript_id "Phchi.S4G026000.t1"; gene_id "Phchi.S4G026000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6946.t1 is derived from g4118.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26097829	26102280	.	+	.	Phchi.S1G410500
Phchi.S1	AUGUSTUS	transcript	26097829	26102280	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	start_codon	26097829	26097831	.	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26097829	26098018	0.98	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26097829	26098018	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098019	26098136	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098137	26098188	1	+	2	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098137	26098188	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098189	26098265	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098266	26098325	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098266	26098325	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098326	26098480	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098481	26098505	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098481	26098505	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098506	26098622	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098623	26098708	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098623	26098708	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098709	26098892	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098893	26099004	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098893	26099004	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099005	26099101	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099102	26099164	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099102	26099164	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099165	26099297	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099298	26099317	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099298	26099317	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099318	26099406	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099407	26099504	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099407	26099504	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099505	26099646	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099647	26099675	1	+	2	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099647	26099675	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099676	26099796	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099797	26099828	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099797	26099828	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099829	26100026	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100027	26100074	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100027	26100074	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100075	26100247	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100248	26100308	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100248	26100308	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100309	26100407	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100408	26100505	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100408	26100505	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100506	26100629	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100630	26100705	0.99	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100630	26100705	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100706	26100801	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100802	26100868	0.52	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100802	26100868	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100869	26101153	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101154	26101263	0.94	+	2	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101154	26101263	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101264	26101342	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101343	26101429	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101343	26101429	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101430	26101545	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101546	26101643	1	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101546	26101643	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101644	26101767	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101768	26101850	1	+	1	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101768	26101850	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101851	26102182	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26102183	26102280	1	+	2	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26102183	26102280	.	+	.	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	stop_codon	26102281	26102283	.	+	0	transcript_id "Phchi.S1G410500.t1"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	transcript	26097829	26102049	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	start_codon	26097829	26097831	.	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26097829	26098018	0.95	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26097829	26098018	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098019	26098136	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098137	26098188	1	+	2	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098137	26098188	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098189	26098265	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098266	26098325	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098266	26098325	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098326	26098480	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098481	26098505	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098481	26098505	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098506	26098622	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098623	26098708	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098623	26098708	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26098709	26098892	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26098893	26099004	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26098893	26099004	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099005	26099101	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099102	26099164	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099102	26099164	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099165	26099297	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099298	26099317	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099298	26099317	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099318	26099406	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099407	26099504	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099407	26099504	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099505	26099646	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099647	26099675	1	+	2	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099647	26099675	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099676	26099796	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26099797	26099828	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26099797	26099828	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26099829	26100026	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100027	26100074	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100027	26100074	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100075	26100247	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100248	26100308	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100248	26100308	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100309	26100407	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100408	26100505	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100408	26100505	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100506	26100629	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100630	26100705	0.98	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100630	26100705	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100706	26100801	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26100802	26100868	0.54	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26100802	26100868	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26100869	26101153	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101154	26101263	0.89	+	2	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101154	26101263	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101264	26101342	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101343	26101429	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101343	26101429	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101430	26101545	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101546	26101643	1	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101546	26101643	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101644	26101767	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101768	26101850	1	+	1	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101768	26101850	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	intron	26101851	26101990	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	CDS	26101991	26102049	0.97	+	2	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	exon	26101991	26102049	.	+	.	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
Phchi.S1	AUGUSTUS	stop_codon	26102050	26102052	.	+	0	transcript_id "Phchi.S1G410500.t2"; gene_id "Phchi.S1G410500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6493.t1 is derived from g3665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23281325	23285209	.	-	.	Phchi.S1G365200
Phchi.S1	AUGUSTUS	transcript	23281325	23285209	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	stop_codon	23281322	23281324	.	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23281325	23281544	1	-	1	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23281325	23281544	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23281545	23281717	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23281718	23281889	1	-	2	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23281718	23281889	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23281890	23281983	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23281984	23282073	0.97	-	2	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23281984	23282073	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23282074	23282150	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23282151	23282257	1	-	1	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23282151	23282257	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23282258	23282352	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23282353	23282427	1	-	1	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23282353	23282427	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23282428	23282518	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23282519	23282627	1	-	2	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23282519	23282627	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23282628	23282718	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23282719	23282842	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23282719	23282842	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23282843	23282921	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23282922	23282996	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23282922	23282996	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23282997	23283090	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23283091	23283264	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23283091	23283264	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23283265	23283344	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23283345	23283501	1	-	1	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23283345	23283501	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23283502	23283627	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23283628	23283668	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23283628	23283668	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23283669	23283756	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23283757	23283822	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23283757	23283822	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23283823	23283934	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23283935	23283971	0.99	-	1	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23283935	23283971	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23283972	23284119	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23284120	23284196	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23284120	23284196	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23284197	23284371	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23284372	23284428	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23284372	23284428	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23284429	23284503	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23284504	23284554	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23284504	23284554	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23284555	23284643	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23284644	23284709	1	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23284644	23284709	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23284710	23284789	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23284790	23284925	0.84	-	1	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23284790	23284925	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23284926	23285027	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23285028	23285070	0.84	-	2	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23285028	23285070	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	intron	23285071	23285145	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	CDS	23285146	23285209	0.91	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	exon	23285146	23285209	.	-	.	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
Phchi.S1	AUGUSTUS	start_codon	23285207	23285209	.	-	0	transcript_id "Phchi.S1G365200.t1"; gene_id "Phchi.S1G365200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3460.t1 is derived from g629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3877097	3879136	.	+	.	Phchi.S1G061900
Phchi.S1	AUGUSTUS	transcript	3877097	3879136	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	start_codon	3877097	3877099	.	+	0	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877097	3877268	0.9	+	0	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877097	3877268	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3877269	3877432	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877433	3877649	1	+	2	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877433	3877649	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3877650	3877736	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877737	3877816	0.86	+	1	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877737	3877816	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3877817	3877918	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877919	3878078	0.84	+	2	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877919	3878078	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878079	3878180	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878181	3878262	1	+	1	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878181	3878262	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878263	3878360	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878361	3878490	1	+	0	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878361	3878490	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878491	3878704	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878705	3878768	1	+	2	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878705	3878768	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878769	3878879	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878880	3878948	1	+	1	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878880	3878948	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878949	3879039	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3879040	3879136	0.98	+	1	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3879040	3879136	.	+	.	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	stop_codon	3879137	3879139	.	+	0	transcript_id "Phchi.S1G061900.t1"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	transcript	3877097	3879136	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	start_codon	3877097	3877099	.	+	0	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877097	3877268	0.9	+	0	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877097	3877268	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3877269	3877432	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877433	3877532	0.81	+	2	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877433	3877532	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3877533	3877736	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877737	3877816	0.82	+	1	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877737	3877816	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3877817	3877918	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3877919	3878078	0.81	+	2	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3877919	3878078	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878079	3878180	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878181	3878262	1	+	1	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878181	3878262	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878263	3878360	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878361	3878490	1	+	0	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878361	3878490	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878491	3878704	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878705	3878768	1	+	2	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878705	3878768	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878769	3878879	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3878880	3878948	1	+	1	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3878880	3878948	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	intron	3878949	3879039	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	CDS	3879040	3879136	0.97	+	1	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	exon	3879040	3879136	.	+	.	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
Phchi.S1	AUGUSTUS	stop_codon	3879137	3879139	.	+	0	transcript_id "Phchi.S1G061900.t2"; gene_id "Phchi.S1G061900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11454.t1 is derived from g15504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6443956	6444963	.	-	.	Phchi.S4G103600
Phchi.S4	AUGUSTUS	transcript	6443956	6444963	.	-	.	transcript_id "Phchi.S4G103600.t1"; gene_id "Phchi.S4G103600"
Phchi.S4	AUGUSTUS	stop_codon	6443953	6443955	.	-	0	transcript_id "Phchi.S4G103600.t1"; gene_id "Phchi.S4G103600"
Phchi.S4	AUGUSTUS	CDS	6443956	6444963	0.31	-	0	transcript_id "Phchi.S4G103600.t1"; gene_id "Phchi.S4G103600"
Phchi.S4	AUGUSTUS	exon	6443956	6444963	.	-	.	transcript_id "Phchi.S4G103600.t1"; gene_id "Phchi.S4G103600"
Phchi.S4	AUGUSTUS	start_codon	6444961	6444963	.	-	0	transcript_id "Phchi.S4G103600.t1"; gene_id "Phchi.S4G103600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8073.t1 is derived from g5248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32806234	32807915	.	+	.	Phchi.S1G523200
Phchi.S1	AUGUSTUS	transcript	32806234	32807915	.	+	.	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	start_codon	32806234	32806236	.	+	0	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	CDS	32806234	32806258	0.98	+	0	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	exon	32806234	32806258	.	+	.	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	intron	32806259	32806397	.	+	.	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	CDS	32806398	32806862	1	+	2	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	exon	32806398	32806862	.	+	.	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	intron	32806863	32807277	.	+	.	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	CDS	32807278	32807915	1	+	2	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	exon	32807278	32807915	.	+	.	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
Phchi.S1	AUGUSTUS	stop_codon	32807916	32807918	.	+	0	transcript_id "Phchi.S1G523200.t1"; gene_id "Phchi.S1G523200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7971.t1 is derived from g5146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32189979	32190950	.	+	.	Phchi.S1G513000
Phchi.S1	AUGUSTUS	transcript	32189979	32190950	.	+	.	transcript_id "Phchi.S1G513000.t1"; gene_id "Phchi.S1G513000"
Phchi.S1	AUGUSTUS	start_codon	32189979	32189981	.	+	0	transcript_id "Phchi.S1G513000.t1"; gene_id "Phchi.S1G513000"
Phchi.S1	AUGUSTUS	CDS	32189979	32190950	0.55	+	0	transcript_id "Phchi.S1G513000.t1"; gene_id "Phchi.S1G513000"
Phchi.S1	AUGUSTUS	exon	32189979	32190950	.	+	.	transcript_id "Phchi.S1G513000.t1"; gene_id "Phchi.S1G513000"
Phchi.S1	AUGUSTUS	stop_codon	32190951	32190953	.	+	0	transcript_id "Phchi.S1G513000.t1"; gene_id "Phchi.S1G513000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15320.t1 is derived from g13788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18381063	18381464	.	-	.	Phchi.S3G263900
Phchi.S3	AUGUSTUS	transcript	18381063	18381464	.	-	.	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	stop_codon	18381060	18381062	.	-	0	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	CDS	18381063	18381181	0.78	-	2	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	exon	18381063	18381181	.	-	.	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	intron	18381182	18381274	.	-	.	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	CDS	18381275	18381464	0.35	-	0	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	exon	18381275	18381464	.	-	.	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
Phchi.S3	AUGUSTUS	start_codon	18381462	18381464	.	-	0	transcript_id "Phchi.S3G263900.t1"; gene_id "Phchi.S3G263900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7498.t1 is derived from g4672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29670897	29671403	.	+	.	Phchi.S1G465700
Phchi.S1	AUGUSTUS	transcript	29670897	29671403	.	+	.	transcript_id "Phchi.S1G465700.t1"; gene_id "Phchi.S1G465700"
Phchi.S1	AUGUSTUS	start_codon	29670897	29670899	.	+	0	transcript_id "Phchi.S1G465700.t1"; gene_id "Phchi.S1G465700"
Phchi.S1	AUGUSTUS	CDS	29670897	29671403	0.39	+	0	transcript_id "Phchi.S1G465700.t1"; gene_id "Phchi.S1G465700"
Phchi.S1	AUGUSTUS	exon	29670897	29671403	.	+	.	transcript_id "Phchi.S1G465700.t1"; gene_id "Phchi.S1G465700"
Phchi.S1	AUGUSTUS	stop_codon	29671404	29671406	.	+	0	transcript_id "Phchi.S1G465700.t1"; gene_id "Phchi.S1G465700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg186.t1 is derived from g9968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1066674	1067595	.	-	.	Phchi.S6G014500
Phchi.S6	AUGUSTUS	transcript	1066674	1067595	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	stop_codon	1066671	1066673	.	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	CDS	1066674	1066784	0.82	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	exon	1066674	1066784	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	intron	1066785	1066869	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	CDS	1066870	1066935	1	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	exon	1066870	1066935	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	intron	1066936	1067048	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	CDS	1067049	1067174	1	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	exon	1067049	1067174	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	intron	1067175	1067263	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	CDS	1067264	1067425	1	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	exon	1067264	1067425	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	intron	1067426	1067592	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	CDS	1067593	1067595	1	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	exon	1067593	1067595	.	-	.	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
Phchi.S6	AUGUSTUS	start_codon	1067593	1067595	.	-	0	transcript_id "Phchi.S6G014500.t1"; gene_id "Phchi.S6G014500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3567.t1 is derived from g736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4538402	4538950	.	-	.	Phchi.S1G072600
Phchi.S1	AUGUSTUS	transcript	4538402	4538950	.	-	.	transcript_id "Phchi.S1G072600.t1"; gene_id "Phchi.S1G072600"
Phchi.S1	AUGUSTUS	stop_codon	4538399	4538401	.	-	0	transcript_id "Phchi.S1G072600.t1"; gene_id "Phchi.S1G072600"
Phchi.S1	AUGUSTUS	CDS	4538402	4538950	0.82	-	0	transcript_id "Phchi.S1G072600.t1"; gene_id "Phchi.S1G072600"
Phchi.S1	AUGUSTUS	exon	4538402	4538950	.	-	.	transcript_id "Phchi.S1G072600.t1"; gene_id "Phchi.S1G072600"
Phchi.S1	AUGUSTUS	start_codon	4538948	4538950	.	-	0	transcript_id "Phchi.S1G072600.t1"; gene_id "Phchi.S1G072600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14228.t1 is derived from g12695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11655072	11656432	.	+	.	Phchi.S3G154700
Phchi.S3	AUGUSTUS	transcript	11655072	11656432	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	start_codon	11655072	11655074	.	+	0	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	CDS	11655072	11655303	0.85	+	0	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	exon	11655072	11655303	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	intron	11655304	11655405	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	CDS	11655406	11655465	1	+	2	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	exon	11655406	11655465	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	intron	11655466	11655568	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	CDS	11655569	11655868	1	+	2	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	exon	11655569	11655868	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	intron	11655869	11655968	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	CDS	11655969	11656033	1	+	2	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	exon	11655969	11656033	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	intron	11656034	11656129	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	CDS	11656130	11656432	0.91	+	0	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	exon	11656130	11656432	.	+	.	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
Phchi.S3	AUGUSTUS	stop_codon	11656433	11656435	.	+	0	transcript_id "Phchi.S3G154700.t1"; gene_id "Phchi.S3G154700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7889.t1 is derived from g5063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31771269	31772740	.	+	.	Phchi.S1G504800
Phchi.S1	AUGUSTUS	transcript	31771269	31772740	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	start_codon	31771269	31771271	.	+	0	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31771269	31771456	0.92	+	0	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31771269	31771456	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31771457	31771673	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31771674	31771742	1	+	1	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31771674	31771742	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31771743	31771857	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31771858	31771941	1	+	1	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31771858	31771941	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31771942	31772140	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31772141	31772303	0.99	+	1	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31772141	31772303	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31772304	31772410	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31772411	31772740	0.77	+	0	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31772411	31772740	.	+	.	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	stop_codon	31772741	31772743	.	+	0	transcript_id "Phchi.S1G504800.t1"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	transcript	31771269	31772740	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	start_codon	31771269	31771271	.	+	0	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31771269	31771456	0.97	+	0	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31771269	31771456	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31771457	31771673	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31771674	31771742	1	+	1	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31771674	31771742	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31771743	31771857	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31771858	31771941	1	+	1	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31771858	31771941	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31771942	31772137	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31772138	31772303	0.97	+	1	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31772138	31772303	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	intron	31772304	31772410	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	CDS	31772411	31772740	0.67	+	0	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	exon	31772411	31772740	.	+	.	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
Phchi.S1	AUGUSTUS	stop_codon	31772741	31772743	.	+	0	transcript_id "Phchi.S1G504800.t2"; gene_id "Phchi.S1G504800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1868.t1 is derived from g8788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3621136	3621678	.	-	.	Phchi.S5G047700
Phchi.S5	AUGUSTUS	transcript	3621136	3621678	.	-	.	transcript_id "Phchi.S5G047700.t1"; gene_id "Phchi.S5G047700"
Phchi.S5	AUGUSTUS	stop_codon	3621133	3621135	.	-	0	transcript_id "Phchi.S5G047700.t1"; gene_id "Phchi.S5G047700"
Phchi.S5	AUGUSTUS	CDS	3621136	3621678	0.63	-	0	transcript_id "Phchi.S5G047700.t1"; gene_id "Phchi.S5G047700"
Phchi.S5	AUGUSTUS	exon	3621136	3621678	.	-	.	transcript_id "Phchi.S5G047700.t1"; gene_id "Phchi.S5G047700"
Phchi.S5	AUGUSTUS	start_codon	3621676	3621678	.	-	0	transcript_id "Phchi.S5G047700.t1"; gene_id "Phchi.S5G047700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12688.t1 is derived from g11153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	232845	235534	.	+	.	Phchi.S3G000700
Phchi.S3	AUGUSTUS	transcript	232845	235534	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	start_codon	232845	232847	.	+	0	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	CDS	232845	232868	0.65	+	0	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	exon	232845	232868	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	intron	232869	232946	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	CDS	232947	232978	0.68	+	0	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	exon	232947	232978	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	intron	232979	233287	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	CDS	233288	233328	0.76	+	1	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	exon	233288	233328	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	intron	233329	233603	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	CDS	233604	235534	0.65	+	2	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	exon	233604	235534	.	+	.	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
Phchi.S3	AUGUSTUS	stop_codon	235535	235537	.	+	0	transcript_id "Phchi.S3G000700.t1"; gene_id "Phchi.S3G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2060.t1 is derived from g8980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4657985	4659341	.	+	.	Phchi.S5G066900
Phchi.S5	AUGUSTUS	transcript	4657985	4659341	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	start_codon	4657985	4657987	.	+	0	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	CDS	4657985	4658073	0.44	+	0	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	exon	4657985	4658073	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	intron	4658074	4658295	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	CDS	4658296	4658361	0.37	+	1	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	exon	4658296	4658361	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	intron	4658362	4658458	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	CDS	4658459	4658571	0.33	+	1	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	exon	4658459	4658571	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	intron	4658572	4658730	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	CDS	4658731	4658857	0.7	+	2	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	exon	4658731	4658857	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	intron	4658858	4659033	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	CDS	4659034	4659189	0.99	+	1	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	exon	4659034	4659189	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	intron	4659190	4659325	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	CDS	4659326	4659341	0.99	+	1	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	exon	4659326	4659341	.	+	.	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
Phchi.S5	AUGUSTUS	stop_codon	4659342	4659344	.	+	0	transcript_id "Phchi.S5G066900.t1"; gene_id "Phchi.S5G066900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14572.t1 is derived from g13040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13540778	13542676	.	+	.	Phchi.S3G189100
Phchi.S3	AUGUSTUS	transcript	13540778	13542676	.	+	.	transcript_id "Phchi.S3G189100.t1"; gene_id "Phchi.S3G189100"
Phchi.S3	AUGUSTUS	start_codon	13540778	13540780	.	+	0	transcript_id "Phchi.S3G189100.t1"; gene_id "Phchi.S3G189100"
Phchi.S3	AUGUSTUS	CDS	13540778	13542676	0.58	+	0	transcript_id "Phchi.S3G189100.t1"; gene_id "Phchi.S3G189100"
Phchi.S3	AUGUSTUS	exon	13540778	13542676	.	+	.	transcript_id "Phchi.S3G189100.t1"; gene_id "Phchi.S3G189100"
Phchi.S3	AUGUSTUS	stop_codon	13542677	13542679	.	+	0	transcript_id "Phchi.S3G189100.t1"; gene_id "Phchi.S3G189100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1445.t1 is derived from g8364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	919412	920200	.	+	.	Phchi.S5G005400
Phchi.S5	AUGUSTUS	transcript	919412	920200	.	+	.	transcript_id "Phchi.S5G005400.t1"; gene_id "Phchi.S5G005400"
Phchi.S5	AUGUSTUS	start_codon	919412	919414	.	+	0	transcript_id "Phchi.S5G005400.t1"; gene_id "Phchi.S5G005400"
Phchi.S5	AUGUSTUS	CDS	919412	920200	0.99	+	0	transcript_id "Phchi.S5G005400.t1"; gene_id "Phchi.S5G005400"
Phchi.S5	AUGUSTUS	exon	919412	920200	.	+	.	transcript_id "Phchi.S5G005400.t1"; gene_id "Phchi.S5G005400"
Phchi.S5	AUGUSTUS	stop_codon	920201	920203	.	+	0	transcript_id "Phchi.S5G005400.t1"; gene_id "Phchi.S5G005400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2855.t1 is derived from g24.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37142	39545	.	-	.	Phchi.S1G001400
Phchi.S1	AUGUSTUS	transcript	37142	39545	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	stop_codon	37139	37141	.	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	CDS	37142	37393	1	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	exon	37142	37393	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	intron	37394	37497	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	CDS	37498	37695	0.98	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	exon	37498	37695	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	intron	37696	37788	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	CDS	37789	38031	1	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	exon	37789	38031	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	intron	38032	38145	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	CDS	38146	38319	0.98	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	exon	38146	38319	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	intron	38320	38441	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	CDS	38442	39545	0.93	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	exon	38442	39545	.	-	.	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
Phchi.S1	AUGUSTUS	start_codon	39543	39545	.	-	0	transcript_id "Phchi.S1G001400.t1"; gene_id "Phchi.S1G001400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4800.t1 is derived from g1970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12884046	12892658	.	+	.	Phchi.S1G195900
Phchi.S1	AUGUSTUS	transcript	12884046	12892658	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	start_codon	12884046	12884048	.	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12884046	12885450	0.85	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12884046	12885450	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12885451	12885551	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12885552	12886870	0.73	+	2	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12885552	12886870	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12886871	12886973	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12886974	12888442	0.68	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12886974	12888442	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12888443	12888667	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12888668	12888853	0.34	+	1	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12888668	12888853	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12888854	12889008	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12889009	12889234	0.38	+	1	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12889009	12889234	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12889235	12889316	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12889317	12889517	1	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12889317	12889517	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12889518	12889618	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12889619	12890055	0.73	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12889619	12890055	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12890056	12890140	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12890141	12891344	0.97	+	1	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12890141	12891344	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12891345	12891543	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12891544	12891644	1	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12891544	12891644	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12891645	12891760	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12891761	12891872	1	+	1	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12891761	12891872	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12891873	12891954	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12891955	12892128	1	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12891955	12892128	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	intron	12892129	12892229	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	CDS	12892230	12892658	0.93	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	exon	12892230	12892658	.	+	.	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
Phchi.S1	AUGUSTUS	stop_codon	12892659	12892661	.	+	0	transcript_id "Phchi.S1G195900.t1"; gene_id "Phchi.S1G195900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11463.t1 is derived from g15513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6491176	6492807	.	-	.	Phchi.S4G104500
Phchi.S4	AUGUSTUS	transcript	6491176	6492807	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	stop_codon	6491173	6491175	.	-	0	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	CDS	6491176	6491465	0.52	-	2	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	exon	6491176	6491465	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	intron	6491466	6491563	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	CDS	6491564	6492003	1	-	1	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	exon	6491564	6492003	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	intron	6492004	6492093	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	CDS	6492094	6492176	1	-	0	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	exon	6492094	6492176	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	intron	6492177	6492263	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	CDS	6492264	6492435	0.58	-	1	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	exon	6492264	6492435	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	intron	6492436	6492559	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	CDS	6492560	6492807	0.94	-	0	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	exon	6492560	6492807	.	-	.	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
Phchi.S4	AUGUSTUS	start_codon	6492805	6492807	.	-	0	transcript_id "Phchi.S4G104500.t1"; gene_id "Phchi.S4G104500"
# This transcript jg5354.t2 is derived from g2524.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5354.t3 is derived from g2524.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5355.t1 is derived from g2525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16447565	16449233	.	+	.	Phchi.S1G251400
Phchi.S1	AUGUSTUS	transcript	16447565	16449233	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	start_codon	16447565	16447567	.	+	0	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	CDS	16447565	16447661	1	+	0	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	exon	16447565	16447661	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	intron	16447662	16447888	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	CDS	16447889	16448026	1	+	2	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	exon	16447889	16448026	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	intron	16448027	16448226	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	CDS	16448227	16448322	0.9	+	2	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	exon	16448227	16448322	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	intron	16448323	16448423	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	CDS	16448424	16448659	1	+	2	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	exon	16448424	16448659	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	intron	16448660	16448814	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	CDS	16448815	16448868	1	+	0	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	exon	16448815	16448868	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	intron	16448869	16449014	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	CDS	16449015	16449233	0.64	+	0	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	exon	16449015	16449233	.	+	.	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
Phchi.S1	AUGUSTUS	stop_codon	16449234	16449236	.	+	0	transcript_id "Phchi.S1G251400.t1"; gene_id "Phchi.S1G251400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10631.t1 is derived from g14681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1343677	1344617	.	+	.	Phchi.S4G021300
Phchi.S4	AUGUSTUS	transcript	1343677	1344617	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	start_codon	1343677	1343679	.	+	0	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	CDS	1343677	1343796	0.68	+	0	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	exon	1343677	1343796	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	intron	1343797	1343894	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	CDS	1343895	1344003	1	+	0	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	exon	1343895	1344003	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	intron	1344004	1344127	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	CDS	1344128	1344296	1	+	2	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	exon	1344128	1344296	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	intron	1344297	1344445	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	CDS	1344446	1344617	0.99	+	1	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	exon	1344446	1344617	.	+	.	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
Phchi.S4	AUGUSTUS	stop_codon	1344618	1344620	.	+	0	transcript_id "Phchi.S4G021300.t1"; gene_id "Phchi.S4G021300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15861.t1 is derived from g14331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21900308	21902952	.	-	.	Phchi.S3G318000
Phchi.S3	AUGUSTUS	transcript	21900308	21902952	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	stop_codon	21900305	21900307	.	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	CDS	21900308	21900598	0.56	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	exon	21900308	21900598	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	intron	21900599	21900727	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	CDS	21900728	21900814	1	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	exon	21900728	21900814	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	intron	21900815	21900902	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	CDS	21900903	21901223	1	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	exon	21900903	21901223	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	intron	21901224	21901355	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	CDS	21901356	21901895	0.69	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	exon	21901356	21901895	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	intron	21901896	21902079	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	CDS	21902080	21902952	0.97	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	exon	21902080	21902952	.	-	.	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
Phchi.S3	AUGUSTUS	start_codon	21902950	21902952	.	-	0	transcript_id "Phchi.S3G318000.t1"; gene_id "Phchi.S3G318000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3293.t1 is derived from g462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2702011	2703690	.	-	.	Phchi.S1G045200
Phchi.S1	AUGUSTUS	transcript	2702011	2703690	.	-	.	transcript_id "Phchi.S1G045200.t1"; gene_id "Phchi.S1G045200"
Phchi.S1	AUGUSTUS	stop_codon	2702008	2702010	.	-	0	transcript_id "Phchi.S1G045200.t1"; gene_id "Phchi.S1G045200"
Phchi.S1	AUGUSTUS	CDS	2702011	2703690	1	-	0	transcript_id "Phchi.S1G045200.t1"; gene_id "Phchi.S1G045200"
Phchi.S1	AUGUSTUS	exon	2702011	2703690	.	-	.	transcript_id "Phchi.S1G045200.t1"; gene_id "Phchi.S1G045200"
Phchi.S1	AUGUSTUS	start_codon	2703688	2703690	.	-	0	transcript_id "Phchi.S1G045200.t1"; gene_id "Phchi.S1G045200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6688.t1 is derived from g3860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24512425	24514382	.	-	.	Phchi.S1G384700
Phchi.S1	AUGUSTUS	transcript	24512425	24514382	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	stop_codon	24512422	24512424	.	-	0	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	CDS	24512425	24512796	0.89	-	0	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	exon	24512425	24512796	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	intron	24512797	24512907	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	CDS	24512908	24513156	1	-	0	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	exon	24512908	24513156	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	intron	24513157	24513292	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	CDS	24513293	24513873	1	-	2	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	exon	24513293	24513873	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	intron	24513874	24513991	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	CDS	24513992	24514382	0.94	-	0	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	exon	24513992	24514382	.	-	.	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	start_codon	24514380	24514382	.	-	0	transcript_id "Phchi.S1G384700.t1"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	transcript	24512425	24513123	.	-	.	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	stop_codon	24512422	24512424	.	-	0	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	CDS	24512425	24512796	0.92	-	0	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	exon	24512425	24512796	.	-	.	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	intron	24512797	24512907	.	-	.	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	CDS	24512908	24513123	0.46	-	0	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	exon	24512908	24513123	.	-	.	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
Phchi.S1	AUGUSTUS	start_codon	24513121	24513123	.	-	0	transcript_id "Phchi.S1G384700.t2"; gene_id "Phchi.S1G384700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13901.t1 is derived from g12368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9549354	9552169	.	+	.	Phchi.S3G122000
Phchi.S3	AUGUSTUS	transcript	9549354	9552169	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	start_codon	9549354	9549356	.	+	0	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	CDS	9549354	9549624	1	+	0	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	exon	9549354	9549624	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	intron	9549625	9549732	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	CDS	9549733	9549914	1	+	2	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	exon	9549733	9549914	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	intron	9549915	9550034	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	CDS	9550035	9550307	0.56	+	0	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	exon	9550035	9550307	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	intron	9550308	9550388	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	CDS	9550389	9551230	0.57	+	0	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	exon	9550389	9551230	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	intron	9551231	9551326	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	CDS	9551327	9551582	0.96	+	1	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	exon	9551327	9551582	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	intron	9551583	9551746	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	CDS	9551747	9552169	0.94	+	0	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	exon	9551747	9552169	.	+	.	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
Phchi.S3	AUGUSTUS	stop_codon	9552170	9552172	.	+	0	transcript_id "Phchi.S3G122000.t1"; gene_id "Phchi.S3G122000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14851.t1 is derived from g13319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15049321	15049959	.	+	.	Phchi.S3G217000
Phchi.S3	AUGUSTUS	transcript	15049321	15049959	.	+	.	transcript_id "Phchi.S3G217000.t1"; gene_id "Phchi.S3G217000"
Phchi.S3	AUGUSTUS	start_codon	15049321	15049323	.	+	0	transcript_id "Phchi.S3G217000.t1"; gene_id "Phchi.S3G217000"
Phchi.S3	AUGUSTUS	CDS	15049321	15049959	0.96	+	0	transcript_id "Phchi.S3G217000.t1"; gene_id "Phchi.S3G217000"
Phchi.S3	AUGUSTUS	exon	15049321	15049959	.	+	.	transcript_id "Phchi.S3G217000.t1"; gene_id "Phchi.S3G217000"
Phchi.S3	AUGUSTUS	stop_codon	15049960	15049962	.	+	0	transcript_id "Phchi.S3G217000.t1"; gene_id "Phchi.S3G217000"
# This transcript jg14198.t2 is derived from g12665.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14199.t1 is derived from g12666.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11435204	11450796	.	-	.	Phchi.S3G151800
Phchi.S3	AUGUSTUS	transcript	11435204	11450796	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	stop_codon	11435201	11435203	.	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11435204	11435436	0.96	-	2	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11435204	11435436	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11435437	11435537	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11435538	11435742	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11435538	11435742	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11435743	11435818	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11435819	11436103	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11435819	11436103	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436104	11436191	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11436192	11436360	0.94	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11436192	11436360	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436361	11436523	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11436524	11436647	0.8	-	2	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11436524	11436647	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436648	11436731	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11436732	11436881	1	-	2	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11436732	11436881	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436882	11437014	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11437015	11437165	0.99	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11437015	11437165	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11437166	11437272	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11437273	11438739	0.99	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11437273	11438739	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11438740	11438830	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11438831	11439178	0.99	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11438831	11439178	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11439179	11439313	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11439314	11439466	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11439314	11439466	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11439467	11439690	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11439691	11439783	0.97	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11439691	11439783	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11439784	11439995	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11439996	11440214	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11439996	11440214	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440215	11440304	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11440305	11440565	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11440305	11440565	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440566	11440676	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11440677	11440775	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11440677	11440775	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440776	11440879	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11440880	11440981	0.99	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11440880	11440981	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440982	11441201	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11441202	11441325	0.5	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11441202	11441325	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11441326	11441451	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11441452	11441605	0.55	-	2	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11441452	11441605	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11441606	11441751	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11441752	11442058	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11441752	11442058	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11442059	11442208	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11442209	11442469	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11442209	11442469	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11442470	11442556	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11442557	11442808	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11442557	11442808	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11442809	11443045	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11443046	11443300	0.98	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11443046	11443300	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11443301	11443373	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11443374	11445356	0.52	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11443374	11445356	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11445357	11445432	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11445433	11445757	0.96	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11445433	11445757	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11445758	11445855	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11445856	11446048	0.97	-	2	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11445856	11446048	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446049	11446155	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11446156	11446166	1	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11446156	11446166	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446167	11446337	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11446338	11446506	1	-	2	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11446338	11446506	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446507	11446662	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11446663	11446883	1	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11446663	11446883	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446884	11447021	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447022	11447240	1	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447022	11447240	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447241	11447329	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447330	11447460	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447330	11447460	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447461	11447570	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447571	11447711	0.99	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447571	11447711	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447712	11447793	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447794	11447968	0.99	-	1	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447794	11447968	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447969	11448078	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11448079	11448242	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11448079	11448242	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11448243	11448358	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11448359	11448493	0.87	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11448359	11448493	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11448494	11448682	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11448683	11448922	0.65	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11448683	11448922	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11448923	11449037	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449038	11449130	0.97	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449038	11449130	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11449131	11449461	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449462	11449563	0.91	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449462	11449563	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11449564	11449639	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449640	11449729	0.95	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449640	11449729	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11449730	11449862	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449863	11450060	1	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449863	11450060	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11450061	11450157	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11450158	11450796	0.95	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11450158	11450796	.	-	.	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	start_codon	11450794	11450796	.	-	0	transcript_id "Phchi.S3G151800.t1"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	transcript	11435204	11450796	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	stop_codon	11435201	11435203	.	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11435204	11435436	0.98	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11435204	11435436	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11435437	11435537	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11435538	11435742	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11435538	11435742	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11435743	11435818	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11435819	11436103	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11435819	11436103	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436104	11436191	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11436192	11436360	0.93	-	1	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11436192	11436360	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436361	11436523	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11436524	11436647	0.84	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11436524	11436647	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436648	11436731	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11436732	11436881	1	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11436732	11436881	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11436882	11437014	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11437015	11437165	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11437015	11437165	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11437166	11437272	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11437273	11438739	0.94	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11437273	11438739	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11438740	11438830	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11438831	11439178	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11438831	11439178	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11439179	11439313	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11439314	11439466	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11439314	11439466	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11439467	11439690	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11439691	11439783	0.98	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11439691	11439783	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11439784	11439995	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11439996	11440214	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11439996	11440214	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440215	11440304	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11440305	11440565	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11440305	11440565	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440566	11440676	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11440677	11440775	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11440677	11440775	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440776	11440879	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11440880	11440981	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11440880	11440981	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11440982	11441201	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11441202	11441325	0.37	-	1	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11441202	11441325	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11441326	11441451	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11441452	11441605	0.39	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11441452	11441605	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11441606	11441751	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11441752	11442058	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11441752	11442058	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11442059	11442208	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11442209	11442469	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11442209	11442469	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11442470	11442556	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11442557	11442808	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11442557	11442808	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11442809	11443045	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11443046	11443300	0.97	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11443046	11443300	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11443301	11443373	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11443374	11445356	0.55	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11443374	11445356	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11445357	11445432	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11445433	11445533	0.63	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11445433	11445533	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11445534	11445649	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11445650	11445757	0.65	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11445650	11445757	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11445758	11445943	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11445944	11446048	0.78	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11445944	11446048	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446049	11446155	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11446156	11446166	0.99	-	1	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11446156	11446166	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446167	11446337	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11446338	11446506	1	-	2	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11446338	11446506	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446507	11446662	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11446663	11446883	1	-	1	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11446663	11446883	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11446884	11447021	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447022	11447240	1	-	1	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447022	11447240	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447241	11447329	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447330	11447460	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447330	11447460	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447461	11447570	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447571	11447711	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447571	11447711	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447712	11447793	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11447794	11447968	0.98	-	1	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11447794	11447968	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11447969	11448078	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11448079	11448242	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11448079	11448242	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11448243	11448358	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11448359	11448493	0.74	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11448359	11448493	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11448494	11448682	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11448683	11448922	0.48	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11448683	11448922	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11448923	11449037	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449038	11449130	0.95	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449038	11449130	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11449131	11449461	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449462	11449563	0.93	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449462	11449563	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11449564	11449862	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11449863	11450060	1	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11449863	11450060	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	intron	11450061	11450157	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	CDS	11450158	11450796	0.98	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	exon	11450158	11450796	.	-	.	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
Phchi.S3	AUGUSTUS	start_codon	11450794	11450796	.	-	0	transcript_id "Phchi.S3G151800.t2"; gene_id "Phchi.S3G151800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14316.t1 is derived from g12783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12067900	12068553	.	+	.	Phchi.S3G163500
Phchi.S3	AUGUSTUS	transcript	12067900	12068553	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	start_codon	12067900	12067902	.	+	0	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12067900	12067944	1	+	0	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12067900	12067944	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12067945	12068030	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068031	12068208	1	+	0	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068031	12068208	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12068209	12068281	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068282	12068326	1	+	2	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068282	12068326	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12068327	12068408	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068409	12068418	1	+	2	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068409	12068418	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12068419	12068516	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068517	12068553	0.98	+	1	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068517	12068553	.	+	.	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	stop_codon	12068554	12068556	.	+	0	transcript_id "Phchi.S3G163500.t1"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	transcript	12067900	12068553	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	start_codon	12067900	12067902	.	+	0	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12067900	12067944	1	+	0	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12067900	12067944	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12067945	12068030	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068031	12068208	1	+	0	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068031	12068208	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12068209	12068287	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068288	12068326	0.99	+	2	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068288	12068326	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12068327	12068408	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068409	12068418	0.99	+	2	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068409	12068418	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	intron	12068419	12068516	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	CDS	12068517	12068553	0.97	+	1	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	exon	12068517	12068553	.	+	.	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
Phchi.S3	AUGUSTUS	stop_codon	12068554	12068556	.	+	0	transcript_id "Phchi.S3G163500.t2"; gene_id "Phchi.S3G163500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11544.t1 is derived from g15594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6977596	6978671	.	+	.	Phchi.S4G112600
Phchi.S4	AUGUSTUS	transcript	6977596	6978671	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	start_codon	6977596	6977598	.	+	0	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6977596	6977713	1	+	0	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6977596	6977713	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	intron	6977714	6977855	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6977856	6977994	1	+	2	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6977856	6977994	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	intron	6977995	6978091	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6978092	6978103	0.99	+	1	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6978092	6978103	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	intron	6978104	6978176	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6978177	6978181	0.99	+	1	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6978177	6978181	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	intron	6978182	6978267	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6978268	6978327	1	+	2	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6978268	6978327	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	intron	6978328	6978469	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6978470	6978481	0.39	+	2	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6978470	6978481	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	intron	6978482	6978624	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	CDS	6978625	6978671	0.37	+	2	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	exon	6978625	6978671	.	+	.	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
Phchi.S4	AUGUSTUS	stop_codon	6978672	6978674	.	+	0	transcript_id "Phchi.S4G112600.t1"; gene_id "Phchi.S4G112600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6607.t1 is derived from g3779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23991787	23995302	.	-	.	Phchi.S1G376600
Phchi.S1	AUGUSTUS	transcript	23991787	23995302	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	stop_codon	23991784	23991786	.	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23991787	23991924	1	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23991787	23991924	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23991925	23992130	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23992131	23992184	1	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23992131	23992184	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23992185	23992477	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23992478	23992522	1	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23992478	23992522	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23992523	23992611	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23992612	23992668	1	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23992612	23992668	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23992669	23992787	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23992788	23992853	1	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23992788	23992853	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23992854	23992946	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23992947	23993010	1	-	1	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23992947	23993010	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23993011	23993544	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23993545	23993609	1	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23993545	23993609	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23993610	23993743	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23993744	23993817	1	-	2	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23993744	23993817	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23993818	23993973	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23993974	23994057	1	-	2	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23993974	23994057	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23994058	23994304	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23994305	23994419	0.37	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23994305	23994419	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23994420	23994533	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23994534	23994605	0.95	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23994534	23994605	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23994606	23994985	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23994986	23995060	0.67	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23994986	23995060	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	intron	23995061	23995212	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	CDS	23995213	23995302	0.67	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	exon	23995213	23995302	.	-	.	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
Phchi.S1	AUGUSTUS	start_codon	23995300	23995302	.	-	0	transcript_id "Phchi.S1G376600.t1"; gene_id "Phchi.S1G376600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5730.t1 is derived from g2900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18589136	18590558	.	-	.	Phchi.S1G288900
Phchi.S1	AUGUSTUS	transcript	18589136	18590558	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	stop_codon	18589133	18589135	.	-	0	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18589136	18589186	1	-	0	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18589136	18589186	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18589187	18589305	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18589306	18589387	1	-	1	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18589306	18589387	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18589388	18589511	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18589512	18589603	1	-	0	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18589512	18589603	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18589604	18590251	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18590252	18590362	1	-	0	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18590252	18590362	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18590363	18590507	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18590508	18590558	1	-	0	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18590508	18590558	.	-	.	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	start_codon	18590556	18590558	.	-	0	transcript_id "Phchi.S1G288900.t1"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	transcript	18589136	18590558	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	stop_codon	18589133	18589135	.	-	0	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18589136	18589186	0.99	-	0	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18589136	18589186	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18589187	18589305	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18589306	18589387	1	-	1	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18589306	18589387	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18589388	18589511	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18589512	18589603	1	-	0	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18589512	18589603	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18589604	18590251	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18590252	18590362	0.99	-	0	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18590252	18590362	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	intron	18590363	18590468	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	CDS	18590469	18590558	0.74	-	0	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	exon	18590469	18590558	.	-	.	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
Phchi.S1	AUGUSTUS	start_codon	18590556	18590558	.	-	0	transcript_id "Phchi.S1G288900.t2"; gene_id "Phchi.S1G288900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4763.t1 is derived from g1933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12702279	12707956	.	+	.	Phchi.S1G192200
Phchi.S1	AUGUSTUS	transcript	12702279	12707956	.	+	.	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	start_codon	12702279	12702281	.	+	0	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	CDS	12702279	12704785	0.21	+	0	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	exon	12702279	12704785	.	+	.	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	intron	12704786	12704880	.	+	.	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	CDS	12704881	12707826	0.24	+	1	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	exon	12704881	12707826	.	+	.	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	intron	12707827	12707910	.	+	.	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	CDS	12707911	12707956	1	+	1	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	exon	12707911	12707956	.	+	.	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
Phchi.S1	AUGUSTUS	stop_codon	12707957	12707959	.	+	0	transcript_id "Phchi.S1G192200.t1"; gene_id "Phchi.S1G192200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5948.t1 is derived from g3119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19983765	19985749	.	-	.	Phchi.S1G310700
Phchi.S1	AUGUSTUS	transcript	19983765	19985749	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	stop_codon	19983762	19983764	.	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19983765	19983862	0.96	-	2	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19983765	19983862	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19983863	19983954	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19983955	19984014	0.96	-	2	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19983955	19984014	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19984015	19984158	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19984159	19984194	1	-	2	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19984159	19984194	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19984195	19984398	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19984399	19984450	0.42	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19984399	19984450	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19984451	19984590	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19984591	19984614	0.54	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19984591	19984614	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19984615	19984706	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19984707	19984952	1	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19984707	19984952	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19984953	19985119	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19985120	19985253	0.94	-	2	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19985120	19985253	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19985254	19985362	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19985363	19985543	0.99	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19985363	19985543	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	intron	19985544	19985656	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	CDS	19985657	19985749	0.6	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	exon	19985657	19985749	.	-	.	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
Phchi.S1	AUGUSTUS	start_codon	19985747	19985749	.	-	0	transcript_id "Phchi.S1G310700.t1"; gene_id "Phchi.S1G310700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13032.t1 is derived from g11497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3791878	3792993	.	+	.	Phchi.S3G035100
Phchi.S3	AUGUSTUS	transcript	3791878	3792993	.	+	.	transcript_id "Phchi.S3G035100.t1"; gene_id "Phchi.S3G035100"
Phchi.S3	AUGUSTUS	start_codon	3791878	3791880	.	+	0	transcript_id "Phchi.S3G035100.t1"; gene_id "Phchi.S3G035100"
Phchi.S3	AUGUSTUS	CDS	3791878	3792993	0.99	+	0	transcript_id "Phchi.S3G035100.t1"; gene_id "Phchi.S3G035100"
Phchi.S3	AUGUSTUS	exon	3791878	3792993	.	+	.	transcript_id "Phchi.S3G035100.t1"; gene_id "Phchi.S3G035100"
Phchi.S3	AUGUSTUS	stop_codon	3792994	3792996	.	+	0	transcript_id "Phchi.S3G035100.t1"; gene_id "Phchi.S3G035100"
# This transcript jg12296.t2 is derived from g7972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12297.t1 is derived from g7973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9595627	9597486	.	+	.	Phchi.S2G037700
Phchi.S2	AUGUSTUS	transcript	9595627	9597486	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	start_codon	9595627	9595629	.	+	0	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9595627	9595950	0.77	+	0	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9595627	9595950	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9595951	9596026	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9596027	9596096	1	+	0	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9596027	9596096	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9596097	9596220	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9596221	9596318	1	+	2	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9596221	9596318	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9596319	9596501	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9596502	9596584	1	+	0	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9596502	9596584	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9596585	9596703	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9596704	9596819	1	+	1	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9596704	9596819	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9596820	9596899	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9596900	9596996	1	+	2	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9596900	9596996	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9596997	9597129	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9597130	9597214	1	+	1	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9597130	9597214	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	intron	9597215	9597399	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	CDS	9597400	9597486	0.57	+	0	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	exon	9597400	9597486	.	+	.	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
Phchi.S2	AUGUSTUS	stop_codon	9597487	9597489	.	+	0	transcript_id "Phchi.S2G037700.t1"; gene_id "Phchi.S2G037700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg150.t1 is derived from g9932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	842848	843761	.	+	.	Phchi.S6G010900
Phchi.S6	AUGUSTUS	transcript	842848	843761	.	+	.	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	start_codon	842848	842850	.	+	0	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	CDS	842848	842871	0.6	+	0	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	exon	842848	842871	.	+	.	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	intron	842872	843024	.	+	.	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	CDS	843025	843584	0.98	+	0	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	exon	843025	843584	.	+	.	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	intron	843585	843718	.	+	.	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	CDS	843719	843761	1	+	1	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	exon	843719	843761	.	+	.	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
Phchi.S6	AUGUSTUS	stop_codon	843762	843764	.	+	0	transcript_id "Phchi.S6G010900.t1"; gene_id "Phchi.S6G010900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7059.t1 is derived from g4231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26659017	26660905	.	-	.	Phchi.S1G421800
Phchi.S1	AUGUSTUS	transcript	26659017	26660905	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	stop_codon	26659014	26659016	.	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26659017	26659553	0.98	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26659017	26659553	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	intron	26659554	26659652	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26659653	26659796	1	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26659653	26659796	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	intron	26659797	26659972	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26659973	26660062	1	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26659973	26660062	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	intron	26660063	26660152	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26660153	26660346	1	-	2	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26660153	26660346	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	intron	26660347	26660501	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26660502	26660560	1	-	1	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26660502	26660560	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	intron	26660561	26660688	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26660689	26660771	1	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26660689	26660771	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	intron	26660772	26660890	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	CDS	26660891	26660905	1	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	exon	26660891	26660905	.	-	.	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
Phchi.S1	AUGUSTUS	start_codon	26660903	26660905	.	-	0	transcript_id "Phchi.S1G421800.t1"; gene_id "Phchi.S1G421800"
# This transcript jg8471.t2 is derived from g5646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8472.t1 is derived from g5647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36107601	36109620	.	-	.	Phchi.S1G563100
Phchi.S1	AUGUSTUS	transcript	36107601	36109620	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	stop_codon	36107598	36107600	.	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36107601	36107615	0.94	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36107601	36107615	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	intron	36107616	36107734	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36107735	36107839	0.95	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36107735	36107839	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	intron	36107840	36107930	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36107931	36108004	1	-	2	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36107931	36108004	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	intron	36108005	36108150	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36108151	36108211	1	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36108151	36108211	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	intron	36108212	36108349	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36108350	36108424	1	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36108350	36108424	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	intron	36108425	36108535	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36108536	36108646	0.99	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36108536	36108646	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	intron	36108647	36109176	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	CDS	36109177	36109620	0.56	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	exon	36109177	36109620	.	-	.	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
Phchi.S1	AUGUSTUS	start_codon	36109618	36109620	.	-	0	transcript_id "Phchi.S1G563100.t1"; gene_id "Phchi.S1G563100"
# This transcript jg232.t2 is derived from g10014.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg233.t1 is derived from g10015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1587745	1590226	.	-	.	Phchi.S6G019200
Phchi.S6	AUGUSTUS	transcript	1587745	1590226	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	stop_codon	1587742	1587744	.	-	0	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	CDS	1587745	1588242	0.69	-	0	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	exon	1587745	1588242	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	intron	1588243	1588427	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	CDS	1588428	1588546	0.3	-	2	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	exon	1588428	1588546	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	intron	1588547	1588749	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	CDS	1588750	1589287	0.6	-	0	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	exon	1588750	1589287	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	intron	1589288	1589374	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	CDS	1589375	1589453	0.49	-	1	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	exon	1589375	1589453	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	intron	1589454	1589548	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	CDS	1589549	1589820	0.46	-	0	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	exon	1589549	1589820	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	intron	1589821	1590010	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	CDS	1590011	1590226	0.63	-	0	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	exon	1590011	1590226	.	-	.	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
Phchi.S6	AUGUSTUS	start_codon	1590224	1590226	.	-	0	transcript_id "Phchi.S6G019200.t1"; gene_id "Phchi.S6G019200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4395.t1 is derived from g1564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10224002	10224646	.	-	.	Phchi.S1G155400
Phchi.S1	AUGUSTUS	transcript	10224002	10224646	.	-	.	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	stop_codon	10223999	10224001	.	-	0	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	CDS	10224002	10224094	1	-	0	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	exon	10224002	10224094	.	-	.	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	intron	10224095	10224191	.	-	.	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	CDS	10224192	10224255	1	-	1	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	exon	10224192	10224255	.	-	.	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	intron	10224256	10224347	.	-	.	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	CDS	10224348	10224646	1	-	0	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	exon	10224348	10224646	.	-	.	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
Phchi.S1	AUGUSTUS	start_codon	10224644	10224646	.	-	0	transcript_id "Phchi.S1G155400.t1"; gene_id "Phchi.S1G155400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4309.t1 is derived from g1478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9553092	9553475	.	+	.	Phchi.S1G146800
Phchi.S1	AUGUSTUS	transcript	9553092	9553475	.	+	.	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	start_codon	9553092	9553094	.	+	0	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	CDS	9553092	9553355	0.87	+	0	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	exon	9553092	9553355	.	+	.	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	intron	9553356	9553448	.	+	.	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	CDS	9553449	9553475	0.57	+	0	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	exon	9553449	9553475	.	+	.	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
Phchi.S1	AUGUSTUS	stop_codon	9553476	9553478	.	+	0	transcript_id "Phchi.S1G146800.t1"; gene_id "Phchi.S1G146800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14011.t1 is derived from g12478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10303411	10304971	.	+	.	Phchi.S3G133000
Phchi.S3	AUGUSTUS	transcript	10303411	10304971	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	start_codon	10303411	10303413	.	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10303411	10303428	0.31	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10303411	10303428	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10303429	10303510	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10303511	10303646	0.26	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10303511	10303646	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10303647	10303728	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10303729	10303861	1	+	2	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10303729	10303861	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10303862	10303945	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10303946	10303991	1	+	1	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10303946	10303991	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10303992	10304070	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10304071	10304130	1	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10304071	10304130	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10304131	10304204	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10304205	10304241	1	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10304205	10304241	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10304242	10304348	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10304349	10304428	0.48	+	2	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10304349	10304428	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10304429	10304504	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10304505	10304596	1	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10304505	10304596	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10304597	10304688	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10304689	10304749	1	+	1	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10304689	10304749	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	intron	10304750	10304911	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	CDS	10304912	10304971	1	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	exon	10304912	10304971	.	+	.	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
Phchi.S3	AUGUSTUS	stop_codon	10304972	10304974	.	+	0	transcript_id "Phchi.S3G133000.t1"; gene_id "Phchi.S3G133000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5751.t1 is derived from g2921.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18717611	18719617	.	-	.	Phchi.S1G291000
Phchi.S1	AUGUSTUS	transcript	18717611	18719490	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	stop_codon	18717608	18717610	.	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18717611	18717690	1	-	2	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18717611	18717690	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18717691	18717776	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18717777	18717879	1	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18717777	18717879	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18717880	18717969	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18717970	18718500	0.98	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18717970	18718500	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718501	18718594	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18718595	18718639	1	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18718595	18718639	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718640	18718716	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18718717	18718817	1	-	2	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18718717	18718817	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718818	18718906	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18718907	18718973	1	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18718907	18718973	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718974	18719064	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18719065	18719130	1	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18719065	18719130	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18719131	18719252	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18719253	18719333	1	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18719253	18719333	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18719334	18719424	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18719425	18719490	1	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18719425	18719490	.	-	.	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	start_codon	18719488	18719490	.	-	0	transcript_id "Phchi.S1G291000.t1"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	transcript	18717611	18719617	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	stop_codon	18717608	18717610	.	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18717611	18717690	1	-	2	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18717611	18717690	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18717691	18717776	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18717777	18717879	1	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18717777	18717879	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18717880	18717969	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18717970	18718500	0.97	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18717970	18718500	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718501	18718594	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18718595	18718639	1	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18718595	18718639	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718640	18718716	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18718717	18718817	1	-	2	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18718717	18718817	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718818	18718906	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18718907	18718973	1	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18718907	18718973	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18718974	18719064	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18719065	18719130	1	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18719065	18719130	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18719131	18719252	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18719253	18719333	1	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18719253	18719333	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	intron	18719334	18719551	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	CDS	18719552	18719617	0.45	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	exon	18719552	18719617	.	-	.	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
Phchi.S1	AUGUSTUS	start_codon	18719615	18719617	.	-	0	transcript_id "Phchi.S1G291000.t2"; gene_id "Phchi.S1G291000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4032.t1 is derived from g1201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7270338	7278375	.	+	.	Phchi.S1G119100
Phchi.S1	AUGUSTUS	transcript	7270338	7278375	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	start_codon	7270338	7270340	.	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7270338	7270550	0.62	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7270338	7270550	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7270551	7270694	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7270695	7270985	0.96	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7270695	7270985	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7270986	7271077	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7271078	7271086	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7271078	7271086	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7271087	7271701	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7271702	7271818	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7271702	7271818	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7271819	7271972	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7271973	7272119	0.54	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7271973	7272119	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7272120	7272225	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7272226	7272679	0.67	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7272226	7272679	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7272680	7272829	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7272830	7272941	1	+	2	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7272830	7272941	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7272942	7273068	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7273069	7273190	1	+	1	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7273069	7273190	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7273191	7273312	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7273313	7273407	1	+	2	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7273313	7273407	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7273408	7273516	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7273517	7273591	0.99	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7273517	7273591	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7273592	7273784	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7273785	7274022	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7273785	7274022	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7274023	7274098	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7274099	7274174	1	+	2	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7274099	7274174	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7274175	7274397	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7274398	7274445	1	+	1	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7274398	7274445	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7274446	7274552	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7274553	7274698	0.28	+	1	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7274553	7274698	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7274699	7274802	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7274803	7274873	1	+	2	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7274803	7274873	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7274874	7275032	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7275033	7275206	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7275033	7275206	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7275207	7275331	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7275332	7275403	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7275332	7275403	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7275404	7275551	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7275552	7275653	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7275552	7275653	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7275654	7275751	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7275752	7275841	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7275752	7275841	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7275842	7275943	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7275944	7276019	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7275944	7276019	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7276020	7276222	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7276223	7276319	1	+	2	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7276223	7276319	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7276320	7276424	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7276425	7276494	1	+	1	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7276425	7276494	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7276495	7276574	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7276575	7276754	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7276575	7276754	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7276755	7276891	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7276892	7277014	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7276892	7277014	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7277015	7277094	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7277095	7277178	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7277095	7277178	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7277179	7277295	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7277296	7277480	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7277296	7277480	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7277481	7277647	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7277648	7277786	1	+	1	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7277648	7277786	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7277787	7277889	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7277890	7277949	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7277890	7277949	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7277950	7278041	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7278042	7278158	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7278042	7278158	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	intron	7278159	7278264	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	CDS	7278265	7278375	1	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	exon	7278265	7278375	.	+	.	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
Phchi.S1	AUGUSTUS	stop_codon	7278376	7278378	.	+	0	transcript_id "Phchi.S1G119100.t1"; gene_id "Phchi.S1G119100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2259.t1 is derived from g9179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5716073	5717953	.	+	.	Phchi.S5G086800
Phchi.S5	AUGUSTUS	transcript	5716073	5717953	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	start_codon	5716073	5716075	.	+	0	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5716073	5716304	0.98	+	0	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5716073	5716304	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	intron	5716305	5716370	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5716371	5716618	1	+	2	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5716371	5716618	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	intron	5716619	5716702	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5716703	5716890	1	+	0	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5716703	5716890	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	intron	5716891	5716981	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5716982	5717073	0.49	+	1	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5716982	5717073	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	intron	5717074	5717163	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5717164	5717433	1	+	2	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5717164	5717433	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	intron	5717434	5717530	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5717531	5717666	1	+	2	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5717531	5717666	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	intron	5717667	5717754	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	CDS	5717755	5717953	1	+	1	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	exon	5717755	5717953	.	+	.	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
Phchi.S5	AUGUSTUS	stop_codon	5717954	5717956	.	+	0	transcript_id "Phchi.S5G086800.t1"; gene_id "Phchi.S5G086800"
# This transcript jg7531.t2 is derived from g4705.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7532.t1 is derived from g4706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29920359	29921098	.	+	.	Phchi.S1G469100
Phchi.S1	AUGUSTUS	transcript	29920359	29921098	.	+	.	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	start_codon	29920359	29920361	.	+	0	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	CDS	29920359	29920842	0.29	+	0	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	exon	29920359	29920842	.	+	.	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	intron	29920843	29920985	.	+	.	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	CDS	29920986	29921098	0.53	+	2	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	exon	29920986	29921098	.	+	.	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
Phchi.S1	AUGUSTUS	stop_codon	29921099	29921101	.	+	0	transcript_id "Phchi.S1G469100.t1"; gene_id "Phchi.S1G469100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg933.t1 is derived from g10715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6491952	6494976	.	-	.	Phchi.S6G089200
Phchi.S6	AUGUSTUS	transcript	6491952	6494976	.	-	.	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	stop_codon	6491949	6491951	.	-	0	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	CDS	6491952	6494234	0.99	-	0	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	exon	6491952	6494234	.	-	.	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	intron	6494235	6494340	.	-	.	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	CDS	6494341	6494976	0.94	-	0	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	exon	6494341	6494976	.	-	.	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
Phchi.S6	AUGUSTUS	start_codon	6494974	6494976	.	-	0	transcript_id "Phchi.S6G089200.t1"; gene_id "Phchi.S6G089200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10121.t1 is derived from g7297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45833056	45836189	.	+	.	Phchi.S1G728000
Phchi.S1	AUGUSTUS	transcript	45833056	45836189	.	+	.	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	start_codon	45833056	45833058	.	+	0	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	CDS	45833056	45833160	1	+	0	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	exon	45833056	45833160	.	+	.	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	intron	45833161	45834147	.	+	.	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	CDS	45834148	45834668	0.95	+	0	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	exon	45834148	45834668	.	+	.	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	intron	45834669	45836167	.	+	.	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	CDS	45836168	45836189	0.01	+	1	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	exon	45836168	45836189	.	+	.	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
Phchi.S1	AUGUSTUS	stop_codon	45836190	45836192	.	+	0	transcript_id "Phchi.S1G728000.t1"; gene_id "Phchi.S1G728000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13105.t1 is derived from g11570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4157981	4158391	.	-	.	Phchi.S3G042400
Phchi.S3	AUGUSTUS	transcript	4157981	4158391	.	-	.	transcript_id "Phchi.S3G042400.t1"; gene_id "Phchi.S3G042400"
Phchi.S3	AUGUSTUS	stop_codon	4157978	4157980	.	-	0	transcript_id "Phchi.S3G042400.t1"; gene_id "Phchi.S3G042400"
Phchi.S3	AUGUSTUS	CDS	4157981	4158391	0.88	-	0	transcript_id "Phchi.S3G042400.t1"; gene_id "Phchi.S3G042400"
Phchi.S3	AUGUSTUS	exon	4157981	4158391	.	-	.	transcript_id "Phchi.S3G042400.t1"; gene_id "Phchi.S3G042400"
Phchi.S3	AUGUSTUS	start_codon	4158389	4158391	.	-	0	transcript_id "Phchi.S3G042400.t1"; gene_id "Phchi.S3G042400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11332.t1 is derived from g15382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5603895	5604184	.	-	.	Phchi.S4G091400
Phchi.S4	AUGUSTUS	transcript	5603895	5604184	.	-	.	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	stop_codon	5603892	5603894	.	-	0	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	CDS	5603895	5604002	0.63	-	0	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	exon	5603895	5604002	.	-	.	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	intron	5604003	5604094	.	-	.	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	CDS	5604095	5604184	0.49	-	0	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	exon	5604095	5604184	.	-	.	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
Phchi.S4	AUGUSTUS	start_codon	5604182	5604184	.	-	0	transcript_id "Phchi.S4G091400.t1"; gene_id "Phchi.S4G091400"
# This transcript jg14694.t2 is derived from g13162.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14695.t1 is derived from g13163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14202434	14203132	.	-	.	Phchi.S3G201400
Phchi.S3	AUGUSTUS	transcript	14202434	14203132	.	-	.	transcript_id "Phchi.S3G201400.t1"; gene_id "Phchi.S3G201400"
Phchi.S3	AUGUSTUS	stop_codon	14202431	14202433	.	-	0	transcript_id "Phchi.S3G201400.t1"; gene_id "Phchi.S3G201400"
Phchi.S3	AUGUSTUS	CDS	14202434	14203132	0.77	-	0	transcript_id "Phchi.S3G201400.t1"; gene_id "Phchi.S3G201400"
Phchi.S3	AUGUSTUS	exon	14202434	14203132	.	-	.	transcript_id "Phchi.S3G201400.t1"; gene_id "Phchi.S3G201400"
Phchi.S3	AUGUSTUS	start_codon	14203130	14203132	.	-	0	transcript_id "Phchi.S3G201400.t1"; gene_id "Phchi.S3G201400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1980.t1 is derived from g8900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4214198	4215802	.	-	.	Phchi.S5G058900
Phchi.S5	AUGUSTUS	transcript	4214198	4215802	.	-	.	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	stop_codon	4214195	4214197	.	-	0	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	CDS	4214198	4215415	1	-	0	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	exon	4214198	4215415	.	-	.	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	intron	4215416	4215745	.	-	.	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	CDS	4215746	4215802	1	-	0	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	exon	4215746	4215802	.	-	.	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
Phchi.S5	AUGUSTUS	start_codon	4215800	4215802	.	-	0	transcript_id "Phchi.S5G058900.t1"; gene_id "Phchi.S5G058900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14964.t1 is derived from g13432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15778798	15779490	.	+	.	Phchi.S3G228300
Phchi.S3	AUGUSTUS	transcript	15778798	15779490	.	+	.	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	start_codon	15778798	15778800	.	+	0	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	CDS	15778798	15779049	1	+	0	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	exon	15778798	15779049	.	+	.	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	intron	15779050	15779172	.	+	.	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	CDS	15779173	15779490	1	+	0	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	exon	15779173	15779490	.	+	.	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
Phchi.S3	AUGUSTUS	stop_codon	15779491	15779493	.	+	0	transcript_id "Phchi.S3G228300.t1"; gene_id "Phchi.S3G228300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9792.t1 is derived from g6968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43717445	43718302	.	-	.	Phchi.S1G695100
Phchi.S1	AUGUSTUS	transcript	43717445	43718302	.	-	.	transcript_id "Phchi.S1G695100.t1"; gene_id "Phchi.S1G695100"
Phchi.S1	AUGUSTUS	stop_codon	43717442	43717444	.	-	0	transcript_id "Phchi.S1G695100.t1"; gene_id "Phchi.S1G695100"
Phchi.S1	AUGUSTUS	CDS	43717445	43718302	0.76	-	0	transcript_id "Phchi.S1G695100.t1"; gene_id "Phchi.S1G695100"
Phchi.S1	AUGUSTUS	exon	43717445	43718302	.	-	.	transcript_id "Phchi.S1G695100.t1"; gene_id "Phchi.S1G695100"
Phchi.S1	AUGUSTUS	start_codon	43718300	43718302	.	-	0	transcript_id "Phchi.S1G695100.t1"; gene_id "Phchi.S1G695100"
# This transcript jg2626.t2 is derived from g9546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2627.t1 is derived from g9547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7836420	7837444	.	+	.	Phchi.S5G123600
Phchi.S5	AUGUSTUS	transcript	7836420	7837444	.	+	.	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	start_codon	7836420	7836422	.	+	0	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	CDS	7836420	7836434	0.18	+	0	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	exon	7836420	7836434	.	+	.	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	intron	7836435	7837399	.	+	.	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	CDS	7837400	7837444	0.56	+	0	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	exon	7837400	7837444	.	+	.	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
Phchi.S5	AUGUSTUS	stop_codon	7837445	7837447	.	+	0	transcript_id "Phchi.S5G123600.t1"; gene_id "Phchi.S5G123600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14908.t1 is derived from g13376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15463408	15464442	.	+	.	Phchi.S3G222700
Phchi.S3	AUGUSTUS	transcript	15463408	15464442	.	+	.	transcript_id "Phchi.S3G222700.t1"; gene_id "Phchi.S3G222700"
Phchi.S3	AUGUSTUS	start_codon	15463408	15463410	.	+	0	transcript_id "Phchi.S3G222700.t1"; gene_id "Phchi.S3G222700"
Phchi.S3	AUGUSTUS	CDS	15463408	15464442	0.76	+	0	transcript_id "Phchi.S3G222700.t1"; gene_id "Phchi.S3G222700"
Phchi.S3	AUGUSTUS	exon	15463408	15464442	.	+	.	transcript_id "Phchi.S3G222700.t1"; gene_id "Phchi.S3G222700"
Phchi.S3	AUGUSTUS	stop_codon	15464443	15464445	.	+	0	transcript_id "Phchi.S3G222700.t1"; gene_id "Phchi.S3G222700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8494.t1 is derived from g5669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36247142	36250582	.	+	.	Phchi.S1G565300
Phchi.S1	AUGUSTUS	transcript	36247142	36250582	.	+	.	transcript_id "Phchi.S1G565300.t1"; gene_id "Phchi.S1G565300"
Phchi.S1	AUGUSTUS	start_codon	36247142	36247144	.	+	0	transcript_id "Phchi.S1G565300.t1"; gene_id "Phchi.S1G565300"
Phchi.S1	AUGUSTUS	CDS	36247142	36250582	0.79	+	0	transcript_id "Phchi.S1G565300.t1"; gene_id "Phchi.S1G565300"
Phchi.S1	AUGUSTUS	exon	36247142	36250582	.	+	.	transcript_id "Phchi.S1G565300.t1"; gene_id "Phchi.S1G565300"
Phchi.S1	AUGUSTUS	stop_codon	36250583	36250585	.	+	0	transcript_id "Phchi.S1G565300.t1"; gene_id "Phchi.S1G565300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13279.t1 is derived from g11744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5142258	5143388	.	-	.	Phchi.S3G059800
Phchi.S3	AUGUSTUS	transcript	5142258	5143388	.	-	.	transcript_id "Phchi.S3G059800.t1"; gene_id "Phchi.S3G059800"
Phchi.S3	AUGUSTUS	stop_codon	5142255	5142257	.	-	0	transcript_id "Phchi.S3G059800.t1"; gene_id "Phchi.S3G059800"
Phchi.S3	AUGUSTUS	CDS	5142258	5143388	0.7	-	0	transcript_id "Phchi.S3G059800.t1"; gene_id "Phchi.S3G059800"
Phchi.S3	AUGUSTUS	exon	5142258	5143388	.	-	.	transcript_id "Phchi.S3G059800.t1"; gene_id "Phchi.S3G059800"
Phchi.S3	AUGUSTUS	start_codon	5143386	5143388	.	-	0	transcript_id "Phchi.S3G059800.t1"; gene_id "Phchi.S3G059800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11967.t1 is derived from g7642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	239517	241016	.	+	.	Phchi.S2G004700
Phchi.S2	AUGUSTUS	transcript	239517	241016	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	start_codon	239517	239519	.	+	0	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	CDS	239517	239597	0.46	+	0	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	exon	239517	239597	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	intron	239598	239687	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	CDS	239688	239801	1	+	0	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	exon	239688	239801	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	intron	239802	239934	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	CDS	239935	240071	1	+	0	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	exon	239935	240071	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	intron	240072	240170	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	CDS	240171	240250	1	+	1	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	exon	240171	240250	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	intron	240251	240330	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	CDS	240331	240362	0.97	+	2	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	exon	240331	240362	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	intron	240363	240977	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	CDS	240978	241016	1	+	0	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	exon	240978	241016	.	+	.	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
Phchi.S2	AUGUSTUS	stop_codon	241017	241019	.	+	0	transcript_id "Phchi.S2G004700.t1"; gene_id "Phchi.S2G004700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12298.t1 is derived from g7974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9598281	9598823	.	-	.	Phchi.S2G037800
Phchi.S2	AUGUSTUS	transcript	9598281	9598823	.	-	.	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	stop_codon	9598278	9598280	.	-	0	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	CDS	9598281	9598418	0.53	-	0	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	exon	9598281	9598418	.	-	.	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	intron	9598419	9598565	.	-	.	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	CDS	9598566	9598823	0.66	-	0	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	exon	9598566	9598823	.	-	.	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
Phchi.S2	AUGUSTUS	start_codon	9598821	9598823	.	-	0	transcript_id "Phchi.S2G037800.t1"; gene_id "Phchi.S2G037800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8260.t1 is derived from g5435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34939807	34941555	.	-	.	Phchi.S1G541900
Phchi.S1	AUGUSTUS	transcript	34939807	34941555	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	stop_codon	34939804	34939806	.	-	0	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34939807	34940025	0.9	-	0	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34939807	34940025	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34940026	34940135	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34940136	34940241	0.92	-	1	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34940136	34940241	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34940242	34940320	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34940321	34940514	1	-	0	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34940321	34940514	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34940515	34940587	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34940588	34940688	1	-	2	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34940588	34940688	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34940689	34940773	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34940774	34940894	1	-	0	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34940774	34940894	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34940895	34940964	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34940965	34941203	1	-	2	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34940965	34941203	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34941204	34941286	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34941287	34941454	0.97	-	2	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34941287	34941454	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	intron	34941455	34941548	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	CDS	34941549	34941555	0.97	-	0	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	exon	34941549	34941555	.	-	.	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
Phchi.S1	AUGUSTUS	start_codon	34941553	34941555	.	-	0	transcript_id "Phchi.S1G541900.t1"; gene_id "Phchi.S1G541900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12849.t1 is derived from g11314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2695650	2696265	.	+	.	Phchi.S3G016800
Phchi.S3	AUGUSTUS	transcript	2695650	2696265	.	+	.	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	start_codon	2695650	2695652	.	+	0	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	CDS	2695650	2695949	0.78	+	0	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	exon	2695650	2695949	.	+	.	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	intron	2695950	2696055	.	+	.	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	CDS	2696056	2696265	0.81	+	0	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	exon	2696056	2696265	.	+	.	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
Phchi.S3	AUGUSTUS	stop_codon	2696266	2696268	.	+	0	transcript_id "Phchi.S3G016800.t1"; gene_id "Phchi.S3G016800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2309.t1 is derived from g9229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5999411	6003073	.	-	.	Phchi.S5G091800
Phchi.S5	AUGUSTUS	transcript	5999411	6003073	.	-	.	transcript_id "Phchi.S5G091800.t1"; gene_id "Phchi.S5G091800"
Phchi.S5	AUGUSTUS	stop_codon	5999408	5999410	.	-	0	transcript_id "Phchi.S5G091800.t1"; gene_id "Phchi.S5G091800"
Phchi.S5	AUGUSTUS	CDS	5999411	6003073	0.57	-	0	transcript_id "Phchi.S5G091800.t1"; gene_id "Phchi.S5G091800"
Phchi.S5	AUGUSTUS	exon	5999411	6003073	.	-	.	transcript_id "Phchi.S5G091800.t1"; gene_id "Phchi.S5G091800"
Phchi.S5	AUGUSTUS	start_codon	6003071	6003073	.	-	0	transcript_id "Phchi.S5G091800.t1"; gene_id "Phchi.S5G091800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15283.t1 is derived from g13751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18152778	18157221	.	-	.	Phchi.S3G260200
Phchi.S3	AUGUSTUS	transcript	18152778	18157221	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	stop_codon	18152775	18152777	.	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18152778	18153866	1	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18152778	18153866	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	intron	18153867	18154046	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18154047	18154281	0.81	-	1	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18154047	18154281	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	intron	18154282	18154368	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18154369	18155058	0.97	-	1	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18154369	18155058	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	intron	18155059	18155175	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18155176	18155372	1	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18155176	18155372	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	intron	18155373	18155487	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18155488	18155631	1	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18155488	18155631	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	intron	18155632	18155715	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18155716	18156360	0.99	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18155716	18156360	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	intron	18156361	18156450	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	CDS	18156451	18157221	0.58	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	exon	18156451	18157221	.	-	.	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
Phchi.S3	AUGUSTUS	start_codon	18157219	18157221	.	-	0	transcript_id "Phchi.S3G260200.t1"; gene_id "Phchi.S3G260200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg7478.t1 is derived from g4651.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29550192	29551764	.	+	.	Phchi.S1G463700
Phchi.S1	AUGUSTUS	transcript	29550192	29551764	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	start_codon	29550192	29550194	.	+	0	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550192	29550329	0.92	+	0	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550192	29550329	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550330	29550486	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550487	29550589	1	+	0	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550487	29550589	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550590	29550834	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550835	29550911	1	+	2	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550835	29550911	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550912	29550989	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550990	29551093	1	+	0	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550990	29551093	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551094	29551202	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551203	29551290	1	+	1	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551203	29551290	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551291	29551393	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551394	29551521	1	+	0	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551394	29551521	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551522	29551718	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551719	29551764	1	+	1	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551719	29551764	.	+	.	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	stop_codon	29551765	29551767	.	+	0	transcript_id "Phchi.S1G463700.t1"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	transcript	29550192	29551764	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	start_codon	29550192	29550194	.	+	0	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550192	29550329	0.89	+	0	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550192	29550329	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550330	29550486	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550487	29550589	1	+	0	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550487	29550589	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550590	29550834	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550835	29550911	1	+	2	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550835	29550911	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550912	29550989	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550990	29551093	1	+	0	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550990	29551093	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551094	29551202	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551203	29551290	1	+	1	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551203	29551290	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551291	29551393	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551394	29551464	1	+	0	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551394	29551464	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551465	29551718	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551719	29551764	1	+	1	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551719	29551764	.	+	.	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	stop_codon	29551765	29551767	.	+	0	transcript_id "Phchi.S1G463700.t2"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	transcript	29550192	29551764	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	start_codon	29550192	29550194	.	+	0	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550192	29550329	0.92	+	0	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550192	29550329	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550330	29550486	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550487	29550589	1	+	0	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550487	29550589	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550590	29550834	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550835	29550911	1	+	2	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550835	29550911	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29550912	29550989	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29550990	29551093	1	+	0	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29550990	29551093	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551094	29551202	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551203	29551290	1	+	1	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551203	29551290	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551291	29551393	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551394	29551500	0.98	+	0	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551394	29551500	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	intron	29551501	29551718	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	CDS	29551719	29551764	1	+	1	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	exon	29551719	29551764	.	+	.	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
Phchi.S1	AUGUSTUS	stop_codon	29551765	29551767	.	+	0	transcript_id "Phchi.S1G463700.t3"; gene_id "Phchi.S1G463700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4050.t1 is derived from g1219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7536801	7537544	.	+	.	Phchi.S1G120900
Phchi.S1	AUGUSTUS	transcript	7536801	7537544	.	+	.	transcript_id "Phchi.S1G120900.t1"; gene_id "Phchi.S1G120900"
Phchi.S1	AUGUSTUS	start_codon	7536801	7536803	.	+	0	transcript_id "Phchi.S1G120900.t1"; gene_id "Phchi.S1G120900"
Phchi.S1	AUGUSTUS	CDS	7536801	7537544	0.97	+	0	transcript_id "Phchi.S1G120900.t1"; gene_id "Phchi.S1G120900"
Phchi.S1	AUGUSTUS	exon	7536801	7537544	.	+	.	transcript_id "Phchi.S1G120900.t1"; gene_id "Phchi.S1G120900"
Phchi.S1	AUGUSTUS	stop_codon	7537545	7537547	.	+	0	transcript_id "Phchi.S1G120900.t1"; gene_id "Phchi.S1G120900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg827.t1 is derived from g10609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5768259	5769277	.	+	.	Phchi.S6G078600
Phchi.S6	AUGUSTUS	transcript	5768259	5769277	.	+	.	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	start_codon	5768259	5768261	.	+	0	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	CDS	5768259	5768785	0.96	+	0	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	exon	5768259	5768785	.	+	.	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	intron	5768786	5768910	.	+	.	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	CDS	5768911	5769277	0.41	+	1	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	exon	5768911	5769277	.	+	.	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
Phchi.S6	AUGUSTUS	stop_codon	5769278	5769280	.	+	0	transcript_id "Phchi.S6G078600.t1"; gene_id "Phchi.S6G078600"
# This transcript jg14298.t2 is derived from g12765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14298.t3 is derived from g12765.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14299.t1 is derived from g12766.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11991923	11993707	.	+	.	Phchi.S3G161800
Phchi.S3	AUGUSTUS	transcript	11991923	11993707	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	start_codon	11991923	11991925	.	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11991923	11992248	0.53	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11991923	11992248	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11992249	11992332	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11992333	11992420	1	+	1	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11992333	11992420	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11992421	11992573	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11992574	11992582	0.99	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11992574	11992582	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11992583	11992670	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11992671	11992756	1	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11992671	11992756	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11992757	11992854	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11992855	11992933	1	+	1	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11992855	11992933	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11992934	11993054	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11993055	11993114	1	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11993055	11993114	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11993115	11993200	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11993201	11993322	1	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11993201	11993322	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11993323	11993423	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11993424	11993495	0.97	+	1	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11993424	11993495	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	intron	11993496	11993607	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	CDS	11993608	11993707	0.99	+	1	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	exon	11993608	11993707	.	+	.	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
Phchi.S3	AUGUSTUS	stop_codon	11993708	11993710	.	+	0	transcript_id "Phchi.S3G161800.t1"; gene_id "Phchi.S3G161800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13396.t1 is derived from g11862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6520879	6521333	.	-	.	Phchi.S3G071500
Phchi.S3	AUGUSTUS	transcript	6520879	6521333	.	-	.	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	stop_codon	6520876	6520878	.	-	0	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	CDS	6520879	6520950	1	-	0	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	exon	6520879	6520950	.	-	.	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	intron	6520951	6521036	.	-	.	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	CDS	6521037	6521189	0.76	-	0	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	exon	6521037	6521189	.	-	.	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	intron	6521190	6521318	.	-	.	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	CDS	6521319	6521333	0.76	-	0	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	exon	6521319	6521333	.	-	.	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
Phchi.S3	AUGUSTUS	start_codon	6521331	6521333	.	-	0	transcript_id "Phchi.S3G071500.t1"; gene_id "Phchi.S3G071500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8738.t1 is derived from g5913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37750967	37752062	.	-	.	Phchi.S1G589700
Phchi.S1	AUGUSTUS	transcript	37750967	37752062	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	stop_codon	37750964	37750966	.	-	0	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	CDS	37750967	37751036	0.54	-	1	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	exon	37750967	37751036	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	intron	37751037	37751139	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	CDS	37751140	37751223	0.54	-	1	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	exon	37751140	37751223	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	intron	37751224	37751434	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	CDS	37751435	37751553	1	-	0	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	exon	37751435	37751553	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	intron	37751554	37751694	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	CDS	37751695	37751804	1	-	2	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	exon	37751695	37751804	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	intron	37751805	37751893	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	CDS	37751894	37752062	0.72	-	0	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	exon	37751894	37752062	.	-	.	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
Phchi.S1	AUGUSTUS	start_codon	37752060	37752062	.	-	0	transcript_id "Phchi.S1G589700.t1"; gene_id "Phchi.S1G589700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7601.t1 is derived from g4775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30209331	30212606	.	-	.	Phchi.S1G476000
Phchi.S1	AUGUSTUS	transcript	30209331	30212606	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	stop_codon	30209328	30209330	.	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30209331	30209489	0.99	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30209331	30209489	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30209490	30209571	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30209572	30209685	1	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30209572	30209685	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30209686	30209764	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30209765	30210374	1	-	1	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30209765	30210374	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30210375	30210545	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30210546	30210793	0.99	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30210546	30210793	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30210794	30210890	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30210891	30211228	0.98	-	2	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30210891	30211228	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30211229	30211348	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30211349	30211688	0.78	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30211349	30211688	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30211689	30211931	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30211932	30212222	1	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30211932	30212222	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	intron	30212223	30212444	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	CDS	30212445	30212606	1	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	exon	30212445	30212606	.	-	.	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
Phchi.S1	AUGUSTUS	start_codon	30212604	30212606	.	-	0	transcript_id "Phchi.S1G476000.t1"; gene_id "Phchi.S1G476000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11414.t1 is derived from g15464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6246284	6246595	.	-	.	Phchi.S4G099600
Phchi.S4	AUGUSTUS	transcript	6246284	6246595	.	-	.	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	stop_codon	6246281	6246283	.	-	0	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	CDS	6246284	6246379	0.84	-	0	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	exon	6246284	6246379	.	-	.	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	intron	6246380	6246481	.	-	.	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	CDS	6246482	6246595	0.77	-	0	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	exon	6246482	6246595	.	-	.	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
Phchi.S4	AUGUSTUS	start_codon	6246593	6246595	.	-	0	transcript_id "Phchi.S4G099600.t1"; gene_id "Phchi.S4G099600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg858.t1 is derived from g10640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5957283	5962385	.	+	.	Phchi.S6G081700
Phchi.S6	AUGUSTUS	transcript	5957283	5962385	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	start_codon	5957283	5957285	.	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5957283	5957532	0.52	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5957283	5957532	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5957533	5957596	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5957597	5957793	0.81	+	2	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5957597	5957793	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5957794	5957908	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5957909	5958045	0.98	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5957909	5958045	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5958046	5958116	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5958117	5958171	0.58	+	1	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5958117	5958171	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5958172	5958468	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5958469	5959136	0.58	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5958469	5959136	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5959137	5959337	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5959338	5960201	0.85	+	1	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5959338	5960201	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5960202	5960355	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5960356	5960494	0.62	+	1	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5960356	5960494	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5960495	5960793	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5960794	5960808	0.89	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5960794	5960808	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5960809	5960902	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5960903	5961089	0.84	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5960903	5961089	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5961090	5961184	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5961185	5961388	1	+	2	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5961185	5961388	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5961389	5961469	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5961470	5961612	1	+	2	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5961470	5961612	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5961613	5961708	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5961709	5961988	1	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5961709	5961988	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	intron	5961989	5962080	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	CDS	5962081	5962385	1	+	2	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	exon	5962081	5962385	.	+	.	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
Phchi.S6	AUGUSTUS	stop_codon	5962386	5962388	.	+	0	transcript_id "Phchi.S6G081700.t1"; gene_id "Phchi.S6G081700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5121.t1 is derived from g2291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14820904	14825057	.	-	.	Phchi.S1G228000
Phchi.S1	AUGUSTUS	transcript	14820904	14825057	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	stop_codon	14820901	14820903	.	-	0	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	CDS	14820904	14822186	0.27	-	2	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	exon	14820904	14822186	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	intron	14822187	14822404	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	CDS	14822405	14822978	0.31	-	0	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	exon	14822405	14822978	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	intron	14822979	14823084	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	CDS	14823085	14823373	0.85	-	1	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	exon	14823085	14823373	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	intron	14823374	14823768	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	CDS	14823769	14825057	0.78	-	0	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	exon	14823769	14825057	.	-	.	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
Phchi.S1	AUGUSTUS	start_codon	14825055	14825057	.	-	0	transcript_id "Phchi.S1G228000.t1"; gene_id "Phchi.S1G228000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2286.t1 is derived from g9206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5872072	5873745	.	-	.	Phchi.S5G089500
Phchi.S5	AUGUSTUS	transcript	5872072	5873745	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	stop_codon	5872069	5872071	.	-	0	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	CDS	5872072	5872147	1	-	1	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	exon	5872072	5872147	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	intron	5872148	5872346	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	CDS	5872347	5872402	1	-	0	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	exon	5872347	5872402	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	intron	5872403	5872533	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	CDS	5872534	5872642	1	-	1	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	exon	5872534	5872642	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	intron	5872643	5872969	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	CDS	5872970	5873013	1	-	0	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	exon	5872970	5873013	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	intron	5873014	5873649	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	CDS	5873650	5873745	0.61	-	0	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	exon	5873650	5873745	.	-	.	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
Phchi.S5	AUGUSTUS	start_codon	5873743	5873745	.	-	0	transcript_id "Phchi.S5G089500.t1"; gene_id "Phchi.S5G089500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8799.t1 is derived from g5974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38047121	38050271	.	-	.	Phchi.S1G595800
Phchi.S1	AUGUSTUS	transcript	38047121	38050271	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	stop_codon	38047118	38047120	.	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38047121	38047573	0.65	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38047121	38047573	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38047574	38047693	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38047694	38047801	0.78	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38047694	38047801	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38047802	38047891	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38047892	38047970	1	-	1	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38047892	38047970	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38047971	38048050	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38048051	38048186	1	-	2	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38048051	38048186	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38048187	38048287	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38048288	38048382	0.99	-	1	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38048288	38048382	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38048383	38048530	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38048531	38049083	0.99	-	2	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38048531	38049083	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38049084	38049175	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38049176	38049524	1	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38049176	38049524	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38049525	38049598	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38049599	38049702	1	-	2	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38049599	38049702	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38049703	38049791	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38049792	38049872	0.83	-	2	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38049792	38049872	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38049873	38049954	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38049955	38050048	0.58	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38049955	38050048	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	intron	38050049	38050160	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	CDS	38050161	38050271	0.86	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	exon	38050161	38050271	.	-	.	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
Phchi.S1	AUGUSTUS	start_codon	38050269	38050271	.	-	0	transcript_id "Phchi.S1G595800.t1"; gene_id "Phchi.S1G595800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15748.t1 is derived from g14218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21047060	21050818	.	-	.	Phchi.S3G306700
Phchi.S3	AUGUSTUS	transcript	21047060	21050818	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	stop_codon	21047057	21047059	.	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21047060	21047179	1	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21047060	21047179	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21047180	21047258	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21047259	21047386	1	-	2	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21047259	21047386	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21047387	21047536	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21047537	21047609	1	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21047537	21047609	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21047610	21047732	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21047733	21047889	1	-	1	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21047733	21047889	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21047890	21048036	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21048037	21048157	1	-	2	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21048037	21048157	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21048158	21048254	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21048255	21048374	1	-	2	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21048255	21048374	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21048375	21048463	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21048464	21048899	1	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21048464	21048899	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21048900	21049142	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21049143	21049204	1	-	2	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21049143	21049204	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21049205	21049302	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21049303	21049487	1	-	1	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21049303	21049487	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21049488	21049662	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21049663	21049745	1	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21049663	21049745	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21049746	21049816	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21049817	21049995	0.96	-	2	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21049817	21049995	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21049996	21050105	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21050106	21050223	1	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21050106	21050223	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21050224	21050345	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21050346	21050425	1	-	2	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21050346	21050425	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	intron	21050426	21050685	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	CDS	21050686	21050818	0.99	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	exon	21050686	21050818	.	-	.	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
Phchi.S3	AUGUSTUS	start_codon	21050816	21050818	.	-	0	transcript_id "Phchi.S3G306700.t1"; gene_id "Phchi.S3G306700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2701.t1 is derived from g9621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8252694	8252981	.	+	.	Phchi.S5G131000
Phchi.S5	AUGUSTUS	transcript	8252694	8252981	.	+	.	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	start_codon	8252694	8252696	.	+	0	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	CDS	8252694	8252844	0.98	+	0	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	exon	8252694	8252844	.	+	.	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	intron	8252845	8252925	.	+	.	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	CDS	8252926	8252981	0.72	+	2	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	exon	8252926	8252981	.	+	.	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
Phchi.S5	AUGUSTUS	stop_codon	8252982	8252984	.	+	0	transcript_id "Phchi.S5G131000.t1"; gene_id "Phchi.S5G131000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5885.t1 is derived from g3055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19579411	19582104	.	-	.	Phchi.S1G304400
Phchi.S1	AUGUSTUS	transcript	19579411	19582104	.	-	.	transcript_id "Phchi.S1G304400.t1"; gene_id "Phchi.S1G304400"
Phchi.S1	AUGUSTUS	stop_codon	19579408	19579410	.	-	0	transcript_id "Phchi.S1G304400.t1"; gene_id "Phchi.S1G304400"
Phchi.S1	AUGUSTUS	CDS	19579411	19582104	0.91	-	0	transcript_id "Phchi.S1G304400.t1"; gene_id "Phchi.S1G304400"
Phchi.S1	AUGUSTUS	exon	19579411	19582104	.	-	.	transcript_id "Phchi.S1G304400.t1"; gene_id "Phchi.S1G304400"
Phchi.S1	AUGUSTUS	start_codon	19582102	19582104	.	-	0	transcript_id "Phchi.S1G304400.t1"; gene_id "Phchi.S1G304400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6274.t1 is derived from g3446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21954378	21955499	.	-	.	Phchi.S1G343300
Phchi.S1	AUGUSTUS	transcript	21954378	21955499	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	stop_codon	21954375	21954377	.	-	0	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	CDS	21954378	21954438	0.66	-	1	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	exon	21954378	21954438	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	intron	21954439	21954530	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	CDS	21954531	21954850	1	-	0	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	exon	21954531	21954850	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	intron	21954851	21955000	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	CDS	21955001	21955200	0.89	-	2	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	exon	21955001	21955200	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	intron	21955201	21955283	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	CDS	21955284	21955334	0.85	-	2	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	exon	21955284	21955334	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	intron	21955335	21955447	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	CDS	21955448	21955499	0.99	-	0	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	exon	21955448	21955499	.	-	.	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
Phchi.S1	AUGUSTUS	start_codon	21955497	21955499	.	-	0	transcript_id "Phchi.S1G343300.t1"; gene_id "Phchi.S1G343300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1745.t1 is derived from g8665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2837555	2841307	.	-	.	Phchi.S5G035400
Phchi.S5	AUGUSTUS	transcript	2837555	2841307	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	stop_codon	2837552	2837554	.	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2837555	2837965	1	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2837555	2837965	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2837966	2838081	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2838082	2838224	0.99	-	2	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2838082	2838224	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2838225	2838296	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2838297	2838392	1	-	2	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2838297	2838392	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2838393	2838486	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2838487	2838536	0.99	-	1	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2838487	2838536	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2838537	2838625	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2838626	2838679	0.58	-	1	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2838626	2838679	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2838680	2838776	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2838777	2838917	1	-	1	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2838777	2838917	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2838918	2838995	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2838996	2839133	1	-	1	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2838996	2839133	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2839134	2839248	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2839249	2839454	0.99	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2839249	2839454	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2839455	2839557	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2839558	2839680	0.99	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2839558	2839680	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2839681	2839768	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2839769	2839929	1	-	2	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2839769	2839929	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2839930	2840008	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2840009	2840171	0.98	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2840009	2840171	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2840172	2840277	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2840278	2840387	0.98	-	2	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2840278	2840387	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2840388	2840466	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2840467	2840512	1	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2840467	2840512	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2840513	2840673	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2840674	2840781	1	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2840674	2840781	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2840782	2840853	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2840854	2840985	1	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2840854	2840985	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	intron	2840986	2841082	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	CDS	2841083	2841307	0.52	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	exon	2841083	2841307	.	-	.	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
Phchi.S5	AUGUSTUS	start_codon	2841305	2841307	.	-	0	transcript_id "Phchi.S5G035400.t1"; gene_id "Phchi.S5G035400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg175.t1 is derived from g9957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1017807	1018815	.	+	.	Phchi.S6G013400
Phchi.S6	AUGUSTUS	transcript	1017807	1018815	.	+	.	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	start_codon	1017807	1017809	.	+	0	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	CDS	1017807	1018479	0.85	+	0	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	exon	1017807	1018479	.	+	.	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	intron	1018480	1018771	.	+	.	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	CDS	1018772	1018815	0.88	+	2	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	exon	1018772	1018815	.	+	.	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
Phchi.S6	AUGUSTUS	stop_codon	1018816	1018818	.	+	0	transcript_id "Phchi.S6G013400.t1"; gene_id "Phchi.S6G013400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2246.t1 is derived from g9166.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5635616	5638944	.	+	.	Phchi.S5G085500
Phchi.S5	AUGUSTUS	transcript	5635616	5638944	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	start_codon	5635616	5635618	.	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5635616	5635824	0.84	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5635616	5635824	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5635825	5636076	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636077	5636154	1	+	1	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636077	5636154	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636155	5636267	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636268	5636432	0.96	+	1	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636268	5636432	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636433	5636524	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636525	5636574	1	+	1	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636525	5636574	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636575	5636670	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636671	5636779	1	+	2	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636671	5636779	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636780	5636865	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636866	5636917	1	+	1	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636866	5636917	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636918	5636999	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637000	5637089	1	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637000	5637089	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637090	5637207	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637208	5637276	1	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637208	5637276	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637277	5637360	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637361	5637447	1	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637361	5637447	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637448	5637574	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637575	5637605	1	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637575	5637605	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637606	5637749	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637750	5638084	1	+	2	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637750	5638084	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5638085	5638188	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5638189	5638581	0.95	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5638189	5638581	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5638582	5638662	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5638663	5638944	1	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5638663	5638944	.	+	.	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	stop_codon	5638945	5638947	.	+	0	transcript_id "Phchi.S5G085500.t1"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	transcript	5635616	5638944	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	start_codon	5635616	5635618	.	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5635616	5635824	0.83	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5635616	5635824	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5635825	5636076	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636077	5636154	0.99	+	1	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636077	5636154	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636155	5636267	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636268	5636432	0.95	+	1	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636268	5636432	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636433	5636524	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636525	5636574	1	+	1	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636525	5636574	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636575	5636670	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636671	5636779	1	+	2	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636671	5636779	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636780	5636865	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5636866	5636917	1	+	1	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5636866	5636917	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5636918	5636999	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637000	5637089	1	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637000	5637089	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637090	5637207	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637208	5637276	1	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637208	5637276	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637277	5637360	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637361	5637447	1	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637361	5637447	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637448	5637574	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637575	5637605	1	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637575	5637605	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5637606	5637695	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5637696	5638084	0.98	+	2	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5637696	5638084	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5638085	5638188	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5638189	5638581	0.95	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5638189	5638581	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	intron	5638582	5638662	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	CDS	5638663	5638944	1	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	exon	5638663	5638944	.	+	.	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
Phchi.S5	AUGUSTUS	stop_codon	5638945	5638947	.	+	0	transcript_id "Phchi.S5G085500.t2"; gene_id "Phchi.S5G085500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2766.t1 is derived from g9686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8720844	8721547	.	+	.	Phchi.S5G137500
Phchi.S5	AUGUSTUS	transcript	8720844	8721547	.	+	.	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	start_codon	8720844	8720846	.	+	0	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	CDS	8720844	8720928	0.95	+	0	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	exon	8720844	8720928	.	+	.	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	intron	8720929	8721051	.	+	.	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	CDS	8721052	8721102	1	+	2	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	exon	8721052	8721102	.	+	.	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	intron	8721103	8721182	.	+	.	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	CDS	8721183	8721547	0.99	+	2	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	exon	8721183	8721547	.	+	.	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
Phchi.S5	AUGUSTUS	stop_codon	8721548	8721550	.	+	0	transcript_id "Phchi.S5G137500.t1"; gene_id "Phchi.S5G137500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13782.t1 is derived from g12249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8874069	8878559	.	-	.	Phchi.S3G110100
Phchi.S3	AUGUSTUS	transcript	8874069	8878559	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	stop_codon	8874066	8874068	.	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8874069	8874777	0.96	-	1	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8874069	8874777	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8874778	8874860	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8874861	8874973	1	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8874861	8874973	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8874974	8875125	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8875126	8875218	1	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8875126	8875218	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8875219	8875375	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8875376	8875615	0.87	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8875376	8875615	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8875616	8875743	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8875744	8875893	0.83	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8875744	8875893	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8875894	8876008	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8876009	8876059	0.42	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8876009	8876059	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8876060	8876172	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8876173	8876371	0.75	-	1	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8876173	8876371	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8876372	8876457	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8876458	8876615	0.97	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8876458	8876615	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8876616	8876741	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8876742	8877703	0.94	-	2	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8876742	8877703	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8877704	8877890	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8877891	8877974	1	-	2	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8877891	8877974	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8877975	8878068	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8878069	8878138	0.96	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8878069	8878138	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8878139	8878310	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8878311	8878386	0.99	-	1	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8878311	8878386	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	intron	8878387	8878482	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	CDS	8878483	8878559	0.86	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	exon	8878483	8878559	.	-	.	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
Phchi.S3	AUGUSTUS	start_codon	8878557	8878559	.	-	0	transcript_id "Phchi.S3G110100.t1"; gene_id "Phchi.S3G110100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10681.t1 is derived from g14731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1567075	1567680	.	+	.	Phchi.S4G026300
Phchi.S4	AUGUSTUS	transcript	1567075	1567680	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	start_codon	1567075	1567077	.	+	0	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	CDS	1567075	1567114	0.72	+	0	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	exon	1567075	1567114	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	intron	1567115	1567233	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	CDS	1567234	1567335	0.73	+	2	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	exon	1567234	1567335	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	intron	1567336	1567426	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	CDS	1567427	1567516	1	+	2	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	exon	1567427	1567516	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	intron	1567517	1567675	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	CDS	1567676	1567680	1	+	2	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	exon	1567676	1567680	.	+	.	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
Phchi.S4	AUGUSTUS	stop_codon	1567681	1567683	.	+	0	transcript_id "Phchi.S4G026300.t1"; gene_id "Phchi.S4G026300"
# This transcript jg12195.t2 is derived from g7871.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12195.t3 is derived from g7871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12195.t4 is derived from g7871.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12196.t1 is derived from g7872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6673111	6674572	.	+	.	Phchi.S2G027600
Phchi.S2	AUGUSTUS	transcript	6673111	6674572	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	start_codon	6673111	6673113	.	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6673111	6673218	1	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6673111	6673218	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	intron	6673219	6673304	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6673305	6673466	1	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6673305	6673466	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	intron	6673467	6673550	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6673551	6673649	1	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6673551	6673649	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	intron	6673650	6673899	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6673900	6673980	1	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6673900	6673980	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	intron	6673981	6674070	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6674071	6674148	1	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6674071	6674148	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	intron	6674149	6674232	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6674233	6674322	0.95	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6674233	6674322	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	intron	6674323	6674434	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	CDS	6674435	6674572	0.94	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	exon	6674435	6674572	.	+	.	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
Phchi.S2	AUGUSTUS	stop_codon	6674573	6674575	.	+	0	transcript_id "Phchi.S2G027600.t1"; gene_id "Phchi.S2G027600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10636.t1 is derived from g14686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1359561	1361776	.	+	.	Phchi.S4G021800
Phchi.S4	AUGUSTUS	transcript	1359561	1361776	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	start_codon	1359561	1359563	.	+	0	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1359561	1359770	0.83	+	0	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1359561	1359770	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1359771	1359860	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1359861	1360074	1	+	0	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1359861	1360074	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1360075	1360145	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1360146	1360283	0.79	+	2	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1360146	1360283	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1360284	1360384	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1360385	1360527	0.88	+	2	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1360385	1360527	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1360528	1360616	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1360617	1360645	0.84	+	0	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1360617	1360645	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1360646	1360785	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1360786	1361045	0.87	+	1	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1360786	1361045	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1361046	1361164	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1361165	1361245	0.99	+	2	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1361165	1361245	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1361246	1361382	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1361383	1361573	1	+	2	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1361383	1361573	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	intron	1361574	1361656	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	CDS	1361657	1361776	0.99	+	0	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	exon	1361657	1361776	.	+	.	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
Phchi.S4	AUGUSTUS	stop_codon	1361777	1361779	.	+	0	transcript_id "Phchi.S4G021800.t1"; gene_id "Phchi.S4G021800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11594.t1 is derived from g15645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7264434	7265750	.	+	.	Phchi.S4G117600
Phchi.S4	AUGUSTUS	transcript	7264434	7265750	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	start_codon	7264434	7264436	.	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7264434	7264466	0.98	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7264434	7264466	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7264467	7264579	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7264580	7264616	1	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7264580	7264616	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7264617	7264754	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7264755	7264840	1	+	2	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7264755	7264840	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7264841	7264974	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7264975	7265070	1	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7264975	7265070	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7265071	7265158	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7265159	7265300	1	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7265159	7265300	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7265301	7265442	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7265443	7265450	0.59	+	2	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7265443	7265450	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7265451	7265539	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7265540	7265604	0.95	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7265540	7265604	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	intron	7265605	7265677	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	CDS	7265678	7265750	0.97	+	1	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	exon	7265678	7265750	.	+	.	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
Phchi.S4	AUGUSTUS	stop_codon	7265751	7265753	.	+	0	transcript_id "Phchi.S4G117600.t1"; gene_id "Phchi.S4G117600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8215.t1 is derived from g5390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34453595	34457192	.	-	.	Phchi.S1G537400
Phchi.S1	AUGUSTUS	transcript	34453595	34457192	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	stop_codon	34453592	34453594	.	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34453595	34453715	1	-	1	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34453595	34453715	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34453716	34453808	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34453809	34453939	1	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34453809	34453939	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34453940	34454023	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34454024	34454362	1	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34454024	34454362	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34454363	34454554	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34454555	34454722	1	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34454555	34454722	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34454723	34454954	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34454955	34455161	1	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34454955	34455161	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34455162	34455366	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34455367	34455562	0.98	-	1	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34455367	34455562	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34455563	34455667	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34455668	34455954	0.89	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34455668	34455954	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34455955	34456075	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34456076	34456429	0.68	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34456076	34456429	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34456430	34456535	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34456536	34456714	0.66	-	2	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34456536	34456714	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34456715	34456804	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34456805	34456856	1	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34456805	34456856	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	intron	34456857	34457084	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	CDS	34457085	34457192	0.73	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	exon	34457085	34457192	.	-	.	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
Phchi.S1	AUGUSTUS	start_codon	34457190	34457192	.	-	0	transcript_id "Phchi.S1G537400.t1"; gene_id "Phchi.S1G537400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7695.t1 is derived from g4869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30686256	30692460	.	+	.	Phchi.S1G485400
Phchi.S1	AUGUSTUS	transcript	30686256	30692460	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	start_codon	30686256	30686258	.	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30686256	30686623	0.99	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30686256	30686623	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30686624	30686749	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30686750	30686910	1	+	1	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30686750	30686910	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30686911	30687120	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30687121	30687154	0.78	+	2	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30687121	30687154	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30687155	30687312	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30687313	30687365	0.78	+	1	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30687313	30687365	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30687366	30687508	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30687509	30687618	1	+	2	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30687509	30687618	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30687619	30687693	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30687694	30687771	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30687694	30687771	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30687772	30687917	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30687918	30687942	0.54	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30687918	30687942	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30687943	30688144	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30688145	30688230	0.55	+	2	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30688145	30688230	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30688231	30688319	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30688320	30688436	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30688320	30688436	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30688437	30688581	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30688582	30688685	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30688582	30688685	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30688686	30688845	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30688846	30688932	0.99	+	1	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30688846	30688932	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30688933	30689042	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30689043	30689118	1	+	1	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30689043	30689118	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30689119	30689210	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30689211	30689400	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30689211	30689400	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30689401	30689527	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30689528	30689598	0.84	+	2	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30689528	30689598	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30689599	30689708	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30689709	30689789	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30689709	30689789	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30689790	30690020	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30690021	30690091	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30690021	30690091	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30690092	30690264	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30690265	30690364	1	+	1	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30690265	30690364	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30690365	30690477	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30690478	30690537	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30690478	30690537	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30690538	30690728	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30690729	30690783	1	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30690729	30690783	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30690784	30690907	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30690908	30691317	1	+	2	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30690908	30691317	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	intron	30691318	30691401	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	CDS	30691402	30692460	0.4	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	exon	30691402	30692460	.	+	.	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
Phchi.S1	AUGUSTUS	stop_codon	30692461	30692463	.	+	0	transcript_id "Phchi.S1G485400.t1"; gene_id "Phchi.S1G485400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11653.t1 is derived from g15704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7520890	7523440	.	+	.	Phchi.S4G123500
Phchi.S4	AUGUSTUS	transcript	7520890	7523440	.	+	.	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	start_codon	7520890	7520892	.	+	0	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	CDS	7520890	7522483	0.96	+	0	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	exon	7520890	7522483	.	+	.	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	intron	7522484	7522595	.	+	.	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	CDS	7522596	7523440	0.99	+	2	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	exon	7522596	7523440	.	+	.	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
Phchi.S4	AUGUSTUS	stop_codon	7523441	7523443	.	+	0	transcript_id "Phchi.S4G123500.t1"; gene_id "Phchi.S4G123500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3525.t1 is derived from g694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4227229	4228592	.	-	.	Phchi.S1G068400
Phchi.S1	AUGUSTUS	transcript	4227229	4228592	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	stop_codon	4227226	4227228	.	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4227229	4227341	1	-	2	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4227229	4227341	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	intron	4227342	4227424	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4227425	4227527	1	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4227425	4227527	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	intron	4227528	4227626	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4227627	4227719	1	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4227627	4227719	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	intron	4227720	4227815	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4227816	4227926	1	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4227816	4227926	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	intron	4227927	4228029	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4228030	4228134	1	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4228030	4228134	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	intron	4228135	4228216	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4228217	4228386	1	-	2	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4228217	4228386	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	intron	4228387	4228474	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	CDS	4228475	4228592	0.97	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	exon	4228475	4228592	.	-	.	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
Phchi.S1	AUGUSTUS	start_codon	4228590	4228592	.	-	0	transcript_id "Phchi.S1G068400.t1"; gene_id "Phchi.S1G068400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7665.t1 is derived from g4839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30499586	30500952	.	+	.	Phchi.S1G482400
Phchi.S1	AUGUSTUS	transcript	30499586	30500952	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	start_codon	30499586	30499588	.	+	0	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	CDS	30499586	30499714	1	+	0	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	exon	30499586	30499714	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	intron	30499715	30500034	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	CDS	30500035	30500169	1	+	0	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	exon	30500035	30500169	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	intron	30500170	30500350	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	CDS	30500351	30500437	1	+	0	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	exon	30500351	30500437	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	intron	30500438	30500582	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	CDS	30500583	30500730	1	+	0	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	exon	30500583	30500730	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	intron	30500731	30500923	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	CDS	30500924	30500952	1	+	2	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	exon	30500924	30500952	.	+	.	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
Phchi.S1	AUGUSTUS	stop_codon	30500953	30500955	.	+	0	transcript_id "Phchi.S1G482400.t1"; gene_id "Phchi.S1G482400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9810.t1 is derived from g6986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43849880	43851720	.	+	.	Phchi.S1G696900
Phchi.S1	AUGUSTUS	transcript	43849880	43851720	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	start_codon	43849880	43849882	.	+	0	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	CDS	43849880	43850377	0.77	+	0	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	exon	43849880	43850377	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	intron	43850378	43850487	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	CDS	43850488	43850980	0.34	+	0	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	exon	43850488	43850980	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	intron	43850981	43851477	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	CDS	43851478	43851495	1	+	2	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	exon	43851478	43851495	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	intron	43851496	43851664	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	CDS	43851665	43851720	1	+	2	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	exon	43851665	43851720	.	+	.	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
Phchi.S1	AUGUSTUS	stop_codon	43851721	43851723	.	+	0	transcript_id "Phchi.S1G696900.t1"; gene_id "Phchi.S1G696900"
# This transcript jg8161.t2 is derived from g5336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8162.t1 is derived from g5337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34233621	34238317	.	+	.	Phchi.S1G532100
Phchi.S1	AUGUSTUS	transcript	34233621	34238317	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	start_codon	34233621	34233623	.	+	0	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34233621	34234233	0.83	+	0	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34233621	34234233	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34234234	34234426	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34234427	34234491	1	+	2	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34234427	34234491	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34234492	34234576	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34234577	34234632	0.61	+	0	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34234577	34234632	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34234633	34234737	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34234738	34235575	0.77	+	1	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34234738	34235575	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34235576	34235676	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34235677	34236052	0.54	+	0	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34235677	34236052	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34236053	34236215	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34236216	34236237	1	+	2	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34236216	34236237	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34236238	34236429	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34236430	34236736	0.99	+	1	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34236430	34236736	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	intron	34236737	34237132	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	CDS	34237133	34238317	0.34	+	0	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	exon	34237133	34238317	.	+	.	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
Phchi.S1	AUGUSTUS	stop_codon	34238318	34238320	.	+	0	transcript_id "Phchi.S1G532100.t1"; gene_id "Phchi.S1G532100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3507.t1 is derived from g676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4124986	4125555	.	+	.	Phchi.S1G066600
Phchi.S1	AUGUSTUS	transcript	4124986	4125555	.	+	.	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	start_codon	4124986	4124988	.	+	0	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	CDS	4124986	4125277	0.65	+	0	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	exon	4124986	4125277	.	+	.	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	intron	4125278	4125385	.	+	.	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	CDS	4125386	4125555	0.93	+	2	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	exon	4125386	4125555	.	+	.	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
Phchi.S1	AUGUSTUS	stop_codon	4125556	4125558	.	+	0	transcript_id "Phchi.S1G066600.t1"; gene_id "Phchi.S1G066600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9316.t1 is derived from g6491.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40915567	40917402	.	-	.	Phchi.S1G647500
Phchi.S1	AUGUSTUS	transcript	40916069	40917402	.	-	.	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	stop_codon	40916066	40916068	.	-	0	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	CDS	40916069	40916114	0.8	-	1	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	exon	40916069	40916114	.	-	.	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	intron	40916115	40916245	.	-	.	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	CDS	40916246	40917402	0.84	-	0	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	exon	40916246	40917402	.	-	.	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	start_codon	40917400	40917402	.	-	0	transcript_id "Phchi.S1G647500.t1"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	transcript	40915567	40917402	.	-	.	transcript_id "Phchi.S1G647500.t2"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	stop_codon	40915564	40915566	.	-	0	transcript_id "Phchi.S1G647500.t2"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	CDS	40915567	40917402	1	-	0	transcript_id "Phchi.S1G647500.t2"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	exon	40915567	40917402	.	-	.	transcript_id "Phchi.S1G647500.t2"; gene_id "Phchi.S1G647500"
Phchi.S1	AUGUSTUS	start_codon	40917400	40917402	.	-	0	transcript_id "Phchi.S1G647500.t2"; gene_id "Phchi.S1G647500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13657.t1 is derived from g12124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8040080	8041126	.	+	.	Phchi.S3G097600
Phchi.S3	AUGUSTUS	transcript	8040080	8041126	.	+	.	transcript_id "Phchi.S3G097600.t1"; gene_id "Phchi.S3G097600"
Phchi.S3	AUGUSTUS	start_codon	8040080	8040082	.	+	0	transcript_id "Phchi.S3G097600.t1"; gene_id "Phchi.S3G097600"
Phchi.S3	AUGUSTUS	CDS	8040080	8041126	0.99	+	0	transcript_id "Phchi.S3G097600.t1"; gene_id "Phchi.S3G097600"
Phchi.S3	AUGUSTUS	exon	8040080	8041126	.	+	.	transcript_id "Phchi.S3G097600.t1"; gene_id "Phchi.S3G097600"
Phchi.S3	AUGUSTUS	stop_codon	8041127	8041129	.	+	0	transcript_id "Phchi.S3G097600.t1"; gene_id "Phchi.S3G097600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13686.t1 is derived from g12153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8199424	8202416	.	-	.	Phchi.S3G100500
Phchi.S3	AUGUSTUS	transcript	8199424	8202416	.	-	.	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	stop_codon	8199421	8199423	.	-	0	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	CDS	8199424	8199504	0.03	-	0	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	exon	8199424	8199504	.	-	.	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	intron	8199505	8199651	.	-	.	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	CDS	8199652	8199760	1	-	1	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	exon	8199652	8199760	.	-	.	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	intron	8199761	8202381	.	-	.	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	CDS	8202382	8202416	0.01	-	0	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	exon	8202382	8202416	.	-	.	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
Phchi.S3	AUGUSTUS	start_codon	8202414	8202416	.	-	0	transcript_id "Phchi.S3G100500.t1"; gene_id "Phchi.S3G100500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10302.t1 is derived from g7478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47049580	47050214	.	+	.	Phchi.S1G746100
Phchi.S1	AUGUSTUS	transcript	47049580	47050214	.	+	.	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	start_codon	47049580	47049582	.	+	0	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	CDS	47049580	47049757	0.45	+	0	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	exon	47049580	47049757	.	+	.	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	intron	47049758	47049856	.	+	.	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	CDS	47049857	47050016	1	+	2	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	exon	47049857	47050016	.	+	.	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	intron	47050017	47050102	.	+	.	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	CDS	47050103	47050214	1	+	1	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	exon	47050103	47050214	.	+	.	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
Phchi.S1	AUGUSTUS	stop_codon	47050215	47050217	.	+	0	transcript_id "Phchi.S1G746100.t1"; gene_id "Phchi.S1G746100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11687.t1 is derived from g15738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7681230	7683588	.	-	.	Phchi.S4G126900
Phchi.S4	AUGUSTUS	transcript	7681230	7683588	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	stop_codon	7681227	7681229	.	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7681230	7681379	0.73	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7681230	7681379	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7681380	7681461	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7681462	7681767	0.89	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7681462	7681767	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7681768	7681898	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7681899	7682200	1	-	2	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7681899	7682200	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7682201	7682295	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7682296	7682398	0.99	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7682296	7682398	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7682399	7682508	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7682509	7682612	1	-	2	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7682509	7682612	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7682613	7682713	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7682714	7682780	0.96	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7682714	7682780	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7682781	7682876	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7682877	7682999	1	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7682877	7682999	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	intron	7683000	7683087	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	CDS	7683088	7683588	0.65	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	exon	7683088	7683588	.	-	.	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
Phchi.S4	AUGUSTUS	start_codon	7683586	7683588	.	-	0	transcript_id "Phchi.S4G126900.t1"; gene_id "Phchi.S4G126900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3992.t1 is derived from g1161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6892787	6895101	.	+	.	Phchi.S1G115100
Phchi.S1	AUGUSTUS	transcript	6892787	6895101	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	start_codon	6892787	6892789	.	+	0	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	CDS	6892787	6893116	0.71	+	0	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	exon	6892787	6893116	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	intron	6893117	6893218	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	CDS	6893219	6893685	0.97	+	0	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	exon	6893219	6893685	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	intron	6893686	6893764	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	CDS	6893765	6893878	1	+	1	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	exon	6893765	6893878	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	intron	6893879	6894033	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	CDS	6894034	6894626	1	+	1	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	exon	6894034	6894626	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	intron	6894627	6894712	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	CDS	6894713	6894888	0.98	+	2	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	exon	6894713	6894888	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	intron	6894889	6894984	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	CDS	6894985	6895101	1	+	0	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	exon	6894985	6895101	.	+	.	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
Phchi.S1	AUGUSTUS	stop_codon	6895102	6895104	.	+	0	transcript_id "Phchi.S1G115100.t1"; gene_id "Phchi.S1G115100"
# This transcript jg12805.t1 is derived from g11270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2458176	2459233	.	+	.	Phchi.S3G012400
Phchi.S3	AUGUSTUS	transcript	2458176	2459233	.	+	.	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	start_codon	2458176	2458178	.	+	0	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	CDS	2458176	2458435	0.41	+	0	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	exon	2458176	2458435	.	+	.	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	intron	2458436	2458565	.	+	.	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	CDS	2458566	2459135	0.29	+	1	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	exon	2458566	2459135	.	+	.	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	intron	2459136	2459220	.	+	.	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	CDS	2459221	2459233	0.21	+	1	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	exon	2459221	2459233	.	+	.	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
Phchi.S3	AUGUSTUS	stop_codon	2459234	2459236	.	+	0	transcript_id "Phchi.S3G012400.t1"; gene_id "Phchi.S3G012400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14420.t1 is derived from g12888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12725642	12731107	.	+	.	Phchi.S3G173900
Phchi.S3	AUGUSTUS	transcript	12725642	12731107	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	start_codon	12725642	12725644	.	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12725642	12725767	0.96	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12725642	12725767	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12725768	12726078	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12726079	12726222	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12726079	12726222	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12726223	12726614	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12726615	12726825	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12726615	12726825	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12726826	12726921	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12726922	12727320	0.89	+	2	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12726922	12727320	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12727321	12727513	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12727514	12727567	0.96	+	2	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12727514	12727567	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12727568	12727723	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12727724	12727824	1	+	2	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12727724	12727824	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12727825	12727958	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12727959	12728078	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12727959	12728078	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12728079	12728221	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12728222	12728311	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12728222	12728311	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12728312	12728395	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12728396	12728511	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12728396	12728511	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12728512	12728675	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12728676	12728775	1	+	1	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12728676	12728775	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12728776	12728944	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12728945	12729016	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12728945	12729016	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12729017	12729099	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12729100	12729147	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12729100	12729147	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12729148	12729253	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12729254	12729331	0.98	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12729254	12729331	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12729332	12729453	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12729454	12729573	0.91	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12729454	12729573	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12729574	12729675	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12729676	12729781	0.99	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12729676	12729781	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12729782	12729867	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12729868	12730031	1	+	2	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12729868	12730031	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12730032	12730124	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12730125	12730259	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12730125	12730259	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12730260	12730341	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12730342	12730472	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12730342	12730472	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12730473	12730557	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12730558	12730620	1	+	1	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12730558	12730620	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12730621	12730731	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12730732	12730810	1	+	1	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12730732	12730810	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	intron	12730811	12731002	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	CDS	12731003	12731107	1	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	exon	12731003	12731107	.	+	.	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
Phchi.S3	AUGUSTUS	stop_codon	12731108	12731110	.	+	0	transcript_id "Phchi.S3G173900.t1"; gene_id "Phchi.S3G173900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6124.t1 is derived from g3295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21039842	21044262	.	+	.	Phchi.S1G328300
Phchi.S1	AUGUSTUS	transcript	21039842	21044262	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	start_codon	21039842	21039844	.	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21039842	21039846	0.71	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21039842	21039846	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21039847	21040059	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21040060	21040111	0.51	+	1	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21040060	21040111	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21040112	21040221	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21040222	21040352	0.44	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21040222	21040352	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21040353	21040427	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21040428	21042408	0.99	+	1	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21040428	21042408	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21042409	21042499	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21042500	21042726	1	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21042500	21042726	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21042727	21042914	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21042915	21042951	1	+	1	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21042915	21042951	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21042952	21043081	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21043082	21043137	1	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21043082	21043137	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21043138	21043232	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21043233	21043818	0.59	+	1	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21043233	21043818	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	intron	21043819	21043905	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	CDS	21043906	21044262	0.51	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	exon	21043906	21044262	.	+	.	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
Phchi.S1	AUGUSTUS	stop_codon	21044263	21044265	.	+	0	transcript_id "Phchi.S1G328300.t1"; gene_id "Phchi.S1G328300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5271.t1 is derived from g2441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15985866	15986492	.	+	.	Phchi.S1G243000
Phchi.S1	AUGUSTUS	transcript	15985866	15986492	.	+	.	transcript_id "Phchi.S1G243000.t1"; gene_id "Phchi.S1G243000"
Phchi.S1	AUGUSTUS	start_codon	15985866	15985868	.	+	0	transcript_id "Phchi.S1G243000.t1"; gene_id "Phchi.S1G243000"
Phchi.S1	AUGUSTUS	CDS	15985866	15986492	0.39	+	0	transcript_id "Phchi.S1G243000.t1"; gene_id "Phchi.S1G243000"
Phchi.S1	AUGUSTUS	exon	15985866	15986492	.	+	.	transcript_id "Phchi.S1G243000.t1"; gene_id "Phchi.S1G243000"
Phchi.S1	AUGUSTUS	stop_codon	15986493	15986495	.	+	0	transcript_id "Phchi.S1G243000.t1"; gene_id "Phchi.S1G243000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14758.t1 is derived from g13226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14574113	14574808	.	+	.	Phchi.S3G207700
Phchi.S3	AUGUSTUS	transcript	14574113	14574808	.	+	.	transcript_id "Phchi.S3G207700.t1"; gene_id "Phchi.S3G207700"
Phchi.S3	AUGUSTUS	start_codon	14574113	14574115	.	+	0	transcript_id "Phchi.S3G207700.t1"; gene_id "Phchi.S3G207700"
Phchi.S3	AUGUSTUS	CDS	14574113	14574808	0.57	+	0	transcript_id "Phchi.S3G207700.t1"; gene_id "Phchi.S3G207700"
Phchi.S3	AUGUSTUS	exon	14574113	14574808	.	+	.	transcript_id "Phchi.S3G207700.t1"; gene_id "Phchi.S3G207700"
Phchi.S3	AUGUSTUS	stop_codon	14574809	14574811	.	+	0	transcript_id "Phchi.S3G207700.t1"; gene_id "Phchi.S3G207700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13223.t1 is derived from g11688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4765761	4766586	.	+	.	Phchi.S3G054200
Phchi.S3	AUGUSTUS	transcript	4765761	4766586	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	start_codon	4765761	4765763	.	+	0	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	CDS	4765761	4765809	0.96	+	0	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	exon	4765761	4765809	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	intron	4765810	4765903	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	CDS	4765904	4766211	0.78	+	2	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	exon	4765904	4766211	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	intron	4766212	4766366	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	CDS	4766367	4766464	1	+	0	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	exon	4766367	4766464	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	intron	4766465	4766558	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	CDS	4766559	4766586	1	+	1	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	exon	4766559	4766586	.	+	.	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
Phchi.S3	AUGUSTUS	stop_codon	4766587	4766589	.	+	0	transcript_id "Phchi.S3G054200.t1"; gene_id "Phchi.S3G054200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7334.t1 is derived from g4506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28559431	28563110	.	+	.	Phchi.S1G449300
Phchi.S1	AUGUSTUS	transcript	28559431	28563110	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	start_codon	28559431	28559433	.	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28559431	28559446	0.46	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28559431	28559446	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28559447	28559576	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28559577	28559627	1	+	2	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28559577	28559627	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28559628	28559859	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28559860	28560011	1	+	2	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28559860	28560011	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28560012	28560192	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28560193	28560252	1	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28560193	28560252	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28560253	28560343	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28560344	28560462	0.8	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28560344	28560462	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28560463	28560546	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28560547	28560611	0.8	+	1	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28560547	28560611	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28560612	28560710	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28560711	28560763	0.57	+	2	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28560711	28560763	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28560764	28560871	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28560872	28560925	0.78	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28560872	28560925	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28560926	28561043	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28561044	28561103	1	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28561044	28561103	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28561104	28561261	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28561262	28561323	1	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28561262	28561323	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28561324	28561410	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28561411	28561781	1	+	1	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28561411	28561781	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28561782	28561870	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28561871	28561988	1	+	2	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28561871	28561988	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28561989	28562077	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28562078	28562126	1	+	1	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28562078	28562126	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28562127	28562268	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28562269	28562352	1	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28562269	28562352	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28562353	28562457	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28562458	28562537	1	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28562458	28562537	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28562538	28562644	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28562645	28562734	1	+	1	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28562645	28562734	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28562735	28562852	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28562853	28562905	1	+	1	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28562853	28562905	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	intron	28562906	28562979	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	CDS	28562980	28563110	0.5	+	2	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	exon	28562980	28563110	.	+	.	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
Phchi.S1	AUGUSTUS	stop_codon	28563111	28563113	.	+	0	transcript_id "Phchi.S1G449300.t1"; gene_id "Phchi.S1G449300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5183.t1 is derived from g2353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15372677	15373287	.	+	.	Phchi.S1G234200
Phchi.S1	AUGUSTUS	transcript	15372677	15373287	.	+	.	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	start_codon	15372677	15372679	.	+	0	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	CDS	15372677	15372869	0.43	+	0	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	exon	15372677	15372869	.	+	.	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	intron	15372870	15372955	.	+	.	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	CDS	15372956	15373287	0.42	+	2	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	exon	15372956	15373287	.	+	.	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
Phchi.S1	AUGUSTUS	stop_codon	15373288	15373290	.	+	0	transcript_id "Phchi.S1G234200.t1"; gene_id "Phchi.S1G234200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4779.t1 is derived from g1949.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12778939	12784781	.	+	.	Phchi.S1G193800
Phchi.S1	AUGUSTUS	transcript	12778939	12784781	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	start_codon	12778939	12778941	.	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12778939	12779181	0.96	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12778939	12779181	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779182	12779282	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12779283	12779519	0.99	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12779283	12779519	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779520	12779595	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12779596	12779841	0.96	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12779596	12779841	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779842	12779935	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12779936	12779958	0.95	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12779936	12779958	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779959	12780129	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780130	12780235	0.97	+	1	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780130	12780235	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780236	12780311	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780312	12780425	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780312	12780425	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780426	12780523	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780524	12780622	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780524	12780622	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780623	12780698	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780699	12780788	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780699	12780788	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780789	12780926	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780927	12781033	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780927	12781033	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781034	12781116	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781117	12781257	1	+	1	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781117	12781257	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781258	12781350	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781351	12781622	0.54	+	1	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781351	12781622	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781623	12781741	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781742	12781808	0.6	+	2	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781742	12781808	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781809	12781938	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781939	12782007	0.92	+	1	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781939	12782007	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782008	12782228	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782229	12782337	1	+	1	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782229	12782337	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782338	12782488	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782489	12782602	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782489	12782602	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782603	12782709	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782710	12782772	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782710	12782772	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782773	12782889	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782890	12783051	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782890	12783051	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783052	12783170	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783171	12783251	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783171	12783251	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783252	12783393	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783394	12783665	0.76	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783394	12783665	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783666	12783771	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783772	12783853	1	+	1	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783772	12783853	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783854	12783929	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783930	12784025	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783930	12784025	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784026	12784101	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784102	12784203	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784102	12784203	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784204	12784319	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784320	12784436	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784320	12784436	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784437	12784520	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784521	12784637	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784521	12784637	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784638	12784712	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784713	12784781	1	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784713	12784781	.	+	.	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	stop_codon	12784782	12784784	.	+	0	transcript_id "Phchi.S1G193800.t1"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	transcript	12778939	12784781	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	start_codon	12778939	12778941	.	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12778939	12779181	0.93	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12778939	12779181	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779182	12779282	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12779283	12779519	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12779283	12779519	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779520	12779595	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12779596	12779841	0.68	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12779596	12779841	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12779842	12779948	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12779949	12780028	0.7	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12779949	12780028	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780029	12780129	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780130	12780235	0.97	+	1	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780130	12780235	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780236	12780311	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780312	12780425	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780312	12780425	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780426	12780523	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780524	12780622	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780524	12780622	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780623	12780698	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780699	12780788	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780699	12780788	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12780789	12780926	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12780927	12781033	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12780927	12781033	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781034	12781116	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781117	12781257	1	+	1	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781117	12781257	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781258	12781350	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781351	12781622	0.54	+	1	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781351	12781622	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781623	12781741	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781742	12781808	0.6	+	2	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781742	12781808	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12781809	12781938	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12781939	12782007	0.86	+	1	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12781939	12782007	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782008	12782228	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782229	12782337	1	+	1	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782229	12782337	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782338	12782488	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782489	12782602	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782489	12782602	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782603	12782709	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782710	12782772	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782710	12782772	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12782773	12782889	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12782890	12783051	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12782890	12783051	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783052	12783170	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783171	12783251	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783171	12783251	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783252	12783393	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783394	12783665	0.77	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783394	12783665	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783666	12783771	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783772	12783853	1	+	1	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783772	12783853	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12783854	12783929	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12783930	12784025	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12783930	12784025	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784026	12784101	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784102	12784203	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784102	12784203	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784204	12784319	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784320	12784436	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784320	12784436	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784437	12784520	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784521	12784637	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784521	12784637	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	intron	12784638	12784712	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	CDS	12784713	12784781	1	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	exon	12784713	12784781	.	+	.	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
Phchi.S1	AUGUSTUS	stop_codon	12784782	12784784	.	+	0	transcript_id "Phchi.S1G193800.t2"; gene_id "Phchi.S1G193800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg49.t1 is derived from g9831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	83386	85725	.	-	.	Phchi.S6G000800
Phchi.S6	AUGUSTUS	transcript	83386	85725	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	stop_codon	83383	83385	.	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	83386	83402	1	-	2	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	83386	83402	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	83403	83819	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	83820	83852	0.99	-	2	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	83820	83852	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	83853	83986	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	83987	84023	0.99	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	83987	84023	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	84024	84105	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	84106	84231	1	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	84106	84231	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	84232	84318	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	84319	84402	1	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	84319	84402	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	84403	84547	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	84548	84675	1	-	2	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	84548	84675	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	84676	84783	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	84784	84838	1	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	84784	84838	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	84839	84924	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	84925	85104	1	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	84925	85104	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	intron	85105	85344	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	CDS	85345	85725	0.92	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	exon	85345	85725	.	-	.	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
Phchi.S6	AUGUSTUS	start_codon	85723	85725	.	-	0	transcript_id "Phchi.S6G000800.t1"; gene_id "Phchi.S6G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5554.t1 is derived from g2724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17576739	17577637	.	-	.	Phchi.S1G271300
Phchi.S1	AUGUSTUS	transcript	17576739	17577637	.	-	.	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	stop_codon	17576736	17576738	.	-	0	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	CDS	17576739	17577117	0.65	-	1	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	exon	17576739	17577117	.	-	.	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	intron	17577118	17577272	.	-	.	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	CDS	17577273	17577637	0.35	-	0	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	exon	17577273	17577637	.	-	.	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
Phchi.S1	AUGUSTUS	start_codon	17577635	17577637	.	-	0	transcript_id "Phchi.S1G271300.t1"; gene_id "Phchi.S1G271300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12221.t1 is derived from g7897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6822366	6824378	.	+	.	Phchi.S2G030100
Phchi.S2	AUGUSTUS	transcript	6822366	6824378	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	start_codon	6822366	6822368	.	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6822366	6822590	1	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6822366	6822590	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	intron	6822591	6823082	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6823083	6823292	1	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6823083	6823292	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	intron	6823293	6823439	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6823440	6823610	1	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6823440	6823610	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	intron	6823611	6823691	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6823692	6823815	1	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6823692	6823815	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	intron	6823816	6823903	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6823904	6823965	1	+	2	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6823904	6823965	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	intron	6823966	6824075	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6824076	6824157	1	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6824076	6824157	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	intron	6824158	6824244	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	CDS	6824245	6824378	1	+	2	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	exon	6824245	6824378	.	+	.	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
Phchi.S2	AUGUSTUS	stop_codon	6824379	6824381	.	+	0	transcript_id "Phchi.S2G030100.t1"; gene_id "Phchi.S2G030100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15648.t1 is derived from g14117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20472159	20472467	.	+	.	Phchi.S3G296700
Phchi.S3	AUGUSTUS	transcript	20472159	20472467	.	+	.	transcript_id "Phchi.S3G296700.t1"; gene_id "Phchi.S3G296700"
Phchi.S3	AUGUSTUS	start_codon	20472159	20472161	.	+	0	transcript_id "Phchi.S3G296700.t1"; gene_id "Phchi.S3G296700"
Phchi.S3	AUGUSTUS	CDS	20472159	20472467	1	+	0	transcript_id "Phchi.S3G296700.t1"; gene_id "Phchi.S3G296700"
Phchi.S3	AUGUSTUS	exon	20472159	20472467	.	+	.	transcript_id "Phchi.S3G296700.t1"; gene_id "Phchi.S3G296700"
Phchi.S3	AUGUSTUS	stop_codon	20472468	20472470	.	+	0	transcript_id "Phchi.S3G296700.t1"; gene_id "Phchi.S3G296700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2501.t1 is derived from g9421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6997680	6999866	.	-	.	Phchi.S5G111000
Phchi.S5	AUGUSTUS	transcript	6997847	6999866	.	-	.	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	stop_codon	6997844	6997846	.	-	0	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	CDS	6997847	6997858	1	-	0	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	exon	6997847	6997858	.	-	.	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	intron	6997859	6997946	.	-	.	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	CDS	6997947	6999866	1	-	0	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	exon	6997947	6999866	.	-	.	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	start_codon	6999864	6999866	.	-	0	transcript_id "Phchi.S5G111000.t1"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	transcript	6997680	6999866	.	-	.	transcript_id "Phchi.S5G111000.t2"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	stop_codon	6997677	6997679	.	-	0	transcript_id "Phchi.S5G111000.t2"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	CDS	6997680	6999866	1	-	0	transcript_id "Phchi.S5G111000.t2"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	exon	6997680	6999866	.	-	.	transcript_id "Phchi.S5G111000.t2"; gene_id "Phchi.S5G111000"
Phchi.S5	AUGUSTUS	start_codon	6999864	6999866	.	-	0	transcript_id "Phchi.S5G111000.t2"; gene_id "Phchi.S5G111000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14464.t1 is derived from g12932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13001223	13002172	.	+	.	Phchi.S3G178300
Phchi.S3	AUGUSTUS	transcript	13001223	13002172	.	+	.	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	start_codon	13001223	13001225	.	+	0	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	CDS	13001223	13001292	0.36	+	0	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	exon	13001223	13001292	.	+	.	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	intron	13001293	13001520	.	+	.	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	CDS	13001521	13001747	0.3	+	2	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	exon	13001521	13001747	.	+	.	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	intron	13001748	13001851	.	+	.	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	CDS	13001852	13002172	0.57	+	0	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	exon	13001852	13002172	.	+	.	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
Phchi.S3	AUGUSTUS	stop_codon	13002173	13002175	.	+	0	transcript_id "Phchi.S3G178300.t1"; gene_id "Phchi.S3G178300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9857.t1 is derived from g7033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44104335	44105263	.	-	.	Phchi.S1G701600
Phchi.S1	AUGUSTUS	transcript	44104335	44105263	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	stop_codon	44104332	44104334	.	-	0	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	CDS	44104335	44104386	0.86	-	1	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	exon	44104335	44104386	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	intron	44104387	44104482	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	CDS	44104483	44104536	0.8	-	1	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	exon	44104483	44104536	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	intron	44104537	44104987	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	CDS	44104988	44105014	0.73	-	1	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	exon	44104988	44105014	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	intron	44105015	44105097	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	CDS	44105098	44105120	0.72	-	0	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	exon	44105098	44105120	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	intron	44105121	44105200	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	CDS	44105201	44105263	0.78	-	0	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	exon	44105201	44105263	.	-	.	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
Phchi.S1	AUGUSTUS	start_codon	44105261	44105263	.	-	0	transcript_id "Phchi.S1G701600.t1"; gene_id "Phchi.S1G701600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg624.t1 is derived from g10406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4453803	4454838	.	-	.	Phchi.S6G058300
Phchi.S6	AUGUSTUS	transcript	4453803	4454838	.	-	.	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	stop_codon	4453800	4453802	.	-	0	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	CDS	4453803	4454120	1	-	0	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	exon	4453803	4454120	.	-	.	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	intron	4454121	4454287	.	-	.	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	CDS	4454288	4454419	1	-	0	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	exon	4454288	4454419	.	-	.	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	intron	4454420	4454709	.	-	.	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	CDS	4454710	4454838	0.99	-	0	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	exon	4454710	4454838	.	-	.	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
Phchi.S6	AUGUSTUS	start_codon	4454836	4454838	.	-	0	transcript_id "Phchi.S6G058300.t1"; gene_id "Phchi.S6G058300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2183.t1 is derived from g9103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5258046	5260733	.	-	.	Phchi.S5G079200
Phchi.S5	AUGUSTUS	transcript	5258046	5260733	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	stop_codon	5258043	5258045	.	-	0	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	CDS	5258046	5258507	0.53	-	0	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	exon	5258046	5258507	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	intron	5258508	5258599	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	CDS	5258600	5258890	1	-	0	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	exon	5258600	5258890	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	intron	5258891	5258991	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	CDS	5258992	5259418	1	-	1	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	exon	5258992	5259418	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	intron	5259419	5259502	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	CDS	5259503	5259995	0.65	-	2	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	exon	5259503	5259995	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	intron	5259996	5260108	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	CDS	5260109	5260733	0.6	-	0	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	exon	5260109	5260733	.	-	.	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
Phchi.S5	AUGUSTUS	start_codon	5260731	5260733	.	-	0	transcript_id "Phchi.S5G079200.t1"; gene_id "Phchi.S5G079200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2893.t1 is derived from g62.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	367854	370560	.	+	.	Phchi.S1G005200
Phchi.S1	AUGUSTUS	transcript	367854	370560	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	start_codon	367854	367856	.	+	0	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	367854	367917	0.44	+	0	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	367854	367917	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	367918	368025	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368026	368095	0.99	+	2	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368026	368095	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	368096	368207	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368208	368323	1	+	1	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368208	368323	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	368324	368411	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368412	368515	0.52	+	2	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368412	368515	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	368516	368655	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368656	369602	0.73	+	0	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368656	369602	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	369603	369708	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	369709	370047	0.89	+	1	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	369709	370047	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	370048	370140	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	370141	370305	1	+	1	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	370141	370305	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	370306	370451	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	370452	370560	1	+	1	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	370452	370560	.	+	.	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	stop_codon	370561	370563	.	+	0	transcript_id "Phchi.S1G005200.t1"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	transcript	367854	370560	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	start_codon	367854	367856	.	+	0	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	367854	367917	0.48	+	0	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	367854	367917	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	367918	368025	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368026	368095	1	+	2	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368026	368095	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	368096	368207	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368208	368323	1	+	1	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368208	368323	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	368324	368411	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368412	368515	0.49	+	2	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368412	368515	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	368516	368655	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	368656	369602	0.62	+	0	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	368656	369602	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	369603	369708	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	369709	370047	0.89	+	1	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	369709	370047	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	370048	370137	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	370138	370305	1	+	1	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	370138	370305	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	intron	370306	370451	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	CDS	370452	370560	1	+	1	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	exon	370452	370560	.	+	.	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
Phchi.S1	AUGUSTUS	stop_codon	370561	370563	.	+	0	transcript_id "Phchi.S1G005200.t2"; gene_id "Phchi.S1G005200"
# This transcript jg11975.t2 is derived from g7650.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11976.t1 is derived from g7651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	265260	266501	.	-	.	Phchi.S2G005600
Phchi.S2	AUGUSTUS	transcript	265260	266501	.	-	.	transcript_id "Phchi.S2G005600.t1"; gene_id "Phchi.S2G005600"
Phchi.S2	AUGUSTUS	stop_codon	265257	265259	.	-	0	transcript_id "Phchi.S2G005600.t1"; gene_id "Phchi.S2G005600"
Phchi.S2	AUGUSTUS	CDS	265260	266501	1	-	0	transcript_id "Phchi.S2G005600.t1"; gene_id "Phchi.S2G005600"
Phchi.S2	AUGUSTUS	exon	265260	266501	.	-	.	transcript_id "Phchi.S2G005600.t1"; gene_id "Phchi.S2G005600"
Phchi.S2	AUGUSTUS	start_codon	266499	266501	.	-	0	transcript_id "Phchi.S2G005600.t1"; gene_id "Phchi.S2G005600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3733.t1 is derived from g902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5439932	5442598	.	+	.	Phchi.S1G089200
Phchi.S1	AUGUSTUS	transcript	5439932	5442598	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	start_codon	5439932	5439934	.	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5439932	5440047	0.97	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5439932	5440047	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5440048	5440240	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5440241	5440341	1	+	1	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5440241	5440341	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5440342	5440656	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5440657	5440829	0.96	+	2	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5440657	5440829	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5440830	5440930	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5440931	5441162	0.98	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5440931	5441162	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5441163	5441346	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5441347	5441465	1	+	2	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5441347	5441465	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5441466	5441695	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5441696	5441752	1	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5441696	5441752	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5441753	5441848	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5441849	5442033	1	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5441849	5442033	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5442034	5442123	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5442124	5442268	1	+	1	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5442124	5442268	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5442269	5442357	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5442358	5442441	1	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5442358	5442441	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	intron	5442442	5442523	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	CDS	5442524	5442598	0.95	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	exon	5442524	5442598	.	+	.	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
Phchi.S1	AUGUSTUS	stop_codon	5442599	5442601	.	+	0	transcript_id "Phchi.S1G089200.t1"; gene_id "Phchi.S1G089200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15385.t1 is derived from g13853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18751904	18752660	.	-	.	Phchi.S3G270400
Phchi.S3	AUGUSTUS	transcript	18751904	18752660	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	stop_codon	18751901	18751903	.	-	0	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	CDS	18751904	18751979	1	-	1	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	exon	18751904	18751979	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	intron	18751980	18752074	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	CDS	18752075	18752157	1	-	0	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	exon	18752075	18752157	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	intron	18752158	18752248	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	CDS	18752249	18752317	1	-	0	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	exon	18752249	18752317	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	intron	18752318	18752415	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	CDS	18752416	18752458	0.82	-	1	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	exon	18752416	18752458	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	intron	18752459	18752631	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	CDS	18752632	18752660	0.78	-	0	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	exon	18752632	18752660	.	-	.	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
Phchi.S3	AUGUSTUS	start_codon	18752658	18752660	.	-	0	transcript_id "Phchi.S3G270400.t1"; gene_id "Phchi.S3G270400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14368.t1 is derived from g12835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12388958	12390146	.	-	.	Phchi.S3G168700
Phchi.S3	AUGUSTUS	transcript	12388958	12390146	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	stop_codon	12388955	12388957	.	-	0	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	CDS	12388958	12388969	0.92	-	0	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	exon	12388958	12388969	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	intron	12388970	12389069	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	CDS	12389070	12389114	0.91	-	0	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	exon	12389070	12389114	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	intron	12389115	12389259	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	CDS	12389260	12389473	0.91	-	1	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	exon	12389260	12389473	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	intron	12389474	12389607	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	CDS	12389608	12389623	1	-	2	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	exon	12389608	12389623	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	intron	12389624	12389749	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	CDS	12389750	12390146	0.51	-	0	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	exon	12389750	12390146	.	-	.	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
Phchi.S3	AUGUSTUS	start_codon	12390144	12390146	.	-	0	transcript_id "Phchi.S3G168700.t1"; gene_id "Phchi.S3G168700"
# This transcript jg114.t2 is derived from g9896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg115.t1 is derived from g9897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	605576	607786	.	+	.	Phchi.S6G007400
Phchi.S6	AUGUSTUS	transcript	605576	607786	.	+	.	transcript_id "Phchi.S6G007400.t1"; gene_id "Phchi.S6G007400"
Phchi.S6	AUGUSTUS	start_codon	605576	605578	.	+	0	transcript_id "Phchi.S6G007400.t1"; gene_id "Phchi.S6G007400"
Phchi.S6	AUGUSTUS	CDS	605576	607786	0.49	+	0	transcript_id "Phchi.S6G007400.t1"; gene_id "Phchi.S6G007400"
Phchi.S6	AUGUSTUS	exon	605576	607786	.	+	.	transcript_id "Phchi.S6G007400.t1"; gene_id "Phchi.S6G007400"
Phchi.S6	AUGUSTUS	stop_codon	607787	607789	.	+	0	transcript_id "Phchi.S6G007400.t1"; gene_id "Phchi.S6G007400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14903.t1 is derived from g13371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15450061	15451006	.	-	.	Phchi.S3G222200
Phchi.S3	AUGUSTUS	transcript	15450061	15451006	.	-	.	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	stop_codon	15450058	15450060	.	-	0	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	CDS	15450061	15450297	0.92	-	0	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	exon	15450061	15450297	.	-	.	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	intron	15450298	15450661	.	-	.	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	CDS	15450662	15451006	0.58	-	0	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	exon	15450662	15451006	.	-	.	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
Phchi.S3	AUGUSTUS	start_codon	15451004	15451006	.	-	0	transcript_id "Phchi.S3G222200.t1"; gene_id "Phchi.S3G222200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7285.t1 is derived from g4457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28137444	28143367	.	+	.	Phchi.S1G444400
Phchi.S1	AUGUSTUS	transcript	28137444	28143367	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	start_codon	28137444	28137446	.	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28137444	28137483	0.64	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28137444	28137483	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28137484	28137574	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28137575	28137596	0.98	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28137575	28137596	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28137597	28137694	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28137695	28137780	0.98	+	1	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28137695	28137780	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28137781	28137963	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28137964	28138057	1	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28137964	28138057	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28138058	28138176	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28138177	28138273	1	+	1	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28138177	28138273	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28138274	28138353	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28138354	28138512	0.99	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28138354	28138512	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28138513	28138643	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28138644	28138650	0.89	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28138644	28138650	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28138651	28138740	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28138741	28138859	0.87	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28138741	28138859	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28138860	28138940	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28138941	28139116	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28138941	28139116	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28139117	28139203	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28139204	28139351	0.58	+	1	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28139204	28139351	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28139352	28139456	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28139457	28139552	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28139457	28139552	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28139553	28139712	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28139713	28139848	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28139713	28139848	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28139849	28139988	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28139989	28140110	1	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28139989	28140110	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28140111	28140219	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28140220	28140402	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28140220	28140402	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28140403	28140502	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28140503	28140542	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28140503	28140542	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28140543	28140611	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28140612	28140673	1	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28140612	28140673	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28140674	28140806	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28140807	28140944	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28140807	28140944	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28140945	28141024	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28141025	28141179	1	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28141025	28141179	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28141180	28141344	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28141345	28141488	1	+	1	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28141345	28141488	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28141489	28141575	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28141576	28141723	1	+	1	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28141576	28141723	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28141724	28141813	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28141814	28141888	0.62	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28141814	28141888	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28141889	28142279	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28142280	28142307	0.92	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28142280	28142307	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28142308	28142389	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28142390	28142506	0.8	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28142390	28142506	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	intron	28142507	28142588	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	CDS	28142589	28143367	0.8	+	2	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	exon	28142589	28143367	.	+	.	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
Phchi.S1	AUGUSTUS	stop_codon	28143368	28143370	.	+	0	transcript_id "Phchi.S1G444400.t1"; gene_id "Phchi.S1G444400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10767.t1 is derived from g14817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2010843	2011986	.	+	.	Phchi.S4G034900
Phchi.S4	AUGUSTUS	transcript	2010843	2011986	.	+	.	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	start_codon	2010843	2010845	.	+	0	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	CDS	2010843	2010893	0.01	+	0	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	exon	2010843	2010893	.	+	.	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	intron	2010894	2011262	.	+	.	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	CDS	2011263	2011354	1	+	0	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	exon	2011263	2011354	.	+	.	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	intron	2011355	2011982	.	+	.	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	CDS	2011983	2011986	0.01	+	1	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	exon	2011983	2011986	.	+	.	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
Phchi.S4	AUGUSTUS	stop_codon	2011987	2011989	.	+	0	transcript_id "Phchi.S4G034900.t1"; gene_id "Phchi.S4G034900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12438.t1 is derived from g8115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20311224	20318476	.	-	.	Phchi.S2G051800
Phchi.S2	AUGUSTUS	transcript	20311224	20318476	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	stop_codon	20311221	20311223	.	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20311224	20311262	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20311224	20311262	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20311263	20311375	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20311376	20311462	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20311376	20311462	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20311463	20311550	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20311551	20311625	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20311551	20311625	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20311626	20311732	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20311733	20311846	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20311733	20311846	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20311847	20311933	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20311934	20312020	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20311934	20312020	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20312021	20312288	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20312289	20312354	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20312289	20312354	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20312355	20312444	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20312445	20312510	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20312445	20312510	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20312511	20312606	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20312607	20312678	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20312607	20312678	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20312679	20312830	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20312831	20312932	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20312831	20312932	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20312933	20313022	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20313023	20313200	1	-	1	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20313023	20313200	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20313201	20313306	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20313307	20313362	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20313307	20313362	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20313363	20313593	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20313594	20313704	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20313594	20313704	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20313705	20313796	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20313797	20313865	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20313797	20313865	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20313866	20313997	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20313998	20314106	1	-	1	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20313998	20314106	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20314107	20314196	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20314197	20314279	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20314197	20314279	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20314280	20314391	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20314392	20314472	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20314392	20314472	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20314473	20314549	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20314550	20314672	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20314550	20314672	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20314673	20314824	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20314825	20314944	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20314825	20314944	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20314945	20315042	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20315043	20315123	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20315043	20315123	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20315124	20315228	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20315229	20315375	0.95	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20315229	20315375	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20315376	20315461	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20315462	20315540	1	-	1	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20315462	20315540	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20315541	20315760	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20315761	20315835	0.98	-	1	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20315761	20315835	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20315836	20315946	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20315947	20316056	0.99	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20315947	20316056	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20316057	20316181	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20316182	20316280	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20316182	20316280	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20316281	20316429	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20316430	20316545	1	-	2	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20316430	20316545	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20316546	20316704	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20316705	20316813	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20316705	20316813	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20316814	20316898	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20316899	20317117	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20316899	20317117	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20317118	20317372	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20317373	20317638	1	-	2	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20317373	20317638	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20317639	20317748	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20317749	20317906	0.67	-	1	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20317749	20317906	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20317907	20318025	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20318026	20318176	1	-	2	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20318026	20318176	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20318177	20318248	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20318249	20318309	1	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20318249	20318309	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	intron	20318310	20318449	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	CDS	20318450	20318476	0.78	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	exon	20318450	20318476	.	-	.	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
Phchi.S2	AUGUSTUS	start_codon	20318474	20318476	.	-	0	transcript_id "Phchi.S2G051800.t1"; gene_id "Phchi.S2G051800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11204.t1 is derived from g15254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4669441	4672121	.	+	.	Phchi.S4G078600
Phchi.S4	AUGUSTUS	transcript	4669441	4672121	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	start_codon	4669441	4669443	.	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4669441	4670364	0.33	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4669441	4670364	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4670365	4670698	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4670699	4670818	0.97	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4670699	4670818	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4670819	4670916	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4670917	4671039	1	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4670917	4671039	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4671040	4671120	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4671121	4671198	1	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4671121	4671198	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4671199	4671303	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4671304	4671386	0.97	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4671304	4671386	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4671387	4671481	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4671482	4671590	1	+	1	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4671482	4671590	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4671591	4671708	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4671709	4671777	1	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4671709	4671777	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	intron	4671778	4671854	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	CDS	4671855	4672121	0.68	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	exon	4671855	4672121	.	+	.	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
Phchi.S4	AUGUSTUS	stop_codon	4672122	4672124	.	+	0	transcript_id "Phchi.S4G078600.t1"; gene_id "Phchi.S4G078600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14646.t1 is derived from g13114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13932967	13936290	.	+	.	Phchi.S3G196500
Phchi.S3	AUGUSTUS	transcript	13932967	13936290	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	start_codon	13932967	13932969	.	+	0	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13932967	13933019	1	+	0	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13932967	13933019	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13933020	13933259	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13933260	13933328	0.74	+	1	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13933260	13933328	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13933329	13933477	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13933478	13933536	0.71	+	1	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13933478	13933536	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13933537	13933682	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13933683	13933812	0.67	+	2	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13933683	13933812	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13933813	13934056	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13934057	13934076	0.56	+	1	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13934057	13934076	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13934077	13934387	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13934388	13934614	0.61	+	2	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13934388	13934614	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13934615	13934717	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13934718	13934876	0.97	+	0	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13934718	13934876	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13934877	13935257	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13935258	13935354	0.62	+	0	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13935258	13935354	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13935355	13935435	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13935436	13935548	0.37	+	2	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13935436	13935548	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13935549	13935628	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13935629	13935756	0.66	+	0	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13935629	13935756	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	intron	13935757	13936205	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	CDS	13936206	13936290	0.64	+	1	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	exon	13936206	13936290	.	+	.	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
Phchi.S3	AUGUSTUS	stop_codon	13936291	13936293	.	+	0	transcript_id "Phchi.S3G196500.t1"; gene_id "Phchi.S3G196500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3871.t1 is derived from g1040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6148757	6150393	.	-	.	Phchi.S1G103000
Phchi.S1	AUGUSTUS	transcript	6148757	6150393	.	-	.	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	stop_codon	6148754	6148756	.	-	0	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	CDS	6148757	6149774	0.99	-	1	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	exon	6148757	6149774	.	-	.	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	intron	6149775	6149896	.	-	.	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	CDS	6149897	6150393	0.96	-	0	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	exon	6149897	6150393	.	-	.	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
Phchi.S1	AUGUSTUS	start_codon	6150391	6150393	.	-	0	transcript_id "Phchi.S1G103000.t1"; gene_id "Phchi.S1G103000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11686.t1 is derived from g15737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7660984	7662038	.	-	.	Phchi.S4G126800
Phchi.S4	AUGUSTUS	transcript	7660984	7662038	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	stop_codon	7660981	7660983	.	-	0	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	CDS	7660984	7661100	0.62	-	0	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	exon	7660984	7661100	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	intron	7661101	7661324	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	CDS	7661325	7661409	0.92	-	1	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	exon	7661325	7661409	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	intron	7661410	7661507	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	CDS	7661508	7661581	1	-	0	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	exon	7661508	7661581	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	intron	7661582	7661758	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	CDS	7661759	7661825	1	-	1	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	exon	7661759	7661825	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	intron	7661826	7661964	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	CDS	7661965	7662038	1	-	0	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	exon	7661965	7662038	.	-	.	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
Phchi.S4	AUGUSTUS	start_codon	7662036	7662038	.	-	0	transcript_id "Phchi.S4G126800.t1"; gene_id "Phchi.S4G126800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4935.t1 is derived from g2105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13644836	13646840	.	-	.	Phchi.S1G209400
Phchi.S1	AUGUSTUS	transcript	13644836	13646840	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	stop_codon	13644833	13644835	.	-	0	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13644836	13645017	1	-	2	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13644836	13645017	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	intron	13645018	13645146	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13645147	13645393	1	-	0	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13645147	13645393	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	intron	13645394	13645490	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13645491	13645802	0.99	-	0	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13645491	13645802	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	intron	13645803	13645886	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13645887	13645966	0.98	-	2	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13645887	13645966	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	intron	13645967	13646061	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13646062	13646099	0.66	-	1	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13646062	13646099	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	intron	13646100	13646209	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13646210	13646243	0.98	-	2	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13646210	13646243	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	intron	13646244	13646350	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	CDS	13646351	13646840	1	-	0	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	exon	13646351	13646840	.	-	.	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
Phchi.S1	AUGUSTUS	start_codon	13646838	13646840	.	-	0	transcript_id "Phchi.S1G209400.t1"; gene_id "Phchi.S1G209400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9737.t1 is derived from g6913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43455181	43457343	.	-	.	Phchi.S1G689600
Phchi.S1	AUGUSTUS	transcript	43455181	43457343	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	stop_codon	43455178	43455180	.	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43455181	43455228	0.95	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43455181	43455228	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43455229	43455376	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43455377	43455636	0.96	-	2	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43455377	43455636	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43455637	43455735	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43455736	43455828	1	-	2	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43455736	43455828	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43455829	43455914	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43455915	43456014	1	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43455915	43456014	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43456015	43456113	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43456114	43456218	1	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43456114	43456218	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43456219	43456301	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43456302	43456442	1	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43456302	43456442	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43456443	43456563	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43456564	43457151	1	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43456564	43457151	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	intron	43457152	43457235	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	CDS	43457236	43457343	0.78	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	exon	43457236	43457343	.	-	.	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
Phchi.S1	AUGUSTUS	start_codon	43457341	43457343	.	-	0	transcript_id "Phchi.S1G689600.t1"; gene_id "Phchi.S1G689600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13322.t1 is derived from g11788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6097140	6098255	.	+	.	Phchi.S3G064100
Phchi.S3	AUGUSTUS	transcript	6097140	6098255	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	start_codon	6097140	6097142	.	+	0	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	CDS	6097140	6097319	1	+	0	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	exon	6097140	6097319	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	intron	6097320	6097474	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	CDS	6097475	6097609	1	+	0	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	exon	6097475	6097609	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	intron	6097610	6097688	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	CDS	6097689	6097917	1	+	0	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	exon	6097689	6097917	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	intron	6097918	6098007	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	CDS	6098008	6098255	0.49	+	2	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	exon	6098008	6098255	.	+	.	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
Phchi.S3	AUGUSTUS	stop_codon	6098256	6098258	.	+	0	transcript_id "Phchi.S3G064100.t1"; gene_id "Phchi.S3G064100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10750.t1 is derived from g14800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1927125	1928486	.	-	.	Phchi.S4G033200
Phchi.S4	AUGUSTUS	transcript	1927125	1928486	.	-	.	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	stop_codon	1927122	1927124	.	-	0	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	CDS	1927125	1927271	0.98	-	0	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	exon	1927125	1927271	.	-	.	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	intron	1927272	1927458	.	-	.	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	CDS	1927459	1928156	0.52	-	2	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	exon	1927459	1928156	.	-	.	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	intron	1928157	1928281	.	-	.	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	CDS	1928282	1928486	1	-	0	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	exon	1928282	1928486	.	-	.	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
Phchi.S4	AUGUSTUS	start_codon	1928484	1928486	.	-	0	transcript_id "Phchi.S4G033200.t1"; gene_id "Phchi.S4G033200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10734.t1 is derived from g14784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1832770	1833437	.	+	.	Phchi.S4G031600
Phchi.S4	AUGUSTUS	transcript	1832770	1833437	.	+	.	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	start_codon	1832770	1832772	.	+	0	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	CDS	1832770	1832941	0.91	+	0	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	exon	1832770	1832941	.	+	.	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	intron	1832942	1833078	.	+	.	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	CDS	1833079	1833437	0.98	+	2	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	exon	1833079	1833437	.	+	.	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
Phchi.S4	AUGUSTUS	stop_codon	1833438	1833440	.	+	0	transcript_id "Phchi.S4G031600.t1"; gene_id "Phchi.S4G031600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4607.t1 is derived from g1777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11371383	11372504	.	+	.	Phchi.S1G176600
Phchi.S1	AUGUSTUS	transcript	11371383	11372504	.	+	.	transcript_id "Phchi.S1G176600.t1"; gene_id "Phchi.S1G176600"
Phchi.S1	AUGUSTUS	start_codon	11371383	11371385	.	+	0	transcript_id "Phchi.S1G176600.t1"; gene_id "Phchi.S1G176600"
Phchi.S1	AUGUSTUS	CDS	11371383	11372504	1	+	0	transcript_id "Phchi.S1G176600.t1"; gene_id "Phchi.S1G176600"
Phchi.S1	AUGUSTUS	exon	11371383	11372504	.	+	.	transcript_id "Phchi.S1G176600.t1"; gene_id "Phchi.S1G176600"
Phchi.S1	AUGUSTUS	stop_codon	11372505	11372507	.	+	0	transcript_id "Phchi.S1G176600.t1"; gene_id "Phchi.S1G176600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5312.t1 is derived from g2482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16239329	16240225	.	-	.	Phchi.S1G247100
Phchi.S1	AUGUSTUS	transcript	16239329	16240225	.	-	.	transcript_id "Phchi.S1G247100.t1"; gene_id "Phchi.S1G247100"
Phchi.S1	AUGUSTUS	stop_codon	16239326	16239328	.	-	0	transcript_id "Phchi.S1G247100.t1"; gene_id "Phchi.S1G247100"
Phchi.S1	AUGUSTUS	CDS	16239329	16240225	0.97	-	0	transcript_id "Phchi.S1G247100.t1"; gene_id "Phchi.S1G247100"
Phchi.S1	AUGUSTUS	exon	16239329	16240225	.	-	.	transcript_id "Phchi.S1G247100.t1"; gene_id "Phchi.S1G247100"
Phchi.S1	AUGUSTUS	start_codon	16240223	16240225	.	-	0	transcript_id "Phchi.S1G247100.t1"; gene_id "Phchi.S1G247100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg699.t1 is derived from g10481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4969280	4969667	.	+	.	Phchi.S6G065800
Phchi.S6	AUGUSTUS	transcript	4969280	4969667	.	+	.	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	start_codon	4969280	4969282	.	+	0	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	CDS	4969280	4969288	0.83	+	0	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	exon	4969280	4969288	.	+	.	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	intron	4969289	4969394	.	+	.	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	CDS	4969395	4969667	0.57	+	0	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	exon	4969395	4969667	.	+	.	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
Phchi.S6	AUGUSTUS	stop_codon	4969668	4969670	.	+	0	transcript_id "Phchi.S6G065800.t1"; gene_id "Phchi.S6G065800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7893.t1 is derived from g5067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31784470	31785609	.	+	.	Phchi.S1G505200
Phchi.S1	AUGUSTUS	transcript	31784470	31785609	.	+	.	transcript_id "Phchi.S1G505200.t1"; gene_id "Phchi.S1G505200"
Phchi.S1	AUGUSTUS	start_codon	31784470	31784472	.	+	0	transcript_id "Phchi.S1G505200.t1"; gene_id "Phchi.S1G505200"
Phchi.S1	AUGUSTUS	CDS	31784470	31785609	0.59	+	0	transcript_id "Phchi.S1G505200.t1"; gene_id "Phchi.S1G505200"
Phchi.S1	AUGUSTUS	exon	31784470	31785609	.	+	.	transcript_id "Phchi.S1G505200.t1"; gene_id "Phchi.S1G505200"
Phchi.S1	AUGUSTUS	stop_codon	31785610	31785612	.	+	0	transcript_id "Phchi.S1G505200.t1"; gene_id "Phchi.S1G505200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6706.t1 is derived from g3878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24639362	24640350	.	-	.	Phchi.S1G386500
Phchi.S1	AUGUSTUS	transcript	24639362	24640350	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	stop_codon	24639359	24639361	.	-	0	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	CDS	24639362	24639393	1	-	2	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	exon	24639362	24639393	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	intron	24639394	24639675	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	CDS	24639676	24639715	1	-	0	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	exon	24639676	24639715	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	intron	24639716	24639813	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	CDS	24639814	24640026	0.87	-	0	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	exon	24639814	24640026	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	intron	24640027	24640173	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	CDS	24640174	24640214	0.98	-	2	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	exon	24640174	24640214	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	intron	24640215	24640307	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	CDS	24640308	24640350	0.99	-	0	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	exon	24640308	24640350	.	-	.	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
Phchi.S1	AUGUSTUS	start_codon	24640348	24640350	.	-	0	transcript_id "Phchi.S1G386500.t1"; gene_id "Phchi.S1G386500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4983.t1 is derived from g2153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13878528	13879952	.	-	.	Phchi.S1G214200
Phchi.S1	AUGUSTUS	transcript	13878528	13879952	.	-	.	transcript_id "Phchi.S1G214200.t1"; gene_id "Phchi.S1G214200"
Phchi.S1	AUGUSTUS	stop_codon	13878525	13878527	.	-	0	transcript_id "Phchi.S1G214200.t1"; gene_id "Phchi.S1G214200"
Phchi.S1	AUGUSTUS	CDS	13878528	13879952	0.84	-	0	transcript_id "Phchi.S1G214200.t1"; gene_id "Phchi.S1G214200"
Phchi.S1	AUGUSTUS	exon	13878528	13879952	.	-	.	transcript_id "Phchi.S1G214200.t1"; gene_id "Phchi.S1G214200"
Phchi.S1	AUGUSTUS	start_codon	13879950	13879952	.	-	0	transcript_id "Phchi.S1G214200.t1"; gene_id "Phchi.S1G214200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg793.t1 is derived from g10575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5606469	5607638	.	+	.	Phchi.S6G075200
Phchi.S6	AUGUSTUS	transcript	5606469	5607638	.	+	.	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	start_codon	5606469	5606471	.	+	0	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	CDS	5606469	5606893	0.55	+	0	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	exon	5606469	5606893	.	+	.	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	intron	5606894	5607089	.	+	.	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	CDS	5607090	5607323	1	+	1	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	exon	5607090	5607323	.	+	.	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	intron	5607324	5607421	.	+	.	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	CDS	5607422	5607638	1	+	1	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	exon	5607422	5607638	.	+	.	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
Phchi.S6	AUGUSTUS	stop_codon	5607639	5607641	.	+	0	transcript_id "Phchi.S6G075200.t1"; gene_id "Phchi.S6G075200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9438.t1 is derived from g6614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41456148	41457865	.	+	.	Phchi.S1G659700
Phchi.S1	AUGUSTUS	transcript	41456148	41457865	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	start_codon	41456148	41456150	.	+	0	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	CDS	41456148	41456211	0.75	+	0	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	exon	41456148	41456211	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	intron	41456212	41456378	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	CDS	41456379	41456462	0.78	+	2	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	exon	41456379	41456462	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	intron	41456463	41456815	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	CDS	41456816	41457099	0.86	+	2	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	exon	41456816	41457099	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	intron	41457100	41457192	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	CDS	41457193	41457300	1	+	0	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	exon	41457193	41457300	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	intron	41457301	41457388	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	CDS	41457389	41457865	1	+	0	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	exon	41457389	41457865	.	+	.	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
Phchi.S1	AUGUSTUS	stop_codon	41457866	41457868	.	+	0	transcript_id "Phchi.S1G659700.t1"; gene_id "Phchi.S1G659700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6144.t1 is derived from g3315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21142653	21145909	.	-	.	Phchi.S1G330300
Phchi.S1	AUGUSTUS	transcript	21142653	21145909	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	stop_codon	21142650	21142652	.	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21142653	21142853	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21142653	21142853	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21142854	21142956	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21142957	21143079	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21142957	21143079	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21143080	21143183	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21143184	21143308	0.99	-	2	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21143184	21143308	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21143309	21143404	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21143405	21143528	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21143405	21143528	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21143529	21143640	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21143641	21143694	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21143641	21143694	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21143695	21143771	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21143772	21143861	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21143772	21143861	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21143862	21143962	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21143963	21144058	0.78	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21143963	21144058	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21144059	21144164	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21144165	21144234	0.78	-	1	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21144165	21144234	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21144235	21144352	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21144353	21144495	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21144353	21144495	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21144496	21144628	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21144629	21144772	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21144629	21144772	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21144773	21144898	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21144899	21145054	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21144899	21145054	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21145055	21145175	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21145176	21145226	1	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21145176	21145226	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21145227	21145309	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21145310	21145458	0.99	-	2	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21145310	21145458	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21145459	21145569	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21145570	21145743	0.99	-	2	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21145570	21145743	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	intron	21145744	21145863	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	CDS	21145864	21145909	0.82	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	exon	21145864	21145909	.	-	.	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
Phchi.S1	AUGUSTUS	start_codon	21145907	21145909	.	-	0	transcript_id "Phchi.S1G330300.t1"; gene_id "Phchi.S1G330300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3018.t1 is derived from g187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1167249	1168867	.	-	.	Phchi.S1G017700
Phchi.S1	AUGUSTUS	transcript	1167249	1168867	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	stop_codon	1167246	1167248	.	-	0	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	CDS	1167249	1167411	0.96	-	1	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	exon	1167249	1167411	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	intron	1167412	1167501	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	CDS	1167502	1167629	1	-	0	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	exon	1167502	1167629	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	intron	1167630	1167729	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	CDS	1167730	1168019	1	-	2	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	exon	1167730	1168019	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	intron	1168020	1168146	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	CDS	1168147	1168295	1	-	1	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	exon	1168147	1168295	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	intron	1168296	1168392	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	CDS	1168393	1168702	1	-	2	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	exon	1168393	1168702	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	intron	1168703	1168833	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	CDS	1168834	1168867	0.49	-	0	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	exon	1168834	1168867	.	-	.	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
Phchi.S1	AUGUSTUS	start_codon	1168865	1168867	.	-	0	transcript_id "Phchi.S1G017700.t1"; gene_id "Phchi.S1G017700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3769.t1 is derived from g938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5616976	5617846	.	-	.	Phchi.S1G092800
Phchi.S1	AUGUSTUS	transcript	5616976	5617846	.	-	.	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	stop_codon	5616973	5616975	.	-	0	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	CDS	5616976	5617047	1	-	0	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	exon	5616976	5617047	.	-	.	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	intron	5617048	5617135	.	-	.	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	CDS	5617136	5617846	0.98	-	0	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	exon	5617136	5617846	.	-	.	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
Phchi.S1	AUGUSTUS	start_codon	5617844	5617846	.	-	0	transcript_id "Phchi.S1G092800.t1"; gene_id "Phchi.S1G092800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14680.t1 is derived from g13148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14143645	14144276	.	+	.	Phchi.S3G199900
Phchi.S3	AUGUSTUS	transcript	14143645	14144276	.	+	.	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	start_codon	14143645	14143647	.	+	0	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	CDS	14143645	14143824	0.65	+	0	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	exon	14143645	14143824	.	+	.	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	intron	14143825	14143996	.	+	.	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	CDS	14143997	14144071	0.95	+	0	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	exon	14143997	14144071	.	+	.	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	intron	14144072	14144171	.	+	.	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	CDS	14144172	14144276	1	+	0	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	exon	14144172	14144276	.	+	.	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
Phchi.S3	AUGUSTUS	stop_codon	14144277	14144279	.	+	0	transcript_id "Phchi.S3G199900.t1"; gene_id "Phchi.S3G199900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12592.t1 is derived from g8269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36325457	36326043	.	+	.	Phchi.S2G067200
Phchi.S2	AUGUSTUS	transcript	36325457	36326043	.	+	.	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	start_codon	36325457	36325459	.	+	0	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	CDS	36325457	36325640	0.97	+	0	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	exon	36325457	36325640	.	+	.	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	intron	36325641	36325729	.	+	.	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	CDS	36325730	36326043	0.91	+	2	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	exon	36325730	36326043	.	+	.	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
Phchi.S2	AUGUSTUS	stop_codon	36326044	36326046	.	+	0	transcript_id "Phchi.S2G067200.t1"; gene_id "Phchi.S2G067200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11340.t1 is derived from g15390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5636824	5637720	.	-	.	Phchi.S4G092200
Phchi.S4	AUGUSTUS	transcript	5636824	5637720	.	-	.	transcript_id "Phchi.S4G092200.t1"; gene_id "Phchi.S4G092200"
Phchi.S4	AUGUSTUS	stop_codon	5636821	5636823	.	-	0	transcript_id "Phchi.S4G092200.t1"; gene_id "Phchi.S4G092200"
Phchi.S4	AUGUSTUS	CDS	5636824	5637720	0.41	-	0	transcript_id "Phchi.S4G092200.t1"; gene_id "Phchi.S4G092200"
Phchi.S4	AUGUSTUS	exon	5636824	5637720	.	-	.	transcript_id "Phchi.S4G092200.t1"; gene_id "Phchi.S4G092200"
Phchi.S4	AUGUSTUS	start_codon	5637718	5637720	.	-	0	transcript_id "Phchi.S4G092200.t1"; gene_id "Phchi.S4G092200"
# This transcript jg14799.t2 is derived from g13267.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14800.t1 is derived from g13268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14779364	14782505	.	-	.	Phchi.S3G211900
Phchi.S3	AUGUSTUS	transcript	14779364	14782505	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	stop_codon	14779361	14779363	.	-	0	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	CDS	14779364	14779449	0.97	-	2	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	exon	14779364	14779449	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	intron	14779450	14779553	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	CDS	14779554	14779720	0.98	-	1	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	exon	14779554	14779720	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	intron	14779721	14779809	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	CDS	14779810	14779947	1	-	1	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	exon	14779810	14779947	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	intron	14779948	14780059	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	CDS	14780060	14780209	0.77	-	1	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	exon	14780060	14780209	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	intron	14780210	14780350	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	CDS	14780351	14780415	0.85	-	0	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	exon	14780351	14780415	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	intron	14780416	14780600	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	CDS	14780601	14782505	0.19	-	0	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	exon	14780601	14782505	.	-	.	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
Phchi.S3	AUGUSTUS	start_codon	14782503	14782505	.	-	0	transcript_id "Phchi.S3G211900.t1"; gene_id "Phchi.S3G211900"
# This transcript jg3868.t2 is derived from g1037.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3869.t1 is derived from g1038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6138901	6140020	.	+	.	Phchi.S1G102800
Phchi.S1	AUGUSTUS	transcript	6138901	6140020	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	start_codon	6138901	6138903	.	+	0	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6138901	6139035	0.99	+	0	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6138901	6139035	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139036	6139142	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139143	6139197	1	+	0	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139143	6139197	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139198	6139283	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139284	6139460	0.99	+	2	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139284	6139460	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139461	6139534	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139535	6139736	0.98	+	2	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139535	6139736	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139737	6139911	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139912	6140020	0.98	+	1	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139912	6140020	.	+	.	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	stop_codon	6140021	6140023	.	+	0	transcript_id "Phchi.S1G102800.t1"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	transcript	6138901	6140020	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	start_codon	6138901	6138903	.	+	0	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6138901	6139035	1	+	0	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6138901	6139035	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139036	6139142	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139143	6139197	1	+	0	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139143	6139197	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139198	6139283	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139284	6139460	1	+	2	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139284	6139460	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139461	6139534	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139535	6139614	0.15	+	2	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139535	6139614	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139615	6139690	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139691	6139740	0.11	+	0	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139691	6139740	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	intron	6139741	6139911	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	CDS	6139912	6140020	0.21	+	1	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	exon	6139912	6140020	.	+	.	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
Phchi.S1	AUGUSTUS	stop_codon	6140021	6140023	.	+	0	transcript_id "Phchi.S1G102800.t2"; gene_id "Phchi.S1G102800"
# This transcript jg6577.t2 is derived from g3749.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6578.t1 is derived from g3750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23833151	23836098	.	-	.	Phchi.S1G373700
Phchi.S1	AUGUSTUS	transcript	23833151	23836098	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	stop_codon	23833148	23833150	.	-	0	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	CDS	23833151	23833334	0.76	-	1	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	exon	23833151	23833334	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	intron	23833335	23833432	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	CDS	23833433	23833509	1	-	0	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	exon	23833433	23833509	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	intron	23833510	23833593	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	CDS	23833594	23833627	0.8	-	1	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	exon	23833594	23833627	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	intron	23833628	23834103	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	CDS	23834104	23834187	0.6	-	1	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	exon	23834104	23834187	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	intron	23834188	23834955	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	CDS	23834956	23835313	1	-	2	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	exon	23834956	23835313	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	intron	23835314	23835719	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	CDS	23835720	23836098	0.89	-	0	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	exon	23835720	23836098	.	-	.	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
Phchi.S1	AUGUSTUS	start_codon	23836096	23836098	.	-	0	transcript_id "Phchi.S1G373700.t1"; gene_id "Phchi.S1G373700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg476.t1 is derived from g10258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3345481	3345884	.	-	.	Phchi.S6G043500
Phchi.S6	AUGUSTUS	transcript	3345481	3345884	.	-	.	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	stop_codon	3345478	3345480	.	-	0	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	CDS	3345481	3345605	0.56	-	2	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	exon	3345481	3345605	.	-	.	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	intron	3345606	3345763	.	-	.	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	CDS	3345764	3345884	0.57	-	0	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	exon	3345764	3345884	.	-	.	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
Phchi.S6	AUGUSTUS	start_codon	3345882	3345884	.	-	0	transcript_id "Phchi.S6G043500.t1"; gene_id "Phchi.S6G043500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8610.t1 is derived from g5785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36906235	36907796	.	+	.	Phchi.S1G576900
Phchi.S1	AUGUSTUS	transcript	36906235	36907796	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	start_codon	36906235	36906237	.	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36906235	36906358	0.81	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36906235	36906358	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36906359	36906496	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36906497	36906618	0.7	+	2	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36906497	36906618	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36906619	36906729	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36906730	36906810	1	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36906730	36906810	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36906811	36906962	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36906963	36907076	1	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36906963	36907076	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36907077	36907174	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36907175	36907249	1	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36907175	36907249	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36907250	36907354	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36907355	36907420	0.97	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36907355	36907420	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36907421	36907539	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36907540	36907583	1	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36907540	36907583	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	intron	36907584	36907663	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	CDS	36907664	36907796	1	+	1	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	exon	36907664	36907796	.	+	.	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
Phchi.S1	AUGUSTUS	stop_codon	36907797	36907799	.	+	0	transcript_id "Phchi.S1G576900.t1"; gene_id "Phchi.S1G576900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg58.t1 is derived from g9840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	294977	295967	.	-	.	Phchi.S6G001700
Phchi.S6	AUGUSTUS	transcript	294977	295967	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	stop_codon	294974	294976	.	-	0	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	CDS	294977	295129	0.99	-	0	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	exon	294977	295129	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	intron	295130	295283	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	CDS	295284	295360	1	-	2	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	exon	295284	295360	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	intron	295361	295446	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	CDS	295447	295496	0.59	-	1	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	exon	295447	295496	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	intron	295497	295661	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	CDS	295662	295777	0.79	-	0	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	exon	295662	295777	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	intron	295778	295907	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	CDS	295908	295967	0.31	-	0	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	exon	295908	295967	.	-	.	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
Phchi.S6	AUGUSTUS	start_codon	295965	295967	.	-	0	transcript_id "Phchi.S6G001700.t1"; gene_id "Phchi.S6G001700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3151.t1 is derived from g320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1988170	1988508	.	-	.	Phchi.S1G031000
Phchi.S1	AUGUSTUS	transcript	1988170	1988508	.	-	.	transcript_id "Phchi.S1G031000.t1"; gene_id "Phchi.S1G031000"
Phchi.S1	AUGUSTUS	stop_codon	1988167	1988169	.	-	0	transcript_id "Phchi.S1G031000.t1"; gene_id "Phchi.S1G031000"
Phchi.S1	AUGUSTUS	CDS	1988170	1988508	0.75	-	0	transcript_id "Phchi.S1G031000.t1"; gene_id "Phchi.S1G031000"
Phchi.S1	AUGUSTUS	exon	1988170	1988508	.	-	.	transcript_id "Phchi.S1G031000.t1"; gene_id "Phchi.S1G031000"
Phchi.S1	AUGUSTUS	start_codon	1988506	1988508	.	-	0	transcript_id "Phchi.S1G031000.t1"; gene_id "Phchi.S1G031000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3322.t1 is derived from g491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2890102	2891338	.	+	.	Phchi.S1G048100
Phchi.S1	AUGUSTUS	transcript	2890102	2891338	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	start_codon	2890102	2890104	.	+	0	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	CDS	2890102	2890200	0.84	+	0	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	exon	2890102	2890200	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	intron	2890201	2890363	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	CDS	2890364	2890592	1	+	0	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	exon	2890364	2890592	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	intron	2890593	2890678	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	CDS	2890679	2890727	1	+	2	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	exon	2890679	2890727	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	intron	2890728	2890953	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	CDS	2890954	2891338	1	+	1	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	exon	2890954	2891338	.	+	.	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
Phchi.S1	AUGUSTUS	stop_codon	2891339	2891341	.	+	0	transcript_id "Phchi.S1G048100.t1"; gene_id "Phchi.S1G048100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6308.t1 is derived from g3480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22197470	22198503	.	+	.	Phchi.S1G346700
Phchi.S1	AUGUSTUS	transcript	22197470	22198503	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	start_codon	22197470	22197472	.	+	0	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	CDS	22197470	22197565	0.78	+	0	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	exon	22197470	22197565	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	intron	22197566	22197683	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	CDS	22197684	22197839	1	+	0	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	exon	22197684	22197839	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	intron	22197840	22197930	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	CDS	22197931	22198129	0.99	+	0	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	exon	22197931	22198129	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	intron	22198130	22198282	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	CDS	22198283	22198503	1	+	2	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	exon	22198283	22198503	.	+	.	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
Phchi.S1	AUGUSTUS	stop_codon	22198504	22198506	.	+	0	transcript_id "Phchi.S1G346700.t1"; gene_id "Phchi.S1G346700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8022.t1 is derived from g5197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32521721	32522041	.	+	.	Phchi.S1G518100
Phchi.S1	AUGUSTUS	transcript	32521721	32522041	.	+	.	transcript_id "Phchi.S1G518100.t1"; gene_id "Phchi.S1G518100"
Phchi.S1	AUGUSTUS	start_codon	32521721	32521723	.	+	0	transcript_id "Phchi.S1G518100.t1"; gene_id "Phchi.S1G518100"
Phchi.S1	AUGUSTUS	CDS	32521721	32522041	0.66	+	0	transcript_id "Phchi.S1G518100.t1"; gene_id "Phchi.S1G518100"
Phchi.S1	AUGUSTUS	exon	32521721	32522041	.	+	.	transcript_id "Phchi.S1G518100.t1"; gene_id "Phchi.S1G518100"
Phchi.S1	AUGUSTUS	stop_codon	32522042	32522044	.	+	0	transcript_id "Phchi.S1G518100.t1"; gene_id "Phchi.S1G518100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2229.t1 is derived from g9149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5558918	5561093	.	+	.	Phchi.S5G083800
Phchi.S5	AUGUSTUS	transcript	5558918	5561093	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	start_codon	5558918	5558920	.	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5558918	5558920	0.98	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5558918	5558920	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5558921	5559036	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559037	5559159	1	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559037	5559159	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559160	5559294	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559295	5559461	1	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559295	5559461	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559462	5559591	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559592	5559753	1	+	1	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559592	5559753	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559754	5559904	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559905	5559993	1	+	1	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559905	5559993	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559994	5560092	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560093	5560211	0.99	+	2	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560093	5560211	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560212	5560329	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560330	5560426	1	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560330	5560426	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560427	5560525	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560526	5560656	1	+	2	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560526	5560656	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560657	5560746	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560747	5560920	1	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560747	5560920	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560921	5561015	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5561016	5561093	1	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5561016	5561093	.	+	.	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	stop_codon	5561094	5561096	.	+	0	transcript_id "Phchi.S5G083800.t1"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	transcript	5558918	5561093	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	start_codon	5558918	5558920	.	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5558918	5558920	0.98	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5558918	5558920	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5558921	5559036	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559037	5559159	1	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559037	5559159	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559160	5559294	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559295	5559461	1	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559295	5559461	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559462	5559591	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559592	5559687	0.85	+	1	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559592	5559687	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559688	5559795	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559796	5559810	0.85	+	1	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559796	5559810	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559811	5559904	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5559905	5559993	1	+	1	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5559905	5559993	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5559994	5560092	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560093	5560211	1	+	2	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560093	5560211	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560212	5560329	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560330	5560426	1	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560330	5560426	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560427	5560525	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560526	5560656	1	+	2	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560526	5560656	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560657	5560746	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5560747	5560920	1	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5560747	5560920	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	intron	5560921	5561015	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	CDS	5561016	5561093	1	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	exon	5561016	5561093	.	+	.	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
Phchi.S5	AUGUSTUS	stop_codon	5561094	5561096	.	+	0	transcript_id "Phchi.S5G083800.t2"; gene_id "Phchi.S5G083800"
# This transcript jg2247.t2 is derived from g9167.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2248.t1 is derived from g9168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5654580	5666680	.	-	.	Phchi.S5G085700
Phchi.S5	AUGUSTUS	transcript	5654580	5666680	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	stop_codon	5654577	5654579	.	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5654580	5654810	0.99	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5654580	5654810	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5654811	5654889	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5654890	5654955	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5654890	5654955	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5654956	5655058	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5655059	5655229	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5655059	5655229	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5655230	5655316	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5655317	5655427	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5655317	5655427	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5655428	5655505	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5655506	5655617	0.99	-	1	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5655506	5655617	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5655618	5655722	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5655723	5655781	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5655723	5655781	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5655782	5655873	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5655874	5655948	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5655874	5655948	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5655949	5656021	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5656022	5656120	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5656022	5656120	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5656121	5656202	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5656203	5656535	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5656203	5656535	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5656536	5656613	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5656614	5656721	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5656614	5656721	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5656722	5656846	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5656847	5661790	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5656847	5661790	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5661791	5661877	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5661878	5662264	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5661878	5662264	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5662265	5662341	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5662342	5662677	0.96	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5662342	5662677	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5662678	5662812	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5662813	5662875	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5662813	5662875	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5662876	5662976	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5662977	5663046	0.96	-	1	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5662977	5663046	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5663047	5663117	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5663118	5663353	0.54	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5663118	5663353	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5663354	5663431	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5663432	5663536	0.98	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5663432	5663536	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5663537	5663630	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5663631	5663828	0.97	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5663631	5663828	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5663829	5663911	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5663912	5663977	0.98	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5663912	5663977	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5663978	5664147	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5664148	5664258	0.98	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5664148	5664258	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5664259	5664330	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5664331	5664418	1	-	1	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5664331	5664418	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5664419	5664521	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5664522	5664596	0.97	-	1	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5664522	5664596	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5664597	5664693	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5664694	5664764	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5664694	5664764	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5664765	5664863	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5664864	5664953	1	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5664864	5664953	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5664954	5665041	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5665042	5665248	0.99	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5665042	5665248	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5665249	5665338	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5665339	5665542	0.87	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5665339	5665542	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5665543	5665648	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5665649	5665804	0.93	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5665649	5665804	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5665805	5665921	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5665922	5666175	0.94	-	2	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5665922	5666175	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	intron	5666176	5666286	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	CDS	5666287	5666680	0.65	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	exon	5666287	5666680	.	-	.	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
Phchi.S5	AUGUSTUS	start_codon	5666678	5666680	.	-	0	transcript_id "Phchi.S5G085700.t1"; gene_id "Phchi.S5G085700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6803.t1 is derived from g3975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25134519	25136062	.	-	.	Phchi.S1G396200
Phchi.S1	AUGUSTUS	transcript	25134519	25136062	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	stop_codon	25134516	25134518	.	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25134519	25134617	1	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25134519	25134617	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25134618	25134716	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25134717	25134806	1	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25134717	25134806	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25134807	25134889	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25134890	25134973	1	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25134890	25134973	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25134974	25135048	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25135049	25135208	1	-	1	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25135049	25135208	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25135209	25135300	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25135301	25135368	1	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25135301	25135368	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25135369	25135483	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25135484	25135555	1	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25135484	25135555	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25135556	25135762	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25135763	25135889	0.52	-	1	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25135763	25135889	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	intron	25135890	25135976	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	CDS	25135977	25136062	0.38	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	exon	25135977	25136062	.	-	.	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
Phchi.S1	AUGUSTUS	start_codon	25136060	25136062	.	-	0	transcript_id "Phchi.S1G396200.t1"; gene_id "Phchi.S1G396200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4754.t1 is derived from g1924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12662967	12664350	.	-	.	Phchi.S1G191300
Phchi.S1	AUGUSTUS	transcript	12662967	12664350	.	-	.	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	stop_codon	12662964	12662966	.	-	0	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	CDS	12662967	12663749	0.94	-	0	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	exon	12662967	12663749	.	-	.	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	intron	12663750	12663839	.	-	.	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	CDS	12663840	12664064	1	-	0	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	exon	12663840	12664064	.	-	.	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	intron	12664065	12664185	.	-	.	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	CDS	12664186	12664350	1	-	0	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	exon	12664186	12664350	.	-	.	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
Phchi.S1	AUGUSTUS	start_codon	12664348	12664350	.	-	0	transcript_id "Phchi.S1G191300.t1"; gene_id "Phchi.S1G191300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7609.t1 is derived from g4783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30239718	30240810	.	+	.	Phchi.S1G476800
Phchi.S1	AUGUSTUS	transcript	30239718	30240810	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	start_codon	30239718	30239720	.	+	0	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	CDS	30239718	30239982	0.42	+	0	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	exon	30239718	30239982	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	intron	30239983	30240053	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	CDS	30240054	30240089	0.99	+	2	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	exon	30240054	30240089	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	intron	30240090	30240158	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	CDS	30240159	30240313	1	+	2	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	exon	30240159	30240313	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	intron	30240314	30240398	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	CDS	30240399	30240566	1	+	0	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	exon	30240399	30240566	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	intron	30240567	30240705	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	CDS	30240706	30240810	1	+	0	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	exon	30240706	30240810	.	+	.	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
Phchi.S1	AUGUSTUS	stop_codon	30240811	30240813	.	+	0	transcript_id "Phchi.S1G476800.t1"; gene_id "Phchi.S1G476800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8436.t1 is derived from g5611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35932617	35933984	.	-	.	Phchi.S1G559500
Phchi.S1	AUGUSTUS	transcript	35932617	35933984	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	stop_codon	35932614	35932616	.	-	0	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	CDS	35932617	35933162	0.99	-	0	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	exon	35932617	35933162	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	intron	35933163	35933275	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	CDS	35933276	35933514	1	-	2	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	exon	35933276	35933514	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	intron	35933515	35933614	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	CDS	35933615	35933706	1	-	1	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	exon	35933615	35933706	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	intron	35933707	35933780	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	CDS	35933781	35933834	1	-	1	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	exon	35933781	35933834	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	intron	35933835	35933913	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	CDS	35933914	35933984	1	-	0	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	exon	35933914	35933984	.	-	.	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
Phchi.S1	AUGUSTUS	start_codon	35933982	35933984	.	-	0	transcript_id "Phchi.S1G559500.t1"; gene_id "Phchi.S1G559500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg348.t1 is derived from g10130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2531630	2531967	.	+	.	Phchi.S6G030700
Phchi.S6	AUGUSTUS	transcript	2531630	2531967	.	+	.	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	start_codon	2531630	2531632	.	+	0	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	CDS	2531630	2531831	0.99	+	0	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	exon	2531630	2531831	.	+	.	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	intron	2531832	2531926	.	+	.	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	CDS	2531927	2531967	1	+	2	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	exon	2531927	2531967	.	+	.	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
Phchi.S6	AUGUSTUS	stop_codon	2531968	2531970	.	+	0	transcript_id "Phchi.S6G030700.t1"; gene_id "Phchi.S6G030700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15894.t1 is derived from g14364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22053102	22054162	.	+	.	Phchi.S3G321300
Phchi.S3	AUGUSTUS	transcript	22053102	22054162	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	start_codon	22053102	22053104	.	+	0	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22053102	22053402	0.62	+	0	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22053102	22053402	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	intron	22053403	22053503	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22053504	22053637	0.98	+	2	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22053504	22053637	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	intron	22053638	22053731	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22053732	22054016	1	+	0	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22053732	22054016	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	intron	22054017	22054111	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22054112	22054162	1	+	0	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22054112	22054162	.	+	.	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	stop_codon	22054163	22054165	.	+	0	transcript_id "Phchi.S3G321300.t1"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	transcript	22053102	22054162	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	start_codon	22053102	22053104	.	+	0	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22053102	22053402	0.64	+	0	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22053102	22053402	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	intron	22053403	22053503	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22053504	22053637	0.93	+	2	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22053504	22053637	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	intron	22053638	22053731	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22053732	22054016	1	+	0	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22053732	22054016	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	intron	22054017	22054108	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	CDS	22054109	22054162	0.56	+	0	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	exon	22054109	22054162	.	+	.	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
Phchi.S3	AUGUSTUS	stop_codon	22054163	22054165	.	+	0	transcript_id "Phchi.S3G321300.t2"; gene_id "Phchi.S3G321300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6391.t1 is derived from g3563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22705869	22707782	.	+	.	Phchi.S1G355000
Phchi.S1	AUGUSTUS	transcript	22705869	22707782	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	start_codon	22705869	22705871	.	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22705869	22705973	1	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22705869	22705973	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22705974	22706062	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22706063	22706132	1	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22706063	22706132	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22706133	22706296	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22706297	22706343	1	+	2	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22706297	22706343	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22706344	22706471	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22706472	22706580	1	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22706472	22706580	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22706581	22706700	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22706701	22706786	1	+	2	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22706701	22706786	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22706787	22706915	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22706916	22707006	1	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22706916	22707006	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22707007	22707130	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22707131	22707216	1	+	2	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22707131	22707216	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22707217	22707500	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22707501	22707587	1	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22707501	22707587	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	intron	22707588	22707665	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	CDS	22707666	22707782	1	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	exon	22707666	22707782	.	+	.	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
Phchi.S1	AUGUSTUS	stop_codon	22707783	22707785	.	+	0	transcript_id "Phchi.S1G355000.t1"; gene_id "Phchi.S1G355000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11146.t1 is derived from g15196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4378371	4379558	.	-	.	Phchi.S4G072800
Phchi.S4	AUGUSTUS	transcript	4378371	4379558	.	-	.	transcript_id "Phchi.S4G072800.t1"; gene_id "Phchi.S4G072800"
Phchi.S4	AUGUSTUS	stop_codon	4378368	4378370	.	-	0	transcript_id "Phchi.S4G072800.t1"; gene_id "Phchi.S4G072800"
Phchi.S4	AUGUSTUS	CDS	4378371	4379558	0.87	-	0	transcript_id "Phchi.S4G072800.t1"; gene_id "Phchi.S4G072800"
Phchi.S4	AUGUSTUS	exon	4378371	4379558	.	-	.	transcript_id "Phchi.S4G072800.t1"; gene_id "Phchi.S4G072800"
Phchi.S4	AUGUSTUS	start_codon	4379556	4379558	.	-	0	transcript_id "Phchi.S4G072800.t1"; gene_id "Phchi.S4G072800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14955.t1 is derived from g13423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15707349	15710591	.	-	.	Phchi.S3G227400
Phchi.S3	AUGUSTUS	transcript	15707349	15710591	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	stop_codon	15707346	15707348	.	-	0	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15707349	15708271	1	-	2	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15707349	15708271	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15708272	15708375	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15708376	15708745	1	-	0	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15708376	15708745	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15708746	15708900	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15708901	15708953	1	-	2	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15708901	15708953	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15708954	15709055	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15709056	15709316	1	-	2	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15709056	15709316	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15709317	15709429	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15709430	15709504	0.99	-	2	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15709430	15709504	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15709505	15709675	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15709676	15709924	1	-	2	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15709676	15709924	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15709925	15710023	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15710024	15710246	1	-	0	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15710024	15710246	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	intron	15710247	15710351	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	CDS	15710352	15710591	0.96	-	0	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	exon	15710352	15710591	.	-	.	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
Phchi.S3	AUGUSTUS	start_codon	15710589	15710591	.	-	0	transcript_id "Phchi.S3G227400.t1"; gene_id "Phchi.S3G227400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3278.t1 is derived from g447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2651381	2652935	.	-	.	Phchi.S1G043700
Phchi.S1	AUGUSTUS	transcript	2651381	2652935	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	stop_codon	2651378	2651380	.	-	0	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2651381	2651498	1	-	1	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2651381	2651498	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	intron	2651499	2651591	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2651592	2651639	1	-	1	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2651592	2651639	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	intron	2651640	2651746	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2651747	2651844	1	-	0	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2651747	2651844	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	intron	2651845	2651965	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2651966	2652011	1	-	1	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2651966	2652011	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	intron	2652012	2652106	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2652107	2652234	1	-	0	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2652107	2652234	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	intron	2652235	2652326	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2652327	2652419	1	-	0	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2652327	2652419	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	intron	2652420	2652848	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	CDS	2652849	2652935	0.48	-	0	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	exon	2652849	2652935	.	-	.	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
Phchi.S1	AUGUSTUS	start_codon	2652933	2652935	.	-	0	transcript_id "Phchi.S1G043700.t1"; gene_id "Phchi.S1G043700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14904.t1 is derived from g13372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15452440	15453983	.	-	.	Phchi.S3G222300
Phchi.S3	AUGUSTUS	transcript	15452440	15453983	.	-	.	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	stop_codon	15452437	15452439	.	-	0	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	CDS	15452440	15452503	0.99	-	1	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	exon	15452440	15452503	.	-	.	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	intron	15452504	15452662	.	-	.	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	CDS	15452663	15452721	0.78	-	0	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	exon	15452663	15452721	.	-	.	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	intron	15452722	15452855	.	-	.	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	CDS	15452856	15453983	0.44	-	0	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	exon	15452856	15453983	.	-	.	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
Phchi.S3	AUGUSTUS	start_codon	15453981	15453983	.	-	0	transcript_id "Phchi.S3G222300.t1"; gene_id "Phchi.S3G222300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1794.t1 is derived from g8714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3062852	3063931	.	+	.	Phchi.S5G040300
Phchi.S5	AUGUSTUS	transcript	3062852	3063931	.	+	.	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	start_codon	3062852	3062854	.	+	0	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	CDS	3062852	3063544	0.55	+	0	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	exon	3062852	3063544	.	+	.	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	intron	3063545	3063643	.	+	.	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	CDS	3063644	3063931	0.47	+	0	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	exon	3063644	3063931	.	+	.	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
Phchi.S5	AUGUSTUS	stop_codon	3063932	3063934	.	+	0	transcript_id "Phchi.S5G040300.t1"; gene_id "Phchi.S5G040300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9346.t1 is derived from g6521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41066709	41067767	.	+	.	Phchi.S1G650500
Phchi.S1	AUGUSTUS	transcript	41066709	41067767	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	start_codon	41066709	41066711	.	+	0	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	CDS	41066709	41066739	0.53	+	0	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	exon	41066709	41066739	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	intron	41066740	41066912	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	CDS	41066913	41067007	0.54	+	2	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	exon	41066913	41067007	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	intron	41067008	41067115	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	CDS	41067116	41067141	0.54	+	0	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	exon	41067116	41067141	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	intron	41067142	41067325	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	CDS	41067326	41067452	0.48	+	1	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	exon	41067326	41067452	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	intron	41067453	41067650	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	CDS	41067651	41067767	0.46	+	0	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	exon	41067651	41067767	.	+	.	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
Phchi.S1	AUGUSTUS	stop_codon	41067768	41067770	.	+	0	transcript_id "Phchi.S1G650500.t1"; gene_id "Phchi.S1G650500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11001.t1 is derived from g15051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3587709	3588953	.	-	.	Phchi.S4G058300
Phchi.S4	AUGUSTUS	transcript	3587709	3588953	.	-	.	transcript_id "Phchi.S4G058300.t1"; gene_id "Phchi.S4G058300"
Phchi.S4	AUGUSTUS	stop_codon	3587706	3587708	.	-	0	transcript_id "Phchi.S4G058300.t1"; gene_id "Phchi.S4G058300"
Phchi.S4	AUGUSTUS	CDS	3587709	3588953	0.52	-	0	transcript_id "Phchi.S4G058300.t1"; gene_id "Phchi.S4G058300"
Phchi.S4	AUGUSTUS	exon	3587709	3588953	.	-	.	transcript_id "Phchi.S4G058300.t1"; gene_id "Phchi.S4G058300"
Phchi.S4	AUGUSTUS	start_codon	3588951	3588953	.	-	0	transcript_id "Phchi.S4G058300.t1"; gene_id "Phchi.S4G058300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10194.t1 is derived from g7370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46332223	46332981	.	-	.	Phchi.S1G735300
Phchi.S1	AUGUSTUS	transcript	46332223	46332981	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	stop_codon	46332220	46332222	.	-	0	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	CDS	46332223	46332405	0.72	-	0	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	exon	46332223	46332405	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	intron	46332406	46332500	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	CDS	46332501	46332587	0.73	-	0	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	exon	46332501	46332587	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	intron	46332588	46332669	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	CDS	46332670	46332762	1	-	0	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	exon	46332670	46332762	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	intron	46332763	46332843	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	CDS	46332844	46332981	0.35	-	0	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	exon	46332844	46332981	.	-	.	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
Phchi.S1	AUGUSTUS	start_codon	46332979	46332981	.	-	0	transcript_id "Phchi.S1G735300.t1"; gene_id "Phchi.S1G735300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7642.t1 is derived from g4816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30376710	30378078	.	-	.	Phchi.S1G480100
Phchi.S1	AUGUSTUS	transcript	30376710	30378078	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	stop_codon	30376707	30376709	.	-	0	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	CDS	30376710	30376990	1	-	2	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	exon	30376710	30376990	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	intron	30376991	30377089	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	CDS	30377090	30377315	1	-	0	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	exon	30377090	30377315	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	intron	30377316	30377394	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	CDS	30377395	30377545	1	-	1	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	exon	30377395	30377545	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	intron	30377546	30377654	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	CDS	30377655	30377879	1	-	1	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	exon	30377655	30377879	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	intron	30377880	30378034	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	CDS	30378035	30378078	1	-	0	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	exon	30378035	30378078	.	-	.	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
Phchi.S1	AUGUSTUS	start_codon	30378076	30378078	.	-	0	transcript_id "Phchi.S1G480100.t1"; gene_id "Phchi.S1G480100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10503.t1 is derived from g14552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	740290	740910	.	-	.	Phchi.S4G008500
Phchi.S4	AUGUSTUS	transcript	740290	740910	.	-	.	transcript_id "Phchi.S4G008500.t1"; gene_id "Phchi.S4G008500"
Phchi.S4	AUGUSTUS	stop_codon	740287	740289	.	-	0	transcript_id "Phchi.S4G008500.t1"; gene_id "Phchi.S4G008500"
Phchi.S4	AUGUSTUS	CDS	740290	740910	1	-	0	transcript_id "Phchi.S4G008500.t1"; gene_id "Phchi.S4G008500"
Phchi.S4	AUGUSTUS	exon	740290	740910	.	-	.	transcript_id "Phchi.S4G008500.t1"; gene_id "Phchi.S4G008500"
Phchi.S4	AUGUSTUS	start_codon	740908	740910	.	-	0	transcript_id "Phchi.S4G008500.t1"; gene_id "Phchi.S4G008500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg458.t1 is derived from g10240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3229091	3230493	.	-	.	Phchi.S6G041700
Phchi.S6	AUGUSTUS	transcript	3229091	3230493	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	stop_codon	3229088	3229090	.	-	0	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	CDS	3229091	3229093	1	-	0	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	exon	3229091	3229093	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	intron	3229094	3229185	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	CDS	3229186	3229267	1	-	1	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	exon	3229186	3229267	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	intron	3229268	3229411	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	CDS	3229412	3229530	1	-	0	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	exon	3229412	3229530	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	intron	3229531	3229816	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	CDS	3229817	3229936	1	-	0	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	exon	3229817	3229936	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	intron	3229937	3230076	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	CDS	3230077	3230147	1	-	2	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	exon	3230077	3230147	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	intron	3230148	3230345	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	CDS	3230346	3230493	0.99	-	0	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	exon	3230346	3230493	.	-	.	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
Phchi.S6	AUGUSTUS	start_codon	3230491	3230493	.	-	0	transcript_id "Phchi.S6G041700.t1"; gene_id "Phchi.S6G041700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5447.t1 is derived from g2617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16906928	16908591	.	-	.	Phchi.S1G260600
Phchi.S1	AUGUSTUS	transcript	16906928	16908591	.	-	.	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	stop_codon	16906925	16906927	.	-	0	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	CDS	16906928	16907391	0.9	-	2	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	exon	16906928	16907391	.	-	.	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	intron	16907392	16907555	.	-	.	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	CDS	16907556	16908591	0.54	-	0	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	exon	16907556	16908591	.	-	.	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
Phchi.S1	AUGUSTUS	start_codon	16908589	16908591	.	-	0	transcript_id "Phchi.S1G260600.t1"; gene_id "Phchi.S1G260600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14959.t1 is derived from g13427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15729428	15729935	.	+	.	Phchi.S3G227800
Phchi.S3	AUGUSTUS	transcript	15729428	15729935	.	+	.	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	start_codon	15729428	15729430	.	+	0	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	CDS	15729428	15729731	0.97	+	0	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	exon	15729428	15729731	.	+	.	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	intron	15729732	15729906	.	+	.	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	CDS	15729907	15729935	1	+	2	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	exon	15729907	15729935	.	+	.	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
Phchi.S3	AUGUSTUS	stop_codon	15729936	15729938	.	+	0	transcript_id "Phchi.S3G227800.t1"; gene_id "Phchi.S3G227800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11298.t1 is derived from g15348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5289413	5290963	.	-	.	Phchi.S4G088000
Phchi.S4	AUGUSTUS	transcript	5289413	5290963	.	-	.	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	stop_codon	5289410	5289412	.	-	0	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	CDS	5289413	5290376	0.22	-	1	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	exon	5289413	5290376	.	-	.	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	intron	5290377	5290655	.	-	.	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	CDS	5290656	5290963	0.3	-	0	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	exon	5290656	5290963	.	-	.	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
Phchi.S4	AUGUSTUS	start_codon	5290961	5290963	.	-	0	transcript_id "Phchi.S4G088000.t1"; gene_id "Phchi.S4G088000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4870.t1 is derived from g2040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13175221	13176723	.	+	.	Phchi.S1G202900
Phchi.S1	AUGUSTUS	transcript	13175221	13176723	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	start_codon	13175221	13175223	.	+	0	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	CDS	13175221	13175620	0.98	+	0	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	exon	13175221	13175620	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	intron	13175621	13175696	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	CDS	13175697	13176140	0.99	+	2	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	exon	13175697	13176140	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	intron	13176141	13176238	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	CDS	13176239	13176319	1	+	2	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	exon	13176239	13176319	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	intron	13176320	13176446	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	CDS	13176447	13176522	0.81	+	2	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	exon	13176447	13176522	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	intron	13176523	13176599	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	CDS	13176600	13176723	0.59	+	1	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	exon	13176600	13176723	.	+	.	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
Phchi.S1	AUGUSTUS	stop_codon	13176724	13176726	.	+	0	transcript_id "Phchi.S1G202900.t1"; gene_id "Phchi.S1G202900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8591.t1 is derived from g5766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36783675	36788419	.	-	.	Phchi.S1G575000
Phchi.S1	AUGUSTUS	transcript	36783675	36788419	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	stop_codon	36783672	36783674	.	-	0	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	CDS	36783675	36785326	0.97	-	2	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	exon	36783675	36785326	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	intron	36785327	36785654	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	CDS	36785655	36785790	1	-	0	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	exon	36785655	36785790	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	intron	36785791	36786202	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	CDS	36786203	36787479	0.54	-	2	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	exon	36786203	36787479	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	intron	36787480	36787589	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	CDS	36787590	36787801	0.48	-	1	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	exon	36787590	36787801	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	intron	36787802	36787888	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	CDS	36787889	36788008	0.84	-	1	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	exon	36787889	36788008	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	intron	36788009	36788330	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	CDS	36788331	36788419	0.75	-	0	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	exon	36788331	36788419	.	-	.	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
Phchi.S1	AUGUSTUS	start_codon	36788417	36788419	.	-	0	transcript_id "Phchi.S1G575000.t1"; gene_id "Phchi.S1G575000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4209.t1 is derived from g1378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8913271	8916542	.	-	.	Phchi.S1G136800
Phchi.S1	AUGUSTUS	transcript	8913271	8916542	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	stop_codon	8913268	8913270	.	-	0	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8913271	8914296	1	-	0	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8913271	8914296	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8914297	8914392	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8914393	8914495	1	-	1	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8914393	8914495	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8914496	8914580	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8914581	8914720	1	-	0	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8914581	8914720	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8914721	8914811	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8914812	8914911	1	-	1	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8914812	8914911	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8914912	8915043	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8915044	8915133	1	-	1	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8915044	8915133	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8915134	8915213	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8915214	8915253	1	-	2	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8915214	8915253	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8915254	8915372	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8915373	8915481	1	-	0	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8915373	8915481	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8915482	8915577	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8915578	8915750	1	-	2	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8915578	8915750	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8915751	8915974	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8915975	8916085	0.35	-	2	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8915975	8916085	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8916086	8916184	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8916185	8916249	0.39	-	1	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8916185	8916249	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8916250	8916340	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8916341	8916361	0.95	-	1	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8916341	8916361	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	intron	8916362	8916495	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	CDS	8916496	8916542	0.82	-	0	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	exon	8916496	8916542	.	-	.	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
Phchi.S1	AUGUSTUS	start_codon	8916540	8916542	.	-	0	transcript_id "Phchi.S1G136800.t1"; gene_id "Phchi.S1G136800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10256.t1 is derived from g7432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46705956	46711113	.	-	.	Phchi.S1G741500
Phchi.S1	AUGUSTUS	transcript	46705956	46711113	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	stop_codon	46705953	46705955	.	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46705956	46706438	1	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46705956	46706438	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46706439	46706534	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46706535	46706863	0.59	-	2	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46706535	46706863	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46706864	46707058	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46707059	46708453	0.67	-	2	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46707059	46708453	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46708454	46708542	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46708543	46708981	0.8	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46708543	46708981	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46708982	46709052	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46709053	46709240	0.69	-	2	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46709053	46709240	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46709241	46709371	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46709372	46709477	0.65	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46709372	46709477	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46709478	46709647	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46709648	46709833	1	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46709648	46709833	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46709834	46709960	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46709961	46710173	1	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46709961	46710173	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46710174	46710335	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46710336	46710446	1	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46710336	46710446	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46710447	46710573	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46710574	46710660	1	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46710574	46710660	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	intron	46710661	46710873	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	CDS	46710874	46711113	0.77	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	exon	46710874	46711113	.	-	.	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
Phchi.S1	AUGUSTUS	start_codon	46711111	46711113	.	-	0	transcript_id "Phchi.S1G741500.t1"; gene_id "Phchi.S1G741500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5108.t1 is derived from g2278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14775950	14776661	.	-	.	Phchi.S1G226700
Phchi.S1	AUGUSTUS	transcript	14775950	14776661	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	stop_codon	14775947	14775949	.	-	0	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	CDS	14775950	14776106	1	-	1	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	exon	14775950	14776106	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	intron	14776107	14776195	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	CDS	14776196	14776252	1	-	1	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	exon	14776196	14776252	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	intron	14776253	14776336	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	CDS	14776337	14776395	1	-	0	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	exon	14776337	14776395	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	intron	14776396	14776475	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	CDS	14776476	14776661	0.78	-	0	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	exon	14776476	14776661	.	-	.	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
Phchi.S1	AUGUSTUS	start_codon	14776659	14776661	.	-	0	transcript_id "Phchi.S1G226700.t1"; gene_id "Phchi.S1G226700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11628.t1 is derived from g15679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7381393	7384015	.	-	.	Phchi.S4G121000
Phchi.S4	AUGUSTUS	transcript	7381393	7384015	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	stop_codon	7381390	7381392	.	-	0	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7381393	7381598	1	-	2	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7381393	7381598	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	intron	7381599	7381680	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7381681	7381885	1	-	0	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7381681	7381885	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	intron	7381886	7381964	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7381965	7382329	0.85	-	2	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7381965	7382329	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	intron	7382330	7382492	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7382493	7382633	0.85	-	2	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7382493	7382633	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	intron	7382634	7382731	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7382732	7383638	0.88	-	0	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7382732	7383638	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	intron	7383639	7383772	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7383773	7383807	0.93	-	2	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7383773	7383807	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	intron	7383808	7383918	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	CDS	7383919	7384015	0.91	-	0	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	exon	7383919	7384015	.	-	.	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
Phchi.S4	AUGUSTUS	start_codon	7384013	7384015	.	-	0	transcript_id "Phchi.S4G121000.t1"; gene_id "Phchi.S4G121000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14396.t1 is derived from g12864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12599542	12602066	.	-	.	Phchi.S3G171500
Phchi.S3	AUGUSTUS	transcript	12599542	12602066	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	stop_codon	12599539	12599541	.	-	0	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	CDS	12599542	12599943	0.97	-	0	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	exon	12599542	12599943	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	intron	12599944	12600036	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	CDS	12600037	12600564	1	-	0	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	exon	12600037	12600564	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	intron	12600565	12600646	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	CDS	12600647	12600848	1	-	1	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	exon	12600647	12600848	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	intron	12600849	12600952	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	CDS	12600953	12601161	1	-	0	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	exon	12600953	12601161	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	intron	12601162	12601356	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	CDS	12601357	12601652	1	-	2	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	exon	12601357	12601652	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	intron	12601653	12601744	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	CDS	12601745	12602066	0.95	-	0	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	exon	12601745	12602066	.	-	.	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
Phchi.S3	AUGUSTUS	start_codon	12602064	12602066	.	-	0	transcript_id "Phchi.S3G171500.t1"; gene_id "Phchi.S3G171500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11881.t1 is derived from g15933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8960301	8962128	.	-	.	Phchi.S4G146300
Phchi.S4	AUGUSTUS	transcript	8960301	8962128	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	stop_codon	8960298	8960300	.	-	0	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	CDS	8960301	8960729	0.73	-	0	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	exon	8960301	8960729	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	intron	8960730	8960804	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	CDS	8960805	8961050	0.58	-	0	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	exon	8960805	8961050	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	intron	8961051	8961160	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	CDS	8961161	8961894	0.68	-	2	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	exon	8961161	8961894	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	intron	8961895	8962010	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	CDS	8962011	8962128	0.78	-	0	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	exon	8962011	8962128	.	-	.	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
Phchi.S4	AUGUSTUS	start_codon	8962126	8962128	.	-	0	transcript_id "Phchi.S4G146300.t1"; gene_id "Phchi.S4G146300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6551.t1 is derived from g3723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23670208	23670684	.	-	.	Phchi.S1G371000
Phchi.S1	AUGUSTUS	transcript	23670208	23670684	.	-	.	transcript_id "Phchi.S1G371000.t1"; gene_id "Phchi.S1G371000"
Phchi.S1	AUGUSTUS	stop_codon	23670205	23670207	.	-	0	transcript_id "Phchi.S1G371000.t1"; gene_id "Phchi.S1G371000"
Phchi.S1	AUGUSTUS	CDS	23670208	23670684	1	-	0	transcript_id "Phchi.S1G371000.t1"; gene_id "Phchi.S1G371000"
Phchi.S1	AUGUSTUS	exon	23670208	23670684	.	-	.	transcript_id "Phchi.S1G371000.t1"; gene_id "Phchi.S1G371000"
Phchi.S1	AUGUSTUS	start_codon	23670682	23670684	.	-	0	transcript_id "Phchi.S1G371000.t1"; gene_id "Phchi.S1G371000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg10388.t1 is derived from g7564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47501335	47505396	.	+	.	Phchi.S1G754700
Phchi.S1	AUGUSTUS	transcript	47501391	47505396	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	start_codon	47501391	47501393	.	+	0	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501391	47501442	0.67	+	0	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501391	47501442	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501443	47501614	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501615	47501694	0.98	+	2	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501615	47501694	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501695	47501787	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501788	47501891	1	+	0	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501788	47501891	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501892	47502043	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502044	47502053	0.82	+	1	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502044	47502053	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502054	47502348	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502349	47502922	0.48	+	0	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502349	47502922	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502923	47503195	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503196	47503327	0.45	+	2	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503196	47503327	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503328	47503513	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503514	47503630	0.25	+	2	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503514	47503630	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503631	47503723	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503724	47504117	0.47	+	2	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503724	47504117	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504118	47504408	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504409	47504542	0.52	+	1	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504409	47504542	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504543	47504627	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504628	47504686	0.93	+	2	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504628	47504686	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504687	47504838	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504839	47505396	0.96	+	0	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504839	47505396	.	+	.	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	stop_codon	47505397	47505399	.	+	0	transcript_id "Phchi.S1G754700.t1"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	transcript	47501335	47505396	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	start_codon	47501335	47501337	.	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501335	47501442	0.52	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501335	47501442	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501443	47501619	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501620	47501694	1	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501620	47501694	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501695	47501787	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501788	47501891	1	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501788	47501891	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501892	47502043	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502044	47502053	0.8	+	1	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502044	47502053	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502054	47502348	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502349	47502922	0.4	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502349	47502922	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502923	47503195	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503196	47503327	0.42	+	2	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503196	47503327	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503328	47503513	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503514	47503630	0.24	+	2	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503514	47503630	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503631	47503723	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503724	47504117	0.47	+	2	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503724	47504117	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504118	47504408	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504409	47504542	0.59	+	1	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504409	47504542	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504543	47504627	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504628	47504686	0.97	+	2	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504628	47504686	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504687	47504838	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504839	47505396	0.97	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504839	47505396	.	+	.	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	stop_codon	47505397	47505399	.	+	0	transcript_id "Phchi.S1G754700.t2"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	transcript	47501335	47505396	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	start_codon	47501335	47501337	.	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501335	47501442	0.4	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501335	47501442	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501443	47501619	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501620	47501694	1	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501620	47501694	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501695	47501781	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501782	47501891	1	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501782	47501891	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501892	47502043	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502044	47502053	0.81	+	1	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502044	47502053	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502054	47502348	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502349	47502922	0.42	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502349	47502922	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502923	47503195	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503196	47503327	0.36	+	2	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503196	47503327	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503328	47503513	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503514	47503630	0.11	+	2	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503514	47503630	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503631	47503723	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503724	47504117	0.44	+	2	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503724	47504117	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504118	47504408	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504409	47504542	0.59	+	1	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504409	47504542	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504543	47504627	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504628	47504686	0.93	+	2	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504628	47504686	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504687	47504838	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504839	47505396	0.96	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504839	47505396	.	+	.	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	stop_codon	47505397	47505399	.	+	0	transcript_id "Phchi.S1G754700.t3"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	transcript	47501335	47505396	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	start_codon	47501335	47501337	.	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501335	47501442	0.5	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501335	47501442	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501443	47501619	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501620	47501694	1	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501620	47501694	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501695	47501787	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47501788	47501891	0.97	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47501788	47501891	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47501892	47502035	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502036	47502073	0.65	+	1	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502036	47502073	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502074	47502227	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502228	47502253	0.6	+	2	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502228	47502253	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502254	47502348	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47502349	47502922	0.48	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47502349	47502922	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47502923	47503195	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503196	47503327	0.38	+	2	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503196	47503327	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503328	47503513	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503514	47503630	0.12	+	2	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503514	47503630	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47503631	47503723	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47503724	47504117	0.43	+	2	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47503724	47504117	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504118	47504408	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504409	47504542	0.51	+	1	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504409	47504542	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504543	47504627	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504628	47504686	0.96	+	2	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504628	47504686	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	intron	47504687	47504838	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	CDS	47504839	47505396	0.96	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	exon	47504839	47505396	.	+	.	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
Phchi.S1	AUGUSTUS	stop_codon	47505397	47505399	.	+	0	transcript_id "Phchi.S1G754700.t4"; gene_id "Phchi.S1G754700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5661.t1 is derived from g2831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18176149	18177358	.	-	.	Phchi.S1G282000
Phchi.S1	AUGUSTUS	transcript	18176149	18177358	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	stop_codon	18176146	18176148	.	-	0	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	CDS	18176149	18176243	0.87	-	2	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	exon	18176149	18176243	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	intron	18176244	18176315	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	CDS	18176316	18176424	1	-	0	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	exon	18176316	18176424	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	intron	18176425	18176497	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	CDS	18176498	18176570	1	-	1	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	exon	18176498	18176570	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	intron	18176571	18176650	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	CDS	18176651	18176737	1	-	1	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	exon	18176651	18176737	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	intron	18176738	18176841	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	CDS	18176842	18177026	1	-	0	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	exon	18176842	18177026	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	intron	18177027	18177118	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	CDS	18177119	18177358	0.89	-	0	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	exon	18177119	18177358	.	-	.	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
Phchi.S1	AUGUSTUS	start_codon	18177356	18177358	.	-	0	transcript_id "Phchi.S1G282000.t1"; gene_id "Phchi.S1G282000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7132.t1 is derived from g4304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27098495	27102799	.	-	.	Phchi.S1G429100
Phchi.S1	AUGUSTUS	transcript	27098495	27102799	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	stop_codon	27098492	27098494	.	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27098495	27098557	0.71	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27098495	27098557	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27098558	27099119	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27099120	27099335	0.89	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27099120	27099335	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27099336	27099809	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27099810	27099955	1	-	2	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27099810	27099955	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27099956	27100278	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27100279	27100342	1	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27100279	27100342	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27100343	27100474	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27100475	27100548	1	-	2	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27100475	27100548	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27100549	27100672	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27100673	27100799	1	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27100673	27100799	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27100800	27100876	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27100877	27100961	1	-	1	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27100877	27100961	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27100962	27101041	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27101042	27101105	1	-	2	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27101042	27101105	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27101106	27101202	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27101203	27101264	1	-	1	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27101203	27101264	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27101265	27101378	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27101379	27101449	1	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27101379	27101449	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27101450	27101605	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27101606	27101701	1	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27101606	27101701	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27101702	27101860	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27101861	27102009	1	-	2	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27101861	27102009	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27102010	27102117	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27102118	27102187	1	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27102118	27102187	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27102188	27102479	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27102480	27102520	1	-	2	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27102480	27102520	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	intron	27102521	27102723	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	CDS	27102724	27102799	1	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	exon	27102724	27102799	.	-	.	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
Phchi.S1	AUGUSTUS	start_codon	27102797	27102799	.	-	0	transcript_id "Phchi.S1G429100.t1"; gene_id "Phchi.S1G429100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10159.t1 is derived from g7335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46040225	46041983	.	-	.	Phchi.S1G731800
Phchi.S1	AUGUSTUS	transcript	46040225	46041983	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	stop_codon	46040222	46040224	.	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46040225	46040305	1	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46040225	46040305	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	intron	46040306	46040414	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46040415	46040468	1	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46040415	46040468	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	intron	46040469	46040567	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46040568	46040623	1	-	2	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46040568	46040623	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	intron	46040624	46040737	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46040738	46040804	1	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46040738	46040804	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	intron	46040805	46040957	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46040958	46041015	1	-	1	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46040958	46041015	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	intron	46041016	46041125	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46041126	46041181	0.94	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46041126	46041181	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	intron	46041182	46041299	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	CDS	46041300	46041983	0.96	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	exon	46041300	46041983	.	-	.	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
Phchi.S1	AUGUSTUS	start_codon	46041981	46041983	.	-	0	transcript_id "Phchi.S1G731800.t1"; gene_id "Phchi.S1G731800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15876.t1 is derived from g14346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22004502	22007594	.	+	.	Phchi.S3G319500
Phchi.S3	AUGUSTUS	transcript	22004502	22007594	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	start_codon	22004502	22004504	.	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22004502	22004608	1	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22004502	22004608	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22004609	22004803	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22004804	22004882	0.59	+	1	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22004804	22004882	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22004883	22004992	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22004993	22005131	0.62	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22004993	22005131	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22005132	22005215	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22005216	22005282	1	+	2	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22005216	22005282	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22005283	22005440	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22005441	22006282	0.98	+	1	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22005441	22006282	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22006283	22006443	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22006444	22006676	0.47	+	2	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22006444	22006676	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22006677	22006789	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22006790	22006861	0.98	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22006790	22006861	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22006862	22006992	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22006993	22007214	1	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22006993	22007214	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22007215	22007291	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22007292	22007324	0.54	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22007292	22007324	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22007325	22007419	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22007420	22007440	0.49	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22007420	22007440	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	intron	22007441	22007582	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	CDS	22007583	22007594	0.49	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	exon	22007583	22007594	.	+	.	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
Phchi.S3	AUGUSTUS	stop_codon	22007595	22007597	.	+	0	transcript_id "Phchi.S3G319500.t1"; gene_id "Phchi.S3G319500"
# This transcript jg656.t2 is derived from g10438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg656.t3 is derived from g10438.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg657.t1 is derived from g10439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4615591	4616793	.	+	.	Phchi.S6G061600
Phchi.S6	AUGUSTUS	transcript	4615591	4616793	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	start_codon	4615591	4615593	.	+	0	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	CDS	4615591	4615687	0.85	+	0	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	exon	4615591	4615687	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	intron	4615688	4615830	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	CDS	4615831	4616204	0.77	+	2	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	exon	4615831	4616204	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	intron	4616205	4616333	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	CDS	4616334	4616449	0.51	+	0	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	exon	4616334	4616449	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	intron	4616450	4616552	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	CDS	4616553	4616625	0.6	+	1	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	exon	4616553	4616625	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	intron	4616626	4616763	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	CDS	4616764	4616793	0.6	+	0	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	exon	4616764	4616793	.	+	.	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
Phchi.S6	AUGUSTUS	stop_codon	4616794	4616796	.	+	0	transcript_id "Phchi.S6G061600.t1"; gene_id "Phchi.S6G061600"
# This transcript jg12900.t2 is derived from g11365.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12900.t3 is derived from g11365.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12900.t4 is derived from g11365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12901.t1 is derived from g11366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3075393	3077043	.	-	.	Phchi.S3G022000
Phchi.S3	AUGUSTUS	transcript	3075393	3077043	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	stop_codon	3075390	3075392	.	-	0	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3075393	3075492	1	-	1	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3075393	3075492	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3075493	3075614	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3075615	3075628	1	-	0	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3075615	3075628	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3075629	3075741	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3075742	3075895	0.95	-	1	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3075742	3075895	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3075896	3076004	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3076005	3076058	1	-	1	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3076005	3076058	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3076059	3076169	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3076170	3076255	0.86	-	0	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3076170	3076255	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3076256	3076332	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3076333	3076451	1	-	2	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3076333	3076451	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3076452	3076529	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3076530	3076606	1	-	1	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3076530	3076606	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3076607	3076713	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3076714	3076807	1	-	2	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3076714	3076807	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	intron	3076808	3076883	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	CDS	3076884	3077043	1	-	0	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	exon	3076884	3077043	.	-	.	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
Phchi.S3	AUGUSTUS	start_codon	3077041	3077043	.	-	0	transcript_id "Phchi.S3G022000.t1"; gene_id "Phchi.S3G022000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1925.t1 is derived from g8845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3872282	3875291	.	-	.	Phchi.S5G053400
Phchi.S5	AUGUSTUS	transcript	3872282	3875291	.	-	.	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	stop_codon	3872279	3872281	.	-	0	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	CDS	3872282	3873937	0.85	-	0	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	exon	3872282	3873937	.	-	.	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	intron	3873938	3874079	.	-	.	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	CDS	3874080	3874830	0.87	-	1	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	exon	3874080	3874830	.	-	.	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	intron	3874831	3874932	.	-	.	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	CDS	3874933	3875291	0.93	-	0	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	exon	3874933	3875291	.	-	.	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
Phchi.S5	AUGUSTUS	start_codon	3875289	3875291	.	-	0	transcript_id "Phchi.S5G053400.t1"; gene_id "Phchi.S5G053400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2643.t1 is derived from g9563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7922939	7927239	.	-	.	Phchi.S5G125200
Phchi.S5	AUGUSTUS	transcript	7922939	7927239	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	stop_codon	7922936	7922938	.	-	0	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	CDS	7922939	7922986	0.93	-	0	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	exon	7922939	7922986	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	intron	7922987	7923071	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	CDS	7923072	7923083	0.93	-	0	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	exon	7923072	7923083	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	intron	7923084	7923139	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	CDS	7923140	7923146	0.93	-	1	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	exon	7923140	7923146	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	intron	7923147	7923289	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	CDS	7923290	7923370	0.44	-	1	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	exon	7923290	7923370	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	intron	7923371	7923608	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	CDS	7923609	7925219	0.37	-	1	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	exon	7923609	7925219	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	intron	7925220	7925320	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	CDS	7925321	7927239	0.89	-	0	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	exon	7925321	7927239	.	-	.	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
Phchi.S5	AUGUSTUS	start_codon	7927237	7927239	.	-	0	transcript_id "Phchi.S5G125200.t1"; gene_id "Phchi.S5G125200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11254.t1 is derived from g15304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5019250	5022698	.	+	.	Phchi.S4G083600
Phchi.S4	AUGUSTUS	transcript	5019250	5022698	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	start_codon	5019250	5019252	.	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5019250	5019534	0.96	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5019250	5019534	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	intron	5019535	5019685	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5019686	5020240	0.99	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5019686	5020240	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	intron	5020241	5020345	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5020346	5021014	0.99	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5020346	5021014	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	intron	5021015	5021107	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5021108	5021212	1	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5021108	5021212	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	intron	5021213	5021326	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5021327	5021590	1	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5021327	5021590	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	intron	5021591	5021682	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5021683	5022103	0.46	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5021683	5022103	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	intron	5022104	5022252	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	CDS	5022253	5022698	0.79	+	2	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	exon	5022253	5022698	.	+	.	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
Phchi.S4	AUGUSTUS	stop_codon	5022699	5022701	.	+	0	transcript_id "Phchi.S4G083600.t1"; gene_id "Phchi.S4G083600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12411.t1 is derived from g8088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18480738	18481010	.	+	.	Phchi.S2G049100
Phchi.S2	AUGUSTUS	transcript	18480738	18481010	.	+	.	transcript_id "Phchi.S2G049100.t1"; gene_id "Phchi.S2G049100"
Phchi.S2	AUGUSTUS	start_codon	18480738	18480740	.	+	0	transcript_id "Phchi.S2G049100.t1"; gene_id "Phchi.S2G049100"
Phchi.S2	AUGUSTUS	CDS	18480738	18481010	0.69	+	0	transcript_id "Phchi.S2G049100.t1"; gene_id "Phchi.S2G049100"
Phchi.S2	AUGUSTUS	exon	18480738	18481010	.	+	.	transcript_id "Phchi.S2G049100.t1"; gene_id "Phchi.S2G049100"
Phchi.S2	AUGUSTUS	stop_codon	18481011	18481013	.	+	0	transcript_id "Phchi.S2G049100.t1"; gene_id "Phchi.S2G049100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13951.t1 is derived from g12418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9884564	9885892	.	+	.	Phchi.S3G127000
Phchi.S3	AUGUSTUS	transcript	9884564	9885892	.	+	.	transcript_id "Phchi.S3G127000.t1"; gene_id "Phchi.S3G127000"
Phchi.S3	AUGUSTUS	start_codon	9884564	9884566	.	+	0	transcript_id "Phchi.S3G127000.t1"; gene_id "Phchi.S3G127000"
Phchi.S3	AUGUSTUS	CDS	9884564	9885892	0.64	+	0	transcript_id "Phchi.S3G127000.t1"; gene_id "Phchi.S3G127000"
Phchi.S3	AUGUSTUS	exon	9884564	9885892	.	+	.	transcript_id "Phchi.S3G127000.t1"; gene_id "Phchi.S3G127000"
Phchi.S3	AUGUSTUS	stop_codon	9885893	9885895	.	+	0	transcript_id "Phchi.S3G127000.t1"; gene_id "Phchi.S3G127000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13288.t1 is derived from g11754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5190404	5191895	.	+	.	Phchi.S3G060700
Phchi.S3	AUGUSTUS	transcript	5190404	5191895	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	start_codon	5190404	5190406	.	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5190404	5190454	1	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5190404	5190454	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	intron	5190455	5190657	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5190658	5190771	1	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5190658	5190771	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	intron	5190772	5190979	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5190980	5191093	1	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5190980	5191093	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	intron	5191094	5191192	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5191193	5191362	1	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5191193	5191362	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	intron	5191363	5191461	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5191462	5191552	1	+	1	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5191462	5191552	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	intron	5191553	5191638	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5191639	5191704	1	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5191639	5191704	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	intron	5191705	5191790	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	CDS	5191791	5191895	1	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	exon	5191791	5191895	.	+	.	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
Phchi.S3	AUGUSTUS	stop_codon	5191896	5191898	.	+	0	transcript_id "Phchi.S3G060700.t1"; gene_id "Phchi.S3G060700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13988.t1 is derived from g12455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10129243	10130430	.	-	.	Phchi.S3G130700
Phchi.S3	AUGUSTUS	transcript	10129243	10130430	.	-	.	transcript_id "Phchi.S3G130700.t1"; gene_id "Phchi.S3G130700"
Phchi.S3	AUGUSTUS	stop_codon	10129240	10129242	.	-	0	transcript_id "Phchi.S3G130700.t1"; gene_id "Phchi.S3G130700"
Phchi.S3	AUGUSTUS	CDS	10129243	10130430	0.58	-	0	transcript_id "Phchi.S3G130700.t1"; gene_id "Phchi.S3G130700"
Phchi.S3	AUGUSTUS	exon	10129243	10130430	.	-	.	transcript_id "Phchi.S3G130700.t1"; gene_id "Phchi.S3G130700"
Phchi.S3	AUGUSTUS	start_codon	10130428	10130430	.	-	0	transcript_id "Phchi.S3G130700.t1"; gene_id "Phchi.S3G130700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6248.t1 is derived from g3420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21864421	21866401	.	+	.	Phchi.S1G340700
Phchi.S1	AUGUSTUS	transcript	21864421	21866401	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	start_codon	21864421	21864423	.	+	0	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	CDS	21864421	21865463	0.94	+	0	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	exon	21864421	21865463	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	intron	21865464	21865586	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	CDS	21865587	21865794	1	+	1	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	exon	21865587	21865794	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	intron	21865795	21865888	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	CDS	21865889	21866075	0.85	+	0	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	exon	21865889	21866075	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	intron	21866076	21866195	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	CDS	21866196	21866231	0.9	+	2	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	exon	21866196	21866231	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	intron	21866232	21866351	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	CDS	21866352	21866401	0.9	+	2	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	exon	21866352	21866401	.	+	.	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
Phchi.S1	AUGUSTUS	stop_codon	21866402	21866404	.	+	0	transcript_id "Phchi.S1G340700.t1"; gene_id "Phchi.S1G340700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7163.t1 is derived from g4335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27344570	27346703	.	-	.	Phchi.S1G432200
Phchi.S1	AUGUSTUS	transcript	27344570	27346703	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	stop_codon	27344567	27344569	.	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27344570	27344716	0.74	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27344570	27344716	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27344717	27344808	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27344809	27344950	1	-	1	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27344809	27344950	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27344951	27345050	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27345051	27345199	1	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27345051	27345199	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27345200	27345279	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27345280	27345411	1	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27345280	27345411	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27345412	27345530	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27345531	27345668	1	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27345531	27345668	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27345669	27345755	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27345756	27345838	1	-	2	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27345756	27345838	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27345839	27345982	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27345983	27346073	1	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27345983	27346073	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	intron	27346074	27346412	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	CDS	27346413	27346703	0.92	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	exon	27346413	27346703	.	-	.	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
Phchi.S1	AUGUSTUS	start_codon	27346701	27346703	.	-	0	transcript_id "Phchi.S1G432200.t1"; gene_id "Phchi.S1G432200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13357.t1 is derived from g11823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6305430	6308049	.	+	.	Phchi.S3G067600
Phchi.S3	AUGUSTUS	transcript	6305430	6308049	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	start_codon	6305430	6305432	.	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6305430	6305522	0.29	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6305430	6305522	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6305523	6305608	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6305609	6305671	1	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6305609	6305671	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6305672	6305748	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6305749	6305839	1	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6305749	6305839	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6305840	6305927	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6305928	6306095	1	+	2	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6305928	6306095	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6306096	6306235	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6306236	6306312	0.99	+	2	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6306236	6306312	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6306313	6306413	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6306414	6306515	0.99	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6306414	6306515	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6306516	6306608	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6306609	6306683	1	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6306609	6306683	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6306684	6306771	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6306772	6306863	0.99	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6306772	6306863	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6306864	6306971	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6306972	6307020	0.99	+	1	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6306972	6307020	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6307021	6307145	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6307146	6307259	1	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6307146	6307259	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6307260	6307348	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6307349	6307435	1	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6307349	6307435	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6307436	6307539	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6307540	6307639	0.42	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6307540	6307639	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6307640	6307743	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6307744	6307871	0.73	+	2	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6307744	6307871	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	intron	6307872	6307959	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	CDS	6307960	6308049	0.94	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	exon	6307960	6308049	.	+	.	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
Phchi.S3	AUGUSTUS	stop_codon	6308050	6308052	.	+	0	transcript_id "Phchi.S3G067600.t1"; gene_id "Phchi.S3G067600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9242.t1 is derived from g6417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40563639	40566647	.	-	.	Phchi.S1G640100
Phchi.S1	AUGUSTUS	transcript	40563639	40566647	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	stop_codon	40563636	40563638	.	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40563639	40563643	1	-	2	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40563639	40563643	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40563644	40563771	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40563772	40563937	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40563772	40563937	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40563938	40564031	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40564032	40564185	1	-	1	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40564032	40564185	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40564186	40564284	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40564285	40564433	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40564285	40564433	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40564434	40564522	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40564523	40564630	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40564523	40564630	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40564631	40564749	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40564750	40564857	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40564750	40564857	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40564858	40564963	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40564964	40565101	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40564964	40565101	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40565102	40565198	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40565199	40565372	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40565199	40565372	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40565373	40565491	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40565492	40565605	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40565492	40565605	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40565606	40565705	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40565706	40565813	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40565706	40565813	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40565814	40565892	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40565893	40566015	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40565893	40566015	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40566016	40566122	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40566123	40566167	1	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40566123	40566167	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	intron	40566168	40566521	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	CDS	40566522	40566647	0.45	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	exon	40566522	40566647	.	-	.	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
Phchi.S1	AUGUSTUS	start_codon	40566645	40566647	.	-	0	transcript_id "Phchi.S1G640100.t1"; gene_id "Phchi.S1G640100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6932.t1 is derived from g4104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26040551	26044306	.	+	.	Phchi.S1G409100
Phchi.S1	AUGUSTUS	transcript	26040551	26044306	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	start_codon	26040551	26040553	.	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26040551	26040571	0.51	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26040551	26040571	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26040572	26040759	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26040760	26040866	0.49	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26040760	26040866	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26040867	26040956	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26040957	26041043	0.26	+	1	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26040957	26041043	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26041044	26041378	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26041379	26041436	0.32	+	1	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26041379	26041436	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26041437	26041549	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26041550	26042142	0.53	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26041550	26042142	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26042143	26042273	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26042274	26042325	0.99	+	1	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26042274	26042325	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26042326	26042459	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26042460	26042726	1	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26042460	26042726	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26042727	26042830	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26042831	26042977	0.75	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26042831	26042977	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26042978	26043049	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26043050	26043397	1	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26043050	26043397	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26043398	26043510	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26043511	26043798	1	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26043511	26043798	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	intron	26043799	26044075	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	CDS	26044076	26044306	0.99	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	exon	26044076	26044306	.	+	.	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
Phchi.S1	AUGUSTUS	stop_codon	26044307	26044309	.	+	0	transcript_id "Phchi.S1G409100.t1"; gene_id "Phchi.S1G409100"
# This transcript jg806.t1 is derived from g10588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5683749	5687763	.	-	.	Phchi.S6G076500
Phchi.S6	AUGUSTUS	transcript	5683749	5687763	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	stop_codon	5683746	5683748	.	-	0	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5683749	5683828	0.96	-	2	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5683749	5683828	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5683829	5684022	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5684023	5684091	0.98	-	2	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5684023	5684091	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5684092	5684235	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5684236	5684301	0.98	-	2	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5684236	5684301	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5684302	5684497	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5684498	5684540	0.83	-	0	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5684498	5684540	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5684541	5684611	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5684612	5684680	0.79	-	0	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5684612	5684680	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5684681	5684839	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5684840	5684846	0.85	-	1	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5684840	5684846	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5684847	5684948	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5684949	5686238	0.83	-	1	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5684949	5686238	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5686239	5686328	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5686329	5686369	0.93	-	0	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5686329	5686369	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	intron	5686370	5686479	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	CDS	5686480	5687763	0.66	-	0	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	exon	5686480	5687763	.	-	.	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
Phchi.S6	AUGUSTUS	start_codon	5687761	5687763	.	-	0	transcript_id "Phchi.S6G076500.t1"; gene_id "Phchi.S6G076500"
# This transcript jg1950.t2 is derived from g8870.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1951.t1 is derived from g8871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3965211	3967975	.	-	.	Phchi.S5G056000
Phchi.S5	AUGUSTUS	transcript	3965211	3967975	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	stop_codon	3965208	3965210	.	-	0	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	CDS	3965211	3965276	1	-	0	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	exon	3965211	3965276	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	intron	3965277	3965696	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	CDS	3965697	3965878	1	-	2	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	exon	3965697	3965878	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	intron	3965879	3966025	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	CDS	3966026	3966093	1	-	1	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	exon	3966026	3966093	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	intron	3966094	3966371	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	CDS	3966372	3967975	0.61	-	0	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	exon	3966372	3967975	.	-	.	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
Phchi.S5	AUGUSTUS	start_codon	3967973	3967975	.	-	0	transcript_id "Phchi.S5G056000.t1"; gene_id "Phchi.S5G056000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11600.t1 is derived from g15651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7280882	7282670	.	-	.	Phchi.S4G118200
Phchi.S4	AUGUSTUS	transcript	7280882	7282670	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	stop_codon	7280879	7280881	.	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7280882	7280923	1	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7280882	7280923	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7280924	7281003	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7281004	7281217	1	-	1	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7281004	7281217	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7281218	7281302	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7281303	7281437	1	-	1	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7281303	7281437	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7281438	7281515	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7281516	7281598	1	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7281516	7281598	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7281599	7281677	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7281678	7281749	1	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7281678	7281749	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7281750	7281835	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7281836	7281904	1	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7281836	7281904	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7281905	7281989	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7281990	7282127	1	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7281990	7282127	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	intron	7282128	7282217	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	CDS	7282218	7282670	1	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	exon	7282218	7282670	.	-	.	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
Phchi.S4	AUGUSTUS	start_codon	7282668	7282670	.	-	0	transcript_id "Phchi.S4G118200.t1"; gene_id "Phchi.S4G118200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9827.t1 is derived from g7003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43991367	43991690	.	-	.	Phchi.S1G698600
Phchi.S1	AUGUSTUS	transcript	43991367	43991690	.	-	.	transcript_id "Phchi.S1G698600.t1"; gene_id "Phchi.S1G698600"
Phchi.S1	AUGUSTUS	stop_codon	43991364	43991366	.	-	0	transcript_id "Phchi.S1G698600.t1"; gene_id "Phchi.S1G698600"
Phchi.S1	AUGUSTUS	CDS	43991367	43991690	0.81	-	0	transcript_id "Phchi.S1G698600.t1"; gene_id "Phchi.S1G698600"
Phchi.S1	AUGUSTUS	exon	43991367	43991690	.	-	.	transcript_id "Phchi.S1G698600.t1"; gene_id "Phchi.S1G698600"
Phchi.S1	AUGUSTUS	start_codon	43991688	43991690	.	-	0	transcript_id "Phchi.S1G698600.t1"; gene_id "Phchi.S1G698600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10507.t1 is derived from g14556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	754204	755300	.	+	.	Phchi.S4G008900
Phchi.S4	AUGUSTUS	transcript	754204	755300	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	start_codon	754204	754206	.	+	0	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	CDS	754204	754434	0.91	+	0	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	exon	754204	754434	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	intron	754435	754515	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	CDS	754516	754599	0.97	+	0	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	exon	754516	754599	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	intron	754600	754687	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	CDS	754688	754777	1	+	0	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	exon	754688	754777	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	intron	754778	754875	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	CDS	754876	754943	1	+	0	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	exon	754876	754943	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	intron	754944	755029	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	CDS	755030	755300	0.71	+	1	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	exon	755030	755300	.	+	.	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
Phchi.S4	AUGUSTUS	stop_codon	755301	755303	.	+	0	transcript_id "Phchi.S4G008900.t1"; gene_id "Phchi.S4G008900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2050.t1 is derived from g8970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4599696	4600946	.	-	.	Phchi.S5G065900
Phchi.S5	AUGUSTUS	transcript	4599696	4600946	.	-	.	transcript_id "Phchi.S5G065900.t1"; gene_id "Phchi.S5G065900"
Phchi.S5	AUGUSTUS	stop_codon	4599693	4599695	.	-	0	transcript_id "Phchi.S5G065900.t1"; gene_id "Phchi.S5G065900"
Phchi.S5	AUGUSTUS	CDS	4599696	4600946	0.99	-	0	transcript_id "Phchi.S5G065900.t1"; gene_id "Phchi.S5G065900"
Phchi.S5	AUGUSTUS	exon	4599696	4600946	.	-	.	transcript_id "Phchi.S5G065900.t1"; gene_id "Phchi.S5G065900"
Phchi.S5	AUGUSTUS	start_codon	4600944	4600946	.	-	0	transcript_id "Phchi.S5G065900.t1"; gene_id "Phchi.S5G065900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13449.t1 is derived from g11916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6776082	6778330	.	-	.	Phchi.S3G076800
Phchi.S3	AUGUSTUS	transcript	6776082	6778330	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	stop_codon	6776079	6776081	.	-	0	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6776082	6776093	1	-	0	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6776082	6776093	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6776094	6776182	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6776183	6776255	1	-	1	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6776183	6776255	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6776256	6776344	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6776345	6776413	0.99	-	1	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6776345	6776413	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6776414	6776531	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6776532	6776646	0.92	-	2	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6776532	6776646	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6776647	6776749	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6776750	6776988	0.97	-	1	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6776750	6776988	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6776989	6777097	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6777098	6777364	1	-	1	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6777098	6777364	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6777365	6777458	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6777459	6777736	1	-	0	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6777459	6777736	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6777737	6777841	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6777842	6778125	0.8	-	2	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6777842	6778125	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	intron	6778126	6778230	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	CDS	6778231	6778330	0.75	-	0	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	exon	6778231	6778330	.	-	.	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
Phchi.S3	AUGUSTUS	start_codon	6778328	6778330	.	-	0	transcript_id "Phchi.S3G076800.t1"; gene_id "Phchi.S3G076800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg841.t1 is derived from g10623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5841269	5846647	.	-	.	Phchi.S6G080000
Phchi.S6	AUGUSTUS	transcript	5841269	5846647	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	stop_codon	5841266	5841268	.	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5841269	5842852	0.88	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5841269	5842852	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5842853	5842947	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5842948	5843736	0.81	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5842948	5843736	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5843737	5843852	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5843853	5844158	1	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5843853	5844158	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5844159	5844288	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5844289	5844471	1	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5844289	5844471	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5844472	5844599	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5844600	5845470	0.98	-	1	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5844600	5845470	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5845471	5845572	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5845573	5845732	0.98	-	2	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5845573	5845732	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5845733	5845847	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5845848	5845892	1	-	2	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5845848	5845892	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5845893	5846005	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5846006	5846305	1	-	2	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5846006	5846305	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	intron	5846306	5846406	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	CDS	5846407	5846647	1	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	exon	5846407	5846647	.	-	.	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
Phchi.S6	AUGUSTUS	start_codon	5846645	5846647	.	-	0	transcript_id "Phchi.S6G080000.t1"; gene_id "Phchi.S6G080000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6754.t1 is derived from g3926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24856161	24858465	.	+	.	Phchi.S1G391300
Phchi.S1	AUGUSTUS	transcript	24856161	24858465	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	start_codon	24856161	24856163	.	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24856161	24856593	0.99	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24856161	24856593	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24856594	24856668	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24856669	24856888	1	+	2	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24856669	24856888	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24856889	24856972	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24856973	24857084	1	+	1	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24856973	24857084	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24857085	24857174	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24857175	24857447	1	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24857175	24857447	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24857448	24857535	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24857536	24857801	1	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24857536	24857801	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24857802	24857918	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24857919	24858075	1	+	1	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24857919	24858075	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24858076	24858165	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24858166	24858249	1	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24858166	24858249	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	intron	24858250	24858327	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	CDS	24858328	24858465	1	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	exon	24858328	24858465	.	+	.	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
Phchi.S1	AUGUSTUS	stop_codon	24858466	24858468	.	+	0	transcript_id "Phchi.S1G391300.t1"; gene_id "Phchi.S1G391300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6460.t1 is derived from g3632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23124219	23125051	.	-	.	Phchi.S1G361900
Phchi.S1	AUGUSTUS	transcript	23124219	23125051	.	-	.	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	stop_codon	23124216	23124218	.	-	0	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	CDS	23124219	23124414	0.62	-	1	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	exon	23124219	23124414	.	-	.	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	intron	23124415	23124827	.	-	.	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	CDS	23124828	23125051	0.71	-	0	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	exon	23124828	23125051	.	-	.	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
Phchi.S1	AUGUSTUS	start_codon	23125049	23125051	.	-	0	transcript_id "Phchi.S1G361900.t1"; gene_id "Phchi.S1G361900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9074.t1 is derived from g6249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39726966	39728391	.	-	.	Phchi.S1G623300
Phchi.S1	AUGUSTUS	transcript	39726966	39728391	.	-	.	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	stop_codon	39726963	39726965	.	-	0	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	CDS	39726966	39727013	0.56	-	0	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	exon	39726966	39727013	.	-	.	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	intron	39727014	39727164	.	-	.	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	CDS	39727165	39728391	0.52	-	0	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	exon	39727165	39728391	.	-	.	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	start_codon	39728389	39728391	.	-	0	transcript_id "Phchi.S1G623300.t1"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	transcript	39727127	39728391	.	-	.	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	stop_codon	39727124	39727126	.	-	0	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	CDS	39727127	39727139	0.54	-	1	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	exon	39727127	39727139	.	-	.	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	intron	39727140	39727231	.	-	.	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	CDS	39727232	39728391	0.14	-	0	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	exon	39727232	39728391	.	-	.	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
Phchi.S1	AUGUSTUS	start_codon	39728389	39728391	.	-	0	transcript_id "Phchi.S1G623300.t2"; gene_id "Phchi.S1G623300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6880.t1 is derived from g4052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25803758	25805178	.	+	.	Phchi.S1G403900
Phchi.S1	AUGUSTUS	transcript	25803758	25805178	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	start_codon	25803758	25803760	.	+	0	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	CDS	25803758	25804363	0.86	+	0	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	exon	25803758	25804363	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	intron	25804364	25804528	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	CDS	25804529	25804618	0.99	+	0	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	exon	25804529	25804618	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	intron	25804619	25804727	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	CDS	25804728	25804853	0.83	+	0	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	exon	25804728	25804853	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	intron	25804854	25804950	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	CDS	25804951	25805178	0.71	+	0	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	exon	25804951	25805178	.	+	.	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
Phchi.S1	AUGUSTUS	stop_codon	25805179	25805181	.	+	0	transcript_id "Phchi.S1G403900.t1"; gene_id "Phchi.S1G403900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10435.t1 is derived from g14484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	329650	331042	.	+	.	Phchi.S4G001700
Phchi.S4	AUGUSTUS	transcript	329650	331042	.	+	.	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	start_codon	329650	329652	.	+	0	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	CDS	329650	329808	1	+	0	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	exon	329650	329808	.	+	.	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	intron	329809	329897	.	+	.	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	CDS	329898	330853	0.46	+	0	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	exon	329898	330853	.	+	.	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	intron	330854	331035	.	+	.	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	CDS	331036	331042	0.6	+	1	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	exon	331036	331042	.	+	.	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
Phchi.S4	AUGUSTUS	stop_codon	331043	331045	.	+	0	transcript_id "Phchi.S4G001700.t1"; gene_id "Phchi.S4G001700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4904.t1 is derived from g2074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13333452	13334453	.	+	.	Phchi.S1G206300
Phchi.S1	AUGUSTUS	transcript	13333452	13334453	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	start_codon	13333452	13333454	.	+	0	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	CDS	13333452	13333578	0.97	+	0	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	exon	13333452	13333578	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	intron	13333579	13333654	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	CDS	13333655	13333786	1	+	2	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	exon	13333655	13333786	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	intron	13333787	13333932	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	CDS	13333933	13334165	1	+	2	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	exon	13333933	13334165	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	intron	13334166	13334255	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	CDS	13334256	13334453	1	+	0	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	exon	13334256	13334453	.	+	.	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
Phchi.S1	AUGUSTUS	stop_codon	13334454	13334456	.	+	0	transcript_id "Phchi.S1G206300.t1"; gene_id "Phchi.S1G206300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2949.t1 is derived from g118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	719831	721458	.	-	.	Phchi.S1G010800
Phchi.S1	AUGUSTUS	transcript	719831	721458	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	stop_codon	719828	719830	.	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	719831	719950	0.99	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	719831	719950	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	719951	720080	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	720081	720169	1	-	2	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	720081	720169	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	720170	720337	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	720338	720411	0.99	-	1	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	720338	720411	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	720412	720516	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	720517	720611	1	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	720517	720611	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	720612	720753	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	720754	720846	1	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	720754	720846	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	720847	720932	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	720933	720980	0.61	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	720933	720980	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	720981	721092	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	721093	721141	0.65	-	1	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	721093	721141	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	721142	721229	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	721230	721274	0.71	-	1	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	721230	721274	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	intron	721275	721405	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	CDS	721406	721458	1	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	exon	721406	721458	.	-	.	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
Phchi.S1	AUGUSTUS	start_codon	721456	721458	.	-	0	transcript_id "Phchi.S1G010800.t1"; gene_id "Phchi.S1G010800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14245.t1 is derived from g12712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11735382	11737132	.	+	.	Phchi.S3G156400
Phchi.S3	AUGUSTUS	transcript	11735382	11737132	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	start_codon	11735382	11735384	.	+	0	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	CDS	11735382	11735490	1	+	0	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	exon	11735382	11735490	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	intron	11735491	11735568	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	CDS	11735569	11735657	0.96	+	2	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	exon	11735569	11735657	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	intron	11735658	11735777	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	CDS	11735778	11735923	0.89	+	0	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	exon	11735778	11735923	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	intron	11735924	11736036	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	CDS	11736037	11737132	0.93	+	1	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	exon	11736037	11737132	.	+	.	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
Phchi.S3	AUGUSTUS	stop_codon	11737133	11737135	.	+	0	transcript_id "Phchi.S3G156400.t1"; gene_id "Phchi.S3G156400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12960.t1 is derived from g11425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3334857	3335712	.	-	.	Phchi.S3G027900
Phchi.S3	AUGUSTUS	transcript	3334857	3335712	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	stop_codon	3334854	3334856	.	-	0	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	CDS	3334857	3334955	1	-	0	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	exon	3334857	3334955	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	intron	3334956	3335108	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	CDS	3335109	3335186	1	-	0	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	exon	3335109	3335186	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	intron	3335187	3335340	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	CDS	3335341	3335444	1	-	2	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	exon	3335341	3335444	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	intron	3335445	3335525	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	CDS	3335526	3335712	1	-	0	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	exon	3335526	3335712	.	-	.	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
Phchi.S3	AUGUSTUS	start_codon	3335710	3335712	.	-	0	transcript_id "Phchi.S3G027900.t1"; gene_id "Phchi.S3G027900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12270.t1 is derived from g7946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7398450	7399704	.	-	.	Phchi.S2G035000
Phchi.S2	AUGUSTUS	transcript	7398450	7399704	.	-	.	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	stop_codon	7398447	7398449	.	-	0	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	CDS	7398450	7398751	0.39	-	2	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	exon	7398450	7398751	.	-	.	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	intron	7398752	7398836	.	-	.	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	CDS	7398837	7399704	0.43	-	0	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	exon	7398837	7399704	.	-	.	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
Phchi.S2	AUGUSTUS	start_codon	7399702	7399704	.	-	0	transcript_id "Phchi.S2G035000.t1"; gene_id "Phchi.S2G035000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1810.t1 is derived from g8730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3157307	3159104	.	-	.	Phchi.S5G041900
Phchi.S5	AUGUSTUS	transcript	3157307	3159104	.	-	.	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	stop_codon	3157304	3157306	.	-	0	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	CDS	3157307	3157321	1	-	0	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	exon	3157307	3157321	.	-	.	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	intron	3157322	3157415	.	-	.	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	CDS	3157416	3157725	0.48	-	1	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	exon	3157416	3157725	.	-	.	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	intron	3157726	3158151	.	-	.	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	CDS	3158152	3159104	0.17	-	0	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	exon	3158152	3159104	.	-	.	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
Phchi.S5	AUGUSTUS	start_codon	3159102	3159104	.	-	0	transcript_id "Phchi.S5G041900.t1"; gene_id "Phchi.S5G041900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg615.t1 is derived from g10397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4419057	4421302	.	+	.	Phchi.S6G057400
Phchi.S6	AUGUSTUS	transcript	4419057	4421302	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	start_codon	4419057	4419059	.	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4419057	4419167	0.49	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4419057	4419167	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4419168	4419257	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4419258	4419398	1	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4419258	4419398	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4419399	4419563	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4419564	4419642	1	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4419564	4419642	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4419643	4419802	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4419803	4419861	1	+	2	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4419803	4419861	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4419862	4420059	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4420060	4420137	0.88	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4420060	4420137	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4420138	4420255	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4420256	4420337	1	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4420256	4420337	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4420338	4420483	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4420484	4420532	1	+	2	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4420484	4420532	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4420533	4420646	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4420647	4420708	1	+	1	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4420647	4420708	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4420709	4420796	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4420797	4420864	1	+	2	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4420797	4420864	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4420865	4420953	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4420954	4421009	1	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4420954	4421009	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4421010	4421134	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4421135	4421182	1	+	1	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4421135	4421182	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	intron	4421183	4421253	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	CDS	4421254	4421302	1	+	1	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	exon	4421254	4421302	.	+	.	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
Phchi.S6	AUGUSTUS	stop_codon	4421303	4421305	.	+	0	transcript_id "Phchi.S6G057400.t1"; gene_id "Phchi.S6G057400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1236.t1 is derived from g11019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8546694	8547990	.	-	.	Phchi.S6G119500
Phchi.S6	AUGUSTUS	transcript	8546694	8547990	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	stop_codon	8546691	8546693	.	-	0	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	CDS	8546694	8546804	1	-	0	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	exon	8546694	8546804	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	intron	8546805	8546901	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	CDS	8546902	8546961	1	-	0	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	exon	8546902	8546961	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	intron	8546962	8547047	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	CDS	8547048	8547332	1	-	0	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	exon	8547048	8547332	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	intron	8547333	8547413	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	CDS	8547414	8547534	1	-	1	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	exon	8547414	8547534	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	intron	8547535	8547630	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	CDS	8547631	8547711	1	-	1	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	exon	8547631	8547711	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	intron	8547712	8547799	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	CDS	8547800	8547990	0.98	-	0	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	exon	8547800	8547990	.	-	.	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
Phchi.S6	AUGUSTUS	start_codon	8547988	8547990	.	-	0	transcript_id "Phchi.S6G119500.t1"; gene_id "Phchi.S6G119500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3678.t1 is derived from g847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5148222	5148659	.	-	.	Phchi.S1G083700
Phchi.S1	AUGUSTUS	transcript	5148222	5148659	.	-	.	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	stop_codon	5148219	5148221	.	-	0	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	CDS	5148222	5148441	0.86	-	1	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	exon	5148222	5148441	.	-	.	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	intron	5148442	5148534	.	-	.	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	CDS	5148535	5148659	0.81	-	0	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	exon	5148535	5148659	.	-	.	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
Phchi.S1	AUGUSTUS	start_codon	5148657	5148659	.	-	0	transcript_id "Phchi.S1G083700.t1"; gene_id "Phchi.S1G083700"
# This transcript jg14613.t2 is derived from g13081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14614.t1 is derived from g13082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13779131	13780627	.	+	.	Phchi.S3G193300
Phchi.S3	AUGUSTUS	transcript	13779131	13780627	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	start_codon	13779131	13779133	.	+	0	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	CDS	13779131	13779322	0.57	+	0	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	exon	13779131	13779322	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	intron	13779323	13779445	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	CDS	13779446	13779625	1	+	0	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	exon	13779446	13779625	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	intron	13779626	13779718	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	CDS	13779719	13779881	1	+	0	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	exon	13779719	13779881	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	intron	13779882	13780010	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	CDS	13780011	13780329	1	+	2	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	exon	13780011	13780329	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	intron	13780330	13780462	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	CDS	13780463	13780476	0.54	+	1	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	exon	13780463	13780476	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	intron	13780477	13780565	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	CDS	13780566	13780627	1	+	2	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	exon	13780566	13780627	.	+	.	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
Phchi.S3	AUGUSTUS	stop_codon	13780628	13780630	.	+	0	transcript_id "Phchi.S3G193300.t1"; gene_id "Phchi.S3G193300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6303.t1 is derived from g3475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22172103	22173152	.	-	.	Phchi.S1G346200
Phchi.S1	AUGUSTUS	transcript	22172103	22173152	.	-	.	transcript_id "Phchi.S1G346200.t1"; gene_id "Phchi.S1G346200"
Phchi.S1	AUGUSTUS	stop_codon	22172100	22172102	.	-	0	transcript_id "Phchi.S1G346200.t1"; gene_id "Phchi.S1G346200"
Phchi.S1	AUGUSTUS	CDS	22172103	22173152	0.99	-	0	transcript_id "Phchi.S1G346200.t1"; gene_id "Phchi.S1G346200"
Phchi.S1	AUGUSTUS	exon	22172103	22173152	.	-	.	transcript_id "Phchi.S1G346200.t1"; gene_id "Phchi.S1G346200"
Phchi.S1	AUGUSTUS	start_codon	22173150	22173152	.	-	0	transcript_id "Phchi.S1G346200.t1"; gene_id "Phchi.S1G346200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11041.t1 is derived from g15091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3789146	3792310	.	-	.	Phchi.S4G062300
Phchi.S4	AUGUSTUS	transcript	3789146	3792310	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	stop_codon	3789143	3789145	.	-	0	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	CDS	3789146	3789990	0.97	-	2	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	exon	3789146	3789990	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	intron	3789991	3790128	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	CDS	3790129	3790617	1	-	2	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	exon	3790129	3790617	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	intron	3790618	3790700	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	CDS	3790701	3790849	0.95	-	1	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	exon	3790701	3790849	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	intron	3790850	3790971	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	CDS	3790972	3791114	0.97	-	0	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	exon	3790972	3791114	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	intron	3791115	3791238	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	CDS	3791239	3791291	1	-	2	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	exon	3791239	3791291	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	intron	3791292	3791385	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	CDS	3791386	3792310	0.78	-	0	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	exon	3791386	3792310	.	-	.	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
Phchi.S4	AUGUSTUS	start_codon	3792308	3792310	.	-	0	transcript_id "Phchi.S4G062300.t1"; gene_id "Phchi.S4G062300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4564.t1 is derived from g1734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11129344	11130568	.	+	.	Phchi.S1G172300
Phchi.S1	AUGUSTUS	transcript	11129344	11130568	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	start_codon	11129344	11129346	.	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	CDS	11129344	11129346	1	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	exon	11129344	11129346	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	intron	11129347	11129431	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	CDS	11129432	11129488	1	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	exon	11129432	11129488	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	intron	11129489	11129572	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	CDS	11129573	11129780	1	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	exon	11129573	11129780	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	intron	11129781	11129881	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	CDS	11129882	11130051	1	+	2	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	exon	11129882	11130051	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	intron	11130052	11130131	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	CDS	11130132	11130353	1	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	exon	11130132	11130353	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	intron	11130354	11130439	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	CDS	11130440	11130568	0.97	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	exon	11130440	11130568	.	+	.	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
Phchi.S1	AUGUSTUS	stop_codon	11130569	11130571	.	+	0	transcript_id "Phchi.S1G172300.t1"; gene_id "Phchi.S1G172300"
# This transcript jg9115.t2 is derived from g6290.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9115.t3 is derived from g6290.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9115.t4 is derived from g6290.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9116.t1 is derived from g6291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39897190	39898975	.	-	.	Phchi.S1G627500
Phchi.S1	AUGUSTUS	transcript	39897190	39898975	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	stop_codon	39897187	39897189	.	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39897190	39897363	0.96	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39897190	39897363	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39897364	39897441	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39897442	39897588	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39897442	39897588	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39897589	39897670	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39897671	39897742	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39897671	39897742	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39897743	39897825	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39897826	39897906	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39897826	39897906	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39897907	39897982	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39897983	39898057	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39897983	39898057	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39898058	39898155	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39898156	39898368	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39898156	39898368	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39898369	39898462	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39898463	39898618	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39898463	39898618	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	intron	39898619	39898702	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	CDS	39898703	39898975	1	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	exon	39898703	39898975	.	-	.	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
Phchi.S1	AUGUSTUS	start_codon	39898973	39898975	.	-	0	transcript_id "Phchi.S1G627500.t1"; gene_id "Phchi.S1G627500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15850.t1 is derived from g14320.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21811669	21814893	.	-	.	Phchi.S3G316900
Phchi.S3	AUGUSTUS	transcript	21811669	21814893	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	stop_codon	21811666	21811668	.	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21811669	21811680	0.58	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21811669	21811680	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21811681	21811881	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21811882	21811974	0.57	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21811882	21811974	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21811975	21812075	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812076	21812139	0.52	-	1	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812076	21812139	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21812140	21812250	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812251	21812344	0.93	-	2	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812251	21812344	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21812345	21812506	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812507	21812668	0.62	-	2	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812507	21812668	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21812669	21812818	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812819	21813012	0.66	-	1	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812819	21813012	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813013	21813097	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813098	21813132	1	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813098	21813132	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813133	21813501	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813502	21813595	1	-	1	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813502	21813595	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813596	21813676	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813677	21813719	0.87	-	2	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813677	21813719	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813720	21813825	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813826	21813848	1	-	1	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813826	21813848	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813849	21813948	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813949	21814046	1	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813949	21814046	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21814047	21814130	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21814131	21814301	1	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21814131	21814301	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21814302	21814370	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21814371	21814604	1	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21814371	21814604	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21814605	21814731	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21814732	21814893	1	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21814732	21814893	.	-	.	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	start_codon	21814891	21814893	.	-	0	transcript_id "Phchi.S3G316900.t1"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	transcript	21811669	21814893	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	stop_codon	21811666	21811668	.	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21811669	21811680	0.42	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21811669	21811680	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21811681	21811881	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21811882	21811974	0.42	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21811882	21811974	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21811975	21812075	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812076	21812139	0.42	-	1	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812076	21812139	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21812140	21812250	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812251	21812344	0.98	-	2	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812251	21812344	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21812345	21812506	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812507	21812668	0.65	-	2	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812507	21812668	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21812669	21812818	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21812819	21813012	0.69	-	1	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21812819	21813012	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813013	21813097	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813098	21813132	1	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813098	21813132	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813133	21813501	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813502	21813595	1	-	1	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813502	21813595	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813596	21813676	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813677	21813880	0.99	-	1	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813677	21813880	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21813881	21813948	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21813949	21814046	1	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21813949	21814046	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21814047	21814130	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21814131	21814301	1	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21814131	21814301	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21814302	21814370	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21814371	21814604	1	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21814371	21814604	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	intron	21814605	21814731	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	CDS	21814732	21814893	0.98	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	exon	21814732	21814893	.	-	.	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
Phchi.S3	AUGUSTUS	start_codon	21814891	21814893	.	-	0	transcript_id "Phchi.S3G316900.t2"; gene_id "Phchi.S3G316900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9590.t1 is derived from g6766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42813980	42814373	.	+	.	Phchi.S1G674900
Phchi.S1	AUGUSTUS	transcript	42813980	42814373	.	+	.	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	start_codon	42813980	42813982	.	+	0	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	CDS	42813980	42813995	0.36	+	0	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	exon	42813980	42813995	.	+	.	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	intron	42813996	42814149	.	+	.	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	CDS	42814150	42814373	1	+	2	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	exon	42814150	42814373	.	+	.	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
Phchi.S1	AUGUSTUS	stop_codon	42814374	42814376	.	+	0	transcript_id "Phchi.S1G674900.t1"; gene_id "Phchi.S1G674900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11497.t1 is derived from g15547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6644717	6646756	.	+	.	Phchi.S4G107900
Phchi.S4	AUGUSTUS	transcript	6644717	6646756	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	start_codon	6644717	6644719	.	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6644717	6644879	1	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6644717	6644879	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	intron	6644880	6644996	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6644997	6645328	1	+	2	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6644997	6645328	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	intron	6645329	6645428	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6645429	6645587	1	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6645429	6645587	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	intron	6645588	6645672	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6645673	6645867	1	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6645673	6645867	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	intron	6645868	6645961	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6645962	6646099	1	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6645962	6646099	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	intron	6646100	6646217	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6646218	6646450	1	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6646218	6646450	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	intron	6646451	6646551	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	CDS	6646552	6646756	1	+	1	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	exon	6646552	6646756	.	+	.	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
Phchi.S4	AUGUSTUS	stop_codon	6646757	6646759	.	+	0	transcript_id "Phchi.S4G107900.t1"; gene_id "Phchi.S4G107900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4864.t1 is derived from g2034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13155971	13156954	.	-	.	Phchi.S1G202300
Phchi.S1	AUGUSTUS	transcript	13155971	13156954	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	stop_codon	13155968	13155970	.	-	0	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	CDS	13155971	13156101	1	-	2	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	exon	13155971	13156101	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	intron	13156102	13156187	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	CDS	13156188	13156295	1	-	2	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	exon	13156188	13156295	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	intron	13156296	13156379	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	CDS	13156380	13156566	1	-	0	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	exon	13156380	13156566	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	intron	13156567	13156738	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	CDS	13156739	13156954	0.33	-	0	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	exon	13156739	13156954	.	-	.	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
Phchi.S1	AUGUSTUS	start_codon	13156952	13156954	.	-	0	transcript_id "Phchi.S1G202300.t1"; gene_id "Phchi.S1G202300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1698.t1 is derived from g8617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2571166	2576052	.	+	.	Phchi.S5G030700
Phchi.S5	AUGUSTUS	transcript	2571166	2576052	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	start_codon	2571166	2571168	.	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2571166	2571303	0.56	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2571166	2571303	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2571304	2571403	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2571404	2571494	1	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2571404	2571494	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2571495	2571581	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2571582	2571676	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2571582	2571676	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2571677	2571857	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2571858	2571961	1	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2571858	2571961	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2571962	2572053	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2572054	2572115	1	+	1	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2572054	2572115	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2572116	2572208	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2572209	2572283	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2572209	2572283	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2572284	2572402	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2572403	2572575	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2572403	2572575	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2572576	2572740	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2572741	2572816	1	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2572741	2572816	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2572817	2572895	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2572896	2572997	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2572896	2572997	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2572998	2573084	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2573085	2573162	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2573085	2573162	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2573163	2573241	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2573242	2573383	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2573242	2573383	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2573384	2573472	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2573473	2573956	1	+	1	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2573473	2573956	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2573957	2574114	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2574115	2574411	1	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2574115	2574411	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2574412	2574552	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2574553	2574669	1	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2574553	2574669	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2574670	2574841	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2574842	2575072	1	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2574842	2575072	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2575073	2575190	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2575191	2575606	0.96	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2575191	2575606	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2575607	2575719	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2575720	2575814	0.96	+	1	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2575720	2575814	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	intron	2575815	2575978	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	CDS	2575979	2576052	1	+	2	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	exon	2575979	2576052	.	+	.	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
Phchi.S5	AUGUSTUS	stop_codon	2576053	2576055	.	+	0	transcript_id "Phchi.S5G030700.t1"; gene_id "Phchi.S5G030700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3306.t1 is derived from g475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2758653	2759683	.	+	.	Phchi.S1G046500
Phchi.S1	AUGUSTUS	transcript	2758653	2759683	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	start_codon	2758653	2758655	.	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	CDS	2758653	2758709	0.52	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	exon	2758653	2758709	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	intron	2758710	2758888	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	CDS	2758889	2758921	1	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	exon	2758889	2758921	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	intron	2758922	2759037	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	CDS	2759038	2759148	1	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	exon	2759038	2759148	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	intron	2759149	2759275	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	CDS	2759276	2759371	1	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	exon	2759276	2759371	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	intron	2759372	2759487	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	CDS	2759488	2759562	1	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	exon	2759488	2759562	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	intron	2759563	2759650	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	CDS	2759651	2759683	1	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	exon	2759651	2759683	.	+	.	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
Phchi.S1	AUGUSTUS	stop_codon	2759684	2759686	.	+	0	transcript_id "Phchi.S1G046500.t1"; gene_id "Phchi.S1G046500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12453.t1 is derived from g8130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23457392	23460077	.	-	.	Phchi.S2G053300
Phchi.S2	AUGUSTUS	transcript	23457392	23460077	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	stop_codon	23457389	23457391	.	-	0	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23457392	23457546	1	-	2	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23457392	23457546	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	intron	23457547	23457619	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23457620	23457729	1	-	1	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23457620	23457729	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	intron	23457730	23457833	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23457834	23457895	1	-	0	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23457834	23457895	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	intron	23457896	23458041	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23458042	23458155	1	-	0	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23458042	23458155	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	intron	23458156	23458308	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23458309	23458553	1	-	2	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23458309	23458553	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	intron	23458554	23458628	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23458629	23459360	1	-	2	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23458629	23459360	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	intron	23459361	23459953	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	CDS	23459954	23460077	0.73	-	0	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	exon	23459954	23460077	.	-	.	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
Phchi.S2	AUGUSTUS	start_codon	23460075	23460077	.	-	0	transcript_id "Phchi.S2G053300.t1"; gene_id "Phchi.S2G053300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9579.t1 is derived from g6755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42749465	42750932	.	+	.	Phchi.S1G673800
Phchi.S1	AUGUSTUS	transcript	42749465	42750932	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	start_codon	42749465	42749467	.	+	0	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	CDS	42749465	42749606	0.22	+	0	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	exon	42749465	42749606	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	intron	42749607	42749968	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	CDS	42749969	42750052	0.69	+	2	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	exon	42749969	42750052	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	intron	42750053	42750288	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	CDS	42750289	42750361	0.97	+	2	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	exon	42750289	42750361	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	intron	42750362	42750445	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	CDS	42750446	42750612	1	+	1	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	exon	42750446	42750612	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	intron	42750613	42750749	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	CDS	42750750	42750790	1	+	2	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	exon	42750750	42750790	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	intron	42750791	42750881	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	CDS	42750882	42750932	0.64	+	0	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	exon	42750882	42750932	.	+	.	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
Phchi.S1	AUGUSTUS	stop_codon	42750933	42750935	.	+	0	transcript_id "Phchi.S1G673800.t1"; gene_id "Phchi.S1G673800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3831.t1 is derived from g1000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5929926	5932853	.	-	.	Phchi.S1G099000
Phchi.S1	AUGUSTUS	transcript	5929926	5932853	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	stop_codon	5929923	5929925	.	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5929926	5929983	0.22	-	1	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5929926	5929983	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5929984	5930068	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5930069	5930130	0.97	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5930069	5930130	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5930131	5930298	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5930299	5930533	0.92	-	1	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5930299	5930533	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5930534	5930622	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5930623	5930664	1	-	1	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5930623	5930664	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5930665	5931054	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5931055	5931313	0.65	-	2	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5931055	5931313	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5931314	5931419	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5931420	5931515	1	-	2	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5931420	5931515	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5931516	5931590	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5931591	5931678	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5931591	5931678	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5931679	5931768	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5931769	5931882	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5931769	5931882	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5931883	5931980	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5931981	5932052	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5931981	5932052	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5932053	5932136	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5932137	5932223	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5932137	5932223	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5932224	5932356	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5932357	5932440	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5932357	5932440	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5932441	5932565	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5932566	5932664	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5932566	5932664	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	intron	5932665	5932751	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	CDS	5932752	5932853	1	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	exon	5932752	5932853	.	-	.	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
Phchi.S1	AUGUSTUS	start_codon	5932851	5932853	.	-	0	transcript_id "Phchi.S1G099000.t1"; gene_id "Phchi.S1G099000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9023.t1 is derived from g6198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39190531	39192365	.	+	.	Phchi.S1G618200
Phchi.S1	AUGUSTUS	transcript	39190531	39192365	.	+	.	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	start_codon	39190531	39190533	.	+	0	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	CDS	39190531	39190561	0.85	+	0	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	exon	39190531	39190561	.	+	.	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	intron	39190562	39190670	.	+	.	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	CDS	39190671	39191748	0.81	+	2	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	exon	39190671	39191748	.	+	.	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	intron	39191749	39191830	.	+	.	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	CDS	39191831	39192365	1	+	1	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	exon	39191831	39192365	.	+	.	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
Phchi.S1	AUGUSTUS	stop_codon	39192366	39192368	.	+	0	transcript_id "Phchi.S1G618200.t1"; gene_id "Phchi.S1G618200"
# This transcript jg9935.t2 is derived from g7111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9936.t1 is derived from g7112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44544567	44548783	.	-	.	Phchi.S1G709500
Phchi.S1	AUGUSTUS	transcript	44544567	44548783	.	-	.	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	stop_codon	44544564	44544566	.	-	0	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	CDS	44544567	44545700	0.71	-	0	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	exon	44544567	44545700	.	-	.	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	intron	44545701	44545813	.	-	.	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	CDS	44545814	44547186	0.89	-	2	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	exon	44545814	44547186	.	-	.	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	intron	44547187	44547300	.	-	.	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	CDS	44547301	44548783	0.6	-	0	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	exon	44547301	44548783	.	-	.	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
Phchi.S1	AUGUSTUS	start_codon	44548781	44548783	.	-	0	transcript_id "Phchi.S1G709500.t1"; gene_id "Phchi.S1G709500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15029.t1 is derived from g13497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16603522	16605397	.	-	.	Phchi.S3G234800
Phchi.S3	AUGUSTUS	transcript	16603522	16605397	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	stop_codon	16603519	16603521	.	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16603522	16603522	1	-	1	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16603522	16603522	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16603523	16603701	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16603702	16603773	1	-	1	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16603702	16603773	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16603774	16603865	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16603866	16604086	0.87	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16603866	16604086	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16604087	16604186	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16604187	16604249	0.87	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16604187	16604249	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16604250	16604339	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16604340	16604402	0.98	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16604340	16604402	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16604403	16604484	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16604485	16604493	0.74	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16604485	16604493	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16604494	16604592	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16604593	16604621	0.88	-	2	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16604593	16604621	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16604622	16604808	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16604809	16604867	0.87	-	1	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16604809	16604867	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16604868	16604974	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16604975	16605033	0.86	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16604975	16605033	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	intron	16605034	16605211	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	CDS	16605212	16605397	0.61	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	exon	16605212	16605397	.	-	.	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
Phchi.S3	AUGUSTUS	start_codon	16605395	16605397	.	-	0	transcript_id "Phchi.S3G234800.t1"; gene_id "Phchi.S3G234800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4881.t1 is derived from g2051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13201174	13202679	.	+	.	Phchi.S1G204000
Phchi.S1	AUGUSTUS	transcript	13201174	13202679	.	+	.	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	start_codon	13201174	13201176	.	+	0	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	CDS	13201174	13201596	0.91	+	0	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	exon	13201174	13201596	.	+	.	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	intron	13201597	13201764	.	+	.	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	CDS	13201765	13202679	1	+	0	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	exon	13201765	13202679	.	+	.	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
Phchi.S1	AUGUSTUS	stop_codon	13202680	13202682	.	+	0	transcript_id "Phchi.S1G204000.t1"; gene_id "Phchi.S1G204000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9395.t1 is derived from g6571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41316384	41318585	.	+	.	Phchi.S1G655400
Phchi.S1	AUGUSTUS	transcript	41316384	41318585	.	+	.	transcript_id "Phchi.S1G655400.t1"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	start_codon	41316384	41316386	.	+	0	transcript_id "Phchi.S1G655400.t1"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	CDS	41316384	41318585	0.92	+	0	transcript_id "Phchi.S1G655400.t1"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	exon	41316384	41318585	.	+	.	transcript_id "Phchi.S1G655400.t1"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	stop_codon	41318586	41318588	.	+	0	transcript_id "Phchi.S1G655400.t1"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	transcript	41316384	41318225	.	+	.	transcript_id "Phchi.S1G655400.t2"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	start_codon	41316384	41316386	.	+	0	transcript_id "Phchi.S1G655400.t2"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	CDS	41316384	41318225	0.74	+	0	transcript_id "Phchi.S1G655400.t2"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	exon	41316384	41318225	.	+	.	transcript_id "Phchi.S1G655400.t2"; gene_id "Phchi.S1G655400"
Phchi.S1	AUGUSTUS	stop_codon	41318308	41318310	.	+	0	transcript_id "Phchi.S1G655400.t2"; gene_id "Phchi.S1G655400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1625.t1 is derived from g8544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2082389	2083189	.	+	.	Phchi.S5G023400
Phchi.S5	AUGUSTUS	transcript	2082389	2083189	.	+	.	transcript_id "Phchi.S5G023400.t1"; gene_id "Phchi.S5G023400"
Phchi.S5	AUGUSTUS	start_codon	2082389	2082391	.	+	0	transcript_id "Phchi.S5G023400.t1"; gene_id "Phchi.S5G023400"
Phchi.S5	AUGUSTUS	CDS	2082389	2083189	1	+	0	transcript_id "Phchi.S5G023400.t1"; gene_id "Phchi.S5G023400"
Phchi.S5	AUGUSTUS	exon	2082389	2083189	.	+	.	transcript_id "Phchi.S5G023400.t1"; gene_id "Phchi.S5G023400"
Phchi.S5	AUGUSTUS	stop_codon	2083190	2083192	.	+	0	transcript_id "Phchi.S5G023400.t1"; gene_id "Phchi.S5G023400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2522.t1 is derived from g9442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7128908	7129432	.	-	.	Phchi.S5G113100
Phchi.S5	AUGUSTUS	transcript	7128908	7129432	.	-	.	transcript_id "Phchi.S5G113100.t1"; gene_id "Phchi.S5G113100"
Phchi.S5	AUGUSTUS	stop_codon	7128905	7128907	.	-	0	transcript_id "Phchi.S5G113100.t1"; gene_id "Phchi.S5G113100"
Phchi.S5	AUGUSTUS	CDS	7128908	7129432	1	-	0	transcript_id "Phchi.S5G113100.t1"; gene_id "Phchi.S5G113100"
Phchi.S5	AUGUSTUS	exon	7128908	7129432	.	-	.	transcript_id "Phchi.S5G113100.t1"; gene_id "Phchi.S5G113100"
Phchi.S5	AUGUSTUS	start_codon	7129430	7129432	.	-	0	transcript_id "Phchi.S5G113100.t1"; gene_id "Phchi.S5G113100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2840.t1 is derived from g9760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9136288	9136617	.	-	.	Phchi.S5G144900
Phchi.S5	AUGUSTUS	transcript	9136288	9136617	.	-	.	transcript_id "Phchi.S5G144900.t1"; gene_id "Phchi.S5G144900"
Phchi.S5	AUGUSTUS	stop_codon	9136285	9136287	.	-	0	transcript_id "Phchi.S5G144900.t1"; gene_id "Phchi.S5G144900"
Phchi.S5	AUGUSTUS	CDS	9136288	9136617	0.85	-	0	transcript_id "Phchi.S5G144900.t1"; gene_id "Phchi.S5G144900"
Phchi.S5	AUGUSTUS	exon	9136288	9136617	.	-	.	transcript_id "Phchi.S5G144900.t1"; gene_id "Phchi.S5G144900"
Phchi.S5	AUGUSTUS	start_codon	9136615	9136617	.	-	0	transcript_id "Phchi.S5G144900.t1"; gene_id "Phchi.S5G144900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12865.t1 is derived from g11330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2817190	2819819	.	+	.	Phchi.S3G018400
Phchi.S3	AUGUSTUS	transcript	2817190	2819819	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	start_codon	2817190	2817192	.	+	0	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	CDS	2817190	2818521	0.62	+	0	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	exon	2817190	2818521	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	intron	2818522	2818630	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	CDS	2818631	2818947	0.97	+	0	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	exon	2818631	2818947	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	intron	2818948	2819030	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	CDS	2819031	2819173	0.72	+	1	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	exon	2819031	2819173	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	intron	2819174	2819274	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	CDS	2819275	2819819	0.66	+	2	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	exon	2819275	2819819	.	+	.	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
Phchi.S3	AUGUSTUS	stop_codon	2819820	2819822	.	+	0	transcript_id "Phchi.S3G018400.t1"; gene_id "Phchi.S3G018400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5390.t1 is derived from g2560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16645420	16646703	.	+	.	Phchi.S1G254900
Phchi.S1	AUGUSTUS	transcript	16645420	16646703	.	+	.	transcript_id "Phchi.S1G254900.t1"; gene_id "Phchi.S1G254900"
Phchi.S1	AUGUSTUS	start_codon	16645420	16645422	.	+	0	transcript_id "Phchi.S1G254900.t1"; gene_id "Phchi.S1G254900"
Phchi.S1	AUGUSTUS	CDS	16645420	16646703	1	+	0	transcript_id "Phchi.S1G254900.t1"; gene_id "Phchi.S1G254900"
Phchi.S1	AUGUSTUS	exon	16645420	16646703	.	+	.	transcript_id "Phchi.S1G254900.t1"; gene_id "Phchi.S1G254900"
Phchi.S1	AUGUSTUS	stop_codon	16646704	16646706	.	+	0	transcript_id "Phchi.S1G254900.t1"; gene_id "Phchi.S1G254900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6184.t1 is derived from g3355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21368328	21368839	.	-	.	Phchi.S1G334300
Phchi.S1	AUGUSTUS	transcript	21368328	21368839	.	-	.	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	stop_codon	21368325	21368327	.	-	0	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	CDS	21368328	21368414	0.58	-	0	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	exon	21368328	21368414	.	-	.	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	intron	21368415	21368502	.	-	.	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	CDS	21368503	21368579	0.76	-	2	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	exon	21368503	21368579	.	-	.	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	intron	21368580	21368760	.	-	.	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	CDS	21368761	21368839	1	-	0	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	exon	21368761	21368839	.	-	.	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
Phchi.S1	AUGUSTUS	start_codon	21368837	21368839	.	-	0	transcript_id "Phchi.S1G334300.t1"; gene_id "Phchi.S1G334300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6123.t1 is derived from g3294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21031594	21033765	.	-	.	Phchi.S1G328200
Phchi.S1	AUGUSTUS	transcript	21031594	21033765	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	stop_codon	21031591	21031593	.	-	0	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21031594	21031918	0.89	-	1	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21031594	21031918	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21031919	21032010	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21032011	21032348	0.89	-	0	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21032011	21032348	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21032349	21032452	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21032453	21032641	0.91	-	0	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21032453	21032641	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21032642	21032725	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21032726	21032806	1	-	0	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21032726	21032806	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21032807	21032908	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21032909	21033023	0.86	-	1	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21032909	21033023	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21033024	21033130	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21033131	21033226	0.81	-	1	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21033131	21033226	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21033227	21033320	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21033321	21033530	0.99	-	1	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21033321	21033530	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	intron	21033531	21033640	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	CDS	21033641	21033765	0.99	-	0	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	exon	21033641	21033765	.	-	.	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
Phchi.S1	AUGUSTUS	start_codon	21033763	21033765	.	-	0	transcript_id "Phchi.S1G328200.t1"; gene_id "Phchi.S1G328200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11357.t1 is derived from g15407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5737772	5738785	.	-	.	Phchi.S4G093900
Phchi.S4	AUGUSTUS	transcript	5737772	5738785	.	-	.	transcript_id "Phchi.S4G093900.t1"; gene_id "Phchi.S4G093900"
Phchi.S4	AUGUSTUS	stop_codon	5737769	5737771	.	-	0	transcript_id "Phchi.S4G093900.t1"; gene_id "Phchi.S4G093900"
Phchi.S4	AUGUSTUS	CDS	5737772	5738785	0.98	-	0	transcript_id "Phchi.S4G093900.t1"; gene_id "Phchi.S4G093900"
Phchi.S4	AUGUSTUS	exon	5737772	5738785	.	-	.	transcript_id "Phchi.S4G093900.t1"; gene_id "Phchi.S4G093900"
Phchi.S4	AUGUSTUS	start_codon	5738783	5738785	.	-	0	transcript_id "Phchi.S4G093900.t1"; gene_id "Phchi.S4G093900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6743.t1 is derived from g3915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24809728	24811770	.	-	.	Phchi.S1G390200
Phchi.S1	AUGUSTUS	transcript	24809728	24811770	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	stop_codon	24809725	24809727	.	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24809728	24809748	1	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24809728	24809748	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24809749	24809827	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24809828	24809908	1	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24809828	24809908	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24809909	24809993	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24809994	24810248	1	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24809994	24810248	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24810249	24810345	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24810346	24810486	1	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24810346	24810486	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24810487	24810574	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24810575	24810718	1	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24810575	24810718	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24810719	24810816	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24810817	24810983	1	-	2	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24810817	24810983	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24810984	24811071	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24811072	24811133	1	-	1	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24811072	24811133	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24811134	24811233	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24811234	24811377	1	-	1	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24811234	24811377	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	intron	24811378	24811483	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	CDS	24811484	24811770	0.68	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	exon	24811484	24811770	.	-	.	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
Phchi.S1	AUGUSTUS	start_codon	24811768	24811770	.	-	0	transcript_id "Phchi.S1G390200.t1"; gene_id "Phchi.S1G390200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14478.t1 is derived from g12946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13047444	13048171	.	+	.	Phchi.S3G179700
Phchi.S3	AUGUSTUS	transcript	13047444	13048171	.	+	.	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	start_codon	13047444	13047446	.	+	0	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	CDS	13047444	13048054	0.8	+	0	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	exon	13047444	13048054	.	+	.	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	intron	13048055	13048146	.	+	.	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	CDS	13048147	13048171	0.98	+	1	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	exon	13048147	13048171	.	+	.	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
Phchi.S3	AUGUSTUS	stop_codon	13048172	13048174	.	+	0	transcript_id "Phchi.S3G179700.t1"; gene_id "Phchi.S3G179700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12908.t1 is derived from g11373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3091005	3092943	.	+	.	Phchi.S3G022700
Phchi.S3	AUGUSTUS	transcript	3091005	3092943	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	start_codon	3091005	3091007	.	+	0	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3091005	3091100	0.75	+	0	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3091005	3091100	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3091101	3091198	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3091199	3091278	1	+	0	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3091199	3091278	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3091279	3091422	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3091423	3091513	1	+	1	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3091423	3091513	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3091514	3091627	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3091628	3091680	1	+	0	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3091628	3091680	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3091681	3091795	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3091796	3091838	0.93	+	1	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3091796	3091838	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3091839	3091960	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3091961	3092064	1	+	0	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3091961	3092064	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3092065	3092195	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3092196	3092261	1	+	1	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3092196	3092261	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3092262	3092348	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3092349	3092579	1	+	1	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3092349	3092579	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	intron	3092580	3092684	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	CDS	3092685	3092943	0.71	+	1	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	exon	3092685	3092943	.	+	.	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
Phchi.S3	AUGUSTUS	stop_codon	3092944	3092946	.	+	0	transcript_id "Phchi.S3G022700.t1"; gene_id "Phchi.S3G022700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13248.t1 is derived from g11713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4918027	4920848	.	+	.	Phchi.S3G056700
Phchi.S3	AUGUSTUS	transcript	4918027	4920848	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	start_codon	4918027	4918029	.	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4918027	4918224	0.66	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4918027	4918224	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4918225	4918386	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4918387	4918554	1	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4918387	4918554	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4918555	4918755	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4918756	4918878	1	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4918756	4918878	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4918879	4918963	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4918964	4919074	1	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4918964	4919074	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4919075	4919153	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4919154	4919279	1	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4919154	4919279	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4919280	4919435	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4919436	4919555	1	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4919436	4919555	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4919556	4919656	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4919657	4920061	0.71	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4919657	4920061	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	intron	4920062	4920524	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	CDS	4920525	4920848	0.82	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	exon	4920525	4920848	.	+	.	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
Phchi.S3	AUGUSTUS	stop_codon	4920849	4920851	.	+	0	transcript_id "Phchi.S3G056700.t1"; gene_id "Phchi.S3G056700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9248.t1 is derived from g6423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40581694	40586596	.	+	.	Phchi.S1G640700
Phchi.S1	AUGUSTUS	transcript	40581694	40586596	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	start_codon	40581694	40581696	.	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40581694	40581861	0.83	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40581694	40581861	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40581862	40581995	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40581996	40582148	0.8	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40581996	40582148	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40582149	40582231	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40582232	40582303	1	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40582232	40582303	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40582304	40582452	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40582453	40582749	0.69	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40582453	40582749	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40582750	40582873	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40582874	40582922	0.56	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40582874	40582922	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40582923	40583002	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40583003	40583130	0.61	+	2	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40583003	40583130	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40583131	40583482	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40583483	40583642	0.34	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40583483	40583642	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40583643	40584012	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40584013	40584030	0.99	+	2	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40584013	40584030	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40584031	40584165	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40584166	40584284	0.99	+	2	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40584166	40584284	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40584285	40584490	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40584491	40584778	0.99	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40584491	40584778	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40584779	40584883	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40584884	40584975	1	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40584884	40584975	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40584976	40585070	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40585071	40585193	1	+	1	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40585071	40585193	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40585194	40585280	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40585281	40585437	1	+	1	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40585281	40585437	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40585438	40585539	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40585540	40585660	1	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40585540	40585660	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40585661	40585746	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40585747	40585847	1	+	2	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40585747	40585847	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40585848	40585940	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40585941	40586048	1	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40585941	40586048	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40586049	40586146	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40586147	40586368	1	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40586147	40586368	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	intron	40586369	40586443	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	CDS	40586444	40586596	1	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	exon	40586444	40586596	.	+	.	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
Phchi.S1	AUGUSTUS	stop_codon	40586597	40586599	.	+	0	transcript_id "Phchi.S1G640700.t1"; gene_id "Phchi.S1G640700"
# This transcript jg6564.t2 is derived from g3736.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6565.t1 is derived from g3737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23737922	23738315	.	+	.	Phchi.S1G372400
Phchi.S1	AUGUSTUS	transcript	23737922	23738315	.	+	.	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	start_codon	23737922	23737924	.	+	0	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	CDS	23737922	23737927	0.47	+	0	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	exon	23737922	23737927	.	+	.	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	intron	23737928	23738020	.	+	.	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	CDS	23738021	23738097	0.7	+	0	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	exon	23738021	23738097	.	+	.	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	intron	23738098	23738173	.	+	.	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	CDS	23738174	23738315	0.69	+	1	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	exon	23738174	23738315	.	+	.	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
Phchi.S1	AUGUSTUS	stop_codon	23738316	23738318	.	+	0	transcript_id "Phchi.S1G372400.t1"; gene_id "Phchi.S1G372400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10217.t1 is derived from g7393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46423300	46423888	.	+	.	Phchi.S1G737600
Phchi.S1	AUGUSTUS	transcript	46423300	46423888	.	+	.	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	start_codon	46423300	46423302	.	+	0	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	CDS	46423300	46423446	0.86	+	0	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	exon	46423300	46423446	.	+	.	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	intron	46423447	46423583	.	+	.	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	CDS	46423584	46423611	0.97	+	0	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	exon	46423584	46423611	.	+	.	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	intron	46423612	46423751	.	+	.	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	CDS	46423752	46423888	1	+	2	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	exon	46423752	46423888	.	+	.	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
Phchi.S1	AUGUSTUS	stop_codon	46423889	46423891	.	+	0	transcript_id "Phchi.S1G737600.t1"; gene_id "Phchi.S1G737600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg992.t1 is derived from g10775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6949423	6950989	.	+	.	Phchi.S6G095100
Phchi.S6	AUGUSTUS	transcript	6949423	6950989	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	start_codon	6949423	6949425	.	+	0	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	CDS	6949423	6949447	1	+	0	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	exon	6949423	6949447	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	intron	6949448	6949594	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	CDS	6949595	6949672	1	+	2	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	exon	6949595	6949672	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	intron	6949673	6949763	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	CDS	6949764	6950305	1	+	2	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	exon	6949764	6950305	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	intron	6950306	6950417	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	CDS	6950418	6950567	0.98	+	0	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	exon	6950418	6950567	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	intron	6950568	6950686	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	CDS	6950687	6950989	0.94	+	0	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	exon	6950687	6950989	.	+	.	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
Phchi.S6	AUGUSTUS	stop_codon	6950990	6950992	.	+	0	transcript_id "Phchi.S6G095100.t1"; gene_id "Phchi.S6G095100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14574.t1 is derived from g13042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13544722	13547171	.	+	.	Phchi.S3G189300
Phchi.S3	AUGUSTUS	transcript	13544722	13547171	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	start_codon	13544722	13544724	.	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13544722	13544989	0.75	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13544722	13544989	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13544990	13545214	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13545215	13545411	1	+	2	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13545215	13545411	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13545412	13545553	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13545554	13545733	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13545554	13545733	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13545734	13545814	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13545815	13545946	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13545815	13545946	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13545947	13546042	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13546043	13546117	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13546043	13546117	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13546118	13546234	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13546235	13546340	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13546235	13546340	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13546341	13546439	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13546440	13546534	1	+	2	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13546440	13546534	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13546535	13546625	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13546626	13546811	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13546626	13546811	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13546812	13546929	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13546930	13547016	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13546930	13547016	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	intron	13547017	13547108	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	CDS	13547109	13547171	1	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	exon	13547109	13547171	.	+	.	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
Phchi.S3	AUGUSTUS	stop_codon	13547172	13547174	.	+	0	transcript_id "Phchi.S3G189300.t1"; gene_id "Phchi.S3G189300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5207.t1 is derived from g2377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15471282	15474580	.	+	.	Phchi.S1G236600
Phchi.S1	AUGUSTUS	transcript	15471282	15474580	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	start_codon	15471282	15471284	.	+	0	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	CDS	15471282	15472283	0.73	+	0	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	exon	15471282	15472283	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	intron	15472284	15472406	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	CDS	15472407	15472656	0.99	+	0	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	exon	15472407	15472656	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	intron	15472657	15472738	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	CDS	15472739	15473035	1	+	2	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	exon	15472739	15473035	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	intron	15473036	15473134	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	CDS	15473135	15473802	1	+	2	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	exon	15473135	15473802	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	intron	15473803	15473891	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	CDS	15473892	15474421	0.66	+	0	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	exon	15473892	15474421	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	intron	15474422	15474534	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	CDS	15474535	15474580	0.67	+	1	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	exon	15474535	15474580	.	+	.	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
Phchi.S1	AUGUSTUS	stop_codon	15474581	15474583	.	+	0	transcript_id "Phchi.S1G236600.t1"; gene_id "Phchi.S1G236600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13647.t1 is derived from g12114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8002804	8003196	.	-	.	Phchi.S3G096600
Phchi.S3	AUGUSTUS	transcript	8002804	8003196	.	-	.	transcript_id "Phchi.S3G096600.t1"; gene_id "Phchi.S3G096600"
Phchi.S3	AUGUSTUS	stop_codon	8002801	8002803	.	-	0	transcript_id "Phchi.S3G096600.t1"; gene_id "Phchi.S3G096600"
Phchi.S3	AUGUSTUS	CDS	8002804	8003196	0.99	-	0	transcript_id "Phchi.S3G096600.t1"; gene_id "Phchi.S3G096600"
Phchi.S3	AUGUSTUS	exon	8002804	8003196	.	-	.	transcript_id "Phchi.S3G096600.t1"; gene_id "Phchi.S3G096600"
Phchi.S3	AUGUSTUS	start_codon	8003194	8003196	.	-	0	transcript_id "Phchi.S3G096600.t1"; gene_id "Phchi.S3G096600"
# This transcript jg6939.t2 is derived from g4111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6940.t1 is derived from g4112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26075372	26077606	.	+	.	Phchi.S1G409900
Phchi.S1	AUGUSTUS	transcript	26075372	26077606	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	start_codon	26075372	26075374	.	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26075372	26075423	0.65	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26075372	26075423	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	intron	26075424	26075553	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26075554	26075639	0.48	+	2	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26075554	26075639	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	intron	26075640	26075796	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26075797	26076771	0.87	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26075797	26076771	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	intron	26076772	26076935	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26076936	26077007	1	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26076936	26077007	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	intron	26077008	26077147	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26077148	26077171	0.87	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26077148	26077171	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	intron	26077172	26077274	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26077275	26077362	1	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26077275	26077362	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	intron	26077363	26077589	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	CDS	26077590	26077606	1	+	2	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	exon	26077590	26077606	.	+	.	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
Phchi.S1	AUGUSTUS	stop_codon	26077607	26077609	.	+	0	transcript_id "Phchi.S1G409900.t1"; gene_id "Phchi.S1G409900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7100.t1 is derived from g4272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26909268	26913112	.	-	.	Phchi.S1G425900
Phchi.S1	AUGUSTUS	transcript	26909268	26913112	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	stop_codon	26909265	26909267	.	-	0	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26909268	26909274	1	-	1	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26909268	26909274	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26909275	26909688	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26909689	26909852	1	-	0	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26909689	26909852	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26909853	26910057	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26910058	26910241	1	-	1	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26910058	26910241	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26910242	26910371	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26910372	26910462	1	-	2	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26910372	26910462	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26910463	26910955	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26910956	26911096	1	-	2	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26910956	26911096	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26911097	26911265	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26911266	26911285	1	-	1	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26911266	26911285	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26911286	26911591	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26911592	26911737	1	-	0	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26911592	26911737	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26911738	26911831	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26911832	26911988	1	-	1	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26911832	26911988	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26911989	26912263	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26912264	26912493	1	-	0	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26912264	26912493	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	intron	26912494	26912770	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	CDS	26912771	26913112	0.7	-	0	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	exon	26912771	26913112	.	-	.	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
Phchi.S1	AUGUSTUS	start_codon	26913110	26913112	.	-	0	transcript_id "Phchi.S1G425900.t1"; gene_id "Phchi.S1G425900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11138.t1 is derived from g15188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4359240	4360471	.	+	.	Phchi.S4G072000
Phchi.S4	AUGUSTUS	transcript	4359240	4360471	.	+	.	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	start_codon	4359240	4359242	.	+	0	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	CDS	4359240	4360121	0.83	+	0	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	exon	4359240	4360121	.	+	.	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	intron	4360122	4360201	.	+	.	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	CDS	4360202	4360471	0.95	+	0	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	exon	4360202	4360471	.	+	.	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
Phchi.S4	AUGUSTUS	stop_codon	4360472	4360474	.	+	0	transcript_id "Phchi.S4G072000.t1"; gene_id "Phchi.S4G072000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14516.t1 is derived from g12984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13271198	13273217	.	-	.	Phchi.S3G183500
Phchi.S3	AUGUSTUS	transcript	13271198	13273217	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	stop_codon	13271195	13271197	.	-	0	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13271198	13271388	0.96	-	2	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13271198	13271388	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13271389	13271470	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13271471	13271638	1	-	2	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13271471	13271638	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13271639	13271735	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13271736	13271784	1	-	0	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13271736	13271784	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13271785	13271892	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13271893	13271930	1	-	2	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13271893	13271930	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13271931	13272085	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13272086	13272219	1	-	1	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13272086	13272219	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13272220	13272331	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13272332	13272394	1	-	1	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13272332	13272394	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13272395	13272531	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13272532	13272699	1	-	1	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13272532	13272699	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13272700	13272794	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13272795	13272849	0.99	-	2	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13272795	13272849	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13272850	13272968	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13272969	13273049	1	-	2	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13272969	13273049	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	intron	13273050	13273123	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	CDS	13273124	13273217	1	-	0	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	exon	13273124	13273217	.	-	.	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
Phchi.S3	AUGUSTUS	start_codon	13273215	13273217	.	-	0	transcript_id "Phchi.S3G183500.t1"; gene_id "Phchi.S3G183500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4222.t1 is derived from g1391.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8994479	8995110	.	+	.	Phchi.S1G138100
Phchi.S1	AUGUSTUS	transcript	8994479	8995110	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	start_codon	8994479	8994481	.	+	0	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	CDS	8994479	8994631	0.31	+	0	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	exon	8994479	8994631	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	intron	8994632	8994732	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	CDS	8994733	8994768	0.81	+	0	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	exon	8994733	8994768	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	intron	8994769	8994864	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	CDS	8994865	8994950	1	+	0	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	exon	8994865	8994950	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	intron	8994951	8995049	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	CDS	8995050	8995110	1	+	1	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	exon	8995050	8995110	.	+	.	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
Phchi.S1	AUGUSTUS	stop_codon	8995111	8995113	.	+	0	transcript_id "Phchi.S1G138100.t1"; gene_id "Phchi.S1G138100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7829.t1 is derived from g5003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31396129	31398700	.	-	.	Phchi.S1G498800
Phchi.S1	AUGUSTUS	transcript	31396129	31398700	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	stop_codon	31396126	31396128	.	-	0	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31396129	31396250	0.94	-	2	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31396129	31396250	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31396251	31396354	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31396355	31396427	0.88	-	0	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31396355	31396427	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31396428	31396579	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31396580	31396602	0.93	-	2	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31396580	31396602	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31396603	31396692	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31396693	31396820	1	-	1	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31396693	31396820	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31396821	31396926	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31396927	31397082	1	-	1	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31396927	31397082	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31397083	31397245	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31397246	31397302	1	-	1	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31397246	31397302	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31397303	31397423	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31397424	31398026	0.81	-	1	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31397424	31398026	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31398027	31398127	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31398128	31398341	0.82	-	2	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31398128	31398341	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	intron	31398342	31398630	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	CDS	31398631	31398700	0.97	-	0	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	exon	31398631	31398700	.	-	.	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
Phchi.S1	AUGUSTUS	start_codon	31398698	31398700	.	-	0	transcript_id "Phchi.S1G498800.t1"; gene_id "Phchi.S1G498800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6956.t1 is derived from g4128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26132754	26138197	.	+	.	Phchi.S1G411500
Phchi.S1	AUGUSTUS	transcript	26132754	26138197	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	start_codon	26132754	26132756	.	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26132754	26132897	0.99	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26132754	26132897	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26132898	26133032	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26133033	26133105	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26133033	26133105	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26133106	26133235	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26133236	26133457	1	+	2	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26133236	26133457	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26133458	26133564	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26133565	26133611	1	+	2	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26133565	26133611	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26133612	26133731	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26133732	26133830	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26133732	26133830	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26133831	26134240	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26134241	26134315	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26134241	26134315	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26134316	26134407	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26134408	26134496	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26134408	26134496	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26134497	26134682	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26134683	26134823	0.74	+	1	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26134683	26134823	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26134824	26134936	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26134937	26135007	0.84	+	1	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26134937	26135007	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26135008	26135110	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26135111	26135190	1	+	2	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26135111	26135190	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26135191	26135305	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26135306	26135452	0.98	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26135306	26135452	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26135453	26135568	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26135569	26135631	0.98	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26135569	26135631	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26135632	26135764	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26135765	26135839	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26135765	26135839	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26135840	26135977	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26135978	26136132	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26135978	26136132	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26136133	26136236	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26136237	26136372	1	+	1	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26136237	26136372	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26136373	26136462	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26136463	26136594	0.99	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26136463	26136594	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26136595	26136700	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26136701	26136778	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26136701	26136778	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26136779	26136855	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26136856	26136911	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26136856	26136911	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26136912	26136993	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26136994	26137077	0.99	+	1	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26136994	26137077	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26137078	26137184	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26137185	26137341	0.89	+	1	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26137185	26137341	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26137342	26137450	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26137451	26137552	0.97	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26137451	26137552	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26137553	26137633	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26137634	26137680	1	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26137634	26137680	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26137681	26137865	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26137866	26137914	0.55	+	1	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26137866	26137914	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26137915	26137988	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26137989	26138024	0.63	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26137989	26138024	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	intron	26138025	26138176	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	CDS	26138177	26138197	0.64	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	exon	26138177	26138197	.	+	.	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
Phchi.S1	AUGUSTUS	stop_codon	26138198	26138200	.	+	0	transcript_id "Phchi.S1G411500.t1"; gene_id "Phchi.S1G411500"
# This transcript jg12862.t2 is derived from g11327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12863.t1 is derived from g11328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2810460	2812708	.	-	.	Phchi.S3G018200
Phchi.S3	AUGUSTUS	transcript	2810460	2812708	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	stop_codon	2810457	2810459	.	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2810460	2810627	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2810460	2810627	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2810628	2810717	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2810718	2810795	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2810718	2810795	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2810796	2810892	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2810893	2810974	1	-	1	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2810893	2810974	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2810975	2811066	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2811067	2811138	1	-	1	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2811067	2811138	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2811139	2811230	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2811231	2811352	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2811231	2811352	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2811353	2811438	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2811439	2811494	1	-	2	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2811439	2811494	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2811495	2811610	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2811611	2811680	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2811611	2811680	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2811681	2811780	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2811781	2811864	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2811781	2811864	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2811865	2811988	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2811989	2812057	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2811989	2812057	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2812058	2812141	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2812142	2812215	1	-	2	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2812142	2812215	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2812216	2812290	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2812291	2812402	1	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2812291	2812402	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	intron	2812403	2812495	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	CDS	2812496	2812708	0.27	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	exon	2812496	2812708	.	-	.	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
Phchi.S3	AUGUSTUS	start_codon	2812706	2812708	.	-	0	transcript_id "Phchi.S3G018200.t1"; gene_id "Phchi.S3G018200"
# This transcript jg1714.t2 is derived from g8634.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1715.t1 is derived from g8635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2669368	2670665	.	-	.	Phchi.S5G032400
Phchi.S5	AUGUSTUS	transcript	2669368	2670665	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	stop_codon	2669365	2669367	.	-	0	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	CDS	2669368	2669370	0.97	-	0	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	exon	2669368	2669370	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	intron	2669371	2669595	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	CDS	2669596	2669671	1	-	1	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	exon	2669596	2669671	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	intron	2669672	2669779	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	CDS	2669780	2669874	1	-	0	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	exon	2669780	2669874	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	intron	2669875	2669957	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	CDS	2669958	2670052	0.96	-	2	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	exon	2669958	2670052	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	intron	2670053	2670242	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	CDS	2670243	2670397	0.96	-	1	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	exon	2670243	2670397	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	intron	2670398	2670486	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	CDS	2670487	2670665	0.91	-	0	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	exon	2670487	2670665	.	-	.	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
Phchi.S5	AUGUSTUS	start_codon	2670663	2670665	.	-	0	transcript_id "Phchi.S5G032400.t1"; gene_id "Phchi.S5G032400"
# This transcript jg10949.t2 is derived from g14999.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10950.t1 is derived from g15000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3235269	3237004	.	-	.	Phchi.S4G053200
Phchi.S4	AUGUSTUS	transcript	3235269	3237004	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	stop_codon	3235266	3235268	.	-	0	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	CDS	3235269	3235582	0.99	-	2	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	exon	3235269	3235582	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	intron	3235583	3235723	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	CDS	3235724	3235980	0.69	-	1	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	exon	3235724	3235980	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	intron	3235981	3236129	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	CDS	3236130	3236179	0.98	-	0	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	exon	3236130	3236179	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	intron	3236180	3236252	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	CDS	3236253	3236306	0.67	-	0	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	exon	3236253	3236306	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	intron	3236307	3236617	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	CDS	3236618	3236678	0.54	-	1	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	exon	3236618	3236678	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	intron	3236679	3236894	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	CDS	3236895	3237004	0.54	-	0	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	exon	3236895	3237004	.	-	.	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
Phchi.S4	AUGUSTUS	start_codon	3237002	3237004	.	-	0	transcript_id "Phchi.S4G053200.t1"; gene_id "Phchi.S4G053200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15415.t1 is derived from g13883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18959273	18959863	.	+	.	Phchi.S3G273400
Phchi.S3	AUGUSTUS	transcript	18959273	18959863	.	+	.	transcript_id "Phchi.S3G273400.t1"; gene_id "Phchi.S3G273400"
Phchi.S3	AUGUSTUS	start_codon	18959273	18959275	.	+	0	transcript_id "Phchi.S3G273400.t1"; gene_id "Phchi.S3G273400"
Phchi.S3	AUGUSTUS	CDS	18959273	18959863	0.24	+	0	transcript_id "Phchi.S3G273400.t1"; gene_id "Phchi.S3G273400"
Phchi.S3	AUGUSTUS	exon	18959273	18959863	.	+	.	transcript_id "Phchi.S3G273400.t1"; gene_id "Phchi.S3G273400"
Phchi.S3	AUGUSTUS	stop_codon	18959864	18959866	.	+	0	transcript_id "Phchi.S3G273400.t1"; gene_id "Phchi.S3G273400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7596.t1 is derived from g4770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30194954	30195912	.	+	.	Phchi.S1G475500
Phchi.S1	AUGUSTUS	transcript	30194954	30195912	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	start_codon	30194954	30194956	.	+	0	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	CDS	30194954	30195087	1	+	0	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	exon	30194954	30195087	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	intron	30195088	30195181	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	CDS	30195182	30195289	1	+	1	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	exon	30195182	30195289	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	intron	30195290	30195407	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	CDS	30195408	30195479	1	+	1	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	exon	30195408	30195479	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	intron	30195480	30195571	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	CDS	30195572	30195651	1	+	1	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	exon	30195572	30195651	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	intron	30195652	30195742	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	CDS	30195743	30195912	0.97	+	2	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	exon	30195743	30195912	.	+	.	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
Phchi.S1	AUGUSTUS	stop_codon	30195913	30195915	.	+	0	transcript_id "Phchi.S1G475500.t1"; gene_id "Phchi.S1G475500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg984.t1 is derived from g10767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6882498	6883342	.	-	.	Phchi.S6G094300
Phchi.S6	AUGUSTUS	transcript	6882498	6883342	.	-	.	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	stop_codon	6882495	6882497	.	-	0	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	CDS	6882498	6882629	0.92	-	0	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	exon	6882498	6882629	.	-	.	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	intron	6882630	6882715	.	-	.	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	CDS	6882716	6883342	0.96	-	0	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	exon	6882716	6883342	.	-	.	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
Phchi.S6	AUGUSTUS	start_codon	6883340	6883342	.	-	0	transcript_id "Phchi.S6G094300.t1"; gene_id "Phchi.S6G094300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12950.t1 is derived from g11415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3284763	3285888	.	+	.	Phchi.S3G026900
Phchi.S3	AUGUSTUS	transcript	3284763	3285888	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	start_codon	3284763	3284765	.	+	0	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	CDS	3284763	3284849	0.37	+	0	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	exon	3284763	3284849	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	intron	3284850	3285102	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	CDS	3285103	3285115	0.92	+	0	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	exon	3285103	3285115	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	intron	3285116	3285192	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	CDS	3285193	3285225	1	+	2	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	exon	3285193	3285225	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	intron	3285226	3285362	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	CDS	3285363	3285424	1	+	2	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	exon	3285363	3285424	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	intron	3285425	3285670	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	CDS	3285671	3285736	1	+	0	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	exon	3285671	3285736	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	intron	3285737	3285873	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	CDS	3285874	3285888	1	+	0	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	exon	3285874	3285888	.	+	.	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
Phchi.S3	AUGUSTUS	stop_codon	3285889	3285891	.	+	0	transcript_id "Phchi.S3G026900.t1"; gene_id "Phchi.S3G026900"
# This transcript jg9545.t2 is derived from g6721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9546.t1 is derived from g6722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42408996	42411451	.	+	.	Phchi.S1G670500
Phchi.S1	AUGUSTUS	transcript	42408996	42411451	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	start_codon	42408996	42408998	.	+	0	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	CDS	42408996	42409031	0.88	+	0	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	exon	42408996	42409031	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	intron	42409032	42409352	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	CDS	42409353	42410386	0.95	+	0	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	exon	42409353	42410386	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	intron	42410387	42410635	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	CDS	42410636	42410967	0.84	+	1	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	exon	42410636	42410967	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	intron	42410968	42411098	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	CDS	42411099	42411451	0.4	+	2	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	exon	42411099	42411451	.	+	.	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
Phchi.S1	AUGUSTUS	stop_codon	42411452	42411454	.	+	0	transcript_id "Phchi.S1G670500.t1"; gene_id "Phchi.S1G670500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2809.t1 is derived from g9729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8972294	8974524	.	-	.	Phchi.S5G141800
Phchi.S5	AUGUSTUS	transcript	8972294	8974524	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	stop_codon	8972291	8972293	.	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8972294	8972423	1	-	1	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8972294	8972423	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8972424	8972545	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8972546	8972595	1	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8972546	8972595	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8972596	8972677	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8972678	8972770	1	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8972678	8972770	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8972771	8972872	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8972873	8972973	1	-	2	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8972873	8972973	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8972974	8973088	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8973089	8973173	0.99	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8973089	8973173	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8973174	8973278	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8973279	8973485	1	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8973279	8973485	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8973486	8973578	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8973579	8973610	1	-	2	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8973579	8973610	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8973611	8973745	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8973746	8973831	1	-	1	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8973746	8973831	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8973832	8973951	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8973952	8974058	1	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8973952	8974058	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8974059	8974168	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8974169	8974345	0.98	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8974169	8974345	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	intron	8974346	8974521	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	CDS	8974522	8974524	0.99	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	exon	8974522	8974524	.	-	.	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
Phchi.S5	AUGUSTUS	start_codon	8974522	8974524	.	-	0	transcript_id "Phchi.S5G141800.t1"; gene_id "Phchi.S5G141800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg255.t1 is derived from g10037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1730931	1731734	.	+	.	Phchi.S6G021400
Phchi.S6	AUGUSTUS	transcript	1730931	1731734	.	+	.	transcript_id "Phchi.S6G021400.t1"; gene_id "Phchi.S6G021400"
Phchi.S6	AUGUSTUS	start_codon	1730931	1730933	.	+	0	transcript_id "Phchi.S6G021400.t1"; gene_id "Phchi.S6G021400"
Phchi.S6	AUGUSTUS	CDS	1730931	1731734	0.9	+	0	transcript_id "Phchi.S6G021400.t1"; gene_id "Phchi.S6G021400"
Phchi.S6	AUGUSTUS	exon	1730931	1731734	.	+	.	transcript_id "Phchi.S6G021400.t1"; gene_id "Phchi.S6G021400"
Phchi.S6	AUGUSTUS	stop_codon	1731735	1731737	.	+	0	transcript_id "Phchi.S6G021400.t1"; gene_id "Phchi.S6G021400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2647.t1 is derived from g9567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7984633	7986253	.	+	.	Phchi.S5G125600
Phchi.S5	AUGUSTUS	transcript	7984633	7986253	.	+	.	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	start_codon	7984633	7984635	.	+	0	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	CDS	7984633	7986069	0.5	+	0	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	exon	7984633	7986069	.	+	.	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	intron	7986070	7986187	.	+	.	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	CDS	7986188	7986253	0.99	+	0	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	exon	7986188	7986253	.	+	.	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
Phchi.S5	AUGUSTUS	stop_codon	7986254	7986256	.	+	0	transcript_id "Phchi.S5G125600.t1"; gene_id "Phchi.S5G125600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12035.t1 is derived from g7710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	781766	785644	.	+	.	Phchi.S2G011500
Phchi.S2	AUGUSTUS	transcript	781766	785644	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	start_codon	781766	781768	.	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	781766	782060	1	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	781766	782060	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	782061	782164	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	782165	782277	0.98	+	2	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	782165	782277	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	782278	782374	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	782375	782683	1	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	782375	782683	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	782684	782894	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	782895	783007	1	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	782895	783007	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	783008	783111	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	783112	783442	1	+	1	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	783112	783442	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	783443	783587	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	783588	783803	1	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	783588	783803	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	783804	783975	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	783976	784212	0.94	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	783976	784212	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	784213	784324	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	784325	784510	0.99	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	784325	784510	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	784511	784666	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	784667	784807	1	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	784667	784807	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	784808	784904	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	784905	785173	0.99	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	784905	785173	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	785174	785323	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	785324	785405	1	+	1	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	785324	785405	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	intron	785406	785515	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	CDS	785516	785644	1	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	exon	785516	785644	.	+	.	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
Phchi.S2	AUGUSTUS	stop_codon	785645	785647	.	+	0	transcript_id "Phchi.S2G011500.t1"; gene_id "Phchi.S2G011500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10897.t1 is derived from g14947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2808436	2808970	.	+	.	Phchi.S4G047900
Phchi.S4	AUGUSTUS	transcript	2808436	2808970	.	+	.	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	start_codon	2808436	2808438	.	+	0	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	CDS	2808436	2808737	0.99	+	0	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	exon	2808436	2808737	.	+	.	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	intron	2808738	2808936	.	+	.	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	CDS	2808937	2808970	1	+	1	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	exon	2808937	2808970	.	+	.	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
Phchi.S4	AUGUSTUS	stop_codon	2808971	2808973	.	+	0	transcript_id "Phchi.S4G047900.t1"; gene_id "Phchi.S4G047900"
# This transcript jg10890.t2 is derived from g14940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10891.t1 is derived from g14941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2784250	2784991	.	-	.	Phchi.S4G047300
Phchi.S4	AUGUSTUS	transcript	2784250	2784991	.	-	.	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	stop_codon	2784247	2784249	.	-	0	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	CDS	2784250	2784279	0.84	-	0	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	exon	2784250	2784279	.	-	.	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	intron	2784280	2784574	.	-	.	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	CDS	2784575	2784838	0.92	-	0	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	exon	2784575	2784838	.	-	.	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	intron	2784839	2784919	.	-	.	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	CDS	2784920	2784991	0.94	-	0	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	exon	2784920	2784991	.	-	.	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
Phchi.S4	AUGUSTUS	start_codon	2784989	2784991	.	-	0	transcript_id "Phchi.S4G047300.t1"; gene_id "Phchi.S4G047300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4822.t1 is derived from g1992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13005747	13007744	.	-	.	Phchi.S1G198100
Phchi.S1	AUGUSTUS	transcript	13005747	13007744	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	stop_codon	13005744	13005746	.	-	0	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	CDS	13005747	13005780	0.87	-	1	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	exon	13005747	13005780	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	intron	13005781	13005872	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	CDS	13005873	13006972	1	-	0	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	exon	13005873	13006972	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	intron	13006973	13007055	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	CDS	13007056	13007150	1	-	2	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	exon	13007056	13007150	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	intron	13007151	13007240	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	CDS	13007241	13007409	1	-	0	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	exon	13007241	13007409	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	intron	13007410	13007490	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	CDS	13007491	13007594	0.94	-	2	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	exon	13007491	13007594	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	intron	13007595	13007683	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	CDS	13007684	13007744	0.35	-	0	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	exon	13007684	13007744	.	-	.	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
Phchi.S1	AUGUSTUS	start_codon	13007742	13007744	.	-	0	transcript_id "Phchi.S1G198100.t1"; gene_id "Phchi.S1G198100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15193.t1 is derived from g13661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17500007	17501089	.	-	.	Phchi.S3G251200
Phchi.S3	AUGUSTUS	transcript	17500007	17501089	.	-	.	transcript_id "Phchi.S3G251200.t1"; gene_id "Phchi.S3G251200"
Phchi.S3	AUGUSTUS	stop_codon	17500004	17500006	.	-	0	transcript_id "Phchi.S3G251200.t1"; gene_id "Phchi.S3G251200"
Phchi.S3	AUGUSTUS	CDS	17500007	17501089	0.28	-	0	transcript_id "Phchi.S3G251200.t1"; gene_id "Phchi.S3G251200"
Phchi.S3	AUGUSTUS	exon	17500007	17501089	.	-	.	transcript_id "Phchi.S3G251200.t1"; gene_id "Phchi.S3G251200"
Phchi.S3	AUGUSTUS	start_codon	17501087	17501089	.	-	0	transcript_id "Phchi.S3G251200.t1"; gene_id "Phchi.S3G251200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3438.t1 is derived from g607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3662220	3663013	.	-	.	Phchi.S1G059700
Phchi.S1	AUGUSTUS	transcript	3662220	3663013	.	-	.	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	stop_codon	3662217	3662219	.	-	0	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	CDS	3662220	3662490	0.57	-	1	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	exon	3662220	3662490	.	-	.	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	intron	3662491	3662734	.	-	.	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	CDS	3662735	3662835	0.85	-	0	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	exon	3662735	3662835	.	-	.	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	intron	3662836	3662905	.	-	.	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	CDS	3662906	3663013	0.52	-	0	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	exon	3662906	3663013	.	-	.	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
Phchi.S1	AUGUSTUS	start_codon	3663011	3663013	.	-	0	transcript_id "Phchi.S1G059700.t1"; gene_id "Phchi.S1G059700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10519.t1 is derived from g14569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	803497	805895	.	-	.	Phchi.S4G010100
Phchi.S4	AUGUSTUS	transcript	803497	805895	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	stop_codon	803494	803496	.	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	803497	803553	1	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	803497	803553	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	803554	803644	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	803645	803695	1	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	803645	803695	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	803696	803799	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	803800	803886	1	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	803800	803886	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	803887	803953	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	803954	804072	1	-	2	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	803954	804072	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	804073	804190	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	804191	804429	1	-	1	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	804191	804429	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	804430	804547	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	804548	804604	0.99	-	1	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	804548	804604	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	804605	804710	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	804711	804797	1	-	1	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	804711	804797	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	804798	804894	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	804895	805442	1	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	804895	805442	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	intron	805443	805583	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	CDS	805584	805895	0.99	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	exon	805584	805895	.	-	.	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
Phchi.S4	AUGUSTUS	start_codon	805893	805895	.	-	0	transcript_id "Phchi.S4G010100.t1"; gene_id "Phchi.S4G010100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3619.t1 is derived from g788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4784531	4787910	.	+	.	Phchi.S1G077800
Phchi.S1	AUGUSTUS	transcript	4784531	4787910	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	start_codon	4784531	4784533	.	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4784531	4784697	0.97	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4784531	4784697	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4784698	4784820	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4784821	4784941	1	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4784821	4784941	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4784942	4785067	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4785068	4785240	1	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4785068	4785240	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4785241	4785331	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4785332	4785425	1	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4785332	4785425	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4785426	4785567	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4785568	4785618	0.83	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4785568	4785618	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4785619	4785766	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4785767	4785832	0.99	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4785767	4785832	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4785833	4785946	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4785947	4786006	1	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4785947	4786006	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4786007	4786121	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4786122	4786186	1	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4786122	4786186	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4786187	4786276	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4786277	4786355	1	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4786277	4786355	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4786356	4786440	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4786441	4786682	1	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4786441	4786682	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4786683	4786772	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4786773	4786847	0.99	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4786773	4786847	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4786848	4786955	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4786956	4787057	0.69	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4786956	4787057	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4787058	4787131	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4787132	4787240	0.42	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4787132	4787240	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4787241	4787355	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4787356	4787429	0.77	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4787356	4787429	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	intron	4787430	4787825	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	CDS	4787826	4787910	0.79	+	1	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	exon	4787826	4787910	.	+	.	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
Phchi.S1	AUGUSTUS	stop_codon	4787911	4787913	.	+	0	transcript_id "Phchi.S1G077800.t1"; gene_id "Phchi.S1G077800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6534.t1 is derived from g3706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23523958	23524323	.	+	.	Phchi.S1G369300
Phchi.S1	AUGUSTUS	transcript	23523958	23524323	.	+	.	transcript_id "Phchi.S1G369300.t1"; gene_id "Phchi.S1G369300"
Phchi.S1	AUGUSTUS	start_codon	23523958	23523960	.	+	0	transcript_id "Phchi.S1G369300.t1"; gene_id "Phchi.S1G369300"
Phchi.S1	AUGUSTUS	CDS	23523958	23524323	0.97	+	0	transcript_id "Phchi.S1G369300.t1"; gene_id "Phchi.S1G369300"
Phchi.S1	AUGUSTUS	exon	23523958	23524323	.	+	.	transcript_id "Phchi.S1G369300.t1"; gene_id "Phchi.S1G369300"
Phchi.S1	AUGUSTUS	stop_codon	23524324	23524326	.	+	0	transcript_id "Phchi.S1G369300.t1"; gene_id "Phchi.S1G369300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3085.t1 is derived from g254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1554389	1554857	.	-	.	Phchi.S1G024400
Phchi.S1	AUGUSTUS	transcript	1554389	1554857	.	-	.	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	stop_codon	1554386	1554388	.	-	0	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	CDS	1554389	1554535	0.72	-	0	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	exon	1554389	1554535	.	-	.	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	intron	1554536	1554608	.	-	.	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	CDS	1554609	1554712	1	-	2	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	exon	1554609	1554712	.	-	.	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	intron	1554713	1554799	.	-	.	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	CDS	1554800	1554857	0.85	-	0	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	exon	1554800	1554857	.	-	.	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	start_codon	1554855	1554857	.	-	0	transcript_id "Phchi.S1G024400.t1"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	transcript	1554415	1554857	.	-	.	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	stop_codon	1554412	1554414	.	-	0	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	CDS	1554415	1554525	0.87	-	0	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	exon	1554415	1554525	.	-	.	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	intron	1554526	1554608	.	-	.	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	CDS	1554609	1554712	0.89	-	2	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	exon	1554609	1554712	.	-	.	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	intron	1554713	1554799	.	-	.	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	CDS	1554800	1554857	0.91	-	0	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	exon	1554800	1554857	.	-	.	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
Phchi.S1	AUGUSTUS	start_codon	1554855	1554857	.	-	0	transcript_id "Phchi.S1G024400.t2"; gene_id "Phchi.S1G024400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3903.t1 is derived from g1072.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6319382	6321695	.	+	.	Phchi.S1G106200
Phchi.S1	AUGUSTUS	transcript	6319961	6321695	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	start_codon	6319961	6319963	.	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6319961	6320074	0.83	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6319961	6320074	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320075	6320221	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6320222	6320281	1	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6320222	6320281	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320282	6320375	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6320376	6320612	1	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6320376	6320612	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320613	6320767	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6320768	6320928	1	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6320768	6320928	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320929	6321044	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6321045	6321142	1	+	1	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6321045	6321142	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6321143	6321318	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6321319	6321443	1	+	2	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6321319	6321443	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6321444	6321536	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6321537	6321695	1	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6321537	6321695	.	+	.	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	stop_codon	6321696	6321698	.	+	0	transcript_id "Phchi.S1G106200.t1"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	transcript	6319382	6321695	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	start_codon	6319382	6319384	.	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6319382	6319666	0.72	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6319382	6319666	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6319667	6319795	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6319796	6320074	0.92	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6319796	6320074	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320075	6320221	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6320222	6320281	1	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6320222	6320281	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320282	6320375	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6320376	6320612	1	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6320376	6320612	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320613	6320767	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6320768	6320928	0.98	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6320768	6320928	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6320929	6321044	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6321045	6321142	0.99	+	1	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6321045	6321142	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6321143	6321318	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6321319	6321443	1	+	2	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6321319	6321443	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6321444	6321536	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6321537	6321695	1	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6321537	6321695	.	+	.	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	stop_codon	6321696	6321698	.	+	0	transcript_id "Phchi.S1G106200.t2"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	transcript	6319382	6319823	.	+	.	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	start_codon	6319382	6319384	.	+	0	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6319382	6319666	0.77	+	0	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6319382	6319666	.	+	.	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	intron	6319667	6319808	.	+	.	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	CDS	6319809	6319823	1	+	0	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	exon	6319809	6319823	.	+	.	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
Phchi.S1	AUGUSTUS	stop_codon	6319824	6319826	.	+	0	transcript_id "Phchi.S1G106200.t3"; gene_id "Phchi.S1G106200"
# This transcript jg3643.t2 is derived from g812.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3643.t3 is derived from g812.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3643.t4 is derived from g812.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3644.t1 is derived from g813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4922676	4925593	.	+	.	Phchi.S1G080300
Phchi.S1	AUGUSTUS	transcript	4922676	4925593	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	start_codon	4922676	4922678	.	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4922676	4922798	1	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4922676	4922798	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4922799	4922983	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4922984	4923028	1	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4922984	4923028	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4923029	4923119	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4923120	4923175	1	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4923120	4923175	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4923176	4923264	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4923265	4923414	1	+	1	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4923265	4923414	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4923415	4923500	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4923501	4923611	1	+	1	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4923501	4923611	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4923612	4923705	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4923706	4923805	1	+	1	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4923706	4923805	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4923806	4923902	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4923903	4924187	1	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4923903	4924187	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4924188	4924323	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4924324	4924493	0.99	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4924324	4924493	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4924494	4924618	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4924619	4924747	1	+	1	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4924619	4924747	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4924748	4924872	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4924873	4924969	1	+	1	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4924873	4924969	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4924970	4925050	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4925051	4925128	1	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4925051	4925128	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	intron	4925129	4925206	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	CDS	4925207	4925593	1	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	exon	4925207	4925593	.	+	.	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
Phchi.S1	AUGUSTUS	stop_codon	4925594	4925596	.	+	0	transcript_id "Phchi.S1G080300.t1"; gene_id "Phchi.S1G080300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7929.t1 is derived from g5103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31938415	31939953	.	+	.	Phchi.S1G508800
Phchi.S1	AUGUSTUS	transcript	31938415	31939953	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	start_codon	31938415	31938417	.	+	0	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	CDS	31938415	31938762	1	+	0	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	exon	31938415	31938762	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	intron	31938763	31938962	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	CDS	31938963	31939164	1	+	0	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	exon	31938963	31939164	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	intron	31939165	31939318	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	CDS	31939319	31939553	1	+	2	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	exon	31939319	31939553	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	intron	31939554	31939634	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	CDS	31939635	31939953	1	+	1	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	exon	31939635	31939953	.	+	.	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
Phchi.S1	AUGUSTUS	stop_codon	31939954	31939956	.	+	0	transcript_id "Phchi.S1G508800.t1"; gene_id "Phchi.S1G508800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10097.t1 is derived from g7273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45731605	45733534	.	-	.	Phchi.S1G725600
Phchi.S1	AUGUSTUS	transcript	45731605	45733534	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	stop_codon	45731602	45731604	.	-	0	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45731605	45732103	0.98	-	1	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45731605	45732103	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45732104	45732234	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45732235	45732338	0.99	-	0	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45732235	45732338	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45732339	45732449	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45732450	45732512	0.98	-	0	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45732450	45732512	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45732513	45732619	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45732620	45732648	0.99	-	2	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45732620	45732648	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45732649	45732734	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45732735	45732773	1	-	2	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45732735	45732773	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45732774	45732869	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45732870	45732919	1	-	1	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45732870	45732919	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45732920	45732999	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45733000	45733227	1	-	1	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45733000	45733227	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	intron	45733228	45733415	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	CDS	45733416	45733534	0.96	-	0	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	exon	45733416	45733534	.	-	.	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
Phchi.S1	AUGUSTUS	start_codon	45733532	45733534	.	-	0	transcript_id "Phchi.S1G725600.t1"; gene_id "Phchi.S1G725600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6609.t1 is derived from g3781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23996562	23996858	.	+	.	Phchi.S1G376800
Phchi.S1	AUGUSTUS	transcript	23996562	23996858	.	+	.	transcript_id "Phchi.S1G376800.t1"; gene_id "Phchi.S1G376800"
Phchi.S1	AUGUSTUS	start_codon	23996562	23996564	.	+	0	transcript_id "Phchi.S1G376800.t1"; gene_id "Phchi.S1G376800"
Phchi.S1	AUGUSTUS	CDS	23996562	23996858	0.45	+	0	transcript_id "Phchi.S1G376800.t1"; gene_id "Phchi.S1G376800"
Phchi.S1	AUGUSTUS	exon	23996562	23996858	.	+	.	transcript_id "Phchi.S1G376800.t1"; gene_id "Phchi.S1G376800"
Phchi.S1	AUGUSTUS	stop_codon	23996859	23996861	.	+	0	transcript_id "Phchi.S1G376800.t1"; gene_id "Phchi.S1G376800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7000.t1 is derived from g4172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26331403	26336326	.	-	.	Phchi.S1G415900
Phchi.S1	AUGUSTUS	transcript	26331403	26336326	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	stop_codon	26331400	26331402	.	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26331403	26331878	1	-	2	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26331403	26331878	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26331879	26331957	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26331958	26332201	1	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26331958	26332201	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26332202	26332292	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26332293	26332358	1	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26332293	26332358	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26332359	26332435	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26332436	26332622	1	-	1	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26332436	26332622	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26332623	26332707	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26332708	26332953	1	-	1	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26332708	26332953	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26332954	26333053	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26333054	26333193	1	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26333054	26333193	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26333194	26333293	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26333294	26333482	1	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26333294	26333482	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26333483	26333602	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26333603	26334600	0.47	-	2	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26333603	26334600	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26334601	26334688	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26334689	26335202	0.26	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26334689	26335202	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26335203	26335447	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26335448	26335531	0.54	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26335448	26335531	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26335532	26335623	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26335624	26335734	0.99	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26335624	26335734	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26335735	26335853	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26335854	26335928	0.94	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26335854	26335928	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	intron	26335929	26336173	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	CDS	26336174	26336326	0.52	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	exon	26336174	26336326	.	-	.	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
Phchi.S1	AUGUSTUS	start_codon	26336324	26336326	.	-	0	transcript_id "Phchi.S1G415900.t1"; gene_id "Phchi.S1G415900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11170.t1 is derived from g15220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4450587	4451368	.	+	.	Phchi.S4G075200
Phchi.S4	AUGUSTUS	transcript	4450587	4451368	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	start_codon	4450587	4450589	.	+	0	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	CDS	4450587	4450612	0.47	+	0	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	exon	4450587	4450612	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	intron	4450613	4450699	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	CDS	4450700	4450883	0.5	+	1	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	exon	4450700	4450883	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	intron	4450884	4450989	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	CDS	4450990	4451080	0.92	+	0	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	exon	4450990	4451080	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	intron	4451081	4451258	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	CDS	4451259	4451368	0.57	+	2	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	exon	4451259	4451368	.	+	.	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
Phchi.S4	AUGUSTUS	stop_codon	4451369	4451371	.	+	0	transcript_id "Phchi.S4G075200.t1"; gene_id "Phchi.S4G075200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5120.t1 is derived from g2290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14819707	14820322	.	-	.	Phchi.S1G227900
Phchi.S1	AUGUSTUS	transcript	14819707	14820322	.	-	.	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	stop_codon	14819704	14819706	.	-	0	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	CDS	14819707	14820184	0.79	-	1	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	exon	14819707	14820184	.	-	.	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	intron	14820185	14820290	.	-	.	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	CDS	14820291	14820322	0.93	-	0	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	exon	14820291	14820322	.	-	.	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
Phchi.S1	AUGUSTUS	start_codon	14820320	14820322	.	-	0	transcript_id "Phchi.S1G227900.t1"; gene_id "Phchi.S1G227900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7804.t1 is derived from g4978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31263491	31264669	.	+	.	Phchi.S1G496300
Phchi.S1	AUGUSTUS	transcript	31263491	31264669	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	start_codon	31263491	31263493	.	+	0	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	CDS	31263491	31263532	1	+	0	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	exon	31263491	31263532	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	intron	31263533	31263842	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	CDS	31263843	31263850	0.96	+	0	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	exon	31263843	31263850	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	intron	31263851	31264117	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	CDS	31264118	31264244	0.91	+	1	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	exon	31264118	31264244	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	intron	31264245	31264341	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	CDS	31264342	31264410	1	+	0	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	exon	31264342	31264410	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	intron	31264411	31264501	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	CDS	31264502	31264669	1	+	0	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	exon	31264502	31264669	.	+	.	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
Phchi.S1	AUGUSTUS	stop_codon	31264670	31264672	.	+	0	transcript_id "Phchi.S1G496300.t1"; gene_id "Phchi.S1G496300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6665.t1 is derived from g3837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24397653	24400017	.	+	.	Phchi.S1G382400
Phchi.S1	AUGUSTUS	transcript	24397653	24400017	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	start_codon	24397653	24397655	.	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24397653	24397770	0.99	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24397653	24397770	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24397771	24397930	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24397931	24398128	1	+	2	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24397931	24398128	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24398129	24398251	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24398252	24398363	1	+	2	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24398252	24398363	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24398364	24398481	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24398482	24398830	0.96	+	1	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24398482	24398830	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24398831	24398941	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24398942	24399079	1	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24398942	24399079	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399080	24399167	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399168	24399284	1	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399168	24399284	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399285	24399390	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399391	24399576	1	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399391	24399576	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399577	24399705	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399706	24399762	1	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399706	24399762	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399763	24399846	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399847	24400017	0.99	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399847	24400017	.	+	.	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	stop_codon	24400018	24400020	.	+	0	transcript_id "Phchi.S1G382400.t1"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	transcript	24397653	24400017	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	start_codon	24397653	24397655	.	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24397653	24397770	1	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24397653	24397770	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24397771	24397927	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24397928	24398128	1	+	2	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24397928	24398128	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24398129	24398251	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24398252	24398363	1	+	2	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24398252	24398363	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24398364	24398481	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24398482	24398830	0.91	+	1	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24398482	24398830	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24398831	24398941	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24398942	24399079	1	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24398942	24399079	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399080	24399167	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399168	24399284	1	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399168	24399284	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399285	24399390	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399391	24399576	1	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399391	24399576	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399577	24399705	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399706	24399762	1	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399706	24399762	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	intron	24399763	24399846	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	CDS	24399847	24400017	0.98	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	exon	24399847	24400017	.	+	.	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
Phchi.S1	AUGUSTUS	stop_codon	24400018	24400020	.	+	0	transcript_id "Phchi.S1G382400.t2"; gene_id "Phchi.S1G382400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12831.t1 is derived from g11296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2594615	2601639	.	-	.	Phchi.S3G015000
Phchi.S3	AUGUSTUS	transcript	2594615	2601639	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	stop_codon	2594612	2594614	.	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2594615	2595800	0.99	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2594615	2595800	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2595801	2595881	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2595882	2596056	1	-	2	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2595882	2596056	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596057	2596134	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596135	2596303	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596135	2596303	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596304	2596394	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596395	2596485	1	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596395	2596485	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596486	2596580	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596581	2596639	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596581	2596639	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596640	2596734	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596735	2596824	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596735	2596824	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596825	2596963	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596964	2597050	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596964	2597050	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597051	2597207	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597208	2597250	1	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597208	2597250	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597251	2597403	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597404	2597483	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597404	2597483	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597484	2597563	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597564	2597620	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597564	2597620	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597621	2597736	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597737	2597862	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597737	2597862	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597863	2597970	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597971	2598058	1	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597971	2598058	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598059	2598201	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598202	2598531	0.97	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598202	2598531	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598532	2598652	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598653	2598750	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598653	2598750	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598751	2598833	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598834	2598902	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598834	2598902	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598903	2598982	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598983	2599036	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598983	2599036	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599037	2599214	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599215	2599343	0.96	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599215	2599343	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599344	2599465	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599466	2599557	0.98	-	2	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599466	2599557	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599558	2599676	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599677	2599761	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599677	2599761	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599762	2599984	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599985	2600138	1	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599985	2600138	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600139	2600291	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600292	2600491	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600292	2600491	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600492	2600585	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600586	2600652	1	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600586	2600652	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600653	2600758	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600759	2600901	0.93	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600759	2600901	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600902	2600985	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600986	2601364	1	-	1	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600986	2601364	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2601365	2601511	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2601512	2601639	1	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2601512	2601639	.	-	.	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	start_codon	2601637	2601639	.	-	0	transcript_id "Phchi.S3G015000.t1"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	transcript	2594615	2601639	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	stop_codon	2594612	2594614	.	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2594615	2595800	1	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2594615	2595800	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2595801	2595881	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2595882	2596056	1	-	2	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2595882	2596056	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596057	2596134	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596135	2596303	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596135	2596303	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596304	2596394	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596395	2596485	1	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596395	2596485	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596486	2596580	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596581	2596639	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596581	2596639	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596640	2596734	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596735	2596824	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596735	2596824	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2596825	2596963	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2596964	2597050	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2596964	2597050	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597051	2597207	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597208	2597250	1	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597208	2597250	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597251	2597403	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597404	2597483	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597404	2597483	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597484	2597563	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597564	2597620	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597564	2597620	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597621	2597736	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597737	2597862	0.99	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597737	2597862	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2597863	2597970	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2597971	2598026	0.56	-	2	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2597971	2598026	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598027	2598201	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598202	2598276	0.53	-	2	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598202	2598276	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598277	2598394	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598395	2598531	0.41	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598395	2598531	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598532	2598652	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598653	2598750	0.97	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598653	2598750	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598751	2598833	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598834	2598902	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598834	2598902	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2598903	2598982	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2598983	2599036	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2598983	2599036	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599037	2599214	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599215	2599343	0.95	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599215	2599343	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599344	2599465	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599466	2599557	0.95	-	2	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599466	2599557	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599558	2599676	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599677	2599761	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599677	2599761	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2599762	2599984	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2599985	2600138	1	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2599985	2600138	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600139	2600291	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600292	2600491	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600292	2600491	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600492	2600585	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600586	2600652	1	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600586	2600652	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600653	2600758	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600759	2600901	0.96	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600759	2600901	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2600902	2600985	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2600986	2601364	1	-	1	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2600986	2601364	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	intron	2601365	2601511	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	CDS	2601512	2601639	1	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	exon	2601512	2601639	.	-	.	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
Phchi.S3	AUGUSTUS	start_codon	2601637	2601639	.	-	0	transcript_id "Phchi.S3G015000.t2"; gene_id "Phchi.S3G015000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4925.t1 is derived from g2095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13598806	13601588	.	-	.	Phchi.S1G208400
Phchi.S1	AUGUSTUS	transcript	13598806	13601588	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	stop_codon	13598803	13598805	.	-	0	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	CDS	13598806	13599439	0.96	-	1	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	exon	13598806	13599439	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	intron	13599440	13599719	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	CDS	13599720	13599760	0.95	-	0	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	exon	13599720	13599760	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	intron	13599761	13599833	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	CDS	13599834	13599854	0.95	-	0	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	exon	13599834	13599854	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	intron	13599855	13599999	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	CDS	13600000	13600952	0.61	-	2	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	exon	13600000	13600952	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	intron	13600953	13601233	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	CDS	13601234	13601588	0.45	-	0	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	exon	13601234	13601588	.	-	.	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
Phchi.S1	AUGUSTUS	start_codon	13601586	13601588	.	-	0	transcript_id "Phchi.S1G208400.t1"; gene_id "Phchi.S1G208400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7481.t1 is derived from g4654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29560052	29560562	.	+	.	Phchi.S1G464000
Phchi.S1	AUGUSTUS	transcript	29560052	29560562	.	+	.	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	start_codon	29560052	29560054	.	+	0	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	CDS	29560052	29560087	0.91	+	0	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	exon	29560052	29560087	.	+	.	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	intron	29560088	29560165	.	+	.	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	CDS	29560166	29560388	0.93	+	0	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	exon	29560166	29560388	.	+	.	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	intron	29560389	29560536	.	+	.	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	CDS	29560537	29560562	0.93	+	2	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	exon	29560537	29560562	.	+	.	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
Phchi.S1	AUGUSTUS	stop_codon	29560563	29560565	.	+	0	transcript_id "Phchi.S1G464000.t1"; gene_id "Phchi.S1G464000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6011.t1 is derived from g3182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20421760	20422115	.	+	.	Phchi.S1G317000
Phchi.S1	AUGUSTUS	transcript	20421760	20422115	.	+	.	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	start_codon	20421760	20421762	.	+	0	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	CDS	20421760	20421819	1	+	0	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	exon	20421760	20421819	.	+	.	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	intron	20421820	20421968	.	+	.	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	CDS	20421969	20422115	0.82	+	0	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	exon	20421969	20422115	.	+	.	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
Phchi.S1	AUGUSTUS	stop_codon	20422116	20422118	.	+	0	transcript_id "Phchi.S1G317000.t1"; gene_id "Phchi.S1G317000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11209.t1 is derived from g15259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4793931	4797757	.	+	.	Phchi.S4G079100
Phchi.S4	AUGUSTUS	transcript	4793931	4797757	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	start_codon	4793931	4793933	.	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4793931	4794116	0.93	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4793931	4794116	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4794117	4794547	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4794548	4794757	1	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4794548	4794757	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4794758	4795680	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4795681	4795743	1	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4795681	4795743	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4795744	4795899	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4795900	4795997	1	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4795900	4795997	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4795998	4796108	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796109	4796204	1	+	1	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796109	4796204	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796205	4796302	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796303	4796360	1	+	1	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796303	4796360	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796361	4796447	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796448	4796555	1	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796448	4796555	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796556	4796641	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796642	4796723	1	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796642	4796723	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796724	4796884	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796885	4796997	1	+	2	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796885	4796997	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796998	4797148	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4797149	4797757	0.99	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4797149	4797757	.	+	.	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	stop_codon	4797758	4797760	.	+	0	transcript_id "Phchi.S4G079100.t1"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	transcript	4793931	4797757	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	start_codon	4793931	4793933	.	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4793931	4794116	0.91	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4793931	4794116	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4794117	4794547	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4794548	4794757	1	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4794548	4794757	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4794758	4795680	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4795681	4795743	1	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4795681	4795743	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4795744	4795923	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4795924	4795997	1	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4795924	4795997	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4795998	4796108	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796109	4796204	1	+	1	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796109	4796204	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796205	4796302	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796303	4796360	1	+	1	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796303	4796360	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796361	4796447	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796448	4796555	1	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796448	4796555	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796556	4796641	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796642	4796723	1	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796642	4796723	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796724	4796884	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796885	4796997	1	+	2	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796885	4796997	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796998	4797148	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4797149	4797757	0.98	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4797149	4797757	.	+	.	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	stop_codon	4797758	4797760	.	+	0	transcript_id "Phchi.S4G079100.t2"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	transcript	4793931	4797757	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	start_codon	4793931	4793933	.	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4793931	4794116	0.86	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4793931	4794116	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4794117	4794547	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4794548	4794757	1	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4794548	4794757	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4794758	4795680	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4795681	4795743	1	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4795681	4795743	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4795744	4795899	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4795900	4795997	1	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4795900	4795997	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4795998	4796108	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796109	4796204	1	+	1	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796109	4796204	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796205	4796302	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796303	4796360	1	+	1	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796303	4796360	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796361	4796447	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796448	4796555	1	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796448	4796555	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796556	4796641	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796642	4796723	1	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796642	4796723	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796724	4796884	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4796885	4796991	1	+	2	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4796885	4796991	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	intron	4796992	4797148	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	CDS	4797149	4797757	0.99	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	exon	4797149	4797757	.	+	.	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
Phchi.S4	AUGUSTUS	stop_codon	4797758	4797760	.	+	0	transcript_id "Phchi.S4G079100.t3"; gene_id "Phchi.S4G079100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4301.t1 is derived from g1470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9510373	9511761	.	-	.	Phchi.S1G146000
Phchi.S1	AUGUSTUS	transcript	9510373	9511761	.	-	.	transcript_id "Phchi.S1G146000.t1"; gene_id "Phchi.S1G146000"
Phchi.S1	AUGUSTUS	stop_codon	9510370	9510372	.	-	0	transcript_id "Phchi.S1G146000.t1"; gene_id "Phchi.S1G146000"
Phchi.S1	AUGUSTUS	CDS	9510373	9511761	0.84	-	0	transcript_id "Phchi.S1G146000.t1"; gene_id "Phchi.S1G146000"
Phchi.S1	AUGUSTUS	exon	9510373	9511761	.	-	.	transcript_id "Phchi.S1G146000.t1"; gene_id "Phchi.S1G146000"
Phchi.S1	AUGUSTUS	start_codon	9511759	9511761	.	-	0	transcript_id "Phchi.S1G146000.t1"; gene_id "Phchi.S1G146000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3556.t1 is derived from g725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4460676	4462631	.	+	.	Phchi.S1G071500
Phchi.S1	AUGUSTUS	transcript	4460676	4462631	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	start_codon	4460676	4460678	.	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4460676	4460797	0.49	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4460676	4460797	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4460798	4460947	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4460948	4461047	1	+	1	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4460948	4461047	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4461048	4461137	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4461138	4461194	1	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4461138	4461194	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4461195	4461497	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4461498	4461563	1	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4461498	4461563	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4461564	4461703	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4461704	4461898	1	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4461704	4461898	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4461899	4461996	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4461997	4462108	1	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4461997	4462108	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4462109	4462204	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4462205	4462428	1	+	2	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4462205	4462428	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	intron	4462429	4462541	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	CDS	4462542	4462631	0.99	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	exon	4462542	4462631	.	+	.	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
Phchi.S1	AUGUSTUS	stop_codon	4462632	4462634	.	+	0	transcript_id "Phchi.S1G071500.t1"; gene_id "Phchi.S1G071500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11079.t1 is derived from g15129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3987622	3988417	.	+	.	Phchi.S4G066100
Phchi.S4	AUGUSTUS	transcript	3987622	3988417	.	+	.	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	start_codon	3987622	3987624	.	+	0	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	CDS	3987622	3987909	0.94	+	0	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	exon	3987622	3987909	.	+	.	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	intron	3987910	3988104	.	+	.	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	CDS	3988105	3988175	0.75	+	0	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	exon	3988105	3988175	.	+	.	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	intron	3988176	3988263	.	+	.	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	CDS	3988264	3988417	0.77	+	1	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	exon	3988264	3988417	.	+	.	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
Phchi.S4	AUGUSTUS	stop_codon	3988418	3988420	.	+	0	transcript_id "Phchi.S4G066100.t1"; gene_id "Phchi.S4G066100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9721.t1 is derived from g6897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43398252	43399139	.	+	.	Phchi.S1G688000
Phchi.S1	AUGUSTUS	transcript	43398252	43399139	.	+	.	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	start_codon	43398252	43398254	.	+	0	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	CDS	43398252	43398593	0.56	+	0	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	exon	43398252	43398593	.	+	.	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	intron	43398594	43398872	.	+	.	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	CDS	43398873	43399139	0.99	+	0	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	exon	43398873	43399139	.	+	.	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
Phchi.S1	AUGUSTUS	stop_codon	43399140	43399142	.	+	0	transcript_id "Phchi.S1G688000.t1"; gene_id "Phchi.S1G688000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7603.t1 is derived from g4777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30214592	30216338	.	-	.	Phchi.S1G476200
Phchi.S1	AUGUSTUS	transcript	30214592	30216338	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	stop_codon	30214589	30214591	.	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30214592	30214762	0.84	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30214592	30214762	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30214763	30214894	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30214895	30214974	1	-	2	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30214895	30214974	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30214975	30215068	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30215069	30215150	0.99	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30215069	30215150	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30215151	30215257	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30215258	30215320	0.99	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30215258	30215320	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30215321	30215453	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30215454	30215565	0.99	-	1	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30215454	30215565	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30215566	30215674	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30215675	30215755	0.99	-	1	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30215675	30215755	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30215756	30215877	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30215878	30215982	0.93	-	1	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30215878	30215982	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30215983	30216085	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30216086	30216132	0.97	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30216086	30216132	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	intron	30216133	30216218	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	CDS	30216219	30216338	0.98	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	exon	30216219	30216338	.	-	.	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
Phchi.S1	AUGUSTUS	start_codon	30216336	30216338	.	-	0	transcript_id "Phchi.S1G476200.t1"; gene_id "Phchi.S1G476200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg722.t1 is derived from g10504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5126227	5129334	.	-	.	Phchi.S6G068100
Phchi.S6	AUGUSTUS	transcript	5126227	5129334	.	-	.	transcript_id "Phchi.S6G068100.t1"; gene_id "Phchi.S6G068100"
Phchi.S6	AUGUSTUS	stop_codon	5126224	5126226	.	-	0	transcript_id "Phchi.S6G068100.t1"; gene_id "Phchi.S6G068100"
Phchi.S6	AUGUSTUS	CDS	5126227	5129334	0.62	-	0	transcript_id "Phchi.S6G068100.t1"; gene_id "Phchi.S6G068100"
Phchi.S6	AUGUSTUS	exon	5126227	5129334	.	-	.	transcript_id "Phchi.S6G068100.t1"; gene_id "Phchi.S6G068100"
Phchi.S6	AUGUSTUS	start_codon	5129332	5129334	.	-	0	transcript_id "Phchi.S6G068100.t1"; gene_id "Phchi.S6G068100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11469.t1 is derived from g15519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6510081	6511888	.	-	.	Phchi.S4G105100
Phchi.S4	AUGUSTUS	transcript	6510081	6511888	.	-	.	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	stop_codon	6510078	6510080	.	-	0	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	CDS	6510081	6511103	1	-	0	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	exon	6510081	6511103	.	-	.	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	intron	6511104	6511219	.	-	.	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	CDS	6511220	6511698	0.89	-	2	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	exon	6511220	6511698	.	-	.	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	intron	6511699	6511818	.	-	.	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	CDS	6511819	6511888	0.99	-	0	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	exon	6511819	6511888	.	-	.	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
Phchi.S4	AUGUSTUS	start_codon	6511886	6511888	.	-	0	transcript_id "Phchi.S4G105100.t1"; gene_id "Phchi.S4G105100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14450.t1 is derived from g12918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12899645	12902045	.	+	.	Phchi.S3G176900
Phchi.S3	AUGUSTUS	transcript	12899645	12902045	.	+	.	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	start_codon	12899645	12899647	.	+	0	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	CDS	12899645	12899827	0.97	+	0	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	exon	12899645	12899827	.	+	.	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	intron	12899828	12899937	.	+	.	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	CDS	12899938	12901290	0.9	+	0	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	exon	12899938	12901290	.	+	.	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	intron	12901291	12901415	.	+	.	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	CDS	12901416	12902045	0.45	+	0	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	exon	12901416	12902045	.	+	.	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
Phchi.S3	AUGUSTUS	stop_codon	12902046	12902048	.	+	0	transcript_id "Phchi.S3G176900.t1"; gene_id "Phchi.S3G176900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4812.t1 is derived from g1982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12940498	12943434	.	+	.	Phchi.S1G197100
Phchi.S1	AUGUSTUS	transcript	12940498	12943434	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	start_codon	12940498	12940500	.	+	0	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	CDS	12940498	12940698	0.99	+	0	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	exon	12940498	12940698	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	intron	12940699	12940853	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	CDS	12940854	12940936	0.92	+	0	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	exon	12940854	12940936	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	intron	12940937	12941045	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	CDS	12941046	12941207	0.92	+	1	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	exon	12941046	12941207	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	intron	12941208	12941462	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	CDS	12941463	12941814	0.95	+	1	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	exon	12941463	12941814	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	intron	12941815	12941976	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	CDS	12941977	12942216	0.95	+	0	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	exon	12941977	12942216	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	intron	12942217	12942378	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	CDS	12942379	12943434	0.76	+	0	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	exon	12942379	12943434	.	+	.	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
Phchi.S1	AUGUSTUS	stop_codon	12943435	12943437	.	+	0	transcript_id "Phchi.S1G197100.t1"; gene_id "Phchi.S1G197100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5267.t1 is derived from g2437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15956610	15957907	.	+	.	Phchi.S1G242600
Phchi.S1	AUGUSTUS	transcript	15956610	15957907	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	start_codon	15956610	15956612	.	+	0	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	CDS	15956610	15956900	0.4	+	0	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	exon	15956610	15956900	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	intron	15956901	15957076	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	CDS	15957077	15957328	0.95	+	0	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	exon	15957077	15957328	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	intron	15957329	15957435	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	CDS	15957436	15957816	0.99	+	0	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	exon	15957436	15957816	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	intron	15957817	15957904	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	CDS	15957905	15957907	1	+	0	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	exon	15957905	15957907	.	+	.	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
Phchi.S1	AUGUSTUS	stop_codon	15957908	15957910	.	+	0	transcript_id "Phchi.S1G242600.t1"; gene_id "Phchi.S1G242600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9706.t1 is derived from g6882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43351180	43353048	.	+	.	Phchi.S1G686500
Phchi.S1	AUGUSTUS	transcript	43351180	43353048	.	+	.	transcript_id "Phchi.S1G686500.t1"; gene_id "Phchi.S1G686500"
Phchi.S1	AUGUSTUS	start_codon	43351180	43351182	.	+	0	transcript_id "Phchi.S1G686500.t1"; gene_id "Phchi.S1G686500"
Phchi.S1	AUGUSTUS	CDS	43351180	43353048	0.83	+	0	transcript_id "Phchi.S1G686500.t1"; gene_id "Phchi.S1G686500"
Phchi.S1	AUGUSTUS	exon	43351180	43353048	.	+	.	transcript_id "Phchi.S1G686500.t1"; gene_id "Phchi.S1G686500"
Phchi.S1	AUGUSTUS	stop_codon	43353049	43353051	.	+	0	transcript_id "Phchi.S1G686500.t1"; gene_id "Phchi.S1G686500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2632.t1 is derived from g9552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7860112	7860426	.	-	.	Phchi.S5G124100
Phchi.S5	AUGUSTUS	transcript	7860112	7860426	.	-	.	transcript_id "Phchi.S5G124100.t1"; gene_id "Phchi.S5G124100"
Phchi.S5	AUGUSTUS	stop_codon	7860109	7860111	.	-	0	transcript_id "Phchi.S5G124100.t1"; gene_id "Phchi.S5G124100"
Phchi.S5	AUGUSTUS	CDS	7860112	7860426	0.72	-	0	transcript_id "Phchi.S5G124100.t1"; gene_id "Phchi.S5G124100"
Phchi.S5	AUGUSTUS	exon	7860112	7860426	.	-	.	transcript_id "Phchi.S5G124100.t1"; gene_id "Phchi.S5G124100"
Phchi.S5	AUGUSTUS	start_codon	7860424	7860426	.	-	0	transcript_id "Phchi.S5G124100.t1"; gene_id "Phchi.S5G124100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg842.t1 is derived from g10624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5849273	5850555	.	-	.	Phchi.S6G080100
Phchi.S6	AUGUSTUS	transcript	5849273	5850555	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	stop_codon	5849270	5849272	.	-	0	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	CDS	5849273	5849661	0.99	-	2	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	exon	5849273	5849661	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	intron	5849662	5849773	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	CDS	5849774	5849939	0.99	-	0	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	exon	5849774	5849939	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	intron	5849940	5850030	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	CDS	5850031	5850222	1	-	0	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	exon	5850031	5850222	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	intron	5850223	5850339	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	CDS	5850340	5850555	0.87	-	0	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	exon	5850340	5850555	.	-	.	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
Phchi.S6	AUGUSTUS	start_codon	5850553	5850555	.	-	0	transcript_id "Phchi.S6G080100.t1"; gene_id "Phchi.S6G080100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15631.t1 is derived from g14100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20378541	20379404	.	+	.	Phchi.S3G295000
Phchi.S3	AUGUSTUS	transcript	20378541	20379404	.	+	.	transcript_id "Phchi.S3G295000.t1"; gene_id "Phchi.S3G295000"
Phchi.S3	AUGUSTUS	start_codon	20378541	20378543	.	+	0	transcript_id "Phchi.S3G295000.t1"; gene_id "Phchi.S3G295000"
Phchi.S3	AUGUSTUS	CDS	20378541	20379404	1	+	0	transcript_id "Phchi.S3G295000.t1"; gene_id "Phchi.S3G295000"
Phchi.S3	AUGUSTUS	exon	20378541	20379404	.	+	.	transcript_id "Phchi.S3G295000.t1"; gene_id "Phchi.S3G295000"
Phchi.S3	AUGUSTUS	stop_codon	20379405	20379407	.	+	0	transcript_id "Phchi.S3G295000.t1"; gene_id "Phchi.S3G295000"
# This transcript jg1526.t2 is derived from g8445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1527.t1 is derived from g8446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1590567	1591026	.	+	.	Phchi.S5G013600
Phchi.S5	AUGUSTUS	transcript	1590567	1591026	.	+	.	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	start_codon	1590567	1590569	.	+	0	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	CDS	1590567	1590599	0.78	+	0	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	exon	1590567	1590599	.	+	.	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	intron	1590600	1590694	.	+	.	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	CDS	1590695	1590859	0.87	+	0	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	exon	1590695	1590859	.	+	.	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	intron	1590860	1590993	.	+	.	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	CDS	1590994	1591026	0.89	+	0	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	exon	1590994	1591026	.	+	.	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
Phchi.S5	AUGUSTUS	stop_codon	1591027	1591029	.	+	0	transcript_id "Phchi.S5G013600.t1"; gene_id "Phchi.S5G013600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1131.t1 is derived from g10914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7868635	7870383	.	+	.	Phchi.S6G109000
Phchi.S6	AUGUSTUS	transcript	7868635	7870383	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	start_codon	7868635	7868637	.	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7868635	7868877	0.42	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7868635	7868877	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	intron	7868878	7868986	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7868987	7869097	1	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7868987	7869097	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	intron	7869098	7869219	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7869220	7869228	0.56	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7869220	7869228	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	intron	7869229	7869341	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7869342	7869717	0.35	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7869342	7869717	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	intron	7869718	7869830	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7869831	7869949	0.88	+	2	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7869831	7869949	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	intron	7869950	7870085	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7870086	7870136	0.79	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7870086	7870136	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	intron	7870137	7870215	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	CDS	7870216	7870383	0.82	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	exon	7870216	7870383	.	+	.	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
Phchi.S6	AUGUSTUS	stop_codon	7870384	7870386	.	+	0	transcript_id "Phchi.S6G109000.t1"; gene_id "Phchi.S6G109000"
# This transcript jg8897.t2 is derived from g6072.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8898.t1 is derived from g6073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38545508	38546131	.	+	.	Phchi.S1G605700
Phchi.S1	AUGUSTUS	transcript	38545508	38546131	.	+	.	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	start_codon	38545508	38545510	.	+	0	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	CDS	38545508	38545571	0.92	+	0	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	exon	38545508	38545571	.	+	.	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	intron	38545572	38545707	.	+	.	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	CDS	38545708	38545865	1	+	2	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	exon	38545708	38545865	.	+	.	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	intron	38545866	38546050	.	+	.	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	CDS	38546051	38546131	1	+	0	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	exon	38546051	38546131	.	+	.	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
Phchi.S1	AUGUSTUS	stop_codon	38546132	38546134	.	+	0	transcript_id "Phchi.S1G605700.t1"; gene_id "Phchi.S1G605700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13798.t1 is derived from g12265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8945872	8947129	.	+	.	Phchi.S3G111700
Phchi.S3	AUGUSTUS	transcript	8945872	8947129	.	+	.	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	start_codon	8945872	8945874	.	+	0	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	CDS	8945872	8946365	1	+	0	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	exon	8945872	8946365	.	+	.	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	intron	8946366	8946472	.	+	.	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	CDS	8946473	8946797	1	+	1	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	exon	8946473	8946797	.	+	.	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	intron	8946798	8946886	.	+	.	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	CDS	8946887	8947129	1	+	0	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	exon	8946887	8947129	.	+	.	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
Phchi.S3	AUGUSTUS	stop_codon	8947130	8947132	.	+	0	transcript_id "Phchi.S3G111700.t1"; gene_id "Phchi.S3G111700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg126.t1 is derived from g9908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	700259	701523	.	-	.	Phchi.S6G008500
Phchi.S6	AUGUSTUS	transcript	700259	701523	.	-	.	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	stop_codon	700256	700258	.	-	0	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	CDS	700259	700898	0.83	-	1	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	exon	700259	700898	.	-	.	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	intron	700899	701059	.	-	.	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	CDS	701060	701523	0.54	-	0	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	exon	701060	701523	.	-	.	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
Phchi.S6	AUGUSTUS	start_codon	701521	701523	.	-	0	transcript_id "Phchi.S6G008500.t1"; gene_id "Phchi.S6G008500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5093.t1 is derived from g2263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14711234	14715887	.	-	.	Phchi.S1G225200
Phchi.S1	AUGUSTUS	transcript	14711234	14715887	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	stop_codon	14711231	14711233	.	-	0	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14711234	14711356	0.96	-	0	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14711234	14711356	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14711357	14711853	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14711854	14712083	0.56	-	2	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14711854	14712083	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14712084	14712393	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14712394	14712576	0.36	-	2	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14712394	14712576	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14712577	14712706	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14712707	14712927	0.98	-	1	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14712707	14712927	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14712928	14713248	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14713249	14713320	0.99	-	1	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14713249	14713320	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14713321	14713434	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14713435	14713532	0.99	-	0	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14713435	14713532	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14713533	14713649	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14713650	14713706	0.79	-	0	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14713650	14713706	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14713707	14713846	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14713847	14713851	0.78	-	2	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14713847	14713851	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14713852	14713928	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14713929	14714005	0.78	-	1	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14713929	14714005	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14714006	14714103	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14714104	14714185	1	-	2	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14714104	14714185	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14714186	14714383	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14714384	14714524	1	-	2	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14714384	14714524	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	intron	14714525	14715745	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	CDS	14715746	14715887	0.99	-	0	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	exon	14715746	14715887	.	-	.	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
Phchi.S1	AUGUSTUS	start_codon	14715885	14715887	.	-	0	transcript_id "Phchi.S1G225200.t1"; gene_id "Phchi.S1G225200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14679.t1 is derived from g13147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14137668	14140943	.	-	.	Phchi.S3G199800
Phchi.S3	AUGUSTUS	transcript	14137668	14140943	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	stop_codon	14137665	14137667	.	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14137668	14138020	1	-	2	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14137668	14138020	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14138021	14138129	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14138130	14138278	0.75	-	1	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14138130	14138278	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14138279	14138395	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14138396	14138994	0.71	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14138396	14138994	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14138995	14139126	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14139127	14139282	1	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14139127	14139282	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14139283	14139396	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14139397	14139588	1	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14139397	14139588	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14139589	14139712	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14139713	14140036	1	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14139713	14140036	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14140037	14140159	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14140160	14140435	0.97	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14140160	14140435	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	intron	14140436	14140514	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	CDS	14140515	14140943	0.72	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	exon	14140515	14140943	.	-	.	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
Phchi.S3	AUGUSTUS	start_codon	14140941	14140943	.	-	0	transcript_id "Phchi.S3G199800.t1"; gene_id "Phchi.S3G199800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10531.t1 is derived from g14581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	846509	848092	.	-	.	Phchi.S4G011300
Phchi.S4	AUGUSTUS	transcript	846509	848092	.	-	.	transcript_id "Phchi.S4G011300.t1"; gene_id "Phchi.S4G011300"
Phchi.S4	AUGUSTUS	stop_codon	846506	846508	.	-	0	transcript_id "Phchi.S4G011300.t1"; gene_id "Phchi.S4G011300"
Phchi.S4	AUGUSTUS	CDS	846509	848092	0.99	-	0	transcript_id "Phchi.S4G011300.t1"; gene_id "Phchi.S4G011300"
Phchi.S4	AUGUSTUS	exon	846509	848092	.	-	.	transcript_id "Phchi.S4G011300.t1"; gene_id "Phchi.S4G011300"
Phchi.S4	AUGUSTUS	start_codon	848090	848092	.	-	0	transcript_id "Phchi.S4G011300.t1"; gene_id "Phchi.S4G011300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7710.t1 is derived from g4884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30740131	30741638	.	+	.	Phchi.S1G486900
Phchi.S1	AUGUSTUS	transcript	30740131	30741638	.	+	.	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	start_codon	30740131	30740133	.	+	0	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	CDS	30740131	30740796	1	+	0	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	exon	30740131	30740796	.	+	.	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	intron	30740797	30740930	.	+	.	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	CDS	30740931	30741638	1	+	0	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	exon	30740931	30741638	.	+	.	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
Phchi.S1	AUGUSTUS	stop_codon	30741639	30741641	.	+	0	transcript_id "Phchi.S1G486900.t1"; gene_id "Phchi.S1G486900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10232.t1 is derived from g7408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46500151	46500777	.	-	.	Phchi.S1G739100
Phchi.S1	AUGUSTUS	transcript	46500151	46500777	.	-	.	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	stop_codon	46500148	46500150	.	-	0	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	CDS	46500151	46500611	0.98	-	2	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	exon	46500151	46500611	.	-	.	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	intron	46500612	46500704	.	-	.	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	CDS	46500705	46500777	0.96	-	0	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	exon	46500705	46500777	.	-	.	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
Phchi.S1	AUGUSTUS	start_codon	46500775	46500777	.	-	0	transcript_id "Phchi.S1G739100.t1"; gene_id "Phchi.S1G739100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15855.t1 is derived from g14325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21859076	21859673	.	+	.	Phchi.S3G317400
Phchi.S3	AUGUSTUS	transcript	21859076	21859673	.	+	.	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	start_codon	21859076	21859078	.	+	0	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	CDS	21859076	21859492	0.46	+	0	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	exon	21859076	21859492	.	+	.	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	intron	21859493	21859565	.	+	.	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	CDS	21859566	21859673	0.26	+	0	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	exon	21859566	21859673	.	+	.	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
Phchi.S3	AUGUSTUS	stop_codon	21859674	21859676	.	+	0	transcript_id "Phchi.S3G317400.t1"; gene_id "Phchi.S3G317400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg219.t1 is derived from g10001.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1450797	1451879	.	+	.	Phchi.S6G017800
Phchi.S6	AUGUSTUS	transcript	1450797	1451879	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	start_codon	1450797	1450799	.	+	0	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1450797	1450901	0.61	+	0	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1450797	1450901	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	intron	1450902	1451014	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1451015	1451101	0.91	+	0	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1451015	1451101	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	intron	1451102	1451281	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1451282	1451414	0.99	+	0	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1451282	1451414	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	intron	1451415	1451742	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1451743	1451879	0.98	+	2	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1451743	1451879	.	+	.	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	stop_codon	1451880	1451882	.	+	0	transcript_id "Phchi.S6G017800.t1"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	transcript	1450906	1451879	.	+	.	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	start_codon	1450906	1450908	.	+	0	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1450906	1450975	0.42	+	0	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1450906	1450975	.	+	.	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	intron	1450976	1451281	.	+	.	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1451282	1451434	0.62	+	2	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1451282	1451434	.	+	.	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	intron	1451435	1451742	.	+	.	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	CDS	1451743	1451879	0.62	+	2	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	exon	1451743	1451879	.	+	.	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
Phchi.S6	AUGUSTUS	stop_codon	1451880	1451882	.	+	0	transcript_id "Phchi.S6G017800.t2"; gene_id "Phchi.S6G017800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11711.t1 is derived from g15762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7790573	7792699	.	+	.	Phchi.S4G129300
Phchi.S4	AUGUSTUS	transcript	7790573	7792699	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	start_codon	7790573	7790575	.	+	0	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7790573	7790592	0.58	+	0	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7790573	7790592	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7790593	7790683	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7790684	7790757	1	+	1	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7790684	7790757	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7790758	7790880	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7790881	7790953	0.8	+	2	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7790881	7790953	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7790954	7791039	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7791040	7791156	1	+	1	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7791040	7791156	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7791157	7791286	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7791287	7791347	1	+	1	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7791287	7791347	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7791348	7791474	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7791475	7791494	1	+	0	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7791475	7791494	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7791495	7791601	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7791602	7791625	1	+	1	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7791602	7791625	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7791626	7791708	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7791709	7791776	1	+	1	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7791709	7791776	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7791777	7791857	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7791858	7791949	1	+	2	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7791858	7791949	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7791950	7792107	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7792108	7792206	1	+	0	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7792108	7792206	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7792207	7792335	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7792336	7792429	1	+	0	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7792336	7792429	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	intron	7792430	7792556	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	CDS	7792557	7792699	1	+	2	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	exon	7792557	7792699	.	+	.	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
Phchi.S4	AUGUSTUS	stop_codon	7792700	7792702	.	+	0	transcript_id "Phchi.S4G129300.t1"; gene_id "Phchi.S4G129300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9468.t1 is derived from g6644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41604105	41604464	.	+	.	Phchi.S1G662700
Phchi.S1	AUGUSTUS	transcript	41604105	41604464	.	+	.	transcript_id "Phchi.S1G662700.t1"; gene_id "Phchi.S1G662700"
Phchi.S1	AUGUSTUS	start_codon	41604105	41604107	.	+	0	transcript_id "Phchi.S1G662700.t1"; gene_id "Phchi.S1G662700"
Phchi.S1	AUGUSTUS	CDS	41604105	41604464	0.95	+	0	transcript_id "Phchi.S1G662700.t1"; gene_id "Phchi.S1G662700"
Phchi.S1	AUGUSTUS	exon	41604105	41604464	.	+	.	transcript_id "Phchi.S1G662700.t1"; gene_id "Phchi.S1G662700"
Phchi.S1	AUGUSTUS	stop_codon	41604465	41604467	.	+	0	transcript_id "Phchi.S1G662700.t1"; gene_id "Phchi.S1G662700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5293.t1 is derived from g2463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16046840	16048516	.	+	.	Phchi.S1G245200
Phchi.S1	AUGUSTUS	transcript	16046840	16048516	.	+	.	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	start_codon	16046840	16046842	.	+	0	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	CDS	16046840	16047965	1	+	0	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	exon	16046840	16047965	.	+	.	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	intron	16047966	16048092	.	+	.	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	CDS	16048093	16048226	1	+	2	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	exon	16048093	16048226	.	+	.	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	intron	16048227	16048321	.	+	.	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	CDS	16048322	16048516	1	+	0	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	exon	16048322	16048516	.	+	.	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
Phchi.S1	AUGUSTUS	stop_codon	16048517	16048519	.	+	0	transcript_id "Phchi.S1G245200.t1"; gene_id "Phchi.S1G245200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2462.t1 is derived from g9382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6777019	6780540	.	+	.	Phchi.S5G107100
Phchi.S5	AUGUSTUS	transcript	6777019	6780540	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	start_codon	6777019	6777021	.	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6777019	6777441	0.92	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6777019	6777441	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6777442	6777823	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6777824	6778322	0.99	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6777824	6778322	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6778323	6778425	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6778426	6778490	1	+	2	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6778426	6778490	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6778491	6778579	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6778580	6778657	1	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6778580	6778657	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6778658	6778798	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6778799	6778909	1	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6778799	6778909	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6778910	6779002	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6779003	6779047	1	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6779003	6779047	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6779048	6779247	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6779248	6779421	1	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6779248	6779421	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	intron	6779422	6779586	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	CDS	6779587	6780540	0.95	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	exon	6779587	6780540	.	+	.	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
Phchi.S5	AUGUSTUS	stop_codon	6780541	6780543	.	+	0	transcript_id "Phchi.S5G107100.t1"; gene_id "Phchi.S5G107100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13209.t1 is derived from g11674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4688226	4691228	.	-	.	Phchi.S3G052800
Phchi.S3	AUGUSTUS	transcript	4688226	4691228	.	-	.	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	stop_codon	4688223	4688225	.	-	0	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	CDS	4688226	4688737	1	-	2	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	exon	4688226	4688737	.	-	.	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	intron	4688738	4688841	.	-	.	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	CDS	4688842	4690155	0.94	-	2	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	exon	4688842	4690155	.	-	.	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	intron	4690156	4690231	.	-	.	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	CDS	4690232	4691228	0.94	-	0	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	exon	4690232	4691228	.	-	.	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
Phchi.S3	AUGUSTUS	start_codon	4691226	4691228	.	-	0	transcript_id "Phchi.S3G052800.t1"; gene_id "Phchi.S3G052800"
# This transcript jg12140.t2 is derived from g7816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12141.t1 is derived from g7817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4837222	4838090	.	-	.	Phchi.S2G022100
Phchi.S2	AUGUSTUS	transcript	4837222	4838090	.	-	.	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	stop_codon	4837219	4837221	.	-	0	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	CDS	4837222	4837521	0.8	-	0	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	exon	4837222	4837521	.	-	.	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	intron	4837522	4837603	.	-	.	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	CDS	4837604	4837711	1	-	0	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	exon	4837604	4837711	.	-	.	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	intron	4837712	4837793	.	-	.	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	CDS	4837794	4838090	1	-	0	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	exon	4837794	4838090	.	-	.	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
Phchi.S2	AUGUSTUS	start_codon	4838088	4838090	.	-	0	transcript_id "Phchi.S2G022100.t1"; gene_id "Phchi.S2G022100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8812.t1 is derived from g5987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38098586	38099798	.	-	.	Phchi.S1G597100
Phchi.S1	AUGUSTUS	transcript	38098586	38099798	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	stop_codon	38098583	38098585	.	-	0	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	CDS	38098586	38098911	0.97	-	2	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	exon	38098586	38098911	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	intron	38098912	38099011	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	CDS	38099012	38099084	1	-	0	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	exon	38099012	38099084	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	intron	38099085	38099199	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	CDS	38099200	38099364	0.99	-	0	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	exon	38099200	38099364	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	intron	38099365	38099492	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	CDS	38099493	38099798	0.76	-	0	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	exon	38099493	38099798	.	-	.	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
Phchi.S1	AUGUSTUS	start_codon	38099796	38099798	.	-	0	transcript_id "Phchi.S1G597100.t1"; gene_id "Phchi.S1G597100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8990.t1 is derived from g6165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39003847	39005361	.	-	.	Phchi.S1G614900
Phchi.S1	AUGUSTUS	transcript	39003847	39005361	.	-	.	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	stop_codon	39003844	39003846	.	-	0	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	CDS	39003847	39004741	0.49	-	1	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	exon	39003847	39004741	.	-	.	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	intron	39004742	39004879	.	-	.	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	CDS	39004880	39004949	0.97	-	2	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	exon	39004880	39004949	.	-	.	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	intron	39004950	39005039	.	-	.	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	CDS	39005040	39005361	0.6	-	0	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	exon	39005040	39005361	.	-	.	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
Phchi.S1	AUGUSTUS	start_codon	39005359	39005361	.	-	0	transcript_id "Phchi.S1G614900.t1"; gene_id "Phchi.S1G614900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7977.t1 is derived from g5152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32202057	32203535	.	-	.	Phchi.S1G513600
Phchi.S1	AUGUSTUS	transcript	32202057	32203535	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	stop_codon	32202054	32202056	.	-	0	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	CDS	32202057	32202452	0.94	-	0	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	exon	32202057	32202452	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	intron	32202453	32202618	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	CDS	32202619	32202713	1	-	2	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	exon	32202619	32202713	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	intron	32202714	32202842	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	CDS	32202843	32202931	0.96	-	1	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	exon	32202843	32202931	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	intron	32202932	32203035	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	CDS	32203036	32203130	0.96	-	0	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	exon	32203036	32203130	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	intron	32203131	32203439	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	CDS	32203440	32203535	0.63	-	0	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	exon	32203440	32203535	.	-	.	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
Phchi.S1	AUGUSTUS	start_codon	32203533	32203535	.	-	0	transcript_id "Phchi.S1G513600.t1"; gene_id "Phchi.S1G513600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12570.t1 is derived from g8247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35606117	35607053	.	+	.	Phchi.S2G065000
Phchi.S2	AUGUSTUS	transcript	35606117	35607053	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	start_codon	35606117	35606119	.	+	0	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	CDS	35606117	35606146	0.76	+	0	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	exon	35606117	35606146	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	intron	35606147	35606223	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	CDS	35606224	35606598	0.56	+	0	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	exon	35606224	35606598	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	intron	35606599	35606702	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	CDS	35606703	35606855	1	+	0	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	exon	35606703	35606855	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	intron	35606856	35606930	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	CDS	35606931	35607053	0.46	+	0	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	exon	35606931	35607053	.	+	.	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
Phchi.S2	AUGUSTUS	stop_codon	35607054	35607056	.	+	0	transcript_id "Phchi.S2G065000.t1"; gene_id "Phchi.S2G065000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3877.t1 is derived from g1046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6178396	6181658	.	-	.	Phchi.S1G103600
Phchi.S1	AUGUSTUS	transcript	6178396	6181658	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	stop_codon	6178393	6178395	.	-	0	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6178396	6178510	1	-	1	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6178396	6178510	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6178511	6178598	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6178599	6178698	1	-	2	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6178599	6178698	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6178699	6178816	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6178817	6178982	1	-	0	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6178817	6178982	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6178983	6179105	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6179106	6179403	1	-	1	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6179106	6179403	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6179404	6179580	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6179581	6179844	1	-	1	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6179581	6179844	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6179845	6179957	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6179958	6180076	1	-	0	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6179958	6180076	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6180077	6180168	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6180169	6181420	0.68	-	1	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6180169	6181420	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	intron	6181421	6181509	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	CDS	6181510	6181658	0.53	-	0	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	exon	6181510	6181658	.	-	.	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
Phchi.S1	AUGUSTUS	start_codon	6181656	6181658	.	-	0	transcript_id "Phchi.S1G103600.t1"; gene_id "Phchi.S1G103600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg577.t1 is derived from g10359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4252554	4253591	.	+	.	Phchi.S6G053600
Phchi.S6	AUGUSTUS	transcript	4252554	4253591	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	start_codon	4252554	4252556	.	+	0	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	CDS	4252554	4252910	0.56	+	0	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	exon	4252554	4252910	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	intron	4252911	4252990	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	CDS	4252991	4253089	0.28	+	0	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	exon	4252991	4253089	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	intron	4253090	4253372	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	CDS	4253373	4253424	0.36	+	0	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	exon	4253373	4253424	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	intron	4253425	4253502	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	CDS	4253503	4253591	0.61	+	2	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	exon	4253503	4253591	.	+	.	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
Phchi.S6	AUGUSTUS	stop_codon	4253592	4253594	.	+	0	transcript_id "Phchi.S6G053600.t1"; gene_id "Phchi.S6G053600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10642.t1 is derived from g14692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1390281	1391063	.	+	.	Phchi.S4G022400
Phchi.S4	AUGUSTUS	transcript	1390281	1391063	.	+	.	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	start_codon	1390281	1390283	.	+	0	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	CDS	1390281	1390323	0.91	+	0	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	exon	1390281	1390323	.	+	.	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	intron	1390324	1390524	.	+	.	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	CDS	1390525	1391063	1	+	2	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	exon	1390525	1391063	.	+	.	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
Phchi.S4	AUGUSTUS	stop_codon	1391064	1391066	.	+	0	transcript_id "Phchi.S4G022400.t1"; gene_id "Phchi.S4G022400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3750.t1 is derived from g919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5487769	5488342	.	-	.	Phchi.S1G090900
Phchi.S1	AUGUSTUS	transcript	5487769	5488342	.	-	.	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	stop_codon	5487766	5487768	.	-	0	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	CDS	5487769	5487769	0.81	-	1	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	exon	5487769	5487769	.	-	.	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	intron	5487770	5488029	.	-	.	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	CDS	5488030	5488125	0.58	-	1	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	exon	5488030	5488125	.	-	.	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	intron	5488126	5488238	.	-	.	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	CDS	5488239	5488342	0.58	-	0	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	exon	5488239	5488342	.	-	.	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
Phchi.S1	AUGUSTUS	start_codon	5488340	5488342	.	-	0	transcript_id "Phchi.S1G090900.t1"; gene_id "Phchi.S1G090900"
# This transcript jg8555.t2 is derived from g5730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8556.t1 is derived from g5731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36611732	36614101	.	+	.	Phchi.S1G571500
Phchi.S1	AUGUSTUS	transcript	36611732	36614101	.	+	.	transcript_id "Phchi.S1G571500.t1"; gene_id "Phchi.S1G571500"
Phchi.S1	AUGUSTUS	start_codon	36611732	36611734	.	+	0	transcript_id "Phchi.S1G571500.t1"; gene_id "Phchi.S1G571500"
Phchi.S1	AUGUSTUS	CDS	36611732	36614101	0.87	+	0	transcript_id "Phchi.S1G571500.t1"; gene_id "Phchi.S1G571500"
Phchi.S1	AUGUSTUS	exon	36611732	36614101	.	+	.	transcript_id "Phchi.S1G571500.t1"; gene_id "Phchi.S1G571500"
Phchi.S1	AUGUSTUS	stop_codon	36614102	36614104	.	+	0	transcript_id "Phchi.S1G571500.t1"; gene_id "Phchi.S1G571500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10155.t1 is derived from g7331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46017740	46019719	.	+	.	Phchi.S1G731400
Phchi.S1	AUGUSTUS	transcript	46017740	46019719	.	+	.	transcript_id "Phchi.S1G731400.t1"; gene_id "Phchi.S1G731400"
Phchi.S1	AUGUSTUS	start_codon	46017740	46017742	.	+	0	transcript_id "Phchi.S1G731400.t1"; gene_id "Phchi.S1G731400"
Phchi.S1	AUGUSTUS	CDS	46017740	46019719	1	+	0	transcript_id "Phchi.S1G731400.t1"; gene_id "Phchi.S1G731400"
Phchi.S1	AUGUSTUS	exon	46017740	46019719	.	+	.	transcript_id "Phchi.S1G731400.t1"; gene_id "Phchi.S1G731400"
Phchi.S1	AUGUSTUS	stop_codon	46019720	46019722	.	+	0	transcript_id "Phchi.S1G731400.t1"; gene_id "Phchi.S1G731400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8045.t1 is derived from g5220.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32704613	32706279	.	+	.	Phchi.S1G520400
Phchi.S1	AUGUSTUS	transcript	32704613	32706279	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	start_codon	32704613	32704615	.	+	0	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32704613	32704840	0.43	+	0	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32704613	32704840	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32704841	32704927	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32704928	32705085	0.74	+	0	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32704928	32705085	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705086	32705177	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705178	32705192	0.96	+	1	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705178	32705192	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705193	32705289	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705290	32705297	0.92	+	1	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705290	32705297	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705298	32705396	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705397	32705539	0.81	+	2	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705397	32705539	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705540	32705788	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705789	32705916	0.66	+	0	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705789	32705916	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705917	32706116	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32706117	32706170	0.77	+	1	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32706117	32706170	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32706171	32706254	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32706255	32706279	0.77	+	1	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32706255	32706279	.	+	.	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	stop_codon	32706280	32706282	.	+	0	transcript_id "Phchi.S1G520400.t1"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	transcript	32704613	32706279	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	start_codon	32704613	32704615	.	+	0	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32704613	32704840	0.46	+	0	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32704613	32704840	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32704841	32704927	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32704928	32705090	0.69	+	0	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32704928	32705090	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705091	32705177	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705178	32705192	1	+	2	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705178	32705192	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705193	32705396	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705397	32705539	0.85	+	2	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705397	32705539	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705540	32705788	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32705789	32705916	0.57	+	0	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32705789	32705916	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32705917	32706116	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32706117	32706170	0.75	+	1	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32706117	32706170	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	intron	32706171	32706254	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	CDS	32706255	32706279	0.75	+	1	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	exon	32706255	32706279	.	+	.	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
Phchi.S1	AUGUSTUS	stop_codon	32706280	32706282	.	+	0	transcript_id "Phchi.S1G520400.t2"; gene_id "Phchi.S1G520400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15685.t1 is derived from g14154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20642345	20643955	.	+	.	Phchi.S3G300400
Phchi.S3	AUGUSTUS	transcript	20642345	20643955	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	start_codon	20642345	20642347	.	+	0	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	CDS	20642345	20642570	0.97	+	0	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	exon	20642345	20642570	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	intron	20642571	20642699	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	CDS	20642700	20642821	1	+	2	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	exon	20642700	20642821	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	intron	20642822	20642993	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	CDS	20642994	20643217	1	+	0	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	exon	20642994	20643217	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	intron	20643218	20643309	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	CDS	20643310	20643503	1	+	1	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	exon	20643310	20643503	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	intron	20643504	20643605	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	CDS	20643606	20643955	0.96	+	2	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	exon	20643606	20643955	.	+	.	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
Phchi.S3	AUGUSTUS	stop_codon	20643956	20643958	.	+	0	transcript_id "Phchi.S3G300400.t1"; gene_id "Phchi.S3G300400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9545.t1 is derived from g6721.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42402883	42403822	.	+	.	Phchi.S1G670400
Phchi.S1	AUGUSTUS	transcript	42402883	42403822	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	start_codon	42402883	42402885	.	+	0	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	CDS	42402883	42403271	0.96	+	0	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	exon	42402883	42403271	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	intron	42403272	42403419	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	CDS	42403420	42403442	0.82	+	1	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	exon	42403420	42403442	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	intron	42403443	42403528	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	CDS	42403529	42403614	0.8	+	2	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	exon	42403529	42403614	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	intron	42403615	42403744	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	CDS	42403745	42403822	0.79	+	0	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	exon	42403745	42403822	.	+	.	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	stop_codon	42403823	42403825	.	+	0	transcript_id "Phchi.S1G670400.t1"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	transcript	42402883	42403604	.	+	.	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	start_codon	42402883	42402885	.	+	0	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	CDS	42402883	42403271	0.6	+	0	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	exon	42402883	42403271	.	+	.	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	intron	42403272	42403528	.	+	.	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	CDS	42403529	42403604	0.64	+	1	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	exon	42403529	42403604	.	+	.	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
Phchi.S1	AUGUSTUS	stop_codon	42403605	42403607	.	+	0	transcript_id "Phchi.S1G670400.t2"; gene_id "Phchi.S1G670400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg653.t1 is derived from g10435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4598612	4599996	.	+	.	Phchi.S6G061200
Phchi.S6	AUGUSTUS	transcript	4598612	4599996	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	start_codon	4598612	4598614	.	+	0	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	CDS	4598612	4598899	1	+	0	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	exon	4598612	4598899	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	intron	4598900	4599230	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	CDS	4599231	4599335	1	+	0	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	exon	4599231	4599335	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	intron	4599336	4599451	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	CDS	4599452	4599499	1	+	0	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	exon	4599452	4599499	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	intron	4599500	4599756	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	CDS	4599757	4599996	0.52	+	0	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	exon	4599757	4599996	.	+	.	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
Phchi.S6	AUGUSTUS	stop_codon	4599997	4599999	.	+	0	transcript_id "Phchi.S6G061200.t1"; gene_id "Phchi.S6G061200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg256.t1 is derived from g10038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1732574	1733779	.	+	.	Phchi.S6G021500
Phchi.S6	AUGUSTUS	transcript	1732574	1733779	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	start_codon	1732574	1732576	.	+	0	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	CDS	1732574	1732828	0.89	+	0	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	exon	1732574	1732828	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	intron	1732829	1732913	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	CDS	1732914	1733035	1	+	0	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	exon	1732914	1733035	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	intron	1733036	1733118	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	CDS	1733119	1733320	1	+	1	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	exon	1733119	1733320	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	intron	1733321	1733408	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	CDS	1733409	1733533	1	+	0	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	exon	1733409	1733533	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	intron	1733534	1733613	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	CDS	1733614	1733779	1	+	1	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	exon	1733614	1733779	.	+	.	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
Phchi.S6	AUGUSTUS	stop_codon	1733780	1733782	.	+	0	transcript_id "Phchi.S6G021500.t1"; gene_id "Phchi.S6G021500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13520.t1 is derived from g11987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7286460	7288445	.	-	.	Phchi.S3G083900
Phchi.S3	AUGUSTUS	transcript	7286460	7288445	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	stop_codon	7286457	7286459	.	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7286460	7286462	1	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7286460	7286462	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7286463	7286650	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7286651	7286755	1	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7286651	7286755	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7286756	7286833	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7286834	7286904	1	-	2	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7286834	7286904	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7286905	7287002	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7287003	7287156	1	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7287003	7287156	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7287157	7287308	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7287309	7287372	1	-	1	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7287309	7287372	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7287373	7287553	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7287554	7287637	1	-	1	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7287554	7287637	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7287638	7287743	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7287744	7287790	1	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7287744	7287790	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7287791	7287928	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7287929	7287988	1	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7287929	7287988	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7287989	7288141	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7288142	7288271	0.62	-	1	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7288142	7288271	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	intron	7288272	7288362	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	CDS	7288363	7288445	0.62	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	exon	7288363	7288445	.	-	.	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
Phchi.S3	AUGUSTUS	start_codon	7288443	7288445	.	-	0	transcript_id "Phchi.S3G083900.t1"; gene_id "Phchi.S3G083900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9559.t1 is derived from g6735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42661796	42664513	.	+	.	Phchi.S1G671800
Phchi.S1	AUGUSTUS	transcript	42661796	42664513	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	start_codon	42661796	42661798	.	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42661796	42661987	0.28	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42661796	42661987	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42661988	42662095	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42662096	42662239	1	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42662096	42662239	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42662240	42662331	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42662332	42662425	0.98	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42662332	42662425	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42662426	42662541	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42662542	42662708	1	+	2	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42662542	42662708	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42662709	42662831	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42662832	42662960	0.99	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42662832	42662960	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42662961	42663094	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42663095	42663336	0.98	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42663095	42663336	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42663337	42663424	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42663425	42663607	0.96	+	1	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42663425	42663607	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42663608	42663684	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42663685	42663769	0.68	+	1	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42663685	42663769	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	intron	42663770	42663937	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	CDS	42663938	42664513	0.88	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	exon	42663938	42664513	.	+	.	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
Phchi.S1	AUGUSTUS	stop_codon	42664514	42664516	.	+	0	transcript_id "Phchi.S1G671800.t1"; gene_id "Phchi.S1G671800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8341.t1 is derived from g5516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35403154	35404134	.	-	.	Phchi.S1G550000
Phchi.S1	AUGUSTUS	transcript	35403154	35404134	.	-	.	transcript_id "Phchi.S1G550000.t1"; gene_id "Phchi.S1G550000"
Phchi.S1	AUGUSTUS	stop_codon	35403151	35403153	.	-	0	transcript_id "Phchi.S1G550000.t1"; gene_id "Phchi.S1G550000"
Phchi.S1	AUGUSTUS	CDS	35403154	35404134	0.5	-	0	transcript_id "Phchi.S1G550000.t1"; gene_id "Phchi.S1G550000"
Phchi.S1	AUGUSTUS	exon	35403154	35404134	.	-	.	transcript_id "Phchi.S1G550000.t1"; gene_id "Phchi.S1G550000"
Phchi.S1	AUGUSTUS	start_codon	35404132	35404134	.	-	0	transcript_id "Phchi.S1G550000.t1"; gene_id "Phchi.S1G550000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11459.t1 is derived from g15509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6465719	6465937	.	-	.	Phchi.S4G104100
Phchi.S4	AUGUSTUS	transcript	6465719	6465937	.	-	.	transcript_id "Phchi.S4G104100.t1"; gene_id "Phchi.S4G104100"
Phchi.S4	AUGUSTUS	stop_codon	6465716	6465718	.	-	0	transcript_id "Phchi.S4G104100.t1"; gene_id "Phchi.S4G104100"
Phchi.S4	AUGUSTUS	CDS	6465719	6465937	0.97	-	0	transcript_id "Phchi.S4G104100.t1"; gene_id "Phchi.S4G104100"
Phchi.S4	AUGUSTUS	exon	6465719	6465937	.	-	.	transcript_id "Phchi.S4G104100.t1"; gene_id "Phchi.S4G104100"
Phchi.S4	AUGUSTUS	start_codon	6465935	6465937	.	-	0	transcript_id "Phchi.S4G104100.t1"; gene_id "Phchi.S4G104100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3147.t1 is derived from g316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1981442	1982832	.	-	.	Phchi.S1G030600
Phchi.S1	AUGUSTUS	transcript	1981442	1982224	.	-	.	transcript_id "Phchi.S1G030600.t1"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	stop_codon	1981439	1981441	.	-	0	transcript_id "Phchi.S1G030600.t1"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	CDS	1981442	1982224	0.53	-	0	transcript_id "Phchi.S1G030600.t1"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	exon	1981442	1982224	.	-	.	transcript_id "Phchi.S1G030600.t1"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	start_codon	1982222	1982224	.	-	0	transcript_id "Phchi.S1G030600.t1"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	transcript	1981442	1982832	.	-	.	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	stop_codon	1981439	1981441	.	-	0	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	CDS	1981442	1982411	0.38	-	1	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	exon	1981442	1982411	.	-	.	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	intron	1982412	1982590	.	-	.	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	CDS	1982591	1982832	0.1	-	0	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	exon	1982591	1982832	.	-	.	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
Phchi.S1	AUGUSTUS	start_codon	1982830	1982832	.	-	0	transcript_id "Phchi.S1G030600.t2"; gene_id "Phchi.S1G030600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7632.t1 is derived from g4806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30328666	30329941	.	+	.	Phchi.S1G479100
Phchi.S1	AUGUSTUS	transcript	30328666	30329941	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	start_codon	30328666	30328668	.	+	0	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	CDS	30328666	30328832	1	+	0	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	exon	30328666	30328832	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	intron	30328833	30329038	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	CDS	30329039	30329141	1	+	1	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	exon	30329039	30329141	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	intron	30329142	30329345	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	CDS	30329346	30329483	1	+	0	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	exon	30329346	30329483	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	intron	30329484	30329581	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	CDS	30329582	30329683	1	+	0	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	exon	30329582	30329683	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	intron	30329684	30329788	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	CDS	30329789	30329941	1	+	0	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	exon	30329789	30329941	.	+	.	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
Phchi.S1	AUGUSTUS	stop_codon	30329942	30329944	.	+	0	transcript_id "Phchi.S1G479100.t1"; gene_id "Phchi.S1G479100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7333.t1 is derived from g4505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28551906	28555971	.	-	.	Phchi.S1G449200
Phchi.S1	AUGUSTUS	transcript	28551906	28555971	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	stop_codon	28551903	28551905	.	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28551906	28552112	0.95	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28551906	28552112	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28552113	28552248	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28552249	28552357	1	-	1	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28552249	28552357	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28552358	28552475	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28552476	28552624	1	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28552476	28552624	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28552625	28552777	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28552778	28552863	1	-	2	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28552778	28552863	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28552864	28553024	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28553025	28553072	0.67	-	2	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28553025	28553072	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28553073	28553159	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28553160	28553166	1	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28553160	28553166	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28553167	28553299	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28553300	28553455	1	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28553300	28553455	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28553456	28553616	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28553617	28553884	1	-	1	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28553617	28553884	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28553885	28554059	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28554060	28554445	0.89	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28554060	28554445	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	intron	28554446	28554603	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	CDS	28554604	28555971	0.58	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	exon	28554604	28555971	.	-	.	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
Phchi.S1	AUGUSTUS	start_codon	28555969	28555971	.	-	0	transcript_id "Phchi.S1G449200.t1"; gene_id "Phchi.S1G449200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4907.t1 is derived from g2077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13345232	13345903	.	-	.	Phchi.S1G206600
Phchi.S1	AUGUSTUS	transcript	13345232	13345903	.	-	.	transcript_id "Phchi.S1G206600.t1"; gene_id "Phchi.S1G206600"
Phchi.S1	AUGUSTUS	stop_codon	13345229	13345231	.	-	0	transcript_id "Phchi.S1G206600.t1"; gene_id "Phchi.S1G206600"
Phchi.S1	AUGUSTUS	CDS	13345232	13345903	0.52	-	0	transcript_id "Phchi.S1G206600.t1"; gene_id "Phchi.S1G206600"
Phchi.S1	AUGUSTUS	exon	13345232	13345903	.	-	.	transcript_id "Phchi.S1G206600.t1"; gene_id "Phchi.S1G206600"
Phchi.S1	AUGUSTUS	start_codon	13345901	13345903	.	-	0	transcript_id "Phchi.S1G206600.t1"; gene_id "Phchi.S1G206600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4544.t1 is derived from g1714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11033830	11036031	.	-	.	Phchi.S1G170300
Phchi.S1	AUGUSTUS	transcript	11034007	11036031	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	stop_codon	11034004	11034006	.	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034007	11034156	1	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034007	11034156	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034157	11034234	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034235	11034330	1	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034235	11034330	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034331	11034422	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034423	11034534	0.95	-	1	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034423	11034534	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034535	11034646	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034647	11034840	1	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034647	11034840	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034841	11034930	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034931	11035012	1	-	1	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034931	11035012	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11035013	11035084	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11035085	11035225	0.99	-	1	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11035085	11035225	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11035226	11035315	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11035316	11035413	1	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11035316	11035413	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11035414	11035488	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11035489	11036031	0.31	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11035489	11036031	.	-	.	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	start_codon	11036029	11036031	.	-	0	transcript_id "Phchi.S1G170300.t1"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	transcript	11033830	11036031	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	stop_codon	11033827	11033829	.	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11033830	11033976	1	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11033830	11033976	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11033977	11034234	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034235	11034330	1	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034235	11034330	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034331	11034422	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034423	11034534	0.93	-	1	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034423	11034534	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034535	11034646	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034647	11034840	1	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034647	11034840	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11034841	11034930	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11034931	11035012	1	-	1	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11034931	11035012	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11035013	11035084	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11035085	11035225	0.98	-	1	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11035085	11035225	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11035226	11035315	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11035316	11035413	1	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11035316	11035413	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	intron	11035414	11035488	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	CDS	11035489	11036031	0.33	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	exon	11035489	11036031	.	-	.	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
Phchi.S1	AUGUSTUS	start_codon	11036029	11036031	.	-	0	transcript_id "Phchi.S1G170300.t2"; gene_id "Phchi.S1G170300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9723.t1 is derived from g6899.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43402202	43405055	.	+	.	Phchi.S1G688200
Phchi.S1	AUGUSTUS	transcript	43402353	43405055	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	start_codon	43402353	43402355	.	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43402353	43402422	0.98	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43402353	43402422	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43402423	43402740	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43402741	43402874	0.99	+	2	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43402741	43402874	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43402875	43402972	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43402973	43403040	1	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43402973	43403040	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403041	43403167	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403168	43403381	0.87	+	1	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403168	43403381	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403382	43403498	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403499	43403591	0.97	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403499	43403591	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403592	43403713	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403714	43403842	0.75	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403714	43403842	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403843	43403923	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403924	43404018	0.99	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403924	43404018	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43404019	43404121	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43404122	43405055	0.98	+	1	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43404122	43405055	.	+	.	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	stop_codon	43405056	43405058	.	+	0	transcript_id "Phchi.S1G688200.t1"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	transcript	43402202	43405055	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	start_codon	43402202	43402204	.	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43402202	43402422	0.95	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43402202	43402422	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43402423	43402558	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43402559	43402874	0.65	+	1	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43402559	43402874	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43402875	43402972	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43402973	43403040	1	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43402973	43403040	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403041	43403167	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403168	43403381	0.91	+	1	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403168	43403381	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403382	43403498	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403499	43403591	0.98	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403499	43403591	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403592	43403713	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403714	43403842	0.82	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403714	43403842	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43403843	43403923	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43403924	43404018	0.99	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43403924	43404018	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	intron	43404019	43404121	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	CDS	43404122	43405055	0.98	+	1	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	exon	43404122	43405055	.	+	.	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
Phchi.S1	AUGUSTUS	stop_codon	43405056	43405058	.	+	0	transcript_id "Phchi.S1G688200.t2"; gene_id "Phchi.S1G688200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5320.t1 is derived from g2490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16275817	16277174	.	+	.	Phchi.S1G247900
Phchi.S1	AUGUSTUS	transcript	16275817	16277174	.	+	.	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	start_codon	16275817	16275819	.	+	0	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	CDS	16275817	16275957	1	+	0	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	exon	16275817	16275957	.	+	.	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	intron	16275958	16276138	.	+	.	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	CDS	16276139	16277008	0.69	+	0	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	exon	16276139	16277008	.	+	.	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	intron	16277009	16277150	.	+	.	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	CDS	16277151	16277174	0.86	+	0	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	exon	16277151	16277174	.	+	.	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
Phchi.S1	AUGUSTUS	stop_codon	16277175	16277177	.	+	0	transcript_id "Phchi.S1G247900.t1"; gene_id "Phchi.S1G247900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14590.t1 is derived from g13058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13609672	13611271	.	-	.	Phchi.S3G190900
Phchi.S3	AUGUSTUS	transcript	13609672	13611271	.	-	.	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	stop_codon	13609669	13609671	.	-	0	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	CDS	13609672	13610705	1	-	2	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	exon	13609672	13610705	.	-	.	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	intron	13610706	13610850	.	-	.	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	CDS	13610851	13610947	1	-	0	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	exon	13610851	13610947	.	-	.	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	intron	13610948	13611034	.	-	.	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	CDS	13611035	13611271	0.26	-	0	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	exon	13611035	13611271	.	-	.	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
Phchi.S3	AUGUSTUS	start_codon	13611269	13611271	.	-	0	transcript_id "Phchi.S3G190900.t1"; gene_id "Phchi.S3G190900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3.t1 is derived from g7595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C129	AUGUSTUS	gene	22603	27824	.	+	.	Phchi.C129G000100
Phchi.C129	AUGUSTUS	transcript	22603	27824	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	start_codon	22603	22605	.	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	22603	22625	1	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	22603	22625	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	22626	22707	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	22708	22764	0.97	+	1	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	22708	22764	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	22765	22865	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	22866	22980	0.65	+	1	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	22866	22980	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	22981	23644	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	23645	24103	0.51	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	23645	24103	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	24104	24208	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	24209	24661	0.97	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	24209	24661	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	24662	24826	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	24827	25069	1	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	24827	25069	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	25070	25226	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	25227	26051	0.82	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	25227	26051	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	26052	26144	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	26145	26168	0.96	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	26145	26168	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	26169	26263	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	26264	26319	0.83	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	26264	26319	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	26320	26514	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	26515	26720	1	+	1	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	26515	26720	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	26721	26988	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	26989	27744	0.99	+	2	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	26989	27744	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	intron	27745	27822	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	CDS	27823	27824	1	+	2	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	exon	27823	27824	.	+	.	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
Phchi.C129	AUGUSTUS	stop_codon	27825	27827	.	+	0	transcript_id "Phchi.C129G000100.t1"; gene_id "Phchi.C129G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15771.t1 is derived from g14241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21275699	21276916	.	+	.	Phchi.S3G309000
Phchi.S3	AUGUSTUS	transcript	21275699	21276916	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	start_codon	21275699	21275701	.	+	0	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	CDS	21275699	21275878	1	+	0	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	exon	21275699	21275878	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	intron	21275879	21275999	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	CDS	21276000	21276364	0.99	+	0	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	exon	21276000	21276364	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	intron	21276365	21276473	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	CDS	21276474	21276700	1	+	1	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	exon	21276474	21276700	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	intron	21276701	21276854	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	CDS	21276855	21276916	1	+	2	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	exon	21276855	21276916	.	+	.	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
Phchi.S3	AUGUSTUS	stop_codon	21276917	21276919	.	+	0	transcript_id "Phchi.S3G309000.t1"; gene_id "Phchi.S3G309000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14887.t1 is derived from g13355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15285121	15286143	.	+	.	Phchi.S3G220600
Phchi.S3	AUGUSTUS	transcript	15285121	15286143	.	+	.	transcript_id "Phchi.S3G220600.t1"; gene_id "Phchi.S3G220600"
Phchi.S3	AUGUSTUS	start_codon	15285121	15285123	.	+	0	transcript_id "Phchi.S3G220600.t1"; gene_id "Phchi.S3G220600"
Phchi.S3	AUGUSTUS	CDS	15285121	15286143	1	+	0	transcript_id "Phchi.S3G220600.t1"; gene_id "Phchi.S3G220600"
Phchi.S3	AUGUSTUS	exon	15285121	15286143	.	+	.	transcript_id "Phchi.S3G220600.t1"; gene_id "Phchi.S3G220600"
Phchi.S3	AUGUSTUS	stop_codon	15286144	15286146	.	+	0	transcript_id "Phchi.S3G220600.t1"; gene_id "Phchi.S3G220600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7414.t1 is derived from g4586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29032932	29037036	.	+	.	Phchi.S1G457300
Phchi.S1	AUGUSTUS	transcript	29032932	29037036	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	start_codon	29032932	29032934	.	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29032932	29033572	1	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29032932	29033572	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29033573	29033650	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29033651	29034056	0.99	+	1	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29033651	29034056	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29034057	29034155	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29034156	29034371	1	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29034156	29034371	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29034372	29034550	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29034551	29034658	1	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29034551	29034658	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29034659	29034779	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29034780	29035054	1	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29034780	29035054	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29035055	29035130	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29035131	29035403	1	+	1	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29035131	29035403	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29035404	29035558	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29035559	29035604	0.75	+	1	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29035559	29035604	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29035605	29035829	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29035830	29036432	0.47	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29035830	29036432	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29036433	29036512	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29036513	29036776	1	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29036513	29036776	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	intron	29036777	29036877	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	CDS	29036878	29037036	0.97	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	exon	29036878	29037036	.	+	.	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
Phchi.S1	AUGUSTUS	stop_codon	29037037	29037039	.	+	0	transcript_id "Phchi.S1G457300.t1"; gene_id "Phchi.S1G457300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12781.t1 is derived from g11246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2172851	2178548	.	+	.	Phchi.S3G010000
Phchi.S3	AUGUSTUS	transcript	2172851	2178548	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	start_codon	2172851	2172853	.	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2172851	2173019	0.99	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2172851	2173019	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2173020	2173295	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2173296	2173449	0.99	+	2	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2173296	2173449	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2173450	2173556	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2173557	2173629	0.99	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2173557	2173629	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2173630	2173726	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2173727	2173792	1	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2173727	2173792	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2173793	2173890	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2173891	2174101	1	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2173891	2174101	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2174102	2174323	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2174324	2174405	1	+	2	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2174324	2174405	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2174406	2174506	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2174507	2174579	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2174507	2174579	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2174580	2174721	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2174722	2174832	0.98	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2174722	2174832	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2174833	2174935	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2174936	2175121	1	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2174936	2175121	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2175122	2175240	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2175241	2175494	1	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2175241	2175494	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2175495	2175604	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2175605	2175916	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2175605	2175916	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2175917	2176026	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2176027	2176356	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2176027	2176356	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2176357	2176466	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2176467	2176796	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2176467	2176796	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2176797	2176906	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2176907	2177236	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2176907	2177236	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2177237	2177346	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2177347	2178126	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2177347	2178126	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2178127	2178216	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2178217	2178402	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2178217	2178402	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	intron	2178403	2178487	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	CDS	2178488	2178548	1	+	1	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	exon	2178488	2178548	.	+	.	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
Phchi.S3	AUGUSTUS	stop_codon	2178549	2178551	.	+	0	transcript_id "Phchi.S3G010000.t1"; gene_id "Phchi.S3G010000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11475.t1 is derived from g15525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6532462	6532981	.	-	.	Phchi.S4G105700
Phchi.S4	AUGUSTUS	transcript	6532462	6532981	.	-	.	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	stop_codon	6532459	6532461	.	-	0	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	CDS	6532462	6532485	0.9	-	0	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	exon	6532462	6532485	.	-	.	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	intron	6532486	6532689	.	-	.	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	CDS	6532690	6532782	0.63	-	0	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	exon	6532690	6532782	.	-	.	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	intron	6532783	6532870	.	-	.	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	CDS	6532871	6532981	0.6	-	0	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	exon	6532871	6532981	.	-	.	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
Phchi.S4	AUGUSTUS	start_codon	6532979	6532981	.	-	0	transcript_id "Phchi.S4G105700.t1"; gene_id "Phchi.S4G105700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7358.t1 is derived from g4530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28759088	28762447	.	-	.	Phchi.S1G451700
Phchi.S1	AUGUSTUS	transcript	28759088	28762447	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	stop_codon	28759085	28759087	.	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28759088	28759384	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28759088	28759384	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28759385	28759471	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28759472	28759642	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28759472	28759642	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28759643	28759760	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28759761	28759841	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28759761	28759841	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28759842	28760026	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28760027	28760125	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28760027	28760125	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28760126	28760286	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28760287	28760395	1	-	1	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28760287	28760395	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28760396	28760529	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28760530	28760595	1	-	1	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28760530	28760595	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28760596	28760678	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28760679	28760803	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28760679	28760803	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28760804	28760901	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28760902	28760991	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28760902	28760991	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28760992	28761090	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28761091	28761262	0.84	-	1	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28761091	28761262	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28761263	28761342	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28761343	28761438	1	-	1	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28761343	28761438	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28761439	28761511	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28761512	28761624	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28761512	28761624	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28761625	28761734	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28761735	28761965	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28761735	28761965	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28761966	28762092	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28762093	28762140	1	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28762093	28762140	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	intron	28762141	28762288	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	CDS	28762289	28762447	0.99	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	exon	28762289	28762447	.	-	.	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
Phchi.S1	AUGUSTUS	start_codon	28762445	28762447	.	-	0	transcript_id "Phchi.S1G451700.t1"; gene_id "Phchi.S1G451700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8537.t1 is derived from g5712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36536587	36538433	.	-	.	Phchi.S1G569600
Phchi.S1	AUGUSTUS	transcript	36536587	36538433	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	stop_codon	36536584	36536586	.	-	0	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36536587	36536884	0.35	-	1	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36536587	36536884	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	intron	36536885	36537270	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36537271	36537475	0.37	-	2	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36537271	36537475	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	intron	36537476	36537559	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36537560	36537671	1	-	0	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36537560	36537671	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	intron	36537672	36537761	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36537762	36537850	1	-	2	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36537762	36537850	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	intron	36537851	36538020	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36538021	36538114	1	-	0	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36538021	36538114	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	intron	36538115	36538203	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36538204	36538293	0.75	-	0	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36538204	36538293	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	intron	36538294	36538397	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	CDS	36538398	36538433	0.75	-	0	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	exon	36538398	36538433	.	-	.	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
Phchi.S1	AUGUSTUS	start_codon	36538431	36538433	.	-	0	transcript_id "Phchi.S1G569600.t1"; gene_id "Phchi.S1G569600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12723.t1 is derived from g11188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1122676	1123064	.	-	.	Phchi.S3G004200
Phchi.S3	AUGUSTUS	transcript	1122676	1123064	.	-	.	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	stop_codon	1122673	1122675	.	-	0	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	CDS	1122676	1122786	0.93	-	0	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	exon	1122676	1122786	.	-	.	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	intron	1122787	1122878	.	-	.	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	CDS	1122879	1122928	0.62	-	2	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	exon	1122879	1122928	.	-	.	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	intron	1122929	1123024	.	-	.	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	CDS	1123025	1123064	0.24	-	0	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	exon	1123025	1123064	.	-	.	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
Phchi.S3	AUGUSTUS	start_codon	1123062	1123064	.	-	0	transcript_id "Phchi.S3G004200.t1"; gene_id "Phchi.S3G004200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9917.t1 is derived from g7093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44433695	44436485	.	-	.	Phchi.S1G707600
Phchi.S1	AUGUSTUS	transcript	44433695	44436485	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	stop_codon	44433692	44433694	.	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44433695	44433895	1	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44433695	44433895	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44433896	44433989	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44433990	44434106	1	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44433990	44434106	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44434107	44434225	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44434226	44434395	0.76	-	2	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44434226	44434395	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44434396	44434474	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44434475	44434512	0.82	-	1	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44434475	44434512	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44434513	44434621	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44434622	44434878	0.96	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44434622	44434878	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44434879	44434959	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44434960	44435327	0.99	-	2	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44434960	44435327	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44435328	44435444	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44435445	44435520	0.99	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44435445	44435520	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44435521	44435656	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44435657	44435746	1	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44435657	44435746	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44435747	44435832	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44435833	44435924	1	-	2	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44435833	44435924	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44435925	44436024	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44436025	44436128	1	-	1	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44436025	44436128	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44436129	44436207	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44436208	44436270	1	-	1	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44436208	44436270	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	intron	44436271	44436357	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	CDS	44436358	44436485	0.95	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	exon	44436358	44436485	.	-	.	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
Phchi.S1	AUGUSTUS	start_codon	44436483	44436485	.	-	0	transcript_id "Phchi.S1G707600.t1"; gene_id "Phchi.S1G707600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11417.t1 is derived from g15467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6254583	6255222	.	+	.	Phchi.S4G099900
Phchi.S4	AUGUSTUS	transcript	6254583	6255222	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	start_codon	6254583	6254585	.	+	0	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	CDS	6254583	6254649	0.93	+	0	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	exon	6254583	6254649	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	intron	6254650	6254805	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	CDS	6254806	6254915	0.98	+	2	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	exon	6254806	6254915	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	intron	6254916	6255036	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	CDS	6255037	6255083	1	+	0	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	exon	6255037	6255083	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	intron	6255084	6255167	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	CDS	6255168	6255222	1	+	1	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	exon	6255168	6255222	.	+	.	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
Phchi.S4	AUGUSTUS	stop_codon	6255223	6255225	.	+	0	transcript_id "Phchi.S4G099900.t1"; gene_id "Phchi.S4G099900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4723.t1 is derived from g1893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12481209	12484824	.	+	.	Phchi.S1G188200
Phchi.S1	AUGUSTUS	transcript	12481209	12484824	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	start_codon	12481209	12481211	.	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12481209	12481379	0.95	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12481209	12481379	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12481380	12481458	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12481459	12481617	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12481459	12481617	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12481618	12481778	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12481779	12481868	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12481779	12481868	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12481869	12481982	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12481983	12482111	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12481983	12482111	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12482112	12482254	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12482255	12482355	0.53	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12482255	12482355	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12482356	12482457	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12482458	12482575	0.45	+	1	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12482458	12482575	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12482576	12482666	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12482667	12482798	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12482667	12482798	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12482799	12482918	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12482919	12482984	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12482919	12482984	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12482985	12483115	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12483116	12483169	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12483116	12483169	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12483170	12483282	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12483283	12483318	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12483283	12483318	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12483319	12483647	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12483648	12483743	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12483648	12483743	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12483744	12483836	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12483837	12483980	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12483837	12483980	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12483981	12484073	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12484074	12484156	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12484074	12484156	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12484157	12484246	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12484247	12484284	1	+	1	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12484247	12484284	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12484285	12484376	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12484377	12484588	1	+	2	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12484377	12484588	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	intron	12484589	12484686	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	CDS	12484687	12484824	1	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	exon	12484687	12484824	.	+	.	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
Phchi.S1	AUGUSTUS	stop_codon	12484825	12484827	.	+	0	transcript_id "Phchi.S1G188200.t1"; gene_id "Phchi.S1G188200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13111.t1 is derived from g11576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4188528	4189447	.	-	.	Phchi.S3G043000
Phchi.S3	AUGUSTUS	transcript	4188528	4189447	.	-	.	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	stop_codon	4188525	4188527	.	-	0	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	CDS	4188528	4188870	1	-	1	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	exon	4188528	4188870	.	-	.	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	intron	4188871	4189196	.	-	.	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	CDS	4189197	4189447	1	-	0	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	exon	4189197	4189447	.	-	.	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
Phchi.S3	AUGUSTUS	start_codon	4189445	4189447	.	-	0	transcript_id "Phchi.S3G043000.t1"; gene_id "Phchi.S3G043000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1798.t1 is derived from g8718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3072150	3072539	.	-	.	Phchi.S5G040700
Phchi.S5	AUGUSTUS	transcript	3072150	3072539	.	-	.	transcript_id "Phchi.S5G040700.t1"; gene_id "Phchi.S5G040700"
Phchi.S5	AUGUSTUS	stop_codon	3072147	3072149	.	-	0	transcript_id "Phchi.S5G040700.t1"; gene_id "Phchi.S5G040700"
Phchi.S5	AUGUSTUS	CDS	3072150	3072539	0.63	-	0	transcript_id "Phchi.S5G040700.t1"; gene_id "Phchi.S5G040700"
Phchi.S5	AUGUSTUS	exon	3072150	3072539	.	-	.	transcript_id "Phchi.S5G040700.t1"; gene_id "Phchi.S5G040700"
Phchi.S5	AUGUSTUS	start_codon	3072537	3072539	.	-	0	transcript_id "Phchi.S5G040700.t1"; gene_id "Phchi.S5G040700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4231.t1 is derived from g1400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9033839	9036370	.	+	.	Phchi.S1G139000
Phchi.S1	AUGUSTUS	transcript	9033839	9036370	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	start_codon	9033839	9033841	.	+	0	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9033839	9034076	0.53	+	0	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9033839	9034076	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	intron	9034077	9034195	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9034196	9034788	0.54	+	2	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9034196	9034788	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	intron	9034789	9034883	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9034884	9035234	0.86	+	0	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9034884	9035234	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	intron	9035235	9035316	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9035317	9035603	1	+	0	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9035317	9035603	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	intron	9035604	9035690	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9035691	9035783	1	+	1	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9035691	9035783	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	intron	9035784	9035874	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9035875	9035980	0.94	+	1	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9035875	9035980	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	intron	9035981	9036106	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	CDS	9036107	9036370	0.96	+	0	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	exon	9036107	9036370	.	+	.	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
Phchi.S1	AUGUSTUS	stop_codon	9036371	9036373	.	+	0	transcript_id "Phchi.S1G139000.t1"; gene_id "Phchi.S1G139000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10184.t1 is derived from g7360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46203907	46206276	.	-	.	Phchi.S1G734300
Phchi.S1	AUGUSTUS	transcript	46203907	46206276	.	-	.	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	stop_codon	46203904	46203906	.	-	0	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	CDS	46203907	46205769	1	-	0	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	exon	46203907	46205769	.	-	.	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	intron	46205770	46205859	.	-	.	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	CDS	46205860	46206276	0.75	-	0	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	exon	46205860	46206276	.	-	.	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
Phchi.S1	AUGUSTUS	start_codon	46206274	46206276	.	-	0	transcript_id "Phchi.S1G734300.t1"; gene_id "Phchi.S1G734300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12085.t1 is derived from g7760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2178210	2179348	.	+	.	Phchi.S2G016500
Phchi.S2	AUGUSTUS	transcript	2178210	2179348	.	+	.	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	start_codon	2178210	2178212	.	+	0	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	CDS	2178210	2179115	0.54	+	0	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	exon	2178210	2179115	.	+	.	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	intron	2179116	2179189	.	+	.	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	CDS	2179190	2179348	1	+	0	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	exon	2179190	2179348	.	+	.	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
Phchi.S2	AUGUSTUS	stop_codon	2179349	2179351	.	+	0	transcript_id "Phchi.S2G016500.t1"; gene_id "Phchi.S2G016500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3205.t1 is derived from g374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2233743	2235443	.	-	.	Phchi.S1G036400
Phchi.S1	AUGUSTUS	transcript	2233743	2235443	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	stop_codon	2233740	2233742	.	-	0	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	CDS	2233743	2234020	1	-	2	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	exon	2233743	2234020	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	intron	2234021	2234123	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	CDS	2234124	2234327	1	-	2	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	exon	2234124	2234327	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	intron	2234328	2234418	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	CDS	2234419	2234819	0.45	-	1	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	exon	2234419	2234819	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	intron	2234820	2234932	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	CDS	2234933	2235087	0.45	-	0	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	exon	2234933	2235087	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	intron	2235088	2235251	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	CDS	2235252	2235443	1	-	0	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	exon	2235252	2235443	.	-	.	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
Phchi.S1	AUGUSTUS	start_codon	2235441	2235443	.	-	0	transcript_id "Phchi.S1G036400.t1"; gene_id "Phchi.S1G036400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12158.t1 is derived from g7834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5067113	5071964	.	-	.	Phchi.S2G023800
Phchi.S2	AUGUSTUS	transcript	5067113	5071964	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	stop_codon	5067110	5067112	.	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5067113	5067187	1	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5067113	5067187	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5067188	5067384	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5067385	5067503	1	-	2	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5067385	5067503	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5067504	5067647	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5067648	5067723	0.66	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5067648	5067723	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5067724	5067949	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5067950	5068149	0.99	-	2	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5067950	5068149	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5068150	5068455	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5068456	5068535	1	-	1	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5068456	5068535	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5068536	5068604	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5068605	5068664	0.96	-	1	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5068605	5068664	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5068665	5068768	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5068769	5068821	0.87	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5068769	5068821	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5068822	5068989	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5068990	5069052	1	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5068990	5069052	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5069053	5069172	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5069173	5069264	1	-	2	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5069173	5069264	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5069265	5069417	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5069418	5069460	1	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5069418	5069460	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5069461	5069843	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5069844	5069923	1	-	2	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5069844	5069923	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5069924	5070058	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5070059	5070152	1	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5070059	5070152	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5070153	5070461	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5070462	5070517	1	-	2	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5070462	5070517	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5070518	5070708	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5070709	5070764	1	-	1	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5070709	5070764	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5070765	5071328	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5071329	5071417	1	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5071329	5071417	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5071418	5071534	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5071535	5071658	1	-	1	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5071535	5071658	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	intron	5071659	5071899	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	CDS	5071900	5071964	1	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	exon	5071900	5071964	.	-	.	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
Phchi.S2	AUGUSTUS	start_codon	5071962	5071964	.	-	0	transcript_id "Phchi.S2G023800.t1"; gene_id "Phchi.S2G023800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3499.t1 is derived from g668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4104963	4105532	.	+	.	Phchi.S1G065800
Phchi.S1	AUGUSTUS	transcript	4104963	4105532	.	+	.	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	start_codon	4104963	4104965	.	+	0	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	CDS	4104963	4105254	0.9	+	0	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	exon	4104963	4105254	.	+	.	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	intron	4105255	4105362	.	+	.	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	CDS	4105363	4105532	0.94	+	2	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	exon	4105363	4105532	.	+	.	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
Phchi.S1	AUGUSTUS	stop_codon	4105533	4105535	.	+	0	transcript_id "Phchi.S1G065800.t1"; gene_id "Phchi.S1G065800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4995.t1 is derived from g2165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13934688	13935259	.	+	.	Phchi.S1G215400
Phchi.S1	AUGUSTUS	transcript	13934688	13935259	.	+	.	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	start_codon	13934688	13934690	.	+	0	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	CDS	13934688	13935123	0.82	+	0	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	exon	13934688	13935123	.	+	.	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	intron	13935124	13935257	.	+	.	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	CDS	13935258	13935259	0.99	+	2	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	exon	13935258	13935259	.	+	.	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
Phchi.S1	AUGUSTUS	stop_codon	13935260	13935262	.	+	0	transcript_id "Phchi.S1G215400.t1"; gene_id "Phchi.S1G215400"
# This transcript jg12762.t2 is derived from g11227.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12763.t1 is derived from g11228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1945908	1947364	.	-	.	Phchi.S3G008200
Phchi.S3	AUGUSTUS	transcript	1945908	1947364	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	stop_codon	1945905	1945907	.	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1945908	1946054	0.99	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1945908	1946054	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	intron	1946055	1946136	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1946137	1946172	1	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1946137	1946172	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	intron	1946173	1946254	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1946255	1946443	1	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1946255	1946443	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	intron	1946444	1946524	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1946525	1946595	0.98	-	2	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1946525	1946595	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	intron	1946596	1946702	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1946703	1946970	1	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1946703	1946970	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	intron	1946971	1947056	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1947057	1947082	1	-	2	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1947057	1947082	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	intron	1947083	1947348	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	CDS	1947349	1947364	1	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	exon	1947349	1947364	.	-	.	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
Phchi.S3	AUGUSTUS	start_codon	1947362	1947364	.	-	0	transcript_id "Phchi.S3G008200.t1"; gene_id "Phchi.S3G008200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7853.t1 is derived from g5027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31527038	31529431	.	-	.	Phchi.S1G501200
Phchi.S1	AUGUSTUS	transcript	31527038	31529431	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	stop_codon	31527035	31527037	.	-	0	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31527038	31527162	1	-	2	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31527038	31527162	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31527163	31527268	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31527269	31527332	1	-	0	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31527269	31527332	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31527333	31527422	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31527423	31527571	1	-	2	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31527423	31527571	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31527572	31527751	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31527752	31527827	1	-	0	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31527752	31527827	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31527828	31527973	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31527974	31528019	1	-	1	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31527974	31528019	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31528020	31528153	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31528154	31528352	1	-	2	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31528154	31528352	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31528353	31528465	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31528466	31528579	1	-	2	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31528466	31528579	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31528580	31528689	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31528690	31528819	1	-	0	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31528690	31528819	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	intron	31528820	31529368	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	CDS	31529369	31529431	1	-	0	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	exon	31529369	31529431	.	-	.	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
Phchi.S1	AUGUSTUS	start_codon	31529429	31529431	.	-	0	transcript_id "Phchi.S1G501200.t1"; gene_id "Phchi.S1G501200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13772.t1 is derived from g12239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8839414	8839966	.	-	.	Phchi.S3G109100
Phchi.S3	AUGUSTUS	transcript	8839414	8839966	.	-	.	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	stop_codon	8839411	8839413	.	-	0	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	CDS	8839414	8839459	1	-	1	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	exon	8839414	8839459	.	-	.	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	intron	8839460	8839640	.	-	.	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	CDS	8839641	8839966	0.97	-	0	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	exon	8839641	8839966	.	-	.	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
Phchi.S3	AUGUSTUS	start_codon	8839964	8839966	.	-	0	transcript_id "Phchi.S3G109100.t1"; gene_id "Phchi.S3G109100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3330.t1 is derived from g499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2940894	2942815	.	+	.	Phchi.S1G048900
Phchi.S1	AUGUSTUS	transcript	2940894	2942815	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	start_codon	2940894	2940896	.	+	0	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	CDS	2940894	2941987	0.63	+	0	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	exon	2940894	2941987	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	intron	2941988	2942099	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	CDS	2942100	2942533	0.28	+	1	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	exon	2942100	2942533	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	intron	2942534	2942623	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	CDS	2942624	2942678	0.56	+	2	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	exon	2942624	2942678	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	intron	2942679	2942808	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	CDS	2942809	2942815	0.56	+	1	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	exon	2942809	2942815	.	+	.	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
Phchi.S1	AUGUSTUS	stop_codon	2942816	2942818	.	+	0	transcript_id "Phchi.S1G048900.t1"; gene_id "Phchi.S1G048900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5327.t1 is derived from g2497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16305229	16305619	.	+	.	Phchi.S1G248600
Phchi.S1	AUGUSTUS	transcript	16305229	16305619	.	+	.	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	start_codon	16305229	16305231	.	+	0	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	CDS	16305229	16305231	1	+	0	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	exon	16305229	16305231	.	+	.	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	intron	16305232	16305327	.	+	.	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	CDS	16305328	16305484	1	+	0	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	exon	16305328	16305484	.	+	.	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	intron	16305485	16305575	.	+	.	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	CDS	16305576	16305619	1	+	2	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	exon	16305576	16305619	.	+	.	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
Phchi.S1	AUGUSTUS	stop_codon	16305620	16305622	.	+	0	transcript_id "Phchi.S1G248600.t1"; gene_id "Phchi.S1G248600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6231.t1 is derived from g3403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21785145	21786653	.	+	.	Phchi.S1G339000
Phchi.S1	AUGUSTUS	transcript	21785145	21786653	.	+	.	transcript_id "Phchi.S1G339000.t1"; gene_id "Phchi.S1G339000"
Phchi.S1	AUGUSTUS	start_codon	21785145	21785147	.	+	0	transcript_id "Phchi.S1G339000.t1"; gene_id "Phchi.S1G339000"
Phchi.S1	AUGUSTUS	CDS	21785145	21786653	0.86	+	0	transcript_id "Phchi.S1G339000.t1"; gene_id "Phchi.S1G339000"
Phchi.S1	AUGUSTUS	exon	21785145	21786653	.	+	.	transcript_id "Phchi.S1G339000.t1"; gene_id "Phchi.S1G339000"
Phchi.S1	AUGUSTUS	stop_codon	21786654	21786656	.	+	0	transcript_id "Phchi.S1G339000.t1"; gene_id "Phchi.S1G339000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9227.t1 is derived from g6402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40509583	40511015	.	-	.	Phchi.S1G638600
Phchi.S1	AUGUSTUS	transcript	40509583	40511015	.	-	.	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	stop_codon	40509580	40509582	.	-	0	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	CDS	40509583	40509945	1	-	0	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	exon	40509583	40509945	.	-	.	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	intron	40509946	40510082	.	-	.	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	CDS	40510083	40510388	1	-	0	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	exon	40510083	40510388	.	-	.	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	intron	40510389	40510478	.	-	.	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	CDS	40510479	40511015	0.99	-	0	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	exon	40510479	40511015	.	-	.	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
Phchi.S1	AUGUSTUS	start_codon	40511013	40511015	.	-	0	transcript_id "Phchi.S1G638600.t1"; gene_id "Phchi.S1G638600"
# This transcript jg12040.t2 is derived from g7715.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12041.t1 is derived from g7716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	893579	899225	.	+	.	Phchi.S2G012100
Phchi.S2	AUGUSTUS	transcript	893579	899225	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	start_codon	893579	893581	.	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	893579	893781	0.79	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	893579	893781	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	893782	893887	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	893888	894185	0.71	+	1	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	893888	894185	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	894186	894341	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	894342	894485	0.82	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	894342	894485	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	894486	894612	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	894613	894699	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	894613	894699	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	894700	894838	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	894839	894970	0.61	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	894839	894970	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	894971	895044	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	895045	895209	0.9	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	895045	895209	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	895210	895304	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	895305	895483	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	895305	895483	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	895484	895690	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	895691	895775	1	+	1	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	895691	895775	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	895776	896006	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	896007	896063	0.6	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	896007	896063	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	896064	896145	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	896146	896198	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	896146	896198	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	896199	896288	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	896289	896497	1	+	1	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	896289	896497	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	896498	896701	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	896702	896820	1	+	2	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	896702	896820	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	896821	896939	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	896940	897010	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	896940	897010	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	897011	897144	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	897145	897262	1	+	1	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	897145	897262	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	897263	897384	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	897385	897471	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	897385	897471	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	897472	897561	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	897562	897648	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	897562	897648	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	897649	897725	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	897726	897802	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	897726	897802	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	897803	897890	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	897891	898068	1	+	1	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	897891	898068	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	898069	898151	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	898152	898254	1	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	898152	898254	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	intron	898255	898326	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	CDS	898327	899225	0.99	+	2	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	exon	898327	899225	.	+	.	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
Phchi.S2	AUGUSTUS	stop_codon	899226	899228	.	+	0	transcript_id "Phchi.S2G012100.t1"; gene_id "Phchi.S2G012100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg542.t1 is derived from g10324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3986741	3989849	.	-	.	Phchi.S6G050100
Phchi.S6	AUGUSTUS	transcript	3986741	3989849	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	stop_codon	3986738	3986740	.	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3986741	3987080	0.99	-	1	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3986741	3987080	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3987081	3987183	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3987184	3987299	1	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3987184	3987299	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3987300	3987397	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3987398	3987495	1	-	2	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3987398	3987495	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3987496	3987584	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3987585	3987633	1	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3987585	3987633	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3987634	3987714	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3987715	3987768	1	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3987715	3987768	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3987769	3987902	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3987903	3988014	0.95	-	1	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3987903	3988014	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3988015	3988094	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3988095	3988225	0.95	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3988095	3988225	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3988226	3988318	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3988319	3988421	1	-	1	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3988319	3988421	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3988422	3988526	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3988527	3988604	1	-	1	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3988527	3988604	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3988605	3988721	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3988722	3989005	1	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3988722	3989005	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	intron	3989006	3989087	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	CDS	3989088	3989849	0.62	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	exon	3989088	3989849	.	-	.	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
Phchi.S6	AUGUSTUS	start_codon	3989847	3989849	.	-	0	transcript_id "Phchi.S6G050100.t1"; gene_id "Phchi.S6G050100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8920.t1 is derived from g6095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38673835	38674062	.	-	.	Phchi.S1G607900
Phchi.S1	AUGUSTUS	transcript	38673835	38674062	.	-	.	transcript_id "Phchi.S1G607900.t1"; gene_id "Phchi.S1G607900"
Phchi.S1	AUGUSTUS	stop_codon	38673832	38673834	.	-	0	transcript_id "Phchi.S1G607900.t1"; gene_id "Phchi.S1G607900"
Phchi.S1	AUGUSTUS	CDS	38673835	38674062	0.62	-	0	transcript_id "Phchi.S1G607900.t1"; gene_id "Phchi.S1G607900"
Phchi.S1	AUGUSTUS	exon	38673835	38674062	.	-	.	transcript_id "Phchi.S1G607900.t1"; gene_id "Phchi.S1G607900"
Phchi.S1	AUGUSTUS	start_codon	38674060	38674062	.	-	0	transcript_id "Phchi.S1G607900.t1"; gene_id "Phchi.S1G607900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2792.t1 is derived from g9712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8924882	8925822	.	+	.	Phchi.S5G140100
Phchi.S5	AUGUSTUS	transcript	8924882	8925822	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	start_codon	8924882	8924884	.	+	0	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	CDS	8924882	8924901	1	+	0	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	exon	8924882	8924901	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	intron	8924902	8925003	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	CDS	8925004	8925265	1	+	1	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	exon	8925004	8925265	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	intron	8925266	8925430	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	CDS	8925431	8925607	1	+	0	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	exon	8925431	8925607	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	intron	8925608	8925741	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	CDS	8925742	8925822	1	+	0	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	exon	8925742	8925822	.	+	.	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
Phchi.S5	AUGUSTUS	stop_codon	8925823	8925825	.	+	0	transcript_id "Phchi.S5G140100.t1"; gene_id "Phchi.S5G140100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2602.t1 is derived from g9522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7720620	7721294	.	-	.	Phchi.S5G121100
Phchi.S5	AUGUSTUS	transcript	7720620	7721294	.	-	.	transcript_id "Phchi.S5G121100.t1"; gene_id "Phchi.S5G121100"
Phchi.S5	AUGUSTUS	stop_codon	7720617	7720619	.	-	0	transcript_id "Phchi.S5G121100.t1"; gene_id "Phchi.S5G121100"
Phchi.S5	AUGUSTUS	CDS	7720620	7721294	0.73	-	0	transcript_id "Phchi.S5G121100.t1"; gene_id "Phchi.S5G121100"
Phchi.S5	AUGUSTUS	exon	7720620	7721294	.	-	.	transcript_id "Phchi.S5G121100.t1"; gene_id "Phchi.S5G121100"
Phchi.S5	AUGUSTUS	start_codon	7721292	7721294	.	-	0	transcript_id "Phchi.S5G121100.t1"; gene_id "Phchi.S5G121100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1618.t1 is derived from g8537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2049578	2050888	.	-	.	Phchi.S5G022700
Phchi.S5	AUGUSTUS	transcript	2049578	2050888	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	stop_codon	2049575	2049577	.	-	0	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	CDS	2049578	2050024	0.92	-	0	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	exon	2049578	2050024	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	intron	2050025	2050109	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	CDS	2050110	2050207	1	-	2	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	exon	2050110	2050207	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	intron	2050208	2050293	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	CDS	2050294	2050474	1	-	0	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	exon	2050294	2050474	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	intron	2050475	2050700	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	CDS	2050701	2050778	1	-	0	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	exon	2050701	2050778	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	intron	2050779	2050885	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	CDS	2050886	2050888	0.98	-	0	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	exon	2050886	2050888	.	-	.	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
Phchi.S5	AUGUSTUS	start_codon	2050886	2050888	.	-	0	transcript_id "Phchi.S5G022700.t1"; gene_id "Phchi.S5G022700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg13432.t1 is derived from g11899.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6675411	6678931	.	+	.	Phchi.S3G075100
Phchi.S3	AUGUSTUS	transcript	6675411	6678931	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	start_codon	6675411	6675413	.	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675411	6675667	0.93	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675411	6675667	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675668	6675759	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675760	6675931	1	+	1	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675760	6675931	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675932	6676023	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676024	6676092	1	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676024	6676092	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676093	6676238	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676239	6676306	1	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676239	6676306	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676307	6676410	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676411	6676479	1	+	1	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676411	6676479	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676480	6676574	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676575	6676665	1	+	1	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676575	6676665	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676666	6676756	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676757	6676790	0.99	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676757	6676790	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676791	6676894	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676895	6676901	0.99	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676895	6676901	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676902	6677006	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677007	6677056	0.99	+	1	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677007	6677056	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677057	6677151	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677152	6677197	0.99	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677152	6677197	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677198	6677352	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677353	6677398	1	+	1	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677353	6677398	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677399	6677484	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677485	6677551	1	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677485	6677551	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677552	6677627	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677628	6677693	1	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677628	6677693	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677694	6677775	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677776	6677868	1	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677776	6677868	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677869	6677996	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677997	6678085	1	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677997	6678085	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678086	6678176	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678177	6678243	1	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678177	6678243	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678244	6678343	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678344	6678386	1	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678344	6678386	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678387	6678471	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678472	6678541	1	+	1	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678472	6678541	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678542	6678611	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678612	6678684	1	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678612	6678684	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678685	6678782	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678783	6678931	0.99	+	2	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678783	6678931	.	+	.	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	stop_codon	6678932	6678934	.	+	0	transcript_id "Phchi.S3G075100.t1"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	transcript	6675411	6678931	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	start_codon	6675411	6675413	.	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675411	6675667	0.88	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675411	6675667	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675668	6675759	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675760	6675931	1	+	1	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675760	6675931	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675932	6676023	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676024	6676092	1	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676024	6676092	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676093	6676238	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676239	6676306	1	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676239	6676306	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676307	6676410	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676411	6676479	1	+	1	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676411	6676479	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676480	6676574	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676575	6676665	1	+	1	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676575	6676665	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676666	6676756	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676757	6676790	0.97	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676757	6676790	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676791	6676894	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676895	6676901	0.96	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676895	6676901	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676902	6677006	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677007	6677056	0.97	+	1	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677007	6677056	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677057	6677151	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677152	6677197	1	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677152	6677197	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677198	6677352	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677353	6677398	1	+	1	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677353	6677398	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677399	6677493	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677494	6677551	1	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677494	6677551	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677552	6677627	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677628	6677693	1	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677628	6677693	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677694	6677775	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677776	6677868	1	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677776	6677868	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677869	6677996	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677997	6678085	1	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677997	6678085	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678086	6678176	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678177	6678243	1	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678177	6678243	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678244	6678343	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678344	6678386	1	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678344	6678386	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678387	6678471	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678472	6678541	1	+	1	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678472	6678541	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678542	6678611	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678612	6678684	1	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678612	6678684	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678685	6678782	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678783	6678931	1	+	2	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678783	6678931	.	+	.	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	stop_codon	6678932	6678934	.	+	0	transcript_id "Phchi.S3G075100.t2"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	transcript	6675411	6678931	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	start_codon	6675411	6675413	.	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675411	6675667	0.93	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675411	6675667	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675668	6675759	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675760	6675931	1	+	1	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675760	6675931	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675932	6676023	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676024	6676092	1	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676024	6676092	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676093	6676238	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676239	6676306	1	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676239	6676306	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676307	6676410	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676411	6676479	1	+	1	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676411	6676479	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676480	6676574	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676575	6676665	1	+	1	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676575	6676665	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676666	6676756	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676757	6676841	0.99	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676757	6676841	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676842	6677151	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677152	6677197	0.99	+	2	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677152	6677197	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677198	6677352	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677353	6677398	1	+	1	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677353	6677398	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677399	6677493	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677494	6677551	0.72	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677494	6677551	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677552	6677627	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677628	6677693	1	+	2	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677628	6677693	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677694	6677775	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677776	6677868	1	+	2	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677776	6677868	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677869	6677996	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677997	6678085	1	+	2	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677997	6678085	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678086	6678176	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678177	6678243	1	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678177	6678243	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678244	6678343	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678344	6678386	1	+	2	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678344	6678386	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678387	6678471	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678472	6678541	1	+	1	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678472	6678541	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678542	6678611	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678612	6678684	1	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678612	6678684	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678685	6678782	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678783	6678931	0.99	+	2	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678783	6678931	.	+	.	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	stop_codon	6678932	6678934	.	+	0	transcript_id "Phchi.S3G075100.t3"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	transcript	6675411	6678931	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	start_codon	6675411	6675413	.	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675411	6675667	0.92	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675411	6675667	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675668	6675759	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6675760	6675931	1	+	1	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6675760	6675931	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6675932	6676023	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676024	6676092	1	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676024	6676092	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676093	6676238	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676239	6676306	1	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676239	6676306	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676307	6676410	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676411	6676479	1	+	1	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676411	6676479	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676480	6676574	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676575	6676665	1	+	1	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676575	6676665	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676666	6676756	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676757	6676841	0.73	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676757	6676841	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6676842	6676956	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6676957	6677056	0.92	+	2	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6676957	6677056	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677057	6677146	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677147	6677197	1	+	1	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677147	6677197	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677198	6677352	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677353	6677398	1	+	1	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677353	6677398	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677399	6677493	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677494	6677551	0.71	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677494	6677551	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677552	6677627	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677628	6677693	1	+	2	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677628	6677693	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677694	6677775	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677776	6677868	1	+	2	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677776	6677868	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6677869	6677996	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6677997	6678085	1	+	2	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6677997	6678085	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678086	6678176	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678177	6678243	1	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678177	6678243	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678244	6678343	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678344	6678386	1	+	2	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678344	6678386	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678387	6678471	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678472	6678541	1	+	1	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678472	6678541	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678542	6678611	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678612	6678684	1	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678612	6678684	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	intron	6678685	6678782	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	CDS	6678783	6678931	0.97	+	2	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	exon	6678783	6678931	.	+	.	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
Phchi.S3	AUGUSTUS	stop_codon	6678932	6678934	.	+	0	transcript_id "Phchi.S3G075100.t4"; gene_id "Phchi.S3G075100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14044.t1 is derived from g12511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10449849	10450121	.	+	.	Phchi.S3G136300
Phchi.S3	AUGUSTUS	transcript	10449849	10450121	.	+	.	transcript_id "Phchi.S3G136300.t1"; gene_id "Phchi.S3G136300"
Phchi.S3	AUGUSTUS	start_codon	10449849	10449851	.	+	0	transcript_id "Phchi.S3G136300.t1"; gene_id "Phchi.S3G136300"
Phchi.S3	AUGUSTUS	CDS	10449849	10450121	0.88	+	0	transcript_id "Phchi.S3G136300.t1"; gene_id "Phchi.S3G136300"
Phchi.S3	AUGUSTUS	exon	10449849	10450121	.	+	.	transcript_id "Phchi.S3G136300.t1"; gene_id "Phchi.S3G136300"
Phchi.S3	AUGUSTUS	stop_codon	10450122	10450124	.	+	0	transcript_id "Phchi.S3G136300.t1"; gene_id "Phchi.S3G136300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4841.t1 is derived from g2011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13058249	13059318	.	-	.	Phchi.S1G200000
Phchi.S1	AUGUSTUS	transcript	13058249	13059318	.	-	.	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	stop_codon	13058246	13058248	.	-	0	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	CDS	13058249	13058628	0.85	-	2	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	exon	13058249	13058628	.	-	.	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	intron	13058629	13058732	.	-	.	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	CDS	13058733	13058919	0.96	-	0	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	exon	13058733	13058919	.	-	.	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	intron	13058920	13059012	.	-	.	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	CDS	13059013	13059318	0.99	-	0	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	exon	13059013	13059318	.	-	.	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
Phchi.S1	AUGUSTUS	start_codon	13059316	13059318	.	-	0	transcript_id "Phchi.S1G200000.t1"; gene_id "Phchi.S1G200000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15224.t1 is derived from g13692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17815254	17819018	.	+	.	Phchi.S3G254300
Phchi.S3	AUGUSTUS	transcript	17815254	17819018	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	start_codon	17815254	17815256	.	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17815254	17815538	1	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17815254	17815538	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17815539	17815891	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17815892	17815981	1	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17815892	17815981	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17815982	17816083	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17816084	17816203	1	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17816084	17816203	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17816204	17816372	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17816373	17816474	1	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17816373	17816474	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17816475	17816556	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17816557	17816849	1	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17816557	17816849	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17816850	17816937	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17816938	17817083	1	+	1	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17816938	17817083	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17817084	17817178	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17817179	17817350	0.99	+	2	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17817179	17817350	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17817351	17817456	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17817457	17818156	0.94	+	1	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17817457	17818156	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17818157	17818252	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17818253	17818600	1	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17818253	17818600	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	intron	17818601	17818739	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	CDS	17818740	17819018	0.98	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	exon	17818740	17819018	.	+	.	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
Phchi.S3	AUGUSTUS	stop_codon	17819019	17819021	.	+	0	transcript_id "Phchi.S3G254300.t1"; gene_id "Phchi.S3G254300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5698.t1 is derived from g2868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18384389	18388427	.	-	.	Phchi.S1G285700
Phchi.S1	AUGUSTUS	transcript	18384389	18388427	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	stop_codon	18384386	18384388	.	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18384389	18384550	0.99	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18384389	18384550	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18384551	18384644	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18384645	18384797	1	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18384645	18384797	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18384798	18384879	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18384880	18385044	1	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18384880	18385044	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18385045	18385135	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18385136	18385301	1	-	1	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18385136	18385301	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18385302	18385457	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18385458	18385589	0.61	-	1	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18385458	18385589	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18385590	18385711	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18385712	18386411	0.6	-	2	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18385712	18386411	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18386412	18386514	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18386515	18386712	0.94	-	2	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18386515	18386712	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18386713	18386803	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18386804	18386867	1	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18386804	18386867	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18386868	18386954	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18386955	18387005	0.97	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18386955	18387005	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18387006	18387117	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18387118	18387186	0.62	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18387118	18387186	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18387187	18387276	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18387277	18387396	1	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18387277	18387396	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18387397	18387489	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18387490	18387690	0.83	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18387490	18387690	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18387691	18387803	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18387804	18387902	0.99	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18387804	18387902	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18387903	18388054	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18388055	18388135	1	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18388055	18388135	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	intron	18388136	18388274	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	CDS	18388275	18388427	0.75	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	exon	18388275	18388427	.	-	.	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
Phchi.S1	AUGUSTUS	start_codon	18388425	18388427	.	-	0	transcript_id "Phchi.S1G285700.t1"; gene_id "Phchi.S1G285700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15050.t1 is derived from g13518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16751169	16751818	.	+	.	Phchi.S3G236900
Phchi.S3	AUGUSTUS	transcript	16751169	16751818	.	+	.	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	start_codon	16751169	16751171	.	+	0	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	CDS	16751169	16751220	0.98	+	0	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	exon	16751169	16751220	.	+	.	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	intron	16751221	16751466	.	+	.	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	CDS	16751467	16751580	0.92	+	2	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	exon	16751467	16751580	.	+	.	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	intron	16751581	16751726	.	+	.	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	CDS	16751727	16751818	0.93	+	2	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	exon	16751727	16751818	.	+	.	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
Phchi.S3	AUGUSTUS	stop_codon	16751819	16751821	.	+	0	transcript_id "Phchi.S3G236900.t1"; gene_id "Phchi.S3G236900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3331.t1 is derived from g500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2954785	2955562	.	-	.	Phchi.S1G049000
Phchi.S1	AUGUSTUS	transcript	2954785	2955562	.	-	.	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	stop_codon	2954782	2954784	.	-	0	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	CDS	2954785	2954811	0.99	-	0	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	exon	2954785	2954811	.	-	.	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	intron	2954812	2955000	.	-	.	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	CDS	2955001	2955132	1	-	0	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	exon	2955001	2955132	.	-	.	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	intron	2955133	2955226	.	-	.	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	CDS	2955227	2955562	0.99	-	0	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	exon	2955227	2955562	.	-	.	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
Phchi.S1	AUGUSTUS	start_codon	2955560	2955562	.	-	0	transcript_id "Phchi.S1G049000.t1"; gene_id "Phchi.S1G049000"
# This transcript jg448.t2 is derived from g10230.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg449.t1 is derived from g10231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3136480	3138365	.	+	.	Phchi.S6G040800
Phchi.S6	AUGUSTUS	transcript	3136480	3138365	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	start_codon	3136480	3136482	.	+	0	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	CDS	3136480	3136731	0.37	+	0	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	exon	3136480	3136731	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	intron	3136732	3136811	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	CDS	3136812	3136832	1	+	0	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	exon	3136812	3136832	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	intron	3136833	3136986	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	CDS	3136987	3137121	1	+	0	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	exon	3136987	3137121	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	intron	3137122	3137251	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	CDS	3137252	3137412	1	+	0	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	exon	3137252	3137412	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	intron	3137413	3137524	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	CDS	3137525	3138365	0.91	+	1	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	exon	3137525	3138365	.	+	.	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
Phchi.S6	AUGUSTUS	stop_codon	3138366	3138368	.	+	0	transcript_id "Phchi.S6G040800.t1"; gene_id "Phchi.S6G040800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7952.t1 is derived from g5126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32075165	32078970	.	+	.	Phchi.S1G511100
Phchi.S1	AUGUSTUS	transcript	32075165	32078970	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	start_codon	32075165	32075167	.	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32075165	32075275	0.99	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32075165	32075275	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32075276	32075463	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32075464	32075583	0.84	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32075464	32075583	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32075584	32075695	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32075696	32075816	0.79	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32075696	32075816	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32075817	32075902	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32075903	32075951	0.72	+	2	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32075903	32075951	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32075952	32076216	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32076217	32076361	0.69	+	1	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32076217	32076361	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32076362	32076479	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32076480	32076542	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32076480	32076542	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32076543	32076687	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32076688	32076798	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32076688	32076798	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32076799	32076958	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32076959	32077024	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32076959	32077024	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32077025	32077128	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32077129	32077206	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32077129	32077206	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32077207	32077318	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32077319	32077396	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32077319	32077396	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32077397	32077533	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32077534	32077600	0.98	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32077534	32077600	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32077601	32077702	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32077703	32077788	1	+	2	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32077703	32077788	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32077789	32077942	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32077943	32077975	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32077943	32077975	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32077976	32078106	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32078107	32078139	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32078107	32078139	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32078140	32078265	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32078266	32078366	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32078266	32078366	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32078367	32078434	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32078435	32078520	1	+	1	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32078435	32078520	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32078521	32078594	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32078595	32078701	1	+	2	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32078595	32078701	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32078702	32078781	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32078782	32078859	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32078782	32078859	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	intron	32078860	32078937	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	CDS	32078938	32078970	1	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	exon	32078938	32078970	.	+	.	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
Phchi.S1	AUGUSTUS	stop_codon	32078971	32078973	.	+	0	transcript_id "Phchi.S1G511100.t1"; gene_id "Phchi.S1G511100"
# This transcript jg2393.t2 is derived from g9313.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2393.t3 is derived from g9313.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2394.t1 is derived from g9314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6468667	6469922	.	+	.	Phchi.S5G100300
Phchi.S5	AUGUSTUS	transcript	6468667	6469922	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	start_codon	6468667	6468669	.	+	0	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	CDS	6468667	6469075	0.61	+	0	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	exon	6468667	6469075	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	intron	6469076	6469159	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	CDS	6469160	6469232	0.99	+	2	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	exon	6469160	6469232	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	intron	6469233	6469331	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	CDS	6469332	6469458	1	+	1	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	exon	6469332	6469458	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	intron	6469459	6469541	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	CDS	6469542	6469717	0.65	+	0	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	exon	6469542	6469717	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	intron	6469718	6469789	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	CDS	6469790	6469922	0.62	+	1	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	exon	6469790	6469922	.	+	.	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
Phchi.S5	AUGUSTUS	stop_codon	6469923	6469925	.	+	0	transcript_id "Phchi.S5G100300.t1"; gene_id "Phchi.S5G100300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4855.t1 is derived from g2025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13117279	13119221	.	-	.	Phchi.S1G201400
Phchi.S1	AUGUSTUS	transcript	13117279	13117908	.	-	.	transcript_id "Phchi.S1G201400.t1"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	stop_codon	13117276	13117278	.	-	0	transcript_id "Phchi.S1G201400.t1"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	CDS	13117279	13117908	0.78	-	0	transcript_id "Phchi.S1G201400.t1"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	exon	13117279	13117908	.	-	.	transcript_id "Phchi.S1G201400.t1"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	start_codon	13117906	13117908	.	-	0	transcript_id "Phchi.S1G201400.t1"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	transcript	13117279	13118603	.	-	.	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	stop_codon	13117276	13117278	.	-	0	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	CDS	13117279	13118234	0.44	-	2	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	exon	13117279	13118234	.	-	.	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	intron	13118235	13118347	.	-	.	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	CDS	13118348	13118603	0.3	-	0	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	exon	13118348	13118603	.	-	.	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	start_codon	13118601	13118603	.	-	0	transcript_id "Phchi.S1G201400.t2"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	transcript	13117279	13119221	.	-	.	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	stop_codon	13117276	13117278	.	-	0	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	CDS	13117279	13118234	0.33	-	2	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	exon	13117279	13118234	.	-	.	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	intron	13118235	13118347	.	-	.	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	CDS	13118348	13119221	0.23	-	0	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	exon	13118348	13119221	.	-	.	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
Phchi.S1	AUGUSTUS	start_codon	13119219	13119221	.	-	0	transcript_id "Phchi.S1G201400.t3"; gene_id "Phchi.S1G201400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3763.t1 is derived from g932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5574937	5577564	.	+	.	Phchi.S1G092200
Phchi.S1	AUGUSTUS	transcript	5574937	5577564	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	start_codon	5574937	5574939	.	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5574937	5574992	0.36	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5574937	5574992	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5574993	5575103	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5575104	5575175	0.63	+	1	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5575104	5575175	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5575176	5575254	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5575255	5575346	0.97	+	1	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5575255	5575346	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5575347	5575419	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5575420	5575916	0.97	+	2	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5575420	5575916	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5575917	5576017	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5576018	5576209	0.99	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5576018	5576209	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5576210	5576292	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5576293	5576499	0.98	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5576293	5576499	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5576500	5576590	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5576591	5576701	0.9	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5576591	5576701	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5576702	5577031	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5577032	5577044	1	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5577032	5577044	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5577045	5577186	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5577187	5577217	1	+	2	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5577187	5577217	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	intron	5577218	5577434	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	CDS	5577435	5577564	0.7	+	1	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	exon	5577435	5577564	.	+	.	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
Phchi.S1	AUGUSTUS	stop_codon	5577565	5577567	.	+	0	transcript_id "Phchi.S1G092200.t1"; gene_id "Phchi.S1G092200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8527.t1 is derived from g5702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36447267	36447884	.	+	.	Phchi.S1G568600
Phchi.S1	AUGUSTUS	transcript	36447267	36447884	.	+	.	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	start_codon	36447267	36447269	.	+	0	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	CDS	36447267	36447342	0.38	+	0	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	exon	36447267	36447342	.	+	.	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	intron	36447343	36447432	.	+	.	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	CDS	36447433	36447501	0.4	+	2	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	exon	36447433	36447501	.	+	.	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	intron	36447502	36447627	.	+	.	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	CDS	36447628	36447884	0.64	+	2	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	exon	36447628	36447884	.	+	.	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
Phchi.S1	AUGUSTUS	stop_codon	36447885	36447887	.	+	0	transcript_id "Phchi.S1G568600.t1"; gene_id "Phchi.S1G568600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg260.t1 is derived from g10042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1752516	1754726	.	+	.	Phchi.S6G021900
Phchi.S6	AUGUSTUS	transcript	1752516	1754726	.	+	.	transcript_id "Phchi.S6G021900.t1"; gene_id "Phchi.S6G021900"
Phchi.S6	AUGUSTUS	start_codon	1752516	1752518	.	+	0	transcript_id "Phchi.S6G021900.t1"; gene_id "Phchi.S6G021900"
Phchi.S6	AUGUSTUS	CDS	1752516	1754726	0.89	+	0	transcript_id "Phchi.S6G021900.t1"; gene_id "Phchi.S6G021900"
Phchi.S6	AUGUSTUS	exon	1752516	1754726	.	+	.	transcript_id "Phchi.S6G021900.t1"; gene_id "Phchi.S6G021900"
Phchi.S6	AUGUSTUS	stop_codon	1754727	1754729	.	+	0	transcript_id "Phchi.S6G021900.t1"; gene_id "Phchi.S6G021900"
# This transcript jg1615.t2 is derived from g8534.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1616.t1 is derived from g8535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2035624	2038241	.	+	.	Phchi.S5G022500
Phchi.S5	AUGUSTUS	transcript	2035624	2038241	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	start_codon	2035624	2035626	.	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2035624	2035869	0.98	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2035624	2035869	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2035870	2035976	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2035977	2036092	1	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2035977	2036092	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2036093	2036174	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2036175	2036283	1	+	1	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2036175	2036283	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2036284	2036426	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2036427	2036541	1	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2036427	2036541	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2036542	2036631	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2036632	2036719	0.77	+	2	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2036632	2036719	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2036720	2036838	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2036839	2036945	1	+	1	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2036839	2036945	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2036946	2037026	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2037027	2037060	1	+	2	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2037027	2037060	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2037061	2037229	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2037230	2037278	1	+	1	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2037230	2037278	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2037279	2037354	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2037355	2037408	1	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2037355	2037408	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2037409	2037562	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2037563	2037706	0.97	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2037563	2037706	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2037707	2037808	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2037809	2037873	0.99	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2037809	2037873	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2037874	2037954	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2037955	2038009	1	+	1	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2037955	2038009	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	intron	2038010	2038088	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	CDS	2038089	2038241	0.99	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	exon	2038089	2038241	.	+	.	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
Phchi.S5	AUGUSTUS	stop_codon	2038242	2038244	.	+	0	transcript_id "Phchi.S5G022500.t1"; gene_id "Phchi.S5G022500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10438.t1 is derived from g14487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	338685	339254	.	-	.	Phchi.S4G002000
Phchi.S4	AUGUSTUS	transcript	338685	339254	.	-	.	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	stop_codon	338682	338684	.	-	0	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	CDS	338685	339021	0.8	-	1	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	exon	338685	339021	.	-	.	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	intron	339022	339114	.	-	.	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	CDS	339115	339254	0.91	-	0	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	exon	339115	339254	.	-	.	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
Phchi.S4	AUGUSTUS	start_codon	339252	339254	.	-	0	transcript_id "Phchi.S4G002000.t1"; gene_id "Phchi.S4G002000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14340.t1 is derived from g12807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12303066	12304622	.	+	.	Phchi.S3G165900
Phchi.S3	AUGUSTUS	transcript	12303066	12304622	.	+	.	transcript_id "Phchi.S3G165900.t1"; gene_id "Phchi.S3G165900"
Phchi.S3	AUGUSTUS	start_codon	12303066	12303068	.	+	0	transcript_id "Phchi.S3G165900.t1"; gene_id "Phchi.S3G165900"
Phchi.S3	AUGUSTUS	CDS	12303066	12304622	0.7	+	0	transcript_id "Phchi.S3G165900.t1"; gene_id "Phchi.S3G165900"
Phchi.S3	AUGUSTUS	exon	12303066	12304622	.	+	.	transcript_id "Phchi.S3G165900.t1"; gene_id "Phchi.S3G165900"
Phchi.S3	AUGUSTUS	stop_codon	12304623	12304625	.	+	0	transcript_id "Phchi.S3G165900.t1"; gene_id "Phchi.S3G165900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11990.t1 is derived from g7665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	404445	405994	.	-	.	Phchi.S2G007000
Phchi.S2	AUGUSTUS	transcript	404445	405994	.	-	.	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	stop_codon	404442	404444	.	-	0	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	CDS	404445	404719	0.13	-	2	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	exon	404445	404719	.	-	.	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	intron	404720	405825	.	-	.	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	CDS	405826	405994	0.01	-	0	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	exon	405826	405994	.	-	.	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
Phchi.S2	AUGUSTUS	start_codon	405992	405994	.	-	0	transcript_id "Phchi.S2G007000.t1"; gene_id "Phchi.S2G007000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg396.t1 is derived from g10178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2873884	2875584	.	+	.	Phchi.S6G035500
Phchi.S6	AUGUSTUS	transcript	2873884	2875584	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	start_codon	2873884	2873886	.	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2873884	2873892	0.99	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2873884	2873892	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2873893	2873981	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2873982	2874008	0.99	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2873982	2874008	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2874009	2874090	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2874091	2874121	0.99	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2874091	2874121	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2874122	2874341	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2874342	2874424	1	+	2	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2874342	2874424	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2874425	2874562	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2874563	2874646	1	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2874563	2874646	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2874647	2874768	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2874769	2874863	1	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2874769	2874863	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2874864	2875009	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2875010	2875115	1	+	1	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2875010	2875115	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2875116	2875200	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2875201	2875290	1	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2875201	2875290	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2875291	2875386	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2875387	2875473	1	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2875387	2875473	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	intron	2875474	2875548	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	CDS	2875549	2875584	0.99	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	exon	2875549	2875584	.	+	.	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
Phchi.S6	AUGUSTUS	stop_codon	2875585	2875587	.	+	0	transcript_id "Phchi.S6G035500.t1"; gene_id "Phchi.S6G035500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14769.t1 is derived from g13237.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14633236	14634577	.	-	.	Phchi.S3G208800
Phchi.S3	AUGUSTUS	transcript	14633236	14634577	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	stop_codon	14633233	14633235	.	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633236	14633268	1	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633236	14633268	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633269	14633349	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633350	14633463	1	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633350	14633463	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633464	14633542	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633543	14633668	1	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633543	14633668	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633669	14633749	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633750	14633818	1	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633750	14633818	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633819	14633899	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633900	14633973	0.98	-	2	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633900	14633973	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633974	14634062	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14634063	14634150	0.98	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14634063	14634150	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14634151	14634313	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14634314	14634577	0.71	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14634314	14634577	.	-	.	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	start_codon	14634575	14634577	.	-	0	transcript_id "Phchi.S3G208800.t1"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	transcript	14633236	14634577	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	stop_codon	14633233	14633235	.	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633236	14633268	1	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633236	14633268	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633269	14633349	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633350	14633463	1	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633350	14633463	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633464	14633542	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633543	14633668	1	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633543	14633668	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633669	14633749	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633750	14633818	1	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633750	14633818	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633819	14633899	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633900	14634012	1	-	2	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633900	14634012	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14634013	14634104	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14634105	14634150	1	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14634105	14634150	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14634151	14634313	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14634314	14634577	0.58	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14634314	14634577	.	-	.	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	start_codon	14634575	14634577	.	-	0	transcript_id "Phchi.S3G208800.t2"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	transcript	14633236	14634577	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	stop_codon	14633233	14633235	.	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633236	14633271	0.99	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633236	14633271	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633272	14633349	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633350	14633463	1	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633350	14633463	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633464	14633542	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633543	14633668	1	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633543	14633668	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633669	14633749	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633750	14633818	1	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633750	14633818	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633819	14633899	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14633900	14633973	0.99	-	2	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14633900	14633973	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14633974	14634062	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14634063	14634150	0.99	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14634063	14634150	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	intron	14634151	14634313	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	CDS	14634314	14634577	0.58	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	exon	14634314	14634577	.	-	.	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
Phchi.S3	AUGUSTUS	start_codon	14634575	14634577	.	-	0	transcript_id "Phchi.S3G208800.t3"; gene_id "Phchi.S3G208800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13626.t1 is derived from g12093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7820863	7823323	.	-	.	Phchi.S3G094500
Phchi.S3	AUGUSTUS	transcript	7820863	7823323	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	stop_codon	7820860	7820862	.	-	0	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	CDS	7820863	7822315	0.99	-	1	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	exon	7820863	7822315	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	intron	7822316	7822418	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	CDS	7822419	7822589	0.72	-	1	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	exon	7822419	7822589	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	intron	7822590	7822675	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	CDS	7822676	7823188	0.68	-	1	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	exon	7822676	7823188	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	intron	7823189	7823279	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	CDS	7823280	7823323	1	-	0	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	exon	7823280	7823323	.	-	.	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
Phchi.S3	AUGUSTUS	start_codon	7823321	7823323	.	-	0	transcript_id "Phchi.S3G094500.t1"; gene_id "Phchi.S3G094500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3455.t1 is derived from g624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3861517	3864992	.	-	.	Phchi.S1G061400
Phchi.S1	AUGUSTUS	transcript	3861517	3864992	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	stop_codon	3861514	3861516	.	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3861517	3861522	1	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3861517	3861522	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3861523	3861855	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3861856	3861921	0.48	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3861856	3861921	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3861922	3862045	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3862046	3862100	0.51	-	1	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3862046	3862100	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3862101	3862368	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3862369	3862452	1	-	1	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3862369	3862452	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3862453	3862577	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3862578	3862696	1	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3862578	3862696	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3862697	3862873	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3862874	3862959	1	-	2	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3862874	3862959	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3862960	3863141	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3863142	3863254	1	-	1	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3863142	3863254	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3863255	3863354	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3863355	3863417	1	-	1	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3863355	3863417	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3863418	3863557	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3863558	3863637	1	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3863558	3863637	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3863638	3863796	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3863797	3863917	1	-	1	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3863797	3863917	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3863918	3864051	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3864052	3864146	1	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3864052	3864146	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3864147	3864308	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3864309	3864389	1	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3864309	3864389	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3864390	3864542	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3864543	3864611	1	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3864543	3864611	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	intron	3864612	3864863	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	CDS	3864864	3864992	0.57	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	exon	3864864	3864992	.	-	.	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
Phchi.S1	AUGUSTUS	start_codon	3864990	3864992	.	-	0	transcript_id "Phchi.S1G061400.t1"; gene_id "Phchi.S1G061400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15790.t1 is derived from g14260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21353757	21358724	.	-	.	Phchi.S3G310900
Phchi.S3	AUGUSTUS	transcript	21353757	21358724	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	stop_codon	21353754	21353756	.	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21353757	21353924	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21353757	21353924	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21353925	21354003	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354004	21354066	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354004	21354066	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354067	21354174	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354175	21354341	0.96	-	2	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354175	21354341	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354342	21354448	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354449	21354489	1	-	1	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354449	21354489	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354490	21354604	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354605	21354690	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354605	21354690	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354691	21354836	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354837	21354964	1	-	2	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354837	21354964	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354965	21355050	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355051	21355156	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355051	21355156	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355157	21355347	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355348	21355498	0.97	-	1	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355348	21355498	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355499	21355577	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355578	21355630	0.95	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355578	21355630	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355631	21355763	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355764	21355931	0.48	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355764	21355931	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355932	21356025	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356026	21356184	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356026	21356184	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21356185	21356276	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356277	21356393	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356277	21356393	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21356394	21356564	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356565	21356699	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356565	21356699	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21356700	21356810	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356811	21357008	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356811	21357008	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21357009	21357098	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21357099	21357395	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21357099	21357395	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21357396	21357509	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21357510	21358295	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21357510	21358295	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21358296	21358496	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21358497	21358724	1	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21358497	21358724	.	-	.	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	start_codon	21358722	21358724	.	-	0	transcript_id "Phchi.S3G310900.t1"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	transcript	21353757	21358724	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	stop_codon	21353754	21353756	.	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21353757	21353924	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21353757	21353924	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21353925	21354003	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354004	21354066	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354004	21354066	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354067	21354174	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354175	21354341	0.95	-	2	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354175	21354341	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354342	21354448	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354449	21354489	0.99	-	1	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354449	21354489	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354490	21354604	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354605	21354690	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354605	21354690	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354691	21354836	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21354837	21354964	1	-	2	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21354837	21354964	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21354965	21355050	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355051	21355156	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355051	21355156	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355157	21355347	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355348	21355487	0.99	-	2	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355348	21355487	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355488	21355577	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355578	21355630	0.87	-	1	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355578	21355630	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355631	21355734	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21355735	21355931	0.47	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21355735	21355931	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21355932	21356025	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356026	21356184	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356026	21356184	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21356185	21356276	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356277	21356393	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356277	21356393	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21356394	21356564	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356565	21356699	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356565	21356699	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21356700	21356810	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21356811	21357008	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21356811	21357008	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21357009	21357098	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21357099	21357395	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21357099	21357395	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21357396	21357509	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21357510	21358295	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21357510	21358295	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	intron	21358296	21358496	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	CDS	21358497	21358724	1	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	exon	21358497	21358724	.	-	.	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
Phchi.S3	AUGUSTUS	start_codon	21358722	21358724	.	-	0	transcript_id "Phchi.S3G310900.t2"; gene_id "Phchi.S3G310900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4741.t1 is derived from g1911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12579901	12580827	.	-	.	Phchi.S1G190000
Phchi.S1	AUGUSTUS	transcript	12579901	12580827	.	-	.	transcript_id "Phchi.S1G190000.t1"; gene_id "Phchi.S1G190000"
Phchi.S1	AUGUSTUS	stop_codon	12579898	12579900	.	-	0	transcript_id "Phchi.S1G190000.t1"; gene_id "Phchi.S1G190000"
Phchi.S1	AUGUSTUS	CDS	12579901	12580827	0.33	-	0	transcript_id "Phchi.S1G190000.t1"; gene_id "Phchi.S1G190000"
Phchi.S1	AUGUSTUS	exon	12579901	12580827	.	-	.	transcript_id "Phchi.S1G190000.t1"; gene_id "Phchi.S1G190000"
Phchi.S1	AUGUSTUS	start_codon	12580825	12580827	.	-	0	transcript_id "Phchi.S1G190000.t1"; gene_id "Phchi.S1G190000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8416.t1 is derived from g5591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35844708	35846866	.	+	.	Phchi.S1G557500
Phchi.S1	AUGUSTUS	transcript	35844708	35846866	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	start_codon	35844708	35844710	.	+	0	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	CDS	35844708	35845229	0.24	+	0	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	exon	35844708	35845229	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	intron	35845230	35845339	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	CDS	35845340	35845552	1	+	0	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	exon	35845340	35845552	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	intron	35845553	35845633	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	CDS	35845634	35846421	0.98	+	0	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	exon	35845634	35846421	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	intron	35846422	35846505	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	CDS	35846506	35846866	1	+	1	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	exon	35846506	35846866	.	+	.	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
Phchi.S1	AUGUSTUS	stop_codon	35846867	35846869	.	+	0	transcript_id "Phchi.S1G557500.t1"; gene_id "Phchi.S1G557500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8362.t1 is derived from g5537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35513674	35517337	.	+	.	Phchi.S1G552100
Phchi.S1	AUGUSTUS	transcript	35513674	35517337	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	start_codon	35513674	35513676	.	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35513674	35513780	1	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35513674	35513780	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35513781	35514593	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35514594	35514672	1	+	1	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35514594	35514672	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35514673	35514854	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35514855	35514953	1	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35514855	35514953	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35514954	35515059	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35515060	35515173	1	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35515060	35515173	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35515174	35515256	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35515257	35515414	1	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35515257	35515414	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35515415	35515683	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35515684	35515765	1	+	1	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35515684	35515765	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35515766	35515863	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35515864	35515949	1	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35515864	35515949	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35515950	35516042	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35516043	35516237	1	+	1	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35516043	35516237	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	intron	35516238	35516364	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	CDS	35516365	35517337	0.82	+	1	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	exon	35516365	35517337	.	+	.	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
Phchi.S1	AUGUSTUS	stop_codon	35517338	35517340	.	+	0	transcript_id "Phchi.S1G552100.t1"; gene_id "Phchi.S1G552100"
# This transcript jg3026.t2 is derived from g195.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3027.t1 is derived from g196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1206492	1208805	.	+	.	Phchi.S1G018600
Phchi.S1	AUGUSTUS	transcript	1206492	1208805	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	start_codon	1206492	1206494	.	+	0	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1206492	1206506	0.41	+	0	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1206492	1206506	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	intron	1206507	1206613	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1206614	1206776	0.95	+	0	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1206614	1206776	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	intron	1206777	1206864	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1206865	1207082	0.77	+	2	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1206865	1207082	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	intron	1207083	1207156	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1207157	1207450	0.97	+	0	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1207157	1207450	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	intron	1207451	1207530	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1207531	1207799	0.99	+	0	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1207531	1207799	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	intron	1207800	1207907	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1207908	1208805	0.97	+	1	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1207908	1208805	.	+	.	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	stop_codon	1208806	1208808	.	+	0	transcript_id "Phchi.S1G018600.t1"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	transcript	1207576	1208805	.	+	.	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	start_codon	1207576	1207578	.	+	0	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1207576	1207799	0.45	+	0	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1207576	1207799	.	+	.	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	intron	1207800	1207907	.	+	.	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	CDS	1207908	1208805	0.95	+	1	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	exon	1207908	1208805	.	+	.	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
Phchi.S1	AUGUSTUS	stop_codon	1208806	1208808	.	+	0	transcript_id "Phchi.S1G018600.t2"; gene_id "Phchi.S1G018600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10381.t1 is derived from g7557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47480631	47482558	.	+	.	Phchi.S1G754000
Phchi.S1	AUGUSTUS	transcript	47480631	47482558	.	+	.	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	start_codon	47480631	47480633	.	+	0	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	CDS	47480631	47480850	0.55	+	0	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	exon	47480631	47480850	.	+	.	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	intron	47480851	47480994	.	+	.	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	CDS	47480995	47481141	0.68	+	2	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	exon	47480995	47481141	.	+	.	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	intron	47481142	47481254	.	+	.	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	CDS	47481255	47482558	0.88	+	2	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	exon	47481255	47482558	.	+	.	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
Phchi.S1	AUGUSTUS	stop_codon	47482559	47482561	.	+	0	transcript_id "Phchi.S1G754000.t1"; gene_id "Phchi.S1G754000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4886.t1 is derived from g2056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13220409	13221734	.	+	.	Phchi.S1G204500
Phchi.S1	AUGUSTUS	transcript	13220409	13221734	.	+	.	transcript_id "Phchi.S1G204500.t1"; gene_id "Phchi.S1G204500"
Phchi.S1	AUGUSTUS	start_codon	13220409	13220411	.	+	0	transcript_id "Phchi.S1G204500.t1"; gene_id "Phchi.S1G204500"
Phchi.S1	AUGUSTUS	CDS	13220409	13221734	0.46	+	0	transcript_id "Phchi.S1G204500.t1"; gene_id "Phchi.S1G204500"
Phchi.S1	AUGUSTUS	exon	13220409	13221734	.	+	.	transcript_id "Phchi.S1G204500.t1"; gene_id "Phchi.S1G204500"
Phchi.S1	AUGUSTUS	stop_codon	13221735	13221737	.	+	0	transcript_id "Phchi.S1G204500.t1"; gene_id "Phchi.S1G204500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13855.t1 is derived from g12322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9249550	9250388	.	-	.	Phchi.S3G117400
Phchi.S3	AUGUSTUS	transcript	9249550	9250388	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	stop_codon	9249547	9249549	.	-	0	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	CDS	9249550	9249663	1	-	0	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	exon	9249550	9249663	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	intron	9249664	9249744	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	CDS	9249745	9249825	1	-	0	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	exon	9249745	9249825	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	intron	9249826	9249943	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	CDS	9249944	9250066	1	-	0	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	exon	9249944	9250066	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	intron	9250067	9250148	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	CDS	9250149	9250388	0.94	-	0	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	exon	9250149	9250388	.	-	.	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
Phchi.S3	AUGUSTUS	start_codon	9250386	9250388	.	-	0	transcript_id "Phchi.S3G117400.t1"; gene_id "Phchi.S3G117400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5721.t1 is derived from g2891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18545906	18547699	.	+	.	Phchi.S1G288000
Phchi.S1	AUGUSTUS	transcript	18545906	18547699	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	start_codon	18545906	18545908	.	+	0	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18545906	18546044	0.97	+	0	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18545906	18546044	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	intron	18546045	18546139	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18546140	18546359	1	+	2	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18546140	18546359	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	intron	18546360	18546449	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18546450	18546676	1	+	1	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18546450	18546676	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	intron	18546677	18546759	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18546760	18546975	1	+	2	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18546760	18546975	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	intron	18546976	18547056	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18547057	18547258	1	+	2	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18547057	18547258	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	intron	18547259	18547350	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18547351	18547520	1	+	1	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18547351	18547520	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	intron	18547521	18547613	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	CDS	18547614	18547699	1	+	2	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	exon	18547614	18547699	.	+	.	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
Phchi.S1	AUGUSTUS	stop_codon	18547700	18547702	.	+	0	transcript_id "Phchi.S1G288000.t1"; gene_id "Phchi.S1G288000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7140.t1 is derived from g4312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27141200	27142806	.	-	.	Phchi.S1G429900
Phchi.S1	AUGUSTUS	transcript	27141200	27142806	.	-	.	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	stop_codon	27141197	27141199	.	-	0	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	CDS	27141200	27141321	1	-	2	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	exon	27141200	27141321	.	-	.	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	intron	27141322	27142574	.	-	.	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	CDS	27142575	27142704	1	-	0	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	exon	27142575	27142704	.	-	.	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	intron	27142705	27142791	.	-	.	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	CDS	27142792	27142806	1	-	0	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	exon	27142792	27142806	.	-	.	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
Phchi.S1	AUGUSTUS	start_codon	27142804	27142806	.	-	0	transcript_id "Phchi.S1G429900.t1"; gene_id "Phchi.S1G429900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10007.t1 is derived from g7183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45020850	45021847	.	+	.	Phchi.S1G716600
Phchi.S1	AUGUSTUS	transcript	45020850	45021847	.	+	.	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	start_codon	45020850	45020852	.	+	0	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	CDS	45020850	45021026	0.8	+	0	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	exon	45020850	45021026	.	+	.	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	intron	45021027	45021115	.	+	.	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	CDS	45021116	45021847	0.87	+	0	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	exon	45021116	45021847	.	+	.	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
Phchi.S1	AUGUSTUS	stop_codon	45021848	45021850	.	+	0	transcript_id "Phchi.S1G716600.t1"; gene_id "Phchi.S1G716600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg312.t1 is derived from g10094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2222234	2224939	.	-	.	Phchi.S6G027100
Phchi.S6	AUGUSTUS	transcript	2222234	2224939	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	stop_codon	2222231	2222233	.	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2222234	2222520	0.96	-	2	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2222234	2222520	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2222521	2222601	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2222602	2222660	1	-	1	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2222602	2222660	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2222661	2222753	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2222754	2222878	1	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2222754	2222878	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2222879	2222975	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2222976	2223038	1	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2222976	2223038	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2223039	2223163	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2223164	2223294	0.64	-	2	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2223164	2223294	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2223295	2223362	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2223363	2223376	0.64	-	1	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2223363	2223376	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2223377	2223507	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2223508	2223626	0.89	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2223508	2223626	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2223627	2223735	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2223736	2223819	0.96	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2223736	2223819	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2223820	2224049	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2224050	2224182	1	-	1	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2224050	2224182	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2224183	2224281	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2224282	2224441	1	-	2	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2224282	2224441	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2224442	2224568	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2224569	2224635	1	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2224569	2224635	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	intron	2224636	2224807	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	CDS	2224808	2224939	0.6	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	exon	2224808	2224939	.	-	.	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
Phchi.S6	AUGUSTUS	start_codon	2224937	2224939	.	-	0	transcript_id "Phchi.S6G027100.t1"; gene_id "Phchi.S6G027100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10866.t1 is derived from g14916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2663234	2663917	.	+	.	Phchi.S4G044800
Phchi.S4	AUGUSTUS	transcript	2663234	2663917	.	+	.	transcript_id "Phchi.S4G044800.t1"; gene_id "Phchi.S4G044800"
Phchi.S4	AUGUSTUS	start_codon	2663234	2663236	.	+	0	transcript_id "Phchi.S4G044800.t1"; gene_id "Phchi.S4G044800"
Phchi.S4	AUGUSTUS	CDS	2663234	2663917	0.94	+	0	transcript_id "Phchi.S4G044800.t1"; gene_id "Phchi.S4G044800"
Phchi.S4	AUGUSTUS	exon	2663234	2663917	.	+	.	transcript_id "Phchi.S4G044800.t1"; gene_id "Phchi.S4G044800"
Phchi.S4	AUGUSTUS	stop_codon	2663918	2663920	.	+	0	transcript_id "Phchi.S4G044800.t1"; gene_id "Phchi.S4G044800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg467.t1 is derived from g10249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3282798	3283963	.	-	.	Phchi.S6G042600
Phchi.S6	AUGUSTUS	transcript	3282798	3283963	.	-	.	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	stop_codon	3282795	3282797	.	-	0	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	CDS	3282798	3283220	0.98	-	0	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	exon	3282798	3283220	.	-	.	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	intron	3283221	3283306	.	-	.	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	CDS	3283307	3283963	0.93	-	0	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	exon	3283307	3283963	.	-	.	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
Phchi.S6	AUGUSTUS	start_codon	3283961	3283963	.	-	0	transcript_id "Phchi.S6G042600.t1"; gene_id "Phchi.S6G042600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12574.t1 is derived from g8251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35680729	35682850	.	+	.	Phchi.S2G065400
Phchi.S2	AUGUSTUS	transcript	35680729	35682850	.	+	.	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	start_codon	35680729	35680731	.	+	0	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	CDS	35680729	35682527	0.73	+	0	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	exon	35680729	35682527	.	+	.	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	intron	35682528	35682621	.	+	.	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	CDS	35682622	35682850	0.99	+	1	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	exon	35682622	35682850	.	+	.	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
Phchi.S2	AUGUSTUS	stop_codon	35682851	35682853	.	+	0	transcript_id "Phchi.S2G065400.t1"; gene_id "Phchi.S2G065400"
# This transcript jg1401.t2 is derived from g8320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1402.t1 is derived from g8321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	144251	146803	.	+	.	Phchi.S5G001100
Phchi.S5	AUGUSTUS	transcript	144251	146803	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	start_codon	144251	144253	.	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	144251	144338	1	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	144251	144338	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	144339	144435	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	144436	144707	1	+	2	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	144436	144707	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	144708	144821	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	144822	144886	1	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	144822	144886	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	144887	144975	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	144976	145138	1	+	1	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	144976	145138	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	145139	145339	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	145340	145488	0.99	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	145340	145488	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	145489	145607	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	145608	145877	1	+	1	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	145608	145877	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	145878	146003	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	146004	146172	1	+	1	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	146004	146172	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	146173	146276	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	146277	146369	1	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	146277	146369	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	intron	146370	146488	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	CDS	146489	146803	1	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	exon	146489	146803	.	+	.	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
Phchi.S5	AUGUSTUS	stop_codon	146804	146806	.	+	0	transcript_id "Phchi.S5G001100.t1"; gene_id "Phchi.S5G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15110.t1 is derived from g13578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17117815	17119606	.	+	.	Phchi.S3G242900
Phchi.S3	AUGUSTUS	transcript	17117815	17119606	.	+	.	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	start_codon	17117815	17117817	.	+	0	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	CDS	17117815	17118007	0.82	+	0	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	exon	17117815	17118007	.	+	.	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	intron	17118008	17118095	.	+	.	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	CDS	17118096	17119606	0.84	+	2	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	exon	17118096	17119606	.	+	.	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
Phchi.S3	AUGUSTUS	stop_codon	17119607	17119609	.	+	0	transcript_id "Phchi.S3G242900.t1"; gene_id "Phchi.S3G242900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8766.t1 is derived from g5941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37864277	37864534	.	+	.	Phchi.S1G592500
Phchi.S1	AUGUSTUS	transcript	37864277	37864534	.	+	.	transcript_id "Phchi.S1G592500.t1"; gene_id "Phchi.S1G592500"
Phchi.S1	AUGUSTUS	start_codon	37864277	37864279	.	+	0	transcript_id "Phchi.S1G592500.t1"; gene_id "Phchi.S1G592500"
Phchi.S1	AUGUSTUS	CDS	37864277	37864534	0.2	+	0	transcript_id "Phchi.S1G592500.t1"; gene_id "Phchi.S1G592500"
Phchi.S1	AUGUSTUS	exon	37864277	37864534	.	+	.	transcript_id "Phchi.S1G592500.t1"; gene_id "Phchi.S1G592500"
Phchi.S1	AUGUSTUS	stop_codon	37864535	37864537	.	+	0	transcript_id "Phchi.S1G592500.t1"; gene_id "Phchi.S1G592500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14343.t1 is derived from g12810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12309937	12310411	.	+	.	Phchi.S3G166200
Phchi.S3	AUGUSTUS	transcript	12309937	12310411	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	start_codon	12309937	12309939	.	+	0	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	CDS	12309937	12309959	0.89	+	0	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	exon	12309937	12309959	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	intron	12309960	12310038	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	CDS	12310039	12310087	0.93	+	1	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	exon	12310039	12310087	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	intron	12310088	12310166	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	CDS	12310167	12310204	0.85	+	0	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	exon	12310167	12310204	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	intron	12310205	12310278	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	CDS	12310279	12310411	0.85	+	1	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	exon	12310279	12310411	.	+	.	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
Phchi.S3	AUGUSTUS	stop_codon	12310412	12310414	.	+	0	transcript_id "Phchi.S3G166200.t1"; gene_id "Phchi.S3G166200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2006.t1 is derived from g8926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4413313	4414577	.	-	.	Phchi.S5G061500
Phchi.S5	AUGUSTUS	transcript	4413313	4414577	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	stop_codon	4413310	4413312	.	-	0	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	CDS	4413313	4413695	1	-	2	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	exon	4413313	4413695	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	intron	4413696	4413789	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	CDS	4413790	4413955	0.99	-	0	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	exon	4413790	4413955	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	intron	4413956	4414060	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	CDS	4414061	4414249	0.99	-	0	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	exon	4414061	4414249	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	intron	4414250	4414352	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	CDS	4414353	4414577	0.59	-	0	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	exon	4414353	4414577	.	-	.	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
Phchi.S5	AUGUSTUS	start_codon	4414575	4414577	.	-	0	transcript_id "Phchi.S5G061500.t1"; gene_id "Phchi.S5G061500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg240.t1 is derived from g10022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1661419	1662342	.	-	.	Phchi.S6G019900
Phchi.S6	AUGUSTUS	transcript	1661419	1662342	.	-	.	transcript_id "Phchi.S6G019900.t1"; gene_id "Phchi.S6G019900"
Phchi.S6	AUGUSTUS	stop_codon	1661416	1661418	.	-	0	transcript_id "Phchi.S6G019900.t1"; gene_id "Phchi.S6G019900"
Phchi.S6	AUGUSTUS	CDS	1661419	1662342	1	-	0	transcript_id "Phchi.S6G019900.t1"; gene_id "Phchi.S6G019900"
Phchi.S6	AUGUSTUS	exon	1661419	1662342	.	-	.	transcript_id "Phchi.S6G019900.t1"; gene_id "Phchi.S6G019900"
Phchi.S6	AUGUSTUS	start_codon	1662340	1662342	.	-	0	transcript_id "Phchi.S6G019900.t1"; gene_id "Phchi.S6G019900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13533.t1 is derived from g12000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7395553	7397390	.	+	.	Phchi.S3G085200
Phchi.S3	AUGUSTUS	transcript	7395553	7397390	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	start_codon	7395553	7395555	.	+	0	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	CDS	7395553	7395688	0.24	+	0	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	exon	7395553	7395688	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	intron	7395689	7395927	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	CDS	7395928	7396079	1	+	2	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	exon	7395928	7396079	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	intron	7396080	7396281	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	CDS	7396282	7396398	1	+	0	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	exon	7396282	7396398	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	intron	7396399	7396493	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	CDS	7396494	7396589	1	+	0	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	exon	7396494	7396589	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	intron	7396590	7396703	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	CDS	7396704	7397390	0.96	+	0	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	exon	7396704	7397390	.	+	.	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
Phchi.S3	AUGUSTUS	stop_codon	7397391	7397393	.	+	0	transcript_id "Phchi.S3G085200.t1"; gene_id "Phchi.S3G085200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8457.t1 is derived from g5632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36016195	36018192	.	+	.	Phchi.S1G561600
Phchi.S1	AUGUSTUS	transcript	36016195	36018167	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	start_codon	36016195	36016197	.	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36016195	36016245	0.88	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36016195	36016245	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36016246	36016355	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36016356	36016793	0.95	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36016356	36016793	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36016794	36016945	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36016946	36017197	0.98	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36016946	36017197	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017198	36017290	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017291	36017381	0.78	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017291	36017381	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017382	36017510	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017511	36017682	0.8	+	2	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017511	36017682	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017683	36017816	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017817	36017899	1	+	1	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017817	36017899	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017900	36017981	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017982	36017995	1	+	2	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017982	36017995	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017996	36018140	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36018141	36018167	1	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36018141	36018167	.	+	.	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	stop_codon	36018168	36018170	.	+	0	transcript_id "Phchi.S1G561600.t1"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	transcript	36016195	36018192	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	start_codon	36016195	36016197	.	+	0	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36016195	36016245	0.87	+	0	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36016195	36016245	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36016246	36016355	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36016356	36016793	0.93	+	0	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36016356	36016793	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36016794	36016945	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36016946	36017197	1	+	0	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36016946	36017197	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017198	36017290	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017291	36017381	0.68	+	0	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017291	36017381	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017382	36017510	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017511	36017682	0.67	+	2	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017511	36017682	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017683	36017816	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017817	36017899	1	+	1	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017817	36017899	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	intron	36017900	36017995	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	CDS	36017996	36018192	1	+	2	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	exon	36017996	36018192	.	+	.	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
Phchi.S1	AUGUSTUS	stop_codon	36018193	36018195	.	+	0	transcript_id "Phchi.S1G561600.t2"; gene_id "Phchi.S1G561600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4844.t1 is derived from g2014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13071137	13072113	.	+	.	Phchi.S1G200300
Phchi.S1	AUGUSTUS	transcript	13071137	13072113	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	start_codon	13071137	13071139	.	+	0	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	CDS	13071137	13071164	1	+	0	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	exon	13071137	13071164	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	intron	13071165	13071238	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	CDS	13071239	13071378	1	+	2	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	exon	13071239	13071378	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	intron	13071379	13071557	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	CDS	13071558	13071683	1	+	0	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	exon	13071558	13071683	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	intron	13071684	13071975	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	CDS	13071976	13072113	1	+	0	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	exon	13071976	13072113	.	+	.	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
Phchi.S1	AUGUSTUS	stop_codon	13072114	13072116	.	+	0	transcript_id "Phchi.S1G200300.t1"; gene_id "Phchi.S1G200300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4310.t1 is derived from g1479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9570462	9571275	.	-	.	Phchi.S1G146900
Phchi.S1	AUGUSTUS	transcript	9570462	9571275	.	-	.	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	stop_codon	9570459	9570461	.	-	0	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	CDS	9570462	9570470	0.9	-	0	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	exon	9570462	9570470	.	-	.	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	intron	9570471	9570600	.	-	.	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	CDS	9570601	9571275	0.59	-	0	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	exon	9570601	9571275	.	-	.	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
Phchi.S1	AUGUSTUS	start_codon	9571273	9571275	.	-	0	transcript_id "Phchi.S1G146900.t1"; gene_id "Phchi.S1G146900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4146.t1 is derived from g1315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8637348	8637815	.	-	.	Phchi.S1G130500
Phchi.S1	AUGUSTUS	transcript	8637348	8637815	.	-	.	transcript_id "Phchi.S1G130500.t1"; gene_id "Phchi.S1G130500"
Phchi.S1	AUGUSTUS	stop_codon	8637345	8637347	.	-	0	transcript_id "Phchi.S1G130500.t1"; gene_id "Phchi.S1G130500"
Phchi.S1	AUGUSTUS	CDS	8637348	8637815	0.91	-	0	transcript_id "Phchi.S1G130500.t1"; gene_id "Phchi.S1G130500"
Phchi.S1	AUGUSTUS	exon	8637348	8637815	.	-	.	transcript_id "Phchi.S1G130500.t1"; gene_id "Phchi.S1G130500"
Phchi.S1	AUGUSTUS	start_codon	8637813	8637815	.	-	0	transcript_id "Phchi.S1G130500.t1"; gene_id "Phchi.S1G130500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5437.t1 is derived from g2607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16870608	16872128	.	-	.	Phchi.S1G259600
Phchi.S1	AUGUSTUS	transcript	16870608	16872128	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	stop_codon	16870605	16870607	.	-	0	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	CDS	16870608	16871147	0.91	-	0	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	exon	16870608	16871147	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	intron	16871148	16871255	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	CDS	16871256	16871430	0.95	-	1	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	exon	16871256	16871430	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	intron	16871431	16871514	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	CDS	16871515	16871582	1	-	0	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	exon	16871515	16871582	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	intron	16871583	16871704	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	CDS	16871705	16871823	1	-	2	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	exon	16871705	16871823	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	intron	16871824	16871902	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	CDS	16871903	16872128	1	-	0	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	exon	16871903	16872128	.	-	.	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
Phchi.S1	AUGUSTUS	start_codon	16872126	16872128	.	-	0	transcript_id "Phchi.S1G259600.t1"; gene_id "Phchi.S1G259600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2335.t1 is derived from g9255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6218988	6222892	.	+	.	Phchi.S5G094400
Phchi.S5	AUGUSTUS	transcript	6218988	6222892	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	start_codon	6218988	6218990	.	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6218988	6219191	0.66	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6218988	6219191	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6219192	6219289	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6219290	6219490	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6219290	6219490	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6219491	6219587	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6219588	6219702	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6219588	6219702	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6219703	6219783	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6219784	6219871	1	+	2	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6219784	6219871	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6219872	6220013	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6220014	6220225	1	+	1	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6220014	6220225	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6220226	6220305	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6220306	6220418	1	+	2	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6220306	6220418	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6220419	6220535	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6220536	6220685	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6220536	6220685	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6220686	6220775	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6220776	6220843	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6220776	6220843	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6220844	6220946	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6220947	6221052	1	+	1	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6220947	6221052	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6221053	6221150	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6221151	6221309	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6221151	6221309	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6221310	6221409	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6221410	6221463	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6221410	6221463	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6221464	6221577	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6221578	6221658	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6221578	6221658	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6221659	6221750	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6221751	6221888	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6221751	6221888	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6221889	6221975	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6221976	6222135	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6221976	6222135	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6222136	6222243	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6222244	6222323	1	+	2	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6222244	6222323	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6222324	6222414	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6222415	6222560	1	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6222415	6222560	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6222561	6222644	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6222645	6222702	1	+	1	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6222645	6222702	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	intron	6222703	6222790	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	CDS	6222791	6222892	0.9	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	exon	6222791	6222892	.	+	.	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
Phchi.S5	AUGUSTUS	stop_codon	6222893	6222895	.	+	0	transcript_id "Phchi.S5G094400.t1"; gene_id "Phchi.S5G094400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13642.t1 is derived from g12109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7985960	7987755	.	-	.	Phchi.S3G096100
Phchi.S3	AUGUSTUS	transcript	7985960	7987755	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	stop_codon	7985957	7985959	.	-	0	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	CDS	7985960	7986965	0.41	-	1	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	exon	7985960	7986965	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	intron	7986966	7987078	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	CDS	7987079	7987301	0.99	-	2	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	exon	7987079	7987301	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	intron	7987302	7987390	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	CDS	7987391	7987440	0.96	-	1	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	exon	7987391	7987440	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	intron	7987441	7987597	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	CDS	7987598	7987659	0.52	-	0	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	exon	7987598	7987659	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	intron	7987660	7987746	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	CDS	7987747	7987755	0.58	-	0	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	exon	7987747	7987755	.	-	.	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
Phchi.S3	AUGUSTUS	start_codon	7987753	7987755	.	-	0	transcript_id "Phchi.S3G096100.t1"; gene_id "Phchi.S3G096100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9530.t1 is derived from g6706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42326186	42329410	.	+	.	Phchi.S1G668900
Phchi.S1	AUGUSTUS	transcript	42326186	42329410	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	start_codon	42326186	42326188	.	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42326186	42326532	0.96	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42326186	42326532	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42326533	42326775	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42326776	42326861	1	+	1	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42326776	42326861	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42326862	42327099	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42327100	42327233	1	+	2	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42327100	42327233	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42327234	42327398	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42327399	42327509	1	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42327399	42327509	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42327510	42327593	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42327594	42327692	1	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42327594	42327692	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42327693	42327775	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42327776	42327797	0.68	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42327776	42327797	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42327798	42327889	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42327890	42327898	0.74	+	2	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42327890	42327898	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42327899	42327991	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42327992	42328053	1	+	2	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42327992	42328053	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42328054	42328149	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42328150	42328214	1	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42328150	42328214	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42328215	42328349	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42328350	42328459	1	+	1	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42328350	42328459	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42328460	42328608	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42328609	42328723	1	+	2	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42328609	42328723	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42328724	42328821	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42328822	42328887	1	+	1	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42328822	42328887	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42328888	42328975	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42328976	42329086	1	+	1	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42328976	42329086	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42329087	42329179	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42329180	42329246	1	+	1	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42329180	42329246	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	intron	42329247	42329365	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	CDS	42329366	42329410	1	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	exon	42329366	42329410	.	+	.	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
Phchi.S1	AUGUSTUS	stop_codon	42329411	42329413	.	+	0	transcript_id "Phchi.S1G668900.t1"; gene_id "Phchi.S1G668900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12376.t1 is derived from g8052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14075370	14076619	.	+	.	Phchi.S2G045600
Phchi.S2	AUGUSTUS	transcript	14075370	14076619	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	start_codon	14075370	14075372	.	+	0	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14075370	14075375	0.83	+	0	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14075370	14075375	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14075376	14075685	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14075686	14075779	0.79	+	0	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14075686	14075779	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14075780	14075853	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14075854	14075872	0.71	+	2	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14075854	14075872	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14075873	14076028	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14076029	14076104	0.97	+	1	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14076029	14076104	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14076105	14076434	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14076435	14076442	0.88	+	0	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14076435	14076442	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14076443	14076618	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14076619	14076619	0.91	+	1	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14076619	14076619	.	+	.	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	stop_codon	14076620	14076622	.	+	0	transcript_id "Phchi.S2G045600.t1"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	transcript	14075370	14076619	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	start_codon	14075370	14075372	.	+	0	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14075370	14075375	0.74	+	0	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14075370	14075375	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14075376	14075685	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14075686	14075779	0.67	+	0	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14075686	14075779	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14075780	14075853	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14075854	14075872	0.62	+	2	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14075854	14075872	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14075873	14076025	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14076026	14076104	0.95	+	1	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14076026	14076104	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14076105	14076434	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14076435	14076442	0.85	+	0	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14076435	14076442	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	intron	14076443	14076618	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	CDS	14076619	14076619	0.9	+	1	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	exon	14076619	14076619	.	+	.	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
Phchi.S2	AUGUSTUS	stop_codon	14076620	14076622	.	+	0	transcript_id "Phchi.S2G045600.t2"; gene_id "Phchi.S2G045600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2603.t1 is derived from g9523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7729404	7730078	.	-	.	Phchi.S5G121200
Phchi.S5	AUGUSTUS	transcript	7729404	7730078	.	-	.	transcript_id "Phchi.S5G121200.t1"; gene_id "Phchi.S5G121200"
Phchi.S5	AUGUSTUS	stop_codon	7729401	7729403	.	-	0	transcript_id "Phchi.S5G121200.t1"; gene_id "Phchi.S5G121200"
Phchi.S5	AUGUSTUS	CDS	7729404	7730078	0.76	-	0	transcript_id "Phchi.S5G121200.t1"; gene_id "Phchi.S5G121200"
Phchi.S5	AUGUSTUS	exon	7729404	7730078	.	-	.	transcript_id "Phchi.S5G121200.t1"; gene_id "Phchi.S5G121200"
Phchi.S5	AUGUSTUS	start_codon	7730076	7730078	.	-	0	transcript_id "Phchi.S5G121200.t1"; gene_id "Phchi.S5G121200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15841.t1 is derived from g14311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21735573	21736702	.	+	.	Phchi.S3G316000
Phchi.S3	AUGUSTUS	transcript	21735573	21736702	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	start_codon	21735573	21735575	.	+	0	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	CDS	21735573	21735851	0.93	+	0	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	exon	21735573	21735851	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	intron	21735852	21735953	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	CDS	21735954	21736085	0.94	+	0	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	exon	21735954	21736085	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	intron	21736086	21736164	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	CDS	21736165	21736281	1	+	0	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	exon	21736165	21736281	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	intron	21736282	21736366	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	CDS	21736367	21736702	1	+	0	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	exon	21736367	21736702	.	+	.	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
Phchi.S3	AUGUSTUS	stop_codon	21736703	21736705	.	+	0	transcript_id "Phchi.S3G316000.t1"; gene_id "Phchi.S3G316000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7146.t1 is derived from g4318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27171691	27172605	.	-	.	Phchi.S1G430500
Phchi.S1	AUGUSTUS	transcript	27171691	27172605	.	-	.	transcript_id "Phchi.S1G430500.t1"; gene_id "Phchi.S1G430500"
Phchi.S1	AUGUSTUS	stop_codon	27171688	27171690	.	-	0	transcript_id "Phchi.S1G430500.t1"; gene_id "Phchi.S1G430500"
Phchi.S1	AUGUSTUS	CDS	27171691	27172605	0.38	-	0	transcript_id "Phchi.S1G430500.t1"; gene_id "Phchi.S1G430500"
Phchi.S1	AUGUSTUS	exon	27171691	27172605	.	-	.	transcript_id "Phchi.S1G430500.t1"; gene_id "Phchi.S1G430500"
Phchi.S1	AUGUSTUS	start_codon	27172603	27172605	.	-	0	transcript_id "Phchi.S1G430500.t1"; gene_id "Phchi.S1G430500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12183.t1 is derived from g7859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6118324	6119371	.	-	.	Phchi.S2G026300
Phchi.S2	AUGUSTUS	transcript	6118324	6119371	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	stop_codon	6118321	6118323	.	-	0	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	CDS	6118324	6118501	1	-	1	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	exon	6118324	6118501	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	intron	6118502	6118587	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	CDS	6118588	6118657	1	-	2	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	exon	6118588	6118657	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	intron	6118658	6118747	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	CDS	6118748	6118812	1	-	1	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	exon	6118748	6118812	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	intron	6118813	6118900	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	CDS	6118901	6118996	1	-	1	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	exon	6118901	6118996	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	intron	6118997	6119073	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	CDS	6119074	6119220	1	-	1	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	exon	6119074	6119220	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	intron	6119221	6119303	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	CDS	6119304	6119371	0.85	-	0	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	exon	6119304	6119371	.	-	.	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
Phchi.S2	AUGUSTUS	start_codon	6119369	6119371	.	-	0	transcript_id "Phchi.S2G026300.t1"; gene_id "Phchi.S2G026300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12619.t1 is derived from g8296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37596515	37601387	.	+	.	Phchi.S2G069900
Phchi.S2	AUGUSTUS	transcript	37596515	37601387	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	start_codon	37596515	37596517	.	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37596515	37596542	0.62	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37596515	37596542	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37596543	37596642	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37596643	37596683	1	+	2	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37596643	37596683	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37596684	37596762	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37596763	37596907	1	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37596763	37596907	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37596908	37597034	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37597035	37597176	1	+	2	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37597035	37597176	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37597177	37597306	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37597307	37597381	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37597307	37597381	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37597382	37597593	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37597594	37597665	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37597594	37597665	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37597666	37597890	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37597891	37597962	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37597891	37597962	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37597963	37598156	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37598157	37598225	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37598157	37598225	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37598226	37598419	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37598420	37598491	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37598420	37598491	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37598492	37598762	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37598763	37598837	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37598763	37598837	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37598838	37598967	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37598968	37599039	1	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37598968	37599039	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37599040	37599139	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37599140	37599258	0.88	+	1	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37599140	37599258	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37599259	37599460	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37599461	37599517	0.6	+	2	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37599461	37599517	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37599518	37599716	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37599717	37599928	1	+	2	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37599717	37599928	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37599929	37600068	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37600069	37600264	1	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37600069	37600264	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37600265	37600475	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37600476	37600651	1	+	2	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37600476	37600651	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37600652	37600734	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37600735	37600839	1	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37600735	37600839	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37600840	37600924	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37600925	37601050	1	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37600925	37601050	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	intron	37601051	37601147	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	CDS	37601148	37601387	1	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	exon	37601148	37601387	.	+	.	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
Phchi.S2	AUGUSTUS	stop_codon	37601388	37601390	.	+	0	transcript_id "Phchi.S2G069900.t1"; gene_id "Phchi.S2G069900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13705.t1 is derived from g12172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8288428	8288762	.	+	.	Phchi.S3G102400
Phchi.S3	AUGUSTUS	transcript	8288428	8288762	.	+	.	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	start_codon	8288428	8288430	.	+	0	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	CDS	8288428	8288542	1	+	0	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	exon	8288428	8288542	.	+	.	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	intron	8288543	8288628	.	+	.	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	CDS	8288629	8288762	1	+	2	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	exon	8288629	8288762	.	+	.	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
Phchi.S3	AUGUSTUS	stop_codon	8288763	8288765	.	+	0	transcript_id "Phchi.S3G102400.t1"; gene_id "Phchi.S3G102400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4247.t1 is derived from g1416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9157521	9159902	.	+	.	Phchi.S1G140600
Phchi.S1	AUGUSTUS	transcript	9157521	9159902	.	+	.	transcript_id "Phchi.S1G140600.t1"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	start_codon	9157521	9157523	.	+	0	transcript_id "Phchi.S1G140600.t1"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	CDS	9157521	9159902	0.98	+	0	transcript_id "Phchi.S1G140600.t1"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	exon	9157521	9159902	.	+	.	transcript_id "Phchi.S1G140600.t1"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	stop_codon	9159903	9159905	.	+	0	transcript_id "Phchi.S1G140600.t1"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	transcript	9157521	9158023	.	+	.	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	start_codon	9157521	9157523	.	+	0	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	CDS	9157521	9157814	0.36	+	0	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	exon	9157521	9157814	.	+	.	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	intron	9157815	9157957	.	+	.	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	CDS	9157958	9158023	0.61	+	0	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	exon	9157958	9158023	.	+	.	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
Phchi.S1	AUGUSTUS	stop_codon	9158024	9158026	.	+	0	transcript_id "Phchi.S1G140600.t2"; gene_id "Phchi.S1G140600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2000.t1 is derived from g8920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4400342	4402497	.	+	.	Phchi.S5G060900
Phchi.S5	AUGUSTUS	transcript	4400342	4402497	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	start_codon	4400342	4400344	.	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	CDS	4400342	4400410	1	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	exon	4400342	4400410	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	intron	4400411	4400507	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	CDS	4400508	4400588	1	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	exon	4400508	4400588	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	intron	4400589	4400701	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	CDS	4400702	4400782	1	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	exon	4400702	4400782	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	intron	4400783	4400928	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	CDS	4400929	4401102	1	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	exon	4400929	4401102	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	intron	4401103	4401247	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	CDS	4401248	4401346	1	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	exon	4401248	4401346	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	intron	4401347	4401429	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	CDS	4401430	4402497	0.63	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	exon	4401430	4402497	.	+	.	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
Phchi.S5	AUGUSTUS	stop_codon	4402498	4402500	.	+	0	transcript_id "Phchi.S5G060900.t1"; gene_id "Phchi.S5G060900"
# This transcript jg10152.t2 is derived from g7328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10153.t1 is derived from g7329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46002824	46003152	.	+	.	Phchi.S1G731200
Phchi.S1	AUGUSTUS	transcript	46002824	46003152	.	+	.	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	start_codon	46002824	46002826	.	+	0	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	CDS	46002824	46003009	0.71	+	0	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	exon	46002824	46003009	.	+	.	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	intron	46003010	46003122	.	+	.	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	CDS	46003123	46003152	0.8	+	0	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	exon	46003123	46003152	.	+	.	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
Phchi.S1	AUGUSTUS	stop_codon	46003153	46003155	.	+	0	transcript_id "Phchi.S1G731200.t1"; gene_id "Phchi.S1G731200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg642.t1 is derived from g10424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4559703	4560218	.	+	.	Phchi.S6G060100
Phchi.S6	AUGUSTUS	transcript	4559703	4560218	.	+	.	transcript_id "Phchi.S6G060100.t1"; gene_id "Phchi.S6G060100"
Phchi.S6	AUGUSTUS	start_codon	4559703	4559705	.	+	0	transcript_id "Phchi.S6G060100.t1"; gene_id "Phchi.S6G060100"
Phchi.S6	AUGUSTUS	CDS	4559703	4560218	1	+	0	transcript_id "Phchi.S6G060100.t1"; gene_id "Phchi.S6G060100"
Phchi.S6	AUGUSTUS	exon	4559703	4560218	.	+	.	transcript_id "Phchi.S6G060100.t1"; gene_id "Phchi.S6G060100"
Phchi.S6	AUGUSTUS	stop_codon	4560219	4560221	.	+	0	transcript_id "Phchi.S6G060100.t1"; gene_id "Phchi.S6G060100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg664.t1 is derived from g10446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4639137	4639774	.	-	.	Phchi.S6G062300
Phchi.S6	AUGUSTUS	transcript	4639137	4639774	.	-	.	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	stop_codon	4639134	4639136	.	-	0	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	CDS	4639137	4639526	0.95	-	0	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	exon	4639137	4639526	.	-	.	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	intron	4639527	4639606	.	-	.	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	CDS	4639607	4639774	0.96	-	0	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	exon	4639607	4639774	.	-	.	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
Phchi.S6	AUGUSTUS	start_codon	4639772	4639774	.	-	0	transcript_id "Phchi.S6G062300.t1"; gene_id "Phchi.S6G062300"
# This transcript jg11790.t2 is derived from g15842.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11791.t1 is derived from g15843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8179435	8181088	.	+	.	Phchi.S4G137300
Phchi.S4	AUGUSTUS	transcript	8179435	8181088	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	start_codon	8179435	8179437	.	+	0	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	CDS	8179435	8179549	0.9	+	0	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	exon	8179435	8179549	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	intron	8179550	8179875	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	CDS	8179876	8180049	1	+	2	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	exon	8179876	8180049	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	intron	8180050	8180258	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	CDS	8180259	8180282	1	+	2	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	exon	8180259	8180282	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	intron	8180283	8180364	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	CDS	8180365	8180441	1	+	2	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	exon	8180365	8180441	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	intron	8180442	8180572	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	CDS	8180573	8181088	0.76	+	0	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	exon	8180573	8181088	.	+	.	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
Phchi.S4	AUGUSTUS	stop_codon	8181089	8181091	.	+	0	transcript_id "Phchi.S4G137300.t1"; gene_id "Phchi.S4G137300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6648.t1 is derived from g3820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24273200	24276349	.	+	.	Phchi.S1G380700
Phchi.S1	AUGUSTUS	transcript	24273200	24276349	.	+	.	transcript_id "Phchi.S1G380700.t1"; gene_id "Phchi.S1G380700"
Phchi.S1	AUGUSTUS	start_codon	24273200	24273202	.	+	0	transcript_id "Phchi.S1G380700.t1"; gene_id "Phchi.S1G380700"
Phchi.S1	AUGUSTUS	CDS	24273200	24276349	1	+	0	transcript_id "Phchi.S1G380700.t1"; gene_id "Phchi.S1G380700"
Phchi.S1	AUGUSTUS	exon	24273200	24276349	.	+	.	transcript_id "Phchi.S1G380700.t1"; gene_id "Phchi.S1G380700"
Phchi.S1	AUGUSTUS	stop_codon	24276350	24276352	.	+	0	transcript_id "Phchi.S1G380700.t1"; gene_id "Phchi.S1G380700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1053.t1 is derived from g10836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7313474	7314390	.	-	.	Phchi.S6G101200
Phchi.S6	AUGUSTUS	transcript	7313474	7314390	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	stop_codon	7313471	7313473	.	-	0	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	CDS	7313474	7313616	0.6	-	2	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	exon	7313474	7313616	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	intron	7313617	7313713	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	CDS	7313714	7313985	1	-	1	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	exon	7313714	7313985	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	intron	7313986	7314076	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	CDS	7314077	7314118	0.98	-	1	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	exon	7314077	7314118	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	intron	7314119	7314307	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	CDS	7314308	7314390	0.67	-	0	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	exon	7314308	7314390	.	-	.	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
Phchi.S6	AUGUSTUS	start_codon	7314388	7314390	.	-	0	transcript_id "Phchi.S6G101200.t1"; gene_id "Phchi.S6G101200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12249.t1 is derived from g7925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7008399	7010945	.	-	.	Phchi.S2G032900
Phchi.S2	AUGUSTUS	transcript	7008399	7010945	.	-	.	transcript_id "Phchi.S2G032900.t1"; gene_id "Phchi.S2G032900"
Phchi.S2	AUGUSTUS	stop_codon	7008396	7008398	.	-	0	transcript_id "Phchi.S2G032900.t1"; gene_id "Phchi.S2G032900"
Phchi.S2	AUGUSTUS	CDS	7008399	7010945	0.75	-	0	transcript_id "Phchi.S2G032900.t1"; gene_id "Phchi.S2G032900"
Phchi.S2	AUGUSTUS	exon	7008399	7010945	.	-	.	transcript_id "Phchi.S2G032900.t1"; gene_id "Phchi.S2G032900"
Phchi.S2	AUGUSTUS	start_codon	7010943	7010945	.	-	0	transcript_id "Phchi.S2G032900.t1"; gene_id "Phchi.S2G032900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7555.t1 is derived from g4729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30016135	30021993	.	-	.	Phchi.S1G471400
Phchi.S1	AUGUSTUS	transcript	30016135	30021993	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	stop_codon	30016132	30016134	.	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30016135	30016805	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30016135	30016805	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30016806	30016901	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30016902	30016948	1	-	1	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30016902	30016948	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30016949	30017039	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30017040	30017265	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30017040	30017265	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30017266	30017349	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30017350	30017435	1	-	1	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30017350	30017435	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30017436	30017543	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30017544	30017561	0.99	-	1	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30017544	30017561	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30017562	30017689	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30017690	30017739	0.99	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30017690	30017739	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30017740	30017847	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30017848	30018099	0.99	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30017848	30018099	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30018100	30018208	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30018209	30018397	0.96	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30018209	30018397	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30018398	30018483	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30018484	30018680	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30018484	30018680	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30018681	30018753	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30018754	30018879	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30018754	30018879	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30018880	30018968	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30018969	30019052	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30018969	30019052	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30019053	30019129	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30019130	30019193	1	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30019130	30019193	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30019194	30019377	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30019378	30019495	1	-	1	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30019378	30019495	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30019496	30019578	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30019579	30019628	1	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30019579	30019628	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30019629	30019723	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30019724	30019795	0.91	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30019724	30019795	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30019796	30019900	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30019901	30019952	0.9	-	1	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30019901	30019952	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30019953	30020073	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30020074	30020230	0.99	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30020074	30020230	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30020231	30020388	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30020389	30020601	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30020389	30020601	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30020602	30020685	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30020686	30020707	1	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30020686	30020707	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30020708	30020832	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30020833	30020870	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30020833	30020870	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30020871	30020962	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30020963	30021009	1	-	1	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30020963	30021009	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30021010	30021079	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30021080	30021116	1	-	2	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30021080	30021116	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30021117	30021209	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30021210	30021447	1	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30021210	30021447	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30021448	30021529	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30021530	30021694	0.82	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30021530	30021694	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	intron	30021695	30021783	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	CDS	30021784	30021993	0.7	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	exon	30021784	30021993	.	-	.	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
Phchi.S1	AUGUSTUS	start_codon	30021991	30021993	.	-	0	transcript_id "Phchi.S1G471400.t1"; gene_id "Phchi.S1G471400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8060.t1 is derived from g5235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32744507	32745029	.	+	.	Phchi.S1G521900
Phchi.S1	AUGUSTUS	transcript	32744507	32745029	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	start_codon	32744507	32744509	.	+	0	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	CDS	32744507	32744553	0.95	+	0	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	exon	32744507	32744553	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	intron	32744554	32744643	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	CDS	32744644	32744686	0.95	+	1	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	exon	32744644	32744686	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	intron	32744687	32744766	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	CDS	32744767	32744883	1	+	0	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	exon	32744767	32744883	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	intron	32744884	32745023	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	CDS	32745024	32745029	1	+	0	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	exon	32745024	32745029	.	+	.	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
Phchi.S1	AUGUSTUS	stop_codon	32745030	32745032	.	+	0	transcript_id "Phchi.S1G521900.t1"; gene_id "Phchi.S1G521900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg285.t1 is derived from g10067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2026601	2027464	.	-	.	Phchi.S6G024400
Phchi.S6	AUGUSTUS	transcript	2026601	2027464	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	stop_codon	2026598	2026600	.	-	0	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	CDS	2026601	2026622	0.67	-	1	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	exon	2026601	2026622	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	intron	2026623	2026741	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	CDS	2026742	2026875	0.43	-	0	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	exon	2026742	2026875	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	intron	2026876	2026968	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	CDS	2026969	2026980	0.47	-	0	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	exon	2026969	2026980	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	intron	2026981	2027122	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	CDS	2027123	2027146	0.59	-	0	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	exon	2027123	2027146	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	intron	2027147	2027356	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	CDS	2027357	2027464	0.56	-	0	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	exon	2027357	2027464	.	-	.	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
Phchi.S6	AUGUSTUS	start_codon	2027462	2027464	.	-	0	transcript_id "Phchi.S6G024400.t1"; gene_id "Phchi.S6G024400"
# This transcript jg10714.t2 is derived from g14764.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10715.t1 is derived from g14765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1737335	1737808	.	-	.	Phchi.S4G029700
Phchi.S4	AUGUSTUS	transcript	1737335	1737808	.	-	.	transcript_id "Phchi.S4G029700.t1"; gene_id "Phchi.S4G029700"
Phchi.S4	AUGUSTUS	stop_codon	1737332	1737334	.	-	0	transcript_id "Phchi.S4G029700.t1"; gene_id "Phchi.S4G029700"
Phchi.S4	AUGUSTUS	CDS	1737335	1737808	0.62	-	0	transcript_id "Phchi.S4G029700.t1"; gene_id "Phchi.S4G029700"
Phchi.S4	AUGUSTUS	exon	1737335	1737808	.	-	.	transcript_id "Phchi.S4G029700.t1"; gene_id "Phchi.S4G029700"
Phchi.S4	AUGUSTUS	start_codon	1737806	1737808	.	-	0	transcript_id "Phchi.S4G029700.t1"; gene_id "Phchi.S4G029700"
# This transcript jg4681.t2 is derived from g1851.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4682.t1 is derived from g1852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11829697	11830571	.	-	.	Phchi.S1G184100
Phchi.S1	AUGUSTUS	transcript	11829697	11830571	.	-	.	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	stop_codon	11829694	11829696	.	-	0	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	CDS	11829697	11830191	0.96	-	0	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	exon	11829697	11830191	.	-	.	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	intron	11830192	11830285	.	-	.	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	CDS	11830286	11830400	1	-	1	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	exon	11830286	11830400	.	-	.	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	intron	11830401	11830482	.	-	.	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	CDS	11830483	11830571	0.58	-	0	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	exon	11830483	11830571	.	-	.	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
Phchi.S1	AUGUSTUS	start_codon	11830569	11830571	.	-	0	transcript_id "Phchi.S1G184100.t1"; gene_id "Phchi.S1G184100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7600.t1 is derived from g4774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30205282	30209038	.	+	.	Phchi.S1G475900
Phchi.S1	AUGUSTUS	transcript	30205282	30209038	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	start_codon	30205282	30205284	.	+	0	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30205282	30206209	0.61	+	0	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30205282	30206209	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	intron	30206210	30206298	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30206299	30206615	0.62	+	2	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30206299	30206615	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	intron	30206616	30206773	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30206774	30206941	1	+	0	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30206774	30206941	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	intron	30206942	30207109	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30207110	30207789	0.95	+	0	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30207110	30207789	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	intron	30207790	30207923	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30207924	30208206	1	+	1	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30207924	30208206	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	intron	30208207	30208373	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30208374	30208663	1	+	0	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30208374	30208663	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	intron	30208664	30208848	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	CDS	30208849	30209038	1	+	1	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	exon	30208849	30209038	.	+	.	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
Phchi.S1	AUGUSTUS	stop_codon	30209039	30209041	.	+	0	transcript_id "Phchi.S1G475900.t1"; gene_id "Phchi.S1G475900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2306.t1 is derived from g9226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5971301	5982667	.	-	.	Phchi.S5G091500
Phchi.S5	AUGUSTUS	transcript	5971301	5982667	.	-	.	transcript_id "Phchi.S5G091500.t1"; gene_id "Phchi.S5G091500"
Phchi.S5	AUGUSTUS	stop_codon	5971298	5971300	.	-	0	transcript_id "Phchi.S5G091500.t1"; gene_id "Phchi.S5G091500"
Phchi.S5	AUGUSTUS	CDS	5971301	5982667	0.79	-	0	transcript_id "Phchi.S5G091500.t1"; gene_id "Phchi.S5G091500"
Phchi.S5	AUGUSTUS	exon	5971301	5982667	.	-	.	transcript_id "Phchi.S5G091500.t1"; gene_id "Phchi.S5G091500"
Phchi.S5	AUGUSTUS	start_codon	5982665	5982667	.	-	0	transcript_id "Phchi.S5G091500.t1"; gene_id "Phchi.S5G091500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5277.t1 is derived from g2447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16004721	16006491	.	-	.	Phchi.S1G243600
Phchi.S1	AUGUSTUS	transcript	16004721	16006491	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	stop_codon	16004718	16004720	.	-	0	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	CDS	16004721	16004956	1	-	2	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	exon	16004721	16004956	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	intron	16004957	16005050	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	CDS	16005051	16005152	1	-	2	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	exon	16005051	16005152	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	intron	16005153	16005257	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	CDS	16005258	16005648	1	-	0	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	exon	16005258	16005648	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	intron	16005649	16005813	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	CDS	16005814	16006491	1	-	0	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	exon	16005814	16006491	.	-	.	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
Phchi.S1	AUGUSTUS	start_codon	16006489	16006491	.	-	0	transcript_id "Phchi.S1G243600.t1"; gene_id "Phchi.S1G243600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2952.t1 is derived from g121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	746899	748620	.	-	.	Phchi.S1G011100
Phchi.S1	AUGUSTUS	transcript	746899	748620	.	-	.	transcript_id "Phchi.S1G011100.t1"; gene_id "Phchi.S1G011100"
Phchi.S1	AUGUSTUS	stop_codon	746896	746898	.	-	0	transcript_id "Phchi.S1G011100.t1"; gene_id "Phchi.S1G011100"
Phchi.S1	AUGUSTUS	CDS	746899	748620	1	-	0	transcript_id "Phchi.S1G011100.t1"; gene_id "Phchi.S1G011100"
Phchi.S1	AUGUSTUS	exon	746899	748620	.	-	.	transcript_id "Phchi.S1G011100.t1"; gene_id "Phchi.S1G011100"
Phchi.S1	AUGUSTUS	start_codon	748618	748620	.	-	0	transcript_id "Phchi.S1G011100.t1"; gene_id "Phchi.S1G011100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15724.t1 is derived from g14194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20902564	20903987	.	-	.	Phchi.S3G304300
Phchi.S3	AUGUSTUS	transcript	20902564	20903987	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	stop_codon	20902561	20902563	.	-	0	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	CDS	20902564	20902623	1	-	0	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	exon	20902564	20902623	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	intron	20902624	20902704	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	CDS	20902705	20902786	1	-	1	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	exon	20902705	20902786	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	intron	20902787	20902976	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	CDS	20902977	20902994	1	-	1	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	exon	20902977	20902994	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	intron	20902995	20903125	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	CDS	20903126	20903256	0.79	-	0	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	exon	20903126	20903256	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	intron	20903257	20903425	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	CDS	20903426	20903788	0.63	-	0	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	exon	20903426	20903788	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	intron	20903789	20903978	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	CDS	20903979	20903987	0.77	-	0	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	exon	20903979	20903987	.	-	.	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
Phchi.S3	AUGUSTUS	start_codon	20903985	20903987	.	-	0	transcript_id "Phchi.S3G304300.t1"; gene_id "Phchi.S3G304300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5662.t1 is derived from g2832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18177681	18178674	.	+	.	Phchi.S1G282100
Phchi.S1	AUGUSTUS	transcript	18177681	18178674	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	start_codon	18177681	18177683	.	+	0	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	CDS	18177681	18177761	1	+	0	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	exon	18177681	18177761	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	intron	18177762	18178013	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	CDS	18178014	18178099	1	+	0	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	exon	18178014	18178099	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	intron	18178100	18178203	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	CDS	18178204	18178265	0.41	+	1	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	exon	18178204	18178265	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	intron	18178266	18178388	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	CDS	18178389	18178474	0.31	+	2	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	exon	18178389	18178474	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	intron	18178475	18178584	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	CDS	18178585	18178674	0.36	+	0	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	exon	18178585	18178674	.	+	.	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
Phchi.S1	AUGUSTUS	stop_codon	18178675	18178677	.	+	0	transcript_id "Phchi.S1G282100.t1"; gene_id "Phchi.S1G282100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15278.t1 is derived from g13746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18132925	18133863	.	-	.	Phchi.S3G259700
Phchi.S3	AUGUSTUS	transcript	18132925	18133863	.	-	.	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	stop_codon	18132922	18132924	.	-	0	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	CDS	18132925	18133296	0.93	-	0	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	exon	18132925	18133296	.	-	.	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	intron	18133297	18133704	.	-	.	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	CDS	18133705	18133863	1	-	0	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	exon	18133705	18133863	.	-	.	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
Phchi.S3	AUGUSTUS	start_codon	18133861	18133863	.	-	0	transcript_id "Phchi.S3G259700.t1"; gene_id "Phchi.S3G259700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10258.t1 is derived from g7434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46718820	46719191	.	+	.	Phchi.S1G741700
Phchi.S1	AUGUSTUS	transcript	46718820	46719191	.	+	.	transcript_id "Phchi.S1G741700.t1"; gene_id "Phchi.S1G741700"
Phchi.S1	AUGUSTUS	start_codon	46718820	46718822	.	+	0	transcript_id "Phchi.S1G741700.t1"; gene_id "Phchi.S1G741700"
Phchi.S1	AUGUSTUS	CDS	46718820	46719191	0.63	+	0	transcript_id "Phchi.S1G741700.t1"; gene_id "Phchi.S1G741700"
Phchi.S1	AUGUSTUS	exon	46718820	46719191	.	+	.	transcript_id "Phchi.S1G741700.t1"; gene_id "Phchi.S1G741700"
Phchi.S1	AUGUSTUS	stop_codon	46719192	46719194	.	+	0	transcript_id "Phchi.S1G741700.t1"; gene_id "Phchi.S1G741700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9862.t1 is derived from g7038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44128673	44129581	.	+	.	Phchi.S1G702100
Phchi.S1	AUGUSTUS	transcript	44128673	44129581	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	start_codon	44128673	44128675	.	+	0	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	CDS	44128673	44128759	1	+	0	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	exon	44128673	44128759	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	intron	44128760	44128859	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	CDS	44128860	44128912	1	+	0	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	exon	44128860	44128912	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	intron	44128913	44128991	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	CDS	44128992	44129141	1	+	1	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	exon	44128992	44129141	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	intron	44129142	44129234	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	CDS	44129235	44129342	0.99	+	1	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	exon	44129235	44129342	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	intron	44129343	44129454	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	CDS	44129455	44129581	0.85	+	1	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	exon	44129455	44129581	.	+	.	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
Phchi.S1	AUGUSTUS	stop_codon	44129582	44129584	.	+	0	transcript_id "Phchi.S1G702100.t1"; gene_id "Phchi.S1G702100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg692.t1 is derived from g10474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4938451	4939176	.	+	.	Phchi.S6G065100
Phchi.S6	AUGUSTUS	transcript	4938451	4939176	.	+	.	transcript_id "Phchi.S6G065100.t1"; gene_id "Phchi.S6G065100"
Phchi.S6	AUGUSTUS	start_codon	4938451	4938453	.	+	0	transcript_id "Phchi.S6G065100.t1"; gene_id "Phchi.S6G065100"
Phchi.S6	AUGUSTUS	CDS	4938451	4939176	0.7	+	0	transcript_id "Phchi.S6G065100.t1"; gene_id "Phchi.S6G065100"
Phchi.S6	AUGUSTUS	exon	4938451	4939176	.	+	.	transcript_id "Phchi.S6G065100.t1"; gene_id "Phchi.S6G065100"
Phchi.S6	AUGUSTUS	stop_codon	4939177	4939179	.	+	0	transcript_id "Phchi.S6G065100.t1"; gene_id "Phchi.S6G065100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2058.t1 is derived from g8978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4647013	4648074	.	+	.	Phchi.S5G066700
Phchi.S5	AUGUSTUS	transcript	4647013	4648074	.	+	.	transcript_id "Phchi.S5G066700.t1"; gene_id "Phchi.S5G066700"
Phchi.S5	AUGUSTUS	start_codon	4647013	4647015	.	+	0	transcript_id "Phchi.S5G066700.t1"; gene_id "Phchi.S5G066700"
Phchi.S5	AUGUSTUS	CDS	4647013	4648074	0.99	+	0	transcript_id "Phchi.S5G066700.t1"; gene_id "Phchi.S5G066700"
Phchi.S5	AUGUSTUS	exon	4647013	4648074	.	+	.	transcript_id "Phchi.S5G066700.t1"; gene_id "Phchi.S5G066700"
Phchi.S5	AUGUSTUS	stop_codon	4648075	4648077	.	+	0	transcript_id "Phchi.S5G066700.t1"; gene_id "Phchi.S5G066700"
# This transcript jg15491.t2 is derived from g13960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15491.t3 is derived from g13960.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15492.t1 is derived from g13961.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19485922	19486440	.	+	.	Phchi.S3G281100
Phchi.S3	AUGUSTUS	transcript	19485922	19486440	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	start_codon	19485922	19485924	.	+	0	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19485922	19485950	0.97	+	0	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19485922	19485950	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	intron	19485951	19486066	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19486067	19486118	0.97	+	1	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19486067	19486118	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	intron	19486119	19486213	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19486214	19486297	1	+	0	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19486214	19486297	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	intron	19486298	19486386	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19486387	19486440	0.95	+	0	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19486387	19486440	.	+	.	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	stop_codon	19486441	19486443	.	+	0	transcript_id "Phchi.S3G281100.t1"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	transcript	19485922	19486440	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	start_codon	19485922	19485924	.	+	0	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19485922	19485946	0.43	+	0	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19485922	19485946	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	intron	19485947	19486082	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19486083	19486118	0.53	+	2	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19486083	19486118	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	intron	19486119	19486202	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19486203	19486297	1	+	2	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19486203	19486297	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	intron	19486298	19486386	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	CDS	19486387	19486440	0.93	+	0	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	exon	19486387	19486440	.	+	.	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
Phchi.S3	AUGUSTUS	stop_codon	19486441	19486443	.	+	0	transcript_id "Phchi.S3G281100.t2"; gene_id "Phchi.S3G281100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10376.t1 is derived from g7552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47437894	47439345	.	+	.	Phchi.S1G753500
Phchi.S1	AUGUSTUS	transcript	47437894	47439345	.	+	.	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	start_codon	47437894	47437896	.	+	0	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	CDS	47437894	47438535	0.71	+	0	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	exon	47437894	47438535	.	+	.	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	intron	47438536	47438663	.	+	.	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	CDS	47438664	47438924	1	+	0	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	exon	47438664	47438924	.	+	.	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	intron	47438925	47439075	.	+	.	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	CDS	47439076	47439345	1	+	0	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	exon	47439076	47439345	.	+	.	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
Phchi.S1	AUGUSTUS	stop_codon	47439346	47439348	.	+	0	transcript_id "Phchi.S1G753500.t1"; gene_id "Phchi.S1G753500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9025.t1 is derived from g6200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39198759	39201595	.	+	.	Phchi.S1G618400
Phchi.S1	AUGUSTUS	transcript	39198759	39201595	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	start_codon	39198759	39198761	.	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39198759	39198850	0.91	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39198759	39198850	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39198851	39198939	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39198940	39199084	0.99	+	1	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39198940	39199084	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39199085	39199167	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39199168	39199226	1	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39199168	39199226	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39199227	39199361	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39199362	39199454	0.89	+	1	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39199362	39199454	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39199455	39199526	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39199527	39199610	1	+	1	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39199527	39199610	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39199611	39199780	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39199781	39199878	1	+	1	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39199781	39199878	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39199879	39200012	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39200013	39200090	1	+	2	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39200013	39200090	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39200091	39200236	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39200237	39200370	1	+	2	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39200237	39200370	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39200371	39200470	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39200471	39200512	1	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39200471	39200512	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39200513	39200647	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39200648	39200766	0.9	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39200648	39200766	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39200767	39200843	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39200844	39200943	1	+	1	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39200844	39200943	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39200944	39201071	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39201072	39201153	1	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39201072	39201153	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39201154	39201241	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39201242	39201314	1	+	2	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39201242	39201314	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	intron	39201315	39201429	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	CDS	39201430	39201595	1	+	1	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	exon	39201430	39201595	.	+	.	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
Phchi.S1	AUGUSTUS	stop_codon	39201596	39201598	.	+	0	transcript_id "Phchi.S1G618400.t1"; gene_id "Phchi.S1G618400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6804.t1 is derived from g3976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25136217	25136997	.	-	.	Phchi.S1G396300
Phchi.S1	AUGUSTUS	transcript	25136217	25136997	.	-	.	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	stop_codon	25136214	25136216	.	-	0	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	CDS	25136217	25136288	0.96	-	0	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	exon	25136217	25136288	.	-	.	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	intron	25136289	25136429	.	-	.	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	CDS	25136430	25136479	0.57	-	2	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	exon	25136430	25136479	.	-	.	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	intron	25136480	25136891	.	-	.	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	CDS	25136892	25136997	0.01	-	0	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	exon	25136892	25136997	.	-	.	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
Phchi.S1	AUGUSTUS	start_codon	25136995	25136997	.	-	0	transcript_id "Phchi.S1G396300.t1"; gene_id "Phchi.S1G396300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11351.t1 is derived from g15401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5694406	5696046	.	-	.	Phchi.S4G093300
Phchi.S4	AUGUSTUS	transcript	5694406	5696046	.	-	.	transcript_id "Phchi.S4G093300.t1"; gene_id "Phchi.S4G093300"
Phchi.S4	AUGUSTUS	stop_codon	5694403	5694405	.	-	0	transcript_id "Phchi.S4G093300.t1"; gene_id "Phchi.S4G093300"
Phchi.S4	AUGUSTUS	CDS	5694406	5696046	0.41	-	0	transcript_id "Phchi.S4G093300.t1"; gene_id "Phchi.S4G093300"
Phchi.S4	AUGUSTUS	exon	5694406	5696046	.	-	.	transcript_id "Phchi.S4G093300.t1"; gene_id "Phchi.S4G093300"
Phchi.S4	AUGUSTUS	start_codon	5696044	5696046	.	-	0	transcript_id "Phchi.S4G093300.t1"; gene_id "Phchi.S4G093300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15709.t1 is derived from g14179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20805889	20806956	.	+	.	Phchi.S3G302800
Phchi.S3	AUGUSTUS	transcript	20805889	20806956	.	+	.	transcript_id "Phchi.S3G302800.t1"; gene_id "Phchi.S3G302800"
Phchi.S3	AUGUSTUS	start_codon	20805889	20805891	.	+	0	transcript_id "Phchi.S3G302800.t1"; gene_id "Phchi.S3G302800"
Phchi.S3	AUGUSTUS	CDS	20805889	20806956	0.96	+	0	transcript_id "Phchi.S3G302800.t1"; gene_id "Phchi.S3G302800"
Phchi.S3	AUGUSTUS	exon	20805889	20806956	.	+	.	transcript_id "Phchi.S3G302800.t1"; gene_id "Phchi.S3G302800"
Phchi.S3	AUGUSTUS	stop_codon	20806957	20806959	.	+	0	transcript_id "Phchi.S3G302800.t1"; gene_id "Phchi.S3G302800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5932.t1 is derived from g3103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19925603	19927444	.	-	.	Phchi.S1G309100
Phchi.S1	AUGUSTUS	transcript	19925603	19927444	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	stop_codon	19925600	19925602	.	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19925603	19925734	0.96	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19925603	19925734	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19925735	19925887	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19925888	19925986	1	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19925888	19925986	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19925987	19926071	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19926072	19926140	1	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19926072	19926140	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19926141	19926246	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19926247	19926348	0.98	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19926247	19926348	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19926349	19926450	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19926451	19926575	0.99	-	2	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19926451	19926575	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19926576	19926700	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19926701	19926779	1	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19926701	19926779	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19926780	19926902	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19926903	19927044	1	-	1	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19926903	19927044	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	intron	19927045	19927205	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	CDS	19927206	19927444	1	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	exon	19927206	19927444	.	-	.	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
Phchi.S1	AUGUSTUS	start_codon	19927442	19927444	.	-	0	transcript_id "Phchi.S1G309100.t1"; gene_id "Phchi.S1G309100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15604.t1 is derived from g14073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20241178	20250542	.	+	.	Phchi.S3G292300
Phchi.S3	AUGUSTUS	transcript	20241178	20250542	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	start_codon	20241178	20241180	.	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20241178	20241357	0.68	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20241178	20241357	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20241358	20241513	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20241514	20241613	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20241514	20241613	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20241614	20241709	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20241710	20241768	1	+	2	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20241710	20241768	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20241769	20241859	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20241860	20241991	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20241860	20241991	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20241992	20242176	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20242177	20242317	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20242177	20242317	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20242318	20242481	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20242482	20242553	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20242482	20242553	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20242554	20242645	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20242646	20242740	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20242646	20242740	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20242741	20242944	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20242945	20243077	1	+	1	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20242945	20243077	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20243078	20243227	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20243228	20243410	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20243228	20243410	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20243411	20243547	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20243548	20243738	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20243548	20243738	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20243739	20243833	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20243834	20243900	1	+	1	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20243834	20243900	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20243901	20244021	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20244022	20244155	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20244022	20244155	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20244156	20244269	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20244270	20244336	1	+	1	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20244270	20244336	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20244337	20244448	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20244449	20244511	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20244449	20244511	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20244512	20244618	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20244619	20244896	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20244619	20244896	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20244897	20244989	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20244990	20245092	0.47	+	1	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20244990	20245092	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20245093	20245172	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20245173	20245340	0.55	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20245173	20245340	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20245341	20245442	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20245443	20245945	0.55	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20245443	20245945	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20245946	20246033	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20246034	20246040	1	+	1	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20246034	20246040	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20246041	20246233	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20246234	20246273	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20246234	20246273	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20246274	20246363	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20246364	20246374	1	+	2	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20246364	20246374	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20246375	20246472	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20246473	20246550	0.74	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20246473	20246550	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20246551	20246675	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20246676	20246837	0.4	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20246676	20246837	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20246838	20247368	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20247369	20247462	0.9	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20247369	20247462	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20247463	20247657	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20247658	20249201	1	+	2	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20247658	20249201	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20249202	20249339	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20249340	20250223	1	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20249340	20250223	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	intron	20250224	20250307	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	CDS	20250308	20250542	1	+	1	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	exon	20250308	20250542	.	+	.	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
Phchi.S3	AUGUSTUS	stop_codon	20250543	20250545	.	+	0	transcript_id "Phchi.S3G292300.t1"; gene_id "Phchi.S3G292300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8726.t1 is derived from g5901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37690543	37694381	.	+	.	Phchi.S1G588500
Phchi.S1	AUGUSTUS	transcript	37690543	37694381	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	start_codon	37690543	37690545	.	+	0	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	CDS	37690543	37692398	0.26	+	0	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	exon	37690543	37692398	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	intron	37692399	37692511	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	CDS	37692512	37693816	0.34	+	1	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	exon	37692512	37693816	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	intron	37693817	37693969	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	CDS	37693970	37694016	0.94	+	1	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	exon	37693970	37694016	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	intron	37694017	37694364	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	CDS	37694365	37694381	0.94	+	2	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	exon	37694365	37694381	.	+	.	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
Phchi.S1	AUGUSTUS	stop_codon	37694382	37694384	.	+	0	transcript_id "Phchi.S1G588500.t1"; gene_id "Phchi.S1G588500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13594.t1 is derived from g12061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7623390	7626590	.	+	.	Phchi.S3G091300
Phchi.S3	AUGUSTUS	transcript	7623390	7626590	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	start_codon	7623390	7623392	.	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7623390	7623537	0.91	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7623390	7623537	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7623538	7623713	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7623714	7623768	0.8	+	2	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7623714	7623768	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7623769	7623928	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7623929	7624047	1	+	1	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7623929	7624047	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7624048	7624143	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7624144	7624265	1	+	2	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7624144	7624265	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7624266	7624358	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7624359	7624541	1	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7624359	7624541	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7624542	7624816	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7624817	7624935	1	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7624817	7624935	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7624936	7625026	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7625027	7625075	1	+	1	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7625027	7625075	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7625076	7625172	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7625173	7625274	1	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7625173	7625274	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7625275	7625387	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7625388	7625490	1	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7625388	7625490	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7625491	7625592	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7625593	7625656	1	+	2	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7625593	7625656	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7625657	7625745	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7625746	7625860	1	+	1	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7625746	7625860	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7625861	7625947	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7625948	7626048	1	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7625948	7626048	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7626049	7626132	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7626133	7626289	1	+	1	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7626133	7626289	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	intron	7626290	7626365	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	CDS	7626366	7626590	1	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	exon	7626366	7626590	.	+	.	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
Phchi.S3	AUGUSTUS	stop_codon	7626591	7626593	.	+	0	transcript_id "Phchi.S3G091300.t1"; gene_id "Phchi.S3G091300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6555.t1 is derived from g3727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23700946	23703688	.	+	.	Phchi.S1G371400
Phchi.S1	AUGUSTUS	transcript	23700946	23703688	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	start_codon	23700946	23700948	.	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23700946	23701422	1	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23700946	23701422	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23701423	23701575	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23701576	23701682	1	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23701576	23701682	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23701683	23701780	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23701781	23701869	1	+	1	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23701781	23701869	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23701870	23701962	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23701963	23702036	1	+	2	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23701963	23702036	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23702037	23702223	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23702224	23702364	0.36	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23702224	23702364	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23702365	23702538	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23702539	23702644	0.92	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23702539	23702644	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23702645	23702735	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23702736	23702833	1	+	2	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23702736	23702833	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23702834	23702954	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23702955	23703077	1	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23702955	23703077	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23703078	23703162	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23703163	23703231	1	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23703163	23703231	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23703232	23703322	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23703323	23703384	0.37	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23703323	23703384	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	intron	23703385	23703615	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	CDS	23703616	23703688	0.31	+	1	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	exon	23703616	23703688	.	+	.	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
Phchi.S1	AUGUSTUS	stop_codon	23703689	23703691	.	+	0	transcript_id "Phchi.S1G371400.t1"; gene_id "Phchi.S1G371400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5883.t1 is derived from g3053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19575127	19576475	.	+	.	Phchi.S1G304200
Phchi.S1	AUGUSTUS	transcript	19575127	19576475	.	+	.	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	start_codon	19575127	19575129	.	+	0	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	CDS	19575127	19575204	0.86	+	0	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	exon	19575127	19575204	.	+	.	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	intron	19575205	19575284	.	+	.	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	CDS	19575285	19576475	0.75	+	0	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	exon	19575285	19576475	.	+	.	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
Phchi.S1	AUGUSTUS	stop_codon	19576476	19576478	.	+	0	transcript_id "Phchi.S1G304200.t1"; gene_id "Phchi.S1G304200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13359.t1 is derived from g11825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6323903	6325297	.	+	.	Phchi.S3G067800
Phchi.S3	AUGUSTUS	transcript	6323903	6325297	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	start_codon	6323903	6323905	.	+	0	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	CDS	6323903	6323953	0.51	+	0	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	exon	6323903	6323953	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	intron	6323954	6324142	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	CDS	6324143	6324257	0.85	+	0	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	exon	6324143	6324257	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	intron	6324258	6324389	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	CDS	6324390	6324519	0.53	+	2	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	exon	6324390	6324519	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	intron	6324520	6324715	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	CDS	6324716	6324785	0.62	+	1	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	exon	6324716	6324785	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	intron	6324786	6324943	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	CDS	6324944	6325038	0.48	+	0	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	exon	6324944	6325038	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	intron	6325039	6325209	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	CDS	6325210	6325297	0.74	+	1	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	exon	6325210	6325297	.	+	.	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
Phchi.S3	AUGUSTUS	stop_codon	6325298	6325300	.	+	0	transcript_id "Phchi.S3G067800.t1"; gene_id "Phchi.S3G067800"
# This transcript jg11727.t2 is derived from g15779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11728.t1 is derived from g15780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7865618	7866818	.	+	.	Phchi.S4G131000
Phchi.S4	AUGUSTUS	transcript	7865618	7866818	.	+	.	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	start_codon	7865618	7865620	.	+	0	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	CDS	7865618	7865971	0.98	+	0	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	exon	7865618	7865971	.	+	.	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	intron	7865972	7866071	.	+	.	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	CDS	7866072	7866818	0.99	+	0	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	exon	7866072	7866818	.	+	.	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
Phchi.S4	AUGUSTUS	stop_codon	7866819	7866821	.	+	0	transcript_id "Phchi.S4G131000.t1"; gene_id "Phchi.S4G131000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3518.t1 is derived from g687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4168109	4168848	.	-	.	Phchi.S1G067700
Phchi.S1	AUGUSTUS	transcript	4168109	4168848	.	-	.	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	stop_codon	4168106	4168108	.	-	0	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	CDS	4168109	4168600	0.71	-	0	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	exon	4168109	4168600	.	-	.	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	intron	4168601	4168704	.	-	.	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	CDS	4168705	4168848	0.74	-	0	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	exon	4168705	4168848	.	-	.	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
Phchi.S1	AUGUSTUS	start_codon	4168846	4168848	.	-	0	transcript_id "Phchi.S1G067700.t1"; gene_id "Phchi.S1G067700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10054.t1 is derived from g7230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45500682	45502685	.	-	.	Phchi.S1G721300
Phchi.S1	AUGUSTUS	transcript	45500682	45502685	.	-	.	transcript_id "Phchi.S1G721300.t1"; gene_id "Phchi.S1G721300"
Phchi.S1	AUGUSTUS	stop_codon	45500679	45500681	.	-	0	transcript_id "Phchi.S1G721300.t1"; gene_id "Phchi.S1G721300"
Phchi.S1	AUGUSTUS	CDS	45500682	45502685	0.75	-	0	transcript_id "Phchi.S1G721300.t1"; gene_id "Phchi.S1G721300"
Phchi.S1	AUGUSTUS	exon	45500682	45502685	.	-	.	transcript_id "Phchi.S1G721300.t1"; gene_id "Phchi.S1G721300"
Phchi.S1	AUGUSTUS	start_codon	45502683	45502685	.	-	0	transcript_id "Phchi.S1G721300.t1"; gene_id "Phchi.S1G721300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15297.t1 is derived from g13765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18273519	18275048	.	+	.	Phchi.S3G261600
Phchi.S3	AUGUSTUS	transcript	18273519	18275048	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	start_codon	18273519	18273521	.	+	0	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	CDS	18273519	18273822	0.49	+	0	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	exon	18273519	18273822	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	intron	18273823	18273963	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	CDS	18273964	18274076	0.51	+	2	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	exon	18273964	18274076	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	intron	18274077	18274159	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	CDS	18274160	18274399	1	+	0	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	exon	18274160	18274399	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	intron	18274400	18274491	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	CDS	18274492	18274744	0.97	+	0	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	exon	18274492	18274744	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	intron	18274745	18274827	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	CDS	18274828	18275048	0.98	+	2	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	exon	18274828	18275048	.	+	.	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
Phchi.S3	AUGUSTUS	stop_codon	18275049	18275051	.	+	0	transcript_id "Phchi.S3G261600.t1"; gene_id "Phchi.S3G261600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1901.t1 is derived from g8821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3782077	3783067	.	-	.	Phchi.S5G051000
Phchi.S5	AUGUSTUS	transcript	3782077	3783067	.	-	.	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	stop_codon	3782074	3782076	.	-	0	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	CDS	3782077	3782091	0.99	-	0	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	exon	3782077	3782091	.	-	.	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	intron	3782092	3782279	.	-	.	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	CDS	3782280	3782545	0.99	-	2	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	exon	3782280	3782545	.	-	.	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	intron	3782546	3783051	.	-	.	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	CDS	3783052	3783067	0.64	-	0	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	exon	3783052	3783067	.	-	.	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
Phchi.S5	AUGUSTUS	start_codon	3783065	3783067	.	-	0	transcript_id "Phchi.S5G051000.t1"; gene_id "Phchi.S5G051000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9972.t1 is derived from g7148.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44716784	44720528	.	-	.	Phchi.S1G713100
Phchi.S1	AUGUSTUS	transcript	44716784	44720528	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	stop_codon	44716781	44716783	.	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44716784	44717740	0.74	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44716784	44717740	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44717741	44718143	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44718144	44718206	0.7	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44718144	44718206	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44718207	44718347	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44718348	44718407	1	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44718348	44718407	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44718408	44718543	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44718544	44718600	0.49	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44718544	44718600	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44718601	44718710	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44718711	44718795	1	-	1	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44718711	44718795	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44718796	44718988	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44718989	44719181	1	-	2	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44718989	44719181	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44719182	44719277	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44719278	44719331	1	-	2	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44719278	44719331	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44719332	44719408	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44719409	44719590	0.83	-	1	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44719409	44719590	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44719591	44719781	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44719782	44719921	0.49	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44719782	44719921	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	intron	44719922	44720000	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	CDS	44720001	44720528	1	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	exon	44720001	44720528	.	-	.	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
Phchi.S1	AUGUSTUS	start_codon	44720526	44720528	.	-	0	transcript_id "Phchi.S1G713100.t1"; gene_id "Phchi.S1G713100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8930.t1 is derived from g6105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38718913	38720098	.	-	.	Phchi.S1G608900
Phchi.S1	AUGUSTUS	transcript	38718913	38720098	.	-	.	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	stop_codon	38718910	38718912	.	-	0	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	CDS	38718913	38719545	0.5	-	0	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	exon	38718913	38719545	.	-	.	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	intron	38719546	38719636	.	-	.	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	CDS	38719637	38720098	1	-	0	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	exon	38719637	38720098	.	-	.	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
Phchi.S1	AUGUSTUS	start_codon	38720096	38720098	.	-	0	transcript_id "Phchi.S1G608900.t1"; gene_id "Phchi.S1G608900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15901.t1 is derived from g14371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22070437	22071365	.	-	.	Phchi.S3G322000
Phchi.S3	AUGUSTUS	transcript	22070437	22071365	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	stop_codon	22070434	22070436	.	-	0	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	CDS	22070437	22070601	1	-	0	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	exon	22070437	22070601	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	intron	22070602	22070723	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	CDS	22070724	22070792	1	-	0	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	exon	22070724	22070792	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	intron	22070793	22070877	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	CDS	22070878	22070972	1	-	2	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	exon	22070878	22070972	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	intron	22070973	22071109	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	CDS	22071110	22071199	1	-	2	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	exon	22071110	22071199	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	intron	22071200	22071280	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	CDS	22071281	22071365	1	-	0	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	exon	22071281	22071365	.	-	.	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
Phchi.S3	AUGUSTUS	start_codon	22071363	22071365	.	-	0	transcript_id "Phchi.S3G322000.t1"; gene_id "Phchi.S3G322000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6795.t1 is derived from g3967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25113114	25113905	.	+	.	Phchi.S1G395400
Phchi.S1	AUGUSTUS	transcript	25113114	25113905	.	+	.	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	start_codon	25113114	25113116	.	+	0	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	CDS	25113114	25113536	1	+	0	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	exon	25113114	25113536	.	+	.	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	intron	25113537	25113623	.	+	.	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	CDS	25113624	25113706	1	+	0	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	exon	25113624	25113706	.	+	.	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	intron	25113707	25113796	.	+	.	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	CDS	25113797	25113905	1	+	1	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	exon	25113797	25113905	.	+	.	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
Phchi.S1	AUGUSTUS	stop_codon	25113906	25113908	.	+	0	transcript_id "Phchi.S1G395400.t1"; gene_id "Phchi.S1G395400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7121.t1 is derived from g4293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27065007	27067940	.	+	.	Phchi.S1G428000
Phchi.S1	AUGUSTUS	transcript	27065007	27067940	.	+	.	transcript_id "Phchi.S1G428000.t1"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	start_codon	27065007	27065009	.	+	0	transcript_id "Phchi.S1G428000.t1"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	CDS	27065007	27067940	1	+	0	transcript_id "Phchi.S1G428000.t1"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	exon	27065007	27067940	.	+	.	transcript_id "Phchi.S1G428000.t1"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	stop_codon	27067941	27067943	.	+	0	transcript_id "Phchi.S1G428000.t1"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	transcript	27066078	27067940	.	+	.	transcript_id "Phchi.S1G428000.t2"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	start_codon	27066078	27066080	.	+	0	transcript_id "Phchi.S1G428000.t2"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	CDS	27066078	27067940	0.98	+	0	transcript_id "Phchi.S1G428000.t2"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	exon	27066078	27067940	.	+	.	transcript_id "Phchi.S1G428000.t2"; gene_id "Phchi.S1G428000"
Phchi.S1	AUGUSTUS	stop_codon	27067941	27067943	.	+	0	transcript_id "Phchi.S1G428000.t2"; gene_id "Phchi.S1G428000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6227.t1 is derived from g3399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21770799	21773822	.	+	.	Phchi.S1G338600
Phchi.S1	AUGUSTUS	transcript	21770799	21773822	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	start_codon	21770799	21770801	.	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21770799	21770832	0.99	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21770799	21770832	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21770833	21771043	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21771044	21771109	0.89	+	2	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21771044	21771109	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21771110	21771209	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21771210	21771427	0.46	+	2	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21771210	21771427	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21771428	21771513	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21771514	21771588	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21771514	21771588	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21771589	21771771	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21771772	21771816	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21771772	21771816	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21771817	21771936	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21771937	21772011	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21771937	21772011	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21772012	21772133	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21772134	21772221	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21772134	21772221	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21772222	21772532	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21772533	21772657	1	+	2	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21772533	21772657	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21772658	21772830	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21772831	21772926	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21772831	21772926	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21772927	21773019	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21773020	21773128	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21773020	21773128	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21773129	21773198	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21773199	21773314	1	+	2	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21773199	21773314	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21773315	21773396	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21773397	21773475	1	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21773397	21773475	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21773476	21773563	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21773564	21773650	1	+	2	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21773564	21773650	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	intron	21773651	21773811	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	CDS	21773812	21773822	0.87	+	2	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	exon	21773812	21773822	.	+	.	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
Phchi.S1	AUGUSTUS	stop_codon	21773823	21773825	.	+	0	transcript_id "Phchi.S1G338600.t1"; gene_id "Phchi.S1G338600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1639.t1 is derived from g8558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2148367	2151665	.	+	.	Phchi.S5G024800
Phchi.S5	AUGUSTUS	transcript	2148367	2151665	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	start_codon	2148367	2148369	.	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2148367	2148456	0.98	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2148367	2148456	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2148457	2148584	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2148585	2148780	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2148585	2148780	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2148781	2148890	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2148891	2148970	0.98	+	2	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2148891	2148970	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2148971	2149388	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149389	2149616	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149389	2149616	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2149617	2149739	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149740	2149865	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149740	2149865	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2149866	2149966	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149967	2150047	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149967	2150047	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150048	2150180	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150181	2150322	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150181	2150322	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150323	2150419	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150420	2150598	1	+	2	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150420	2150598	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150599	2150697	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150698	2150853	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150698	2150853	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150854	2150984	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150985	2151092	1	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150985	2151092	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2151093	2151170	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2151171	2151295	0.65	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2151171	2151295	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2151296	2151402	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2151403	2151537	1	+	1	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2151403	2151537	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2151538	2151607	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2151608	2151665	1	+	1	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2151608	2151665	.	+	.	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	stop_codon	2151666	2151668	.	+	0	transcript_id "Phchi.S5G024800.t1"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	transcript	2148367	2151665	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	start_codon	2148367	2148369	.	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2148367	2148456	0.99	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2148367	2148456	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2148457	2148584	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2148585	2148780	1	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2148585	2148780	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2148781	2148890	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2148891	2148970	0.99	+	2	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2148891	2148970	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2148971	2149303	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149304	2149390	0.89	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149304	2149390	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2149391	2149499	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149500	2149616	0.61	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149500	2149616	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2149617	2149739	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149740	2149865	1	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149740	2149865	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2149866	2149966	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2149967	2150047	1	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2149967	2150047	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150048	2150180	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150181	2150322	1	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150181	2150322	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150323	2150419	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150420	2150598	1	+	2	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150420	2150598	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150599	2150697	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150698	2150853	1	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150698	2150853	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2150854	2150984	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2150985	2151092	1	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2150985	2151092	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2151093	2151170	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2151171	2151295	0.7	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2151171	2151295	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2151296	2151402	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2151403	2151537	1	+	1	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2151403	2151537	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	intron	2151538	2151607	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	CDS	2151608	2151665	1	+	1	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	exon	2151608	2151665	.	+	.	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
Phchi.S5	AUGUSTUS	stop_codon	2151666	2151668	.	+	0	transcript_id "Phchi.S5G024800.t2"; gene_id "Phchi.S5G024800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5518.t1 is derived from g2688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17199531	17200257	.	+	.	Phchi.S1G267700
Phchi.S1	AUGUSTUS	transcript	17199531	17200257	.	+	.	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	start_codon	17199531	17199533	.	+	0	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	CDS	17199531	17199835	0.73	+	0	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	exon	17199531	17199835	.	+	.	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	intron	17199836	17200028	.	+	.	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	CDS	17200029	17200109	0.93	+	1	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	exon	17200029	17200109	.	+	.	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	intron	17200110	17200253	.	+	.	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	CDS	17200254	17200257	1	+	1	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	exon	17200254	17200257	.	+	.	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
Phchi.S1	AUGUSTUS	stop_codon	17200258	17200260	.	+	0	transcript_id "Phchi.S1G267700.t1"; gene_id "Phchi.S1G267700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3218.t1 is derived from g387.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2301850	2302584	.	-	.	Phchi.S1G037700
Phchi.S1	AUGUSTUS	transcript	2302185	2302584	.	-	.	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	stop_codon	2302182	2302184	.	-	0	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2302185	2302274	0.66	-	0	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2302185	2302274	.	-	.	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	intron	2302275	2302467	.	-	.	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2302468	2302584	1	-	0	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2302468	2302584	.	-	.	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	start_codon	2302582	2302584	.	-	0	transcript_id "Phchi.S1G037700.t1"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	transcript	2301850	2302584	.	-	.	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	stop_codon	2301847	2301849	.	-	0	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2301850	2301896	0.64	-	2	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2301850	2301896	.	-	.	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	intron	2301897	2302157	.	-	.	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2302158	2302203	0.64	-	0	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2302158	2302203	.	-	.	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	intron	2302204	2302467	.	-	.	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2302468	2302584	0.97	-	0	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2302468	2302584	.	-	.	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	start_codon	2302582	2302584	.	-	0	transcript_id "Phchi.S1G037700.t2"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	transcript	2301850	2302584	.	-	.	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	stop_codon	2301847	2301849	.	-	0	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2301850	2301896	0.54	-	2	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2301850	2301896	.	-	.	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	intron	2301897	2302157	.	-	.	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2302158	2302197	0.55	-	0	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2302158	2302197	.	-	.	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	intron	2302198	2302467	.	-	.	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	CDS	2302468	2302584	0.96	-	0	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	exon	2302468	2302584	.	-	.	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
Phchi.S1	AUGUSTUS	start_codon	2302582	2302584	.	-	0	transcript_id "Phchi.S1G037700.t3"; gene_id "Phchi.S1G037700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15163.t1 is derived from g13631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17327318	17328606	.	-	.	Phchi.S3G248200
Phchi.S3	AUGUSTUS	transcript	17327318	17328606	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	stop_codon	17327315	17327317	.	-	0	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	CDS	17327318	17327414	1	-	1	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	exon	17327318	17327414	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	intron	17327415	17327547	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	CDS	17327548	17327623	0.85	-	2	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	exon	17327548	17327623	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	intron	17327624	17327738	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	CDS	17327739	17327848	1	-	1	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	exon	17327739	17327848	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	intron	17327849	17328059	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	CDS	17328060	17328142	1	-	0	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	exon	17328060	17328142	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	intron	17328143	17328233	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	CDS	17328234	17328356	1	-	0	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	exon	17328234	17328356	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	intron	17328357	17328465	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	CDS	17328466	17328606	0.89	-	0	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	exon	17328466	17328606	.	-	.	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
Phchi.S3	AUGUSTUS	start_codon	17328604	17328606	.	-	0	transcript_id "Phchi.S3G248200.t1"; gene_id "Phchi.S3G248200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8068.t1 is derived from g5243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32792122	32798502	.	+	.	Phchi.S1G522700
Phchi.S1	AUGUSTUS	transcript	32792122	32798502	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	start_codon	32792122	32792124	.	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32792122	32792199	0.91	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32792122	32792199	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32792200	32792293	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32792294	32792378	1	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32792294	32792378	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32792379	32792573	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32792574	32792613	1	+	2	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32792574	32792613	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32792614	32792742	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32792743	32792991	0.98	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32792743	32792991	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32792992	32793081	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32793082	32793180	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32793082	32793180	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32793181	32793333	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32793334	32793344	0.88	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32793334	32793344	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32793345	32793527	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32793528	32793610	0.87	+	2	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32793528	32793610	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32793611	32793683	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32793684	32793800	0.98	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32793684	32793800	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32793801	32793906	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32793907	32794022	0.98	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32793907	32794022	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32794023	32794105	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32794106	32794208	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32794106	32794208	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32794209	32794362	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32794363	32794715	1	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32794363	32794715	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32794716	32794815	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32794816	32795146	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32794816	32795146	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32795147	32795239	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32795240	32795421	0.98	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32795240	32795421	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32795422	32795527	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32795528	32795746	0.97	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32795528	32795746	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32795747	32795818	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32795819	32796011	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32795819	32796011	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32796012	32796124	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32796125	32796378	1	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32796125	32796378	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32796379	32796541	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32796542	32796634	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32796542	32796634	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32796635	32796878	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32796879	32796980	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32796879	32796980	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32796981	32797108	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32797109	32797517	1	+	1	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32797109	32797517	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32797518	32797685	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32797686	32797823	1	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32797686	32797823	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	intron	32797824	32797911	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	CDS	32797912	32798502	1	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	exon	32797912	32798502	.	+	.	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
Phchi.S1	AUGUSTUS	stop_codon	32798503	32798505	.	+	0	transcript_id "Phchi.S1G522700.t1"; gene_id "Phchi.S1G522700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9523.t1 is derived from g6699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42265862	42266677	.	+	.	Phchi.S1G668200
Phchi.S1	AUGUSTUS	transcript	42265862	42266677	.	+	.	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	start_codon	42265862	42265864	.	+	0	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	CDS	42265862	42266224	0.47	+	0	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	exon	42265862	42266224	.	+	.	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	intron	42266225	42266304	.	+	.	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	CDS	42266305	42266326	0.47	+	0	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	exon	42266305	42266326	.	+	.	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	intron	42266327	42266498	.	+	.	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	CDS	42266499	42266677	0.47	+	2	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	exon	42266499	42266677	.	+	.	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
Phchi.S1	AUGUSTUS	stop_codon	42266678	42266680	.	+	0	transcript_id "Phchi.S1G668200.t1"; gene_id "Phchi.S1G668200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4081.t1 is derived from g1250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7692411	7694688	.	+	.	Phchi.S1G124000
Phchi.S1	AUGUSTUS	transcript	7692411	7694688	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	start_codon	7692411	7692413	.	+	0	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	CDS	7692411	7692664	0.71	+	0	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	exon	7692411	7692664	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	intron	7692665	7692767	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	CDS	7692768	7692845	0.93	+	1	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	exon	7692768	7692845	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	intron	7692846	7692996	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	CDS	7692997	7694574	0.44	+	1	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	exon	7692997	7694574	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	intron	7694575	7694666	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	CDS	7694667	7694688	1	+	1	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	exon	7694667	7694688	.	+	.	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
Phchi.S1	AUGUSTUS	stop_codon	7694689	7694691	.	+	0	transcript_id "Phchi.S1G124000.t1"; gene_id "Phchi.S1G124000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2037.t1 is derived from g8957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4549725	4551062	.	+	.	Phchi.S5G064600
Phchi.S5	AUGUSTUS	transcript	4549725	4551062	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	start_codon	4549725	4549727	.	+	0	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4549725	4549747	0.93	+	0	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4549725	4549747	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	intron	4549748	4549875	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4549876	4549924	1	+	1	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4549876	4549924	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	intron	4549925	4550020	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4550021	4550129	1	+	0	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4550021	4550129	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	intron	4550130	4550298	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4550299	4550392	1	+	2	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4550299	4550392	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	intron	4550393	4550508	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4550509	4550642	1	+	1	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4550509	4550642	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	intron	4550643	4550726	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4550727	4550890	1	+	2	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4550727	4550890	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	intron	4550891	4550990	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	CDS	4550991	4551062	1	+	0	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	exon	4550991	4551062	.	+	.	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
Phchi.S5	AUGUSTUS	stop_codon	4551063	4551065	.	+	0	transcript_id "Phchi.S5G064600.t1"; gene_id "Phchi.S5G064600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1498.t1 is derived from g8417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1207171	1208520	.	-	.	Phchi.S5G010700
Phchi.S5	AUGUSTUS	transcript	1207171	1208520	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	stop_codon	1207168	1207170	.	-	0	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	CDS	1207171	1207315	0.97	-	1	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	exon	1207171	1207315	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	intron	1207316	1207404	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	CDS	1207405	1207538	1	-	0	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	exon	1207405	1207538	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	intron	1207539	1207632	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	CDS	1207633	1207986	0.99	-	0	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	exon	1207633	1207986	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	intron	1207987	1208059	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	CDS	1208060	1208256	1	-	2	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	exon	1208060	1208256	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	intron	1208257	1208375	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	CDS	1208376	1208520	0.42	-	0	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	exon	1208376	1208520	.	-	.	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
Phchi.S5	AUGUSTUS	start_codon	1208518	1208520	.	-	0	transcript_id "Phchi.S5G010700.t1"; gene_id "Phchi.S5G010700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1334.t1 is derived from g11117.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9085633	9087081	.	+	.	Phchi.S6G129300
Phchi.S6	AUGUSTUS	transcript	9085633	9087081	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	start_codon	9085633	9085635	.	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9085633	9085726	0.97	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9085633	9085726	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9085727	9085817	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9085818	9085942	1	+	2	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9085818	9085942	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9085943	9086030	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086031	9086183	1	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086031	9086183	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086184	9086316	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086317	9086373	1	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086317	9086373	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086374	9086652	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086653	9086695	0.94	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086653	9086695	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086696	9086777	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086778	9086791	0.53	+	2	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086778	9086791	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086792	9086985	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086986	9086998	0.56	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086986	9086998	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086999	9087073	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9087074	9087081	0.7	+	2	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9087074	9087081	.	+	.	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	stop_codon	9087082	9087084	.	+	0	transcript_id "Phchi.S6G129300.t1"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	transcript	9085633	9087081	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	start_codon	9085633	9085635	.	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9085633	9085726	0.93	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9085633	9085726	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9085727	9085817	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9085818	9085942	1	+	2	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9085818	9085942	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9085943	9086105	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086106	9086183	1	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086106	9086183	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086184	9086316	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086317	9086373	0.99	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086317	9086373	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086374	9086652	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086653	9086695	0.9	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086653	9086695	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086696	9086777	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086778	9086791	0.5	+	2	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086778	9086791	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086792	9086985	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9086986	9086998	0.57	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9086986	9086998	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	intron	9086999	9087073	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	CDS	9087074	9087081	0.76	+	2	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	exon	9087074	9087081	.	+	.	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
Phchi.S6	AUGUSTUS	stop_codon	9087082	9087084	.	+	0	transcript_id "Phchi.S6G129300.t2"; gene_id "Phchi.S6G129300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12115.t1 is derived from g7791.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3580130	3581992	.	-	.	Phchi.S2G019500
Phchi.S2	AUGUSTUS	transcript	3580130	3581992	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	stop_codon	3580127	3580129	.	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580130	3580270	0.95	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580130	3580270	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580271	3580435	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580436	3580455	1	-	2	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580436	3580455	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580456	3580589	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580590	3580692	1	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580590	3580692	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580693	3580768	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580769	3580861	1	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580769	3580861	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580862	3580999	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581000	3581132	1	-	1	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581000	3581132	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581133	3581319	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581320	3581408	1	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581320	3581408	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581409	3581484	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581485	3581647	0.99	-	1	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581485	3581647	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581648	3581742	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581743	3581798	1	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581743	3581798	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581799	3581893	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581894	3581992	0.85	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581894	3581992	.	-	.	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	start_codon	3581990	3581992	.	-	0	transcript_id "Phchi.S2G019500.t1"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	transcript	3580261	3581992	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	stop_codon	3580258	3580260	.	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580261	3580266	1	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580261	3580266	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580267	3580435	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580436	3580455	1	-	2	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580436	3580455	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580456	3580589	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580590	3580692	1	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580590	3580692	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580693	3580768	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3580769	3580861	1	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3580769	3580861	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3580862	3580999	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581000	3581132	1	-	1	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581000	3581132	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581133	3581319	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581320	3581408	1	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581320	3581408	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581409	3581484	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581485	3581647	1	-	1	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581485	3581647	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581648	3581742	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581743	3581798	1	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581743	3581798	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	intron	3581799	3581893	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	CDS	3581894	3581992	0.77	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	exon	3581894	3581992	.	-	.	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
Phchi.S2	AUGUSTUS	start_codon	3581990	3581992	.	-	0	transcript_id "Phchi.S2G019500.t2"; gene_id "Phchi.S2G019500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5879.t1 is derived from g3049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19558044	19564829	.	-	.	Phchi.S1G303800
Phchi.S1	AUGUSTUS	transcript	19558044	19564829	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	stop_codon	19558041	19558043	.	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19558044	19558220	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19558044	19558220	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19558221	19558296	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19558297	19558389	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19558297	19558389	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19558390	19558487	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19558488	19558621	1	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19558488	19558621	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19558622	19558701	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19558702	19558807	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19558702	19558807	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19558808	19558888	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19558889	19558972	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19558889	19558972	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19558973	19559058	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19559059	19559175	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19559059	19559175	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19559176	19559255	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19559256	19559352	1	-	1	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19559256	19559352	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19559353	19559579	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19559580	19559717	1	-	1	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19559580	19559717	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19559718	19559802	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19559803	19559974	1	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19559803	19559974	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19559975	19560065	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19560066	19560196	1	-	1	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19560066	19560196	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19560197	19560300	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19560301	19560383	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19560301	19560383	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19560384	19560464	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19560465	19560583	1	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19560465	19560583	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19560584	19560690	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19560691	19560804	0.89	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19560691	19560804	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19560805	19560942	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19560943	19561086	1	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19560943	19561086	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19561087	19561424	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19561425	19561503	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19561425	19561503	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19561504	19561606	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19561607	19561717	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19561607	19561717	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19561718	19561790	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19561791	19561968	1	-	1	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19561791	19561968	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19561969	19562644	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19562645	19562760	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19562645	19562760	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19562761	19562875	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19562876	19562974	0.65	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19562876	19562974	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19562975	19563058	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19563059	19563081	0.65	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19563059	19563081	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19563082	19563231	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19563232	19563391	0.48	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19563232	19563391	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19563392	19563487	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19563488	19563516	0.41	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19563488	19563516	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19563517	19563569	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19563570	19563638	0.41	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19563570	19563638	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19563639	19563737	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19563738	19563863	0.99	-	2	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19563738	19563863	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19563864	19564000	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19564001	19564166	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19564001	19564166	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19564167	19564251	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19564252	19564419	1	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19564252	19564419	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	intron	19564420	19564691	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	CDS	19564692	19564829	0.98	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	exon	19564692	19564829	.	-	.	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
Phchi.S1	AUGUSTUS	start_codon	19564827	19564829	.	-	0	transcript_id "Phchi.S1G303800.t1"; gene_id "Phchi.S1G303800"
# This transcript jg9617.t2 is derived from g6793.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9618.t1 is derived from g6794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42947116	42949060	.	+	.	Phchi.S1G677700
Phchi.S1	AUGUSTUS	transcript	42947116	42949060	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	start_codon	42947116	42947118	.	+	0	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	CDS	42947116	42947820	0.99	+	0	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	exon	42947116	42947820	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	intron	42947821	42947923	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	CDS	42947924	42947982	0.99	+	0	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	exon	42947924	42947982	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	intron	42947983	42948203	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	CDS	42948204	42948332	1	+	1	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	exon	42948204	42948332	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	intron	42948333	42948423	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	CDS	42948424	42948559	1	+	1	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	exon	42948424	42948559	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	intron	42948560	42948628	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	CDS	42948629	42949060	1	+	0	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	exon	42948629	42949060	.	+	.	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
Phchi.S1	AUGUSTUS	stop_codon	42949061	42949063	.	+	0	transcript_id "Phchi.S1G677700.t1"; gene_id "Phchi.S1G677700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13781.t1 is derived from g12248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8872151	8873518	.	+	.	Phchi.S3G110000
Phchi.S3	AUGUSTUS	transcript	8872151	8873518	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	start_codon	8872151	8872153	.	+	0	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	CDS	8872151	8872357	0.56	+	0	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	exon	8872151	8872357	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	intron	8872358	8872897	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	CDS	8872898	8873077	0.96	+	0	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	exon	8872898	8873077	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	intron	8873078	8873183	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	CDS	8873184	8873297	1	+	0	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	exon	8873184	8873297	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	intron	8873298	8873395	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	CDS	8873396	8873518	0.63	+	0	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	exon	8873396	8873518	.	+	.	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
Phchi.S3	AUGUSTUS	stop_codon	8873519	8873521	.	+	0	transcript_id "Phchi.S3G110000.t1"; gene_id "Phchi.S3G110000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8785.t1 is derived from g5960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37944961	37948057	.	-	.	Phchi.S1G594400
Phchi.S1	AUGUSTUS	transcript	37944961	37948057	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	stop_codon	37944958	37944960	.	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37944961	37945393	0.89	-	1	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37944961	37945393	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37945394	37945509	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37945510	37946069	1	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37945510	37946069	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37946070	37946193	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37946194	37946322	1	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37946194	37946322	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37946323	37946405	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37946406	37946496	1	-	1	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37946406	37946496	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37946497	37946622	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37946623	37946735	1	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37946623	37946735	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37946736	37946823	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37946824	37947067	1	-	1	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37946824	37947067	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37947068	37947217	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37947218	37947306	1	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37947218	37947306	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37947307	37947405	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37947406	37947476	1	-	2	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37947406	37947476	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37947477	37947623	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37947624	37947717	1	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37947624	37947717	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	intron	37947718	37947874	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	CDS	37947875	37948057	0.72	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	exon	37947875	37948057	.	-	.	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
Phchi.S1	AUGUSTUS	start_codon	37948055	37948057	.	-	0	transcript_id "Phchi.S1G594400.t1"; gene_id "Phchi.S1G594400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3908.t1 is derived from g1077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6395039	6396853	.	-	.	Phchi.S1G106700
Phchi.S1	AUGUSTUS	transcript	6395039	6396853	.	-	.	transcript_id "Phchi.S1G106700.t1"; gene_id "Phchi.S1G106700"
Phchi.S1	AUGUSTUS	stop_codon	6395036	6395038	.	-	0	transcript_id "Phchi.S1G106700.t1"; gene_id "Phchi.S1G106700"
Phchi.S1	AUGUSTUS	CDS	6395039	6396853	0.72	-	0	transcript_id "Phchi.S1G106700.t1"; gene_id "Phchi.S1G106700"
Phchi.S1	AUGUSTUS	exon	6395039	6396853	.	-	.	transcript_id "Phchi.S1G106700.t1"; gene_id "Phchi.S1G106700"
Phchi.S1	AUGUSTUS	start_codon	6396851	6396853	.	-	0	transcript_id "Phchi.S1G106700.t1"; gene_id "Phchi.S1G106700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3232.t1 is derived from g401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2369591	2370728	.	-	.	Phchi.S1G039100
Phchi.S1	AUGUSTUS	transcript	2369591	2370728	.	-	.	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	stop_codon	2369588	2369590	.	-	0	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	CDS	2369591	2369591	0.98	-	1	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	exon	2369591	2369591	.	-	.	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	intron	2369592	2369794	.	-	.	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	CDS	2369795	2369810	0.68	-	2	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	exon	2369795	2369810	.	-	.	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	intron	2369811	2369947	.	-	.	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	CDS	2369948	2370728	0.61	-	0	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	exon	2369948	2370728	.	-	.	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
Phchi.S1	AUGUSTUS	start_codon	2370726	2370728	.	-	0	transcript_id "Phchi.S1G039100.t1"; gene_id "Phchi.S1G039100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9426.t1 is derived from g6602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41417968	41418688	.	+	.	Phchi.S1G658500
Phchi.S1	AUGUSTUS	transcript	41417968	41418688	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	start_codon	41417968	41417970	.	+	0	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	CDS	41417968	41418150	0.74	+	0	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	exon	41417968	41418150	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	intron	41418151	41418230	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	CDS	41418231	41418330	0.43	+	0	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	exon	41418231	41418330	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	intron	41418331	41418421	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	CDS	41418422	41418548	0.43	+	2	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	exon	41418422	41418548	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	intron	41418549	41418624	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	CDS	41418625	41418688	0.43	+	1	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	exon	41418625	41418688	.	+	.	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
Phchi.S1	AUGUSTUS	stop_codon	41418689	41418691	.	+	0	transcript_id "Phchi.S1G658500.t1"; gene_id "Phchi.S1G658500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9035.t1 is derived from g6210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39234581	39236773	.	+	.	Phchi.S1G619400
Phchi.S1	AUGUSTUS	transcript	39234581	39236773	.	+	.	transcript_id "Phchi.S1G619400.t1"; gene_id "Phchi.S1G619400"
Phchi.S1	AUGUSTUS	start_codon	39234581	39234583	.	+	0	transcript_id "Phchi.S1G619400.t1"; gene_id "Phchi.S1G619400"
Phchi.S1	AUGUSTUS	CDS	39234581	39236773	1	+	0	transcript_id "Phchi.S1G619400.t1"; gene_id "Phchi.S1G619400"
Phchi.S1	AUGUSTUS	exon	39234581	39236773	.	+	.	transcript_id "Phchi.S1G619400.t1"; gene_id "Phchi.S1G619400"
Phchi.S1	AUGUSTUS	stop_codon	39236774	39236776	.	+	0	transcript_id "Phchi.S1G619400.t1"; gene_id "Phchi.S1G619400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15191.t1 is derived from g13659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17490056	17491138	.	-	.	Phchi.S3G251000
Phchi.S3	AUGUSTUS	transcript	17490056	17491138	.	-	.	transcript_id "Phchi.S3G251000.t1"; gene_id "Phchi.S3G251000"
Phchi.S3	AUGUSTUS	stop_codon	17490053	17490055	.	-	0	transcript_id "Phchi.S3G251000.t1"; gene_id "Phchi.S3G251000"
Phchi.S3	AUGUSTUS	CDS	17490056	17491138	0.34	-	0	transcript_id "Phchi.S3G251000.t1"; gene_id "Phchi.S3G251000"
Phchi.S3	AUGUSTUS	exon	17490056	17491138	.	-	.	transcript_id "Phchi.S3G251000.t1"; gene_id "Phchi.S3G251000"
Phchi.S3	AUGUSTUS	start_codon	17491136	17491138	.	-	0	transcript_id "Phchi.S3G251000.t1"; gene_id "Phchi.S3G251000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14424.t1 is derived from g12892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12750145	12753622	.	+	.	Phchi.S3G174300
Phchi.S3	AUGUSTUS	transcript	12750145	12753622	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	start_codon	12750145	12750147	.	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12750145	12750459	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12750145	12750459	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12750460	12750552	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12750553	12750884	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12750553	12750884	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12750885	12750970	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12750971	12751163	1	+	1	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12750971	12751163	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12751164	12751244	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12751245	12751420	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12751245	12751420	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12751421	12751555	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12751556	12751625	1	+	1	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12751556	12751625	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12751626	12751775	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12751776	12751968	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12751776	12751968	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12751969	12752065	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12752066	12752161	1	+	2	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12752066	12752161	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12752162	12752283	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12752284	12752378	1	+	2	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12752284	12752378	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12752379	12752486	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12752487	12752606	0.92	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12752487	12752606	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12752607	12752713	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12752714	12752833	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12752714	12752833	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12752834	12752966	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12752967	12753065	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12752967	12753065	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12753066	12753163	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12753164	12753268	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12753164	12753268	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	intron	12753269	12753361	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	CDS	12753362	12753622	1	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	exon	12753362	12753622	.	+	.	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
Phchi.S3	AUGUSTUS	stop_codon	12753623	12753625	.	+	0	transcript_id "Phchi.S3G174300.t1"; gene_id "Phchi.S3G174300"
# This transcript jg1379.t2 is derived from g15987.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1380.t1 is derived from g15988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C149	AUGUSTUS	gene	14761	15668	.	-	.	Phchi.C149G000300
Phchi.C149	AUGUSTUS	transcript	14761	15668	.	-	.	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	stop_codon	14758	14760	.	-	0	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	CDS	14761	14959	0.87	-	1	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	exon	14761	14959	.	-	.	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	intron	14960	15057	.	-	.	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	CDS	15058	15134	1	-	0	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	exon	15058	15134	.	-	.	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	intron	15135	15548	.	-	.	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	CDS	15549	15668	0.75	-	0	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	exon	15549	15668	.	-	.	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
Phchi.C149	AUGUSTUS	start_codon	15666	15668	.	-	0	transcript_id "Phchi.C149G000300.t1"; gene_id "Phchi.C149G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10236.t1 is derived from g7412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46509484	46511686	.	-	.	Phchi.S1G739500
Phchi.S1	AUGUSTUS	transcript	46509484	46511686	.	-	.	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	stop_codon	46509481	46509483	.	-	0	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	CDS	46509484	46511400	0.88	-	0	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	exon	46509484	46511400	.	-	.	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	intron	46511401	46511494	.	-	.	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	CDS	46511495	46511686	1	-	0	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	exon	46511495	46511686	.	-	.	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
Phchi.S1	AUGUSTUS	start_codon	46511684	46511686	.	-	0	transcript_id "Phchi.S1G739500.t1"; gene_id "Phchi.S1G739500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13093.t1 is derived from g11558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4113780	4116942	.	+	.	Phchi.S3G041200
Phchi.S3	AUGUSTUS	transcript	4113780	4116942	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	start_codon	4113780	4113782	.	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4113780	4113920	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4113780	4113920	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4113921	4114016	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4114017	4114094	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4114017	4114094	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4114095	4114166	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4114167	4114271	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4114167	4114271	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4114272	4114351	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4114352	4114443	0.98	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4114352	4114443	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4114444	4114547	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4114548	4114741	0.98	+	1	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4114548	4114741	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4114742	4114921	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4114922	4115043	1	+	2	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4114922	4115043	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4115044	4115249	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4115250	4115324	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4115250	4115324	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4115325	4115401	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4115402	4115512	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4115402	4115512	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4115513	4115669	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4115670	4115813	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4115670	4115813	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4115814	4115919	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4115920	4116039	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4115920	4116039	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4116040	4116124	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4116125	4116341	1	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4116125	4116341	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4116342	4116423	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4116424	4116547	0.61	+	2	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4116424	4116547	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	intron	4116548	4116653	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	CDS	4116654	4116942	0.48	+	1	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	exon	4116654	4116942	.	+	.	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
Phchi.S3	AUGUSTUS	stop_codon	4116943	4116945	.	+	0	transcript_id "Phchi.S3G041200.t1"; gene_id "Phchi.S3G041200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5978.t1 is derived from g3149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20211620	20213342	.	-	.	Phchi.S1G313700
Phchi.S1	AUGUSTUS	transcript	20211620	20213342	.	-	.	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	stop_codon	20211617	20211619	.	-	0	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	CDS	20211620	20212627	1	-	0	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	exon	20211620	20212627	.	-	.	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	intron	20212628	20212706	.	-	.	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	CDS	20212707	20213342	0.51	-	0	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	exon	20212707	20213342	.	-	.	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
Phchi.S1	AUGUSTUS	start_codon	20213340	20213342	.	-	0	transcript_id "Phchi.S1G313700.t1"; gene_id "Phchi.S1G313700"
# This transcript jg4420.t2 is derived from g1589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4421.t1 is derived from g1590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10427362	10428586	.	+	.	Phchi.S1G158000
Phchi.S1	AUGUSTUS	transcript	10427362	10428586	.	+	.	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	start_codon	10427362	10427364	.	+	0	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	CDS	10427362	10428133	0.48	+	0	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	exon	10427362	10428133	.	+	.	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	intron	10428134	10428212	.	+	.	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	CDS	10428213	10428586	0.99	+	2	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	exon	10428213	10428586	.	+	.	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
Phchi.S1	AUGUSTUS	stop_codon	10428587	10428589	.	+	0	transcript_id "Phchi.S1G158000.t1"; gene_id "Phchi.S1G158000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1932.t1 is derived from g8852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3898387	3899300	.	-	.	Phchi.S5G054100
Phchi.S5	AUGUSTUS	transcript	3898387	3899300	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	stop_codon	3898384	3898386	.	-	0	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	CDS	3898387	3898420	1	-	1	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	exon	3898387	3898420	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	intron	3898421	3898549	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	CDS	3898550	3898579	1	-	1	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	exon	3898550	3898579	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	intron	3898580	3898669	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	CDS	3898670	3898752	1	-	0	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	exon	3898670	3898752	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	intron	3898753	3898827	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	CDS	3898828	3898890	1	-	0	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	exon	3898828	3898890	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	intron	3898891	3899039	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	CDS	3899040	3899300	0.48	-	0	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	exon	3899040	3899300	.	-	.	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
Phchi.S5	AUGUSTUS	start_codon	3899298	3899300	.	-	0	transcript_id "Phchi.S5G054100.t1"; gene_id "Phchi.S5G054100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12194.t1 is derived from g7870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6602373	6605720	.	+	.	Phchi.S2G027400
Phchi.S2	AUGUSTUS	transcript	6602373	6605720	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	start_codon	6602373	6602375	.	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6602373	6602734	0.54	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6602373	6602734	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6602735	6603136	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6603137	6603208	1	+	1	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6603137	6603208	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6603209	6603535	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6603536	6603601	1	+	1	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6603536	6603601	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6603602	6603698	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6603699	6603777	0.99	+	1	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6603699	6603777	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6603778	6603890	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6603891	6604011	1	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6603891	6604011	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6604012	6604096	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6604097	6604192	1	+	2	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6604097	6604192	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6604193	6604405	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6604406	6604518	1	+	2	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6604406	6604518	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6604519	6604626	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6604627	6604704	1	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6604627	6604704	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6604705	6604966	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6604967	6605083	1	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6604967	6605083	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6605084	6605210	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6605211	6605310	1	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6605211	6605310	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6605311	6605496	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6605497	6605597	1	+	2	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6605497	6605597	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	intron	6605598	6605690	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	CDS	6605691	6605720	1	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	exon	6605691	6605720	.	+	.	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
Phchi.S2	AUGUSTUS	stop_codon	6605721	6605723	.	+	0	transcript_id "Phchi.S2G027400.t1"; gene_id "Phchi.S2G027400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15197.t1 is derived from g13665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17515479	17516174	.	-	.	Phchi.S3G251600
Phchi.S3	AUGUSTUS	transcript	17515479	17516174	.	-	.	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	stop_codon	17515476	17515478	.	-	0	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	CDS	17515479	17515790	0.89	-	0	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	exon	17515479	17515790	.	-	.	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	intron	17515791	17515985	.	-	.	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	CDS	17515986	17516174	0.42	-	0	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	exon	17515986	17516174	.	-	.	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
Phchi.S3	AUGUSTUS	start_codon	17516172	17516174	.	-	0	transcript_id "Phchi.S3G251600.t1"; gene_id "Phchi.S3G251600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7103.t1 is derived from g4275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26946449	26955081	.	-	.	Phchi.S1G426200
Phchi.S1	AUGUSTUS	transcript	26946449	26955081	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	stop_codon	26946446	26946448	.	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26946449	26946999	0.97	-	2	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26946449	26946999	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26947000	26947098	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26947099	26947297	0.98	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26947099	26947297	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26947298	26947485	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26947486	26948096	0.5	-	2	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26947486	26948096	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26948097	26948212	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26948213	26948653	0.99	-	2	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26948213	26948653	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26948654	26948801	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26948802	26949012	0.98	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26948802	26949012	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26949013	26949157	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26949158	26949228	0.72	-	2	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26949158	26949228	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26949229	26949407	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26949408	26949576	0.85	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26949408	26949576	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26949577	26949669	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26949670	26949860	0.83	-	2	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26949670	26949860	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26949861	26950215	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26950216	26951028	0.35	-	2	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26950216	26951028	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26951029	26951138	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26951139	26951919	0.19	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26951139	26951919	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26951920	26952211	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26952212	26953309	0.62	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26952212	26953309	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	intron	26953310	26953461	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	CDS	26953462	26955081	0.77	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	exon	26953462	26955081	.	-	.	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
Phchi.S1	AUGUSTUS	start_codon	26955079	26955081	.	-	0	transcript_id "Phchi.S1G426200.t1"; gene_id "Phchi.S1G426200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11695.t1 is derived from g15746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7710688	7711787	.	-	.	Phchi.S4G127700
Phchi.S4	AUGUSTUS	transcript	7710688	7711787	.	-	.	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	stop_codon	7710685	7710687	.	-	0	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	CDS	7710688	7711292	1	-	2	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	exon	7710688	7711292	.	-	.	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	intron	7711293	7711479	.	-	.	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	CDS	7711480	7711537	1	-	0	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	exon	7711480	7711537	.	-	.	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	intron	7711538	7711682	.	-	.	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	CDS	7711683	7711787	0.78	-	0	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	exon	7711683	7711787	.	-	.	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
Phchi.S4	AUGUSTUS	start_codon	7711785	7711787	.	-	0	transcript_id "Phchi.S4G127700.t1"; gene_id "Phchi.S4G127700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg946.t1 is derived from g10728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6611291	6612378	.	+	.	Phchi.S6G090500
Phchi.S6	AUGUSTUS	transcript	6611291	6612378	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	start_codon	6611291	6611293	.	+	0	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	CDS	6611291	6611613	0.8	+	0	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	exon	6611291	6611613	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	intron	6611614	6611740	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	CDS	6611741	6611936	1	+	1	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	exon	6611741	6611936	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	intron	6611937	6612041	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	CDS	6612042	6612173	0.77	+	0	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	exon	6612042	6612173	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	intron	6612174	6612267	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	CDS	6612268	6612378	0.81	+	0	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	exon	6612268	6612378	.	+	.	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
Phchi.S6	AUGUSTUS	stop_codon	6612379	6612381	.	+	0	transcript_id "Phchi.S6G090500.t1"; gene_id "Phchi.S6G090500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9505.t1 is derived from g6681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42104393	42104719	.	-	.	Phchi.S1G666400
Phchi.S1	AUGUSTUS	transcript	42104393	42104719	.	-	.	transcript_id "Phchi.S1G666400.t1"; gene_id "Phchi.S1G666400"
Phchi.S1	AUGUSTUS	stop_codon	42104390	42104392	.	-	0	transcript_id "Phchi.S1G666400.t1"; gene_id "Phchi.S1G666400"
Phchi.S1	AUGUSTUS	CDS	42104393	42104719	0.7	-	0	transcript_id "Phchi.S1G666400.t1"; gene_id "Phchi.S1G666400"
Phchi.S1	AUGUSTUS	exon	42104393	42104719	.	-	.	transcript_id "Phchi.S1G666400.t1"; gene_id "Phchi.S1G666400"
Phchi.S1	AUGUSTUS	start_codon	42104717	42104719	.	-	0	transcript_id "Phchi.S1G666400.t1"; gene_id "Phchi.S1G666400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13234.t1 is derived from g11699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4853263	4853871	.	-	.	Phchi.S3G055300
Phchi.S3	AUGUSTUS	transcript	4853263	4853871	.	-	.	transcript_id "Phchi.S3G055300.t1"; gene_id "Phchi.S3G055300"
Phchi.S3	AUGUSTUS	stop_codon	4853260	4853262	.	-	0	transcript_id "Phchi.S3G055300.t1"; gene_id "Phchi.S3G055300"
Phchi.S3	AUGUSTUS	CDS	4853263	4853871	0.45	-	0	transcript_id "Phchi.S3G055300.t1"; gene_id "Phchi.S3G055300"
Phchi.S3	AUGUSTUS	exon	4853263	4853871	.	-	.	transcript_id "Phchi.S3G055300.t1"; gene_id "Phchi.S3G055300"
Phchi.S3	AUGUSTUS	start_codon	4853869	4853871	.	-	0	transcript_id "Phchi.S3G055300.t1"; gene_id "Phchi.S3G055300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11319.t1 is derived from g15369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5338410	5339854	.	-	.	Phchi.S4G090100
Phchi.S4	AUGUSTUS	transcript	5338410	5339854	.	-	.	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	stop_codon	5338407	5338409	.	-	0	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	CDS	5338410	5339375	1	-	0	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	exon	5338410	5339375	.	-	.	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	intron	5339376	5339635	.	-	.	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	CDS	5339636	5339854	0.97	-	0	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	exon	5339636	5339854	.	-	.	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
Phchi.S4	AUGUSTUS	start_codon	5339852	5339854	.	-	0	transcript_id "Phchi.S4G090100.t1"; gene_id "Phchi.S4G090100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11968.t1 is derived from g7643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	243451	244618	.	-	.	Phchi.S2G004800
Phchi.S2	AUGUSTUS	transcript	243451	244618	.	-	.	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	stop_codon	243448	243450	.	-	0	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	CDS	243451	243461	0.94	-	2	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	exon	243451	243461	.	-	.	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	intron	243462	243537	.	-	.	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	CDS	243538	243898	0.94	-	0	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	exon	243538	243898	.	-	.	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	intron	243899	243988	.	-	.	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	CDS	243989	244618	0.88	-	0	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	exon	243989	244618	.	-	.	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
Phchi.S2	AUGUSTUS	start_codon	244616	244618	.	-	0	transcript_id "Phchi.S2G004800.t1"; gene_id "Phchi.S2G004800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8314.t1 is derived from g5489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35252145	35254517	.	-	.	Phchi.S1G547300
Phchi.S1	AUGUSTUS	transcript	35252145	35254517	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	stop_codon	35252142	35252144	.	-	0	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252145	35252296	1	-	2	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252145	35252296	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252297	35252384	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252385	35252510	1	-	2	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252385	35252510	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252511	35252591	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252592	35252715	1	-	0	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252592	35252715	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252716	35252847	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252848	35252895	1	-	0	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252848	35252895	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252896	35252995	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252996	35253031	1	-	0	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252996	35253031	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253032	35253128	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253129	35253228	1	-	1	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253129	35253228	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253229	35253302	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253303	35253399	1	-	2	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253303	35253399	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253400	35253706	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253707	35253852	1	-	1	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253707	35253852	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253853	35253948	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253949	35254517	0.55	-	0	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253949	35254517	.	-	.	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	start_codon	35254515	35254517	.	-	0	transcript_id "Phchi.S1G547300.t1"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	transcript	35252145	35254517	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	stop_codon	35252142	35252144	.	-	0	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252145	35252296	1	-	2	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252145	35252296	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252297	35252384	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252385	35252510	1	-	2	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252385	35252510	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252511	35252591	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252592	35252715	1	-	0	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252592	35252715	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252716	35252847	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252848	35252895	1	-	0	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252848	35252895	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35252896	35252995	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35252996	35253031	1	-	0	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35252996	35253031	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253032	35253128	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253129	35253228	1	-	1	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253129	35253228	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253229	35253302	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253303	35253417	0.69	-	2	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253303	35253417	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253418	35253547	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253548	35253585	0.57	-	1	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253548	35253585	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253586	35253702	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253703	35253852	0.58	-	1	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253703	35253852	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	intron	35253853	35253948	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	CDS	35253949	35254517	0.47	-	0	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	exon	35253949	35254517	.	-	.	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
Phchi.S1	AUGUSTUS	start_codon	35254515	35254517	.	-	0	transcript_id "Phchi.S1G547300.t2"; gene_id "Phchi.S1G547300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10527.t1 is derived from g14577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	838716	839646	.	-	.	Phchi.S4G010900
Phchi.S4	AUGUSTUS	transcript	838716	839646	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	stop_codon	838713	838715	.	-	0	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	CDS	838716	838722	1	-	1	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	exon	838716	838722	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	intron	838723	838820	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	CDS	838821	838866	1	-	2	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	exon	838821	838866	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	intron	838867	839116	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	CDS	839117	839195	1	-	0	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	exon	839117	839195	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	intron	839196	839314	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	CDS	839315	839377	1	-	0	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	exon	839315	839377	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	intron	839378	839467	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	CDS	839468	839494	1	-	0	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	exon	839468	839494	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	intron	839495	839604	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	CDS	839605	839646	0.9	-	0	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	exon	839605	839646	.	-	.	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
Phchi.S4	AUGUSTUS	start_codon	839644	839646	.	-	0	transcript_id "Phchi.S4G010900.t1"; gene_id "Phchi.S4G010900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8459.t1 is derived from g5634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36039649	36040939	.	-	.	Phchi.S1G561800
Phchi.S1	AUGUSTUS	transcript	36039649	36040939	.	-	.	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	stop_codon	36039646	36039648	.	-	0	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	CDS	36039649	36040523	0.58	-	2	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	exon	36039649	36040523	.	-	.	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	intron	36040524	36040633	.	-	.	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	CDS	36040634	36040675	0.98	-	2	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	exon	36040634	36040675	.	-	.	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	intron	36040676	36040803	.	-	.	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	CDS	36040804	36040939	0.37	-	0	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	exon	36040804	36040939	.	-	.	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
Phchi.S1	AUGUSTUS	start_codon	36040937	36040939	.	-	0	transcript_id "Phchi.S1G561800.t1"; gene_id "Phchi.S1G561800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13367.t1 is derived from g11833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6367965	6368755	.	+	.	Phchi.S3G068600
Phchi.S3	AUGUSTUS	transcript	6367965	6368755	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	start_codon	6367965	6367967	.	+	0	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	CDS	6367965	6367975	0.45	+	0	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	exon	6367965	6367975	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	intron	6367976	6368062	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	CDS	6368063	6368156	0.5	+	1	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	exon	6368063	6368156	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	intron	6368157	6368253	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	CDS	6368254	6368344	0.85	+	0	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	exon	6368254	6368344	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	intron	6368345	6368449	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	CDS	6368450	6368578	0.86	+	2	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	exon	6368450	6368578	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	intron	6368579	6368669	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	CDS	6368670	6368755	1	+	2	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	exon	6368670	6368755	.	+	.	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
Phchi.S3	AUGUSTUS	stop_codon	6368756	6368758	.	+	0	transcript_id "Phchi.S3G068600.t1"; gene_id "Phchi.S3G068600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15991.t1 is derived from g9763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C297	AUGUSTUS	gene	7308	8868	.	-	.	Phchi.C297G000300
Phchi.C297	AUGUSTUS	transcript	7308	8868	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	stop_codon	7305	7307	.	-	0	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	CDS	7308	7720	0.48	-	2	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	exon	7308	7720	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	intron	7721	7916	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	CDS	7917	8273	0.93	-	2	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	exon	7917	8273	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	intron	8274	8366	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	CDS	8367	8414	0.94	-	2	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	exon	8367	8414	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	intron	8415	8603	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	CDS	8604	8868	0.96	-	0	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	exon	8604	8868	.	-	.	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
Phchi.C297	AUGUSTUS	start_codon	8866	8868	.	-	0	transcript_id "Phchi.C297G000300.t1"; gene_id "Phchi.C297G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6182.t1 is derived from g3353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21334224	21334735	.	-	.	Phchi.S1G334100
Phchi.S1	AUGUSTUS	transcript	21334224	21334735	.	-	.	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	stop_codon	21334221	21334223	.	-	0	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	CDS	21334224	21334310	0.67	-	0	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	exon	21334224	21334310	.	-	.	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	intron	21334311	21334398	.	-	.	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	CDS	21334399	21334475	0.85	-	2	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	exon	21334399	21334475	.	-	.	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	intron	21334476	21334656	.	-	.	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	CDS	21334657	21334735	1	-	0	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	exon	21334657	21334735	.	-	.	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
Phchi.S1	AUGUSTUS	start_codon	21334733	21334735	.	-	0	transcript_id "Phchi.S1G334100.t1"; gene_id "Phchi.S1G334100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5580.t1 is derived from g2750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17711126	17714464	.	-	.	Phchi.S1G273900
Phchi.S1	AUGUSTUS	transcript	17711126	17714464	.	-	.	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	stop_codon	17711123	17711125	.	-	0	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	CDS	17711126	17711432	0.01	-	1	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	exon	17711126	17711432	.	-	.	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	intron	17711433	17712562	.	-	.	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	CDS	17712563	17712636	0.91	-	0	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	exon	17712563	17712636	.	-	.	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	intron	17712637	17714383	.	-	.	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	CDS	17714384	17714464	0.03	-	0	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	exon	17714384	17714464	.	-	.	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
Phchi.S1	AUGUSTUS	start_codon	17714462	17714464	.	-	0	transcript_id "Phchi.S1G273900.t1"; gene_id "Phchi.S1G273900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1325.t1 is derived from g11108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9027334	9030143	.	+	.	Phchi.S6G128400
Phchi.S6	AUGUSTUS	transcript	9027334	9030143	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	start_codon	9027334	9027336	.	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9027334	9027663	0.96	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9027334	9027663	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9027664	9027811	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9027812	9027865	1	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9027812	9027865	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9027866	9027967	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9027968	9028038	0.99	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9027968	9028038	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9028039	9028141	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9028142	9028916	0.92	+	1	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9028142	9028916	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9028917	9029055	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9029056	9029190	1	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9029056	9029190	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9029191	9029342	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9029343	9029482	1	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9029343	9029482	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9029483	9029732	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9029733	9029913	1	+	1	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9029733	9029913	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	intron	9029914	9029993	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	CDS	9029994	9030143	1	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	exon	9029994	9030143	.	+	.	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
Phchi.S6	AUGUSTUS	stop_codon	9030144	9030146	.	+	0	transcript_id "Phchi.S6G128400.t1"; gene_id "Phchi.S6G128400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg30.t1 is derived from g9808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C246	AUGUSTUS	gene	15872	16853	.	+	.	Phchi.C246G000300
Phchi.C246	AUGUSTUS	transcript	15872	16853	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	start_codon	15872	15874	.	+	0	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	CDS	15872	15918	1	+	0	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	exon	15872	15918	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	intron	15919	16068	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	CDS	16069	16102	1	+	1	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	exon	16069	16102	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	intron	16103	16184	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	CDS	16185	16351	0.99	+	0	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	exon	16185	16351	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	intron	16352	16473	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	CDS	16474	16525	1	+	1	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	exon	16474	16525	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	intron	16526	16615	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	CDS	16616	16683	1	+	0	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	exon	16616	16683	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	intron	16684	16789	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	CDS	16790	16853	1	+	1	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	exon	16790	16853	.	+	.	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
Phchi.C246	AUGUSTUS	stop_codon	16854	16856	.	+	0	transcript_id "Phchi.C246G000300.t1"; gene_id "Phchi.C246G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8187.t1 is derived from g5362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34338836	34339550	.	+	.	Phchi.S1G534600
Phchi.S1	AUGUSTUS	transcript	34338836	34339550	.	+	.	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	start_codon	34338836	34338838	.	+	0	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	CDS	34338836	34339288	0.79	+	0	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	exon	34338836	34339288	.	+	.	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	intron	34339289	34339448	.	+	.	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	CDS	34339449	34339550	0.47	+	0	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	exon	34339449	34339550	.	+	.	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
Phchi.S1	AUGUSTUS	stop_codon	34339551	34339553	.	+	0	transcript_id "Phchi.S1G534600.t1"; gene_id "Phchi.S1G534600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10893.t1 is derived from g14943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2788161	2790957	.	+	.	Phchi.S4G047500
Phchi.S4	AUGUSTUS	transcript	2788161	2790957	.	+	.	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	start_codon	2788161	2788163	.	+	0	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	CDS	2788161	2790491	0.98	+	0	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	exon	2788161	2790491	.	+	.	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	intron	2790492	2790569	.	+	.	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	CDS	2790570	2790720	0.91	+	0	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	exon	2790570	2790720	.	+	.	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	intron	2790721	2790856	.	+	.	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	CDS	2790857	2790957	1	+	2	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	exon	2790857	2790957	.	+	.	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
Phchi.S4	AUGUSTUS	stop_codon	2790958	2790960	.	+	0	transcript_id "Phchi.S4G047500.t1"; gene_id "Phchi.S4G047500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7096.t1 is derived from g4268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26886711	26887823	.	-	.	Phchi.S1G425500
Phchi.S1	AUGUSTUS	transcript	26886711	26887823	.	-	.	transcript_id "Phchi.S1G425500.t1"; gene_id "Phchi.S1G425500"
Phchi.S1	AUGUSTUS	stop_codon	26886708	26886710	.	-	0	transcript_id "Phchi.S1G425500.t1"; gene_id "Phchi.S1G425500"
Phchi.S1	AUGUSTUS	CDS	26886711	26887823	0.94	-	0	transcript_id "Phchi.S1G425500.t1"; gene_id "Phchi.S1G425500"
Phchi.S1	AUGUSTUS	exon	26886711	26887823	.	-	.	transcript_id "Phchi.S1G425500.t1"; gene_id "Phchi.S1G425500"
Phchi.S1	AUGUSTUS	start_codon	26887821	26887823	.	-	0	transcript_id "Phchi.S1G425500.t1"; gene_id "Phchi.S1G425500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg746.t1 is derived from g10528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5316539	5318158	.	+	.	Phchi.S6G070500
Phchi.S6	AUGUSTUS	transcript	5316539	5318158	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	start_codon	5316539	5316541	.	+	0	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	CDS	5316539	5316576	0.51	+	0	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	exon	5316539	5316576	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	intron	5316577	5316701	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	CDS	5316702	5317071	0.85	+	1	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	exon	5316702	5317071	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	intron	5317072	5317181	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	CDS	5317182	5317436	1	+	0	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	exon	5317182	5317436	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	intron	5317437	5317527	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	CDS	5317528	5317850	0.76	+	0	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	exon	5317528	5317850	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	intron	5317851	5318016	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	CDS	5318017	5318158	0.76	+	1	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	exon	5318017	5318158	.	+	.	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
Phchi.S6	AUGUSTUS	stop_codon	5318159	5318161	.	+	0	transcript_id "Phchi.S6G070500.t1"; gene_id "Phchi.S6G070500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15058.t1 is derived from g13526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16784862	16786027	.	-	.	Phchi.S3G237700
Phchi.S3	AUGUSTUS	transcript	16784862	16786027	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	stop_codon	16784859	16784861	.	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16784862	16784889	1	-	1	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16784862	16784889	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	intron	16784890	16785060	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16785061	16785119	0.96	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16785061	16785119	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	intron	16785120	16785222	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16785223	16785261	0.62	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16785223	16785261	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	intron	16785262	16785344	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16785345	16785423	0.93	-	1	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16785345	16785423	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	intron	16785424	16785548	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16785549	16785637	0.83	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16785549	16785637	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	intron	16785638	16785728	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16785729	16785860	0.8	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16785729	16785860	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	intron	16785861	16786006	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	CDS	16786007	16786027	0.68	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	exon	16786007	16786027	.	-	.	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
Phchi.S3	AUGUSTUS	start_codon	16786025	16786027	.	-	0	transcript_id "Phchi.S3G237700.t1"; gene_id "Phchi.S3G237700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4290.t1 is derived from g1459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9441284	9442078	.	-	.	Phchi.S1G144900
Phchi.S1	AUGUSTUS	transcript	9441284	9441787	.	-	.	transcript_id "Phchi.S1G144900.t1"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	stop_codon	9441281	9441283	.	-	0	transcript_id "Phchi.S1G144900.t1"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	CDS	9441284	9441787	0.66	-	0	transcript_id "Phchi.S1G144900.t1"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	exon	9441284	9441787	.	-	.	transcript_id "Phchi.S1G144900.t1"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	start_codon	9441785	9441787	.	-	0	transcript_id "Phchi.S1G144900.t1"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	transcript	9441284	9442078	.	-	.	transcript_id "Phchi.S1G144900.t2"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	stop_codon	9441281	9441283	.	-	0	transcript_id "Phchi.S1G144900.t2"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	CDS	9441284	9442078	0.49	-	0	transcript_id "Phchi.S1G144900.t2"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	exon	9441284	9442078	.	-	.	transcript_id "Phchi.S1G144900.t2"; gene_id "Phchi.S1G144900"
Phchi.S1	AUGUSTUS	start_codon	9442076	9442078	.	-	0	transcript_id "Phchi.S1G144900.t2"; gene_id "Phchi.S1G144900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2003.t1 is derived from g8923.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4406878	4409602	.	-	.	Phchi.S5G061200
Phchi.S5	AUGUSTUS	transcript	4406878	4407891	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	stop_codon	4406875	4406877	.	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4406878	4407162	0.99	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4406878	4407162	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407163	4407239	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407240	4407395	1	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407240	4407395	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407396	4407477	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407478	4407567	1	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407478	4407567	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407568	4407654	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407655	4407723	1	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407655	4407723	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407724	4407888	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407889	4407891	1	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407889	4407891	.	-	.	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	start_codon	4407889	4407891	.	-	0	transcript_id "Phchi.S5G061200.t1"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	transcript	4406878	4409602	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	stop_codon	4406875	4406877	.	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4406878	4407162	0.99	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4406878	4407162	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407163	4407239	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407240	4407395	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407240	4407395	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407396	4407477	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407478	4407567	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407478	4407567	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407568	4407654	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407655	4407723	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407655	4407723	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407724	4408036	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408037	4408195	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408037	4408195	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408196	4408278	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408279	4408383	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408279	4408383	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408384	4408507	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408508	4408651	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408508	4408651	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408652	4408758	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408759	4408872	1	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408759	4408872	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408873	4408962	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408963	4409056	1	-	1	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408963	4409056	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4409057	4409225	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4409226	4409602	0.58	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4409226	4409602	.	-	.	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	start_codon	4409600	4409602	.	-	0	transcript_id "Phchi.S5G061200.t2"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	transcript	4407930	4409602	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	stop_codon	4407927	4407929	.	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4407930	4407968	1	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4407930	4407968	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4407969	4408102	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408103	4408195	1	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408103	4408195	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408196	4408278	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408279	4408383	1	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408279	4408383	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408384	4408507	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408508	4408651	1	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408508	4408651	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408652	4408758	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408759	4408872	1	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408759	4408872	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4408873	4408962	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4408963	4409056	1	-	1	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4408963	4409056	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	intron	4409057	4409225	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	CDS	4409226	4409602	0.56	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	exon	4409226	4409602	.	-	.	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
Phchi.S5	AUGUSTUS	start_codon	4409600	4409602	.	-	0	transcript_id "Phchi.S5G061200.t3"; gene_id "Phchi.S5G061200"
# This transcript jg11407.t2 is derived from g15457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11408.t1 is derived from g15458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6220808	6222841	.	-	.	Phchi.S4G099000
Phchi.S4	AUGUSTUS	transcript	6220808	6222841	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	stop_codon	6220805	6220807	.	-	0	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	CDS	6220808	6220875	0.99	-	2	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	exon	6220808	6220875	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	intron	6220876	6220976	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	CDS	6220977	6221053	0.99	-	1	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	exon	6220977	6221053	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	intron	6221054	6221140	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	CDS	6221141	6221215	0.4	-	1	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	exon	6221141	6221215	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	intron	6221216	6221315	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	CDS	6221316	6222841	0.34	-	0	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	exon	6221316	6222841	.	-	.	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
Phchi.S4	AUGUSTUS	start_codon	6222839	6222841	.	-	0	transcript_id "Phchi.S4G099000.t1"; gene_id "Phchi.S4G099000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15053.t1 is derived from g13521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16762232	16764557	.	-	.	Phchi.S3G237200
Phchi.S3	AUGUSTUS	transcript	16762232	16764557	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	stop_codon	16762229	16762231	.	-	0	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	CDS	16762232	16762453	0.91	-	0	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	exon	16762232	16762453	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	intron	16762454	16762577	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	CDS	16762578	16762638	0.87	-	1	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	exon	16762578	16762638	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	intron	16762639	16762920	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	CDS	16762921	16762976	0.94	-	0	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	exon	16762921	16762976	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	intron	16762977	16763089	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	CDS	16763090	16763172	0.99	-	2	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	exon	16763090	16763172	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	intron	16763173	16763257	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	CDS	16763258	16764557	0.99	-	0	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	exon	16763258	16764557	.	-	.	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
Phchi.S3	AUGUSTUS	start_codon	16764555	16764557	.	-	0	transcript_id "Phchi.S3G237200.t1"; gene_id "Phchi.S3G237200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7694.t1 is derived from g4868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30685286	30685837	.	-	.	Phchi.S1G485300
Phchi.S1	AUGUSTUS	transcript	30685286	30685837	.	-	.	transcript_id "Phchi.S1G485300.t1"; gene_id "Phchi.S1G485300"
Phchi.S1	AUGUSTUS	stop_codon	30685283	30685285	.	-	0	transcript_id "Phchi.S1G485300.t1"; gene_id "Phchi.S1G485300"
Phchi.S1	AUGUSTUS	CDS	30685286	30685837	0.06	-	0	transcript_id "Phchi.S1G485300.t1"; gene_id "Phchi.S1G485300"
Phchi.S1	AUGUSTUS	exon	30685286	30685837	.	-	.	transcript_id "Phchi.S1G485300.t1"; gene_id "Phchi.S1G485300"
Phchi.S1	AUGUSTUS	start_codon	30685835	30685837	.	-	0	transcript_id "Phchi.S1G485300.t1"; gene_id "Phchi.S1G485300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6628.t1 is derived from g3800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24164477	24167298	.	+	.	Phchi.S1G378700
Phchi.S1	AUGUSTUS	transcript	24164477	24167298	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	start_codon	24164477	24164479	.	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24164477	24164606	0.75	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24164477	24164606	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24164607	24164683	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24164684	24164859	0.76	+	2	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24164684	24164859	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24164860	24165185	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24165186	24165260	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24165186	24165260	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24165261	24165494	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24165495	24165602	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24165495	24165602	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24165603	24165718	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24165719	24165879	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24165719	24165879	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24165880	24165991	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24165992	24166106	1	+	1	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24165992	24166106	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24166107	24166192	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24166193	24166347	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24166193	24166347	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24166348	24166503	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24166504	24166555	1	+	1	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24166504	24166555	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24166556	24166646	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24166647	24166715	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24166647	24166715	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24166716	24166799	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24166800	24166877	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24166800	24166877	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	intron	24166878	24166977	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	CDS	24166978	24167298	1	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	exon	24166978	24167298	.	+	.	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
Phchi.S1	AUGUSTUS	stop_codon	24167299	24167301	.	+	0	transcript_id "Phchi.S1G378700.t1"; gene_id "Phchi.S1G378700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15586.t1 is derived from g14055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20134541	20135039	.	-	.	Phchi.S3G290500
Phchi.S3	AUGUSTUS	transcript	20134541	20135039	.	-	.	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	stop_codon	20134538	20134540	.	-	0	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	CDS	20134541	20134562	0.89	-	1	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	exon	20134541	20134562	.	-	.	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	intron	20134563	20134672	.	-	.	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	CDS	20134673	20134893	0.92	-	0	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	exon	20134673	20134893	.	-	.	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	intron	20134894	20135024	.	-	.	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	CDS	20135025	20135039	0.94	-	0	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	exon	20135025	20135039	.	-	.	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
Phchi.S3	AUGUSTUS	start_codon	20135037	20135039	.	-	0	transcript_id "Phchi.S3G290500.t1"; gene_id "Phchi.S3G290500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4257.t1 is derived from g1426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9181636	9182738	.	+	.	Phchi.S1G141600
Phchi.S1	AUGUSTUS	transcript	9181636	9182738	.	+	.	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	start_codon	9181636	9181638	.	+	0	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	CDS	9181636	9182112	0.99	+	0	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	exon	9181636	9182112	.	+	.	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	intron	9182113	9182192	.	+	.	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	CDS	9182193	9182738	0.98	+	0	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	exon	9182193	9182738	.	+	.	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
Phchi.S1	AUGUSTUS	stop_codon	9182739	9182741	.	+	0	transcript_id "Phchi.S1G141600.t1"; gene_id "Phchi.S1G141600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12057.t1 is derived from g7732.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1106970	1112937	.	+	.	Phchi.S2G013700
Phchi.S2	AUGUSTUS	transcript	1106970	1112937	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	start_codon	1106970	1106972	.	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1106970	1107047	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1106970	1107047	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107048	1107210	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107211	1107411	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107211	1107411	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107412	1107511	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107512	1107634	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107512	1107634	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107635	1107813	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107814	1107851	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107814	1107851	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107852	1107979	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107980	1108148	1	+	1	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107980	1108148	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1108149	1108267	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1108268	1108309	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1108268	1108309	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1108310	1108488	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1108489	1111371	0.44	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1108489	1111371	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1111372	1111454	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1111455	1111580	0.45	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1111455	1111580	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1111581	1111672	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1111673	1111831	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1111673	1111831	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1111832	1111984	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1111985	1112080	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1111985	1112080	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1112081	1112167	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1112168	1112310	1	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1112168	1112310	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1112311	1112397	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1112398	1112535	1	+	1	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1112398	1112535	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1112536	1112699	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1112700	1112937	0.73	+	1	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1112700	1112937	.	+	.	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	stop_codon	1112938	1112940	.	+	0	transcript_id "Phchi.S2G013700.t1"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	transcript	1106970	1112937	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	start_codon	1106970	1106972	.	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1106970	1107047	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1106970	1107047	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107048	1107210	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107211	1107411	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107211	1107411	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107412	1107511	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107512	1107634	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107512	1107634	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107635	1107813	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107814	1107851	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107814	1107851	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1107852	1107979	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1107980	1108148	1	+	1	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1107980	1108148	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1108149	1108267	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1108268	1108309	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1108268	1108309	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1108310	1108488	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1108489	1111371	0.38	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1108489	1111371	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1111372	1111454	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1111455	1111580	0.39	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1111455	1111580	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1111581	1111672	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1111673	1111831	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1111673	1111831	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1111832	1111969	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1111970	1112080	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1111970	1112080	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1112081	1112167	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1112168	1112310	1	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1112168	1112310	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1112311	1112397	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1112398	1112535	1	+	1	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1112398	1112535	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	intron	1112536	1112699	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	CDS	1112700	1112937	0.67	+	1	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	exon	1112700	1112937	.	+	.	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
Phchi.S2	AUGUSTUS	stop_codon	1112938	1112940	.	+	0	transcript_id "Phchi.S2G013700.t2"; gene_id "Phchi.S2G013700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15977.t1 is derived from g9820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C54	AUGUSTUS	gene	53061	53703	.	+	.	Phchi.C54G000400
Phchi.C54	AUGUSTUS	transcript	53061	53703	.	+	.	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	start_codon	53061	53063	.	+	0	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	CDS	53061	53076	0.87	+	0	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	exon	53061	53076	.	+	.	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	intron	53077	53236	.	+	.	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	CDS	53237	53703	0.94	+	2	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	exon	53237	53703	.	+	.	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
Phchi.C54	AUGUSTUS	stop_codon	53704	53706	.	+	0	transcript_id "Phchi.C54G000400.t1"; gene_id "Phchi.C54G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2187.t1 is derived from g9107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5273027	5274490	.	+	.	Phchi.S5G079600
Phchi.S5	AUGUSTUS	transcript	5273027	5274490	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	start_codon	5273027	5273029	.	+	0	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5273027	5273070	0.43	+	0	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5273027	5273070	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	intron	5273071	5273357	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5273358	5273394	0.47	+	1	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5273358	5273394	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	intron	5273395	5273484	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5273485	5273650	0.84	+	0	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5273485	5273650	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	intron	5273651	5273848	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5273849	5273863	0.84	+	2	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5273849	5273863	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	intron	5273864	5273974	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5273975	5274033	0.82	+	2	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5273975	5274033	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	intron	5274034	5274149	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5274150	5274219	0.86	+	0	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5274150	5274219	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	intron	5274220	5274452	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	CDS	5274453	5274490	0.99	+	2	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	exon	5274453	5274490	.	+	.	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
Phchi.S5	AUGUSTUS	stop_codon	5274491	5274493	.	+	0	transcript_id "Phchi.S5G079600.t1"; gene_id "Phchi.S5G079600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3149.t1 is derived from g318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1986308	1986952	.	+	.	Phchi.S1G030800
Phchi.S1	AUGUSTUS	transcript	1986308	1986952	.	+	.	transcript_id "Phchi.S1G030800.t1"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	start_codon	1986308	1986310	.	+	0	transcript_id "Phchi.S1G030800.t1"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	CDS	1986308	1986952	0.86	+	0	transcript_id "Phchi.S1G030800.t1"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	exon	1986308	1986952	.	+	.	transcript_id "Phchi.S1G030800.t1"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	stop_codon	1986953	1986955	.	+	0	transcript_id "Phchi.S1G030800.t1"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	transcript	1986515	1986952	.	+	.	transcript_id "Phchi.S1G030800.t2"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	start_codon	1986515	1986517	.	+	0	transcript_id "Phchi.S1G030800.t2"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	CDS	1986515	1986952	0.82	+	0	transcript_id "Phchi.S1G030800.t2"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	exon	1986515	1986952	.	+	.	transcript_id "Phchi.S1G030800.t2"; gene_id "Phchi.S1G030800"
Phchi.S1	AUGUSTUS	stop_codon	1986953	1986955	.	+	0	transcript_id "Phchi.S1G030800.t2"; gene_id "Phchi.S1G030800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5934.t1 is derived from g3105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19936669	19941830	.	+	.	Phchi.S1G309300
Phchi.S1	AUGUSTUS	transcript	19936669	19941830	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	start_codon	19936669	19936671	.	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19936669	19936801	0.71	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19936669	19936801	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19936802	19937312	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19937313	19937375	0.97	+	2	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19937313	19937375	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19937376	19937568	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19937569	19938094	0.75	+	2	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19937569	19938094	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19938095	19938197	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19938198	19938801	0.18	+	1	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19938198	19938801	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19938802	19938902	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19938903	19939972	0.42	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19938903	19939972	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19939973	19940089	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19940090	19940285	1	+	1	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19940090	19940285	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19940286	19940408	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19940409	19940578	1	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19940409	19940578	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19940579	19940671	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19940672	19941005	0.98	+	1	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19940672	19941005	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19941006	19941130	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19941131	19941347	1	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19941131	19941347	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19941348	19941459	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19941460	19941566	1	+	2	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19941460	19941566	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	intron	19941567	19941680	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	CDS	19941681	19941830	0.97	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	exon	19941681	19941830	.	+	.	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
Phchi.S1	AUGUSTUS	stop_codon	19941831	19941833	.	+	0	transcript_id "Phchi.S1G309300.t1"; gene_id "Phchi.S1G309300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9670.t1 is derived from g6846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43202020	43203887	.	-	.	Phchi.S1G682900
Phchi.S1	AUGUSTUS	transcript	43202020	43203887	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	stop_codon	43202017	43202019	.	-	0	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	CDS	43202020	43202346	0.99	-	0	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	exon	43202020	43202346	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	intron	43202347	43202419	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	CDS	43202420	43202850	0.68	-	2	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	exon	43202420	43202850	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	intron	43202851	43202933	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	CDS	43202934	43203149	0.97	-	2	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	exon	43202934	43203149	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	intron	43203150	43203245	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	CDS	43203246	43203386	0.59	-	2	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	exon	43203246	43203386	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	intron	43203387	43203529	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	CDS	43203530	43203887	0.21	-	0	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	exon	43203530	43203887	.	-	.	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
Phchi.S1	AUGUSTUS	start_codon	43203885	43203887	.	-	0	transcript_id "Phchi.S1G682900.t1"; gene_id "Phchi.S1G682900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1204.t1 is derived from g10987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8408629	8409966	.	-	.	Phchi.S6G116300
Phchi.S6	AUGUSTUS	transcript	8408629	8409966	.	-	.	transcript_id "Phchi.S6G116300.t1"; gene_id "Phchi.S6G116300"
Phchi.S6	AUGUSTUS	stop_codon	8408626	8408628	.	-	0	transcript_id "Phchi.S6G116300.t1"; gene_id "Phchi.S6G116300"
Phchi.S6	AUGUSTUS	CDS	8408629	8409966	0.8	-	0	transcript_id "Phchi.S6G116300.t1"; gene_id "Phchi.S6G116300"
Phchi.S6	AUGUSTUS	exon	8408629	8409966	.	-	.	transcript_id "Phchi.S6G116300.t1"; gene_id "Phchi.S6G116300"
Phchi.S6	AUGUSTUS	start_codon	8409964	8409966	.	-	0	transcript_id "Phchi.S6G116300.t1"; gene_id "Phchi.S6G116300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14036.t1 is derived from g12503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10402902	10403162	.	+	.	Phchi.S3G135500
Phchi.S3	AUGUSTUS	transcript	10402902	10403162	.	+	.	transcript_id "Phchi.S3G135500.t1"; gene_id "Phchi.S3G135500"
Phchi.S3	AUGUSTUS	start_codon	10402902	10402904	.	+	0	transcript_id "Phchi.S3G135500.t1"; gene_id "Phchi.S3G135500"
Phchi.S3	AUGUSTUS	CDS	10402902	10403162	0.61	+	0	transcript_id "Phchi.S3G135500.t1"; gene_id "Phchi.S3G135500"
Phchi.S3	AUGUSTUS	exon	10402902	10403162	.	+	.	transcript_id "Phchi.S3G135500.t1"; gene_id "Phchi.S3G135500"
Phchi.S3	AUGUSTUS	stop_codon	10403163	10403165	.	+	0	transcript_id "Phchi.S3G135500.t1"; gene_id "Phchi.S3G135500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8030.t1 is derived from g5205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32561547	32563210	.	-	.	Phchi.S1G518900
Phchi.S1	AUGUSTUS	transcript	32561547	32563210	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	stop_codon	32561544	32561546	.	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32561547	32561625	0.46	-	1	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32561547	32561625	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32561626	32561733	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32561734	32561804	0.56	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32561734	32561804	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32561805	32561880	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32561881	32561970	1	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32561881	32561970	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32561971	32562064	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32562065	32562117	1	-	2	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32562065	32562117	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32562118	32562203	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32562204	32562257	1	-	2	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32562204	32562257	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32562258	32562396	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32562397	32562460	0.81	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32562397	32562460	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32562461	32562572	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32562573	32562632	0.91	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32562573	32562632	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32562633	32562740	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32562741	32562980	0.44	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32562741	32562980	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	intron	32562981	32563120	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	CDS	32563121	32563210	0.79	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	exon	32563121	32563210	.	-	.	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
Phchi.S1	AUGUSTUS	start_codon	32563208	32563210	.	-	0	transcript_id "Phchi.S1G518900.t1"; gene_id "Phchi.S1G518900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12930.t1 is derived from g11395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3198736	3199706	.	-	.	Phchi.S3G024900
Phchi.S3	AUGUSTUS	transcript	3198736	3199706	.	-	.	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	stop_codon	3198733	3198735	.	-	0	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	CDS	3198736	3198828	1	-	0	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	exon	3198736	3198828	.	-	.	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	intron	3198829	3198986	.	-	.	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	CDS	3198987	3199045	1	-	2	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	exon	3198987	3199045	.	-	.	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	intron	3199046	3199138	.	-	.	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	CDS	3199139	3199706	0.57	-	0	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	exon	3199139	3199706	.	-	.	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	start_codon	3199704	3199706	.	-	0	transcript_id "Phchi.S3G024900.t1"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	transcript	3198736	3199706	.	-	.	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	stop_codon	3198733	3198735	.	-	0	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	CDS	3198736	3198828	1	-	0	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	exon	3198736	3198828	.	-	.	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	intron	3198829	3198986	.	-	.	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	CDS	3198987	3199054	0.99	-	2	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	exon	3198987	3199054	.	-	.	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	intron	3199055	3199138	.	-	.	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	CDS	3199139	3199706	0.55	-	0	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	exon	3199139	3199706	.	-	.	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
Phchi.S3	AUGUSTUS	start_codon	3199704	3199706	.	-	0	transcript_id "Phchi.S3G024900.t2"; gene_id "Phchi.S3G024900"
# This transcript jg2467.t2 is derived from g9387.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2468.t1 is derived from g9388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6812670	6813903	.	-	.	Phchi.S5G107700
Phchi.S5	AUGUSTUS	transcript	6812670	6813903	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	stop_codon	6812667	6812669	.	-	0	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	CDS	6812670	6812700	0.8	-	1	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	exon	6812670	6812700	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	intron	6812701	6812798	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	CDS	6812799	6812862	0.8	-	2	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	exon	6812799	6812862	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	intron	6812863	6812935	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	CDS	6812936	6813041	1	-	0	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	exon	6812936	6813041	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	intron	6813042	6813171	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	CDS	6813172	6813280	1	-	1	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	exon	6813172	6813280	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	intron	6813281	6813516	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	CDS	6813517	6813563	0.94	-	0	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	exon	6813517	6813563	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	intron	6813564	6813822	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	CDS	6813823	6813903	0.59	-	0	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	exon	6813823	6813903	.	-	.	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
Phchi.S5	AUGUSTUS	start_codon	6813901	6813903	.	-	0	transcript_id "Phchi.S5G107700.t1"; gene_id "Phchi.S5G107700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6692.t1 is derived from g3864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24550316	24551834	.	+	.	Phchi.S1G385100
Phchi.S1	AUGUSTUS	transcript	24550316	24551834	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	start_codon	24550316	24550318	.	+	0	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24550316	24550481	1	+	0	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24550316	24550481	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	intron	24550482	24550615	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24550616	24550723	0.72	+	2	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24550616	24550723	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	intron	24550724	24550845	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24550846	24550909	0.74	+	2	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24550846	24550909	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	intron	24550910	24551061	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24551062	24551168	1	+	1	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24551062	24551168	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	intron	24551169	24551264	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24551265	24551299	1	+	2	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24551265	24551299	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	intron	24551300	24551416	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24551417	24551545	1	+	0	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24551417	24551545	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	intron	24551546	24551636	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	CDS	24551637	24551834	0.95	+	0	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	exon	24551637	24551834	.	+	.	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
Phchi.S1	AUGUSTUS	stop_codon	24551835	24551837	.	+	0	transcript_id "Phchi.S1G385100.t1"; gene_id "Phchi.S1G385100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1725.t1 is derived from g8645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2722661	2725102	.	-	.	Phchi.S5G033400
Phchi.S5	AUGUSTUS	transcript	2722661	2725102	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	stop_codon	2722658	2722660	.	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2722661	2722802	1	-	1	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2722661	2722802	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2722803	2722941	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2722942	2723115	1	-	1	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2722942	2723115	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2723116	2723237	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2723238	2723434	1	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2723238	2723434	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2723435	2723526	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2723527	2723640	0.99	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2723527	2723640	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2723641	2723755	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2723756	2723892	0.98	-	2	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2723756	2723892	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2723893	2723990	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2723991	2724101	0.99	-	2	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2723991	2724101	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2724102	2724210	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2724211	2724463	1	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2724211	2724463	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2724464	2724590	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2724591	2724689	1	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2724591	2724689	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	intron	2724690	2724805	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	CDS	2724806	2725102	0.95	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	exon	2724806	2725102	.	-	.	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
Phchi.S5	AUGUSTUS	start_codon	2725100	2725102	.	-	0	transcript_id "Phchi.S5G033400.t1"; gene_id "Phchi.S5G033400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4495.t1 is derived from g1665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10809379	10810949	.	+	.	Phchi.S1G165400
Phchi.S1	AUGUSTUS	transcript	10809379	10810949	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	start_codon	10809379	10809381	.	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	CDS	10809379	10809451	1	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	exon	10809379	10809451	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	intron	10809452	10809577	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	CDS	10809578	10809723	1	+	2	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	exon	10809578	10809723	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	intron	10809724	10809837	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	CDS	10809838	10810056	1	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	exon	10809838	10810056	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	intron	10810057	10810169	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	CDS	10810170	10810385	1	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	exon	10810170	10810385	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	intron	10810386	10810562	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	CDS	10810563	10810649	0.83	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	exon	10810563	10810649	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	intron	10810650	10810751	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	CDS	10810752	10810949	1	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	exon	10810752	10810949	.	+	.	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
Phchi.S1	AUGUSTUS	stop_codon	10810950	10810952	.	+	0	transcript_id "Phchi.S1G165400.t1"; gene_id "Phchi.S1G165400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3073.t1 is derived from g242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1439089	1439780	.	+	.	Phchi.S1G023200
Phchi.S1	AUGUSTUS	transcript	1439089	1439780	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	start_codon	1439089	1439091	.	+	0	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	CDS	1439089	1439121	1	+	0	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	exon	1439089	1439121	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	intron	1439122	1439213	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	CDS	1439214	1439292	1	+	0	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	exon	1439214	1439292	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	intron	1439293	1439380	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	CDS	1439381	1439401	0.62	+	2	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	exon	1439381	1439401	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	intron	1439402	1439496	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	CDS	1439497	1439780	0.53	+	2	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	exon	1439497	1439780	.	+	.	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
Phchi.S1	AUGUSTUS	stop_codon	1439781	1439783	.	+	0	transcript_id "Phchi.S1G023200.t1"; gene_id "Phchi.S1G023200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13381.t1 is derived from g11847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6439230	6442112	.	+	.	Phchi.S3G070000
Phchi.S3	AUGUSTUS	transcript	6439230	6442112	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	start_codon	6439230	6439232	.	+	0	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6439230	6439320	0.95	+	0	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6439230	6439320	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6439321	6439439	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6439440	6439606	0.8	+	2	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6439440	6439606	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6439607	6439709	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6439710	6439923	0.46	+	0	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6439710	6439923	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6439924	6440023	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6440024	6440649	0.68	+	2	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6440024	6440649	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6440650	6440793	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6440794	6441010	1	+	0	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6440794	6441010	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6441011	6441096	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6441097	6441275	0.99	+	2	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6441097	6441275	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6441276	6441376	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6441377	6441615	0.99	+	0	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6441377	6441615	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	intron	6441616	6441703	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	CDS	6441704	6442112	1	+	1	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	exon	6441704	6442112	.	+	.	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
Phchi.S3	AUGUSTUS	stop_codon	6442113	6442115	.	+	0	transcript_id "Phchi.S3G070000.t1"; gene_id "Phchi.S3G070000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10948.t1 is derived from g14998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3228859	3231427	.	+	.	Phchi.S4G053000
Phchi.S4	AUGUSTUS	transcript	3228859	3231427	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	start_codon	3228859	3228861	.	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3228859	3229221	1	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3228859	3229221	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3229222	3229336	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3229337	3229476	1	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3229337	3229476	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3229477	3229565	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3229566	3229665	1	+	1	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3229566	3229665	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3229666	3229849	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3229850	3229948	1	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3229850	3229948	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3229949	3230134	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3230135	3230482	0.9	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3230135	3230482	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3230483	3230577	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3230578	3230670	1	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3230578	3230670	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3230671	3230829	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3230830	3231036	1	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3230830	3231036	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	intron	3231037	3231118	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	CDS	3231119	3231427	1	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	exon	3231119	3231427	.	+	.	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
Phchi.S4	AUGUSTUS	stop_codon	3231428	3231430	.	+	0	transcript_id "Phchi.S4G053000.t1"; gene_id "Phchi.S4G053000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8718.t1 is derived from g5893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37658651	37659444	.	-	.	Phchi.S1G587700
Phchi.S1	AUGUSTUS	transcript	37658651	37659444	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	stop_codon	37658648	37658650	.	-	0	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	CDS	37658651	37658731	1	-	0	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	exon	37658651	37658731	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	intron	37658732	37658814	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	CDS	37658815	37658954	1	-	2	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	exon	37658815	37658954	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	intron	37658955	37659033	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	CDS	37659034	37659082	1	-	0	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	exon	37659034	37659082	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	intron	37659083	37659171	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	CDS	37659172	37659320	1	-	2	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	exon	37659172	37659320	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	intron	37659321	37659395	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	CDS	37659396	37659444	1	-	0	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	exon	37659396	37659444	.	-	.	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
Phchi.S1	AUGUSTUS	start_codon	37659442	37659444	.	-	0	transcript_id "Phchi.S1G587700.t1"; gene_id "Phchi.S1G587700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5072.t1 is derived from g2242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14542607	14543367	.	-	.	Phchi.S1G223100
Phchi.S1	AUGUSTUS	transcript	14542607	14543367	.	-	.	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	stop_codon	14542604	14542606	.	-	0	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	CDS	14542607	14543192	0.63	-	1	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	exon	14542607	14543192	.	-	.	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	intron	14543193	14543302	.	-	.	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	CDS	14543303	14543367	0.52	-	0	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	exon	14543303	14543367	.	-	.	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
Phchi.S1	AUGUSTUS	start_codon	14543365	14543367	.	-	0	transcript_id "Phchi.S1G223100.t1"; gene_id "Phchi.S1G223100"
# This transcript jg388.t2 is derived from g10170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg389.t1 is derived from g10171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2847373	2848170	.	-	.	Phchi.S6G034800
Phchi.S6	AUGUSTUS	transcript	2847373	2848170	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	stop_codon	2847370	2847372	.	-	0	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	CDS	2847373	2847420	0.98	-	0	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	exon	2847373	2847420	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	intron	2847421	2847534	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	CDS	2847535	2847615	1	-	0	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	exon	2847535	2847615	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	intron	2847616	2847743	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	CDS	2847744	2847854	1	-	0	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	exon	2847744	2847854	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	intron	2847855	2848002	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	CDS	2848003	2848170	1	-	0	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	exon	2848003	2848170	.	-	.	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
Phchi.S6	AUGUSTUS	start_codon	2848168	2848170	.	-	0	transcript_id "Phchi.S6G034800.t1"; gene_id "Phchi.S6G034800"
# This transcript jg2232.t2 is derived from g9152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2233.t1 is derived from g9153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5578828	5580658	.	+	.	Phchi.S5G084200
Phchi.S5	AUGUSTUS	transcript	5578828	5580658	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	start_codon	5578828	5578830	.	+	0	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	CDS	5578828	5578932	0.99	+	0	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	exon	5578828	5578932	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	intron	5578933	5579093	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	CDS	5579094	5579363	1	+	0	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	exon	5579094	5579363	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	intron	5579364	5579452	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	CDS	5579453	5579676	0.99	+	0	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	exon	5579453	5579676	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	intron	5579677	5579787	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	CDS	5579788	5580658	1	+	1	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	exon	5579788	5580658	.	+	.	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
Phchi.S5	AUGUSTUS	stop_codon	5580659	5580661	.	+	0	transcript_id "Phchi.S5G084200.t1"; gene_id "Phchi.S5G084200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3353.t1 is derived from g522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3096259	3096598	.	-	.	Phchi.S1G051200
Phchi.S1	AUGUSTUS	transcript	3096259	3096598	.	-	.	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	stop_codon	3096256	3096258	.	-	0	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	CDS	3096259	3096306	0.83	-	0	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	exon	3096259	3096306	.	-	.	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	intron	3096307	3096409	.	-	.	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	CDS	3096410	3096598	0.87	-	0	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	exon	3096410	3096598	.	-	.	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
Phchi.S1	AUGUSTUS	start_codon	3096596	3096598	.	-	0	transcript_id "Phchi.S1G051200.t1"; gene_id "Phchi.S1G051200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12510.t1 is derived from g8187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31818284	31818960	.	+	.	Phchi.S2G059000
Phchi.S2	AUGUSTUS	transcript	31818284	31818960	.	+	.	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	start_codon	31818284	31818286	.	+	0	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	CDS	31818284	31818552	0.6	+	0	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	exon	31818284	31818552	.	+	.	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	intron	31818553	31818656	.	+	.	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	CDS	31818657	31818960	0.96	+	1	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	exon	31818657	31818960	.	+	.	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
Phchi.S2	AUGUSTUS	stop_codon	31818961	31818963	.	+	0	transcript_id "Phchi.S2G059000.t1"; gene_id "Phchi.S2G059000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12795.t1 is derived from g11260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2421266	2422687	.	+	.	Phchi.S3G011400
Phchi.S3	AUGUSTUS	transcript	2421266	2422687	.	+	.	transcript_id "Phchi.S3G011400.t1"; gene_id "Phchi.S3G011400"
Phchi.S3	AUGUSTUS	start_codon	2421266	2421268	.	+	0	transcript_id "Phchi.S3G011400.t1"; gene_id "Phchi.S3G011400"
Phchi.S3	AUGUSTUS	CDS	2421266	2422687	0.74	+	0	transcript_id "Phchi.S3G011400.t1"; gene_id "Phchi.S3G011400"
Phchi.S3	AUGUSTUS	exon	2421266	2422687	.	+	.	transcript_id "Phchi.S3G011400.t1"; gene_id "Phchi.S3G011400"
Phchi.S3	AUGUSTUS	stop_codon	2422688	2422690	.	+	0	transcript_id "Phchi.S3G011400.t1"; gene_id "Phchi.S3G011400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5484.t1 is derived from g2654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17073343	17077034	.	-	.	Phchi.S1G264300
Phchi.S1	AUGUSTUS	transcript	17073343	17077034	.	-	.	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	stop_codon	17073340	17073342	.	-	0	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	CDS	17073343	17075357	0.4	-	2	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	exon	17073343	17075357	.	-	.	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	intron	17075358	17075482	.	-	.	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	CDS	17075483	17077034	0.12	-	0	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	exon	17075483	17077034	.	-	.	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
Phchi.S1	AUGUSTUS	start_codon	17077032	17077034	.	-	0	transcript_id "Phchi.S1G264300.t1"; gene_id "Phchi.S1G264300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12239.t1 is derived from g7915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6933755	6935110	.	+	.	Phchi.S2G031900
Phchi.S2	AUGUSTUS	transcript	6933755	6935110	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	start_codon	6933755	6933757	.	+	0	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	CDS	6933755	6934020	0.79	+	0	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	exon	6933755	6934020	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	intron	6934021	6934131	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	CDS	6934132	6934187	1	+	1	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	exon	6934132	6934187	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	intron	6934188	6934281	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	CDS	6934282	6934343	1	+	2	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	exon	6934282	6934343	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	intron	6934344	6934443	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	CDS	6934444	6934503	1	+	0	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	exon	6934444	6934503	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	intron	6934504	6934574	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	CDS	6934575	6934759	1	+	0	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	exon	6934575	6934759	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	intron	6934760	6934842	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	CDS	6934843	6935110	0.95	+	1	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	exon	6934843	6935110	.	+	.	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
Phchi.S2	AUGUSTUS	stop_codon	6935111	6935113	.	+	0	transcript_id "Phchi.S2G031900.t1"; gene_id "Phchi.S2G031900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14345.t1 is derived from g12812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12315050	12317755	.	+	.	Phchi.S3G166400
Phchi.S3	AUGUSTUS	transcript	12315050	12317755	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	start_codon	12315050	12315052	.	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12315050	12315245	0.95	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12315050	12315245	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	intron	12315246	12315325	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12315326	12315750	0.88	+	2	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12315326	12315750	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	intron	12315751	12315971	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12315972	12316490	0.99	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12315972	12316490	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	intron	12316491	12316584	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12316585	12316820	0.99	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12316585	12316820	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	intron	12316821	12316927	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12316928	12317192	1	+	1	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12316928	12317192	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	intron	12317193	12317272	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12317273	12317410	1	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12317273	12317410	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	intron	12317411	12317488	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	CDS	12317489	12317755	0.22	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	exon	12317489	12317755	.	+	.	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
Phchi.S3	AUGUSTUS	stop_codon	12317756	12317758	.	+	0	transcript_id "Phchi.S3G166400.t1"; gene_id "Phchi.S3G166400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6580.t1 is derived from g3752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23840217	23840942	.	-	.	Phchi.S1G373900
Phchi.S1	AUGUSTUS	transcript	23840217	23840942	.	-	.	transcript_id "Phchi.S1G373900.t1"; gene_id "Phchi.S1G373900"
Phchi.S1	AUGUSTUS	stop_codon	23840214	23840216	.	-	0	transcript_id "Phchi.S1G373900.t1"; gene_id "Phchi.S1G373900"
Phchi.S1	AUGUSTUS	CDS	23840217	23840942	0.56	-	0	transcript_id "Phchi.S1G373900.t1"; gene_id "Phchi.S1G373900"
Phchi.S1	AUGUSTUS	exon	23840217	23840942	.	-	.	transcript_id "Phchi.S1G373900.t1"; gene_id "Phchi.S1G373900"
Phchi.S1	AUGUSTUS	start_codon	23840940	23840942	.	-	0	transcript_id "Phchi.S1G373900.t1"; gene_id "Phchi.S1G373900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7164.t1 is derived from g4336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27352580	27353956	.	-	.	Phchi.S1G432300
Phchi.S1	AUGUSTUS	transcript	27352580	27353956	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	stop_codon	27352577	27352579	.	-	0	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27352580	27352666	0.74	-	0	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27352580	27352666	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27352667	27352751	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27352752	27352850	1	-	0	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27352752	27352850	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27352851	27352949	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27352950	27353039	1	-	0	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27352950	27353039	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27353040	27353137	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27353138	27353258	1	-	1	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27353138	27353258	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27353259	27353888	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27353889	27353956	0.86	-	0	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27353889	27353956	.	-	.	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	start_codon	27353954	27353956	.	-	0	transcript_id "Phchi.S1G432300.t1"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	transcript	27352580	27353956	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	stop_codon	27352577	27352579	.	-	0	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27352580	27352666	0.8	-	0	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27352580	27352666	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27352667	27352751	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27352752	27352850	1	-	0	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27352752	27352850	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27352851	27352949	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27352950	27353039	1	-	0	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27352950	27353039	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27353040	27353137	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27353138	27353258	0.91	-	1	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27353138	27353258	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27353259	27353480	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27353481	27353571	0.92	-	2	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27353481	27353571	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	intron	27353572	27353715	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	CDS	27353716	27353956	0.49	-	0	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	exon	27353716	27353956	.	-	.	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
Phchi.S1	AUGUSTUS	start_codon	27353954	27353956	.	-	0	transcript_id "Phchi.S1G432300.t2"; gene_id "Phchi.S1G432300"
# This transcript jg8096.t2 is derived from g5271.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8096.t3 is derived from g5271.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8097.t1 is derived from g5272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32937278	32940141	.	-	.	Phchi.S1G525600
Phchi.S1	AUGUSTUS	transcript	32937278	32940141	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	stop_codon	32937275	32937277	.	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32937278	32937330	0.76	-	2	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32937278	32937330	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32937331	32937422	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32937423	32937438	0.54	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32937423	32937438	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32937439	32937634	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32937635	32937703	0.56	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32937635	32937703	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32937704	32937793	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32937794	32937908	1	-	1	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32937794	32937908	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32937909	32938065	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32938066	32938155	1	-	1	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32938066	32938155	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32938156	32938252	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32938253	32938371	1	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32938253	32938371	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32938372	32938446	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32938447	32938504	1	-	1	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32938447	32938504	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32938505	32938611	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32938612	32938787	0.98	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32938612	32938787	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32938788	32938923	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32938924	32939105	1	-	2	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32938924	32939105	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32939106	32939198	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32939199	32939352	1	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32939199	32939352	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	intron	32939353	32939448	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	CDS	32939449	32940141	0.84	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	exon	32939449	32940141	.	-	.	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
Phchi.S1	AUGUSTUS	start_codon	32940139	32940141	.	-	0	transcript_id "Phchi.S1G525600.t1"; gene_id "Phchi.S1G525600"
# This transcript jg5037.t2 is derived from g2207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5038.t1 is derived from g2208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14200224	14200914	.	-	.	Phchi.S1G219700
Phchi.S1	AUGUSTUS	transcript	14200224	14200914	.	-	.	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	stop_codon	14200221	14200223	.	-	0	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	CDS	14200224	14200244	1	-	0	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	exon	14200224	14200244	.	-	.	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	intron	14200245	14200326	.	-	.	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	CDS	14200327	14200914	0.85	-	0	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	exon	14200327	14200914	.	-	.	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
Phchi.S1	AUGUSTUS	start_codon	14200912	14200914	.	-	0	transcript_id "Phchi.S1G219700.t1"; gene_id "Phchi.S1G219700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4807.t1 is derived from g1977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12910708	12911268	.	-	.	Phchi.S1G196600
Phchi.S1	AUGUSTUS	transcript	12910708	12911268	.	-	.	transcript_id "Phchi.S1G196600.t1"; gene_id "Phchi.S1G196600"
Phchi.S1	AUGUSTUS	stop_codon	12910705	12910707	.	-	0	transcript_id "Phchi.S1G196600.t1"; gene_id "Phchi.S1G196600"
Phchi.S1	AUGUSTUS	CDS	12910708	12911268	0.9	-	0	transcript_id "Phchi.S1G196600.t1"; gene_id "Phchi.S1G196600"
Phchi.S1	AUGUSTUS	exon	12910708	12911268	.	-	.	transcript_id "Phchi.S1G196600.t1"; gene_id "Phchi.S1G196600"
Phchi.S1	AUGUSTUS	start_codon	12911266	12911268	.	-	0	transcript_id "Phchi.S1G196600.t1"; gene_id "Phchi.S1G196600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2221.t1 is derived from g9141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5502233	5504722	.	-	.	Phchi.S5G083000
Phchi.S5	AUGUSTUS	transcript	5502233	5504722	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	stop_codon	5502230	5502232	.	-	0	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	CDS	5502233	5502679	0.54	-	0	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	exon	5502233	5502679	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	intron	5502680	5502777	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	CDS	5502778	5503865	0.93	-	2	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	exon	5502778	5503865	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	intron	5503866	5503985	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	CDS	5503986	5504066	1	-	2	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	exon	5503986	5504066	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	intron	5504067	5504168	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	CDS	5504169	5504408	1	-	2	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	exon	5504169	5504408	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	intron	5504409	5504520	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	CDS	5504521	5504722	1	-	0	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	exon	5504521	5504722	.	-	.	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
Phchi.S5	AUGUSTUS	start_codon	5504720	5504722	.	-	0	transcript_id "Phchi.S5G083000.t1"; gene_id "Phchi.S5G083000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6217.t1 is derived from g3389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21498096	21498693	.	+	.	Phchi.S1G337600
Phchi.S1	AUGUSTUS	transcript	21498096	21498693	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	start_codon	21498096	21498098	.	+	0	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	CDS	21498096	21498253	1	+	0	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	exon	21498096	21498253	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	intron	21498254	21498330	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	CDS	21498331	21498411	1	+	1	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	exon	21498331	21498411	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	intron	21498412	21498503	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	CDS	21498504	21498561	1	+	1	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	exon	21498504	21498561	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	intron	21498562	21498651	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	CDS	21498652	21498693	1	+	0	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	exon	21498652	21498693	.	+	.	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
Phchi.S1	AUGUSTUS	stop_codon	21498694	21498696	.	+	0	transcript_id "Phchi.S1G337600.t1"; gene_id "Phchi.S1G337600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6472.t1 is derived from g3644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23173747	23177121	.	-	.	Phchi.S1G363100
Phchi.S1	AUGUSTUS	transcript	23173747	23177121	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	stop_codon	23173744	23173746	.	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23173747	23174034	0.98	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23173747	23174034	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23174035	23174150	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23174151	23174287	1	-	2	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23174151	23174287	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23174288	23174455	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23174456	23174962	0.33	-	2	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23174456	23174962	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23174963	23175068	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23175069	23175429	0.46	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23175069	23175429	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23175430	23175557	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23175558	23175818	0.5	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23175558	23175818	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23175819	23175933	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23175934	23176158	0.98	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23175934	23176158	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23176159	23176245	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23176246	23176476	1	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23176246	23176476	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23176477	23176671	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23176672	23176756	0.93	-	1	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23176672	23176756	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23176757	23176871	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23176872	23176917	0.7	-	2	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23176872	23176917	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	intron	23176918	23177075	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	CDS	23177076	23177121	0.7	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	exon	23177076	23177121	.	-	.	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
Phchi.S1	AUGUSTUS	start_codon	23177119	23177121	.	-	0	transcript_id "Phchi.S1G363100.t1"; gene_id "Phchi.S1G363100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3815.t1 is derived from g984.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5877365	5877951	.	-	.	Phchi.S1G097400
Phchi.S1	AUGUSTUS	transcript	5877365	5877951	.	-	.	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	stop_codon	5877362	5877364	.	-	0	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	CDS	5877365	5877637	1	-	0	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	exon	5877365	5877637	.	-	.	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	intron	5877638	5877807	.	-	.	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	CDS	5877808	5877951	0.6	-	0	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	exon	5877808	5877951	.	-	.	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	start_codon	5877949	5877951	.	-	0	transcript_id "Phchi.S1G097400.t1"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	transcript	5877365	5877951	.	-	.	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	stop_codon	5877362	5877364	.	-	0	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	CDS	5877365	5877634	0.99	-	0	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	exon	5877365	5877634	.	-	.	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	intron	5877635	5877807	.	-	.	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	CDS	5877808	5877951	0.51	-	0	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	exon	5877808	5877951	.	-	.	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
Phchi.S1	AUGUSTUS	start_codon	5877949	5877951	.	-	0	transcript_id "Phchi.S1G097400.t2"; gene_id "Phchi.S1G097400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3813.t1 is derived from g982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5850737	5853523	.	-	.	Phchi.S1G097200
Phchi.S1	AUGUSTUS	transcript	5850737	5853523	.	-	.	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	stop_codon	5850734	5850736	.	-	0	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	CDS	5850737	5852990	0.71	-	1	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	exon	5850737	5852990	.	-	.	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	intron	5852991	5853137	.	-	.	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	CDS	5853138	5853220	1	-	0	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	exon	5853138	5853220	.	-	.	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	intron	5853221	5853358	.	-	.	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	CDS	5853359	5853523	0.83	-	0	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	exon	5853359	5853523	.	-	.	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	start_codon	5853521	5853523	.	-	0	transcript_id "Phchi.S1G097200.t1"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	transcript	5853131	5853523	.	-	.	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	stop_codon	5853128	5853130	.	-	0	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	CDS	5853131	5853220	0.88	-	0	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	exon	5853131	5853220	.	-	.	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	intron	5853221	5853358	.	-	.	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	CDS	5853359	5853523	0.76	-	0	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	exon	5853359	5853523	.	-	.	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
Phchi.S1	AUGUSTUS	start_codon	5853521	5853523	.	-	0	transcript_id "Phchi.S1G097200.t2"; gene_id "Phchi.S1G097200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7137.t1 is derived from g4309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27133223	27136975	.	+	.	Phchi.S1G429600
Phchi.S1	AUGUSTUS	transcript	27133223	27136975	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	start_codon	27133223	27133225	.	+	0	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	CDS	27133223	27133708	0.74	+	0	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	exon	27133223	27133708	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	intron	27133709	27133841	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	CDS	27133842	27133991	1	+	0	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	exon	27133842	27133991	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	intron	27133992	27134072	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	CDS	27134073	27134105	1	+	0	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	exon	27134073	27134105	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	intron	27134106	27134209	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	CDS	27134210	27136975	1	+	0	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	exon	27134210	27136975	.	+	.	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
Phchi.S1	AUGUSTUS	stop_codon	27136976	27136978	.	+	0	transcript_id "Phchi.S1G429600.t1"; gene_id "Phchi.S1G429600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10012.t1 is derived from g7188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45045732	45050181	.	-	.	Phchi.S1G717100
Phchi.S1	AUGUSTUS	transcript	45045732	45050181	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	stop_codon	45045729	45045731	.	-	0	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	CDS	45045732	45046090	0.46	-	2	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	exon	45045732	45046090	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	intron	45046091	45046188	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	CDS	45046189	45046867	0.55	-	0	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	exon	45046189	45046867	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	intron	45046868	45046986	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	CDS	45046987	45047860	0.57	-	1	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	exon	45046987	45047860	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	intron	45047861	45048033	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	CDS	45048034	45048439	0.49	-	2	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	exon	45048034	45048439	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	intron	45048440	45048551	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	CDS	45048552	45050181	0.67	-	0	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	exon	45048552	45050181	.	-	.	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
Phchi.S1	AUGUSTUS	start_codon	45050179	45050181	.	-	0	transcript_id "Phchi.S1G717100.t1"; gene_id "Phchi.S1G717100"
# This transcript jg9626.t2 is derived from g6802.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9627.t1 is derived from g6803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42969659	42971443	.	-	.	Phchi.S1G678600
Phchi.S1	AUGUSTUS	transcript	42969659	42971443	.	-	.	transcript_id "Phchi.S1G678600.t1"; gene_id "Phchi.S1G678600"
Phchi.S1	AUGUSTUS	stop_codon	42969656	42969658	.	-	0	transcript_id "Phchi.S1G678600.t1"; gene_id "Phchi.S1G678600"
Phchi.S1	AUGUSTUS	CDS	42969659	42971443	0.64	-	0	transcript_id "Phchi.S1G678600.t1"; gene_id "Phchi.S1G678600"
Phchi.S1	AUGUSTUS	exon	42969659	42971443	.	-	.	transcript_id "Phchi.S1G678600.t1"; gene_id "Phchi.S1G678600"
Phchi.S1	AUGUSTUS	start_codon	42971441	42971443	.	-	0	transcript_id "Phchi.S1G678600.t1"; gene_id "Phchi.S1G678600"
# This transcript jg11959.t2 is derived from g7634.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11960.t1 is derived from g7635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	203604	206052	.	+	.	Phchi.S2G004000
Phchi.S2	AUGUSTUS	transcript	203604	206052	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	start_codon	203604	203606	.	+	0	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	203604	204117	0.78	+	0	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	203604	204117	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	204118	204220	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	204221	204434	0.59	+	2	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	204221	204434	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	204435	204638	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	204639	204722	1	+	1	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	204639	204722	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	204723	204868	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	204869	204915	1	+	1	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	204869	204915	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	204916	204996	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	204997	205097	1	+	2	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	204997	205097	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	205098	205345	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	205346	205453	1	+	0	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	205346	205453	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	205454	205648	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	205649	205870	1	+	0	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	205649	205870	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	intron	205871	205959	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	CDS	205960	206052	0.7	+	0	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	exon	205960	206052	.	+	.	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
Phchi.S2	AUGUSTUS	stop_codon	206053	206055	.	+	0	transcript_id "Phchi.S2G004000.t1"; gene_id "Phchi.S2G004000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10535.t1 is derived from g14585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	862370	867801	.	+	.	Phchi.S4G011700
Phchi.S4	AUGUSTUS	transcript	862370	867801	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	start_codon	862370	862372	.	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	862370	862664	0.76	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	862370	862664	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	862665	862804	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	862805	862979	1	+	2	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	862805	862979	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	862980	863105	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	863106	863280	1	+	1	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	863106	863280	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	863281	863479	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	863480	863612	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	863480	863612	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	863613	863771	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	863772	863842	1	+	2	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	863772	863842	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	863843	863947	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	863948	864031	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	863948	864031	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	864032	864168	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	864169	864259	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	864169	864259	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	864260	864355	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	864356	864876	1	+	2	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	864356	864876	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	864877	864995	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	864996	865160	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	864996	865160	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	865161	865292	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	865293	865511	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	865293	865511	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	865512	865611	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	865612	865739	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	865612	865739	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	865740	865877	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	865878	866067	1	+	1	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	865878	866067	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	866068	866164	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	866165	866248	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	866165	866248	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	866249	866339	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	866340	866437	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	866340	866437	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	866438	866588	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	866589	866850	1	+	1	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	866589	866850	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	866851	866951	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	866952	867114	1	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	866952	867114	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	867115	867228	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	867229	867409	1	+	2	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	867229	867409	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	867410	867495	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	867496	867567	1	+	1	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	867496	867567	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	intron	867568	867662	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	CDS	867663	867801	0.82	+	1	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	exon	867663	867801	.	+	.	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
Phchi.S4	AUGUSTUS	stop_codon	867802	867804	.	+	0	transcript_id "Phchi.S4G011700.t1"; gene_id "Phchi.S4G011700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4575.t1 is derived from g1745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11173113	11176070	.	+	.	Phchi.S1G173400
Phchi.S1	AUGUSTUS	transcript	11173113	11176070	.	+	.	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	start_codon	11173113	11173115	.	+	0	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	CDS	11173113	11175663	0.47	+	0	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	exon	11173113	11175663	.	+	.	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	intron	11175664	11175813	.	+	.	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	CDS	11175814	11175867	0.44	+	2	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	exon	11175814	11175867	.	+	.	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	intron	11175868	11176005	.	+	.	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	CDS	11176006	11176070	0.83	+	2	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	exon	11176006	11176070	.	+	.	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
Phchi.S1	AUGUSTUS	stop_codon	11176071	11176073	.	+	0	transcript_id "Phchi.S1G173400.t1"; gene_id "Phchi.S1G173400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14874.t1 is derived from g13342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15234387	15235464	.	-	.	Phchi.S3G219300
Phchi.S3	AUGUSTUS	transcript	15234387	15235464	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	stop_codon	15234384	15234386	.	-	0	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	CDS	15234387	15234411	0.96	-	1	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	exon	15234387	15234411	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	intron	15234412	15234552	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	CDS	15234553	15234593	1	-	0	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	exon	15234553	15234593	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	intron	15234594	15234755	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	CDS	15234756	15234813	0.95	-	1	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	exon	15234756	15234813	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	intron	15234814	15234942	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	CDS	15234943	15234996	0.3	-	1	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	exon	15234943	15234996	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	intron	15234997	15235253	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	CDS	15235254	15235260	0.84	-	2	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	exon	15235254	15235260	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	intron	15235261	15235433	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	CDS	15235434	15235464	0.95	-	0	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	exon	15235434	15235464	.	-	.	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
Phchi.S3	AUGUSTUS	start_codon	15235462	15235464	.	-	0	transcript_id "Phchi.S3G219300.t1"; gene_id "Phchi.S3G219300"
# This transcript jg3955.t2 is derived from g1124.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3955.t3 is derived from g1124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3956.t1 is derived from g1125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6702374	6703204	.	-	.	Phchi.S1G111500
Phchi.S1	AUGUSTUS	transcript	6702374	6703204	.	-	.	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	stop_codon	6702371	6702373	.	-	0	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	CDS	6702374	6702419	0.98	-	1	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	exon	6702374	6702419	.	-	.	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	intron	6702420	6702551	.	-	.	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	CDS	6702552	6703204	0.82	-	0	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	exon	6702552	6703204	.	-	.	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	start_codon	6703202	6703204	.	-	0	transcript_id "Phchi.S1G111500.t1"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	transcript	6702465	6703204	.	-	.	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	stop_codon	6702462	6702464	.	-	0	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	CDS	6702465	6702472	0.93	-	2	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	exon	6702465	6702472	.	-	.	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	intron	6702473	6702648	.	-	.	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	CDS	6702649	6703204	0.57	-	0	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	exon	6702649	6703204	.	-	.	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
Phchi.S1	AUGUSTUS	start_codon	6703202	6703204	.	-	0	transcript_id "Phchi.S1G111500.t2"; gene_id "Phchi.S1G111500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2156.t1 is derived from g9076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5093874	5096109	.	+	.	Phchi.S5G076500
Phchi.S5	AUGUSTUS	transcript	5093874	5096109	.	+	.	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	start_codon	5093874	5093876	.	+	0	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	CDS	5093874	5094034	0.66	+	0	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	exon	5093874	5094034	.	+	.	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	intron	5094035	5094140	.	+	.	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	CDS	5094141	5094238	0.51	+	1	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	exon	5094141	5094238	.	+	.	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	intron	5094239	5094349	.	+	.	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	CDS	5094350	5096109	0.98	+	2	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	exon	5094350	5096109	.	+	.	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
Phchi.S5	AUGUSTUS	stop_codon	5096110	5096112	.	+	0	transcript_id "Phchi.S5G076500.t1"; gene_id "Phchi.S5G076500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2440.t1 is derived from g9360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6643628	6644605	.	-	.	Phchi.S5G104900
Phchi.S5	AUGUSTUS	transcript	6643628	6644605	.	-	.	transcript_id "Phchi.S5G104900.t1"; gene_id "Phchi.S5G104900"
Phchi.S5	AUGUSTUS	stop_codon	6643625	6643627	.	-	0	transcript_id "Phchi.S5G104900.t1"; gene_id "Phchi.S5G104900"
Phchi.S5	AUGUSTUS	CDS	6643628	6644605	0.49	-	0	transcript_id "Phchi.S5G104900.t1"; gene_id "Phchi.S5G104900"
Phchi.S5	AUGUSTUS	exon	6643628	6644605	.	-	.	transcript_id "Phchi.S5G104900.t1"; gene_id "Phchi.S5G104900"
Phchi.S5	AUGUSTUS	start_codon	6644603	6644605	.	-	0	transcript_id "Phchi.S5G104900.t1"; gene_id "Phchi.S5G104900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5612.t1 is derived from g2782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17891339	17892004	.	+	.	Phchi.S1G277100
Phchi.S1	AUGUSTUS	transcript	17891339	17892004	.	+	.	transcript_id "Phchi.S1G277100.t1"; gene_id "Phchi.S1G277100"
Phchi.S1	AUGUSTUS	start_codon	17891339	17891341	.	+	0	transcript_id "Phchi.S1G277100.t1"; gene_id "Phchi.S1G277100"
Phchi.S1	AUGUSTUS	CDS	17891339	17892004	1	+	0	transcript_id "Phchi.S1G277100.t1"; gene_id "Phchi.S1G277100"
Phchi.S1	AUGUSTUS	exon	17891339	17892004	.	+	.	transcript_id "Phchi.S1G277100.t1"; gene_id "Phchi.S1G277100"
Phchi.S1	AUGUSTUS	stop_codon	17892005	17892007	.	+	0	transcript_id "Phchi.S1G277100.t1"; gene_id "Phchi.S1G277100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2078.t1 is derived from g8998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4750535	4752628	.	-	.	Phchi.S5G068700
Phchi.S5	AUGUSTUS	transcript	4750535	4752628	.	-	.	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	stop_codon	4750532	4750534	.	-	0	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	CDS	4750535	4751441	1	-	1	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	exon	4750535	4751441	.	-	.	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	intron	4751442	4751566	.	-	.	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	CDS	4751567	4752138	0.99	-	0	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	exon	4751567	4752138	.	-	.	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	intron	4752139	4752232	.	-	.	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	CDS	4752233	4752628	0.4	-	0	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	exon	4752233	4752628	.	-	.	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
Phchi.S5	AUGUSTUS	start_codon	4752626	4752628	.	-	0	transcript_id "Phchi.S5G068700.t1"; gene_id "Phchi.S5G068700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6884.t1 is derived from g4056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25819934	25821006	.	-	.	Phchi.S1G404300
Phchi.S1	AUGUSTUS	transcript	25819934	25821006	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	stop_codon	25819931	25819933	.	-	0	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	CDS	25819934	25819971	0.98	-	2	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	exon	25819934	25819971	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	intron	25819972	25820048	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	CDS	25820049	25820106	0.98	-	0	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	exon	25820049	25820106	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	intron	25820107	25820317	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	CDS	25820318	25820697	0.9	-	2	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	exon	25820318	25820697	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	intron	25820698	25820768	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	CDS	25820769	25821006	0.93	-	0	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	exon	25820769	25821006	.	-	.	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
Phchi.S1	AUGUSTUS	start_codon	25821004	25821006	.	-	0	transcript_id "Phchi.S1G404300.t1"; gene_id "Phchi.S1G404300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7530.t1 is derived from g4704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29913392	29915972	.	-	.	Phchi.S1G468900
Phchi.S1	AUGUSTUS	transcript	29913392	29915972	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	stop_codon	29913389	29913391	.	-	0	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29913392	29914303	0.88	-	0	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29913392	29914303	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29914304	29914470	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29914471	29914523	0.81	-	2	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29914471	29914523	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29914524	29914627	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29914628	29914633	0.81	-	2	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29914628	29914633	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29914634	29914782	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29914783	29914864	1	-	0	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29914783	29914864	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29914865	29914982	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29914983	29915085	1	-	1	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29914983	29915085	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29915086	29915203	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29915204	29915284	1	-	1	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29915204	29915284	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29915285	29915373	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29915374	29915415	1	-	1	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29915374	29915415	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29915416	29915592	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29915593	29915660	1	-	0	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29915593	29915660	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29915661	29915760	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29915761	29915885	1	-	2	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29915761	29915885	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	intron	29915886	29915968	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	CDS	29915969	29915972	1	-	0	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	exon	29915969	29915972	.	-	.	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
Phchi.S1	AUGUSTUS	start_codon	29915970	29915972	.	-	0	transcript_id "Phchi.S1G468900.t1"; gene_id "Phchi.S1G468900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14503.t1 is derived from g12971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13218026	13220491	.	+	.	Phchi.S3G182200
Phchi.S3	AUGUSTUS	transcript	13218026	13220491	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	start_codon	13218026	13218028	.	+	0	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13218026	13218545	1	+	0	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13218026	13218545	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13218546	13218694	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13218695	13218857	1	+	2	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13218695	13218857	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13218858	13218981	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13218982	13219212	0.97	+	1	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13218982	13219212	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13219213	13219317	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13219318	13219563	1	+	1	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13219318	13219563	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13219564	13219654	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13219655	13219805	1	+	1	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13219655	13219805	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13219806	13219903	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13219904	13220491	0.94	+	0	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13219904	13220491	.	+	.	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	stop_codon	13220492	13220494	.	+	0	transcript_id "Phchi.S3G182200.t1"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	transcript	13218026	13220491	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	start_codon	13218026	13218028	.	+	0	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13218026	13218545	0.98	+	0	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13218026	13218545	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13218546	13218694	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13218695	13218857	1	+	2	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13218695	13218857	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13218858	13218981	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13218982	13219212	1	+	1	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13218982	13219212	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13219213	13219317	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13219318	13219563	0.99	+	1	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13219318	13219563	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13219564	13219651	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13219652	13219805	0.97	+	1	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13219652	13219805	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	intron	13219806	13219903	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	CDS	13219904	13220491	0.87	+	0	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	exon	13219904	13220491	.	+	.	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
Phchi.S3	AUGUSTUS	stop_codon	13220492	13220494	.	+	0	transcript_id "Phchi.S3G182200.t2"; gene_id "Phchi.S3G182200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8501.t1 is derived from g5676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36347333	36350084	.	+	.	Phchi.S1G566000
Phchi.S1	AUGUSTUS	transcript	36347333	36349677	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	start_codon	36347333	36347335	.	+	0	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36347333	36348089	0.76	+	0	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36347333	36348089	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36348090	36348349	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36348350	36349143	0.95	+	2	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36348350	36349143	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349144	36349276	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349277	36349408	1	+	0	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349277	36349408	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349409	36349647	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349648	36349677	1	+	0	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349648	36349677	.	+	.	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	stop_codon	36349678	36349680	.	+	0	transcript_id "Phchi.S1G566000.t1"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	transcript	36347333	36350084	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	start_codon	36347333	36347335	.	+	0	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36347333	36348089	0.71	+	0	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36347333	36348089	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36348090	36348349	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36348350	36349143	0.94	+	2	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36348350	36349143	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349144	36349276	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349277	36349332	0.61	+	0	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349277	36349332	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349333	36349467	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349468	36349476	0.98	+	1	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349468	36349476	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349477	36349647	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349648	36349715	0.92	+	1	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349648	36349715	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349716	36349801	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349802	36349892	0.97	+	2	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349802	36349892	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349893	36350065	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36350066	36350084	1	+	1	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36350066	36350084	.	+	.	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	stop_codon	36350085	36350087	.	+	0	transcript_id "Phchi.S1G566000.t2"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	transcript	36347333	36350084	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	start_codon	36347333	36347335	.	+	0	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36347333	36348089	0.73	+	0	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36347333	36348089	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36348090	36348349	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36348350	36349143	0.9	+	2	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36348350	36349143	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349144	36349276	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349277	36349332	0.43	+	0	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349277	36349332	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349333	36349474	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349475	36349519	0.65	+	1	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349475	36349519	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349520	36349647	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349648	36349715	0.62	+	1	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349648	36349715	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349716	36349801	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36349802	36349892	0.72	+	2	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36349802	36349892	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	intron	36349893	36350065	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	CDS	36350066	36350084	1	+	1	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	exon	36350066	36350084	.	+	.	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
Phchi.S1	AUGUSTUS	stop_codon	36350085	36350087	.	+	0	transcript_id "Phchi.S1G566000.t3"; gene_id "Phchi.S1G566000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14388.t1 is derived from g12856.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12562878	12565013	.	+	.	Phchi.S3G170700
Phchi.S3	AUGUSTUS	transcript	12562878	12565013	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	start_codon	12562878	12562880	.	+	0	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	CDS	12562878	12562994	0.97	+	0	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	exon	12562878	12562994	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	intron	12562995	12563106	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	CDS	12563107	12563442	0.87	+	0	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	exon	12563107	12563442	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	intron	12563443	12563701	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	CDS	12563702	12563731	0.57	+	0	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	exon	12563702	12563731	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	intron	12563732	12563837	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	CDS	12563838	12563898	0.97	+	0	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	exon	12563838	12563898	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	intron	12563899	12563985	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	CDS	12563986	12565013	1	+	2	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	exon	12563986	12565013	.	+	.	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
Phchi.S3	AUGUSTUS	stop_codon	12565014	12565016	.	+	0	transcript_id "Phchi.S3G170700.t1"; gene_id "Phchi.S3G170700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9949.t1 is derived from g7125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44625729	44627712	.	+	.	Phchi.S1G710800
Phchi.S1	AUGUSTUS	transcript	44625729	44627712	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	start_codon	44625729	44625731	.	+	0	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	CDS	44625729	44626490	0.93	+	0	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	exon	44625729	44626490	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	intron	44626491	44626573	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	CDS	44626574	44626725	1	+	0	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	exon	44626574	44626725	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	intron	44626726	44626816	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	CDS	44626817	44627145	1	+	1	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	exon	44626817	44627145	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	intron	44627146	44627272	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	CDS	44627273	44627388	0.62	+	2	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	exon	44627273	44627388	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	intron	44627389	44627592	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	CDS	44627593	44627712	0.56	+	0	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	exon	44627593	44627712	.	+	.	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
Phchi.S1	AUGUSTUS	stop_codon	44627713	44627715	.	+	0	transcript_id "Phchi.S1G710800.t1"; gene_id "Phchi.S1G710800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5304.t1 is derived from g2474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16159194	16161464	.	+	.	Phchi.S1G246300
Phchi.S1	AUGUSTUS	transcript	16159194	16161464	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	start_codon	16159194	16159196	.	+	0	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16159194	16159213	0.47	+	0	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16159194	16159213	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16159214	16159363	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16159364	16159429	1	+	1	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16159364	16159429	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16159430	16159520	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16159521	16159765	1	+	1	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16159521	16159765	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16159766	16159902	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16159903	16160129	0.49	+	2	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16159903	16160129	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16160130	16160253	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16160254	16160350	0.69	+	0	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16160254	16160350	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16160351	16160440	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16160441	16160506	1	+	2	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16160441	16160506	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16160507	16160586	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16160587	16160632	0.99	+	2	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16160587	16160632	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16160633	16160715	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16160716	16160862	1	+	1	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16160716	16160862	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16160863	16160947	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16160948	16161086	1	+	1	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16160948	16161086	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	intron	16161087	16161176	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	CDS	16161177	16161464	1	+	0	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	exon	16161177	16161464	.	+	.	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
Phchi.S1	AUGUSTUS	stop_codon	16161465	16161467	.	+	0	transcript_id "Phchi.S1G246300.t1"; gene_id "Phchi.S1G246300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12821.t1 is derived from g11286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2563485	2568479	.	+	.	Phchi.S3G014000
Phchi.S3	AUGUSTUS	transcript	2563485	2568479	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	start_codon	2563485	2563487	.	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2563485	2563699	0.86	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2563485	2563699	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2563700	2563784	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2563785	2563846	1	+	1	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2563785	2563846	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2563847	2563938	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2563939	2564307	1	+	2	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2563939	2564307	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2564308	2564465	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2564466	2564554	1	+	2	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2564466	2564554	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2564555	2564669	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2564670	2564988	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2564670	2564988	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2564989	2565141	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2565142	2565194	1	+	2	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2565142	2565194	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2565195	2565407	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2565408	2565631	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2565408	2565631	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2565632	2565713	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2565714	2565801	1	+	1	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2565714	2565801	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2565802	2565891	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2565892	2566005	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2565892	2566005	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2566006	2566117	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2566118	2566216	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2566118	2566216	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2566217	2566352	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2566353	2566547	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2566353	2566547	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2566548	2566633	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2566634	2566716	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2566634	2566716	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2566717	2566815	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2566816	2567044	1	+	1	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2566816	2567044	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2567045	2567250	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2567251	2567411	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2567251	2567411	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2567412	2567503	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2567504	2567639	0.99	+	1	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2567504	2567639	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2567640	2567747	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2567748	2567828	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2567748	2567828	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2567829	2568027	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2568028	2568114	1	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2568028	2568114	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	intron	2568115	2568200	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	CDS	2568201	2568479	0.98	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	exon	2568201	2568479	.	+	.	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
Phchi.S3	AUGUSTUS	stop_codon	2568480	2568482	.	+	0	transcript_id "Phchi.S3G014000.t1"; gene_id "Phchi.S3G014000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2419.t1 is derived from g9339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6558786	6559600	.	-	.	Phchi.S5G102800
Phchi.S5	AUGUSTUS	transcript	6558786	6559600	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	stop_codon	6558783	6558785	.	-	0	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	CDS	6558786	6558866	0.82	-	0	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	exon	6558786	6558866	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	intron	6558867	6558942	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	CDS	6558943	6558953	0.82	-	2	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	exon	6558943	6558953	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	intron	6558954	6559054	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	CDS	6559055	6559165	0.83	-	2	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	exon	6559055	6559165	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	intron	6559166	6559476	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	CDS	6559477	6559600	0.84	-	0	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	exon	6559477	6559600	.	-	.	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
Phchi.S5	AUGUSTUS	start_codon	6559598	6559600	.	-	0	transcript_id "Phchi.S5G102800.t1"; gene_id "Phchi.S5G102800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11965.t1 is derived from g7640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	228554	234648	.	-	.	Phchi.S2G004500
Phchi.S2	AUGUSTUS	transcript	228554	234648	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	stop_codon	228551	228553	.	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	228554	228596	1	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	228554	228596	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	228597	228685	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	228686	228913	1	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	228686	228913	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	228914	229032	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	229033	229284	1	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	229033	229284	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	229285	229365	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	229366	229583	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	229366	229583	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	229584	229708	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	229709	229879	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	229709	229879	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	229880	230073	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	230074	230183	1	-	2	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	230074	230183	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	230184	230267	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	230268	230437	1	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	230268	230437	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	230438	230580	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	230581	230789	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	230581	230789	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	230790	230919	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	230920	231009	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	230920	231009	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	231010	231095	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	231096	231235	1	-	2	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	231096	231235	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	231236	231308	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	231309	231345	0.84	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	231309	231345	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	231346	231398	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	231399	231415	1	-	2	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	231399	231415	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	231416	231654	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	231655	231764	1	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	231655	231764	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	231765	231912	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	231913	232037	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	231913	232037	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	232038	232180	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	232181	232451	0.64	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	232181	232451	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	232452	232587	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	232588	232854	1	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	232588	232854	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	232855	232962	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	232963	233201	0.98	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	232963	233201	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	233202	233372	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	233373	233469	0.68	-	1	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	233373	233469	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	233470	233590	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	233591	233607	0.64	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	233591	233607	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	233608	233811	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	233812	234048	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	233812	234048	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	intron	234049	234204	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	CDS	234205	234648	1	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	exon	234205	234648	.	-	.	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
Phchi.S2	AUGUSTUS	start_codon	234646	234648	.	-	0	transcript_id "Phchi.S2G004500.t1"; gene_id "Phchi.S2G004500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9261.t1 is derived from g6436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40629697	40630520	.	+	.	Phchi.S1G642000
Phchi.S1	AUGUSTUS	transcript	40629697	40630520	.	+	.	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	start_codon	40629697	40629699	.	+	0	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	CDS	40629697	40630208	0.52	+	0	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	exon	40629697	40630208	.	+	.	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	intron	40630209	40630396	.	+	.	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	CDS	40630397	40630520	0.6	+	1	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	exon	40630397	40630520	.	+	.	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
Phchi.S1	AUGUSTUS	stop_codon	40630521	40630523	.	+	0	transcript_id "Phchi.S1G642000.t1"; gene_id "Phchi.S1G642000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5758.t1 is derived from g2928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18827959	18829385	.	-	.	Phchi.S1G291700
Phchi.S1	AUGUSTUS	transcript	18827959	18829385	.	-	.	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	stop_codon	18827956	18827958	.	-	0	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	CDS	18827959	18828129	0.97	-	0	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	exon	18827959	18828129	.	-	.	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	intron	18828130	18828305	.	-	.	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	CDS	18828306	18829385	0.73	-	0	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	exon	18828306	18829385	.	-	.	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
Phchi.S1	AUGUSTUS	start_codon	18829383	18829385	.	-	0	transcript_id "Phchi.S1G291700.t1"; gene_id "Phchi.S1G291700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg708.t1 is derived from g10490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5012732	5015419	.	-	.	Phchi.S6G066700
Phchi.S6	AUGUSTUS	transcript	5012732	5015419	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	stop_codon	5012729	5012731	.	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5012732	5012833	0.96	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5012732	5012833	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5012834	5012944	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5012945	5013065	0.92	-	1	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5012945	5013065	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5013066	5013152	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5013153	5013240	0.95	-	2	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5013153	5013240	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5013241	5013379	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5013380	5013431	1	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5013380	5013431	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5013432	5013537	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5013538	5013642	1	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5013538	5013642	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5013643	5013762	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5013763	5013906	1	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5013763	5013906	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5013907	5013994	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5013995	5014087	1	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5013995	5014087	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5014088	5014221	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5014222	5014253	1	-	2	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5014222	5014253	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5014254	5014366	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5014367	5014489	0.99	-	2	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5014367	5014489	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5014490	5014593	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5014594	5014645	0.95	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5014594	5014645	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5014646	5014726	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5014727	5014834	1	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5014727	5014834	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5014835	5014915	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5014916	5015059	1	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5014916	5015059	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	intron	5015060	5015143	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	CDS	5015144	5015419	0.82	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	exon	5015144	5015419	.	-	.	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
Phchi.S6	AUGUSTUS	start_codon	5015417	5015419	.	-	0	transcript_id "Phchi.S6G066700.t1"; gene_id "Phchi.S6G066700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6158.t1 is derived from g3329.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21230900	21231795	.	+	.	Phchi.S1G331700
Phchi.S1	AUGUSTUS	transcript	21230900	21231795	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	start_codon	21230900	21230902	.	+	0	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21230900	21231082	0.47	+	0	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21230900	21231082	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	intron	21231083	21231236	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21231237	21231243	0.95	+	0	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21231237	21231243	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	intron	21231244	21231440	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21231441	21231582	0.95	+	2	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21231441	21231582	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	intron	21231583	21231776	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21231777	21231795	0.95	+	1	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21231777	21231795	.	+	.	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	stop_codon	21231796	21231798	.	+	0	transcript_id "Phchi.S1G331700.t1"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	transcript	21230900	21231795	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	start_codon	21230900	21230902	.	+	0	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21230900	21231082	0.4	+	0	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21230900	21231082	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	intron	21231083	21231236	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21231237	21231243	0.97	+	0	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21231237	21231243	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	intron	21231244	21231440	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21231441	21231582	0.97	+	2	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21231441	21231582	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	intron	21231583	21231773	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	CDS	21231774	21231795	0.97	+	1	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	exon	21231774	21231795	.	+	.	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
Phchi.S1	AUGUSTUS	stop_codon	21231796	21231798	.	+	0	transcript_id "Phchi.S1G331700.t2"; gene_id "Phchi.S1G331700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13843.t1 is derived from g12310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9162271	9163118	.	+	.	Phchi.S3G116200
Phchi.S3	AUGUSTUS	transcript	9162271	9163118	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	start_codon	9162271	9162273	.	+	0	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	CDS	9162271	9162422	0.79	+	0	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	exon	9162271	9162422	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	intron	9162423	9162504	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	CDS	9162505	9162627	1	+	1	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	exon	9162505	9162627	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	intron	9162628	9162763	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	CDS	9162764	9162824	1	+	1	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	exon	9162764	9162824	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	intron	9162825	9162914	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	CDS	9162915	9163118	1	+	0	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	exon	9162915	9163118	.	+	.	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
Phchi.S3	AUGUSTUS	stop_codon	9163119	9163121	.	+	0	transcript_id "Phchi.S3G116200.t1"; gene_id "Phchi.S3G116200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10463.t1 is derived from g14512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	485740	486966	.	+	.	Phchi.S4G004500
Phchi.S4	AUGUSTUS	transcript	485740	486966	.	+	.	transcript_id "Phchi.S4G004500.t1"; gene_id "Phchi.S4G004500"
Phchi.S4	AUGUSTUS	start_codon	485740	485742	.	+	0	transcript_id "Phchi.S4G004500.t1"; gene_id "Phchi.S4G004500"
Phchi.S4	AUGUSTUS	CDS	485740	486966	0.46	+	0	transcript_id "Phchi.S4G004500.t1"; gene_id "Phchi.S4G004500"
Phchi.S4	AUGUSTUS	exon	485740	486966	.	+	.	transcript_id "Phchi.S4G004500.t1"; gene_id "Phchi.S4G004500"
Phchi.S4	AUGUSTUS	stop_codon	486967	486969	.	+	0	transcript_id "Phchi.S4G004500.t1"; gene_id "Phchi.S4G004500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7995.t1 is derived from g5170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32343939	32344849	.	+	.	Phchi.S1G515400
Phchi.S1	AUGUSTUS	transcript	32343939	32344849	.	+	.	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	start_codon	32343939	32343941	.	+	0	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	CDS	32343939	32344049	0.99	+	0	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	exon	32343939	32344049	.	+	.	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	intron	32344050	32344205	.	+	.	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	CDS	32344206	32344210	1	+	0	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	exon	32344206	32344210	.	+	.	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	intron	32344211	32344290	.	+	.	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	CDS	32344291	32344849	0.94	+	1	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	exon	32344291	32344849	.	+	.	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
Phchi.S1	AUGUSTUS	stop_codon	32344850	32344852	.	+	0	transcript_id "Phchi.S1G515400.t1"; gene_id "Phchi.S1G515400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5639.t1 is derived from g2809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18009909	18012634	.	+	.	Phchi.S1G279800
Phchi.S1	AUGUSTUS	transcript	18009909	18012634	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	start_codon	18009909	18009911	.	+	0	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18009909	18010166	0.99	+	0	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18009909	18010166	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18010167	18010410	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18010411	18010559	1	+	0	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18010411	18010559	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18010560	18010644	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18010645	18010840	1	+	1	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18010645	18010840	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18010841	18010991	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18010992	18011202	1	+	0	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18010992	18011202	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18011203	18011338	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18011339	18011645	1	+	2	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18011339	18011645	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18011646	18011754	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18011755	18012126	1	+	1	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18011755	18012126	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18012127	18012211	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18012212	18012289	1	+	1	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18012212	18012289	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	intron	18012290	18012390	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	CDS	18012391	18012634	0.99	+	1	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	exon	18012391	18012634	.	+	.	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
Phchi.S1	AUGUSTUS	stop_codon	18012635	18012637	.	+	0	transcript_id "Phchi.S1G279800.t1"; gene_id "Phchi.S1G279800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2559.t1 is derived from g9479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7355743	7357310	.	+	.	Phchi.S5G116800
Phchi.S5	AUGUSTUS	transcript	7355743	7357310	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	start_codon	7355743	7355745	.	+	0	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7355743	7356033	0.52	+	0	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7355743	7356033	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7356034	7356446	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356447	7356516	0.96	+	0	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356447	7356516	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7356517	7356708	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356709	7356761	0.96	+	2	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356709	7356761	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7356762	7356955	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356956	7357025	0.83	+	0	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356956	7357025	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7357026	7357116	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7357117	7357172	0.92	+	2	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7357117	7357172	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7357173	7357259	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7357260	7357310	0.94	+	0	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7357260	7357310	.	+	.	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	stop_codon	7357311	7357313	.	+	0	transcript_id "Phchi.S5G116800.t1"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	transcript	7356084	7357310	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	start_codon	7356084	7356086	.	+	0	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356084	7356344	0.4	+	0	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356084	7356344	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7356345	7356446	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356447	7356516	0.94	+	0	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356447	7356516	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7356517	7356708	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356709	7356761	0.92	+	2	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356709	7356761	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7356762	7356955	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7356956	7357025	0.85	+	0	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7356956	7357025	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7357026	7357116	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7357117	7357172	0.87	+	2	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7357117	7357172	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	intron	7357173	7357259	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	CDS	7357260	7357310	0.9	+	0	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	exon	7357260	7357310	.	+	.	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
Phchi.S5	AUGUSTUS	stop_codon	7357311	7357313	.	+	0	transcript_id "Phchi.S5G116800.t2"; gene_id "Phchi.S5G116800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15233.t1 is derived from g13701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17851882	17857022	.	+	.	Phchi.S3G255200
Phchi.S3	AUGUSTUS	transcript	17851882	17857022	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	start_codon	17851882	17851884	.	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17851882	17851977	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17851882	17851977	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17851978	17852073	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17852074	17852178	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17852074	17852178	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17852179	17852437	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17852438	17852763	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17852438	17852763	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17852764	17852969	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17852970	17853113	1	+	1	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17852970	17853113	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17853114	17853283	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17853284	17853368	1	+	1	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17853284	17853368	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17853369	17853621	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17853622	17853852	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17853622	17853852	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17853853	17854003	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17854004	17854051	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17854004	17854051	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17854052	17854132	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17854133	17854207	0.99	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17854133	17854207	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17854208	17854325	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17854326	17854422	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17854326	17854422	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17854423	17854555	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17854556	17854862	0.98	+	2	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17854556	17854862	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17854863	17855110	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17855111	17855243	0.86	+	1	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17855111	17855243	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17855244	17855355	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17855356	17855654	0.17	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17855356	17855654	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17855655	17855740	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17855741	17855812	0.33	+	1	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17855741	17855812	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17855813	17855996	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17855997	17856087	1	+	1	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17855997	17856087	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17856088	17856211	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17856212	17856259	0.99	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17856212	17856259	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17856260	17856363	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17856364	17856492	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17856364	17856492	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17856493	17856621	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17856622	17856699	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17856622	17856699	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	intron	17856700	17856776	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	CDS	17856777	17857022	1	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	exon	17856777	17857022	.	+	.	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
Phchi.S3	AUGUSTUS	stop_codon	17857023	17857025	.	+	0	transcript_id "Phchi.S3G255200.t1"; gene_id "Phchi.S3G255200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13824.t1 is derived from g12291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9081795	9082250	.	-	.	Phchi.S3G114300
Phchi.S3	AUGUSTUS	transcript	9081795	9082250	.	-	.	transcript_id "Phchi.S3G114300.t1"; gene_id "Phchi.S3G114300"
Phchi.S3	AUGUSTUS	stop_codon	9081792	9081794	.	-	0	transcript_id "Phchi.S3G114300.t1"; gene_id "Phchi.S3G114300"
Phchi.S3	AUGUSTUS	CDS	9081795	9082250	0.46	-	0	transcript_id "Phchi.S3G114300.t1"; gene_id "Phchi.S3G114300"
Phchi.S3	AUGUSTUS	exon	9081795	9082250	.	-	.	transcript_id "Phchi.S3G114300.t1"; gene_id "Phchi.S3G114300"
Phchi.S3	AUGUSTUS	start_codon	9082248	9082250	.	-	0	transcript_id "Phchi.S3G114300.t1"; gene_id "Phchi.S3G114300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8919.t1 is derived from g6094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38669149	38670438	.	-	.	Phchi.S1G607800
Phchi.S1	AUGUSTUS	transcript	38669149	38670438	.	-	.	transcript_id "Phchi.S1G607800.t1"; gene_id "Phchi.S1G607800"
Phchi.S1	AUGUSTUS	stop_codon	38669146	38669148	.	-	0	transcript_id "Phchi.S1G607800.t1"; gene_id "Phchi.S1G607800"
Phchi.S1	AUGUSTUS	CDS	38669149	38670438	1	-	0	transcript_id "Phchi.S1G607800.t1"; gene_id "Phchi.S1G607800"
Phchi.S1	AUGUSTUS	exon	38669149	38670438	.	-	.	transcript_id "Phchi.S1G607800.t1"; gene_id "Phchi.S1G607800"
Phchi.S1	AUGUSTUS	start_codon	38670436	38670438	.	-	0	transcript_id "Phchi.S1G607800.t1"; gene_id "Phchi.S1G607800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6929.t1 is derived from g4101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26032071	26034066	.	-	.	Phchi.S1G408800
Phchi.S1	AUGUSTUS	transcript	26032071	26034066	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	stop_codon	26032068	26032070	.	-	0	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26032071	26032733	0.99	-	0	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26032071	26032733	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	intron	26032734	26032887	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26032888	26033021	1	-	2	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26032888	26033021	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	intron	26033022	26033118	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26033119	26033210	1	-	1	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26033119	26033210	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	intron	26033211	26033327	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26033328	26033374	1	-	0	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26033328	26033374	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	intron	26033375	26033460	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26033461	26033549	1	-	2	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26033461	26033549	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	intron	26033550	26033752	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26033753	26033870	1	-	0	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26033753	26033870	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	intron	26033871	26033973	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	CDS	26033974	26034066	0.82	-	0	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	exon	26033974	26034066	.	-	.	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
Phchi.S1	AUGUSTUS	start_codon	26034064	26034066	.	-	0	transcript_id "Phchi.S1G408800.t1"; gene_id "Phchi.S1G408800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3479.t1 is derived from g648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3993889	3995250	.	+	.	Phchi.S1G063800
Phchi.S1	AUGUSTUS	transcript	3993889	3995250	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	start_codon	3993889	3993891	.	+	0	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	CDS	3993889	3994032	0.51	+	0	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	exon	3993889	3994032	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	intron	3994033	3994127	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	CDS	3994128	3994301	0.45	+	0	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	exon	3994128	3994301	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	intron	3994302	3994435	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	CDS	3994436	3995027	0.47	+	0	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	exon	3994436	3995027	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	intron	3995028	3995131	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	CDS	3995132	3995250	0.42	+	2	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	exon	3995132	3995250	.	+	.	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
Phchi.S1	AUGUSTUS	stop_codon	3995251	3995253	.	+	0	transcript_id "Phchi.S1G063800.t1"; gene_id "Phchi.S1G063800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5816.t1 is derived from g2986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19091602	19092526	.	+	.	Phchi.S1G297500
Phchi.S1	AUGUSTUS	transcript	19091602	19092526	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	start_codon	19091602	19091604	.	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	CDS	19091602	19091700	0.89	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	exon	19091602	19091700	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	intron	19091701	19091800	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	CDS	19091801	19091836	1	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	exon	19091801	19091836	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	intron	19091837	19091910	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	CDS	19091911	19092048	1	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	exon	19091911	19092048	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	intron	19092049	19092140	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	CDS	19092141	19092227	1	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	exon	19092141	19092227	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	intron	19092228	19092310	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	CDS	19092311	19092358	1	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	exon	19092311	19092358	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	intron	19092359	19092448	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	CDS	19092449	19092526	0.88	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	exon	19092449	19092526	.	+	.	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
Phchi.S1	AUGUSTUS	stop_codon	19092527	19092529	.	+	0	transcript_id "Phchi.S1G297500.t1"; gene_id "Phchi.S1G297500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1577.t1 is derived from g8496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1852023	1853547	.	-	.	Phchi.S5G018600
Phchi.S5	AUGUSTUS	transcript	1852023	1853547	.	-	.	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	stop_codon	1852020	1852022	.	-	0	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	CDS	1852023	1852385	0.97	-	0	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	exon	1852023	1852385	.	-	.	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	intron	1852386	1852545	.	-	.	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	CDS	1852546	1852780	0.62	-	1	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	exon	1852546	1852780	.	-	.	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	intron	1852781	1852999	.	-	.	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	CDS	1853000	1853547	0.71	-	0	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	exon	1853000	1853547	.	-	.	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
Phchi.S5	AUGUSTUS	start_codon	1853545	1853547	.	-	0	transcript_id "Phchi.S5G018600.t1"; gene_id "Phchi.S5G018600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6056.t1 is derived from g3227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20666338	20666763	.	+	.	Phchi.S1G321500
Phchi.S1	AUGUSTUS	transcript	20666338	20666763	.	+	.	transcript_id "Phchi.S1G321500.t1"; gene_id "Phchi.S1G321500"
Phchi.S1	AUGUSTUS	start_codon	20666338	20666340	.	+	0	transcript_id "Phchi.S1G321500.t1"; gene_id "Phchi.S1G321500"
Phchi.S1	AUGUSTUS	CDS	20666338	20666763	0.62	+	0	transcript_id "Phchi.S1G321500.t1"; gene_id "Phchi.S1G321500"
Phchi.S1	AUGUSTUS	exon	20666338	20666763	.	+	.	transcript_id "Phchi.S1G321500.t1"; gene_id "Phchi.S1G321500"
Phchi.S1	AUGUSTUS	stop_codon	20666764	20666766	.	+	0	transcript_id "Phchi.S1G321500.t1"; gene_id "Phchi.S1G321500"
# This transcript jg1421.t2 is derived from g8340.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1421.t3 is derived from g8340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1422.t1 is derived from g8341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	780825	782733	.	+	.	Phchi.S5G003100
Phchi.S5	AUGUSTUS	transcript	780825	782733	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	start_codon	780825	780827	.	+	0	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	CDS	780825	781094	0.65	+	0	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	exon	780825	781094	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	intron	781095	781213	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	CDS	781214	782438	0.77	+	0	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	exon	781214	782438	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	intron	782439	782536	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	CDS	782537	782579	0.95	+	2	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	exon	782537	782579	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	intron	782580	782669	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	CDS	782670	782733	1	+	1	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	exon	782670	782733	.	+	.	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
Phchi.S5	AUGUSTUS	stop_codon	782734	782736	.	+	0	transcript_id "Phchi.S5G003100.t1"; gene_id "Phchi.S5G003100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14107.t1 is derived from g12574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10883321	10884452	.	-	.	Phchi.S3G142600
Phchi.S3	AUGUSTUS	transcript	10883321	10884452	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	stop_codon	10883318	10883320	.	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	CDS	10883321	10883371	1	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	exon	10883321	10883371	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	intron	10883372	10883458	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	CDS	10883459	10883539	1	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	exon	10883459	10883539	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	intron	10883540	10883636	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	CDS	10883637	10883754	1	-	1	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	exon	10883637	10883754	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	intron	10883755	10883877	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	CDS	10883878	10883918	1	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	exon	10883878	10883918	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	intron	10883919	10884011	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	CDS	10884012	10884107	1	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	exon	10884012	10884107	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	intron	10884108	10884224	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	CDS	10884225	10884452	1	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	exon	10884225	10884452	.	-	.	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
Phchi.S3	AUGUSTUS	start_codon	10884450	10884452	.	-	0	transcript_id "Phchi.S3G142600.t1"; gene_id "Phchi.S3G142600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8551.t1 is derived from g5726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36582611	36584391	.	+	.	Phchi.S1G571000
Phchi.S1	AUGUSTUS	transcript	36582611	36584391	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	start_codon	36582611	36582613	.	+	0	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36582611	36582954	0.78	+	0	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36582611	36582954	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	intron	36582955	36583065	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36583066	36583139	0.57	+	1	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36583066	36583139	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	intron	36583140	36583247	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36583248	36583330	0.58	+	2	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36583248	36583330	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	intron	36583331	36583425	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36583426	36583447	1	+	0	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36583426	36583447	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	intron	36583448	36583571	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36583572	36583591	1	+	2	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36583572	36583591	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	intron	36583592	36583767	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36583768	36583923	1	+	0	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36583768	36583923	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	intron	36583924	36584031	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	CDS	36584032	36584391	1	+	0	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	exon	36584032	36584391	.	+	.	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
Phchi.S1	AUGUSTUS	stop_codon	36584392	36584394	.	+	0	transcript_id "Phchi.S1G571000.t1"; gene_id "Phchi.S1G571000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4622.t1 is derived from g1792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11446775	11448944	.	-	.	Phchi.S1G178100
Phchi.S1	AUGUSTUS	transcript	11446775	11448944	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	stop_codon	11446772	11446774	.	-	0	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11446775	11446895	1	-	1	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11446775	11446895	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	intron	11446896	11447054	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11447055	11447230	0.84	-	0	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11447055	11447230	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	intron	11447231	11447309	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11447310	11447423	0.84	-	0	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11447310	11447423	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	intron	11447424	11447507	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11447508	11447700	1	-	1	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11447508	11447700	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	intron	11447701	11447784	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11447785	11447977	1	-	2	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11447785	11447977	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	intron	11447978	11448056	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11448057	11448283	0.97	-	1	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11448057	11448283	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	intron	11448284	11448387	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	CDS	11448388	11448944	0.77	-	0	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	exon	11448388	11448944	.	-	.	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
Phchi.S1	AUGUSTUS	start_codon	11448942	11448944	.	-	0	transcript_id "Phchi.S1G178100.t1"; gene_id "Phchi.S1G178100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8982.t1 is derived from g6157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38971014	38971940	.	+	.	Phchi.S1G614100
Phchi.S1	AUGUSTUS	transcript	38971014	38971940	.	+	.	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	start_codon	38971014	38971016	.	+	0	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	CDS	38971014	38971020	0.98	+	0	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	exon	38971014	38971020	.	+	.	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	intron	38971021	38971137	.	+	.	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	CDS	38971138	38971940	0.98	+	2	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	exon	38971138	38971940	.	+	.	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
Phchi.S1	AUGUSTUS	stop_codon	38971941	38971943	.	+	0	transcript_id "Phchi.S1G614100.t1"; gene_id "Phchi.S1G614100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5779.t1 is derived from g2949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18908873	18912112	.	+	.	Phchi.S1G293800
Phchi.S1	AUGUSTUS	transcript	18908873	18912112	.	+	.	transcript_id "Phchi.S1G293800.t1"; gene_id "Phchi.S1G293800"
Phchi.S1	AUGUSTUS	start_codon	18908873	18908875	.	+	0	transcript_id "Phchi.S1G293800.t1"; gene_id "Phchi.S1G293800"
Phchi.S1	AUGUSTUS	CDS	18908873	18912112	1	+	0	transcript_id "Phchi.S1G293800.t1"; gene_id "Phchi.S1G293800"
Phchi.S1	AUGUSTUS	exon	18908873	18912112	.	+	.	transcript_id "Phchi.S1G293800.t1"; gene_id "Phchi.S1G293800"
Phchi.S1	AUGUSTUS	stop_codon	18912113	18912115	.	+	0	transcript_id "Phchi.S1G293800.t1"; gene_id "Phchi.S1G293800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2245.t1 is derived from g9165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5629401	5635181	.	-	.	Phchi.S5G085400
Phchi.S5	AUGUSTUS	transcript	5629401	5635181	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	stop_codon	5629398	5629400	.	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5629401	5629546	0.99	-	2	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5629401	5629546	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5629547	5629634	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5629635	5629874	1	-	2	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5629635	5629874	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5629875	5629954	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5629955	5630018	1	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5629955	5630018	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5630019	5630202	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5630203	5630508	1	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5630203	5630508	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5630509	5630643	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5630644	5630858	1	-	2	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5630644	5630858	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5630859	5630948	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5630949	5631240	0.73	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5630949	5631240	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5631241	5631397	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5631398	5631562	1	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5631398	5631562	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5631563	5631702	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5631703	5631850	0.49	-	1	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5631703	5631850	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5631851	5631953	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5631954	5631969	1	-	2	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5631954	5631969	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5631970	5632064	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5632065	5632413	1	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5632065	5632413	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5632414	5632511	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5632512	5632598	1	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5632512	5632598	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5632599	5632670	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5632671	5632991	1	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5632671	5632991	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5632992	5633115	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5633116	5634143	0.38	-	2	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5633116	5634143	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	intron	5634144	5634220	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	CDS	5634221	5635181	0.37	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	exon	5634221	5635181	.	-	.	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
Phchi.S5	AUGUSTUS	start_codon	5635179	5635181	.	-	0	transcript_id "Phchi.S5G085400.t1"; gene_id "Phchi.S5G085400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9919.t1 is derived from g7095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44468496	44468702	.	+	.	Phchi.S1G707800
Phchi.S1	AUGUSTUS	transcript	44468496	44468702	.	+	.	transcript_id "Phchi.S1G707800.t1"; gene_id "Phchi.S1G707800"
Phchi.S1	AUGUSTUS	start_codon	44468496	44468498	.	+	0	transcript_id "Phchi.S1G707800.t1"; gene_id "Phchi.S1G707800"
Phchi.S1	AUGUSTUS	CDS	44468496	44468702	0.92	+	0	transcript_id "Phchi.S1G707800.t1"; gene_id "Phchi.S1G707800"
Phchi.S1	AUGUSTUS	exon	44468496	44468702	.	+	.	transcript_id "Phchi.S1G707800.t1"; gene_id "Phchi.S1G707800"
Phchi.S1	AUGUSTUS	stop_codon	44468703	44468705	.	+	0	transcript_id "Phchi.S1G707800.t1"; gene_id "Phchi.S1G707800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8481.t1 is derived from g5656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36143106	36143459	.	-	.	Phchi.S1G564000
Phchi.S1	AUGUSTUS	transcript	36143106	36143459	.	-	.	transcript_id "Phchi.S1G564000.t1"; gene_id "Phchi.S1G564000"
Phchi.S1	AUGUSTUS	stop_codon	36143103	36143105	.	-	0	transcript_id "Phchi.S1G564000.t1"; gene_id "Phchi.S1G564000"
Phchi.S1	AUGUSTUS	CDS	36143106	36143459	0.74	-	0	transcript_id "Phchi.S1G564000.t1"; gene_id "Phchi.S1G564000"
Phchi.S1	AUGUSTUS	exon	36143106	36143459	.	-	.	transcript_id "Phchi.S1G564000.t1"; gene_id "Phchi.S1G564000"
Phchi.S1	AUGUSTUS	start_codon	36143457	36143459	.	-	0	transcript_id "Phchi.S1G564000.t1"; gene_id "Phchi.S1G564000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5666.t1 is derived from g2836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18197698	18203397	.	+	.	Phchi.S1G282500
Phchi.S1	AUGUSTUS	transcript	18197698	18203397	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	start_codon	18197698	18197700	.	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18197698	18197871	0.98	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18197698	18197871	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18197872	18197948	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18197949	18198040	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18197949	18198040	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18198041	18198291	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18198292	18198463	1	+	1	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18198292	18198463	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18198464	18198559	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18198560	18198614	0.85	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18198560	18198614	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18198615	18198730	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18198731	18198849	0.97	+	2	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18198731	18198849	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18198850	18198954	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18198955	18199010	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18198955	18199010	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18199011	18199168	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18199169	18199217	1	+	1	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18199169	18199217	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18199218	18199335	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18199336	18199470	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18199336	18199470	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18199471	18199635	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18199636	18199767	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18199636	18199767	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18199768	18200045	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18200046	18200129	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18200046	18200129	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18200130	18200218	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18200219	18200317	0.95	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18200219	18200317	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18200318	18200430	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18200431	18200522	0.94	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18200431	18200522	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18200523	18200624	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18200625	18200697	0.99	+	1	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18200625	18200697	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18200698	18200769	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18200770	18200922	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18200770	18200922	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18200923	18201009	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18201010	18201123	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18201010	18201123	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18201124	18201233	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18201234	18201287	0.95	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18201234	18201287	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18201288	18201459	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18201460	18201543	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18201460	18201543	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18201544	18201695	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18201696	18201770	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18201696	18201770	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18201771	18201875	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18201876	18202034	0.98	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18201876	18202034	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18202035	18202145	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18202146	18202271	0.98	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18202146	18202271	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18202272	18202395	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18202396	18202503	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18202396	18202503	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18202504	18202588	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18202589	18202651	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18202589	18202651	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18202652	18202752	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18202753	18202827	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18202753	18202827	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18202828	18202980	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18202981	18203192	1	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18202981	18203192	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	intron	18203193	18203273	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	CDS	18203274	18203397	1	+	1	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	exon	18203274	18203397	.	+	.	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
Phchi.S1	AUGUSTUS	stop_codon	18203398	18203400	.	+	0	transcript_id "Phchi.S1G282500.t1"; gene_id "Phchi.S1G282500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10785.t1 is derived from g14835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2107188	2109620	.	+	.	Phchi.S4G036700
Phchi.S4	AUGUSTUS	transcript	2107188	2109620	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	start_codon	2107188	2107190	.	+	0	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	CDS	2107188	2107476	0.76	+	0	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	exon	2107188	2107476	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	intron	2107477	2107776	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	CDS	2107777	2108585	0.99	+	2	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	exon	2107777	2108585	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	intron	2108586	2108683	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	CDS	2108684	2108844	1	+	0	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	exon	2108684	2108844	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	intron	2108845	2108942	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	CDS	2108943	2109201	0.95	+	1	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	exon	2108943	2109201	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	intron	2109202	2109314	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	CDS	2109315	2109620	0.99	+	0	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	exon	2109315	2109620	.	+	.	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
Phchi.S4	AUGUSTUS	stop_codon	2109621	2109623	.	+	0	transcript_id "Phchi.S4G036700.t1"; gene_id "Phchi.S4G036700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7337.t1 is derived from g4509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28570374	28571161	.	+	.	Phchi.S1G449600
Phchi.S1	AUGUSTUS	transcript	28570374	28571161	.	+	.	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	start_codon	28570374	28570376	.	+	0	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28570374	28570534	0.6	+	0	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28570374	28570534	.	+	.	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	intron	28570535	28570855	.	+	.	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28570856	28571023	0.97	+	1	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28570856	28571023	.	+	.	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	intron	28571024	28571121	.	+	.	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28571122	28571161	0.8	+	1	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28571122	28571161	.	+	.	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	stop_codon	28571162	28571164	.	+	0	transcript_id "Phchi.S1G449600.t1"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	transcript	28570439	28571161	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	start_codon	28570439	28570441	.	+	0	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28570439	28570534	0.99	+	0	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28570439	28570534	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	intron	28570535	28570634	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28570635	28570720	0.66	+	0	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28570635	28570720	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	intron	28570721	28570855	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28570856	28571023	0.89	+	1	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28570856	28571023	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	intron	28571024	28571121	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	CDS	28571122	28571161	0.79	+	1	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	exon	28571122	28571161	.	+	.	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
Phchi.S1	AUGUSTUS	stop_codon	28571162	28571164	.	+	0	transcript_id "Phchi.S1G449600.t2"; gene_id "Phchi.S1G449600"
# This transcript jg14860.t2 is derived from g13328.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14861.t1 is derived from g13329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15091475	15092386	.	+	.	Phchi.S3G218000
Phchi.S3	AUGUSTUS	transcript	15091475	15092386	.	+	.	transcript_id "Phchi.S3G218000.t1"; gene_id "Phchi.S3G218000"
Phchi.S3	AUGUSTUS	start_codon	15091475	15091477	.	+	0	transcript_id "Phchi.S3G218000.t1"; gene_id "Phchi.S3G218000"
Phchi.S3	AUGUSTUS	CDS	15091475	15092386	1	+	0	transcript_id "Phchi.S3G218000.t1"; gene_id "Phchi.S3G218000"
Phchi.S3	AUGUSTUS	exon	15091475	15092386	.	+	.	transcript_id "Phchi.S3G218000.t1"; gene_id "Phchi.S3G218000"
Phchi.S3	AUGUSTUS	stop_codon	15092387	15092389	.	+	0	transcript_id "Phchi.S3G218000.t1"; gene_id "Phchi.S3G218000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7578.t1 is derived from g4752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30134880	30135300	.	-	.	Phchi.S1G473700
Phchi.S1	AUGUSTUS	transcript	30134880	30135300	.	-	.	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	stop_codon	30134877	30134879	.	-	0	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	CDS	30134880	30134992	0.68	-	2	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	exon	30134880	30134992	.	-	.	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	intron	30134993	30135212	.	-	.	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	CDS	30135213	30135300	0.96	-	0	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	exon	30135213	30135300	.	-	.	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
Phchi.S1	AUGUSTUS	start_codon	30135298	30135300	.	-	0	transcript_id "Phchi.S1G473700.t1"; gene_id "Phchi.S1G473700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12557.t1 is derived from g8234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34747400	34749831	.	-	.	Phchi.S2G063700
Phchi.S2	AUGUSTUS	transcript	34747400	34749831	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	stop_codon	34747397	34747399	.	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34747400	34747763	0.91	-	1	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34747400	34747763	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34747764	34747856	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34747857	34747963	1	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34747857	34747963	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34747964	34748047	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34748048	34748410	0.99	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34748048	34748410	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34748411	34748547	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34748548	34748715	1	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34748548	34748715	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34748716	34748794	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34748795	34749016	1	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34748795	34749016	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34749017	34749175	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34749176	34749415	0.99	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34749176	34749415	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34749416	34749532	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34749533	34749612	1	-	2	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34749533	34749612	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	intron	34749613	34749803	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	CDS	34749804	34749831	0.88	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	exon	34749804	34749831	.	-	.	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
Phchi.S2	AUGUSTUS	start_codon	34749829	34749831	.	-	0	transcript_id "Phchi.S2G063700.t1"; gene_id "Phchi.S2G063700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7044.t1 is derived from g4216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26574867	26575427	.	+	.	Phchi.S1G420300
Phchi.S1	AUGUSTUS	transcript	26574867	26575427	.	+	.	transcript_id "Phchi.S1G420300.t1"; gene_id "Phchi.S1G420300"
Phchi.S1	AUGUSTUS	start_codon	26574867	26574869	.	+	0	transcript_id "Phchi.S1G420300.t1"; gene_id "Phchi.S1G420300"
Phchi.S1	AUGUSTUS	CDS	26574867	26575427	0.45	+	0	transcript_id "Phchi.S1G420300.t1"; gene_id "Phchi.S1G420300"
Phchi.S1	AUGUSTUS	exon	26574867	26575427	.	+	.	transcript_id "Phchi.S1G420300.t1"; gene_id "Phchi.S1G420300"
Phchi.S1	AUGUSTUS	stop_codon	26575428	26575430	.	+	0	transcript_id "Phchi.S1G420300.t1"; gene_id "Phchi.S1G420300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9291.t1 is derived from g6466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40784138	40786450	.	+	.	Phchi.S1G645000
Phchi.S1	AUGUSTUS	transcript	40784138	40786450	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	start_codon	40784138	40784140	.	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40784138	40784538	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40784138	40784538	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40784539	40784624	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40784625	40784730	1	+	1	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40784625	40784730	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40784731	40784809	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40784810	40785026	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40784810	40785026	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40785027	40785104	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40785105	40785226	1	+	2	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40785105	40785226	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40785227	40785352	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40785353	40785451	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40785353	40785451	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40785452	40785545	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40785546	40785599	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40785546	40785599	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40785600	40785700	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40785701	40785799	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40785701	40785799	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40785800	40785887	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40785888	40785989	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40785888	40785989	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	intron	40785990	40786069	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	CDS	40786070	40786450	1	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	exon	40786070	40786450	.	+	.	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
Phchi.S1	AUGUSTUS	stop_codon	40786451	40786453	.	+	0	transcript_id "Phchi.S1G645000.t1"; gene_id "Phchi.S1G645000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg942.t1 is derived from g10724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6565700	6566539	.	-	.	Phchi.S6G090100
Phchi.S6	AUGUSTUS	transcript	6565700	6566539	.	-	.	transcript_id "Phchi.S6G090100.t1"; gene_id "Phchi.S6G090100"
Phchi.S6	AUGUSTUS	stop_codon	6565697	6565699	.	-	0	transcript_id "Phchi.S6G090100.t1"; gene_id "Phchi.S6G090100"
Phchi.S6	AUGUSTUS	CDS	6565700	6566539	0.82	-	0	transcript_id "Phchi.S6G090100.t1"; gene_id "Phchi.S6G090100"
Phchi.S6	AUGUSTUS	exon	6565700	6566539	.	-	.	transcript_id "Phchi.S6G090100.t1"; gene_id "Phchi.S6G090100"
Phchi.S6	AUGUSTUS	start_codon	6566537	6566539	.	-	0	transcript_id "Phchi.S6G090100.t1"; gene_id "Phchi.S6G090100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15317.t1 is derived from g13785.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18368035	18369812	.	+	.	Phchi.S3G263600
Phchi.S3	AUGUSTUS	transcript	18368035	18369812	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	start_codon	18368035	18368037	.	+	0	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368035	18368157	1	+	0	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368035	18368157	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368158	18368239	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368240	18368339	1	+	0	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368240	18368339	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368340	18368423	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368424	18368654	1	+	2	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368424	18368654	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368655	18368770	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368771	18368884	1	+	2	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368771	18368884	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368885	18368974	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368975	18369107	1	+	2	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368975	18369107	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18369108	18369187	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18369188	18369812	1	+	1	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18369188	18369812	.	+	.	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	stop_codon	18369813	18369815	.	+	0	transcript_id "Phchi.S3G263600.t1"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	transcript	18368035	18369812	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	start_codon	18368035	18368037	.	+	0	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368035	18368157	1	+	0	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368035	18368157	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368158	18368239	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368240	18368339	1	+	0	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368240	18368339	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368340	18368423	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368424	18368654	1	+	2	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368424	18368654	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368655	18368770	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368771	18368884	0.97	+	2	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368771	18368884	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18368885	18368977	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18368978	18369107	0.67	+	2	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18368978	18369107	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	intron	18369108	18369187	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	CDS	18369188	18369812	1	+	1	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	exon	18369188	18369812	.	+	.	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
Phchi.S3	AUGUSTUS	stop_codon	18369813	18369815	.	+	0	transcript_id "Phchi.S3G263600.t2"; gene_id "Phchi.S3G263600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3651.t1 is derived from g820.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4971002	4974245	.	-	.	Phchi.S1G081000
Phchi.S1	AUGUSTUS	transcript	4971002	4974245	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	stop_codon	4970999	4971001	.	-	0	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	CDS	4971002	4971375	0.56	-	2	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	exon	4971002	4971375	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	intron	4971376	4971508	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	CDS	4971509	4971927	0.58	-	1	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	exon	4971509	4971927	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	intron	4971928	4972233	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	CDS	4972234	4972602	0.81	-	1	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	exon	4972234	4972602	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	intron	4972603	4972893	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	CDS	4972894	4973479	0.37	-	2	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	exon	4972894	4973479	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	intron	4973480	4973842	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	CDS	4973843	4974245	0.37	-	0	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	exon	4973843	4974245	.	-	.	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	start_codon	4974243	4974245	.	-	0	transcript_id "Phchi.S1G081000.t1"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	transcript	4971002	4971337	.	-	.	transcript_id "Phchi.S1G081000.t2"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	stop_codon	4970999	4971001	.	-	0	transcript_id "Phchi.S1G081000.t2"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	CDS	4971002	4971337	0.93	-	0	transcript_id "Phchi.S1G081000.t2"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	exon	4971002	4971337	.	-	.	transcript_id "Phchi.S1G081000.t2"; gene_id "Phchi.S1G081000"
Phchi.S1	AUGUSTUS	start_codon	4971335	4971337	.	-	0	transcript_id "Phchi.S1G081000.t2"; gene_id "Phchi.S1G081000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10385.t1 is derived from g7561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47489753	47493610	.	+	.	Phchi.S1G754400
Phchi.S1	AUGUSTUS	transcript	47489753	47493610	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	start_codon	47489753	47489755	.	+	0	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47489753	47489818	0.96	+	0	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47489753	47489818	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	intron	47489819	47489918	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47489919	47490510	0.73	+	0	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47489919	47490510	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	intron	47490511	47490798	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47490799	47492503	0.51	+	2	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47490799	47492503	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	intron	47492504	47493086	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47493087	47493146	0.31	+	1	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47493087	47493146	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	intron	47493147	47493250	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47493251	47493285	0.47	+	1	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47493251	47493285	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	intron	47493286	47493375	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47493376	47493452	1	+	2	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47493376	47493452	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	intron	47493453	47493598	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	CDS	47493599	47493610	1	+	0	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	exon	47493599	47493610	.	+	.	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
Phchi.S1	AUGUSTUS	stop_codon	47493611	47493613	.	+	0	transcript_id "Phchi.S1G754400.t1"; gene_id "Phchi.S1G754400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6482.t1 is derived from g3654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23206751	23207527	.	-	.	Phchi.S1G364100
Phchi.S1	AUGUSTUS	transcript	23206751	23207527	.	-	.	transcript_id "Phchi.S1G364100.t1"; gene_id "Phchi.S1G364100"
Phchi.S1	AUGUSTUS	stop_codon	23206748	23206750	.	-	0	transcript_id "Phchi.S1G364100.t1"; gene_id "Phchi.S1G364100"
Phchi.S1	AUGUSTUS	CDS	23206751	23207527	0.99	-	0	transcript_id "Phchi.S1G364100.t1"; gene_id "Phchi.S1G364100"
Phchi.S1	AUGUSTUS	exon	23206751	23207527	.	-	.	transcript_id "Phchi.S1G364100.t1"; gene_id "Phchi.S1G364100"
Phchi.S1	AUGUSTUS	start_codon	23207525	23207527	.	-	0	transcript_id "Phchi.S1G364100.t1"; gene_id "Phchi.S1G364100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4182.t1 is derived from g1351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8794056	8796475	.	-	.	Phchi.S1G134100
Phchi.S1	AUGUSTUS	transcript	8794056	8796475	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	stop_codon	8794053	8794055	.	-	0	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	CDS	8794056	8794274	1	-	0	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	exon	8794056	8794274	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	intron	8794275	8794364	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	CDS	8794365	8794536	1	-	1	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	exon	8794365	8794536	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	intron	8794537	8794618	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	CDS	8794619	8794802	1	-	2	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	exon	8794619	8794802	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	intron	8794803	8794884	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	CDS	8794885	8796475	1	-	0	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	exon	8794885	8796475	.	-	.	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
Phchi.S1	AUGUSTUS	start_codon	8796473	8796475	.	-	0	transcript_id "Phchi.S1G134100.t1"; gene_id "Phchi.S1G134100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2844.t1 is derived from g13.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6106	7975	.	-	.	Phchi.S1G000300
Phchi.S1	AUGUSTUS	transcript	6106	7975	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	stop_codon	6103	6105	.	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	6106	6276	0.99	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	6106	6276	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	6277	6410	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	6411	6456	1	-	1	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	6411	6456	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	6457	6530	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	6531	6550	1	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	6531	6550	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	6551	7118	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7119	7181	1	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7119	7181	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7182	7273	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7274	7354	1	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7274	7354	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7355	7450	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7451	7525	1	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7451	7525	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7526	7626	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7627	7762	1	-	1	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7627	7762	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7763	7913	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7914	7975	0.4	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7914	7975	.	-	.	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	start_codon	7973	7975	.	-	0	transcript_id "Phchi.S1G000300.t1"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	transcript	6106	7975	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	stop_codon	6103	6105	.	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	6106	6276	0.98	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	6106	6276	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	6277	6410	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	6411	6456	0.95	-	1	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	6411	6456	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	6457	6530	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	6531	6550	1	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	6531	6550	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	6551	7118	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7119	7181	1	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7119	7181	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7182	7273	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7274	7363	0.99	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7274	7363	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7364	7450	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7451	7525	1	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7451	7525	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7526	7626	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7627	7762	1	-	1	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7627	7762	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	intron	7763	7913	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	CDS	7914	7975	0.32	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	exon	7914	7975	.	-	.	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
Phchi.S1	AUGUSTUS	start_codon	7973	7975	.	-	0	transcript_id "Phchi.S1G000300.t2"; gene_id "Phchi.S1G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8776.t1 is derived from g5951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37902341	37902772	.	-	.	Phchi.S1G593500
Phchi.S1	AUGUSTUS	transcript	37902341	37902772	.	-	.	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	stop_codon	37902338	37902340	.	-	0	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	CDS	37902341	37902542	0.93	-	1	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	exon	37902341	37902542	.	-	.	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	intron	37902543	37902758	.	-	.	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	CDS	37902759	37902772	0.92	-	0	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	exon	37902759	37902772	.	-	.	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
Phchi.S1	AUGUSTUS	start_codon	37902770	37902772	.	-	0	transcript_id "Phchi.S1G593500.t1"; gene_id "Phchi.S1G593500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7899.t1 is derived from g5073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31800367	31801991	.	-	.	Phchi.S1G505800
Phchi.S1	AUGUSTUS	transcript	31800367	31801991	.	-	.	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	stop_codon	31800364	31800366	.	-	0	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	CDS	31800367	31800709	1	-	1	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	exon	31800367	31800709	.	-	.	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	intron	31800710	31800804	.	-	.	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	CDS	31800805	31801991	0.86	-	0	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	exon	31800805	31801991	.	-	.	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
Phchi.S1	AUGUSTUS	start_codon	31801989	31801991	.	-	0	transcript_id "Phchi.S1G505800.t1"; gene_id "Phchi.S1G505800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2538.t1 is derived from g9458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7216139	7220950	.	+	.	Phchi.S5G114700
Phchi.S5	AUGUSTUS	transcript	7216139	7220950	.	+	.	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	start_codon	7216139	7216141	.	+	0	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	CDS	7216139	7216211	0.23	+	0	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	exon	7216139	7216211	.	+	.	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	intron	7216212	7220882	.	+	.	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	CDS	7220883	7220950	0.03	+	2	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	exon	7220883	7220950	.	+	.	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
Phchi.S5	AUGUSTUS	stop_codon	7220951	7220953	.	+	0	transcript_id "Phchi.S5G114700.t1"; gene_id "Phchi.S5G114700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1561.t1 is derived from g8480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1773368	1773763	.	+	.	Phchi.S5G017000
Phchi.S5	AUGUSTUS	transcript	1773368	1773763	.	+	.	transcript_id "Phchi.S5G017000.t1"; gene_id "Phchi.S5G017000"
Phchi.S5	AUGUSTUS	start_codon	1773368	1773370	.	+	0	transcript_id "Phchi.S5G017000.t1"; gene_id "Phchi.S5G017000"
Phchi.S5	AUGUSTUS	CDS	1773368	1773763	0.53	+	0	transcript_id "Phchi.S5G017000.t1"; gene_id "Phchi.S5G017000"
Phchi.S5	AUGUSTUS	exon	1773368	1773763	.	+	.	transcript_id "Phchi.S5G017000.t1"; gene_id "Phchi.S5G017000"
Phchi.S5	AUGUSTUS	stop_codon	1773764	1773766	.	+	0	transcript_id "Phchi.S5G017000.t1"; gene_id "Phchi.S5G017000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3932.t1 is derived from g1101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6554454	6556265	.	-	.	Phchi.S1G109100
Phchi.S1	AUGUSTUS	transcript	6554454	6556265	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	stop_codon	6554451	6554453	.	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6554454	6554504	0.56	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6554454	6554504	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6554505	6554606	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6554607	6554748	0.78	-	1	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6554607	6554748	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6554749	6554871	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6554872	6554969	1	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6554872	6554969	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6554970	6555062	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6555063	6555111	1	-	1	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6555063	6555111	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6555112	6555191	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6555192	6555252	1	-	2	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6555192	6555252	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6555253	6555384	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6555385	6555535	1	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6555385	6555535	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6555536	6555655	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6555656	6555700	0.99	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6555656	6555700	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	intron	6555701	6555779	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	CDS	6555780	6556265	0.64	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	exon	6555780	6556265	.	-	.	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
Phchi.S1	AUGUSTUS	start_codon	6556263	6556265	.	-	0	transcript_id "Phchi.S1G109100.t1"; gene_id "Phchi.S1G109100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10005.t1 is derived from g7181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45008318	45009070	.	-	.	Phchi.S1G716400
Phchi.S1	AUGUSTUS	transcript	45008318	45009070	.	-	.	transcript_id "Phchi.S1G716400.t1"; gene_id "Phchi.S1G716400"
Phchi.S1	AUGUSTUS	stop_codon	45008315	45008317	.	-	0	transcript_id "Phchi.S1G716400.t1"; gene_id "Phchi.S1G716400"
Phchi.S1	AUGUSTUS	CDS	45008318	45009070	0.81	-	0	transcript_id "Phchi.S1G716400.t1"; gene_id "Phchi.S1G716400"
Phchi.S1	AUGUSTUS	exon	45008318	45009070	.	-	.	transcript_id "Phchi.S1G716400.t1"; gene_id "Phchi.S1G716400"
Phchi.S1	AUGUSTUS	start_codon	45009068	45009070	.	-	0	transcript_id "Phchi.S1G716400.t1"; gene_id "Phchi.S1G716400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2878.t1 is derived from g47.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	240288	241786	.	-	.	Phchi.S1G003700
Phchi.S1	AUGUSTUS	transcript	240288	241786	.	-	.	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	stop_codon	240285	240287	.	-	0	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	CDS	240288	241336	0.43	-	2	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	exon	240288	241336	.	-	.	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	intron	241337	241413	.	-	.	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	CDS	241414	241786	0.54	-	0	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	exon	241414	241786	.	-	.	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
Phchi.S1	AUGUSTUS	start_codon	241784	241786	.	-	0	transcript_id "Phchi.S1G003700.t1"; gene_id "Phchi.S1G003700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13491.t1 is derived from g11958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7150621	7151403	.	-	.	Phchi.S3G081000
Phchi.S3	AUGUSTUS	transcript	7150621	7151403	.	-	.	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	stop_codon	7150618	7150620	.	-	0	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	CDS	7150621	7150786	0.67	-	1	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	exon	7150621	7150786	.	-	.	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	intron	7150787	7151017	.	-	.	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	CDS	7151018	7151403	0.46	-	0	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	exon	7151018	7151403	.	-	.	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
Phchi.S3	AUGUSTUS	start_codon	7151401	7151403	.	-	0	transcript_id "Phchi.S3G081000.t1"; gene_id "Phchi.S3G081000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13385.t1 is derived from g11851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6482001	6484800	.	+	.	Phchi.S3G070400
Phchi.S3	AUGUSTUS	transcript	6482001	6484800	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	start_codon	6482001	6482003	.	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6482001	6482101	0.48	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6482001	6482101	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6482102	6482272	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6482273	6482399	0.27	+	1	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6482273	6482399	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6482400	6482542	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6482543	6482794	1	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6482543	6482794	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6482795	6482925	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6482926	6483125	1	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6482926	6483125	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6483126	6483230	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6483231	6483441	1	+	1	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6483231	6483441	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6483442	6483574	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6483575	6483676	1	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6483575	6483676	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6483677	6483760	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6483761	6484008	1	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6483761	6484008	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6484009	6484106	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6484107	6484238	0.66	+	1	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6484107	6484238	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6484239	6484359	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6484360	6484523	0.5	+	1	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6484360	6484523	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	intron	6484524	6484639	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	CDS	6484640	6484800	0.99	+	2	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	exon	6484640	6484800	.	+	.	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
Phchi.S3	AUGUSTUS	stop_codon	6484801	6484803	.	+	0	transcript_id "Phchi.S3G070400.t1"; gene_id "Phchi.S3G070400"
# This transcript jg15036.t2 is derived from g13504.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15037.t1 is derived from g13505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16680831	16683632	.	+	.	Phchi.S3G235600
Phchi.S3	AUGUSTUS	transcript	16680831	16683632	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	start_codon	16680831	16680833	.	+	0	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	CDS	16680831	16680960	1	+	0	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	exon	16680831	16680960	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	intron	16680961	16681033	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	CDS	16681034	16681101	1	+	2	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	exon	16681034	16681101	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	intron	16681102	16681196	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	CDS	16681197	16681333	0.89	+	0	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	exon	16681197	16681333	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	intron	16681334	16681471	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	CDS	16681472	16681515	0.39	+	1	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	exon	16681472	16681515	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	intron	16681516	16681773	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	CDS	16681774	16683632	0.4	+	2	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	exon	16681774	16683632	.	+	.	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
Phchi.S3	AUGUSTUS	stop_codon	16683633	16683635	.	+	0	transcript_id "Phchi.S3G235600.t1"; gene_id "Phchi.S3G235600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg581.t1 is derived from g10363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4276524	4277126	.	+	.	Phchi.S6G054000
Phchi.S6	AUGUSTUS	transcript	4276524	4277126	.	+	.	transcript_id "Phchi.S6G054000.t1"; gene_id "Phchi.S6G054000"
Phchi.S6	AUGUSTUS	start_codon	4276524	4276526	.	+	0	transcript_id "Phchi.S6G054000.t1"; gene_id "Phchi.S6G054000"
Phchi.S6	AUGUSTUS	CDS	4276524	4277126	0.67	+	0	transcript_id "Phchi.S6G054000.t1"; gene_id "Phchi.S6G054000"
Phchi.S6	AUGUSTUS	exon	4276524	4277126	.	+	.	transcript_id "Phchi.S6G054000.t1"; gene_id "Phchi.S6G054000"
Phchi.S6	AUGUSTUS	stop_codon	4277127	4277129	.	+	0	transcript_id "Phchi.S6G054000.t1"; gene_id "Phchi.S6G054000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6364.t1 is derived from g3536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22580618	22580890	.	+	.	Phchi.S1G352300
Phchi.S1	AUGUSTUS	transcript	22580618	22580890	.	+	.	transcript_id "Phchi.S1G352300.t1"; gene_id "Phchi.S1G352300"
Phchi.S1	AUGUSTUS	start_codon	22580618	22580620	.	+	0	transcript_id "Phchi.S1G352300.t1"; gene_id "Phchi.S1G352300"
Phchi.S1	AUGUSTUS	CDS	22580618	22580890	0.41	+	0	transcript_id "Phchi.S1G352300.t1"; gene_id "Phchi.S1G352300"
Phchi.S1	AUGUSTUS	exon	22580618	22580890	.	+	.	transcript_id "Phchi.S1G352300.t1"; gene_id "Phchi.S1G352300"
Phchi.S1	AUGUSTUS	stop_codon	22580891	22580893	.	+	0	transcript_id "Phchi.S1G352300.t1"; gene_id "Phchi.S1G352300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11221.t1 is derived from g15271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4855884	4856468	.	-	.	Phchi.S4G080300
Phchi.S4	AUGUSTUS	transcript	4855884	4856468	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	stop_codon	4855881	4855883	.	-	0	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	CDS	4855884	4855947	1	-	1	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	exon	4855884	4855947	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	intron	4855948	4856053	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	CDS	4856054	4856121	1	-	0	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	exon	4856054	4856121	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	intron	4856122	4856211	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	CDS	4856212	4856263	0.72	-	1	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	exon	4856212	4856263	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	intron	4856264	4856385	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	CDS	4856386	4856468	0.7	-	0	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	exon	4856386	4856468	.	-	.	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
Phchi.S4	AUGUSTUS	start_codon	4856466	4856468	.	-	0	transcript_id "Phchi.S4G080300.t1"; gene_id "Phchi.S4G080300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1937.t1 is derived from g8857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3910078	3916589	.	-	.	Phchi.S5G054600
Phchi.S5	AUGUSTUS	transcript	3910078	3916589	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	stop_codon	3910075	3910077	.	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3910078	3910174	0.99	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3910078	3910174	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3910175	3910265	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3910266	3910370	1	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3910266	3910370	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3910371	3910458	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3910459	3910523	1	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3910459	3910523	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3910524	3910653	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3910654	3910677	1	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3910654	3910677	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3910678	3910815	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3910816	3910899	1	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3910816	3910899	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3910900	3910981	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3910982	3911119	1	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3910982	3911119	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3911120	3911465	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3911466	3911520	1	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3911466	3911520	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3911521	3911697	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3911698	3911901	0.98	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3911698	3911901	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3911902	3912138	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3912139	3912367	0.99	-	2	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3912139	3912367	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3912368	3912475	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3912476	3912491	0.55	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3912476	3912491	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3912492	3912695	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3912696	3912818	0.43	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3912696	3912818	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3912819	3913208	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3913209	3913322	0.93	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3913209	3913322	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3913323	3913430	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3913431	3913571	0.94	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3913431	3913571	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3913572	3913676	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3913677	3913713	1	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3913677	3913713	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3913714	3913800	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3913801	3913885	0.85	-	2	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3913801	3913885	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3913886	3913981	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3913982	3914060	1	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3913982	3914060	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3914061	3914154	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3914155	3914502	0.98	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3914155	3914502	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3914503	3914672	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3914673	3914862	1	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3914673	3914862	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3914863	3915171	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3915172	3915301	0.9	-	2	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3915172	3915301	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3915302	3915383	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3915384	3915517	0.95	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3915384	3915517	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3915518	3915620	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3915621	3915726	0.86	-	2	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3915621	3915726	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3915727	3915895	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3915896	3915990	0.79	-	1	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3915896	3915990	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	intron	3915991	3916071	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	CDS	3916072	3916589	0.95	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	exon	3916072	3916589	.	-	.	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
Phchi.S5	AUGUSTUS	start_codon	3916587	3916589	.	-	0	transcript_id "Phchi.S5G054600.t1"; gene_id "Phchi.S5G054600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9701.t1 is derived from g6877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43338313	43338819	.	+	.	Phchi.S1G686000
Phchi.S1	AUGUSTUS	transcript	43338313	43338819	.	+	.	transcript_id "Phchi.S1G686000.t1"; gene_id "Phchi.S1G686000"
Phchi.S1	AUGUSTUS	start_codon	43338313	43338315	.	+	0	transcript_id "Phchi.S1G686000.t1"; gene_id "Phchi.S1G686000"
Phchi.S1	AUGUSTUS	CDS	43338313	43338819	0.88	+	0	transcript_id "Phchi.S1G686000.t1"; gene_id "Phchi.S1G686000"
Phchi.S1	AUGUSTUS	exon	43338313	43338819	.	+	.	transcript_id "Phchi.S1G686000.t1"; gene_id "Phchi.S1G686000"
Phchi.S1	AUGUSTUS	stop_codon	43338820	43338822	.	+	0	transcript_id "Phchi.S1G686000.t1"; gene_id "Phchi.S1G686000"
# This transcript jg11267.t2 is derived from g15317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11268.t1 is derived from g15318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5094002	5098354	.	+	.	Phchi.S4G085000
Phchi.S4	AUGUSTUS	transcript	5094002	5098354	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	start_codon	5094002	5094004	.	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5094002	5094326	0.51	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5094002	5094326	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5094327	5094447	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5094448	5095643	1	+	2	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5094448	5095643	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5095644	5095742	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5095743	5096067	1	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5095743	5096067	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5096068	5096261	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5096262	5096444	1	+	2	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5096262	5096444	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5096445	5096523	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5096524	5096807	0.99	+	2	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5096524	5096807	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5096808	5096895	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5096896	5097012	1	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5096896	5097012	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5097013	5097093	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5097094	5097365	0.99	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5097094	5097365	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5097366	5097479	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5097480	5097666	1	+	1	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5097480	5097666	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5097667	5097746	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5097747	5098025	0.97	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5097747	5098025	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	intron	5098026	5098120	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	CDS	5098121	5098354	0.78	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	exon	5098121	5098354	.	+	.	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
Phchi.S4	AUGUSTUS	stop_codon	5098355	5098357	.	+	0	transcript_id "Phchi.S4G085000.t1"; gene_id "Phchi.S4G085000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6417.t1 is derived from g3589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22898972	22899713	.	-	.	Phchi.S1G357600
Phchi.S1	AUGUSTUS	transcript	22898972	22899713	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	stop_codon	22898969	22898971	.	-	0	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	CDS	22898972	22899031	0.96	-	0	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	exon	22898972	22899031	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	intron	22899032	22899146	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	CDS	22899147	22899257	0.99	-	0	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	exon	22899147	22899257	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	intron	22899258	22899353	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	CDS	22899354	22899460	0.99	-	2	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	exon	22899354	22899460	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	intron	22899461	22899553	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	CDS	22899554	22899713	0.98	-	0	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	exon	22899554	22899713	.	-	.	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
Phchi.S1	AUGUSTUS	start_codon	22899711	22899713	.	-	0	transcript_id "Phchi.S1G357600.t1"; gene_id "Phchi.S1G357600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg7216.t1 is derived from g4388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27672826	27677780	.	+	.	Phchi.S1G437500
Phchi.S1	AUGUSTUS	transcript	27672826	27677124	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	start_codon	27672826	27672828	.	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27672826	27672894	0.92	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27672826	27672894	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27672895	27673001	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673002	27673284	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673002	27673284	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673285	27673423	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673424	27673452	1	+	2	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673424	27673452	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673453	27673546	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673547	27673648	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673547	27673648	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673649	27673775	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673776	27673844	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673776	27673844	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673845	27673962	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673963	27674022	0.98	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673963	27674022	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674023	27674105	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674106	27674241	0.97	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674106	27674241	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674242	27674497	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674498	27674546	1	+	2	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674498	27674546	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674547	27674669	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674670	27674778	1	+	1	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674670	27674778	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674779	27674862	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674863	27674955	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674863	27674955	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674956	27675041	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675042	27675134	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675042	27675134	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675135	27675271	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675272	27675409	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675272	27675409	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675410	27675497	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675498	27675584	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675498	27675584	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675585	27675754	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675755	27675868	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675755	27675868	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675869	27676017	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676018	27676072	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676018	27676072	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676073	27676210	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676211	27676353	1	+	2	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676211	27676353	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676354	27676445	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676446	27676592	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676446	27676592	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676593	27676676	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676677	27676729	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676677	27676729	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676730	27676824	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676825	27676924	1	+	1	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676825	27676924	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676925	27677106	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27677107	27677124	1	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27677107	27677124	.	+	.	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	stop_codon	27677125	27677127	.	+	0	transcript_id "Phchi.S1G437500.t1"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	transcript	27672826	27677780	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	start_codon	27672826	27672828	.	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27672826	27672894	0.95	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27672826	27672894	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27672895	27673001	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673002	27673284	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673002	27673284	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673285	27673423	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673424	27673452	1	+	2	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673424	27673452	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673453	27673546	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673547	27673648	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673547	27673648	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673649	27673775	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673776	27673844	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673776	27673844	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673845	27673962	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673963	27674022	0.99	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673963	27674022	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674023	27674105	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674106	27674241	0.98	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674106	27674241	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674242	27674497	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674498	27674546	1	+	2	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674498	27674546	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674547	27674669	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674670	27674778	1	+	1	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674670	27674778	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674779	27674862	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674863	27674955	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674863	27674955	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674956	27675041	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675042	27675134	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675042	27675134	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675135	27675271	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675272	27675409	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675272	27675409	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675410	27675497	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675498	27675584	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675498	27675584	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675585	27675754	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675755	27675868	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675755	27675868	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675869	27676017	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676018	27676072	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676018	27676072	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676073	27676210	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676211	27676353	1	+	2	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676211	27676353	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676354	27676445	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676446	27676592	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676446	27676592	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676593	27676676	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676677	27676729	1	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676677	27676729	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676730	27676824	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676825	27676924	1	+	1	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676825	27676924	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676925	27677483	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27677484	27677780	0.88	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27677484	27677780	.	+	.	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	stop_codon	27677781	27677783	.	+	0	transcript_id "Phchi.S1G437500.t2"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	transcript	27672826	27677780	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	start_codon	27672826	27672828	.	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27672826	27672894	0.89	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27672826	27672894	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27672895	27673001	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673002	27673284	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673002	27673284	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673285	27673423	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673424	27673452	1	+	2	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673424	27673452	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673453	27673546	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673547	27673648	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673547	27673648	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673649	27673775	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673776	27673844	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673776	27673844	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673845	27673962	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673963	27674022	0.96	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673963	27674022	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674023	27674105	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674106	27674241	0.96	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674106	27674241	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674242	27674497	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674498	27674546	1	+	2	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674498	27674546	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674547	27674669	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674670	27674778	1	+	1	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674670	27674778	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674779	27674862	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674863	27674955	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674863	27674955	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674956	27675041	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675042	27675134	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675042	27675134	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675135	27675271	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675272	27675409	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675272	27675409	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675410	27675497	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675498	27675584	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675498	27675584	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675585	27675754	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675755	27675817	0.99	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675755	27675817	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675818	27676017	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676018	27676072	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676018	27676072	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676073	27676210	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676211	27676353	1	+	2	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676211	27676353	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676354	27676445	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676446	27676592	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676446	27676592	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676593	27676676	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676677	27676729	1	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676677	27676729	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676730	27676824	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676825	27676924	1	+	1	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676825	27676924	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676925	27677483	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27677484	27677780	0.85	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27677484	27677780	.	+	.	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	stop_codon	27677781	27677783	.	+	0	transcript_id "Phchi.S1G437500.t3"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	transcript	27672826	27677780	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	start_codon	27672826	27672828	.	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27672826	27672894	0.83	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27672826	27672894	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27672895	27673001	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673002	27673284	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673002	27673284	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673285	27673423	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673424	27673452	1	+	2	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673424	27673452	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673453	27673546	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673547	27673648	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673547	27673648	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673649	27673775	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673776	27673844	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673776	27673844	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27673845	27673962	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27673963	27674022	0.98	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27673963	27674022	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674023	27674105	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674106	27674241	0.96	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674106	27674241	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674242	27674497	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674498	27674546	1	+	2	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674498	27674546	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674547	27674669	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674670	27674778	1	+	1	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674670	27674778	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674779	27674862	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27674863	27674955	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27674863	27674955	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27674956	27675041	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675042	27675134	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675042	27675134	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675135	27675271	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675272	27675409	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675272	27675409	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675410	27675497	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675498	27675611	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675498	27675611	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675612	27675754	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27675755	27675868	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27675755	27675868	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27675869	27676017	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676018	27676072	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676018	27676072	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676073	27676210	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676211	27676353	1	+	2	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676211	27676353	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676354	27676445	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676446	27676592	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676446	27676592	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676593	27676676	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676677	27676729	1	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676677	27676729	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676730	27676824	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27676825	27676924	1	+	1	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27676825	27676924	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	intron	27676925	27677483	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	CDS	27677484	27677780	0.84	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	exon	27677484	27677780	.	+	.	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
Phchi.S1	AUGUSTUS	stop_codon	27677781	27677783	.	+	0	transcript_id "Phchi.S1G437500.t4"; gene_id "Phchi.S1G437500"
# This transcript jg4331.t2 is derived from g1500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4332.t1 is derived from g1501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9821558	9822831	.	-	.	Phchi.S1G149100
Phchi.S1	AUGUSTUS	transcript	9821558	9822831	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	stop_codon	9821555	9821557	.	-	0	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	CDS	9821558	9821609	1	-	1	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	exon	9821558	9821609	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	intron	9821610	9821701	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	CDS	9821702	9821984	1	-	2	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	exon	9821702	9821984	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	intron	9821985	9822076	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	CDS	9822077	9822293	0.99	-	0	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	exon	9822077	9822293	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	intron	9822294	9822366	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	CDS	9822367	9822831	0.76	-	0	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	exon	9822367	9822831	.	-	.	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
Phchi.S1	AUGUSTUS	start_codon	9822829	9822831	.	-	0	transcript_id "Phchi.S1G149100.t1"; gene_id "Phchi.S1G149100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3514.t1 is derived from g683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4155347	4157206	.	-	.	Phchi.S1G067300
Phchi.S1	AUGUSTUS	transcript	4155347	4157206	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	stop_codon	4155344	4155346	.	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4155347	4155586	1	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4155347	4155586	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	intron	4155587	4155683	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4155684	4155771	1	-	1	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4155684	4155771	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	intron	4155772	4155866	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4155867	4156063	1	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4155867	4156063	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	intron	4156064	4156178	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4156179	4156229	1	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4156179	4156229	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	intron	4156230	4156311	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4156312	4156485	1	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4156312	4156485	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	intron	4156486	4156573	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4156574	4157095	0.99	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4156574	4157095	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	intron	4157096	4157191	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	CDS	4157192	4157206	1	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	exon	4157192	4157206	.	-	.	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
Phchi.S1	AUGUSTUS	start_codon	4157204	4157206	.	-	0	transcript_id "Phchi.S1G067300.t1"; gene_id "Phchi.S1G067300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8965.t1 is derived from g6140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38872721	38877825	.	+	.	Phchi.S1G612400
Phchi.S1	AUGUSTUS	transcript	38872721	38877825	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	start_codon	38872721	38872723	.	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38872721	38872944	0.97	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38872721	38872944	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38872945	38873045	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38873046	38873076	0.98	+	1	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38873046	38873076	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38873077	38873179	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38873180	38873373	0.96	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38873180	38873373	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38873374	38873495	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38873496	38873721	1	+	1	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38873496	38873721	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38873722	38873853	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38873854	38874102	1	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38873854	38874102	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38874103	38874299	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38874300	38874415	1	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38874300	38874415	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38874416	38874597	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38874598	38874693	0.98	+	1	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38874598	38874693	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38874694	38874810	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38874811	38874898	1	+	1	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38874811	38874898	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38874899	38874991	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38874992	38875224	1	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38874992	38875224	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38875225	38875323	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38875324	38875508	0.65	+	1	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38875324	38875508	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38875509	38875610	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38875611	38875810	0.99	+	2	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38875611	38875810	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38875811	38875917	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38875918	38876035	0.77	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38875918	38876035	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38876036	38876143	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38876144	38876250	0.77	+	2	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38876144	38876250	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38876251	38876346	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38876347	38876448	1	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38876347	38876448	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38876449	38876579	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38876580	38876835	0.81	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38876580	38876835	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38876836	38876989	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38876990	38877138	0.92	+	2	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38876990	38877138	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38877139	38877233	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38877234	38877518	1	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38877234	38877518	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	intron	38877519	38877645	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	CDS	38877646	38877825	0.8	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	exon	38877646	38877825	.	+	.	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
Phchi.S1	AUGUSTUS	stop_codon	38877826	38877828	.	+	0	transcript_id "Phchi.S1G612400.t1"; gene_id "Phchi.S1G612400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14194.t1 is derived from g12661.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11410438	11414516	.	-	.	Phchi.S3G151300
Phchi.S3	AUGUSTUS	transcript	11410438	11414516	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	stop_codon	11410435	11410437	.	-	0	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11410438	11410553	1	-	2	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11410438	11410553	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11410554	11410702	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11410703	11410928	1	-	0	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11410703	11410928	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11410929	11411144	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11411145	11411181	0.99	-	1	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11411145	11411181	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11411182	11411284	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11411285	11411384	0.99	-	2	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11411285	11411384	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11411385	11412520	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11412521	11412656	1	-	0	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11412521	11412656	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11412657	11412761	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11412762	11412994	0.65	-	2	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11412762	11412994	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11412995	11413233	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11413234	11413325	0.87	-	1	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11413234	11413325	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11413326	11414379	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11414380	11414516	0.95	-	0	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11414380	11414516	.	-	.	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	start_codon	11414514	11414516	.	-	0	transcript_id "Phchi.S3G151300.t1"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	transcript	11410551	11414516	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	stop_codon	11410548	11410550	.	-	0	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11410551	11410553	0.84	-	0	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11410551	11410553	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11410554	11410643	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11410644	11410928	0.84	-	0	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11410644	11410928	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11410929	11411144	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11411145	11411181	1	-	1	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11411145	11411181	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11411182	11411284	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11411285	11411384	1	-	2	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11411285	11411384	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11411385	11412520	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11412521	11412656	1	-	0	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11412521	11412656	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11412657	11412761	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11412762	11412994	0.68	-	2	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11412762	11412994	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11412995	11413233	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11413234	11413325	0.86	-	1	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11413234	11413325	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11413326	11414379	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11414380	11414516	0.89	-	0	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11414380	11414516	.	-	.	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	start_codon	11414514	11414516	.	-	0	transcript_id "Phchi.S3G151300.t2"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	transcript	11410551	11414516	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	stop_codon	11410548	11410550	.	-	0	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11410551	11410553	0.79	-	0	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11410551	11410553	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11410554	11410643	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11410644	11410958	0.79	-	0	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11410644	11410958	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11410959	11411144	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11411145	11411181	1	-	1	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11411145	11411181	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11411182	11411284	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11411285	11411384	1	-	2	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11411285	11411384	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11411385	11412520	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11412521	11412656	1	-	0	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11412521	11412656	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11412657	11412761	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11412762	11412994	0.68	-	2	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11412762	11412994	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11412995	11413233	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11413234	11413325	0.81	-	1	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11413234	11413325	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	intron	11413326	11414379	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	CDS	11414380	11414516	0.88	-	0	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	exon	11414380	11414516	.	-	.	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
Phchi.S3	AUGUSTUS	start_codon	11414514	11414516	.	-	0	transcript_id "Phchi.S3G151300.t3"; gene_id "Phchi.S3G151300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10882.t1 is derived from g14932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2742747	2743381	.	+	.	Phchi.S4G046400
Phchi.S4	AUGUSTUS	transcript	2742747	2743381	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	start_codon	2742747	2742749	.	+	0	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	CDS	2742747	2742787	0.92	+	0	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	exon	2742747	2742787	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	intron	2742788	2742870	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	CDS	2742871	2742943	1	+	1	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	exon	2742871	2742943	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	intron	2742944	2743017	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	CDS	2743018	2743080	1	+	0	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	exon	2743018	2743080	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	intron	2743081	2743150	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	CDS	2743151	2743381	0.88	+	0	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	exon	2743151	2743381	.	+	.	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
Phchi.S4	AUGUSTUS	stop_codon	2743382	2743384	.	+	0	transcript_id "Phchi.S4G046400.t1"; gene_id "Phchi.S4G046400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5452.t1 is derived from g2622.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16919551	16920952	.	+	.	Phchi.S1G261100
Phchi.S1	AUGUSTUS	transcript	16919551	16920952	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	start_codon	16919551	16919553	.	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16919551	16919901	1	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16919551	16919901	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	intron	16919902	16920064	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16920065	16920142	1	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16920065	16920142	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	intron	16920143	16920232	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16920233	16920256	1	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16920233	16920256	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	intron	16920257	16920374	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16920375	16920422	1	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16920375	16920422	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	intron	16920423	16920518	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16920519	16920583	0.99	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16920519	16920583	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	intron	16920584	16920686	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16920687	16920764	0.99	+	1	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16920687	16920764	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	intron	16920765	16920849	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	CDS	16920850	16920952	1	+	1	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	exon	16920850	16920952	.	+	.	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
Phchi.S1	AUGUSTUS	stop_codon	16920953	16920955	.	+	0	transcript_id "Phchi.S1G261100.t1"; gene_id "Phchi.S1G261100"
# This transcript jg6793.t2 is derived from g3965.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6793.t3 is derived from g3965.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6794.t1 is derived from g3966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25109655	25111230	.	+	.	Phchi.S1G395300
Phchi.S1	AUGUSTUS	transcript	25109655	25111230	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	start_codon	25109655	25109657	.	+	0	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	CDS	25109655	25109709	0.95	+	0	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	exon	25109655	25109709	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	intron	25109710	25109788	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	CDS	25109789	25109924	0.87	+	2	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	exon	25109789	25109924	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	intron	25109925	25110201	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	CDS	25110202	25110308	0.9	+	1	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	exon	25110202	25110308	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	intron	25110309	25110447	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	CDS	25110448	25110502	0.9	+	2	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	exon	25110448	25110502	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	intron	25110503	25110808	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	CDS	25110809	25110910	1	+	1	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	exon	25110809	25110910	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	intron	25110911	25111079	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	CDS	25111080	25111230	0.97	+	1	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	exon	25111080	25111230	.	+	.	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
Phchi.S1	AUGUSTUS	stop_codon	25111231	25111233	.	+	0	transcript_id "Phchi.S1G395300.t1"; gene_id "Phchi.S1G395300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1893.t1 is derived from g8813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3754776	3755261	.	+	.	Phchi.S5G050200
Phchi.S5	AUGUSTUS	transcript	3754776	3755261	.	+	.	transcript_id "Phchi.S5G050200.t1"; gene_id "Phchi.S5G050200"
Phchi.S5	AUGUSTUS	start_codon	3754776	3754778	.	+	0	transcript_id "Phchi.S5G050200.t1"; gene_id "Phchi.S5G050200"
Phchi.S5	AUGUSTUS	CDS	3754776	3755261	0.9	+	0	transcript_id "Phchi.S5G050200.t1"; gene_id "Phchi.S5G050200"
Phchi.S5	AUGUSTUS	exon	3754776	3755261	.	+	.	transcript_id "Phchi.S5G050200.t1"; gene_id "Phchi.S5G050200"
Phchi.S5	AUGUSTUS	stop_codon	3755262	3755264	.	+	0	transcript_id "Phchi.S5G050200.t1"; gene_id "Phchi.S5G050200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12691.t1 is derived from g11156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	567627	570538	.	-	.	Phchi.S3G001000
Phchi.S3	AUGUSTUS	transcript	567627	570538	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	stop_codon	567624	567626	.	-	0	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	CDS	567627	569779	0.73	-	2	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	exon	567627	569779	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	intron	569780	570054	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	CDS	570055	570095	0.85	-	1	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	exon	570055	570095	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	intron	570096	570404	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	CDS	570405	570436	0.74	-	0	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	exon	570405	570436	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	intron	570437	570514	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	CDS	570515	570538	0.74	-	0	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	exon	570515	570538	.	-	.	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
Phchi.S3	AUGUSTUS	start_codon	570536	570538	.	-	0	transcript_id "Phchi.S3G001000.t1"; gene_id "Phchi.S3G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13693.t1 is derived from g12160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8230391	8231110	.	-	.	Phchi.S3G101200
Phchi.S3	AUGUSTUS	transcript	8230391	8231110	.	-	.	transcript_id "Phchi.S3G101200.t1"; gene_id "Phchi.S3G101200"
Phchi.S3	AUGUSTUS	stop_codon	8230388	8230390	.	-	0	transcript_id "Phchi.S3G101200.t1"; gene_id "Phchi.S3G101200"
Phchi.S3	AUGUSTUS	CDS	8230391	8231110	0.7	-	0	transcript_id "Phchi.S3G101200.t1"; gene_id "Phchi.S3G101200"
Phchi.S3	AUGUSTUS	exon	8230391	8231110	.	-	.	transcript_id "Phchi.S3G101200.t1"; gene_id "Phchi.S3G101200"
Phchi.S3	AUGUSTUS	start_codon	8231108	8231110	.	-	0	transcript_id "Phchi.S3G101200.t1"; gene_id "Phchi.S3G101200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14487.t1 is derived from g12955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13091504	13091880	.	-	.	Phchi.S3G180600
Phchi.S3	AUGUSTUS	transcript	13091504	13091880	.	-	.	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	stop_codon	13091501	13091503	.	-	0	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	CDS	13091504	13091595	0.62	-	2	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	exon	13091504	13091595	.	-	.	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	intron	13091596	13091762	.	-	.	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	CDS	13091763	13091880	0.59	-	0	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	exon	13091763	13091880	.	-	.	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
Phchi.S3	AUGUSTUS	start_codon	13091878	13091880	.	-	0	transcript_id "Phchi.S3G180600.t1"; gene_id "Phchi.S3G180600"
# This transcript jg139.t2 is derived from g9921.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg140.t1 is derived from g9922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	771120	774814	.	-	.	Phchi.S6G009900
Phchi.S6	AUGUSTUS	transcript	771120	774814	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	stop_codon	771117	771119	.	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	771120	771227	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	771120	771227	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	771228	771308	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	771309	771407	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	771309	771407	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	771408	771499	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	771500	771568	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	771500	771568	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	771569	771668	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	771669	771758	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	771669	771758	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	771759	771865	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	771866	771935	1	-	1	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	771866	771935	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	771936	772034	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	772035	772104	1	-	2	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	772035	772104	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	772105	772235	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	772236	772422	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	772236	772422	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	772423	772504	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	772505	772589	1	-	1	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	772505	772589	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	772590	772705	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	772706	772884	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	772706	772884	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	772885	772974	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	772975	773079	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	772975	773079	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	773080	773174	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	773175	773258	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	773175	773258	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	773259	773349	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	773350	773430	0.99	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	773350	773430	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	773431	773536	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	773537	773752	0.86	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	773537	773752	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	773753	773844	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	773845	773946	1	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	773845	773946	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	773947	774046	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	774047	774119	1	-	1	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	774047	774119	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	intron	774120	774308	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	CDS	774309	774814	0.89	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	exon	774309	774814	.	-	.	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
Phchi.S6	AUGUSTUS	start_codon	774812	774814	.	-	0	transcript_id "Phchi.S6G009900.t1"; gene_id "Phchi.S6G009900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13655.t1 is derived from g12122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8031427	8035552	.	-	.	Phchi.S3G097400
Phchi.S3	AUGUSTUS	transcript	8031427	8035552	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	stop_codon	8031424	8031426	.	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8031427	8031466	0.89	-	1	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8031427	8031466	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8031467	8031550	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8031551	8031592	0.88	-	1	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8031551	8031592	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8031593	8031749	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8031750	8031871	0.89	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8031750	8031871	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8031872	8032020	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8032021	8032164	1	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8032021	8032164	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8032165	8032250	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8032251	8032338	0.98	-	1	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8032251	8032338	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8032339	8032446	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8032447	8032552	0.56	-	2	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8032447	8032552	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8032553	8032628	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8032629	8032783	1	-	1	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8032629	8032783	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8032784	8032909	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8032910	8032979	1	-	2	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8032910	8032979	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8032980	8033108	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8033109	8033278	0.99	-	1	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8033109	8033278	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8033279	8033385	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8033386	8033453	1	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8033386	8033453	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8033454	8033565	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8033566	8033669	0.93	-	2	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8033566	8033669	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8033670	8033801	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8033802	8033972	1	-	2	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8033802	8033972	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8033973	8034103	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8034104	8034241	1	-	2	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8034104	8034241	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8034242	8034387	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8034388	8034571	1	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8034388	8034571	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8034572	8034756	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8034757	8035149	1	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8034757	8035149	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	intron	8035150	8035372	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	CDS	8035373	8035552	0.88	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	exon	8035373	8035552	.	-	.	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
Phchi.S3	AUGUSTUS	start_codon	8035550	8035552	.	-	0	transcript_id "Phchi.S3G097400.t1"; gene_id "Phchi.S3G097400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12381.t1 is derived from g8057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14464197	14465195	.	-	.	Phchi.S2G046100
Phchi.S2	AUGUSTUS	transcript	14464197	14465195	.	-	.	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	stop_codon	14464194	14464196	.	-	0	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	CDS	14464197	14464538	0.42	-	0	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	exon	14464197	14464538	.	-	.	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	intron	14464539	14464632	.	-	.	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	CDS	14464633	14464768	0.38	-	1	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	exon	14464633	14464768	.	-	.	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	intron	14464769	14464857	.	-	.	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	CDS	14464858	14465195	0.86	-	0	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	exon	14464858	14465195	.	-	.	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
Phchi.S2	AUGUSTUS	start_codon	14465193	14465195	.	-	0	transcript_id "Phchi.S2G046100.t1"; gene_id "Phchi.S2G046100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14027.t1 is derived from g12494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10368135	10368591	.	+	.	Phchi.S3G134600
Phchi.S3	AUGUSTUS	transcript	10368135	10368591	.	+	.	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	start_codon	10368135	10368137	.	+	0	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	CDS	10368135	10368245	1	+	0	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	exon	10368135	10368245	.	+	.	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	intron	10368246	10368330	.	+	.	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	CDS	10368331	10368438	1	+	0	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	exon	10368331	10368438	.	+	.	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	intron	10368439	10368531	.	+	.	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	CDS	10368532	10368591	0.97	+	0	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	exon	10368532	10368591	.	+	.	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
Phchi.S3	AUGUSTUS	stop_codon	10368592	10368594	.	+	0	transcript_id "Phchi.S3G134600.t1"; gene_id "Phchi.S3G134600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12000.t1 is derived from g7675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	454694	455314	.	-	.	Phchi.S2G008000
Phchi.S2	AUGUSTUS	transcript	454694	455314	.	-	.	transcript_id "Phchi.S2G008000.t1"; gene_id "Phchi.S2G008000"
Phchi.S2	AUGUSTUS	stop_codon	454691	454693	.	-	0	transcript_id "Phchi.S2G008000.t1"; gene_id "Phchi.S2G008000"
Phchi.S2	AUGUSTUS	CDS	454694	455314	0.97	-	0	transcript_id "Phchi.S2G008000.t1"; gene_id "Phchi.S2G008000"
Phchi.S2	AUGUSTUS	exon	454694	455314	.	-	.	transcript_id "Phchi.S2G008000.t1"; gene_id "Phchi.S2G008000"
Phchi.S2	AUGUSTUS	start_codon	455312	455314	.	-	0	transcript_id "Phchi.S2G008000.t1"; gene_id "Phchi.S2G008000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14612.t1 is derived from g13080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13751735	13752705	.	-	.	Phchi.S3G193100
Phchi.S3	AUGUSTUS	transcript	13751735	13752705	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	stop_codon	13751732	13751734	.	-	0	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	CDS	13751735	13751854	0.85	-	0	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	exon	13751735	13751854	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	intron	13751855	13751962	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	CDS	13751963	13752146	0.86	-	1	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	exon	13751963	13752146	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	intron	13752147	13752251	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	CDS	13752252	13752365	1	-	1	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	exon	13752252	13752365	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	intron	13752366	13752457	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	CDS	13752458	13752705	0.99	-	0	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	exon	13752458	13752705	.	-	.	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
Phchi.S3	AUGUSTUS	start_codon	13752703	13752705	.	-	0	transcript_id "Phchi.S3G193100.t1"; gene_id "Phchi.S3G193100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10728.t1 is derived from g14778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1782335	1782815	.	+	.	Phchi.S4G031000
Phchi.S4	AUGUSTUS	transcript	1782335	1782815	.	+	.	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	start_codon	1782335	1782337	.	+	0	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	CDS	1782335	1782632	0.84	+	0	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	exon	1782335	1782632	.	+	.	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	intron	1782633	1782720	.	+	.	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	CDS	1782721	1782815	1	+	2	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	exon	1782721	1782815	.	+	.	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
Phchi.S4	AUGUSTUS	stop_codon	1782816	1782818	.	+	0	transcript_id "Phchi.S4G031000.t1"; gene_id "Phchi.S4G031000"
# This transcript jg10388.t2 is derived from g7564.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10388.t3 is derived from g7564.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10388.t4 is derived from g7564.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10389.t1 is derived from g7565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47506480	47508195	.	+	.	Phchi.S1G754800
Phchi.S1	AUGUSTUS	transcript	47506480	47508195	.	+	.	transcript_id "Phchi.S1G754800.t1"; gene_id "Phchi.S1G754800"
Phchi.S1	AUGUSTUS	start_codon	47506480	47506482	.	+	0	transcript_id "Phchi.S1G754800.t1"; gene_id "Phchi.S1G754800"
Phchi.S1	AUGUSTUS	CDS	47506480	47508195	0.67	+	0	transcript_id "Phchi.S1G754800.t1"; gene_id "Phchi.S1G754800"
Phchi.S1	AUGUSTUS	exon	47506480	47508195	.	+	.	transcript_id "Phchi.S1G754800.t1"; gene_id "Phchi.S1G754800"
Phchi.S1	AUGUSTUS	stop_codon	47508196	47508198	.	+	0	transcript_id "Phchi.S1G754800.t1"; gene_id "Phchi.S1G754800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3873.t1 is derived from g1042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6155947	6158086	.	-	.	Phchi.S1G103200
Phchi.S1	AUGUSTUS	transcript	6155947	6158086	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	stop_codon	6155944	6155946	.	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6155947	6156075	1	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6155947	6156075	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6156076	6156161	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6156162	6156302	1	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6156162	6156302	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6156303	6156404	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6156405	6156547	1	-	2	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6156405	6156547	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6156548	6156668	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6156669	6156826	1	-	1	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6156669	6156826	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6156827	6156902	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6156903	6157011	1	-	2	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6156903	6157011	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6157012	6157168	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6157169	6157266	1	-	1	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6157169	6157266	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6157267	6157364	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6157365	6157519	1	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6157365	6157519	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6157520	6157614	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6157615	6157698	0.88	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6157615	6157698	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	intron	6157699	6157804	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	CDS	6157805	6158086	0.72	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	exon	6157805	6158086	.	-	.	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
Phchi.S1	AUGUSTUS	start_codon	6158084	6158086	.	-	0	transcript_id "Phchi.S1G103200.t1"; gene_id "Phchi.S1G103200"
# This transcript jg3121.t2 is derived from g290.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3122.t1 is derived from g291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1840284	1843973	.	-	.	Phchi.S1G028100
Phchi.S1	AUGUSTUS	transcript	1840284	1843973	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	stop_codon	1840281	1840283	.	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1840284	1840383	1	-	1	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1840284	1840383	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1840384	1840476	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1840477	1840616	1	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1840477	1840616	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1840617	1840703	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1840704	1840971	0.9	-	1	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1840704	1840971	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1840972	1841115	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1841116	1841268	0.8	-	1	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1841116	1841268	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1841269	1841357	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1841358	1841404	1	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1841358	1841404	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1841405	1841488	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1841489	1841596	1	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1841489	1841596	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1841597	1841727	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1841728	1841986	1	-	1	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1841728	1841986	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1841987	1842082	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1842083	1842203	0.98	-	2	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1842083	1842203	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1842204	1842378	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1842379	1842433	0.85	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1842379	1842433	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1842434	1842539	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1842540	1842611	1	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1842540	1842611	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1842612	1842704	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1842705	1842753	1	-	1	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1842705	1842753	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1842754	1842886	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1842887	1843262	1	-	2	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1842887	1843262	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1843263	1843341	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1843342	1843618	0.93	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1843342	1843618	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	intron	1843619	1843733	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	CDS	1843734	1843973	0.44	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	exon	1843734	1843973	.	-	.	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
Phchi.S1	AUGUSTUS	start_codon	1843971	1843973	.	-	0	transcript_id "Phchi.S1G028100.t1"; gene_id "Phchi.S1G028100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9483.t1 is derived from g6659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41966410	41969566	.	-	.	Phchi.S1G664200
Phchi.S1	AUGUSTUS	transcript	41966410	41969566	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	stop_codon	41966407	41966409	.	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41966410	41966650	0.85	-	1	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41966410	41966650	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41966651	41966759	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41966760	41966839	0.85	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41966760	41966839	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41966840	41966987	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41966988	41967204	0.99	-	1	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41966988	41967204	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41967205	41967305	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41967306	41967667	0.99	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41967306	41967667	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41967668	41967755	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41967756	41967839	1	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41967756	41967839	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41967840	41967947	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41967948	41968046	1	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41967948	41968046	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41968047	41968232	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41968233	41969027	0.65	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41968233	41969027	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	intron	41969028	41969170	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	CDS	41969171	41969566	0.74	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	exon	41969171	41969566	.	-	.	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
Phchi.S1	AUGUSTUS	start_codon	41969564	41969566	.	-	0	transcript_id "Phchi.S1G664200.t1"; gene_id "Phchi.S1G664200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg41.t1 is derived from g9802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C201	AUGUSTUS	gene	11302	11580	.	+	.	Phchi.C201G000100
Phchi.C201	AUGUSTUS	transcript	11302	11580	.	+	.	transcript_id "Phchi.C201G000100.t1"; gene_id "Phchi.C201G000100"
Phchi.C201	AUGUSTUS	start_codon	11302	11304	.	+	0	transcript_id "Phchi.C201G000100.t1"; gene_id "Phchi.C201G000100"
Phchi.C201	AUGUSTUS	CDS	11302	11580	0.69	+	0	transcript_id "Phchi.C201G000100.t1"; gene_id "Phchi.C201G000100"
Phchi.C201	AUGUSTUS	exon	11302	11580	.	+	.	transcript_id "Phchi.C201G000100.t1"; gene_id "Phchi.C201G000100"
Phchi.C201	AUGUSTUS	stop_codon	11581	11583	.	+	0	transcript_id "Phchi.C201G000100.t1"; gene_id "Phchi.C201G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4388.t1 is derived from g1557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10185134	10187992	.	-	.	Phchi.S1G154700
Phchi.S1	AUGUSTUS	transcript	10185134	10187992	.	-	.	transcript_id "Phchi.S1G154700.t1"; gene_id "Phchi.S1G154700"
Phchi.S1	AUGUSTUS	stop_codon	10185131	10185133	.	-	0	transcript_id "Phchi.S1G154700.t1"; gene_id "Phchi.S1G154700"
Phchi.S1	AUGUSTUS	CDS	10185134	10187992	0.89	-	0	transcript_id "Phchi.S1G154700.t1"; gene_id "Phchi.S1G154700"
Phchi.S1	AUGUSTUS	exon	10185134	10187992	.	-	.	transcript_id "Phchi.S1G154700.t1"; gene_id "Phchi.S1G154700"
Phchi.S1	AUGUSTUS	start_codon	10187990	10187992	.	-	0	transcript_id "Phchi.S1G154700.t1"; gene_id "Phchi.S1G154700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1931.t1 is derived from g8851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3883947	3887038	.	-	.	Phchi.S5G054000
Phchi.S5	AUGUSTUS	transcript	3883947	3887038	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	stop_codon	3883944	3883946	.	-	0	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	CDS	3883947	3884939	1	-	0	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	exon	3883947	3884939	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	intron	3884940	3885038	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	CDS	3885039	3886258	1	-	2	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	exon	3885039	3886258	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	intron	3886259	3886380	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	CDS	3886381	3886512	1	-	2	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	exon	3886381	3886512	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	intron	3886513	3886629	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	CDS	3886630	3887038	0.79	-	0	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	exon	3886630	3887038	.	-	.	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
Phchi.S5	AUGUSTUS	start_codon	3887036	3887038	.	-	0	transcript_id "Phchi.S5G054000.t1"; gene_id "Phchi.S5G054000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10025.t1 is derived from g7201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45148389	45148718	.	-	.	Phchi.S1G718400
Phchi.S1	AUGUSTUS	transcript	45148389	45148718	.	-	.	transcript_id "Phchi.S1G718400.t1"; gene_id "Phchi.S1G718400"
Phchi.S1	AUGUSTUS	stop_codon	45148386	45148388	.	-	0	transcript_id "Phchi.S1G718400.t1"; gene_id "Phchi.S1G718400"
Phchi.S1	AUGUSTUS	CDS	45148389	45148718	0.52	-	0	transcript_id "Phchi.S1G718400.t1"; gene_id "Phchi.S1G718400"
Phchi.S1	AUGUSTUS	exon	45148389	45148718	.	-	.	transcript_id "Phchi.S1G718400.t1"; gene_id "Phchi.S1G718400"
Phchi.S1	AUGUSTUS	start_codon	45148716	45148718	.	-	0	transcript_id "Phchi.S1G718400.t1"; gene_id "Phchi.S1G718400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9783.t1 is derived from g6959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43668386	43669542	.	+	.	Phchi.S1G694200
Phchi.S1	AUGUSTUS	transcript	43668386	43669542	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	start_codon	43668386	43668388	.	+	0	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	CDS	43668386	43668464	1	+	0	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	exon	43668386	43668464	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	intron	43668465	43668559	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	CDS	43668560	43668795	1	+	2	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	exon	43668560	43668795	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	intron	43668796	43668908	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	CDS	43668909	43669391	1	+	0	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	exon	43668909	43669391	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	intron	43669392	43669533	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	CDS	43669534	43669542	1	+	0	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	exon	43669534	43669542	.	+	.	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
Phchi.S1	AUGUSTUS	stop_codon	43669543	43669545	.	+	0	transcript_id "Phchi.S1G694200.t1"; gene_id "Phchi.S1G694200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12163.t1 is derived from g7839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5078620	5080907	.	-	.	Phchi.S2G024300
Phchi.S2	AUGUSTUS	transcript	5078620	5080907	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	stop_codon	5078617	5078619	.	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5078620	5078717	1	-	2	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5078620	5078717	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5078718	5078805	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5078806	5078863	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5078806	5078863	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5078864	5078947	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5078948	5079097	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5078948	5079097	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079098	5079172	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079173	5079289	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079173	5079289	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079290	5079404	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079405	5079545	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079405	5079545	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079546	5079812	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079813	5079877	1	-	2	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079813	5079877	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079878	5079964	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079965	5080045	1	-	2	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079965	5080045	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080046	5080145	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080146	5080233	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080146	5080233	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080234	5080309	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080310	5080483	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080310	5080483	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080484	5080645	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080646	5080709	1	-	1	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080646	5080709	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080710	5080797	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080798	5080907	1	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080798	5080907	.	-	.	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	start_codon	5080905	5080907	.	-	0	transcript_id "Phchi.S2G024300.t1"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	transcript	5078620	5080907	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	stop_codon	5078617	5078619	.	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5078620	5078717	1	-	2	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5078620	5078717	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5078718	5078805	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5078806	5078863	1	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5078806	5078863	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5078864	5078947	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5078948	5079094	0.75	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5078948	5079094	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079095	5079172	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079173	5079289	1	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079173	5079289	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079290	5079404	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079405	5079545	1	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079405	5079545	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079546	5079812	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079813	5079877	1	-	2	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079813	5079877	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5079878	5079964	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5079965	5080045	1	-	2	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5079965	5080045	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080046	5080145	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080146	5080233	1	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080146	5080233	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080234	5080309	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080310	5080483	1	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080310	5080483	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080484	5080645	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080646	5080709	1	-	1	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080646	5080709	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	intron	5080710	5080797	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	CDS	5080798	5080907	0.99	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	exon	5080798	5080907	.	-	.	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
Phchi.S2	AUGUSTUS	start_codon	5080905	5080907	.	-	0	transcript_id "Phchi.S2G024300.t2"; gene_id "Phchi.S2G024300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4938.t1 is derived from g2108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13660728	13662476	.	+	.	Phchi.S1G209700
Phchi.S1	AUGUSTUS	transcript	13660728	13662476	.	+	.	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	start_codon	13660728	13660730	.	+	0	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	CDS	13660728	13660981	0.14	+	0	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	exon	13660728	13660981	.	+	.	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	intron	13660982	13661518	.	+	.	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	CDS	13661519	13662476	0.97	+	1	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	exon	13661519	13662476	.	+	.	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
Phchi.S1	AUGUSTUS	stop_codon	13662477	13662479	.	+	0	transcript_id "Phchi.S1G209700.t1"; gene_id "Phchi.S1G209700"
# This transcript jg15201.t2 is derived from g13669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15202.t1 is derived from g13670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17535902	17536750	.	+	.	Phchi.S3G252100
Phchi.S3	AUGUSTUS	transcript	17535902	17536750	.	+	.	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	start_codon	17535902	17535904	.	+	0	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	CDS	17535902	17535908	0.94	+	0	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	exon	17535902	17535908	.	+	.	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	intron	17535909	17536025	.	+	.	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	CDS	17536026	17536750	0.94	+	2	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	exon	17536026	17536750	.	+	.	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
Phchi.S3	AUGUSTUS	stop_codon	17536751	17536753	.	+	0	transcript_id "Phchi.S3G252100.t1"; gene_id "Phchi.S3G252100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14607.t1 is derived from g13075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13733562	13734134	.	+	.	Phchi.S3G192600
Phchi.S3	AUGUSTUS	transcript	13733562	13734134	.	+	.	transcript_id "Phchi.S3G192600.t1"; gene_id "Phchi.S3G192600"
Phchi.S3	AUGUSTUS	start_codon	13733562	13733564	.	+	0	transcript_id "Phchi.S3G192600.t1"; gene_id "Phchi.S3G192600"
Phchi.S3	AUGUSTUS	CDS	13733562	13734134	0.96	+	0	transcript_id "Phchi.S3G192600.t1"; gene_id "Phchi.S3G192600"
Phchi.S3	AUGUSTUS	exon	13733562	13734134	.	+	.	transcript_id "Phchi.S3G192600.t1"; gene_id "Phchi.S3G192600"
Phchi.S3	AUGUSTUS	stop_codon	13734135	13734137	.	+	0	transcript_id "Phchi.S3G192600.t1"; gene_id "Phchi.S3G192600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1155.t1 is derived from g10938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8069388	8074943	.	+	.	Phchi.S6G111400
Phchi.S6	AUGUSTUS	transcript	8069388	8074943	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	start_codon	8069388	8069390	.	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8069388	8069633	0.56	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8069388	8069633	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8069634	8069725	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8069726	8072320	0.99	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8069726	8072320	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8072321	8072413	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8072414	8072521	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8072414	8072521	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8072522	8072708	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8072709	8072809	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8072709	8072809	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8072810	8072897	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8072898	8072988	1	+	1	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8072898	8072988	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8072989	8073091	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8073092	8073202	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8073092	8073202	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8073203	8073292	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8073293	8073358	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8073293	8073358	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8073359	8073488	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8073489	8073548	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8073489	8073548	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8073549	8073747	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8073748	8074308	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8073748	8074308	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8074309	8074424	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8074425	8074562	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8074425	8074562	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8074563	8074677	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8074678	8074797	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8074678	8074797	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	intron	8074798	8074880	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	CDS	8074881	8074943	1	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	exon	8074881	8074943	.	+	.	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
Phchi.S6	AUGUSTUS	stop_codon	8074944	8074946	.	+	0	transcript_id "Phchi.S6G111400.t1"; gene_id "Phchi.S6G111400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2784.t1 is derived from g9704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8855217	8856449	.	+	.	Phchi.S5G139300
Phchi.S5	AUGUSTUS	transcript	8855217	8856449	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	start_codon	8855217	8855219	.	+	0	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	CDS	8855217	8855370	0.78	+	0	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	exon	8855217	8855370	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	intron	8855371	8855768	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	CDS	8855769	8855878	1	+	2	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	exon	8855769	8855878	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	intron	8855879	8855981	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	CDS	8855982	8856089	0.87	+	0	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	exon	8855982	8856089	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	intron	8856090	8856181	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	CDS	8856182	8856253	1	+	0	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	exon	8856182	8856253	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	intron	8856254	8856368	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	CDS	8856369	8856449	1	+	0	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	exon	8856369	8856449	.	+	.	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
Phchi.S5	AUGUSTUS	stop_codon	8856450	8856452	.	+	0	transcript_id "Phchi.S5G139300.t1"; gene_id "Phchi.S5G139300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11800.t1 is derived from g15852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8208822	8212112	.	-	.	Phchi.S4G138200
Phchi.S4	AUGUSTUS	transcript	8208822	8212112	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	stop_codon	8208819	8208821	.	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8208822	8208917	1	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8208822	8208917	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8208918	8209004	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8209005	8209210	0.97	-	2	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8209005	8209210	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8209211	8209314	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8209315	8209355	0.99	-	1	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8209315	8209355	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8209356	8209463	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8209464	8209599	0.7	-	2	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8209464	8209599	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8209600	8209717	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8209718	8209810	0.85	-	2	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8209718	8209810	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8209811	8209913	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8209914	8210043	0.86	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8209914	8210043	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8210044	8210182	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8210183	8210265	1	-	2	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8210183	8210265	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8210266	8210401	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8210402	8210485	1	-	2	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8210402	8210485	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8210486	8210613	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8210614	8210677	1	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8210614	8210677	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8210678	8210784	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8210785	8210841	0.98	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8210785	8210841	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8210842	8210938	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8210939	8211001	1	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8210939	8211001	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8211002	8211221	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8211222	8211260	1	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8211222	8211260	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8211261	8211466	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8211467	8211526	1	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8211467	8211526	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8211527	8211613	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8211614	8211671	1	-	1	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8211614	8211671	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8211672	8211836	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8211837	8211942	0.91	-	2	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8211837	8211942	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	intron	8211943	8212081	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	CDS	8212082	8212112	0.91	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	exon	8212082	8212112	.	-	.	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
Phchi.S4	AUGUSTUS	start_codon	8212110	8212112	.	-	0	transcript_id "Phchi.S4G138200.t1"; gene_id "Phchi.S4G138200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6287.t1 is derived from g3459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22092686	22093861	.	-	.	Phchi.S1G344600
Phchi.S1	AUGUSTUS	transcript	22092686	22093861	.	-	.	transcript_id "Phchi.S1G344600.t1"; gene_id "Phchi.S1G344600"
Phchi.S1	AUGUSTUS	stop_codon	22092683	22092685	.	-	0	transcript_id "Phchi.S1G344600.t1"; gene_id "Phchi.S1G344600"
Phchi.S1	AUGUSTUS	CDS	22092686	22093861	1	-	0	transcript_id "Phchi.S1G344600.t1"; gene_id "Phchi.S1G344600"
Phchi.S1	AUGUSTUS	exon	22092686	22093861	.	-	.	transcript_id "Phchi.S1G344600.t1"; gene_id "Phchi.S1G344600"
Phchi.S1	AUGUSTUS	start_codon	22093859	22093861	.	-	0	transcript_id "Phchi.S1G344600.t1"; gene_id "Phchi.S1G344600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4302.t1 is derived from g1471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9513056	9514135	.	-	.	Phchi.S1G146100
Phchi.S1	AUGUSTUS	transcript	9513056	9514135	.	-	.	transcript_id "Phchi.S1G146100.t1"; gene_id "Phchi.S1G146100"
Phchi.S1	AUGUSTUS	stop_codon	9513053	9513055	.	-	0	transcript_id "Phchi.S1G146100.t1"; gene_id "Phchi.S1G146100"
Phchi.S1	AUGUSTUS	CDS	9513056	9514135	0.52	-	0	transcript_id "Phchi.S1G146100.t1"; gene_id "Phchi.S1G146100"
Phchi.S1	AUGUSTUS	exon	9513056	9514135	.	-	.	transcript_id "Phchi.S1G146100.t1"; gene_id "Phchi.S1G146100"
Phchi.S1	AUGUSTUS	start_codon	9514133	9514135	.	-	0	transcript_id "Phchi.S1G146100.t1"; gene_id "Phchi.S1G146100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14883.t1 is derived from g13351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15269338	15270297	.	-	.	Phchi.S3G220200
Phchi.S3	AUGUSTUS	transcript	15269338	15270297	.	-	.	transcript_id "Phchi.S3G220200.t1"; gene_id "Phchi.S3G220200"
Phchi.S3	AUGUSTUS	stop_codon	15269335	15269337	.	-	0	transcript_id "Phchi.S3G220200.t1"; gene_id "Phchi.S3G220200"
Phchi.S3	AUGUSTUS	CDS	15269338	15270297	0.54	-	0	transcript_id "Phchi.S3G220200.t1"; gene_id "Phchi.S3G220200"
Phchi.S3	AUGUSTUS	exon	15269338	15270297	.	-	.	transcript_id "Phchi.S3G220200.t1"; gene_id "Phchi.S3G220200"
Phchi.S3	AUGUSTUS	start_codon	15270295	15270297	.	-	0	transcript_id "Phchi.S3G220200.t1"; gene_id "Phchi.S3G220200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13729.t1 is derived from g12196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8573820	8574968	.	+	.	Phchi.S3G104800
Phchi.S3	AUGUSTUS	transcript	8573820	8574968	.	+	.	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	start_codon	8573820	8573822	.	+	0	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	CDS	8573820	8573834	0.35	+	0	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	exon	8573820	8573834	.	+	.	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	intron	8573835	8573923	.	+	.	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	CDS	8573924	8574484	1	+	0	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	exon	8573924	8574484	.	+	.	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	intron	8574485	8574668	.	+	.	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	CDS	8574669	8574968	0.84	+	0	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	exon	8574669	8574968	.	+	.	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
Phchi.S3	AUGUSTUS	stop_codon	8574969	8574971	.	+	0	transcript_id "Phchi.S3G104800.t1"; gene_id "Phchi.S3G104800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7559.t1 is derived from g4733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30031538	30033653	.	-	.	Phchi.S1G471800
Phchi.S1	AUGUSTUS	transcript	30031538	30033653	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	stop_codon	30031535	30031537	.	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30031538	30031681	1	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30031538	30031681	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30031682	30031773	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30031774	30031932	1	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30031774	30031932	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30031933	30032012	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30032013	30032094	1	-	1	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30032013	30032094	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30032095	30032217	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30032218	30032306	1	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30032218	30032306	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30032307	30032406	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30032407	30032484	1	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30032407	30032484	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30032485	30032618	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30032619	30032676	1	-	1	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30032619	30032676	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30032677	30032781	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30032782	30033011	0.98	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30032782	30033011	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30033012	30033114	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30033115	30033259	1	-	1	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30033115	30033259	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30033260	30033350	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30033351	30033392	1	-	1	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30033351	30033392	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	intron	30033393	30033525	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	CDS	30033526	30033653	0.65	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	exon	30033526	30033653	.	-	.	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
Phchi.S1	AUGUSTUS	start_codon	30033651	30033653	.	-	0	transcript_id "Phchi.S1G471800.t1"; gene_id "Phchi.S1G471800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10309.t1 is derived from g7485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47073594	47075110	.	-	.	Phchi.S1G746800
Phchi.S1	AUGUSTUS	transcript	47073594	47075110	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	stop_codon	47073591	47073593	.	-	0	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	CDS	47073594	47073716	1	-	0	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	exon	47073594	47073716	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	intron	47073717	47073793	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	CDS	47073794	47074030	1	-	0	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	exon	47073794	47074030	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	intron	47074031	47074125	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	CDS	47074126	47074299	1	-	0	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	exon	47074126	47074299	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	intron	47074300	47074391	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	CDS	47074392	47074531	1	-	2	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	exon	47074392	47074531	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	intron	47074532	47074611	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	CDS	47074612	47075110	0.99	-	0	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	exon	47074612	47075110	.	-	.	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
Phchi.S1	AUGUSTUS	start_codon	47075108	47075110	.	-	0	transcript_id "Phchi.S1G746800.t1"; gene_id "Phchi.S1G746800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4186.t1 is derived from g1355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8806995	8808047	.	-	.	Phchi.S1G134500
Phchi.S1	AUGUSTUS	transcript	8806995	8808047	.	-	.	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	stop_codon	8806992	8806994	.	-	0	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	CDS	8806995	8807193	0.85	-	1	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	exon	8806995	8807193	.	-	.	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	intron	8807194	8807541	.	-	.	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	CDS	8807542	8808047	0.77	-	0	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	exon	8807542	8808047	.	-	.	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
Phchi.S1	AUGUSTUS	start_codon	8808045	8808047	.	-	0	transcript_id "Phchi.S1G134500.t1"; gene_id "Phchi.S1G134500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9489.t1 is derived from g6665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41992582	41994084	.	-	.	Phchi.S1G664800
Phchi.S1	AUGUSTUS	transcript	41992582	41994084	.	-	.	transcript_id "Phchi.S1G664800.t1"; gene_id "Phchi.S1G664800"
Phchi.S1	AUGUSTUS	stop_codon	41992579	41992581	.	-	0	transcript_id "Phchi.S1G664800.t1"; gene_id "Phchi.S1G664800"
Phchi.S1	AUGUSTUS	CDS	41992582	41994084	0.53	-	0	transcript_id "Phchi.S1G664800.t1"; gene_id "Phchi.S1G664800"
Phchi.S1	AUGUSTUS	exon	41992582	41994084	.	-	.	transcript_id "Phchi.S1G664800.t1"; gene_id "Phchi.S1G664800"
Phchi.S1	AUGUSTUS	start_codon	41994082	41994084	.	-	0	transcript_id "Phchi.S1G664800.t1"; gene_id "Phchi.S1G664800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1443.t1 is derived from g8362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	915139	917619	.	+	.	Phchi.S5G005200
Phchi.S5	AUGUSTUS	transcript	915139	917619	.	+	.	transcript_id "Phchi.S5G005200.t1"; gene_id "Phchi.S5G005200"
Phchi.S5	AUGUSTUS	start_codon	915139	915141	.	+	0	transcript_id "Phchi.S5G005200.t1"; gene_id "Phchi.S5G005200"
Phchi.S5	AUGUSTUS	CDS	915139	917619	0.94	+	0	transcript_id "Phchi.S5G005200.t1"; gene_id "Phchi.S5G005200"
Phchi.S5	AUGUSTUS	exon	915139	917619	.	+	.	transcript_id "Phchi.S5G005200.t1"; gene_id "Phchi.S5G005200"
Phchi.S5	AUGUSTUS	stop_codon	917620	917622	.	+	0	transcript_id "Phchi.S5G005200.t1"; gene_id "Phchi.S5G005200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14393.t1 is derived from g12861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12585765	12587555	.	+	.	Phchi.S3G171200
Phchi.S3	AUGUSTUS	transcript	12585765	12587555	.	+	.	transcript_id "Phchi.S3G171200.t1"; gene_id "Phchi.S3G171200"
Phchi.S3	AUGUSTUS	start_codon	12585765	12585767	.	+	0	transcript_id "Phchi.S3G171200.t1"; gene_id "Phchi.S3G171200"
Phchi.S3	AUGUSTUS	CDS	12585765	12587555	0.83	+	0	transcript_id "Phchi.S3G171200.t1"; gene_id "Phchi.S3G171200"
Phchi.S3	AUGUSTUS	exon	12585765	12587555	.	+	.	transcript_id "Phchi.S3G171200.t1"; gene_id "Phchi.S3G171200"
Phchi.S3	AUGUSTUS	stop_codon	12587556	12587558	.	+	0	transcript_id "Phchi.S3G171200.t1"; gene_id "Phchi.S3G171200"
# This transcript jg13605.t2 is derived from g12072.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13606.t1 is derived from g12073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7672480	7676378	.	-	.	Phchi.S3G092500
Phchi.S3	AUGUSTUS	transcript	7672480	7676378	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	stop_codon	7672477	7672479	.	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7672480	7672554	0.84	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7672480	7672554	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7672555	7672643	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7672644	7672739	1	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7672644	7672739	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7672740	7672830	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7672831	7672892	1	-	2	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7672831	7672892	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7672893	7672981	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7672982	7673046	1	-	1	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7672982	7673046	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7673047	7673124	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7673125	7673193	1	-	1	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7673125	7673193	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7673194	7673263	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7673264	7673356	1	-	1	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7673264	7673356	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7673357	7673478	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7673479	7673582	0.76	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7673479	7673582	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7673583	7673709	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7673710	7673793	1	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7673710	7673793	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7673794	7673887	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7673888	7673980	1	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7673888	7673980	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7673981	7674078	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7674079	7674130	0.78	-	1	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7674079	7674130	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7674131	7674232	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7674233	7674304	0.77	-	1	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7674233	7674304	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7674305	7674397	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7674398	7674473	1	-	2	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7674398	7674473	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7674474	7674565	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7674566	7674678	0.89	-	1	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7674566	7674678	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7674679	7674787	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7674788	7674935	0.78	-	2	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7674788	7674935	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7674936	7675053	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7675054	7675131	1	-	2	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7675054	7675131	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7675132	7675214	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7675215	7675344	1	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7675215	7675344	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7675345	7675418	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7675419	7675594	1	-	2	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7675419	7675594	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7675595	7675674	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7675675	7675735	1	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7675675	7675735	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7675736	7675833	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7675834	7675943	0.98	-	2	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7675834	7675943	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7675944	7676205	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7676206	7676263	0.53	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7676206	7676263	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	intron	7676264	7676354	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	CDS	7676355	7676378	0.8	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	exon	7676355	7676378	.	-	.	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
Phchi.S3	AUGUSTUS	start_codon	7676376	7676378	.	-	0	transcript_id "Phchi.S3G092500.t1"; gene_id "Phchi.S3G092500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5328.t1 is derived from g2498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16306205	16307831	.	-	.	Phchi.S1G248700
Phchi.S1	AUGUSTUS	transcript	16306205	16307831	.	-	.	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	stop_codon	16306202	16306204	.	-	0	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	CDS	16306205	16306633	0.84	-	0	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	exon	16306205	16306633	.	-	.	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	intron	16306634	16306868	.	-	.	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	CDS	16306869	16307831	1	-	0	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	exon	16306869	16307831	.	-	.	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
Phchi.S1	AUGUSTUS	start_codon	16307829	16307831	.	-	0	transcript_id "Phchi.S1G248700.t1"; gene_id "Phchi.S1G248700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7680.t1 is derived from g4854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30590502	30591756	.	+	.	Phchi.S1G483900
Phchi.S1	AUGUSTUS	transcript	30590502	30591756	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	start_codon	30590502	30590504	.	+	0	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	CDS	30590502	30590723	0.46	+	0	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	exon	30590502	30590723	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	intron	30590724	30590826	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	CDS	30590827	30591113	0.38	+	0	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	exon	30590827	30591113	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	intron	30591114	30591227	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	CDS	30591228	30591294	0.86	+	1	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	exon	30591228	30591294	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	intron	30591295	30591369	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	CDS	30591370	30591756	0.86	+	0	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	exon	30591370	30591756	.	+	.	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
Phchi.S1	AUGUSTUS	stop_codon	30591757	30591759	.	+	0	transcript_id "Phchi.S1G483900.t1"; gene_id "Phchi.S1G483900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2961.t1 is derived from g130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	801861	808089	.	+	.	Phchi.S1G012000
Phchi.S1	AUGUSTUS	transcript	801861	808089	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	start_codon	801861	801863	.	+	0	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	801861	802101	0.94	+	0	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	801861	802101	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	802102	802258	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	802259	802557	1	+	2	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	802259	802557	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	802558	802672	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	802673	802890	0.77	+	0	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	802673	802890	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	802891	803034	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	803035	803298	0.97	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	803035	803298	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	803299	803399	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	803400	803638	0.84	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	803400	803638	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	803639	803802	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	803803	803923	1	+	2	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	803803	803923	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	803924	804049	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	804050	804118	1	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	804050	804118	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	804119	804211	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	804212	804283	1	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	804212	804283	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	804284	804370	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	804371	804439	1	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	804371	804439	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	804440	804559	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	804560	804792	0.95	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	804560	804792	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	804793	804897	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	804898	805109	1	+	2	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	804898	805109	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	805110	805310	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	805311	805437	0.98	+	0	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	805311	805437	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	805438	805539	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	805540	805608	1	+	2	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	805540	805608	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	805609	805728	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	805729	805778	1	+	2	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	805729	805778	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	805779	805905	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	805906	806516	0.84	+	0	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	805906	806516	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	806517	806705	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	806706	806876	0.8	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	806706	806876	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	806877	806982	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	806983	807072	0.39	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	806983	807072	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	807073	807261	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	807262	807747	0.8	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	807262	807747	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	intron	807748	807845	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	CDS	807846	808089	1	+	1	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	exon	807846	808089	.	+	.	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
Phchi.S1	AUGUSTUS	stop_codon	808090	808092	.	+	0	transcript_id "Phchi.S1G012000.t1"; gene_id "Phchi.S1G012000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3156.t1 is derived from g325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2012142	2013742	.	-	.	Phchi.S1G031500
Phchi.S1	AUGUSTUS	transcript	2012142	2013742	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	stop_codon	2012139	2012141	.	-	0	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	CDS	2012142	2012374	0.95	-	2	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	exon	2012142	2012374	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	intron	2012375	2012470	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	CDS	2012471	2012723	1	-	0	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	exon	2012471	2012723	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	intron	2012724	2012828	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	CDS	2012829	2012961	0.95	-	1	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	exon	2012829	2012961	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	intron	2012962	2013033	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	CDS	2013034	2013065	0.95	-	0	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	exon	2013034	2013065	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	intron	2013066	2013188	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	CDS	2013189	2013328	0.99	-	2	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	exon	2013189	2013328	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	intron	2013329	2013417	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	CDS	2013418	2013742	0.99	-	0	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	exon	2013418	2013742	.	-	.	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
Phchi.S1	AUGUSTUS	start_codon	2013740	2013742	.	-	0	transcript_id "Phchi.S1G031500.t1"; gene_id "Phchi.S1G031500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg177.t1 is derived from g9959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1024852	1025597	.	-	.	Phchi.S6G013600
Phchi.S6	AUGUSTUS	transcript	1024852	1025597	.	-	.	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	stop_codon	1024849	1024851	.	-	0	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	CDS	1024852	1025427	1	-	0	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	exon	1024852	1025427	.	-	.	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	intron	1025428	1025495	.	-	.	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	CDS	1025496	1025597	0.47	-	0	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	exon	1025496	1025597	.	-	.	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
Phchi.S6	AUGUSTUS	start_codon	1025595	1025597	.	-	0	transcript_id "Phchi.S6G013600.t1"; gene_id "Phchi.S6G013600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1828.t1 is derived from g8748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3370066	3372583	.	+	.	Phchi.S5G043700
Phchi.S5	AUGUSTUS	transcript	3370066	3372583	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	start_codon	3370066	3370068	.	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3370066	3370280	1	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3370066	3370280	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3370281	3370379	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3370380	3370692	1	+	1	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3370380	3370692	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3370693	3370816	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3370817	3370972	1	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3370817	3370972	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3370973	3371114	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3371115	3371375	1	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3371115	3371375	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3371376	3371500	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3371501	3371590	1	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3371501	3371590	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3371591	3371799	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3371800	3371878	1	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3371800	3371878	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3371879	3372015	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3372016	3372122	1	+	2	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3372016	3372122	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3372123	3372235	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3372236	3372354	1	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3372236	3372354	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	intron	3372355	3372483	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	CDS	3372484	3372583	1	+	1	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	exon	3372484	3372583	.	+	.	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
Phchi.S5	AUGUSTUS	stop_codon	3372584	3372586	.	+	0	transcript_id "Phchi.S5G043700.t1"; gene_id "Phchi.S5G043700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13368.t1 is derived from g11834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6369805	6371198	.	-	.	Phchi.S3G068700
Phchi.S3	AUGUSTUS	transcript	6369805	6371198	.	-	.	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	stop_codon	6369802	6369804	.	-	0	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	CDS	6369805	6370752	0.63	-	0	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	exon	6369805	6370752	.	-	.	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	intron	6370753	6370820	.	-	.	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	CDS	6370821	6371198	0.49	-	0	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	exon	6370821	6371198	.	-	.	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
Phchi.S3	AUGUSTUS	start_codon	6371196	6371198	.	-	0	transcript_id "Phchi.S3G068700.t1"; gene_id "Phchi.S3G068700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11613.t1 is derived from g15664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7330133	7331744	.	+	.	Phchi.S4G119500
Phchi.S4	AUGUSTUS	transcript	7330133	7331744	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	start_codon	7330133	7330135	.	+	0	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	CDS	7330133	7330359	1	+	0	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	exon	7330133	7330359	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	intron	7330360	7330458	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	CDS	7330459	7330624	1	+	1	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	exon	7330459	7330624	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	intron	7330625	7330719	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	CDS	7330720	7330799	1	+	0	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	exon	7330720	7330799	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	intron	7330800	7330896	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	CDS	7330897	7331324	1	+	1	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	exon	7330897	7331324	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	intron	7331325	7331424	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	CDS	7331425	7331744	0.99	+	2	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	exon	7331425	7331744	.	+	.	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
Phchi.S4	AUGUSTUS	stop_codon	7331745	7331747	.	+	0	transcript_id "Phchi.S4G119500.t1"; gene_id "Phchi.S4G119500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9290.t1 is derived from g6465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40783405	40783846	.	-	.	Phchi.S1G644900
Phchi.S1	AUGUSTUS	transcript	40783405	40783846	.	-	.	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	stop_codon	40783402	40783404	.	-	0	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	CDS	40783405	40783671	0.88	-	0	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	exon	40783405	40783671	.	-	.	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	intron	40783672	40783762	.	-	.	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	CDS	40783763	40783846	0.97	-	0	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	exon	40783763	40783846	.	-	.	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
Phchi.S1	AUGUSTUS	start_codon	40783844	40783846	.	-	0	transcript_id "Phchi.S1G644900.t1"; gene_id "Phchi.S1G644900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3739.t1 is derived from g908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5457532	5459238	.	+	.	Phchi.S1G089800
Phchi.S1	AUGUSTUS	transcript	5457532	5459238	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	start_codon	5457532	5457534	.	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5457532	5457672	0.39	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5457532	5457672	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	intron	5457673	5457813	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5457814	5457930	0.92	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5457814	5457930	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	intron	5457931	5458028	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5458029	5458163	0.94	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5458029	5458163	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	intron	5458164	5458261	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5458262	5458360	0.97	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5458262	5458360	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	intron	5458361	5458473	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5458474	5458777	0.99	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5458474	5458777	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	intron	5458778	5458864	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5458865	5459088	1	+	2	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5458865	5459088	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	intron	5459089	5459178	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	CDS	5459179	5459238	1	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	exon	5459179	5459238	.	+	.	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
Phchi.S1	AUGUSTUS	stop_codon	5459239	5459241	.	+	0	transcript_id "Phchi.S1G089800.t1"; gene_id "Phchi.S1G089800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg477.t1 is derived from g10259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3348238	3348796	.	+	.	Phchi.S6G043600
Phchi.S6	AUGUSTUS	transcript	3348238	3348796	.	+	.	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	start_codon	3348238	3348240	.	+	0	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	CDS	3348238	3348444	1	+	0	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	exon	3348238	3348444	.	+	.	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	intron	3348445	3348519	.	+	.	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	CDS	3348520	3348622	0.95	+	0	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	exon	3348520	3348622	.	+	.	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	intron	3348623	3348752	.	+	.	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	CDS	3348753	3348796	0.77	+	2	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	exon	3348753	3348796	.	+	.	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
Phchi.S6	AUGUSTUS	stop_codon	3348797	3348799	.	+	0	transcript_id "Phchi.S6G043600.t1"; gene_id "Phchi.S6G043600"
# This transcript jg12115.t2 is derived from g7791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12116.t1 is derived from g7792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3642927	3648014	.	-	.	Phchi.S2G019600
Phchi.S2	AUGUSTUS	transcript	3642927	3648014	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	stop_codon	3642924	3642926	.	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3642927	3642997	1	-	2	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3642927	3642997	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3642998	3643120	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3643121	3643307	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3643121	3643307	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3643308	3643437	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3643438	3643588	1	-	1	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3643438	3643588	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3643589	3643731	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3643732	3643844	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3643732	3643844	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3643845	3643947	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3643948	3644017	0.61	-	1	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3643948	3644017	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3644018	3644112	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3644113	3644324	0.81	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3644113	3644324	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3644325	3644503	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3644504	3644585	1	-	1	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3644504	3644585	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3644586	3645240	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3645241	3645296	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3645241	3645296	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3645297	3645427	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3645428	3645496	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3645428	3645496	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3645497	3645686	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3645687	3645941	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3645687	3645941	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3645942	3646185	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3646186	3646362	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3646186	3646362	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3646363	3646907	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3646908	3647054	1	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3646908	3647054	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3647055	3647363	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3647364	3647496	1	-	1	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3647364	3647496	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	intron	3647497	3647808	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	CDS	3647809	3648014	0.97	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	exon	3647809	3648014	.	-	.	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
Phchi.S2	AUGUSTUS	start_codon	3648012	3648014	.	-	0	transcript_id "Phchi.S2G019600.t1"; gene_id "Phchi.S2G019600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5501.t1 is derived from g2671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17147491	17148986	.	-	.	Phchi.S1G266000
Phchi.S1	AUGUSTUS	transcript	17147491	17148986	.	-	.	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	stop_codon	17147488	17147490	.	-	0	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	CDS	17147491	17148216	1	-	0	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	exon	17147491	17148216	.	-	.	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	intron	17148217	17148317	.	-	.	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	CDS	17148318	17148986	1	-	0	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	exon	17148318	17148986	.	-	.	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
Phchi.S1	AUGUSTUS	start_codon	17148984	17148986	.	-	0	transcript_id "Phchi.S1G266000.t1"; gene_id "Phchi.S1G266000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg280.t1 is derived from g10062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2010667	2011818	.	-	.	Phchi.S6G023900
Phchi.S6	AUGUSTUS	transcript	2010667	2011818	.	-	.	transcript_id "Phchi.S6G023900.t1"; gene_id "Phchi.S6G023900"
Phchi.S6	AUGUSTUS	stop_codon	2010664	2010666	.	-	0	transcript_id "Phchi.S6G023900.t1"; gene_id "Phchi.S6G023900"
Phchi.S6	AUGUSTUS	CDS	2010667	2011818	1	-	0	transcript_id "Phchi.S6G023900.t1"; gene_id "Phchi.S6G023900"
Phchi.S6	AUGUSTUS	exon	2010667	2011818	.	-	.	transcript_id "Phchi.S6G023900.t1"; gene_id "Phchi.S6G023900"
Phchi.S6	AUGUSTUS	start_codon	2011816	2011818	.	-	0	transcript_id "Phchi.S6G023900.t1"; gene_id "Phchi.S6G023900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9177.t1 is derived from g6352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40232658	40233837	.	+	.	Phchi.S1G633600
Phchi.S1	AUGUSTUS	transcript	40232658	40233837	.	+	.	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	start_codon	40232658	40232660	.	+	0	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	CDS	40232658	40232672	0.34	+	0	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	exon	40232658	40232672	.	+	.	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	intron	40232673	40232871	.	+	.	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	CDS	40232872	40233837	1	+	0	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	exon	40232872	40233837	.	+	.	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
Phchi.S1	AUGUSTUS	stop_codon	40233838	40233840	.	+	0	transcript_id "Phchi.S1G633600.t1"; gene_id "Phchi.S1G633600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1924.t1 is derived from g8844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3871191	3872228	.	-	.	Phchi.S5G053300
Phchi.S5	AUGUSTUS	transcript	3871191	3872228	.	-	.	transcript_id "Phchi.S5G053300.t1"; gene_id "Phchi.S5G053300"
Phchi.S5	AUGUSTUS	stop_codon	3871188	3871190	.	-	0	transcript_id "Phchi.S5G053300.t1"; gene_id "Phchi.S5G053300"
Phchi.S5	AUGUSTUS	CDS	3871191	3872228	0.53	-	0	transcript_id "Phchi.S5G053300.t1"; gene_id "Phchi.S5G053300"
Phchi.S5	AUGUSTUS	exon	3871191	3872228	.	-	.	transcript_id "Phchi.S5G053300.t1"; gene_id "Phchi.S5G053300"
Phchi.S5	AUGUSTUS	start_codon	3872226	3872228	.	-	0	transcript_id "Phchi.S5G053300.t1"; gene_id "Phchi.S5G053300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2769.t1 is derived from g9689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8747060	8749126	.	+	.	Phchi.S5G137800
Phchi.S5	AUGUSTUS	transcript	8747060	8749126	.	+	.	transcript_id "Phchi.S5G137800.t1"; gene_id "Phchi.S5G137800"
Phchi.S5	AUGUSTUS	start_codon	8747060	8747062	.	+	0	transcript_id "Phchi.S5G137800.t1"; gene_id "Phchi.S5G137800"
Phchi.S5	AUGUSTUS	CDS	8747060	8749126	0.98	+	0	transcript_id "Phchi.S5G137800.t1"; gene_id "Phchi.S5G137800"
Phchi.S5	AUGUSTUS	exon	8747060	8749126	.	+	.	transcript_id "Phchi.S5G137800.t1"; gene_id "Phchi.S5G137800"
Phchi.S5	AUGUSTUS	stop_codon	8749127	8749129	.	+	0	transcript_id "Phchi.S5G137800.t1"; gene_id "Phchi.S5G137800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12963.t1 is derived from g11428.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3352668	3356019	.	+	.	Phchi.S3G028200
Phchi.S3	AUGUSTUS	transcript	3353150	3356019	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	start_codon	3353150	3353152	.	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3353150	3353205	0.98	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3353150	3353205	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3353206	3353288	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3353289	3353661	0.98	+	1	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3353289	3353661	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3353662	3353745	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3353746	3353936	1	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3353746	3353936	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3353937	3354122	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3354123	3354258	1	+	1	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3354123	3354258	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3354259	3354355	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3354356	3354496	1	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3354356	3354496	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3354497	3354605	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3354606	3354964	1	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3354606	3354964	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3354965	3355041	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3355042	3355306	1	+	1	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3355042	3355306	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3355307	3355424	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3355425	3355496	1	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3355425	3355496	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3355497	3355596	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3355597	3356019	0.86	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3355597	3356019	.	+	.	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	stop_codon	3356020	3356022	.	+	0	transcript_id "Phchi.S3G028200.t1"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	transcript	3352668	3356019	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	start_codon	3352668	3352670	.	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3352668	3352699	0.2	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3352668	3352699	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3352700	3353288	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3353289	3353661	0.33	+	1	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3353289	3353661	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3353662	3353745	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3353746	3353936	1	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3353746	3353936	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3353937	3354122	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3354123	3354258	1	+	1	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3354123	3354258	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3354259	3354355	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3354356	3354496	1	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3354356	3354496	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3354497	3354605	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3354606	3354964	1	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3354606	3354964	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3354965	3355041	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3355042	3355306	0.97	+	1	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3355042	3355306	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3355307	3355424	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3355425	3355496	1	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3355425	3355496	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	intron	3355497	3355596	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	CDS	3355597	3356019	0.93	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	exon	3355597	3356019	.	+	.	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
Phchi.S3	AUGUSTUS	stop_codon	3356020	3356022	.	+	0	transcript_id "Phchi.S3G028200.t2"; gene_id "Phchi.S3G028200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1435.t1 is derived from g8354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	828021	830887	.	-	.	Phchi.S5G004400
Phchi.S5	AUGUSTUS	transcript	828021	830887	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	stop_codon	828018	828020	.	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	828021	828114	0.78	-	1	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	828021	828114	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	828115	828226	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	828227	828933	0.51	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	828227	828933	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	828934	829024	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	829025	829168	1	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	829025	829168	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	829169	829287	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	829288	829344	1	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	829288	829344	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	829345	829432	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	829433	829498	1	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	829433	829498	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	829499	829597	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	829598	829680	1	-	2	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	829598	829680	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	829681	829770	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	829771	829849	1	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	829771	829849	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	829850	830008	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	830009	830096	0.87	-	1	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	830009	830096	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	830097	830202	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	830203	830303	0.86	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	830203	830303	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	830304	830418	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	830419	830496	0.99	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	830419	830496	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	830497	830653	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	830654	830697	1	-	2	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	830654	830697	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	intron	830698	830769	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	CDS	830770	830887	1	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	exon	830770	830887	.	-	.	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
Phchi.S5	AUGUSTUS	start_codon	830885	830887	.	-	0	transcript_id "Phchi.S5G004400.t1"; gene_id "Phchi.S5G004400"
# This transcript jg1918.t2 is derived from g8838.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1919.t1 is derived from g8839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3846762	3849209	.	+	.	Phchi.S5G052800
Phchi.S5	AUGUSTUS	transcript	3846762	3849209	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	start_codon	3846762	3846764	.	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3846762	3847014	0.88	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3846762	3847014	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3847015	3847275	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3847276	3847442	1	+	2	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3847276	3847442	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3847443	3847581	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3847582	3847680	1	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3847582	3847680	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3847681	3847762	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3847763	3847873	0.99	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3847763	3847873	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3847874	3847974	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3847975	3848037	0.99	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3847975	3848037	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3848038	3848130	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3848131	3848240	0.9	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3848131	3848240	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3848241	3848318	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3848319	3848427	0.62	+	1	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3848319	3848427	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3848428	3848523	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3848524	3848625	1	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3848524	3848625	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3848626	3848745	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3848746	3848859	1	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3848746	3848859	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3848860	3848952	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3848953	3849027	1	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3848953	3849027	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	intron	3849028	3849107	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	CDS	3849108	3849209	1	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	exon	3849108	3849209	.	+	.	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
Phchi.S5	AUGUSTUS	stop_codon	3849210	3849212	.	+	0	transcript_id "Phchi.S5G052800.t1"; gene_id "Phchi.S5G052800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9443.t1 is derived from g6619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41490901	41493163	.	-	.	Phchi.S1G660200
Phchi.S1	AUGUSTUS	transcript	41490901	41493163	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	stop_codon	41490898	41490900	.	-	0	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	CDS	41490901	41491134	0.74	-	0	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	exon	41490901	41491134	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	intron	41491135	41491218	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	CDS	41491219	41491302	0.75	-	0	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	exon	41491219	41491302	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	intron	41491303	41491439	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	CDS	41491440	41491477	0.37	-	2	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	exon	41491440	41491477	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	intron	41491478	41491687	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	CDS	41491688	41491866	0.21	-	1	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	exon	41491688	41491866	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	intron	41491867	41491976	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	CDS	41491977	41493163	0.12	-	0	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	exon	41491977	41493163	.	-	.	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
Phchi.S1	AUGUSTUS	start_codon	41493161	41493163	.	-	0	transcript_id "Phchi.S1G660200.t1"; gene_id "Phchi.S1G660200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2615.t1 is derived from g9535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7792322	7793719	.	-	.	Phchi.S5G122400
Phchi.S5	AUGUSTUS	transcript	7792322	7793719	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	stop_codon	7792319	7792321	.	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	CDS	7792322	7792425	0.66	-	2	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	exon	7792322	7792425	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	intron	7792426	7792556	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	CDS	7792557	7792668	0.47	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	exon	7792557	7792668	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	intron	7792669	7792754	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	CDS	7792755	7792805	1	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	exon	7792755	7792805	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	intron	7792806	7792933	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	CDS	7792934	7793077	1	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	exon	7792934	7793077	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	intron	7793078	7793308	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	CDS	7793309	7793389	0.89	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	exon	7793309	7793389	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	intron	7793390	7793611	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	CDS	7793612	7793719	0.98	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	exon	7793612	7793719	.	-	.	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
Phchi.S5	AUGUSTUS	start_codon	7793717	7793719	.	-	0	transcript_id "Phchi.S5G122400.t1"; gene_id "Phchi.S5G122400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5870.t1 is derived from g3040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19486867	19487514	.	+	.	Phchi.S1G302900
Phchi.S1	AUGUSTUS	transcript	19486867	19487514	.	+	.	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	start_codon	19486867	19486869	.	+	0	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	CDS	19486867	19486871	0.43	+	0	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	exon	19486867	19486871	.	+	.	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	intron	19486872	19486993	.	+	.	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	CDS	19486994	19487139	0.86	+	1	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	exon	19486994	19487139	.	+	.	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	intron	19487140	19487218	.	+	.	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	CDS	19487219	19487514	0.9	+	2	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	exon	19487219	19487514	.	+	.	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
Phchi.S1	AUGUSTUS	stop_codon	19487515	19487517	.	+	0	transcript_id "Phchi.S1G302900.t1"; gene_id "Phchi.S1G302900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14541.t1 is derived from g13009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13403682	13404386	.	-	.	Phchi.S3G186000
Phchi.S3	AUGUSTUS	transcript	13403682	13404386	.	-	.	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	stop_codon	13403679	13403681	.	-	0	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	CDS	13403682	13403893	1	-	2	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	exon	13403682	13403893	.	-	.	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	intron	13403894	13403980	.	-	.	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	CDS	13403981	13404244	0.94	-	2	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	exon	13403981	13404244	.	-	.	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	intron	13404245	13404352	.	-	.	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	CDS	13404353	13404386	0.94	-	0	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	exon	13404353	13404386	.	-	.	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
Phchi.S3	AUGUSTUS	start_codon	13404384	13404386	.	-	0	transcript_id "Phchi.S3G186000.t1"; gene_id "Phchi.S3G186000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg192.t1 is derived from g9974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1081737	1082806	.	+	.	Phchi.S6G015100
Phchi.S6	AUGUSTUS	transcript	1081737	1082806	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	start_codon	1081737	1081739	.	+	0	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	CDS	1081737	1081949	0.96	+	0	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	exon	1081737	1081949	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	intron	1081950	1082028	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	CDS	1082029	1082247	1	+	0	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	exon	1082029	1082247	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	intron	1082248	1082334	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	CDS	1082335	1082438	1	+	0	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	exon	1082335	1082438	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	intron	1082439	1082520	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	CDS	1082521	1082806	0.97	+	1	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	exon	1082521	1082806	.	+	.	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
Phchi.S6	AUGUSTUS	stop_codon	1082807	1082809	.	+	0	transcript_id "Phchi.S6G015100.t1"; gene_id "Phchi.S6G015100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5595.t1 is derived from g2765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17805237	17806073	.	-	.	Phchi.S1G275400
Phchi.S1	AUGUSTUS	transcript	17805237	17806073	.	-	.	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	stop_codon	17805234	17805236	.	-	0	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	CDS	17805237	17805603	0.74	-	1	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	exon	17805237	17805603	.	-	.	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	intron	17805604	17805794	.	-	.	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	CDS	17805795	17805803	0.84	-	1	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	exon	17805795	17805803	.	-	.	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	intron	17805804	17806059	.	-	.	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	CDS	17806060	17806073	0.98	-	0	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	exon	17806060	17806073	.	-	.	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
Phchi.S1	AUGUSTUS	start_codon	17806071	17806073	.	-	0	transcript_id "Phchi.S1G275400.t1"; gene_id "Phchi.S1G275400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1661.t1 is derived from g8580.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2287121	2288454	.	-	.	Phchi.S5G027000
Phchi.S5	AUGUSTUS	transcript	2287121	2288454	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	stop_codon	2287118	2287120	.	-	0	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287121	2287348	0.21	-	0	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287121	2287348	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287349	2287443	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287444	2287509	1	-	0	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287444	2287509	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287510	2287607	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287608	2287712	1	-	0	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287608	2287712	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287713	2287804	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287805	2287836	1	-	2	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287805	2287836	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287837	2288037	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288038	2288079	1	-	2	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288038	2288079	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2288080	2288173	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288174	2288254	1	-	2	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288174	2288254	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2288255	2288387	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288388	2288454	0.62	-	0	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288388	2288454	.	-	.	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	start_codon	2288452	2288454	.	-	0	transcript_id "Phchi.S5G027000.t1"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	transcript	2287121	2288454	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	stop_codon	2287118	2287120	.	-	0	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287121	2287348	0.26	-	0	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287121	2287348	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287349	2287443	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287444	2287509	1	-	0	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287444	2287509	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287510	2287607	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287608	2287704	0.76	-	1	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287608	2287704	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287705	2287804	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287805	2287955	0.6	-	2	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287805	2287955	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287956	2288037	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288038	2288079	0.88	-	2	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288038	2288079	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2288080	2288173	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288174	2288254	0.97	-	2	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288174	2288254	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2288255	2288387	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288388	2288454	0.55	-	0	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288388	2288454	.	-	.	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	start_codon	2288452	2288454	.	-	0	transcript_id "Phchi.S5G027000.t2"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	transcript	2287121	2288454	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	stop_codon	2287118	2287120	.	-	0	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287121	2287348	0.26	-	0	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287121	2287348	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287349	2287443	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287444	2287509	1	-	0	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287444	2287509	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287510	2287607	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287608	2287704	0.95	-	1	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287608	2287704	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2287705	2287804	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2287805	2288054	0.55	-	2	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2287805	2288054	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2288055	2288173	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288174	2288254	0.59	-	2	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288174	2288254	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	intron	2288255	2288387	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	CDS	2288388	2288454	0.32	-	0	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	exon	2288388	2288454	.	-	.	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
Phchi.S5	AUGUSTUS	start_codon	2288452	2288454	.	-	0	transcript_id "Phchi.S5G027000.t3"; gene_id "Phchi.S5G027000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11155.t1 is derived from g15205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4408432	4409378	.	+	.	Phchi.S4G073700
Phchi.S4	AUGUSTUS	transcript	4408432	4409378	.	+	.	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	start_codon	4408432	4408434	.	+	0	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	CDS	4408432	4408857	0.77	+	0	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	exon	4408432	4408857	.	+	.	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	intron	4408858	4408970	.	+	.	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	CDS	4408971	4409378	0.65	+	0	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	exon	4408971	4409378	.	+	.	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
Phchi.S4	AUGUSTUS	stop_codon	4409379	4409381	.	+	0	transcript_id "Phchi.S4G073700.t1"; gene_id "Phchi.S4G073700"
# This transcript jg11295.t2 is derived from g15345.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11296.t1 is derived from g15346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5285245	5287587	.	+	.	Phchi.S4G087800
Phchi.S4	AUGUSTUS	transcript	5285245	5287587	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	start_codon	5285245	5285247	.	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5285245	5285436	1	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5285245	5285436	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5285437	5285523	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5285524	5285583	1	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5285524	5285583	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5285584	5285707	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5285708	5285899	1	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5285708	5285899	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5285900	5286029	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5286030	5286212	1	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5286030	5286212	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5286213	5286347	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5286348	5286478	1	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5286348	5286478	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5286479	5286562	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5286563	5286731	1	+	1	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5286563	5286731	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5286732	5286817	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5286818	5286947	1	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5286818	5286947	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	intron	5286948	5287138	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	CDS	5287139	5287587	1	+	2	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	exon	5287139	5287587	.	+	.	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
Phchi.S4	AUGUSTUS	stop_codon	5287588	5287590	.	+	0	transcript_id "Phchi.S4G087800.t1"; gene_id "Phchi.S4G087800"
# This transcript jg4456.t2 is derived from g1626.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4457.t1 is derived from g1627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10588057	10588712	.	-	.	Phchi.S1G161600
Phchi.S1	AUGUSTUS	transcript	10588057	10588712	.	-	.	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	stop_codon	10588054	10588056	.	-	0	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	CDS	10588057	10588228	0.26	-	1	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	exon	10588057	10588228	.	-	.	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	intron	10588229	10588485	.	-	.	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	CDS	10588486	10588712	0.42	-	0	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	exon	10588486	10588712	.	-	.	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
Phchi.S1	AUGUSTUS	start_codon	10588710	10588712	.	-	0	transcript_id "Phchi.S1G161600.t1"; gene_id "Phchi.S1G161600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13966.t1 is derived from g12433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9954968	9956820	.	-	.	Phchi.S3G128500
Phchi.S3	AUGUSTUS	transcript	9954968	9956820	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	stop_codon	9954965	9954967	.	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9954968	9955032	0.98	-	2	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9954968	9955032	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9955033	9955107	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9955108	9955378	0.81	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9955108	9955378	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9955379	9955467	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9955468	9955516	1	-	1	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9955468	9955516	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9955517	9955615	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9955616	9955827	0.79	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9955616	9955827	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9955828	9955956	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9955957	9956079	1	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9955957	9956079	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9956080	9956190	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9956191	9956256	0.86	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9956191	9956256	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9956257	9956349	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9956350	9956420	0.72	-	2	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9956350	9956420	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9956421	9956506	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9956507	9956611	0.7	-	2	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9956507	9956611	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	intron	9956612	9956696	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	CDS	9956697	9956820	0.91	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	exon	9956697	9956820	.	-	.	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
Phchi.S3	AUGUSTUS	start_codon	9956818	9956820	.	-	0	transcript_id "Phchi.S3G128500.t1"; gene_id "Phchi.S3G128500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8299.t1 is derived from g5474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35145711	35147178	.	+	.	Phchi.S1G545800
Phchi.S1	AUGUSTUS	transcript	35145711	35147178	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	start_codon	35145711	35145713	.	+	0	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35145711	35145814	0.91	+	0	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35145711	35145814	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35145815	35145924	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35145925	35146024	0.99	+	1	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35145925	35146024	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35146025	35146176	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35146177	35146210	1	+	0	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35146177	35146210	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35146211	35146317	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35146318	35146394	0.99	+	2	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35146318	35146394	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35146395	35146487	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35146488	35146513	1	+	0	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35146488	35146513	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35146514	35146619	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35146620	35146784	1	+	1	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35146620	35146784	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35146785	35146869	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35146870	35146984	1	+	1	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35146870	35146984	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	intron	35146985	35147076	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	CDS	35147077	35147178	0.98	+	0	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	exon	35147077	35147178	.	+	.	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
Phchi.S1	AUGUSTUS	stop_codon	35147179	35147181	.	+	0	transcript_id "Phchi.S1G545800.t1"; gene_id "Phchi.S1G545800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10833.t1 is derived from g14883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2332479	2333671	.	+	.	Phchi.S4G041500
Phchi.S4	AUGUSTUS	transcript	2332479	2333671	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	start_codon	2332479	2332481	.	+	0	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	CDS	2332479	2332621	1	+	0	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	exon	2332479	2332621	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	intron	2332622	2332720	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	CDS	2332721	2332797	1	+	1	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	exon	2332721	2332797	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	intron	2332798	2333029	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	CDS	2333030	2333265	0.99	+	2	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	exon	2333030	2333265	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	intron	2333266	2333357	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	CDS	2333358	2333434	1	+	0	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	exon	2333358	2333434	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	intron	2333435	2333523	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	CDS	2333524	2333671	1	+	1	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	exon	2333524	2333671	.	+	.	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
Phchi.S4	AUGUSTUS	stop_codon	2333672	2333674	.	+	0	transcript_id "Phchi.S4G041500.t1"; gene_id "Phchi.S4G041500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14220.t1 is derived from g12687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11564120	11566344	.	+	.	Phchi.S3G153900
Phchi.S3	AUGUSTUS	transcript	11564120	11566344	.	+	.	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	start_codon	11564120	11564122	.	+	0	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	CDS	11564120	11565405	0.97	+	0	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	exon	11564120	11565405	.	+	.	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	intron	11565406	11565497	.	+	.	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	CDS	11565498	11565793	1	+	1	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	exon	11565498	11565793	.	+	.	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	intron	11565794	11565952	.	+	.	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	CDS	11565953	11566344	0.89	+	2	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	exon	11565953	11566344	.	+	.	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
Phchi.S3	AUGUSTUS	stop_codon	11566345	11566347	.	+	0	transcript_id "Phchi.S3G153900.t1"; gene_id "Phchi.S3G153900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5405.t1 is derived from g2575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16710232	16710889	.	-	.	Phchi.S1G256400
Phchi.S1	AUGUSTUS	transcript	16710232	16710889	.	-	.	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	stop_codon	16710229	16710231	.	-	0	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	CDS	16710232	16710676	0.92	-	1	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	exon	16710232	16710676	.	-	.	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	intron	16710677	16710752	.	-	.	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	CDS	16710753	16710889	1	-	0	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	exon	16710753	16710889	.	-	.	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
Phchi.S1	AUGUSTUS	start_codon	16710887	16710889	.	-	0	transcript_id "Phchi.S1G256400.t1"; gene_id "Phchi.S1G256400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4003.t1 is derived from g1172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6981941	6984460	.	-	.	Phchi.S1G116200
Phchi.S1	AUGUSTUS	transcript	6981941	6984460	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	stop_codon	6981938	6981940	.	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6981941	6981958	1	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6981941	6981958	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6981959	6982198	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6982199	6982337	1	-	1	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6982199	6982337	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6982338	6982435	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6982436	6982555	0.99	-	1	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6982436	6982555	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6982556	6982675	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6982676	6982831	1	-	1	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6982676	6982831	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6982832	6982924	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6982925	6982973	1	-	2	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6982925	6982973	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6982974	6983055	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6983056	6983107	0.76	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6983056	6983107	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6983108	6983217	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6983218	6983288	0.53	-	2	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6983218	6983288	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6983289	6983400	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6983401	6983497	0.93	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6983401	6983497	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6983498	6983614	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6983615	6983773	1	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6983615	6983773	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6983774	6983903	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6983904	6984078	1	-	1	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6983904	6984078	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6984079	6984213	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6984214	6984297	0.75	-	1	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6984214	6984297	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	intron	6984298	6984398	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	CDS	6984399	6984460	0.41	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	exon	6984399	6984460	.	-	.	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
Phchi.S1	AUGUSTUS	start_codon	6984458	6984460	.	-	0	transcript_id "Phchi.S1G116200.t1"; gene_id "Phchi.S1G116200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3757.t1 is derived from g926.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5549019	5550849	.	-	.	Phchi.S1G091600
Phchi.S1	AUGUSTUS	transcript	5549019	5550849	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	stop_codon	5549016	5549018	.	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549019	5549180	1	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549019	5549180	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5549181	5549296	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549297	5549458	1	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549297	5549458	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5549459	5549689	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549690	5549765	1	-	1	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549690	5549765	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5549766	5549939	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549940	5550019	1	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549940	5550019	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550020	5550230	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550231	5550449	0.99	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550231	5550449	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550450	5550550	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550551	5550630	0.88	-	2	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550551	5550630	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550631	5550782	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550783	5550849	0.96	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550783	5550849	.	-	.	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	start_codon	5550847	5550849	.	-	0	transcript_id "Phchi.S1G091600.t1"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	transcript	5549019	5550849	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	stop_codon	5549016	5549018	.	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549019	5549180	1	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549019	5549180	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5549181	5549296	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549297	5549458	1	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549297	5549458	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5549459	5549689	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549690	5549765	1	-	1	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549690	5549765	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5549766	5549939	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5549940	5550019	1	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5549940	5550019	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550020	5550234	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550235	5550289	1	-	1	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550235	5550289	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550290	5550372	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550373	5550449	0.97	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550373	5550449	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550450	5550550	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550551	5550630	0.88	-	2	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550551	5550630	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	intron	5550631	5550782	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	CDS	5550783	5550849	0.95	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	exon	5550783	5550849	.	-	.	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
Phchi.S1	AUGUSTUS	start_codon	5550847	5550849	.	-	0	transcript_id "Phchi.S1G091600.t2"; gene_id "Phchi.S1G091600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10185.t1 is derived from g7361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46208898	46212828	.	+	.	Phchi.S1G734400
Phchi.S1	AUGUSTUS	transcript	46208898	46212828	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	start_codon	46208898	46208900	.	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46208898	46208961	0.96	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46208898	46208961	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46208962	46209287	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46209288	46209309	0.94	+	2	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46209288	46209309	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46209310	46209428	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46209429	46209500	0.95	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46209429	46209500	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46209501	46209636	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46209637	46209727	1	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46209637	46209727	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46209728	46209935	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46209936	46210030	1	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46209936	46210030	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46210031	46210177	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46210178	46210235	1	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46210178	46210235	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46210236	46210436	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46210437	46210639	1	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46210437	46210639	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46210640	46210754	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46210755	46210812	1	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46210755	46210812	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46210813	46210979	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46210980	46211020	1	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46210980	46211020	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46211021	46211138	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46211139	46211213	1	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46211139	46211213	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46211214	46211334	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46211335	46211391	1	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46211335	46211391	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46211392	46211638	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46211639	46211705	1	+	1	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46211639	46211705	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46211706	46211808	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46211809	46211949	0.61	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46211809	46211949	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46211950	46212038	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46212039	46212254	1	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46212039	46212254	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46212255	46212352	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46212353	46212514	1	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46212353	46212514	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46212515	46212601	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46212602	46212679	1	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46212602	46212679	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	intron	46212680	46212753	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	CDS	46212754	46212828	0.95	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	exon	46212754	46212828	.	+	.	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
Phchi.S1	AUGUSTUS	stop_codon	46212829	46212831	.	+	0	transcript_id "Phchi.S1G734400.t1"; gene_id "Phchi.S1G734400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10967.t1 is derived from g15017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3398220	3399782	.	+	.	Phchi.S4G054900
Phchi.S4	AUGUSTUS	transcript	3398220	3399782	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	start_codon	3398220	3398222	.	+	0	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	CDS	3398220	3398459	0.9	+	0	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	exon	3398220	3398459	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	intron	3398460	3398554	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	CDS	3398555	3398625	1	+	0	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	exon	3398555	3398625	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	intron	3398626	3398715	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	CDS	3398716	3398833	1	+	1	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	exon	3398716	3398833	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	intron	3398834	3398930	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	CDS	3398931	3399782	1	+	0	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	exon	3398931	3399782	.	+	.	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
Phchi.S4	AUGUSTUS	stop_codon	3399783	3399785	.	+	0	transcript_id "Phchi.S4G054900.t1"; gene_id "Phchi.S4G054900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11253.t1 is derived from g15303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5014915	5019183	.	+	.	Phchi.S4G083500
Phchi.S4	AUGUSTUS	transcript	5014915	5019183	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	start_codon	5014915	5014917	.	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5014915	5015008	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5014915	5015008	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5015009	5015194	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5015195	5015776	1	+	2	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5015195	5015776	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5015777	5015869	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5015870	5015958	1	+	2	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5015870	5015958	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5015959	5016112	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5016113	5016679	0.99	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5016113	5016679	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5016680	5016872	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5016873	5016938	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5016873	5016938	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5016939	5017030	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5017031	5017141	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5017031	5017141	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5017142	5017227	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5017228	5017379	0.88	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5017228	5017379	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5017380	5017558	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5017559	5017661	0.88	+	1	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5017559	5017661	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5017662	5017756	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5017757	5017843	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5017757	5017843	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5017844	5017930	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5017931	5018083	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5017931	5018083	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5018084	5018168	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5018169	5018324	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5018169	5018324	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5018325	5018407	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5018408	5018617	1	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5018408	5018617	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	intron	5018618	5018772	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	CDS	5018773	5019183	0.97	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	exon	5018773	5019183	.	+	.	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
Phchi.S4	AUGUSTUS	stop_codon	5019184	5019186	.	+	0	transcript_id "Phchi.S4G083500.t1"; gene_id "Phchi.S4G083500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5335.t1 is derived from g2505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16353046	16354040	.	+	.	Phchi.S1G249400
Phchi.S1	AUGUSTUS	transcript	16353046	16354040	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	start_codon	16353046	16353048	.	+	0	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	CDS	16353046	16353124	0.93	+	0	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	exon	16353046	16353124	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	intron	16353125	16353272	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	CDS	16353273	16353558	1	+	2	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	exon	16353273	16353558	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	intron	16353559	16353693	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	CDS	16353694	16353782	1	+	1	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	exon	16353694	16353782	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	intron	16353783	16354005	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	CDS	16354006	16354040	0.95	+	2	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	exon	16354006	16354040	.	+	.	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
Phchi.S1	AUGUSTUS	stop_codon	16354041	16354043	.	+	0	transcript_id "Phchi.S1G249400.t1"; gene_id "Phchi.S1G249400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10126.t1 is derived from g7302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45851536	45854319	.	-	.	Phchi.S1G728500
Phchi.S1	AUGUSTUS	transcript	45851536	45854319	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	stop_codon	45851533	45851535	.	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45851536	45851772	1	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45851536	45851772	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45851773	45851936	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45851937	45852155	1	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45851937	45852155	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45852156	45852484	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45852485	45852639	0.89	-	2	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45852485	45852639	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45852640	45852786	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45852787	45852874	1	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45852787	45852874	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45852875	45853057	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853058	45853191	0.89	-	2	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853058	45853191	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45853192	45853317	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853318	45853615	0.89	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853318	45853615	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45853616	45853718	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853719	45853843	0.98	-	2	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853719	45853843	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45853844	45853964	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853965	45854097	0.96	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853965	45854097	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45854098	45854214	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45854215	45854319	0.72	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45854215	45854319	.	-	.	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	start_codon	45854317	45854319	.	-	0	transcript_id "Phchi.S1G728500.t1"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	transcript	45851536	45854319	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	stop_codon	45851533	45851535	.	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45851536	45851772	1	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45851536	45851772	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45851773	45851936	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45851937	45852155	1	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45851937	45852155	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45852156	45852484	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45852485	45852667	0.96	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45852485	45852667	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45852668	45852767	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45852768	45852920	0.94	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45852768	45852920	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45852921	45853057	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853058	45853191	0.91	-	2	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853058	45853191	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45853192	45853317	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853318	45853615	0.9	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853318	45853615	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45853616	45853718	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853719	45853843	0.96	-	2	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853719	45853843	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45853844	45853964	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45853965	45854097	0.96	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45853965	45854097	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	intron	45854098	45854214	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	CDS	45854215	45854319	0.69	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	exon	45854215	45854319	.	-	.	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
Phchi.S1	AUGUSTUS	start_codon	45854317	45854319	.	-	0	transcript_id "Phchi.S1G728500.t2"; gene_id "Phchi.S1G728500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4446.t1 is derived from g1615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10551236	10552168	.	-	.	Phchi.S1G160500
Phchi.S1	AUGUSTUS	transcript	10551236	10552168	.	-	.	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	stop_codon	10551233	10551235	.	-	0	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	CDS	10551236	10551403	0.98	-	0	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	exon	10551236	10551403	.	-	.	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	intron	10551404	10551479	.	-	.	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	CDS	10551480	10551525	0.98	-	1	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	exon	10551480	10551525	.	-	.	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	intron	10551526	10551620	.	-	.	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	CDS	10551621	10552168	0.46	-	0	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	exon	10551621	10552168	.	-	.	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
Phchi.S1	AUGUSTUS	start_codon	10552166	10552168	.	-	0	transcript_id "Phchi.S1G160500.t1"; gene_id "Phchi.S1G160500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6492.t1 is derived from g3664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23278941	23280449	.	+	.	Phchi.S1G365100
Phchi.S1	AUGUSTUS	transcript	23278941	23280449	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	start_codon	23278941	23278943	.	+	0	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	CDS	23278941	23279021	1	+	0	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	exon	23278941	23279021	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	intron	23279022	23279093	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	CDS	23279094	23279361	0.86	+	0	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	exon	23279094	23279361	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	intron	23279362	23279440	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	CDS	23279441	23279484	0.69	+	2	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	exon	23279441	23279484	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	intron	23279485	23279840	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	CDS	23279841	23279891	0.87	+	0	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	exon	23279841	23279891	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	intron	23279892	23280248	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	CDS	23280249	23280449	0.91	+	0	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	exon	23280249	23280449	.	+	.	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
Phchi.S1	AUGUSTUS	stop_codon	23280450	23280452	.	+	0	transcript_id "Phchi.S1G365100.t1"; gene_id "Phchi.S1G365100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5364.t1 is derived from g2534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16508408	16511197	.	+	.	Phchi.S1G252300
Phchi.S1	AUGUSTUS	transcript	16508408	16511197	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	start_codon	16508408	16508410	.	+	0	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	CDS	16508408	16508470	0.99	+	0	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	exon	16508408	16508470	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	intron	16508471	16508687	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	CDS	16508688	16508820	1	+	0	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	exon	16508688	16508820	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	intron	16508821	16508912	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	CDS	16508913	16509130	0.77	+	2	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	exon	16508913	16509130	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	intron	16509131	16509239	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	CDS	16509240	16509796	0.85	+	0	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	exon	16509240	16509796	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	intron	16509797	16509906	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	CDS	16509907	16510790	0.7	+	1	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	exon	16509907	16510790	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	intron	16510791	16511000	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	CDS	16511001	16511197	0.63	+	2	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	exon	16511001	16511197	.	+	.	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
Phchi.S1	AUGUSTUS	stop_codon	16511198	16511200	.	+	0	transcript_id "Phchi.S1G252300.t1"; gene_id "Phchi.S1G252300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1381.t1 is derived from g15973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C41	AUGUSTUS	gene	68	871	.	-	.	Phchi.C41G000100
Phchi.C41	AUGUSTUS	transcript	68	871	.	-	.	transcript_id "Phchi.C41G000100.t1"; gene_id "Phchi.C41G000100"
Phchi.C41	AUGUSTUS	stop_codon	65	67	.	-	0	transcript_id "Phchi.C41G000100.t1"; gene_id "Phchi.C41G000100"
Phchi.C41	AUGUSTUS	CDS	68	871	0.75	-	0	transcript_id "Phchi.C41G000100.t1"; gene_id "Phchi.C41G000100"
Phchi.C41	AUGUSTUS	exon	68	871	.	-	.	transcript_id "Phchi.C41G000100.t1"; gene_id "Phchi.C41G000100"
Phchi.C41	AUGUSTUS	start_codon	869	871	.	-	0	transcript_id "Phchi.C41G000100.t1"; gene_id "Phchi.C41G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1473.t1 is derived from g8392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1099005	1100928	.	-	.	Phchi.S5G008200
Phchi.S5	AUGUSTUS	transcript	1099005	1100928	.	-	.	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	stop_codon	1099002	1099004	.	-	0	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	CDS	1099005	1099253	0.94	-	0	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	exon	1099005	1099253	.	-	.	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	intron	1099254	1099335	.	-	.	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	CDS	1099336	1099864	0.97	-	1	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	exon	1099336	1099864	.	-	.	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	intron	1099865	1099969	.	-	.	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	CDS	1099970	1100928	0.89	-	0	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	exon	1099970	1100928	.	-	.	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
Phchi.S5	AUGUSTUS	start_codon	1100926	1100928	.	-	0	transcript_id "Phchi.S5G008200.t1"; gene_id "Phchi.S5G008200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10353.t1 is derived from g7529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47324448	47325116	.	+	.	Phchi.S1G751200
Phchi.S1	AUGUSTUS	transcript	47324448	47325116	.	+	.	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	start_codon	47324448	47324450	.	+	0	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	CDS	47324448	47324642	0.12	+	0	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	exon	47324448	47324642	.	+	.	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	intron	47324643	47325080	.	+	.	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	CDS	47325081	47325116	0.97	+	0	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	exon	47325081	47325116	.	+	.	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
Phchi.S1	AUGUSTUS	stop_codon	47325117	47325119	.	+	0	transcript_id "Phchi.S1G751200.t1"; gene_id "Phchi.S1G751200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10026.t1 is derived from g7202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45151930	45153985	.	+	.	Phchi.S1G718500
Phchi.S1	AUGUSTUS	transcript	45151930	45153985	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	start_codon	45151930	45151932	.	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45151930	45151986	1	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45151930	45151986	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45151987	45152084	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45152085	45152135	1	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45152085	45152135	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45152136	45152216	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45152217	45152324	1	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45152217	45152324	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45152325	45152408	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45152409	45152428	0.62	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45152409	45152428	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45152429	45152507	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45152508	45152523	0.62	+	1	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45152508	45152523	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45152524	45152744	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45152745	45152812	0.99	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45152745	45152812	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45152813	45152913	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45152914	45153039	1	+	1	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45152914	45153039	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45153040	45153124	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45153125	45153231	1	+	1	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45153125	45153231	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45153232	45153451	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45153452	45153523	1	+	2	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45153452	45153523	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	intron	45153524	45153596	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	CDS	45153597	45153985	0.91	+	2	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	exon	45153597	45153985	.	+	.	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
Phchi.S1	AUGUSTUS	stop_codon	45153986	45153988	.	+	0	transcript_id "Phchi.S1G718500.t1"; gene_id "Phchi.S1G718500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4875.t1 is derived from g2045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13185232	13186302	.	+	.	Phchi.S1G203400
Phchi.S1	AUGUSTUS	transcript	13185232	13186302	.	+	.	transcript_id "Phchi.S1G203400.t1"; gene_id "Phchi.S1G203400"
Phchi.S1	AUGUSTUS	start_codon	13185232	13185234	.	+	0	transcript_id "Phchi.S1G203400.t1"; gene_id "Phchi.S1G203400"
Phchi.S1	AUGUSTUS	CDS	13185232	13186302	0.97	+	0	transcript_id "Phchi.S1G203400.t1"; gene_id "Phchi.S1G203400"
Phchi.S1	AUGUSTUS	exon	13185232	13186302	.	+	.	transcript_id "Phchi.S1G203400.t1"; gene_id "Phchi.S1G203400"
Phchi.S1	AUGUSTUS	stop_codon	13186303	13186305	.	+	0	transcript_id "Phchi.S1G203400.t1"; gene_id "Phchi.S1G203400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6629.t1 is derived from g3801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24168690	24169708	.	-	.	Phchi.S1G378800
Phchi.S1	AUGUSTUS	transcript	24168690	24169708	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	stop_codon	24168687	24168689	.	-	0	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	CDS	24168690	24168857	0.99	-	0	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	exon	24168690	24168857	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	intron	24168858	24168968	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	CDS	24168969	24169285	0.97	-	2	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	exon	24168969	24169285	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	intron	24169286	24169493	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	CDS	24169494	24169610	0.51	-	2	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	exon	24169494	24169610	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	intron	24169611	24169689	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	CDS	24169690	24169708	0.51	-	0	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	exon	24169690	24169708	.	-	.	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
Phchi.S1	AUGUSTUS	start_codon	24169706	24169708	.	-	0	transcript_id "Phchi.S1G378800.t1"; gene_id "Phchi.S1G378800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13344.t1 is derived from g11810.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 3 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6191787	6197119	.	+	.	Phchi.S3G066300
Phchi.S3	AUGUSTUS	transcript	6191787	6197119	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	start_codon	6191787	6191789	.	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6191787	6191806	0.82	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6191787	6191806	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6191807	6192306	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6192307	6192468	0.54	+	1	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6192307	6192468	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6192469	6192610	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6192611	6192762	0.96	+	1	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6192611	6192762	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6192763	6192864	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6192865	6192978	0.98	+	2	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6192865	6192978	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6192979	6193115	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6193116	6193148	0.97	+	2	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6193116	6193148	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6193149	6193820	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6193821	6193871	1	+	2	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6193821	6193871	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6193872	6193959	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6193960	6194030	1	+	2	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6193960	6194030	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194031	6194117	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194118	6194162	1	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194118	6194162	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194163	6194303	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194304	6194363	1	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194304	6194363	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194364	6194472	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194473	6194533	1	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194473	6194533	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194534	6194634	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194635	6194747	1	+	2	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194635	6194747	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194748	6194837	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194838	6194953	1	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194838	6194953	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194954	6195053	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195054	6195152	1	+	1	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195054	6195152	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195153	6195333	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195334	6195409	1	+	1	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195334	6195409	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195410	6195698	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195699	6195767	0.89	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195699	6195767	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195768	6195845	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195846	6195934	0.9	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195846	6195934	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195935	6196254	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196255	6196318	0.99	+	1	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196255	6196318	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196319	6196424	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196425	6196586	0.99	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196425	6196586	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196587	6196668	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196669	6196750	1	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196669	6196750	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196751	6196836	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196837	6196901	1	+	2	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196837	6196901	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196902	6196984	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196985	6197119	1	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196985	6197119	.	+	.	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	stop_codon	6197120	6197122	.	+	0	transcript_id "Phchi.S3G066300.t1"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	transcript	6191787	6197119	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	start_codon	6191787	6191789	.	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6191787	6191806	0.9	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6191787	6191806	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6191807	6192306	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6192307	6192468	0.45	+	1	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6192307	6192468	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6192469	6192610	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6192611	6192762	0.93	+	1	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6192611	6192762	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6192763	6192864	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6192865	6192978	0.99	+	2	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6192865	6192978	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6192979	6193115	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6193116	6193148	0.98	+	2	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6193116	6193148	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6193149	6193820	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6193821	6193871	1	+	2	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6193821	6193871	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6193872	6193959	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6193960	6194030	1	+	2	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6193960	6194030	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194031	6194117	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194118	6194162	1	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194118	6194162	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194163	6194303	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194304	6194363	1	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194304	6194363	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194364	6194472	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194473	6194533	1	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194473	6194533	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194534	6194634	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194635	6194747	1	+	2	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194635	6194747	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194748	6194837	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6194838	6194953	1	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6194838	6194953	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6194954	6195050	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195051	6195152	1	+	1	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195051	6195152	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195153	6195333	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195334	6195409	1	+	1	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195334	6195409	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195410	6195698	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195699	6195767	0.87	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195699	6195767	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195768	6195845	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6195846	6195934	0.87	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6195846	6195934	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6195935	6196254	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196255	6196318	0.97	+	1	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196255	6196318	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196319	6196424	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196425	6196586	1	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196425	6196586	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196587	6196668	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196669	6196750	1	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196669	6196750	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196751	6196836	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196837	6196901	1	+	2	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196837	6196901	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	intron	6196902	6196984	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	CDS	6196985	6197119	0.97	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	exon	6196985	6197119	.	+	.	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
Phchi.S3	AUGUSTUS	stop_codon	6197120	6197122	.	+	0	transcript_id "Phchi.S3G066300.t2"; gene_id "Phchi.S3G066300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11179.t1 is derived from g15229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4515668	4517854	.	-	.	Phchi.S4G076100
Phchi.S4	AUGUSTUS	transcript	4515668	4517854	.	-	.	transcript_id "Phchi.S4G076100.t1"; gene_id "Phchi.S4G076100"
Phchi.S4	AUGUSTUS	stop_codon	4515665	4515667	.	-	0	transcript_id "Phchi.S4G076100.t1"; gene_id "Phchi.S4G076100"
Phchi.S4	AUGUSTUS	CDS	4515668	4517854	0.57	-	0	transcript_id "Phchi.S4G076100.t1"; gene_id "Phchi.S4G076100"
Phchi.S4	AUGUSTUS	exon	4515668	4517854	.	-	.	transcript_id "Phchi.S4G076100.t1"; gene_id "Phchi.S4G076100"
Phchi.S4	AUGUSTUS	start_codon	4517852	4517854	.	-	0	transcript_id "Phchi.S4G076100.t1"; gene_id "Phchi.S4G076100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4328.t1 is derived from g1497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9805319	9809067	.	-	.	Phchi.S1G148700
Phchi.S1	AUGUSTUS	transcript	9805319	9809067	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	stop_codon	9805316	9805318	.	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9805319	9806482	1	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9805319	9806482	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9806483	9806580	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9806581	9806722	1	-	1	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9806581	9806722	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9806723	9806820	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9806821	9807004	1	-	2	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9806821	9807004	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9807005	9807094	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9807095	9807184	1	-	2	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9807095	9807184	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9807185	9807274	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9807275	9807365	1	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9807275	9807365	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9807366	9807535	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9807536	9807577	1	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9807536	9807577	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9807578	9807677	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9807678	9807830	0.87	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9807678	9807830	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9807831	9807915	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9807916	9808047	0.67	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9807916	9808047	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9808048	9808154	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9808155	9808250	0.99	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9808155	9808250	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9808251	9808446	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9808447	9808587	1	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9808447	9808587	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9808588	9808741	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9808742	9808816	0.91	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9808742	9808816	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	intron	9808817	9808923	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	CDS	9808924	9809067	0.77	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	exon	9808924	9809067	.	-	.	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
Phchi.S1	AUGUSTUS	start_codon	9809065	9809067	.	-	0	transcript_id "Phchi.S1G148700.t1"; gene_id "Phchi.S1G148700"
# This transcript jg12581.t2 is derived from g8258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12582.t1 is derived from g8259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35967678	35970212	.	-	.	Phchi.S2G066200
Phchi.S2	AUGUSTUS	transcript	35967678	35970212	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	stop_codon	35967675	35967677	.	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35967678	35968055	0.96	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35967678	35968055	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35968056	35968160	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35968161	35968242	1	-	1	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35968161	35968242	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35968243	35968404	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35968405	35968505	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35968405	35968505	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35968506	35968629	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35968630	35968713	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35968630	35968713	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35968714	35968799	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35968800	35968871	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35968800	35968871	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35968872	35968969	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35968970	35969083	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35968970	35969083	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35969084	35969174	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35969175	35969321	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35969175	35969321	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35969322	35969442	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35969443	35969508	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35969443	35969508	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35969509	35969634	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35969635	35969763	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35969635	35969763	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	intron	35969764	35970134	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	CDS	35970135	35970212	1	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	exon	35970135	35970212	.	-	.	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
Phchi.S2	AUGUSTUS	start_codon	35970210	35970212	.	-	0	transcript_id "Phchi.S2G066200.t1"; gene_id "Phchi.S2G066200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg968.t1 is derived from g10750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6713136	6713997	.	+	.	Phchi.S6G092700
Phchi.S6	AUGUSTUS	transcript	6713136	6713997	.	+	.	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	start_codon	6713136	6713138	.	+	0	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	CDS	6713136	6713238	0.64	+	0	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	exon	6713136	6713238	.	+	.	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	intron	6713239	6713632	.	+	.	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	CDS	6713633	6713997	0.77	+	2	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	exon	6713633	6713997	.	+	.	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
Phchi.S6	AUGUSTUS	stop_codon	6713998	6714000	.	+	0	transcript_id "Phchi.S6G092700.t1"; gene_id "Phchi.S6G092700"
# This transcript jg6748.t2 is derived from g3920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6749.t1 is derived from g3921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24841428	24842114	.	+	.	Phchi.S1G390800
Phchi.S1	AUGUSTUS	transcript	24841428	24842114	.	+	.	transcript_id "Phchi.S1G390800.t1"; gene_id "Phchi.S1G390800"
Phchi.S1	AUGUSTUS	start_codon	24841428	24841430	.	+	0	transcript_id "Phchi.S1G390800.t1"; gene_id "Phchi.S1G390800"
Phchi.S1	AUGUSTUS	CDS	24841428	24842114	0.99	+	0	transcript_id "Phchi.S1G390800.t1"; gene_id "Phchi.S1G390800"
Phchi.S1	AUGUSTUS	exon	24841428	24842114	.	+	.	transcript_id "Phchi.S1G390800.t1"; gene_id "Phchi.S1G390800"
Phchi.S1	AUGUSTUS	stop_codon	24842115	24842117	.	+	0	transcript_id "Phchi.S1G390800.t1"; gene_id "Phchi.S1G390800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13715.t1 is derived from g12182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8418869	8419300	.	-	.	Phchi.S3G103400
Phchi.S3	AUGUSTUS	transcript	8418869	8419300	.	-	.	transcript_id "Phchi.S3G103400.t1"; gene_id "Phchi.S3G103400"
Phchi.S3	AUGUSTUS	stop_codon	8418866	8418868	.	-	0	transcript_id "Phchi.S3G103400.t1"; gene_id "Phchi.S3G103400"
Phchi.S3	AUGUSTUS	CDS	8418869	8419300	0.84	-	0	transcript_id "Phchi.S3G103400.t1"; gene_id "Phchi.S3G103400"
Phchi.S3	AUGUSTUS	exon	8418869	8419300	.	-	.	transcript_id "Phchi.S3G103400.t1"; gene_id "Phchi.S3G103400"
Phchi.S3	AUGUSTUS	start_codon	8419298	8419300	.	-	0	transcript_id "Phchi.S3G103400.t1"; gene_id "Phchi.S3G103400"
# This transcript jg9104.t2 is derived from g6279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9105.t1 is derived from g6280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39846422	39847765	.	+	.	Phchi.S1G626400
Phchi.S1	AUGUSTUS	transcript	39846422	39847765	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	start_codon	39846422	39846424	.	+	0	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	CDS	39846422	39846526	1	+	0	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	exon	39846422	39846526	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	intron	39846527	39846607	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	CDS	39846608	39846932	0.61	+	0	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	exon	39846608	39846932	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	intron	39846933	39847002	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	CDS	39847003	39847078	0.48	+	2	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	exon	39847003	39847078	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	intron	39847079	39847206	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	CDS	39847207	39847451	0.42	+	1	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	exon	39847207	39847451	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	intron	39847452	39847529	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	CDS	39847530	39847619	0.7	+	2	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	exon	39847530	39847619	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	intron	39847620	39847709	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	CDS	39847710	39847765	0.94	+	2	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	exon	39847710	39847765	.	+	.	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
Phchi.S1	AUGUSTUS	stop_codon	39847766	39847768	.	+	0	transcript_id "Phchi.S1G626400.t1"; gene_id "Phchi.S1G626400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4733.t1 is derived from g1903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12518778	12520593	.	-	.	Phchi.S1G189200
Phchi.S1	AUGUSTUS	transcript	12518778	12520593	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	stop_codon	12518775	12518777	.	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12518778	12518790	0.62	-	1	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12518778	12518790	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12518791	12518914	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12518915	12519077	0.66	-	2	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12518915	12519077	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519078	12519146	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519147	12519258	1	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519147	12519258	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519259	12519332	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519333	12519394	1	-	2	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519333	12519394	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519395	12519477	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519478	12519586	1	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519478	12519586	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519587	12519674	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519675	12519721	1	-	2	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519675	12519721	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519722	12519808	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519809	12519951	0.99	-	1	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519809	12519951	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519952	12520059	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520060	12520133	1	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520060	12520133	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12520134	12520209	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520210	12520275	1	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520210	12520275	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12520276	12520404	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520405	12520593	0.82	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520405	12520593	.	-	.	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	start_codon	12520591	12520593	.	-	0	transcript_id "Phchi.S1G189200.t1"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	transcript	12518778	12520593	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	stop_codon	12518775	12518777	.	-	0	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12518778	12518790	0.55	-	1	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12518778	12518790	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12518791	12518914	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12518915	12519077	0.57	-	2	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12518915	12519077	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519078	12519146	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519147	12519258	1	-	0	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519147	12519258	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519259	12519332	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519333	12519394	1	-	2	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519333	12519394	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519395	12519477	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519478	12519586	1	-	0	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519478	12519586	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519587	12519674	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519675	12519721	1	-	2	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519675	12519721	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519722	12519808	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12519809	12519951	1	-	1	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12519809	12519951	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12519952	12520059	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520060	12520133	1	-	0	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520060	12520133	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12520134	12520209	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520210	12520310	0.75	-	2	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520210	12520310	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12520311	12520404	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520405	12520461	0.64	-	2	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520405	12520461	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	intron	12520462	12520538	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	CDS	12520539	12520593	0.41	-	0	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	exon	12520539	12520593	.	-	.	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
Phchi.S1	AUGUSTUS	start_codon	12520591	12520593	.	-	0	transcript_id "Phchi.S1G189200.t2"; gene_id "Phchi.S1G189200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10072.t1 is derived from g7248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45628383	45629072	.	+	.	Phchi.S1G723100
Phchi.S1	AUGUSTUS	transcript	45628383	45629072	.	+	.	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	start_codon	45628383	45628385	.	+	0	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	CDS	45628383	45628619	0.94	+	0	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	exon	45628383	45628619	.	+	.	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	intron	45628620	45628711	.	+	.	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	CDS	45628712	45628868	1	+	0	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	exon	45628712	45628868	.	+	.	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	intron	45628869	45628950	.	+	.	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	CDS	45628951	45629072	0.99	+	2	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	exon	45628951	45629072	.	+	.	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
Phchi.S1	AUGUSTUS	stop_codon	45629073	45629075	.	+	0	transcript_id "Phchi.S1G723100.t1"; gene_id "Phchi.S1G723100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10451.t1 is derived from g14500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	394208	396188	.	+	.	Phchi.S4G003300
Phchi.S4	AUGUSTUS	transcript	394208	396188	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	start_codon	394208	394210	.	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	394208	394517	0.88	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	394208	394517	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	intron	394518	394631	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	394632	394776	0.32	+	2	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	394632	394776	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	intron	394777	394925	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	394926	395136	0.61	+	1	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	394926	395136	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	intron	395137	395249	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	395250	395321	1	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	395250	395321	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	intron	395322	395448	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	395449	395544	1	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	395449	395544	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	intron	395545	395671	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	395672	395944	0.99	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	395672	395944	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	intron	395945	396080	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	CDS	396081	396188	1	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	exon	396081	396188	.	+	.	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
Phchi.S4	AUGUSTUS	stop_codon	396189	396191	.	+	0	transcript_id "Phchi.S4G003300.t1"; gene_id "Phchi.S4G003300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13763.t1 is derived from g12230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8771751	8775592	.	+	.	Phchi.S3G108200
Phchi.S3	AUGUSTUS	transcript	8771751	8775592	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	start_codon	8771751	8771753	.	+	0	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8771751	8771859	1	+	0	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8771751	8771859	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8771860	8771948	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8771949	8772525	0.94	+	2	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8771949	8772525	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8772526	8772620	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8772621	8773180	1	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8772621	8773180	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8773181	8773270	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8773271	8773406	0.99	+	2	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8773271	8773406	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8773407	8773507	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8773508	8773579	0.7	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8773508	8773579	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8773580	8773684	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8773685	8773756	1	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8773685	8773756	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8773757	8773853	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8773854	8773925	1	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8773854	8773925	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8773926	8774017	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8774018	8774034	0.6	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8774018	8774034	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8774035	8774207	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8774208	8774506	0.55	+	2	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8774208	8774506	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8774507	8774597	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8774598	8774724	1	+	0	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8774598	8774724	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8774725	8774804	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8774805	8774873	1	+	2	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8774805	8774873	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8774874	8774968	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8774969	8775001	1	+	2	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8774969	8775001	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8775002	8775093	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8775094	8775256	1	+	2	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8775094	8775256	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8775257	8775332	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8775333	8775464	1	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8775333	8775464	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	intron	8775465	8775564	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	CDS	8775565	8775592	1	+	1	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	exon	8775565	8775592	.	+	.	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
Phchi.S3	AUGUSTUS	stop_codon	8775593	8775595	.	+	0	transcript_id "Phchi.S3G108200.t1"; gene_id "Phchi.S3G108200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg991.t1 is derived from g10774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6922988	6925476	.	+	.	Phchi.S6G095000
Phchi.S6	AUGUSTUS	transcript	6922988	6925476	.	+	.	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	start_codon	6922988	6922990	.	+	0	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	CDS	6922988	6923212	0.79	+	0	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	exon	6922988	6923212	.	+	.	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	intron	6923213	6923292	.	+	.	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	CDS	6923293	6923416	1	+	0	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	exon	6923293	6923416	.	+	.	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	intron	6923417	6923542	.	+	.	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	CDS	6923543	6925476	1	+	2	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	exon	6923543	6925476	.	+	.	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
Phchi.S6	AUGUSTUS	stop_codon	6925477	6925479	.	+	0	transcript_id "Phchi.S6G095000.t1"; gene_id "Phchi.S6G095000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2628.t1 is derived from g9548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7838620	7842734	.	+	.	Phchi.S5G123700
Phchi.S5	AUGUSTUS	transcript	7838620	7842734	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	start_codon	7838620	7838622	.	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7838620	7838769	1	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7838620	7838769	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7838770	7838856	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7838857	7838955	1	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7838857	7838955	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7838956	7839043	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7839044	7839147	1	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7839044	7839147	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7839148	7839232	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7839233	7839608	0.28	+	1	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7839233	7839608	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7839609	7839748	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7839749	7840103	0.58	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7839749	7840103	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7840104	7840222	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7840223	7840345	1	+	2	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7840223	7840345	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7840346	7840543	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7840544	7840632	1	+	2	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7840544	7840632	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7840633	7840727	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7840728	7840928	1	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7840728	7840928	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7840929	7841028	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7841029	7841415	0.99	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7841029	7841415	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7841416	7841532	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7841533	7841616	1	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7841533	7841616	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7841617	7841934	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7841935	7841951	0.9	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7841935	7841951	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7841952	7842029	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7842030	7842125	0.9	+	1	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7842030	7842125	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	intron	7842126	7842460	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	CDS	7842461	7842734	0.72	+	1	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	exon	7842461	7842734	.	+	.	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
Phchi.S5	AUGUSTUS	stop_codon	7842735	7842737	.	+	0	transcript_id "Phchi.S5G123700.t1"; gene_id "Phchi.S5G123700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12325.t1 is derived from g8001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10899999	10900747	.	+	.	Phchi.S2G040500
Phchi.S2	AUGUSTUS	transcript	10899999	10900747	.	+	.	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	start_codon	10899999	10900001	.	+	0	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	CDS	10899999	10900210	0.67	+	0	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	exon	10899999	10900210	.	+	.	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	intron	10900211	10900416	.	+	.	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	CDS	10900417	10900747	0.25	+	1	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	exon	10900417	10900747	.	+	.	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
Phchi.S2	AUGUSTUS	stop_codon	10900748	10900750	.	+	0	transcript_id "Phchi.S2G040500.t1"; gene_id "Phchi.S2G040500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg711.t1 is derived from g10493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5018973	5019985	.	+	.	Phchi.S6G067000
Phchi.S6	AUGUSTUS	transcript	5018973	5019985	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	start_codon	5018973	5018975	.	+	0	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	CDS	5018973	5019077	0.99	+	0	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	exon	5018973	5019077	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	intron	5019078	5019181	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	CDS	5019182	5019453	0.76	+	0	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	exon	5019182	5019453	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	intron	5019454	5019544	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	CDS	5019545	5019641	1	+	1	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	exon	5019545	5019641	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	intron	5019642	5019775	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	CDS	5019776	5019985	0.97	+	0	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	exon	5019776	5019985	.	+	.	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
Phchi.S6	AUGUSTUS	stop_codon	5019986	5019988	.	+	0	transcript_id "Phchi.S6G067000.t1"; gene_id "Phchi.S6G067000"
# This transcript jg11836.t2 is derived from g15888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11837.t1 is derived from g15889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8497709	8499078	.	+	.	Phchi.S4G141900
Phchi.S4	AUGUSTUS	transcript	8497709	8499078	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	start_codon	8497709	8497711	.	+	0	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	CDS	8497709	8497823	1	+	0	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	exon	8497709	8497823	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	intron	8497824	8498084	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	CDS	8498085	8498284	1	+	2	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	exon	8498085	8498284	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	intron	8498285	8498379	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	CDS	8498380	8498469	1	+	0	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	exon	8498380	8498469	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	intron	8498470	8498554	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	CDS	8498555	8498626	1	+	0	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	exon	8498555	8498626	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	intron	8498627	8498767	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	CDS	8498768	8498897	1	+	0	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	exon	8498768	8498897	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	intron	8498898	8498983	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	CDS	8498984	8499078	0.99	+	2	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	exon	8498984	8499078	.	+	.	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
Phchi.S4	AUGUSTUS	stop_codon	8499079	8499081	.	+	0	transcript_id "Phchi.S4G141900.t1"; gene_id "Phchi.S4G141900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1917.t1 is derived from g8837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3843511	3844325	.	+	.	Phchi.S5G052600
Phchi.S5	AUGUSTUS	transcript	3843511	3844325	.	+	.	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	start_codon	3843511	3843513	.	+	0	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	CDS	3843511	3843740	0.73	+	0	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	exon	3843511	3843740	.	+	.	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	intron	3843741	3843811	.	+	.	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	CDS	3843812	3844031	1	+	1	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	exon	3843812	3844031	.	+	.	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	intron	3844032	3844112	.	+	.	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	CDS	3844113	3844325	0.74	+	0	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	exon	3844113	3844325	.	+	.	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
Phchi.S5	AUGUSTUS	stop_codon	3844326	3844328	.	+	0	transcript_id "Phchi.S5G052600.t1"; gene_id "Phchi.S5G052600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12040.t1 is derived from g7715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	853355	858142	.	-	.	Phchi.S2G012000
Phchi.S2	AUGUSTUS	transcript	853355	858142	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	stop_codon	853352	853354	.	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	853355	853540	0.42	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	853355	853540	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	853541	853668	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	853669	853836	0.98	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	853669	853836	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	853837	853938	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	853939	854013	0.99	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	853939	854013	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	854014	854141	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	854142	854292	0.92	-	1	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	854142	854292	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	854293	854383	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	854384	854392	0.67	-	1	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	854384	854392	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	854393	854481	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	854482	857519	0.81	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	854482	857519	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	857520	857917	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	857918	858142	0.57	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	857918	858142	.	-	.	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	start_codon	858140	858142	.	-	0	transcript_id "Phchi.S2G012000.t1"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	transcript	853355	858142	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	stop_codon	853352	853354	.	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	853355	853540	0.52	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	853355	853540	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	853541	853668	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	853669	853836	0.98	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	853669	853836	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	853837	853938	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	853939	854013	1	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	853939	854013	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	854014	854141	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	854142	854292	0.94	-	1	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	854142	854292	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	854293	854383	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	854384	854392	0.68	-	1	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	854384	854392	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	854393	854481	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	854482	857561	0.44	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	854482	857561	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	857562	857674	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	857675	857719	0.87	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	857675	857719	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	intron	857720	857917	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	CDS	857918	858142	0.58	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	exon	857918	858142	.	-	.	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
Phchi.S2	AUGUSTUS	start_codon	858140	858142	.	-	0	transcript_id "Phchi.S2G012000.t2"; gene_id "Phchi.S2G012000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9158.t1 is derived from g6333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40143577	40145382	.	+	.	Phchi.S1G631700
Phchi.S1	AUGUSTUS	transcript	40143577	40145382	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	start_codon	40143577	40143579	.	+	0	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	CDS	40143577	40143678	0.97	+	0	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	exon	40143577	40143678	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	intron	40143679	40143761	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	CDS	40143762	40144412	0.99	+	0	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	exon	40143762	40144412	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	intron	40144413	40144499	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	CDS	40144500	40145018	0.99	+	0	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	exon	40144500	40145018	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	intron	40145019	40145109	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	CDS	40145110	40145382	0.52	+	0	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	exon	40145110	40145382	.	+	.	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
Phchi.S1	AUGUSTUS	stop_codon	40145383	40145385	.	+	0	transcript_id "Phchi.S1G631700.t1"; gene_id "Phchi.S1G631700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6237.t1 is derived from g3409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21811441	21813733	.	-	.	Phchi.S1G339600
Phchi.S1	AUGUSTUS	transcript	21811441	21813733	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	stop_codon	21811438	21811440	.	-	0	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21811441	21811441	1	-	1	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21811441	21811441	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	intron	21811442	21811606	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21811607	21811773	1	-	0	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21811607	21811773	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	intron	21811774	21812157	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21812158	21812198	1	-	2	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21812158	21812198	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	intron	21812199	21812369	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21812370	21812759	1	-	2	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21812370	21812759	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	intron	21812760	21812906	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21812907	21813242	1	-	2	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21812907	21813242	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	intron	21813243	21813450	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21813451	21813490	1	-	0	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21813451	21813490	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	intron	21813491	21813604	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	CDS	21813605	21813733	0.95	-	0	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	exon	21813605	21813733	.	-	.	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
Phchi.S1	AUGUSTUS	start_codon	21813731	21813733	.	-	0	transcript_id "Phchi.S1G339600.t1"; gene_id "Phchi.S1G339600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15153.t1 is derived from g13621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17288125	17292927	.	+	.	Phchi.S3G247200
Phchi.S3	AUGUSTUS	transcript	17288125	17292927	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	start_codon	17288125	17288127	.	+	0	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	CDS	17288125	17288327	0.01	+	0	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	exon	17288125	17288327	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	intron	17288328	17288836	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	CDS	17288837	17288906	0.98	+	1	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	exon	17288837	17288906	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	intron	17288907	17290506	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	CDS	17290507	17290593	0.62	+	0	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	exon	17290507	17290593	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	intron	17290594	17292714	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	CDS	17292715	17292927	0.91	+	0	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	exon	17292715	17292927	.	+	.	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
Phchi.S3	AUGUSTUS	stop_codon	17292928	17292930	.	+	0	transcript_id "Phchi.S3G247200.t1"; gene_id "Phchi.S3G247200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8438.t1 is derived from g5613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35936009	35938563	.	+	.	Phchi.S1G559700
Phchi.S1	AUGUSTUS	transcript	35936009	35938563	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	start_codon	35936009	35936011	.	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936009	35936024	0.75	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936009	35936024	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936025	35936113	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936114	35936277	1	+	2	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936114	35936277	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936278	35936358	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936359	35936414	1	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936359	35936414	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936415	35936512	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936513	35936630	1	+	1	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936513	35936630	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936631	35936795	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936796	35936858	1	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936796	35936858	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936859	35936950	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936951	35937019	1	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936951	35937019	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937020	35937120	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937121	35937287	0.74	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937121	35937287	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937288	35937401	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937402	35937469	0.95	+	1	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937402	35937469	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937470	35937546	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937547	35937602	1	+	2	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937547	35937602	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937603	35937683	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937684	35937728	0.97	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937684	35937728	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937729	35937840	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937841	35937891	0.99	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937841	35937891	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937892	35938051	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35938052	35938153	0.6	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35938052	35938153	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35938154	35938261	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35938262	35938352	0.43	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35938262	35938352	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35938353	35938456	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35938457	35938563	0.43	+	2	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35938457	35938563	.	+	.	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	stop_codon	35938564	35938566	.	+	0	transcript_id "Phchi.S1G559700.t1"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	transcript	35936009	35938563	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	start_codon	35936009	35936011	.	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936009	35936024	0.82	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936009	35936024	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936025	35936113	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936114	35936277	1	+	2	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936114	35936277	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936278	35936358	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936359	35936414	1	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936359	35936414	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936415	35936512	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936513	35936630	1	+	1	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936513	35936630	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936631	35936795	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936796	35936858	1	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936796	35936858	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35936859	35936950	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35936951	35937019	1	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35936951	35937019	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937020	35937120	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937121	35937287	0.8	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937121	35937287	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937288	35937401	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937402	35937469	0.96	+	1	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937402	35937469	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937470	35937537	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937538	35937602	1	+	2	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937538	35937602	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937603	35937683	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937684	35937728	0.98	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937684	35937728	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937729	35937840	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35937841	35937891	1	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35937841	35937891	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35937892	35938051	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35938052	35938153	0.47	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35938052	35938153	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35938154	35938261	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35938262	35938352	0.22	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35938262	35938352	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	intron	35938353	35938456	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	CDS	35938457	35938563	0.22	+	2	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	exon	35938457	35938563	.	+	.	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
Phchi.S1	AUGUSTUS	stop_codon	35938564	35938566	.	+	0	transcript_id "Phchi.S1G559700.t2"; gene_id "Phchi.S1G559700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg321.t1 is derived from g10103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2262627	2263744	.	+	.	Phchi.S6G028000
Phchi.S6	AUGUSTUS	transcript	2262627	2263744	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	start_codon	2262627	2262629	.	+	0	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	CDS	2262627	2262738	0.98	+	0	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	exon	2262627	2262738	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	intron	2262739	2262835	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	CDS	2262836	2262909	0.96	+	2	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	exon	2262836	2262909	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	intron	2262910	2263048	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	CDS	2263049	2263169	0.99	+	0	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	exon	2263049	2263169	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	intron	2263170	2263258	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	CDS	2263259	2263469	1	+	2	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	exon	2263259	2263469	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	intron	2263470	2263566	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	CDS	2263567	2263744	1	+	1	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	exon	2263567	2263744	.	+	.	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
Phchi.S6	AUGUSTUS	stop_codon	2263745	2263747	.	+	0	transcript_id "Phchi.S6G028000.t1"; gene_id "Phchi.S6G028000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11847.t1 is derived from g15899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8566926	8568211	.	+	.	Phchi.S4G142900
Phchi.S4	AUGUSTUS	transcript	8566926	8568211	.	+	.	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	start_codon	8566926	8566928	.	+	0	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	CDS	8566926	8567662	0.55	+	0	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	exon	8566926	8567662	.	+	.	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	intron	8567663	8567802	.	+	.	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	CDS	8567803	8568211	0.97	+	1	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	exon	8567803	8568211	.	+	.	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
Phchi.S4	AUGUSTUS	stop_codon	8568212	8568214	.	+	0	transcript_id "Phchi.S4G142900.t1"; gene_id "Phchi.S4G142900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10240.t1 is derived from g7416.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46518956	46521999	.	-	.	Phchi.S1G739900
Phchi.S1	AUGUSTUS	transcript	46518956	46521999	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	stop_codon	46518953	46518955	.	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46518956	46519138	0.95	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46518956	46519138	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519139	46519232	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519233	46519316	1	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519233	46519316	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519317	46519402	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519403	46519455	1	-	2	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519403	46519455	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519456	46519552	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519553	46519639	1	-	2	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519553	46519639	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519640	46519784	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519785	46519829	1	-	2	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519785	46519829	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519830	46519922	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519923	46520073	1	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519923	46520073	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520074	46520156	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520157	46520294	1	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520157	46520294	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520295	46520411	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520412	46520543	0.98	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520412	46520543	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520544	46520627	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520628	46520833	1	-	2	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520628	46520833	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520834	46520916	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520917	46521028	1	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520917	46521028	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521029	46521133	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521134	46521193	0.96	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521134	46521193	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521194	46521299	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521300	46521398	1	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521300	46521398	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521399	46521618	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521619	46521674	1	-	2	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521619	46521674	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521675	46521941	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521942	46521999	0.87	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521942	46521999	.	-	.	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	start_codon	46521997	46521999	.	-	0	transcript_id "Phchi.S1G739900.t1"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	transcript	46518956	46521999	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	stop_codon	46518953	46518955	.	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46518956	46519138	0.98	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46518956	46519138	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519139	46519232	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519233	46519316	1	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519233	46519316	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519317	46519402	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519403	46519455	1	-	2	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519403	46519455	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519456	46519552	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519553	46519639	0.99	-	2	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519553	46519639	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519640	46519784	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519785	46519829	1	-	2	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519785	46519829	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46519830	46519922	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46519923	46520073	1	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46519923	46520073	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520074	46520156	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520157	46520294	1	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520157	46520294	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520295	46520411	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520412	46520540	1	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520412	46520540	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520541	46520627	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520628	46520833	1	-	2	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520628	46520833	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46520834	46520916	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46520917	46521028	1	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46520917	46521028	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521029	46521133	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521134	46521193	0.92	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521134	46521193	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521194	46521299	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521300	46521398	1	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521300	46521398	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521399	46521618	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521619	46521674	1	-	2	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521619	46521674	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	intron	46521675	46521941	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	CDS	46521942	46521999	0.94	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	exon	46521942	46521999	.	-	.	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
Phchi.S1	AUGUSTUS	start_codon	46521997	46521999	.	-	0	transcript_id "Phchi.S1G739900.t2"; gene_id "Phchi.S1G739900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10921.t1 is derived from g14971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2977136	2978549	.	-	.	Phchi.S4G050300
Phchi.S4	AUGUSTUS	transcript	2977136	2978549	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	stop_codon	2977133	2977135	.	-	0	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	CDS	2977136	2977358	0.98	-	1	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	exon	2977136	2977358	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	intron	2977359	2977444	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	CDS	2977445	2977533	0.36	-	0	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	exon	2977445	2977533	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	intron	2977534	2977857	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	CDS	2977858	2977871	0.63	-	2	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	exon	2977858	2977871	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	intron	2977872	2977954	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	CDS	2977955	2978334	0.65	-	1	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	exon	2977955	2978334	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	intron	2978335	2978417	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	CDS	2978418	2978456	0.96	-	1	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	exon	2978418	2978456	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	intron	2978457	2978544	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	CDS	2978545	2978549	0.96	-	0	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	exon	2978545	2978549	.	-	.	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
Phchi.S4	AUGUSTUS	start_codon	2978547	2978549	.	-	0	transcript_id "Phchi.S4G050300.t1"; gene_id "Phchi.S4G050300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13936.t1 is derived from g12403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9804733	9805712	.	-	.	Phchi.S3G125500
Phchi.S3	AUGUSTUS	transcript	9804733	9805712	.	-	.	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	stop_codon	9804730	9804732	.	-	0	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	CDS	9804733	9805118	0.79	-	2	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	exon	9804733	9805118	.	-	.	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	intron	9805119	9805222	.	-	.	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	CDS	9805223	9805388	0.97	-	0	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	exon	9805223	9805388	.	-	.	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	intron	9805389	9805496	.	-	.	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	CDS	9805497	9805712	0.97	-	0	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	exon	9805497	9805712	.	-	.	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
Phchi.S3	AUGUSTUS	start_codon	9805710	9805712	.	-	0	transcript_id "Phchi.S3G125500.t1"; gene_id "Phchi.S3G125500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7326.t1 is derived from g4498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28524859	28526196	.	+	.	Phchi.S1G448500
Phchi.S1	AUGUSTUS	transcript	28524859	28526196	.	+	.	transcript_id "Phchi.S1G448500.t1"; gene_id "Phchi.S1G448500"
Phchi.S1	AUGUSTUS	start_codon	28524859	28524861	.	+	0	transcript_id "Phchi.S1G448500.t1"; gene_id "Phchi.S1G448500"
Phchi.S1	AUGUSTUS	CDS	28524859	28526196	1	+	0	transcript_id "Phchi.S1G448500.t1"; gene_id "Phchi.S1G448500"
Phchi.S1	AUGUSTUS	exon	28524859	28526196	.	+	.	transcript_id "Phchi.S1G448500.t1"; gene_id "Phchi.S1G448500"
Phchi.S1	AUGUSTUS	stop_codon	28526197	28526199	.	+	0	transcript_id "Phchi.S1G448500.t1"; gene_id "Phchi.S1G448500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg54.t1 is derived from g9836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	145544	147106	.	+	.	Phchi.S6G001300
Phchi.S6	AUGUSTUS	transcript	145544	147106	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	start_codon	145544	145546	.	+	0	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	CDS	145544	145624	0.45	+	0	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	exon	145544	145624	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	intron	145625	146006	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	CDS	146007	146016	0.49	+	0	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	exon	146007	146016	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	intron	146017	146197	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	CDS	146198	146216	0.49	+	2	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	exon	146198	146216	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	intron	146217	146409	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	CDS	146410	146547	0.65	+	1	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	exon	146410	146547	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	intron	146548	146876	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	CDS	146877	147006	0.27	+	1	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	exon	146877	147006	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	intron	147007	147097	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	CDS	147098	147106	0.91	+	0	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	exon	147098	147106	.	+	.	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
Phchi.S6	AUGUSTUS	stop_codon	147107	147109	.	+	0	transcript_id "Phchi.S6G001300.t1"; gene_id "Phchi.S6G001300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9229.t1 is derived from g6404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40514173	40516231	.	+	.	Phchi.S1G638800
Phchi.S1	AUGUSTUS	transcript	40514173	40516231	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	start_codon	40514173	40514175	.	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40514173	40514289	0.67	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40514173	40514289	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40514290	40514576	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40514577	40514649	0.93	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40514577	40514649	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40514650	40514777	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40514778	40514879	0.77	+	2	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40514778	40514879	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40514880	40514994	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40514995	40515080	1	+	2	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40514995	40515080	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40515081	40515291	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40515292	40515438	1	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40515292	40515438	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40515439	40515543	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40515544	40515667	1	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40515544	40515667	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40515668	40515761	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40515762	40516051	0.75	+	2	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40515762	40516051	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	intron	40516052	40516141	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	CDS	40516142	40516231	1	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	exon	40516142	40516231	.	+	.	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
Phchi.S1	AUGUSTUS	stop_codon	40516232	40516234	.	+	0	transcript_id "Phchi.S1G638800.t1"; gene_id "Phchi.S1G638800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg422.t1 is derived from g10204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3000368	3000881	.	-	.	Phchi.S6G038100
Phchi.S6	AUGUSTUS	transcript	3000368	3000881	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	stop_codon	3000365	3000367	.	-	0	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	CDS	3000368	3000382	0.8	-	0	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	exon	3000368	3000382	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	intron	3000383	3000477	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	CDS	3000478	3000547	0.8	-	1	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	exon	3000478	3000547	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	intron	3000548	3000653	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	CDS	3000654	3000713	0.74	-	1	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	exon	3000654	3000713	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	intron	3000714	3000816	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	CDS	3000817	3000881	0.71	-	0	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	exon	3000817	3000881	.	-	.	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
Phchi.S6	AUGUSTUS	start_codon	3000879	3000881	.	-	0	transcript_id "Phchi.S6G038100.t1"; gene_id "Phchi.S6G038100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5063.t1 is derived from g2233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14496920	14498008	.	+	.	Phchi.S1G222200
Phchi.S1	AUGUSTUS	transcript	14496920	14498008	.	+	.	transcript_id "Phchi.S1G222200.t1"; gene_id "Phchi.S1G222200"
Phchi.S1	AUGUSTUS	start_codon	14496920	14496922	.	+	0	transcript_id "Phchi.S1G222200.t1"; gene_id "Phchi.S1G222200"
Phchi.S1	AUGUSTUS	CDS	14496920	14498008	1	+	0	transcript_id "Phchi.S1G222200.t1"; gene_id "Phchi.S1G222200"
Phchi.S1	AUGUSTUS	exon	14496920	14498008	.	+	.	transcript_id "Phchi.S1G222200.t1"; gene_id "Phchi.S1G222200"
Phchi.S1	AUGUSTUS	stop_codon	14498009	14498011	.	+	0	transcript_id "Phchi.S1G222200.t1"; gene_id "Phchi.S1G222200"
# This transcript jg6138.t2 is derived from g3309.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6139.t1 is derived from g3310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21125010	21127610	.	-	.	Phchi.S1G329800
Phchi.S1	AUGUSTUS	transcript	21125010	21127610	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	stop_codon	21125007	21125009	.	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21125010	21125023	0.9	-	2	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21125010	21125023	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21125024	21125179	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21125180	21125393	0.9	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21125180	21125393	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21125394	21125481	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21125482	21125718	1	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21125482	21125718	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21125719	21125815	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21125816	21126268	0.44	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21125816	21126268	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21126269	21126350	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21126351	21126638	0.99	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21126351	21126638	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21126639	21126744	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21126745	21126798	1	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21126745	21126798	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21126799	21126926	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21126927	21127037	1	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21126927	21127037	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21127038	21127114	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21127115	21127338	1	-	2	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21127115	21127338	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	intron	21127339	21127426	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	CDS	21127427	21127610	0.55	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	exon	21127427	21127610	.	-	.	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
Phchi.S1	AUGUSTUS	start_codon	21127608	21127610	.	-	0	transcript_id "Phchi.S1G329800.t1"; gene_id "Phchi.S1G329800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14809.t1 is derived from g13277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14810960	14811972	.	+	.	Phchi.S3G212800
Phchi.S3	AUGUSTUS	transcript	14810960	14811972	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	start_codon	14810960	14810962	.	+	0	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14810960	14810987	0.86	+	0	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14810960	14810987	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	intron	14810988	14811126	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14811127	14811209	1	+	2	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14811127	14811209	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	intron	14811210	14811358	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14811359	14811438	1	+	0	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14811359	14811438	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	intron	14811439	14811513	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14811514	14811658	1	+	1	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14811514	14811658	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	intron	14811659	14811736	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14811737	14811766	0.68	+	0	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14811737	14811766	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	intron	14811767	14811834	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14811835	14811884	0.99	+	0	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14811835	14811884	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	intron	14811885	14811971	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	CDS	14811972	14811972	0.99	+	1	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	exon	14811972	14811972	.	+	.	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
Phchi.S3	AUGUSTUS	stop_codon	14811973	14811975	.	+	0	transcript_id "Phchi.S3G212800.t1"; gene_id "Phchi.S3G212800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3692.t1 is derived from g861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5213163	5214380	.	-	.	Phchi.S1G085100
Phchi.S1	AUGUSTUS	transcript	5213163	5214380	.	-	.	transcript_id "Phchi.S1G085100.t1"; gene_id "Phchi.S1G085100"
Phchi.S1	AUGUSTUS	stop_codon	5213160	5213162	.	-	0	transcript_id "Phchi.S1G085100.t1"; gene_id "Phchi.S1G085100"
Phchi.S1	AUGUSTUS	CDS	5213163	5214380	0.92	-	0	transcript_id "Phchi.S1G085100.t1"; gene_id "Phchi.S1G085100"
Phchi.S1	AUGUSTUS	exon	5213163	5214380	.	-	.	transcript_id "Phchi.S1G085100.t1"; gene_id "Phchi.S1G085100"
Phchi.S1	AUGUSTUS	start_codon	5214378	5214380	.	-	0	transcript_id "Phchi.S1G085100.t1"; gene_id "Phchi.S1G085100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3504.t1 is derived from g673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4120720	4121100	.	+	.	Phchi.S1G066300
Phchi.S1	AUGUSTUS	transcript	4120720	4121100	.	+	.	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	start_codon	4120720	4120722	.	+	0	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	CDS	4120720	4120731	0.99	+	0	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	exon	4120720	4120731	.	+	.	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	intron	4120732	4120827	.	+	.	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	CDS	4120828	4121100	0.52	+	0	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	exon	4120828	4121100	.	+	.	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
Phchi.S1	AUGUSTUS	stop_codon	4121101	4121103	.	+	0	transcript_id "Phchi.S1G066300.t1"; gene_id "Phchi.S1G066300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8176.t1 is derived from g5351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34288220	34289581	.	+	.	Phchi.S1G533500
Phchi.S1	AUGUSTUS	transcript	34288220	34289581	.	+	.	transcript_id "Phchi.S1G533500.t1"; gene_id "Phchi.S1G533500"
Phchi.S1	AUGUSTUS	start_codon	34288220	34288222	.	+	0	transcript_id "Phchi.S1G533500.t1"; gene_id "Phchi.S1G533500"
Phchi.S1	AUGUSTUS	CDS	34288220	34289581	1	+	0	transcript_id "Phchi.S1G533500.t1"; gene_id "Phchi.S1G533500"
Phchi.S1	AUGUSTUS	exon	34288220	34289581	.	+	.	transcript_id "Phchi.S1G533500.t1"; gene_id "Phchi.S1G533500"
Phchi.S1	AUGUSTUS	stop_codon	34289582	34289584	.	+	0	transcript_id "Phchi.S1G533500.t1"; gene_id "Phchi.S1G533500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7207.t1 is derived from g4379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27636596	27637761	.	+	.	Phchi.S1G436600
Phchi.S1	AUGUSTUS	transcript	27636596	27637761	.	+	.	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	start_codon	27636596	27636598	.	+	0	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	CDS	27636596	27636826	0.13	+	0	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	exon	27636596	27636826	.	+	.	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	intron	27636827	27636914	.	+	.	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	CDS	27636915	27637008	1	+	0	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	exon	27636915	27637008	.	+	.	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	intron	27637009	27637528	.	+	.	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	CDS	27637529	27637761	0.01	+	2	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	exon	27637529	27637761	.	+	.	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
Phchi.S1	AUGUSTUS	stop_codon	27637762	27637764	.	+	0	transcript_id "Phchi.S1G436600.t1"; gene_id "Phchi.S1G436600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2990.t1 is derived from g159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1025081	1026704	.	-	.	Phchi.S1G014900
Phchi.S1	AUGUSTUS	transcript	1025081	1026704	.	-	.	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	stop_codon	1025078	1025080	.	-	0	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	CDS	1025081	1025116	1	-	0	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	exon	1025081	1025116	.	-	.	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	intron	1025117	1026197	.	-	.	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	CDS	1026198	1026704	0.93	-	0	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	exon	1026198	1026704	.	-	.	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
Phchi.S1	AUGUSTUS	start_codon	1026702	1026704	.	-	0	transcript_id "Phchi.S1G014900.t1"; gene_id "Phchi.S1G014900"
# This transcript jg14519.t2 is derived from g12987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14519.t3 is derived from g12987.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14520.t1 is derived from g12988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13297287	13298883	.	-	.	Phchi.S3G183900
Phchi.S3	AUGUSTUS	transcript	13297287	13298883	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	stop_codon	13297284	13297286	.	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13297287	13297376	1	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13297287	13297376	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	intron	13297377	13297466	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13297467	13297595	1	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13297467	13297595	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	intron	13297596	13297702	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13297703	13297867	0.97	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13297703	13297867	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	intron	13297868	13297959	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13297960	13298394	1	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13297960	13298394	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	intron	13298395	13298493	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13298494	13298521	0.97	-	1	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13298494	13298521	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	intron	13298522	13298594	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13298595	13298736	0.97	-	2	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13298595	13298736	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	intron	13298737	13298834	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	CDS	13298835	13298883	0.97	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	exon	13298835	13298883	.	-	.	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
Phchi.S3	AUGUSTUS	start_codon	13298881	13298883	.	-	0	transcript_id "Phchi.S3G183900.t1"; gene_id "Phchi.S3G183900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14265.t1 is derived from g12732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11837025	11839882	.	-	.	Phchi.S3G158400
Phchi.S3	AUGUSTUS	transcript	11837025	11839882	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	stop_codon	11837022	11837024	.	-	0	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11837025	11837631	1	-	1	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11837025	11837631	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	intron	11837632	11837732	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11837733	11837926	0.99	-	0	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11837733	11837926	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	intron	11837927	11838037	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11838038	11838360	0.6	-	2	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11838038	11838360	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	intron	11838361	11838432	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11838433	11838568	0.55	-	0	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11838433	11838568	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	intron	11838569	11838913	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11838914	11839118	0.98	-	1	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11838914	11839118	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	intron	11839119	11839632	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11839633	11839649	1	-	0	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11839633	11839649	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	intron	11839650	11839867	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	CDS	11839868	11839882	0.96	-	0	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	exon	11839868	11839882	.	-	.	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
Phchi.S3	AUGUSTUS	start_codon	11839880	11839882	.	-	0	transcript_id "Phchi.S3G158400.t1"; gene_id "Phchi.S3G158400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8496.t1 is derived from g5671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36253336	36255247	.	+	.	Phchi.S1G565500
Phchi.S1	AUGUSTUS	transcript	36253336	36255247	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	start_codon	36253336	36253338	.	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36253336	36253428	0.56	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36253336	36253428	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36253429	36253512	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36253513	36253534	0.76	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36253513	36253534	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36253535	36253634	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36253635	36253747	0.99	+	2	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36253635	36253747	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36253748	36253841	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36253842	36253961	1	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36253842	36253961	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36253962	36254050	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36254051	36254117	1	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36254051	36254117	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36254118	36254250	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36254251	36254297	1	+	2	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36254251	36254297	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36254298	36254525	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36254526	36254613	1	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36254526	36254613	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36254614	36254755	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36254756	36254889	1	+	2	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36254756	36254889	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36254890	36254990	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36254991	36255089	1	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36254991	36255089	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	intron	36255090	36255178	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	CDS	36255179	36255247	1	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	exon	36255179	36255247	.	+	.	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
Phchi.S1	AUGUSTUS	stop_codon	36255248	36255250	.	+	0	transcript_id "Phchi.S1G565500.t1"; gene_id "Phchi.S1G565500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11839.t1 is derived from g15891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8514301	8516734	.	+	.	Phchi.S4G142100
Phchi.S4	AUGUSTUS	transcript	8514301	8516734	.	+	.	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	start_codon	8514301	8514303	.	+	0	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	CDS	8514301	8514308	0.93	+	0	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	exon	8514301	8514308	.	+	.	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	intron	8514309	8514486	.	+	.	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	CDS	8514487	8514532	0.56	+	1	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	exon	8514487	8514532	.	+	.	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	intron	8514533	8514631	.	+	.	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	CDS	8514632	8516734	0.69	+	0	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	exon	8514632	8516734	.	+	.	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
Phchi.S4	AUGUSTUS	stop_codon	8516735	8516737	.	+	0	transcript_id "Phchi.S4G142100.t1"; gene_id "Phchi.S4G142100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15639.t1 is derived from g14108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20430065	20431864	.	-	.	Phchi.S3G295800
Phchi.S3	AUGUSTUS	transcript	20430065	20431864	.	-	.	transcript_id "Phchi.S3G295800.t1"; gene_id "Phchi.S3G295800"
Phchi.S3	AUGUSTUS	stop_codon	20430062	20430064	.	-	0	transcript_id "Phchi.S3G295800.t1"; gene_id "Phchi.S3G295800"
Phchi.S3	AUGUSTUS	CDS	20430065	20431864	0.94	-	0	transcript_id "Phchi.S3G295800.t1"; gene_id "Phchi.S3G295800"
Phchi.S3	AUGUSTUS	exon	20430065	20431864	.	-	.	transcript_id "Phchi.S3G295800.t1"; gene_id "Phchi.S3G295800"
Phchi.S3	AUGUSTUS	start_codon	20431862	20431864	.	-	0	transcript_id "Phchi.S3G295800.t1"; gene_id "Phchi.S3G295800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15883.t1 is derived from g14353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22023588	22025457	.	-	.	Phchi.S3G320200
Phchi.S3	AUGUSTUS	transcript	22023588	22025457	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	stop_codon	22023585	22023587	.	-	0	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	CDS	22023588	22023818	1	-	0	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	exon	22023588	22023818	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	intron	22023819	22023902	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	CDS	22023903	22024183	0.98	-	2	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	exon	22023903	22024183	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	intron	22024184	22024304	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	CDS	22024305	22025154	0.97	-	0	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	exon	22024305	22025154	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	intron	22025155	22025307	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	CDS	22025308	22025457	0.2	-	0	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	exon	22025308	22025457	.	-	.	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
Phchi.S3	AUGUSTUS	start_codon	22025455	22025457	.	-	0	transcript_id "Phchi.S3G320200.t1"; gene_id "Phchi.S3G320200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11188.t1 is derived from g15238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4548825	4550060	.	-	.	Phchi.S4G077000
Phchi.S4	AUGUSTUS	transcript	4548825	4550060	.	-	.	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	stop_codon	4548822	4548824	.	-	0	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	CDS	4548825	4548896	0.9	-	0	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	exon	4548825	4548896	.	-	.	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	intron	4548897	4549367	.	-	.	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	CDS	4549368	4549752	0.66	-	1	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	exon	4549368	4549752	.	-	.	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	intron	4549753	4549842	.	-	.	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	CDS	4549843	4550060	0.66	-	0	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	exon	4549843	4550060	.	-	.	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
Phchi.S4	AUGUSTUS	start_codon	4550058	4550060	.	-	0	transcript_id "Phchi.S4G077000.t1"; gene_id "Phchi.S4G077000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9543.t1 is derived from g6719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42400702	42401476	.	-	.	Phchi.S1G670200
Phchi.S1	AUGUSTUS	transcript	42400702	42401476	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	stop_codon	42400699	42400701	.	-	0	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	CDS	42400702	42400774	1	-	1	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	exon	42400702	42400774	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	intron	42400775	42400868	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	CDS	42400869	42400927	0.92	-	0	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	exon	42400869	42400927	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	intron	42400928	42401025	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	CDS	42401026	42401091	0.41	-	0	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	exon	42401026	42401091	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	intron	42401092	42401205	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	CDS	42401206	42401280	1	-	0	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	exon	42401206	42401280	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	intron	42401281	42401374	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	CDS	42401375	42401476	0.96	-	0	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	exon	42401375	42401476	.	-	.	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
Phchi.S1	AUGUSTUS	start_codon	42401474	42401476	.	-	0	transcript_id "Phchi.S1G670200.t1"; gene_id "Phchi.S1G670200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9151.t1 is derived from g6326.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40109237	40111155	.	+	.	Phchi.S1G631000
Phchi.S1	AUGUSTUS	transcript	40109237	40110928	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	start_codon	40109237	40109239	.	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109237	40109425	0.63	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109237	40109425	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40109426	40109537	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109538	40109635	1	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109538	40109635	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40109636	40109760	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109761	40109858	1	+	1	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109761	40109858	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40109859	40109947	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109948	40110000	1	+	2	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109948	40110000	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110001	40110094	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110095	40110190	1	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110095	40110190	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110191	40110315	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110316	40110405	1	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110316	40110405	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110406	40110494	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110495	40110587	1	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110495	40110587	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110588	40110682	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110683	40110778	1	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110683	40110778	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110779	40110856	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110857	40110928	1	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110857	40110928	.	+	.	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	stop_codon	40110929	40110931	.	+	0	transcript_id "Phchi.S1G631000.t1"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	transcript	40109237	40111155	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	start_codon	40109237	40109239	.	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109237	40109425	0.74	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109237	40109425	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40109426	40109537	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109538	40109635	0.98	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109538	40109635	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40109636	40109760	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109761	40109858	1	+	1	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109761	40109858	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40109859	40109947	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40109948	40110000	1	+	2	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40109948	40110000	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110001	40110094	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110095	40110190	1	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110095	40110190	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110191	40110315	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110316	40110405	1	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110316	40110405	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110406	40110494	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110495	40110587	1	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110495	40110587	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110588	40110682	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110683	40110778	1	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110683	40110778	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110779	40110856	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40110857	40110922	0.73	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40110857	40110922	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	intron	40110923	40111023	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	CDS	40111024	40111155	0.72	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	exon	40111024	40111155	.	+	.	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
Phchi.S1	AUGUSTUS	stop_codon	40111156	40111158	.	+	0	transcript_id "Phchi.S1G631000.t2"; gene_id "Phchi.S1G631000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13390.t1 is derived from g11856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6503765	6506255	.	+	.	Phchi.S3G070900
Phchi.S3	AUGUSTUS	transcript	6503765	6506255	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	start_codon	6503765	6503767	.	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6503765	6504073	0.99	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6503765	6504073	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6504074	6504227	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6504228	6504302	0.96	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6504228	6504302	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6504303	6504408	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6504409	6504514	0.76	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6504409	6504514	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6504515	6504600	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6504601	6504685	0.95	+	2	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6504601	6504685	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6504686	6504831	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6504832	6504952	1	+	1	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6504832	6504952	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6504953	6505028	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6505029	6505105	1	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6505029	6505105	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6505106	6505252	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6505253	6505315	1	+	1	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6505253	6505315	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6505316	6505441	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6505442	6505584	1	+	1	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6505442	6505584	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6505585	6505661	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6505662	6505747	1	+	2	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6505662	6505747	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6505748	6505881	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6505882	6506006	1	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6505882	6506006	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	intron	6506007	6506095	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	CDS	6506096	6506255	0.96	+	1	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	exon	6506096	6506255	.	+	.	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
Phchi.S3	AUGUSTUS	stop_codon	6506256	6506258	.	+	0	transcript_id "Phchi.S3G070900.t1"; gene_id "Phchi.S3G070900"
# This transcript jg930.t2 is derived from g10712.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg931.t1 is derived from g10713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6489640	6490036	.	-	.	Phchi.S6G089000
Phchi.S6	AUGUSTUS	transcript	6489640	6490036	.	-	.	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	stop_codon	6489637	6489639	.	-	0	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	CDS	6489640	6489743	0.9	-	2	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	exon	6489640	6489743	.	-	.	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	intron	6489744	6489828	.	-	.	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	CDS	6489829	6490036	0.99	-	0	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	exon	6489829	6490036	.	-	.	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
Phchi.S6	AUGUSTUS	start_codon	6490034	6490036	.	-	0	transcript_id "Phchi.S6G089000.t1"; gene_id "Phchi.S6G089000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12220.t1 is derived from g7896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6815702	6820474	.	-	.	Phchi.S2G030000
Phchi.S2	AUGUSTUS	transcript	6815702	6820474	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	stop_codon	6815699	6815701	.	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6815702	6815932	1	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6815702	6815932	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6815933	6816083	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6816084	6817679	0.99	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6816084	6817679	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6817680	6817956	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6817957	6817985	0.97	-	2	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6817957	6817985	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6817986	6818068	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6818069	6818548	0.86	-	2	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6818069	6818548	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6818549	6818656	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6818657	6819032	1	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6818657	6819032	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6819033	6819180	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6819181	6819951	1	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6819181	6819951	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6819952	6820039	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6820040	6820276	1	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6820040	6820276	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	intron	6820277	6820369	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	CDS	6820370	6820474	0.84	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	exon	6820370	6820474	.	-	.	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
Phchi.S2	AUGUSTUS	start_codon	6820472	6820474	.	-	0	transcript_id "Phchi.S2G030000.t1"; gene_id "Phchi.S2G030000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13643.t1 is derived from g12110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7989444	7993353	.	+	.	Phchi.S3G096200
Phchi.S3	AUGUSTUS	transcript	7989444	7993353	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	start_codon	7989444	7989446	.	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7989444	7990018	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7989444	7990018	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7990019	7990113	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7990114	7990182	1	+	1	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7990114	7990182	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7990183	7990257	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7990258	7990365	1	+	1	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7990258	7990365	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7990366	7990505	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7990506	7990686	0.99	+	1	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7990506	7990686	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7990687	7990788	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7990789	7990868	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7990789	7990868	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7990869	7990989	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7990990	7991109	1	+	1	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7990990	7991109	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7991110	7991234	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7991235	7991340	1	+	1	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7991235	7991340	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7991341	7991423	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7991424	7991513	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7991424	7991513	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7991514	7991667	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7991668	7991736	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7991668	7991736	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7991737	7991906	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7991907	7991972	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7991907	7991972	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7991973	7992066	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7992067	7992234	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7992067	7992234	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7992235	7992337	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7992338	7992460	0.86	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7992338	7992460	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7992461	7992553	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7992554	7992583	0.86	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7992554	7992583	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7992584	7992781	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7992782	7992837	1	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7992782	7992837	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	intron	7992838	7993352	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	CDS	7993353	7993353	1	+	1	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	exon	7993353	7993353	.	+	.	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
Phchi.S3	AUGUSTUS	stop_codon	7993354	7993356	.	+	0	transcript_id "Phchi.S3G096200.t1"; gene_id "Phchi.S3G096200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg410.t1 is derived from g10192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2944254	2946764	.	-	.	Phchi.S6G036900
Phchi.S6	AUGUSTUS	transcript	2944254	2946764	.	-	.	transcript_id "Phchi.S6G036900.t1"; gene_id "Phchi.S6G036900"
Phchi.S6	AUGUSTUS	stop_codon	2944251	2944253	.	-	0	transcript_id "Phchi.S6G036900.t1"; gene_id "Phchi.S6G036900"
Phchi.S6	AUGUSTUS	CDS	2944254	2946764	0.95	-	0	transcript_id "Phchi.S6G036900.t1"; gene_id "Phchi.S6G036900"
Phchi.S6	AUGUSTUS	exon	2944254	2946764	.	-	.	transcript_id "Phchi.S6G036900.t1"; gene_id "Phchi.S6G036900"
Phchi.S6	AUGUSTUS	start_codon	2946762	2946764	.	-	0	transcript_id "Phchi.S6G036900.t1"; gene_id "Phchi.S6G036900"
# This transcript jg10883.t2 is derived from g14933.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10884.t1 is derived from g14934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2752762	2755468	.	+	.	Phchi.S4G046600
Phchi.S4	AUGUSTUS	transcript	2752762	2755468	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	start_codon	2752762	2752764	.	+	0	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	CDS	2752762	2753131	0.88	+	0	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	exon	2752762	2753131	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	intron	2753132	2753234	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	CDS	2753235	2753481	0.87	+	2	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	exon	2753235	2753481	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	intron	2753482	2753579	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	CDS	2753580	2753874	1	+	1	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	exon	2753580	2753874	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	intron	2753875	2754047	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	CDS	2754048	2754428	1	+	0	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	exon	2754048	2754428	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	intron	2754429	2754544	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	CDS	2754545	2755468	1	+	0	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	exon	2754545	2755468	.	+	.	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
Phchi.S4	AUGUSTUS	stop_codon	2755469	2755471	.	+	0	transcript_id "Phchi.S4G046600.t1"; gene_id "Phchi.S4G046600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6419.t1 is derived from g3591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22901088	22903148	.	+	.	Phchi.S1G357800
Phchi.S1	AUGUSTUS	transcript	22901088	22903148	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	start_codon	22901088	22901090	.	+	0	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	CDS	22901088	22901203	0.45	+	0	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	exon	22901088	22901203	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	intron	22901204	22901482	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	CDS	22901483	22902377	0.58	+	1	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	exon	22901483	22902377	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	intron	22902378	22902583	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	CDS	22902584	22902608	1	+	0	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	exon	22902584	22902608	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	intron	22902609	22902864	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	CDS	22902865	22902978	1	+	2	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	exon	22902865	22902978	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	intron	22902979	22903071	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	CDS	22903072	22903148	1	+	2	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	exon	22903072	22903148	.	+	.	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
Phchi.S1	AUGUSTUS	stop_codon	22903149	22903151	.	+	0	transcript_id "Phchi.S1G357800.t1"; gene_id "Phchi.S1G357800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3055.t1 is derived from g224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1368794	1369340	.	-	.	Phchi.S1G021400
Phchi.S1	AUGUSTUS	transcript	1368794	1369340	.	-	.	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	stop_codon	1368791	1368793	.	-	0	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	CDS	1368794	1368857	0.91	-	1	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	exon	1368794	1368857	.	-	.	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	intron	1368858	1369038	.	-	.	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	CDS	1369039	1369340	0.87	-	0	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	exon	1369039	1369340	.	-	.	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
Phchi.S1	AUGUSTUS	start_codon	1369338	1369340	.	-	0	transcript_id "Phchi.S1G021400.t1"; gene_id "Phchi.S1G021400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13098.t1 is derived from g11563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4133659	4133963	.	+	.	Phchi.S3G041700
Phchi.S3	AUGUSTUS	transcript	4133659	4133963	.	+	.	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	start_codon	4133659	4133661	.	+	0	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	CDS	4133659	4133846	0.6	+	0	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	exon	4133659	4133846	.	+	.	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	intron	4133847	4133938	.	+	.	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	CDS	4133939	4133963	1	+	1	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	exon	4133939	4133963	.	+	.	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
Phchi.S3	AUGUSTUS	stop_codon	4133964	4133966	.	+	0	transcript_id "Phchi.S3G041700.t1"; gene_id "Phchi.S3G041700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5421.t1 is derived from g2591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16800150	16800940	.	-	.	Phchi.S1G258000
Phchi.S1	AUGUSTUS	transcript	16800150	16800940	.	-	.	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	stop_codon	16800147	16800149	.	-	0	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	CDS	16800150	16800378	0.86	-	1	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	exon	16800150	16800378	.	-	.	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	intron	16800379	16800451	.	-	.	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	CDS	16800452	16800606	0.84	-	0	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	exon	16800452	16800606	.	-	.	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	intron	16800607	16800682	.	-	.	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	CDS	16800683	16800940	0.6	-	0	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	exon	16800683	16800940	.	-	.	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
Phchi.S1	AUGUSTUS	start_codon	16800938	16800940	.	-	0	transcript_id "Phchi.S1G258000.t1"; gene_id "Phchi.S1G258000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14172.t1 is derived from g12639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11260746	11263697	.	-	.	Phchi.S3G149100
Phchi.S3	AUGUSTUS	transcript	11260746	11263697	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	stop_codon	11260743	11260745	.	-	0	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	CDS	11260746	11262074	0.46	-	0	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	exon	11260746	11262074	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	intron	11262075	11262260	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	CDS	11262261	11262702	0.7	-	1	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	exon	11262261	11262702	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	intron	11262703	11262876	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	CDS	11262877	11262971	0.88	-	0	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	exon	11262877	11262971	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	intron	11262972	11263071	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	CDS	11263072	11263142	0.82	-	2	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	exon	11263072	11263142	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	intron	11263143	11263237	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	CDS	11263238	11263429	0.93	-	2	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	exon	11263238	11263429	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	intron	11263430	11263564	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	CDS	11263565	11263697	0.38	-	0	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	exon	11263565	11263697	.	-	.	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
Phchi.S3	AUGUSTUS	start_codon	11263695	11263697	.	-	0	transcript_id "Phchi.S3G149100.t1"; gene_id "Phchi.S3G149100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10877.t1 is derived from g14927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2718954	2720977	.	-	.	Phchi.S4G045900
Phchi.S4	AUGUSTUS	transcript	2718954	2720977	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	stop_codon	2718951	2718953	.	-	0	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2718954	2719058	1	-	0	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2718954	2719058	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2719059	2719176	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2719177	2719418	0.95	-	2	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2719177	2719418	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2719419	2719639	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2719640	2719866	1	-	1	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2719640	2719866	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2719867	2720036	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720037	2720167	1	-	0	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720037	2720167	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720168	2720249	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720250	2720371	1	-	2	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720250	2720371	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720372	2720484	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720485	2720517	0.65	-	2	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720485	2720517	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720518	2720709	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720710	2720734	0.66	-	0	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720710	2720734	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720735	2720869	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720870	2720977	0.64	-	0	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720870	2720977	.	-	.	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	start_codon	2720975	2720977	.	-	0	transcript_id "Phchi.S4G045900.t1"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	transcript	2718954	2720977	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	stop_codon	2718951	2718953	.	-	0	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2718954	2719058	1	-	0	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2718954	2719058	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2719059	2719176	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2719177	2719418	0.97	-	2	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2719177	2719418	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2719419	2719639	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2719640	2719828	0.71	-	2	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2719640	2719828	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2719829	2720036	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720037	2720087	0.42	-	2	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720037	2720087	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720088	2720139	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720140	2720167	0.42	-	0	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720140	2720167	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720168	2720249	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720250	2720371	0.99	-	2	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720250	2720371	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720372	2720484	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720485	2720517	0.72	-	2	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720485	2720517	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720518	2720709	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720710	2720734	0.73	-	0	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720710	2720734	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	intron	2720735	2720869	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	CDS	2720870	2720977	0.54	-	0	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	exon	2720870	2720977	.	-	.	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
Phchi.S4	AUGUSTUS	start_codon	2720975	2720977	.	-	0	transcript_id "Phchi.S4G045900.t2"; gene_id "Phchi.S4G045900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg716.t1 is derived from g10498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5056616	5060102	.	+	.	Phchi.S6G067500
Phchi.S6	AUGUSTUS	transcript	5056616	5060102	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	start_codon	5056616	5056618	.	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5056616	5056670	0.28	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5056616	5056670	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5056671	5056819	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5056820	5056860	0.31	+	2	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5056820	5056860	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5056861	5056954	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5056955	5057161	1	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5056955	5057161	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5057162	5057242	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5057243	5057476	0.98	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5057243	5057476	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5057477	5057635	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5057636	5057810	0.44	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5057636	5057810	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5057811	5057884	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5057885	5058897	0.85	+	2	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5057885	5058897	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5058898	5059046	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5059047	5059163	0.69	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5059047	5059163	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5059164	5059261	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5059262	5059543	0.97	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5059262	5059543	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5059544	5059649	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5059650	5059871	0.9	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5059650	5059871	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	intron	5059872	5060075	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	CDS	5060076	5060102	0.27	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	exon	5060076	5060102	.	+	.	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
Phchi.S6	AUGUSTUS	stop_codon	5060103	5060105	.	+	0	transcript_id "Phchi.S6G067500.t1"; gene_id "Phchi.S6G067500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1777.t1 is derived from g8697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2968839	2969362	.	+	.	Phchi.S5G038600
Phchi.S5	AUGUSTUS	transcript	2968839	2969362	.	+	.	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	start_codon	2968839	2968841	.	+	0	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	CDS	2968839	2968936	0.95	+	0	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	exon	2968839	2968936	.	+	.	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	intron	2968937	2969007	.	+	.	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	CDS	2969008	2969362	1	+	1	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	exon	2969008	2969362	.	+	.	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
Phchi.S5	AUGUSTUS	stop_codon	2969363	2969365	.	+	0	transcript_id "Phchi.S5G038600.t1"; gene_id "Phchi.S5G038600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12428.t1 is derived from g8105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19583008	19584346	.	-	.	Phchi.S2G050800
Phchi.S2	AUGUSTUS	transcript	19583008	19584346	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	stop_codon	19583005	19583007	.	-	0	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583008	19583178	0.99	-	0	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583008	19583178	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583179	19583345	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583346	19583436	0.81	-	1	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583346	19583436	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583437	19583552	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583553	19583595	0.98	-	2	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583553	19583595	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583596	19583693	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583694	19583775	1	-	0	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583694	19583775	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583776	19583934	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583935	19584051	1	-	0	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583935	19584051	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19584052	19584121	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19584122	19584346	0.6	-	0	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19584122	19584346	.	-	.	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	start_codon	19584344	19584346	.	-	0	transcript_id "Phchi.S2G050800.t1"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	transcript	19583008	19584346	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	stop_codon	19583005	19583007	.	-	0	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583008	19583178	1	-	0	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583008	19583178	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583179	19583276	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583277	19583436	0.76	-	1	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583277	19583436	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583437	19583552	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583553	19583595	0.87	-	2	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583553	19583595	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583596	19583693	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583694	19583775	1	-	0	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583694	19583775	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19583776	19583934	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19583935	19584051	0.98	-	0	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19583935	19584051	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	intron	19584052	19584121	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	CDS	19584122	19584346	0.65	-	0	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	exon	19584122	19584346	.	-	.	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
Phchi.S2	AUGUSTUS	start_codon	19584344	19584346	.	-	0	transcript_id "Phchi.S2G050800.t2"; gene_id "Phchi.S2G050800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6014.t1 is derived from g3185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20434156	20434603	.	-	.	Phchi.S1G317300
Phchi.S1	AUGUSTUS	transcript	20434156	20434603	.	-	.	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	stop_codon	20434153	20434155	.	-	0	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	CDS	20434156	20434423	0.88	-	1	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	exon	20434156	20434423	.	-	.	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	intron	20434424	20434523	.	-	.	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	CDS	20434524	20434603	0.82	-	0	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	exon	20434524	20434603	.	-	.	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
Phchi.S1	AUGUSTUS	start_codon	20434601	20434603	.	-	0	transcript_id "Phchi.S1G317300.t1"; gene_id "Phchi.S1G317300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14764.t1 is derived from g13232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14586887	14590101	.	+	.	Phchi.S3G208300
Phchi.S3	AUGUSTUS	transcript	14586887	14590101	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	start_codon	14586887	14586889	.	+	0	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14586887	14586959	0.99	+	0	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14586887	14586959	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14586960	14587150	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14587151	14587264	1	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14587151	14587264	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14587265	14587350	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14587351	14587446	1	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14587351	14587446	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14587447	14587535	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14587536	14587775	0.9	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14587536	14587775	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14587776	14588033	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14588034	14588477	0.84	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14588034	14588477	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14588478	14588636	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14588637	14588747	1	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14588637	14588747	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14588748	14588874	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14588875	14588976	1	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14588875	14588976	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14588977	14589090	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14589091	14589148	1	+	2	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14589091	14589148	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14589149	14589276	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14589277	14589345	1	+	1	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14589277	14589345	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14589346	14589536	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14589537	14589624	1	+	1	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14589537	14589624	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14589625	14589743	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14589744	14589805	1	+	0	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14589744	14589805	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14589806	14589886	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14589887	14589938	0.87	+	1	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14589887	14589938	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	intron	14589939	14590044	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	CDS	14590045	14590101	0.87	+	0	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	exon	14590045	14590101	.	+	.	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
Phchi.S3	AUGUSTUS	stop_codon	14590102	14590104	.	+	0	transcript_id "Phchi.S3G208300.t1"; gene_id "Phchi.S3G208300"
# This transcript jg11439.t2 is derived from g15489.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11440.t1 is derived from g15490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6383917	6386020	.	-	.	Phchi.S4G102200
Phchi.S4	AUGUSTUS	transcript	6383917	6386020	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	stop_codon	6383914	6383916	.	-	0	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	CDS	6383917	6384222	0.96	-	0	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	exon	6383917	6384222	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	intron	6384223	6384312	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	CDS	6384313	6384456	1	-	0	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	exon	6384313	6384456	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	intron	6384457	6384553	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	CDS	6384554	6384676	1	-	0	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	exon	6384554	6384676	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	intron	6384677	6384776	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	CDS	6384777	6384889	1	-	2	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	exon	6384777	6384889	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	intron	6384890	6384988	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	CDS	6384989	6385819	0.64	-	2	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	exon	6384989	6385819	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	intron	6385820	6385908	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	CDS	6385909	6386020	0.52	-	0	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	exon	6385909	6386020	.	-	.	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
Phchi.S4	AUGUSTUS	start_codon	6386018	6386020	.	-	0	transcript_id "Phchi.S4G102200.t1"; gene_id "Phchi.S4G102200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2793.t1 is derived from g9713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8928660	8929372	.	-	.	Phchi.S5G140200
Phchi.S5	AUGUSTUS	transcript	8928660	8929372	.	-	.	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	stop_codon	8928657	8928659	.	-	0	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	CDS	8928660	8929121	0.92	-	0	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	exon	8928660	8929121	.	-	.	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	intron	8929122	8929210	.	-	.	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	CDS	8929211	8929372	0.78	-	0	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	exon	8929211	8929372	.	-	.	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
Phchi.S5	AUGUSTUS	start_codon	8929370	8929372	.	-	0	transcript_id "Phchi.S5G140200.t1"; gene_id "Phchi.S5G140200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3465.t1 is derived from g634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3890111	3891873	.	-	.	Phchi.S1G062400
Phchi.S1	AUGUSTUS	transcript	3890111	3891873	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	stop_codon	3890108	3890110	.	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	CDS	3890111	3890296	1	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	exon	3890111	3890296	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	intron	3890297	3890387	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	CDS	3890388	3890750	0.85	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	exon	3890388	3890750	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	intron	3890751	3890864	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	CDS	3890865	3891305	1	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	exon	3890865	3891305	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	intron	3891306	3891442	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	CDS	3891443	3891559	1	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	exon	3891443	3891559	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	intron	3891560	3891816	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	CDS	3891817	3891873	1	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	exon	3891817	3891873	.	-	.	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
Phchi.S1	AUGUSTUS	start_codon	3891871	3891873	.	-	0	transcript_id "Phchi.S1G062400.t1"; gene_id "Phchi.S1G062400"
# This transcript jg14518.t2 is derived from g12986.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14518.t3 is derived from g12986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14518.t4 is derived from g12986.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14519.t1 is derived from g12987.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13283991	13289836	.	-	.	Phchi.S3G183800
Phchi.S3	AUGUSTUS	transcript	13283991	13289836	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	stop_codon	13283988	13283990	.	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13283991	13284101	0.99	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13283991	13284101	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284102	13284268	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284269	13284370	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284269	13284370	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284371	13284466	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284467	13284562	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284467	13284562	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284563	13284654	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284655	13284798	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284655	13284798	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284799	13284883	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284884	13284928	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284884	13284928	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284929	13285017	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285018	13285119	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285018	13285119	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285120	13285194	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285195	13285358	1	-	2	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285195	13285358	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285359	13285448	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285449	13285488	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285449	13285488	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285489	13285709	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285710	13285793	0.8	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285710	13285793	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285794	13286116	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286117	13286209	0.51	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286117	13286209	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286210	13286328	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286329	13286399	0.94	-	2	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286329	13286399	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286400	13286500	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286501	13286565	0.94	-	1	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286501	13286565	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286566	13286702	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286703	13286798	1	-	1	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286703	13286798	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286799	13286916	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286917	13287017	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286917	13287017	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287018	13287090	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287091	13287131	1	-	2	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287091	13287131	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287132	13287221	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287222	13287335	1	-	2	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287222	13287335	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287336	13287488	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287489	13287577	0.99	-	1	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287489	13287577	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287578	13287651	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287652	13287761	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287652	13287761	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287762	13287846	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287847	13287912	0.98	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287847	13287912	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287913	13288017	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288018	13288071	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288018	13288071	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13288072	13288670	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288671	13288745	1	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288671	13288745	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13288746	13288962	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288963	13289015	0.68	-	2	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288963	13289015	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289016	13289149	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289150	13289209	0.68	-	2	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289150	13289209	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289210	13289306	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289307	13289337	0.8	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289307	13289337	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289338	13289413	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289414	13289836	0.62	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289414	13289836	.	-	.	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	start_codon	13289834	13289836	.	-	0	transcript_id "Phchi.S3G183800.t1"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	transcript	13283991	13289836	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	stop_codon	13283988	13283990	.	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13283991	13284101	0.98	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13283991	13284101	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284102	13284268	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284269	13284370	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284269	13284370	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284371	13284466	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284467	13284562	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284467	13284562	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284563	13284654	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284655	13284798	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284655	13284798	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284799	13284883	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284884	13284928	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284884	13284928	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284929	13285017	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285018	13285119	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285018	13285119	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285120	13285194	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285195	13285358	1	-	2	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285195	13285358	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285359	13285448	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285449	13285488	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285449	13285488	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285489	13285709	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285710	13285793	0.76	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285710	13285793	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285794	13286116	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286117	13286209	0.6	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286117	13286209	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286210	13286328	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286329	13286399	0.93	-	2	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286329	13286399	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286400	13286500	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286501	13286565	0.93	-	1	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286501	13286565	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286566	13286702	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286703	13286798	0.99	-	1	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286703	13286798	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286799	13286916	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286917	13287017	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286917	13287017	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287018	13287090	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287091	13287131	1	-	2	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287091	13287131	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287132	13287221	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287222	13287335	1	-	2	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287222	13287335	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287336	13287488	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287489	13287577	1	-	1	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287489	13287577	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287578	13287651	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287652	13287761	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287652	13287761	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287762	13287846	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287847	13287912	0.98	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287847	13287912	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287913	13288017	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288018	13288071	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288018	13288071	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13288072	13288670	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288671	13288745	1	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288671	13288745	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13288746	13288983	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288984	13289015	0.51	-	2	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288984	13289015	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289016	13289149	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289150	13289209	0.51	-	2	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289150	13289209	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289210	13289306	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289307	13289337	0.77	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289307	13289337	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289338	13289413	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289414	13289836	0.59	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289414	13289836	.	-	.	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	start_codon	13289834	13289836	.	-	0	transcript_id "Phchi.S3G183800.t2"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	transcript	13283991	13289836	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	stop_codon	13283988	13283990	.	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13283991	13284101	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13283991	13284101	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284102	13284268	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284269	13284370	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284269	13284370	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284371	13284466	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284467	13284562	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284467	13284562	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284563	13284654	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284655	13284798	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284655	13284798	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284799	13284883	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13284884	13284928	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13284884	13284928	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13284929	13285017	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285018	13285119	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285018	13285119	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285120	13285194	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285195	13285358	1	-	2	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285195	13285358	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285359	13285448	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285449	13285488	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285449	13285488	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285489	13285709	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13285710	13285793	0.73	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13285710	13285793	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13285794	13286116	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286117	13286209	0.46	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286117	13286209	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286210	13286328	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286329	13286399	0.96	-	2	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286329	13286399	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286400	13286500	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286501	13286565	0.96	-	1	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286501	13286565	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286566	13286702	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286703	13286798	0.99	-	1	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286703	13286798	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13286799	13286916	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13286917	13287017	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13286917	13287017	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287018	13287090	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287091	13287131	1	-	2	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287091	13287131	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287132	13287221	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287222	13287347	0.98	-	2	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287222	13287347	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287348	13287488	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287489	13287577	1	-	1	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287489	13287577	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287578	13287651	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287652	13287761	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287652	13287761	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287762	13287846	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13287847	13287912	0.97	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13287847	13287912	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13287913	13288017	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288018	13288071	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288018	13288071	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13288072	13288670	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288671	13288745	1	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288671	13288745	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13288746	13288983	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13288984	13289015	0.46	-	2	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13288984	13289015	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289016	13289149	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289150	13289209	0.46	-	2	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289150	13289209	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289210	13289306	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289307	13289337	0.72	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289307	13289337	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	intron	13289338	13289413	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	CDS	13289414	13289836	0.53	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	exon	13289414	13289836	.	-	.	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
Phchi.S3	AUGUSTUS	start_codon	13289834	13289836	.	-	0	transcript_id "Phchi.S3G183800.t3"; gene_id "Phchi.S3G183800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12421.t1 is derived from g8098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19448300	19448920	.	+	.	Phchi.S2G050100
Phchi.S2	AUGUSTUS	transcript	19448300	19448920	.	+	.	transcript_id "Phchi.S2G050100.t1"; gene_id "Phchi.S2G050100"
Phchi.S2	AUGUSTUS	start_codon	19448300	19448302	.	+	0	transcript_id "Phchi.S2G050100.t1"; gene_id "Phchi.S2G050100"
Phchi.S2	AUGUSTUS	CDS	19448300	19448920	0.92	+	0	transcript_id "Phchi.S2G050100.t1"; gene_id "Phchi.S2G050100"
Phchi.S2	AUGUSTUS	exon	19448300	19448920	.	+	.	transcript_id "Phchi.S2G050100.t1"; gene_id "Phchi.S2G050100"
Phchi.S2	AUGUSTUS	stop_codon	19448921	19448923	.	+	0	transcript_id "Phchi.S2G050100.t1"; gene_id "Phchi.S2G050100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3190.t1 is derived from g359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2152141	2154554	.	-	.	Phchi.S1G034900
Phchi.S1	AUGUSTUS	transcript	2152141	2154554	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	stop_codon	2152138	2152140	.	-	0	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2152141	2152340	1	-	2	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2152141	2152340	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2152341	2152563	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2152564	2152743	1	-	2	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2152564	2152743	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2152744	2152842	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2152843	2152991	1	-	1	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2152843	2152991	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2152992	2153073	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2153074	2153326	1	-	2	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2153074	2153326	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2153327	2153516	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2153517	2153704	1	-	1	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2153517	2153704	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2153705	2153803	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2153804	2153961	1	-	0	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2153804	2153961	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2153962	2154040	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2154041	2154082	1	-	0	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2154041	2154082	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2154083	2154204	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2154205	2154254	0.87	-	2	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2154205	2154254	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	intron	2154255	2154349	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	CDS	2154350	2154554	1	-	0	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	exon	2154350	2154554	.	-	.	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
Phchi.S1	AUGUSTUS	start_codon	2154552	2154554	.	-	0	transcript_id "Phchi.S1G034900.t1"; gene_id "Phchi.S1G034900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg448.t1 is derived from g10230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3131788	3135823	.	+	.	Phchi.S6G040700
Phchi.S6	AUGUSTUS	transcript	3131788	3135823	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	start_codon	3131788	3131790	.	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3131788	3131795	0.83	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3131788	3131795	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3131796	3131895	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3131896	3131947	0.99	+	1	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3131896	3131947	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3131948	3132024	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132025	3132056	1	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132025	3132056	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132057	3132361	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132362	3132439	1	+	1	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132362	3132439	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132440	3132538	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132539	3132635	1	+	1	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132539	3132635	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132636	3132766	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132767	3132812	0.9	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132767	3132812	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132813	3132972	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132973	3132983	0.91	+	2	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132973	3132983	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132984	3133081	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133082	3133194	1	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133082	3133194	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133195	3133286	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133287	3133314	1	+	1	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133287	3133314	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133315	3133454	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133455	3133547	1	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133455	3133547	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133548	3133631	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133632	3133719	1	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133632	3133719	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133720	3133792	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133793	3133854	0.99	+	2	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133793	3133854	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133855	3133960	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133961	3134031	0.97	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133961	3134031	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3134032	3134450	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3134451	3135081	0.97	+	1	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3134451	3135081	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135082	3135162	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135163	3135243	0.62	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135163	3135243	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135244	3135337	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135338	3135469	1	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135338	3135469	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135470	3135557	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135558	3135623	0.76	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135558	3135623	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135624	3135724	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135725	3135823	0.42	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135725	3135823	.	+	.	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	stop_codon	3135824	3135826	.	+	0	transcript_id "Phchi.S6G040700.t1"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	transcript	3131788	3135823	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	start_codon	3131788	3131790	.	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3131788	3131795	0.89	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3131788	3131795	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3131796	3131895	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3131896	3131947	0.99	+	1	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3131896	3131947	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3131948	3132024	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132025	3132056	1	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132025	3132056	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132057	3132361	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132362	3132439	1	+	1	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132362	3132439	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132440	3132538	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132539	3132635	1	+	1	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132539	3132635	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132636	3132766	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132767	3132812	1	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132767	3132812	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132813	3132895	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3132896	3132990	0.52	+	2	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3132896	3132990	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3132991	3133081	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133082	3133194	1	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133082	3133194	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133195	3133286	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133287	3133314	1	+	1	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133287	3133314	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133315	3133454	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133455	3133547	1	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133455	3133547	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133548	3133631	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133632	3133719	1	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133632	3133719	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133720	3133792	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133793	3133854	0.99	+	2	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133793	3133854	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3133855	3133960	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3133961	3134031	0.96	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3133961	3134031	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3134032	3134450	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3134451	3135081	0.95	+	1	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3134451	3135081	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135082	3135162	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135163	3135243	0.54	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135163	3135243	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135244	3135337	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135338	3135469	1	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135338	3135469	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135470	3135557	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135558	3135623	0.78	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135558	3135623	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	intron	3135624	3135724	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	CDS	3135725	3135823	0.52	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	exon	3135725	3135823	.	+	.	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
Phchi.S6	AUGUSTUS	stop_codon	3135824	3135826	.	+	0	transcript_id "Phchi.S6G040700.t2"; gene_id "Phchi.S6G040700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2715.t1 is derived from g9635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8308402	8311551	.	-	.	Phchi.S5G132400
Phchi.S5	AUGUSTUS	transcript	8308402	8311551	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	stop_codon	8308399	8308401	.	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8308402	8308587	0.98	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8308402	8308587	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8308588	8308714	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8308715	8308907	0.99	-	1	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8308715	8308907	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8308908	8309056	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8309057	8309179	1	-	1	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8309057	8309179	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8309180	8309319	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8309320	8309459	1	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8309320	8309459	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8309460	8309636	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8309637	8309705	1	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8309637	8309705	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8309706	8309825	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8309826	8309982	1	-	1	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8309826	8309982	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8309983	8310132	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8310133	8310207	0.98	-	1	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8310133	8310207	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8310208	8310317	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8310318	8310453	1	-	2	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8310318	8310453	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8310454	8310642	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8310643	8310721	1	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8310643	8310721	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	intron	8310722	8310858	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	CDS	8310859	8311551	0.7	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	exon	8310859	8311551	.	-	.	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
Phchi.S5	AUGUSTUS	start_codon	8311549	8311551	.	-	0	transcript_id "Phchi.S5G132400.t1"; gene_id "Phchi.S5G132400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9178.t1 is derived from g6353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40234390	40234908	.	+	.	Phchi.S1G633700
Phchi.S1	AUGUSTUS	transcript	40234390	40234908	.	+	.	transcript_id "Phchi.S1G633700.t1"; gene_id "Phchi.S1G633700"
Phchi.S1	AUGUSTUS	start_codon	40234390	40234392	.	+	0	transcript_id "Phchi.S1G633700.t1"; gene_id "Phchi.S1G633700"
Phchi.S1	AUGUSTUS	CDS	40234390	40234908	0.89	+	0	transcript_id "Phchi.S1G633700.t1"; gene_id "Phchi.S1G633700"
Phchi.S1	AUGUSTUS	exon	40234390	40234908	.	+	.	transcript_id "Phchi.S1G633700.t1"; gene_id "Phchi.S1G633700"
Phchi.S1	AUGUSTUS	stop_codon	40234909	40234911	.	+	0	transcript_id "Phchi.S1G633700.t1"; gene_id "Phchi.S1G633700"
# This transcript jg3888.t2 is derived from g1057.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3889.t1 is derived from g1058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6216791	6222057	.	+	.	Phchi.S1G104800
Phchi.S1	AUGUSTUS	transcript	6216791	6222057	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	start_codon	6216791	6216793	.	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6216791	6217159	0.78	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6216791	6217159	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6217160	6217291	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6217292	6217384	0.81	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6217292	6217384	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6217385	6217510	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6217511	6218227	0.62	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6217511	6218227	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6218228	6218324	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6218325	6218435	1	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6218325	6218435	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6218436	6218594	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6218595	6219171	0.59	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6218595	6219171	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6219172	6219292	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6219293	6219648	0.92	+	2	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6219293	6219648	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6219649	6219787	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6219788	6220048	1	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6219788	6220048	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6220049	6220147	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6220148	6220333	0.9	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6220148	6220333	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6220334	6220447	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6220448	6221602	0.71	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6220448	6221602	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6221603	6221688	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6221689	6221897	0.99	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6221689	6221897	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	intron	6221898	6221969	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	CDS	6221970	6222057	0.99	+	1	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	exon	6221970	6222057	.	+	.	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
Phchi.S1	AUGUSTUS	stop_codon	6222058	6222060	.	+	0	transcript_id "Phchi.S1G104800.t1"; gene_id "Phchi.S1G104800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13933.t1 is derived from g12400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9793054	9798174	.	+	.	Phchi.S3G125200
Phchi.S3	AUGUSTUS	transcript	9793054	9798174	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	start_codon	9793054	9793056	.	+	0	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9793054	9793160	0.99	+	0	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9793054	9793160	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9793161	9793303	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9793304	9793389	0.95	+	1	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9793304	9793389	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9793390	9793511	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9793512	9793627	0.91	+	2	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9793512	9793627	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9793628	9793859	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9793860	9793945	1	+	0	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9793860	9793945	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9793946	9794102	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9794103	9795523	1	+	1	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9794103	9795523	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9795524	9795676	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9795677	9795850	0.87	+	2	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9795677	9795850	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9795851	9795937	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9795938	9796148	0.6	+	2	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9795938	9796148	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9796149	9796237	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9796238	9797011	0.64	+	1	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9796238	9797011	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9797012	9797098	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9797099	9797338	1	+	1	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9797099	9797338	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9797339	9797626	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9797627	9797754	1	+	1	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9797627	9797754	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	intron	9797755	9797878	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	CDS	9797879	9798174	0.81	+	2	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	exon	9797879	9798174	.	+	.	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
Phchi.S3	AUGUSTUS	stop_codon	9798175	9798177	.	+	0	transcript_id "Phchi.S3G125200.t1"; gene_id "Phchi.S3G125200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4185.t1 is derived from g1354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8803717	8805152	.	+	.	Phchi.S1G134400
Phchi.S1	AUGUSTUS	transcript	8803717	8805152	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	start_codon	8803717	8803719	.	+	0	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	CDS	8803717	8803988	0.67	+	0	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	exon	8803717	8803988	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	intron	8803989	8804071	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	CDS	8804072	8804399	1	+	1	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	exon	8804072	8804399	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	intron	8804400	8804486	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	CDS	8804487	8804636	1	+	0	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	exon	8804487	8804636	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	intron	8804637	8804734	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	CDS	8804735	8804995	1	+	0	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	exon	8804735	8804995	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	intron	8804996	8805086	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	CDS	8805087	8805152	1	+	0	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	exon	8805087	8805152	.	+	.	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
Phchi.S1	AUGUSTUS	stop_codon	8805153	8805155	.	+	0	transcript_id "Phchi.S1G134400.t1"; gene_id "Phchi.S1G134400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2848.t1 is derived from g17.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14654	16195	.	+	.	Phchi.S1G000700
Phchi.S1	AUGUSTUS	transcript	14654	16195	.	+	.	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	start_codon	14654	14656	.	+	0	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	CDS	14654	15142	0.97	+	0	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	exon	14654	15142	.	+	.	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	intron	15143	15513	.	+	.	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	CDS	15514	15999	0.59	+	0	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	exon	15514	15999	.	+	.	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	intron	16000	16075	.	+	.	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	CDS	16076	16195	1	+	0	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	exon	16076	16195	.	+	.	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
Phchi.S1	AUGUSTUS	stop_codon	16196	16198	.	+	0	transcript_id "Phchi.S1G000700.t1"; gene_id "Phchi.S1G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5193.t1 is derived from g2363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15408043	15412792	.	+	.	Phchi.S1G235200
Phchi.S1	AUGUSTUS	transcript	15408043	15412792	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	start_codon	15408043	15408045	.	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15408043	15408151	0.97	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15408043	15408151	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15408152	15408379	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15408380	15409572	1	+	2	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15408380	15409572	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15409573	15409693	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15409694	15409832	0.9	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15409694	15409832	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15409833	15409937	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15409938	15410128	0.89	+	2	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15409938	15410128	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15410129	15410253	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15410254	15410361	0.98	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15410254	15410361	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15410362	15410465	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15410466	15410669	0.82	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15410466	15410669	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15410670	15410770	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15410771	15411002	1	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15410771	15411002	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15411003	15411108	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15411109	15411258	1	+	2	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15411109	15411258	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15411259	15411402	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15411403	15411559	1	+	2	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15411403	15411559	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15411560	15411700	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15411701	15411828	1	+	1	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15411701	15411828	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15411829	15411954	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15411955	15412274	0.96	+	2	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15411955	15412274	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15412275	15412352	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15412353	15412550	1	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15412353	15412550	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	intron	15412551	15412642	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	CDS	15412643	15412792	0.99	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	exon	15412643	15412792	.	+	.	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
Phchi.S1	AUGUSTUS	stop_codon	15412793	15412795	.	+	0	transcript_id "Phchi.S1G235200.t1"; gene_id "Phchi.S1G235200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg93.t1 is derived from g9875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	476302	478359	.	+	.	Phchi.S6G005200
Phchi.S6	AUGUSTUS	transcript	476302	478359	.	+	.	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	start_codon	476302	476304	.	+	0	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	CDS	476302	477209	0.65	+	0	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	exon	476302	477209	.	+	.	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	intron	477210	477368	.	+	.	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	CDS	477369	478359	0.76	+	1	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	exon	477369	478359	.	+	.	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	stop_codon	478360	478362	.	+	0	transcript_id "Phchi.S6G005200.t1"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	transcript	476302	477628	.	+	.	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	start_codon	476302	476304	.	+	0	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	CDS	476302	477209	0.52	+	0	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	exon	476302	477209	.	+	.	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	intron	477210	477368	.	+	.	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	CDS	477369	477490	0.3	+	1	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	exon	477369	477490	.	+	.	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	intron	477491	477587	.	+	.	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	CDS	477588	477628	0.3	+	2	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	exon	477588	477628	.	+	.	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
Phchi.S6	AUGUSTUS	stop_codon	477629	477631	.	+	0	transcript_id "Phchi.S6G005200.t2"; gene_id "Phchi.S6G005200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12335.t1 is derived from g8011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11007641	11008503	.	-	.	Phchi.S2G041500
Phchi.S2	AUGUSTUS	transcript	11007641	11008503	.	-	.	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	stop_codon	11007638	11007640	.	-	0	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	CDS	11007641	11007757	1	-	0	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	exon	11007641	11007757	.	-	.	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	intron	11007758	11007941	.	-	.	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	CDS	11007942	11007982	1	-	2	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	exon	11007942	11007982	.	-	.	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	intron	11007983	11008427	.	-	.	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	CDS	11008428	11008503	1	-	0	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	exon	11008428	11008503	.	-	.	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
Phchi.S2	AUGUSTUS	start_codon	11008501	11008503	.	-	0	transcript_id "Phchi.S2G041500.t1"; gene_id "Phchi.S2G041500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3238.t1 is derived from g407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2397261	2398623	.	+	.	Phchi.S1G039700
Phchi.S1	AUGUSTUS	transcript	2397261	2398623	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	start_codon	2397261	2397263	.	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2397261	2397383	0.52	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2397261	2397383	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2397384	2397479	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2397480	2397572	0.88	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2397480	2397572	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2397573	2397695	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2397696	2397770	0.77	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2397696	2397770	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2397771	2397874	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2397875	2397991	0.8	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2397875	2397991	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2397992	2398119	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2398120	2398191	1	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2398120	2398191	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2398192	2398280	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2398281	2398331	1	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2398281	2398331	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2398332	2398408	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2398409	2398456	1	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2398409	2398456	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	intron	2398457	2398545	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	CDS	2398546	2398623	1	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	exon	2398546	2398623	.	+	.	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
Phchi.S1	AUGUSTUS	stop_codon	2398624	2398626	.	+	0	transcript_id "Phchi.S1G039700.t1"; gene_id "Phchi.S1G039700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4241.t1 is derived from g1410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9119046	9119730	.	+	.	Phchi.S1G140000
Phchi.S1	AUGUSTUS	transcript	9119046	9119730	.	+	.	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	start_codon	9119046	9119048	.	+	0	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	CDS	9119046	9119102	0.52	+	0	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	exon	9119046	9119102	.	+	.	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	intron	9119103	9119278	.	+	.	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	CDS	9119279	9119310	0.69	+	0	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	exon	9119279	9119310	.	+	.	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	intron	9119311	9119525	.	+	.	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	CDS	9119526	9119730	0.63	+	1	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	exon	9119526	9119730	.	+	.	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
Phchi.S1	AUGUSTUS	stop_codon	9119731	9119733	.	+	0	transcript_id "Phchi.S1G140000.t1"; gene_id "Phchi.S1G140000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12728.t1 is derived from g11193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1418938	1420261	.	-	.	Phchi.S3G004700
Phchi.S3	AUGUSTUS	transcript	1418938	1420261	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	stop_codon	1418935	1418937	.	-	0	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	CDS	1418938	1419028	0.97	-	1	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	exon	1418938	1419028	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	intron	1419029	1419130	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	CDS	1419131	1419210	0.96	-	0	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	exon	1419131	1419210	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	intron	1419211	1419393	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	CDS	1419394	1419614	0.57	-	2	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	exon	1419394	1419614	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	intron	1419615	1419732	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	CDS	1419733	1420261	0.95	-	0	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	exon	1419733	1420261	.	-	.	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
Phchi.S3	AUGUSTUS	start_codon	1420259	1420261	.	-	0	transcript_id "Phchi.S3G004700.t1"; gene_id "Phchi.S3G004700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4668.t1 is derived from g1838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11722718	11723958	.	-	.	Phchi.S1G182700
Phchi.S1	AUGUSTUS	transcript	11722718	11723958	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	stop_codon	11722715	11722717	.	-	0	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	CDS	11722718	11723106	0.99	-	2	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	exon	11722718	11723106	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	intron	11723107	11723272	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	CDS	11723273	11723390	0.69	-	0	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	exon	11723273	11723390	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	intron	11723391	11723465	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	CDS	11723466	11723663	0.98	-	0	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	exon	11723466	11723663	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	intron	11723664	11723748	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	CDS	11723749	11723958	0.77	-	0	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	exon	11723749	11723958	.	-	.	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
Phchi.S1	AUGUSTUS	start_codon	11723956	11723958	.	-	0	transcript_id "Phchi.S1G182700.t1"; gene_id "Phchi.S1G182700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4848.t1 is derived from g2018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13085177	13085957	.	+	.	Phchi.S1G200700
Phchi.S1	AUGUSTUS	transcript	13085177	13085957	.	+	.	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	start_codon	13085177	13085179	.	+	0	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	CDS	13085177	13085298	0.98	+	0	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	exon	13085177	13085298	.	+	.	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	intron	13085299	13085384	.	+	.	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	CDS	13085385	13085556	0.67	+	1	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	exon	13085385	13085556	.	+	.	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	intron	13085557	13085636	.	+	.	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	CDS	13085637	13085957	0.95	+	0	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	exon	13085637	13085957	.	+	.	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
Phchi.S1	AUGUSTUS	stop_codon	13085958	13085960	.	+	0	transcript_id "Phchi.S1G200700.t1"; gene_id "Phchi.S1G200700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6354.t1 is derived from g3526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22473933	22475960	.	-	.	Phchi.S1G351300
Phchi.S1	AUGUSTUS	transcript	22473933	22475960	.	-	.	transcript_id "Phchi.S1G351300.t1"; gene_id "Phchi.S1G351300"
Phchi.S1	AUGUSTUS	stop_codon	22473930	22473932	.	-	0	transcript_id "Phchi.S1G351300.t1"; gene_id "Phchi.S1G351300"
Phchi.S1	AUGUSTUS	CDS	22473933	22475960	0.99	-	0	transcript_id "Phchi.S1G351300.t1"; gene_id "Phchi.S1G351300"
Phchi.S1	AUGUSTUS	exon	22473933	22475960	.	-	.	transcript_id "Phchi.S1G351300.t1"; gene_id "Phchi.S1G351300"
Phchi.S1	AUGUSTUS	start_codon	22475958	22475960	.	-	0	transcript_id "Phchi.S1G351300.t1"; gene_id "Phchi.S1G351300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8760.t1 is derived from g5935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37849137	37851461	.	-	.	Phchi.S1G591900
Phchi.S1	AUGUSTUS	transcript	37849137	37851461	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	stop_codon	37849134	37849136	.	-	0	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	CDS	37849137	37849710	1	-	1	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	exon	37849137	37849710	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	intron	37849711	37849880	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	CDS	37849881	37850065	1	-	0	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	exon	37849881	37850065	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	intron	37850066	37850157	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	CDS	37850158	37850331	1	-	0	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	exon	37850158	37850331	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	intron	37850332	37850465	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	CDS	37850466	37850557	0.87	-	2	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	exon	37850466	37850557	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	intron	37850558	37851097	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	CDS	37851098	37851461	0.52	-	0	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	exon	37851098	37851461	.	-	.	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
Phchi.S1	AUGUSTUS	start_codon	37851459	37851461	.	-	0	transcript_id "Phchi.S1G591900.t1"; gene_id "Phchi.S1G591900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11172.t1 is derived from g15222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4480592	4481218	.	+	.	Phchi.S4G075400
Phchi.S4	AUGUSTUS	transcript	4480592	4481218	.	+	.	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	start_codon	4480592	4480594	.	+	0	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	CDS	4480592	4481047	0.93	+	0	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	exon	4480592	4481047	.	+	.	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	intron	4481048	4481179	.	+	.	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	CDS	4481180	4481218	1	+	0	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	exon	4481180	4481218	.	+	.	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
Phchi.S4	AUGUSTUS	stop_codon	4481219	4481221	.	+	0	transcript_id "Phchi.S4G075400.t1"; gene_id "Phchi.S4G075400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7741.t1 is derived from g4915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30919056	30919711	.	+	.	Phchi.S1G490000
Phchi.S1	AUGUSTUS	transcript	30919056	30919711	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	start_codon	30919056	30919058	.	+	0	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	CDS	30919056	30919146	0.74	+	0	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	exon	30919056	30919146	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	intron	30919147	30919227	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	CDS	30919228	30919244	0.87	+	2	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	exon	30919228	30919244	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	intron	30919245	30919316	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	CDS	30919317	30919321	0.8	+	0	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	exon	30919317	30919321	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	intron	30919322	30919514	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	CDS	30919515	30919619	0.87	+	1	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	exon	30919515	30919619	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	intron	30919620	30919707	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	CDS	30919708	30919711	0.87	+	1	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	exon	30919708	30919711	.	+	.	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
Phchi.S1	AUGUSTUS	stop_codon	30919712	30919714	.	+	0	transcript_id "Phchi.S1G490000.t1"; gene_id "Phchi.S1G490000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5780.t1 is derived from g2950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18912388	18917500	.	+	.	Phchi.S1G293900
Phchi.S1	AUGUSTUS	transcript	18912388	18917500	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	start_codon	18912388	18912390	.	+	0	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18912388	18912519	0.98	+	0	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18912388	18912519	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18912520	18912645	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18912646	18913091	1	+	0	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18912646	18913091	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18913092	18914345	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18914346	18914449	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18914346	18914449	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18914450	18914741	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18914742	18914811	1	+	2	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18914742	18914811	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18914812	18914904	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18914905	18914979	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18914905	18914979	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18914980	18915074	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18915075	18915149	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18915075	18915149	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18915150	18915229	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18915230	18915277	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18915230	18915277	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18915278	18915412	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18915413	18915481	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18915413	18915481	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18915482	18915577	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18915578	18916372	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18915578	18916372	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18916373	18916466	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18916467	18916518	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18916467	18916518	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18916519	18916597	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18916598	18917016	1	+	0	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18916598	18917016	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18917017	18917109	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18917110	18917361	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18917110	18917361	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	intron	18917362	18917442	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	CDS	18917443	18917500	1	+	1	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	exon	18917443	18917500	.	+	.	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
Phchi.S1	AUGUSTUS	stop_codon	18917501	18917503	.	+	0	transcript_id "Phchi.S1G293900.t1"; gene_id "Phchi.S1G293900"
# This transcript jg4440.t2 is derived from g1609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4441.t1 is derived from g1610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10534383	10536474	.	+	.	Phchi.S1G160000
Phchi.S1	AUGUSTUS	transcript	10534383	10536474	.	+	.	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	start_codon	10534383	10534385	.	+	0	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	CDS	10534383	10534805	0.99	+	0	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	exon	10534383	10534805	.	+	.	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	intron	10534806	10534914	.	+	.	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	CDS	10534915	10536474	0.98	+	0	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	exon	10534915	10536474	.	+	.	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
Phchi.S1	AUGUSTUS	stop_codon	10536475	10536477	.	+	0	transcript_id "Phchi.S1G160000.t1"; gene_id "Phchi.S1G160000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4782.t1 is derived from g1952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12796758	12797988	.	-	.	Phchi.S1G194100
Phchi.S1	AUGUSTUS	transcript	12796758	12797988	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	stop_codon	12796755	12796757	.	-	0	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12796758	12796866	1	-	1	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12796758	12796866	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	intron	12796867	12796947	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12796948	12797072	1	-	0	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12796948	12797072	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	intron	12797073	12797145	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12797146	12797261	1	-	2	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12797146	12797261	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	intron	12797262	12797360	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12797361	12797475	1	-	0	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12797361	12797475	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	intron	12797476	12797553	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12797554	12797613	1	-	0	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12797554	12797613	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	intron	12797614	12797682	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12797683	12797752	1	-	1	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12797683	12797752	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	intron	12797753	12797911	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	CDS	12797912	12797988	1	-	0	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	exon	12797912	12797988	.	-	.	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
Phchi.S1	AUGUSTUS	start_codon	12797986	12797988	.	-	0	transcript_id "Phchi.S1G194100.t1"; gene_id "Phchi.S1G194100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1604.t1 is derived from g8523.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1982253	1989147	.	+	.	Phchi.S5G021300
Phchi.S5	AUGUSTUS	transcript	1982253	1989147	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	start_codon	1982253	1982255	.	+	0	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1982253	1983429	0.91	+	0	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1982253	1983429	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1983430	1983542	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1983543	1984676	0.79	+	2	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1983543	1984676	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1984677	1984746	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1984747	1985803	0.33	+	2	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1984747	1985803	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1985804	1985916	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1985917	1986155	0.55	+	1	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1985917	1986155	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1986156	1986239	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1986240	1986441	0.57	+	2	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1986240	1986441	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1986442	1986548	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1986549	1987569	0.47	+	1	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1986549	1987569	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1987570	1987656	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1987657	1989147	0.99	+	0	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1987657	1989147	.	+	.	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	stop_codon	1989148	1989150	.	+	0	transcript_id "Phchi.S5G021300.t1"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	transcript	1982253	1989147	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	start_codon	1982253	1982255	.	+	0	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1982253	1983429	0.91	+	0	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1982253	1983429	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1983430	1983542	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1983543	1984676	0.82	+	2	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1983543	1984676	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1984677	1984758	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1984759	1985803	0.39	+	2	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1984759	1985803	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1985804	1985916	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1985917	1986155	0.4	+	1	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1985917	1986155	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1986156	1986239	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1986240	1986441	0.58	+	2	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1986240	1986441	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1986442	1986548	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1986549	1987569	0.5	+	1	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1986549	1987569	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	intron	1987570	1987656	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	CDS	1987657	1989147	0.93	+	0	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	exon	1987657	1989147	.	+	.	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
Phchi.S5	AUGUSTUS	stop_codon	1989148	1989150	.	+	0	transcript_id "Phchi.S5G021300.t2"; gene_id "Phchi.S5G021300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14667.t1 is derived from g13135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14055083	14058016	.	-	.	Phchi.S3G198600
Phchi.S3	AUGUSTUS	transcript	14055083	14058016	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	stop_codon	14055080	14055082	.	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14055083	14055190	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14055083	14055190	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14055191	14055321	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14055322	14055376	1	-	1	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14055322	14055376	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14055377	14055483	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14055484	14055536	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14055484	14055536	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14055537	14055710	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14055711	14055830	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14055711	14055830	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14055831	14055951	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14055952	14055987	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14055952	14055987	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14055988	14056107	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14056108	14056236	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14056108	14056236	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14056237	14056356	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14056357	14056422	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14056357	14056422	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14056423	14056518	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14056519	14056581	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14056519	14056581	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14056582	14056706	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14056707	14056736	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14056707	14056736	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14056737	14056879	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14056880	14056930	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14056880	14056930	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14056931	14057093	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14057094	14057177	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14057094	14057177	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14057178	14057327	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14057328	14057441	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14057328	14057441	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14057442	14057591	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14057592	14057661	1	-	1	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14057592	14057661	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	intron	14057662	14057765	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	CDS	14057766	14058016	1	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	exon	14057766	14058016	.	-	.	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
Phchi.S3	AUGUSTUS	start_codon	14058014	14058016	.	-	0	transcript_id "Phchi.S3G198600.t1"; gene_id "Phchi.S3G198600"
# This transcript jg4016.t2 is derived from g1185.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4017.t1 is derived from g1186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7190128	7192244	.	+	.	Phchi.S1G117600
Phchi.S1	AUGUSTUS	transcript	7190128	7192244	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	start_codon	7190128	7190130	.	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7190128	7190413	0.7	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7190128	7190413	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7190414	7190502	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7190503	7190573	1	+	2	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7190503	7190573	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7190574	7190680	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7190681	7190735	0.99	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7190681	7190735	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7190736	7190948	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7190949	7191021	1	+	2	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7190949	7191021	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7191022	7191124	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7191125	7191206	1	+	1	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7191125	7191206	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7191207	7191407	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7191408	7191490	0.94	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7191408	7191490	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7191491	7191598	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7191599	7191737	0.99	+	1	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7191599	7191737	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7191738	7191875	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7191876	7191954	1	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7191876	7191954	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7191955	7192035	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7192036	7192100	1	+	2	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7192036	7192100	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	intron	7192101	7192187	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	CDS	7192188	7192244	1	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	exon	7192188	7192244	.	+	.	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
Phchi.S1	AUGUSTUS	stop_codon	7192245	7192247	.	+	0	transcript_id "Phchi.S1G117600.t1"; gene_id "Phchi.S1G117600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9989.t1 is derived from g7165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44834614	44835402	.	+	.	Phchi.S1G714800
Phchi.S1	AUGUSTUS	transcript	44834614	44835402	.	+	.	transcript_id "Phchi.S1G714800.t1"; gene_id "Phchi.S1G714800"
Phchi.S1	AUGUSTUS	start_codon	44834614	44834616	.	+	0	transcript_id "Phchi.S1G714800.t1"; gene_id "Phchi.S1G714800"
Phchi.S1	AUGUSTUS	CDS	44834614	44835402	0.29	+	0	transcript_id "Phchi.S1G714800.t1"; gene_id "Phchi.S1G714800"
Phchi.S1	AUGUSTUS	exon	44834614	44835402	.	+	.	transcript_id "Phchi.S1G714800.t1"; gene_id "Phchi.S1G714800"
Phchi.S1	AUGUSTUS	stop_codon	44835403	44835405	.	+	0	transcript_id "Phchi.S1G714800.t1"; gene_id "Phchi.S1G714800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14463.t1 is derived from g12931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12999608	13000691	.	+	.	Phchi.S3G178200
Phchi.S3	AUGUSTUS	transcript	12999608	13000691	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	start_codon	12999608	12999610	.	+	0	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	CDS	12999608	12999715	0.72	+	0	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	exon	12999608	12999715	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	intron	12999716	12999839	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	CDS	12999840	13000001	1	+	0	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	exon	12999840	13000001	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	intron	13000002	13000087	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	CDS	13000088	13000288	1	+	0	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	exon	13000088	13000288	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	intron	13000289	13000385	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	CDS	13000386	13000691	1	+	0	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	exon	13000386	13000691	.	+	.	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
Phchi.S3	AUGUSTUS	stop_codon	13000692	13000694	.	+	0	transcript_id "Phchi.S3G178200.t1"; gene_id "Phchi.S3G178200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2743.t1 is derived from g9663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8527169	8527664	.	+	.	Phchi.S5G135200
Phchi.S5	AUGUSTUS	transcript	8527169	8527664	.	+	.	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	start_codon	8527169	8527171	.	+	0	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	CDS	8527169	8527359	1	+	0	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	exon	8527169	8527359	.	+	.	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	intron	8527360	8527501	.	+	.	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	CDS	8527502	8527664	0.96	+	1	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	exon	8527502	8527664	.	+	.	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
Phchi.S5	AUGUSTUS	stop_codon	8527665	8527667	.	+	0	transcript_id "Phchi.S5G135200.t1"; gene_id "Phchi.S5G135200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14641.t1 is derived from g13109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13893680	13894942	.	-	.	Phchi.S3G196000
Phchi.S3	AUGUSTUS	transcript	13893680	13894942	.	-	.	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	stop_codon	13893677	13893679	.	-	0	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	CDS	13893680	13894287	0.85	-	2	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	exon	13893680	13894287	.	-	.	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	intron	13894288	13894368	.	-	.	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	CDS	13894369	13894942	0.97	-	0	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	exon	13894369	13894942	.	-	.	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
Phchi.S3	AUGUSTUS	start_codon	13894940	13894942	.	-	0	transcript_id "Phchi.S3G196000.t1"; gene_id "Phchi.S3G196000"
# This transcript jg13892.t2 is derived from g12359.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13893.t1 is derived from g12360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9492266	9494071	.	-	.	Phchi.S3G121200
Phchi.S3	AUGUSTUS	transcript	9492266	9494071	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	stop_codon	9492263	9492265	.	-	0	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	CDS	9492266	9492310	1	-	0	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	exon	9492266	9492310	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	intron	9492311	9492463	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	CDS	9492464	9492625	0.99	-	0	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	exon	9492464	9492625	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	intron	9492626	9493010	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	CDS	9493011	9493030	0.92	-	2	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	exon	9493011	9493030	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	intron	9493031	9493092	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	CDS	9493093	9493142	0.79	-	1	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	exon	9493093	9493142	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	intron	9493143	9493331	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	CDS	9493332	9493384	0.93	-	0	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	exon	9493332	9493384	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	intron	9493385	9493603	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	CDS	9493604	9494071	0.82	-	0	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	exon	9493604	9494071	.	-	.	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
Phchi.S3	AUGUSTUS	start_codon	9494069	9494071	.	-	0	transcript_id "Phchi.S3G121200.t1"; gene_id "Phchi.S3G121200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12769.t1 is derived from g11234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1956811	1958988	.	-	.	Phchi.S3G008800
Phchi.S3	AUGUSTUS	transcript	1956811	1958988	.	-	.	transcript_id "Phchi.S3G008800.t1"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	stop_codon	1956808	1956810	.	-	0	transcript_id "Phchi.S3G008800.t1"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	CDS	1956811	1958988	0.97	-	0	transcript_id "Phchi.S3G008800.t1"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	exon	1956811	1958988	.	-	.	transcript_id "Phchi.S3G008800.t1"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	start_codon	1958986	1958988	.	-	0	transcript_id "Phchi.S3G008800.t1"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	transcript	1956811	1957236	.	-	.	transcript_id "Phchi.S3G008800.t2"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	stop_codon	1956808	1956810	.	-	0	transcript_id "Phchi.S3G008800.t2"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	CDS	1956811	1957236	0.6	-	0	transcript_id "Phchi.S3G008800.t2"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	exon	1956811	1957236	.	-	.	transcript_id "Phchi.S3G008800.t2"; gene_id "Phchi.S3G008800"
Phchi.S3	AUGUSTUS	start_codon	1957234	1957236	.	-	0	transcript_id "Phchi.S3G008800.t2"; gene_id "Phchi.S3G008800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4418.t1 is derived from g1587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10391894	10393616	.	-	.	Phchi.S1G157700
Phchi.S1	AUGUSTUS	transcript	10391894	10393616	.	-	.	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	stop_codon	10391891	10391893	.	-	0	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	CDS	10391894	10392799	1	-	0	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	exon	10391894	10392799	.	-	.	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	intron	10392800	10392908	.	-	.	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	CDS	10392909	10393342	1	-	2	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	exon	10392909	10393342	.	-	.	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	intron	10393343	10393474	.	-	.	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	CDS	10393475	10393616	0.93	-	0	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	exon	10393475	10393616	.	-	.	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
Phchi.S1	AUGUSTUS	start_codon	10393614	10393616	.	-	0	transcript_id "Phchi.S1G157700.t1"; gene_id "Phchi.S1G157700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8001.t1 is derived from g5176.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32371835	32373964	.	+	.	Phchi.S1G516000
Phchi.S1	AUGUSTUS	transcript	32371835	32373964	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	start_codon	32371835	32371837	.	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32371835	32371973	1	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32371835	32371973	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32371974	32372054	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372055	32372114	1	+	2	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372055	32372114	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372115	32372189	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372190	32372338	1	+	2	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372190	32372338	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372339	32372425	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372426	32372519	1	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372426	32372519	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372520	32372703	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372704	32372774	1	+	2	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372704	32372774	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372775	32372861	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372862	32372968	1	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372862	32372968	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372969	32373057	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373058	32373086	0.9	+	1	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373058	32373086	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373087	32373166	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373167	32373178	1	+	2	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373167	32373178	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373179	32373344	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373345	32373433	1	+	2	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373345	32373433	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373434	32373531	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373532	32373591	1	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373532	32373591	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373592	32373681	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373682	32373765	1	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373682	32373765	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373766	32373844	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373845	32373964	1	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373845	32373964	.	+	.	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	stop_codon	32373965	32373967	.	+	0	transcript_id "Phchi.S1G516000.t1"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	transcript	32371835	32373964	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	start_codon	32371835	32371837	.	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32371835	32371973	1	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32371835	32371973	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32371974	32372054	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372055	32372114	1	+	2	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372055	32372114	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372115	32372180	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372181	32372338	1	+	2	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372181	32372338	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372339	32372425	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372426	32372519	1	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372426	32372519	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372520	32372703	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372704	32372774	1	+	2	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372704	32372774	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372775	32372861	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32372862	32372968	1	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32372862	32372968	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32372969	32373057	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373058	32373086	0.86	+	1	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373058	32373086	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373087	32373166	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373167	32373178	1	+	2	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373167	32373178	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373179	32373344	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373345	32373433	1	+	2	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373345	32373433	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373434	32373531	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373532	32373591	1	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373532	32373591	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373592	32373681	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373682	32373765	1	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373682	32373765	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	intron	32373766	32373844	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	CDS	32373845	32373964	1	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	exon	32373845	32373964	.	+	.	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
Phchi.S1	AUGUSTUS	stop_codon	32373965	32373967	.	+	0	transcript_id "Phchi.S1G516000.t2"; gene_id "Phchi.S1G516000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5172.t1 is derived from g2342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15308845	15310236	.	-	.	Phchi.S1G233100
Phchi.S1	AUGUSTUS	transcript	15308845	15310236	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	stop_codon	15308842	15308844	.	-	0	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	CDS	15308845	15309477	0.84	-	0	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	exon	15308845	15309477	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	intron	15309478	15309723	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	CDS	15309724	15309775	1	-	1	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	exon	15309724	15309775	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	intron	15309776	15309874	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	CDS	15309875	15309976	1	-	1	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	exon	15309875	15309976	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	intron	15309977	15310138	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	CDS	15310139	15310236	0.98	-	0	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	exon	15310139	15310236	.	-	.	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
Phchi.S1	AUGUSTUS	start_codon	15310234	15310236	.	-	0	transcript_id "Phchi.S1G233100.t1"; gene_id "Phchi.S1G233100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9235.t1 is derived from g6410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40536211	40540338	.	-	.	Phchi.S1G639400
Phchi.S1	AUGUSTUS	transcript	40536211	40540338	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	stop_codon	40536208	40536210	.	-	0	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40536211	40536250	1	-	1	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40536211	40536250	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40536251	40536345	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40536346	40536417	0.91	-	1	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40536346	40536417	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40536418	40536503	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40536504	40536596	0.73	-	1	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40536504	40536596	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40536597	40536989	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40536990	40537256	0.39	-	1	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40536990	40537256	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40537257	40537763	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40537764	40538601	0.2	-	2	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40537764	40538601	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40538602	40539237	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40539238	40539781	0.36	-	0	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40539238	40539781	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40539782	40539979	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40539980	40540015	0.45	-	0	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40539980	40540015	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40540016	40540097	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40540098	40540153	0.45	-	2	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40540098	40540153	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	intron	40540154	40540241	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	CDS	40540242	40540338	0.51	-	0	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	exon	40540242	40540338	.	-	.	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
Phchi.S1	AUGUSTUS	start_codon	40540336	40540338	.	-	0	transcript_id "Phchi.S1G639400.t1"; gene_id "Phchi.S1G639400"
# This transcript jg14126.t2 is derived from g12593.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14127.t1 is derived from g12594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11024389	11034691	.	+	.	Phchi.S3G144600
Phchi.S3	AUGUSTUS	transcript	11024389	11034691	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	start_codon	11024389	11024391	.	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11024389	11024721	0.98	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11024389	11024721	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11024722	11024877	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11024878	11024947	1	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11024878	11024947	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11024948	11025046	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11025047	11025152	1	+	2	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11025047	11025152	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11025153	11025251	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11025252	11025513	0.99	+	1	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11025252	11025513	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11025514	11025607	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11025608	11025645	1	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11025608	11025645	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11025646	11025728	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11025729	11025785	1	+	1	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11025729	11025785	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11025786	11025886	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11025887	11025950	1	+	1	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11025887	11025950	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11025951	11026051	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11026052	11026504	0.95	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11026052	11026504	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11026505	11026596	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11026597	11026698	1	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11026597	11026698	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11026699	11026867	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11026868	11027183	0.64	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11026868	11027183	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11027184	11027296	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11027297	11027385	0.85	+	2	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11027297	11027385	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11027386	11027525	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11027526	11028492	0.83	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11027526	11028492	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11028493	11028575	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11028576	11030293	0.99	+	2	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11028576	11030293	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11030294	11030415	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11030416	11030555	1	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11030416	11030555	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11030556	11030656	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11030657	11030774	1	+	1	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11030657	11030774	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11030775	11030937	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11030938	11031008	1	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11030938	11031008	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11031009	11031104	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11031105	11031903	0.96	+	1	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11031105	11031903	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11031904	11032031	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11032032	11032736	1	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11032032	11032736	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11032737	11032946	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11032947	11033838	0.29	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11032947	11033838	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	intron	11033839	11034185	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	CDS	11034186	11034691	0.44	+	2	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	exon	11034186	11034691	.	+	.	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
Phchi.S3	AUGUSTUS	stop_codon	11034692	11034694	.	+	0	transcript_id "Phchi.S3G144600.t1"; gene_id "Phchi.S3G144600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13665.t1 is derived from g12132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8063686	8067703	.	+	.	Phchi.S3G098400
Phchi.S3	AUGUSTUS	transcript	8063686	8067703	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	start_codon	8063686	8063688	.	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8063686	8065026	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8063686	8065026	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8065027	8065168	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8065169	8065366	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8065169	8065366	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8065367	8065450	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8065451	8065660	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8065451	8065660	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8065661	8065742	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8065743	8065832	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8065743	8065832	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8065833	8065909	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8065910	8066113	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8065910	8066113	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8066114	8066229	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8066230	8066442	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8066230	8066442	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8066443	8066539	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8066540	8066718	0.98	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8066540	8066718	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8066719	8066819	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8066820	8067057	1	+	1	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8066820	8067057	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8067058	8067153	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8067154	8067403	1	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8067154	8067403	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	intron	8067404	8067494	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	CDS	8067495	8067703	1	+	2	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	exon	8067495	8067703	.	+	.	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
Phchi.S3	AUGUSTUS	stop_codon	8067704	8067706	.	+	0	transcript_id "Phchi.S3G098400.t1"; gene_id "Phchi.S3G098400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11315.t1 is derived from g15365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5329327	5331403	.	+	.	Phchi.S4G089700
Phchi.S4	AUGUSTUS	transcript	5329327	5331403	.	+	.	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	start_codon	5329327	5329329	.	+	0	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	CDS	5329327	5330694	0.51	+	0	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	exon	5329327	5330694	.	+	.	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	intron	5330695	5330851	.	+	.	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	CDS	5330852	5331041	1	+	0	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	exon	5330852	5331041	.	+	.	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	intron	5331042	5331140	.	+	.	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	CDS	5331141	5331403	0.53	+	2	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	exon	5331141	5331403	.	+	.	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
Phchi.S4	AUGUSTUS	stop_codon	5331404	5331406	.	+	0	transcript_id "Phchi.S4G089700.t1"; gene_id "Phchi.S4G089700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7133.t1 is derived from g4305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27120084	27121961	.	-	.	Phchi.S1G429200
Phchi.S1	AUGUSTUS	transcript	27120084	27121961	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	stop_codon	27120081	27120083	.	-	0	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27120084	27120321	1	-	1	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27120084	27120321	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	intron	27120322	27120421	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27120422	27120573	1	-	0	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27120422	27120573	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	intron	27120574	27120683	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27120684	27120839	1	-	0	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27120684	27120839	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	intron	27120840	27120930	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27120931	27121216	0.98	-	1	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27120931	27121216	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	intron	27121217	27121363	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27121364	27121480	1	-	1	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27121364	27121480	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	intron	27121481	27121594	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27121595	27121657	1	-	1	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27121595	27121657	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	intron	27121658	27121782	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	CDS	27121783	27121961	0.94	-	0	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	exon	27121783	27121961	.	-	.	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
Phchi.S1	AUGUSTUS	start_codon	27121959	27121961	.	-	0	transcript_id "Phchi.S1G429200.t1"; gene_id "Phchi.S1G429200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11784.t1 is derived from g15836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8147885	8150608	.	+	.	Phchi.S4G136600
Phchi.S4	AUGUSTUS	transcript	8147885	8150608	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	start_codon	8147885	8147887	.	+	0	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	CDS	8147885	8148466	0.99	+	0	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	exon	8147885	8148466	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	intron	8148467	8148563	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	CDS	8148564	8149657	1	+	0	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	exon	8148564	8149657	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	intron	8149658	8149788	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	CDS	8149789	8150083	1	+	1	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	exon	8149789	8150083	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	intron	8150084	8150172	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	CDS	8150173	8150299	1	+	0	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	exon	8150173	8150299	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	intron	8150300	8150384	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	CDS	8150385	8150608	0.79	+	2	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	exon	8150385	8150608	.	+	.	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
Phchi.S4	AUGUSTUS	stop_codon	8150609	8150611	.	+	0	transcript_id "Phchi.S4G136600.t1"; gene_id "Phchi.S4G136600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1535.t1 is derived from g8454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1656177	1661539	.	-	.	Phchi.S5G014400
Phchi.S5	AUGUSTUS	transcript	1656177	1661539	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	stop_codon	1656174	1656176	.	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1656177	1656356	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1656177	1656356	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1656357	1656470	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1656471	1656659	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1656471	1656659	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1656660	1656756	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1656757	1657032	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1656757	1657032	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1657033	1657194	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1657195	1657419	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1657195	1657419	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1657420	1657522	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1657523	1657588	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1657523	1657588	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1657589	1657685	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1657686	1657841	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1657686	1657841	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1657842	1657926	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1657927	1657989	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1657927	1657989	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1657990	1658219	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1658220	1658318	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1658220	1658318	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1658319	1658471	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1658472	1658621	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1658472	1658621	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1658622	1658712	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1658713	1658826	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1658713	1658826	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1658827	1659056	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1659057	1659089	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1659057	1659089	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1659090	1659229	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1659230	1660626	1	-	2	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1659230	1660626	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1660627	1660912	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1660913	1661371	1	-	2	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1660913	1661371	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	intron	1661372	1661487	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	CDS	1661488	1661539	1	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	exon	1661488	1661539	.	-	.	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
Phchi.S5	AUGUSTUS	start_codon	1661537	1661539	.	-	0	transcript_id "Phchi.S5G014400.t1"; gene_id "Phchi.S5G014400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1606.t1 is derived from g8525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1999905	2006382	.	+	.	Phchi.S5G021500
Phchi.S5	AUGUSTUS	transcript	1999905	2006382	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	start_codon	1999905	1999907	.	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	1999905	1999990	0.8	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	1999905	1999990	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	1999991	2000090	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2000091	2000193	1	+	1	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2000091	2000193	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2000194	2000300	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2000301	2000367	1	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2000301	2000367	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2000368	2000465	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2000466	2000701	1	+	2	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2000466	2000701	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2000702	2000792	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2000793	2000903	0.76	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2000793	2000903	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2000904	2001027	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2001028	2001116	0.66	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2001028	2001116	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2001117	2001183	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2001184	2001256	0.7	+	1	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2001184	2001256	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2001257	2001423	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2001424	2001693	1	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2001424	2001693	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2001694	2001775	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2001776	2002404	0.73	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2001776	2002404	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2002405	2002607	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2002608	2005147	0.83	+	1	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2002608	2005147	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2005148	2005225	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2005226	2005927	0.5	+	2	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2005226	2005927	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2005928	2006105	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2006106	2006175	0.97	+	2	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2006106	2006175	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	intron	2006176	2006321	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	CDS	2006322	2006382	1	+	1	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	exon	2006322	2006382	.	+	.	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
Phchi.S5	AUGUSTUS	stop_codon	2006383	2006385	.	+	0	transcript_id "Phchi.S5G021500.t1"; gene_id "Phchi.S5G021500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8970.t1 is derived from g6145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38895379	38895923	.	-	.	Phchi.S1G612900
Phchi.S1	AUGUSTUS	transcript	38895379	38895923	.	-	.	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	stop_codon	38895376	38895378	.	-	0	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	CDS	38895379	38895403	0.6	-	1	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	exon	38895379	38895403	.	-	.	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	intron	38895404	38895558	.	-	.	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	CDS	38895559	38895923	0.56	-	0	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	exon	38895559	38895923	.	-	.	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
Phchi.S1	AUGUSTUS	start_codon	38895921	38895923	.	-	0	transcript_id "Phchi.S1G612900.t1"; gene_id "Phchi.S1G612900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8078.t1 is derived from g5253.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32843613	32845100	.	-	.	Phchi.S1G523700
Phchi.S1	AUGUSTUS	transcript	32843613	32845100	.	-	.	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	stop_codon	32843610	32843612	.	-	0	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	CDS	32843613	32843821	0.71	-	2	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	exon	32843613	32843821	.	-	.	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	intron	32843822	32843914	.	-	.	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	CDS	32843915	32845100	0.58	-	0	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	exon	32843915	32845100	.	-	.	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	start_codon	32845098	32845100	.	-	0	transcript_id "Phchi.S1G523700.t1"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	transcript	32843613	32845100	.	-	.	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	stop_codon	32843610	32843612	.	-	0	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	CDS	32843613	32843764	0.5	-	2	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	exon	32843613	32843764	.	-	.	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	intron	32843765	32843914	.	-	.	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	CDS	32843915	32845100	0.42	-	0	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	exon	32843915	32845100	.	-	.	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
Phchi.S1	AUGUSTUS	start_codon	32845098	32845100	.	-	0	transcript_id "Phchi.S1G523700.t2"; gene_id "Phchi.S1G523700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13746.t1 is derived from g12213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8678278	8679669	.	+	.	Phchi.S3G106500
Phchi.S3	AUGUSTUS	transcript	8678278	8679669	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	start_codon	8678278	8678280	.	+	0	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	CDS	8678278	8678387	0.99	+	0	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	exon	8678278	8678387	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	intron	8678388	8678807	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	CDS	8678808	8678918	0.84	+	1	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	exon	8678808	8678918	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	intron	8678919	8679144	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	CDS	8679145	8679174	0.43	+	1	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	exon	8679145	8679174	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	intron	8679175	8679318	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	CDS	8679319	8679414	0.61	+	1	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	exon	8679319	8679414	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	intron	8679415	8679569	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	CDS	8679570	8679669	1	+	1	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	exon	8679570	8679669	.	+	.	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
Phchi.S3	AUGUSTUS	stop_codon	8679670	8679672	.	+	0	transcript_id "Phchi.S3G106500.t1"; gene_id "Phchi.S3G106500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8632.t1 is derived from g5807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37166904	37169600	.	+	.	Phchi.S1G579100
Phchi.S1	AUGUSTUS	transcript	37166904	37169600	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	start_codon	37166904	37166906	.	+	0	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	CDS	37166904	37167229	1	+	0	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	exon	37166904	37167229	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	intron	37167230	37167348	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	CDS	37167349	37167604	0.99	+	1	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	exon	37167349	37167604	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	intron	37167605	37167690	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	CDS	37167691	37168671	0.57	+	0	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	exon	37167691	37168671	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	intron	37168672	37168762	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	CDS	37168763	37169006	0.73	+	0	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	exon	37168763	37169006	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	intron	37169007	37169101	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	CDS	37169102	37169487	0.76	+	2	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	exon	37169102	37169487	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	intron	37169488	37169591	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	CDS	37169592	37169600	0.72	+	0	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	exon	37169592	37169600	.	+	.	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
Phchi.S1	AUGUSTUS	stop_codon	37169601	37169603	.	+	0	transcript_id "Phchi.S1G579100.t1"; gene_id "Phchi.S1G579100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12009.t1 is derived from g7684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	511642	514301	.	-	.	Phchi.S2G008900
Phchi.S2	AUGUSTUS	transcript	511642	514301	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	stop_codon	511639	511641	.	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	511642	511845	1	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	511642	511845	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	511846	511953	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	511954	512096	1	-	2	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	511954	512096	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	512097	512185	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	512186	512279	1	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	512186	512279	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	512280	512428	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	512429	512590	1	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	512429	512590	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	512591	512698	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	512699	512767	0.91	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	512699	512767	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	512768	512868	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	512869	513078	0.86	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	512869	513078	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	513079	513411	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	513412	513474	1	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	513412	513474	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	513475	513635	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	513636	513724	1	-	2	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	513636	513724	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	513725	513852	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	513853	513955	0.5	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	513853	513955	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	intron	513956	514154	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	CDS	514155	514301	0.6	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	exon	514155	514301	.	-	.	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
Phchi.S2	AUGUSTUS	start_codon	514299	514301	.	-	0	transcript_id "Phchi.S2G008900.t1"; gene_id "Phchi.S2G008900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8059.t1 is derived from g5234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32741711	32743518	.	-	.	Phchi.S1G521800
Phchi.S1	AUGUSTUS	transcript	32741711	32743518	.	-	.	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	stop_codon	32741708	32741710	.	-	0	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	CDS	32741711	32742748	1	-	0	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	exon	32741711	32742748	.	-	.	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	intron	32742749	32742840	.	-	.	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	CDS	32742841	32743518	0.95	-	0	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	exon	32742841	32743518	.	-	.	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
Phchi.S1	AUGUSTUS	start_codon	32743516	32743518	.	-	0	transcript_id "Phchi.S1G521800.t1"; gene_id "Phchi.S1G521800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg323.t1 is derived from g10105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2265750	2268031	.	+	.	Phchi.S6G028200
Phchi.S6	AUGUSTUS	transcript	2265750	2268031	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	start_codon	2265750	2265752	.	+	0	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	CDS	2265750	2265985	0.68	+	0	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	exon	2265750	2265985	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	intron	2265986	2266188	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	CDS	2266189	2266232	0.93	+	1	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	exon	2266189	2266232	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	intron	2266233	2266508	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	CDS	2266509	2266862	0.44	+	2	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	exon	2266509	2266862	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	intron	2266863	2266958	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	CDS	2266959	2268031	0.61	+	2	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	exon	2266959	2268031	.	+	.	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
Phchi.S6	AUGUSTUS	stop_codon	2268032	2268034	.	+	0	transcript_id "Phchi.S6G028200.t1"; gene_id "Phchi.S6G028200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13285.t1 is derived from g11751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5183804	5184550	.	+	.	Phchi.S3G060400
Phchi.S3	AUGUSTUS	transcript	5183804	5184550	.	+	.	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	start_codon	5183804	5183806	.	+	0	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	CDS	5183804	5183995	0.88	+	0	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	exon	5183804	5183995	.	+	.	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	intron	5183996	5184134	.	+	.	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	CDS	5184135	5184359	0.77	+	0	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	exon	5184135	5184359	.	+	.	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	intron	5184360	5184442	.	+	.	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	CDS	5184443	5184550	0.83	+	0	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	exon	5184443	5184550	.	+	.	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
Phchi.S3	AUGUSTUS	stop_codon	5184551	5184553	.	+	0	transcript_id "Phchi.S3G060400.t1"; gene_id "Phchi.S3G060400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7099.t1 is derived from g4271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26906867	26909241	.	-	.	Phchi.S1G425800
Phchi.S1	AUGUSTUS	transcript	26906867	26909241	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	stop_codon	26906864	26906866	.	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26906867	26906990	1	-	1	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26906867	26906990	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26906991	26907076	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26907077	26907238	1	-	1	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26907077	26907238	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26907239	26907358	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26907359	26907447	1	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26907359	26907447	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26907448	26907535	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26907536	26907787	0.95	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26907536	26907787	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26907788	26907882	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26907883	26907993	1	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26907883	26907993	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26907994	26908086	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26908087	26908234	1	-	1	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26908087	26908234	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26908235	26908376	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26908377	26908556	1	-	1	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26908377	26908556	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26908557	26908698	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26908699	26908802	0.85	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26908699	26908802	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26908803	26908907	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26908908	26909156	0.87	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26908908	26909156	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	intron	26909157	26909226	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	CDS	26909227	26909241	0.58	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	exon	26909227	26909241	.	-	.	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
Phchi.S1	AUGUSTUS	start_codon	26909239	26909241	.	-	0	transcript_id "Phchi.S1G425800.t1"; gene_id "Phchi.S1G425800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13974.t1 is derived from g12441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10006108	10007518	.	+	.	Phchi.S3G129300
Phchi.S3	AUGUSTUS	transcript	10006108	10007518	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	start_codon	10006108	10006110	.	+	0	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10006108	10006159	0.53	+	0	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10006108	10006159	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	intron	10006160	10006285	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10006286	10006413	1	+	2	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10006286	10006413	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	intron	10006414	10006538	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10006539	10006626	1	+	0	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10006539	10006626	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	intron	10006627	10006730	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10006731	10006804	1	+	2	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10006731	10006804	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	intron	10006805	10006893	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10006894	10007082	1	+	0	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10006894	10007082	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	intron	10007083	10007153	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10007154	10007251	1	+	0	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10007154	10007251	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	intron	10007252	10007367	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	CDS	10007368	10007518	0.99	+	1	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	exon	10007368	10007518	.	+	.	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
Phchi.S3	AUGUSTUS	stop_codon	10007519	10007521	.	+	0	transcript_id "Phchi.S3G129300.t1"; gene_id "Phchi.S3G129300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1115.t1 is derived from g10898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7772831	7773859	.	-	.	Phchi.S6G107400
Phchi.S6	AUGUSTUS	transcript	7772831	7773859	.	-	.	transcript_id "Phchi.S6G107400.t1"; gene_id "Phchi.S6G107400"
Phchi.S6	AUGUSTUS	stop_codon	7772828	7772830	.	-	0	transcript_id "Phchi.S6G107400.t1"; gene_id "Phchi.S6G107400"
Phchi.S6	AUGUSTUS	CDS	7772831	7773859	0.56	-	0	transcript_id "Phchi.S6G107400.t1"; gene_id "Phchi.S6G107400"
Phchi.S6	AUGUSTUS	exon	7772831	7773859	.	-	.	transcript_id "Phchi.S6G107400.t1"; gene_id "Phchi.S6G107400"
Phchi.S6	AUGUSTUS	start_codon	7773857	7773859	.	-	0	transcript_id "Phchi.S6G107400.t1"; gene_id "Phchi.S6G107400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8800.t1 is derived from g5975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38051758	38052936	.	+	.	Phchi.S1G595900
Phchi.S1	AUGUSTUS	transcript	38051758	38052936	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	start_codon	38051758	38051760	.	+	0	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	CDS	38051758	38051805	0.56	+	0	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	exon	38051758	38051805	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	intron	38051806	38051892	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	CDS	38051893	38051926	0.94	+	0	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	exon	38051893	38051926	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	intron	38051927	38052137	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	CDS	38052138	38052190	0.62	+	2	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	exon	38052138	38052190	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	intron	38052191	38052282	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	CDS	38052283	38052573	1	+	0	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	exon	38052283	38052573	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	intron	38052574	38052711	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	CDS	38052712	38052936	0.99	+	0	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	exon	38052712	38052936	.	+	.	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
Phchi.S1	AUGUSTUS	stop_codon	38052937	38052939	.	+	0	transcript_id "Phchi.S1G595900.t1"; gene_id "Phchi.S1G595900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15889.t1 is derived from g14359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22037421	22040275	.	+	.	Phchi.S3G320800
Phchi.S3	AUGUSTUS	transcript	22037421	22040275	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	start_codon	22037421	22037423	.	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22037421	22037705	0.45	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22037421	22037705	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22037706	22037820	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22037821	22037916	1	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22037821	22037916	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22037917	22038094	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22038095	22038205	1	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22038095	22038205	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22038206	22038290	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22038291	22038600	1	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22038291	22038600	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22038601	22038765	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22038766	22038856	1	+	2	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22038766	22038856	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22038857	22038967	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22038968	22039298	0.92	+	1	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22038968	22039298	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22039299	22039405	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22039406	22039554	1	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22039406	22039554	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	intron	22039555	22039743	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	CDS	22039744	22040275	0.99	+	1	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	exon	22039744	22040275	.	+	.	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
Phchi.S3	AUGUSTUS	stop_codon	22040276	22040278	.	+	0	transcript_id "Phchi.S3G320800.t1"; gene_id "Phchi.S3G320800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2351.t1 is derived from g9271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6314570	6316656	.	-	.	Phchi.S5G096000
Phchi.S5	AUGUSTUS	transcript	6314570	6316656	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	stop_codon	6314567	6314569	.	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6314570	6314680	1	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6314570	6314680	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6314681	6314835	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6314836	6314922	1	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6314836	6314922	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6314923	6315043	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6315044	6315211	0.99	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6315044	6315211	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6315212	6315312	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6315313	6315432	0.94	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6315313	6315432	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6315433	6315637	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6315638	6315745	1	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6315638	6315745	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6315746	6315892	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6315893	6315973	1	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6315893	6315973	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6315974	6316062	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6316063	6316303	0.99	-	1	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6316063	6316303	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	intron	6316304	6316411	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	CDS	6316412	6316656	0.99	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	exon	6316412	6316656	.	-	.	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
Phchi.S5	AUGUSTUS	start_codon	6316654	6316656	.	-	0	transcript_id "Phchi.S5G096000.t1"; gene_id "Phchi.S5G096000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10690.t1 is derived from g14740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1594384	1594953	.	-	.	Phchi.S4G027200
Phchi.S4	AUGUSTUS	transcript	1594384	1594953	.	-	.	transcript_id "Phchi.S4G027200.t1"; gene_id "Phchi.S4G027200"
Phchi.S4	AUGUSTUS	stop_codon	1594381	1594383	.	-	0	transcript_id "Phchi.S4G027200.t1"; gene_id "Phchi.S4G027200"
Phchi.S4	AUGUSTUS	CDS	1594384	1594953	0.91	-	0	transcript_id "Phchi.S4G027200.t1"; gene_id "Phchi.S4G027200"
Phchi.S4	AUGUSTUS	exon	1594384	1594953	.	-	.	transcript_id "Phchi.S4G027200.t1"; gene_id "Phchi.S4G027200"
Phchi.S4	AUGUSTUS	start_codon	1594951	1594953	.	-	0	transcript_id "Phchi.S4G027200.t1"; gene_id "Phchi.S4G027200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13696.t1 is derived from g12163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8247485	8250950	.	+	.	Phchi.S3G101500
Phchi.S3	AUGUSTUS	transcript	8247485	8250950	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	start_codon	8247485	8247487	.	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8247485	8247724	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8247485	8247724	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8247725	8248027	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8248028	8248126	0.7	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8248028	8248126	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8248127	8248228	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8248229	8248300	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8248229	8248300	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8248301	8248421	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8248422	8248484	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8248422	8248484	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8248485	8248604	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8248605	8248745	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8248605	8248745	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8248746	8248843	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8248844	8248939	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8248844	8248939	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8248940	8249030	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8249031	8249315	0.99	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8249031	8249315	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8249316	8249430	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8249431	8249575	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8249431	8249575	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8249576	8249648	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8249649	8249791	1	+	2	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8249649	8249791	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8249792	8249870	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8249871	8250065	1	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8249871	8250065	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8250066	8250156	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8250157	8250423	0.97	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8250157	8250423	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8250424	8250524	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8250525	8250625	0.92	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8250525	8250625	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8250626	8250726	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8250727	8250739	0.81	+	1	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8250727	8250739	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	intron	8250740	8250869	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	CDS	8250870	8250950	0.82	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	exon	8250870	8250950	.	+	.	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
Phchi.S3	AUGUSTUS	stop_codon	8250951	8250953	.	+	0	transcript_id "Phchi.S3G101500.t1"; gene_id "Phchi.S3G101500"
# This transcript jg15894.t2 is derived from g14364.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15895.t1 is derived from g14365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22054599	22056738	.	+	.	Phchi.S3G321400
Phchi.S3	AUGUSTUS	transcript	22054599	22056738	.	+	.	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	start_codon	22054599	22054601	.	+	0	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	CDS	22054599	22056002	0.45	+	0	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	exon	22054599	22056002	.	+	.	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	intron	22056003	22056144	.	+	.	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	CDS	22056145	22056738	0.9	+	0	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	exon	22056145	22056738	.	+	.	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	stop_codon	22056739	22056741	.	+	0	transcript_id "Phchi.S3G321400.t1"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	transcript	22055622	22056738	.	+	.	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	start_codon	22055622	22055624	.	+	0	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	CDS	22055622	22056002	0.46	+	0	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	exon	22055622	22056002	.	+	.	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	intron	22056003	22056144	.	+	.	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	CDS	22056145	22056738	0.79	+	0	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	exon	22056145	22056738	.	+	.	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
Phchi.S3	AUGUSTUS	stop_codon	22056739	22056741	.	+	0	transcript_id "Phchi.S3G321400.t2"; gene_id "Phchi.S3G321400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2994.t1 is derived from g163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1047264	1052195	.	-	.	Phchi.S1G015300
Phchi.S1	AUGUSTUS	transcript	1047264	1052195	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	stop_codon	1047261	1047263	.	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1047264	1047587	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1047264	1047587	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1047588	1047675	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1047676	1047813	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1047676	1047813	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1047814	1047921	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1047922	1048171	1	-	1	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1047922	1048171	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1048172	1048269	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1048270	1048382	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1048270	1048382	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1048383	1048455	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1048456	1048539	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1048456	1048539	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1048540	1048705	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1048706	1048980	1	-	2	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1048706	1048980	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1048981	1049146	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1049147	1049261	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1049147	1049261	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1049262	1049355	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1049356	1049551	1	-	1	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1049356	1049551	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1049552	1049631	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1049632	1049684	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1049632	1049684	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1049685	1049770	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1049771	1049899	0.93	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1049771	1049899	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1049900	1050004	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1050005	1050100	0.96	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1050005	1050100	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1050101	1050261	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1050262	1050327	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1050262	1050327	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1050328	1050427	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1050428	1050481	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1050428	1050481	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1050482	1050571	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1050572	1050654	0.76	-	2	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1050572	1050654	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1050655	1050782	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1050783	1051029	0.75	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1050783	1051029	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1051030	1051128	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1051129	1051213	1	-	1	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1051129	1051213	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	intron	1051214	1051296	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	CDS	1051297	1052195	1	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	exon	1051297	1052195	.	-	.	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
Phchi.S1	AUGUSTUS	start_codon	1052193	1052195	.	-	0	transcript_id "Phchi.S1G015300.t1"; gene_id "Phchi.S1G015300"
# This transcript jg15214.t2 is derived from g13682.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15215.t1 is derived from g13683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17723188	17724924	.	+	.	Phchi.S3G253400
Phchi.S3	AUGUSTUS	transcript	17723188	17724924	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	start_codon	17723188	17723190	.	+	0	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	CDS	17723188	17723679	0.93	+	0	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	exon	17723188	17723679	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	intron	17723680	17723801	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	CDS	17723802	17724293	0.96	+	0	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	exon	17723802	17724293	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	intron	17724294	17724378	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	CDS	17724379	17724596	1	+	0	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	exon	17724379	17724596	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	intron	17724597	17724677	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	CDS	17724678	17724924	1	+	1	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	exon	17724678	17724924	.	+	.	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
Phchi.S3	AUGUSTUS	stop_codon	17724925	17724927	.	+	0	transcript_id "Phchi.S3G253400.t1"; gene_id "Phchi.S3G253400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8863.t1 is derived from g6038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38337907	38341477	.	+	.	Phchi.S1G602200
Phchi.S1	AUGUSTUS	transcript	38337907	38341477	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	start_codon	38337907	38337909	.	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38337907	38338350	0.8	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38337907	38338350	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38338351	38338879	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38338880	38339365	1	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38338880	38339365	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38339366	38339543	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38339544	38339628	1	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38339544	38339628	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38339629	38339759	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38339760	38339830	1	+	2	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38339760	38339830	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38339831	38339912	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38339913	38340001	1	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38339913	38340001	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38340002	38340130	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38340131	38340263	1	+	1	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38340131	38340263	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38340264	38340352	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38340353	38340582	1	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38340353	38340582	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38340583	38340668	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38340669	38341148	1	+	1	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38340669	38341148	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	intron	38341149	38341236	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	CDS	38341237	38341477	0.68	+	1	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	exon	38341237	38341477	.	+	.	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
Phchi.S1	AUGUSTUS	stop_codon	38341478	38341480	.	+	0	transcript_id "Phchi.S1G602200.t1"; gene_id "Phchi.S1G602200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg844.t1 is derived from g10626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5853907	5858555	.	-	.	Phchi.S6G080300
Phchi.S6	AUGUSTUS	transcript	5853907	5858555	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	stop_codon	5853904	5853906	.	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5853907	5853954	0.64	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5853907	5853954	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5853955	5854106	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5854107	5854123	0.65	-	2	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5854107	5854123	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5854124	5854251	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5854252	5854327	0.69	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5854252	5854327	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5854328	5854412	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5854413	5854562	1	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5854413	5854562	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5854563	5854661	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5854662	5854809	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5854662	5854809	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5854810	5854944	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5854945	5855090	0.98	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5854945	5855090	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5855091	5855195	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5855196	5855287	0.97	-	2	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5855196	5855287	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5855288	5855395	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5855396	5855447	0.99	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5855396	5855447	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5855448	5855602	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5855603	5855928	1	-	2	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5855603	5855928	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5855929	5856053	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5856054	5856230	1	-	2	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5856054	5856230	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5856231	5856318	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5856319	5856425	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5856319	5856425	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5856426	5856520	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5856521	5856577	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5856521	5856577	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5856578	5856666	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5856667	5856732	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5856667	5856732	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5856733	5856847	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5856848	5856928	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5856848	5856928	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5856929	5857044	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5857045	5857116	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5857045	5857116	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5857117	5857203	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5857204	5857275	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5857204	5857275	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5857276	5857446	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5857447	5857521	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5857447	5857521	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5857522	5857618	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5857619	5857690	1	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5857619	5857690	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5857691	5857975	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5857976	5858122	0.98	-	1	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5857976	5858122	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5858123	5858224	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5858225	5858351	1	-	2	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5858225	5858351	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	intron	5858352	5858473	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	CDS	5858474	5858555	1	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	exon	5858474	5858555	.	-	.	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
Phchi.S6	AUGUSTUS	start_codon	5858553	5858555	.	-	0	transcript_id "Phchi.S6G080300.t1"; gene_id "Phchi.S6G080300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8237.t1 is derived from g5412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34582981	34584025	.	+	.	Phchi.S1G539600
Phchi.S1	AUGUSTUS	transcript	34582981	34584025	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	start_codon	34582981	34582983	.	+	0	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	CDS	34582981	34583270	1	+	0	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	exon	34582981	34583270	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	intron	34583271	34583368	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	CDS	34583369	34583489	0.98	+	1	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	exon	34583369	34583489	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	intron	34583490	34583604	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	CDS	34583605	34583754	1	+	0	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	exon	34583605	34583754	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	intron	34583755	34583866	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	CDS	34583867	34584025	1	+	0	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	exon	34583867	34584025	.	+	.	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
Phchi.S1	AUGUSTUS	stop_codon	34584026	34584028	.	+	0	transcript_id "Phchi.S1G539600.t1"; gene_id "Phchi.S1G539600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1291.t1 is derived from g11074.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8862520	8870012	.	-	.	Phchi.S6G125000
Phchi.S6	AUGUSTUS	transcript	8862520	8870012	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	stop_codon	8862517	8862519	.	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8862520	8862707	1	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8862520	8862707	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8862708	8862790	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8862791	8863009	1	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8862791	8863009	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863010	8863083	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863084	8863311	0.54	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863084	8863311	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863312	8863399	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863400	8863420	0.53	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863400	8863420	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863421	8863506	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863507	8863730	0.53	-	1	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863507	8863730	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863731	8863824	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863825	8864061	0.99	-	1	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863825	8864061	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864062	8864206	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8864207	8864289	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8864207	8864289	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864290	8864442	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8864443	8864822	1	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8864443	8864822	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864823	8864936	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8864937	8864988	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8864937	8864988	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864989	8865098	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865099	8865317	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865099	8865317	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865318	8865429	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865430	8865495	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865430	8865495	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865496	8865589	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865590	8865647	1	-	1	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865590	8865647	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865648	8865752	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865753	8865874	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865753	8865874	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865875	8865973	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865974	8866145	1	-	1	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865974	8866145	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866146	8866239	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8866240	8866511	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8866240	8866511	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866512	8866686	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8866687	8866767	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8866687	8866767	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866768	8866843	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8866844	8866984	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8866844	8866984	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866985	8867083	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867084	8867179	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867084	8867179	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867180	8867255	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867256	8867306	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867256	8867306	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867307	8867467	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867468	8867551	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867468	8867551	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867552	8867730	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867731	8867853	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867731	8867853	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867854	8867946	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867947	8867978	0.98	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867947	8867978	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867979	8868049	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868050	8868158	0.59	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868050	8868158	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868159	8868241	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868242	8868451	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868242	8868451	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868452	8868572	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868573	8868620	0.87	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868573	8868620	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868621	8868729	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868730	8868943	0.87	-	1	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868730	8868943	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868944	8869028	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869029	8869100	1	-	1	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869029	8869100	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8869101	8869214	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869215	8869491	0.94	-	2	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869215	8869491	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8869492	8869579	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869580	8869808	1	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869580	8869808	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8869809	8869955	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869956	8870012	0.8	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869956	8870012	.	-	.	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	start_codon	8870010	8870012	.	-	0	transcript_id "Phchi.S6G125000.t1"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	transcript	8862520	8870012	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	stop_codon	8862517	8862519	.	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8862520	8862707	0.99	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8862520	8862707	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8862708	8862790	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8862791	8863009	1	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8862791	8863009	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863010	8863083	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863084	8863320	0.57	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863084	8863320	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863321	8863399	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863400	8863420	0.55	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863400	8863420	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863421	8863506	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863507	8863730	0.55	-	1	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863507	8863730	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8863731	8863824	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8863825	8864061	1	-	1	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8863825	8864061	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864062	8864206	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8864207	8864289	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8864207	8864289	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864290	8864442	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8864443	8864822	1	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8864443	8864822	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864823	8864936	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8864937	8864988	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8864937	8864988	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8864989	8865098	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865099	8865317	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865099	8865317	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865318	8865429	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865430	8865495	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865430	8865495	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865496	8865589	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865590	8865647	1	-	1	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865590	8865647	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865648	8865752	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865753	8865874	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865753	8865874	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8865875	8865973	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8865974	8866145	1	-	1	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8865974	8866145	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866146	8866239	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8866240	8866511	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8866240	8866511	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866512	8866686	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8866687	8866767	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8866687	8866767	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866768	8866843	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8866844	8866984	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8866844	8866984	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8866985	8867083	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867084	8867179	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867084	8867179	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867180	8867255	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867256	8867306	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867256	8867306	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867307	8867467	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867468	8867551	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867468	8867551	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867552	8867730	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867731	8867853	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867731	8867853	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867854	8867946	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8867947	8867978	0.99	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8867947	8867978	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8867979	8868049	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868050	8868158	0.5	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868050	8868158	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868159	8868241	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868242	8868451	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868242	8868451	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868452	8868572	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868573	8868620	0.81	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868573	8868620	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868621	8868729	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8868730	8868943	0.87	-	1	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8868730	8868943	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8868944	8869028	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869029	8869100	1	-	1	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869029	8869100	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8869101	8869214	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869215	8869491	0.9	-	2	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869215	8869491	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8869492	8869579	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869580	8869808	1	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869580	8869808	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	intron	8869809	8869955	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	CDS	8869956	8870012	0.71	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	exon	8869956	8870012	.	-	.	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
Phchi.S6	AUGUSTUS	start_codon	8870010	8870012	.	-	0	transcript_id "Phchi.S6G125000.t2"; gene_id "Phchi.S6G125000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6120.t1 is derived from g3291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21022925	21023929	.	+	.	Phchi.S1G327900
Phchi.S1	AUGUSTUS	transcript	21022925	21023929	.	+	.	transcript_id "Phchi.S1G327900.t1"; gene_id "Phchi.S1G327900"
Phchi.S1	AUGUSTUS	start_codon	21022925	21022927	.	+	0	transcript_id "Phchi.S1G327900.t1"; gene_id "Phchi.S1G327900"
Phchi.S1	AUGUSTUS	CDS	21022925	21023929	0.35	+	0	transcript_id "Phchi.S1G327900.t1"; gene_id "Phchi.S1G327900"
Phchi.S1	AUGUSTUS	exon	21022925	21023929	.	+	.	transcript_id "Phchi.S1G327900.t1"; gene_id "Phchi.S1G327900"
Phchi.S1	AUGUSTUS	stop_codon	21023930	21023932	.	+	0	transcript_id "Phchi.S1G327900.t1"; gene_id "Phchi.S1G327900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2752.t1 is derived from g9672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8623331	8623733	.	-	.	Phchi.S5G136100
Phchi.S5	AUGUSTUS	transcript	8623331	8623733	.	-	.	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	stop_codon	8623328	8623330	.	-	0	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	CDS	8623331	8623375	0.99	-	0	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	exon	8623331	8623375	.	-	.	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	intron	8623376	8623463	.	-	.	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	CDS	8623464	8623733	0.95	-	0	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	exon	8623464	8623733	.	-	.	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
Phchi.S5	AUGUSTUS	start_codon	8623731	8623733	.	-	0	transcript_id "Phchi.S5G136100.t1"; gene_id "Phchi.S5G136100"
# This transcript jg1791.t2 is derived from g8711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1792.t1 is derived from g8712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3048401	3051660	.	+	.	Phchi.S5G040100
Phchi.S5	AUGUSTUS	transcript	3048401	3048882	.	+	.	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	start_codon	3048401	3048403	.	+	0	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3048401	3048646	0.98	+	0	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3048401	3048646	.	+	.	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3048647	3048729	.	+	.	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3048730	3048882	0.85	+	0	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3048730	3048882	.	+	.	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	stop_codon	3048883	3048885	.	+	0	transcript_id "Phchi.S5G040100.t1"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	transcript	3048401	3051660	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	start_codon	3048401	3048403	.	+	0	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3048401	3048646	0.99	+	0	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3048401	3048646	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3048647	3048729	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3048730	3048874	0.85	+	0	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3048730	3048874	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3048875	3049033	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3049034	3050818	0.76	+	2	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3049034	3050818	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3050819	3050933	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3050934	3050996	0.87	+	2	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3050934	3050996	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3050997	3051081	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3051082	3051272	0.79	+	2	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3051082	3051272	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3051273	3051372	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3051373	3051452	0.82	+	0	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3051373	3051452	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	intron	3051453	3051560	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	CDS	3051561	3051660	0.86	+	1	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	exon	3051561	3051660	.	+	.	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
Phchi.S5	AUGUSTUS	stop_codon	3051661	3051663	.	+	0	transcript_id "Phchi.S5G040100.t2"; gene_id "Phchi.S5G040100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8359.t1 is derived from g5534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35483431	35488150	.	-	.	Phchi.S1G551800
Phchi.S1	AUGUSTUS	transcript	35483431	35488150	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	stop_codon	35483428	35483430	.	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35483431	35483553	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35483431	35483553	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35483554	35483628	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35483629	35483733	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35483629	35483733	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35483734	35483818	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35483819	35483878	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35483819	35483878	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35483879	35483985	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35483986	35484081	0.99	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35483986	35484081	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35484082	35484225	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35484226	35484282	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35484226	35484282	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35484283	35484406	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35484407	35484466	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35484407	35484466	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35484467	35484649	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35484650	35484782	1	-	1	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35484650	35484782	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35484783	35485007	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35485008	35485088	1	-	1	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35485008	35485088	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35485089	35485228	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35485229	35485305	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35485229	35485305	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35485306	35485426	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35485427	35485503	0.99	-	2	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35485427	35485503	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35485504	35485630	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35485631	35485694	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35485631	35485694	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35485695	35485818	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35485819	35485846	0.81	-	1	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35485819	35485846	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35485847	35485931	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35485932	35485975	0.85	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35485932	35485975	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35485976	35486174	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35486175	35486262	0.38	-	1	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35486175	35486262	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35486263	35486831	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35486832	35487010	0.54	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35486832	35487010	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35487011	35487106	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35487107	35487220	0.89	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35487107	35487220	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35487221	35487383	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35487384	35487468	0.53	-	1	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35487384	35487468	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35487469	35487565	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35487566	35487644	0.95	-	2	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35487566	35487644	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35487645	35487778	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35487779	35487888	1	-	1	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35487779	35487888	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	intron	35487889	35487986	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	CDS	35487987	35488150	1	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	exon	35487987	35488150	.	-	.	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
Phchi.S1	AUGUSTUS	start_codon	35488148	35488150	.	-	0	transcript_id "Phchi.S1G551800.t1"; gene_id "Phchi.S1G551800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15177.t1 is derived from g13645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17375390	17376628	.	+	.	Phchi.S3G249600
Phchi.S3	AUGUSTUS	transcript	17375390	17376628	.	+	.	transcript_id "Phchi.S3G249600.t1"; gene_id "Phchi.S3G249600"
Phchi.S3	AUGUSTUS	start_codon	17375390	17375392	.	+	0	transcript_id "Phchi.S3G249600.t1"; gene_id "Phchi.S3G249600"
Phchi.S3	AUGUSTUS	CDS	17375390	17376628	0.24	+	0	transcript_id "Phchi.S3G249600.t1"; gene_id "Phchi.S3G249600"
Phchi.S3	AUGUSTUS	exon	17375390	17376628	.	+	.	transcript_id "Phchi.S3G249600.t1"; gene_id "Phchi.S3G249600"
Phchi.S3	AUGUSTUS	stop_codon	17376629	17376631	.	+	0	transcript_id "Phchi.S3G249600.t1"; gene_id "Phchi.S3G249600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10602.t1 is derived from g14652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1157965	1158558	.	-	.	Phchi.S4G018400
Phchi.S4	AUGUSTUS	transcript	1157965	1158558	.	-	.	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	stop_codon	1157962	1157964	.	-	0	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	CDS	1157965	1158136	0.42	-	1	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	exon	1157965	1158136	.	-	.	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	intron	1158137	1158220	.	-	.	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	CDS	1158221	1158354	0.78	-	0	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	exon	1158221	1158354	.	-	.	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	intron	1158355	1158516	.	-	.	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	CDS	1158517	1158558	0.78	-	0	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	exon	1158517	1158558	.	-	.	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
Phchi.S4	AUGUSTUS	start_codon	1158556	1158558	.	-	0	transcript_id "Phchi.S4G018400.t1"; gene_id "Phchi.S4G018400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8504.t1 is derived from g5679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36359586	36361426	.	+	.	Phchi.S1G566300
Phchi.S1	AUGUSTUS	transcript	36359586	36361426	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	start_codon	36359586	36359588	.	+	0	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36359586	36359749	1	+	0	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36359586	36359749	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36359750	36359829	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36359830	36359920	1	+	1	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36359830	36359920	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36359921	36359999	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36360000	36360204	1	+	0	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36360000	36360204	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36360205	36360290	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36360291	36360328	1	+	2	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36360291	36360328	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36360329	36360447	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36360448	36360551	1	+	0	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36360448	36360551	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36360552	36360642	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36360643	36360719	1	+	1	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36360643	36360719	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36360720	36360814	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36360815	36360855	0.99	+	2	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36360815	36360855	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	intron	36360856	36360961	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	CDS	36360962	36361426	0.92	+	0	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	exon	36360962	36361426	.	+	.	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
Phchi.S1	AUGUSTUS	stop_codon	36361427	36361429	.	+	0	transcript_id "Phchi.S1G566300.t1"; gene_id "Phchi.S1G566300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5533.t1 is derived from g2703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17436588	17438395	.	-	.	Phchi.S1G269200
Phchi.S1	AUGUSTUS	transcript	17436588	17438395	.	-	.	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	stop_codon	17436585	17436587	.	-	0	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	CDS	17436588	17436968	1	-	0	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	exon	17436588	17436968	.	-	.	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	intron	17436969	17437095	.	-	.	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	CDS	17437096	17437327	0.99	-	1	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	exon	17437096	17437327	.	-	.	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	intron	17437328	17437427	.	-	.	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	CDS	17437428	17438395	0.99	-	0	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	exon	17437428	17438395	.	-	.	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	start_codon	17438393	17438395	.	-	0	transcript_id "Phchi.S1G269200.t1"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	transcript	17436926	17438395	.	-	.	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	stop_codon	17436923	17436925	.	-	0	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	CDS	17436926	17436937	0.41	-	0	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	exon	17436926	17436937	.	-	.	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	intron	17436938	17437095	.	-	.	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	CDS	17437096	17437327	0.75	-	1	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	exon	17437096	17437327	.	-	.	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	intron	17437328	17437427	.	-	.	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	CDS	17437428	17438395	0.99	-	0	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	exon	17437428	17438395	.	-	.	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
Phchi.S1	AUGUSTUS	start_codon	17438393	17438395	.	-	0	transcript_id "Phchi.S1G269200.t2"; gene_id "Phchi.S1G269200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9129.t1 is derived from g6304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40004222	40006516	.	+	.	Phchi.S1G628800
Phchi.S1	AUGUSTUS	transcript	40004222	40006516	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	start_codon	40004222	40004224	.	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40004222	40004290	0.43	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40004222	40004290	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40004291	40004379	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40004380	40004628	1	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40004380	40004628	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40004629	40004808	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40004809	40004850	1	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40004809	40004850	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40004851	40004945	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40004946	40005122	1	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40004946	40005122	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40005123	40005205	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40005206	40005356	1	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40005206	40005356	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40005357	40005465	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40005466	40005552	1	+	2	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40005466	40005552	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40005553	40005672	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40005673	40005797	1	+	2	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40005673	40005797	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40005798	40005928	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40005929	40006047	1	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40005929	40006047	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40006048	40006204	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40006205	40006228	0.95	+	1	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40006205	40006228	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40006229	40006316	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40006317	40006375	0.86	+	1	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40006317	40006375	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	intron	40006376	40006508	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	CDS	40006509	40006516	0.95	+	2	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	exon	40006509	40006516	.	+	.	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
Phchi.S1	AUGUSTUS	stop_codon	40006517	40006519	.	+	0	transcript_id "Phchi.S1G628800.t1"; gene_id "Phchi.S1G628800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13473.t1 is derived from g11940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7069656	7071427	.	-	.	Phchi.S3G079200
Phchi.S3	AUGUSTUS	transcript	7069656	7071427	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	stop_codon	7069653	7069655	.	-	0	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	CDS	7069656	7069946	0.65	-	0	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	exon	7069656	7069946	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	intron	7069947	7070026	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	CDS	7070027	7070599	0.5	-	0	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	exon	7070027	7070599	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	intron	7070600	7070676	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	CDS	7070677	7070799	0.84	-	0	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	exon	7070677	7070799	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	intron	7070800	7070932	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	CDS	7070933	7071427	0.48	-	0	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	exon	7070933	7071427	.	-	.	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
Phchi.S3	AUGUSTUS	start_codon	7071425	7071427	.	-	0	transcript_id "Phchi.S3G079200.t1"; gene_id "Phchi.S3G079200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14474.t1 is derived from g12942.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13035242	13038525	.	-	.	Phchi.S3G179300
Phchi.S3	AUGUSTUS	transcript	13035242	13036712	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	stop_codon	13035239	13035241	.	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035242	13035364	0.74	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035242	13035364	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035365	13035446	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035447	13035545	1	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035447	13035545	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035546	13035688	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035689	13035799	1	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035689	13035799	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035800	13035887	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035888	13035998	1	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035888	13035998	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035999	13036094	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036095	13036250	1	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036095	13036250	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036251	13036375	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036376	13036490	0.99	-	1	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036376	13036490	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036491	13036683	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036684	13036712	0.83	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036684	13036712	.	-	.	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	start_codon	13036710	13036712	.	-	0	transcript_id "Phchi.S3G179300.t1"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	transcript	13036865	13038525	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	stop_codon	13036862	13036864	.	-	0	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036865	13036882	1	-	0	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036865	13036882	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036883	13037015	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037016	13037101	1	-	2	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037016	13037101	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037102	13037211	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037212	13037248	1	-	0	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037212	13037248	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037249	13037380	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037381	13037457	1	-	2	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037381	13037457	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037458	13037535	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037536	13037609	1	-	1	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037536	13037609	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037610	13037691	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037692	13037812	0.96	-	2	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037692	13037812	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037813	13037917	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037918	13038008	0.74	-	0	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037918	13038008	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13038009	13038126	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13038127	13038525	0.45	-	0	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13038127	13038525	.	-	.	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	start_codon	13038523	13038525	.	-	0	transcript_id "Phchi.S3G179300.t2"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	transcript	13035242	13038525	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	stop_codon	13035239	13035241	.	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035242	13035364	0.76	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035242	13035364	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035365	13035446	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035447	13035545	1	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035447	13035545	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035546	13035688	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035689	13035799	1	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035689	13035799	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035800	13035887	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13035888	13035998	1	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13035888	13035998	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13035999	13036094	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036095	13036250	1	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036095	13036250	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036251	13036375	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036376	13036490	0.74	-	1	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036376	13036490	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036491	13036651	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036652	13036737	0.46	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036652	13036737	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036738	13036841	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13036842	13036901	0.36	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13036842	13036901	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13036902	13037015	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037016	13037101	0.5	-	2	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037016	13037101	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037102	13037211	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037212	13037248	0.96	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037212	13037248	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037249	13037380	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037381	13037457	1	-	2	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037381	13037457	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037458	13037535	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037536	13037609	1	-	1	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037536	13037609	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037610	13037691	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037692	13037812	0.98	-	2	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037692	13037812	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13037813	13037917	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13037918	13038008	0.82	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13037918	13038008	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	intron	13038009	13038126	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	CDS	13038127	13038525	0.4	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	exon	13038127	13038525	.	-	.	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
Phchi.S3	AUGUSTUS	start_codon	13038523	13038525	.	-	0	transcript_id "Phchi.S3G179300.t3"; gene_id "Phchi.S3G179300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1551.t1 is derived from g8470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1717153	1718378	.	-	.	Phchi.S5G016000
Phchi.S5	AUGUSTUS	transcript	1717153	1718378	.	-	.	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	stop_codon	1717150	1717152	.	-	0	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	CDS	1717153	1718235	0.79	-	0	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	exon	1717153	1718235	.	-	.	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	intron	1718236	1718357	.	-	.	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	CDS	1718358	1718378	0.84	-	0	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	exon	1718358	1718378	.	-	.	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
Phchi.S5	AUGUSTUS	start_codon	1718376	1718378	.	-	0	transcript_id "Phchi.S5G016000.t1"; gene_id "Phchi.S5G016000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14645.t1 is derived from g13113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13932093	13932732	.	-	.	Phchi.S3G196400
Phchi.S3	AUGUSTUS	transcript	13932093	13932732	.	-	.	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	stop_codon	13932090	13932092	.	-	0	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	CDS	13932093	13932326	0.98	-	0	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	exon	13932093	13932326	.	-	.	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	intron	13932327	13932405	.	-	.	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	CDS	13932406	13932471	1	-	0	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	exon	13932406	13932471	.	-	.	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	intron	13932472	13932555	.	-	.	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	CDS	13932556	13932732	1	-	0	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	exon	13932556	13932732	.	-	.	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
Phchi.S3	AUGUSTUS	start_codon	13932730	13932732	.	-	0	transcript_id "Phchi.S3G196400.t1"; gene_id "Phchi.S3G196400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9004.t1 is derived from g6179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39117412	39119135	.	+	.	Phchi.S1G616300
Phchi.S1	AUGUSTUS	transcript	39117412	39119135	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	start_codon	39117412	39117414	.	+	0	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	CDS	39117412	39117517	0.99	+	0	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	exon	39117412	39117517	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	intron	39117518	39117984	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	CDS	39117985	39118128	1	+	2	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	exon	39117985	39118128	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	intron	39118129	39118434	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	CDS	39118435	39118560	1	+	2	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	exon	39118435	39118560	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	intron	39118561	39118654	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	CDS	39118655	39118806	1	+	2	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	exon	39118655	39118806	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	intron	39118807	39118904	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	CDS	39118905	39119135	1	+	0	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	exon	39118905	39119135	.	+	.	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
Phchi.S1	AUGUSTUS	stop_codon	39119136	39119138	.	+	0	transcript_id "Phchi.S1G616300.t1"; gene_id "Phchi.S1G616300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13585.t1 is derived from g12052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7582881	7585316	.	+	.	Phchi.S3G090400
Phchi.S3	AUGUSTUS	transcript	7582881	7585316	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	start_codon	7582881	7582883	.	+	0	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	CDS	7582881	7582955	0.63	+	0	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	exon	7582881	7582955	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	intron	7582956	7583056	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	CDS	7583057	7583118	0.86	+	0	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	exon	7583057	7583118	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	intron	7583119	7583253	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	CDS	7583254	7584017	0.62	+	1	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	exon	7583254	7584017	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	intron	7584018	7584120	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	CDS	7584121	7585316	0.63	+	2	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	exon	7584121	7585316	.	+	.	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
Phchi.S3	AUGUSTUS	stop_codon	7585317	7585319	.	+	0	transcript_id "Phchi.S3G090400.t1"; gene_id "Phchi.S3G090400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16011.t1 is derived from g14462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C22	AUGUSTUS	gene	21995	22773	.	+	.	Phchi.C22G000100
Phchi.C22	AUGUSTUS	transcript	21995	22773	.	+	.	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	start_codon	21995	21997	.	+	0	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	CDS	21995	22338	0.61	+	0	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	exon	21995	22338	.	+	.	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	intron	22339	22514	.	+	.	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	CDS	22515	22773	0.6	+	1	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	exon	22515	22773	.	+	.	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
Phchi.C22	AUGUSTUS	stop_codon	22774	22776	.	+	0	transcript_id "Phchi.C22G000100.t1"; gene_id "Phchi.C22G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4384.t1 is derived from g1553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10172803	10174302	.	-	.	Phchi.S1G154300
Phchi.S1	AUGUSTUS	transcript	10172803	10174302	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	stop_codon	10172800	10172802	.	-	0	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	CDS	10172803	10172845	0.83	-	1	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	exon	10172803	10172845	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	intron	10172846	10172995	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	CDS	10172996	10173320	0.56	-	2	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	exon	10172996	10173320	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	intron	10173321	10173396	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	CDS	10173397	10173526	0.92	-	0	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	exon	10173397	10173526	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	intron	10173527	10173608	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	CDS	10173609	10173686	1	-	0	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	exon	10173609	10173686	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	intron	10173687	10173766	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	CDS	10173767	10173856	0.96	-	0	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	exon	10173767	10173856	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	intron	10173857	10173963	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	CDS	10173964	10174302	0.57	-	0	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	exon	10173964	10174302	.	-	.	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
Phchi.S1	AUGUSTUS	start_codon	10174300	10174302	.	-	0	transcript_id "Phchi.S1G154300.t1"; gene_id "Phchi.S1G154300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9466.t1 is derived from g6642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41585388	41587049	.	-	.	Phchi.S1G662500
Phchi.S1	AUGUSTUS	transcript	41585388	41587049	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	stop_codon	41585385	41585387	.	-	0	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41585388	41585564	1	-	0	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41585388	41585564	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41585565	41585637	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41585638	41585684	1	-	2	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41585638	41585684	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41585685	41585759	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41585760	41585844	1	-	0	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41585760	41585844	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41585845	41585914	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41585915	41585993	1	-	1	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41585915	41585993	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41585994	41586079	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41586080	41586233	1	-	2	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41586080	41586233	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41586234	41586316	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41586317	41586396	1	-	1	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41586317	41586396	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41586397	41586504	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41586505	41586736	1	-	2	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41586505	41586736	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	intron	41586737	41586925	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	CDS	41586926	41587049	0.99	-	0	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	exon	41586926	41587049	.	-	.	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
Phchi.S1	AUGUSTUS	start_codon	41587047	41587049	.	-	0	transcript_id "Phchi.S1G662500.t1"; gene_id "Phchi.S1G662500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2596.t1 is derived from g9516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7619252	7619740	.	+	.	Phchi.S5G120500
Phchi.S5	AUGUSTUS	transcript	7619252	7619740	.	+	.	transcript_id "Phchi.S5G120500.t1"; gene_id "Phchi.S5G120500"
Phchi.S5	AUGUSTUS	start_codon	7619252	7619254	.	+	0	transcript_id "Phchi.S5G120500.t1"; gene_id "Phchi.S5G120500"
Phchi.S5	AUGUSTUS	CDS	7619252	7619740	0.81	+	0	transcript_id "Phchi.S5G120500.t1"; gene_id "Phchi.S5G120500"
Phchi.S5	AUGUSTUS	exon	7619252	7619740	.	+	.	transcript_id "Phchi.S5G120500.t1"; gene_id "Phchi.S5G120500"
Phchi.S5	AUGUSTUS	stop_codon	7619741	7619743	.	+	0	transcript_id "Phchi.S5G120500.t1"; gene_id "Phchi.S5G120500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8.t1 is derived from g9781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C156	AUGUSTUS	gene	20323	20613	.	+	.	Phchi.C156G000100
Phchi.C156	AUGUSTUS	transcript	20323	20613	.	+	.	transcript_id "Phchi.C156G000100.t1"; gene_id "Phchi.C156G000100"
Phchi.C156	AUGUSTUS	start_codon	20323	20325	.	+	0	transcript_id "Phchi.C156G000100.t1"; gene_id "Phchi.C156G000100"
Phchi.C156	AUGUSTUS	CDS	20323	20613	0.63	+	0	transcript_id "Phchi.C156G000100.t1"; gene_id "Phchi.C156G000100"
Phchi.C156	AUGUSTUS	exon	20323	20613	.	+	.	transcript_id "Phchi.C156G000100.t1"; gene_id "Phchi.C156G000100"
Phchi.C156	AUGUSTUS	stop_codon	20614	20616	.	+	0	transcript_id "Phchi.C156G000100.t1"; gene_id "Phchi.C156G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5166.t1 is derived from g2336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15267133	15268701	.	+	.	Phchi.S1G232500
Phchi.S1	AUGUSTUS	transcript	15267133	15268701	.	+	.	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	start_codon	15267133	15267135	.	+	0	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	CDS	15267133	15267614	0.73	+	0	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	exon	15267133	15267614	.	+	.	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	intron	15267615	15267750	.	+	.	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	CDS	15267751	15267774	0.93	+	1	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	exon	15267751	15267774	.	+	.	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	intron	15267775	15267881	.	+	.	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	CDS	15267882	15268701	1	+	1	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	exon	15267882	15268701	.	+	.	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
Phchi.S1	AUGUSTUS	stop_codon	15268702	15268704	.	+	0	transcript_id "Phchi.S1G232500.t1"; gene_id "Phchi.S1G232500"
# This transcript jg12400.t2 is derived from g8077.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12401.t1 is derived from g8078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17630087	17632297	.	+	.	Phchi.S2G048100
Phchi.S2	AUGUSTUS	transcript	17630087	17632297	.	+	.	transcript_id "Phchi.S2G048100.t1"; gene_id "Phchi.S2G048100"
Phchi.S2	AUGUSTUS	start_codon	17630087	17630089	.	+	0	transcript_id "Phchi.S2G048100.t1"; gene_id "Phchi.S2G048100"
Phchi.S2	AUGUSTUS	CDS	17630087	17632297	0.99	+	0	transcript_id "Phchi.S2G048100.t1"; gene_id "Phchi.S2G048100"
Phchi.S2	AUGUSTUS	exon	17630087	17632297	.	+	.	transcript_id "Phchi.S2G048100.t1"; gene_id "Phchi.S2G048100"
Phchi.S2	AUGUSTUS	stop_codon	17632298	17632300	.	+	0	transcript_id "Phchi.S2G048100.t1"; gene_id "Phchi.S2G048100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10809.t1 is derived from g14859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2201929	2204196	.	-	.	Phchi.S4G039100
Phchi.S4	AUGUSTUS	transcript	2201929	2204196	.	-	.	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	stop_codon	2201926	2201928	.	-	0	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	CDS	2201929	2202608	0.84	-	2	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	exon	2201929	2202608	.	-	.	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	intron	2202609	2202697	.	-	.	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	CDS	2202698	2203121	0.35	-	0	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	exon	2202698	2203121	.	-	.	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	intron	2203122	2203428	.	-	.	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	CDS	2203429	2204196	0.61	-	0	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	exon	2203429	2204196	.	-	.	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	start_codon	2204194	2204196	.	-	0	transcript_id "Phchi.S4G039100.t1"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	transcript	2203632	2204196	.	-	.	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	stop_codon	2203629	2203631	.	-	0	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	CDS	2203632	2203648	0.42	-	2	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	exon	2203632	2203648	.	-	.	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	intron	2203649	2203721	.	-	.	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	CDS	2203722	2204196	0.37	-	0	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	exon	2203722	2204196	.	-	.	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
Phchi.S4	AUGUSTUS	start_codon	2204194	2204196	.	-	0	transcript_id "Phchi.S4G039100.t2"; gene_id "Phchi.S4G039100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12775.t1 is derived from g11240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1986530	1987072	.	-	.	Phchi.S3G009400
Phchi.S3	AUGUSTUS	transcript	1986530	1987072	.	-	.	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	stop_codon	1986527	1986529	.	-	0	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	CDS	1986530	1986588	0.98	-	2	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	exon	1986530	1986588	.	-	.	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	intron	1986589	1986726	.	-	.	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	CDS	1986727	1987072	0.94	-	0	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	exon	1986727	1987072	.	-	.	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
Phchi.S3	AUGUSTUS	start_codon	1987070	1987072	.	-	0	transcript_id "Phchi.S3G009400.t1"; gene_id "Phchi.S3G009400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7622.t1 is derived from g4796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30302693	30303301	.	-	.	Phchi.S1G478100
Phchi.S1	AUGUSTUS	transcript	30302693	30303301	.	-	.	transcript_id "Phchi.S1G478100.t1"; gene_id "Phchi.S1G478100"
Phchi.S1	AUGUSTUS	stop_codon	30302690	30302692	.	-	0	transcript_id "Phchi.S1G478100.t1"; gene_id "Phchi.S1G478100"
Phchi.S1	AUGUSTUS	CDS	30302693	30303301	0.69	-	0	transcript_id "Phchi.S1G478100.t1"; gene_id "Phchi.S1G478100"
Phchi.S1	AUGUSTUS	exon	30302693	30303301	.	-	.	transcript_id "Phchi.S1G478100.t1"; gene_id "Phchi.S1G478100"
Phchi.S1	AUGUSTUS	start_codon	30303299	30303301	.	-	0	transcript_id "Phchi.S1G478100.t1"; gene_id "Phchi.S1G478100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11250.t1 is derived from g15300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5005743	5007432	.	+	.	Phchi.S4G083200
Phchi.S4	AUGUSTUS	transcript	5005743	5007432	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	start_codon	5005743	5005745	.	+	0	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	CDS	5005743	5006011	1	+	0	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	exon	5005743	5006011	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	intron	5006012	5006138	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	CDS	5006139	5006304	0.93	+	1	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	exon	5006139	5006304	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	intron	5006305	5006411	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	CDS	5006412	5006491	0.91	+	0	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	exon	5006412	5006491	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	intron	5006492	5006589	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	CDS	5006590	5007023	1	+	1	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	exon	5006590	5007023	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	intron	5007024	5007163	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	CDS	5007164	5007432	1	+	2	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	exon	5007164	5007432	.	+	.	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
Phchi.S4	AUGUSTUS	stop_codon	5007433	5007435	.	+	0	transcript_id "Phchi.S4G083200.t1"; gene_id "Phchi.S4G083200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4992.t1 is derived from g2162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13921792	13928403	.	-	.	Phchi.S1G215100
Phchi.S1	AUGUSTUS	transcript	13921792	13928403	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	stop_codon	13921789	13921791	.	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13921792	13921815	0.41	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13921792	13921815	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13921816	13921955	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13921956	13921984	0.4	-	2	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13921956	13921984	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13921985	13922125	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13922126	13922207	0.41	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13922126	13922207	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13922208	13922376	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13922377	13922434	1	-	1	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13922377	13922434	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13922435	13922516	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13922517	13922573	0.76	-	1	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13922517	13922573	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13922574	13922679	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13922680	13922789	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13922680	13922789	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13922790	13922916	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13922917	13923126	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13922917	13923126	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13923127	13923293	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13923294	13923338	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13923294	13923338	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13923339	13923434	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13923435	13923593	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13923435	13923593	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13923594	13923691	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13923692	13923796	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13923692	13923796	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13923797	13923884	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13923885	13924067	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13923885	13924067	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13924068	13924277	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13924278	13924370	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13924278	13924370	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13924371	13924494	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13924495	13924629	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13924495	13924629	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13924630	13924706	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13924707	13924781	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13924707	13924781	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13924782	13925062	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13925063	13925162	1	-	1	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13925063	13925162	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13925163	13925318	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13925319	13925367	0.85	-	2	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13925319	13925367	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13925368	13925445	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13925446	13925491	0.85	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13925446	13925491	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13925492	13925580	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13925581	13925728	1	-	1	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13925581	13925728	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13925729	13925865	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13925866	13926038	0.76	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13925866	13926038	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13926039	13926130	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13926131	13926261	0.43	-	2	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13926131	13926261	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13926262	13926344	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13926345	13926411	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13926345	13926411	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13926412	13926527	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13926528	13926749	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13926528	13926749	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13926750	13926900	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13926901	13927042	1	-	1	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13926901	13927042	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13927043	13927339	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13927340	13927401	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13927340	13927401	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13927402	13927480	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13927481	13927553	1	-	1	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13927481	13927553	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13927554	13927705	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13927706	13927815	1	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13927706	13927815	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13927816	13927900	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13927901	13927953	0.91	-	2	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13927901	13927953	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13927954	13928033	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13928034	13928060	0.91	-	2	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13928034	13928060	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	intron	13928061	13928288	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	CDS	13928289	13928403	0.91	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	exon	13928289	13928403	.	-	.	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
Phchi.S1	AUGUSTUS	start_codon	13928401	13928403	.	-	0	transcript_id "Phchi.S1G215100.t1"; gene_id "Phchi.S1G215100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8088.t1 is derived from g5263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32891743	32892591	.	-	.	Phchi.S1G524700
Phchi.S1	AUGUSTUS	transcript	32891743	32892591	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	stop_codon	32891740	32891742	.	-	0	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	CDS	32891743	32891823	0.98	-	0	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	exon	32891743	32891823	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	intron	32891824	32891914	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	CDS	32891915	32891988	1	-	2	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	exon	32891915	32891988	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	intron	32891989	32892183	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	CDS	32892184	32892230	0.92	-	1	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	exon	32892184	32892230	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	intron	32892231	32892346	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	CDS	32892347	32892436	0.92	-	1	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	exon	32892347	32892436	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	intron	32892437	32892583	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	CDS	32892584	32892591	0.93	-	0	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	exon	32892584	32892591	.	-	.	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
Phchi.S1	AUGUSTUS	start_codon	32892589	32892591	.	-	0	transcript_id "Phchi.S1G524700.t1"; gene_id "Phchi.S1G524700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14922.t1 is derived from g13390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15515040	15515999	.	+	.	Phchi.S3G224100
Phchi.S3	AUGUSTUS	transcript	15515040	15515999	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	start_codon	15515040	15515042	.	+	0	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	CDS	15515040	15515358	0.75	+	0	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	exon	15515040	15515358	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	intron	15515359	15515482	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	CDS	15515483	15515619	1	+	2	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	exon	15515483	15515619	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	intron	15515620	15515732	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	CDS	15515733	15515805	1	+	0	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	exon	15515733	15515805	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	intron	15515806	15515892	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	CDS	15515893	15515999	0.97	+	2	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	exon	15515893	15515999	.	+	.	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
Phchi.S3	AUGUSTUS	stop_codon	15516000	15516002	.	+	0	transcript_id "Phchi.S3G224100.t1"; gene_id "Phchi.S3G224100"
# This transcript jg977.t2 is derived from g10760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg978.t1 is derived from g10761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6760445	6763290	.	+	.	Phchi.S6G093700
Phchi.S6	AUGUSTUS	transcript	6760445	6763290	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	start_codon	6760445	6760447	.	+	0	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	CDS	6760445	6760502	0.93	+	0	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	exon	6760445	6760502	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	intron	6760503	6760604	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	CDS	6760605	6761612	0.62	+	2	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	exon	6760605	6761612	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	intron	6761613	6761710	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	CDS	6761711	6763056	0.69	+	2	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	exon	6761711	6763056	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	intron	6763057	6763140	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	CDS	6763141	6763290	1	+	0	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	exon	6763141	6763290	.	+	.	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
Phchi.S6	AUGUSTUS	stop_codon	6763291	6763293	.	+	0	transcript_id "Phchi.S6G093700.t1"; gene_id "Phchi.S6G093700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15139.t1 is derived from g13607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17243021	17245272	.	+	.	Phchi.S3G245800
Phchi.S3	AUGUSTUS	transcript	17243021	17245272	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	start_codon	17243021	17243023	.	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17243021	17243107	0.68	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17243021	17243107	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17243108	17243217	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17243218	17243317	0.94	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17243218	17243317	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17243318	17243392	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17243393	17243527	1	+	2	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17243393	17243527	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17243528	17243602	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17243603	17243661	1	+	2	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17243603	17243661	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17243662	17243747	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17243748	17243815	1	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17243748	17243815	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17243816	17243918	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17243919	17243970	1	+	1	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17243919	17243970	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17243971	17244074	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17244075	17244278	1	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17244075	17244278	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17244279	17244360	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17244361	17244966	1	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17244361	17244966	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	intron	17244967	17245062	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	CDS	17245063	17245272	1	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	exon	17245063	17245272	.	+	.	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
Phchi.S3	AUGUSTUS	stop_codon	17245273	17245275	.	+	0	transcript_id "Phchi.S3G245800.t1"; gene_id "Phchi.S3G245800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1212.t1 is derived from g10995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8432711	8433181	.	-	.	Phchi.S6G117100
Phchi.S6	AUGUSTUS	transcript	8432711	8433181	.	-	.	transcript_id "Phchi.S6G117100.t1"; gene_id "Phchi.S6G117100"
Phchi.S6	AUGUSTUS	stop_codon	8432708	8432710	.	-	0	transcript_id "Phchi.S6G117100.t1"; gene_id "Phchi.S6G117100"
Phchi.S6	AUGUSTUS	CDS	8432711	8433181	0.97	-	0	transcript_id "Phchi.S6G117100.t1"; gene_id "Phchi.S6G117100"
Phchi.S6	AUGUSTUS	exon	8432711	8433181	.	-	.	transcript_id "Phchi.S6G117100.t1"; gene_id "Phchi.S6G117100"
Phchi.S6	AUGUSTUS	start_codon	8433179	8433181	.	-	0	transcript_id "Phchi.S6G117100.t1"; gene_id "Phchi.S6G117100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11704.t1 is derived from g15755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7768117	7769513	.	+	.	Phchi.S4G128600
Phchi.S4	AUGUSTUS	transcript	7768117	7769513	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	start_codon	7768117	7768119	.	+	0	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7768117	7768494	0.82	+	0	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7768117	7768494	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7768495	7768663	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7768664	7768944	1	+	0	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7768664	7768944	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7768945	7769059	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769060	7769131	1	+	1	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769060	7769131	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7769132	7769318	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769319	7769408	1	+	1	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769319	7769408	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7769409	7769500	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769501	7769513	1	+	1	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769501	7769513	.	+	.	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	stop_codon	7769514	7769516	.	+	0	transcript_id "Phchi.S4G128600.t1"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	transcript	7768117	7769513	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	start_codon	7768117	7768119	.	+	0	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7768117	7768494	0.82	+	0	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7768117	7768494	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7768495	7768663	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7768664	7768944	0.98	+	0	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7768664	7768944	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7768945	7769059	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769060	7769131	1	+	1	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769060	7769131	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7769132	7769211	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769212	7769261	0.64	+	1	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769212	7769261	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7769262	7769353	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769354	7769408	0.76	+	2	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769354	7769408	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	intron	7769409	7769500	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	CDS	7769501	7769513	1	+	1	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	exon	7769501	7769513	.	+	.	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
Phchi.S4	AUGUSTUS	stop_codon	7769514	7769516	.	+	0	transcript_id "Phchi.S4G128600.t2"; gene_id "Phchi.S4G128600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1978.t1 is derived from g8898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4172739	4174659	.	-	.	Phchi.S5G058700
Phchi.S5	AUGUSTUS	transcript	4172739	4174659	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	stop_codon	4172736	4172738	.	-	0	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	CDS	4172739	4173528	0.58	-	1	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	exon	4172739	4173528	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	intron	4173529	4173610	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	CDS	4173611	4173999	0.22	-	0	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	exon	4173611	4173999	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	intron	4174000	4174147	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	CDS	4174148	4174324	0.3	-	0	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	exon	4174148	4174324	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	intron	4174325	4174398	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	CDS	4174399	4174659	0.99	-	0	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	exon	4174399	4174659	.	-	.	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
Phchi.S5	AUGUSTUS	start_codon	4174657	4174659	.	-	0	transcript_id "Phchi.S5G058700.t1"; gene_id "Phchi.S5G058700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5791.t1 is derived from g2961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18968789	18970342	.	+	.	Phchi.S1G295000
Phchi.S1	AUGUSTUS	transcript	18968789	18970342	.	+	.	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	start_codon	18968789	18968791	.	+	0	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	CDS	18968789	18968910	0.93	+	0	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	exon	18968789	18968910	.	+	.	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	intron	18968911	18969026	.	+	.	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	CDS	18969027	18969154	0.74	+	1	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	exon	18969027	18969154	.	+	.	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	intron	18969155	18969305	.	+	.	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	CDS	18969306	18970342	0.7	+	2	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	exon	18969306	18970342	.	+	.	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
Phchi.S1	AUGUSTUS	stop_codon	18970343	18970345	.	+	0	transcript_id "Phchi.S1G295000.t1"; gene_id "Phchi.S1G295000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8294.t1 is derived from g5469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35131495	35133402	.	+	.	Phchi.S1G545300
Phchi.S1	AUGUSTUS	transcript	35131495	35133402	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	start_codon	35131495	35131497	.	+	0	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	CDS	35131495	35131979	0.78	+	0	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	exon	35131495	35131979	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	intron	35131980	35132073	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	CDS	35132074	35132323	1	+	1	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	exon	35132074	35132323	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	intron	35132324	35132435	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	CDS	35132436	35132831	1	+	0	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	exon	35132436	35132831	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	intron	35132832	35132914	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	CDS	35132915	35133007	0.94	+	0	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	exon	35132915	35133007	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	intron	35133008	35133141	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	CDS	35133142	35133402	0.92	+	0	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	exon	35133142	35133402	.	+	.	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
Phchi.S1	AUGUSTUS	stop_codon	35133403	35133405	.	+	0	transcript_id "Phchi.S1G545300.t1"; gene_id "Phchi.S1G545300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5469.t1 is derived from g2639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16994047	16995733	.	+	.	Phchi.S1G262800
Phchi.S1	AUGUSTUS	transcript	16994047	16995733	.	+	.	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	start_codon	16994047	16994049	.	+	0	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	CDS	16994047	16994170	0.93	+	0	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	exon	16994047	16994170	.	+	.	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	intron	16994171	16994556	.	+	.	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	CDS	16994557	16995553	0.27	+	2	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	exon	16994557	16995553	.	+	.	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	intron	16995554	16995681	.	+	.	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	CDS	16995682	16995733	0.14	+	1	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	exon	16995682	16995733	.	+	.	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
Phchi.S1	AUGUSTUS	stop_codon	16995734	16995736	.	+	0	transcript_id "Phchi.S1G262800.t1"; gene_id "Phchi.S1G262800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6253.t1 is derived from g3425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21882015	21885047	.	+	.	Phchi.S1G341200
Phchi.S1	AUGUSTUS	transcript	21882015	21885047	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	start_codon	21882015	21882017	.	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21882015	21882082	0.31	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21882015	21882082	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21882083	21882170	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21882171	21882364	1	+	1	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21882171	21882364	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21882365	21882464	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21882465	21882547	1	+	2	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21882465	21882547	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21882548	21882635	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21882636	21882737	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21882636	21882737	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21882738	21882825	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21882826	21882955	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21882826	21882955	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21882956	21883104	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21883105	21883163	1	+	2	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21883105	21883163	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21883164	21883269	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21883270	21883362	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21883270	21883362	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21883363	21883444	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21883445	21883512	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21883445	21883512	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21883513	21883618	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21883619	21883715	0.99	+	1	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21883619	21883715	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21883716	21883828	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21883829	21883903	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21883829	21883903	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21883904	21884035	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21884036	21884134	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21884036	21884134	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21884135	21884313	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21884314	21884466	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21884314	21884466	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21884467	21884559	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21884560	21884589	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21884560	21884589	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21884590	21884669	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21884670	21884732	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21884670	21884732	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21884733	21884821	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21884822	21884899	1	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21884822	21884899	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	intron	21884900	21884981	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	CDS	21884982	21885047	0.97	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	exon	21884982	21885047	.	+	.	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
Phchi.S1	AUGUSTUS	stop_codon	21885048	21885050	.	+	0	transcript_id "Phchi.S1G341200.t1"; gene_id "Phchi.S1G341200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg548.t1 is derived from g10330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4010275	4011127	.	-	.	Phchi.S6G050700
Phchi.S6	AUGUSTUS	transcript	4010275	4011127	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	stop_codon	4010272	4010274	.	-	0	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	CDS	4010275	4010430	1	-	0	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	exon	4010275	4010430	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	intron	4010431	4010540	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	CDS	4010541	4010701	1	-	2	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	exon	4010541	4010701	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	intron	4010702	4010836	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	CDS	4010837	4010935	1	-	2	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	exon	4010837	4010935	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	intron	4010936	4011033	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	CDS	4011034	4011127	1	-	0	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	exon	4011034	4011127	.	-	.	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
Phchi.S6	AUGUSTUS	start_codon	4011125	4011127	.	-	0	transcript_id "Phchi.S6G050700.t1"; gene_id "Phchi.S6G050700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9430.t1 is derived from g6606.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41431239	41432270	.	+	.	Phchi.S1G658900
Phchi.S1	AUGUSTUS	transcript	41431239	41431999	.	+	.	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	start_codon	41431239	41431241	.	+	0	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	CDS	41431239	41431901	0.8	+	0	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	exon	41431239	41431901	.	+	.	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	intron	41431902	41431987	.	+	.	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	CDS	41431988	41431999	0.83	+	0	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	exon	41431988	41431999	.	+	.	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	stop_codon	41432000	41432002	.	+	0	transcript_id "Phchi.S1G658900.t1"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	transcript	41431239	41432270	.	+	.	transcript_id "Phchi.S1G658900.t2"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	start_codon	41431239	41431241	.	+	0	transcript_id "Phchi.S1G658900.t2"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	CDS	41431239	41432270	1	+	0	transcript_id "Phchi.S1G658900.t2"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	exon	41431239	41432270	.	+	.	transcript_id "Phchi.S1G658900.t2"; gene_id "Phchi.S1G658900"
Phchi.S1	AUGUSTUS	stop_codon	41432271	41432273	.	+	0	transcript_id "Phchi.S1G658900.t2"; gene_id "Phchi.S1G658900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12850.t1 is derived from g11315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2698869	2701761	.	-	.	Phchi.S3G016900
Phchi.S3	AUGUSTUS	transcript	2698869	2701761	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	stop_codon	2698866	2698868	.	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2698869	2698936	1	-	2	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2698869	2698936	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2698937	2699026	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2699027	2699267	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2699027	2699267	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2699268	2699391	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2699392	2699454	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2699392	2699454	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2699455	2699574	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2699575	2699640	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2699575	2699640	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2699641	2699733	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2699734	2699817	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2699734	2699817	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2699818	2699959	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2699960	2700165	1	-	2	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2699960	2700165	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2700166	2700275	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2700276	2700366	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2700276	2700366	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2700367	2700506	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2700507	2700611	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2700507	2700611	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2700612	2700801	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2700802	2700876	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2700802	2700876	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2700877	2701016	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2701017	2701109	1	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2701017	2701109	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2701110	2701209	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2701210	2701285	1	-	1	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2701210	2701285	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	intron	2701286	2701588	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	CDS	2701589	2701761	0.91	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	exon	2701589	2701761	.	-	.	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
Phchi.S3	AUGUSTUS	start_codon	2701759	2701761	.	-	0	transcript_id "Phchi.S3G016900.t1"; gene_id "Phchi.S3G016900"
# This transcript jg13411.t2 is derived from g11877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13412.t1 is derived from g11878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6589855	6590574	.	+	.	Phchi.S3G073100
Phchi.S3	AUGUSTUS	transcript	6589855	6590574	.	+	.	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	start_codon	6589855	6589857	.	+	0	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	CDS	6589855	6590082	0.84	+	0	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	exon	6589855	6590082	.	+	.	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	intron	6590083	6590208	.	+	.	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	CDS	6590209	6590574	1	+	0	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	exon	6590209	6590574	.	+	.	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
Phchi.S3	AUGUSTUS	stop_codon	6590575	6590577	.	+	0	transcript_id "Phchi.S3G073100.t1"; gene_id "Phchi.S3G073100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6523.t1 is derived from g3695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23475509	23477104	.	-	.	Phchi.S1G368200
Phchi.S1	AUGUSTUS	transcript	23475509	23477104	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	stop_codon	23475506	23475508	.	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23475509	23475625	0.7	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23475509	23475625	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23475626	23475722	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23475723	23475824	1	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23475723	23475824	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23475825	23475961	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23475962	23476033	1	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23475962	23476033	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23476034	23476104	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23476105	23476147	1	-	1	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23476105	23476147	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23476148	23476244	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23476245	23476288	1	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23476245	23476288	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23476289	23476379	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23476380	23476439	1	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23476380	23476439	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23476440	23476528	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23476529	23476609	1	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23476529	23476609	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	intron	23476610	23476705	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	CDS	23476706	23477104	0.84	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	exon	23476706	23477104	.	-	.	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
Phchi.S1	AUGUSTUS	start_codon	23477102	23477104	.	-	0	transcript_id "Phchi.S1G368200.t1"; gene_id "Phchi.S1G368200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1088.t1 is derived from g10871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7527553	7528505	.	-	.	Phchi.S6G104700
Phchi.S6	AUGUSTUS	transcript	7527553	7528505	.	-	.	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	stop_codon	7527550	7527552	.	-	0	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	CDS	7527553	7527708	0.23	-	0	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	exon	7527553	7527708	.	-	.	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	intron	7527709	7527793	.	-	.	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	CDS	7527794	7528015	0.24	-	0	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	exon	7527794	7528015	.	-	.	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	intron	7528016	7528127	.	-	.	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	CDS	7528128	7528505	1	-	0	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	exon	7528128	7528505	.	-	.	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
Phchi.S6	AUGUSTUS	start_codon	7528503	7528505	.	-	0	transcript_id "Phchi.S6G104700.t1"; gene_id "Phchi.S6G104700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8482.t1 is derived from g5657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36144046	36144619	.	-	.	Phchi.S1G564100
Phchi.S1	AUGUSTUS	transcript	36144046	36144619	.	-	.	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	stop_codon	36144043	36144045	.	-	0	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	CDS	36144046	36144321	0.51	-	0	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	exon	36144046	36144321	.	-	.	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	intron	36144322	36144478	.	-	.	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	CDS	36144479	36144619	0.73	-	0	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	exon	36144479	36144619	.	-	.	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
Phchi.S1	AUGUSTUS	start_codon	36144617	36144619	.	-	0	transcript_id "Phchi.S1G564100.t1"; gene_id "Phchi.S1G564100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2660.t1 is derived from g9580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8096321	8096995	.	+	.	Phchi.S5G126900
Phchi.S5	AUGUSTUS	transcript	8096321	8096995	.	+	.	transcript_id "Phchi.S5G126900.t1"; gene_id "Phchi.S5G126900"
Phchi.S5	AUGUSTUS	start_codon	8096321	8096323	.	+	0	transcript_id "Phchi.S5G126900.t1"; gene_id "Phchi.S5G126900"
Phchi.S5	AUGUSTUS	CDS	8096321	8096995	0.79	+	0	transcript_id "Phchi.S5G126900.t1"; gene_id "Phchi.S5G126900"
Phchi.S5	AUGUSTUS	exon	8096321	8096995	.	+	.	transcript_id "Phchi.S5G126900.t1"; gene_id "Phchi.S5G126900"
Phchi.S5	AUGUSTUS	stop_codon	8096996	8096998	.	+	0	transcript_id "Phchi.S5G126900.t1"; gene_id "Phchi.S5G126900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg507.t1 is derived from g10289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3513832	3514288	.	+	.	Phchi.S6G046600
Phchi.S6	AUGUSTUS	transcript	3513832	3514288	.	+	.	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	start_codon	3513832	3513834	.	+	0	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	CDS	3513832	3513978	0.87	+	0	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	exon	3513832	3513978	.	+	.	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	intron	3513979	3514117	.	+	.	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	CDS	3514118	3514288	0.93	+	0	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	exon	3514118	3514288	.	+	.	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
Phchi.S6	AUGUSTUS	stop_codon	3514289	3514291	.	+	0	transcript_id "Phchi.S6G046600.t1"; gene_id "Phchi.S6G046600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5676.t1 is derived from g2846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18253706	18254446	.	+	.	Phchi.S1G283500
Phchi.S1	AUGUSTUS	transcript	18253706	18254446	.	+	.	transcript_id "Phchi.S1G283500.t1"; gene_id "Phchi.S1G283500"
Phchi.S1	AUGUSTUS	start_codon	18253706	18253708	.	+	0	transcript_id "Phchi.S1G283500.t1"; gene_id "Phchi.S1G283500"
Phchi.S1	AUGUSTUS	CDS	18253706	18254446	1	+	0	transcript_id "Phchi.S1G283500.t1"; gene_id "Phchi.S1G283500"
Phchi.S1	AUGUSTUS	exon	18253706	18254446	.	+	.	transcript_id "Phchi.S1G283500.t1"; gene_id "Phchi.S1G283500"
Phchi.S1	AUGUSTUS	stop_codon	18254447	18254449	.	+	0	transcript_id "Phchi.S1G283500.t1"; gene_id "Phchi.S1G283500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15627.t1 is derived from g14096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20369357	20371102	.	-	.	Phchi.S3G294600
Phchi.S3	AUGUSTUS	transcript	20369357	20371102	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	stop_codon	20369354	20369356	.	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20369357	20369409	0.99	-	2	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20369357	20369409	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20369410	20369607	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20369608	20369671	1	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20369608	20369671	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20369672	20369762	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20369763	20369829	1	-	1	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20369763	20369829	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20369830	20369969	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20369970	20370026	1	-	1	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20369970	20370026	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20370027	20370251	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20370252	20370328	1	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20370252	20370328	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20370329	20370482	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20370483	20370542	1	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20370483	20370542	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20370543	20370717	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20370718	20370849	1	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20370718	20370849	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	intron	20370850	20371030	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	CDS	20371031	20371102	0.54	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	exon	20371031	20371102	.	-	.	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
Phchi.S3	AUGUSTUS	start_codon	20371100	20371102	.	-	0	transcript_id "Phchi.S3G294600.t1"; gene_id "Phchi.S3G294600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12483.t1 is derived from g8160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28714867	28715112	.	-	.	Phchi.S2G056300
Phchi.S2	AUGUSTUS	transcript	28714867	28715112	.	-	.	transcript_id "Phchi.S2G056300.t1"; gene_id "Phchi.S2G056300"
Phchi.S2	AUGUSTUS	stop_codon	28714864	28714866	.	-	0	transcript_id "Phchi.S2G056300.t1"; gene_id "Phchi.S2G056300"
Phchi.S2	AUGUSTUS	CDS	28714867	28715112	0.67	-	0	transcript_id "Phchi.S2G056300.t1"; gene_id "Phchi.S2G056300"
Phchi.S2	AUGUSTUS	exon	28714867	28715112	.	-	.	transcript_id "Phchi.S2G056300.t1"; gene_id "Phchi.S2G056300"
Phchi.S2	AUGUSTUS	start_codon	28715110	28715112	.	-	0	transcript_id "Phchi.S2G056300.t1"; gene_id "Phchi.S2G056300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13957.t1 is derived from g12424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9916367	9917277	.	+	.	Phchi.S3G127600
Phchi.S3	AUGUSTUS	transcript	9916367	9917277	.	+	.	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	start_codon	9916367	9916369	.	+	0	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	CDS	9916367	9916638	0.65	+	0	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	exon	9916367	9916638	.	+	.	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	intron	9916639	9916727	.	+	.	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	CDS	9916728	9917277	0.98	+	1	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	exon	9916728	9917277	.	+	.	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
Phchi.S3	AUGUSTUS	stop_codon	9917278	9917280	.	+	0	transcript_id "Phchi.S3G127600.t1"; gene_id "Phchi.S3G127600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4134.t1 is derived from g1303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8448364	8450675	.	+	.	Phchi.S1G129300
Phchi.S1	AUGUSTUS	transcript	8448364	8450675	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	start_codon	8448364	8448366	.	+	0	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8448364	8448702	0.72	+	0	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8448364	8448702	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8448703	8448795	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8448796	8449012	0.72	+	0	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8448796	8449012	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449013	8449086	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8449087	8449440	1	+	2	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8449087	8449440	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449441	8449538	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8449539	8449625	1	+	2	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8449539	8449625	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449626	8449739	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8449740	8449932	0.99	+	2	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8449740	8449932	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449933	8450054	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8450055	8450187	1	+	1	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8450055	8450187	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8450188	8450315	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8450316	8450675	0.99	+	0	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8450316	8450675	.	+	.	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	stop_codon	8450676	8450678	.	+	0	transcript_id "Phchi.S1G129300.t1"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	transcript	8448364	8450675	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	start_codon	8448364	8448366	.	+	0	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8448364	8448702	0.71	+	0	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8448364	8448702	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8448703	8448795	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8448796	8448988	0.71	+	0	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8448796	8448988	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8448989	8449086	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8449087	8449440	1	+	2	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8449087	8449440	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449441	8449538	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8449539	8449625	1	+	2	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8449539	8449625	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449626	8449739	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8449740	8449932	1	+	2	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8449740	8449932	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8449933	8450054	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8450055	8450187	1	+	1	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8450055	8450187	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	intron	8450188	8450315	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	CDS	8450316	8450675	0.99	+	0	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	exon	8450316	8450675	.	+	.	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
Phchi.S1	AUGUSTUS	stop_codon	8450676	8450678	.	+	0	transcript_id "Phchi.S1G129300.t2"; gene_id "Phchi.S1G129300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg426.t1 is derived from g10208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3033517	3035628	.	+	.	Phchi.S6G038500
Phchi.S6	AUGUSTUS	transcript	3033517	3035628	.	+	.	transcript_id "Phchi.S6G038500.t1"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	start_codon	3033517	3033519	.	+	0	transcript_id "Phchi.S6G038500.t1"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	CDS	3033517	3035628	0.96	+	0	transcript_id "Phchi.S6G038500.t1"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	exon	3033517	3035628	.	+	.	transcript_id "Phchi.S6G038500.t1"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	stop_codon	3035629	3035631	.	+	0	transcript_id "Phchi.S6G038500.t1"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	transcript	3033973	3035628	.	+	.	transcript_id "Phchi.S6G038500.t2"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	start_codon	3033973	3033975	.	+	0	transcript_id "Phchi.S6G038500.t2"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	CDS	3033973	3035628	0.55	+	0	transcript_id "Phchi.S6G038500.t2"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	exon	3033973	3035628	.	+	.	transcript_id "Phchi.S6G038500.t2"; gene_id "Phchi.S6G038500"
Phchi.S6	AUGUSTUS	stop_codon	3035629	3035631	.	+	0	transcript_id "Phchi.S6G038500.t2"; gene_id "Phchi.S6G038500"
# This transcript jg3035.t2 is derived from g204.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3036.t1 is derived from g205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1262734	1263829	.	+	.	Phchi.S1G019500
Phchi.S1	AUGUSTUS	transcript	1262734	1263829	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	start_codon	1262734	1262736	.	+	0	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	CDS	1262734	1262823	1	+	0	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	exon	1262734	1262823	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	intron	1262824	1262922	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	CDS	1262923	1263046	0.54	+	0	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	exon	1262923	1263046	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	intron	1263047	1263230	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	CDS	1263231	1263289	0.94	+	2	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	exon	1263231	1263289	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	intron	1263290	1263429	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	CDS	1263430	1263475	1	+	0	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	exon	1263430	1263475	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	intron	1263476	1263626	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	CDS	1263627	1263829	0.69	+	2	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	exon	1263627	1263829	.	+	.	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
Phchi.S1	AUGUSTUS	stop_codon	1263830	1263832	.	+	0	transcript_id "Phchi.S1G019500.t1"; gene_id "Phchi.S1G019500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13144.t1 is derived from g11609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4385816	4386667	.	-	.	Phchi.S3G046300
Phchi.S3	AUGUSTUS	transcript	4385816	4386667	.	-	.	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	stop_codon	4385813	4385815	.	-	0	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	CDS	4385816	4386078	1	-	2	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	exon	4385816	4386078	.	-	.	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	intron	4386079	4386321	.	-	.	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	CDS	4386322	4386667	0.49	-	0	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	exon	4386322	4386667	.	-	.	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
Phchi.S3	AUGUSTUS	start_codon	4386665	4386667	.	-	0	transcript_id "Phchi.S3G046300.t1"; gene_id "Phchi.S3G046300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14152.t1 is derived from g12619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11175807	11176405	.	+	.	Phchi.S3G147100
Phchi.S3	AUGUSTUS	transcript	11175807	11176405	.	+	.	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	start_codon	11175807	11175809	.	+	0	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	CDS	11175807	11175939	0.8	+	0	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	exon	11175807	11175939	.	+	.	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	intron	11175940	11176012	.	+	.	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	CDS	11176013	11176173	1	+	2	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	exon	11176013	11176173	.	+	.	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	intron	11176174	11176309	.	+	.	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	CDS	11176310	11176405	1	+	0	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	exon	11176310	11176405	.	+	.	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
Phchi.S3	AUGUSTUS	stop_codon	11176406	11176408	.	+	0	transcript_id "Phchi.S3G147100.t1"; gene_id "Phchi.S3G147100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13106.t1 is derived from g11571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4176013	4177400	.	-	.	Phchi.S3G042500
Phchi.S3	AUGUSTUS	transcript	4176013	4177400	.	-	.	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	stop_codon	4176010	4176012	.	-	0	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	CDS	4176013	4176653	0.63	-	2	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	exon	4176013	4176653	.	-	.	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	intron	4176654	4176847	.	-	.	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	CDS	4176848	4176894	0.64	-	1	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	exon	4176848	4176894	.	-	.	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	intron	4176895	4176978	.	-	.	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	CDS	4176979	4177400	0.63	-	0	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	exon	4176979	4177400	.	-	.	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
Phchi.S3	AUGUSTUS	start_codon	4177398	4177400	.	-	0	transcript_id "Phchi.S3G042500.t1"; gene_id "Phchi.S3G042500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1326.t1 is derived from g11109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9031061	9033147	.	-	.	Phchi.S6G128500
Phchi.S6	AUGUSTUS	transcript	9031061	9033147	.	-	.	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	stop_codon	9031058	9031060	.	-	0	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	CDS	9031061	9031761	0.99	-	2	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	exon	9031061	9031761	.	-	.	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	intron	9031762	9031850	.	-	.	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	CDS	9031851	9032669	1	-	2	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	exon	9031851	9032669	.	-	.	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	intron	9032670	9032849	.	-	.	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	CDS	9032850	9033147	0.93	-	0	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	exon	9032850	9033147	.	-	.	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
Phchi.S6	AUGUSTUS	start_codon	9033145	9033147	.	-	0	transcript_id "Phchi.S6G128500.t1"; gene_id "Phchi.S6G128500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10350.t1 is derived from g7526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47314041	47316188	.	-	.	Phchi.S1G750900
Phchi.S1	AUGUSTUS	transcript	47314041	47316188	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	stop_codon	47314038	47314040	.	-	0	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47314041	47314495	0.61	-	2	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47314041	47314495	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	intron	47314496	47314921	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47314922	47315021	0.61	-	0	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47314922	47315021	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	intron	47315022	47315201	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47315202	47315372	0.99	-	0	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47315202	47315372	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	intron	47315373	47315551	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47315552	47315582	0.97	-	1	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47315552	47315582	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	intron	47315583	47315893	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47315894	47315928	1	-	0	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47315894	47315928	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	intron	47315929	47316010	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47316011	47316083	1	-	1	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47316011	47316083	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	intron	47316084	47316162	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	CDS	47316163	47316188	1	-	0	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	exon	47316163	47316188	.	-	.	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
Phchi.S1	AUGUSTUS	start_codon	47316186	47316188	.	-	0	transcript_id "Phchi.S1G750900.t1"; gene_id "Phchi.S1G750900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5433.t1 is derived from g2603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16843077	16846052	.	+	.	Phchi.S1G259200
Phchi.S1	AUGUSTUS	transcript	16843077	16846052	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	start_codon	16843077	16843079	.	+	0	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	CDS	16843077	16843263	0.74	+	0	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	exon	16843077	16843263	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	intron	16843264	16843351	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	CDS	16843352	16843422	1	+	2	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	exon	16843352	16843422	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	intron	16843423	16843509	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	CDS	16843510	16843672	1	+	0	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	exon	16843510	16843672	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	intron	16843673	16843752	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	CDS	16843753	16843847	1	+	2	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	exon	16843753	16843847	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	intron	16843848	16843933	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	CDS	16843934	16845907	0.41	+	0	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	exon	16843934	16845907	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	intron	16845908	16846004	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	CDS	16846005	16846052	0.57	+	0	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	exon	16846005	16846052	.	+	.	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
Phchi.S1	AUGUSTUS	stop_codon	16846053	16846055	.	+	0	transcript_id "Phchi.S1G259200.t1"; gene_id "Phchi.S1G259200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5097.t1 is derived from g2267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14727337	14728077	.	+	.	Phchi.S1G225600
Phchi.S1	AUGUSTUS	transcript	14727337	14728077	.	+	.	transcript_id "Phchi.S1G225600.t1"; gene_id "Phchi.S1G225600"
Phchi.S1	AUGUSTUS	start_codon	14727337	14727339	.	+	0	transcript_id "Phchi.S1G225600.t1"; gene_id "Phchi.S1G225600"
Phchi.S1	AUGUSTUS	CDS	14727337	14728077	0.96	+	0	transcript_id "Phchi.S1G225600.t1"; gene_id "Phchi.S1G225600"
Phchi.S1	AUGUSTUS	exon	14727337	14728077	.	+	.	transcript_id "Phchi.S1G225600.t1"; gene_id "Phchi.S1G225600"
Phchi.S1	AUGUSTUS	stop_codon	14728078	14728080	.	+	0	transcript_id "Phchi.S1G225600.t1"; gene_id "Phchi.S1G225600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1450.t1 is derived from g8369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	953472	954798	.	+	.	Phchi.S5G005900
Phchi.S5	AUGUSTUS	transcript	953472	954798	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	start_codon	953472	953474	.	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	953472	953711	1	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	953472	953711	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	953712	953809	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	953810	953851	1	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	953810	953851	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	953852	953939	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	953940	954055	1	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	953940	954055	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954056	954136	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954137	954242	1	+	1	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954137	954242	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954243	954342	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954343	954396	1	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954343	954396	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954397	954481	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954482	954494	0.59	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954482	954494	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954495	954583	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954584	954659	0.59	+	2	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954584	954659	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954660	954743	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954744	954798	1	+	1	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954744	954798	.	+	.	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	stop_codon	954799	954801	.	+	0	transcript_id "Phchi.S5G005900.t1"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	transcript	953472	954798	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	start_codon	953472	953474	.	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	953472	953711	1	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	953472	953711	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	953712	953809	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	953810	953851	1	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	953810	953851	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	953852	953926	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	953927	953961	0.55	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	953927	953961	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	953962	954034	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954035	954055	0.89	+	1	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954035	954055	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954056	954136	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954137	954242	1	+	1	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954137	954242	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954243	954342	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954343	954396	1	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954343	954396	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954397	954481	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954482	954494	0.5	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954482	954494	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954495	954583	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954584	954659	0.5	+	2	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954584	954659	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	intron	954660	954743	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	CDS	954744	954798	1	+	1	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	exon	954744	954798	.	+	.	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
Phchi.S5	AUGUSTUS	stop_codon	954799	954801	.	+	0	transcript_id "Phchi.S5G005900.t2"; gene_id "Phchi.S5G005900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9671.t1 is derived from g6847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43219381	43221987	.	+	.	Phchi.S1G683000
Phchi.S1	AUGUSTUS	transcript	43219381	43221987	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	start_codon	43219381	43219383	.	+	0	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	CDS	43219381	43219691	0.96	+	0	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	exon	43219381	43219691	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	intron	43219692	43219785	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	CDS	43219786	43220066	1	+	1	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	exon	43219786	43220066	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	intron	43220067	43220154	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	CDS	43220155	43220398	1	+	2	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	exon	43220155	43220398	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	intron	43220399	43220483	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	CDS	43220484	43220687	1	+	1	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	exon	43220484	43220687	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	intron	43220688	43220831	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	CDS	43220832	43221987	0.98	+	1	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	exon	43220832	43221987	.	+	.	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
Phchi.S1	AUGUSTUS	stop_codon	43221988	43221990	.	+	0	transcript_id "Phchi.S1G683000.t1"; gene_id "Phchi.S1G683000"
# This transcript jg6280.t2 is derived from g3452.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6280.t3 is derived from g3452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6281.t1 is derived from g3453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22074994	22075495	.	+	.	Phchi.S1G344000
Phchi.S1	AUGUSTUS	transcript	22074994	22075495	.	+	.	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	start_codon	22074994	22074996	.	+	0	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	CDS	22074994	22075090	0.64	+	0	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	exon	22074994	22075090	.	+	.	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	intron	22075091	22075313	.	+	.	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	CDS	22075314	22075495	0.95	+	2	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	exon	22075314	22075495	.	+	.	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
Phchi.S1	AUGUSTUS	stop_codon	22075496	22075498	.	+	0	transcript_id "Phchi.S1G344000.t1"; gene_id "Phchi.S1G344000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16008.t1 is derived from g14432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	140470	140856	.	+	.	Phchi.C10G000600
Phchi.C10	AUGUSTUS	transcript	140470	140856	.	+	.	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	start_codon	140470	140472	.	+	0	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	CDS	140470	140585	0.93	+	0	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	exon	140470	140585	.	+	.	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	intron	140586	140693	.	+	.	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	CDS	140694	140856	0.97	+	1	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	exon	140694	140856	.	+	.	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
Phchi.C10	AUGUSTUS	stop_codon	140857	140859	.	+	0	transcript_id "Phchi.C10G000600.t1"; gene_id "Phchi.C10G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg141.t1 is derived from g9923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	778387	781133	.	-	.	Phchi.S6G010000
Phchi.S6	AUGUSTUS	transcript	778387	781133	.	-	.	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	stop_codon	778384	778386	.	-	0	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	CDS	778387	779594	0.95	-	2	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	exon	778387	779594	.	-	.	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	intron	779595	779700	.	-	.	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	CDS	779701	780322	0.42	-	0	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	exon	779701	780322	.	-	.	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	intron	780323	780410	.	-	.	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	CDS	780411	781133	0.34	-	0	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	exon	780411	781133	.	-	.	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
Phchi.S6	AUGUSTUS	start_codon	781131	781133	.	-	0	transcript_id "Phchi.S6G010000.t1"; gene_id "Phchi.S6G010000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5552.t1 is derived from g2722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17562469	17563659	.	-	.	Phchi.S1G271100
Phchi.S1	AUGUSTUS	transcript	17562469	17563659	.	-	.	transcript_id "Phchi.S1G271100.t1"; gene_id "Phchi.S1G271100"
Phchi.S1	AUGUSTUS	stop_codon	17562466	17562468	.	-	0	transcript_id "Phchi.S1G271100.t1"; gene_id "Phchi.S1G271100"
Phchi.S1	AUGUSTUS	CDS	17562469	17563659	0.53	-	0	transcript_id "Phchi.S1G271100.t1"; gene_id "Phchi.S1G271100"
Phchi.S1	AUGUSTUS	exon	17562469	17563659	.	-	.	transcript_id "Phchi.S1G271100.t1"; gene_id "Phchi.S1G271100"
Phchi.S1	AUGUSTUS	start_codon	17563657	17563659	.	-	0	transcript_id "Phchi.S1G271100.t1"; gene_id "Phchi.S1G271100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15184.t1 is derived from g13652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17462765	17464012	.	+	.	Phchi.S3G250300
Phchi.S3	AUGUSTUS	transcript	17462765	17464012	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	start_codon	17462765	17462767	.	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17462765	17462918	0.63	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17462765	17462918	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	intron	17462919	17463024	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17463025	17463098	0.92	+	2	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17463025	17463098	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	intron	17463099	17463194	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17463195	17463341	1	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17463195	17463341	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	intron	17463342	17463430	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17463431	17463446	0.98	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17463431	17463446	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	intron	17463447	17463512	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17463513	17463547	0.98	+	2	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17463513	17463547	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	intron	17463548	17463683	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17463684	17463758	0.98	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17463684	17463758	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	intron	17463759	17463904	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	CDS	17463905	17464012	0.98	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	exon	17463905	17464012	.	+	.	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
Phchi.S3	AUGUSTUS	stop_codon	17464013	17464015	.	+	0	transcript_id "Phchi.S3G250300.t1"; gene_id "Phchi.S3G250300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11731.t1 is derived from g15783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7898993	7901036	.	+	.	Phchi.S4G131300
Phchi.S4	AUGUSTUS	transcript	7898993	7901036	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	start_codon	7898993	7898995	.	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7898993	7899035	0.91	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7898993	7899035	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7899036	7899213	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7899214	7899323	1	+	2	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7899214	7899323	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7899324	7899399	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7899400	7899483	1	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7899400	7899483	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7899484	7899565	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7899566	7899883	1	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7899566	7899883	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7899884	7899994	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7899995	7900163	0.98	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7899995	7900163	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7900164	7900271	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7900272	7900516	0.89	+	2	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7900272	7900516	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7900517	7900613	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7900614	7900801	1	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7900614	7900801	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	intron	7900802	7900879	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	CDS	7900880	7901036	0.99	+	1	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	exon	7900880	7901036	.	+	.	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
Phchi.S4	AUGUSTUS	stop_codon	7901037	7901039	.	+	0	transcript_id "Phchi.S4G131300.t1"; gene_id "Phchi.S4G131300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4326.t1 is derived from g1495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9798636	9800387	.	-	.	Phchi.S1G148500
Phchi.S1	AUGUSTUS	transcript	9798636	9800387	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	stop_codon	9798633	9798635	.	-	0	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9798636	9798983	0.98	-	0	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9798636	9798983	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	intron	9798984	9799065	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9799066	9799292	1	-	2	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9799066	9799292	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	intron	9799293	9799381	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9799382	9799583	1	-	0	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9799382	9799583	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	intron	9799584	9799658	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9799659	9799765	1	-	2	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9799659	9799765	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	intron	9799766	9799855	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9799856	9800057	1	-	0	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9799856	9800057	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	intron	9800058	9800217	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9800218	9800279	0.73	-	2	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9800218	9800279	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	intron	9800280	9800365	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	CDS	9800366	9800387	0.73	-	0	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	exon	9800366	9800387	.	-	.	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
Phchi.S1	AUGUSTUS	start_codon	9800385	9800387	.	-	0	transcript_id "Phchi.S1G148500.t1"; gene_id "Phchi.S1G148500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2199.t1 is derived from g9119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5403353	5403759	.	-	.	Phchi.S5G080800
Phchi.S5	AUGUSTUS	transcript	5403353	5403759	.	-	.	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	stop_codon	5403350	5403352	.	-	0	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	CDS	5403353	5403530	0.96	-	1	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	exon	5403353	5403530	.	-	.	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	intron	5403531	5403715	.	-	.	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	CDS	5403716	5403759	0.96	-	0	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	exon	5403716	5403759	.	-	.	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
Phchi.S5	AUGUSTUS	start_codon	5403757	5403759	.	-	0	transcript_id "Phchi.S5G080800.t1"; gene_id "Phchi.S5G080800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4401.t1 is derived from g1570.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10242825	10244127	.	-	.	Phchi.S1G156000
Phchi.S1	AUGUSTUS	transcript	10242825	10244127	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	stop_codon	10242822	10242824	.	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10242825	10243325	1	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10242825	10243325	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243326	10243400	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243401	10243470	1	-	1	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243401	10243470	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243471	10243549	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243550	10243638	1	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243550	10243638	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243639	10243720	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243721	10243831	0.99	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243721	10243831	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243832	10243921	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243922	10244017	0.66	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243922	10244017	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10244018	10244109	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10244110	10244127	0.48	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10244110	10244127	.	-	.	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	start_codon	10244125	10244127	.	-	0	transcript_id "Phchi.S1G156000.t1"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	transcript	10242825	10244127	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	stop_codon	10242822	10242824	.	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10242825	10243322	0.98	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10242825	10243322	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243323	10243400	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243401	10243470	1	-	1	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243401	10243470	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243471	10243549	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243550	10243638	0.99	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243550	10243638	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243639	10243720	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243721	10243831	0.98	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243721	10243831	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10243832	10243921	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10243922	10244017	0.68	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10243922	10244017	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	intron	10244018	10244109	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	CDS	10244110	10244127	0.47	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	exon	10244110	10244127	.	-	.	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
Phchi.S1	AUGUSTUS	start_codon	10244125	10244127	.	-	0	transcript_id "Phchi.S1G156000.t2"; gene_id "Phchi.S1G156000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2374.t1 is derived from g9294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6400617	6405405	.	-	.	Phchi.S5G098300
Phchi.S5	AUGUSTUS	transcript	6400617	6405405	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	stop_codon	6400614	6400616	.	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6400617	6401729	1	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6400617	6401729	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6401730	6401864	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6401865	6402676	0.32	-	2	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6401865	6402676	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6402677	6403127	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6403128	6403210	0.65	-	1	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6403128	6403210	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6403211	6403327	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6403328	6403395	0.99	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6403328	6403395	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6403396	6403475	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6403476	6403607	1	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6403476	6403607	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6403608	6403730	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6403731	6403936	1	-	2	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6403731	6403936	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6403937	6404029	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6404030	6404263	1	-	2	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6404030	6404263	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6404264	6404450	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6404451	6404541	1	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6404451	6404541	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6404542	6404703	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6404704	6404848	1	-	1	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6404704	6404848	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6404849	6404936	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6404937	6404992	0.9	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6404937	6404992	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6404993	6405074	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6405075	6405146	0.71	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6405075	6405146	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	intron	6405147	6405219	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	CDS	6405220	6405405	0.67	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	exon	6405220	6405405	.	-	.	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
Phchi.S5	AUGUSTUS	start_codon	6405403	6405405	.	-	0	transcript_id "Phchi.S5G098300.t1"; gene_id "Phchi.S5G098300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3052.t1 is derived from g221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1362886	1363360	.	+	.	Phchi.S1G021100
Phchi.S1	AUGUSTUS	transcript	1362886	1363360	.	+	.	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	start_codon	1362886	1362888	.	+	0	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	CDS	1362886	1363065	0.99	+	0	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	exon	1362886	1363065	.	+	.	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	intron	1363066	1363189	.	+	.	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	CDS	1363190	1363360	1	+	0	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	exon	1363190	1363360	.	+	.	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
Phchi.S1	AUGUSTUS	stop_codon	1363361	1363363	.	+	0	transcript_id "Phchi.S1G021100.t1"; gene_id "Phchi.S1G021100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12103.t1 is derived from g7779.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3292423	3295314	.	-	.	Phchi.S2G018300
Phchi.S2	AUGUSTUS	transcript	3292423	3295314	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	stop_codon	3292420	3292422	.	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292423	3292427	1	-	2	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292423	3292427	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292428	3292500	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292501	3292634	1	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292501	3292634	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292635	3292723	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292724	3292791	1	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292724	3292791	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292792	3292895	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292896	3293048	0.73	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292896	3293048	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293049	3293253	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293254	3293275	0.7	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293254	3293275	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293276	3293481	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293482	3293571	1	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293482	3293571	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293572	3293648	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293649	3293780	1	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293649	3293780	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293781	3293860	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293861	3293968	1	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293861	3293968	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293969	3294125	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294126	3294217	1	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294126	3294217	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294218	3294328	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294329	3294377	1	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294329	3294377	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294378	3294510	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294511	3294601	1	-	2	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294511	3294601	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294602	3294690	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294691	3294725	0.99	-	1	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294691	3294725	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294726	3294850	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294851	3294975	0.97	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294851	3294975	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294976	3295083	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3295084	3295314	0.83	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3295084	3295314	.	-	.	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	start_codon	3295312	3295314	.	-	0	transcript_id "Phchi.S2G018300.t1"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	transcript	3292423	3295314	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	stop_codon	3292420	3292422	.	-	0	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292423	3292427	1	-	2	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292423	3292427	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292428	3292500	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292501	3292634	1	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292501	3292634	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292635	3292723	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292724	3292791	0.98	-	0	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292724	3292791	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292792	3292895	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292896	3293048	0.64	-	0	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292896	3293048	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293049	3293253	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293254	3293275	0.63	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293254	3293275	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293276	3293481	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293482	3293571	1	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293482	3293571	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293572	3293648	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293649	3293780	1	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293649	3293780	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293781	3293860	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293861	3293968	1	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293861	3293968	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293969	3294125	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294126	3294217	1	-	0	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294126	3294217	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294218	3294328	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294329	3294377	1	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294329	3294377	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294378	3294510	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294511	3294601	1	-	2	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294511	3294601	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294602	3294709	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294710	3294975	0.95	-	1	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294710	3294975	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294976	3295123	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3295124	3295314	0.87	-	0	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3295124	3295314	.	-	.	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	start_codon	3295312	3295314	.	-	0	transcript_id "Phchi.S2G018300.t2"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	transcript	3292423	3295314	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	stop_codon	3292420	3292422	.	-	0	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292423	3292427	1	-	2	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292423	3292427	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292428	3292500	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292501	3292634	1	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292501	3292634	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292635	3292723	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292724	3292791	0.99	-	0	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292724	3292791	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3292792	3292895	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3292896	3293048	0.67	-	0	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3292896	3293048	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293049	3293253	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293254	3293275	0.69	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293254	3293275	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293276	3293481	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293482	3293571	1	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293482	3293571	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293572	3293648	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293649	3293780	1	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293649	3293780	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293781	3293860	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3293861	3293968	1	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3293861	3293968	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3293969	3294125	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294126	3294217	1	-	0	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294126	3294217	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294218	3294328	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294329	3294377	1	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294329	3294377	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294378	3294510	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294511	3294601	1	-	2	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294511	3294601	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294602	3294690	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294691	3294725	0.62	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294691	3294725	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294726	3294876	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3294877	3294975	0.43	-	1	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3294877	3294975	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	intron	3294976	3295123	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	CDS	3295124	3295314	0.65	-	0	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	exon	3295124	3295314	.	-	.	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
Phchi.S2	AUGUSTUS	start_codon	3295312	3295314	.	-	0	transcript_id "Phchi.S2G018300.t3"; gene_id "Phchi.S2G018300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11064.t1 is derived from g15114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3944476	3946398	.	-	.	Phchi.S4G064600
Phchi.S4	AUGUSTUS	transcript	3944476	3946398	.	-	.	transcript_id "Phchi.S4G064600.t1"; gene_id "Phchi.S4G064600"
Phchi.S4	AUGUSTUS	stop_codon	3944473	3944475	.	-	0	transcript_id "Phchi.S4G064600.t1"; gene_id "Phchi.S4G064600"
Phchi.S4	AUGUSTUS	CDS	3944476	3946398	0.5	-	0	transcript_id "Phchi.S4G064600.t1"; gene_id "Phchi.S4G064600"
Phchi.S4	AUGUSTUS	exon	3944476	3946398	.	-	.	transcript_id "Phchi.S4G064600.t1"; gene_id "Phchi.S4G064600"
Phchi.S4	AUGUSTUS	start_codon	3946396	3946398	.	-	0	transcript_id "Phchi.S4G064600.t1"; gene_id "Phchi.S4G064600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg685.t1 is derived from g10467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4781647	4783599	.	-	.	Phchi.S6G064400
Phchi.S6	AUGUSTUS	transcript	4781647	4783599	.	-	.	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	stop_codon	4781644	4781646	.	-	0	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	CDS	4781647	4782079	0.89	-	1	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	exon	4781647	4782079	.	-	.	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	intron	4782080	4782158	.	-	.	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	CDS	4782159	4782442	1	-	0	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	exon	4782159	4782442	.	-	.	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	intron	4782443	4782612	.	-	.	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	CDS	4782613	4783599	0.82	-	0	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	exon	4782613	4783599	.	-	.	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
Phchi.S6	AUGUSTUS	start_codon	4783597	4783599	.	-	0	transcript_id "Phchi.S6G064400.t1"; gene_id "Phchi.S6G064400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8782.t1 is derived from g5957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37924348	37925030	.	+	.	Phchi.S1G594100
Phchi.S1	AUGUSTUS	transcript	37924348	37925030	.	+	.	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	start_codon	37924348	37924350	.	+	0	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	CDS	37924348	37924663	0.83	+	0	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	exon	37924348	37924663	.	+	.	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	intron	37924664	37924746	.	+	.	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	CDS	37924747	37925030	1	+	2	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	exon	37924747	37925030	.	+	.	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
Phchi.S1	AUGUSTUS	stop_codon	37925031	37925033	.	+	0	transcript_id "Phchi.S1G594100.t1"; gene_id "Phchi.S1G594100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9948.t1 is derived from g7124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44621468	44625287	.	-	.	Phchi.S1G710700
Phchi.S1	AUGUSTUS	transcript	44621468	44625287	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	stop_codon	44621465	44621467	.	-	0	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44621468	44622071	0.83	-	1	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44621468	44622071	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	intron	44622072	44622148	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44622149	44622386	1	-	2	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44622149	44622386	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	intron	44622387	44622481	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44622482	44622925	0.99	-	2	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44622482	44622925	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	intron	44622926	44623046	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44623047	44623219	0.72	-	1	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44623047	44623219	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	intron	44623220	44623324	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44623325	44624394	0.85	-	0	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44623325	44624394	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	intron	44624395	44624484	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44624485	44624733	1	-	0	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44624485	44624733	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	intron	44624734	44624831	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	CDS	44624832	44625287	0.96	-	0	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	exon	44624832	44625287	.	-	.	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
Phchi.S1	AUGUSTUS	start_codon	44625285	44625287	.	-	0	transcript_id "Phchi.S1G710700.t1"; gene_id "Phchi.S1G710700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1843.t1 is derived from g8763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3529742	3530265	.	-	.	Phchi.S5G045200
Phchi.S5	AUGUSTUS	transcript	3529742	3530265	.	-	.	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	stop_codon	3529739	3529741	.	-	0	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	CDS	3529742	3529765	1	-	0	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	exon	3529742	3529765	.	-	.	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	intron	3529766	3529946	.	-	.	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	CDS	3529947	3530157	1	-	1	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	exon	3529947	3530157	.	-	.	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	intron	3530158	3530257	.	-	.	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	CDS	3530258	3530265	0.41	-	0	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	exon	3530258	3530265	.	-	.	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
Phchi.S5	AUGUSTUS	start_codon	3530263	3530265	.	-	0	transcript_id "Phchi.S5G045200.t1"; gene_id "Phchi.S5G045200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10805.t1 is derived from g14855.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2183776	2186554	.	-	.	Phchi.S4G038700
Phchi.S4	AUGUSTUS	transcript	2183776	2186554	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	stop_codon	2183773	2183775	.	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2183776	2184585	1	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2183776	2184585	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2184586	2184937	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2184938	2185456	0.96	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2184938	2185456	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2185457	2185574	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2185575	2185582	0.97	-	2	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2185575	2185582	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2185583	2185776	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2185777	2186019	0.94	-	2	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2185777	2186019	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2186020	2186098	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2186099	2186177	0.96	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2186099	2186177	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2186178	2186269	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2186270	2186359	0.96	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2186270	2186359	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2186360	2186497	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2186498	2186554	0.9	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2186498	2186554	.	-	.	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	start_codon	2186552	2186554	.	-	0	transcript_id "Phchi.S4G038700.t1"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	transcript	2183776	2186554	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	stop_codon	2183773	2183775	.	-	0	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2183776	2184585	1	-	0	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2183776	2184585	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2184586	2184937	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2184938	2185382	0.56	-	1	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2184938	2185382	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2185383	2185555	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2185556	2185582	0.18	-	1	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2185556	2185582	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2185583	2185790	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2185791	2186019	0.48	-	2	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2185791	2186019	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2186020	2186098	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2186099	2186177	0.99	-	0	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2186099	2186177	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2186178	2186269	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2186270	2186359	0.99	-	0	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2186270	2186359	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	intron	2186360	2186497	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	CDS	2186498	2186554	0.96	-	0	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	exon	2186498	2186554	.	-	.	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
Phchi.S4	AUGUSTUS	start_codon	2186552	2186554	.	-	0	transcript_id "Phchi.S4G038700.t2"; gene_id "Phchi.S4G038700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2500.t1 is derived from g9420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6993266	6994328	.	-	.	Phchi.S5G110900
Phchi.S5	AUGUSTUS	transcript	6993266	6994328	.	-	.	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	stop_codon	6993263	6993265	.	-	0	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	CDS	6993266	6993670	1	-	0	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	exon	6993266	6993670	.	-	.	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	intron	6993671	6993943	.	-	.	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	CDS	6993944	6993955	0.81	-	0	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	exon	6993944	6993955	.	-	.	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	intron	6993956	6994247	.	-	.	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	CDS	6994248	6994328	0.7	-	0	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	exon	6994248	6994328	.	-	.	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
Phchi.S5	AUGUSTUS	start_codon	6994326	6994328	.	-	0	transcript_id "Phchi.S5G110900.t1"; gene_id "Phchi.S5G110900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10284.t1 is derived from g7460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46811968	46813507	.	+	.	Phchi.S1G744300
Phchi.S1	AUGUSTUS	transcript	46811968	46813507	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	start_codon	46811968	46811970	.	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46811968	46812070	1	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46811968	46812070	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812071	46812147	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812148	46812318	1	+	2	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812148	46812318	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812319	46812417	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812418	46812473	1	+	2	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812418	46812473	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812474	46812603	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812604	46812659	1	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812604	46812659	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812660	46812780	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812781	46812838	1	+	1	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812781	46812838	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812839	46812923	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812924	46812998	1	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812924	46812998	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812999	46813082	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46813083	46813172	1	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46813083	46813172	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46813173	46813272	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46813273	46813350	1	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46813273	46813350	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46813351	46813441	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46813442	46813507	0.99	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46813442	46813507	.	+	.	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	stop_codon	46813508	46813510	.	+	0	transcript_id "Phchi.S1G744300.t1"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	transcript	46811968	46813507	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	start_codon	46811968	46811970	.	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46811968	46812070	0.98	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46811968	46812070	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812071	46812150	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812151	46812318	0.99	+	2	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812151	46812318	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812319	46812417	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812418	46812473	1	+	2	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812418	46812473	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812474	46812603	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812604	46812659	1	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812604	46812659	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812660	46812780	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812781	46812838	1	+	1	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812781	46812838	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812839	46812923	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46812924	46812998	1	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46812924	46812998	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46812999	46813082	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46813083	46813172	1	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46813083	46813172	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46813173	46813272	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46813273	46813350	1	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46813273	46813350	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	intron	46813351	46813441	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	CDS	46813442	46813507	0.99	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	exon	46813442	46813507	.	+	.	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
Phchi.S1	AUGUSTUS	stop_codon	46813508	46813510	.	+	0	transcript_id "Phchi.S1G744300.t2"; gene_id "Phchi.S1G744300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11610.t1 is derived from g15661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7315351	7316888	.	-	.	Phchi.S4G119200
Phchi.S4	AUGUSTUS	transcript	7315351	7316888	.	-	.	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	stop_codon	7315348	7315350	.	-	0	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	CDS	7315351	7315898	0.95	-	2	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	exon	7315351	7315898	.	-	.	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	intron	7315899	7315969	.	-	.	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	CDS	7315970	7316888	0.83	-	0	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	exon	7315970	7316888	.	-	.	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
Phchi.S4	AUGUSTUS	start_codon	7316886	7316888	.	-	0	transcript_id "Phchi.S4G119200.t1"; gene_id "Phchi.S4G119200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1546.t1 is derived from g8465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1693898	1694566	.	-	.	Phchi.S5G015500
Phchi.S5	AUGUSTUS	transcript	1693898	1694566	.	-	.	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	stop_codon	1693895	1693897	.	-	0	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	CDS	1693898	1694159	1	-	1	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	exon	1693898	1694159	.	-	.	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	intron	1694160	1694241	.	-	.	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	CDS	1694242	1694459	1	-	0	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	exon	1694242	1694459	.	-	.	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	intron	1694460	1694551	.	-	.	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	CDS	1694552	1694566	0.97	-	0	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	exon	1694552	1694566	.	-	.	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
Phchi.S5	AUGUSTUS	start_codon	1694564	1694566	.	-	0	transcript_id "Phchi.S5G015500.t1"; gene_id "Phchi.S5G015500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12362.t1 is derived from g8038.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12735863	12740876	.	-	.	Phchi.S2G044200
Phchi.S2	AUGUSTUS	transcript	12735863	12740876	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	stop_codon	12735860	12735862	.	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12735863	12735896	1	-	1	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12735863	12735896	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12735897	12735980	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12735981	12736060	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12735981	12736060	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736061	12736156	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736157	12736262	1	-	1	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736157	12736262	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736263	12736355	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736356	12736390	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736356	12736390	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736391	12736518	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736519	12736605	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736519	12736605	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736606	12736741	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736742	12736819	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736742	12736819	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736820	12736975	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736976	12737044	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736976	12737044	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737045	12737269	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737270	12737377	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737270	12737377	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737378	12737547	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737548	12737611	1	-	1	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737548	12737611	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737612	12737843	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737844	12738199	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737844	12738199	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738200	12738281	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738282	12738369	0.61	-	1	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738282	12738369	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738370	12738468	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738469	12738521	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738469	12738521	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738522	12738841	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738842	12738911	1	-	1	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738842	12738911	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738912	12738993	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738994	12739064	1	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738994	12739064	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739065	12739189	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739190	12739244	0.53	-	1	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739190	12739244	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739245	12739302	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739303	12739333	0.53	-	2	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739303	12739333	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739334	12739565	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739566	12739739	0.77	-	2	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739566	12739739	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739740	12739825	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739826	12739913	0.94	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739826	12739913	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739914	12740135	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12740136	12740218	0.94	-	2	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12740136	12740218	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12740219	12740782	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12740783	12740876	0.53	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12740783	12740876	.	-	.	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	start_codon	12740874	12740876	.	-	0	transcript_id "Phchi.S2G044200.t1"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	transcript	12735863	12740876	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	stop_codon	12735860	12735862	.	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12735863	12735896	1	-	1	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12735863	12735896	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12735897	12735980	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12735981	12736060	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12735981	12736060	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736061	12736156	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736157	12736262	1	-	1	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736157	12736262	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736263	12736355	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736356	12736390	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736356	12736390	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736391	12736518	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736519	12736605	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736519	12736605	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736606	12736741	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736742	12736819	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736742	12736819	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736820	12736975	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736976	12737044	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736976	12737044	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737045	12737269	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737270	12737377	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737270	12737377	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737378	12737547	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737548	12737611	1	-	1	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737548	12737611	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737612	12737843	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737844	12738199	0.99	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737844	12738199	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738200	12738281	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738282	12738369	0.59	-	1	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738282	12738369	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738370	12738468	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738469	12738521	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738469	12738521	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738522	12738841	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738842	12738911	1	-	1	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738842	12738911	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738912	12738993	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738994	12739064	1	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738994	12739064	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739065	12739189	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739190	12739244	0.57	-	1	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739190	12739244	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739245	12739302	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739303	12739333	0.57	-	2	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739303	12739333	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739334	12739565	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739566	12739739	0.72	-	2	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739566	12739739	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739740	12739825	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739826	12739919	0.92	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739826	12739919	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739920	12740135	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12740136	12740218	0.92	-	2	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12740136	12740218	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12740219	12740782	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12740783	12740876	0.5	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12740783	12740876	.	-	.	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	start_codon	12740874	12740876	.	-	0	transcript_id "Phchi.S2G044200.t2"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	transcript	12735863	12740876	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	stop_codon	12735860	12735862	.	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12735863	12735896	1	-	1	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12735863	12735896	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12735897	12735980	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12735981	12736060	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12735981	12736060	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736061	12736156	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736157	12736262	1	-	1	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736157	12736262	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736263	12736355	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736356	12736390	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736356	12736390	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736391	12736518	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736519	12736605	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736519	12736605	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736606	12736741	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736742	12736819	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736742	12736819	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12736820	12736975	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12736976	12737044	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12736976	12737044	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737045	12737269	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737270	12737377	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737270	12737377	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737378	12737547	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737548	12737611	1	-	1	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737548	12737611	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12737612	12737843	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12737844	12738199	0.98	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12737844	12738199	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738200	12738281	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738282	12738369	0.56	-	1	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738282	12738369	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738370	12738468	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738469	12738521	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738469	12738521	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738522	12738841	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738842	12738911	1	-	1	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738842	12738911	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12738912	12738993	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12738994	12739064	1	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12738994	12739064	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739065	12739189	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739190	12739244	0.39	-	1	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739190	12739244	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739245	12739302	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739303	12739333	0.4	-	2	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739303	12739333	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739334	12739565	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739566	12739739	0.66	-	2	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739566	12739739	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739740	12739825	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12739826	12739913	0.56	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12739826	12739913	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12739914	12740174	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12740175	12740218	0.57	-	2	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12740175	12740218	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	intron	12740219	12740782	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	CDS	12740783	12740876	0.45	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	exon	12740783	12740876	.	-	.	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
Phchi.S2	AUGUSTUS	start_codon	12740874	12740876	.	-	0	transcript_id "Phchi.S2G044200.t3"; gene_id "Phchi.S2G044200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9471.t1 is derived from g6647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41678278	41680450	.	-	.	Phchi.S1G663000
Phchi.S1	AUGUSTUS	transcript	41678278	41680450	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	stop_codon	41678275	41678277	.	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41678278	41678460	0.97	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41678278	41678460	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41678461	41678549	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41678550	41678654	1	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41678550	41678654	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41678655	41678741	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41678742	41678842	1	-	2	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41678742	41678842	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41678843	41679033	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41679034	41679103	1	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41679034	41679103	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41679104	41679217	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41679218	41679280	1	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41679218	41679280	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41679281	41679359	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41679360	41679426	1	-	1	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41679360	41679426	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41679427	41679519	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41679520	41679644	1	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41679520	41679644	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41679645	41679749	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41679750	41679827	0.99	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41679750	41679827	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41679828	41679936	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41679937	41679983	1	-	2	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41679937	41679983	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41679984	41680083	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41680084	41680208	1	-	1	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41680084	41680208	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	intron	41680209	41680307	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	CDS	41680308	41680450	0.86	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	exon	41680308	41680450	.	-	.	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
Phchi.S1	AUGUSTUS	start_codon	41680448	41680450	.	-	0	transcript_id "Phchi.S1G663000.t1"; gene_id "Phchi.S1G663000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4606.t1 is derived from g1776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11323386	11323733	.	-	.	Phchi.S1G176500
Phchi.S1	AUGUSTUS	transcript	11323386	11323733	.	-	.	transcript_id "Phchi.S1G176500.t1"; gene_id "Phchi.S1G176500"
Phchi.S1	AUGUSTUS	stop_codon	11323383	11323385	.	-	0	transcript_id "Phchi.S1G176500.t1"; gene_id "Phchi.S1G176500"
Phchi.S1	AUGUSTUS	CDS	11323386	11323733	1	-	0	transcript_id "Phchi.S1G176500.t1"; gene_id "Phchi.S1G176500"
Phchi.S1	AUGUSTUS	exon	11323386	11323733	.	-	.	transcript_id "Phchi.S1G176500.t1"; gene_id "Phchi.S1G176500"
Phchi.S1	AUGUSTUS	start_codon	11323731	11323733	.	-	0	transcript_id "Phchi.S1G176500.t1"; gene_id "Phchi.S1G176500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7749.t1 is derived from g4923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30950471	30953636	.	+	.	Phchi.S1G490800
Phchi.S1	AUGUSTUS	transcript	30950471	30953636	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	start_codon	30950471	30950473	.	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30950471	30950572	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30950471	30950572	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30950573	30950699	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30950700	30950871	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30950700	30950871	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30950872	30950963	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30950964	30951127	1	+	2	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30950964	30951127	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30951128	30951305	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30951306	30951416	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30951306	30951416	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30951417	30951506	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30951507	30951586	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30951507	30951586	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30951587	30951727	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30951728	30951878	1	+	1	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30951728	30951878	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30951879	30951997	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30951998	30952091	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30951998	30952091	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30952092	30952223	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30952224	30952312	1	+	2	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30952224	30952312	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30952313	30952393	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30952394	30952467	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30952394	30952467	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30952468	30952544	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30952545	30952707	1	+	1	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30952545	30952707	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30952708	30952802	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30952803	30952885	1	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30952803	30952885	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30952886	30953021	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30953022	30953102	1	+	1	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30953022	30953102	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30953103	30953277	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30953278	30953461	1	+	1	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30953278	30953461	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	intron	30953462	30953555	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	CDS	30953556	30953636	0.72	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	exon	30953556	30953636	.	+	.	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
Phchi.S1	AUGUSTUS	stop_codon	30953637	30953639	.	+	0	transcript_id "Phchi.S1G490800.t1"; gene_id "Phchi.S1G490800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4892.t1 is derived from g2062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13269214	13269843	.	-	.	Phchi.S1G205100
Phchi.S1	AUGUSTUS	transcript	13269214	13269843	.	-	.	transcript_id "Phchi.S1G205100.t1"; gene_id "Phchi.S1G205100"
Phchi.S1	AUGUSTUS	stop_codon	13269211	13269213	.	-	0	transcript_id "Phchi.S1G205100.t1"; gene_id "Phchi.S1G205100"
Phchi.S1	AUGUSTUS	CDS	13269214	13269843	1	-	0	transcript_id "Phchi.S1G205100.t1"; gene_id "Phchi.S1G205100"
Phchi.S1	AUGUSTUS	exon	13269214	13269843	.	-	.	transcript_id "Phchi.S1G205100.t1"; gene_id "Phchi.S1G205100"
Phchi.S1	AUGUSTUS	start_codon	13269841	13269843	.	-	0	transcript_id "Phchi.S1G205100.t1"; gene_id "Phchi.S1G205100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11129.t1 is derived from g15179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4303212	4306743	.	+	.	Phchi.S4G071100
Phchi.S4	AUGUSTUS	transcript	4303212	4306743	.	+	.	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	start_codon	4303212	4303214	.	+	0	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	CDS	4303212	4303442	1	+	0	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	exon	4303212	4303442	.	+	.	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	intron	4303443	4303549	.	+	.	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	CDS	4303550	4303636	0.78	+	0	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	exon	4303550	4303636	.	+	.	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	intron	4303637	4303722	.	+	.	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	CDS	4303723	4306743	1	+	0	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	exon	4303723	4306743	.	+	.	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
Phchi.S4	AUGUSTUS	stop_codon	4306744	4306746	.	+	0	transcript_id "Phchi.S4G071100.t1"; gene_id "Phchi.S4G071100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg721.t1 is derived from g10503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5124746	5125801	.	-	.	Phchi.S6G068000
Phchi.S6	AUGUSTUS	transcript	5124746	5125801	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	stop_codon	5124743	5124745	.	-	0	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	CDS	5124746	5124933	1	-	2	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	exon	5124746	5124933	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	intron	5124934	5125038	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	CDS	5125039	5125218	1	-	2	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	exon	5125039	5125218	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	intron	5125219	5125294	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	CDS	5125295	5125418	1	-	0	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	exon	5125295	5125418	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	intron	5125419	5125513	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	CDS	5125514	5125801	0.83	-	0	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	exon	5125514	5125801	.	-	.	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
Phchi.S6	AUGUSTUS	start_codon	5125799	5125801	.	-	0	transcript_id "Phchi.S6G068000.t1"; gene_id "Phchi.S6G068000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7906.t1 is derived from g5080.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31830786	31835277	.	-	.	Phchi.S1G506500
Phchi.S1	AUGUSTUS	transcript	31830786	31835277	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	stop_codon	31830783	31830785	.	-	0	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31830786	31830987	0.99	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31830786	31830987	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31830988	31831072	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831073	31831206	1	-	0	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831073	31831206	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831207	31831295	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831296	31831428	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831296	31831428	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831429	31831509	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831510	31831653	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831510	31831653	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831654	31831743	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831744	31831858	1	-	2	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831744	31831858	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831859	31831957	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831958	31832084	1	-	0	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831958	31832084	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832085	31832173	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31832174	31832454	1	-	2	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31832174	31832454	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832455	31832543	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31832544	31832725	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31832544	31832725	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832726	31832849	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31832850	31832921	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31832850	31832921	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832922	31833033	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833034	31833105	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833034	31833105	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833106	31833235	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833236	31833304	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833236	31833304	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833305	31833436	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833437	31833508	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833437	31833508	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833509	31833596	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833597	31833726	0.92	-	2	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833597	31833726	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833727	31833832	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833833	31834347	1	-	1	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833833	31834347	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31834348	31834444	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31834445	31834788	1	-	0	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31834445	31834788	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31834789	31834871	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31834872	31835068	1	-	2	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31834872	31835068	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31835069	31835159	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31835160	31835277	0.72	-	0	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31835160	31835277	.	-	.	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	start_codon	31835275	31835277	.	-	0	transcript_id "Phchi.S1G506500.t1"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	transcript	31830830	31835277	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	stop_codon	31830827	31830829	.	-	0	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31830830	31830992	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31830830	31830992	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31830993	31831072	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831073	31831206	1	-	0	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831073	31831206	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831207	31831295	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831296	31831428	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831296	31831428	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831429	31831509	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831510	31831653	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831510	31831653	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831654	31831743	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831744	31831858	1	-	2	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831744	31831858	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31831859	31831957	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31831958	31832084	1	-	0	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31831958	31832084	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832085	31832173	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31832174	31832454	1	-	2	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31832174	31832454	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832455	31832543	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31832544	31832725	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31832544	31832725	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832726	31832849	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31832850	31832921	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31832850	31832921	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31832922	31833033	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833034	31833105	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833034	31833105	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833106	31833235	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833236	31833304	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833236	31833304	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833305	31833436	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833437	31833508	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833437	31833508	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833509	31833596	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833597	31833726	0.82	-	2	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833597	31833726	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31833727	31833832	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31833833	31834347	1	-	1	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31833833	31834347	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31834348	31834444	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31834445	31834788	1	-	0	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31834445	31834788	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31834789	31834871	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31834872	31835068	1	-	2	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31834872	31835068	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	intron	31835069	31835159	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	CDS	31835160	31835277	0.68	-	0	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	exon	31835160	31835277	.	-	.	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
Phchi.S1	AUGUSTUS	start_codon	31835275	31835277	.	-	0	transcript_id "Phchi.S1G506500.t2"; gene_id "Phchi.S1G506500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6833.t1 is derived from g4005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25468870	25470678	.	-	.	Phchi.S1G399200
Phchi.S1	AUGUSTUS	transcript	25468870	25470678	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	stop_codon	25468867	25468869	.	-	0	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	CDS	25468870	25469357	0.62	-	2	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	exon	25468870	25469357	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	intron	25469358	25469544	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	CDS	25469545	25469731	0.98	-	0	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	exon	25469545	25469731	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	intron	25469732	25469818	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	CDS	25469819	25469983	0.96	-	0	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	exon	25469819	25469983	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	intron	25469984	25470099	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	CDS	25470100	25470678	0.9	-	0	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	exon	25470100	25470678	.	-	.	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
Phchi.S1	AUGUSTUS	start_codon	25470676	25470678	.	-	0	transcript_id "Phchi.S1G399200.t1"; gene_id "Phchi.S1G399200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4053.t1 is derived from g1222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7547697	7553035	.	-	.	Phchi.S1G121200
Phchi.S1	AUGUSTUS	transcript	7547697	7553035	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	stop_codon	7547694	7547696	.	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7547697	7547904	1	-	1	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7547697	7547904	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7547905	7548004	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7548005	7548118	1	-	1	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7548005	7548118	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7548119	7548214	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7548215	7548318	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7548215	7548318	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7548319	7548440	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7548441	7548548	0.94	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7548441	7548548	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7548549	7548656	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7548657	7548737	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7548657	7548737	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7548738	7548864	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7548865	7548933	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7548865	7548933	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7548934	7549153	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7549154	7549234	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7549154	7549234	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7549235	7549343	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7549344	7549433	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7549344	7549433	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7549434	7549557	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7549558	7549647	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7549558	7549647	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7549648	7549775	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7549776	7549844	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7549776	7549844	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7549845	7549936	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7549937	7550176	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7549937	7550176	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7550177	7550293	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7550294	7550410	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7550294	7550410	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7550411	7550631	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7550632	7550691	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7550632	7550691	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7550692	7550773	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7550774	7550848	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7550774	7550848	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7550849	7550950	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7550951	7551073	0.98	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7550951	7551073	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7551074	7551159	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7551160	7551249	0.97	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7551160	7551249	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7551250	7551356	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7551357	7551413	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7551357	7551413	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7551414	7551619	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7551620	7551707	1	-	1	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7551620	7551707	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7551708	7551788	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7551789	7551974	1	-	1	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7551789	7551974	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7551975	7552137	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7552138	7552261	1	-	2	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7552138	7552261	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7552262	7552350	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7552351	7552447	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7552351	7552447	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	intron	7552448	7552933	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	CDS	7552934	7553035	1	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	exon	7552934	7553035	.	-	.	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
Phchi.S1	AUGUSTUS	start_codon	7553033	7553035	.	-	0	transcript_id "Phchi.S1G121200.t1"; gene_id "Phchi.S1G121200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15822.t1 is derived from g14292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21589087	21590770	.	+	.	Phchi.S3G314100
Phchi.S3	AUGUSTUS	transcript	21589087	21590770	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	start_codon	21589087	21589089	.	+	0	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	CDS	21589087	21589797	0.76	+	0	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	exon	21589087	21589797	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	intron	21589798	21589947	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	CDS	21589948	21590029	0.89	+	0	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	exon	21589948	21590029	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	intron	21590030	21590144	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	CDS	21590145	21590170	0.95	+	2	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	exon	21590145	21590170	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	intron	21590171	21590248	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	CDS	21590249	21590361	0.64	+	0	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	exon	21590249	21590361	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	intron	21590362	21590446	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	CDS	21590447	21590465	0.66	+	1	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	exon	21590447	21590465	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	intron	21590466	21590689	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	CDS	21590690	21590770	0.66	+	0	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	exon	21590690	21590770	.	+	.	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
Phchi.S3	AUGUSTUS	stop_codon	21590771	21590773	.	+	0	transcript_id "Phchi.S3G314100.t1"; gene_id "Phchi.S3G314100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11097.t1 is derived from g15147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4101868	4102883	.	-	.	Phchi.S4G067900
Phchi.S4	AUGUSTUS	transcript	4101868	4102883	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	stop_codon	4101865	4101867	.	-	0	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	CDS	4101868	4102037	0.7	-	2	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	exon	4101868	4102037	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	intron	4102038	4102146	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	CDS	4102147	4102207	0.37	-	0	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	exon	4102147	4102207	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	intron	4102208	4102278	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	CDS	4102279	4102384	1	-	1	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	exon	4102279	4102384	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	intron	4102385	4102479	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	CDS	4102480	4102529	1	-	0	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	exon	4102480	4102529	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	intron	4102530	4102709	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	CDS	4102710	4102883	0.94	-	0	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	exon	4102710	4102883	.	-	.	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
Phchi.S4	AUGUSTUS	start_codon	4102881	4102883	.	-	0	transcript_id "Phchi.S4G067900.t1"; gene_id "Phchi.S4G067900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3627.t1 is derived from g796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4836662	4841633	.	+	.	Phchi.S1G078600
Phchi.S1	AUGUSTUS	transcript	4836662	4841633	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	start_codon	4836662	4836664	.	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4836662	4836729	0.57	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4836662	4836729	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4836730	4837349	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4837350	4837416	1	+	1	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4837350	4837416	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4837417	4837562	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4837563	4837628	1	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4837563	4837628	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4837629	4837780	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4837781	4837827	1	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4837781	4837827	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4837828	4837904	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4837905	4837961	0.67	+	1	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4837905	4837961	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4837962	4838080	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4838081	4838150	0.67	+	1	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4838081	4838150	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4838151	4838236	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4838237	4838279	1	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4838237	4838279	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4838280	4838420	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4838421	4838470	1	+	2	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4838421	4838470	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4838471	4838553	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4838554	4838635	1	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4838554	4838635	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4838636	4838759	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4838760	4838809	1	+	2	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4838760	4838809	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4838810	4838895	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4838896	4838969	1	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4838896	4838969	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4838970	4839088	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4839089	4839140	1	+	1	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4839089	4839140	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4839141	4839240	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4839241	4839777	0.82	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4839241	4839777	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4839778	4839962	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4839963	4841297	0.82	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4839963	4841297	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	intron	4841298	4841621	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	CDS	4841622	4841633	1	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	exon	4841622	4841633	.	+	.	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
Phchi.S1	AUGUSTUS	stop_codon	4841634	4841636	.	+	0	transcript_id "Phchi.S1G078600.t1"; gene_id "Phchi.S1G078600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8730.t1 is derived from g5905.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37701632	37704622	.	-	.	Phchi.S1G588900
Phchi.S1	AUGUSTUS	transcript	37703625	37704622	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	stop_codon	37703622	37703624	.	-	0	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37703625	37703656	0.99	-	2	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37703625	37703656	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37703657	37703925	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37703926	37704114	1	-	2	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37703926	37704114	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37704115	37704220	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37704221	37704317	0.96	-	0	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37704221	37704317	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37704318	37704478	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37704479	37704622	0.99	-	0	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37704479	37704622	.	-	.	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	start_codon	37704620	37704622	.	-	0	transcript_id "Phchi.S1G588900.t1"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	transcript	37701632	37704622	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	stop_codon	37701629	37701631	.	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37701632	37701793	0.99	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37701632	37701793	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37701794	37701887	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37701888	37701986	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37701888	37701986	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37701987	37702073	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37702074	37702142	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37702074	37702142	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37702143	37702238	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37702239	37702277	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37702239	37702277	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37702278	37702419	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37702420	37702533	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37702420	37702533	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37702534	37702624	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37702625	37702774	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37702625	37702774	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37702775	37702887	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37702888	37703013	0.55	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37702888	37703013	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37703014	37703164	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37703165	37703248	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37703165	37703248	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37703249	37703349	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37703350	37703421	1	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37703350	37703421	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37703422	37703497	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37703498	37703598	1	-	2	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37703498	37703598	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37703599	37703925	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37703926	37704114	0.99	-	2	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37703926	37704114	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37704115	37704220	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37704221	37704317	0.98	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37704221	37704317	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	intron	37704318	37704478	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	CDS	37704479	37704622	0.99	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	exon	37704479	37704622	.	-	.	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
Phchi.S1	AUGUSTUS	start_codon	37704620	37704622	.	-	0	transcript_id "Phchi.S1G588900.t2"; gene_id "Phchi.S1G588900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9542.t1 is derived from g6718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42398406	42399764	.	+	.	Phchi.S1G670100
Phchi.S1	AUGUSTUS	transcript	42398406	42399764	.	+	.	transcript_id "Phchi.S1G670100.t1"; gene_id "Phchi.S1G670100"
Phchi.S1	AUGUSTUS	start_codon	42398406	42398408	.	+	0	transcript_id "Phchi.S1G670100.t1"; gene_id "Phchi.S1G670100"
Phchi.S1	AUGUSTUS	CDS	42398406	42399764	0.81	+	0	transcript_id "Phchi.S1G670100.t1"; gene_id "Phchi.S1G670100"
Phchi.S1	AUGUSTUS	exon	42398406	42399764	.	+	.	transcript_id "Phchi.S1G670100.t1"; gene_id "Phchi.S1G670100"
Phchi.S1	AUGUSTUS	stop_codon	42399765	42399767	.	+	0	transcript_id "Phchi.S1G670100.t1"; gene_id "Phchi.S1G670100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg46.t1 is derived from g9828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	62830	63625	.	-	.	Phchi.S6G000500
Phchi.S6	AUGUSTUS	transcript	62830	63625	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	stop_codon	62827	62829	.	-	0	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	CDS	62830	62830	0.88	-	1	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	exon	62830	62830	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	intron	62831	62916	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	CDS	62917	63032	0.88	-	0	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	exon	62917	63032	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	intron	63033	63273	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	CDS	63274	63389	0.51	-	2	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	exon	63274	63389	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	intron	63390	63570	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	CDS	63571	63625	0.51	-	0	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	exon	63571	63625	.	-	.	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
Phchi.S6	AUGUSTUS	start_codon	63623	63625	.	-	0	transcript_id "Phchi.S6G000500.t1"; gene_id "Phchi.S6G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7747.t1 is derived from g4921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30938566	30940652	.	-	.	Phchi.S1G490600
Phchi.S1	AUGUSTUS	transcript	30938566	30940652	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	stop_codon	30938563	30938565	.	-	0	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	CDS	30938566	30939012	1	-	0	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	exon	30938566	30939012	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	intron	30939013	30939466	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	CDS	30939467	30939686	0.96	-	1	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	exon	30939467	30939686	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	intron	30939687	30939815	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	CDS	30939816	30940142	0.95	-	1	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	exon	30939816	30940142	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	intron	30940143	30940307	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	CDS	30940308	30940362	1	-	2	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	exon	30940308	30940362	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	intron	30940363	30940639	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	CDS	30940640	30940652	0.38	-	0	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	exon	30940640	30940652	.	-	.	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
Phchi.S1	AUGUSTUS	start_codon	30940650	30940652	.	-	0	transcript_id "Phchi.S1G490600.t1"; gene_id "Phchi.S1G490600"
# This transcript jg6913.t2 is derived from g4085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6914.t1 is derived from g4086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25975963	25977612	.	-	.	Phchi.S1G407300
Phchi.S1	AUGUSTUS	transcript	25975963	25977612	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	stop_codon	25975960	25975962	.	-	0	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	CDS	25975963	25976091	1	-	0	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	exon	25975963	25976091	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	intron	25976092	25976180	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	CDS	25976181	25976231	1	-	0	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	exon	25976181	25976231	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	intron	25976232	25976311	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	CDS	25976312	25976378	1	-	1	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	exon	25976312	25976378	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	intron	25976379	25976475	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	CDS	25976476	25976738	1	-	0	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	exon	25976476	25976738	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	intron	25976739	25976835	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	CDS	25976836	25977612	0.93	-	0	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	exon	25976836	25977612	.	-	.	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
Phchi.S1	AUGUSTUS	start_codon	25977610	25977612	.	-	0	transcript_id "Phchi.S1G407300.t1"; gene_id "Phchi.S1G407300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3382.t1 is derived from g551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3266625	3267681	.	-	.	Phchi.S1G054100
Phchi.S1	AUGUSTUS	transcript	3266625	3267681	.	-	.	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	stop_codon	3266622	3266624	.	-	0	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	CDS	3266625	3267097	0.72	-	2	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	exon	3266625	3267097	.	-	.	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	intron	3267098	3267234	.	-	.	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	CDS	3267235	3267427	0.36	-	0	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	exon	3267235	3267427	.	-	.	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	intron	3267428	3267546	.	-	.	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	CDS	3267547	3267681	0.53	-	0	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	exon	3267547	3267681	.	-	.	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	start_codon	3267679	3267681	.	-	0	transcript_id "Phchi.S1G054100.t1"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	transcript	3267065	3267681	.	-	.	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	stop_codon	3267062	3267064	.	-	0	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	CDS	3267065	3267097	0.42	-	0	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	exon	3267065	3267097	.	-	.	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	intron	3267098	3267256	.	-	.	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	CDS	3267257	3267427	0.27	-	0	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	exon	3267257	3267427	.	-	.	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	intron	3267428	3267546	.	-	.	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	CDS	3267547	3267681	0.55	-	0	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	exon	3267547	3267681	.	-	.	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
Phchi.S1	AUGUSTUS	start_codon	3267679	3267681	.	-	0	transcript_id "Phchi.S1G054100.t2"; gene_id "Phchi.S1G054100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12338.t1 is derived from g8014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11297217	11298917	.	+	.	Phchi.S2G041800
Phchi.S2	AUGUSTUS	transcript	11297217	11298917	.	+	.	transcript_id "Phchi.S2G041800.t1"; gene_id "Phchi.S2G041800"
Phchi.S2	AUGUSTUS	start_codon	11297217	11297219	.	+	0	transcript_id "Phchi.S2G041800.t1"; gene_id "Phchi.S2G041800"
Phchi.S2	AUGUSTUS	CDS	11297217	11298917	0.81	+	0	transcript_id "Phchi.S2G041800.t1"; gene_id "Phchi.S2G041800"
Phchi.S2	AUGUSTUS	exon	11297217	11298917	.	+	.	transcript_id "Phchi.S2G041800.t1"; gene_id "Phchi.S2G041800"
Phchi.S2	AUGUSTUS	stop_codon	11298918	11298920	.	+	0	transcript_id "Phchi.S2G041800.t1"; gene_id "Phchi.S2G041800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10675.t1 is derived from g14725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1551473	1551949	.	+	.	Phchi.S4G025700
Phchi.S4	AUGUSTUS	transcript	1551473	1551949	.	+	.	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	start_codon	1551473	1551475	.	+	0	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	CDS	1551473	1551673	0.61	+	0	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	exon	1551473	1551673	.	+	.	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	intron	1551674	1551793	.	+	.	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	CDS	1551794	1551949	0.59	+	0	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	exon	1551794	1551949	.	+	.	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
Phchi.S4	AUGUSTUS	stop_codon	1551950	1551952	.	+	0	transcript_id "Phchi.S4G025700.t1"; gene_id "Phchi.S4G025700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6186.t1 is derived from g3357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21376162	21377236	.	-	.	Phchi.S1G334500
Phchi.S1	AUGUSTUS	transcript	21376162	21377236	.	-	.	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	stop_codon	21376159	21376161	.	-	0	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	CDS	21376162	21376824	1	-	0	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	exon	21376162	21376824	.	-	.	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	intron	21376825	21376896	.	-	.	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	CDS	21376897	21377122	0.41	-	1	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	exon	21376897	21377122	.	-	.	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	intron	21377123	21377207	.	-	.	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	CDS	21377208	21377236	0.42	-	0	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	exon	21377208	21377236	.	-	.	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
Phchi.S1	AUGUSTUS	start_codon	21377234	21377236	.	-	0	transcript_id "Phchi.S1G334500.t1"; gene_id "Phchi.S1G334500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2135.t1 is derived from g9055.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5015007	5016006	.	-	.	Phchi.S5G074400
Phchi.S5	AUGUSTUS	transcript	5015007	5016006	.	-	.	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	stop_codon	5015004	5015006	.	-	0	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	CDS	5015007	5015049	0.92	-	1	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	exon	5015007	5015049	.	-	.	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	intron	5015050	5015482	.	-	.	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	CDS	5015483	5015596	1	-	1	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	exon	5015483	5015596	.	-	.	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	intron	5015597	5015731	.	-	.	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	CDS	5015732	5016006	0.29	-	0	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	exon	5015732	5016006	.	-	.	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	start_codon	5016004	5016006	.	-	0	transcript_id "Phchi.S5G074400.t1"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	transcript	5015257	5016006	.	-	.	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	stop_codon	5015254	5015256	.	-	0	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	CDS	5015257	5015281	0.79	-	1	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	exon	5015257	5015281	.	-	.	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	intron	5015282	5015482	.	-	.	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	CDS	5015483	5015596	1	-	1	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	exon	5015483	5015596	.	-	.	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	intron	5015597	5015731	.	-	.	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	CDS	5015732	5016006	0.27	-	0	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	exon	5015732	5016006	.	-	.	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
Phchi.S5	AUGUSTUS	start_codon	5016004	5016006	.	-	0	transcript_id "Phchi.S5G074400.t2"; gene_id "Phchi.S5G074400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5024.t1 is derived from g2194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14098548	14100577	.	+	.	Phchi.S1G218300
Phchi.S1	AUGUSTUS	transcript	14098548	14100577	.	+	.	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	start_codon	14098548	14098550	.	+	0	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	CDS	14098548	14099741	1	+	0	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	exon	14098548	14099741	.	+	.	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	intron	14099742	14099944	.	+	.	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	CDS	14099945	14100052	0.93	+	0	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	exon	14099945	14100052	.	+	.	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	intron	14100053	14100118	.	+	.	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	CDS	14100119	14100577	0.78	+	0	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	exon	14100119	14100577	.	+	.	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
Phchi.S1	AUGUSTUS	stop_codon	14100578	14100580	.	+	0	transcript_id "Phchi.S1G218300.t1"; gene_id "Phchi.S1G218300"
# This transcript jg10746.t2 is derived from g14796.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10747.t1 is derived from g14797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1902638	1903551	.	+	.	Phchi.S4G032900
Phchi.S4	AUGUSTUS	transcript	1902638	1903551	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	start_codon	1902638	1902640	.	+	0	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	CDS	1902638	1902817	0.9	+	0	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	exon	1902638	1902817	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	intron	1902818	1902984	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	CDS	1902985	1903155	1	+	0	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	exon	1902985	1903155	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	intron	1903156	1903239	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	CDS	1903240	1903332	1	+	0	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	exon	1903240	1903332	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	intron	1903333	1903431	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	CDS	1903432	1903551	1	+	0	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	exon	1903432	1903551	.	+	.	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
Phchi.S4	AUGUSTUS	stop_codon	1903552	1903554	.	+	0	transcript_id "Phchi.S4G032900.t1"; gene_id "Phchi.S4G032900"
# This transcript jg10501.t2 is derived from g14550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10502.t1 is derived from g14551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	728794	729342	.	-	.	Phchi.S4G008400
Phchi.S4	AUGUSTUS	transcript	728794	729342	.	-	.	transcript_id "Phchi.S4G008400.t1"; gene_id "Phchi.S4G008400"
Phchi.S4	AUGUSTUS	stop_codon	728791	728793	.	-	0	transcript_id "Phchi.S4G008400.t1"; gene_id "Phchi.S4G008400"
Phchi.S4	AUGUSTUS	CDS	728794	729342	0.88	-	0	transcript_id "Phchi.S4G008400.t1"; gene_id "Phchi.S4G008400"
Phchi.S4	AUGUSTUS	exon	728794	729342	.	-	.	transcript_id "Phchi.S4G008400.t1"; gene_id "Phchi.S4G008400"
Phchi.S4	AUGUSTUS	start_codon	729340	729342	.	-	0	transcript_id "Phchi.S4G008400.t1"; gene_id "Phchi.S4G008400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13550.t1 is derived from g12017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7459565	7460138	.	-	.	Phchi.S3G086900
Phchi.S3	AUGUSTUS	transcript	7459565	7460138	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	stop_codon	7459562	7459564	.	-	0	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	CDS	7459565	7459600	1	-	0	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	exon	7459565	7459600	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	intron	7459601	7459686	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	CDS	7459687	7459751	1	-	2	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	exon	7459687	7459751	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	intron	7459752	7459864	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	CDS	7459865	7459926	1	-	1	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	exon	7459865	7459926	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	intron	7459927	7460058	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	CDS	7460059	7460138	0.84	-	0	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	exon	7460059	7460138	.	-	.	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
Phchi.S3	AUGUSTUS	start_codon	7460136	7460138	.	-	0	transcript_id "Phchi.S3G086900.t1"; gene_id "Phchi.S3G086900"
# This transcript jg3637.t2 is derived from g806.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3638.t1 is derived from g807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4894476	4895177	.	+	.	Phchi.S1G079700
Phchi.S1	AUGUSTUS	transcript	4894476	4895177	.	+	.	transcript_id "Phchi.S1G079700.t1"; gene_id "Phchi.S1G079700"
Phchi.S1	AUGUSTUS	start_codon	4894476	4894478	.	+	0	transcript_id "Phchi.S1G079700.t1"; gene_id "Phchi.S1G079700"
Phchi.S1	AUGUSTUS	CDS	4894476	4895177	0.55	+	0	transcript_id "Phchi.S1G079700.t1"; gene_id "Phchi.S1G079700"
Phchi.S1	AUGUSTUS	exon	4894476	4895177	.	+	.	transcript_id "Phchi.S1G079700.t1"; gene_id "Phchi.S1G079700"
Phchi.S1	AUGUSTUS	stop_codon	4895178	4895180	.	+	0	transcript_id "Phchi.S1G079700.t1"; gene_id "Phchi.S1G079700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2575.t1 is derived from g9495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7441561	7442363	.	-	.	Phchi.S5G118400
Phchi.S5	AUGUSTUS	transcript	7441561	7442363	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	stop_codon	7441558	7441560	.	-	0	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	CDS	7441561	7441655	0.99	-	2	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	exon	7441561	7441655	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	intron	7441656	7441747	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	CDS	7441748	7441971	0.75	-	1	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	exon	7441748	7441971	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	intron	7441972	7442071	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	CDS	7442072	7442104	1	-	1	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	exon	7442072	7442104	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	intron	7442105	7442244	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	CDS	7442245	7442363	0.41	-	0	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	exon	7442245	7442363	.	-	.	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
Phchi.S5	AUGUSTUS	start_codon	7442361	7442363	.	-	0	transcript_id "Phchi.S5G118400.t1"; gene_id "Phchi.S5G118400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5005.t1 is derived from g2175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13965632	13967845	.	+	.	Phchi.S1G216400
Phchi.S1	AUGUSTUS	transcript	13965632	13967845	.	+	.	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	start_codon	13965632	13965634	.	+	0	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	CDS	13965632	13967292	0.39	+	0	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	exon	13965632	13967292	.	+	.	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	intron	13967293	13967442	.	+	.	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	CDS	13967443	13967845	0.9	+	1	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	exon	13967443	13967845	.	+	.	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
Phchi.S1	AUGUSTUS	stop_codon	13967846	13967848	.	+	0	transcript_id "Phchi.S1G216400.t1"; gene_id "Phchi.S1G216400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13865.t1 is derived from g12332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9304398	9305027	.	+	.	Phchi.S3G118400
Phchi.S3	AUGUSTUS	transcript	9304398	9305027	.	+	.	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	start_codon	9304398	9304400	.	+	0	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	CDS	9304398	9304509	0.96	+	0	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	exon	9304398	9304509	.	+	.	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	intron	9304510	9304632	.	+	.	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	CDS	9304633	9304738	0.98	+	2	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	exon	9304633	9304738	.	+	.	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	intron	9304739	9304960	.	+	.	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	CDS	9304961	9305027	0.98	+	1	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	exon	9304961	9305027	.	+	.	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
Phchi.S3	AUGUSTUS	stop_codon	9305028	9305030	.	+	0	transcript_id "Phchi.S3G118400.t1"; gene_id "Phchi.S3G118400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1245.t1 is derived from g11028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8622424	8622862	.	-	.	Phchi.S6G120400
Phchi.S6	AUGUSTUS	transcript	8622424	8622862	.	-	.	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	stop_codon	8622421	8622423	.	-	0	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	CDS	8622424	8622469	0.77	-	1	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	exon	8622424	8622469	.	-	.	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	intron	8622470	8622557	.	-	.	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	CDS	8622558	8622625	0.74	-	0	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	exon	8622558	8622625	.	-	.	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	intron	8622626	8622721	.	-	.	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	CDS	8622722	8622862	0.26	-	0	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	exon	8622722	8622862	.	-	.	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
Phchi.S6	AUGUSTUS	start_codon	8622860	8622862	.	-	0	transcript_id "Phchi.S6G120400.t1"; gene_id "Phchi.S6G120400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6325.t1 is derived from g3497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22289355	22291018	.	+	.	Phchi.S1G348400
Phchi.S1	AUGUSTUS	transcript	22289355	22291018	.	+	.	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	start_codon	22289355	22289357	.	+	0	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	CDS	22289355	22290174	0.56	+	0	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	exon	22289355	22290174	.	+	.	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	intron	22290175	22290353	.	+	.	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	CDS	22290354	22291018	0.38	+	2	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	exon	22290354	22291018	.	+	.	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
Phchi.S1	AUGUSTUS	stop_codon	22291019	22291021	.	+	0	transcript_id "Phchi.S1G348400.t1"; gene_id "Phchi.S1G348400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13210.t1 is derived from g11675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4699078	4700939	.	-	.	Phchi.S3G052900
Phchi.S3	AUGUSTUS	transcript	4699078	4700939	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	stop_codon	4699075	4699077	.	-	0	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	CDS	4699078	4699586	1	-	2	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	exon	4699078	4699586	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	intron	4699587	4699705	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	CDS	4699706	4700257	0.69	-	2	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	exon	4699706	4700257	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	intron	4700258	4700372	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	CDS	4700373	4700602	0.71	-	1	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	exon	4700373	4700602	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	intron	4700603	4700679	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	CDS	4700680	4700939	0.37	-	0	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	exon	4700680	4700939	.	-	.	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
Phchi.S3	AUGUSTUS	start_codon	4700937	4700939	.	-	0	transcript_id "Phchi.S3G052900.t1"; gene_id "Phchi.S3G052900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9437.t1 is derived from g6613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41451975	41455582	.	+	.	Phchi.S1G659600
Phchi.S1	AUGUSTUS	transcript	41451975	41455582	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	start_codon	41451975	41451977	.	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41451975	41452072	0.95	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41451975	41452072	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41452073	41452292	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41452293	41452397	1	+	1	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41452293	41452397	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41452398	41452548	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41452549	41452666	1	+	1	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41452549	41452666	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41452667	41452747	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41452748	41452798	1	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41452748	41452798	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41452799	41452890	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41452891	41452982	1	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41452891	41452982	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41452983	41453245	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41453246	41453345	1	+	1	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41453246	41453345	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41453346	41453524	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41453525	41453644	1	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41453525	41453644	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41453645	41453726	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41453727	41453804	1	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41453727	41453804	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41453805	41453897	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41453898	41453944	1	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41453898	41453944	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41453945	41454078	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41454079	41454134	1	+	1	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41454079	41454134	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41454135	41454230	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41454231	41454271	1	+	2	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41454231	41454271	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41454272	41454389	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41454390	41454501	1	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41454390	41454501	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41454502	41454626	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41454627	41454789	1	+	2	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41454627	41454789	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	intron	41454790	41454876	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	CDS	41454877	41455582	1	+	1	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	exon	41454877	41455582	.	+	.	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
Phchi.S1	AUGUSTUS	stop_codon	41455583	41455585	.	+	0	transcript_id "Phchi.S1G659600.t1"; gene_id "Phchi.S1G659600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5525.t1 is derived from g2695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17414981	17416565	.	+	.	Phchi.S1G268400
Phchi.S1	AUGUSTUS	transcript	17414981	17416565	.	+	.	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	start_codon	17414981	17414983	.	+	0	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	CDS	17414981	17415379	0.98	+	0	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	exon	17414981	17415379	.	+	.	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	intron	17415380	17415593	.	+	.	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	CDS	17415594	17416565	0.95	+	0	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	exon	17415594	17416565	.	+	.	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
Phchi.S1	AUGUSTUS	stop_codon	17416566	17416568	.	+	0	transcript_id "Phchi.S1G268400.t1"; gene_id "Phchi.S1G268400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4273.t1 is derived from g1442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9338238	9339170	.	+	.	Phchi.S1G143200
Phchi.S1	AUGUSTUS	transcript	9338238	9339170	.	+	.	transcript_id "Phchi.S1G143200.t1"; gene_id "Phchi.S1G143200"
Phchi.S1	AUGUSTUS	start_codon	9338238	9338240	.	+	0	transcript_id "Phchi.S1G143200.t1"; gene_id "Phchi.S1G143200"
Phchi.S1	AUGUSTUS	CDS	9338238	9339170	0.88	+	0	transcript_id "Phchi.S1G143200.t1"; gene_id "Phchi.S1G143200"
Phchi.S1	AUGUSTUS	exon	9338238	9339170	.	+	.	transcript_id "Phchi.S1G143200.t1"; gene_id "Phchi.S1G143200"
Phchi.S1	AUGUSTUS	stop_codon	9339171	9339173	.	+	0	transcript_id "Phchi.S1G143200.t1"; gene_id "Phchi.S1G143200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10555.t1 is derived from g14605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	967385	971171	.	+	.	Phchi.S4G013700
Phchi.S4	AUGUSTUS	transcript	967385	971171	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	start_codon	967385	967387	.	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	967385	967560	0.59	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	967385	967560	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	967561	967715	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	967716	967752	1	+	1	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	967716	967752	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	967753	967845	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	967846	967949	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	967846	967949	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	967950	968130	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	968131	968326	1	+	1	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	968131	968326	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	968327	968424	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	968425	968491	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	968425	968491	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	968492	968570	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	968571	968674	1	+	2	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	968571	968674	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	968675	968845	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	968846	968924	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	968846	968924	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	968925	969094	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	969095	969152	0.99	+	2	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	969095	969152	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	969153	969254	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	969255	969386	1	+	1	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	969255	969386	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	969387	969504	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	969505	969574	1	+	1	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	969505	969574	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	969575	969658	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	969659	969716	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	969659	969716	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	969717	969815	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	969816	969871	1	+	2	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	969816	969871	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	969872	969956	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	969957	970109	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	969957	970109	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	970110	970281	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	970282	970393	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	970282	970393	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	970394	970471	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	970472	970613	1	+	2	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	970472	970613	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	970614	970715	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	970716	970791	1	+	1	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	970716	970791	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	970792	970868	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	970869	970964	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	970869	970964	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	intron	970965	971045	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	CDS	971046	971171	1	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	exon	971046	971171	.	+	.	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
Phchi.S4	AUGUSTUS	stop_codon	971172	971174	.	+	0	transcript_id "Phchi.S4G013700.t1"; gene_id "Phchi.S4G013700"
# This transcript jg13607.t2 is derived from g12074.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13608.t1 is derived from g12075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7679332	7681017	.	-	.	Phchi.S3G092700
Phchi.S3	AUGUSTUS	transcript	7679332	7681017	.	-	.	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	stop_codon	7679329	7679331	.	-	0	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	CDS	7679332	7680361	1	-	1	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	exon	7679332	7680361	.	-	.	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	intron	7680362	7680544	.	-	.	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	CDS	7680545	7681017	0.56	-	0	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	exon	7680545	7681017	.	-	.	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
Phchi.S3	AUGUSTUS	start_codon	7681015	7681017	.	-	0	transcript_id "Phchi.S3G092700.t1"; gene_id "Phchi.S3G092700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14875.t1 is derived from g13343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15236752	15238277	.	+	.	Phchi.S3G219400
Phchi.S3	AUGUSTUS	transcript	15236752	15238277	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	start_codon	15236752	15236754	.	+	0	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	CDS	15236752	15236763	0.89	+	0	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	exon	15236752	15236763	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	intron	15236764	15236857	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	CDS	15236858	15236872	0.98	+	0	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	exon	15236858	15236872	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	intron	15236873	15236943	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	CDS	15236944	15237246	0.65	+	0	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	exon	15236944	15237246	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	intron	15237247	15237398	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	CDS	15237399	15238277	0.77	+	0	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	exon	15237399	15238277	.	+	.	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
Phchi.S3	AUGUSTUS	stop_codon	15238278	15238280	.	+	0	transcript_id "Phchi.S3G219400.t1"; gene_id "Phchi.S3G219400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6811.t1 is derived from g3983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25164686	25166046	.	-	.	Phchi.S1G397000
Phchi.S1	AUGUSTUS	transcript	25164686	25166046	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	stop_codon	25164683	25164685	.	-	0	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	CDS	25164686	25164990	1	-	2	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	exon	25164686	25164990	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	intron	25164991	25165120	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	CDS	25165121	25165233	0.99	-	1	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	exon	25165121	25165233	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	intron	25165234	25165380	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	CDS	25165381	25165643	0.99	-	0	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	exon	25165381	25165643	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	intron	25165644	25165740	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	CDS	25165741	25166046	1	-	0	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	exon	25165741	25166046	.	-	.	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
Phchi.S1	AUGUSTUS	start_codon	25166044	25166046	.	-	0	transcript_id "Phchi.S1G397000.t1"; gene_id "Phchi.S1G397000"
# This transcript jg14134.t2 is derived from g12601.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14134.t3 is derived from g12601.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14135.t1 is derived from g12602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11080765	11081569	.	+	.	Phchi.S3G145400
Phchi.S3	AUGUSTUS	transcript	11080765	11081569	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	start_codon	11080765	11080767	.	+	0	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	CDS	11080765	11080896	0.89	+	0	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	exon	11080765	11080896	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	intron	11080897	11081007	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	CDS	11081008	11081165	0.96	+	0	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	exon	11081008	11081165	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	intron	11081166	11081256	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	CDS	11081257	11081323	1	+	1	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	exon	11081257	11081323	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	intron	11081324	11081473	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	CDS	11081474	11081569	1	+	0	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	exon	11081474	11081569	.	+	.	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
Phchi.S3	AUGUSTUS	stop_codon	11081570	11081572	.	+	0	transcript_id "Phchi.S3G145400.t1"; gene_id "Phchi.S3G145400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8132.t1 is derived from g5307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33722775	33726284	.	-	.	Phchi.S1G529100
Phchi.S1	AUGUSTUS	transcript	33722775	33726284	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	stop_codon	33722772	33722774	.	-	0	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	CDS	33722775	33723062	0.82	-	0	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	exon	33722775	33723062	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	intron	33723063	33723342	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	CDS	33723343	33723627	0.99	-	0	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	exon	33723343	33723627	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	intron	33723628	33723779	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	CDS	33723780	33723960	1	-	1	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	exon	33723780	33723960	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	intron	33723961	33724139	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	CDS	33724140	33724290	1	-	2	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	exon	33724140	33724290	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	intron	33724291	33724387	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	CDS	33724388	33726284	0.65	-	0	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	exon	33724388	33726284	.	-	.	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
Phchi.S1	AUGUSTUS	start_codon	33726282	33726284	.	-	0	transcript_id "Phchi.S1G529100.t1"; gene_id "Phchi.S1G529100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3824.t1 is derived from g993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5896876	5897895	.	-	.	Phchi.S1G098300
Phchi.S1	AUGUSTUS	transcript	5896876	5897895	.	-	.	transcript_id "Phchi.S1G098300.t1"; gene_id "Phchi.S1G098300"
Phchi.S1	AUGUSTUS	stop_codon	5896873	5896875	.	-	0	transcript_id "Phchi.S1G098300.t1"; gene_id "Phchi.S1G098300"
Phchi.S1	AUGUSTUS	CDS	5896876	5897895	0.69	-	0	transcript_id "Phchi.S1G098300.t1"; gene_id "Phchi.S1G098300"
Phchi.S1	AUGUSTUS	exon	5896876	5897895	.	-	.	transcript_id "Phchi.S1G098300.t1"; gene_id "Phchi.S1G098300"
Phchi.S1	AUGUSTUS	start_codon	5897893	5897895	.	-	0	transcript_id "Phchi.S1G098300.t1"; gene_id "Phchi.S1G098300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8282.t1 is derived from g5457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35081866	35082654	.	-	.	Phchi.S1G544100
Phchi.S1	AUGUSTUS	transcript	35081866	35082654	.	-	.	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	stop_codon	35081863	35081865	.	-	0	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	CDS	35081866	35081933	0.98	-	2	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	exon	35081866	35081933	.	-	.	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	intron	35081934	35082005	.	-	.	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	CDS	35082006	35082654	0.46	-	0	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	exon	35082006	35082654	.	-	.	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
Phchi.S1	AUGUSTUS	start_codon	35082652	35082654	.	-	0	transcript_id "Phchi.S1G544100.t1"; gene_id "Phchi.S1G544100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12999.t1 is derived from g11464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3574357	3577882	.	+	.	Phchi.S3G031800
Phchi.S3	AUGUSTUS	transcript	3574357	3577882	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	start_codon	3574357	3574359	.	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3574357	3574431	0.55	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3574357	3574431	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3574432	3574518	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3574519	3574718	0.6	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3574519	3574718	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3574719	3574798	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3574799	3575017	0.99	+	1	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3574799	3575017	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3575018	3575101	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3575102	3575275	1	+	1	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3575102	3575275	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3575276	3575375	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3575376	3575676	1	+	1	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3575376	3575676	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3575677	3575757	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3575758	3575943	1	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3575758	3575943	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3575944	3576028	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3576029	3576062	0.24	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3576029	3576062	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3576063	3576223	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3576224	3576246	0.54	+	2	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3576224	3576246	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	intron	3576247	3576334	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	CDS	3576335	3577882	0.86	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	exon	3576335	3577882	.	+	.	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
Phchi.S3	AUGUSTUS	stop_codon	3577883	3577885	.	+	0	transcript_id "Phchi.S3G031800.t1"; gene_id "Phchi.S3G031800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6250.t1 is derived from g3422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21871905	21874452	.	-	.	Phchi.S1G340900
Phchi.S1	AUGUSTUS	transcript	21871905	21874452	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	stop_codon	21871902	21871904	.	-	0	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	CDS	21871905	21871929	0.62	-	1	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	exon	21871905	21871929	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	intron	21871930	21872123	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	CDS	21872124	21872156	0.62	-	1	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	exon	21872124	21872156	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	intron	21872157	21872253	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	CDS	21872254	21873251	0.9	-	0	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	exon	21872254	21873251	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	intron	21873252	21873353	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	CDS	21873354	21873563	0.98	-	0	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	exon	21873354	21873563	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	intron	21873564	21873681	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	CDS	21873682	21874452	0.48	-	0	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	exon	21873682	21874452	.	-	.	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
Phchi.S1	AUGUSTUS	start_codon	21874450	21874452	.	-	0	transcript_id "Phchi.S1G340900.t1"; gene_id "Phchi.S1G340900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg132.t1 is derived from g9914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	713707	719561	.	-	.	Phchi.S6G009100
Phchi.S6	AUGUSTUS	transcript	713707	719561	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	stop_codon	713704	713706	.	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	713707	714494	0.99	-	2	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	713707	714494	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	714495	714593	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	714594	714711	1	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	714594	714711	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	714712	714807	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	714808	714984	1	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	714808	714984	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	714985	715079	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	715080	715203	1	-	1	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	715080	715203	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	715204	715301	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	715302	715368	0.95	-	2	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	715302	715368	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	715369	715471	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	715472	715576	1	-	2	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	715472	715576	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	715577	715718	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	715719	715830	1	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	715719	715830	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	715831	715934	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	715935	716047	1	-	2	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	715935	716047	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	716048	716147	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	716148	716271	1	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	716148	716271	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	716272	716382	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	716383	717493	1	-	1	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	716383	717493	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	717494	717634	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	717635	717742	1	-	1	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	717635	717742	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	717743	717846	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	717847	717938	1	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	717847	717938	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	717939	718086	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	718087	718296	0.51	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	718087	718296	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	718297	718525	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	718526	719182	0.92	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	718526	719182	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	intron	719183	719267	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	CDS	719268	719561	0.92	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	exon	719268	719561	.	-	.	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
Phchi.S6	AUGUSTUS	start_codon	719559	719561	.	-	0	transcript_id "Phchi.S6G009100.t1"; gene_id "Phchi.S6G009100"
# This transcript jg8414.t2 is derived from g5589.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8415.t1 is derived from g5590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35842267	35844574	.	+	.	Phchi.S1G557400
Phchi.S1	AUGUSTUS	transcript	35842267	35844574	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	start_codon	35842267	35842269	.	+	0	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	CDS	35842267	35842401	0.44	+	0	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	exon	35842267	35842401	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	intron	35842402	35842499	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	CDS	35842500	35842554	0.89	+	0	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	exon	35842500	35842554	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	intron	35842555	35842725	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	CDS	35842726	35842904	0.94	+	2	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	exon	35842726	35842904	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	intron	35842905	35843063	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	CDS	35843064	35843521	0.98	+	0	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	exon	35843064	35843521	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	intron	35843522	35843618	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	CDS	35843619	35844145	0.83	+	1	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	exon	35843619	35844145	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	intron	35844146	35844266	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	CDS	35844267	35844574	0.23	+	2	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	exon	35844267	35844574	.	+	.	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
Phchi.S1	AUGUSTUS	stop_codon	35844575	35844577	.	+	0	transcript_id "Phchi.S1G557400.t1"; gene_id "Phchi.S1G557400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1373.t1 is derived from g16015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C216	AUGUSTUS	gene	20582	21100	.	-	.	Phchi.C216G000100
Phchi.C216	AUGUSTUS	transcript	20582	21100	.	-	.	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	stop_codon	20579	20581	.	-	0	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	CDS	20582	20916	0.57	-	2	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	exon	20582	20916	.	-	.	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	intron	20917	21045	.	-	.	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	CDS	21046	21100	0.35	-	0	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	exon	21046	21100	.	-	.	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
Phchi.C216	AUGUSTUS	start_codon	21098	21100	.	-	0	transcript_id "Phchi.C216G000100.t1"; gene_id "Phchi.C216G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14870.t1 is derived from g13338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15210643	15211835	.	-	.	Phchi.S3G218900
Phchi.S3	AUGUSTUS	transcript	15210643	15211835	.	-	.	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	stop_codon	15210640	15210642	.	-	0	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	CDS	15210643	15211203	1	-	0	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	exon	15210643	15211203	.	-	.	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	intron	15211204	15211300	.	-	.	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	CDS	15211301	15211492	1	-	0	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	exon	15211301	15211492	.	-	.	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	intron	15211493	15211601	.	-	.	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	CDS	15211602	15211835	0.92	-	0	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	exon	15211602	15211835	.	-	.	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
Phchi.S3	AUGUSTUS	start_codon	15211833	15211835	.	-	0	transcript_id "Phchi.S3G218900.t1"; gene_id "Phchi.S3G218900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8477.t1 is derived from g5652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36133729	36136000	.	-	.	Phchi.S1G563600
Phchi.S1	AUGUSTUS	transcript	36133729	36136000	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	stop_codon	36133726	36133728	.	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36133729	36133812	0.71	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36133729	36133812	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36133813	36133889	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36133890	36134063	1	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36133890	36134063	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134064	36134158	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134159	36134225	1	-	1	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134159	36134225	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134226	36134313	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134314	36134511	1	-	1	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134314	36134511	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134512	36134619	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134620	36134721	0.99	-	1	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134620	36134721	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134722	36134822	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134823	36134944	0.98	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134823	36134944	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134945	36135018	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36135019	36135105	1	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36135019	36135105	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36135106	36135191	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36135192	36135746	0.81	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36135192	36135746	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36135747	36135868	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36135869	36136000	0.55	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36135869	36136000	.	-	.	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	start_codon	36135998	36136000	.	-	0	transcript_id "Phchi.S1G563600.t1"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	transcript	36133729	36136000	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	stop_codon	36133726	36133728	.	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36133729	36133812	0.68	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36133729	36133812	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36133813	36133889	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36133890	36134063	1	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36133890	36134063	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134064	36134158	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134159	36134225	1	-	1	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134159	36134225	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134226	36134313	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134314	36134511	1	-	1	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134314	36134511	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134512	36134619	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134620	36134721	0.99	-	1	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134620	36134721	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134722	36134842	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36134843	36134934	0.81	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36134843	36134934	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36134935	36135018	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36135019	36135105	1	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36135019	36135105	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36135106	36135191	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36135192	36135746	0.8	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36135192	36135746	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	intron	36135747	36135868	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	CDS	36135869	36136000	0.63	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	exon	36135869	36136000	.	-	.	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
Phchi.S1	AUGUSTUS	start_codon	36135998	36136000	.	-	0	transcript_id "Phchi.S1G563600.t2"; gene_id "Phchi.S1G563600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5968.t1 is derived from g3139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20138102	20138856	.	-	.	Phchi.S1G312700
Phchi.S1	AUGUSTUS	transcript	20138102	20138856	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	stop_codon	20138099	20138101	.	-	0	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	CDS	20138102	20138268	0.91	-	2	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	exon	20138102	20138268	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	intron	20138269	20138364	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	CDS	20138365	20138431	0.76	-	0	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	exon	20138365	20138431	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	intron	20138432	20138583	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	CDS	20138584	20138619	0.93	-	0	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	exon	20138584	20138619	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	intron	20138620	20138829	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	CDS	20138830	20138856	0.92	-	0	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	exon	20138830	20138856	.	-	.	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
Phchi.S1	AUGUSTUS	start_codon	20138854	20138856	.	-	0	transcript_id "Phchi.S1G312700.t1"; gene_id "Phchi.S1G312700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5556.t1 is derived from g2726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17579563	17580673	.	+	.	Phchi.S1G271500
Phchi.S1	AUGUSTUS	transcript	17579563	17580673	.	+	.	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	start_codon	17579563	17579565	.	+	0	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	CDS	17579563	17579602	0.75	+	0	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	exon	17579563	17579602	.	+	.	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	intron	17579603	17580004	.	+	.	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	CDS	17580005	17580043	1	+	2	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	exon	17580005	17580043	.	+	.	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	intron	17580044	17580212	.	+	.	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	CDS	17580213	17580673	0.57	+	2	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	exon	17580213	17580673	.	+	.	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
Phchi.S1	AUGUSTUS	stop_codon	17580674	17580676	.	+	0	transcript_id "Phchi.S1G271500.t1"; gene_id "Phchi.S1G271500"
# This transcript jg3545.t2 is derived from g714.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3546.t1 is derived from g715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4397876	4399544	.	-	.	Phchi.S1G070500
Phchi.S1	AUGUSTUS	transcript	4398718	4399544	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	stop_codon	4398715	4398717	.	-	0	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4398718	4398796	0.69	-	1	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4398718	4398796	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4398797	4398913	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4398914	4399092	0.8	-	0	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4398914	4399092	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4399093	4399251	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4399252	4399304	1	-	2	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4399252	4399304	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4399305	4399444	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4399445	4399544	1	-	0	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4399445	4399544	.	-	.	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	start_codon	4399542	4399544	.	-	0	transcript_id "Phchi.S1G070500.t1"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	transcript	4397876	4399544	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	stop_codon	4397873	4397875	.	-	0	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4397876	4398042	0.56	-	2	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4397876	4398042	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4398043	4398116	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4398117	4398452	0.35	-	2	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4398117	4398452	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4398453	4398670	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4398671	4398796	0.43	-	2	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4398671	4398796	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4398797	4399051	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4399052	4399112	0.56	-	0	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4399052	4399112	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4399113	4399251	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4399252	4399304	0.85	-	2	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4399252	4399304	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	intron	4399305	4399444	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	CDS	4399445	4399544	0.85	-	0	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	exon	4399445	4399544	.	-	.	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
Phchi.S1	AUGUSTUS	start_codon	4399542	4399544	.	-	0	transcript_id "Phchi.S1G070500.t2"; gene_id "Phchi.S1G070500"
# This transcript jg14833.t2 is derived from g13301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14834.t1 is derived from g13302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14926445	14928052	.	+	.	Phchi.S3G215300
Phchi.S3	AUGUSTUS	transcript	14926445	14928052	.	+	.	transcript_id "Phchi.S3G215300.t1"; gene_id "Phchi.S3G215300"
Phchi.S3	AUGUSTUS	start_codon	14926445	14926447	.	+	0	transcript_id "Phchi.S3G215300.t1"; gene_id "Phchi.S3G215300"
Phchi.S3	AUGUSTUS	CDS	14926445	14928052	0.46	+	0	transcript_id "Phchi.S3G215300.t1"; gene_id "Phchi.S3G215300"
Phchi.S3	AUGUSTUS	exon	14926445	14928052	.	+	.	transcript_id "Phchi.S3G215300.t1"; gene_id "Phchi.S3G215300"
Phchi.S3	AUGUSTUS	stop_codon	14928053	14928055	.	+	0	transcript_id "Phchi.S3G215300.t1"; gene_id "Phchi.S3G215300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6016.t1 is derived from g3187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20443437	20444686	.	-	.	Phchi.S1G317500
Phchi.S1	AUGUSTUS	transcript	20443437	20444686	.	-	.	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	stop_codon	20443434	20443436	.	-	0	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	CDS	20443437	20443866	0.84	-	1	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	exon	20443437	20443866	.	-	.	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	intron	20443867	20443952	.	-	.	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	CDS	20443953	20444686	0.75	-	0	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	exon	20443953	20444686	.	-	.	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
Phchi.S1	AUGUSTUS	start_codon	20444684	20444686	.	-	0	transcript_id "Phchi.S1G317500.t1"; gene_id "Phchi.S1G317500"
# This transcript jg13564.t2 is derived from g12031.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13565.t1 is derived from g12032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7520300	7521596	.	-	.	Phchi.S3G088400
Phchi.S3	AUGUSTUS	transcript	7520300	7521596	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	stop_codon	7520297	7520299	.	-	0	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	CDS	7520300	7520391	0.99	-	2	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	exon	7520300	7520391	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	intron	7520392	7520488	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	CDS	7520489	7520710	1	-	2	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	exon	7520489	7520710	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	intron	7520711	7520881	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	CDS	7520882	7521217	1	-	2	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	exon	7520882	7521217	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	intron	7521218	7521472	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	CDS	7521473	7521596	1	-	0	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	exon	7521473	7521596	.	-	.	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
Phchi.S3	AUGUSTUS	start_codon	7521594	7521596	.	-	0	transcript_id "Phchi.S3G088400.t1"; gene_id "Phchi.S3G088400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14204.t1 is derived from g12671.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11493574	11496585	.	-	.	Phchi.S3G152300
Phchi.S3	AUGUSTUS	transcript	11493574	11496585	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	stop_codon	11493571	11493573	.	-	0	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11493574	11493646	0.95	-	1	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11493574	11493646	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11493647	11493735	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11493736	11493846	1	-	1	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11493736	11493846	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11493847	11493928	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11493929	11494086	1	-	0	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11493929	11494086	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11494087	11494178	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11494179	11494361	0.95	-	0	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11494179	11494361	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11494362	11494464	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11494465	11495697	0.54	-	0	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11494465	11495697	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11495698	11496435	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11496436	11496585	0.98	-	0	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11496436	11496585	.	-	.	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	start_codon	11496583	11496585	.	-	0	transcript_id "Phchi.S3G152300.t1"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	transcript	11493574	11496195	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	stop_codon	11493571	11493573	.	-	0	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11493574	11493646	0.95	-	1	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11493574	11493646	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11493647	11493735	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11493736	11493846	1	-	1	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11493736	11493846	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11493847	11493928	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11493929	11494086	1	-	0	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11493929	11494086	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11494087	11494178	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11494179	11494361	0.94	-	0	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11494179	11494361	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11494362	11494464	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11494465	11495697	0.48	-	0	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11494465	11495697	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	intron	11495698	11496162	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	CDS	11496163	11496195	0.99	-	0	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	exon	11496163	11496195	.	-	.	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
Phchi.S3	AUGUSTUS	start_codon	11496193	11496195	.	-	0	transcript_id "Phchi.S3G152300.t2"; gene_id "Phchi.S3G152300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12994.t1 is derived from g11459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3546925	3548348	.	+	.	Phchi.S3G031300
Phchi.S3	AUGUSTUS	transcript	3546925	3548348	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	start_codon	3546925	3546927	.	+	0	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	CDS	3546925	3547209	1	+	0	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	exon	3546925	3547209	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	intron	3547210	3547302	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	CDS	3547303	3547509	1	+	0	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	exon	3547303	3547509	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	intron	3547510	3547613	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	CDS	3547614	3547694	1	+	0	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	exon	3547614	3547694	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	intron	3547695	3547799	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	CDS	3547800	3548182	1	+	0	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	exon	3547800	3548182	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	intron	3548183	3548320	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	CDS	3548321	3548348	1	+	1	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	exon	3548321	3548348	.	+	.	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
Phchi.S3	AUGUSTUS	stop_codon	3548349	3548351	.	+	0	transcript_id "Phchi.S3G031300.t1"; gene_id "Phchi.S3G031300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4857.t1 is derived from g2027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13121130	13124370	.	-	.	Phchi.S1G201600
Phchi.S1	AUGUSTUS	transcript	13121130	13124370	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	stop_codon	13121127	13121129	.	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13121130	13121336	0.99	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13121130	13121336	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13121337	13121423	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13121424	13121498	1	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13121424	13121498	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13121499	13121576	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13121577	13121688	1	-	1	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13121577	13121688	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13121689	13121789	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13121790	13121872	0.99	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13121790	13121872	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13121873	13121958	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13121959	13122203	0.95	-	2	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13121959	13122203	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13122204	13122304	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13122305	13122466	0.88	-	2	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13122305	13122466	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13122467	13122576	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13122577	13122774	0.81	-	2	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13122577	13122774	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13122775	13122868	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13122869	13122887	0.82	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13122869	13122887	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13122888	13122985	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13122986	13123132	0.68	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13122986	13123132	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13123133	13123218	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13123219	13123307	1	-	2	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13123219	13123307	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13123308	13123429	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13123430	13123584	1	-	1	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13123430	13123584	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13123585	13123742	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13123743	13123858	1	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13123743	13123858	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13123859	13124039	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13124040	13124201	1	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13124040	13124201	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	intron	13124202	13124280	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	CDS	13124281	13124370	1	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	exon	13124281	13124370	.	-	.	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
Phchi.S1	AUGUSTUS	start_codon	13124368	13124370	.	-	0	transcript_id "Phchi.S1G201600.t1"; gene_id "Phchi.S1G201600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15169.t1 is derived from g13637.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17348170	17351038	.	+	.	Phchi.S3G248800
Phchi.S3	AUGUSTUS	transcript	17348170	17351038	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	start_codon	17348170	17348172	.	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348170	17348526	0.61	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348170	17348526	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348527	17348643	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348644	17348708	1	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348644	17348708	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348709	17348863	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348864	17348871	0.98	+	1	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348864	17348871	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348872	17348944	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348945	17348954	0.98	+	2	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348945	17348954	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348955	17349129	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349130	17349201	1	+	1	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349130	17349201	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349202	17349322	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349323	17349491	1	+	1	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349323	17349491	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349492	17349621	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349622	17349665	1	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349622	17349665	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349666	17349763	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349764	17349863	1	+	1	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349764	17349863	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349864	17349988	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349989	17350057	1	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349989	17350057	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350058	17350150	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350151	17350205	1	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350151	17350205	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350206	17350309	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350310	17350425	0.99	+	2	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350310	17350425	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350426	17350552	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350553	17350676	0.81	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350553	17350676	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350677	17350747	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350748	17350889	1	+	2	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350748	17350889	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350890	17350971	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350972	17351038	0.47	+	1	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350972	17351038	.	+	.	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	stop_codon	17351039	17351041	.	+	0	transcript_id "Phchi.S3G248800.t1"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	transcript	17348170	17351038	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	start_codon	17348170	17348172	.	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348170	17348526	0.56	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348170	17348526	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348527	17348643	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348644	17348708	1	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348644	17348708	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348709	17348863	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17348864	17348944	1	+	1	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17348864	17348944	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17348945	17349129	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349130	17349201	0.99	+	1	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349130	17349201	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349202	17349322	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349323	17349491	0.99	+	1	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349323	17349491	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349492	17349621	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349622	17349665	1	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349622	17349665	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349666	17349763	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349764	17349863	1	+	1	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349764	17349863	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17349864	17349988	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17349989	17350057	1	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17349989	17350057	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350058	17350150	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350151	17350205	1	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350151	17350205	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350206	17350309	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350310	17350425	1	+	2	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350310	17350425	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350426	17350552	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350553	17350676	0.85	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350553	17350676	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350677	17350747	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350748	17350889	1	+	2	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350748	17350889	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	intron	17350890	17350971	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	CDS	17350972	17351038	0.44	+	1	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	exon	17350972	17351038	.	+	.	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
Phchi.S3	AUGUSTUS	stop_codon	17351039	17351041	.	+	0	transcript_id "Phchi.S3G248800.t2"; gene_id "Phchi.S3G248800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11231.t1 is derived from g15281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4910911	4913798	.	-	.	Phchi.S4G081300
Phchi.S4	AUGUSTUS	transcript	4910911	4913798	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	stop_codon	4910908	4910910	.	-	0	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	CDS	4910911	4910970	0.98	-	0	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	exon	4910911	4910970	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	intron	4910971	4911135	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	CDS	4911136	4911196	0.85	-	1	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	exon	4911136	4911196	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	intron	4911197	4911287	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	CDS	4911288	4913458	0.67	-	0	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	exon	4911288	4913458	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	intron	4913459	4913723	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	CDS	4913724	4913798	0.78	-	0	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	exon	4913724	4913798	.	-	.	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
Phchi.S4	AUGUSTUS	start_codon	4913796	4913798	.	-	0	transcript_id "Phchi.S4G081300.t1"; gene_id "Phchi.S4G081300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1541.t1 is derived from g8460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1681225	1683453	.	-	.	Phchi.S5G015000
Phchi.S5	AUGUSTUS	transcript	1681225	1683453	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	stop_codon	1681222	1681224	.	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	CDS	1681225	1682066	1	-	2	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	exon	1681225	1682066	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	intron	1682067	1682165	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	CDS	1682166	1682628	0.85	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	exon	1682166	1682628	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	intron	1682629	1682870	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	CDS	1682871	1682921	0.84	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	exon	1682871	1682921	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	intron	1682922	1683089	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	CDS	1683090	1683104	0.84	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	exon	1683090	1683104	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	intron	1683105	1683174	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	CDS	1683175	1683219	0.54	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	exon	1683175	1683219	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	intron	1683220	1683417	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	CDS	1683418	1683453	0.67	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	exon	1683418	1683453	.	-	.	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
Phchi.S5	AUGUSTUS	start_codon	1683451	1683453	.	-	0	transcript_id "Phchi.S5G015000.t1"; gene_id "Phchi.S5G015000"
# This transcript jg712.t2 is derived from g10494.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg713.t1 is derived from g10495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5044618	5045955	.	+	.	Phchi.S6G067200
Phchi.S6	AUGUSTUS	transcript	5044618	5045955	.	+	.	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	start_codon	5044618	5044620	.	+	0	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	CDS	5044618	5045235	0.57	+	0	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	exon	5044618	5045235	.	+	.	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	intron	5045236	5045338	.	+	.	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	CDS	5045339	5045588	0.77	+	0	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	exon	5045339	5045588	.	+	.	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	intron	5045589	5045695	.	+	.	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	CDS	5045696	5045955	0.77	+	2	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	exon	5045696	5045955	.	+	.	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
Phchi.S6	AUGUSTUS	stop_codon	5045956	5045958	.	+	0	transcript_id "Phchi.S6G067200.t1"; gene_id "Phchi.S6G067200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11962.t1 is derived from g7637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	207988	210231	.	+	.	Phchi.S2G004200
Phchi.S2	AUGUSTUS	transcript	207988	210231	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	start_codon	207988	207990	.	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	207988	208254	0.55	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	207988	208254	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208255	208378	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208379	208456	0.98	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208379	208456	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208457	208644	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208645	208649	0.77	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208645	208649	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208650	208698	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208699	208780	0.7	+	1	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208699	208780	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208781	208935	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208936	209040	1	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208936	209040	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209041	209145	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209146	209225	1	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209146	209225	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209226	209318	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209319	209409	1	+	1	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209319	209409	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209410	209493	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209494	209601	1	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209494	209601	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209602	209771	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209772	209858	1	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209772	209858	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209859	209936	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209937	210005	1	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209937	210005	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	210006	210096	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	210097	210231	0.53	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	210097	210231	.	+	.	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	stop_codon	210232	210234	.	+	0	transcript_id "Phchi.S2G004200.t1"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	transcript	207988	210231	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	start_codon	207988	207990	.	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	207988	208254	0.62	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	207988	208254	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208255	208407	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208408	208456	0.68	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208408	208456	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208457	208685	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208686	208780	0.96	+	2	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208686	208780	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	208781	208935	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	208936	209040	1	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	208936	209040	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209041	209145	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209146	209225	1	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209146	209225	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209226	209318	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209319	209409	1	+	1	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209319	209409	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209410	209493	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209494	209601	1	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209494	209601	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209602	209771	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209772	209858	1	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209772	209858	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	209859	209936	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	209937	210005	1	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	209937	210005	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	intron	210006	210096	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	CDS	210097	210231	0.52	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	exon	210097	210231	.	+	.	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
Phchi.S2	AUGUSTUS	stop_codon	210232	210234	.	+	0	transcript_id "Phchi.S2G004200.t2"; gene_id "Phchi.S2G004200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5472.t1 is derived from g2642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16999785	17000650	.	+	.	Phchi.S1G263100
Phchi.S1	AUGUSTUS	transcript	16999785	17000650	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	start_codon	16999785	16999787	.	+	0	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	CDS	16999785	16999890	1	+	0	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	exon	16999785	16999890	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	intron	16999891	16999988	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	CDS	16999989	17000130	1	+	2	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	exon	16999989	17000130	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	intron	17000131	17000209	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	CDS	17000210	17000299	0.62	+	1	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	exon	17000210	17000299	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	intron	17000300	17000386	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	CDS	17000387	17000465	0.99	+	1	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	exon	17000387	17000465	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	intron	17000466	17000554	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	CDS	17000555	17000650	1	+	0	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	exon	17000555	17000650	.	+	.	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
Phchi.S1	AUGUSTUS	stop_codon	17000651	17000653	.	+	0	transcript_id "Phchi.S1G263100.t1"; gene_id "Phchi.S1G263100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14258.t1 is derived from g12725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11785857	11786997	.	-	.	Phchi.S3G157700
Phchi.S3	AUGUSTUS	transcript	11785857	11786997	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	stop_codon	11785854	11785856	.	-	0	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	CDS	11785857	11785916	1	-	0	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	exon	11785857	11785916	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	intron	11785917	11786014	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	CDS	11786015	11786224	0.78	-	0	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	exon	11786015	11786224	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	intron	11786225	11786323	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	CDS	11786324	11786579	0.79	-	1	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	exon	11786324	11786579	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	intron	11786580	11786725	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	CDS	11786726	11786997	0.94	-	0	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	exon	11786726	11786997	.	-	.	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
Phchi.S3	AUGUSTUS	start_codon	11786995	11786997	.	-	0	transcript_id "Phchi.S3G157700.t1"; gene_id "Phchi.S3G157700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9683.t1 is derived from g6859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43265749	43266965	.	+	.	Phchi.S1G684200
Phchi.S1	AUGUSTUS	transcript	43265749	43266965	.	+	.	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	start_codon	43265749	43265751	.	+	0	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	CDS	43265749	43266123	0.81	+	0	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	exon	43265749	43266123	.	+	.	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	intron	43266124	43266302	.	+	.	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	CDS	43266303	43266965	0.57	+	0	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	exon	43266303	43266965	.	+	.	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
Phchi.S1	AUGUSTUS	stop_codon	43266966	43266968	.	+	0	transcript_id "Phchi.S1G684200.t1"; gene_id "Phchi.S1G684200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7449.t1 is derived from g4621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29262883	29268622	.	-	.	Phchi.S1G460800
Phchi.S1	AUGUSTUS	transcript	29262883	29268622	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	stop_codon	29262880	29262882	.	-	0	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	CDS	29262883	29264770	1	-	1	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	exon	29262883	29264770	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	intron	29264771	29265202	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	CDS	29265203	29265295	1	-	1	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	exon	29265203	29265295	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	intron	29265296	29265469	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	CDS	29265470	29267002	1	-	1	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	exon	29265470	29267002	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	intron	29267003	29267105	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	CDS	29267106	29268622	0.67	-	0	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	exon	29267106	29268622	.	-	.	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
Phchi.S1	AUGUSTUS	start_codon	29268620	29268622	.	-	0	transcript_id "Phchi.S1G460800.t1"; gene_id "Phchi.S1G460800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3227.t1 is derived from g396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2355000	2357132	.	+	.	Phchi.S1G038600
Phchi.S1	AUGUSTUS	transcript	2355000	2357132	.	+	.	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	start_codon	2355000	2355002	.	+	0	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	CDS	2355000	2355033	0.4	+	0	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	exon	2355000	2355033	.	+	.	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	intron	2355034	2355195	.	+	.	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	CDS	2355196	2356859	0.35	+	2	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	exon	2355196	2356859	.	+	.	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	intron	2356860	2356940	.	+	.	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	CDS	2356941	2357132	0.86	+	0	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	exon	2356941	2357132	.	+	.	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
Phchi.S1	AUGUSTUS	stop_codon	2357133	2357135	.	+	0	transcript_id "Phchi.S1G038600.t1"; gene_id "Phchi.S1G038600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13887.t1 is derived from g12354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9462832	9464688	.	+	.	Phchi.S3G120600
Phchi.S3	AUGUSTUS	transcript	9462832	9464688	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	start_codon	9462832	9462834	.	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9462832	9463266	0.84	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9462832	9463266	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9463267	9463384	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9463385	9463525	0.88	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9463385	9463525	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9463526	9463613	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9463614	9463676	0.99	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9463614	9463676	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9463677	9463784	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9463785	9463874	1	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9463785	9463874	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9463875	9463987	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9463988	9464110	1	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9463988	9464110	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9464111	9464204	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9464205	9464292	1	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9464205	9464292	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9464293	9464364	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9464365	9464439	1	+	2	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9464365	9464439	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	intron	9464440	9464521	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	CDS	9464522	9464688	1	+	2	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	exon	9464522	9464688	.	+	.	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
Phchi.S3	AUGUSTUS	stop_codon	9464689	9464691	.	+	0	transcript_id "Phchi.S3G120600.t1"; gene_id "Phchi.S3G120600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10187.t1 is derived from g7363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46213959	46218448	.	+	.	Phchi.S1G734600
Phchi.S1	AUGUSTUS	transcript	46213959	46218448	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	start_codon	46213959	46213961	.	+	0	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46213959	46213969	0.67	+	0	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46213959	46213969	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46213970	46214266	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214267	46214354	0.81	+	1	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214267	46214354	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214355	46214481	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214482	46214551	0.98	+	0	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214482	46214551	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214552	46214670	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214671	46214739	0.7	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214671	46214739	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214740	46214975	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214976	46215064	1	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214976	46215064	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215065	46215199	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215200	46215224	1	+	0	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215200	46215224	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215225	46215315	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215316	46215354	1	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215316	46215354	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215355	46215453	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215454	46215571	1	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215454	46215571	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215572	46216070	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216071	46216231	1	+	1	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216071	46216231	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216232	46216350	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216351	46216401	1	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216351	46216401	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216402	46216523	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216524	46216728	1	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216524	46216728	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216729	46216829	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216830	46216969	0.98	+	1	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216830	46216969	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216970	46217130	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217131	46217350	1	+	2	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217131	46217350	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217351	46217441	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217442	46217816	0.97	+	1	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217442	46217816	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217817	46217892	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217893	46217973	0.97	+	1	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217893	46217973	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217974	46218048	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46218049	46218448	0.69	+	1	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46218049	46218448	.	+	.	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	stop_codon	46218449	46218451	.	+	0	transcript_id "Phchi.S1G734600.t1"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	transcript	46213959	46218448	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	start_codon	46213959	46213961	.	+	0	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46213959	46213969	0.71	+	0	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46213959	46213969	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46213970	46214266	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214267	46214354	0.84	+	1	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214267	46214354	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214355	46214481	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214482	46214551	0.98	+	0	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214482	46214551	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214552	46214670	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214671	46214739	0.65	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214671	46214739	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214740	46214975	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214976	46215064	1	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214976	46215064	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215065	46215199	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215200	46215224	1	+	0	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215200	46215224	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215225	46215315	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215316	46215354	1	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215316	46215354	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215355	46215453	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215454	46215571	1	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215454	46215571	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215572	46216070	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216071	46216231	1	+	1	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216071	46216231	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216232	46216350	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216351	46216401	1	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216351	46216401	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216402	46216523	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216524	46216728	0.98	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216524	46216728	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216729	46216829	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216830	46216969	0.95	+	1	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216830	46216969	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216970	46217130	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217131	46217350	0.99	+	2	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217131	46217350	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217351	46217450	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217451	46217816	0.91	+	1	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217451	46217816	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217817	46217892	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217893	46217973	0.96	+	1	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217893	46217973	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217974	46218048	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46218049	46218448	0.72	+	1	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46218049	46218448	.	+	.	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	stop_codon	46218449	46218451	.	+	0	transcript_id "Phchi.S1G734600.t2"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	transcript	46213959	46218448	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	start_codon	46213959	46213961	.	+	0	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46213959	46213969	0.71	+	0	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46213959	46213969	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46213970	46214266	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214267	46214354	0.87	+	1	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214267	46214354	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214355	46214481	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214482	46214551	0.96	+	0	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214482	46214551	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214552	46214670	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214671	46214739	0.62	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214671	46214739	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46214740	46214975	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46214976	46215064	1	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46214976	46215064	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215065	46215199	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215200	46215224	1	+	0	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215200	46215224	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215225	46215315	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215316	46215354	1	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215316	46215354	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215355	46215453	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215454	46215571	1	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215454	46215571	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215572	46215865	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46215866	46215935	0.54	+	1	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46215866	46215935	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46215936	46216092	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216093	46216231	0.5	+	0	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216093	46216231	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216232	46216350	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216351	46216401	1	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216351	46216401	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216402	46216523	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216524	46216728	0.97	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216524	46216728	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216729	46216829	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46216830	46216969	1	+	1	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46216830	46216969	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46216970	46217130	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217131	46217350	0.99	+	2	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217131	46217350	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217351	46217441	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217442	46217816	0.99	+	1	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217442	46217816	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217817	46217892	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46217893	46217973	0.99	+	1	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46217893	46217973	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	intron	46217974	46218048	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	CDS	46218049	46218448	0.73	+	1	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	exon	46218049	46218448	.	+	.	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
Phchi.S1	AUGUSTUS	stop_codon	46218449	46218451	.	+	0	transcript_id "Phchi.S1G734600.t3"; gene_id "Phchi.S1G734600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13521.t1 is derived from g11988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7336105	7338282	.	+	.	Phchi.S3G084000
Phchi.S3	AUGUSTUS	transcript	7336105	7338282	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	start_codon	7336105	7336107	.	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7336105	7336350	1	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7336105	7336350	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7336351	7336459	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7336460	7336658	0.98	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7336460	7336658	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7336659	7336761	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7336762	7336828	0.99	+	2	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7336762	7336828	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7336829	7336913	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7336914	7336977	0.45	+	1	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7336914	7336977	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7336978	7337083	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7337084	7337164	0.45	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7337084	7337164	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7337165	7337246	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7337247	7337333	1	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7337247	7337333	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7337334	7337401	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7337402	7337559	1	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7337402	7337559	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7337560	7337657	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7337658	7337706	1	+	1	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7337658	7337706	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7337707	7337800	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7337801	7337925	1	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7337801	7337925	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	intron	7337926	7338059	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	CDS	7338060	7338282	0.97	+	1	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	exon	7338060	7338282	.	+	.	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
Phchi.S3	AUGUSTUS	stop_codon	7338283	7338285	.	+	0	transcript_id "Phchi.S3G084000.t1"; gene_id "Phchi.S3G084000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2920.t1 is derived from g89.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	568433	569429	.	-	.	Phchi.S1G007900
Phchi.S1	AUGUSTUS	transcript	568433	569429	.	-	.	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	stop_codon	568430	568432	.	-	0	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	CDS	568433	568466	0.99	-	1	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	exon	568433	568466	.	-	.	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	intron	568467	568632	.	-	.	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	CDS	568633	569429	0.69	-	0	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	exon	568633	569429	.	-	.	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	start_codon	569427	569429	.	-	0	transcript_id "Phchi.S1G007900.t1"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	transcript	568433	569429	.	-	.	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	stop_codon	568430	568432	.	-	0	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	CDS	568433	568461	0.68	-	2	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	exon	568433	568461	.	-	.	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	intron	568462	568636	.	-	.	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	CDS	568637	569429	0.46	-	0	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	exon	568637	569429	.	-	.	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
Phchi.S1	AUGUSTUS	start_codon	569427	569429	.	-	0	transcript_id "Phchi.S1G007900.t2"; gene_id "Phchi.S1G007900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12371.t1 is derived from g8047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13121272	13122327	.	-	.	Phchi.S2G045100
Phchi.S2	AUGUSTUS	transcript	13121272	13122327	.	-	.	transcript_id "Phchi.S2G045100.t1"; gene_id "Phchi.S2G045100"
Phchi.S2	AUGUSTUS	stop_codon	13121269	13121271	.	-	0	transcript_id "Phchi.S2G045100.t1"; gene_id "Phchi.S2G045100"
Phchi.S2	AUGUSTUS	CDS	13121272	13122327	0.93	-	0	transcript_id "Phchi.S2G045100.t1"; gene_id "Phchi.S2G045100"
Phchi.S2	AUGUSTUS	exon	13121272	13122327	.	-	.	transcript_id "Phchi.S2G045100.t1"; gene_id "Phchi.S2G045100"
Phchi.S2	AUGUSTUS	start_codon	13122325	13122327	.	-	0	transcript_id "Phchi.S2G045100.t1"; gene_id "Phchi.S2G045100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10840.t1 is derived from g14890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2417381	2418628	.	+	.	Phchi.S4G042200
Phchi.S4	AUGUSTUS	transcript	2417381	2418628	.	+	.	transcript_id "Phchi.S4G042200.t1"; gene_id "Phchi.S4G042200"
Phchi.S4	AUGUSTUS	start_codon	2417381	2417383	.	+	0	transcript_id "Phchi.S4G042200.t1"; gene_id "Phchi.S4G042200"
Phchi.S4	AUGUSTUS	CDS	2417381	2418628	1	+	0	transcript_id "Phchi.S4G042200.t1"; gene_id "Phchi.S4G042200"
Phchi.S4	AUGUSTUS	exon	2417381	2418628	.	+	.	transcript_id "Phchi.S4G042200.t1"; gene_id "Phchi.S4G042200"
Phchi.S4	AUGUSTUS	stop_codon	2418629	2418631	.	+	0	transcript_id "Phchi.S4G042200.t1"; gene_id "Phchi.S4G042200"
# This transcript jg15663.t2 is derived from g14132.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15663.t3 is derived from g14132.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15664.t1 is derived from g14133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20571049	20572554	.	+	.	Phchi.S3G298300
Phchi.S3	AUGUSTUS	transcript	20571049	20572554	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	start_codon	20571049	20571051	.	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20571049	20571236	0.73	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20571049	20571236	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	intron	20571237	20571339	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20571340	20571460	0.82	+	1	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20571340	20571460	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	intron	20571461	20571551	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20571552	20571689	1	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20571552	20571689	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	intron	20571690	20571799	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20571800	20571916	1	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20571800	20571916	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	intron	20571917	20572003	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20572004	20572072	1	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20572004	20572072	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	intron	20572073	20572225	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20572226	20572321	1	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20572226	20572321	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	intron	20572322	20572416	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	CDS	20572417	20572554	1	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	exon	20572417	20572554	.	+	.	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
Phchi.S3	AUGUSTUS	stop_codon	20572555	20572557	.	+	0	transcript_id "Phchi.S3G298300.t1"; gene_id "Phchi.S3G298300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9262.t1 is derived from g6437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40643451	40648706	.	+	.	Phchi.S1G642100
Phchi.S1	AUGUSTUS	transcript	40643451	40648706	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	start_codon	40643451	40643453	.	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40643451	40643571	0.99	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40643451	40643571	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40643572	40643815	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40643816	40643943	1	+	2	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40643816	40643943	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40643944	40644104	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40644105	40644268	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40644105	40644268	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40644269	40644421	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40644422	40644512	1	+	1	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40644422	40644512	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40644513	40644707	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40644708	40644887	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40644708	40644887	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40644888	40644986	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40644987	40645067	0.94	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40644987	40645067	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40645068	40645169	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40645170	40645250	0.98	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40645170	40645250	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40645251	40645380	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40645381	40645473	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40645381	40645473	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40645474	40645551	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40645552	40645632	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40645552	40645632	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40645633	40645744	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40645745	40645907	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40645745	40645907	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40645908	40646024	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40646025	40646145	1	+	2	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40646025	40646145	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40646146	40646236	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40646237	40646309	1	+	1	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40646237	40646309	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40646310	40646395	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40646396	40646503	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40646396	40646503	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40646504	40646647	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40646648	40646745	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40646648	40646745	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40646746	40646826	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40646827	40646872	1	+	1	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40646827	40646872	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40646873	40647022	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40647023	40647119	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40647023	40647119	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40647120	40647264	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40647265	40647338	1	+	2	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40647265	40647338	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40647339	40647408	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40647409	40647513	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40647409	40647513	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40647514	40647646	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40647647	40647727	0.99	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40647647	40647727	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40647728	40647829	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40647830	40647923	1	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40647830	40647923	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40647924	40648262	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40648263	40648363	1	+	2	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40648263	40648363	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	intron	40648364	40648445	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	CDS	40648446	40648706	0.99	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	exon	40648446	40648706	.	+	.	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
Phchi.S1	AUGUSTUS	stop_codon	40648707	40648709	.	+	0	transcript_id "Phchi.S1G642100.t1"; gene_id "Phchi.S1G642100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10914.t1 is derived from g14964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2915353	2918508	.	-	.	Phchi.S4G049600
Phchi.S4	AUGUSTUS	transcript	2915353	2918508	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	stop_codon	2915350	2915352	.	-	0	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	CDS	2915353	2915895	1	-	0	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	exon	2915353	2915895	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	intron	2915896	2916015	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	CDS	2916016	2916710	1	-	2	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	exon	2916016	2916710	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	intron	2916711	2916801	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	CDS	2916802	2917098	1	-	2	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	exon	2916802	2917098	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	intron	2917099	2917191	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	CDS	2917192	2917438	1	-	0	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	exon	2917192	2917438	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	intron	2917439	2917542	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	CDS	2917543	2918508	1	-	0	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	exon	2917543	2918508	.	-	.	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
Phchi.S4	AUGUSTUS	start_codon	2918506	2918508	.	-	0	transcript_id "Phchi.S4G049600.t1"; gene_id "Phchi.S4G049600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3041.t1 is derived from g210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1305882	1306814	.	+	.	Phchi.S1G020000
Phchi.S1	AUGUSTUS	transcript	1305882	1306814	.	+	.	transcript_id "Phchi.S1G020000.t1"; gene_id "Phchi.S1G020000"
Phchi.S1	AUGUSTUS	start_codon	1305882	1305884	.	+	0	transcript_id "Phchi.S1G020000.t1"; gene_id "Phchi.S1G020000"
Phchi.S1	AUGUSTUS	CDS	1305882	1306814	1	+	0	transcript_id "Phchi.S1G020000.t1"; gene_id "Phchi.S1G020000"
Phchi.S1	AUGUSTUS	exon	1305882	1306814	.	+	.	transcript_id "Phchi.S1G020000.t1"; gene_id "Phchi.S1G020000"
Phchi.S1	AUGUSTUS	stop_codon	1306815	1306817	.	+	0	transcript_id "Phchi.S1G020000.t1"; gene_id "Phchi.S1G020000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15500.t1 is derived from g13969.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 2 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19542204	19557273	.	-	.	Phchi.S3G281900
Phchi.S3	AUGUSTUS	transcript	19542204	19557273	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	stop_codon	19542201	19542203	.	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19542204	19542516	0.49	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19542204	19542516	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19542517	19542722	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19542723	19543057	0.3	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19542723	19543057	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19543058	19543270	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19543271	19543621	0.76	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19543271	19543621	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19543622	19543758	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19543759	19543839	0.35	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19543759	19543839	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19543840	19543947	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19543948	19544061	0.82	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19543948	19544061	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19544062	19544216	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19544217	19544286	0.73	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19544217	19544286	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19544287	19544750	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19544751	19544845	0.65	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19544751	19544845	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19544846	19544977	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19544978	19545043	0.5	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19544978	19545043	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19545044	19545133	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19545134	19545190	0.97	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19545134	19545190	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19545191	19545269	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19545270	19545370	0.98	-	2	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19545270	19545370	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19545371	19545469	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19545470	19545560	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19545470	19545560	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19545561	19545654	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19545655	19545768	0.98	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19545655	19545768	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19545769	19545889	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19545890	19545989	0.98	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19545890	19545989	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19545990	19546103	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19546104	19546253	1	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19546104	19546253	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19546254	19546351	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19546352	19546440	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19546352	19546440	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19546441	19546516	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19546517	19546822	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19546517	19546822	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19546823	19546920	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19546921	19547025	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19546921	19547025	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19547026	19547164	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19547165	19547321	0.9	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19547165	19547321	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19547322	19547437	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19547438	19547556	0.98	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19547438	19547556	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19547557	19547641	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19547642	19547728	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19547642	19547728	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19547729	19547810	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19547811	19547990	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19547811	19547990	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19547991	19548077	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19548078	19548374	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19548078	19548374	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19548375	19548482	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19548483	19548563	0.99	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19548483	19548563	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19548564	19548643	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19548644	19548997	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19548644	19548997	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19548998	19549079	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19549080	19549319	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19549080	19549319	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19549320	19549416	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19549417	19549728	0.8	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19549417	19549728	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19549729	19549843	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19549844	19549952	0.79	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19549844	19549952	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19549953	19550040	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19550041	19550102	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19550041	19550102	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19550103	19550263	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19550264	19550565	0.65	-	2	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19550264	19550565	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19550566	19550657	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19550658	19550767	0.65	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19550658	19550767	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19550768	19550848	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19550849	19550976	0.98	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19550849	19550976	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19550977	19551198	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19551199	19551336	0.95	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19551199	19551336	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19551337	19551423	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19551424	19551531	0.95	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19551424	19551531	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19551532	19551659	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19551660	19551889	0.9	-	2	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19551660	19551889	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19551890	19552121	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19552122	19552149	0.93	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19552122	19552149	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19552150	19552286	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19552287	19552380	1	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19552287	19552380	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19552381	19552480	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19552481	19552575	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19552481	19552575	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19552576	19552654	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19552655	19552828	0.58	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19552655	19552828	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19552829	19552947	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19552948	19553163	0.77	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19552948	19553163	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19553164	19553250	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19553251	19553367	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19553251	19553367	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19553368	19553507	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19553508	19553571	1	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19553508	19553571	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19553572	19553647	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19553648	19553749	1	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19553648	19553749	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19553750	19553836	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19553837	19553937	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19553837	19553937	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19553938	19554014	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19554015	19554080	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19554015	19554080	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19554081	19554161	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19554162	19554321	1	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19554162	19554321	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19554322	19554427	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19554428	19554501	0.88	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19554428	19554501	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19554502	19554583	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19554584	19554802	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19554584	19554802	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19554803	19554901	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19554902	19554976	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19554902	19554976	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19554977	19555054	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19555055	19555150	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19555055	19555150	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19555151	19555254	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19555255	19555300	0.91	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19555255	19555300	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19555301	19555395	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19555396	19555499	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19555396	19555499	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19555500	19555578	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19555579	19555723	1	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19555579	19555723	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19555724	19555798	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19555799	19555899	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19555799	19555899	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19555900	19555982	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19555983	19556147	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19555983	19556147	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19556148	19556229	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19556230	19556358	1	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19556230	19556358	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19556359	19556454	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19556455	19556536	0.63	-	1	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19556455	19556536	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19556537	19556671	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19556672	19556964	0.47	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19556672	19556964	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	intron	19556965	19557090	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	CDS	19557091	19557273	0.79	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	exon	19557091	19557273	.	-	.	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
Phchi.S3	AUGUSTUS	start_codon	19557271	19557273	.	-	0	transcript_id "Phchi.S3G281900.t1"; gene_id "Phchi.S3G281900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10836.t1 is derived from g14886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2379691	2380938	.	+	.	Phchi.S4G041800
Phchi.S4	AUGUSTUS	transcript	2379691	2380938	.	+	.	transcript_id "Phchi.S4G041800.t1"; gene_id "Phchi.S4G041800"
Phchi.S4	AUGUSTUS	start_codon	2379691	2379693	.	+	0	transcript_id "Phchi.S4G041800.t1"; gene_id "Phchi.S4G041800"
Phchi.S4	AUGUSTUS	CDS	2379691	2380938	1	+	0	transcript_id "Phchi.S4G041800.t1"; gene_id "Phchi.S4G041800"
Phchi.S4	AUGUSTUS	exon	2379691	2380938	.	+	.	transcript_id "Phchi.S4G041800.t1"; gene_id "Phchi.S4G041800"
Phchi.S4	AUGUSTUS	stop_codon	2380939	2380941	.	+	0	transcript_id "Phchi.S4G041800.t1"; gene_id "Phchi.S4G041800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12133.t1 is derived from g7809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4080880	4082771	.	-	.	Phchi.S2G021300
Phchi.S2	AUGUSTUS	transcript	4080880	4082771	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	stop_codon	4080877	4080879	.	-	0	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4080880	4080954	0.63	-	0	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4080880	4080954	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	intron	4080955	4081073	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4081074	4081101	0.65	-	1	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4081074	4081101	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	intron	4081102	4081192	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4081193	4081337	0.89	-	2	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4081193	4081337	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	intron	4081338	4081429	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4081430	4081698	0.63	-	1	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4081430	4081698	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	intron	4081699	4081812	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4081813	4082180	0.74	-	0	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4081813	4082180	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	intron	4082181	4082272	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4082273	4082383	1	-	0	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4082273	4082383	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	intron	4082384	4082570	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	CDS	4082571	4082771	1	-	0	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	exon	4082571	4082771	.	-	.	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
Phchi.S2	AUGUSTUS	start_codon	4082769	4082771	.	-	0	transcript_id "Phchi.S2G021300.t1"; gene_id "Phchi.S2G021300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg420.t1 is derived from g10202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2965873	2966850	.	+	.	Phchi.S6G037900
Phchi.S6	AUGUSTUS	transcript	2965873	2966850	.	+	.	transcript_id "Phchi.S6G037900.t1"; gene_id "Phchi.S6G037900"
Phchi.S6	AUGUSTUS	start_codon	2965873	2965875	.	+	0	transcript_id "Phchi.S6G037900.t1"; gene_id "Phchi.S6G037900"
Phchi.S6	AUGUSTUS	CDS	2965873	2966850	0.54	+	0	transcript_id "Phchi.S6G037900.t1"; gene_id "Phchi.S6G037900"
Phchi.S6	AUGUSTUS	exon	2965873	2966850	.	+	.	transcript_id "Phchi.S6G037900.t1"; gene_id "Phchi.S6G037900"
Phchi.S6	AUGUSTUS	stop_codon	2966851	2966853	.	+	0	transcript_id "Phchi.S6G037900.t1"; gene_id "Phchi.S6G037900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11652.t1 is derived from g15703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7518203	7520126	.	-	.	Phchi.S4G123400
Phchi.S4	AUGUSTUS	transcript	7518203	7520126	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	stop_codon	7518200	7518202	.	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7518203	7518235	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7518203	7518235	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7518236	7518432	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7518433	7518600	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7518433	7518600	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7518601	7518679	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7518680	7518742	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7518680	7518742	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7518743	7518826	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7518827	7518919	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7518827	7518919	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7518920	7518992	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7518993	7519067	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7518993	7519067	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7519068	7519185	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7519186	7519286	1	-	2	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7519186	7519286	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7519287	7519363	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7519364	7519489	1	-	2	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7519364	7519489	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7519490	7519579	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7519580	7519673	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7519580	7519673	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7519674	7519751	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7519752	7519817	0.99	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7519752	7519817	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7519818	7519925	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7519926	7519992	1	-	1	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7519926	7519992	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	intron	7519993	7520115	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	CDS	7520116	7520126	1	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	exon	7520116	7520126	.	-	.	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
Phchi.S4	AUGUSTUS	start_codon	7520124	7520126	.	-	0	transcript_id "Phchi.S4G123400.t1"; gene_id "Phchi.S4G123400"
# This transcript jg11015.t2 is derived from g15065.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11016.t1 is derived from g15066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3647266	3647971	.	+	.	Phchi.S4G059800
Phchi.S4	AUGUSTUS	transcript	3647266	3647971	.	+	.	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	start_codon	3647266	3647268	.	+	0	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	CDS	3647266	3647465	0.36	+	0	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	exon	3647266	3647465	.	+	.	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	intron	3647466	3647698	.	+	.	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	CDS	3647699	3647749	0.86	+	1	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	exon	3647699	3647749	.	+	.	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	intron	3647750	3647892	.	+	.	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	CDS	3647893	3647971	0.93	+	1	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	exon	3647893	3647971	.	+	.	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
Phchi.S4	AUGUSTUS	stop_codon	3647972	3647974	.	+	0	transcript_id "Phchi.S4G059800.t1"; gene_id "Phchi.S4G059800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9070.t1 is derived from g6245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39654259	39656322	.	-	.	Phchi.S1G622900
Phchi.S1	AUGUSTUS	transcript	39654259	39655284	.	-	.	transcript_id "Phchi.S1G622900.t1"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	stop_codon	39654256	39654258	.	-	0	transcript_id "Phchi.S1G622900.t1"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	CDS	39654259	39655284	0.99	-	0	transcript_id "Phchi.S1G622900.t1"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	exon	39654259	39655284	.	-	.	transcript_id "Phchi.S1G622900.t1"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	start_codon	39655282	39655284	.	-	0	transcript_id "Phchi.S1G622900.t1"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	transcript	39654259	39656322	.	-	.	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	stop_codon	39654256	39654258	.	-	0	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	CDS	39654259	39655274	0.56	-	2	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	exon	39654259	39655274	.	-	.	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	intron	39655275	39655532	.	-	.	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	CDS	39655533	39656322	0.2	-	0	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	exon	39655533	39656322	.	-	.	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
Phchi.S1	AUGUSTUS	start_codon	39656320	39656322	.	-	0	transcript_id "Phchi.S1G622900.t2"; gene_id "Phchi.S1G622900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14294.t1 is derived from g12761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11969057	11970586	.	+	.	Phchi.S3G161300
Phchi.S3	AUGUSTUS	transcript	11969057	11970586	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	start_codon	11969057	11969059	.	+	0	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	CDS	11969057	11969115	0.98	+	0	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	exon	11969057	11969115	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	intron	11969116	11969193	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	CDS	11969194	11969329	1	+	1	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	exon	11969194	11969329	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	intron	11969330	11969411	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	CDS	11969412	11969641	1	+	0	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	exon	11969412	11969641	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	intron	11969642	11969759	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	CDS	11969760	11970236	1	+	1	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	exon	11969760	11970236	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	intron	11970237	11970366	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	CDS	11970367	11970586	0.63	+	1	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	exon	11970367	11970586	.	+	.	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
Phchi.S3	AUGUSTUS	stop_codon	11970587	11970589	.	+	0	transcript_id "Phchi.S3G161300.t1"; gene_id "Phchi.S3G161300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3423.t1 is derived from g592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3573931	3575464	.	+	.	Phchi.S1G058200
Phchi.S1	AUGUSTUS	transcript	3573931	3575464	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	start_codon	3573931	3573933	.	+	0	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	CDS	3573931	3574143	0.56	+	0	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	exon	3573931	3574143	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	intron	3574144	3574240	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	CDS	3574241	3574340	0.55	+	0	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	exon	3574241	3574340	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	intron	3574341	3574514	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	CDS	3574515	3574572	0.78	+	2	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	exon	3574515	3574572	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	intron	3574573	3574830	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	CDS	3574831	3575464	0.72	+	1	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	exon	3574831	3575464	.	+	.	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
Phchi.S1	AUGUSTUS	stop_codon	3575465	3575467	.	+	0	transcript_id "Phchi.S1G058200.t1"; gene_id "Phchi.S1G058200"
# This transcript jg2755.t2 is derived from g9675.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2756.t1 is derived from g9676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8653165	8654989	.	-	.	Phchi.S5G136500
Phchi.S5	AUGUSTUS	transcript	8653165	8654989	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	stop_codon	8653162	8653164	.	-	0	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	CDS	8653165	8653267	0.99	-	1	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	exon	8653165	8653267	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	intron	8653268	8653569	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	CDS	8653570	8653628	1	-	0	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	exon	8653570	8653628	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	intron	8653629	8653801	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	CDS	8653802	8653939	0.83	-	0	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	exon	8653802	8653939	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	intron	8653940	8654050	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	CDS	8654051	8654305	0.78	-	0	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	exon	8654051	8654305	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	intron	8654306	8654382	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	CDS	8654383	8654627	0.54	-	2	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	exon	8654383	8654627	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	intron	8654628	8654733	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	CDS	8654734	8654989	0.5	-	0	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	exon	8654734	8654989	.	-	.	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
Phchi.S5	AUGUSTUS	start_codon	8654987	8654989	.	-	0	transcript_id "Phchi.S5G136500.t1"; gene_id "Phchi.S5G136500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2385.t1 is derived from g9305.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6446649	6450133	.	-	.	Phchi.S5G099400
Phchi.S5	AUGUSTUS	transcript	6446649	6450133	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	stop_codon	6446646	6446648	.	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6446649	6446780	1	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6446649	6446780	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6446781	6446873	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6446874	6446982	1	-	1	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6446874	6446982	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6446983	6447070	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447071	6447129	1	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447071	6447129	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447130	6447214	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447215	6447247	0.58	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447215	6447247	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447248	6447416	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447417	6447554	0.34	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447417	6447554	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447555	6447636	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447637	6447712	1	-	1	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447637	6447712	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447713	6447842	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447843	6447905	1	-	1	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447843	6447905	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447906	6447991	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447992	6448086	1	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447992	6448086	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448087	6448225	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448226	6448325	1	-	1	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448226	6448325	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448326	6448405	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448406	6448500	1	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448406	6448500	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448501	6448641	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448642	6448649	0.99	-	2	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448642	6448649	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448650	6448699	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448700	6448723	0.99	-	2	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448700	6448723	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448724	6448866	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448867	6448971	1	-	2	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448867	6448971	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448972	6449079	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449080	6449177	1	-	1	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449080	6449177	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6449178	6449278	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449279	6449376	0.99	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449279	6449376	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6449377	6449571	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449572	6449651	0.84	-	2	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449572	6449651	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6449652	6449742	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449743	6450133	0.94	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449743	6450133	.	-	.	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	start_codon	6450131	6450133	.	-	0	transcript_id "Phchi.S5G099400.t1"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	transcript	6446649	6450133	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	stop_codon	6446646	6446648	.	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6446649	6446780	1	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6446649	6446780	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6446781	6446873	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6446874	6446982	1	-	1	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6446874	6446982	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6446983	6447070	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447071	6447129	1	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447071	6447129	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447130	6447214	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447215	6447247	0.46	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447215	6447247	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447248	6447416	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447417	6447554	0.33	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447417	6447554	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447555	6447636	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447637	6447712	1	-	1	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447637	6447712	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447713	6447842	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447843	6447905	1	-	1	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447843	6447905	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6447906	6447991	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6447992	6448086	1	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6447992	6448086	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448087	6448225	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448226	6448325	1	-	1	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448226	6448325	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448326	6448405	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448406	6448500	1	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448406	6448500	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448501	6448649	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448650	6448723	0.9	-	2	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448650	6448723	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448724	6448866	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6448867	6448971	0.99	-	2	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6448867	6448971	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6448972	6449079	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449080	6449177	1	-	1	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449080	6449177	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6449178	6449278	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449279	6449376	0.99	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449279	6449376	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6449377	6449571	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449572	6449651	0.79	-	2	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449572	6449651	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	intron	6449652	6449742	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	CDS	6449743	6450133	0.93	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	exon	6449743	6450133	.	-	.	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
Phchi.S5	AUGUSTUS	start_codon	6450131	6450133	.	-	0	transcript_id "Phchi.S5G099400.t2"; gene_id "Phchi.S5G099400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5802.t1 is derived from g2972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19026155	19027027	.	+	.	Phchi.S1G296100
Phchi.S1	AUGUSTUS	transcript	19026155	19027027	.	+	.	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	start_codon	19026155	19026157	.	+	0	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	CDS	19026155	19026221	1	+	0	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	exon	19026155	19026221	.	+	.	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	intron	19026222	19026407	.	+	.	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	CDS	19026408	19027027	0.97	+	2	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	exon	19026408	19027027	.	+	.	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
Phchi.S1	AUGUSTUS	stop_codon	19027028	19027030	.	+	0	transcript_id "Phchi.S1G296100.t1"; gene_id "Phchi.S1G296100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6302.t1 is derived from g3474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22171461	22171919	.	-	.	Phchi.S1G346100
Phchi.S1	AUGUSTUS	transcript	22171461	22171919	.	-	.	transcript_id "Phchi.S1G346100.t1"; gene_id "Phchi.S1G346100"
Phchi.S1	AUGUSTUS	stop_codon	22171458	22171460	.	-	0	transcript_id "Phchi.S1G346100.t1"; gene_id "Phchi.S1G346100"
Phchi.S1	AUGUSTUS	CDS	22171461	22171919	0.81	-	0	transcript_id "Phchi.S1G346100.t1"; gene_id "Phchi.S1G346100"
Phchi.S1	AUGUSTUS	exon	22171461	22171919	.	-	.	transcript_id "Phchi.S1G346100.t1"; gene_id "Phchi.S1G346100"
Phchi.S1	AUGUSTUS	start_codon	22171917	22171919	.	-	0	transcript_id "Phchi.S1G346100.t1"; gene_id "Phchi.S1G346100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11027.t1 is derived from g15077.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3706324	3707487	.	-	.	Phchi.S4G060900
Phchi.S4	AUGUSTUS	transcript	3706324	3707487	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	stop_codon	3706321	3706323	.	-	0	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3706324	3706418	1	-	2	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3706324	3706418	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	intron	3706419	3706854	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3706855	3706965	1	-	2	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3706855	3706965	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	intron	3706966	3707253	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3707254	3707329	0.67	-	0	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3707254	3707329	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	intron	3707330	3707415	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3707416	3707487	0.32	-	0	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3707416	3707487	.	-	.	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	start_codon	3707485	3707487	.	-	0	transcript_id "Phchi.S4G060900.t1"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	transcript	3706324	3707487	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	stop_codon	3706321	3706323	.	-	0	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3706324	3706418	1	-	2	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3706324	3706418	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	intron	3706419	3706854	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3706855	3706959	0.89	-	2	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3706855	3706959	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	intron	3706960	3707253	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3707254	3707329	0.58	-	0	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3707254	3707329	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	intron	3707330	3707415	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	CDS	3707416	3707487	0.3	-	0	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	exon	3707416	3707487	.	-	.	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
Phchi.S4	AUGUSTUS	start_codon	3707485	3707487	.	-	0	transcript_id "Phchi.S4G060900.t2"; gene_id "Phchi.S4G060900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5500.t1 is derived from g2670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17139428	17140592	.	+	.	Phchi.S1G265900
Phchi.S1	AUGUSTUS	transcript	17139428	17140592	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	start_codon	17139428	17139430	.	+	0	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	CDS	17139428	17139584	0.96	+	0	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	exon	17139428	17139584	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	intron	17139585	17139694	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	CDS	17139695	17140010	0.85	+	2	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	exon	17139695	17140010	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	intron	17140011	17140101	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	CDS	17140102	17140228	0.86	+	1	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	exon	17140102	17140228	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	intron	17140229	17140394	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	CDS	17140395	17140592	0.87	+	0	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	exon	17140395	17140592	.	+	.	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
Phchi.S1	AUGUSTUS	stop_codon	17140593	17140595	.	+	0	transcript_id "Phchi.S1G265900.t1"; gene_id "Phchi.S1G265900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2736.t1 is derived from g9656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8499673	8501006	.	-	.	Phchi.S5G134500
Phchi.S5	AUGUSTUS	transcript	8499673	8501006	.	-	.	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	stop_codon	8499670	8499672	.	-	0	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	CDS	8499673	8500247	0.74	-	2	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	exon	8499673	8500247	.	-	.	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	intron	8500248	8500378	.	-	.	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	CDS	8500379	8501006	1	-	0	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	exon	8500379	8501006	.	-	.	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
Phchi.S5	AUGUSTUS	start_codon	8501004	8501006	.	-	0	transcript_id "Phchi.S5G134500.t1"; gene_id "Phchi.S5G134500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2842.t1 is derived from g11.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1922	2887	.	+	.	Phchi.S1G000100
Phchi.S1	AUGUSTUS	transcript	1922	2887	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	start_codon	1922	1924	.	+	0	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	CDS	1922	2093	0.82	+	0	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	exon	1922	2093	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	intron	2094	2215	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	CDS	2216	2438	0.99	+	2	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	exon	2216	2438	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	intron	2439	2537	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	CDS	2538	2659	1	+	1	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	exon	2538	2659	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	intron	2660	2858	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	CDS	2859	2887	0.71	+	2	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	exon	2859	2887	.	+	.	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
Phchi.S1	AUGUSTUS	stop_codon	2888	2890	.	+	0	transcript_id "Phchi.S1G000100.t1"; gene_id "Phchi.S1G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg519.t1 is derived from g10301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3736048	3736943	.	+	.	Phchi.S6G047800
Phchi.S6	AUGUSTUS	transcript	3736048	3736943	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	start_codon	3736048	3736050	.	+	0	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	CDS	3736048	3736112	0.98	+	0	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	exon	3736048	3736112	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	intron	3736113	3736190	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	CDS	3736191	3736301	1	+	1	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	exon	3736191	3736301	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	intron	3736302	3736388	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	CDS	3736389	3736551	1	+	1	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	exon	3736389	3736551	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	intron	3736552	3736638	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	CDS	3736639	3736719	1	+	0	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	exon	3736639	3736719	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	intron	3736720	3736808	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	CDS	3736809	3736943	1	+	0	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	exon	3736809	3736943	.	+	.	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
Phchi.S6	AUGUSTUS	stop_codon	3736944	3736946	.	+	0	transcript_id "Phchi.S6G047800.t1"; gene_id "Phchi.S6G047800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12824.t1 is derived from g11289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2579142	2580044	.	+	.	Phchi.S3G014300
Phchi.S3	AUGUSTUS	transcript	2579142	2580044	.	+	.	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	start_codon	2579142	2579144	.	+	0	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	CDS	2579142	2579288	1	+	0	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	exon	2579142	2579288	.	+	.	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	intron	2579289	2579404	.	+	.	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	CDS	2579405	2579453	1	+	0	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	exon	2579405	2579453	.	+	.	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	intron	2579454	2579574	.	+	.	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	CDS	2579575	2580044	0.98	+	2	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	exon	2579575	2580044	.	+	.	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
Phchi.S3	AUGUSTUS	stop_codon	2580045	2580047	.	+	0	transcript_id "Phchi.S3G014300.t1"; gene_id "Phchi.S3G014300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1851.t1 is derived from g8771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3552456	3553245	.	-	.	Phchi.S5G046000
Phchi.S5	AUGUSTUS	transcript	3552456	3553245	.	-	.	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	stop_codon	3552453	3552455	.	-	0	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	CDS	3552456	3552812	1	-	0	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	exon	3552456	3552812	.	-	.	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	intron	3552813	3552888	.	-	.	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	CDS	3552889	3553245	0.43	-	0	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	exon	3552889	3553245	.	-	.	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
Phchi.S5	AUGUSTUS	start_codon	3553243	3553245	.	-	0	transcript_id "Phchi.S5G046000.t1"; gene_id "Phchi.S5G046000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2437.t1 is derived from g9357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6630276	6635262	.	-	.	Phchi.S5G104600
Phchi.S5	AUGUSTUS	transcript	6630276	6635262	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	stop_codon	6630273	6630275	.	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6630276	6630343	0.99	-	2	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6630276	6630343	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6630344	6630437	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6630438	6630468	0.94	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6630438	6630468	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6630469	6630580	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6630581	6630631	0.76	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6630581	6630631	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6630632	6630719	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6630720	6630861	1	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6630720	6630861	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6630862	6630942	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6630943	6631026	1	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6630943	6631026	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6631027	6631139	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6631140	6631262	1	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6631140	6631262	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6631263	6631340	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6631341	6631546	1	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6631341	6631546	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6631547	6631633	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6631634	6631726	1	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6631634	6631726	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6631727	6631831	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6631832	6631894	1	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6631832	6631894	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6631895	6632048	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6632049	6632251	1	-	2	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6632049	6632251	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6632252	6632399	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6632400	6632568	1	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6632400	6632568	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6632569	6632693	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6632694	6632902	1	-	2	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6632694	6632902	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6632903	6633081	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6633082	6633236	1	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6633082	6633236	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6633237	6633377	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6633378	6633614	0.94	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6633378	6633614	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6633615	6633728	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6633729	6633967	0.94	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6633729	6633967	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6633968	6634050	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6634051	6634181	1	-	2	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6634051	6634181	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6634182	6634274	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6634275	6634483	1	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6634275	6634483	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6634484	6634580	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6634581	6634693	1	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6634581	6634693	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6634694	6634778	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6634779	6634829	0.91	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6634779	6634829	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6634830	6634927	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6634928	6635000	0.92	-	1	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6634928	6635000	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	intron	6635001	6635143	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	CDS	6635144	6635262	0.75	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	exon	6635144	6635262	.	-	.	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
Phchi.S5	AUGUSTUS	start_codon	6635260	6635262	.	-	0	transcript_id "Phchi.S5G104600.t1"; gene_id "Phchi.S5G104600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12423.t1 is derived from g8100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19547531	19550120	.	+	.	Phchi.S2G050300
Phchi.S2	AUGUSTUS	transcript	19547531	19550120	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	start_codon	19547531	19547533	.	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19547531	19547618	0.97	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19547531	19547618	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19547619	19547735	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19547736	19548017	0.97	+	2	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19547736	19548017	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19548018	19548198	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19548199	19548229	0.93	+	2	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19548199	19548229	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19548230	19548360	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19548361	19548475	0.93	+	1	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19548361	19548475	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19548476	19548569	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19548570	19548671	1	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19548570	19548671	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19548672	19548821	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19548822	19548875	1	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19548822	19548875	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19548876	19548971	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19548972	19549064	1	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19548972	19549064	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19549065	19549260	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19549261	19549353	0.95	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19549261	19549353	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19549354	19549465	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19549466	19549570	1	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19549466	19549570	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19549571	19549651	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19549652	19549750	1	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19549652	19549750	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	intron	19549751	19549850	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	CDS	19549851	19550120	0.83	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	exon	19549851	19550120	.	+	.	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
Phchi.S2	AUGUSTUS	stop_codon	19550121	19550123	.	+	0	transcript_id "Phchi.S2G050300.t1"; gene_id "Phchi.S2G050300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6125.t1 is derived from g3296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21057782	21058783	.	+	.	Phchi.S1G328400
Phchi.S1	AUGUSTUS	transcript	21057782	21058783	.	+	.	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	start_codon	21057782	21057784	.	+	0	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	CDS	21057782	21058288	1	+	0	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	exon	21057782	21058288	.	+	.	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	intron	21058289	21058392	.	+	.	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	CDS	21058393	21058443	1	+	0	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	exon	21058393	21058443	.	+	.	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	intron	21058444	21058525	.	+	.	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	CDS	21058526	21058783	1	+	0	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	exon	21058526	21058783	.	+	.	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
Phchi.S1	AUGUSTUS	stop_codon	21058784	21058786	.	+	0	transcript_id "Phchi.S1G328400.t1"; gene_id "Phchi.S1G328400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8054.t1 is derived from g5229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32723094	32725303	.	+	.	Phchi.S1G521300
Phchi.S1	AUGUSTUS	transcript	32723094	32725303	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	start_codon	32723094	32723096	.	+	0	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32723094	32723325	0.97	+	0	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32723094	32723325	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	intron	32723326	32724018	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32724019	32724054	1	+	2	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32724019	32724054	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	intron	32724055	32724143	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32724144	32724243	0.97	+	2	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32724144	32724243	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	intron	32724244	32724376	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32724377	32724431	1	+	1	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32724377	32724431	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	intron	32724432	32724513	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32724514	32724630	1	+	0	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32724514	32724630	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	intron	32724631	32724793	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32724794	32724958	1	+	0	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32724794	32724958	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	intron	32724959	32725075	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	CDS	32725076	32725303	0.51	+	0	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	exon	32725076	32725303	.	+	.	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
Phchi.S1	AUGUSTUS	stop_codon	32725304	32725306	.	+	0	transcript_id "Phchi.S1G521300.t1"; gene_id "Phchi.S1G521300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12230.t1 is derived from g7906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6851550	6852843	.	+	.	Phchi.S2G031000
Phchi.S2	AUGUSTUS	transcript	6851550	6852843	.	+	.	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	start_codon	6851550	6851552	.	+	0	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	CDS	6851550	6851563	0.69	+	0	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	exon	6851550	6851563	.	+	.	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	intron	6851564	6851686	.	+	.	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	CDS	6851687	6851834	0.98	+	1	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	exon	6851687	6851834	.	+	.	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	intron	6851835	6852450	.	+	.	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	CDS	6852451	6852843	0.65	+	0	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	exon	6852451	6852843	.	+	.	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
Phchi.S2	AUGUSTUS	stop_codon	6852844	6852846	.	+	0	transcript_id "Phchi.S2G031000.t1"; gene_id "Phchi.S2G031000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2266.t1 is derived from g9186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5741283	5744169	.	+	.	Phchi.S5G087500
Phchi.S5	AUGUSTUS	transcript	5741283	5744169	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	start_codon	5741283	5741285	.	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5741283	5741441	0.39	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5741283	5741441	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5741442	5741526	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5741527	5741643	1	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5741527	5741643	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5741644	5741753	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5741754	5741854	1	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5741754	5741854	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5741855	5742040	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742041	5742112	1	+	1	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742041	5742112	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742113	5742188	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742189	5742270	1	+	1	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742189	5742270	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742271	5742379	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742380	5742460	1	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742380	5742460	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742461	5742743	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742744	5742782	1	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742744	5742782	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742783	5742922	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742923	5742994	1	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742923	5742994	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742995	5743758	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5743759	5743899	1	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5743759	5743899	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5743900	5743983	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5743984	5744169	0.92	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5743984	5744169	.	+	.	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	stop_codon	5744170	5744172	.	+	0	transcript_id "Phchi.S5G087500.t1"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	transcript	5741283	5743253	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	start_codon	5741283	5741285	.	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5741283	5741441	0.32	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5741283	5741441	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5741442	5741526	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5741527	5741643	0.98	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5741527	5741643	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5741644	5741753	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5741754	5741854	1	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5741754	5741854	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5741855	5742040	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742041	5742112	1	+	1	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742041	5742112	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742113	5742188	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742189	5742270	1	+	1	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742189	5742270	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742271	5742379	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742380	5742460	1	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742380	5742460	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742461	5742743	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742744	5742782	1	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742744	5742782	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742783	5742922	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5742923	5742994	1	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5742923	5742994	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	intron	5742995	5743241	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	CDS	5743242	5743253	0.44	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	exon	5743242	5743253	.	+	.	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
Phchi.S5	AUGUSTUS	stop_codon	5743254	5743256	.	+	0	transcript_id "Phchi.S5G087500.t2"; gene_id "Phchi.S5G087500"
# This transcript jg10597.t2 is derived from g14647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10597.t3 is derived from g14647.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10598.t1 is derived from g14648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1135305	1137841	.	-	.	Phchi.S4G018000
Phchi.S4	AUGUSTUS	transcript	1135305	1137841	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	stop_codon	1135302	1135304	.	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1135305	1135373	1	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1135305	1135373	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1135374	1135449	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1135450	1135522	1	-	1	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1135450	1135522	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1135523	1135614	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1135615	1135736	1	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1135615	1135736	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1135737	1135825	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1135826	1135984	1	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1135826	1135984	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1135985	1136073	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1136074	1136163	1	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1136074	1136163	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1136164	1136250	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1136251	1136313	1	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1136251	1136313	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1136314	1136396	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1136397	1136486	1	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1136397	1136486	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1136487	1136677	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1136678	1136735	1	-	1	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1136678	1136735	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1136736	1136852	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1136853	1137117	0.92	-	2	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1136853	1137117	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1137118	1137212	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1137213	1137328	0.9	-	1	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1137213	1137328	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1137329	1137464	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1137465	1137573	0.87	-	2	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1137465	1137573	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	intron	1137574	1137828	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	CDS	1137829	1137841	0.91	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	exon	1137829	1137841	.	-	.	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
Phchi.S4	AUGUSTUS	start_codon	1137839	1137841	.	-	0	transcript_id "Phchi.S4G018000.t1"; gene_id "Phchi.S4G018000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3450.t1 is derived from g619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3802437	3810358	.	+	.	Phchi.S1G060900
Phchi.S1	AUGUSTUS	transcript	3802437	3810358	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	start_codon	3802437	3802439	.	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3802437	3803159	0.74	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3802437	3803159	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3803160	3803246	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3803247	3803568	0.81	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3803247	3803568	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3803569	3803680	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3803681	3803936	0.38	+	2	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3803681	3803936	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3803937	3804042	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3804043	3804175	0.79	+	1	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3804043	3804175	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3804176	3804337	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3804338	3804696	0.83	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3804338	3804696	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3804697	3804783	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3804784	3805278	0.98	+	1	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3804784	3805278	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3805279	3805364	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3805365	3805523	0.76	+	1	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3805365	3805523	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3805524	3805588	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3805589	3806705	0.65	+	1	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3805589	3806705	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3806706	3806846	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3806847	3807206	0.98	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3806847	3807206	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3807207	3807330	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3807331	3807565	0.55	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3807331	3807565	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	intron	3807566	3807671	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	CDS	3807672	3810358	0.95	+	2	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	exon	3807672	3810358	.	+	.	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
Phchi.S1	AUGUSTUS	stop_codon	3810359	3810361	.	+	0	transcript_id "Phchi.S1G060900.t1"; gene_id "Phchi.S1G060900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5384.t1 is derived from g2554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16617869	16622144	.	-	.	Phchi.S1G254300
Phchi.S1	AUGUSTUS	transcript	16617869	16622144	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	stop_codon	16617866	16617868	.	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16617869	16617928	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16617869	16617928	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16617929	16618005	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16618006	16618089	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16618006	16618089	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16618090	16618187	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16618188	16618301	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16618188	16618301	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16618302	16618390	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16618391	16618504	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16618391	16618504	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16618505	16618619	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16618620	16618680	1	-	1	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16618620	16618680	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16618681	16618812	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16618813	16619019	1	-	1	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16618813	16619019	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16619020	16619218	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16619219	16620537	0.97	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16619219	16620537	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16620538	16620621	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16620622	16620747	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16620622	16620747	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16620748	16620836	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16620837	16620904	1	-	2	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16620837	16620904	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16620905	16620998	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16620999	16621107	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16620999	16621107	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16621108	16621305	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16621306	16621390	1	-	1	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16621306	16621390	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16621391	16621481	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16621482	16621598	1	-	1	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16621482	16621598	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16621599	16621695	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16621696	16621734	1	-	1	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16621696	16621734	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16621735	16621840	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16621841	16621849	0.92	-	1	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16621841	16621849	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	intron	16621850	16622052	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	CDS	16622053	16622144	1	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	exon	16622053	16622144	.	-	.	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
Phchi.S1	AUGUSTUS	start_codon	16622142	16622144	.	-	0	transcript_id "Phchi.S1G254300.t1"; gene_id "Phchi.S1G254300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9608.t1 is derived from g6784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42916902	42917579	.	+	.	Phchi.S1G676700
Phchi.S1	AUGUSTUS	transcript	42916902	42917579	.	+	.	transcript_id "Phchi.S1G676700.t1"; gene_id "Phchi.S1G676700"
Phchi.S1	AUGUSTUS	start_codon	42916902	42916904	.	+	0	transcript_id "Phchi.S1G676700.t1"; gene_id "Phchi.S1G676700"
Phchi.S1	AUGUSTUS	CDS	42916902	42917579	0.61	+	0	transcript_id "Phchi.S1G676700.t1"; gene_id "Phchi.S1G676700"
Phchi.S1	AUGUSTUS	exon	42916902	42917579	.	+	.	transcript_id "Phchi.S1G676700.t1"; gene_id "Phchi.S1G676700"
Phchi.S1	AUGUSTUS	stop_codon	42917580	42917582	.	+	0	transcript_id "Phchi.S1G676700.t1"; gene_id "Phchi.S1G676700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15277.t1 is derived from g13745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18116389	18119811	.	-	.	Phchi.S3G259600
Phchi.S3	AUGUSTUS	transcript	18116389	18119811	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	stop_codon	18116386	18116388	.	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18116389	18116817	0.52	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18116389	18116817	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18116818	18117011	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18117012	18117084	0.6	-	1	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18117012	18117084	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18117085	18117239	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18117240	18117325	0.81	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18117240	18117325	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18117326	18117508	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18117509	18117558	0.44	-	2	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18117509	18117558	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18117559	18117754	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18117755	18117879	0.72	-	1	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18117755	18117879	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18117880	18117976	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18117977	18118155	1	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18117977	18118155	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18118156	18118307	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18118308	18118442	1	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18118308	18118442	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18118443	18118563	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18118564	18118741	0.99	-	1	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18118564	18118741	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18118742	18118844	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18118845	18118990	0.99	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18118845	18118990	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	intron	18118991	18119160	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	CDS	18119161	18119811	0.96	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	exon	18119161	18119811	.	-	.	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
Phchi.S3	AUGUSTUS	start_codon	18119809	18119811	.	-	0	transcript_id "Phchi.S3G259600.t1"; gene_id "Phchi.S3G259600"
# This transcript jg9855.t1 is derived from g7030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44096462	44098584	.	+	.	Phchi.S1G701300
Phchi.S1	AUGUSTUS	transcript	44096462	44098584	.	+	.	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	start_codon	44096462	44096464	.	+	0	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	CDS	44096462	44098076	0.42	+	0	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	exon	44096462	44098076	.	+	.	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	intron	44098077	44098162	.	+	.	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	CDS	44098163	44098584	0.29	+	2	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	exon	44098163	44098584	.	+	.	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
Phchi.S1	AUGUSTUS	stop_codon	44098585	44098587	.	+	0	transcript_id "Phchi.S1G701300.t1"; gene_id "Phchi.S1G701300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg465.t1 is derived from g10247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3266407	3269418	.	+	.	Phchi.S6G042400
Phchi.S6	AUGUSTUS	transcript	3266407	3269418	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	start_codon	3266407	3266409	.	+	0	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	CDS	3266407	3268391	0.38	+	0	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	exon	3266407	3268391	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	intron	3268392	3268622	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	CDS	3268623	3268643	0.93	+	1	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	exon	3268623	3268643	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	intron	3268644	3268775	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	CDS	3268776	3268804	0.85	+	1	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	exon	3268776	3268804	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	intron	3268805	3269009	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	CDS	3269010	3269160	0.96	+	2	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	exon	3269010	3269160	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	intron	3269161	3269258	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	CDS	3269259	3269418	0.98	+	1	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	exon	3269259	3269418	.	+	.	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
Phchi.S6	AUGUSTUS	stop_codon	3269419	3269421	.	+	0	transcript_id "Phchi.S6G042400.t1"; gene_id "Phchi.S6G042400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11390.t1 is derived from g15440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6108448	6109274	.	+	.	Phchi.S4G097200
Phchi.S4	AUGUSTUS	transcript	6108448	6109274	.	+	.	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	start_codon	6108448	6108450	.	+	0	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	CDS	6108448	6109120	0.36	+	0	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	exon	6108448	6109120	.	+	.	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	intron	6109121	6109251	.	+	.	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	CDS	6109252	6109274	0.17	+	2	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	exon	6109252	6109274	.	+	.	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
Phchi.S4	AUGUSTUS	stop_codon	6109275	6109277	.	+	0	transcript_id "Phchi.S4G097200.t1"; gene_id "Phchi.S4G097200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3853.t1 is derived from g1022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6044026	6044772	.	-	.	Phchi.S1G101200
Phchi.S1	AUGUSTUS	transcript	6044026	6044772	.	-	.	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	stop_codon	6044023	6044025	.	-	0	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	CDS	6044026	6044026	0.99	-	1	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	exon	6044026	6044026	.	-	.	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	intron	6044027	6044343	.	-	.	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	CDS	6044344	6044538	0.99	-	1	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	exon	6044344	6044538	.	-	.	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	intron	6044539	6044617	.	-	.	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	CDS	6044618	6044772	1	-	0	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	exon	6044618	6044772	.	-	.	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	start_codon	6044770	6044772	.	-	0	transcript_id "Phchi.S1G101200.t1"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	transcript	6044026	6044705	.	-	.	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	stop_codon	6044023	6044025	.	-	0	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	CDS	6044026	6044026	0.95	-	1	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	exon	6044026	6044026	.	-	.	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	intron	6044027	6044343	.	-	.	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	CDS	6044344	6044521	0.95	-	2	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	exon	6044344	6044521	.	-	.	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	intron	6044522	6044617	.	-	.	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	CDS	6044618	6044705	0.87	-	0	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	exon	6044618	6044705	.	-	.	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
Phchi.S1	AUGUSTUS	start_codon	6044703	6044705	.	-	0	transcript_id "Phchi.S1G101200.t2"; gene_id "Phchi.S1G101200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13918.t1 is derived from g12385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9655421	9657576	.	-	.	Phchi.S3G123700
Phchi.S3	AUGUSTUS	transcript	9655421	9657576	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	stop_codon	9655418	9655420	.	-	0	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9655421	9655469	0.93	-	1	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9655421	9655469	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9655470	9655694	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9655695	9656041	0.93	-	0	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9655695	9656041	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9656042	9656132	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9656133	9656248	1	-	2	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9656133	9656248	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9656249	9656383	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9656384	9656512	1	-	2	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9656384	9656512	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9656513	9656612	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9656613	9656680	1	-	1	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9656613	9656680	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9656681	9656803	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9656804	9656864	1	-	2	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9656804	9656864	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9656865	9656964	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9656965	9657053	1	-	1	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9656965	9657053	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9657054	9657130	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9657131	9657257	1	-	2	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9657131	9657257	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	intron	9657258	9657338	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	CDS	9657339	9657576	0.82	-	0	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	exon	9657339	9657576	.	-	.	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
Phchi.S3	AUGUSTUS	start_codon	9657574	9657576	.	-	0	transcript_id "Phchi.S3G123700.t1"; gene_id "Phchi.S3G123700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12107.t1 is derived from g7783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3488013	3490814	.	-	.	Phchi.S2G018700
Phchi.S2	AUGUSTUS	transcript	3488013	3490814	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	stop_codon	3488010	3488012	.	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3488013	3488348	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3488013	3488348	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3488349	3488465	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3488466	3488582	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3488466	3488582	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3488583	3488662	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3488663	3488750	1	-	1	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3488663	3488750	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3488751	3488952	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3488953	3489027	1	-	1	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3488953	3489027	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3489028	3489111	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3489112	3489179	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3489112	3489179	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3489180	3489313	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3489314	3489396	1	-	2	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3489314	3489396	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3489397	3489546	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3489547	3489595	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3489547	3489595	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3489596	3489687	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3489688	3489808	1	-	1	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3489688	3489808	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3489809	3489913	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3489914	3489999	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3489914	3489999	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3490000	3490153	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3490154	3490282	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3490154	3490282	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3490283	3490362	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3490363	3490485	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3490363	3490485	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	intron	3490486	3490607	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	CDS	3490608	3490814	1	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	exon	3490608	3490814	.	-	.	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
Phchi.S2	AUGUSTUS	start_codon	3490812	3490814	.	-	0	transcript_id "Phchi.S2G018700.t1"; gene_id "Phchi.S2G018700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1597.t1 is derived from g8516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1943725	1944162	.	-	.	Phchi.S5G020600
Phchi.S5	AUGUSTUS	transcript	1943725	1944162	.	-	.	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	stop_codon	1943722	1943724	.	-	0	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	CDS	1943725	1943917	1	-	1	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	exon	1943725	1943917	.	-	.	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	intron	1943918	1944076	.	-	.	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	CDS	1944077	1944162	0.99	-	0	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	exon	1944077	1944162	.	-	.	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
Phchi.S5	AUGUSTUS	start_codon	1944160	1944162	.	-	0	transcript_id "Phchi.S5G020600.t1"; gene_id "Phchi.S5G020600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13837.t1 is derived from g12304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9134402	9136128	.	-	.	Phchi.S3G115600
Phchi.S3	AUGUSTUS	transcript	9134402	9136128	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	stop_codon	9134399	9134401	.	-	0	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9134402	9134912	1	-	1	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9134402	9134912	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	intron	9134913	9135048	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9135049	9135152	1	-	0	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9135049	9135152	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	intron	9135153	9135268	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9135269	9135331	1	-	0	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9135269	9135331	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	intron	9135332	9135436	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9135437	9135465	0.99	-	2	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9135437	9135465	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	intron	9135466	9135545	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9135546	9135584	1	-	2	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9135546	9135584	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	intron	9135585	9135681	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9135682	9135731	1	-	1	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9135682	9135731	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	intron	9135732	9135817	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	CDS	9135818	9136128	0.62	-	0	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	exon	9135818	9136128	.	-	.	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
Phchi.S3	AUGUSTUS	start_codon	9136126	9136128	.	-	0	transcript_id "Phchi.S3G115600.t1"; gene_id "Phchi.S3G115600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13624.t1 is derived from g12091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7813976	7814528	.	-	.	Phchi.S3G094300
Phchi.S3	AUGUSTUS	transcript	7813976	7814528	.	-	.	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	stop_codon	7813973	7813975	.	-	0	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	CDS	7813976	7814069	0.75	-	1	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	exon	7813976	7814069	.	-	.	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	intron	7814070	7814208	.	-	.	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	CDS	7814209	7814528	0.66	-	0	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	exon	7814209	7814528	.	-	.	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
Phchi.S3	AUGUSTUS	start_codon	7814526	7814528	.	-	0	transcript_id "Phchi.S3G094300.t1"; gene_id "Phchi.S3G094300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6172.t1 is derived from g3343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21291851	21292813	.	-	.	Phchi.S1G333100
Phchi.S1	AUGUSTUS	transcript	21291851	21292813	.	-	.	transcript_id "Phchi.S1G333100.t1"; gene_id "Phchi.S1G333100"
Phchi.S1	AUGUSTUS	stop_codon	21291848	21291850	.	-	0	transcript_id "Phchi.S1G333100.t1"; gene_id "Phchi.S1G333100"
Phchi.S1	AUGUSTUS	CDS	21291851	21292813	0.82	-	0	transcript_id "Phchi.S1G333100.t1"; gene_id "Phchi.S1G333100"
Phchi.S1	AUGUSTUS	exon	21291851	21292813	.	-	.	transcript_id "Phchi.S1G333100.t1"; gene_id "Phchi.S1G333100"
Phchi.S1	AUGUSTUS	start_codon	21292811	21292813	.	-	0	transcript_id "Phchi.S1G333100.t1"; gene_id "Phchi.S1G333100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4530.t1 is derived from g1700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10981872	10982335	.	-	.	Phchi.S1G168900
Phchi.S1	AUGUSTUS	transcript	10981872	10982335	.	-	.	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	stop_codon	10981869	10981871	.	-	0	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	CDS	10981872	10982053	1	-	2	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	exon	10981872	10982053	.	-	.	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	intron	10982054	10982156	.	-	.	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	CDS	10982157	10982232	1	-	0	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	exon	10982157	10982232	.	-	.	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	intron	10982233	10982326	.	-	.	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	CDS	10982327	10982335	0.88	-	0	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	exon	10982327	10982335	.	-	.	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
Phchi.S1	AUGUSTUS	start_codon	10982333	10982335	.	-	0	transcript_id "Phchi.S1G168900.t1"; gene_id "Phchi.S1G168900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8830.t1 is derived from g6005.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38164738	38166261	.	+	.	Phchi.S1G598900
Phchi.S1	AUGUSTUS	transcript	38164738	38165900	.	+	.	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	start_codon	38164738	38164740	.	+	0	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	CDS	38164738	38165355	1	+	0	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	exon	38164738	38165355	.	+	.	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	intron	38165356	38165468	.	+	.	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	CDS	38165469	38165724	1	+	0	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	exon	38165469	38165724	.	+	.	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	intron	38165725	38165874	.	+	.	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	CDS	38165875	38165900	1	+	2	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	exon	38165875	38165900	.	+	.	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	stop_codon	38165901	38165903	.	+	0	transcript_id "Phchi.S1G598900.t1"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	transcript	38164738	38166261	.	+	.	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	start_codon	38164738	38164740	.	+	0	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	CDS	38164738	38165355	0.98	+	0	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	exon	38164738	38165355	.	+	.	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	intron	38165356	38165468	.	+	.	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	CDS	38165469	38165732	1	+	0	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	exon	38165469	38165732	.	+	.	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	intron	38165733	38165874	.	+	.	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	CDS	38165875	38166261	0.45	+	0	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	exon	38165875	38166261	.	+	.	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
Phchi.S1	AUGUSTUS	stop_codon	38166262	38166264	.	+	0	transcript_id "Phchi.S1G598900.t2"; gene_id "Phchi.S1G598900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9991.t1 is derived from g7167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44842869	44844706	.	-	.	Phchi.S1G715000
Phchi.S1	AUGUSTUS	transcript	44842869	44844706	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	stop_codon	44842866	44842868	.	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	CDS	44842869	44843030	0.77	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	exon	44842869	44843030	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	intron	44843031	44843149	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	CDS	44843150	44843419	0.43	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	exon	44843150	44843419	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	intron	44843420	44843513	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	CDS	44843514	44843642	1	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	exon	44843514	44843642	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	intron	44843643	44843731	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	CDS	44843732	44843875	0.98	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	exon	44843732	44843875	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	intron	44843876	44843961	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	CDS	44843962	44844135	0.94	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	exon	44843962	44844135	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	intron	44844136	44844421	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	CDS	44844422	44844706	0.58	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	exon	44844422	44844706	.	-	.	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
Phchi.S1	AUGUSTUS	start_codon	44844704	44844706	.	-	0	transcript_id "Phchi.S1G715000.t1"; gene_id "Phchi.S1G715000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9749.t1 is derived from g6925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43491329	43495687	.	-	.	Phchi.S1G690800
Phchi.S1	AUGUSTUS	transcript	43491329	43495687	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	stop_codon	43491326	43491328	.	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43491329	43491364	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43491329	43491364	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43491365	43491448	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43491449	43491587	1	-	1	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43491449	43491587	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43491588	43491689	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43491690	43491838	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43491690	43491838	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43491839	43491916	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43491917	43492038	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43491917	43492038	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43492039	43492156	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43492157	43492278	1	-	1	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43492157	43492278	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43492279	43492357	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43492358	43492612	1	-	1	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43492358	43492612	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43492613	43492700	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43492701	43492864	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43492701	43492864	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43492865	43493104	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43493105	43493226	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43493105	43493226	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43493227	43493320	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43493321	43493495	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43493321	43493495	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43493496	43493581	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43493582	43493668	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43493582	43493668	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43493669	43493750	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43493751	43494053	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43493751	43494053	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43494054	43494322	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43494323	43494378	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43494323	43494378	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43494379	43494516	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43494517	43494598	1	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43494517	43494598	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43494599	43494715	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43494716	43494783	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43494716	43494783	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43494784	43494926	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43494927	43494983	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43494927	43494983	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43494984	43495087	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43495088	43495150	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43495088	43495150	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43495151	43495359	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43495360	43495431	1	-	2	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43495360	43495431	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	intron	43495432	43495593	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	CDS	43495594	43495687	0.96	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	exon	43495594	43495687	.	-	.	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
Phchi.S1	AUGUSTUS	start_codon	43495685	43495687	.	-	0	transcript_id "Phchi.S1G690800.t1"; gene_id "Phchi.S1G690800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11780.t1 is derived from g15832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8139953	8143131	.	+	.	Phchi.S4G136200
Phchi.S4	AUGUSTUS	transcript	8139953	8143131	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	start_codon	8139953	8139955	.	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8139953	8140083	0.8	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8139953	8140083	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8140084	8140160	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8140161	8140236	0.81	+	1	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8140161	8140236	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8140237	8140659	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8140660	8140804	1	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8140660	8140804	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8140805	8140928	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8140929	8141080	0.74	+	2	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8140929	8141080	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8141081	8141277	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8141278	8141463	0.98	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8141278	8141463	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8141464	8141553	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8141554	8141629	1	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8141554	8141629	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8141630	8141733	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8141734	8141811	0.95	+	2	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8141734	8141811	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8141812	8141919	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8141920	8142005	1	+	2	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8141920	8142005	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8142006	8142146	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8142147	8142220	1	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8142147	8142220	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8142221	8142328	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8142329	8142374	1	+	1	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8142329	8142374	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8142375	8142470	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8142471	8142580	1	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8142471	8142580	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8142581	8142666	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8142667	8142841	1	+	1	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8142667	8142841	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	intron	8142842	8142921	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	CDS	8142922	8143131	0.97	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	exon	8142922	8143131	.	+	.	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
Phchi.S4	AUGUSTUS	stop_codon	8143132	8143134	.	+	0	transcript_id "Phchi.S4G136200.t1"; gene_id "Phchi.S4G136200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11115.t1 is derived from g15165.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4224356	4230600	.	-	.	Phchi.S4G069700
Phchi.S4	AUGUSTUS	transcript	4224356	4230600	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	stop_codon	4224353	4224355	.	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4224356	4225785	1	-	2	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4224356	4225785	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4225786	4225860	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4225861	4226191	0.45	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4225861	4226191	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4226192	4226312	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4226313	4226431	0.28	-	2	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4226313	4226431	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4226432	4226733	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4226734	4226881	0.59	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4226734	4226881	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4226882	4226949	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4226950	4227156	0.7	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4226950	4227156	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4227157	4227269	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4227270	4227538	0.5	-	2	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4227270	4227538	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4227539	4227659	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4227660	4228008	0.93	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4227660	4228008	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4228009	4228091	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4228092	4228351	1	-	2	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4228092	4228351	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4228352	4228447	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4228448	4228676	0.97	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4228448	4228676	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4228677	4228762	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4228763	4228927	1	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4228763	4228927	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4228928	4229063	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4229064	4229390	1	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4229064	4229390	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4229391	4229524	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4229525	4229614	0.83	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4229525	4229614	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4229615	4229751	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4229752	4229819	0.99	-	2	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4229752	4229819	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4229820	4229925	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4229926	4230112	1	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4229926	4230112	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	intron	4230113	4230210	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	CDS	4230211	4230600	1	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	exon	4230211	4230600	.	-	.	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
Phchi.S4	AUGUSTUS	start_codon	4230598	4230600	.	-	0	transcript_id "Phchi.S4G069700.t1"; gene_id "Phchi.S4G069700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg118.t1 is derived from g9900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	645944	646882	.	+	.	Phchi.S6G007700
Phchi.S6	AUGUSTUS	transcript	645944	646882	.	+	.	transcript_id "Phchi.S6G007700.t1"; gene_id "Phchi.S6G007700"
Phchi.S6	AUGUSTUS	start_codon	645944	645946	.	+	0	transcript_id "Phchi.S6G007700.t1"; gene_id "Phchi.S6G007700"
Phchi.S6	AUGUSTUS	CDS	645944	646882	0.8	+	0	transcript_id "Phchi.S6G007700.t1"; gene_id "Phchi.S6G007700"
Phchi.S6	AUGUSTUS	exon	645944	646882	.	+	.	transcript_id "Phchi.S6G007700.t1"; gene_id "Phchi.S6G007700"
Phchi.S6	AUGUSTUS	stop_codon	646883	646885	.	+	0	transcript_id "Phchi.S6G007700.t1"; gene_id "Phchi.S6G007700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5850.t1 is derived from g3020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19330524	19338447	.	-	.	Phchi.S1G300900
Phchi.S1	AUGUSTUS	transcript	19330524	19338447	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	stop_codon	19330521	19330523	.	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19330524	19330978	0.53	-	2	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19330524	19330978	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19330979	19331091	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19331092	19331221	0.52	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19331092	19331221	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19331222	19331428	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19331429	19331515	0.58	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19331429	19331515	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19331516	19331608	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19331609	19331641	1	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19331609	19331641	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19331642	19331832	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19331833	19331925	1	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19331833	19331925	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19331926	19332249	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19332250	19332340	0.81	-	1	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19332250	19332340	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19332341	19332765	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19332766	19335248	0.47	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19332766	19335248	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19335249	19335421	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19335422	19335680	1	-	1	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19335422	19335680	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19335681	19335763	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19335764	19336050	1	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19335764	19336050	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19336051	19336127	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19336128	19336463	0.94	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19336128	19336463	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19336464	19336548	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19336549	19336690	1	-	1	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19336549	19336690	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19336691	19336781	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19336782	19337002	1	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19336782	19337002	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19337003	19337083	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19337084	19337245	1	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19337084	19337245	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19337246	19337330	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19337331	19337489	1	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19337331	19337489	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19337490	19337582	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19337583	19337891	0.92	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19337583	19337891	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19337892	19337996	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19337997	19338260	0.84	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19337997	19338260	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	intron	19338261	19338363	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	CDS	19338364	19338447	0.89	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	exon	19338364	19338447	.	-	.	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
Phchi.S1	AUGUSTUS	start_codon	19338445	19338447	.	-	0	transcript_id "Phchi.S1G300900.t1"; gene_id "Phchi.S1G300900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4979.t1 is derived from g2149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13854126	13858952	.	+	.	Phchi.S1G213800
Phchi.S1	AUGUSTUS	transcript	13854126	13858952	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	start_codon	13854126	13854128	.	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13854126	13854131	0.94	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13854126	13854131	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13854132	13854368	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13854369	13854455	0.39	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13854369	13854455	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13854456	13854629	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13854630	13854761	0.81	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13854630	13854761	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13854762	13854856	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13854857	13854928	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13854857	13854928	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13854929	13855024	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13855025	13855230	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13855025	13855230	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13855231	13855320	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13855321	13855792	0.99	+	1	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13855321	13855792	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13855793	13855947	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13855948	13856088	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13855948	13856088	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13856089	13856183	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13856184	13856322	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13856184	13856322	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13856323	13856485	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13856486	13856679	1	+	2	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13856486	13856679	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13856680	13856784	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13856785	13856943	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13856785	13856943	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13856944	13857028	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13857029	13857105	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13857029	13857105	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13857106	13857184	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13857185	13857565	0.84	+	1	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13857185	13857565	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13857566	13857652	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13857653	13858079	1	+	1	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13857653	13858079	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13858080	13858174	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13858175	13858468	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13858175	13858468	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13858469	13858554	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13858555	13858673	1	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13858555	13858673	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	intron	13858674	13858768	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	CDS	13858769	13858952	0.96	+	1	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	exon	13858769	13858952	.	+	.	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
Phchi.S1	AUGUSTUS	stop_codon	13858953	13858955	.	+	0	transcript_id "Phchi.S1G213800.t1"; gene_id "Phchi.S1G213800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6098.t1 is derived from g3269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20944163	20947486	.	-	.	Phchi.S1G325700
Phchi.S1	AUGUSTUS	transcript	20944163	20947486	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	stop_codon	20944160	20944162	.	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20944163	20944740	1	-	2	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20944163	20944740	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20944741	20944827	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20944828	20945035	1	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20944828	20945035	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20945036	20945109	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20945110	20945221	0.98	-	1	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20945110	20945221	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20945222	20945323	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20945324	20945560	0.97	-	1	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20945324	20945560	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20945561	20945644	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20945645	20945745	1	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20945645	20945745	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20945746	20945819	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20945820	20946146	1	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20945820	20946146	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20946147	20946238	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20946239	20946449	1	-	1	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20946239	20946449	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20946450	20946549	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20946550	20946661	0.99	-	2	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20946550	20946661	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20946662	20946744	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20946745	20946900	1	-	2	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20946745	20946900	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20946901	20946991	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20946992	20947083	1	-	1	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20946992	20947083	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20947084	20947168	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20947169	20947263	0.94	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20947169	20947263	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	intron	20947264	20947360	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	CDS	20947361	20947486	0.78	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	exon	20947361	20947486	.	-	.	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
Phchi.S1	AUGUSTUS	start_codon	20947484	20947486	.	-	0	transcript_id "Phchi.S1G325700.t1"; gene_id "Phchi.S1G325700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5177.t1 is derived from g2347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15341726	15342979	.	+	.	Phchi.S1G233600
Phchi.S1	AUGUSTUS	transcript	15341726	15342979	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	start_codon	15341726	15341728	.	+	0	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	CDS	15341726	15341859	0.82	+	0	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	exon	15341726	15341859	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	intron	15341860	15341968	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	CDS	15341969	15342207	1	+	1	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	exon	15341969	15342207	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	intron	15342208	15342284	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	CDS	15342285	15342435	1	+	2	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	exon	15342285	15342435	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	intron	15342436	15342515	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	CDS	15342516	15342601	1	+	1	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	exon	15342516	15342601	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	intron	15342602	15342708	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	CDS	15342709	15342813	0.98	+	2	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	exon	15342709	15342813	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	intron	15342814	15342920	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	CDS	15342921	15342979	0.97	+	2	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	exon	15342921	15342979	.	+	.	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
Phchi.S1	AUGUSTUS	stop_codon	15342980	15342982	.	+	0	transcript_id "Phchi.S1G233600.t1"; gene_id "Phchi.S1G233600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4560.t1 is derived from g1730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11116759	11119694	.	-	.	Phchi.S1G171900
Phchi.S1	AUGUSTUS	transcript	11116759	11119694	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	stop_codon	11116756	11116758	.	-	0	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	CDS	11116759	11117016	1	-	0	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	exon	11116759	11117016	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	intron	11117017	11117218	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	CDS	11117219	11117255	0.99	-	1	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	exon	11117219	11117255	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	intron	11117256	11117326	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	CDS	11117327	11117608	0.01	-	1	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	exon	11117327	11117608	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	intron	11117609	11117700	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	CDS	11117701	11117932	0.98	-	2	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	exon	11117701	11117932	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	intron	11117933	11118319	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	CDS	11118320	11119694	0.76	-	0	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	exon	11118320	11119694	.	-	.	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
Phchi.S1	AUGUSTUS	start_codon	11119692	11119694	.	-	0	transcript_id "Phchi.S1G171900.t1"; gene_id "Phchi.S1G171900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6997.t1 is derived from g4169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26317238	26318010	.	-	.	Phchi.S1G415600
Phchi.S1	AUGUSTUS	transcript	26317238	26318010	.	-	.	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	stop_codon	26317235	26317237	.	-	0	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	CDS	26317238	26317296	1	-	2	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	exon	26317238	26317296	.	-	.	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	intron	26317297	26317507	.	-	.	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	CDS	26317508	26317639	1	-	2	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	exon	26317508	26317639	.	-	.	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	intron	26317640	26317865	.	-	.	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	CDS	26317866	26318010	1	-	0	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	exon	26317866	26318010	.	-	.	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
Phchi.S1	AUGUSTUS	start_codon	26318008	26318010	.	-	0	transcript_id "Phchi.S1G415600.t1"; gene_id "Phchi.S1G415600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9688.t1 is derived from g6864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43289811	43290107	.	-	.	Phchi.S1G684700
Phchi.S1	AUGUSTUS	transcript	43289811	43290107	.	-	.	transcript_id "Phchi.S1G684700.t1"; gene_id "Phchi.S1G684700"
Phchi.S1	AUGUSTUS	stop_codon	43289808	43289810	.	-	0	transcript_id "Phchi.S1G684700.t1"; gene_id "Phchi.S1G684700"
Phchi.S1	AUGUSTUS	CDS	43289811	43290107	0.33	-	0	transcript_id "Phchi.S1G684700.t1"; gene_id "Phchi.S1G684700"
Phchi.S1	AUGUSTUS	exon	43289811	43290107	.	-	.	transcript_id "Phchi.S1G684700.t1"; gene_id "Phchi.S1G684700"
Phchi.S1	AUGUSTUS	start_codon	43290105	43290107	.	-	0	transcript_id "Phchi.S1G684700.t1"; gene_id "Phchi.S1G684700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9472.t1 is derived from g6648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41681522	41682235	.	-	.	Phchi.S1G663100
Phchi.S1	AUGUSTUS	transcript	41681522	41682235	.	-	.	transcript_id "Phchi.S1G663100.t1"; gene_id "Phchi.S1G663100"
Phchi.S1	AUGUSTUS	stop_codon	41681519	41681521	.	-	0	transcript_id "Phchi.S1G663100.t1"; gene_id "Phchi.S1G663100"
Phchi.S1	AUGUSTUS	CDS	41681522	41682235	0.3	-	0	transcript_id "Phchi.S1G663100.t1"; gene_id "Phchi.S1G663100"
Phchi.S1	AUGUSTUS	exon	41681522	41682235	.	-	.	transcript_id "Phchi.S1G663100.t1"; gene_id "Phchi.S1G663100"
Phchi.S1	AUGUSTUS	start_codon	41682233	41682235	.	-	0	transcript_id "Phchi.S1G663100.t1"; gene_id "Phchi.S1G663100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6751.t1 is derived from g3923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24845663	24848242	.	-	.	Phchi.S1G391000
Phchi.S1	AUGUSTUS	transcript	24845663	24848242	.	-	.	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	stop_codon	24845660	24845662	.	-	0	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	CDS	24845663	24846051	0.8	-	2	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	exon	24845663	24846051	.	-	.	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	intron	24846052	24846360	.	-	.	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	CDS	24846361	24848242	0.57	-	0	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	exon	24846361	24848242	.	-	.	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	start_codon	24848240	24848242	.	-	0	transcript_id "Phchi.S1G391000.t1"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	transcript	24845663	24846034	.	-	.	transcript_id "Phchi.S1G391000.t2"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	stop_codon	24845660	24845662	.	-	0	transcript_id "Phchi.S1G391000.t2"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	CDS	24845663	24846034	0.4	-	0	transcript_id "Phchi.S1G391000.t2"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	exon	24845663	24846034	.	-	.	transcript_id "Phchi.S1G391000.t2"; gene_id "Phchi.S1G391000"
Phchi.S1	AUGUSTUS	start_codon	24846032	24846034	.	-	0	transcript_id "Phchi.S1G391000.t2"; gene_id "Phchi.S1G391000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3765.t1 is derived from g934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5587301	5589217	.	-	.	Phchi.S1G092400
Phchi.S1	AUGUSTUS	transcript	5587301	5589217	.	-	.	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	stop_codon	5587298	5587300	.	-	0	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	CDS	5587301	5588837	0.58	-	1	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	exon	5587301	5588837	.	-	.	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	intron	5588838	5588984	.	-	.	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	CDS	5588985	5589217	0.66	-	0	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	exon	5588985	5589217	.	-	.	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
Phchi.S1	AUGUSTUS	start_codon	5589215	5589217	.	-	0	transcript_id "Phchi.S1G092400.t1"; gene_id "Phchi.S1G092400"
# This transcript jg14905.t2 is derived from g13373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14906.t1 is derived from g13374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15457838	15459210	.	-	.	Phchi.S3G222500
Phchi.S3	AUGUSTUS	transcript	15457838	15459210	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	stop_codon	15457835	15457837	.	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	CDS	15457838	15457876	0.79	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	exon	15457838	15457876	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	intron	15457877	15457978	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	CDS	15457979	15458038	0.78	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	exon	15457979	15458038	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	intron	15458039	15458156	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	CDS	15458157	15458330	1	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	exon	15458157	15458330	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	intron	15458331	15458504	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	CDS	15458505	15458555	1	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	exon	15458505	15458555	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	intron	15458556	15458738	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	CDS	15458739	15458837	1	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	exon	15458739	15458837	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	intron	15458838	15459207	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	CDS	15459208	15459210	0.93	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	exon	15459208	15459210	.	-	.	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
Phchi.S3	AUGUSTUS	start_codon	15459208	15459210	.	-	0	transcript_id "Phchi.S3G222500.t1"; gene_id "Phchi.S3G222500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3185.t1 is derived from g354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2136374	2137582	.	-	.	Phchi.S1G034400
Phchi.S1	AUGUSTUS	transcript	2136374	2137582	.	-	.	transcript_id "Phchi.S1G034400.t1"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	stop_codon	2136371	2136373	.	-	0	transcript_id "Phchi.S1G034400.t1"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	CDS	2136374	2137582	0.99	-	0	transcript_id "Phchi.S1G034400.t1"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	exon	2136374	2137582	.	-	.	transcript_id "Phchi.S1G034400.t1"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	start_codon	2137580	2137582	.	-	0	transcript_id "Phchi.S1G034400.t1"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	transcript	2136374	2137363	.	-	.	transcript_id "Phchi.S1G034400.t2"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	stop_codon	2136371	2136373	.	-	0	transcript_id "Phchi.S1G034400.t2"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	CDS	2136374	2137363	0.93	-	0	transcript_id "Phchi.S1G034400.t2"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	exon	2136374	2137363	.	-	.	transcript_id "Phchi.S1G034400.t2"; gene_id "Phchi.S1G034400"
Phchi.S1	AUGUSTUS	start_codon	2137361	2137363	.	-	0	transcript_id "Phchi.S1G034400.t2"; gene_id "Phchi.S1G034400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12353.t1 is derived from g8029.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12578666	12583064	.	+	.	Phchi.S2G043300
Phchi.S2	AUGUSTUS	transcript	12578666	12583064	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	start_codon	12578666	12578668	.	+	0	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12578666	12578831	0.51	+	0	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12578666	12578831	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12578832	12578957	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12578958	12579214	1	+	2	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12578958	12579214	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12579215	12579311	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12579312	12580420	0.81	+	0	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12579312	12580420	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12580421	12580636	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12580637	12580715	0.92	+	1	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12580637	12580715	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12580716	12580786	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12580787	12580942	0.99	+	0	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12580787	12580942	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12580943	12581039	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12581040	12583064	0.99	+	0	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12581040	12583064	.	+	.	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	stop_codon	12583065	12583067	.	+	0	transcript_id "Phchi.S2G043300.t1"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	transcript	12578666	12583064	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	start_codon	12578666	12578668	.	+	0	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12578666	12578831	0.56	+	0	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12578666	12578831	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12578832	12578957	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12578958	12579214	0.99	+	2	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12578958	12579214	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12579215	12579311	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12579312	12580420	0.72	+	0	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12579312	12580420	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12580421	12580569	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12580570	12580663	0.89	+	1	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12580570	12580663	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12580664	12580786	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12580787	12580942	0.97	+	0	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12580787	12580942	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	intron	12580943	12581039	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	CDS	12581040	12583064	1	+	0	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	exon	12581040	12583064	.	+	.	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
Phchi.S2	AUGUSTUS	stop_codon	12583065	12583067	.	+	0	transcript_id "Phchi.S2G043300.t2"; gene_id "Phchi.S2G043300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12771.t1 is derived from g11236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1967184	1972388	.	-	.	Phchi.S3G009000
Phchi.S3	AUGUSTUS	transcript	1967184	1972388	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	stop_codon	1967181	1967183	.	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967184	1967381	1	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967184	1967381	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1967382	1967477	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967478	1967645	1	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967478	1967645	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1967646	1967731	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967732	1967844	1	-	2	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967732	1967844	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1967845	1967936	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967937	1968142	1	-	1	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967937	1968142	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1968143	1968255	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1968256	1968374	1	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1968256	1968374	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1968375	1968588	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1968589	1970050	1	-	1	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1968589	1970050	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1970051	1970448	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1970449	1970650	1	-	2	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1970449	1970650	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1970651	1970747	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1970748	1970911	0.98	-	1	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1970748	1970911	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1970912	1971026	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1971027	1971279	0.98	-	2	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1971027	1971279	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1971280	1971360	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1971361	1971582	0.89	-	2	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1971361	1971582	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1971583	1971743	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1971744	1971906	0.74	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1971744	1971906	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1971907	1972235	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1972236	1972388	1	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1972236	1972388	.	-	.	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	start_codon	1972386	1972388	.	-	0	transcript_id "Phchi.S3G009000.t1"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	transcript	1967184	1972388	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	stop_codon	1967181	1967183	.	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967184	1967381	1	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967184	1967381	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1967382	1967477	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967478	1967645	1	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967478	1967645	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1967646	1967731	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967732	1967844	1	-	2	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967732	1967844	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1967845	1967936	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1967937	1968142	1	-	1	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1967937	1968142	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1968143	1968255	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1968256	1968374	1	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1968256	1968374	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1968375	1968588	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1968589	1969917	0.79	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1968589	1969917	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1969918	1970018	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1970019	1970055	0.97	-	1	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1970019	1970055	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1970056	1970448	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1970449	1970650	1	-	2	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1970449	1970650	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1970651	1970747	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1970748	1970911	0.98	-	1	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1970748	1970911	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1970912	1971026	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1971027	1971279	0.99	-	2	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1971027	1971279	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1971280	1971360	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1971361	1971582	0.92	-	2	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1971361	1971582	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1971583	1971743	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1971744	1971906	0.75	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1971744	1971906	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	intron	1971907	1972235	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	CDS	1972236	1972388	1	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	exon	1972236	1972388	.	-	.	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
Phchi.S3	AUGUSTUS	start_codon	1972386	1972388	.	-	0	transcript_id "Phchi.S3G009000.t2"; gene_id "Phchi.S3G009000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13904.t1 is derived from g12371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9600611	9602552	.	-	.	Phchi.S3G122300
Phchi.S3	AUGUSTUS	transcript	9600611	9602552	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	stop_codon	9600608	9600610	.	-	0	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9600611	9600778	1	-	0	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9600611	9600778	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	intron	9600779	9600876	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9600877	9600944	1	-	2	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9600877	9600944	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	intron	9600945	9601040	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9601041	9601329	0.98	-	0	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9601041	9601329	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	intron	9601330	9601423	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9601424	9601681	1	-	0	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9601424	9601681	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	intron	9601682	9601772	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9601773	9601861	1	-	2	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9601773	9601861	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	intron	9601862	9601967	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9601968	9602288	0.78	-	2	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9601968	9602288	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	intron	9602289	9602404	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	CDS	9602405	9602552	0.85	-	0	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	exon	9602405	9602552	.	-	.	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
Phchi.S3	AUGUSTUS	start_codon	9602550	9602552	.	-	0	transcript_id "Phchi.S3G122300.t1"; gene_id "Phchi.S3G122300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14735.t1 is derived from g13203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14445748	14449178	.	+	.	Phchi.S3G205400
Phchi.S3	AUGUSTUS	transcript	14445748	14449178	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	start_codon	14445748	14445750	.	+	0	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	CDS	14445748	14445791	0.59	+	0	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	exon	14445748	14445791	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	intron	14445792	14445899	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	CDS	14445900	14446007	0.39	+	1	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	exon	14445900	14446007	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	intron	14446008	14446169	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	CDS	14446170	14447043	0.36	+	1	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	exon	14446170	14447043	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	intron	14447044	14447132	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	CDS	14447133	14448083	1	+	0	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	exon	14447133	14448083	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	intron	14448084	14448176	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	CDS	14448177	14449178	0.98	+	0	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	exon	14448177	14449178	.	+	.	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
Phchi.S3	AUGUSTUS	stop_codon	14449179	14449181	.	+	0	transcript_id "Phchi.S3G205400.t1"; gene_id "Phchi.S3G205400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10885.t1 is derived from g14935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2756693	2758522	.	+	.	Phchi.S4G046700
Phchi.S4	AUGUSTUS	transcript	2756693	2758522	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	start_codon	2756693	2756695	.	+	0	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	CDS	2756693	2757084	0.94	+	0	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	exon	2756693	2757084	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	intron	2757085	2757183	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	CDS	2757184	2757436	1	+	1	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	exon	2757184	2757436	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	intron	2757437	2757517	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	CDS	2757518	2757823	1	+	0	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	exon	2757518	2757823	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	intron	2757824	2757918	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	CDS	2757919	2758104	0.64	+	0	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	exon	2757919	2758104	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	intron	2758105	2758231	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	CDS	2758232	2758522	0.6	+	0	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	exon	2758232	2758522	.	+	.	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
Phchi.S4	AUGUSTUS	stop_codon	2758523	2758525	.	+	0	transcript_id "Phchi.S4G046700.t1"; gene_id "Phchi.S4G046700"
# This transcript jg15808.t2 is derived from g14278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15809.t1 is derived from g14279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21501738	21505093	.	+	.	Phchi.S3G312800
Phchi.S3	AUGUSTUS	transcript	21501738	21505093	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	start_codon	21501738	21501740	.	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21501738	21501852	0.52	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21501738	21501852	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21501853	21501934	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21501935	21502009	0.63	+	2	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21501935	21502009	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21502010	21502143	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21502144	21502251	0.99	+	2	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21502144	21502251	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21502252	21502373	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21502374	21502552	1	+	2	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21502374	21502552	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21502553	21502667	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21502668	21502814	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21502668	21502814	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21502815	21503068	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21503069	21503179	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21503069	21503179	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21503180	21503272	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21503273	21503488	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21503273	21503488	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21503489	21503577	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21503578	21503639	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21503578	21503639	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21503640	21503733	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21503734	21503785	1	+	1	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21503734	21503785	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21503786	21503898	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21503899	21504018	0.68	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21503899	21504018	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21504019	21504100	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21504101	21504148	0.85	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21504101	21504148	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21504149	21504294	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21504295	21504453	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21504295	21504453	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21504454	21504590	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21504591	21504776	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21504591	21504776	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	intron	21504777	21504862	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	CDS	21504863	21505093	1	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	exon	21504863	21505093	.	+	.	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
Phchi.S3	AUGUSTUS	stop_codon	21505094	21505096	.	+	0	transcript_id "Phchi.S3G312800.t1"; gene_id "Phchi.S3G312800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11198.t1 is derived from g15248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4653485	4656347	.	+	.	Phchi.S4G078000
Phchi.S4	AUGUSTUS	transcript	4653485	4656347	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	start_codon	4653485	4653487	.	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4653485	4653545	1	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4653485	4653545	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4653546	4653626	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4653627	4653882	1	+	2	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4653627	4653882	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4653883	4654111	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4654112	4654196	1	+	1	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4654112	4654196	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4654197	4654365	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4654366	4654559	1	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4654366	4654559	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4654560	4654653	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4654654	4654783	1	+	1	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4654654	4654783	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4654784	4654908	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4654909	4654967	1	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4654909	4654967	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4654968	4655051	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4655052	4655120	1	+	1	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4655052	4655120	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4655121	4655248	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4655249	4655295	1	+	1	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4655249	4655295	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4655296	4655376	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4655377	4655463	1	+	2	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4655377	4655463	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4655464	4655652	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4655653	4655717	1	+	2	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4655653	4655717	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4655718	4655809	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4655810	4655893	1	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4655810	4655893	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4655894	4655964	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4655965	4656030	1	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4655965	4656030	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4656031	4656103	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4656104	4656179	0.85	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4656104	4656179	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	intron	4656180	4656330	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	CDS	4656331	4656347	0.85	+	2	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	exon	4656331	4656347	.	+	.	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
Phchi.S4	AUGUSTUS	stop_codon	4656348	4656350	.	+	0	transcript_id "Phchi.S4G078000.t1"; gene_id "Phchi.S4G078000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11088.t1 is derived from g15138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4031426	4034648	.	+	.	Phchi.S4G067000
Phchi.S4	AUGUSTUS	transcript	4031426	4034648	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	start_codon	4031426	4031428	.	+	0	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	CDS	4031426	4031657	1	+	0	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	exon	4031426	4031657	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	intron	4031658	4031751	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	CDS	4031752	4032207	0.8	+	2	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	exon	4031752	4032207	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	intron	4032208	4032303	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	CDS	4032304	4033270	0.12	+	2	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	exon	4032304	4033270	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	intron	4033271	4033486	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	CDS	4033487	4034648	0.7	+	1	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	exon	4033487	4034648	.	+	.	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
Phchi.S4	AUGUSTUS	stop_codon	4034649	4034651	.	+	0	transcript_id "Phchi.S4G067000.t1"; gene_id "Phchi.S4G067000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9789.t1 is derived from g6965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43695781	43696155	.	-	.	Phchi.S1G694800
Phchi.S1	AUGUSTUS	transcript	43695781	43696155	.	-	.	transcript_id "Phchi.S1G694800.t1"; gene_id "Phchi.S1G694800"
Phchi.S1	AUGUSTUS	stop_codon	43695778	43695780	.	-	0	transcript_id "Phchi.S1G694800.t1"; gene_id "Phchi.S1G694800"
Phchi.S1	AUGUSTUS	CDS	43695781	43696155	0.58	-	0	transcript_id "Phchi.S1G694800.t1"; gene_id "Phchi.S1G694800"
Phchi.S1	AUGUSTUS	exon	43695781	43696155	.	-	.	transcript_id "Phchi.S1G694800.t1"; gene_id "Phchi.S1G694800"
Phchi.S1	AUGUSTUS	start_codon	43696153	43696155	.	-	0	transcript_id "Phchi.S1G694800.t1"; gene_id "Phchi.S1G694800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5834.t1 is derived from g3004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19171307	19172363	.	-	.	Phchi.S1G299300
Phchi.S1	AUGUSTUS	transcript	19171307	19172363	.	-	.	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	stop_codon	19171304	19171306	.	-	0	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	CDS	19171307	19171658	0.99	-	1	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	exon	19171307	19171658	.	-	.	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	intron	19171659	19171743	.	-	.	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	CDS	19171744	19172363	0.97	-	0	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	exon	19171744	19172363	.	-	.	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
Phchi.S1	AUGUSTUS	start_codon	19172361	19172363	.	-	0	transcript_id "Phchi.S1G299300.t1"; gene_id "Phchi.S1G299300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg310.t1 is derived from g10092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2218263	2219085	.	-	.	Phchi.S6G026900
Phchi.S6	AUGUSTUS	transcript	2218263	2219085	.	-	.	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	stop_codon	2218260	2218262	.	-	0	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	CDS	2218263	2218478	1	-	0	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	exon	2218263	2218478	.	-	.	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	intron	2218479	2218560	.	-	.	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	CDS	2218561	2218722	1	-	0	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	exon	2218561	2218722	.	-	.	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	intron	2218723	2218800	.	-	.	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	CDS	2218801	2219085	1	-	0	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	exon	2218801	2219085	.	-	.	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
Phchi.S6	AUGUSTUS	start_codon	2219083	2219085	.	-	0	transcript_id "Phchi.S6G026900.t1"; gene_id "Phchi.S6G026900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7826.t1 is derived from g5000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31384422	31385104	.	+	.	Phchi.S1G498500
Phchi.S1	AUGUSTUS	transcript	31384422	31385104	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	start_codon	31384422	31384424	.	+	0	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	CDS	31384422	31384623	0.97	+	0	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	exon	31384422	31384623	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	intron	31384624	31384699	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	CDS	31384700	31384792	1	+	2	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	exon	31384700	31384792	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	intron	31384793	31384866	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	CDS	31384867	31384963	1	+	2	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	exon	31384867	31384963	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	intron	31384964	31385052	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	CDS	31385053	31385104	1	+	1	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	exon	31385053	31385104	.	+	.	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
Phchi.S1	AUGUSTUS	stop_codon	31385105	31385107	.	+	0	transcript_id "Phchi.S1G498500.t1"; gene_id "Phchi.S1G498500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5588.t1 is derived from g2758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17772592	17772849	.	-	.	Phchi.S1G274700
Phchi.S1	AUGUSTUS	transcript	17772592	17772849	.	-	.	transcript_id "Phchi.S1G274700.t1"; gene_id "Phchi.S1G274700"
Phchi.S1	AUGUSTUS	stop_codon	17772589	17772591	.	-	0	transcript_id "Phchi.S1G274700.t1"; gene_id "Phchi.S1G274700"
Phchi.S1	AUGUSTUS	CDS	17772592	17772849	0.45	-	0	transcript_id "Phchi.S1G274700.t1"; gene_id "Phchi.S1G274700"
Phchi.S1	AUGUSTUS	exon	17772592	17772849	.	-	.	transcript_id "Phchi.S1G274700.t1"; gene_id "Phchi.S1G274700"
Phchi.S1	AUGUSTUS	start_codon	17772847	17772849	.	-	0	transcript_id "Phchi.S1G274700.t1"; gene_id "Phchi.S1G274700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4369.t1 is derived from g1538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10099446	10100066	.	-	.	Phchi.S1G152800
Phchi.S1	AUGUSTUS	transcript	10099446	10100066	.	-	.	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	stop_codon	10099443	10099445	.	-	0	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	CDS	10099446	10099678	0.6	-	2	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	exon	10099446	10099678	.	-	.	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	intron	10099679	10099776	.	-	.	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	CDS	10099777	10099905	0.58	-	2	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	exon	10099777	10099905	.	-	.	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	intron	10099906	10100002	.	-	.	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	CDS	10100003	10100066	0.33	-	0	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	exon	10100003	10100066	.	-	.	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
Phchi.S1	AUGUSTUS	start_codon	10100064	10100066	.	-	0	transcript_id "Phchi.S1G152800.t1"; gene_id "Phchi.S1G152800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12109.t1 is derived from g7785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3567331	3567687	.	+	.	Phchi.S2G018900
Phchi.S2	AUGUSTUS	transcript	3567331	3567687	.	+	.	transcript_id "Phchi.S2G018900.t1"; gene_id "Phchi.S2G018900"
Phchi.S2	AUGUSTUS	start_codon	3567331	3567333	.	+	0	transcript_id "Phchi.S2G018900.t1"; gene_id "Phchi.S2G018900"
Phchi.S2	AUGUSTUS	CDS	3567331	3567687	0.99	+	0	transcript_id "Phchi.S2G018900.t1"; gene_id "Phchi.S2G018900"
Phchi.S2	AUGUSTUS	exon	3567331	3567687	.	+	.	transcript_id "Phchi.S2G018900.t1"; gene_id "Phchi.S2G018900"
Phchi.S2	AUGUSTUS	stop_codon	3567688	3567690	.	+	0	transcript_id "Phchi.S2G018900.t1"; gene_id "Phchi.S2G018900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7002.t1 is derived from g4174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26350696	26353989	.	-	.	Phchi.S1G416100
Phchi.S1	AUGUSTUS	transcript	26350696	26353989	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	stop_codon	26350693	26350695	.	-	0	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	CDS	26350696	26350705	0.85	-	1	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	exon	26350696	26350705	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	intron	26350706	26351409	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	CDS	26351410	26351447	0.83	-	0	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	exon	26351410	26351447	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	intron	26351448	26351520	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	CDS	26351521	26351543	0.87	-	2	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	exon	26351521	26351543	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	intron	26351544	26351627	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	CDS	26351628	26353989	0.77	-	0	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	exon	26351628	26353989	.	-	.	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
Phchi.S1	AUGUSTUS	start_codon	26353987	26353989	.	-	0	transcript_id "Phchi.S1G416100.t1"; gene_id "Phchi.S1G416100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13315.t1 is derived from g11781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5959541	5962052	.	+	.	Phchi.S3G063400
Phchi.S3	AUGUSTUS	transcript	5959541	5962052	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	start_codon	5959541	5959543	.	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5959541	5959764	0.98	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5959541	5959764	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5959765	5959913	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5959914	5960238	1	+	1	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5959914	5960238	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5960239	5960356	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5960357	5960506	1	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5960357	5960506	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5960507	5960596	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5960597	5960857	1	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5960597	5960857	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5960858	5960988	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5960989	5961075	1	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5960989	5961075	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5961076	5961196	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5961197	5961275	1	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5961197	5961275	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5961276	5961423	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5961424	5961530	0.96	+	2	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5961424	5961530	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5961531	5961633	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5961634	5961752	0.96	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5961634	5961752	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	intron	5961753	5961913	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	CDS	5961914	5962052	0.96	+	1	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	exon	5961914	5962052	.	+	.	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
Phchi.S3	AUGUSTUS	stop_codon	5962053	5962055	.	+	0	transcript_id "Phchi.S3G063400.t1"; gene_id "Phchi.S3G063400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13980.t1 is derived from g12447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10034771	10037712	.	+	.	Phchi.S3G129900
Phchi.S3	AUGUSTUS	transcript	10034771	10037712	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	start_codon	10034771	10034773	.	+	0	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10034771	10034843	1	+	0	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10034771	10034843	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10034844	10035339	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10035340	10035488	1	+	2	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10035340	10035488	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10035489	10035618	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10035619	10035680	1	+	0	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10035619	10035680	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10035681	10035812	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10035813	10035998	1	+	1	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10035813	10035998	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10035999	10036153	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036154	10036290	1	+	1	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036154	10036290	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036291	10036443	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036444	10036574	1	+	2	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036444	10036574	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036575	10036739	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036740	10036902	1	+	0	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036740	10036902	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036903	10036978	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036979	10037150	1	+	2	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036979	10037150	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10037151	10037234	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10037235	10037712	1	+	1	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10037235	10037712	.	+	.	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	stop_codon	10037713	10037715	.	+	0	transcript_id "Phchi.S3G129900.t1"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	transcript	10034771	10037712	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	start_codon	10034771	10034773	.	+	0	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10034771	10034843	1	+	0	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10034771	10034843	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10034844	10035339	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10035340	10035488	1	+	2	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10035340	10035488	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10035489	10035618	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10035619	10035680	1	+	0	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10035619	10035680	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10035681	10035812	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10035813	10035998	1	+	1	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10035813	10035998	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10035999	10036153	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036154	10036188	0.55	+	1	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036154	10036188	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036189	10036330	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036331	10036360	0.55	+	2	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036331	10036360	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036361	10036443	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036444	10036574	1	+	2	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036444	10036574	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036575	10036739	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036740	10036902	1	+	0	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036740	10036902	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10036903	10036978	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10036979	10037150	1	+	2	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10036979	10037150	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	intron	10037151	10037234	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	CDS	10037235	10037712	0.99	+	1	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	exon	10037235	10037712	.	+	.	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
Phchi.S3	AUGUSTUS	stop_codon	10037713	10037715	.	+	0	transcript_id "Phchi.S3G129900.t2"; gene_id "Phchi.S3G129900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11306.t1 is derived from g15356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5307023	5307938	.	-	.	Phchi.S4G088800
Phchi.S4	AUGUSTUS	transcript	5307023	5307938	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	stop_codon	5307020	5307022	.	-	0	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	CDS	5307023	5307067	1	-	0	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	exon	5307023	5307067	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	intron	5307068	5307158	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	CDS	5307159	5307267	1	-	1	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	exon	5307159	5307267	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	intron	5307268	5307359	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	CDS	5307360	5307431	0.81	-	1	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	exon	5307360	5307431	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	intron	5307432	5307521	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	CDS	5307522	5307829	0.81	-	0	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	exon	5307522	5307829	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	intron	5307830	5307929	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	CDS	5307930	5307938	1	-	0	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	exon	5307930	5307938	.	-	.	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
Phchi.S4	AUGUSTUS	start_codon	5307936	5307938	.	-	0	transcript_id "Phchi.S4G088800.t1"; gene_id "Phchi.S4G088800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11208.t1 is derived from g15258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4768846	4771825	.	+	.	Phchi.S4G079000
Phchi.S4	AUGUSTUS	transcript	4768846	4771825	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	start_codon	4768846	4768848	.	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4768846	4768891	0.98	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4768846	4768891	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4768892	4768975	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4768976	4769041	0.98	+	2	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4768976	4769041	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4769042	4769141	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4769142	4769589	0.99	+	2	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4769142	4769589	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4769590	4769665	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4769666	4769824	1	+	1	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4769666	4769824	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4769825	4769915	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4769916	4769972	1	+	1	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4769916	4769972	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4769973	4770048	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4770049	4770304	1	+	1	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4770049	4770304	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4770305	4770382	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4770383	4770522	1	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4770383	4770522	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4770523	4770619	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4770620	4770727	1	+	1	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4770620	4770727	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4770728	4770862	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4770863	4770941	1	+	1	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4770863	4770941	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4770942	4771029	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4771030	4771192	0.9	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4771030	4771192	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4771193	4771336	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4771337	4771383	0.98	+	2	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4771337	4771383	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4771384	4771489	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4771490	4771669	1	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4771490	4771669	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	intron	4771670	4771750	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	CDS	4771751	4771825	1	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	exon	4771751	4771825	.	+	.	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
Phchi.S4	AUGUSTUS	stop_codon	4771826	4771828	.	+	0	transcript_id "Phchi.S4G079000.t1"; gene_id "Phchi.S4G079000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6958.t1 is derived from g4130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26141440	26143014	.	-	.	Phchi.S1G411700
Phchi.S1	AUGUSTUS	transcript	26141440	26143014	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	stop_codon	26141437	26141439	.	-	0	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	CDS	26141440	26141578	0.58	-	1	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	exon	26141440	26141578	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	intron	26141579	26141666	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	CDS	26141667	26141847	0.48	-	2	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	exon	26141667	26141847	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	intron	26141848	26141965	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	CDS	26141966	26142719	0.39	-	0	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	exon	26141966	26142719	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	intron	26142720	26142816	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	CDS	26142817	26142930	1	-	0	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	exon	26142817	26142930	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	intron	26142931	26143005	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	CDS	26143006	26143014	0.98	-	0	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	exon	26143006	26143014	.	-	.	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
Phchi.S1	AUGUSTUS	start_codon	26143012	26143014	.	-	0	transcript_id "Phchi.S1G411700.t1"; gene_id "Phchi.S1G411700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6910.t1 is derived from g4082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25966608	25967150	.	-	.	Phchi.S1G406900
Phchi.S1	AUGUSTUS	transcript	25966608	25967150	.	-	.	transcript_id "Phchi.S1G406900.t1"; gene_id "Phchi.S1G406900"
Phchi.S1	AUGUSTUS	stop_codon	25966605	25966607	.	-	0	transcript_id "Phchi.S1G406900.t1"; gene_id "Phchi.S1G406900"
Phchi.S1	AUGUSTUS	CDS	25966608	25967150	0.89	-	0	transcript_id "Phchi.S1G406900.t1"; gene_id "Phchi.S1G406900"
Phchi.S1	AUGUSTUS	exon	25966608	25967150	.	-	.	transcript_id "Phchi.S1G406900.t1"; gene_id "Phchi.S1G406900"
Phchi.S1	AUGUSTUS	start_codon	25967148	25967150	.	-	0	transcript_id "Phchi.S1G406900.t1"; gene_id "Phchi.S1G406900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9610.t1 is derived from g6786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42926435	42928040	.	+	.	Phchi.S1G676900
Phchi.S1	AUGUSTUS	transcript	42926435	42928040	.	+	.	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	start_codon	42926435	42926437	.	+	0	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	CDS	42926435	42926776	0.35	+	0	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	exon	42926435	42926776	.	+	.	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	intron	42926777	42926983	.	+	.	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	CDS	42926984	42927922	0.42	+	0	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	exon	42926984	42927922	.	+	.	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	intron	42927923	42928019	.	+	.	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	CDS	42928020	42928040	0.46	+	0	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	exon	42928020	42928040	.	+	.	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
Phchi.S1	AUGUSTUS	stop_codon	42928041	42928043	.	+	0	transcript_id "Phchi.S1G676900.t1"; gene_id "Phchi.S1G676900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3262.t1 is derived from g431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2576986	2577869	.	+	.	Phchi.S1G042100
Phchi.S1	AUGUSTUS	transcript	2576986	2577869	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	start_codon	2576986	2576988	.	+	0	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	CDS	2576986	2577148	0.68	+	0	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	exon	2576986	2577148	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	intron	2577149	2577246	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	CDS	2577247	2577371	1	+	2	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	exon	2577247	2577371	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	intron	2577372	2577477	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	CDS	2577478	2577591	1	+	0	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	exon	2577478	2577591	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	intron	2577592	2577687	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	CDS	2577688	2577776	1	+	0	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	exon	2577688	2577776	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	intron	2577777	2577862	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	CDS	2577863	2577869	1	+	1	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	exon	2577863	2577869	.	+	.	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
Phchi.S1	AUGUSTUS	stop_codon	2577870	2577872	.	+	0	transcript_id "Phchi.S1G042100.t1"; gene_id "Phchi.S1G042100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6661.t1 is derived from g3833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24360500	24361451	.	+	.	Phchi.S1G382000
Phchi.S1	AUGUSTUS	transcript	24360500	24361451	.	+	.	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	start_codon	24360500	24360502	.	+	0	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	CDS	24360500	24360716	0.5	+	0	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	exon	24360500	24360716	.	+	.	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	intron	24360717	24360870	.	+	.	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	CDS	24360871	24361451	0.52	+	2	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	exon	24360871	24361451	.	+	.	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
Phchi.S1	AUGUSTUS	stop_codon	24361452	24361454	.	+	0	transcript_id "Phchi.S1G382000.t1"; gene_id "Phchi.S1G382000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2451.t1 is derived from g9371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6679727	6680183	.	+	.	Phchi.S5G106000
Phchi.S5	AUGUSTUS	transcript	6679727	6680183	.	+	.	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	start_codon	6679727	6679729	.	+	0	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	CDS	6679727	6679772	0.8	+	0	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	exon	6679727	6679772	.	+	.	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	intron	6679773	6679944	.	+	.	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	CDS	6679945	6680183	0.77	+	2	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	exon	6679945	6680183	.	+	.	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
Phchi.S5	AUGUSTUS	stop_codon	6680184	6680186	.	+	0	transcript_id "Phchi.S5G106000.t1"; gene_id "Phchi.S5G106000"
# This transcript jg1953.t2 is derived from g8873.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1954.t1 is derived from g8874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4005588	4006694	.	-	.	Phchi.S5G056300
Phchi.S5	AUGUSTUS	transcript	4005588	4006694	.	-	.	transcript_id "Phchi.S5G056300.t1"; gene_id "Phchi.S5G056300"
Phchi.S5	AUGUSTUS	stop_codon	4005585	4005587	.	-	0	transcript_id "Phchi.S5G056300.t1"; gene_id "Phchi.S5G056300"
Phchi.S5	AUGUSTUS	CDS	4005588	4006694	1	-	0	transcript_id "Phchi.S5G056300.t1"; gene_id "Phchi.S5G056300"
Phchi.S5	AUGUSTUS	exon	4005588	4006694	.	-	.	transcript_id "Phchi.S5G056300.t1"; gene_id "Phchi.S5G056300"
Phchi.S5	AUGUSTUS	start_codon	4006692	4006694	.	-	0	transcript_id "Phchi.S5G056300.t1"; gene_id "Phchi.S5G056300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2357.t1 is derived from g9277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6328165	6330449	.	+	.	Phchi.S5G096600
Phchi.S5	AUGUSTUS	transcript	6328165	6330449	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	start_codon	6328165	6328167	.	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6328165	6328326	0.96	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6328165	6328326	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6328327	6328802	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6328803	6328843	1	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6328803	6328843	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6328844	6328965	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6328966	6329015	1	+	1	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6328966	6329015	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6329016	6329160	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6329161	6329305	1	+	2	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6329161	6329305	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6329306	6329422	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6329423	6329476	1	+	1	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6329423	6329476	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6329477	6329564	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6329565	6329694	0.8	+	1	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6329565	6329694	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6329695	6329803	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6329804	6330043	0.42	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6329804	6330043	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6330044	6330209	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6330210	6330245	0.44	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6330210	6330245	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	intron	6330246	6330398	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	CDS	6330399	6330449	0.98	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	exon	6330399	6330449	.	+	.	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
Phchi.S5	AUGUSTUS	stop_codon	6330450	6330452	.	+	0	transcript_id "Phchi.S5G096600.t1"; gene_id "Phchi.S5G096600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11970.t1 is derived from g7645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	247674	248873	.	+	.	Phchi.S2G005000
Phchi.S2	AUGUSTUS	transcript	247674	248873	.	+	.	transcript_id "Phchi.S2G005000.t1"; gene_id "Phchi.S2G005000"
Phchi.S2	AUGUSTUS	start_codon	247674	247676	.	+	0	transcript_id "Phchi.S2G005000.t1"; gene_id "Phchi.S2G005000"
Phchi.S2	AUGUSTUS	CDS	247674	248873	0.73	+	0	transcript_id "Phchi.S2G005000.t1"; gene_id "Phchi.S2G005000"
Phchi.S2	AUGUSTUS	exon	247674	248873	.	+	.	transcript_id "Phchi.S2G005000.t1"; gene_id "Phchi.S2G005000"
Phchi.S2	AUGUSTUS	stop_codon	248874	248876	.	+	0	transcript_id "Phchi.S2G005000.t1"; gene_id "Phchi.S2G005000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6289.t1 is derived from g3461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22096968	22099314	.	+	.	Phchi.S1G344800
Phchi.S1	AUGUSTUS	transcript	22096968	22099314	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	start_codon	22096968	22096970	.	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22096968	22097009	0.59	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22096968	22097009	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097010	22097136	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097137	22097220	1	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097137	22097220	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097221	22097304	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097305	22097437	1	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097305	22097437	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097438	22097547	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097548	22097665	1	+	2	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097548	22097665	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097666	22097758	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097759	22097858	1	+	1	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097759	22097858	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097859	22097947	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097948	22098075	1	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097948	22098075	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098076	22098294	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098295	22098373	1	+	1	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098295	22098373	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098374	22098444	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098445	22098533	1	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098445	22098533	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098534	22098636	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098637	22098682	1	+	1	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098637	22098682	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098683	22098762	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098763	22098833	0.96	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098763	22098833	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098834	22098944	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098945	22099018	0.96	+	1	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098945	22099018	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22099019	22099099	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22099100	22099158	1	+	2	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22099100	22099158	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22099159	22099266	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22099267	22099314	0.94	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22099267	22099314	.	+	.	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	stop_codon	22099315	22099317	.	+	0	transcript_id "Phchi.S1G344800.t1"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	transcript	22096968	22099314	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	start_codon	22096968	22096970	.	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22096968	22097009	0.57	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22096968	22097009	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097010	22097136	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097137	22097220	1	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097137	22097220	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097221	22097304	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097305	22097437	1	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097305	22097437	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097438	22097547	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097548	22097665	1	+	2	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097548	22097665	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097666	22097758	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097759	22097858	1	+	1	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097759	22097858	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22097859	22097947	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22097948	22098022	0.79	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22097948	22098022	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098023	22098095	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098096	22098106	0.98	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098096	22098106	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098107	22098294	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098295	22098373	1	+	1	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098295	22098373	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098374	22098444	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098445	22098533	1	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098445	22098533	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098534	22098636	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098637	22098682	1	+	1	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098637	22098682	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098683	22098762	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098763	22098833	0.97	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098763	22098833	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22098834	22098944	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22098945	22099018	0.97	+	1	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22098945	22099018	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22099019	22099099	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22099100	22099158	1	+	2	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22099100	22099158	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	intron	22099159	22099266	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	CDS	22099267	22099314	0.99	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	exon	22099267	22099314	.	+	.	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
Phchi.S1	AUGUSTUS	stop_codon	22099315	22099317	.	+	0	transcript_id "Phchi.S1G344800.t2"; gene_id "Phchi.S1G344800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6826.t1 is derived from g3998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25232523	25233949	.	+	.	Phchi.S1G398500
Phchi.S1	AUGUSTUS	transcript	25232523	25233949	.	+	.	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	start_codon	25232523	25232525	.	+	0	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	CDS	25232523	25232781	1	+	0	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	exon	25232523	25232781	.	+	.	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	intron	25232782	25232872	.	+	.	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	CDS	25232873	25233290	1	+	2	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	exon	25232873	25233290	.	+	.	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	intron	25233291	25233375	.	+	.	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	CDS	25233376	25233949	1	+	1	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	exon	25233376	25233949	.	+	.	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
Phchi.S1	AUGUSTUS	stop_codon	25233950	25233952	.	+	0	transcript_id "Phchi.S1G398500.t1"; gene_id "Phchi.S1G398500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10538.t1 is derived from g14588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	871488	873038	.	-	.	Phchi.S4G012000
Phchi.S4	AUGUSTUS	transcript	871488	873038	.	-	.	transcript_id "Phchi.S4G012000.t1"; gene_id "Phchi.S4G012000"
Phchi.S4	AUGUSTUS	stop_codon	871485	871487	.	-	0	transcript_id "Phchi.S4G012000.t1"; gene_id "Phchi.S4G012000"
Phchi.S4	AUGUSTUS	CDS	871488	873038	1	-	0	transcript_id "Phchi.S4G012000.t1"; gene_id "Phchi.S4G012000"
Phchi.S4	AUGUSTUS	exon	871488	873038	.	-	.	transcript_id "Phchi.S4G012000.t1"; gene_id "Phchi.S4G012000"
Phchi.S4	AUGUSTUS	start_codon	873036	873038	.	-	0	transcript_id "Phchi.S4G012000.t1"; gene_id "Phchi.S4G012000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9159.t1 is derived from g6334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40145983	40147935	.	-	.	Phchi.S1G631800
Phchi.S1	AUGUSTUS	transcript	40145983	40147935	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	stop_codon	40145980	40145982	.	-	0	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	CDS	40145983	40146060	0.99	-	0	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	exon	40145983	40146060	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	intron	40146061	40146274	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	CDS	40146275	40146307	1	-	0	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	exon	40146275	40146307	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	intron	40146308	40146801	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	CDS	40146802	40146949	1	-	1	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	exon	40146802	40146949	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	intron	40146950	40147085	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	CDS	40147086	40147408	1	-	0	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	exon	40147086	40147408	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	intron	40147409	40147608	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	CDS	40147609	40147935	0.99	-	0	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	exon	40147609	40147935	.	-	.	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
Phchi.S1	AUGUSTUS	start_codon	40147933	40147935	.	-	0	transcript_id "Phchi.S1G631800.t1"; gene_id "Phchi.S1G631800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg473.t1 is derived from g10255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3333974	3335325	.	-	.	Phchi.S6G043200
Phchi.S6	AUGUSTUS	transcript	3333974	3335325	.	-	.	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	stop_codon	3333971	3333973	.	-	0	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	CDS	3333974	3334657	0.4	-	0	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	exon	3333974	3334657	.	-	.	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	intron	3334658	3334758	.	-	.	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	CDS	3334759	3335325	0.54	-	0	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	exon	3334759	3335325	.	-	.	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
Phchi.S6	AUGUSTUS	start_codon	3335323	3335325	.	-	0	transcript_id "Phchi.S6G043200.t1"; gene_id "Phchi.S6G043200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4403.t1 is derived from g1572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10250569	10251278	.	+	.	Phchi.S1G156200
Phchi.S1	AUGUSTUS	transcript	10250569	10251278	.	+	.	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	start_codon	10250569	10250571	.	+	0	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	CDS	10250569	10250710	0.96	+	0	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	exon	10250569	10250710	.	+	.	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	intron	10250711	10251105	.	+	.	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	CDS	10251106	10251278	1	+	2	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	exon	10251106	10251278	.	+	.	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
Phchi.S1	AUGUSTUS	stop_codon	10251279	10251281	.	+	0	transcript_id "Phchi.S1G156200.t1"; gene_id "Phchi.S1G156200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5573.t1 is derived from g2743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17670865	17672403	.	-	.	Phchi.S1G273200
Phchi.S1	AUGUSTUS	transcript	17670865	17672403	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	stop_codon	17670862	17670864	.	-	0	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	CDS	17670865	17670910	0.99	-	1	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	exon	17670865	17670910	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	intron	17670911	17671003	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	CDS	17671004	17671143	0.94	-	0	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	exon	17671004	17671143	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	intron	17671144	17671262	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	CDS	17671263	17671331	0.99	-	0	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	exon	17671263	17671331	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	intron	17671332	17671762	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	CDS	17671763	17671865	1	-	1	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	exon	17671763	17671865	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	intron	17671866	17671961	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	CDS	17671962	17672083	1	-	0	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	exon	17671962	17672083	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	intron	17672084	17672247	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	CDS	17672248	17672403	0.9	-	0	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	exon	17672248	17672403	.	-	.	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
Phchi.S1	AUGUSTUS	start_codon	17672401	17672403	.	-	0	transcript_id "Phchi.S1G273200.t1"; gene_id "Phchi.S1G273200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6954.t1 is derived from g4126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26125001	26125732	.	+	.	Phchi.S1G411300
Phchi.S1	AUGUSTUS	transcript	26125001	26125732	.	+	.	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	start_codon	26125001	26125003	.	+	0	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	CDS	26125001	26125192	0.43	+	0	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	exon	26125001	26125192	.	+	.	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	intron	26125193	26125431	.	+	.	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	CDS	26125432	26125495	1	+	0	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	exon	26125432	26125495	.	+	.	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	intron	26125496	26125676	.	+	.	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	CDS	26125677	26125732	1	+	2	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	exon	26125677	26125732	.	+	.	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
Phchi.S1	AUGUSTUS	stop_codon	26125733	26125735	.	+	0	transcript_id "Phchi.S1G411300.t1"; gene_id "Phchi.S1G411300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4966.t1 is derived from g2136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13794621	13798087	.	+	.	Phchi.S1G212500
Phchi.S1	AUGUSTUS	transcript	13794621	13798087	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	start_codon	13794621	13794623	.	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13794621	13794776	0.29	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13794621	13794776	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13794777	13795279	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13795280	13795498	0.53	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13795280	13795498	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13795499	13795662	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13795663	13795800	0.79	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13795663	13795800	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13795801	13795872	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13795873	13795982	0.45	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13795873	13795982	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13795983	13796130	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13796131	13796203	0.79	+	1	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13796131	13796203	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13796204	13796339	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13796340	13796458	0.85	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13796340	13796458	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13796459	13796570	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13796571	13796685	1	+	1	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13796571	13796685	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13796686	13796765	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13796766	13796882	0.98	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13796766	13796882	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13796883	13796985	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13796986	13797077	0.98	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13796986	13797077	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13797078	13797169	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13797170	13797236	1	+	1	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13797170	13797236	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13797237	13797365	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13797366	13797435	0.79	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13797366	13797435	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13797436	13797514	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13797515	13797606	1	+	2	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13797515	13797606	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13797607	13797705	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13797706	13797849	1	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13797706	13797849	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	intron	13797850	13797943	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	CDS	13797944	13798087	0.86	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	exon	13797944	13798087	.	+	.	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
Phchi.S1	AUGUSTUS	stop_codon	13798088	13798090	.	+	0	transcript_id "Phchi.S1G212500.t1"; gene_id "Phchi.S1G212500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7081.t1 is derived from g4253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26798105	26801089	.	+	.	Phchi.S1G424000
Phchi.S1	AUGUSTUS	transcript	26798105	26801089	.	+	.	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	start_codon	26798105	26798107	.	+	0	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	CDS	26798105	26800481	0.98	+	0	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	exon	26798105	26800481	.	+	.	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	intron	26800482	26800724	.	+	.	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	CDS	26800725	26801089	1	+	2	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	exon	26800725	26801089	.	+	.	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
Phchi.S1	AUGUSTUS	stop_codon	26801090	26801092	.	+	0	transcript_id "Phchi.S1G424000.t1"; gene_id "Phchi.S1G424000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14390.t1 is derived from g12858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12569330	12569677	.	+	.	Phchi.S3G170900
Phchi.S3	AUGUSTUS	transcript	12569330	12569677	.	+	.	transcript_id "Phchi.S3G170900.t1"; gene_id "Phchi.S3G170900"
Phchi.S3	AUGUSTUS	start_codon	12569330	12569332	.	+	0	transcript_id "Phchi.S3G170900.t1"; gene_id "Phchi.S3G170900"
Phchi.S3	AUGUSTUS	CDS	12569330	12569677	1	+	0	transcript_id "Phchi.S3G170900.t1"; gene_id "Phchi.S3G170900"
Phchi.S3	AUGUSTUS	exon	12569330	12569677	.	+	.	transcript_id "Phchi.S3G170900.t1"; gene_id "Phchi.S3G170900"
Phchi.S3	AUGUSTUS	stop_codon	12569678	12569680	.	+	0	transcript_id "Phchi.S3G170900.t1"; gene_id "Phchi.S3G170900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14153.t1 is derived from g12620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11176946	11177610	.	+	.	Phchi.S3G147200
Phchi.S3	AUGUSTUS	transcript	11176946	11177610	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	start_codon	11176946	11176948	.	+	0	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	CDS	11176946	11177050	0.94	+	0	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	exon	11176946	11177050	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	intron	11177051	11177163	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	CDS	11177164	11177229	1	+	0	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	exon	11177164	11177229	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	intron	11177230	11177369	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	CDS	11177370	11177495	1	+	0	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	exon	11177370	11177495	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	intron	11177496	11177589	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	CDS	11177590	11177610	1	+	0	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	exon	11177590	11177610	.	+	.	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
Phchi.S3	AUGUSTUS	stop_codon	11177611	11177613	.	+	0	transcript_id "Phchi.S3G147200.t1"; gene_id "Phchi.S3G147200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2996.t1 is derived from g165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1058389	1059294	.	-	.	Phchi.S1G015500
Phchi.S1	AUGUSTUS	transcript	1058389	1059294	.	-	.	transcript_id "Phchi.S1G015500.t1"; gene_id "Phchi.S1G015500"
Phchi.S1	AUGUSTUS	stop_codon	1058386	1058388	.	-	0	transcript_id "Phchi.S1G015500.t1"; gene_id "Phchi.S1G015500"
Phchi.S1	AUGUSTUS	CDS	1058389	1059294	1	-	0	transcript_id "Phchi.S1G015500.t1"; gene_id "Phchi.S1G015500"
Phchi.S1	AUGUSTUS	exon	1058389	1059294	.	-	.	transcript_id "Phchi.S1G015500.t1"; gene_id "Phchi.S1G015500"
Phchi.S1	AUGUSTUS	start_codon	1059292	1059294	.	-	0	transcript_id "Phchi.S1G015500.t1"; gene_id "Phchi.S1G015500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7717.t1 is derived from g4891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30782714	30784336	.	+	.	Phchi.S1G487600
Phchi.S1	AUGUSTUS	transcript	30782714	30784336	.	+	.	transcript_id "Phchi.S1G487600.t1"; gene_id "Phchi.S1G487600"
Phchi.S1	AUGUSTUS	start_codon	30782714	30782716	.	+	0	transcript_id "Phchi.S1G487600.t1"; gene_id "Phchi.S1G487600"
Phchi.S1	AUGUSTUS	CDS	30782714	30784336	0.95	+	0	transcript_id "Phchi.S1G487600.t1"; gene_id "Phchi.S1G487600"
Phchi.S1	AUGUSTUS	exon	30782714	30784336	.	+	.	transcript_id "Phchi.S1G487600.t1"; gene_id "Phchi.S1G487600"
Phchi.S1	AUGUSTUS	stop_codon	30784337	30784339	.	+	0	transcript_id "Phchi.S1G487600.t1"; gene_id "Phchi.S1G487600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12087.t1 is derived from g7762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2181962	2183019	.	-	.	Phchi.S2G016700
Phchi.S2	AUGUSTUS	transcript	2181962	2183019	.	-	.	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	stop_codon	2181959	2181961	.	-	0	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	CDS	2181962	2181963	0.84	-	2	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	exon	2181962	2181963	.	-	.	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	intron	2181964	2182142	.	-	.	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	CDS	2182143	2183019	0.56	-	0	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	exon	2182143	2183019	.	-	.	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
Phchi.S2	AUGUSTUS	start_codon	2183017	2183019	.	-	0	transcript_id "Phchi.S2G016700.t1"; gene_id "Phchi.S2G016700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3153.t1 is derived from g322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1989830	1992327	.	-	.	Phchi.S1G031200
Phchi.S1	AUGUSTUS	transcript	1989830	1992327	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	stop_codon	1989827	1989829	.	-	0	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	CDS	1989830	1991660	0.94	-	1	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	exon	1989830	1991660	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	intron	1991661	1991777	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	CDS	1991778	1991842	0.77	-	0	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	exon	1991778	1991842	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	intron	1991843	1991933	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	CDS	1991934	1992060	0.67	-	1	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	exon	1991934	1992060	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	intron	1992061	1992262	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	CDS	1992263	1992327	0.5	-	0	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	exon	1992263	1992327	.	-	.	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
Phchi.S1	AUGUSTUS	start_codon	1992325	1992327	.	-	0	transcript_id "Phchi.S1G031200.t1"; gene_id "Phchi.S1G031200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3837.t1 is derived from g1006.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5947440	5949158	.	+	.	Phchi.S1G099600
Phchi.S1	AUGUSTUS	transcript	5947440	5949158	.	+	.	transcript_id "Phchi.S1G099600.t1"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	start_codon	5947440	5947442	.	+	0	transcript_id "Phchi.S1G099600.t1"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	CDS	5947440	5949158	1	+	0	transcript_id "Phchi.S1G099600.t1"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	exon	5947440	5949158	.	+	.	transcript_id "Phchi.S1G099600.t1"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	stop_codon	5949159	5949161	.	+	0	transcript_id "Phchi.S1G099600.t1"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	transcript	5947596	5949158	.	+	.	transcript_id "Phchi.S1G099600.t2"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	start_codon	5947596	5947598	.	+	0	transcript_id "Phchi.S1G099600.t2"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	CDS	5947596	5949158	1	+	0	transcript_id "Phchi.S1G099600.t2"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	exon	5947596	5949158	.	+	.	transcript_id "Phchi.S1G099600.t2"; gene_id "Phchi.S1G099600"
Phchi.S1	AUGUSTUS	stop_codon	5949159	5949161	.	+	0	transcript_id "Phchi.S1G099600.t2"; gene_id "Phchi.S1G099600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8138.t1 is derived from g5313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33822025	33822746	.	-	.	Phchi.S1G529700
Phchi.S1	AUGUSTUS	transcript	33822025	33822746	.	-	.	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	stop_codon	33822022	33822024	.	-	0	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	CDS	33822025	33822255	0.94	-	0	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	exon	33822025	33822255	.	-	.	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	intron	33822256	33822341	.	-	.	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	CDS	33822342	33822746	1	-	0	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	exon	33822342	33822746	.	-	.	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
Phchi.S1	AUGUSTUS	start_codon	33822744	33822746	.	-	0	transcript_id "Phchi.S1G529700.t1"; gene_id "Phchi.S1G529700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1018.t1 is derived from g10801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7137133	7139287	.	-	.	Phchi.S6G097700
Phchi.S6	AUGUSTUS	transcript	7137133	7139287	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	stop_codon	7137130	7137132	.	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7137133	7137164	1	-	2	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7137133	7137164	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7137165	7137254	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7137255	7137387	1	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7137255	7137387	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7137388	7137503	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7137504	7137582	0.99	-	1	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7137504	7137582	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7137583	7137705	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7137706	7137792	1	-	1	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7137706	7137792	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7137793	7137868	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7137869	7137968	0.57	-	2	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7137869	7137968	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7137969	7138070	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7138071	7138128	1	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7138071	7138128	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7138129	7138213	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7138214	7138282	1	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7138214	7138282	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7138283	7138366	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7138367	7138458	1	-	2	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7138367	7138458	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7138459	7138670	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7138671	7138800	1	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7138671	7138800	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7138801	7138895	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7138896	7138991	1	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7138896	7138991	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	intron	7138992	7139149	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	CDS	7139150	7139287	1	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	exon	7139150	7139287	.	-	.	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
Phchi.S6	AUGUSTUS	start_codon	7139285	7139287	.	-	0	transcript_id "Phchi.S6G097700.t1"; gene_id "Phchi.S6G097700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg723.t1 is derived from g10505.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5135512	5136511	.	+	.	Phchi.S6G068200
Phchi.S6	AUGUSTUS	transcript	5135512	5136511	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	start_codon	5135512	5135514	.	+	0	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5135512	5135608	0.71	+	0	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5135512	5135608	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5135609	5135702	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5135703	5135708	1	+	2	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5135703	5135708	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5135709	5135853	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5135854	5136019	0.98	+	2	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5135854	5136019	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136020	5136102	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136103	5136187	0.98	+	1	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136103	5136187	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136188	5136277	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136278	5136420	1	+	0	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136278	5136420	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136421	5136507	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136508	5136511	1	+	1	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136508	5136511	.	+	.	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	stop_codon	5136512	5136514	.	+	0	transcript_id "Phchi.S6G068200.t1"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	transcript	5135512	5136511	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	start_codon	5135512	5135514	.	+	0	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5135512	5135608	0.58	+	0	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5135512	5135608	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5135609	5135702	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5135703	5135708	1	+	2	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5135703	5135708	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5135709	5135853	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5135854	5136015	0.74	+	2	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5135854	5136015	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136016	5136102	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136103	5136114	0.99	+	2	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136103	5136114	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136115	5136187	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136188	5136195	1	+	2	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136188	5136195	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136196	5136277	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136278	5136420	1	+	0	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136278	5136420	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	intron	5136421	5136507	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	CDS	5136508	5136511	1	+	1	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	exon	5136508	5136511	.	+	.	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
Phchi.S6	AUGUSTUS	stop_codon	5136512	5136514	.	+	0	transcript_id "Phchi.S6G068200.t2"; gene_id "Phchi.S6G068200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2288.t1 is derived from g9208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5877132	5880237	.	-	.	Phchi.S5G089700
Phchi.S5	AUGUSTUS	transcript	5877132	5880237	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	stop_codon	5877129	5877131	.	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5877132	5877212	0.51	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5877132	5877212	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5877213	5877359	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5877360	5877533	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5877360	5877533	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5877534	5877620	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5877621	5877710	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5877621	5877710	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5877711	5877807	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5877808	5877909	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5877808	5877909	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5877910	5878034	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5878035	5878095	1	-	1	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5878035	5878095	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5878096	5878176	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5878177	5878321	1	-	2	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5878177	5878321	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5878322	5878409	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5878410	5878563	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5878410	5878563	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5878564	5878647	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5878648	5878884	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5878648	5878884	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5878885	5879014	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5879015	5879125	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5879015	5879125	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5879126	5879220	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5879221	5879344	1	-	1	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5879221	5879344	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5879345	5879437	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5879438	5879655	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5879438	5879655	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5879656	5879743	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5879744	5879944	1	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5879744	5879944	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	intron	5879945	5880081	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	CDS	5880082	5880237	0.53	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	exon	5880082	5880237	.	-	.	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
Phchi.S5	AUGUSTUS	start_codon	5880235	5880237	.	-	0	transcript_id "Phchi.S5G089700.t1"; gene_id "Phchi.S5G089700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg916.t1 is derived from g10698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6417851	6421191	.	-	.	Phchi.S6G087500
Phchi.S6	AUGUSTUS	transcript	6417851	6421191	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	stop_codon	6417848	6417850	.	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6417851	6417925	0.44	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6417851	6417925	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6417926	6418119	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6418120	6418305	0.75	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6418120	6418305	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6418306	6418403	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6418404	6418700	0.98	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6418404	6418700	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6418701	6418825	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6418826	6418884	1	-	2	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6418826	6418884	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6418885	6419133	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419134	6419206	1	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419134	6419206	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419207	6419311	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419312	6419462	0.59	-	1	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419312	6419462	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419463	6419566	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419567	6419646	0.94	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419567	6419646	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419647	6419765	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419766	6419953	1	-	2	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419766	6419953	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419954	6420088	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6420089	6420191	1	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6420089	6420191	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6420192	6420337	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6420338	6420482	1	-	1	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6420338	6420482	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6420483	6420621	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6420622	6420853	1	-	2	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6420622	6420853	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6420854	6421121	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6421122	6421191	1	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6421122	6421191	.	-	.	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	start_codon	6421189	6421191	.	-	0	transcript_id "Phchi.S6G087500.t1"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	transcript	6417851	6421191	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	stop_codon	6417848	6417850	.	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6417851	6417925	0.47	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6417851	6417925	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6417926	6418119	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6418120	6418305	0.76	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6418120	6418305	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6418306	6418403	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6418404	6418700	0.98	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6418404	6418700	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6418701	6418825	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6418826	6418884	1	-	2	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6418826	6418884	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6418885	6419118	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419119	6419206	1	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419119	6419206	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419207	6419311	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419312	6419462	0.54	-	1	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419312	6419462	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419463	6419566	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419567	6419646	0.94	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419567	6419646	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419647	6419765	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6419766	6419953	1	-	2	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6419766	6419953	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6419954	6420088	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6420089	6420191	1	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6420089	6420191	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6420192	6420337	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6420338	6420482	1	-	1	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6420338	6420482	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6420483	6420621	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6420622	6420853	1	-	2	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6420622	6420853	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	intron	6420854	6421121	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	CDS	6421122	6421191	1	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	exon	6421122	6421191	.	-	.	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
Phchi.S6	AUGUSTUS	start_codon	6421189	6421191	.	-	0	transcript_id "Phchi.S6G087500.t2"; gene_id "Phchi.S6G087500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3676.t1 is derived from g845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5145286	5146022	.	-	.	Phchi.S1G083500
Phchi.S1	AUGUSTUS	transcript	5145286	5146022	.	-	.	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	stop_codon	5145283	5145285	.	-	0	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	CDS	5145286	5145511	0.96	-	1	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	exon	5145286	5145511	.	-	.	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	intron	5145512	5145638	.	-	.	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	CDS	5145639	5145772	0.99	-	0	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	exon	5145639	5145772	.	-	.	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	intron	5145773	5145914	.	-	.	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	CDS	5145915	5146022	0.78	-	0	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	exon	5145915	5146022	.	-	.	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
Phchi.S1	AUGUSTUS	start_codon	5146020	5146022	.	-	0	transcript_id "Phchi.S1G083500.t1"; gene_id "Phchi.S1G083500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3527.t1 is derived from g696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4234078	4236422	.	-	.	Phchi.S1G068600
Phchi.S1	AUGUSTUS	transcript	4234078	4236422	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	stop_codon	4234075	4234077	.	-	0	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234078	4234225	0.99	-	1	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234078	4234225	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234226	4234308	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234309	4234351	0.99	-	2	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234309	4234351	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234352	4234430	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234431	4234487	0.99	-	2	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234431	4234487	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234488	4234568	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234569	4234593	0.93	-	0	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234569	4234593	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234594	4234697	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234698	4234713	0.91	-	1	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234698	4234713	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234714	4235178	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4235179	4235221	0.94	-	2	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4235179	4235221	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4235222	4235315	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4235316	4235835	0.92	-	0	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4235316	4235835	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4235836	4235984	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4235985	4236422	0.95	-	0	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4235985	4236422	.	-	.	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	start_codon	4236420	4236422	.	-	0	transcript_id "Phchi.S1G068600.t1"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	transcript	4234078	4236422	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	stop_codon	4234075	4234077	.	-	0	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234078	4234225	0.99	-	1	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234078	4234225	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234226	4234308	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234309	4234351	0.99	-	2	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234309	4234351	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234352	4234430	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234431	4234487	0.99	-	2	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234431	4234487	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234488	4234568	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234569	4234593	0.86	-	0	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234569	4234593	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234594	4234697	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4234698	4234713	0.84	-	1	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4234698	4234713	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4234714	4235178	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4235179	4235221	0.87	-	2	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4235179	4235221	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4235222	4235315	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4235316	4235786	0.8	-	2	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4235316	4235786	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4235787	4235984	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4235985	4236033	0.82	-	0	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4235985	4236033	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	intron	4236034	4236128	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	CDS	4236129	4236422	0.78	-	0	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	exon	4236129	4236422	.	-	.	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
Phchi.S1	AUGUSTUS	start_codon	4236420	4236422	.	-	0	transcript_id "Phchi.S1G068600.t2"; gene_id "Phchi.S1G068600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14756.t1 is derived from g13224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14561191	14565782	.	+	.	Phchi.S3G207500
Phchi.S3	AUGUSTUS	transcript	14561191	14565782	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	start_codon	14561191	14561193	.	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14561191	14562092	0.95	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14561191	14562092	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14562093	14562206	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14562207	14562360	1	+	1	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14562207	14562360	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14562361	14562489	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14562490	14562582	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14562490	14562582	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14562583	14562678	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14562679	14562767	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14562679	14562767	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14562768	14562947	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14562948	14563074	1	+	1	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14562948	14563074	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14563075	14563183	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14563184	14563303	0.98	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14563184	14563303	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14563304	14563498	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14563499	14563549	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14563499	14563549	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14563550	14563653	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14563654	14563715	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14563654	14563715	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14563716	14563803	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14563804	14563861	1	+	1	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14563804	14563861	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14563862	14563957	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14563958	14564083	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14563958	14564083	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14564084	14564297	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14564298	14564378	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14564298	14564378	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14564379	14564472	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14564473	14564602	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14564473	14564602	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14564603	14564732	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14564733	14564881	1	+	2	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14564733	14564881	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14564882	14564965	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14564966	14565132	0.86	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14564966	14565132	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14565133	14565209	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14565210	14565246	0.86	+	1	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14565210	14565246	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14565247	14565320	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14565321	14565419	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14565321	14565419	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14565420	14565508	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14565509	14565562	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14565509	14565562	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	intron	14565563	14565641	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	CDS	14565642	14565782	1	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	exon	14565642	14565782	.	+	.	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
Phchi.S3	AUGUSTUS	stop_codon	14565783	14565785	.	+	0	transcript_id "Phchi.S3G207500.t1"; gene_id "Phchi.S3G207500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9499.t1 is derived from g6675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42065016	42066693	.	-	.	Phchi.S1G665800
Phchi.S1	AUGUSTUS	transcript	42065016	42066693	.	-	.	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	stop_codon	42065013	42065015	.	-	0	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	CDS	42065016	42065048	0.67	-	0	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	exon	42065016	42065048	.	-	.	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	intron	42065049	42065412	.	-	.	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	CDS	42065413	42066693	0.28	-	0	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	exon	42065413	42066693	.	-	.	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
Phchi.S1	AUGUSTUS	start_codon	42066691	42066693	.	-	0	transcript_id "Phchi.S1G665800.t1"; gene_id "Phchi.S1G665800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7092.t1 is derived from g4264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26866748	26873706	.	-	.	Phchi.S1G425100
Phchi.S1	AUGUSTUS	transcript	26866748	26873706	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	stop_codon	26866745	26866747	.	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26866748	26867560	0.98	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26866748	26867560	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26867561	26867745	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26867746	26867912	1	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26867746	26867912	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26867913	26867994	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26867995	26868141	1	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26867995	26868141	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26868142	26868237	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26868238	26868367	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26868238	26868367	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26868368	26868477	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26868478	26868616	0.99	-	1	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26868478	26868616	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26868617	26868711	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26868712	26868917	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26868712	26868917	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26868918	26869002	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26869003	26869190	0.58	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26869003	26869190	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26869191	26869372	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26869373	26869478	0.82	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26869373	26869478	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26869479	26869594	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26869595	26869672	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26869595	26869672	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26869673	26869786	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26869787	26869876	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26869787	26869876	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26869877	26869958	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26869959	26870111	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26869959	26870111	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26870112	26870253	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26870254	26870372	1	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26870254	26870372	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26870373	26870462	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26870463	26870601	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26870463	26870601	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26870602	26870693	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26870694	26870797	1	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26870694	26870797	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26870798	26870895	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26870896	26870980	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26870896	26870980	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26870981	26871105	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26871106	26871119	1	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26871106	26871119	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26871120	26871244	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26871245	26871308	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26871245	26871308	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26871309	26871432	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26871433	26871598	1	-	1	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26871433	26871598	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26871599	26871689	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26871690	26871717	1	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26871690	26871717	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26871718	26871834	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26871835	26871991	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26871835	26871991	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26871992	26872106	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26872107	26872250	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26872107	26872250	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26872251	26872332	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26872333	26872434	1	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26872333	26872434	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26872435	26872783	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26872784	26872926	0.32	-	2	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26872784	26872926	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26872927	26873000	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26873001	26873091	0.41	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26873001	26873091	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	intron	26873092	26873316	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	CDS	26873317	26873706	0.33	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	exon	26873317	26873706	.	-	.	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
Phchi.S1	AUGUSTUS	start_codon	26873704	26873706	.	-	0	transcript_id "Phchi.S1G425100.t1"; gene_id "Phchi.S1G425100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4961.t1 is derived from g2131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13773331	13774358	.	-	.	Phchi.S1G212000
Phchi.S1	AUGUSTUS	transcript	13773331	13774358	.	-	.	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	stop_codon	13773328	13773330	.	-	0	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	CDS	13773331	13773600	0.74	-	0	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	exon	13773331	13773600	.	-	.	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	intron	13773601	13773752	.	-	.	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	CDS	13773753	13774358	0.45	-	0	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	exon	13773753	13774358	.	-	.	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
Phchi.S1	AUGUSTUS	start_codon	13774356	13774358	.	-	0	transcript_id "Phchi.S1G212000.t1"; gene_id "Phchi.S1G212000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7184.t1 is derived from g4356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27445377	27448154	.	+	.	Phchi.S1G434300
Phchi.S1	AUGUSTUS	transcript	27445377	27448154	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	start_codon	27445377	27445379	.	+	0	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27445377	27445547	0.92	+	0	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27445377	27445547	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27445548	27445631	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27445632	27445723	1	+	0	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27445632	27445723	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27445724	27445857	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27445858	27445929	1	+	1	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27445858	27445929	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27445930	27446016	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27446017	27446123	1	+	1	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27446017	27446123	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27446124	27446299	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27446300	27446355	1	+	2	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27446300	27446355	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27446356	27446478	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27446479	27446680	1	+	0	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27446479	27446680	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27446681	27446776	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27446777	27446869	1	+	2	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27446777	27446869	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	intron	27446870	27446961	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	CDS	27446962	27448154	0.34	+	2	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	exon	27446962	27448154	.	+	.	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
Phchi.S1	AUGUSTUS	stop_codon	27448155	27448157	.	+	0	transcript_id "Phchi.S1G434300.t1"; gene_id "Phchi.S1G434300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6723.t1 is derived from g3895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24748152	24749027	.	-	.	Phchi.S1G388200
Phchi.S1	AUGUSTUS	transcript	24748152	24749027	.	-	.	transcript_id "Phchi.S1G388200.t1"; gene_id "Phchi.S1G388200"
Phchi.S1	AUGUSTUS	stop_codon	24748149	24748151	.	-	0	transcript_id "Phchi.S1G388200.t1"; gene_id "Phchi.S1G388200"
Phchi.S1	AUGUSTUS	CDS	24748152	24749027	0.94	-	0	transcript_id "Phchi.S1G388200.t1"; gene_id "Phchi.S1G388200"
Phchi.S1	AUGUSTUS	exon	24748152	24749027	.	-	.	transcript_id "Phchi.S1G388200.t1"; gene_id "Phchi.S1G388200"
Phchi.S1	AUGUSTUS	start_codon	24749025	24749027	.	-	0	transcript_id "Phchi.S1G388200.t1"; gene_id "Phchi.S1G388200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2478.t1 is derived from g9398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6843346	6845122	.	+	.	Phchi.S5G108700
Phchi.S5	AUGUSTUS	transcript	6843346	6845122	.	+	.	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	start_codon	6843346	6843348	.	+	0	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	CDS	6843346	6843733	0.65	+	0	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	exon	6843346	6843733	.	+	.	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	intron	6843734	6843818	.	+	.	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	CDS	6843819	6845122	1	+	2	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	exon	6843819	6845122	.	+	.	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
Phchi.S5	AUGUSTUS	stop_codon	6845123	6845125	.	+	0	transcript_id "Phchi.S5G108700.t1"; gene_id "Phchi.S5G108700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12478.t1 is derived from g8155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	27937474	27938106	.	-	.	Phchi.S2G055800
Phchi.S2	AUGUSTUS	transcript	27937474	27938106	.	-	.	transcript_id "Phchi.S2G055800.t1"; gene_id "Phchi.S2G055800"
Phchi.S2	AUGUSTUS	stop_codon	27937471	27937473	.	-	0	transcript_id "Phchi.S2G055800.t1"; gene_id "Phchi.S2G055800"
Phchi.S2	AUGUSTUS	CDS	27937474	27938106	0.95	-	0	transcript_id "Phchi.S2G055800.t1"; gene_id "Phchi.S2G055800"
Phchi.S2	AUGUSTUS	exon	27937474	27938106	.	-	.	transcript_id "Phchi.S2G055800.t1"; gene_id "Phchi.S2G055800"
Phchi.S2	AUGUSTUS	start_codon	27938104	27938106	.	-	0	transcript_id "Phchi.S2G055800.t1"; gene_id "Phchi.S2G055800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg371.t1 is derived from g10153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2691822	2693342	.	-	.	Phchi.S6G033000
Phchi.S6	AUGUSTUS	transcript	2691822	2693342	.	-	.	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	stop_codon	2691819	2691821	.	-	0	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	CDS	2691822	2692544	1	-	0	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	exon	2691822	2692544	.	-	.	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	intron	2692545	2692691	.	-	.	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	CDS	2692692	2693342	0.62	-	0	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	exon	2692692	2693342	.	-	.	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
Phchi.S6	AUGUSTUS	start_codon	2693340	2693342	.	-	0	transcript_id "Phchi.S6G033000.t1"; gene_id "Phchi.S6G033000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6295.t1 is derived from g3467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22149704	22150696	.	+	.	Phchi.S1G345400
Phchi.S1	AUGUSTUS	transcript	22149704	22150696	.	+	.	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	start_codon	22149704	22149706	.	+	0	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	CDS	22149704	22150129	0.64	+	0	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	exon	22149704	22150129	.	+	.	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	intron	22150130	22150244	.	+	.	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	CDS	22150245	22150404	1	+	0	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	exon	22150245	22150404	.	+	.	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	intron	22150405	22150502	.	+	.	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	CDS	22150503	22150696	0.77	+	2	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	exon	22150503	22150696	.	+	.	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
Phchi.S1	AUGUSTUS	stop_codon	22150697	22150699	.	+	0	transcript_id "Phchi.S1G345400.t1"; gene_id "Phchi.S1G345400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2850.t1 is derived from g19.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17998	18972	.	-	.	Phchi.S1G000900
Phchi.S1	AUGUSTUS	transcript	17998	18708	.	-	.	transcript_id "Phchi.S1G000900.t1"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	stop_codon	17995	17997	.	-	0	transcript_id "Phchi.S1G000900.t1"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	CDS	17998	18708	0.89	-	0	transcript_id "Phchi.S1G000900.t1"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	exon	17998	18708	.	-	.	transcript_id "Phchi.S1G000900.t1"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	start_codon	18706	18708	.	-	0	transcript_id "Phchi.S1G000900.t1"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	transcript	17998	18972	.	-	.	transcript_id "Phchi.S1G000900.t2"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	stop_codon	17995	17997	.	-	0	transcript_id "Phchi.S1G000900.t2"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	CDS	17998	18972	0.53	-	0	transcript_id "Phchi.S1G000900.t2"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	exon	17998	18972	.	-	.	transcript_id "Phchi.S1G000900.t2"; gene_id "Phchi.S1G000900"
Phchi.S1	AUGUSTUS	start_codon	18970	18972	.	-	0	transcript_id "Phchi.S1G000900.t2"; gene_id "Phchi.S1G000900"
# This transcript jg2012.t2 is derived from g8932.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2013.t1 is derived from g8933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4462095	4462739	.	-	.	Phchi.S5G062200
Phchi.S5	AUGUSTUS	transcript	4462095	4462739	.	-	.	transcript_id "Phchi.S5G062200.t1"; gene_id "Phchi.S5G062200"
Phchi.S5	AUGUSTUS	stop_codon	4462092	4462094	.	-	0	transcript_id "Phchi.S5G062200.t1"; gene_id "Phchi.S5G062200"
Phchi.S5	AUGUSTUS	CDS	4462095	4462739	0.99	-	0	transcript_id "Phchi.S5G062200.t1"; gene_id "Phchi.S5G062200"
Phchi.S5	AUGUSTUS	exon	4462095	4462739	.	-	.	transcript_id "Phchi.S5G062200.t1"; gene_id "Phchi.S5G062200"
Phchi.S5	AUGUSTUS	start_codon	4462737	4462739	.	-	0	transcript_id "Phchi.S5G062200.t1"; gene_id "Phchi.S5G062200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9703.t1 is derived from g6879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43342091	43343056	.	+	.	Phchi.S1G686200
Phchi.S1	AUGUSTUS	transcript	43342091	43343056	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	start_codon	43342091	43342093	.	+	0	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	CDS	43342091	43342390	1	+	0	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	exon	43342091	43342390	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	intron	43342391	43342490	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	CDS	43342491	43342544	1	+	0	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	exon	43342491	43342544	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	intron	43342545	43342718	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	CDS	43342719	43342778	1	+	0	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	exon	43342719	43342778	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	intron	43342779	43342864	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	CDS	43342865	43343056	1	+	0	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	exon	43342865	43343056	.	+	.	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
Phchi.S1	AUGUSTUS	stop_codon	43343057	43343059	.	+	0	transcript_id "Phchi.S1G686200.t1"; gene_id "Phchi.S1G686200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10504.t1 is derived from g14553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	742029	742940	.	-	.	Phchi.S4G008600
Phchi.S4	AUGUSTUS	transcript	742029	742940	.	-	.	transcript_id "Phchi.S4G008600.t1"; gene_id "Phchi.S4G008600"
Phchi.S4	AUGUSTUS	stop_codon	742026	742028	.	-	0	transcript_id "Phchi.S4G008600.t1"; gene_id "Phchi.S4G008600"
Phchi.S4	AUGUSTUS	CDS	742029	742940	0.76	-	0	transcript_id "Phchi.S4G008600.t1"; gene_id "Phchi.S4G008600"
Phchi.S4	AUGUSTUS	exon	742029	742940	.	-	.	transcript_id "Phchi.S4G008600.t1"; gene_id "Phchi.S4G008600"
Phchi.S4	AUGUSTUS	start_codon	742938	742940	.	-	0	transcript_id "Phchi.S4G008600.t1"; gene_id "Phchi.S4G008600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10522.t1 is derived from g14572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	817621	819648	.	-	.	Phchi.S4G010400
Phchi.S4	AUGUSTUS	transcript	817621	819648	.	-	.	transcript_id "Phchi.S4G010400.t1"; gene_id "Phchi.S4G010400"
Phchi.S4	AUGUSTUS	stop_codon	817618	817620	.	-	0	transcript_id "Phchi.S4G010400.t1"; gene_id "Phchi.S4G010400"
Phchi.S4	AUGUSTUS	CDS	817621	819648	0.98	-	0	transcript_id "Phchi.S4G010400.t1"; gene_id "Phchi.S4G010400"
Phchi.S4	AUGUSTUS	exon	817621	819648	.	-	.	transcript_id "Phchi.S4G010400.t1"; gene_id "Phchi.S4G010400"
Phchi.S4	AUGUSTUS	start_codon	819646	819648	.	-	0	transcript_id "Phchi.S4G010400.t1"; gene_id "Phchi.S4G010400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13230.t1 is derived from g11695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4796191	4797462	.	-	.	Phchi.S3G054900
Phchi.S3	AUGUSTUS	transcript	4796191	4797462	.	-	.	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	stop_codon	4796188	4796190	.	-	0	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	CDS	4796191	4796598	0.73	-	0	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	exon	4796191	4796598	.	-	.	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	intron	4796599	4796878	.	-	.	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	CDS	4796879	4796986	0.73	-	0	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	exon	4796879	4796986	.	-	.	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	intron	4796987	4797327	.	-	.	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	CDS	4797328	4797462	0.42	-	0	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	exon	4797328	4797462	.	-	.	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
Phchi.S3	AUGUSTUS	start_codon	4797460	4797462	.	-	0	transcript_id "Phchi.S3G054900.t1"; gene_id "Phchi.S3G054900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15424.t1 is derived from g13892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19015758	19018354	.	+	.	Phchi.S3G274300
Phchi.S3	AUGUSTUS	transcript	19015758	19018354	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	start_codon	19015758	19015760	.	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19015758	19015760	0.75	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19015758	19015760	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19015761	19016272	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19016273	19016308	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19016273	19016308	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19016309	19016439	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19016440	19016511	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19016440	19016511	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19016512	19016635	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19016636	19016740	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19016636	19016740	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19016741	19016872	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19016873	19016964	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19016873	19016964	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19016965	19017060	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19017061	19017202	1	+	1	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19017061	19017202	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19017203	19017343	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19017344	19017441	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19017344	19017441	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19017442	19017531	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19017532	19017661	1	+	1	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19017532	19017661	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19017662	19017738	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19017739	19017883	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19017739	19017883	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19017884	19017964	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19017965	19018023	1	+	2	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19017965	19018023	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	intron	19018024	19018111	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	CDS	19018112	19018354	1	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	exon	19018112	19018354	.	+	.	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
Phchi.S3	AUGUSTUS	stop_codon	19018355	19018357	.	+	0	transcript_id "Phchi.S3G274300.t1"; gene_id "Phchi.S3G274300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10287.t1 is derived from g7463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46821285	46823624	.	-	.	Phchi.S1G744600
Phchi.S1	AUGUSTUS	transcript	46821285	46823624	.	-	.	transcript_id "Phchi.S1G744600.t1"; gene_id "Phchi.S1G744600"
Phchi.S1	AUGUSTUS	stop_codon	46821282	46821284	.	-	0	transcript_id "Phchi.S1G744600.t1"; gene_id "Phchi.S1G744600"
Phchi.S1	AUGUSTUS	CDS	46821285	46823624	0.72	-	0	transcript_id "Phchi.S1G744600.t1"; gene_id "Phchi.S1G744600"
Phchi.S1	AUGUSTUS	exon	46821285	46823624	.	-	.	transcript_id "Phchi.S1G744600.t1"; gene_id "Phchi.S1G744600"
Phchi.S1	AUGUSTUS	start_codon	46823622	46823624	.	-	0	transcript_id "Phchi.S1G744600.t1"; gene_id "Phchi.S1G744600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9171.t1 is derived from g6346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40203747	40206311	.	+	.	Phchi.S1G633000
Phchi.S1	AUGUSTUS	transcript	40203747	40206311	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	start_codon	40203747	40203749	.	+	0	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	CDS	40203747	40203824	0.7	+	0	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	exon	40203747	40203824	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	intron	40203825	40204036	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	CDS	40204037	40204111	0.78	+	0	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	exon	40204037	40204111	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	intron	40204112	40204257	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	CDS	40204258	40204333	0.93	+	0	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	exon	40204258	40204333	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	intron	40204334	40204471	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	CDS	40204472	40205829	0.41	+	2	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	exon	40204472	40205829	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	intron	40205830	40205936	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	CDS	40205937	40206311	0.5	+	0	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	exon	40205937	40206311	.	+	.	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
Phchi.S1	AUGUSTUS	stop_codon	40206312	40206314	.	+	0	transcript_id "Phchi.S1G633000.t1"; gene_id "Phchi.S1G633000"
# This transcript jg14514.t2 is derived from g12982.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14515.t1 is derived from g12983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13269112	13271013	.	+	.	Phchi.S3G183400
Phchi.S3	AUGUSTUS	transcript	13269112	13271013	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	start_codon	13269112	13269114	.	+	0	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	CDS	13269112	13269694	1	+	0	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	exon	13269112	13269694	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	intron	13269695	13269975	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	CDS	13269976	13270173	1	+	2	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	exon	13269976	13270173	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	intron	13270174	13270308	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	CDS	13270309	13270597	1	+	2	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	exon	13270309	13270597	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	intron	13270598	13270688	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	CDS	13270689	13270851	1	+	1	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	exon	13270689	13270851	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	intron	13270852	13270935	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	CDS	13270936	13271013	1	+	0	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	exon	13270936	13271013	.	+	.	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
Phchi.S3	AUGUSTUS	stop_codon	13271014	13271016	.	+	0	transcript_id "Phchi.S3G183400.t1"; gene_id "Phchi.S3G183400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5463.t1 is derived from g2633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16964081	16966365	.	-	.	Phchi.S1G262200
Phchi.S1	AUGUSTUS	transcript	16964081	16966365	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	stop_codon	16964078	16964080	.	-	0	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16964081	16964087	0.36	-	1	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16964081	16964087	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	intron	16964088	16964194	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16964195	16964906	0.28	-	2	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16964195	16964906	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	intron	16964907	16965043	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16965044	16965647	0.49	-	0	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16965044	16965647	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	intron	16965648	16965743	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16965744	16965838	1	-	2	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16965744	16965838	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	intron	16965839	16965924	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16965925	16965986	0.8	-	1	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16965925	16965986	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	intron	16965987	16966153	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16966154	16966223	0.7	-	2	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16966154	16966223	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	intron	16966224	16966301	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	CDS	16966302	16966365	1	-	0	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	exon	16966302	16966365	.	-	.	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
Phchi.S1	AUGUSTUS	start_codon	16966363	16966365	.	-	0	transcript_id "Phchi.S1G262200.t1"; gene_id "Phchi.S1G262200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6395.t1 is derived from g3567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22724556	22725256	.	+	.	Phchi.S1G355400
Phchi.S1	AUGUSTUS	transcript	22724556	22725256	.	+	.	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	start_codon	22724556	22724558	.	+	0	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	CDS	22724556	22724560	0.95	+	0	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	exon	22724556	22724560	.	+	.	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	intron	22724561	22724694	.	+	.	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	CDS	22724695	22725256	0.95	+	1	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	exon	22724695	22725256	.	+	.	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
Phchi.S1	AUGUSTUS	stop_codon	22725257	22725259	.	+	0	transcript_id "Phchi.S1G355400.t1"; gene_id "Phchi.S1G355400"
# This transcript jg6634.t2 is derived from g3806.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6635.t1 is derived from g3807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24184139	24189290	.	+	.	Phchi.S1G379400
Phchi.S1	AUGUSTUS	transcript	24184139	24189290	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	start_codon	24184139	24184141	.	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24184139	24184206	0.54	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24184139	24184206	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24184207	24184326	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24184327	24184432	0.5	+	1	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24184327	24184432	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24184433	24184524	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24184525	24184935	0.93	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24184525	24184935	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24184936	24185084	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24185085	24185240	0.92	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24185085	24185240	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24185241	24185349	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24185350	24185507	0.85	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24185350	24185507	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24185508	24185624	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24185625	24185708	0.87	+	1	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24185625	24185708	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24185709	24185805	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24185806	24185904	0.88	+	1	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24185806	24185904	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24185905	24186029	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24186030	24186080	1	+	1	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24186030	24186080	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24186081	24186435	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24186436	24186538	1	+	1	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24186436	24186538	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24186539	24186618	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24186619	24186701	1	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24186619	24186701	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24186702	24186838	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24186839	24186884	1	+	1	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24186839	24186884	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24186885	24187029	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24187030	24187117	1	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24187030	24187117	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24187118	24187199	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24187200	24188368	0.92	+	2	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24187200	24188368	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	intron	24188369	24188465	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	CDS	24188466	24189290	1	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	exon	24188466	24189290	.	+	.	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
Phchi.S1	AUGUSTUS	stop_codon	24189291	24189293	.	+	0	transcript_id "Phchi.S1G379400.t1"; gene_id "Phchi.S1G379400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1834.t1 is derived from g8754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3484362	3484607	.	-	.	Phchi.S5G044300
Phchi.S5	AUGUSTUS	transcript	3484362	3484607	.	-	.	transcript_id "Phchi.S5G044300.t1"; gene_id "Phchi.S5G044300"
Phchi.S5	AUGUSTUS	stop_codon	3484359	3484361	.	-	0	transcript_id "Phchi.S5G044300.t1"; gene_id "Phchi.S5G044300"
Phchi.S5	AUGUSTUS	CDS	3484362	3484607	0.75	-	0	transcript_id "Phchi.S5G044300.t1"; gene_id "Phchi.S5G044300"
Phchi.S5	AUGUSTUS	exon	3484362	3484607	.	-	.	transcript_id "Phchi.S5G044300.t1"; gene_id "Phchi.S5G044300"
Phchi.S5	AUGUSTUS	start_codon	3484605	3484607	.	-	0	transcript_id "Phchi.S5G044300.t1"; gene_id "Phchi.S5G044300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1506.t1 is derived from g8425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1281970	1283855	.	-	.	Phchi.S5G011500
Phchi.S5	AUGUSTUS	transcript	1281987	1283855	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	stop_codon	1281984	1281986	.	-	0	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1281987	1282066	0.63	-	2	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1281987	1282066	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282067	1282139	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282140	1282265	0.65	-	2	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282140	1282265	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282266	1282361	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282362	1282439	0.65	-	2	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282362	1282439	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282440	1282559	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282560	1282647	0.67	-	0	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282560	1282647	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282648	1282773	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282774	1282835	1	-	2	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282774	1282835	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282836	1282962	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282963	1283070	1	-	2	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282963	1283070	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1283071	1283198	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1283199	1283544	1	-	0	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1283199	1283544	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1283545	1283639	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1283640	1283855	0.67	-	0	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1283640	1283855	.	-	.	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	start_codon	1283853	1283855	.	-	0	transcript_id "Phchi.S5G011500.t1"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	transcript	1281970	1283855	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	stop_codon	1281967	1281969	.	-	0	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1281970	1282057	0.69	-	1	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1281970	1282057	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282058	1282139	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282140	1282265	0.69	-	1	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282140	1282265	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282266	1282361	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282362	1282453	0.62	-	0	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282362	1282453	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282454	1282548	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282549	1282647	0.62	-	0	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282549	1282647	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282648	1282773	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282774	1282835	1	-	2	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282774	1282835	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1282836	1282962	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1282963	1283070	1	-	2	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1282963	1283070	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1283071	1283198	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1283199	1283544	1	-	0	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1283199	1283544	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	intron	1283545	1283639	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	CDS	1283640	1283855	0.62	-	0	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	exon	1283640	1283855	.	-	.	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
Phchi.S5	AUGUSTUS	start_codon	1283853	1283855	.	-	0	transcript_id "Phchi.S5G011500.t2"; gene_id "Phchi.S5G011500"
# This transcript jg14787.t2 is derived from g13255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14788.t1 is derived from g13256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14712515	14715179	.	-	.	Phchi.S3G210700
Phchi.S3	AUGUSTUS	transcript	14712515	14715179	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	stop_codon	14712512	14712514	.	-	0	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	CDS	14712515	14712532	0.99	-	0	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	exon	14712515	14712532	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	intron	14712533	14712624	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	CDS	14712625	14712773	0.99	-	2	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	exon	14712625	14712773	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	intron	14712774	14712852	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	CDS	14712853	14712868	0.9	-	0	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	exon	14712853	14712868	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	intron	14712869	14713046	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	CDS	14713047	14715179	0.59	-	0	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	exon	14713047	14715179	.	-	.	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
Phchi.S3	AUGUSTUS	start_codon	14715177	14715179	.	-	0	transcript_id "Phchi.S3G210700.t1"; gene_id "Phchi.S3G210700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2939.t1 is derived from g108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	671571	672355	.	-	.	Phchi.S1G009800
Phchi.S1	AUGUSTUS	transcript	671571	672355	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	stop_codon	671568	671570	.	-	0	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	CDS	671571	671619	1	-	1	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	exon	671571	671619	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	intron	671620	671719	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	CDS	671720	671841	1	-	0	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	exon	671720	671841	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	intron	671842	671955	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	CDS	671956	672070	1	-	1	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	exon	671956	672070	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	intron	672071	672176	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	CDS	672177	672355	0.84	-	0	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	exon	672177	672355	.	-	.	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
Phchi.S1	AUGUSTUS	start_codon	672353	672355	.	-	0	transcript_id "Phchi.S1G009800.t1"; gene_id "Phchi.S1G009800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg821.t1 is derived from g10603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5718028	5718494	.	+	.	Phchi.S6G078000
Phchi.S6	AUGUSTUS	transcript	5718028	5718494	.	+	.	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	start_codon	5718028	5718030	.	+	0	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	CDS	5718028	5718217	0.98	+	0	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	exon	5718028	5718217	.	+	.	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	intron	5718218	5718303	.	+	.	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	CDS	5718304	5718494	0.6	+	2	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	exon	5718304	5718494	.	+	.	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
Phchi.S6	AUGUSTUS	stop_codon	5718495	5718497	.	+	0	transcript_id "Phchi.S6G078000.t1"; gene_id "Phchi.S6G078000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13572.t1 is derived from g12039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7547130	7548174	.	-	.	Phchi.S3G089100
Phchi.S3	AUGUSTUS	transcript	7547130	7548174	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	stop_codon	7547127	7547129	.	-	0	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	CDS	7547130	7547283	1	-	1	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	exon	7547130	7547283	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	intron	7547284	7547385	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	CDS	7547386	7547504	1	-	0	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	exon	7547386	7547504	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	intron	7547505	7547604	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	CDS	7547605	7547717	1	-	2	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	exon	7547605	7547717	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	intron	7547718	7547801	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	CDS	7547802	7548174	1	-	0	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	exon	7547802	7548174	.	-	.	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
Phchi.S3	AUGUSTUS	start_codon	7548172	7548174	.	-	0	transcript_id "Phchi.S3G089100.t1"; gene_id "Phchi.S3G089100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15723.t1 is derived from g14193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20895734	20898400	.	+	.	Phchi.S3G304200
Phchi.S3	AUGUSTUS	transcript	20895734	20898400	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	start_codon	20895734	20895736	.	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20895734	20895952	1	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20895734	20895952	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20895953	20896029	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20896030	20896068	0.65	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20896030	20896068	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20896069	20896187	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20896188	20896654	1	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20896188	20896654	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20896655	20896745	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20896746	20896860	1	+	1	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20896746	20896860	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20896861	20896980	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20896981	20897646	0.9	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20896981	20897646	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20897647	20897748	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20897749	20897826	1	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20897749	20897826	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20897827	20897932	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20897933	20898061	1	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20897933	20898061	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	intron	20898062	20898157	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	CDS	20898158	20898400	0.88	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	exon	20898158	20898400	.	+	.	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
Phchi.S3	AUGUSTUS	stop_codon	20898401	20898403	.	+	0	transcript_id "Phchi.S3G304200.t1"; gene_id "Phchi.S3G304200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12890.t1 is derived from g11355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3010168	3011425	.	-	.	Phchi.S3G020900
Phchi.S3	AUGUSTUS	transcript	3010168	3011425	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	stop_codon	3010165	3010167	.	-	0	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3010168	3010223	0.99	-	2	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3010168	3010223	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	intron	3010224	3010322	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3010323	3010420	0.75	-	1	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3010323	3010420	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	intron	3010421	3010680	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3010681	3010690	0.59	-	2	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3010681	3010690	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	intron	3010691	3010842	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3010843	3010905	0.56	-	2	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3010843	3010905	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	intron	3010906	3011042	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3011043	3011143	0.33	-	1	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3011043	3011143	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	intron	3011144	3011231	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3011232	3011248	0.93	-	0	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3011232	3011248	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	intron	3011249	3011389	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	CDS	3011390	3011425	0.97	-	0	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	exon	3011390	3011425	.	-	.	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
Phchi.S3	AUGUSTUS	start_codon	3011423	3011425	.	-	0	transcript_id "Phchi.S3G020900.t1"; gene_id "Phchi.S3G020900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7946.t1 is derived from g5120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32045578	32046312	.	-	.	Phchi.S1G510500
Phchi.S1	AUGUSTUS	transcript	32045578	32046312	.	-	.	transcript_id "Phchi.S1G510500.t1"; gene_id "Phchi.S1G510500"
Phchi.S1	AUGUSTUS	stop_codon	32045575	32045577	.	-	0	transcript_id "Phchi.S1G510500.t1"; gene_id "Phchi.S1G510500"
Phchi.S1	AUGUSTUS	CDS	32045578	32046312	0.4	-	0	transcript_id "Phchi.S1G510500.t1"; gene_id "Phchi.S1G510500"
Phchi.S1	AUGUSTUS	exon	32045578	32046312	.	-	.	transcript_id "Phchi.S1G510500.t1"; gene_id "Phchi.S1G510500"
Phchi.S1	AUGUSTUS	start_codon	32046310	32046312	.	-	0	transcript_id "Phchi.S1G510500.t1"; gene_id "Phchi.S1G510500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2059.t1 is derived from g8979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4648588	4650367	.	-	.	Phchi.S5G066800
Phchi.S5	AUGUSTUS	transcript	4648588	4650367	.	-	.	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	stop_codon	4648585	4648587	.	-	0	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	CDS	4648588	4649153	1	-	2	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	exon	4648588	4649153	.	-	.	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	intron	4649154	4649314	.	-	.	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	CDS	4649315	4649513	0.98	-	0	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	exon	4649315	4649513	.	-	.	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	intron	4649514	4649734	.	-	.	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	CDS	4649735	4650367	0.55	-	0	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	exon	4649735	4650367	.	-	.	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
Phchi.S5	AUGUSTUS	start_codon	4650365	4650367	.	-	0	transcript_id "Phchi.S5G066800.t1"; gene_id "Phchi.S5G066800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12810.t1 is derived from g11275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2474928	2475630	.	+	.	Phchi.S3G012900
Phchi.S3	AUGUSTUS	transcript	2474928	2475630	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	start_codon	2474928	2474930	.	+	0	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	CDS	2474928	2475134	0.69	+	0	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	exon	2474928	2475134	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	intron	2475135	2475249	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	CDS	2475250	2475282	0.77	+	0	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	exon	2475250	2475282	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	intron	2475283	2475362	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	CDS	2475363	2475412	0.81	+	0	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	exon	2475363	2475412	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	intron	2475413	2475497	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	CDS	2475498	2475630	0.81	+	1	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	exon	2475498	2475630	.	+	.	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
Phchi.S3	AUGUSTUS	stop_codon	2475631	2475633	.	+	0	transcript_id "Phchi.S3G012900.t1"; gene_id "Phchi.S3G012900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6545.t1 is derived from g3717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23569056	23570581	.	-	.	Phchi.S1G370400
Phchi.S1	AUGUSTUS	transcript	23569056	23570581	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	stop_codon	23569053	23569055	.	-	0	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	CDS	23569056	23569114	1	-	2	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	exon	23569056	23569114	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	intron	23569115	23569262	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	CDS	23569263	23569382	0.98	-	2	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	exon	23569263	23569382	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	intron	23569383	23569485	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	CDS	23569486	23569608	0.98	-	2	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	exon	23569486	23569608	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	intron	23569609	23569823	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	CDS	23569824	23569898	0.99	-	2	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	exon	23569824	23569898	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	intron	23569899	23570544	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	CDS	23570545	23570581	0.87	-	0	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	exon	23570545	23570581	.	-	.	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
Phchi.S1	AUGUSTUS	start_codon	23570579	23570581	.	-	0	transcript_id "Phchi.S1G370400.t1"; gene_id "Phchi.S1G370400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15272.t1 is derived from g13740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18045682	18047142	.	+	.	Phchi.S3G259100
Phchi.S3	AUGUSTUS	transcript	18045682	18047142	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	start_codon	18045682	18045684	.	+	0	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18045682	18045706	0.98	+	0	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18045682	18045706	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	intron	18045707	18045850	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18045851	18046258	0.98	+	2	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18045851	18046258	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	intron	18046259	18046332	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18046333	18046384	0.99	+	2	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18046333	18046384	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	intron	18046385	18046496	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18046497	18046623	0.99	+	1	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18046497	18046623	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	intron	18046624	18046721	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18046722	18046792	1	+	0	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18046722	18046792	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	intron	18046793	18046865	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18046866	18046938	1	+	1	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18046866	18046938	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	intron	18046939	18047031	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	CDS	18047032	18047142	1	+	0	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	exon	18047032	18047142	.	+	.	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
Phchi.S3	AUGUSTUS	stop_codon	18047143	18047145	.	+	0	transcript_id "Phchi.S3G259100.t1"; gene_id "Phchi.S3G259100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10443.t1 is derived from g14492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	360979	361438	.	-	.	Phchi.S4G002500
Phchi.S4	AUGUSTUS	transcript	360979	361438	.	-	.	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	stop_codon	360976	360978	.	-	0	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	CDS	360979	361009	0.99	-	1	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	exon	360979	361009	.	-	.	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	intron	361010	361217	.	-	.	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	CDS	361218	361438	0.86	-	0	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	exon	361218	361438	.	-	.	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
Phchi.S4	AUGUSTUS	start_codon	361436	361438	.	-	0	transcript_id "Phchi.S4G002500.t1"; gene_id "Phchi.S4G002500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9389.t1 is derived from g6565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41294062	41294427	.	-	.	Phchi.S1G654800
Phchi.S1	AUGUSTUS	transcript	41294062	41294427	.	-	.	transcript_id "Phchi.S1G654800.t1"; gene_id "Phchi.S1G654800"
Phchi.S1	AUGUSTUS	stop_codon	41294059	41294061	.	-	0	transcript_id "Phchi.S1G654800.t1"; gene_id "Phchi.S1G654800"
Phchi.S1	AUGUSTUS	CDS	41294062	41294427	0.73	-	0	transcript_id "Phchi.S1G654800.t1"; gene_id "Phchi.S1G654800"
Phchi.S1	AUGUSTUS	exon	41294062	41294427	.	-	.	transcript_id "Phchi.S1G654800.t1"; gene_id "Phchi.S1G654800"
Phchi.S1	AUGUSTUS	start_codon	41294425	41294427	.	-	0	transcript_id "Phchi.S1G654800.t1"; gene_id "Phchi.S1G654800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8835.t1 is derived from g6010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38214470	38215804	.	-	.	Phchi.S1G599400
Phchi.S1	AUGUSTUS	transcript	38214470	38215804	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	stop_codon	38214467	38214469	.	-	0	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	CDS	38214470	38214911	1	-	1	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	exon	38214470	38214911	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	intron	38214912	38215112	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	CDS	38215113	38215348	0.95	-	0	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	exon	38215113	38215348	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	intron	38215349	38215475	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	CDS	38215476	38215541	0.96	-	0	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	exon	38215476	38215541	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	intron	38215542	38215639	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	CDS	38215640	38215804	1	-	0	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	exon	38215640	38215804	.	-	.	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
Phchi.S1	AUGUSTUS	start_codon	38215802	38215804	.	-	0	transcript_id "Phchi.S1G599400.t1"; gene_id "Phchi.S1G599400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13857.t1 is derived from g12324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9266423	9268060	.	+	.	Phchi.S3G117600
Phchi.S3	AUGUSTUS	transcript	9266423	9268060	.	+	.	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	start_codon	9266423	9266425	.	+	0	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	CDS	9266423	9266572	0.56	+	0	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	exon	9266423	9266572	.	+	.	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	intron	9266573	9266716	.	+	.	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	CDS	9266717	9268060	0.59	+	0	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	exon	9266717	9268060	.	+	.	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
Phchi.S3	AUGUSTUS	stop_codon	9268061	9268063	.	+	0	transcript_id "Phchi.S3G117600.t1"; gene_id "Phchi.S3G117600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10321.t1 is derived from g7497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47096601	47103532	.	+	.	Phchi.S1G748000
Phchi.S1	AUGUSTUS	transcript	47096601	47103532	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	start_codon	47096601	47096603	.	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47096601	47097460	0.62	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47096601	47097460	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47097461	47097567	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47097568	47097892	0.42	+	1	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47097568	47097892	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47097893	47097991	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47097992	47099783	0.5	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47097992	47099783	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47099784	47099918	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47099919	47100160	0.57	+	2	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47099919	47100160	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47100161	47100248	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47100249	47100671	0.97	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47100249	47100671	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47100672	47100757	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47100758	47101069	1	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47100758	47101069	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47101070	47101154	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47101155	47101256	1	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47101155	47101256	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47101257	47101354	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47101355	47101516	1	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47101355	47101516	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47101517	47101760	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47101761	47101823	1	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47101761	47101823	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47101824	47101962	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47101963	47102566	0.96	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47101963	47102566	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47102567	47102650	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47102651	47102754	1	+	2	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47102651	47102754	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47102755	47103217	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47103218	47103373	1	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47103218	47103373	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	intron	47103374	47103439	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	CDS	47103440	47103532	1	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	exon	47103440	47103532	.	+	.	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
Phchi.S1	AUGUSTUS	stop_codon	47103533	47103535	.	+	0	transcript_id "Phchi.S1G748000.t1"; gene_id "Phchi.S1G748000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10332.t1 is derived from g7508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47211536	47215560	.	-	.	Phchi.S1G749100
Phchi.S1	AUGUSTUS	transcript	47211536	47215560	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	stop_codon	47211533	47211535	.	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47211536	47211604	0.92	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47211536	47211604	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47211605	47211698	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47211699	47211800	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47211699	47211800	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47211801	47211881	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47211882	47211962	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47211882	47211962	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47211963	47212059	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47212060	47212155	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47212060	47212155	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47212156	47212244	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47212245	47212349	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47212245	47212349	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47212350	47212462	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47212463	47212537	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47212463	47212537	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47212538	47212621	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47212622	47212681	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47212622	47212681	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47212682	47212786	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47212787	47212917	0.99	-	2	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47212787	47212917	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47212918	47213051	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47213052	47213127	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47213052	47213127	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47213128	47213206	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47213207	47213276	1	-	1	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47213207	47213276	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47213277	47213371	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47213372	47213433	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47213372	47213433	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47213434	47213560	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47213561	47213644	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47213561	47213644	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47213645	47213768	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47213769	47213843	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47213769	47213843	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47213844	47214033	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47214034	47214171	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47214034	47214171	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47214172	47214250	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47214251	47214309	1	-	2	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47214251	47214309	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47214310	47214416	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47214417	47214575	0.99	-	2	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47214417	47214575	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47214576	47214801	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47214802	47214856	1	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47214802	47214856	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	intron	47214857	47214969	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	CDS	47214970	47215560	0.93	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	exon	47214970	47215560	.	-	.	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
Phchi.S1	AUGUSTUS	start_codon	47215558	47215560	.	-	0	transcript_id "Phchi.S1G749100.t1"; gene_id "Phchi.S1G749100"
# This transcript jg2289.t2 is derived from g9209.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2289.t3 is derived from g9209.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2290.t1 is derived from g9210.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5886685	5888718	.	-	.	Phchi.S5G089900
Phchi.S5	AUGUSTUS	transcript	5887145	5888718	.	-	.	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	stop_codon	5887142	5887144	.	-	0	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	CDS	5887145	5887254	0.51	-	2	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	exon	5887145	5887254	.	-	.	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	intron	5887255	5887358	.	-	.	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	CDS	5887359	5888718	0.3	-	0	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	exon	5887359	5888718	.	-	.	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	start_codon	5888716	5888718	.	-	0	transcript_id "Phchi.S5G089900.t1"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	transcript	5886685	5888718	.	-	.	transcript_id "Phchi.S5G089900.t2"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	stop_codon	5886682	5886684	.	-	0	transcript_id "Phchi.S5G089900.t2"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	CDS	5886685	5888718	0.64	-	0	transcript_id "Phchi.S5G089900.t2"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	exon	5886685	5888718	.	-	.	transcript_id "Phchi.S5G089900.t2"; gene_id "Phchi.S5G089900"
Phchi.S5	AUGUSTUS	start_codon	5888716	5888718	.	-	0	transcript_id "Phchi.S5G089900.t2"; gene_id "Phchi.S5G089900"
# This transcript jg1499.t2 is derived from g8418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1500.t1 is derived from g8419.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1210291	1222608	.	+	.	Phchi.S5G010900
Phchi.S5	AUGUSTUS	transcript	1210291	1222608	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	start_codon	1210291	1210293	.	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1210291	1210596	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1210291	1210596	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1210597	1210695	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1210696	1210842	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1210696	1210842	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1210843	1210934	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1210935	1211033	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1210935	1211033	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211034	1211133	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211134	1211262	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211134	1211262	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211263	1211337	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211338	1211430	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211338	1211430	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211431	1211543	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211544	1211609	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211544	1211609	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211610	1211732	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211733	1211822	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211733	1211822	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211823	1211899	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211900	1211956	0.97	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211900	1211956	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211957	1212062	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212063	1212175	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212063	1212175	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212176	1212256	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212257	1212365	1	+	1	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212257	1212365	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212366	1212503	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212504	1212596	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212504	1212596	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212597	1212671	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212672	1212720	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212672	1212720	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212721	1212902	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212903	1213006	1	+	2	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212903	1213006	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213007	1213112	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213113	1213181	0.98	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213113	1213181	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213182	1213290	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213291	1213437	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213291	1213437	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213438	1213526	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213527	1213631	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213527	1213631	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213632	1213715	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213716	1213829	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213716	1213829	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213830	1213946	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213947	1214022	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213947	1214022	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214023	1214202	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214203	1214246	0.99	+	2	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214203	1214246	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214247	1214351	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214352	1214425	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214352	1214425	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214426	1214542	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214543	1214645	1	+	1	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214543	1214645	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214646	1214735	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214736	1214870	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214736	1214870	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214871	1214948	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214949	1215047	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214949	1215047	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215048	1215169	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215170	1215211	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215170	1215211	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215212	1215319	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215320	1215373	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215320	1215373	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215374	1215459	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215460	1215639	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215460	1215639	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215640	1215734	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215735	1215782	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215735	1215782	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215783	1215879	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215880	1215945	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215880	1215945	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215946	1216074	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216075	1216158	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216075	1216158	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216159	1216240	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216241	1216315	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216241	1216315	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216316	1216387	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216388	1216572	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216388	1216572	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216573	1216663	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216664	1216766	1	+	1	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216664	1216766	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216767	1216927	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216928	1217044	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216928	1217044	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217045	1217139	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217140	1217232	0.99	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217140	1217232	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217233	1217338	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217339	1217476	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217339	1217476	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217477	1217557	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217558	1217611	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217558	1217611	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217612	1217834	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217835	1217948	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217835	1217948	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217949	1218029	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218030	1218107	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218030	1218107	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218108	1218195	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218196	1218345	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218196	1218345	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218346	1218423	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218424	1218495	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218424	1218495	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218496	1218577	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218578	1218733	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218578	1218733	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218734	1218811	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218812	1218865	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218812	1218865	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218866	1218976	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218977	1219070	0.97	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218977	1219070	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219071	1219150	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219151	1219254	1	+	2	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219151	1219254	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219255	1219343	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219344	1219451	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219344	1219451	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219452	1219650	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219651	1219701	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219651	1219701	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219702	1219823	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219824	1220295	0.66	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219824	1220295	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1220296	1220438	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1220439	1220509	0.87	+	2	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1220439	1220509	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1220510	1220631	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1220632	1220850	0.99	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1220632	1220850	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1220851	1220920	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1220921	1222273	0.98	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1220921	1222273	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1222274	1222356	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1222357	1222420	1	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1222357	1222420	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1222421	1222516	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1222517	1222608	1	+	2	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1222517	1222608	.	+	.	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	stop_codon	1222609	1222611	.	+	0	transcript_id "Phchi.S5G010900.t1"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	transcript	1210291	1222608	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	start_codon	1210291	1210293	.	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1210291	1210596	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1210291	1210596	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1210597	1210695	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1210696	1210842	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1210696	1210842	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1210843	1210934	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1210935	1211033	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1210935	1211033	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211034	1211133	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211134	1211262	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211134	1211262	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211263	1211337	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211338	1211430	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211338	1211430	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211431	1211543	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211544	1211609	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211544	1211609	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211610	1211732	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211733	1211822	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211733	1211822	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211823	1211899	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1211900	1211977	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1211900	1211977	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1211978	1212062	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212063	1212175	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212063	1212175	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212176	1212256	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212257	1212365	1	+	1	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212257	1212365	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212366	1212503	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212504	1212596	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212504	1212596	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212597	1212671	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212672	1212720	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212672	1212720	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1212721	1212902	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1212903	1213006	1	+	2	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1212903	1213006	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213007	1213112	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213113	1213181	0.96	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213113	1213181	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213182	1213290	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213291	1213437	0.99	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213291	1213437	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213438	1213526	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213527	1213631	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213527	1213631	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213632	1213715	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213716	1213829	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213716	1213829	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1213830	1213946	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1213947	1214022	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1213947	1214022	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214023	1214202	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214203	1214246	0.98	+	2	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214203	1214246	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214247	1214351	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214352	1214425	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214352	1214425	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214426	1214542	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214543	1214645	1	+	1	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214543	1214645	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214646	1214735	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214736	1214870	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214736	1214870	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1214871	1214948	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1214949	1215047	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1214949	1215047	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215048	1215169	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215170	1215211	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215170	1215211	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215212	1215319	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215320	1215373	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215320	1215373	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215374	1215459	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215460	1215639	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215460	1215639	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215640	1215734	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215735	1215782	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215735	1215782	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215783	1215879	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1215880	1215945	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1215880	1215945	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1215946	1216074	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216075	1216158	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216075	1216158	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216159	1216240	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216241	1216315	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216241	1216315	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216316	1216387	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216388	1216572	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216388	1216572	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216573	1216663	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216664	1216766	1	+	1	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216664	1216766	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1216767	1216927	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1216928	1217044	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1216928	1217044	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217045	1217139	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217140	1217232	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217140	1217232	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217233	1217338	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217339	1217476	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217339	1217476	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217477	1217557	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217558	1217611	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217558	1217611	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217612	1217834	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1217835	1217948	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1217835	1217948	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1217949	1218029	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218030	1218107	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218030	1218107	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218108	1218195	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218196	1218345	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218196	1218345	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218346	1218423	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218424	1218495	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218424	1218495	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218496	1218577	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218578	1218733	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218578	1218733	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218734	1218811	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218812	1218865	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218812	1218865	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1218866	1218976	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1218977	1219070	0.97	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1218977	1219070	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219071	1219150	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219151	1219254	1	+	2	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219151	1219254	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219255	1219343	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219344	1219451	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219344	1219451	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219452	1219650	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219651	1219701	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219651	1219701	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1219702	1219823	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1219824	1220295	0.57	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1219824	1220295	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1220296	1220438	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1220439	1220509	0.81	+	2	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1220439	1220509	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1220510	1220631	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1220632	1220850	0.98	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1220632	1220850	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1220851	1220920	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1220921	1222273	0.98	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1220921	1222273	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1222274	1222356	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1222357	1222420	1	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1222357	1222420	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	intron	1222421	1222516	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	CDS	1222517	1222608	1	+	2	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	exon	1222517	1222608	.	+	.	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
Phchi.S5	AUGUSTUS	stop_codon	1222609	1222611	.	+	0	transcript_id "Phchi.S5G010900.t2"; gene_id "Phchi.S5G010900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1351.t1 is derived from g15991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C113	AUGUSTUS	gene	40288	43815	.	+	.	Phchi.C113G000100
Phchi.C113	AUGUSTUS	transcript	40288	43815	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	start_codon	40288	40290	.	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	40288	40404	0.97	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	40288	40404	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	40405	40496	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	40497	40574	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	40497	40574	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	40575	40697	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	40698	40820	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	40698	40820	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	40821	40928	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	40929	40995	0.79	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	40929	40995	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	40996	41105	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	41106	41167	0.79	+	2	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	41106	41167	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	41168	41290	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	41291	41430	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	41291	41430	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	41431	41523	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	41524	41650	1	+	1	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	41524	41650	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	41651	41755	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	41756	41864	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	41756	41864	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	41865	41947	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	41948	42036	1	+	2	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	41948	42036	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	42037	42121	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	42122	42205	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	42122	42205	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	42206	42282	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	42283	42654	0.98	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	42283	42654	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	42655	42770	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	42771	43484	0.99	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	42771	43484	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	43485	43627	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	43628	43687	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	43628	43687	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	intron	43688	43767	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	CDS	43768	43815	1	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	exon	43768	43815	.	+	.	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
Phchi.C113	AUGUSTUS	stop_codon	43816	43818	.	+	0	transcript_id "Phchi.C113G000100.t1"; gene_id "Phchi.C113G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12096.t1 is derived from g7771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2630240	2634657	.	-	.	Phchi.S2G017600
Phchi.S2	AUGUSTUS	transcript	2630240	2634657	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	stop_codon	2630237	2630239	.	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2630240	2630247	1	-	2	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2630240	2630247	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2630248	2630413	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2630414	2630456	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2630414	2630456	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2630457	2630555	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2630556	2630609	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2630556	2630609	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2630610	2630759	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2630760	2630828	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2630760	2630828	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2630829	2630939	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2630940	2631008	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2630940	2631008	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2631009	2631233	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2631234	2631356	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2631234	2631356	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2631357	2631480	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2631481	2631582	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2631481	2631582	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2631583	2631732	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2631733	2631807	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2631733	2631807	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2631808	2631934	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2631935	2632025	1	-	1	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2631935	2632025	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2632026	2632371	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2632372	2632442	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2632372	2632442	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2632443	2632681	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2632682	2632863	1	-	2	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2632682	2632863	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2632864	2633095	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2633096	2633180	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2633096	2633180	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2633181	2633302	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2633303	2633389	1	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2633303	2633389	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2633390	2633529	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2633530	2633632	1	-	1	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2633530	2633632	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2633633	2634430	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2634431	2634558	0.66	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2634431	2634558	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	intron	2634559	2634645	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	CDS	2634646	2634657	0.55	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	exon	2634646	2634657	.	-	.	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
Phchi.S2	AUGUSTUS	start_codon	2634655	2634657	.	-	0	transcript_id "Phchi.S2G017600.t1"; gene_id "Phchi.S2G017600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14085.t1 is derived from g12552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10786665	10788457	.	-	.	Phchi.S3G140400
Phchi.S3	AUGUSTUS	transcript	10786665	10788457	.	-	.	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	stop_codon	10786662	10786664	.	-	0	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	CDS	10786665	10787191	1	-	2	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	exon	10786665	10787191	.	-	.	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	intron	10787192	10787295	.	-	.	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	CDS	10787296	10788142	0.73	-	0	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	exon	10787296	10788142	.	-	.	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	intron	10788143	10788427	.	-	.	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	CDS	10788428	10788457	0.73	-	0	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	exon	10788428	10788457	.	-	.	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
Phchi.S3	AUGUSTUS	start_codon	10788455	10788457	.	-	0	transcript_id "Phchi.S3G140400.t1"; gene_id "Phchi.S3G140400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg127.t1 is derived from g9909.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	702948	705332	.	-	.	Phchi.S6G008600
Phchi.S6	AUGUSTUS	transcript	702948	705332	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	stop_codon	702945	702947	.	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	702948	702986	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	702948	702986	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	702987	703083	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	703084	703158	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	703084	703158	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	703159	703271	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	703272	703367	0.99	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	703272	703367	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	703368	703450	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	703451	703519	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	703451	703519	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	703520	703643	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	703644	703709	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	703644	703709	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	703710	703793	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	703794	703852	1	-	2	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	703794	703852	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	703853	703936	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	703937	703994	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	703937	703994	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	703995	704127	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	704128	704214	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	704128	704214	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	704215	704362	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	704363	704464	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	704363	704464	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	704465	704550	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	704551	704613	1	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	704551	704613	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	704614	704707	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	704708	704800	0.99	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	704708	704800	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	704801	704851	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	704852	704884	0.98	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	704852	704884	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	intron	704885	705032	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	CDS	705033	705332	0.97	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	exon	705033	705332	.	-	.	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
Phchi.S6	AUGUSTUS	start_codon	705330	705332	.	-	0	transcript_id "Phchi.S6G008600.t1"; gene_id "Phchi.S6G008600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6653.t1 is derived from g3825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24314091	24314819	.	+	.	Phchi.S1G381200
Phchi.S1	AUGUSTUS	transcript	24314091	24314819	.	+	.	transcript_id "Phchi.S1G381200.t1"; gene_id "Phchi.S1G381200"
Phchi.S1	AUGUSTUS	start_codon	24314091	24314093	.	+	0	transcript_id "Phchi.S1G381200.t1"; gene_id "Phchi.S1G381200"
Phchi.S1	AUGUSTUS	CDS	24314091	24314819	0.34	+	0	transcript_id "Phchi.S1G381200.t1"; gene_id "Phchi.S1G381200"
Phchi.S1	AUGUSTUS	exon	24314091	24314819	.	+	.	transcript_id "Phchi.S1G381200.t1"; gene_id "Phchi.S1G381200"
Phchi.S1	AUGUSTUS	stop_codon	24314820	24314822	.	+	0	transcript_id "Phchi.S1G381200.t1"; gene_id "Phchi.S1G381200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg424.t1 is derived from g10206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3016677	3018082	.	+	.	Phchi.S6G038300
Phchi.S6	AUGUSTUS	transcript	3016677	3018082	.	+	.	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	start_codon	3016677	3016679	.	+	0	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	CDS	3016677	3017346	0.48	+	0	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	exon	3016677	3017346	.	+	.	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	intron	3017347	3017468	.	+	.	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	CDS	3017469	3017699	0.9	+	2	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	exon	3017469	3017699	.	+	.	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	intron	3017700	3017786	.	+	.	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	CDS	3017787	3018082	0.87	+	2	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	exon	3017787	3018082	.	+	.	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
Phchi.S6	AUGUSTUS	stop_codon	3018083	3018085	.	+	0	transcript_id "Phchi.S6G038300.t1"; gene_id "Phchi.S6G038300"
# This transcript jg12073.t2 is derived from g7748.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12074.t1 is derived from g7749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2115001	2119093	.	-	.	Phchi.S2G015400
Phchi.S2	AUGUSTUS	transcript	2115001	2119093	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	stop_codon	2114998	2115000	.	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2115001	2115242	0.61	-	2	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2115001	2115242	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2115243	2115363	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2115364	2115487	1	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2115364	2115487	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2115488	2115593	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2115594	2115809	1	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2115594	2115809	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2115810	2115938	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2115939	2116067	1	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2115939	2116067	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2116068	2116182	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2116183	2116429	0.99	-	1	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2116183	2116429	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2116430	2116512	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2116513	2116845	1	-	1	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2116513	2116845	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2116846	2116932	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2116933	2117159	0.98	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2116933	2117159	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2117160	2117368	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2117369	2117423	1	-	1	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2117369	2117423	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	intron	2117424	2117540	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	CDS	2117541	2119093	1	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	exon	2117541	2119093	.	-	.	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
Phchi.S2	AUGUSTUS	start_codon	2119091	2119093	.	-	0	transcript_id "Phchi.S2G015400.t1"; gene_id "Phchi.S2G015400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13309.t1 is derived from g11775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5696550	5698624	.	+	.	Phchi.S3G062800
Phchi.S3	AUGUSTUS	transcript	5696550	5698624	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	start_codon	5696550	5696552	.	+	0	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	CDS	5696550	5696938	1	+	0	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	exon	5696550	5696938	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	intron	5696939	5697048	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	CDS	5697049	5697337	1	+	1	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	exon	5697049	5697337	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	intron	5697338	5697451	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	CDS	5697452	5697745	1	+	0	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	exon	5697452	5697745	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	intron	5697746	5697885	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	CDS	5697886	5698253	1	+	0	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	exon	5697886	5698253	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	intron	5698254	5698371	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	CDS	5698372	5698624	1	+	1	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	exon	5698372	5698624	.	+	.	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
Phchi.S3	AUGUSTUS	stop_codon	5698625	5698627	.	+	0	transcript_id "Phchi.S3G062800.t1"; gene_id "Phchi.S3G062800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10034.t1 is derived from g7210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45175823	45177171	.	-	.	Phchi.S1G719300
Phchi.S1	AUGUSTUS	transcript	45175823	45177171	.	-	.	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	stop_codon	45175820	45175822	.	-	0	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	CDS	45175823	45176770	0.9	-	0	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	exon	45175823	45176770	.	-	.	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	intron	45176771	45176841	.	-	.	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	CDS	45176842	45177171	0.27	-	0	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	exon	45176842	45177171	.	-	.	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
Phchi.S1	AUGUSTUS	start_codon	45177169	45177171	.	-	0	transcript_id "Phchi.S1G719300.t1"; gene_id "Phchi.S1G719300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11690.t1 is derived from g15741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7691823	7693611	.	-	.	Phchi.S4G127200
Phchi.S4	AUGUSTUS	transcript	7691823	7693611	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	stop_codon	7691820	7691822	.	-	0	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	CDS	7691823	7691907	0.98	-	1	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	exon	7691823	7691907	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	intron	7691908	7691990	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	CDS	7691991	7692021	1	-	2	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	exon	7691991	7692021	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	intron	7692022	7692115	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	CDS	7692116	7693447	0.93	-	2	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	exon	7692116	7693447	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	intron	7693448	7693541	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	CDS	7693542	7693611	1	-	0	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	exon	7693542	7693611	.	-	.	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
Phchi.S4	AUGUSTUS	start_codon	7693609	7693611	.	-	0	transcript_id "Phchi.S4G127200.t1"; gene_id "Phchi.S4G127200"
# This transcript jg11240.t2 is derived from g15290.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11241.t1 is derived from g15291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4965649	4968930	.	+	.	Phchi.S4G082300
Phchi.S4	AUGUSTUS	transcript	4965649	4967664	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	start_codon	4965649	4965651	.	+	0	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4965649	4966128	0.99	+	0	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4965649	4966128	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4966129	4966376	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4966377	4966730	0.96	+	0	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4966377	4966730	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4966731	4966881	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4966882	4967048	0.93	+	0	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4966882	4967048	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4967049	4967213	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4967214	4967664	0.95	+	1	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4967214	4967664	.	+	.	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	stop_codon	4967665	4967667	.	+	0	transcript_id "Phchi.S4G082300.t1"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	transcript	4965649	4968930	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	start_codon	4965649	4965651	.	+	0	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4965649	4966128	0.99	+	0	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4965649	4966128	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4966129	4966376	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4966377	4966730	0.98	+	0	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4966377	4966730	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4966731	4966881	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4966882	4967048	0.91	+	0	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4966882	4967048	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4967049	4967213	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4967214	4967659	0.99	+	1	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4967214	4967659	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4967660	4967832	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4967833	4968255	0.98	+	2	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4967833	4968255	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	intron	4968256	4968358	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	CDS	4968359	4968930	0.74	+	2	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	exon	4968359	4968930	.	+	.	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
Phchi.S4	AUGUSTUS	stop_codon	4968931	4968933	.	+	0	transcript_id "Phchi.S4G082300.t2"; gene_id "Phchi.S4G082300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11803.t1 is derived from g15855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8213683	8215218	.	-	.	Phchi.S4G138500
Phchi.S4	AUGUSTUS	transcript	8213683	8215218	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	stop_codon	8213680	8213682	.	-	0	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	CDS	8213683	8213687	1	-	2	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	exon	8213683	8213687	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	intron	8213688	8213767	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	CDS	8213768	8213828	1	-	0	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	exon	8213768	8213828	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	intron	8213829	8213917	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	CDS	8213918	8214056	1	-	1	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	exon	8213918	8214056	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	intron	8214057	8214142	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	CDS	8214143	8214587	1	-	2	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	exon	8214143	8214587	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	intron	8214588	8214677	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	CDS	8214678	8215218	0.97	-	0	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	exon	8214678	8215218	.	-	.	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
Phchi.S4	AUGUSTUS	start_codon	8215216	8215218	.	-	0	transcript_id "Phchi.S4G138500.t1"; gene_id "Phchi.S4G138500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11978.t1 is derived from g7653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	271771	272136	.	-	.	Phchi.S2G005800
Phchi.S2	AUGUSTUS	transcript	271771	272136	.	-	.	transcript_id "Phchi.S2G005800.t1"; gene_id "Phchi.S2G005800"
Phchi.S2	AUGUSTUS	stop_codon	271768	271770	.	-	0	transcript_id "Phchi.S2G005800.t1"; gene_id "Phchi.S2G005800"
Phchi.S2	AUGUSTUS	CDS	271771	272136	0.25	-	0	transcript_id "Phchi.S2G005800.t1"; gene_id "Phchi.S2G005800"
Phchi.S2	AUGUSTUS	exon	271771	272136	.	-	.	transcript_id "Phchi.S2G005800.t1"; gene_id "Phchi.S2G005800"
Phchi.S2	AUGUSTUS	start_codon	272134	272136	.	-	0	transcript_id "Phchi.S2G005800.t1"; gene_id "Phchi.S2G005800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12599.t1 is derived from g8276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37402635	37404080	.	+	.	Phchi.S2G067900
Phchi.S2	AUGUSTUS	transcript	37402635	37404080	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	start_codon	37402635	37402637	.	+	0	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	CDS	37402635	37402758	1	+	0	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	exon	37402635	37402758	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	intron	37402759	37403036	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	CDS	37403037	37403196	1	+	2	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	exon	37403037	37403196	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	intron	37403197	37403355	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	CDS	37403356	37403436	1	+	1	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	exon	37403356	37403436	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	intron	37403437	37403757	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	CDS	37403758	37403881	1	+	1	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	exon	37403758	37403881	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	intron	37403882	37404029	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	CDS	37404030	37404080	1	+	0	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	exon	37404030	37404080	.	+	.	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
Phchi.S2	AUGUSTUS	stop_codon	37404081	37404083	.	+	0	transcript_id "Phchi.S2G067900.t1"; gene_id "Phchi.S2G067900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14575.t1 is derived from g13043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13547827	13548933	.	+	.	Phchi.S3G189400
Phchi.S3	AUGUSTUS	transcript	13547827	13548933	.	+	.	transcript_id "Phchi.S3G189400.t1"; gene_id "Phchi.S3G189400"
Phchi.S3	AUGUSTUS	start_codon	13547827	13547829	.	+	0	transcript_id "Phchi.S3G189400.t1"; gene_id "Phchi.S3G189400"
Phchi.S3	AUGUSTUS	CDS	13547827	13548933	1	+	0	transcript_id "Phchi.S3G189400.t1"; gene_id "Phchi.S3G189400"
Phchi.S3	AUGUSTUS	exon	13547827	13548933	.	+	.	transcript_id "Phchi.S3G189400.t1"; gene_id "Phchi.S3G189400"
Phchi.S3	AUGUSTUS	stop_codon	13548934	13548936	.	+	0	transcript_id "Phchi.S3G189400.t1"; gene_id "Phchi.S3G189400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5094.t1 is derived from g2264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14716058	14716651	.	+	.	Phchi.S1G225300
Phchi.S1	AUGUSTUS	transcript	14716058	14716651	.	+	.	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	start_codon	14716058	14716060	.	+	0	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	CDS	14716058	14716176	0.67	+	0	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	exon	14716058	14716176	.	+	.	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	intron	14716177	14716439	.	+	.	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	CDS	14716440	14716517	0.95	+	1	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	exon	14716440	14716517	.	+	.	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	intron	14716518	14716590	.	+	.	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	CDS	14716591	14716651	1	+	1	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	exon	14716591	14716651	.	+	.	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
Phchi.S1	AUGUSTUS	stop_codon	14716652	14716654	.	+	0	transcript_id "Phchi.S1G225300.t1"; gene_id "Phchi.S1G225300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14348.t1 is derived from g12815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12322239	12324707	.	+	.	Phchi.S3G166700
Phchi.S3	AUGUSTUS	transcript	12322239	12324707	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	start_codon	12322239	12322241	.	+	0	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12322239	12322284	1	+	0	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12322239	12322284	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12322285	12322702	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12322703	12322831	0.98	+	2	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12322703	12322831	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12322832	12322940	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12322941	12322980	1	+	2	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12322941	12322980	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12322981	12323300	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12323301	12323376	1	+	1	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12323301	12323376	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12323377	12323471	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12323472	12323672	1	+	0	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12323472	12323672	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12323673	12323800	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12323801	12324013	1	+	0	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12323801	12324013	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12324014	12324143	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12324144	12324352	0.91	+	0	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12324144	12324352	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	intron	12324353	12324673	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	CDS	12324674	12324707	0.52	+	1	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	exon	12324674	12324707	.	+	.	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
Phchi.S3	AUGUSTUS	stop_codon	12324708	12324710	.	+	0	transcript_id "Phchi.S3G166700.t1"; gene_id "Phchi.S3G166700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6092.t1 is derived from g3263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20922437	20926101	.	+	.	Phchi.S1G325100
Phchi.S1	AUGUSTUS	transcript	20922437	20926101	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	start_codon	20922437	20922439	.	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20922437	20922650	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20922437	20922650	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20922651	20923240	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20923241	20923326	0.99	+	2	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20923241	20923326	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20923327	20923437	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20923438	20923509	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20923438	20923509	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20923510	20923602	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20923603	20923716	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20923603	20923716	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20923717	20923837	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20923838	20923906	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20923838	20923906	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20923907	20924031	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20924032	20924088	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20924032	20924088	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20924089	20924190	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20924191	20924244	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20924191	20924244	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20924245	20924365	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20924366	20924428	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20924366	20924428	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20924429	20924539	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20924540	20924602	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20924540	20924602	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20924603	20924679	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20924680	20924745	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20924680	20924745	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20924746	20924891	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20924892	20925056	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20924892	20925056	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20925057	20925140	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20925141	20925296	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20925141	20925296	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20925297	20925379	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20925380	20925460	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20925380	20925460	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20925461	20925580	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20925581	20925654	1	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20925581	20925654	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20925655	20925923	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20925924	20925989	0.99	+	1	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20925924	20925989	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	intron	20925990	20926076	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	CDS	20926077	20926101	0.99	+	1	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	exon	20926077	20926101	.	+	.	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
Phchi.S1	AUGUSTUS	stop_codon	20926102	20926104	.	+	0	transcript_id "Phchi.S1G325100.t1"; gene_id "Phchi.S1G325100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6407.t1 is derived from g3579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22811659	22812798	.	-	.	Phchi.S1G356600
Phchi.S1	AUGUSTUS	transcript	22811659	22812798	.	-	.	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	stop_codon	22811656	22811658	.	-	0	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	CDS	22811659	22812636	0.69	-	0	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	exon	22811659	22812636	.	-	.	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	intron	22812637	22812720	.	-	.	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	CDS	22812721	22812798	0.88	-	0	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	exon	22812721	22812798	.	-	.	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
Phchi.S1	AUGUSTUS	start_codon	22812796	22812798	.	-	0	transcript_id "Phchi.S1G356600.t1"; gene_id "Phchi.S1G356600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9845.t1 is derived from g7021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44044947	44045440	.	-	.	Phchi.S1G700400
Phchi.S1	AUGUSTUS	transcript	44044947	44045440	.	-	.	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	stop_codon	44044944	44044946	.	-	0	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	CDS	44044947	44045222	0.45	-	0	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	exon	44044947	44045222	.	-	.	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	intron	44045223	44045335	.	-	.	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	CDS	44045336	44045440	0.45	-	0	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	exon	44045336	44045440	.	-	.	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
Phchi.S1	AUGUSTUS	start_codon	44045438	44045440	.	-	0	transcript_id "Phchi.S1G700400.t1"; gene_id "Phchi.S1G700400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12235.t1 is derived from g7911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6925069	6927180	.	-	.	Phchi.S2G031500
Phchi.S2	AUGUSTUS	transcript	6925069	6927180	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	stop_codon	6925066	6925068	.	-	0	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	CDS	6925069	6925392	0.69	-	0	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	exon	6925069	6925392	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	intron	6925393	6925472	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	CDS	6925473	6925521	1	-	1	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	exon	6925473	6925521	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	intron	6925522	6925629	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	CDS	6925630	6926123	0.96	-	0	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	exon	6925630	6926123	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	intron	6926124	6926218	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	CDS	6926219	6926430	1	-	2	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	exon	6926219	6926430	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	intron	6926431	6926527	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	CDS	6926528	6926696	1	-	0	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	exon	6926528	6926696	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	intron	6926697	6926784	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	CDS	6926785	6927180	0.55	-	0	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	exon	6926785	6927180	.	-	.	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
Phchi.S2	AUGUSTUS	start_codon	6927178	6927180	.	-	0	transcript_id "Phchi.S2G031500.t1"; gene_id "Phchi.S2G031500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8666.t1 is derived from g5841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37352329	37355301	.	+	.	Phchi.S1G582500
Phchi.S1	AUGUSTUS	transcript	37352329	37355301	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	start_codon	37352329	37352331	.	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37352329	37352382	0.91	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37352329	37352382	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37352383	37352482	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37352483	37352524	0.98	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37352483	37352524	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37352525	37352661	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37352662	37352787	0.96	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37352662	37352787	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37352788	37352900	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37352901	37353062	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37352901	37353062	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37353063	37353171	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37353172	37353199	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37353172	37353199	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37353200	37353280	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37353281	37353349	1	+	2	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37353281	37353349	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37353350	37353437	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37353438	37353532	0.91	+	2	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37353438	37353532	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37353533	37353679	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37353680	37353692	0.88	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37353680	37353692	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37353693	37353814	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37353815	37353888	0.97	+	2	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37353815	37353888	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37353889	37353977	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37353978	37354166	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37353978	37354166	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37354167	37354244	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37354245	37354395	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37354245	37354395	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37354396	37354492	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37354493	37354569	1	+	2	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37354493	37354569	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37354570	37354649	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37354650	37354713	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37354650	37354713	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37354714	37354800	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37354801	37354958	1	+	2	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37354801	37354958	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37354959	37355045	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37355046	37355180	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37355046	37355180	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	intron	37355181	37355253	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	CDS	37355254	37355301	1	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	exon	37355254	37355301	.	+	.	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
Phchi.S1	AUGUSTUS	stop_codon	37355302	37355304	.	+	0	transcript_id "Phchi.S1G582500.t1"; gene_id "Phchi.S1G582500"
# This transcript jg6191.t2 is derived from g3362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6192.t1 is derived from g3363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21408510	21409561	.	-	.	Phchi.S1G335100
Phchi.S1	AUGUSTUS	transcript	21408510	21409561	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	stop_codon	21408507	21408509	.	-	0	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	CDS	21408510	21408615	0.76	-	1	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	exon	21408510	21408615	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	intron	21408616	21408720	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	CDS	21408721	21408827	0.76	-	0	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	exon	21408721	21408827	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	intron	21408828	21408957	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	CDS	21408958	21409069	1	-	1	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	exon	21408958	21409069	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	intron	21409070	21409312	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	CDS	21409313	21409432	1	-	1	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	exon	21409313	21409432	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	intron	21409433	21409532	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	CDS	21409533	21409561	0.98	-	0	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	exon	21409533	21409561	.	-	.	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
Phchi.S1	AUGUSTUS	start_codon	21409559	21409561	.	-	0	transcript_id "Phchi.S1G335100.t1"; gene_id "Phchi.S1G335100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10464.t1 is derived from g14513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	494092	494770	.	-	.	Phchi.S4G004600
Phchi.S4	AUGUSTUS	transcript	494092	494770	.	-	.	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	stop_codon	494089	494091	.	-	0	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	CDS	494092	494159	0.68	-	2	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	exon	494092	494159	.	-	.	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	intron	494160	494252	.	-	.	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	CDS	494253	494303	0.36	-	2	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	exon	494253	494303	.	-	.	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	intron	494304	494499	.	-	.	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	CDS	494500	494770	0.17	-	0	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	exon	494500	494770	.	-	.	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
Phchi.S4	AUGUSTUS	start_codon	494768	494770	.	-	0	transcript_id "Phchi.S4G004600.t1"; gene_id "Phchi.S4G004600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1441.t1 is derived from g8360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	874514	876082	.	-	.	Phchi.S5G005000
Phchi.S5	AUGUSTUS	transcript	874514	876082	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	stop_codon	874511	874513	.	-	0	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	CDS	874514	874773	0.98	-	2	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	exon	874514	874773	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	intron	874774	874874	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	CDS	874875	875145	0.95	-	0	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	exon	874875	875145	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	intron	875146	875270	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	CDS	875271	875440	0.64	-	2	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	exon	875271	875440	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	intron	875441	875551	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	CDS	875552	875593	0.57	-	2	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	exon	875552	875593	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	intron	875594	875829	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	CDS	875830	876082	0.95	-	0	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	exon	875830	876082	.	-	.	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
Phchi.S5	AUGUSTUS	start_codon	876080	876082	.	-	0	transcript_id "Phchi.S5G005000.t1"; gene_id "Phchi.S5G005000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10043.t1 is derived from g7219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45222489	45223069	.	+	.	Phchi.S1G720200
Phchi.S1	AUGUSTUS	transcript	45222489	45223069	.	+	.	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	start_codon	45222489	45222491	.	+	0	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	CDS	45222489	45222615	0.97	+	0	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	exon	45222489	45222615	.	+	.	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	intron	45222616	45222733	.	+	.	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	CDS	45222734	45222865	1	+	2	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	exon	45222734	45222865	.	+	.	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	intron	45222866	45222965	.	+	.	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	CDS	45222966	45223069	1	+	2	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	exon	45222966	45223069	.	+	.	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
Phchi.S1	AUGUSTUS	stop_codon	45223070	45223072	.	+	0	transcript_id "Phchi.S1G720200.t1"; gene_id "Phchi.S1G720200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9524.t1 is derived from g6700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42267303	42270844	.	-	.	Phchi.S1G668300
Phchi.S1	AUGUSTUS	transcript	42267303	42270844	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	stop_codon	42267300	42267302	.	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42267303	42267354	1	-	1	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42267303	42267354	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42267355	42267871	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42267872	42268096	1	-	1	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42267872	42268096	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42268097	42269041	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42269042	42269116	0.86	-	1	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42269042	42269116	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42269117	42269196	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42269197	42269267	0.99	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42269197	42269267	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42269268	42269359	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42269360	42269485	1	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42269360	42269485	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42269486	42269570	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42269571	42269678	1	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42269571	42269678	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42269679	42269798	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42269799	42269862	1	-	1	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42269799	42269862	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42269863	42269993	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42269994	42270147	0.99	-	2	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42269994	42270147	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42270148	42270254	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42270255	42270426	1	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42270255	42270426	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	intron	42270427	42270628	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	CDS	42270629	42270844	0.72	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	exon	42270629	42270844	.	-	.	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
Phchi.S1	AUGUSTUS	start_codon	42270842	42270844	.	-	0	transcript_id "Phchi.S1G668300.t1"; gene_id "Phchi.S1G668300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15043.t1 is derived from g13511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16714813	16715927	.	-	.	Phchi.S3G236200
Phchi.S3	AUGUSTUS	transcript	16714813	16715927	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	stop_codon	16714810	16714812	.	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	CDS	16714813	16714818	1	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	exon	16714813	16714818	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	intron	16714819	16714911	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	CDS	16714912	16715013	1	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	exon	16714912	16715013	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	intron	16715014	16715098	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	CDS	16715099	16715305	1	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	exon	16715099	16715305	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	intron	16715306	16715422	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	CDS	16715423	16715758	0.99	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	exon	16715423	16715758	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	intron	16715759	16715846	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	CDS	16715847	16715927	0.62	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	exon	16715847	16715927	.	-	.	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
Phchi.S3	AUGUSTUS	start_codon	16715925	16715927	.	-	0	transcript_id "Phchi.S3G236200.t1"; gene_id "Phchi.S3G236200"
# This transcript jg5144.t2 is derived from g2314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5145.t1 is derived from g2315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15138296	15140488	.	+	.	Phchi.S1G230400
Phchi.S1	AUGUSTUS	transcript	15138296	15140488	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	start_codon	15138296	15138298	.	+	0	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15138296	15138338	0.88	+	0	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15138296	15138338	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	intron	15138339	15138476	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15138477	15138486	0.95	+	2	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15138477	15138486	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	intron	15138487	15138609	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15138610	15138653	0.99	+	1	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15138610	15138653	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	intron	15138654	15138833	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15138834	15139120	1	+	2	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15138834	15139120	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	intron	15139121	15139243	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15139244	15139295	1	+	0	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15139244	15139295	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	intron	15139296	15139486	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15139487	15139554	1	+	2	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15139487	15139554	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	intron	15139555	15139654	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	CDS	15139655	15140488	0.53	+	0	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	exon	15139655	15140488	.	+	.	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
Phchi.S1	AUGUSTUS	stop_codon	15140489	15140491	.	+	0	transcript_id "Phchi.S1G230400.t1"; gene_id "Phchi.S1G230400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10980.t1 is derived from g15030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3501505	3504254	.	-	.	Phchi.S4G056200
Phchi.S4	AUGUSTUS	transcript	3501505	3504254	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	stop_codon	3501502	3501504	.	-	0	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	CDS	3501505	3502426	0.15	-	1	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	exon	3501505	3502426	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	intron	3502427	3502777	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	CDS	3502778	3503358	0.34	-	0	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	exon	3502778	3503358	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	intron	3503359	3503535	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	CDS	3503536	3503617	0.61	-	1	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	exon	3503536	3503617	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	intron	3503618	3503714	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	CDS	3503715	3503878	1	-	0	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	exon	3503715	3503878	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	intron	3503879	3503967	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	CDS	3503968	3504041	1	-	2	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	exon	3503968	3504041	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	intron	3504042	3504127	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	CDS	3504128	3504254	1	-	0	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	exon	3504128	3504254	.	-	.	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
Phchi.S4	AUGUSTUS	start_codon	3504252	3504254	.	-	0	transcript_id "Phchi.S4G056200.t1"; gene_id "Phchi.S4G056200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3500.t1 is derived from g669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4111037	4111636	.	-	.	Phchi.S1G065900
Phchi.S1	AUGUSTUS	transcript	4111037	4111636	.	-	.	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	stop_codon	4111034	4111036	.	-	0	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	CDS	4111037	4111360	1	-	0	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	exon	4111037	4111360	.	-	.	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	intron	4111361	4111450	.	-	.	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	CDS	4111451	4111636	0.76	-	0	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	exon	4111451	4111636	.	-	.	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
Phchi.S1	AUGUSTUS	start_codon	4111634	4111636	.	-	0	transcript_id "Phchi.S1G065900.t1"; gene_id "Phchi.S1G065900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5393.t1 is derived from g2563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16649839	16652074	.	+	.	Phchi.S1G255200
Phchi.S1	AUGUSTUS	transcript	16649839	16652074	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	start_codon	16649839	16649841	.	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16649839	16649919	1	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16649839	16649919	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16649920	16650010	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16650011	16650229	1	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16650011	16650229	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16650230	16650306	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16650307	16650402	0.99	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16650307	16650402	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16650403	16650522	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16650523	16650617	0.99	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16650523	16650617	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16650618	16650741	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16650742	16650870	1	+	1	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16650742	16650870	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16650871	16651000	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16651001	16651121	0.99	+	1	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16651001	16651121	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16651122	16651236	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16651237	16651333	1	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16651237	16651333	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16651334	16651460	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16651461	16651573	0.99	+	2	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16651461	16651573	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16651574	16651670	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16651671	16651795	1	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16651671	16651795	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	intron	16651796	16651908	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	CDS	16651909	16652074	0.89	+	1	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	exon	16651909	16652074	.	+	.	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
Phchi.S1	AUGUSTUS	stop_codon	16652075	16652077	.	+	0	transcript_id "Phchi.S1G255200.t1"; gene_id "Phchi.S1G255200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5855.t1 is derived from g3025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19377416	19381821	.	-	.	Phchi.S1G301400
Phchi.S1	AUGUSTUS	transcript	19377416	19381821	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	stop_codon	19377413	19377415	.	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19377416	19377661	0.92	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19377416	19377661	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19377662	19377758	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19377759	19377842	0.74	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19377759	19377842	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19377843	19378021	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19378022	19378176	0.52	-	2	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19378022	19378176	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19378177	19378341	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19378342	19378410	1	-	2	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19378342	19378410	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19378411	19378495	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19378496	19378628	1	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19378496	19378628	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19378629	19378712	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19378713	19378936	1	-	2	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19378713	19378936	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19378937	19379027	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19379028	19379076	0.77	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19379028	19379076	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19379077	19379186	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19379187	19379325	0.65	-	1	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19379187	19379325	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19379326	19379423	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19379424	19379492	1	-	1	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19379424	19379492	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19379493	19379731	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19379732	19379803	1	-	1	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19379732	19379803	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19379804	19379901	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19379902	19379973	1	-	1	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19379902	19379973	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19379974	19380045	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19380046	19380160	1	-	2	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19380046	19380160	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19380161	19380272	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19380273	19380511	1	-	1	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19380273	19380511	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19380512	19380603	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19380604	19380876	1	-	1	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19380604	19380876	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19380877	19381002	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19381003	19381576	0.87	-	2	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19381003	19381576	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	intron	19381577	19381727	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	CDS	19381728	19381821	0.58	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	exon	19381728	19381821	.	-	.	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
Phchi.S1	AUGUSTUS	start_codon	19381819	19381821	.	-	0	transcript_id "Phchi.S1G301400.t1"; gene_id "Phchi.S1G301400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11934.t1 is derived from g7609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	94063	95019	.	-	.	Phchi.S2G001400
Phchi.S2	AUGUSTUS	transcript	94063	95019	.	-	.	transcript_id "Phchi.S2G001400.t1"; gene_id "Phchi.S2G001400"
Phchi.S2	AUGUSTUS	stop_codon	94060	94062	.	-	0	transcript_id "Phchi.S2G001400.t1"; gene_id "Phchi.S2G001400"
Phchi.S2	AUGUSTUS	CDS	94063	95019	0.97	-	0	transcript_id "Phchi.S2G001400.t1"; gene_id "Phchi.S2G001400"
Phchi.S2	AUGUSTUS	exon	94063	95019	.	-	.	transcript_id "Phchi.S2G001400.t1"; gene_id "Phchi.S2G001400"
Phchi.S2	AUGUSTUS	start_codon	95017	95019	.	-	0	transcript_id "Phchi.S2G001400.t1"; gene_id "Phchi.S2G001400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3576.t1 is derived from g745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4591418	4592774	.	+	.	Phchi.S1G073500
Phchi.S1	AUGUSTUS	transcript	4591418	4592774	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	start_codon	4591418	4591420	.	+	0	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	CDS	4591418	4591509	0.86	+	0	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	exon	4591418	4591509	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	intron	4591510	4591583	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	CDS	4591584	4591860	0.89	+	1	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	exon	4591584	4591860	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	intron	4591861	4592140	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	CDS	4592141	4592282	0.93	+	0	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	exon	4592141	4592282	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	intron	4592283	4592376	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	CDS	4592377	4592457	1	+	2	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	exon	4592377	4592457	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	intron	4592458	4592552	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	CDS	4592553	4592596	1	+	2	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	exon	4592553	4592596	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	intron	4592597	4592696	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	CDS	4592697	4592774	1	+	0	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	exon	4592697	4592774	.	+	.	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
Phchi.S1	AUGUSTUS	stop_codon	4592775	4592777	.	+	0	transcript_id "Phchi.S1G073500.t1"; gene_id "Phchi.S1G073500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6068.t1 is derived from g3239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20715302	20719124	.	-	.	Phchi.S1G322700
Phchi.S1	AUGUSTUS	transcript	20715302	20719124	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	stop_codon	20715299	20715301	.	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20715302	20715392	0.99	-	1	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20715302	20715392	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20715393	20715491	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20715492	20715628	1	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20715492	20715628	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20715629	20715713	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20715714	20715994	0.78	-	2	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20715714	20715994	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20715995	20716179	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20716180	20716252	0.63	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20716180	20716252	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20716253	20716356	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20716357	20716401	1	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20716357	20716401	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20716402	20716506	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20716507	20716611	1	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20716507	20716611	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20716612	20716706	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20716707	20716965	1	-	1	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20716707	20716965	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20716966	20717058	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20717059	20717176	0.96	-	2	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20717059	20717176	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20717177	20717262	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20717263	20717395	0.95	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20717263	20717395	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20717396	20717506	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20717507	20717578	1	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20717507	20717578	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20717579	20717672	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20717673	20717721	0.98	-	1	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20717673	20717721	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20717722	20717815	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20717816	20718302	0.99	-	2	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20717816	20718302	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20718303	20718405	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20718406	20718727	0.99	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20718406	20718727	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	intron	20718728	20718824	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	CDS	20718825	20719124	0.77	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	exon	20718825	20719124	.	-	.	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
Phchi.S1	AUGUSTUS	start_codon	20719122	20719124	.	-	0	transcript_id "Phchi.S1G322700.t1"; gene_id "Phchi.S1G322700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8976.t1 is derived from g6151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38936039	38939722	.	-	.	Phchi.S1G613500
Phchi.S1	AUGUSTUS	transcript	38936039	38939722	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	stop_codon	38936036	38936038	.	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38936039	38936107	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38936039	38936107	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38936108	38936190	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38936191	38936357	1	-	2	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38936191	38936357	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38936358	38936447	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38936448	38936553	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38936448	38936553	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38936554	38936647	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38936648	38936685	1	-	2	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38936648	38936685	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38936686	38936771	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38936772	38936859	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38936772	38936859	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38936860	38936980	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38936981	38937034	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38936981	38937034	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38937035	38937118	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38937119	38937227	1	-	1	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38937119	38937227	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38937228	38937337	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38937338	38937420	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38937338	38937420	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38937421	38937492	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38937493	38937555	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38937493	38937555	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38937556	38937639	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38937640	38937702	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38937640	38937702	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38937703	38937795	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38937796	38937894	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38937796	38937894	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38937895	38938061	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38938062	38938121	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38938062	38938121	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38938122	38938235	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38938236	38938294	1	-	2	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38938236	38938294	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38938295	38938429	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38938430	38938544	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38938430	38938544	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38938545	38938684	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38938685	38938854	1	-	2	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38938685	38938854	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38938855	38938999	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38939000	38939103	1	-	1	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38939000	38939103	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38939104	38939182	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38939183	38939277	1	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38939183	38939277	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38939278	38939373	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38939374	38939456	1	-	2	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38939374	38939456	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	intron	38939457	38939538	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	CDS	38939539	38939722	0.99	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	exon	38939539	38939722	.	-	.	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
Phchi.S1	AUGUSTUS	start_codon	38939720	38939722	.	-	0	transcript_id "Phchi.S1G613500.t1"; gene_id "Phchi.S1G613500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4392.t1 is derived from g1561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10209218	10209855	.	-	.	Phchi.S1G155100
Phchi.S1	AUGUSTUS	transcript	10209218	10209855	.	-	.	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	stop_codon	10209215	10209217	.	-	0	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	CDS	10209218	10209390	0.95	-	2	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	exon	10209218	10209390	.	-	.	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	intron	10209391	10209514	.	-	.	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	CDS	10209515	10209764	0.99	-	0	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	exon	10209515	10209764	.	-	.	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	intron	10209765	10209852	.	-	.	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	CDS	10209853	10209855	0.6	-	0	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	exon	10209853	10209855	.	-	.	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
Phchi.S1	AUGUSTUS	start_codon	10209853	10209855	.	-	0	transcript_id "Phchi.S1G155100.t1"; gene_id "Phchi.S1G155100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13232.t1 is derived from g11697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4802695	4804053	.	+	.	Phchi.S3G055100
Phchi.S3	AUGUSTUS	transcript	4802695	4804053	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	start_codon	4802695	4802697	.	+	0	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	CDS	4802695	4802763	0.6	+	0	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	exon	4802695	4802763	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	intron	4802764	4802960	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	CDS	4802961	4803151	0.42	+	0	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	exon	4802961	4803151	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	intron	4803152	4803318	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	CDS	4803319	4803392	0.99	+	1	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	exon	4803319	4803392	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	intron	4803393	4803549	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	CDS	4803550	4803576	0.58	+	2	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	exon	4803550	4803576	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	intron	4803577	4803979	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	CDS	4803980	4804053	0.48	+	2	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	exon	4803980	4804053	.	+	.	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
Phchi.S3	AUGUSTUS	stop_codon	4804054	4804056	.	+	0	transcript_id "Phchi.S3G055100.t1"; gene_id "Phchi.S3G055100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13020.t1 is derived from g11485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3653299	3653731	.	+	.	Phchi.S3G033900
Phchi.S3	AUGUSTUS	transcript	3653299	3653731	.	+	.	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	start_codon	3653299	3653301	.	+	0	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	CDS	3653299	3653352	0.95	+	0	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	exon	3653299	3653352	.	+	.	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	intron	3653353	3653469	.	+	.	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	CDS	3653470	3653529	1	+	0	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	exon	3653470	3653529	.	+	.	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	intron	3653530	3653620	.	+	.	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	CDS	3653621	3653731	1	+	0	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	exon	3653621	3653731	.	+	.	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
Phchi.S3	AUGUSTUS	stop_codon	3653732	3653734	.	+	0	transcript_id "Phchi.S3G033900.t1"; gene_id "Phchi.S3G033900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9460.t1 is derived from g6636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41567507	41568724	.	+	.	Phchi.S1G661900
Phchi.S1	AUGUSTUS	transcript	41567507	41568724	.	+	.	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	start_codon	41567507	41567509	.	+	0	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	CDS	41567507	41567843	0.85	+	0	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	exon	41567507	41567843	.	+	.	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	intron	41567844	41567921	.	+	.	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	CDS	41567922	41567979	1	+	2	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	exon	41567922	41567979	.	+	.	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	intron	41567980	41568093	.	+	.	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	CDS	41568094	41568724	0.56	+	1	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	exon	41568094	41568724	.	+	.	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
Phchi.S1	AUGUSTUS	stop_codon	41568725	41568727	.	+	0	transcript_id "Phchi.S1G661900.t1"; gene_id "Phchi.S1G661900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14042.t1 is derived from g12509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10429818	10431488	.	-	.	Phchi.S3G136100
Phchi.S3	AUGUSTUS	transcript	10430883	10431488	.	-	.	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	stop_codon	10430880	10430882	.	-	0	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10430883	10430936	0.68	-	0	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10430883	10430936	.	-	.	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10430937	10431030	.	-	.	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10431031	10431150	1	-	0	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10431031	10431150	.	-	.	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10431151	10431242	.	-	.	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10431243	10431488	1	-	0	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10431243	10431488	.	-	.	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	start_codon	10431486	10431488	.	-	0	transcript_id "Phchi.S3G136100.t1"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	transcript	10429818	10431488	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	stop_codon	10429815	10429817	.	-	0	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10429818	10429831	0.68	-	2	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10429818	10429831	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10429832	10429910	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10429911	10429983	0.46	-	0	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10429911	10429983	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10429984	10430074	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10430075	10430277	0.67	-	2	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10430075	10430277	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10430278	10430358	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10430359	10430528	1	-	1	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10430359	10430528	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10430529	10430636	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10430637	10430936	0.88	-	1	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10430637	10430936	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10430937	10431025	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10431026	10431150	1	-	0	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10431026	10431150	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	intron	10431151	10431242	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	CDS	10431243	10431488	1	-	0	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	exon	10431243	10431488	.	-	.	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
Phchi.S3	AUGUSTUS	start_codon	10431486	10431488	.	-	0	transcript_id "Phchi.S3G136100.t2"; gene_id "Phchi.S3G136100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14054.t1 is derived from g12521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10507141	10508171	.	+	.	Phchi.S3G137300
Phchi.S3	AUGUSTUS	transcript	10507141	10508171	.	+	.	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	start_codon	10507141	10507143	.	+	0	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	CDS	10507141	10507222	1	+	0	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	exon	10507141	10507222	.	+	.	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	intron	10507223	10507365	.	+	.	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	CDS	10507366	10508171	0.84	+	2	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	exon	10507366	10508171	.	+	.	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
Phchi.S3	AUGUSTUS	stop_codon	10508172	10508174	.	+	0	transcript_id "Phchi.S3G137300.t1"; gene_id "Phchi.S3G137300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7886.t1 is derived from g5060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31762314	31763821	.	+	.	Phchi.S1G504500
Phchi.S1	AUGUSTUS	transcript	31762314	31763821	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	start_codon	31762314	31762316	.	+	0	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	CDS	31762314	31762329	1	+	0	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	exon	31762314	31762329	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	intron	31762330	31762491	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	CDS	31762492	31762622	1	+	2	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	exon	31762492	31762622	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	intron	31762623	31762972	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	CDS	31762973	31763109	1	+	0	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	exon	31762973	31763109	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	intron	31763110	31763195	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	CDS	31763196	31763346	1	+	1	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	exon	31763196	31763346	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	intron	31763347	31763480	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	CDS	31763481	31763637	1	+	0	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	exon	31763481	31763637	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	intron	31763638	31763729	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	CDS	31763730	31763821	1	+	2	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	exon	31763730	31763821	.	+	.	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
Phchi.S1	AUGUSTUS	stop_codon	31763822	31763824	.	+	0	transcript_id "Phchi.S1G504500.t1"; gene_id "Phchi.S1G504500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10386.t1 is derived from g7562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47493635	47496973	.	-	.	Phchi.S1G754500
Phchi.S1	AUGUSTUS	transcript	47493635	47496973	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	stop_codon	47493632	47493634	.	-	0	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	CDS	47493635	47495394	0.59	-	2	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	exon	47493635	47495394	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	intron	47495395	47495783	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	CDS	47495784	47496411	0.36	-	0	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	exon	47495784	47496411	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	intron	47496412	47496492	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	CDS	47496493	47496587	1	-	2	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	exon	47496493	47496587	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	intron	47496588	47496825	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	CDS	47496826	47496973	0.91	-	0	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	exon	47496826	47496973	.	-	.	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
Phchi.S1	AUGUSTUS	start_codon	47496971	47496973	.	-	0	transcript_id "Phchi.S1G754500.t1"; gene_id "Phchi.S1G754500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13985.t1 is derived from g12452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10053931	10055671	.	+	.	Phchi.S3G130400
Phchi.S3	AUGUSTUS	transcript	10053931	10055671	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	start_codon	10053931	10053933	.	+	0	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	CDS	10053931	10053979	0.57	+	0	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	exon	10053931	10053979	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	intron	10053980	10054097	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	CDS	10054098	10054249	0.59	+	2	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	exon	10054098	10054249	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	intron	10054250	10054376	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	CDS	10054377	10054412	0.99	+	0	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	exon	10054377	10054412	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	intron	10054413	10054502	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	CDS	10054503	10054829	0.48	+	0	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	exon	10054503	10054829	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	intron	10054830	10054903	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	CDS	10054904	10055671	0.54	+	0	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	exon	10054904	10055671	.	+	.	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
Phchi.S3	AUGUSTUS	stop_codon	10055672	10055674	.	+	0	transcript_id "Phchi.S3G130400.t1"; gene_id "Phchi.S3G130400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6908.t1 is derived from g4080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25933827	25935573	.	+	.	Phchi.S1G406700
Phchi.S1	AUGUSTUS	transcript	25933827	25935573	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	start_codon	25933827	25933829	.	+	0	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25933827	25934048	1	+	0	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25933827	25934048	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25934049	25934184	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25934185	25934261	1	+	0	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25934185	25934261	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25934262	25934395	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25934396	25934467	1	+	1	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25934396	25934467	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25934468	25934557	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25934558	25934595	1	+	1	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25934558	25934595	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25934596	25934669	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25934670	25934713	1	+	2	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25934670	25934713	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25934714	25934837	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25934838	25934884	1	+	0	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25934838	25934884	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25934885	25935025	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25935026	25935200	1	+	1	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25935026	25935200	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25935201	25935293	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25935294	25935370	0.98	+	0	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25935294	25935370	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	intron	25935371	25935455	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	CDS	25935456	25935573	0.84	+	1	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	exon	25935456	25935573	.	+	.	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
Phchi.S1	AUGUSTUS	stop_codon	25935574	25935576	.	+	0	transcript_id "Phchi.S1G406700.t1"; gene_id "Phchi.S1G406700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7220.t1 is derived from g4392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27698830	27699529	.	+	.	Phchi.S1G437900
Phchi.S1	AUGUSTUS	transcript	27698830	27699529	.	+	.	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	start_codon	27698830	27698832	.	+	0	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	CDS	27698830	27699112	1	+	0	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	exon	27698830	27699112	.	+	.	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	intron	27699113	27699194	.	+	.	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	CDS	27699195	27699253	1	+	2	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	exon	27699195	27699253	.	+	.	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	intron	27699254	27699370	.	+	.	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	CDS	27699371	27699529	1	+	0	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	exon	27699371	27699529	.	+	.	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
Phchi.S1	AUGUSTUS	stop_codon	27699530	27699532	.	+	0	transcript_id "Phchi.S1G437900.t1"; gene_id "Phchi.S1G437900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14332.t1 is derived from g12799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12128105	12129937	.	-	.	Phchi.S3G165100
Phchi.S3	AUGUSTUS	transcript	12128105	12129937	.	-	.	transcript_id "Phchi.S3G165100.t1"; gene_id "Phchi.S3G165100"
Phchi.S3	AUGUSTUS	stop_codon	12128102	12128104	.	-	0	transcript_id "Phchi.S3G165100.t1"; gene_id "Phchi.S3G165100"
Phchi.S3	AUGUSTUS	CDS	12128105	12129937	0.99	-	0	transcript_id "Phchi.S3G165100.t1"; gene_id "Phchi.S3G165100"
Phchi.S3	AUGUSTUS	exon	12128105	12129937	.	-	.	transcript_id "Phchi.S3G165100.t1"; gene_id "Phchi.S3G165100"
Phchi.S3	AUGUSTUS	start_codon	12129935	12129937	.	-	0	transcript_id "Phchi.S3G165100.t1"; gene_id "Phchi.S3G165100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2783.t1 is derived from g9703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8852083	8854316	.	-	.	Phchi.S5G139200
Phchi.S5	AUGUSTUS	transcript	8852083	8854316	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	stop_codon	8852080	8852082	.	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8852083	8852181	1	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8852083	8852181	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8852182	8852266	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8852267	8852524	1	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8852267	8852524	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8852525	8852622	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8852623	8852742	1	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8852623	8852742	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8852743	8852873	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8852874	8852991	1	-	1	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8852874	8852991	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8852992	8853177	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8853178	8853281	1	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8853178	8853281	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8853282	8853370	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8853371	8853680	1	-	1	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8853371	8853680	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8853681	8853814	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8853815	8854110	0.89	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8853815	8854110	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	intron	8854111	8854280	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	CDS	8854281	8854316	0.5	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	exon	8854281	8854316	.	-	.	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
Phchi.S5	AUGUSTUS	start_codon	8854314	8854316	.	-	0	transcript_id "Phchi.S5G139200.t1"; gene_id "Phchi.S5G139200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10298.t1 is derived from g7474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46992458	46992877	.	-	.	Phchi.S1G745700
Phchi.S1	AUGUSTUS	transcript	46992458	46992877	.	-	.	transcript_id "Phchi.S1G745700.t1"; gene_id "Phchi.S1G745700"
Phchi.S1	AUGUSTUS	stop_codon	46992455	46992457	.	-	0	transcript_id "Phchi.S1G745700.t1"; gene_id "Phchi.S1G745700"
Phchi.S1	AUGUSTUS	CDS	46992458	46992877	0.62	-	0	transcript_id "Phchi.S1G745700.t1"; gene_id "Phchi.S1G745700"
Phchi.S1	AUGUSTUS	exon	46992458	46992877	.	-	.	transcript_id "Phchi.S1G745700.t1"; gene_id "Phchi.S1G745700"
Phchi.S1	AUGUSTUS	start_codon	46992875	46992877	.	-	0	transcript_id "Phchi.S1G745700.t1"; gene_id "Phchi.S1G745700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7731.t1 is derived from g4905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30881100	30882188	.	-	.	Phchi.S1G489000
Phchi.S1	AUGUSTUS	transcript	30881100	30882188	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	stop_codon	30881097	30881099	.	-	0	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	CDS	30881100	30881204	0.93	-	0	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	exon	30881100	30881204	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	intron	30881205	30881283	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	CDS	30881284	30881355	1	-	0	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	exon	30881284	30881355	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	intron	30881356	30881451	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	CDS	30881452	30881514	1	-	0	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	exon	30881452	30881514	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	intron	30881515	30881606	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	CDS	30881607	30882188	0.81	-	0	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	exon	30881607	30882188	.	-	.	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
Phchi.S1	AUGUSTUS	start_codon	30882186	30882188	.	-	0	transcript_id "Phchi.S1G489000.t1"; gene_id "Phchi.S1G489000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2599.t1 is derived from g9519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7666382	7666699	.	+	.	Phchi.S5G120800
Phchi.S5	AUGUSTUS	transcript	7666382	7666699	.	+	.	transcript_id "Phchi.S5G120800.t1"; gene_id "Phchi.S5G120800"
Phchi.S5	AUGUSTUS	start_codon	7666382	7666384	.	+	0	transcript_id "Phchi.S5G120800.t1"; gene_id "Phchi.S5G120800"
Phchi.S5	AUGUSTUS	CDS	7666382	7666699	0.75	+	0	transcript_id "Phchi.S5G120800.t1"; gene_id "Phchi.S5G120800"
Phchi.S5	AUGUSTUS	exon	7666382	7666699	.	+	.	transcript_id "Phchi.S5G120800.t1"; gene_id "Phchi.S5G120800"
Phchi.S5	AUGUSTUS	stop_codon	7666700	7666702	.	+	0	transcript_id "Phchi.S5G120800.t1"; gene_id "Phchi.S5G120800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11997.t1 is derived from g7672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	448902	450279	.	-	.	Phchi.S2G007700
Phchi.S2	AUGUSTUS	transcript	448902	450279	.	-	.	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	stop_codon	448899	448901	.	-	0	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	CDS	448902	449297	0.61	-	0	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	exon	448902	449297	.	-	.	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	intron	449298	449379	.	-	.	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	CDS	449380	450279	0.31	-	0	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	exon	449380	450279	.	-	.	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
Phchi.S2	AUGUSTUS	start_codon	450277	450279	.	-	0	transcript_id "Phchi.S2G007700.t1"; gene_id "Phchi.S2G007700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5408.t1 is derived from g2578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16719011	16720301	.	-	.	Phchi.S1G256700
Phchi.S1	AUGUSTUS	transcript	16719011	16720301	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	stop_codon	16719008	16719010	.	-	0	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	CDS	16719011	16719315	0.99	-	2	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	exon	16719011	16719315	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	intron	16719316	16719421	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	CDS	16719422	16719536	1	-	0	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	exon	16719422	16719536	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	intron	16719537	16719716	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	CDS	16719717	16719799	1	-	2	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	exon	16719717	16719799	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	intron	16719800	16719919	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	CDS	16719920	16720055	1	-	0	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	exon	16719920	16720055	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	intron	16720056	16720157	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	CDS	16720158	16720301	0.95	-	0	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	exon	16720158	16720301	.	-	.	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
Phchi.S1	AUGUSTUS	start_codon	16720299	16720301	.	-	0	transcript_id "Phchi.S1G256700.t1"; gene_id "Phchi.S1G256700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5633.t1 is derived from g2803.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17979278	17979948	.	+	.	Phchi.S1G279200
Phchi.S1	AUGUSTUS	transcript	17979278	17979948	.	+	.	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	start_codon	17979278	17979280	.	+	0	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	CDS	17979278	17979485	0.38	+	0	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	exon	17979278	17979485	.	+	.	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	intron	17979486	17979598	.	+	.	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	CDS	17979599	17979948	0.35	+	2	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	exon	17979599	17979948	.	+	.	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	stop_codon	17979949	17979951	.	+	0	transcript_id "Phchi.S1G279200.t1"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	transcript	17979601	17979948	.	+	.	transcript_id "Phchi.S1G279200.t2"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	start_codon	17979601	17979603	.	+	0	transcript_id "Phchi.S1G279200.t2"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	CDS	17979601	17979948	0.52	+	0	transcript_id "Phchi.S1G279200.t2"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	exon	17979601	17979948	.	+	.	transcript_id "Phchi.S1G279200.t2"; gene_id "Phchi.S1G279200"
Phchi.S1	AUGUSTUS	stop_codon	17979949	17979951	.	+	0	transcript_id "Phchi.S1G279200.t2"; gene_id "Phchi.S1G279200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5840.t1 is derived from g3010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19282429	19285770	.	+	.	Phchi.S1G299900
Phchi.S1	AUGUSTUS	transcript	19282429	19285770	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	start_codon	19282429	19282431	.	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19282429	19282586	0.99	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19282429	19282586	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19282587	19282900	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19282901	19282985	1	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19282901	19282985	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19282986	19283125	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19283126	19283223	1	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19283126	19283223	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19283224	19283338	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19283339	19283394	1	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19283339	19283394	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19283395	19283507	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19283508	19283625	1	+	2	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19283508	19283625	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19283626	19283738	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19283739	19283766	1	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19283739	19283766	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19283767	19283849	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19283850	19283941	1	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19283850	19283941	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19283942	19284033	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19284034	19284190	1	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19284034	19284190	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19284191	19284273	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19284274	19284377	0.92	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19284274	19284377	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19284378	19284502	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19284503	19284602	0.92	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19284503	19284602	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19284603	19284689	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19284690	19284781	0.83	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19284690	19284781	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19284782	19285165	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19285166	19285232	0.75	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19285166	19285232	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19285233	19285361	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19285362	19285421	1	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19285362	19285421	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19285422	19285522	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19285523	19285569	1	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19285523	19285569	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	intron	19285570	19285658	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	CDS	19285659	19285770	1	+	1	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	exon	19285659	19285770	.	+	.	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
Phchi.S1	AUGUSTUS	stop_codon	19285771	19285773	.	+	0	transcript_id "Phchi.S1G299900.t1"; gene_id "Phchi.S1G299900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2313.t1 is derived from g9233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6022765	6025491	.	-	.	Phchi.S5G092200
Phchi.S5	AUGUSTUS	transcript	6022765	6025491	.	-	.	transcript_id "Phchi.S5G092200.t1"; gene_id "Phchi.S5G092200"
Phchi.S5	AUGUSTUS	stop_codon	6022762	6022764	.	-	0	transcript_id "Phchi.S5G092200.t1"; gene_id "Phchi.S5G092200"
Phchi.S5	AUGUSTUS	CDS	6022765	6025491	0.79	-	0	transcript_id "Phchi.S5G092200.t1"; gene_id "Phchi.S5G092200"
Phchi.S5	AUGUSTUS	exon	6022765	6025491	.	-	.	transcript_id "Phchi.S5G092200.t1"; gene_id "Phchi.S5G092200"
Phchi.S5	AUGUSTUS	start_codon	6025489	6025491	.	-	0	transcript_id "Phchi.S5G092200.t1"; gene_id "Phchi.S5G092200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg361.t1 is derived from g10143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2647311	2648612	.	-	.	Phchi.S6G032000
Phchi.S6	AUGUSTUS	transcript	2647311	2648612	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	stop_codon	2647308	2647310	.	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	CDS	2647311	2647469	0.57	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	exon	2647311	2647469	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	intron	2647470	2647553	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	CDS	2647554	2647687	0.64	-	2	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	exon	2647554	2647687	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	intron	2647688	2647857	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	CDS	2647858	2647996	0.56	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	exon	2647858	2647996	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	intron	2647997	2648073	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	CDS	2648074	2648148	0.68	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	exon	2648074	2648148	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	intron	2648149	2648359	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	CDS	2648360	2648416	0.85	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	exon	2648360	2648416	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	intron	2648417	2648495	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	CDS	2648496	2648612	0.95	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	exon	2648496	2648612	.	-	.	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
Phchi.S6	AUGUSTUS	start_codon	2648610	2648612	.	-	0	transcript_id "Phchi.S6G032000.t1"; gene_id "Phchi.S6G032000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4068.t1 is derived from g1237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7620752	7621255	.	+	.	Phchi.S1G122700
Phchi.S1	AUGUSTUS	transcript	7620752	7621255	.	+	.	transcript_id "Phchi.S1G122700.t1"; gene_id "Phchi.S1G122700"
Phchi.S1	AUGUSTUS	start_codon	7620752	7620754	.	+	0	transcript_id "Phchi.S1G122700.t1"; gene_id "Phchi.S1G122700"
Phchi.S1	AUGUSTUS	CDS	7620752	7621255	0.93	+	0	transcript_id "Phchi.S1G122700.t1"; gene_id "Phchi.S1G122700"
Phchi.S1	AUGUSTUS	exon	7620752	7621255	.	+	.	transcript_id "Phchi.S1G122700.t1"; gene_id "Phchi.S1G122700"
Phchi.S1	AUGUSTUS	stop_codon	7621256	7621258	.	+	0	transcript_id "Phchi.S1G122700.t1"; gene_id "Phchi.S1G122700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10637.t1 is derived from g14687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1362448	1365289	.	+	.	Phchi.S4G021900
Phchi.S4	AUGUSTUS	transcript	1362448	1365289	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	start_codon	1362448	1362450	.	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1362448	1362490	0.89	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1362448	1362490	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1362491	1362579	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1362580	1362765	1	+	2	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1362580	1362765	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1362766	1362843	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1362844	1362931	0.96	+	2	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1362844	1362931	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1362932	1363064	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1363065	1363086	0.96	+	1	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1363065	1363086	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1363087	1363237	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1363238	1363477	1	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1363238	1363477	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1363478	1363577	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1363578	1363640	1	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1363578	1363640	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1363641	1363729	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1363730	1363798	1	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1363730	1363798	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1363799	1363886	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1363887	1363932	1	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1363887	1363932	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1363933	1364026	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1364027	1364077	1	+	2	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1364027	1364077	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1364078	1364699	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1364700	1365067	0.99	+	2	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1364700	1365067	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	intron	1365068	1365178	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	CDS	1365179	1365289	0.98	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	exon	1365179	1365289	.	+	.	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
Phchi.S4	AUGUSTUS	stop_codon	1365290	1365292	.	+	0	transcript_id "Phchi.S4G021900.t1"; gene_id "Phchi.S4G021900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3357.t1 is derived from g526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3105144	3110031	.	-	.	Phchi.S1G051600
Phchi.S1	AUGUSTUS	transcript	3105144	3110031	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	stop_codon	3105141	3105143	.	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3105144	3105488	0.64	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3105144	3105488	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3105489	3105594	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3105595	3105691	0.76	-	1	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3105595	3105691	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3105692	3105867	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3105868	3106191	0.86	-	1	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3105868	3106191	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3106192	3106336	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3106337	3106461	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3106337	3106461	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3106462	3106548	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3106549	3106818	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3106549	3106818	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3106819	3106907	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3106908	3107096	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3106908	3107096	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3107097	3107180	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3107181	3107258	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3107181	3107258	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3107259	3107336	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3107337	3107537	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3107337	3107537	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3107538	3107621	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3107622	3107772	1	-	1	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3107622	3107772	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3107773	3107874	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3107875	3108098	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3107875	3108098	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3108099	3108188	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3108189	3108531	1	-	1	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3108189	3108531	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3108532	3108672	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3108673	3108911	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3108673	3108911	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3108912	3109044	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3109045	3109149	1	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3109045	3109149	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3109150	3109269	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3109270	3109360	1	-	1	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3109270	3109360	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3109361	3109488	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3109489	3109645	0.99	-	2	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3109489	3109645	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	intron	3109646	3109766	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	CDS	3109767	3110031	0.83	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	exon	3109767	3110031	.	-	.	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
Phchi.S1	AUGUSTUS	start_codon	3110029	3110031	.	-	0	transcript_id "Phchi.S1G051600.t1"; gene_id "Phchi.S1G051600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4574.t1 is derived from g1744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11171141	11172096	.	-	.	Phchi.S1G173300
Phchi.S1	AUGUSTUS	transcript	11171141	11172096	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	stop_codon	11171138	11171140	.	-	0	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	CDS	11171141	11171407	1	-	0	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	exon	11171141	11171407	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	intron	11171408	11171498	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	CDS	11171499	11171786	0.83	-	0	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	exon	11171499	11171786	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	intron	11171787	11171902	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	CDS	11171903	11171962	0.98	-	0	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	exon	11171903	11171962	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	intron	11171963	11172054	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	CDS	11172055	11172096	0.99	-	0	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	exon	11172055	11172096	.	-	.	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
Phchi.S1	AUGUSTUS	start_codon	11172094	11172096	.	-	0	transcript_id "Phchi.S1G173300.t1"; gene_id "Phchi.S1G173300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6346.t1 is derived from g3518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22426640	22427611	.	-	.	Phchi.S1G350500
Phchi.S1	AUGUSTUS	transcript	22426640	22427611	.	-	.	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	stop_codon	22426637	22426639	.	-	0	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	CDS	22426640	22426821	1	-	2	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	exon	22426640	22426821	.	-	.	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	intron	22426822	22426895	.	-	.	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	CDS	22426896	22427299	1	-	1	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	exon	22426896	22427299	.	-	.	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	intron	22427300	22427456	.	-	.	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	CDS	22427457	22427611	0.94	-	0	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	exon	22427457	22427611	.	-	.	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
Phchi.S1	AUGUSTUS	start_codon	22427609	22427611	.	-	0	transcript_id "Phchi.S1G350500.t1"; gene_id "Phchi.S1G350500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14470.t1 is derived from g12938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13025193	13025915	.	+	.	Phchi.S3G178900
Phchi.S3	AUGUSTUS	transcript	13025193	13025915	.	+	.	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	start_codon	13025193	13025195	.	+	0	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	CDS	13025193	13025364	0.73	+	0	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	exon	13025193	13025364	.	+	.	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	intron	13025365	13025727	.	+	.	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	CDS	13025728	13025915	1	+	2	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	exon	13025728	13025915	.	+	.	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
Phchi.S3	AUGUSTUS	stop_codon	13025916	13025918	.	+	0	transcript_id "Phchi.S3G178900.t1"; gene_id "Phchi.S3G178900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10500.t1 is derived from g14549.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	721642	725310	.	+	.	Phchi.S4G008200
Phchi.S4	AUGUSTUS	transcript	721642	724322	.	+	.	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	start_codon	721642	721644	.	+	0	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	CDS	721642	724236	0.62	+	0	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	exon	721642	724236	.	+	.	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	intron	724237	724304	.	+	.	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	CDS	724305	724322	0.9	+	0	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	exon	724305	724322	.	+	.	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	stop_codon	724323	724325	.	+	0	transcript_id "Phchi.S4G008200.t1"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	transcript	721642	725310	.	+	.	transcript_id "Phchi.S4G008200.t2"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	start_codon	721642	721644	.	+	0	transcript_id "Phchi.S4G008200.t2"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	CDS	721642	725310	1	+	0	transcript_id "Phchi.S4G008200.t2"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	exon	721642	725310	.	+	.	transcript_id "Phchi.S4G008200.t2"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	stop_codon	725311	725313	.	+	0	transcript_id "Phchi.S4G008200.t2"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	transcript	723112	725310	.	+	.	transcript_id "Phchi.S4G008200.t3"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	start_codon	723112	723114	.	+	0	transcript_id "Phchi.S4G008200.t3"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	CDS	723112	725310	0.62	+	0	transcript_id "Phchi.S4G008200.t3"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	exon	723112	725310	.	+	.	transcript_id "Phchi.S4G008200.t3"; gene_id "Phchi.S4G008200"
Phchi.S4	AUGUSTUS	stop_codon	725311	725313	.	+	0	transcript_id "Phchi.S4G008200.t3"; gene_id "Phchi.S4G008200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5465.t1 is derived from g2635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16978616	16980187	.	+	.	Phchi.S1G262400
Phchi.S1	AUGUSTUS	transcript	16978616	16980187	.	+	.	transcript_id "Phchi.S1G262400.t1"; gene_id "Phchi.S1G262400"
Phchi.S1	AUGUSTUS	start_codon	16978616	16978618	.	+	0	transcript_id "Phchi.S1G262400.t1"; gene_id "Phchi.S1G262400"
Phchi.S1	AUGUSTUS	CDS	16978616	16980187	0.98	+	0	transcript_id "Phchi.S1G262400.t1"; gene_id "Phchi.S1G262400"
Phchi.S1	AUGUSTUS	exon	16978616	16980187	.	+	.	transcript_id "Phchi.S1G262400.t1"; gene_id "Phchi.S1G262400"
Phchi.S1	AUGUSTUS	stop_codon	16980188	16980190	.	+	0	transcript_id "Phchi.S1G262400.t1"; gene_id "Phchi.S1G262400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15547.t1 is derived from g14016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19825245	19827480	.	+	.	Phchi.S3G286600
Phchi.S3	AUGUSTUS	transcript	19825245	19827480	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	start_codon	19825245	19825247	.	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19825245	19825277	0.58	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19825245	19825277	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19825278	19825426	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19825427	19825546	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19825427	19825546	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19825547	19825632	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19825633	19825746	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19825633	19825746	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19825747	19825819	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19825820	19825909	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19825820	19825909	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19825910	19825989	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19825990	19826074	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19825990	19826074	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19826075	19826187	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19826188	19826243	1	+	2	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19826188	19826243	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19826244	19826335	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19826336	19826414	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19826336	19826414	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19826415	19826504	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19826505	19826639	1	+	2	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19826505	19826639	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19826640	19826734	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19826735	19826967	1	+	2	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19826735	19826967	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19826968	19827077	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19827078	19827233	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19827078	19827233	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	intron	19827234	19827312	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	CDS	19827313	19827480	1	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	exon	19827313	19827480	.	+	.	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
Phchi.S3	AUGUSTUS	stop_codon	19827481	19827483	.	+	0	transcript_id "Phchi.S3G286600.t1"; gene_id "Phchi.S3G286600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12462.t1 is derived from g8139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24378263	24378658	.	-	.	Phchi.S2G054200
Phchi.S2	AUGUSTUS	transcript	24378263	24378658	.	-	.	transcript_id "Phchi.S2G054200.t1"; gene_id "Phchi.S2G054200"
Phchi.S2	AUGUSTUS	stop_codon	24378260	24378262	.	-	0	transcript_id "Phchi.S2G054200.t1"; gene_id "Phchi.S2G054200"
Phchi.S2	AUGUSTUS	CDS	24378263	24378658	0.88	-	0	transcript_id "Phchi.S2G054200.t1"; gene_id "Phchi.S2G054200"
Phchi.S2	AUGUSTUS	exon	24378263	24378658	.	-	.	transcript_id "Phchi.S2G054200.t1"; gene_id "Phchi.S2G054200"
Phchi.S2	AUGUSTUS	start_codon	24378656	24378658	.	-	0	transcript_id "Phchi.S2G054200.t1"; gene_id "Phchi.S2G054200"
# This transcript jg7409.t2 is derived from g4581.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7410.t1 is derived from g4582.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29025746	29029004	.	+	.	Phchi.S1G456900
Phchi.S1	AUGUSTUS	transcript	29025746	29029004	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	start_codon	29025746	29025748	.	+	0	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29025746	29026254	1	+	0	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29025746	29026254	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29026255	29026461	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29026462	29026684	1	+	1	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29026462	29026684	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29026685	29026842	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29026843	29026917	0.4	+	0	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29026843	29026917	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29026918	29027033	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29027034	29027125	0.66	+	0	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29027034	29027125	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29027126	29027214	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29027215	29027572	0.98	+	1	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29027215	29027572	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29027573	29027660	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29027661	29027932	1	+	0	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29027661	29027932	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29027933	29028024	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29028025	29028483	0.64	+	1	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29028025	29028483	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29028484	29028706	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29028707	29029004	0.59	+	1	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29028707	29029004	.	+	.	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	stop_codon	29029005	29029007	.	+	0	transcript_id "Phchi.S1G456900.t1"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	transcript	29025746	29029004	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	start_codon	29025746	29025748	.	+	0	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29025746	29026254	1	+	0	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29025746	29026254	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29026255	29026461	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29026462	29026684	0.44	+	1	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29026462	29026684	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29026685	29026853	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29026854	29026894	0.38	+	0	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29026854	29026894	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29026895	29026978	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29026979	29027125	0.41	+	1	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29026979	29027125	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29027126	29027214	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29027215	29027572	1	+	1	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29027215	29027572	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29027573	29027660	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29027661	29027932	1	+	0	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29027661	29027932	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29027933	29028024	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29028025	29028483	0.72	+	1	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29028025	29028483	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	intron	29028484	29028706	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	CDS	29028707	29029004	0.53	+	1	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	exon	29028707	29029004	.	+	.	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
Phchi.S1	AUGUSTUS	stop_codon	29029005	29029007	.	+	0	transcript_id "Phchi.S1G456900.t2"; gene_id "Phchi.S1G456900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10821.t1 is derived from g14871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2293141	2293656	.	-	.	Phchi.S4G040300
Phchi.S4	AUGUSTUS	transcript	2293141	2293656	.	-	.	transcript_id "Phchi.S4G040300.t1"; gene_id "Phchi.S4G040300"
Phchi.S4	AUGUSTUS	stop_codon	2293138	2293140	.	-	0	transcript_id "Phchi.S4G040300.t1"; gene_id "Phchi.S4G040300"
Phchi.S4	AUGUSTUS	CDS	2293141	2293656	0.56	-	0	transcript_id "Phchi.S4G040300.t1"; gene_id "Phchi.S4G040300"
Phchi.S4	AUGUSTUS	exon	2293141	2293656	.	-	.	transcript_id "Phchi.S4G040300.t1"; gene_id "Phchi.S4G040300"
Phchi.S4	AUGUSTUS	start_codon	2293654	2293656	.	-	0	transcript_id "Phchi.S4G040300.t1"; gene_id "Phchi.S4G040300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg750.t1 is derived from g10532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5333859	5335748	.	+	.	Phchi.S6G070900
Phchi.S6	AUGUSTUS	transcript	5333859	5335748	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	start_codon	5333859	5333861	.	+	0	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	CDS	5333859	5333886	0.57	+	0	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	exon	5333859	5333886	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	intron	5333887	5334042	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	CDS	5334043	5334970	0.59	+	2	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	exon	5334043	5334970	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	intron	5334971	5335056	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	CDS	5335057	5335288	0.98	+	1	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	exon	5335057	5335288	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	intron	5335289	5335373	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	CDS	5335374	5335748	1	+	0	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	exon	5335374	5335748	.	+	.	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
Phchi.S6	AUGUSTUS	stop_codon	5335749	5335751	.	+	0	transcript_id "Phchi.S6G070900.t1"; gene_id "Phchi.S6G070900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15303.t1 is derived from g13771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18303511	18305616	.	+	.	Phchi.S3G262200
Phchi.S3	AUGUSTUS	transcript	18303511	18305616	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	start_codon	18303511	18303513	.	+	0	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	CDS	18303511	18303656	0.86	+	0	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	exon	18303511	18303656	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	intron	18303657	18303771	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	CDS	18303772	18303972	1	+	1	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	exon	18303772	18303972	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	intron	18303973	18304123	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	CDS	18304124	18304301	0.99	+	1	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	exon	18304124	18304301	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	intron	18304302	18304400	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	CDS	18304401	18304663	0.96	+	0	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	exon	18304401	18304663	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	intron	18304664	18304775	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	CDS	18304776	18305051	0.92	+	1	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	exon	18304776	18305051	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	intron	18305052	18305138	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	CDS	18305139	18305616	0.93	+	1	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	exon	18305139	18305616	.	+	.	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
Phchi.S3	AUGUSTUS	stop_codon	18305617	18305619	.	+	0	transcript_id "Phchi.S3G262200.t1"; gene_id "Phchi.S3G262200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7149.t1 is derived from g4321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27198384	27199832	.	+	.	Phchi.S1G430800
Phchi.S1	AUGUSTUS	transcript	27198384	27199832	.	+	.	transcript_id "Phchi.S1G430800.t1"; gene_id "Phchi.S1G430800"
Phchi.S1	AUGUSTUS	start_codon	27198384	27198386	.	+	0	transcript_id "Phchi.S1G430800.t1"; gene_id "Phchi.S1G430800"
Phchi.S1	AUGUSTUS	CDS	27198384	27199832	0.39	+	0	transcript_id "Phchi.S1G430800.t1"; gene_id "Phchi.S1G430800"
Phchi.S1	AUGUSTUS	exon	27198384	27199832	.	+	.	transcript_id "Phchi.S1G430800.t1"; gene_id "Phchi.S1G430800"
Phchi.S1	AUGUSTUS	stop_codon	27199833	27199835	.	+	0	transcript_id "Phchi.S1G430800.t1"; gene_id "Phchi.S1G430800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8964.t1 is derived from g6139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38867781	38869385	.	+	.	Phchi.S1G612300
Phchi.S1	AUGUSTUS	transcript	38867781	38869385	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	start_codon	38867781	38867783	.	+	0	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	CDS	38867781	38868248	0.33	+	0	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	exon	38867781	38868248	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	intron	38868249	38868334	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	CDS	38868335	38868345	0.99	+	0	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	exon	38868335	38868345	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	intron	38868346	38868451	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	CDS	38868452	38868572	0.96	+	1	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	exon	38868452	38868572	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	intron	38868573	38868668	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	CDS	38868669	38868673	0.99	+	0	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	exon	38868669	38868673	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	intron	38868674	38868758	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	CDS	38868759	38869174	0.89	+	1	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	exon	38868759	38869174	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	intron	38869175	38869356	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	CDS	38869357	38869385	0.98	+	2	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	exon	38869357	38869385	.	+	.	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
Phchi.S1	AUGUSTUS	stop_codon	38869386	38869388	.	+	0	transcript_id "Phchi.S1G612300.t1"; gene_id "Phchi.S1G612300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13553.t1 is derived from g12020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7471749	7473843	.	+	.	Phchi.S3G087200
Phchi.S3	AUGUSTUS	transcript	7471749	7473843	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	start_codon	7471749	7471751	.	+	0	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	CDS	7471749	7472094	0.94	+	0	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	exon	7471749	7472094	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	intron	7472095	7472766	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	CDS	7472767	7473001	0.98	+	2	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	exon	7472767	7473001	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	intron	7473002	7473114	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	CDS	7473115	7473244	1	+	1	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	exon	7473115	7473244	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	intron	7473245	7473401	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	CDS	7473402	7473407	1	+	0	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	exon	7473402	7473407	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	intron	7473408	7473506	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	CDS	7473507	7473598	1	+	0	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	exon	7473507	7473598	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	intron	7473599	7473773	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	CDS	7473774	7473843	1	+	1	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	exon	7473774	7473843	.	+	.	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
Phchi.S3	AUGUSTUS	stop_codon	7473844	7473846	.	+	0	transcript_id "Phchi.S3G087200.t1"; gene_id "Phchi.S3G087200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg955.t1 is derived from g10737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6640945	6641382	.	+	.	Phchi.S6G091400
Phchi.S6	AUGUSTUS	transcript	6640945	6641382	.	+	.	transcript_id "Phchi.S6G091400.t1"; gene_id "Phchi.S6G091400"
Phchi.S6	AUGUSTUS	start_codon	6640945	6640947	.	+	0	transcript_id "Phchi.S6G091400.t1"; gene_id "Phchi.S6G091400"
Phchi.S6	AUGUSTUS	CDS	6640945	6641382	0.78	+	0	transcript_id "Phchi.S6G091400.t1"; gene_id "Phchi.S6G091400"
Phchi.S6	AUGUSTUS	exon	6640945	6641382	.	+	.	transcript_id "Phchi.S6G091400.t1"; gene_id "Phchi.S6G091400"
Phchi.S6	AUGUSTUS	stop_codon	6641383	6641385	.	+	0	transcript_id "Phchi.S6G091400.t1"; gene_id "Phchi.S6G091400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15035.t1 is derived from g13503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16644072	16644379	.	-	.	Phchi.S3G235400
Phchi.S3	AUGUSTUS	transcript	16644072	16644379	.	-	.	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	stop_codon	16644069	16644071	.	-	0	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	CDS	16644072	16644243	0.87	-	1	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	exon	16644072	16644243	.	-	.	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	intron	16644244	16644335	.	-	.	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	CDS	16644336	16644379	0.89	-	0	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	exon	16644336	16644379	.	-	.	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
Phchi.S3	AUGUSTUS	start_codon	16644377	16644379	.	-	0	transcript_id "Phchi.S3G235400.t1"; gene_id "Phchi.S3G235400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4896.t1 is derived from g2066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13290536	13290950	.	+	.	Phchi.S1G205500
Phchi.S1	AUGUSTUS	transcript	13290536	13290950	.	+	.	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	start_codon	13290536	13290538	.	+	0	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	CDS	13290536	13290730	0.94	+	0	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	exon	13290536	13290730	.	+	.	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	intron	13290731	13290869	.	+	.	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	CDS	13290870	13290950	0.81	+	0	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	exon	13290870	13290950	.	+	.	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
Phchi.S1	AUGUSTUS	stop_codon	13290951	13290953	.	+	0	transcript_id "Phchi.S1G205500.t1"; gene_id "Phchi.S1G205500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15250.t1 is derived from g13718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17899878	17903046	.	-	.	Phchi.S3G256900
Phchi.S3	AUGUSTUS	transcript	17899878	17903046	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	stop_codon	17899875	17899877	.	-	0	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17899878	17900328	1	-	1	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17899878	17900328	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17900329	17900415	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17900416	17900645	1	-	0	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17900416	17900645	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17900646	17900764	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17900765	17900885	0.98	-	1	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17900765	17900885	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17900886	17901002	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17901003	17901152	1	-	1	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17901003	17901152	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17901153	17901253	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17901254	17901459	1	-	0	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17901254	17901459	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17901460	17901963	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17901964	17902078	1	-	1	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17901964	17902078	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17902079	17902289	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17902290	17902384	1	-	0	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17902290	17902384	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17902385	17902537	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17902538	17902743	0.96	-	2	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17902538	17902743	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	intron	17902744	17902865	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	CDS	17902866	17903046	0.88	-	0	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	exon	17902866	17903046	.	-	.	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
Phchi.S3	AUGUSTUS	start_codon	17903044	17903046	.	-	0	transcript_id "Phchi.S3G256900.t1"; gene_id "Phchi.S3G256900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7331.t1 is derived from g4503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28545245	28546936	.	-	.	Phchi.S1G449000
Phchi.S1	AUGUSTUS	transcript	28545245	28546936	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	stop_codon	28545242	28545244	.	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	CDS	28545245	28545622	0.93	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	exon	28545245	28545622	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	intron	28545623	28545713	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	CDS	28545714	28545842	1	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	exon	28545714	28545842	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	intron	28545843	28545930	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	CDS	28545931	28546245	0.97	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	exon	28545931	28546245	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	intron	28546246	28546373	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	CDS	28546374	28546499	0.92	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	exon	28546374	28546499	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	intron	28546500	28546615	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	CDS	28546616	28546936	0.95	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	exon	28546616	28546936	.	-	.	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
Phchi.S1	AUGUSTUS	start_codon	28546934	28546936	.	-	0	transcript_id "Phchi.S1G449000.t1"; gene_id "Phchi.S1G449000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2963.t1 is derived from g132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	850154	850750	.	+	.	Phchi.S1G012200
Phchi.S1	AUGUSTUS	transcript	850154	850750	.	+	.	transcript_id "Phchi.S1G012200.t1"; gene_id "Phchi.S1G012200"
Phchi.S1	AUGUSTUS	start_codon	850154	850156	.	+	0	transcript_id "Phchi.S1G012200.t1"; gene_id "Phchi.S1G012200"
Phchi.S1	AUGUSTUS	CDS	850154	850750	0.46	+	0	transcript_id "Phchi.S1G012200.t1"; gene_id "Phchi.S1G012200"
Phchi.S1	AUGUSTUS	exon	850154	850750	.	+	.	transcript_id "Phchi.S1G012200.t1"; gene_id "Phchi.S1G012200"
Phchi.S1	AUGUSTUS	stop_codon	850751	850753	.	+	0	transcript_id "Phchi.S1G012200.t1"; gene_id "Phchi.S1G012200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9428.t1 is derived from g6604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41427897	41429039	.	-	.	Phchi.S1G658700
Phchi.S1	AUGUSTUS	transcript	41427897	41429039	.	-	.	transcript_id "Phchi.S1G658700.t1"; gene_id "Phchi.S1G658700"
Phchi.S1	AUGUSTUS	stop_codon	41427894	41427896	.	-	0	transcript_id "Phchi.S1G658700.t1"; gene_id "Phchi.S1G658700"
Phchi.S1	AUGUSTUS	CDS	41427897	41429039	1	-	0	transcript_id "Phchi.S1G658700.t1"; gene_id "Phchi.S1G658700"
Phchi.S1	AUGUSTUS	exon	41427897	41429039	.	-	.	transcript_id "Phchi.S1G658700.t1"; gene_id "Phchi.S1G658700"
Phchi.S1	AUGUSTUS	start_codon	41429037	41429039	.	-	0	transcript_id "Phchi.S1G658700.t1"; gene_id "Phchi.S1G658700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5853.t1 is derived from g3023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19347516	19348590	.	+	.	Phchi.S1G301200
Phchi.S1	AUGUSTUS	transcript	19347516	19348590	.	+	.	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	start_codon	19347516	19347518	.	+	0	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	CDS	19347516	19348371	0.89	+	0	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	exon	19347516	19348371	.	+	.	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	intron	19348372	19348489	.	+	.	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	CDS	19348490	19348590	0.8	+	2	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	exon	19348490	19348590	.	+	.	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
Phchi.S1	AUGUSTUS	stop_codon	19348591	19348593	.	+	0	transcript_id "Phchi.S1G301200.t1"; gene_id "Phchi.S1G301200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15117.t1 is derived from g13585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17159346	17159855	.	+	.	Phchi.S3G243600
Phchi.S3	AUGUSTUS	transcript	17159346	17159855	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	start_codon	17159346	17159348	.	+	0	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	CDS	17159346	17159457	0.96	+	0	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	exon	17159346	17159457	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	intron	17159458	17159591	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	CDS	17159592	17159597	0.94	+	2	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	exon	17159592	17159597	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	intron	17159598	17159679	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	CDS	17159680	17159752	0.84	+	2	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	exon	17159680	17159752	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	intron	17159753	17159848	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	CDS	17159849	17159855	1	+	1	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	exon	17159849	17159855	.	+	.	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
Phchi.S3	AUGUSTUS	stop_codon	17159856	17159858	.	+	0	transcript_id "Phchi.S3G243600.t1"; gene_id "Phchi.S3G243600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9623.t1 is derived from g6799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42961867	42962280	.	-	.	Phchi.S1G678200
Phchi.S1	AUGUSTUS	transcript	42961867	42962280	.	-	.	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	stop_codon	42961864	42961866	.	-	0	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	CDS	42961867	42961903	0.75	-	1	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	exon	42961867	42961903	.	-	.	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	intron	42961904	42961993	.	-	.	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	CDS	42961994	42962079	0.97	-	0	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	exon	42961994	42962079	.	-	.	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	intron	42962080	42962157	.	-	.	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	CDS	42962158	42962280	0.94	-	0	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	exon	42962158	42962280	.	-	.	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
Phchi.S1	AUGUSTUS	start_codon	42962278	42962280	.	-	0	transcript_id "Phchi.S1G678200.t1"; gene_id "Phchi.S1G678200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11345.t1 is derived from g15395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5666113	5667525	.	-	.	Phchi.S4G092700
Phchi.S4	AUGUSTUS	transcript	5666113	5667525	.	-	.	transcript_id "Phchi.S4G092700.t1"; gene_id "Phchi.S4G092700"
Phchi.S4	AUGUSTUS	stop_codon	5666110	5666112	.	-	0	transcript_id "Phchi.S4G092700.t1"; gene_id "Phchi.S4G092700"
Phchi.S4	AUGUSTUS	CDS	5666113	5667525	1	-	0	transcript_id "Phchi.S4G092700.t1"; gene_id "Phchi.S4G092700"
Phchi.S4	AUGUSTUS	exon	5666113	5667525	.	-	.	transcript_id "Phchi.S4G092700.t1"; gene_id "Phchi.S4G092700"
Phchi.S4	AUGUSTUS	start_codon	5667523	5667525	.	-	0	transcript_id "Phchi.S4G092700.t1"; gene_id "Phchi.S4G092700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2909.t1 is derived from g78.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	448081	448887	.	+	.	Phchi.S1G006800
Phchi.S1	AUGUSTUS	transcript	448081	448887	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	start_codon	448081	448083	.	+	0	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	CDS	448081	448102	0.56	+	0	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	exon	448081	448102	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	intron	448103	448294	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	CDS	448295	448340	0.52	+	2	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	exon	448295	448340	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	intron	448341	448650	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	CDS	448651	448728	0.76	+	1	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	exon	448651	448728	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	intron	448729	448820	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	CDS	448821	448887	1	+	1	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	exon	448821	448887	.	+	.	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
Phchi.S1	AUGUSTUS	stop_codon	448888	448890	.	+	0	transcript_id "Phchi.S1G006800.t1"; gene_id "Phchi.S1G006800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14436.t1 is derived from g12904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12813357	12813966	.	-	.	Phchi.S3G175500
Phchi.S3	AUGUSTUS	transcript	12813357	12813966	.	-	.	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	stop_codon	12813354	12813356	.	-	0	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	CDS	12813357	12813526	0.97	-	2	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	exon	12813357	12813526	.	-	.	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	intron	12813527	12813648	.	-	.	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	CDS	12813649	12813754	1	-	0	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	exon	12813649	12813754	.	-	.	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	intron	12813755	12813903	.	-	.	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	CDS	12813904	12813966	0.99	-	0	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	exon	12813904	12813966	.	-	.	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
Phchi.S3	AUGUSTUS	start_codon	12813964	12813966	.	-	0	transcript_id "Phchi.S3G175500.t1"; gene_id "Phchi.S3G175500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg96.t1 is derived from g9878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	487169	487903	.	-	.	Phchi.S6G005500
Phchi.S6	AUGUSTUS	transcript	487169	487903	.	-	.	transcript_id "Phchi.S6G005500.t1"; gene_id "Phchi.S6G005500"
Phchi.S6	AUGUSTUS	stop_codon	487166	487168	.	-	0	transcript_id "Phchi.S6G005500.t1"; gene_id "Phchi.S6G005500"
Phchi.S6	AUGUSTUS	CDS	487169	487903	1	-	0	transcript_id "Phchi.S6G005500.t1"; gene_id "Phchi.S6G005500"
Phchi.S6	AUGUSTUS	exon	487169	487903	.	-	.	transcript_id "Phchi.S6G005500.t1"; gene_id "Phchi.S6G005500"
Phchi.S6	AUGUSTUS	start_codon	487901	487903	.	-	0	transcript_id "Phchi.S6G005500.t1"; gene_id "Phchi.S6G005500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15086.t1 is derived from g13554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16953294	16954830	.	-	.	Phchi.S3G240500
Phchi.S3	AUGUSTUS	transcript	16953294	16954830	.	-	.	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	stop_codon	16953291	16953293	.	-	0	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	CDS	16953294	16954060	0.96	-	2	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	exon	16953294	16954060	.	-	.	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	intron	16954061	16954165	.	-	.	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	CDS	16954166	16954391	1	-	0	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	exon	16954166	16954391	.	-	.	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	intron	16954392	16954587	.	-	.	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	CDS	16954588	16954830	1	-	0	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	exon	16954588	16954830	.	-	.	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
Phchi.S3	AUGUSTUS	start_codon	16954828	16954830	.	-	0	transcript_id "Phchi.S3G240500.t1"; gene_id "Phchi.S3G240500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14197.t1 is derived from g12664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11429912	11432659	.	-	.	Phchi.S3G151600
Phchi.S3	AUGUSTUS	transcript	11429912	11432659	.	-	.	transcript_id "Phchi.S3G151600.t1"; gene_id "Phchi.S3G151600"
Phchi.S3	AUGUSTUS	stop_codon	11429909	11429911	.	-	0	transcript_id "Phchi.S3G151600.t1"; gene_id "Phchi.S3G151600"
Phchi.S3	AUGUSTUS	CDS	11429912	11432659	1	-	0	transcript_id "Phchi.S3G151600.t1"; gene_id "Phchi.S3G151600"
Phchi.S3	AUGUSTUS	exon	11429912	11432659	.	-	.	transcript_id "Phchi.S3G151600.t1"; gene_id "Phchi.S3G151600"
Phchi.S3	AUGUSTUS	start_codon	11432657	11432659	.	-	0	transcript_id "Phchi.S3G151600.t1"; gene_id "Phchi.S3G151600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5095.t1 is derived from g2265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14717920	14721699	.	+	.	Phchi.S1G225400
Phchi.S1	AUGUSTUS	transcript	14717920	14721699	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	start_codon	14717920	14717922	.	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14717920	14717977	0.99	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14717920	14717977	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14717978	14718069	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718070	14718125	1	+	2	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718070	14718125	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718126	14718207	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718208	14718305	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718208	14718305	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718306	14718388	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718389	14718518	1	+	1	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718389	14718518	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718519	14718614	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718615	14718730	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718615	14718730	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718731	14718814	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718815	14718881	1	+	1	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718815	14718881	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718882	14719032	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719033	14719074	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719033	14719074	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719075	14719157	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719158	14719199	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719158	14719199	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719200	14719353	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719354	14719430	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719354	14719430	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719431	14719542	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719543	14719669	1	+	1	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719543	14719669	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719670	14719760	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719761	14719928	0.99	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719761	14719928	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719929	14720040	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720041	14720169	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720041	14720169	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720170	14720269	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720270	14720380	0.96	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720270	14720380	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720381	14720497	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720498	14720632	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720498	14720632	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720633	14720765	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720766	14720840	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720766	14720840	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720841	14720929	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720930	14721037	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720930	14721037	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14721038	14721172	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14721173	14721268	1	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14721173	14721268	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14721269	14721420	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14721421	14721504	0.96	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14721421	14721504	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14721505	14721609	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14721610	14721699	0.96	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14721610	14721699	.	+	.	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	stop_codon	14721700	14721702	.	+	0	transcript_id "Phchi.S1G225400.t1"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	transcript	14717920	14721699	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	start_codon	14717920	14717922	.	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14717920	14717977	0.98	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14717920	14717977	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14717978	14718069	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718070	14718125	1	+	2	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718070	14718125	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718126	14718207	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718208	14718305	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718208	14718305	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718306	14718388	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718389	14718518	1	+	1	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718389	14718518	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718519	14718614	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718615	14718730	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718615	14718730	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718731	14718814	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14718815	14718881	1	+	1	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14718815	14718881	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14718882	14719032	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719033	14719074	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719033	14719074	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719075	14719157	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719158	14719199	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719158	14719199	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719200	14719353	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719354	14719430	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719354	14719430	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719431	14719542	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719543	14719673	0.82	+	1	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719543	14719673	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719674	14719760	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14719761	14719777	0.61	+	2	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14719761	14719777	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14719778	14720040	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720041	14720169	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720041	14720169	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720170	14720269	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720270	14720380	0.97	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720270	14720380	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720381	14720497	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720498	14720632	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720498	14720632	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720633	14720765	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720766	14720840	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720766	14720840	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14720841	14720929	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14720930	14721037	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14720930	14721037	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14721038	14721172	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14721173	14721268	1	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14721173	14721268	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14721269	14721420	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14721421	14721504	0.97	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14721421	14721504	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	intron	14721505	14721609	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	CDS	14721610	14721699	0.97	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	exon	14721610	14721699	.	+	.	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
Phchi.S1	AUGUSTUS	stop_codon	14721700	14721702	.	+	0	transcript_id "Phchi.S1G225400.t2"; gene_id "Phchi.S1G225400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4534.t1 is derived from g1704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10989134	10996951	.	+	.	Phchi.S1G169300
Phchi.S1	AUGUSTUS	transcript	10989134	10996951	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	start_codon	10989134	10989136	.	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10989134	10989468	0.91	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10989134	10989468	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10989469	10989729	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10989730	10991503	0.84	+	1	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10989730	10991503	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10991504	10991611	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10991612	10993042	0.92	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10991612	10993042	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10993043	10993177	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10993178	10993569	0.82	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10993178	10993569	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10993570	10993670	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10993671	10993786	0.93	+	1	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10993671	10993786	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10993787	10993922	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10993923	10994341	0.4	+	2	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10993923	10994341	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10994342	10994467	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10994468	10994527	0.27	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10994468	10994527	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10994528	10994616	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10994617	10994830	0.47	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10994617	10994830	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10994831	10995126	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10995127	10995531	0.72	+	2	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10995127	10995531	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10995532	10995631	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10995632	10995772	0.73	+	2	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10995632	10995772	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10995773	10995973	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10995974	10996085	0.77	+	2	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10995974	10996085	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10996086	10996178	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10996179	10996253	0.5	+	1	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10996179	10996253	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10996254	10996398	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10996399	10996569	0.51	+	1	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10996399	10996569	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10996570	10996672	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10996673	10996764	0.99	+	1	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10996673	10996764	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	intron	10996765	10996877	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	CDS	10996878	10996951	0.99	+	2	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	exon	10996878	10996951	.	+	.	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
Phchi.S1	AUGUSTUS	stop_codon	10996952	10996954	.	+	0	transcript_id "Phchi.S1G169300.t1"; gene_id "Phchi.S1G169300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6392.t1 is derived from g3564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22711506	22714083	.	+	.	Phchi.S1G355100
Phchi.S1	AUGUSTUS	transcript	22711506	22714083	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	start_codon	22711506	22711508	.	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22711506	22712285	0.98	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22711506	22712285	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22712286	22712374	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22712375	22712572	1	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22712375	22712572	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22712573	22712714	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22712715	22712774	1	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22712715	22712774	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22712775	22712879	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22712880	22712975	0.99	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22712880	22712975	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22712976	22713101	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22713102	22713126	1	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22713102	22713126	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22713127	22713268	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22713269	22713363	1	+	2	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22713269	22713363	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22713364	22713576	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22713577	22713743	1	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22713577	22713743	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22713744	22713824	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22713825	22713898	1	+	1	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22713825	22713898	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	intron	22713899	22713994	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	CDS	22713995	22714083	1	+	2	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	exon	22713995	22714083	.	+	.	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
Phchi.S1	AUGUSTUS	stop_codon	22714084	22714086	.	+	0	transcript_id "Phchi.S1G355100.t1"; gene_id "Phchi.S1G355100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5567.t1 is derived from g2737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17625763	17628180	.	+	.	Phchi.S1G272600
Phchi.S1	AUGUSTUS	transcript	17625763	17628180	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	start_codon	17625763	17625765	.	+	0	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	CDS	17625763	17626643	1	+	0	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	exon	17625763	17626643	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	intron	17626644	17626733	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	CDS	17626734	17627038	0.99	+	1	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	exon	17626734	17627038	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	intron	17627039	17627140	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	CDS	17627141	17627178	0.69	+	2	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	exon	17627141	17627178	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	intron	17627179	17627397	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	CDS	17627398	17628180	0.33	+	0	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	exon	17627398	17628180	.	+	.	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
Phchi.S1	AUGUSTUS	stop_codon	17628181	17628183	.	+	0	transcript_id "Phchi.S1G272600.t1"; gene_id "Phchi.S1G272600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4440.t1 is derived from g1609.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10529198	10530849	.	-	.	Phchi.S1G159900
Phchi.S1	AUGUSTUS	transcript	10529198	10530849	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	stop_codon	10529195	10529197	.	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529198	10529249	1	-	1	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529198	10529249	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529250	10529375	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529376	10529436	1	-	2	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529376	10529436	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529437	10529555	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529556	10529637	1	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529556	10529637	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529638	10529745	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529746	10529807	1	-	2	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529746	10529807	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529808	10529933	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529934	10530006	1	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529934	10530006	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10530007	10530132	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10530133	10530228	0.86	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10530133	10530228	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10530229	10530331	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10530332	10530430	0.89	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10530332	10530430	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10530431	10530582	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10530583	10530849	0.99	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10530583	10530849	.	-	.	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	start_codon	10530847	10530849	.	-	0	transcript_id "Phchi.S1G159900.t1"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	transcript	10529198	10530849	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	stop_codon	10529195	10529197	.	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529198	10529249	1	-	1	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529198	10529249	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529250	10529375	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529376	10529436	1	-	2	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529376	10529436	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529437	10529555	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529556	10529637	1	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529556	10529637	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529638	10529745	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529746	10529807	1	-	2	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529746	10529807	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10529808	10529933	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10529934	10530006	1	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10529934	10530006	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10530007	10530132	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10530133	10530228	0.76	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10530133	10530228	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10530229	10530331	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10530332	10530457	0.53	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10530332	10530457	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	intron	10530458	10530582	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	CDS	10530583	10530849	0.95	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	exon	10530583	10530849	.	-	.	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
Phchi.S1	AUGUSTUS	start_codon	10530847	10530849	.	-	0	transcript_id "Phchi.S1G159900.t2"; gene_id "Phchi.S1G159900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13208.t1 is derived from g11673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4669437	4670537	.	-	.	Phchi.S3G052700
Phchi.S3	AUGUSTUS	transcript	4669437	4670537	.	-	.	transcript_id "Phchi.S3G052700.t1"; gene_id "Phchi.S3G052700"
Phchi.S3	AUGUSTUS	stop_codon	4669434	4669436	.	-	0	transcript_id "Phchi.S3G052700.t1"; gene_id "Phchi.S3G052700"
Phchi.S3	AUGUSTUS	CDS	4669437	4670537	0.95	-	0	transcript_id "Phchi.S3G052700.t1"; gene_id "Phchi.S3G052700"
Phchi.S3	AUGUSTUS	exon	4669437	4670537	.	-	.	transcript_id "Phchi.S3G052700.t1"; gene_id "Phchi.S3G052700"
Phchi.S3	AUGUSTUS	start_codon	4670535	4670537	.	-	0	transcript_id "Phchi.S3G052700.t1"; gene_id "Phchi.S3G052700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3509.t1 is derived from g678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4133820	4134326	.	-	.	Phchi.S1G066800
Phchi.S1	AUGUSTUS	transcript	4133820	4134326	.	-	.	transcript_id "Phchi.S1G066800.t1"; gene_id "Phchi.S1G066800"
Phchi.S1	AUGUSTUS	stop_codon	4133817	4133819	.	-	0	transcript_id "Phchi.S1G066800.t1"; gene_id "Phchi.S1G066800"
Phchi.S1	AUGUSTUS	CDS	4133820	4134326	0.87	-	0	transcript_id "Phchi.S1G066800.t1"; gene_id "Phchi.S1G066800"
Phchi.S1	AUGUSTUS	exon	4133820	4134326	.	-	.	transcript_id "Phchi.S1G066800.t1"; gene_id "Phchi.S1G066800"
Phchi.S1	AUGUSTUS	start_codon	4134324	4134326	.	-	0	transcript_id "Phchi.S1G066800.t1"; gene_id "Phchi.S1G066800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4571.t1 is derived from g1741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11162942	11164369	.	+	.	Phchi.S1G173000
Phchi.S1	AUGUSTUS	transcript	11162942	11164369	.	+	.	transcript_id "Phchi.S1G173000.t1"; gene_id "Phchi.S1G173000"
Phchi.S1	AUGUSTUS	start_codon	11162942	11162944	.	+	0	transcript_id "Phchi.S1G173000.t1"; gene_id "Phchi.S1G173000"
Phchi.S1	AUGUSTUS	CDS	11162942	11164369	1	+	0	transcript_id "Phchi.S1G173000.t1"; gene_id "Phchi.S1G173000"
Phchi.S1	AUGUSTUS	exon	11162942	11164369	.	+	.	transcript_id "Phchi.S1G173000.t1"; gene_id "Phchi.S1G173000"
Phchi.S1	AUGUSTUS	stop_codon	11164370	11164372	.	+	0	transcript_id "Phchi.S1G173000.t1"; gene_id "Phchi.S1G173000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8717.t1 is derived from g5892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37631867	37636405	.	-	.	Phchi.S1G587600
Phchi.S1	AUGUSTUS	transcript	37631867	37636405	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	stop_codon	37631864	37631866	.	-	0	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37631867	37632079	1	-	0	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37631867	37632079	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	intron	37632080	37632204	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37632205	37632420	1	-	0	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37632205	37632420	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	intron	37632421	37632494	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37632495	37633225	1	-	2	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37632495	37633225	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	intron	37633226	37633414	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37633415	37634527	1	-	2	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37633415	37634527	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	intron	37634528	37634892	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37634893	37635017	0.71	-	1	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37634893	37635017	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	intron	37635018	37635121	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37635122	37635310	0.82	-	1	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37635122	37635310	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	intron	37635311	37635470	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	CDS	37635471	37636405	0.3	-	0	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	exon	37635471	37636405	.	-	.	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
Phchi.S1	AUGUSTUS	start_codon	37636403	37636405	.	-	0	transcript_id "Phchi.S1G587600.t1"; gene_id "Phchi.S1G587600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6922.t1 is derived from g4094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26009846	26011912	.	-	.	Phchi.S1G408100
Phchi.S1	AUGUSTUS	transcript	26009846	26011912	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	stop_codon	26009843	26009845	.	-	0	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	CDS	26009846	26009992	0.56	-	0	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	exon	26009846	26009992	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	intron	26009993	26010118	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	CDS	26010119	26010336	0.84	-	2	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	exon	26010119	26010336	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	intron	26010337	26010479	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	CDS	26010480	26010509	0.27	-	2	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	exon	26010480	26010509	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	intron	26010510	26010640	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	CDS	26010641	26010714	0.26	-	1	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	exon	26010641	26010714	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	intron	26010715	26010824	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	CDS	26010825	26011272	0.54	-	2	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	exon	26010825	26011272	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	intron	26011273	26011587	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	CDS	26011588	26011912	0.32	-	0	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	exon	26011588	26011912	.	-	.	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
Phchi.S1	AUGUSTUS	start_codon	26011910	26011912	.	-	0	transcript_id "Phchi.S1G408100.t1"; gene_id "Phchi.S1G408100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8814.t1 is derived from g5989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38110408	38114407	.	-	.	Phchi.S1G597300
Phchi.S1	AUGUSTUS	transcript	38110408	38114407	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	stop_codon	38110405	38110407	.	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38110408	38110464	0.58	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38110408	38110464	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38110465	38110552	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38110553	38110720	0.48	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38110553	38110720	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38110721	38110810	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38110811	38110876	1	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38110811	38110876	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38110877	38110998	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38110999	38111755	0.99	-	1	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38110999	38111755	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38111756	38111986	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38111987	38112029	0.86	-	2	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38111987	38112029	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38112030	38112110	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38112111	38112205	0.86	-	1	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38112111	38112205	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38112206	38112355	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38112356	38112658	1	-	1	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38112356	38112658	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38112659	38112866	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38112867	38113025	1	-	1	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38112867	38113025	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38113026	38113122	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38113123	38113208	1	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38113123	38113208	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38113209	38113333	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38113334	38113411	1	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38113334	38113411	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38113412	38113612	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38113613	38113720	1	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38113613	38113720	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38113721	38113903	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38113904	38114107	1	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38113904	38114107	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	intron	38114108	38114314	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	CDS	38114315	38114407	1	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	exon	38114315	38114407	.	-	.	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
Phchi.S1	AUGUSTUS	start_codon	38114405	38114407	.	-	0	transcript_id "Phchi.S1G597300.t1"; gene_id "Phchi.S1G597300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14344.t1 is derived from g12811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12312291	12314466	.	+	.	Phchi.S3G166300
Phchi.S3	AUGUSTUS	transcript	12312291	12314466	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	start_codon	12312291	12312293	.	+	0	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12312291	12312718	0.91	+	0	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12312291	12312718	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	intron	12312719	12312873	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12312874	12313052	1	+	1	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12312874	12313052	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	intron	12313053	12313186	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12313187	12313398	1	+	2	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12313187	12313398	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	intron	12313399	12313515	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12313516	12313770	1	+	0	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12313516	12313770	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	intron	12313771	12313912	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12313913	12313999	1	+	0	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12313913	12313999	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	intron	12314000	12314090	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12314091	12314263	1	+	0	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12314091	12314263	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	intron	12314264	12314363	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	CDS	12314364	12314466	1	+	1	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	exon	12314364	12314466	.	+	.	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
Phchi.S3	AUGUSTUS	stop_codon	12314467	12314469	.	+	0	transcript_id "Phchi.S3G166300.t1"; gene_id "Phchi.S3G166300"
# This transcript jg11122.t2 is derived from g15172.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11123.t1 is derived from g15173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4266184	4266807	.	-	.	Phchi.S4G070500
Phchi.S4	AUGUSTUS	transcript	4266184	4266807	.	-	.	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	stop_codon	4266181	4266183	.	-	0	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	CDS	4266184	4266314	0.83	-	2	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	exon	4266184	4266314	.	-	.	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	intron	4266315	4266503	.	-	.	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	CDS	4266504	4266807	0.86	-	0	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	exon	4266504	4266807	.	-	.	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	start_codon	4266805	4266807	.	-	0	transcript_id "Phchi.S4G070500.t1"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	transcript	4266260	4266807	.	-	.	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	stop_codon	4266257	4266259	.	-	0	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	CDS	4266260	4266342	0.62	-	2	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	exon	4266260	4266342	.	-	.	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	intron	4266343	4266503	.	-	.	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	CDS	4266504	4266807	0.6	-	0	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	exon	4266504	4266807	.	-	.	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
Phchi.S4	AUGUSTUS	start_codon	4266805	4266807	.	-	0	transcript_id "Phchi.S4G070500.t2"; gene_id "Phchi.S4G070500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14823.t1 is derived from g13291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14892160	14896986	.	-	.	Phchi.S3G214200
Phchi.S3	AUGUSTUS	transcript	14892160	14896986	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	stop_codon	14892157	14892159	.	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14892160	14892257	1	-	2	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14892160	14892257	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14892258	14892354	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14892355	14892484	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14892355	14892484	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14892485	14892608	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14892609	14892698	0.98	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14892609	14892698	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14892699	14892804	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14892805	14892910	1	-	1	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14892805	14892910	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14892911	14892995	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14892996	14893096	0.87	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14892996	14893096	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14893097	14893200	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14893201	14893296	0.74	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14893201	14893296	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14893297	14893377	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14893378	14893474	1	-	1	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14893378	14893474	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14893475	14893545	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14893546	14893682	0.99	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14893546	14893682	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14893683	14893800	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14893801	14893932	0.98	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14893801	14893932	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14893933	14894023	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14894024	14894122	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14894024	14894122	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14894123	14894318	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14894319	14894516	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14894319	14894516	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14894517	14894593	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14894594	14894680	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14894594	14894680	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14894681	14894838	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14894839	14894929	1	-	1	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14894839	14894929	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14894930	14895062	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14895063	14895118	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14895063	14895118	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14895119	14895264	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14895265	14895417	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14895265	14895417	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14895418	14895502	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14895503	14895595	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14895503	14895595	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14895596	14895713	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14895714	14895812	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14895714	14895812	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14895813	14895902	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14895903	14895964	1	-	2	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14895903	14895964	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14895965	14896075	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14896076	14896171	1	-	2	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14896076	14896171	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14896172	14896309	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14896310	14896409	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14896310	14896409	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14896410	14896520	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14896521	14896592	1	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14896521	14896592	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14896593	14896680	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14896681	14896731	0.94	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14896681	14896731	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	intron	14896732	14896836	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	CDS	14896837	14896986	0.92	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	exon	14896837	14896986	.	-	.	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
Phchi.S3	AUGUSTUS	start_codon	14896984	14896986	.	-	0	transcript_id "Phchi.S3G214200.t1"; gene_id "Phchi.S3G214200"
# This transcript jg3959.t2 is derived from g1128.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3960.t1 is derived from g1129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6729298	6730831	.	+	.	Phchi.S1G111900
Phchi.S1	AUGUSTUS	transcript	6729298	6730831	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	start_codon	6729298	6729300	.	+	0	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	CDS	6729298	6729471	0.41	+	0	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	exon	6729298	6729471	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	intron	6729472	6729661	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	CDS	6729662	6729785	0.5	+	0	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	exon	6729662	6729785	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	intron	6729786	6729858	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	CDS	6729859	6729923	0.83	+	2	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	exon	6729859	6729923	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	intron	6729924	6730172	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	CDS	6730173	6730334	0.95	+	0	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	exon	6730173	6730334	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	intron	6730335	6730540	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	CDS	6730541	6730831	0.95	+	0	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	exon	6730541	6730831	.	+	.	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
Phchi.S1	AUGUSTUS	stop_codon	6730832	6730834	.	+	0	transcript_id "Phchi.S1G111900.t1"; gene_id "Phchi.S1G111900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6702.t1 is derived from g3874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24598474	24601035	.	+	.	Phchi.S1G386100
Phchi.S1	AUGUSTUS	transcript	24598474	24601035	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	start_codon	24598474	24598476	.	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24598474	24598612	0.53	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24598474	24598612	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24598613	24598686	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24598687	24598769	1	+	2	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24598687	24598769	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24598770	24598963	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24598964	24599041	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24598964	24599041	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24599042	24599127	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24599128	24599277	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24599128	24599277	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24599278	24599369	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24599370	24599456	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24599370	24599456	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24599457	24599643	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24599644	24599697	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24599644	24599697	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24599698	24599829	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24599830	24599920	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24599830	24599920	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24599921	24600040	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24600041	24600111	0.99	+	2	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24600041	24600111	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24600112	24600241	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24600242	24600311	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24600242	24600311	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24600312	24600415	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24600416	24600468	0.84	+	2	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24600416	24600468	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24600469	24600558	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24600559	24600652	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24600559	24600652	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24600653	24600762	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24600763	24600860	1	+	2	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24600763	24600860	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	intron	24600861	24600951	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	CDS	24600952	24601035	1	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	exon	24600952	24601035	.	+	.	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
Phchi.S1	AUGUSTUS	stop_codon	24601036	24601038	.	+	0	transcript_id "Phchi.S1G386100.t1"; gene_id "Phchi.S1G386100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7208.t1 is derived from g4380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27640851	27641186	.	-	.	Phchi.S1G436700
Phchi.S1	AUGUSTUS	transcript	27640851	27641186	.	-	.	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	stop_codon	27640848	27640850	.	-	0	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	CDS	27640851	27640986	0.04	-	1	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	exon	27640851	27640986	.	-	.	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	intron	27640987	27641067	.	-	.	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	CDS	27641068	27641186	0.35	-	0	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	exon	27641068	27641186	.	-	.	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
Phchi.S1	AUGUSTUS	start_codon	27641184	27641186	.	-	0	transcript_id "Phchi.S1G436700.t1"; gene_id "Phchi.S1G436700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4937.t1 is derived from g2107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13657605	13659989	.	-	.	Phchi.S1G209600
Phchi.S1	AUGUSTUS	transcript	13657605	13659989	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	stop_codon	13657602	13657604	.	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13657605	13657653	0.97	-	1	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13657605	13657653	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	intron	13657654	13657973	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13657974	13658710	0.91	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13657974	13658710	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	intron	13658711	13658817	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13658818	13658880	0.95	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13658818	13658880	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	intron	13658881	13659028	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13659029	13659406	1	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13659029	13659406	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	intron	13659407	13659516	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13659517	13659593	1	-	2	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13659517	13659593	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	intron	13659594	13659665	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13659666	13659741	1	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13659666	13659741	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	intron	13659742	13659824	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	CDS	13659825	13659989	0.92	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	exon	13659825	13659989	.	-	.	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
Phchi.S1	AUGUSTUS	start_codon	13659987	13659989	.	-	0	transcript_id "Phchi.S1G209600.t1"; gene_id "Phchi.S1G209600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10094.t1 is derived from g7270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45724248	45727366	.	-	.	Phchi.S1G725300
Phchi.S1	AUGUSTUS	transcript	45724248	45727366	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	stop_codon	45724245	45724247	.	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45724248	45724303	0.66	-	2	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45724248	45724303	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45724304	45724388	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45724389	45724494	0.64	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45724389	45724494	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45724495	45724597	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45724598	45724693	0.89	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45724598	45724693	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45724694	45724771	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45724772	45724841	1	-	1	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45724772	45724841	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45724842	45725016	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45725017	45725297	0.92	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45725017	45725297	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45725298	45725401	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45725402	45725476	0.92	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45725402	45725476	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45725477	45725556	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45725557	45725743	1	-	1	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45725557	45725743	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45725744	45725843	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45725844	45725920	1	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45725844	45725920	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45725921	45726000	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45726001	45726096	1	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45726001	45726096	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45726097	45726251	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45726252	45726305	1	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45726252	45726305	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45726306	45726432	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45726433	45726521	0.69	-	2	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45726433	45726521	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45726522	45726631	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45726632	45726702	0.98	-	1	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45726632	45726702	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45726703	45726776	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45726777	45726979	1	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45726777	45726979	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	intron	45726980	45727051	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	CDS	45727052	45727366	0.99	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	exon	45727052	45727366	.	-	.	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
Phchi.S1	AUGUSTUS	start_codon	45727364	45727366	.	-	0	transcript_id "Phchi.S1G725300.t1"; gene_id "Phchi.S1G725300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15744.t1 is derived from g14214.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21028493	21031222	.	-	.	Phchi.S3G306300
Phchi.S3	AUGUSTUS	transcript	21028493	21031222	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	stop_codon	21028490	21028492	.	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21028493	21028744	0.95	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21028493	21028744	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21028745	21028870	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21028871	21029013	0.99	-	2	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21028871	21029013	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029014	21029126	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029127	21029194	1	-	1	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029127	21029194	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029195	21029363	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029364	21029427	1	-	2	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029364	21029427	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029428	21029500	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029501	21029520	0.7	-	1	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029501	21029520	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029521	21029865	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029866	21029899	0.85	-	2	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029866	21029899	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029900	21029983	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029984	21030057	1	-	1	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029984	21030057	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030058	21030143	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030144	21030253	1	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030144	21030253	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030254	21030339	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030340	21030456	1	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030340	21030456	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030457	21030541	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030542	21030595	0.96	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030542	21030595	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030596	21030699	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030700	21030813	0.98	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030700	21030813	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030814	21030905	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030906	21031010	1	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030906	21031010	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21031011	21031087	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21031088	21031222	0.6	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21031088	21031222	.	-	.	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	start_codon	21031220	21031222	.	-	0	transcript_id "Phchi.S3G306300.t1"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	transcript	21028493	21031222	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	stop_codon	21028490	21028492	.	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21028493	21028744	0.98	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21028493	21028744	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21028745	21028870	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21028871	21029013	0.99	-	2	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21028871	21029013	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029014	21029126	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029127	21029194	1	-	1	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029127	21029194	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029195	21029363	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029364	21029427	1	-	2	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029364	21029427	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029428	21029500	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029501	21029561	0.61	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029501	21029561	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029562	21029820	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029821	21029882	0.61	-	2	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029821	21029882	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21029883	21029983	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21029984	21030057	0.92	-	1	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21029984	21030057	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030058	21030143	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030144	21030253	1	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030144	21030253	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030254	21030339	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030340	21030456	1	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030340	21030456	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030457	21030541	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030542	21030595	0.98	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030542	21030595	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030596	21030699	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030700	21030813	0.99	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030700	21030813	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21030814	21030905	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21030906	21031010	1	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21030906	21031010	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	intron	21031011	21031087	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	CDS	21031088	21031222	0.57	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	exon	21031088	21031222	.	-	.	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
Phchi.S3	AUGUSTUS	start_codon	21031220	21031222	.	-	0	transcript_id "Phchi.S3G306300.t2"; gene_id "Phchi.S3G306300"
# This transcript jg2432.t2 is derived from g9352.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2433.t1 is derived from g9353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6622707	6624637	.	-	.	Phchi.S5G104200
Phchi.S5	AUGUSTUS	transcript	6622707	6624637	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	stop_codon	6622704	6622706	.	-	0	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6622707	6622724	0.51	-	0	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6622707	6622724	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6622725	6622909	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6622910	6622925	0.99	-	1	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6622910	6622925	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6622926	6623001	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6623002	6623076	1	-	1	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6623002	6623076	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6623077	6623164	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6623165	6623293	1	-	1	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6623165	6623293	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6623294	6623379	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6623380	6623640	1	-	1	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6623380	6623640	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6623641	6623740	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6623741	6623900	1	-	2	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6623741	6623900	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6623901	6623981	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6623982	6624074	1	-	2	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6623982	6624074	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6624075	6624152	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6624153	6624402	0.99	-	0	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6624153	6624402	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	intron	6624403	6624592	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	CDS	6624593	6624637	0.85	-	0	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	exon	6624593	6624637	.	-	.	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
Phchi.S5	AUGUSTUS	start_codon	6624635	6624637	.	-	0	transcript_id "Phchi.S5G104200.t1"; gene_id "Phchi.S5G104200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12317.t1 is derived from g7993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10422836	10423243	.	-	.	Phchi.S2G039700
Phchi.S2	AUGUSTUS	transcript	10422836	10423243	.	-	.	transcript_id "Phchi.S2G039700.t1"; gene_id "Phchi.S2G039700"
Phchi.S2	AUGUSTUS	stop_codon	10422833	10422835	.	-	0	transcript_id "Phchi.S2G039700.t1"; gene_id "Phchi.S2G039700"
Phchi.S2	AUGUSTUS	CDS	10422836	10423243	0.93	-	0	transcript_id "Phchi.S2G039700.t1"; gene_id "Phchi.S2G039700"
Phchi.S2	AUGUSTUS	exon	10422836	10423243	.	-	.	transcript_id "Phchi.S2G039700.t1"; gene_id "Phchi.S2G039700"
Phchi.S2	AUGUSTUS	start_codon	10423241	10423243	.	-	0	transcript_id "Phchi.S2G039700.t1"; gene_id "Phchi.S2G039700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15959.t1 is derived from g11142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	36683	37986	.	-	.	Phchi.C91G000600
Phchi.C91	AUGUSTUS	transcript	36683	37986	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	stop_codon	36680	36682	.	-	0	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	36683	36720	0.51	-	2	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	36683	36720	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	intron	36721	36824	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	36825	36922	0.55	-	1	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	36825	36922	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	intron	36923	37087	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	37088	37139	0.73	-	2	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	37088	37139	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	intron	37140	37327	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	37328	37351	0.43	-	2	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	37328	37351	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	intron	37352	37498	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	37499	37561	1	-	2	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	37499	37561	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	intron	37562	37661	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	37662	37809	1	-	0	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	37662	37809	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	intron	37810	37896	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	CDS	37897	37986	0.8	-	0	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	exon	37897	37986	.	-	.	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
Phchi.C91	AUGUSTUS	start_codon	37984	37986	.	-	0	transcript_id "Phchi.C91G000600.t1"; gene_id "Phchi.C91G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2796.t1 is derived from g9716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8934419	8934781	.	+	.	Phchi.S5G140500
Phchi.S5	AUGUSTUS	transcript	8934419	8934781	.	+	.	transcript_id "Phchi.S5G140500.t1"; gene_id "Phchi.S5G140500"
Phchi.S5	AUGUSTUS	start_codon	8934419	8934421	.	+	0	transcript_id "Phchi.S5G140500.t1"; gene_id "Phchi.S5G140500"
Phchi.S5	AUGUSTUS	CDS	8934419	8934781	0.9	+	0	transcript_id "Phchi.S5G140500.t1"; gene_id "Phchi.S5G140500"
Phchi.S5	AUGUSTUS	exon	8934419	8934781	.	+	.	transcript_id "Phchi.S5G140500.t1"; gene_id "Phchi.S5G140500"
Phchi.S5	AUGUSTUS	stop_codon	8934782	8934784	.	+	0	transcript_id "Phchi.S5G140500.t1"; gene_id "Phchi.S5G140500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15155.t1 is derived from g13623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17294705	17298049	.	+	.	Phchi.S3G247400
Phchi.S3	AUGUSTUS	transcript	17294705	17298049	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	start_codon	17294705	17294707	.	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17294705	17294839	0.99	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17294705	17294839	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17294840	17294936	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17294937	17295169	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17294937	17295169	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17295170	17295255	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17295256	17295374	1	+	1	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17295256	17295374	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17295375	17295458	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17295459	17295520	1	+	2	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17295459	17295520	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17295521	17295685	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17295686	17295804	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17295686	17295804	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17295805	17295912	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17295913	17296030	1	+	1	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17295913	17296030	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17296031	17296160	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17296161	17296309	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17296161	17296309	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17296310	17296441	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17296442	17296515	0.96	+	1	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17296442	17296515	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17296516	17296627	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17296628	17296797	0.95	+	2	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17296628	17296797	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17296798	17296899	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17296900	17297010	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17296900	17297010	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17297011	17297129	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17297130	17297297	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17297130	17297297	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17297298	17297390	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17297391	17297462	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17297391	17297462	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17297463	17297627	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17297628	17297679	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17297628	17297679	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17297680	17297778	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17297779	17297858	1	+	2	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17297779	17297858	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	intron	17297859	17297947	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	CDS	17297948	17298049	1	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	exon	17297948	17298049	.	+	.	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
Phchi.S3	AUGUSTUS	stop_codon	17298050	17298052	.	+	0	transcript_id "Phchi.S3G247400.t1"; gene_id "Phchi.S3G247400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg907.t1 is derived from g10689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6376447	6378896	.	+	.	Phchi.S6G086600
Phchi.S6	AUGUSTUS	transcript	6376447	6378896	.	+	.	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	start_codon	6376447	6376449	.	+	0	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	CDS	6376447	6377064	0.98	+	0	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	exon	6376447	6377064	.	+	.	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	intron	6377065	6377183	.	+	.	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	CDS	6377184	6378896	0.7	+	0	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	exon	6377184	6378896	.	+	.	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
Phchi.S6	AUGUSTUS	stop_codon	6378897	6378899	.	+	0	transcript_id "Phchi.S6G086600.t1"; gene_id "Phchi.S6G086600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5448.t1 is derived from g2618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16908838	16909511	.	-	.	Phchi.S1G260700
Phchi.S1	AUGUSTUS	transcript	16908838	16909511	.	-	.	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	stop_codon	16908835	16908837	.	-	0	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	CDS	16908838	16909013	1	-	2	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	exon	16908838	16909013	.	-	.	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	intron	16909014	16909101	.	-	.	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	CDS	16909102	16909183	0.58	-	0	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	exon	16909102	16909183	.	-	.	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	intron	16909184	16909391	.	-	.	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	CDS	16909392	16909511	0.95	-	0	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	exon	16909392	16909511	.	-	.	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
Phchi.S1	AUGUSTUS	start_codon	16909509	16909511	.	-	0	transcript_id "Phchi.S1G260700.t1"; gene_id "Phchi.S1G260700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7278.t1 is derived from g4450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28105660	28107036	.	+	.	Phchi.S1G443700
Phchi.S1	AUGUSTUS	transcript	28105660	28107036	.	+	.	transcript_id "Phchi.S1G443700.t1"; gene_id "Phchi.S1G443700"
Phchi.S1	AUGUSTUS	start_codon	28105660	28105662	.	+	0	transcript_id "Phchi.S1G443700.t1"; gene_id "Phchi.S1G443700"
Phchi.S1	AUGUSTUS	CDS	28105660	28107036	0.68	+	0	transcript_id "Phchi.S1G443700.t1"; gene_id "Phchi.S1G443700"
Phchi.S1	AUGUSTUS	exon	28105660	28107036	.	+	.	transcript_id "Phchi.S1G443700.t1"; gene_id "Phchi.S1G443700"
Phchi.S1	AUGUSTUS	stop_codon	28107037	28107039	.	+	0	transcript_id "Phchi.S1G443700.t1"; gene_id "Phchi.S1G443700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4679.t1 is derived from g1849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11794421	11795767	.	-	.	Phchi.S1G183800
Phchi.S1	AUGUSTUS	transcript	11794421	11795767	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	stop_codon	11794418	11794420	.	-	0	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	CDS	11794421	11794981	1	-	0	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	exon	11794421	11794981	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	intron	11794982	11795071	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	CDS	11795072	11795263	0.99	-	0	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	exon	11795072	11795263	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	intron	11795264	11795365	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	CDS	11795366	11795598	0.99	-	2	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	exon	11795366	11795598	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	intron	11795599	11795682	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	CDS	11795683	11795767	0.36	-	0	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	exon	11795683	11795767	.	-	.	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
Phchi.S1	AUGUSTUS	start_codon	11795765	11795767	.	-	0	transcript_id "Phchi.S1G183800.t1"; gene_id "Phchi.S1G183800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11061.t1 is derived from g15111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3937071	3938529	.	-	.	Phchi.S4G064300
Phchi.S4	AUGUSTUS	transcript	3937071	3938529	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	stop_codon	3937068	3937070	.	-	0	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	CDS	3937071	3937256	1	-	0	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	exon	3937071	3937256	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	intron	3937257	3937337	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	CDS	3937338	3937547	0.6	-	0	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	exon	3937338	3937547	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	intron	3937548	3937659	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	CDS	3937660	3937765	0.7	-	1	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	exon	3937660	3937765	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	intron	3937766	3937857	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	CDS	3937858	3938028	0.7	-	1	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	exon	3937858	3938028	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	intron	3938029	3938110	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	CDS	3938111	3938340	0.63	-	0	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	exon	3938111	3938340	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	intron	3938341	3938421	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	CDS	3938422	3938529	0.66	-	0	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	exon	3938422	3938529	.	-	.	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
Phchi.S4	AUGUSTUS	start_codon	3938527	3938529	.	-	0	transcript_id "Phchi.S4G064300.t1"; gene_id "Phchi.S4G064300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5727.t1 is derived from g2897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18575128	18575727	.	+	.	Phchi.S1G288600
Phchi.S1	AUGUSTUS	transcript	18575128	18575727	.	+	.	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	start_codon	18575128	18575130	.	+	0	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	CDS	18575128	18575161	0.82	+	0	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	exon	18575128	18575161	.	+	.	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	intron	18575162	18575491	.	+	.	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	CDS	18575492	18575727	0.02	+	2	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	exon	18575492	18575727	.	+	.	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
Phchi.S1	AUGUSTUS	stop_codon	18575728	18575730	.	+	0	transcript_id "Phchi.S1G288600.t1"; gene_id "Phchi.S1G288600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15943.t1 is derived from g5.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C101	AUGUSTUS	gene	30008	31740	.	-	.	Phchi.C101G000200
Phchi.C101	AUGUSTUS	transcript	30008	31740	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	stop_codon	30005	30007	.	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30008	30070	1	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30008	30070	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30071	30196	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30197	30465	1	-	2	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30197	30465	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30466	30622	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30623	30887	1	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30623	30887	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30888	30960	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30961	31026	1	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30961	31026	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31027	31168	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31169	31243	1	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31169	31243	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31244	31328	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31329	31406	1	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31329	31406	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31407	31559	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31560	31581	1	-	1	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31560	31581	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31582	31660	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31661	31740	0.85	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31661	31740	.	-	.	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	start_codon	31738	31740	.	-	0	transcript_id "Phchi.C101G000200.t1"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	transcript	30008	31740	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	stop_codon	30005	30007	.	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30008	30070	1	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30008	30070	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30071	30196	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30197	30465	1	-	2	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30197	30465	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30466	30622	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30623	30887	0.96	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30623	30887	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30888	30960	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30961	31026	0.97	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30961	31026	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31027	31168	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31169	31234	0.99	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31169	31234	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31235	31328	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31329	31406	0.99	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31329	31406	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31407	31559	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31560	31581	0.99	-	1	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31560	31581	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	31582	31660	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	31661	31740	0.73	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	31661	31740	.	-	.	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	start_codon	31738	31740	.	-	0	transcript_id "Phchi.C101G000200.t2"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	transcript	30008	30697	.	-	.	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	stop_codon	30005	30007	.	-	0	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30008	30070	0.92	-	0	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30008	30070	.	-	.	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30071	30196	.	-	.	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30197	30457	0.81	-	0	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30197	30457	.	-	.	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	intron	30458	30622	.	-	.	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	CDS	30623	30697	0.41	-	0	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	exon	30623	30697	.	-	.	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
Phchi.C101	AUGUSTUS	start_codon	30695	30697	.	-	0	transcript_id "Phchi.C101G000200.t3"; gene_id "Phchi.C101G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7138.t1 is derived from g4310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27137243	27138611	.	-	.	Phchi.S1G429700
Phchi.S1	AUGUSTUS	transcript	27137243	27138611	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	stop_codon	27137240	27137242	.	-	0	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27137243	27137582	0.65	-	1	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27137243	27137582	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	intron	27137583	27137669	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27137670	27137790	0.66	-	2	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27137670	27137790	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	intron	27137791	27137894	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27137895	27137950	0.66	-	1	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27137895	27137950	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	intron	27137951	27138032	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27138033	27138106	0.66	-	0	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27138033	27138106	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	intron	27138107	27138243	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27138244	27138314	1	-	2	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27138244	27138314	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	intron	27138315	27138402	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27138403	27138451	1	-	0	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27138403	27138451	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	intron	27138452	27138608	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	CDS	27138609	27138611	1	-	0	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	exon	27138609	27138611	.	-	.	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
Phchi.S1	AUGUSTUS	start_codon	27138609	27138611	.	-	0	transcript_id "Phchi.S1G429700.t1"; gene_id "Phchi.S1G429700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11824.t1 is derived from g15876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8412877	8413467	.	+	.	Phchi.S4G140600
Phchi.S4	AUGUSTUS	transcript	8412877	8413467	.	+	.	transcript_id "Phchi.S4G140600.t1"; gene_id "Phchi.S4G140600"
Phchi.S4	AUGUSTUS	start_codon	8412877	8412879	.	+	0	transcript_id "Phchi.S4G140600.t1"; gene_id "Phchi.S4G140600"
Phchi.S4	AUGUSTUS	CDS	8412877	8413467	0.99	+	0	transcript_id "Phchi.S4G140600.t1"; gene_id "Phchi.S4G140600"
Phchi.S4	AUGUSTUS	exon	8412877	8413467	.	+	.	transcript_id "Phchi.S4G140600.t1"; gene_id "Phchi.S4G140600"
Phchi.S4	AUGUSTUS	stop_codon	8413468	8413470	.	+	0	transcript_id "Phchi.S4G140600.t1"; gene_id "Phchi.S4G140600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2967.t1 is derived from g136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	886091	888439	.	+	.	Phchi.S1G012600
Phchi.S1	AUGUSTUS	transcript	886091	888439	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	start_codon	886091	886093	.	+	0	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886091	886185	0.98	+	0	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886091	886185	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886186	886310	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886311	886416	1	+	1	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886311	886416	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886417	886582	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886583	886650	1	+	0	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886583	886650	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886651	886759	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886760	886974	1	+	1	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886760	886974	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886975	887053	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887054	887117	1	+	2	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887054	887117	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887118	887216	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887217	887289	1	+	1	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887217	887289	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887290	887416	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887417	887537	1	+	0	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887417	887537	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887538	887672	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887673	887760	1	+	2	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887673	887760	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887761	887856	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887857	887982	0.99	+	1	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887857	887982	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887983	888091	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	888092	888201	1	+	1	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	888092	888201	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	888202	888293	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	888294	888439	0.96	+	2	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	888294	888439	.	+	.	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	stop_codon	888440	888442	.	+	0	transcript_id "Phchi.S1G012600.t1"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	transcript	886091	888439	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	start_codon	886091	886093	.	+	0	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886091	886185	0.98	+	0	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886091	886185	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886186	886310	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886311	886416	1	+	1	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886311	886416	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886417	886579	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886580	886650	1	+	0	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886580	886650	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886651	886759	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	886760	886974	1	+	1	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	886760	886974	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	886975	887053	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887054	887117	1	+	2	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887054	887117	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887118	887216	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887217	887289	1	+	1	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887217	887289	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887290	887416	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887417	887537	1	+	0	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887417	887537	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887538	887672	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887673	887760	1	+	2	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887673	887760	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887761	887856	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	887857	887982	1	+	1	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	887857	887982	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	887983	888091	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	888092	888201	0.98	+	1	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	888092	888201	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	intron	888202	888293	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	CDS	888294	888439	0.96	+	2	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	exon	888294	888439	.	+	.	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
Phchi.S1	AUGUSTUS	stop_codon	888440	888442	.	+	0	transcript_id "Phchi.S1G012600.t2"; gene_id "Phchi.S1G012600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13375.t1 is derived from g11841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6417537	6418780	.	+	.	Phchi.S3G069400
Phchi.S3	AUGUSTUS	transcript	6417537	6418780	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	start_codon	6417537	6417539	.	+	0	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	CDS	6417537	6417739	1	+	0	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	exon	6417537	6417739	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	intron	6417740	6418022	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	CDS	6418023	6418263	1	+	1	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	exon	6418023	6418263	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	intron	6418264	6418343	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	CDS	6418344	6418464	1	+	0	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	exon	6418344	6418464	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	intron	6418465	6418565	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	CDS	6418566	6418780	0.99	+	2	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	exon	6418566	6418780	.	+	.	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
Phchi.S3	AUGUSTUS	stop_codon	6418781	6418783	.	+	0	transcript_id "Phchi.S3G069400.t1"; gene_id "Phchi.S3G069400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6718.t1 is derived from g3890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24700177	24703408	.	-	.	Phchi.S1G387700
Phchi.S1	AUGUSTUS	transcript	24700177	24703408	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	stop_codon	24700174	24700176	.	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24700177	24700239	0.99	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24700177	24700239	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24700240	24700324	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24700325	24700528	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24700325	24700528	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24700529	24700647	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24700648	24700749	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24700648	24700749	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24700750	24700835	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24700836	24700900	1	-	2	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24700836	24700900	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24700901	24701046	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24701047	24701130	1	-	2	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24701047	24701130	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24701131	24701295	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24701296	24701368	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24701296	24701368	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24701369	24701455	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24701456	24701557	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24701456	24701557	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24701558	24701667	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24701668	24701787	0.99	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24701668	24701787	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24701788	24701924	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24701925	24702035	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24701925	24702035	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24702036	24702158	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24702159	24702230	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24702159	24702230	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24702231	24702339	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24702340	24702453	0.82	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24702340	24702453	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24702454	24702590	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24702591	24702689	1	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24702591	24702689	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	intron	24702690	24702964	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	CDS	24702965	24703408	0.48	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	exon	24702965	24703408	.	-	.	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
Phchi.S1	AUGUSTUS	start_codon	24703406	24703408	.	-	0	transcript_id "Phchi.S1G387700.t1"; gene_id "Phchi.S1G387700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2696.t1 is derived from g9616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8239007	8243055	.	+	.	Phchi.S5G130500
Phchi.S5	AUGUSTUS	transcript	8239007	8243055	.	+	.	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	start_codon	8239007	8239009	.	+	0	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	CDS	8239007	8239171	0.86	+	0	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	exon	8239007	8239171	.	+	.	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	intron	8239172	8239269	.	+	.	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	CDS	8239270	8239480	1	+	0	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	exon	8239270	8239480	.	+	.	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	intron	8239481	8239576	.	+	.	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	CDS	8239577	8243055	1	+	2	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	exon	8239577	8243055	.	+	.	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
Phchi.S5	AUGUSTUS	stop_codon	8243056	8243058	.	+	0	transcript_id "Phchi.S5G130500.t1"; gene_id "Phchi.S5G130500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10150.t1 is derived from g7326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45995993	45996633	.	+	.	Phchi.S1G730900
Phchi.S1	AUGUSTUS	transcript	45995993	45996633	.	+	.	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	start_codon	45995993	45995995	.	+	0	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	CDS	45995993	45996094	1	+	0	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	exon	45995993	45996094	.	+	.	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	intron	45996095	45996258	.	+	.	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	CDS	45996259	45996339	0.97	+	0	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	exon	45996259	45996339	.	+	.	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	intron	45996340	45996417	.	+	.	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	CDS	45996418	45996633	0.85	+	0	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	exon	45996418	45996633	.	+	.	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
Phchi.S1	AUGUSTUS	stop_codon	45996634	45996636	.	+	0	transcript_id "Phchi.S1G730900.t1"; gene_id "Phchi.S1G730900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9769.t1 is derived from g6945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43601473	43606013	.	-	.	Phchi.S1G692800
Phchi.S1	AUGUSTUS	transcript	43601473	43606013	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	stop_codon	43601470	43601472	.	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43601473	43601708	0.99	-	2	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43601473	43601708	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43601709	43601784	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43601785	43601878	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43601785	43601878	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43601879	43601968	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43601969	43602049	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43601969	43602049	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43602050	43602150	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43602151	43602199	1	-	1	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43602151	43602199	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43602200	43602288	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43602289	43602374	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43602289	43602374	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43602375	43602478	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43602479	43602556	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43602479	43602556	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43602557	43602648	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43602649	43602798	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43602649	43602798	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43602799	43602877	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43602878	43602916	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43602878	43602916	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43602917	43603009	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43603010	43603099	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43603010	43603099	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43603100	43603528	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43603529	43603591	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43603529	43603591	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43603592	43603713	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43603714	43603783	0.71	-	1	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43603714	43603783	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43603784	43603884	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43603885	43603928	0.95	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43603885	43603928	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43603929	43604032	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43604033	43604050	0.56	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43604033	43604050	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43604051	43604198	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43604199	43604249	0.97	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43604199	43604249	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43604250	43604389	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43604390	43604473	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43604390	43604473	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43604474	43604577	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43604578	43604642	0.98	-	2	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43604578	43604642	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43604643	43604744	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43604745	43604801	0.98	-	2	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43604745	43604801	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43604802	43604890	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43604891	43605008	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43604891	43605008	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43605009	43605138	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43605139	43605189	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43605139	43605189	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43605190	43605286	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43605287	43605373	1	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43605287	43605373	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43605374	43605540	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43605541	43605620	1	-	2	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43605541	43605620	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	intron	43605621	43605694	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	CDS	43605695	43606013	0.5	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	exon	43605695	43606013	.	-	.	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
Phchi.S1	AUGUSTUS	start_codon	43606011	43606013	.	-	0	transcript_id "Phchi.S1G692800.t1"; gene_id "Phchi.S1G692800"
# This transcript jg13816.t2 is derived from g12283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13817.t1 is derived from g12284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9048741	9051109	.	-	.	Phchi.S3G113600
Phchi.S3	AUGUSTUS	transcript	9048741	9051109	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	stop_codon	9048738	9048740	.	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9048741	9049011	0.99	-	1	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9048741	9049011	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9049012	9049106	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9049107	9049168	1	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9049107	9049168	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9049169	9049253	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9049254	9049391	0.99	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9049254	9049391	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9049392	9049497	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9049498	9049635	1	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9049498	9049635	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9049636	9049721	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9049722	9049895	1	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9049722	9049895	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9049896	9049986	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9049987	9050076	0.98	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9049987	9050076	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9050077	9050181	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9050182	9050411	1	-	2	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9050182	9050411	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9050412	9050520	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9050521	9050671	1	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9050521	9050671	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9050672	9050766	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9050767	9050909	1	-	2	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9050767	9050909	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	intron	9050910	9051003	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	CDS	9051004	9051109	0.99	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	exon	9051004	9051109	.	-	.	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
Phchi.S3	AUGUSTUS	start_codon	9051107	9051109	.	-	0	transcript_id "Phchi.S3G113600.t1"; gene_id "Phchi.S3G113600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12889.t1 is derived from g11354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3007441	3009639	.	+	.	Phchi.S3G020800
Phchi.S3	AUGUSTUS	transcript	3007441	3009639	.	+	.	transcript_id "Phchi.S3G020800.t1"; gene_id "Phchi.S3G020800"
Phchi.S3	AUGUSTUS	start_codon	3007441	3007443	.	+	0	transcript_id "Phchi.S3G020800.t1"; gene_id "Phchi.S3G020800"
Phchi.S3	AUGUSTUS	CDS	3007441	3009639	0.55	+	0	transcript_id "Phchi.S3G020800.t1"; gene_id "Phchi.S3G020800"
Phchi.S3	AUGUSTUS	exon	3007441	3009639	.	+	.	transcript_id "Phchi.S3G020800.t1"; gene_id "Phchi.S3G020800"
Phchi.S3	AUGUSTUS	stop_codon	3009640	3009642	.	+	0	transcript_id "Phchi.S3G020800.t1"; gene_id "Phchi.S3G020800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg130.t1 is derived from g9912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	710939	712290	.	-	.	Phchi.S6G008900
Phchi.S6	AUGUSTUS	transcript	710939	712290	.	-	.	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	stop_codon	710936	710938	.	-	0	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	CDS	710939	711058	0.91	-	0	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	exon	710939	711058	.	-	.	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	intron	711059	711189	.	-	.	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	CDS	711190	712290	0.99	-	0	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	exon	711190	712290	.	-	.	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
Phchi.S6	AUGUSTUS	start_codon	712288	712290	.	-	0	transcript_id "Phchi.S6G008900.t1"; gene_id "Phchi.S6G008900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1057.t1 is derived from g10840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7322489	7323183	.	+	.	Phchi.S6G101600
Phchi.S6	AUGUSTUS	transcript	7322489	7323183	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	start_codon	7322489	7322491	.	+	0	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	CDS	7322489	7322537	0.92	+	0	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	exon	7322489	7322537	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	intron	7322538	7322624	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	CDS	7322625	7322828	0.8	+	2	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	exon	7322625	7322828	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	intron	7322829	7322984	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	CDS	7322985	7323050	0.61	+	2	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	exon	7322985	7323050	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	intron	7323051	7323133	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	CDS	7323134	7323183	0.78	+	2	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	exon	7323134	7323183	.	+	.	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
Phchi.S6	AUGUSTUS	stop_codon	7323184	7323186	.	+	0	transcript_id "Phchi.S6G101600.t1"; gene_id "Phchi.S6G101600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15216.t1 is derived from g13684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17727900	17728988	.	-	.	Phchi.S3G253500
Phchi.S3	AUGUSTUS	transcript	17727900	17728865	.	-	.	transcript_id "Phchi.S3G253500.t1"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	stop_codon	17727897	17727899	.	-	0	transcript_id "Phchi.S3G253500.t1"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	CDS	17727900	17728865	0.35	-	0	transcript_id "Phchi.S3G253500.t1"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	exon	17727900	17728865	.	-	.	transcript_id "Phchi.S3G253500.t1"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	start_codon	17728863	17728865	.	-	0	transcript_id "Phchi.S3G253500.t1"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	transcript	17727900	17728988	.	-	.	transcript_id "Phchi.S3G253500.t2"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	stop_codon	17727897	17727899	.	-	0	transcript_id "Phchi.S3G253500.t2"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	CDS	17727900	17728988	0.34	-	0	transcript_id "Phchi.S3G253500.t2"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	exon	17727900	17728988	.	-	.	transcript_id "Phchi.S3G253500.t2"; gene_id "Phchi.S3G253500"
Phchi.S3	AUGUSTUS	start_codon	17728986	17728988	.	-	0	transcript_id "Phchi.S3G253500.t2"; gene_id "Phchi.S3G253500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11085.t1 is derived from g15135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4006111	4006584	.	-	.	Phchi.S4G066700
Phchi.S4	AUGUSTUS	transcript	4006111	4006584	.	-	.	transcript_id "Phchi.S4G066700.t1"; gene_id "Phchi.S4G066700"
Phchi.S4	AUGUSTUS	stop_codon	4006108	4006110	.	-	0	transcript_id "Phchi.S4G066700.t1"; gene_id "Phchi.S4G066700"
Phchi.S4	AUGUSTUS	CDS	4006111	4006584	0.96	-	0	transcript_id "Phchi.S4G066700.t1"; gene_id "Phchi.S4G066700"
Phchi.S4	AUGUSTUS	exon	4006111	4006584	.	-	.	transcript_id "Phchi.S4G066700.t1"; gene_id "Phchi.S4G066700"
Phchi.S4	AUGUSTUS	start_codon	4006582	4006584	.	-	0	transcript_id "Phchi.S4G066700.t1"; gene_id "Phchi.S4G066700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13391.t1 is derived from g11857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6513563	6513790	.	-	.	Phchi.S3G071000
Phchi.S3	AUGUSTUS	transcript	6513563	6513790	.	-	.	transcript_id "Phchi.S3G071000.t1"; gene_id "Phchi.S3G071000"
Phchi.S3	AUGUSTUS	stop_codon	6513560	6513562	.	-	0	transcript_id "Phchi.S3G071000.t1"; gene_id "Phchi.S3G071000"
Phchi.S3	AUGUSTUS	CDS	6513563	6513790	0.79	-	0	transcript_id "Phchi.S3G071000.t1"; gene_id "Phchi.S3G071000"
Phchi.S3	AUGUSTUS	exon	6513563	6513790	.	-	.	transcript_id "Phchi.S3G071000.t1"; gene_id "Phchi.S3G071000"
Phchi.S3	AUGUSTUS	start_codon	6513788	6513790	.	-	0	transcript_id "Phchi.S3G071000.t1"; gene_id "Phchi.S3G071000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1611.t1 is derived from g8530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2019835	2021050	.	-	.	Phchi.S5G022000
Phchi.S5	AUGUSTUS	transcript	2019835	2021050	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	stop_codon	2019832	2019834	.	-	0	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	CDS	2019835	2020116	0.99	-	0	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	exon	2019835	2020116	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	intron	2020117	2020209	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	CDS	2020210	2020394	1	-	2	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	exon	2020210	2020394	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	intron	2020395	2020488	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	CDS	2020489	2020882	1	-	0	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	exon	2020489	2020882	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	intron	2020883	2020963	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	CDS	2020964	2021050	0.83	-	0	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	exon	2020964	2021050	.	-	.	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
Phchi.S5	AUGUSTUS	start_codon	2021048	2021050	.	-	0	transcript_id "Phchi.S5G022000.t1"; gene_id "Phchi.S5G022000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12796.t1 is derived from g11261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2428566	2428889	.	+	.	Phchi.S3G011500
Phchi.S3	AUGUSTUS	transcript	2428566	2428889	.	+	.	transcript_id "Phchi.S3G011500.t1"; gene_id "Phchi.S3G011500"
Phchi.S3	AUGUSTUS	start_codon	2428566	2428568	.	+	0	transcript_id "Phchi.S3G011500.t1"; gene_id "Phchi.S3G011500"
Phchi.S3	AUGUSTUS	CDS	2428566	2428889	0.28	+	0	transcript_id "Phchi.S3G011500.t1"; gene_id "Phchi.S3G011500"
Phchi.S3	AUGUSTUS	exon	2428566	2428889	.	+	.	transcript_id "Phchi.S3G011500.t1"; gene_id "Phchi.S3G011500"
Phchi.S3	AUGUSTUS	stop_codon	2428890	2428892	.	+	0	transcript_id "Phchi.S3G011500.t1"; gene_id "Phchi.S3G011500"
# This transcript jg5672.t2 is derived from g2842.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5673.t1 is derived from g2843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18243380	18243815	.	+	.	Phchi.S1G283200
Phchi.S1	AUGUSTUS	transcript	18243380	18243815	.	+	.	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	start_codon	18243380	18243382	.	+	0	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	CDS	18243380	18243588	1	+	0	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	exon	18243380	18243588	.	+	.	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	intron	18243589	18243778	.	+	.	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	CDS	18243779	18243815	0.86	+	1	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	exon	18243779	18243815	.	+	.	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
Phchi.S1	AUGUSTUS	stop_codon	18243816	18243818	.	+	0	transcript_id "Phchi.S1G283200.t1"; gene_id "Phchi.S1G283200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1370.t1 is derived from g9815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C217	AUGUSTUS	gene	23567	24004	.	+	.	Phchi.C217G000400
Phchi.C217	AUGUSTUS	transcript	23567	24004	.	+	.	transcript_id "Phchi.C217G000400.t1"; gene_id "Phchi.C217G000400"
Phchi.C217	AUGUSTUS	start_codon	23567	23569	.	+	0	transcript_id "Phchi.C217G000400.t1"; gene_id "Phchi.C217G000400"
Phchi.C217	AUGUSTUS	CDS	23567	24004	1	+	0	transcript_id "Phchi.C217G000400.t1"; gene_id "Phchi.C217G000400"
Phchi.C217	AUGUSTUS	exon	23567	24004	.	+	.	transcript_id "Phchi.C217G000400.t1"; gene_id "Phchi.C217G000400"
Phchi.C217	AUGUSTUS	stop_codon	24005	24007	.	+	0	transcript_id "Phchi.C217G000400.t1"; gene_id "Phchi.C217G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4131.t1 is derived from g1300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8402353	8403790	.	+	.	Phchi.S1G129000
Phchi.S1	AUGUSTUS	transcript	8402353	8403790	.	+	.	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	start_codon	8402353	8402355	.	+	0	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	CDS	8402353	8402394	0.42	+	0	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	exon	8402353	8402394	.	+	.	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	intron	8402395	8402491	.	+	.	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	CDS	8402492	8403790	0.99	+	0	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	exon	8402492	8403790	.	+	.	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
Phchi.S1	AUGUSTUS	stop_codon	8403791	8403793	.	+	0	transcript_id "Phchi.S1G129000.t1"; gene_id "Phchi.S1G129000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15378.t1 is derived from g13846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18689650	18690094	.	-	.	Phchi.S3G269700
Phchi.S3	AUGUSTUS	transcript	18689650	18690094	.	-	.	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	stop_codon	18689647	18689649	.	-	0	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	CDS	18689650	18689717	0.67	-	2	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	exon	18689650	18689717	.	-	.	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	intron	18689718	18689907	.	-	.	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	CDS	18689908	18690094	0.67	-	0	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	exon	18689908	18690094	.	-	.	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
Phchi.S3	AUGUSTUS	start_codon	18690092	18690094	.	-	0	transcript_id "Phchi.S3G269700.t1"; gene_id "Phchi.S3G269700"
# This transcript jg14503.t2 is derived from g12971.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14504.t1 is derived from g12972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13220662	13222969	.	-	.	Phchi.S3G182300
Phchi.S3	AUGUSTUS	transcript	13220662	13222969	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	stop_codon	13220659	13220661	.	-	0	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13220662	13221292	0.77	-	1	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13220662	13221292	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221293	13221396	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221397	13221454	1	-	2	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221397	13221454	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221455	13221613	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221614	13221669	1	-	1	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221614	13221669	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221670	13221816	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221817	13221891	1	-	1	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221817	13221891	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221892	13221986	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221987	13222095	1	-	2	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221987	13222095	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13222096	13222242	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13222243	13222381	1	-	0	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13222243	13222381	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13222382	13222465	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13222466	13222969	0.56	-	0	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13222466	13222969	.	-	.	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	start_codon	13222967	13222969	.	-	0	transcript_id "Phchi.S3G182300.t1"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	transcript	13220662	13222044	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	stop_codon	13220659	13220661	.	-	0	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13220662	13221292	0.75	-	1	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13220662	13221292	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221293	13221396	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221397	13221454	1	-	2	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221397	13221454	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221455	13221613	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221614	13221669	1	-	1	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221614	13221669	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221670	13221816	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221817	13221913	0.36	-	2	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221817	13221913	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	intron	13221914	13221986	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	CDS	13221987	13222044	0.21	-	0	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	exon	13221987	13222044	.	-	.	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
Phchi.S3	AUGUSTUS	start_codon	13222042	13222044	.	-	0	transcript_id "Phchi.S3G182300.t2"; gene_id "Phchi.S3G182300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8418.t1 is derived from g5593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35867779	35869717	.	-	.	Phchi.S1G557700
Phchi.S1	AUGUSTUS	transcript	35867779	35869717	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	stop_codon	35867776	35867778	.	-	0	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	CDS	35867779	35868028	1	-	1	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	exon	35867779	35868028	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	intron	35868029	35868114	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	CDS	35868115	35868485	1	-	0	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	exon	35868115	35868485	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	intron	35868486	35868576	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	CDS	35868577	35868896	0.67	-	2	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	exon	35868577	35868896	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	intron	35868897	35868999	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	CDS	35869000	35869244	0.59	-	1	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	exon	35869000	35869244	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	intron	35869245	35869328	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	CDS	35869329	35869717	1	-	0	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	exon	35869329	35869717	.	-	.	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
Phchi.S1	AUGUSTUS	start_codon	35869715	35869717	.	-	0	transcript_id "Phchi.S1G557700.t1"; gene_id "Phchi.S1G557700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5707.t1 is derived from g2877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18469453	18471162	.	-	.	Phchi.S1G286600
Phchi.S1	AUGUSTUS	transcript	18469453	18471162	.	-	.	transcript_id "Phchi.S1G286600.t1"; gene_id "Phchi.S1G286600"
Phchi.S1	AUGUSTUS	stop_codon	18469450	18469452	.	-	0	transcript_id "Phchi.S1G286600.t1"; gene_id "Phchi.S1G286600"
Phchi.S1	AUGUSTUS	CDS	18469453	18471162	1	-	0	transcript_id "Phchi.S1G286600.t1"; gene_id "Phchi.S1G286600"
Phchi.S1	AUGUSTUS	exon	18469453	18471162	.	-	.	transcript_id "Phchi.S1G286600.t1"; gene_id "Phchi.S1G286600"
Phchi.S1	AUGUSTUS	start_codon	18471160	18471162	.	-	0	transcript_id "Phchi.S1G286600.t1"; gene_id "Phchi.S1G286600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12681.t1 is derived from g14415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	41221	42010	.	+	.	Phchi.C62G001200
Phchi.C62	AUGUSTUS	transcript	41221	42010	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	start_codon	41221	41223	.	+	0	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	CDS	41221	41231	0.87	+	0	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	exon	41221	41231	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	intron	41232	41318	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	CDS	41319	41412	0.94	+	1	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	exon	41319	41412	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	intron	41413	41509	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	CDS	41510	41535	0.53	+	0	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	exon	41510	41535	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	intron	41536	41780	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	CDS	41781	41833	0.45	+	1	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	exon	41781	41833	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	intron	41834	41924	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	CDS	41925	42010	1	+	2	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	exon	41925	42010	.	+	.	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
Phchi.C62	AUGUSTUS	stop_codon	42011	42013	.	+	0	transcript_id "Phchi.C62G001200.t1"; gene_id "Phchi.C62G001200"
# This transcript jg9533.t2 is derived from g6709.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9534.t1 is derived from g6710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42358265	42361352	.	+	.	Phchi.S1G669300
Phchi.S1	AUGUSTUS	transcript	42358265	42361352	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	start_codon	42358265	42358267	.	+	0	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	CDS	42358265	42358267	1	+	0	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	exon	42358265	42358267	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	intron	42358268	42358356	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	CDS	42358357	42359391	0.43	+	0	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	exon	42358357	42359391	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	intron	42359392	42359468	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	CDS	42359469	42359703	0.46	+	0	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	exon	42359469	42359703	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	intron	42359704	42359900	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	CDS	42359901	42360127	0.86	+	2	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	exon	42359901	42360127	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	intron	42360128	42360317	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	CDS	42360318	42361352	0.81	+	0	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	exon	42360318	42361352	.	+	.	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
Phchi.S1	AUGUSTUS	stop_codon	42361353	42361355	.	+	0	transcript_id "Phchi.S1G669300.t1"; gene_id "Phchi.S1G669300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15125.t1 is derived from g13593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17178210	17181919	.	+	.	Phchi.S3G244400
Phchi.S3	AUGUSTUS	transcript	17178210	17181919	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	start_codon	17178210	17178212	.	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17178210	17178833	0.86	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17178210	17178833	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17178834	17178924	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17178925	17179018	1	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17178925	17179018	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17179019	17179166	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17179167	17179249	1	+	2	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17179167	17179249	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17179250	17179335	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17179336	17179433	1	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17179336	17179433	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17179434	17179533	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17179534	17179603	1	+	1	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17179534	17179603	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17179604	17179713	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17179714	17179807	0.97	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17179714	17179807	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17179808	17179900	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17179901	17179985	1	+	2	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17179901	17179985	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17179986	17180152	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17180153	17180188	1	+	1	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17180153	17180188	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17180189	17180269	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17180270	17180423	1	+	1	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17180270	17180423	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17180424	17180543	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17180544	17180705	1	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17180544	17180705	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17180706	17180825	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17180826	17180896	0.96	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17180826	17180896	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17180897	17180999	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17181000	17181078	0.98	+	1	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17181000	17181078	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17181079	17181202	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17181203	17181318	1	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17181203	17181318	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17181319	17181454	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17181455	17181602	1	+	1	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17181455	17181602	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17181603	17181683	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17181684	17181753	1	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17181684	17181753	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	intron	17181754	17181845	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	CDS	17181846	17181919	1	+	2	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	exon	17181846	17181919	.	+	.	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
Phchi.S3	AUGUSTUS	stop_codon	17181920	17181922	.	+	0	transcript_id "Phchi.S3G244400.t1"; gene_id "Phchi.S3G244400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4738.t1 is derived from g1908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12546477	12549366	.	+	.	Phchi.S1G189700
Phchi.S1	AUGUSTUS	transcript	12546477	12549366	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	start_codon	12546477	12546479	.	+	0	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	CDS	12546477	12546624	0.56	+	0	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	exon	12546477	12546624	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	intron	12546625	12546703	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	CDS	12546704	12546798	1	+	2	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	exon	12546704	12546798	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	intron	12546799	12546886	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	CDS	12546887	12549126	0.78	+	0	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	exon	12546887	12549126	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	intron	12549127	12549314	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	CDS	12549315	12549366	0.9	+	1	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	exon	12549315	12549366	.	+	.	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
Phchi.S1	AUGUSTUS	stop_codon	12549367	12549369	.	+	0	transcript_id "Phchi.S1G189700.t1"; gene_id "Phchi.S1G189700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13500.t1 is derived from g11967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7197767	7198640	.	-	.	Phchi.S3G081900
Phchi.S3	AUGUSTUS	transcript	7197767	7198640	.	-	.	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	stop_codon	7197764	7197766	.	-	0	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	CDS	7197767	7198216	1	-	0	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	exon	7197767	7198216	.	-	.	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	intron	7198217	7198313	.	-	.	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	CDS	7198314	7198640	0.51	-	0	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	exon	7198314	7198640	.	-	.	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
Phchi.S3	AUGUSTUS	start_codon	7198638	7198640	.	-	0	transcript_id "Phchi.S3G081900.t1"; gene_id "Phchi.S3G081900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12262.t1 is derived from g7938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7142986	7143510	.	+	.	Phchi.S2G034200
Phchi.S2	AUGUSTUS	transcript	7142986	7143510	.	+	.	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	start_codon	7142986	7142988	.	+	0	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	CDS	7142986	7143167	0.72	+	0	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	exon	7142986	7143167	.	+	.	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	intron	7143168	7143281	.	+	.	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	CDS	7143282	7143510	0.91	+	1	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	exon	7143282	7143510	.	+	.	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
Phchi.S2	AUGUSTUS	stop_codon	7143511	7143513	.	+	0	transcript_id "Phchi.S2G034200.t1"; gene_id "Phchi.S2G034200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14578.t1 is derived from g13046.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13560751	13562086	.	-	.	Phchi.S3G189700
Phchi.S3	AUGUSTUS	transcript	13560751	13562086	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	stop_codon	13560748	13560750	.	-	0	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	CDS	13560751	13561103	1	-	2	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	exon	13560751	13561103	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	intron	13561104	13561228	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	CDS	13561229	13561288	0.86	-	2	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	exon	13561229	13561288	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	intron	13561289	13561588	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	CDS	13561589	13561731	1	-	1	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	exon	13561589	13561731	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	intron	13561732	13561820	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	CDS	13561821	13562086	1	-	0	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	exon	13561821	13562086	.	-	.	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
Phchi.S3	AUGUSTUS	start_codon	13562084	13562086	.	-	0	transcript_id "Phchi.S3G189700.t1"; gene_id "Phchi.S3G189700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1600.t1 is derived from g8519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1963003	1964542	.	+	.	Phchi.S5G020900
Phchi.S5	AUGUSTUS	transcript	1963003	1964542	.	+	.	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	start_codon	1963003	1963005	.	+	0	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	CDS	1963003	1963343	0.4	+	0	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	exon	1963003	1963343	.	+	.	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	intron	1963344	1963444	.	+	.	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	CDS	1963445	1963753	1	+	1	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	exon	1963445	1963753	.	+	.	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	intron	1963754	1963839	.	+	.	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	CDS	1963840	1964542	1	+	1	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	exon	1963840	1964542	.	+	.	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
Phchi.S5	AUGUSTUS	stop_codon	1964543	1964545	.	+	0	transcript_id "Phchi.S5G020900.t1"; gene_id "Phchi.S5G020900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10465.t1 is derived from g14514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	528142	529699	.	+	.	Phchi.S4G004700
Phchi.S4	AUGUSTUS	transcript	528142	529699	.	+	.	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	start_codon	528142	528144	.	+	0	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	CDS	528142	528828	0.54	+	0	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	exon	528142	528828	.	+	.	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	intron	528829	528934	.	+	.	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	CDS	528935	529699	0.94	+	0	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	exon	528935	529699	.	+	.	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
Phchi.S4	AUGUSTUS	stop_codon	529700	529702	.	+	0	transcript_id "Phchi.S4G004700.t1"; gene_id "Phchi.S4G004700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10868.t1 is derived from g14918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2667032	2667703	.	+	.	Phchi.S4G045000
Phchi.S4	AUGUSTUS	transcript	2667032	2667703	.	+	.	transcript_id "Phchi.S4G045000.t1"; gene_id "Phchi.S4G045000"
Phchi.S4	AUGUSTUS	start_codon	2667032	2667034	.	+	0	transcript_id "Phchi.S4G045000.t1"; gene_id "Phchi.S4G045000"
Phchi.S4	AUGUSTUS	CDS	2667032	2667703	0.64	+	0	transcript_id "Phchi.S4G045000.t1"; gene_id "Phchi.S4G045000"
Phchi.S4	AUGUSTUS	exon	2667032	2667703	.	+	.	transcript_id "Phchi.S4G045000.t1"; gene_id "Phchi.S4G045000"
Phchi.S4	AUGUSTUS	stop_codon	2667704	2667706	.	+	0	transcript_id "Phchi.S4G045000.t1"; gene_id "Phchi.S4G045000"
# This transcript jg11495.t2 is derived from g15545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11496.t1 is derived from g15546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6644170	6644691	.	+	.	Phchi.S4G107800
Phchi.S4	AUGUSTUS	transcript	6644170	6644691	.	+	.	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	start_codon	6644170	6644172	.	+	0	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	CDS	6644170	6644325	0.98	+	0	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	exon	6644170	6644325	.	+	.	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	intron	6644326	6644601	.	+	.	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	CDS	6644602	6644691	1	+	0	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	exon	6644602	6644691	.	+	.	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
Phchi.S4	AUGUSTUS	stop_codon	6644692	6644694	.	+	0	transcript_id "Phchi.S4G107800.t1"; gene_id "Phchi.S4G107800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2341.t1 is derived from g9261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6250462	6252012	.	+	.	Phchi.S5G095000
Phchi.S5	AUGUSTUS	transcript	6250462	6252012	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	start_codon	6250462	6250464	.	+	0	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	CDS	6250462	6251043	0.71	+	0	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	exon	6250462	6251043	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	intron	6251044	6251148	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	CDS	6251149	6251181	0.98	+	0	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	exon	6251149	6251181	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	intron	6251182	6251306	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	CDS	6251307	6251397	1	+	0	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	exon	6251307	6251397	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	intron	6251398	6251479	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	CDS	6251480	6251743	1	+	2	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	exon	6251480	6251743	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	intron	6251744	6251839	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	CDS	6251840	6252012	0.93	+	2	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	exon	6251840	6252012	.	+	.	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
Phchi.S5	AUGUSTUS	stop_codon	6252013	6252015	.	+	0	transcript_id "Phchi.S5G095000.t1"; gene_id "Phchi.S5G095000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8295.t1 is derived from g5470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35134595	35137625	.	-	.	Phchi.S1G545400
Phchi.S1	AUGUSTUS	transcript	35134595	35137625	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	stop_codon	35134592	35134594	.	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35134595	35134708	0.82	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35134595	35134708	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35134709	35134821	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35134822	35134888	0.93	-	1	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35134822	35134888	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35134889	35134994	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35134995	35135134	0.95	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35134995	35135134	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35135135	35135248	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35135249	35135341	1	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35135249	35135341	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35135342	35135431	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35135432	35135614	1	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35135432	35135614	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35135615	35135763	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35135764	35135868	1	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35135764	35135868	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35135869	35135998	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35135999	35136079	1	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35135999	35136079	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35136080	35136176	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35136177	35136318	1	-	1	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35136177	35136318	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35136319	35136409	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35136410	35136489	1	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35136410	35136489	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35136490	35136633	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35136634	35136746	1	-	2	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35136634	35136746	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35136747	35136864	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35136865	35137111	1	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35136865	35137111	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	intron	35137112	35137220	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	CDS	35137221	35137625	0.78	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	exon	35137221	35137625	.	-	.	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
Phchi.S1	AUGUSTUS	start_codon	35137623	35137625	.	-	0	transcript_id "Phchi.S1G545400.t1"; gene_id "Phchi.S1G545400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6431.t1 is derived from g3603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22995750	22996430	.	+	.	Phchi.S1G359000
Phchi.S1	AUGUSTUS	transcript	22995750	22996430	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	start_codon	22995750	22995752	.	+	0	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	CDS	22995750	22995762	0.96	+	0	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	exon	22995750	22995762	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	intron	22995763	22995861	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	CDS	22995862	22995920	1	+	2	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	exon	22995862	22995920	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	intron	22995921	22996013	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	CDS	22996014	22996084	1	+	0	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	exon	22996014	22996084	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	intron	22996085	22996182	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	CDS	22996183	22996251	1	+	1	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	exon	22996183	22996251	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	intron	22996252	22996393	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	CDS	22996394	22996430	1	+	1	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	exon	22996394	22996430	.	+	.	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
Phchi.S1	AUGUSTUS	stop_codon	22996431	22996433	.	+	0	transcript_id "Phchi.S1G359000.t1"; gene_id "Phchi.S1G359000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12768.t1 is derived from g11233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1955150	1955859	.	-	.	Phchi.S3G008700
Phchi.S3	AUGUSTUS	transcript	1955150	1955859	.	-	.	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	stop_codon	1955147	1955149	.	-	0	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	CDS	1955150	1955190	0.61	-	2	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	exon	1955150	1955190	.	-	.	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	intron	1955191	1955289	.	-	.	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	CDS	1955290	1955476	0.93	-	0	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	exon	1955290	1955476	.	-	.	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	intron	1955477	1955574	.	-	.	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	CDS	1955575	1955859	0.9	-	0	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	exon	1955575	1955859	.	-	.	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
Phchi.S3	AUGUSTUS	start_codon	1955857	1955859	.	-	0	transcript_id "Phchi.S3G008700.t1"; gene_id "Phchi.S3G008700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7963.t1 is derived from g5138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32118523	32121330	.	-	.	Phchi.S1G512200
Phchi.S1	AUGUSTUS	transcript	32118523	32121330	.	-	.	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	stop_codon	32118520	32118522	.	-	0	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	CDS	32118523	32120656	0.95	-	1	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	exon	32118523	32120656	.	-	.	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	intron	32120657	32120823	.	-	.	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	CDS	32120824	32120953	0.99	-	2	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	exon	32120824	32120953	.	-	.	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	intron	32120954	32121197	.	-	.	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	CDS	32121198	32121330	0.99	-	0	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	exon	32121198	32121330	.	-	.	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
Phchi.S1	AUGUSTUS	start_codon	32121328	32121330	.	-	0	transcript_id "Phchi.S1G512200.t1"; gene_id "Phchi.S1G512200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1424.t1 is derived from g8343.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	784890	789114	.	+	.	Phchi.S5G003300
Phchi.S5	AUGUSTUS	transcript	784890	789114	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	start_codon	784890	784892	.	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	784890	785462	0.94	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	784890	785462	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	785463	785680	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	785681	785686	0.75	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	785681	785686	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	785687	785846	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	785847	785915	1	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	785847	785915	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	785916	786061	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	786062	786169	1	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	786062	786169	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	786170	786313	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	786314	786379	1	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	786314	786379	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	786380	786561	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	786562	786765	0.69	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	786562	786765	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	786766	786849	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	786850	786936	1	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	786850	786936	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	786937	787081	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	787082	787188	1	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	787082	787188	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	787189	787288	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	787289	787387	1	+	1	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	787289	787387	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	787388	787553	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	787554	787605	0.86	+	1	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	787554	787605	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	787606	787706	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	787707	788419	0.8	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	787707	788419	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	788420	788527	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	788528	788740	0.53	+	1	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	788528	788740	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	788741	788831	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	788832	788955	1	+	1	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	788832	788955	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	intron	788956	789045	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	CDS	789046	789114	1	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	exon	789046	789114	.	+	.	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
Phchi.S5	AUGUSTUS	stop_codon	789115	789117	.	+	0	transcript_id "Phchi.S5G003300.t1"; gene_id "Phchi.S5G003300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1864.t1 is derived from g8784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3608908	3610046	.	+	.	Phchi.S5G047300
Phchi.S5	AUGUSTUS	transcript	3608908	3610046	.	+	.	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	start_codon	3608908	3608910	.	+	0	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	CDS	3608908	3609421	0.52	+	0	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	exon	3608908	3609421	.	+	.	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	intron	3609422	3609619	.	+	.	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	CDS	3609620	3609848	0.33	+	2	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	exon	3609620	3609848	.	+	.	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	intron	3609849	3609970	.	+	.	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	CDS	3609971	3610046	0.38	+	1	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	exon	3609971	3610046	.	+	.	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
Phchi.S5	AUGUSTUS	stop_codon	3610047	3610049	.	+	0	transcript_id "Phchi.S5G047300.t1"; gene_id "Phchi.S5G047300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10852.t1 is derived from g14902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2513728	2514105	.	+	.	Phchi.S4G043400
Phchi.S4	AUGUSTUS	transcript	2513728	2514105	.	+	.	transcript_id "Phchi.S4G043400.t1"; gene_id "Phchi.S4G043400"
Phchi.S4	AUGUSTUS	start_codon	2513728	2513730	.	+	0	transcript_id "Phchi.S4G043400.t1"; gene_id "Phchi.S4G043400"
Phchi.S4	AUGUSTUS	CDS	2513728	2514105	0.61	+	0	transcript_id "Phchi.S4G043400.t1"; gene_id "Phchi.S4G043400"
Phchi.S4	AUGUSTUS	exon	2513728	2514105	.	+	.	transcript_id "Phchi.S4G043400.t1"; gene_id "Phchi.S4G043400"
Phchi.S4	AUGUSTUS	stop_codon	2514106	2514108	.	+	0	transcript_id "Phchi.S4G043400.t1"; gene_id "Phchi.S4G043400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5851.t1 is derived from g3021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19339979	19341470	.	-	.	Phchi.S1G301000
Phchi.S1	AUGUSTUS	transcript	19339979	19341470	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	stop_codon	19339976	19339978	.	-	0	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	CDS	19339979	19340647	1	-	0	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	exon	19339979	19340647	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	intron	19340648	19340770	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	CDS	19340771	19341010	1	-	0	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	exon	19340771	19341010	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	intron	19341011	19341116	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	CDS	19341117	19341179	1	-	0	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	exon	19341117	19341179	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	intron	19341180	19341359	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	CDS	19341360	19341470	1	-	0	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	exon	19341360	19341470	.	-	.	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
Phchi.S1	AUGUSTUS	start_codon	19341468	19341470	.	-	0	transcript_id "Phchi.S1G301000.t1"; gene_id "Phchi.S1G301000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg658.t1 is derived from g10440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4617480	4618781	.	-	.	Phchi.S6G061700
Phchi.S6	AUGUSTUS	transcript	4617480	4618781	.	-	.	transcript_id "Phchi.S6G061700.t1"; gene_id "Phchi.S6G061700"
Phchi.S6	AUGUSTUS	stop_codon	4617477	4617479	.	-	0	transcript_id "Phchi.S6G061700.t1"; gene_id "Phchi.S6G061700"
Phchi.S6	AUGUSTUS	CDS	4617480	4618781	1	-	0	transcript_id "Phchi.S6G061700.t1"; gene_id "Phchi.S6G061700"
Phchi.S6	AUGUSTUS	exon	4617480	4618781	.	-	.	transcript_id "Phchi.S6G061700.t1"; gene_id "Phchi.S6G061700"
Phchi.S6	AUGUSTUS	start_codon	4618779	4618781	.	-	0	transcript_id "Phchi.S6G061700.t1"; gene_id "Phchi.S6G061700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14457.t1 is derived from g12925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12974154	12975780	.	-	.	Phchi.S3G177600
Phchi.S3	AUGUSTUS	transcript	12974154	12975780	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	stop_codon	12974151	12974153	.	-	0	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12974154	12974429	0.61	-	0	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12974154	12974429	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12974430	12974507	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12974508	12974586	1	-	1	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12974508	12974586	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12974587	12974724	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12974725	12974800	1	-	2	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12974725	12974800	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12974801	12974881	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12974882	12974972	1	-	0	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12974882	12974972	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12974973	12975093	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12975094	12975164	1	-	2	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12975094	12975164	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12975165	12975324	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12975325	12975376	1	-	0	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12975325	12975376	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12975377	12975467	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12975468	12975565	1	-	2	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12975468	12975565	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	intron	12975566	12975641	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	CDS	12975642	12975780	0.98	-	0	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	exon	12975642	12975780	.	-	.	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
Phchi.S3	AUGUSTUS	start_codon	12975778	12975780	.	-	0	transcript_id "Phchi.S3G177600.t1"; gene_id "Phchi.S3G177600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5184.t1 is derived from g2354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15375661	15377505	.	-	.	Phchi.S1G234300
Phchi.S1	AUGUSTUS	transcript	15375661	15377505	.	-	.	transcript_id "Phchi.S1G234300.t1"; gene_id "Phchi.S1G234300"
Phchi.S1	AUGUSTUS	stop_codon	15375658	15375660	.	-	0	transcript_id "Phchi.S1G234300.t1"; gene_id "Phchi.S1G234300"
Phchi.S1	AUGUSTUS	CDS	15375661	15377505	0.99	-	0	transcript_id "Phchi.S1G234300.t1"; gene_id "Phchi.S1G234300"
Phchi.S1	AUGUSTUS	exon	15375661	15377505	.	-	.	transcript_id "Phchi.S1G234300.t1"; gene_id "Phchi.S1G234300"
Phchi.S1	AUGUSTUS	start_codon	15377503	15377505	.	-	0	transcript_id "Phchi.S1G234300.t1"; gene_id "Phchi.S1G234300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6326.t1 is derived from g3498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22292006	22295407	.	-	.	Phchi.S1G348500
Phchi.S1	AUGUSTUS	transcript	22292006	22295407	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	stop_codon	22292003	22292005	.	-	0	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22292006	22292050	0.99	-	0	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22292006	22292050	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22292051	22292124	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22292125	22293555	0.32	-	0	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22292125	22293555	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22293556	22293731	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22293732	22294306	0.61	-	2	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22293732	22294306	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22294307	22294397	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22294398	22294570	0.84	-	1	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22294398	22294570	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22294571	22294704	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22294705	22294723	0.36	-	2	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22294705	22294723	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22294724	22294906	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22294907	22294943	0.39	-	0	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22294907	22294943	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22294944	22295086	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22295087	22295163	0.42	-	2	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22295087	22295163	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22295164	22295257	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22295258	22295299	0.29	-	2	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22295258	22295299	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	intron	22295300	22295382	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	CDS	22295383	22295407	0.31	-	0	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	exon	22295383	22295407	.	-	.	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
Phchi.S1	AUGUSTUS	start_codon	22295405	22295407	.	-	0	transcript_id "Phchi.S1G348500.t1"; gene_id "Phchi.S1G348500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2966.t1 is derived from g135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	861219	866732	.	+	.	Phchi.S1G012500
Phchi.S1	AUGUSTUS	transcript	861219	866732	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	start_codon	861219	861221	.	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	861219	861240	0.97	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	861219	861240	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	861241	861406	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	861407	861590	0.41	+	2	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	861407	861590	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	861591	861785	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	861786	863430	0.4	+	1	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	861786	863430	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	863431	863536	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	863537	863857	0.96	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	863537	863857	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	863858	863948	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	863949	864035	1	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	863949	864035	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	864036	864132	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	864133	864462	0.72	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	864133	864462	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	864463	864552	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	864553	864819	0.77	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	864553	864819	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	864820	864920	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	864921	865085	0.98	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	864921	865085	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	865086	865165	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	865166	865280	1	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	865166	865280	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	865281	865434	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	865435	865460	1	+	2	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	865435	865460	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	865461	865609	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	865610	865666	1	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	865610	865666	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	865667	865748	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	865749	865812	1	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	865749	865812	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	865813	865921	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	865922	866161	1	+	2	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	865922	866161	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	866162	866254	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	866255	866322	0.92	+	2	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	866255	866322	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	866323	866438	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	866439	866503	0.93	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	866439	866503	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	intron	866504	866593	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	CDS	866594	866732	0.88	+	1	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	exon	866594	866732	.	+	.	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
Phchi.S1	AUGUSTUS	stop_codon	866733	866735	.	+	0	transcript_id "Phchi.S1G012500.t1"; gene_id "Phchi.S1G012500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14223.t1 is derived from g12690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11639217	11639675	.	-	.	Phchi.S3G154200
Phchi.S3	AUGUSTUS	transcript	11639217	11639675	.	-	.	transcript_id "Phchi.S3G154200.t1"; gene_id "Phchi.S3G154200"
Phchi.S3	AUGUSTUS	stop_codon	11639214	11639216	.	-	0	transcript_id "Phchi.S3G154200.t1"; gene_id "Phchi.S3G154200"
Phchi.S3	AUGUSTUS	CDS	11639217	11639675	0.98	-	0	transcript_id "Phchi.S3G154200.t1"; gene_id "Phchi.S3G154200"
Phchi.S3	AUGUSTUS	exon	11639217	11639675	.	-	.	transcript_id "Phchi.S3G154200.t1"; gene_id "Phchi.S3G154200"
Phchi.S3	AUGUSTUS	start_codon	11639673	11639675	.	-	0	transcript_id "Phchi.S3G154200.t1"; gene_id "Phchi.S3G154200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9752.t1 is derived from g6928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43507995	43509232	.	+	.	Phchi.S1G691100
Phchi.S1	AUGUSTUS	transcript	43507995	43509232	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	start_codon	43507995	43507997	.	+	0	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	CDS	43507995	43508073	1	+	0	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	exon	43507995	43508073	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	intron	43508074	43508193	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	CDS	43508194	43508273	1	+	2	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	exon	43508194	43508273	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	intron	43508274	43508378	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	CDS	43508379	43508838	0.98	+	0	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	exon	43508379	43508838	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	intron	43508839	43508927	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	CDS	43508928	43509013	0.71	+	2	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	exon	43508928	43509013	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	intron	43509014	43509175	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	CDS	43509176	43509232	0.69	+	0	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	exon	43509176	43509232	.	+	.	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
Phchi.S1	AUGUSTUS	stop_codon	43509233	43509235	.	+	0	transcript_id "Phchi.S1G691100.t1"; gene_id "Phchi.S1G691100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9898.t1 is derived from g7074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44327281	44330742	.	+	.	Phchi.S1G705700
Phchi.S1	AUGUSTUS	transcript	44327281	44330742	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	start_codon	44327281	44327283	.	+	0	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44327281	44327299	1	+	0	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44327281	44327299	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	intron	44327300	44327443	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44327444	44327542	1	+	2	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44327444	44327542	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	intron	44327543	44327633	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44327634	44327681	0.7	+	2	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44327634	44327681	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	intron	44327682	44327905	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44327906	44328025	0.43	+	2	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44327906	44328025	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	intron	44328026	44328117	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44328118	44328722	0.78	+	2	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44328118	44328722	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	intron	44328723	44328813	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44328814	44330547	1	+	0	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44328814	44330547	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	intron	44330548	44330628	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	CDS	44330629	44330742	1	+	0	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	exon	44330629	44330742	.	+	.	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
Phchi.S1	AUGUSTUS	stop_codon	44330743	44330745	.	+	0	transcript_id "Phchi.S1G705700.t1"; gene_id "Phchi.S1G705700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2810.t1 is derived from g9730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8976597	8977259	.	+	.	Phchi.S5G141900
Phchi.S5	AUGUSTUS	transcript	8976597	8977259	.	+	.	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	start_codon	8976597	8976599	.	+	0	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	CDS	8976597	8976730	1	+	0	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	exon	8976597	8976730	.	+	.	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	intron	8976731	8976812	.	+	.	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	CDS	8976813	8977156	1	+	1	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	exon	8976813	8977156	.	+	.	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	intron	8977157	8977248	.	+	.	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	CDS	8977249	8977259	1	+	2	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	exon	8977249	8977259	.	+	.	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
Phchi.S5	AUGUSTUS	stop_codon	8977260	8977262	.	+	0	transcript_id "Phchi.S5G141900.t1"; gene_id "Phchi.S5G141900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5206.t1 is derived from g2376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15469730	15470424	.	-	.	Phchi.S1G236500
Phchi.S1	AUGUSTUS	transcript	15469730	15470424	.	-	.	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	stop_codon	15469727	15469729	.	-	0	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	CDS	15469730	15470014	0.67	-	0	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	exon	15469730	15470014	.	-	.	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	intron	15470015	15470166	.	-	.	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	CDS	15470167	15470424	0.74	-	0	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	exon	15470167	15470424	.	-	.	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
Phchi.S1	AUGUSTUS	start_codon	15470422	15470424	.	-	0	transcript_id "Phchi.S1G236500.t1"; gene_id "Phchi.S1G236500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg686.t1 is derived from g10468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4784013	4785476	.	+	.	Phchi.S6G064500
Phchi.S6	AUGUSTUS	transcript	4784013	4785476	.	+	.	transcript_id "Phchi.S6G064500.t1"; gene_id "Phchi.S6G064500"
Phchi.S6	AUGUSTUS	start_codon	4784013	4784015	.	+	0	transcript_id "Phchi.S6G064500.t1"; gene_id "Phchi.S6G064500"
Phchi.S6	AUGUSTUS	CDS	4784013	4785476	0.99	+	0	transcript_id "Phchi.S6G064500.t1"; gene_id "Phchi.S6G064500"
Phchi.S6	AUGUSTUS	exon	4784013	4785476	.	+	.	transcript_id "Phchi.S6G064500.t1"; gene_id "Phchi.S6G064500"
Phchi.S6	AUGUSTUS	stop_codon	4785477	4785479	.	+	0	transcript_id "Phchi.S6G064500.t1"; gene_id "Phchi.S6G064500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8207.t1 is derived from g5382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34434644	34435106	.	+	.	Phchi.S1G536600
Phchi.S1	AUGUSTUS	transcript	34434644	34435106	.	+	.	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	start_codon	34434644	34434646	.	+	0	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	CDS	34434644	34434773	1	+	0	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	exon	34434644	34434773	.	+	.	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	intron	34434774	34434945	.	+	.	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	CDS	34434946	34435106	0.99	+	2	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	exon	34434946	34435106	.	+	.	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
Phchi.S1	AUGUSTUS	stop_codon	34435107	34435109	.	+	0	transcript_id "Phchi.S1G536600.t1"; gene_id "Phchi.S1G536600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15479.t1 is derived from g13947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19394242	19396766	.	-	.	Phchi.S3G279800
Phchi.S3	AUGUSTUS	transcript	19394242	19396766	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	stop_codon	19394239	19394241	.	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19394242	19394514	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19394242	19394514	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19394515	19394648	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19394649	19394714	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19394649	19394714	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19394715	19394812	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19394813	19394973	1	-	2	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19394813	19394973	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19394974	19395069	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19395070	19395178	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19395070	19395178	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19395179	19395311	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19395312	19395417	1	-	1	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19395312	19395417	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19395418	19395495	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19395496	19395572	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19395496	19395572	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19395573	19395653	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19395654	19395716	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19395654	19395716	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19395717	19395939	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19395940	19396086	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19395940	19396086	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19396087	19396172	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19396173	19396319	1	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19396173	19396319	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	intron	19396320	19396433	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	CDS	19396434	19396766	0.97	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	exon	19396434	19396766	.	-	.	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
Phchi.S3	AUGUSTUS	start_codon	19396764	19396766	.	-	0	transcript_id "Phchi.S3G279800.t1"; gene_id "Phchi.S3G279800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8448.t1 is derived from g5623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35985965	35987788	.	-	.	Phchi.S1G560700
Phchi.S1	AUGUSTUS	transcript	35985965	35987788	.	-	.	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	stop_codon	35985962	35985964	.	-	0	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	CDS	35985965	35987557	1	-	0	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	exon	35985965	35987557	.	-	.	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	intron	35987558	35987647	.	-	.	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	CDS	35987648	35987788	0.35	-	0	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	exon	35987648	35987788	.	-	.	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
Phchi.S1	AUGUSTUS	start_codon	35987786	35987788	.	-	0	transcript_id "Phchi.S1G560700.t1"; gene_id "Phchi.S1G560700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12783.t1 is derived from g11248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2185443	2186113	.	+	.	Phchi.S3G010200
Phchi.S3	AUGUSTUS	transcript	2185443	2186113	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	start_codon	2185443	2185445	.	+	0	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	CDS	2185443	2185495	0.91	+	0	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	exon	2185443	2185495	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	intron	2185496	2185588	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	CDS	2185589	2185711	0.83	+	1	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	exon	2185589	2185711	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	intron	2185712	2185896	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	CDS	2185897	2185926	0.55	+	1	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	exon	2185897	2185926	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	intron	2185927	2186070	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	CDS	2186071	2186113	0.84	+	1	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	exon	2186071	2186113	.	+	.	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
Phchi.S3	AUGUSTUS	stop_codon	2186114	2186116	.	+	0	transcript_id "Phchi.S3G010200.t1"; gene_id "Phchi.S3G010200"
# This transcript jg12700.t2 is derived from g11165.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12700.t3 is derived from g11165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12701.t1 is derived from g11166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	629956	631127	.	+	.	Phchi.S3G002000
Phchi.S3	AUGUSTUS	transcript	629956	631127	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	start_codon	629956	629958	.	+	0	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	CDS	629956	630218	0.98	+	0	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	exon	629956	630218	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	intron	630219	630305	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	CDS	630306	630420	1	+	1	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	exon	630306	630420	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	intron	630421	630514	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	CDS	630515	631003	1	+	0	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	exon	630515	631003	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	intron	631004	631103	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	CDS	631104	631127	1	+	0	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	exon	631104	631127	.	+	.	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
Phchi.S3	AUGUSTUS	stop_codon	631128	631130	.	+	0	transcript_id "Phchi.S3G002000.t1"; gene_id "Phchi.S3G002000"
# This transcript jg7213.t2 is derived from g4385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7214.t1 is derived from g4386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27664921	27669032	.	+	.	Phchi.S1G437300
Phchi.S1	AUGUSTUS	transcript	27664921	27669032	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	start_codon	27664921	27664923	.	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27664921	27664954	0.99	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27664921	27664954	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27664955	27665069	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27665070	27665189	1	+	2	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27665070	27665189	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27665190	27665365	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27665366	27665463	1	+	2	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27665366	27665463	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27665464	27665558	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27665559	27665642	1	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27665559	27665642	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27665643	27665723	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27665724	27665924	0.62	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27665724	27665924	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27665925	27666029	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27666030	27666133	0.99	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27666030	27666133	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27666134	27666285	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27666286	27666484	0.85	+	1	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27666286	27666484	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27666485	27666612	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27666613	27666639	0.6	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27666613	27666639	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27666640	27666716	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27666717	27666788	0.81	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27666717	27666788	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27666789	27666981	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27666982	27667368	1	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27666982	27667368	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27667369	27667456	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27667457	27667521	1	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27667457	27667521	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27667522	27667673	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27667674	27667722	1	+	1	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27667674	27667722	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27667723	27667847	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27667848	27668016	1	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27667848	27668016	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27668017	27668113	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27668114	27668198	1	+	2	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27668114	27668198	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27668199	27668310	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27668311	27668380	1	+	1	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27668311	27668380	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27668381	27668497	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27668498	27668641	1	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27668498	27668641	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	intron	27668642	27668741	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	CDS	27668742	27669032	0.97	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	exon	27668742	27669032	.	+	.	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
Phchi.S1	AUGUSTUS	stop_codon	27669033	27669035	.	+	0	transcript_id "Phchi.S1G437300.t1"; gene_id "Phchi.S1G437300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9932.t1 is derived from g7108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44531508	44533559	.	-	.	Phchi.S1G709100
Phchi.S1	AUGUSTUS	transcript	44531508	44533559	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	stop_codon	44531505	44531507	.	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44531508	44531658	1	-	1	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44531508	44531658	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44531659	44531730	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44531731	44531846	1	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44531731	44531846	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44531847	44531929	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44531930	44532004	1	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44531930	44532004	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44532005	44532213	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44532214	44532336	1	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44532214	44532336	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44532337	44532480	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44532481	44532598	1	-	1	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44532481	44532598	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44532599	44532662	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44532663	44532781	1	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44532663	44532781	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44532782	44532872	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44532873	44533102	1	-	2	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44532873	44533102	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	intron	44533103	44533228	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	CDS	44533229	44533559	1	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	exon	44533229	44533559	.	-	.	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
Phchi.S1	AUGUSTUS	start_codon	44533557	44533559	.	-	0	transcript_id "Phchi.S1G709100.t1"; gene_id "Phchi.S1G709100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13745.t1 is derived from g12212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8676220	8677419	.	+	.	Phchi.S3G106400
Phchi.S3	AUGUSTUS	transcript	8676220	8677419	.	+	.	transcript_id "Phchi.S3G106400.t1"; gene_id "Phchi.S3G106400"
Phchi.S3	AUGUSTUS	start_codon	8676220	8676222	.	+	0	transcript_id "Phchi.S3G106400.t1"; gene_id "Phchi.S3G106400"
Phchi.S3	AUGUSTUS	CDS	8676220	8677419	1	+	0	transcript_id "Phchi.S3G106400.t1"; gene_id "Phchi.S3G106400"
Phchi.S3	AUGUSTUS	exon	8676220	8677419	.	+	.	transcript_id "Phchi.S3G106400.t1"; gene_id "Phchi.S3G106400"
Phchi.S3	AUGUSTUS	stop_codon	8677420	8677422	.	+	0	transcript_id "Phchi.S3G106400.t1"; gene_id "Phchi.S3G106400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11796.t1 is derived from g15848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8197343	8198752	.	-	.	Phchi.S4G137800
Phchi.S4	AUGUSTUS	transcript	8197343	8198752	.	-	.	transcript_id "Phchi.S4G137800.t1"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	stop_codon	8197340	8197342	.	-	0	transcript_id "Phchi.S4G137800.t1"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	CDS	8197343	8198752	1	-	0	transcript_id "Phchi.S4G137800.t1"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	exon	8197343	8198752	.	-	.	transcript_id "Phchi.S4G137800.t1"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	start_codon	8198750	8198752	.	-	0	transcript_id "Phchi.S4G137800.t1"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	transcript	8197762	8198752	.	-	.	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	stop_codon	8197759	8197761	.	-	0	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	CDS	8197762	8197777	0.36	-	1	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	exon	8197762	8197777	.	-	.	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	intron	8197778	8197952	.	-	.	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	CDS	8197953	8198752	0.38	-	0	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	exon	8197953	8198752	.	-	.	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
Phchi.S4	AUGUSTUS	start_codon	8198750	8198752	.	-	0	transcript_id "Phchi.S4G137800.t2"; gene_id "Phchi.S4G137800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg302.t1 is derived from g10084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2130723	2132054	.	+	.	Phchi.S6G026100
Phchi.S6	AUGUSTUS	transcript	2130723	2132054	.	+	.	transcript_id "Phchi.S6G026100.t1"; gene_id "Phchi.S6G026100"
Phchi.S6	AUGUSTUS	start_codon	2130723	2130725	.	+	0	transcript_id "Phchi.S6G026100.t1"; gene_id "Phchi.S6G026100"
Phchi.S6	AUGUSTUS	CDS	2130723	2132054	0.82	+	0	transcript_id "Phchi.S6G026100.t1"; gene_id "Phchi.S6G026100"
Phchi.S6	AUGUSTUS	exon	2130723	2132054	.	+	.	transcript_id "Phchi.S6G026100.t1"; gene_id "Phchi.S6G026100"
Phchi.S6	AUGUSTUS	stop_codon	2132055	2132057	.	+	0	transcript_id "Phchi.S6G026100.t1"; gene_id "Phchi.S6G026100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10071.t1 is derived from g7247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45625604	45628160	.	+	.	Phchi.S1G723000
Phchi.S1	AUGUSTUS	transcript	45625604	45628160	.	+	.	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	start_codon	45625604	45625606	.	+	0	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	CDS	45625604	45626557	0.61	+	0	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	exon	45625604	45626557	.	+	.	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	intron	45626558	45626649	.	+	.	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	CDS	45626650	45627864	0.5	+	0	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	exon	45626650	45627864	.	+	.	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	intron	45627865	45627971	.	+	.	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	CDS	45627972	45628160	0.88	+	0	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	exon	45627972	45628160	.	+	.	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
Phchi.S1	AUGUSTUS	stop_codon	45628161	45628163	.	+	0	transcript_id "Phchi.S1G723000.t1"; gene_id "Phchi.S1G723000"
# This transcript jg12103.t2 is derived from g7779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12103.t3 is derived from g7779.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12104.t1 is derived from g7780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3350846	3351205	.	+	.	Phchi.S2G018400
Phchi.S2	AUGUSTUS	transcript	3350846	3351205	.	+	.	transcript_id "Phchi.S2G018400.t1"; gene_id "Phchi.S2G018400"
Phchi.S2	AUGUSTUS	start_codon	3350846	3350848	.	+	0	transcript_id "Phchi.S2G018400.t1"; gene_id "Phchi.S2G018400"
Phchi.S2	AUGUSTUS	CDS	3350846	3351205	0.95	+	0	transcript_id "Phchi.S2G018400.t1"; gene_id "Phchi.S2G018400"
Phchi.S2	AUGUSTUS	exon	3350846	3351205	.	+	.	transcript_id "Phchi.S2G018400.t1"; gene_id "Phchi.S2G018400"
Phchi.S2	AUGUSTUS	stop_codon	3351206	3351208	.	+	0	transcript_id "Phchi.S2G018400.t1"; gene_id "Phchi.S2G018400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2818.t1 is derived from g9738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9017497	9019570	.	+	.	Phchi.S5G142700
Phchi.S5	AUGUSTUS	transcript	9017497	9019570	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	start_codon	9017497	9017499	.	+	0	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	CDS	9017497	9017890	0.65	+	0	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	exon	9017497	9017890	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	intron	9017891	9018183	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	CDS	9018184	9018204	0.35	+	2	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	exon	9018184	9018204	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	intron	9018205	9018312	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	CDS	9018313	9018440	0.36	+	2	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	exon	9018313	9018440	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	intron	9018441	9018539	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	CDS	9018540	9018992	0.82	+	0	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	exon	9018540	9018992	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	intron	9018993	9019087	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	CDS	9019088	9019237	0.98	+	0	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	exon	9019088	9019237	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	intron	9019238	9019354	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	CDS	9019355	9019570	0.98	+	0	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	exon	9019355	9019570	.	+	.	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
Phchi.S5	AUGUSTUS	stop_codon	9019571	9019573	.	+	0	transcript_id "Phchi.S5G142700.t1"; gene_id "Phchi.S5G142700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8945.t1 is derived from g6120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38791536	38794625	.	+	.	Phchi.S1G610400
Phchi.S1	AUGUSTUS	transcript	38791536	38794625	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	start_codon	38791536	38791538	.	+	0	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38791536	38791747	0.83	+	0	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38791536	38791747	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	intron	38791748	38791843	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38791844	38792048	0.9	+	1	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38791844	38792048	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	intron	38792049	38792266	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38792267	38792716	0.9	+	0	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38792267	38792716	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	intron	38792717	38792820	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38792821	38793026	0.47	+	0	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38792821	38793026	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	intron	38793027	38793142	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38793143	38793473	0.24	+	1	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38793143	38793473	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	intron	38793474	38793657	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38793658	38793752	0.55	+	0	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38793658	38793752	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	intron	38793753	38793862	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	CDS	38793863	38794625	0.67	+	1	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	exon	38793863	38794625	.	+	.	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
Phchi.S1	AUGUSTUS	stop_codon	38794626	38794628	.	+	0	transcript_id "Phchi.S1G610400.t1"; gene_id "Phchi.S1G610400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13190.t1 is derived from g11655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4611383	4614986	.	+	.	Phchi.S3G050900
Phchi.S3	AUGUSTUS	transcript	4611822	4614986	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	start_codon	4611822	4611824	.	+	0	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4611822	4611824	0.51	+	0	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4611822	4611824	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4611825	4611913	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4611914	4612188	0.58	+	0	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4611914	4612188	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4612189	4612289	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4612290	4612960	0.96	+	1	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4612290	4612960	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4612961	4613043	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613044	4613274	1	+	2	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613044	4613274	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4613275	4613400	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613401	4613505	0.99	+	2	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613401	4613505	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4613506	4613669	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613670	4613685	0.98	+	2	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613670	4613685	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4613686	4613779	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613780	4614986	0.49	+	1	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613780	4614986	.	+	.	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	stop_codon	4614987	4614989	.	+	0	transcript_id "Phchi.S3G050900.t1"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	transcript	4611383	4614986	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	start_codon	4611383	4611385	.	+	0	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4611383	4611395	0.51	+	0	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4611383	4611395	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4611396	4611492	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4611493	4611575	0.23	+	2	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4611493	4611575	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4611576	4611913	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4611914	4612188	0.73	+	0	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4611914	4612188	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4612189	4612289	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4612290	4612960	0.98	+	1	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4612290	4612960	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4612961	4613043	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613044	4613274	1	+	2	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613044	4613274	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4613275	4613400	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613401	4613505	1	+	2	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613401	4613505	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4613506	4613669	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613670	4613685	0.98	+	2	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613670	4613685	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	intron	4613686	4613779	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	CDS	4613780	4614986	0.52	+	1	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	exon	4613780	4614986	.	+	.	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
Phchi.S3	AUGUSTUS	stop_codon	4614987	4614989	.	+	0	transcript_id "Phchi.S3G050900.t2"; gene_id "Phchi.S3G050900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12500.t1 is derived from g8177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30848903	30849846	.	-	.	Phchi.S2G058000
Phchi.S2	AUGUSTUS	transcript	30848903	30849846	.	-	.	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	stop_codon	30848900	30848902	.	-	0	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	CDS	30848903	30849138	0.3	-	2	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	exon	30848903	30849138	.	-	.	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	intron	30849139	30849307	.	-	.	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	CDS	30849308	30849459	0.4	-	1	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	exon	30849308	30849459	.	-	.	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	intron	30849460	30849634	.	-	.	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	CDS	30849635	30849846	0.83	-	0	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	exon	30849635	30849846	.	-	.	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
Phchi.S2	AUGUSTUS	start_codon	30849844	30849846	.	-	0	transcript_id "Phchi.S2G058000.t1"; gene_id "Phchi.S2G058000"
# This transcript jg11358.t2 is derived from g15408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11359.t1 is derived from g15409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5755918	5756930	.	-	.	Phchi.S4G094100
Phchi.S4	AUGUSTUS	transcript	5755918	5756930	.	-	.	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	stop_codon	5755915	5755917	.	-	0	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	CDS	5755918	5756388	0.49	-	0	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	exon	5755918	5756388	.	-	.	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	intron	5756389	5756456	.	-	.	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	CDS	5756457	5756930	0.91	-	0	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	exon	5756457	5756930	.	-	.	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
Phchi.S4	AUGUSTUS	start_codon	5756928	5756930	.	-	0	transcript_id "Phchi.S4G094100.t1"; gene_id "Phchi.S4G094100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5194.t1 is derived from g2364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15413178	15414702	.	-	.	Phchi.S1G235300
Phchi.S1	AUGUSTUS	transcript	15413178	15414702	.	-	.	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	stop_codon	15413175	15413177	.	-	0	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	CDS	15413178	15413450	0.59	-	0	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	exon	15413178	15413450	.	-	.	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	intron	15413451	15413545	.	-	.	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	CDS	15413546	15414121	0.58	-	0	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	exon	15413546	15414121	.	-	.	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	intron	15414122	15414204	.	-	.	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	CDS	15414205	15414702	0.98	-	0	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	exon	15414205	15414702	.	-	.	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
Phchi.S1	AUGUSTUS	start_codon	15414700	15414702	.	-	0	transcript_id "Phchi.S1G235300.t1"; gene_id "Phchi.S1G235300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7173.t1 is derived from g4345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27395909	27396937	.	-	.	Phchi.S1G433200
Phchi.S1	AUGUSTUS	transcript	27395909	27396937	.	-	.	transcript_id "Phchi.S1G433200.t1"; gene_id "Phchi.S1G433200"
Phchi.S1	AUGUSTUS	stop_codon	27395906	27395908	.	-	0	transcript_id "Phchi.S1G433200.t1"; gene_id "Phchi.S1G433200"
Phchi.S1	AUGUSTUS	CDS	27395909	27396937	1	-	0	transcript_id "Phchi.S1G433200.t1"; gene_id "Phchi.S1G433200"
Phchi.S1	AUGUSTUS	exon	27395909	27396937	.	-	.	transcript_id "Phchi.S1G433200.t1"; gene_id "Phchi.S1G433200"
Phchi.S1	AUGUSTUS	start_codon	27396935	27396937	.	-	0	transcript_id "Phchi.S1G433200.t1"; gene_id "Phchi.S1G433200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8810.t1 is derived from g5985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38093227	38096425	.	-	.	Phchi.S1G596900
Phchi.S1	AUGUSTUS	transcript	38093227	38096425	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	stop_codon	38093224	38093226	.	-	0	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38093227	38093302	0.98	-	1	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38093227	38093302	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38093303	38093425	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38093426	38094058	0.72	-	1	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38093426	38094058	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38094059	38094165	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38094166	38094249	0.94	-	1	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38094166	38094249	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38094250	38094360	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38094361	38094539	1	-	0	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38094361	38094539	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38094540	38094630	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38094631	38094750	1	-	0	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38094631	38094750	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38094751	38094842	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38094843	38094936	0.97	-	1	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38094843	38094936	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38094937	38095031	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38095032	38095318	1	-	0	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38095032	38095318	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38095319	38095419	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38095420	38095516	0.99	-	1	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38095420	38095516	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38095517	38095607	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38095608	38095742	0.98	-	1	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38095608	38095742	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	intron	38095743	38095844	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	CDS	38095845	38096425	0.98	-	0	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	exon	38095845	38096425	.	-	.	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
Phchi.S1	AUGUSTUS	start_codon	38096423	38096425	.	-	0	transcript_id "Phchi.S1G596900.t1"; gene_id "Phchi.S1G596900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4436.t1 is derived from g1605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10491878	10495369	.	+	.	Phchi.S1G159500
Phchi.S1	AUGUSTUS	transcript	10491878	10495369	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	start_codon	10491878	10491880	.	+	0	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	CDS	10491878	10492110	0.74	+	0	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	exon	10491878	10492110	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	intron	10492111	10492220	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	CDS	10492221	10493374	0.94	+	1	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	exon	10492221	10493374	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	intron	10493375	10493464	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	CDS	10493465	10493963	0.99	+	2	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	exon	10493465	10493963	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	intron	10493964	10494058	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	CDS	10494059	10494293	1	+	1	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	exon	10494059	10494293	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	intron	10494294	10494406	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	CDS	10494407	10495369	1	+	0	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	exon	10494407	10495369	.	+	.	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
Phchi.S1	AUGUSTUS	stop_codon	10495370	10495372	.	+	0	transcript_id "Phchi.S1G159500.t1"; gene_id "Phchi.S1G159500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5616.t1 is derived from g2786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17910321	17912636	.	+	.	Phchi.S1G277500
Phchi.S1	AUGUSTUS	transcript	17910321	17911050	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	start_codon	17910321	17910323	.	+	0	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910321	17910327	0.73	+	0	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910321	17910327	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17910328	17910470	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910471	17910584	0.82	+	2	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910471	17910584	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17910585	17910695	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910696	17910803	0.65	+	2	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910696	17910803	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17910804	17910997	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910998	17911050	0.65	+	2	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910998	17911050	.	+	.	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	stop_codon	17911051	17911053	.	+	0	transcript_id "Phchi.S1G277500.t1"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	transcript	17910321	17912636	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	start_codon	17910321	17910323	.	+	0	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910321	17910327	0.75	+	0	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910321	17910327	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17910328	17910470	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910471	17910584	0.85	+	2	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910471	17910584	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17910585	17910695	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910696	17910803	0.7	+	2	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910696	17910803	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17910804	17910989	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17910990	17911266	0.46	+	2	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17910990	17911266	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17911267	17911590	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17911591	17911712	0.91	+	1	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17911591	17911712	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17911713	17911822	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17911823	17911834	0.72	+	2	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17911823	17911834	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17911835	17911909	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17911910	17912024	0.42	+	2	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17911910	17912024	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	intron	17912025	17912095	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	CDS	17912096	17912636	0.42	+	1	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	exon	17912096	17912636	.	+	.	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
Phchi.S1	AUGUSTUS	stop_codon	17912637	17912639	.	+	0	transcript_id "Phchi.S1G277500.t2"; gene_id "Phchi.S1G277500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14820.t1 is derived from g13288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14867111	14867581	.	+	.	Phchi.S3G213900
Phchi.S3	AUGUSTUS	transcript	14867111	14867581	.	+	.	transcript_id "Phchi.S3G213900.t1"; gene_id "Phchi.S3G213900"
Phchi.S3	AUGUSTUS	start_codon	14867111	14867113	.	+	0	transcript_id "Phchi.S3G213900.t1"; gene_id "Phchi.S3G213900"
Phchi.S3	AUGUSTUS	CDS	14867111	14867581	0.65	+	0	transcript_id "Phchi.S3G213900.t1"; gene_id "Phchi.S3G213900"
Phchi.S3	AUGUSTUS	exon	14867111	14867581	.	+	.	transcript_id "Phchi.S3G213900.t1"; gene_id "Phchi.S3G213900"
Phchi.S3	AUGUSTUS	stop_codon	14867582	14867584	.	+	0	transcript_id "Phchi.S3G213900.t1"; gene_id "Phchi.S3G213900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg194.t1 is derived from g9976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1085240	1087968	.	+	.	Phchi.S6G015300
Phchi.S6	AUGUSTUS	transcript	1085240	1087968	.	+	.	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	start_codon	1085240	1085242	.	+	0	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	CDS	1085240	1085505	0.98	+	0	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	exon	1085240	1085505	.	+	.	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	intron	1085506	1085648	.	+	.	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	CDS	1085649	1087968	1	+	1	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	exon	1085649	1087968	.	+	.	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
Phchi.S6	AUGUSTUS	stop_codon	1087969	1087971	.	+	0	transcript_id "Phchi.S6G015300.t1"; gene_id "Phchi.S6G015300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7295.t1 is derived from g4467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28372433	28373490	.	-	.	Phchi.S1G445400
Phchi.S1	AUGUSTUS	transcript	28372433	28373490	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	stop_codon	28372430	28372432	.	-	0	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	CDS	28372433	28372547	1	-	1	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	exon	28372433	28372547	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	intron	28372548	28372660	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	CDS	28372661	28372744	1	-	1	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	exon	28372661	28372744	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	intron	28372745	28372854	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	CDS	28372855	28372962	1	-	1	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	exon	28372855	28372962	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	intron	28372963	28373048	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	CDS	28373049	28373106	1	-	2	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	exon	28373049	28373106	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	intron	28373107	28373369	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	CDS	28373370	28373490	0.97	-	0	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	exon	28373370	28373490	.	-	.	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
Phchi.S1	AUGUSTUS	start_codon	28373488	28373490	.	-	0	transcript_id "Phchi.S1G445400.t1"; gene_id "Phchi.S1G445400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5951.t1 is derived from g3122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20011711	20012214	.	-	.	Phchi.S1G311000
Phchi.S1	AUGUSTUS	transcript	20011711	20012214	.	-	.	transcript_id "Phchi.S1G311000.t1"; gene_id "Phchi.S1G311000"
Phchi.S1	AUGUSTUS	stop_codon	20011708	20011710	.	-	0	transcript_id "Phchi.S1G311000.t1"; gene_id "Phchi.S1G311000"
Phchi.S1	AUGUSTUS	CDS	20011711	20012214	0.85	-	0	transcript_id "Phchi.S1G311000.t1"; gene_id "Phchi.S1G311000"
Phchi.S1	AUGUSTUS	exon	20011711	20012214	.	-	.	transcript_id "Phchi.S1G311000.t1"; gene_id "Phchi.S1G311000"
Phchi.S1	AUGUSTUS	start_codon	20012212	20012214	.	-	0	transcript_id "Phchi.S1G311000.t1"; gene_id "Phchi.S1G311000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3025.t1 is derived from g194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1199573	1200631	.	-	.	Phchi.S1G018400
Phchi.S1	AUGUSTUS	transcript	1199573	1200631	.	-	.	transcript_id "Phchi.S1G018400.t1"; gene_id "Phchi.S1G018400"
Phchi.S1	AUGUSTUS	stop_codon	1199570	1199572	.	-	0	transcript_id "Phchi.S1G018400.t1"; gene_id "Phchi.S1G018400"
Phchi.S1	AUGUSTUS	CDS	1199573	1200631	0.59	-	0	transcript_id "Phchi.S1G018400.t1"; gene_id "Phchi.S1G018400"
Phchi.S1	AUGUSTUS	exon	1199573	1200631	.	-	.	transcript_id "Phchi.S1G018400.t1"; gene_id "Phchi.S1G018400"
Phchi.S1	AUGUSTUS	start_codon	1200629	1200631	.	-	0	transcript_id "Phchi.S1G018400.t1"; gene_id "Phchi.S1G018400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8425.t1 is derived from g5600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35888612	35889236	.	+	.	Phchi.S1G558400
Phchi.S1	AUGUSTUS	transcript	35888612	35889236	.	+	.	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	start_codon	35888612	35888614	.	+	0	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	CDS	35888612	35888850	0.63	+	0	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	exon	35888612	35888850	.	+	.	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	intron	35888851	35888938	.	+	.	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	CDS	35888939	35889236	0.66	+	1	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	exon	35888939	35889236	.	+	.	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
Phchi.S1	AUGUSTUS	stop_codon	35889237	35889239	.	+	0	transcript_id "Phchi.S1G558400.t1"; gene_id "Phchi.S1G558400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10066.t1 is derived from g7242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45611983	45612715	.	-	.	Phchi.S1G722500
Phchi.S1	AUGUSTUS	transcript	45611983	45612715	.	-	.	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	stop_codon	45611980	45611982	.	-	0	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	CDS	45611983	45612506	0.98	-	2	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	exon	45611983	45612506	.	-	.	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	intron	45612507	45612633	.	-	.	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	CDS	45612634	45612715	1	-	0	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	exon	45612634	45612715	.	-	.	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
Phchi.S1	AUGUSTUS	start_codon	45612713	45612715	.	-	0	transcript_id "Phchi.S1G722500.t1"; gene_id "Phchi.S1G722500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7775.t1 is derived from g4949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31175629	31176381	.	+	.	Phchi.S1G493400
Phchi.S1	AUGUSTUS	transcript	31175629	31176381	.	+	.	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	start_codon	31175629	31175631	.	+	0	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	CDS	31175629	31175732	0.26	+	0	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	exon	31175629	31175732	.	+	.	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	intron	31175733	31175915	.	+	.	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	CDS	31175916	31176381	0.21	+	1	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	exon	31175916	31176381	.	+	.	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
Phchi.S1	AUGUSTUS	stop_codon	31176382	31176384	.	+	0	transcript_id "Phchi.S1G493400.t1"; gene_id "Phchi.S1G493400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2418.t1 is derived from g9338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6555716	6556045	.	+	.	Phchi.S5G102700
Phchi.S5	AUGUSTUS	transcript	6555716	6556045	.	+	.	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	start_codon	6555716	6555718	.	+	0	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	CDS	6555716	6555771	0.99	+	0	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	exon	6555716	6555771	.	+	.	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	intron	6555772	6555870	.	+	.	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	CDS	6555871	6556045	0.98	+	1	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	exon	6555871	6556045	.	+	.	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
Phchi.S5	AUGUSTUS	stop_codon	6556046	6556048	.	+	0	transcript_id "Phchi.S5G102700.t1"; gene_id "Phchi.S5G102700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1286.t1 is derived from g11069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8814694	8817227	.	-	.	Phchi.S6G124500
Phchi.S6	AUGUSTUS	transcript	8814694	8817227	.	-	.	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	stop_codon	8814691	8814693	.	-	0	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	CDS	8814694	8816789	0.38	-	2	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	exon	8814694	8816789	.	-	.	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	intron	8816790	8816902	.	-	.	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	CDS	8816903	8817227	1	-	0	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	exon	8816903	8817227	.	-	.	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
Phchi.S6	AUGUSTUS	start_codon	8817225	8817227	.	-	0	transcript_id "Phchi.S6G124500.t1"; gene_id "Phchi.S6G124500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15462.t1 is derived from g13930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19300186	19300725	.	+	.	Phchi.S3G278100
Phchi.S3	AUGUSTUS	transcript	19300186	19300725	.	+	.	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	start_codon	19300186	19300188	.	+	0	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	CDS	19300186	19300448	0.39	+	0	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	exon	19300186	19300448	.	+	.	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	intron	19300449	19300709	.	+	.	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	CDS	19300710	19300725	0.42	+	1	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	exon	19300710	19300725	.	+	.	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
Phchi.S3	AUGUSTUS	stop_codon	19300726	19300728	.	+	0	transcript_id "Phchi.S3G278100.t1"; gene_id "Phchi.S3G278100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1058.t1 is derived from g10841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7354658	7355592	.	+	.	Phchi.S6G101700
Phchi.S6	AUGUSTUS	transcript	7354658	7355592	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	start_codon	7354658	7354660	.	+	0	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	CDS	7354658	7354669	0.41	+	0	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	exon	7354658	7354669	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	intron	7354670	7354741	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	CDS	7354742	7354869	0.4	+	0	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	exon	7354742	7354869	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	intron	7354870	7355234	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	CDS	7355235	7355267	0.44	+	1	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	exon	7355235	7355267	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	intron	7355268	7355420	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	CDS	7355421	7355592	0.69	+	1	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	exon	7355421	7355592	.	+	.	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
Phchi.S6	AUGUSTUS	stop_codon	7355593	7355595	.	+	0	transcript_id "Phchi.S6G101700.t1"; gene_id "Phchi.S6G101700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7213.t1 is derived from g4385.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27660688	27663352	.	+	.	Phchi.S1G437200
Phchi.S1	AUGUSTUS	transcript	27660688	27663352	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	start_codon	27660688	27660690	.	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27660688	27660909	0.96	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27660688	27660909	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27660910	27661051	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661052	27661062	0.98	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661052	27661062	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661063	27661135	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661136	27661178	0.98	+	1	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661136	27661178	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661179	27661266	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661267	27661386	1	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661267	27661386	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661387	27661497	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661498	27661613	1	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661498	27661613	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661614	27661798	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661799	27661838	0.5	+	1	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661799	27661838	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661839	27661956	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661957	27662175	1	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661957	27662175	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662176	27662318	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27662319	27662413	0.43	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27662319	27662413	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662414	27662487	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27662488	27662593	0.99	+	1	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27662488	27662593	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662594	27662728	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27662729	27662956	1	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27662729	27662956	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662957	27663051	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27663052	27663136	1	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27663052	27663136	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27663137	27663230	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27663231	27663352	0.95	+	2	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27663231	27663352	.	+	.	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	stop_codon	27663353	27663355	.	+	0	transcript_id "Phchi.S1G437200.t1"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	transcript	27660688	27663352	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	start_codon	27660688	27660690	.	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27660688	27660884	0.94	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27660688	27660884	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27660885	27661051	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661052	27661178	1	+	1	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661052	27661178	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661179	27661266	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661267	27661386	1	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661267	27661386	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661387	27661497	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661498	27661613	1	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661498	27661613	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661614	27661798	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661799	27661838	0.45	+	1	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661799	27661838	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27661839	27661956	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27661957	27662175	1	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27661957	27662175	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662176	27662318	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27662319	27662413	0.46	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27662319	27662413	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662414	27662487	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27662488	27662593	0.98	+	1	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27662488	27662593	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662594	27662728	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27662729	27662956	1	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27662729	27662956	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27662957	27663051	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27663052	27663136	1	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27663052	27663136	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	intron	27663137	27663230	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	CDS	27663231	27663352	0.91	+	2	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	exon	27663231	27663352	.	+	.	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
Phchi.S1	AUGUSTUS	stop_codon	27663353	27663355	.	+	0	transcript_id "Phchi.S1G437200.t2"; gene_id "Phchi.S1G437200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6200.t1 is derived from g3371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21450396	21451022	.	-	.	Phchi.S1G335900
Phchi.S1	AUGUSTUS	transcript	21450396	21451022	.	-	.	transcript_id "Phchi.S1G335900.t1"; gene_id "Phchi.S1G335900"
Phchi.S1	AUGUSTUS	stop_codon	21450393	21450395	.	-	0	transcript_id "Phchi.S1G335900.t1"; gene_id "Phchi.S1G335900"
Phchi.S1	AUGUSTUS	CDS	21450396	21451022	0.64	-	0	transcript_id "Phchi.S1G335900.t1"; gene_id "Phchi.S1G335900"
Phchi.S1	AUGUSTUS	exon	21450396	21451022	.	-	.	transcript_id "Phchi.S1G335900.t1"; gene_id "Phchi.S1G335900"
Phchi.S1	AUGUSTUS	start_codon	21451020	21451022	.	-	0	transcript_id "Phchi.S1G335900.t1"; gene_id "Phchi.S1G335900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3345.t1 is derived from g514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3049479	3050575	.	-	.	Phchi.S1G050400
Phchi.S1	AUGUSTUS	transcript	3049479	3050575	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	stop_codon	3049476	3049478	.	-	0	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	CDS	3049479	3049499	0.79	-	0	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	exon	3049479	3049499	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	intron	3049500	3049776	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	CDS	3049777	3049803	0.96	-	0	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	exon	3049777	3049803	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	intron	3049804	3049873	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	CDS	3049874	3050005	1	-	0	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	exon	3049874	3050005	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	intron	3050006	3050094	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	CDS	3050095	3050155	0.84	-	1	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	exon	3050095	3050155	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	intron	3050156	3050270	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	CDS	3050271	3050575	0.43	-	0	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	exon	3050271	3050575	.	-	.	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
Phchi.S1	AUGUSTUS	start_codon	3050573	3050575	.	-	0	transcript_id "Phchi.S1G050400.t1"; gene_id "Phchi.S1G050400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg222.t1 is derived from g10004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1468830	1470450	.	-	.	Phchi.S6G018100
Phchi.S6	AUGUSTUS	transcript	1468830	1470450	.	-	.	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	stop_codon	1468827	1468829	.	-	0	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	CDS	1468830	1469795	1	-	0	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	exon	1468830	1469795	.	-	.	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	intron	1469796	1469990	.	-	.	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	CDS	1469991	1470199	0.66	-	2	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	exon	1469991	1470199	.	-	.	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	intron	1470200	1470302	.	-	.	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	CDS	1470303	1470450	0.55	-	0	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	exon	1470303	1470450	.	-	.	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
Phchi.S6	AUGUSTUS	start_codon	1470448	1470450	.	-	0	transcript_id "Phchi.S6G018100.t1"; gene_id "Phchi.S6G018100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9798.t1 is derived from g6974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43736321	43738743	.	+	.	Phchi.S1G695700
Phchi.S1	AUGUSTUS	transcript	43736321	43738743	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	start_codon	43736321	43736323	.	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43736321	43736395	1	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43736321	43736395	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43736396	43736527	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43736528	43737034	0.8	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43736528	43737034	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737035	43737172	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737173	43737336	1	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737173	43737336	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737337	43737484	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737485	43737536	1	+	1	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737485	43737536	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737537	43737711	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737712	43737939	1	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737712	43737939	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737940	43738029	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43738030	43738539	0.95	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43738030	43738539	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43738540	43738626	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43738627	43738743	1	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43738627	43738743	.	+	.	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	stop_codon	43738744	43738746	.	+	0	transcript_id "Phchi.S1G695700.t1"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	transcript	43736321	43738743	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	start_codon	43736321	43736323	.	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43736321	43736395	1	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43736321	43736395	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43736396	43736527	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43736528	43736767	0.71	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43736528	43736767	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43736768	43737018	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737019	43737034	0.7	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737019	43737034	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737035	43737200	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737201	43737336	0.7	+	2	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737201	43737336	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737337	43737484	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737485	43737536	1	+	1	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737485	43737536	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737537	43737711	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43737712	43737939	1	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43737712	43737939	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43737940	43738029	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43738030	43738539	0.91	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43738030	43738539	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	intron	43738540	43738626	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	CDS	43738627	43738743	1	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	exon	43738627	43738743	.	+	.	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
Phchi.S1	AUGUSTUS	stop_codon	43738744	43738746	.	+	0	transcript_id "Phchi.S1G695700.t2"; gene_id "Phchi.S1G695700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3994.t1 is derived from g1163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6897274	6897781	.	-	.	Phchi.S1G115300
Phchi.S1	AUGUSTUS	transcript	6897274	6897781	.	-	.	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	stop_codon	6897271	6897273	.	-	0	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	CDS	6897274	6897427	0.98	-	1	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	exon	6897274	6897427	.	-	.	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	intron	6897428	6897515	.	-	.	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	CDS	6897516	6897781	0.58	-	0	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	exon	6897516	6897781	.	-	.	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
Phchi.S1	AUGUSTUS	start_codon	6897779	6897781	.	-	0	transcript_id "Phchi.S1G115300.t1"; gene_id "Phchi.S1G115300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5957.t1 is derived from g3128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20069734	20074823	.	-	.	Phchi.S1G311600
Phchi.S1	AUGUSTUS	transcript	20069734	20074823	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	stop_codon	20069731	20069733	.	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20069734	20069872	1	-	1	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20069734	20069872	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20069873	20069948	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20069949	20070052	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20069949	20070052	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20070053	20070125	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20070126	20070195	1	-	1	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20070126	20070195	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20070196	20070364	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20070365	20070408	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20070365	20070408	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20070409	20070491	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20070492	20070593	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20070492	20070593	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20070594	20070738	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20070739	20070909	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20070739	20070909	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20070910	20070981	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20070982	20071068	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20070982	20071068	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20071069	20071173	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20071174	20071245	0.65	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20071174	20071245	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20071246	20071346	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20071347	20071427	0.32	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20071347	20071427	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20071428	20071553	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20071554	20071796	0.47	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20071554	20071796	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20071797	20071874	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20071875	20071941	1	-	1	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20071875	20071941	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20071942	20072025	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20072026	20072084	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20072026	20072084	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20072085	20072183	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20072184	20072414	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20072184	20072414	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20072415	20072502	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20072503	20072568	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20072503	20072568	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20072569	20072657	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20072658	20072839	1	-	2	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20072658	20072839	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20072840	20072971	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20072972	20073059	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20072972	20073059	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20073060	20073133	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20073134	20073256	0.7	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20073134	20073256	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20073257	20073368	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20073369	20073512	0.68	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20073369	20073512	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20073513	20073616	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20073617	20073713	0.99	-	1	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20073617	20073713	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20073714	20073802	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20073803	20073846	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20073803	20073846	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	intron	20073847	20073935	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	CDS	20073936	20074823	1	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	exon	20073936	20074823	.	-	.	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
Phchi.S1	AUGUSTUS	start_codon	20074821	20074823	.	-	0	transcript_id "Phchi.S1G311600.t1"; gene_id "Phchi.S1G311600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2832.t1 is derived from g9752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9096429	9097578	.	+	.	Phchi.S5G144100
Phchi.S5	AUGUSTUS	transcript	9096429	9097578	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	start_codon	9096429	9096431	.	+	0	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	CDS	9096429	9096716	0.42	+	0	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	exon	9096429	9096716	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	intron	9096717	9096808	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	CDS	9096809	9097065	1	+	0	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	exon	9096809	9097065	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	intron	9097066	9097206	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	CDS	9097207	9097374	0.35	+	1	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	exon	9097207	9097374	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	intron	9097375	9097496	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	CDS	9097497	9097578	0.47	+	1	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	exon	9097497	9097578	.	+	.	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
Phchi.S5	AUGUSTUS	stop_codon	9097579	9097581	.	+	0	transcript_id "Phchi.S5G144100.t1"; gene_id "Phchi.S5G144100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7925.t1 is derived from g5099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31929103	31931337	.	-	.	Phchi.S1G508400
Phchi.S1	AUGUSTUS	transcript	31929103	31931337	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	stop_codon	31929100	31929102	.	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31929103	31929537	0.65	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31929103	31929537	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31929538	31929636	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31929637	31929697	1	-	1	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31929637	31929697	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31929698	31929777	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31929778	31929887	1	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31929778	31929887	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31929888	31929994	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31929995	31930054	0.99	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31929995	31930054	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31930055	31930141	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31930142	31930220	1	-	1	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31930142	31930220	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31930221	31930348	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31930349	31930419	1	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31930349	31930419	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31930420	31930527	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31930528	31930584	1	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31930528	31930584	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31930585	31930665	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31930666	31930837	1	-	1	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31930666	31930837	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31930838	31930944	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31930945	31931109	0.99	-	1	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31930945	31931109	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	intron	31931110	31931191	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	CDS	31931192	31931337	0.74	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	exon	31931192	31931337	.	-	.	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
Phchi.S1	AUGUSTUS	start_codon	31931335	31931337	.	-	0	transcript_id "Phchi.S1G508400.t1"; gene_id "Phchi.S1G508400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg996.t1 is derived from g10779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6966186	6968336	.	+	.	Phchi.S6G095500
Phchi.S6	AUGUSTUS	transcript	6966186	6968336	.	+	.	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	start_codon	6966186	6966188	.	+	0	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	CDS	6966186	6967212	0.99	+	0	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	exon	6966186	6967212	.	+	.	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	intron	6967213	6967302	.	+	.	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	CDS	6967303	6968336	0.98	+	2	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	exon	6967303	6968336	.	+	.	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
Phchi.S6	AUGUSTUS	stop_codon	6968337	6968339	.	+	0	transcript_id "Phchi.S6G095500.t1"; gene_id "Phchi.S6G095500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3053.t1 is derived from g222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1364597	1366480	.	+	.	Phchi.S1G021200
Phchi.S1	AUGUSTUS	transcript	1364597	1366480	.	+	.	transcript_id "Phchi.S1G021200.t1"; gene_id "Phchi.S1G021200"
Phchi.S1	AUGUSTUS	start_codon	1364597	1364599	.	+	0	transcript_id "Phchi.S1G021200.t1"; gene_id "Phchi.S1G021200"
Phchi.S1	AUGUSTUS	CDS	1364597	1366480	1	+	0	transcript_id "Phchi.S1G021200.t1"; gene_id "Phchi.S1G021200"
Phchi.S1	AUGUSTUS	exon	1364597	1366480	.	+	.	transcript_id "Phchi.S1G021200.t1"; gene_id "Phchi.S1G021200"
Phchi.S1	AUGUSTUS	stop_codon	1366481	1366483	.	+	0	transcript_id "Phchi.S1G021200.t1"; gene_id "Phchi.S1G021200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2540.t1 is derived from g9460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7232209	7232832	.	-	.	Phchi.S5G114900
Phchi.S5	AUGUSTUS	transcript	7232209	7232832	.	-	.	transcript_id "Phchi.S5G114900.t1"; gene_id "Phchi.S5G114900"
Phchi.S5	AUGUSTUS	stop_codon	7232206	7232208	.	-	0	transcript_id "Phchi.S5G114900.t1"; gene_id "Phchi.S5G114900"
Phchi.S5	AUGUSTUS	CDS	7232209	7232832	0.92	-	0	transcript_id "Phchi.S5G114900.t1"; gene_id "Phchi.S5G114900"
Phchi.S5	AUGUSTUS	exon	7232209	7232832	.	-	.	transcript_id "Phchi.S5G114900.t1"; gene_id "Phchi.S5G114900"
Phchi.S5	AUGUSTUS	start_codon	7232830	7232832	.	-	0	transcript_id "Phchi.S5G114900.t1"; gene_id "Phchi.S5G114900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7748.t1 is derived from g4922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30942730	30950158	.	-	.	Phchi.S1G490700
Phchi.S1	AUGUSTUS	transcript	30942730	30950158	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	stop_codon	30942727	30942729	.	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30942730	30944050	0.68	-	1	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30942730	30944050	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30944051	30944153	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30944154	30944251	1	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30944154	30944251	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30944252	30944342	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30944343	30944432	1	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30944343	30944432	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30944433	30944539	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30944540	30945244	0.64	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30944540	30945244	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30945245	30945367	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30945368	30945496	1	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30945368	30945496	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30945497	30945623	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30945624	30945743	0.69	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30945624	30945743	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30945744	30945861	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30945862	30946059	0.67	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30945862	30946059	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30946060	30946294	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30946295	30946510	1	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30946295	30946510	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30946511	30946711	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30946712	30947395	0.85	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30946712	30947395	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30947396	30947463	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30947464	30947592	0.93	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30947464	30947592	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30947593	30947742	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30947743	30948303	0.98	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30947743	30948303	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30948304	30948476	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30948477	30948542	0.66	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30948477	30948542	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30948543	30948788	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30948789	30948858	1	-	1	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30948789	30948858	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30948859	30948956	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30948957	30949685	0.4	-	1	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30948957	30949685	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30949686	30949831	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30949832	30949890	0.49	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30949832	30949890	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	intron	30949891	30950032	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	CDS	30950033	30950158	0.42	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	exon	30950033	30950158	.	-	.	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
Phchi.S1	AUGUSTUS	start_codon	30950156	30950158	.	-	0	transcript_id "Phchi.S1G490700.t1"; gene_id "Phchi.S1G490700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg413.t1 is derived from g10195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2953620	2954297	.	+	.	Phchi.S6G037200
Phchi.S6	AUGUSTUS	transcript	2953620	2954297	.	+	.	transcript_id "Phchi.S6G037200.t1"; gene_id "Phchi.S6G037200"
Phchi.S6	AUGUSTUS	start_codon	2953620	2953622	.	+	0	transcript_id "Phchi.S6G037200.t1"; gene_id "Phchi.S6G037200"
Phchi.S6	AUGUSTUS	CDS	2953620	2954297	0.78	+	0	transcript_id "Phchi.S6G037200.t1"; gene_id "Phchi.S6G037200"
Phchi.S6	AUGUSTUS	exon	2953620	2954297	.	+	.	transcript_id "Phchi.S6G037200.t1"; gene_id "Phchi.S6G037200"
Phchi.S6	AUGUSTUS	stop_codon	2954298	2954300	.	+	0	transcript_id "Phchi.S6G037200.t1"; gene_id "Phchi.S6G037200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8470.t1 is derived from g5645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36100018	36104797	.	-	.	Phchi.S1G562900
Phchi.S1	AUGUSTUS	transcript	36100018	36104797	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	stop_codon	36100015	36100017	.	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36100018	36100550	1	-	2	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36100018	36100550	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36100551	36100657	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36100658	36100871	1	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36100658	36100871	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36100872	36101027	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101028	36101142	0.99	-	1	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101028	36101142	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101143	36101251	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101252	36101482	1	-	1	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101252	36101482	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101483	36101579	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101580	36101683	1	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101580	36101683	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101684	36101765	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101766	36101984	1	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101766	36101984	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101985	36102084	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102085	36102406	0.98	-	1	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102085	36102406	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36102407	36102519	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102520	36102631	1	-	2	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102520	36102631	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36102632	36102721	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102722	36102877	1	-	2	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102722	36102877	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36102878	36102994	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102995	36103092	1	-	1	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102995	36103092	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103093	36103185	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36103186	36103280	1	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36103186	36103280	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103281	36103404	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36103405	36103502	0.57	-	2	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36103405	36103502	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103503	36103582	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36103583	36103966	0.55	-	2	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36103583	36103966	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103967	36104044	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104045	36104163	0.76	-	1	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104045	36104163	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36104164	36104290	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104291	36104317	0.51	-	1	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104291	36104317	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36104318	36104411	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104412	36104586	1	-	2	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104412	36104586	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36104587	36104769	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104770	36104797	0.81	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104770	36104797	.	-	.	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	start_codon	36104795	36104797	.	-	0	transcript_id "Phchi.S1G562900.t1"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	transcript	36100018	36104797	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	stop_codon	36100015	36100017	.	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36100018	36100550	1	-	2	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36100018	36100550	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36100551	36100657	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36100658	36100871	1	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36100658	36100871	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36100872	36101027	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101028	36101142	1	-	1	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101028	36101142	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101143	36101251	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101252	36101482	1	-	1	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101252	36101482	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101483	36101579	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101580	36101683	1	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101580	36101683	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101684	36101765	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36101766	36101984	1	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36101766	36101984	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36101985	36102084	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102085	36102406	0.92	-	1	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102085	36102406	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36102407	36102519	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102520	36102631	1	-	2	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102520	36102631	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36102632	36102721	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102722	36102877	1	-	2	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102722	36102877	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36102878	36102994	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36102995	36103092	1	-	1	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36102995	36103092	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103093	36103185	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36103186	36103280	1	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36103186	36103280	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103281	36103404	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36103405	36103502	0.45	-	2	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36103405	36103502	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103503	36103582	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36103583	36103966	0.42	-	2	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36103583	36103966	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36103967	36104044	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104045	36104163	0.68	-	1	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104045	36104163	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36104164	36104290	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104291	36104317	0.37	-	1	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104291	36104317	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36104318	36104411	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104412	36104562	0.98	-	2	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104412	36104562	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	intron	36104563	36104769	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	CDS	36104770	36104797	0.88	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	exon	36104770	36104797	.	-	.	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
Phchi.S1	AUGUSTUS	start_codon	36104795	36104797	.	-	0	transcript_id "Phchi.S1G562900.t2"; gene_id "Phchi.S1G562900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15262.t1 is derived from g13730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18012001	18013800	.	-	.	Phchi.S3G258100
Phchi.S3	AUGUSTUS	transcript	18012001	18013800	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	stop_codon	18011998	18012000	.	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18012001	18012012	1	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18012001	18012012	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	intron	18012013	18012106	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18012107	18012196	1	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18012107	18012196	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	intron	18012197	18012277	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18012278	18012526	0.99	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18012278	18012526	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	intron	18012527	18012662	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18012663	18012908	1	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18012663	18012908	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	intron	18012909	18012996	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18012997	18013369	0.65	-	1	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18012997	18013369	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	intron	18013370	18013655	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18013656	18013673	0.86	-	1	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18013656	18013673	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	intron	18013674	18013756	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	CDS	18013757	18013800	0.98	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	exon	18013757	18013800	.	-	.	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
Phchi.S3	AUGUSTUS	start_codon	18013798	18013800	.	-	0	transcript_id "Phchi.S3G258100.t1"; gene_id "Phchi.S3G258100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4590.t1 is derived from g1760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11225658	11226277	.	+	.	Phchi.S1G174900
Phchi.S1	AUGUSTUS	transcript	11225658	11226277	.	+	.	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	start_codon	11225658	11225660	.	+	0	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	CDS	11225658	11225666	0.99	+	0	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	exon	11225658	11225666	.	+	.	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	intron	11225667	11225764	.	+	.	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	CDS	11225765	11226277	0.98	+	0	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	exon	11225765	11226277	.	+	.	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
Phchi.S1	AUGUSTUS	stop_codon	11226278	11226280	.	+	0	transcript_id "Phchi.S1G174900.t1"; gene_id "Phchi.S1G174900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7322.t1 is derived from g4494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28514885	28517094	.	+	.	Phchi.S1G448100
Phchi.S1	AUGUSTUS	transcript	28514885	28517094	.	+	.	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	start_codon	28514885	28514887	.	+	0	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	CDS	28514885	28515272	0.34	+	0	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	exon	28514885	28515272	.	+	.	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	intron	28515273	28515673	.	+	.	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	CDS	28515674	28515882	0.34	+	2	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	exon	28515674	28515882	.	+	.	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	intron	28515883	28515963	.	+	.	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	CDS	28515964	28517094	0.85	+	0	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	exon	28515964	28517094	.	+	.	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
Phchi.S1	AUGUSTUS	stop_codon	28517095	28517097	.	+	0	transcript_id "Phchi.S1G448100.t1"; gene_id "Phchi.S1G448100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4849.t1 is derived from g2019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13087378	13087807	.	-	.	Phchi.S1G200800
Phchi.S1	AUGUSTUS	transcript	13087378	13087807	.	-	.	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	stop_codon	13087375	13087377	.	-	0	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	CDS	13087378	13087421	0.73	-	2	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	exon	13087378	13087421	.	-	.	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	intron	13087422	13087515	.	-	.	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	CDS	13087516	13087807	0.96	-	0	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	exon	13087516	13087807	.	-	.	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
Phchi.S1	AUGUSTUS	start_codon	13087805	13087807	.	-	0	transcript_id "Phchi.S1G200800.t1"; gene_id "Phchi.S1G200800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15722.t1 is derived from g14192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20894701	20895537	.	-	.	Phchi.S3G304100
Phchi.S3	AUGUSTUS	transcript	20894701	20895537	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	stop_codon	20894698	20894700	.	-	0	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	CDS	20894701	20894747	0.97	-	2	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	exon	20894701	20894747	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	intron	20894748	20894915	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	CDS	20894916	20895017	1	-	2	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	exon	20894916	20895017	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	intron	20895018	20895104	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	CDS	20895105	20895240	1	-	0	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	exon	20895105	20895240	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	intron	20895241	20895534	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	CDS	20895535	20895537	0.99	-	0	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	exon	20895535	20895537	.	-	.	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
Phchi.S3	AUGUSTUS	start_codon	20895535	20895537	.	-	0	transcript_id "Phchi.S3G304100.t1"; gene_id "Phchi.S3G304100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4321.t1 is derived from g1490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9621518	9624289	.	+	.	Phchi.S1G148000
Phchi.S1	AUGUSTUS	transcript	9621518	9624289	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	start_codon	9621518	9621520	.	+	0	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9621518	9622505	0.68	+	0	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9621518	9622505	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9622506	9622640	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9622641	9622873	1	+	2	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9622641	9622873	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9622874	9623001	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9623002	9623146	1	+	0	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9623002	9623146	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9623147	9623241	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9623242	9623310	1	+	2	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9623242	9623310	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9623311	9623417	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9623418	9623610	1	+	2	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9623418	9623610	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9623611	9623721	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9623722	9623851	1	+	1	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9623722	9623851	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9623852	9623946	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9623947	9624053	0.62	+	0	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9623947	9624053	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	intron	9624054	9624222	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	CDS	9624223	9624289	0.37	+	1	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	exon	9624223	9624289	.	+	.	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
Phchi.S1	AUGUSTUS	stop_codon	9624290	9624292	.	+	0	transcript_id "Phchi.S1G148000.t1"; gene_id "Phchi.S1G148000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4206.t1 is derived from g1375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8905246	8906018	.	+	.	Phchi.S1G136500
Phchi.S1	AUGUSTUS	transcript	8905246	8906018	.	+	.	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	start_codon	8905246	8905248	.	+	0	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	CDS	8905246	8905329	0.87	+	0	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	exon	8905246	8905329	.	+	.	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	intron	8905330	8905485	.	+	.	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	CDS	8905486	8905565	1	+	0	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	exon	8905486	8905565	.	+	.	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	intron	8905566	8905861	.	+	.	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	CDS	8905862	8906018	1	+	1	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	exon	8905862	8906018	.	+	.	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
Phchi.S1	AUGUSTUS	stop_codon	8906019	8906021	.	+	0	transcript_id "Phchi.S1G136500.t1"; gene_id "Phchi.S1G136500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7926.t1 is derived from g5100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31931523	31932693	.	-	.	Phchi.S1G508500
Phchi.S1	AUGUSTUS	transcript	31931523	31932693	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	stop_codon	31931520	31931522	.	-	0	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	CDS	31931523	31931910	1	-	1	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	exon	31931523	31931910	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	intron	31931911	31931997	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	CDS	31931998	31932154	1	-	2	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	exon	31931998	31932154	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	intron	31932155	31932242	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	CDS	31932243	31932510	1	-	0	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	exon	31932243	31932510	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	intron	31932511	31932594	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	CDS	31932595	31932693	1	-	0	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	exon	31932595	31932693	.	-	.	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
Phchi.S1	AUGUSTUS	start_codon	31932691	31932693	.	-	0	transcript_id "Phchi.S1G508500.t1"; gene_id "Phchi.S1G508500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14376.t1 is derived from g12843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12447354	12447925	.	-	.	Phchi.S3G169500
Phchi.S3	AUGUSTUS	transcript	12447354	12447925	.	-	.	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	stop_codon	12447351	12447353	.	-	0	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	CDS	12447354	12447557	0.92	-	0	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	exon	12447354	12447557	.	-	.	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	intron	12447558	12447685	.	-	.	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	CDS	12447686	12447925	0.55	-	0	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	exon	12447686	12447925	.	-	.	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
Phchi.S3	AUGUSTUS	start_codon	12447923	12447925	.	-	0	transcript_id "Phchi.S3G169500.t1"; gene_id "Phchi.S3G169500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2160.t1 is derived from g9080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5123928	5124919	.	-	.	Phchi.S5G076900
Phchi.S5	AUGUSTUS	transcript	5123928	5124919	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	stop_codon	5123925	5123927	.	-	0	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	CDS	5123928	5124042	0.98	-	1	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	exon	5123928	5124042	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	intron	5124043	5124201	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	CDS	5124202	5124279	1	-	1	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	exon	5124202	5124279	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	intron	5124280	5124374	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	CDS	5124375	5124466	1	-	0	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	exon	5124375	5124466	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	intron	5124467	5124548	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	CDS	5124549	5124599	1	-	0	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	exon	5124549	5124599	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	intron	5124600	5124709	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	CDS	5124710	5124764	0.99	-	1	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	exon	5124710	5124764	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	intron	5124765	5124854	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	CDS	5124855	5124919	0.76	-	0	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	exon	5124855	5124919	.	-	.	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
Phchi.S5	AUGUSTUS	start_codon	5124917	5124919	.	-	0	transcript_id "Phchi.S5G076900.t1"; gene_id "Phchi.S5G076900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12037.t1 is derived from g7712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	791876	794336	.	+	.	Phchi.S2G011700
Phchi.S2	AUGUSTUS	transcript	791876	794336	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	start_codon	791876	791878	.	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	791876	792257	0.61	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	791876	792257	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	792258	792410	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	792411	792499	0.78	+	2	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	792411	792499	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	792500	792636	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	792637	792693	0.86	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	792637	792693	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	792694	792772	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	792773	792877	0.98	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	792773	792877	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	792878	792957	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	792958	793014	1	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	792958	793014	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	793015	793095	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	793096	793179	1	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	793096	793179	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	793180	793258	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	793259	793327	1	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	793259	793327	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	793328	793420	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	793421	793533	1	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	793421	793533	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	793534	793658	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	793659	793828	1	+	1	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	793659	793828	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	793829	793995	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	793996	794074	0.92	+	2	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	793996	794074	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	intron	794075	794185	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	CDS	794186	794336	0.99	+	1	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	exon	794186	794336	.	+	.	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
Phchi.S2	AUGUSTUS	stop_codon	794337	794339	.	+	0	transcript_id "Phchi.S2G011700.t1"; gene_id "Phchi.S2G011700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13876.t1 is derived from g12343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9428495	9430286	.	-	.	Phchi.S3G119500
Phchi.S3	AUGUSTUS	transcript	9428495	9430286	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	stop_codon	9428492	9428494	.	-	0	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	CDS	9428495	9429309	0.37	-	2	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	exon	9428495	9429309	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	intron	9429310	9429433	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	CDS	9429434	9429611	0.91	-	0	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	exon	9429434	9429611	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	intron	9429612	9429694	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	CDS	9429695	9429996	1	-	2	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	exon	9429695	9429996	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	intron	9429997	9430165	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	CDS	9430166	9430286	0.78	-	0	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	exon	9430166	9430286	.	-	.	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
Phchi.S3	AUGUSTUS	start_codon	9430284	9430286	.	-	0	transcript_id "Phchi.S3G119500.t1"; gene_id "Phchi.S3G119500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8391.t1 is derived from g5566.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35674452	35678587	.	-	.	Phchi.S1G555000
Phchi.S1	AUGUSTUS	transcript	35674452	35678587	.	-	.	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	stop_codon	35674449	35674451	.	-	0	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	CDS	35674452	35677259	0.84	-	0	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	exon	35674452	35677259	.	-	.	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	intron	35677260	35677363	.	-	.	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	CDS	35677364	35678587	0.67	-	0	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	exon	35677364	35678587	.	-	.	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	start_codon	35678585	35678587	.	-	0	transcript_id "Phchi.S1G555000.t1"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	transcript	35674452	35675576	.	-	.	transcript_id "Phchi.S1G555000.t2"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	stop_codon	35674449	35674451	.	-	0	transcript_id "Phchi.S1G555000.t2"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	CDS	35674452	35675576	1	-	0	transcript_id "Phchi.S1G555000.t2"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	exon	35674452	35675576	.	-	.	transcript_id "Phchi.S1G555000.t2"; gene_id "Phchi.S1G555000"
Phchi.S1	AUGUSTUS	start_codon	35675574	35675576	.	-	0	transcript_id "Phchi.S1G555000.t2"; gene_id "Phchi.S1G555000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9537.t1 is derived from g6713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42380566	42383662	.	+	.	Phchi.S1G669600
Phchi.S1	AUGUSTUS	transcript	42380566	42383662	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	start_codon	42380566	42380568	.	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42380566	42380646	0.91	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42380566	42380646	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42380647	42380814	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42380815	42380930	1	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42380815	42380930	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42380931	42381025	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381026	42381116	1	+	1	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381026	42381116	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381117	42381203	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381204	42381324	1	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381204	42381324	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381325	42381420	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381421	42381613	1	+	2	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381421	42381613	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381614	42381799	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381800	42381944	1	+	1	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381800	42381944	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381945	42382033	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382034	42382124	1	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382034	42382124	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382125	42382272	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382273	42382331	1	+	2	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382273	42382331	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382332	42382434	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382435	42382512	1	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382435	42382512	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382513	42382590	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382591	42382674	1	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382591	42382674	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382675	42382755	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382756	42382901	1	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382756	42382901	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382902	42383000	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383001	42383132	1	+	1	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383001	42383132	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42383133	42383213	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383214	42383286	1	+	1	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383214	42383286	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42383287	42383377	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383378	42383463	0.78	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383378	42383463	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42383464	42383565	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383566	42383662	0.98	+	1	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383566	42383662	.	+	.	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	stop_codon	42383663	42383665	.	+	0	transcript_id "Phchi.S1G669600.t1"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	transcript	42380566	42383662	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	start_codon	42380566	42380568	.	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42380566	42380646	0.92	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42380566	42380646	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42380647	42380814	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42380815	42380930	1	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42380815	42380930	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42380931	42381025	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381026	42381116	1	+	1	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381026	42381116	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381117	42381203	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381204	42381324	1	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381204	42381324	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381325	42381420	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381421	42381613	1	+	2	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381421	42381613	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381614	42381799	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42381800	42381944	1	+	1	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42381800	42381944	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42381945	42382033	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382034	42382124	1	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382034	42382124	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382125	42382272	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382273	42382303	0.33	+	2	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382273	42382303	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382304	42382474	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382475	42382512	0.75	+	1	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382475	42382512	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382513	42382603	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382604	42382674	0.97	+	2	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382604	42382674	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382675	42382755	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42382756	42382901	1	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42382756	42382901	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42382902	42383000	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383001	42383132	1	+	1	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383001	42383132	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42383133	42383213	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383214	42383286	1	+	1	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383214	42383286	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42383287	42383377	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383378	42383463	0.71	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383378	42383463	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	intron	42383464	42383565	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	CDS	42383566	42383662	0.93	+	1	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	exon	42383566	42383662	.	+	.	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
Phchi.S1	AUGUSTUS	stop_codon	42383663	42383665	.	+	0	transcript_id "Phchi.S1G669600.t2"; gene_id "Phchi.S1G669600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4794.t1 is derived from g1964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12830417	12831207	.	-	.	Phchi.S1G195300
Phchi.S1	AUGUSTUS	transcript	12830417	12831207	.	-	.	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	stop_codon	12830414	12830416	.	-	0	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	CDS	12830417	12830495	0.98	-	1	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	exon	12830417	12830495	.	-	.	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	intron	12830496	12830741	.	-	.	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	CDS	12830742	12830814	0.57	-	2	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	exon	12830742	12830814	.	-	.	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	intron	12830815	12831074	.	-	.	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	CDS	12831075	12831207	0.32	-	0	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	exon	12831075	12831207	.	-	.	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
Phchi.S1	AUGUSTUS	start_codon	12831205	12831207	.	-	0	transcript_id "Phchi.S1G195300.t1"; gene_id "Phchi.S1G195300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12818.t1 is derived from g11283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2547086	2549148	.	-	.	Phchi.S3G013700
Phchi.S3	AUGUSTUS	transcript	2547086	2549148	.	-	.	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	stop_codon	2547083	2547085	.	-	0	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	CDS	2547086	2547447	0.53	-	2	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	exon	2547086	2547447	.	-	.	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	intron	2547448	2547909	.	-	.	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	CDS	2547910	2548392	0.33	-	2	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	exon	2547910	2548392	.	-	.	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	intron	2548393	2548499	.	-	.	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	CDS	2548500	2549148	0.98	-	0	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	exon	2548500	2549148	.	-	.	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
Phchi.S3	AUGUSTUS	start_codon	2549146	2549148	.	-	0	transcript_id "Phchi.S3G013700.t1"; gene_id "Phchi.S3G013700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14109.t1 is derived from g12576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10887230	10888174	.	+	.	Phchi.S3G142800
Phchi.S3	AUGUSTUS	transcript	10887230	10888174	.	+	.	transcript_id "Phchi.S3G142800.t1"; gene_id "Phchi.S3G142800"
Phchi.S3	AUGUSTUS	start_codon	10887230	10887232	.	+	0	transcript_id "Phchi.S3G142800.t1"; gene_id "Phchi.S3G142800"
Phchi.S3	AUGUSTUS	CDS	10887230	10888174	0.62	+	0	transcript_id "Phchi.S3G142800.t1"; gene_id "Phchi.S3G142800"
Phchi.S3	AUGUSTUS	exon	10887230	10888174	.	+	.	transcript_id "Phchi.S3G142800.t1"; gene_id "Phchi.S3G142800"
Phchi.S3	AUGUSTUS	stop_codon	10888175	10888177	.	+	0	transcript_id "Phchi.S3G142800.t1"; gene_id "Phchi.S3G142800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6311.t1 is derived from g3483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22210998	22211896	.	-	.	Phchi.S1G347000
Phchi.S1	AUGUSTUS	transcript	22210998	22211896	.	-	.	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	stop_codon	22210995	22210997	.	-	0	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	CDS	22210998	22211114	1	-	0	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	exon	22210998	22211114	.	-	.	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	intron	22211115	22211252	.	-	.	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	CDS	22211253	22211534	1	-	0	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	exon	22211253	22211534	.	-	.	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	intron	22211535	22211845	.	-	.	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	CDS	22211846	22211896	1	-	0	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	exon	22211846	22211896	.	-	.	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
Phchi.S1	AUGUSTUS	start_codon	22211894	22211896	.	-	0	transcript_id "Phchi.S1G347000.t1"; gene_id "Phchi.S1G347000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8672.t1 is derived from g5847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37368400	37369055	.	+	.	Phchi.S1G583100
Phchi.S1	AUGUSTUS	transcript	37368400	37369055	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	start_codon	37368400	37368402	.	+	0	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	CDS	37368400	37368529	1	+	0	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	exon	37368400	37368529	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	intron	37368530	37368631	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	CDS	37368632	37368693	1	+	2	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	exon	37368632	37368693	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	intron	37368694	37368785	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	CDS	37368786	37368858	1	+	0	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	exon	37368786	37368858	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	intron	37368859	37368957	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	CDS	37368958	37369055	1	+	2	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	exon	37368958	37369055	.	+	.	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
Phchi.S1	AUGUSTUS	stop_codon	37369056	37369058	.	+	0	transcript_id "Phchi.S1G583100.t1"; gene_id "Phchi.S1G583100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11562.t1 is derived from g15613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7070785	7072719	.	-	.	Phchi.S4G114400
Phchi.S4	AUGUSTUS	transcript	7070785	7072719	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	stop_codon	7070782	7070784	.	-	0	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7070785	7070804	1	-	2	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7070785	7070804	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7070805	7070961	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7070962	7071015	0.46	-	2	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7070962	7071015	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7071016	7071092	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7071093	7071228	0.41	-	0	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7071093	7071228	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7071229	7071349	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7071350	7071418	1	-	0	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7071350	7071418	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7071419	7071538	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7071539	7071710	1	-	1	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7071539	7071710	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7071711	7071804	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7071805	7071924	0.89	-	1	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7071805	7071924	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7071925	7072039	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7072040	7072173	1	-	0	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7072040	7072173	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	intron	7072174	7072281	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	CDS	7072282	7072719	1	-	0	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	exon	7072282	7072719	.	-	.	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
Phchi.S4	AUGUSTUS	start_codon	7072717	7072719	.	-	0	transcript_id "Phchi.S4G114400.t1"; gene_id "Phchi.S4G114400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14148.t1 is derived from g12615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11162912	11168700	.	+	.	Phchi.S3G146700
Phchi.S3	AUGUSTUS	transcript	11162912	11168700	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	start_codon	11162912	11162914	.	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11162912	11163013	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11162912	11163013	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11163014	11163175	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11163176	11163414	0.96	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11163176	11163414	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11163415	11163523	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11163524	11163663	0.76	+	1	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11163524	11163663	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11163664	11163749	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11163750	11163831	1	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11163750	11163831	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11163832	11163980	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11163981	11164131	1	+	1	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11163981	11164131	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11164132	11164242	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11164243	11164405	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11164243	11164405	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11164406	11164495	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11164496	11164672	0.78	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11164496	11164672	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11164673	11164789	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11164790	11164905	0.78	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11164790	11164905	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11164906	11165014	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11165015	11165063	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11165015	11165063	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11165064	11165141	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11165142	11165286	1	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11165142	11165286	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11165287	11165379	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11165380	11165534	0.94	+	1	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11165380	11165534	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11165535	11165611	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11165612	11165745	0.76	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11165612	11165745	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11165746	11165885	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11165886	11165993	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11165886	11165993	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11165994	11166079	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11166080	11166148	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11166080	11166148	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11166149	11166227	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11166228	11166314	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11166228	11166314	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11166315	11166412	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11166413	11166475	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11166413	11166475	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11166476	11166655	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11166656	11166771	0.99	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11166656	11166771	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11166772	11166874	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11166875	11166932	1	+	1	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11166875	11166932	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11166933	11167074	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11167075	11167162	0.89	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11167075	11167162	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11167163	11167264	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11167265	11167357	0.9	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11167265	11167357	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11167358	11167441	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11167442	11167527	1	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11167442	11167527	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11167528	11167617	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11167618	11168082	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11167618	11168082	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11168083	11168163	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11168164	11168309	1	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11168164	11168309	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11168310	11168400	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11168401	11168486	1	+	1	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11168401	11168486	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	intron	11168487	11168572	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	CDS	11168573	11168700	1	+	2	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	exon	11168573	11168700	.	+	.	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
Phchi.S3	AUGUSTUS	stop_codon	11168701	11168703	.	+	0	transcript_id "Phchi.S3G146700.t1"; gene_id "Phchi.S3G146700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12513.t1 is derived from g8190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32404110	32404352	.	+	.	Phchi.S2G059300
Phchi.S2	AUGUSTUS	transcript	32404110	32404352	.	+	.	transcript_id "Phchi.S2G059300.t1"; gene_id "Phchi.S2G059300"
Phchi.S2	AUGUSTUS	start_codon	32404110	32404112	.	+	0	transcript_id "Phchi.S2G059300.t1"; gene_id "Phchi.S2G059300"
Phchi.S2	AUGUSTUS	CDS	32404110	32404352	0.95	+	0	transcript_id "Phchi.S2G059300.t1"; gene_id "Phchi.S2G059300"
Phchi.S2	AUGUSTUS	exon	32404110	32404352	.	+	.	transcript_id "Phchi.S2G059300.t1"; gene_id "Phchi.S2G059300"
Phchi.S2	AUGUSTUS	stop_codon	32404353	32404355	.	+	0	transcript_id "Phchi.S2G059300.t1"; gene_id "Phchi.S2G059300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13483.t1 is derived from g11950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7113807	7115451	.	-	.	Phchi.S3G080200
Phchi.S3	AUGUSTUS	transcript	7113807	7115451	.	-	.	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	stop_codon	7113804	7113806	.	-	0	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	CDS	7113807	7113871	0.98	-	2	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	exon	7113807	7113871	.	-	.	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	intron	7113872	7114004	.	-	.	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	CDS	7114005	7115451	0.59	-	0	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	exon	7114005	7115451	.	-	.	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
Phchi.S3	AUGUSTUS	start_codon	7115449	7115451	.	-	0	transcript_id "Phchi.S3G080200.t1"; gene_id "Phchi.S3G080200"
# This transcript jg10080.t2 is derived from g7256.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10080.t3 is derived from g7256.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10081.t1 is derived from g7257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45648258	45652455	.	-	.	Phchi.S1G724000
Phchi.S1	AUGUSTUS	transcript	45648258	45652455	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	stop_codon	45648255	45648257	.	-	0	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	CDS	45648258	45648970	0.58	-	2	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	exon	45648258	45648970	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	intron	45648971	45649028	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	CDS	45649029	45649047	0.52	-	0	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	exon	45649029	45649047	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	intron	45649048	45649217	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	CDS	45649218	45649358	0.71	-	0	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	exon	45649218	45649358	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	intron	45649359	45649439	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	CDS	45649440	45650812	0.99	-	2	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	exon	45649440	45650812	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	intron	45650813	45650936	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	CDS	45650937	45652455	1	-	0	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	exon	45650937	45652455	.	-	.	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
Phchi.S1	AUGUSTUS	start_codon	45652453	45652455	.	-	0	transcript_id "Phchi.S1G724000.t1"; gene_id "Phchi.S1G724000"
# This transcript jg11525.t2 is derived from g15575.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11526.t1 is derived from g15576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6903311	6904324	.	+	.	Phchi.S4G110800
Phchi.S4	AUGUSTUS	transcript	6903311	6904324	.	+	.	transcript_id "Phchi.S4G110800.t1"; gene_id "Phchi.S4G110800"
Phchi.S4	AUGUSTUS	start_codon	6903311	6903313	.	+	0	transcript_id "Phchi.S4G110800.t1"; gene_id "Phchi.S4G110800"
Phchi.S4	AUGUSTUS	CDS	6903311	6904324	0.59	+	0	transcript_id "Phchi.S4G110800.t1"; gene_id "Phchi.S4G110800"
Phchi.S4	AUGUSTUS	exon	6903311	6904324	.	+	.	transcript_id "Phchi.S4G110800.t1"; gene_id "Phchi.S4G110800"
Phchi.S4	AUGUSTUS	stop_codon	6904325	6904327	.	+	0	transcript_id "Phchi.S4G110800.t1"; gene_id "Phchi.S4G110800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2661.t1 is derived from g9581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8097667	8098641	.	-	.	Phchi.S5G127000
Phchi.S5	AUGUSTUS	transcript	8097667	8098641	.	-	.	transcript_id "Phchi.S5G127000.t1"; gene_id "Phchi.S5G127000"
Phchi.S5	AUGUSTUS	stop_codon	8097664	8097666	.	-	0	transcript_id "Phchi.S5G127000.t1"; gene_id "Phchi.S5G127000"
Phchi.S5	AUGUSTUS	CDS	8097667	8098641	0.62	-	0	transcript_id "Phchi.S5G127000.t1"; gene_id "Phchi.S5G127000"
Phchi.S5	AUGUSTUS	exon	8097667	8098641	.	-	.	transcript_id "Phchi.S5G127000.t1"; gene_id "Phchi.S5G127000"
Phchi.S5	AUGUSTUS	start_codon	8098639	8098641	.	-	0	transcript_id "Phchi.S5G127000.t1"; gene_id "Phchi.S5G127000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10915.t1 is derived from g14965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2919327	2923514	.	-	.	Phchi.S4G049700
Phchi.S4	AUGUSTUS	transcript	2919327	2923514	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	stop_codon	2919324	2919326	.	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2919327	2919405	1	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2919327	2919405	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2919406	2919507	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2919508	2919579	0.99	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2919508	2919579	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2919580	2919687	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2919688	2919759	1	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2919688	2919759	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2919760	2919883	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2919884	2920027	1	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2919884	2920027	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2920028	2920197	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2920198	2920269	1	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2920198	2920269	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2920270	2920358	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2920359	2920491	1	-	2	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2920359	2920491	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2920492	2920632	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2920633	2920770	1	-	2	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2920633	2920770	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2920771	2920997	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2920998	2921197	0.85	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2920998	2921197	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2921198	2921363	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2921364	2921386	0.92	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2921364	2921386	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2921387	2921515	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2921516	2921628	0.98	-	2	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2921516	2921628	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2921629	2921706	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2921707	2921734	1	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2921707	2921734	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2921735	2921818	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2921819	2921863	1	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2921819	2921863	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2921864	2921950	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2921951	2922089	1	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2921951	2922089	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2922090	2922189	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2922190	2922321	1	-	1	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2922190	2922321	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2922322	2922417	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2922418	2922542	1	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2922418	2922542	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2922543	2922626	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2922627	2922677	1	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2922627	2922677	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	intron	2922678	2922914	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	CDS	2922915	2923514	1	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	exon	2922915	2923514	.	-	.	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
Phchi.S4	AUGUSTUS	start_codon	2923512	2923514	.	-	0	transcript_id "Phchi.S4G049700.t1"; gene_id "Phchi.S4G049700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5713.t1 is derived from g2883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18487018	18492744	.	-	.	Phchi.S1G287200
Phchi.S1	AUGUSTUS	transcript	18487018	18492744	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	stop_codon	18487015	18487017	.	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18487018	18487219	1	-	1	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18487018	18487219	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18487220	18487297	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18487298	18487388	1	-	2	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18487298	18487388	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18487389	18488159	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18488160	18488175	0.99	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18488160	18488175	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18488176	18488257	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18488258	18488290	0.85	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18488258	18488290	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18488291	18488511	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18488512	18488582	1	-	2	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18488512	18488582	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18488583	18488665	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18488666	18488761	1	-	2	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18488666	18488761	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18488762	18488848	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18488849	18488939	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18488849	18488939	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18488940	18489045	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18489046	18489392	1	-	2	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18489046	18489392	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18489393	18489509	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18489510	18489648	0.62	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18489510	18489648	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18489649	18489934	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18489935	18490105	0.99	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18489935	18490105	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18490106	18490298	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18490299	18490441	1	-	2	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18490299	18490441	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18490442	18490563	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18490564	18490669	0.99	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18490564	18490669	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18490670	18490784	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18490785	18490902	1	-	1	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18490785	18490902	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18490903	18490997	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18490998	18491113	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18490998	18491113	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18491114	18491330	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18491331	18491459	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18491331	18491459	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18491460	18491649	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18491650	18491760	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18491650	18491760	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18491761	18491942	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18491943	18492077	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18491943	18492077	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18492078	18492162	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18492163	18492240	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18492163	18492240	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18492241	18492358	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18492359	18492451	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18492359	18492451	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	intron	18492452	18492672	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	CDS	18492673	18492744	1	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	exon	18492673	18492744	.	-	.	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
Phchi.S1	AUGUSTUS	start_codon	18492742	18492744	.	-	0	transcript_id "Phchi.S1G287200.t1"; gene_id "Phchi.S1G287200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9259.t1 is derived from g6434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40622758	40624311	.	+	.	Phchi.S1G641800
Phchi.S1	AUGUSTUS	transcript	40622758	40624311	.	+	.	transcript_id "Phchi.S1G641800.t1"; gene_id "Phchi.S1G641800"
Phchi.S1	AUGUSTUS	start_codon	40622758	40622760	.	+	0	transcript_id "Phchi.S1G641800.t1"; gene_id "Phchi.S1G641800"
Phchi.S1	AUGUSTUS	CDS	40622758	40624311	0.97	+	0	transcript_id "Phchi.S1G641800.t1"; gene_id "Phchi.S1G641800"
Phchi.S1	AUGUSTUS	exon	40622758	40624311	.	+	.	transcript_id "Phchi.S1G641800.t1"; gene_id "Phchi.S1G641800"
Phchi.S1	AUGUSTUS	stop_codon	40624312	40624314	.	+	0	transcript_id "Phchi.S1G641800.t1"; gene_id "Phchi.S1G641800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7066.t1 is derived from g4238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26703803	26704893	.	+	.	Phchi.S1G422500
Phchi.S1	AUGUSTUS	transcript	26703803	26704893	.	+	.	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	start_codon	26703803	26703805	.	+	0	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	CDS	26703803	26703965	1	+	0	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	exon	26703803	26703965	.	+	.	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	intron	26703966	26704060	.	+	.	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	CDS	26704061	26704893	0.99	+	2	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	exon	26704061	26704893	.	+	.	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
Phchi.S1	AUGUSTUS	stop_codon	26704894	26704896	.	+	0	transcript_id "Phchi.S1G422500.t1"; gene_id "Phchi.S1G422500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11174.t1 is derived from g15224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4492895	4494815	.	-	.	Phchi.S4G075600
Phchi.S4	AUGUSTUS	transcript	4492895	4494815	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	stop_codon	4492892	4492894	.	-	0	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4492895	4493304	0.91	-	2	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4492895	4493304	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493305	4493390	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4493391	4493628	1	-	0	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4493391	4493628	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493629	4493718	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4493719	4493925	1	-	0	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4493719	4493925	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493926	4494035	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4494036	4494815	0.6	-	0	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4494036	4494815	.	-	.	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	start_codon	4494813	4494815	.	-	0	transcript_id "Phchi.S4G075600.t1"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	transcript	4492895	4494815	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	stop_codon	4492892	4492894	.	-	0	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4492895	4493304	0.95	-	2	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4492895	4493304	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493305	4493390	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4493391	4493628	1	-	0	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4493391	4493628	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493629	4493718	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4493719	4493831	0.78	-	2	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4493719	4493831	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493832	4493916	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4493917	4493941	0.84	-	0	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4493917	4493941	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	intron	4493942	4494035	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	CDS	4494036	4494815	0.53	-	0	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	exon	4494036	4494815	.	-	.	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
Phchi.S4	AUGUSTUS	start_codon	4494813	4494815	.	-	0	transcript_id "Phchi.S4G075600.t2"; gene_id "Phchi.S4G075600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6719.t1 is derived from g3891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24704943	24708021	.	-	.	Phchi.S1G387800
Phchi.S1	AUGUSTUS	transcript	24704943	24708021	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	stop_codon	24704940	24704942	.	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24704943	24704955	0.64	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24704943	24704955	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24704956	24705120	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24705121	24705390	0.51	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24705121	24705390	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24705391	24705467	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24705468	24705499	0.6	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24705468	24705499	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24705500	24705625	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24705626	24705689	0.99	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24705626	24705689	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24705690	24705900	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24705901	24705934	0.84	-	2	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24705901	24705934	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24705935	24706086	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24706087	24706127	0.85	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24706087	24706127	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24706128	24706243	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24706244	24706405	0.85	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24706244	24706405	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24706406	24706537	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24706538	24706620	1	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24706538	24706620	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24706621	24706718	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24706719	24706790	1	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24706719	24706790	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24706791	24706885	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24706886	24706943	1	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24706886	24706943	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24706944	24707058	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24707059	24707219	1	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24707059	24707219	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24707220	24707358	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24707359	24707451	1	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24707359	24707451	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24707452	24707594	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24707595	24707619	1	-	1	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24707595	24707619	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	intron	24707620	24707866	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	CDS	24707867	24708021	0.66	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	exon	24707867	24708021	.	-	.	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
Phchi.S1	AUGUSTUS	start_codon	24708019	24708021	.	-	0	transcript_id "Phchi.S1G387800.t1"; gene_id "Phchi.S1G387800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4179.t1 is derived from g1348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8780826	8781518	.	+	.	Phchi.S1G133800
Phchi.S1	AUGUSTUS	transcript	8780826	8781518	.	+	.	transcript_id "Phchi.S1G133800.t1"; gene_id "Phchi.S1G133800"
Phchi.S1	AUGUSTUS	start_codon	8780826	8780828	.	+	0	transcript_id "Phchi.S1G133800.t1"; gene_id "Phchi.S1G133800"
Phchi.S1	AUGUSTUS	CDS	8780826	8781518	0.6	+	0	transcript_id "Phchi.S1G133800.t1"; gene_id "Phchi.S1G133800"
Phchi.S1	AUGUSTUS	exon	8780826	8781518	.	+	.	transcript_id "Phchi.S1G133800.t1"; gene_id "Phchi.S1G133800"
Phchi.S1	AUGUSTUS	stop_codon	8781519	8781521	.	+	0	transcript_id "Phchi.S1G133800.t1"; gene_id "Phchi.S1G133800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14301.t1 is derived from g12768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12002736	12005874	.	+	.	Phchi.S3G162000
Phchi.S3	AUGUSTUS	transcript	12002736	12005874	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	start_codon	12002736	12002738	.	+	0	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12002736	12003284	0.9	+	0	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12002736	12003284	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12003285	12003382	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12003383	12003416	0.98	+	0	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12003383	12003416	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12003417	12003769	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12003770	12003814	0.98	+	2	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12003770	12003814	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12003815	12004084	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12004085	12004283	1	+	2	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12004085	12004283	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12004284	12004351	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12004352	12004658	0.98	+	1	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12004352	12004658	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12004659	12004769	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12004770	12005081	1	+	0	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12004770	12005081	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12005082	12005205	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12005206	12005456	0.92	+	0	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12005206	12005456	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	intron	12005457	12005537	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	CDS	12005538	12005874	0.99	+	1	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	exon	12005538	12005874	.	+	.	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
Phchi.S3	AUGUSTUS	stop_codon	12005875	12005877	.	+	0	transcript_id "Phchi.S3G162000.t1"; gene_id "Phchi.S3G162000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3584.t1 is derived from g753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4609515	4611953	.	-	.	Phchi.S1G074300
Phchi.S1	AUGUSTUS	transcript	4609515	4611953	.	-	.	transcript_id "Phchi.S1G074300.t1"; gene_id "Phchi.S1G074300"
Phchi.S1	AUGUSTUS	stop_codon	4609512	4609514	.	-	0	transcript_id "Phchi.S1G074300.t1"; gene_id "Phchi.S1G074300"
Phchi.S1	AUGUSTUS	CDS	4609515	4611953	0.96	-	0	transcript_id "Phchi.S1G074300.t1"; gene_id "Phchi.S1G074300"
Phchi.S1	AUGUSTUS	exon	4609515	4611953	.	-	.	transcript_id "Phchi.S1G074300.t1"; gene_id "Phchi.S1G074300"
Phchi.S1	AUGUSTUS	start_codon	4611951	4611953	.	-	0	transcript_id "Phchi.S1G074300.t1"; gene_id "Phchi.S1G074300"
# This transcript jg7726.t2 is derived from g4900.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7727.t1 is derived from g4901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30840645	30842673	.	-	.	Phchi.S1G488600
Phchi.S1	AUGUSTUS	transcript	30840645	30842673	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	stop_codon	30840642	30840644	.	-	0	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	CDS	30840645	30840646	0.67	-	2	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	exon	30840645	30840646	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	intron	30840647	30840876	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	CDS	30840877	30841091	0.6	-	1	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	exon	30840877	30841091	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	intron	30841092	30841227	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	CDS	30841228	30841423	0.3	-	2	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	exon	30841228	30841423	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	intron	30841424	30841502	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	CDS	30841503	30841854	0.82	-	0	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	exon	30841503	30841854	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	intron	30841855	30841947	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	CDS	30841948	30842423	0.94	-	2	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	exon	30841948	30842423	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	intron	30842424	30842561	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	CDS	30842562	30842673	1	-	0	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	exon	30842562	30842673	.	-	.	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
Phchi.S1	AUGUSTUS	start_codon	30842671	30842673	.	-	0	transcript_id "Phchi.S1G488600.t1"; gene_id "Phchi.S1G488600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9184.t1 is derived from g6359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40245654	40245854	.	-	.	Phchi.S1G634300
Phchi.S1	AUGUSTUS	transcript	40245654	40245854	.	-	.	transcript_id "Phchi.S1G634300.t1"; gene_id "Phchi.S1G634300"
Phchi.S1	AUGUSTUS	stop_codon	40245651	40245653	.	-	0	transcript_id "Phchi.S1G634300.t1"; gene_id "Phchi.S1G634300"
Phchi.S1	AUGUSTUS	CDS	40245654	40245854	0.53	-	0	transcript_id "Phchi.S1G634300.t1"; gene_id "Phchi.S1G634300"
Phchi.S1	AUGUSTUS	exon	40245654	40245854	.	-	.	transcript_id "Phchi.S1G634300.t1"; gene_id "Phchi.S1G634300"
Phchi.S1	AUGUSTUS	start_codon	40245852	40245854	.	-	0	transcript_id "Phchi.S1G634300.t1"; gene_id "Phchi.S1G634300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3880.t1 is derived from g1049.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6192678	6195651	.	-	.	Phchi.S1G103900
Phchi.S1	AUGUSTUS	transcript	6192757	6195651	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	stop_codon	6192754	6192756	.	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6192757	6192836	1	-	2	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6192757	6192836	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6192837	6192907	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6192908	6192977	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6192908	6192977	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6192978	6193073	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193074	6193151	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193074	6193151	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193152	6193280	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193281	6193334	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193281	6193334	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193335	6193428	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193429	6193492	1	-	1	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193429	6193492	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193493	6193590	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193591	6193636	1	-	2	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193591	6193636	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193637	6193712	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193713	6193785	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193713	6193785	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193786	6193876	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193877	6193948	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193877	6193948	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193949	6194293	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194294	6194386	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194294	6194386	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6194387	6194574	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194575	6194627	1	-	2	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194575	6194627	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6194628	6194711	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194712	6194802	1	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194712	6194802	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6194803	6194921	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194922	6195019	0.68	-	2	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194922	6195019	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6195020	6195118	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6195119	6195202	0.87	-	2	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6195119	6195202	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6195203	6195535	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6195536	6195564	0.97	-	1	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6195536	6195564	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6195565	6195622	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6195623	6195651	0.98	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6195623	6195651	.	-	.	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	start_codon	6195649	6195651	.	-	0	transcript_id "Phchi.S1G103900.t1"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	transcript	6192678	6195651	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	stop_codon	6192675	6192677	.	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6192678	6192709	0.95	-	2	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6192678	6192709	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6192710	6192907	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6192908	6192977	0.95	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6192908	6192977	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6192978	6193073	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193074	6193151	1	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193074	6193151	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193152	6193280	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193281	6193334	1	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193281	6193334	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193335	6193428	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193429	6193492	1	-	1	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193429	6193492	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193493	6193590	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193591	6193636	1	-	2	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193591	6193636	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193637	6193712	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193713	6193785	1	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193713	6193785	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193786	6193876	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6193877	6193948	1	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6193877	6193948	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6193949	6194293	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194294	6194386	1	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194294	6194386	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6194387	6194574	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194575	6194627	1	-	2	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194575	6194627	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6194628	6194711	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194712	6194802	1	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194712	6194802	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6194803	6194921	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6194922	6195019	0.57	-	2	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6194922	6195019	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6195020	6195118	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6195119	6195202	0.81	-	2	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6195119	6195202	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6195203	6195535	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6195536	6195564	0.96	-	1	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6195536	6195564	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	intron	6195565	6195622	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	CDS	6195623	6195651	0.96	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	exon	6195623	6195651	.	-	.	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
Phchi.S1	AUGUSTUS	start_codon	6195649	6195651	.	-	0	transcript_id "Phchi.S1G103900.t2"; gene_id "Phchi.S1G103900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4117.t1 is derived from g1286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8258405	8259917	.	-	.	Phchi.S1G127600
Phchi.S1	AUGUSTUS	transcript	8258405	8259917	.	-	.	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	stop_codon	8258402	8258404	.	-	0	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	CDS	8258405	8259173	0.84	-	1	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	exon	8258405	8259173	.	-	.	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	intron	8259174	8259298	.	-	.	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	CDS	8259299	8259344	0.76	-	2	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	exon	8259299	8259344	.	-	.	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	intron	8259345	8259496	.	-	.	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	CDS	8259497	8259917	0.83	-	0	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	exon	8259497	8259917	.	-	.	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
Phchi.S1	AUGUSTUS	start_codon	8259915	8259917	.	-	0	transcript_id "Phchi.S1G127600.t1"; gene_id "Phchi.S1G127600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13728.t1 is derived from g12195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8571064	8573373	.	+	.	Phchi.S3G104700
Phchi.S3	AUGUSTUS	transcript	8571064	8573373	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	start_codon	8571064	8571066	.	+	0	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8571064	8571253	0.81	+	0	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8571064	8571253	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	intron	8571254	8571359	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8571360	8571946	0.31	+	2	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8571360	8571946	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	intron	8571947	8572043	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8572044	8572179	1	+	0	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8572044	8572179	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	intron	8572180	8572283	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8572284	8572483	0.99	+	2	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8572284	8572483	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	intron	8572484	8572575	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8572576	8572644	1	+	0	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8572576	8572644	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	intron	8572645	8572743	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8572744	8572802	1	+	0	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8572744	8572802	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	intron	8572803	8572904	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	CDS	8572905	8573373	0.71	+	1	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	exon	8572905	8573373	.	+	.	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
Phchi.S3	AUGUSTUS	stop_codon	8573374	8573376	.	+	0	transcript_id "Phchi.S3G104700.t1"; gene_id "Phchi.S3G104700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15662.t1 is derived from g14131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20554696	20557259	.	-	.	Phchi.S3G298100
Phchi.S3	AUGUSTUS	transcript	20554696	20557259	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	stop_codon	20554693	20554695	.	-	0	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20554696	20554824	0.97	-	0	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20554696	20554824	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20554825	20554961	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20554962	20555121	0.92	-	1	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20554962	20555121	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20555122	20555202	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20555203	20556004	0.97	-	2	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20555203	20556004	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20556005	20556203	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20556204	20556264	1	-	0	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20556204	20556264	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20556265	20556434	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20556435	20556507	0.75	-	1	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20556435	20556507	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20556508	20556620	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20556621	20556652	0.75	-	0	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20556621	20556652	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20556653	20556774	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20556775	20556884	1	-	2	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20556775	20556884	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	intron	20556885	20557009	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	CDS	20557010	20557259	1	-	0	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	exon	20557010	20557259	.	-	.	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
Phchi.S3	AUGUSTUS	start_codon	20557257	20557259	.	-	0	transcript_id "Phchi.S3G298100.t1"; gene_id "Phchi.S3G298100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6585.t1 is derived from g3757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23881853	23883432	.	-	.	Phchi.S1G374400
Phchi.S1	AUGUSTUS	transcript	23881853	23883432	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	stop_codon	23881850	23881852	.	-	0	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	CDS	23881853	23881965	1	-	2	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	exon	23881853	23881965	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	intron	23881966	23882057	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	CDS	23882058	23882169	1	-	0	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	exon	23882058	23882169	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	intron	23882170	23882266	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	CDS	23882267	23882342	1	-	1	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	exon	23882267	23882342	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	intron	23882343	23882423	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	CDS	23882424	23883270	1	-	2	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	exon	23882424	23883270	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	intron	23883271	23883338	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	CDS	23883339	23883432	0.88	-	0	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	exon	23883339	23883432	.	-	.	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
Phchi.S1	AUGUSTUS	start_codon	23883430	23883432	.	-	0	transcript_id "Phchi.S1G374400.t1"; gene_id "Phchi.S1G374400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9557.t1 is derived from g6733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42653508	42656670	.	+	.	Phchi.S1G671600
Phchi.S1	AUGUSTUS	transcript	42653508	42656670	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	start_codon	42653508	42653510	.	+	0	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	CDS	42653508	42653755	0.75	+	0	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	exon	42653508	42653755	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	intron	42653756	42653841	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	CDS	42653842	42654874	0.79	+	1	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	exon	42653842	42654874	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	intron	42654875	42654966	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	CDS	42654967	42655278	0.79	+	0	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	exon	42654967	42655278	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	intron	42655279	42655444	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	CDS	42655445	42655521	0.7	+	0	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	exon	42655445	42655521	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	intron	42655522	42655638	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	CDS	42655639	42656087	1	+	1	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	exon	42655639	42656087	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	intron	42656088	42656161	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	CDS	42656162	42656670	1	+	2	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	exon	42656162	42656670	.	+	.	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
Phchi.S1	AUGUSTUS	stop_codon	42656671	42656673	.	+	0	transcript_id "Phchi.S1G671600.t1"; gene_id "Phchi.S1G671600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14356.t1 is derived from g12823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12349329	12350875	.	+	.	Phchi.S3G167500
Phchi.S3	AUGUSTUS	transcript	12349329	12350875	.	+	.	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	start_codon	12349329	12349331	.	+	0	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	CDS	12349329	12350340	0.99	+	0	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	exon	12349329	12350340	.	+	.	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	intron	12350341	12350418	.	+	.	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	CDS	12350419	12350483	0.99	+	2	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	exon	12350419	12350483	.	+	.	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	intron	12350484	12350563	.	+	.	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	CDS	12350564	12350875	0.99	+	0	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	exon	12350564	12350875	.	+	.	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
Phchi.S3	AUGUSTUS	stop_codon	12350876	12350878	.	+	0	transcript_id "Phchi.S3G167500.t1"; gene_id "Phchi.S3G167500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4518.t1 is derived from g1688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10918138	10920328	.	+	.	Phchi.S1G167700
Phchi.S1	AUGUSTUS	transcript	10918138	10920328	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	start_codon	10918138	10918140	.	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10918138	10918185	1	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10918138	10918185	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10918186	10918488	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10918489	10918548	0.99	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10918489	10918548	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10918549	10918650	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10918651	10918690	1	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10918651	10918690	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10918691	10918805	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10918806	10918920	0.93	+	2	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10918806	10918920	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10918921	10919065	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10919066	10919135	1	+	1	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10919066	10919135	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10919136	10919226	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10919227	10919265	1	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10919227	10919265	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10919266	10919373	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10919374	10919460	1	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10919374	10919460	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10919461	10919546	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10919547	10919607	1	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10919547	10919607	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10919608	10919756	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10919757	10919881	1	+	2	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10919757	10919881	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10919882	10920032	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10920033	10920124	1	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10920033	10920124	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	intron	10920125	10920216	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	CDS	10920217	10920328	1	+	1	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	exon	10920217	10920328	.	+	.	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
Phchi.S1	AUGUSTUS	stop_codon	10920329	10920331	.	+	0	transcript_id "Phchi.S1G167700.t1"; gene_id "Phchi.S1G167700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7168.t1 is derived from g4340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27362496	27363325	.	-	.	Phchi.S1G432700
Phchi.S1	AUGUSTUS	transcript	27362496	27363325	.	-	.	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	stop_codon	27362493	27362495	.	-	0	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	CDS	27362496	27362744	1	-	0	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	exon	27362496	27362744	.	-	.	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	intron	27362745	27362830	.	-	.	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	CDS	27362831	27363007	1	-	0	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	exon	27362831	27363007	.	-	.	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	intron	27363008	27363100	.	-	.	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	CDS	27363101	27363325	0.93	-	0	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	exon	27363101	27363325	.	-	.	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
Phchi.S1	AUGUSTUS	start_codon	27363323	27363325	.	-	0	transcript_id "Phchi.S1G432700.t1"; gene_id "Phchi.S1G432700"
# This transcript jg4026.t2 is derived from g1195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4027.t1 is derived from g1196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7226375	7227793	.	+	.	Phchi.S1G118600
Phchi.S1	AUGUSTUS	transcript	7226375	7227793	.	+	.	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	start_codon	7226375	7226377	.	+	0	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	CDS	7226375	7226492	0.45	+	0	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	exon	7226375	7226492	.	+	.	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	intron	7226493	7226594	.	+	.	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	CDS	7226595	7227793	1	+	2	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	exon	7226595	7227793	.	+	.	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
Phchi.S1	AUGUSTUS	stop_codon	7227794	7227796	.	+	0	transcript_id "Phchi.S1G118600.t1"; gene_id "Phchi.S1G118600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1308.t1 is derived from g11091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8932069	8935094	.	-	.	Phchi.S6G126700
Phchi.S6	AUGUSTUS	transcript	8932069	8935094	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	stop_codon	8932066	8932068	.	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932069	8932209	0.97	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932069	8932209	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8932210	8932342	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932343	8932419	0.97	-	2	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932343	8932419	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8932420	8932519	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932520	8932882	1	-	2	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932520	8932882	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8932883	8932992	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932993	8933126	1	-	1	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932993	8933126	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8933127	8933262	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8933263	8933351	1	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8933263	8933351	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8933352	8933485	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8933486	8933661	1	-	2	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8933486	8933661	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8933662	8933760	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8933761	8934188	1	-	1	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8933761	8934188	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8934189	8934334	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8934335	8934420	1	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8934335	8934420	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8934421	8934505	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8934506	8934619	1	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8934506	8934619	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8934620	8934704	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8934705	8935094	1	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8934705	8935094	.	-	.	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	start_codon	8935092	8935094	.	-	0	transcript_id "Phchi.S6G126700.t1"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	transcript	8932353	8935094	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	stop_codon	8932350	8932352	.	-	0	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932353	8932435	0.62	-	2	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932353	8932435	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8932436	8932519	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932520	8932882	0.97	-	2	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932520	8932882	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8932883	8932992	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8932993	8933126	1	-	1	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8932993	8933126	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8933127	8933262	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8933263	8933351	1	-	0	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8933263	8933351	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8933352	8933485	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8933486	8933661	1	-	2	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8933486	8933661	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8933662	8933760	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8933761	8934188	1	-	1	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8933761	8934188	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8934189	8934334	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8934335	8934420	1	-	0	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8934335	8934420	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8934421	8934505	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8934506	8934619	1	-	0	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8934506	8934619	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	intron	8934620	8934704	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	CDS	8934705	8935094	1	-	0	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	exon	8934705	8935094	.	-	.	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
Phchi.S6	AUGUSTUS	start_codon	8935092	8935094	.	-	0	transcript_id "Phchi.S6G126700.t2"; gene_id "Phchi.S6G126700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10181.t1 is derived from g7357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46178979	46180797	.	+	.	Phchi.S1G734000
Phchi.S1	AUGUSTUS	transcript	46178979	46180797	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	start_codon	46178979	46178981	.	+	0	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46178979	46179227	1	+	0	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46178979	46179227	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	intron	46179228	46179314	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46179315	46179471	1	+	0	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46179315	46179471	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	intron	46179472	46179630	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46179631	46179762	1	+	2	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46179631	46179762	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	intron	46179763	46179956	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46179957	46180105	1	+	2	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46179957	46180105	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	intron	46180106	46180232	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46180233	46180361	1	+	0	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46180233	46180361	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	intron	46180362	46180452	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46180453	46180520	1	+	0	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46180453	46180520	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	intron	46180521	46180601	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	CDS	46180602	46180797	1	+	1	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	exon	46180602	46180797	.	+	.	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
Phchi.S1	AUGUSTUS	stop_codon	46180798	46180800	.	+	0	transcript_id "Phchi.S1G734000.t1"; gene_id "Phchi.S1G734000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11951.t1 is derived from g7626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	174909	176490	.	+	.	Phchi.S2G003100
Phchi.S2	AUGUSTUS	transcript	174909	176490	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	start_codon	174909	174911	.	+	0	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	CDS	174909	175359	0.91	+	0	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	exon	174909	175359	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	intron	175360	175673	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	CDS	175674	175773	1	+	2	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	exon	175674	175773	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	intron	175774	175922	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	CDS	175923	176085	1	+	1	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	exon	175923	176085	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	intron	176086	176180	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	CDS	176181	176276	1	+	0	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	exon	176181	176276	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	intron	176277	176370	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	CDS	176371	176490	1	+	0	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	exon	176371	176490	.	+	.	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
Phchi.S2	AUGUSTUS	stop_codon	176491	176493	.	+	0	transcript_id "Phchi.S2G003100.t1"; gene_id "Phchi.S2G003100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5631.t1 is derived from g2801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17966356	17970122	.	-	.	Phchi.S1G279000
Phchi.S1	AUGUSTUS	transcript	17966356	17970122	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	stop_codon	17966353	17966355	.	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17966356	17966736	1	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17966356	17966736	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17966737	17966907	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17966908	17967010	1	-	1	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17966908	17967010	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17967011	17967186	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17967187	17967237	0.65	-	1	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17967187	17967237	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17967238	17967363	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17967364	17967446	0.65	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17967364	17967446	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17967447	17967577	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17967578	17967670	0.84	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17967578	17967670	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17967671	17967781	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17967782	17967835	1	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17967782	17967835	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17967836	17968037	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17968038	17968131	0.84	-	1	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17968038	17968131	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17968132	17968239	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17968240	17968319	0.84	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17968240	17968319	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17968320	17968516	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17968517	17968625	1	-	1	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17968517	17968625	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17968626	17968784	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17968785	17968885	1	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17968785	17968885	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17968886	17969061	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17969062	17969181	1	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17969062	17969181	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17969182	17969285	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17969286	17969378	1	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17969286	17969378	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17969379	17969529	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17969530	17969559	1	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17969530	17969559	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	intron	17969560	17970023	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	CDS	17970024	17970122	0.97	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	exon	17970024	17970122	.	-	.	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
Phchi.S1	AUGUSTUS	start_codon	17970120	17970122	.	-	0	transcript_id "Phchi.S1G279000.t1"; gene_id "Phchi.S1G279000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6202.t1 is derived from g3373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21456538	21460886	.	+	.	Phchi.S1G336100
Phchi.S1	AUGUSTUS	transcript	21456538	21460886	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	start_codon	21456538	21456540	.	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21456538	21456645	0.98	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21456538	21456645	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21456646	21456774	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21456775	21456922	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21456775	21456922	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21456923	21457089	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21457090	21457796	1	+	2	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21457090	21457796	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21457797	21458167	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458168	21458374	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458168	21458374	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21458375	21458514	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458515	21458589	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458515	21458589	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21458590	21458672	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458673	21458800	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458673	21458800	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21458801	21458899	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458900	21459006	1	+	1	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458900	21459006	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459007	21459184	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459185	21459244	1	+	2	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459185	21459244	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459245	21459346	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459347	21459420	1	+	2	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459347	21459420	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459421	21459514	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459515	21459565	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459515	21459565	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459566	21459661	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459662	21459711	0.91	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459662	21459711	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459712	21459831	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459832	21459934	0.91	+	1	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459832	21459934	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459935	21460047	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460048	21460137	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460048	21460137	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460138	21460222	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460223	21460285	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460223	21460285	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460286	21460363	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460364	21460459	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460364	21460459	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460460	21460581	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460582	21460709	1	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460582	21460709	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460710	21460879	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460880	21460886	1	+	1	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460880	21460886	.	+	.	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	stop_codon	21460887	21460889	.	+	0	transcript_id "Phchi.S1G336100.t1"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	transcript	21456538	21460886	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	start_codon	21456538	21456540	.	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21456538	21456645	0.96	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21456538	21456645	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21456646	21456774	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21456775	21456922	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21456775	21456922	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21456923	21457077	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21457078	21457796	1	+	2	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21457078	21457796	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21457797	21458167	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458168	21458374	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458168	21458374	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21458375	21458514	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458515	21458589	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458515	21458589	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21458590	21458672	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458673	21458800	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458673	21458800	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21458801	21458899	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21458900	21459006	1	+	1	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21458900	21459006	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459007	21459184	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459185	21459244	1	+	2	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459185	21459244	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459245	21459346	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459347	21459420	1	+	2	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459347	21459420	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459421	21459514	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459515	21459565	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459515	21459565	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459566	21459661	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459662	21459711	0.86	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459662	21459711	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459712	21459831	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21459832	21459934	0.86	+	1	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21459832	21459934	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21459935	21460047	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460048	21460137	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460048	21460137	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460138	21460222	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460223	21460285	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460223	21460285	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460286	21460363	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460364	21460459	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460364	21460459	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460460	21460581	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460582	21460709	1	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460582	21460709	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	intron	21460710	21460879	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	CDS	21460880	21460886	1	+	1	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	exon	21460880	21460886	.	+	.	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
Phchi.S1	AUGUSTUS	stop_codon	21460887	21460889	.	+	0	transcript_id "Phchi.S1G336100.t2"; gene_id "Phchi.S1G336100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14677.t1 is derived from g13145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14134403	14134807	.	-	.	Phchi.S3G199600
Phchi.S3	AUGUSTUS	transcript	14134403	14134807	.	-	.	transcript_id "Phchi.S3G199600.t1"; gene_id "Phchi.S3G199600"
Phchi.S3	AUGUSTUS	stop_codon	14134400	14134402	.	-	0	transcript_id "Phchi.S3G199600.t1"; gene_id "Phchi.S3G199600"
Phchi.S3	AUGUSTUS	CDS	14134403	14134807	0.56	-	0	transcript_id "Phchi.S3G199600.t1"; gene_id "Phchi.S3G199600"
Phchi.S3	AUGUSTUS	exon	14134403	14134807	.	-	.	transcript_id "Phchi.S3G199600.t1"; gene_id "Phchi.S3G199600"
Phchi.S3	AUGUSTUS	start_codon	14134805	14134807	.	-	0	transcript_id "Phchi.S3G199600.t1"; gene_id "Phchi.S3G199600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1108.t1 is derived from g10891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7658883	7660276	.	+	.	Phchi.S6G106700
Phchi.S6	AUGUSTUS	transcript	7658883	7660276	.	+	.	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	start_codon	7658883	7658885	.	+	0	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	CDS	7658883	7659011	0.4	+	0	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	exon	7658883	7659011	.	+	.	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	intron	7659012	7659105	.	+	.	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	CDS	7659106	7659492	0.83	+	0	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	exon	7659106	7659492	.	+	.	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	intron	7659493	7659700	.	+	.	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	CDS	7659701	7660276	0.71	+	0	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	exon	7659701	7660276	.	+	.	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
Phchi.S6	AUGUSTUS	stop_codon	7660277	7660279	.	+	0	transcript_id "Phchi.S6G106700.t1"; gene_id "Phchi.S6G106700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3811.t1 is derived from g980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5831862	5832902	.	-	.	Phchi.S1G097000
Phchi.S1	AUGUSTUS	transcript	5831862	5832902	.	-	.	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	stop_codon	5831859	5831861	.	-	0	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	CDS	5831862	5832365	1	-	0	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	exon	5831862	5832365	.	-	.	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	intron	5832366	5832476	.	-	.	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	CDS	5832477	5832902	0.98	-	0	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	exon	5832477	5832902	.	-	.	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
Phchi.S1	AUGUSTUS	start_codon	5832900	5832902	.	-	0	transcript_id "Phchi.S1G097000.t1"; gene_id "Phchi.S1G097000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6930.t1 is derived from g4102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26034758	26035072	.	+	.	Phchi.S1G408900
Phchi.S1	AUGUSTUS	transcript	26034758	26035072	.	+	.	transcript_id "Phchi.S1G408900.t1"; gene_id "Phchi.S1G408900"
Phchi.S1	AUGUSTUS	start_codon	26034758	26034760	.	+	0	transcript_id "Phchi.S1G408900.t1"; gene_id "Phchi.S1G408900"
Phchi.S1	AUGUSTUS	CDS	26034758	26035072	0.76	+	0	transcript_id "Phchi.S1G408900.t1"; gene_id "Phchi.S1G408900"
Phchi.S1	AUGUSTUS	exon	26034758	26035072	.	+	.	transcript_id "Phchi.S1G408900.t1"; gene_id "Phchi.S1G408900"
Phchi.S1	AUGUSTUS	stop_codon	26035073	26035075	.	+	0	transcript_id "Phchi.S1G408900.t1"; gene_id "Phchi.S1G408900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6434.t1 is derived from g3606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23025976	23026260	.	+	.	Phchi.S1G359300
Phchi.S1	AUGUSTUS	transcript	23025976	23026260	.	+	.	transcript_id "Phchi.S1G359300.t1"; gene_id "Phchi.S1G359300"
Phchi.S1	AUGUSTUS	start_codon	23025976	23025978	.	+	0	transcript_id "Phchi.S1G359300.t1"; gene_id "Phchi.S1G359300"
Phchi.S1	AUGUSTUS	CDS	23025976	23026260	0.79	+	0	transcript_id "Phchi.S1G359300.t1"; gene_id "Phchi.S1G359300"
Phchi.S1	AUGUSTUS	exon	23025976	23026260	.	+	.	transcript_id "Phchi.S1G359300.t1"; gene_id "Phchi.S1G359300"
Phchi.S1	AUGUSTUS	stop_codon	23026261	23026263	.	+	0	transcript_id "Phchi.S1G359300.t1"; gene_id "Phchi.S1G359300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9391.t1 is derived from g6567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41309760	41310182	.	+	.	Phchi.S1G655000
Phchi.S1	AUGUSTUS	transcript	41309760	41310182	.	+	.	transcript_id "Phchi.S1G655000.t1"; gene_id "Phchi.S1G655000"
Phchi.S1	AUGUSTUS	start_codon	41309760	41309762	.	+	0	transcript_id "Phchi.S1G655000.t1"; gene_id "Phchi.S1G655000"
Phchi.S1	AUGUSTUS	CDS	41309760	41310182	1	+	0	transcript_id "Phchi.S1G655000.t1"; gene_id "Phchi.S1G655000"
Phchi.S1	AUGUSTUS	exon	41309760	41310182	.	+	.	transcript_id "Phchi.S1G655000.t1"; gene_id "Phchi.S1G655000"
Phchi.S1	AUGUSTUS	stop_codon	41310183	41310185	.	+	0	transcript_id "Phchi.S1G655000.t1"; gene_id "Phchi.S1G655000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4260.t1 is derived from g1429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9211368	9211913	.	+	.	Phchi.S1G141900
Phchi.S1	AUGUSTUS	transcript	9211368	9211913	.	+	.	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	start_codon	9211368	9211370	.	+	0	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	CDS	9211368	9211479	0.71	+	0	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	exon	9211368	9211479	.	+	.	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	intron	9211480	9211564	.	+	.	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	CDS	9211565	9211622	1	+	2	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	exon	9211565	9211622	.	+	.	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	intron	9211623	9211759	.	+	.	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	CDS	9211760	9211913	0.99	+	1	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	exon	9211760	9211913	.	+	.	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
Phchi.S1	AUGUSTUS	stop_codon	9211914	9211916	.	+	0	transcript_id "Phchi.S1G141900.t1"; gene_id "Phchi.S1G141900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1648.t1 is derived from g8567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2207702	2210317	.	+	.	Phchi.S5G025700
Phchi.S5	AUGUSTUS	transcript	2207702	2210317	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	start_codon	2207702	2207704	.	+	0	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	CDS	2207702	2208837	0.99	+	0	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	exon	2207702	2208837	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	intron	2208838	2208967	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	CDS	2208968	2209061	0.79	+	1	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	exon	2208968	2209061	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	intron	2209062	2209168	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	CDS	2209169	2209893	0.57	+	0	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	exon	2209169	2209893	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	intron	2209894	2209983	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	CDS	2209984	2210080	0.57	+	1	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	exon	2209984	2210080	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	intron	2210081	2210164	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	CDS	2210165	2210317	0.93	+	0	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	exon	2210165	2210317	.	+	.	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
Phchi.S5	AUGUSTUS	stop_codon	2210318	2210320	.	+	0	transcript_id "Phchi.S5G025700.t1"; gene_id "Phchi.S5G025700"
# This transcript jg15575.t2 is derived from g14044.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15576.t1 is derived from g14045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20096039	20097583	.	+	.	Phchi.S3G289500
Phchi.S3	AUGUSTUS	transcript	20096039	20097583	.	+	.	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	start_codon	20096039	20096041	.	+	0	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	CDS	20096039	20096375	0.62	+	0	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	exon	20096039	20096375	.	+	.	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	intron	20096376	20096651	.	+	.	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	CDS	20096652	20097583	0.78	+	2	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	exon	20096652	20097583	.	+	.	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
Phchi.S3	AUGUSTUS	stop_codon	20097584	20097586	.	+	0	transcript_id "Phchi.S3G289500.t1"; gene_id "Phchi.S3G289500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4319.t1 is derived from g1488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9603802	9605277	.	+	.	Phchi.S1G147800
Phchi.S1	AUGUSTUS	transcript	9603802	9605277	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	start_codon	9603802	9603804	.	+	0	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	CDS	9603802	9604098	0.91	+	0	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	exon	9603802	9604098	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	intron	9604099	9604689	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	CDS	9604690	9604859	0.99	+	0	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	exon	9604690	9604859	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	intron	9604860	9605034	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	CDS	9605035	9605065	0.71	+	1	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	exon	9605035	9605065	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	intron	9605066	9605151	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	CDS	9605152	9605277	0.99	+	0	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	exon	9605152	9605277	.	+	.	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
Phchi.S1	AUGUSTUS	stop_codon	9605278	9605280	.	+	0	transcript_id "Phchi.S1G147800.t1"; gene_id "Phchi.S1G147800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13062.t1 is derived from g11527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3964420	3965549	.	+	.	Phchi.S3G038100
Phchi.S3	AUGUSTUS	transcript	3964420	3965549	.	+	.	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	start_codon	3964420	3964422	.	+	0	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	CDS	3964420	3964747	0.83	+	0	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	exon	3964420	3964747	.	+	.	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	intron	3964748	3964887	.	+	.	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	CDS	3964888	3965178	0.79	+	2	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	exon	3964888	3965178	.	+	.	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	intron	3965179	3965277	.	+	.	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	CDS	3965278	3965549	0.8	+	2	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	exon	3965278	3965549	.	+	.	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
Phchi.S3	AUGUSTUS	stop_codon	3965550	3965552	.	+	0	transcript_id "Phchi.S3G038100.t1"; gene_id "Phchi.S3G038100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14610.t1 is derived from g13078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13741568	13745572	.	-	.	Phchi.S3G192900
Phchi.S3	AUGUSTUS	transcript	13741568	13745572	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	stop_codon	13741565	13741567	.	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	CDS	13741568	13741828	1	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	exon	13741568	13741828	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	intron	13741829	13741916	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	CDS	13741917	13741997	1	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	exon	13741917	13741997	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	intron	13741998	13742079	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	CDS	13742080	13742226	1	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	exon	13742080	13742226	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	intron	13742227	13742370	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	CDS	13742371	13743344	0.67	-	2	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	exon	13742371	13743344	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	intron	13743345	13743752	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	CDS	13743753	13745109	0.69	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	exon	13743753	13745109	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	intron	13745110	13745329	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	CDS	13745330	13745572	0.88	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	exon	13745330	13745572	.	-	.	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
Phchi.S3	AUGUSTUS	start_codon	13745570	13745572	.	-	0	transcript_id "Phchi.S3G192900.t1"; gene_id "Phchi.S3G192900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7417.t1 is derived from g4589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29042018	29042734	.	+	.	Phchi.S1G457600
Phchi.S1	AUGUSTUS	transcript	29042018	29042734	.	+	.	transcript_id "Phchi.S1G457600.t1"; gene_id "Phchi.S1G457600"
Phchi.S1	AUGUSTUS	start_codon	29042018	29042020	.	+	0	transcript_id "Phchi.S1G457600.t1"; gene_id "Phchi.S1G457600"
Phchi.S1	AUGUSTUS	CDS	29042018	29042734	0.65	+	0	transcript_id "Phchi.S1G457600.t1"; gene_id "Phchi.S1G457600"
Phchi.S1	AUGUSTUS	exon	29042018	29042734	.	+	.	transcript_id "Phchi.S1G457600.t1"; gene_id "Phchi.S1G457600"
Phchi.S1	AUGUSTUS	stop_codon	29042735	29042737	.	+	0	transcript_id "Phchi.S1G457600.t1"; gene_id "Phchi.S1G457600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5300.t1 is derived from g2470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16093041	16094921	.	-	.	Phchi.S1G245900
Phchi.S1	AUGUSTUS	transcript	16093041	16094921	.	-	.	transcript_id "Phchi.S1G245900.t1"; gene_id "Phchi.S1G245900"
Phchi.S1	AUGUSTUS	stop_codon	16093038	16093040	.	-	0	transcript_id "Phchi.S1G245900.t1"; gene_id "Phchi.S1G245900"
Phchi.S1	AUGUSTUS	CDS	16093041	16094921	0.87	-	0	transcript_id "Phchi.S1G245900.t1"; gene_id "Phchi.S1G245900"
Phchi.S1	AUGUSTUS	exon	16093041	16094921	.	-	.	transcript_id "Phchi.S1G245900.t1"; gene_id "Phchi.S1G245900"
Phchi.S1	AUGUSTUS	start_codon	16094919	16094921	.	-	0	transcript_id "Phchi.S1G245900.t1"; gene_id "Phchi.S1G245900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9048.t1 is derived from g6223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39390960	39391828	.	-	.	Phchi.S1G620700
Phchi.S1	AUGUSTUS	transcript	39390960	39391828	.	-	.	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	stop_codon	39390957	39390959	.	-	0	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	CDS	39390960	39391153	1	-	2	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	exon	39390960	39391153	.	-	.	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	intron	39391154	39391353	.	-	.	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	CDS	39391354	39391581	1	-	2	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	exon	39391354	39391581	.	-	.	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	intron	39391582	39391716	.	-	.	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	CDS	39391717	39391828	0.81	-	0	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	exon	39391717	39391828	.	-	.	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
Phchi.S1	AUGUSTUS	start_codon	39391826	39391828	.	-	0	transcript_id "Phchi.S1G620700.t1"; gene_id "Phchi.S1G620700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10846.t1 is derived from g14896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2454801	2456048	.	+	.	Phchi.S4G042800
Phchi.S4	AUGUSTUS	transcript	2454801	2456048	.	+	.	transcript_id "Phchi.S4G042800.t1"; gene_id "Phchi.S4G042800"
Phchi.S4	AUGUSTUS	start_codon	2454801	2454803	.	+	0	transcript_id "Phchi.S4G042800.t1"; gene_id "Phchi.S4G042800"
Phchi.S4	AUGUSTUS	CDS	2454801	2456048	1	+	0	transcript_id "Phchi.S4G042800.t1"; gene_id "Phchi.S4G042800"
Phchi.S4	AUGUSTUS	exon	2454801	2456048	.	+	.	transcript_id "Phchi.S4G042800.t1"; gene_id "Phchi.S4G042800"
Phchi.S4	AUGUSTUS	stop_codon	2456049	2456051	.	+	0	transcript_id "Phchi.S4G042800.t1"; gene_id "Phchi.S4G042800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14362.t1 is derived from g12829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12364561	12365572	.	+	.	Phchi.S3G168100
Phchi.S3	AUGUSTUS	transcript	12364561	12365572	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	start_codon	12364561	12364563	.	+	0	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	CDS	12364561	12364648	1	+	0	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	exon	12364561	12364648	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	intron	12364649	12364724	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	CDS	12364725	12364820	1	+	2	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	exon	12364725	12364820	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	intron	12364821	12364919	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	CDS	12364920	12365047	1	+	2	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	exon	12364920	12365047	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	intron	12365048	12365155	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	CDS	12365156	12365237	1	+	0	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	exon	12365156	12365237	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	intron	12365238	12365313	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	CDS	12365314	12365403	1	+	2	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	exon	12365314	12365403	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	intron	12365404	12365495	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	CDS	12365496	12365572	1	+	2	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	exon	12365496	12365572	.	+	.	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
Phchi.S3	AUGUSTUS	stop_codon	12365573	12365575	.	+	0	transcript_id "Phchi.S3G168100.t1"; gene_id "Phchi.S3G168100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8978.t1 is derived from g6153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38941793	38942627	.	-	.	Phchi.S1G613700
Phchi.S1	AUGUSTUS	transcript	38941793	38942627	.	-	.	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	stop_codon	38941790	38941792	.	-	0	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	CDS	38941793	38942185	1	-	0	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	exon	38941793	38942185	.	-	.	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	intron	38942186	38942276	.	-	.	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	CDS	38942277	38942488	1	-	2	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	exon	38942277	38942488	.	-	.	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	intron	38942489	38942557	.	-	.	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	CDS	38942558	38942627	1	-	0	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	exon	38942558	38942627	.	-	.	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
Phchi.S1	AUGUSTUS	start_codon	38942625	38942627	.	-	0	transcript_id "Phchi.S1G613700.t1"; gene_id "Phchi.S1G613700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6345.t1 is derived from g3517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22425217	22426019	.	+	.	Phchi.S1G350400
Phchi.S1	AUGUSTUS	transcript	22425217	22426019	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	start_codon	22425217	22425219	.	+	0	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	CDS	22425217	22425421	0.95	+	0	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	exon	22425217	22425421	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	intron	22425422	22425519	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	CDS	22425520	22425638	1	+	2	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	exon	22425520	22425638	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	intron	22425639	22425737	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	CDS	22425738	22425856	1	+	0	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	exon	22425738	22425856	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	intron	22425857	22425931	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	CDS	22425932	22426019	1	+	1	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	exon	22425932	22426019	.	+	.	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
Phchi.S1	AUGUSTUS	stop_codon	22426020	22426022	.	+	0	transcript_id "Phchi.S1G350400.t1"; gene_id "Phchi.S1G350400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11040.t1 is derived from g15090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3786413	3788517	.	+	.	Phchi.S4G062200
Phchi.S4	AUGUSTUS	transcript	3786413	3788517	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	start_codon	3786413	3786415	.	+	0	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	CDS	3786413	3787549	0.69	+	0	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	exon	3786413	3787549	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	intron	3787550	3787645	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	CDS	3787646	3787874	1	+	0	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	exon	3787646	3787874	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	intron	3787875	3787970	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	CDS	3787971	3788110	0.94	+	2	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	exon	3787971	3788110	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	intron	3788111	3788354	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	CDS	3788355	3788376	0.94	+	0	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	exon	3788355	3788376	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	intron	3788377	3788470	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	CDS	3788471	3788517	0.92	+	2	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	exon	3788471	3788517	.	+	.	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
Phchi.S4	AUGUSTUS	stop_codon	3788518	3788520	.	+	0	transcript_id "Phchi.S4G062200.t1"; gene_id "Phchi.S4G062200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5585.t1 is derived from g2755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17746408	17753000	.	+	.	Phchi.S1G274400
Phchi.S1	AUGUSTUS	transcript	17746408	17753000	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	start_codon	17746408	17746410	.	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17746408	17746684	0.83	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17746408	17746684	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17746685	17746818	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17746819	17746911	0.62	+	2	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17746819	17746911	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17746912	17747149	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17747150	17747222	0.58	+	2	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17747150	17747222	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17747223	17747385	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17747386	17747499	0.66	+	1	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17747386	17747499	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17747500	17747717	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17747718	17748127	0.4	+	1	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17747718	17748127	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17748128	17748230	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17748231	17748964	0.33	+	2	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17748231	17748964	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17748965	17749121	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17749122	17749214	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17749122	17749214	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17749215	17749390	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17749391	17749462	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17749391	17749462	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17749463	17749545	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17749546	17749596	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17749546	17749596	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17749597	17749779	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17749780	17749950	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17749780	17749950	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17749951	17750072	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17750073	17750183	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17750073	17750183	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17750184	17750388	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17750389	17750498	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17750389	17750498	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17750499	17750650	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17750651	17750808	1	+	1	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17750651	17750808	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17750809	17750971	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17750972	17751069	1	+	2	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17750972	17751069	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17751070	17751158	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17751159	17751212	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17751159	17751212	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17751213	17751336	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17751337	17751393	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17751337	17751393	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17751394	17751471	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17751472	17751723	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17751472	17751723	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17751724	17751796	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17751797	17751940	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17751797	17751940	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17751941	17752034	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17752035	17752186	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17752035	17752186	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17752187	17752283	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17752284	17752392	1	+	1	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17752284	17752392	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17752393	17752511	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17752512	17752595	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17752512	17752595	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17752596	17752686	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17752687	17752830	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17752687	17752830	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	intron	17752831	17752955	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	CDS	17752956	17753000	1	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	exon	17752956	17753000	.	+	.	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
Phchi.S1	AUGUSTUS	stop_codon	17753001	17753003	.	+	0	transcript_id "Phchi.S1G274400.t1"; gene_id "Phchi.S1G274400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11425.t1 is derived from g15475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6276866	6277161	.	+	.	Phchi.S4G100700
Phchi.S4	AUGUSTUS	transcript	6276866	6277161	.	+	.	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	start_codon	6276866	6276868	.	+	0	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	CDS	6276866	6277001	0.69	+	0	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	exon	6276866	6277001	.	+	.	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	intron	6277002	6277096	.	+	.	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	CDS	6277097	6277161	0.88	+	2	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	exon	6277097	6277161	.	+	.	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
Phchi.S4	AUGUSTUS	stop_codon	6277162	6277164	.	+	0	transcript_id "Phchi.S4G100700.t1"; gene_id "Phchi.S4G100700"
# This transcript jg14204.t2 is derived from g12671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14205.t1 is derived from g12672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11498719	11500442	.	-	.	Phchi.S3G152400
Phchi.S3	AUGUSTUS	transcript	11498719	11500277	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	stop_codon	11498716	11498718	.	-	0	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11498719	11498941	1	-	1	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11498719	11498941	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11498942	11499039	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499040	11499134	1	-	0	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499040	11499134	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499135	11499289	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499290	11499370	1	-	0	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499290	11499370	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499371	11499465	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499466	11499750	1	-	0	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499466	11499750	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499751	11499885	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499886	11499980	1	-	2	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499886	11499980	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499981	11500183	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11500184	11500277	0.25	-	0	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11500184	11500277	.	-	.	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	start_codon	11500275	11500277	.	-	0	transcript_id "Phchi.S3G152400.t1"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	transcript	11498719	11500442	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	stop_codon	11498716	11498718	.	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11498719	11498941	1	-	1	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11498719	11498941	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11498942	11499039	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499040	11499134	1	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499040	11499134	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499135	11499289	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499290	11499370	1	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499290	11499370	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499371	11499465	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499466	11499750	1	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499466	11499750	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499751	11499885	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11499886	11499980	0.92	-	2	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11499886	11499980	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11499981	11500077	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11500078	11500096	0.48	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11500078	11500096	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11500097	11500183	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11500184	11500242	0.89	-	2	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11500184	11500242	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	intron	11500243	11500336	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	CDS	11500337	11500442	0.23	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	exon	11500337	11500442	.	-	.	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
Phchi.S3	AUGUSTUS	start_codon	11500440	11500442	.	-	0	transcript_id "Phchi.S3G152400.t2"; gene_id "Phchi.S3G152400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14708.t1 is derived from g13176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14321869	14323254	.	+	.	Phchi.S3G202700
Phchi.S3	AUGUSTUS	transcript	14321869	14323254	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	start_codon	14321869	14321871	.	+	0	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	CDS	14321869	14321944	1	+	0	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	exon	14321869	14321944	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	intron	14321945	14322021	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	CDS	14322022	14322714	1	+	2	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	exon	14322022	14322714	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	intron	14322715	14322864	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	CDS	14322865	14322968	1	+	2	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	exon	14322865	14322968	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	intron	14322969	14323224	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	CDS	14323225	14323254	1	+	0	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	exon	14323225	14323254	.	+	.	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
Phchi.S3	AUGUSTUS	stop_codon	14323255	14323257	.	+	0	transcript_id "Phchi.S3G202700.t1"; gene_id "Phchi.S3G202700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3843.t1 is derived from g1012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5989781	5991817	.	-	.	Phchi.S1G100200
Phchi.S1	AUGUSTUS	transcript	5989781	5991817	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	stop_codon	5989778	5989780	.	-	0	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	CDS	5989781	5989816	1	-	0	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	exon	5989781	5989816	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	intron	5989817	5989901	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	CDS	5989902	5990716	0.59	-	2	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	exon	5989902	5990716	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	intron	5990717	5991439	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	CDS	5991440	5991479	0.99	-	0	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	exon	5991440	5991479	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	intron	5991480	5991736	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	CDS	5991737	5991817	0.83	-	0	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	exon	5991737	5991817	.	-	.	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
Phchi.S1	AUGUSTUS	start_codon	5991815	5991817	.	-	0	transcript_id "Phchi.S1G100200.t1"; gene_id "Phchi.S1G100200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7361.t1 is derived from g4533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28768489	28770151	.	-	.	Phchi.S1G452000
Phchi.S1	AUGUSTUS	transcript	28768489	28770151	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	stop_codon	28768486	28768488	.	-	0	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28768489	28768752	0.97	-	0	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28768489	28768752	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	intron	28768753	28768891	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28768892	28769106	0.99	-	2	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28768892	28769106	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	intron	28769107	28769222	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28769223	28769357	1	-	2	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28769223	28769357	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	intron	28769358	28769444	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28769445	28769517	0.99	-	0	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28769445	28769517	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	intron	28769518	28769621	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28769622	28769651	0.65	-	0	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28769622	28769651	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	intron	28769652	28769764	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28769765	28769909	0.97	-	1	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28769765	28769909	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	intron	28769910	28770047	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	CDS	28770048	28770151	0.98	-	0	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	exon	28770048	28770151	.	-	.	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
Phchi.S1	AUGUSTUS	start_codon	28770149	28770151	.	-	0	transcript_id "Phchi.S1G452000.t1"; gene_id "Phchi.S1G452000"
# This transcript jg1548.t2 is derived from g8467.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1549.t1 is derived from g8468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1704955	1707210	.	-	.	Phchi.S5G015800
Phchi.S5	AUGUSTUS	transcript	1704955	1707210	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	stop_codon	1704952	1704954	.	-	0	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1704955	1705104	1	-	0	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1704955	1705104	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	intron	1705105	1705179	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1705180	1705554	1	-	0	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1705180	1705554	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	intron	1705555	1705854	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1705855	1706000	1	-	2	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1705855	1706000	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	intron	1706001	1706150	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1706151	1706203	1	-	1	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1706151	1706203	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	intron	1706204	1706302	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1706303	1706474	0.92	-	2	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1706303	1706474	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	intron	1706475	1706689	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1706690	1706828	1	-	0	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1706690	1706828	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	intron	1706829	1706973	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	CDS	1706974	1707210	0.68	-	0	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	exon	1706974	1707210	.	-	.	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
Phchi.S5	AUGUSTUS	start_codon	1707208	1707210	.	-	0	transcript_id "Phchi.S5G015800.t1"; gene_id "Phchi.S5G015800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6188.t1 is derived from g3359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21379608	21380258	.	+	.	Phchi.S1G334700
Phchi.S1	AUGUSTUS	transcript	21379608	21380258	.	+	.	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	start_codon	21379608	21379610	.	+	0	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	CDS	21379608	21379736	1	+	0	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	exon	21379608	21379736	.	+	.	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	intron	21379737	21379974	.	+	.	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	CDS	21379975	21380104	1	+	0	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	exon	21379975	21380104	.	+	.	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	intron	21380105	21380238	.	+	.	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	CDS	21380239	21380258	1	+	2	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	exon	21380239	21380258	.	+	.	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
Phchi.S1	AUGUSTUS	stop_codon	21380259	21380261	.	+	0	transcript_id "Phchi.S1G334700.t1"; gene_id "Phchi.S1G334700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1175.t1 is derived from g10958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8278458	8281304	.	-	.	Phchi.S6G113400
Phchi.S6	AUGUSTUS	transcript	8278458	8281304	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	stop_codon	8278455	8278457	.	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8278458	8279135	0.98	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8278458	8279135	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8279136	8279236	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8279237	8279487	1	-	2	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8279237	8279487	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8279488	8279575	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8279576	8279812	0.7	-	2	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8279576	8279812	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8279813	8280013	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8280014	8280087	0.98	-	1	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8280014	8280087	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8280088	8280176	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8280177	8280211	1	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8280177	8280211	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8280212	8280332	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8280333	8280356	1	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8280333	8280356	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8280357	8280480	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8280481	8280538	1	-	1	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8280481	8280538	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8280539	8280633	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8280634	8280701	0.96	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8280634	8280701	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8280702	8280787	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8280788	8280968	1	-	1	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8280788	8280968	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	intron	8280969	8281080	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	CDS	8281081	8281304	0.99	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	exon	8281081	8281304	.	-	.	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
Phchi.S6	AUGUSTUS	start_codon	8281302	8281304	.	-	0	transcript_id "Phchi.S6G113400.t1"; gene_id "Phchi.S6G113400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2269.t1 is derived from g9189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5780935	5783192	.	-	.	Phchi.S5G087800
Phchi.S5	AUGUSTUS	transcript	5780935	5783192	.	-	.	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	stop_codon	5780932	5780934	.	-	0	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	CDS	5780935	5782406	0.71	-	2	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	exon	5780935	5782406	.	-	.	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	intron	5782407	5782486	.	-	.	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	CDS	5782487	5783192	0.31	-	0	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	exon	5782487	5783192	.	-	.	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
Phchi.S5	AUGUSTUS	start_codon	5783190	5783192	.	-	0	transcript_id "Phchi.S5G087800.t1"; gene_id "Phchi.S5G087800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10028.t1 is derived from g7204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45159081	45160188	.	-	.	Phchi.S1G718700
Phchi.S1	AUGUSTUS	transcript	45159081	45160188	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	stop_codon	45159078	45159080	.	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	CDS	45159081	45159254	0.99	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	exon	45159081	45159254	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	intron	45159255	45159360	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	CDS	45159361	45159408	1	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	exon	45159361	45159408	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	intron	45159409	45159501	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	CDS	45159502	45159588	1	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	exon	45159502	45159588	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	intron	45159589	45159676	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	CDS	45159677	45159814	1	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	exon	45159677	45159814	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	intron	45159815	45159912	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	CDS	45159913	45160188	0.54	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	exon	45159913	45160188	.	-	.	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
Phchi.S1	AUGUSTUS	start_codon	45160186	45160188	.	-	0	transcript_id "Phchi.S1G718700.t1"; gene_id "Phchi.S1G718700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7765.t1 is derived from g4939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31161794	31162265	.	+	.	Phchi.S1G492400
Phchi.S1	AUGUSTUS	transcript	31161794	31162265	.	+	.	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	start_codon	31161794	31161796	.	+	0	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	CDS	31161794	31161924	0.79	+	0	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	exon	31161794	31161924	.	+	.	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	intron	31161925	31162066	.	+	.	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	CDS	31162067	31162265	0.78	+	1	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	exon	31162067	31162265	.	+	.	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
Phchi.S1	AUGUSTUS	stop_codon	31162266	31162268	.	+	0	transcript_id "Phchi.S1G492400.t1"; gene_id "Phchi.S1G492400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3066.t1 is derived from g235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1411510	1415634	.	-	.	Phchi.S1G022500
Phchi.S1	AUGUSTUS	transcript	1411510	1415634	.	-	.	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	stop_codon	1411507	1411509	.	-	0	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	CDS	1411510	1412118	1	-	0	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	exon	1411510	1412118	.	-	.	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	intron	1412119	1415592	.	-	.	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	CDS	1415593	1415634	0.34	-	0	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	exon	1415593	1415634	.	-	.	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
Phchi.S1	AUGUSTUS	start_codon	1415632	1415634	.	-	0	transcript_id "Phchi.S1G022500.t1"; gene_id "Phchi.S1G022500"
# This transcript jg7458.t2 is derived from g4630.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7459.t1 is derived from g4632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29384935	29385522	.	-	.	Phchi.S1G461800
Phchi.S1	AUGUSTUS	transcript	29384935	29385522	.	-	.	transcript_id "Phchi.S1G461800.t1"; gene_id "Phchi.S1G461800"
Phchi.S1	AUGUSTUS	stop_codon	29384932	29384934	.	-	0	transcript_id "Phchi.S1G461800.t1"; gene_id "Phchi.S1G461800"
Phchi.S1	AUGUSTUS	CDS	29384935	29385522	0.48	-	0	transcript_id "Phchi.S1G461800.t1"; gene_id "Phchi.S1G461800"
Phchi.S1	AUGUSTUS	exon	29384935	29385522	.	-	.	transcript_id "Phchi.S1G461800.t1"; gene_id "Phchi.S1G461800"
Phchi.S1	AUGUSTUS	start_codon	29385520	29385522	.	-	0	transcript_id "Phchi.S1G461800.t1"; gene_id "Phchi.S1G461800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9741.t1 is derived from g6917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43470861	43471610	.	+	.	Phchi.S1G690000
Phchi.S1	AUGUSTUS	transcript	43470861	43471610	.	+	.	transcript_id "Phchi.S1G690000.t1"; gene_id "Phchi.S1G690000"
Phchi.S1	AUGUSTUS	start_codon	43470861	43470863	.	+	0	transcript_id "Phchi.S1G690000.t1"; gene_id "Phchi.S1G690000"
Phchi.S1	AUGUSTUS	CDS	43470861	43471610	0.99	+	0	transcript_id "Phchi.S1G690000.t1"; gene_id "Phchi.S1G690000"
Phchi.S1	AUGUSTUS	exon	43470861	43471610	.	+	.	transcript_id "Phchi.S1G690000.t1"; gene_id "Phchi.S1G690000"
Phchi.S1	AUGUSTUS	stop_codon	43471611	43471613	.	+	0	transcript_id "Phchi.S1G690000.t1"; gene_id "Phchi.S1G690000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10964.t1 is derived from g15014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3324998	3325525	.	-	.	Phchi.S4G054600
Phchi.S4	AUGUSTUS	transcript	3324998	3325525	.	-	.	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	stop_codon	3324995	3324997	.	-	0	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	CDS	3324998	3325025	0.94	-	1	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	exon	3324998	3325025	.	-	.	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	intron	3325026	3325190	.	-	.	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	CDS	3325191	3325263	0.88	-	2	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	exon	3325191	3325263	.	-	.	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	intron	3325264	3325353	.	-	.	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	CDS	3325354	3325525	0.72	-	0	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	exon	3325354	3325525	.	-	.	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
Phchi.S4	AUGUSTUS	start_codon	3325523	3325525	.	-	0	transcript_id "Phchi.S4G054600.t1"; gene_id "Phchi.S4G054600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6814.t1 is derived from g3986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25180220	25181931	.	-	.	Phchi.S1G397300
Phchi.S1	AUGUSTUS	transcript	25180220	25181931	.	-	.	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	stop_codon	25180217	25180219	.	-	0	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	CDS	25180220	25180746	0.27	-	2	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	exon	25180220	25180746	.	-	.	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	intron	25180747	25180829	.	-	.	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	CDS	25180830	25181931	0.43	-	0	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	exon	25180830	25181931	.	-	.	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
Phchi.S1	AUGUSTUS	start_codon	25181929	25181931	.	-	0	transcript_id "Phchi.S1G397300.t1"; gene_id "Phchi.S1G397300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15229.t1 is derived from g13697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17838064	17840265	.	-	.	Phchi.S3G254800
Phchi.S3	AUGUSTUS	transcript	17838064	17840265	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	stop_codon	17838061	17838063	.	-	0	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	CDS	17838064	17838241	1	-	1	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	exon	17838064	17838241	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	intron	17838242	17838321	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	CDS	17838322	17838539	1	-	0	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	exon	17838322	17838539	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	intron	17838540	17838643	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	CDS	17838644	17839045	0.99	-	0	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	exon	17838644	17839045	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	intron	17839046	17839123	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	CDS	17839124	17839314	1	-	2	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	exon	17839124	17839314	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	intron	17839315	17839400	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	CDS	17839401	17840265	0.88	-	0	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	exon	17839401	17840265	.	-	.	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
Phchi.S3	AUGUSTUS	start_codon	17840263	17840265	.	-	0	transcript_id "Phchi.S3G254800.t1"; gene_id "Phchi.S3G254800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14486.t1 is derived from g12954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13088184	13091113	.	+	.	Phchi.S3G180500
Phchi.S3	AUGUSTUS	transcript	13088184	13091113	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	start_codon	13088184	13088186	.	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13088184	13088316	0.99	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13088184	13088316	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13088317	13088582	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13088583	13088668	1	+	2	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13088583	13088668	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13088669	13088751	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13088752	13088859	1	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13088752	13088859	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13088860	13089062	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13089063	13089312	0.65	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13089063	13089312	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13089313	13089398	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13089399	13089442	1	+	2	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13089399	13089442	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13089443	13089589	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13089590	13089657	1	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13089590	13089657	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13089658	13089736	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13089737	13089842	1	+	1	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13089737	13089842	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13089843	13089985	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13089986	13090146	1	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13089986	13090146	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13090147	13090263	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13090264	13090333	1	+	1	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13090264	13090333	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13090334	13090460	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13090461	13090511	1	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13090461	13090511	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13090512	13090606	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13090607	13090659	1	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13090607	13090659	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13090660	13090772	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13090773	13090902	1	+	1	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13090773	13090902	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	intron	13090903	13091023	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	CDS	13091024	13091113	0.93	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	exon	13091024	13091113	.	+	.	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
Phchi.S3	AUGUSTUS	stop_codon	13091114	13091116	.	+	0	transcript_id "Phchi.S3G180500.t1"; gene_id "Phchi.S3G180500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2361.t1 is derived from g9281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6348710	6350998	.	+	.	Phchi.S5G097000
Phchi.S5	AUGUSTUS	transcript	6348710	6350998	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	start_codon	6348710	6348712	.	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6348710	6348767	0.65	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6348710	6348767	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6348768	6348972	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6348973	6349118	1	+	2	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6348973	6349118	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349119	6349217	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349218	6349265	1	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349218	6349265	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349266	6349346	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349347	6349428	1	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349347	6349428	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349429	6349820	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349821	6349918	0.99	+	2	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349821	6349918	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349919	6350206	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350207	6350254	1	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350207	6350254	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350255	6350373	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350374	6350457	1	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350374	6350457	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350458	6350540	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350541	6350605	1	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350541	6350605	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350606	6350677	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350678	6350729	1	+	1	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350678	6350729	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350730	6350953	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350954	6350998	1	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350954	6350998	.	+	.	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	stop_codon	6350999	6351001	.	+	0	transcript_id "Phchi.S5G097000.t1"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	transcript	6348710	6350998	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	start_codon	6348710	6348712	.	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6348710	6348767	0.68	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6348710	6348767	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6348768	6348972	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6348973	6349118	1	+	2	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6348973	6349118	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349119	6349217	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349218	6349265	1	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349218	6349265	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349266	6349346	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349347	6349428	1	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349347	6349428	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349429	6349797	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349798	6349821	0.91	+	2	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349798	6349821	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349822	6349880	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6349881	6349918	0.91	+	2	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6349881	6349918	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6349919	6350206	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350207	6350254	1	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350207	6350254	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350255	6350373	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350374	6350457	1	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350374	6350457	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350458	6350540	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350541	6350605	1	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350541	6350605	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350606	6350677	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350678	6350729	1	+	1	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350678	6350729	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	intron	6350730	6350953	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	CDS	6350954	6350998	1	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	exon	6350954	6350998	.	+	.	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
Phchi.S5	AUGUSTUS	stop_codon	6350999	6351001	.	+	0	transcript_id "Phchi.S5G097000.t2"; gene_id "Phchi.S5G097000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5132.t1 is derived from g2302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15073339	15075215	.	+	.	Phchi.S1G229100
Phchi.S1	AUGUSTUS	transcript	15073339	15075215	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	start_codon	15073339	15073341	.	+	0	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	CDS	15073339	15073908	0.35	+	0	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	exon	15073339	15073908	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	intron	15073909	15074045	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	CDS	15074046	15074330	0.33	+	0	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	exon	15074046	15074330	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	intron	15074331	15074451	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	CDS	15074452	15074732	1	+	0	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	exon	15074452	15074732	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	intron	15074733	15074821	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	CDS	15074822	15075215	1	+	1	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	exon	15074822	15075215	.	+	.	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
Phchi.S1	AUGUSTUS	stop_codon	15075216	15075218	.	+	0	transcript_id "Phchi.S1G229100.t1"; gene_id "Phchi.S1G229100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1916.t1 is derived from g8836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3841848	3842519	.	+	.	Phchi.S5G052500
Phchi.S5	AUGUSTUS	transcript	3841848	3842519	.	+	.	transcript_id "Phchi.S5G052500.t1"; gene_id "Phchi.S5G052500"
Phchi.S5	AUGUSTUS	start_codon	3841848	3841850	.	+	0	transcript_id "Phchi.S5G052500.t1"; gene_id "Phchi.S5G052500"
Phchi.S5	AUGUSTUS	CDS	3841848	3842519	0.44	+	0	transcript_id "Phchi.S5G052500.t1"; gene_id "Phchi.S5G052500"
Phchi.S5	AUGUSTUS	exon	3841848	3842519	.	+	.	transcript_id "Phchi.S5G052500.t1"; gene_id "Phchi.S5G052500"
Phchi.S5	AUGUSTUS	stop_codon	3842520	3842522	.	+	0	transcript_id "Phchi.S5G052500.t1"; gene_id "Phchi.S5G052500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10892.t1 is derived from g14942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2787307	2787991	.	-	.	Phchi.S4G047400
Phchi.S4	AUGUSTUS	transcript	2787307	2787991	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	stop_codon	2787304	2787306	.	-	0	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	CDS	2787307	2787363	1	-	0	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	exon	2787307	2787363	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	intron	2787364	2787454	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	CDS	2787455	2787529	1	-	0	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	exon	2787455	2787529	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	intron	2787530	2787613	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	CDS	2787614	2787681	1	-	2	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	exon	2787614	2787681	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	intron	2787682	2787876	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	CDS	2787877	2787991	1	-	0	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	exon	2787877	2787991	.	-	.	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
Phchi.S4	AUGUSTUS	start_codon	2787989	2787991	.	-	0	transcript_id "Phchi.S4G047400.t1"; gene_id "Phchi.S4G047400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10296.t1 is derived from g7472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46983493	46984403	.	-	.	Phchi.S1G745500
Phchi.S1	AUGUSTUS	transcript	46983493	46984403	.	-	.	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	stop_codon	46983490	46983492	.	-	0	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	CDS	46983493	46983530	0.34	-	2	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	exon	46983493	46983530	.	-	.	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	intron	46983531	46983607	.	-	.	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	CDS	46983608	46983713	0.22	-	0	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	exon	46983608	46983713	.	-	.	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	intron	46983714	46983947	.	-	.	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	CDS	46983948	46984403	0.59	-	0	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	exon	46983948	46984403	.	-	.	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
Phchi.S1	AUGUSTUS	start_codon	46984401	46984403	.	-	0	transcript_id "Phchi.S1G745500.t1"; gene_id "Phchi.S1G745500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7617.t1 is derived from g4791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30286824	30288651	.	-	.	Phchi.S1G477600
Phchi.S1	AUGUSTUS	transcript	30286824	30288651	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	stop_codon	30286821	30286823	.	-	0	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	CDS	30286824	30287149	1	-	2	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	exon	30286824	30287149	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	intron	30287150	30287232	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	CDS	30287233	30287346	1	-	2	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	exon	30287233	30287346	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	intron	30287347	30287453	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	CDS	30287454	30287645	1	-	2	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	exon	30287454	30287645	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	intron	30287646	30287739	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	CDS	30287740	30287921	1	-	1	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	exon	30287740	30287921	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	intron	30287922	30288017	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	CDS	30288018	30288140	0.66	-	1	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	exon	30288018	30288140	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	intron	30288141	30288211	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	CDS	30288212	30288651	0.35	-	0	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	exon	30288212	30288651	.	-	.	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
Phchi.S1	AUGUSTUS	start_codon	30288649	30288651	.	-	0	transcript_id "Phchi.S1G477600.t1"; gene_id "Phchi.S1G477600"
# This transcript jg502.t2 is derived from g10284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg503.t1 is derived from g10285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3494817	3495273	.	+	.	Phchi.S6G046200
Phchi.S6	AUGUSTUS	transcript	3494817	3495273	.	+	.	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	start_codon	3494817	3494819	.	+	0	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	CDS	3494817	3494963	0.96	+	0	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	exon	3494817	3494963	.	+	.	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	intron	3494964	3495102	.	+	.	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	CDS	3495103	3495273	1	+	0	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	exon	3495103	3495273	.	+	.	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
Phchi.S6	AUGUSTUS	stop_codon	3495274	3495276	.	+	0	transcript_id "Phchi.S6G046200.t1"; gene_id "Phchi.S6G046200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15412.t1 is derived from g13880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18887571	18890714	.	+	.	Phchi.S3G273100
Phchi.S3	AUGUSTUS	transcript	18887571	18890714	.	+	.	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	start_codon	18887571	18887573	.	+	0	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	CDS	18887571	18888198	1	+	0	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	exon	18887571	18888198	.	+	.	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	intron	18888199	18888359	.	+	.	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	CDS	18888360	18888649	0.81	+	2	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	exon	18888360	18888649	.	+	.	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	intron	18888650	18888884	.	+	.	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	CDS	18888885	18890714	0.99	+	0	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	exon	18888885	18890714	.	+	.	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
Phchi.S3	AUGUSTUS	stop_codon	18890715	18890717	.	+	0	transcript_id "Phchi.S3G273100.t1"; gene_id "Phchi.S3G273100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13306.t1 is derived from g11772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5662772	5664077	.	+	.	Phchi.S3G062500
Phchi.S3	AUGUSTUS	transcript	5662772	5664077	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	start_codon	5662772	5662774	.	+	0	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	CDS	5662772	5662951	1	+	0	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	exon	5662772	5662951	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	intron	5662952	5663043	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	CDS	5663044	5663178	1	+	0	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	exon	5663044	5663178	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	intron	5663179	5663274	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	CDS	5663275	5663506	1	+	0	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	exon	5663275	5663506	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	intron	5663507	5663613	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	CDS	5663614	5663817	1	+	2	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	exon	5663614	5663817	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	intron	5663818	5663916	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	CDS	5663917	5664077	1	+	2	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	exon	5663917	5664077	.	+	.	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
Phchi.S3	AUGUSTUS	stop_codon	5664078	5664080	.	+	0	transcript_id "Phchi.S3G062500.t1"; gene_id "Phchi.S3G062500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7937.t1 is derived from g5111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32002780	32003202	.	-	.	Phchi.S1G509600
Phchi.S1	AUGUSTUS	transcript	32002780	32003202	.	-	.	transcript_id "Phchi.S1G509600.t1"; gene_id "Phchi.S1G509600"
Phchi.S1	AUGUSTUS	stop_codon	32002777	32002779	.	-	0	transcript_id "Phchi.S1G509600.t1"; gene_id "Phchi.S1G509600"
Phchi.S1	AUGUSTUS	CDS	32002780	32003202	0.52	-	0	transcript_id "Phchi.S1G509600.t1"; gene_id "Phchi.S1G509600"
Phchi.S1	AUGUSTUS	exon	32002780	32003202	.	-	.	transcript_id "Phchi.S1G509600.t1"; gene_id "Phchi.S1G509600"
Phchi.S1	AUGUSTUS	start_codon	32003200	32003202	.	-	0	transcript_id "Phchi.S1G509600.t1"; gene_id "Phchi.S1G509600"
# This transcript jg4614.t2 is derived from g1784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4615.t1 is derived from g1785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11420964	11422871	.	-	.	Phchi.S1G177400
Phchi.S1	AUGUSTUS	transcript	11420964	11422871	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	stop_codon	11420961	11420963	.	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11420964	11421056	1	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11420964	11421056	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11421057	11421136	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11421137	11421243	1	-	2	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11421137	11421243	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11421244	11421320	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11421321	11421422	1	-	2	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11421321	11421422	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11421423	11421508	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11421509	11421558	1	-	1	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11421509	11421558	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11421559	11421640	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11421641	11421859	1	-	1	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11421641	11421859	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11421860	11421943	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11421944	11422041	1	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11421944	11422041	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11422042	11422123	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11422124	11422246	1	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11422124	11422246	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11422247	11422329	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11422330	11422389	1	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11422330	11422389	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	intron	11422390	11422469	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	CDS	11422470	11422871	0.99	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	exon	11422470	11422871	.	-	.	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
Phchi.S1	AUGUSTUS	start_codon	11422869	11422871	.	-	0	transcript_id "Phchi.S1G177400.t1"; gene_id "Phchi.S1G177400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13666.t1 is derived from g12133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8068130	8069145	.	+	.	Phchi.S3G098500
Phchi.S3	AUGUSTUS	transcript	8068130	8069145	.	+	.	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	start_codon	8068130	8068132	.	+	0	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	CDS	8068130	8068660	0.96	+	0	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	exon	8068130	8068660	.	+	.	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	intron	8068661	8068755	.	+	.	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	CDS	8068756	8069145	0.99	+	0	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	exon	8068756	8069145	.	+	.	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
Phchi.S3	AUGUSTUS	stop_codon	8069146	8069148	.	+	0	transcript_id "Phchi.S3G098500.t1"; gene_id "Phchi.S3G098500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12444.t1 is derived from g8121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20867139	20867453	.	-	.	Phchi.S2G052400
Phchi.S2	AUGUSTUS	transcript	20867139	20867453	.	-	.	transcript_id "Phchi.S2G052400.t1"; gene_id "Phchi.S2G052400"
Phchi.S2	AUGUSTUS	stop_codon	20867136	20867138	.	-	0	transcript_id "Phchi.S2G052400.t1"; gene_id "Phchi.S2G052400"
Phchi.S2	AUGUSTUS	CDS	20867139	20867453	0.81	-	0	transcript_id "Phchi.S2G052400.t1"; gene_id "Phchi.S2G052400"
Phchi.S2	AUGUSTUS	exon	20867139	20867453	.	-	.	transcript_id "Phchi.S2G052400.t1"; gene_id "Phchi.S2G052400"
Phchi.S2	AUGUSTUS	start_codon	20867451	20867453	.	-	0	transcript_id "Phchi.S2G052400.t1"; gene_id "Phchi.S2G052400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1874.t1 is derived from g8794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3642227	3644901	.	+	.	Phchi.S5G048300
Phchi.S5	AUGUSTUS	transcript	3642227	3644901	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	start_codon	3642227	3642229	.	+	0	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	CDS	3642227	3642496	0.99	+	0	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	exon	3642227	3642496	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	intron	3642497	3642719	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	CDS	3642720	3643481	1	+	0	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	exon	3642720	3643481	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	intron	3643482	3643579	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	CDS	3643580	3643803	1	+	0	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	exon	3643580	3643803	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	intron	3643804	3643991	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	CDS	3643992	3644138	1	+	1	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	exon	3643992	3644138	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	intron	3644139	3644357	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	CDS	3644358	3644579	1	+	1	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	exon	3644358	3644579	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	intron	3644580	3644666	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	CDS	3644667	3644901	1	+	1	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	exon	3644667	3644901	.	+	.	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
Phchi.S5	AUGUSTUS	stop_codon	3644902	3644904	.	+	0	transcript_id "Phchi.S5G048300.t1"; gene_id "Phchi.S5G048300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7520.t1 is derived from g4694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29814295	29815899	.	+	.	Phchi.S1G467900
Phchi.S1	AUGUSTUS	transcript	29814295	29815899	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	start_codon	29814295	29814297	.	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	CDS	29814295	29814353	1	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	exon	29814295	29814353	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	intron	29814354	29814606	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	CDS	29814607	29814712	1	+	1	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	exon	29814607	29814712	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	intron	29814713	29814892	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	CDS	29814893	29815030	1	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	exon	29814893	29815030	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	intron	29815031	29815180	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	CDS	29815181	29815366	1	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	exon	29815181	29815366	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	intron	29815367	29815510	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	CDS	29815511	29815711	1	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	exon	29815511	29815711	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	intron	29815712	29815800	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	CDS	29815801	29815899	1	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	exon	29815801	29815899	.	+	.	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
Phchi.S1	AUGUSTUS	stop_codon	29815900	29815902	.	+	0	transcript_id "Phchi.S1G467900.t1"; gene_id "Phchi.S1G467900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5438.t1 is derived from g2608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16872590	16873078	.	+	.	Phchi.S1G259700
Phchi.S1	AUGUSTUS	transcript	16872590	16873078	.	+	.	transcript_id "Phchi.S1G259700.t1"; gene_id "Phchi.S1G259700"
Phchi.S1	AUGUSTUS	start_codon	16872590	16872592	.	+	0	transcript_id "Phchi.S1G259700.t1"; gene_id "Phchi.S1G259700"
Phchi.S1	AUGUSTUS	CDS	16872590	16873078	0.96	+	0	transcript_id "Phchi.S1G259700.t1"; gene_id "Phchi.S1G259700"
Phchi.S1	AUGUSTUS	exon	16872590	16873078	.	+	.	transcript_id "Phchi.S1G259700.t1"; gene_id "Phchi.S1G259700"
Phchi.S1	AUGUSTUS	stop_codon	16873079	16873081	.	+	0	transcript_id "Phchi.S1G259700.t1"; gene_id "Phchi.S1G259700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11639.t1 is derived from g15690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7417932	7420641	.	+	.	Phchi.S4G122100
Phchi.S4	AUGUSTUS	transcript	7417932	7420641	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	start_codon	7417932	7417934	.	+	0	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7417932	7418061	0.73	+	0	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7417932	7418061	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7418062	7418197	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7418198	7418274	0.92	+	2	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7418198	7418274	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7418275	7418516	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7418517	7418804	0.92	+	0	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7418517	7418804	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7418805	7418886	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7418887	7418997	1	+	0	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7418887	7418997	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7418998	7419116	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7419117	7419336	0.95	+	0	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7419117	7419336	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7419337	7419439	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7419440	7419773	0.96	+	2	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7419440	7419773	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7419774	7419870	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7419871	7419932	1	+	1	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7419871	7419932	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7419933	7420087	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7420088	7420154	0.94	+	2	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7420088	7420154	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	intron	7420155	7420586	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	CDS	7420587	7420641	0.94	+	1	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	exon	7420587	7420641	.	+	.	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
Phchi.S4	AUGUSTUS	stop_codon	7420642	7420644	.	+	0	transcript_id "Phchi.S4G122100.t1"; gene_id "Phchi.S4G122100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3991.t1 is derived from g1160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6889937	6892736	.	+	.	Phchi.S1G115000
Phchi.S1	AUGUSTUS	transcript	6889937	6892736	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	start_codon	6889937	6889939	.	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6889937	6890030	0.98	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6889937	6890030	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6890031	6890213	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6890214	6890366	1	+	2	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6890214	6890366	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6890367	6890474	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6890475	6890634	0.97	+	2	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6890475	6890634	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6890635	6890740	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6890741	6891044	0.97	+	1	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6890741	6891044	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6891045	6891149	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6891150	6891287	0.96	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6891150	6891287	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6891288	6891403	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6891404	6891596	0.96	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6891404	6891596	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6891597	6891671	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6891672	6891802	1	+	2	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6891672	6891802	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6891803	6891884	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6891885	6892076	1	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6891885	6892076	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6892077	6892182	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6892183	6892361	1	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6892183	6892361	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6892362	6892475	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6892476	6892557	0.97	+	1	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6892476	6892557	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	intron	6892558	6892652	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	CDS	6892653	6892736	0.71	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	exon	6892653	6892736	.	+	.	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
Phchi.S1	AUGUSTUS	stop_codon	6892737	6892739	.	+	0	transcript_id "Phchi.S1G115000.t1"; gene_id "Phchi.S1G115000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3722.t1 is derived from g891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5374369	5376475	.	+	.	Phchi.S1G088100
Phchi.S1	AUGUSTUS	transcript	5374369	5376475	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	start_codon	5374369	5374371	.	+	0	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	CDS	5374369	5374693	0.51	+	0	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	exon	5374369	5374693	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	intron	5374694	5374801	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	CDS	5374802	5375031	0.49	+	2	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	exon	5374802	5375031	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	intron	5375032	5375119	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	CDS	5375120	5375391	0.99	+	0	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	exon	5375120	5375391	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	intron	5375392	5375493	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	CDS	5375494	5375917	1	+	1	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	exon	5375494	5375917	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	intron	5375918	5376055	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	CDS	5376056	5376475	1	+	0	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	exon	5376056	5376475	.	+	.	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
Phchi.S1	AUGUSTUS	stop_codon	5376476	5376478	.	+	0	transcript_id "Phchi.S1G088100.t1"; gene_id "Phchi.S1G088100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13628.t1 is derived from g12095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7827123	7828136	.	-	.	Phchi.S3G094700
Phchi.S3	AUGUSTUS	transcript	7827123	7828136	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	stop_codon	7827120	7827122	.	-	0	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7827123	7827243	1	-	1	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7827123	7827243	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	intron	7827244	7827357	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7827358	7827421	1	-	2	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7827358	7827421	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	intron	7827422	7827508	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7827509	7827561	1	-	1	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7827509	7827561	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	intron	7827562	7827642	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7827643	7827681	1	-	1	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7827643	7827681	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	intron	7827682	7827765	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7827766	7827848	1	-	0	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7827766	7827848	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	intron	7827849	7827948	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7827949	7827991	1	-	1	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7827949	7827991	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	intron	7827992	7828083	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	CDS	7828084	7828136	1	-	0	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	exon	7828084	7828136	.	-	.	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
Phchi.S3	AUGUSTUS	start_codon	7828134	7828136	.	-	0	transcript_id "Phchi.S3G094700.t1"; gene_id "Phchi.S3G094700"
# This transcript jg9230.t2 is derived from g6405.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9230.t3 is derived from g6405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9231.t1 is derived from g6406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40520504	40521160	.	+	.	Phchi.S1G639000
Phchi.S1	AUGUSTUS	transcript	40520504	40521160	.	+	.	transcript_id "Phchi.S1G639000.t1"; gene_id "Phchi.S1G639000"
Phchi.S1	AUGUSTUS	start_codon	40520504	40520506	.	+	0	transcript_id "Phchi.S1G639000.t1"; gene_id "Phchi.S1G639000"
Phchi.S1	AUGUSTUS	CDS	40520504	40521160	0.77	+	0	transcript_id "Phchi.S1G639000.t1"; gene_id "Phchi.S1G639000"
Phchi.S1	AUGUSTUS	exon	40520504	40521160	.	+	.	transcript_id "Phchi.S1G639000.t1"; gene_id "Phchi.S1G639000"
Phchi.S1	AUGUSTUS	stop_codon	40521161	40521163	.	+	0	transcript_id "Phchi.S1G639000.t1"; gene_id "Phchi.S1G639000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg926.t1 is derived from g10708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6476589	6478741	.	-	.	Phchi.S6G088500
Phchi.S6	AUGUSTUS	transcript	6476589	6478741	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	stop_codon	6476586	6476588	.	-	0	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	CDS	6476589	6476977	0.99	-	2	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	exon	6476589	6476977	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	intron	6476978	6477069	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	CDS	6477070	6477319	1	-	0	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	exon	6477070	6477319	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	intron	6477320	6477407	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	CDS	6477408	6477619	1	-	2	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	exon	6477408	6477619	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	intron	6477620	6477750	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	CDS	6477751	6478299	1	-	2	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	exon	6477751	6478299	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	intron	6478300	6478530	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	CDS	6478531	6478570	0.77	-	0	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	exon	6478531	6478570	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	intron	6478571	6478636	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	CDS	6478637	6478741	0.46	-	0	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	exon	6478637	6478741	.	-	.	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
Phchi.S6	AUGUSTUS	start_codon	6478739	6478741	.	-	0	transcript_id "Phchi.S6G088500.t1"; gene_id "Phchi.S6G088500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7403.t1 is derived from g4575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28961439	28961714	.	+	.	Phchi.S1G456200
Phchi.S1	AUGUSTUS	transcript	28961439	28961714	.	+	.	transcript_id "Phchi.S1G456200.t1"; gene_id "Phchi.S1G456200"
Phchi.S1	AUGUSTUS	start_codon	28961439	28961441	.	+	0	transcript_id "Phchi.S1G456200.t1"; gene_id "Phchi.S1G456200"
Phchi.S1	AUGUSTUS	CDS	28961439	28961714	0.86	+	0	transcript_id "Phchi.S1G456200.t1"; gene_id "Phchi.S1G456200"
Phchi.S1	AUGUSTUS	exon	28961439	28961714	.	+	.	transcript_id "Phchi.S1G456200.t1"; gene_id "Phchi.S1G456200"
Phchi.S1	AUGUSTUS	stop_codon	28961715	28961717	.	+	0	transcript_id "Phchi.S1G456200.t1"; gene_id "Phchi.S1G456200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4515.t1 is derived from g1685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10908929	10909672	.	-	.	Phchi.S1G167400
Phchi.S1	AUGUSTUS	transcript	10908929	10909672	.	-	.	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	stop_codon	10908926	10908928	.	-	0	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	CDS	10908929	10909211	0.98	-	1	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	exon	10908929	10909211	.	-	.	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	intron	10909212	10909424	.	-	.	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	CDS	10909425	10909672	0.83	-	0	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	exon	10909425	10909672	.	-	.	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
Phchi.S1	AUGUSTUS	start_codon	10909670	10909672	.	-	0	transcript_id "Phchi.S1G167400.t1"; gene_id "Phchi.S1G167400"
# This transcript jg1955.t2 is derived from g8875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1956.t1 is derived from g8876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4011699	4012860	.	+	.	Phchi.S5G056500
Phchi.S5	AUGUSTUS	transcript	4011699	4012860	.	+	.	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	start_codon	4011699	4011701	.	+	0	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	CDS	4011699	4012222	0.73	+	0	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	exon	4011699	4012222	.	+	.	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	intron	4012223	4012305	.	+	.	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	CDS	4012306	4012615	0.92	+	1	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	exon	4012306	4012615	.	+	.	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	intron	4012616	4012743	.	+	.	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	CDS	4012744	4012860	1	+	0	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	exon	4012744	4012860	.	+	.	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
Phchi.S5	AUGUSTUS	stop_codon	4012861	4012863	.	+	0	transcript_id "Phchi.S5G056500.t1"; gene_id "Phchi.S5G056500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5745.t1 is derived from g2915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18692068	18692718	.	+	.	Phchi.S1G290400
Phchi.S1	AUGUSTUS	transcript	18692068	18692718	.	+	.	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	start_codon	18692068	18692070	.	+	0	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	CDS	18692068	18692211	0.73	+	0	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	exon	18692068	18692211	.	+	.	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	intron	18692212	18692297	.	+	.	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	CDS	18692298	18692417	0.8	+	0	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	exon	18692298	18692417	.	+	.	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	intron	18692418	18692511	.	+	.	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	CDS	18692512	18692718	0.97	+	0	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	exon	18692512	18692718	.	+	.	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
Phchi.S1	AUGUSTUS	stop_codon	18692719	18692721	.	+	0	transcript_id "Phchi.S1G290400.t1"; gene_id "Phchi.S1G290400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1581.t1 is derived from g8500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1866461	1870578	.	-	.	Phchi.S5G019000
Phchi.S5	AUGUSTUS	transcript	1866461	1870578	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	stop_codon	1866458	1866460	.	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1866461	1866560	0.43	-	1	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1866461	1866560	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1866561	1866704	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1866705	1866736	0.84	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1866705	1866736	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1866737	1867028	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867029	1867100	0.85	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867029	1867100	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867101	1867234	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867235	1867388	1	-	1	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867235	1867388	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867389	1867480	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867481	1867608	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867481	1867608	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867609	1867698	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867699	1867791	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867699	1867791	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867792	1867879	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867880	1867949	1	-	1	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867880	1867949	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867950	1868049	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868050	1868192	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868050	1868192	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868193	1868312	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868313	1868435	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868313	1868435	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868436	1868560	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868561	1868671	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868561	1868671	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868672	1868848	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868849	1869112	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868849	1869112	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1869113	1869305	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1869306	1869385	0.74	-	2	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1869306	1869385	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1869386	1869494	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1869495	1869643	0.74	-	1	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1869495	1869643	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1869644	1869872	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1869873	1870006	1	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1869873	1870006	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1870007	1870138	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1870139	1870296	1	-	2	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1870139	1870296	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1870297	1870430	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1870431	1870578	0.81	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1870431	1870578	.	-	.	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	start_codon	1870576	1870578	.	-	0	transcript_id "Phchi.S5G019000.t1"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	transcript	1866461	1870578	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	stop_codon	1866458	1866460	.	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1866461	1866560	0.5	-	1	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1866461	1866560	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1866561	1866704	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1866705	1866736	0.84	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1866705	1866736	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1866737	1867028	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867029	1867100	0.84	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867029	1867100	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867101	1867234	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867235	1867388	1	-	1	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867235	1867388	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867389	1867480	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867481	1867608	1	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867481	1867608	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867609	1867698	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867699	1867791	1	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867699	1867791	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867792	1867879	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1867880	1867949	1	-	1	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1867880	1867949	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1867950	1868049	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868050	1868192	1	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868050	1868192	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868193	1868312	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868313	1868435	1	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868313	1868435	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868436	1868560	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868561	1868649	0.98	-	2	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868561	1868649	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868650	1868848	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868849	1868853	0.76	-	1	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868849	1868853	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1868854	1868960	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1868961	1869112	0.59	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1868961	1869112	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1869113	1869305	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1869306	1869385	0.75	-	2	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1869306	1869385	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1869386	1869494	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1869495	1869643	0.72	-	1	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1869495	1869643	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1869644	1869872	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1869873	1870006	1	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1869873	1870006	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1870007	1870138	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1870139	1870296	1	-	2	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1870139	1870296	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	intron	1870297	1870430	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	CDS	1870431	1870578	0.72	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	exon	1870431	1870578	.	-	.	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
Phchi.S5	AUGUSTUS	start_codon	1870576	1870578	.	-	0	transcript_id "Phchi.S5G019000.t2"; gene_id "Phchi.S5G019000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2243.t1 is derived from g9163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5618395	5620874	.	-	.	Phchi.S5G085200
Phchi.S5	AUGUSTUS	transcript	5618395	5620874	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	stop_codon	5618392	5618394	.	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5618395	5618534	1	-	2	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5618395	5618534	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5618535	5618623	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5618624	5618726	1	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5618624	5618726	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5618727	5618835	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5618836	5619216	1	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5618836	5619216	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5619217	5619316	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5619317	5619517	1	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5619317	5619517	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5619518	5619601	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5619602	5619733	1	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5619602	5619733	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5619734	5619818	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5619819	5619930	1	-	1	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5619819	5619930	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5619931	5620034	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5620035	5620259	1	-	1	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5620035	5620259	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5620260	5620341	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5620342	5620415	1	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5620342	5620415	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	intron	5620416	5620508	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	CDS	5620509	5620874	1	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	exon	5620509	5620874	.	-	.	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
Phchi.S5	AUGUSTUS	start_codon	5620872	5620874	.	-	0	transcript_id "Phchi.S5G085200.t1"; gene_id "Phchi.S5G085200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11470.t1 is derived from g15520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6512528	6514551	.	+	.	Phchi.S4G105200
Phchi.S4	AUGUSTUS	transcript	6512528	6514551	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	start_codon	6512528	6512530	.	+	0	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	CDS	6512528	6512573	1	+	0	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	exon	6512528	6512573	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	intron	6512574	6512662	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	CDS	6512663	6513156	0.99	+	2	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	exon	6512663	6513156	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	intron	6513157	6513265	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	CDS	6513266	6513557	1	+	0	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	exon	6513266	6513557	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	intron	6513558	6513733	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	CDS	6513734	6513850	1	+	2	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	exon	6513734	6513850	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	intron	6513851	6513928	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	CDS	6513929	6514551	1	+	2	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	exon	6513929	6514551	.	+	.	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
Phchi.S4	AUGUSTUS	stop_codon	6514552	6514554	.	+	0	transcript_id "Phchi.S4G105200.t1"; gene_id "Phchi.S4G105200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8274.t1 is derived from g5449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35060924	35063015	.	-	.	Phchi.S1G543300
Phchi.S1	AUGUSTUS	transcript	35060924	35063015	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	stop_codon	35060921	35060923	.	-	0	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35060924	35061226	0.98	-	0	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35060924	35061226	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35061227	35061310	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35061311	35061494	1	-	1	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35061311	35061494	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35061495	35061585	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35061586	35061775	1	-	2	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35061586	35061775	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35061776	35061902	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35061903	35062144	1	-	1	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35061903	35062144	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35062145	35062322	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35062323	35062408	1	-	0	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35062323	35062408	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35062409	35062547	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35062548	35062652	1	-	0	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35062548	35062652	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35062653	35062732	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35062733	35062835	1	-	1	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35062733	35062835	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	intron	35062836	35062956	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	CDS	35062957	35063015	1	-	0	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	exon	35062957	35063015	.	-	.	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
Phchi.S1	AUGUSTUS	start_codon	35063013	35063015	.	-	0	transcript_id "Phchi.S1G543300.t1"; gene_id "Phchi.S1G543300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15955.t1 is derived from g11138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	17913	19315	.	-	.	Phchi.C91G000200
Phchi.C91	AUGUSTUS	transcript	17913	19315	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	stop_codon	17910	17912	.	-	0	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	CDS	17913	18575	1	-	0	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	exon	17913	18575	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	intron	18576	18693	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	CDS	18694	18786	1	-	0	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	exon	18694	18786	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	intron	18787	18903	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	CDS	18904	18979	1	-	1	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	exon	18904	18979	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	intron	18980	19063	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	CDS	19064	19176	1	-	0	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	exon	19064	19176	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	intron	19177	19309	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	CDS	19310	19315	1	-	0	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	exon	19310	19315	.	-	.	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
Phchi.C91	AUGUSTUS	start_codon	19313	19315	.	-	0	transcript_id "Phchi.C91G000200.t1"; gene_id "Phchi.C91G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14128.t1 is derived from g12595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11035641	11038868	.	+	.	Phchi.S3G144700
Phchi.S3	AUGUSTUS	transcript	11035641	11038868	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	start_codon	11035641	11035643	.	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11035641	11036000	0.72	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11035641	11036000	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11036001	11036282	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11036283	11036546	0.96	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11036283	11036546	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11036547	11036670	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11036671	11036705	0.55	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11036671	11036705	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11036706	11036891	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11036892	11037064	0.92	+	1	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11036892	11037064	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11037065	11037168	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11037169	11037559	0.92	+	2	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11037169	11037559	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11037560	11037663	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11037664	11037916	0.97	+	1	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11037664	11037916	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11037917	11038000	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11038001	11038183	1	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11038001	11038183	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	intron	11038184	11038259	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	CDS	11038260	11038868	0.75	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	exon	11038260	11038868	.	+	.	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
Phchi.S3	AUGUSTUS	stop_codon	11038869	11038871	.	+	0	transcript_id "Phchi.S3G144700.t1"; gene_id "Phchi.S3G144700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7299.t1 is derived from g4471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28382642	28383119	.	+	.	Phchi.S1G445800
Phchi.S1	AUGUSTUS	transcript	28382642	28383119	.	+	.	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	start_codon	28382642	28382644	.	+	0	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	CDS	28382642	28382833	1	+	0	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	exon	28382642	28382833	.	+	.	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	intron	28382834	28382930	.	+	.	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	CDS	28382931	28383119	1	+	0	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	exon	28382931	28383119	.	+	.	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
Phchi.S1	AUGUSTUS	stop_codon	28383120	28383122	.	+	0	transcript_id "Phchi.S1G445800.t1"; gene_id "Phchi.S1G445800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg850.t1 is derived from g10632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5900729	5901764	.	+	.	Phchi.S6G080900
Phchi.S6	AUGUSTUS	transcript	5900729	5901764	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	start_codon	5900729	5900731	.	+	0	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	CDS	5900729	5900762	0.78	+	0	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	exon	5900729	5900762	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	intron	5900763	5900947	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	CDS	5900948	5901013	0.8	+	2	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	exon	5900948	5901013	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	intron	5901014	5901375	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	CDS	5901376	5901420	0.84	+	2	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	exon	5901376	5901420	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	intron	5901421	5901504	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	CDS	5901505	5901574	0.83	+	2	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	exon	5901505	5901574	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	intron	5901575	5901721	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	CDS	5901722	5901764	0.84	+	1	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	exon	5901722	5901764	.	+	.	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
Phchi.S6	AUGUSTUS	stop_codon	5901765	5901767	.	+	0	transcript_id "Phchi.S6G080900.t1"; gene_id "Phchi.S6G080900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1417.t1 is derived from g8336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	721612	723647	.	+	.	Phchi.S5G002600
Phchi.S5	AUGUSTUS	transcript	721612	723647	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	start_codon	721612	721614	.	+	0	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	721612	721628	0.46	+	0	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	721612	721628	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	intron	721629	721763	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	721764	721819	0.43	+	1	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	721764	721819	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	intron	721820	721952	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	721953	722063	0.43	+	2	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	721953	722063	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	intron	722064	722386	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	722387	722614	1	+	2	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	722387	722614	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	intron	722615	722735	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	722736	723149	0.93	+	2	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	722736	723149	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	intron	723150	723238	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	723239	723366	1	+	2	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	723239	723366	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	intron	723367	723569	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	CDS	723570	723647	1	+	0	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	exon	723570	723647	.	+	.	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
Phchi.S5	AUGUSTUS	stop_codon	723648	723650	.	+	0	transcript_id "Phchi.S5G002600.t1"; gene_id "Phchi.S5G002600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14653.t1 is derived from g13121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13954947	13955806	.	-	.	Phchi.S3G197200
Phchi.S3	AUGUSTUS	transcript	13954947	13955806	.	-	.	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	stop_codon	13954944	13954946	.	-	0	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	CDS	13954947	13955507	1	-	0	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	exon	13954947	13955507	.	-	.	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	intron	13955508	13955734	.	-	.	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	CDS	13955735	13955806	0.9	-	0	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	exon	13955735	13955806	.	-	.	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
Phchi.S3	AUGUSTUS	start_codon	13955804	13955806	.	-	0	transcript_id "Phchi.S3G197200.t1"; gene_id "Phchi.S3G197200"
# This transcript jg15814.t2 is derived from g14284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15814.t3 is derived from g14284.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15815.t1 is derived from g14285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21523346	21525138	.	+	.	Phchi.S3G313400
Phchi.S3	AUGUSTUS	transcript	21523346	21525138	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	start_codon	21523346	21523348	.	+	0	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	CDS	21523346	21523979	0.34	+	0	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	exon	21523346	21523979	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	intron	21523980	21524215	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	CDS	21524216	21524281	0.66	+	2	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	exon	21524216	21524281	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	intron	21524282	21524588	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	CDS	21524589	21524685	0.49	+	2	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	exon	21524589	21524685	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	intron	21524686	21524761	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	CDS	21524762	21524777	0.32	+	1	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	exon	21524762	21524777	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	intron	21524778	21525084	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	CDS	21525085	21525138	0.72	+	0	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	exon	21525085	21525138	.	+	.	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
Phchi.S3	AUGUSTUS	stop_codon	21525139	21525141	.	+	0	transcript_id "Phchi.S3G313400.t1"; gene_id "Phchi.S3G313400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8495.t1 is derived from g5670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36250976	36251752	.	-	.	Phchi.S1G565400
Phchi.S1	AUGUSTUS	transcript	36250976	36251752	.	-	.	transcript_id "Phchi.S1G565400.t1"; gene_id "Phchi.S1G565400"
Phchi.S1	AUGUSTUS	stop_codon	36250973	36250975	.	-	0	transcript_id "Phchi.S1G565400.t1"; gene_id "Phchi.S1G565400"
Phchi.S1	AUGUSTUS	CDS	36250976	36251752	1	-	0	transcript_id "Phchi.S1G565400.t1"; gene_id "Phchi.S1G565400"
Phchi.S1	AUGUSTUS	exon	36250976	36251752	.	-	.	transcript_id "Phchi.S1G565400.t1"; gene_id "Phchi.S1G565400"
Phchi.S1	AUGUSTUS	start_codon	36251750	36251752	.	-	0	transcript_id "Phchi.S1G565400.t1"; gene_id "Phchi.S1G565400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3766.t1 is derived from g935.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5589842	5598780	.	+	.	Phchi.S1G092500
Phchi.S1	AUGUSTUS	transcript	5589842	5598780	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	start_codon	5589842	5589844	.	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5589842	5589995	0.7	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5589842	5589995	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5589996	5590108	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590109	5590191	1	+	2	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590109	5590191	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590192	5590277	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590278	5590335	1	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590278	5590335	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590336	5590442	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590443	5590492	1	+	2	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590443	5590492	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590493	5590585	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590586	5590670	0.46	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590586	5590670	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590671	5590814	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590815	5590843	0.88	+	2	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590815	5590843	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590844	5590960	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590961	5591029	0.92	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590961	5591029	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5591030	5591170	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5591171	5591543	1	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5591171	5591543	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5591544	5591634	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5591635	5591726	1	+	2	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5591635	5591726	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5591727	5591872	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5591873	5592409	0.99	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5591873	5592409	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5592410	5592485	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5592486	5594487	0.99	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5592486	5594487	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5594488	5594572	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5594573	5595027	0.62	+	2	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5594573	5595027	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5595028	5595152	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5595153	5595413	0.41	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5595153	5595413	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5595414	5595491	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5595492	5595646	1	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5595492	5595646	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5595647	5595736	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5595737	5596325	0.99	+	1	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5595737	5596325	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5596326	5596410	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5596411	5596557	1	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5596411	5596557	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5596558	5596641	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5596642	5596916	0.67	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5596642	5596916	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5596917	5596990	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5596991	5597108	0.68	+	1	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5596991	5597108	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597109	5597183	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597184	5597389	1	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597184	5597389	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597390	5597475	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597476	5597779	1	+	1	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597476	5597779	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597780	5597849	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597850	5597882	0.98	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597850	5597882	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597883	5597950	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597951	5598523	0.92	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597951	5598523	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5598524	5598612	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5598613	5598780	1	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5598613	5598780	.	+	.	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	stop_codon	5598781	5598783	.	+	0	transcript_id "Phchi.S1G092500.t1"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	transcript	5589842	5598780	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	start_codon	5589842	5589844	.	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5589842	5589995	0.69	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5589842	5589995	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5589996	5590108	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590109	5590191	1	+	2	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590109	5590191	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590192	5590277	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590278	5590335	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590278	5590335	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590336	5590442	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590443	5590492	1	+	2	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590443	5590492	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590493	5590585	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590586	5590670	0.42	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590586	5590670	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590671	5590814	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590815	5590843	0.88	+	2	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590815	5590843	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5590844	5590960	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5590961	5591029	0.98	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5590961	5591029	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5591030	5591170	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5591171	5591543	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5591171	5591543	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5591544	5591634	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5591635	5591726	1	+	2	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5591635	5591726	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5591727	5591872	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5591873	5592409	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5591873	5592409	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5592410	5592485	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5592486	5594487	0.99	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5592486	5594487	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5594488	5594572	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5594573	5595027	0.68	+	2	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5594573	5595027	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5595028	5595152	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5595153	5595413	0.44	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5595153	5595413	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5595414	5595491	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5595492	5595646	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5595492	5595646	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5595647	5595736	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5595737	5596325	0.95	+	1	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5595737	5596325	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5596326	5596410	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5596411	5596488	0.78	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5596411	5596488	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5596489	5596641	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5596642	5596916	0.58	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5596642	5596916	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5596917	5596990	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5596991	5597108	0.61	+	1	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5596991	5597108	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597109	5597183	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597184	5597389	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597184	5597389	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597390	5597475	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597476	5597779	1	+	1	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597476	5597779	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597780	5597849	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597850	5597882	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597850	5597882	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5597883	5597950	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5597951	5598523	0.87	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5597951	5598523	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	intron	5598524	5598612	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	CDS	5598613	5598780	1	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	exon	5598613	5598780	.	+	.	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
Phchi.S1	AUGUSTUS	stop_codon	5598781	5598783	.	+	0	transcript_id "Phchi.S1G092500.t2"; gene_id "Phchi.S1G092500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4338.t1 is derived from g1507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9846888	9847986	.	+	.	Phchi.S1G149700
Phchi.S1	AUGUSTUS	transcript	9846888	9847986	.	+	.	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	start_codon	9846888	9846890	.	+	0	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	CDS	9846888	9847138	0.54	+	0	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	exon	9846888	9847138	.	+	.	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	intron	9847139	9847337	.	+	.	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	CDS	9847338	9847986	1	+	1	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	exon	9847338	9847986	.	+	.	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
Phchi.S1	AUGUSTUS	stop_codon	9847987	9847989	.	+	0	transcript_id "Phchi.S1G149700.t1"; gene_id "Phchi.S1G149700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13915.t1 is derived from g12382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9640615	9644584	.	-	.	Phchi.S3G123400
Phchi.S3	AUGUSTUS	transcript	9640615	9644584	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	stop_codon	9640612	9640614	.	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9640615	9640773	1	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9640615	9640773	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9640774	9640853	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9640854	9640988	1	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9640854	9640988	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9640989	9641071	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9641072	9641266	1	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9641072	9641266	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9641267	9641357	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9641358	9641462	1	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9641358	9641462	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9641463	9641561	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9641562	9641669	1	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9641562	9641669	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9641670	9641757	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9641758	9641917	1	-	1	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9641758	9641917	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9641918	9641995	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9641996	9642060	1	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9641996	9642060	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9642061	9642165	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9642166	9642489	0.9	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9642166	9642489	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9642490	9642610	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9642611	9642728	1	-	1	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9642611	9642728	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9642729	9642894	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9642895	9642987	1	-	1	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9642895	9642987	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9642988	9643150	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9643151	9643282	1	-	1	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9643151	9643282	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9643283	9643387	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9643388	9644127	0.92	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9643388	9644127	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9644128	9644204	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9644205	9644262	0.91	-	1	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9644205	9644262	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	intron	9644263	9644360	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	CDS	9644361	9644584	0.86	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	exon	9644361	9644584	.	-	.	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
Phchi.S3	AUGUSTUS	start_codon	9644582	9644584	.	-	0	transcript_id "Phchi.S3G123400.t1"; gene_id "Phchi.S3G123400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10792.t1 is derived from g14842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2137012	2139447	.	-	.	Phchi.S4G037400
Phchi.S4	AUGUSTUS	transcript	2137012	2139447	.	-	.	transcript_id "Phchi.S4G037400.t1"; gene_id "Phchi.S4G037400"
Phchi.S4	AUGUSTUS	stop_codon	2137009	2137011	.	-	0	transcript_id "Phchi.S4G037400.t1"; gene_id "Phchi.S4G037400"
Phchi.S4	AUGUSTUS	CDS	2137012	2139447	1	-	0	transcript_id "Phchi.S4G037400.t1"; gene_id "Phchi.S4G037400"
Phchi.S4	AUGUSTUS	exon	2137012	2139447	.	-	.	transcript_id "Phchi.S4G037400.t1"; gene_id "Phchi.S4G037400"
Phchi.S4	AUGUSTUS	start_codon	2139445	2139447	.	-	0	transcript_id "Phchi.S4G037400.t1"; gene_id "Phchi.S4G037400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg489.t1 is derived from g10271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3414188	3417455	.	+	.	Phchi.S6G044800
Phchi.S6	AUGUSTUS	transcript	3414188	3417455	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	start_codon	3414188	3414190	.	+	0	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	CDS	3414188	3414344	0.52	+	0	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	exon	3414188	3414344	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	intron	3414345	3414437	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	CDS	3414438	3414526	1	+	2	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	exon	3414438	3414526	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	intron	3414527	3414609	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	CDS	3414610	3414821	1	+	0	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	exon	3414610	3414821	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	intron	3414822	3414950	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	CDS	3414951	3415351	0.53	+	1	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	exon	3414951	3415351	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	intron	3415352	3415452	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	CDS	3415453	3417455	0.55	+	2	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	exon	3415453	3417455	.	+	.	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
Phchi.S6	AUGUSTUS	stop_codon	3417456	3417458	.	+	0	transcript_id "Phchi.S6G044800.t1"; gene_id "Phchi.S6G044800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9163.t1 is derived from g6338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40159833	40161688	.	-	.	Phchi.S1G632200
Phchi.S1	AUGUSTUS	transcript	40159833	40161688	.	-	.	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	stop_codon	40159830	40159832	.	-	0	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	CDS	40159833	40161244	0.92	-	2	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	exon	40159833	40161244	.	-	.	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	intron	40161245	40161348	.	-	.	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	CDS	40161349	40161688	0.52	-	0	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	exon	40161349	40161688	.	-	.	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
Phchi.S1	AUGUSTUS	start_codon	40161686	40161688	.	-	0	transcript_id "Phchi.S1G632200.t1"; gene_id "Phchi.S1G632200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4493.t1 is derived from g1663.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10800887	10803296	.	-	.	Phchi.S1G165200
Phchi.S1	AUGUSTUS	transcript	10800887	10803296	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	stop_codon	10800884	10800886	.	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10800887	10800911	1	-	1	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10800887	10800911	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10800912	10800995	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10800996	10801105	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10800996	10801105	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801106	10801182	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801183	10801224	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801183	10801224	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801225	10801324	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801325	10801426	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801325	10801426	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801427	10801513	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801514	10801612	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801514	10801612	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801613	10801689	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801690	10801750	1	-	1	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801690	10801750	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801751	10801832	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801833	10801954	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801833	10801954	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801955	10802037	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802038	10802123	1	-	2	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802038	10802123	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802124	10802233	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802234	10802318	0.94	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802234	10802318	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802319	10802400	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802401	10802484	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802401	10802484	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802485	10802568	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802569	10802645	1	-	2	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802569	10802645	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802646	10802739	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802740	10802803	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802740	10802803	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802804	10802886	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802887	10802955	1	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802887	10802955	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802956	10803060	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10803061	10803144	0.98	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10803061	10803144	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10803145	10803245	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10803246	10803296	0.84	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10803246	10803296	.	-	.	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	start_codon	10803294	10803296	.	-	0	transcript_id "Phchi.S1G165200.t1"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	transcript	10800887	10803296	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	stop_codon	10800884	10800886	.	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10800887	10800911	1	-	1	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10800887	10800911	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10800912	10800995	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10800996	10801105	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10800996	10801105	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801106	10801182	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801183	10801224	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801183	10801224	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801225	10801324	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801325	10801426	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801325	10801426	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801427	10801513	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801514	10801612	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801514	10801612	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801613	10801689	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801690	10801750	1	-	1	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801690	10801750	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801751	10801832	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10801833	10801954	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10801833	10801954	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10801955	10802037	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802038	10802123	1	-	2	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802038	10802123	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802124	10802233	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802234	10802318	0.94	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802234	10802318	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802319	10802400	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802401	10802484	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802401	10802484	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802485	10802568	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802569	10802645	1	-	2	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802569	10802645	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802646	10802739	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802740	10802803	1	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802740	10802803	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802804	10802886	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10802887	10802955	0.99	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10802887	10802955	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10802956	10803060	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10803061	10803147	0.85	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10803061	10803147	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	intron	10803148	10803245	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	CDS	10803246	10803296	0.89	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	exon	10803246	10803296	.	-	.	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
Phchi.S1	AUGUSTUS	start_codon	10803294	10803296	.	-	0	transcript_id "Phchi.S1G165200.t2"; gene_id "Phchi.S1G165200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4163.t1 is derived from g1332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8698460	8699218	.	+	.	Phchi.S1G132200
Phchi.S1	AUGUSTUS	transcript	8698460	8699218	.	+	.	transcript_id "Phchi.S1G132200.t1"; gene_id "Phchi.S1G132200"
Phchi.S1	AUGUSTUS	start_codon	8698460	8698462	.	+	0	transcript_id "Phchi.S1G132200.t1"; gene_id "Phchi.S1G132200"
Phchi.S1	AUGUSTUS	CDS	8698460	8699218	1	+	0	transcript_id "Phchi.S1G132200.t1"; gene_id "Phchi.S1G132200"
Phchi.S1	AUGUSTUS	exon	8698460	8699218	.	+	.	transcript_id "Phchi.S1G132200.t1"; gene_id "Phchi.S1G132200"
Phchi.S1	AUGUSTUS	stop_codon	8699219	8699221	.	+	0	transcript_id "Phchi.S1G132200.t1"; gene_id "Phchi.S1G132200"
# This transcript jg9328.t2 is derived from g6503.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9328.t3 is derived from g6503.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9329.t1 is derived from g6504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40960275	40961648	.	-	.	Phchi.S1G648800
Phchi.S1	AUGUSTUS	transcript	40960275	40961648	.	-	.	transcript_id "Phchi.S1G648800.t1"; gene_id "Phchi.S1G648800"
Phchi.S1	AUGUSTUS	stop_codon	40960272	40960274	.	-	0	transcript_id "Phchi.S1G648800.t1"; gene_id "Phchi.S1G648800"
Phchi.S1	AUGUSTUS	CDS	40960275	40961648	0.92	-	0	transcript_id "Phchi.S1G648800.t1"; gene_id "Phchi.S1G648800"
Phchi.S1	AUGUSTUS	exon	40960275	40961648	.	-	.	transcript_id "Phchi.S1G648800.t1"; gene_id "Phchi.S1G648800"
Phchi.S1	AUGUSTUS	start_codon	40961646	40961648	.	-	0	transcript_id "Phchi.S1G648800.t1"; gene_id "Phchi.S1G648800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13877.t1 is derived from g12344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9430456	9432395	.	+	.	Phchi.S3G119600
Phchi.S3	AUGUSTUS	transcript	9430456	9432395	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	start_codon	9430456	9430458	.	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9430456	9430623	0.95	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9430456	9430623	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9430624	9430773	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9430774	9430882	1	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9430774	9430882	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9430883	9430969	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9430970	9431085	1	+	2	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9430970	9431085	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9431086	9431242	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9431243	9431368	1	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9431243	9431368	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9431369	9431494	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9431495	9431615	1	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9431495	9431615	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9431616	9431700	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9431701	9431785	1	+	2	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9431701	9431785	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9431786	9431880	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9431881	9431994	0.99	+	1	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9431881	9431994	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9431995	9432111	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9432112	9432151	0.95	+	1	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9432112	9432151	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	intron	9432152	9432242	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	CDS	9432243	9432395	0.95	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	exon	9432243	9432395	.	+	.	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
Phchi.S3	AUGUSTUS	stop_codon	9432396	9432398	.	+	0	transcript_id "Phchi.S3G119600.t1"; gene_id "Phchi.S3G119600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5620.t1 is derived from g2790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17918155	17918766	.	-	.	Phchi.S1G277900
Phchi.S1	AUGUSTUS	transcript	17918155	17918766	.	-	.	transcript_id "Phchi.S1G277900.t1"; gene_id "Phchi.S1G277900"
Phchi.S1	AUGUSTUS	stop_codon	17918152	17918154	.	-	0	transcript_id "Phchi.S1G277900.t1"; gene_id "Phchi.S1G277900"
Phchi.S1	AUGUSTUS	CDS	17918155	17918766	0.75	-	0	transcript_id "Phchi.S1G277900.t1"; gene_id "Phchi.S1G277900"
Phchi.S1	AUGUSTUS	exon	17918155	17918766	.	-	.	transcript_id "Phchi.S1G277900.t1"; gene_id "Phchi.S1G277900"
Phchi.S1	AUGUSTUS	start_codon	17918764	17918766	.	-	0	transcript_id "Phchi.S1G277900.t1"; gene_id "Phchi.S1G277900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg980.t1 is derived from g10763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6830018	6830909	.	+	.	Phchi.S6G093900
Phchi.S6	AUGUSTUS	transcript	6830018	6830909	.	+	.	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	start_codon	6830018	6830020	.	+	0	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	CDS	6830018	6830240	0.56	+	0	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	exon	6830018	6830240	.	+	.	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	intron	6830241	6830443	.	+	.	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	CDS	6830444	6830520	0.88	+	2	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	exon	6830444	6830520	.	+	.	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	intron	6830521	6830621	.	+	.	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	CDS	6830622	6830909	0.98	+	0	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	exon	6830622	6830909	.	+	.	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
Phchi.S6	AUGUSTUS	stop_codon	6830910	6830912	.	+	0	transcript_id "Phchi.S6G093900.t1"; gene_id "Phchi.S6G093900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13903.t1 is derived from g12370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9596309	9599899	.	-	.	Phchi.S3G122200
Phchi.S3	AUGUSTUS	transcript	9596309	9599899	.	-	.	transcript_id "Phchi.S3G122200.t1"; gene_id "Phchi.S3G122200"
Phchi.S3	AUGUSTUS	stop_codon	9596306	9596308	.	-	0	transcript_id "Phchi.S3G122200.t1"; gene_id "Phchi.S3G122200"
Phchi.S3	AUGUSTUS	CDS	9596309	9599899	0.9	-	0	transcript_id "Phchi.S3G122200.t1"; gene_id "Phchi.S3G122200"
Phchi.S3	AUGUSTUS	exon	9596309	9599899	.	-	.	transcript_id "Phchi.S3G122200.t1"; gene_id "Phchi.S3G122200"
Phchi.S3	AUGUSTUS	start_codon	9599897	9599899	.	-	0	transcript_id "Phchi.S3G122200.t1"; gene_id "Phchi.S3G122200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9507.t1 is derived from g6683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42113832	42116298	.	+	.	Phchi.S1G666600
Phchi.S1	AUGUSTUS	transcript	42113832	42116298	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	start_codon	42113832	42113834	.	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42113832	42113902	0.92	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42113832	42113902	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42113903	42114112	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42114113	42114152	1	+	1	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42114113	42114152	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42114153	42114482	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42114483	42114492	0.73	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42114483	42114492	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42114493	42114554	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42114555	42114585	0.98	+	2	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42114555	42114585	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42114586	42114682	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42114683	42114731	0.98	+	1	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42114683	42114731	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42114732	42114847	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42114848	42114954	0.98	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42114848	42114954	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42114955	42115061	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42115062	42115149	1	+	1	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42115062	42115149	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42115150	42115232	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42115233	42115436	1	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42115233	42115436	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42115437	42115523	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42115524	42115577	1	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42115524	42115577	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42115578	42115685	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42115686	42115723	1	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42115686	42115723	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42115724	42115810	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42115811	42115970	1	+	1	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42115811	42115970	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42115971	42116049	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42116050	42116110	1	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42116050	42116110	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	intron	42116111	42116206	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	CDS	42116207	42116298	1	+	2	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	exon	42116207	42116298	.	+	.	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
Phchi.S1	AUGUSTUS	stop_codon	42116299	42116301	.	+	0	transcript_id "Phchi.S1G666600.t1"; gene_id "Phchi.S1G666600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13043.t1 is derived from g11508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3853822	3854961	.	-	.	Phchi.S3G036200
Phchi.S3	AUGUSTUS	transcript	3853822	3854961	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	stop_codon	3853819	3853821	.	-	0	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	CDS	3853822	3853831	1	-	1	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	exon	3853822	3853831	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	intron	3853832	3854021	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	CDS	3854022	3854256	0.46	-	2	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	exon	3854022	3854256	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	intron	3854257	3854436	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	CDS	3854437	3854686	0.47	-	0	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	exon	3854437	3854686	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	intron	3854687	3854775	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	CDS	3854776	3854961	0.3	-	0	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	exon	3854776	3854961	.	-	.	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
Phchi.S3	AUGUSTUS	start_codon	3854959	3854961	.	-	0	transcript_id "Phchi.S3G036200.t1"; gene_id "Phchi.S3G036200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15327.t1 is derived from g13795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18401429	18402361	.	-	.	Phchi.S3G264600
Phchi.S3	AUGUSTUS	transcript	18401429	18402361	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	stop_codon	18401426	18401428	.	-	0	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	CDS	18401429	18401569	1	-	0	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	exon	18401429	18401569	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	intron	18401570	18401664	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	CDS	18401665	18401745	1	-	0	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	exon	18401665	18401745	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	intron	18401746	18401851	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	CDS	18401852	18401974	1	-	0	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	exon	18401852	18401974	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	intron	18401975	18402082	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	CDS	18402083	18402361	0.96	-	0	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	exon	18402083	18402361	.	-	.	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
Phchi.S3	AUGUSTUS	start_codon	18402359	18402361	.	-	0	transcript_id "Phchi.S3G264600.t1"; gene_id "Phchi.S3G264600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5056.t1 is derived from g2226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14422851	14424214	.	+	.	Phchi.S1G221500
Phchi.S1	AUGUSTUS	transcript	14422851	14424214	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	start_codon	14422851	14422853	.	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14422851	14422869	0.88	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14422851	14422869	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14422870	14422946	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14422947	14423136	1	+	2	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14422947	14423136	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14423137	14423210	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14423211	14423298	1	+	1	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14423211	14423298	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14423299	14423398	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14423399	14423462	1	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14423399	14423462	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14423463	14423521	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14423522	14423627	1	+	2	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14423522	14423627	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14423628	14423716	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14423717	14423771	1	+	1	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14423717	14423771	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14423772	14423857	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14423858	14423911	1	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14423858	14423911	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14423912	14423993	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14423994	14424080	1	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14423994	14424080	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	intron	14424081	14424157	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	CDS	14424158	14424214	1	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	exon	14424158	14424214	.	+	.	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
Phchi.S1	AUGUSTUS	stop_codon	14424215	14424217	.	+	0	transcript_id "Phchi.S1G221500.t1"; gene_id "Phchi.S1G221500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14141.t1 is derived from g12608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11109117	11112410	.	+	.	Phchi.S3G146000
Phchi.S3	AUGUSTUS	transcript	11109117	11112410	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	start_codon	11109117	11109119	.	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11109117	11109158	0.76	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11109117	11109158	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11109159	11109239	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11109240	11109317	1	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11109240	11109317	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11109318	11109405	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11109406	11109488	1	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11109406	11109488	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11109489	11109583	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11109584	11109685	1	+	1	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11109584	11109685	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11109686	11109776	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11109777	11110038	1	+	1	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11109777	11110038	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11110039	11110177	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11110178	11110282	1	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11110178	11110282	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11110283	11110452	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11110453	11110553	1	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11110453	11110553	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11110554	11110631	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11110632	11110770	1	+	1	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11110632	11110770	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11110771	11110863	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11110864	11110976	1	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11110864	11110976	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11110977	11111134	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11111135	11111628	0.71	+	1	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11111135	11111628	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	intron	11111629	11111742	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	CDS	11111743	11112410	0.88	+	2	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	exon	11111743	11112410	.	+	.	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
Phchi.S3	AUGUSTUS	stop_codon	11112411	11112413	.	+	0	transcript_id "Phchi.S3G146000.t1"; gene_id "Phchi.S3G146000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11353.t1 is derived from g15403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5711844	5713645	.	-	.	Phchi.S4G093500
Phchi.S4	AUGUSTUS	transcript	5711844	5713645	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	stop_codon	5711841	5711843	.	-	0	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	CDS	5711844	5712699	1	-	1	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	exon	5711844	5712699	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	intron	5712700	5712796	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	CDS	5712797	5713020	0.99	-	0	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	exon	5712797	5713020	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	intron	5713021	5713110	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	CDS	5713111	5713380	1	-	0	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	exon	5713111	5713380	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	intron	5713381	5713540	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	CDS	5713541	5713645	1	-	0	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	exon	5713541	5713645	.	-	.	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
Phchi.S4	AUGUSTUS	start_codon	5713643	5713645	.	-	0	transcript_id "Phchi.S4G093500.t1"; gene_id "Phchi.S4G093500"
# This transcript jg10910.t2 is derived from g14960.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10911.t1 is derived from g14961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2898224	2899590	.	+	.	Phchi.S4G049300
Phchi.S4	AUGUSTUS	transcript	2898224	2899590	.	+	.	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	start_codon	2898224	2898226	.	+	0	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	CDS	2898224	2898934	0.39	+	0	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	exon	2898224	2898934	.	+	.	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	intron	2898935	2899008	.	+	.	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	CDS	2899009	2899590	1	+	0	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	exon	2899009	2899590	.	+	.	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
Phchi.S4	AUGUSTUS	stop_codon	2899591	2899593	.	+	0	transcript_id "Phchi.S4G049300.t1"; gene_id "Phchi.S4G049300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15769.t1 is derived from g14239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21270368	21272799	.	-	.	Phchi.S3G308800
Phchi.S3	AUGUSTUS	transcript	21270368	21272799	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	stop_codon	21270365	21270367	.	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21270368	21270535	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21270368	21270535	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21270536	21270620	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21270621	21270669	1	-	1	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21270621	21270669	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21270670	21270765	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21270766	21270820	1	-	2	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21270766	21270820	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21270821	21270909	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21270910	21271030	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21270910	21271030	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21271031	21271135	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21271136	21271173	0.99	-	2	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21271136	21271173	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21271174	21271263	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21271264	21271327	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21271264	21271327	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21271328	21271400	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21271401	21271508	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21271401	21271508	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21271509	21271599	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21271600	21271695	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21271600	21271695	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21271696	21271777	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21271778	21271899	1	-	2	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21271778	21271899	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21271900	21272004	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21272005	21272077	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21272005	21272077	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21272078	21272166	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21272167	21272243	1	-	2	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21272167	21272243	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21272244	21272319	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21272320	21272638	1	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21272320	21272638	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	intron	21272639	21272787	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	CDS	21272788	21272799	0.92	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	exon	21272788	21272799	.	-	.	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
Phchi.S3	AUGUSTUS	start_codon	21272797	21272799	.	-	0	transcript_id "Phchi.S3G308800.t1"; gene_id "Phchi.S3G308800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9681.t1 is derived from g6857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43259691	43261402	.	+	.	Phchi.S1G684000
Phchi.S1	AUGUSTUS	transcript	43259691	43261402	.	+	.	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	start_codon	43259691	43259693	.	+	0	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	CDS	43259691	43260803	0.14	+	0	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	exon	43259691	43260803	.	+	.	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	intron	43260804	43261339	.	+	.	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	CDS	43261340	43261402	0.93	+	0	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	exon	43261340	43261402	.	+	.	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
Phchi.S1	AUGUSTUS	stop_codon	43261403	43261405	.	+	0	transcript_id "Phchi.S1G684000.t1"; gene_id "Phchi.S1G684000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4342.t1 is derived from g1511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9860065	9861180	.	-	.	Phchi.S1G150100
Phchi.S1	AUGUSTUS	transcript	9860065	9861180	.	-	.	transcript_id "Phchi.S1G150100.t1"; gene_id "Phchi.S1G150100"
Phchi.S1	AUGUSTUS	stop_codon	9860062	9860064	.	-	0	transcript_id "Phchi.S1G150100.t1"; gene_id "Phchi.S1G150100"
Phchi.S1	AUGUSTUS	CDS	9860065	9861180	0.55	-	0	transcript_id "Phchi.S1G150100.t1"; gene_id "Phchi.S1G150100"
Phchi.S1	AUGUSTUS	exon	9860065	9861180	.	-	.	transcript_id "Phchi.S1G150100.t1"; gene_id "Phchi.S1G150100"
Phchi.S1	AUGUSTUS	start_codon	9861178	9861180	.	-	0	transcript_id "Phchi.S1G150100.t1"; gene_id "Phchi.S1G150100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9332.t1 is derived from g6507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40966991	40967224	.	+	.	Phchi.S1G649100
Phchi.S1	AUGUSTUS	transcript	40966991	40967224	.	+	.	transcript_id "Phchi.S1G649100.t1"; gene_id "Phchi.S1G649100"
Phchi.S1	AUGUSTUS	start_codon	40966991	40966993	.	+	0	transcript_id "Phchi.S1G649100.t1"; gene_id "Phchi.S1G649100"
Phchi.S1	AUGUSTUS	CDS	40966991	40967224	0.99	+	0	transcript_id "Phchi.S1G649100.t1"; gene_id "Phchi.S1G649100"
Phchi.S1	AUGUSTUS	exon	40966991	40967224	.	+	.	transcript_id "Phchi.S1G649100.t1"; gene_id "Phchi.S1G649100"
Phchi.S1	AUGUSTUS	stop_codon	40967225	40967227	.	+	0	transcript_id "Phchi.S1G649100.t1"; gene_id "Phchi.S1G649100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12393.t1 is derived from g8070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	16810320	16810778	.	-	.	Phchi.S2G047300
Phchi.S2	AUGUSTUS	transcript	16810320	16810778	.	-	.	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	stop_codon	16810317	16810319	.	-	0	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	CDS	16810320	16810571	0.01	-	0	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	exon	16810320	16810571	.	-	.	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	intron	16810572	16810694	.	-	.	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	CDS	16810695	16810778	0.01	-	0	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	exon	16810695	16810778	.	-	.	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
Phchi.S2	AUGUSTUS	start_codon	16810776	16810778	.	-	0	transcript_id "Phchi.S2G047300.t1"; gene_id "Phchi.S2G047300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4187.t1 is derived from g1356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8821448	8822086	.	-	.	Phchi.S1G134600
Phchi.S1	AUGUSTUS	transcript	8821448	8822086	.	-	.	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	stop_codon	8821445	8821447	.	-	0	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	CDS	8821448	8821480	0.76	-	0	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	exon	8821448	8821480	.	-	.	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	intron	8821481	8821616	.	-	.	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	CDS	8821617	8821830	0.76	-	1	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	exon	8821617	8821830	.	-	.	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	intron	8821831	8822018	.	-	.	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	CDS	8822019	8822086	0.98	-	0	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	exon	8822019	8822086	.	-	.	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
Phchi.S1	AUGUSTUS	start_codon	8822084	8822086	.	-	0	transcript_id "Phchi.S1G134600.t1"; gene_id "Phchi.S1G134600"
# This transcript jg2326.t2 is derived from g9246.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2327.t1 is derived from g9247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6195056	6195534	.	+	.	Phchi.S5G093600
Phchi.S5	AUGUSTUS	transcript	6195056	6195534	.	+	.	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	start_codon	6195056	6195058	.	+	0	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	CDS	6195056	6195355	0.94	+	0	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	exon	6195056	6195355	.	+	.	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	intron	6195356	6195438	.	+	.	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	CDS	6195439	6195534	1	+	0	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	exon	6195439	6195534	.	+	.	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
Phchi.S5	AUGUSTUS	stop_codon	6195535	6195537	.	+	0	transcript_id "Phchi.S5G093600.t1"; gene_id "Phchi.S5G093600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9033.t1 is derived from g6208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39228968	39232233	.	+	.	Phchi.S1G619200
Phchi.S1	AUGUSTUS	transcript	39228968	39232233	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	start_codon	39228968	39228970	.	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39228968	39229072	0.59	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39228968	39229072	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39229073	39229213	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39229214	39229287	0.93	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39229214	39229287	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39229288	39229429	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39229430	39229559	0.99	+	1	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39229430	39229559	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39229560	39229808	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39229809	39229872	1	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39229809	39229872	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39229873	39230070	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39230071	39230138	1	+	2	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39230071	39230138	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39230139	39230299	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39230300	39230388	1	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39230300	39230388	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39230389	39230487	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39230488	39230668	1	+	1	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39230488	39230668	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39230669	39230798	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39230799	39230927	1	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39230799	39230927	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39230928	39231014	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39231015	39231148	1	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39231015	39231148	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39231149	39231230	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39231231	39231444	1	+	1	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39231231	39231444	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39231445	39231542	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39231543	39231727	1	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39231543	39231727	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39231728	39231809	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39231810	39231905	0.99	+	1	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39231810	39231905	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	intron	39231906	39232007	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	CDS	39232008	39232233	0.96	+	1	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	exon	39232008	39232233	.	+	.	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
Phchi.S1	AUGUSTUS	stop_codon	39232234	39232236	.	+	0	transcript_id "Phchi.S1G619200.t1"; gene_id "Phchi.S1G619200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2714.t1 is derived from g9634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8306440	8307207	.	-	.	Phchi.S5G132300
Phchi.S5	AUGUSTUS	transcript	8306440	8307207	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	stop_codon	8306437	8306439	.	-	0	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	CDS	8306440	8306502	0.99	-	0	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	exon	8306440	8306502	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	intron	8306503	8306588	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	CDS	8306589	8306801	1	-	0	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	exon	8306589	8306801	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	intron	8306802	8306910	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	CDS	8306911	8306991	1	-	0	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	exon	8306911	8306991	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	intron	8306992	8307093	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	CDS	8307094	8307207	0.58	-	0	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	exon	8307094	8307207	.	-	.	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
Phchi.S5	AUGUSTUS	start_codon	8307205	8307207	.	-	0	transcript_id "Phchi.S5G132300.t1"; gene_id "Phchi.S5G132300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15783.t1 is derived from g14253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21319284	21324320	.	-	.	Phchi.S3G310200
Phchi.S3	AUGUSTUS	transcript	21319284	21324320	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	stop_codon	21319281	21319283	.	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21319284	21319499	0.9	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21319284	21319499	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21319500	21319577	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21319578	21319841	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21319578	21319841	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21319842	21320064	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21320065	21320157	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21320065	21320157	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21320158	21320285	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21320286	21320480	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21320286	21320480	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21320481	21320687	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21320688	21320786	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21320688	21320786	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21320787	21321279	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21321280	21321528	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21321280	21321528	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21321529	21321612	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21321613	21321816	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21321613	21321816	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21321817	21321962	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21321963	21322022	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21321963	21322022	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21322023	21322192	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21322193	21322375	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21322193	21322375	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21322376	21322490	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21322491	21323093	0.92	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21322491	21323093	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21323094	21323177	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21323178	21323267	1	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21323178	21323267	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21323268	21323356	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21323357	21324092	0.68	-	1	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21323357	21324092	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21324093	21324175	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21324176	21324199	0.87	-	1	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21324176	21324199	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	intron	21324200	21324297	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	CDS	21324298	21324320	0.99	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	exon	21324298	21324320	.	-	.	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
Phchi.S3	AUGUSTUS	start_codon	21324318	21324320	.	-	0	transcript_id "Phchi.S3G310200.t1"; gene_id "Phchi.S3G310200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg18.t1 is derived from g16028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C11	AUGUSTUS	gene	20630	24176	.	+	.	Phchi.C11G000200
Phchi.C11	AUGUSTUS	transcript	20630	24176	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	start_codon	20630	20632	.	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	20630	20687	0.52	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	20630	20687	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	20688	20835	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	20836	20908	1	+	2	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	20836	20908	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	20909	20988	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	20989	21090	1	+	1	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	20989	21090	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	21091	21174	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	21175	21205	1	+	1	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	21175	21205	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	21206	21370	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	21371	21427	1	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	21371	21427	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	21428	21554	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	21555	21650	1	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	21555	21650	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	21651	21872	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	21873	21995	1	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	21873	21995	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	21996	22172	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	22173	22277	0.97	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	22173	22277	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	22278	22358	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	22359	22431	0.97	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	22359	22431	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	22432	22640	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	22641	22770	1	+	2	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	22641	22770	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	22771	22921	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	22922	23024	1	+	1	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	22922	23024	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	23025	23122	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	23123	23185	1	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	23123	23185	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	23186	23274	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	23275	23355	1	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	23275	23355	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	23356	23505	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	23506	23569	1	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	23506	23569	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	23570	23695	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	23696	23808	0.95	+	2	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	23696	23808	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	intron	23809	23909	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	CDS	23910	24176	0.93	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	exon	23910	24176	.	+	.	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
Phchi.C11	AUGUSTUS	stop_codon	24177	24179	.	+	0	transcript_id "Phchi.C11G000200.t1"; gene_id "Phchi.C11G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2884.t1 is derived from g53.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	266663	271601	.	-	.	Phchi.S1G004300
Phchi.S1	AUGUSTUS	transcript	266663	271601	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	stop_codon	266660	266662	.	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	266663	266817	0.98	-	2	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	266663	266817	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	266818	266907	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	266908	267012	0.89	-	2	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	266908	267012	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	267013	267205	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	267206	267596	0.81	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	267206	267596	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	267597	267700	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	267701	267826	0.5	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	267701	267826	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	267827	267912	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	267913	270738	0.89	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	267913	270738	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	270739	270815	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	270816	270974	0.93	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	270816	270974	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	270975	271193	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	271194	271205	0.73	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	271194	271205	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	intron	271206	271577	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	CDS	271578	271601	0.96	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	exon	271578	271601	.	-	.	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
Phchi.S1	AUGUSTUS	start_codon	271599	271601	.	-	0	transcript_id "Phchi.S1G004300.t1"; gene_id "Phchi.S1G004300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15223.t1 is derived from g13691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17813191	17814436	.	-	.	Phchi.S3G254200
Phchi.S3	AUGUSTUS	transcript	17813191	17814436	.	-	.	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	stop_codon	17813188	17813190	.	-	0	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	CDS	17813191	17813779	0.93	-	1	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	exon	17813191	17813779	.	-	.	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	intron	17813780	17813931	.	-	.	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	CDS	17813932	17814240	0.7	-	1	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	exon	17813932	17814240	.	-	.	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	intron	17814241	17814347	.	-	.	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	CDS	17814348	17814436	0.8	-	0	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	exon	17814348	17814436	.	-	.	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
Phchi.S3	AUGUSTUS	start_codon	17814434	17814436	.	-	0	transcript_id "Phchi.S3G254200.t1"; gene_id "Phchi.S3G254200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7638.t1 is derived from g4812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30356266	30359816	.	-	.	Phchi.S1G479700
Phchi.S1	AUGUSTUS	transcript	30356266	30359816	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	stop_codon	30356263	30356265	.	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30356266	30356647	0.67	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30356266	30356647	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30356648	30356738	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30356739	30356878	1	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30356739	30356878	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30356879	30356976	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30356977	30357388	1	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30356977	30357388	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30357389	30357485	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30357486	30357587	1	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30357486	30357587	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30357588	30357662	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30357663	30357788	1	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30357663	30357788	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30357789	30357890	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30357891	30357929	0.99	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30357891	30357929	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30357930	30358035	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30358036	30358148	0.99	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30358036	30358148	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30358149	30358336	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30358337	30358402	0.75	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30358337	30358402	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30358403	30358517	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30358518	30358594	1	-	2	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30358518	30358594	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30358595	30358756	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30358757	30358911	0.99	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30358757	30358911	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30358912	30359131	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30359132	30359146	0.97	-	1	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30359132	30359146	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30359147	30359298	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30359299	30359480	0.99	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30359299	30359480	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	intron	30359481	30359654	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	CDS	30359655	30359816	0.97	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	exon	30359655	30359816	.	-	.	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
Phchi.S1	AUGUSTUS	start_codon	30359814	30359816	.	-	0	transcript_id "Phchi.S1G479700.t1"; gene_id "Phchi.S1G479700"
# This transcript jg11708.t2 is derived from g15759.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11709.t1 is derived from g15760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7786033	7787245	.	+	.	Phchi.S4G129100
Phchi.S4	AUGUSTUS	transcript	7786033	7787245	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	start_codon	7786033	7786035	.	+	0	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	CDS	7786033	7786153	1	+	0	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	exon	7786033	7786153	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	intron	7786154	7786743	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	CDS	7786744	7786856	1	+	2	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	exon	7786744	7786856	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	intron	7786857	7787019	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	CDS	7787020	7787062	1	+	0	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	exon	7787020	7787062	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	intron	7787063	7787207	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	CDS	7787208	7787245	1	+	2	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	exon	7787208	7787245	.	+	.	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
Phchi.S4	AUGUSTUS	stop_codon	7787246	7787248	.	+	0	transcript_id "Phchi.S4G129100.t1"; gene_id "Phchi.S4G129100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4339.t1 is derived from g1508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9854119	9856067	.	+	.	Phchi.S1G149800
Phchi.S1	AUGUSTUS	transcript	9854119	9856067	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	start_codon	9854119	9854121	.	+	0	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	CDS	9854119	9854392	0.88	+	0	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	exon	9854119	9854392	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	intron	9854393	9854506	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	CDS	9854507	9854705	0.87	+	2	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	exon	9854507	9854705	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	intron	9854706	9854824	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	CDS	9854825	9855122	0.99	+	1	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	exon	9854825	9855122	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	intron	9855123	9855226	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	CDS	9855227	9855506	0.83	+	0	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	exon	9855227	9855506	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	intron	9855507	9855615	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	CDS	9855616	9856067	0.83	+	2	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	exon	9855616	9856067	.	+	.	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
Phchi.S1	AUGUSTUS	stop_codon	9856068	9856070	.	+	0	transcript_id "Phchi.S1G149800.t1"; gene_id "Phchi.S1G149800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4136.t1 is derived from g1305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8461530	8463842	.	+	.	Phchi.S1G129500
Phchi.S1	AUGUSTUS	transcript	8461530	8463842	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	start_codon	8461530	8461532	.	+	0	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	CDS	8461530	8462178	0.6	+	0	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	exon	8461530	8462178	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	intron	8462179	8462252	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	CDS	8462253	8462606	1	+	2	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	exon	8462253	8462606	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	intron	8462607	8462704	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	CDS	8462705	8462791	1	+	2	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	exon	8462705	8462791	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	intron	8462792	8462905	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	CDS	8462906	8463098	0.97	+	2	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	exon	8462906	8463098	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	intron	8463099	8463220	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	CDS	8463221	8463353	0.93	+	1	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	exon	8463221	8463353	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	intron	8463354	8463482	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	CDS	8463483	8463842	1	+	0	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	exon	8463483	8463842	.	+	.	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
Phchi.S1	AUGUSTUS	stop_codon	8463843	8463845	.	+	0	transcript_id "Phchi.S1G129500.t1"; gene_id "Phchi.S1G129500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2541.t1 is derived from g9461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7234844	7235440	.	+	.	Phchi.S5G115000
Phchi.S5	AUGUSTUS	transcript	7234844	7235440	.	+	.	transcript_id "Phchi.S5G115000.t1"; gene_id "Phchi.S5G115000"
Phchi.S5	AUGUSTUS	start_codon	7234844	7234846	.	+	0	transcript_id "Phchi.S5G115000.t1"; gene_id "Phchi.S5G115000"
Phchi.S5	AUGUSTUS	CDS	7234844	7235440	0.91	+	0	transcript_id "Phchi.S5G115000.t1"; gene_id "Phchi.S5G115000"
Phchi.S5	AUGUSTUS	exon	7234844	7235440	.	+	.	transcript_id "Phchi.S5G115000.t1"; gene_id "Phchi.S5G115000"
Phchi.S5	AUGUSTUS	stop_codon	7235441	7235443	.	+	0	transcript_id "Phchi.S5G115000.t1"; gene_id "Phchi.S5G115000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3002.t1 is derived from g171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1083595	1085535	.	-	.	Phchi.S1G016100
Phchi.S1	AUGUSTUS	transcript	1083595	1085535	.	-	.	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	stop_codon	1083592	1083594	.	-	0	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	CDS	1083595	1083632	1	-	2	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	exon	1083595	1083632	.	-	.	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	intron	1083633	1083711	.	-	.	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	CDS	1083712	1085080	1	-	0	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	exon	1083712	1085080	.	-	.	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	intron	1085081	1085169	.	-	.	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	CDS	1085170	1085535	0.35	-	0	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	exon	1085170	1085535	.	-	.	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
Phchi.S1	AUGUSTUS	start_codon	1085533	1085535	.	-	0	transcript_id "Phchi.S1G016100.t1"; gene_id "Phchi.S1G016100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5987.t1 is derived from g3158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20267588	20268841	.	+	.	Phchi.S1G314600
Phchi.S1	AUGUSTUS	transcript	20267588	20268841	.	+	.	transcript_id "Phchi.S1G314600.t1"; gene_id "Phchi.S1G314600"
Phchi.S1	AUGUSTUS	start_codon	20267588	20267590	.	+	0	transcript_id "Phchi.S1G314600.t1"; gene_id "Phchi.S1G314600"
Phchi.S1	AUGUSTUS	CDS	20267588	20268841	0.88	+	0	transcript_id "Phchi.S1G314600.t1"; gene_id "Phchi.S1G314600"
Phchi.S1	AUGUSTUS	exon	20267588	20268841	.	+	.	transcript_id "Phchi.S1G314600.t1"; gene_id "Phchi.S1G314600"
Phchi.S1	AUGUSTUS	stop_codon	20268842	20268844	.	+	0	transcript_id "Phchi.S1G314600.t1"; gene_id "Phchi.S1G314600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2140.t1 is derived from g9060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5024652	5026157	.	+	.	Phchi.S5G074900
Phchi.S5	AUGUSTUS	transcript	5024652	5026157	.	+	.	transcript_id "Phchi.S5G074900.t1"; gene_id "Phchi.S5G074900"
Phchi.S5	AUGUSTUS	start_codon	5024652	5024654	.	+	0	transcript_id "Phchi.S5G074900.t1"; gene_id "Phchi.S5G074900"
Phchi.S5	AUGUSTUS	CDS	5024652	5026157	0.6	+	0	transcript_id "Phchi.S5G074900.t1"; gene_id "Phchi.S5G074900"
Phchi.S5	AUGUSTUS	exon	5024652	5026157	.	+	.	transcript_id "Phchi.S5G074900.t1"; gene_id "Phchi.S5G074900"
Phchi.S5	AUGUSTUS	stop_codon	5026158	5026160	.	+	0	transcript_id "Phchi.S5G074900.t1"; gene_id "Phchi.S5G074900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14248.t1 is derived from g12715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11750174	11750775	.	-	.	Phchi.S3G156700
Phchi.S3	AUGUSTUS	transcript	11750174	11750775	.	-	.	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	stop_codon	11750171	11750173	.	-	0	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	CDS	11750174	11750600	0.83	-	1	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	exon	11750174	11750600	.	-	.	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	intron	11750601	11750698	.	-	.	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	CDS	11750699	11750775	0.85	-	0	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	exon	11750699	11750775	.	-	.	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
Phchi.S3	AUGUSTUS	start_codon	11750773	11750775	.	-	0	transcript_id "Phchi.S3G156700.t1"; gene_id "Phchi.S3G156700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2898.t1 is derived from g67.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	381459	382753	.	-	.	Phchi.S1G005700
Phchi.S1	AUGUSTUS	transcript	381459	382753	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	stop_codon	381456	381458	.	-	0	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	CDS	381459	381499	1	-	2	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	exon	381459	381499	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	intron	381500	381580	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	CDS	381581	381698	1	-	0	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	exon	381581	381698	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	intron	381699	381803	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	CDS	381804	381986	1	-	0	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	exon	381804	381986	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	intron	381987	382176	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	CDS	382177	382245	0.47	-	0	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	exon	382177	382245	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	intron	382246	382404	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	CDS	382405	382543	1	-	1	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	exon	382405	382543	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	intron	382544	382739	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	CDS	382740	382753	0.51	-	0	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	exon	382740	382753	.	-	.	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
Phchi.S1	AUGUSTUS	start_codon	382751	382753	.	-	0	transcript_id "Phchi.S1G005700.t1"; gene_id "Phchi.S1G005700"
# This transcript jg11245.t2 is derived from g15295.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11246.t1 is derived from g15296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4990266	4991342	.	-	.	Phchi.S4G082800
Phchi.S4	AUGUSTUS	transcript	4990266	4991342	.	-	.	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	stop_codon	4990263	4990265	.	-	0	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	CDS	4990266	4990266	1	-	1	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	exon	4990266	4990266	.	-	.	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	intron	4990267	4990909	.	-	.	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	CDS	4990910	4991134	0.89	-	1	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	exon	4990910	4991134	.	-	.	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	intron	4991135	4991211	.	-	.	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	CDS	4991212	4991342	0.85	-	0	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	exon	4991212	4991342	.	-	.	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
Phchi.S4	AUGUSTUS	start_codon	4991340	4991342	.	-	0	transcript_id "Phchi.S4G082800.t1"; gene_id "Phchi.S4G082800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg769.t1 is derived from g10551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5428324	5429606	.	-	.	Phchi.S6G072800
Phchi.S6	AUGUSTUS	transcript	5428324	5429606	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	stop_codon	5428321	5428323	.	-	0	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	CDS	5428324	5428374	1	-	0	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	exon	5428324	5428374	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	intron	5428375	5428472	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	CDS	5428473	5428550	1	-	0	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	exon	5428473	5428550	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	intron	5428551	5428640	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	CDS	5428641	5428895	1	-	0	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	exon	5428641	5428895	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	intron	5428896	5428987	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	CDS	5428988	5429172	1	-	2	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	exon	5428988	5429172	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	intron	5429173	5429252	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	CDS	5429253	5429393	1	-	2	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	exon	5429253	5429393	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	intron	5429394	5429587	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	CDS	5429588	5429606	1	-	0	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	exon	5429588	5429606	.	-	.	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
Phchi.S6	AUGUSTUS	start_codon	5429604	5429606	.	-	0	transcript_id "Phchi.S6G072800.t1"; gene_id "Phchi.S6G072800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg813.t1 is derived from g10595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5700924	5701730	.	-	.	Phchi.S6G077200
Phchi.S6	AUGUSTUS	transcript	5700924	5701730	.	-	.	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	stop_codon	5700921	5700923	.	-	0	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	CDS	5700924	5701172	1	-	0	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	exon	5700924	5701172	.	-	.	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	intron	5701173	5701304	.	-	.	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	CDS	5701305	5701515	1	-	1	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	exon	5701305	5701515	.	-	.	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	intron	5701516	5701704	.	-	.	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	CDS	5701705	5701730	0.94	-	0	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	exon	5701705	5701730	.	-	.	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
Phchi.S6	AUGUSTUS	start_codon	5701728	5701730	.	-	0	transcript_id "Phchi.S6G077200.t1"; gene_id "Phchi.S6G077200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1299.t1 is derived from g11082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8899180	8900688	.	-	.	Phchi.S6G125800
Phchi.S6	AUGUSTUS	transcript	8899180	8900688	.	-	.	transcript_id "Phchi.S6G125800.t1"; gene_id "Phchi.S6G125800"
Phchi.S6	AUGUSTUS	stop_codon	8899177	8899179	.	-	0	transcript_id "Phchi.S6G125800.t1"; gene_id "Phchi.S6G125800"
Phchi.S6	AUGUSTUS	CDS	8899180	8900688	0.4	-	0	transcript_id "Phchi.S6G125800.t1"; gene_id "Phchi.S6G125800"
Phchi.S6	AUGUSTUS	exon	8899180	8900688	.	-	.	transcript_id "Phchi.S6G125800.t1"; gene_id "Phchi.S6G125800"
Phchi.S6	AUGUSTUS	start_codon	8900686	8900688	.	-	0	transcript_id "Phchi.S6G125800.t1"; gene_id "Phchi.S6G125800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13021.t1 is derived from g11486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3654479	3657630	.	+	.	Phchi.S3G034000
Phchi.S3	AUGUSTUS	transcript	3654479	3657630	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	start_codon	3654479	3654481	.	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3654479	3655177	0.46	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3654479	3655177	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3655178	3655262	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3655263	3655405	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3655263	3655405	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3655406	3655480	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3655481	3655597	1	+	1	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3655481	3655597	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3655598	3655725	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3655726	3655840	1	+	1	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3655726	3655840	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3655841	3655949	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3655950	3656087	0.96	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3655950	3656087	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3656088	3656213	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3656214	3656309	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3656214	3656309	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3656310	3656398	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3656399	3656512	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3656399	3656512	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3656513	3656610	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3656611	3656679	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3656611	3656679	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3656680	3656775	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3656776	3656846	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3656776	3656846	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3656847	3656940	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3656941	3657034	1	+	1	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3656941	3657034	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3657035	3657125	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3657126	3657254	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3657126	3657254	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3657255	3657350	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3657351	3657440	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3657351	3657440	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	intron	3657441	3657537	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	CDS	3657538	3657630	1	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	exon	3657538	3657630	.	+	.	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
Phchi.S3	AUGUSTUS	stop_codon	3657631	3657633	.	+	0	transcript_id "Phchi.S3G034000.t1"; gene_id "Phchi.S3G034000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10168.t1 is derived from g7344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46073732	46076784	.	-	.	Phchi.S1G732700
Phchi.S1	AUGUSTUS	transcript	46073732	46076784	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	stop_codon	46073729	46073731	.	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46073732	46073908	1	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46073732	46073908	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46073909	46074001	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46074002	46074151	1	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46074002	46074151	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46074152	46074243	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46074244	46074379	1	-	1	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46074244	46074379	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46074380	46074479	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46074480	46074559	1	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46074480	46074559	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46074560	46074651	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46074652	46074809	1	-	2	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46074652	46074809	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46074810	46074899	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46074900	46075151	1	-	2	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46074900	46075151	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46075152	46075239	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46075240	46075818	0.89	-	2	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46075240	46075818	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46075819	46075921	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46075922	46076025	0.97	-	1	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46075922	46076025	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46076026	46076114	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46076115	46076236	0.99	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46076115	46076236	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46076237	46076350	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46076351	46076451	1	-	2	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46076351	46076451	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	intron	46076452	46076555	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	CDS	46076556	46076784	0.43	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	exon	46076556	46076784	.	-	.	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
Phchi.S1	AUGUSTUS	start_codon	46076782	46076784	.	-	0	transcript_id "Phchi.S1G732700.t1"; gene_id "Phchi.S1G732700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5303.t1 is derived from g2473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16156750	16158972	.	+	.	Phchi.S1G246200
Phchi.S1	AUGUSTUS	transcript	16156750	16158972	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	start_codon	16156750	16156752	.	+	0	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16156750	16157023	0.91	+	0	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16156750	16157023	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16157024	16157121	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16157122	16157438	1	+	2	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16157122	16157438	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16157439	16157517	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16157518	16157777	0.99	+	0	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16157518	16157777	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16157778	16157886	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16157887	16158147	1	+	1	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16157887	16158147	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16158148	16158232	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16158233	16158456	0.98	+	1	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16158233	16158456	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16158457	16158565	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16158566	16158655	0.49	+	2	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16158566	16158655	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16158656	16158794	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16158795	16158868	0.78	+	2	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16158795	16158868	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	intron	16158869	16158960	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	CDS	16158961	16158972	0.82	+	0	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	exon	16158961	16158972	.	+	.	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
Phchi.S1	AUGUSTUS	stop_codon	16158973	16158975	.	+	0	transcript_id "Phchi.S1G246200.t1"; gene_id "Phchi.S1G246200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3721.t1 is derived from g890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5371935	5372849	.	-	.	Phchi.S1G088000
Phchi.S1	AUGUSTUS	transcript	5371935	5372849	.	-	.	transcript_id "Phchi.S1G088000.t1"; gene_id "Phchi.S1G088000"
Phchi.S1	AUGUSTUS	stop_codon	5371932	5371934	.	-	0	transcript_id "Phchi.S1G088000.t1"; gene_id "Phchi.S1G088000"
Phchi.S1	AUGUSTUS	CDS	5371935	5372849	0.33	-	0	transcript_id "Phchi.S1G088000.t1"; gene_id "Phchi.S1G088000"
Phchi.S1	AUGUSTUS	exon	5371935	5372849	.	-	.	transcript_id "Phchi.S1G088000.t1"; gene_id "Phchi.S1G088000"
Phchi.S1	AUGUSTUS	start_codon	5372847	5372849	.	-	0	transcript_id "Phchi.S1G088000.t1"; gene_id "Phchi.S1G088000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4362.t1 is derived from g1531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10050236	10050716	.	-	.	Phchi.S1G152100
Phchi.S1	AUGUSTUS	transcript	10050236	10050716	.	-	.	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	stop_codon	10050233	10050235	.	-	0	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	CDS	10050236	10050421	0.42	-	0	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	exon	10050236	10050421	.	-	.	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	intron	10050422	10050611	.	-	.	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	CDS	10050612	10050716	0.56	-	0	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	exon	10050612	10050716	.	-	.	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
Phchi.S1	AUGUSTUS	start_codon	10050714	10050716	.	-	0	transcript_id "Phchi.S1G152100.t1"; gene_id "Phchi.S1G152100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4000.t1 is derived from g1169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6915732	6918950	.	-	.	Phchi.S1G115900
Phchi.S1	AUGUSTUS	transcript	6915732	6918950	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	stop_codon	6915729	6915731	.	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6915732	6915845	0.79	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6915732	6915845	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6915846	6916106	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6916107	6916165	0.6	-	2	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6916107	6916165	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6916166	6916271	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6916272	6916347	0.7	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6916272	6916347	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6916348	6916563	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6916564	6916663	1	-	1	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6916564	6916663	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6916664	6916753	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6916754	6916881	1	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6916754	6916881	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6916882	6916980	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6916981	6917148	1	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6916981	6917148	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6917149	6917250	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6917251	6917366	1	-	2	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6917251	6917366	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6917367	6917501	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6917502	6917654	1	-	2	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6917502	6917654	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6917655	6917778	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6917779	6917922	1	-	2	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6917779	6917922	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6917923	6918230	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6918231	6918267	1	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6918231	6918267	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	intron	6918268	6918362	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	CDS	6918363	6918950	1	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	exon	6918363	6918950	.	-	.	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
Phchi.S1	AUGUSTUS	start_codon	6918948	6918950	.	-	0	transcript_id "Phchi.S1G115900.t1"; gene_id "Phchi.S1G115900"
# This transcript jg1008.t2 is derived from g10791.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1009.t1 is derived from g10792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7083009	7085326	.	+	.	Phchi.S6G096800
Phchi.S6	AUGUSTUS	transcript	7083009	7085326	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	start_codon	7083009	7083011	.	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7083009	7083030	0.86	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7083009	7083030	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7083031	7083142	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7083143	7083219	0.89	+	2	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7083143	7083219	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7083220	7083345	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7083346	7083462	1	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7083346	7083462	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7083463	7083538	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7083539	7083648	1	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7083539	7083648	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7083649	7083749	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7083750	7083816	1	+	1	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7083750	7083816	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7083817	7083968	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7083969	7084102	1	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7083969	7084102	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7084103	7084271	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7084272	7084320	1	+	1	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7084272	7084320	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7084321	7084402	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7084403	7084474	1	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7084403	7084474	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7084475	7084573	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7084574	7084675	1	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7084574	7084675	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7084676	7084772	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7084773	7084840	1	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7084773	7084840	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7084841	7085002	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7085003	7085155	1	+	1	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7085003	7085155	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	intron	7085156	7085271	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	CDS	7085272	7085326	1	+	1	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	exon	7085272	7085326	.	+	.	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
Phchi.S6	AUGUSTUS	stop_codon	7085327	7085329	.	+	0	transcript_id "Phchi.S6G096800.t1"; gene_id "Phchi.S6G096800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg480.t1 is derived from g10262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3352225	3354202	.	-	.	Phchi.S6G043900
Phchi.S6	AUGUSTUS	transcript	3352225	3354202	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	stop_codon	3352222	3352224	.	-	0	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	CDS	3352225	3352255	0.99	-	1	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	exon	3352225	3352255	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	intron	3352256	3352348	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	CDS	3352349	3352655	0.99	-	2	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	exon	3352349	3352655	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	intron	3352656	3352776	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	CDS	3352777	3353222	0.99	-	1	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	exon	3352777	3353222	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	intron	3353223	3353441	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	CDS	3353442	3353524	1	-	0	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	exon	3353442	3353524	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	intron	3353525	3353645	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	CDS	3353646	3353817	0.98	-	1	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	exon	3353646	3353817	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	intron	3353818	3353921	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	CDS	3353922	3354202	0.81	-	0	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	exon	3353922	3354202	.	-	.	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
Phchi.S6	AUGUSTUS	start_codon	3354200	3354202	.	-	0	transcript_id "Phchi.S6G043900.t1"; gene_id "Phchi.S6G043900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3119.t1 is derived from g288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1822164	1826139	.	-	.	Phchi.S1G027800
Phchi.S1	AUGUSTUS	transcript	1822164	1826139	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	stop_codon	1822161	1822163	.	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1822164	1822229	0.99	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1822164	1822229	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1822230	1822326	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1822327	1823861	0.52	-	2	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1822327	1823861	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1823862	1824005	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1824006	1824318	0.18	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1824006	1824318	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1824319	1824425	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1824426	1824924	0.25	-	1	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1824426	1824924	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1824925	1825050	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1825051	1825112	1	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1825051	1825112	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1825113	1825214	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1825215	1825369	1	-	2	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1825215	1825369	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1825370	1825468	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1825469	1825524	1	-	1	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1825469	1825524	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1825525	1825660	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1825661	1825746	1	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1825661	1825746	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1825747	1825867	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1825868	1825962	1	-	2	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1825868	1825962	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	intron	1825963	1826051	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	CDS	1826052	1826139	0.98	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	exon	1826052	1826139	.	-	.	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
Phchi.S1	AUGUSTUS	start_codon	1826137	1826139	.	-	0	transcript_id "Phchi.S1G027800.t1"; gene_id "Phchi.S1G027800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7990.t1 is derived from g5165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32270768	32275882	.	-	.	Phchi.S1G514900
Phchi.S1	AUGUSTUS	transcript	32270768	32275882	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	stop_codon	32270765	32270767	.	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32270768	32270833	0.95	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32270768	32270833	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32270834	32270913	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32270914	32270971	1	-	1	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32270914	32270971	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32270972	32271094	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32271095	32271186	0.97	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32271095	32271186	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32271187	32271288	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32271289	32271408	0.93	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32271289	32271408	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32271409	32271520	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32271521	32271610	1	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32271521	32271610	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32271611	32271780	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32271781	32271873	1	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32271781	32271873	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32271874	32271995	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32271996	32272089	1	-	1	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32271996	32272089	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32272090	32272188	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32272189	32272307	0.83	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32272189	32272307	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32272308	32272409	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32272410	32272523	0.98	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32272410	32272523	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32272524	32272632	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32272633	32272758	0.99	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32272633	32272758	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32272759	32272949	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32272950	32273052	1	-	1	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32272950	32273052	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32273053	32273180	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32273181	32273256	1	-	2	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32273181	32273256	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32273257	32273482	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32273483	32273734	1	-	2	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32273483	32273734	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32273735	32273923	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32273924	32274068	1	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32273924	32274068	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32274069	32274197	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32274198	32274318	1	-	1	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32274198	32274318	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32274319	32274412	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32274413	32274479	1	-	2	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32274413	32274479	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32274480	32274589	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32274590	32274829	0.8	-	2	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32274590	32274829	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	intron	32274830	32275695	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	CDS	32275696	32275882	0.6	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	exon	32275696	32275882	.	-	.	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
Phchi.S1	AUGUSTUS	start_codon	32275880	32275882	.	-	0	transcript_id "Phchi.S1G514900.t1"; gene_id "Phchi.S1G514900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6169.t1 is derived from g3340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21280034	21282185	.	+	.	Phchi.S1G332800
Phchi.S1	AUGUSTUS	transcript	21280034	21282185	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	start_codon	21280034	21280036	.	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21280034	21280459	0.94	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21280034	21280459	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21280460	21280551	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21280552	21280655	1	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21280552	21280655	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21280656	21280743	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21280744	21280815	1	+	1	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21280744	21280815	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21280816	21280905	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21280906	21281044	1	+	1	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21280906	21281044	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21281045	21281126	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21281127	21281230	1	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21281127	21281230	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21281231	21281319	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21281320	21281413	1	+	1	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21281320	21281413	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21281414	21281512	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21281513	21281551	1	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21281513	21281551	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21281552	21281634	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21281635	21281745	1	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21281635	21281745	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21281746	21281825	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21281826	21281891	1	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21281826	21281891	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21281892	21281978	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21281979	21282094	1	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21281979	21282094	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	intron	21282095	21282184	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	CDS	21282185	21282185	1	+	1	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	exon	21282185	21282185	.	+	.	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
Phchi.S1	AUGUSTUS	stop_codon	21282186	21282188	.	+	0	transcript_id "Phchi.S1G332800.t1"; gene_id "Phchi.S1G332800"
# This transcript jg1701.t2 is derived from g8620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1702.t1 is derived from g8621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2586478	2589370	.	-	.	Phchi.S5G031100
Phchi.S5	AUGUSTUS	transcript	2586478	2589370	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	stop_codon	2586475	2586477	.	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2586478	2586481	1	-	1	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2586478	2586481	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2586482	2586572	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2586573	2586660	1	-	2	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2586573	2586660	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2586661	2586838	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2586839	2586988	1	-	2	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2586839	2586988	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2586989	2587085	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2587086	2587299	0.53	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2587086	2587299	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2587300	2587410	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2587411	2587632	0.64	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2587411	2587632	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2587633	2587739	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2587740	2587925	0.94	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2587740	2587925	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2587926	2588090	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2588091	2588213	1	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2588091	2588213	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2588214	2588335	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2588336	2588436	1	-	2	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2588336	2588436	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2588437	2588917	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2588918	2588971	0.91	-	2	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2588918	2588971	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2588972	2589095	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2589096	2589259	0.9	-	1	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2589096	2589259	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	intron	2589260	2589347	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	CDS	2589348	2589370	0.99	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	exon	2589348	2589370	.	-	.	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
Phchi.S5	AUGUSTUS	start_codon	2589368	2589370	.	-	0	transcript_id "Phchi.S5G031100.t1"; gene_id "Phchi.S5G031100"
# This transcript jg2875.t2 is derived from g44.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2876.t1 is derived from g45.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	226715	229518	.	+	.	Phchi.S1G003500
Phchi.S1	AUGUSTUS	transcript	226715	229518	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	start_codon	226715	226717	.	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	226715	226795	0.86	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	226715	226795	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	226796	226966	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	226967	227060	1	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	226967	227060	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	227061	227308	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	227309	227394	1	+	2	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	227309	227394	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	227395	227492	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	227493	227542	1	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	227493	227542	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	227543	227658	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	227659	227728	1	+	1	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	227659	227728	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	227729	227811	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	227812	227893	1	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	227812	227893	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	227894	228016	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	228017	228118	0.48	+	2	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	228017	228118	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	228119	228335	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	228336	228433	0.94	+	2	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	228336	228433	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	228434	228543	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	228544	229212	0.89	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	228544	229212	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	intron	229213	229323	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	CDS	229324	229518	0.93	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	exon	229324	229518	.	+	.	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
Phchi.S1	AUGUSTUS	stop_codon	229519	229521	.	+	0	transcript_id "Phchi.S1G003500.t1"; gene_id "Phchi.S1G003500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8211.t1 is derived from g5386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34441501	34441707	.	+	.	Phchi.S1G537000
Phchi.S1	AUGUSTUS	transcript	34441501	34441707	.	+	.	transcript_id "Phchi.S1G537000.t1"; gene_id "Phchi.S1G537000"
Phchi.S1	AUGUSTUS	start_codon	34441501	34441503	.	+	0	transcript_id "Phchi.S1G537000.t1"; gene_id "Phchi.S1G537000"
Phchi.S1	AUGUSTUS	CDS	34441501	34441707	0.92	+	0	transcript_id "Phchi.S1G537000.t1"; gene_id "Phchi.S1G537000"
Phchi.S1	AUGUSTUS	exon	34441501	34441707	.	+	.	transcript_id "Phchi.S1G537000.t1"; gene_id "Phchi.S1G537000"
Phchi.S1	AUGUSTUS	stop_codon	34441708	34441710	.	+	0	transcript_id "Phchi.S1G537000.t1"; gene_id "Phchi.S1G537000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10329.t1 is derived from g7505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47202497	47202870	.	-	.	Phchi.S1G748800
Phchi.S1	AUGUSTUS	transcript	47202497	47202870	.	-	.	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	stop_codon	47202494	47202496	.	-	0	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	CDS	47202497	47202523	0.82	-	0	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	exon	47202497	47202523	.	-	.	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	intron	47202524	47202600	.	-	.	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	CDS	47202601	47202693	0.97	-	0	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	exon	47202601	47202693	.	-	.	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	intron	47202694	47202777	.	-	.	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	CDS	47202778	47202870	0.52	-	0	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	exon	47202778	47202870	.	-	.	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
Phchi.S1	AUGUSTUS	start_codon	47202868	47202870	.	-	0	transcript_id "Phchi.S1G748800.t1"; gene_id "Phchi.S1G748800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2293.t1 is derived from g9213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5906941	5911713	.	-	.	Phchi.S5G090200
Phchi.S5	AUGUSTUS	transcript	5906941	5911713	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	stop_codon	5906938	5906940	.	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5906941	5907015	0.95	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5906941	5907015	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5907016	5907100	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5907101	5907192	0.89	-	2	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5907101	5907192	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5907193	5907277	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5907278	5907503	0.66	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5907278	5907503	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5907504	5907581	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5907582	5907634	0.97	-	2	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5907582	5907634	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5907635	5907715	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5907716	5907742	0.85	-	2	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5907716	5907742	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5907743	5907861	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5907862	5908090	0.59	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5907862	5908090	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5908091	5908188	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5908189	5908800	0.75	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5908189	5908800	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5908801	5908973	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5908974	5910728	0.88	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5908974	5910728	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5910729	5910898	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5910899	5911270	0.81	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5910899	5911270	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5911271	5911353	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5911354	5911713	0.59	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5911354	5911713	.	-	.	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	start_codon	5911711	5911713	.	-	0	transcript_id "Phchi.S5G090200.t1"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	transcript	5910719	5911713	.	-	.	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	stop_codon	5910716	5910718	.	-	0	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5910719	5910728	0.48	-	1	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5910719	5910728	.	-	.	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5910729	5910881	.	-	.	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5910882	5911270	0.33	-	0	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5910882	5911270	.	-	.	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	intron	5911271	5911353	.	-	.	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	CDS	5911354	5911713	0.54	-	0	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	exon	5911354	5911713	.	-	.	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
Phchi.S5	AUGUSTUS	start_codon	5911711	5911713	.	-	0	transcript_id "Phchi.S5G090200.t2"; gene_id "Phchi.S5G090200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14833.t1 is derived from g13301.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14922916	14925018	.	-	.	Phchi.S3G215200
Phchi.S3	AUGUSTUS	transcript	14922916	14925018	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	stop_codon	14922913	14922915	.	-	0	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14922916	14923432	1	-	1	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14922916	14923432	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14923433	14923525	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14923526	14923597	1	-	1	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14923526	14923597	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14923598	14923753	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14923754	14924441	1	-	2	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14923754	14924441	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14924442	14924521	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14924522	14924738	1	-	0	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14924522	14924738	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14924739	14924895	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14924896	14925018	1	-	0	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14924896	14925018	.	-	.	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	start_codon	14925016	14925018	.	-	0	transcript_id "Phchi.S3G215200.t1"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	transcript	14922916	14925018	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	stop_codon	14922913	14922915	.	-	0	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14922916	14923435	0.96	-	1	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14922916	14923435	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14923436	14923525	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14923526	14923597	1	-	1	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14923526	14923597	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14923598	14923753	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14923754	14924441	1	-	2	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14923754	14924441	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14924442	14924521	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14924522	14924738	1	-	0	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14924522	14924738	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	intron	14924739	14924895	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	CDS	14924896	14925018	1	-	0	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	exon	14924896	14925018	.	-	.	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
Phchi.S3	AUGUSTUS	start_codon	14925016	14925018	.	-	0	transcript_id "Phchi.S3G215200.t2"; gene_id "Phchi.S3G215200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14531.t1 is derived from g12999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13329012	13329541	.	-	.	Phchi.S3G185000
Phchi.S3	AUGUSTUS	transcript	13329012	13329541	.	-	.	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	stop_codon	13329009	13329011	.	-	0	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	CDS	13329012	13329101	0.96	-	0	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	exon	13329012	13329101	.	-	.	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	intron	13329102	13329339	.	-	.	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	CDS	13329340	13329435	1	-	0	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	exon	13329340	13329435	.	-	.	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	intron	13329436	13329520	.	-	.	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	CDS	13329521	13329541	0.67	-	0	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	exon	13329521	13329541	.	-	.	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
Phchi.S3	AUGUSTUS	start_codon	13329539	13329541	.	-	0	transcript_id "Phchi.S3G185000.t1"; gene_id "Phchi.S3G185000"
# This transcript jg10807.t2 is derived from g14857.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10808.t1 is derived from g14858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2199231	2201342	.	+	.	Phchi.S4G039000
Phchi.S4	AUGUSTUS	transcript	2199231	2201342	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	start_codon	2199231	2199233	.	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2199231	2199254	0.8	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2199231	2199254	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2199255	2199471	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2199472	2199546	1	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2199472	2199546	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2199547	2199636	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2199637	2199757	1	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2199637	2199757	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2199758	2199901	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2199902	2199996	1	+	2	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2199902	2199996	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2199997	2200096	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2200097	2200168	1	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2200097	2200168	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2200169	2200282	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2200283	2200609	1	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2200283	2200609	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2200610	2200750	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2200751	2200871	1	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2200751	2200871	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2200872	2201020	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2201021	2201203	1	+	2	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2201021	2201203	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	intron	2201204	2201325	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	CDS	2201326	2201342	1	+	2	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	exon	2201326	2201342	.	+	.	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
Phchi.S4	AUGUSTUS	stop_codon	2201343	2201345	.	+	0	transcript_id "Phchi.S4G039000.t1"; gene_id "Phchi.S4G039000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3170.t1 is derived from g339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2086927	2088017	.	-	.	Phchi.S1G032900
Phchi.S1	AUGUSTUS	transcript	2086927	2088017	.	-	.	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	stop_codon	2086924	2086926	.	-	0	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	CDS	2086927	2087758	0.69	-	1	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	exon	2086927	2087758	.	-	.	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	intron	2087759	2087862	.	-	.	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	CDS	2087863	2088017	0.71	-	0	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	exon	2087863	2088017	.	-	.	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
Phchi.S1	AUGUSTUS	start_codon	2088015	2088017	.	-	0	transcript_id "Phchi.S1G032900.t1"; gene_id "Phchi.S1G032900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13086.t1 is derived from g11551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4092141	4093929	.	+	.	Phchi.S3G040500
Phchi.S3	AUGUSTUS	transcript	4092141	4093929	.	+	.	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	start_codon	4092141	4092143	.	+	0	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	CDS	4092141	4092776	0.53	+	0	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	exon	4092141	4092776	.	+	.	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	intron	4092777	4092970	.	+	.	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	CDS	4092971	4093319	0.52	+	0	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	exon	4092971	4093319	.	+	.	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	intron	4093320	4093411	.	+	.	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	CDS	4093412	4093929	1	+	2	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	exon	4093412	4093929	.	+	.	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
Phchi.S3	AUGUSTUS	stop_codon	4093930	4093932	.	+	0	transcript_id "Phchi.S3G040500.t1"; gene_id "Phchi.S3G040500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10070.t1 is derived from g7246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45623226	45624891	.	-	.	Phchi.S1G722900
Phchi.S1	AUGUSTUS	transcript	45623226	45624891	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	stop_codon	45623223	45623225	.	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45623226	45623315	1	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45623226	45623315	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45623316	45623398	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45623399	45623471	1	-	1	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45623399	45623471	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45623472	45623572	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45623573	45623621	0.99	-	2	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45623573	45623621	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45623622	45623707	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45623708	45623765	1	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45623708	45623765	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45623766	45623866	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45623867	45623927	0.99	-	1	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45623867	45623927	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45623928	45624079	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45624080	45624162	1	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45624080	45624162	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45624163	45624300	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45624301	45624582	1	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45624301	45624582	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	intron	45624583	45624663	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	CDS	45624664	45624891	0.71	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	exon	45624664	45624891	.	-	.	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
Phchi.S1	AUGUSTUS	start_codon	45624889	45624891	.	-	0	transcript_id "Phchi.S1G722900.t1"; gene_id "Phchi.S1G722900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8175.t1 is derived from g5350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34283319	34287029	.	+	.	Phchi.S1G533400
Phchi.S1	AUGUSTUS	transcript	34283319	34287029	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	start_codon	34283319	34283321	.	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34283319	34283690	0.99	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34283319	34283690	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34283691	34283839	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34283840	34283959	1	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34283840	34283959	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34283960	34284127	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34284128	34284562	0.96	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34284128	34284562	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34284563	34284762	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34284763	34284853	1	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34284763	34284853	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34284854	34285011	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34285012	34285256	1	+	2	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34285012	34285256	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34285257	34285400	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34285401	34285565	1	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34285401	34285565	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34285566	34285682	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34285683	34285757	1	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34285683	34285757	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34285758	34285857	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34285858	34285989	1	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34285858	34285989	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34285990	34286077	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34286078	34286134	1	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34286078	34286134	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34286135	34286220	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34286221	34286394	0.82	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34286221	34286394	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34286395	34286658	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34286659	34286743	0.49	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34286659	34286743	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34286744	34286826	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34286827	34286846	0.85	+	2	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34286827	34286846	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	intron	34286847	34286942	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	CDS	34286943	34287029	0.85	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	exon	34286943	34287029	.	+	.	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
Phchi.S1	AUGUSTUS	stop_codon	34287030	34287032	.	+	0	transcript_id "Phchi.S1G533400.t1"; gene_id "Phchi.S1G533400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15540.t1 is derived from g14009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19778050	19780249	.	+	.	Phchi.S3G285900
Phchi.S3	AUGUSTUS	transcript	19778050	19780249	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	start_codon	19778050	19778052	.	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778050	19778232	0.86	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778050	19778232	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778233	19778317	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778318	19778443	1	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778318	19778443	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778444	19778523	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778524	19778589	1	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778524	19778589	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778590	19778710	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778711	19778928	1	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778711	19778928	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778929	19779069	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19779070	19779154	1	+	1	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19779070	19779154	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19779155	19779436	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19779437	19779472	1	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19779437	19779472	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19779473	19779582	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19779583	19779894	0.99	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19779583	19779894	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19779895	19780057	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19780058	19780099	1	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19780058	19780099	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19780100	19780186	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19780187	19780249	0.99	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19780187	19780249	.	+	.	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	stop_codon	19780250	19780252	.	+	0	transcript_id "Phchi.S3G285900.t1"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	transcript	19778050	19780249	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	start_codon	19778050	19778052	.	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778050	19778232	0.88	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778050	19778232	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778233	19778317	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778318	19778443	1	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778318	19778443	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778444	19778523	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778524	19778589	1	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778524	19778589	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778590	19778710	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19778711	19778928	1	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19778711	19778928	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19778929	19779069	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19779070	19779154	0.87	+	1	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19779070	19779154	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19779155	19779405	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19779406	19779447	0.37	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19779406	19779447	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19779448	19779582	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19779583	19779894	0.51	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19779583	19779894	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19779895	19780057	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19780058	19780099	1	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19780058	19780099	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	intron	19780100	19780186	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	CDS	19780187	19780249	1	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	exon	19780187	19780249	.	+	.	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
Phchi.S3	AUGUSTUS	stop_codon	19780250	19780252	.	+	0	transcript_id "Phchi.S3G285900.t2"; gene_id "Phchi.S3G285900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6950.t1 is derived from g4122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26115342	26115794	.	-	.	Phchi.S1G410900
Phchi.S1	AUGUSTUS	transcript	26115342	26115794	.	-	.	transcript_id "Phchi.S1G410900.t1"; gene_id "Phchi.S1G410900"
Phchi.S1	AUGUSTUS	stop_codon	26115339	26115341	.	-	0	transcript_id "Phchi.S1G410900.t1"; gene_id "Phchi.S1G410900"
Phchi.S1	AUGUSTUS	CDS	26115342	26115794	1	-	0	transcript_id "Phchi.S1G410900.t1"; gene_id "Phchi.S1G410900"
Phchi.S1	AUGUSTUS	exon	26115342	26115794	.	-	.	transcript_id "Phchi.S1G410900.t1"; gene_id "Phchi.S1G410900"
Phchi.S1	AUGUSTUS	start_codon	26115792	26115794	.	-	0	transcript_id "Phchi.S1G410900.t1"; gene_id "Phchi.S1G410900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3569.t1 is derived from g738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4548016	4548400	.	-	.	Phchi.S1G072800
Phchi.S1	AUGUSTUS	transcript	4548016	4548400	.	-	.	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	stop_codon	4548013	4548015	.	-	0	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	CDS	4548016	4548215	0.38	-	2	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	exon	4548016	4548215	.	-	.	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	intron	4548216	4548315	.	-	.	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	CDS	4548316	4548400	0.62	-	0	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	exon	4548316	4548400	.	-	.	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
Phchi.S1	AUGUSTUS	start_codon	4548398	4548400	.	-	0	transcript_id "Phchi.S1G072800.t1"; gene_id "Phchi.S1G072800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3140.t1 is derived from g309.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1958734	1960585	.	+	.	Phchi.S1G029900
Phchi.S1	AUGUSTUS	transcript	1958734	1960585	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	start_codon	1958734	1958736	.	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1958734	1958808	1	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1958734	1958808	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1958809	1958917	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1958918	1959113	1	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1958918	1959113	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959114	1959209	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1959210	1959364	1	+	2	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1959210	1959364	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959365	1959529	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1959530	1959616	0.99	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1959530	1959616	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959617	1959692	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1959693	1959836	1	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1959693	1959836	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959837	1960024	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1960025	1960131	1	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1960025	1960131	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1960132	1960221	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1960222	1960402	1	+	1	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1960222	1960402	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1960403	1960501	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1960502	1960585	1	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1960502	1960585	.	+	.	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	stop_codon	1960586	1960588	.	+	0	transcript_id "Phchi.S1G029900.t1"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	transcript	1958734	1960585	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	start_codon	1958734	1958736	.	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1958734	1958808	1	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1958734	1958808	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1958809	1958917	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1958918	1959113	1	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1958918	1959113	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959114	1959209	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1959210	1959364	1	+	2	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1959210	1959364	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959365	1959523	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1959524	1959616	0.97	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1959524	1959616	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959617	1959692	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1959693	1959836	1	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1959693	1959836	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1959837	1960024	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1960025	1960131	1	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1960025	1960131	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1960132	1960221	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1960222	1960402	1	+	1	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1960222	1960402	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	intron	1960403	1960501	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	CDS	1960502	1960585	1	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	exon	1960502	1960585	.	+	.	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
Phchi.S1	AUGUSTUS	stop_codon	1960586	1960588	.	+	0	transcript_id "Phchi.S1G029900.t2"; gene_id "Phchi.S1G029900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10823.t1 is derived from g14873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2301959	2303005	.	+	.	Phchi.S4G040500
Phchi.S4	AUGUSTUS	transcript	2301959	2303005	.	+	.	transcript_id "Phchi.S4G040500.t1"; gene_id "Phchi.S4G040500"
Phchi.S4	AUGUSTUS	start_codon	2301959	2301961	.	+	0	transcript_id "Phchi.S4G040500.t1"; gene_id "Phchi.S4G040500"
Phchi.S4	AUGUSTUS	CDS	2301959	2303005	0.43	+	0	transcript_id "Phchi.S4G040500.t1"; gene_id "Phchi.S4G040500"
Phchi.S4	AUGUSTUS	exon	2301959	2303005	.	+	.	transcript_id "Phchi.S4G040500.t1"; gene_id "Phchi.S4G040500"
Phchi.S4	AUGUSTUS	stop_codon	2303006	2303008	.	+	0	transcript_id "Phchi.S4G040500.t1"; gene_id "Phchi.S4G040500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15254.t1 is derived from g13722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17919237	17921849	.	-	.	Phchi.S3G257300
Phchi.S3	AUGUSTUS	transcript	17919237	17921849	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	stop_codon	17919234	17919236	.	-	0	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17919237	17919547	1	-	2	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17919237	17919547	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17919548	17919646	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17919647	17919845	1	-	0	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17919647	17919845	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17919846	17919936	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17919937	17920079	1	-	2	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17919937	17920079	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17920080	17920194	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17920195	17920328	1	-	1	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17920195	17920328	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17920329	17920439	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17920440	17920584	0.94	-	2	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17920440	17920584	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17920585	17920707	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17920708	17920879	1	-	0	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17920708	17920879	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17920880	17921069	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17921070	17921164	1	-	2	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17921070	17921164	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17921165	17921247	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17921248	17921272	0.99	-	0	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17921248	17921272	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17921273	17921398	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17921399	17921723	0.62	-	1	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17921399	17921723	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	intron	17921724	17921844	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	CDS	17921845	17921849	0.64	-	0	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	exon	17921845	17921849	.	-	.	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
Phchi.S3	AUGUSTUS	start_codon	17921847	17921849	.	-	0	transcript_id "Phchi.S3G257300.t1"; gene_id "Phchi.S3G257300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12218.t1 is derived from g7894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6810927	6813525	.	-	.	Phchi.S2G029800
Phchi.S2	AUGUSTUS	transcript	6810927	6813525	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	stop_codon	6810924	6810926	.	-	0	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6810927	6810998	0.96	-	0	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6810927	6810998	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6810999	6811085	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811086	6811323	1	-	1	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811086	6811323	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811324	6811404	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811405	6811531	0.86	-	2	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811405	6811531	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811532	6811617	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811618	6811708	0.56	-	0	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811618	6811708	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811709	6811791	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811792	6811865	0.98	-	2	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811792	6811865	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811866	6812108	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812109	6812431	0.98	-	1	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812109	6812431	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6812432	6812619	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812620	6812728	1	-	2	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812620	6812728	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6812729	6812868	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812869	6813012	1	-	2	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812869	6813012	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6813013	6813097	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6813098	6813207	1	-	1	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6813098	6813207	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6813208	6813297	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6813298	6813370	1	-	2	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6813298	6813370	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6813371	6813461	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6813462	6813525	0.79	-	0	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6813462	6813525	.	-	.	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	start_codon	6813523	6813525	.	-	0	transcript_id "Phchi.S2G029800.t1"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	transcript	6810927	6813525	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	stop_codon	6810924	6810926	.	-	0	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6810927	6810998	0.97	-	0	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6810927	6810998	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6810999	6811085	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811086	6811323	1	-	1	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811086	6811323	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811324	6811404	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811405	6811531	0.79	-	2	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811405	6811531	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811532	6811617	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811618	6811708	0.51	-	0	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811618	6811708	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811709	6811791	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6811792	6811855	0.99	-	1	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6811792	6811855	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6811856	6812108	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812109	6812130	0.99	-	2	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812109	6812130	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6812131	6812255	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812256	6812431	0.94	-	1	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812256	6812431	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6812432	6812619	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812620	6812728	1	-	2	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812620	6812728	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6812729	6812868	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6812869	6813012	1	-	2	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6812869	6813012	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6813013	6813097	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6813098	6813207	1	-	1	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6813098	6813207	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6813208	6813297	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6813298	6813370	1	-	2	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6813298	6813370	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	intron	6813371	6813461	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	CDS	6813462	6813525	0.79	-	0	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	exon	6813462	6813525	.	-	.	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
Phchi.S2	AUGUSTUS	start_codon	6813523	6813525	.	-	0	transcript_id "Phchi.S2G029800.t2"; gene_id "Phchi.S2G029800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11317.t1 is derived from g15367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5333724	5334031	.	+	.	Phchi.S4G089900
Phchi.S4	AUGUSTUS	transcript	5333724	5334031	.	+	.	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	start_codon	5333724	5333726	.	+	0	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	CDS	5333724	5333738	0.87	+	0	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	exon	5333724	5333738	.	+	.	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	intron	5333739	5333815	.	+	.	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	CDS	5333816	5334031	0.73	+	0	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	exon	5333816	5334031	.	+	.	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
Phchi.S4	AUGUSTUS	stop_codon	5334032	5334034	.	+	0	transcript_id "Phchi.S4G089900.t1"; gene_id "Phchi.S4G089900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15167.t1 is derived from g13635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17346532	17347252	.	-	.	Phchi.S3G248600
Phchi.S3	AUGUSTUS	transcript	17346532	17347252	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	stop_codon	17346529	17346531	.	-	0	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	CDS	17346532	17346618	0.98	-	0	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	exon	17346532	17346618	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	intron	17346619	17346740	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	CDS	17346741	17346800	0.99	-	0	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	exon	17346741	17346800	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	intron	17346801	17346940	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	CDS	17346941	17346997	1	-	0	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	exon	17346941	17346997	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	intron	17346998	17347072	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	CDS	17347073	17347252	0.49	-	0	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	exon	17347073	17347252	.	-	.	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
Phchi.S3	AUGUSTUS	start_codon	17347250	17347252	.	-	0	transcript_id "Phchi.S3G248600.t1"; gene_id "Phchi.S3G248600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11541.t1 is derived from g15591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6968721	6969336	.	+	.	Phchi.S4G112300
Phchi.S4	AUGUSTUS	transcript	6968721	6969336	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	start_codon	6968721	6968723	.	+	0	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	CDS	6968721	6968728	0.5	+	0	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	exon	6968721	6968728	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	intron	6968729	6968884	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	CDS	6968885	6968981	0.66	+	1	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	exon	6968885	6968981	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	intron	6968982	6969062	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	CDS	6969063	6969118	1	+	0	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	exon	6969063	6969118	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	intron	6969119	6969218	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	CDS	6969219	6969336	0.86	+	1	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	exon	6969219	6969336	.	+	.	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
Phchi.S4	AUGUSTUS	stop_codon	6969337	6969339	.	+	0	transcript_id "Phchi.S4G112300.t1"; gene_id "Phchi.S4G112300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6978.t1 is derived from g4150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26249101	26253159	.	+	.	Phchi.S1G413700
Phchi.S1	AUGUSTUS	transcript	26249101	26253159	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	start_codon	26249101	26249103	.	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249101	26249142	0.38	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249101	26249142	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249143	26249254	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249255	26249378	0.46	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249255	26249378	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249379	26249470	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249471	26249682	0.93	+	2	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249471	26249682	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249683	26249780	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249781	26249876	1	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249781	26249876	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249877	26249984	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249985	26250410	1	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249985	26250410	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26250411	26250590	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26250591	26251353	0.57	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26250591	26251353	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26251354	26251487	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26251488	26252114	0.78	+	2	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26251488	26252114	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252115	26252208	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252209	26252261	0.97	+	2	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252209	26252261	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252262	26252311	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252312	26252429	0.87	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252312	26252429	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252430	26252511	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252512	26252679	1	+	2	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252512	26252679	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252680	26252758	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252759	26252815	1	+	2	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252759	26252815	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252816	26253043	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26253044	26253159	1	+	2	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26253044	26253159	.	+	.	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	stop_codon	26253160	26253162	.	+	0	transcript_id "Phchi.S1G413700.t1"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	transcript	26249101	26253159	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	start_codon	26249101	26249103	.	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249101	26249142	0.33	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249101	26249142	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249143	26249254	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249255	26249378	0.45	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249255	26249378	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249379	26249470	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249471	26249682	0.97	+	2	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249471	26249682	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249683	26249780	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249781	26249876	1	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249781	26249876	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26249877	26249984	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26249985	26250410	0.99	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26249985	26250410	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26250411	26250590	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26250591	26251353	0.59	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26250591	26251353	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26251354	26251487	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26251488	26252114	0.79	+	2	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26251488	26252114	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252115	26252208	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252209	26252261	0.96	+	2	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252209	26252261	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252262	26252311	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252312	26252429	0.92	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252312	26252429	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252430	26252511	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252512	26252527	0.66	+	2	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252512	26252527	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252528	26252618	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252619	26252679	0.66	+	1	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252619	26252679	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252680	26252758	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26252759	26252864	0.66	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26252759	26252864	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	intron	26252865	26253043	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	CDS	26253044	26253159	0.91	+	2	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	exon	26253044	26253159	.	+	.	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
Phchi.S1	AUGUSTUS	stop_codon	26253160	26253162	.	+	0	transcript_id "Phchi.S1G413700.t2"; gene_id "Phchi.S1G413700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13156.t1 is derived from g11621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4436328	4436868	.	-	.	Phchi.S3G047500
Phchi.S3	AUGUSTUS	transcript	4436328	4436868	.	-	.	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	stop_codon	4436325	4436327	.	-	0	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	CDS	4436328	4436387	0.92	-	0	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	exon	4436328	4436387	.	-	.	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	intron	4436388	4436586	.	-	.	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	CDS	4436587	4436868	0.65	-	0	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	exon	4436587	4436868	.	-	.	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
Phchi.S3	AUGUSTUS	start_codon	4436866	4436868	.	-	0	transcript_id "Phchi.S3G047500.t1"; gene_id "Phchi.S3G047500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13952.t1 is derived from g12419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9886444	9886899	.	-	.	Phchi.S3G127100
Phchi.S3	AUGUSTUS	transcript	9886444	9886899	.	-	.	transcript_id "Phchi.S3G127100.t1"; gene_id "Phchi.S3G127100"
Phchi.S3	AUGUSTUS	stop_codon	9886441	9886443	.	-	0	transcript_id "Phchi.S3G127100.t1"; gene_id "Phchi.S3G127100"
Phchi.S3	AUGUSTUS	CDS	9886444	9886899	0.9	-	0	transcript_id "Phchi.S3G127100.t1"; gene_id "Phchi.S3G127100"
Phchi.S3	AUGUSTUS	exon	9886444	9886899	.	-	.	transcript_id "Phchi.S3G127100.t1"; gene_id "Phchi.S3G127100"
Phchi.S3	AUGUSTUS	start_codon	9886897	9886899	.	-	0	transcript_id "Phchi.S3G127100.t1"; gene_id "Phchi.S3G127100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6448.t1 is derived from g3620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23067754	23070267	.	-	.	Phchi.S1G360700
Phchi.S1	AUGUSTUS	transcript	23067754	23070267	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	stop_codon	23067751	23067753	.	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23067754	23067897	1	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23067754	23067897	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23067898	23067981	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23067982	23068212	1	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23067982	23068212	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23068213	23068307	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23068308	23068523	0.98	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23068308	23068523	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23068524	23068624	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23068625	23068749	1	-	2	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23068625	23068749	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23068750	23068873	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23068874	23069063	1	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23068874	23069063	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23069064	23069183	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23069184	23069278	0.98	-	2	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23069184	23069278	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23069279	23069716	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23069717	23069941	0.96	-	2	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23069717	23069941	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	intron	23069942	23070089	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	CDS	23070090	23070267	1	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	exon	23070090	23070267	.	-	.	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
Phchi.S1	AUGUSTUS	start_codon	23070265	23070267	.	-	0	transcript_id "Phchi.S1G360700.t1"; gene_id "Phchi.S1G360700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9836.t1 is derived from g7012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44009819	44011424	.	+	.	Phchi.S1G699500
Phchi.S1	AUGUSTUS	transcript	44009819	44011424	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	start_codon	44009819	44009821	.	+	0	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	CDS	44009819	44010175	0.85	+	0	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	exon	44009819	44010175	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	intron	44010176	44010344	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	CDS	44010345	44010395	1	+	0	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	exon	44010345	44010395	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	intron	44010396	44010587	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	CDS	44010588	44010721	1	+	0	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	exon	44010588	44010721	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	intron	44010722	44010927	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	CDS	44010928	44011028	0.91	+	1	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	exon	44010928	44011028	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	intron	44011029	44011129	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	CDS	44011130	44011240	0.29	+	2	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	exon	44011130	44011240	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	intron	44011241	44011326	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	CDS	44011327	44011424	0.31	+	2	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	exon	44011327	44011424	.	+	.	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
Phchi.S1	AUGUSTUS	stop_codon	44011425	44011427	.	+	0	transcript_id "Phchi.S1G699500.t1"; gene_id "Phchi.S1G699500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8170.t1 is derived from g5345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34264026	34264698	.	-	.	Phchi.S1G532900
Phchi.S1	AUGUSTUS	transcript	34264026	34264698	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	stop_codon	34264023	34264025	.	-	0	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	CDS	34264026	34264160	0.78	-	0	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	exon	34264026	34264160	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	intron	34264161	34264248	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	CDS	34264249	34264272	0.56	-	0	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	exon	34264249	34264272	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	intron	34264273	34264342	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	CDS	34264343	34264396	0.77	-	0	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	exon	34264343	34264396	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	intron	34264397	34264635	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	CDS	34264636	34264698	0.7	-	0	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	exon	34264636	34264698	.	-	.	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
Phchi.S1	AUGUSTUS	start_codon	34264696	34264698	.	-	0	transcript_id "Phchi.S1G532900.t1"; gene_id "Phchi.S1G532900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10963.t1 is derived from g15013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3320009	3322047	.	-	.	Phchi.S4G054500
Phchi.S4	AUGUSTUS	transcript	3320009	3322047	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	stop_codon	3320006	3320008	.	-	0	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3320009	3320273	1	-	1	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3320009	3320273	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3320274	3320362	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3320363	3320565	1	-	0	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3320363	3320565	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3320566	3320684	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3320685	3320742	1	-	1	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3320685	3320742	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3320743	3320922	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3320923	3320978	1	-	0	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3320923	3320978	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3320979	3321195	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3321196	3321242	1	-	2	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3321196	3321242	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3321243	3321418	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3321419	3321565	0.9	-	2	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3321419	3321565	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3321566	3321686	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3321687	3321732	1	-	0	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3321687	3321732	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3321733	3321815	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3321816	3321825	1	-	1	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3321816	3321825	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	intron	3321826	3322003	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	CDS	3322004	3322047	0.78	-	0	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	exon	3322004	3322047	.	-	.	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
Phchi.S4	AUGUSTUS	start_codon	3322045	3322047	.	-	0	transcript_id "Phchi.S4G054500.t1"; gene_id "Phchi.S4G054500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12773.t1 is derived from g11238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1981445	1981732	.	+	.	Phchi.S3G009200
Phchi.S3	AUGUSTUS	transcript	1981445	1981732	.	+	.	transcript_id "Phchi.S3G009200.t1"; gene_id "Phchi.S3G009200"
Phchi.S3	AUGUSTUS	start_codon	1981445	1981447	.	+	0	transcript_id "Phchi.S3G009200.t1"; gene_id "Phchi.S3G009200"
Phchi.S3	AUGUSTUS	CDS	1981445	1981732	0.8	+	0	transcript_id "Phchi.S3G009200.t1"; gene_id "Phchi.S3G009200"
Phchi.S3	AUGUSTUS	exon	1981445	1981732	.	+	.	transcript_id "Phchi.S3G009200.t1"; gene_id "Phchi.S3G009200"
Phchi.S3	AUGUSTUS	stop_codon	1981733	1981735	.	+	0	transcript_id "Phchi.S3G009200.t1"; gene_id "Phchi.S3G009200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13888.t1 is derived from g12355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9465273	9466749	.	-	.	Phchi.S3G120700
Phchi.S3	AUGUSTUS	transcript	9465273	9466749	.	-	.	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	stop_codon	9465270	9465272	.	-	0	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	CDS	9465273	9466109	0.96	-	0	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	exon	9465273	9466109	.	-	.	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	intron	9466110	9466281	.	-	.	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	CDS	9466282	9466749	0.86	-	0	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	exon	9466282	9466749	.	-	.	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
Phchi.S3	AUGUSTUS	start_codon	9466747	9466749	.	-	0	transcript_id "Phchi.S3G120700.t1"; gene_id "Phchi.S3G120700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10095.t1 is derived from g7271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45729040	45729561	.	-	.	Phchi.S1G725400
Phchi.S1	AUGUSTUS	transcript	45729040	45729561	.	-	.	transcript_id "Phchi.S1G725400.t1"; gene_id "Phchi.S1G725400"
Phchi.S1	AUGUSTUS	stop_codon	45729037	45729039	.	-	0	transcript_id "Phchi.S1G725400.t1"; gene_id "Phchi.S1G725400"
Phchi.S1	AUGUSTUS	CDS	45729040	45729561	0.99	-	0	transcript_id "Phchi.S1G725400.t1"; gene_id "Phchi.S1G725400"
Phchi.S1	AUGUSTUS	exon	45729040	45729561	.	-	.	transcript_id "Phchi.S1G725400.t1"; gene_id "Phchi.S1G725400"
Phchi.S1	AUGUSTUS	start_codon	45729559	45729561	.	-	0	transcript_id "Phchi.S1G725400.t1"; gene_id "Phchi.S1G725400"
# This transcript jg4173.t2 is derived from g1342.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4174.t1 is derived from g1343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8741736	8743082	.	+	.	Phchi.S1G133300
Phchi.S1	AUGUSTUS	transcript	8741736	8743082	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	start_codon	8741736	8741738	.	+	0	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	CDS	8741736	8742038	0.61	+	0	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	exon	8741736	8742038	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	intron	8742039	8742184	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	CDS	8742185	8742278	0.39	+	0	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	exon	8742185	8742278	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	intron	8742279	8742387	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	CDS	8742388	8742462	0.36	+	2	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	exon	8742388	8742462	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	intron	8742463	8742798	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	CDS	8742799	8743082	0.42	+	2	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	exon	8742799	8743082	.	+	.	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
Phchi.S1	AUGUSTUS	stop_codon	8743083	8743085	.	+	0	transcript_id "Phchi.S1G133300.t1"; gene_id "Phchi.S1G133300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8528.t1 is derived from g5703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36475153	36475491	.	+	.	Phchi.S1G568700
Phchi.S1	AUGUSTUS	transcript	36475153	36475491	.	+	.	transcript_id "Phchi.S1G568700.t1"; gene_id "Phchi.S1G568700"
Phchi.S1	AUGUSTUS	start_codon	36475153	36475155	.	+	0	transcript_id "Phchi.S1G568700.t1"; gene_id "Phchi.S1G568700"
Phchi.S1	AUGUSTUS	CDS	36475153	36475491	0.18	+	0	transcript_id "Phchi.S1G568700.t1"; gene_id "Phchi.S1G568700"
Phchi.S1	AUGUSTUS	exon	36475153	36475491	.	+	.	transcript_id "Phchi.S1G568700.t1"; gene_id "Phchi.S1G568700"
Phchi.S1	AUGUSTUS	stop_codon	36475492	36475494	.	+	0	transcript_id "Phchi.S1G568700.t1"; gene_id "Phchi.S1G568700"
# This transcript jg13618.t2 is derived from g12085.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13619.t1 is derived from g12086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7775158	7776495	.	-	.	Phchi.S3G093800
Phchi.S3	AUGUSTUS	transcript	7775158	7776495	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	stop_codon	7775155	7775157	.	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	CDS	7775158	7775166	0.99	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	exon	7775158	7775166	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	intron	7775167	7775356	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	CDS	7775357	7775485	0.99	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	exon	7775357	7775485	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	intron	7775486	7775731	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	CDS	7775732	7775897	0.99	-	1	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	exon	7775732	7775897	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	intron	7775898	7775995	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	CDS	7775996	7776168	0.68	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	exon	7775996	7776168	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	intron	7776169	7776283	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	CDS	7776284	7776313	0.6	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	exon	7776284	7776313	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	intron	7776314	7776387	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	CDS	7776388	7776495	1	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	exon	7776388	7776495	.	-	.	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
Phchi.S3	AUGUSTUS	start_codon	7776493	7776495	.	-	0	transcript_id "Phchi.S3G093800.t1"; gene_id "Phchi.S3G093800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8467.t1 is derived from g5642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36068286	36070544	.	+	.	Phchi.S1G562600
Phchi.S1	AUGUSTUS	transcript	36068286	36070544	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	start_codon	36068286	36068288	.	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36068286	36068297	0.74	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36068286	36068297	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36068298	36068443	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36068444	36068545	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36068444	36068545	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36068546	36068640	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36068641	36068703	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36068641	36068703	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36068704	36068785	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36068786	36068918	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36068786	36068918	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36068919	36068995	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36068996	36069102	1	+	2	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36068996	36069102	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36069103	36069235	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36069236	36069430	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36069236	36069430	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36069431	36069519	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36069520	36069606	0.95	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36069520	36069606	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36069607	36069707	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36069708	36069812	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36069708	36069812	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36069813	36069890	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36069891	36069988	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36069891	36069988	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36069989	36070080	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36070081	36070159	1	+	1	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36070081	36070159	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36070160	36070247	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36070248	36070336	1	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36070248	36070336	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	intron	36070337	36070432	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	CDS	36070433	36070544	0.95	+	1	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	exon	36070433	36070544	.	+	.	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
Phchi.S1	AUGUSTUS	stop_codon	36070545	36070547	.	+	0	transcript_id "Phchi.S1G562600.t1"; gene_id "Phchi.S1G562600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3487.t1 is derived from g656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4022537	4023564	.	-	.	Phchi.S1G064600
Phchi.S1	AUGUSTUS	transcript	4022537	4023564	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	stop_codon	4022534	4022536	.	-	0	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	CDS	4022537	4022607	0.99	-	2	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	exon	4022537	4022607	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	intron	4022608	4022764	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	CDS	4022765	4022951	0.92	-	0	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	exon	4022765	4022951	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	intron	4022952	4023249	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	CDS	4023250	4023414	0.9	-	0	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	exon	4023250	4023414	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	intron	4023415	4023495	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	CDS	4023496	4023564	0.83	-	0	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	exon	4023496	4023564	.	-	.	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
Phchi.S1	AUGUSTUS	start_codon	4023562	4023564	.	-	0	transcript_id "Phchi.S1G064600.t1"; gene_id "Phchi.S1G064600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15856.t1 is derived from g14326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21862947	21867976	.	+	.	Phchi.S3G317500
Phchi.S3	AUGUSTUS	transcript	21862947	21867976	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	start_codon	21862947	21862949	.	+	0	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	CDS	21862947	21867271	0.71	+	0	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	exon	21862947	21867271	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	intron	21867272	21867384	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	CDS	21867385	21867426	1	+	1	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	exon	21867385	21867426	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	intron	21867427	21867564	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	CDS	21867565	21867854	0.71	+	1	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	exon	21867565	21867854	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	intron	21867855	21867959	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	CDS	21867960	21867976	0.6	+	2	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	exon	21867960	21867976	.	+	.	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
Phchi.S3	AUGUSTUS	stop_codon	21867977	21867979	.	+	0	transcript_id "Phchi.S3G317500.t1"; gene_id "Phchi.S3G317500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3255.t1 is derived from g424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2529978	2530996	.	+	.	Phchi.S1G041400
Phchi.S1	AUGUSTUS	transcript	2529978	2530996	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	start_codon	2529978	2529980	.	+	0	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	CDS	2529978	2530077	0.81	+	0	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	exon	2529978	2530077	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	intron	2530078	2530236	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	CDS	2530237	2530338	0.94	+	2	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	exon	2530237	2530338	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	intron	2530339	2530450	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	CDS	2530451	2530608	0.9	+	2	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	exon	2530451	2530608	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	intron	2530609	2530798	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	CDS	2530799	2530996	0.81	+	0	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	exon	2530799	2530996	.	+	.	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
Phchi.S1	AUGUSTUS	stop_codon	2530997	2530999	.	+	0	transcript_id "Phchi.S1G041400.t1"; gene_id "Phchi.S1G041400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1833.t1 is derived from g8753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3475474	3476864	.	-	.	Phchi.S5G044200
Phchi.S5	AUGUSTUS	transcript	3475474	3476864	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	stop_codon	3475471	3475473	.	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3475474	3475478	1	-	2	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3475474	3475478	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3475479	3475639	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3475640	3475694	1	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3475640	3475694	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3475695	3475870	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3475871	3475964	1	-	1	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3475871	3475964	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3475965	3476043	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3476044	3476117	1	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3476044	3476117	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3476118	3476209	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3476210	3476272	1	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3476210	3476272	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3476273	3476444	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3476445	3476489	1	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3476445	3476489	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3476490	3476613	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3476614	3476659	1	-	1	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3476614	3476659	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	intron	3476660	3476751	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	CDS	3476752	3476864	1	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	exon	3476752	3476864	.	-	.	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
Phchi.S5	AUGUSTUS	start_codon	3476862	3476864	.	-	0	transcript_id "Phchi.S5G044200.t1"; gene_id "Phchi.S5G044200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3888.t1 is derived from g1057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6211438	6213440	.	+	.	Phchi.S1G104700
Phchi.S1	AUGUSTUS	transcript	6211438	6213440	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	start_codon	6211438	6211440	.	+	0	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6211438	6211557	0.43	+	0	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6211438	6211557	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6211558	6211664	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6211665	6211910	0.6	+	0	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6211665	6211910	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6211911	6211996	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6211997	6212279	1	+	0	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6211997	6212279	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6212280	6212367	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6212368	6212522	1	+	2	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6212368	6212522	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6212523	6212705	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6212706	6212839	1	+	0	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6212706	6212839	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6212840	6213144	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6213145	6213179	1	+	1	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6213145	6213179	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6213180	6213243	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6213244	6213321	0.98	+	2	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6213244	6213321	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6213322	6213402	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6213403	6213440	0.94	+	2	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6213403	6213440	.	+	.	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	stop_codon	6213441	6213443	.	+	0	transcript_id "Phchi.S1G104700.t1"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	transcript	6211438	6213440	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	start_codon	6211438	6211440	.	+	0	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6211438	6211557	0.4	+	0	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6211438	6211557	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6211558	6211664	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6211665	6211910	0.71	+	0	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6211665	6211910	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6211911	6211996	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6211997	6212279	1	+	0	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6211997	6212279	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6212280	6212367	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6212368	6212522	1	+	2	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6212368	6212522	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6212523	6212705	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6212706	6212839	1	+	0	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6212706	6212839	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6212840	6213141	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6213142	6213179	1	+	1	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6213142	6213179	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6213180	6213243	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6213244	6213321	0.94	+	2	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6213244	6213321	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	intron	6213322	6213402	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	CDS	6213403	6213440	0.96	+	2	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	exon	6213403	6213440	.	+	.	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
Phchi.S1	AUGUSTUS	stop_codon	6213441	6213443	.	+	0	transcript_id "Phchi.S1G104700.t2"; gene_id "Phchi.S1G104700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6878.t1 is derived from g4050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25771772	25773642	.	-	.	Phchi.S1G403700
Phchi.S1	AUGUSTUS	transcript	25771772	25773642	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	stop_codon	25771769	25771771	.	-	0	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25771772	25771880	0.75	-	1	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25771772	25771880	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25771881	25771990	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25771991	25772061	0.97	-	0	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25771991	25772061	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25772062	25772139	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25772140	25772302	1	-	1	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25772140	25772302	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25772303	25772429	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25772430	25772546	1	-	1	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25772430	25772546	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25772547	25772675	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25772676	25772741	1	-	1	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25772676	25772741	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25772742	25772841	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25772842	25772968	1	-	2	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25772842	25772968	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25772969	25773075	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25773076	25773124	1	-	0	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25773076	25773124	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25773125	25773270	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25773271	25773431	1	-	2	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25773271	25773431	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	intron	25773432	25773521	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	CDS	25773522	25773642	0.44	-	0	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	exon	25773522	25773642	.	-	.	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
Phchi.S1	AUGUSTUS	start_codon	25773640	25773642	.	-	0	transcript_id "Phchi.S1G403700.t1"; gene_id "Phchi.S1G403700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15680.t1 is derived from g14149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20631550	20634709	.	+	.	Phchi.S3G299900
Phchi.S3	AUGUSTUS	transcript	20631550	20634709	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	start_codon	20631550	20631552	.	+	0	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20631550	20631845	1	+	0	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20631550	20631845	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	intron	20631846	20631940	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20631941	20632053	0.97	+	1	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20631941	20632053	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	intron	20632054	20632158	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20632159	20632557	0.93	+	2	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20632159	20632557	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	intron	20632558	20632661	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20632662	20633575	0.99	+	2	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20632662	20633575	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	intron	20633576	20633674	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20633675	20633863	1	+	0	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20633675	20633863	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	intron	20633864	20633958	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20633959	20634120	1	+	0	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20633959	20634120	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	intron	20634121	20634217	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	CDS	20634218	20634709	0.99	+	0	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	exon	20634218	20634709	.	+	.	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
Phchi.S3	AUGUSTUS	stop_codon	20634710	20634712	.	+	0	transcript_id "Phchi.S3G299900.t1"; gene_id "Phchi.S3G299900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3800.t1 is derived from g969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5804715	5805597	.	-	.	Phchi.S1G095900
Phchi.S1	AUGUSTUS	transcript	5804715	5805597	.	-	.	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	stop_codon	5804712	5804714	.	-	0	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	CDS	5804715	5804844	1	-	1	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	exon	5804715	5804844	.	-	.	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	intron	5804845	5804944	.	-	.	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	CDS	5804945	5805261	0.95	-	0	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	exon	5804945	5805261	.	-	.	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	intron	5805262	5805402	.	-	.	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	CDS	5805403	5805597	0.92	-	0	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	exon	5805403	5805597	.	-	.	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
Phchi.S1	AUGUSTUS	start_codon	5805595	5805597	.	-	0	transcript_id "Phchi.S1G095900.t1"; gene_id "Phchi.S1G095900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7212.t1 is derived from g4384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27651321	27653133	.	-	.	Phchi.S1G437100
Phchi.S1	AUGUSTUS	transcript	27651321	27653133	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	stop_codon	27651318	27651320	.	-	0	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27651321	27651408	1	-	1	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27651321	27651408	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27651409	27651490	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27651491	27651584	1	-	2	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27651491	27651584	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27651585	27651674	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27651675	27651757	1	-	1	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27651675	27651757	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27651758	27651840	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27651841	27652006	1	-	2	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27651841	27652006	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27652007	27652080	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27652081	27652185	1	-	2	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27652081	27652185	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27652186	27652303	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27652304	27652373	1	-	0	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27652304	27652373	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27652374	27652515	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27652516	27652552	1	-	1	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27652516	27652552	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27652553	27652729	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27652730	27652826	1	-	2	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27652730	27652826	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	intron	27652827	27653084	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	CDS	27653085	27653133	0.87	-	0	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	exon	27653085	27653133	.	-	.	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
Phchi.S1	AUGUSTUS	start_codon	27653131	27653133	.	-	0	transcript_id "Phchi.S1G437100.t1"; gene_id "Phchi.S1G437100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3550.t1 is derived from g719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4438732	4440014	.	-	.	Phchi.S1G070900
Phchi.S1	AUGUSTUS	transcript	4438732	4440014	.	-	.	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	stop_codon	4438729	4438731	.	-	0	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	CDS	4438732	4438732	0.48	-	1	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	exon	4438732	4438732	.	-	.	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	intron	4438733	4438947	.	-	.	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	CDS	4438948	4439648	0.63	-	0	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	exon	4438948	4439648	.	-	.	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	intron	4439649	4439750	.	-	.	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	CDS	4439751	4440014	0.85	-	0	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	exon	4439751	4440014	.	-	.	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
Phchi.S1	AUGUSTUS	start_codon	4440012	4440014	.	-	0	transcript_id "Phchi.S1G070900.t1"; gene_id "Phchi.S1G070900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1130.t1 is derived from g10913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7866834	7867929	.	+	.	Phchi.S6G108900
Phchi.S6	AUGUSTUS	transcript	7866834	7867929	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	start_codon	7866834	7866836	.	+	0	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	CDS	7866834	7867183	0.66	+	0	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	exon	7866834	7867183	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	intron	7867184	7867300	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	CDS	7867301	7867388	1	+	1	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	exon	7867301	7867388	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	intron	7867389	7867474	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	CDS	7867475	7867602	1	+	0	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	exon	7867475	7867602	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	intron	7867603	7867732	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	CDS	7867733	7867791	0.6	+	1	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	exon	7867733	7867791	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	intron	7867792	7867888	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	CDS	7867889	7867929	0.27	+	2	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	exon	7867889	7867929	.	+	.	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
Phchi.S6	AUGUSTUS	stop_codon	7867930	7867932	.	+	0	transcript_id "Phchi.S6G108900.t1"; gene_id "Phchi.S6G108900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4422.t1 is derived from g1591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10428802	10429815	.	-	.	Phchi.S1G158100
Phchi.S1	AUGUSTUS	transcript	10428802	10429815	.	-	.	transcript_id "Phchi.S1G158100.t1"; gene_id "Phchi.S1G158100"
Phchi.S1	AUGUSTUS	stop_codon	10428799	10428801	.	-	0	transcript_id "Phchi.S1G158100.t1"; gene_id "Phchi.S1G158100"
Phchi.S1	AUGUSTUS	CDS	10428802	10429815	0.99	-	0	transcript_id "Phchi.S1G158100.t1"; gene_id "Phchi.S1G158100"
Phchi.S1	AUGUSTUS	exon	10428802	10429815	.	-	.	transcript_id "Phchi.S1G158100.t1"; gene_id "Phchi.S1G158100"
Phchi.S1	AUGUSTUS	start_codon	10429813	10429815	.	-	0	transcript_id "Phchi.S1G158100.t1"; gene_id "Phchi.S1G158100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13389.t1 is derived from g11855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6497350	6503497	.	-	.	Phchi.S3G070800
Phchi.S3	AUGUSTUS	transcript	6497350	6503497	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	stop_codon	6497347	6497349	.	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6497350	6498157	1	-	1	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6497350	6498157	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6498158	6498244	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6498245	6498438	1	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6498245	6498438	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6498439	6498526	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6498527	6498743	0.82	-	1	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6498527	6498743	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6498744	6498863	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6498864	6498993	0.94	-	2	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6498864	6498993	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6498994	6499092	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6499093	6499207	1	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6499093	6499207	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6499208	6499311	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6499312	6499399	1	-	1	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6499312	6499399	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6499400	6499494	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6499495	6499586	0.94	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6499495	6499586	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6499587	6499702	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6499703	6500284	0.94	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6499703	6500284	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6500285	6500446	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6500447	6500760	0.67	-	2	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6500447	6500760	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6500761	6500920	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6500921	6501251	0.66	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6500921	6501251	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	intron	6501252	6501337	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	CDS	6501338	6503497	0.79	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	exon	6501338	6503497	.	-	.	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
Phchi.S3	AUGUSTUS	start_codon	6503495	6503497	.	-	0	transcript_id "Phchi.S3G070800.t1"; gene_id "Phchi.S3G070800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10000.t1 is derived from g7176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44991374	44992365	.	+	.	Phchi.S1G715900
Phchi.S1	AUGUSTUS	transcript	44991374	44992365	.	+	.	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	start_codon	44991374	44991376	.	+	0	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	CDS	44991374	44991550	0.49	+	0	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	exon	44991374	44991550	.	+	.	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	intron	44991551	44991633	.	+	.	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	CDS	44991634	44992365	0.81	+	0	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	exon	44991634	44992365	.	+	.	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
Phchi.S1	AUGUSTUS	stop_codon	44992366	44992368	.	+	0	transcript_id "Phchi.S1G715900.t1"; gene_id "Phchi.S1G715900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8321.t1 is derived from g5496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35281929	35283320	.	-	.	Phchi.S1G548000
Phchi.S1	AUGUSTUS	transcript	35281929	35283320	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	stop_codon	35281926	35281928	.	-	0	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	CDS	35281929	35281982	1	-	0	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	exon	35281929	35281982	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	intron	35281983	35282063	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	CDS	35282064	35282247	1	-	1	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	exon	35282064	35282247	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	intron	35282248	35282359	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	CDS	35282360	35282610	0.92	-	0	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	exon	35282360	35282610	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	intron	35282611	35282722	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	CDS	35282723	35282855	0.89	-	1	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	exon	35282723	35282855	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	intron	35282856	35282951	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	CDS	35282952	35283085	0.77	-	0	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	exon	35282952	35283085	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	intron	35283086	35283194	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	CDS	35283195	35283320	0.47	-	0	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	exon	35283195	35283320	.	-	.	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
Phchi.S1	AUGUSTUS	start_codon	35283318	35283320	.	-	0	transcript_id "Phchi.S1G548000.t1"; gene_id "Phchi.S1G548000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2278.t1 is derived from g9198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5838064	5839077	.	+	.	Phchi.S5G088700
Phchi.S5	AUGUSTUS	transcript	5838064	5839077	.	+	.	transcript_id "Phchi.S5G088700.t1"; gene_id "Phchi.S5G088700"
Phchi.S5	AUGUSTUS	start_codon	5838064	5838066	.	+	0	transcript_id "Phchi.S5G088700.t1"; gene_id "Phchi.S5G088700"
Phchi.S5	AUGUSTUS	CDS	5838064	5839077	0.97	+	0	transcript_id "Phchi.S5G088700.t1"; gene_id "Phchi.S5G088700"
Phchi.S5	AUGUSTUS	exon	5838064	5839077	.	+	.	transcript_id "Phchi.S5G088700.t1"; gene_id "Phchi.S5G088700"
Phchi.S5	AUGUSTUS	stop_codon	5839078	5839080	.	+	0	transcript_id "Phchi.S5G088700.t1"; gene_id "Phchi.S5G088700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11195.t1 is derived from g15245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4640217	4641869	.	+	.	Phchi.S4G077700
Phchi.S4	AUGUSTUS	transcript	4640217	4641869	.	+	.	transcript_id "Phchi.S4G077700.t1"; gene_id "Phchi.S4G077700"
Phchi.S4	AUGUSTUS	start_codon	4640217	4640219	.	+	0	transcript_id "Phchi.S4G077700.t1"; gene_id "Phchi.S4G077700"
Phchi.S4	AUGUSTUS	CDS	4640217	4641869	0.8	+	0	transcript_id "Phchi.S4G077700.t1"; gene_id "Phchi.S4G077700"
Phchi.S4	AUGUSTUS	exon	4640217	4641869	.	+	.	transcript_id "Phchi.S4G077700.t1"; gene_id "Phchi.S4G077700"
Phchi.S4	AUGUSTUS	stop_codon	4641870	4641872	.	+	0	transcript_id "Phchi.S4G077700.t1"; gene_id "Phchi.S4G077700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4883.t1 is derived from g2053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13209718	13210812	.	-	.	Phchi.S1G204200
Phchi.S1	AUGUSTUS	transcript	13209718	13210812	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	stop_codon	13209715	13209717	.	-	0	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	CDS	13209718	13209816	1	-	0	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	exon	13209718	13209816	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	intron	13209817	13209957	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	CDS	13209958	13210044	1	-	0	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	exon	13209958	13210044	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	intron	13210045	13210153	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	CDS	13210154	13210218	1	-	2	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	exon	13210154	13210218	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	intron	13210219	13210420	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	CDS	13210421	13210502	1	-	0	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	exon	13210421	13210502	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	intron	13210503	13210656	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	CDS	13210657	13210812	1	-	0	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	exon	13210657	13210812	.	-	.	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
Phchi.S1	AUGUSTUS	start_codon	13210810	13210812	.	-	0	transcript_id "Phchi.S1G204200.t1"; gene_id "Phchi.S1G204200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10399.t1 is derived from g7575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47544320	47547127	.	+	.	Phchi.S1G755800
Phchi.S1	AUGUSTUS	transcript	47544320	47547127	.	+	.	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	start_codon	47544320	47544322	.	+	0	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	CDS	47544320	47544412	0.92	+	0	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	exon	47544320	47544412	.	+	.	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	intron	47544413	47544495	.	+	.	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	CDS	47544496	47546940	0.65	+	0	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	exon	47544496	47546940	.	+	.	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	intron	47546941	47547076	.	+	.	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	CDS	47547077	47547127	0.66	+	0	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	exon	47547077	47547127	.	+	.	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
Phchi.S1	AUGUSTUS	stop_codon	47547128	47547130	.	+	0	transcript_id "Phchi.S1G755800.t1"; gene_id "Phchi.S1G755800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3997.t1 is derived from g1166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6905352	6906480	.	-	.	Phchi.S1G115600
Phchi.S1	AUGUSTUS	transcript	6905352	6906480	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	stop_codon	6905349	6905351	.	-	0	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	CDS	6905352	6905618	0.96	-	0	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	exon	6905352	6905618	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	intron	6905619	6905789	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	CDS	6905790	6905833	1	-	2	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	exon	6905790	6905833	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	intron	6905834	6905925	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	CDS	6905926	6905983	1	-	0	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	exon	6905926	6905983	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	intron	6905984	6906130	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	CDS	6906131	6906224	1	-	1	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	exon	6906131	6906224	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	intron	6906225	6906334	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	CDS	6906335	6906480	0.86	-	0	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	exon	6906335	6906480	.	-	.	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
Phchi.S1	AUGUSTUS	start_codon	6906478	6906480	.	-	0	transcript_id "Phchi.S1G115600.t1"; gene_id "Phchi.S1G115600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7660.t1 is derived from g4834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30458185	30461192	.	+	.	Phchi.S1G481900
Phchi.S1	AUGUSTUS	transcript	30458185	30461192	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	start_codon	30458185	30458187	.	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	CDS	30458185	30459396	1	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	exon	30458185	30459396	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	intron	30459397	30459540	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	CDS	30459541	30459585	1	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	exon	30459541	30459585	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	intron	30459586	30459706	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	CDS	30459707	30460120	0.99	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	exon	30459707	30460120	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	intron	30460121	30460236	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	CDS	30460237	30460338	0.11	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	exon	30460237	30460338	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	intron	30460339	30460617	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	CDS	30460618	30460738	0.3	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	exon	30460618	30460738	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	intron	30460739	30460908	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	CDS	30460909	30461192	0.77	+	2	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	exon	30460909	30461192	.	+	.	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
Phchi.S1	AUGUSTUS	stop_codon	30461193	30461195	.	+	0	transcript_id "Phchi.S1G481900.t1"; gene_id "Phchi.S1G481900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3920.t1 is derived from g1089.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6431818	6434627	.	-	.	Phchi.S1G107900
Phchi.S1	AUGUSTUS	transcript	6431818	6433079	.	-	.	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	stop_codon	6431815	6431817	.	-	0	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	CDS	6431818	6431988	0.72	-	0	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	exon	6431818	6431988	.	-	.	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	intron	6431989	6432179	.	-	.	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	CDS	6432180	6433079	0.49	-	0	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	exon	6432180	6433079	.	-	.	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	start_codon	6433077	6433079	.	-	0	transcript_id "Phchi.S1G107900.t1"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	transcript	6432054	6434627	.	-	.	transcript_id "Phchi.S1G107900.t2"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	stop_codon	6432051	6432053	.	-	0	transcript_id "Phchi.S1G107900.t2"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	CDS	6432054	6434627	0.78	-	0	transcript_id "Phchi.S1G107900.t2"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	exon	6432054	6434627	.	-	.	transcript_id "Phchi.S1G107900.t2"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	start_codon	6434625	6434627	.	-	0	transcript_id "Phchi.S1G107900.t2"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	transcript	6432054	6434354	.	-	.	transcript_id "Phchi.S1G107900.t3"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	stop_codon	6432051	6432053	.	-	0	transcript_id "Phchi.S1G107900.t3"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	CDS	6432054	6434354	0.77	-	0	transcript_id "Phchi.S1G107900.t3"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	exon	6432054	6434354	.	-	.	transcript_id "Phchi.S1G107900.t3"; gene_id "Phchi.S1G107900"
Phchi.S1	AUGUSTUS	start_codon	6434352	6434354	.	-	0	transcript_id "Phchi.S1G107900.t3"; gene_id "Phchi.S1G107900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11507.t1 is derived from g15557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6804508	6804759	.	-	.	Phchi.S4G108900
Phchi.S4	AUGUSTUS	transcript	6804508	6804759	.	-	.	transcript_id "Phchi.S4G108900.t1"; gene_id "Phchi.S4G108900"
Phchi.S4	AUGUSTUS	stop_codon	6804505	6804507	.	-	0	transcript_id "Phchi.S4G108900.t1"; gene_id "Phchi.S4G108900"
Phchi.S4	AUGUSTUS	CDS	6804508	6804759	0.97	-	0	transcript_id "Phchi.S4G108900.t1"; gene_id "Phchi.S4G108900"
Phchi.S4	AUGUSTUS	exon	6804508	6804759	.	-	.	transcript_id "Phchi.S4G108900.t1"; gene_id "Phchi.S4G108900"
Phchi.S4	AUGUSTUS	start_codon	6804757	6804759	.	-	0	transcript_id "Phchi.S4G108900.t1"; gene_id "Phchi.S4G108900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7743.t1 is derived from g4917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30921544	30922745	.	-	.	Phchi.S1G490200
Phchi.S1	AUGUSTUS	transcript	30921544	30922745	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	stop_codon	30921541	30921543	.	-	0	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	CDS	30921544	30921733	1	-	1	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	exon	30921544	30921733	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	intron	30921734	30921822	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	CDS	30921823	30922032	1	-	1	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	exon	30921823	30922032	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	intron	30922033	30922116	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	CDS	30922117	30922355	0.94	-	0	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	exon	30922117	30922355	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	intron	30922356	30922472	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	CDS	30922473	30922745	0.56	-	0	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	exon	30922473	30922745	.	-	.	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
Phchi.S1	AUGUSTUS	start_codon	30922743	30922745	.	-	0	transcript_id "Phchi.S1G490200.t1"; gene_id "Phchi.S1G490200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5428.t1 is derived from g2598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16822350	16826024	.	+	.	Phchi.S1G258700
Phchi.S1	AUGUSTUS	transcript	16822350	16826024	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	start_codon	16822350	16822352	.	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16822350	16822372	0.63	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16822350	16822372	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16822373	16822546	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16822547	16822850	0.44	+	1	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16822547	16822850	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16822851	16822976	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16822977	16823220	1	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16822977	16823220	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16823221	16823352	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16823353	16823618	1	+	2	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16823353	16823618	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16823619	16823747	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16823748	16823842	1	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16823748	16823842	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16823843	16823981	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16823982	16824096	1	+	1	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16823982	16824096	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16824097	16824223	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16824224	16824429	1	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16824224	16824429	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16824430	16824511	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16824512	16824620	0.98	+	1	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16824512	16824620	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16824621	16824705	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16824706	16824761	0.93	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16824706	16824761	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16824762	16824871	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16824872	16824992	0.98	+	1	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16824872	16824992	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16824993	16825066	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16825067	16825302	0.98	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16825067	16825302	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16825303	16825380	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16825381	16825581	1	+	1	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16825381	16825581	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16825582	16825687	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16825688	16825835	1	+	1	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16825688	16825835	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	intron	16825836	16826015	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	CDS	16826016	16826024	1	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	exon	16826016	16826024	.	+	.	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
Phchi.S1	AUGUSTUS	stop_codon	16826025	16826027	.	+	0	transcript_id "Phchi.S1G258700.t1"; gene_id "Phchi.S1G258700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4095.t1 is derived from g1264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7797318	7799451	.	-	.	Phchi.S1G125400
Phchi.S1	AUGUSTUS	transcript	7797318	7799451	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	stop_codon	7797315	7797317	.	-	0	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	CDS	7797318	7797668	0.96	-	0	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	exon	7797318	7797668	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	intron	7797669	7797764	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	CDS	7797765	7798685	1	-	0	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	exon	7797765	7798685	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	intron	7798686	7798792	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	CDS	7798793	7799058	0.9	-	2	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	exon	7798793	7799058	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	intron	7799059	7799159	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	CDS	7799160	7799451	0.44	-	0	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	exon	7799160	7799451	.	-	.	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
Phchi.S1	AUGUSTUS	start_codon	7799449	7799451	.	-	0	transcript_id "Phchi.S1G125400.t1"; gene_id "Phchi.S1G125400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2254.t1 is derived from g9174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5702985	5703634	.	-	.	Phchi.S5G086300
Phchi.S5	AUGUSTUS	transcript	5702985	5703634	.	-	.	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	stop_codon	5702982	5702984	.	-	0	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	CDS	5702985	5703512	0.42	-	0	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	exon	5702985	5703512	.	-	.	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	intron	5703513	5703589	.	-	.	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	CDS	5703590	5703634	0.4	-	0	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	exon	5703590	5703634	.	-	.	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
Phchi.S5	AUGUSTUS	start_codon	5703632	5703634	.	-	0	transcript_id "Phchi.S5G086300.t1"; gene_id "Phchi.S5G086300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9220.t1 is derived from g6395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40465307	40466332	.	-	.	Phchi.S1G637900
Phchi.S1	AUGUSTUS	transcript	40465307	40466332	.	-	.	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	stop_codon	40465304	40465306	.	-	0	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	CDS	40465307	40465350	0.76	-	2	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	exon	40465307	40465350	.	-	.	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	intron	40465351	40465493	.	-	.	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	CDS	40465494	40465637	0.51	-	2	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	exon	40465494	40465637	.	-	.	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	intron	40465638	40465872	.	-	.	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	CDS	40465873	40466332	0.98	-	0	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	exon	40465873	40466332	.	-	.	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
Phchi.S1	AUGUSTUS	start_codon	40466330	40466332	.	-	0	transcript_id "Phchi.S1G637900.t1"; gene_id "Phchi.S1G637900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14630.t1 is derived from g13098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13839017	13840340	.	-	.	Phchi.S3G194900
Phchi.S3	AUGUSTUS	transcript	13839017	13840340	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	stop_codon	13839014	13839016	.	-	0	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	CDS	13839017	13839066	0.77	-	2	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	exon	13839017	13839066	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	intron	13839067	13839166	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	CDS	13839167	13839238	1	-	2	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	exon	13839167	13839238	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	intron	13839239	13839332	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	CDS	13839333	13839402	1	-	0	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	exon	13839333	13839402	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	intron	13839403	13839503	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	CDS	13839504	13839686	0.98	-	0	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	exon	13839504	13839686	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	intron	13839687	13840007	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	CDS	13840008	13840340	0.51	-	0	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	exon	13840008	13840340	.	-	.	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
Phchi.S3	AUGUSTUS	start_codon	13840338	13840340	.	-	0	transcript_id "Phchi.S3G194900.t1"; gene_id "Phchi.S3G194900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8158.t1 is derived from g5333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34173269	34183073	.	-	.	Phchi.S1G531700
Phchi.S1	AUGUSTUS	transcript	34173269	34183073	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	stop_codon	34173266	34173268	.	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34173269	34173562	0.72	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34173269	34173562	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34173563	34173709	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34173710	34173841	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34173710	34173841	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34173842	34173959	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34173960	34174052	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34173960	34174052	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34174053	34174143	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34174144	34174450	0.99	-	1	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34174144	34174450	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34174451	34174559	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34174560	34174844	1	-	1	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34174560	34174844	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34174845	34174937	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34174938	34175071	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34174938	34175071	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175072	34175186	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34175187	34175423	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34175187	34175423	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175424	34175521	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34175522	34175626	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34175522	34175626	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175627	34175827	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34175828	34175989	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34175828	34175989	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175990	34176141	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34176142	34176265	1	-	1	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34176142	34176265	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34176266	34176500	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34176501	34176670	0.99	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34176501	34176670	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34176671	34176772	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34176773	34176925	0.96	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34176773	34176925	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34176926	34177084	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34177085	34177384	0.7	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34177085	34177384	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34177385	34177680	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34177681	34177695	0.39	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34177681	34177695	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34177696	34177802	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34177803	34177847	0.55	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34177803	34177847	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34177848	34178115	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34178116	34178274	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34178116	34178274	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34178275	34178391	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34178392	34178442	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34178392	34178442	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34178443	34178671	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34178672	34178730	0.46	-	2	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34178672	34178730	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34178731	34179027	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179028	34179085	0.3	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179028	34179085	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34179086	34179218	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179219	34179250	0.47	-	2	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179219	34179250	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34179251	34179340	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179341	34179542	0.97	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179341	34179542	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34179543	34179623	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179624	34180040	0.97	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179624	34180040	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180041	34180180	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180181	34180367	1	-	1	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180181	34180367	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180368	34180447	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180448	34180462	1	-	1	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180448	34180462	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180463	34180515	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180516	34180552	1	-	2	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180516	34180552	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180553	34180649	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180650	34180764	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180650	34180764	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180765	34180962	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180963	34181070	1	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180963	34181070	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181071	34181185	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181186	34181221	0.88	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181186	34181221	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181222	34181307	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181308	34181438	1	-	2	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181308	34181438	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181439	34181514	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181515	34181620	0.77	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181515	34181620	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181621	34181923	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181924	34181947	0.44	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181924	34181947	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181948	34182003	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182004	34182071	0.5	-	2	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182004	34182071	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182072	34182215	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182216	34182328	1	-	1	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182216	34182328	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182329	34182449	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182450	34182568	0.44	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182450	34182568	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182569	34182858	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182859	34182888	0.54	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182859	34182888	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182889	34183055	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34183056	34183073	0.86	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34183056	34183073	.	-	.	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	start_codon	34183071	34183073	.	-	0	transcript_id "Phchi.S1G531700.t1"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	transcript	34173269	34183073	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	stop_codon	34173266	34173268	.	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34173269	34173562	0.73	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34173269	34173562	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34173563	34173709	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34173710	34173841	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34173710	34173841	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34173842	34173959	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34173960	34174052	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34173960	34174052	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34174053	34174143	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34174144	34174450	0.97	-	1	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34174144	34174450	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34174451	34174559	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34174560	34174844	0.97	-	1	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34174560	34174844	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34174845	34174937	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34174938	34175071	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34174938	34175071	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175072	34175186	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34175187	34175423	0.98	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34175187	34175423	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175424	34175521	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34175522	34175626	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34175522	34175626	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175627	34175827	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34175828	34175989	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34175828	34175989	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34175990	34176141	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34176142	34176265	1	-	1	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34176142	34176265	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34176266	34176500	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34176501	34176685	0.98	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34176501	34176685	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34176686	34176772	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34176773	34176925	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34176773	34176925	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34176926	34177084	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34177085	34177384	0.73	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34177085	34177384	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34177385	34177680	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34177681	34177695	0.5	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34177681	34177695	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34177696	34177802	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34177803	34177847	0.57	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34177803	34177847	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34177848	34178115	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34178116	34178274	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34178116	34178274	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34178275	34178391	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34178392	34178442	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34178392	34178442	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34178443	34178671	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34178672	34178730	0.47	-	2	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34178672	34178730	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34178731	34179027	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179028	34179085	0.29	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179028	34179085	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34179086	34179218	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179219	34179250	0.44	-	2	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179219	34179250	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34179251	34179340	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179341	34179542	0.97	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179341	34179542	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34179543	34179623	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34179624	34180040	0.98	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34179624	34180040	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180041	34180180	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180181	34180367	1	-	1	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180181	34180367	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180368	34180447	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180448	34180462	1	-	1	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180448	34180462	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180463	34180515	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180516	34180552	1	-	2	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180516	34180552	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180553	34180649	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180650	34180764	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180650	34180764	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34180765	34180962	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34180963	34181070	1	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34180963	34181070	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181071	34181185	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181186	34181221	0.87	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181186	34181221	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181222	34181307	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181308	34181438	1	-	2	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181308	34181438	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181439	34181514	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181515	34181620	0.79	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181515	34181620	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181621	34181923	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34181924	34181947	0.35	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34181924	34181947	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34181948	34182003	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182004	34182071	0.47	-	2	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182004	34182071	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182072	34182215	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182216	34182328	1	-	1	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182216	34182328	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182329	34182449	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182450	34182568	0.4	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182450	34182568	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182569	34182858	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34182859	34182888	0.54	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34182859	34182888	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	intron	34182889	34183055	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	CDS	34183056	34183073	0.82	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	exon	34183056	34183073	.	-	.	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
Phchi.S1	AUGUSTUS	start_codon	34183071	34183073	.	-	0	transcript_id "Phchi.S1G531700.t2"; gene_id "Phchi.S1G531700"
# This transcript jg13577.t2 is derived from g12044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13578.t1 is derived from g12045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7561332	7562491	.	+	.	Phchi.S3G089700
Phchi.S3	AUGUSTUS	transcript	7561332	7562491	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	start_codon	7561332	7561334	.	+	0	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	CDS	7561332	7561446	0.55	+	0	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	exon	7561332	7561446	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	intron	7561447	7561592	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	CDS	7561593	7561598	0.94	+	2	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	exon	7561593	7561598	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	intron	7561599	7561908	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	CDS	7561909	7562260	0.91	+	2	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	exon	7561909	7562260	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	intron	7562261	7562334	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	CDS	7562335	7562491	1	+	1	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	exon	7562335	7562491	.	+	.	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
Phchi.S3	AUGUSTUS	stop_codon	7562492	7562494	.	+	0	transcript_id "Phchi.S3G089700.t1"; gene_id "Phchi.S3G089700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4845.t1 is derived from g2015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13077369	13078219	.	+	.	Phchi.S1G200400
Phchi.S1	AUGUSTUS	transcript	13077369	13078219	.	+	.	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	start_codon	13077369	13077371	.	+	0	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	CDS	13077369	13077665	0.99	+	0	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	exon	13077369	13077665	.	+	.	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	intron	13077666	13077780	.	+	.	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	CDS	13077781	13077921	0.98	+	0	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	exon	13077781	13077921	.	+	.	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	intron	13077922	13078024	.	+	.	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	CDS	13078025	13078219	0.75	+	0	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	exon	13078025	13078219	.	+	.	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
Phchi.S1	AUGUSTUS	stop_codon	13078220	13078222	.	+	0	transcript_id "Phchi.S1G200400.t1"; gene_id "Phchi.S1G200400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8194.t1 is derived from g5369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34370916	34374315	.	-	.	Phchi.S1G535300
Phchi.S1	AUGUSTUS	transcript	34370916	34374315	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	stop_codon	34370913	34370915	.	-	0	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34370916	34371062	0.99	-	0	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34370916	34371062	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	intron	34371063	34371156	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34371157	34371460	1	-	1	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34371157	34371460	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	intron	34371461	34371545	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34371546	34371792	1	-	2	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34371546	34371792	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	intron	34371793	34371945	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34371946	34372121	1	-	1	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34371946	34372121	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	intron	34372122	34372274	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34372275	34373602	1	-	0	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34372275	34373602	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	intron	34373603	34373763	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34373764	34374022	1	-	1	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34373764	34374022	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	intron	34374023	34374178	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	CDS	34374179	34374315	0.93	-	0	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	exon	34374179	34374315	.	-	.	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
Phchi.S1	AUGUSTUS	start_codon	34374313	34374315	.	-	0	transcript_id "Phchi.S1G535300.t1"; gene_id "Phchi.S1G535300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12003.t1 is derived from g7678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	495159	499594	.	+	.	Phchi.S2G008300
Phchi.S2	AUGUSTUS	transcript	495159	499594	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	start_codon	495159	495161	.	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	495159	495323	0.52	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	495159	495323	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	495324	495513	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	495514	495573	1	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	495514	495573	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	495574	495660	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	495661	495775	1	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	495661	495775	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	495776	495871	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	495872	496197	1	+	2	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	495872	496197	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	496198	496311	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	496312	496368	1	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	496312	496368	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	496369	496643	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	496644	496728	1	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	496644	496728	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	496729	497083	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	497084	497133	1	+	2	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	497084	497133	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	497134	497219	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	497220	497314	1	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	497220	497314	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	497315	497433	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	497434	497513	1	+	1	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	497434	497513	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	497514	497696	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	497697	497780	1	+	2	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	497697	497780	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	497781	497872	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	497873	497989	0.62	+	2	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	497873	497989	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	497990	498113	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	498114	498190	0.46	+	2	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	498114	498190	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	498191	498296	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	498297	498407	0.61	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	498297	498407	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	498408	498540	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	498541	498607	0.61	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	498541	498607	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	498608	498716	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	498717	498793	0.72	+	2	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	498717	498793	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	intron	498794	498886	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	CDS	498887	499594	0.86	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	exon	498887	499594	.	+	.	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
Phchi.S2	AUGUSTUS	stop_codon	499595	499597	.	+	0	transcript_id "Phchi.S2G008300.t1"; gene_id "Phchi.S2G008300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10263.t1 is derived from g7439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46733410	46737042	.	-	.	Phchi.S1G742200
Phchi.S1	AUGUSTUS	transcript	46733410	46737042	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	stop_codon	46733407	46733409	.	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46733410	46733506	1	-	1	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46733410	46733506	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46733507	46733603	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46733604	46733689	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46733604	46733689	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46733690	46733790	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46733791	46733973	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46733791	46733973	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46733974	46734063	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734064	46734337	0.64	-	1	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734064	46734337	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734338	46734424	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734425	46734509	0.94	-	2	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734425	46734509	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734510	46734615	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734616	46734769	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734616	46734769	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734770	46734841	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734842	46734982	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734842	46734982	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734983	46735082	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735083	46735164	1	-	1	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735083	46735164	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735165	46735250	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735251	46735306	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735251	46735306	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735307	46735401	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735402	46735437	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735402	46735437	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735438	46735612	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735613	46735657	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735613	46735657	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735658	46735761	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735762	46735824	0.97	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735762	46735824	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735825	46735933	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735934	46735986	0.97	-	2	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735934	46735986	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735987	46736130	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736131	46736221	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736131	46736221	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736222	46736357	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736358	46736465	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736358	46736465	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736466	46736567	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736568	46736675	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736568	46736675	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736676	46736758	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736759	46736847	1	-	2	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736759	46736847	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736848	46736942	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736943	46737042	1	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736943	46737042	.	-	.	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	start_codon	46737040	46737042	.	-	0	transcript_id "Phchi.S1G742200.t1"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	transcript	46733410	46737042	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	stop_codon	46733407	46733409	.	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46733410	46733506	1	-	1	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46733410	46733506	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46733507	46733603	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46733604	46733689	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46733604	46733689	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46733690	46733790	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46733791	46733973	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46733791	46733973	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46733974	46734063	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734064	46734337	0.59	-	1	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734064	46734337	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734338	46734424	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734425	46734509	0.93	-	2	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734425	46734509	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734510	46734615	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734616	46734766	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734616	46734766	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734767	46734841	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46734842	46734982	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46734842	46734982	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46734983	46735082	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735083	46735164	1	-	1	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735083	46735164	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735165	46735250	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735251	46735306	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735251	46735306	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735307	46735401	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735402	46735437	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735402	46735437	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735438	46735612	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735613	46735657	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735613	46735657	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735658	46735761	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735762	46735824	0.96	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735762	46735824	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735825	46735933	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46735934	46735986	0.99	-	2	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46735934	46735986	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46735987	46736130	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736131	46736221	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736131	46736221	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736222	46736357	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736358	46736465	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736358	46736465	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736466	46736567	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736568	46736675	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736568	46736675	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736676	46736758	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736759	46736847	1	-	2	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736759	46736847	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	intron	46736848	46736942	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	CDS	46736943	46737042	1	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	exon	46736943	46737042	.	-	.	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
Phchi.S1	AUGUSTUS	start_codon	46737040	46737042	.	-	0	transcript_id "Phchi.S1G742200.t2"; gene_id "Phchi.S1G742200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10943.t1 is derived from g14993.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3214658	3217086	.	-	.	Phchi.S4G052500
Phchi.S4	AUGUSTUS	transcript	3214658	3217086	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	stop_codon	3214655	3214657	.	-	0	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3214658	3214713	0.64	-	2	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3214658	3214713	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3214714	3214861	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3214862	3214902	0.85	-	1	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3214862	3214902	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3214903	3215002	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3215003	3215073	0.49	-	0	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3215003	3215073	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3215074	3215162	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3215163	3215224	0.49	-	2	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3215163	3215224	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3215225	3215330	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3215331	3217086	0.48	-	0	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3215331	3217086	.	-	.	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	start_codon	3217084	3217086	.	-	0	transcript_id "Phchi.S4G052500.t1"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	transcript	3214658	3217086	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	stop_codon	3214655	3214657	.	-	0	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3214658	3214713	0.62	-	2	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3214658	3214713	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3214714	3214861	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3214862	3214905	0.78	-	1	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3214862	3214905	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3214906	3215002	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3215003	3215073	0.36	-	0	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3215003	3215073	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3215074	3215162	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3215163	3215224	0.34	-	2	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3215163	3215224	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	intron	3215225	3215330	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	CDS	3215331	3217086	0.35	-	0	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	exon	3215331	3217086	.	-	.	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
Phchi.S4	AUGUSTUS	start_codon	3217084	3217086	.	-	0	transcript_id "Phchi.S4G052500.t2"; gene_id "Phchi.S4G052500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4625.t1 is derived from g1795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11451032	11451712	.	-	.	Phchi.S1G178400
Phchi.S1	AUGUSTUS	transcript	11451032	11451712	.	-	.	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	stop_codon	11451029	11451031	.	-	0	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	CDS	11451032	11451097	1	-	0	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	exon	11451032	11451097	.	-	.	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	intron	11451098	11451194	.	-	.	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	CDS	11451195	11451298	0.7	-	2	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	exon	11451195	11451298	.	-	.	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	intron	11451299	11451639	.	-	.	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	CDS	11451640	11451712	0.7	-	0	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	exon	11451640	11451712	.	-	.	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
Phchi.S1	AUGUSTUS	start_codon	11451710	11451712	.	-	0	transcript_id "Phchi.S1G178400.t1"; gene_id "Phchi.S1G178400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9738.t1 is derived from g6914.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43457558	43459466	.	-	.	Phchi.S1G689700
Phchi.S1	AUGUSTUS	transcript	43457558	43459466	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	stop_codon	43457555	43457557	.	-	0	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	CDS	43457558	43457905	1	-	0	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	exon	43457558	43457905	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	intron	43457906	43458028	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	CDS	43458029	43458442	0.99	-	0	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	exon	43458029	43458442	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	intron	43458443	43458697	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	CDS	43458698	43458706	0.88	-	0	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	exon	43458698	43458706	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	intron	43458707	43458828	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	CDS	43458829	43458901	0.89	-	1	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	exon	43458829	43458901	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	intron	43458902	43459152	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	CDS	43459153	43459466	0.55	-	0	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	exon	43459153	43459466	.	-	.	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
Phchi.S1	AUGUSTUS	start_codon	43459464	43459466	.	-	0	transcript_id "Phchi.S1G689700.t1"; gene_id "Phchi.S1G689700"
# This transcript jg9418.t2 is derived from g6594.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9418.t3 is derived from g6594.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9419.t1 is derived from g6595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41399599	41401173	.	-	.	Phchi.S1G657800
Phchi.S1	AUGUSTUS	transcript	41399599	41401173	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	stop_codon	41399596	41399598	.	-	0	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41399599	41399612	0.94	-	2	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41399599	41399612	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41399613	41399697	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41399698	41399769	0.94	-	2	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41399698	41399769	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41399770	41399965	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41399966	41400096	0.65	-	1	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41399966	41400096	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41400097	41400182	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41400183	41400295	1	-	0	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41400183	41400295	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41400296	41400446	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41400447	41400569	1	-	0	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41400447	41400569	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41400570	41400646	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41400647	41400789	1	-	2	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41400647	41400789	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41400790	41400932	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41400933	41401047	1	-	0	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41400933	41401047	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	intron	41401048	41401131	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	CDS	41401132	41401173	0.99	-	0	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	exon	41401132	41401173	.	-	.	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
Phchi.S1	AUGUSTUS	start_codon	41401171	41401173	.	-	0	transcript_id "Phchi.S1G657800.t1"; gene_id "Phchi.S1G657800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15946.t1 is derived from g14439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	6501	7133	.	-	.	Phchi.C116G000200
Phchi.C116	AUGUSTUS	transcript	6501	7133	.	-	.	transcript_id "Phchi.C116G000200.t1"; gene_id "Phchi.C116G000200"
Phchi.C116	AUGUSTUS	stop_codon	6498	6500	.	-	0	transcript_id "Phchi.C116G000200.t1"; gene_id "Phchi.C116G000200"
Phchi.C116	AUGUSTUS	CDS	6501	7133	0.51	-	0	transcript_id "Phchi.C116G000200.t1"; gene_id "Phchi.C116G000200"
Phchi.C116	AUGUSTUS	exon	6501	7133	.	-	.	transcript_id "Phchi.C116G000200.t1"; gene_id "Phchi.C116G000200"
Phchi.C116	AUGUSTUS	start_codon	7131	7133	.	-	0	transcript_id "Phchi.C116G000200.t1"; gene_id "Phchi.C116G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2611.t1 is derived from g9531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7784530	7786066	.	+	.	Phchi.S5G122000
Phchi.S5	AUGUSTUS	transcript	7784530	7786066	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	start_codon	7784530	7784532	.	+	0	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	CDS	7784530	7784756	0.98	+	0	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	exon	7784530	7784756	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	intron	7784757	7784851	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	CDS	7784852	7785176	0.96	+	1	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	exon	7784852	7785176	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	intron	7785177	7785289	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	CDS	7785290	7785445	1	+	0	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	exon	7785290	7785445	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	intron	7785446	7785530	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	CDS	7785531	7785806	1	+	0	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	exon	7785531	7785806	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	intron	7785807	7785893	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	CDS	7785894	7785967	1	+	0	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	exon	7785894	7785967	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	intron	7785968	7786050	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	CDS	7786051	7786066	1	+	1	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	exon	7786051	7786066	.	+	.	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
Phchi.S5	AUGUSTUS	stop_codon	7786067	7786069	.	+	0	transcript_id "Phchi.S5G122000.t1"; gene_id "Phchi.S5G122000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15920.t1 is derived from g14390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22221232	22222210	.	+	.	Phchi.S3G323900
Phchi.S3	AUGUSTUS	transcript	22221232	22222210	.	+	.	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	start_codon	22221232	22221234	.	+	0	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	CDS	22221232	22221457	0.83	+	0	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	exon	22221232	22221457	.	+	.	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	intron	22221458	22222175	.	+	.	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	CDS	22222176	22222210	0.01	+	2	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	exon	22222176	22222210	.	+	.	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
Phchi.S3	AUGUSTUS	stop_codon	22222211	22222213	.	+	0	transcript_id "Phchi.S3G323900.t1"; gene_id "Phchi.S3G323900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13788.t1 is derived from g12255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8892138	8894665	.	-	.	Phchi.S3G110700
Phchi.S3	AUGUSTUS	transcript	8892138	8894665	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	stop_codon	8892135	8892137	.	-	0	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8892138	8892342	0.78	-	1	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8892138	8892342	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8892343	8892429	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8892430	8892501	1	-	1	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8892430	8892501	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8892502	8892603	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8892604	8892681	1	-	1	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8892604	8892681	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8892682	8892777	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8892778	8892849	1	-	1	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8892778	8892849	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8892850	8892941	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8892942	8893013	1	-	1	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8892942	8893013	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8893014	8893116	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8893117	8893240	1	-	2	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8893117	8893240	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8893241	8893338	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8893339	8893832	1	-	1	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8893339	8893832	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8893833	8893927	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8893928	8894477	0.98	-	2	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8893928	8894477	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	intron	8894478	8894577	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	CDS	8894578	8894665	0.99	-	0	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	exon	8894578	8894665	.	-	.	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
Phchi.S3	AUGUSTUS	start_codon	8894663	8894665	.	-	0	transcript_id "Phchi.S3G110700.t1"; gene_id "Phchi.S3G110700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11733.t1 is derived from g15785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7903006	7905113	.	-	.	Phchi.S4G131500
Phchi.S4	AUGUSTUS	transcript	7903006	7905113	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	stop_codon	7903003	7903005	.	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7903006	7903179	1	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7903006	7903179	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	intron	7903180	7903264	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7903265	7903324	1	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7903265	7903324	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	intron	7903325	7903408	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7903409	7903616	1	-	1	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7903409	7903616	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	intron	7903617	7903700	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7903701	7903939	1	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7903701	7903939	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	intron	7903940	7904028	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7904029	7904139	0.56	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7904029	7904139	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	intron	7904140	7904251	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7904252	7904306	0.67	-	1	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7904252	7904306	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	intron	7904307	7904382	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	CDS	7904383	7905113	1	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	exon	7904383	7905113	.	-	.	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
Phchi.S4	AUGUSTUS	start_codon	7905111	7905113	.	-	0	transcript_id "Phchi.S4G131500.t1"; gene_id "Phchi.S4G131500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10936.t1 is derived from g14986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3179387	3179680	.	+	.	Phchi.S4G051800
Phchi.S4	AUGUSTUS	transcript	3179387	3179680	.	+	.	transcript_id "Phchi.S4G051800.t1"; gene_id "Phchi.S4G051800"
Phchi.S4	AUGUSTUS	start_codon	3179387	3179389	.	+	0	transcript_id "Phchi.S4G051800.t1"; gene_id "Phchi.S4G051800"
Phchi.S4	AUGUSTUS	CDS	3179387	3179680	0.57	+	0	transcript_id "Phchi.S4G051800.t1"; gene_id "Phchi.S4G051800"
Phchi.S4	AUGUSTUS	exon	3179387	3179680	.	+	.	transcript_id "Phchi.S4G051800.t1"; gene_id "Phchi.S4G051800"
Phchi.S4	AUGUSTUS	stop_codon	3179681	3179683	.	+	0	transcript_id "Phchi.S4G051800.t1"; gene_id "Phchi.S4G051800"
# This transcript jg10903.t2 is derived from g14953.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10904.t1 is derived from g14954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2838172	2839213	.	-	.	Phchi.S4G048600
Phchi.S4	AUGUSTUS	transcript	2838172	2839213	.	-	.	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	stop_codon	2838169	2838171	.	-	0	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	CDS	2838172	2838227	0.79	-	2	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	exon	2838172	2838227	.	-	.	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	intron	2838228	2838504	.	-	.	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	CDS	2838505	2839213	0.77	-	0	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	exon	2838505	2839213	.	-	.	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
Phchi.S4	AUGUSTUS	start_codon	2839211	2839213	.	-	0	transcript_id "Phchi.S4G048600.t1"; gene_id "Phchi.S4G048600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg36.t1 is derived from g9796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C67	AUGUSTUS	gene	11074	11625	.	-	.	Phchi.C67G000200
Phchi.C67	AUGUSTUS	transcript	11074	11625	.	-	.	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	stop_codon	11071	11073	.	-	0	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	CDS	11074	11172	0.72	-	0	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	exon	11074	11172	.	-	.	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	intron	11173	11370	.	-	.	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	CDS	11371	11625	0.48	-	0	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	exon	11371	11625	.	-	.	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
Phchi.C67	AUGUSTUS	start_codon	11623	11625	.	-	0	transcript_id "Phchi.C67G000200.t1"; gene_id "Phchi.C67G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10128.t1 is derived from g7304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45858096	45861357	.	+	.	Phchi.S1G728700
Phchi.S1	AUGUSTUS	transcript	45858096	45861357	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	start_codon	45858096	45858098	.	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45858096	45858392	0.96	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45858096	45858392	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45858393	45858492	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45858493	45858684	0.89	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45858493	45858684	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45858685	45858808	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45858809	45859015	0.89	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45858809	45859015	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45859016	45859101	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45859102	45859367	0.98	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45859102	45859367	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45859368	45859448	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45859449	45859611	1	+	1	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45859449	45859611	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45859612	45859698	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45859699	45859926	1	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45859699	45859926	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45859927	45860012	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45860013	45860205	1	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45860013	45860205	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45860206	45860303	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45860304	45860452	1	+	2	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45860304	45860452	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45860453	45860551	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45860552	45861093	0.99	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45860552	45861093	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	intron	45861094	45861173	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	CDS	45861174	45861357	0.99	+	1	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	exon	45861174	45861357	.	+	.	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
Phchi.S1	AUGUSTUS	stop_codon	45861358	45861360	.	+	0	transcript_id "Phchi.S1G728700.t1"; gene_id "Phchi.S1G728700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3457.t1 is derived from g626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3867215	3869750	.	-	.	Phchi.S1G061600
Phchi.S1	AUGUSTUS	transcript	3867215	3869750	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	stop_codon	3867212	3867214	.	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3867215	3867301	0.7	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3867215	3867301	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3867302	3867393	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3867394	3867480	0.95	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3867394	3867480	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3867481	3867587	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3867588	3867629	0.99	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3867588	3867629	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3867630	3867766	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3867767	3867877	1	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3867767	3867877	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3867878	3867976	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3867977	3868076	1	-	1	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3867977	3868076	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3868077	3868189	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3868190	3868272	1	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3868190	3868272	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3868273	3868371	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3868372	3868437	0.99	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3868372	3868437	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3868438	3868566	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3868567	3868618	0.85	-	1	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3868567	3868618	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3868619	3868713	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3868714	3868854	0.89	-	1	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3868714	3868854	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3868855	3869041	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3869042	3869147	1	-	2	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3869042	3869147	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	intron	3869148	3869317	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	CDS	3869318	3869750	0.88	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	exon	3869318	3869750	.	-	.	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
Phchi.S1	AUGUSTUS	start_codon	3869748	3869750	.	-	0	transcript_id "Phchi.S1G061600.t1"; gene_id "Phchi.S1G061600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15227.t1 is derived from g13695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17830534	17833586	.	+	.	Phchi.S3G254600
Phchi.S3	AUGUSTUS	transcript	17830534	17833586	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	start_codon	17830534	17830536	.	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17830534	17830688	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17830534	17830688	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17830689	17830785	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17830786	17830885	1	+	1	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17830786	17830885	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17830886	17831024	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17831025	17831102	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17831025	17831102	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17831103	17831185	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17831186	17831257	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17831186	17831257	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17831258	17831395	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17831396	17831517	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17831396	17831517	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17831518	17831645	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17831646	17831730	0.84	+	1	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17831646	17831730	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17831731	17831834	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17831835	17831924	0.97	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17831835	17831924	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17831925	17832043	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17832044	17832145	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17832044	17832145	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17832146	17832256	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17832257	17832346	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17832257	17832346	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17832347	17832485	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17832486	17832566	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17832486	17832566	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17832567	17832670	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17832671	17832742	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17832671	17832742	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17832743	17832826	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17832827	17832921	1	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17832827	17832921	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17832922	17832999	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17833000	17833088	1	+	1	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17833000	17833088	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17833089	17833165	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17833166	17833228	1	+	2	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17833166	17833228	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17833229	17833304	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17833305	17833345	0.95	+	2	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17833305	17833345	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	intron	17833346	17833448	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	CDS	17833449	17833586	0.95	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	exon	17833449	17833586	.	+	.	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
Phchi.S3	AUGUSTUS	stop_codon	17833587	17833589	.	+	0	transcript_id "Phchi.S3G254600.t1"; gene_id "Phchi.S3G254600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3385.t1 is derived from g554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3287775	3292010	.	-	.	Phchi.S1G054400
Phchi.S1	AUGUSTUS	transcript	3287775	3292010	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	stop_codon	3287772	3287774	.	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3287775	3287918	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3287775	3287918	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3287919	3288009	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3288010	3288156	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3288010	3288156	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3288157	3288253	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3288254	3288365	1	-	1	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3288254	3288365	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3288366	3288471	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3288472	3288653	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3288472	3288653	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3288654	3288736	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3288737	3288868	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3288737	3288868	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3288869	3288965	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3288966	3290231	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3288966	3290231	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3290232	3290330	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3290331	3291560	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3290331	3291560	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3291561	3291661	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3291662	3291753	0.99	-	2	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3291662	3291753	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	intron	3291754	3291913	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	CDS	3291914	3292010	1	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	exon	3291914	3292010	.	-	.	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
Phchi.S1	AUGUSTUS	start_codon	3292008	3292010	.	-	0	transcript_id "Phchi.S1G054400.t1"; gene_id "Phchi.S1G054400"
# This transcript jg13980.t2 is derived from g12447.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13981.t1 is derived from g12448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10037899	10039951	.	-	.	Phchi.S3G130000
Phchi.S3	AUGUSTUS	transcript	10037899	10039951	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	stop_codon	10037896	10037898	.	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10037899	10038108	0.98	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10037899	10038108	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10038109	10038187	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10038188	10038388	0.61	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10038188	10038388	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10038389	10038567	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10038568	10038693	0.93	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10038568	10038693	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10038694	10038838	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10038839	10038985	0.9	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10038839	10038985	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10038986	10039058	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10039059	10039247	1	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10039059	10039247	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10039248	10039418	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10039419	10039577	1	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10039419	10039577	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10039578	10039695	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10039696	10039758	1	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10039696	10039758	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	intron	10039759	10039870	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	CDS	10039871	10039951	1	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	exon	10039871	10039951	.	-	.	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
Phchi.S3	AUGUSTUS	start_codon	10039949	10039951	.	-	0	transcript_id "Phchi.S3G130000.t1"; gene_id "Phchi.S3G130000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13688.t1 is derived from g12155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8207902	8209236	.	-	.	Phchi.S3G100700
Phchi.S3	AUGUSTUS	transcript	8207902	8209236	.	-	.	transcript_id "Phchi.S3G100700.t1"; gene_id "Phchi.S3G100700"
Phchi.S3	AUGUSTUS	stop_codon	8207899	8207901	.	-	0	transcript_id "Phchi.S3G100700.t1"; gene_id "Phchi.S3G100700"
Phchi.S3	AUGUSTUS	CDS	8207902	8209236	1	-	0	transcript_id "Phchi.S3G100700.t1"; gene_id "Phchi.S3G100700"
Phchi.S3	AUGUSTUS	exon	8207902	8209236	.	-	.	transcript_id "Phchi.S3G100700.t1"; gene_id "Phchi.S3G100700"
Phchi.S3	AUGUSTUS	start_codon	8209234	8209236	.	-	0	transcript_id "Phchi.S3G100700.t1"; gene_id "Phchi.S3G100700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg595.t1 is derived from g10377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4332860	4334194	.	-	.	Phchi.S6G055400
Phchi.S6	AUGUSTUS	transcript	4332860	4334194	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	stop_codon	4332857	4332859	.	-	0	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4332860	4332948	0.97	-	2	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4332860	4332948	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	intron	4332949	4333060	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4333061	4333261	0.98	-	2	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4333061	4333261	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	intron	4333262	4333362	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4333363	4333446	1	-	2	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4333363	4333446	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	intron	4333447	4333570	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4333571	4333632	1	-	1	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4333571	4333632	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	intron	4333633	4333706	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4333707	4333748	1	-	1	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4333707	4333748	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	intron	4333749	4333885	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4333886	4333934	1	-	2	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4333886	4333934	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	intron	4333935	4334130	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	CDS	4334131	4334194	0.48	-	0	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	exon	4334131	4334194	.	-	.	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
Phchi.S6	AUGUSTUS	start_codon	4334192	4334194	.	-	0	transcript_id "Phchi.S6G055400.t1"; gene_id "Phchi.S6G055400"
# This transcript jg14657.t2 is derived from g13125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14658.t1 is derived from g13126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13995004	13996096	.	+	.	Phchi.S3G197700
Phchi.S3	AUGUSTUS	transcript	13995004	13996096	.	+	.	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	start_codon	13995004	13995006	.	+	0	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	CDS	13995004	13995289	0.75	+	0	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	exon	13995004	13995289	.	+	.	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	intron	13995290	13995527	.	+	.	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	CDS	13995528	13996096	0.9	+	2	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	exon	13995528	13996096	.	+	.	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
Phchi.S3	AUGUSTUS	stop_codon	13996097	13996099	.	+	0	transcript_id "Phchi.S3G197700.t1"; gene_id "Phchi.S3G197700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11358.t1 is derived from g15408.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5739514	5742110	.	+	.	Phchi.S4G094000
Phchi.S4	AUGUSTUS	transcript	5739514	5742110	.	+	.	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	start_codon	5739514	5739516	.	+	0	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	CDS	5739514	5740416	0.32	+	0	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	exon	5739514	5740416	.	+	.	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	intron	5740417	5740520	.	+	.	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	CDS	5740521	5742110	0.76	+	0	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	exon	5740521	5742110	.	+	.	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	stop_codon	5742111	5742113	.	+	0	transcript_id "Phchi.S4G094000.t1"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	transcript	5739838	5742110	.	+	.	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	start_codon	5739838	5739840	.	+	0	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	CDS	5739838	5740416	0.38	+	0	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	exon	5739838	5740416	.	+	.	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	intron	5740417	5740520	.	+	.	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	CDS	5740521	5742110	0.75	+	0	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	exon	5740521	5742110	.	+	.	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
Phchi.S4	AUGUSTUS	stop_codon	5742111	5742113	.	+	0	transcript_id "Phchi.S4G094000.t2"; gene_id "Phchi.S4G094000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6977.t1 is derived from g4149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26248378	26248803	.	-	.	Phchi.S1G413600
Phchi.S1	AUGUSTUS	transcript	26248378	26248803	.	-	.	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	stop_codon	26248375	26248377	.	-	0	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	CDS	26248378	26248394	0.83	-	2	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	exon	26248378	26248394	.	-	.	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	intron	26248395	26248488	.	-	.	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	CDS	26248489	26248633	0.83	-	0	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	exon	26248489	26248633	.	-	.	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	intron	26248634	26248731	.	-	.	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	CDS	26248732	26248803	0.99	-	0	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	exon	26248732	26248803	.	-	.	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
Phchi.S1	AUGUSTUS	start_codon	26248801	26248803	.	-	0	transcript_id "Phchi.S1G413600.t1"; gene_id "Phchi.S1G413600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9690.t1 is derived from g6866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43297830	43299752	.	+	.	Phchi.S1G684900
Phchi.S1	AUGUSTUS	transcript	43297830	43299752	.	+	.	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	start_codon	43297830	43297832	.	+	0	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	CDS	43297830	43298478	0.65	+	0	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	exon	43297830	43298478	.	+	.	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	intron	43298479	43298572	.	+	.	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	CDS	43298573	43299002	0.68	+	2	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	exon	43298573	43299002	.	+	.	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	intron	43299003	43299076	.	+	.	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	CDS	43299077	43299752	0.53	+	1	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	exon	43299077	43299752	.	+	.	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
Phchi.S1	AUGUSTUS	stop_codon	43299753	43299755	.	+	0	transcript_id "Phchi.S1G684900.t1"; gene_id "Phchi.S1G684900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9157.t1 is derived from g6332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40137902	40142204	.	-	.	Phchi.S1G631600
Phchi.S1	AUGUSTUS	transcript	40137902	40142204	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	stop_codon	40137899	40137901	.	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40137902	40138880	0.97	-	1	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40137902	40138880	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40138881	40139090	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40139091	40139404	0.99	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40139091	40139404	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40139405	40139523	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40139524	40139583	1	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40139524	40139583	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40139584	40139699	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40139700	40139835	0.98	-	1	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40139700	40139835	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40139836	40139970	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40139971	40140246	1	-	1	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40139971	40140246	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40140247	40140398	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40140399	40140583	1	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40140399	40140583	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40140584	40140678	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40140679	40141192	0.99	-	1	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40140679	40141192	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40141193	40141307	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40141308	40141348	1	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40141308	40141348	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40141349	40141619	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40141620	40141695	1	-	1	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40141620	40141695	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	intron	40141696	40142013	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	CDS	40142014	40142204	1	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	exon	40142014	40142204	.	-	.	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
Phchi.S1	AUGUSTUS	start_codon	40142202	40142204	.	-	0	transcript_id "Phchi.S1G631600.t1"; gene_id "Phchi.S1G631600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11389.t1 is derived from g15439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6106777	6107412	.	-	.	Phchi.S4G097100
Phchi.S4	AUGUSTUS	transcript	6106777	6107412	.	-	.	transcript_id "Phchi.S4G097100.t1"; gene_id "Phchi.S4G097100"
Phchi.S4	AUGUSTUS	stop_codon	6106774	6106776	.	-	0	transcript_id "Phchi.S4G097100.t1"; gene_id "Phchi.S4G097100"
Phchi.S4	AUGUSTUS	CDS	6106777	6107412	0.73	-	0	transcript_id "Phchi.S4G097100.t1"; gene_id "Phchi.S4G097100"
Phchi.S4	AUGUSTUS	exon	6106777	6107412	.	-	.	transcript_id "Phchi.S4G097100.t1"; gene_id "Phchi.S4G097100"
Phchi.S4	AUGUSTUS	start_codon	6107410	6107412	.	-	0	transcript_id "Phchi.S4G097100.t1"; gene_id "Phchi.S4G097100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2139.t1 is derived from g9059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5023407	5024121	.	+	.	Phchi.S5G074800
Phchi.S5	AUGUSTUS	transcript	5023407	5024121	.	+	.	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	start_codon	5023407	5023409	.	+	0	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	CDS	5023407	5023742	0.97	+	0	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	exon	5023407	5023742	.	+	.	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	intron	5023743	5023837	.	+	.	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	CDS	5023838	5023844	1	+	0	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	exon	5023838	5023844	.	+	.	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	intron	5023845	5024011	.	+	.	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	CDS	5024012	5024121	1	+	2	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	exon	5024012	5024121	.	+	.	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
Phchi.S5	AUGUSTUS	stop_codon	5024122	5024124	.	+	0	transcript_id "Phchi.S5G074800.t1"; gene_id "Phchi.S5G074800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4745.t1 is derived from g1915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12604628	12605885	.	-	.	Phchi.S1G190400
Phchi.S1	AUGUSTUS	transcript	12604628	12605885	.	-	.	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	stop_codon	12604625	12604627	.	-	0	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	CDS	12604628	12605635	0.99	-	0	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	exon	12604628	12605635	.	-	.	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	intron	12605636	12605714	.	-	.	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	CDS	12605715	12605885	1	-	0	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	exon	12605715	12605885	.	-	.	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
Phchi.S1	AUGUSTUS	start_codon	12605883	12605885	.	-	0	transcript_id "Phchi.S1G190400.t1"; gene_id "Phchi.S1G190400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13640.t1 is derived from g12107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7968957	7969220	.	+	.	Phchi.S3G095900
Phchi.S3	AUGUSTUS	transcript	7968957	7969220	.	+	.	transcript_id "Phchi.S3G095900.t1"; gene_id "Phchi.S3G095900"
Phchi.S3	AUGUSTUS	start_codon	7968957	7968959	.	+	0	transcript_id "Phchi.S3G095900.t1"; gene_id "Phchi.S3G095900"
Phchi.S3	AUGUSTUS	CDS	7968957	7969220	0.4	+	0	transcript_id "Phchi.S3G095900.t1"; gene_id "Phchi.S3G095900"
Phchi.S3	AUGUSTUS	exon	7968957	7969220	.	+	.	transcript_id "Phchi.S3G095900.t1"; gene_id "Phchi.S3G095900"
Phchi.S3	AUGUSTUS	stop_codon	7969221	7969223	.	+	0	transcript_id "Phchi.S3G095900.t1"; gene_id "Phchi.S3G095900"
# This transcript jg14862.t2 is derived from g13330.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14863.t1 is derived from g13331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15094971	15095704	.	+	.	Phchi.S3G218200
Phchi.S3	AUGUSTUS	transcript	15094971	15095704	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	start_codon	15094971	15094973	.	+	0	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	CDS	15094971	15094989	0.36	+	0	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	exon	15094971	15094989	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	intron	15094990	15095140	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	CDS	15095141	15095177	0.47	+	2	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	exon	15095141	15095177	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	intron	15095178	15095314	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	CDS	15095315	15095342	1	+	1	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	exon	15095315	15095342	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	intron	15095343	15095477	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	CDS	15095478	15095532	1	+	0	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	exon	15095478	15095532	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	intron	15095533	15095609	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	CDS	15095610	15095704	1	+	2	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	exon	15095610	15095704	.	+	.	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
Phchi.S3	AUGUSTUS	stop_codon	15095705	15095707	.	+	0	transcript_id "Phchi.S3G218200.t1"; gene_id "Phchi.S3G218200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14118.t1 is derived from g12585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10958315	10962347	.	-	.	Phchi.S3G143700
Phchi.S3	AUGUSTUS	transcript	10958315	10962347	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	stop_codon	10958312	10958314	.	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10958315	10958416	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10958315	10958416	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10958417	10958506	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10958507	10958584	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10958507	10958584	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10958585	10958669	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10958670	10958766	1	-	1	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10958670	10958766	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10958767	10958851	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10958852	10959006	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10958852	10959006	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10959007	10959094	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10959095	10959190	0.99	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10959095	10959190	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10959191	10959294	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10959295	10959356	1	-	2	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10959295	10959356	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10959357	10959453	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10959454	10959526	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10959454	10959526	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10959527	10959600	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10959601	10959682	0.84	-	1	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10959601	10959682	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10959683	10959787	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10959788	10959905	0.8	-	2	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10959788	10959905	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10959906	10960115	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10960116	10960176	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10960116	10960176	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10960177	10960271	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10960272	10960336	1	-	2	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10960272	10960336	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10960337	10960509	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10960510	10960746	1	-	2	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10960510	10960746	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10960747	10960833	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10960834	10960922	1	-	1	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10960834	10960922	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10960923	10961108	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10961109	10961161	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10961109	10961161	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10961162	10961288	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10961289	10961472	1	-	1	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10961289	10961472	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10961473	10961608	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10961609	10961690	0.93	-	2	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10961609	10961690	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10961691	10961802	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10961803	10961997	0.68	-	2	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10961803	10961997	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	intron	10961998	10962337	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	CDS	10962338	10962347	1	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	exon	10962338	10962347	.	-	.	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
Phchi.S3	AUGUSTUS	start_codon	10962345	10962347	.	-	0	transcript_id "Phchi.S3G143700.t1"; gene_id "Phchi.S3G143700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6971.t1 is derived from g4143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26229276	26232750	.	-	.	Phchi.S1G413000
Phchi.S1	AUGUSTUS	transcript	26229276	26232750	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	stop_codon	26229273	26229275	.	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26229276	26229377	1	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26229276	26229377	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26229378	26229463	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26229464	26229604	1	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26229464	26229604	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26229605	26229708	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26229709	26229764	1	-	2	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26229709	26229764	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26229765	26229849	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26229850	26229984	1	-	2	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26229850	26229984	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26229985	26230071	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26230072	26230258	1	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26230072	26230258	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26230259	26230347	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26230348	26230486	1	-	1	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26230348	26230486	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26230487	26230649	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26230650	26230712	0.99	-	1	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26230650	26230712	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26230713	26230819	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26230820	26230901	0.93	-	2	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26230820	26230901	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26230902	26231002	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26231003	26231081	0.93	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26231003	26231081	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26231082	26231174	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26231175	26231357	1	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26231175	26231357	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26231358	26231487	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26231488	26231732	1	-	2	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26231488	26231732	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26231733	26231863	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26231864	26231966	0.98	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26231864	26231966	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26231967	26232076	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26232077	26232208	0.88	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26232077	26232208	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26232209	26232346	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26232347	26232523	0.99	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26232347	26232523	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	intron	26232524	26232636	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	CDS	26232637	26232750	0.83	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	exon	26232637	26232750	.	-	.	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
Phchi.S1	AUGUSTUS	start_codon	26232748	26232750	.	-	0	transcript_id "Phchi.S1G413000.t1"; gene_id "Phchi.S1G413000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8699.t1 is derived from g5874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37520369	37521325	.	-	.	Phchi.S1G585800
Phchi.S1	AUGUSTUS	transcript	37520369	37521325	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	stop_codon	37520366	37520368	.	-	0	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	CDS	37520369	37520469	1	-	2	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	exon	37520369	37520469	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	intron	37520470	37520742	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	CDS	37520743	37520784	1	-	2	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	exon	37520743	37520784	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	intron	37520785	37520890	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	CDS	37520891	37520952	0.98	-	1	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	exon	37520891	37520952	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	intron	37520953	37521299	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	CDS	37521300	37521325	0.77	-	0	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	exon	37521300	37521325	.	-	.	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
Phchi.S1	AUGUSTUS	start_codon	37521323	37521325	.	-	0	transcript_id "Phchi.S1G585800.t1"; gene_id "Phchi.S1G585800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8710.t1 is derived from g5885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37589970	37590664	.	+	.	Phchi.S1G586900
Phchi.S1	AUGUSTUS	transcript	37589970	37590664	.	+	.	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	start_codon	37589970	37589972	.	+	0	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	CDS	37589970	37590175	0.77	+	0	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	exon	37589970	37590175	.	+	.	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	intron	37590176	37590284	.	+	.	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	CDS	37590285	37590308	0.95	+	1	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	exon	37590285	37590308	.	+	.	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	intron	37590309	37590639	.	+	.	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	CDS	37590640	37590664	1	+	1	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	exon	37590640	37590664	.	+	.	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
Phchi.S1	AUGUSTUS	stop_codon	37590665	37590667	.	+	0	transcript_id "Phchi.S1G586900.t1"; gene_id "Phchi.S1G586900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4720.t1 is derived from g1890.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12457655	12460331	.	-	.	Phchi.S1G187900
Phchi.S1	AUGUSTUS	transcript	12457655	12460331	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	stop_codon	12457652	12457654	.	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12457655	12457724	1	-	1	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12457655	12457724	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12457725	12457801	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12457802	12457899	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12457802	12457899	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12457900	12458007	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458008	12458073	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458008	12458073	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458074	12458202	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458203	12458256	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458203	12458256	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458257	12458332	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458333	12458422	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458333	12458422	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458423	12458507	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458508	12458556	1	-	1	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458508	12458556	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458557	12458692	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458693	12458823	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458693	12458823	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458824	12459045	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459046	12459144	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459046	12459144	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459145	12459280	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459281	12459316	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459281	12459316	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459317	12459551	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459552	12459642	1	-	1	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459552	12459642	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459643	12459724	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459725	12459911	1	-	2	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459725	12459911	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459912	12459986	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459987	12460074	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459987	12460074	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12460075	12460247	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12460248	12460331	1	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12460248	12460331	.	-	.	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	start_codon	12460329	12460331	.	-	0	transcript_id "Phchi.S1G187900.t1"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	transcript	12457655	12460331	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	stop_codon	12457652	12457654	.	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12457655	12457724	1	-	1	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12457655	12457724	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12457725	12457801	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12457802	12457899	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12457802	12457899	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12457900	12458007	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458008	12458073	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458008	12458073	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458074	12458202	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458203	12458256	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458203	12458256	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458257	12458332	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458333	12458422	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458333	12458422	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458423	12458507	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458508	12458556	1	-	1	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458508	12458556	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458557	12458692	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12458693	12458823	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12458693	12458823	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12458824	12459045	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459046	12459144	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459046	12459144	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459145	12459280	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459281	12459316	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459281	12459316	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459317	12459551	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459552	12459642	1	-	1	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459552	12459642	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459643	12459724	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459725	12459818	0.52	-	2	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459725	12459818	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12459819	12459986	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12459987	12460074	0.96	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12459987	12460074	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	intron	12460075	12460247	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	CDS	12460248	12460331	1	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	exon	12460248	12460331	.	-	.	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
Phchi.S1	AUGUSTUS	start_codon	12460329	12460331	.	-	0	transcript_id "Phchi.S1G187900.t2"; gene_id "Phchi.S1G187900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13580.t1 is derived from g12047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7569742	7570650	.	-	.	Phchi.S3G089900
Phchi.S3	AUGUSTUS	transcript	7569742	7570650	.	-	.	transcript_id "Phchi.S3G089900.t1"; gene_id "Phchi.S3G089900"
Phchi.S3	AUGUSTUS	stop_codon	7569739	7569741	.	-	0	transcript_id "Phchi.S3G089900.t1"; gene_id "Phchi.S3G089900"
Phchi.S3	AUGUSTUS	CDS	7569742	7570650	0.7	-	0	transcript_id "Phchi.S3G089900.t1"; gene_id "Phchi.S3G089900"
Phchi.S3	AUGUSTUS	exon	7569742	7570650	.	-	.	transcript_id "Phchi.S3G089900.t1"; gene_id "Phchi.S3G089900"
Phchi.S3	AUGUSTUS	start_codon	7570648	7570650	.	-	0	transcript_id "Phchi.S3G089900.t1"; gene_id "Phchi.S3G089900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10411.t1 is derived from g7587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47722851	47724692	.	-	.	Phchi.S1G757000
Phchi.S1	AUGUSTUS	transcript	47722851	47724692	.	-	.	transcript_id "Phchi.S1G757000.t1"; gene_id "Phchi.S1G757000"
Phchi.S1	AUGUSTUS	stop_codon	47722848	47722850	.	-	0	transcript_id "Phchi.S1G757000.t1"; gene_id "Phchi.S1G757000"
Phchi.S1	AUGUSTUS	CDS	47722851	47724692	0.41	-	0	transcript_id "Phchi.S1G757000.t1"; gene_id "Phchi.S1G757000"
Phchi.S1	AUGUSTUS	exon	47722851	47724692	.	-	.	transcript_id "Phchi.S1G757000.t1"; gene_id "Phchi.S1G757000"
Phchi.S1	AUGUSTUS	start_codon	47724690	47724692	.	-	0	transcript_id "Phchi.S1G757000.t1"; gene_id "Phchi.S1G757000"
# This transcript jg5442.t2 is derived from g2612.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5443.t1 is derived from g2613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16891233	16891834	.	+	.	Phchi.S1G260200
Phchi.S1	AUGUSTUS	transcript	16891233	16891834	.	+	.	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	start_codon	16891233	16891235	.	+	0	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	CDS	16891233	16891245	0.89	+	0	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	exon	16891233	16891245	.	+	.	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	intron	16891246	16891471	.	+	.	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	CDS	16891472	16891563	0.9	+	2	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	exon	16891472	16891563	.	+	.	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	intron	16891564	16891639	.	+	.	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	CDS	16891640	16891834	0.94	+	0	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	exon	16891640	16891834	.	+	.	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
Phchi.S1	AUGUSTUS	stop_codon	16891835	16891837	.	+	0	transcript_id "Phchi.S1G260200.t1"; gene_id "Phchi.S1G260200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9996.t1 is derived from g7172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44917502	44918254	.	+	.	Phchi.S1G715500
Phchi.S1	AUGUSTUS	transcript	44917502	44918254	.	+	.	transcript_id "Phchi.S1G715500.t1"; gene_id "Phchi.S1G715500"
Phchi.S1	AUGUSTUS	start_codon	44917502	44917504	.	+	0	transcript_id "Phchi.S1G715500.t1"; gene_id "Phchi.S1G715500"
Phchi.S1	AUGUSTUS	CDS	44917502	44918254	0.88	+	0	transcript_id "Phchi.S1G715500.t1"; gene_id "Phchi.S1G715500"
Phchi.S1	AUGUSTUS	exon	44917502	44918254	.	+	.	transcript_id "Phchi.S1G715500.t1"; gene_id "Phchi.S1G715500"
Phchi.S1	AUGUSTUS	stop_codon	44918255	44918257	.	+	0	transcript_id "Phchi.S1G715500.t1"; gene_id "Phchi.S1G715500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14907.t1 is derived from g13375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15460261	15462285	.	+	.	Phchi.S3G222600
Phchi.S3	AUGUSTUS	transcript	15460261	15462285	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	start_codon	15460261	15460263	.	+	0	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15460261	15460330	0.97	+	0	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15460261	15460330	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15460331	15460405	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15460406	15460743	0.99	+	2	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15460406	15460743	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15460744	15460842	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15460843	15461046	0.97	+	0	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15460843	15461046	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15461047	15461170	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15461171	15461210	0.84	+	0	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15461171	15461210	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15461211	15461405	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15461406	15461532	0.87	+	2	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15461406	15461532	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15461533	15461611	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15461612	15461647	0.43	+	1	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15461612	15461647	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15461648	15461872	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15461873	15461959	0.42	+	1	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15461873	15461959	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15461960	15462070	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15462071	15462112	0.96	+	1	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15462071	15462112	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	intron	15462113	15462200	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	CDS	15462201	15462285	0.92	+	1	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	exon	15462201	15462285	.	+	.	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
Phchi.S3	AUGUSTUS	stop_codon	15462286	15462288	.	+	0	transcript_id "Phchi.S3G222600.t1"; gene_id "Phchi.S3G222600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12472.t1 is derived from g8149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	26442718	26443928	.	+	.	Phchi.S2G055200
Phchi.S2	AUGUSTUS	transcript	26442718	26443928	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	start_codon	26442718	26442720	.	+	0	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	CDS	26442718	26442860	0.63	+	0	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	exon	26442718	26442860	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	intron	26442861	26442939	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	CDS	26442940	26443054	1	+	1	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	exon	26442940	26443054	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	intron	26443055	26443135	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	CDS	26443136	26443204	1	+	0	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	exon	26443136	26443204	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	intron	26443205	26443293	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	CDS	26443294	26443352	1	+	0	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	exon	26443294	26443352	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	intron	26443353	26443445	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	CDS	26443446	26443560	1	+	1	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	exon	26443446	26443560	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	intron	26443561	26443658	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	CDS	26443659	26443928	0.99	+	0	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	exon	26443659	26443928	.	+	.	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
Phchi.S2	AUGUSTUS	stop_codon	26443929	26443931	.	+	0	transcript_id "Phchi.S2G055200.t1"; gene_id "Phchi.S2G055200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14542.t1 is derived from g13010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13404628	13405182	.	+	.	Phchi.S3G186100
Phchi.S3	AUGUSTUS	transcript	13404628	13405182	.	+	.	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	start_codon	13404628	13404630	.	+	0	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	CDS	13404628	13404779	0.72	+	0	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	exon	13404628	13404779	.	+	.	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	intron	13404780	13405130	.	+	.	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	CDS	13405131	13405182	0.87	+	1	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	exon	13405131	13405182	.	+	.	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
Phchi.S3	AUGUSTUS	stop_codon	13405183	13405185	.	+	0	transcript_id "Phchi.S3G186100.t1"; gene_id "Phchi.S3G186100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1235.t1 is derived from g11018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8543992	8546529	.	+	.	Phchi.S6G119400
Phchi.S6	AUGUSTUS	transcript	8543992	8546529	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	start_codon	8543992	8543994	.	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8543992	8544126	0.98	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8543992	8544126	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8544127	8544212	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8544213	8544275	1	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8544213	8544275	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8544276	8544378	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8544379	8544463	1	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8544379	8544463	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8544464	8544559	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8544560	8544627	1	+	2	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8544560	8544627	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8544628	8544716	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8544717	8544805	1	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8544717	8544805	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8544806	8544972	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8544973	8545176	1	+	1	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8544973	8545176	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8545177	8545338	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8545339	8545594	1	+	1	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8545339	8545594	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8545595	8545688	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8545689	8545916	1	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8545689	8545916	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8545917	8546007	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8546008	8546205	1	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8546008	8546205	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	intron	8546206	8546322	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	CDS	8546323	8546529	0.98	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	exon	8546323	8546529	.	+	.	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
Phchi.S6	AUGUSTUS	stop_codon	8546530	8546532	.	+	0	transcript_id "Phchi.S6G119400.t1"; gene_id "Phchi.S6G119400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1976.t1 is derived from g8896.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4102651	4105965	.	+	.	Phchi.S5G058500
Phchi.S5	AUGUSTUS	transcript	4102651	4105965	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	start_codon	4102651	4102653	.	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4102651	4102703	0.73	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4102651	4102703	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4102704	4102811	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4102812	4102935	1	+	1	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4102812	4102935	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4102936	4103129	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103130	4103275	1	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103130	4103275	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103276	4103357	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103358	4103532	1	+	1	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103358	4103532	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103533	4103617	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103618	4103749	1	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103618	4103749	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103750	4103876	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103877	4103912	1	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103877	4103912	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103913	4104182	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4104183	4104445	0.99	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4104183	4104445	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4104446	4104519	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4104520	4104676	1	+	1	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4104520	4104676	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4104677	4104762	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4104763	4105230	1	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4104763	4105230	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4105231	4105322	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4105323	4105411	1	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4105323	4105411	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4105412	4105499	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4105500	4105639	1	+	1	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4105500	4105639	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4105640	4105726	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4105727	4105965	0.81	+	2	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4105727	4105965	.	+	.	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	stop_codon	4105966	4105968	.	+	0	transcript_id "Phchi.S5G058500.t1"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	transcript	4102651	4105965	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	start_codon	4102651	4102653	.	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4102651	4102703	0.66	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4102651	4102703	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4102704	4102811	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4102812	4102935	1	+	1	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4102812	4102935	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4102936	4103129	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103130	4103275	1	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103130	4103275	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103276	4103357	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103358	4103532	1	+	1	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103358	4103532	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103533	4103617	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103618	4103749	1	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103618	4103749	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4103750	4103876	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4103877	4104044	0.99	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4103877	4104044	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4104045	4104182	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4104183	4104445	1	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4104183	4104445	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4104446	4104519	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4104520	4104676	1	+	1	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4104520	4104676	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4104677	4104762	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4104763	4105230	1	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4104763	4105230	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4105231	4105322	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4105323	4105411	1	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4105323	4105411	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4105412	4105499	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4105500	4105639	1	+	1	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4105500	4105639	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	intron	4105640	4105726	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	CDS	4105727	4105965	0.88	+	2	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	exon	4105727	4105965	.	+	.	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
Phchi.S5	AUGUSTUS	stop_codon	4105966	4105968	.	+	0	transcript_id "Phchi.S5G058500.t2"; gene_id "Phchi.S5G058500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg969.t1 is derived from g10752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6714598	6715118	.	+	.	Phchi.S6G092800
Phchi.S6	AUGUSTUS	transcript	6714598	6715118	.	+	.	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	start_codon	6714598	6714600	.	+	0	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	CDS	6714598	6714743	0.79	+	0	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	exon	6714598	6714743	.	+	.	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	intron	6714744	6714970	.	+	.	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	CDS	6714971	6715118	0.93	+	1	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	exon	6714971	6715118	.	+	.	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
Phchi.S6	AUGUSTUS	stop_codon	6715119	6715121	.	+	0	transcript_id "Phchi.S6G092800.t1"; gene_id "Phchi.S6G092800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11196.t1 is derived from g15246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4642930	4643216	.	-	.	Phchi.S4G077800
Phchi.S4	AUGUSTUS	transcript	4642930	4643216	.	-	.	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	stop_codon	4642927	4642929	.	-	0	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	CDS	4642930	4643088	0.95	-	0	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	exon	4642930	4643088	.	-	.	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	intron	4643089	4643168	.	-	.	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	CDS	4643169	4643216	0.83	-	0	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	exon	4643169	4643216	.	-	.	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
Phchi.S4	AUGUSTUS	start_codon	4643214	4643216	.	-	0	transcript_id "Phchi.S4G077800.t1"; gene_id "Phchi.S4G077800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5824.t1 is derived from g2994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19130915	19132330	.	-	.	Phchi.S1G298300
Phchi.S1	AUGUSTUS	transcript	19130915	19132330	.	-	.	transcript_id "Phchi.S1G298300.t1"; gene_id "Phchi.S1G298300"
Phchi.S1	AUGUSTUS	stop_codon	19130912	19130914	.	-	0	transcript_id "Phchi.S1G298300.t1"; gene_id "Phchi.S1G298300"
Phchi.S1	AUGUSTUS	CDS	19130915	19132330	0.99	-	0	transcript_id "Phchi.S1G298300.t1"; gene_id "Phchi.S1G298300"
Phchi.S1	AUGUSTUS	exon	19130915	19132330	.	-	.	transcript_id "Phchi.S1G298300.t1"; gene_id "Phchi.S1G298300"
Phchi.S1	AUGUSTUS	start_codon	19132328	19132330	.	-	0	transcript_id "Phchi.S1G298300.t1"; gene_id "Phchi.S1G298300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13724.t1 is derived from g12191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8549132	8549551	.	-	.	Phchi.S3G104300
Phchi.S3	AUGUSTUS	transcript	8549132	8549551	.	-	.	transcript_id "Phchi.S3G104300.t1"; gene_id "Phchi.S3G104300"
Phchi.S3	AUGUSTUS	stop_codon	8549129	8549131	.	-	0	transcript_id "Phchi.S3G104300.t1"; gene_id "Phchi.S3G104300"
Phchi.S3	AUGUSTUS	CDS	8549132	8549551	0.99	-	0	transcript_id "Phchi.S3G104300.t1"; gene_id "Phchi.S3G104300"
Phchi.S3	AUGUSTUS	exon	8549132	8549551	.	-	.	transcript_id "Phchi.S3G104300.t1"; gene_id "Phchi.S3G104300"
Phchi.S3	AUGUSTUS	start_codon	8549549	8549551	.	-	0	transcript_id "Phchi.S3G104300.t1"; gene_id "Phchi.S3G104300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4459.t1 is derived from g1629.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10591337	10594533	.	+	.	Phchi.S1G161800
Phchi.S1	AUGUSTUS	transcript	10591337	10594533	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	start_codon	10591337	10591339	.	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591337	10591402	1	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591337	10591402	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591403	10591476	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591477	10591608	0.98	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591477	10591608	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591609	10591734	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591735	10591791	0.98	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591735	10591791	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591792	10591880	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591881	10591952	0.99	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591881	10591952	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591953	10592096	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592097	10592123	0.95	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592097	10592123	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592124	10592267	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592268	10592351	0.95	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592268	10592351	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592352	10592478	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592479	10592553	0.99	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592479	10592553	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592554	10592659	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592660	10592774	0.98	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592660	10592774	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592775	10592861	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592862	10592919	0.97	+	2	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592862	10592919	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592920	10593021	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593022	10593093	0.99	+	1	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593022	10593093	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593094	10593177	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593178	10593308	1	+	1	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593178	10593308	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593309	10593371	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593372	10593495	0.88	+	2	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593372	10593495	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593496	10593596	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593597	10593616	0.5	+	1	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593597	10593616	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593617	10593724	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593725	10593761	0.5	+	2	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593725	10593761	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593762	10593861	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593862	10593906	1	+	1	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593862	10593906	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593907	10594077	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594078	10594116	0.99	+	1	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594078	10594116	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10594117	10594204	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594205	10594440	0.99	+	1	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594205	10594440	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10594441	10594528	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594529	10594533	1	+	2	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594529	10594533	.	+	.	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	stop_codon	10594534	10594536	.	+	0	transcript_id "Phchi.S1G161800.t1"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	transcript	10591337	10594533	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	start_codon	10591337	10591339	.	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591337	10591402	1	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591337	10591402	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591403	10591476	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591477	10591608	0.99	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591477	10591608	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591609	10591734	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591735	10591791	0.99	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591735	10591791	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591792	10591880	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591881	10591952	0.99	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591881	10591952	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591953	10592096	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592097	10592123	0.94	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592097	10592123	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592124	10592267	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592268	10592351	0.94	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592268	10592351	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592352	10592478	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592479	10592553	0.96	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592479	10592553	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592554	10592712	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592713	10592774	0.92	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592713	10592774	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592775	10593021	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593022	10593093	1	+	1	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593022	10593093	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593094	10593177	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593178	10593308	1	+	1	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593178	10593308	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593309	10593371	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593372	10593495	0.85	+	2	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593372	10593495	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593496	10593596	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593597	10593616	0.4	+	1	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593597	10593616	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593617	10593724	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593725	10593761	0.41	+	2	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593725	10593761	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593762	10593861	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593862	10593906	1	+	1	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593862	10593906	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593907	10594077	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594078	10594116	0.99	+	1	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594078	10594116	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10594117	10594204	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594205	10594440	0.99	+	1	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594205	10594440	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10594441	10594528	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594529	10594533	1	+	2	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594529	10594533	.	+	.	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	stop_codon	10594534	10594536	.	+	0	transcript_id "Phchi.S1G161800.t2"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	transcript	10591337	10594533	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	start_codon	10591337	10591339	.	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591337	10591402	1	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591337	10591402	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591403	10591476	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591477	10591506	0.54	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591477	10591506	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591507	10591606	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591607	10591664	0.54	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591607	10591664	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591665	10591880	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10591881	10591952	0.91	+	2	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10591881	10591952	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10591953	10592096	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592097	10592166	1	+	2	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592097	10592166	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592167	10592272	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592273	10592351	1	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592273	10592351	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592352	10592478	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592479	10592553	1	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592479	10592553	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592554	10592659	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592660	10592774	0.96	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592660	10592774	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592775	10592861	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10592862	10592919	0.94	+	2	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10592862	10592919	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10592920	10593021	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593022	10593093	0.99	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593022	10593093	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593094	10593177	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593178	10593308	1	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593178	10593308	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593309	10593371	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593372	10593495	0.87	+	2	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593372	10593495	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593496	10593596	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593597	10593616	0.4	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593597	10593616	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593617	10593724	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593725	10593761	0.4	+	2	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593725	10593761	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593762	10593861	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10593862	10593906	1	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10593862	10593906	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10593907	10594077	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594078	10594116	1	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594078	10594116	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10594117	10594204	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594205	10594440	1	+	1	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594205	10594440	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	intron	10594441	10594528	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	CDS	10594529	10594533	1	+	2	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	exon	10594529	10594533	.	+	.	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
Phchi.S1	AUGUSTUS	stop_codon	10594534	10594536	.	+	0	transcript_id "Phchi.S1G161800.t3"; gene_id "Phchi.S1G161800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1366.t1 is derived from g11146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C72	AUGUSTUS	gene	40809	41030	.	+	.	Phchi.C72G000200
Phchi.C72	AUGUSTUS	transcript	40809	41030	.	+	.	transcript_id "Phchi.C72G000200.t1"; gene_id "Phchi.C72G000200"
Phchi.C72	AUGUSTUS	start_codon	40809	40811	.	+	0	transcript_id "Phchi.C72G000200.t1"; gene_id "Phchi.C72G000200"
Phchi.C72	AUGUSTUS	CDS	40809	41030	0.57	+	0	transcript_id "Phchi.C72G000200.t1"; gene_id "Phchi.C72G000200"
Phchi.C72	AUGUSTUS	exon	40809	41030	.	+	.	transcript_id "Phchi.C72G000200.t1"; gene_id "Phchi.C72G000200"
Phchi.C72	AUGUSTUS	stop_codon	41031	41033	.	+	0	transcript_id "Phchi.C72G000200.t1"; gene_id "Phchi.C72G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4806.t1 is derived from g1976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12906273	12909864	.	+	.	Phchi.S1G196500
Phchi.S1	AUGUSTUS	transcript	12906273	12909864	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	start_codon	12906273	12906275	.	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12906273	12906937	0.35	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12906273	12906937	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12906938	12907219	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12907220	12907359	0.6	+	1	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12907220	12907359	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12907360	12907446	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12907447	12907541	0.38	+	2	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12907447	12907541	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12907542	12907633	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12907634	12908488	0.4	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12907634	12908488	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12908489	12908582	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12908583	12908718	1	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12908583	12908718	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12908719	12908835	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12908836	12908933	1	+	2	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12908836	12908933	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12908934	12909068	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12909069	12909134	1	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12909069	12909134	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12909135	12909273	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12909274	12909363	1	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12909274	12909363	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12909364	12909542	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12909543	12909719	0.98	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12909543	12909719	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	intron	12909720	12909828	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	CDS	12909829	12909864	0.97	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	exon	12909829	12909864	.	+	.	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
Phchi.S1	AUGUSTUS	stop_codon	12909865	12909867	.	+	0	transcript_id "Phchi.S1G196500.t1"; gene_id "Phchi.S1G196500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13119.t1 is derived from g11584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4214752	4215947	.	-	.	Phchi.S3G043800
Phchi.S3	AUGUSTUS	transcript	4214752	4215947	.	-	.	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	stop_codon	4214749	4214751	.	-	0	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	CDS	4214752	4215162	0.58	-	0	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	exon	4214752	4215162	.	-	.	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	intron	4215163	4215944	.	-	.	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	CDS	4215945	4215947	0.58	-	0	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	exon	4215945	4215947	.	-	.	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
Phchi.S3	AUGUSTUS	start_codon	4215945	4215947	.	-	0	transcript_id "Phchi.S3G043800.t1"; gene_id "Phchi.S3G043800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5750.t1 is derived from g2920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18708159	18716592	.	+	.	Phchi.S1G290900
Phchi.S1	AUGUSTUS	transcript	18708159	18716592	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	start_codon	18708159	18708161	.	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18708159	18708784	1	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18708159	18708784	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18708785	18708892	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18708893	18708969	1	+	1	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18708893	18708969	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18708970	18709209	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18709210	18709262	1	+	2	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18709210	18709262	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18709263	18709366	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18709367	18709675	0.9	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18709367	18709675	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18709676	18710352	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18710353	18710615	0.59	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18710353	18710615	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18710616	18710710	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18710711	18711551	0.72	+	1	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18710711	18711551	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18711552	18711641	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18711642	18711986	0.94	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18711642	18711986	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18711987	18712100	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18712101	18712217	0.72	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18712101	18712217	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18712218	18712303	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18712304	18712717	0.93	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18712304	18712717	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18712718	18712845	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18712846	18713899	0.99	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18712846	18713899	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18713900	18714023	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18714024	18714580	0.96	+	2	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18714024	18714580	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18714581	18714842	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18714843	18714965	1	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18714843	18714965	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18714966	18715128	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18715129	18715209	0.92	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18715129	18715209	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18715210	18715322	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18715323	18715376	0.99	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18715323	18715376	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18715377	18715507	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18715508	18715659	0.96	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18715508	18715659	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18715660	18715811	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18715812	18715818	0.67	+	1	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18715812	18715818	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18715819	18715974	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18715975	18716063	0.43	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18715975	18716063	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	intron	18716064	18716534	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	CDS	18716535	18716592	1	+	1	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	exon	18716535	18716592	.	+	.	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
Phchi.S1	AUGUSTUS	stop_codon	18716593	18716595	.	+	0	transcript_id "Phchi.S1G290900.t1"; gene_id "Phchi.S1G290900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8115.t1 is derived from g5290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33231666	33233566	.	+	.	Phchi.S1G527400
Phchi.S1	AUGUSTUS	transcript	33231666	33233566	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	start_codon	33231666	33231668	.	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33231666	33231765	1	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33231666	33231765	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33231766	33232109	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33232110	33232271	1	+	2	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33232110	33232271	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33232272	33232363	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33232364	33232506	1	+	2	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33232364	33232506	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33232507	33232634	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33232635	33232676	1	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33232635	33232676	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33232677	33232789	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33232790	33232864	1	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33232790	33232864	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33232865	33233021	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33233022	33233076	1	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33233022	33233076	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33233077	33233173	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33233174	33233277	1	+	2	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33233174	33233277	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	intron	33233278	33233401	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	CDS	33233402	33233566	0.88	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	exon	33233402	33233566	.	+	.	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
Phchi.S1	AUGUSTUS	stop_codon	33233567	33233569	.	+	0	transcript_id "Phchi.S1G527400.t1"; gene_id "Phchi.S1G527400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7125.t1 is derived from g4297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27080177	27083764	.	-	.	Phchi.S1G428400
Phchi.S1	AUGUSTUS	transcript	27080177	27083764	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	stop_codon	27080174	27080176	.	-	0	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27080177	27080267	1	-	1	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27080177	27080267	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27080268	27080556	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27080557	27080602	1	-	2	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27080557	27080602	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27080603	27080705	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27080706	27080750	1	-	2	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27080706	27080750	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27080751	27080836	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27080837	27080851	1	-	2	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27080837	27080851	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27080852	27080924	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27080925	27080942	1	-	2	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27080925	27080942	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27080943	27081031	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27081032	27081161	0.51	-	0	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27081032	27081161	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27081162	27081293	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27081294	27081345	0.56	-	1	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27081294	27081345	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27081346	27081431	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27081432	27081468	0.65	-	2	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27081432	27081468	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27081469	27081572	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27081573	27081689	0.98	-	2	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27081573	27081689	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	intron	27081690	27081771	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	CDS	27081772	27083764	0.96	-	0	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	exon	27081772	27083764	.	-	.	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
Phchi.S1	AUGUSTUS	start_codon	27083762	27083764	.	-	0	transcript_id "Phchi.S1G428400.t1"; gene_id "Phchi.S1G428400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6561.t1 is derived from g3733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23728780	23729307	.	+	.	Phchi.S1G372000
Phchi.S1	AUGUSTUS	transcript	23728780	23729307	.	+	.	transcript_id "Phchi.S1G372000.t1"; gene_id "Phchi.S1G372000"
Phchi.S1	AUGUSTUS	start_codon	23728780	23728782	.	+	0	transcript_id "Phchi.S1G372000.t1"; gene_id "Phchi.S1G372000"
Phchi.S1	AUGUSTUS	CDS	23728780	23729307	1	+	0	transcript_id "Phchi.S1G372000.t1"; gene_id "Phchi.S1G372000"
Phchi.S1	AUGUSTUS	exon	23728780	23729307	.	+	.	transcript_id "Phchi.S1G372000.t1"; gene_id "Phchi.S1G372000"
Phchi.S1	AUGUSTUS	stop_codon	23729308	23729310	.	+	0	transcript_id "Phchi.S1G372000.t1"; gene_id "Phchi.S1G372000"
# This transcript jg14466.t2 is derived from g12934.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14467.t1 is derived from g12935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13010472	13013272	.	+	.	Phchi.S3G178600
Phchi.S3	AUGUSTUS	transcript	13010472	13013272	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	start_codon	13010472	13010474	.	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13010472	13010577	0.93	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13010472	13010577	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13010578	13010659	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13010660	13010723	0.97	+	2	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13010660	13010723	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13010724	13011035	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13011036	13011145	0.85	+	1	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13011036	13011145	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13011146	13011235	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13011236	13011303	0.82	+	2	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13011236	13011303	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13011304	13011415	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13011416	13011522	0.94	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13011416	13011522	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13011523	13011604	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13011605	13011709	1	+	1	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13011605	13011709	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13011710	13011816	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13011817	13011906	1	+	1	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13011817	13011906	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13011907	13011983	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13011984	13012059	1	+	1	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13011984	13012059	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13012060	13012154	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13012155	13012224	1	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13012155	13012224	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13012225	13012307	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13012308	13012378	0.99	+	2	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13012308	13012378	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13012379	13012476	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13012477	13012567	0.9	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13012477	13012567	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13012568	13012683	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13012684	13012808	0.99	+	2	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13012684	13012808	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13012809	13012906	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13012907	13013035	1	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13012907	13013035	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	intron	13013036	13013122	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	CDS	13013123	13013272	1	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	exon	13013123	13013272	.	+	.	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
Phchi.S3	AUGUSTUS	stop_codon	13013273	13013275	.	+	0	transcript_id "Phchi.S3G178600.t1"; gene_id "Phchi.S3G178600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8355.t1 is derived from g5530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35473553	35475127	.	+	.	Phchi.S1G551400
Phchi.S1	AUGUSTUS	transcript	35473553	35475127	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	start_codon	35473553	35473555	.	+	0	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35473553	35473734	0.93	+	0	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35473553	35473734	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	intron	35473735	35473819	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35473820	35474070	1	+	1	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35473820	35474070	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	intron	35474071	35474201	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35474202	35474281	1	+	2	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35474202	35474281	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	intron	35474282	35474419	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35474420	35474496	1	+	0	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35474420	35474496	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	intron	35474497	35474577	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35474578	35474750	0.85	+	1	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35474578	35474750	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	intron	35474751	35474860	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35474861	35474957	0.85	+	2	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35474861	35474957	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	intron	35474958	35475090	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	CDS	35475091	35475127	0.99	+	1	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	exon	35475091	35475127	.	+	.	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
Phchi.S1	AUGUSTUS	stop_codon	35475128	35475130	.	+	0	transcript_id "Phchi.S1G551400.t1"; gene_id "Phchi.S1G551400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12673.t1 is derived from g14407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	9793	10109	.	+	.	Phchi.C62G000400
Phchi.C62	AUGUSTUS	transcript	9793	10109	.	+	.	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	start_codon	9793	9795	.	+	0	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	CDS	9793	9990	0.82	+	0	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	exon	9793	9990	.	+	.	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	intron	9991	10082	.	+	.	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	CDS	10083	10109	0.97	+	0	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	exon	10083	10109	.	+	.	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
Phchi.C62	AUGUSTUS	stop_codon	10110	10112	.	+	0	transcript_id "Phchi.C62G000400.t1"; gene_id "Phchi.C62G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7970.t1 is derived from g5145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32179095	32180120	.	-	.	Phchi.S1G512900
Phchi.S1	AUGUSTUS	transcript	32179095	32180120	.	-	.	transcript_id "Phchi.S1G512900.t1"; gene_id "Phchi.S1G512900"
Phchi.S1	AUGUSTUS	stop_codon	32179092	32179094	.	-	0	transcript_id "Phchi.S1G512900.t1"; gene_id "Phchi.S1G512900"
Phchi.S1	AUGUSTUS	CDS	32179095	32180120	0.81	-	0	transcript_id "Phchi.S1G512900.t1"; gene_id "Phchi.S1G512900"
Phchi.S1	AUGUSTUS	exon	32179095	32180120	.	-	.	transcript_id "Phchi.S1G512900.t1"; gene_id "Phchi.S1G512900"
Phchi.S1	AUGUSTUS	start_codon	32180118	32180120	.	-	0	transcript_id "Phchi.S1G512900.t1"; gene_id "Phchi.S1G512900"
# This transcript jg916.t2 is derived from g10698.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg917.t1 is derived from g10699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6421589	6421931	.	-	.	Phchi.S6G087600
Phchi.S6	AUGUSTUS	transcript	6421589	6421931	.	-	.	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	stop_codon	6421586	6421588	.	-	0	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	CDS	6421589	6421690	0.97	-	0	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	exon	6421589	6421690	.	-	.	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	intron	6421691	6421784	.	-	.	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	CDS	6421785	6421931	1	-	0	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	exon	6421785	6421931	.	-	.	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
Phchi.S6	AUGUSTUS	start_codon	6421929	6421931	.	-	0	transcript_id "Phchi.S6G087600.t1"; gene_id "Phchi.S6G087600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6008.t1 is derived from g3179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20412063	20412656	.	-	.	Phchi.S1G316700
Phchi.S1	AUGUSTUS	transcript	20412063	20412656	.	-	.	transcript_id "Phchi.S1G316700.t1"; gene_id "Phchi.S1G316700"
Phchi.S1	AUGUSTUS	stop_codon	20412060	20412062	.	-	0	transcript_id "Phchi.S1G316700.t1"; gene_id "Phchi.S1G316700"
Phchi.S1	AUGUSTUS	CDS	20412063	20412656	0.69	-	0	transcript_id "Phchi.S1G316700.t1"; gene_id "Phchi.S1G316700"
Phchi.S1	AUGUSTUS	exon	20412063	20412656	.	-	.	transcript_id "Phchi.S1G316700.t1"; gene_id "Phchi.S1G316700"
Phchi.S1	AUGUSTUS	start_codon	20412654	20412656	.	-	0	transcript_id "Phchi.S1G316700.t1"; gene_id "Phchi.S1G316700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4382.t1 is derived from g1551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10170093	10171000	.	+	.	Phchi.S1G154100
Phchi.S1	AUGUSTUS	transcript	10170093	10171000	.	+	.	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	start_codon	10170093	10170095	.	+	0	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	CDS	10170093	10170758	0.52	+	0	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	exon	10170093	10170758	.	+	.	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	intron	10170759	10170841	.	+	.	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	CDS	10170842	10171000	0.98	+	0	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	exon	10170842	10171000	.	+	.	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
Phchi.S1	AUGUSTUS	stop_codon	10171001	10171003	.	+	0	transcript_id "Phchi.S1G154100.t1"; gene_id "Phchi.S1G154100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9702.t1 is derived from g6878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43341480	43341902	.	-	.	Phchi.S1G686100
Phchi.S1	AUGUSTUS	transcript	43341480	43341902	.	-	.	transcript_id "Phchi.S1G686100.t1"; gene_id "Phchi.S1G686100"
Phchi.S1	AUGUSTUS	stop_codon	43341477	43341479	.	-	0	transcript_id "Phchi.S1G686100.t1"; gene_id "Phchi.S1G686100"
Phchi.S1	AUGUSTUS	CDS	43341480	43341902	0.96	-	0	transcript_id "Phchi.S1G686100.t1"; gene_id "Phchi.S1G686100"
Phchi.S1	AUGUSTUS	exon	43341480	43341902	.	-	.	transcript_id "Phchi.S1G686100.t1"; gene_id "Phchi.S1G686100"
Phchi.S1	AUGUSTUS	start_codon	43341900	43341902	.	-	0	transcript_id "Phchi.S1G686100.t1"; gene_id "Phchi.S1G686100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3972.t1 is derived from g1141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6805377	6809573	.	+	.	Phchi.S1G113100
Phchi.S1	AUGUSTUS	transcript	6805377	6809573	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	start_codon	6805377	6805379	.	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6805377	6805790	0.85	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6805377	6805790	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6805791	6805865	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6805866	6806150	0.99	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6805866	6806150	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6806151	6806310	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6806311	6806628	1	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6806311	6806628	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6806629	6806876	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6806877	6807104	1	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6806877	6807104	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6807105	6807238	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6807239	6807339	1	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6807239	6807339	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6807340	6807498	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6807499	6807616	1	+	1	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6807499	6807616	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6807617	6807919	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6807920	6808576	0.85	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6807920	6808576	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6808577	6808772	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6808773	6809164	1	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6808773	6809164	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6809165	6809256	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6809257	6809324	1	+	1	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6809257	6809324	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6809325	6809481	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6809482	6809573	0.94	+	2	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6809482	6809573	.	+	.	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	stop_codon	6809574	6809576	.	+	0	transcript_id "Phchi.S1G113100.t1"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	transcript	6805377	6809491	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	start_codon	6805377	6805379	.	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6805377	6805790	0.85	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6805377	6805790	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6805791	6805865	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6805866	6806150	0.99	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6805866	6806150	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6806151	6806310	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6806311	6806628	1	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6806311	6806628	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6806629	6806876	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6806877	6807104	1	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6806877	6807104	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6807105	6807238	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6807239	6807339	1	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6807239	6807339	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6807340	6807498	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6807499	6807616	1	+	1	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6807499	6807616	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6807617	6807919	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6807920	6808576	0.88	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6807920	6808576	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6808577	6808772	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6808773	6809164	0.93	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6808773	6809164	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6809165	6809256	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6809257	6809324	0.94	+	1	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6809257	6809324	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	intron	6809325	6809477	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	CDS	6809478	6809491	0.94	+	2	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	exon	6809478	6809491	.	+	.	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
Phchi.S1	AUGUSTUS	stop_codon	6809492	6809494	.	+	0	transcript_id "Phchi.S1G113100.t2"; gene_id "Phchi.S1G113100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14434.t1 is derived from g12902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12776207	12777598	.	-	.	Phchi.S3G175300
Phchi.S3	AUGUSTUS	transcript	12776207	12777598	.	-	.	transcript_id "Phchi.S3G175300.t1"; gene_id "Phchi.S3G175300"
Phchi.S3	AUGUSTUS	stop_codon	12776204	12776206	.	-	0	transcript_id "Phchi.S3G175300.t1"; gene_id "Phchi.S3G175300"
Phchi.S3	AUGUSTUS	CDS	12776207	12777598	0.26	-	0	transcript_id "Phchi.S3G175300.t1"; gene_id "Phchi.S3G175300"
Phchi.S3	AUGUSTUS	exon	12776207	12777598	.	-	.	transcript_id "Phchi.S3G175300.t1"; gene_id "Phchi.S3G175300"
Phchi.S3	AUGUSTUS	start_codon	12777596	12777598	.	-	0	transcript_id "Phchi.S3G175300.t1"; gene_id "Phchi.S3G175300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12064.t1 is derived from g7739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1578020	1578358	.	+	.	Phchi.S2G014400
Phchi.S2	AUGUSTUS	transcript	1578020	1578358	.	+	.	transcript_id "Phchi.S2G014400.t1"; gene_id "Phchi.S2G014400"
Phchi.S2	AUGUSTUS	start_codon	1578020	1578022	.	+	0	transcript_id "Phchi.S2G014400.t1"; gene_id "Phchi.S2G014400"
Phchi.S2	AUGUSTUS	CDS	1578020	1578358	0.96	+	0	transcript_id "Phchi.S2G014400.t1"; gene_id "Phchi.S2G014400"
Phchi.S2	AUGUSTUS	exon	1578020	1578358	.	+	.	transcript_id "Phchi.S2G014400.t1"; gene_id "Phchi.S2G014400"
Phchi.S2	AUGUSTUS	stop_codon	1578359	1578361	.	+	0	transcript_id "Phchi.S2G014400.t1"; gene_id "Phchi.S2G014400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9394.t1 is derived from g6570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41314804	41316205	.	-	.	Phchi.S1G655300
Phchi.S1	AUGUSTUS	transcript	41314804	41316205	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	stop_codon	41314801	41314803	.	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41314804	41314848	0.99	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41314804	41314848	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	intron	41314849	41314931	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41314932	41315024	1	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41314932	41315024	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	intron	41315025	41315108	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41315109	41315162	1	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41315109	41315162	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	intron	41315163	41315312	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41315313	41315453	1	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41315313	41315453	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	intron	41315454	41315552	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41315553	41315618	1	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41315553	41315618	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	intron	41315619	41315726	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41315727	41315931	1	-	1	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41315727	41315931	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	intron	41315932	41316011	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	CDS	41316012	41316205	0.84	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	exon	41316012	41316205	.	-	.	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
Phchi.S1	AUGUSTUS	start_codon	41316203	41316205	.	-	0	transcript_id "Phchi.S1G655300.t1"; gene_id "Phchi.S1G655300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8124.t1 is derived from g5299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33518972	33521171	.	-	.	Phchi.S1G528300
Phchi.S1	AUGUSTUS	transcript	33518972	33521171	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	stop_codon	33518969	33518971	.	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33518972	33519001	1	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33518972	33519001	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519002	33519070	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33519071	33519119	1	-	1	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33519071	33519119	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519120	33519246	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33519247	33519302	1	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33519247	33519302	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519303	33519384	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33519385	33519452	1	-	2	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33519385	33519452	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519453	33519540	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33519541	33519602	1	-	1	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33519541	33519602	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519603	33519716	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33519717	33519765	1	-	2	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33519717	33519765	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519766	33519879	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33519880	33519993	0.95	-	2	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33519880	33519993	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33519994	33520155	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33520156	33520326	0.59	-	2	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33520156	33520326	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33520327	33520611	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33520612	33520687	1	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33520612	33520687	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33520688	33520833	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33520834	33520874	1	-	2	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33520834	33520874	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33520875	33520954	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33520955	33520970	1	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33520955	33520970	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	intron	33520971	33521060	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	CDS	33521061	33521171	0.58	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	exon	33521061	33521171	.	-	.	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
Phchi.S1	AUGUSTUS	start_codon	33521169	33521171	.	-	0	transcript_id "Phchi.S1G528300.t1"; gene_id "Phchi.S1G528300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg1959.t1 is derived from g8879.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4031746	4034888	.	+	.	Phchi.S5G056800
Phchi.S5	AUGUSTUS	transcript	4031746	4032831	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	start_codon	4031746	4031748	.	+	0	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4031746	4031843	0.94	+	0	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4031746	4031843	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4031844	4032025	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032026	4032073	0.94	+	1	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032026	4032073	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032074	4032305	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032306	4032317	0.94	+	1	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032306	4032317	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032318	4032401	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032402	4032429	0.94	+	1	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032402	4032429	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032430	4032523	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032524	4032652	0.94	+	0	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032524	4032652	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032653	4032819	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032820	4032831	0.8	+	0	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032820	4032831	.	+	.	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	stop_codon	4032832	4032834	.	+	0	transcript_id "Phchi.S5G056800.t1"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	transcript	4031746	4034888	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	start_codon	4031746	4031748	.	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4031746	4031843	0.96	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4031746	4031843	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4031844	4032025	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032026	4032073	0.96	+	1	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032026	4032073	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032074	4032305	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032306	4032317	0.96	+	1	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032306	4032317	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032318	4032401	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032402	4032429	0.96	+	1	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032402	4032429	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032430	4032523	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032524	4032652	0.96	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032524	4032652	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032653	4032784	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032785	4032900	0.21	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032785	4032900	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032901	4033197	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033198	4033236	0.69	+	1	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033198	4033236	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033237	4033319	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033320	4033452	0.72	+	1	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033320	4033452	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033453	4033745	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033746	4033865	1	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033746	4033865	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033866	4034014	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034015	4034110	1	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034015	4034110	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4034111	4034202	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034203	4034355	1	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034203	4034355	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4034356	4034448	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034449	4034526	1	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034449	4034526	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4034527	4034654	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034655	4034888	1	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034655	4034888	.	+	.	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	stop_codon	4034889	4034891	.	+	0	transcript_id "Phchi.S5G056800.t2"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	transcript	4031746	4032831	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	start_codon	4031746	4031748	.	+	0	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4031746	4031843	0.9	+	0	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4031746	4031843	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4031844	4032025	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032026	4032073	0.91	+	1	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032026	4032073	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032074	4032305	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032306	4032317	0.91	+	1	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032306	4032317	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032318	4032401	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032402	4032429	0.91	+	1	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032402	4032429	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032430	4032526	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032527	4032652	0.91	+	0	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032527	4032652	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4032653	4032819	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4032820	4032831	0.57	+	0	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4032820	4032831	.	+	.	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	stop_codon	4032832	4032834	.	+	0	transcript_id "Phchi.S5G056800.t3"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	transcript	4033080	4034888	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	start_codon	4033080	4033082	.	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033080	4033236	0.47	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033080	4033236	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033237	4033319	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033320	4033359	0.55	+	2	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033320	4033359	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033360	4033424	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033425	4033452	0.53	+	1	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033425	4033452	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033453	4033745	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4033746	4033865	1	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4033746	4033865	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4033866	4034014	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034015	4034110	1	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034015	4034110	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4034111	4034202	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034203	4034355	1	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034203	4034355	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4034356	4034448	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034449	4034526	1	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034449	4034526	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	intron	4034527	4034654	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	CDS	4034655	4034888	1	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	exon	4034655	4034888	.	+	.	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
Phchi.S5	AUGUSTUS	stop_codon	4034889	4034891	.	+	0	transcript_id "Phchi.S5G056800.t4"; gene_id "Phchi.S5G056800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14046.t1 is derived from g12513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10465189	10465927	.	+	.	Phchi.S3G136500
Phchi.S3	AUGUSTUS	transcript	10465189	10465927	.	+	.	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	start_codon	10465189	10465191	.	+	0	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	CDS	10465189	10465423	0.87	+	0	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	exon	10465189	10465423	.	+	.	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	intron	10465424	10465530	.	+	.	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	CDS	10465531	10465634	0.92	+	2	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	exon	10465531	10465634	.	+	.	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	intron	10465635	10465747	.	+	.	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	CDS	10465748	10465927	0.91	+	0	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	exon	10465748	10465927	.	+	.	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
Phchi.S3	AUGUSTUS	stop_codon	10465928	10465930	.	+	0	transcript_id "Phchi.S3G136500.t1"; gene_id "Phchi.S3G136500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15829.t1 is derived from g14299.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21642172	21643012	.	-	.	Phchi.S3G314800
Phchi.S3	AUGUSTUS	transcript	21642172	21643012	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	stop_codon	21642169	21642171	.	-	0	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642172	21642254	0.67	-	2	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642172	21642254	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	intron	21642255	21642406	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642407	21642516	0.6	-	1	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642407	21642516	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	intron	21642517	21642622	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642623	21642732	1	-	0	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642623	21642732	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	intron	21642733	21642943	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642944	21643012	1	-	0	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642944	21643012	.	-	.	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	start_codon	21643010	21643012	.	-	0	transcript_id "Phchi.S3G314800.t1"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	transcript	21642172	21643012	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	stop_codon	21642169	21642171	.	-	0	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642172	21642254	0.57	-	2	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642172	21642254	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	intron	21642255	21642406	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642407	21642516	0.66	-	1	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642407	21642516	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	intron	21642517	21642622	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642623	21642735	0.97	-	0	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642623	21642735	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	intron	21642736	21642943	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	CDS	21642944	21643012	1	-	0	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	exon	21642944	21643012	.	-	.	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
Phchi.S3	AUGUSTUS	start_codon	21643010	21643012	.	-	0	transcript_id "Phchi.S3G314800.t2"; gene_id "Phchi.S3G314800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg276.t1 is derived from g10058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1990199	1995085	.	-	.	Phchi.S6G023500
Phchi.S6	AUGUSTUS	transcript	1990199	1995085	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	stop_codon	1990196	1990198	.	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1990199	1991218	0.91	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1990199	1991218	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1991219	1991307	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1991308	1991433	0.34	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1991308	1991433	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1991434	1991549	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1991550	1991791	0.99	-	2	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1991550	1991791	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1991792	1991928	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1991929	1992002	0.98	-	1	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1991929	1992002	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1992003	1992094	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1992095	1993085	0.97	-	2	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1992095	1993085	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1993086	1993192	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1993193	1993509	0.96	-	1	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1993193	1993509	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1993510	1993676	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1993677	1993936	0.62	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1993677	1993936	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1993937	1994047	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1994048	1994248	0.62	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1994048	1994248	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1994249	1994333	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1994334	1994509	1	-	2	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1994334	1994509	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1994510	1994604	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1994605	1994659	0.99	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1994605	1994659	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	intron	1994660	1994815	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1994816	1995085	0.99	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1994816	1995085	.	-	.	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	start_codon	1995083	1995085	.	-	0	transcript_id "Phchi.S6G023500.t1"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	transcript	1990199	1991443	.	-	.	transcript_id "Phchi.S6G023500.t2"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	stop_codon	1990196	1990198	.	-	0	transcript_id "Phchi.S6G023500.t2"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	CDS	1990199	1991443	0.71	-	0	transcript_id "Phchi.S6G023500.t2"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	exon	1990199	1991443	.	-	.	transcript_id "Phchi.S6G023500.t2"; gene_id "Phchi.S6G023500"
Phchi.S6	AUGUSTUS	start_codon	1991441	1991443	.	-	0	transcript_id "Phchi.S6G023500.t2"; gene_id "Phchi.S6G023500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7147.t1 is derived from g4319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27177006	27186265	.	-	.	Phchi.S1G430600
Phchi.S1	AUGUSTUS	transcript	27177006	27186265	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	stop_codon	27177003	27177005	.	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27177006	27177182	0.99	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27177006	27177182	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27177183	27177299	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27177300	27177512	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27177300	27177512	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27177513	27177588	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27177589	27177671	1	-	2	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27177589	27177671	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27177672	27177762	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27177763	27177872	1	-	1	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27177763	27177872	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27177873	27177961	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27177962	27178011	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27177962	27178011	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27178012	27178103	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27178104	27178367	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27178104	27178367	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27178368	27178465	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27178466	27178693	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27178466	27178693	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27178694	27178781	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27178782	27178886	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27178782	27178886	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27178887	27179004	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27179005	27179073	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27179005	27179073	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27179074	27179317	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27179318	27179825	1	-	1	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27179318	27179825	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27179826	27179969	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27179970	27180131	0.36	-	1	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27179970	27180131	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27180132	27180226	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27180227	27180510	0.37	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27180227	27180510	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27180511	27180593	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27180594	27181076	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27180594	27181076	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27181077	27181160	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27181161	27181280	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27181161	27181280	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27181281	27181375	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27181376	27181795	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27181376	27181795	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27181796	27181887	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27181888	27182280	0.86	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27181888	27182280	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27182281	27182363	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27182364	27182525	0.99	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27182364	27182525	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27182526	27182659	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27182660	27182864	0.99	-	1	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27182660	27182864	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27182865	27183010	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27183011	27183222	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27183011	27183222	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27183223	27183377	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27183378	27183446	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27183378	27183446	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27183447	27183535	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27183536	27183668	1	-	1	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27183536	27183668	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27183669	27183751	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27183752	27184361	1	-	2	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27183752	27184361	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27184362	27184442	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27184443	27184551	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27184443	27184551	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27184552	27184665	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27184666	27185015	0.9	-	2	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27184666	27185015	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27185016	27185099	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27185100	27185181	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27185100	27185181	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27185182	27185413	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27185414	27185471	1	-	1	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27185414	27185471	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27185472	27185554	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27185555	27185772	1	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27185555	27185772	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27185773	27186007	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27186008	27186102	1	-	2	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27186008	27186102	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	intron	27186103	27186201	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	CDS	27186202	27186265	0.66	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	exon	27186202	27186265	.	-	.	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
Phchi.S1	AUGUSTUS	start_codon	27186263	27186265	.	-	0	transcript_id "Phchi.S1G430600.t1"; gene_id "Phchi.S1G430600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12234.t1 is derived from g7910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6923763	6924866	.	+	.	Phchi.S2G031400
Phchi.S2	AUGUSTUS	transcript	6923763	6924866	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	start_codon	6923763	6923765	.	+	0	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	CDS	6923763	6923991	1	+	0	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	exon	6923763	6923991	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	intron	6923992	6924157	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	CDS	6924158	6924210	1	+	2	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	exon	6924158	6924210	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	intron	6924211	6924301	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	CDS	6924302	6924466	1	+	0	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	exon	6924302	6924466	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	intron	6924467	6924553	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	CDS	6924554	6924664	1	+	0	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	exon	6924554	6924664	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	intron	6924665	6924746	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	CDS	6924747	6924866	1	+	0	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	exon	6924747	6924866	.	+	.	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
Phchi.S2	AUGUSTUS	stop_codon	6924867	6924869	.	+	0	transcript_id "Phchi.S2G031400.t1"; gene_id "Phchi.S2G031400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4730.t1 is derived from g1900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12505510	12507564	.	-	.	Phchi.S1G188900
Phchi.S1	AUGUSTUS	transcript	12505510	12507564	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	stop_codon	12505507	12505509	.	-	0	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12505510	12505543	1	-	1	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12505510	12505543	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12505544	12505691	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12505692	12505743	0.68	-	2	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12505692	12505743	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12505744	12505886	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12505887	12505900	0.68	-	1	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12505887	12505900	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12505901	12506035	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12506036	12506159	1	-	2	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12506036	12506159	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12506160	12506248	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12506249	12506336	1	-	0	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12506249	12506336	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12506337	12506504	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12506505	12506642	1	-	0	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12506505	12506642	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12506643	12506888	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12506889	12506976	1	-	1	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12506889	12506976	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12506977	12507062	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12507063	12507186	1	-	2	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12507063	12507186	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12507187	12507324	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12507325	12507396	1	-	2	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12507325	12507396	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	intron	12507397	12507488	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	CDS	12507489	12507564	0.9	-	0	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	exon	12507489	12507564	.	-	.	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
Phchi.S1	AUGUSTUS	start_codon	12507562	12507564	.	-	0	transcript_id "Phchi.S1G188900.t1"; gene_id "Phchi.S1G188900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1674.t1 is derived from g8593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2413560	2414715	.	-	.	Phchi.S5G028300
Phchi.S5	AUGUSTUS	transcript	2413560	2414715	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	stop_codon	2413557	2413559	.	-	0	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	CDS	2413560	2413590	0.53	-	1	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	exon	2413560	2413590	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	intron	2413591	2413721	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	CDS	2413722	2414003	0.49	-	1	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	exon	2413722	2414003	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	intron	2414004	2414197	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	CDS	2414198	2414268	0.49	-	0	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	exon	2414198	2414268	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	intron	2414269	2414544	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	CDS	2414545	2414715	0.97	-	0	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	exon	2414545	2414715	.	-	.	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
Phchi.S5	AUGUSTUS	start_codon	2414713	2414715	.	-	0	transcript_id "Phchi.S5G028300.t1"; gene_id "Phchi.S5G028300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8924.t1 is derived from g6099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38686990	38688049	.	-	.	Phchi.S1G608300
Phchi.S1	AUGUSTUS	transcript	38686990	38688049	.	-	.	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	stop_codon	38686987	38686989	.	-	0	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	CDS	38686990	38687340	0.69	-	0	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	exon	38686990	38687340	.	-	.	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	intron	38687341	38687530	.	-	.	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	CDS	38687531	38687791	0.94	-	0	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	exon	38687531	38687791	.	-	.	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	intron	38687792	38687953	.	-	.	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	CDS	38687954	38688049	0.94	-	0	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	exon	38687954	38688049	.	-	.	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
Phchi.S1	AUGUSTUS	start_codon	38688047	38688049	.	-	0	transcript_id "Phchi.S1G608300.t1"; gene_id "Phchi.S1G608300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg760.t1 is derived from g10542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5370120	5372156	.	-	.	Phchi.S6G071900
Phchi.S6	AUGUSTUS	transcript	5370120	5372156	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	stop_codon	5370117	5370119	.	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5370120	5370316	1	-	2	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5370120	5370316	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5370317	5370390	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5370391	5370652	0.69	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5370391	5370652	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5370653	5370730	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5370731	5370823	1	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5370731	5370823	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5370824	5370916	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5370917	5370969	1	-	2	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5370917	5370969	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5370970	5371068	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5371069	5371129	1	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5371069	5371129	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5371130	5371220	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5371221	5371329	1	-	1	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5371221	5371329	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5371330	5371586	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5371587	5371636	1	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5371587	5371636	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5371637	5371734	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5371735	5371784	1	-	2	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5371735	5371784	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5371785	5371877	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5371878	5371971	1	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5371878	5371971	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	intron	5371972	5372129	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	CDS	5372130	5372156	1	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	exon	5372130	5372156	.	-	.	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
Phchi.S6	AUGUSTUS	start_codon	5372154	5372156	.	-	0	transcript_id "Phchi.S6G071900.t1"; gene_id "Phchi.S6G071900"
# This transcript jg8475.t2 is derived from g5650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8476.t1 is derived from g5651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36132919	36133333	.	-	.	Phchi.S1G563500
Phchi.S1	AUGUSTUS	transcript	36132919	36133333	.	-	.	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	stop_codon	36132916	36132918	.	-	0	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	CDS	36132919	36133054	1	-	1	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	exon	36132919	36133054	.	-	.	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	intron	36133055	36133153	.	-	.	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	CDS	36133154	36133247	1	-	2	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	exon	36133154	36133247	.	-	.	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	intron	36133248	36133329	.	-	.	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	CDS	36133330	36133333	0.42	-	0	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	exon	36133330	36133333	.	-	.	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
Phchi.S1	AUGUSTUS	start_codon	36133331	36133333	.	-	0	transcript_id "Phchi.S1G563500.t1"; gene_id "Phchi.S1G563500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14062.t1 is derived from g12529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10611143	10613081	.	+	.	Phchi.S3G138100
Phchi.S3	AUGUSTUS	transcript	10611143	10613081	.	+	.	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	start_codon	10611143	10611145	.	+	0	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	CDS	10611143	10612990	0.24	+	0	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	exon	10611143	10612990	.	+	.	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	intron	10612991	10613063	.	+	.	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	CDS	10613064	10613081	0.22	+	0	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	exon	10613064	10613081	.	+	.	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
Phchi.S3	AUGUSTUS	stop_codon	10613082	10613084	.	+	0	transcript_id "Phchi.S3G138100.t1"; gene_id "Phchi.S3G138100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8505.t1 is derived from g5680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36368852	36369393	.	-	.	Phchi.S1G566400
Phchi.S1	AUGUSTUS	transcript	36368852	36369393	.	-	.	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	stop_codon	36368849	36368851	.	-	0	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	CDS	36368852	36368948	0.41	-	1	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	exon	36368852	36368948	.	-	.	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	intron	36368949	36369046	.	-	.	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	CDS	36369047	36369393	0.49	-	0	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	exon	36369047	36369393	.	-	.	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
Phchi.S1	AUGUSTUS	start_codon	36369391	36369393	.	-	0	transcript_id "Phchi.S1G566400.t1"; gene_id "Phchi.S1G566400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1080.t1 is derived from g10863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7489575	7494034	.	-	.	Phchi.S6G103900
Phchi.S6	AUGUSTUS	transcript	7489575	7494034	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	stop_codon	7489572	7489574	.	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7489575	7490091	0.61	-	1	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7489575	7490091	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7490092	7490174	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7490175	7492351	0.87	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7490175	7492351	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7492352	7492536	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7492537	7492740	1	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7492537	7492740	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7492741	7492832	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7492833	7492940	1	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7492833	7492940	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7492941	7493051	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493052	7493237	0.94	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493052	7493237	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7493238	7493357	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493358	7493803	0.91	-	2	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493358	7493803	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7493804	7493913	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493914	7494034	0.74	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493914	7494034	.	-	.	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	start_codon	7494032	7494034	.	-	0	transcript_id "Phchi.S6G103900.t1"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	transcript	7489575	7494034	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	stop_codon	7489572	7489574	.	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7489575	7490091	0.57	-	1	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7489575	7490091	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7490092	7490174	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7490175	7492351	0.91	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7490175	7492351	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7492352	7492536	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7492537	7492740	1	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7492537	7492740	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7492741	7492832	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7492833	7492940	1	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7492833	7492940	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7492941	7493051	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493052	7493260	0.96	-	2	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493052	7493260	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7493261	7493357	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493358	7493481	0.67	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493358	7493481	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7493482	7493606	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493607	7493803	0.67	-	2	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493607	7493803	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	intron	7493804	7493913	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	CDS	7493914	7494034	0.79	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	exon	7493914	7494034	.	-	.	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
Phchi.S6	AUGUSTUS	start_codon	7494032	7494034	.	-	0	transcript_id "Phchi.S6G103900.t2"; gene_id "Phchi.S6G103900"
# This transcript jg5652.t2 is derived from g2822.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5653.t1 is derived from g2823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18151875	18152957	.	+	.	Phchi.S1G281200
Phchi.S1	AUGUSTUS	transcript	18151875	18152957	.	+	.	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	start_codon	18151875	18151877	.	+	0	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	CDS	18151875	18151981	0.46	+	0	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	exon	18151875	18151981	.	+	.	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	intron	18151982	18152068	.	+	.	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	CDS	18152069	18152957	0.46	+	1	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	exon	18152069	18152957	.	+	.	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
Phchi.S1	AUGUSTUS	stop_codon	18152958	18152960	.	+	0	transcript_id "Phchi.S1G281200.t1"; gene_id "Phchi.S1G281200"
# This transcript jg12218.t2 is derived from g7894.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12219.t1 is derived from g7895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6814221	6814919	.	+	.	Phchi.S2G029900
Phchi.S2	AUGUSTUS	transcript	6814221	6814919	.	+	.	transcript_id "Phchi.S2G029900.t1"; gene_id "Phchi.S2G029900"
Phchi.S2	AUGUSTUS	start_codon	6814221	6814223	.	+	0	transcript_id "Phchi.S2G029900.t1"; gene_id "Phchi.S2G029900"
Phchi.S2	AUGUSTUS	CDS	6814221	6814919	1	+	0	transcript_id "Phchi.S2G029900.t1"; gene_id "Phchi.S2G029900"
Phchi.S2	AUGUSTUS	exon	6814221	6814919	.	+	.	transcript_id "Phchi.S2G029900.t1"; gene_id "Phchi.S2G029900"
Phchi.S2	AUGUSTUS	stop_codon	6814920	6814922	.	+	0	transcript_id "Phchi.S2G029900.t1"; gene_id "Phchi.S2G029900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11569.t1 is derived from g15620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7094468	7097960	.	-	.	Phchi.S4G115100
Phchi.S4	AUGUSTUS	transcript	7094468	7097960	.	-	.	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	stop_codon	7094465	7094467	.	-	0	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	CDS	7094468	7094473	0.92	-	0	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	exon	7094468	7094473	.	-	.	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	intron	7094474	7094740	.	-	.	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	CDS	7094741	7095114	0.91	-	2	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	exon	7094741	7095114	.	-	.	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	intron	7095115	7095307	.	-	.	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	CDS	7095308	7097960	0.53	-	0	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	exon	7095308	7097960	.	-	.	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
Phchi.S4	AUGUSTUS	start_codon	7097958	7097960	.	-	0	transcript_id "Phchi.S4G115100.t1"; gene_id "Phchi.S4G115100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7509.t1 is derived from g4683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29745951	29751005	.	-	.	Phchi.S1G466800
Phchi.S1	AUGUSTUS	transcript	29745951	29751005	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	stop_codon	29745948	29745950	.	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29745951	29746007	1	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29745951	29746007	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29746008	29746097	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29746098	29746295	1	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29746098	29746295	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29746296	29746378	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29746379	29747314	1	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29746379	29747314	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29747315	29747392	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29747393	29747665	1	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29747393	29747665	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29747666	29747763	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29747764	29748272	0.94	-	2	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29747764	29748272	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29748273	29748387	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29748388	29748583	0.61	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29748388	29748583	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29748584	29748691	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29748692	29748850	0.97	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29748692	29748850	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29748851	29748934	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29748935	29749888	1	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29748935	29749888	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29749889	29749980	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29749981	29750244	0.98	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29749981	29750244	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29750245	29750334	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29750335	29750595	0.99	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29750335	29750595	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29750596	29750681	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29750682	29750834	0.99	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29750682	29750834	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	intron	29750835	29750933	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	CDS	29750934	29751005	0.4	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	exon	29750934	29751005	.	-	.	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
Phchi.S1	AUGUSTUS	start_codon	29751003	29751005	.	-	0	transcript_id "Phchi.S1G466800.t1"; gene_id "Phchi.S1G466800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1189.t1 is derived from g10972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8351907	8352999	.	-	.	Phchi.S6G114800
Phchi.S6	AUGUSTUS	transcript	8351907	8352999	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	stop_codon	8351904	8351906	.	-	0	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	CDS	8351907	8351959	0.45	-	2	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	exon	8351907	8351959	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	intron	8351960	8352044	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	CDS	8352045	8352100	0.71	-	1	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	exon	8352045	8352100	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	intron	8352101	8352230	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	CDS	8352231	8352358	1	-	0	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	exon	8352231	8352358	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	intron	8352359	8352444	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	CDS	8352445	8352532	1	-	1	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	exon	8352445	8352532	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	intron	8352533	8352649	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	CDS	8352650	8352999	0.65	-	0	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	exon	8352650	8352999	.	-	.	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
Phchi.S6	AUGUSTUS	start_codon	8352997	8352999	.	-	0	transcript_id "Phchi.S6G114800.t1"; gene_id "Phchi.S6G114800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7009.t1 is derived from g4181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26383356	26390998	.	+	.	Phchi.S1G416800
Phchi.S1	AUGUSTUS	transcript	26383356	26390998	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	start_codon	26383356	26383358	.	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26383356	26383835	0.62	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26383356	26383835	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26383836	26384312	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26384313	26384378	0.86	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26384313	26384378	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26384379	26384533	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26384534	26384695	0.91	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26384534	26384695	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26384696	26384848	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26384849	26384979	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26384849	26384979	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26384980	26385113	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26385114	26385190	1	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26385114	26385190	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26385191	26385322	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26385323	26385504	1	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26385323	26385504	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26385505	26385682	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26385683	26385760	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26385683	26385760	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26385761	26385925	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26385926	26386058	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26385926	26386058	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26386059	26386157	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26386158	26386218	1	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26386158	26386218	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26386219	26386375	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26386376	26386457	1	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26386376	26386457	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26386458	26386550	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26386551	26386678	0.88	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26386551	26386678	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26386679	26386752	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26386753	26386775	0.81	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26386753	26386775	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26386776	26386861	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26386862	26386896	0.88	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26386862	26386896	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26386897	26386983	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26386984	26387086	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26386984	26387086	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26387087	26387167	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26387168	26387305	1	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26387168	26387305	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26387306	26387462	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26387463	26387536	1	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26387463	26387536	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26387537	26387631	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26387632	26387804	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26387632	26387804	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26387805	26387887	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26387888	26387981	1	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26387888	26387981	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26387982	26388101	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26388102	26388199	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26388102	26388199	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26388200	26388281	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26388282	26388417	1	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26388282	26388417	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26388418	26388509	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26388510	26388616	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26388510	26388616	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26388617	26388705	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26388706	26388801	1	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26388706	26388801	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26388802	26388880	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26388881	26388968	1	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26388881	26388968	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26388969	26389057	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26389058	26389178	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26389058	26389178	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26389179	26389388	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26389389	26389509	1	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26389389	26389509	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26389510	26389595	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26389596	26389722	0.56	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26389596	26389722	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26389723	26389802	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26389803	26389880	0.73	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26389803	26389880	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26389881	26389976	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26389977	26390092	0.99	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26389977	26390092	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26390093	26390198	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26390199	26390258	0.99	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26390199	26390258	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26390259	26390359	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26390360	26390462	0.99	+	1	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26390360	26390462	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26390463	26390553	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26390554	26390682	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26390554	26390682	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26390683	26390761	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26390762	26390873	1	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26390762	26390873	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	intron	26390874	26390960	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	CDS	26390961	26390998	1	+	2	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	exon	26390961	26390998	.	+	.	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
Phchi.S1	AUGUSTUS	stop_codon	26390999	26391001	.	+	0	transcript_id "Phchi.S1G416800.t1"; gene_id "Phchi.S1G416800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5769.t1 is derived from g2939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18874779	18877743	.	-	.	Phchi.S1G292800
Phchi.S1	AUGUSTUS	transcript	18874779	18877743	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	stop_codon	18874776	18874778	.	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18874779	18874985	0.96	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18874779	18874985	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18874986	18875086	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18875087	18875194	1	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18875087	18875194	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18875195	18875271	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18875272	18875451	0.95	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18875272	18875451	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18875452	18875564	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18875565	18875693	0.98	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18875565	18875693	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18875694	18875802	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18875803	18876078	0.94	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18875803	18876078	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18876079	18876268	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18876269	18876480	1	-	2	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18876269	18876480	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18876481	18876583	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18876584	18877432	0.8	-	2	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18876584	18877432	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18877433	18877528	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18877529	18877549	0.72	-	2	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18877529	18877549	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	intron	18877550	18877643	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	CDS	18877644	18877743	0.68	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	exon	18877644	18877743	.	-	.	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
Phchi.S1	AUGUSTUS	start_codon	18877741	18877743	.	-	0	transcript_id "Phchi.S1G292800.t1"; gene_id "Phchi.S1G292800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10849.t1 is derived from g14899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2474931	2476178	.	+	.	Phchi.S4G043100
Phchi.S4	AUGUSTUS	transcript	2474931	2476178	.	+	.	transcript_id "Phchi.S4G043100.t1"; gene_id "Phchi.S4G043100"
Phchi.S4	AUGUSTUS	start_codon	2474931	2474933	.	+	0	transcript_id "Phchi.S4G043100.t1"; gene_id "Phchi.S4G043100"
Phchi.S4	AUGUSTUS	CDS	2474931	2476178	1	+	0	transcript_id "Phchi.S4G043100.t1"; gene_id "Phchi.S4G043100"
Phchi.S4	AUGUSTUS	exon	2474931	2476178	.	+	.	transcript_id "Phchi.S4G043100.t1"; gene_id "Phchi.S4G043100"
Phchi.S4	AUGUSTUS	stop_codon	2476179	2476181	.	+	0	transcript_id "Phchi.S4G043100.t1"; gene_id "Phchi.S4G043100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg164.t1 is derived from g9946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	938574	939722	.	+	.	Phchi.S6G012300
Phchi.S6	AUGUSTUS	transcript	938574	939722	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	start_codon	938574	938576	.	+	0	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	CDS	938574	938780	0.88	+	0	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	exon	938574	938780	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	intron	938781	938868	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	CDS	938869	939041	0.95	+	0	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	exon	938869	939041	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	intron	939042	939269	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	CDS	939270	939364	0.95	+	1	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	exon	939270	939364	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	intron	939365	939702	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	CDS	939703	939722	0.99	+	2	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	exon	939703	939722	.	+	.	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
Phchi.S6	AUGUSTUS	stop_codon	939723	939725	.	+	0	transcript_id "Phchi.S6G012300.t1"; gene_id "Phchi.S6G012300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10196.t1 is derived from g7372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46334723	46336661	.	+	.	Phchi.S1G735500
Phchi.S1	AUGUSTUS	transcript	46334723	46336661	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	start_codon	46334723	46334725	.	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	CDS	46334723	46335079	0.98	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	exon	46334723	46335079	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	intron	46335080	46335383	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	CDS	46335384	46335485	0.74	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	exon	46335384	46335485	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	intron	46335486	46335619	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	CDS	46335620	46335808	0.38	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	exon	46335620	46335808	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	intron	46335809	46335900	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	CDS	46335901	46336404	0.7	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	exon	46335901	46336404	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	intron	46336405	46336490	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	CDS	46336491	46336661	0.75	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	exon	46336491	46336661	.	+	.	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
Phchi.S1	AUGUSTUS	stop_codon	46336662	46336664	.	+	0	transcript_id "Phchi.S1G735500.t1"; gene_id "Phchi.S1G735500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14498.t1 is derived from g12966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13182088	13191220	.	+	.	Phchi.S3G181700
Phchi.S3	AUGUSTUS	transcript	13182088	13191220	.	+	.	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	start_codon	13182088	13182090	.	+	0	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	CDS	13182088	13182196	0.36	+	0	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	exon	13182088	13182196	.	+	.	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	intron	13182197	13182320	.	+	.	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	CDS	13182321	13191220	0.74	+	2	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	exon	13182321	13191220	.	+	.	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
Phchi.S3	AUGUSTUS	stop_codon	13191221	13191223	.	+	0	transcript_id "Phchi.S3G181700.t1"; gene_id "Phchi.S3G181700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg683.t1 is derived from g10465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4773731	4774117	.	+	.	Phchi.S6G064200
Phchi.S6	AUGUSTUS	transcript	4773731	4774117	.	+	.	transcript_id "Phchi.S6G064200.t1"; gene_id "Phchi.S6G064200"
Phchi.S6	AUGUSTUS	start_codon	4773731	4773733	.	+	0	transcript_id "Phchi.S6G064200.t1"; gene_id "Phchi.S6G064200"
Phchi.S6	AUGUSTUS	CDS	4773731	4774117	0.54	+	0	transcript_id "Phchi.S6G064200.t1"; gene_id "Phchi.S6G064200"
Phchi.S6	AUGUSTUS	exon	4773731	4774117	.	+	.	transcript_id "Phchi.S6G064200.t1"; gene_id "Phchi.S6G064200"
Phchi.S6	AUGUSTUS	stop_codon	4774118	4774120	.	+	0	transcript_id "Phchi.S6G064200.t1"; gene_id "Phchi.S6G064200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9958.t1 is derived from g7134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44660590	44664960	.	+	.	Phchi.S1G711700
Phchi.S1	AUGUSTUS	transcript	44660590	44664960	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	start_codon	44660590	44660592	.	+	0	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	CDS	44660590	44662138	0.68	+	0	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	exon	44660590	44662138	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	intron	44662139	44662254	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	CDS	44662255	44663702	1	+	2	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	exon	44662255	44663702	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	intron	44663703	44663821	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	CDS	44663822	44664626	0.54	+	0	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	exon	44663822	44664626	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	intron	44664627	44664730	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	CDS	44664731	44664960	0.6	+	2	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	exon	44664731	44664960	.	+	.	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
Phchi.S1	AUGUSTUS	stop_codon	44664961	44664963	.	+	0	transcript_id "Phchi.S1G711700.t1"; gene_id "Phchi.S1G711700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8809.t1 is derived from g5984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38090453	38091982	.	+	.	Phchi.S1G596800
Phchi.S1	AUGUSTUS	transcript	38090453	38091982	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	start_codon	38090453	38090455	.	+	0	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38090453	38090536	0.86	+	0	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38090453	38090536	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	intron	38090537	38090637	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38090638	38090767	0.98	+	0	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38090638	38090767	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	intron	38090768	38091007	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38091008	38091114	1	+	2	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38091008	38091114	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	intron	38091115	38091224	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38091225	38091359	1	+	0	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38091225	38091359	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	intron	38091360	38091469	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38091470	38091573	1	+	0	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38091470	38091573	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	intron	38091574	38091660	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38091661	38091761	1	+	1	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38091661	38091761	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	intron	38091762	38091857	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	CDS	38091858	38091982	0.98	+	2	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	exon	38091858	38091982	.	+	.	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
Phchi.S1	AUGUSTUS	stop_codon	38091983	38091985	.	+	0	transcript_id "Phchi.S1G596800.t1"; gene_id "Phchi.S1G596800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13053.t1 is derived from g11518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3918078	3919865	.	+	.	Phchi.S3G037200
Phchi.S3	AUGUSTUS	transcript	3918078	3919865	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	start_codon	3918078	3918080	.	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	CDS	3918078	3918355	0.81	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	exon	3918078	3918355	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	intron	3918356	3918446	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	CDS	3918447	3918774	1	+	1	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	exon	3918447	3918774	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	intron	3918775	3918900	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	CDS	3918901	3919050	0.95	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	exon	3918901	3919050	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	intron	3919051	3919154	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	CDS	3919155	3919415	0.82	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	exon	3919155	3919415	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	intron	3919416	3919545	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	CDS	3919546	3919629	1	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	exon	3919546	3919629	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	intron	3919630	3919742	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	CDS	3919743	3919865	0.66	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	exon	3919743	3919865	.	+	.	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
Phchi.S3	AUGUSTUS	stop_codon	3919866	3919868	.	+	0	transcript_id "Phchi.S3G037200.t1"; gene_id "Phchi.S3G037200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7349.t1 is derived from g4521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28647134	28648559	.	-	.	Phchi.S1G450800
Phchi.S1	AUGUSTUS	transcript	28647134	28648559	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	stop_codon	28647131	28647133	.	-	0	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	CDS	28647134	28647336	1	-	2	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	exon	28647134	28647336	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	intron	28647337	28647410	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	CDS	28647411	28647569	1	-	2	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	exon	28647411	28647569	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	intron	28647570	28647677	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	CDS	28647678	28647785	1	-	2	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	exon	28647678	28647785	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	intron	28647786	28647863	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	CDS	28647864	28647945	1	-	0	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	exon	28647864	28647945	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	intron	28647946	28648034	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	CDS	28648035	28648214	1	-	0	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	exon	28648035	28648214	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	intron	28648215	28648304	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	CDS	28648305	28648559	1	-	0	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	exon	28648305	28648559	.	-	.	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
Phchi.S1	AUGUSTUS	start_codon	28648557	28648559	.	-	0	transcript_id "Phchi.S1G450800.t1"; gene_id "Phchi.S1G450800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13301.t1 is derived from g11767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5592294	5594671	.	-	.	Phchi.S3G062000
Phchi.S3	AUGUSTUS	transcript	5592294	5594671	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	stop_codon	5592291	5592293	.	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5592294	5592375	0.97	-	1	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5592294	5592375	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5592376	5592500	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5592501	5592619	0.97	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5592501	5592619	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5592620	5592722	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5592723	5592829	1	-	2	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5592723	5592829	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5592830	5592973	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5592974	5593052	0.69	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5592974	5593052	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5593053	5593173	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5593174	5593248	0.33	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5593174	5593248	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5593249	5593371	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5593372	5593632	0.7	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5593372	5593632	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5593633	5593712	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5593713	5593862	1	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5593713	5593862	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5593863	5593980	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5593981	5594305	1	-	1	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5593981	5594305	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	intron	5594306	5594453	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	CDS	5594454	5594671	0.88	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	exon	5594454	5594671	.	-	.	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
Phchi.S3	AUGUSTUS	start_codon	5594669	5594671	.	-	0	transcript_id "Phchi.S3G062000.t1"; gene_id "Phchi.S3G062000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11313.t1 is derived from g15363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5324160	5326231	.	+	.	Phchi.S4G089500
Phchi.S4	AUGUSTUS	transcript	5324160	5326231	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	start_codon	5324160	5324162	.	+	0	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5324160	5324194	0.8	+	0	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5324160	5324194	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5324195	5324293	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5324294	5324330	0.29	+	1	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5324294	5324330	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5324331	5324421	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5324422	5324515	0.41	+	0	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5324422	5324515	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5324516	5324755	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5324756	5324826	0.38	+	2	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5324756	5324826	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5324827	5324910	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5324911	5325158	0.99	+	0	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5324911	5325158	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5325159	5325259	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5325260	5325469	0.99	+	1	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5325260	5325469	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5325470	5325614	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5325615	5325825	1	+	1	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5325615	5325825	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	intron	5325826	5325988	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	CDS	5325989	5326231	0.81	+	0	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	exon	5325989	5326231	.	+	.	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
Phchi.S4	AUGUSTUS	stop_codon	5326232	5326234	.	+	0	transcript_id "Phchi.S4G089500.t1"; gene_id "Phchi.S4G089500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15687.t1 is derived from g14156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20665102	20667569	.	-	.	Phchi.S3G300600
Phchi.S3	AUGUSTUS	transcript	20665102	20667569	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	stop_codon	20665099	20665101	.	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20665102	20665143	1	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20665102	20665143	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20665144	20665277	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20665278	20665355	1	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20665278	20665355	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20665356	20665443	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20665444	20665516	1	-	1	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20665444	20665516	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20665517	20665606	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20665607	20665687	1	-	1	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20665607	20665687	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20665688	20665776	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20665777	20665827	1	-	1	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20665777	20665827	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20665828	20665916	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20665917	20666011	1	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20665917	20666011	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20666012	20666107	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20666108	20666188	1	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20666108	20666188	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20666189	20666343	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20666344	20666428	1	-	1	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20666344	20666428	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20666429	20666535	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20666536	20666615	0.99	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20666536	20666615	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20666616	20666691	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20666692	20666696	1	-	2	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20666692	20666696	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20666697	20666760	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20666761	20666807	1	-	1	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20666761	20666807	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20666808	20667067	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20667068	20667138	1	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20667068	20667138	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20667139	20667236	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20667237	20667321	1	-	1	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20667237	20667321	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	intron	20667322	20667450	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	CDS	20667451	20667569	1	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	exon	20667451	20667569	.	-	.	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
Phchi.S3	AUGUSTUS	start_codon	20667567	20667569	.	-	0	transcript_id "Phchi.S3G300600.t1"; gene_id "Phchi.S3G300600"
# This transcript jg11366.t2 is derived from g15416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11367.t1 is derived from g15417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5796421	5799797	.	+	.	Phchi.S4G094900
Phchi.S4	AUGUSTUS	transcript	5796421	5799797	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	start_codon	5796421	5796423	.	+	0	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	CDS	5796421	5797239	0.99	+	0	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	exon	5796421	5797239	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	intron	5797240	5797519	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	CDS	5797520	5798847	0.97	+	0	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	exon	5797520	5798847	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	intron	5798848	5798990	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	CDS	5798991	5799251	0.6	+	1	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	exon	5798991	5799251	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	intron	5799252	5799379	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	CDS	5799380	5799797	0.84	+	1	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	exon	5799380	5799797	.	+	.	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	stop_codon	5799798	5799800	.	+	0	transcript_id "Phchi.S4G094900.t1"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	transcript	5796421	5796953	.	+	.	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	start_codon	5796421	5796423	.	+	0	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	CDS	5796421	5796849	0.63	+	0	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	exon	5796421	5796849	.	+	.	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	intron	5796850	5796923	.	+	.	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	CDS	5796924	5796953	0.83	+	0	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	exon	5796924	5796953	.	+	.	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
Phchi.S4	AUGUSTUS	stop_codon	5796954	5796956	.	+	0	transcript_id "Phchi.S4G094900.t2"; gene_id "Phchi.S4G094900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg953.t1 is derived from g10735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6635763	6637445	.	-	.	Phchi.S6G091200
Phchi.S6	AUGUSTUS	transcript	6635763	6637445	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	stop_codon	6635760	6635762	.	-	0	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6635763	6635870	1	-	0	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6635763	6635870	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	intron	6635871	6636068	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6636069	6636187	1	-	2	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6636069	6636187	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	intron	6636188	6636341	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6636342	6636473	1	-	2	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6636342	6636473	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	intron	6636474	6636554	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6636555	6636662	1	-	2	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6636555	6636662	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	intron	6636663	6636845	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6636846	6636941	0.51	-	2	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6636846	6636941	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	intron	6636942	6637133	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6637134	6637194	1	-	0	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6637134	6637194	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	intron	6637195	6637427	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	CDS	6637428	6637445	1	-	0	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	exon	6637428	6637445	.	-	.	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
Phchi.S6	AUGUSTUS	start_codon	6637443	6637445	.	-	0	transcript_id "Phchi.S6G091200.t1"; gene_id "Phchi.S6G091200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3731.t1 is derived from g900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5430187	5432072	.	+	.	Phchi.S1G089000
Phchi.S1	AUGUSTUS	transcript	5430187	5432072	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	start_codon	5430187	5430189	.	+	0	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	CDS	5430187	5430450	1	+	0	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	exon	5430187	5430450	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	intron	5430451	5430525	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	CDS	5430526	5431296	0.99	+	0	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	exon	5430526	5431296	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	intron	5431297	5431415	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	CDS	5431416	5431776	1	+	0	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	exon	5431416	5431776	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	intron	5431777	5431863	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	CDS	5431864	5432072	1	+	2	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	exon	5431864	5432072	.	+	.	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
Phchi.S1	AUGUSTUS	stop_codon	5432073	5432075	.	+	0	transcript_id "Phchi.S1G089000.t1"; gene_id "Phchi.S1G089000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8405.t1 is derived from g5580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35804949	35807632	.	-	.	Phchi.S1G556400
Phchi.S1	AUGUSTUS	transcript	35804949	35807632	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	stop_codon	35804946	35804948	.	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35804949	35804997	0.84	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35804949	35804997	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35804998	35805079	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35805080	35805174	1	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35805080	35805174	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35805175	35805254	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35805255	35805303	1	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35805255	35805303	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35805304	35805429	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35805430	35805489	1	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35805430	35805489	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35805490	35805662	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35805663	35805784	1	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35805663	35805784	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35805785	35805879	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35805880	35805921	1	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35805880	35805921	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35805922	35805999	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35806000	35806048	1	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35806000	35806048	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35806049	35806193	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35806194	35806265	1	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35806194	35806265	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35806266	35806352	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35806353	35806453	1	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35806353	35806453	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35806454	35806527	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35806528	35806603	1	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35806528	35806603	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35806604	35806823	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35806824	35806903	1	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35806824	35806903	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35806904	35806987	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35806988	35807099	0.92	-	1	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35806988	35807099	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35807100	35807225	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35807226	35807274	0.91	-	2	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35807226	35807274	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35807275	35807397	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35807398	35807449	0.94	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35807398	35807449	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	intron	35807450	35807593	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	CDS	35807594	35807632	1	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	exon	35807594	35807632	.	-	.	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
Phchi.S1	AUGUSTUS	start_codon	35807630	35807632	.	-	0	transcript_id "Phchi.S1G556400.t1"; gene_id "Phchi.S1G556400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12543.t1 is derived from g8220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34116500	34119609	.	-	.	Phchi.S2G062300
Phchi.S2	AUGUSTUS	transcript	34116500	34119609	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	stop_codon	34116497	34116499	.	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34116500	34116573	1	-	2	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34116500	34116573	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34116574	34116668	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34116669	34116806	1	-	2	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34116669	34116806	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34116807	34116933	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34116934	34117024	1	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34116934	34117024	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34117025	34117118	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34117119	34117511	0.93	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34117119	34117511	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34117512	34117716	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34117717	34117898	1	-	2	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34117717	34117898	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34117899	34118165	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34118166	34118342	0.91	-	2	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34118166	34118342	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34118343	34118435	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34118436	34118604	0.68	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34118436	34118604	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34118605	34118717	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34118718	34118957	1	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34118718	34118957	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34118958	34119214	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34119215	34119295	1	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34119215	34119295	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	intron	34119296	34119513	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	CDS	34119514	34119609	1	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	exon	34119514	34119609	.	-	.	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
Phchi.S2	AUGUSTUS	start_codon	34119607	34119609	.	-	0	transcript_id "Phchi.S2G062300.t1"; gene_id "Phchi.S2G062300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg265.t1 is derived from g10047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1873943	1874783	.	-	.	Phchi.S6G022400
Phchi.S6	AUGUSTUS	transcript	1873943	1874783	.	-	.	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	stop_codon	1873940	1873942	.	-	0	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	CDS	1873943	1874032	0.87	-	0	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	exon	1873943	1874032	.	-	.	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	intron	1874033	1874126	.	-	.	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	CDS	1874127	1874783	0.85	-	0	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	exon	1874127	1874783	.	-	.	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
Phchi.S6	AUGUSTUS	start_codon	1874781	1874783	.	-	0	transcript_id "Phchi.S6G022400.t1"; gene_id "Phchi.S6G022400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11952.t1 is derived from g7627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	177019	179198	.	-	.	Phchi.S2G003200
Phchi.S2	AUGUSTUS	transcript	177019	179198	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	stop_codon	177016	177018	.	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177019	177076	1	-	1	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177019	177076	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177077	177161	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177162	177281	1	-	1	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177162	177281	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177282	177398	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177399	177484	1	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177399	177484	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177485	177593	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177594	177690	1	-	1	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177594	177690	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177691	177772	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177773	177860	1	-	2	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177773	177860	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177861	177975	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177976	178072	1	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177976	178072	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	178073	178168	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	178169	178264	1	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	178169	178264	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	178265	178379	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	178380	178479	0.99	-	1	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	178380	178479	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	178480	178585	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	178586	178704	1	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	178586	178704	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	178705	178790	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	178791	178848	1	-	1	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	178791	178848	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	178849	178943	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	178944	179069	1	-	1	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	178944	179069	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	179070	179160	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	179161	179198	1	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	179161	179198	.	-	.	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	start_codon	179196	179198	.	-	0	transcript_id "Phchi.S2G003200.t1"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	transcript	177019	178200	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	stop_codon	177016	177018	.	-	0	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177019	177076	1	-	1	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177019	177076	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177077	177161	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177162	177281	1	-	1	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177162	177281	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177282	177398	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177399	177484	1	-	0	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177399	177484	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177485	177593	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177594	177690	1	-	1	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177594	177690	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177691	177772	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177773	177860	1	-	2	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177773	177860	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	177861	177975	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	177976	178076	1	-	1	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	177976	178076	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	intron	178077	178168	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	CDS	178169	178200	0.98	-	0	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	exon	178169	178200	.	-	.	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
Phchi.S2	AUGUSTUS	start_codon	178198	178200	.	-	0	transcript_id "Phchi.S2G003200.t2"; gene_id "Phchi.S2G003200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14098.t1 is derived from g12565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10833797	10834108	.	-	.	Phchi.S3G141700
Phchi.S3	AUGUSTUS	transcript	10833797	10834108	.	-	.	transcript_id "Phchi.S3G141700.t1"; gene_id "Phchi.S3G141700"
Phchi.S3	AUGUSTUS	stop_codon	10833794	10833796	.	-	0	transcript_id "Phchi.S3G141700.t1"; gene_id "Phchi.S3G141700"
Phchi.S3	AUGUSTUS	CDS	10833797	10834108	0.75	-	0	transcript_id "Phchi.S3G141700.t1"; gene_id "Phchi.S3G141700"
Phchi.S3	AUGUSTUS	exon	10833797	10834108	.	-	.	transcript_id "Phchi.S3G141700.t1"; gene_id "Phchi.S3G141700"
Phchi.S3	AUGUSTUS	start_codon	10834106	10834108	.	-	0	transcript_id "Phchi.S3G141700.t1"; gene_id "Phchi.S3G141700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2106.t1 is derived from g9026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4904596	4906374	.	+	.	Phchi.S5G071500
Phchi.S5	AUGUSTUS	transcript	4904596	4906374	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	start_codon	4904596	4904598	.	+	0	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	CDS	4904596	4904779	0.65	+	0	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	exon	4904596	4904779	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	intron	4904780	4904862	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	CDS	4904863	4905102	1	+	2	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	exon	4904863	4905102	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	intron	4905103	4905236	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	CDS	4905237	4905348	0.95	+	2	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	exon	4905237	4905348	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	intron	4905349	4905449	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	CDS	4905450	4905624	1	+	1	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	exon	4905450	4905624	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	intron	4905625	4905715	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	CDS	4905716	4905959	1	+	0	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	exon	4905716	4905959	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	intron	4905960	4906048	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	CDS	4906049	4906374	1	+	2	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	exon	4906049	4906374	.	+	.	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
Phchi.S5	AUGUSTUS	stop_codon	4906375	4906377	.	+	0	transcript_id "Phchi.S5G071500.t1"; gene_id "Phchi.S5G071500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5830.t1 is derived from g3000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19152369	19153777	.	-	.	Phchi.S1G298900
Phchi.S1	AUGUSTUS	transcript	19152369	19153777	.	-	.	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	stop_codon	19152366	19152368	.	-	0	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	CDS	19152369	19152918	0.71	-	1	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	exon	19152369	19152918	.	-	.	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	intron	19152919	19153088	.	-	.	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	CDS	19153089	19153777	0.56	-	0	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	exon	19153089	19153777	.	-	.	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
Phchi.S1	AUGUSTUS	start_codon	19153775	19153777	.	-	0	transcript_id "Phchi.S1G298900.t1"; gene_id "Phchi.S1G298900"
# This transcript jg8045.t2 is derived from g5220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8046.t1 is derived from g5221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32707160	32709795	.	-	.	Phchi.S1G520500
Phchi.S1	AUGUSTUS	transcript	32707160	32709795	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	stop_codon	32707157	32707159	.	-	0	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32707160	32707423	1	-	0	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32707160	32707423	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32707424	32707516	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32707517	32707579	1	-	0	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32707517	32707579	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32707580	32707680	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32707681	32707952	1	-	2	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32707681	32707952	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32707953	32708104	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32708105	32708259	1	-	1	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32708105	32708259	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32708260	32708463	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32708464	32708735	1	-	0	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32708464	32708735	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32708736	32708835	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32708836	32708980	0.67	-	1	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32708836	32708980	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32708981	32709355	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32709356	32709493	0.4	-	1	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32709356	32709493	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32709494	32709654	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32709655	32709663	0.76	-	1	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32709655	32709663	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	intron	32709664	32709745	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	CDS	32709746	32709795	0.65	-	0	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	exon	32709746	32709795	.	-	.	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
Phchi.S1	AUGUSTUS	start_codon	32709793	32709795	.	-	0	transcript_id "Phchi.S1G520500.t1"; gene_id "Phchi.S1G520500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2200.t1 is derived from g9120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5404856	5405558	.	-	.	Phchi.S5G080900
Phchi.S5	AUGUSTUS	transcript	5404856	5405558	.	-	.	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	stop_codon	5404853	5404855	.	-	0	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	CDS	5404856	5404907	0.87	-	1	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	exon	5404856	5404907	.	-	.	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	intron	5404908	5405052	.	-	.	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	CDS	5405053	5405227	0.51	-	2	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	exon	5405053	5405227	.	-	.	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	intron	5405228	5405299	.	-	.	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	CDS	5405300	5405558	0.24	-	0	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	exon	5405300	5405558	.	-	.	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
Phchi.S5	AUGUSTUS	start_codon	5405556	5405558	.	-	0	transcript_id "Phchi.S5G080900.t1"; gene_id "Phchi.S5G080900"
# This transcript jg4490.t2 is derived from g1660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4491.t1 is derived from g1661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10784700	10786310	.	-	.	Phchi.S1G165000
Phchi.S1	AUGUSTUS	transcript	10784700	10786310	.	-	.	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	stop_codon	10784697	10784699	.	-	0	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	CDS	10784700	10785966	0.97	-	1	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	exon	10784700	10785966	.	-	.	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	intron	10785967	10786107	.	-	.	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	CDS	10786108	10786310	0.95	-	0	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	exon	10786108	10786310	.	-	.	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
Phchi.S1	AUGUSTUS	start_codon	10786308	10786310	.	-	0	transcript_id "Phchi.S1G165000.t1"; gene_id "Phchi.S1G165000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4029.t1 is derived from g1198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7230194	7231705	.	+	.	Phchi.S1G118800
Phchi.S1	AUGUSTUS	transcript	7230194	7231705	.	+	.	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	start_codon	7230194	7230196	.	+	0	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	CDS	7230194	7230493	0.28	+	0	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	exon	7230194	7230493	.	+	.	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	intron	7230494	7230652	.	+	.	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	CDS	7230653	7231705	0.51	+	0	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	exon	7230653	7231705	.	+	.	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
Phchi.S1	AUGUSTUS	stop_codon	7231706	7231708	.	+	0	transcript_id "Phchi.S1G118800.t1"; gene_id "Phchi.S1G118800"
# This transcript jg2550.t2 is derived from g9470.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2551.t1 is derived from g9471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7291150	7291815	.	-	.	Phchi.S5G116000
Phchi.S5	AUGUSTUS	transcript	7291150	7291815	.	-	.	transcript_id "Phchi.S5G116000.t1"; gene_id "Phchi.S5G116000"
Phchi.S5	AUGUSTUS	stop_codon	7291147	7291149	.	-	0	transcript_id "Phchi.S5G116000.t1"; gene_id "Phchi.S5G116000"
Phchi.S5	AUGUSTUS	CDS	7291150	7291815	0.87	-	0	transcript_id "Phchi.S5G116000.t1"; gene_id "Phchi.S5G116000"
Phchi.S5	AUGUSTUS	exon	7291150	7291815	.	-	.	transcript_id "Phchi.S5G116000.t1"; gene_id "Phchi.S5G116000"
Phchi.S5	AUGUSTUS	start_codon	7291813	7291815	.	-	0	transcript_id "Phchi.S5G116000.t1"; gene_id "Phchi.S5G116000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14776.t1 is derived from g13244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14651448	14652611	.	-	.	Phchi.S3G209500
Phchi.S3	AUGUSTUS	transcript	14651448	14652611	.	-	.	transcript_id "Phchi.S3G209500.t1"; gene_id "Phchi.S3G209500"
Phchi.S3	AUGUSTUS	stop_codon	14651445	14651447	.	-	0	transcript_id "Phchi.S3G209500.t1"; gene_id "Phchi.S3G209500"
Phchi.S3	AUGUSTUS	CDS	14651448	14652611	0.99	-	0	transcript_id "Phchi.S3G209500.t1"; gene_id "Phchi.S3G209500"
Phchi.S3	AUGUSTUS	exon	14651448	14652611	.	-	.	transcript_id "Phchi.S3G209500.t1"; gene_id "Phchi.S3G209500"
Phchi.S3	AUGUSTUS	start_codon	14652609	14652611	.	-	0	transcript_id "Phchi.S3G209500.t1"; gene_id "Phchi.S3G209500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13103.t1 is derived from g11568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4144251	4145138	.	-	.	Phchi.S3G042200
Phchi.S3	AUGUSTUS	transcript	4144251	4145138	.	-	.	transcript_id "Phchi.S3G042200.t1"; gene_id "Phchi.S3G042200"
Phchi.S3	AUGUSTUS	stop_codon	4144248	4144250	.	-	0	transcript_id "Phchi.S3G042200.t1"; gene_id "Phchi.S3G042200"
Phchi.S3	AUGUSTUS	CDS	4144251	4145138	0.21	-	0	transcript_id "Phchi.S3G042200.t1"; gene_id "Phchi.S3G042200"
Phchi.S3	AUGUSTUS	exon	4144251	4145138	.	-	.	transcript_id "Phchi.S3G042200.t1"; gene_id "Phchi.S3G042200"
Phchi.S3	AUGUSTUS	start_codon	4145136	4145138	.	-	0	transcript_id "Phchi.S3G042200.t1"; gene_id "Phchi.S3G042200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8893.t1 is derived from g6068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38521567	38524338	.	-	.	Phchi.S1G605200
Phchi.S1	AUGUSTUS	transcript	38521567	38524338	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	stop_codon	38521564	38521566	.	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	CDS	38521567	38521863	1	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	exon	38521567	38521863	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	intron	38521864	38521947	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	CDS	38521948	38522229	1	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	exon	38521948	38522229	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	intron	38522230	38522346	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	CDS	38522347	38522919	0.6	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	exon	38522347	38522919	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	intron	38522920	38522992	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	CDS	38522993	38524075	0.62	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	exon	38522993	38524075	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	intron	38524076	38524161	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	CDS	38524162	38524338	0.98	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	exon	38524162	38524338	.	-	.	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
Phchi.S1	AUGUSTUS	start_codon	38524336	38524338	.	-	0	transcript_id "Phchi.S1G605200.t1"; gene_id "Phchi.S1G605200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11177.t1 is derived from g15227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4503213	4504660	.	-	.	Phchi.S4G075900
Phchi.S4	AUGUSTUS	transcript	4503213	4504660	.	-	.	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	stop_codon	4503210	4503212	.	-	0	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	CDS	4503213	4503306	0.78	-	1	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	exon	4503213	4503306	.	-	.	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	intron	4503307	4503398	.	-	.	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	CDS	4503399	4504660	0.83	-	0	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	exon	4503399	4504660	.	-	.	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
Phchi.S4	AUGUSTUS	start_codon	4504658	4504660	.	-	0	transcript_id "Phchi.S4G075900.t1"; gene_id "Phchi.S4G075900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5652.t1 is derived from g2822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18147546	18151147	.	+	.	Phchi.S1G281100
Phchi.S1	AUGUSTUS	transcript	18147546	18151147	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	start_codon	18147546	18147548	.	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18147546	18147776	1	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18147546	18147776	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18147777	18147932	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18147933	18148165	1	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18147933	18148165	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18148166	18148306	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18148307	18148926	0.95	+	1	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18148307	18148926	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18148927	18149002	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18149003	18149037	1	+	2	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18149003	18149037	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18149038	18149310	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18149311	18149695	0.75	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18149311	18149695	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18149696	18149809	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18149810	18149892	1	+	2	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18149810	18149892	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18149893	18150100	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18150101	18150295	1	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18150101	18150295	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18150296	18150469	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18150470	18151147	1	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18150470	18151147	.	+	.	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	stop_codon	18151148	18151150	.	+	0	transcript_id "Phchi.S1G281100.t1"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	transcript	18147546	18151147	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	start_codon	18147546	18147548	.	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18147546	18147776	1	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18147546	18147776	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18147777	18147932	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18147933	18148165	0.99	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18147933	18148165	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18148166	18148306	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18148307	18148926	0.97	+	1	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18148307	18148926	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18148927	18149002	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18149003	18149037	0.98	+	2	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18149003	18149037	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18149038	18149310	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18149311	18149695	0.84	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18149311	18149695	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18149696	18149809	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18149810	18149892	0.98	+	2	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18149810	18149892	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18149893	18150100	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18150101	18150299	0.87	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18150101	18150299	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18150300	18150374	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18150375	18150394	0.84	+	2	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18150375	18150394	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	intron	18150395	18150469	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	CDS	18150470	18151147	0.99	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	exon	18150470	18151147	.	+	.	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
Phchi.S1	AUGUSTUS	stop_codon	18151148	18151150	.	+	0	transcript_id "Phchi.S1G281100.t2"; gene_id "Phchi.S1G281100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14989.t1 is derived from g13457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16096958	16099311	.	+	.	Phchi.S3G230800
Phchi.S3	AUGUSTUS	transcript	16096958	16099311	.	+	.	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	start_codon	16096958	16096960	.	+	0	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	CDS	16096958	16097536	0.5	+	0	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	exon	16096958	16097536	.	+	.	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	intron	16097537	16097792	.	+	.	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	CDS	16097793	16098033	0.97	+	0	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	exon	16097793	16098033	.	+	.	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	intron	16098034	16098268	.	+	.	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	CDS	16098269	16099311	1	+	2	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	exon	16098269	16099311	.	+	.	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
Phchi.S3	AUGUSTUS	stop_codon	16099312	16099314	.	+	0	transcript_id "Phchi.S3G230800.t1"; gene_id "Phchi.S3G230800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2045.t1 is derived from g8965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4572939	4574183	.	+	.	Phchi.S5G065400
Phchi.S5	AUGUSTUS	transcript	4572939	4574183	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	start_codon	4572939	4572941	.	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	CDS	4572939	4572960	0.98	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	exon	4572939	4572960	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	intron	4572961	4573053	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	CDS	4573054	4573142	1	+	2	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	exon	4573054	4573142	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	intron	4573143	4573320	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	CDS	4573321	4573395	1	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	exon	4573321	4573395	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	intron	4573396	4573533	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	CDS	4573534	4573644	1	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	exon	4573534	4573644	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	intron	4573645	4573726	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	CDS	4573727	4573822	1	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	exon	4573727	4573822	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	intron	4573823	4573910	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	CDS	4573911	4574183	1	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	exon	4573911	4574183	.	+	.	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
Phchi.S5	AUGUSTUS	stop_codon	4574184	4574186	.	+	0	transcript_id "Phchi.S5G065400.t1"; gene_id "Phchi.S5G065400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2512.t1 is derived from g9432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7075950	7078811	.	+	.	Phchi.S5G112100
Phchi.S5	AUGUSTUS	transcript	7075950	7078811	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	start_codon	7075950	7075952	.	+	0	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	CDS	7075950	7077828	0.9	+	0	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	exon	7075950	7077828	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	intron	7077829	7078002	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	CDS	7078003	7078056	0.99	+	2	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	exon	7078003	7078056	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	intron	7078057	7078612	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	CDS	7078613	7078668	0.93	+	2	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	exon	7078613	7078668	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	intron	7078669	7078766	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	CDS	7078767	7078811	0.95	+	0	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	exon	7078767	7078811	.	+	.	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
Phchi.S5	AUGUSTUS	stop_codon	7078812	7078814	.	+	0	transcript_id "Phchi.S5G112100.t1"; gene_id "Phchi.S5G112100"
# This transcript jg1093.t2 is derived from g10876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1094.t1 is derived from g10877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7575963	7576743	.	+	.	Phchi.S6G105300
Phchi.S6	AUGUSTUS	transcript	7575963	7576743	.	+	.	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	start_codon	7575963	7575965	.	+	0	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	CDS	7575963	7576091	0.73	+	0	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	exon	7575963	7576091	.	+	.	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	intron	7576092	7576242	.	+	.	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	CDS	7576243	7576743	0.9	+	0	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	exon	7576243	7576743	.	+	.	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
Phchi.S6	AUGUSTUS	stop_codon	7576744	7576746	.	+	0	transcript_id "Phchi.S6G105300.t1"; gene_id "Phchi.S6G105300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14435.t1 is derived from g12903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12778006	12778511	.	-	.	Phchi.S3G175400
Phchi.S3	AUGUSTUS	transcript	12778006	12778511	.	-	.	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	stop_codon	12778003	12778005	.	-	0	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	CDS	12778006	12778082	0.47	-	2	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	exon	12778006	12778082	.	-	.	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	intron	12778083	12778162	.	-	.	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	CDS	12778163	12778511	0.5	-	0	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	exon	12778163	12778511	.	-	.	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
Phchi.S3	AUGUSTUS	start_codon	12778509	12778511	.	-	0	transcript_id "Phchi.S3G175400.t1"; gene_id "Phchi.S3G175400"
# This transcript jg11962.t2 is derived from g7637.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11963.t1 is derived from g7638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	215948	223843	.	-	.	Phchi.S2G004300
Phchi.S2	AUGUSTUS	transcript	215948	223843	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	stop_codon	215945	215947	.	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	215948	215997	0.97	-	2	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	215948	215997	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	215998	217080	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	217081	217415	0.86	-	1	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	217081	217415	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	217416	217512	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	217513	217737	1	-	1	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	217513	217737	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	217738	217822	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	217823	218805	0.99	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	217823	218805	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	218806	218934	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	218935	219031	1	-	1	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	218935	219031	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	219032	219108	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	219109	219242	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	219109	219242	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	219243	219399	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	219400	219525	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	219400	219525	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	219526	219704	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	219705	219815	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	219705	219815	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	219816	219945	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	219946	220027	1	-	1	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	219946	220027	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	220028	220131	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	220132	220277	0.91	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	220132	220277	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	220278	220399	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	220400	220626	1	-	2	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	220400	220626	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	220627	220711	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	220712	220790	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	220712	220790	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	220791	220902	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	220903	221013	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	220903	221013	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	221014	221149	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	221150	221282	1	-	1	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	221150	221282	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	221283	221409	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	221410	221552	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	221410	221552	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	221553	221650	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	221651	221695	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	221651	221695	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	221696	221851	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	221852	221959	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	221852	221959	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	221960	222112	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	222113	222238	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	222113	222238	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	222239	222388	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	222389	222473	1	-	1	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	222389	222473	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	222474	222587	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	222588	222670	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	222588	222670	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	222671	222766	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	222767	222847	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	222767	222847	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	222848	222959	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	222960	223040	0.73	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	222960	223040	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	223041	223239	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	223240	223314	1	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	223240	223314	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	intron	223315	223396	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	CDS	223397	223843	0.99	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	exon	223397	223843	.	-	.	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
Phchi.S2	AUGUSTUS	start_codon	223841	223843	.	-	0	transcript_id "Phchi.S2G004300.t1"; gene_id "Phchi.S2G004300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3229.t1 is derived from g398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2360895	2363047	.	-	.	Phchi.S1G038800
Phchi.S1	AUGUSTUS	transcript	2360895	2363047	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	stop_codon	2360892	2360894	.	-	0	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	CDS	2360895	2360934	1	-	1	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	exon	2360895	2360934	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	intron	2360935	2361082	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	CDS	2361083	2361299	0.49	-	2	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	exon	2361083	2361299	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	intron	2361300	2361755	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	CDS	2361756	2362434	0.21	-	0	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	exon	2361756	2362434	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	intron	2362435	2362978	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	CDS	2362979	2363047	0.01	-	0	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	exon	2362979	2363047	.	-	.	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
Phchi.S1	AUGUSTUS	start_codon	2363045	2363047	.	-	0	transcript_id "Phchi.S1G038800.t1"; gene_id "Phchi.S1G038800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9813.t1 is derived from g6989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43863962	43865840	.	-	.	Phchi.S1G697200
Phchi.S1	AUGUSTUS	transcript	43863962	43865840	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	stop_codon	43863959	43863961	.	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43863962	43864189	0.98	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43863962	43864189	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43864190	43864261	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43864262	43864474	1	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43864262	43864474	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43864475	43864626	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43864627	43864869	0.65	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43864627	43864869	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43864870	43865043	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43865044	43865113	0.67	-	1	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43865044	43865113	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43865114	43865199	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43865200	43865328	1	-	1	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43865200	43865328	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43865329	43865428	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43865429	43865548	0.99	-	1	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43865429	43865548	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43865549	43865704	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43865705	43865724	0.99	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43865705	43865724	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	intron	43865725	43865825	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	CDS	43865826	43865840	0.57	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	exon	43865826	43865840	.	-	.	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
Phchi.S1	AUGUSTUS	start_codon	43865838	43865840	.	-	0	transcript_id "Phchi.S1G697200.t1"; gene_id "Phchi.S1G697200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14095.t1 is derived from g12562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10825968	10831355	.	+	.	Phchi.S3G141400
Phchi.S3	AUGUSTUS	transcript	10825968	10831355	.	+	.	transcript_id "Phchi.S3G141400.t1"; gene_id "Phchi.S3G141400"
Phchi.S3	AUGUSTUS	start_codon	10825968	10825970	.	+	0	transcript_id "Phchi.S3G141400.t1"; gene_id "Phchi.S3G141400"
Phchi.S3	AUGUSTUS	CDS	10825968	10831355	0.74	+	0	transcript_id "Phchi.S3G141400.t1"; gene_id "Phchi.S3G141400"
Phchi.S3	AUGUSTUS	exon	10825968	10831355	.	+	.	transcript_id "Phchi.S3G141400.t1"; gene_id "Phchi.S3G141400"
Phchi.S3	AUGUSTUS	stop_codon	10831356	10831358	.	+	0	transcript_id "Phchi.S3G141400.t1"; gene_id "Phchi.S3G141400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14852.t1 is derived from g13320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15056785	15058219	.	-	.	Phchi.S3G217100
Phchi.S3	AUGUSTUS	transcript	15056785	15058219	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	stop_codon	15056782	15056784	.	-	0	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	CDS	15056785	15057191	1	-	2	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	exon	15056785	15057191	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	intron	15057192	15057306	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	CDS	15057307	15057472	1	-	0	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	exon	15057307	15057472	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	intron	15057473	15057590	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	CDS	15057591	15057779	1	-	0	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	exon	15057591	15057779	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	intron	15057780	15057994	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	CDS	15057995	15058219	1	-	0	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	exon	15057995	15058219	.	-	.	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
Phchi.S3	AUGUSTUS	start_codon	15058217	15058219	.	-	0	transcript_id "Phchi.S3G217100.t1"; gene_id "Phchi.S3G217100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11545.t1 is derived from g15595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6980507	6981709	.	-	.	Phchi.S4G112700
Phchi.S4	AUGUSTUS	transcript	6980507	6981709	.	-	.	transcript_id "Phchi.S4G112700.t1"; gene_id "Phchi.S4G112700"
Phchi.S4	AUGUSTUS	stop_codon	6980504	6980506	.	-	0	transcript_id "Phchi.S4G112700.t1"; gene_id "Phchi.S4G112700"
Phchi.S4	AUGUSTUS	CDS	6980507	6981709	0.63	-	0	transcript_id "Phchi.S4G112700.t1"; gene_id "Phchi.S4G112700"
Phchi.S4	AUGUSTUS	exon	6980507	6981709	.	-	.	transcript_id "Phchi.S4G112700.t1"; gene_id "Phchi.S4G112700"
Phchi.S4	AUGUSTUS	start_codon	6981707	6981709	.	-	0	transcript_id "Phchi.S4G112700.t1"; gene_id "Phchi.S4G112700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11734.t1 is derived from g15786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7905404	7908115	.	+	.	Phchi.S4G131600
Phchi.S4	AUGUSTUS	transcript	7905404	7908115	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	start_codon	7905404	7905406	.	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7905404	7905476	1	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7905404	7905476	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7905477	7905780	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7905781	7906040	1	+	2	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7905781	7906040	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906041	7906231	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906232	7906271	1	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906232	7906271	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906272	7906399	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906400	7906548	1	+	2	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906400	7906548	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906549	7906645	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906646	7906724	1	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906646	7906724	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906725	7906808	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906809	7906908	1	+	2	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906809	7906908	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906909	7906990	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906991	7907154	1	+	1	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906991	7907154	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7907155	7907253	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7907254	7907300	1	+	2	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7907254	7907300	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7907301	7907489	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7907490	7907570	1	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7907490	7907570	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7907571	7907671	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7907672	7908115	0.97	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7907672	7908115	.	+	.	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	stop_codon	7908116	7908118	.	+	0	transcript_id "Phchi.S4G131600.t1"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	transcript	7905404	7908115	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	start_codon	7905404	7905406	.	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7905404	7905476	1	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7905404	7905476	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7905477	7905780	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7905781	7906040	1	+	2	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7905781	7906040	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906041	7906231	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906232	7906271	1	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906232	7906271	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906272	7906399	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906400	7906548	1	+	2	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906400	7906548	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906549	7906645	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906646	7906724	1	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906646	7906724	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906725	7906808	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906809	7906908	1	+	2	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906809	7906908	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7906909	7906990	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7906991	7907154	1	+	1	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7906991	7907154	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7907155	7907253	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7907254	7907300	1	+	2	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7907254	7907300	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7907301	7907489	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7907490	7907570	1	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7907490	7907570	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	intron	7907571	7907668	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	CDS	7907669	7908115	0.83	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	exon	7907669	7908115	.	+	.	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
Phchi.S4	AUGUSTUS	stop_codon	7908116	7908118	.	+	0	transcript_id "Phchi.S4G131600.t2"; gene_id "Phchi.S4G131600"
# This transcript jg14941.t2 is derived from g13409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14942.t1 is derived from g13410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15646730	15650045	.	-	.	Phchi.S3G226100
Phchi.S3	AUGUSTUS	transcript	15646730	15650045	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	stop_codon	15646727	15646729	.	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15646730	15646769	0.57	-	1	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15646730	15646769	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15646770	15646956	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15646957	15647171	0.56	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15646957	15647171	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15647172	15647273	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15647274	15647354	0.81	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15647274	15647354	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15647355	15647453	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15647454	15647501	1	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15647454	15647501	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15647502	15647578	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15647579	15647716	1	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15647579	15647716	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15647717	15647795	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15647796	15647906	1	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15647796	15647906	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15647907	15647998	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15647999	15648612	1	-	2	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15647999	15648612	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15648613	15648703	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15648704	15648786	1	-	1	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15648704	15648786	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15648787	15648879	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15648880	15648998	1	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15648880	15648998	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15648999	15649084	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15649085	15649343	1	-	1	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15649085	15649343	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15649344	15649532	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15649533	15649750	0.96	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15649533	15649750	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	intron	15649751	15649967	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	CDS	15649968	15650045	0.95	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	exon	15649968	15650045	.	-	.	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
Phchi.S3	AUGUSTUS	start_codon	15650043	15650045	.	-	0	transcript_id "Phchi.S3G226100.t1"; gene_id "Phchi.S3G226100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5053.t1 is derived from g2223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14397089	14397493	.	-	.	Phchi.S1G221200
Phchi.S1	AUGUSTUS	transcript	14397089	14397493	.	-	.	transcript_id "Phchi.S1G221200.t1"; gene_id "Phchi.S1G221200"
Phchi.S1	AUGUSTUS	stop_codon	14397086	14397088	.	-	0	transcript_id "Phchi.S1G221200.t1"; gene_id "Phchi.S1G221200"
Phchi.S1	AUGUSTUS	CDS	14397089	14397493	0.97	-	0	transcript_id "Phchi.S1G221200.t1"; gene_id "Phchi.S1G221200"
Phchi.S1	AUGUSTUS	exon	14397089	14397493	.	-	.	transcript_id "Phchi.S1G221200.t1"; gene_id "Phchi.S1G221200"
Phchi.S1	AUGUSTUS	start_codon	14397491	14397493	.	-	0	transcript_id "Phchi.S1G221200.t1"; gene_id "Phchi.S1G221200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12207.t1 is derived from g7883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6736409	6738407	.	+	.	Phchi.S2G028700
Phchi.S2	AUGUSTUS	transcript	6736409	6738407	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	start_codon	6736409	6736411	.	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6736409	6736758	1	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6736409	6736758	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6736759	6736828	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6736829	6736979	1	+	1	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6736829	6736979	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6736980	6737074	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6737075	6737242	1	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6737075	6737242	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6737243	6737340	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6737341	6737567	1	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6737341	6737567	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6737568	6737667	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6737668	6737685	0.5	+	1	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6737668	6737685	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6737686	6737756	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6737757	6737790	0.57	+	1	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6737757	6737790	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6737791	6737865	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6737866	6737928	1	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6737866	6737928	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6737929	6738051	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6738052	6738195	1	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6738052	6738195	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	intron	6738196	6738278	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	CDS	6738279	6738407	1	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	exon	6738279	6738407	.	+	.	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
Phchi.S2	AUGUSTUS	stop_codon	6738408	6738410	.	+	0	transcript_id "Phchi.S2G028700.t1"; gene_id "Phchi.S2G028700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13270.t1 is derived from g11735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4997840	4999989	.	+	.	Phchi.S3G058900
Phchi.S3	AUGUSTUS	transcript	4997840	4999989	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	start_codon	4997840	4997842	.	+	0	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4997840	4998198	0.99	+	0	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4997840	4998198	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4998199	4998280	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4998281	4998382	1	+	1	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4998281	4998382	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4998383	4998477	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4998478	4998500	1	+	1	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4998478	4998500	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4998501	4998569	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4998570	4998676	1	+	2	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4998570	4998676	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4998677	4998767	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4998768	4999353	1	+	0	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4998768	4999353	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4999354	4999436	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4999437	4999623	0.98	+	2	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4999437	4999623	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4999624	4999703	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4999704	4999834	0.53	+	1	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4999704	4999834	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	intron	4999835	4999924	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	CDS	4999925	4999989	0.49	+	2	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	exon	4999925	4999989	.	+	.	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
Phchi.S3	AUGUSTUS	stop_codon	4999990	4999992	.	+	0	transcript_id "Phchi.S3G058900.t1"; gene_id "Phchi.S3G058900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6489.t1 is derived from g3661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23268668	23269825	.	+	.	Phchi.S1G364800
Phchi.S1	AUGUSTUS	transcript	23268668	23269825	.	+	.	transcript_id "Phchi.S1G364800.t1"; gene_id "Phchi.S1G364800"
Phchi.S1	AUGUSTUS	start_codon	23268668	23268670	.	+	0	transcript_id "Phchi.S1G364800.t1"; gene_id "Phchi.S1G364800"
Phchi.S1	AUGUSTUS	CDS	23268668	23269825	0.37	+	0	transcript_id "Phchi.S1G364800.t1"; gene_id "Phchi.S1G364800"
Phchi.S1	AUGUSTUS	exon	23268668	23269825	.	+	.	transcript_id "Phchi.S1G364800.t1"; gene_id "Phchi.S1G364800"
Phchi.S1	AUGUSTUS	stop_codon	23269826	23269828	.	+	0	transcript_id "Phchi.S1G364800.t1"; gene_id "Phchi.S1G364800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11661.t1 is derived from g15712.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7562040	7564565	.	-	.	Phchi.S4G124300
Phchi.S4	AUGUSTUS	transcript	7562040	7564565	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	stop_codon	7562037	7562039	.	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562040	7562117	1	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562040	7562117	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562118	7562219	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562220	7562303	0.98	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562220	7562303	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562304	7562387	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562388	7562444	1	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562388	7562444	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562445	7562522	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562523	7562651	1	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562523	7562651	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562652	7562744	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562745	7562831	1	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562745	7562831	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562832	7562939	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562940	7562987	1	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562940	7562987	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562988	7563200	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563201	7563357	1	-	1	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563201	7563357	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563358	7563470	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563471	7563612	0.98	-	2	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563471	7563612	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563613	7563699	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563700	7563723	0.74	-	2	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563700	7563723	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563724	7563819	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563820	7563888	0.91	-	2	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563820	7563888	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563889	7564010	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7564011	7564042	0.96	-	1	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7564011	7564042	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7564043	7564269	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7564270	7564565	0.97	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7564270	7564565	.	-	.	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	start_codon	7564563	7564565	.	-	0	transcript_id "Phchi.S4G124300.t1"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	transcript	7562040	7564565	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	stop_codon	7562037	7562039	.	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562040	7562117	1	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562040	7562117	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562118	7562219	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562220	7562303	0.96	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562220	7562303	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562304	7562387	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562388	7562444	1	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562388	7562444	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562445	7562522	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562523	7562651	1	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562523	7562651	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562652	7562744	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562745	7562831	1	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562745	7562831	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562832	7562939	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7562940	7562987	1	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7562940	7562987	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7562988	7563200	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563201	7563357	1	-	1	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563201	7563357	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563358	7563470	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563471	7563612	1	-	2	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563471	7563612	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563613	7563888	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7563889	7563938	0.51	-	1	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7563889	7563938	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7563939	7564012	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7564013	7564042	0.51	-	1	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7564013	7564042	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	intron	7564043	7564269	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	CDS	7564270	7564565	0.49	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	exon	7564270	7564565	.	-	.	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
Phchi.S4	AUGUSTUS	start_codon	7564563	7564565	.	-	0	transcript_id "Phchi.S4G124300.t2"; gene_id "Phchi.S4G124300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1056.t1 is derived from g10839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7320271	7321863	.	-	.	Phchi.S6G101500
Phchi.S6	AUGUSTUS	transcript	7320271	7321863	.	-	.	transcript_id "Phchi.S6G101500.t1"; gene_id "Phchi.S6G101500"
Phchi.S6	AUGUSTUS	stop_codon	7320268	7320270	.	-	0	transcript_id "Phchi.S6G101500.t1"; gene_id "Phchi.S6G101500"
Phchi.S6	AUGUSTUS	CDS	7320271	7321863	0.81	-	0	transcript_id "Phchi.S6G101500.t1"; gene_id "Phchi.S6G101500"
Phchi.S6	AUGUSTUS	exon	7320271	7321863	.	-	.	transcript_id "Phchi.S6G101500.t1"; gene_id "Phchi.S6G101500"
Phchi.S6	AUGUSTUS	start_codon	7321861	7321863	.	-	0	transcript_id "Phchi.S6G101500.t1"; gene_id "Phchi.S6G101500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2148.t1 is derived from g9068.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5074313	5076744	.	-	.	Phchi.S5G075700
Phchi.S5	AUGUSTUS	transcript	5074313	5076744	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	stop_codon	5074310	5074312	.	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5074313	5074494	0.95	-	2	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5074313	5074494	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5074495	5074590	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5074591	5074642	1	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5074591	5074642	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5074643	5074842	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5074843	5075009	0.39	-	2	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5074843	5075009	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5075010	5075347	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5075348	5075360	0.38	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5075348	5075360	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5075361	5075517	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5075518	5075667	1	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5075518	5075667	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5075668	5075765	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5075766	5075937	1	-	1	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5075766	5075937	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5075938	5076069	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5076070	5076144	1	-	1	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5076070	5076144	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5076145	5076280	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5076281	5076306	1	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5076281	5076306	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5076307	5076454	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5076455	5076503	1	-	1	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5076455	5076503	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	intron	5076504	5076691	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	CDS	5076692	5076744	1	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	exon	5076692	5076744	.	-	.	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
Phchi.S5	AUGUSTUS	start_codon	5076742	5076744	.	-	0	transcript_id "Phchi.S5G075700.t1"; gene_id "Phchi.S5G075700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12259.t1 is derived from g7935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7057046	7057784	.	+	.	Phchi.S2G033900
Phchi.S2	AUGUSTUS	transcript	7057046	7057784	.	+	.	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	start_codon	7057046	7057048	.	+	0	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	CDS	7057046	7057213	0.41	+	0	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	exon	7057046	7057213	.	+	.	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	intron	7057214	7057352	.	+	.	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	CDS	7057353	7057784	0.77	+	0	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	exon	7057353	7057784	.	+	.	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
Phchi.S2	AUGUSTUS	stop_codon	7057785	7057787	.	+	0	transcript_id "Phchi.S2G033900.t1"; gene_id "Phchi.S2G033900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2524.t1 is derived from g9444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7132912	7133435	.	-	.	Phchi.S5G113300
Phchi.S5	AUGUSTUS	transcript	7132912	7133435	.	-	.	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	stop_codon	7132909	7132911	.	-	0	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	CDS	7132912	7133043	0.99	-	0	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	exon	7132912	7133043	.	-	.	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	intron	7133044	7133255	.	-	.	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	CDS	7133256	7133435	0.9	-	0	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	exon	7133256	7133435	.	-	.	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
Phchi.S5	AUGUSTUS	start_codon	7133433	7133435	.	-	0	transcript_id "Phchi.S5G113300.t1"; gene_id "Phchi.S5G113300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9463.t1 is derived from g6639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41576919	41578823	.	+	.	Phchi.S1G662200
Phchi.S1	AUGUSTUS	transcript	41576919	41578823	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	start_codon	41576919	41576921	.	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41576919	41577001	0.95	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41576919	41577001	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41577002	41577079	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41577080	41577149	1	+	1	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41577080	41577149	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41577150	41577247	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41577248	41577385	1	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41577248	41577385	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41577386	41577465	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41577466	41577632	0.98	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41577466	41577632	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41577633	41577762	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41577763	41577847	0.81	+	1	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41577763	41577847	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41577848	41577956	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41577957	41578013	0.82	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41577957	41578013	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41578014	41578113	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41578114	41578215	0.99	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41578114	41578215	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41578216	41578321	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41578322	41578392	0.99	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41578322	41578392	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	intron	41578393	41578498	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	CDS	41578499	41578823	1	+	1	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	exon	41578499	41578823	.	+	.	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
Phchi.S1	AUGUSTUS	stop_codon	41578824	41578826	.	+	0	transcript_id "Phchi.S1G662200.t1"; gene_id "Phchi.S1G662200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8567.t1 is derived from g5742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36641335	36646097	.	+	.	Phchi.S1G572600
Phchi.S1	AUGUSTUS	transcript	36641335	36646097	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	start_codon	36641335	36641337	.	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36641335	36641519	0.76	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36641335	36641519	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36641520	36641647	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36641648	36641852	0.8	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36641648	36641852	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36641853	36641985	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36641986	36642123	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36641986	36642123	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36642124	36642199	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36642200	36642274	0.87	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36642200	36642274	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36642275	36642377	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36642378	36642416	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36642378	36642416	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36642417	36642513	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36642514	36642606	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36642514	36642606	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36642607	36642798	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36642799	36642854	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36642799	36642854	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36642855	36643051	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36643052	36643130	0.99	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36643052	36643130	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36643131	36643236	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36643237	36643301	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36643237	36643301	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36643302	36643384	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36643385	36643430	1	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36643385	36643430	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36643431	36643520	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36643521	36643654	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36643521	36643654	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36643655	36643788	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36643789	36643881	1	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36643789	36643881	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36643882	36643968	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36643969	36644083	1	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36643969	36644083	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36644084	36644213	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36644214	36644363	0.87	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36644214	36644363	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36644364	36644452	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36644453	36644508	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36644453	36644508	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36644509	36644609	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36644610	36644691	1	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36644610	36644691	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36644692	36644786	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36644787	36644919	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36644787	36644919	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36644920	36644998	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36644999	36645093	1	+	2	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36644999	36645093	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36645094	36645234	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36645235	36645687	0.99	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36645235	36645687	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36645688	36645765	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36645766	36645854	1	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36645766	36645854	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	intron	36645855	36645940	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	CDS	36645941	36646097	0.92	+	1	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	exon	36645941	36646097	.	+	.	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
Phchi.S1	AUGUSTUS	stop_codon	36646098	36646100	.	+	0	transcript_id "Phchi.S1G572600.t1"; gene_id "Phchi.S1G572600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15938.t1 is derived from g14401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C58	AUGUSTUS	gene	22183	22551	.	-	.	Phchi.C58G000200
Phchi.C58	AUGUSTUS	transcript	22183	22551	.	-	.	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	stop_codon	22180	22182	.	-	0	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	CDS	22183	22386	0.99	-	0	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	exon	22183	22386	.	-	.	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	intron	22387	22473	.	-	.	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	CDS	22474	22551	1	-	0	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	exon	22474	22551	.	-	.	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
Phchi.C58	AUGUSTUS	start_codon	22549	22551	.	-	0	transcript_id "Phchi.C58G000200.t1"; gene_id "Phchi.C58G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12023.t1 is derived from g7698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	616674	619307	.	+	.	Phchi.S2G010300
Phchi.S2	AUGUSTUS	transcript	616674	619307	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	start_codon	616674	616676	.	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	616674	616901	0.97	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	616674	616901	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	intron	616902	616999	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	617000	617168	0.97	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	617000	617168	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	intron	617169	617247	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	617248	617831	0.95	+	2	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	617248	617831	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	intron	617832	618010	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	618011	618065	1	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	618011	618065	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	intron	618066	618170	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	618171	618475	0.98	+	2	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	618171	618475	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	intron	618476	618721	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	618722	618844	1	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	618722	618844	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	intron	618845	619190	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	CDS	619191	619307	0.43	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	exon	619191	619307	.	+	.	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
Phchi.S2	AUGUSTUS	stop_codon	619308	619310	.	+	0	transcript_id "Phchi.S2G010300.t1"; gene_id "Phchi.S2G010300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14916.t1 is derived from g13384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15485265	15485846	.	+	.	Phchi.S3G223500
Phchi.S3	AUGUSTUS	transcript	15485265	15485846	.	+	.	transcript_id "Phchi.S3G223500.t1"; gene_id "Phchi.S3G223500"
Phchi.S3	AUGUSTUS	start_codon	15485265	15485267	.	+	0	transcript_id "Phchi.S3G223500.t1"; gene_id "Phchi.S3G223500"
Phchi.S3	AUGUSTUS	CDS	15485265	15485846	0.33	+	0	transcript_id "Phchi.S3G223500.t1"; gene_id "Phchi.S3G223500"
Phchi.S3	AUGUSTUS	exon	15485265	15485846	.	+	.	transcript_id "Phchi.S3G223500.t1"; gene_id "Phchi.S3G223500"
Phchi.S3	AUGUSTUS	stop_codon	15485847	15485849	.	+	0	transcript_id "Phchi.S3G223500.t1"; gene_id "Phchi.S3G223500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1696.t1 is derived from g8615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2567224	2568234	.	+	.	Phchi.S5G030500
Phchi.S5	AUGUSTUS	transcript	2567224	2568234	.	+	.	transcript_id "Phchi.S5G030500.t1"; gene_id "Phchi.S5G030500"
Phchi.S5	AUGUSTUS	start_codon	2567224	2567226	.	+	0	transcript_id "Phchi.S5G030500.t1"; gene_id "Phchi.S5G030500"
Phchi.S5	AUGUSTUS	CDS	2567224	2568234	0.61	+	0	transcript_id "Phchi.S5G030500.t1"; gene_id "Phchi.S5G030500"
Phchi.S5	AUGUSTUS	exon	2567224	2568234	.	+	.	transcript_id "Phchi.S5G030500.t1"; gene_id "Phchi.S5G030500"
Phchi.S5	AUGUSTUS	stop_codon	2568235	2568237	.	+	0	transcript_id "Phchi.S5G030500.t1"; gene_id "Phchi.S5G030500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3694.t1 is derived from g863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5217663	5218058	.	+	.	Phchi.S1G085300
Phchi.S1	AUGUSTUS	transcript	5217663	5218058	.	+	.	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	start_codon	5217663	5217665	.	+	0	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	CDS	5217663	5217778	1	+	0	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	exon	5217663	5217778	.	+	.	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	intron	5217779	5217898	.	+	.	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	CDS	5217899	5218058	0.94	+	1	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	exon	5217899	5218058	.	+	.	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
Phchi.S1	AUGUSTUS	stop_codon	5218059	5218061	.	+	0	transcript_id "Phchi.S1G085300.t1"; gene_id "Phchi.S1G085300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9222.t1 is derived from g6397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40470209	40471104	.	+	.	Phchi.S1G638100
Phchi.S1	AUGUSTUS	transcript	40470209	40471104	.	+	.	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	start_codon	40470209	40470211	.	+	0	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	CDS	40470209	40470407	0.99	+	0	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	exon	40470209	40470407	.	+	.	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	intron	40470408	40470544	.	+	.	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	CDS	40470545	40471104	0.98	+	2	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	exon	40470545	40471104	.	+	.	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
Phchi.S1	AUGUSTUS	stop_codon	40471105	40471107	.	+	0	transcript_id "Phchi.S1G638100.t1"; gene_id "Phchi.S1G638100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15344.t1 is derived from g13812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18481012	18481483	.	-	.	Phchi.S3G266300
Phchi.S3	AUGUSTUS	transcript	18481012	18481483	.	-	.	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	stop_codon	18481009	18481011	.	-	0	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	CDS	18481012	18481097	0.51	-	2	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	exon	18481012	18481097	.	-	.	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	intron	18481098	18481233	.	-	.	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	CDS	18481234	18481483	0.67	-	0	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	exon	18481234	18481483	.	-	.	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
Phchi.S3	AUGUSTUS	start_codon	18481481	18481483	.	-	0	transcript_id "Phchi.S3G266300.t1"; gene_id "Phchi.S3G266300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9984.t1 is derived from g7160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44784449	44786277	.	+	.	Phchi.S1G714300
Phchi.S1	AUGUSTUS	transcript	44784449	44786277	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	start_codon	44784449	44784451	.	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	CDS	44784449	44784766	0.94	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	exon	44784449	44784766	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	intron	44784767	44785015	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	CDS	44785016	44785189	1	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	exon	44785016	44785189	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	intron	44785190	44785275	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	CDS	44785276	44785419	0.98	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	exon	44785276	44785419	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	intron	44785420	44785507	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	CDS	44785508	44785636	1	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	exon	44785508	44785636	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	intron	44785637	44785902	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	CDS	44785903	44785958	0.35	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	exon	44785903	44785958	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	intron	44785959	44786102	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	CDS	44786103	44786277	0.67	+	1	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	exon	44786103	44786277	.	+	.	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
Phchi.S1	AUGUSTUS	stop_codon	44786278	44786280	.	+	0	transcript_id "Phchi.S1G714300.t1"; gene_id "Phchi.S1G714300"
# This transcript jg14568.t2 is derived from g13036.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14569.t1 is derived from g13037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13515164	13516846	.	+	.	Phchi.S3G188800
Phchi.S3	AUGUSTUS	transcript	13515164	13516846	.	+	.	transcript_id "Phchi.S3G188800.t1"; gene_id "Phchi.S3G188800"
Phchi.S3	AUGUSTUS	start_codon	13515164	13515166	.	+	0	transcript_id "Phchi.S3G188800.t1"; gene_id "Phchi.S3G188800"
Phchi.S3	AUGUSTUS	CDS	13515164	13516846	1	+	0	transcript_id "Phchi.S3G188800.t1"; gene_id "Phchi.S3G188800"
Phchi.S3	AUGUSTUS	exon	13515164	13516846	.	+	.	transcript_id "Phchi.S3G188800.t1"; gene_id "Phchi.S3G188800"
Phchi.S3	AUGUSTUS	stop_codon	13516847	13516849	.	+	0	transcript_id "Phchi.S3G188800.t1"; gene_id "Phchi.S3G188800"
# This transcript jg12163.t2 is derived from g7839.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12164.t1 is derived from g7840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5081017	5082085	.	+	.	Phchi.S2G024400
Phchi.S2	AUGUSTUS	transcript	5081017	5082085	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	start_codon	5081017	5081019	.	+	0	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5081017	5081075	0.98	+	0	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5081017	5081075	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	intron	5081076	5081195	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5081196	5081258	0.98	+	1	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5081196	5081258	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	intron	5081259	5081348	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5081349	5081438	1	+	1	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5081349	5081438	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	intron	5081439	5081506	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5081507	5081564	1	+	1	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5081507	5081564	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	intron	5081565	5081640	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5081641	5081730	1	+	0	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5081641	5081730	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	intron	5081731	5081820	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5081821	5081938	1	+	0	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5081821	5081938	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	intron	5081939	5082020	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	CDS	5082021	5082085	0.94	+	2	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	exon	5082021	5082085	.	+	.	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
Phchi.S2	AUGUSTUS	stop_codon	5082086	5082088	.	+	0	transcript_id "Phchi.S2G024400.t1"; gene_id "Phchi.S2G024400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15373.t1 is derived from g13841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18676613	18678631	.	+	.	Phchi.S3G269200
Phchi.S3	AUGUSTUS	transcript	18676613	18678631	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	start_codon	18676613	18676615	.	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18676613	18676894	0.38	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18676613	18676894	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18676895	18677133	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18677134	18677193	1	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18677134	18677193	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18677194	18677328	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18677329	18677426	1	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18677329	18677426	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18677427	18677575	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18677576	18677654	1	+	1	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18677576	18677654	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18677655	18677768	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18677769	18677862	1	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18677769	18677862	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18677863	18677982	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18677983	18678095	1	+	2	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18677983	18678095	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18678096	18678174	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18678175	18678220	1	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18678175	18678220	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18678221	18678317	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18678318	18678358	0.99	+	2	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18678318	18678358	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	intron	18678359	18678466	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	CDS	18678467	18678631	0.99	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	exon	18678467	18678631	.	+	.	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
Phchi.S3	AUGUSTUS	stop_codon	18678632	18678634	.	+	0	transcript_id "Phchi.S3G269200.t1"; gene_id "Phchi.S3G269200"
# This transcript jg15213.t2 is derived from g13681.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15214.t1 is derived from g13682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17720716	17722823	.	-	.	Phchi.S3G253300
Phchi.S3	AUGUSTUS	transcript	17720716	17722823	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	stop_codon	17720713	17720715	.	-	0	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	CDS	17720716	17720893	1	-	1	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	exon	17720716	17720893	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	intron	17720894	17720985	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	CDS	17720986	17721203	0.97	-	0	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	exon	17720986	17721203	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	intron	17721204	17721320	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	CDS	17721321	17721743	1	-	0	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	exon	17721321	17721743	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	intron	17721744	17721833	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	CDS	17721834	17722027	0.98	-	2	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	exon	17721834	17722027	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	intron	17722028	17722132	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	CDS	17722133	17722823	0.79	-	0	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	exon	17722133	17722823	.	-	.	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	start_codon	17722821	17722823	.	-	0	transcript_id "Phchi.S3G253300.t1"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	transcript	17722080	17722823	.	-	.	transcript_id "Phchi.S3G253300.t2"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	stop_codon	17722077	17722079	.	-	0	transcript_id "Phchi.S3G253300.t2"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	CDS	17722080	17722823	0.66	-	0	transcript_id "Phchi.S3G253300.t2"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	exon	17722080	17722823	.	-	.	transcript_id "Phchi.S3G253300.t2"; gene_id "Phchi.S3G253300"
Phchi.S3	AUGUSTUS	start_codon	17722821	17722823	.	-	0	transcript_id "Phchi.S3G253300.t2"; gene_id "Phchi.S3G253300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14783.t1 is derived from g13251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14679704	14681933	.	+	.	Phchi.S3G210200
Phchi.S3	AUGUSTUS	transcript	14679704	14681933	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	start_codon	14679704	14679706	.	+	0	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	CDS	14679704	14679730	1	+	0	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	exon	14679704	14679730	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	intron	14679731	14680188	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	CDS	14680189	14680256	1	+	0	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	exon	14680189	14680256	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	intron	14680257	14680393	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	CDS	14680394	14680480	1	+	1	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	exon	14680394	14680480	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	intron	14680481	14680630	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	CDS	14680631	14680740	1	+	1	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	exon	14680631	14680740	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	intron	14680741	14680874	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	CDS	14680875	14681091	0.87	+	2	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	exon	14680875	14681091	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	intron	14681092	14681680	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	CDS	14681681	14681933	0.6	+	1	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	exon	14681681	14681933	.	+	.	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
Phchi.S3	AUGUSTUS	stop_codon	14681934	14681936	.	+	0	transcript_id "Phchi.S3G210200.t1"; gene_id "Phchi.S3G210200"
# This transcript jg6674.t2 is derived from g3846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6675.t1 is derived from g3847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24450963	24451892	.	-	.	Phchi.S1G383400
Phchi.S1	AUGUSTUS	transcript	24450963	24451892	.	-	.	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	stop_codon	24450960	24450962	.	-	0	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	CDS	24450963	24451273	1	-	2	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	exon	24450963	24451273	.	-	.	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	intron	24451274	24451360	.	-	.	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	CDS	24451361	24451765	1	-	2	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	exon	24451361	24451765	.	-	.	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	intron	24451766	24451846	.	-	.	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	CDS	24451847	24451892	0.98	-	0	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	exon	24451847	24451892	.	-	.	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
Phchi.S1	AUGUSTUS	start_codon	24451890	24451892	.	-	0	transcript_id "Phchi.S1G383400.t1"; gene_id "Phchi.S1G383400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10776.t1 is derived from g14826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2059012	2062470	.	+	.	Phchi.S4G035800
Phchi.S4	AUGUSTUS	transcript	2059012	2062470	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	start_codon	2059012	2059014	.	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2059012	2059728	0.77	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2059012	2059728	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2059729	2059799	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2059800	2060045	0.93	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2059800	2060045	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2060046	2060280	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2060281	2060473	0.93	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2060281	2060473	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2060474	2060583	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2060584	2060729	1	+	2	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2060584	2060729	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2060730	2060885	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2060886	2060953	1	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2060886	2060953	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2060954	2061078	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2061079	2061181	1	+	1	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2061079	2061181	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2061182	2061266	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2061267	2061293	0.57	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2061267	2061293	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2061294	2061513	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2061514	2061610	0.5	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2061514	2061610	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2061611	2061696	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2061697	2061812	0.62	+	2	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2061697	2061812	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2061813	2061901	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2061902	2062060	0.99	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2061902	2062060	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2062061	2062151	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2062152	2062315	1	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2062152	2062315	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	intron	2062316	2062466	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	CDS	2062467	2062470	1	+	1	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	exon	2062467	2062470	.	+	.	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
Phchi.S4	AUGUSTUS	stop_codon	2062471	2062473	.	+	0	transcript_id "Phchi.S4G035800.t1"; gene_id "Phchi.S4G035800"
# This transcript jg959.t2 is derived from g10741.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg960.t1 is derived from g10742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6659649	6661913	.	+	.	Phchi.S6G091900
Phchi.S6	AUGUSTUS	transcript	6659649	6661913	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	start_codon	6659649	6659651	.	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6659649	6659774	0.72	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6659649	6659774	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6659775	6659978	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6659979	6660041	1	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6659979	6660041	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6660042	6660161	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6660162	6660217	1	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6660162	6660217	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6660218	6660357	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6660358	6660451	1	+	1	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6660358	6660451	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6660452	6660530	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6660531	6660591	1	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6660531	6660591	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6660592	6660681	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6660682	6660763	1	+	2	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6660682	6660763	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6660764	6660876	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6660877	6660932	1	+	1	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6660877	6660932	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6660933	6661024	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6661025	6661300	0.83	+	2	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6661025	6661300	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6661301	6661453	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6661454	6661460	0.46	+	2	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6661454	6661460	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6661461	6661557	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6661558	6661678	0.4	+	1	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6661558	6661678	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	intron	6661679	6661901	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	CDS	6661902	6661913	0.87	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	exon	6661902	6661913	.	+	.	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
Phchi.S6	AUGUSTUS	stop_codon	6661914	6661916	.	+	0	transcript_id "Phchi.S6G091900.t1"; gene_id "Phchi.S6G091900"
# This transcript jg1246.t2 is derived from g11029.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1247.t1 is derived from g11030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8626583	8627707	.	-	.	Phchi.S6G120600
Phchi.S6	AUGUSTUS	transcript	8626583	8627707	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	stop_codon	8626580	8626582	.	-	0	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	CDS	8626583	8626631	0.76	-	1	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	exon	8626583	8626631	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	intron	8626632	8626779	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	CDS	8626780	8626820	0.77	-	0	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	exon	8626780	8626820	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	intron	8626821	8626950	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	CDS	8626951	8627016	1	-	0	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	exon	8626951	8627016	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	intron	8627017	8627271	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	CDS	8627272	8627578	1	-	1	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	exon	8627272	8627578	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	intron	8627579	8627696	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	CDS	8627697	8627707	1	-	0	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	exon	8627697	8627707	.	-	.	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
Phchi.S6	AUGUSTUS	start_codon	8627705	8627707	.	-	0	transcript_id "Phchi.S6G120600.t1"; gene_id "Phchi.S6G120600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6683.t1 is derived from g3855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24497163	24498980	.	-	.	Phchi.S1G384200
Phchi.S1	AUGUSTUS	transcript	24497163	24498980	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	stop_codon	24497160	24497162	.	-	0	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	CDS	24497163	24497540	1	-	0	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	exon	24497163	24497540	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	intron	24497541	24497691	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	CDS	24497692	24497940	1	-	0	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	exon	24497692	24497940	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	intron	24497941	24498029	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	CDS	24498030	24498625	0.79	-	2	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	exon	24498030	24498625	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	intron	24498626	24498736	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	CDS	24498737	24498980	0.36	-	0	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	exon	24498737	24498980	.	-	.	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
Phchi.S1	AUGUSTUS	start_codon	24498978	24498980	.	-	0	transcript_id "Phchi.S1G384200.t1"; gene_id "Phchi.S1G384200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1631.t1 is derived from g8550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2102961	2103691	.	-	.	Phchi.S5G024000
Phchi.S5	AUGUSTUS	transcript	2102961	2103691	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	stop_codon	2102958	2102960	.	-	0	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	CDS	2102961	2103117	0.47	-	1	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	exon	2102961	2103117	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	intron	2103118	2103258	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	CDS	2103259	2103357	0.51	-	1	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	exon	2103259	2103357	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	intron	2103358	2103435	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	CDS	2103436	2103533	0.47	-	0	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	exon	2103436	2103533	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	intron	2103534	2103685	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	CDS	2103686	2103691	0.44	-	0	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	exon	2103686	2103691	.	-	.	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
Phchi.S5	AUGUSTUS	start_codon	2103689	2103691	.	-	0	transcript_id "Phchi.S5G024000.t1"; gene_id "Phchi.S5G024000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6791.t1 is derived from g3963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25096674	25098508	.	-	.	Phchi.S1G395000
Phchi.S1	AUGUSTUS	transcript	25096674	25098508	.	-	.	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	stop_codon	25096671	25096673	.	-	0	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	CDS	25096674	25098017	0.63	-	0	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	exon	25096674	25098017	.	-	.	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	intron	25098018	25098135	.	-	.	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	CDS	25098136	25098154	0.63	-	1	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	exon	25098136	25098154	.	-	.	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	intron	25098155	25098248	.	-	.	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	CDS	25098249	25098508	0.95	-	0	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	exon	25098249	25098508	.	-	.	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
Phchi.S1	AUGUSTUS	start_codon	25098506	25098508	.	-	0	transcript_id "Phchi.S1G395000.t1"; gene_id "Phchi.S1G395000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8962.t1 is derived from g6137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38862033	38863674	.	+	.	Phchi.S1G612100
Phchi.S1	AUGUSTUS	transcript	38862033	38863674	.	+	.	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	start_codon	38862033	38862035	.	+	0	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	CDS	38862033	38862754	0.46	+	0	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	exon	38862033	38862754	.	+	.	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	intron	38862755	38862892	.	+	.	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	CDS	38862893	38863040	1	+	1	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	exon	38862893	38863040	.	+	.	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	intron	38863041	38863125	.	+	.	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	CDS	38863126	38863674	1	+	0	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	exon	38863126	38863674	.	+	.	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
Phchi.S1	AUGUSTUS	stop_codon	38863675	38863677	.	+	0	transcript_id "Phchi.S1G612100.t1"; gene_id "Phchi.S1G612100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13598.t1 is derived from g12065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7641508	7642662	.	+	.	Phchi.S3G091700
Phchi.S3	AUGUSTUS	transcript	7641508	7642662	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	start_codon	7641508	7641510	.	+	0	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	CDS	7641508	7641569	1	+	0	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	exon	7641508	7641569	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	intron	7641570	7641741	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	CDS	7641742	7641927	1	+	1	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	exon	7641742	7641927	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	intron	7641928	7642019	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	CDS	7642020	7642164	0.67	+	1	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	exon	7642020	7642164	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	intron	7642165	7642247	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	CDS	7642248	7642434	0.44	+	0	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	exon	7642248	7642434	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	intron	7642435	7642528	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	CDS	7642529	7642662	0.91	+	2	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	exon	7642529	7642662	.	+	.	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
Phchi.S3	AUGUSTUS	stop_codon	7642663	7642665	.	+	0	transcript_id "Phchi.S3G091700.t1"; gene_id "Phchi.S3G091700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8352.t1 is derived from g5527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35463263	35465043	.	+	.	Phchi.S1G551100
Phchi.S1	AUGUSTUS	transcript	35463263	35465043	.	+	.	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	start_codon	35463263	35463265	.	+	0	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	CDS	35463263	35463732	0.99	+	0	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	exon	35463263	35463732	.	+	.	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	intron	35463733	35463806	.	+	.	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	CDS	35463807	35465043	0.97	+	1	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	exon	35463807	35465043	.	+	.	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
Phchi.S1	AUGUSTUS	stop_codon	35465044	35465046	.	+	0	transcript_id "Phchi.S1G551100.t1"; gene_id "Phchi.S1G551100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8627.t1 is derived from g5802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37147814	37148900	.	+	.	Phchi.S1G578600
Phchi.S1	AUGUSTUS	transcript	37147814	37148900	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	start_codon	37147814	37147816	.	+	0	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	CDS	37147814	37147957	1	+	0	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	exon	37147814	37147957	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	intron	37147958	37148047	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	CDS	37148048	37148231	1	+	0	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	exon	37148048	37148231	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	intron	37148232	37148318	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	CDS	37148319	37148452	1	+	2	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	exon	37148319	37148452	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	intron	37148453	37148535	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	CDS	37148536	37148718	1	+	0	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	exon	37148536	37148718	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	intron	37148719	37148804	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	CDS	37148805	37148900	0.49	+	0	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	exon	37148805	37148900	.	+	.	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
Phchi.S1	AUGUSTUS	stop_codon	37148901	37148903	.	+	0	transcript_id "Phchi.S1G578600.t1"; gene_id "Phchi.S1G578600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11725.t1 is derived from g15777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7849507	7855763	.	-	.	Phchi.S4G130700
Phchi.S4	AUGUSTUS	transcript	7849507	7855763	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	stop_codon	7849504	7849506	.	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7849507	7849670	0.52	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7849507	7849670	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7849671	7849801	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7849802	7849925	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7849802	7849925	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7849926	7850040	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850041	7850210	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850041	7850210	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850211	7850296	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850297	7850445	1	-	1	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850297	7850445	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850446	7850526	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850527	7850666	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850527	7850666	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850667	7850770	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850771	7850950	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850771	7850950	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850951	7851069	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851070	7851173	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851070	7851173	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7851174	7851333	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851334	7851465	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851334	7851465	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7851466	7851603	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851604	7851802	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851604	7851802	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7851803	7851908	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851909	7852027	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851909	7852027	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852028	7852148	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852149	7852190	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852149	7852190	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852191	7852356	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852357	7852516	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852357	7852516	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852517	7852623	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852624	7852804	0.98	-	1	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852624	7852804	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852805	7852921	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852922	7853051	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852922	7853051	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7853052	7853208	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7853209	7853354	1	-	1	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7853209	7853354	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7853355	7853676	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7853677	7853850	1	-	1	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7853677	7853850	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7853851	7853962	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7853963	7854147	0.99	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7853963	7854147	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7854148	7854305	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7854306	7854471	1	-	1	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7854306	7854471	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7854472	7854705	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7854706	7854864	1	-	1	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7854706	7854864	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7854865	7854984	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7854985	7855072	1	-	2	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7854985	7855072	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7855073	7855164	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7855165	7855300	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7855165	7855300	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7855301	7855673	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7855674	7855763	1	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7855674	7855763	.	-	.	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	start_codon	7855761	7855763	.	-	0	transcript_id "Phchi.S4G130700.t1"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	transcript	7849507	7855763	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	stop_codon	7849504	7849506	.	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7849507	7849670	0.56	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7849507	7849670	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7849671	7849801	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7849802	7849925	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7849802	7849925	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7849926	7850040	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850041	7850198	0.97	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850041	7850198	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850199	7850296	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850297	7850445	0.99	-	1	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850297	7850445	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850446	7850526	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850527	7850666	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850527	7850666	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850667	7850770	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7850771	7850950	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7850771	7850950	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7850951	7851069	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851070	7851173	1	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851070	7851173	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7851174	7851333	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851334	7851465	1	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851334	7851465	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7851466	7851603	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851604	7851802	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851604	7851802	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7851803	7851908	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7851909	7852027	0.99	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7851909	7852027	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852028	7852148	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852149	7852190	1	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852149	7852190	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852191	7852356	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852357	7852516	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852357	7852516	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852517	7852623	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852624	7852804	0.93	-	1	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852624	7852804	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7852805	7852921	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7852922	7853051	1	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7852922	7853051	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7853052	7853208	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7853209	7853354	1	-	1	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7853209	7853354	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7853355	7853676	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7853677	7853850	1	-	1	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7853677	7853850	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7853851	7853962	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7853963	7854147	0.99	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7853963	7854147	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7854148	7854305	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7854306	7854471	1	-	1	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7854306	7854471	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7854472	7854705	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7854706	7854864	1	-	1	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7854706	7854864	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7854865	7854984	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7854985	7855072	1	-	2	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7854985	7855072	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7855073	7855164	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7855165	7855300	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7855165	7855300	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	intron	7855301	7855673	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	CDS	7855674	7855763	1	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	exon	7855674	7855763	.	-	.	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
Phchi.S4	AUGUSTUS	start_codon	7855761	7855763	.	-	0	transcript_id "Phchi.S4G130700.t2"; gene_id "Phchi.S4G130700"
# This transcript jg3382.t2 is derived from g551.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3383.t1 is derived from g552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3267885	3268428	.	-	.	Phchi.S1G054200
Phchi.S1	AUGUSTUS	transcript	3267885	3268428	.	-	.	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	stop_codon	3267882	3267884	.	-	0	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	CDS	3267885	3268228	0.79	-	2	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	exon	3267885	3268228	.	-	.	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	intron	3268229	3268364	.	-	.	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	CDS	3268365	3268428	0.89	-	0	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	exon	3268365	3268428	.	-	.	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
Phchi.S1	AUGUSTUS	start_codon	3268426	3268428	.	-	0	transcript_id "Phchi.S1G054200.t1"; gene_id "Phchi.S1G054200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14429.t1 is derived from g12897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12764596	12765221	.	-	.	Phchi.S3G174800
Phchi.S3	AUGUSTUS	transcript	12764596	12765221	.	-	.	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	stop_codon	12764593	12764595	.	-	0	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	CDS	12764596	12764700	0.72	-	0	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	exon	12764596	12764700	.	-	.	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	intron	12764701	12764870	.	-	.	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	CDS	12764871	12765221	0.67	-	0	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	exon	12764871	12765221	.	-	.	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
Phchi.S3	AUGUSTUS	start_codon	12765219	12765221	.	-	0	transcript_id "Phchi.S3G174800.t1"; gene_id "Phchi.S3G174800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14218.t1 is derived from g12685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11559037	11561531	.	+	.	Phchi.S3G153700
Phchi.S3	AUGUSTUS	transcript	11559037	11561531	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	start_codon	11559037	11559039	.	+	0	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	CDS	11559037	11559162	0.67	+	0	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	exon	11559037	11559162	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	intron	11559163	11559251	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	CDS	11559252	11559461	0.8	+	0	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	exon	11559252	11559461	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	intron	11559462	11559566	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	CDS	11559567	11561303	0.85	+	0	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	exon	11559567	11561303	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	intron	11561304	11561384	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	CDS	11561385	11561531	1	+	0	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	exon	11561385	11561531	.	+	.	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
Phchi.S3	AUGUSTUS	stop_codon	11561532	11561534	.	+	0	transcript_id "Phchi.S3G153700.t1"; gene_id "Phchi.S3G153700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13972.t1 is derived from g12439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10001030	10002848	.	+	.	Phchi.S3G129100
Phchi.S3	AUGUSTUS	transcript	10001030	10002848	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	start_codon	10001030	10001032	.	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10001030	10001146	0.67	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10001030	10001146	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10001147	10001328	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10001329	10001380	0.55	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10001329	10001380	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10001381	10001504	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10001505	10001594	1	+	2	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10001505	10001594	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10001595	10001715	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10001716	10001900	1	+	2	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10001716	10001900	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10001901	10002007	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10002008	10002130	0.91	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10002008	10002130	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10002131	10002224	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10002225	10002293	0.99	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10002225	10002293	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10002294	10002367	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10002368	10002376	0.99	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10002368	10002376	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	intron	10002377	10002527	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	CDS	10002528	10002848	0.97	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	exon	10002528	10002848	.	+	.	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
Phchi.S3	AUGUSTUS	stop_codon	10002849	10002851	.	+	0	transcript_id "Phchi.S3G129100.t1"; gene_id "Phchi.S3G129100"
# This transcript jg9647.t2 is derived from g6823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9648.t1 is derived from g6824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43050708	43052039	.	-	.	Phchi.S1G680700
Phchi.S1	AUGUSTUS	transcript	43050708	43052039	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	stop_codon	43050705	43050707	.	-	0	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	CDS	43050708	43050801	0.99	-	1	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	exon	43050708	43050801	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	intron	43050802	43050905	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	CDS	43050906	43051048	1	-	0	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	exon	43050906	43051048	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	intron	43051049	43051162	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	CDS	43051163	43051244	1	-	1	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	exon	43051163	43051244	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	intron	43051245	43051392	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	CDS	43051393	43051544	1	-	0	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	exon	43051393	43051544	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	intron	43051545	43051745	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	CDS	43051746	43051922	1	-	0	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	exon	43051746	43051922	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	intron	43051923	43052006	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	CDS	43052007	43052039	0.98	-	0	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	exon	43052007	43052039	.	-	.	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
Phchi.S1	AUGUSTUS	start_codon	43052037	43052039	.	-	0	transcript_id "Phchi.S1G680700.t1"; gene_id "Phchi.S1G680700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6744.t1 is derived from g3916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24820008	24822220	.	+	.	Phchi.S1G390300
Phchi.S1	AUGUSTUS	transcript	24820008	24822220	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	start_codon	24820008	24820010	.	+	0	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24820008	24820245	0.78	+	0	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24820008	24820245	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24820246	24820324	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24820325	24820432	0.99	+	2	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24820325	24820432	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24820433	24820553	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24820554	24820616	0.89	+	2	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24820554	24820616	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24820617	24820707	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24820708	24820967	0.52	+	2	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24820708	24820967	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24820968	24821074	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24821075	24821377	0.99	+	0	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24821075	24821377	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24821378	24821479	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24821480	24821610	1	+	0	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24821480	24821610	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24821611	24821695	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24821696	24821797	1	+	1	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24821696	24821797	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24821798	24821880	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24821881	24821986	1	+	1	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24821881	24821986	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	intron	24821987	24822073	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	CDS	24822074	24822220	0.7	+	0	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	exon	24822074	24822220	.	+	.	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
Phchi.S1	AUGUSTUS	stop_codon	24822221	24822223	.	+	0	transcript_id "Phchi.S1G390300.t1"; gene_id "Phchi.S1G390300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14886.t1 is derived from g13354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15278698	15280064	.	+	.	Phchi.S3G220500
Phchi.S3	AUGUSTUS	transcript	15278698	15280064	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	start_codon	15278698	15278700	.	+	0	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	CDS	15278698	15278817	0.77	+	0	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	exon	15278698	15278817	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	intron	15278818	15278900	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	CDS	15278901	15279024	0.85	+	0	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	exon	15278901	15279024	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	intron	15279025	15279116	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	CDS	15279117	15279418	0.85	+	2	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	exon	15279117	15279418	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	intron	15279419	15279524	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	CDS	15279525	15279689	0.81	+	0	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	exon	15279525	15279689	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	intron	15279690	15279791	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	CDS	15279792	15280064	0.8	+	0	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	exon	15279792	15280064	.	+	.	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
Phchi.S3	AUGUSTUS	stop_codon	15280065	15280067	.	+	0	transcript_id "Phchi.S3G220500.t1"; gene_id "Phchi.S3G220500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8916.t1 is derived from g6091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38659924	38661766	.	+	.	Phchi.S1G607500
Phchi.S1	AUGUSTUS	transcript	38659924	38661766	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	start_codon	38659924	38659926	.	+	0	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	CDS	38659924	38659962	0.66	+	0	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	exon	38659924	38659962	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	intron	38659963	38660152	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	CDS	38660153	38660214	0.78	+	0	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	exon	38660153	38660214	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	intron	38660215	38660379	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	CDS	38660380	38660461	0.78	+	1	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	exon	38660380	38660461	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	intron	38660462	38660612	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	CDS	38660613	38660789	0.78	+	0	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	exon	38660613	38660789	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	intron	38660790	38661468	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	CDS	38661469	38661569	0.9	+	0	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	exon	38661469	38661569	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	intron	38661570	38661681	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	CDS	38661682	38661766	0.89	+	1	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	exon	38661682	38661766	.	+	.	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
Phchi.S1	AUGUSTUS	stop_codon	38661767	38661769	.	+	0	transcript_id "Phchi.S1G607500.t1"; gene_id "Phchi.S1G607500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13434.t1 is derived from g11901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6684236	6685577	.	-	.	Phchi.S3G075300
Phchi.S3	AUGUSTUS	transcript	6684236	6685577	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	stop_codon	6684233	6684235	.	-	0	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684236	6684400	0.94	-	0	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684236	6684400	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6684401	6684476	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684477	6684701	1	-	0	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684477	6684701	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6684702	6684867	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684868	6685043	1	-	2	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684868	6685043	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6685044	6685123	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6685124	6685283	1	-	0	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6685124	6685283	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6685284	6685361	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6685362	6685577	0.99	-	0	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6685362	6685577	.	-	.	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	start_codon	6685575	6685577	.	-	0	transcript_id "Phchi.S3G075300.t1"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	transcript	6684236	6685577	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	stop_codon	6684233	6684235	.	-	0	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684236	6684400	0.9	-	0	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684236	6684400	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6684401	6684476	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684477	6684570	0.8	-	1	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684477	6684570	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6684571	6684668	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684669	6684701	0.8	-	1	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684669	6684701	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6684702	6684895	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6684896	6685043	0.8	-	2	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6684896	6685043	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6685044	6685123	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6685124	6685283	1	-	0	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6685124	6685283	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	intron	6685284	6685361	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	CDS	6685362	6685577	0.99	-	0	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	exon	6685362	6685577	.	-	.	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
Phchi.S3	AUGUSTUS	start_codon	6685575	6685577	.	-	0	transcript_id "Phchi.S3G075300.t2"; gene_id "Phchi.S3G075300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11609.t1 is derived from g15660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7314151	7315215	.	+	.	Phchi.S4G119100
Phchi.S4	AUGUSTUS	transcript	7314151	7315215	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	start_codon	7314151	7314153	.	+	0	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	CDS	7314151	7314492	1	+	0	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	exon	7314151	7314492	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	intron	7314493	7314586	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	CDS	7314587	7314777	0.43	+	0	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	exon	7314587	7314777	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	intron	7314778	7314997	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	CDS	7314998	7315049	0.98	+	1	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	exon	7314998	7315049	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	intron	7315050	7315155	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	CDS	7315156	7315215	0.98	+	0	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	exon	7315156	7315215	.	+	.	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
Phchi.S4	AUGUSTUS	stop_codon	7315216	7315218	.	+	0	transcript_id "Phchi.S4G119100.t1"; gene_id "Phchi.S4G119100"
# This transcript jg7673.t2 is derived from g4847.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7674.t1 is derived from g4848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30570146	30571882	.	+	.	Phchi.S1G483300
Phchi.S1	AUGUSTUS	transcript	30570146	30571882	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	start_codon	30570146	30570148	.	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30570146	30570190	1	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30570146	30570190	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30570191	30570271	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30570272	30570383	1	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30570272	30570383	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30570384	30570483	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30570484	30570542	1	+	2	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30570484	30570542	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30570543	30570639	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30570640	30570694	1	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30570640	30570694	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30570695	30570826	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30570827	30570921	1	+	2	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30570827	30570921	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30570922	30571120	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30571121	30571266	1	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30571121	30571266	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30571267	30571399	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30571400	30571542	1	+	1	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30571400	30571542	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30571543	30571635	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30571636	30571721	1	+	2	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30571636	30571721	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	intron	30571722	30571807	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	CDS	30571808	30571882	0.99	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	exon	30571808	30571882	.	+	.	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
Phchi.S1	AUGUSTUS	stop_codon	30571883	30571885	.	+	0	transcript_id "Phchi.S1G483300.t1"; gene_id "Phchi.S1G483300"
# This transcript jg13497.t2 is derived from g11964.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13498.t1 is derived from g11965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7169205	7169942	.	-	.	Phchi.S3G081700
Phchi.S3	AUGUSTUS	transcript	7169205	7169942	.	-	.	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	stop_codon	7169202	7169204	.	-	0	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	CDS	7169205	7169769	0.99	-	1	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	exon	7169205	7169769	.	-	.	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	intron	7169770	7169907	.	-	.	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	CDS	7169908	7169942	1	-	0	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	exon	7169908	7169942	.	-	.	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
Phchi.S3	AUGUSTUS	start_codon	7169940	7169942	.	-	0	transcript_id "Phchi.S3G081700.t1"; gene_id "Phchi.S3G081700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5085.t1 is derived from g2255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14603960	14606129	.	+	.	Phchi.S1G224400
Phchi.S1	AUGUSTUS	transcript	14603960	14606129	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	start_codon	14603960	14603962	.	+	0	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14603960	14604050	0.97	+	0	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14603960	14604050	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604051	14604211	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604212	14604294	1	+	2	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604212	14604294	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604295	14604381	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604382	14604511	1	+	0	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604382	14604511	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604512	14604648	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604649	14604700	0.97	+	2	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604649	14604700	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604701	14604782	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604783	14605952	0.27	+	1	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604783	14605952	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14605953	14606074	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14606075	14606129	0.37	+	1	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14606075	14606129	.	+	.	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	stop_codon	14606130	14606132	.	+	0	transcript_id "Phchi.S1G224400.t1"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	transcript	14604021	14606129	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	start_codon	14604021	14604023	.	+	0	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604021	14604102	0.42	+	0	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604021	14604102	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604103	14604211	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604212	14604294	0.84	+	2	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604212	14604294	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604295	14604381	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604382	14604511	1	+	0	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604382	14604511	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604512	14604648	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604649	14604700	0.95	+	2	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604649	14604700	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14604701	14604782	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14604783	14605952	0.29	+	1	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14604783	14605952	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	intron	14605953	14606074	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	CDS	14606075	14606129	0.45	+	1	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	exon	14606075	14606129	.	+	.	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
Phchi.S1	AUGUSTUS	stop_codon	14606130	14606132	.	+	0	transcript_id "Phchi.S1G224400.t2"; gene_id "Phchi.S1G224400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4577.t1 is derived from g1747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11181798	11184118	.	+	.	Phchi.S1G173600
Phchi.S1	AUGUSTUS	transcript	11181798	11184118	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	start_codon	11181798	11181800	.	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11181798	11182277	1	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11181798	11182277	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11182278	11182363	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11182364	11182494	0.99	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11182364	11182494	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11182495	11182593	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11182594	11182653	0.5	+	1	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11182594	11182653	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11182654	11182829	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11182830	11183004	1	+	1	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11182830	11183004	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11183005	11183115	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11183116	11183284	0.92	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11183116	11183284	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11183285	11183423	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11183424	11183554	0.98	+	2	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11183424	11183554	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11183555	11183638	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11183639	11183791	0.92	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11183639	11183791	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	intron	11183792	11183875	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	CDS	11183876	11184118	1	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	exon	11183876	11184118	.	+	.	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
Phchi.S1	AUGUSTUS	stop_codon	11184119	11184121	.	+	0	transcript_id "Phchi.S1G173600.t1"; gene_id "Phchi.S1G173600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5720.t1 is derived from g2890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18508910	18511281	.	+	.	Phchi.S1G287900
Phchi.S1	AUGUSTUS	transcript	18508910	18511281	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	start_codon	18508910	18508912	.	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	CDS	18508910	18509422	0.88	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	exon	18508910	18509422	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	intron	18509423	18509528	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	CDS	18509529	18509750	1	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	exon	18509529	18509750	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	intron	18509751	18509917	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	CDS	18509918	18510243	1	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	exon	18509918	18510243	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	intron	18510244	18510369	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	CDS	18510370	18510499	1	+	1	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	exon	18510370	18510499	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	intron	18510500	18510580	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	CDS	18510581	18510877	1	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	exon	18510581	18510877	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	intron	18510878	18511017	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	CDS	18511018	18511281	1	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	exon	18511018	18511281	.	+	.	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
Phchi.S1	AUGUSTUS	stop_codon	18511282	18511284	.	+	0	transcript_id "Phchi.S1G287900.t1"; gene_id "Phchi.S1G287900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4632.t1 is derived from g1802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11483004	11484818	.	+	.	Phchi.S1G179100
Phchi.S1	AUGUSTUS	transcript	11483004	11484818	.	+	.	transcript_id "Phchi.S1G179100.t1"; gene_id "Phchi.S1G179100"
Phchi.S1	AUGUSTUS	start_codon	11483004	11483006	.	+	0	transcript_id "Phchi.S1G179100.t1"; gene_id "Phchi.S1G179100"
Phchi.S1	AUGUSTUS	CDS	11483004	11484818	1	+	0	transcript_id "Phchi.S1G179100.t1"; gene_id "Phchi.S1G179100"
Phchi.S1	AUGUSTUS	exon	11483004	11484818	.	+	.	transcript_id "Phchi.S1G179100.t1"; gene_id "Phchi.S1G179100"
Phchi.S1	AUGUSTUS	stop_codon	11484819	11484821	.	+	0	transcript_id "Phchi.S1G179100.t1"; gene_id "Phchi.S1G179100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg330.t1 is derived from g10112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2286768	2288141	.	+	.	Phchi.S6G028900
Phchi.S6	AUGUSTUS	transcript	2286768	2288141	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	start_codon	2286768	2286770	.	+	0	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2286768	2286779	0.99	+	0	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2286768	2286779	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2286780	2286918	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2286919	2287027	0.86	+	0	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2286919	2287027	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2287028	2287134	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2287135	2287229	1	+	2	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2287135	2287229	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2287230	2287330	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2287331	2287445	1	+	0	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2287331	2287445	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2287446	2287527	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2287528	2287652	1	+	2	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2287528	2287652	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2287653	2287741	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2287742	2287821	1	+	0	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2287742	2287821	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2287822	2287927	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2287928	2287998	0.93	+	1	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2287928	2287998	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	intron	2287999	2288085	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	CDS	2288086	2288141	0.93	+	2	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	exon	2288086	2288141	.	+	.	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
Phchi.S6	AUGUSTUS	stop_codon	2288142	2288144	.	+	0	transcript_id "Phchi.S6G028900.t1"; gene_id "Phchi.S6G028900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5852.t1 is derived from g3022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19342954	19344565	.	-	.	Phchi.S1G301100
Phchi.S1	AUGUSTUS	transcript	19342954	19344565	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	stop_codon	19342951	19342953	.	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19342954	19342989	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19342954	19342989	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	intron	19342990	19343148	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19343149	19343322	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19343149	19343322	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	intron	19343323	19343448	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19343449	19343544	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19343449	19343544	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	intron	19343545	19343628	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19343629	19343709	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19343629	19343709	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	intron	19343710	19343836	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19343837	19343911	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19343837	19343911	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	intron	19343912	19344164	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19344165	19344239	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19344165	19344239	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	intron	19344240	19344415	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	CDS	19344416	19344565	1	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	exon	19344416	19344565	.	-	.	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
Phchi.S1	AUGUSTUS	start_codon	19344563	19344565	.	-	0	transcript_id "Phchi.S1G301100.t1"; gene_id "Phchi.S1G301100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5319.t1 is derived from g2489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16265361	16266719	.	+	.	Phchi.S1G247800
Phchi.S1	AUGUSTUS	transcript	16265361	16266719	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	start_codon	16265361	16265363	.	+	0	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16265361	16265388	1	+	0	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16265361	16265388	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16265389	16265476	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16265477	16265642	1	+	2	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16265477	16265642	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16265643	16265740	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16265741	16265831	1	+	1	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16265741	16265831	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16265832	16265917	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16265918	16265976	1	+	0	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16265918	16265976	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16265977	16266067	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16266068	16266128	1	+	1	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16266068	16266128	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16266129	16266236	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16266237	16266327	1	+	0	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16266237	16266327	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16266328	16266433	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16266434	16266510	1	+	2	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16266434	16266510	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	intron	16266511	16266599	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	CDS	16266600	16266719	0.99	+	0	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	exon	16266600	16266719	.	+	.	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
Phchi.S1	AUGUSTUS	stop_codon	16266720	16266722	.	+	0	transcript_id "Phchi.S1G247800.t1"; gene_id "Phchi.S1G247800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11384.t1 is derived from g15434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6044857	6045240	.	-	.	Phchi.S4G096600
Phchi.S4	AUGUSTUS	transcript	6044857	6045240	.	-	.	transcript_id "Phchi.S4G096600.t1"; gene_id "Phchi.S4G096600"
Phchi.S4	AUGUSTUS	stop_codon	6044854	6044856	.	-	0	transcript_id "Phchi.S4G096600.t1"; gene_id "Phchi.S4G096600"
Phchi.S4	AUGUSTUS	CDS	6044857	6045240	0.96	-	0	transcript_id "Phchi.S4G096600.t1"; gene_id "Phchi.S4G096600"
Phchi.S4	AUGUSTUS	exon	6044857	6045240	.	-	.	transcript_id "Phchi.S4G096600.t1"; gene_id "Phchi.S4G096600"
Phchi.S4	AUGUSTUS	start_codon	6045238	6045240	.	-	0	transcript_id "Phchi.S4G096600.t1"; gene_id "Phchi.S4G096600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7988.t1 is derived from g5163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32266756	32268296	.	+	.	Phchi.S1G514700
Phchi.S1	AUGUSTUS	transcript	32266756	32268296	.	+	.	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	start_codon	32266756	32266758	.	+	0	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	CDS	32266756	32267485	0.91	+	0	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	exon	32266756	32267485	.	+	.	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	intron	32267486	32267694	.	+	.	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	CDS	32267695	32268296	0.9	+	2	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	exon	32267695	32268296	.	+	.	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	stop_codon	32268297	32268299	.	+	0	transcript_id "Phchi.S1G514700.t1"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	transcript	32267517	32268296	.	+	.	transcript_id "Phchi.S1G514700.t2"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	start_codon	32267517	32267519	.	+	0	transcript_id "Phchi.S1G514700.t2"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	CDS	32267517	32268296	0.72	+	0	transcript_id "Phchi.S1G514700.t2"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	exon	32267517	32268296	.	+	.	transcript_id "Phchi.S1G514700.t2"; gene_id "Phchi.S1G514700"
Phchi.S1	AUGUSTUS	stop_codon	32268297	32268299	.	+	0	transcript_id "Phchi.S1G514700.t2"; gene_id "Phchi.S1G514700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5341.t1 is derived from g2511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16371018	16373238	.	-	.	Phchi.S1G250000
Phchi.S1	AUGUSTUS	transcript	16371018	16373238	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	stop_codon	16371015	16371017	.	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16371018	16371350	1	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16371018	16371350	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16371351	16371424	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16371425	16371493	1	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16371425	16371493	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16371494	16371575	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16371576	16371647	1	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16371576	16371647	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16371648	16371730	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16371731	16371830	1	-	1	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16371731	16371830	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16371831	16372042	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16372043	16372119	1	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16372043	16372119	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16372120	16372246	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16372247	16372346	0.99	-	1	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16372247	16372346	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16372347	16372442	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16372443	16372573	0.52	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16372443	16372573	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16372574	16372664	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16372665	16372725	1	-	1	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16372665	16372725	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	intron	16372726	16372885	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	CDS	16372886	16373238	0.95	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	exon	16372886	16373238	.	-	.	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
Phchi.S1	AUGUSTUS	start_codon	16373236	16373238	.	-	0	transcript_id "Phchi.S1G250000.t1"; gene_id "Phchi.S1G250000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14236.t1 is derived from g12703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11685340	11687137	.	-	.	Phchi.S3G155500
Phchi.S3	AUGUSTUS	transcript	11685340	11687137	.	-	.	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	stop_codon	11685337	11685339	.	-	0	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	CDS	11685340	11685786	1	-	0	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	exon	11685340	11685786	.	-	.	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	intron	11685787	11685880	.	-	.	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	CDS	11685881	11687137	1	-	0	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	exon	11685881	11687137	.	-	.	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
Phchi.S3	AUGUSTUS	start_codon	11687135	11687137	.	-	0	transcript_id "Phchi.S3G155500.t1"; gene_id "Phchi.S3G155500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2239.t1 is derived from g9159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5604993	5605653	.	+	.	Phchi.S5G084800
Phchi.S5	AUGUSTUS	transcript	5604993	5605653	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	start_codon	5604993	5604995	.	+	0	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	CDS	5604993	5605127	0.61	+	0	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	exon	5604993	5605127	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	intron	5605128	5605243	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	CDS	5605244	5605295	1	+	0	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	exon	5605244	5605295	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	intron	5605296	5605394	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	CDS	5605395	5605461	0.92	+	2	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	exon	5605395	5605461	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	intron	5605462	5605565	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	CDS	5605566	5605653	0.81	+	1	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	exon	5605566	5605653	.	+	.	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
Phchi.S5	AUGUSTUS	stop_codon	5605654	5605656	.	+	0	transcript_id "Phchi.S5G084800.t1"; gene_id "Phchi.S5G084800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3519.t1 is derived from g688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4179880	4180753	.	+	.	Phchi.S1G067800
Phchi.S1	AUGUSTUS	transcript	4179880	4180753	.	+	.	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	start_codon	4179880	4179882	.	+	0	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	CDS	4179880	4180009	0.88	+	0	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	exon	4179880	4180009	.	+	.	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	intron	4180010	4180304	.	+	.	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	CDS	4180305	4180753	0.69	+	2	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	exon	4180305	4180753	.	+	.	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
Phchi.S1	AUGUSTUS	stop_codon	4180754	4180756	.	+	0	transcript_id "Phchi.S1G067800.t1"; gene_id "Phchi.S1G067800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7004.t1 is derived from g4176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26361618	26366296	.	+	.	Phchi.S1G416300
Phchi.S1	AUGUSTUS	transcript	26361618	26366296	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	start_codon	26361618	26361620	.	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26361618	26361791	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26361618	26361791	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26361792	26361953	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26361954	26362265	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26361954	26362265	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26362266	26362377	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26362378	26362650	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26362378	26362650	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26362651	26362799	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26362800	26362847	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26362800	26362847	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26362848	26362945	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26362946	26363011	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26362946	26363011	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26363012	26363097	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26363098	26363201	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26363098	26363201	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26363202	26363358	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26363359	26363452	1	+	1	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26363359	26363452	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26363453	26363550	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26363551	26363607	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26363551	26363607	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26363608	26363734	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26363735	26364173	0.93	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26363735	26364173	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26364174	26364269	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26364270	26364424	1	+	2	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26364270	26364424	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26364425	26364521	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26364522	26364587	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26364522	26364587	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26364588	26364725	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26364726	26364794	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26364726	26364794	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26364795	26364894	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26364895	26364990	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26364895	26364990	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26364991	26365073	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26365074	26365142	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26365074	26365142	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26365143	26365243	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26365244	26365290	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26365244	26365290	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26365291	26365391	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26365392	26365455	1	+	1	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26365392	26365455	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26365456	26365545	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26365546	26365623	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26365546	26365623	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26365624	26365821	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26365822	26365884	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26365822	26365884	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26365885	26366012	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26366013	26366096	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26366013	26366096	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	intron	26366097	26366176	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	CDS	26366177	26366296	1	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	exon	26366177	26366296	.	+	.	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
Phchi.S1	AUGUSTUS	stop_codon	26366297	26366299	.	+	0	transcript_id "Phchi.S1G416300.t1"; gene_id "Phchi.S1G416300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11316.t1 is derived from g15366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5332041	5332967	.	-	.	Phchi.S4G089800
Phchi.S4	AUGUSTUS	transcript	5332041	5332967	.	-	.	transcript_id "Phchi.S4G089800.t1"; gene_id "Phchi.S4G089800"
Phchi.S4	AUGUSTUS	stop_codon	5332038	5332040	.	-	0	transcript_id "Phchi.S4G089800.t1"; gene_id "Phchi.S4G089800"
Phchi.S4	AUGUSTUS	CDS	5332041	5332967	0.33	-	0	transcript_id "Phchi.S4G089800.t1"; gene_id "Phchi.S4G089800"
Phchi.S4	AUGUSTUS	exon	5332041	5332967	.	-	.	transcript_id "Phchi.S4G089800.t1"; gene_id "Phchi.S4G089800"
Phchi.S4	AUGUSTUS	start_codon	5332965	5332967	.	-	0	transcript_id "Phchi.S4G089800.t1"; gene_id "Phchi.S4G089800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15185.t1 is derived from g13653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17464861	17466000	.	-	.	Phchi.S3G250400
Phchi.S3	AUGUSTUS	transcript	17464861	17466000	.	-	.	transcript_id "Phchi.S3G250400.t1"; gene_id "Phchi.S3G250400"
Phchi.S3	AUGUSTUS	stop_codon	17464858	17464860	.	-	0	transcript_id "Phchi.S3G250400.t1"; gene_id "Phchi.S3G250400"
Phchi.S3	AUGUSTUS	CDS	17464861	17466000	0.93	-	0	transcript_id "Phchi.S3G250400.t1"; gene_id "Phchi.S3G250400"
Phchi.S3	AUGUSTUS	exon	17464861	17466000	.	-	.	transcript_id "Phchi.S3G250400.t1"; gene_id "Phchi.S3G250400"
Phchi.S3	AUGUSTUS	start_codon	17465998	17466000	.	-	0	transcript_id "Phchi.S3G250400.t1"; gene_id "Phchi.S3G250400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4235.t1 is derived from g1404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9043321	9043947	.	-	.	Phchi.S1G139400
Phchi.S1	AUGUSTUS	transcript	9043321	9043947	.	-	.	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	stop_codon	9043318	9043320	.	-	0	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	CDS	9043321	9043390	1	-	1	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	exon	9043321	9043390	.	-	.	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	intron	9043391	9043543	.	-	.	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	CDS	9043544	9043661	1	-	2	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	exon	9043544	9043661	.	-	.	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	intron	9043662	9043760	.	-	.	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	CDS	9043761	9043947	0.99	-	0	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	exon	9043761	9043947	.	-	.	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
Phchi.S1	AUGUSTUS	start_codon	9043945	9043947	.	-	0	transcript_id "Phchi.S1G139400.t1"; gene_id "Phchi.S1G139400"
# This transcript jg13015.t2 is derived from g11480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13016.t1 is derived from g11481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3639537	3640303	.	+	.	Phchi.S3G033500
Phchi.S3	AUGUSTUS	transcript	3639537	3640303	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	start_codon	3639537	3639539	.	+	0	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	CDS	3639537	3639539	1	+	0	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	exon	3639537	3639539	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	intron	3639540	3639629	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	CDS	3639630	3639722	1	+	0	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	exon	3639630	3639722	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	intron	3639723	3639825	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	CDS	3639826	3639910	1	+	0	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	exon	3639826	3639910	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	intron	3639911	3640011	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	CDS	3640012	3640142	1	+	2	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	exon	3640012	3640142	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	intron	3640143	3640234	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	CDS	3640235	3640303	1	+	0	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	exon	3640235	3640303	.	+	.	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
Phchi.S3	AUGUSTUS	stop_codon	3640304	3640306	.	+	0	transcript_id "Phchi.S3G033500.t1"; gene_id "Phchi.S3G033500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg540.t1 is derived from g10322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3980528	3981697	.	-	.	Phchi.S6G049900
Phchi.S6	AUGUSTUS	transcript	3980528	3981697	.	-	.	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	stop_codon	3980525	3980527	.	-	0	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	CDS	3980528	3980961	0.69	-	2	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	exon	3980528	3980961	.	-	.	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	intron	3980962	3981081	.	-	.	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	CDS	3981082	3981499	0.99	-	0	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	exon	3981082	3981499	.	-	.	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	intron	3981500	3981586	.	-	.	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	CDS	3981587	3981697	0.7	-	0	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	exon	3981587	3981697	.	-	.	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
Phchi.S6	AUGUSTUS	start_codon	3981695	3981697	.	-	0	transcript_id "Phchi.S6G049900.t1"; gene_id "Phchi.S6G049900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15917.t1 is derived from g14387.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22200016	22202415	.	+	.	Phchi.S3G323600
Phchi.S3	AUGUSTUS	transcript	22200016	22202415	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	start_codon	22200016	22200018	.	+	0	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200016	22200192	0.62	+	0	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200016	22200192	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22200193	22200399	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200400	22200632	0.99	+	0	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200400	22200632	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22200633	22200738	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200739	22200793	0.99	+	1	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200739	22200793	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22200794	22200881	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200882	22201137	1	+	0	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200882	22201137	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22201138	22201259	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22201260	22202233	0.99	+	2	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22201260	22202233	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22202234	22202325	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22202326	22202415	1	+	0	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22202326	22202415	.	+	.	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	stop_codon	22202416	22202418	.	+	0	transcript_id "Phchi.S3G323600.t1"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	transcript	22200016	22202415	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	start_codon	22200016	22200018	.	+	0	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200016	22200192	0.66	+	0	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200016	22200192	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22200193	22200399	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200400	22200666	1	+	0	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200400	22200666	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22200667	22200881	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22200882	22201137	0.96	+	0	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22200882	22201137	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22201138	22201259	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22201260	22202233	0.99	+	2	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22201260	22202233	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	intron	22202234	22202325	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	CDS	22202326	22202415	1	+	0	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	exon	22202326	22202415	.	+	.	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
Phchi.S3	AUGUSTUS	stop_codon	22202416	22202418	.	+	0	transcript_id "Phchi.S3G323600.t2"; gene_id "Phchi.S3G323600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4930.t1 is derived from g2100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13618580	13618873	.	+	.	Phchi.S1G208900
Phchi.S1	AUGUSTUS	transcript	13618580	13618873	.	+	.	transcript_id "Phchi.S1G208900.t1"; gene_id "Phchi.S1G208900"
Phchi.S1	AUGUSTUS	start_codon	13618580	13618582	.	+	0	transcript_id "Phchi.S1G208900.t1"; gene_id "Phchi.S1G208900"
Phchi.S1	AUGUSTUS	CDS	13618580	13618873	0.47	+	0	transcript_id "Phchi.S1G208900.t1"; gene_id "Phchi.S1G208900"
Phchi.S1	AUGUSTUS	exon	13618580	13618873	.	+	.	transcript_id "Phchi.S1G208900.t1"; gene_id "Phchi.S1G208900"
Phchi.S1	AUGUSTUS	stop_codon	13618874	13618876	.	+	0	transcript_id "Phchi.S1G208900.t1"; gene_id "Phchi.S1G208900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3620.t1 is derived from g789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4793197	4793832	.	+	.	Phchi.S1G077900
Phchi.S1	AUGUSTUS	transcript	4793197	4793832	.	+	.	transcript_id "Phchi.S1G077900.t1"; gene_id "Phchi.S1G077900"
Phchi.S1	AUGUSTUS	start_codon	4793197	4793199	.	+	0	transcript_id "Phchi.S1G077900.t1"; gene_id "Phchi.S1G077900"
Phchi.S1	AUGUSTUS	CDS	4793197	4793832	0.46	+	0	transcript_id "Phchi.S1G077900.t1"; gene_id "Phchi.S1G077900"
Phchi.S1	AUGUSTUS	exon	4793197	4793832	.	+	.	transcript_id "Phchi.S1G077900.t1"; gene_id "Phchi.S1G077900"
Phchi.S1	AUGUSTUS	stop_codon	4793833	4793835	.	+	0	transcript_id "Phchi.S1G077900.t1"; gene_id "Phchi.S1G077900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg617.t1 is derived from g10399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4436728	4437492	.	-	.	Phchi.S6G057600
Phchi.S6	AUGUSTUS	transcript	4436728	4437492	.	-	.	transcript_id "Phchi.S6G057600.t1"; gene_id "Phchi.S6G057600"
Phchi.S6	AUGUSTUS	stop_codon	4436725	4436727	.	-	0	transcript_id "Phchi.S6G057600.t1"; gene_id "Phchi.S6G057600"
Phchi.S6	AUGUSTUS	CDS	4436728	4437492	0.94	-	0	transcript_id "Phchi.S6G057600.t1"; gene_id "Phchi.S6G057600"
Phchi.S6	AUGUSTUS	exon	4436728	4437492	.	-	.	transcript_id "Phchi.S6G057600.t1"; gene_id "Phchi.S6G057600"
Phchi.S6	AUGUSTUS	start_codon	4437490	4437492	.	-	0	transcript_id "Phchi.S6G057600.t1"; gene_id "Phchi.S6G057600"
# This transcript jg15509.t2 is derived from g13978.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15510.t1 is derived from g13979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19610392	19612458	.	-	.	Phchi.S3G282900
Phchi.S3	AUGUSTUS	transcript	19610392	19612458	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	stop_codon	19610389	19610391	.	-	0	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	CDS	19610392	19610501	0.93	-	2	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	exon	19610392	19610501	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	intron	19610502	19610598	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	CDS	19610599	19611957	0.58	-	2	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	exon	19610599	19611957	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	intron	19611958	19612049	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	CDS	19612050	19612154	0.54	-	2	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	exon	19612050	19612154	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	intron	19612155	19612409	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	CDS	19612410	19612458	0.99	-	0	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	exon	19612410	19612458	.	-	.	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
Phchi.S3	AUGUSTUS	start_codon	19612456	19612458	.	-	0	transcript_id "Phchi.S3G282900.t1"; gene_id "Phchi.S3G282900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11961.t1 is derived from g7636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	206304	207087	.	+	.	Phchi.S2G004100
Phchi.S2	AUGUSTUS	transcript	206304	207087	.	+	.	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	start_codon	206304	206306	.	+	0	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	CDS	206304	206383	0.58	+	0	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	exon	206304	206383	.	+	.	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	intron	206384	206486	.	+	.	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	CDS	206487	207087	0.72	+	1	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	exon	206487	207087	.	+	.	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
Phchi.S2	AUGUSTUS	stop_codon	207088	207090	.	+	0	transcript_id "Phchi.S2G004100.t1"; gene_id "Phchi.S2G004100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3203.t1 is derived from g372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2228224	2230011	.	+	.	Phchi.S1G036200
Phchi.S1	AUGUSTUS	transcript	2228224	2230011	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	start_codon	2228224	2228226	.	+	0	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	CDS	2228224	2228654	0.95	+	0	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	exon	2228224	2228654	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	intron	2228655	2228797	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	CDS	2228798	2228821	1	+	1	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	exon	2228798	2228821	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	intron	2228822	2228983	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	CDS	2228984	2229234	1	+	1	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	exon	2228984	2229234	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	intron	2229235	2229325	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	CDS	2229326	2229621	1	+	2	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	exon	2229326	2229621	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	intron	2229622	2229726	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	CDS	2229727	2230011	1	+	0	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	exon	2229727	2230011	.	+	.	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
Phchi.S1	AUGUSTUS	stop_codon	2230012	2230014	.	+	0	transcript_id "Phchi.S1G036200.t1"; gene_id "Phchi.S1G036200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12645.t1 is derived from g16012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	8993	11285	.	-	.	Phchi.C136G000500
Phchi.C136	AUGUSTUS	transcript	8993	11285	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	stop_codon	8990	8992	.	-	0	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	8993	9095	1	-	1	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	8993	9095	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	9096	9249	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	9250	9371	1	-	0	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	9250	9371	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	9372	9495	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	9496	9584	0.52	-	2	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	9496	9584	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	9585	9687	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	9688	9766	0.7	-	0	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	9688	9766	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	9767	9882	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	9883	9969	1	-	0	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	9883	9969	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	9970	10053	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	10054	10286	0.63	-	2	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	10054	10286	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	10287	10423	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	10424	10572	0.84	-	1	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	10424	10572	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	10573	10647	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	10648	10992	0.58	-	1	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	10648	10992	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	intron	10993	11076	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	CDS	11077	11285	0.99	-	0	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	exon	11077	11285	.	-	.	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
Phchi.C136	AUGUSTUS	start_codon	11283	11285	.	-	0	transcript_id "Phchi.C136G000500.t1"; gene_id "Phchi.C136G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg551.t1 is derived from g10333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4017537	4020471	.	+	.	Phchi.S6G051000
Phchi.S6	AUGUSTUS	transcript	4017537	4020471	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	start_codon	4017537	4017539	.	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4017537	4017666	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4017537	4017666	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4017667	4017755	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4017756	4017827	1	+	2	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4017756	4017827	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4017828	4017904	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4017905	4018014	1	+	2	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4017905	4018014	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4018015	4018086	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4018087	4018206	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4018087	4018206	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4018207	4018279	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4018280	4018372	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4018280	4018372	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4018373	4018465	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4018466	4018508	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4018466	4018508	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4018509	4018597	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4018598	4018707	1	+	2	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4018598	4018707	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4018708	4018792	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4018793	4018926	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4018793	4018926	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4018927	4019012	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4019013	4019085	1	+	1	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4019013	4019085	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4019086	4019207	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4019208	4019291	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4019208	4019291	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4019292	4019367	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4019368	4019454	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4019368	4019454	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4019455	4019520	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4019521	4020003	0.25	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4019521	4020003	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4020004	4020071	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4020072	4020239	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4020072	4020239	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	intron	4020240	4020330	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	CDS	4020331	4020471	1	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	exon	4020331	4020471	.	+	.	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
Phchi.S6	AUGUSTUS	stop_codon	4020472	4020474	.	+	0	transcript_id "Phchi.S6G051000.t1"; gene_id "Phchi.S6G051000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7539.t1 is derived from g4713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29956464	29958080	.	-	.	Phchi.S1G469800
Phchi.S1	AUGUSTUS	transcript	29956464	29958080	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	stop_codon	29956461	29956463	.	-	0	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	CDS	29956464	29956666	1	-	2	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	exon	29956464	29956666	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	intron	29956667	29956757	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	CDS	29956758	29956902	0.88	-	0	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	exon	29956758	29956902	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	intron	29956903	29957007	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	CDS	29957008	29957157	1	-	0	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	exon	29957008	29957157	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	intron	29957158	29957240	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	CDS	29957241	29957407	0.99	-	2	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	exon	29957241	29957407	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	intron	29957408	29957509	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	CDS	29957510	29957771	1	-	0	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	exon	29957510	29957771	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	intron	29957772	29957867	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	CDS	29957868	29958080	0.69	-	0	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	exon	29957868	29958080	.	-	.	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
Phchi.S1	AUGUSTUS	start_codon	29958078	29958080	.	-	0	transcript_id "Phchi.S1G469800.t1"; gene_id "Phchi.S1G469800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5353.t1 is derived from g2523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16442712	16443815	.	+	.	Phchi.S1G251200
Phchi.S1	AUGUSTUS	transcript	16442712	16443815	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	start_codon	16442712	16442714	.	+	0	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	CDS	16442712	16442792	0.39	+	0	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	exon	16442712	16442792	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	intron	16442793	16442872	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	CDS	16442873	16442940	1	+	0	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	exon	16442873	16442940	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	intron	16442941	16443068	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	CDS	16443069	16443182	0.99	+	1	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	exon	16443069	16443182	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	intron	16443183	16443311	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	CDS	16443312	16443474	1	+	1	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	exon	16443312	16443474	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	intron	16443475	16443550	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	CDS	16443551	16443697	1	+	0	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	exon	16443551	16443697	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	intron	16443698	16443791	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	CDS	16443792	16443815	0.99	+	0	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	exon	16443792	16443815	.	+	.	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
Phchi.S1	AUGUSTUS	stop_codon	16443816	16443818	.	+	0	transcript_id "Phchi.S1G251200.t1"; gene_id "Phchi.S1G251200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11405.t1 is derived from g15455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6201434	6202842	.	-	.	Phchi.S4G098700
Phchi.S4	AUGUSTUS	transcript	6201434	6202842	.	-	.	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	stop_codon	6201431	6201433	.	-	0	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	CDS	6201434	6202453	0.65	-	0	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	exon	6201434	6202453	.	-	.	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	intron	6202454	6202524	.	-	.	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	CDS	6202525	6202842	0.64	-	0	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	exon	6202525	6202842	.	-	.	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
Phchi.S4	AUGUSTUS	start_codon	6202840	6202842	.	-	0	transcript_id "Phchi.S4G098700.t1"; gene_id "Phchi.S4G098700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7714.t1 is derived from g4888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30772113	30774177	.	+	.	Phchi.S1G487300
Phchi.S1	AUGUSTUS	transcript	30772113	30774177	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	start_codon	30772113	30772115	.	+	0	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	CDS	30772113	30772529	0.99	+	0	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	exon	30772113	30772529	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	intron	30772530	30772835	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	CDS	30772836	30772956	0.92	+	0	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	exon	30772836	30772956	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	intron	30772957	30773068	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	CDS	30773069	30773314	1	+	2	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	exon	30773069	30773314	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	intron	30773315	30773456	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	CDS	30773457	30773610	1	+	2	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	exon	30773457	30773610	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	intron	30773611	30773702	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	CDS	30773703	30774177	0.99	+	1	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	exon	30773703	30774177	.	+	.	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
Phchi.S1	AUGUSTUS	stop_codon	30774178	30774180	.	+	0	transcript_id "Phchi.S1G487300.t1"; gene_id "Phchi.S1G487300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7287.t1 is derived from g4459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28321841	28329376	.	+	.	Phchi.S1G444600
Phchi.S1	AUGUSTUS	transcript	28321841	28329376	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	start_codon	28321841	28321843	.	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28321841	28322114	0.99	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28321841	28322114	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28322115	28322377	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28322378	28322553	1	+	2	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28322378	28322553	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28322554	28322637	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28322638	28322755	1	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28322638	28322755	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28322756	28322837	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28322838	28323913	0.83	+	2	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28322838	28323913	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28323914	28324019	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28324020	28324069	0.93	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28324020	28324069	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28324070	28324149	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28324150	28324312	0.94	+	1	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28324150	28324312	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28324313	28324406	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28324407	28324471	1	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28324407	28324471	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28324472	28324610	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28324611	28325059	1	+	1	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28324611	28325059	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28325060	28325229	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28325230	28325354	1	+	2	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28325230	28325354	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28325355	28325505	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28325506	28325698	0.94	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28325506	28325698	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28325699	28325811	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28325812	28325900	0.99	+	2	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28325812	28325900	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28325901	28325994	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28325995	28326185	1	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28325995	28326185	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28326186	28326287	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28326288	28326442	0.9	+	1	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28326288	28326442	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28326443	28326533	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28326534	28326592	0.99	+	2	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28326534	28326592	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28326593	28326693	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28326694	28326789	0.97	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28326694	28326789	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28326790	28326979	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28326980	28327092	1	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28326980	28327092	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28327093	28327191	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28327192	28327312	1	+	1	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28327192	28327312	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28327313	28327449	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28327450	28327477	0.99	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28327450	28327477	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28327478	28327594	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28327595	28328355	0.88	+	2	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28327595	28328355	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28328356	28328639	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28328640	28328737	0.87	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28328640	28328737	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	intron	28328738	28329372	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	CDS	28329373	28329376	0.83	+	1	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	exon	28329373	28329376	.	+	.	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
Phchi.S1	AUGUSTUS	stop_codon	28329377	28329379	.	+	0	transcript_id "Phchi.S1G444600.t1"; gene_id "Phchi.S1G444600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6596.t1 is derived from g3768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23914288	23915084	.	-	.	Phchi.S1G375500
Phchi.S1	AUGUSTUS	transcript	23914288	23915084	.	-	.	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	stop_codon	23914285	23914287	.	-	0	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	CDS	23914288	23914292	0.92	-	2	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	exon	23914288	23914292	.	-	.	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	intron	23914293	23914645	.	-	.	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	CDS	23914646	23915084	0.89	-	0	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	exon	23914646	23915084	.	-	.	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
Phchi.S1	AUGUSTUS	start_codon	23915082	23915084	.	-	0	transcript_id "Phchi.S1G375500.t1"; gene_id "Phchi.S1G375500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1684.t1 is derived from g8603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2489042	2490762	.	-	.	Phchi.S5G029300
Phchi.S5	AUGUSTUS	transcript	2489042	2490762	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	stop_codon	2489039	2489041	.	-	0	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	CDS	2489042	2489690	0.76	-	1	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	exon	2489042	2489690	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	intron	2489691	2489811	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	CDS	2489812	2489943	1	-	1	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	exon	2489812	2489943	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	intron	2489944	2490056	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	CDS	2490057	2490409	0.77	-	0	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	exon	2490057	2490409	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	intron	2490410	2490504	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	CDS	2490505	2490762	0.61	-	0	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	exon	2490505	2490762	.	-	.	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
Phchi.S5	AUGUSTUS	start_codon	2490760	2490762	.	-	0	transcript_id "Phchi.S5G029300.t1"; gene_id "Phchi.S5G029300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9790.t1 is derived from g6966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43697778	43699821	.	+	.	Phchi.S1G694900
Phchi.S1	AUGUSTUS	transcript	43697778	43699821	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	start_codon	43697778	43697780	.	+	0	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	CDS	43697778	43697820	1	+	0	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	exon	43697778	43697820	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	intron	43697821	43697903	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	CDS	43697904	43697970	0.5	+	2	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	exon	43697904	43697970	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	intron	43697971	43698153	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	CDS	43698154	43698161	0.49	+	1	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	exon	43698154	43698161	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	intron	43698162	43698298	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	CDS	43698299	43699821	0.86	+	2	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	exon	43698299	43699821	.	+	.	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
Phchi.S1	AUGUSTUS	stop_codon	43699822	43699824	.	+	0	transcript_id "Phchi.S1G694900.t1"; gene_id "Phchi.S1G694900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6230.t1 is derived from g3402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21778954	21779306	.	-	.	Phchi.S1G338900
Phchi.S1	AUGUSTUS	transcript	21778954	21779306	.	-	.	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	stop_codon	21778951	21778953	.	-	0	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	CDS	21778954	21779167	0.64	-	1	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	exon	21778954	21779167	.	-	.	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	intron	21779168	21779259	.	-	.	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	CDS	21779260	21779306	0.54	-	0	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	exon	21779260	21779306	.	-	.	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
Phchi.S1	AUGUSTUS	start_codon	21779304	21779306	.	-	0	transcript_id "Phchi.S1G338900.t1"; gene_id "Phchi.S1G338900"
# This transcript jg9614.t2 is derived from g6790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9615.t1 is derived from g6791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42937613	42940375	.	+	.	Phchi.S1G677400
Phchi.S1	AUGUSTUS	transcript	42937613	42940375	.	+	.	transcript_id "Phchi.S1G677400.t1"; gene_id "Phchi.S1G677400"
Phchi.S1	AUGUSTUS	start_codon	42937613	42937615	.	+	0	transcript_id "Phchi.S1G677400.t1"; gene_id "Phchi.S1G677400"
Phchi.S1	AUGUSTUS	CDS	42937613	42940375	0.84	+	0	transcript_id "Phchi.S1G677400.t1"; gene_id "Phchi.S1G677400"
Phchi.S1	AUGUSTUS	exon	42937613	42940375	.	+	.	transcript_id "Phchi.S1G677400.t1"; gene_id "Phchi.S1G677400"
Phchi.S1	AUGUSTUS	stop_codon	42940376	42940378	.	+	0	transcript_id "Phchi.S1G677400.t1"; gene_id "Phchi.S1G677400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2198.t1 is derived from g9118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5368538	5369977	.	-	.	Phchi.S5G080700
Phchi.S5	AUGUSTUS	transcript	5368538	5369977	.	-	.	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	stop_codon	5368535	5368537	.	-	0	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	CDS	5368538	5369431	1	-	0	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	exon	5368538	5369431	.	-	.	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	intron	5369432	5369557	.	-	.	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	CDS	5369558	5369977	0.49	-	0	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	exon	5369558	5369977	.	-	.	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
Phchi.S5	AUGUSTUS	start_codon	5369975	5369977	.	-	0	transcript_id "Phchi.S5G080700.t1"; gene_id "Phchi.S5G080700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11573.t1 is derived from g15624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7135072	7140079	.	-	.	Phchi.S4G115500
Phchi.S4	AUGUSTUS	transcript	7135072	7140079	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	stop_codon	7135069	7135071	.	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7135072	7135094	1	-	2	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7135072	7135094	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7135095	7135310	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7135311	7135353	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7135311	7135353	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7135354	7135531	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7135532	7135582	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7135532	7135582	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7135583	7135669	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7135670	7135816	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7135670	7135816	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7135817	7135903	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7135904	7136002	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7135904	7136002	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7136003	7136095	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7136096	7136161	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7136096	7136161	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7136162	7136315	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7136316	7136489	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7136316	7136489	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7136490	7136604	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7136605	7136769	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7136605	7136769	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7136770	7137016	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7137017	7137112	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7137017	7137112	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7137113	7137282	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7137283	7137345	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7137283	7137345	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7137346	7137487	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7137488	7137547	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7137488	7137547	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7137548	7137623	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7137624	7137725	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7137624	7137725	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7137726	7137877	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7137878	7137967	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7137878	7137967	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7137968	7138100	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7138101	7138178	1	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7138101	7138178	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	intron	7138179	7138318	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	CDS	7138319	7140079	0.98	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	exon	7138319	7140079	.	-	.	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
Phchi.S4	AUGUSTUS	start_codon	7140077	7140079	.	-	0	transcript_id "Phchi.S4G115500.t1"; gene_id "Phchi.S4G115500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8568.t1 is derived from g5743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36646358	36648121	.	-	.	Phchi.S1G572700
Phchi.S1	AUGUSTUS	transcript	36646358	36648121	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	stop_codon	36646355	36646357	.	-	0	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36646358	36646451	0.97	-	1	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36646358	36646451	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36646452	36646549	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36646550	36646744	1	-	1	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36646550	36646744	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36646745	36646844	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36646845	36646919	1	-	1	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36646845	36646919	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36646920	36647009	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36647010	36647065	1	-	0	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36647010	36647065	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36647066	36647186	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36647187	36647239	0.9	-	2	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36647187	36647239	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36647240	36647351	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36647352	36647415	0.9	-	0	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36647352	36647415	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36647416	36647515	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36647516	36647658	1	-	2	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36647516	36647658	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36647659	36647727	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36647728	36647908	1	-	0	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36647728	36647908	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	intron	36647909	36648013	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	CDS	36648014	36648121	0.99	-	0	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	exon	36648014	36648121	.	-	.	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
Phchi.S1	AUGUSTUS	start_codon	36648119	36648121	.	-	0	transcript_id "Phchi.S1G572700.t1"; gene_id "Phchi.S1G572700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9415.t1 is derived from g6591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41376456	41376980	.	-	.	Phchi.S1G657400
Phchi.S1	AUGUSTUS	transcript	41376456	41376980	.	-	.	transcript_id "Phchi.S1G657400.t1"; gene_id "Phchi.S1G657400"
Phchi.S1	AUGUSTUS	stop_codon	41376453	41376455	.	-	0	transcript_id "Phchi.S1G657400.t1"; gene_id "Phchi.S1G657400"
Phchi.S1	AUGUSTUS	CDS	41376456	41376980	0.75	-	0	transcript_id "Phchi.S1G657400.t1"; gene_id "Phchi.S1G657400"
Phchi.S1	AUGUSTUS	exon	41376456	41376980	.	-	.	transcript_id "Phchi.S1G657400.t1"; gene_id "Phchi.S1G657400"
Phchi.S1	AUGUSTUS	start_codon	41376978	41376980	.	-	0	transcript_id "Phchi.S1G657400.t1"; gene_id "Phchi.S1G657400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14375.t1 is derived from g12842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12420062	12428327	.	+	.	Phchi.S3G169400
Phchi.S3	AUGUSTUS	transcript	12420062	12428327	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	start_codon	12420062	12420064	.	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12420062	12420197	0.58	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12420062	12420197	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12420198	12420349	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12420350	12420792	0.84	+	2	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12420350	12420792	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12420793	12420892	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12420893	12421024	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12420893	12421024	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12421025	12421147	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12421148	12421246	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12421148	12421246	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12421247	12421361	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12421362	12421432	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12421362	12421432	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12421433	12421512	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12421513	12421606	1	+	1	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12421513	12421606	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12421607	12421745	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12421746	12421838	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12421746	12421838	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12421839	12421928	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12421929	12422074	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12421929	12422074	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12422075	12422222	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12422223	12422382	1	+	1	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12422223	12422382	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12422383	12422490	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12422491	12422601	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12422491	12422601	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12422602	12422830	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12422831	12423046	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12422831	12423046	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12423047	12423138	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12423139	12423296	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12423139	12423296	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12423297	12423402	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12423403	12423532	1	+	1	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12423403	12423532	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12423533	12423645	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12423646	12423704	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12423646	12423704	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12423705	12423866	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12423867	12423972	1	+	1	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12423867	12423972	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12423973	12424097	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12424098	12424194	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12424098	12424194	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12424195	12424308	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12424309	12424424	0.99	+	2	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12424309	12424424	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12424425	12424529	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12424530	12424727	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12424530	12424727	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12424728	12424825	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12424826	12424936	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12424826	12424936	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12424937	12425012	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12425013	12425252	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12425013	12425252	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12425253	12425538	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12425539	12425637	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12425539	12425637	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12425638	12425726	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12425727	12425822	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12425727	12425822	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12425823	12425925	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12425926	12426123	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12425926	12426123	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12426124	12426278	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12426279	12426353	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12426279	12426353	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12426354	12426503	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12426504	12426632	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12426504	12426632	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12426633	12426746	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12426747	12426845	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12426747	12426845	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12426846	12426956	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12426957	12427099	0.99	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12426957	12427099	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12427100	12427228	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12427229	12427322	1	+	1	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12427229	12427322	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12427323	12427417	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12427418	12427620	0.81	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12427418	12427620	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12427621	12427765	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12427766	12427844	0.94	+	1	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12427766	12427844	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12427845	12427957	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12427958	12428041	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12427958	12428041	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	intron	12428042	12428159	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	CDS	12428160	12428327	1	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	exon	12428160	12428327	.	+	.	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
Phchi.S3	AUGUSTUS	stop_codon	12428328	12428330	.	+	0	transcript_id "Phchi.S3G169400.t1"; gene_id "Phchi.S3G169400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3689.t1 is derived from g858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5187827	5188222	.	+	.	Phchi.S1G084800
Phchi.S1	AUGUSTUS	transcript	5187827	5188222	.	+	.	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	start_codon	5187827	5187829	.	+	0	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	CDS	5187827	5187942	1	+	0	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	exon	5187827	5187942	.	+	.	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	intron	5187943	5188062	.	+	.	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	CDS	5188063	5188222	0.94	+	1	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	exon	5188063	5188222	.	+	.	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
Phchi.S1	AUGUSTUS	stop_codon	5188223	5188225	.	+	0	transcript_id "Phchi.S1G084800.t1"; gene_id "Phchi.S1G084800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6674.t1 is derived from g3846.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24448674	24450944	.	+	.	Phchi.S1G383300
Phchi.S1	AUGUSTUS	transcript	24448674	24450944	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	start_codon	24448674	24448676	.	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24448674	24448756	0.91	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24448674	24448756	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24448757	24448998	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24448999	24449108	0.94	+	1	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24448999	24449108	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449109	24449250	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449251	24449342	0.95	+	2	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449251	24449342	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449343	24449433	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449434	24449544	0.99	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449434	24449544	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449545	24449650	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449651	24449729	1	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449651	24449729	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449730	24449811	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449812	24449911	1	+	2	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449812	24449911	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449912	24450030	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24450031	24450232	0.77	+	1	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24450031	24450232	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24450233	24450372	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24450373	24450576	1	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24450373	24450576	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24450577	24450668	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24450669	24450944	1	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24450669	24450944	.	+	.	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	stop_codon	24450945	24450947	.	+	0	transcript_id "Phchi.S1G383300.t1"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	transcript	24449019	24450944	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	start_codon	24449019	24449021	.	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449019	24449108	0.49	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449019	24449108	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449109	24449243	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449244	24449342	0.92	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449244	24449342	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449343	24449433	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449434	24449544	0.97	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449434	24449544	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449545	24449650	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449651	24449729	1	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449651	24449729	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449730	24449811	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24449812	24449911	1	+	2	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24449812	24449911	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24449912	24450030	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24450031	24450232	0.81	+	1	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24450031	24450232	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24450233	24450372	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24450373	24450576	1	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24450373	24450576	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	intron	24450577	24450668	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	CDS	24450669	24450944	1	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	exon	24450669	24450944	.	+	.	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
Phchi.S1	AUGUSTUS	stop_codon	24450945	24450947	.	+	0	transcript_id "Phchi.S1G383300.t2"; gene_id "Phchi.S1G383300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11958.t1 is derived from g7633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	194613	195296	.	-	.	Phchi.S2G003800
Phchi.S2	AUGUSTUS	transcript	194613	195296	.	-	.	transcript_id "Phchi.S2G003800.t1"; gene_id "Phchi.S2G003800"
Phchi.S2	AUGUSTUS	stop_codon	194610	194612	.	-	0	transcript_id "Phchi.S2G003800.t1"; gene_id "Phchi.S2G003800"
Phchi.S2	AUGUSTUS	CDS	194613	195296	0.39	-	0	transcript_id "Phchi.S2G003800.t1"; gene_id "Phchi.S2G003800"
Phchi.S2	AUGUSTUS	exon	194613	195296	.	-	.	transcript_id "Phchi.S2G003800.t1"; gene_id "Phchi.S2G003800"
Phchi.S2	AUGUSTUS	start_codon	195294	195296	.	-	0	transcript_id "Phchi.S2G003800.t1"; gene_id "Phchi.S2G003800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7732.t1 is derived from g4906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30884365	30885281	.	+	.	Phchi.S1G489100
Phchi.S1	AUGUSTUS	transcript	30884365	30885281	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	start_codon	30884365	30884367	.	+	0	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	CDS	30884365	30884721	0.96	+	0	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	exon	30884365	30884721	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	intron	30884722	30884819	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	CDS	30884820	30884882	0.83	+	0	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	exon	30884820	30884882	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	intron	30884883	30884988	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	CDS	30884989	30885060	0.92	+	0	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	exon	30884989	30885060	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	intron	30885061	30885164	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	CDS	30885165	30885281	0.98	+	0	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	exon	30885165	30885281	.	+	.	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
Phchi.S1	AUGUSTUS	stop_codon	30885282	30885284	.	+	0	transcript_id "Phchi.S1G489100.t1"; gene_id "Phchi.S1G489100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9664.t1 is derived from g6840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43132226	43135208	.	-	.	Phchi.S1G682300
Phchi.S1	AUGUSTUS	transcript	43132226	43135208	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	stop_codon	43132223	43132225	.	-	0	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43132226	43132842	0.31	-	2	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43132226	43132842	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43132843	43132941	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43132942	43133222	0.79	-	1	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43132942	43133222	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43133223	43133352	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43133353	43133465	1	-	0	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43133353	43133465	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43133466	43133568	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43133569	43134502	0.97	-	1	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43133569	43134502	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43134503	43134670	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43134671	43134770	0.98	-	2	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43134671	43134770	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43134771	43134884	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43134885	43134976	0.99	-	1	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43134885	43134976	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43134977	43135104	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43135105	43135208	1	-	0	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43135105	43135208	.	-	.	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	start_codon	43135206	43135208	.	-	0	transcript_id "Phchi.S1G682300.t1"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	transcript	43132226	43135208	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	stop_codon	43132223	43132225	.	-	0	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43132226	43132842	0.22	-	2	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43132226	43132842	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43132843	43132941	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43132942	43133222	0.83	-	1	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43132942	43133222	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43133223	43133352	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43133353	43133465	1	-	0	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43133353	43133465	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43133466	43133568	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43133569	43134502	0.97	-	1	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43133569	43134502	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43134503	43134670	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43134671	43134770	0.56	-	2	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43134671	43134770	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43134771	43134930	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43134931	43134956	0.77	-	1	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43134931	43134956	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	intron	43134957	43135104	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	CDS	43135105	43135208	0.99	-	0	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	exon	43135105	43135208	.	-	.	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
Phchi.S1	AUGUSTUS	start_codon	43135206	43135208	.	-	0	transcript_id "Phchi.S1G682300.t2"; gene_id "Phchi.S1G682300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11184.t1 is derived from g15234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4537706	4539455	.	+	.	Phchi.S4G076600
Phchi.S4	AUGUSTUS	transcript	4537706	4539455	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	start_codon	4537706	4537708	.	+	0	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	CDS	4537706	4537942	1	+	0	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	exon	4537706	4537942	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	intron	4537943	4538068	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	CDS	4538069	4538236	1	+	0	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	exon	4538069	4538236	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	intron	4538237	4538415	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	CDS	4538416	4538595	1	+	0	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	exon	4538416	4538595	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	intron	4538596	4538691	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	CDS	4538692	4538926	1	+	0	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	exon	4538692	4538926	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	intron	4538927	4539030	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	CDS	4539031	4539253	0.97	+	2	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	exon	4539031	4539253	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	intron	4539254	4539349	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	CDS	4539350	4539455	1	+	1	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	exon	4539350	4539455	.	+	.	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
Phchi.S4	AUGUSTUS	stop_codon	4539456	4539458	.	+	0	transcript_id "Phchi.S4G076600.t1"; gene_id "Phchi.S4G076600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2091.t1 is derived from g9011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4836301	4837990	.	-	.	Phchi.S5G070000
Phchi.S5	AUGUSTUS	transcript	4836301	4837990	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	stop_codon	4836298	4836300	.	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	CDS	4836301	4836696	0.98	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	exon	4836301	4836696	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	intron	4836697	4836803	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	CDS	4836804	4836868	0.98	-	2	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	exon	4836804	4836868	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	intron	4836869	4836970	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	CDS	4836971	4837052	1	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	exon	4836971	4837052	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	intron	4837053	4837140	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	CDS	4837141	4837275	0.77	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	exon	4837141	4837275	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	intron	4837276	4837424	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	CDS	4837425	4837547	1	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	exon	4837425	4837547	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	intron	4837548	4837696	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	CDS	4837697	4837990	1	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	exon	4837697	4837990	.	-	.	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
Phchi.S5	AUGUSTUS	start_codon	4837988	4837990	.	-	0	transcript_id "Phchi.S5G070000.t1"; gene_id "Phchi.S5G070000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15313.t1 is derived from g13781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18351550	18354960	.	+	.	Phchi.S3G263200
Phchi.S3	AUGUSTUS	transcript	18351550	18354960	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	start_codon	18351550	18351552	.	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18351550	18351708	0.77	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18351550	18351708	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18351709	18351801	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18351802	18351986	0.98	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18351802	18351986	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18351987	18352109	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18352110	18352266	0.88	+	1	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18352110	18352266	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18352267	18352352	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18352353	18352438	1	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18352353	18352438	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18352439	18352609	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18352610	18352700	1	+	1	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18352610	18352700	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18352701	18352841	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18352842	18352961	1	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18352842	18352961	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18352962	18353099	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18353100	18353201	1	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18353100	18353201	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18353202	18353315	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18353316	18353423	1	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18353316	18353423	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18353424	18353546	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18353547	18353611	0.99	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18353547	18353611	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18353612	18353837	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18353838	18353955	1	+	1	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18353838	18353955	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18353956	18354069	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18354070	18354243	1	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18354070	18354243	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18354244	18354359	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18354360	18354427	1	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18354360	18354427	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	intron	18354428	18354515	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	CDS	18354516	18354960	0.27	+	1	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	exon	18354516	18354960	.	+	.	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
Phchi.S3	AUGUSTUS	stop_codon	18354961	18354963	.	+	0	transcript_id "Phchi.S3G263200.t1"; gene_id "Phchi.S3G263200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8238.t1 is derived from g5413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34585719	34587844	.	-	.	Phchi.S1G539700
Phchi.S1	AUGUSTUS	transcript	34585719	34587844	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	stop_codon	34585716	34585718	.	-	0	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	CDS	34585719	34586039	1	-	0	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	exon	34585719	34586039	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	intron	34586040	34586175	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	CDS	34586176	34586226	0.97	-	0	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	exon	34586176	34586226	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	intron	34586227	34586457	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	CDS	34586458	34586524	0.92	-	1	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	exon	34586458	34586524	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	intron	34586525	34586649	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	CDS	34586650	34586861	0.92	-	0	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	exon	34586650	34586861	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	intron	34586862	34586932	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	CDS	34586933	34587844	0.9	-	0	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	exon	34586933	34587844	.	-	.	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
Phchi.S1	AUGUSTUS	start_codon	34587842	34587844	.	-	0	transcript_id "Phchi.S1G539700.t1"; gene_id "Phchi.S1G539700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8867.t1 is derived from g6042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38377766	38380336	.	-	.	Phchi.S1G602600
Phchi.S1	AUGUSTUS	transcript	38377766	38380336	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	stop_codon	38377763	38377765	.	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38377766	38377889	0.71	-	1	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38377766	38377889	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38377890	38377994	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38377995	38378109	0.98	-	2	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38377995	38378109	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38378110	38378208	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38378209	38378324	1	-	1	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38378209	38378324	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38378325	38378406	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38378407	38378486	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38378407	38378486	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38378487	38378637	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38378638	38378691	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38378638	38378691	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38378692	38378782	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38378783	38378893	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38378783	38378893	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38378894	38378994	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38378995	38379285	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38378995	38379285	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38379286	38379377	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38379378	38379491	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38379378	38379491	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38379492	38379590	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38379591	38379701	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38379591	38379701	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	intron	38379702	38379847	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	CDS	38379848	38380336	1	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	exon	38379848	38380336	.	-	.	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
Phchi.S1	AUGUSTUS	start_codon	38380334	38380336	.	-	0	transcript_id "Phchi.S1G602600.t1"; gene_id "Phchi.S1G602600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2749.t1 is derived from g9669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8613056	8613969	.	-	.	Phchi.S5G135800
Phchi.S5	AUGUSTUS	transcript	8613056	8613969	.	-	.	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	stop_codon	8613053	8613055	.	-	0	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	CDS	8613056	8613238	0.96	-	0	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	exon	8613056	8613238	.	-	.	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	intron	8613239	8613466	.	-	.	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	CDS	8613467	8613619	0.88	-	0	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	exon	8613467	8613619	.	-	.	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	intron	8613620	8613693	.	-	.	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	CDS	8613694	8613969	0.94	-	0	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	exon	8613694	8613969	.	-	.	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
Phchi.S5	AUGUSTUS	start_codon	8613967	8613969	.	-	0	transcript_id "Phchi.S5G135800.t1"; gene_id "Phchi.S5G135800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2130.t1 is derived from g9050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4983536	4986336	.	-	.	Phchi.S5G073900
Phchi.S5	AUGUSTUS	transcript	4983536	4986336	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	stop_codon	4983533	4983535	.	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4983536	4983560	0.72	-	1	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4983536	4983560	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4983561	4983708	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4983709	4983884	0.55	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4983709	4983884	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4983885	4984106	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4984107	4984313	0.56	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4984107	4984313	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4984314	4984417	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4984418	4984669	0.93	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4984418	4984669	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4984670	4984770	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4984771	4985056	0.33	-	1	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4984771	4985056	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4985057	4985175	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4985176	4985264	1	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4985176	4985264	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4985265	4985378	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4985379	4985570	0.62	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4985379	4985570	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4985571	4985759	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4985760	4985783	0.62	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4985760	4985783	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4985784	4985948	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4985949	4986005	1	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4985949	4986005	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	intron	4986006	4986177	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	CDS	4986178	4986336	0.98	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	exon	4986178	4986336	.	-	.	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
Phchi.S5	AUGUSTUS	start_codon	4986334	4986336	.	-	0	transcript_id "Phchi.S5G073900.t1"; gene_id "Phchi.S5G073900"
# This transcript jg5984.t2 is derived from g3155.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5984.t3 is derived from g3155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5985.t1 is derived from g3156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20266152	20266724	.	-	.	Phchi.S1G314400
Phchi.S1	AUGUSTUS	transcript	20266152	20266724	.	-	.	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	stop_codon	20266149	20266151	.	-	0	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	CDS	20266152	20266226	0.97	-	0	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	exon	20266152	20266226	.	-	.	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	intron	20266227	20266361	.	-	.	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	CDS	20266362	20266724	0.48	-	0	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	exon	20266362	20266724	.	-	.	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
Phchi.S1	AUGUSTUS	start_codon	20266722	20266724	.	-	0	transcript_id "Phchi.S1G314400.t1"; gene_id "Phchi.S1G314400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15888.t1 is derived from g14358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22034037	22035887	.	+	.	Phchi.S3G320700
Phchi.S3	AUGUSTUS	transcript	22034037	22035887	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	start_codon	22034037	22034039	.	+	0	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	CDS	22034037	22034107	1	+	0	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	exon	22034037	22034107	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	intron	22034108	22034358	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	CDS	22034359	22034425	0.97	+	1	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	exon	22034359	22034425	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	intron	22034426	22034535	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	CDS	22034536	22034869	0.75	+	0	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	exon	22034536	22034869	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	intron	22034870	22034962	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	CDS	22034963	22035418	0.46	+	2	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	exon	22034963	22035418	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	intron	22035419	22035543	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	CDS	22035544	22035887	0.5	+	2	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	exon	22035544	22035887	.	+	.	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
Phchi.S3	AUGUSTUS	stop_codon	22035888	22035890	.	+	0	transcript_id "Phchi.S3G320700.t1"; gene_id "Phchi.S3G320700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15990.t1 is derived from g9762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C297	AUGUSTUS	gene	6305	7270	.	-	.	Phchi.C297G000200
Phchi.C297	AUGUSTUS	transcript	6305	7270	.	-	.	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	stop_codon	6302	6304	.	-	0	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	CDS	6305	6805	0.78	-	0	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	exon	6305	6805	.	-	.	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	intron	6806	6905	.	-	.	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	CDS	6906	7066	0.47	-	2	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	exon	6906	7066	.	-	.	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	intron	7067	7227	.	-	.	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	CDS	7228	7270	0.5	-	0	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	exon	7228	7270	.	-	.	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
Phchi.C297	AUGUSTUS	start_codon	7268	7270	.	-	0	transcript_id "Phchi.C297G000200.t1"; gene_id "Phchi.C297G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4969.t1 is derived from g2139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13809323	13811690	.	+	.	Phchi.S1G212800
Phchi.S1	AUGUSTUS	transcript	13809323	13811690	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	start_codon	13809323	13809325	.	+	0	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13809323	13809543	0.34	+	0	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13809323	13809543	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13809544	13809629	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13809630	13809764	1	+	1	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13809630	13809764	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13809765	13809860	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13809861	13810115	1	+	1	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13809861	13810115	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13810116	13810202	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13810203	13810284	1	+	1	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13810203	13810284	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13810285	13810393	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13810394	13810509	1	+	0	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13810394	13810509	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13810510	13810629	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13810630	13810684	1	+	1	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13810630	13810684	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13810685	13810970	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13810971	13811082	1	+	0	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13810971	13811082	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13811083	13811173	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13811174	13811343	1	+	2	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13811174	13811343	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	intron	13811344	13811426	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	CDS	13811427	13811690	0.99	+	0	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	exon	13811427	13811690	.	+	.	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
Phchi.S1	AUGUSTUS	stop_codon	13811691	13811693	.	+	0	transcript_id "Phchi.S1G212800.t1"; gene_id "Phchi.S1G212800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14350.t1 is derived from g12817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12327394	12327979	.	-	.	Phchi.S3G166900
Phchi.S3	AUGUSTUS	transcript	12327394	12327979	.	-	.	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	stop_codon	12327391	12327393	.	-	0	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	CDS	12327394	12327404	1	-	2	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	exon	12327394	12327404	.	-	.	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	intron	12327405	12327621	.	-	.	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	CDS	12327622	12327979	1	-	0	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	exon	12327622	12327979	.	-	.	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
Phchi.S3	AUGUSTUS	start_codon	12327977	12327979	.	-	0	transcript_id "Phchi.S3G166900.t1"; gene_id "Phchi.S3G166900"
# This transcript jg4780.t2 is derived from g1950.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4781.t1 is derived from g1951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12795482	12796486	.	+	.	Phchi.S1G194000
Phchi.S1	AUGUSTUS	transcript	12795482	12796486	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	start_codon	12795482	12795484	.	+	0	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	CDS	12795482	12795492	1	+	0	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	exon	12795482	12795492	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	intron	12795493	12795629	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	CDS	12795630	12795705	1	+	1	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	exon	12795630	12795705	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	intron	12795706	12795780	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	CDS	12795781	12795882	1	+	0	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	exon	12795781	12795882	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	intron	12795883	12796016	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	CDS	12796017	12796165	1	+	0	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	exon	12796017	12796165	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	intron	12796166	12796260	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	CDS	12796261	12796486	0.99	+	1	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	exon	12796261	12796486	.	+	.	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
Phchi.S1	AUGUSTUS	stop_codon	12796487	12796489	.	+	0	transcript_id "Phchi.S1G194000.t1"; gene_id "Phchi.S1G194000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6224.t1 is derived from g3396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21762559	21763889	.	+	.	Phchi.S1G338300
Phchi.S1	AUGUSTUS	transcript	21762559	21763889	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	start_codon	21762559	21762561	.	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21762559	21762807	0.91	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21762559	21762807	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	intron	21762808	21762892	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21762893	21762953	1	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21762893	21762953	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	intron	21762954	21763063	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21763064	21763146	1	+	2	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21763064	21763146	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	intron	21763147	21763306	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21763307	21763345	1	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21763307	21763345	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	intron	21763346	21763427	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21763428	21763498	1	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21763428	21763498	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	intron	21763499	21763619	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21763620	21763734	1	+	1	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21763620	21763734	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	intron	21763735	21763823	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	CDS	21763824	21763889	1	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	exon	21763824	21763889	.	+	.	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
Phchi.S1	AUGUSTUS	stop_codon	21763890	21763892	.	+	0	transcript_id "Phchi.S1G338300.t1"; gene_id "Phchi.S1G338300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13143.t1 is derived from g11608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4383745	4385455	.	-	.	Phchi.S3G046200
Phchi.S3	AUGUSTUS	transcript	4383745	4385455	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	stop_codon	4383742	4383744	.	-	0	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	CDS	4383745	4383871	0.95	-	1	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	exon	4383745	4383871	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	intron	4383872	4383952	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	CDS	4383953	4384094	1	-	2	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	exon	4383953	4384094	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	intron	4384095	4384185	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	CDS	4384186	4384520	1	-	1	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	exon	4384186	4384520	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	intron	4384521	4384642	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	CDS	4384643	4384679	1	-	2	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	exon	4384643	4384679	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	intron	4384680	4384785	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	CDS	4384786	4384977	1	-	2	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	exon	4384786	4384977	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	intron	4384978	4385346	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	CDS	4385347	4385455	1	-	0	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	exon	4385347	4385455	.	-	.	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
Phchi.S3	AUGUSTUS	start_codon	4385453	4385455	.	-	0	transcript_id "Phchi.S3G046200.t1"; gene_id "Phchi.S3G046200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3702.t1 is derived from g871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5236622	5237296	.	-	.	Phchi.S1G086100
Phchi.S1	AUGUSTUS	transcript	5236622	5237296	.	-	.	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	stop_codon	5236619	5236621	.	-	0	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	CDS	5236622	5236969	0.7	-	0	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	exon	5236622	5236969	.	-	.	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	intron	5236970	5237059	.	-	.	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	CDS	5237060	5237296	0.86	-	0	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	exon	5237060	5237296	.	-	.	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
Phchi.S1	AUGUSTUS	start_codon	5237294	5237296	.	-	0	transcript_id "Phchi.S1G086100.t1"; gene_id "Phchi.S1G086100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2049.t1 is derived from g8969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4593881	4599385	.	-	.	Phchi.S5G065800
Phchi.S5	AUGUSTUS	transcript	4593881	4599385	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	stop_codon	4593878	4593880	.	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4593881	4594003	0.99	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4593881	4594003	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4594004	4594100	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4594101	4594184	0.98	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4594101	4594184	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4594185	4594296	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4594297	4594471	0.98	-	1	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4594297	4594471	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4594472	4594624	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4594625	4594666	1	-	1	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4594625	4594666	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4594667	4594754	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4594755	4594881	1	-	2	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4594755	4594881	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4594882	4595026	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4595027	4595609	0.52	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4595027	4595609	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4595610	4595759	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4595760	4595851	1	-	2	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4595760	4595851	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4595852	4596002	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4596003	4596693	0.55	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4596003	4596693	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4596694	4596772	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4596773	4596902	0.99	-	1	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4596773	4596902	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4596903	4597027	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4597028	4597083	1	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4597028	4597083	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4597084	4597167	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4597168	4597206	1	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4597168	4597206	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4597207	4597349	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4597350	4597427	1	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4597350	4597427	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4597428	4597525	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4597526	4597651	1	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4597526	4597651	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4597652	4597748	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4597749	4597826	1	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4597749	4597826	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4597827	4598000	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4598001	4598084	0.99	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4598001	4598084	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4598085	4598205	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4598206	4598325	0.97	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4598206	4598325	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4598326	4598421	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4598422	4598511	1	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4598422	4598511	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4598512	4598592	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4598593	4598669	0.38	-	2	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4598593	4598669	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4598670	4598816	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4598817	4598854	0.64	-	1	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4598817	4598854	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	intron	4598855	4599026	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	CDS	4599027	4599385	0.99	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	exon	4599027	4599385	.	-	.	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
Phchi.S5	AUGUSTUS	start_codon	4599383	4599385	.	-	0	transcript_id "Phchi.S5G065800.t1"; gene_id "Phchi.S5G065800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10825.t1 is derived from g14875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2305549	2306466	.	+	.	Phchi.S4G040700
Phchi.S4	AUGUSTUS	transcript	2305549	2306466	.	+	.	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	start_codon	2305549	2305551	.	+	0	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	CDS	2305549	2305800	0.44	+	0	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	exon	2305549	2305800	.	+	.	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	intron	2305801	2305889	.	+	.	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	CDS	2305890	2306213	0.33	+	0	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	exon	2305890	2306213	.	+	.	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	intron	2306214	2306451	.	+	.	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	CDS	2306452	2306466	0.37	+	0	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	exon	2306452	2306466	.	+	.	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
Phchi.S4	AUGUSTUS	stop_codon	2306467	2306469	.	+	0	transcript_id "Phchi.S4G040700.t1"; gene_id "Phchi.S4G040700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4705.t1 is derived from g1875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12407070	12409080	.	-	.	Phchi.S1G186400
Phchi.S1	AUGUSTUS	transcript	12407070	12409080	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	stop_codon	12407067	12407069	.	-	0	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	CDS	12407070	12407107	1	-	2	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	exon	12407070	12407107	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	intron	12407108	12407445	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	CDS	12407446	12407527	1	-	0	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	exon	12407446	12407527	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	intron	12407528	12407749	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	CDS	12407750	12408279	0.65	-	2	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	exon	12407750	12408279	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	intron	12408280	12408399	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	CDS	12408400	12408458	0.73	-	1	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	exon	12408400	12408458	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	intron	12408459	12408721	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	CDS	12408722	12408778	0.88	-	1	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	exon	12408722	12408778	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	intron	12408779	12408982	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	CDS	12408983	12409080	0.71	-	0	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	exon	12408983	12409080	.	-	.	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
Phchi.S1	AUGUSTUS	start_codon	12409078	12409080	.	-	0	transcript_id "Phchi.S1G186400.t1"; gene_id "Phchi.S1G186400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg913.t1 is derived from g10695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6409924	6412214	.	-	.	Phchi.S6G087200
Phchi.S6	AUGUSTUS	transcript	6409924	6412214	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	stop_codon	6409921	6409923	.	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6409924	6410017	1	-	1	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6409924	6410017	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6410018	6410088	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6410089	6410210	1	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6410089	6410210	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6410211	6410299	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6410300	6410406	1	-	2	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6410300	6410406	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6410407	6410501	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6410502	6410580	1	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6410502	6410580	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6410581	6410670	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6410671	6410769	1	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6410671	6410769	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6410770	6410880	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6410881	6411068	1	-	2	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6410881	6411068	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6411069	6411160	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6411161	6411224	1	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6411161	6411224	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6411225	6411316	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6411317	6411466	1	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6411317	6411466	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6411467	6411547	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6411548	6411866	1	-	1	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6411548	6411866	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	intron	6411867	6411960	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	CDS	6411961	6412214	0.91	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	exon	6411961	6412214	.	-	.	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
Phchi.S6	AUGUSTUS	start_codon	6412212	6412214	.	-	0	transcript_id "Phchi.S6G087200.t1"; gene_id "Phchi.S6G087200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11694.t1 is derived from g15745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7709606	7710416	.	+	.	Phchi.S4G127600
Phchi.S4	AUGUSTUS	transcript	7709606	7710416	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	start_codon	7709606	7709608	.	+	0	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	CDS	7709606	7709704	0.71	+	0	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	exon	7709606	7709704	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	intron	7709705	7709806	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	CDS	7709807	7709869	0.84	+	0	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	exon	7709807	7709869	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	intron	7709870	7710009	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	CDS	7710010	7710084	0.99	+	0	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	exon	7710010	7710084	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	intron	7710085	7710192	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	CDS	7710193	7710251	0.94	+	0	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	exon	7710193	7710251	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	intron	7710252	7710370	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	CDS	7710371	7710416	0.94	+	1	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	exon	7710371	7710416	.	+	.	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
Phchi.S4	AUGUSTUS	stop_codon	7710417	7710419	.	+	0	transcript_id "Phchi.S4G127600.t1"; gene_id "Phchi.S4G127600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1513.t1 is derived from g8432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1329704	1331403	.	+	.	Phchi.S5G012200
Phchi.S5	AUGUSTUS	transcript	1329704	1331403	.	+	.	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	start_codon	1329704	1329706	.	+	0	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	CDS	1329704	1330723	0.47	+	0	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	exon	1329704	1330723	.	+	.	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	intron	1330724	1330827	.	+	.	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	CDS	1330828	1331403	0.92	+	0	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	exon	1330828	1331403	.	+	.	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
Phchi.S5	AUGUSTUS	stop_codon	1331404	1331406	.	+	0	transcript_id "Phchi.S5G012200.t1"; gene_id "Phchi.S5G012200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11290.t1 is derived from g15340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5245428	5245836	.	-	.	Phchi.S4G087200
Phchi.S4	AUGUSTUS	transcript	5245428	5245836	.	-	.	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	stop_codon	5245425	5245427	.	-	0	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	CDS	5245428	5245553	0.64	-	0	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	exon	5245428	5245553	.	-	.	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	intron	5245554	5245695	.	-	.	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	CDS	5245696	5245836	0.69	-	0	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	exon	5245696	5245836	.	-	.	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
Phchi.S4	AUGUSTUS	start_codon	5245834	5245836	.	-	0	transcript_id "Phchi.S4G087200.t1"; gene_id "Phchi.S4G087200"
# This transcript jg706.t2 is derived from g10488.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg707.t1 is derived from g10489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5010581	5012615	.	+	.	Phchi.S6G066600
Phchi.S6	AUGUSTUS	transcript	5010581	5012615	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	start_codon	5010581	5010583	.	+	0	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	CDS	5010581	5012156	0.8	+	0	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	exon	5010581	5012156	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	intron	5012157	5012262	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	CDS	5012263	5012368	0.98	+	2	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	exon	5012263	5012368	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	intron	5012369	5012472	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	CDS	5012473	5012494	0.91	+	1	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	exon	5012473	5012494	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	intron	5012495	5012576	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	CDS	5012577	5012615	0.98	+	0	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	exon	5012577	5012615	.	+	.	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
Phchi.S6	AUGUSTUS	stop_codon	5012616	5012618	.	+	0	transcript_id "Phchi.S6G066600.t1"; gene_id "Phchi.S6G066600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11267.t1 is derived from g15317.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5089078	5091217	.	-	.	Phchi.S4G084900
Phchi.S4	AUGUSTUS	transcript	5089078	5091217	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	stop_codon	5089075	5089077	.	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089078	5089242	0.98	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089078	5089242	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089243	5089382	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089383	5089472	0.99	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089383	5089472	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089473	5089712	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089713	5089759	0.93	-	2	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089713	5089759	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089760	5089862	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089863	5089882	0.99	-	1	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089863	5089882	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089883	5090004	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090005	5090164	1	-	2	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090005	5090164	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090165	5090344	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090345	5090403	1	-	1	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090345	5090403	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090404	5090499	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090500	5090570	1	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090500	5090570	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090571	5090645	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090646	5090708	1	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090646	5090708	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090709	5090854	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090855	5090869	0.96	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090855	5090869	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090870	5090927	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090928	5090972	0.93	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090928	5090972	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090973	5091139	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5091140	5091217	0.43	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5091140	5091217	.	-	.	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	start_codon	5091215	5091217	.	-	0	transcript_id "Phchi.S4G084900.t1"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	transcript	5089078	5091217	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	stop_codon	5089075	5089077	.	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089078	5089242	1	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089078	5089242	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089243	5089382	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089383	5089472	1	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089383	5089472	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089473	5089557	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089558	5089638	1	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089558	5089638	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089639	5089712	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089713	5089759	0.92	-	2	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089713	5089759	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089760	5089862	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5089863	5089882	0.96	-	1	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5089863	5089882	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5089883	5090004	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090005	5090164	1	-	2	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090005	5090164	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090165	5090344	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090345	5090403	1	-	1	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090345	5090403	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090404	5090499	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090500	5090570	1	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090500	5090570	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090571	5090645	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090646	5090708	1	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090646	5090708	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090709	5090854	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090855	5090869	0.99	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090855	5090869	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090870	5090927	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5090928	5090972	0.97	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5090928	5090972	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	intron	5090973	5091157	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	CDS	5091158	5091217	0.24	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	exon	5091158	5091217	.	-	.	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
Phchi.S4	AUGUSTUS	start_codon	5091215	5091217	.	-	0	transcript_id "Phchi.S4G084900.t2"; gene_id "Phchi.S4G084900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg824.t1 is derived from g10606.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5721912	5724506	.	+	.	Phchi.S6G078300
Phchi.S6	AUGUSTUS	transcript	5721912	5723865	.	+	.	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	start_codon	5721912	5721914	.	+	0	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	CDS	5721912	5723705	0.96	+	0	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	exon	5721912	5723705	.	+	.	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	intron	5723706	5723841	.	+	.	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	CDS	5723842	5723865	0.96	+	0	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	exon	5723842	5723865	.	+	.	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	stop_codon	5723866	5723868	.	+	0	transcript_id "Phchi.S6G078300.t1"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	transcript	5721912	5724506	.	+	.	transcript_id "Phchi.S6G078300.t2"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	start_codon	5721912	5721914	.	+	0	transcript_id "Phchi.S6G078300.t2"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	CDS	5721912	5724506	1	+	0	transcript_id "Phchi.S6G078300.t2"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	exon	5721912	5724506	.	+	.	transcript_id "Phchi.S6G078300.t2"; gene_id "Phchi.S6G078300"
Phchi.S6	AUGUSTUS	stop_codon	5724507	5724509	.	+	0	transcript_id "Phchi.S6G078300.t2"; gene_id "Phchi.S6G078300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1701.t1 is derived from g8620.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2583316	2586361	.	-	.	Phchi.S5G031000
Phchi.S5	AUGUSTUS	transcript	2583316	2586361	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	stop_codon	2583313	2583315	.	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2583316	2583476	1	-	2	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2583316	2583476	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2583477	2583558	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2583559	2583687	1	-	2	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2583559	2583687	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2583688	2583805	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2583806	2583937	0.61	-	2	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2583806	2583937	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2583938	2584046	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584047	2584172	0.94	-	2	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584047	2584172	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584173	2584268	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584269	2584394	1	-	2	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584269	2584394	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584395	2584557	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584558	2584650	1	-	2	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584558	2584650	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584651	2584812	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584813	2584954	1	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584813	2584954	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584955	2585101	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585102	2585224	0.99	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585102	2585224	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2585225	2585329	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585330	2585479	1	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585330	2585479	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2585480	2585636	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585637	2585810	0.99	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585637	2585810	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2585811	2585919	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585920	2586066	0.99	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585920	2586066	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2586067	2586268	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2586269	2586361	0.59	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2586269	2586361	.	-	.	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	start_codon	2586359	2586361	.	-	0	transcript_id "Phchi.S5G031000.t1"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	transcript	2583316	2586361	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	stop_codon	2583313	2583315	.	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2583316	2583476	1	-	2	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2583316	2583476	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2583477	2583558	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2583559	2583687	1	-	2	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2583559	2583687	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2583688	2583805	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2583806	2583937	0.55	-	2	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2583806	2583937	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2583938	2584046	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584047	2584172	0.96	-	2	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584047	2584172	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584173	2584268	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584269	2584394	1	-	2	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584269	2584394	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584395	2584557	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584558	2584650	1	-	2	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584558	2584650	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584651	2584812	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2584813	2584957	1	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2584813	2584957	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2584958	2585101	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585102	2585224	1	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585102	2585224	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2585225	2585329	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585330	2585479	1	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585330	2585479	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2585480	2585636	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585637	2585810	0.99	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585637	2585810	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2585811	2585919	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2585920	2586066	0.97	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2585920	2586066	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	intron	2586067	2586268	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	CDS	2586269	2586361	0.5	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	exon	2586269	2586361	.	-	.	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
Phchi.S5	AUGUSTUS	start_codon	2586359	2586361	.	-	0	transcript_id "Phchi.S5G031000.t2"; gene_id "Phchi.S5G031000"
# This transcript jg7991.t2 is derived from g5166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7992.t1 is derived from g5167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32283958	32284746	.	-	.	Phchi.S1G515100
Phchi.S1	AUGUSTUS	transcript	32283958	32284746	.	-	.	transcript_id "Phchi.S1G515100.t1"; gene_id "Phchi.S1G515100"
Phchi.S1	AUGUSTUS	stop_codon	32283955	32283957	.	-	0	transcript_id "Phchi.S1G515100.t1"; gene_id "Phchi.S1G515100"
Phchi.S1	AUGUSTUS	CDS	32283958	32284746	0.93	-	0	transcript_id "Phchi.S1G515100.t1"; gene_id "Phchi.S1G515100"
Phchi.S1	AUGUSTUS	exon	32283958	32284746	.	-	.	transcript_id "Phchi.S1G515100.t1"; gene_id "Phchi.S1G515100"
Phchi.S1	AUGUSTUS	start_codon	32284744	32284746	.	-	0	transcript_id "Phchi.S1G515100.t1"; gene_id "Phchi.S1G515100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12819.t1 is derived from g11284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2551526	2555817	.	+	.	Phchi.S3G013800
Phchi.S3	AUGUSTUS	transcript	2551526	2555817	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	start_codon	2551526	2551528	.	+	0	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2551526	2552228	0.99	+	0	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2551526	2552228	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2552229	2552341	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2552342	2552482	0.8	+	2	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2552342	2552482	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2552483	2552632	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2552633	2552748	0.94	+	2	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2552633	2552748	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2552749	2552823	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2552824	2552975	0.94	+	0	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2552824	2552975	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2552976	2553063	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2553064	2553212	0.94	+	1	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2553064	2553212	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2553213	2553605	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2553606	2553724	1	+	2	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2553606	2553724	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2553725	2553838	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2553839	2553996	1	+	0	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2553839	2553996	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2553997	2554151	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2554152	2554192	0.99	+	1	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2554152	2554192	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2554193	2554287	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2554288	2554407	0.85	+	2	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2554288	2554407	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2554408	2554578	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2554579	2555006	0.41	+	2	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2554579	2555006	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2555007	2555359	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2555360	2555549	0.9	+	0	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2555360	2555549	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	intron	2555550	2555635	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	CDS	2555636	2555817	0.92	+	2	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	exon	2555636	2555817	.	+	.	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
Phchi.S3	AUGUSTUS	stop_codon	2555818	2555820	.	+	0	transcript_id "Phchi.S3G013800.t1"; gene_id "Phchi.S3G013800"
# This transcript jg6829.t2 is derived from g4001.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6830.t1 is derived from g4002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25443872	25444321	.	-	.	Phchi.S1G398900
Phchi.S1	AUGUSTUS	transcript	25443872	25444321	.	-	.	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	stop_codon	25443869	25443871	.	-	0	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	CDS	25443872	25443986	0.62	-	1	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	exon	25443872	25443986	.	-	.	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	intron	25443987	25444067	.	-	.	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	CDS	25444068	25444321	0.6	-	0	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	exon	25444068	25444321	.	-	.	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
Phchi.S1	AUGUSTUS	start_codon	25444319	25444321	.	-	0	transcript_id "Phchi.S1G398900.t1"; gene_id "Phchi.S1G398900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15237.t1 is derived from g13705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17867876	17872819	.	+	.	Phchi.S3G255600
Phchi.S3	AUGUSTUS	transcript	17867876	17872819	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	start_codon	17867876	17867878	.	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17867876	17868065	0.78	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17867876	17868065	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17868066	17868174	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17868175	17868343	0.82	+	2	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17868175	17868343	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17868344	17868523	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17868524	17868608	1	+	1	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17868524	17868608	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17868609	17868711	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17868712	17868762	0.99	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17868712	17868762	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17868763	17868867	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17868868	17869038	0.99	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17868868	17869038	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17869039	17869146	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17869147	17869301	0.92	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17869147	17869301	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17869302	17869402	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17869403	17869511	1	+	1	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17869403	17869511	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17869512	17869685	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17869686	17869785	0.99	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17869686	17869785	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17869786	17869895	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17869896	17869951	1	+	2	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17869896	17869951	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17869952	17870050	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17870051	17870116	1	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17870051	17870116	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17870117	17870343	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17870344	17870426	1	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17870344	17870426	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17870427	17870634	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17870635	17870768	0.98	+	1	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17870635	17870768	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17870769	17870919	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17870920	17871130	1	+	2	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17870920	17871130	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17871131	17871270	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17871271	17871402	0.97	+	1	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17871271	17871402	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17871403	17871514	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17871515	17871575	0.97	+	1	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17871515	17871575	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17871576	17871701	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17871702	17871761	1	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17871702	17871761	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17871762	17871925	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17871926	17871984	1	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17871926	17871984	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17871985	17872095	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17872096	17872183	1	+	1	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17872096	17872183	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17872184	17872262	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17872263	17872385	1	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17872263	17872385	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17872386	17872469	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17872470	17872538	1	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17872470	17872538	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	intron	17872539	17872684	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	CDS	17872685	17872819	0.99	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	exon	17872685	17872819	.	+	.	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
Phchi.S3	AUGUSTUS	stop_codon	17872820	17872822	.	+	0	transcript_id "Phchi.S3G255600.t1"; gene_id "Phchi.S3G255600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4357.t1 is derived from g1526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9986433	9986939	.	-	.	Phchi.S1G151600
Phchi.S1	AUGUSTUS	transcript	9986433	9986939	.	-	.	transcript_id "Phchi.S1G151600.t1"; gene_id "Phchi.S1G151600"
Phchi.S1	AUGUSTUS	stop_codon	9986430	9986432	.	-	0	transcript_id "Phchi.S1G151600.t1"; gene_id "Phchi.S1G151600"
Phchi.S1	AUGUSTUS	CDS	9986433	9986939	0.48	-	0	transcript_id "Phchi.S1G151600.t1"; gene_id "Phchi.S1G151600"
Phchi.S1	AUGUSTUS	exon	9986433	9986939	.	-	.	transcript_id "Phchi.S1G151600.t1"; gene_id "Phchi.S1G151600"
Phchi.S1	AUGUSTUS	start_codon	9986937	9986939	.	-	0	transcript_id "Phchi.S1G151600.t1"; gene_id "Phchi.S1G151600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2208.t1 is derived from g9128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5426563	5427498	.	+	.	Phchi.S5G081700
Phchi.S5	AUGUSTUS	transcript	5426563	5427498	.	+	.	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	start_codon	5426563	5426565	.	+	0	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	CDS	5426563	5427045	0.99	+	0	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	exon	5426563	5427045	.	+	.	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	intron	5427046	5427150	.	+	.	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	CDS	5427151	5427204	1	+	0	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	exon	5427151	5427204	.	+	.	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	intron	5427205	5427363	.	+	.	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	CDS	5427364	5427498	0.94	+	0	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	exon	5427364	5427498	.	+	.	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
Phchi.S5	AUGUSTUS	stop_codon	5427499	5427501	.	+	0	transcript_id "Phchi.S5G081700.t1"; gene_id "Phchi.S5G081700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6840.t1 is derived from g4012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25503252	25504873	.	-	.	Phchi.S1G399900
Phchi.S1	AUGUSTUS	transcript	25503252	25504873	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	stop_codon	25503249	25503251	.	-	0	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25503252	25503404	1	-	0	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25503252	25503404	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	intron	25503405	25503502	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25503503	25503562	1	-	0	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25503503	25503562	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	intron	25503563	25503641	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25503642	25503743	1	-	0	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25503642	25503743	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	intron	25503744	25503831	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25503832	25504178	1	-	2	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25503832	25504178	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	intron	25504179	25504271	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25504272	25504349	1	-	2	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25504272	25504349	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	intron	25504350	25504471	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25504472	25504537	0.78	-	2	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25504472	25504537	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	intron	25504538	25504650	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	CDS	25504651	25504873	0.93	-	0	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	exon	25504651	25504873	.	-	.	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
Phchi.S1	AUGUSTUS	start_codon	25504871	25504873	.	-	0	transcript_id "Phchi.S1G399900.t1"; gene_id "Phchi.S1G399900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11706.t1 is derived from g15757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7772809	7773643	.	+	.	Phchi.S4G128800
Phchi.S4	AUGUSTUS	transcript	7772809	7773643	.	+	.	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	start_codon	7772809	7772811	.	+	0	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	CDS	7772809	7773100	1	+	0	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	exon	7772809	7773100	.	+	.	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	intron	7773101	7773224	.	+	.	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	CDS	7773225	7773643	1	+	2	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	exon	7773225	7773643	.	+	.	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
Phchi.S4	AUGUSTUS	stop_codon	7773644	7773646	.	+	0	transcript_id "Phchi.S4G128800.t1"; gene_id "Phchi.S4G128800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7200.t1 is derived from g4372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27617048	27619288	.	-	.	Phchi.S1G435900
Phchi.S1	AUGUSTUS	transcript	27617048	27619288	.	-	.	transcript_id "Phchi.S1G435900.t1"; gene_id "Phchi.S1G435900"
Phchi.S1	AUGUSTUS	stop_codon	27617045	27617047	.	-	0	transcript_id "Phchi.S1G435900.t1"; gene_id "Phchi.S1G435900"
Phchi.S1	AUGUSTUS	CDS	27617048	27619288	0.99	-	0	transcript_id "Phchi.S1G435900.t1"; gene_id "Phchi.S1G435900"
Phchi.S1	AUGUSTUS	exon	27617048	27619288	.	-	.	transcript_id "Phchi.S1G435900.t1"; gene_id "Phchi.S1G435900"
Phchi.S1	AUGUSTUS	start_codon	27619286	27619288	.	-	0	transcript_id "Phchi.S1G435900.t1"; gene_id "Phchi.S1G435900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14239.t1 is derived from g12706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11695978	11697752	.	+	.	Phchi.S3G155800
Phchi.S3	AUGUSTUS	transcript	11695978	11697752	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	start_codon	11695978	11695980	.	+	0	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	CDS	11695978	11696139	0.76	+	0	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	exon	11695978	11696139	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	intron	11696140	11696231	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	CDS	11696232	11696831	0.52	+	0	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	exon	11696232	11696831	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	intron	11696832	11697020	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	CDS	11697021	11697234	1	+	0	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	exon	11697021	11697234	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	intron	11697235	11697321	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	CDS	11697322	11697752	0.48	+	2	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	exon	11697322	11697752	.	+	.	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
Phchi.S3	AUGUSTUS	stop_codon	11697753	11697755	.	+	0	transcript_id "Phchi.S3G155800.t1"; gene_id "Phchi.S3G155800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3254.t1 is derived from g423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2523595	2524460	.	-	.	Phchi.S1G041300
Phchi.S1	AUGUSTUS	transcript	2523595	2524460	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	stop_codon	2523592	2523594	.	-	0	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	CDS	2523595	2523717	1	-	0	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	exon	2523595	2523717	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	intron	2523718	2523802	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	CDS	2523803	2523871	1	-	0	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	exon	2523803	2523871	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	intron	2523872	2523968	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	CDS	2523969	2524109	0.99	-	0	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	exon	2523969	2524109	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	intron	2524110	2524334	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	CDS	2524335	2524460	0.47	-	0	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	exon	2524335	2524460	.	-	.	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
Phchi.S1	AUGUSTUS	start_codon	2524458	2524460	.	-	0	transcript_id "Phchi.S1G041300.t1"; gene_id "Phchi.S1G041300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11176.t1 is derived from g15226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4501136	4502653	.	+	.	Phchi.S4G075800
Phchi.S4	AUGUSTUS	transcript	4501136	4502653	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	start_codon	4501136	4501138	.	+	0	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	CDS	4501136	4501473	0.51	+	0	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	exon	4501136	4501473	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	intron	4501474	4501681	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	CDS	4501682	4501692	0.53	+	1	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	exon	4501682	4501692	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	intron	4501693	4501805	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	CDS	4501806	4501939	0.51	+	2	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	exon	4501806	4501939	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	intron	4501940	4502207	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	CDS	4502208	4502411	1	+	0	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	exon	4502208	4502411	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	intron	4502412	4502536	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	CDS	4502537	4502653	1	+	0	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	exon	4502537	4502653	.	+	.	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
Phchi.S4	AUGUSTUS	stop_codon	4502654	4502656	.	+	0	transcript_id "Phchi.S4G075800.t1"; gene_id "Phchi.S4G075800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15096.t1 is derived from g13564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16995328	16995750	.	+	.	Phchi.S3G241500
Phchi.S3	AUGUSTUS	transcript	16995328	16995750	.	+	.	transcript_id "Phchi.S3G241500.t1"; gene_id "Phchi.S3G241500"
Phchi.S3	AUGUSTUS	start_codon	16995328	16995330	.	+	0	transcript_id "Phchi.S3G241500.t1"; gene_id "Phchi.S3G241500"
Phchi.S3	AUGUSTUS	CDS	16995328	16995750	0.94	+	0	transcript_id "Phchi.S3G241500.t1"; gene_id "Phchi.S3G241500"
Phchi.S3	AUGUSTUS	exon	16995328	16995750	.	+	.	transcript_id "Phchi.S3G241500.t1"; gene_id "Phchi.S3G241500"
Phchi.S3	AUGUSTUS	stop_codon	16995751	16995753	.	+	0	transcript_id "Phchi.S3G241500.t1"; gene_id "Phchi.S3G241500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5669.t1 is derived from g2839.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18208299	18211021	.	+	.	Phchi.S1G282800
Phchi.S1	AUGUSTUS	transcript	18208299	18211021	.	+	.	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	start_codon	18208299	18208301	.	+	0	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	CDS	18208299	18208707	0.77	+	0	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	exon	18208299	18208707	.	+	.	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	intron	18208708	18208811	.	+	.	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	CDS	18208812	18211021	0.84	+	2	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	exon	18208812	18211021	.	+	.	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	stop_codon	18211022	18211024	.	+	0	transcript_id "Phchi.S1G282800.t1"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	transcript	18208299	18208871	.	+	.	transcript_id "Phchi.S1G282800.t2"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	start_codon	18208299	18208301	.	+	0	transcript_id "Phchi.S1G282800.t2"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	CDS	18208299	18208871	0.9	+	0	transcript_id "Phchi.S1G282800.t2"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	exon	18208299	18208871	.	+	.	transcript_id "Phchi.S1G282800.t2"; gene_id "Phchi.S1G282800"
Phchi.S1	AUGUSTUS	stop_codon	18208872	18208874	.	+	0	transcript_id "Phchi.S1G282800.t2"; gene_id "Phchi.S1G282800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1225.t1 is derived from g11008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8470491	8473440	.	+	.	Phchi.S6G118400
Phchi.S6	AUGUSTUS	transcript	8470491	8473440	.	+	.	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	start_codon	8470491	8470493	.	+	0	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	CDS	8470491	8472839	1	+	0	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	exon	8470491	8472839	.	+	.	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	intron	8472840	8473015	.	+	.	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	CDS	8473016	8473104	1	+	0	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	exon	8473016	8473104	.	+	.	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	intron	8473105	8473223	.	+	.	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	CDS	8473224	8473440	1	+	1	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	exon	8473224	8473440	.	+	.	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
Phchi.S6	AUGUSTUS	stop_codon	8473441	8473443	.	+	0	transcript_id "Phchi.S6G118400.t1"; gene_id "Phchi.S6G118400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8816.t1 is derived from g5991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38119397	38120191	.	+	.	Phchi.S1G597500
Phchi.S1	AUGUSTUS	transcript	38119397	38120191	.	+	.	transcript_id "Phchi.S1G597500.t1"; gene_id "Phchi.S1G597500"
Phchi.S1	AUGUSTUS	start_codon	38119397	38119399	.	+	0	transcript_id "Phchi.S1G597500.t1"; gene_id "Phchi.S1G597500"
Phchi.S1	AUGUSTUS	CDS	38119397	38120191	0.7	+	0	transcript_id "Phchi.S1G597500.t1"; gene_id "Phchi.S1G597500"
Phchi.S1	AUGUSTUS	exon	38119397	38120191	.	+	.	transcript_id "Phchi.S1G597500.t1"; gene_id "Phchi.S1G597500"
Phchi.S1	AUGUSTUS	stop_codon	38120192	38120194	.	+	0	transcript_id "Phchi.S1G597500.t1"; gene_id "Phchi.S1G597500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15157.t1 is derived from g13625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17301338	17302302	.	+	.	Phchi.S3G247600
Phchi.S3	AUGUSTUS	transcript	17301338	17302302	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	start_codon	17301338	17301340	.	+	0	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	CDS	17301338	17301340	1	+	0	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	exon	17301338	17301340	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	intron	17301341	17301575	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	CDS	17301576	17301677	1	+	0	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	exon	17301576	17301677	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	intron	17301678	17301813	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	CDS	17301814	17301943	1	+	0	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	exon	17301814	17301943	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	intron	17301944	17302046	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	CDS	17302047	17302159	1	+	2	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	exon	17302047	17302159	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	intron	17302160	17302251	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	CDS	17302252	17302302	0.99	+	0	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	exon	17302252	17302302	.	+	.	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
Phchi.S3	AUGUSTUS	stop_codon	17302303	17302305	.	+	0	transcript_id "Phchi.S3G247600.t1"; gene_id "Phchi.S3G247600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2087.t1 is derived from g9007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4806402	4807868	.	+	.	Phchi.S5G069600
Phchi.S5	AUGUSTUS	transcript	4806402	4807868	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	start_codon	4806402	4806404	.	+	0	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	CDS	4806402	4806763	0.94	+	0	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	exon	4806402	4806763	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	intron	4806764	4806924	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	CDS	4806925	4806994	1	+	1	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	exon	4806925	4806994	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	intron	4806995	4807079	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	CDS	4807080	4807251	1	+	0	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	exon	4807080	4807251	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	intron	4807252	4807372	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	CDS	4807373	4807516	1	+	2	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	exon	4807373	4807516	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	intron	4807517	4807611	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	CDS	4807612	4807868	0.56	+	2	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	exon	4807612	4807868	.	+	.	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
Phchi.S5	AUGUSTUS	stop_codon	4807869	4807871	.	+	0	transcript_id "Phchi.S5G069600.t1"; gene_id "Phchi.S5G069600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6187.t1 is derived from g3358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21377811	21379315	.	-	.	Phchi.S1G334600
Phchi.S1	AUGUSTUS	transcript	21377811	21379315	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	stop_codon	21377808	21377810	.	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21377811	21377846	1	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21377811	21377846	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21377847	21377992	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21377993	21378072	1	-	2	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21377993	21378072	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21378073	21378159	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21378160	21378204	1	-	2	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21378160	21378204	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21378205	21378397	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21378398	21378449	1	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21378398	21378449	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21378450	21378533	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21378534	21378596	1	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21378534	21378596	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21378597	21378686	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21378687	21378794	1	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21378687	21378794	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21378795	21378877	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21378878	21378916	1	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21378878	21378916	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21378917	21379008	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21379009	21379125	1	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21379009	21379125	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	intron	21379126	21379210	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	CDS	21379211	21379315	0.41	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	exon	21379211	21379315	.	-	.	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
Phchi.S1	AUGUSTUS	start_codon	21379313	21379315	.	-	0	transcript_id "Phchi.S1G334600.t1"; gene_id "Phchi.S1G334600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12123.t1 is derived from g7799.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3967024	3969214	.	-	.	Phchi.S2G020300
Phchi.S2	AUGUSTUS	transcript	3967024	3969214	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	stop_codon	3967021	3967023	.	-	0	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3967024	3967208	1	-	2	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3967024	3967208	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3967209	3967313	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3967314	3967818	1	-	0	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3967314	3967818	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3967819	3967900	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3967901	3968053	1	-	0	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3967901	3968053	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968054	3968181	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968182	3968465	1	-	2	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968182	3968465	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968466	3968596	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968597	3968689	1	-	2	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968597	3968689	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968690	3968778	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968779	3968861	1	-	1	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968779	3968861	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968862	3968942	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968943	3969081	1	-	2	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968943	3969081	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3969082	3969171	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3969172	3969214	0.59	-	0	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3969172	3969214	.	-	.	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	start_codon	3969212	3969214	.	-	0	transcript_id "Phchi.S2G020300.t1"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	transcript	3967024	3969214	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	stop_codon	3967021	3967023	.	-	0	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3967024	3967208	1	-	2	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3967024	3967208	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3967209	3967313	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3967314	3967818	0.98	-	0	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3967314	3967818	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3967819	3967900	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3967901	3968053	1	-	0	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3967901	3968053	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968054	3968181	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968182	3968480	0.55	-	2	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968182	3968480	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968481	3968596	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968597	3968689	0.98	-	2	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968597	3968689	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968690	3968778	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968779	3968861	1	-	1	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968779	3968861	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3968862	3968942	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3968943	3969081	1	-	2	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3968943	3969081	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	intron	3969082	3969171	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	CDS	3969172	3969214	0.62	-	0	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	exon	3969172	3969214	.	-	.	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
Phchi.S2	AUGUSTUS	start_codon	3969212	3969214	.	-	0	transcript_id "Phchi.S2G020300.t2"; gene_id "Phchi.S2G020300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15515.t1 is derived from g13984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19635331	19637352	.	+	.	Phchi.S3G283400
Phchi.S3	AUGUSTUS	transcript	19635331	19637352	.	+	.	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	start_codon	19635331	19635333	.	+	0	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	CDS	19635331	19636172	0.57	+	0	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	exon	19635331	19636172	.	+	.	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	intron	19636173	19636258	.	+	.	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	CDS	19636259	19636790	0.98	+	1	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	exon	19636259	19636790	.	+	.	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	intron	19636791	19636902	.	+	.	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	CDS	19636903	19637352	1	+	0	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	exon	19636903	19637352	.	+	.	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
Phchi.S3	AUGUSTUS	stop_codon	19637353	19637355	.	+	0	transcript_id "Phchi.S3G283400.t1"; gene_id "Phchi.S3G283400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15450.t1 is derived from g13918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19222838	19227384	.	+	.	Phchi.S3G276900
Phchi.S3	AUGUSTUS	transcript	19222838	19227384	.	+	.	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	start_codon	19222838	19222840	.	+	0	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	CDS	19222838	19224769	0.74	+	0	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	exon	19222838	19224769	.	+	.	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	intron	19224770	19224885	.	+	.	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	CDS	19224886	19227384	1	+	0	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	exon	19224886	19227384	.	+	.	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
Phchi.S3	AUGUSTUS	stop_codon	19227385	19227387	.	+	0	transcript_id "Phchi.S3G276900.t1"; gene_id "Phchi.S3G276900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10913.t1 is derived from g14963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2902072	2903523	.	+	.	Phchi.S4G049500
Phchi.S4	AUGUSTUS	transcript	2902072	2903523	.	+	.	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	start_codon	2902072	2902074	.	+	0	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	CDS	2902072	2902484	0.84	+	0	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	exon	2902072	2902484	.	+	.	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	intron	2902485	2902613	.	+	.	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	CDS	2902614	2903523	1	+	1	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	exon	2902614	2903523	.	+	.	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
Phchi.S4	AUGUSTUS	stop_codon	2903524	2903526	.	+	0	transcript_id "Phchi.S4G049500.t1"; gene_id "Phchi.S4G049500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1632.t1 is derived from g8551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2103945	2106618	.	-	.	Phchi.S5G024100
Phchi.S5	AUGUSTUS	transcript	2103945	2106618	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	stop_codon	2103942	2103944	.	-	0	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2103945	2104076	0.88	-	0	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2103945	2104076	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104077	2104494	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2104495	2104539	1	-	0	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2104495	2104539	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104540	2104689	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2104690	2104756	1	-	1	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2104690	2104756	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104757	2104901	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2104902	2104949	0.7	-	1	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2104902	2104949	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104950	2105228	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2105229	2105607	0.6	-	2	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2105229	2105607	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2105608	2105720	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2105721	2106618	0.59	-	0	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2105721	2106618	.	-	.	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	start_codon	2106616	2106618	.	-	0	transcript_id "Phchi.S5G024100.t1"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	transcript	2103945	2106618	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	stop_codon	2103942	2103944	.	-	0	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2103945	2104076	0.91	-	0	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2103945	2104076	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104077	2104494	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2104495	2104539	1	-	0	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2104495	2104539	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104540	2104689	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2104690	2104805	0.97	-	2	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2104690	2104805	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104806	2104901	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2104902	2104949	0.74	-	2	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2104902	2104949	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2104950	2105053	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2105054	2105095	0.29	-	2	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2105054	2105095	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2105096	2105202	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2105203	2105607	0.46	-	2	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2105203	2105607	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	intron	2105608	2105720	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	CDS	2105721	2106618	0.5	-	0	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	exon	2105721	2106618	.	-	.	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
Phchi.S5	AUGUSTUS	start_codon	2106616	2106618	.	-	0	transcript_id "Phchi.S5G024100.t2"; gene_id "Phchi.S5G024100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14177.t1 is derived from g12644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11301563	11304765	.	-	.	Phchi.S3G149600
Phchi.S3	AUGUSTUS	transcript	11301563	11304765	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	stop_codon	11301560	11301562	.	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11301563	11301634	0.97	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11301563	11301634	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11301635	11301722	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11301723	11301781	0.97	-	2	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11301723	11301781	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11301782	11301890	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11301891	11301927	0.97	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11301891	11301927	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11301928	11302068	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11302069	11302111	1	-	1	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11302069	11302111	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11302112	11302225	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11302226	11302317	1	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11302226	11302317	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11302318	11302413	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11302414	11302482	1	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11302414	11302482	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11302483	11302575	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11302576	11302620	1	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11302576	11302620	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11302621	11302719	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11302720	11302828	1	-	1	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11302720	11302828	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11302829	11303002	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11303003	11303103	1	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11303003	11303103	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11303104	11303201	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11303202	11303294	1	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11303202	11303294	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11303295	11303394	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11303395	11303455	1	-	1	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11303395	11303455	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11303456	11303599	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11303600	11303703	1	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11303600	11303703	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11303704	11304231	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11304232	11304383	1	-	2	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11304232	11304383	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	intron	11304384	11304620	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	CDS	11304621	11304765	0.99	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	exon	11304621	11304765	.	-	.	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
Phchi.S3	AUGUSTUS	start_codon	11304763	11304765	.	-	0	transcript_id "Phchi.S3G149600.t1"; gene_id "Phchi.S3G149600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3683.t1 is derived from g852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5162542	5162880	.	-	.	Phchi.S1G084200
Phchi.S1	AUGUSTUS	transcript	5162542	5162880	.	-	.	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	stop_codon	5162539	5162541	.	-	0	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	CDS	5162542	5162656	0.9	-	1	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	exon	5162542	5162656	.	-	.	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	intron	5162657	5162764	.	-	.	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	CDS	5162765	5162880	0.88	-	0	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	exon	5162765	5162880	.	-	.	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
Phchi.S1	AUGUSTUS	start_codon	5162878	5162880	.	-	0	transcript_id "Phchi.S1G084200.t1"; gene_id "Phchi.S1G084200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13000.t1 is derived from g11465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3580591	3581480	.	-	.	Phchi.S3G031900
Phchi.S3	AUGUSTUS	transcript	3580591	3581480	.	-	.	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	stop_codon	3580588	3580590	.	-	0	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	CDS	3580591	3581203	0.73	-	1	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	exon	3580591	3581203	.	-	.	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	intron	3581204	3581292	.	-	.	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	CDS	3581293	3581480	0.9	-	0	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	exon	3581293	3581480	.	-	.	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
Phchi.S3	AUGUSTUS	start_codon	3581478	3581480	.	-	0	transcript_id "Phchi.S3G031900.t1"; gene_id "Phchi.S3G031900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1496.t1 is derived from g8415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1203445	1203737	.	+	.	Phchi.S5G010500
Phchi.S5	AUGUSTUS	transcript	1203445	1203737	.	+	.	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	start_codon	1203445	1203447	.	+	0	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	CDS	1203445	1203583	0.62	+	0	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	exon	1203445	1203583	.	+	.	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	intron	1203584	1203678	.	+	.	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	CDS	1203679	1203737	0.62	+	2	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	exon	1203679	1203737	.	+	.	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
Phchi.S5	AUGUSTUS	stop_codon	1203738	1203740	.	+	0	transcript_id "Phchi.S5G010500.t1"; gene_id "Phchi.S5G010500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6405.t1 is derived from g3577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22799750	22802775	.	+	.	Phchi.S1G356400
Phchi.S1	AUGUSTUS	transcript	22799750	22802775	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	start_codon	22799750	22799752	.	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22799750	22799807	0.51	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22799750	22799807	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22799808	22799947	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22799948	22800100	0.51	+	2	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22799948	22800100	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22800101	22800183	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22800184	22800281	1	+	2	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22800184	22800281	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22800282	22800422	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22800423	22800465	1	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22800423	22800465	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22800466	22800547	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22800548	22800633	0.56	+	2	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22800548	22800633	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22800634	22800791	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22800792	22800831	0.55	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22800792	22800831	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22800832	22800923	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22800924	22801753	0.52	+	2	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22800924	22801753	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22801754	22801837	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22801838	22802005	0.95	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22801838	22802005	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22802006	22802211	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22802212	22802236	0.99	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22802212	22802236	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22802237	22802492	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22802493	22802606	1	+	2	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22802493	22802606	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	intron	22802607	22802698	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	CDS	22802699	22802775	1	+	2	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	exon	22802699	22802775	.	+	.	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
Phchi.S1	AUGUSTUS	stop_codon	22802776	22802778	.	+	0	transcript_id "Phchi.S1G356400.t1"; gene_id "Phchi.S1G356400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14441.t1 is derived from g12909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12843646	12847102	.	-	.	Phchi.S3G176000
Phchi.S3	AUGUSTUS	transcript	12843646	12847102	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	stop_codon	12843643	12843645	.	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12843646	12843727	1	-	1	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12843646	12843727	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12843728	12843811	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12843812	12843935	1	-	2	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12843812	12843935	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12843936	12844008	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12844009	12844057	1	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12844009	12844057	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12844058	12844145	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12844146	12844211	1	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12844146	12844211	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12844212	12844289	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12844290	12844655	0.93	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12844290	12844655	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12844656	12844762	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12844763	12844921	0.99	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12844763	12844921	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12844922	12845041	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12845042	12845333	1	-	1	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12845042	12845333	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12845334	12845470	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12845471	12845817	1	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12845471	12845817	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12845818	12845964	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12845965	12846162	1	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12845965	12846162	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12846163	12846275	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12846276	12846559	1	-	2	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12846276	12846559	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	intron	12846560	12846648	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	CDS	12846649	12847102	0.63	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	exon	12846649	12847102	.	-	.	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
Phchi.S3	AUGUSTUS	start_codon	12847100	12847102	.	-	0	transcript_id "Phchi.S3G176000.t1"; gene_id "Phchi.S3G176000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1195.t1 is derived from g10978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8368736	8370857	.	+	.	Phchi.S6G115400
Phchi.S6	AUGUSTUS	transcript	8368736	8370857	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	start_codon	8368736	8368738	.	+	0	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	CDS	8368736	8368939	0.48	+	0	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	exon	8368736	8368939	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	intron	8368940	8369125	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	CDS	8369126	8369194	0.99	+	0	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	exon	8369126	8369194	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	intron	8369195	8369314	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	CDS	8369315	8369909	1	+	0	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	exon	8369315	8369909	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	intron	8369910	8370007	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	CDS	8370008	8370149	0.93	+	2	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	exon	8370008	8370149	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	intron	8370150	8370244	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	CDS	8370245	8370452	0.6	+	1	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	exon	8370245	8370452	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	intron	8370453	8370557	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	CDS	8370558	8370857	0.57	+	0	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	exon	8370558	8370857	.	+	.	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
Phchi.S6	AUGUSTUS	stop_codon	8370858	8370860	.	+	0	transcript_id "Phchi.S6G115400.t1"; gene_id "Phchi.S6G115400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14676.t1 is derived from g13144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14129509	14132214	.	+	.	Phchi.S3G199500
Phchi.S3	AUGUSTUS	transcript	14129509	14132214	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	start_codon	14129509	14129511	.	+	0	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	CDS	14129509	14129560	0.76	+	0	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	exon	14129509	14129560	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	intron	14129561	14129688	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	CDS	14129689	14131021	0.99	+	2	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	exon	14129689	14131021	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	intron	14131022	14131595	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	CDS	14131596	14131763	0.67	+	1	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	exon	14131596	14131763	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	intron	14131764	14131897	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	CDS	14131898	14131984	0.72	+	1	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	exon	14131898	14131984	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	intron	14131985	14132081	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	CDS	14132082	14132214	0.82	+	1	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	exon	14132082	14132214	.	+	.	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
Phchi.S3	AUGUSTUS	stop_codon	14132215	14132217	.	+	0	transcript_id "Phchi.S3G199500.t1"; gene_id "Phchi.S3G199500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1359.t1 is derived from g15995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C81	AUGUSTUS	gene	2462	3551	.	-	.	Phchi.C81G000100
Phchi.C81	AUGUSTUS	transcript	2462	3551	.	-	.	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	stop_codon	2459	2461	.	-	0	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	CDS	2462	2871	0.52	-	2	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	exon	2462	2871	.	-	.	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	intron	2872	3054	.	-	.	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	CDS	3055	3142	0.68	-	0	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	exon	3055	3142	.	-	.	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	intron	3143	3368	.	-	.	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	CDS	3369	3551	0.59	-	0	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	exon	3369	3551	.	-	.	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
Phchi.C81	AUGUSTUS	start_codon	3549	3551	.	-	0	transcript_id "Phchi.C81G000100.t1"; gene_id "Phchi.C81G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg269.t1 is derived from g10051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1920696	1921257	.	-	.	Phchi.S6G022800
Phchi.S6	AUGUSTUS	transcript	1920696	1921257	.	-	.	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	stop_codon	1920693	1920695	.	-	0	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	CDS	1920696	1921079	1	-	0	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	exon	1920696	1921079	.	-	.	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	intron	1921080	1921185	.	-	.	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	CDS	1921186	1921257	0.94	-	0	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	exon	1921186	1921257	.	-	.	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
Phchi.S6	AUGUSTUS	start_codon	1921255	1921257	.	-	0	transcript_id "Phchi.S6G022800.t1"; gene_id "Phchi.S6G022800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2656.t1 is derived from g9576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8053529	8055870	.	+	.	Phchi.S5G126500
Phchi.S5	AUGUSTUS	transcript	8053529	8055870	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	start_codon	8053529	8053531	.	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8053529	8053702	0.89	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8053529	8053702	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8053703	8053828	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8053829	8054056	0.82	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8053829	8054056	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8054057	8054145	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8054146	8054320	0.73	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8054146	8054320	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8054321	8054448	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8054449	8054651	0.77	+	2	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8054449	8054651	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8054652	8054759	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8054760	8054887	0.98	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8054760	8054887	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8054888	8054970	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8054971	8055076	1	+	1	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8054971	8055076	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8055077	8055162	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8055163	8055243	0.81	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8055163	8055243	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8055244	8055348	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8055349	8055459	0.87	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8055349	8055459	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8055460	8055534	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8055535	8055678	0.55	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8055535	8055678	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	intron	8055679	8055786	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	CDS	8055787	8055870	0.78	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	exon	8055787	8055870	.	+	.	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
Phchi.S5	AUGUSTUS	stop_codon	8055871	8055873	.	+	0	transcript_id "Phchi.S5G126500.t1"; gene_id "Phchi.S5G126500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4129.t1 is derived from g1298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8396360	8397209	.	+	.	Phchi.S1G128800
Phchi.S1	AUGUSTUS	transcript	8396360	8397209	.	+	.	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	start_codon	8396360	8396362	.	+	0	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	CDS	8396360	8396607	0.75	+	0	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	exon	8396360	8396607	.	+	.	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	intron	8396608	8396719	.	+	.	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	CDS	8396720	8396766	0.88	+	1	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	exon	8396720	8396766	.	+	.	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	intron	8396767	8396934	.	+	.	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	CDS	8396935	8397209	0.99	+	2	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	exon	8396935	8397209	.	+	.	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
Phchi.S1	AUGUSTUS	stop_codon	8397210	8397212	.	+	0	transcript_id "Phchi.S1G128800.t1"; gene_id "Phchi.S1G128800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12845.t1 is derived from g11310.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2667021	2677405	.	-	.	Phchi.S3G016400
Phchi.S3	AUGUSTUS	transcript	2667021	2677405	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	stop_codon	2667018	2667020	.	-	0	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667021	2667302	1	-	0	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667021	2667302	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667303	2667392	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667393	2667494	1	-	0	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667393	2667494	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667495	2667565	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667566	2667639	0.62	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667566	2667639	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667640	2667857	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667858	2668008	0.99	-	0	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667858	2668008	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668009	2668120	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668121	2668359	0.99	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668121	2668359	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668360	2668456	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668457	2668671	0.97	-	1	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668457	2668671	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668672	2668921	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668922	2669158	0.99	-	1	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668922	2669158	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669159	2669235	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669236	2669380	0.95	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669236	2669380	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669381	2669492	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669493	2669813	0.9	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669493	2669813	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669814	2669906	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669907	2670218	0.95	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669907	2670218	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2670219	2670362	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2670363	2670686	0.91	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2670363	2670686	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2670687	2670771	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2670772	2671083	0.98	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2670772	2671083	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671084	2671178	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2671179	2671517	0.91	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2671179	2671517	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671518	2671621	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2671622	2671972	0.91	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2671622	2671972	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671973	2672070	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672071	2672373	1	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672071	2672373	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2672374	2672457	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672458	2672505	1	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672458	2672505	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2672506	2672666	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672667	2673011	0.99	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672667	2673011	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673012	2673175	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2673176	2673538	1	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2673176	2673538	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673539	2673633	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2673634	2673972	0.61	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2673634	2673972	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673973	2674102	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674103	2674465	0.92	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674103	2674465	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2674466	2674571	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674572	2674688	0.55	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674572	2674688	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2674689	2674847	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674848	2675012	0.49	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674848	2675012	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675013	2675232	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2675233	2675583	0.31	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2675233	2675583	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675584	2675675	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2675676	2675960	0.62	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2675676	2675960	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675961	2676114	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2676115	2676471	0.96	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2676115	2676471	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2676472	2676603	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2676604	2677278	0.95	-	2	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2676604	2677278	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2677279	2677377	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2677378	2677405	0.77	-	0	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2677378	2677405	.	-	.	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	start_codon	2677403	2677405	.	-	0	transcript_id "Phchi.S3G016400.t1"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	transcript	2667021	2677405	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	stop_codon	2667018	2667020	.	-	0	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667021	2667302	1	-	0	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667021	2667302	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667303	2667392	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667393	2667494	1	-	0	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667393	2667494	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667495	2667565	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667566	2667753	0.66	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667566	2667753	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667754	2667857	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667858	2668008	0.98	-	0	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667858	2668008	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668009	2668120	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668121	2668359	1	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668121	2668359	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668360	2668456	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668457	2668671	0.93	-	1	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668457	2668671	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668672	2668921	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668922	2669158	1	-	1	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668922	2669158	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669159	2669235	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669236	2669380	0.93	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669236	2669380	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669381	2669492	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669493	2669813	0.94	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669493	2669813	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669814	2669906	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669907	2670218	1	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669907	2670218	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2670219	2670362	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2670363	2670686	0.92	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2670363	2670686	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2670687	2670771	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2670772	2671083	0.98	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2670772	2671083	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671084	2671178	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2671179	2671517	0.89	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2671179	2671517	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671518	2671621	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2671622	2671972	0.92	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2671622	2671972	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671973	2672070	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672071	2672373	1	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672071	2672373	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2672374	2672457	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672458	2672505	1	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672458	2672505	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2672506	2672666	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672667	2673011	0.98	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672667	2673011	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673012	2673175	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2673176	2673538	1	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2673176	2673538	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673539	2673633	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2673634	2673972	0.67	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2673634	2673972	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673973	2674102	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674103	2674465	0.95	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674103	2674465	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2674466	2674571	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674572	2674688	0.48	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674572	2674688	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2674689	2674847	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674848	2675012	0.52	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674848	2675012	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675013	2675232	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2675233	2675583	0.28	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2675233	2675583	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675584	2675675	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2675676	2675960	0.57	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2675676	2675960	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675961	2676114	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2676115	2676471	0.99	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2676115	2676471	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2676472	2676705	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2676706	2677278	0.93	-	2	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2676706	2677278	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2677279	2677377	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2677378	2677405	0.75	-	0	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2677378	2677405	.	-	.	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	start_codon	2677403	2677405	.	-	0	transcript_id "Phchi.S3G016400.t2"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	transcript	2667021	2677405	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	stop_codon	2667018	2667020	.	-	0	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667021	2667302	1	-	0	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667021	2667302	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667303	2667392	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667393	2667494	1	-	0	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667393	2667494	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667495	2667565	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667566	2667639	0.59	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667566	2667639	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2667640	2667857	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2667858	2668008	0.99	-	0	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2667858	2668008	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668009	2668120	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668121	2668359	0.99	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668121	2668359	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668360	2668456	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668457	2668671	0.97	-	1	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668457	2668671	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2668672	2668921	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2668922	2669158	1	-	1	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2668922	2669158	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669159	2669235	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669236	2669380	0.93	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669236	2669380	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669381	2669492	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669493	2669813	0.95	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669493	2669813	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2669814	2669906	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2669907	2670218	0.96	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2669907	2670218	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2670219	2670362	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2670363	2670686	0.9	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2670363	2670686	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2670687	2670771	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2670772	2671083	0.99	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2670772	2671083	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671084	2671178	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2671179	2671517	0.83	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2671179	2671517	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671518	2671621	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2671622	2671972	0.89	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2671622	2671972	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2671973	2672070	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672071	2672373	1	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672071	2672373	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2672374	2672457	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672458	2672505	1	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672458	2672505	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2672506	2672666	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2672667	2673011	1	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2672667	2673011	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673012	2673175	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2673176	2673538	1	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2673176	2673538	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673539	2673633	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2673634	2673972	0.64	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2673634	2673972	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2673973	2674102	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674103	2674465	0.95	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674103	2674465	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2674466	2674571	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674572	2674688	0.54	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674572	2674688	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2674689	2674847	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2674848	2675012	0.46	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2674848	2675012	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675013	2675232	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2675233	2675583	0.24	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2675233	2675583	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675584	2675675	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2675676	2675960	0.62	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2675676	2675960	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2675961	2676114	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2676115	2676471	1	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2676115	2676471	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2676472	2676705	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2676706	2677278	0.96	-	2	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2676706	2677278	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	intron	2677279	2677377	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	CDS	2677378	2677405	0.72	-	0	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	exon	2677378	2677405	.	-	.	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
Phchi.S3	AUGUSTUS	start_codon	2677403	2677405	.	-	0	transcript_id "Phchi.S3G016400.t3"; gene_id "Phchi.S3G016400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2717.t1 is derived from g9637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8330470	8332343	.	-	.	Phchi.S5G132600
Phchi.S5	AUGUSTUS	transcript	8330470	8332343	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	stop_codon	8330467	8330469	.	-	0	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	CDS	8330470	8330707	1	-	1	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	exon	8330470	8330707	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	intron	8330708	8330836	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	CDS	8330837	8331054	1	-	0	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	exon	8330837	8331054	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	intron	8331055	8331143	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	CDS	8331144	8331629	0.91	-	0	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	exon	8331144	8331629	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	intron	8331630	8331702	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	CDS	8331703	8331887	1	-	2	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	exon	8331703	8331887	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	intron	8331888	8332003	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	CDS	8332004	8332343	0.21	-	0	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	exon	8332004	8332343	.	-	.	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
Phchi.S5	AUGUSTUS	start_codon	8332341	8332343	.	-	0	transcript_id "Phchi.S5G132600.t1"; gene_id "Phchi.S5G132600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1375.t1 is derived from g11134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C13	AUGUSTUS	gene	58460	59608	.	-	.	Phchi.C13G000200
Phchi.C13	AUGUSTUS	transcript	58460	59608	.	-	.	transcript_id "Phchi.C13G000200.t1"; gene_id "Phchi.C13G000200"
Phchi.C13	AUGUSTUS	stop_codon	58457	58459	.	-	0	transcript_id "Phchi.C13G000200.t1"; gene_id "Phchi.C13G000200"
Phchi.C13	AUGUSTUS	CDS	58460	59608	1	-	0	transcript_id "Phchi.C13G000200.t1"; gene_id "Phchi.C13G000200"
Phchi.C13	AUGUSTUS	exon	58460	59608	.	-	.	transcript_id "Phchi.C13G000200.t1"; gene_id "Phchi.C13G000200"
Phchi.C13	AUGUSTUS	start_codon	59606	59608	.	-	0	transcript_id "Phchi.C13G000200.t1"; gene_id "Phchi.C13G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7306.t1 is derived from g4478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28429278	28432459	.	+	.	Phchi.S1G446500
Phchi.S1	AUGUSTUS	transcript	28429278	28432459	.	+	.	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	start_codon	28429278	28429280	.	+	0	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	CDS	28429278	28429673	0.96	+	0	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	exon	28429278	28429673	.	+	.	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	intron	28429674	28429753	.	+	.	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	CDS	28429754	28432459	0.9	+	0	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	exon	28429754	28432459	.	+	.	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	stop_codon	28432460	28432462	.	+	0	transcript_id "Phchi.S1G446500.t1"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	transcript	28429991	28432459	.	+	.	transcript_id "Phchi.S1G446500.t2"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	start_codon	28429991	28429993	.	+	0	transcript_id "Phchi.S1G446500.t2"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	CDS	28429991	28432459	0.5	+	0	transcript_id "Phchi.S1G446500.t2"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	exon	28429991	28432459	.	+	.	transcript_id "Phchi.S1G446500.t2"; gene_id "Phchi.S1G446500"
Phchi.S1	AUGUSTUS	stop_codon	28432460	28432462	.	+	0	transcript_id "Phchi.S1G446500.t2"; gene_id "Phchi.S1G446500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2733.t1 is derived from g9653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8490086	8491465	.	+	.	Phchi.S5G134200
Phchi.S5	AUGUSTUS	transcript	8490086	8491465	.	+	.	transcript_id "Phchi.S5G134200.t1"; gene_id "Phchi.S5G134200"
Phchi.S5	AUGUSTUS	start_codon	8490086	8490088	.	+	0	transcript_id "Phchi.S5G134200.t1"; gene_id "Phchi.S5G134200"
Phchi.S5	AUGUSTUS	CDS	8490086	8491465	0.97	+	0	transcript_id "Phchi.S5G134200.t1"; gene_id "Phchi.S5G134200"
Phchi.S5	AUGUSTUS	exon	8490086	8491465	.	+	.	transcript_id "Phchi.S5G134200.t1"; gene_id "Phchi.S5G134200"
Phchi.S5	AUGUSTUS	stop_codon	8491466	8491468	.	+	0	transcript_id "Phchi.S5G134200.t1"; gene_id "Phchi.S5G134200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8316.t1 is derived from g5491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35255350	35257433	.	+	.	Phchi.S1G547500
Phchi.S1	AUGUSTUS	transcript	35255350	35257433	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	start_codon	35255350	35255352	.	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35255350	35255472	0.58	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35255350	35255472	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35255473	35255611	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35255612	35255836	1	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35255612	35255836	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35255837	35255932	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35255933	35256124	1	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35255933	35256124	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35256125	35256269	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35256270	35256461	1	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35256270	35256461	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35256462	35256538	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35256539	35256657	1	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35256539	35256657	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35256658	35256744	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35256745	35256832	1	+	1	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35256745	35256832	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35256833	35256941	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35256942	35257061	0.81	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35256942	35257061	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35257062	35257140	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35257141	35257281	1	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35257141	35257281	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	intron	35257282	35257358	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	CDS	35257359	35257433	1	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	exon	35257359	35257433	.	+	.	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
Phchi.S1	AUGUSTUS	stop_codon	35257434	35257436	.	+	0	transcript_id "Phchi.S1G547500.t1"; gene_id "Phchi.S1G547500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11994.t1 is derived from g7669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	430742	435453	.	-	.	Phchi.S2G007400
Phchi.S2	AUGUSTUS	transcript	430742	435453	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	stop_codon	430739	430741	.	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	430742	430772	0.92	-	1	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	430742	430772	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	430773	430854	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	430855	430992	1	-	1	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	430855	430992	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	430993	431104	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	431105	431214	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	431105	431214	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	431215	431314	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	431315	431344	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	431315	431344	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	431345	431450	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	431451	431516	0.98	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	431451	431516	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	431517	431685	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	431686	431765	1	-	2	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	431686	431765	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	431766	431866	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	431867	432005	0.95	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	431867	432005	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	432006	432104	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	432105	432185	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	432105	432185	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	432186	432258	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	432259	432294	0.89	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	432259	432294	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	432295	432405	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	432406	432531	0.66	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	432406	432531	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	432532	432633	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	432634	432672	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	432634	432672	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	432673	433476	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	433477	433557	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	433477	433557	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	433558	433855	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	433856	433930	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	433856	433930	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	433931	434091	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	434092	434238	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	434092	434238	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	434239	434317	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	434318	434452	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	434318	434452	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	434453	434699	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	434700	434828	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	434700	434828	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	434829	434933	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	434934	435035	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	434934	435035	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	intron	435036	435240	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	CDS	435241	435453	1	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	exon	435241	435453	.	-	.	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
Phchi.S2	AUGUSTUS	start_codon	435451	435453	.	-	0	transcript_id "Phchi.S2G007400.t1"; gene_id "Phchi.S2G007400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10145.t1 is derived from g7321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45979644	45979961	.	-	.	Phchi.S1G730400
Phchi.S1	AUGUSTUS	transcript	45979644	45979961	.	-	.	transcript_id "Phchi.S1G730400.t1"; gene_id "Phchi.S1G730400"
Phchi.S1	AUGUSTUS	stop_codon	45979641	45979643	.	-	0	transcript_id "Phchi.S1G730400.t1"; gene_id "Phchi.S1G730400"
Phchi.S1	AUGUSTUS	CDS	45979644	45979961	0.96	-	0	transcript_id "Phchi.S1G730400.t1"; gene_id "Phchi.S1G730400"
Phchi.S1	AUGUSTUS	exon	45979644	45979961	.	-	.	transcript_id "Phchi.S1G730400.t1"; gene_id "Phchi.S1G730400"
Phchi.S1	AUGUSTUS	start_codon	45979959	45979961	.	-	0	transcript_id "Phchi.S1G730400.t1"; gene_id "Phchi.S1G730400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7877.t1 is derived from g5051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31676220	31677329	.	+	.	Phchi.S1G503600
Phchi.S1	AUGUSTUS	transcript	31676220	31677329	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	start_codon	31676220	31676222	.	+	0	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	CDS	31676220	31676348	0.98	+	0	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	exon	31676220	31676348	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	intron	31676349	31676505	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	CDS	31676506	31676653	1	+	0	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	exon	31676506	31676653	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	intron	31676654	31676771	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	CDS	31676772	31676910	1	+	2	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	exon	31676772	31676910	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	intron	31676911	31677048	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	CDS	31677049	31677134	1	+	1	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	exon	31677049	31677134	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	intron	31677135	31677216	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	CDS	31677217	31677329	1	+	2	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	exon	31677217	31677329	.	+	.	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
Phchi.S1	AUGUSTUS	stop_codon	31677330	31677332	.	+	0	transcript_id "Phchi.S1G503600.t1"; gene_id "Phchi.S1G503600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13512.t1 is derived from g11979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7249809	7252379	.	+	.	Phchi.S3G083100
Phchi.S3	AUGUSTUS	transcript	7249809	7252379	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	start_codon	7249809	7249811	.	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7249809	7249823	1	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7249809	7249823	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7249824	7249911	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7249912	7249957	0.79	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7249912	7249957	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7249958	7250058	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7250059	7250747	0.75	+	2	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7250059	7250747	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7250748	7250994	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7250995	7251123	1	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7250995	7251123	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7251124	7251201	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7251202	7251540	1	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7251202	7251540	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7251541	7251849	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7251850	7251897	1	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7251850	7251897	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7251898	7252003	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7252004	7252143	1	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7252004	7252143	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	intron	7252144	7252336	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	CDS	7252337	7252379	0.99	+	1	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	exon	7252337	7252379	.	+	.	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
Phchi.S3	AUGUSTUS	stop_codon	7252380	7252382	.	+	0	transcript_id "Phchi.S3G083100.t1"; gene_id "Phchi.S3G083100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2317.t1 is derived from g9237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6118970	6119374	.	-	.	Phchi.S5G092600
Phchi.S5	AUGUSTUS	transcript	6118970	6119374	.	-	.	transcript_id "Phchi.S5G092600.t1"; gene_id "Phchi.S5G092600"
Phchi.S5	AUGUSTUS	stop_codon	6118967	6118969	.	-	0	transcript_id "Phchi.S5G092600.t1"; gene_id "Phchi.S5G092600"
Phchi.S5	AUGUSTUS	CDS	6118970	6119374	0.75	-	0	transcript_id "Phchi.S5G092600.t1"; gene_id "Phchi.S5G092600"
Phchi.S5	AUGUSTUS	exon	6118970	6119374	.	-	.	transcript_id "Phchi.S5G092600.t1"; gene_id "Phchi.S5G092600"
Phchi.S5	AUGUSTUS	start_codon	6119372	6119374	.	-	0	transcript_id "Phchi.S5G092600.t1"; gene_id "Phchi.S5G092600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6097.t1 is derived from g3268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20943046	20944086	.	+	.	Phchi.S1G325600
Phchi.S1	AUGUSTUS	transcript	20943046	20944086	.	+	.	transcript_id "Phchi.S1G325600.t1"; gene_id "Phchi.S1G325600"
Phchi.S1	AUGUSTUS	start_codon	20943046	20943048	.	+	0	transcript_id "Phchi.S1G325600.t1"; gene_id "Phchi.S1G325600"
Phchi.S1	AUGUSTUS	CDS	20943046	20944086	1	+	0	transcript_id "Phchi.S1G325600.t1"; gene_id "Phchi.S1G325600"
Phchi.S1	AUGUSTUS	exon	20943046	20944086	.	+	.	transcript_id "Phchi.S1G325600.t1"; gene_id "Phchi.S1G325600"
Phchi.S1	AUGUSTUS	stop_codon	20944087	20944089	.	+	0	transcript_id "Phchi.S1G325600.t1"; gene_id "Phchi.S1G325600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9815.t1 is derived from g6991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43872655	43873907	.	+	.	Phchi.S1G697400
Phchi.S1	AUGUSTUS	transcript	43872655	43873907	.	+	.	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	start_codon	43872655	43872657	.	+	0	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	CDS	43872655	43873098	1	+	0	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	exon	43872655	43873098	.	+	.	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	intron	43873099	43873202	.	+	.	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	CDS	43873203	43873392	1	+	0	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	exon	43873203	43873392	.	+	.	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	intron	43873393	43873497	.	+	.	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	CDS	43873498	43873907	1	+	2	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	exon	43873498	43873907	.	+	.	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
Phchi.S1	AUGUSTUS	stop_codon	43873908	43873910	.	+	0	transcript_id "Phchi.S1G697400.t1"; gene_id "Phchi.S1G697400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3551.t1 is derived from g720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4440559	4441090	.	+	.	Phchi.S1G071000
Phchi.S1	AUGUSTUS	transcript	4440559	4441090	.	+	.	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	start_codon	4440559	4440561	.	+	0	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	CDS	4440559	4440604	0.99	+	0	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	exon	4440559	4440604	.	+	.	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	intron	4440605	4440824	.	+	.	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	CDS	4440825	4441090	0.95	+	2	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	exon	4440825	4441090	.	+	.	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
Phchi.S1	AUGUSTUS	stop_codon	4441091	4441093	.	+	0	transcript_id "Phchi.S1G071000.t1"; gene_id "Phchi.S1G071000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11262.t1 is derived from g15312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5066279	5067901	.	+	.	Phchi.S4G084400
Phchi.S4	AUGUSTUS	transcript	5066279	5067901	.	+	.	transcript_id "Phchi.S4G084400.t1"; gene_id "Phchi.S4G084400"
Phchi.S4	AUGUSTUS	start_codon	5066279	5066281	.	+	0	transcript_id "Phchi.S4G084400.t1"; gene_id "Phchi.S4G084400"
Phchi.S4	AUGUSTUS	CDS	5066279	5067901	0.88	+	0	transcript_id "Phchi.S4G084400.t1"; gene_id "Phchi.S4G084400"
Phchi.S4	AUGUSTUS	exon	5066279	5067901	.	+	.	transcript_id "Phchi.S4G084400.t1"; gene_id "Phchi.S4G084400"
Phchi.S4	AUGUSTUS	stop_codon	5067902	5067904	.	+	0	transcript_id "Phchi.S4G084400.t1"; gene_id "Phchi.S4G084400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3754.t1 is derived from g923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5506096	5511835	.	-	.	Phchi.S1G091300
Phchi.S1	AUGUSTUS	transcript	5506096	5511835	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	stop_codon	5506093	5506095	.	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5506096	5506143	0.94	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5506096	5506143	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5506144	5506227	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5506228	5506395	1	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5506228	5506395	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5506396	5506494	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5506495	5506684	1	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5506495	5506684	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5506685	5506766	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5506767	5506829	1	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5506767	5506829	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5506830	5506922	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5506923	5507080	1	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5506923	5507080	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5507081	5507170	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5507171	5507386	0.95	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5507171	5507386	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5507387	5507472	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5507473	5507662	1	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5507473	5507662	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5507663	5507801	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5507802	5507873	1	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5507802	5507873	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5507874	5507959	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5507960	5508071	1	-	2	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5507960	5508071	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5508072	5508171	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5508172	5508247	1	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5508172	5508247	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5508248	5508365	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5508366	5508416	0.99	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5508366	5508416	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5508417	5508493	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5508494	5508575	0.98	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5508494	5508575	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5508576	5508833	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5508834	5508870	0.46	-	2	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5508834	5508870	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5508871	5508996	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5508997	5509076	0.71	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5508997	5509076	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5509077	5509169	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5509170	5509324	0.49	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5509170	5509324	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5509325	5509481	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5509482	5509710	0.57	-	1	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5509482	5509710	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5509711	5509798	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5509799	5511357	1	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5509799	5511357	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5511358	5511482	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5511483	5511529	0.97	-	2	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5511483	5511529	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	intron	5511530	5511609	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	CDS	5511610	5511835	0.76	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	exon	5511610	5511835	.	-	.	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
Phchi.S1	AUGUSTUS	start_codon	5511833	5511835	.	-	0	transcript_id "Phchi.S1G091300.t1"; gene_id "Phchi.S1G091300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6511.t1 is derived from g3683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23379299	23384663	.	+	.	Phchi.S1G367000
Phchi.S1	AUGUSTUS	transcript	23379299	23384663	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	start_codon	23379299	23379301	.	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23379299	23379366	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23379299	23379366	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23379367	23379457	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23379458	23379587	1	+	1	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23379458	23379587	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23379588	23379815	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23379816	23379974	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23379816	23379974	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23379975	23380174	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23380175	23380270	0.96	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23380175	23380270	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23380271	23380416	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23380417	23380514	0.96	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23380417	23380514	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23380515	23380602	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23380603	23380741	1	+	1	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23380603	23380741	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23380742	23380827	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23380828	23380925	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23380828	23380925	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23380926	23381001	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23381002	23381158	0.99	+	1	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23381002	23381158	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23381159	23381241	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23381242	23381311	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23381242	23381311	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23381312	23381411	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23381412	23381488	1	+	2	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23381412	23381488	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23381489	23381615	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23381616	23381669	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23381616	23381669	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23381670	23381755	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23381756	23381836	0.99	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23381756	23381836	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23381837	23381952	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23381953	23382064	0.73	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23381953	23382064	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23382065	23382151	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23382152	23382238	1	+	2	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23382152	23382238	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23382239	23382322	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23382323	23382498	0.95	+	2	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23382323	23382498	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23382499	23382601	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23382602	23382763	0.91	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23382602	23382763	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23382764	23382879	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23382880	23382987	0.85	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23382880	23382987	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23382988	23383080	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23383081	23383239	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23383081	23383239	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23383240	23383323	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23383324	23383407	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23383324	23383407	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23383408	23383488	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23383489	23383694	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23383489	23383694	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23383695	23383784	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23383785	23383886	1	+	1	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23383785	23383886	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23383887	23384000	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23384001	23384110	1	+	1	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23384001	23384110	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23384111	23384191	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23384192	23384343	1	+	2	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23384192	23384343	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	intron	23384344	23384420	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	CDS	23384421	23384663	1	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	exon	23384421	23384663	.	+	.	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
Phchi.S1	AUGUSTUS	stop_codon	23384664	23384666	.	+	0	transcript_id "Phchi.S1G367000.t1"; gene_id "Phchi.S1G367000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14439.t1 is derived from g12907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12836658	12837856	.	-	.	Phchi.S3G175800
Phchi.S3	AUGUSTUS	transcript	12836658	12837856	.	-	.	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	stop_codon	12836655	12836657	.	-	0	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	CDS	12836658	12837315	0.65	-	1	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	exon	12836658	12837315	.	-	.	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	intron	12837316	12837401	.	-	.	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	CDS	12837402	12837856	0.06	-	0	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	exon	12837402	12837856	.	-	.	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
Phchi.S3	AUGUSTUS	start_codon	12837854	12837856	.	-	0	transcript_id "Phchi.S3G175800.t1"; gene_id "Phchi.S3G175800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10858.t1 is derived from g14908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2577719	2578351	.	-	.	Phchi.S4G044000
Phchi.S4	AUGUSTUS	transcript	2577719	2578351	.	-	.	transcript_id "Phchi.S4G044000.t1"; gene_id "Phchi.S4G044000"
Phchi.S4	AUGUSTUS	stop_codon	2577716	2577718	.	-	0	transcript_id "Phchi.S4G044000.t1"; gene_id "Phchi.S4G044000"
Phchi.S4	AUGUSTUS	CDS	2577719	2578351	0.51	-	0	transcript_id "Phchi.S4G044000.t1"; gene_id "Phchi.S4G044000"
Phchi.S4	AUGUSTUS	exon	2577719	2578351	.	-	.	transcript_id "Phchi.S4G044000.t1"; gene_id "Phchi.S4G044000"
Phchi.S4	AUGUSTUS	start_codon	2578349	2578351	.	-	0	transcript_id "Phchi.S4G044000.t1"; gene_id "Phchi.S4G044000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11742.t1 is derived from g15794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7953527	7960973	.	-	.	Phchi.S4G132400
Phchi.S4	AUGUSTUS	transcript	7953527	7960973	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	stop_codon	7953524	7953526	.	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7953527	7953640	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7953527	7953640	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7953641	7953717	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7953718	7953840	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7953718	7953840	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7953841	7953918	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7953919	7954024	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7953919	7954024	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7954025	7954129	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7954130	7954206	0.97	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7954130	7954206	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7954207	7954353	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7954354	7954473	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7954354	7954473	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7954474	7954558	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7954559	7954695	1	-	2	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7954559	7954695	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7954696	7954822	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7954823	7954931	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7954823	7954931	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7954932	7955033	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7955034	7955114	0.98	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7955034	7955114	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7955115	7955191	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7955192	7955323	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7955192	7955323	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7955324	7955474	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7955475	7955531	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7955475	7955531	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7955532	7955607	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7955608	7955688	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7955608	7955688	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7955689	7955765	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7955766	7955859	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7955766	7955859	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7955860	7956070	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7956071	7956353	1	-	2	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7956071	7956353	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7956354	7956493	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7956494	7956746	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7956494	7956746	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7956747	7956936	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7956937	7957091	1	-	2	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7956937	7957091	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7957092	7957172	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7957173	7957360	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7957173	7957360	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7957361	7957522	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7957523	7957704	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7957523	7957704	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7957705	7957935	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7957936	7957990	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7957936	7957990	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7957991	7958117	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7958118	7958235	1	-	2	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7958118	7958235	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7958236	7958422	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7958423	7958540	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7958423	7958540	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7958541	7958689	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7958690	7958806	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7958690	7958806	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7958807	7958940	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7958941	7959027	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7958941	7959027	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7959028	7959172	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7959173	7959307	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7959173	7959307	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7959308	7959473	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7959474	7959983	0.99	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7959474	7959983	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7959984	7960174	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960175	7960288	1	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960175	7960288	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960289	7960360	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960361	7960466	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960361	7960466	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960467	7960544	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960545	7960604	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960545	7960604	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960605	7960687	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960688	7960759	1	-	1	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960688	7960759	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960760	7960842	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960843	7960973	0.95	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960843	7960973	.	-	.	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	start_codon	7960971	7960973	.	-	0	transcript_id "Phchi.S4G132400.t1"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	transcript	7958791	7960973	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	stop_codon	7958788	7958790	.	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7958791	7958806	0.96	-	1	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7958791	7958806	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7958807	7958899	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7958900	7959027	0.96	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7958900	7959027	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7959028	7959172	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7959173	7959307	1	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7959173	7959307	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7959308	7959473	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7959474	7959983	1	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7959474	7959983	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7959984	7960174	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960175	7960288	1	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960175	7960288	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960289	7960360	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960361	7960466	1	-	1	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960361	7960466	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960467	7960544	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960545	7960604	1	-	1	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960545	7960604	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960605	7960687	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960688	7960759	1	-	1	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960688	7960759	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	intron	7960760	7960842	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	CDS	7960843	7960973	0.96	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	exon	7960843	7960973	.	-	.	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
Phchi.S4	AUGUSTUS	start_codon	7960971	7960973	.	-	0	transcript_id "Phchi.S4G132400.t2"; gene_id "Phchi.S4G132400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3630.t1 is derived from g799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4854236	4855755	.	+	.	Phchi.S1G078900
Phchi.S1	AUGUSTUS	transcript	4854236	4855755	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	start_codon	4854236	4854238	.	+	0	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	CDS	4854236	4854264	0.81	+	0	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	exon	4854236	4854264	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	intron	4854265	4854360	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	CDS	4854361	4854434	0.81	+	1	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	exon	4854361	4854434	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	intron	4854435	4854538	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	CDS	4854539	4854750	0.98	+	2	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	exon	4854539	4854750	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	intron	4854751	4854857	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	CDS	4854858	4855040	0.99	+	0	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	exon	4854858	4855040	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	intron	4855041	4855153	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	CDS	4855154	4855392	1	+	0	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	exon	4855154	4855392	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	intron	4855393	4855505	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	CDS	4855506	4855755	0.97	+	1	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	exon	4855506	4855755	.	+	.	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
Phchi.S1	AUGUSTUS	stop_codon	4855756	4855758	.	+	0	transcript_id "Phchi.S1G078900.t1"; gene_id "Phchi.S1G078900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8560.t1 is derived from g5735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36621379	36623002	.	-	.	Phchi.S1G571900
Phchi.S1	AUGUSTUS	transcript	36621379	36623002	.	-	.	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	stop_codon	36621376	36621378	.	-	0	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	CDS	36621379	36622455	1	-	0	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	exon	36621379	36622455	.	-	.	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	intron	36622456	36622588	.	-	.	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	CDS	36622589	36623002	0.7	-	0	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	exon	36622589	36623002	.	-	.	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
Phchi.S1	AUGUSTUS	start_codon	36623000	36623002	.	-	0	transcript_id "Phchi.S1G571900.t1"; gene_id "Phchi.S1G571900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12868.t1 is derived from g11333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2828690	2831972	.	+	.	Phchi.S3G018700
Phchi.S3	AUGUSTUS	transcript	2828690	2831972	.	+	.	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	start_codon	2828690	2828692	.	+	0	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	CDS	2828690	2828805	0.47	+	0	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	exon	2828690	2828805	.	+	.	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	intron	2828806	2828890	.	+	.	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	CDS	2828891	2831972	0.49	+	1	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	exon	2828891	2831972	.	+	.	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
Phchi.S3	AUGUSTUS	stop_codon	2831973	2831975	.	+	0	transcript_id "Phchi.S3G018700.t1"; gene_id "Phchi.S3G018700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7629.t1 is derived from g4803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30322193	30323489	.	-	.	Phchi.S1G478800
Phchi.S1	AUGUSTUS	transcript	30322193	30323489	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	stop_codon	30322190	30322192	.	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	CDS	30322193	30322276	0.56	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	exon	30322193	30322276	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	intron	30322277	30322363	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	CDS	30322364	30322399	0.56	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	exon	30322364	30322399	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	intron	30322400	30322514	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	CDS	30322515	30322565	0.89	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	exon	30322515	30322565	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	intron	30322566	30322643	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	CDS	30322644	30322978	0.97	-	2	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	exon	30322644	30322978	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	intron	30322979	30323069	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	CDS	30323070	30323085	1	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	exon	30323070	30323085	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	intron	30323086	30323210	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	CDS	30323211	30323489	0.98	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	exon	30323211	30323489	.	-	.	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
Phchi.S1	AUGUSTUS	start_codon	30323487	30323489	.	-	0	transcript_id "Phchi.S1G478800.t1"; gene_id "Phchi.S1G478800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12286.t1 is derived from g7962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8837540	8838291	.	-	.	Phchi.S2G036600
Phchi.S2	AUGUSTUS	transcript	8837540	8838291	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	stop_codon	8837537	8837539	.	-	0	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	CDS	8837540	8837573	0.95	-	1	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	exon	8837540	8837573	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	intron	8837574	8837661	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	CDS	8837662	8837822	0.94	-	0	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	exon	8837662	8837822	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	intron	8837823	8838016	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	CDS	8838017	8838193	0.88	-	0	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	exon	8838017	8838193	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	intron	8838194	8838282	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	CDS	8838283	8838291	0.43	-	0	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	exon	8838283	8838291	.	-	.	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
Phchi.S2	AUGUSTUS	start_codon	8838289	8838291	.	-	0	transcript_id "Phchi.S2G036600.t1"; gene_id "Phchi.S2G036600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2802.t1 is derived from g9722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8946100	8948810	.	+	.	Phchi.S5G141100
Phchi.S5	AUGUSTUS	transcript	8946100	8948810	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	start_codon	8946100	8946102	.	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8946100	8946150	0.88	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8946100	8946150	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8946151	8946249	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8946250	8946403	1	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8946250	8946403	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8946404	8946573	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8946574	8946725	1	+	2	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8946574	8946725	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8946726	8946810	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8946811	8946924	1	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8946811	8946924	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8946925	8947014	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8947015	8947203	0.99	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8947015	8947203	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8947204	8947305	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8947306	8947461	0.96	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8947306	8947461	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8947462	8947551	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8947552	8947817	1	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8947552	8947817	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8947818	8947910	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8947911	8948008	1	+	1	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8947911	8948008	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8948009	8948096	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8948097	8948275	1	+	2	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8948097	8948275	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8948276	8948367	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8948368	8948478	1	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8948368	8948478	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	intron	8948479	8948606	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	CDS	8948607	8948810	0.98	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	exon	8948607	8948810	.	+	.	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
Phchi.S5	AUGUSTUS	stop_codon	8948811	8948813	.	+	0	transcript_id "Phchi.S5G141100.t1"; gene_id "Phchi.S5G141100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13159.t1 is derived from g11624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4441750	4444668	.	+	.	Phchi.S3G047800
Phchi.S3	AUGUSTUS	transcript	4441750	4444668	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	start_codon	4441750	4441752	.	+	0	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	CDS	4441750	4443962	0.8	+	0	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	exon	4441750	4443962	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	intron	4443963	4444060	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	CDS	4444061	4444096	0.82	+	1	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	exon	4444061	4444096	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	intron	4444097	4444194	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	CDS	4444195	4444299	0.61	+	1	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	exon	4444195	4444299	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	intron	4444300	4444410	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	CDS	4444411	4444579	0.54	+	1	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	exon	4444411	4444579	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	intron	4444580	4444665	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	CDS	4444666	4444668	0.46	+	0	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	exon	4444666	4444668	.	+	.	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
Phchi.S3	AUGUSTUS	stop_codon	4444669	4444671	.	+	0	transcript_id "Phchi.S3G047800.t1"; gene_id "Phchi.S3G047800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11056.t1 is derived from g15106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3875207	3877468	.	-	.	Phchi.S4G063800
Phchi.S4	AUGUSTUS	transcript	3875207	3877468	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	stop_codon	3875204	3875206	.	-	0	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3875207	3875670	0.99	-	2	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3875207	3875670	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3875671	3875872	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3875873	3876134	1	-	0	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3875873	3876134	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3876135	3876257	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3876258	3876846	1	-	1	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3876258	3876846	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3876847	3876945	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3876946	3877047	1	-	1	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3876946	3877047	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3877048	3877160	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3877161	3877468	1	-	0	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3877161	3877468	.	-	.	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	start_codon	3877466	3877468	.	-	0	transcript_id "Phchi.S4G063800.t1"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	transcript	3876850	3877468	.	-	.	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	stop_codon	3876847	3876849	.	-	0	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3876850	3876850	0.74	-	1	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3876850	3876850	.	-	.	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3876851	3876945	.	-	.	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3876946	3877047	0.74	-	1	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3876946	3877047	.	-	.	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3877048	3877160	.	-	.	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3877161	3877468	0.96	-	0	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3877161	3877468	.	-	.	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	start_codon	3877466	3877468	.	-	0	transcript_id "Phchi.S4G063800.t2"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	transcript	3875207	3877468	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	stop_codon	3875204	3875206	.	-	0	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3875207	3875670	1	-	2	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3875207	3875670	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3875671	3875872	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3875873	3876134	1	-	0	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3875873	3876134	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3876135	3876257	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3876258	3876850	0.44	-	2	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3876258	3876850	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3876851	3876956	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3876957	3877033	0.38	-	1	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3876957	3877033	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	intron	3877034	3877160	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	CDS	3877161	3877468	0.93	-	0	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	exon	3877161	3877468	.	-	.	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
Phchi.S4	AUGUSTUS	start_codon	3877466	3877468	.	-	0	transcript_id "Phchi.S4G063800.t3"; gene_id "Phchi.S4G063800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5757.t1 is derived from g2927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18825334	18827444	.	+	.	Phchi.S1G291600
Phchi.S1	AUGUSTUS	transcript	18825334	18827444	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	start_codon	18825334	18825336	.	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	CDS	18825334	18825501	0.86	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	exon	18825334	18825501	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	intron	18825502	18825599	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	CDS	18825600	18825893	0.79	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	exon	18825600	18825893	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	intron	18825894	18826015	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	CDS	18826016	18826129	0.91	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	exon	18826016	18826129	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	intron	18826130	18826230	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	CDS	18826231	18826255	0.91	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	exon	18826231	18826255	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	intron	18826256	18826387	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	CDS	18826388	18826818	0.63	+	2	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	exon	18826388	18826818	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	intron	18826819	18826904	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	CDS	18826905	18827444	0.98	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	exon	18826905	18827444	.	+	.	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
Phchi.S1	AUGUSTUS	stop_codon	18827445	18827447	.	+	0	transcript_id "Phchi.S1G291600.t1"; gene_id "Phchi.S1G291600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5514.t1 is derived from g2684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17180193	17184083	.	-	.	Phchi.S1G267300
Phchi.S1	AUGUSTUS	transcript	17180193	17184083	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	stop_codon	17180190	17180192	.	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17180193	17180282	1	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17180193	17180282	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17180283	17180392	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17180393	17180495	1	-	1	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17180393	17180495	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17180496	17180586	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17180587	17180658	1	-	1	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17180587	17180658	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17180659	17180754	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17180755	17180816	1	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17180755	17180816	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17180817	17180895	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17180896	17181021	1	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17180896	17181021	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17181022	17181187	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17181188	17181245	1	-	1	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17181188	17181245	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17181246	17181339	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17181340	17181438	1	-	1	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17181340	17181438	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17181439	17181591	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17181592	17181684	1	-	1	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17181592	17181684	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17181685	17181862	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17181863	17182050	1	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17181863	17182050	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17182051	17182193	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17182194	17182343	1	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17182194	17182343	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17182344	17182435	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17182436	17182510	1	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17182436	17182510	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17182511	17182596	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17182597	17183152	0.99	-	1	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17182597	17183152	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	intron	17183153	17183673	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	CDS	17183674	17184083	0.65	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	exon	17183674	17184083	.	-	.	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
Phchi.S1	AUGUSTUS	start_codon	17184081	17184083	.	-	0	transcript_id "Phchi.S1G267300.t1"; gene_id "Phchi.S1G267300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5324.t1 is derived from g2494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16287897	16295586	.	-	.	Phchi.S1G248300
Phchi.S1	AUGUSTUS	transcript	16287897	16295586	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	stop_codon	16287894	16287896	.	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16287897	16287960	0.6	-	1	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16287897	16287960	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16287961	16288040	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16288041	16288237	1	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16288041	16288237	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16288238	16288364	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16288365	16288564	1	-	2	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16288365	16288564	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16288565	16288658	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16288659	16288791	1	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16288659	16288791	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16288792	16288982	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16288983	16289090	1	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16288983	16289090	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16289091	16289181	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16289182	16289295	0.99	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16289182	16289295	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16289296	16289405	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16289406	16289565	1	-	1	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16289406	16289565	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16289566	16289653	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16289654	16289766	1	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16289654	16289766	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16289767	16289848	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16289849	16290946	0.58	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16289849	16290946	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16290947	16291056	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16291057	16291876	0.83	-	1	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16291057	16291876	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16291877	16292112	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16292113	16293329	0.95	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16292113	16293329	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16293330	16293430	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16293431	16293672	1	-	2	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16293431	16293672	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16293673	16293810	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16293811	16293959	1	-	1	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16293811	16293959	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16293960	16294055	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16294056	16295188	1	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16294056	16295188	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	intron	16295189	16295418	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	CDS	16295419	16295586	0.87	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	exon	16295419	16295586	.	-	.	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
Phchi.S1	AUGUSTUS	start_codon	16295584	16295586	.	-	0	transcript_id "Phchi.S1G248300.t1"; gene_id "Phchi.S1G248300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7070.t1 is derived from g4242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26740136	26741622	.	+	.	Phchi.S1G422900
Phchi.S1	AUGUSTUS	transcript	26740136	26741622	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	start_codon	26740136	26740138	.	+	0	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	CDS	26740136	26740359	0.47	+	0	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	exon	26740136	26740359	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	intron	26740360	26740540	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	CDS	26740541	26740560	0.52	+	1	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	exon	26740541	26740560	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	intron	26740561	26740732	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	CDS	26740733	26740841	0.24	+	2	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	exon	26740733	26740841	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	intron	26740842	26740941	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	CDS	26740942	26741429	0.55	+	1	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	exon	26740942	26741429	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	intron	26741430	26741608	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	CDS	26741609	26741622	0.57	+	2	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	exon	26741609	26741622	.	+	.	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
Phchi.S1	AUGUSTUS	stop_codon	26741623	26741625	.	+	0	transcript_id "Phchi.S1G422900.t1"; gene_id "Phchi.S1G422900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10357.t1 is derived from g7533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47331532	47333643	.	+	.	Phchi.S1G751600
Phchi.S1	AUGUSTUS	transcript	47331532	47333643	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	start_codon	47331532	47331534	.	+	0	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	CDS	47331532	47331563	0.79	+	0	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	exon	47331532	47331563	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	intron	47331564	47331709	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	CDS	47331710	47331773	0.61	+	1	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	exon	47331710	47331773	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	intron	47331774	47332101	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	CDS	47332102	47332172	1	+	0	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	exon	47332102	47332172	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	intron	47332173	47332294	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	CDS	47332295	47332401	1	+	1	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	exon	47332295	47332401	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	intron	47332402	47332489	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	CDS	47332490	47332920	0.99	+	2	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	exon	47332490	47332920	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	intron	47332921	47333010	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	CDS	47333011	47333643	1	+	0	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	exon	47333011	47333643	.	+	.	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
Phchi.S1	AUGUSTUS	stop_codon	47333644	47333646	.	+	0	transcript_id "Phchi.S1G751600.t1"; gene_id "Phchi.S1G751600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10799.t1 is derived from g14849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2163626	2165430	.	-	.	Phchi.S4G038100
Phchi.S4	AUGUSTUS	transcript	2163626	2165430	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	stop_codon	2163623	2163625	.	-	0	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	CDS	2163626	2163867	1	-	2	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	exon	2163626	2163867	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	intron	2163868	2163959	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	CDS	2163960	2164118	1	-	2	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	exon	2163960	2164118	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	intron	2164119	2164246	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	CDS	2164247	2164345	1	-	2	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	exon	2164247	2164345	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	intron	2164346	2164452	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	CDS	2164453	2164703	0.98	-	1	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	exon	2164453	2164703	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	intron	2164704	2164849	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	CDS	2164850	2165430	1	-	0	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	exon	2164850	2165430	.	-	.	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
Phchi.S4	AUGUSTUS	start_codon	2165428	2165430	.	-	0	transcript_id "Phchi.S4G038100.t1"; gene_id "Phchi.S4G038100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4275.t1 is derived from g1444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9342697	9343741	.	+	.	Phchi.S1G143400
Phchi.S1	AUGUSTUS	transcript	9342697	9343741	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	start_codon	9342697	9342699	.	+	0	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	CDS	9342697	9342738	0.44	+	0	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	exon	9342697	9342738	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	intron	9342739	9342955	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	CDS	9342956	9342989	0.71	+	0	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	exon	9342956	9342989	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	intron	9342990	9343507	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	CDS	9343508	9343604	0.71	+	2	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	exon	9343508	9343604	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	intron	9343605	9343701	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	CDS	9343702	9343741	0.7	+	1	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	exon	9343702	9343741	.	+	.	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
Phchi.S1	AUGUSTUS	stop_codon	9343742	9343744	.	+	0	transcript_id "Phchi.S1G143400.t1"; gene_id "Phchi.S1G143400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2055.t1 is derived from g8975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4630640	4632055	.	-	.	Phchi.S5G066400
Phchi.S5	AUGUSTUS	transcript	4630640	4632055	.	-	.	transcript_id "Phchi.S5G066400.t1"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	stop_codon	4630637	4630639	.	-	0	transcript_id "Phchi.S5G066400.t1"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	CDS	4630640	4632055	1	-	0	transcript_id "Phchi.S5G066400.t1"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	exon	4630640	4632055	.	-	.	transcript_id "Phchi.S5G066400.t1"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	start_codon	4632053	4632055	.	-	0	transcript_id "Phchi.S5G066400.t1"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	transcript	4630640	4631692	.	-	.	transcript_id "Phchi.S5G066400.t2"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	stop_codon	4630637	4630639	.	-	0	transcript_id "Phchi.S5G066400.t2"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	CDS	4630640	4631692	0.99	-	0	transcript_id "Phchi.S5G066400.t2"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	exon	4630640	4631692	.	-	.	transcript_id "Phchi.S5G066400.t2"; gene_id "Phchi.S5G066400"
Phchi.S5	AUGUSTUS	start_codon	4631690	4631692	.	-	0	transcript_id "Phchi.S5G066400.t2"; gene_id "Phchi.S5G066400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14255.t1 is derived from g12722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11777803	11780500	.	+	.	Phchi.S3G157400
Phchi.S3	AUGUSTUS	transcript	11777803	11780500	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	start_codon	11777803	11777805	.	+	0	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	CDS	11777803	11778377	0.45	+	0	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	exon	11777803	11778377	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	intron	11778378	11778651	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	CDS	11778652	11779576	0.26	+	1	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	exon	11778652	11779576	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	intron	11779577	11779721	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	CDS	11779722	11779784	1	+	0	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	exon	11779722	11779784	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	intron	11779785	11779900	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	CDS	11779901	11780062	1	+	0	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	exon	11779901	11780062	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	intron	11780063	11780167	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	CDS	11780168	11780276	1	+	0	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	exon	11780168	11780276	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	intron	11780277	11780360	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	CDS	11780361	11780500	0.91	+	2	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	exon	11780361	11780500	.	+	.	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
Phchi.S3	AUGUSTUS	stop_codon	11780501	11780503	.	+	0	transcript_id "Phchi.S3G157400.t1"; gene_id "Phchi.S3G157400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8108.t1 is derived from g5283.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33161267	33162909	.	+	.	Phchi.S1G526700
Phchi.S1	AUGUSTUS	transcript	33161267	33162909	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	start_codon	33161267	33161269	.	+	0	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33161267	33161309	0.73	+	0	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33161267	33161309	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33161310	33161637	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33161638	33161742	1	+	2	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33161638	33161742	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33161743	33161846	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33161847	33161924	1	+	2	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33161847	33161924	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33161925	33162021	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162022	33162089	1	+	2	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162022	33162089	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162090	33162166	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162167	33162248	1	+	0	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162167	33162248	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162249	33162417	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162418	33162485	1	+	2	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162418	33162485	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162486	33162660	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162661	33162744	1	+	0	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162661	33162744	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162745	33162852	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162853	33162909	1	+	0	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162853	33162909	.	+	.	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	stop_codon	33162910	33162912	.	+	0	transcript_id "Phchi.S1G526700.t1"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	transcript	33161267	33162909	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	start_codon	33161267	33161269	.	+	0	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33161267	33161309	0.67	+	0	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33161267	33161309	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33161310	33161637	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33161638	33161742	1	+	2	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33161638	33161742	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33161743	33161846	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33161847	33161924	1	+	2	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33161847	33161924	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33161925	33162012	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162013	33162089	1	+	2	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162013	33162089	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162090	33162166	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162167	33162248	1	+	0	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162167	33162248	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162249	33162417	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162418	33162485	1	+	2	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162418	33162485	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162486	33162660	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162661	33162744	1	+	0	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162661	33162744	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	intron	33162745	33162852	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	CDS	33162853	33162909	1	+	0	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	exon	33162853	33162909	.	+	.	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
Phchi.S1	AUGUSTUS	stop_codon	33162910	33162912	.	+	0	transcript_id "Phchi.S1G526700.t2"; gene_id "Phchi.S1G526700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13535.t1 is derived from g12002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7403266	7406344	.	-	.	Phchi.S3G085400
Phchi.S3	AUGUSTUS	transcript	7403266	7406344	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	stop_codon	7403263	7403265	.	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7403266	7403388	0.94	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7403266	7403388	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7403389	7403475	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7403476	7403569	1	-	1	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7403476	7403569	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7403570	7403654	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7403655	7403752	1	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7403655	7403752	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7403753	7403833	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7403834	7403942	1	-	1	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7403834	7403942	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7403943	7404148	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7404149	7404190	1	-	1	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7404149	7404190	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7404191	7404346	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7404347	7404422	1	-	2	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7404347	7404422	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7404423	7404562	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7404563	7404681	1	-	1	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7404563	7404681	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7404682	7404772	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7404773	7404841	1	-	1	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7404773	7404841	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7404842	7404918	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7404919	7405127	0.98	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7404919	7405127	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7405128	7405257	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7405258	7405340	0.94	-	2	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7405258	7405340	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7405341	7405421	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7405422	7405571	1	-	2	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7405422	7405571	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7405572	7405695	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7405696	7405999	0.98	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7405696	7405999	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7406000	7406126	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7406127	7406192	1	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7406127	7406192	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	intron	7406193	7406332	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	CDS	7406333	7406344	0.96	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	exon	7406333	7406344	.	-	.	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
Phchi.S3	AUGUSTUS	start_codon	7406342	7406344	.	-	0	transcript_id "Phchi.S3G085400.t1"; gene_id "Phchi.S3G085400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3409.t1 is derived from g578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3376758	3377373	.	+	.	Phchi.S1G056800
Phchi.S1	AUGUSTUS	transcript	3376758	3377373	.	+	.	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	start_codon	3376758	3376760	.	+	0	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	CDS	3376758	3377131	0.69	+	0	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	exon	3376758	3377131	.	+	.	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	intron	3377132	3377333	.	+	.	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	CDS	3377334	3377373	0.97	+	1	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	exon	3377334	3377373	.	+	.	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
Phchi.S1	AUGUSTUS	stop_codon	3377374	3377376	.	+	0	transcript_id "Phchi.S1G056800.t1"; gene_id "Phchi.S1G056800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9676.t1 is derived from g6852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43241180	43241656	.	-	.	Phchi.S1G683500
Phchi.S1	AUGUSTUS	transcript	43241180	43241656	.	-	.	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	stop_codon	43241177	43241179	.	-	0	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	CDS	43241180	43241382	0.78	-	2	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	exon	43241180	43241382	.	-	.	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	intron	43241383	43241460	.	-	.	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	CDS	43241461	43241656	0.84	-	0	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	exon	43241461	43241656	.	-	.	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
Phchi.S1	AUGUSTUS	start_codon	43241654	43241656	.	-	0	transcript_id "Phchi.S1G683500.t1"; gene_id "Phchi.S1G683500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11977.t1 is derived from g7652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	267925	268551	.	+	.	Phchi.S2G005700
Phchi.S2	AUGUSTUS	transcript	267925	268551	.	+	.	transcript_id "Phchi.S2G005700.t1"; gene_id "Phchi.S2G005700"
Phchi.S2	AUGUSTUS	start_codon	267925	267927	.	+	0	transcript_id "Phchi.S2G005700.t1"; gene_id "Phchi.S2G005700"
Phchi.S2	AUGUSTUS	CDS	267925	268551	0.83	+	0	transcript_id "Phchi.S2G005700.t1"; gene_id "Phchi.S2G005700"
Phchi.S2	AUGUSTUS	exon	267925	268551	.	+	.	transcript_id "Phchi.S2G005700.t1"; gene_id "Phchi.S2G005700"
Phchi.S2	AUGUSTUS	stop_codon	268552	268554	.	+	0	transcript_id "Phchi.S2G005700.t1"; gene_id "Phchi.S2G005700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5379.t1 is derived from g2549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16584679	16588303	.	+	.	Phchi.S1G253800
Phchi.S1	AUGUSTUS	transcript	16584679	16588303	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	start_codon	16584679	16584681	.	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16584679	16585388	0.91	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16584679	16585388	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16585389	16585475	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16585476	16585578	0.98	+	1	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16585476	16585578	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16585579	16585701	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16585702	16585802	0.99	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16585702	16585802	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16585803	16585898	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16585899	16585977	1	+	1	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16585899	16585977	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16585978	16586061	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16586062	16586127	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16586062	16586127	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16586128	16586203	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16586204	16586272	0.97	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16586204	16586272	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16586273	16586379	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16586380	16586480	0.83	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16586380	16586480	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16586481	16586571	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16586572	16586650	1	+	1	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16586572	16586650	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16586651	16586737	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16586738	16586803	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16586738	16586803	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16586804	16586893	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16586894	16586962	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16586894	16586962	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16586963	16587055	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16587056	16587133	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16587056	16587133	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16587134	16587211	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16587212	16587331	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16587212	16587331	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16587332	16587423	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16587424	16587590	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16587424	16587590	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16587591	16587673	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16587674	16587782	1	+	1	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16587674	16587782	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16587783	16587872	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16587873	16587932	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16587873	16587932	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16587933	16588015	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16588016	16588110	1	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16588016	16588110	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	intron	16588111	16588191	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	CDS	16588192	16588303	1	+	1	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	exon	16588192	16588303	.	+	.	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
Phchi.S1	AUGUSTUS	stop_codon	16588304	16588306	.	+	0	transcript_id "Phchi.S1G253800.t1"; gene_id "Phchi.S1G253800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12996.t1 is derived from g11461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3557768	3560269	.	+	.	Phchi.S3G031500
Phchi.S3	AUGUSTUS	transcript	3557768	3560269	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	start_codon	3557768	3557770	.	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3557768	3557782	0.98	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3557768	3557782	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3557783	3558147	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3558148	3558244	1	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3558148	3558244	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3558245	3558330	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3558331	3558608	0.99	+	2	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3558331	3558608	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3558609	3558717	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3558718	3559494	1	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3558718	3559494	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3559495	3559597	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3559598	3559687	1	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3559598	3559687	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3559688	3559849	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3559850	3559917	1	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3559850	3559917	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3559918	3560014	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3560015	3560108	0.92	+	1	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3560015	3560108	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	intron	3560109	3560212	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	CDS	3560213	3560269	0.92	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	exon	3560213	3560269	.	+	.	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
Phchi.S3	AUGUSTUS	stop_codon	3560270	3560272	.	+	0	transcript_id "Phchi.S3G031500.t1"; gene_id "Phchi.S3G031500"
# This transcript jg13140.t2 is derived from g11605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13141.t1 is derived from g11606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4361252	4363133	.	+	.	Phchi.S3G046000
Phchi.S3	AUGUSTUS	transcript	4361252	4363133	.	+	.	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	start_codon	4361252	4361254	.	+	0	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	CDS	4361252	4361279	1	+	0	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	exon	4361252	4361279	.	+	.	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	intron	4361280	4362087	.	+	.	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	CDS	4362088	4363133	0.99	+	2	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	exon	4362088	4363133	.	+	.	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
Phchi.S3	AUGUSTUS	stop_codon	4363134	4363136	.	+	0	transcript_id "Phchi.S3G046000.t1"; gene_id "Phchi.S3G046000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1881.t1 is derived from g8801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3692165	3697642	.	+	.	Phchi.S5G049000
Phchi.S5	AUGUSTUS	transcript	3692165	3697642	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	start_codon	3692165	3692167	.	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3692165	3692934	0.49	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3692165	3692934	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3692935	3693005	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3693006	3693071	1	+	1	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3693006	3693071	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3693072	3693155	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3693156	3693273	0.99	+	1	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3693156	3693273	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3693274	3693418	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3693419	3693478	0.93	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3693419	3693478	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3693479	3693575	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3693576	3693606	0.96	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3693576	3693606	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3693607	3693734	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3693735	3693780	0.86	+	2	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3693735	3693780	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3693781	3693888	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3693889	3693943	1	+	1	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3693889	3693943	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3693944	3694049	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3694050	3694103	0.99	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3694050	3694103	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3694104	3694185	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3694186	3694269	0.91	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3694186	3694269	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3694270	3694368	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3694369	3694461	0.86	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3694369	3694461	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3694462	3694569	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3694570	3694698	0.86	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3694570	3694698	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3694699	3694876	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3694877	3694978	0.98	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3694877	3694978	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3694979	3695099	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3695100	3695177	0.98	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3695100	3695177	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3695178	3695261	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3695262	3695324	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3695262	3695324	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3695325	3695418	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3695419	3695484	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3695419	3695484	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3695485	3695570	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3695571	3695666	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3695571	3695666	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3695667	3695736	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3695737	3695836	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3695737	3695836	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3695837	3695998	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3695999	3696174	1	+	2	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3695999	3696174	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3696175	3696319	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3696320	3696424	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3696320	3696424	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3696425	3696531	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3696532	3696598	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3696532	3696598	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3696599	3696697	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3696698	3696780	1	+	2	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3696698	3696780	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3696781	3696852	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3696853	3696966	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3696853	3696966	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3696967	3697058	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3697059	3697176	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3697059	3697176	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3697177	3697259	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3697260	3697315	1	+	2	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3697260	3697315	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3697316	3697393	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3697394	3697441	1	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3697394	3697441	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	intron	3697442	3697531	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	CDS	3697532	3697642	0.99	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	exon	3697532	3697642	.	+	.	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
Phchi.S5	AUGUSTUS	stop_codon	3697643	3697645	.	+	0	transcript_id "Phchi.S5G049000.t1"; gene_id "Phchi.S5G049000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11846.t1 is derived from g15898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8559824	8560150	.	-	.	Phchi.S4G142800
Phchi.S4	AUGUSTUS	transcript	8559824	8560150	.	-	.	transcript_id "Phchi.S4G142800.t1"; gene_id "Phchi.S4G142800"
Phchi.S4	AUGUSTUS	stop_codon	8559821	8559823	.	-	0	transcript_id "Phchi.S4G142800.t1"; gene_id "Phchi.S4G142800"
Phchi.S4	AUGUSTUS	CDS	8559824	8560150	0.79	-	0	transcript_id "Phchi.S4G142800.t1"; gene_id "Phchi.S4G142800"
Phchi.S4	AUGUSTUS	exon	8559824	8560150	.	-	.	transcript_id "Phchi.S4G142800.t1"; gene_id "Phchi.S4G142800"
Phchi.S4	AUGUSTUS	start_codon	8560148	8560150	.	-	0	transcript_id "Phchi.S4G142800.t1"; gene_id "Phchi.S4G142800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15764.t1 is derived from g14234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21122447	21123217	.	+	.	Phchi.S3G308300
Phchi.S3	AUGUSTUS	transcript	21122447	21123217	.	+	.	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	start_codon	21122447	21122449	.	+	0	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	CDS	21122447	21122626	0.45	+	0	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	exon	21122447	21122626	.	+	.	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	intron	21122627	21123000	.	+	.	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	CDS	21123001	21123038	0.92	+	0	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	exon	21123001	21123038	.	+	.	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	intron	21123039	21123132	.	+	.	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	CDS	21123133	21123217	0.92	+	1	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	exon	21123133	21123217	.	+	.	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
Phchi.S3	AUGUSTUS	stop_codon	21123218	21123220	.	+	0	transcript_id "Phchi.S3G308300.t1"; gene_id "Phchi.S3G308300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13263.t1 is derived from g11728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4975106	4975959	.	-	.	Phchi.S3G058200
Phchi.S3	AUGUSTUS	transcript	4975106	4975959	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	stop_codon	4975103	4975105	.	-	0	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	CDS	4975106	4975112	0.98	-	1	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	exon	4975106	4975112	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	intron	4975113	4975278	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	CDS	4975279	4975356	0.98	-	1	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	exon	4975279	4975356	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	intron	4975357	4975514	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	CDS	4975515	4975616	0.97	-	1	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	exon	4975515	4975616	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	intron	4975617	4975698	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	CDS	4975699	4975763	0.99	-	0	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	exon	4975699	4975763	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	intron	4975764	4975902	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	CDS	4975903	4975959	0.99	-	0	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	exon	4975903	4975959	.	-	.	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
Phchi.S3	AUGUSTUS	start_codon	4975957	4975959	.	-	0	transcript_id "Phchi.S3G058200.t1"; gene_id "Phchi.S3G058200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1905.t1 is derived from g8825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3793143	3794306	.	-	.	Phchi.S5G051400
Phchi.S5	AUGUSTUS	transcript	3793143	3794306	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	stop_codon	3793140	3793142	.	-	0	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3793143	3793208	1	-	0	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3793143	3793208	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	intron	3793209	3793288	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3793289	3793341	1	-	2	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3793289	3793341	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	intron	3793342	3793420	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3793421	3793464	1	-	1	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3793421	3793464	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	intron	3793465	3793555	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3793556	3793705	1	-	1	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3793556	3793705	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	intron	3793706	3793792	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3793793	3793875	1	-	0	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3793793	3793875	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	intron	3793876	3793945	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3793946	3794110	1	-	0	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3793946	3794110	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	intron	3794111	3794183	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	CDS	3794184	3794306	1	-	0	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	exon	3794184	3794306	.	-	.	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
Phchi.S5	AUGUSTUS	start_codon	3794304	3794306	.	-	0	transcript_id "Phchi.S5G051400.t1"; gene_id "Phchi.S5G051400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10182.t1 is derived from g7358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46195579	46197560	.	-	.	Phchi.S1G734100
Phchi.S1	AUGUSTUS	transcript	46195579	46197560	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	stop_codon	46195576	46195578	.	-	0	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	CDS	46195579	46195579	0.45	-	1	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	exon	46195579	46195579	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	intron	46195580	46195662	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	CDS	46195663	46195997	0.26	-	0	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	exon	46195663	46195997	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	intron	46195998	46196153	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	CDS	46196154	46196266	0.55	-	2	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	exon	46196154	46196266	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	intron	46196267	46196494	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	CDS	46196495	46197560	0.39	-	0	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	exon	46196495	46197560	.	-	.	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
Phchi.S1	AUGUSTUS	start_codon	46197558	46197560	.	-	0	transcript_id "Phchi.S1G734100.t1"; gene_id "Phchi.S1G734100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9902.t1 is derived from g7078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44369121	44371721	.	-	.	Phchi.S1G706100
Phchi.S1	AUGUSTUS	transcript	44369121	44371721	.	-	.	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	stop_codon	44369118	44369120	.	-	0	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	CDS	44369121	44369680	0.55	-	2	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	exon	44369121	44369680	.	-	.	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	intron	44369681	44369802	.	-	.	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	CDS	44369803	44371462	0.6	-	0	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	exon	44369803	44371462	.	-	.	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	intron	44371463	44371610	.	-	.	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	CDS	44371611	44371721	0.69	-	0	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	exon	44371611	44371721	.	-	.	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
Phchi.S1	AUGUSTUS	start_codon	44371719	44371721	.	-	0	transcript_id "Phchi.S1G706100.t1"; gene_id "Phchi.S1G706100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15860.t1 is derived from g14330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21897708	21900281	.	-	.	Phchi.S3G317900
Phchi.S3	AUGUSTUS	transcript	21897708	21900281	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	stop_codon	21897705	21897707	.	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21897708	21897862	1	-	2	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21897708	21897862	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21897863	21897956	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21897957	21898196	1	-	2	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21897957	21898196	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21898197	21898283	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21898284	21898347	1	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21898284	21898347	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21898348	21898459	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21898460	21898602	0.95	-	2	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21898460	21898602	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21898603	21898691	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21898692	21898764	0.98	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21898692	21898764	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21898765	21898885	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21898886	21899100	1	-	2	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21898886	21899100	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21899101	21899183	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21899184	21899478	1	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21899184	21899478	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21899479	21899595	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21899596	21899760	1	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21899596	21899760	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	intron	21899761	21899846	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	CDS	21899847	21900281	0.46	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	exon	21899847	21900281	.	-	.	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
Phchi.S3	AUGUSTUS	start_codon	21900279	21900281	.	-	0	transcript_id "Phchi.S3G317900.t1"; gene_id "Phchi.S3G317900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12077.t1 is derived from g7752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2140456	2141895	.	-	.	Phchi.S2G015700
Phchi.S2	AUGUSTUS	transcript	2140456	2141895	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	stop_codon	2140453	2140455	.	-	0	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	CDS	2140456	2140537	0.94	-	1	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	exon	2140456	2140537	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	intron	2140538	2140654	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	CDS	2140655	2140763	0.95	-	2	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	exon	2140655	2140763	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	intron	2140764	2140887	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	CDS	2140888	2140915	1	-	0	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	exon	2140888	2140915	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	intron	2140916	2141046	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	CDS	2141047	2141246	1	-	2	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	exon	2141047	2141246	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	intron	2141247	2141374	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	CDS	2141375	2141480	1	-	0	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	exon	2141375	2141480	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	intron	2141481	2141601	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	CDS	2141602	2141895	1	-	0	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	exon	2141602	2141895	.	-	.	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
Phchi.S2	AUGUSTUS	start_codon	2141893	2141895	.	-	0	transcript_id "Phchi.S2G015700.t1"; gene_id "Phchi.S2G015700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13477.t1 is derived from g11944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7079278	7080794	.	-	.	Phchi.S3G079600
Phchi.S3	AUGUSTUS	transcript	7079278	7080794	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	stop_codon	7079275	7079277	.	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	CDS	7079278	7079496	0.99	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	exon	7079278	7079496	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	intron	7079497	7079584	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	CDS	7079585	7079710	1	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	exon	7079585	7079710	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	intron	7079711	7079795	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	CDS	7079796	7079900	0.93	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	exon	7079796	7079900	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	intron	7079901	7080035	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	CDS	7080036	7080199	0.99	-	2	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	exon	7080036	7080199	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	intron	7080200	7080285	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	CDS	7080286	7080484	0.99	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	exon	7080286	7080484	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	intron	7080485	7080596	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	CDS	7080597	7080794	0.35	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	exon	7080597	7080794	.	-	.	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
Phchi.S3	AUGUSTUS	start_codon	7080792	7080794	.	-	0	transcript_id "Phchi.S3G079600.t1"; gene_id "Phchi.S3G079600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4112.t1 is derived from g1281.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7927850	7928629	.	-	.	Phchi.S1G127100
Phchi.S1	AUGUSTUS	transcript	7927850	7928629	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	stop_codon	7927847	7927849	.	-	0	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7927850	7927871	0.81	-	1	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7927850	7927871	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7927872	7927954	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7927955	7928059	0.8	-	1	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7927955	7928059	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7928060	7928170	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7928171	7928318	0.68	-	2	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7928171	7928318	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7928319	7928511	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7928512	7928629	0.66	-	0	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7928512	7928629	.	-	.	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	start_codon	7928627	7928629	.	-	0	transcript_id "Phchi.S1G127100.t1"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	transcript	7927850	7928629	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	stop_codon	7927847	7927849	.	-	0	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7927850	7927871	0.8	-	1	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7927850	7927871	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7927872	7927954	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7927955	7928059	0.78	-	1	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7927955	7928059	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7928060	7928170	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7928171	7928348	0.59	-	2	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7928171	7928348	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7928349	7928511	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7928512	7928629	0.66	-	0	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7928512	7928629	.	-	.	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	start_codon	7928627	7928629	.	-	0	transcript_id "Phchi.S1G127100.t2"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	transcript	7927867	7928629	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	stop_codon	7927864	7927866	.	-	0	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7927867	7927876	0.6	-	1	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7927867	7927876	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7927877	7927954	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7927955	7928059	0.6	-	1	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7927955	7928059	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7928060	7928170	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7928171	7928348	0.47	-	2	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7928171	7928348	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	intron	7928349	7928511	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	CDS	7928512	7928629	0.65	-	0	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	exon	7928512	7928629	.	-	.	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
Phchi.S1	AUGUSTUS	start_codon	7928627	7928629	.	-	0	transcript_id "Phchi.S1G127100.t3"; gene_id "Phchi.S1G127100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11060.t1 is derived from g15110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3935561	3936780	.	+	.	Phchi.S4G064200
Phchi.S4	AUGUSTUS	transcript	3935561	3936780	.	+	.	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	start_codon	3935561	3935563	.	+	0	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	CDS	3935561	3935884	0.57	+	0	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	exon	3935561	3935884	.	+	.	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	intron	3935885	3935976	.	+	.	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	CDS	3935977	3936780	0.46	+	0	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	exon	3935977	3936780	.	+	.	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
Phchi.S4	AUGUSTUS	stop_codon	3936781	3936783	.	+	0	transcript_id "Phchi.S4G064200.t1"; gene_id "Phchi.S4G064200"
# This transcript jg8838.t2 is derived from g6013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8839.t1 is derived from g6014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38222525	38227250	.	+	.	Phchi.S1G599800
Phchi.S1	AUGUSTUS	transcript	38222525	38227250	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	start_codon	38222525	38222527	.	+	0	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	CDS	38222525	38222638	0.55	+	0	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	exon	38222525	38222638	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	intron	38222639	38223014	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	CDS	38223015	38223183	0.55	+	0	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	exon	38223015	38223183	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	intron	38223184	38223301	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	CDS	38223302	38223694	0.51	+	2	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	exon	38223302	38223694	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	intron	38223695	38223762	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	CDS	38223763	38227250	0.58	+	2	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	exon	38223763	38227250	.	+	.	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
Phchi.S1	AUGUSTUS	stop_codon	38227251	38227253	.	+	0	transcript_id "Phchi.S1G599800.t1"; gene_id "Phchi.S1G599800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12508.t1 is derived from g8185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31612820	31614919	.	-	.	Phchi.S2G058800
Phchi.S2	AUGUSTUS	transcript	31612820	31614919	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	stop_codon	31612817	31612819	.	-	0	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	CDS	31612820	31612960	1	-	0	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	exon	31612820	31612960	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	intron	31612961	31613079	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	CDS	31613080	31613184	1	-	0	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	exon	31613080	31613184	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	intron	31613185	31613733	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	CDS	31613734	31613861	1	-	2	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	exon	31613734	31613861	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	intron	31613862	31614651	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	CDS	31614652	31614738	1	-	2	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	exon	31614652	31614738	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	intron	31614739	31614828	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	CDS	31614829	31614919	0.49	-	0	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	exon	31614829	31614919	.	-	.	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
Phchi.S2	AUGUSTUS	start_codon	31614917	31614919	.	-	0	transcript_id "Phchi.S2G058800.t1"; gene_id "Phchi.S2G058800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg144.t1 is derived from g9926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	787148	788032	.	+	.	Phchi.S6G010300
Phchi.S6	AUGUSTUS	transcript	787148	788032	.	+	.	transcript_id "Phchi.S6G010300.t1"; gene_id "Phchi.S6G010300"
Phchi.S6	AUGUSTUS	start_codon	787148	787150	.	+	0	transcript_id "Phchi.S6G010300.t1"; gene_id "Phchi.S6G010300"
Phchi.S6	AUGUSTUS	CDS	787148	788032	0.59	+	0	transcript_id "Phchi.S6G010300.t1"; gene_id "Phchi.S6G010300"
Phchi.S6	AUGUSTUS	exon	787148	788032	.	+	.	transcript_id "Phchi.S6G010300.t1"; gene_id "Phchi.S6G010300"
Phchi.S6	AUGUSTUS	stop_codon	788033	788035	.	+	0	transcript_id "Phchi.S6G010300.t1"; gene_id "Phchi.S6G010300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15472.t1 is derived from g13940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19364303	19365224	.	+	.	Phchi.S3G279100
Phchi.S3	AUGUSTUS	transcript	19364303	19365224	.	+	.	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	start_codon	19364303	19364305	.	+	0	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	CDS	19364303	19364680	0.45	+	0	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	exon	19364303	19364680	.	+	.	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	intron	19364681	19364753	.	+	.	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	CDS	19364754	19365019	1	+	0	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	exon	19364754	19365019	.	+	.	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	intron	19365020	19365175	.	+	.	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	CDS	19365176	19365224	1	+	1	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	exon	19365176	19365224	.	+	.	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
Phchi.S3	AUGUSTUS	stop_codon	19365225	19365227	.	+	0	transcript_id "Phchi.S3G279100.t1"; gene_id "Phchi.S3G279100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11116.t1 is derived from g15166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4231033	4234478	.	+	.	Phchi.S4G069800
Phchi.S4	AUGUSTUS	transcript	4231033	4234478	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	start_codon	4231033	4231035	.	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4231033	4231274	0.76	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4231033	4231274	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4231275	4231358	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4231359	4231605	1	+	1	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4231359	4231605	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4231606	4231687	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4231688	4231813	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4231688	4231813	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4231814	4231904	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4231905	4232060	0.96	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4231905	4232060	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4232061	4232170	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4232171	4232289	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4232171	4232289	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4232290	4232424	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4232425	4232513	1	+	1	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4232425	4232513	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4232514	4232605	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4232606	4232886	0.91	+	2	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4232606	4232886	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4232887	4232998	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4232999	4233232	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4232999	4233232	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4233233	4233310	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4233311	4233384	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4233311	4233384	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4233385	4233484	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4233485	4233578	1	+	1	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4233485	4233578	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4233579	4233668	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4233669	4233818	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4233669	4233818	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4233819	4233916	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4233917	4233991	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4233917	4233991	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4233992	4234123	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4234124	4234223	1	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4234124	4234223	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	intron	4234224	4234305	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	CDS	4234306	4234478	1	+	2	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	exon	4234306	4234478	.	+	.	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
Phchi.S4	AUGUSTUS	stop_codon	4234479	4234481	.	+	0	transcript_id "Phchi.S4G069800.t1"; gene_id "Phchi.S4G069800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15826.t1 is derived from g14296.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21609622	21610998	.	+	.	Phchi.S3G314500
Phchi.S3	AUGUSTUS	transcript	21609622	21610913	.	+	.	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	start_codon	21609622	21609624	.	+	0	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	CDS	21609622	21610729	0.51	+	0	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	exon	21609622	21610729	.	+	.	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	intron	21610730	21610803	.	+	.	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	CDS	21610804	21610913	0.75	+	2	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	exon	21610804	21610913	.	+	.	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	stop_codon	21610914	21610916	.	+	0	transcript_id "Phchi.S3G314500.t1"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	transcript	21609622	21610998	.	+	.	transcript_id "Phchi.S3G314500.t2"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	start_codon	21609622	21609624	.	+	0	transcript_id "Phchi.S3G314500.t2"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	CDS	21609622	21610998	0.75	+	0	transcript_id "Phchi.S3G314500.t2"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	exon	21609622	21610998	.	+	.	transcript_id "Phchi.S3G314500.t2"; gene_id "Phchi.S3G314500"
Phchi.S3	AUGUSTUS	stop_codon	21610999	21611001	.	+	0	transcript_id "Phchi.S3G314500.t2"; gene_id "Phchi.S3G314500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg627.t1 is derived from g10409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4462158	4464849	.	-	.	Phchi.S6G058600
Phchi.S6	AUGUSTUS	transcript	4462158	4464849	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	stop_codon	4462155	4462157	.	-	0	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	CDS	4462158	4464164	0.5	-	0	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	exon	4462158	4464164	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	intron	4464165	4464242	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	CDS	4464243	4464493	0.72	-	2	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	exon	4464243	4464493	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	intron	4464494	4464625	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	CDS	4464626	4464685	0.88	-	2	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	exon	4464626	4464685	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	intron	4464686	4464776	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	CDS	4464777	4464849	0.84	-	0	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	exon	4464777	4464849	.	-	.	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
Phchi.S6	AUGUSTUS	start_codon	4464847	4464849	.	-	0	transcript_id "Phchi.S6G058600.t1"; gene_id "Phchi.S6G058600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15898.t1 is derived from g14368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22060959	22061904	.	+	.	Phchi.S3G321700
Phchi.S3	AUGUSTUS	transcript	22060959	22061904	.	+	.	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	start_codon	22060959	22060961	.	+	0	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	CDS	22060959	22061270	0.99	+	0	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	exon	22060959	22061270	.	+	.	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	intron	22061271	22061367	.	+	.	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	CDS	22061368	22061904	0.99	+	0	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	exon	22061368	22061904	.	+	.	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
Phchi.S3	AUGUSTUS	stop_codon	22061905	22061907	.	+	0	transcript_id "Phchi.S3G321700.t1"; gene_id "Phchi.S3G321700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13376.t1 is derived from g11842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6419367	6421769	.	-	.	Phchi.S3G069500
Phchi.S3	AUGUSTUS	transcript	6419367	6421769	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	stop_codon	6419364	6419366	.	-	0	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	CDS	6419367	6419724	0.99	-	1	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	exon	6419367	6419724	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	intron	6419725	6419813	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	CDS	6419814	6420732	0.62	-	2	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	exon	6419814	6420732	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	intron	6420733	6420870	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	CDS	6420871	6421218	0.54	-	2	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	exon	6420871	6421218	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	intron	6421219	6421416	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	CDS	6421417	6421445	0.37	-	1	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	exon	6421417	6421445	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	intron	6421446	6421550	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	CDS	6421551	6421591	0.42	-	0	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	exon	6421551	6421591	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	intron	6421592	6421694	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	CDS	6421695	6421769	0.21	-	0	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	exon	6421695	6421769	.	-	.	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
Phchi.S3	AUGUSTUS	start_codon	6421767	6421769	.	-	0	transcript_id "Phchi.S3G069500.t1"; gene_id "Phchi.S3G069500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1783.t1 is derived from g8703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2990763	2993035	.	+	.	Phchi.S5G039200
Phchi.S5	AUGUSTUS	transcript	2990763	2993035	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	start_codon	2990763	2990765	.	+	0	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2990763	2990852	0.91	+	0	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2990763	2990852	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2990853	2990928	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2990929	2990989	0.88	+	0	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2990929	2990989	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2990990	2991177	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2991178	2991324	0.73	+	2	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2991178	2991324	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2991325	2991642	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2991643	2991676	0.95	+	2	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2991643	2991676	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2991677	2991892	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2991893	2991934	0.99	+	1	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2991893	2991934	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2991935	2992177	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2992178	2992313	0.99	+	1	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2992178	2992313	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2992314	2992540	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2992541	2992646	1	+	0	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2992541	2992646	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	intron	2992647	2992955	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	CDS	2992956	2993035	0.94	+	2	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	exon	2992956	2993035	.	+	.	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
Phchi.S5	AUGUSTUS	stop_codon	2993036	2993038	.	+	0	transcript_id "Phchi.S5G039200.t1"; gene_id "Phchi.S5G039200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2270.t1 is derived from g9190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5790623	5792674	.	-	.	Phchi.S5G087900
Phchi.S5	AUGUSTUS	transcript	5790623	5792674	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	stop_codon	5790620	5790622	.	-	0	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	CDS	5790623	5790633	0.76	-	2	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	exon	5790623	5790633	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	intron	5790634	5790884	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	CDS	5790885	5790946	0.54	-	1	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	exon	5790885	5790946	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	intron	5790947	5791038	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	CDS	5791039	5792458	0.72	-	2	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	exon	5791039	5792458	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	intron	5792459	5792577	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	CDS	5792578	5792674	0.59	-	0	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	exon	5792578	5792674	.	-	.	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
Phchi.S5	AUGUSTUS	start_codon	5792672	5792674	.	-	0	transcript_id "Phchi.S5G087900.t1"; gene_id "Phchi.S5G087900"
# This transcript jg15511.t2 is derived from g13980.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15511.t3 is derived from g13980.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15512.t1 is derived from g13981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19622186	19622815	.	-	.	Phchi.S3G283100
Phchi.S3	AUGUSTUS	transcript	19622186	19622815	.	-	.	transcript_id "Phchi.S3G283100.t1"; gene_id "Phchi.S3G283100"
Phchi.S3	AUGUSTUS	stop_codon	19622183	19622185	.	-	0	transcript_id "Phchi.S3G283100.t1"; gene_id "Phchi.S3G283100"
Phchi.S3	AUGUSTUS	CDS	19622186	19622815	0.86	-	0	transcript_id "Phchi.S3G283100.t1"; gene_id "Phchi.S3G283100"
Phchi.S3	AUGUSTUS	exon	19622186	19622815	.	-	.	transcript_id "Phchi.S3G283100.t1"; gene_id "Phchi.S3G283100"
Phchi.S3	AUGUSTUS	start_codon	19622813	19622815	.	-	0	transcript_id "Phchi.S3G283100.t1"; gene_id "Phchi.S3G283100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8480.t1 is derived from g5655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36141627	36142601	.	-	.	Phchi.S1G563900
Phchi.S1	AUGUSTUS	transcript	36141627	36142601	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	stop_codon	36141624	36141626	.	-	0	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	CDS	36141627	36142075	0.99	-	2	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	exon	36141627	36142075	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	intron	36142076	36142175	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	CDS	36142176	36142239	0.39	-	0	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	exon	36142176	36142239	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	intron	36142240	36142331	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	CDS	36142332	36142383	0.39	-	1	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	exon	36142332	36142383	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	intron	36142384	36142572	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	CDS	36142573	36142601	0.39	-	0	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	exon	36142573	36142601	.	-	.	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
Phchi.S1	AUGUSTUS	start_codon	36142599	36142601	.	-	0	transcript_id "Phchi.S1G563900.t1"; gene_id "Phchi.S1G563900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5173.t1 is derived from g2343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15318904	15320327	.	-	.	Phchi.S1G233200
Phchi.S1	AUGUSTUS	transcript	15318904	15320327	.	-	.	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	stop_codon	15318901	15318903	.	-	0	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	CDS	15318904	15319579	1	-	1	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	exon	15318904	15319579	.	-	.	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	intron	15319580	15319686	.	-	.	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	CDS	15319687	15319710	0.83	-	1	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	exon	15319687	15319710	.	-	.	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	intron	15319711	15319845	.	-	.	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	CDS	15319846	15320327	0.78	-	0	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	exon	15319846	15320327	.	-	.	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
Phchi.S1	AUGUSTUS	start_codon	15320325	15320327	.	-	0	transcript_id "Phchi.S1G233200.t1"; gene_id "Phchi.S1G233200"
# This transcript jg9335.t2 is derived from g6510.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9336.t1 is derived from g6511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40992896	40995375	.	+	.	Phchi.S1G649500
Phchi.S1	AUGUSTUS	transcript	40992896	40995375	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	start_codon	40992896	40992898	.	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	CDS	40992896	40992913	0.58	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	exon	40992896	40992913	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	intron	40992914	40993128	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	CDS	40993129	40993209	0.92	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	exon	40993129	40993209	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	intron	40993210	40993364	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	CDS	40993365	40993583	1	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	exon	40993365	40993583	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	intron	40993584	40993744	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	CDS	40993745	40994506	0.99	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	exon	40993745	40994506	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	intron	40994507	40995174	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	CDS	40995175	40995375	0.74	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	exon	40995175	40995375	.	+	.	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
Phchi.S1	AUGUSTUS	stop_codon	40995376	40995378	.	+	0	transcript_id "Phchi.S1G649500.t1"; gene_id "Phchi.S1G649500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9606.t1 is derived from g6782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42910823	42912485	.	+	.	Phchi.S1G676500
Phchi.S1	AUGUSTUS	transcript	42910823	42912485	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	start_codon	42910823	42910825	.	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42910823	42910882	1	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42910823	42910882	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42910883	42910971	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42910972	42911058	1	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42910972	42911058	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42911059	42911155	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42911156	42911224	1	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42911156	42911224	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42911225	42911319	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42911320	42911513	1	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42911320	42911513	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42911514	42911588	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42911589	42911730	1	+	1	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42911589	42911730	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42911731	42911827	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42911828	42912037	1	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42911828	42912037	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42912038	42912130	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42912131	42912208	1	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42912131	42912208	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	intron	42912209	42912287	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	CDS	42912288	42912485	0.96	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	exon	42912288	42912485	.	+	.	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
Phchi.S1	AUGUSTUS	stop_codon	42912486	42912488	.	+	0	transcript_id "Phchi.S1G676500.t1"; gene_id "Phchi.S1G676500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2826.t1 is derived from g9746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9063343	9064677	.	-	.	Phchi.S5G143500
Phchi.S5	AUGUSTUS	transcript	9063343	9064677	.	-	.	transcript_id "Phchi.S5G143500.t1"; gene_id "Phchi.S5G143500"
Phchi.S5	AUGUSTUS	stop_codon	9063340	9063342	.	-	0	transcript_id "Phchi.S5G143500.t1"; gene_id "Phchi.S5G143500"
Phchi.S5	AUGUSTUS	CDS	9063343	9064677	0.66	-	0	transcript_id "Phchi.S5G143500.t1"; gene_id "Phchi.S5G143500"
Phchi.S5	AUGUSTUS	exon	9063343	9064677	.	-	.	transcript_id "Phchi.S5G143500.t1"; gene_id "Phchi.S5G143500"
Phchi.S5	AUGUSTUS	start_codon	9064675	9064677	.	-	0	transcript_id "Phchi.S5G143500.t1"; gene_id "Phchi.S5G143500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6267.t1 is derived from g3439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21933656	21935937	.	-	.	Phchi.S1G342600
Phchi.S1	AUGUSTUS	transcript	21933656	21935937	.	-	.	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	stop_codon	21933653	21933655	.	-	0	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	CDS	21933656	21934012	0.96	-	0	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	exon	21933656	21934012	.	-	.	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	intron	21934013	21934101	.	-	.	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	CDS	21934102	21934362	1	-	0	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	exon	21934102	21934362	.	-	.	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	intron	21934363	21934467	.	-	.	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	CDS	21934468	21935937	0.21	-	0	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	exon	21934468	21935937	.	-	.	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
Phchi.S1	AUGUSTUS	start_codon	21935935	21935937	.	-	0	transcript_id "Phchi.S1G342600.t1"; gene_id "Phchi.S1G342600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12197.t1 is derived from g7873.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6674753	6679027	.	-	.	Phchi.S2G027700
Phchi.S2	AUGUSTUS	transcript	6674753	6679027	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	stop_codon	6674750	6674752	.	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6674753	6674824	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6674753	6674824	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6674825	6674903	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6674904	6674973	1	-	1	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6674904	6674973	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6674974	6675065	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6675066	6675160	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6675066	6675160	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6675161	6675261	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6675262	6675301	1	-	1	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6675262	6675301	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6675302	6675404	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6675405	6675463	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6675405	6675463	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6675464	6675560	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6675561	6675642	1	-	1	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6675561	6675642	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6675643	6675732	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6675733	6675872	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6675733	6675872	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6675873	6675984	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6675985	6676047	0.99	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6675985	6676047	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6676048	6676130	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6676131	6676250	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6676131	6676250	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6676251	6676323	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6676324	6676425	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6676324	6676425	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6676426	6676540	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6676541	6676627	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6676541	6676627	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6676628	6676745	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6676746	6676838	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6676746	6676838	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6676839	6676979	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6676980	6677057	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6676980	6677057	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6677058	6677196	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6677197	6677254	0.61	-	1	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6677197	6677254	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6677255	6677556	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6677557	6677654	0.69	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6677557	6677654	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6677655	6677765	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6677766	6677873	0.9	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6677766	6677873	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6677874	6677992	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6677993	6678055	0.99	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6677993	6678055	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6678056	6678154	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6678155	6678283	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6678155	6678283	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6678284	6678387	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6678388	6678537	0.99	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6678388	6678537	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	intron	6678538	6678766	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	CDS	6678767	6679027	1	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	exon	6678767	6679027	.	-	.	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
Phchi.S2	AUGUSTUS	start_codon	6679025	6679027	.	-	0	transcript_id "Phchi.S2G027700.t1"; gene_id "Phchi.S2G027700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg511.t1 is derived from g10293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3527398	3528290	.	-	.	Phchi.S6G047000
Phchi.S6	AUGUSTUS	transcript	3527398	3528290	.	-	.	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	stop_codon	3527395	3527397	.	-	0	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	CDS	3527398	3527400	1	-	0	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	exon	3527398	3527400	.	-	.	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	intron	3527401	3527649	.	-	.	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	CDS	3527650	3527766	1	-	0	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	exon	3527650	3527766	.	-	.	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	intron	3527767	3528197	.	-	.	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	CDS	3528198	3528290	0.74	-	0	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	exon	3528198	3528290	.	-	.	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
Phchi.S6	AUGUSTUS	start_codon	3528288	3528290	.	-	0	transcript_id "Phchi.S6G047000.t1"; gene_id "Phchi.S6G047000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12135.t1 is derived from g7811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4466356	4466880	.	-	.	Phchi.S2G021500
Phchi.S2	AUGUSTUS	transcript	4466356	4466880	.	-	.	transcript_id "Phchi.S2G021500.t1"; gene_id "Phchi.S2G021500"
Phchi.S2	AUGUSTUS	stop_codon	4466353	4466355	.	-	0	transcript_id "Phchi.S2G021500.t1"; gene_id "Phchi.S2G021500"
Phchi.S2	AUGUSTUS	CDS	4466356	4466880	0.77	-	0	transcript_id "Phchi.S2G021500.t1"; gene_id "Phchi.S2G021500"
Phchi.S2	AUGUSTUS	exon	4466356	4466880	.	-	.	transcript_id "Phchi.S2G021500.t1"; gene_id "Phchi.S2G021500"
Phchi.S2	AUGUSTUS	start_codon	4466878	4466880	.	-	0	transcript_id "Phchi.S2G021500.t1"; gene_id "Phchi.S2G021500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg537.t1 is derived from g10319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3915411	3916813	.	-	.	Phchi.S6G049600
Phchi.S6	AUGUSTUS	transcript	3915411	3916813	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	stop_codon	3915408	3915410	.	-	0	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	CDS	3915411	3915471	0.59	-	1	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	exon	3915411	3915471	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	intron	3915472	3915868	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	CDS	3915869	3915942	0.59	-	0	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	exon	3915869	3915942	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	intron	3915943	3916232	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	CDS	3916233	3916314	0.64	-	1	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	exon	3916233	3916314	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	intron	3916315	3916418	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	CDS	3916419	3916813	0.91	-	0	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	exon	3916419	3916813	.	-	.	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
Phchi.S6	AUGUSTUS	start_codon	3916811	3916813	.	-	0	transcript_id "Phchi.S6G049600.t1"; gene_id "Phchi.S6G049600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8363.t1 is derived from g5538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35521502	35522332	.	-	.	Phchi.S1G552200
Phchi.S1	AUGUSTUS	transcript	35521502	35522332	.	-	.	transcript_id "Phchi.S1G552200.t1"; gene_id "Phchi.S1G552200"
Phchi.S1	AUGUSTUS	stop_codon	35521499	35521501	.	-	0	transcript_id "Phchi.S1G552200.t1"; gene_id "Phchi.S1G552200"
Phchi.S1	AUGUSTUS	CDS	35521502	35522332	0.92	-	0	transcript_id "Phchi.S1G552200.t1"; gene_id "Phchi.S1G552200"
Phchi.S1	AUGUSTUS	exon	35521502	35522332	.	-	.	transcript_id "Phchi.S1G552200.t1"; gene_id "Phchi.S1G552200"
Phchi.S1	AUGUSTUS	start_codon	35522330	35522332	.	-	0	transcript_id "Phchi.S1G552200.t1"; gene_id "Phchi.S1G552200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3755.t1 is derived from g924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5544991	5546304	.	-	.	Phchi.S1G091400
Phchi.S1	AUGUSTUS	transcript	5544991	5546304	.	-	.	transcript_id "Phchi.S1G091400.t1"; gene_id "Phchi.S1G091400"
Phchi.S1	AUGUSTUS	stop_codon	5544988	5544990	.	-	0	transcript_id "Phchi.S1G091400.t1"; gene_id "Phchi.S1G091400"
Phchi.S1	AUGUSTUS	CDS	5544991	5546304	0.53	-	0	transcript_id "Phchi.S1G091400.t1"; gene_id "Phchi.S1G091400"
Phchi.S1	AUGUSTUS	exon	5544991	5546304	.	-	.	transcript_id "Phchi.S1G091400.t1"; gene_id "Phchi.S1G091400"
Phchi.S1	AUGUSTUS	start_codon	5546302	5546304	.	-	0	transcript_id "Phchi.S1G091400.t1"; gene_id "Phchi.S1G091400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12981.t1 is derived from g11446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3439828	3445071	.	-	.	Phchi.S3G030000
Phchi.S3	AUGUSTUS	transcript	3439828	3445071	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	stop_codon	3439825	3439827	.	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3439828	3440194	1	-	1	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3439828	3440194	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3440195	3440310	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3440311	3440894	0.98	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3440311	3440894	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3440895	3440965	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3440966	3441094	0.45	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3440966	3441094	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3441095	3441176	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3441177	3441389	1	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3441177	3441389	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3441390	3441475	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3441476	3442546	0.95	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3441476	3442546	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3442547	3442630	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3442631	3442941	0.94	-	2	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3442631	3442941	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3442942	3443035	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3443036	3443265	1	-	1	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3443036	3443265	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3443266	3443353	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3443354	3443811	1	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3443354	3443811	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3443812	3443901	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3443902	3444080	1	-	2	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3443902	3444080	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3444081	3444204	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3444205	3444259	1	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3444205	3444259	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	intron	3444260	3444417	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	CDS	3444418	3445071	1	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	exon	3444418	3445071	.	-	.	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
Phchi.S3	AUGUSTUS	start_codon	3445069	3445071	.	-	0	transcript_id "Phchi.S3G030000.t1"; gene_id "Phchi.S3G030000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8507.t1 is derived from g5682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36371381	36372696	.	-	.	Phchi.S1G566600
Phchi.S1	AUGUSTUS	transcript	36371381	36372696	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	stop_codon	36371378	36371380	.	-	0	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36371381	36371403	1	-	2	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36371381	36371403	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	intron	36371404	36371743	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36371744	36371802	0.95	-	1	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36371744	36371802	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	intron	36371803	36371898	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36371899	36371969	0.7	-	0	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36371899	36371969	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	intron	36371970	36372056	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36372057	36372110	1	-	0	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36372057	36372110	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	intron	36372111	36372201	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36372202	36372240	1	-	0	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36372202	36372240	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	intron	36372241	36372336	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36372337	36372541	1	-	1	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36372337	36372541	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	intron	36372542	36372637	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	CDS	36372638	36372696	1	-	0	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	exon	36372638	36372696	.	-	.	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
Phchi.S1	AUGUSTUS	start_codon	36372694	36372696	.	-	0	transcript_id "Phchi.S1G566600.t1"; gene_id "Phchi.S1G566600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5983.t1 is derived from g3154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20234137	20239690	.	+	.	Phchi.S1G314200
Phchi.S1	AUGUSTUS	transcript	20234137	20239690	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	start_codon	20234137	20234139	.	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20234137	20234262	0.9	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20234137	20234262	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20234263	20234362	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20234363	20234414	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20234363	20234414	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20234415	20234484	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20234485	20234532	1	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20234485	20234532	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20234533	20234702	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20234703	20234857	1	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20234703	20234857	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20234858	20234956	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20234957	20235014	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20234957	20235014	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20235015	20235154	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20235155	20235212	1	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20235155	20235212	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20235213	20235304	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20235305	20235397	1	+	1	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20235305	20235397	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20235398	20235490	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20235491	20235675	0.9	+	1	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20235491	20235675	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20235676	20235816	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20235817	20235828	0.56	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20235817	20235828	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20235829	20235969	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20235970	20236085	0.97	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20235970	20236085	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20236086	20236248	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20236249	20236348	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20236249	20236348	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20236349	20236432	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20236433	20237276	0.65	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20236433	20237276	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20237277	20237378	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20237379	20237434	1	+	1	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20237379	20237434	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20237435	20237555	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20237556	20237698	1	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20237556	20237698	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20237699	20237823	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20237824	20238009	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20237824	20238009	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20238010	20238098	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20238099	20238143	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20238099	20238143	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20238144	20238315	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20238316	20238372	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20238316	20238372	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20238373	20238488	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20238489	20238583	0.98	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20238489	20238583	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20238584	20238739	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20238740	20238770	1	+	1	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20238740	20238770	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20238771	20238893	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20238894	20238953	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20238894	20238953	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20238954	20239039	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20239040	20239112	1	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20239040	20239112	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20239113	20239208	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20239209	20239294	1	+	2	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20239209	20239294	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	intron	20239295	20239384	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	CDS	20239385	20239690	0.79	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	exon	20239385	20239690	.	+	.	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
Phchi.S1	AUGUSTUS	stop_codon	20239691	20239693	.	+	0	transcript_id "Phchi.S1G314200.t1"; gene_id "Phchi.S1G314200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8267.t1 is derived from g5442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35032376	35034629	.	-	.	Phchi.S1G542600
Phchi.S1	AUGUSTUS	transcript	35032376	35034629	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	stop_codon	35032373	35032375	.	-	0	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35032376	35032470	1	-	2	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35032376	35032470	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	intron	35032471	35032562	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35032563	35032674	1	-	0	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35032563	35032674	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	intron	35032675	35032760	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35032761	35032896	1	-	1	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35032761	35032896	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	intron	35032897	35032993	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35032994	35033259	1	-	0	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35032994	35033259	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	intron	35033260	35033333	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35033334	35033509	0.91	-	2	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35033334	35033509	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	intron	35033510	35033615	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35033616	35033774	0.98	-	2	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35033616	35033774	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	intron	35033775	35034586	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	CDS	35034587	35034629	1	-	0	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	exon	35034587	35034629	.	-	.	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
Phchi.S1	AUGUSTUS	start_codon	35034627	35034629	.	-	0	transcript_id "Phchi.S1G542600.t1"; gene_id "Phchi.S1G542600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5213.t1 is derived from g2383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15504012	15506966	.	-	.	Phchi.S1G237200
Phchi.S1	AUGUSTUS	transcript	15504012	15506966	.	-	.	transcript_id "Phchi.S1G237200.t1"; gene_id "Phchi.S1G237200"
Phchi.S1	AUGUSTUS	stop_codon	15504009	15504011	.	-	0	transcript_id "Phchi.S1G237200.t1"; gene_id "Phchi.S1G237200"
Phchi.S1	AUGUSTUS	CDS	15504012	15506966	0.75	-	0	transcript_id "Phchi.S1G237200.t1"; gene_id "Phchi.S1G237200"
Phchi.S1	AUGUSTUS	exon	15504012	15506966	.	-	.	transcript_id "Phchi.S1G237200.t1"; gene_id "Phchi.S1G237200"
Phchi.S1	AUGUSTUS	start_codon	15506964	15506966	.	-	0	transcript_id "Phchi.S1G237200.t1"; gene_id "Phchi.S1G237200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9745.t1 is derived from g6921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43480346	43482492	.	-	.	Phchi.S1G690400
Phchi.S1	AUGUSTUS	transcript	43480346	43482492	.	-	.	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	stop_codon	43480343	43480345	.	-	0	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	CDS	43480346	43482282	0.69	-	2	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	exon	43480346	43482282	.	-	.	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	intron	43482283	43482404	.	-	.	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	CDS	43482405	43482492	0.68	-	0	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	exon	43482405	43482492	.	-	.	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
Phchi.S1	AUGUSTUS	start_codon	43482490	43482492	.	-	0	transcript_id "Phchi.S1G690400.t1"; gene_id "Phchi.S1G690400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10050.t1 is derived from g7226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45387878	45389551	.	+	.	Phchi.S1G720900
Phchi.S1	AUGUSTUS	transcript	45387878	45389551	.	+	.	transcript_id "Phchi.S1G720900.t1"; gene_id "Phchi.S1G720900"
Phchi.S1	AUGUSTUS	start_codon	45387878	45387880	.	+	0	transcript_id "Phchi.S1G720900.t1"; gene_id "Phchi.S1G720900"
Phchi.S1	AUGUSTUS	CDS	45387878	45389551	0.29	+	0	transcript_id "Phchi.S1G720900.t1"; gene_id "Phchi.S1G720900"
Phchi.S1	AUGUSTUS	exon	45387878	45389551	.	+	.	transcript_id "Phchi.S1G720900.t1"; gene_id "Phchi.S1G720900"
Phchi.S1	AUGUSTUS	stop_codon	45389552	45389554	.	+	0	transcript_id "Phchi.S1G720900.t1"; gene_id "Phchi.S1G720900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8771.t1 is derived from g5946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37890953	37893282	.	+	.	Phchi.S1G593000
Phchi.S1	AUGUSTUS	transcript	37890953	37893282	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	start_codon	37890953	37890955	.	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37890953	37890971	1	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37890953	37890971	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37890972	37891064	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37891065	37891165	0.81	+	2	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37891065	37891165	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37891166	37891283	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37891284	37891451	1	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37891284	37891451	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37891452	37891548	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37891549	37891679	1	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37891549	37891679	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37891680	37891802	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37891803	37892033	0.65	+	1	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37891803	37892033	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37892034	37892140	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37892141	37892316	0.51	+	1	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37892141	37892316	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37892317	37892419	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37892420	37892517	1	+	2	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37892420	37892517	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37892518	37892603	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37892604	37892887	1	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37892604	37892887	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37892888	37893010	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37893011	37893128	1	+	1	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37893011	37893128	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	intron	37893129	37893264	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	CDS	37893265	37893282	1	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	exon	37893265	37893282	.	+	.	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
Phchi.S1	AUGUSTUS	stop_codon	37893283	37893285	.	+	0	transcript_id "Phchi.S1G593000.t1"; gene_id "Phchi.S1G593000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13826.t1 is derived from g12293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9085481	9087894	.	+	.	Phchi.S3G114500
Phchi.S3	AUGUSTUS	transcript	9085481	9087894	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	start_codon	9085481	9085483	.	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9085481	9085648	0.64	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9085481	9085648	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9085649	9085745	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9085746	9085869	1	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9085746	9085869	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9085870	9085946	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9085947	9086086	0.52	+	2	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9085947	9086086	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9086087	9086244	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9086245	9086283	0.94	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9086245	9086283	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9086284	9086379	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9086380	9086424	0.82	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9086380	9086424	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9086425	9086502	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9086503	9086583	0.97	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9086503	9086583	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9086584	9086674	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9086675	9086754	1	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9086675	9086754	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9086755	9086856	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9086857	9087055	1	+	1	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9086857	9087055	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9087056	9087155	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9087156	9087211	1	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9087156	9087211	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9087212	9087293	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9087294	9087440	1	+	1	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9087294	9087440	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9087441	9087524	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9087525	9087702	1	+	1	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9087525	9087702	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	intron	9087703	9087801	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	CDS	9087802	9087894	0.86	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	exon	9087802	9087894	.	+	.	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
Phchi.S3	AUGUSTUS	stop_codon	9087895	9087897	.	+	0	transcript_id "Phchi.S3G114500.t1"; gene_id "Phchi.S3G114500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6260.t1 is derived from g3432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21917370	21919844	.	-	.	Phchi.S1G341900
Phchi.S1	AUGUSTUS	transcript	21917370	21919844	.	-	.	transcript_id "Phchi.S1G341900.t1"; gene_id "Phchi.S1G341900"
Phchi.S1	AUGUSTUS	stop_codon	21917367	21917369	.	-	0	transcript_id "Phchi.S1G341900.t1"; gene_id "Phchi.S1G341900"
Phchi.S1	AUGUSTUS	CDS	21917370	21919844	0.95	-	0	transcript_id "Phchi.S1G341900.t1"; gene_id "Phchi.S1G341900"
Phchi.S1	AUGUSTUS	exon	21917370	21919844	.	-	.	transcript_id "Phchi.S1G341900.t1"; gene_id "Phchi.S1G341900"
Phchi.S1	AUGUSTUS	start_codon	21919842	21919844	.	-	0	transcript_id "Phchi.S1G341900.t1"; gene_id "Phchi.S1G341900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3209.t1 is derived from g378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2242352	2243374	.	-	.	Phchi.S1G036800
Phchi.S1	AUGUSTUS	transcript	2242352	2243374	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	stop_codon	2242349	2242351	.	-	0	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	CDS	2242352	2242466	0.99	-	1	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	exon	2242352	2242466	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	intron	2242467	2242601	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	CDS	2242602	2242759	1	-	0	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	exon	2242602	2242759	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	intron	2242760	2242873	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	CDS	2242874	2243002	1	-	0	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	exon	2242874	2243002	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	intron	2243003	2243123	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	CDS	2243124	2243197	1	-	2	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	exon	2243124	2243197	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	intron	2243198	2243346	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	CDS	2243347	2243374	0.98	-	0	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	exon	2243347	2243374	.	-	.	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
Phchi.S1	AUGUSTUS	start_codon	2243372	2243374	.	-	0	transcript_id "Phchi.S1G036800.t1"; gene_id "Phchi.S1G036800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15408.t1 is derived from g13876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18862301	18864177	.	+	.	Phchi.S3G272700
Phchi.S3	AUGUSTUS	transcript	18862301	18864177	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	start_codon	18862301	18862303	.	+	0	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18862301	18862385	0.95	+	0	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18862301	18862385	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	intron	18862386	18862655	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18862656	18862852	0.39	+	2	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18862656	18862852	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	intron	18862853	18863063	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18863064	18863068	1	+	0	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18863064	18863068	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	intron	18863069	18863167	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18863168	18863301	1	+	1	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18863168	18863301	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	intron	18863302	18863539	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18863540	18863648	1	+	2	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18863540	18863648	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	intron	18863649	18863774	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18863775	18863892	1	+	1	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18863775	18863892	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	intron	18863893	18864108	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	CDS	18864109	18864177	1	+	0	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	exon	18864109	18864177	.	+	.	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
Phchi.S3	AUGUSTUS	stop_codon	18864178	18864180	.	+	0	transcript_id "Phchi.S3G272700.t1"; gene_id "Phchi.S3G272700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11385.t1 is derived from g15435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6045267	6045554	.	-	.	Phchi.S4G096700
Phchi.S4	AUGUSTUS	transcript	6045267	6045554	.	-	.	transcript_id "Phchi.S4G096700.t1"; gene_id "Phchi.S4G096700"
Phchi.S4	AUGUSTUS	stop_codon	6045264	6045266	.	-	0	transcript_id "Phchi.S4G096700.t1"; gene_id "Phchi.S4G096700"
Phchi.S4	AUGUSTUS	CDS	6045267	6045554	0.98	-	0	transcript_id "Phchi.S4G096700.t1"; gene_id "Phchi.S4G096700"
Phchi.S4	AUGUSTUS	exon	6045267	6045554	.	-	.	transcript_id "Phchi.S4G096700.t1"; gene_id "Phchi.S4G096700"
Phchi.S4	AUGUSTUS	start_codon	6045552	6045554	.	-	0	transcript_id "Phchi.S4G096700.t1"; gene_id "Phchi.S4G096700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14244.t1 is derived from g12711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11712466	11717526	.	+	.	Phchi.S3G156300
Phchi.S3	AUGUSTUS	transcript	11712466	11717526	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	start_codon	11712466	11712468	.	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11712466	11712498	0.47	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11712466	11712498	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11712499	11712639	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11712640	11712782	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11712640	11712782	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11712783	11712868	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11712869	11712893	0.99	+	1	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11712869	11712893	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11712894	11712990	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11712991	11713065	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11712991	11713065	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11713066	11713168	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11713169	11713270	0.91	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11713169	11713270	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11713271	11713384	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11713385	11713435	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11713385	11713435	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11713436	11713649	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11713650	11713755	0.99	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11713650	11713755	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11713756	11713868	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11713869	11713982	0.99	+	2	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11713869	11713982	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11713983	11714060	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11714061	11714152	0.97	+	2	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11714061	11714152	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11714153	11714361	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11714362	11714443	0.86	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11714362	11714443	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11714444	11714620	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11714621	11714697	1	+	2	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11714621	11714697	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11714698	11714776	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11714777	11714875	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11714777	11714875	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11714876	11714953	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11714954	11715044	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11714954	11715044	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11715045	11715287	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11715288	11715373	1	+	2	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11715288	11715373	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11715374	11715471	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11715472	11715630	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11715472	11715630	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11715631	11715758	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11715759	11715812	0.88	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11715759	11715812	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11715813	11715914	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11715915	11716043	0.96	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11715915	11716043	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11716044	11716183	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11716184	11716276	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11716184	11716276	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11716277	11716365	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11716366	11716512	0.98	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11716366	11716512	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11716513	11716619	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11716620	11716717	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11716620	11716717	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11716718	11716788	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11716789	11716873	1	+	1	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11716789	11716873	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11716874	11716958	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11716959	11717017	1	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11716959	11717017	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11717018	11717113	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11717114	11717212	1	+	1	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11717114	11717212	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11717213	11717292	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11717293	11717379	1	+	1	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11717293	11717379	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	intron	11717380	11717456	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	CDS	11717457	11717526	1	+	1	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	exon	11717457	11717526	.	+	.	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
Phchi.S3	AUGUSTUS	stop_codon	11717527	11717529	.	+	0	transcript_id "Phchi.S3G156300.t1"; gene_id "Phchi.S3G156300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6057.t1 is derived from g3228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20667919	20669702	.	-	.	Phchi.S1G321600
Phchi.S1	AUGUSTUS	transcript	20667919	20669702	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	stop_codon	20667916	20667918	.	-	0	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	CDS	20667919	20668174	1	-	1	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	exon	20667919	20668174	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	intron	20668175	20668275	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	CDS	20668276	20668493	1	-	0	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	exon	20668276	20668493	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	intron	20668494	20668577	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	CDS	20668578	20669069	1	-	0	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	exon	20668578	20669069	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	intron	20669070	20669186	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	CDS	20669187	20669702	0.98	-	0	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	exon	20669187	20669702	.	-	.	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
Phchi.S1	AUGUSTUS	start_codon	20669700	20669702	.	-	0	transcript_id "Phchi.S1G321600.t1"; gene_id "Phchi.S1G321600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12932.t1 is derived from g11397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3205584	3206573	.	+	.	Phchi.S3G025100
Phchi.S3	AUGUSTUS	transcript	3205584	3206573	.	+	.	transcript_id "Phchi.S3G025100.t1"; gene_id "Phchi.S3G025100"
Phchi.S3	AUGUSTUS	start_codon	3205584	3205586	.	+	0	transcript_id "Phchi.S3G025100.t1"; gene_id "Phchi.S3G025100"
Phchi.S3	AUGUSTUS	CDS	3205584	3206573	0.72	+	0	transcript_id "Phchi.S3G025100.t1"; gene_id "Phchi.S3G025100"
Phchi.S3	AUGUSTUS	exon	3205584	3206573	.	+	.	transcript_id "Phchi.S3G025100.t1"; gene_id "Phchi.S3G025100"
Phchi.S3	AUGUSTUS	stop_codon	3206574	3206576	.	+	0	transcript_id "Phchi.S3G025100.t1"; gene_id "Phchi.S3G025100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15750.t1 is derived from g14220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21053785	21054498	.	+	.	Phchi.S3G306900
Phchi.S3	AUGUSTUS	transcript	21053785	21054498	.	+	.	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	start_codon	21053785	21053787	.	+	0	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	CDS	21053785	21054245	1	+	0	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	exon	21053785	21054245	.	+	.	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	intron	21054246	21054386	.	+	.	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	CDS	21054387	21054498	1	+	1	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	exon	21054387	21054498	.	+	.	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
Phchi.S3	AUGUSTUS	stop_codon	21054499	21054501	.	+	0	transcript_id "Phchi.S3G306900.t1"; gene_id "Phchi.S3G306900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14661.t1 is derived from g13129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14003535	14006610	.	+	.	Phchi.S3G198000
Phchi.S3	AUGUSTUS	transcript	14003535	14006610	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	start_codon	14003535	14003537	.	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14003535	14003666	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14003535	14003666	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14003667	14003788	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14003789	14003827	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14003789	14003827	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14003828	14003940	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14003941	14004003	0.98	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14003941	14004003	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004004	14004112	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004113	14004193	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004113	14004193	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004194	14004285	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004286	14004344	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004286	14004344	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004345	14004491	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004492	14004600	1	+	1	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004492	14004600	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004601	14004705	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004706	14004876	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004706	14004876	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004877	14005032	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005033	14005102	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005033	14005102	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005103	14005418	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005419	14005511	1	+	2	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005419	14005511	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005512	14005612	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005613	14005656	0.97	+	2	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005613	14005656	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005657	14005766	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005767	14005802	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005767	14005802	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005803	14005966	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005967	14006119	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005967	14006119	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14006120	14006235	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14006236	14006330	1	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14006236	14006330	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14006331	14006408	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14006409	14006610	1	+	1	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14006409	14006610	.	+	.	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	stop_codon	14006611	14006613	.	+	0	transcript_id "Phchi.S3G198000.t1"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	transcript	14003535	14006610	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	start_codon	14003535	14003537	.	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14003535	14003666	1	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14003535	14003666	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14003667	14003788	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14003789	14003827	0.91	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14003789	14003827	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14003828	14003940	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14003941	14004003	0.9	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14003941	14004003	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004004	14004173	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004174	14004193	0.72	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004174	14004193	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004194	14004285	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004286	14004348	0.83	+	1	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004286	14004348	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004349	14004491	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004492	14004600	1	+	1	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004492	14004600	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004601	14004705	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14004706	14004876	1	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14004706	14004876	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14004877	14005032	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005033	14005102	1	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005033	14005102	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005103	14005418	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005419	14005511	1	+	2	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005419	14005511	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005512	14005612	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005613	14005656	0.97	+	2	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005613	14005656	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005657	14005766	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005767	14005802	0.99	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005767	14005802	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14005803	14005966	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14005967	14006119	1	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14005967	14006119	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14006120	14006235	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14006236	14006330	1	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14006236	14006330	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	intron	14006331	14006408	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	CDS	14006409	14006610	0.99	+	1	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	exon	14006409	14006610	.	+	.	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
Phchi.S3	AUGUSTUS	stop_codon	14006611	14006613	.	+	0	transcript_id "Phchi.S3G198000.t2"; gene_id "Phchi.S3G198000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3442.t1 is derived from g611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3713912	3714589	.	-	.	Phchi.S1G060100
Phchi.S1	AUGUSTUS	transcript	3713912	3714589	.	-	.	transcript_id "Phchi.S1G060100.t1"; gene_id "Phchi.S1G060100"
Phchi.S1	AUGUSTUS	stop_codon	3713909	3713911	.	-	0	transcript_id "Phchi.S1G060100.t1"; gene_id "Phchi.S1G060100"
Phchi.S1	AUGUSTUS	CDS	3713912	3714589	0.99	-	0	transcript_id "Phchi.S1G060100.t1"; gene_id "Phchi.S1G060100"
Phchi.S1	AUGUSTUS	exon	3713912	3714589	.	-	.	transcript_id "Phchi.S1G060100.t1"; gene_id "Phchi.S1G060100"
Phchi.S1	AUGUSTUS	start_codon	3714587	3714589	.	-	0	transcript_id "Phchi.S1G060100.t1"; gene_id "Phchi.S1G060100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13868.t1 is derived from g12335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9388408	9389720	.	+	.	Phchi.S3G118700
Phchi.S3	AUGUSTUS	transcript	9388408	9389720	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	start_codon	9388408	9388410	.	+	0	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	CDS	9388408	9388587	1	+	0	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	exon	9388408	9388587	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	intron	9388588	9388680	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	CDS	9388681	9388815	1	+	0	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	exon	9388681	9388815	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	intron	9388816	9388915	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	CDS	9388916	9389147	1	+	0	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	exon	9388916	9389147	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	intron	9389148	9389254	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	CDS	9389255	9389458	1	+	2	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	exon	9389255	9389458	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	intron	9389459	9389559	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	CDS	9389560	9389720	1	+	2	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	exon	9389560	9389720	.	+	.	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
Phchi.S3	AUGUSTUS	stop_codon	9389721	9389723	.	+	0	transcript_id "Phchi.S3G118700.t1"; gene_id "Phchi.S3G118700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15925.t1 is derived from g14395.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22247120	22249814	.	-	.	Phchi.S3G324400
Phchi.S3	AUGUSTUS	transcript	22247120	22249814	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	stop_codon	22247117	22247119	.	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247120	22247264	1	-	1	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247120	22247264	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22247265	22247360	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247361	22247551	1	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247361	22247551	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22247552	22247639	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247640	22247807	1	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247640	22247807	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22247808	22247896	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247897	22248064	1	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247897	22248064	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22248065	22248182	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22248183	22248390	1	-	1	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22248183	22248390	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22248391	22248618	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22248619	22248813	1	-	1	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22248619	22248813	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22248814	22248917	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22248918	22249006	1	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22248918	22249006	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22249007	22249129	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22249130	22249197	1	-	2	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22249130	22249197	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22249198	22249280	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22249281	22249362	1	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22249281	22249362	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22249363	22249457	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22249458	22249814	0.76	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22249458	22249814	.	-	.	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	start_codon	22249812	22249814	.	-	0	transcript_id "Phchi.S3G324400.t1"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	transcript	22247120	22249814	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	stop_codon	22247117	22247119	.	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247120	22247264	1	-	1	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247120	22247264	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22247265	22247360	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247361	22247551	1	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247361	22247551	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22247552	22247639	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247640	22247807	1	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247640	22247807	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22247808	22247896	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22247897	22248064	1	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22247897	22248064	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22248065	22248182	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22248183	22248390	0.99	-	1	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22248183	22248390	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22248391	22248618	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22248619	22248813	1	-	1	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22248619	22248813	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22248814	22248917	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22248918	22249006	1	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22248918	22249006	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22249007	22249129	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22249130	22249197	1	-	2	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22249130	22249197	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22249198	22249280	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22249281	22249359	1	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22249281	22249359	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	intron	22249360	22249457	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	CDS	22249458	22249814	0.76	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	exon	22249458	22249814	.	-	.	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
Phchi.S3	AUGUSTUS	start_codon	22249812	22249814	.	-	0	transcript_id "Phchi.S3G324400.t2"; gene_id "Phchi.S3G324400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1752.t1 is derived from g8672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2881437	2886066	.	+	.	Phchi.S5G036100
Phchi.S5	AUGUSTUS	transcript	2881437	2886066	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	start_codon	2881437	2881439	.	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2881437	2883002	0.51	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2881437	2883002	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2883003	2883094	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2883095	2883342	1	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2883095	2883342	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2883343	2883485	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2883486	2883612	1	+	1	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2883486	2883612	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2883613	2883724	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2883725	2884000	0.99	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2883725	2884000	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2884001	2884091	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2884092	2884449	0.99	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2884092	2884449	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2884450	2884553	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2884554	2884817	0.85	+	2	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2884554	2884817	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2884818	2885007	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2885008	2885123	0.67	+	2	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2885008	2885123	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2885124	2885340	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2885341	2885436	1	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2885341	2885436	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2885437	2885522	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2885523	2885599	1	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2885523	2885599	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2885600	2885712	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2885713	2885803	1	+	1	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2885713	2885803	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	intron	2885804	2885898	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	CDS	2885899	2886066	1	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	exon	2885899	2886066	.	+	.	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
Phchi.S5	AUGUSTUS	stop_codon	2886067	2886069	.	+	0	transcript_id "Phchi.S5G036100.t1"; gene_id "Phchi.S5G036100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14566.t1 is derived from g13034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13502618	13504977	.	-	.	Phchi.S3G188500
Phchi.S3	AUGUSTUS	transcript	13502880	13504977	.	-	.	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	stop_codon	13502877	13502879	.	-	0	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	CDS	13502880	13502888	0.93	-	0	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	exon	13502880	13502888	.	-	.	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	intron	13502889	13502968	.	-	.	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	CDS	13502969	13504689	0.56	-	2	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	exon	13502969	13504689	.	-	.	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	intron	13504690	13504760	.	-	.	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	CDS	13504761	13504977	0.57	-	0	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	exon	13504761	13504977	.	-	.	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	start_codon	13504975	13504977	.	-	0	transcript_id "Phchi.S3G188500.t1"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	transcript	13502618	13504977	.	-	.	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	stop_codon	13502615	13502617	.	-	0	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	CDS	13502618	13504689	0.59	-	2	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	exon	13502618	13504689	.	-	.	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	intron	13504690	13504760	.	-	.	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	CDS	13504761	13504977	0.58	-	0	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	exon	13504761	13504977	.	-	.	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
Phchi.S3	AUGUSTUS	start_codon	13504975	13504977	.	-	0	transcript_id "Phchi.S3G188500.t2"; gene_id "Phchi.S3G188500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15702.t1 is derived from g14172.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20776816	20778143	.	-	.	Phchi.S3G302100
Phchi.S3	AUGUSTUS	transcript	20776816	20778143	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	stop_codon	20776813	20776815	.	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20776816	20776866	1	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20776816	20776866	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20776867	20776957	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20776958	20777020	1	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20776958	20777020	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777021	20777101	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777102	20777161	1	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777102	20777161	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777162	20777349	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777350	20777430	1	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777350	20777430	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777431	20777600	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777601	20777722	0.95	-	2	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777601	20777722	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777723	20777808	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777809	20777820	0.97	-	2	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777809	20777820	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777821	20777989	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777990	20778143	0.87	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777990	20778143	.	-	.	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	start_codon	20778141	20778143	.	-	0	transcript_id "Phchi.S3G302100.t1"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	transcript	20776816	20778143	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	stop_codon	20776813	20776815	.	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20776816	20776866	1	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20776816	20776866	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20776867	20776957	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20776958	20777020	1	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20776958	20777020	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777021	20777101	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777102	20777161	1	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777102	20777161	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777162	20777331	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777332	20777430	1	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777332	20777430	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777431	20777600	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777601	20777722	0.92	-	2	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777601	20777722	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777723	20777808	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777809	20777820	0.95	-	2	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777809	20777820	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	intron	20777821	20777989	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	CDS	20777990	20778143	0.88	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	exon	20777990	20778143	.	-	.	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
Phchi.S3	AUGUSTUS	start_codon	20778141	20778143	.	-	0	transcript_id "Phchi.S3G302100.t2"; gene_id "Phchi.S3G302100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6771.t1 is derived from g3943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25005031	25005933	.	+	.	Phchi.S1G393000
Phchi.S1	AUGUSTUS	transcript	25005031	25005933	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	start_codon	25005031	25005033	.	+	0	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	CDS	25005031	25005168	0.92	+	0	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	exon	25005031	25005168	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	intron	25005169	25005253	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	CDS	25005254	25005676	0.5	+	0	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	exon	25005254	25005676	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	intron	25005677	25005728	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	CDS	25005729	25005785	0.85	+	0	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	exon	25005729	25005785	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	intron	25005786	25005876	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	CDS	25005877	25005933	1	+	0	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	exon	25005877	25005933	.	+	.	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
Phchi.S1	AUGUSTUS	stop_codon	25005934	25005936	.	+	0	transcript_id "Phchi.S1G393000.t1"; gene_id "Phchi.S1G393000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3013.t1 is derived from g182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1125244	1126363	.	+	.	Phchi.S1G017200
Phchi.S1	AUGUSTUS	transcript	1125244	1126363	.	+	.	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	start_codon	1125244	1125246	.	+	0	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	CDS	1125244	1125729	0.66	+	0	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	exon	1125244	1125729	.	+	.	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	intron	1125730	1125815	.	+	.	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	CDS	1125816	1126012	0.98	+	0	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	exon	1125816	1126012	.	+	.	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	intron	1126013	1126116	.	+	.	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	CDS	1126117	1126363	0.96	+	1	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	exon	1126117	1126363	.	+	.	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
Phchi.S1	AUGUSTUS	stop_codon	1126364	1126366	.	+	0	transcript_id "Phchi.S1G017200.t1"; gene_id "Phchi.S1G017200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2185.t1 is derived from g9105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5263446	5266102	.	+	.	Phchi.S5G079400
Phchi.S5	AUGUSTUS	transcript	5263446	5266102	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	start_codon	5263446	5263448	.	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5263446	5263655	1	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5263446	5263655	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5263656	5263793	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5263794	5263893	1	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5263794	5263893	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5263894	5264054	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5264055	5264146	1	+	2	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5264055	5264146	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5264147	5264299	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5264300	5264431	1	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5264300	5264431	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5264432	5264560	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5264561	5264746	0.98	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5264561	5264746	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5264747	5264854	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5264855	5265018	0.99	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5264855	5265018	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5265019	5265115	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5265116	5265194	1	+	1	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5265116	5265194	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5265195	5265299	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5265300	5265428	1	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5265300	5265428	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5265429	5265498	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5265499	5265626	1	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5265499	5265626	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	intron	5265627	5265732	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	CDS	5265733	5266102	0.97	+	1	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	exon	5265733	5266102	.	+	.	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
Phchi.S5	AUGUSTUS	stop_codon	5266103	5266105	.	+	0	transcript_id "Phchi.S5G079400.t1"; gene_id "Phchi.S5G079400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7428.t1 is derived from g4600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29088916	29089661	.	+	.	Phchi.S1G458700
Phchi.S1	AUGUSTUS	transcript	29088916	29089661	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	start_codon	29088916	29088918	.	+	0	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	CDS	29088916	29088941	0.52	+	0	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	exon	29088916	29088941	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	intron	29088942	29089025	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	CDS	29089026	29089092	0.61	+	1	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	exon	29089026	29089092	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	intron	29089093	29089224	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	CDS	29089225	29089230	0.61	+	0	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	exon	29089225	29089230	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	intron	29089231	29089325	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	CDS	29089326	29089428	0.96	+	0	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	exon	29089326	29089428	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	intron	29089429	29089518	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	CDS	29089519	29089661	0.85	+	2	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	exon	29089519	29089661	.	+	.	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
Phchi.S1	AUGUSTUS	stop_codon	29089662	29089664	.	+	0	transcript_id "Phchi.S1G458700.t1"; gene_id "Phchi.S1G458700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15445.t1 is derived from g13913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19198391	19198702	.	+	.	Phchi.S3G276400
Phchi.S3	AUGUSTUS	transcript	19198391	19198702	.	+	.	transcript_id "Phchi.S3G276400.t1"; gene_id "Phchi.S3G276400"
Phchi.S3	AUGUSTUS	start_codon	19198391	19198393	.	+	0	transcript_id "Phchi.S3G276400.t1"; gene_id "Phchi.S3G276400"
Phchi.S3	AUGUSTUS	CDS	19198391	19198702	0.3	+	0	transcript_id "Phchi.S3G276400.t1"; gene_id "Phchi.S3G276400"
Phchi.S3	AUGUSTUS	exon	19198391	19198702	.	+	.	transcript_id "Phchi.S3G276400.t1"; gene_id "Phchi.S3G276400"
Phchi.S3	AUGUSTUS	stop_codon	19198703	19198705	.	+	0	transcript_id "Phchi.S3G276400.t1"; gene_id "Phchi.S3G276400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15555.t1 is derived from g14024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19908109	19909238	.	+	.	Phchi.S3G287400
Phchi.S3	AUGUSTUS	transcript	19908109	19909238	.	+	.	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	start_codon	19908109	19908111	.	+	0	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	CDS	19908109	19908473	1	+	0	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	exon	19908109	19908473	.	+	.	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	intron	19908474	19908815	.	+	.	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	CDS	19908816	19908839	1	+	1	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	exon	19908816	19908839	.	+	.	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	intron	19908840	19908910	.	+	.	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	CDS	19908911	19909238	0.78	+	1	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	exon	19908911	19909238	.	+	.	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
Phchi.S3	AUGUSTUS	stop_codon	19909239	19909241	.	+	0	transcript_id "Phchi.S3G287400.t1"; gene_id "Phchi.S3G287400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3538.t1 is derived from g707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4354212	4356393	.	+	.	Phchi.S1G069700
Phchi.S1	AUGUSTUS	transcript	4354212	4356393	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	start_codon	4354212	4354214	.	+	0	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	CDS	4354212	4354266	1	+	0	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	exon	4354212	4354266	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	intron	4354267	4354350	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	CDS	4354351	4354436	1	+	2	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	exon	4354351	4354436	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	intron	4354437	4354525	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	CDS	4354526	4356279	0.34	+	0	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	exon	4354526	4356279	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	intron	4356280	4356371	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	CDS	4356372	4356393	0.3	+	1	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	exon	4356372	4356393	.	+	.	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
Phchi.S1	AUGUSTUS	stop_codon	4356394	4356396	.	+	0	transcript_id "Phchi.S1G069700.t1"; gene_id "Phchi.S1G069700"
# This transcript jg7381.t2 is derived from g4553.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7382.t1 is derived from g4554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28854726	28855489	.	+	.	Phchi.S1G454100
Phchi.S1	AUGUSTUS	transcript	28854726	28855489	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	start_codon	28854726	28854728	.	+	0	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	CDS	28854726	28855042	0.46	+	0	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	exon	28854726	28855042	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	intron	28855043	28855109	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	CDS	28855110	28855126	0.31	+	1	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	exon	28855110	28855126	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	intron	28855127	28855203	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	CDS	28855204	28855268	0.94	+	2	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	exon	28855204	28855268	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	intron	28855269	28855480	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	CDS	28855481	28855489	0.94	+	0	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	exon	28855481	28855489	.	+	.	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
Phchi.S1	AUGUSTUS	stop_codon	28855490	28855492	.	+	0	transcript_id "Phchi.S1G454100.t1"; gene_id "Phchi.S1G454100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14790.t1 is derived from g13258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14720219	14721322	.	+	.	Phchi.S3G210900
Phchi.S3	AUGUSTUS	transcript	14720219	14721322	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	start_codon	14720219	14720221	.	+	0	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	CDS	14720219	14720253	0.51	+	0	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	exon	14720219	14720253	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	intron	14720254	14720331	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	CDS	14720332	14720358	0.5	+	1	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	exon	14720332	14720358	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	intron	14720359	14720554	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	CDS	14720555	14720618	1	+	1	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	exon	14720555	14720618	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	intron	14720619	14720704	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	CDS	14720705	14721322	1	+	0	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	exon	14720705	14721322	.	+	.	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
Phchi.S3	AUGUSTUS	stop_codon	14721323	14721325	.	+	0	transcript_id "Phchi.S3G210900.t1"; gene_id "Phchi.S3G210900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1699.t1 is derived from g8618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2577284	2578311	.	+	.	Phchi.S5G030800
Phchi.S5	AUGUSTUS	transcript	2577284	2578311	.	+	.	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	start_codon	2577284	2577286	.	+	0	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	CDS	2577284	2577467	0.82	+	0	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	exon	2577284	2577467	.	+	.	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	intron	2577468	2577619	.	+	.	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	CDS	2577620	2578311	0.94	+	2	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	exon	2577620	2578311	.	+	.	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
Phchi.S5	AUGUSTUS	stop_codon	2578312	2578314	.	+	0	transcript_id "Phchi.S5G030800.t1"; gene_id "Phchi.S5G030800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1711.t1 is derived from g8631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2660570	2661472	.	+	.	Phchi.S5G032000
Phchi.S5	AUGUSTUS	transcript	2660570	2661472	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	start_codon	2660570	2660572	.	+	0	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	CDS	2660570	2660646	1	+	0	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	exon	2660570	2660646	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	intron	2660647	2660785	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	CDS	2660786	2660812	1	+	1	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	exon	2660786	2660812	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	intron	2660813	2660921	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	CDS	2660922	2661016	0.97	+	1	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	exon	2660922	2661016	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	intron	2661017	2661106	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	CDS	2661107	2661216	1	+	2	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	exon	2661107	2661216	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	intron	2661217	2661325	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	CDS	2661326	2661472	0.97	+	0	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	exon	2661326	2661472	.	+	.	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
Phchi.S5	AUGUSTUS	stop_codon	2661473	2661475	.	+	0	transcript_id "Phchi.S5G032000.t1"; gene_id "Phchi.S5G032000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15708.t1 is derived from g14178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20800491	20805772	.	-	.	Phchi.S3G302700
Phchi.S3	AUGUSTUS	transcript	20800491	20805772	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	stop_codon	20800488	20800490	.	-	0	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20800491	20800573	0.69	-	2	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20800491	20800573	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20800574	20800738	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20800739	20801632	0.62	-	2	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20800739	20801632	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20801633	20801790	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20801791	20801997	1	-	2	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20801791	20801997	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20801998	20802109	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20802110	20802439	0.52	-	2	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20802110	20802439	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20802440	20802553	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20802554	20802734	0.57	-	0	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20802554	20802734	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20802735	20802829	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20802830	20802985	1	-	0	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20802830	20802985	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20802986	20803119	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20803120	20803234	0.94	-	1	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20803120	20803234	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20803235	20803341	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20803342	20803552	0.94	-	2	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20803342	20803552	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20803553	20803682	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20803683	20804031	0.54	-	0	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20803683	20804031	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20804032	20804119	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20804120	20804217	1	-	2	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20804120	20804217	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20804218	20804360	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20804361	20804683	1	-	1	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20804361	20804683	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20804684	20804784	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20804785	20805141	1	-	1	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20804785	20805141	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20805142	20805234	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20805235	20805345	1	-	1	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20805235	20805345	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	intron	20805346	20805455	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	CDS	20805456	20805772	0.98	-	0	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	exon	20805456	20805772	.	-	.	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
Phchi.S3	AUGUSTUS	start_codon	20805770	20805772	.	-	0	transcript_id "Phchi.S3G302700.t1"; gene_id "Phchi.S3G302700"
# This transcript jg7874.t2 is derived from g5048.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7875.t1 is derived from g5049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31662960	31668288	.	+	.	Phchi.S1G503400
Phchi.S1	AUGUSTUS	transcript	31662960	31668288	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	start_codon	31662960	31662962	.	+	0	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31662960	31665075	0.76	+	0	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31662960	31665075	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31665076	31665337	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31665338	31665792	1	+	2	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31665338	31665792	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31665793	31665886	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31665887	31666040	0.83	+	0	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31665887	31666040	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31666041	31666147	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31666148	31666205	0.95	+	2	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31666148	31666205	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31666206	31666358	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31666359	31666480	1	+	1	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31666359	31666480	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31666481	31666576	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31666577	31667910	0.81	+	2	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31666577	31667910	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31667911	31668090	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31668091	31668136	0.88	+	0	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31668091	31668136	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	intron	31668137	31668259	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	CDS	31668260	31668288	0.92	+	2	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	exon	31668260	31668288	.	+	.	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
Phchi.S1	AUGUSTUS	stop_codon	31668289	31668291	.	+	0	transcript_id "Phchi.S1G503400.t1"; gene_id "Phchi.S1G503400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8737.t1 is derived from g5912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37749059	37750177	.	+	.	Phchi.S1G589600
Phchi.S1	AUGUSTUS	transcript	37749059	37750177	.	+	.	transcript_id "Phchi.S1G589600.t1"; gene_id "Phchi.S1G589600"
Phchi.S1	AUGUSTUS	start_codon	37749059	37749061	.	+	0	transcript_id "Phchi.S1G589600.t1"; gene_id "Phchi.S1G589600"
Phchi.S1	AUGUSTUS	CDS	37749059	37750177	0.76	+	0	transcript_id "Phchi.S1G589600.t1"; gene_id "Phchi.S1G589600"
Phchi.S1	AUGUSTUS	exon	37749059	37750177	.	+	.	transcript_id "Phchi.S1G589600.t1"; gene_id "Phchi.S1G589600"
Phchi.S1	AUGUSTUS	stop_codon	37750178	37750180	.	+	0	transcript_id "Phchi.S1G589600.t1"; gene_id "Phchi.S1G589600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14275.t1 is derived from g12742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11890578	11890913	.	+	.	Phchi.S3G159400
Phchi.S3	AUGUSTUS	transcript	11890578	11890913	.	+	.	transcript_id "Phchi.S3G159400.t1"; gene_id "Phchi.S3G159400"
Phchi.S3	AUGUSTUS	start_codon	11890578	11890580	.	+	0	transcript_id "Phchi.S3G159400.t1"; gene_id "Phchi.S3G159400"
Phchi.S3	AUGUSTUS	CDS	11890578	11890913	0.86	+	0	transcript_id "Phchi.S3G159400.t1"; gene_id "Phchi.S3G159400"
Phchi.S3	AUGUSTUS	exon	11890578	11890913	.	+	.	transcript_id "Phchi.S3G159400.t1"; gene_id "Phchi.S3G159400"
Phchi.S3	AUGUSTUS	stop_codon	11890914	11890916	.	+	0	transcript_id "Phchi.S3G159400.t1"; gene_id "Phchi.S3G159400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4220.t1 is derived from g1389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8989184	8991173	.	+	.	Phchi.S1G137900
Phchi.S1	AUGUSTUS	transcript	8989184	8991173	.	+	.	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	start_codon	8989184	8989186	.	+	0	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	CDS	8989184	8989660	0.82	+	0	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	exon	8989184	8989660	.	+	.	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	intron	8989661	8989760	.	+	.	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	CDS	8989761	8991173	0.88	+	0	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	exon	8989761	8991173	.	+	.	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
Phchi.S1	AUGUSTUS	stop_codon	8991174	8991176	.	+	0	transcript_id "Phchi.S1G137900.t1"; gene_id "Phchi.S1G137900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12512.t1 is derived from g8189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32274907	32275377	.	-	.	Phchi.S2G059200
Phchi.S2	AUGUSTUS	transcript	32274907	32275377	.	-	.	transcript_id "Phchi.S2G059200.t1"; gene_id "Phchi.S2G059200"
Phchi.S2	AUGUSTUS	stop_codon	32274904	32274906	.	-	0	transcript_id "Phchi.S2G059200.t1"; gene_id "Phchi.S2G059200"
Phchi.S2	AUGUSTUS	CDS	32274907	32275377	0.42	-	0	transcript_id "Phchi.S2G059200.t1"; gene_id "Phchi.S2G059200"
Phchi.S2	AUGUSTUS	exon	32274907	32275377	.	-	.	transcript_id "Phchi.S2G059200.t1"; gene_id "Phchi.S2G059200"
Phchi.S2	AUGUSTUS	start_codon	32275375	32275377	.	-	0	transcript_id "Phchi.S2G059200.t1"; gene_id "Phchi.S2G059200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3396.t1 is derived from g565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3332894	3333722	.	-	.	Phchi.S1G055500
Phchi.S1	AUGUSTUS	transcript	3332894	3333722	.	-	.	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	stop_codon	3332891	3332893	.	-	0	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	CDS	3332894	3333016	1	-	0	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	exon	3332894	3333016	.	-	.	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	intron	3333017	3333533	.	-	.	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	CDS	3333534	3333722	1	-	0	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	exon	3333534	3333722	.	-	.	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
Phchi.S1	AUGUSTUS	start_codon	3333720	3333722	.	-	0	transcript_id "Phchi.S1G055500.t1"; gene_id "Phchi.S1G055500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13864.t1 is derived from g12331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9301226	9303184	.	+	.	Phchi.S3G118300
Phchi.S3	AUGUSTUS	transcript	9301226	9303184	.	+	.	transcript_id "Phchi.S3G118300.t1"; gene_id "Phchi.S3G118300"
Phchi.S3	AUGUSTUS	start_codon	9301226	9301228	.	+	0	transcript_id "Phchi.S3G118300.t1"; gene_id "Phchi.S3G118300"
Phchi.S3	AUGUSTUS	CDS	9301226	9303184	1	+	0	transcript_id "Phchi.S3G118300.t1"; gene_id "Phchi.S3G118300"
Phchi.S3	AUGUSTUS	exon	9301226	9303184	.	+	.	transcript_id "Phchi.S3G118300.t1"; gene_id "Phchi.S3G118300"
Phchi.S3	AUGUSTUS	stop_codon	9303185	9303187	.	+	0	transcript_id "Phchi.S3G118300.t1"; gene_id "Phchi.S3G118300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2353.t1 is derived from g9273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6319376	6321100	.	-	.	Phchi.S5G096200
Phchi.S5	AUGUSTUS	transcript	6319376	6321100	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	stop_codon	6319373	6319375	.	-	0	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	CDS	6319376	6319795	1	-	0	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	exon	6319376	6319795	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	intron	6319796	6319920	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	CDS	6319921	6320295	0.97	-	0	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	exon	6319921	6320295	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	intron	6320296	6320395	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	CDS	6320396	6320481	0.75	-	2	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	exon	6320396	6320481	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	intron	6320482	6320562	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	CDS	6320563	6320867	0.55	-	1	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	exon	6320563	6320867	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	intron	6320868	6321011	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	CDS	6321012	6321100	0.58	-	0	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	exon	6321012	6321100	.	-	.	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
Phchi.S5	AUGUSTUS	start_codon	6321098	6321100	.	-	0	transcript_id "Phchi.S5G096200.t1"; gene_id "Phchi.S5G096200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5066.t1 is derived from g2236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14505301	14505749	.	+	.	Phchi.S1G222500
Phchi.S1	AUGUSTUS	transcript	14505301	14505749	.	+	.	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	start_codon	14505301	14505303	.	+	0	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	CDS	14505301	14505459	0.69	+	0	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	exon	14505301	14505459	.	+	.	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	intron	14505460	14505629	.	+	.	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	CDS	14505630	14505749	0.7	+	0	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	exon	14505630	14505749	.	+	.	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
Phchi.S1	AUGUSTUS	stop_codon	14505750	14505752	.	+	0	transcript_id "Phchi.S1G222500.t1"; gene_id "Phchi.S1G222500"
# This transcript jg2472.t2 is derived from g9392.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2473.t1 is derived from g9393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6830455	6833733	.	-	.	Phchi.S5G108200
Phchi.S5	AUGUSTUS	transcript	6830455	6833733	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	stop_codon	6830452	6830454	.	-	0	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6830455	6830611	1	-	1	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6830455	6830611	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6830612	6830705	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6830706	6830801	0.66	-	1	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6830706	6830801	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6830802	6831012	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831013	6831628	0.43	-	2	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831013	6831628	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831629	6831725	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831726	6831788	0.86	-	2	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831726	6831788	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831789	6831873	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831874	6831881	0.77	-	1	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831874	6831881	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831882	6831961	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831962	6832117	0.78	-	1	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831962	6832117	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6832118	6832538	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6832539	6832696	1	-	0	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6832539	6832696	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6832697	6832939	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6832940	6833011	1	-	0	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6832940	6833011	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833012	6833092	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833093	6833168	1	-	1	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833093	6833168	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833169	6833244	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833245	6833326	1	-	2	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833245	6833326	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833327	6833546	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833547	6833733	0.87	-	0	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833547	6833733	.	-	.	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	start_codon	6833731	6833733	.	-	0	transcript_id "Phchi.S5G108200.t1"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	transcript	6830455	6833733	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	stop_codon	6830452	6830454	.	-	0	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6830455	6830611	0.99	-	1	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6830455	6830611	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6830612	6830705	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6830706	6830801	0.65	-	1	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6830706	6830801	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6830802	6831012	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831013	6831628	0.57	-	2	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831013	6831628	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831629	6831725	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831726	6831788	1	-	2	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831726	6831788	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831789	6831873	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831874	6831914	0.92	-	1	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831874	6831914	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831915	6832034	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6832035	6832117	0.7	-	0	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6832035	6832117	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6832118	6832939	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6832940	6833011	0.94	-	0	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6832940	6833011	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833012	6833092	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833093	6833168	1	-	1	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833093	6833168	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833169	6833244	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833245	6833326	1	-	2	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833245	6833326	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833327	6833546	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833547	6833733	0.87	-	0	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833547	6833733	.	-	.	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	start_codon	6833731	6833733	.	-	0	transcript_id "Phchi.S5G108200.t2"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	transcript	6830455	6833733	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	stop_codon	6830452	6830454	.	-	0	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6830455	6830611	1	-	1	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6830455	6830611	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6830612	6830705	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6830706	6830801	0.66	-	1	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6830706	6830801	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6830802	6831012	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831013	6831628	0.37	-	2	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831013	6831628	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831629	6831725	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831726	6831788	0.81	-	2	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831726	6831788	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831789	6831873	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831874	6831881	0.69	-	1	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831874	6831881	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6831882	6831961	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6831962	6832117	0.69	-	1	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6831962	6832117	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6832118	6832538	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6832539	6832696	1	-	0	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6832539	6832696	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6832697	6832939	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6832940	6833011	1	-	0	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6832940	6833011	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833012	6833092	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833093	6833168	1	-	1	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833093	6833168	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833169	6833244	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833245	6833326	1	-	2	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833245	6833326	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	intron	6833327	6833534	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	CDS	6833535	6833733	0.8	-	0	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	exon	6833535	6833733	.	-	.	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
Phchi.S5	AUGUSTUS	start_codon	6833731	6833733	.	-	0	transcript_id "Phchi.S5G108200.t3"; gene_id "Phchi.S5G108200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2011.t1 is derived from g8931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4447953	4448705	.	+	.	Phchi.S5G062000
Phchi.S5	AUGUSTUS	transcript	4447953	4448705	.	+	.	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	start_codon	4447953	4447955	.	+	0	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	CDS	4447953	4448006	0.51	+	0	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	exon	4447953	4448006	.	+	.	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	intron	4448007	4448112	.	+	.	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	CDS	4448113	4448227	0.52	+	0	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	exon	4448113	4448227	.	+	.	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	intron	4448228	4448430	.	+	.	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	CDS	4448431	4448705	0.96	+	2	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	exon	4448431	4448705	.	+	.	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
Phchi.S5	AUGUSTUS	stop_codon	4448706	4448708	.	+	0	transcript_id "Phchi.S5G062000.t1"; gene_id "Phchi.S5G062000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13592.t1 is derived from g12059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7619597	7620979	.	+	.	Phchi.S3G091100
Phchi.S3	AUGUSTUS	transcript	7619597	7620979	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	start_codon	7619597	7619599	.	+	0	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	CDS	7619597	7619988	0.99	+	0	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	exon	7619597	7619988	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	intron	7619989	7620179	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	CDS	7620180	7620217	1	+	1	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	exon	7620180	7620217	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	intron	7620218	7620386	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	CDS	7620387	7620481	1	+	2	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	exon	7620387	7620481	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	intron	7620482	7620674	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	CDS	7620675	7620812	1	+	0	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	exon	7620675	7620812	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	intron	7620813	7620943	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	CDS	7620944	7620979	1	+	0	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	exon	7620944	7620979	.	+	.	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
Phchi.S3	AUGUSTUS	stop_codon	7620980	7620982	.	+	0	transcript_id "Phchi.S3G091100.t1"; gene_id "Phchi.S3G091100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2763.t1 is derived from g9683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8714987	8716903	.	-	.	Phchi.S5G137200
Phchi.S5	AUGUSTUS	transcript	8714987	8716903	.	-	.	transcript_id "Phchi.S5G137200.t1"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	stop_codon	8714984	8714986	.	-	0	transcript_id "Phchi.S5G137200.t1"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	CDS	8714987	8716903	0.93	-	0	transcript_id "Phchi.S5G137200.t1"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	exon	8714987	8716903	.	-	.	transcript_id "Phchi.S5G137200.t1"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	start_codon	8716901	8716903	.	-	0	transcript_id "Phchi.S5G137200.t1"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	transcript	8714987	8715727	.	-	.	transcript_id "Phchi.S5G137200.t2"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	stop_codon	8714984	8714986	.	-	0	transcript_id "Phchi.S5G137200.t2"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	CDS	8714987	8715727	0.5	-	0	transcript_id "Phchi.S5G137200.t2"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	exon	8714987	8715727	.	-	.	transcript_id "Phchi.S5G137200.t2"; gene_id "Phchi.S5G137200"
Phchi.S5	AUGUSTUS	start_codon	8715725	8715727	.	-	0	transcript_id "Phchi.S5G137200.t2"; gene_id "Phchi.S5G137200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4150.t1 is derived from g1319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8651959	8652294	.	+	.	Phchi.S1G130900
Phchi.S1	AUGUSTUS	transcript	8651959	8652294	.	+	.	transcript_id "Phchi.S1G130900.t1"; gene_id "Phchi.S1G130900"
Phchi.S1	AUGUSTUS	start_codon	8651959	8651961	.	+	0	transcript_id "Phchi.S1G130900.t1"; gene_id "Phchi.S1G130900"
Phchi.S1	AUGUSTUS	CDS	8651959	8652294	0.82	+	0	transcript_id "Phchi.S1G130900.t1"; gene_id "Phchi.S1G130900"
Phchi.S1	AUGUSTUS	exon	8651959	8652294	.	+	.	transcript_id "Phchi.S1G130900.t1"; gene_id "Phchi.S1G130900"
Phchi.S1	AUGUSTUS	stop_codon	8652295	8652297	.	+	0	transcript_id "Phchi.S1G130900.t1"; gene_id "Phchi.S1G130900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13891.t1 is derived from g12358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9481539	9483514	.	-	.	Phchi.S3G121000
Phchi.S3	AUGUSTUS	transcript	9481539	9483514	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	stop_codon	9481536	9481538	.	-	0	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	CDS	9481539	9481592	1	-	0	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	exon	9481539	9481592	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	intron	9481593	9481727	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	CDS	9481728	9481942	1	-	2	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	exon	9481728	9481942	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	intron	9481943	9482106	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	CDS	9482107	9482468	1	-	1	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	exon	9482107	9482468	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	intron	9482469	9482561	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	CDS	9482562	9482623	1	-	0	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	exon	9482562	9482623	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	intron	9482624	9482779	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	CDS	9482780	9482863	1	-	0	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	exon	9482780	9482863	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	intron	9482864	9483388	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	CDS	9483389	9483514	1	-	0	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	exon	9483389	9483514	.	-	.	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
Phchi.S3	AUGUSTUS	start_codon	9483512	9483514	.	-	0	transcript_id "Phchi.S3G121000.t1"; gene_id "Phchi.S3G121000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15397.t1 is derived from g13865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18818154	18819308	.	+	.	Phchi.S3G271600
Phchi.S3	AUGUSTUS	transcript	18818154	18819308	.	+	.	transcript_id "Phchi.S3G271600.t1"; gene_id "Phchi.S3G271600"
Phchi.S3	AUGUSTUS	start_codon	18818154	18818156	.	+	0	transcript_id "Phchi.S3G271600.t1"; gene_id "Phchi.S3G271600"
Phchi.S3	AUGUSTUS	CDS	18818154	18819308	0.57	+	0	transcript_id "Phchi.S3G271600.t1"; gene_id "Phchi.S3G271600"
Phchi.S3	AUGUSTUS	exon	18818154	18819308	.	+	.	transcript_id "Phchi.S3G271600.t1"; gene_id "Phchi.S3G271600"
Phchi.S3	AUGUSTUS	stop_codon	18819309	18819311	.	+	0	transcript_id "Phchi.S3G271600.t1"; gene_id "Phchi.S3G271600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5306.t1 is derived from g2476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16210909	16215446	.	+	.	Phchi.S1G246500
Phchi.S1	AUGUSTUS	transcript	16210909	16215446	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	start_codon	16210909	16210911	.	+	0	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16210909	16211002	0.74	+	0	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16210909	16211002	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16211003	16211100	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16211101	16211414	0.98	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16211101	16211414	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16211415	16211493	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16211494	16211753	0.99	+	0	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16211494	16211753	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16211754	16211862	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16211863	16212120	0.99	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16211863	16212120	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16212121	16212205	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16212206	16212429	0.97	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16212206	16212429	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16212430	16212538	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16212539	16212665	1	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16212539	16212665	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16212666	16212770	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16212771	16212845	1	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16212771	16212845	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16212846	16212937	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16212938	16213009	0.98	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16212938	16213009	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16213010	16213127	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16213128	16213190	0.92	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16213128	16213190	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16213191	16213340	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16213341	16213406	1	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16213341	16213406	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16213407	16213497	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16213498	16213742	1	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16213498	16213742	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16213743	16213879	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16213880	16213918	1	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16213880	16213918	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16213919	16214037	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16214038	16214106	0.87	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16214038	16214106	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16214107	16214201	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16214202	16214327	1	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16214202	16214327	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16214328	16214421	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16214422	16214487	1	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16214422	16214487	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16214488	16214567	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16214568	16214613	1	+	2	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16214568	16214613	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16214614	16214696	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16214697	16214843	1	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16214697	16214843	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16214844	16214929	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16214930	16215068	1	+	1	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16214930	16215068	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	intron	16215069	16215158	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	CDS	16215159	16215446	1	+	0	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	exon	16215159	16215446	.	+	.	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
Phchi.S1	AUGUSTUS	stop_codon	16215447	16215449	.	+	0	transcript_id "Phchi.S1G246500.t1"; gene_id "Phchi.S1G246500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5907.t1 is derived from g3077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19741588	19742940	.	+	.	Phchi.S1G306600
Phchi.S1	AUGUSTUS	transcript	19741588	19742940	.	+	.	transcript_id "Phchi.S1G306600.t1"; gene_id "Phchi.S1G306600"
Phchi.S1	AUGUSTUS	start_codon	19741588	19741590	.	+	0	transcript_id "Phchi.S1G306600.t1"; gene_id "Phchi.S1G306600"
Phchi.S1	AUGUSTUS	CDS	19741588	19742940	0.8	+	0	transcript_id "Phchi.S1G306600.t1"; gene_id "Phchi.S1G306600"
Phchi.S1	AUGUSTUS	exon	19741588	19742940	.	+	.	transcript_id "Phchi.S1G306600.t1"; gene_id "Phchi.S1G306600"
Phchi.S1	AUGUSTUS	stop_codon	19742941	19742943	.	+	0	transcript_id "Phchi.S1G306600.t1"; gene_id "Phchi.S1G306600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1566.t1 is derived from g8485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1781467	1784503	.	-	.	Phchi.S5G017500
Phchi.S5	AUGUSTUS	transcript	1781467	1784503	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	stop_codon	1781464	1781466	.	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1781467	1781587	1	-	1	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1781467	1781587	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1781588	1781662	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1781663	1781808	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1781663	1781808	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1781809	1781894	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1781895	1782029	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1781895	1782029	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1782030	1782115	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1782116	1782199	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1782116	1782199	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1782200	1782342	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1782343	1782417	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1782343	1782417	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1782418	1782502	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1782503	1782536	1	-	1	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1782503	1782536	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1782537	1782634	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1782635	1782735	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1782635	1782735	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1782736	1782828	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1782829	1782915	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1782829	1782915	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1782916	1783011	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1783012	1783104	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1783012	1783104	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1783105	1783256	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1783257	1783337	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1783257	1783337	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1783338	1783457	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1783458	1783671	1	-	1	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1783458	1783671	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	intron	1783672	1783796	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	CDS	1783797	1784503	1	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	exon	1783797	1784503	.	-	.	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
Phchi.S5	AUGUSTUS	start_codon	1784501	1784503	.	-	0	transcript_id "Phchi.S5G017500.t1"; gene_id "Phchi.S5G017500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15339.t1 is derived from g13807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18454781	18456844	.	+	.	Phchi.S3G265800
Phchi.S3	AUGUSTUS	transcript	18454781	18456844	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	start_codon	18454781	18454783	.	+	0	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	CDS	18454781	18455149	0.92	+	0	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	exon	18454781	18455149	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	intron	18455150	18455289	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	CDS	18455290	18456412	0.91	+	0	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	exon	18455290	18456412	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	intron	18456413	18456491	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	CDS	18456492	18456561	1	+	2	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	exon	18456492	18456561	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	intron	18456562	18456840	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	CDS	18456841	18456844	1	+	1	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	exon	18456841	18456844	.	+	.	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
Phchi.S3	AUGUSTUS	stop_codon	18456845	18456847	.	+	0	transcript_id "Phchi.S3G265800.t1"; gene_id "Phchi.S3G265800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9214.t1 is derived from g6389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40455298	40456491	.	-	.	Phchi.S1G637300
Phchi.S1	AUGUSTUS	transcript	40455298	40456491	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	stop_codon	40455295	40455297	.	-	0	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40455298	40455390	1	-	0	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40455298	40455390	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	intron	40455391	40455480	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40455481	40455597	1	-	0	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40455481	40455597	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	intron	40455598	40455680	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40455681	40455844	1	-	2	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40455681	40455844	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	intron	40455845	40455924	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40455925	40456002	1	-	2	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40455925	40456002	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	intron	40456003	40456094	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40456095	40456154	1	-	2	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40456095	40456154	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	intron	40456155	40456246	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40456247	40456338	1	-	1	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40456247	40456338	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	intron	40456339	40456417	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	CDS	40456418	40456491	1	-	0	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	exon	40456418	40456491	.	-	.	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
Phchi.S1	AUGUSTUS	start_codon	40456489	40456491	.	-	0	transcript_id "Phchi.S1G637300.t1"; gene_id "Phchi.S1G637300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4838.t1 is derived from g2008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13053415	13054466	.	+	.	Phchi.S1G199700
Phchi.S1	AUGUSTUS	transcript	13053415	13054466	.	+	.	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	start_codon	13053415	13053417	.	+	0	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	CDS	13053415	13053768	0.95	+	0	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	exon	13053415	13053768	.	+	.	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	intron	13053769	13053844	.	+	.	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	CDS	13053845	13054031	0.84	+	0	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	exon	13053845	13054031	.	+	.	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	intron	13054032	13054131	.	+	.	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	CDS	13054132	13054466	0.93	+	2	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	exon	13054132	13054466	.	+	.	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
Phchi.S1	AUGUSTUS	stop_codon	13054467	13054469	.	+	0	transcript_id "Phchi.S1G199700.t1"; gene_id "Phchi.S1G199700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7134.t1 is derived from g4306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27122752	27124227	.	-	.	Phchi.S1G429300
Phchi.S1	AUGUSTUS	transcript	27122752	27124227	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	stop_codon	27122749	27122751	.	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27122752	27122823	0.59	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27122752	27122823	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27122824	27122906	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27122907	27123035	1	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27122907	27123035	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27123036	27123110	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27123111	27123224	1	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27123111	27123224	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27123225	27123320	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27123321	27123385	1	-	2	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27123321	27123385	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27123386	27123476	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27123477	27123516	1	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27123477	27123516	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27123517	27123606	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27123607	27123669	1	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27123607	27123669	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27123670	27123778	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27123779	27124073	1	-	1	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27123779	27124073	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	intron	27124074	27124144	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	CDS	27124145	27124227	1	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	exon	27124145	27124227	.	-	.	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
Phchi.S1	AUGUSTUS	start_codon	27124225	27124227	.	-	0	transcript_id "Phchi.S1G429300.t1"; gene_id "Phchi.S1G429300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1361.t1 is derived from g15997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C81	AUGUSTUS	gene	16510	18275	.	-	.	Phchi.C81G000300
Phchi.C81	AUGUSTUS	transcript	16510	18275	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	stop_codon	16507	16509	.	-	0	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	CDS	16510	16759	1	-	1	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	exon	16510	16759	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	intron	16760	16860	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	CDS	16861	17078	1	-	0	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	exon	16861	17078	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	intron	17079	17162	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	CDS	17163	17654	1	-	0	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	exon	17163	17654	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	intron	17655	17771	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	CDS	17772	18275	0.98	-	0	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	exon	17772	18275	.	-	.	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
Phchi.C81	AUGUSTUS	start_codon	18273	18275	.	-	0	transcript_id "Phchi.C81G000300.t1"; gene_id "Phchi.C81G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13560.t1 is derived from g12027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7492546	7496177	.	+	.	Phchi.S3G087900
Phchi.S3	AUGUSTUS	transcript	7492546	7496177	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	start_codon	7492546	7492548	.	+	0	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7492546	7492819	0.78	+	0	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7492546	7492819	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	intron	7492820	7492920	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7492921	7494287	0.87	+	2	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7492921	7494287	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	intron	7494288	7494413	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7494414	7494694	0.6	+	0	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7494414	7494694	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	intron	7494695	7494806	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7494807	7494838	0.97	+	1	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7494807	7494838	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	intron	7494839	7494945	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7494946	7495349	0.84	+	2	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7494946	7495349	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	intron	7495350	7495452	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7495453	7495944	0.53	+	0	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7495453	7495944	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	intron	7495945	7496120	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	CDS	7496121	7496177	1	+	0	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	exon	7496121	7496177	.	+	.	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
Phchi.S3	AUGUSTUS	stop_codon	7496502	7496504	.	+	0	transcript_id "Phchi.S3G087900.t1"; gene_id "Phchi.S3G087900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15246.t1 is derived from g13714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17888109	17889542	.	-	.	Phchi.S3G256500
Phchi.S3	AUGUSTUS	transcript	17888109	17889542	.	-	.	transcript_id "Phchi.S3G256500.t1"; gene_id "Phchi.S3G256500"
Phchi.S3	AUGUSTUS	stop_codon	17888106	17888108	.	-	0	transcript_id "Phchi.S3G256500.t1"; gene_id "Phchi.S3G256500"
Phchi.S3	AUGUSTUS	CDS	17888109	17889542	0.92	-	0	transcript_id "Phchi.S3G256500.t1"; gene_id "Phchi.S3G256500"
Phchi.S3	AUGUSTUS	exon	17888109	17889542	.	-	.	transcript_id "Phchi.S3G256500.t1"; gene_id "Phchi.S3G256500"
Phchi.S3	AUGUSTUS	start_codon	17889540	17889542	.	-	0	transcript_id "Phchi.S3G256500.t1"; gene_id "Phchi.S3G256500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1517.t1 is derived from g8436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1505049	1507526	.	+	.	Phchi.S5G012600
Phchi.S5	AUGUSTUS	transcript	1505049	1507526	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	start_codon	1505049	1505051	.	+	0	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	CDS	1505049	1505152	1	+	0	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	exon	1505049	1505152	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	intron	1505153	1505242	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	CDS	1505243	1506494	0.89	+	1	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	exon	1505243	1506494	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	intron	1506495	1506713	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	CDS	1506714	1506801	1	+	0	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	exon	1506714	1506801	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	intron	1506802	1506889	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	CDS	1506890	1506961	0.94	+	2	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	exon	1506890	1506961	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	intron	1506962	1507086	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	CDS	1507087	1507526	0.94	+	2	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	exon	1507087	1507526	.	+	.	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
Phchi.S5	AUGUSTUS	stop_codon	1507527	1507529	.	+	0	transcript_id "Phchi.S5G012600.t1"; gene_id "Phchi.S5G012600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11274.t1 is derived from g15324.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5141017	5146526	.	-	.	Phchi.S4G085600
Phchi.S4	AUGUSTUS	transcript	5141017	5146526	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	stop_codon	5141014	5141016	.	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141017	5141083	0.49	-	1	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141017	5141083	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141084	5141179	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141180	5141262	0.99	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141180	5141262	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141263	5141364	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141365	5141427	0.99	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141365	5141427	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141428	5141566	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141567	5141635	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141567	5141635	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141636	5141743	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141744	5141797	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141744	5141797	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141798	5141885	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141886	5141966	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141886	5141966	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141967	5142058	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142059	5142124	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142059	5142124	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142125	5142242	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142243	5142475	0.95	-	2	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142243	5142475	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142476	5142844	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142845	5142939	0.96	-	1	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142845	5142939	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142940	5143013	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5143014	5143096	0.63	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5143014	5143096	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5143097	5143202	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5143203	5143263	0.63	-	1	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5143203	5143263	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5143264	5143434	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5143435	5143469	0.85	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5143435	5143469	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5143470	5143717	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5143718	5143835	0.44	-	1	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5143718	5143835	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5143836	5144015	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5144016	5144198	0.58	-	1	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5144016	5144198	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5144199	5144394	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5144395	5144531	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5144395	5144531	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5144532	5144676	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5144677	5144772	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5144677	5144772	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5144773	5144886	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5144887	5145817	1	-	1	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5144887	5145817	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5145818	5146311	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5146312	5146526	1	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5146312	5146526	.	-	.	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	start_codon	5146524	5146526	.	-	0	transcript_id "Phchi.S4G085600.t1"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	transcript	5141017	5143074	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	stop_codon	5141014	5141016	.	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141017	5141083	0.46	-	1	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141017	5141083	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141084	5141179	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141180	5141262	0.97	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141180	5141262	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141263	5141364	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141365	5141427	0.97	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141365	5141427	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141428	5141566	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141567	5141635	1	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141567	5141635	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141636	5141743	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141744	5141797	1	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141744	5141797	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141798	5141885	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5141886	5141966	1	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5141886	5141966	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5141967	5142058	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142059	5142124	1	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142059	5142124	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142125	5142242	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142243	5142404	0.65	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142243	5142404	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142405	5142540	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142541	5142556	0.48	-	1	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142541	5142556	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142557	5142675	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142676	5142716	0.65	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142676	5142716	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142717	5142844	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5142845	5142939	0.95	-	2	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5142845	5142939	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	intron	5142940	5143013	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	CDS	5143014	5143074	0.92	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	exon	5143014	5143074	.	-	.	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
Phchi.S4	AUGUSTUS	start_codon	5143072	5143074	.	-	0	transcript_id "Phchi.S4G085600.t2"; gene_id "Phchi.S4G085600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8659.t1 is derived from g5834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37310895	37311748	.	+	.	Phchi.S1G581800
Phchi.S1	AUGUSTUS	transcript	37310895	37311748	.	+	.	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	start_codon	37310895	37310897	.	+	0	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	CDS	37310895	37311395	0.49	+	0	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	exon	37310895	37311395	.	+	.	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	intron	37311396	37311514	.	+	.	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	CDS	37311515	37311748	0.75	+	0	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	exon	37311515	37311748	.	+	.	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
Phchi.S1	AUGUSTUS	stop_codon	37311749	37311751	.	+	0	transcript_id "Phchi.S1G581800.t1"; gene_id "Phchi.S1G581800"
# This transcript jg14082.t2 is derived from g12549.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14083.t1 is derived from g12550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10774617	10775845	.	-	.	Phchi.S3G140200
Phchi.S3	AUGUSTUS	transcript	10774617	10775845	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	stop_codon	10774614	10774616	.	-	0	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	CDS	10774617	10774664	1	-	0	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	exon	10774617	10774664	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	intron	10774665	10774740	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	CDS	10774741	10774857	1	-	0	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	exon	10774741	10774857	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	intron	10774858	10774938	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	CDS	10774939	10775026	1	-	1	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	exon	10774939	10775026	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	intron	10775027	10775123	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	CDS	10775124	10775173	1	-	0	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	exon	10775124	10775173	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	intron	10775174	10775282	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	CDS	10775283	10775494	1	-	2	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	exon	10775283	10775494	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	intron	10775495	10775580	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	CDS	10775581	10775845	0.89	-	0	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	exon	10775581	10775845	.	-	.	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
Phchi.S3	AUGUSTUS	start_codon	10775843	10775845	.	-	0	transcript_id "Phchi.S3G140200.t1"; gene_id "Phchi.S3G140200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5489.t1 is derived from g2659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17101583	17103517	.	-	.	Phchi.S1G264800
Phchi.S1	AUGUSTUS	transcript	17101583	17103517	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	stop_codon	17101580	17101582	.	-	0	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	CDS	17101583	17101750	1	-	0	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	exon	17101583	17101750	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	intron	17101751	17101877	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	CDS	17101878	17102049	1	-	1	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	exon	17101878	17102049	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	intron	17102050	17102135	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	CDS	17102136	17102318	1	-	1	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	exon	17102136	17102318	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	intron	17102319	17102419	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	CDS	17102420	17102733	0.6	-	0	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	exon	17102420	17102733	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	intron	17102734	17102812	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	CDS	17102813	17103007	1	-	0	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	exon	17102813	17103007	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	intron	17103008	17103094	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	CDS	17103095	17103517	0.61	-	0	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	exon	17103095	17103517	.	-	.	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
Phchi.S1	AUGUSTUS	start_codon	17103515	17103517	.	-	0	transcript_id "Phchi.S1G264800.t1"; gene_id "Phchi.S1G264800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8641.t1 is derived from g5816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37197206	37198216	.	+	.	Phchi.S1G580000
Phchi.S1	AUGUSTUS	transcript	37197206	37198216	.	+	.	transcript_id "Phchi.S1G580000.t1"; gene_id "Phchi.S1G580000"
Phchi.S1	AUGUSTUS	start_codon	37197206	37197208	.	+	0	transcript_id "Phchi.S1G580000.t1"; gene_id "Phchi.S1G580000"
Phchi.S1	AUGUSTUS	CDS	37197206	37198216	0.92	+	0	transcript_id "Phchi.S1G580000.t1"; gene_id "Phchi.S1G580000"
Phchi.S1	AUGUSTUS	exon	37197206	37198216	.	+	.	transcript_id "Phchi.S1G580000.t1"; gene_id "Phchi.S1G580000"
Phchi.S1	AUGUSTUS	stop_codon	37198217	37198219	.	+	0	transcript_id "Phchi.S1G580000.t1"; gene_id "Phchi.S1G580000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2371.t1 is derived from g9291.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6388652	6389239	.	-	.	Phchi.S5G098000
Phchi.S5	AUGUSTUS	transcript	6388652	6389239	.	-	.	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	stop_codon	6388649	6388651	.	-	0	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	CDS	6388652	6388746	0.99	-	2	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	exon	6388652	6388746	.	-	.	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	intron	6388747	6388926	.	-	.	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	CDS	6388927	6389239	0.99	-	0	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	exon	6388927	6389239	.	-	.	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	start_codon	6389237	6389239	.	-	0	transcript_id "Phchi.S5G098000.t1"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	transcript	6388652	6389239	.	-	.	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	stop_codon	6388649	6388651	.	-	0	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	CDS	6388652	6388755	0.99	-	2	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	exon	6388652	6388755	.	-	.	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	intron	6388756	6388926	.	-	.	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	CDS	6388927	6389239	0.97	-	0	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	exon	6388927	6389239	.	-	.	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
Phchi.S5	AUGUSTUS	start_codon	6389237	6389239	.	-	0	transcript_id "Phchi.S5G098000.t2"; gene_id "Phchi.S5G098000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14615.t1 is derived from g13083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13790674	13793437	.	-	.	Phchi.S3G193400
Phchi.S3	AUGUSTUS	transcript	13790674	13793437	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	stop_codon	13790671	13790673	.	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13790674	13790756	1	-	2	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13790674	13790756	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13790757	13790844	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13790845	13790995	1	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13790845	13790995	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13790996	13791068	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13791069	13791224	0.48	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13791069	13791224	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13791225	13791313	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13791314	13791491	0.99	-	1	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13791314	13791491	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13791492	13791615	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13791616	13792100	1	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13791616	13792100	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13792101	13792192	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13792193	13792272	1	-	2	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13792193	13792272	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13792273	13792393	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13792394	13792460	1	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13792394	13792460	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13792461	13792542	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13792543	13792637	0.46	-	2	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13792543	13792637	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13792638	13792830	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13792831	13792939	0.79	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13792831	13792939	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13792940	13793089	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13793090	13793158	1	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13793090	13793158	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	intron	13793159	13793257	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	CDS	13793258	13793437	0.59	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	exon	13793258	13793437	.	-	.	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
Phchi.S3	AUGUSTUS	start_codon	13793435	13793437	.	-	0	transcript_id "Phchi.S3G193400.t1"; gene_id "Phchi.S3G193400"
# This transcript jg2904.t2 is derived from g73.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2905.t1 is derived from g74.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	411035	413609	.	-	.	Phchi.S1G006400
Phchi.S1	AUGUSTUS	transcript	411035	413609	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	stop_codon	411032	411034	.	-	0	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	411035	411098	0.86	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	411035	411098	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	411099	411222	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	411223	411246	0.86	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	411223	411246	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	411247	411358	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	411359	411475	0.75	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	411359	411475	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	411476	411603	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	411604	411675	1	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	411604	411675	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	411676	411766	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	411767	411817	1	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	411767	411817	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	411818	411958	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	411959	412046	1	-	2	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	411959	412046	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	412047	412175	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	412176	412299	1	-	0	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	412176	412299	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	412300	412418	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	412419	412491	1	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	412419	412491	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	412492	412583	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	412584	412650	1	-	2	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	412584	412650	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	412651	412778	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	412779	412954	0.99	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	412779	412954	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	412955	413105	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	413106	413155	1	-	0	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	413106	413155	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	413156	413341	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	413342	413405	1	-	1	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	413342	413405	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	intron	413406	413496	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	CDS	413497	413609	0.92	-	0	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	exon	413497	413609	.	-	.	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
Phchi.S1	AUGUSTUS	start_codon	413607	413609	.	-	0	transcript_id "Phchi.S1G006400.t1"; gene_id "Phchi.S1G006400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7243.t1 is derived from g4415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27805208	27808510	.	+	.	Phchi.S1G440200
Phchi.S1	AUGUSTUS	transcript	27805208	27808510	.	+	.	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	start_codon	27805208	27805210	.	+	0	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	CDS	27805208	27805970	0.06	+	0	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	exon	27805208	27805970	.	+	.	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	intron	27805971	27808460	.	+	.	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	CDS	27808461	27808510	0.02	+	2	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	exon	27808461	27808510	.	+	.	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
Phchi.S1	AUGUSTUS	stop_codon	27808511	27808513	.	+	0	transcript_id "Phchi.S1G440200.t1"; gene_id "Phchi.S1G440200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2593.t1 is derived from g9513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7557435	7558247	.	+	.	Phchi.S5G120200
Phchi.S5	AUGUSTUS	transcript	7557435	7558247	.	+	.	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	start_codon	7557435	7557437	.	+	0	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	CDS	7557435	7557695	0.21	+	0	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	exon	7557435	7557695	.	+	.	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	intron	7557696	7557797	.	+	.	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	CDS	7557798	7557867	0.85	+	0	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	exon	7557798	7557867	.	+	.	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	intron	7557868	7558062	.	+	.	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	CDS	7558063	7558247	0.8	+	2	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	exon	7558063	7558247	.	+	.	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
Phchi.S5	AUGUSTUS	stop_codon	7558248	7558250	.	+	0	transcript_id "Phchi.S5G120200.t1"; gene_id "Phchi.S5G120200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6189.t1 is derived from g3360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21381402	21385681	.	+	.	Phchi.S1G334800
Phchi.S1	AUGUSTUS	transcript	21381402	21385681	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	start_codon	21381402	21381404	.	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21381402	21382817	0.33	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21381402	21382817	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21382818	21382933	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21382934	21383082	0.5	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21382934	21383082	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21383083	21383322	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21383323	21383602	1	+	1	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21383323	21383602	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21383603	21383701	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21383702	21383809	1	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21383702	21383809	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21383810	21384014	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21384015	21384131	0.7	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21384015	21384131	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21384132	21384397	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21384398	21384541	0.98	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21384398	21384541	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21384542	21384733	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21384734	21384920	0.74	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21384734	21384920	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21384921	21385473	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21385474	21385484	0.87	+	2	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21385474	21385484	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	intron	21385485	21385579	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	CDS	21385580	21385681	0.65	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	exon	21385580	21385681	.	+	.	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
Phchi.S1	AUGUSTUS	stop_codon	21385682	21385684	.	+	0	transcript_id "Phchi.S1G334800.t1"; gene_id "Phchi.S1G334800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6347.t1 is derived from g3519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22431859	22432641	.	+	.	Phchi.S1G350600
Phchi.S1	AUGUSTUS	transcript	22431859	22432641	.	+	.	transcript_id "Phchi.S1G350600.t1"; gene_id "Phchi.S1G350600"
Phchi.S1	AUGUSTUS	start_codon	22431859	22431861	.	+	0	transcript_id "Phchi.S1G350600.t1"; gene_id "Phchi.S1G350600"
Phchi.S1	AUGUSTUS	CDS	22431859	22432641	0.94	+	0	transcript_id "Phchi.S1G350600.t1"; gene_id "Phchi.S1G350600"
Phchi.S1	AUGUSTUS	exon	22431859	22432641	.	+	.	transcript_id "Phchi.S1G350600.t1"; gene_id "Phchi.S1G350600"
Phchi.S1	AUGUSTUS	stop_codon	22432642	22432644	.	+	0	transcript_id "Phchi.S1G350600.t1"; gene_id "Phchi.S1G350600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4239.t1 is derived from g1408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9105896	9109398	.	+	.	Phchi.S1G139800
Phchi.S1	AUGUSTUS	transcript	9105896	9109398	.	+	.	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	start_codon	9105896	9105898	.	+	0	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	CDS	9105896	9106131	0.04	+	0	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	exon	9105896	9106131	.	+	.	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	intron	9106132	9106976	.	+	.	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	CDS	9106977	9107022	0.16	+	1	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	exon	9106977	9107022	.	+	.	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	intron	9107023	9109128	.	+	.	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	CDS	9109129	9109398	0.98	+	0	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	exon	9109129	9109398	.	+	.	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
Phchi.S1	AUGUSTUS	stop_codon	9109399	9109401	.	+	0	transcript_id "Phchi.S1G139800.t1"; gene_id "Phchi.S1G139800"
# This transcript jg12257.t2 is derived from g7933.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12258.t1 is derived from g7934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7055532	7056678	.	+	.	Phchi.S2G033800
Phchi.S2	AUGUSTUS	transcript	7055532	7056678	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	start_codon	7055532	7055534	.	+	0	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	CDS	7055532	7055687	0.69	+	0	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	exon	7055532	7055687	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	intron	7055688	7055838	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	CDS	7055839	7055931	0.67	+	0	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	exon	7055839	7055931	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	intron	7055932	7056062	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	CDS	7056063	7056135	0.66	+	0	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	exon	7056063	7056135	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	intron	7056136	7056277	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	CDS	7056278	7056307	0.87	+	2	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	exon	7056278	7056307	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	intron	7056308	7056451	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	CDS	7056452	7056535	0.88	+	2	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	exon	7056452	7056535	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	intron	7056536	7056625	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	CDS	7056626	7056678	0.94	+	2	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	exon	7056626	7056678	.	+	.	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
Phchi.S2	AUGUSTUS	stop_codon	7056679	7056681	.	+	0	transcript_id "Phchi.S2G033800.t1"; gene_id "Phchi.S2G033800"
# This transcript jg8085.t2 is derived from g5260.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8086.t1 is derived from g5261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32882097	32883611	.	+	.	Phchi.S1G524500
Phchi.S1	AUGUSTUS	transcript	32882097	32883611	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	start_codon	32882097	32882099	.	+	0	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32882097	32882591	0.99	+	0	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32882097	32882591	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	intron	32882592	32882797	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32882798	32883173	1	+	0	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32882798	32883173	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	intron	32883174	32883262	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32883263	32883324	1	+	2	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32883263	32883324	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	intron	32883325	32883527	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32883528	32883611	1	+	0	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32883528	32883611	.	+	.	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	stop_codon	32883612	32883614	.	+	0	transcript_id "Phchi.S1G524500.t1"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	transcript	32882097	32883611	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	start_codon	32882097	32882099	.	+	0	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32882097	32882591	1	+	0	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32882097	32882591	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	intron	32882592	32882797	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32882798	32883173	1	+	0	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32882798	32883173	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	intron	32883174	32883262	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32883263	32883333	0.99	+	2	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32883263	32883333	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	intron	32883334	32883527	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	CDS	32883528	32883611	0.98	+	0	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	exon	32883528	32883611	.	+	.	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
Phchi.S1	AUGUSTUS	stop_codon	32883612	32883614	.	+	0	transcript_id "Phchi.S1G524500.t2"; gene_id "Phchi.S1G524500"
# This transcript jg5198.t1 is derived from g2367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15419605	15420720	.	+	.	Phchi.S1G235600
Phchi.S1	AUGUSTUS	transcript	15419605	15420720	.	+	.	transcript_id "Phchi.S1G235600.t1"; gene_id "Phchi.S1G235600"
Phchi.S1	AUGUSTUS	start_codon	15419605	15419607	.	+	0	transcript_id "Phchi.S1G235600.t1"; gene_id "Phchi.S1G235600"
Phchi.S1	AUGUSTUS	CDS	15419605	15420720	0.32	+	0	transcript_id "Phchi.S1G235600.t1"; gene_id "Phchi.S1G235600"
Phchi.S1	AUGUSTUS	exon	15419605	15420720	.	+	.	transcript_id "Phchi.S1G235600.t1"; gene_id "Phchi.S1G235600"
Phchi.S1	AUGUSTUS	stop_codon	15420721	15420723	.	+	0	transcript_id "Phchi.S1G235600.t1"; gene_id "Phchi.S1G235600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11074.t1 is derived from g15124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3973297	3973764	.	-	.	Phchi.S4G065600
Phchi.S4	AUGUSTUS	transcript	3973297	3973764	.	-	.	transcript_id "Phchi.S4G065600.t1"; gene_id "Phchi.S4G065600"
Phchi.S4	AUGUSTUS	stop_codon	3973294	3973296	.	-	0	transcript_id "Phchi.S4G065600.t1"; gene_id "Phchi.S4G065600"
Phchi.S4	AUGUSTUS	CDS	3973297	3973764	0.82	-	0	transcript_id "Phchi.S4G065600.t1"; gene_id "Phchi.S4G065600"
Phchi.S4	AUGUSTUS	exon	3973297	3973764	.	-	.	transcript_id "Phchi.S4G065600.t1"; gene_id "Phchi.S4G065600"
Phchi.S4	AUGUSTUS	start_codon	3973762	3973764	.	-	0	transcript_id "Phchi.S4G065600.t1"; gene_id "Phchi.S4G065600"
# This transcript jg10902.t1 is derived from g14951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2816330	2816620	.	-	.	Phchi.S4G048300
Phchi.S4	AUGUSTUS	transcript	2816330	2816620	.	-	.	transcript_id "Phchi.S4G048300.t1"; gene_id "Phchi.S4G048300"
Phchi.S4	AUGUSTUS	stop_codon	2816327	2816329	.	-	0	transcript_id "Phchi.S4G048300.t1"; gene_id "Phchi.S4G048300"
Phchi.S4	AUGUSTUS	CDS	2816330	2816620	0.94	-	0	transcript_id "Phchi.S4G048300.t1"; gene_id "Phchi.S4G048300"
Phchi.S4	AUGUSTUS	exon	2816330	2816620	.	-	.	transcript_id "Phchi.S4G048300.t1"; gene_id "Phchi.S4G048300"
Phchi.S4	AUGUSTUS	start_codon	2816618	2816620	.	-	0	transcript_id "Phchi.S4G048300.t1"; gene_id "Phchi.S4G048300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1419.t1 is derived from g8338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	756273	756509	.	-	.	Phchi.S5G002800
Phchi.S5	AUGUSTUS	transcript	756273	756509	.	-	.	transcript_id "Phchi.S5G002800.t1"; gene_id "Phchi.S5G002800"
Phchi.S5	AUGUSTUS	stop_codon	756270	756272	.	-	0	transcript_id "Phchi.S5G002800.t1"; gene_id "Phchi.S5G002800"
Phchi.S5	AUGUSTUS	CDS	756273	756509	0.83	-	0	transcript_id "Phchi.S5G002800.t1"; gene_id "Phchi.S5G002800"
Phchi.S5	AUGUSTUS	exon	756273	756509	.	-	.	transcript_id "Phchi.S5G002800.t1"; gene_id "Phchi.S5G002800"
Phchi.S5	AUGUSTUS	start_codon	756507	756509	.	-	0	transcript_id "Phchi.S5G002800.t1"; gene_id "Phchi.S5G002800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11483.t1 is derived from g15533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6590525	6592691	.	-	.	Phchi.S4G106500
Phchi.S4	AUGUSTUS	transcript	6590525	6592691	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	stop_codon	6590522	6590524	.	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6590525	6590631	1	-	2	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6590525	6590631	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6590632	6590716	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6590717	6590781	1	-	1	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6590717	6590781	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6590782	6590913	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6590914	6590999	1	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6590914	6590999	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6591000	6591274	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6591275	6591448	0.59	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6591275	6591448	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6591449	6591583	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6591584	6591677	1	-	1	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6591584	6591677	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6591678	6591803	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6591804	6591976	1	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6591804	6591976	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6591977	6592088	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6592089	6592296	1	-	1	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6592089	6592296	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6592297	6592496	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6592497	6592585	1	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6592497	6592585	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	intron	6592586	6592682	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	CDS	6592683	6592691	0.35	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	exon	6592683	6592691	.	-	.	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
Phchi.S4	AUGUSTUS	start_codon	6592689	6592691	.	-	0	transcript_id "Phchi.S4G106500.t1"; gene_id "Phchi.S4G106500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12254.t1 is derived from g7930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7023336	7027555	.	+	.	Phchi.S2G033400
Phchi.S2	AUGUSTUS	transcript	7023336	7027555	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	start_codon	7023336	7023338	.	+	0	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7023336	7023432	0.93	+	0	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7023336	7023432	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	intron	7023433	7023525	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7023526	7023671	1	+	2	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7023526	7023671	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	intron	7023672	7023815	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7023816	7024017	0.69	+	0	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7023816	7024017	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	intron	7024018	7024118	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7024119	7024357	0.69	+	2	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7024119	7024357	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	intron	7024358	7024569	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7024570	7024678	1	+	0	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7024570	7024678	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	intron	7024679	7024822	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7024823	7024922	0.38	+	2	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7024823	7024922	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	intron	7024923	7025088	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	CDS	7025089	7027555	0.51	+	1	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	exon	7025089	7027555	.	+	.	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
Phchi.S2	AUGUSTUS	stop_codon	7027556	7027558	.	+	0	transcript_id "Phchi.S2G033400.t1"; gene_id "Phchi.S2G033400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2872.t1 is derived from g41.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	206308	209076	.	-	.	Phchi.S1G003100
Phchi.S1	AUGUSTUS	transcript	206308	209076	.	-	.	transcript_id "Phchi.S1G003100.t1"; gene_id "Phchi.S1G003100"
Phchi.S1	AUGUSTUS	stop_codon	206305	206307	.	-	0	transcript_id "Phchi.S1G003100.t1"; gene_id "Phchi.S1G003100"
Phchi.S1	AUGUSTUS	CDS	206308	209076	0.85	-	0	transcript_id "Phchi.S1G003100.t1"; gene_id "Phchi.S1G003100"
Phchi.S1	AUGUSTUS	exon	206308	209076	.	-	.	transcript_id "Phchi.S1G003100.t1"; gene_id "Phchi.S1G003100"
Phchi.S1	AUGUSTUS	start_codon	209074	209076	.	-	0	transcript_id "Phchi.S1G003100.t1"; gene_id "Phchi.S1G003100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11740.t1 is derived from g15792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7942046	7948453	.	-	.	Phchi.S4G132200
Phchi.S4	AUGUSTUS	transcript	7942046	7948453	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	stop_codon	7942043	7942045	.	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7942046	7942086	0.99	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7942046	7942086	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7942087	7942162	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7942163	7942266	1	-	1	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7942163	7942266	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7942267	7942375	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7942376	7942448	1	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7942376	7942448	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7942449	7942650	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7942651	7942738	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7942651	7942738	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7942739	7942832	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7942833	7942881	1	-	1	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7942833	7942881	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7942882	7943052	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7943053	7943107	1	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7943053	7943107	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7943108	7943244	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7943245	7943344	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7943245	7943344	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7943345	7943417	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7943418	7943495	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7943418	7943495	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7943496	7943598	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7943599	7943715	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7943599	7943715	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7943716	7943843	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7943844	7943947	1	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7943844	7943947	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7943948	7944058	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7944059	7944131	0.99	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7944059	7944131	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7944132	7944247	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7944248	7944325	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7944248	7944325	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7944326	7944414	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7944415	7944539	1	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7944415	7944539	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7944540	7944717	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7944718	7944745	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7944718	7944745	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7944746	7944831	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7944832	7944977	1	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7944832	7944977	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7944978	7945068	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7945069	7945234	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7945069	7945234	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7945235	7945322	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7945323	7945421	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7945323	7945421	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7945422	7945508	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7945509	7945640	0.92	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7945509	7945640	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7945641	7945744	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7945745	7945810	0.99	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7945745	7945810	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7945811	7945898	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7945899	7946043	1	-	1	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7945899	7946043	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7946044	7946202	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7946203	7946324	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7946203	7946324	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7946325	7946511	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7946512	7946673	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7946512	7946673	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7946674	7946757	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7946758	7946869	1	-	1	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7946758	7946869	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7946870	7946966	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7946967	7947112	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7946967	7947112	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7947113	7947225	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7947226	7947330	0.85	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7947226	7947330	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7947331	7947517	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7947518	7947592	0.92	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7947518	7947592	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7947593	7947674	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7947675	7947748	1	-	2	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7947675	7947748	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7947749	7947920	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7947921	7948074	1	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7947921	7948074	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7948075	7948142	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7948143	7948320	1	-	1	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7948143	7948320	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	intron	7948321	7948403	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	CDS	7948404	7948453	0.99	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	exon	7948404	7948453	.	-	.	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
Phchi.S4	AUGUSTUS	start_codon	7948451	7948453	.	-	0	transcript_id "Phchi.S4G132200.t1"; gene_id "Phchi.S4G132200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1007.t1 is derived from g10790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7071631	7077582	.	-	.	Phchi.S6G096600
Phchi.S6	AUGUSTUS	transcript	7071631	7077582	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	stop_codon	7071628	7071630	.	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7071631	7072209	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7071631	7072209	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7072210	7072318	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7072319	7072603	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7072319	7072603	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7072604	7072689	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7072690	7073044	1	-	1	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7072690	7073044	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7073045	7073176	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7073177	7073451	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7073177	7073451	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7073452	7073544	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7073545	7073820	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7073545	7073820	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7073821	7073913	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7073914	7074024	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7073914	7074024	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7074025	7074157	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7074158	7074373	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7074158	7074373	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7074374	7074477	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7074478	7074678	0.99	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7074478	7074678	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7074679	7074758	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7074759	7074867	1	-	1	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7074759	7074867	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7074868	7074947	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7074948	7075054	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7074948	7075054	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7075055	7075270	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7075271	7075321	0.99	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7075271	7075321	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7075322	7075458	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7075459	7075479	0.99	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7075459	7075479	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7075480	7075630	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7075631	7075706	1	-	1	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7075631	7075706	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7075707	7075972	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7075973	7076022	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7075973	7076022	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7076023	7076200	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7076201	7076420	0.58	-	1	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7076201	7076420	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7076421	7076587	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7076588	7076679	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7076588	7076679	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7076680	7076763	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7076764	7076823	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7076764	7076823	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7076824	7076977	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7076978	7077026	1	-	1	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7076978	7077026	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	intron	7077027	7077478	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	CDS	7077479	7077582	1	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	exon	7077479	7077582	.	-	.	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
Phchi.S6	AUGUSTUS	start_codon	7077580	7077582	.	-	0	transcript_id "Phchi.S6G096600.t1"; gene_id "Phchi.S6G096600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10850.t1 is derived from g14900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2497409	2498248	.	-	.	Phchi.S4G043200
Phchi.S4	AUGUSTUS	transcript	2497409	2498248	.	-	.	transcript_id "Phchi.S4G043200.t1"; gene_id "Phchi.S4G043200"
Phchi.S4	AUGUSTUS	stop_codon	2497406	2497408	.	-	0	transcript_id "Phchi.S4G043200.t1"; gene_id "Phchi.S4G043200"
Phchi.S4	AUGUSTUS	CDS	2497409	2498248	1	-	0	transcript_id "Phchi.S4G043200.t1"; gene_id "Phchi.S4G043200"
Phchi.S4	AUGUSTUS	exon	2497409	2498248	.	-	.	transcript_id "Phchi.S4G043200.t1"; gene_id "Phchi.S4G043200"
Phchi.S4	AUGUSTUS	start_codon	2498246	2498248	.	-	0	transcript_id "Phchi.S4G043200.t1"; gene_id "Phchi.S4G043200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1174.t1 is derived from g10957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8276858	8278080	.	-	.	Phchi.S6G113300
Phchi.S6	AUGUSTUS	transcript	8276858	8278080	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	stop_codon	8276855	8276857	.	-	0	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8276858	8276985	0.73	-	2	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8276858	8276985	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	intron	8276986	8277096	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8277097	8277138	0.71	-	2	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8277097	8277138	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	intron	8277139	8277223	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8277224	8277276	1	-	1	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8277224	8277276	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	intron	8277277	8277358	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8277359	8277458	1	-	2	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8277359	8277458	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	intron	8277459	8277533	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8277534	8277603	0.99	-	0	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8277534	8277603	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	intron	8277604	8277704	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8277705	8277878	0.93	-	0	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8277705	8277878	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	intron	8277879	8278032	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	CDS	8278033	8278080	0.79	-	0	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	exon	8278033	8278080	.	-	.	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
Phchi.S6	AUGUSTUS	start_codon	8278078	8278080	.	-	0	transcript_id "Phchi.S6G113300.t1"; gene_id "Phchi.S6G113300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7561.t1 is derived from g4735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30036158	30041256	.	-	.	Phchi.S1G472000
Phchi.S1	AUGUSTUS	transcript	30036158	30041256	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	stop_codon	30036155	30036157	.	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30036158	30036259	0.98	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30036158	30036259	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30036260	30036342	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30036343	30036552	1	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30036343	30036552	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30036553	30036685	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30036686	30037261	0.99	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30036686	30037261	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30037262	30037446	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30037447	30037668	1	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30037447	30037668	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30037669	30037799	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30037800	30037930	1	-	2	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30037800	30037930	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30037931	30038085	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30038086	30039007	0.99	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30038086	30039007	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30039008	30039128	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30039129	30039224	1	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30039129	30039224	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30039225	30039320	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30039321	30039398	1	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30039321	30039398	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30039399	30039489	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30039490	30040445	0.98	-	2	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30039490	30040445	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30040446	30040540	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30040541	30040664	1	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30040541	30040664	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	intron	30040665	30040803	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	CDS	30040804	30041256	0.83	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	exon	30040804	30041256	.	-	.	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
Phchi.S1	AUGUSTUS	start_codon	30041254	30041256	.	-	0	transcript_id "Phchi.S1G472000.t1"; gene_id "Phchi.S1G472000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10327.t1 is derived from g7503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47136727	47137540	.	-	.	Phchi.S1G748600
Phchi.S1	AUGUSTUS	transcript	47136727	47137540	.	-	.	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	stop_codon	47136724	47136726	.	-	0	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	CDS	47136727	47136762	1	-	0	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	exon	47136727	47136762	.	-	.	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	intron	47136763	47136847	.	-	.	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	CDS	47136848	47137540	0.8	-	0	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	exon	47136848	47137540	.	-	.	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
Phchi.S1	AUGUSTUS	start_codon	47137538	47137540	.	-	0	transcript_id "Phchi.S1G748600.t1"; gene_id "Phchi.S1G748600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9555.t1 is derived from g6731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42430530	42431955	.	+	.	Phchi.S1G671400
Phchi.S1	AUGUSTUS	transcript	42430530	42431955	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	start_codon	42430530	42430532	.	+	0	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	CDS	42430530	42431005	1	+	0	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	exon	42430530	42431005	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	intron	42431006	42431106	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	CDS	42431107	42431369	0.99	+	1	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	exon	42431107	42431369	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	intron	42431370	42431468	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	CDS	42431469	42431773	0.44	+	2	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	exon	42431469	42431773	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	intron	42431774	42431874	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	CDS	42431875	42431955	0.44	+	0	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	exon	42431875	42431955	.	+	.	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
Phchi.S1	AUGUSTUS	stop_codon	42431956	42431958	.	+	0	transcript_id "Phchi.S1G671400.t1"; gene_id "Phchi.S1G671400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2774.t1 is derived from g9694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8774155	8775243	.	-	.	Phchi.S5G138300
Phchi.S5	AUGUSTUS	transcript	8774155	8775243	.	-	.	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	stop_codon	8774152	8774154	.	-	0	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	CDS	8774155	8774301	0.63	-	0	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	exon	8774155	8774301	.	-	.	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	intron	8774302	8774505	.	-	.	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	CDS	8774506	8775243	0.17	-	0	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	exon	8774506	8775243	.	-	.	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
Phchi.S5	AUGUSTUS	start_codon	8775241	8775243	.	-	0	transcript_id "Phchi.S5G138300.t1"; gene_id "Phchi.S5G138300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2948.t1 is derived from g117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	714769	719500	.	+	.	Phchi.S1G010700
Phchi.S1	AUGUSTUS	transcript	714769	719500	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	start_codon	714769	714771	.	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	714769	714814	0.71	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	714769	714814	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	714815	714906	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	714907	715486	0.88	+	2	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	714907	715486	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	715487	715620	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	715621	715774	1	+	1	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	715621	715774	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	715775	716076	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	716077	716190	0.97	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	716077	716190	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	716191	716308	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	716309	716386	0.99	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	716309	716386	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	716387	716467	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	716468	716596	1	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	716468	716596	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	716597	716701	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	716702	716926	0.85	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	716702	716926	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	716927	717035	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	717036	717221	1	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	717036	717221	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	717222	717394	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	717395	717457	1	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	717395	717457	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	717458	717548	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	717549	717720	0.89	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	717549	717720	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	717721	717848	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	717849	717921	0.87	+	2	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	717849	717921	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	717922	718024	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	718025	718184	0.9	+	1	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	718025	718184	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	718185	718271	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	718272	718667	0.63	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	718272	718667	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	718668	718759	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	718760	718969	0.72	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	718760	718969	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	718970	719096	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	719097	719142	0.8	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	719097	719142	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	719143	719232	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	719233	719312	0.79	+	2	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	719233	719312	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	intron	719313	719407	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	CDS	719408	719500	0.98	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	exon	719408	719500	.	+	.	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
Phchi.S1	AUGUSTUS	stop_codon	719501	719503	.	+	0	transcript_id "Phchi.S1G010700.t1"; gene_id "Phchi.S1G010700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3015.t1 is derived from g184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1161056	1162306	.	+	.	Phchi.S1G017400
Phchi.S1	AUGUSTUS	transcript	1161056	1162306	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	start_codon	1161056	1161058	.	+	0	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161056	1161060	1	+	0	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161056	1161060	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161061	1161304	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161305	1161491	1	+	1	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161305	1161491	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161492	1161610	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161611	1161776	1	+	0	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161611	1161776	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161777	1161870	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161871	1161908	1	+	2	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161871	1161908	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161909	1162026	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1162027	1162072	1	+	0	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1162027	1162072	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1162073	1162277	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1162278	1162306	1	+	2	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1162278	1162306	.	+	.	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	stop_codon	1162307	1162309	.	+	0	transcript_id "Phchi.S1G017400.t1"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	transcript	1161056	1162306	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	start_codon	1161056	1161058	.	+	0	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161056	1161060	1	+	0	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161056	1161060	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161061	1161304	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161305	1161491	1	+	1	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161305	1161491	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161492	1161610	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161611	1161776	1	+	0	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161611	1161776	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161777	1161870	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1161871	1161908	1	+	2	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1161871	1161908	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1161909	1162026	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1162027	1162072	0.99	+	0	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1162027	1162072	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	intron	1162073	1162286	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	CDS	1162287	1162306	0.98	+	2	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	exon	1162287	1162306	.	+	.	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
Phchi.S1	AUGUSTUS	stop_codon	1162307	1162309	.	+	0	transcript_id "Phchi.S1G017400.t2"; gene_id "Phchi.S1G017400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9856.t1 is derived from g7032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44101143	44101983	.	+	.	Phchi.S1G701500
Phchi.S1	AUGUSTUS	transcript	44101143	44101983	.	+	.	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	start_codon	44101143	44101145	.	+	0	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	CDS	44101143	44101219	0.8	+	0	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	exon	44101143	44101219	.	+	.	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	intron	44101220	44101406	.	+	.	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	CDS	44101407	44101983	0.84	+	1	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	exon	44101407	44101983	.	+	.	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
Phchi.S1	AUGUSTUS	stop_codon	44101984	44101986	.	+	0	transcript_id "Phchi.S1G701500.t1"; gene_id "Phchi.S1G701500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7175.t1 is derived from g4347.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27402317	27412475	.	-	.	Phchi.S1G433400
Phchi.S1	AUGUSTUS	transcript	27402317	27412475	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	stop_codon	27402314	27402316	.	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27402317	27402568	0.98	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27402317	27402568	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27402569	27402654	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27402655	27403629	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27402655	27403629	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27403630	27403788	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27403789	27403974	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27403789	27403974	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27403975	27404066	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27404067	27404399	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27404067	27404399	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27404400	27404574	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27404575	27404922	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27404575	27404922	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27404923	27405098	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405099	27405284	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405099	27405284	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405285	27405371	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405372	27405518	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405372	27405518	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405519	27405612	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405613	27405795	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405613	27405795	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405796	27405873	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405874	27405984	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405874	27405984	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405985	27406125	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406126	27406201	1	-	1	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406126	27406201	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406202	27406298	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406299	27406429	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406299	27406429	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406430	27406528	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406529	27406722	1	-	2	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406529	27406722	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406723	27406818	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406819	27406945	0.87	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406819	27406945	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406946	27407056	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407057	27407201	0.86	-	1	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407057	27407201	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407202	27407301	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407302	27407339	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407302	27407339	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407340	27407427	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407428	27407535	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407428	27407535	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407536	27407687	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407688	27407849	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407688	27407849	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407850	27407939	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407940	27408012	1	-	1	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407940	27408012	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408013	27408181	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27408182	27408225	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27408182	27408225	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408226	27408345	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27408346	27408540	0.98	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27408346	27408540	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408541	27408684	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27408685	27408852	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27408685	27408852	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408853	27409007	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27409008	27409289	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27409008	27409289	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27409290	27409633	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27409634	27409942	0.97	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27409634	27409942	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27409943	27410053	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410054	27410191	0.98	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410054	27410191	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410192	27410338	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410339	27410439	1	-	2	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410339	27410439	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410440	27410718	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410719	27410774	1	-	1	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410719	27410774	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410775	27410864	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410865	27410977	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410865	27410977	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410978	27411369	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27411370	27411494	0.99	-	2	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27411370	27411494	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27411495	27411598	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27411599	27411761	0.69	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27411599	27411761	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27411762	27411865	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27411866	27411952	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27411866	27411952	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27411953	27412460	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27412461	27412475	1	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27412461	27412475	.	-	.	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	start_codon	27412473	27412475	.	-	0	transcript_id "Phchi.S1G433400.t1"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	transcript	27402317	27412475	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	stop_codon	27402314	27402316	.	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27402317	27402568	0.98	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27402317	27402568	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27402569	27402654	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27402655	27403629	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27402655	27403629	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27403630	27403788	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27403789	27403974	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27403789	27403974	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27403975	27404066	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27404067	27404399	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27404067	27404399	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27404400	27404574	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27404575	27404922	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27404575	27404922	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27404923	27405098	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405099	27405284	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405099	27405284	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405285	27405371	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405372	27405518	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405372	27405518	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405519	27405612	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405613	27405795	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405613	27405795	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405796	27405873	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27405874	27405984	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27405874	27405984	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27405985	27406125	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406126	27406201	1	-	1	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406126	27406201	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406202	27406298	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406299	27406429	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406299	27406429	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406430	27406528	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406529	27406722	1	-	2	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406529	27406722	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406723	27406818	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27406819	27406945	0.85	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27406819	27406945	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27406946	27407056	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407057	27407201	0.86	-	1	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407057	27407201	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407202	27407301	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407302	27407339	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407302	27407339	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407340	27407427	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407428	27407562	0.96	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407428	27407562	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407563	27407687	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407688	27407849	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407688	27407849	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27407850	27407939	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27407940	27408012	1	-	1	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27407940	27408012	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408013	27408181	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27408182	27408225	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27408182	27408225	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408226	27408345	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27408346	27408540	0.99	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27408346	27408540	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408541	27408684	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27408685	27408852	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27408685	27408852	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27408853	27409007	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27409008	27409289	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27409008	27409289	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27409290	27409633	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27409634	27409942	0.97	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27409634	27409942	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27409943	27410053	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410054	27410191	0.98	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410054	27410191	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410192	27410338	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410339	27410439	1	-	2	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410339	27410439	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410440	27410718	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410719	27410774	1	-	1	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410719	27410774	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410775	27410864	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27410865	27410977	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27410865	27410977	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27410978	27411369	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27411370	27411494	0.98	-	2	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27411370	27411494	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27411495	27411598	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27411599	27411761	0.68	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27411599	27411761	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27411762	27411865	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27411866	27411952	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27411866	27411952	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	intron	27411953	27412460	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	CDS	27412461	27412475	1	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	exon	27412461	27412475	.	-	.	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
Phchi.S1	AUGUSTUS	start_codon	27412473	27412475	.	-	0	transcript_id "Phchi.S1G433400.t2"; gene_id "Phchi.S1G433400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11691.t1 is derived from g15742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7695354	7696157	.	-	.	Phchi.S4G127300
Phchi.S4	AUGUSTUS	transcript	7695354	7696157	.	-	.	transcript_id "Phchi.S4G127300.t1"; gene_id "Phchi.S4G127300"
Phchi.S4	AUGUSTUS	stop_codon	7695351	7695353	.	-	0	transcript_id "Phchi.S4G127300.t1"; gene_id "Phchi.S4G127300"
Phchi.S4	AUGUSTUS	CDS	7695354	7696157	0.99	-	0	transcript_id "Phchi.S4G127300.t1"; gene_id "Phchi.S4G127300"
Phchi.S4	AUGUSTUS	exon	7695354	7696157	.	-	.	transcript_id "Phchi.S4G127300.t1"; gene_id "Phchi.S4G127300"
Phchi.S4	AUGUSTUS	start_codon	7696155	7696157	.	-	0	transcript_id "Phchi.S4G127300.t1"; gene_id "Phchi.S4G127300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3281.t1 is derived from g450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2672786	2677154	.	+	.	Phchi.S1G044000
Phchi.S1	AUGUSTUS	transcript	2672786	2677154	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	start_codon	2672786	2672788	.	+	0	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	CDS	2672786	2674343	0.73	+	0	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	exon	2672786	2674343	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	intron	2674344	2674451	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	CDS	2674452	2674547	0.95	+	2	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	exon	2674452	2674547	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	intron	2674548	2674648	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	CDS	2674649	2675898	0.97	+	2	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	exon	2674649	2675898	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	intron	2675899	2676017	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	CDS	2676018	2677154	1	+	0	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	exon	2676018	2677154	.	+	.	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
Phchi.S1	AUGUSTUS	stop_codon	2677155	2677157	.	+	0	transcript_id "Phchi.S1G044000.t1"; gene_id "Phchi.S1G044000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13200.t1 is derived from g11665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4649069	4649655	.	-	.	Phchi.S3G051900
Phchi.S3	AUGUSTUS	transcript	4649069	4649655	.	-	.	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	stop_codon	4649066	4649068	.	-	0	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	CDS	4649069	4649290	1	-	0	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	exon	4649069	4649290	.	-	.	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	intron	4649291	4649460	.	-	.	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	CDS	4649461	4649655	1	-	0	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	exon	4649461	4649655	.	-	.	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
Phchi.S3	AUGUSTUS	start_codon	4649653	4649655	.	-	0	transcript_id "Phchi.S3G051900.t1"; gene_id "Phchi.S3G051900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15907.t1 is derived from g14377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22135969	22137696	.	+	.	Phchi.S3G322600
Phchi.S3	AUGUSTUS	transcript	22135969	22137696	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	start_codon	22135969	22135971	.	+	0	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	CDS	22135969	22136050	0.06	+	0	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	exon	22135969	22136050	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	intron	22136051	22136282	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	CDS	22136283	22136322	0.08	+	2	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	exon	22136283	22136322	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	intron	22136323	22137416	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	CDS	22137417	22137519	0.01	+	1	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	exon	22137417	22137519	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	intron	22137520	22137648	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	CDS	22137649	22137696	0.01	+	0	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	exon	22137649	22137696	.	+	.	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
Phchi.S3	AUGUSTUS	stop_codon	22137697	22137699	.	+	0	transcript_id "Phchi.S3G322600.t1"; gene_id "Phchi.S3G322600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6464.t1 is derived from g3636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23130233	23131408	.	-	.	Phchi.S1G362300
Phchi.S1	AUGUSTUS	transcript	23130233	23131408	.	-	.	transcript_id "Phchi.S1G362300.t1"; gene_id "Phchi.S1G362300"
Phchi.S1	AUGUSTUS	stop_codon	23130230	23130232	.	-	0	transcript_id "Phchi.S1G362300.t1"; gene_id "Phchi.S1G362300"
Phchi.S1	AUGUSTUS	CDS	23130233	23131408	0.21	-	0	transcript_id "Phchi.S1G362300.t1"; gene_id "Phchi.S1G362300"
Phchi.S1	AUGUSTUS	exon	23130233	23131408	.	-	.	transcript_id "Phchi.S1G362300.t1"; gene_id "Phchi.S1G362300"
Phchi.S1	AUGUSTUS	start_codon	23131406	23131408	.	-	0	transcript_id "Phchi.S1G362300.t1"; gene_id "Phchi.S1G362300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4987.t1 is derived from g2157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13895552	13896598	.	+	.	Phchi.S1G214600
Phchi.S1	AUGUSTUS	transcript	13895552	13896598	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	start_codon	13895552	13895554	.	+	0	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	CDS	13895552	13895569	0.71	+	0	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	exon	13895552	13895569	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	intron	13895570	13895664	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	CDS	13895665	13895798	1	+	0	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	exon	13895665	13895798	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	intron	13895799	13895973	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	CDS	13895974	13896151	1	+	1	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	exon	13895974	13896151	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	intron	13896152	13896239	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	CDS	13896240	13896315	1	+	0	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	exon	13896240	13896315	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	intron	13896316	13896440	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	CDS	13896441	13896598	1	+	2	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	exon	13896441	13896598	.	+	.	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
Phchi.S1	AUGUSTUS	stop_codon	13896599	13896601	.	+	0	transcript_id "Phchi.S1G214600.t1"; gene_id "Phchi.S1G214600"
# This transcript jg13344.t2 is derived from g11810.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13345.t1 is derived from g11811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6198867	6204169	.	+	.	Phchi.S3G066400
Phchi.S3	AUGUSTUS	transcript	6198867	6204169	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	start_codon	6198867	6198869	.	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6198867	6199768	0.99	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6198867	6199768	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6199769	6199888	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6199889	6202573	1	+	1	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6199889	6202573	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6202574	6202750	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6202751	6202964	1	+	1	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6202751	6202964	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6202965	6203049	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6203050	6203298	1	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6203050	6203298	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6203299	6203436	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6203437	6203496	1	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6203437	6203496	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6203497	6203573	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6203574	6203704	1	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6203574	6203704	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6203705	6203806	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6203807	6203921	0.99	+	1	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6203807	6203921	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	intron	6203922	6204016	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	CDS	6204017	6204169	1	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	exon	6204017	6204169	.	+	.	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
Phchi.S3	AUGUSTUS	stop_codon	6204170	6204172	.	+	0	transcript_id "Phchi.S3G066400.t1"; gene_id "Phchi.S3G066400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15064.t1 is derived from g13532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16838781	16840880	.	-	.	Phchi.S3G238300
Phchi.S3	AUGUSTUS	transcript	16838781	16840880	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	stop_codon	16838778	16838780	.	-	0	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16838781	16838905	0.73	-	2	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16838781	16838905	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16838906	16839040	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839041	16839107	0.79	-	0	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839041	16839107	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839108	16839211	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839212	16839305	0.93	-	1	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839212	16839305	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839306	16839448	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839449	16839477	1	-	0	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839449	16839477	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839478	16839703	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839704	16839904	0.99	-	0	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839704	16839904	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839905	16840222	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16840223	16840454	0.9	-	1	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16840223	16840454	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16840455	16840537	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16840538	16840624	0.92	-	1	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16840538	16840624	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16840625	16840857	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16840858	16840880	0.88	-	0	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16840858	16840880	.	-	.	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	start_codon	16840878	16840880	.	-	0	transcript_id "Phchi.S3G238300.t1"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	transcript	16838781	16840880	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	stop_codon	16838778	16838780	.	-	0	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16838781	16838905	0.72	-	2	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16838781	16838905	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16838906	16839040	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839041	16839107	0.8	-	0	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839041	16839107	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839108	16839211	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839212	16839477	0.89	-	2	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839212	16839477	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839478	16839562	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839563	16839572	0.97	-	0	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839563	16839572	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839573	16839661	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16839662	16839904	0.47	-	0	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16839662	16839904	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16839905	16840222	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16840223	16840454	0.82	-	1	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16840223	16840454	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16840455	16840537	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16840538	16840624	0.84	-	1	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16840538	16840624	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	intron	16840625	16840857	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	CDS	16840858	16840880	0.81	-	0	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	exon	16840858	16840880	.	-	.	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
Phchi.S3	AUGUSTUS	start_codon	16840878	16840880	.	-	0	transcript_id "Phchi.S3G238300.t2"; gene_id "Phchi.S3G238300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4098.t1 is derived from g1267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7813650	7816569	.	-	.	Phchi.S1G125700
Phchi.S1	AUGUSTUS	transcript	7813650	7816569	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	stop_codon	7813647	7813649	.	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	CDS	7813650	7813721	0.78	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	exon	7813650	7813721	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	intron	7813722	7813841	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	CDS	7813842	7813928	0.77	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	exon	7813842	7813928	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	intron	7813929	7814017	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	CDS	7814018	7814029	0.6	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	exon	7814018	7814029	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	intron	7814030	7814118	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	CDS	7814119	7815142	0.42	-	1	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	exon	7814119	7815142	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	intron	7815143	7815565	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	CDS	7815566	7816038	0.64	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	exon	7815566	7816038	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	intron	7816039	7816194	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	CDS	7816195	7816569	0.69	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	exon	7816195	7816569	.	-	.	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
Phchi.S1	AUGUSTUS	start_codon	7816567	7816569	.	-	0	transcript_id "Phchi.S1G125700.t1"; gene_id "Phchi.S1G125700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11612.t1 is derived from g15663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7320722	7321380	.	+	.	Phchi.S4G119400
Phchi.S4	AUGUSTUS	transcript	7320722	7321380	.	+	.	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	start_codon	7320722	7320724	.	+	0	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	CDS	7320722	7320748	0.51	+	0	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	exon	7320722	7320748	.	+	.	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	intron	7320749	7321179	.	+	.	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	CDS	7321180	7321380	0.49	+	0	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	exon	7321180	7321380	.	+	.	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
Phchi.S4	AUGUSTUS	stop_codon	7321381	7321383	.	+	0	transcript_id "Phchi.S4G119400.t1"; gene_id "Phchi.S4G119400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13869.t1 is derived from g12336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9390799	9392894	.	+	.	Phchi.S3G118800
Phchi.S3	AUGUSTUS	transcript	9390799	9392894	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	start_codon	9390799	9390801	.	+	0	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	CDS	9390799	9391187	0.95	+	0	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	exon	9390799	9391187	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	intron	9391188	9391278	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	CDS	9391279	9391567	1	+	1	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	exon	9391279	9391567	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	intron	9391568	9391717	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	CDS	9391718	9392011	0.99	+	0	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	exon	9391718	9392011	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	intron	9392012	9392161	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	CDS	9392162	9392529	1	+	0	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	exon	9392162	9392529	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	intron	9392530	9392638	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	CDS	9392639	9392894	1	+	1	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	exon	9392639	9392894	.	+	.	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
Phchi.S3	AUGUSTUS	stop_codon	9392895	9392897	.	+	0	transcript_id "Phchi.S3G118800.t1"; gene_id "Phchi.S3G118800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11043.t1 is derived from g15093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3793732	3796029	.	-	.	Phchi.S4G062500
Phchi.S4	AUGUSTUS	transcript	3793732	3796029	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	stop_codon	3793729	3793731	.	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3793732	3793935	1	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3793732	3793935	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3793936	3794056	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3794057	3794156	1	-	1	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3794057	3794156	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3794157	3794270	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3794271	3794612	1	-	1	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3794271	3794612	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3794613	3794713	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3794714	3794775	1	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3794714	3794775	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3794776	3794895	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3794896	3794968	1	-	1	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3794896	3794968	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3794969	3795079	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3795080	3795201	1	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3795080	3795201	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3795202	3795297	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3795298	3795375	1	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3795298	3795375	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3795376	3795597	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3795598	3795669	0.98	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3795598	3795669	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3795670	3795772	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3795773	3795846	0.97	-	2	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3795773	3795846	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	intron	3795847	3796019	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	CDS	3796020	3796029	1	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	exon	3796020	3796029	.	-	.	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
Phchi.S4	AUGUSTUS	start_codon	3796027	3796029	.	-	0	transcript_id "Phchi.S4G062500.t1"; gene_id "Phchi.S4G062500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1895.t1 is derived from g8815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3765903	3767630	.	-	.	Phchi.S5G050400
Phchi.S5	AUGUSTUS	transcript	3765903	3767630	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	stop_codon	3765900	3765902	.	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3765903	3766055	1	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3765903	3766055	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	intron	3766056	3766148	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3766149	3766232	1	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3766149	3766232	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	intron	3766233	3766441	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3766442	3766523	1	-	1	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3766442	3766523	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	intron	3766524	3766656	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3766657	3766748	0.99	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3766657	3766748	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	intron	3766749	3766854	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3766855	3766929	0.86	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3766855	3766929	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	intron	3766930	3767229	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3767230	3767284	1	-	1	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3767230	3767284	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	intron	3767285	3767397	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	CDS	3767398	3767630	0.85	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	exon	3767398	3767630	.	-	.	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
Phchi.S5	AUGUSTUS	start_codon	3767628	3767630	.	-	0	transcript_id "Phchi.S5G050400.t1"; gene_id "Phchi.S5G050400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6413.t1 is derived from g3585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22853905	22856958	.	-	.	Phchi.S1G357200
Phchi.S1	AUGUSTUS	transcript	22853905	22856958	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	stop_codon	22853902	22853904	.	-	0	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	CDS	22853905	22854008	0.9	-	2	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	exon	22853905	22854008	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	intron	22854009	22854242	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	CDS	22854243	22854437	0.93	-	2	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	exon	22854243	22854437	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	intron	22854438	22854872	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	CDS	22854873	22856535	0.54	-	0	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	exon	22854873	22856535	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	intron	22856536	22856619	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	CDS	22856620	22856664	0.98	-	0	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	exon	22856620	22856664	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	intron	22856665	22856756	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	CDS	22856757	22856800	0.71	-	2	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	exon	22856757	22856800	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	intron	22856801	22856948	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	CDS	22856949	22856958	0.98	-	0	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	exon	22856949	22856958	.	-	.	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
Phchi.S1	AUGUSTUS	start_codon	22856956	22856958	.	-	0	transcript_id "Phchi.S1G357200.t1"; gene_id "Phchi.S1G357200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6975.t1 is derived from g4147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26243182	26244846	.	-	.	Phchi.S1G413400
Phchi.S1	AUGUSTUS	transcript	26243182	26244846	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	stop_codon	26243179	26243181	.	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26243182	26243259	1	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26243182	26243259	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26243260	26243352	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26243353	26243424	1	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26243353	26243424	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26243425	26243503	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26243504	26243570	1	-	1	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26243504	26243570	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26243571	26243650	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26243651	26243721	1	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26243651	26243721	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26243722	26243800	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26243801	26243852	1	-	1	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26243801	26243852	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26243853	26243977	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26243978	26244042	1	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26243978	26244042	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26244043	26244160	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26244161	26244210	1	-	2	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26244161	26244210	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26244211	26244318	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26244319	26244395	1	-	1	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26244319	26244395	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26244396	26244474	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26244475	26244694	1	-	2	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26244475	26244694	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	intron	26244695	26244788	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	CDS	26244789	26244846	0.71	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	exon	26244789	26244846	.	-	.	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
Phchi.S1	AUGUSTUS	start_codon	26244844	26244846	.	-	0	transcript_id "Phchi.S1G413400.t1"; gene_id "Phchi.S1G413400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5687.t1 is derived from g2857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18317747	18318807	.	-	.	Phchi.S1G284600
Phchi.S1	AUGUSTUS	transcript	18317747	18318807	.	-	.	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	stop_codon	18317744	18317746	.	-	0	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	CDS	18317747	18318127	0.9	-	0	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	exon	18317747	18318127	.	-	.	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	intron	18318128	18318222	.	-	.	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	CDS	18318223	18318489	1	-	0	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	exon	18318223	18318489	.	-	.	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	intron	18318490	18318588	.	-	.	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	CDS	18318589	18318807	0.99	-	0	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	exon	18318589	18318807	.	-	.	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
Phchi.S1	AUGUSTUS	start_codon	18318805	18318807	.	-	0	transcript_id "Phchi.S1G284600.t1"; gene_id "Phchi.S1G284600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8277.t1 is derived from g5452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35066942	35071451	.	-	.	Phchi.S1G543600
Phchi.S1	AUGUSTUS	transcript	35066942	35071451	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	stop_codon	35066939	35066941	.	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35066942	35067542	0.99	-	1	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35066942	35067542	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35067543	35067661	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35067662	35067706	1	-	1	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35067662	35067706	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35067707	35067850	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35067851	35067927	1	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35067851	35067927	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35067928	35068024	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35068025	35068138	1	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35068025	35068138	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35068139	35068253	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35068254	35068342	1	-	2	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35068254	35068342	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35068343	35068460	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35068461	35068530	1	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35068461	35068530	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35068531	35068737	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35068738	35068835	1	-	2	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35068738	35068835	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35068836	35068945	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35068946	35069039	1	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35068946	35069039	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35069040	35069129	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35069130	35069220	1	-	1	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35069130	35069220	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35069221	35069387	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35069388	35069480	1	-	1	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35069388	35069480	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35069481	35069602	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35069603	35069910	1	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35069603	35069910	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35069911	35070101	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35070102	35070414	0.97	-	1	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35070102	35070414	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35070415	35070760	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35070761	35070838	0.53	-	1	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35070761	35070838	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	intron	35070839	35071158	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	CDS	35071159	35071451	0.51	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	exon	35071159	35071451	.	-	.	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
Phchi.S1	AUGUSTUS	start_codon	35071449	35071451	.	-	0	transcript_id "Phchi.S1G543600.t1"; gene_id "Phchi.S1G543600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14280.t1 is derived from g12747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11901060	11905623	.	-	.	Phchi.S3G159900
Phchi.S3	AUGUSTUS	transcript	11901060	11905623	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	stop_codon	11901057	11901059	.	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11901060	11901075	0.59	-	1	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11901060	11901075	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11901076	11901160	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11901161	11901309	0.5	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11901161	11901309	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11901310	11901404	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11901405	11901443	0.59	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11901405	11901443	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11901444	11901570	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11901571	11901654	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11901571	11901654	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11901655	11901742	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11901743	11901838	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11901743	11901838	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11901839	11901942	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11901943	11902044	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11901943	11902044	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11902045	11902128	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11902129	11902171	0.86	-	1	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11902129	11902171	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11902172	11902275	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11902276	11902394	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11902276	11902394	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11902395	11902476	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11902477	11902573	1	-	1	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11902477	11902573	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11902574	11902745	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11902746	11902807	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11902746	11902807	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11902808	11902909	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11902910	11902972	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11902910	11902972	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11902973	11903063	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11903064	11903166	1	-	1	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11903064	11903166	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11903167	11903355	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11903356	11903451	1	-	1	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11903356	11903451	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11903452	11903553	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11903554	11903702	0.98	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11903554	11903702	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11903703	11903936	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11903937	11904110	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11903937	11904110	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11904111	11904221	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11904222	11904300	0.91	-	1	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11904222	11904300	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11904301	11904532	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11904533	11904687	0.49	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11904533	11904687	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11904688	11904914	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11904915	11905088	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11904915	11905088	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	intron	11905089	11905215	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	CDS	11905216	11905623	1	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	exon	11905216	11905623	.	-	.	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
Phchi.S3	AUGUSTUS	start_codon	11905621	11905623	.	-	0	transcript_id "Phchi.S3G159900.t1"; gene_id "Phchi.S3G159900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13912.t1 is derived from g12379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9634904	9635459	.	+	.	Phchi.S3G123100
Phchi.S3	AUGUSTUS	transcript	9634904	9635459	.	+	.	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	start_codon	9634904	9634906	.	+	0	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	CDS	9634904	9635035	0.93	+	0	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	exon	9634904	9635035	.	+	.	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	intron	9635036	9635216	.	+	.	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	CDS	9635217	9635345	0.9	+	0	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	exon	9635217	9635345	.	+	.	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	intron	9635346	9635432	.	+	.	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	CDS	9635433	9635459	0.94	+	0	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	exon	9635433	9635459	.	+	.	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
Phchi.S3	AUGUSTUS	stop_codon	9635460	9635462	.	+	0	transcript_id "Phchi.S3G123100.t1"; gene_id "Phchi.S3G123100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2211.t1 is derived from g9131.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5434073	5435394	.	-	.	Phchi.S5G082000
Phchi.S5	AUGUSTUS	transcript	5434073	5435394	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	stop_codon	5434070	5434072	.	-	0	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434073	5434154	0.95	-	1	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434073	5434154	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	intron	5434155	5434302	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434303	5434356	0.96	-	1	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434303	5434356	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	intron	5434357	5434570	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434571	5434618	0.89	-	1	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434571	5434618	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	intron	5434619	5434921	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434922	5435394	0.93	-	0	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434922	5435394	.	-	.	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	start_codon	5435392	5435394	.	-	0	transcript_id "Phchi.S5G082000.t1"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	transcript	5434073	5435394	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	stop_codon	5434070	5434072	.	-	0	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434073	5434154	0.99	-	1	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434073	5434154	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	intron	5434155	5434302	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434303	5434361	0.99	-	0	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434303	5434361	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	intron	5434362	5434570	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434571	5434741	0.62	-	0	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434571	5434741	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	intron	5434742	5434956	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	CDS	5434957	5435394	0.85	-	0	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	exon	5434957	5435394	.	-	.	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
Phchi.S5	AUGUSTUS	start_codon	5435392	5435394	.	-	0	transcript_id "Phchi.S5G082000.t2"; gene_id "Phchi.S5G082000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12157.t1 is derived from g7833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5066463	5066972	.	-	.	Phchi.S2G023700
Phchi.S2	AUGUSTUS	transcript	5066463	5066972	.	-	.	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	stop_codon	5066460	5066462	.	-	0	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	CDS	5066463	5066522	0.45	-	0	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	exon	5066463	5066522	.	-	.	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	intron	5066523	5066660	.	-	.	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	CDS	5066661	5066802	1	-	1	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	exon	5066661	5066802	.	-	.	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	intron	5066803	5066919	.	-	.	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	CDS	5066920	5066972	0.87	-	0	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	exon	5066920	5066972	.	-	.	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
Phchi.S2	AUGUSTUS	start_codon	5066970	5066972	.	-	0	transcript_id "Phchi.S2G023700.t1"; gene_id "Phchi.S2G023700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6862.t1 is derived from g4034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25624950	25627285	.	+	.	Phchi.S1G402100
Phchi.S1	AUGUSTUS	transcript	25624950	25627285	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	start_codon	25624950	25624952	.	+	0	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25624950	25625056	0.87	+	0	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25624950	25625056	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25625057	25625135	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25625136	25625267	1	+	1	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25625136	25625267	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25625268	25625361	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25625362	25625412	0.76	+	1	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25625362	25625412	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25625413	25625675	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25625676	25625773	0.74	+	1	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25625676	25625773	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25625774	25625863	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25625864	25625934	1	+	2	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25625864	25625934	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25625935	25626092	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25626093	25626171	1	+	0	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25626093	25626171	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25626172	25626253	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25626254	25626320	1	+	2	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25626254	25626320	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25626321	25626410	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25626411	25626493	1	+	1	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25626411	25626493	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25626494	25626573	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25626574	25626665	1	+	2	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25626574	25626665	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25626666	25626753	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25626754	25626860	1	+	0	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25626754	25626860	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25626861	25627025	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25627026	25627089	1	+	1	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25627026	25627089	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	intron	25627090	25627189	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	CDS	25627190	25627285	0.49	+	0	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	exon	25627190	25627285	.	+	.	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
Phchi.S1	AUGUSTUS	stop_codon	25627286	25627288	.	+	0	transcript_id "Phchi.S1G402100.t1"; gene_id "Phchi.S1G402100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg352.t1 is derived from g10134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2559135	2561310	.	-	.	Phchi.S6G031100
Phchi.S6	AUGUSTUS	transcript	2559135	2561310	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	stop_codon	2559132	2559134	.	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2559135	2559246	1	-	1	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2559135	2559246	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2559247	2559342	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2559343	2559461	1	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2559343	2559461	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2559462	2559558	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2559559	2559665	0.66	-	2	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2559559	2559665	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2559666	2559758	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2559759	2559837	0.66	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2559759	2559837	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2559838	2559914	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2559915	2560004	1	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2559915	2560004	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2560005	2560115	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2560116	2560352	1	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2560116	2560352	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2560353	2560447	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2560448	2561000	0.58	-	1	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2560448	2561000	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	intron	2561001	2561098	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	CDS	2561099	2561310	0.97	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	exon	2561099	2561310	.	-	.	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
Phchi.S6	AUGUSTUS	start_codon	2561308	2561310	.	-	0	transcript_id "Phchi.S6G031100.t1"; gene_id "Phchi.S6G031100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2786.t1 is derived from g9706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8859199	8862828	.	+	.	Phchi.S5G139500
Phchi.S5	AUGUSTUS	transcript	8859199	8862828	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	start_codon	8859199	8859201	.	+	0	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8859199	8859479	1	+	0	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8859199	8859479	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8859480	8859657	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8859658	8860452	0.61	+	1	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8859658	8860452	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8860453	8860530	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8860531	8860953	0.48	+	1	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8860531	8860953	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8860954	8861457	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8861458	8862005	0.33	+	1	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8861458	8862005	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8862006	8862096	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8862097	8862292	0.92	+	2	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8862097	8862292	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8862293	8862446	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8862447	8862547	0.94	+	1	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8862447	8862547	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8862548	8862630	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8862631	8862717	0.95	+	2	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8862631	8862717	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	intron	8862718	8862811	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	CDS	8862812	8862828	0.95	+	2	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	exon	8862812	8862828	.	+	.	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
Phchi.S5	AUGUSTUS	stop_codon	8862829	8862831	.	+	0	transcript_id "Phchi.S5G139500.t1"; gene_id "Phchi.S5G139500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15346.t1 is derived from g13814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18487665	18489249	.	-	.	Phchi.S3G266500
Phchi.S3	AUGUSTUS	transcript	18487665	18488293	.	-	.	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	stop_codon	18487662	18487664	.	-	0	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	CDS	18487665	18487686	0.64	-	1	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	exon	18487665	18487686	.	-	.	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	intron	18487687	18487778	.	-	.	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	CDS	18487779	18488293	0.58	-	0	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	exon	18487779	18488293	.	-	.	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	start_codon	18488291	18488293	.	-	0	transcript_id "Phchi.S3G266500.t1"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	transcript	18487665	18489249	.	-	.	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	stop_codon	18487662	18487664	.	-	0	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	CDS	18487665	18487686	0.63	-	1	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	exon	18487665	18487686	.	-	.	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	intron	18487687	18487778	.	-	.	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	CDS	18487779	18488332	0.4	-	0	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	exon	18487779	18488332	.	-	.	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	intron	18488333	18488511	.	-	.	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	CDS	18488512	18489249	0.38	-	0	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	exon	18488512	18489249	.	-	.	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	start_codon	18489247	18489249	.	-	0	transcript_id "Phchi.S3G266500.t2"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	transcript	18488470	18489249	.	-	.	transcript_id "Phchi.S3G266500.t3"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	stop_codon	18488467	18488469	.	-	0	transcript_id "Phchi.S3G266500.t3"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	CDS	18488470	18489249	0.49	-	0	transcript_id "Phchi.S3G266500.t3"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	exon	18488470	18489249	.	-	.	transcript_id "Phchi.S3G266500.t3"; gene_id "Phchi.S3G266500"
Phchi.S3	AUGUSTUS	start_codon	18489247	18489249	.	-	0	transcript_id "Phchi.S3G266500.t3"; gene_id "Phchi.S3G266500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13447.t1 is derived from g11914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6757733	6762408	.	+	.	Phchi.S3G076600
Phchi.S3	AUGUSTUS	transcript	6757733	6762408	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	start_codon	6757733	6757735	.	+	0	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6757733	6757889	0.54	+	0	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6757733	6757889	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6757890	6757969	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6757970	6758271	1	+	2	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6757970	6758271	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6758272	6758359	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6758360	6758625	1	+	0	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6758360	6758625	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6758626	6758729	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6758730	6758990	1	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6758730	6758990	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6758991	6759076	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6759077	6759318	1	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6759077	6759318	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6759319	6759408	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6759409	6759523	1	+	2	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6759409	6759523	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6759524	6759642	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6759643	6759714	1	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6759643	6759714	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6759715	6759827	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6759828	6759899	1	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6759828	6759899	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6759900	6760142	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6760143	6760229	0.99	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6760143	6760229	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6760230	6760334	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6760335	6760600	0.98	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6760335	6760600	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6760601	6760703	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6760704	6760939	0.99	+	2	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6760704	6760939	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6760940	6761018	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6761019	6761145	1	+	0	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6761019	6761145	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6761146	6761280	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6761281	6761349	1	+	2	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6761281	6761349	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6761350	6761472	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6761473	6761518	1	+	2	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6761473	6761518	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6761519	6761638	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6761639	6761779	1	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6761639	6761779	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6761780	6761858	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6761859	6761985	1	+	1	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6761859	6761985	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	intron	6761986	6762075	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	CDS	6762076	6762408	0.97	+	0	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	exon	6762076	6762408	.	+	.	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
Phchi.S3	AUGUSTUS	stop_codon	6762409	6762411	.	+	0	transcript_id "Phchi.S3G076600.t1"; gene_id "Phchi.S3G076600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10841.t1 is derived from g14891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2424115	2426332	.	+	.	Phchi.S4G042300
Phchi.S4	AUGUSTUS	transcript	2424115	2426332	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	start_codon	2424115	2424117	.	+	0	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	CDS	2424115	2425326	0.48	+	0	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	exon	2424115	2425326	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	intron	2425327	2425554	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	CDS	2425555	2425926	0.62	+	0	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	exon	2425555	2425926	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	intron	2425927	2426018	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	CDS	2426019	2426095	1	+	0	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	exon	2426019	2426095	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	intron	2426096	2426184	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	CDS	2426185	2426332	1	+	1	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	exon	2426185	2426332	.	+	.	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
Phchi.S4	AUGUSTUS	stop_codon	2426333	2426335	.	+	0	transcript_id "Phchi.S4G042300.t1"; gene_id "Phchi.S4G042300"
# This transcript jg15538.t2 is derived from g14007.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15539.t1 is derived from g14008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19775518	19777408	.	-	.	Phchi.S3G285800
Phchi.S3	AUGUSTUS	transcript	19775518	19777408	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	stop_codon	19775515	19775517	.	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19775518	19775683	1	-	1	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19775518	19775683	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19775684	19775773	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19775774	19775907	1	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19775774	19775907	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19775908	19775988	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19775989	19776098	1	-	2	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19775989	19776098	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19776099	19776221	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19776222	19776318	1	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19776222	19776318	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19776319	19776435	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19776436	19776615	1	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19776436	19776615	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19776616	19776765	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19776766	19776833	1	-	2	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19776766	19776833	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19776834	19776944	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19776945	19777002	1	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19776945	19777002	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19777003	19777082	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19777083	19777181	1	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19777083	19777181	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	intron	19777182	19777300	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	CDS	19777301	19777408	1	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	exon	19777301	19777408	.	-	.	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
Phchi.S3	AUGUSTUS	start_codon	19777406	19777408	.	-	0	transcript_id "Phchi.S3G285800.t1"; gene_id "Phchi.S3G285800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1594.t1 is derived from g8513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1933359	1933855	.	-	.	Phchi.S5G020300
Phchi.S5	AUGUSTUS	transcript	1933359	1933855	.	-	.	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	stop_codon	1933356	1933358	.	-	0	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	CDS	1933359	1933533	1	-	1	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	exon	1933359	1933533	.	-	.	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	intron	1933534	1933667	.	-	.	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	CDS	1933668	1933855	0.82	-	0	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	exon	1933668	1933855	.	-	.	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
Phchi.S5	AUGUSTUS	start_codon	1933853	1933855	.	-	0	transcript_id "Phchi.S5G020300.t1"; gene_id "Phchi.S5G020300"
# This transcript jg5680.t2 is derived from g2850.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5680.t3 is derived from g2850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5681.t1 is derived from g2851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18300797	18302420	.	-	.	Phchi.S1G284000
Phchi.S1	AUGUSTUS	transcript	18300797	18302420	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	stop_codon	18300794	18300796	.	-	0	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	CDS	18300797	18301606	1	-	0	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	exon	18300797	18301606	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	intron	18301607	18301697	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	CDS	18301698	18301860	0.92	-	1	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	exon	18301698	18301860	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	intron	18301861	18302000	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	CDS	18302001	18302070	0.88	-	2	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	exon	18302001	18302070	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	intron	18302071	18302200	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	CDS	18302201	18302420	0.88	-	0	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	exon	18302201	18302420	.	-	.	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
Phchi.S1	AUGUSTUS	start_codon	18302418	18302420	.	-	0	transcript_id "Phchi.S1G284000.t1"; gene_id "Phchi.S1G284000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg983.t1 is derived from g10766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6880198	6880895	.	-	.	Phchi.S6G094200
Phchi.S6	AUGUSTUS	transcript	6880198	6880895	.	-	.	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	stop_codon	6880195	6880197	.	-	0	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	CDS	6880198	6880329	0.91	-	0	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	exon	6880198	6880329	.	-	.	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	intron	6880330	6880415	.	-	.	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	CDS	6880416	6880895	0.75	-	0	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	exon	6880416	6880895	.	-	.	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
Phchi.S6	AUGUSTUS	start_codon	6880893	6880895	.	-	0	transcript_id "Phchi.S6G094200.t1"; gene_id "Phchi.S6G094200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7825.t1 is derived from g4999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31382453	31383913	.	-	.	Phchi.S1G498400
Phchi.S1	AUGUSTUS	transcript	31382453	31383913	.	-	.	transcript_id "Phchi.S1G498400.t1"; gene_id "Phchi.S1G498400"
Phchi.S1	AUGUSTUS	stop_codon	31382450	31382452	.	-	0	transcript_id "Phchi.S1G498400.t1"; gene_id "Phchi.S1G498400"
Phchi.S1	AUGUSTUS	CDS	31382453	31383913	0.81	-	0	transcript_id "Phchi.S1G498400.t1"; gene_id "Phchi.S1G498400"
Phchi.S1	AUGUSTUS	exon	31382453	31383913	.	-	.	transcript_id "Phchi.S1G498400.t1"; gene_id "Phchi.S1G498400"
Phchi.S1	AUGUSTUS	start_codon	31383911	31383913	.	-	0	transcript_id "Phchi.S1G498400.t1"; gene_id "Phchi.S1G498400"
# This transcript jg7921.t2 is derived from g5095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7922.t1 is derived from g5096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31918797	31921180	.	-	.	Phchi.S1G508100
Phchi.S1	AUGUSTUS	transcript	31918797	31921180	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	stop_codon	31918794	31918796	.	-	0	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31918797	31918894	1	-	2	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31918797	31918894	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31918895	31919018	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31919019	31919063	1	-	2	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31919019	31919063	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31919064	31919150	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31919151	31919202	1	-	0	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31919151	31919202	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31919203	31919291	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31919292	31919366	1	-	0	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31919292	31919366	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31919367	31919483	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31919484	31919520	1	-	1	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31919484	31919520	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31919521	31919676	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31919677	31919745	1	-	1	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31919677	31919745	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31919746	31920006	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31920007	31920109	1	-	2	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31920007	31920109	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31920110	31920214	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31920215	31920290	1	-	0	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31920215	31920290	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31920291	31920416	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31920417	31920588	1	-	1	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31920417	31920588	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	intron	31920589	31920683	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	CDS	31920684	31921180	0.99	-	0	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	exon	31920684	31921180	.	-	.	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
Phchi.S1	AUGUSTUS	start_codon	31921178	31921180	.	-	0	transcript_id "Phchi.S1G508100.t1"; gene_id "Phchi.S1G508100"
# This transcript jg10372.t2 is derived from g7548.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10373.t1 is derived from g7549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47427568	47430389	.	-	.	Phchi.S1G753200
Phchi.S1	AUGUSTUS	transcript	47427568	47430389	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	stop_codon	47427565	47427567	.	-	0	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	CDS	47427568	47427625	0.76	-	1	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	exon	47427568	47427625	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	intron	47427626	47427844	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	CDS	47427845	47427972	0.69	-	0	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	exon	47427845	47427972	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	intron	47427973	47428182	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	CDS	47428183	47430082	0.39	-	1	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	exon	47428183	47430082	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	intron	47430083	47430330	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	CDS	47430331	47430389	0.42	-	0	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	exon	47430331	47430389	.	-	.	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
Phchi.S1	AUGUSTUS	start_codon	47430387	47430389	.	-	0	transcript_id "Phchi.S1G753200.t1"; gene_id "Phchi.S1G753200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2041.t1 is derived from g8961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4564037	4565041	.	-	.	Phchi.S5G065000
Phchi.S5	AUGUSTUS	transcript	4564037	4565041	.	-	.	transcript_id "Phchi.S5G065000.t1"; gene_id "Phchi.S5G065000"
Phchi.S5	AUGUSTUS	stop_codon	4564034	4564036	.	-	0	transcript_id "Phchi.S5G065000.t1"; gene_id "Phchi.S5G065000"
Phchi.S5	AUGUSTUS	CDS	4564037	4565041	0.58	-	0	transcript_id "Phchi.S5G065000.t1"; gene_id "Phchi.S5G065000"
Phchi.S5	AUGUSTUS	exon	4564037	4565041	.	-	.	transcript_id "Phchi.S5G065000.t1"; gene_id "Phchi.S5G065000"
Phchi.S5	AUGUSTUS	start_codon	4565039	4565041	.	-	0	transcript_id "Phchi.S5G065000.t1"; gene_id "Phchi.S5G065000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6845.t1 is derived from g4017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25517591	25519513	.	+	.	Phchi.S1G400400
Phchi.S1	AUGUSTUS	transcript	25517591	25519513	.	+	.	transcript_id "Phchi.S1G400400.t1"; gene_id "Phchi.S1G400400"
Phchi.S1	AUGUSTUS	start_codon	25517591	25517593	.	+	0	transcript_id "Phchi.S1G400400.t1"; gene_id "Phchi.S1G400400"
Phchi.S1	AUGUSTUS	CDS	25517591	25519513	0.99	+	0	transcript_id "Phchi.S1G400400.t1"; gene_id "Phchi.S1G400400"
Phchi.S1	AUGUSTUS	exon	25517591	25519513	.	+	.	transcript_id "Phchi.S1G400400.t1"; gene_id "Phchi.S1G400400"
Phchi.S1	AUGUSTUS	stop_codon	25519514	25519516	.	+	0	transcript_id "Phchi.S1G400400.t1"; gene_id "Phchi.S1G400400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13561.t1 is derived from g12028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7496905	7498485	.	-	.	Phchi.S3G088000
Phchi.S3	AUGUSTUS	transcript	7496905	7498485	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	stop_codon	7496902	7496904	.	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	CDS	7496905	7497195	1	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	exon	7496905	7497195	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	intron	7497196	7497306	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	CDS	7497307	7497474	1	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	exon	7497307	7497474	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	intron	7497475	7497581	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	CDS	7497582	7497713	1	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	exon	7497582	7497713	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	intron	7497714	7497814	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	CDS	7497815	7497897	1	-	2	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	exon	7497815	7497897	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	intron	7497898	7497994	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	CDS	7497995	7498187	1	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	exon	7497995	7498187	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	intron	7498188	7498296	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	CDS	7498297	7498485	0.97	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	exon	7498297	7498485	.	-	.	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
Phchi.S3	AUGUSTUS	start_codon	7498483	7498485	.	-	0	transcript_id "Phchi.S3G088000.t1"; gene_id "Phchi.S3G088000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12558.t1 is derived from g8235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34749945	34755422	.	-	.	Phchi.S2G063800
Phchi.S2	AUGUSTUS	transcript	34749945	34755422	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	stop_codon	34749942	34749944	.	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34749945	34749968	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34749945	34749968	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34749969	34750528	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34750529	34750741	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34750529	34750741	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34750742	34750825	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34750826	34750889	1	-	1	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34750826	34750889	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34750890	34750973	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34750974	34751075	0.98	-	1	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34750974	34751075	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34751076	34751177	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34751178	34751320	0.87	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34751178	34751320	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34751321	34751435	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34751436	34751540	0.88	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34751436	34751540	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34751541	34751623	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34751624	34751773	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34751624	34751773	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34751774	34751995	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34751996	34752112	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34751996	34752112	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34752113	34752236	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34752237	34752314	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34752237	34752314	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34752315	34752609	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34752610	34752694	1	-	1	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34752610	34752694	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34752695	34752808	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34752809	34752930	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34752809	34752930	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34752931	34753084	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34753085	34753150	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34753085	34753150	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34753151	34753269	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34753270	34753376	1	-	2	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34753270	34753376	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34753377	34753626	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34753627	34753723	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34753627	34753723	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34753724	34753823	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34753824	34753901	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34753824	34753901	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34753902	34754062	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34754063	34754173	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34754063	34754173	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34754174	34754437	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34754438	34754519	1	-	1	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34754438	34754519	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34754520	34754670	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34754671	34754732	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34754671	34754732	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34754733	34754879	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34754880	34754945	1	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34754880	34754945	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	intron	34754946	34755275	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	CDS	34755276	34755422	0.65	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	exon	34755276	34755422	.	-	.	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
Phchi.S2	AUGUSTUS	start_codon	34755420	34755422	.	-	0	transcript_id "Phchi.S2G063800.t1"; gene_id "Phchi.S2G063800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9144.t1 is derived from g6319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40064856	40066381	.	+	.	Phchi.S1G630300
Phchi.S1	AUGUSTUS	transcript	40064856	40066381	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	start_codon	40064856	40064858	.	+	0	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40064856	40065007	1	+	0	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40064856	40065007	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	intron	40065008	40065095	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40065096	40065123	1	+	1	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40065096	40065123	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	intron	40065124	40065283	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40065284	40065328	1	+	0	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40065284	40065328	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	intron	40065329	40065428	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40065429	40065514	1	+	0	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40065429	40065514	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	intron	40065515	40065774	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40065775	40065912	0.99	+	1	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40065775	40065912	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	intron	40065913	40066020	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40066021	40066171	0.99	+	1	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40066021	40066171	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	intron	40066172	40066294	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	CDS	40066295	40066381	1	+	0	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	exon	40066295	40066381	.	+	.	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
Phchi.S1	AUGUSTUS	stop_codon	40066382	40066384	.	+	0	transcript_id "Phchi.S1G630300.t1"; gene_id "Phchi.S1G630300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2528.t1 is derived from g9448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7161323	7168139	.	-	.	Phchi.S5G113700
Phchi.S5	AUGUSTUS	transcript	7161323	7168139	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	stop_codon	7161320	7161322	.	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7161323	7161331	0.98	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7161323	7161331	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7161332	7161473	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7161474	7161522	0.98	-	1	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7161474	7161522	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7161523	7161626	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7161627	7165167	0.59	-	2	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7161627	7165167	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7165168	7165292	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7165293	7165614	0.73	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7165293	7165614	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7165615	7165732	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7165733	7165796	1	-	1	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7165733	7165796	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7165797	7165882	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7165883	7165941	1	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7165883	7165941	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7165942	7166020	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7166021	7166099	1	-	1	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7166021	7166099	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7166100	7166182	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7166183	7166236	1	-	1	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7166183	7166236	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7166237	7166387	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7166388	7166458	0.99	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7166388	7166458	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7166459	7166563	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7166564	7166653	1	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7166564	7166653	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7166654	7166743	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7166744	7166833	0.75	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7166744	7166833	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7166834	7166950	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7166951	7167064	1	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7166951	7167064	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7167065	7167146	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7167147	7167449	0.71	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7167147	7167449	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7167450	7167576	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7167577	7167732	0.96	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7167577	7167732	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	intron	7167733	7167812	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	CDS	7167813	7168139	0.99	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	exon	7167813	7168139	.	-	.	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
Phchi.S5	AUGUSTUS	start_codon	7168137	7168139	.	-	0	transcript_id "Phchi.S5G113700.t1"; gene_id "Phchi.S5G113700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1068.t1 is derived from g10851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7411346	7414217	.	-	.	Phchi.S6G102700
Phchi.S6	AUGUSTUS	transcript	7411346	7414217	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	stop_codon	7411343	7411345	.	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7411346	7411383	1	-	2	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7411346	7411383	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7411384	7411549	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7411550	7411704	1	-	1	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7411550	7411704	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7411705	7411791	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7411792	7411849	1	-	2	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7411792	7411849	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7411850	7412138	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7412139	7412253	1	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7412139	7412253	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7412254	7412384	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7412385	7412567	1	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7412385	7412567	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7412568	7412663	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7412664	7412747	1	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7412664	7412747	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7412748	7412835	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7412836	7413153	1	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7412836	7413153	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7413154	7413331	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7413332	7413425	0.68	-	1	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7413332	7413425	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7413426	7413512	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7413513	7413733	0.68	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7413513	7413733	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	intron	7413734	7413854	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	CDS	7413855	7414217	0.99	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	exon	7413855	7414217	.	-	.	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
Phchi.S6	AUGUSTUS	start_codon	7414215	7414217	.	-	0	transcript_id "Phchi.S6G102700.t1"; gene_id "Phchi.S6G102700"
# This transcript jg7273.t2 is derived from g4445.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7274.t1 is derived from g4446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28084346	28087202	.	+	.	Phchi.S1G443300
Phchi.S1	AUGUSTUS	transcript	28084346	28087202	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	start_codon	28084346	28084348	.	+	0	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	CDS	28084346	28084480	0.99	+	0	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	exon	28084346	28084480	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	intron	28084481	28084628	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	CDS	28084629	28085480	0.91	+	0	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	exon	28084629	28085480	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	intron	28085481	28085566	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	CDS	28085567	28086648	0.7	+	0	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	exon	28085567	28086648	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	intron	28086649	28086877	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	CDS	28086878	28086903	0.65	+	1	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	exon	28086878	28086903	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	intron	28086904	28087104	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	CDS	28087105	28087202	0.77	+	2	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	exon	28087105	28087202	.	+	.	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
Phchi.S1	AUGUSTUS	stop_codon	28087203	28087205	.	+	0	transcript_id "Phchi.S1G443300.t1"; gene_id "Phchi.S1G443300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4317.t1 is derived from g1486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9589325	9590590	.	-	.	Phchi.S1G147600
Phchi.S1	AUGUSTUS	transcript	9589325	9590590	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	stop_codon	9589322	9589324	.	-	0	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	CDS	9589325	9589792	0.72	-	0	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	exon	9589325	9589792	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	intron	9589793	9589918	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	CDS	9589919	9590115	0.31	-	2	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	exon	9589919	9590115	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	intron	9590116	9590203	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	CDS	9590204	9590275	0.64	-	2	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	exon	9590204	9590275	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	intron	9590276	9590346	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	CDS	9590347	9590590	0.63	-	0	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	exon	9590347	9590590	.	-	.	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
Phchi.S1	AUGUSTUS	start_codon	9590588	9590590	.	-	0	transcript_id "Phchi.S1G147600.t1"; gene_id "Phchi.S1G147600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6278.t1 is derived from g3450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22046612	22049214	.	+	.	Phchi.S1G343700
Phchi.S1	AUGUSTUS	transcript	22046612	22049214	.	+	.	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	start_codon	22046612	22046614	.	+	0	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22046612	22046961	0.56	+	0	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22046612	22046961	.	+	.	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	intron	22046962	22047485	.	+	.	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22047486	22048538	0.91	+	1	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22047486	22048538	.	+	.	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	intron	22048539	22049084	.	+	.	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22049085	22049214	0.91	+	1	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22049085	22049214	.	+	.	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	stop_codon	22049215	22049217	.	+	0	transcript_id "Phchi.S1G343700.t1"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	transcript	22046612	22049152	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	start_codon	22046612	22046614	.	+	0	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22046612	22046961	0.51	+	0	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22046612	22046961	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	intron	22046962	22047485	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22047486	22048585	0.77	+	1	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22047486	22048585	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	intron	22048586	22048740	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22048741	22048815	0.86	+	2	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22048741	22048815	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	intron	22048816	22049084	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	CDS	22049085	22049152	0.87	+	2	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	exon	22049085	22049152	.	+	.	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
Phchi.S1	AUGUSTUS	stop_codon	22049153	22049155	.	+	0	transcript_id "Phchi.S1G343700.t2"; gene_id "Phchi.S1G343700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9970.t1 is derived from g7146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44712253	44712764	.	-	.	Phchi.S1G712900
Phchi.S1	AUGUSTUS	transcript	44712253	44712764	.	-	.	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	stop_codon	44712250	44712252	.	-	0	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	CDS	44712253	44712384	1	-	0	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	exon	44712253	44712384	.	-	.	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	intron	44712385	44712455	.	-	.	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	CDS	44712456	44712568	1	-	2	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	exon	44712456	44712568	.	-	.	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	intron	44712569	44712649	.	-	.	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	CDS	44712650	44712764	0.93	-	0	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	exon	44712650	44712764	.	-	.	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
Phchi.S1	AUGUSTUS	start_codon	44712762	44712764	.	-	0	transcript_id "Phchi.S1G712900.t1"; gene_id "Phchi.S1G712900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1785.t1 is derived from g8705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2995825	2997019	.	+	.	Phchi.S5G039400
Phchi.S5	AUGUSTUS	transcript	2995825	2997019	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	start_codon	2995825	2995827	.	+	0	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	CDS	2995825	2995836	0.34	+	0	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	exon	2995825	2995836	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	intron	2995837	2995942	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	CDS	2995943	2996108	0.34	+	0	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	exon	2995943	2996108	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	intron	2996109	2996181	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	CDS	2996182	2996270	1	+	2	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	exon	2996182	2996270	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	intron	2996271	2996372	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	CDS	2996373	2996593	1	+	0	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	exon	2996373	2996593	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	intron	2996594	2996666	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	CDS	2996667	2996802	1	+	1	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	exon	2996667	2996802	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	intron	2996803	2996893	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	CDS	2996894	2997019	1	+	0	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	exon	2996894	2997019	.	+	.	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
Phchi.S5	AUGUSTUS	stop_codon	2997020	2997022	.	+	0	transcript_id "Phchi.S5G039400.t1"; gene_id "Phchi.S5G039400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14970.t1 is derived from g13438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15792621	15795119	.	-	.	Phchi.S3G228900
Phchi.S3	AUGUSTUS	transcript	15792621	15795119	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	stop_codon	15792618	15792620	.	-	0	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	CDS	15792621	15793670	0.94	-	0	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	exon	15792621	15793670	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	intron	15793671	15793829	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	CDS	15793830	15793992	0.94	-	1	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	exon	15793830	15793992	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	intron	15793993	15794202	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	CDS	15794203	15794604	0.27	-	1	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	exon	15794203	15794604	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	intron	15794605	15794814	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	CDS	15794815	15795119	0.66	-	0	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	exon	15794815	15795119	.	-	.	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
Phchi.S3	AUGUSTUS	start_codon	15795117	15795119	.	-	0	transcript_id "Phchi.S3G228900.t1"; gene_id "Phchi.S3G228900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2378.t1 is derived from g9298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6419513	6421572	.	-	.	Phchi.S5G098700
Phchi.S5	AUGUSTUS	transcript	6419513	6421572	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	stop_codon	6419510	6419512	.	-	0	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	CDS	6419513	6420172	0.94	-	0	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	exon	6419513	6420172	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	intron	6420173	6420247	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	CDS	6420248	6420347	1	-	1	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	exon	6420248	6420347	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	intron	6420348	6420433	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	CDS	6420434	6420984	1	-	0	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	exon	6420434	6420984	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	intron	6420985	6421064	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	CDS	6421065	6421282	1	-	2	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	exon	6421065	6421282	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	intron	6421283	6421382	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	CDS	6421383	6421572	1	-	0	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	exon	6421383	6421572	.	-	.	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
Phchi.S5	AUGUSTUS	start_codon	6421570	6421572	.	-	0	transcript_id "Phchi.S5G098700.t1"; gene_id "Phchi.S5G098700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8239.t1 is derived from g5414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34631349	34633118	.	-	.	Phchi.S1G539800
Phchi.S1	AUGUSTUS	transcript	34631349	34633118	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	stop_codon	34631346	34631348	.	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34631349	34631375	1	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34631349	34631375	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34631376	34631475	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34631476	34631582	1	-	2	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34631476	34631582	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34631583	34631674	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34631675	34631701	0.98	-	2	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34631675	34631701	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34631702	34631784	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34631785	34631827	0.98	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34631785	34631827	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34631828	34631917	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34631918	34631959	0.97	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34631918	34631959	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34631960	34632395	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34632396	34632401	1	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34632396	34632401	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34632402	34632578	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34632579	34632823	1	-	2	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34632579	34632823	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	intron	34632824	34633042	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	CDS	34633043	34633118	1	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	exon	34633043	34633118	.	-	.	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
Phchi.S1	AUGUSTUS	start_codon	34633116	34633118	.	-	0	transcript_id "Phchi.S1G539800.t1"; gene_id "Phchi.S1G539800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3929.t1 is derived from g1098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6475220	6476002	.	-	.	Phchi.S1G108800
Phchi.S1	AUGUSTUS	transcript	6475220	6476002	.	-	.	transcript_id "Phchi.S1G108800.t1"; gene_id "Phchi.S1G108800"
Phchi.S1	AUGUSTUS	stop_codon	6475217	6475219	.	-	0	transcript_id "Phchi.S1G108800.t1"; gene_id "Phchi.S1G108800"
Phchi.S1	AUGUSTUS	CDS	6475220	6476002	1	-	0	transcript_id "Phchi.S1G108800.t1"; gene_id "Phchi.S1G108800"
Phchi.S1	AUGUSTUS	exon	6475220	6476002	.	-	.	transcript_id "Phchi.S1G108800.t1"; gene_id "Phchi.S1G108800"
Phchi.S1	AUGUSTUS	start_codon	6476000	6476002	.	-	0	transcript_id "Phchi.S1G108800.t1"; gene_id "Phchi.S1G108800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg620.t1 is derived from g10402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4445324	4447202	.	-	.	Phchi.S6G057900
Phchi.S6	AUGUSTUS	transcript	4445324	4447202	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	stop_codon	4445321	4445323	.	-	0	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4445324	4445419	0.99	-	0	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4445324	4445419	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4445420	4445499	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4445500	4445746	1	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4445500	4445746	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4445747	4445858	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4445859	4445933	1	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4445859	4445933	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4445934	4446015	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4446016	4446111	1	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4446016	4446111	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4446112	4446201	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4446202	4446287	1	-	0	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4446202	4446287	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4446288	4446367	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4446368	4446440	1	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4446368	4446440	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4446441	4446527	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4446528	4446605	1	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4446528	4446605	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4446606	4446708	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4446709	4446816	0.95	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4446709	4446816	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4446817	4447014	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4447015	4447092	0.87	-	1	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4447015	4447092	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	intron	4447093	4447185	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	CDS	4447186	4447202	0.87	-	0	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	exon	4447186	4447202	.	-	.	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
Phchi.S6	AUGUSTUS	start_codon	4447200	4447202	.	-	0	transcript_id "Phchi.S6G057900.t1"; gene_id "Phchi.S6G057900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15054.t1 is derived from g13522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16764788	16766833	.	-	.	Phchi.S3G237300
Phchi.S3	AUGUSTUS	transcript	16764788	16766833	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	stop_codon	16764785	16764787	.	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16764788	16764986	1	-	1	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16764788	16764986	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16764987	16765079	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16765080	16765201	1	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16765080	16765201	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16765202	16765319	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16765320	16765376	1	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16765320	16765376	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16765377	16765466	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16765467	16765617	1	-	1	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16765467	16765617	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16765618	16765754	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16765755	16765807	1	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16765755	16765807	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16765808	16765956	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16765957	16766037	1	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16765957	16766037	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16766038	16766123	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16766124	16766223	1	-	1	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16766124	16766223	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16766224	16766326	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16766327	16766446	1	-	1	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16766327	16766446	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16766447	16766595	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16766596	16766657	1	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16766596	16766657	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	intron	16766658	16766827	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	CDS	16766828	16766833	0.97	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	exon	16766828	16766833	.	-	.	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
Phchi.S3	AUGUSTUS	start_codon	16766831	16766833	.	-	0	transcript_id "Phchi.S3G237300.t1"; gene_id "Phchi.S3G237300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2929.t1 is derived from g98.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	594641	596965	.	-	.	Phchi.S1G008800
Phchi.S1	AUGUSTUS	transcript	594641	596965	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	stop_codon	594638	594640	.	-	0	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	CDS	594641	594688	1	-	0	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	exon	594641	594688	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	intron	594689	594784	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	CDS	594785	594855	0.85	-	2	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	exon	594785	594855	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	intron	594856	594964	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	CDS	594965	595118	0.8	-	0	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	exon	594965	595118	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	intron	595119	596524	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	CDS	596525	596965	0.99	-	0	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	exon	596525	596965	.	-	.	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
Phchi.S1	AUGUSTUS	start_codon	596963	596965	.	-	0	transcript_id "Phchi.S1G008800.t1"; gene_id "Phchi.S1G008800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13354.t1 is derived from g11820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6293338	6298649	.	-	.	Phchi.S3G067300
Phchi.S3	AUGUSTUS	transcript	6293338	6298649	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	stop_codon	6293335	6293337	.	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6293338	6293623	0.93	-	1	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6293338	6293623	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6293624	6293715	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6293716	6293882	0.94	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6293716	6293882	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6293883	6293969	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6293970	6294077	1	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6293970	6294077	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6294078	6294157	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6294158	6294412	1	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6294158	6294412	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6294413	6294519	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6294520	6294930	0.94	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6294520	6294930	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6294931	6295015	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6295016	6295216	1	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6295016	6295216	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6295217	6295327	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6295328	6295393	1	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6295328	6295393	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6295394	6295483	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6295484	6296181	0.96	-	2	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6295484	6296181	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6296182	6296329	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6296330	6296413	0.89	-	2	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6296330	6296413	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6296414	6296526	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6296527	6296757	0.99	-	2	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6296527	6296757	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6296758	6296864	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6296865	6297106	0.96	-	1	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6296865	6297106	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6297107	6297216	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6297217	6297409	0.97	-	2	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6297217	6297409	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6297410	6297491	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6297492	6297985	0.96	-	1	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6297492	6297985	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6297986	6298171	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6298172	6298323	1	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6298172	6298323	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	intron	6298324	6298400	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	CDS	6298401	6298649	0.94	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	exon	6298401	6298649	.	-	.	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
Phchi.S3	AUGUSTUS	start_codon	6298647	6298649	.	-	0	transcript_id "Phchi.S3G067300.t1"; gene_id "Phchi.S3G067300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13687.t1 is derived from g12154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8202700	8206816	.	+	.	Phchi.S3G100600
Phchi.S3	AUGUSTUS	transcript	8202700	8206816	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	start_codon	8202700	8202702	.	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8202700	8202765	0.92	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8202700	8202765	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8202766	8202994	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8202995	8203012	0.64	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8202995	8203012	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8203013	8203266	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8203267	8203327	1	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8203267	8203327	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8203328	8203407	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8203408	8203495	0.91	+	2	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8203408	8203495	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8203496	8203583	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8203584	8203668	0.69	+	1	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8203584	8203668	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8203669	8203870	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8203871	8203961	0.34	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8203871	8203961	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8203962	8204049	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8204050	8204114	0.26	+	2	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8204050	8204114	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8204115	8204228	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8204229	8205527	0.28	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8204229	8205527	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8205528	8205760	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8205761	8205910	0.55	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8205761	8205910	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8205911	8206047	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8206048	8206206	0.97	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8206048	8206206	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	intron	8206207	8206318	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	CDS	8206319	8206816	1	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	exon	8206319	8206816	.	+	.	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
Phchi.S3	AUGUSTUS	stop_codon	8206817	8206819	.	+	0	transcript_id "Phchi.S3G100600.t1"; gene_id "Phchi.S3G100600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg826.t1 is derived from g10608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5740945	5745998	.	-	.	Phchi.S6G078500
Phchi.S6	AUGUSTUS	transcript	5740945	5745998	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	stop_codon	5740942	5740944	.	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5740945	5741526	1	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5740945	5741526	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5741527	5741611	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5741612	5741771	1	-	1	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5741612	5741771	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5741772	5741911	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5741912	5743968	0.98	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5741912	5743968	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5743969	5744125	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5744126	5744257	1	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5744126	5744257	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5744258	5744356	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5744357	5744440	1	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5744357	5744440	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5744441	5744526	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5744527	5744797	0.99	-	1	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5744527	5744797	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5744798	5744907	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5744908	5745161	0.99	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5744908	5745161	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5745162	5745352	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5745353	5745562	1	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5745353	5745562	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	intron	5745563	5745734	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	CDS	5745735	5745998	0.49	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	exon	5745735	5745998	.	-	.	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
Phchi.S6	AUGUSTUS	start_codon	5745996	5745998	.	-	0	transcript_id "Phchi.S6G078500.t1"; gene_id "Phchi.S6G078500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3104.t1 is derived from g273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1761996	1762535	.	-	.	Phchi.S1G026300
Phchi.S1	AUGUSTUS	transcript	1761996	1762535	.	-	.	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	stop_codon	1761993	1761995	.	-	0	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	CDS	1761996	1762017	0.35	-	1	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	exon	1761996	1762017	.	-	.	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	intron	1762018	1762212	.	-	.	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	CDS	1762213	1762535	0.29	-	0	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	exon	1762213	1762535	.	-	.	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
Phchi.S1	AUGUSTUS	start_codon	1762533	1762535	.	-	0	transcript_id "Phchi.S1G026300.t1"; gene_id "Phchi.S1G026300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7037.t1 is derived from g4209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26525061	26527334	.	+	.	Phchi.S1G419600
Phchi.S1	AUGUSTUS	transcript	26525061	26527334	.	+	.	transcript_id "Phchi.S1G419600.t1"; gene_id "Phchi.S1G419600"
Phchi.S1	AUGUSTUS	start_codon	26525061	26525063	.	+	0	transcript_id "Phchi.S1G419600.t1"; gene_id "Phchi.S1G419600"
Phchi.S1	AUGUSTUS	CDS	26525061	26527334	0.79	+	0	transcript_id "Phchi.S1G419600.t1"; gene_id "Phchi.S1G419600"
Phchi.S1	AUGUSTUS	exon	26525061	26527334	.	+	.	transcript_id "Phchi.S1G419600.t1"; gene_id "Phchi.S1G419600"
Phchi.S1	AUGUSTUS	stop_codon	26527335	26527337	.	+	0	transcript_id "Phchi.S1G419600.t1"; gene_id "Phchi.S1G419600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6129.t1 is derived from g3300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21065571	21068425	.	-	.	Phchi.S1G328800
Phchi.S1	AUGUSTUS	transcript	21065571	21068425	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	stop_codon	21065568	21065570	.	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21065571	21065966	1	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21065571	21065966	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21065967	21066057	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21066058	21066456	1	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21066058	21066456	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21066457	21066540	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21066541	21066730	1	-	1	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21066541	21066730	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21066731	21066837	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21066838	21066936	1	-	1	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21066838	21066936	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21066937	21067030	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21067031	21067173	1	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21067031	21067173	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21067174	21067268	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21067269	21067348	1	-	2	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21067269	21067348	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21067349	21067446	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21067447	21067699	1	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21067447	21067699	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	intron	21067700	21067840	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	CDS	21067841	21068425	0.92	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	exon	21067841	21068425	.	-	.	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
Phchi.S1	AUGUSTUS	start_codon	21068423	21068425	.	-	0	transcript_id "Phchi.S1G328800.t1"; gene_id "Phchi.S1G328800"
# This transcript jg440.t2 is derived from g10222.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg441.t1 is derived from g10223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3093549	3093986	.	+	.	Phchi.S6G040000
Phchi.S6	AUGUSTUS	transcript	3093549	3093986	.	+	.	transcript_id "Phchi.S6G040000.t1"; gene_id "Phchi.S6G040000"
Phchi.S6	AUGUSTUS	start_codon	3093549	3093551	.	+	0	transcript_id "Phchi.S6G040000.t1"; gene_id "Phchi.S6G040000"
Phchi.S6	AUGUSTUS	CDS	3093549	3093986	0.85	+	0	transcript_id "Phchi.S6G040000.t1"; gene_id "Phchi.S6G040000"
Phchi.S6	AUGUSTUS	exon	3093549	3093986	.	+	.	transcript_id "Phchi.S6G040000.t1"; gene_id "Phchi.S6G040000"
Phchi.S6	AUGUSTUS	stop_codon	3093987	3093989	.	+	0	transcript_id "Phchi.S6G040000.t1"; gene_id "Phchi.S6G040000"
# This transcript jg11658.t2 is derived from g15709.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11659.t1 is derived from g15710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7553606	7556314	.	-	.	Phchi.S4G124100
Phchi.S4	AUGUSTUS	transcript	7553606	7556314	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	stop_codon	7553603	7553605	.	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7553606	7553683	0.99	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7553606	7553683	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	intron	7553684	7553769	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7553770	7553874	1	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7553770	7553874	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	intron	7553875	7554087	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7554088	7554174	1	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7554088	7554174	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	intron	7554175	7554281	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7554282	7554383	0.78	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7554282	7554383	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	intron	7554384	7554535	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7554536	7554648	1	-	2	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7554536	7554648	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	intron	7554649	7554737	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7554738	7556100	0.66	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7554738	7556100	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	intron	7556101	7556206	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	CDS	7556207	7556314	0.64	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	exon	7556207	7556314	.	-	.	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
Phchi.S4	AUGUSTUS	start_codon	7556312	7556314	.	-	0	transcript_id "Phchi.S4G124100.t1"; gene_id "Phchi.S4G124100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4049.t1 is derived from g1218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7535796	7536607	.	-	.	Phchi.S1G120800
Phchi.S1	AUGUSTUS	transcript	7535796	7536607	.	-	.	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	stop_codon	7535793	7535795	.	-	0	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	CDS	7535796	7536018	0.59	-	1	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	exon	7535796	7536018	.	-	.	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	intron	7536019	7536212	.	-	.	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	CDS	7536213	7536607	0.27	-	0	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	exon	7536213	7536607	.	-	.	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
Phchi.S1	AUGUSTUS	start_codon	7536605	7536607	.	-	0	transcript_id "Phchi.S1G120800.t1"; gene_id "Phchi.S1G120800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5954.t1 is derived from g3125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20058491	20062103	.	+	.	Phchi.S1G311300
Phchi.S1	AUGUSTUS	transcript	20058491	20062103	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	start_codon	20058491	20058493	.	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20058491	20058577	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20058491	20058577	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20058578	20059062	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20059063	20059258	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20059063	20059258	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20059259	20059410	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20059411	20059515	1	+	2	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20059411	20059515	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20059516	20059735	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20059736	20059753	1	+	2	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20059736	20059753	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20059754	20059835	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20059836	20059921	0.99	+	2	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20059836	20059921	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20059922	20060029	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20060030	20060182	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20060030	20060182	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20060183	20060371	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20060372	20060506	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20060372	20060506	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20060507	20060591	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20060592	20060758	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20060592	20060758	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20060759	20060854	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20060855	20060949	0.96	+	1	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20060855	20060949	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20060950	20061059	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20061060	20061190	1	+	2	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20061060	20061190	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20061191	20061326	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20061327	20061569	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20061327	20061569	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20061570	20061673	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20061674	20061947	1	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20061674	20061947	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	intron	20061948	20062038	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	CDS	20062039	20062103	0.68	+	2	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	exon	20062039	20062103	.	+	.	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
Phchi.S1	AUGUSTUS	stop_codon	20062104	20062106	.	+	0	transcript_id "Phchi.S1G311300.t1"; gene_id "Phchi.S1G311300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5422.t1 is derived from g2592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16801217	16804332	.	+	.	Phchi.S1G258100
Phchi.S1	AUGUSTUS	transcript	16801217	16804332	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	start_codon	16801217	16801219	.	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801217	16801331	0.99	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801217	16801331	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16801332	16801426	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801427	16801526	1	+	2	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801427	16801526	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16801527	16801627	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801628	16801711	0.64	+	1	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801628	16801711	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16801712	16801879	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801880	16802075	1	+	1	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801880	16802075	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802076	16802159	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802160	16802245	1	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802160	16802245	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802246	16802325	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802326	16802521	1	+	1	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802326	16802521	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802522	16802656	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802657	16802768	0.99	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802657	16802768	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802769	16802878	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802879	16802994	0.99	+	2	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802879	16802994	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802995	16803097	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803098	16803316	0.99	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803098	16803316	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16803317	16803405	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803406	16803515	1	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803406	16803515	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16803516	16803636	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803637	16803757	1	+	1	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803637	16803757	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16803758	16803854	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803855	16804010	1	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803855	16804010	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16804011	16804098	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16804099	16804332	0.99	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16804099	16804332	.	+	.	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	stop_codon	16804333	16804335	.	+	0	transcript_id "Phchi.S1G258100.t1"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	transcript	16801217	16804332	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	start_codon	16801217	16801219	.	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801217	16801331	1	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801217	16801331	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16801332	16801426	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801427	16801526	0.99	+	2	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801427	16801526	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16801527	16801627	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801628	16801711	0.6	+	1	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801628	16801711	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16801712	16801879	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16801880	16802075	1	+	1	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16801880	16802075	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802076	16802159	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802160	16802245	1	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802160	16802245	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802246	16802325	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802326	16802521	1	+	1	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802326	16802521	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802522	16802656	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802657	16802768	1	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802657	16802768	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802769	16802878	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16802879	16802994	1	+	2	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16802879	16802994	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16802995	16803097	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803098	16803316	1	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803098	16803316	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16803317	16803405	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803406	16803515	1	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803406	16803515	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16803516	16803636	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803637	16803757	1	+	1	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803637	16803757	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16803758	16803851	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16803852	16804010	1	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16803852	16804010	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	intron	16804011	16804098	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	CDS	16804099	16804332	0.99	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	exon	16804099	16804332	.	+	.	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
Phchi.S1	AUGUSTUS	stop_codon	16804333	16804335	.	+	0	transcript_id "Phchi.S1G258100.t2"; gene_id "Phchi.S1G258100"
# This transcript jg13710.t2 is derived from g12177.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13711.t1 is derived from g12178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8314438	8315179	.	+	.	Phchi.S3G103000
Phchi.S3	AUGUSTUS	transcript	8314438	8315179	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	start_codon	8314438	8314440	.	+	0	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	CDS	8314438	8314440	0.9	+	0	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	exon	8314438	8314440	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	intron	8314441	8314544	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	CDS	8314545	8314672	0.91	+	0	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	exon	8314545	8314672	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	intron	8314673	8314762	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	CDS	8314763	8314943	0.88	+	1	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	exon	8314763	8314943	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	intron	8314944	8315137	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	CDS	8315138	8315179	0.89	+	0	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	exon	8315138	8315179	.	+	.	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
Phchi.S3	AUGUSTUS	stop_codon	8315180	8315182	.	+	0	transcript_id "Phchi.S3G103000.t1"; gene_id "Phchi.S3G103000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2459.t1 is derived from g9379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6765312	6767540	.	-	.	Phchi.S5G106800
Phchi.S5	AUGUSTUS	transcript	6765312	6767540	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	stop_codon	6765309	6765311	.	-	0	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	CDS	6765312	6765854	0.91	-	0	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	exon	6765312	6765854	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	intron	6765855	6766036	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	CDS	6766037	6766166	0.94	-	1	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	exon	6766037	6766166	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	intron	6766167	6766309	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	CDS	6766310	6766635	0.99	-	0	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	exon	6766310	6766635	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	intron	6766636	6766748	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	CDS	6766749	6766970	0.98	-	0	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	exon	6766749	6766970	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	intron	6766971	6767120	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	CDS	6767121	6767253	0.82	-	1	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	exon	6767121	6767253	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	intron	6767254	6767370	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	CDS	6767371	6767540	0.88	-	0	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	exon	6767371	6767540	.	-	.	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
Phchi.S5	AUGUSTUS	start_codon	6767538	6767540	.	-	0	transcript_id "Phchi.S5G106800.t1"; gene_id "Phchi.S5G106800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6141.t1 is derived from g3312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21135289	21136997	.	-	.	Phchi.S1G330000
Phchi.S1	AUGUSTUS	transcript	21135289	21136997	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	stop_codon	21135286	21135288	.	-	0	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21135289	21135566	0.92	-	2	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21135289	21135566	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21135567	21135660	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21135661	21135763	0.96	-	0	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21135661	21135763	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21135764	21135871	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21135872	21135964	0.92	-	0	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21135872	21135964	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21135965	21136056	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21136057	21136169	1	-	2	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21136057	21136169	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21136170	21136285	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21136286	21136344	1	-	1	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21136286	21136344	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21136345	21136456	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21136457	21136585	1	-	1	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21136457	21136585	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21136586	21136677	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21136678	21136814	1	-	0	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21136678	21136814	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	intron	21136815	21136892	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	CDS	21136893	21136997	0.94	-	0	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	exon	21136893	21136997	.	-	.	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
Phchi.S1	AUGUSTUS	start_codon	21136995	21136997	.	-	0	transcript_id "Phchi.S1G330000.t1"; gene_id "Phchi.S1G330000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4715.t1 is derived from g1885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12436755	12437582	.	-	.	Phchi.S1G187400
Phchi.S1	AUGUSTUS	transcript	12436755	12437582	.	-	.	transcript_id "Phchi.S1G187400.t1"; gene_id "Phchi.S1G187400"
Phchi.S1	AUGUSTUS	stop_codon	12436752	12436754	.	-	0	transcript_id "Phchi.S1G187400.t1"; gene_id "Phchi.S1G187400"
Phchi.S1	AUGUSTUS	CDS	12436755	12437582	0.68	-	0	transcript_id "Phchi.S1G187400.t1"; gene_id "Phchi.S1G187400"
Phchi.S1	AUGUSTUS	exon	12436755	12437582	.	-	.	transcript_id "Phchi.S1G187400.t1"; gene_id "Phchi.S1G187400"
Phchi.S1	AUGUSTUS	start_codon	12437580	12437582	.	-	0	transcript_id "Phchi.S1G187400.t1"; gene_id "Phchi.S1G187400"
# This transcript jg5459.t2 is derived from g2629.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5460.t1 is derived from g2630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16952702	16953940	.	-	.	Phchi.S1G261900
Phchi.S1	AUGUSTUS	transcript	16952702	16953940	.	-	.	transcript_id "Phchi.S1G261900.t1"; gene_id "Phchi.S1G261900"
Phchi.S1	AUGUSTUS	stop_codon	16952699	16952701	.	-	0	transcript_id "Phchi.S1G261900.t1"; gene_id "Phchi.S1G261900"
Phchi.S1	AUGUSTUS	CDS	16952702	16953940	0.93	-	0	transcript_id "Phchi.S1G261900.t1"; gene_id "Phchi.S1G261900"
Phchi.S1	AUGUSTUS	exon	16952702	16953940	.	-	.	transcript_id "Phchi.S1G261900.t1"; gene_id "Phchi.S1G261900"
Phchi.S1	AUGUSTUS	start_codon	16953938	16953940	.	-	0	transcript_id "Phchi.S1G261900.t1"; gene_id "Phchi.S1G261900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11098.t1 is derived from g15148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4103057	4105429	.	+	.	Phchi.S4G068000
Phchi.S4	AUGUSTUS	transcript	4103057	4105429	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	start_codon	4103057	4103059	.	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4103057	4103100	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4103057	4103100	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4103101	4103249	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4103250	4103328	1	+	1	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4103250	4103328	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4103329	4103422	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4103423	4103502	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4103423	4103502	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4103503	4103596	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4103597	4103713	1	+	1	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4103597	4103713	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4103714	4103805	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4103806	4103875	1	+	1	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4103806	4103875	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4103876	4103971	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4103972	4104045	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4103972	4104045	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4104046	4104149	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4104150	4104270	1	+	1	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4104150	4104270	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4104271	4104388	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4104389	4104451	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4104389	4104451	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4104452	4104687	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4104688	4104747	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4104688	4104747	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4104748	4104826	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4104827	4104952	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4104827	4104952	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4104953	4105151	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4105152	4105241	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4105152	4105241	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	intron	4105242	4105318	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	CDS	4105319	4105429	1	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	exon	4105319	4105429	.	+	.	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
Phchi.S4	AUGUSTUS	stop_codon	4105430	4105432	.	+	0	transcript_id "Phchi.S4G068000.t1"; gene_id "Phchi.S4G068000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1487.t1 is derived from g8406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1151625	1152196	.	-	.	Phchi.S5G009600
Phchi.S5	AUGUSTUS	transcript	1151625	1152196	.	-	.	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	stop_codon	1151622	1151624	.	-	0	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	CDS	1151625	1151950	0.53	-	2	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	exon	1151625	1151950	.	-	.	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	intron	1151951	1152111	.	-	.	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	CDS	1152112	1152196	0.37	-	0	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	exon	1152112	1152196	.	-	.	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
Phchi.S5	AUGUSTUS	start_codon	1152194	1152196	.	-	0	transcript_id "Phchi.S5G009600.t1"; gene_id "Phchi.S5G009600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1693.t1 is derived from g8612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2528704	2531239	.	-	.	Phchi.S5G030200
Phchi.S5	AUGUSTUS	transcript	2528704	2531239	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	stop_codon	2528701	2528703	.	-	0	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2528704	2529087	0.93	-	0	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2528704	2529087	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	intron	2529088	2529183	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2529184	2529453	0.59	-	0	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2529184	2529453	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	intron	2529454	2529547	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2529548	2530438	0.8	-	0	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2529548	2530438	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	intron	2530439	2530807	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2530808	2531239	0.78	-	0	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2530808	2531239	.	-	.	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	start_codon	2531237	2531239	.	-	0	transcript_id "Phchi.S5G030200.t1"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	transcript	2528704	2530279	.	-	.	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	stop_codon	2528701	2528703	.	-	0	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2528704	2529087	0.94	-	0	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2528704	2529087	.	-	.	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	intron	2529088	2529183	.	-	.	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2529184	2529453	0.59	-	0	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2529184	2529453	.	-	.	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	intron	2529454	2529547	.	-	.	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	CDS	2529548	2530279	0.49	-	0	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	exon	2529548	2530279	.	-	.	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
Phchi.S5	AUGUSTUS	start_codon	2530277	2530279	.	-	0	transcript_id "Phchi.S5G030200.t2"; gene_id "Phchi.S5G030200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11930.t1 is derived from g7605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	75307	75972	.	+	.	Phchi.S2G001000
Phchi.S2	AUGUSTUS	transcript	75307	75972	.	+	.	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	start_codon	75307	75309	.	+	0	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	CDS	75307	75500	0.54	+	0	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	exon	75307	75500	.	+	.	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	intron	75501	75572	.	+	.	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	CDS	75573	75660	1	+	1	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	exon	75573	75660	.	+	.	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	intron	75661	75915	.	+	.	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	CDS	75916	75972	0.98	+	0	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	exon	75916	75972	.	+	.	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
Phchi.S2	AUGUSTUS	stop_codon	75973	75975	.	+	0	transcript_id "Phchi.S2G001000.t1"; gene_id "Phchi.S2G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9786.t1 is derived from g6962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43684091	43685171	.	-	.	Phchi.S1G694500
Phchi.S1	AUGUSTUS	transcript	43684091	43685171	.	-	.	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	stop_codon	43684088	43684090	.	-	0	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	CDS	43684091	43684627	1	-	0	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	exon	43684091	43684627	.	-	.	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	intron	43684628	43684721	.	-	.	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	CDS	43684722	43684957	0.74	-	2	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	exon	43684722	43684957	.	-	.	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	intron	43684958	43685035	.	-	.	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	CDS	43685036	43685171	0.74	-	0	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	exon	43685036	43685171	.	-	.	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
Phchi.S1	AUGUSTUS	start_codon	43685169	43685171	.	-	0	transcript_id "Phchi.S1G694500.t1"; gene_id "Phchi.S1G694500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7384.t1 is derived from g4556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28870778	28872049	.	-	.	Phchi.S1G454300
Phchi.S1	AUGUSTUS	transcript	28870778	28872049	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	stop_codon	28870775	28870777	.	-	0	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28870778	28870933	0.96	-	0	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28870778	28870933	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28870934	28871073	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871074	28871229	1	-	0	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871074	28871229	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28871230	28871314	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871315	28871425	1	-	0	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871315	28871425	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28871426	28871557	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871558	28871616	1	-	2	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871558	28871616	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28871617	28871709	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871710	28871885	1	-	1	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871710	28871885	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28871886	28871993	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871994	28872049	0.99	-	0	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871994	28872049	.	-	.	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	start_codon	28872047	28872049	.	-	0	transcript_id "Phchi.S1G454300.t1"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	transcript	28871630	28872049	.	-	.	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	stop_codon	28871627	28871629	.	-	0	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871630	28871631	0.67	-	2	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871630	28871631	.	-	.	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28871632	28871709	.	-	.	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871710	28871885	0.99	-	1	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871710	28871885	.	-	.	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	intron	28871886	28871993	.	-	.	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	CDS	28871994	28872049	0.99	-	0	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	exon	28871994	28872049	.	-	.	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
Phchi.S1	AUGUSTUS	start_codon	28872047	28872049	.	-	0	transcript_id "Phchi.S1G454300.t2"; gene_id "Phchi.S1G454300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11409.t1 is derived from g15459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6223379	6226099	.	+	.	Phchi.S4G099100
Phchi.S4	AUGUSTUS	transcript	6223379	6226099	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	start_codon	6223379	6223381	.	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6223379	6223384	0.68	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6223379	6223384	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6223385	6223485	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6223486	6223542	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6223486	6223542	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6223543	6223633	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6223634	6223714	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6223634	6223714	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6223715	6223802	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6223803	6223860	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6223803	6223860	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6223861	6223966	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6223967	6224073	1	+	2	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6223967	6224073	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6224074	6224165	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6224166	6224217	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6224166	6224217	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6224218	6224318	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6224319	6224368	1	+	2	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6224319	6224368	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6224369	6224531	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6224532	6224597	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6224532	6224597	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6224598	6224694	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6224695	6224859	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6224695	6224859	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6224860	6225137	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6225138	6225210	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6225138	6225210	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6225211	6225323	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6225324	6225456	0.97	+	2	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6225324	6225456	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6225457	6225561	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6225562	6225619	1	+	1	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6225562	6225619	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6225620	6225737	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6225738	6225785	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6225738	6225785	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6225786	6225870	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6225871	6225954	1	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6225871	6225954	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	intron	6225955	6226027	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	CDS	6226028	6226099	0.9	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	exon	6226028	6226099	.	+	.	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
Phchi.S4	AUGUSTUS	stop_codon	6226100	6226102	.	+	0	transcript_id "Phchi.S4G099100.t1"; gene_id "Phchi.S4G099100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11327.t1 is derived from g15377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5440721	5441656	.	-	.	Phchi.S4G090900
Phchi.S4	AUGUSTUS	transcript	5440721	5441656	.	-	.	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	stop_codon	5440718	5440720	.	-	0	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	CDS	5440721	5441290	0.62	-	0	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	exon	5440721	5441290	.	-	.	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	intron	5441291	5441403	.	-	.	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	CDS	5441404	5441447	0.76	-	2	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	exon	5441404	5441447	.	-	.	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	intron	5441448	5441538	.	-	.	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	CDS	5441539	5441656	0.98	-	0	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	exon	5441539	5441656	.	-	.	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
Phchi.S4	AUGUSTUS	start_codon	5441654	5441656	.	-	0	transcript_id "Phchi.S4G090900.t1"; gene_id "Phchi.S4G090900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5578.t1 is derived from g2748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17688113	17689585	.	-	.	Phchi.S1G273700
Phchi.S1	AUGUSTUS	transcript	17688113	17689585	.	-	.	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	stop_codon	17688110	17688112	.	-	0	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	CDS	17688113	17688255	0.83	-	2	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	exon	17688113	17688255	.	-	.	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	intron	17688256	17688340	.	-	.	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	CDS	17688341	17688373	0.83	-	2	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	exon	17688341	17688373	.	-	.	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	intron	17688374	17688462	.	-	.	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	CDS	17688463	17689585	0.83	-	0	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	exon	17688463	17689585	.	-	.	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
Phchi.S1	AUGUSTUS	start_codon	17689583	17689585	.	-	0	transcript_id "Phchi.S1G273700.t1"; gene_id "Phchi.S1G273700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15392.t1 is derived from g13860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18812992	18813758	.	-	.	Phchi.S3G271100
Phchi.S3	AUGUSTUS	transcript	18812992	18813758	.	-	.	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	stop_codon	18812989	18812991	.	-	0	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	CDS	18812992	18813265	1	-	1	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	exon	18812992	18813265	.	-	.	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	intron	18813266	18813477	.	-	.	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	CDS	18813478	18813758	1	-	0	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	exon	18813478	18813758	.	-	.	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
Phchi.S3	AUGUSTUS	start_codon	18813756	18813758	.	-	0	transcript_id "Phchi.S3G271100.t1"; gene_id "Phchi.S3G271100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11432.t1 is derived from g15482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6357740	6358542	.	-	.	Phchi.S4G101400
Phchi.S4	AUGUSTUS	transcript	6357740	6358542	.	-	.	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	stop_codon	6357737	6357739	.	-	0	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	CDS	6357740	6358268	0.43	-	1	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	exon	6357740	6358268	.	-	.	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	intron	6358269	6358525	.	-	.	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	CDS	6358526	6358542	0.45	-	0	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	exon	6358526	6358542	.	-	.	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
Phchi.S4	AUGUSTUS	start_codon	6358540	6358542	.	-	0	transcript_id "Phchi.S4G101400.t1"; gene_id "Phchi.S4G101400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10355.t1 is derived from g7531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47327393	47327776	.	-	.	Phchi.S1G751400
Phchi.S1	AUGUSTUS	transcript	47327393	47327776	.	-	.	transcript_id "Phchi.S1G751400.t1"; gene_id "Phchi.S1G751400"
Phchi.S1	AUGUSTUS	stop_codon	47327390	47327392	.	-	0	transcript_id "Phchi.S1G751400.t1"; gene_id "Phchi.S1G751400"
Phchi.S1	AUGUSTUS	CDS	47327393	47327776	0.57	-	0	transcript_id "Phchi.S1G751400.t1"; gene_id "Phchi.S1G751400"
Phchi.S1	AUGUSTUS	exon	47327393	47327776	.	-	.	transcript_id "Phchi.S1G751400.t1"; gene_id "Phchi.S1G751400"
Phchi.S1	AUGUSTUS	start_codon	47327774	47327776	.	-	0	transcript_id "Phchi.S1G751400.t1"; gene_id "Phchi.S1G751400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11322.t1 is derived from g15372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5366741	5367339	.	+	.	Phchi.S4G090400
Phchi.S4	AUGUSTUS	transcript	5366741	5367339	.	+	.	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	start_codon	5366741	5366743	.	+	0	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	CDS	5366741	5366954	0.61	+	0	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	exon	5366741	5366954	.	+	.	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	intron	5366955	5367094	.	+	.	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	CDS	5367095	5367339	1	+	2	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	exon	5367095	5367339	.	+	.	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
Phchi.S4	AUGUSTUS	stop_codon	5367340	5367342	.	+	0	transcript_id "Phchi.S4G090400.t1"; gene_id "Phchi.S4G090400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7880.t1 is derived from g5054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31738736	31740312	.	-	.	Phchi.S1G503900
Phchi.S1	AUGUSTUS	transcript	31738736	31740312	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	stop_codon	31738733	31738735	.	-	0	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31738736	31738739	1	-	1	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31738736	31738739	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	intron	31738740	31738838	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31738839	31738896	1	-	2	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31738839	31738896	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	intron	31738897	31739000	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31739001	31739189	1	-	2	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31739001	31739189	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	intron	31739190	31739392	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31739393	31739492	0.99	-	0	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31739393	31739492	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	intron	31739493	31739601	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31739602	31739723	0.95	-	2	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31739602	31739723	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	intron	31739724	31739870	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31739871	31739958	1	-	0	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31739871	31739958	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	intron	31739959	31740087	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	CDS	31740088	31740312	1	-	0	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	exon	31740088	31740312	.	-	.	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
Phchi.S1	AUGUSTUS	start_codon	31740310	31740312	.	-	0	transcript_id "Phchi.S1G503900.t1"; gene_id "Phchi.S1G503900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8067.t1 is derived from g5242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32770696	32772408	.	+	.	Phchi.S1G522600
Phchi.S1	AUGUSTUS	transcript	32770696	32772408	.	+	.	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	start_codon	32770696	32770698	.	+	0	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	CDS	32770696	32770782	0.83	+	0	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	exon	32770696	32770782	.	+	.	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	intron	32770783	32770995	.	+	.	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	CDS	32770996	32772408	1	+	0	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	exon	32770996	32772408	.	+	.	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
Phchi.S1	AUGUSTUS	stop_codon	32772409	32772411	.	+	0	transcript_id "Phchi.S1G522600.t1"; gene_id "Phchi.S1G522600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14226.t1 is derived from g12693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11644903	11646827	.	-	.	Phchi.S3G154500
Phchi.S3	AUGUSTUS	transcript	11644903	11646827	.	-	.	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	stop_codon	11644900	11644902	.	-	0	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	CDS	11644903	11645643	0.83	-	0	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	exon	11644903	11645643	.	-	.	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	intron	11645644	11645786	.	-	.	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	CDS	11645787	11646827	0.82	-	0	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	exon	11645787	11646827	.	-	.	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
Phchi.S3	AUGUSTUS	start_codon	11646825	11646827	.	-	0	transcript_id "Phchi.S3G154500.t1"; gene_id "Phchi.S3G154500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg142.t1 is derived from g9924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	781635	786215	.	-	.	Phchi.S6G010100
Phchi.S6	AUGUSTUS	transcript	781635	786215	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	stop_codon	781632	781634	.	-	0	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	CDS	781635	783308	0.49	-	0	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	exon	781635	783308	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	intron	783309	783394	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	CDS	783395	784591	0.66	-	0	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	exon	783395	784591	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	intron	784592	784806	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	CDS	784807	785046	0.21	-	0	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	exon	784807	785046	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	intron	785047	785132	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	CDS	785133	785841	0.42	-	1	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	exon	785133	785841	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	intron	785842	785940	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	CDS	785941	786215	0.8	-	0	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	exon	785941	786215	.	-	.	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
Phchi.S6	AUGUSTUS	start_codon	786213	786215	.	-	0	transcript_id "Phchi.S6G010100.t1"; gene_id "Phchi.S6G010100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14469.t1 is derived from g12937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13023006	13024556	.	-	.	Phchi.S3G178800
Phchi.S3	AUGUSTUS	transcript	13023006	13024556	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	stop_codon	13023003	13023005	.	-	0	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	CDS	13023006	13023154	1	-	2	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	exon	13023006	13023154	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	intron	13023155	13023224	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	CDS	13023225	13023296	1	-	2	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	exon	13023225	13023296	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	intron	13023297	13023388	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	CDS	13023389	13023397	0.31	-	2	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	exon	13023389	13023397	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	intron	13023398	13023472	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	CDS	13023473	13024556	0.38	-	0	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	exon	13023473	13024556	.	-	.	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
Phchi.S3	AUGUSTUS	start_codon	13024554	13024556	.	-	0	transcript_id "Phchi.S3G178800.t1"; gene_id "Phchi.S3G178800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8149.t1 is derived from g5324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34076227	34079357	.	+	.	Phchi.S1G530800
Phchi.S1	AUGUSTUS	transcript	34076227	34079357	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	start_codon	34076227	34076229	.	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34076227	34076243	0.99	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34076227	34076243	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34076244	34076445	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34076446	34076649	1	+	1	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34076446	34076649	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34076650	34076716	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34076717	34076798	1	+	1	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34076717	34076798	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34076799	34076897	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34076898	34076972	1	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34076898	34076972	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34076973	34077096	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34077097	34077150	1	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34077097	34077150	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34077151	34077258	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34077259	34077363	0.96	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34077259	34077363	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34077364	34077490	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34077491	34077565	1	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34077491	34077565	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34077566	34077681	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34077682	34077787	1	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34077682	34077787	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34077788	34078017	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34078018	34078114	1	+	2	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34078018	34078114	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34078115	34078257	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34078258	34078411	1	+	1	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34078258	34078411	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34078412	34078545	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34078546	34078644	0.6	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34078546	34078644	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34078645	34078697	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34078698	34078752	0.98	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34078698	34078752	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34078753	34078879	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34078880	34079040	1	+	2	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34078880	34079040	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	intron	34079041	34079132	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	CDS	34079133	34079357	1	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	exon	34079133	34079357	.	+	.	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
Phchi.S1	AUGUSTUS	stop_codon	34079358	34079360	.	+	0	transcript_id "Phchi.S1G530800.t1"; gene_id "Phchi.S1G530800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1617.t1 is derived from g8536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2038661	2039989	.	-	.	Phchi.S5G022600
Phchi.S5	AUGUSTUS	transcript	2038661	2039989	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	stop_codon	2038658	2038660	.	-	0	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	CDS	2038661	2039107	0.96	-	0	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	exon	2038661	2039107	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	intron	2039108	2039192	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	CDS	2039193	2039290	1	-	2	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	exon	2039193	2039290	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	intron	2039291	2039376	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	CDS	2039377	2039557	1	-	0	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	exon	2039377	2039557	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	intron	2039558	2039782	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	CDS	2039783	2039860	1	-	0	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	exon	2039783	2039860	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	intron	2039861	2039986	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	CDS	2039987	2039989	1	-	0	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	exon	2039987	2039989	.	-	.	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
Phchi.S5	AUGUSTUS	start_codon	2039987	2039989	.	-	0	transcript_id "Phchi.S5G022600.t1"; gene_id "Phchi.S5G022600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7015.t1 is derived from g4187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26408015	26409976	.	-	.	Phchi.S1G417400
Phchi.S1	AUGUSTUS	transcript	26408015	26409976	.	-	.	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	stop_codon	26408012	26408014	.	-	0	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	CDS	26408015	26408444	0.99	-	1	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	exon	26408015	26408444	.	-	.	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	intron	26408445	26408523	.	-	.	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	CDS	26408524	26408828	0.87	-	0	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	exon	26408524	26408828	.	-	.	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	intron	26408829	26408938	.	-	.	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	CDS	26408939	26409976	0.86	-	0	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	exon	26408939	26409976	.	-	.	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
Phchi.S1	AUGUSTUS	start_codon	26409974	26409976	.	-	0	transcript_id "Phchi.S1G417400.t1"; gene_id "Phchi.S1G417400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9480.t1 is derived from g6656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41953898	41958491	.	+	.	Phchi.S1G663900
Phchi.S1	AUGUSTUS	transcript	41953898	41958491	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	start_codon	41953898	41953900	.	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41953898	41954224	0.55	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41953898	41954224	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41954225	41954332	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41954333	41955730	0.98	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41954333	41955730	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41955731	41955881	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41955882	41956136	1	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41955882	41956136	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41956137	41956253	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41956254	41956376	1	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41956254	41956376	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41956377	41956477	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41956478	41956954	0.99	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41956478	41956954	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41956955	41957041	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41957042	41957371	0.35	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41957042	41957371	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41957372	41957483	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41957484	41957492	0.73	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41957484	41957492	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41957493	41957580	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41957581	41957617	0.74	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41957581	41957617	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41957618	41957829	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41957830	41957834	1	+	2	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41957830	41957834	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41957835	41957925	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41957926	41958253	1	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41957926	41958253	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	intron	41958254	41958327	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	CDS	41958328	41958491	1	+	2	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	exon	41958328	41958491	.	+	.	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
Phchi.S1	AUGUSTUS	stop_codon	41958492	41958494	.	+	0	transcript_id "Phchi.S1G663900.t1"; gene_id "Phchi.S1G663900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2179.t1 is derived from g9099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5246631	5248449	.	+	.	Phchi.S5G078800
Phchi.S5	AUGUSTUS	transcript	5246631	5248449	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	start_codon	5246631	5246633	.	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5246631	5246765	0.7	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5246631	5246765	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5246766	5246871	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5246872	5247084	0.66	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5246872	5247084	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247085	5247177	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247178	5247300	0.8	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247178	5247300	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247301	5247562	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247563	5247703	0.98	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247563	5247703	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247704	5247792	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247793	5247888	1	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247793	5247888	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247889	5247981	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247982	5248053	1	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247982	5248053	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5248054	5248139	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5248140	5248226	1	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5248140	5248226	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5248227	5248350	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5248351	5248449	1	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5248351	5248449	.	+	.	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	stop_codon	5248450	5248452	.	+	0	transcript_id "Phchi.S5G078800.t1"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	transcript	5246725	5248449	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	start_codon	5246725	5246727	.	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5246725	5246765	0.62	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5246725	5246765	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5246766	5246839	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5246840	5246913	0.38	+	1	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5246840	5246913	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5246914	5247001	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247002	5247084	0.5	+	2	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247002	5247084	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247085	5247177	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247178	5247300	0.78	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247178	5247300	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247301	5247562	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247563	5247703	0.99	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247563	5247703	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247704	5247792	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247793	5247888	1	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247793	5247888	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5247889	5247981	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5247982	5248053	1	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5247982	5248053	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5248054	5248139	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5248140	5248226	1	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5248140	5248226	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	intron	5248227	5248350	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	CDS	5248351	5248449	1	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	exon	5248351	5248449	.	+	.	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
Phchi.S5	AUGUSTUS	stop_codon	5248450	5248452	.	+	0	transcript_id "Phchi.S5G078800.t2"; gene_id "Phchi.S5G078800"
# This transcript jg11167.t2 is derived from g15217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11168.t1 is derived from g15218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4446553	4449377	.	+	.	Phchi.S4G075000
Phchi.S4	AUGUSTUS	transcript	4446553	4449377	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	start_codon	4446553	4446555	.	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4446553	4446684	0.65	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4446553	4446684	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4446685	4446883	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4446884	4446925	1	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4446884	4446925	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4446926	4447002	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4447003	4447126	0.72	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4447003	4447126	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4447127	4447214	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4447215	4447291	1	+	2	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4447215	4447291	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4447292	4447483	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4447484	4447572	1	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4447484	4447572	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4447573	4447691	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4447692	4447881	0.95	+	1	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4447692	4447881	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4447882	4448010	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4448011	4448192	0.99	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4448011	4448192	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4448193	4448298	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4448299	4448401	0.9	+	1	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4448299	4448401	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4448402	4448519	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4448520	4448851	0.86	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4448520	4448851	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	intron	4448852	4448929	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	CDS	4448930	4449377	0.69	+	1	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	exon	4448930	4449377	.	+	.	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
Phchi.S4	AUGUSTUS	stop_codon	4449378	4449380	.	+	0	transcript_id "Phchi.S4G075000.t1"; gene_id "Phchi.S4G075000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13906.t1 is derived from g12373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9604413	9605625	.	+	.	Phchi.S3G122500
Phchi.S3	AUGUSTUS	transcript	9604413	9605625	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	start_codon	9604413	9604415	.	+	0	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	CDS	9604413	9604593	0.9	+	0	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	exon	9604413	9604593	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	intron	9604594	9604700	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	CDS	9604701	9604813	0.99	+	2	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	exon	9604701	9604813	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	intron	9604814	9604901	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	CDS	9604902	9605216	0.93	+	0	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	exon	9604902	9605216	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	intron	9605217	9605430	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	CDS	9605431	9605625	0.88	+	0	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	exon	9605431	9605625	.	+	.	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
Phchi.S3	AUGUSTUS	stop_codon	9605626	9605628	.	+	0	transcript_id "Phchi.S3G122500.t1"; gene_id "Phchi.S3G122500"
# This transcript jg13334.t2 is derived from g11800.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13335.t1 is derived from g11801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6141611	6141909	.	+	.	Phchi.S3G065400
Phchi.S3	AUGUSTUS	transcript	6141611	6141909	.	+	.	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	start_codon	6141611	6141613	.	+	0	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	CDS	6141611	6141668	0.76	+	0	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	exon	6141611	6141668	.	+	.	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	intron	6141669	6141763	.	+	.	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	CDS	6141764	6141909	0.79	+	2	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	exon	6141764	6141909	.	+	.	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
Phchi.S3	AUGUSTUS	stop_codon	6141910	6141912	.	+	0	transcript_id "Phchi.S3G065400.t1"; gene_id "Phchi.S3G065400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11536.t1 is derived from g15586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6956924	6957999	.	+	.	Phchi.S4G111800
Phchi.S4	AUGUSTUS	transcript	6956924	6957999	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	start_codon	6956924	6956926	.	+	0	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	CDS	6956924	6957041	1	+	0	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	exon	6956924	6957041	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	intron	6957042	6957183	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	CDS	6957184	6957218	0.91	+	2	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	exon	6957184	6957218	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	intron	6957219	6957436	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	CDS	6957437	6957509	0.91	+	0	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	exon	6957437	6957509	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	intron	6957510	6957595	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	CDS	6957596	6957655	1	+	2	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	exon	6957596	6957655	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	intron	6957656	6957797	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	CDS	6957798	6957809	0.72	+	2	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	exon	6957798	6957809	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	intron	6957810	6957952	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	CDS	6957953	6957999	0.72	+	2	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	exon	6957953	6957999	.	+	.	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
Phchi.S4	AUGUSTUS	stop_codon	6958000	6958002	.	+	0	transcript_id "Phchi.S4G111800.t1"; gene_id "Phchi.S4G111800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3874.t1 is derived from g1043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6160207	6161772	.	+	.	Phchi.S1G103300
Phchi.S1	AUGUSTUS	transcript	6160207	6161772	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	start_codon	6160207	6160209	.	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6160207	6160278	0.99	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6160207	6160278	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	intron	6160279	6160713	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6160714	6160812	1	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6160714	6160812	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	intron	6160813	6160915	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6160916	6161017	1	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6160916	6161017	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	intron	6161018	6161183	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6161184	6161259	1	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6161184	6161259	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	intron	6161260	6161340	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6161341	6161411	0.99	+	2	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6161341	6161411	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	intron	6161412	6161516	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6161517	6161602	1	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6161517	6161602	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	intron	6161603	6161693	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	CDS	6161694	6161772	0.97	+	1	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	exon	6161694	6161772	.	+	.	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
Phchi.S1	AUGUSTUS	stop_codon	6161773	6161775	.	+	0	transcript_id "Phchi.S1G103300.t1"; gene_id "Phchi.S1G103300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg934.t1 is derived from g10716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6495048	6499405	.	-	.	Phchi.S6G089300
Phchi.S6	AUGUSTUS	transcript	6495048	6499405	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	stop_codon	6495045	6495047	.	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6495048	6495085	0.53	-	2	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6495048	6495085	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6495086	6495407	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6495408	6495462	0.61	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6495408	6495462	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6495463	6495957	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6495958	6496056	0.5	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6495958	6496056	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6496057	6496329	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6496330	6496382	0.72	-	2	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6496330	6496382	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6496383	6496446	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6496447	6496477	1	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6496447	6496477	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6496478	6496570	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6496571	6496640	1	-	1	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6496571	6496640	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6496641	6496744	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6496745	6496796	0.99	-	2	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6496745	6496796	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6496797	6497118	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6497119	6497179	0.73	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6497119	6497179	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6497180	6497371	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6497372	6497460	0.92	-	2	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6497372	6497460	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6497461	6497584	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6497585	6497735	0.75	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6497585	6497735	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6497736	6498115	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6498116	6498361	0.63	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6498116	6498361	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6498362	6498444	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6498445	6498650	1	-	2	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6498445	6498650	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6498651	6498746	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6498747	6498941	1	-	2	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6498747	6498941	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	intron	6498942	6499095	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	CDS	6499096	6499405	0.81	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	exon	6499096	6499405	.	-	.	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
Phchi.S6	AUGUSTUS	start_codon	6499403	6499405	.	-	0	transcript_id "Phchi.S6G089300.t1"; gene_id "Phchi.S6G089300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8953.t1 is derived from g6128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38837632	38838359	.	-	.	Phchi.S1G611200
Phchi.S1	AUGUSTUS	transcript	38837632	38838359	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	stop_codon	38837629	38837631	.	-	0	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	CDS	38837632	38837655	1	-	0	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	exon	38837632	38837655	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	intron	38837656	38837736	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	CDS	38837737	38837803	1	-	1	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	exon	38837737	38837803	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	intron	38837804	38837887	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	CDS	38837888	38837990	0.99	-	2	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	exon	38837888	38837990	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	intron	38837991	38838100	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	CDS	38838101	38838187	0.99	-	2	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	exon	38838101	38838187	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	intron	38838188	38838256	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	CDS	38838257	38838359	1	-	0	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	exon	38838257	38838359	.	-	.	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
Phchi.S1	AUGUSTUS	start_codon	38838357	38838359	.	-	0	transcript_id "Phchi.S1G611200.t1"; gene_id "Phchi.S1G611200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1590.t1 is derived from g8509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1908423	1909827	.	-	.	Phchi.S5G019900
Phchi.S5	AUGUSTUS	transcript	1908423	1909827	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	stop_codon	1908420	1908422	.	-	0	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	CDS	1908423	1908521	1	-	0	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	exon	1908423	1908521	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	intron	1908522	1908606	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	CDS	1908607	1908973	1	-	1	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	exon	1908607	1908973	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	intron	1908974	1909087	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	CDS	1909088	1909266	0.87	-	0	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	exon	1909088	1909266	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	intron	1909267	1909404	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	CDS	1909405	1909827	0.99	-	0	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	exon	1909405	1909827	.	-	.	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
Phchi.S5	AUGUSTUS	start_codon	1909825	1909827	.	-	0	transcript_id "Phchi.S5G019900.t1"; gene_id "Phchi.S5G019900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7873.t1 is derived from g5047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31649720	31654095	.	+	.	Phchi.S1G503200
Phchi.S1	AUGUSTUS	transcript	31649720	31654095	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	start_codon	31649720	31649722	.	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31649720	31649767	0.67	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31649720	31649767	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31649768	31649953	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31649954	31650625	0.56	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31649954	31650625	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31650626	31650713	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31650714	31651774	0.97	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31650714	31651774	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31651775	31651922	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31651923	31652238	1	+	1	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31651923	31652238	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31652239	31652382	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31652383	31652619	1	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31652383	31652619	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31652620	31652820	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31652821	31652994	0.97	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31652821	31652994	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31652995	31653106	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31653107	31653310	0.97	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31653107	31653310	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31653311	31653469	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31653470	31653583	1	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31653470	31653583	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	intron	31653584	31653705	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	CDS	31653706	31654095	0.96	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	exon	31653706	31654095	.	+	.	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
Phchi.S1	AUGUSTUS	stop_codon	31654096	31654098	.	+	0	transcript_id "Phchi.S1G503200.t1"; gene_id "Phchi.S1G503200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13149.t1 is derived from g11614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4404617	4405851	.	-	.	Phchi.S3G046800
Phchi.S3	AUGUSTUS	transcript	4404617	4405851	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	stop_codon	4404614	4404616	.	-	0	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	CDS	4404617	4404810	1	-	2	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	exon	4404617	4404810	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	intron	4404811	4404894	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	CDS	4404895	4405015	1	-	0	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	exon	4404895	4405015	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	intron	4405016	4405155	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	CDS	4405156	4405242	1	-	0	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	exon	4405156	4405242	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	intron	4405243	4405332	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	CDS	4405333	4405485	1	-	0	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	exon	4405333	4405485	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	intron	4405486	4405637	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	CDS	4405638	4405732	0.97	-	2	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	exon	4405638	4405732	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	intron	4405733	4405820	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	CDS	4405821	4405851	0.96	-	0	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	exon	4405821	4405851	.	-	.	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
Phchi.S3	AUGUSTUS	start_codon	4405849	4405851	.	-	0	transcript_id "Phchi.S3G046800.t1"; gene_id "Phchi.S3G046800"
# This transcript jg7988.t2 is derived from g5163.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7989.t1 is derived from g5164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32268761	32270044	.	-	.	Phchi.S1G514800
Phchi.S1	AUGUSTUS	transcript	32268761	32270044	.	-	.	transcript_id "Phchi.S1G514800.t1"; gene_id "Phchi.S1G514800"
Phchi.S1	AUGUSTUS	stop_codon	32268758	32268760	.	-	0	transcript_id "Phchi.S1G514800.t1"; gene_id "Phchi.S1G514800"
Phchi.S1	AUGUSTUS	CDS	32268761	32270044	0.95	-	0	transcript_id "Phchi.S1G514800.t1"; gene_id "Phchi.S1G514800"
Phchi.S1	AUGUSTUS	exon	32268761	32270044	.	-	.	transcript_id "Phchi.S1G514800.t1"; gene_id "Phchi.S1G514800"
Phchi.S1	AUGUSTUS	start_codon	32270042	32270044	.	-	0	transcript_id "Phchi.S1G514800.t1"; gene_id "Phchi.S1G514800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7201.t1 is derived from g4373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27619711	27621152	.	+	.	Phchi.S1G436000
Phchi.S1	AUGUSTUS	transcript	27619711	27621152	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	start_codon	27619711	27619713	.	+	0	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	CDS	27619711	27620079	0.99	+	0	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	exon	27619711	27620079	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	intron	27620080	27620188	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	CDS	27620189	27620266	1	+	0	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	exon	27620189	27620266	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	intron	27620267	27620339	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	CDS	27620340	27620480	1	+	0	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	exon	27620340	27620480	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	intron	27620481	27620584	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	CDS	27620585	27620661	1	+	0	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	exon	27620585	27620661	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	intron	27620662	27620736	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	CDS	27620737	27620901	1	+	1	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	exon	27620737	27620901	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	intron	27620902	27620980	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	CDS	27620981	27621152	1	+	1	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	exon	27620981	27621152	.	+	.	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
Phchi.S1	AUGUSTUS	stop_codon	27621153	27621155	.	+	0	transcript_id "Phchi.S1G436000.t1"; gene_id "Phchi.S1G436000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13984.t1 is derived from g12451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10049670	10053515	.	+	.	Phchi.S3G130300
Phchi.S3	AUGUSTUS	transcript	10049670	10053515	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	start_codon	10049670	10049672	.	+	0	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	CDS	10049670	10052822	0.85	+	0	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	exon	10049670	10052822	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	intron	10052823	10052904	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	CDS	10052905	10053018	1	+	0	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	exon	10052905	10053018	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	intron	10053019	10053097	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	CDS	10053098	10053247	1	+	0	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	exon	10053098	10053247	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	intron	10053248	10053326	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	CDS	10053327	10053515	0.73	+	0	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	exon	10053327	10053515	.	+	.	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
Phchi.S3	AUGUSTUS	stop_codon	10053516	10053518	.	+	0	transcript_id "Phchi.S3G130300.t1"; gene_id "Phchi.S3G130300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9599.t1 is derived from g6775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42881810	42882891	.	+	.	Phchi.S1G675800
Phchi.S1	AUGUSTUS	transcript	42881810	42882891	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	start_codon	42881810	42881812	.	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42881810	42881833	1	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42881810	42881833	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	intron	42881834	42881920	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42881921	42881965	1	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42881921	42881965	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	intron	42881966	42882060	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42882061	42882094	0.66	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42882061	42882094	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	intron	42882095	42882185	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42882186	42882253	0.92	+	2	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42882186	42882253	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	intron	42882254	42882347	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42882348	42882434	1	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42882348	42882434	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	intron	42882435	42882525	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42882526	42882659	1	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42882526	42882659	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	intron	42882660	42882788	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	CDS	42882789	42882891	1	+	1	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	exon	42882789	42882891	.	+	.	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
Phchi.S1	AUGUSTUS	stop_codon	42882892	42882894	.	+	0	transcript_id "Phchi.S1G675800.t1"; gene_id "Phchi.S1G675800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6265.t1 is derived from g3437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21928701	21929812	.	-	.	Phchi.S1G342400
Phchi.S1	AUGUSTUS	transcript	21928701	21929812	.	-	.	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	stop_codon	21928698	21928700	.	-	0	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	CDS	21928701	21928731	0.39	-	1	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	exon	21928701	21928731	.	-	.	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	intron	21928732	21929333	.	-	.	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	CDS	21929334	21929812	0.38	-	0	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	exon	21929334	21929812	.	-	.	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
Phchi.S1	AUGUSTUS	start_codon	21929810	21929812	.	-	0	transcript_id "Phchi.S1G342400.t1"; gene_id "Phchi.S1G342400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2564.t1 is derived from g9484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7408250	7409552	.	+	.	Phchi.S5G117300
Phchi.S5	AUGUSTUS	transcript	7408250	7409552	.	+	.	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	start_codon	7408250	7408252	.	+	0	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	CDS	7408250	7409075	0.66	+	0	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	exon	7408250	7409075	.	+	.	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	intron	7409076	7409166	.	+	.	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	CDS	7409167	7409552	0.86	+	2	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	exon	7409167	7409552	.	+	.	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
Phchi.S5	AUGUSTUS	stop_codon	7409553	7409555	.	+	0	transcript_id "Phchi.S5G117300.t1"; gene_id "Phchi.S5G117300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5733.t1 is derived from g2903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18597806	18601019	.	+	.	Phchi.S1G289200
Phchi.S1	AUGUSTUS	transcript	18597806	18601019	.	+	.	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	start_codon	18597806	18597808	.	+	0	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	CDS	18597806	18599020	1	+	0	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	exon	18597806	18599020	.	+	.	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	intron	18599021	18599159	.	+	.	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	CDS	18599160	18600113	1	+	0	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	exon	18599160	18600113	.	+	.	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	intron	18600114	18600287	.	+	.	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	CDS	18600288	18601019	1	+	0	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	exon	18600288	18601019	.	+	.	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
Phchi.S1	AUGUSTUS	stop_codon	18601020	18601022	.	+	0	transcript_id "Phchi.S1G289200.t1"; gene_id "Phchi.S1G289200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12091.t1 is derived from g7766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2190036	2191878	.	-	.	Phchi.S2G017100
Phchi.S2	AUGUSTUS	transcript	2190036	2191878	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	stop_codon	2190033	2190035	.	-	0	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2190036	2190186	0.95	-	1	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2190036	2190186	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2190187	2190264	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2190265	2190357	1	-	1	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2190265	2190357	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2190358	2190459	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2190460	2190539	1	-	0	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2190460	2190539	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2190540	2190695	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2190696	2190829	1	-	2	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2190696	2190829	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2190830	2190944	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2190945	2191083	1	-	0	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2190945	2191083	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2191084	2191244	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2191245	2191437	0.67	-	1	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2191245	2191437	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2191438	2191553	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2191554	2191628	0.54	-	1	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2191554	2191628	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	intron	2191629	2191783	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	CDS	2191784	2191878	0.37	-	0	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	exon	2191784	2191878	.	-	.	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
Phchi.S2	AUGUSTUS	start_codon	2191876	2191878	.	-	0	transcript_id "Phchi.S2G017100.t1"; gene_id "Phchi.S2G017100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11395.t1 is derived from g15445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6131914	6133520	.	-	.	Phchi.S4G097700
Phchi.S4	AUGUSTUS	transcript	6131914	6133520	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	stop_codon	6131911	6131913	.	-	0	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	CDS	6131914	6132115	0.98	-	1	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	exon	6131914	6132115	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	intron	6132116	6132216	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	CDS	6132217	6132323	1	-	0	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	exon	6132217	6132323	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	intron	6132324	6132419	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	CDS	6132420	6132560	1	-	0	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	exon	6132420	6132560	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	intron	6132561	6132634	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	CDS	6132635	6132775	1	-	0	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	exon	6132635	6132775	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	intron	6132776	6132923	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	CDS	6132924	6133520	0.99	-	0	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	exon	6132924	6133520	.	-	.	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
Phchi.S4	AUGUSTUS	start_codon	6133518	6133520	.	-	0	transcript_id "Phchi.S4G097700.t1"; gene_id "Phchi.S4G097700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7420.t1 is derived from g4592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29065300	29066039	.	-	.	Phchi.S1G457900
Phchi.S1	AUGUSTUS	transcript	29065300	29066039	.	-	.	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	stop_codon	29065297	29065299	.	-	0	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	CDS	29065300	29065863	0.82	-	0	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	exon	29065300	29065863	.	-	.	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	intron	29065864	29066003	.	-	.	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	CDS	29066004	29066039	0.34	-	0	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	exon	29066004	29066039	.	-	.	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
Phchi.S1	AUGUSTUS	start_codon	29066037	29066039	.	-	0	transcript_id "Phchi.S1G457900.t1"; gene_id "Phchi.S1G457900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12813.t1 is derived from g11278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2480010	2482242	.	-	.	Phchi.S3G013200
Phchi.S3	AUGUSTUS	transcript	2480010	2482242	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	stop_codon	2480007	2480009	.	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2480010	2480135	0.79	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2480010	2480135	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2480136	2480226	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2480227	2480319	0.9	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2480227	2480319	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2480320	2480429	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2480430	2480496	1	-	1	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2480430	2480496	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2480497	2480583	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2480584	2480689	1	-	2	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2480584	2480689	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2480690	2480777	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2480778	2480862	1	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2480778	2480862	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2480863	2481006	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2481007	2481098	1	-	2	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2481007	2481098	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2481099	2481201	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2481202	2481324	1	-	2	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2481202	2481324	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2481325	2481562	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2481563	2481668	1	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2481563	2481668	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2481669	2481761	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2481762	2481835	0.51	-	2	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2481762	2481835	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2481836	2481976	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2481977	2482068	0.96	-	1	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2481977	2482068	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	intron	2482069	2482144	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	CDS	2482145	2482242	0.88	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	exon	2482145	2482242	.	-	.	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
Phchi.S3	AUGUSTUS	start_codon	2482240	2482242	.	-	0	transcript_id "Phchi.S3G013200.t1"; gene_id "Phchi.S3G013200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8808.t1 is derived from g5983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38087273	38088053	.	+	.	Phchi.S1G596700
Phchi.S1	AUGUSTUS	transcript	38087273	38088053	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	start_codon	38087273	38087275	.	+	0	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	CDS	38087273	38087413	0.99	+	0	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	exon	38087273	38087413	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	intron	38087414	38087602	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	CDS	38087603	38087695	0.98	+	0	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	exon	38087603	38087695	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	intron	38087696	38087834	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	CDS	38087835	38087873	0.98	+	0	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	exon	38087835	38087873	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	intron	38087874	38088005	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	CDS	38088006	38088053	0.98	+	0	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	exon	38088006	38088053	.	+	.	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
Phchi.S1	AUGUSTUS	stop_codon	38088054	38088056	.	+	0	transcript_id "Phchi.S1G596700.t1"; gene_id "Phchi.S1G596700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10993.t1 is derived from g15043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3565704	3566622	.	+	.	Phchi.S4G057500
Phchi.S4	AUGUSTUS	transcript	3565704	3566622	.	+	.	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	start_codon	3565704	3565706	.	+	0	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	CDS	3565704	3566414	0.38	+	0	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	exon	3565704	3566414	.	+	.	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	intron	3566415	3566562	.	+	.	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	CDS	3566563	3566622	0.74	+	0	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	exon	3566563	3566622	.	+	.	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
Phchi.S4	AUGUSTUS	stop_codon	3566623	3566625	.	+	0	transcript_id "Phchi.S4G057500.t1"; gene_id "Phchi.S4G057500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2778.t1 is derived from g9698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8804173	8804897	.	-	.	Phchi.S5G138700
Phchi.S5	AUGUSTUS	transcript	8804173	8804897	.	-	.	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	stop_codon	8804170	8804172	.	-	0	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	CDS	8804173	8804195	0.05	-	2	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	exon	8804173	8804195	.	-	.	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	intron	8804196	8804269	.	-	.	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	CDS	8804270	8804307	0.01	-	1	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	exon	8804270	8804307	.	-	.	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	intron	8804308	8804793	.	-	.	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	CDS	8804794	8804897	0.02	-	0	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	exon	8804794	8804897	.	-	.	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
Phchi.S5	AUGUSTUS	start_codon	8804895	8804897	.	-	0	transcript_id "Phchi.S5G138700.t1"; gene_id "Phchi.S5G138700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10865.t1 is derived from g14915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2661323	2661541	.	-	.	Phchi.S4G044700
Phchi.S4	AUGUSTUS	transcript	2661323	2661541	.	-	.	transcript_id "Phchi.S4G044700.t1"; gene_id "Phchi.S4G044700"
Phchi.S4	AUGUSTUS	stop_codon	2661320	2661322	.	-	0	transcript_id "Phchi.S4G044700.t1"; gene_id "Phchi.S4G044700"
Phchi.S4	AUGUSTUS	CDS	2661323	2661541	0.45	-	0	transcript_id "Phchi.S4G044700.t1"; gene_id "Phchi.S4G044700"
Phchi.S4	AUGUSTUS	exon	2661323	2661541	.	-	.	transcript_id "Phchi.S4G044700.t1"; gene_id "Phchi.S4G044700"
Phchi.S4	AUGUSTUS	start_codon	2661539	2661541	.	-	0	transcript_id "Phchi.S4G044700.t1"; gene_id "Phchi.S4G044700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4727.t1 is derived from g1897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12502120	12502935	.	-	.	Phchi.S1G188600
Phchi.S1	AUGUSTUS	transcript	12502120	12502935	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	stop_codon	12502117	12502119	.	-	0	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	CDS	12502120	12502218	1	-	0	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	exon	12502120	12502218	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	intron	12502219	12502325	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	CDS	12502326	12502403	0.47	-	0	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	exon	12502326	12502403	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	intron	12502404	12502552	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	CDS	12502553	12502656	1	-	2	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	exon	12502553	12502656	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	intron	12502657	12502748	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	CDS	12502749	12502935	0.98	-	0	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	exon	12502749	12502935	.	-	.	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
Phchi.S1	AUGUSTUS	start_codon	12502933	12502935	.	-	0	transcript_id "Phchi.S1G188600.t1"; gene_id "Phchi.S1G188600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4947.t1 is derived from g2117.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13683936	13684697	.	-	.	Phchi.S1G210600
Phchi.S1	AUGUSTUS	transcript	13683936	13684697	.	-	.	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	stop_codon	13683933	13683935	.	-	0	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	CDS	13683936	13684132	0.97	-	2	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	exon	13683936	13684132	.	-	.	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	intron	13684133	13684300	.	-	.	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	CDS	13684301	13684697	1	-	0	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	exon	13684301	13684697	.	-	.	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	start_codon	13684695	13684697	.	-	0	transcript_id "Phchi.S1G210600.t1"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	transcript	13683936	13684697	.	-	.	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	stop_codon	13683933	13683935	.	-	0	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	CDS	13683936	13684159	0.93	-	2	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	exon	13683936	13684159	.	-	.	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	intron	13684160	13684300	.	-	.	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	CDS	13684301	13684697	0.95	-	0	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	exon	13684301	13684697	.	-	.	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	start_codon	13684695	13684697	.	-	0	transcript_id "Phchi.S1G210600.t2"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	transcript	13684201	13684697	.	-	.	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	stop_codon	13684198	13684200	.	-	0	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	CDS	13684201	13684202	0.94	-	2	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	exon	13684201	13684202	.	-	.	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	intron	13684203	13684300	.	-	.	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	CDS	13684301	13684697	0.92	-	0	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	exon	13684301	13684697	.	-	.	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
Phchi.S1	AUGUSTUS	start_codon	13684695	13684697	.	-	0	transcript_id "Phchi.S1G210600.t3"; gene_id "Phchi.S1G210600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6831.t1 is derived from g4003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25450764	25453248	.	+	.	Phchi.S1G399000
Phchi.S1	AUGUSTUS	transcript	25450764	25453248	.	+	.	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	start_codon	25450764	25450766	.	+	0	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	CDS	25450764	25452390	0.4	+	0	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	exon	25450764	25452390	.	+	.	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	intron	25452391	25452472	.	+	.	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	CDS	25452473	25453248	0.84	+	2	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	exon	25452473	25453248	.	+	.	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
Phchi.S1	AUGUSTUS	stop_codon	25453249	25453251	.	+	0	transcript_id "Phchi.S1G399000.t1"; gene_id "Phchi.S1G399000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6010.t1 is derived from g3181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20421123	20421368	.	+	.	Phchi.S1G316900
Phchi.S1	AUGUSTUS	transcript	20421123	20421368	.	+	.	transcript_id "Phchi.S1G316900.t1"; gene_id "Phchi.S1G316900"
Phchi.S1	AUGUSTUS	start_codon	20421123	20421125	.	+	0	transcript_id "Phchi.S1G316900.t1"; gene_id "Phchi.S1G316900"
Phchi.S1	AUGUSTUS	CDS	20421123	20421368	0.45	+	0	transcript_id "Phchi.S1G316900.t1"; gene_id "Phchi.S1G316900"
Phchi.S1	AUGUSTUS	exon	20421123	20421368	.	+	.	transcript_id "Phchi.S1G316900.t1"; gene_id "Phchi.S1G316900"
Phchi.S1	AUGUSTUS	stop_codon	20421369	20421371	.	+	0	transcript_id "Phchi.S1G316900.t1"; gene_id "Phchi.S1G316900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1205.t1 is derived from g10988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8411028	8413666	.	-	.	Phchi.S6G116400
Phchi.S6	AUGUSTUS	transcript	8411028	8413666	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	stop_codon	8411025	8411027	.	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8411028	8411246	0.82	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8411028	8411246	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8411247	8411349	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8411350	8411427	0.94	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8411350	8411427	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8411428	8411563	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8411564	8411717	1	-	1	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8411564	8411717	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8411718	8411836	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8411837	8411949	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8411837	8411949	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8411950	8412036	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8412037	8412136	1	-	1	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8412037	8412136	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8412137	8412272	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8412273	8412284	1	-	1	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8412273	8412284	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8412285	8412421	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8412422	8412468	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8412422	8412468	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8412469	8412595	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8412596	8412652	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8412596	8412652	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8412653	8412750	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8412751	8412855	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8412751	8412855	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8412856	8412952	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8412953	8413060	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8412953	8413060	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8413061	8413258	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8413259	8413447	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8413259	8413447	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	intron	8413448	8413564	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	CDS	8413565	8413666	1	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	exon	8413565	8413666	.	-	.	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
Phchi.S6	AUGUSTUS	start_codon	8413664	8413666	.	-	0	transcript_id "Phchi.S6G116400.t1"; gene_id "Phchi.S6G116400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10719.t1 is derived from g14769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1745557	1749035	.	-	.	Phchi.S4G030100
Phchi.S4	AUGUSTUS	transcript	1745557	1749035	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	stop_codon	1745554	1745556	.	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1745557	1745784	0.59	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1745557	1745784	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1745785	1745861	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1745862	1747121	0.55	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1745862	1747121	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1747122	1747237	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1747238	1747369	0.97	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1747238	1747369	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1747370	1747482	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1747483	1747566	0.98	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1747483	1747566	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1747567	1747650	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1747651	1747921	1	-	1	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1747651	1747921	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1747922	1748038	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1748039	1748292	0.86	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1748039	1748292	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1748293	1748376	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1748377	1748586	0.81	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1748377	1748586	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	intron	1748587	1748708	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	CDS	1748709	1749035	0.48	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	exon	1748709	1749035	.	-	.	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
Phchi.S4	AUGUSTUS	start_codon	1749033	1749035	.	-	0	transcript_id "Phchi.S4G030100.t1"; gene_id "Phchi.S4G030100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13460.t1 is derived from g11927.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7010842	7011679	.	+	.	Phchi.S3G077900
Phchi.S3	AUGUSTUS	transcript	7010842	7011679	.	+	.	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	start_codon	7010842	7010844	.	+	0	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	CDS	7010842	7010958	0.76	+	0	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	exon	7010842	7010958	.	+	.	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	intron	7010959	7011112	.	+	.	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	CDS	7011113	7011679	0.82	+	0	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	exon	7011113	7011679	.	+	.	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	stop_codon	7011680	7011682	.	+	0	transcript_id "Phchi.S3G077900.t1"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	transcript	7011308	7011679	.	+	.	transcript_id "Phchi.S3G077900.t2"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	start_codon	7011308	7011310	.	+	0	transcript_id "Phchi.S3G077900.t2"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	CDS	7011308	7011679	0.99	+	0	transcript_id "Phchi.S3G077900.t2"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	exon	7011308	7011679	.	+	.	transcript_id "Phchi.S3G077900.t2"; gene_id "Phchi.S3G077900"
Phchi.S3	AUGUSTUS	stop_codon	7011680	7011682	.	+	0	transcript_id "Phchi.S3G077900.t2"; gene_id "Phchi.S3G077900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4207.t1 is derived from g1376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8906214	8908203	.	-	.	Phchi.S1G136600
Phchi.S1	AUGUSTUS	transcript	8906214	8908203	.	-	.	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	stop_codon	8906211	8906213	.	-	0	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	CDS	8906214	8907821	0.94	-	0	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	exon	8906214	8907821	.	-	.	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	intron	8907822	8907930	.	-	.	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	CDS	8907931	8908203	0.61	-	0	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	exon	8907931	8908203	.	-	.	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
Phchi.S1	AUGUSTUS	start_codon	8908201	8908203	.	-	0	transcript_id "Phchi.S1G136600.t1"; gene_id "Phchi.S1G136600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9405.t1 is derived from g6581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41353889	41354424	.	-	.	Phchi.S1G656400
Phchi.S1	AUGUSTUS	transcript	41353889	41354424	.	-	.	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	stop_codon	41353886	41353888	.	-	0	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	CDS	41353889	41354180	0.96	-	1	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	exon	41353889	41354180	.	-	.	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	intron	41354181	41354275	.	-	.	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	CDS	41354276	41354424	0.92	-	0	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	exon	41354276	41354424	.	-	.	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
Phchi.S1	AUGUSTUS	start_codon	41354422	41354424	.	-	0	transcript_id "Phchi.S1G656400.t1"; gene_id "Phchi.S1G656400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3857.t1 is derived from g1026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6055339	6057711	.	+	.	Phchi.S1G101600
Phchi.S1	AUGUSTUS	transcript	6055339	6057711	.	+	.	transcript_id "Phchi.S1G101600.t1"; gene_id "Phchi.S1G101600"
Phchi.S1	AUGUSTUS	start_codon	6055339	6055341	.	+	0	transcript_id "Phchi.S1G101600.t1"; gene_id "Phchi.S1G101600"
Phchi.S1	AUGUSTUS	CDS	6055339	6057711	0.37	+	0	transcript_id "Phchi.S1G101600.t1"; gene_id "Phchi.S1G101600"
Phchi.S1	AUGUSTUS	exon	6055339	6057711	.	+	.	transcript_id "Phchi.S1G101600.t1"; gene_id "Phchi.S1G101600"
Phchi.S1	AUGUSTUS	stop_codon	6057712	6057714	.	+	0	transcript_id "Phchi.S1G101600.t1"; gene_id "Phchi.S1G101600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12418.t1 is derived from g8095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19177317	19177941	.	+	.	Phchi.S2G049800
Phchi.S2	AUGUSTUS	transcript	19177317	19177941	.	+	.	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	start_codon	19177317	19177319	.	+	0	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	CDS	19177317	19177659	0.82	+	0	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	exon	19177317	19177659	.	+	.	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	intron	19177660	19177807	.	+	.	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	CDS	19177808	19177941	0.82	+	2	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	exon	19177808	19177941	.	+	.	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
Phchi.S2	AUGUSTUS	stop_codon	19177942	19177944	.	+	0	transcript_id "Phchi.S2G049800.t1"; gene_id "Phchi.S2G049800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6427.t1 is derived from g3599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22988228	22988601	.	-	.	Phchi.S1G358600
Phchi.S1	AUGUSTUS	transcript	22988228	22988601	.	-	.	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	stop_codon	22988225	22988227	.	-	0	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	CDS	22988228	22988391	0.99	-	2	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	exon	22988228	22988391	.	-	.	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	intron	22988392	22988483	.	-	.	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	CDS	22988484	22988601	0.4	-	0	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	exon	22988484	22988601	.	-	.	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
Phchi.S1	AUGUSTUS	start_codon	22988599	22988601	.	-	0	transcript_id "Phchi.S1G358600.t1"; gene_id "Phchi.S1G358600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9953.t1 is derived from g7129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44638674	44640785	.	+	.	Phchi.S1G711200
Phchi.S1	AUGUSTUS	transcript	44638674	44640785	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	start_codon	44638674	44638676	.	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44638674	44638724	0.74	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44638674	44638724	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44638725	44638814	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44638815	44638928	1	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44638815	44638928	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44638929	44639013	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44639014	44639082	1	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44639014	44639082	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44639083	44639170	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44639171	44639191	0.99	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44639171	44639191	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44639192	44639283	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44639284	44639288	0.99	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44639284	44639288	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44639289	44639370	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44639371	44639527	0.99	+	1	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44639371	44639527	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44639528	44639651	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44639652	44639732	1	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44639652	44639732	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44639733	44639818	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44639819	44639926	1	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44639819	44639926	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44639927	44640018	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44640019	44640087	1	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44640019	44640087	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44640088	44640243	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44640244	44640358	1	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44640244	44640358	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	intron	44640359	44640459	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	CDS	44640460	44640785	0.99	+	2	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	exon	44640460	44640785	.	+	.	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
Phchi.S1	AUGUSTUS	stop_codon	44640786	44640788	.	+	0	transcript_id "Phchi.S1G711200.t1"; gene_id "Phchi.S1G711200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4724.t1 is derived from g1894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12485355	12485678	.	+	.	Phchi.S1G188300
Phchi.S1	AUGUSTUS	transcript	12485355	12485678	.	+	.	transcript_id "Phchi.S1G188300.t1"; gene_id "Phchi.S1G188300"
Phchi.S1	AUGUSTUS	start_codon	12485355	12485357	.	+	0	transcript_id "Phchi.S1G188300.t1"; gene_id "Phchi.S1G188300"
Phchi.S1	AUGUSTUS	CDS	12485355	12485678	0.61	+	0	transcript_id "Phchi.S1G188300.t1"; gene_id "Phchi.S1G188300"
Phchi.S1	AUGUSTUS	exon	12485355	12485678	.	+	.	transcript_id "Phchi.S1G188300.t1"; gene_id "Phchi.S1G188300"
Phchi.S1	AUGUSTUS	stop_codon	12485679	12485681	.	+	0	transcript_id "Phchi.S1G188300.t1"; gene_id "Phchi.S1G188300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15689.t1 is derived from g14158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20669676	20671097	.	-	.	Phchi.S3G300800
Phchi.S3	AUGUSTUS	transcript	20669676	20671097	.	-	.	transcript_id "Phchi.S3G300800.t1"; gene_id "Phchi.S3G300800"
Phchi.S3	AUGUSTUS	stop_codon	20669673	20669675	.	-	0	transcript_id "Phchi.S3G300800.t1"; gene_id "Phchi.S3G300800"
Phchi.S3	AUGUSTUS	CDS	20669676	20671097	0.92	-	0	transcript_id "Phchi.S3G300800.t1"; gene_id "Phchi.S3G300800"
Phchi.S3	AUGUSTUS	exon	20669676	20671097	.	-	.	transcript_id "Phchi.S3G300800.t1"; gene_id "Phchi.S3G300800"
Phchi.S3	AUGUSTUS	start_codon	20671095	20671097	.	-	0	transcript_id "Phchi.S3G300800.t1"; gene_id "Phchi.S3G300800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10014.t1 is derived from g7190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45053860	45055350	.	-	.	Phchi.S1G717300
Phchi.S1	AUGUSTUS	transcript	45053860	45055350	.	-	.	transcript_id "Phchi.S1G717300.t1"; gene_id "Phchi.S1G717300"
Phchi.S1	AUGUSTUS	stop_codon	45053857	45053859	.	-	0	transcript_id "Phchi.S1G717300.t1"; gene_id "Phchi.S1G717300"
Phchi.S1	AUGUSTUS	CDS	45053860	45055350	0.93	-	0	transcript_id "Phchi.S1G717300.t1"; gene_id "Phchi.S1G717300"
Phchi.S1	AUGUSTUS	exon	45053860	45055350	.	-	.	transcript_id "Phchi.S1G717300.t1"; gene_id "Phchi.S1G717300"
Phchi.S1	AUGUSTUS	start_codon	45055348	45055350	.	-	0	transcript_id "Phchi.S1G717300.t1"; gene_id "Phchi.S1G717300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14563.t1 is derived from g13031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13480514	13483412	.	+	.	Phchi.S3G188200
Phchi.S3	AUGUSTUS	transcript	13480514	13483412	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	start_codon	13480514	13480516	.	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13480514	13480856	0.88	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13480514	13480856	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13480857	13480998	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13480999	13481060	0.88	+	2	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13480999	13481060	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13481061	13481181	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13481182	13481272	1	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13481182	13481272	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13481273	13481359	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13481360	13481422	1	+	2	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13481360	13481422	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13481423	13481682	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13481683	13481746	1	+	2	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13481683	13481746	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13481747	13481841	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13481842	13481938	1	+	1	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13481842	13481938	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13481939	13482020	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13482021	13482104	1	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13482021	13482104	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13482105	13482191	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13482192	13482281	1	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13482192	13482281	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13482282	13482405	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13482406	13482430	1	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13482406	13482430	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13482431	13482563	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13482564	13482733	1	+	2	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13482564	13482733	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13482734	13482822	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13482823	13482935	1	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13482823	13482935	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13482936	13483014	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13483015	13483096	1	+	1	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13483015	13483096	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	intron	13483097	13483223	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	CDS	13483224	13483412	1	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	exon	13483224	13483412	.	+	.	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
Phchi.S3	AUGUSTUS	stop_codon	13483413	13483415	.	+	0	transcript_id "Phchi.S3G188200.t1"; gene_id "Phchi.S3G188200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5749.t1 is derived from g2919.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18703868	18706580	.	+	.	Phchi.S1G290800
Phchi.S1	AUGUSTUS	transcript	18703868	18706580	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	start_codon	18703868	18703870	.	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18703868	18704576	0.7	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18703868	18704576	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	intron	18704577	18704700	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18704701	18704873	1	+	2	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18704701	18704873	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	intron	18704874	18705080	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18705081	18705095	1	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18705081	18705095	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	intron	18705096	18705194	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18705195	18705675	0.72	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18705195	18705675	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	intron	18705676	18705780	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18705781	18706043	0.94	+	2	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18705781	18706043	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	intron	18706044	18706131	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18706132	18706209	0.99	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18706132	18706209	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	intron	18706210	18706322	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	CDS	18706323	18706580	0.97	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	exon	18706323	18706580	.	+	.	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
Phchi.S1	AUGUSTUS	stop_codon	18706581	18706583	.	+	0	transcript_id "Phchi.S1G290800.t1"; gene_id "Phchi.S1G290800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5910.t1 is derived from g3081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19745286	19747618	.	+	.	Phchi.S1G306900
Phchi.S1	AUGUSTUS	transcript	19745286	19747618	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	start_codon	19745286	19745288	.	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19745286	19745311	0.9	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19745286	19745311	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19745312	19745400	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19745401	19745749	0.99	+	1	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19745401	19745749	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19745750	19745849	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19745850	19745993	1	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19745850	19745993	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19745994	19746093	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19746094	19746372	1	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19746094	19746372	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19746373	19746540	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19746541	19746743	1	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19746541	19746743	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19746744	19747050	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19747051	19747129	1	+	1	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19747051	19747129	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19747130	19747237	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19747238	19747413	0.99	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19747238	19747413	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19747414	19747488	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19747489	19747618	1	+	1	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19747489	19747618	.	+	.	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	stop_codon	19747619	19747621	.	+	0	transcript_id "Phchi.S1G306900.t1"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	transcript	19745286	19747618	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	start_codon	19745286	19745288	.	+	0	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19745286	19745311	0.96	+	0	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19745286	19745311	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19745312	19745400	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19745401	19745749	0.99	+	1	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19745401	19745749	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19745750	19745849	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19745850	19746000	1	+	0	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19745850	19746000	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19746001	19746093	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19746094	19746132	0.58	+	2	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19746094	19746132	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19746133	19746250	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19746251	19746372	0.58	+	2	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19746251	19746372	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19746373	19746540	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19746541	19746743	1	+	0	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19746541	19746743	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19746744	19747050	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19747051	19747129	1	+	1	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19747051	19747129	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19747130	19747237	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19747238	19747413	0.98	+	0	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19747238	19747413	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	intron	19747414	19747488	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	CDS	19747489	19747618	0.99	+	1	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	exon	19747489	19747618	.	+	.	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
Phchi.S1	AUGUSTUS	stop_codon	19747619	19747621	.	+	0	transcript_id "Phchi.S1G306900.t2"; gene_id "Phchi.S1G306900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5945.t1 is derived from g3116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19965108	19965707	.	-	.	Phchi.S1G310400
Phchi.S1	AUGUSTUS	transcript	19965108	19965707	.	-	.	transcript_id "Phchi.S1G310400.t1"; gene_id "Phchi.S1G310400"
Phchi.S1	AUGUSTUS	stop_codon	19965105	19965107	.	-	0	transcript_id "Phchi.S1G310400.t1"; gene_id "Phchi.S1G310400"
Phchi.S1	AUGUSTUS	CDS	19965108	19965707	1	-	0	transcript_id "Phchi.S1G310400.t1"; gene_id "Phchi.S1G310400"
Phchi.S1	AUGUSTUS	exon	19965108	19965707	.	-	.	transcript_id "Phchi.S1G310400.t1"; gene_id "Phchi.S1G310400"
Phchi.S1	AUGUSTUS	start_codon	19965705	19965707	.	-	0	transcript_id "Phchi.S1G310400.t1"; gene_id "Phchi.S1G310400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8618.t1 is derived from g5793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37005634	37006029	.	+	.	Phchi.S1G577700
Phchi.S1	AUGUSTUS	transcript	37005634	37006029	.	+	.	transcript_id "Phchi.S1G577700.t1"; gene_id "Phchi.S1G577700"
Phchi.S1	AUGUSTUS	start_codon	37005634	37005636	.	+	0	transcript_id "Phchi.S1G577700.t1"; gene_id "Phchi.S1G577700"
Phchi.S1	AUGUSTUS	CDS	37005634	37006029	0.7	+	0	transcript_id "Phchi.S1G577700.t1"; gene_id "Phchi.S1G577700"
Phchi.S1	AUGUSTUS	exon	37005634	37006029	.	+	.	transcript_id "Phchi.S1G577700.t1"; gene_id "Phchi.S1G577700"
Phchi.S1	AUGUSTUS	stop_codon	37006030	37006032	.	+	0	transcript_id "Phchi.S1G577700.t1"; gene_id "Phchi.S1G577700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11352.t1 is derived from g15402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5708129	5709903	.	+	.	Phchi.S4G093400
Phchi.S4	AUGUSTUS	transcript	5708129	5709903	.	+	.	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	start_codon	5708129	5708131	.	+	0	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	CDS	5708129	5709534	0.46	+	0	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	exon	5708129	5709534	.	+	.	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	intron	5709535	5709854	.	+	.	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	CDS	5709855	5709903	1	+	1	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	exon	5709855	5709903	.	+	.	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
Phchi.S4	AUGUSTUS	stop_codon	5709904	5709906	.	+	0	transcript_id "Phchi.S4G093400.t1"; gene_id "Phchi.S4G093400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13525.t1 is derived from g11992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7368073	7373111	.	+	.	Phchi.S3G084400
Phchi.S3	AUGUSTUS	transcript	7368073	7373111	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	start_codon	7368073	7368075	.	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7368073	7368441	0.73	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7368073	7368441	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7368442	7368524	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7368525	7368579	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7368525	7368579	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7368580	7368670	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7368671	7368846	1	+	2	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7368671	7368846	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7368847	7368943	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7368944	7369165	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7368944	7369165	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7369166	7369246	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7369247	7369485	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7369247	7369485	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7369486	7369585	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7369586	7370111	1	+	1	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7369586	7370111	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7370112	7370204	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7370205	7370478	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7370205	7370478	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7370479	7370574	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7370575	7370743	1	+	2	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7370575	7370743	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7370744	7370830	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7370831	7371313	0.91	+	1	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7370831	7371313	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7371314	7371431	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7371432	7371660	0.92	+	1	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7371432	7371660	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7371661	7371741	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7371742	7372008	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7371742	7372008	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7372009	7372084	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7372085	7372348	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7372085	7372348	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	intron	7372349	7372433	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	CDS	7372434	7373111	1	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	exon	7372434	7373111	.	+	.	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
Phchi.S3	AUGUSTUS	stop_codon	7373112	7373114	.	+	0	transcript_id "Phchi.S3G084400.t1"; gene_id "Phchi.S3G084400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1571.t1 is derived from g8490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1820325	1821346	.	+	.	Phchi.S5G018000
Phchi.S5	AUGUSTUS	transcript	1820325	1821346	.	+	.	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	start_codon	1820325	1820327	.	+	0	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	CDS	1820325	1820687	0.19	+	0	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	exon	1820325	1820687	.	+	.	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	intron	1820688	1820782	.	+	.	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	CDS	1820783	1821346	0.52	+	0	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	exon	1820783	1821346	.	+	.	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
Phchi.S5	AUGUSTUS	stop_codon	1821347	1821349	.	+	0	transcript_id "Phchi.S5G018000.t1"; gene_id "Phchi.S5G018000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7465.t1 is derived from g4638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29407214	29414277	.	-	.	Phchi.S1G462400
Phchi.S1	AUGUSTUS	transcript	29407214	29414277	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	stop_codon	29407211	29407213	.	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29407214	29407756	0.74	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29407214	29407756	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29407757	29407829	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29407830	29407988	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29407830	29407988	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29407989	29408093	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29408094	29408234	0.47	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29408094	29408234	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29408235	29408324	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29408325	29408423	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29408325	29408423	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29408424	29408547	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29408548	29409243	0.76	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29408548	29409243	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29409244	29409402	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29409403	29409594	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29409403	29409594	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29409595	29409694	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29409695	29409923	1	-	1	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29409695	29409923	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29409924	29410050	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29410051	29410103	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29410051	29410103	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29410104	29410201	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29410202	29410297	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29410202	29410297	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29410298	29410463	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29410464	29410667	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29410464	29410667	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29410668	29410766	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29410767	29410913	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29410767	29410913	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29410914	29411016	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29411017	29411220	0.87	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29411017	29411220	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29411221	29411349	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29411350	29411501	1	-	2	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29411350	29411501	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29411502	29411657	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29411658	29411749	1	-	1	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29411658	29411749	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29411750	29411830	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29411831	29411992	1	-	1	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29411831	29411992	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29411993	29412103	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29412104	29412264	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29412104	29412264	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29412265	29412470	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29412471	29412485	0.8	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29412471	29412485	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29412486	29412592	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29412593	29412602	0.98	-	1	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29412593	29412602	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29412603	29412754	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29412755	29412860	0.98	-	2	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29412755	29412860	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29412861	29412947	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29412948	29413127	0.99	-	2	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29412948	29413127	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29413128	29413218	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29413219	29413305	1	-	2	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29413219	29413305	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29413306	29413481	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29413482	29413605	1	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29413482	29413605	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	intron	29413606	29413986	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	CDS	29413987	29414277	0.91	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	exon	29413987	29414277	.	-	.	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
Phchi.S1	AUGUSTUS	start_codon	29414275	29414277	.	-	0	transcript_id "Phchi.S1G462400.t1"; gene_id "Phchi.S1G462400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15537.t1 is derived from g14006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19771329	19773391	.	+	.	Phchi.S3G285600
Phchi.S3	AUGUSTUS	transcript	19771329	19773391	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	start_codon	19771329	19771331	.	+	0	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19771329	19771612	1	+	0	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19771329	19771612	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19771613	19771729	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19771730	19771859	1	+	1	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19771730	19771859	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19771860	19771983	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19771984	19772237	0.99	+	0	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19771984	19772237	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19772238	19772361	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19772362	19772566	0.99	+	1	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19772362	19772566	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19772567	19772689	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19772690	19772730	0.99	+	0	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19772690	19772730	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19772731	19772831	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19772832	19772960	1	+	1	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19772832	19772960	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19772961	19773073	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19773074	19773146	0.98	+	1	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19773074	19773146	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	intron	19773147	19773271	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	CDS	19773272	19773391	0.98	+	0	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	exon	19773272	19773391	.	+	.	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
Phchi.S3	AUGUSTUS	stop_codon	19773392	19773394	.	+	0	transcript_id "Phchi.S3G285600.t1"; gene_id "Phchi.S3G285600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8892.t1 is derived from g6067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38500164	38502587	.	-	.	Phchi.S1G605100
Phchi.S1	AUGUSTUS	transcript	38500164	38502587	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	stop_codon	38500161	38500163	.	-	0	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	CDS	38500164	38500387	0.43	-	2	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	exon	38500164	38500387	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	intron	38500388	38500651	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	CDS	38500652	38500678	0.41	-	2	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	exon	38500652	38500678	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	intron	38500679	38500779	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	CDS	38500780	38500900	0.47	-	0	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	exon	38500780	38500900	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	intron	38500901	38500981	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	CDS	38500982	38501104	1	-	0	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	exon	38500982	38501104	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	intron	38501105	38501195	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	CDS	38501196	38501407	1	-	2	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	exon	38501196	38501407	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	intron	38501408	38501488	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	CDS	38501489	38502587	0.62	-	0	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	exon	38501489	38502587	.	-	.	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
Phchi.S1	AUGUSTUS	start_codon	38502585	38502587	.	-	0	transcript_id "Phchi.S1G605100.t1"; gene_id "Phchi.S1G605100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg765.t1 is derived from g10547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5404291	5407016	.	-	.	Phchi.S6G072400
Phchi.S6	AUGUSTUS	transcript	5404291	5407016	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	stop_codon	5404288	5404290	.	-	0	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5404291	5404325	0.55	-	2	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5404291	5404325	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	intron	5404326	5404420	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5404421	5404873	0.56	-	2	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5404421	5404873	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	intron	5404874	5404966	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5404967	5405320	0.63	-	2	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5404967	5405320	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	intron	5405321	5405439	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5405440	5405555	1	-	1	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5405440	5405555	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	intron	5405556	5405761	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5405762	5405931	0.89	-	0	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5405762	5405931	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	intron	5405932	5406052	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5406053	5406409	0.69	-	0	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5406053	5406409	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	intron	5406410	5406569	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	CDS	5406570	5407016	0.96	-	0	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	exon	5406570	5407016	.	-	.	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
Phchi.S6	AUGUSTUS	start_codon	5407014	5407016	.	-	0	transcript_id "Phchi.S6G072400.t1"; gene_id "Phchi.S6G072400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8733.t1 is derived from g5908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37713052	37714273	.	-	.	Phchi.S1G589200
Phchi.S1	AUGUSTUS	transcript	37713052	37714273	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	stop_codon	37713049	37713051	.	-	0	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	CDS	37713052	37713264	0.7	-	0	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	exon	37713052	37713264	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	intron	37713265	37713356	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	CDS	37713357	37713505	1	-	2	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	exon	37713357	37713505	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	intron	37713506	37713592	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	CDS	37713593	37713692	1	-	0	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	exon	37713593	37713692	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	intron	37713693	37713807	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	CDS	37713808	37713885	1	-	0	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	exon	37713808	37713885	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	intron	37713886	37714042	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	CDS	37714043	37714273	0.99	-	0	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	exon	37714043	37714273	.	-	.	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
Phchi.S1	AUGUSTUS	start_codon	37714271	37714273	.	-	0	transcript_id "Phchi.S1G589200.t1"; gene_id "Phchi.S1G589200"
# This transcript jg6709.t2 is derived from g3881.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6710.t1 is derived from g3882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24650834	24652506	.	-	.	Phchi.S1G386900
Phchi.S1	AUGUSTUS	transcript	24650834	24652506	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	stop_codon	24650831	24650833	.	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	CDS	24650834	24651309	1	-	2	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	exon	24650834	24651309	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	intron	24651310	24651450	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	CDS	24651451	24651643	1	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	exon	24651451	24651643	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	intron	24651644	24651725	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	CDS	24651726	24651938	0.58	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	exon	24651726	24651938	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	intron	24651939	24652042	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	CDS	24652043	24652186	0.77	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	exon	24652043	24652186	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	intron	24652187	24652264	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	CDS	24652265	24652384	1	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	exon	24652265	24652384	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	intron	24652385	24652455	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	CDS	24652456	24652506	1	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	exon	24652456	24652506	.	-	.	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
Phchi.S1	AUGUSTUS	start_codon	24652504	24652506	.	-	0	transcript_id "Phchi.S1G386900.t1"; gene_id "Phchi.S1G386900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4944.t1 is derived from g2114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13677162	13679047	.	-	.	Phchi.S1G210300
Phchi.S1	AUGUSTUS	transcript	13677162	13679047	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	stop_codon	13677159	13677161	.	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13677162	13677216	1	-	1	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13677162	13677216	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13677217	13677298	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13677299	13677432	1	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13677299	13677432	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13677433	13677522	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13677523	13677642	1	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13677523	13677642	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13677643	13677735	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13677736	13677918	1	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13677736	13677918	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13677919	13678069	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13678070	13678246	1	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13678070	13678246	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13678247	13678374	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13678375	13678425	1	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13678375	13678425	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13678426	13678533	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13678534	13678627	1	-	1	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13678534	13678627	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	intron	13678628	13678901	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	CDS	13678902	13679047	1	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	exon	13678902	13679047	.	-	.	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
Phchi.S1	AUGUSTUS	start_codon	13679045	13679047	.	-	0	transcript_id "Phchi.S1G210300.t1"; gene_id "Phchi.S1G210300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2931.t1 is derived from g100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	604940	605734	.	+	.	Phchi.S1G009000
Phchi.S1	AUGUSTUS	transcript	604940	605734	.	+	.	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	start_codon	604940	604942	.	+	0	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	CDS	604940	605044	1	+	0	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	exon	604940	605044	.	+	.	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	intron	605045	605509	.	+	.	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	CDS	605510	605734	0.93	+	0	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	exon	605510	605734	.	+	.	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
Phchi.S1	AUGUSTUS	stop_codon	605735	605737	.	+	0	transcript_id "Phchi.S1G009000.t1"; gene_id "Phchi.S1G009000"
# This transcript jg15498.t2 is derived from g13967.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15499.t1 is derived from g13968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19536163	19537668	.	+	.	Phchi.S3G281800
Phchi.S3	AUGUSTUS	transcript	19536163	19537668	.	+	.	transcript_id "Phchi.S3G281800.t1"; gene_id "Phchi.S3G281800"
Phchi.S3	AUGUSTUS	start_codon	19536163	19536165	.	+	0	transcript_id "Phchi.S3G281800.t1"; gene_id "Phchi.S3G281800"
Phchi.S3	AUGUSTUS	CDS	19536163	19537668	1	+	0	transcript_id "Phchi.S3G281800.t1"; gene_id "Phchi.S3G281800"
Phchi.S3	AUGUSTUS	exon	19536163	19537668	.	+	.	transcript_id "Phchi.S3G281800.t1"; gene_id "Phchi.S3G281800"
Phchi.S3	AUGUSTUS	stop_codon	19537669	19537671	.	+	0	transcript_id "Phchi.S3G281800.t1"; gene_id "Phchi.S3G281800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10152.t1 is derived from g7328.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46001202	46002491	.	+	.	Phchi.S1G731100
Phchi.S1	AUGUSTUS	transcript	46001202	46002380	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	start_codon	46001202	46001204	.	+	0	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001202	46001433	0.62	+	0	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001202	46001433	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46001434	46001562	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001563	46001669	1	+	2	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001563	46001669	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46001670	46001749	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001750	46001863	1	+	0	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001750	46001863	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46001864	46001943	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001944	46002027	0.94	+	0	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001944	46002027	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46002028	46002162	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46002163	46002247	0.83	+	0	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46002163	46002247	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46002248	46002333	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46002334	46002380	0.88	+	2	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46002334	46002380	.	+	.	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	stop_codon	46002381	46002383	.	+	0	transcript_id "Phchi.S1G731100.t1"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	transcript	46001202	46002491	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	start_codon	46001202	46001204	.	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001202	46001433	0.63	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001202	46001433	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46001434	46001562	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001563	46001669	1	+	2	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001563	46001669	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46001670	46001749	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001750	46001863	1	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001750	46001863	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46001864	46001943	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46001944	46002027	1	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46001944	46002027	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46002028	46002190	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46002191	46002247	0.64	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46002191	46002247	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	intron	46002248	46002431	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	CDS	46002432	46002491	0.65	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	exon	46002432	46002491	.	+	.	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
Phchi.S1	AUGUSTUS	stop_codon	46002492	46002494	.	+	0	transcript_id "Phchi.S1G731100.t2"; gene_id "Phchi.S1G731100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9755.t1 is derived from g6931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43522278	43523585	.	-	.	Phchi.S1G691400
Phchi.S1	AUGUSTUS	transcript	43522278	43523585	.	-	.	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	stop_codon	43522275	43522277	.	-	0	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	CDS	43522278	43522379	0.92	-	0	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	exon	43522278	43522379	.	-	.	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	intron	43522380	43522632	.	-	.	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	CDS	43522633	43523174	0.92	-	2	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	exon	43522633	43523174	.	-	.	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	intron	43523175	43523437	.	-	.	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	CDS	43523438	43523585	0.83	-	0	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	exon	43523438	43523585	.	-	.	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
Phchi.S1	AUGUSTUS	start_codon	43523583	43523585	.	-	0	transcript_id "Phchi.S1G691400.t1"; gene_id "Phchi.S1G691400"
# This transcript jg14880.t2 is derived from g13348.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14881.t1 is derived from g13349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15256791	15258197	.	-	.	Phchi.S3G220000
Phchi.S3	AUGUSTUS	transcript	15256791	15258197	.	-	.	transcript_id "Phchi.S3G220000.t1"; gene_id "Phchi.S3G220000"
Phchi.S3	AUGUSTUS	stop_codon	15256788	15256790	.	-	0	transcript_id "Phchi.S3G220000.t1"; gene_id "Phchi.S3G220000"
Phchi.S3	AUGUSTUS	CDS	15256791	15258197	1	-	0	transcript_id "Phchi.S3G220000.t1"; gene_id "Phchi.S3G220000"
Phchi.S3	AUGUSTUS	exon	15256791	15258197	.	-	.	transcript_id "Phchi.S3G220000.t1"; gene_id "Phchi.S3G220000"
Phchi.S3	AUGUSTUS	start_codon	15258195	15258197	.	-	0	transcript_id "Phchi.S3G220000.t1"; gene_id "Phchi.S3G220000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2298.t1 is derived from g9218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5928918	5933754	.	+	.	Phchi.S5G090700
Phchi.S5	AUGUSTUS	transcript	5928918	5933754	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	start_codon	5928918	5928920	.	+	0	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5928918	5929626	0.32	+	0	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5928918	5929626	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	intron	5929627	5929724	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5929725	5930915	0.43	+	2	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5929725	5930915	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	intron	5930916	5931091	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5931092	5931866	0.96	+	2	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5931092	5931866	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	intron	5931867	5932000	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5932001	5933398	1	+	1	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5932001	5933398	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	intron	5933399	5933535	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5933536	5933549	0.82	+	1	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5933536	5933549	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	intron	5933550	5933645	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5933646	5933650	0.82	+	2	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5933646	5933650	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	intron	5933651	5933736	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	CDS	5933737	5933754	0.82	+	0	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	exon	5933737	5933754	.	+	.	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
Phchi.S5	AUGUSTUS	stop_codon	5933755	5933757	.	+	0	transcript_id "Phchi.S5G090700.t1"; gene_id "Phchi.S5G090700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14045.t1 is derived from g12512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10450963	10452260	.	+	.	Phchi.S3G136400
Phchi.S3	AUGUSTUS	transcript	10450963	10452260	.	+	.	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	start_codon	10450963	10450965	.	+	0	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	CDS	10450963	10451950	0.37	+	0	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	exon	10450963	10451950	.	+	.	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	intron	10451951	10452165	.	+	.	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	CDS	10452166	10452260	0.53	+	2	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	exon	10452166	10452260	.	+	.	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
Phchi.S3	AUGUSTUS	stop_codon	10452261	10452263	.	+	0	transcript_id "Phchi.S3G136400.t1"; gene_id "Phchi.S3G136400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4322.t1 is derived from g1491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9644832	9645245	.	+	.	Phchi.S1G148100
Phchi.S1	AUGUSTUS	transcript	9644832	9645245	.	+	.	transcript_id "Phchi.S1G148100.t1"; gene_id "Phchi.S1G148100"
Phchi.S1	AUGUSTUS	start_codon	9644832	9644834	.	+	0	transcript_id "Phchi.S1G148100.t1"; gene_id "Phchi.S1G148100"
Phchi.S1	AUGUSTUS	CDS	9644832	9645245	0.61	+	0	transcript_id "Phchi.S1G148100.t1"; gene_id "Phchi.S1G148100"
Phchi.S1	AUGUSTUS	exon	9644832	9645245	.	+	.	transcript_id "Phchi.S1G148100.t1"; gene_id "Phchi.S1G148100"
Phchi.S1	AUGUSTUS	stop_codon	9645246	9645248	.	+	0	transcript_id "Phchi.S1G148100.t1"; gene_id "Phchi.S1G148100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3744.t1 is derived from g913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5469702	5470701	.	-	.	Phchi.S1G090300
Phchi.S1	AUGUSTUS	transcript	5469702	5470701	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	stop_codon	5469699	5469701	.	-	0	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	CDS	5469702	5469739	1	-	2	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	exon	5469702	5469739	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	intron	5469740	5469826	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	CDS	5469827	5469885	1	-	1	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	exon	5469827	5469885	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	intron	5469886	5469969	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	CDS	5469970	5470294	1	-	2	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	exon	5469970	5470294	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	intron	5470295	5470475	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	CDS	5470476	5470701	1	-	0	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	exon	5470476	5470701	.	-	.	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
Phchi.S1	AUGUSTUS	start_codon	5470699	5470701	.	-	0	transcript_id "Phchi.S1G090300.t1"; gene_id "Phchi.S1G090300"
# This transcript jg5633.t2 is derived from g2803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5634.t1 is derived from g2804.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17980725	17984764	.	+	.	Phchi.S1G279300
Phchi.S1	AUGUSTUS	transcript	17980725	17984754	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	start_codon	17980725	17980727	.	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17980725	17981252	0.9	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17980725	17981252	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981253	17981321	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981322	17981480	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981322	17981480	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981481	17981566	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981567	17981667	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981567	17981667	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981668	17981943	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981944	17982016	0.88	+	1	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981944	17982016	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982017	17982141	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982142	17982245	0.88	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982142	17982245	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982246	17982351	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982352	17982484	1	+	1	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982352	17982484	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982485	17982597	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982598	17982654	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982598	17982654	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982655	17982731	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982732	17982848	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982732	17982848	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982849	17982939	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982940	17983031	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982940	17983031	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983032	17983120	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983121	17983199	1	+	1	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983121	17983199	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983200	17983284	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983285	17983350	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983285	17983350	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983351	17983449	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983450	17983498	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983450	17983498	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983499	17983572	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983573	17983671	1	+	2	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983573	17983671	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983672	17983753	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983754	17983863	1	+	2	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983754	17983863	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983864	17983943	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983944	17984027	1	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983944	17984027	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984028	17984117	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984118	17984249	0.33	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984118	17984249	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984250	17984328	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984329	17984521	0.69	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984329	17984521	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984522	17984710	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984711	17984754	0.75	+	2	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984711	17984754	.	+	.	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	stop_codon	17984755	17984757	.	+	0	transcript_id "Phchi.S1G279300.t1"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	transcript	17980725	17984754	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	start_codon	17980725	17980727	.	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17980725	17981252	0.98	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17980725	17981252	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981253	17981321	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981322	17981480	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981322	17981480	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981481	17981566	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981567	17981667	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981567	17981667	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981668	17981764	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981765	17981825	0.99	+	1	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981765	17981825	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981826	17981943	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981944	17981959	0.67	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981944	17981959	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981960	17982112	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982113	17982245	0.96	+	2	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982113	17982245	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982246	17982351	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982352	17982484	1	+	1	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982352	17982484	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982485	17982597	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982598	17982654	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982598	17982654	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982655	17982731	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982732	17982848	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982732	17982848	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982849	17982939	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982940	17983031	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982940	17983031	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983032	17983120	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983121	17983199	1	+	1	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983121	17983199	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983200	17983284	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983285	17983350	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983285	17983350	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983351	17983449	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983450	17983498	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983450	17983498	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983499	17983572	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983573	17983671	1	+	2	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983573	17983671	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983672	17983753	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983754	17983863	1	+	2	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983754	17983863	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983864	17983943	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983944	17984027	1	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983944	17984027	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984028	17984117	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984118	17984249	0.32	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984118	17984249	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984250	17984328	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984329	17984521	0.7	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984329	17984521	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984522	17984710	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984711	17984754	0.76	+	2	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984711	17984754	.	+	.	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	stop_codon	17984755	17984757	.	+	0	transcript_id "Phchi.S1G279300.t2"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	transcript	17980725	17984764	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	start_codon	17980725	17980727	.	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17980725	17981252	0.94	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17980725	17981252	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981253	17981321	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981322	17981480	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981322	17981480	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981481	17981566	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981567	17981667	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981567	17981667	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17981668	17981943	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17981944	17982016	0.93	+	1	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17981944	17982016	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982017	17982141	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982142	17982245	0.93	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982142	17982245	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982246	17982351	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982352	17982484	1	+	1	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982352	17982484	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982485	17982597	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982598	17982654	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982598	17982654	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982655	17982731	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982732	17982848	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982732	17982848	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17982849	17982939	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17982940	17983031	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17982940	17983031	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983032	17983120	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983121	17983199	1	+	1	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983121	17983199	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983200	17983284	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983285	17983350	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983285	17983350	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983351	17983449	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983450	17983498	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983450	17983498	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983499	17983572	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983573	17983671	1	+	2	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983573	17983671	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983672	17983753	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983754	17983863	1	+	2	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983754	17983863	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17983864	17983943	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17983944	17984027	1	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17983944	17984027	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984028	17984117	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984118	17984270	0.32	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984118	17984270	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984271	17984395	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984396	17984521	0.25	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984396	17984521	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	intron	17984522	17984713	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	CDS	17984714	17984764	0.12	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	exon	17984714	17984764	.	+	.	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
Phchi.S1	AUGUSTUS	stop_codon	17984765	17984767	.	+	0	transcript_id "Phchi.S1G279300.t3"; gene_id "Phchi.S1G279300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15645.t1 is derived from g14114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20466088	20467261	.	+	.	Phchi.S3G296400
Phchi.S3	AUGUSTUS	transcript	20466088	20467261	.	+	.	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	start_codon	20466088	20466090	.	+	0	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	CDS	20466088	20466193	0.99	+	0	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	exon	20466088	20466193	.	+	.	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	intron	20466194	20466324	.	+	.	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	CDS	20466325	20466469	0.95	+	2	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	exon	20466325	20466469	.	+	.	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	intron	20466470	20466558	.	+	.	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	CDS	20466559	20467261	0.94	+	1	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	exon	20466559	20467261	.	+	.	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
Phchi.S3	AUGUSTUS	stop_codon	20467262	20467264	.	+	0	transcript_id "Phchi.S3G296400.t1"; gene_id "Phchi.S3G296400"
# This transcript jg15694.t2 is derived from g14163.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15695.t1 is derived from g14164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20730345	20734485	.	-	.	Phchi.S3G301400
Phchi.S3	AUGUSTUS	transcript	20730345	20734485	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	stop_codon	20730342	20730344	.	-	0	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	CDS	20730345	20731357	0.83	-	2	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	exon	20730345	20731357	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	intron	20731358	20731448	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	CDS	20731449	20731635	1	-	0	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	exon	20731449	20731635	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	intron	20731636	20731724	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	CDS	20731725	20732349	0.38	-	1	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	exon	20731725	20732349	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	intron	20732350	20732444	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	CDS	20732445	20732863	0.37	-	0	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	exon	20732445	20732863	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	intron	20732864	20732976	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	CDS	20732977	20733444	0.99	-	0	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	exon	20732977	20733444	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	intron	20733445	20733516	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	CDS	20733517	20734485	0.58	-	0	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	exon	20733517	20734485	.	-	.	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
Phchi.S3	AUGUSTUS	start_codon	20734483	20734485	.	-	0	transcript_id "Phchi.S3G301400.t1"; gene_id "Phchi.S3G301400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3670.t1 is derived from g839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5111044	5111427	.	-	.	Phchi.S1G082900
Phchi.S1	AUGUSTUS	transcript	5111044	5111427	.	-	.	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	stop_codon	5111041	5111043	.	-	0	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	CDS	5111044	5111203	0.97	-	1	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	exon	5111044	5111203	.	-	.	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	intron	5111204	5111311	.	-	.	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	CDS	5111312	5111427	0.89	-	0	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	exon	5111312	5111427	.	-	.	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
Phchi.S1	AUGUSTUS	start_codon	5111425	5111427	.	-	0	transcript_id "Phchi.S1G082900.t1"; gene_id "Phchi.S1G082900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg9115.t1 is derived from g6290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39890509	39896366	.	-	.	Phchi.S1G627400
Phchi.S1	AUGUSTUS	transcript	39890509	39896366	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	stop_codon	39890506	39890508	.	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890509	39890560	1	-	1	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890509	39890560	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890561	39890658	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890659	39890749	0.96	-	2	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890659	39890749	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890750	39890955	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890956	39891123	0.96	-	2	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890956	39891123	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891124	39891278	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891279	39891375	0.99	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891279	39891375	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891376	39891474	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891475	39891612	1	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891475	39891612	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891613	39892665	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892666	39892673	1	-	2	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892666	39892673	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892674	39892753	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892754	39892764	1	-	1	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892754	39892764	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892765	39892932	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892933	39893065	0.98	-	2	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892933	39893065	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893066	39893321	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893322	39893385	1	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893322	39893385	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893386	39893471	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893472	39893501	0.93	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893472	39893501	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893502	39893586	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893587	39893622	1	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893587	39893622	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893623	39893709	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893710	39893835	0.65	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893710	39893835	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893836	39893980	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893981	39894225	0.97	-	2	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893981	39894225	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894226	39894375	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894376	39894478	1	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894376	39894478	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894479	39894582	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894583	39894762	0.98	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894583	39894762	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894763	39894893	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894894	39895112	0.89	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894894	39895112	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895113	39895220	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895221	39895505	0.48	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895221	39895505	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895506	39895589	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895590	39896366	1	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895590	39896366	.	-	.	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	start_codon	39896364	39896366	.	-	0	transcript_id "Phchi.S1G627400.t1"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	transcript	39890509	39896366	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	stop_codon	39890506	39890508	.	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890509	39890560	1	-	1	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890509	39890560	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890561	39890658	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890659	39890749	0.96	-	2	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890659	39890749	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890750	39890955	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890956	39891123	0.96	-	2	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890956	39891123	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891124	39891278	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891279	39891375	1	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891279	39891375	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891376	39891474	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891475	39891612	1	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891475	39891612	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891613	39892665	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892666	39892673	1	-	2	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892666	39892673	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892674	39892753	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892754	39892764	1	-	1	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892754	39892764	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892765	39892947	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892948	39893065	0.99	-	2	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892948	39893065	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893066	39893321	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893322	39893385	1	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893322	39893385	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893386	39893471	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893472	39893501	0.95	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893472	39893501	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893502	39893586	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893587	39893622	1	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893587	39893622	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893623	39893709	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893710	39893835	0.5	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893710	39893835	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893836	39893980	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893981	39894225	0.96	-	2	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893981	39894225	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894226	39894375	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894376	39894478	1	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894376	39894478	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894479	39894582	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894583	39894762	0.97	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894583	39894762	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894763	39894893	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894894	39895112	0.97	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894894	39895112	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895113	39895220	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895221	39895505	0.55	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895221	39895505	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895506	39895589	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895590	39896366	0.99	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895590	39896366	.	-	.	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	start_codon	39896364	39896366	.	-	0	transcript_id "Phchi.S1G627400.t2"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	transcript	39890509	39896366	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	stop_codon	39890506	39890508	.	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890509	39890560	1	-	1	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890509	39890560	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890561	39890658	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890659	39890749	0.93	-	2	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890659	39890749	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890750	39890955	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890956	39891123	0.93	-	2	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890956	39891123	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891124	39891278	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891279	39891375	0.97	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891279	39891375	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891376	39891474	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891475	39891612	1	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891475	39891612	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891613	39892665	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892666	39892673	0.99	-	2	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892666	39892673	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892674	39892753	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892754	39892764	0.98	-	1	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892754	39892764	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892765	39892974	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892975	39893065	0.97	-	2	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892975	39893065	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893066	39893321	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893322	39893385	0.98	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893322	39893385	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893386	39893471	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893472	39893501	0.92	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893472	39893501	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893502	39893586	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893587	39893622	0.99	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893587	39893622	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893623	39893709	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893710	39893835	0.53	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893710	39893835	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893836	39893980	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893981	39894225	0.93	-	2	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893981	39894225	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894226	39894375	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894376	39894478	1	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894376	39894478	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894479	39894582	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894583	39894762	0.96	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894583	39894762	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894763	39894893	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894894	39895112	0.91	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894894	39895112	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895113	39895220	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895221	39895505	0.55	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895221	39895505	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895506	39895589	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895590	39896366	1	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895590	39896366	.	-	.	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	start_codon	39896364	39896366	.	-	0	transcript_id "Phchi.S1G627400.t3"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	transcript	39890509	39896366	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	stop_codon	39890506	39890508	.	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890509	39890560	0.99	-	1	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890509	39890560	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890561	39890658	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890659	39890749	0.98	-	2	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890659	39890749	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39890750	39890955	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39890956	39891123	0.98	-	2	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39890956	39891123	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891124	39891278	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891279	39891375	0.98	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891279	39891375	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891376	39891474	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39891475	39891612	1	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39891475	39891612	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39891613	39892665	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892666	39892673	1	-	2	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892666	39892673	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892674	39892753	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892754	39892764	1	-	1	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892754	39892764	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39892765	39892947	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39892948	39893065	0.99	-	2	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39892948	39893065	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893066	39893321	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893322	39893385	0.98	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893322	39893385	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893386	39893471	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893472	39893501	0.92	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893472	39893501	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893502	39893586	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893587	39893622	1	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893587	39893622	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893623	39893709	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893710	39893835	0.54	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893710	39893835	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39893836	39893980	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39893981	39894225	0.9	-	2	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39893981	39894225	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894226	39894375	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894376	39894478	1	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894376	39894478	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894479	39894582	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894583	39894719	0.98	-	2	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894583	39894719	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39894720	39894893	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39894894	39895021	0.47	-	1	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39894894	39895021	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895022	39895220	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895221	39895330	0.53	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895221	39895330	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895331	39895475	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895476	39895505	0.47	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895476	39895505	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	intron	39895506	39895589	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	CDS	39895590	39896366	1	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	exon	39895590	39896366	.	-	.	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
Phchi.S1	AUGUSTUS	start_codon	39896364	39896366	.	-	0	transcript_id "Phchi.S1G627400.t4"; gene_id "Phchi.S1G627400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12395.t1 is derived from g8072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17114679	17115038	.	+	.	Phchi.S2G047500
Phchi.S2	AUGUSTUS	transcript	17114679	17115038	.	+	.	transcript_id "Phchi.S2G047500.t1"; gene_id "Phchi.S2G047500"
Phchi.S2	AUGUSTUS	start_codon	17114679	17114681	.	+	0	transcript_id "Phchi.S2G047500.t1"; gene_id "Phchi.S2G047500"
Phchi.S2	AUGUSTUS	CDS	17114679	17115038	0.62	+	0	transcript_id "Phchi.S2G047500.t1"; gene_id "Phchi.S2G047500"
Phchi.S2	AUGUSTUS	exon	17114679	17115038	.	+	.	transcript_id "Phchi.S2G047500.t1"; gene_id "Phchi.S2G047500"
Phchi.S2	AUGUSTUS	stop_codon	17115039	17115041	.	+	0	transcript_id "Phchi.S2G047500.t1"; gene_id "Phchi.S2G047500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4820.t1 is derived from g1990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13001339	13003538	.	+	.	Phchi.S1G197900
Phchi.S1	AUGUSTUS	transcript	13001339	13003538	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	start_codon	13001339	13001341	.	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13001339	13001404	0.66	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13001339	13001404	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13001405	13001489	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13001490	13001609	1	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13001490	13001609	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13001610	13001695	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13001696	13001774	0.72	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13001696	13001774	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13001775	13001877	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13001878	13001981	0.73	+	2	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13001878	13001981	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13001982	13002092	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13002093	13002155	0.78	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13002093	13002155	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13002156	13002256	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13002257	13002392	0.81	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13002257	13002392	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13002393	13002478	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13002479	13002598	1	+	2	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13002479	13002598	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13002599	13002698	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13002699	13002847	1	+	2	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13002699	13002847	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13002848	13002944	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13002945	13003022	0.98	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13002945	13003022	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13003023	13003156	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13003157	13003189	0.9	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13003157	13003189	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13003190	13003279	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13003280	13003360	0.9	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13003280	13003360	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	intron	13003361	13003445	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	CDS	13003446	13003538	0.9	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	exon	13003446	13003538	.	+	.	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
Phchi.S1	AUGUSTUS	stop_codon	13003539	13003541	.	+	0	transcript_id "Phchi.S1G197900.t1"; gene_id "Phchi.S1G197900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5370.t1 is derived from g2540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16533343	16534887	.	-	.	Phchi.S1G252900
Phchi.S1	AUGUSTUS	transcript	16533343	16534887	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	stop_codon	16533340	16533342	.	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16533343	16533744	1	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16533343	16533744	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	intron	16533745	16533854	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16533855	16533923	1	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16533855	16533923	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	intron	16533924	16534008	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16534009	16534074	1	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16534009	16534074	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	intron	16534075	16534162	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16534163	16534252	1	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16534163	16534252	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	intron	16534253	16534386	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16534387	16534432	1	-	1	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16534387	16534432	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	intron	16534433	16534553	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16534554	16534655	1	-	1	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16534554	16534655	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	intron	16534656	16534729	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	CDS	16534730	16534887	1	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	exon	16534730	16534887	.	-	.	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
Phchi.S1	AUGUSTUS	start_codon	16534885	16534887	.	-	0	transcript_id "Phchi.S1G252900.t1"; gene_id "Phchi.S1G252900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14193.t1 is derived from g12660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11406620	11408218	.	-	.	Phchi.S3G151200
Phchi.S3	AUGUSTUS	transcript	11406620	11408218	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	stop_codon	11406617	11406619	.	-	0	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	CDS	11406620	11406708	0.83	-	2	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	exon	11406620	11406708	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	intron	11406709	11406801	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	CDS	11406802	11407030	0.84	-	0	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	exon	11406802	11407030	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	intron	11407031	11407146	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	CDS	11407147	11407216	0.99	-	1	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	exon	11407147	11407216	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	intron	11407217	11407421	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	CDS	11407422	11408218	0.77	-	0	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	exon	11407422	11408218	.	-	.	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
Phchi.S3	AUGUSTUS	start_codon	11408216	11408218	.	-	0	transcript_id "Phchi.S3G151200.t1"; gene_id "Phchi.S3G151200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7920.t1 is derived from g5094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31911816	31914663	.	+	.	Phchi.S1G507900
Phchi.S1	AUGUSTUS	transcript	31911816	31914663	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	start_codon	31911816	31911818	.	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31911816	31912307	0.54	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31911816	31912307	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31912308	31912424	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31912425	31912652	1	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31912425	31912652	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31912653	31912742	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31912743	31913078	0.99	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31912743	31913078	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31913079	31913186	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31913187	31913742	0.95	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31913187	31913742	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31913743	31913827	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31913828	31914014	1	+	2	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31913828	31914014	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31914015	31914104	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31914105	31914248	0.83	+	1	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31914105	31914248	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31914249	31914337	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31914338	31914470	0.84	+	1	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31914338	31914470	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	intron	31914471	31914546	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	CDS	31914547	31914663	1	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	exon	31914547	31914663	.	+	.	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
Phchi.S1	AUGUSTUS	stop_codon	31914664	31914666	.	+	0	transcript_id "Phchi.S1G507900.t1"; gene_id "Phchi.S1G507900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg894.t1 is derived from g10676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6340604	6346477	.	-	.	Phchi.S6G085300
Phchi.S6	AUGUSTUS	transcript	6340604	6346477	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	stop_codon	6340601	6340603	.	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6340604	6341044	0.33	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6340604	6341044	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6341045	6341191	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6341192	6341404	1	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6341192	6341404	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6341405	6341539	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6341540	6342415	0.85	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6341540	6342415	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6342416	6342549	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6342550	6342713	0.59	-	2	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6342550	6342713	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6342714	6342817	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6342818	6342929	0.75	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6342818	6342929	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6342930	6343044	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6343045	6343839	0.97	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6343045	6343839	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6343840	6343929	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6343930	6344037	1	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6343930	6344037	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6344038	6344207	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6344208	6344576	1	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6344208	6344576	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6344577	6344704	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6344705	6344830	1	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6344705	6344830	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6344831	6344913	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6344914	6345114	1	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6344914	6345114	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6345115	6345270	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6345271	6345463	0.98	-	1	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6345271	6345463	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6345464	6345593	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6345594	6345717	0.49	-	2	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6345594	6345717	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6345718	6345826	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6345827	6345986	0.49	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6345827	6345986	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6345987	6346062	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6346063	6346150	1	-	1	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6346063	6346150	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6346151	6346228	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6346229	6346331	1	-	2	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6346229	6346331	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	intron	6346332	6346410	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	CDS	6346411	6346477	0.85	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	exon	6346411	6346477	.	-	.	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
Phchi.S6	AUGUSTUS	start_codon	6346475	6346477	.	-	0	transcript_id "Phchi.S6G085300.t1"; gene_id "Phchi.S6G085300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15244.t1 is derived from g13712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17884896	17885315	.	-	.	Phchi.S3G256300
Phchi.S3	AUGUSTUS	transcript	17884896	17885315	.	-	.	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	stop_codon	17884893	17884895	.	-	0	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	CDS	17884896	17884945	0.79	-	2	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	exon	17884896	17884945	.	-	.	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	intron	17884946	17885083	.	-	.	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	CDS	17885084	17885132	0.55	-	0	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	exon	17885084	17885132	.	-	.	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	intron	17885133	17885198	.	-	.	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	CDS	17885199	17885315	0.31	-	0	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	exon	17885199	17885315	.	-	.	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
Phchi.S3	AUGUSTUS	start_codon	17885313	17885315	.	-	0	transcript_id "Phchi.S3G256300.t1"; gene_id "Phchi.S3G256300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2172.t1 is derived from g9092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5171252	5171829	.	-	.	Phchi.S5G078100
Phchi.S5	AUGUSTUS	transcript	5171252	5171829	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	stop_codon	5171249	5171251	.	-	0	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171252	5171305	1	-	0	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171252	5171305	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	intron	5171306	5171401	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171402	5171424	1	-	2	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171402	5171424	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	intron	5171425	5171545	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171546	5171654	1	-	0	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171546	5171654	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	intron	5171655	5171742	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171743	5171829	1	-	0	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171743	5171829	.	-	.	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	start_codon	5171827	5171829	.	-	0	transcript_id "Phchi.S5G078100.t1"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	transcript	5171274	5171829	.	-	.	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	stop_codon	5171271	5171273	.	-	0	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171274	5171305	1	-	2	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171274	5171305	.	-	.	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	intron	5171306	5171545	.	-	.	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171546	5171654	1	-	0	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171546	5171654	.	-	.	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	intron	5171655	5171742	.	-	.	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	CDS	5171743	5171829	1	-	0	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	exon	5171743	5171829	.	-	.	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
Phchi.S5	AUGUSTUS	start_codon	5171827	5171829	.	-	0	transcript_id "Phchi.S5G078100.t2"; gene_id "Phchi.S5G078100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3290.t1 is derived from g459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2698454	2700101	.	-	.	Phchi.S1G044900
Phchi.S1	AUGUSTUS	transcript	2698454	2700101	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	stop_codon	2698451	2698453	.	-	0	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	CDS	2698454	2698724	0.77	-	1	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	exon	2698454	2698724	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	intron	2698725	2698897	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	CDS	2698898	2699286	0.34	-	0	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	exon	2698898	2699286	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	intron	2699287	2699480	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	CDS	2699481	2699563	0.94	-	2	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	exon	2699481	2699563	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	intron	2699564	2699775	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	CDS	2699776	2699817	0.94	-	2	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	exon	2699776	2699817	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	intron	2699818	2699890	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	CDS	2699891	2699927	0.75	-	0	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	exon	2699891	2699927	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	intron	2699928	2700080	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	CDS	2700081	2700101	0.99	-	0	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	exon	2700081	2700101	.	-	.	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
Phchi.S1	AUGUSTUS	start_codon	2700099	2700101	.	-	0	transcript_id "Phchi.S1G044900.t1"; gene_id "Phchi.S1G044900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4078.t1 is derived from g1247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7665691	7666186	.	-	.	Phchi.S1G123700
Phchi.S1	AUGUSTUS	transcript	7665691	7666186	.	-	.	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	stop_codon	7665688	7665690	.	-	0	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	CDS	7665691	7665769	1	-	1	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	exon	7665691	7665769	.	-	.	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	intron	7665770	7665893	.	-	.	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	CDS	7665894	7666186	1	-	0	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	exon	7665894	7666186	.	-	.	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
Phchi.S1	AUGUSTUS	start_codon	7666184	7666186	.	-	0	transcript_id "Phchi.S1G123700.t1"; gene_id "Phchi.S1G123700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3632.t1 is derived from g801.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4859585	4864215	.	+	.	Phchi.S1G079100
Phchi.S1	AUGUSTUS	transcript	4859585	4864215	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	start_codon	4859585	4859587	.	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4859585	4859842	0.67	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4859585	4859842	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4859843	4860009	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860010	4860126	0.99	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860010	4860126	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860127	4860247	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860248	4860312	0.96	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860248	4860312	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860313	4860464	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860465	4860579	1	+	1	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860465	4860579	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860580	4860799	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860800	4860871	1	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860800	4860871	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860872	4860951	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860952	4861011	1	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860952	4861011	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861012	4861155	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4861156	4861331	0.86	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4861156	4861331	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861332	4861522	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4861523	4861591	0.79	+	1	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4861523	4861591	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861592	4861769	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4861770	4861898	0.87	+	1	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4861770	4861898	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861899	4862089	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862090	4862220	1	+	1	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862090	4862220	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4862221	4862410	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862411	4862548	0.55	+	2	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862411	4862548	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4862549	4862628	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862629	4862717	0.95	+	2	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862629	4862717	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4862718	4862811	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862812	4863061	1	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862812	4863061	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4863062	4863169	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4863170	4863316	0.98	+	2	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4863170	4863316	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4863317	4863586	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4863587	4864215	0.97	+	2	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4863587	4864215	.	+	.	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	stop_codon	4864216	4864218	.	+	0	transcript_id "Phchi.S1G079100.t1"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	transcript	4859585	4864215	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	start_codon	4859585	4859587	.	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4859585	4859842	0.66	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4859585	4859842	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4859843	4860009	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860010	4860126	1	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860010	4860126	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860127	4860247	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860248	4860312	0.95	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860248	4860312	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860313	4860464	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860465	4860579	1	+	1	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860465	4860579	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860580	4860799	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860800	4860871	1	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860800	4860871	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4860872	4860951	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4860952	4861011	1	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4860952	4861011	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861012	4861155	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4861156	4861285	0.83	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4861156	4861285	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861286	4861406	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4861407	4861591	0.61	+	2	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4861407	4861591	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861592	4861704	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4861705	4861898	0.92	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4861705	4861898	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4861899	4862089	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862090	4862220	1	+	1	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862090	4862220	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4862221	4862410	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862411	4862548	0.46	+	2	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862411	4862548	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4862549	4862628	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862629	4862717	0.92	+	2	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862629	4862717	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4862718	4862811	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4862812	4863061	0.99	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4862812	4863061	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4863062	4863169	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4863170	4863316	0.99	+	2	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4863170	4863316	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	intron	4863317	4863586	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	CDS	4863587	4864215	0.93	+	2	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	exon	4863587	4864215	.	+	.	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
Phchi.S1	AUGUSTUS	stop_codon	4864216	4864218	.	+	0	transcript_id "Phchi.S1G079100.t2"; gene_id "Phchi.S1G079100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4651.t1 is derived from g1821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11642896	11643201	.	-	.	Phchi.S1G181000
Phchi.S1	AUGUSTUS	transcript	11642896	11643201	.	-	.	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	stop_codon	11642893	11642895	.	-	0	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	CDS	11642896	11642932	0.98	-	1	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	exon	11642896	11642932	.	-	.	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	intron	11642933	11643016	.	-	.	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	CDS	11643017	11643201	0.73	-	0	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	exon	11643017	11643201	.	-	.	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
Phchi.S1	AUGUSTUS	start_codon	11643199	11643201	.	-	0	transcript_id "Phchi.S1G181000.t1"; gene_id "Phchi.S1G181000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2023.t1 is derived from g8943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4491525	4494520	.	+	.	Phchi.S5G063200
Phchi.S5	AUGUSTUS	transcript	4491525	4494520	.	+	.	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	start_codon	4491525	4491527	.	+	0	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	CDS	4491525	4493756	0.99	+	0	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	exon	4491525	4493756	.	+	.	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	intron	4493757	4493865	.	+	.	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	CDS	4493866	4494063	1	+	0	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	exon	4493866	4494063	.	+	.	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	intron	4494064	4494160	.	+	.	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	CDS	4494161	4494520	1	+	0	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	exon	4494161	4494520	.	+	.	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
Phchi.S5	AUGUSTUS	stop_codon	4494521	4494523	.	+	0	transcript_id "Phchi.S5G063200.t1"; gene_id "Phchi.S5G063200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6974.t1 is derived from g4146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26241026	26242982	.	+	.	Phchi.S1G413300
Phchi.S1	AUGUSTUS	transcript	26241026	26242982	.	+	.	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	start_codon	26241026	26241028	.	+	0	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	CDS	26241026	26241247	0.97	+	0	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	exon	26241026	26241247	.	+	.	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	intron	26241248	26241348	.	+	.	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	CDS	26241349	26242328	0.75	+	0	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	exon	26241349	26242328	.	+	.	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	intron	26242329	26242420	.	+	.	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	CDS	26242421	26242982	0.99	+	1	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	exon	26242421	26242982	.	+	.	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
Phchi.S1	AUGUSTUS	stop_codon	26242983	26242985	.	+	0	transcript_id "Phchi.S1G413300.t1"; gene_id "Phchi.S1G413300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5737.t1 is derived from g2907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18618435	18621320	.	-	.	Phchi.S1G289600
Phchi.S1	AUGUSTUS	transcript	18618435	18621320	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	stop_codon	18618432	18618434	.	-	0	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	CDS	18618435	18618583	0.46	-	2	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	exon	18618435	18618583	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	intron	18618584	18618673	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	CDS	18618674	18619035	0.59	-	1	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	exon	18618674	18619035	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	intron	18619036	18619647	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	CDS	18619648	18619801	0.82	-	2	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	exon	18619648	18619801	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	intron	18619802	18619912	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	CDS	18619913	18620029	0.78	-	2	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	exon	18619913	18620029	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	intron	18620030	18620368	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	CDS	18620369	18621320	0.95	-	0	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	exon	18620369	18621320	.	-	.	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
Phchi.S1	AUGUSTUS	start_codon	18621318	18621320	.	-	0	transcript_id "Phchi.S1G289600.t1"; gene_id "Phchi.S1G289600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg472.t1 is derived from g10254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3315249	3316479	.	-	.	Phchi.S6G043100
Phchi.S6	AUGUSTUS	transcript	3315249	3316479	.	-	.	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	stop_codon	3315246	3315248	.	-	0	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	CDS	3315249	3315611	0.38	-	0	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	exon	3315249	3315611	.	-	.	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	intron	3315612	3315760	.	-	.	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	CDS	3315761	3316093	0.56	-	0	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	exon	3315761	3316093	.	-	.	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	intron	3316094	3316161	.	-	.	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	CDS	3316162	3316479	0.4	-	0	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	exon	3316162	3316479	.	-	.	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
Phchi.S6	AUGUSTUS	start_codon	3316477	3316479	.	-	0	transcript_id "Phchi.S6G043100.t1"; gene_id "Phchi.S6G043100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4090.t1 is derived from g1259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7752940	7755138	.	+	.	Phchi.S1G124900
Phchi.S1	AUGUSTUS	transcript	7752940	7755138	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	start_codon	7752940	7752942	.	+	0	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	CDS	7752940	7753539	0.79	+	0	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	exon	7752940	7753539	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	intron	7753540	7753651	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	CDS	7753652	7753819	1	+	0	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	exon	7753652	7753819	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	intron	7753820	7754058	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	CDS	7754059	7754335	1	+	0	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	exon	7754059	7754335	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	intron	7754336	7754825	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	CDS	7754826	7754952	1	+	2	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	exon	7754826	7754952	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	intron	7754953	7755044	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	CDS	7755045	7755138	1	+	1	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	exon	7755045	7755138	.	+	.	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
Phchi.S1	AUGUSTUS	stop_codon	7755139	7755141	.	+	0	transcript_id "Phchi.S1G124900.t1"; gene_id "Phchi.S1G124900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10369.t1 is derived from g7545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47408763	47409338	.	-	.	Phchi.S1G752800
Phchi.S1	AUGUSTUS	transcript	47408763	47409338	.	-	.	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	stop_codon	47408760	47408762	.	-	0	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	CDS	47408763	47409160	1	-	2	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	exon	47408763	47409160	.	-	.	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	intron	47409161	47409325	.	-	.	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	CDS	47409326	47409338	0.99	-	0	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	exon	47409326	47409338	.	-	.	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
Phchi.S1	AUGUSTUS	start_codon	47409336	47409338	.	-	0	transcript_id "Phchi.S1G752800.t1"; gene_id "Phchi.S1G752800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15538.t1 is derived from g14007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19773439	19774978	.	+	.	Phchi.S3G285700
Phchi.S3	AUGUSTUS	transcript	19773439	19774978	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	start_codon	19773439	19773441	.	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773439	19773492	0.99	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773439	19773492	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773493	19773574	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773575	19773669	1	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773575	19773669	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773670	19773779	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773780	19773996	1	+	1	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773780	19773996	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773997	19774114	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774115	19774240	1	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774115	19774240	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19774241	19774324	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774325	19774423	1	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774325	19774423	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19774424	19774541	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774542	19774751	1	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774542	19774751	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19774752	19774837	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774838	19774978	0.98	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774838	19774978	.	+	.	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	stop_codon	19774979	19774981	.	+	0	transcript_id "Phchi.S3G285700.t1"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	transcript	19773439	19774978	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	start_codon	19773439	19773441	.	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773439	19773492	0.98	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773439	19773492	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773493	19773574	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773575	19773669	1	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773575	19773669	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773670	19773760	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773761	19773835	0.84	+	1	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773761	19773835	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773836	19773941	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19773942	19773996	0.84	+	1	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19773942	19773996	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19773997	19774114	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774115	19774240	1	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774115	19774240	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19774241	19774324	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774325	19774423	1	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774325	19774423	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19774424	19774541	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774542	19774751	1	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774542	19774751	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	intron	19774752	19774837	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	CDS	19774838	19774978	0.94	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	exon	19774838	19774978	.	+	.	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
Phchi.S3	AUGUSTUS	stop_codon	19774979	19774981	.	+	0	transcript_id "Phchi.S3G285700.t2"; gene_id "Phchi.S3G285700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15864.t1 is derived from g14334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21932187	21933130	.	+	.	Phchi.S3G318300
Phchi.S3	AUGUSTUS	transcript	21932187	21933130	.	+	.	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	start_codon	21932187	21932189	.	+	0	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	CDS	21932187	21932480	0.82	+	0	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	exon	21932187	21932480	.	+	.	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	intron	21932481	21932629	.	+	.	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	CDS	21932630	21933130	1	+	0	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	exon	21932630	21933130	.	+	.	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
Phchi.S3	AUGUSTUS	stop_codon	21933131	21933133	.	+	0	transcript_id "Phchi.S3G318300.t1"; gene_id "Phchi.S3G318300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg305.t1 is derived from g10087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2157275	2159076	.	+	.	Phchi.S6G026400
Phchi.S6	AUGUSTUS	transcript	2157275	2159076	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	start_codon	2157275	2157277	.	+	0	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2157275	2157284	0.69	+	0	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2157275	2157284	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2157285	2157368	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2157369	2157492	0.69	+	2	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2157369	2157492	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2157493	2157567	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2157568	2157678	0.99	+	1	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2157568	2157678	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2157679	2157817	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2157818	2157941	0.99	+	1	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2157818	2157941	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2157942	2158060	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2158061	2158251	0.87	+	0	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2158061	2158251	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2158252	2158385	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2158386	2158484	0.24	+	1	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2158386	2158484	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2158485	2158591	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2158592	2158701	0.61	+	1	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2158592	2158701	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	intron	2158702	2158906	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	CDS	2158907	2159076	0.95	+	2	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	exon	2158907	2159076	.	+	.	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
Phchi.S6	AUGUSTUS	stop_codon	2159077	2159079	.	+	0	transcript_id "Phchi.S6G026400.t1"; gene_id "Phchi.S6G026400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14985.t1 is derived from g13453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15890131	15890793	.	-	.	Phchi.S3G230400
Phchi.S3	AUGUSTUS	transcript	15890131	15890793	.	-	.	transcript_id "Phchi.S3G230400.t1"; gene_id "Phchi.S3G230400"
Phchi.S3	AUGUSTUS	stop_codon	15890128	15890130	.	-	0	transcript_id "Phchi.S3G230400.t1"; gene_id "Phchi.S3G230400"
Phchi.S3	AUGUSTUS	CDS	15890131	15890793	0.78	-	0	transcript_id "Phchi.S3G230400.t1"; gene_id "Phchi.S3G230400"
Phchi.S3	AUGUSTUS	exon	15890131	15890793	.	-	.	transcript_id "Phchi.S3G230400.t1"; gene_id "Phchi.S3G230400"
Phchi.S3	AUGUSTUS	start_codon	15890791	15890793	.	-	0	transcript_id "Phchi.S3G230400.t1"; gene_id "Phchi.S3G230400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5453.t1 is derived from g2623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16921305	16922120	.	-	.	Phchi.S1G261200
Phchi.S1	AUGUSTUS	transcript	16921305	16922120	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	stop_codon	16921302	16921304	.	-	0	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	CDS	16921305	16921481	1	-	0	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	exon	16921305	16921481	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	intron	16921482	16921577	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	CDS	16921578	16921623	1	-	1	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	exon	16921578	16921623	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	intron	16921624	16921702	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	CDS	16921703	16921871	1	-	2	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	exon	16921703	16921871	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	intron	16921872	16921999	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	CDS	16922000	16922120	0.58	-	0	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	exon	16922000	16922120	.	-	.	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
Phchi.S1	AUGUSTUS	start_codon	16922118	16922120	.	-	0	transcript_id "Phchi.S1G261200.t1"; gene_id "Phchi.S1G261200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1025.t1 is derived from g10808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7172621	7173140	.	+	.	Phchi.S6G098400
Phchi.S6	AUGUSTUS	transcript	7172621	7173140	.	+	.	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	start_codon	7172621	7172623	.	+	0	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	CDS	7172621	7172785	0.22	+	0	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	exon	7172621	7172785	.	+	.	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	intron	7172786	7172876	.	+	.	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	CDS	7172877	7173140	0.24	+	0	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	exon	7172877	7173140	.	+	.	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
Phchi.S6	AUGUSTUS	stop_codon	7173141	7173143	.	+	0	transcript_id "Phchi.S6G098400.t1"; gene_id "Phchi.S6G098400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8310.t1 is derived from g5485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35227211	35227486	.	-	.	Phchi.S1G546900
Phchi.S1	AUGUSTUS	transcript	35227211	35227486	.	-	.	transcript_id "Phchi.S1G546900.t1"; gene_id "Phchi.S1G546900"
Phchi.S1	AUGUSTUS	stop_codon	35227208	35227210	.	-	0	transcript_id "Phchi.S1G546900.t1"; gene_id "Phchi.S1G546900"
Phchi.S1	AUGUSTUS	CDS	35227211	35227486	0.74	-	0	transcript_id "Phchi.S1G546900.t1"; gene_id "Phchi.S1G546900"
Phchi.S1	AUGUSTUS	exon	35227211	35227486	.	-	.	transcript_id "Phchi.S1G546900.t1"; gene_id "Phchi.S1G546900"
Phchi.S1	AUGUSTUS	start_codon	35227484	35227486	.	-	0	transcript_id "Phchi.S1G546900.t1"; gene_id "Phchi.S1G546900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10192.t1 is derived from g7368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46248998	46254141	.	-	.	Phchi.S1G735100
Phchi.S1	AUGUSTUS	transcript	46248998	46254141	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	stop_codon	46248995	46248997	.	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46248998	46252208	0.99	-	1	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46248998	46252208	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46252209	46252298	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46252299	46252618	1	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46252299	46252618	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46252619	46252695	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46252696	46252791	0.58	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46252696	46252791	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46252792	46252919	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46252920	46253051	0.88	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46252920	46253051	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253052	46253141	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46253142	46253262	1	-	1	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46253142	46253262	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253263	46253347	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46253348	46253481	0.94	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46253348	46253481	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253482	46253614	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46253615	46253625	0.85	-	2	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46253615	46253625	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253626	46253717	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46253718	46253728	0.99	-	1	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46253718	46253728	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253729	46253778	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46253779	46253784	0.99	-	1	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46253779	46253784	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253785	46253883	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46253884	46253937	1	-	1	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46253884	46253937	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	intron	46253938	46254109	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	CDS	46254110	46254141	1	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	exon	46254110	46254141	.	-	.	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
Phchi.S1	AUGUSTUS	start_codon	46254139	46254141	.	-	0	transcript_id "Phchi.S1G735100.t1"; gene_id "Phchi.S1G735100"
# This transcript jg6278.t2 is derived from g3450.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg6279.t1 is derived from g3451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22058245	22064568	.	+	.	Phchi.S1G343800
Phchi.S1	AUGUSTUS	transcript	22060715	22064568	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	start_codon	22060715	22060717	.	+	0	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060715	22060721	0.68	+	0	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060715	22060721	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060722	22060813	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060814	22060990	0.82	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060814	22060990	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060991	22061511	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061512	22061555	1	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061512	22061555	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061556	22061651	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061652	22061761	1	+	0	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061652	22061761	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061762	22061879	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061880	22061917	1	+	1	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061880	22061917	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061918	22062125	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062126	22062203	1	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062126	22062203	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062204	22062360	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062361	22062414	1	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062361	22062414	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062415	22062510	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062511	22062612	1	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062511	22062612	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062613	22062699	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062700	22062761	0.84	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062700	22062761	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062762	22062907	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062908	22063011	1	+	0	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062908	22063011	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063012	22063117	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063118	22063186	1	+	1	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063118	22063186	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063187	22063279	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063280	22063395	1	+	1	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063280	22063395	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063396	22063490	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063491	22063525	1	+	2	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063491	22063525	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063526	22063658	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063659	22063801	1	+	0	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063659	22063801	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063802	22063902	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063903	22064025	1	+	1	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063903	22064025	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064026	22064141	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064142	22064237	1	+	1	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064142	22064237	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064238	22064561	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064562	22064568	1	+	1	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064562	22064568	.	+	.	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	stop_codon	22064569	22064571	.	+	0	transcript_id "Phchi.S1G343800.t1"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	transcript	22058245	22064568	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	start_codon	22058245	22058247	.	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22058245	22059625	0.55	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22058245	22059625	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22059626	22059901	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22059902	22059979	0.33	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22059902	22059979	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22059980	22060225	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060226	22060425	0.36	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060226	22060425	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060426	22060597	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060598	22060652	0.8	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060598	22060652	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060653	22060813	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060814	22060990	0.92	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060814	22060990	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060991	22061511	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061512	22061555	1	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061512	22061555	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061556	22061651	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061652	22061761	1	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061652	22061761	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061762	22061879	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061880	22061917	1	+	1	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061880	22061917	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061918	22062125	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062126	22062203	1	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062126	22062203	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062204	22062360	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062361	22062414	1	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062361	22062414	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062415	22062510	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062511	22062612	1	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062511	22062612	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062613	22062699	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062700	22062761	0.87	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062700	22062761	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062762	22062907	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062908	22063011	1	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062908	22063011	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063012	22063117	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063118	22063186	1	+	1	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063118	22063186	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063187	22063279	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063280	22063395	1	+	1	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063280	22063395	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063396	22063490	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063491	22063525	1	+	2	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063491	22063525	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063526	22063658	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063659	22063801	1	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063659	22063801	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063802	22063902	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063903	22064025	1	+	1	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063903	22064025	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064026	22064141	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064142	22064237	1	+	1	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064142	22064237	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064238	22064561	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064562	22064568	1	+	1	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064562	22064568	.	+	.	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	stop_codon	22064569	22064571	.	+	0	transcript_id "Phchi.S1G343800.t2"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	transcript	22058422	22064568	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	start_codon	22058422	22058424	.	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22058422	22059625	0.48	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22058422	22059625	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22059626	22059901	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22059902	22059979	0.35	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22059902	22059979	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22059980	22060225	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060226	22060425	0.34	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060226	22060425	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060426	22060597	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060598	22060652	0.62	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060598	22060652	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060653	22060813	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060814	22060990	0.95	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060814	22060990	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060991	22061511	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061512	22061555	1	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061512	22061555	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061556	22061651	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061652	22061761	1	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061652	22061761	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061762	22061879	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061880	22061917	1	+	1	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061880	22061917	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061918	22062125	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062126	22062203	1	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062126	22062203	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062204	22062360	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062361	22062414	1	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062361	22062414	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062415	22062510	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062511	22062612	1	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062511	22062612	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062613	22062699	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062700	22062761	0.9	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062700	22062761	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062762	22062907	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062908	22063011	1	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062908	22063011	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063012	22063117	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063118	22063186	1	+	1	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063118	22063186	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063187	22063279	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063280	22063395	1	+	1	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063280	22063395	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063396	22063490	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063491	22063525	1	+	2	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063491	22063525	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063526	22063658	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063659	22063801	1	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063659	22063801	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063802	22063902	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063903	22064025	1	+	1	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063903	22064025	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064026	22064141	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064142	22064237	1	+	1	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064142	22064237	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064238	22064561	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064562	22064568	1	+	1	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064562	22064568	.	+	.	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	stop_codon	22064569	22064571	.	+	0	transcript_id "Phchi.S1G343800.t3"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	transcript	22058422	22064568	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	start_codon	22058422	22058424	.	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22058422	22059625	0.47	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22058422	22059625	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22059626	22059901	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22059902	22059979	0.32	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22059902	22059979	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22059980	22060225	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060226	22060425	0.33	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060226	22060425	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060426	22060597	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060598	22060652	0.64	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060598	22060652	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060653	22060813	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22060814	22060990	0.93	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22060814	22060990	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22060991	22061511	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061512	22061555	1	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061512	22061555	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061556	22061651	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061652	22061761	1	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061652	22061761	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061762	22061879	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22061880	22061917	1	+	1	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22061880	22061917	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22061918	22062125	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062126	22062203	1	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062126	22062203	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062204	22062360	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062361	22062414	1	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062361	22062414	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062415	22062510	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062511	22062612	0.86	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062511	22062612	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062613	22062713	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062714	22062802	0.87	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062714	22062802	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22062803	22062907	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22062908	22063011	1	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22062908	22063011	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063012	22063117	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063118	22063186	1	+	1	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063118	22063186	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063187	22063279	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063280	22063395	1	+	1	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063280	22063395	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063396	22063490	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063491	22063525	1	+	2	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063491	22063525	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063526	22063658	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063659	22063801	1	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063659	22063801	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22063802	22063902	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22063903	22064025	1	+	1	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22063903	22064025	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064026	22064141	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064142	22064237	1	+	1	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064142	22064237	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	intron	22064238	22064561	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	CDS	22064562	22064568	1	+	1	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	exon	22064562	22064568	.	+	.	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
Phchi.S1	AUGUSTUS	stop_codon	22064569	22064571	.	+	0	transcript_id "Phchi.S1G343800.t4"; gene_id "Phchi.S1G343800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14287.t1 is derived from g12754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11923313	11924835	.	+	.	Phchi.S3G160600
Phchi.S3	AUGUSTUS	transcript	11923313	11924835	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	start_codon	11923313	11923315	.	+	0	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	CDS	11923313	11923699	0.57	+	0	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	exon	11923313	11923699	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	intron	11923700	11923831	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	CDS	11923832	11923899	1	+	0	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	exon	11923832	11923899	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	intron	11923900	11923988	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	CDS	11923989	11924225	1	+	1	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	exon	11923989	11924225	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	intron	11924226	11924347	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	CDS	11924348	11924480	1	+	1	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	exon	11924348	11924480	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	intron	11924481	11924580	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	CDS	11924581	11924835	1	+	0	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	exon	11924581	11924835	.	+	.	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
Phchi.S3	AUGUSTUS	stop_codon	11924836	11924838	.	+	0	transcript_id "Phchi.S3G160600.t1"; gene_id "Phchi.S3G160600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5450.t1 is derived from g2620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16912608	16917893	.	+	.	Phchi.S1G260900
Phchi.S1	AUGUSTUS	transcript	16912608	16917893	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	start_codon	16912608	16912610	.	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16912608	16912691	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16912608	16912691	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16912692	16912841	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16912842	16912961	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16912842	16912961	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16912962	16913144	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16913145	16913243	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16913145	16913243	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16913244	16913336	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16913337	16913474	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16913337	16913474	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16913475	16913642	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16913643	16913777	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16913643	16913777	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16913778	16913884	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16913885	16914064	0.95	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16913885	16914064	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16914065	16914188	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16914189	16914395	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16914189	16914395	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16914396	16914546	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16914547	16914666	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16914547	16914666	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16914667	16914797	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16914798	16914974	0.67	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16914798	16914974	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16914975	16915048	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16915049	16915171	0.99	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16915049	16915171	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16915172	16915464	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16915465	16915609	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16915465	16915609	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16915610	16915726	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16915727	16915891	1	+	2	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16915727	16915891	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16915892	16915984	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16915985	16916223	0.75	+	2	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16915985	16916223	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16916224	16916337	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16916338	16916370	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16916338	16916370	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16916371	16916518	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16916519	16916600	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16916519	16916600	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16916601	16916713	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16916714	16916874	1	+	2	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16916714	16916874	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16916875	16916983	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16916984	16917172	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16916984	16917172	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16917173	16917256	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16917257	16917439	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16917257	16917439	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16917440	16917529	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16917530	16917708	1	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16917530	16917708	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	intron	16917709	16917799	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	CDS	16917800	16917893	1	+	1	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	exon	16917800	16917893	.	+	.	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
Phchi.S1	AUGUSTUS	stop_codon	16917894	16917896	.	+	0	transcript_id "Phchi.S1G260900.t1"; gene_id "Phchi.S1G260900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3200.t1 is derived from g369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2210961	2212455	.	-	.	Phchi.S1G035900
Phchi.S1	AUGUSTUS	transcript	2210961	2212455	.	-	.	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	stop_codon	2210958	2210960	.	-	0	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	CDS	2210961	2211813	1	-	1	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	exon	2210961	2211813	.	-	.	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	intron	2211814	2211908	.	-	.	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	CDS	2211909	2212231	1	-	0	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	exon	2211909	2212231	.	-	.	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	intron	2212232	2212314	.	-	.	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	CDS	2212315	2212455	1	-	0	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	exon	2212315	2212455	.	-	.	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
Phchi.S1	AUGUSTUS	start_codon	2212453	2212455	.	-	0	transcript_id "Phchi.S1G035900.t1"; gene_id "Phchi.S1G035900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2260.t1 is derived from g9180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5718069	5719229	.	-	.	Phchi.S5G086900
Phchi.S5	AUGUSTUS	transcript	5718069	5719229	.	-	.	transcript_id "Phchi.S5G086900.t1"; gene_id "Phchi.S5G086900"
Phchi.S5	AUGUSTUS	stop_codon	5718066	5718068	.	-	0	transcript_id "Phchi.S5G086900.t1"; gene_id "Phchi.S5G086900"
Phchi.S5	AUGUSTUS	CDS	5718069	5719229	1	-	0	transcript_id "Phchi.S5G086900.t1"; gene_id "Phchi.S5G086900"
Phchi.S5	AUGUSTUS	exon	5718069	5719229	.	-	.	transcript_id "Phchi.S5G086900.t1"; gene_id "Phchi.S5G086900"
Phchi.S5	AUGUSTUS	start_codon	5719227	5719229	.	-	0	transcript_id "Phchi.S5G086900.t1"; gene_id "Phchi.S5G086900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1396.t1 is derived from g8315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	36755	37543	.	+	.	Phchi.S5G000500
Phchi.S5	AUGUSTUS	transcript	36755	37543	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	start_codon	36755	36757	.	+	0	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	CDS	36755	36778	0.94	+	0	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	exon	36755	36778	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	intron	36779	36982	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	CDS	36983	37020	0.99	+	0	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	exon	36983	37020	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	intron	37021	37109	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	CDS	37110	37192	1	+	1	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	exon	37110	37192	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	intron	37193	37334	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	CDS	37335	37543	0.4	+	2	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	exon	37335	37543	.	+	.	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
Phchi.S5	AUGUSTUS	stop_codon	37544	37546	.	+	0	transcript_id "Phchi.S5G000500.t1"; gene_id "Phchi.S5G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15982.t1 is derived from g15990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C20	AUGUSTUS	gene	14972	15568	.	+	.	Phchi.C20G000200
Phchi.C20	AUGUSTUS	transcript	14972	15568	.	+	.	transcript_id "Phchi.C20G000200.t1"; gene_id "Phchi.C20G000200"
Phchi.C20	AUGUSTUS	start_codon	14972	14974	.	+	0	transcript_id "Phchi.C20G000200.t1"; gene_id "Phchi.C20G000200"
Phchi.C20	AUGUSTUS	CDS	14972	15568	1	+	0	transcript_id "Phchi.C20G000200.t1"; gene_id "Phchi.C20G000200"
Phchi.C20	AUGUSTUS	exon	14972	15568	.	+	.	transcript_id "Phchi.C20G000200.t1"; gene_id "Phchi.C20G000200"
Phchi.C20	AUGUSTUS	stop_codon	15569	15571	.	+	0	transcript_id "Phchi.C20G000200.t1"; gene_id "Phchi.C20G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6591.t1 is derived from g3763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23904046	23906214	.	+	.	Phchi.S1G375000
Phchi.S1	AUGUSTUS	transcript	23904046	23906214	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	start_codon	23904046	23904048	.	+	0	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	CDS	23904046	23905283	0.53	+	0	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	exon	23904046	23905283	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	intron	23905284	23905494	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	CDS	23905495	23905636	0.79	+	1	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	exon	23905495	23905636	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	intron	23905637	23905720	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	CDS	23905721	23905930	0.8	+	0	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	exon	23905721	23905930	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	intron	23905931	23906151	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	CDS	23906152	23906214	0.4	+	0	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	exon	23906152	23906214	.	+	.	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
Phchi.S1	AUGUSTUS	stop_codon	23906215	23906217	.	+	0	transcript_id "Phchi.S1G375000.t1"; gene_id "Phchi.S1G375000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10738.t1 is derived from g14788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1864020	1864609	.	-	.	Phchi.S4G032000
Phchi.S4	AUGUSTUS	transcript	1864020	1864609	.	-	.	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	stop_codon	1864017	1864019	.	-	0	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	CDS	1864020	1864309	0.97	-	2	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	exon	1864020	1864309	.	-	.	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	intron	1864310	1864404	.	-	.	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	CDS	1864405	1864609	1	-	0	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	exon	1864405	1864609	.	-	.	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
Phchi.S4	AUGUSTUS	start_codon	1864607	1864609	.	-	0	transcript_id "Phchi.S4G032000.t1"; gene_id "Phchi.S4G032000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11462.t1 is derived from g15512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6484551	6484931	.	+	.	Phchi.S4G104400
Phchi.S4	AUGUSTUS	transcript	6484551	6484931	.	+	.	transcript_id "Phchi.S4G104400.t1"; gene_id "Phchi.S4G104400"
Phchi.S4	AUGUSTUS	start_codon	6484551	6484553	.	+	0	transcript_id "Phchi.S4G104400.t1"; gene_id "Phchi.S4G104400"
Phchi.S4	AUGUSTUS	CDS	6484551	6484931	1	+	0	transcript_id "Phchi.S4G104400.t1"; gene_id "Phchi.S4G104400"
Phchi.S4	AUGUSTUS	exon	6484551	6484931	.	+	.	transcript_id "Phchi.S4G104400.t1"; gene_id "Phchi.S4G104400"
Phchi.S4	AUGUSTUS	stop_codon	6484932	6484934	.	+	0	transcript_id "Phchi.S4G104400.t1"; gene_id "Phchi.S4G104400"
# This transcript jg2211.t2 is derived from g9131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2212.t1 is derived from g9132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5435599	5437263	.	+	.	Phchi.S5G082100
Phchi.S5	AUGUSTUS	transcript	5435599	5437263	.	+	.	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	start_codon	5435599	5435601	.	+	0	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	CDS	5435599	5435758	0.45	+	0	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	exon	5435599	5435758	.	+	.	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	intron	5435759	5435884	.	+	.	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	CDS	5435885	5436475	1	+	2	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	exon	5435885	5436475	.	+	.	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	intron	5436476	5436601	.	+	.	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	CDS	5436602	5437263	0.99	+	2	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	exon	5436602	5437263	.	+	.	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
Phchi.S5	AUGUSTUS	stop_codon	5437264	5437266	.	+	0	transcript_id "Phchi.S5G082100.t1"; gene_id "Phchi.S5G082100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4636.t1 is derived from g1806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11530078	11530656	.	+	.	Phchi.S1G179500
Phchi.S1	AUGUSTUS	transcript	11530078	11530656	.	+	.	transcript_id "Phchi.S1G179500.t1"; gene_id "Phchi.S1G179500"
Phchi.S1	AUGUSTUS	start_codon	11530078	11530080	.	+	0	transcript_id "Phchi.S1G179500.t1"; gene_id "Phchi.S1G179500"
Phchi.S1	AUGUSTUS	CDS	11530078	11530656	0.6	+	0	transcript_id "Phchi.S1G179500.t1"; gene_id "Phchi.S1G179500"
Phchi.S1	AUGUSTUS	exon	11530078	11530656	.	+	.	transcript_id "Phchi.S1G179500.t1"; gene_id "Phchi.S1G179500"
Phchi.S1	AUGUSTUS	stop_codon	11530657	11530659	.	+	0	transcript_id "Phchi.S1G179500.t1"; gene_id "Phchi.S1G179500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg250.t1 is derived from g10032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1706893	1712342	.	+	.	Phchi.S6G020900
Phchi.S6	AUGUSTUS	transcript	1706893	1712342	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	start_codon	1706893	1706895	.	+	0	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1706893	1707189	0.31	+	0	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1706893	1707189	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707190	1707321	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1707322	1707392	0.32	+	0	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1707322	1707392	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707393	1707513	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1707514	1707607	0.29	+	1	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1707514	1707607	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707608	1707863	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1707864	1707903	0.79	+	0	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1707864	1707903	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707904	1708096	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1708097	1710148	0.68	+	2	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1708097	1710148	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1710149	1710508	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1710509	1711422	1	+	2	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1710509	1711422	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1711423	1711776	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1711777	1711829	1	+	0	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1711777	1711829	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1711830	1712050	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1712051	1712342	0.57	+	1	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1712051	1712342	.	+	.	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	stop_codon	1712343	1712345	.	+	0	transcript_id "Phchi.S6G020900.t1"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	transcript	1706893	1710250	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	start_codon	1706893	1706895	.	+	0	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1706893	1707189	0.24	+	0	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1706893	1707189	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707190	1707321	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1707322	1707392	0.35	+	0	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1707322	1707392	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707393	1707513	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1707514	1707607	0.34	+	1	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1707514	1707607	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707608	1707863	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1707864	1707903	0.84	+	0	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1707864	1707903	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1707904	1708096	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1708097	1710148	0.71	+	2	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1708097	1710148	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	intron	1710149	1710233	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	CDS	1710234	1710250	0.93	+	2	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	exon	1710234	1710250	.	+	.	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
Phchi.S6	AUGUSTUS	stop_codon	1710251	1710253	.	+	0	transcript_id "Phchi.S6G020900.t2"; gene_id "Phchi.S6G020900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg266.t1 is derived from g10048.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1908396	1910601	.	-	.	Phchi.S6G022500
Phchi.S6	AUGUSTUS	transcript	1908396	1910601	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	stop_codon	1908393	1908395	.	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1908396	1908704	0.69	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1908396	1908704	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1908705	1908799	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1908800	1908876	0.82	-	2	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1908800	1908876	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1908877	1909044	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909045	1909110	1	-	2	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909045	1909110	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1909111	1909196	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909197	1909374	1	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909197	1909374	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1909375	1909470	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909471	1909659	0.98	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909471	1909659	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1909660	1909763	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909764	1910066	0.93	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909764	1910066	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1910067	1910145	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1910146	1910315	1	-	2	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1910146	1910315	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1910316	1910399	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1910400	1910601	0.9	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1910400	1910601	.	-	.	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	start_codon	1910599	1910601	.	-	0	transcript_id "Phchi.S6G022500.t1"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	transcript	1908396	1910601	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	stop_codon	1908393	1908395	.	-	0	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1908396	1908808	0.68	-	2	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1908396	1908808	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1908809	1908905	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1908906	1908956	0.94	-	2	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1908906	1908956	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1908957	1909044	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909045	1909110	1	-	2	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909045	1909110	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1909111	1909196	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909197	1909374	1	-	0	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909197	1909374	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1909375	1909470	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909471	1909659	0.99	-	0	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909471	1909659	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1909660	1909763	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1909764	1910066	0.92	-	0	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1909764	1910066	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1910067	1910145	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1910146	1910315	1	-	2	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1910146	1910315	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	intron	1910316	1910399	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	CDS	1910400	1910601	0.81	-	0	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	exon	1910400	1910601	.	-	.	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
Phchi.S6	AUGUSTUS	start_codon	1910599	1910601	.	-	0	transcript_id "Phchi.S6G022500.t2"; gene_id "Phchi.S6G022500"
# This transcript jg9078.t2 is derived from g6253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9079.t1 is derived from g6254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39748649	39751415	.	-	.	Phchi.S1G623800
Phchi.S1	AUGUSTUS	transcript	39748649	39751415	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	stop_codon	39748646	39748648	.	-	0	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	CDS	39748649	39748881	0.99	-	2	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	exon	39748649	39748881	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	intron	39748882	39748957	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	CDS	39748958	39749020	0.68	-	2	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	exon	39748958	39749020	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	intron	39749021	39749159	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	CDS	39749160	39749491	0.35	-	1	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	exon	39749160	39749491	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	intron	39749492	39749631	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	CDS	39749632	39749966	0.36	-	0	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	exon	39749632	39749966	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	intron	39749967	39750102	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	CDS	39750103	39750480	0.97	-	0	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	exon	39750103	39750480	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	intron	39750481	39750569	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	CDS	39750570	39751415	0.69	-	0	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	exon	39750570	39751415	.	-	.	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
Phchi.S1	AUGUSTUS	start_codon	39751413	39751415	.	-	0	transcript_id "Phchi.S1G623800.t1"; gene_id "Phchi.S1G623800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8049.t1 is derived from g5224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32713546	32715769	.	+	.	Phchi.S1G520800
Phchi.S1	AUGUSTUS	transcript	32713546	32715769	.	+	.	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	start_codon	32713546	32713548	.	+	0	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	CDS	32713546	32714916	0.84	+	0	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	exon	32713546	32714916	.	+	.	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	intron	32714917	32715019	.	+	.	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	CDS	32715020	32715769	0.7	+	0	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	exon	32715020	32715769	.	+	.	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
Phchi.S1	AUGUSTUS	stop_codon	32715770	32715772	.	+	0	transcript_id "Phchi.S1G520800.t1"; gene_id "Phchi.S1G520800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11587.t1 is derived from g15638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7234131	7234643	.	-	.	Phchi.S4G116900
Phchi.S4	AUGUSTUS	transcript	7234131	7234643	.	-	.	transcript_id "Phchi.S4G116900.t1"; gene_id "Phchi.S4G116900"
Phchi.S4	AUGUSTUS	stop_codon	7234128	7234130	.	-	0	transcript_id "Phchi.S4G116900.t1"; gene_id "Phchi.S4G116900"
Phchi.S4	AUGUSTUS	CDS	7234131	7234643	0.78	-	0	transcript_id "Phchi.S4G116900.t1"; gene_id "Phchi.S4G116900"
Phchi.S4	AUGUSTUS	exon	7234131	7234643	.	-	.	transcript_id "Phchi.S4G116900.t1"; gene_id "Phchi.S4G116900"
Phchi.S4	AUGUSTUS	start_codon	7234641	7234643	.	-	0	transcript_id "Phchi.S4G116900.t1"; gene_id "Phchi.S4G116900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11226.t1 is derived from g15276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4889377	4889937	.	-	.	Phchi.S4G080800
Phchi.S4	AUGUSTUS	transcript	4889377	4889937	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	stop_codon	4889374	4889376	.	-	0	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	CDS	4889377	4889416	1	-	1	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	exon	4889377	4889416	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	intron	4889417	4889522	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	CDS	4889523	4889590	1	-	0	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	exon	4889523	4889590	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	intron	4889591	4889680	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	CDS	4889681	4889732	0.82	-	1	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	exon	4889681	4889732	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	intron	4889733	4889854	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	CDS	4889855	4889937	0.82	-	0	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	exon	4889855	4889937	.	-	.	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
Phchi.S4	AUGUSTUS	start_codon	4889935	4889937	.	-	0	transcript_id "Phchi.S4G080800.t1"; gene_id "Phchi.S4G080800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg289.t1 is derived from g10071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2066871	2067722	.	+	.	Phchi.S6G024800
Phchi.S6	AUGUSTUS	transcript	2066871	2067722	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	start_codon	2066871	2066873	.	+	0	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	CDS	2066871	2066963	0.73	+	0	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	exon	2066871	2066963	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	intron	2066964	2067282	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	CDS	2067283	2067401	0.99	+	0	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	exon	2067283	2067401	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	intron	2067402	2067545	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	CDS	2067546	2067627	1	+	1	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	exon	2067546	2067627	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	intron	2067628	2067719	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	CDS	2067720	2067722	1	+	0	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	exon	2067720	2067722	.	+	.	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
Phchi.S6	AUGUSTUS	stop_codon	2067723	2067725	.	+	0	transcript_id "Phchi.S6G024800.t1"; gene_id "Phchi.S6G024800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14920.t1 is derived from g13388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15508880	15510057	.	-	.	Phchi.S3G223900
Phchi.S3	AUGUSTUS	transcript	15508880	15510057	.	-	.	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	stop_codon	15508877	15508879	.	-	0	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	CDS	15508880	15509265	0.99	-	2	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	exon	15508880	15509265	.	-	.	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	intron	15509266	15509347	.	-	.	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	CDS	15509348	15509702	1	-	0	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	exon	15509348	15509702	.	-	.	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	intron	15509703	15509793	.	-	.	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	CDS	15509794	15510057	0.78	-	0	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	exon	15509794	15510057	.	-	.	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
Phchi.S3	AUGUSTUS	start_codon	15510055	15510057	.	-	0	transcript_id "Phchi.S3G223900.t1"; gene_id "Phchi.S3G223900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10203.t1 is derived from g7379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46358345	46358860	.	+	.	Phchi.S1G736200
Phchi.S1	AUGUSTUS	transcript	46358345	46358860	.	+	.	transcript_id "Phchi.S1G736200.t1"; gene_id "Phchi.S1G736200"
Phchi.S1	AUGUSTUS	start_codon	46358345	46358347	.	+	0	transcript_id "Phchi.S1G736200.t1"; gene_id "Phchi.S1G736200"
Phchi.S1	AUGUSTUS	CDS	46358345	46358860	0.6	+	0	transcript_id "Phchi.S1G736200.t1"; gene_id "Phchi.S1G736200"
Phchi.S1	AUGUSTUS	exon	46358345	46358860	.	+	.	transcript_id "Phchi.S1G736200.t1"; gene_id "Phchi.S1G736200"
Phchi.S1	AUGUSTUS	stop_codon	46358861	46358863	.	+	0	transcript_id "Phchi.S1G736200.t1"; gene_id "Phchi.S1G736200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9889.t1 is derived from g7065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44286632	44290586	.	-	.	Phchi.S1G704800
Phchi.S1	AUGUSTUS	transcript	44286632	44290586	.	-	.	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	stop_codon	44286629	44286631	.	-	0	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44286632	44288499	0.75	-	2	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44286632	44288499	.	-	.	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	intron	44288500	44288591	.	-	.	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44288592	44288853	0.83	-	0	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44288592	44288853	.	-	.	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	intron	44288854	44288960	.	-	.	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44288961	44290586	0.69	-	0	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44288961	44290586	.	-	.	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	start_codon	44290584	44290586	.	-	0	transcript_id "Phchi.S1G704800.t1"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	transcript	44287453	44290586	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	stop_codon	44287450	44287452	.	-	0	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44287453	44287611	1	-	0	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44287453	44287611	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	intron	44287612	44287723	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44287724	44288499	0.37	-	2	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44287724	44288499	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	intron	44288500	44288591	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44288592	44288853	0.78	-	0	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44288592	44288853	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	intron	44288854	44288960	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	CDS	44288961	44290586	0.71	-	0	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	exon	44288961	44290586	.	-	.	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
Phchi.S1	AUGUSTUS	start_codon	44290584	44290586	.	-	0	transcript_id "Phchi.S1G704800.t2"; gene_id "Phchi.S1G704800"
# This transcript jg971.t2 is derived from g10754.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg972.t1 is derived from g10755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6734829	6737033	.	+	.	Phchi.S6G093100
Phchi.S6	AUGUSTUS	transcript	6734829	6737033	.	+	.	transcript_id "Phchi.S6G093100.t1"; gene_id "Phchi.S6G093100"
Phchi.S6	AUGUSTUS	start_codon	6734829	6734831	.	+	0	transcript_id "Phchi.S6G093100.t1"; gene_id "Phchi.S6G093100"
Phchi.S6	AUGUSTUS	CDS	6734829	6737033	0.97	+	0	transcript_id "Phchi.S6G093100.t1"; gene_id "Phchi.S6G093100"
Phchi.S6	AUGUSTUS	exon	6734829	6737033	.	+	.	transcript_id "Phchi.S6G093100.t1"; gene_id "Phchi.S6G093100"
Phchi.S6	AUGUSTUS	stop_codon	6737034	6737036	.	+	0	transcript_id "Phchi.S6G093100.t1"; gene_id "Phchi.S6G093100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1089.t1 is derived from g10872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7529007	7529763	.	+	.	Phchi.S6G104800
Phchi.S6	AUGUSTUS	transcript	7529007	7529763	.	+	.	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	start_codon	7529007	7529009	.	+	0	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	CDS	7529007	7529160	0.79	+	0	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	exon	7529007	7529160	.	+	.	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	intron	7529161	7529326	.	+	.	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	CDS	7529327	7529446	1	+	2	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	exon	7529327	7529446	.	+	.	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	intron	7529447	7529545	.	+	.	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	CDS	7529546	7529763	1	+	2	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	exon	7529546	7529763	.	+	.	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
Phchi.S6	AUGUSTUS	stop_codon	7529764	7529766	.	+	0	transcript_id "Phchi.S6G104800.t1"; gene_id "Phchi.S6G104800"
# This transcript jg15284.t1 is derived from g13752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18157353	18158448	.	-	.	Phchi.S3G260300
Phchi.S3	AUGUSTUS	transcript	18157353	18158448	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	stop_codon	18157350	18157352	.	-	0	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	CDS	18157353	18157370	0.96	-	0	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	exon	18157353	18157370	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	intron	18157371	18157555	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	CDS	18157556	18157604	1	-	1	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	exon	18157556	18157604	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	intron	18157605	18157761	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	CDS	18157762	18157925	1	-	0	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	exon	18157762	18157925	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	intron	18157926	18158014	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	CDS	18158015	18158266	0.57	-	0	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	exon	18158015	18158266	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	intron	18158267	18158358	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	CDS	18158359	18158448	0.44	-	0	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	exon	18158359	18158448	.	-	.	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
Phchi.S3	AUGUSTUS	start_codon	18158446	18158448	.	-	0	transcript_id "Phchi.S3G260300.t1"; gene_id "Phchi.S3G260300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13294.t1 is derived from g11760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5295678	5296823	.	-	.	Phchi.S3G061300
Phchi.S3	AUGUSTUS	transcript	5295678	5296823	.	-	.	transcript_id "Phchi.S3G061300.t1"; gene_id "Phchi.S3G061300"
Phchi.S3	AUGUSTUS	stop_codon	5295675	5295677	.	-	0	transcript_id "Phchi.S3G061300.t1"; gene_id "Phchi.S3G061300"
Phchi.S3	AUGUSTUS	CDS	5295678	5296823	0.36	-	0	transcript_id "Phchi.S3G061300.t1"; gene_id "Phchi.S3G061300"
Phchi.S3	AUGUSTUS	exon	5295678	5296823	.	-	.	transcript_id "Phchi.S3G061300.t1"; gene_id "Phchi.S3G061300"
Phchi.S3	AUGUSTUS	start_codon	5296821	5296823	.	-	0	transcript_id "Phchi.S3G061300.t1"; gene_id "Phchi.S3G061300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5263.t1 is derived from g2433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15910387	15911567	.	-	.	Phchi.S1G242200
Phchi.S1	AUGUSTUS	transcript	15910387	15911567	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	stop_codon	15910384	15910386	.	-	0	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15910387	15910827	0.95	-	0	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15910387	15910827	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	intron	15910828	15910944	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15910945	15911061	1	-	0	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15910945	15911061	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	intron	15911062	15911165	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15911166	15911327	1	-	0	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15911166	15911327	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	intron	15911328	15911483	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15911484	15911567	1	-	0	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15911484	15911567	.	-	.	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	start_codon	15911565	15911567	.	-	0	transcript_id "Phchi.S1G242200.t1"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	transcript	15910387	15911567	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	stop_codon	15910384	15910386	.	-	0	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15910387	15910827	0.92	-	0	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15910387	15910827	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	intron	15910828	15910944	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15910945	15911061	1	-	0	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15910945	15911061	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	intron	15911062	15911165	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15911166	15911330	1	-	0	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15911166	15911330	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	intron	15911331	15911483	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	CDS	15911484	15911567	1	-	0	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	exon	15911484	15911567	.	-	.	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
Phchi.S1	AUGUSTUS	start_codon	15911565	15911567	.	-	0	transcript_id "Phchi.S1G242200.t2"; gene_id "Phchi.S1G242200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13409.t1 is derived from g11875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6565532	6566104	.	+	.	Phchi.S3G072800
Phchi.S3	AUGUSTUS	transcript	6565532	6566104	.	+	.	transcript_id "Phchi.S3G072800.t1"; gene_id "Phchi.S3G072800"
Phchi.S3	AUGUSTUS	start_codon	6565532	6565534	.	+	0	transcript_id "Phchi.S3G072800.t1"; gene_id "Phchi.S3G072800"
Phchi.S3	AUGUSTUS	CDS	6565532	6566104	1	+	0	transcript_id "Phchi.S3G072800.t1"; gene_id "Phchi.S3G072800"
Phchi.S3	AUGUSTUS	exon	6565532	6566104	.	+	.	transcript_id "Phchi.S3G072800.t1"; gene_id "Phchi.S3G072800"
Phchi.S3	AUGUSTUS	stop_codon	6566105	6566107	.	+	0	transcript_id "Phchi.S3G072800.t1"; gene_id "Phchi.S3G072800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4479.t1 is derived from g1649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10708271	10710453	.	+	.	Phchi.S1G163800
Phchi.S1	AUGUSTUS	transcript	10708271	10710453	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	start_codon	10708271	10708273	.	+	0	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	CDS	10708271	10709183	0.88	+	0	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	exon	10708271	10709183	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	intron	10709184	10709260	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	CDS	10709261	10709442	1	+	2	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	exon	10709261	10709442	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	intron	10709443	10709565	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	CDS	10709566	10709655	0.98	+	0	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	exon	10709566	10709655	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	intron	10709656	10709761	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	CDS	10709762	10710031	0.99	+	0	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	exon	10709762	10710031	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	intron	10710032	10710132	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	CDS	10710133	10710453	1	+	0	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	exon	10710133	10710453	.	+	.	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
Phchi.S1	AUGUSTUS	stop_codon	10710454	10710456	.	+	0	transcript_id "Phchi.S1G163800.t1"; gene_id "Phchi.S1G163800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5189.t1 is derived from g2359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15395975	15397944	.	+	.	Phchi.S1G234800
Phchi.S1	AUGUSTUS	transcript	15395975	15397944	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	start_codon	15395975	15395977	.	+	0	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15395975	15396135	1	+	0	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15395975	15396135	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15396136	15396376	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15396377	15396447	1	+	1	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15396377	15396447	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15396448	15396587	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15396588	15396704	1	+	2	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15396588	15396704	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15396705	15396867	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15396868	15397040	0.99	+	2	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15396868	15397040	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15397041	15397142	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15397143	15397228	1	+	0	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15397143	15397228	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15397229	15397313	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15397314	15397365	1	+	1	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15397314	15397365	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15397366	15397471	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15397472	15397537	1	+	0	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15397472	15397537	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15397538	15397623	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15397624	15397751	0.98	+	0	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15397624	15397751	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	intron	15397752	15397853	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	CDS	15397854	15397944	0.98	+	1	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	exon	15397854	15397944	.	+	.	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
Phchi.S1	AUGUSTUS	stop_codon	15397945	15397947	.	+	0	transcript_id "Phchi.S1G234800.t1"; gene_id "Phchi.S1G234800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4037.t1 is derived from g1206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7298057	7301323	.	+	.	Phchi.S1G119600
Phchi.S1	AUGUSTUS	transcript	7298057	7301323	.	+	.	transcript_id "Phchi.S1G119600.t1"; gene_id "Phchi.S1G119600"
Phchi.S1	AUGUSTUS	start_codon	7298057	7298059	.	+	0	transcript_id "Phchi.S1G119600.t1"; gene_id "Phchi.S1G119600"
Phchi.S1	AUGUSTUS	CDS	7298057	7301323	0.78	+	0	transcript_id "Phchi.S1G119600.t1"; gene_id "Phchi.S1G119600"
Phchi.S1	AUGUSTUS	exon	7298057	7301323	.	+	.	transcript_id "Phchi.S1G119600.t1"; gene_id "Phchi.S1G119600"
Phchi.S1	AUGUSTUS	stop_codon	7301324	7301326	.	+	0	transcript_id "Phchi.S1G119600.t1"; gene_id "Phchi.S1G119600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9404.t1 is derived from g6580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41352607	41353399	.	+	.	Phchi.S1G656300
Phchi.S1	AUGUSTUS	transcript	41352607	41353399	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	start_codon	41352607	41352609	.	+	0	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	CDS	41352607	41352754	0.61	+	0	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	exon	41352607	41352754	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	intron	41352755	41352843	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	CDS	41352844	41352912	1	+	2	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	exon	41352844	41352912	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	intron	41352913	41352993	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	CDS	41352994	41353100	1	+	2	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	exon	41352994	41353100	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	intron	41353101	41353219	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	CDS	41353220	41353399	1	+	0	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	exon	41353220	41353399	.	+	.	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
Phchi.S1	AUGUSTUS	stop_codon	41353400	41353402	.	+	0	transcript_id "Phchi.S1G656300.t1"; gene_id "Phchi.S1G656300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2586.t1 is derived from g9506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7495193	7497193	.	-	.	Phchi.S5G119500
Phchi.S5	AUGUSTUS	transcript	7495193	7497193	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	stop_codon	7495190	7495192	.	-	0	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7495193	7495695	0.72	-	2	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7495193	7495695	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7495696	7495797	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7495798	7495994	0.92	-	1	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7495798	7495994	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7495995	7496087	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7496088	7496092	0.98	-	0	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7496088	7496092	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7496093	7496237	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7496238	7496331	1	-	1	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7496238	7496331	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7496332	7496453	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7496454	7496482	1	-	0	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7496454	7496482	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7496483	7496571	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7496572	7496653	0.94	-	1	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7496572	7496653	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7496654	7496754	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7496755	7496861	0.99	-	0	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7496755	7496861	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	intron	7496862	7496965	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	CDS	7496966	7497193	1	-	0	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	exon	7496966	7497193	.	-	.	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
Phchi.S5	AUGUSTUS	start_codon	7497191	7497193	.	-	0	transcript_id "Phchi.S5G119500.t1"; gene_id "Phchi.S5G119500"
# This transcript jg1536.t2 is derived from g8455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1537.t1 is derived from g8456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1667123	1669620	.	+	.	Phchi.S5G014600
Phchi.S5	AUGUSTUS	transcript	1667123	1669620	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	start_codon	1667123	1667125	.	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1667123	1667236	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1667123	1667236	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1667237	1667336	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1667337	1667375	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1667337	1667375	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1667376	1667491	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1667492	1667545	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1667492	1667545	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1667546	1667631	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1667632	1667695	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1667632	1667695	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1667696	1667822	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1667823	1667881	1	+	2	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1667823	1667881	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1667882	1668161	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1668162	1668281	0.61	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1668162	1668281	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1668282	1668440	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1668441	1668469	0.62	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1668441	1668469	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1668470	1668602	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1668603	1668661	0.97	+	1	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1668603	1668661	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1668662	1668766	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1668767	1668852	0.93	+	2	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1668767	1668852	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1668853	1668943	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1668944	1668982	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1668944	1668982	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1668983	1669170	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1669171	1669233	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1669171	1669233	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1669234	1669355	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1669356	1669403	1	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1669356	1669403	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	intron	1669404	1669479	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	CDS	1669480	1669620	0.64	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	exon	1669480	1669620	.	+	.	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
Phchi.S5	AUGUSTUS	stop_codon	1669621	1669623	.	+	0	transcript_id "Phchi.S5G014600.t1"; gene_id "Phchi.S5G014600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7613.t1 is derived from g4787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30263886	30264278	.	+	.	Phchi.S1G477200
Phchi.S1	AUGUSTUS	transcript	30263886	30264278	.	+	.	transcript_id "Phchi.S1G477200.t1"; gene_id "Phchi.S1G477200"
Phchi.S1	AUGUSTUS	start_codon	30263886	30263888	.	+	0	transcript_id "Phchi.S1G477200.t1"; gene_id "Phchi.S1G477200"
Phchi.S1	AUGUSTUS	CDS	30263886	30264278	0.91	+	0	transcript_id "Phchi.S1G477200.t1"; gene_id "Phchi.S1G477200"
Phchi.S1	AUGUSTUS	exon	30263886	30264278	.	+	.	transcript_id "Phchi.S1G477200.t1"; gene_id "Phchi.S1G477200"
Phchi.S1	AUGUSTUS	stop_codon	30264279	30264281	.	+	0	transcript_id "Phchi.S1G477200.t1"; gene_id "Phchi.S1G477200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg284.t1 is derived from g10066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2022621	2024363	.	-	.	Phchi.S6G024300
Phchi.S6	AUGUSTUS	transcript	2022621	2024363	.	-	.	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	stop_codon	2022618	2022620	.	-	0	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	CDS	2022621	2023259	1	-	0	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	exon	2022621	2023259	.	-	.	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	intron	2023260	2023337	.	-	.	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	CDS	2023338	2024363	0.98	-	0	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	exon	2023338	2024363	.	-	.	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
Phchi.S6	AUGUSTUS	start_codon	2024361	2024363	.	-	0	transcript_id "Phchi.S6G024300.t1"; gene_id "Phchi.S6G024300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1287.t1 is derived from g11070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8839022	8839462	.	+	.	Phchi.S6G124600
Phchi.S6	AUGUSTUS	transcript	8839022	8839462	.	+	.	transcript_id "Phchi.S6G124600.t1"; gene_id "Phchi.S6G124600"
Phchi.S6	AUGUSTUS	start_codon	8839022	8839024	.	+	0	transcript_id "Phchi.S6G124600.t1"; gene_id "Phchi.S6G124600"
Phchi.S6	AUGUSTUS	CDS	8839022	8839462	0.78	+	0	transcript_id "Phchi.S6G124600.t1"; gene_id "Phchi.S6G124600"
Phchi.S6	AUGUSTUS	exon	8839022	8839462	.	+	.	transcript_id "Phchi.S6G124600.t1"; gene_id "Phchi.S6G124600"
Phchi.S6	AUGUSTUS	stop_codon	8839463	8839465	.	+	0	transcript_id "Phchi.S6G124600.t1"; gene_id "Phchi.S6G124600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14648.t1 is derived from g13116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13941230	13942723	.	+	.	Phchi.S3G196700
Phchi.S3	AUGUSTUS	transcript	13941230	13942723	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	start_codon	13941230	13941232	.	+	0	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	CDS	13941230	13941236	1	+	0	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	exon	13941230	13941236	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	intron	13941237	13941373	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	CDS	13941374	13941480	1	+	2	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	exon	13941374	13941480	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	intron	13941481	13941567	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	CDS	13941568	13941642	1	+	0	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	exon	13941568	13941642	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	intron	13941643	13941800	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	CDS	13941801	13941860	1	+	0	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	exon	13941801	13941860	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	intron	13941861	13942070	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	CDS	13942071	13942126	0.94	+	0	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	exon	13942071	13942126	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	intron	13942127	13942206	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	CDS	13942207	13942723	0.97	+	1	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	exon	13942207	13942723	.	+	.	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
Phchi.S3	AUGUSTUS	stop_codon	13942724	13942726	.	+	0	transcript_id "Phchi.S3G196700.t1"; gene_id "Phchi.S3G196700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1999.t1 is derived from g8919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4371510	4373475	.	-	.	Phchi.S5G060800
Phchi.S5	AUGUSTUS	transcript	4371510	4373475	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	stop_codon	4371507	4371509	.	-	0	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4371510	4371560	0.95	-	0	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4371510	4371560	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4371561	4371666	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4371667	4371749	0.99	-	2	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4371667	4371749	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4371750	4371839	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4371840	4371921	1	-	0	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4371840	4371921	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4371922	4372039	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4372040	4372100	1	-	1	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4372040	4372100	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4372101	4372188	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4372189	4372278	1	-	1	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4372189	4372278	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4372279	4372422	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4372423	4372456	1	-	2	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4372423	4372456	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4372457	4372551	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4372552	4372687	1	-	0	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4372552	4372687	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4372688	4372782	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4372783	4373065	0.45	-	1	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4372783	4373065	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4373066	4373163	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4373164	4373307	0.51	-	1	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4373164	4373307	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	intron	4373308	4373395	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	CDS	4373396	4373475	0.75	-	0	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	exon	4373396	4373475	.	-	.	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
Phchi.S5	AUGUSTUS	start_codon	4373473	4373475	.	-	0	transcript_id "Phchi.S5G060800.t1"; gene_id "Phchi.S5G060800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2036.t1 is derived from g8956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4548182	4549324	.	-	.	Phchi.S5G064500
Phchi.S5	AUGUSTUS	transcript	4548182	4549324	.	-	.	transcript_id "Phchi.S5G064500.t1"; gene_id "Phchi.S5G064500"
Phchi.S5	AUGUSTUS	stop_codon	4548179	4548181	.	-	0	transcript_id "Phchi.S5G064500.t1"; gene_id "Phchi.S5G064500"
Phchi.S5	AUGUSTUS	CDS	4548182	4549324	0.99	-	0	transcript_id "Phchi.S5G064500.t1"; gene_id "Phchi.S5G064500"
Phchi.S5	AUGUSTUS	exon	4548182	4549324	.	-	.	transcript_id "Phchi.S5G064500.t1"; gene_id "Phchi.S5G064500"
Phchi.S5	AUGUSTUS	start_codon	4549322	4549324	.	-	0	transcript_id "Phchi.S5G064500.t1"; gene_id "Phchi.S5G064500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3747.t1 is derived from g916.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5477728	5478801	.	-	.	Phchi.S1G090600
Phchi.S1	AUGUSTUS	transcript	5477728	5478801	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	stop_codon	5477725	5477727	.	-	0	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5477728	5477741	1	-	2	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5477728	5477741	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5477742	5478132	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478133	5478231	1	-	2	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478133	5478231	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478232	5478375	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478376	5478457	1	-	0	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478376	5478457	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478458	5478575	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478576	5478682	0.95	-	2	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478576	5478682	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478683	5478782	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478783	5478801	0.95	-	0	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478783	5478801	.	-	.	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	start_codon	5478799	5478801	.	-	0	transcript_id "Phchi.S1G090600.t1"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	transcript	5477728	5478801	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	stop_codon	5477725	5477727	.	-	0	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5477728	5477741	1	-	2	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5477728	5477741	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5477742	5478132	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478133	5478252	0.91	-	2	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478133	5478252	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478253	5478375	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478376	5478457	0.93	-	0	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478376	5478457	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478458	5478575	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478576	5478682	0.93	-	2	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478576	5478682	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478683	5478782	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478783	5478801	0.95	-	0	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478783	5478801	.	-	.	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	start_codon	5478799	5478801	.	-	0	transcript_id "Phchi.S1G090600.t2"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	transcript	5477922	5478801	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	stop_codon	5477919	5477921	.	-	0	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5477922	5478004	0.3	-	2	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5477922	5478004	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478005	5478132	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478133	5478231	0.65	-	2	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478133	5478231	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478232	5478375	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478376	5478457	0.71	-	0	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478376	5478457	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478458	5478575	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478576	5478682	0.68	-	2	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478576	5478682	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	intron	5478683	5478782	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	CDS	5478783	5478801	0.71	-	0	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	exon	5478783	5478801	.	-	.	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
Phchi.S1	AUGUSTUS	start_codon	5478799	5478801	.	-	0	transcript_id "Phchi.S1G090600.t3"; gene_id "Phchi.S1G090600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10629.t1 is derived from g14679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1330484	1331236	.	+	.	Phchi.S4G021100
Phchi.S4	AUGUSTUS	transcript	1330484	1331236	.	+	.	transcript_id "Phchi.S4G021100.t1"; gene_id "Phchi.S4G021100"
Phchi.S4	AUGUSTUS	start_codon	1330484	1330486	.	+	0	transcript_id "Phchi.S4G021100.t1"; gene_id "Phchi.S4G021100"
Phchi.S4	AUGUSTUS	CDS	1330484	1331236	0.92	+	0	transcript_id "Phchi.S4G021100.t1"; gene_id "Phchi.S4G021100"
Phchi.S4	AUGUSTUS	exon	1330484	1331236	.	+	.	transcript_id "Phchi.S4G021100.t1"; gene_id "Phchi.S4G021100"
Phchi.S4	AUGUSTUS	stop_codon	1331237	1331239	.	+	0	transcript_id "Phchi.S4G021100.t1"; gene_id "Phchi.S4G021100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15129.t1 is derived from g13597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17197214	17199738	.	+	.	Phchi.S3G244800
Phchi.S3	AUGUSTUS	transcript	17197214	17199738	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	start_codon	17197214	17197216	.	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17197214	17197347	1	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17197214	17197347	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17197348	17197444	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17197445	17197503	0.95	+	1	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17197445	17197503	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17197504	17197613	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17197614	17197670	0.88	+	2	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17197614	17197670	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17197671	17197780	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17197781	17197815	0.98	+	2	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17197781	17197815	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17197816	17197938	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17197939	17198042	0.97	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17197939	17198042	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17198043	17198137	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17198138	17198213	0.79	+	1	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17198138	17198213	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17198214	17198294	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17198295	17198353	0.76	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17198295	17198353	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17198354	17198440	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17198441	17198506	0.63	+	1	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17198441	17198506	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17198507	17198776	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17198777	17198841	0.6	+	1	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17198777	17198841	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17198842	17198934	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17198935	17199017	0.6	+	2	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17198935	17199017	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17199018	17199097	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17199098	17199188	0.74	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17199098	17199188	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17199189	17199274	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17199275	17199333	1	+	2	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17199275	17199333	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17199334	17199401	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17199402	17199542	1	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17199402	17199542	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	intron	17199543	17199633	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	CDS	17199634	17199738	1	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	exon	17199634	17199738	.	+	.	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
Phchi.S3	AUGUSTUS	stop_codon	17199739	17199741	.	+	0	transcript_id "Phchi.S3G244800.t1"; gene_id "Phchi.S3G244800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg829.t1 is derived from g10611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5770522	5772024	.	+	.	Phchi.S6G078800
Phchi.S6	AUGUSTUS	transcript	5770522	5772024	.	+	.	transcript_id "Phchi.S6G078800.t1"; gene_id "Phchi.S6G078800"
Phchi.S6	AUGUSTUS	start_codon	5770522	5770524	.	+	0	transcript_id "Phchi.S6G078800.t1"; gene_id "Phchi.S6G078800"
Phchi.S6	AUGUSTUS	CDS	5770522	5772024	0.94	+	0	transcript_id "Phchi.S6G078800.t1"; gene_id "Phchi.S6G078800"
Phchi.S6	AUGUSTUS	exon	5770522	5772024	.	+	.	transcript_id "Phchi.S6G078800.t1"; gene_id "Phchi.S6G078800"
Phchi.S6	AUGUSTUS	stop_codon	5772025	5772027	.	+	0	transcript_id "Phchi.S6G078800.t1"; gene_id "Phchi.S6G078800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11932.t1 is derived from g7607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	88672	90308	.	+	.	Phchi.S2G001200
Phchi.S2	AUGUSTUS	transcript	88672	90308	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	start_codon	88672	88674	.	+	0	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	CDS	88672	89128	0.53	+	0	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	exon	88672	89128	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	intron	89129	89232	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	CDS	89233	89309	0.98	+	2	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	exon	89233	89309	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	intron	89310	89439	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	CDS	89440	89531	1	+	0	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	exon	89440	89531	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	intron	89532	89737	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	CDS	89738	90308	1	+	1	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	exon	89738	90308	.	+	.	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
Phchi.S2	AUGUSTUS	stop_codon	90309	90311	.	+	0	transcript_id "Phchi.S2G001200.t1"; gene_id "Phchi.S2G001200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5040.t1 is derived from g2210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14208176	14210083	.	-	.	Phchi.S1G219900
Phchi.S1	AUGUSTUS	transcript	14208176	14210083	.	-	.	transcript_id "Phchi.S1G219900.t1"; gene_id "Phchi.S1G219900"
Phchi.S1	AUGUSTUS	stop_codon	14208173	14208175	.	-	0	transcript_id "Phchi.S1G219900.t1"; gene_id "Phchi.S1G219900"
Phchi.S1	AUGUSTUS	CDS	14208176	14210083	0.89	-	0	transcript_id "Phchi.S1G219900.t1"; gene_id "Phchi.S1G219900"
Phchi.S1	AUGUSTUS	exon	14208176	14210083	.	-	.	transcript_id "Phchi.S1G219900.t1"; gene_id "Phchi.S1G219900"
Phchi.S1	AUGUSTUS	start_codon	14210081	14210083	.	-	0	transcript_id "Phchi.S1G219900.t1"; gene_id "Phchi.S1G219900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15316.t1 is derived from g13784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18360776	18362999	.	-	.	Phchi.S3G263500
Phchi.S3	AUGUSTUS	transcript	18360776	18362999	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	stop_codon	18360773	18360775	.	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18360776	18360925	1	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18360776	18360925	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18360926	18361014	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18361015	18361131	1	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18361015	18361131	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18361132	18361230	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18361231	18361410	1	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18361231	18361410	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18361411	18361516	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18361517	18361645	0.99	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18361517	18361645	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18361646	18361741	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18361742	18361984	0.95	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18361742	18361984	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18361985	18362111	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18362112	18362216	1	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18362112	18362216	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18362217	18362333	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18362334	18362426	1	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18362334	18362426	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	intron	18362427	18362513	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	CDS	18362514	18362999	0.8	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	exon	18362514	18362999	.	-	.	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
Phchi.S3	AUGUSTUS	start_codon	18362997	18362999	.	-	0	transcript_id "Phchi.S3G263500.t1"; gene_id "Phchi.S3G263500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11969.t1 is derived from g7644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	246284	246795	.	-	.	Phchi.S2G004900
Phchi.S2	AUGUSTUS	transcript	246284	246795	.	-	.	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	stop_codon	246281	246283	.	-	0	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	CDS	246284	246317	0.85	-	1	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	exon	246284	246317	.	-	.	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	intron	246318	246405	.	-	.	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	CDS	246406	246590	0.73	-	0	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	exon	246406	246590	.	-	.	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	intron	246591	246789	.	-	.	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	CDS	246790	246795	0.76	-	0	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	exon	246790	246795	.	-	.	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
Phchi.S2	AUGUSTUS	start_codon	246793	246795	.	-	0	transcript_id "Phchi.S2G004900.t1"; gene_id "Phchi.S2G004900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14079.t1 is derived from g12546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10685856	10687154	.	-	.	Phchi.S3G139800
Phchi.S3	AUGUSTUS	transcript	10685856	10687154	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	stop_codon	10685853	10685855	.	-	0	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	CDS	10685856	10685876	0.98	-	0	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	exon	10685856	10685876	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	intron	10685877	10685960	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	CDS	10685961	10686055	0.73	-	2	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	exon	10685961	10686055	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	intron	10686056	10686363	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	CDS	10686364	10686403	0.65	-	0	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	exon	10686364	10686403	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	intron	10686404	10686488	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	CDS	10686489	10687154	0.66	-	0	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	exon	10686489	10687154	.	-	.	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
Phchi.S3	AUGUSTUS	start_codon	10687152	10687154	.	-	0	transcript_id "Phchi.S3G139800.t1"; gene_id "Phchi.S3G139800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8290.t1 is derived from g5465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35110449	35111948	.	+	.	Phchi.S1G544900
Phchi.S1	AUGUSTUS	transcript	35110449	35111948	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	start_codon	35110449	35110451	.	+	0	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	CDS	35110449	35110927	1	+	0	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	exon	35110449	35110927	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	intron	35110928	35111014	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	CDS	35111015	35111226	1	+	1	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	exon	35111015	35111226	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	intron	35111227	35111326	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	CDS	35111327	35111706	1	+	2	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	exon	35111327	35111706	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	intron	35111707	35111828	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	CDS	35111829	35111948	1	+	0	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	exon	35111829	35111948	.	+	.	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
Phchi.S1	AUGUSTUS	stop_codon	35111949	35111951	.	+	0	transcript_id "Phchi.S1G544900.t1"; gene_id "Phchi.S1G544900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12464.t1 is derived from g8141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24652870	24653990	.	+	.	Phchi.S2G054400
Phchi.S2	AUGUSTUS	transcript	24652870	24653990	.	+	.	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	start_codon	24652870	24652872	.	+	0	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	CDS	24652870	24652872	0.99	+	0	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	exon	24652870	24652872	.	+	.	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	intron	24652873	24652958	.	+	.	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	CDS	24652959	24653990	0.99	+	0	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	exon	24652959	24653990	.	+	.	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
Phchi.S2	AUGUSTUS	stop_codon	24653991	24653993	.	+	0	transcript_id "Phchi.S2G054400.t1"; gene_id "Phchi.S2G054400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg432.t1 is derived from g10214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3060249	3060968	.	+	.	Phchi.S6G039100
Phchi.S6	AUGUSTUS	transcript	3060249	3060968	.	+	.	transcript_id "Phchi.S6G039100.t1"; gene_id "Phchi.S6G039100"
Phchi.S6	AUGUSTUS	start_codon	3060249	3060251	.	+	0	transcript_id "Phchi.S6G039100.t1"; gene_id "Phchi.S6G039100"
Phchi.S6	AUGUSTUS	CDS	3060249	3060968	1	+	0	transcript_id "Phchi.S6G039100.t1"; gene_id "Phchi.S6G039100"
Phchi.S6	AUGUSTUS	exon	3060249	3060968	.	+	.	transcript_id "Phchi.S6G039100.t1"; gene_id "Phchi.S6G039100"
Phchi.S6	AUGUSTUS	stop_codon	3060969	3060971	.	+	0	transcript_id "Phchi.S6G039100.t1"; gene_id "Phchi.S6G039100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14768.t1 is derived from g13236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14631217	14632992	.	+	.	Phchi.S3G208700
Phchi.S3	AUGUSTUS	transcript	14631217	14632992	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	start_codon	14631217	14631219	.	+	0	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	CDS	14631217	14631572	0.4	+	0	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	exon	14631217	14631572	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	intron	14631573	14631727	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	CDS	14631728	14632274	0.53	+	1	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	exon	14631728	14632274	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	intron	14632275	14632397	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	CDS	14632398	14632573	1	+	0	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	exon	14632398	14632573	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	intron	14632574	14632706	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	CDS	14632707	14632777	1	+	1	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	exon	14632707	14632777	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	intron	14632778	14632906	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	CDS	14632907	14632992	1	+	2	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	exon	14632907	14632992	.	+	.	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
Phchi.S3	AUGUSTUS	stop_codon	14632993	14632995	.	+	0	transcript_id "Phchi.S3G208700.t1"; gene_id "Phchi.S3G208700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9986.t1 is derived from g7162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44794944	44795584	.	+	.	Phchi.S1G714500
Phchi.S1	AUGUSTUS	transcript	44794944	44795584	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	start_codon	44794944	44794946	.	+	0	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	CDS	44794944	44794967	0.4	+	0	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	exon	44794944	44794967	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	intron	44794968	44795046	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	CDS	44795047	44795051	0.99	+	0	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	exon	44795047	44795051	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	intron	44795052	44795189	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	CDS	44795190	44795304	0.99	+	1	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	exon	44795190	44795304	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	intron	44795305	44795386	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	CDS	44795387	44795584	0.61	+	0	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	exon	44795387	44795584	.	+	.	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
Phchi.S1	AUGUSTUS	stop_codon	44795585	44795587	.	+	0	transcript_id "Phchi.S1G714500.t1"; gene_id "Phchi.S1G714500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10614.t1 is derived from g14664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1235877	1237953	.	+	.	Phchi.S4G019600
Phchi.S4	AUGUSTUS	transcript	1235877	1237953	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	start_codon	1235877	1235879	.	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1235877	1235883	0.99	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1235877	1235883	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1235884	1236030	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1236031	1236071	0.86	+	2	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1236031	1236071	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1236072	1236159	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1236160	1236204	0.99	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1236160	1236204	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1236205	1236381	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1236382	1236462	1	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1236382	1236462	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1236463	1236672	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1236673	1236761	1	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1236673	1236761	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1236762	1236873	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1236874	1236948	1	+	1	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1236874	1236948	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1236949	1237083	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1237084	1237145	1	+	1	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1237084	1237145	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1237146	1237320	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1237321	1237392	1	+	2	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1237321	1237392	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1237393	1237489	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1237490	1237513	0.73	+	2	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1237490	1237513	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1237514	1237607	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1237608	1237711	0.98	+	2	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1237608	1237711	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	intron	1237712	1237821	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	CDS	1237822	1237953	0.99	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	exon	1237822	1237953	.	+	.	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
Phchi.S4	AUGUSTUS	stop_codon	1237954	1237956	.	+	0	transcript_id "Phchi.S4G019600.t1"; gene_id "Phchi.S4G019600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg729.t1 is derived from g10511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5201356	5202320	.	+	.	Phchi.S6G068800
Phchi.S6	AUGUSTUS	transcript	5201356	5202320	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	start_codon	5201356	5201358	.	+	0	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	CDS	5201356	5201424	1	+	0	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	exon	5201356	5201424	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	intron	5201425	5201724	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	CDS	5201725	5201848	1	+	0	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	exon	5201725	5201848	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	intron	5201849	5201946	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	CDS	5201947	5202041	1	+	2	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	exon	5201947	5202041	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	intron	5202042	5202269	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	CDS	5202270	5202320	1	+	0	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	exon	5202270	5202320	.	+	.	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
Phchi.S6	AUGUSTUS	stop_codon	5202321	5202323	.	+	0	transcript_id "Phchi.S6G068800.t1"; gene_id "Phchi.S6G068800"
# This transcript jg15807.t2 is derived from g14277.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15808.t1 is derived from g14278.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21497569	21500754	.	-	.	Phchi.S3G312700
Phchi.S3	AUGUSTUS	transcript	21497569	21500754	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	stop_codon	21497566	21497568	.	-	0	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21497569	21497951	0.89	-	2	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21497569	21497951	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21497952	21498364	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21498365	21498767	0.43	-	0	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21498365	21498767	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21498768	21498947	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21498948	21500024	0.46	-	0	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21498948	21500024	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500025	21500110	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500111	21500205	0.93	-	2	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500111	21500205	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500206	21500319	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500320	21500440	0.94	-	0	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500320	21500440	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500441	21500518	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500519	21500583	1	-	2	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500519	21500583	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500584	21500675	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500676	21500754	0.7	-	0	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500676	21500754	.	-	.	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	start_codon	21500752	21500754	.	-	0	transcript_id "Phchi.S3G312700.t1"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	transcript	21497569	21500754	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	stop_codon	21497566	21497568	.	-	0	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21497569	21497951	0.89	-	2	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21497569	21497951	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21497952	21498364	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21498365	21498767	0.38	-	0	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21498365	21498767	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21498768	21498947	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21498948	21500024	0.42	-	0	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21498948	21500024	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500025	21500110	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500111	21500205	0.87	-	2	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500111	21500205	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500206	21500319	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500320	21500408	0.86	-	1	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500320	21500408	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500409	21500489	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500490	21500583	1	-	2	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500490	21500583	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	intron	21500584	21500675	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	CDS	21500676	21500754	0.65	-	0	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	exon	21500676	21500754	.	-	.	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
Phchi.S3	AUGUSTUS	start_codon	21500752	21500754	.	-	0	transcript_id "Phchi.S3G312700.t2"; gene_id "Phchi.S3G312700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1239.t1 is derived from g11022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8553925	8555607	.	-	.	Phchi.S6G119800
Phchi.S6	AUGUSTUS	transcript	8553925	8555607	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	stop_codon	8553922	8553924	.	-	0	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8553925	8553958	1	-	1	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8553925	8553958	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	intron	8553959	8554108	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8554109	8554315	1	-	1	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8554109	8554315	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	intron	8554316	8554402	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8554403	8554579	1	-	1	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8554403	8554579	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	intron	8554580	8554703	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8554704	8554867	1	-	0	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8554704	8554867	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	intron	8554868	8554982	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8554983	8555036	0.99	-	0	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8554983	8555036	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	intron	8555037	8555187	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8555188	8555271	0.67	-	0	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8555188	8555271	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	intron	8555272	8555367	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	CDS	8555368	8555607	0.96	-	0	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	exon	8555368	8555607	.	-	.	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
Phchi.S6	AUGUSTUS	start_codon	8555605	8555607	.	-	0	transcript_id "Phchi.S6G119800.t1"; gene_id "Phchi.S6G119800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12315.t1 is derived from g7991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10419788	10420129	.	+	.	Phchi.S2G039500
Phchi.S2	AUGUSTUS	transcript	10419788	10420129	.	+	.	transcript_id "Phchi.S2G039500.t1"; gene_id "Phchi.S2G039500"
Phchi.S2	AUGUSTUS	start_codon	10419788	10419790	.	+	0	transcript_id "Phchi.S2G039500.t1"; gene_id "Phchi.S2G039500"
Phchi.S2	AUGUSTUS	CDS	10419788	10420129	0.38	+	0	transcript_id "Phchi.S2G039500.t1"; gene_id "Phchi.S2G039500"
Phchi.S2	AUGUSTUS	exon	10419788	10420129	.	+	.	transcript_id "Phchi.S2G039500.t1"; gene_id "Phchi.S2G039500"
Phchi.S2	AUGUSTUS	stop_codon	10420130	10420132	.	+	0	transcript_id "Phchi.S2G039500.t1"; gene_id "Phchi.S2G039500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13892.t1 is derived from g12359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9484362	9489664	.	+	.	Phchi.S3G121100
Phchi.S3	AUGUSTUS	transcript	9484362	9489664	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	start_codon	9484362	9484364	.	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9484362	9484373	0.87	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9484362	9484373	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9484374	9484565	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9484566	9484595	0.64	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9484566	9484595	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9484596	9484716	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9484717	9485019	0.54	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9484717	9485019	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485020	9485214	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485215	9485316	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485215	9485316	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485317	9485491	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485492	9485599	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485492	9485599	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485600	9485695	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485696	9485783	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485696	9485783	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485784	9485913	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485914	9486262	0.61	+	2	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485914	9486262	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9486263	9486508	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9486509	9486854	0.55	+	1	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9486509	9486854	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9486855	9486988	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9486989	9487120	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9486989	9487120	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487121	9487254	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9487255	9487408	0.6	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9487255	9487408	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487409	9487502	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9487503	9487692	0.75	+	2	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9487503	9487692	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487693	9487784	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9487785	9487937	1	+	1	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9487785	9487937	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487938	9488057	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488058	9488241	1	+	1	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488058	9488241	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9488242	9488343	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488344	9488454	0.99	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488344	9488454	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9488455	9488542	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488543	9488758	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488543	9488758	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9488759	9488878	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488879	9489071	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488879	9489071	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9489072	9489149	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9489150	9489220	1	+	2	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9489150	9489220	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9489221	9489334	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9489335	9489454	1	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9489335	9489454	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9489455	9489541	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9489542	9489664	0.98	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9489542	9489664	.	+	.	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	stop_codon	9489665	9489667	.	+	0	transcript_id "Phchi.S3G121100.t1"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	transcript	9484362	9489664	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	start_codon	9484362	9484364	.	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9484362	9484373	0.86	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9484362	9484373	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9484374	9484565	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9484566	9484595	0.68	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9484566	9484595	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9484596	9484716	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9484717	9484934	0.4	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9484717	9484934	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9484935	9485046	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485047	9485059	0.99	+	1	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485047	9485059	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485060	9485214	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485215	9485316	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485215	9485316	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485317	9485491	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485492	9485599	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485492	9485599	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485600	9485695	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485696	9485783	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485696	9485783	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9485784	9485913	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9485914	9486262	0.66	+	2	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9485914	9486262	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9486263	9486508	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9486509	9486854	0.48	+	1	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9486509	9486854	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9486855	9486988	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9486989	9487120	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9486989	9487120	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487121	9487254	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9487255	9487408	0.67	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9487255	9487408	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487409	9487502	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9487503	9487692	0.76	+	2	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9487503	9487692	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487693	9487784	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9487785	9487937	1	+	1	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9487785	9487937	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9487938	9488057	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488058	9488241	1	+	1	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488058	9488241	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9488242	9488343	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488344	9488454	0.99	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488344	9488454	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9488455	9488542	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488543	9488758	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488543	9488758	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9488759	9488878	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9488879	9489071	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9488879	9489071	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9489072	9489149	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9489150	9489220	1	+	2	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9489150	9489220	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9489221	9489334	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9489335	9489454	1	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9489335	9489454	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	intron	9489455	9489541	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	CDS	9489542	9489664	0.99	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	exon	9489542	9489664	.	+	.	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
Phchi.S3	AUGUSTUS	stop_codon	9489665	9489667	.	+	0	transcript_id "Phchi.S3G121100.t2"; gene_id "Phchi.S3G121100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9925.t1 is derived from g7101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44504813	44505061	.	+	.	Phchi.S1G708400
Phchi.S1	AUGUSTUS	transcript	44504813	44505061	.	+	.	transcript_id "Phchi.S1G708400.t1"; gene_id "Phchi.S1G708400"
Phchi.S1	AUGUSTUS	start_codon	44504813	44504815	.	+	0	transcript_id "Phchi.S1G708400.t1"; gene_id "Phchi.S1G708400"
Phchi.S1	AUGUSTUS	CDS	44504813	44505061	0.45	+	0	transcript_id "Phchi.S1G708400.t1"; gene_id "Phchi.S1G708400"
Phchi.S1	AUGUSTUS	exon	44504813	44505061	.	+	.	transcript_id "Phchi.S1G708400.t1"; gene_id "Phchi.S1G708400"
Phchi.S1	AUGUSTUS	stop_codon	44505062	44505064	.	+	0	transcript_id "Phchi.S1G708400.t1"; gene_id "Phchi.S1G708400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9269.t1 is derived from g6444.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40683272	40685465	.	+	.	Phchi.S1G642800
Phchi.S1	AUGUSTUS	transcript	40683272	40685465	.	+	.	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	start_codon	40683272	40683274	.	+	0	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	CDS	40683272	40683813	0.49	+	0	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	exon	40683272	40683813	.	+	.	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	intron	40683814	40683884	.	+	.	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	CDS	40683885	40684770	0.71	+	1	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	exon	40683885	40684770	.	+	.	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	intron	40684771	40685192	.	+	.	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	CDS	40685193	40685465	0.91	+	0	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	exon	40685193	40685465	.	+	.	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	stop_codon	40685466	40685468	.	+	0	transcript_id "Phchi.S1G642800.t1"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	transcript	40683272	40684282	.	+	.	transcript_id "Phchi.S1G642800.t2"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	start_codon	40683272	40683274	.	+	0	transcript_id "Phchi.S1G642800.t2"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	CDS	40683272	40684282	0.81	+	0	transcript_id "Phchi.S1G642800.t2"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	exon	40683272	40684282	.	+	.	transcript_id "Phchi.S1G642800.t2"; gene_id "Phchi.S1G642800"
Phchi.S1	AUGUSTUS	stop_codon	40684283	40684285	.	+	0	transcript_id "Phchi.S1G642800.t2"; gene_id "Phchi.S1G642800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg560.t1 is derived from g10342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4050370	4053964	.	+	.	Phchi.S6G051900
Phchi.S6	AUGUSTUS	transcript	4050370	4053964	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	start_codon	4050370	4050372	.	+	0	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4050370	4052099	0.68	+	0	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4050370	4052099	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4052100	4052218	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4052219	4052333	0.99	+	1	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4052219	4052333	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4052334	4052551	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4052552	4052659	1	+	0	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4052552	4052659	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4052660	4052784	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4052785	4053104	0.5	+	0	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4052785	4053104	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4053105	4053171	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4053172	4053305	0.43	+	1	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4053172	4053305	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4053306	4053399	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4053400	4053508	0.98	+	2	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4053400	4053508	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4053509	4053585	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4053586	4053611	0.6	+	1	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4053586	4053611	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4053612	4053699	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4053700	4053793	0.6	+	2	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4053700	4053793	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	intron	4053794	4053933	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	CDS	4053934	4053964	0.92	+	1	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	exon	4053934	4053964	.	+	.	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
Phchi.S6	AUGUSTUS	stop_codon	4053965	4053967	.	+	0	transcript_id "Phchi.S6G051900.t1"; gene_id "Phchi.S6G051900"
# This transcript jg11181.t2 is derived from g15231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 5 different transcripts
# This transcript jg11182.t1 is derived from g15232.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4531185	4534291	.	+	.	Phchi.S4G076400
Phchi.S4	AUGUSTUS	transcript	4531292	4534291	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	start_codon	4531292	4531294	.	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531292	4531386	0.93	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531292	4531386	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4531387	4531913	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531914	4532026	1	+	1	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531914	4532026	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532027	4532154	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532155	4532228	1	+	2	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532155	4532228	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532229	4532394	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532395	4532592	1	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532395	4532592	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532593	4532741	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532742	4532849	1	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532742	4532849	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532850	4532942	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532943	4533002	1	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532943	4533002	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533003	4533092	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533093	4533170	1	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533093	4533170	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533171	4533261	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533262	4533340	1	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533262	4533340	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533341	4533423	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533424	4533695	1	+	2	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533424	4533695	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533696	4533799	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533800	4534039	0.99	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533800	4534039	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4534040	4534147	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4534148	4534291	0.69	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4534148	4534291	.	+	.	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	stop_codon	4534292	4534294	.	+	0	transcript_id "Phchi.S4G076400.t1"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	transcript	4531185	4534291	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	start_codon	4531185	4531187	.	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531185	4531288	0.56	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531185	4531288	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4531289	4531913	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531914	4532026	1	+	1	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531914	4532026	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532027	4532154	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532155	4532228	1	+	2	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532155	4532228	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532229	4532394	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532395	4532592	1	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532395	4532592	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532593	4532741	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532742	4532849	1	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532742	4532849	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532850	4532942	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532943	4533002	1	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532943	4533002	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533003	4533092	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533093	4533170	1	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533093	4533170	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533171	4533261	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533262	4533340	1	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533262	4533340	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533341	4533423	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533424	4533695	0.98	+	2	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533424	4533695	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533696	4533799	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533800	4534039	1	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533800	4534039	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4534040	4534147	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4534148	4534291	0.7	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4534148	4534291	.	+	.	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	stop_codon	4534292	4534294	.	+	0	transcript_id "Phchi.S4G076400.t2"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	transcript	4531292	4534291	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	start_codon	4531292	4531294	.	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531292	4531386	0.7	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531292	4531386	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4531387	4531913	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531914	4532026	1	+	1	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531914	4532026	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532027	4532154	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532155	4532228	1	+	2	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532155	4532228	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532229	4532394	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532395	4532592	1	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532395	4532592	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532593	4532741	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532742	4532849	1	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532742	4532849	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532850	4532942	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532943	4533002	1	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532943	4533002	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533003	4533092	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533093	4533170	1	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533093	4533170	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533171	4533258	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533259	4533340	1	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533259	4533340	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533341	4533423	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533424	4533695	0.99	+	2	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533424	4533695	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533696	4533799	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533800	4534039	1	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533800	4534039	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4534040	4534147	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4534148	4534291	0.81	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4534148	4534291	.	+	.	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	stop_codon	4534292	4534294	.	+	0	transcript_id "Phchi.S4G076400.t3"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	transcript	4531292	4534291	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	start_codon	4531292	4531294	.	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531292	4531386	0.72	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531292	4531386	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4531387	4531913	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531914	4532026	1	+	1	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531914	4532026	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532027	4532154	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532155	4532228	1	+	2	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532155	4532228	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532229	4532394	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532395	4532604	1	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532395	4532604	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532605	4532741	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532742	4532849	1	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532742	4532849	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532850	4532942	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532943	4533002	1	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532943	4533002	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533003	4533092	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533093	4533170	1	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533093	4533170	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533171	4533261	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533262	4533340	1	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533262	4533340	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533341	4533423	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533424	4533695	1	+	2	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533424	4533695	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533696	4533799	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533800	4534039	0.98	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533800	4534039	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4534040	4534147	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4534148	4534291	0.68	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4534148	4534291	.	+	.	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	stop_codon	4534292	4534294	.	+	0	transcript_id "Phchi.S4G076400.t4"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	transcript	4531292	4534291	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	start_codon	4531292	4531294	.	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531292	4531386	0.75	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531292	4531386	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4531387	4531913	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4531914	4532026	1	+	1	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4531914	4532026	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532027	4532154	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532155	4532228	1	+	2	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532155	4532228	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532229	4532394	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532395	4532592	1	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532395	4532592	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532593	4532741	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532742	4532825	0.48	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532742	4532825	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4532826	4532942	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4532943	4533002	1	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4532943	4533002	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533003	4533092	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533093	4533170	1	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533093	4533170	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533171	4533261	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533262	4533340	1	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533262	4533340	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533341	4533423	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533424	4533695	1	+	2	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533424	4533695	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4533696	4533799	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4533800	4534039	0.99	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4533800	4534039	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	intron	4534040	4534147	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	CDS	4534148	4534291	0.69	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	exon	4534148	4534291	.	+	.	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
Phchi.S4	AUGUSTUS	stop_codon	4534292	4534294	.	+	0	transcript_id "Phchi.S4G076400.t5"; gene_id "Phchi.S4G076400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11430.t1 is derived from g15480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6296633	6297378	.	-	.	Phchi.S4G101200
Phchi.S4	AUGUSTUS	transcript	6296633	6297378	.	-	.	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	stop_codon	6296630	6296632	.	-	0	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	CDS	6296633	6296843	0.61	-	1	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	exon	6296633	6296843	.	-	.	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	intron	6296844	6296914	.	-	.	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	CDS	6296915	6297195	0.46	-	0	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	exon	6296915	6297195	.	-	.	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	intron	6297196	6297270	.	-	.	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	CDS	6297271	6297378	0.62	-	0	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	exon	6297271	6297378	.	-	.	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
Phchi.S4	AUGUSTUS	start_codon	6297376	6297378	.	-	0	transcript_id "Phchi.S4G101200.t1"; gene_id "Phchi.S4G101200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10174.t1 is derived from g7350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46121909	46126253	.	-	.	Phchi.S1G733300
Phchi.S1	AUGUSTUS	transcript	46121909	46126253	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	stop_codon	46121906	46121908	.	-	0	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	CDS	46121909	46122382	0.69	-	0	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	exon	46121909	46122382	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	intron	46122383	46122465	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	CDS	46122466	46123041	0.2	-	0	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	exon	46122466	46123041	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	intron	46123042	46123158	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	CDS	46123159	46124534	0.92	-	2	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	exon	46123159	46124534	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	intron	46124535	46124689	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	CDS	46124690	46126253	0.89	-	0	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	exon	46124690	46126253	.	-	.	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
Phchi.S1	AUGUSTUS	start_codon	46126251	46126253	.	-	0	transcript_id "Phchi.S1G733300.t1"; gene_id "Phchi.S1G733300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3570.t1 is derived from g739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4555719	4556757	.	+	.	Phchi.S1G072900
Phchi.S1	AUGUSTUS	transcript	4555719	4556757	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	start_codon	4555719	4555721	.	+	0	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	CDS	4555719	4555834	1	+	0	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	exon	4555719	4555834	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	intron	4555835	4556182	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	CDS	4556183	4556265	0.88	+	1	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	exon	4556183	4556265	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	intron	4556266	4556398	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	CDS	4556399	4556572	0.59	+	2	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	exon	4556399	4556572	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	intron	4556573	4556665	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	CDS	4556666	4556757	0.34	+	2	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	exon	4556666	4556757	.	+	.	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
Phchi.S1	AUGUSTUS	stop_codon	4556758	4556760	.	+	0	transcript_id "Phchi.S1G072900.t1"; gene_id "Phchi.S1G072900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8869.t1 is derived from g6044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38385323	38387865	.	+	.	Phchi.S1G602800
Phchi.S1	AUGUSTUS	transcript	38385323	38387865	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	start_codon	38385323	38385325	.	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38385323	38385457	1	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38385323	38385457	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38385458	38385551	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38385552	38385860	0.99	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38385552	38385860	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38385861	38385942	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38385943	38386051	1	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38385943	38386051	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38386052	38386243	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38386244	38386337	1	+	2	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38386244	38386337	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38386338	38386683	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38386684	38386771	1	+	1	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38386684	38386771	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38386772	38386941	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38386942	38387025	1	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38386942	38387025	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38387026	38387116	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38387117	38387213	1	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38387117	38387213	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38387214	38387467	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38387468	38387555	1	+	2	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38387468	38387555	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38387556	38387676	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38387677	38387781	0.99	+	1	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38387677	38387781	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	intron	38387782	38387864	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	CDS	38387865	38387865	0.99	+	1	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	exon	38387865	38387865	.	+	.	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
Phchi.S1	AUGUSTUS	stop_codon	38387866	38387868	.	+	0	transcript_id "Phchi.S1G602800.t1"; gene_id "Phchi.S1G602800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10183.t1 is derived from g7359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46201287	46203197	.	-	.	Phchi.S1G734200
Phchi.S1	AUGUSTUS	transcript	46201287	46203197	.	-	.	transcript_id "Phchi.S1G734200.t1"; gene_id "Phchi.S1G734200"
Phchi.S1	AUGUSTUS	stop_codon	46201284	46201286	.	-	0	transcript_id "Phchi.S1G734200.t1"; gene_id "Phchi.S1G734200"
Phchi.S1	AUGUSTUS	CDS	46201287	46203197	0.85	-	0	transcript_id "Phchi.S1G734200.t1"; gene_id "Phchi.S1G734200"
Phchi.S1	AUGUSTUS	exon	46201287	46203197	.	-	.	transcript_id "Phchi.S1G734200.t1"; gene_id "Phchi.S1G734200"
Phchi.S1	AUGUSTUS	start_codon	46203195	46203197	.	-	0	transcript_id "Phchi.S1G734200.t1"; gene_id "Phchi.S1G734200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg324.t1 is derived from g10106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2268125	2272648	.	-	.	Phchi.S6G028300
Phchi.S6	AUGUSTUS	transcript	2268125	2272648	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	stop_codon	2268122	2268124	.	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2268125	2268490	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2268125	2268490	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2268491	2268569	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2268570	2268784	1	-	2	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2268570	2268784	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2268785	2268865	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2268866	2268944	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2268866	2268944	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2268945	2269159	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2269160	2269254	0.82	-	2	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2269160	2269254	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2269255	2269338	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2269339	2269367	0.59	-	1	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2269339	2269367	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2269368	2269426	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2269427	2269445	0.59	-	2	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2269427	2269445	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2269446	2269531	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2269532	2269585	1	-	2	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2269532	2269585	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2269586	2269697	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2269698	2269764	0.99	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2269698	2269764	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2269765	2269990	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2269991	2270056	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2269991	2270056	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2270057	2270154	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2270155	2270232	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2270155	2270232	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2270233	2270337	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2270338	2270390	1	-	2	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2270338	2270390	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2270391	2270469	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2270470	2270503	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2270470	2270503	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2270504	2270617	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2270618	2270654	1	-	1	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2270618	2270654	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2270655	2270808	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2270809	2270897	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2270809	2270897	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2270898	2271008	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2271009	2271131	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2271009	2271131	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2271132	2271214	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2271215	2271319	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2271215	2271319	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2271320	2271494	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2271495	2271599	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2271495	2271599	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2271600	2271702	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2271703	2271915	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2271703	2271915	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2271916	2271993	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2271994	2272140	1	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2271994	2272140	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2272141	2272284	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2272285	2272511	1	-	2	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2272285	2272511	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	intron	2272512	2272587	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	CDS	2272588	2272648	0.92	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	exon	2272588	2272648	.	-	.	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
Phchi.S6	AUGUSTUS	start_codon	2272646	2272648	.	-	0	transcript_id "Phchi.S6G028300.t1"; gene_id "Phchi.S6G028300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6644.t1 is derived from g3816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24224938	24225267	.	-	.	Phchi.S1G380300
Phchi.S1	AUGUSTUS	transcript	24224938	24225267	.	-	.	transcript_id "Phchi.S1G380300.t1"; gene_id "Phchi.S1G380300"
Phchi.S1	AUGUSTUS	stop_codon	24224935	24224937	.	-	0	transcript_id "Phchi.S1G380300.t1"; gene_id "Phchi.S1G380300"
Phchi.S1	AUGUSTUS	CDS	24224938	24225267	0.98	-	0	transcript_id "Phchi.S1G380300.t1"; gene_id "Phchi.S1G380300"
Phchi.S1	AUGUSTUS	exon	24224938	24225267	.	-	.	transcript_id "Phchi.S1G380300.t1"; gene_id "Phchi.S1G380300"
Phchi.S1	AUGUSTUS	start_codon	24225265	24225267	.	-	0	transcript_id "Phchi.S1G380300.t1"; gene_id "Phchi.S1G380300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6473.t1 is derived from g3645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23177631	23178232	.	+	.	Phchi.S1G363200
Phchi.S1	AUGUSTUS	transcript	23177631	23178232	.	+	.	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	start_codon	23177631	23177633	.	+	0	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	CDS	23177631	23177688	0.67	+	0	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	exon	23177631	23177688	.	+	.	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	intron	23177689	23177856	.	+	.	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	CDS	23177857	23178002	0.71	+	2	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	exon	23177857	23178002	.	+	.	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	intron	23178003	23178199	.	+	.	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	CDS	23178200	23178232	0.71	+	0	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	exon	23178200	23178232	.	+	.	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
Phchi.S1	AUGUSTUS	stop_codon	23178233	23178235	.	+	0	transcript_id "Phchi.S1G363200.t1"; gene_id "Phchi.S1G363200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9322.t1 is derived from g6497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40936597	40937277	.	-	.	Phchi.S1G648100
Phchi.S1	AUGUSTUS	transcript	40936597	40937277	.	-	.	transcript_id "Phchi.S1G648100.t1"; gene_id "Phchi.S1G648100"
Phchi.S1	AUGUSTUS	stop_codon	40936594	40936596	.	-	0	transcript_id "Phchi.S1G648100.t1"; gene_id "Phchi.S1G648100"
Phchi.S1	AUGUSTUS	CDS	40936597	40937277	0.94	-	0	transcript_id "Phchi.S1G648100.t1"; gene_id "Phchi.S1G648100"
Phchi.S1	AUGUSTUS	exon	40936597	40937277	.	-	.	transcript_id "Phchi.S1G648100.t1"; gene_id "Phchi.S1G648100"
Phchi.S1	AUGUSTUS	start_codon	40937275	40937277	.	-	0	transcript_id "Phchi.S1G648100.t1"; gene_id "Phchi.S1G648100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12920.t1 is derived from g11385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3167388	3168818	.	+	.	Phchi.S3G023900
Phchi.S3	AUGUSTUS	transcript	3167388	3168818	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	start_codon	3167388	3167390	.	+	0	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	CDS	3167388	3167415	0.44	+	0	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	exon	3167388	3167415	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	intron	3167416	3167516	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	CDS	3167517	3167528	0.59	+	2	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	exon	3167517	3167528	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	intron	3167529	3167660	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	CDS	3167661	3168086	0.79	+	2	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	exon	3167661	3168086	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	intron	3168087	3168175	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	CDS	3168176	3168203	1	+	2	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	exon	3168176	3168203	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	intron	3168204	3168381	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	CDS	3168382	3168465	0.47	+	1	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	exon	3168382	3168465	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	intron	3168466	3168805	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	CDS	3168806	3168818	0.47	+	1	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	exon	3168806	3168818	.	+	.	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
Phchi.S3	AUGUSTUS	stop_codon	3168819	3168821	.	+	0	transcript_id "Phchi.S3G023900.t1"; gene_id "Phchi.S3G023900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8451.t1 is derived from g5626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36000049	36007764	.	+	.	Phchi.S1G561000
Phchi.S1	AUGUSTUS	transcript	36000049	36007764	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	start_codon	36000049	36000051	.	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36000049	36000155	0.46	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36000049	36000155	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36000156	36000251	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36000252	36000490	0.34	+	1	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36000252	36000490	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36000491	36000897	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36000898	36001054	1	+	2	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36000898	36001054	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36001055	36001150	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36001151	36001370	1	+	1	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36001151	36001370	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36001371	36001481	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36001482	36001535	1	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36001482	36001535	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36001536	36001622	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36001623	36001702	1	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36001623	36001702	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36001703	36001910	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36001911	36002001	0.3	+	1	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36001911	36002001	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36002002	36002120	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36002121	36002187	0.31	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36002121	36002187	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36002188	36002275	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36002276	36002686	0.29	+	2	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36002276	36002686	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36002687	36002895	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36002896	36003470	0.68	+	2	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36002896	36003470	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36003471	36003555	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36003556	36003864	1	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36003556	36003864	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36003865	36003954	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36003955	36004110	1	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36003955	36004110	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36004111	36004229	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36004230	36004343	1	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36004230	36004343	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36004344	36004466	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36004467	36005141	0.83	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36004467	36005141	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36005142	36005269	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36005270	36005558	0.75	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36005270	36005558	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36005559	36005671	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36005672	36007656	0.59	+	2	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36005672	36007656	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	intron	36007657	36007746	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	CDS	36007747	36007764	0.61	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	exon	36007747	36007764	.	+	.	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
Phchi.S1	AUGUSTUS	stop_codon	36007765	36007767	.	+	0	transcript_id "Phchi.S1G561000.t1"; gene_id "Phchi.S1G561000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1837.t1 is derived from g8757.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3488028	3491145	.	+	.	Phchi.S5G044600
Phchi.S5	AUGUSTUS	transcript	3488028	3491145	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	start_codon	3488028	3488030	.	+	0	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3488028	3488282	0.99	+	0	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3488028	3488282	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3488283	3488363	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3488364	3488551	1	+	0	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3488364	3488551	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3488552	3488680	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3488681	3489765	1	+	1	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3488681	3489765	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3489766	3490065	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3490066	3490125	0.61	+	2	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3490066	3490125	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3490126	3490226	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3490227	3490352	0.77	+	2	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3490227	3490352	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3490353	3490455	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3490456	3490694	1	+	2	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3490456	3490694	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3490695	3490791	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3490792	3490910	0.99	+	0	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3490792	3490910	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	intron	3490911	3491024	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	CDS	3491025	3491145	1	+	1	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	exon	3491025	3491145	.	+	.	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
Phchi.S5	AUGUSTUS	stop_codon	3491146	3491148	.	+	0	transcript_id "Phchi.S5G044600.t1"; gene_id "Phchi.S5G044600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7815.t1 is derived from g4989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31340174	31341002	.	-	.	Phchi.S1G497400
Phchi.S1	AUGUSTUS	transcript	31340174	31341002	.	-	.	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	stop_codon	31340171	31340173	.	-	0	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	CDS	31340174	31340717	0.7	-	1	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	exon	31340174	31340717	.	-	.	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	intron	31340718	31340811	.	-	.	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	CDS	31340812	31340866	1	-	2	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	exon	31340812	31340866	.	-	.	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	intron	31340867	31340959	.	-	.	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	CDS	31340960	31341002	1	-	0	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	exon	31340960	31341002	.	-	.	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
Phchi.S1	AUGUSTUS	start_codon	31341000	31341002	.	-	0	transcript_id "Phchi.S1G497400.t1"; gene_id "Phchi.S1G497400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5340.t1 is derived from g2510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16369563	16370732	.	+	.	Phchi.S1G249900
Phchi.S1	AUGUSTUS	transcript	16369563	16370732	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	start_codon	16369563	16369565	.	+	0	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	CDS	16369563	16369601	0.35	+	0	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	exon	16369563	16369601	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	intron	16369602	16369707	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	CDS	16369708	16369769	0.97	+	0	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	exon	16369708	16369769	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	intron	16369770	16369873	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	CDS	16369874	16369967	0.97	+	1	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	exon	16369874	16369967	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	intron	16369968	16370054	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	CDS	16370055	16370262	1	+	0	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	exon	16370055	16370262	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	intron	16370263	16370658	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	CDS	16370659	16370732	1	+	2	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	exon	16370659	16370732	.	+	.	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
Phchi.S1	AUGUSTUS	stop_codon	16370733	16370735	.	+	0	transcript_id "Phchi.S1G249900.t1"; gene_id "Phchi.S1G249900"
# This transcript jg2624.t2 is derived from g9544.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2625.t1 is derived from g9545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7820064	7822582	.	-	.	Phchi.S5G123400
Phchi.S5	AUGUSTUS	transcript	7820064	7822582	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	stop_codon	7820061	7820063	.	-	0	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	CDS	7820064	7820658	1	-	1	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	exon	7820064	7820658	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	intron	7820659	7820741	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	CDS	7820742	7820812	0.36	-	0	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	exon	7820742	7820812	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	intron	7820813	7820928	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	CDS	7820929	7821488	0.36	-	2	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	exon	7820929	7821488	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	intron	7821489	7821595	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	CDS	7821596	7821628	0.87	-	2	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	exon	7821596	7821628	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	intron	7821629	7821729	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	CDS	7821730	7822582	0.85	-	0	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	exon	7821730	7822582	.	-	.	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
Phchi.S5	AUGUSTUS	start_codon	7822580	7822582	.	-	0	transcript_id "Phchi.S5G123400.t1"; gene_id "Phchi.S5G123400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6379.t1 is derived from g3551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22647309	22648784	.	+	.	Phchi.S1G353800
Phchi.S1	AUGUSTUS	transcript	22647309	22648784	.	+	.	transcript_id "Phchi.S1G353800.t1"; gene_id "Phchi.S1G353800"
Phchi.S1	AUGUSTUS	start_codon	22647309	22647311	.	+	0	transcript_id "Phchi.S1G353800.t1"; gene_id "Phchi.S1G353800"
Phchi.S1	AUGUSTUS	CDS	22647309	22648784	0.96	+	0	transcript_id "Phchi.S1G353800.t1"; gene_id "Phchi.S1G353800"
Phchi.S1	AUGUSTUS	exon	22647309	22648784	.	+	.	transcript_id "Phchi.S1G353800.t1"; gene_id "Phchi.S1G353800"
Phchi.S1	AUGUSTUS	stop_codon	22648785	22648787	.	+	0	transcript_id "Phchi.S1G353800.t1"; gene_id "Phchi.S1G353800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13363.t1 is derived from g11829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6356266	6357384	.	-	.	Phchi.S3G068200
Phchi.S3	AUGUSTUS	transcript	6356266	6357384	.	-	.	transcript_id "Phchi.S3G068200.t1"; gene_id "Phchi.S3G068200"
Phchi.S3	AUGUSTUS	stop_codon	6356263	6356265	.	-	0	transcript_id "Phchi.S3G068200.t1"; gene_id "Phchi.S3G068200"
Phchi.S3	AUGUSTUS	CDS	6356266	6357384	0.96	-	0	transcript_id "Phchi.S3G068200.t1"; gene_id "Phchi.S3G068200"
Phchi.S3	AUGUSTUS	exon	6356266	6357384	.	-	.	transcript_id "Phchi.S3G068200.t1"; gene_id "Phchi.S3G068200"
Phchi.S3	AUGUSTUS	start_codon	6357382	6357384	.	-	0	transcript_id "Phchi.S3G068200.t1"; gene_id "Phchi.S3G068200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3352.t1 is derived from g521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3071111	3071465	.	-	.	Phchi.S1G051100
Phchi.S1	AUGUSTUS	transcript	3071111	3071465	.	-	.	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	stop_codon	3071108	3071110	.	-	0	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	CDS	3071111	3071246	0.52	-	1	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	exon	3071111	3071246	.	-	.	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	intron	3071247	3071385	.	-	.	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	CDS	3071386	3071465	0.88	-	0	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	exon	3071386	3071465	.	-	.	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
Phchi.S1	AUGUSTUS	start_codon	3071463	3071465	.	-	0	transcript_id "Phchi.S1G051100.t1"; gene_id "Phchi.S1G051100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4842.t1 is derived from g2012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13059580	13060830	.	+	.	Phchi.S1G200100
Phchi.S1	AUGUSTUS	transcript	13060327	13060830	.	+	.	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	start_codon	13060327	13060329	.	+	0	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	CDS	13060327	13060371	0.77	+	0	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	exon	13060327	13060371	.	+	.	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	intron	13060372	13060476	.	+	.	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	CDS	13060477	13060830	0.98	+	0	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	exon	13060477	13060830	.	+	.	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	stop_codon	13060831	13060833	.	+	0	transcript_id "Phchi.S1G200100.t1"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	transcript	13059580	13060830	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	start_codon	13059580	13059582	.	+	0	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	CDS	13059580	13059879	0.5	+	0	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	exon	13059580	13059879	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	intron	13059880	13060001	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	CDS	13060002	13060248	0.47	+	0	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	exon	13060002	13060248	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	intron	13060249	13060324	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	CDS	13060325	13060371	0.61	+	2	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	exon	13060325	13060371	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	intron	13060372	13060476	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	CDS	13060477	13060830	1	+	0	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	exon	13060477	13060830	.	+	.	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
Phchi.S1	AUGUSTUS	stop_codon	13060831	13060833	.	+	0	transcript_id "Phchi.S1G200100.t2"; gene_id "Phchi.S1G200100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6036.t1 is derived from g3207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20528807	20532266	.	+	.	Phchi.S1G319500
Phchi.S1	AUGUSTUS	transcript	20528807	20532266	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	start_codon	20528807	20528809	.	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20528807	20528814	0.5	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20528807	20528814	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20528815	20528969	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20528970	20529079	0.5	+	1	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20528970	20529079	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529080	20529170	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529171	20529218	0.5	+	2	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529171	20529218	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529219	20529323	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529324	20529429	1	+	2	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529324	20529429	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529430	20529856	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529857	20530004	1	+	1	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529857	20530004	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530005	20530130	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530131	20530343	1	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530131	20530343	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530344	20530494	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530495	20530629	1	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530495	20530629	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530630	20530712	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530713	20530847	1	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530713	20530847	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530848	20530923	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530924	20531139	0.98	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530924	20531139	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531140	20531237	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20531238	20531362	1	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20531238	20531362	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531363	20531453	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20531454	20531511	1	+	1	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20531454	20531511	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531512	20531598	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20531599	20531664	0.44	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20531599	20531664	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531665	20532022	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20532023	20532110	0.71	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20532023	20532110	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20532111	20532204	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20532205	20532266	1	+	2	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20532205	20532266	.	+	.	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	stop_codon	20532267	20532269	.	+	0	transcript_id "Phchi.S1G319500.t1"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	transcript	20528807	20532266	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	start_codon	20528807	20528809	.	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20528807	20528814	0.38	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20528807	20528814	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20528815	20528969	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20528970	20529079	0.39	+	1	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20528970	20529079	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529080	20529170	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529171	20529218	0.39	+	2	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529171	20529218	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529219	20529323	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529324	20529429	1	+	2	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529324	20529429	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529430	20529657	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529658	20529736	0.39	+	1	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529658	20529736	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20529737	20529887	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20529888	20530004	0.35	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20529888	20530004	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530005	20530130	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530131	20530343	1	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530131	20530343	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530344	20530494	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530495	20530629	1	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530495	20530629	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530630	20530712	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530713	20530847	1	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530713	20530847	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20530848	20530923	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20530924	20531139	1	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20530924	20531139	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531140	20531237	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20531238	20531362	1	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20531238	20531362	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531363	20531453	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20531454	20531511	1	+	1	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20531454	20531511	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531512	20531598	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20531599	20531664	0.45	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20531599	20531664	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20531665	20532022	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20532023	20532110	0.62	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20532023	20532110	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	intron	20532111	20532204	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	CDS	20532205	20532266	1	+	2	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	exon	20532205	20532266	.	+	.	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
Phchi.S1	AUGUSTUS	stop_codon	20532267	20532269	.	+	0	transcript_id "Phchi.S1G319500.t2"; gene_id "Phchi.S1G319500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10576.t1 is derived from g14626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1038512	1039493	.	+	.	Phchi.S4G015800
Phchi.S4	AUGUSTUS	transcript	1038512	1039493	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	start_codon	1038512	1038514	.	+	0	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	CDS	1038512	1038958	0.37	+	0	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	exon	1038512	1038958	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	intron	1038959	1039081	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	CDS	1039082	1039109	0.26	+	0	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	exon	1039082	1039109	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	intron	1039110	1039207	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	CDS	1039208	1039323	0.41	+	2	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	exon	1039208	1039323	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	intron	1039324	1039418	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	CDS	1039419	1039493	0.68	+	0	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	exon	1039419	1039493	.	+	.	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
Phchi.S4	AUGUSTUS	stop_codon	1039494	1039496	.	+	0	transcript_id "Phchi.S4G015800.t1"; gene_id "Phchi.S4G015800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14864.t1 is derived from g13332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15096385	15098594	.	-	.	Phchi.S3G218300
Phchi.S3	AUGUSTUS	transcript	15096385	15098594	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	stop_codon	15096382	15096384	.	-	0	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	CDS	15096385	15096413	1	-	2	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	exon	15096385	15096413	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	intron	15096414	15096511	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	CDS	15096512	15097185	1	-	1	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	exon	15096512	15097185	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	intron	15097186	15097280	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	CDS	15097281	15097639	0.66	-	0	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	exon	15097281	15097639	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	intron	15097640	15097710	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	CDS	15097711	15098246	0.94	-	2	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	exon	15097711	15098246	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	intron	15098247	15098337	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	CDS	15098338	15098468	0.98	-	1	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	exon	15098338	15098468	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	intron	15098469	15098589	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	CDS	15098590	15098594	0.63	-	0	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	exon	15098590	15098594	.	-	.	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
Phchi.S3	AUGUSTUS	start_codon	15098592	15098594	.	-	0	transcript_id "Phchi.S3G218300.t1"; gene_id "Phchi.S3G218300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11869.t1 is derived from g15921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8918662	8919106	.	-	.	Phchi.S4G145100
Phchi.S4	AUGUSTUS	transcript	8918662	8919106	.	-	.	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	stop_codon	8918659	8918661	.	-	0	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	CDS	8918662	8918699	1	-	2	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	exon	8918662	8918699	.	-	.	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	intron	8918700	8918793	.	-	.	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	CDS	8918794	8918907	1	-	2	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	exon	8918794	8918907	.	-	.	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	intron	8918908	8918985	.	-	.	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	CDS	8918986	8919106	1	-	0	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	exon	8918986	8919106	.	-	.	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
Phchi.S4	AUGUSTUS	start_codon	8919104	8919106	.	-	0	transcript_id "Phchi.S4G145100.t1"; gene_id "Phchi.S4G145100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7477.t1 is derived from g4650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29547902	29549732	.	-	.	Phchi.S1G463600
Phchi.S1	AUGUSTUS	transcript	29547902	29549732	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	stop_codon	29547899	29547901	.	-	0	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29547902	29547999	1	-	2	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29547902	29547999	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29548000	29548162	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29548163	29548238	1	-	0	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29548163	29548238	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29548239	29548320	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29548321	29548419	1	-	0	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29548321	29548419	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29548420	29548517	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29548518	29548651	1	-	2	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29548518	29548651	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29548652	29548735	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29548736	29548884	1	-	1	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29548736	29548884	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29548885	29548984	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29548985	29549069	0.64	-	2	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29548985	29549069	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29549070	29549177	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29549178	29549294	0.95	-	2	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29549178	29549294	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29549295	29549372	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29549373	29549520	1	-	0	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29549373	29549520	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	intron	29549521	29549651	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	CDS	29549652	29549732	1	-	0	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	exon	29549652	29549732	.	-	.	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
Phchi.S1	AUGUSTUS	start_codon	29549730	29549732	.	-	0	transcript_id "Phchi.S1G463600.t1"; gene_id "Phchi.S1G463600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11865.t1 is derived from g15917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8854183	8855186	.	-	.	Phchi.S4G144700
Phchi.S4	AUGUSTUS	transcript	8854183	8855186	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	stop_codon	8854180	8854182	.	-	0	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	CDS	8854183	8854218	0.98	-	0	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	exon	8854183	8854218	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	intron	8854219	8854379	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	CDS	8854380	8854457	1	-	0	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	exon	8854380	8854457	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	intron	8854458	8854628	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	CDS	8854629	8854648	0.54	-	2	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	exon	8854629	8854648	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	intron	8854649	8854765	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	CDS	8854766	8855008	0.9	-	2	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	exon	8854766	8855008	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	intron	8855009	8855098	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	CDS	8855099	8855186	0.84	-	0	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	exon	8855099	8855186	.	-	.	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
Phchi.S4	AUGUSTUS	start_codon	8855184	8855186	.	-	0	transcript_id "Phchi.S4G144700.t1"; gene_id "Phchi.S4G144700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6532.t1 is derived from g3704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23520139	23521017	.	+	.	Phchi.S1G369100
Phchi.S1	AUGUSTUS	transcript	23520139	23521017	.	+	.	transcript_id "Phchi.S1G369100.t1"; gene_id "Phchi.S1G369100"
Phchi.S1	AUGUSTUS	start_codon	23520139	23520141	.	+	0	transcript_id "Phchi.S1G369100.t1"; gene_id "Phchi.S1G369100"
Phchi.S1	AUGUSTUS	CDS	23520139	23521017	0.77	+	0	transcript_id "Phchi.S1G369100.t1"; gene_id "Phchi.S1G369100"
Phchi.S1	AUGUSTUS	exon	23520139	23521017	.	+	.	transcript_id "Phchi.S1G369100.t1"; gene_id "Phchi.S1G369100"
Phchi.S1	AUGUSTUS	stop_codon	23521018	23521020	.	+	0	transcript_id "Phchi.S1G369100.t1"; gene_id "Phchi.S1G369100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10035.t1 is derived from g7211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45180196	45181076	.	-	.	Phchi.S1G719400
Phchi.S1	AUGUSTUS	transcript	45180196	45181076	.	-	.	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	stop_codon	45180193	45180195	.	-	0	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	CDS	45180196	45180460	0.62	-	1	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	exon	45180196	45180460	.	-	.	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	intron	45180461	45180564	.	-	.	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	CDS	45180565	45181076	0.82	-	0	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	exon	45180565	45181076	.	-	.	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
Phchi.S1	AUGUSTUS	start_codon	45181074	45181076	.	-	0	transcript_id "Phchi.S1G719400.t1"; gene_id "Phchi.S1G719400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5743.t1 is derived from g2913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18686517	18688506	.	-	.	Phchi.S1G290200
Phchi.S1	AUGUSTUS	transcript	18686517	18688506	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	stop_codon	18686514	18686516	.	-	0	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18686517	18686727	0.92	-	1	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18686517	18686727	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18686728	18686804	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18686805	18687031	0.99	-	0	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18686805	18687031	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18687032	18687123	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18687124	18687362	1	-	2	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18687124	18687362	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18687363	18687449	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18687450	18687531	1	-	0	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18687450	18687531	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18687532	18687611	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18687612	18687874	0.46	-	2	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18687612	18687874	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18687875	18687965	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18687966	18688071	1	-	0	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18687966	18688071	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18688072	18688161	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18688162	18688261	1	-	1	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18688162	18688261	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	intron	18688262	18688351	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	CDS	18688352	18688506	1	-	0	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	exon	18688352	18688506	.	-	.	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
Phchi.S1	AUGUSTUS	start_codon	18688504	18688506	.	-	0	transcript_id "Phchi.S1G290200.t1"; gene_id "Phchi.S1G290200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4041.t1 is derived from g1210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7310335	7310952	.	-	.	Phchi.S1G120000
Phchi.S1	AUGUSTUS	transcript	7310335	7310952	.	-	.	transcript_id "Phchi.S1G120000.t1"; gene_id "Phchi.S1G120000"
Phchi.S1	AUGUSTUS	stop_codon	7310332	7310334	.	-	0	transcript_id "Phchi.S1G120000.t1"; gene_id "Phchi.S1G120000"
Phchi.S1	AUGUSTUS	CDS	7310335	7310952	1	-	0	transcript_id "Phchi.S1G120000.t1"; gene_id "Phchi.S1G120000"
Phchi.S1	AUGUSTUS	exon	7310335	7310952	.	-	.	transcript_id "Phchi.S1G120000.t1"; gene_id "Phchi.S1G120000"
Phchi.S1	AUGUSTUS	start_codon	7310950	7310952	.	-	0	transcript_id "Phchi.S1G120000.t1"; gene_id "Phchi.S1G120000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13206.t1 is derived from g11671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4663924	4665345	.	-	.	Phchi.S3G052500
Phchi.S3	AUGUSTUS	transcript	4663924	4665345	.	-	.	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	stop_codon	4663921	4663923	.	-	0	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	CDS	4663924	4664002	0.7	-	1	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	exon	4663924	4664002	.	-	.	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	intron	4664003	4664135	.	-	.	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	CDS	4664136	4664409	0.49	-	2	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	exon	4664136	4664409	.	-	.	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	intron	4664410	4664528	.	-	.	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	CDS	4664529	4665345	0.26	-	0	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	exon	4664529	4665345	.	-	.	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
Phchi.S3	AUGUSTUS	start_codon	4665343	4665345	.	-	0	transcript_id "Phchi.S3G052500.t1"; gene_id "Phchi.S3G052500"
# This transcript jg5362.t2 is derived from g2532.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5363.t1 is derived from g2533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16504584	16506802	.	+	.	Phchi.S1G252200
Phchi.S1	AUGUSTUS	transcript	16504584	16506802	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	start_codon	16504584	16504586	.	+	0	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16504584	16504950	0.99	+	0	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16504584	16504950	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16504951	16505044	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16505045	16505100	1	+	2	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16505045	16505100	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16505101	16505235	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16505236	16505318	1	+	0	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16505236	16505318	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16505319	16505403	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16505404	16505482	1	+	1	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16505404	16505482	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16505483	16505568	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16505569	16505679	1	+	0	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16505569	16505679	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16505680	16505758	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16505759	16505868	1	+	0	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16505759	16505868	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16505869	16505964	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16505965	16506048	1	+	1	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16505965	16506048	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16506049	16506138	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16506139	16506176	1	+	1	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16506139	16506176	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16506177	16506289	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16506290	16506356	0.88	+	2	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16506290	16506356	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16506357	16506487	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16506488	16506561	0.77	+	1	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16506488	16506561	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	intron	16506562	16506650	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	CDS	16506651	16506802	0.87	+	2	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	exon	16506651	16506802	.	+	.	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
Phchi.S1	AUGUSTUS	stop_codon	16506803	16506805	.	+	0	transcript_id "Phchi.S1G252200.t1"; gene_id "Phchi.S1G252200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12509.t1 is derived from g8186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31744612	31747733	.	+	.	Phchi.S2G058900
Phchi.S2	AUGUSTUS	transcript	31744612	31747733	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	start_codon	31744612	31744614	.	+	0	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	CDS	31744612	31744765	0.99	+	0	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	exon	31744612	31744765	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	intron	31744766	31745269	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	CDS	31745270	31745324	0.67	+	2	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	exon	31745270	31745324	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	intron	31745325	31745414	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	CDS	31745415	31745666	0.61	+	1	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	exon	31745415	31745666	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	intron	31745667	31746105	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	CDS	31746106	31746395	0.37	+	1	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	exon	31746106	31746395	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	intron	31746396	31746643	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	CDS	31746644	31747231	0.17	+	2	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	exon	31746644	31747231	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	intron	31747232	31747362	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	CDS	31747363	31747733	0.35	+	2	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	exon	31747363	31747733	.	+	.	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
Phchi.S2	AUGUSTUS	stop_codon	31747734	31747736	.	+	0	transcript_id "Phchi.S2G058900.t1"; gene_id "Phchi.S2G058900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3166.t1 is derived from g335.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2040573	2042891	.	+	.	Phchi.S1G032500
Phchi.S1	AUGUSTUS	transcript	2040573	2042891	.	+	.	transcript_id "Phchi.S1G032500.t1"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	start_codon	2040573	2040575	.	+	0	transcript_id "Phchi.S1G032500.t1"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	CDS	2040573	2042891	1	+	0	transcript_id "Phchi.S1G032500.t1"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	exon	2040573	2042891	.	+	.	transcript_id "Phchi.S1G032500.t1"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	stop_codon	2042892	2042894	.	+	0	transcript_id "Phchi.S1G032500.t1"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	transcript	2042058	2042891	.	+	.	transcript_id "Phchi.S1G032500.t2"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	start_codon	2042058	2042060	.	+	0	transcript_id "Phchi.S1G032500.t2"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	CDS	2042058	2042891	1	+	0	transcript_id "Phchi.S1G032500.t2"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	exon	2042058	2042891	.	+	.	transcript_id "Phchi.S1G032500.t2"; gene_id "Phchi.S1G032500"
Phchi.S1	AUGUSTUS	stop_codon	2042892	2042894	.	+	0	transcript_id "Phchi.S1G032500.t2"; gene_id "Phchi.S1G032500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13651.t1 is derived from g12118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8012944	8015824	.	+	.	Phchi.S3G097000
Phchi.S3	AUGUSTUS	transcript	8012944	8015824	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	start_codon	8012944	8012946	.	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8012944	8013033	0.88	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8012944	8013033	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8013034	8013186	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8013187	8013207	0.95	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8013187	8013207	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8013208	8013389	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8013390	8013482	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8013390	8013482	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8013483	8013685	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8013686	8013760	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8013686	8013760	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8013761	8013860	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8013861	8013950	0.61	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8013861	8013950	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8013951	8014056	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8014057	8014146	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8014057	8014146	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8014147	8014237	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8014238	8014297	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8014238	8014297	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8014298	8014422	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8014423	8014580	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8014423	8014580	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8014581	8014703	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8014704	8014761	1	+	1	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8014704	8014761	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8014762	8014857	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8014858	8014897	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8014858	8014897	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8014898	8014983	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8014984	8015315	1	+	2	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8014984	8015315	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8015316	8015484	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8015485	8015562	1	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8015485	8015562	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	intron	8015563	8015659	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	CDS	8015660	8015824	0.8	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	exon	8015660	8015824	.	+	.	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
Phchi.S3	AUGUSTUS	stop_codon	8015825	8015827	.	+	0	transcript_id "Phchi.S3G097000.t1"; gene_id "Phchi.S3G097000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8500.t1 is derived from g5675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36332416	36333342	.	+	.	Phchi.S1G565900
Phchi.S1	AUGUSTUS	transcript	36332416	36333342	.	+	.	transcript_id "Phchi.S1G565900.t1"; gene_id "Phchi.S1G565900"
Phchi.S1	AUGUSTUS	start_codon	36332416	36332418	.	+	0	transcript_id "Phchi.S1G565900.t1"; gene_id "Phchi.S1G565900"
Phchi.S1	AUGUSTUS	CDS	36332416	36333342	0.87	+	0	transcript_id "Phchi.S1G565900.t1"; gene_id "Phchi.S1G565900"
Phchi.S1	AUGUSTUS	exon	36332416	36333342	.	+	.	transcript_id "Phchi.S1G565900.t1"; gene_id "Phchi.S1G565900"
Phchi.S1	AUGUSTUS	stop_codon	36333343	36333345	.	+	0	transcript_id "Phchi.S1G565900.t1"; gene_id "Phchi.S1G565900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4456.t1 is derived from g1626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10583809	10584222	.	-	.	Phchi.S1G161500
Phchi.S1	AUGUSTUS	transcript	10583809	10584045	.	-	.	transcript_id "Phchi.S1G161500.t1"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	stop_codon	10583806	10583808	.	-	0	transcript_id "Phchi.S1G161500.t1"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	CDS	10583809	10584045	0.95	-	0	transcript_id "Phchi.S1G161500.t1"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	exon	10583809	10584045	.	-	.	transcript_id "Phchi.S1G161500.t1"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	start_codon	10584043	10584045	.	-	0	transcript_id "Phchi.S1G161500.t1"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	transcript	10583809	10584222	.	-	.	transcript_id "Phchi.S1G161500.t2"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	stop_codon	10583806	10583808	.	-	0	transcript_id "Phchi.S1G161500.t2"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	CDS	10583809	10584222	0.53	-	0	transcript_id "Phchi.S1G161500.t2"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	exon	10583809	10584222	.	-	.	transcript_id "Phchi.S1G161500.t2"; gene_id "Phchi.S1G161500"
Phchi.S1	AUGUSTUS	start_codon	10584220	10584222	.	-	0	transcript_id "Phchi.S1G161500.t2"; gene_id "Phchi.S1G161500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13265.t1 is derived from g11730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4981277	4983141	.	+	.	Phchi.S3G058400
Phchi.S3	AUGUSTUS	transcript	4981277	4983141	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	start_codon	4981277	4981279	.	+	0	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	CDS	4981277	4981952	0.62	+	0	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	exon	4981277	4981952	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	intron	4981953	4982110	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	CDS	4982111	4982397	0.53	+	2	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	exon	4982111	4982397	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	intron	4982398	4982511	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	CDS	4982512	4982943	0.99	+	0	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	exon	4982512	4982943	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	intron	4982944	4983033	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	CDS	4983034	4983141	1	+	0	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	exon	4983034	4983141	.	+	.	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
Phchi.S3	AUGUSTUS	stop_codon	4983142	4983144	.	+	0	transcript_id "Phchi.S3G058400.t1"; gene_id "Phchi.S3G058400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13364.t1 is derived from g11830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6358345	6359918	.	-	.	Phchi.S3G068300
Phchi.S3	AUGUSTUS	transcript	6358345	6359918	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	stop_codon	6358342	6358344	.	-	0	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	CDS	6358345	6358556	0.97	-	2	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	exon	6358345	6358556	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	intron	6358557	6358643	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	CDS	6358644	6358908	0.96	-	0	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	exon	6358644	6358908	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	intron	6358909	6358978	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	CDS	6358979	6359215	0.76	-	0	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	exon	6358979	6359215	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	intron	6359216	6359346	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	CDS	6359347	6359375	0.95	-	2	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	exon	6359347	6359375	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	intron	6359376	6359549	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	CDS	6359550	6359676	1	-	0	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	exon	6359550	6359676	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	intron	6359677	6359759	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	CDS	6359760	6359918	0.99	-	0	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	exon	6359760	6359918	.	-	.	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
Phchi.S3	AUGUSTUS	start_codon	6359916	6359918	.	-	0	transcript_id "Phchi.S3G068300.t1"; gene_id "Phchi.S3G068300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8825.t1 is derived from g6000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38148071	38150827	.	-	.	Phchi.S1G598400
Phchi.S1	AUGUSTUS	transcript	38148071	38150827	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	stop_codon	38148068	38148070	.	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148071	38148241	0.94	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148071	38148241	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38148242	38148321	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148322	38148510	0.76	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148322	38148510	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38148511	38148617	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148618	38148674	0.58	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148618	38148674	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38148675	38148764	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148765	38149292	0.78	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148765	38149292	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38149293	38149405	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38149406	38149486	1	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38149406	38149486	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38149487	38149667	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38149668	38149815	1	-	1	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38149668	38149815	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38149816	38149982	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38149983	38150085	1	-	2	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38149983	38150085	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150086	38150182	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150183	38150272	1	-	2	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150183	38150272	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150273	38150356	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150357	38150423	1	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150357	38150423	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150424	38150563	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150564	38150624	1	-	1	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150564	38150624	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150625	38150717	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150718	38150827	0.94	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150718	38150827	.	-	.	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	start_codon	38150825	38150827	.	-	0	transcript_id "Phchi.S1G598400.t1"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	transcript	38148071	38150827	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	stop_codon	38148068	38148070	.	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148071	38148241	0.95	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148071	38148241	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38148242	38148321	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148322	38148510	0.68	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148322	38148510	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38148511	38148617	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148618	38148674	0.49	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148618	38148674	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38148675	38148764	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38148765	38149292	0.76	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38148765	38149292	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38149293	38149405	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38149406	38149486	0.99	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38149406	38149486	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38149487	38149667	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38149668	38149815	1	-	1	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38149668	38149815	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38149816	38149982	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38149983	38150085	0.88	-	2	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38149983	38150085	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150086	38150175	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150176	38150272	0.64	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150176	38150272	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150273	38150356	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150357	38150423	1	-	1	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150357	38150423	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150424	38150558	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150559	38150624	1	-	1	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150559	38150624	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	intron	38150625	38150717	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	CDS	38150718	38150827	0.93	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	exon	38150718	38150827	.	-	.	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
Phchi.S1	AUGUSTUS	start_codon	38150825	38150827	.	-	0	transcript_id "Phchi.S1G598400.t2"; gene_id "Phchi.S1G598400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4214.t1 is derived from g1383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8951580	8954459	.	-	.	Phchi.S1G137300
Phchi.S1	AUGUSTUS	transcript	8951580	8954459	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	stop_codon	8951577	8951579	.	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8951580	8951699	1	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8951580	8951699	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8951700	8951818	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8951819	8952046	1	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8951819	8952046	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8952047	8952239	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8952240	8952407	1	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8952240	8952407	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8952408	8952648	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8952649	8952764	1	-	2	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8952649	8952764	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8952765	8952839	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8952840	8952992	1	-	2	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8952840	8952992	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8952993	8953105	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8953106	8953249	1	-	2	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8953106	8953249	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8953250	8953343	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8953344	8953929	0.8	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8953344	8953929	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	intron	8953930	8954006	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	CDS	8954007	8954459	0.65	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	exon	8954007	8954459	.	-	.	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
Phchi.S1	AUGUSTUS	start_codon	8954457	8954459	.	-	0	transcript_id "Phchi.S1G137300.t1"; gene_id "Phchi.S1G137300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12706.t1 is derived from g11171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	653820	656563	.	-	.	Phchi.S3G002500
Phchi.S3	AUGUSTUS	transcript	653820	656563	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	stop_codon	653817	653819	.	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	653820	653895	1	-	1	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	653820	653895	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	653896	654007	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	654008	654081	1	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	654008	654081	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	654082	654163	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	654164	654252	1	-	2	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	654164	654252	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	654253	654423	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	654424	654547	0.44	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	654424	654547	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	654548	654638	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	654639	654890	1	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	654639	654890	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	654891	655222	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	655223	655461	1	-	2	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	655223	655461	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	655462	655586	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	655587	655821	1	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	655587	655821	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	655822	656110	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	656111	656171	0.71	-	1	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	656111	656171	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	intron	656172	656468	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	CDS	656469	656563	0.32	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	exon	656469	656563	.	-	.	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
Phchi.S3	AUGUSTUS	start_codon	656561	656563	.	-	0	transcript_id "Phchi.S3G002500.t1"; gene_id "Phchi.S3G002500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15842.t1 is derived from g14312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21736831	21740795	.	-	.	Phchi.S3G316100
Phchi.S3	AUGUSTUS	transcript	21736831	21740795	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	stop_codon	21736828	21736830	.	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21736831	21736873	0.98	-	1	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21736831	21736873	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21736874	21736980	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21736981	21737255	0.58	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21736981	21737255	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21737256	21737407	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21737408	21737515	0.89	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21737408	21737515	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21737516	21737612	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21737613	21738108	0.96	-	1	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21737613	21738108	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21738109	21738263	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21738264	21738670	0.89	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21738264	21738670	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21738671	21738766	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21738767	21738859	1	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21738767	21738859	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21738860	21738971	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21738972	21739028	0.99	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21738972	21739028	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21739029	21739135	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21739136	21739323	0.91	-	2	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21739136	21739323	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21739324	21739437	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21739438	21739552	0.99	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21739438	21739552	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21739553	21739652	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21739653	21739739	1	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21739653	21739739	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21739740	21739815	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21739816	21739899	1	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21739816	21739899	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21739900	21740055	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21740056	21740154	1	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21740056	21740154	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21740155	21740263	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21740264	21740493	1	-	2	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21740264	21740493	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	intron	21740494	21740575	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	CDS	21740576	21740795	0.48	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	exon	21740576	21740795	.	-	.	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
Phchi.S3	AUGUSTUS	start_codon	21740793	21740795	.	-	0	transcript_id "Phchi.S3G316100.t1"; gene_id "Phchi.S3G316100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14858.t1 is derived from g13326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15083794	15085798	.	+	.	Phchi.S3G217700
Phchi.S3	AUGUSTUS	transcript	15083794	15085798	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	start_codon	15083794	15083796	.	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15083794	15083895	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15083794	15083895	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15083896	15083977	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15083978	15084061	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15083978	15084061	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15084062	15084138	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15084139	15084268	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15084139	15084268	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15084269	15084420	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15084421	15084633	1	+	2	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15084421	15084633	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15084634	15084770	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15084771	15084802	1	+	2	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15084771	15084802	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15084803	15084889	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15084890	15084949	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15084890	15084949	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15084950	15085041	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15085042	15085089	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15085042	15085089	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15085090	15085178	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15085179	15085289	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15085179	15085289	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15085290	15085420	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15085421	15085498	1	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15085421	15085498	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15085499	15085582	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15085583	15085648	0.9	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15085583	15085648	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	intron	15085649	15085750	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	CDS	15085751	15085798	0.9	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	exon	15085751	15085798	.	+	.	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
Phchi.S3	AUGUSTUS	stop_codon	15085799	15085801	.	+	0	transcript_id "Phchi.S3G217700.t1"; gene_id "Phchi.S3G217700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7362.t1 is derived from g4534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28775994	28778184	.	+	.	Phchi.S1G452100
Phchi.S1	AUGUSTUS	transcript	28775994	28778184	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	start_codon	28775994	28775996	.	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	CDS	28775994	28776329	1	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	exon	28775994	28776329	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	intron	28776330	28776418	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	CDS	28776419	28776632	1	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	exon	28776419	28776632	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	intron	28776633	28776788	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	CDS	28776789	28777084	1	+	2	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	exon	28776789	28777084	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	intron	28777085	28777172	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	CDS	28777173	28777370	1	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	exon	28777173	28777370	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	intron	28777371	28777466	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	CDS	28777467	28777517	1	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	exon	28777467	28777517	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	intron	28777518	28777641	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	CDS	28777642	28778184	0.58	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	exon	28777642	28778184	.	+	.	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
Phchi.S1	AUGUSTUS	stop_codon	28778185	28778187	.	+	0	transcript_id "Phchi.S1G452100.t1"; gene_id "Phchi.S1G452100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1002.t1 is derived from g10785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7019950	7020195	.	+	.	Phchi.S6G096100
Phchi.S6	AUGUSTUS	transcript	7019950	7020195	.	+	.	transcript_id "Phchi.S6G096100.t1"; gene_id "Phchi.S6G096100"
Phchi.S6	AUGUSTUS	start_codon	7019950	7019952	.	+	0	transcript_id "Phchi.S6G096100.t1"; gene_id "Phchi.S6G096100"
Phchi.S6	AUGUSTUS	CDS	7019950	7020195	0.41	+	0	transcript_id "Phchi.S6G096100.t1"; gene_id "Phchi.S6G096100"
Phchi.S6	AUGUSTUS	exon	7019950	7020195	.	+	.	transcript_id "Phchi.S6G096100.t1"; gene_id "Phchi.S6G096100"
Phchi.S6	AUGUSTUS	stop_codon	7020196	7020198	.	+	0	transcript_id "Phchi.S6G096100.t1"; gene_id "Phchi.S6G096100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9470.t1 is derived from g6646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41630267	41631484	.	+	.	Phchi.S1G662900
Phchi.S1	AUGUSTUS	transcript	41630267	41631484	.	+	.	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	start_codon	41630267	41630269	.	+	0	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	CDS	41630267	41630668	0.29	+	0	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	exon	41630267	41630668	.	+	.	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	intron	41630669	41630896	.	+	.	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	CDS	41630897	41631484	0.41	+	0	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	exon	41630897	41631484	.	+	.	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
Phchi.S1	AUGUSTUS	stop_codon	41631485	41631487	.	+	0	transcript_id "Phchi.S1G662900.t1"; gene_id "Phchi.S1G662900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12290.t1 is derived from g7966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8855360	8856135	.	-	.	Phchi.S2G037000
Phchi.S2	AUGUSTUS	transcript	8855360	8856135	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	stop_codon	8855357	8855359	.	-	0	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	CDS	8855360	8855416	1	-	0	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	exon	8855360	8855416	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	intron	8855417	8855489	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	CDS	8855490	8855541	1	-	1	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	exon	8855490	8855541	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	intron	8855542	8855629	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	CDS	8855630	8855794	0.98	-	1	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	exon	8855630	8855794	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	intron	8855795	8855902	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	CDS	8855903	8856135	1	-	0	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	exon	8855903	8856135	.	-	.	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
Phchi.S2	AUGUSTUS	start_codon	8856133	8856135	.	-	0	transcript_id "Phchi.S2G037000.t1"; gene_id "Phchi.S2G037000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3264.t1 is derived from g433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2584732	2588641	.	+	.	Phchi.S1G042300
Phchi.S1	AUGUSTUS	transcript	2584732	2588641	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	start_codon	2584732	2584734	.	+	0	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2584732	2584990	0.73	+	0	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2584732	2584990	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2584991	2585171	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2585172	2585380	0.71	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2585172	2585380	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2585381	2585471	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2585472	2585709	1	+	0	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2585472	2585709	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2585710	2585874	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2585875	2586120	0.99	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2585875	2586120	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2586121	2586310	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2586311	2586361	1	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2586311	2586361	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2586362	2586493	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2586494	2586754	1	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2586494	2586754	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2586755	2586870	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2586871	2586923	1	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2586871	2586923	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2586924	2587036	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2587037	2587151	1	+	0	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2587037	2587151	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2587152	2587236	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2587237	2587491	1	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2587237	2587491	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	intron	2587492	2587595	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	CDS	2587596	2588641	0.95	+	2	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	exon	2587596	2588641	.	+	.	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
Phchi.S1	AUGUSTUS	stop_codon	2588642	2588644	.	+	0	transcript_id "Phchi.S1G042300.t1"; gene_id "Phchi.S1G042300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13548.t1 is derived from g12015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7449864	7453615	.	-	.	Phchi.S3G086700
Phchi.S3	AUGUSTUS	transcript	7452217	7453615	.	-	.	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	stop_codon	7452214	7452216	.	-	0	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	CDS	7452217	7452282	1	-	0	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	exon	7452217	7452282	.	-	.	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	intron	7452283	7452409	.	-	.	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	CDS	7452410	7453615	0.66	-	0	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	exon	7452410	7453615	.	-	.	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	start_codon	7453613	7453615	.	-	0	transcript_id "Phchi.S3G086700.t1"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	transcript	7449864	7453615	.	-	.	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	stop_codon	7449861	7449863	.	-	0	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	CDS	7449864	7450484	1	-	0	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	exon	7449864	7450484	.	-	.	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	intron	7450485	7450582	.	-	.	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	CDS	7450583	7453615	0.54	-	0	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	exon	7450583	7453615	.	-	.	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
Phchi.S3	AUGUSTUS	start_codon	7453613	7453615	.	-	0	transcript_id "Phchi.S3G086700.t2"; gene_id "Phchi.S3G086700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5107.t1 is derived from g2277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14774740	14775783	.	+	.	Phchi.S1G226600
Phchi.S1	AUGUSTUS	transcript	14774740	14775783	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	start_codon	14774740	14774742	.	+	0	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	CDS	14774740	14774821	0.95	+	0	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	exon	14774740	14774821	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	intron	14774822	14774894	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	CDS	14774895	14774965	1	+	2	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	exon	14774895	14774965	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	intron	14774966	14775058	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	CDS	14775059	14775084	1	+	0	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	exon	14775059	14775084	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	intron	14775085	14775168	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	CDS	14775169	14775391	1	+	1	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	exon	14775169	14775391	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	intron	14775392	14775460	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	CDS	14775461	14775597	1	+	0	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	exon	14775461	14775597	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	intron	14775598	14775695	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	CDS	14775696	14775783	1	+	1	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	exon	14775696	14775783	.	+	.	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
Phchi.S1	AUGUSTUS	stop_codon	14775784	14775786	.	+	0	transcript_id "Phchi.S1G226600.t1"; gene_id "Phchi.S1G226600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1035.t1 is derived from g10818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7224986	7227872	.	-	.	Phchi.S6G099400
Phchi.S6	AUGUSTUS	transcript	7224986	7227872	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	stop_codon	7224983	7224985	.	-	0	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7224986	7225566	0.73	-	2	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7224986	7225566	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7225567	7225929	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7225930	7226339	0.67	-	1	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7225930	7226339	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7226340	7226681	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7226682	7226959	0.95	-	0	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7226682	7226959	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7226960	7227189	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227190	7227214	0.97	-	1	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227190	7227214	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7227215	7227334	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227335	7227495	0.98	-	0	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227335	7227495	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7227496	7227574	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227575	7227654	1	-	2	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227575	7227654	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7227655	7227745	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227746	7227872	0.98	-	0	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227746	7227872	.	-	.	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	start_codon	7227870	7227872	.	-	0	transcript_id "Phchi.S6G099400.t1"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	transcript	7224986	7227872	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	stop_codon	7224983	7224985	.	-	0	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7224986	7225566	0.65	-	2	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7224986	7225566	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7225567	7225929	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7225930	7226339	0.65	-	1	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7225930	7226339	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7226340	7226681	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7226682	7226959	0.89	-	0	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7226682	7226959	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7226960	7227163	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227164	7227197	0.72	-	1	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227164	7227197	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7227198	7227334	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227335	7227495	1	-	0	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227335	7227495	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7227496	7227574	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227575	7227654	1	-	2	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227575	7227654	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	intron	7227655	7227745	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	CDS	7227746	7227872	0.98	-	0	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	exon	7227746	7227872	.	-	.	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
Phchi.S6	AUGUSTUS	start_codon	7227870	7227872	.	-	0	transcript_id "Phchi.S6G099400.t2"; gene_id "Phchi.S6G099400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4370.t1 is derived from g1539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10101532	10102380	.	-	.	Phchi.S1G152900
Phchi.S1	AUGUSTUS	transcript	10101532	10102380	.	-	.	transcript_id "Phchi.S1G152900.t1"; gene_id "Phchi.S1G152900"
Phchi.S1	AUGUSTUS	stop_codon	10101529	10101531	.	-	0	transcript_id "Phchi.S1G152900.t1"; gene_id "Phchi.S1G152900"
Phchi.S1	AUGUSTUS	CDS	10101532	10102380	0.8	-	0	transcript_id "Phchi.S1G152900.t1"; gene_id "Phchi.S1G152900"
Phchi.S1	AUGUSTUS	exon	10101532	10102380	.	-	.	transcript_id "Phchi.S1G152900.t1"; gene_id "Phchi.S1G152900"
Phchi.S1	AUGUSTUS	start_codon	10102378	10102380	.	-	0	transcript_id "Phchi.S1G152900.t1"; gene_id "Phchi.S1G152900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11073.t1 is derived from g15123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3972047	3972352	.	-	.	Phchi.S4G065500
Phchi.S4	AUGUSTUS	transcript	3972047	3972352	.	-	.	transcript_id "Phchi.S4G065500.t1"; gene_id "Phchi.S4G065500"
Phchi.S4	AUGUSTUS	stop_codon	3972044	3972046	.	-	0	transcript_id "Phchi.S4G065500.t1"; gene_id "Phchi.S4G065500"
Phchi.S4	AUGUSTUS	CDS	3972047	3972352	0.76	-	0	transcript_id "Phchi.S4G065500.t1"; gene_id "Phchi.S4G065500"
Phchi.S4	AUGUSTUS	exon	3972047	3972352	.	-	.	transcript_id "Phchi.S4G065500.t1"; gene_id "Phchi.S4G065500"
Phchi.S4	AUGUSTUS	start_codon	3972350	3972352	.	-	0	transcript_id "Phchi.S4G065500.t1"; gene_id "Phchi.S4G065500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6050.t1 is derived from g3221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20633889	20634432	.	-	.	Phchi.S1G320900
Phchi.S1	AUGUSTUS	transcript	20633889	20634432	.	-	.	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	stop_codon	20633886	20633888	.	-	0	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	CDS	20633889	20633938	0.56	-	2	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	exon	20633889	20633938	.	-	.	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	intron	20633939	20634044	.	-	.	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	CDS	20634045	20634432	0.41	-	0	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	exon	20634045	20634432	.	-	.	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
Phchi.S1	AUGUSTUS	start_codon	20634430	20634432	.	-	0	transcript_id "Phchi.S1G320900.t1"; gene_id "Phchi.S1G320900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1330.t1 is derived from g11113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9054495	9058023	.	-	.	Phchi.S6G128900
Phchi.S6	AUGUSTUS	transcript	9054495	9058023	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	stop_codon	9054492	9054494	.	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9054495	9054589	0.97	-	2	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9054495	9054589	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9054590	9054686	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9054687	9054795	1	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9054687	9054795	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9054796	9054875	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9054876	9054940	1	-	2	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9054876	9054940	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9054941	9055043	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9055044	9055169	1	-	2	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9055044	9055169	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9055170	9055266	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9055267	9055390	0.66	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9055267	9055390	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9055391	9055487	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9055488	9055562	0.68	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9055488	9055562	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9055563	9055657	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9055658	9055744	1	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9055658	9055744	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9055745	9055842	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9055843	9055887	0.99	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9055843	9055887	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9055888	9055965	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9055966	9056028	1	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9055966	9056028	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9056029	9056121	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9056122	9056202	1	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9056122	9056202	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9056203	9056286	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9056287	9056471	1	-	2	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9056287	9056471	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	intron	9056472	9056552	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	CDS	9056553	9058023	0.29	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	exon	9056553	9058023	.	-	.	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
Phchi.S6	AUGUSTUS	start_codon	9058021	9058023	.	-	0	transcript_id "Phchi.S6G128900.t1"; gene_id "Phchi.S6G128900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9486.t1 is derived from g6662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41986524	41989885	.	+	.	Phchi.S1G664500
Phchi.S1	AUGUSTUS	transcript	41986524	41989885	.	+	.	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	start_codon	41986524	41986526	.	+	0	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	CDS	41986524	41989771	0.98	+	0	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	exon	41986524	41989771	.	+	.	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	intron	41989772	41989878	.	+	.	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	CDS	41989879	41989885	0.7	+	1	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	exon	41989879	41989885	.	+	.	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
Phchi.S1	AUGUSTUS	stop_codon	41989886	41989888	.	+	0	transcript_id "Phchi.S1G664500.t1"; gene_id "Phchi.S1G664500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13287.t1 is derived from g11753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5189570	5190071	.	-	.	Phchi.S3G060600
Phchi.S3	AUGUSTUS	transcript	5189570	5190071	.	-	.	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	stop_codon	5189567	5189569	.	-	0	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	CDS	5189570	5189571	1	-	2	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	exon	5189570	5189571	.	-	.	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	intron	5189572	5189663	.	-	.	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	CDS	5189664	5189824	1	-	1	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	exon	5189664	5189824	.	-	.	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	intron	5189825	5190003	.	-	.	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	CDS	5190004	5190071	0.89	-	0	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	exon	5190004	5190071	.	-	.	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
Phchi.S3	AUGUSTUS	start_codon	5190069	5190071	.	-	0	transcript_id "Phchi.S3G060600.t1"; gene_id "Phchi.S3G060600"
# This transcript jg6158.t2 is derived from g3329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6159.t1 is derived from g3330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21245471	21246178	.	+	.	Phchi.S1G331800
Phchi.S1	AUGUSTUS	transcript	21245471	21246178	.	+	.	transcript_id "Phchi.S1G331800.t1"; gene_id "Phchi.S1G331800"
Phchi.S1	AUGUSTUS	start_codon	21245471	21245473	.	+	0	transcript_id "Phchi.S1G331800.t1"; gene_id "Phchi.S1G331800"
Phchi.S1	AUGUSTUS	CDS	21245471	21246178	0.2	+	0	transcript_id "Phchi.S1G331800.t1"; gene_id "Phchi.S1G331800"
Phchi.S1	AUGUSTUS	exon	21245471	21246178	.	+	.	transcript_id "Phchi.S1G331800.t1"; gene_id "Phchi.S1G331800"
Phchi.S1	AUGUSTUS	stop_codon	21246179	21246181	.	+	0	transcript_id "Phchi.S1G331800.t1"; gene_id "Phchi.S1G331800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3469.t1 is derived from g638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3915228	3916932	.	+	.	Phchi.S1G062800
Phchi.S1	AUGUSTUS	transcript	3915228	3916932	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	start_codon	3915228	3915230	.	+	0	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	CDS	3915228	3915480	0.49	+	0	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	exon	3915228	3915480	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	intron	3915481	3915697	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	CDS	3915698	3915726	0.53	+	2	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	exon	3915698	3915726	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	intron	3915727	3915897	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	CDS	3915898	3916270	0.65	+	0	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	exon	3915898	3916270	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	intron	3916271	3916366	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	CDS	3916367	3916932	0.95	+	2	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	exon	3916367	3916932	.	+	.	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
Phchi.S1	AUGUSTUS	stop_codon	3916933	3916935	.	+	0	transcript_id "Phchi.S1G062800.t1"; gene_id "Phchi.S1G062800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1400.t1 is derived from g8319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	133267	135952	.	+	.	Phchi.S5G000900
Phchi.S5	AUGUSTUS	transcript	133267	135952	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	start_codon	133267	133269	.	+	0	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	133267	133315	0.64	+	0	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	133267	133315	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	133316	133426	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	133427	133697	0.66	+	2	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	133427	133697	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	133698	133790	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	133791	134005	1	+	1	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	133791	134005	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	134006	134087	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	134088	134330	1	+	2	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	134088	134330	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	134331	134415	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	134416	134742	0.96	+	2	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	134416	134742	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	134743	134855	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	134856	134894	0.96	+	2	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	134856	134894	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	134895	135046	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	135047	135201	1	+	2	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	135047	135201	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	135202	135280	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	135281	135363	1	+	0	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	135281	135363	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	intron	135364	135456	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	CDS	135457	135952	1	+	1	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	exon	135457	135952	.	+	.	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
Phchi.S5	AUGUSTUS	stop_codon	135953	135955	.	+	0	transcript_id "Phchi.S5G000900.t1"; gene_id "Phchi.S5G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12018.t1 is derived from g7693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	597534	598920	.	-	.	Phchi.S2G009800
Phchi.S2	AUGUSTUS	transcript	597534	598920	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	stop_codon	597531	597533	.	-	0	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	CDS	597534	597613	1	-	2	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	exon	597534	597613	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	intron	597614	597830	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	CDS	597831	598086	1	-	0	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	exon	597831	598086	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	intron	598087	598198	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	CDS	598199	598591	0.55	-	0	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	exon	598199	598591	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	intron	598592	598674	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	CDS	598675	598920	0.81	-	0	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	exon	598675	598920	.	-	.	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
Phchi.S2	AUGUSTUS	start_codon	598918	598920	.	-	0	transcript_id "Phchi.S2G009800.t1"; gene_id "Phchi.S2G009800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2488.t1 is derived from g9408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6921815	6922168	.	-	.	Phchi.S5G109700
Phchi.S5	AUGUSTUS	transcript	6921815	6922168	.	-	.	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	stop_codon	6921812	6921814	.	-	0	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	CDS	6921815	6921991	0.3	-	0	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	exon	6921815	6921991	.	-	.	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	intron	6921992	6922078	.	-	.	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	CDS	6922079	6922168	0.15	-	0	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	exon	6922079	6922168	.	-	.	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
Phchi.S5	AUGUSTUS	start_codon	6922166	6922168	.	-	0	transcript_id "Phchi.S5G109700.t1"; gene_id "Phchi.S5G109700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6981.t1 is derived from g4153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26257091	26262985	.	+	.	Phchi.S1G414000
Phchi.S1	AUGUSTUS	transcript	26257091	26262985	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	start_codon	26257091	26257093	.	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26257091	26257339	0.99	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26257091	26257339	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26257340	26257466	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26257467	26257568	1	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26257467	26257568	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26257569	26257669	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26257670	26257793	1	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26257670	26257793	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26257794	26257925	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26257926	26257987	0.99	+	2	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26257926	26257987	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26257988	26258092	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26258093	26258147	0.99	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26258093	26258147	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26258148	26258268	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26258269	26258475	0.98	+	2	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26258269	26258475	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26258476	26258589	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26258590	26258924	0.99	+	2	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26258590	26258924	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26258925	26259007	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26259008	26259152	1	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26259008	26259152	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26259153	26259238	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26259239	26259513	0.98	+	2	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26259239	26259513	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26259514	26259615	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26259616	26259646	1	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26259616	26259646	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26259647	26259735	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26259736	26259899	1	+	2	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26259736	26259899	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26259900	26259994	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26259995	26260153	1	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26259995	26260153	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26260154	26260284	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26260285	26260452	0.91	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26260285	26260452	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26260453	26260817	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26260818	26260882	0.93	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26260818	26260882	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	intron	26260883	26260983	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	CDS	26260984	26262985	0.97	+	1	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	exon	26260984	26262985	.	+	.	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
Phchi.S1	AUGUSTUS	stop_codon	26262986	26262988	.	+	0	transcript_id "Phchi.S1G414000.t1"; gene_id "Phchi.S1G414000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6273.t1 is derived from g3445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21951697	21953474	.	+	.	Phchi.S1G343200
Phchi.S1	AUGUSTUS	transcript	21951697	21953474	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	start_codon	21951697	21951699	.	+	0	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	CDS	21951697	21951897	1	+	0	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	exon	21951697	21951897	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	intron	21951898	21952177	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	CDS	21952178	21952478	0.96	+	0	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	exon	21952178	21952478	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	intron	21952479	21952580	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	CDS	21952581	21952739	0.96	+	2	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	exon	21952581	21952739	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	intron	21952740	21952844	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	CDS	21952845	21952933	0.94	+	2	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	exon	21952845	21952933	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	intron	21952934	21953021	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	CDS	21953022	21953147	0.93	+	0	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	exon	21953022	21953147	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	intron	21953148	21953249	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	CDS	21953250	21953474	1	+	0	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	exon	21953250	21953474	.	+	.	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
Phchi.S1	AUGUSTUS	stop_codon	21953475	21953477	.	+	0	transcript_id "Phchi.S1G343200.t1"; gene_id "Phchi.S1G343200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15042.t1 is derived from g13510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16714267	16714777	.	-	.	Phchi.S3G236100
Phchi.S3	AUGUSTUS	transcript	16714267	16714777	.	-	.	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	stop_codon	16714264	16714266	.	-	0	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	CDS	16714267	16714351	0.63	-	1	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	exon	16714267	16714351	.	-	.	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	intron	16714352	16714448	.	-	.	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	CDS	16714449	16714592	0.6	-	1	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	exon	16714449	16714592	.	-	.	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	intron	16714593	16714706	.	-	.	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	CDS	16714707	16714777	0.61	-	0	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	exon	16714707	16714777	.	-	.	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
Phchi.S3	AUGUSTUS	start_codon	16714775	16714777	.	-	0	transcript_id "Phchi.S3G236100.t1"; gene_id "Phchi.S3G236100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11058.t1 is derived from g15108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3919822	3923003	.	+	.	Phchi.S4G064000
Phchi.S4	AUGUSTUS	transcript	3919822	3923003	.	+	.	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	start_codon	3919822	3919824	.	+	0	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	CDS	3919822	3919935	0.75	+	0	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	exon	3919822	3919935	.	+	.	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	intron	3919936	3920057	.	+	.	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	CDS	3920058	3923003	0.72	+	0	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	exon	3920058	3923003	.	+	.	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
Phchi.S4	AUGUSTUS	stop_codon	3923004	3923006	.	+	0	transcript_id "Phchi.S4G064000.t1"; gene_id "Phchi.S4G064000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10516.t1 is derived from g14566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	794626	796769	.	+	.	Phchi.S4G009800
Phchi.S4	AUGUSTUS	transcript	794626	796769	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	start_codon	794626	794628	.	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	CDS	794626	794922	0.64	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	exon	794626	794922	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	intron	794923	795032	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	CDS	795033	795248	0.88	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	exon	795033	795248	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	intron	795249	795345	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	CDS	795346	795624	0.99	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	exon	795346	795624	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	intron	795625	795714	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	CDS	795715	796077	0.91	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	exon	795715	796077	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	intron	796078	796192	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	CDS	796193	796393	0.91	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	exon	796193	796393	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	intron	796394	796589	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	CDS	796590	796769	0.93	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	exon	796590	796769	.	+	.	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
Phchi.S4	AUGUSTUS	stop_codon	796770	796772	.	+	0	transcript_id "Phchi.S4G009800.t1"; gene_id "Phchi.S4G009800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13531.t1 is derived from g11998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7389379	7392963	.	+	.	Phchi.S3G085000
Phchi.S3	AUGUSTUS	transcript	7389379	7392963	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	start_codon	7389379	7389381	.	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7389379	7389600	0.6	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7389379	7389600	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7389601	7389693	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7389694	7389811	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7389694	7389811	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7389812	7389894	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7389895	7390082	0.99	+	2	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7389895	7390082	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7390083	7390188	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7390189	7390296	0.99	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7390189	7390296	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7390297	7390423	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7390424	7390488	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7390424	7390488	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7390489	7390624	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7390625	7390730	1	+	1	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7390625	7390730	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7390731	7390881	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7390882	7390965	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7390882	7390965	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7390966	7391057	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7391058	7391204	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7391058	7391204	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7391205	7391300	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7391301	7391429	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7391301	7391429	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7391430	7391508	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7391509	7391576	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7391509	7391576	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7391577	7391658	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7391659	7391692	1	+	1	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7391659	7391692	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7391693	7391798	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7391799	7391883	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7391799	7391883	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7391884	7391968	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7391969	7392036	1	+	2	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7391969	7392036	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7392037	7392202	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7392203	7392316	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7392203	7392316	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7392317	7392413	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7392414	7392449	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7392414	7392449	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7392450	7392533	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7392534	7392620	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7392534	7392620	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7392621	7392701	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7392702	7392793	1	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7392702	7392793	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	intron	7392794	7392872	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	CDS	7392873	7392963	1	+	1	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	exon	7392873	7392963	.	+	.	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
Phchi.S3	AUGUSTUS	stop_codon	7392964	7392966	.	+	0	transcript_id "Phchi.S3G085000.t1"; gene_id "Phchi.S3G085000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1930.t1 is derived from g8850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3882301	3883666	.	+	.	Phchi.S5G053900
Phchi.S5	AUGUSTUS	transcript	3882301	3883666	.	+	.	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	start_codon	3882301	3882303	.	+	0	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	CDS	3882301	3882789	0.81	+	0	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	exon	3882301	3882789	.	+	.	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	intron	3882790	3882995	.	+	.	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	CDS	3882996	3883163	1	+	0	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	exon	3882996	3883163	.	+	.	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	intron	3883164	3883270	.	+	.	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	CDS	3883271	3883666	1	+	0	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	exon	3883271	3883666	.	+	.	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
Phchi.S5	AUGUSTUS	stop_codon	3883667	3883669	.	+	0	transcript_id "Phchi.S5G053900.t1"; gene_id "Phchi.S5G053900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15625.t1 is derived from g14094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20354206	20356695	.	-	.	Phchi.S3G294400
Phchi.S3	AUGUSTUS	transcript	20354206	20356695	.	-	.	transcript_id "Phchi.S3G294400.t1"; gene_id "Phchi.S3G294400"
Phchi.S3	AUGUSTUS	stop_codon	20354203	20354205	.	-	0	transcript_id "Phchi.S3G294400.t1"; gene_id "Phchi.S3G294400"
Phchi.S3	AUGUSTUS	CDS	20354206	20356695	0.47	-	0	transcript_id "Phchi.S3G294400.t1"; gene_id "Phchi.S3G294400"
Phchi.S3	AUGUSTUS	exon	20354206	20356695	.	-	.	transcript_id "Phchi.S3G294400.t1"; gene_id "Phchi.S3G294400"
Phchi.S3	AUGUSTUS	start_codon	20356693	20356695	.	-	0	transcript_id "Phchi.S3G294400.t1"; gene_id "Phchi.S3G294400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7766.t1 is derived from g4940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31164967	31166263	.	+	.	Phchi.S1G492500
Phchi.S1	AUGUSTUS	transcript	31164967	31166263	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	start_codon	31164967	31164969	.	+	0	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	CDS	31164967	31165094	0.53	+	0	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	exon	31164967	31165094	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	intron	31165095	31165179	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	CDS	31165180	31165618	0.78	+	1	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	exon	31165180	31165618	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	intron	31165619	31165695	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	CDS	31165696	31166098	0.7	+	0	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	exon	31165696	31166098	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	intron	31166099	31166189	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	CDS	31166190	31166263	0.45	+	2	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	exon	31166190	31166263	.	+	.	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
Phchi.S1	AUGUSTUS	stop_codon	31166264	31166266	.	+	0	transcript_id "Phchi.S1G492500.t1"; gene_id "Phchi.S1G492500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8203.t1 is derived from g5378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34426088	34426487	.	+	.	Phchi.S1G536200
Phchi.S1	AUGUSTUS	transcript	34426088	34426487	.	+	.	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	start_codon	34426088	34426090	.	+	0	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	CDS	34426088	34426280	0.95	+	0	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	exon	34426088	34426280	.	+	.	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	intron	34426281	34426473	.	+	.	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	CDS	34426474	34426487	0.99	+	2	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	exon	34426474	34426487	.	+	.	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
Phchi.S1	AUGUSTUS	stop_codon	34426488	34426490	.	+	0	transcript_id "Phchi.S1G536200.t1"; gene_id "Phchi.S1G536200"
# This transcript jg10612.t2 is derived from g14662.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10612.t3 is derived from g14662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10613.t1 is derived from g14663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1215561	1218426	.	+	.	Phchi.S4G019500
Phchi.S4	AUGUSTUS	transcript	1215561	1218426	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	start_codon	1215561	1215563	.	+	0	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1215561	1215679	0.9	+	0	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1215561	1215679	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1215680	1215760	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1215761	1215885	1	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1215761	1215885	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1215886	1215958	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1215959	1216088	1	+	2	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1215959	1216088	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1216089	1216263	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1216264	1216345	1	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1216264	1216345	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1216346	1216430	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1216431	1216501	1	+	0	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1216431	1216501	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1216502	1216613	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1216614	1216655	0.99	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1216614	1216655	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1216656	1216816	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1216817	1216941	0.99	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1216817	1216941	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1216942	1217058	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1217059	1217152	1	+	2	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1217059	1217152	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1217153	1217249	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1217250	1217311	1	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1217250	1217311	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1217312	1217404	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1217405	1217468	1	+	2	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1217405	1217468	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1217469	1217693	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1217694	1217849	1	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1217694	1217849	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1217850	1217937	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1217938	1218043	1	+	1	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1217938	1218043	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1218044	1218172	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1218173	1218259	1	+	0	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1218173	1218259	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	intron	1218260	1218348	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	CDS	1218349	1218426	1	+	0	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	exon	1218349	1218426	.	+	.	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
Phchi.S4	AUGUSTUS	stop_codon	1218427	1218429	.	+	0	transcript_id "Phchi.S4G019500.t1"; gene_id "Phchi.S4G019500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3313.t1 is derived from g482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2799469	2801467	.	-	.	Phchi.S1G047200
Phchi.S1	AUGUSTUS	transcript	2799469	2801467	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	stop_codon	2799466	2799468	.	-	0	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	CDS	2799469	2799794	1	-	2	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	exon	2799469	2799794	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	intron	2799795	2799936	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	CDS	2799937	2800051	1	-	0	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	exon	2799937	2800051	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	intron	2800052	2800166	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	CDS	2800167	2800499	0.5	-	0	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	exon	2800167	2800499	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	intron	2800500	2800633	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	CDS	2800634	2801247	0.36	-	2	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	exon	2800634	2801247	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	intron	2801248	2801394	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	CDS	2801395	2801467	0.91	-	0	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	exon	2801395	2801467	.	-	.	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
Phchi.S1	AUGUSTUS	start_codon	2801465	2801467	.	-	0	transcript_id "Phchi.S1G047200.t1"; gene_id "Phchi.S1G047200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9800.t1 is derived from g6976.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43771834	43774246	.	+	.	Phchi.S1G695900
Phchi.S1	AUGUSTUS	transcript	43771834	43774246	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	start_codon	43771834	43771836	.	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43771834	43771908	0.92	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43771834	43771908	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43771909	43772032	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772033	43772189	0.83	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772033	43772189	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43772190	43772299	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772300	43772538	0.83	+	2	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772300	43772538	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43772539	43772676	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772677	43772759	0.98	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772677	43772759	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43772760	43772987	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772988	43773039	1	+	1	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772988	43773039	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43773040	43773214	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43773215	43773442	1	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43773215	43773442	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43773443	43773532	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43773533	43774042	0.88	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43773533	43774042	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43774043	43774129	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43774130	43774246	1	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43774130	43774246	.	+	.	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	stop_codon	43774247	43774249	.	+	0	transcript_id "Phchi.S1G695900.t1"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	transcript	43771834	43774246	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	start_codon	43771834	43771836	.	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43771834	43771908	0.93	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43771834	43771908	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43771909	43772032	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772033	43772189	0.88	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772033	43772189	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43772190	43772299	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772300	43772538	0.51	+	2	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772300	43772538	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43772539	43772704	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772705	43772745	0.49	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772705	43772745	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43772746	43772987	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43772988	43773039	1	+	1	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43772988	43773039	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43773040	43773214	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43773215	43773442	1	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43773215	43773442	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43773443	43773532	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43773533	43774042	0.88	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43773533	43774042	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	intron	43774043	43774129	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	CDS	43774130	43774246	1	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	exon	43774130	43774246	.	+	.	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
Phchi.S1	AUGUSTUS	stop_codon	43774247	43774249	.	+	0	transcript_id "Phchi.S1G695900.t2"; gene_id "Phchi.S1G695900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2525.t1 is derived from g9445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7133957	7140205	.	+	.	Phchi.S5G113400
Phchi.S5	AUGUSTUS	transcript	7133957	7140205	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	start_codon	7133957	7133959	.	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7133957	7134367	0.99	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7133957	7134367	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7134368	7134607	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7134608	7134741	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7134608	7134741	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7134742	7134849	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7134850	7134989	1	+	1	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7134850	7134989	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7134990	7135109	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7135110	7135304	1	+	2	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7135110	7135304	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7135305	7135458	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7135459	7135586	1	+	2	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7135459	7135586	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7135587	7135662	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7135663	7135821	0.98	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7135663	7135821	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7135822	7135934	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7135935	7136039	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7135935	7136039	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7136040	7136312	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7136313	7136387	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7136313	7136387	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7136388	7136503	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7136504	7136641	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7136504	7136641	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7136642	7136749	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7136750	7136944	0.72	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7136750	7136944	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7136945	7137037	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7137038	7137217	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7137038	7137217	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7137218	7137357	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7137358	7137484	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7137358	7137484	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7137485	7137584	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7137585	7137795	1	+	2	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7137585	7137795	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7137796	7137911	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7137912	7138030	1	+	1	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7137912	7138030	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7138031	7138115	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7138116	7138344	1	+	2	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7138116	7138344	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7138345	7138583	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7138584	7138704	1	+	1	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7138584	7138704	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7138705	7138808	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7138809	7138886	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7138809	7138886	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7138887	7139020	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7139021	7139077	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7139021	7139077	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7139078	7139196	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7139197	7139346	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7139197	7139346	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7139347	7139483	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7139484	7139690	1	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7139484	7139690	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	intron	7139691	7139785	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	CDS	7139786	7140205	0.98	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	exon	7139786	7140205	.	+	.	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
Phchi.S5	AUGUSTUS	stop_codon	7140206	7140208	.	+	0	transcript_id "Phchi.S5G113400.t1"; gene_id "Phchi.S5G113400"
# This transcript jg15091.t2 is derived from g13559.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15092.t1 is derived from g13560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16977600	16979353	.	+	.	Phchi.S3G241100
Phchi.S3	AUGUSTUS	transcript	16977600	16979353	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	start_codon	16977600	16977602	.	+	0	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16977600	16977865	0.6	+	0	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16977600	16977865	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16977866	16977953	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16977954	16978042	1	+	1	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16977954	16978042	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16978043	16978178	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16978179	16978244	1	+	2	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16978179	16978244	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16978245	16978362	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16978363	16978445	1	+	2	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16978363	16978445	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16978446	16978547	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16978548	16978594	0.82	+	0	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16978548	16978594	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16978595	16978802	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16978803	16978887	1	+	1	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16978803	16978887	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16978888	16979025	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16979026	16979081	0.98	+	0	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16979026	16979081	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	intron	16979082	16979271	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	CDS	16979272	16979353	0.98	+	1	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	exon	16979272	16979353	.	+	.	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
Phchi.S3	AUGUSTUS	stop_codon	16979354	16979356	.	+	0	transcript_id "Phchi.S3G241100.t1"; gene_id "Phchi.S3G241100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7932.t1 is derived from g5106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31990981	31993150	.	+	.	Phchi.S1G509100
Phchi.S1	AUGUSTUS	transcript	31990981	31993150	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	start_codon	31990981	31990983	.	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31990981	31991092	1	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31990981	31991092	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31991093	31991310	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31991311	31991426	1	+	2	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31991311	31991426	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31991427	31991766	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31991767	31991826	1	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31991767	31991826	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31991827	31991926	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31991927	31992109	1	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31991927	31992109	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31992110	31992196	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31992197	31992301	1	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31992197	31992301	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31992302	31992390	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31992391	31992487	1	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31992391	31992487	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31992488	31992599	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31992600	31992707	1	+	2	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31992600	31992707	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31992708	31992805	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31992806	31992941	1	+	2	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31992806	31992941	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	intron	31992942	31993032	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	CDS	31993033	31993150	0.99	+	1	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	exon	31993033	31993150	.	+	.	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
Phchi.S1	AUGUSTUS	stop_codon	31993151	31993153	.	+	0	transcript_id "Phchi.S1G509100.t1"; gene_id "Phchi.S1G509100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg163.t1 is derived from g9945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	936608	938095	.	-	.	Phchi.S6G012200
Phchi.S6	AUGUSTUS	transcript	936608	938095	.	-	.	transcript_id "Phchi.S6G012200.t1"; gene_id "Phchi.S6G012200"
Phchi.S6	AUGUSTUS	stop_codon	936605	936607	.	-	0	transcript_id "Phchi.S6G012200.t1"; gene_id "Phchi.S6G012200"
Phchi.S6	AUGUSTUS	CDS	936608	938095	0.63	-	0	transcript_id "Phchi.S6G012200.t1"; gene_id "Phchi.S6G012200"
Phchi.S6	AUGUSTUS	exon	936608	938095	.	-	.	transcript_id "Phchi.S6G012200.t1"; gene_id "Phchi.S6G012200"
Phchi.S6	AUGUSTUS	start_codon	938093	938095	.	-	0	transcript_id "Phchi.S6G012200.t1"; gene_id "Phchi.S6G012200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4071.t1 is derived from g1240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7627740	7629990	.	+	.	Phchi.S1G123000
Phchi.S1	AUGUSTUS	transcript	7627740	7629990	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	start_codon	7627740	7627742	.	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7627740	7627745	1	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7627740	7627745	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7627746	7627822	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7627823	7627939	1	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7627823	7627939	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7627940	7628015	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7628016	7628173	1	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7628016	7628173	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7628174	7628303	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7628304	7628425	1	+	1	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7628304	7628425	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7628426	7628566	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7628567	7628760	1	+	2	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7628567	7628760	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7628761	7628908	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7628909	7629091	1	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7628909	7629091	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7629092	7629187	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7629188	7629315	1	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7629188	7629315	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7629316	7629454	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7629455	7629597	1	+	1	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7629455	7629597	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7629598	7629686	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7629687	7629803	1	+	2	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7629687	7629803	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	intron	7629804	7629892	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	CDS	7629893	7629990	1	+	2	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	exon	7629893	7629990	.	+	.	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
Phchi.S1	AUGUSTUS	stop_codon	7629991	7629993	.	+	0	transcript_id "Phchi.S1G123000.t1"; gene_id "Phchi.S1G123000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11419.t1 is derived from g15469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6256372	6257168	.	+	.	Phchi.S4G100100
Phchi.S4	AUGUSTUS	transcript	6256372	6257168	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	start_codon	6256372	6256374	.	+	0	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	CDS	6256372	6256390	0.87	+	0	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	exon	6256372	6256390	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	intron	6256391	6256478	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	CDS	6256479	6256545	0.99	+	2	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	exon	6256479	6256545	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	intron	6256546	6256741	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	CDS	6256742	6256800	0.72	+	1	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	exon	6256742	6256800	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	intron	6256801	6256935	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	CDS	6256936	6257168	1	+	2	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	exon	6256936	6257168	.	+	.	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
Phchi.S4	AUGUSTUS	stop_codon	6257169	6257171	.	+	0	transcript_id "Phchi.S4G100100.t1"; gene_id "Phchi.S4G100100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5559.t1 is derived from g2729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17593767	17595723	.	+	.	Phchi.S1G271800
Phchi.S1	AUGUSTUS	transcript	17593767	17595723	.	+	.	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	start_codon	17593767	17593769	.	+	0	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	CDS	17593767	17595411	0.53	+	0	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	exon	17593767	17595411	.	+	.	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	intron	17595412	17595556	.	+	.	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	CDS	17595557	17595723	0.49	+	2	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	exon	17595557	17595723	.	+	.	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
Phchi.S1	AUGUSTUS	stop_codon	17595724	17595726	.	+	0	transcript_id "Phchi.S1G271800.t1"; gene_id "Phchi.S1G271800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2753.t1 is derived from g9673.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8624758	8630651	.	+	.	Phchi.S5G136200
Phchi.S5	AUGUSTUS	transcript	8624758	8630651	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	start_codon	8624758	8624760	.	+	0	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8624758	8625350	0.98	+	0	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8624758	8625350	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8625351	8625531	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8625532	8626293	1	+	1	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8625532	8626293	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8626294	8626415	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8626416	8627532	0.95	+	1	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8626416	8627532	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8627533	8627693	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8627694	8627982	1	+	0	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8627694	8627982	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8627983	8628122	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8628123	8628304	0.96	+	2	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8628123	8628304	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8628305	8628527	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8628528	8629069	0.94	+	0	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8628528	8629069	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629070	8629171	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8629172	8629200	0.64	+	1	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8629172	8629200	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629201	8629341	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8629342	8629899	0.61	+	2	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8629342	8629899	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629900	8629999	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630000	8630052	0.47	+	2	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630000	8630052	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8630053	8630134	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630135	8630171	0.86	+	0	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630135	8630171	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8630172	8630601	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630602	8630651	0.68	+	2	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630602	8630651	.	+	.	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	stop_codon	8630652	8630654	.	+	0	transcript_id "Phchi.S5G136200.t1"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	transcript	8624758	8630651	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	start_codon	8624758	8624760	.	+	0	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8624758	8625350	0.94	+	0	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8624758	8625350	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8625351	8625531	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8625532	8626293	1	+	1	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8625532	8626293	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8626294	8626415	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8626416	8627532	0.93	+	1	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8626416	8627532	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8627533	8627693	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8627694	8627982	1	+	0	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8627694	8627982	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8627983	8628122	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8628123	8628247	1	+	2	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8628123	8628247	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8628248	8628527	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8628528	8629069	0.89	+	0	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8628528	8629069	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629070	8629171	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8629172	8629200	0.57	+	1	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8629172	8629200	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629201	8629341	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8629342	8629899	0.57	+	2	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8629342	8629899	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629900	8629999	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630000	8630052	0.49	+	2	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630000	8630052	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8630053	8630134	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630135	8630171	0.85	+	0	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630135	8630171	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8630172	8630601	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630602	8630651	0.78	+	2	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630602	8630651	.	+	.	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	stop_codon	8630652	8630654	.	+	0	transcript_id "Phchi.S5G136200.t2"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	transcript	8624758	8630651	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	start_codon	8624758	8624760	.	+	0	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8624758	8625350	0.98	+	0	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8624758	8625350	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8625351	8625531	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8625532	8626293	1	+	1	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8625532	8626293	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8626294	8626415	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8626416	8627532	0.92	+	1	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8626416	8627532	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8627533	8627693	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8627694	8627982	1	+	0	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8627694	8627982	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8627983	8628122	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8628123	8628189	0.99	+	2	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8628123	8628189	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8628190	8628511	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8628512	8629069	0.98	+	1	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8628512	8629069	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629070	8629171	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8629172	8629200	0.43	+	1	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8629172	8629200	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629201	8629341	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8629342	8629899	0.42	+	2	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8629342	8629899	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8629900	8629999	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630000	8630052	0.55	+	2	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630000	8630052	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8630053	8630134	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630135	8630171	0.85	+	0	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630135	8630171	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	intron	8630172	8630601	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	CDS	8630602	8630651	0.7	+	2	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	exon	8630602	8630651	.	+	.	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
Phchi.S5	AUGUSTUS	stop_codon	8630652	8630654	.	+	0	transcript_id "Phchi.S5G136200.t3"; gene_id "Phchi.S5G136200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9174.t1 is derived from g6349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40220118	40225096	.	+	.	Phchi.S1G633300
Phchi.S1	AUGUSTUS	transcript	40220118	40225096	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	start_codon	40220118	40220120	.	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40220118	40220849	0.56	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40220118	40220849	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40220850	40220956	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40220957	40221082	0.89	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40220957	40221082	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40221083	40221190	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40221191	40221217	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40221191	40221217	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40221218	40221369	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40221370	40221426	0.98	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40221370	40221426	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40221427	40221537	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40221538	40221621	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40221538	40221621	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40221622	40221715	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40221716	40221862	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40221716	40221862	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40221863	40221944	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40221945	40222001	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40221945	40222001	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40222002	40222123	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40222124	40222248	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40222124	40222248	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40222249	40222335	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40222336	40222380	1	+	1	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40222336	40222380	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40222381	40222483	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40222484	40222568	0.98	+	1	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40222484	40222568	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40222569	40222648	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40222649	40222704	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40222649	40222704	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40222705	40222801	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40222802	40222898	1	+	1	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40222802	40222898	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40222899	40223077	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40223078	40223208	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40223078	40223208	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40223209	40223329	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40223330	40223468	1	+	1	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40223330	40223468	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40223469	40223588	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40223589	40223699	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40223589	40223699	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40223700	40223784	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40223785	40223866	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40223785	40223866	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40223867	40223960	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40223961	40224061	0.95	+	2	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40223961	40224061	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40224062	40224182	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40224183	40224293	0.97	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40224183	40224293	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40224294	40224377	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40224378	40224485	0.98	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40224378	40224485	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40224486	40224716	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40224717	40224818	1	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40224717	40224818	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	intron	40224819	40225069	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	CDS	40225070	40225096	0.95	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	exon	40225070	40225096	.	+	.	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
Phchi.S1	AUGUSTUS	stop_codon	40225097	40225099	.	+	0	transcript_id "Phchi.S1G633300.t1"; gene_id "Phchi.S1G633300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4939.t1 is derived from g2109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13662717	13666217	.	+	.	Phchi.S1G209800
Phchi.S1	AUGUSTUS	transcript	13662717	13666217	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	start_codon	13662717	13662719	.	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13662717	13662949	0.8	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13662717	13662949	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13662950	13663036	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13663037	13663203	0.86	+	1	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13663037	13663203	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13663204	13663287	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13663288	13663865	0.48	+	2	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13663288	13663865	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13663866	13663964	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13663965	13664056	0.46	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13663965	13664056	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13664057	13664256	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13664257	13664372	0.52	+	1	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13664257	13664372	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13664373	13664491	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13664492	13664766	0.98	+	2	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13664492	13664766	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13664767	13664863	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13664864	13664929	1	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13664864	13664929	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13664930	13665053	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13665054	13665191	1	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13665054	13665191	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13665192	13665269	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13665270	13665347	1	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13665270	13665347	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13665348	13665552	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13665553	13665603	0.79	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13665553	13665603	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13665604	13665709	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13665710	13665744	1	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13665710	13665744	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13665745	13665838	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13665839	13665947	1	+	1	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13665839	13665947	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	intron	13665948	13666028	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	CDS	13666029	13666217	1	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	exon	13666029	13666217	.	+	.	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
Phchi.S1	AUGUSTUS	stop_codon	13666218	13666220	.	+	0	transcript_id "Phchi.S1G209800.t1"; gene_id "Phchi.S1G209800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9080.t1 is derived from g6255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39751970	39756571	.	-	.	Phchi.S1G623900
Phchi.S1	AUGUSTUS	transcript	39751970	39756571	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	stop_codon	39751967	39751969	.	-	0	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39751970	39752110	1	-	0	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39751970	39752110	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752111	39752209	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39752210	39752307	1	-	2	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39752210	39752307	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752308	39752431	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39752432	39752532	0.7	-	1	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39752432	39752532	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752533	39752827	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39752828	39752888	0.97	-	2	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39752828	39752888	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752889	39753049	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39753050	39753609	1	-	1	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39753050	39753609	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39753610	39753722	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39753723	39754753	1	-	0	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39753723	39754753	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39754754	39754882	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39754883	39755139	1	-	2	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39754883	39755139	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39755140	39755253	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39755254	39755581	0.98	-	0	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39755254	39755581	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39755582	39755655	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39755656	39755689	0.97	-	1	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39755656	39755689	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39755690	39755759	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39755760	39756571	0.54	-	0	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39755760	39756571	.	-	.	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	start_codon	39756569	39756571	.	-	0	transcript_id "Phchi.S1G623900.t1"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	transcript	39751970	39756571	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	stop_codon	39751967	39751969	.	-	0	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39751970	39752083	0.95	-	0	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39751970	39752083	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752084	39752209	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39752210	39752307	0.9	-	2	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39752210	39752307	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752308	39752431	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39752432	39752532	0.69	-	1	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39752432	39752532	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752533	39752827	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39752828	39752888	0.9	-	2	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39752828	39752888	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39752889	39753049	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39753050	39753609	0.99	-	1	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39753050	39753609	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39753610	39753722	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39753723	39754753	0.99	-	0	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39753723	39754753	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39754754	39754882	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39754883	39755139	1	-	2	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39754883	39755139	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39755140	39755253	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39755254	39755581	0.94	-	0	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39755254	39755581	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39755582	39755655	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39755656	39755689	0.9	-	1	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39755656	39755689	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	intron	39755690	39755759	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	CDS	39755760	39756571	0.51	-	0	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	exon	39755760	39756571	.	-	.	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
Phchi.S1	AUGUSTUS	start_codon	39756569	39756571	.	-	0	transcript_id "Phchi.S1G623900.t2"; gene_id "Phchi.S1G623900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4729.t1 is derived from g1899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12504537	12505330	.	+	.	Phchi.S1G188800
Phchi.S1	AUGUSTUS	transcript	12504537	12505330	.	+	.	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	start_codon	12504537	12504539	.	+	0	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	CDS	12504537	12505157	0.43	+	0	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	exon	12504537	12505157	.	+	.	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	intron	12505158	12505270	.	+	.	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	CDS	12505271	12505330	0.6	+	0	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	exon	12505271	12505330	.	+	.	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
Phchi.S1	AUGUSTUS	stop_codon	12505331	12505333	.	+	0	transcript_id "Phchi.S1G188800.t1"; gene_id "Phchi.S1G188800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3784.t1 is derived from g953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5710539	5711936	.	+	.	Phchi.S1G094300
Phchi.S1	AUGUSTUS	transcript	5710539	5711936	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	start_codon	5710539	5710541	.	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5710539	5710557	0.38	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5710539	5710557	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	intron	5710558	5710795	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5710796	5710872	0.49	+	2	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5710796	5710872	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	intron	5710873	5710954	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5710955	5711070	0.95	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5710955	5711070	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	intron	5711071	5711208	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5711209	5711332	1	+	1	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5711209	5711332	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	intron	5711333	5711411	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5711412	5711525	0.87	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5711412	5711525	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	intron	5711526	5711634	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5711635	5711715	0.62	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5711635	5711715	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	intron	5711716	5711810	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	CDS	5711811	5711936	0.36	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	exon	5711811	5711936	.	+	.	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
Phchi.S1	AUGUSTUS	stop_codon	5711937	5711939	.	+	0	transcript_id "Phchi.S1G094300.t1"; gene_id "Phchi.S1G094300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14363.t1 is derived from g12830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12365915	12366862	.	-	.	Phchi.S3G168200
Phchi.S3	AUGUSTUS	transcript	12365915	12366862	.	-	.	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	stop_codon	12365912	12365914	.	-	0	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	CDS	12365915	12366022	1	-	0	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	exon	12365915	12366022	.	-	.	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	intron	12366023	12366133	.	-	.	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	CDS	12366134	12366283	1	-	0	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	exon	12366134	12366283	.	-	.	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	intron	12366284	12366451	.	-	.	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	CDS	12366452	12366862	0.87	-	0	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	exon	12366452	12366862	.	-	.	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
Phchi.S3	AUGUSTUS	start_codon	12366860	12366862	.	-	0	transcript_id "Phchi.S3G168200.t1"; gene_id "Phchi.S3G168200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg530.t1 is derived from g10312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3805582	3807704	.	+	.	Phchi.S6G048900
Phchi.S6	AUGUSTUS	transcript	3805582	3807704	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	start_codon	3805582	3805584	.	+	0	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	CDS	3805582	3805982	0.98	+	0	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	exon	3805582	3805982	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	intron	3805983	3806090	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	CDS	3806091	3806325	1	+	1	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	exon	3806091	3806325	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	intron	3806326	3806469	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	CDS	3806470	3806772	0.86	+	0	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	exon	3806470	3806772	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	intron	3806773	3806943	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	CDS	3806944	3807314	1	+	0	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	exon	3806944	3807314	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	intron	3807315	3807448	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	CDS	3807449	3807704	1	+	1	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	exon	3807449	3807704	.	+	.	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
Phchi.S6	AUGUSTUS	stop_codon	3807705	3807707	.	+	0	transcript_id "Phchi.S6G048900.t1"; gene_id "Phchi.S6G048900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12108.t1 is derived from g7784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3553195	3554275	.	-	.	Phchi.S2G018800
Phchi.S2	AUGUSTUS	transcript	3553195	3554275	.	-	.	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	stop_codon	3553192	3553194	.	-	0	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	CDS	3553195	3553547	0.72	-	2	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	exon	3553195	3553547	.	-	.	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	intron	3553548	3553659	.	-	.	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	CDS	3553660	3553954	0.34	-	0	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	exon	3553660	3553954	.	-	.	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	intron	3553955	3554110	.	-	.	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	CDS	3554111	3554275	0.64	-	0	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	exon	3554111	3554275	.	-	.	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
Phchi.S2	AUGUSTUS	start_codon	3554273	3554275	.	-	0	transcript_id "Phchi.S2G018800.t1"; gene_id "Phchi.S2G018800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11354.t1 is derived from g15404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5714455	5714811	.	-	.	Phchi.S4G093600
Phchi.S4	AUGUSTUS	transcript	5714455	5714811	.	-	.	transcript_id "Phchi.S4G093600.t1"; gene_id "Phchi.S4G093600"
Phchi.S4	AUGUSTUS	stop_codon	5714452	5714454	.	-	0	transcript_id "Phchi.S4G093600.t1"; gene_id "Phchi.S4G093600"
Phchi.S4	AUGUSTUS	CDS	5714455	5714811	0.95	-	0	transcript_id "Phchi.S4G093600.t1"; gene_id "Phchi.S4G093600"
Phchi.S4	AUGUSTUS	exon	5714455	5714811	.	-	.	transcript_id "Phchi.S4G093600.t1"; gene_id "Phchi.S4G093600"
Phchi.S4	AUGUSTUS	start_codon	5714809	5714811	.	-	0	transcript_id "Phchi.S4G093600.t1"; gene_id "Phchi.S4G093600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6522.t1 is derived from g3694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23472952	23474605	.	-	.	Phchi.S1G368100
Phchi.S1	AUGUSTUS	transcript	23472952	23474605	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	stop_codon	23472949	23472951	.	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23472952	23473062	1	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23472952	23473062	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23473063	23473172	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23473173	23473247	1	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23473173	23473247	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23473248	23473345	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23473346	23473419	1	-	2	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23473346	23473419	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23473420	23473530	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23473531	23473642	1	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23473531	23473642	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23473643	23473758	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23473759	23473831	1	-	1	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23473759	23473831	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23473832	23474072	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23474073	23474128	1	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23474073	23474128	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23474129	23474221	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23474222	23474298	0.79	-	2	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23474222	23474298	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23474299	23474402	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23474403	23474469	0.39	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23474403	23474469	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	intron	23474470	23474557	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	CDS	23474558	23474605	0.56	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	exon	23474558	23474605	.	-	.	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
Phchi.S1	AUGUSTUS	start_codon	23474603	23474605	.	-	0	transcript_id "Phchi.S1G368100.t1"; gene_id "Phchi.S1G368100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg6993.t1 is derived from g4165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26303975	26308153	.	-	.	Phchi.S1G415200
Phchi.S1	AUGUSTUS	transcript	26303975	26306602	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	stop_codon	26303972	26303974	.	-	0	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26303975	26303991	0.92	-	2	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26303975	26303991	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26303992	26304342	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26304343	26304633	0.92	-	2	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26304343	26304633	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26304634	26304727	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26304728	26304800	0.98	-	0	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26304728	26304800	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26304801	26304924	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26304925	26305094	1	-	2	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26304925	26305094	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26305095	26305577	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26305578	26305680	1	-	0	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26305578	26305680	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26305681	26305882	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26305883	26306046	1	-	2	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26305883	26306046	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306047	26306146	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306147	26306190	1	-	1	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306147	26306190	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306191	26306348	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306349	26306602	0.48	-	0	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306349	26306602	.	-	.	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	start_codon	26306600	26306602	.	-	0	transcript_id "Phchi.S1G415200.t1"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	transcript	26303975	26308153	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	stop_codon	26303972	26303974	.	-	0	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26303975	26303991	0.92	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26303975	26303991	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26303992	26304342	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26304343	26304633	0.92	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26304343	26304633	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26304634	26304727	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26304728	26304800	0.97	-	0	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26304728	26304800	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26304801	26304924	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26304925	26305094	1	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26304925	26305094	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26305095	26305577	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26305578	26305680	1	-	0	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26305578	26305680	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26305681	26305882	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26305883	26306046	1	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26305883	26306046	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306047	26306146	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306147	26306190	1	-	1	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306147	26306190	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306191	26306348	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306349	26306604	0.29	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306349	26306604	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306605	26306727	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306728	26306855	0.61	-	1	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306728	26306855	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306856	26307029	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307030	26307107	0.67	-	1	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307030	26307107	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307108	26307202	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307203	26307278	0.65	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307203	26307278	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307279	26307683	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307684	26307689	0.85	-	2	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307684	26307689	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307690	26307874	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307875	26307911	0.99	-	0	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307875	26307911	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307912	26308024	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26308025	26308153	0.42	-	0	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26308025	26308153	.	-	.	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	start_codon	26308151	26308153	.	-	0	transcript_id "Phchi.S1G415200.t2"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	transcript	26306829	26308153	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	stop_codon	26306826	26306828	.	-	0	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306829	26306855	0.55	-	0	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306829	26306855	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306856	26307029	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307030	26307107	0.56	-	0	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307030	26307107	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307108	26307202	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307203	26307278	0.45	-	1	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307203	26307278	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307279	26307683	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307684	26307801	0.98	-	2	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307684	26307801	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307802	26307874	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307875	26307911	1	-	0	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307875	26307911	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307912	26308024	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26308025	26308153	0.45	-	0	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26308025	26308153	.	-	.	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	start_codon	26308151	26308153	.	-	0	transcript_id "Phchi.S1G415200.t3"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	transcript	26306829	26308153	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	stop_codon	26306826	26306828	.	-	0	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26306829	26306855	0.53	-	0	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26306829	26306855	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26306856	26307029	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307030	26307107	0.53	-	0	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307030	26307107	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307108	26307202	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307203	26307278	0.37	-	1	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307203	26307278	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307279	26307683	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307684	26307807	0.98	-	2	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307684	26307807	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307808	26307874	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26307875	26307911	1	-	0	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26307875	26307911	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	intron	26307912	26308024	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	CDS	26308025	26308153	0.39	-	0	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	exon	26308025	26308153	.	-	.	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
Phchi.S1	AUGUSTUS	start_codon	26308151	26308153	.	-	0	transcript_id "Phchi.S1G415200.t4"; gene_id "Phchi.S1G415200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3936.t1 is derived from g1105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6565655	6566760	.	+	.	Phchi.S1G109500
Phchi.S1	AUGUSTUS	transcript	6565655	6566760	.	+	.	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	start_codon	6565655	6565657	.	+	0	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	CDS	6565655	6565861	1	+	0	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	exon	6565655	6565861	.	+	.	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	intron	6565862	6566367	.	+	.	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	CDS	6566368	6566760	0.96	+	0	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	exon	6566368	6566760	.	+	.	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
Phchi.S1	AUGUSTUS	stop_codon	6566761	6566763	.	+	0	transcript_id "Phchi.S1G109500.t1"; gene_id "Phchi.S1G109500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2021.t1 is derived from g8941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4478327	4479037	.	+	.	Phchi.S5G063000
Phchi.S5	AUGUSTUS	transcript	4478327	4479037	.	+	.	transcript_id "Phchi.S5G063000.t1"; gene_id "Phchi.S5G063000"
Phchi.S5	AUGUSTUS	start_codon	4478327	4478329	.	+	0	transcript_id "Phchi.S5G063000.t1"; gene_id "Phchi.S5G063000"
Phchi.S5	AUGUSTUS	CDS	4478327	4479037	0.52	+	0	transcript_id "Phchi.S5G063000.t1"; gene_id "Phchi.S5G063000"
Phchi.S5	AUGUSTUS	exon	4478327	4479037	.	+	.	transcript_id "Phchi.S5G063000.t1"; gene_id "Phchi.S5G063000"
Phchi.S5	AUGUSTUS	stop_codon	4479038	4479040	.	+	0	transcript_id "Phchi.S5G063000.t1"; gene_id "Phchi.S5G063000"
# This transcript jg927.t2 is derived from g10709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg928.t1 is derived from g10710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6482837	6484741	.	+	.	Phchi.S6G088700
Phchi.S6	AUGUSTUS	transcript	6482837	6484741	.	+	.	transcript_id "Phchi.S6G088700.t1"; gene_id "Phchi.S6G088700"
Phchi.S6	AUGUSTUS	start_codon	6482837	6482839	.	+	0	transcript_id "Phchi.S6G088700.t1"; gene_id "Phchi.S6G088700"
Phchi.S6	AUGUSTUS	CDS	6482837	6484741	0.93	+	0	transcript_id "Phchi.S6G088700.t1"; gene_id "Phchi.S6G088700"
Phchi.S6	AUGUSTUS	exon	6482837	6484741	.	+	.	transcript_id "Phchi.S6G088700.t1"; gene_id "Phchi.S6G088700"
Phchi.S6	AUGUSTUS	stop_codon	6484742	6484744	.	+	0	transcript_id "Phchi.S6G088700.t1"; gene_id "Phchi.S6G088700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8145.t1 is derived from g5320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34066339	34067476	.	-	.	Phchi.S1G530400
Phchi.S1	AUGUSTUS	transcript	34066339	34067476	.	-	.	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	stop_codon	34066336	34066338	.	-	0	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	CDS	34066339	34066682	1	-	2	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	exon	34066339	34066682	.	-	.	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	intron	34066683	34066794	.	-	.	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	CDS	34066795	34066981	1	-	0	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	exon	34066795	34066981	.	-	.	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	intron	34066982	34067086	.	-	.	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	CDS	34067087	34067476	0.4	-	0	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	exon	34067087	34067476	.	-	.	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
Phchi.S1	AUGUSTUS	start_codon	34067474	34067476	.	-	0	transcript_id "Phchi.S1G530400.t1"; gene_id "Phchi.S1G530400"
# This transcript jg6333.t2 is derived from g3505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6334.t1 is derived from g3506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22322994	22324016	.	-	.	Phchi.S1G349300
Phchi.S1	AUGUSTUS	transcript	22322994	22324016	.	-	.	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	stop_codon	22322991	22322993	.	-	0	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	CDS	22322994	22323482	0.91	-	0	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	exon	22322994	22323482	.	-	.	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	intron	22323483	22323613	.	-	.	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	CDS	22323614	22323702	0.84	-	2	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	exon	22323614	22323702	.	-	.	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	intron	22323703	22323805	.	-	.	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	CDS	22323806	22324016	0.58	-	0	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	exon	22323806	22324016	.	-	.	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
Phchi.S1	AUGUSTUS	start_codon	22324014	22324016	.	-	0	transcript_id "Phchi.S1G349300.t1"; gene_id "Phchi.S1G349300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6042.t1 is derived from g3213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20599916	20600407	.	-	.	Phchi.S1G320100
Phchi.S1	AUGUSTUS	transcript	20599916	20600407	.	-	.	transcript_id "Phchi.S1G320100.t1"; gene_id "Phchi.S1G320100"
Phchi.S1	AUGUSTUS	stop_codon	20599913	20599915	.	-	0	transcript_id "Phchi.S1G320100.t1"; gene_id "Phchi.S1G320100"
Phchi.S1	AUGUSTUS	CDS	20599916	20600407	1	-	0	transcript_id "Phchi.S1G320100.t1"; gene_id "Phchi.S1G320100"
Phchi.S1	AUGUSTUS	exon	20599916	20600407	.	-	.	transcript_id "Phchi.S1G320100.t1"; gene_id "Phchi.S1G320100"
Phchi.S1	AUGUSTUS	start_codon	20600405	20600407	.	-	0	transcript_id "Phchi.S1G320100.t1"; gene_id "Phchi.S1G320100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11529.t1 is derived from g15579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6935145	6935773	.	-	.	Phchi.S4G111100
Phchi.S4	AUGUSTUS	transcript	6935145	6935773	.	-	.	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	stop_codon	6935142	6935144	.	-	0	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	CDS	6935145	6935408	0.54	-	0	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	exon	6935145	6935408	.	-	.	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	intron	6935409	6935566	.	-	.	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	CDS	6935567	6935773	0.32	-	0	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	exon	6935567	6935773	.	-	.	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
Phchi.S4	AUGUSTUS	start_codon	6935771	6935773	.	-	0	transcript_id "Phchi.S4G111100.t1"; gene_id "Phchi.S4G111100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13949.t1 is derived from g12416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9862028	9866220	.	+	.	Phchi.S3G126800
Phchi.S3	AUGUSTUS	transcript	9862028	9866220	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	start_codon	9862028	9862030	.	+	0	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9862028	9862204	0.67	+	0	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9862028	9862204	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9862205	9862297	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9862298	9862413	1	+	0	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9862298	9862413	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9862414	9862517	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9862518	9862636	0.99	+	1	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9862518	9862636	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9862637	9862766	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9862767	9862929	0.96	+	2	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9862767	9862929	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9862930	9863013	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9863014	9863246	1	+	1	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9863014	9863246	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9863247	9863370	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9863371	9863546	0.85	+	2	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9863371	9863546	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9863547	9863630	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9863631	9863968	1	+	0	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9863631	9863968	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9863969	9864072	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9864073	9864584	0.51	+	1	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9864073	9864584	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	intron	9864585	9864661	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	CDS	9864662	9866220	0.51	+	2	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	exon	9864662	9866220	.	+	.	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
Phchi.S3	AUGUSTUS	stop_codon	9866221	9866223	.	+	0	transcript_id "Phchi.S3G126800.t1"; gene_id "Phchi.S3G126800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8872.t1 is derived from g6047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38396602	38397309	.	+	.	Phchi.S1G603100
Phchi.S1	AUGUSTUS	transcript	38396602	38397309	.	+	.	transcript_id "Phchi.S1G603100.t1"; gene_id "Phchi.S1G603100"
Phchi.S1	AUGUSTUS	start_codon	38396602	38396604	.	+	0	transcript_id "Phchi.S1G603100.t1"; gene_id "Phchi.S1G603100"
Phchi.S1	AUGUSTUS	CDS	38396602	38397309	0.57	+	0	transcript_id "Phchi.S1G603100.t1"; gene_id "Phchi.S1G603100"
Phchi.S1	AUGUSTUS	exon	38396602	38397309	.	+	.	transcript_id "Phchi.S1G603100.t1"; gene_id "Phchi.S1G603100"
Phchi.S1	AUGUSTUS	stop_codon	38397310	38397312	.	+	0	transcript_id "Phchi.S1G603100.t1"; gene_id "Phchi.S1G603100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1322.t1 is derived from g11105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9017330	9018485	.	-	.	Phchi.S6G128100
Phchi.S6	AUGUSTUS	transcript	9017330	9018485	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	stop_codon	9017327	9017329	.	-	0	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	CDS	9017330	9017605	0.99	-	0	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	exon	9017330	9017605	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	intron	9017606	9017696	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	CDS	9017697	9017762	0.83	-	0	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	exon	9017697	9017762	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	intron	9017763	9017878	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	CDS	9017879	9017925	0.61	-	2	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	exon	9017879	9017925	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	intron	9017926	9018169	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	CDS	9018170	9018485	0.68	-	0	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	exon	9018170	9018485	.	-	.	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
Phchi.S6	AUGUSTUS	start_codon	9018483	9018485	.	-	0	transcript_id "Phchi.S6G128100.t1"; gene_id "Phchi.S6G128100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7913.t1 is derived from g5087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31883886	31886377	.	+	.	Phchi.S1G507200
Phchi.S1	AUGUSTUS	transcript	31883886	31886377	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	start_codon	31883886	31883888	.	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31883886	31883984	1	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31883886	31883984	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31883985	31884068	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31884069	31884140	1	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31884069	31884140	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31884141	31884217	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31884218	31884310	0.98	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31884218	31884310	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31884311	31884423	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31884424	31884505	1	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31884424	31884505	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31884506	31884640	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31884641	31884697	1	+	2	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31884641	31884697	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31884698	31884859	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31884860	31884924	1	+	2	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31884860	31884924	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31884925	31885067	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31885068	31885163	1	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31885068	31885163	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31885164	31885267	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31885268	31885354	1	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31885268	31885354	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31885355	31885449	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31885450	31885530	1	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31885450	31885530	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31885531	31885624	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31885625	31885977	0.48	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31885625	31885977	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31885978	31886107	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31886108	31886126	0.54	+	1	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31886108	31886126	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	intron	31886127	31886335	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	CDS	31886336	31886377	0.44	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	exon	31886336	31886377	.	+	.	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
Phchi.S1	AUGUSTUS	stop_codon	31886378	31886380	.	+	0	transcript_id "Phchi.S1G507200.t1"; gene_id "Phchi.S1G507200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12417.t1 is derived from g8094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18989528	18990399	.	+	.	Phchi.S2G049700
Phchi.S2	AUGUSTUS	transcript	18989528	18990399	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	start_codon	18989528	18989530	.	+	0	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	CDS	18989528	18989693	1	+	0	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	exon	18989528	18989693	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	intron	18989694	18989862	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	CDS	18989863	18989965	1	+	2	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	exon	18989863	18989965	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	intron	18989966	18990107	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	CDS	18990108	18990219	1	+	1	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	exon	18990108	18990219	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	intron	18990220	18990345	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	CDS	18990346	18990399	1	+	0	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	exon	18990346	18990399	.	+	.	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
Phchi.S2	AUGUSTUS	stop_codon	18990400	18990402	.	+	0	transcript_id "Phchi.S2G049700.t1"; gene_id "Phchi.S2G049700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12873.t1 is derived from g11338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2849690	2850709	.	+	.	Phchi.S3G019200
Phchi.S3	AUGUSTUS	transcript	2849690	2850709	.	+	.	transcript_id "Phchi.S3G019200.t1"; gene_id "Phchi.S3G019200"
Phchi.S3	AUGUSTUS	start_codon	2849690	2849692	.	+	0	transcript_id "Phchi.S3G019200.t1"; gene_id "Phchi.S3G019200"
Phchi.S3	AUGUSTUS	CDS	2849690	2850709	0.83	+	0	transcript_id "Phchi.S3G019200.t1"; gene_id "Phchi.S3G019200"
Phchi.S3	AUGUSTUS	exon	2849690	2850709	.	+	.	transcript_id "Phchi.S3G019200.t1"; gene_id "Phchi.S3G019200"
Phchi.S3	AUGUSTUS	stop_codon	2850710	2850712	.	+	0	transcript_id "Phchi.S3G019200.t1"; gene_id "Phchi.S3G019200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15410.t1 is derived from g13878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18879190	18881685	.	+	.	Phchi.S3G272900
Phchi.S3	AUGUSTUS	transcript	18879190	18881685	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	start_codon	18879190	18879192	.	+	0	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879190	18879481	0.46	+	0	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879190	18879481	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879482	18879609	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879610	18879833	1	+	2	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879610	18879833	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879834	18879977	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879978	18880200	1	+	0	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879978	18880200	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880201	18880379	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880380	18880532	1	+	2	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880380	18880532	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880533	18880675	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880676	18880766	0.78	+	2	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880676	18880766	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880767	18880876	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880877	18881063	0.78	+	1	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880877	18881063	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18881064	18881161	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18881162	18881286	1	+	0	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18881162	18881286	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18881287	18881417	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18881418	18881685	1	+	1	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18881418	18881685	.	+	.	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	stop_codon	18881686	18881688	.	+	0	transcript_id "Phchi.S3G272900.t1"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	transcript	18879190	18881685	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	start_codon	18879190	18879192	.	+	0	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879190	18879481	0.38	+	0	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879190	18879481	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879482	18879609	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879610	18879693	0.74	+	2	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879610	18879693	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879694	18879779	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879780	18879844	1	+	2	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879780	18879844	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879845	18879977	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879978	18880200	1	+	0	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879978	18880200	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880201	18880379	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880380	18880532	1	+	2	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880380	18880532	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880533	18880675	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880676	18880766	0.78	+	2	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880676	18880766	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880767	18880876	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880877	18881063	0.78	+	1	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880877	18881063	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18881064	18881161	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18881162	18881286	1	+	0	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18881162	18881286	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18881287	18881417	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18881418	18881685	1	+	1	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18881418	18881685	.	+	.	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	stop_codon	18881686	18881688	.	+	0	transcript_id "Phchi.S3G272900.t2"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	transcript	18879190	18881685	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	start_codon	18879190	18879192	.	+	0	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879190	18879481	0.52	+	0	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879190	18879481	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879482	18879609	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879610	18879833	0.85	+	2	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879610	18879833	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18879834	18879977	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18879978	18880032	0.36	+	0	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18879978	18880032	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880033	18880175	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880176	18880200	0.38	+	2	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880176	18880200	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880201	18880341	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880342	18880532	0.68	+	1	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880342	18880532	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880533	18880675	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880676	18880766	0.74	+	2	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880676	18880766	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18880767	18880876	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18880877	18881063	0.74	+	1	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18880877	18881063	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18881064	18881161	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18881162	18881286	1	+	0	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18881162	18881286	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	intron	18881287	18881417	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	CDS	18881418	18881685	1	+	1	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	exon	18881418	18881685	.	+	.	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
Phchi.S3	AUGUSTUS	stop_codon	18881686	18881688	.	+	0	transcript_id "Phchi.S3G272900.t3"; gene_id "Phchi.S3G272900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4604.t1 is derived from g1774.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11318540	11320060	.	-	.	Phchi.S1G176300
Phchi.S1	AUGUSTUS	transcript	11318540	11320060	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	stop_codon	11318537	11318539	.	-	0	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11318540	11318713	0.43	-	0	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11318540	11318713	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	intron	11318714	11318853	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11318854	11319376	0.26	-	1	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11318854	11319376	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	intron	11319377	11319499	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11319500	11319690	0.57	-	0	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11319500	11319690	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	intron	11319691	11319844	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11319845	11320060	0.33	-	0	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11319845	11320060	.	-	.	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	start_codon	11320058	11320060	.	-	0	transcript_id "Phchi.S1G176300.t1"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	transcript	11318540	11319606	.	-	.	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	stop_codon	11318537	11318539	.	-	0	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11318540	11318713	0.58	-	0	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11318540	11318713	.	-	.	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	intron	11318714	11318853	.	-	.	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11318854	11319376	0.38	-	1	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11318854	11319376	.	-	.	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	intron	11319377	11319499	.	-	.	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11319500	11319606	0.55	-	0	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11319500	11319606	.	-	.	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	start_codon	11319604	11319606	.	-	0	transcript_id "Phchi.S1G176300.t2"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	transcript	11318540	11319306	.	-	.	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	stop_codon	11318537	11318539	.	-	0	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11318540	11318713	0.6	-	0	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11318540	11318713	.	-	.	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	intron	11318714	11318853	.	-	.	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	CDS	11318854	11319306	0.24	-	0	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	exon	11318854	11319306	.	-	.	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
Phchi.S1	AUGUSTUS	start_codon	11319304	11319306	.	-	0	transcript_id "Phchi.S1G176300.t3"; gene_id "Phchi.S1G176300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6488.t1 is derived from g3660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23257362	23257649	.	+	.	Phchi.S1G364700
Phchi.S1	AUGUSTUS	transcript	23257362	23257649	.	+	.	transcript_id "Phchi.S1G364700.t1"; gene_id "Phchi.S1G364700"
Phchi.S1	AUGUSTUS	start_codon	23257362	23257364	.	+	0	transcript_id "Phchi.S1G364700.t1"; gene_id "Phchi.S1G364700"
Phchi.S1	AUGUSTUS	CDS	23257362	23257649	0.87	+	0	transcript_id "Phchi.S1G364700.t1"; gene_id "Phchi.S1G364700"
Phchi.S1	AUGUSTUS	exon	23257362	23257649	.	+	.	transcript_id "Phchi.S1G364700.t1"; gene_id "Phchi.S1G364700"
Phchi.S1	AUGUSTUS	stop_codon	23257650	23257652	.	+	0	transcript_id "Phchi.S1G364700.t1"; gene_id "Phchi.S1G364700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6360.t1 is derived from g3532.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22554484	22557193	.	+	.	Phchi.S1G351900
Phchi.S1	AUGUSTUS	transcript	22554484	22554945	.	+	.	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	start_codon	22554484	22554486	.	+	0	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22554484	22554701	0.97	+	0	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22554484	22554701	.	+	.	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22554702	22554926	.	+	.	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22554927	22554945	0.98	+	1	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22554927	22554945	.	+	.	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	stop_codon	22554946	22554948	.	+	0	transcript_id "Phchi.S1G351900.t1"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	transcript	22554484	22557193	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	start_codon	22554484	22554486	.	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22554484	22554605	0.76	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22554484	22554605	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22554606	22554684	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22554685	22554742	0.76	+	1	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22554685	22554742	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22554743	22554926	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22554927	22555159	0.88	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22554927	22555159	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22555160	22555250	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22555251	22555422	0.98	+	1	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22555251	22555422	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22555423	22555537	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22555538	22555587	1	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22555538	22555587	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22555588	22555682	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22555683	22555986	1	+	1	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22555683	22555986	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22555987	22556088	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22556089	22556277	1	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22556089	22556277	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22556278	22556370	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22556371	22556553	1	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22556371	22556553	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22556554	22556653	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22556654	22556806	0.41	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22556654	22556806	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22556807	22556890	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22556891	22556901	0.56	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22556891	22556901	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	intron	22556902	22557168	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	CDS	22557169	22557193	0.56	+	1	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	exon	22557169	22557193	.	+	.	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
Phchi.S1	AUGUSTUS	stop_codon	22557194	22557196	.	+	0	transcript_id "Phchi.S1G351900.t2"; gene_id "Phchi.S1G351900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2591.t1 is derived from g9511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7536125	7541942	.	+	.	Phchi.S5G120000
Phchi.S5	AUGUSTUS	transcript	7536125	7541942	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	start_codon	7536125	7536127	.	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7536125	7536250	0.82	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7536125	7536250	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7536251	7536342	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7536343	7536403	0.67	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7536343	7536403	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7536404	7536611	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7536612	7536721	0.55	+	2	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7536612	7536721	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7536722	7536826	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7536827	7537216	0.84	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7536827	7537216	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7537217	7537588	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7537589	7537629	0.99	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7537589	7537629	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7537630	7537999	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7538000	7538135	0.95	+	1	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7538000	7538135	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7538136	7538258	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7538259	7540523	0.84	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7538259	7540523	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7540524	7540624	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7540625	7540693	1	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7540625	7540693	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7540694	7540794	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7540795	7541022	0.94	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7540795	7541022	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7541023	7541300	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7541301	7541349	0.97	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7541301	7541349	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7541350	7541442	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7541443	7541510	0.75	+	2	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7541443	7541510	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7541511	7541746	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7541747	7541799	0.67	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7541747	7541799	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	intron	7541800	7541929	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	CDS	7541930	7541942	0.71	+	1	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	exon	7541930	7541942	.	+	.	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
Phchi.S5	AUGUSTUS	stop_codon	7541943	7541945	.	+	0	transcript_id "Phchi.S5G120000.t1"; gene_id "Phchi.S5G120000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg604.t1 is derived from g10386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4370686	4372197	.	-	.	Phchi.S6G056300
Phchi.S6	AUGUSTUS	transcript	4370686	4372197	.	-	.	transcript_id "Phchi.S6G056300.t1"; gene_id "Phchi.S6G056300"
Phchi.S6	AUGUSTUS	stop_codon	4370683	4370685	.	-	0	transcript_id "Phchi.S6G056300.t1"; gene_id "Phchi.S6G056300"
Phchi.S6	AUGUSTUS	CDS	4370686	4372197	0.61	-	0	transcript_id "Phchi.S6G056300.t1"; gene_id "Phchi.S6G056300"
Phchi.S6	AUGUSTUS	exon	4370686	4372197	.	-	.	transcript_id "Phchi.S6G056300.t1"; gene_id "Phchi.S6G056300"
Phchi.S6	AUGUSTUS	start_codon	4372195	4372197	.	-	0	transcript_id "Phchi.S6G056300.t1"; gene_id "Phchi.S6G056300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9926.t1 is derived from g7102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44512027	44512612	.	+	.	Phchi.S1G708500
Phchi.S1	AUGUSTUS	transcript	44512027	44512612	.	+	.	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	start_codon	44512027	44512029	.	+	0	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	CDS	44512027	44512229	0.45	+	0	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	exon	44512027	44512229	.	+	.	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	intron	44512230	44512303	.	+	.	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	CDS	44512304	44512379	0.55	+	1	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	exon	44512304	44512379	.	+	.	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	intron	44512380	44512471	.	+	.	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	CDS	44512472	44512612	0.74	+	0	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	exon	44512472	44512612	.	+	.	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
Phchi.S1	AUGUSTUS	stop_codon	44512613	44512615	.	+	0	transcript_id "Phchi.S1G708500.t1"; gene_id "Phchi.S1G708500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9974.t1 is derived from g7150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44725305	44726485	.	-	.	Phchi.S1G713300
Phchi.S1	AUGUSTUS	transcript	44725305	44726485	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	stop_codon	44725302	44725304	.	-	0	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	CDS	44725305	44725610	0.92	-	0	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	exon	44725305	44725610	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	intron	44725611	44725697	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	CDS	44725698	44726021	1	-	0	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	exon	44725698	44726021	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	intron	44726022	44726114	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	CDS	44726115	44726225	1	-	0	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	exon	44726115	44726225	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	intron	44726226	44726311	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	CDS	44726312	44726485	0.93	-	0	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	exon	44726312	44726485	.	-	.	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
Phchi.S1	AUGUSTUS	start_codon	44726483	44726485	.	-	0	transcript_id "Phchi.S1G713300.t1"; gene_id "Phchi.S1G713300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5091.t1 is derived from g2261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14709343	14710523	.	+	.	Phchi.S1G225000
Phchi.S1	AUGUSTUS	transcript	14709343	14710523	.	+	.	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	start_codon	14709343	14709345	.	+	0	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	CDS	14709343	14710273	1	+	0	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	exon	14709343	14710273	.	+	.	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	intron	14710274	14710452	.	+	.	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	CDS	14710453	14710523	1	+	2	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	exon	14710453	14710523	.	+	.	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
Phchi.S1	AUGUSTUS	stop_codon	14710524	14710526	.	+	0	transcript_id "Phchi.S1G225000.t1"; gene_id "Phchi.S1G225000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13701.t1 is derived from g12168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8270112	8273265	.	-	.	Phchi.S3G102000
Phchi.S3	AUGUSTUS	transcript	8270112	8273265	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	stop_codon	8270109	8270111	.	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8270112	8270180	1	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8270112	8270180	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8270181	8270264	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8270265	8270381	0.82	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8270265	8270381	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8270382	8270471	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8270472	8270539	0.44	-	2	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8270472	8270539	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8270540	8270750	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8270751	8270779	0.49	-	1	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8270751	8270779	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8270780	8270855	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8270856	8270872	0.51	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8270856	8270872	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8270873	8271074	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8271075	8271551	0.64	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8271075	8271551	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8271552	8271747	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8271748	8271878	1	-	2	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8271748	8271878	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8271879	8272066	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8272067	8272229	0.98	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8272067	8272229	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	intron	8272230	8272374	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	CDS	8272375	8273265	0.98	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	exon	8272375	8273265	.	-	.	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
Phchi.S3	AUGUSTUS	start_codon	8273263	8273265	.	-	0	transcript_id "Phchi.S3G102000.t1"; gene_id "Phchi.S3G102000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9056.t1 is derived from g6231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39421866	39424325	.	-	.	Phchi.S1G621500
Phchi.S1	AUGUSTUS	transcript	39421866	39424325	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	stop_codon	39421863	39421865	.	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39421866	39421940	1	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39421866	39421940	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39421941	39422234	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39422235	39422323	1	-	2	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39422235	39422323	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39422324	39422507	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39422508	39422631	1	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39422508	39422631	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39422632	39422719	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39422720	39423005	1	-	1	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39422720	39423005	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39423006	39423167	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39423168	39423233	0.62	-	1	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39423168	39423233	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39423234	39423316	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39423317	39423341	0.6	-	2	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39423317	39423341	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39423342	39423416	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39423417	39423521	1	-	2	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39423417	39423521	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39423522	39423619	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39423620	39423713	0.94	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39423620	39423713	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39423714	39423827	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39423828	39423941	0.94	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39423828	39423941	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	intron	39423942	39424313	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	CDS	39424314	39424325	1	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	exon	39424314	39424325	.	-	.	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
Phchi.S1	AUGUSTUS	start_codon	39424323	39424325	.	-	0	transcript_id "Phchi.S1G621500.t1"; gene_id "Phchi.S1G621500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3850.t1 is derived from g1019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6029912	6030286	.	+	.	Phchi.S1G100900
Phchi.S1	AUGUSTUS	transcript	6029912	6030286	.	+	.	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	start_codon	6029912	6029914	.	+	0	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	CDS	6029912	6029956	1	+	0	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	exon	6029912	6029956	.	+	.	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	intron	6029957	6030049	.	+	.	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	CDS	6030050	6030180	0.89	+	0	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	exon	6030050	6030180	.	+	.	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	intron	6030181	6030255	.	+	.	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	CDS	6030256	6030286	0.95	+	1	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	exon	6030256	6030286	.	+	.	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
Phchi.S1	AUGUSTUS	stop_codon	6030287	6030289	.	+	0	transcript_id "Phchi.S1G100900.t1"; gene_id "Phchi.S1G100900"
# This transcript jg11762.t2 is derived from g15814.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11763.t1 is derived from g15815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8043174	8046305	.	+	.	Phchi.S4G134500
Phchi.S4	AUGUSTUS	transcript	8043174	8046305	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	start_codon	8043174	8043176	.	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8043174	8043249	1	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8043174	8043249	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8043250	8043341	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8043342	8043453	1	+	2	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8043342	8043453	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8043454	8043546	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8043547	8043614	1	+	1	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8043547	8043614	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8043615	8043748	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8043749	8043881	1	+	2	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8043749	8043881	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8043882	8044053	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8044054	8044153	1	+	1	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8044054	8044153	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8044154	8044244	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8044245	8044357	1	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8044245	8044357	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8044358	8044457	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8044458	8044551	1	+	1	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8044458	8044551	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8044552	8044785	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8044786	8044918	1	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8044786	8044918	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8044919	8045059	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8045060	8045206	0.99	+	2	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8045060	8045206	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8045207	8045401	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8045402	8045475	1	+	2	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8045402	8045475	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8045476	8045562	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8045563	8045598	0.69	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8045563	8045598	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8045599	8045693	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8045694	8045782	1	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8045694	8045782	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8045783	8045880	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8045881	8045995	1	+	1	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8045881	8045995	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	intron	8045996	8046125	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	CDS	8046126	8046305	1	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	exon	8046126	8046305	.	+	.	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
Phchi.S4	AUGUSTUS	stop_codon	8046306	8046308	.	+	0	transcript_id "Phchi.S4G134500.t1"; gene_id "Phchi.S4G134500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10676.t1 is derived from g14726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1553405	1555201	.	+	.	Phchi.S4G025800
Phchi.S4	AUGUSTUS	transcript	1553405	1555201	.	+	.	transcript_id "Phchi.S4G025800.t1"; gene_id "Phchi.S4G025800"
Phchi.S4	AUGUSTUS	start_codon	1553405	1553407	.	+	0	transcript_id "Phchi.S4G025800.t1"; gene_id "Phchi.S4G025800"
Phchi.S4	AUGUSTUS	CDS	1553405	1555201	1	+	0	transcript_id "Phchi.S4G025800.t1"; gene_id "Phchi.S4G025800"
Phchi.S4	AUGUSTUS	exon	1553405	1555201	.	+	.	transcript_id "Phchi.S4G025800.t1"; gene_id "Phchi.S4G025800"
Phchi.S4	AUGUSTUS	stop_codon	1555202	1555204	.	+	0	transcript_id "Phchi.S4G025800.t1"; gene_id "Phchi.S4G025800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg737.t1 is derived from g10519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5251188	5252966	.	-	.	Phchi.S6G069600
Phchi.S6	AUGUSTUS	transcript	5251188	5252966	.	-	.	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	stop_codon	5251185	5251187	.	-	0	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	CDS	5251188	5251215	0.85	-	1	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	exon	5251188	5251215	.	-	.	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	intron	5251216	5251465	.	-	.	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	CDS	5251466	5251524	0.83	-	0	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	exon	5251466	5251524	.	-	.	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	intron	5251525	5251814	.	-	.	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	CDS	5251815	5252966	0.46	-	0	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	exon	5251815	5252966	.	-	.	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
Phchi.S6	AUGUSTUS	start_codon	5252964	5252966	.	-	0	transcript_id "Phchi.S6G069600.t1"; gene_id "Phchi.S6G069600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1565.t1 is derived from g8484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1780738	1781073	.	+	.	Phchi.S5G017400
Phchi.S5	AUGUSTUS	transcript	1780738	1781073	.	+	.	transcript_id "Phchi.S5G017400.t1"; gene_id "Phchi.S5G017400"
Phchi.S5	AUGUSTUS	start_codon	1780738	1780740	.	+	0	transcript_id "Phchi.S5G017400.t1"; gene_id "Phchi.S5G017400"
Phchi.S5	AUGUSTUS	CDS	1780738	1781073	0.88	+	0	transcript_id "Phchi.S5G017400.t1"; gene_id "Phchi.S5G017400"
Phchi.S5	AUGUSTUS	exon	1780738	1781073	.	+	.	transcript_id "Phchi.S5G017400.t1"; gene_id "Phchi.S5G017400"
Phchi.S5	AUGUSTUS	stop_codon	1781074	1781076	.	+	0	transcript_id "Phchi.S5G017400.t1"; gene_id "Phchi.S5G017400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6638.t1 is derived from g3810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24197201	24197734	.	+	.	Phchi.S1G379700
Phchi.S1	AUGUSTUS	transcript	24197201	24197734	.	+	.	transcript_id "Phchi.S1G379700.t1"; gene_id "Phchi.S1G379700"
Phchi.S1	AUGUSTUS	start_codon	24197201	24197203	.	+	0	transcript_id "Phchi.S1G379700.t1"; gene_id "Phchi.S1G379700"
Phchi.S1	AUGUSTUS	CDS	24197201	24197734	1	+	0	transcript_id "Phchi.S1G379700.t1"; gene_id "Phchi.S1G379700"
Phchi.S1	AUGUSTUS	exon	24197201	24197734	.	+	.	transcript_id "Phchi.S1G379700.t1"; gene_id "Phchi.S1G379700"
Phchi.S1	AUGUSTUS	stop_codon	24197735	24197737	.	+	0	transcript_id "Phchi.S1G379700.t1"; gene_id "Phchi.S1G379700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4801.t1 is derived from g1971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12893902	12895578	.	+	.	Phchi.S1G196000
Phchi.S1	AUGUSTUS	transcript	12893902	12895578	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	start_codon	12893902	12893904	.	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12893902	12893928	1	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12893902	12893928	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12893929	12894012	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12894013	12894106	1	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12894013	12894106	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12894107	12894188	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12894189	12894221	1	+	2	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12894189	12894221	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12894222	12894298	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12894299	12894445	1	+	2	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12894299	12894445	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12894446	12894547	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12894548	12894678	1	+	2	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12894548	12894678	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12894679	12894784	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12894785	12894922	0.94	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12894785	12894922	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12894923	12895033	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12895034	12895132	1	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12895034	12895132	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	intron	12895133	12895245	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	CDS	12895246	12895578	1	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	exon	12895246	12895578	.	+	.	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
Phchi.S1	AUGUSTUS	stop_codon	12895579	12895581	.	+	0	transcript_id "Phchi.S1G196000.t1"; gene_id "Phchi.S1G196000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15743.t1 is derived from g14213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21025896	21028158	.	+	.	Phchi.S3G306200
Phchi.S3	AUGUSTUS	transcript	21025896	21028158	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	start_codon	21025896	21025898	.	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21025896	21026047	1	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21025896	21026047	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21026048	21026326	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21026327	21026462	1	+	1	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21026327	21026462	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21026463	21026568	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21026569	21026648	0.9	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21026569	21026648	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21026649	21026777	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21026778	21026868	1	+	1	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21026778	21026868	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21026869	21026957	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21026958	21027041	1	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21026958	21027041	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21027042	21027140	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21027141	21027209	1	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21027141	21027209	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21027210	21027290	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21027291	21027352	1	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21027291	21027352	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21027353	21027517	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21027518	21027605	1	+	1	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21027518	21027605	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21027606	21027768	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21027769	21027810	0.99	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21027769	21027810	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21027811	21027920	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21027921	21027968	0.99	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21027921	21027968	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	intron	21027969	21028047	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	CDS	21028048	21028158	0.98	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	exon	21028048	21028158	.	+	.	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
Phchi.S3	AUGUSTUS	stop_codon	21028159	21028161	.	+	0	transcript_id "Phchi.S3G306200.t1"; gene_id "Phchi.S3G306200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15200.t1 is derived from g13668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17531658	17533175	.	-	.	Phchi.S3G251900
Phchi.S3	AUGUSTUS	transcript	17531658	17533175	.	-	.	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	stop_codon	17531655	17531657	.	-	0	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	CDS	17531658	17532150	1	-	1	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	exon	17531658	17532150	.	-	.	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	intron	17532151	17532250	.	-	.	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	CDS	17532251	17532480	0.49	-	0	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	exon	17532251	17532480	.	-	.	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	intron	17532481	17532689	.	-	.	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	CDS	17532690	17533175	0.16	-	0	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	exon	17532690	17533175	.	-	.	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
Phchi.S3	AUGUSTUS	start_codon	17533173	17533175	.	-	0	transcript_id "Phchi.S3G251900.t1"; gene_id "Phchi.S3G251900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4701.t1 is derived from g1871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12351372	12353037	.	+	.	Phchi.S1G186000
Phchi.S1	AUGUSTUS	transcript	12351372	12353037	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	start_codon	12351372	12351374	.	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12351372	12351447	0.7	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12351372	12351447	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	intron	12351448	12351565	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12351566	12351594	0.53	+	2	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12351566	12351594	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	intron	12351595	12351677	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12351678	12351866	1	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12351678	12351866	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	intron	12351867	12352026	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12352027	12352251	0.84	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12352027	12352251	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	intron	12352252	12352368	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12352369	12352584	1	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12352369	12352584	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	intron	12352585	12352694	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12352695	12352756	1	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12352695	12352756	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	intron	12352757	12352853	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	CDS	12352854	12353037	1	+	1	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	exon	12352854	12353037	.	+	.	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
Phchi.S1	AUGUSTUS	stop_codon	12353038	12353040	.	+	0	transcript_id "Phchi.S1G186000.t1"; gene_id "Phchi.S1G186000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8486.t1 is derived from g5661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36162307	36163224	.	-	.	Phchi.S1G564500
Phchi.S1	AUGUSTUS	transcript	36162307	36163224	.	-	.	transcript_id "Phchi.S1G564500.t1"; gene_id "Phchi.S1G564500"
Phchi.S1	AUGUSTUS	stop_codon	36162304	36162306	.	-	0	transcript_id "Phchi.S1G564500.t1"; gene_id "Phchi.S1G564500"
Phchi.S1	AUGUSTUS	CDS	36162307	36163224	0.98	-	0	transcript_id "Phchi.S1G564500.t1"; gene_id "Phchi.S1G564500"
Phchi.S1	AUGUSTUS	exon	36162307	36163224	.	-	.	transcript_id "Phchi.S1G564500.t1"; gene_id "Phchi.S1G564500"
Phchi.S1	AUGUSTUS	start_codon	36163222	36163224	.	-	0	transcript_id "Phchi.S1G564500.t1"; gene_id "Phchi.S1G564500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6038.t1 is derived from g3209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20536184	20542020	.	-	.	Phchi.S1G319700
Phchi.S1	AUGUSTUS	transcript	20536184	20542020	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	stop_codon	20536181	20536183	.	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20536184	20536401	0.99	-	2	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20536184	20536401	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20536402	20536489	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20536490	20536619	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20536490	20536619	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20536620	20536717	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20536718	20536817	1	-	1	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20536718	20536817	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20536818	20536948	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20536949	20537028	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20536949	20537028	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20537029	20537111	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20537112	20537249	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20537112	20537249	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20537250	20537411	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20537412	20537689	0.99	-	2	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20537412	20537689	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20537690	20537794	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20537795	20537957	0.97	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20537795	20537957	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20537958	20538047	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20538048	20538149	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20538048	20538149	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20538150	20538247	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20538248	20538453	1	-	2	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20538248	20538453	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20538454	20538549	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20538550	20538728	1	-	1	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20538550	20538728	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20538729	20538816	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20538817	20538908	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20538817	20538908	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20538909	20538995	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20538996	20539125	0.95	-	1	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20538996	20539125	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20539126	20539236	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20539237	20539775	0.94	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20539237	20539775	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20539776	20539876	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20539877	20540050	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20539877	20540050	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20540051	20540199	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20540200	20540283	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20540200	20540283	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20540284	20540472	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20540473	20540541	1	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20540473	20540541	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20540542	20540690	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20540691	20540765	0.75	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20540691	20540765	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20540766	20540884	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20540885	20540938	0.77	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20540885	20540938	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20540939	20541021	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20541022	20541124	1	-	1	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20541022	20541124	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20541125	20541218	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20541219	20541315	0.99	-	2	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20541219	20541315	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20541316	20541439	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20541440	20541488	0.97	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20541440	20541488	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	intron	20541489	20541573	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	CDS	20541574	20542020	0.56	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	exon	20541574	20542020	.	-	.	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
Phchi.S1	AUGUSTUS	start_codon	20542018	20542020	.	-	0	transcript_id "Phchi.S1G319700.t1"; gene_id "Phchi.S1G319700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13399.t1 is derived from g11865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6525111	6525695	.	+	.	Phchi.S3G071800
Phchi.S3	AUGUSTUS	transcript	6525111	6525695	.	+	.	transcript_id "Phchi.S3G071800.t1"; gene_id "Phchi.S3G071800"
Phchi.S3	AUGUSTUS	start_codon	6525111	6525113	.	+	0	transcript_id "Phchi.S3G071800.t1"; gene_id "Phchi.S3G071800"
Phchi.S3	AUGUSTUS	CDS	6525111	6525695	0.54	+	0	transcript_id "Phchi.S3G071800.t1"; gene_id "Phchi.S3G071800"
Phchi.S3	AUGUSTUS	exon	6525111	6525695	.	+	.	transcript_id "Phchi.S3G071800.t1"; gene_id "Phchi.S3G071800"
Phchi.S3	AUGUSTUS	stop_codon	6525696	6525698	.	+	0	transcript_id "Phchi.S3G071800.t1"; gene_id "Phchi.S3G071800"
# This transcript jg10270.t2 is derived from g7446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10271.t1 is derived from g7447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46781468	46782804	.	+	.	Phchi.S1G743000
Phchi.S1	AUGUSTUS	transcript	46781468	46782804	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	start_codon	46781468	46781470	.	+	0	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	CDS	46781468	46781604	0.92	+	0	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	exon	46781468	46781604	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	intron	46781605	46781702	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	CDS	46781703	46781841	1	+	1	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	exon	46781703	46781841	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	intron	46781842	46781920	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	CDS	46781921	46782051	1	+	0	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	exon	46781921	46782051	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	intron	46782052	46782149	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	CDS	46782150	46782351	1	+	1	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	exon	46782150	46782351	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	intron	46782352	46782447	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	CDS	46782448	46782804	0.99	+	0	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	exon	46782448	46782804	.	+	.	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
Phchi.S1	AUGUSTUS	stop_codon	46782805	46782807	.	+	0	transcript_id "Phchi.S1G743000.t1"; gene_id "Phchi.S1G743000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6136.t1 is derived from g3307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21103028	21106945	.	-	.	Phchi.S1G329500
Phchi.S1	AUGUSTUS	transcript	21103028	21106945	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	stop_codon	21103025	21103027	.	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103028	21103420	0.99	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103028	21103420	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21103421	21103504	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103505	21103650	1	-	2	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103505	21103650	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21103651	21103739	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103740	21103872	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103740	21103872	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21103873	21103990	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103991	21104123	1	-	1	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103991	21104123	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104124	21104218	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104219	21104301	0.86	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104219	21104301	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104302	21104409	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104410	21104488	0.96	-	1	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104410	21104488	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104489	21104680	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104681	21104844	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104681	21104844	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104845	21104938	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104939	21105004	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104939	21105004	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105005	21105158	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105159	21105281	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105159	21105281	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105282	21105368	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105369	21105446	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105369	21105446	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105447	21105532	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105533	21105651	1	-	2	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105533	21105651	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105652	21105734	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105735	21106155	0.83	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105735	21106155	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21106156	21106266	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21106267	21106434	0.84	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21106267	21106434	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21106435	21106513	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21106514	21106699	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21106514	21106699	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21106700	21106825	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21106826	21106945	1	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21106826	21106945	.	-	.	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	start_codon	21106943	21106945	.	-	0	transcript_id "Phchi.S1G329500.t1"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	transcript	21103028	21106945	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	stop_codon	21103025	21103027	.	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103028	21103420	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103028	21103420	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21103421	21103504	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103505	21103650	1	-	2	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103505	21103650	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21103651	21103739	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103740	21103872	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103740	21103872	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21103873	21103990	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21103991	21104123	1	-	1	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21103991	21104123	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104124	21104218	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104219	21104284	0.84	-	1	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104219	21104284	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104285	21104369	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104370	21104483	0.79	-	1	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104370	21104483	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104484	21104680	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104681	21104844	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104681	21104844	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21104845	21104938	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21104939	21105004	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21104939	21105004	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105005	21105158	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105159	21105281	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105159	21105281	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105282	21105368	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105369	21105446	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105369	21105446	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105447	21105532	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105533	21105651	1	-	2	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105533	21105651	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21105652	21105734	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21105735	21106155	0.78	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21105735	21106155	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21106156	21106266	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21106267	21106434	0.78	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21106267	21106434	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21106435	21106513	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21106514	21106699	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21106514	21106699	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	intron	21106700	21106825	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	CDS	21106826	21106945	1	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	exon	21106826	21106945	.	-	.	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
Phchi.S1	AUGUSTUS	start_codon	21106943	21106945	.	-	0	transcript_id "Phchi.S1G329500.t2"; gene_id "Phchi.S1G329500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15628.t1 is derived from g14097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20371953	20373775	.	+	.	Phchi.S3G294700
Phchi.S3	AUGUSTUS	transcript	20371953	20373775	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	start_codon	20371953	20371955	.	+	0	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	CDS	20371953	20372356	0.56	+	0	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	exon	20371953	20372356	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	intron	20372357	20372449	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	CDS	20372450	20373138	1	+	1	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	exon	20372450	20373138	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	intron	20373139	20373316	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	CDS	20373317	20373620	1	+	2	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	exon	20373317	20373620	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	intron	20373621	20373708	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	CDS	20373709	20373775	1	+	1	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	exon	20373709	20373775	.	+	.	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
Phchi.S3	AUGUSTUS	stop_codon	20373776	20373778	.	+	0	transcript_id "Phchi.S3G294700.t1"; gene_id "Phchi.S3G294700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7135.t1 is derived from g4307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27124566	27126414	.	+	.	Phchi.S1G429400
Phchi.S1	AUGUSTUS	transcript	27124566	27126414	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	start_codon	27124566	27124568	.	+	0	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	CDS	27124566	27124791	0.96	+	0	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	exon	27124566	27124791	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	intron	27124792	27124882	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	CDS	27124883	27124962	1	+	2	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	exon	27124883	27124962	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	intron	27124963	27125106	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	CDS	27125107	27125240	1	+	0	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	exon	27125107	27125240	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	intron	27125241	27125378	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	CDS	27125379	27126414	0.77	+	1	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	exon	27125379	27126414	.	+	.	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
Phchi.S1	AUGUSTUS	stop_codon	27126415	27126417	.	+	0	transcript_id "Phchi.S1G429400.t1"; gene_id "Phchi.S1G429400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13738.t1 is derived from g12205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8654726	8659477	.	+	.	Phchi.S3G105700
Phchi.S3	AUGUSTUS	transcript	8654726	8659477	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	start_codon	8654726	8654728	.	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8654726	8654785	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8654726	8654785	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8654786	8655145	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8655146	8655208	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8655146	8655208	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8655209	8655296	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8655297	8655512	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8655297	8655512	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8655513	8655683	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8655684	8655998	0.99	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8655684	8655998	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8655999	8656105	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8656106	8656198	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8656106	8656198	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8656199	8656389	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8656390	8656488	0.99	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8656390	8656488	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8656489	8656599	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8656600	8656629	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8656600	8656629	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8656630	8656728	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8656729	8656782	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8656729	8656782	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8656783	8656877	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8656878	8656931	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8656878	8656931	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8656932	8657014	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8657015	8657092	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8657015	8657092	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8657093	8657173	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8657174	8657265	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8657174	8657265	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8657266	8657394	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8657395	8657452	1	+	1	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8657395	8657452	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8657453	8657554	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8657555	8657629	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8657555	8657629	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8657630	8657736	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8657737	8657784	0.95	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8657737	8657784	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8657785	8657937	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8657938	8658035	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8657938	8658035	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8658036	8658137	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8658138	8658213	1	+	1	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8658138	8658213	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8658214	8658401	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8658402	8658464	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8658402	8658464	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8658465	8658622	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8658623	8658714	1	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8658623	8658714	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8658715	8658900	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8658901	8658969	1	+	1	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8658901	8658969	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8658970	8659039	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8659040	8659103	1	+	1	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8659040	8659103	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8659104	8659180	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8659181	8659246	0.99	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8659181	8659246	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	intron	8659247	8659348	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	CDS	8659349	8659477	0.99	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	exon	8659349	8659477	.	+	.	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
Phchi.S3	AUGUSTUS	stop_codon	8659478	8659480	.	+	0	transcript_id "Phchi.S3G105700.t1"; gene_id "Phchi.S3G105700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13932.t1 is derived from g12399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9790301	9792051	.	+	.	Phchi.S3G125100
Phchi.S3	AUGUSTUS	transcript	9790301	9792051	.	+	.	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	start_codon	9790301	9790303	.	+	0	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	CDS	9790301	9790567	0.99	+	0	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	exon	9790301	9790567	.	+	.	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	intron	9790568	9790689	.	+	.	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	CDS	9790690	9791151	1	+	0	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	exon	9790690	9791151	.	+	.	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	intron	9791152	9791244	.	+	.	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	CDS	9791245	9792051	1	+	0	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	exon	9791245	9792051	.	+	.	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
Phchi.S3	AUGUSTUS	stop_codon	9792052	9792054	.	+	0	transcript_id "Phchi.S3G125100.t1"; gene_id "Phchi.S3G125100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13131.t1 is derived from g11596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4275881	4278119	.	-	.	Phchi.S3G045000
Phchi.S3	AUGUSTUS	transcript	4275881	4278119	.	-	.	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	stop_codon	4275878	4275880	.	-	0	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	CDS	4275881	4277576	1	-	1	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	exon	4275881	4277576	.	-	.	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	intron	4277577	4277650	.	-	.	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	CDS	4277651	4277769	0.43	-	0	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	exon	4277651	4277769	.	-	.	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	intron	4277770	4278074	.	-	.	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	CDS	4278075	4278119	0.58	-	0	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	exon	4278075	4278119	.	-	.	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
Phchi.S3	AUGUSTUS	start_codon	4278117	4278119	.	-	0	transcript_id "Phchi.S3G045000.t1"; gene_id "Phchi.S3G045000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7870.t1 is derived from g5044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31640191	31642916	.	-	.	Phchi.S1G502900
Phchi.S1	AUGUSTUS	transcript	31640191	31642916	.	-	.	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	stop_codon	31640188	31640190	.	-	0	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	CDS	31640191	31641200	0.85	-	2	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	exon	31640191	31641200	.	-	.	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	intron	31641201	31641340	.	-	.	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	CDS	31641341	31642916	0.46	-	0	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	exon	31641341	31642916	.	-	.	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
Phchi.S1	AUGUSTUS	start_codon	31642914	31642916	.	-	0	transcript_id "Phchi.S1G502900.t1"; gene_id "Phchi.S1G502900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14313.t1 is derived from g12780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12058733	12060765	.	-	.	Phchi.S3G163200
Phchi.S3	AUGUSTUS	transcript	12058733	12060765	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	stop_codon	12058730	12058732	.	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12058733	12058914	0.57	-	2	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12058733	12058914	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12058915	12059091	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12059092	12059208	0.52	-	2	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12059092	12059208	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12059209	12059334	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12059335	12059402	1	-	1	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12059335	12059402	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12059403	12059486	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12059487	12059557	1	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12059487	12059557	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12059558	12059698	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12059699	12059799	1	-	2	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12059699	12059799	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12059800	12059968	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12059969	12059987	0.53	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12059969	12059987	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12059988	12060070	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12060071	12060118	0.35	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12060071	12060118	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12060119	12060230	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12060231	12060407	0.72	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12060231	12060407	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	intron	12060408	12060498	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	CDS	12060499	12060765	1	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	exon	12060499	12060765	.	-	.	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
Phchi.S3	AUGUSTUS	start_codon	12060763	12060765	.	-	0	transcript_id "Phchi.S3G163200.t1"; gene_id "Phchi.S3G163200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2693.t1 is derived from g9613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8230305	8232664	.	-	.	Phchi.S5G130200
Phchi.S5	AUGUSTUS	transcript	8230305	8232664	.	-	.	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	stop_codon	8230302	8230304	.	-	0	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	CDS	8230305	8230643	1	-	0	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	exon	8230305	8230643	.	-	.	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	intron	8230644	8230747	.	-	.	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	CDS	8230748	8230915	1	-	0	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	exon	8230748	8230915	.	-	.	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	intron	8230916	8231005	.	-	.	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	CDS	8231006	8232664	0.99	-	0	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	exon	8231006	8232664	.	-	.	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
Phchi.S5	AUGUSTUS	start_codon	8232662	8232664	.	-	0	transcript_id "Phchi.S5G130200.t1"; gene_id "Phchi.S5G130200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13965.t1 is derived from g12432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9953831	9954466	.	-	.	Phchi.S3G128400
Phchi.S3	AUGUSTUS	transcript	9953831	9954466	.	-	.	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	stop_codon	9953828	9953830	.	-	0	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	CDS	9953831	9953942	0.59	-	1	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	exon	9953831	9953942	.	-	.	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	intron	9953943	9954029	.	-	.	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	CDS	9954030	9954466	0.86	-	0	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	exon	9954030	9954466	.	-	.	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
Phchi.S3	AUGUSTUS	start_codon	9954464	9954466	.	-	0	transcript_id "Phchi.S3G128400.t1"; gene_id "Phchi.S3G128400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6455.t1 is derived from g3627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23106303	23108745	.	+	.	Phchi.S1G361400
Phchi.S1	AUGUSTUS	transcript	23106303	23108745	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	start_codon	23106303	23106305	.	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23106303	23106441	0.25	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23106303	23106441	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23106442	23106535	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23106536	23106657	0.21	+	2	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23106536	23106657	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23106658	23106766	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23106767	23106848	0.83	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23106767	23106848	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23106849	23106931	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23106932	23107060	0.38	+	2	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23106932	23107060	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23107061	23107176	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23107177	23107655	0.28	+	2	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23107177	23107655	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23107656	23107746	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23107747	23107809	1	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23107747	23107809	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23107810	23107900	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23107901	23107972	1	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23107901	23107972	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23107973	23108065	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23108066	23108215	0.43	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23108066	23108215	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23108216	23108313	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23108314	23108439	0.87	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23108314	23108439	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23108440	23108531	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23108532	23108588	1	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23108532	23108588	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	intron	23108589	23108673	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	CDS	23108674	23108745	1	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	exon	23108674	23108745	.	+	.	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
Phchi.S1	AUGUSTUS	stop_codon	23108746	23108748	.	+	0	transcript_id "Phchi.S1G361400.t1"; gene_id "Phchi.S1G361400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11821.t1 is derived from g15873.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8394550	8400283	.	+	.	Phchi.S4G140300
Phchi.S4	AUGUSTUS	transcript	8394550	8400283	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	start_codon	8394550	8394552	.	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8394550	8394570	0.98	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8394550	8394570	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8394571	8394713	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8394714	8394950	0.98	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8394714	8394950	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8394951	8395081	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8395082	8395894	0.41	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8395082	8395894	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8395895	8396051	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8396052	8396089	1	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8396052	8396089	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8396090	8396481	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8396482	8396560	1	+	1	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8396482	8396560	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8396561	8396774	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8396775	8397197	0.87	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8396775	8397197	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8397198	8397300	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8397301	8397384	0.67	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8397301	8397384	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8397385	8397640	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8397641	8397781	1	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8397641	8397781	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8397782	8397936	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8397937	8398043	0.77	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8397937	8398043	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8398044	8398353	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8398354	8398458	0.38	+	1	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8398354	8398458	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8398459	8398696	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8398697	8398820	0.97	+	1	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8398697	8398820	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8398821	8398913	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8398914	8399057	1	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8398914	8399057	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8399058	8399242	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8399243	8399389	1	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8399243	8399389	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8399390	8399471	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8399472	8399594	1	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8399472	8399594	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8399595	8399679	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8399680	8399936	0.71	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8399680	8399936	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	intron	8399937	8400168	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	CDS	8400169	8400283	0.55	+	1	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	exon	8400169	8400283	.	+	.	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
Phchi.S4	AUGUSTUS	stop_codon	8400284	8400286	.	+	0	transcript_id "Phchi.S4G140300.t1"; gene_id "Phchi.S4G140300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1812.t1 is derived from g8732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3162164	3162517	.	+	.	Phchi.S5G042100
Phchi.S5	AUGUSTUS	transcript	3162164	3162517	.	+	.	transcript_id "Phchi.S5G042100.t1"; gene_id "Phchi.S5G042100"
Phchi.S5	AUGUSTUS	start_codon	3162164	3162166	.	+	0	transcript_id "Phchi.S5G042100.t1"; gene_id "Phchi.S5G042100"
Phchi.S5	AUGUSTUS	CDS	3162164	3162517	0.35	+	0	transcript_id "Phchi.S5G042100.t1"; gene_id "Phchi.S5G042100"
Phchi.S5	AUGUSTUS	exon	3162164	3162517	.	+	.	transcript_id "Phchi.S5G042100.t1"; gene_id "Phchi.S5G042100"
Phchi.S5	AUGUSTUS	stop_codon	3162518	3162520	.	+	0	transcript_id "Phchi.S5G042100.t1"; gene_id "Phchi.S5G042100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4628.t1 is derived from g1798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11463658	11466089	.	+	.	Phchi.S1G178700
Phchi.S1	AUGUSTUS	transcript	11463658	11466089	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	start_codon	11463658	11463660	.	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	CDS	11463658	11463765	0.42	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	exon	11463658	11463765	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	intron	11463766	11464224	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	CDS	11464225	11464309	0.99	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	exon	11464225	11464309	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	intron	11464310	11464396	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	CDS	11464397	11464410	0.87	+	2	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	exon	11464397	11464410	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	intron	11464411	11464553	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	CDS	11464554	11465750	0.24	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	exon	11464554	11465750	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	intron	11465751	11465859	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	CDS	11465860	11465901	0.56	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	exon	11465860	11465901	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	intron	11465902	11466035	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	CDS	11466036	11466089	0.74	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	exon	11466036	11466089	.	+	.	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
Phchi.S1	AUGUSTUS	stop_codon	11466090	11466092	.	+	0	transcript_id "Phchi.S1G178700.t1"; gene_id "Phchi.S1G178700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6959.t1 is derived from g4131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26143449	26144618	.	+	.	Phchi.S1G411800
Phchi.S1	AUGUSTUS	transcript	26143449	26144618	.	+	.	transcript_id "Phchi.S1G411800.t1"; gene_id "Phchi.S1G411800"
Phchi.S1	AUGUSTUS	start_codon	26143449	26143451	.	+	0	transcript_id "Phchi.S1G411800.t1"; gene_id "Phchi.S1G411800"
Phchi.S1	AUGUSTUS	CDS	26143449	26144618	0.9	+	0	transcript_id "Phchi.S1G411800.t1"; gene_id "Phchi.S1G411800"
Phchi.S1	AUGUSTUS	exon	26143449	26144618	.	+	.	transcript_id "Phchi.S1G411800.t1"; gene_id "Phchi.S1G411800"
Phchi.S1	AUGUSTUS	stop_codon	26144619	26144621	.	+	0	transcript_id "Phchi.S1G411800.t1"; gene_id "Phchi.S1G411800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14755.t1 is derived from g13223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14559060	14560165	.	-	.	Phchi.S3G207400
Phchi.S3	AUGUSTUS	transcript	14559060	14560165	.	-	.	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	stop_codon	14559057	14559059	.	-	0	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	CDS	14559060	14559890	1	-	0	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	exon	14559060	14559890	.	-	.	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	intron	14559891	14560024	.	-	.	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	CDS	14560025	14560165	1	-	0	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	exon	14560025	14560165	.	-	.	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
Phchi.S3	AUGUSTUS	start_codon	14560163	14560165	.	-	0	transcript_id "Phchi.S3G207400.t1"; gene_id "Phchi.S3G207400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15343.t1 is derived from g13811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18467627	18468344	.	+	.	Phchi.S3G266200
Phchi.S3	AUGUSTUS	transcript	18467627	18468344	.	+	.	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	start_codon	18467627	18467629	.	+	0	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	CDS	18467627	18467720	0.56	+	0	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	exon	18467627	18467720	.	+	.	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	intron	18467721	18467856	.	+	.	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	CDS	18467857	18468137	0.84	+	2	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	exon	18467857	18468137	.	+	.	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	intron	18468138	18468239	.	+	.	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	CDS	18468240	18468344	1	+	0	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	exon	18468240	18468344	.	+	.	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
Phchi.S3	AUGUSTUS	stop_codon	18468345	18468347	.	+	0	transcript_id "Phchi.S3G266200.t1"; gene_id "Phchi.S3G266200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4156.t1 is derived from g1325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8673199	8674931	.	-	.	Phchi.S1G131500
Phchi.S1	AUGUSTUS	transcript	8673199	8674931	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	stop_codon	8673196	8673198	.	-	0	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	CDS	8673199	8674288	0.74	-	1	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	exon	8673199	8674288	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	intron	8674289	8674355	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	CDS	8674356	8674405	0.92	-	0	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	exon	8674356	8674405	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	intron	8674406	8674617	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	CDS	8674618	8674713	0.83	-	0	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	exon	8674618	8674713	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	intron	8674714	8674817	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	CDS	8674818	8674931	0.63	-	0	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	exon	8674818	8674931	.	-	.	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
Phchi.S1	AUGUSTUS	start_codon	8674929	8674931	.	-	0	transcript_id "Phchi.S1G131500.t1"; gene_id "Phchi.S1G131500"
# This transcript jg15340.t2 is derived from g13808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15341.t1 is derived from g13809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18466086	18466937	.	+	.	Phchi.S3G266000
Phchi.S3	AUGUSTUS	transcript	18466086	18466937	.	+	.	transcript_id "Phchi.S3G266000.t1"; gene_id "Phchi.S3G266000"
Phchi.S3	AUGUSTUS	start_codon	18466086	18466088	.	+	0	transcript_id "Phchi.S3G266000.t1"; gene_id "Phchi.S3G266000"
Phchi.S3	AUGUSTUS	CDS	18466086	18466937	0.29	+	0	transcript_id "Phchi.S3G266000.t1"; gene_id "Phchi.S3G266000"
Phchi.S3	AUGUSTUS	exon	18466086	18466937	.	+	.	transcript_id "Phchi.S3G266000.t1"; gene_id "Phchi.S3G266000"
Phchi.S3	AUGUSTUS	stop_codon	18466938	18466940	.	+	0	transcript_id "Phchi.S3G266000.t1"; gene_id "Phchi.S3G266000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2697.t1 is derived from g9617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8243557	8246518	.	-	.	Phchi.S5G130600
Phchi.S5	AUGUSTUS	transcript	8243557	8246518	.	-	.	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	stop_codon	8243554	8243556	.	-	0	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	CDS	8243557	8244359	0.91	-	2	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	exon	8243557	8244359	.	-	.	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	intron	8244360	8244478	.	-	.	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	CDS	8244479	8244779	0.98	-	0	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	exon	8244479	8244779	.	-	.	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	intron	8244780	8244898	.	-	.	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	CDS	8244899	8246518	0.98	-	0	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	exon	8244899	8246518	.	-	.	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
Phchi.S5	AUGUSTUS	start_codon	8246516	8246518	.	-	0	transcript_id "Phchi.S5G130600.t1"; gene_id "Phchi.S5G130600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7577.t1 is derived from g4751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30133462	30134795	.	+	.	Phchi.S1G473600
Phchi.S1	AUGUSTUS	transcript	30133462	30134795	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	start_codon	30133462	30133464	.	+	0	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	CDS	30133462	30133750	0.78	+	0	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	exon	30133462	30133750	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	intron	30133751	30133852	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	CDS	30133853	30133885	0.8	+	2	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	exon	30133853	30133885	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	intron	30133886	30134008	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	CDS	30134009	30134136	0.87	+	2	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	exon	30134009	30134136	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	intron	30134137	30134304	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	CDS	30134305	30134434	0.87	+	0	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	exon	30134305	30134434	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	intron	30134435	30134556	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	CDS	30134557	30134628	1	+	2	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	exon	30134557	30134628	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	intron	30134629	30134706	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	CDS	30134707	30134795	0.99	+	2	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	exon	30134707	30134795	.	+	.	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
Phchi.S1	AUGUSTUS	stop_codon	30134796	30134798	.	+	0	transcript_id "Phchi.S1G473600.t1"; gene_id "Phchi.S1G473600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1841.t1 is derived from g8761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3525898	3526856	.	-	.	Phchi.S5G045000
Phchi.S5	AUGUSTUS	transcript	3525898	3526856	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	stop_codon	3525895	3525897	.	-	0	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	CDS	3525898	3525928	0.71	-	1	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	exon	3525898	3525928	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	intron	3525929	3526022	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	CDS	3526023	3526074	1	-	2	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	exon	3526023	3526074	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	intron	3526075	3526153	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	CDS	3526154	3526384	1	-	2	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	exon	3526154	3526384	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	intron	3526385	3526480	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	CDS	3526481	3526553	1	-	0	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	exon	3526481	3526553	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	intron	3526554	3526623	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	CDS	3526624	3526765	1	-	1	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	exon	3526624	3526765	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	intron	3526766	3526845	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	CDS	3526846	3526856	0.92	-	0	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	exon	3526846	3526856	.	-	.	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
Phchi.S5	AUGUSTUS	start_codon	3526854	3526856	.	-	0	transcript_id "Phchi.S5G045000.t1"; gene_id "Phchi.S5G045000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10498.t1 is derived from g14547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	712404	716232	.	+	.	Phchi.S4G008000
Phchi.S4	AUGUSTUS	transcript	712404	716232	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	start_codon	712404	712406	.	+	0	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	CDS	712404	712554	0.75	+	0	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	exon	712404	712554	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	intron	712555	712648	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	CDS	712649	712756	0.95	+	2	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	exon	712649	712756	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	intron	712757	712888	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	CDS	712889	713896	0.76	+	2	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	exon	712889	713896	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	intron	713897	714136	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	CDS	714137	714607	0.83	+	2	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	exon	714137	714607	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	intron	714608	714742	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	CDS	714743	716232	0.81	+	2	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	exon	714743	716232	.	+	.	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
Phchi.S4	AUGUSTUS	stop_codon	716233	716235	.	+	0	transcript_id "Phchi.S4G008000.t1"; gene_id "Phchi.S4G008000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11295.t1 is derived from g15345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5278599	5284950	.	-	.	Phchi.S4G087700
Phchi.S4	AUGUSTUS	transcript	5278599	5284950	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	stop_codon	5278596	5278598	.	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5278599	5278793	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5278599	5278793	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5278794	5278869	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5278870	5279016	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5278870	5279016	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5279017	5279097	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5279098	5279351	1	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5279098	5279351	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5279352	5279425	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5279426	5279803	0.77	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5279426	5279803	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5279804	5279911	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5279912	5280002	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5279912	5280002	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280003	5280095	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280096	5280197	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280096	5280197	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280198	5280377	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280378	5280450	1	-	1	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280378	5280450	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280451	5280533	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280534	5280588	1	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280534	5280588	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280589	5280785	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280786	5280979	1	-	1	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280786	5280979	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280980	5281099	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281100	5281263	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281100	5281263	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281264	5281349	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281350	5281405	1	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281350	5281405	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281406	5281612	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281613	5281692	0.93	-	1	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281613	5281692	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281693	5281794	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281795	5281942	0.93	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281795	5281942	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281943	5282077	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5282078	5282166	1	-	1	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5282078	5282166	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5282167	5282275	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5282276	5282419	1	-	1	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5282276	5282419	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5282420	5282612	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5282613	5282824	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5282613	5282824	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5282825	5283026	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283027	5283218	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283027	5283218	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5283219	5283286	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283287	5283423	1	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283287	5283423	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5283424	5283497	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283498	5283603	0.72	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283498	5283603	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5283604	5283704	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283705	5284014	0.63	-	1	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283705	5284014	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284015	5284108	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284109	5284202	1	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284109	5284202	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284203	5284302	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284303	5284507	0.98	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284303	5284507	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284508	5284579	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284580	5284680	1	-	2	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284580	5284680	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284681	5284760	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284761	5284950	1	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284761	5284950	.	-	.	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	start_codon	5284948	5284950	.	-	0	transcript_id "Phchi.S4G087700.t1"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	transcript	5278599	5284950	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	stop_codon	5278596	5278598	.	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5278599	5278793	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5278599	5278793	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5278794	5278869	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5278870	5279016	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5278870	5279016	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5279017	5279097	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5279098	5279351	1	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5279098	5279351	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5279352	5279425	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5279426	5279803	0.72	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5279426	5279803	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5279804	5279911	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5279912	5280002	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5279912	5280002	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280003	5280095	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280096	5280197	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280096	5280197	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280198	5280377	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280378	5280450	1	-	1	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280378	5280450	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280451	5280533	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280534	5280588	1	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280534	5280588	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280589	5280785	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5280786	5280979	1	-	1	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5280786	5280979	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5280980	5281099	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281100	5281263	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281100	5281263	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281264	5281349	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281350	5281405	0.94	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281350	5281405	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281406	5281599	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281600	5281692	0.76	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281600	5281692	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281693	5281816	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5281817	5281942	0.76	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5281817	5281942	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5281943	5282077	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5282078	5282166	1	-	1	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5282078	5282166	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5282167	5282275	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5282276	5282419	1	-	1	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5282276	5282419	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5282420	5282612	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5282613	5282824	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5282613	5282824	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5282825	5283026	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283027	5283218	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283027	5283218	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5283219	5283286	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283287	5283423	1	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283287	5283423	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5283424	5283497	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283498	5283603	0.72	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283498	5283603	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5283604	5283704	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5283705	5284014	0.62	-	1	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5283705	5284014	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284015	5284108	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284109	5284202	1	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284109	5284202	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284203	5284302	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284303	5284507	0.99	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284303	5284507	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284508	5284579	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284580	5284680	1	-	2	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284580	5284680	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	intron	5284681	5284760	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	CDS	5284761	5284950	1	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	exon	5284761	5284950	.	-	.	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
Phchi.S4	AUGUSTUS	start_codon	5284948	5284950	.	-	0	transcript_id "Phchi.S4G087700.t2"; gene_id "Phchi.S4G087700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg297.t1 is derived from g10079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2108125	2109732	.	+	.	Phchi.S6G025600
Phchi.S6	AUGUSTUS	transcript	2108125	2109732	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	start_codon	2108125	2108127	.	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2108125	2108292	0.92	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2108125	2108292	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	intron	2108293	2108418	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2108419	2108525	1	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2108419	2108525	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	intron	2108526	2108614	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2108615	2108716	1	+	1	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2108615	2108716	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	intron	2108717	2108801	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2108802	2108997	0.99	+	1	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2108802	2108997	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	intron	2108998	2109102	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2109103	2109231	0.99	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2109103	2109231	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	intron	2109232	2109325	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2109326	2109520	1	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2109326	2109520	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	intron	2109521	2109609	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	CDS	2109610	2109732	1	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	exon	2109610	2109732	.	+	.	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
Phchi.S6	AUGUSTUS	stop_codon	2109733	2109735	.	+	0	transcript_id "Phchi.S6G025600.t1"; gene_id "Phchi.S6G025600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6461.t1 is derived from g3633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23125557	23127087	.	-	.	Phchi.S1G362000
Phchi.S1	AUGUSTUS	transcript	23125557	23127087	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	stop_codon	23125554	23125556	.	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23125557	23125632	1	-	1	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23125557	23125632	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23125633	23125723	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23125724	23125770	1	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23125724	23125770	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23125771	23125852	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23125853	23126074	1	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23125853	23126074	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23126075	23126184	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23126185	23126237	1	-	2	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23126185	23126237	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23126238	23126334	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23126335	23126500	1	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23126335	23126500	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23126501	23126580	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23126581	23126622	1	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23126581	23126622	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23126623	23126722	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23126723	23126756	0.99	-	1	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23126723	23126756	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	intron	23126757	23126920	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	CDS	23126921	23127087	0.77	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	exon	23126921	23127087	.	-	.	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
Phchi.S1	AUGUSTUS	start_codon	23127085	23127087	.	-	0	transcript_id "Phchi.S1G362000.t1"; gene_id "Phchi.S1G362000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6503.t1 is derived from g3675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23350066	23352658	.	+	.	Phchi.S1G366200
Phchi.S1	AUGUSTUS	transcript	23350066	23352658	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	start_codon	23350066	23350068	.	+	0	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	CDS	23350066	23350484	0.21	+	0	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	exon	23350066	23350484	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	intron	23350485	23350619	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	CDS	23350620	23350658	1	+	1	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	exon	23350620	23350658	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	intron	23350659	23350747	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	CDS	23350748	23351392	0.42	+	1	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	exon	23350748	23351392	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	intron	23351393	23351484	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	CDS	23351485	23352658	0.43	+	1	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	exon	23351485	23352658	.	+	.	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
Phchi.S1	AUGUSTUS	stop_codon	23352659	23352661	.	+	0	transcript_id "Phchi.S1G366200.t1"; gene_id "Phchi.S1G366200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6086.t1 is derived from g3257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20882241	20885359	.	+	.	Phchi.S1G324500
Phchi.S1	AUGUSTUS	transcript	20882241	20885359	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	start_codon	20882241	20882243	.	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882241	20882379	0.75	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882241	20882379	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882380	20882480	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882481	20882521	0.75	+	2	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882481	20882521	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882522	20882614	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882615	20882675	1	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882615	20882675	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882676	20882752	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882753	20882853	0.26	+	2	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882753	20882853	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882854	20882962	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882963	20883068	0.33	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882963	20883068	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883069	20883198	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883199	20883251	0.69	+	2	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883199	20883251	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883252	20883359	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883360	20883422	0.99	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883360	20883422	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883423	20883575	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883576	20883595	1	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883576	20883595	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883596	20883688	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883689	20883764	0.98	+	1	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883689	20883764	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883765	20883866	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883867	20884103	0.91	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883867	20884103	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884104	20884209	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884210	20884297	1	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884210	20884297	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884298	20884372	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884373	20884458	1	+	2	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884373	20884458	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884459	20884563	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884564	20884671	1	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884564	20884671	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884672	20884759	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884760	20884804	1	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884760	20884804	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884805	20884933	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884934	20885022	1	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884934	20885022	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20885023	20885129	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20885130	20885170	1	+	1	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20885130	20885170	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20885171	20885252	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20885253	20885359	0.97	+	2	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20885253	20885359	.	+	.	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	stop_codon	20885360	20885362	.	+	0	transcript_id "Phchi.S1G324500.t1"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	transcript	20882241	20885359	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	start_codon	20882241	20882243	.	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882241	20882273	0.9	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882241	20882273	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882274	20882412	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882413	20882521	0.96	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882413	20882521	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882522	20882752	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882753	20882853	0.28	+	2	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882753	20882853	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20882854	20882962	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20882963	20883068	0.38	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20882963	20883068	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883069	20883198	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883199	20883251	0.67	+	2	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883199	20883251	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883252	20883359	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883360	20883422	1	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883360	20883422	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883423	20883575	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883576	20883595	1	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883576	20883595	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883596	20883688	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883689	20883764	0.98	+	1	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883689	20883764	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20883765	20883866	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20883867	20884103	0.63	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20883867	20884103	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884104	20884209	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884210	20884297	0.86	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884210	20884297	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884298	20884372	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884373	20884458	1	+	2	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884373	20884458	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884459	20884563	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884564	20884671	1	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884564	20884671	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884672	20884759	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884760	20884804	1	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884760	20884804	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20884805	20884933	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20884934	20885022	1	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20884934	20885022	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20885023	20885129	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20885130	20885170	1	+	1	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20885130	20885170	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	intron	20885171	20885252	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	CDS	20885253	20885359	0.95	+	2	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	exon	20885253	20885359	.	+	.	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
Phchi.S1	AUGUSTUS	stop_codon	20885360	20885362	.	+	0	transcript_id "Phchi.S1G324500.t2"; gene_id "Phchi.S1G324500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10744.t1 is derived from g14794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1891828	1892322	.	-	.	Phchi.S4G032600
Phchi.S4	AUGUSTUS	transcript	1891828	1892322	.	-	.	transcript_id "Phchi.S4G032600.t1"; gene_id "Phchi.S4G032600"
Phchi.S4	AUGUSTUS	stop_codon	1891825	1891827	.	-	0	transcript_id "Phchi.S4G032600.t1"; gene_id "Phchi.S4G032600"
Phchi.S4	AUGUSTUS	CDS	1891828	1892322	0.58	-	0	transcript_id "Phchi.S4G032600.t1"; gene_id "Phchi.S4G032600"
Phchi.S4	AUGUSTUS	exon	1891828	1892322	.	-	.	transcript_id "Phchi.S4G032600.t1"; gene_id "Phchi.S4G032600"
Phchi.S4	AUGUSTUS	start_codon	1892320	1892322	.	-	0	transcript_id "Phchi.S4G032600.t1"; gene_id "Phchi.S4G032600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15825.t1 is derived from g14295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21608567	21609181	.	+	.	Phchi.S3G314400
Phchi.S3	AUGUSTUS	transcript	21608567	21609181	.	+	.	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	start_codon	21608567	21608569	.	+	0	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	CDS	21608567	21608811	0.62	+	0	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	exon	21608567	21608811	.	+	.	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	intron	21608812	21608926	.	+	.	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	CDS	21608927	21608987	0.99	+	1	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	exon	21608927	21608987	.	+	.	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	intron	21608988	21609055	.	+	.	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	CDS	21609056	21609181	1	+	0	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	exon	21609056	21609181	.	+	.	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
Phchi.S3	AUGUSTUS	stop_codon	21609182	21609184	.	+	0	transcript_id "Phchi.S3G314400.t1"; gene_id "Phchi.S3G314400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8926.t1 is derived from g6101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38704605	38707453	.	-	.	Phchi.S1G608500
Phchi.S1	AUGUSTUS	transcript	38704605	38707453	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	stop_codon	38704602	38704604	.	-	0	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38704605	38704616	1	-	0	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38704605	38704616	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38704617	38704783	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38704784	38704835	0.74	-	1	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38704784	38704835	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38704836	38704926	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38704927	38706412	0.34	-	2	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38704927	38706412	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38706413	38706534	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38706535	38706606	1	-	2	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38706535	38706606	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38706607	38706707	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38706708	38706772	0.99	-	1	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38706708	38706772	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38706773	38706876	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38706877	38707055	1	-	0	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38706877	38707055	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38707056	38707213	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38707214	38707258	0.59	-	0	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38707214	38707258	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	intron	38707259	38707381	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	CDS	38707382	38707453	0.32	-	0	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	exon	38707382	38707453	.	-	.	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
Phchi.S1	AUGUSTUS	start_codon	38707451	38707453	.	-	0	transcript_id "Phchi.S1G608500.t1"; gene_id "Phchi.S1G608500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1026.t1 is derived from g10809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7203221	7203637	.	+	.	Phchi.S6G098500
Phchi.S6	AUGUSTUS	transcript	7203221	7203637	.	+	.	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	start_codon	7203221	7203223	.	+	0	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	CDS	7203221	7203415	0.92	+	0	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	exon	7203221	7203415	.	+	.	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	intron	7203416	7203634	.	+	.	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	CDS	7203635	7203637	0.99	+	0	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	exon	7203635	7203637	.	+	.	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
Phchi.S6	AUGUSTUS	stop_codon	7203638	7203640	.	+	0	transcript_id "Phchi.S6G098500.t1"; gene_id "Phchi.S6G098500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5566.t1 is derived from g2736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17608634	17608897	.	-	.	Phchi.S1G272500
Phchi.S1	AUGUSTUS	transcript	17608634	17608897	.	-	.	transcript_id "Phchi.S1G272500.t1"; gene_id "Phchi.S1G272500"
Phchi.S1	AUGUSTUS	stop_codon	17608631	17608633	.	-	0	transcript_id "Phchi.S1G272500.t1"; gene_id "Phchi.S1G272500"
Phchi.S1	AUGUSTUS	CDS	17608634	17608897	0.98	-	0	transcript_id "Phchi.S1G272500.t1"; gene_id "Phchi.S1G272500"
Phchi.S1	AUGUSTUS	exon	17608634	17608897	.	-	.	transcript_id "Phchi.S1G272500.t1"; gene_id "Phchi.S1G272500"
Phchi.S1	AUGUSTUS	start_codon	17608895	17608897	.	-	0	transcript_id "Phchi.S1G272500.t1"; gene_id "Phchi.S1G272500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg990.t1 is derived from g10773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6907983	6909208	.	+	.	Phchi.S6G094900
Phchi.S6	AUGUSTUS	transcript	6907983	6909208	.	+	.	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	start_codon	6907983	6907985	.	+	0	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	CDS	6907983	6908378	1	+	0	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	exon	6907983	6908378	.	+	.	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	intron	6908379	6908466	.	+	.	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	CDS	6908467	6908891	1	+	0	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	exon	6908467	6908891	.	+	.	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	intron	6908892	6908976	.	+	.	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	CDS	6908977	6909208	0.99	+	1	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	exon	6908977	6909208	.	+	.	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
Phchi.S6	AUGUSTUS	stop_codon	6909209	6909211	.	+	0	transcript_id "Phchi.S6G094900.t1"; gene_id "Phchi.S6G094900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg492.t1 is derived from g10274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3422493	3423998	.	+	.	Phchi.S6G045100
Phchi.S6	AUGUSTUS	transcript	3422493	3423998	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	start_codon	3422493	3422495	.	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3422493	3422558	0.72	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3422493	3422558	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3422559	3422662	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3422663	3422758	0.95	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3422663	3422758	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3422759	3422850	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3422851	3422912	0.94	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3422851	3422912	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3422913	3423020	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3423021	3423154	0.9	+	1	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3423021	3423154	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3423155	3423240	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3423241	3423329	0.9	+	2	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3423241	3423329	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3423330	3423442	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3423443	3423488	1	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3423443	3423488	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3423489	3423577	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3423578	3423741	0.95	+	2	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3423578	3423741	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	intron	3423742	3423890	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	CDS	3423891	3423998	0.97	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	exon	3423891	3423998	.	+	.	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
Phchi.S6	AUGUSTUS	stop_codon	3423999	3424001	.	+	0	transcript_id "Phchi.S6G045100.t1"; gene_id "Phchi.S6G045100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4686.t1 is derived from g1856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12070046	12071275	.	-	.	Phchi.S1G184500
Phchi.S1	AUGUSTUS	transcript	12070046	12071275	.	-	.	transcript_id "Phchi.S1G184500.t1"; gene_id "Phchi.S1G184500"
Phchi.S1	AUGUSTUS	stop_codon	12070043	12070045	.	-	0	transcript_id "Phchi.S1G184500.t1"; gene_id "Phchi.S1G184500"
Phchi.S1	AUGUSTUS	CDS	12070046	12071275	0.63	-	0	transcript_id "Phchi.S1G184500.t1"; gene_id "Phchi.S1G184500"
Phchi.S1	AUGUSTUS	exon	12070046	12071275	.	-	.	transcript_id "Phchi.S1G184500.t1"; gene_id "Phchi.S1G184500"
Phchi.S1	AUGUSTUS	start_codon	12071273	12071275	.	-	0	transcript_id "Phchi.S1G184500.t1"; gene_id "Phchi.S1G184500"
# This transcript jg1098.t2 is derived from g10881.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1099.t1 is derived from g10882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7597240	7598596	.	+	.	Phchi.S6G105800
Phchi.S6	AUGUSTUS	transcript	7597240	7598596	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	start_codon	7597240	7597242	.	+	0	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	CDS	7597240	7597804	1	+	0	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	exon	7597240	7597804	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	intron	7597805	7597930	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	CDS	7597931	7598154	1	+	2	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	exon	7597931	7598154	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	intron	7598155	7598282	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	CDS	7598283	7598390	1	+	0	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	exon	7598283	7598390	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	intron	7598391	7598503	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	CDS	7598504	7598596	0.97	+	0	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	exon	7598504	7598596	.	+	.	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
Phchi.S6	AUGUSTUS	stop_codon	7598597	7598599	.	+	0	transcript_id "Phchi.S6G105800.t1"; gene_id "Phchi.S6G105800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12894.t1 is derived from g11359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3027093	3028103	.	+	.	Phchi.S3G021300
Phchi.S3	AUGUSTUS	transcript	3027093	3028103	.	+	.	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	start_codon	3027093	3027095	.	+	0	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	CDS	3027093	3027812	0.51	+	0	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	exon	3027093	3027812	.	+	.	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	intron	3027813	3027920	.	+	.	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	CDS	3027921	3028103	0.77	+	0	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	exon	3027921	3028103	.	+	.	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
Phchi.S3	AUGUSTUS	stop_codon	3028104	3028106	.	+	0	transcript_id "Phchi.S3G021300.t1"; gene_id "Phchi.S3G021300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12182.t1 is derived from g7858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6115374	6117567	.	-	.	Phchi.S2G026200
Phchi.S2	AUGUSTUS	transcript	6115374	6117567	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	stop_codon	6115371	6115373	.	-	0	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	CDS	6115374	6115594	1	-	2	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	exon	6115374	6115594	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	intron	6115595	6115694	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	CDS	6115695	6115950	0.73	-	0	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	exon	6115695	6115950	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	intron	6115951	6116085	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	CDS	6116086	6116349	0.62	-	0	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	exon	6116086	6116349	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	intron	6116350	6116503	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	CDS	6116504	6116628	0.82	-	2	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	exon	6116504	6116628	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	intron	6116629	6116779	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	CDS	6116780	6117001	0.68	-	2	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	exon	6116780	6117001	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	intron	6117002	6117140	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	CDS	6117141	6117567	0.99	-	0	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	exon	6117141	6117567	.	-	.	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
Phchi.S2	AUGUSTUS	start_codon	6117565	6117567	.	-	0	transcript_id "Phchi.S2G026200.t1"; gene_id "Phchi.S2G026200"
# This transcript jg7353.t2 is derived from g4525.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7354.t1 is derived from g4526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28719346	28721919	.	-	.	Phchi.S1G451300
Phchi.S1	AUGUSTUS	transcript	28719346	28721919	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	stop_codon	28719343	28719345	.	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28719346	28719654	0.73	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28719346	28719654	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28719655	28719749	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28719750	28720179	0.99	-	1	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28719750	28720179	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28720180	28720289	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28720290	28720387	1	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28720290	28720387	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28720388	28720500	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28720501	28720603	0.79	-	1	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28720501	28720603	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28720604	28720714	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28720715	28720800	1	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28720715	28720800	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28720801	28720938	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28720939	28721026	1	-	1	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28720939	28721026	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28721027	28721142	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28721143	28721256	1	-	1	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28721143	28721256	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28721257	28721376	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28721377	28721465	1	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28721377	28721465	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28721466	28721561	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28721562	28721671	1	-	2	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28721562	28721671	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	intron	28721672	28721888	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	CDS	28721889	28721919	1	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	exon	28721889	28721919	.	-	.	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
Phchi.S1	AUGUSTUS	start_codon	28721917	28721919	.	-	0	transcript_id "Phchi.S1G451300.t1"; gene_id "Phchi.S1G451300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12053.t1 is derived from g7728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1038999	1042880	.	+	.	Phchi.S2G013300
Phchi.S2	AUGUSTUS	transcript	1038999	1042880	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	start_codon	1038999	1039001	.	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1038999	1039464	1	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1038999	1039464	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1039465	1039626	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1039627	1040785	1	+	2	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1039627	1040785	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1040786	1040923	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1040924	1040981	1	+	1	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1040924	1040981	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1040982	1041104	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1041105	1041218	1	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1041105	1041218	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1041219	1041284	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1041285	1041342	1	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1041285	1041342	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1041343	1041422	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1041423	1041493	0.75	+	2	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1041423	1041493	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1041494	1041595	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1041596	1041651	0.75	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1041596	1041651	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1041652	1041768	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1041769	1041850	1	+	1	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1041769	1041850	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1041851	1041947	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1041948	1042004	1	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1041948	1042004	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1042005	1042099	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1042100	1042346	0.38	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1042100	1042346	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1042347	1042476	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1042477	1042621	0.71	+	2	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1042477	1042621	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	intron	1042622	1042879	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	CDS	1042880	1042880	1	+	1	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	exon	1042880	1042880	.	+	.	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
Phchi.S2	AUGUSTUS	stop_codon	1042881	1042883	.	+	0	transcript_id "Phchi.S2G013300.t1"; gene_id "Phchi.S2G013300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15471.t1 is derived from g13939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19347028	19347459	.	+	.	Phchi.S3G279000
Phchi.S3	AUGUSTUS	transcript	19347028	19347459	.	+	.	transcript_id "Phchi.S3G279000.t1"; gene_id "Phchi.S3G279000"
Phchi.S3	AUGUSTUS	start_codon	19347028	19347030	.	+	0	transcript_id "Phchi.S3G279000.t1"; gene_id "Phchi.S3G279000"
Phchi.S3	AUGUSTUS	CDS	19347028	19347459	0.85	+	0	transcript_id "Phchi.S3G279000.t1"; gene_id "Phchi.S3G279000"
Phchi.S3	AUGUSTUS	exon	19347028	19347459	.	+	.	transcript_id "Phchi.S3G279000.t1"; gene_id "Phchi.S3G279000"
Phchi.S3	AUGUSTUS	stop_codon	19347460	19347462	.	+	0	transcript_id "Phchi.S3G279000.t1"; gene_id "Phchi.S3G279000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4739.t1 is derived from g1909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12550259	12552069	.	-	.	Phchi.S1G189800
Phchi.S1	AUGUSTUS	transcript	12550259	12552069	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	stop_codon	12550256	12550258	.	-	0	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12550259	12550585	0.94	-	0	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12550259	12550585	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12550586	12550664	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12550665	12550975	0.94	-	2	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12550665	12550975	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12550976	12551065	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12551066	12551144	0.95	-	0	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12551066	12551144	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12551145	12551244	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12551245	12551324	0.99	-	2	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12551245	12551324	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12551325	12551433	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12551434	12551537	0.97	-	1	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12551434	12551537	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12551538	12551634	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12551635	12551760	0.33	-	1	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12551635	12551760	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12551761	12551845	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12551846	12551923	0.25	-	1	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12551846	12551923	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	intron	12551924	12552049	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	CDS	12552050	12552069	0.26	-	0	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	exon	12552050	12552069	.	-	.	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
Phchi.S1	AUGUSTUS	start_codon	12552067	12552069	.	-	0	transcript_id "Phchi.S1G189800.t1"; gene_id "Phchi.S1G189800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11063.t1 is derived from g15113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3943413	3944431	.	-	.	Phchi.S4G064500
Phchi.S4	AUGUSTUS	transcript	3943413	3944431	.	-	.	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	stop_codon	3943410	3943412	.	-	0	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	CDS	3943413	3944125	0.75	-	2	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	exon	3943413	3944125	.	-	.	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	intron	3944126	3944208	.	-	.	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	CDS	3944209	3944431	0.45	-	0	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	exon	3944209	3944431	.	-	.	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
Phchi.S4	AUGUSTUS	start_codon	3944429	3944431	.	-	0	transcript_id "Phchi.S4G064500.t1"; gene_id "Phchi.S4G064500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11376.t1 is derived from g15426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5963455	5965464	.	+	.	Phchi.S4G095800
Phchi.S4	AUGUSTUS	transcript	5963455	5965464	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	start_codon	5963455	5963457	.	+	0	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	CDS	5963455	5963551	1	+	0	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	exon	5963455	5963551	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	intron	5963552	5963699	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	CDS	5963700	5964069	1	+	2	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	exon	5963700	5964069	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	intron	5964070	5964193	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	CDS	5964194	5964986	0.84	+	1	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	exon	5964194	5964986	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	intron	5964987	5965065	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	CDS	5965066	5965311	0.75	+	0	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	exon	5965066	5965311	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	intron	5965312	5965425	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	CDS	5965426	5965464	0.94	+	0	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	exon	5965426	5965464	.	+	.	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
Phchi.S4	AUGUSTUS	stop_codon	5965465	5965467	.	+	0	transcript_id "Phchi.S4G095800.t1"; gene_id "Phchi.S4G095800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6599.t1 is derived from g3771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23931634	23932361	.	-	.	Phchi.S1G375800
Phchi.S1	AUGUSTUS	transcript	23931634	23932361	.	-	.	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	stop_codon	23931631	23931633	.	-	0	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	CDS	23931634	23931742	0.8	-	1	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	exon	23931634	23931742	.	-	.	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	intron	23931743	23931918	.	-	.	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	CDS	23931919	23932104	0.63	-	1	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	exon	23931919	23932104	.	-	.	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	intron	23932105	23932236	.	-	.	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	CDS	23932237	23932361	0.44	-	0	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	exon	23932237	23932361	.	-	.	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
Phchi.S1	AUGUSTUS	start_codon	23932359	23932361	.	-	0	transcript_id "Phchi.S1G375800.t1"; gene_id "Phchi.S1G375800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7898.t1 is derived from g5072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31798520	31800212	.	+	.	Phchi.S1G505700
Phchi.S1	AUGUSTUS	transcript	31798520	31800212	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	start_codon	31798520	31798522	.	+	0	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	CDS	31798520	31798798	0.45	+	0	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	exon	31798520	31798798	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	intron	31798799	31799040	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	CDS	31799041	31799636	0.46	+	0	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	exon	31799041	31799636	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	intron	31799637	31799764	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	CDS	31799765	31799840	1	+	1	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	exon	31799765	31799840	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	intron	31799841	31799933	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	CDS	31799934	31800212	0.99	+	0	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	exon	31799934	31800212	.	+	.	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
Phchi.S1	AUGUSTUS	stop_codon	31800213	31800215	.	+	0	transcript_id "Phchi.S1G505700.t1"; gene_id "Phchi.S1G505700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4379.t1 is derived from g1548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10150459	10152753	.	+	.	Phchi.S1G153800
Phchi.S1	AUGUSTUS	transcript	10150459	10152753	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	start_codon	10150459	10150461	.	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10150459	10150563	0.76	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10150459	10150563	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10150564	10150752	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10150753	10150929	0.51	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10150753	10150929	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10150930	10151031	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10151032	10151121	1	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10151032	10151121	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10151122	10151201	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10151202	10151279	0.96	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10151202	10151279	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10151280	10151361	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10151362	10151409	0.61	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10151362	10151409	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10151410	10151574	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10151575	10151913	0.27	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10151575	10151913	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10151914	10152052	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10152053	10152267	0.28	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10152053	10152267	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	intron	10152268	10152356	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	CDS	10152357	10152753	0.71	+	1	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	exon	10152357	10152753	.	+	.	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
Phchi.S1	AUGUSTUS	stop_codon	10152754	10152756	.	+	0	transcript_id "Phchi.S1G153800.t1"; gene_id "Phchi.S1G153800"
# This transcript jg11258.t2 is derived from g15308.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11259.t1 is derived from g15309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5056695	5058650	.	+	.	Phchi.S4G084100
Phchi.S4	AUGUSTUS	transcript	5056695	5058650	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	start_codon	5056695	5056697	.	+	0	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5056695	5056779	0.58	+	0	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5056695	5056779	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5056780	5056959	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5056960	5056987	0.53	+	2	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5056960	5056987	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5056988	5057083	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5057084	5057098	0.57	+	1	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5057084	5057098	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5057099	5057287	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5057288	5057341	0.89	+	1	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5057288	5057341	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5057342	5057509	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5057510	5057545	0.72	+	1	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5057510	5057545	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5057546	5057696	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5057697	5057778	0.57	+	1	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5057697	5057778	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5057779	5057882	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5057883	5057970	0.67	+	0	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5057883	5057970	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5057971	5058051	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5058052	5058120	0.98	+	2	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5058052	5058120	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5058121	5058213	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5058214	5058343	0.56	+	2	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5058214	5058343	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	intron	5058344	5058451	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	CDS	5058452	5058650	0.51	+	1	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	exon	5058452	5058650	.	+	.	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
Phchi.S4	AUGUSTUS	stop_codon	5058651	5058653	.	+	0	transcript_id "Phchi.S4G084100.t1"; gene_id "Phchi.S4G084100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2001.t1 is derived from g8921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4402587	4404453	.	+	.	Phchi.S5G061000
Phchi.S5	AUGUSTUS	transcript	4402587	4404453	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	start_codon	4402587	4402589	.	+	0	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	CDS	4402587	4402825	0.63	+	0	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	exon	4402587	4402825	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	intron	4402826	4402998	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	CDS	4402999	4403219	1	+	1	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	exon	4402999	4403219	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	intron	4403220	4403465	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	CDS	4403466	4403636	0.84	+	2	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	exon	4403466	4403636	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	intron	4403637	4403854	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	CDS	4403855	4403931	0.7	+	2	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	exon	4403855	4403931	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	intron	4403932	4404072	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	CDS	4404073	4404195	0.31	+	0	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	exon	4404073	4404195	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	intron	4404196	4404348	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	CDS	4404349	4404453	0.24	+	0	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	exon	4404349	4404453	.	+	.	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
Phchi.S5	AUGUSTUS	stop_codon	4404454	4404456	.	+	0	transcript_id "Phchi.S5G061000.t1"; gene_id "Phchi.S5G061000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11002.t1 is derived from g15052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3589573	3591251	.	+	.	Phchi.S4G058400
Phchi.S4	AUGUSTUS	transcript	3589573	3591251	.	+	.	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	start_codon	3589573	3589575	.	+	0	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	CDS	3589573	3589937	0.98	+	0	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	exon	3589573	3589937	.	+	.	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	intron	3589938	3590211	.	+	.	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	CDS	3590212	3590260	0.92	+	1	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	exon	3590212	3590260	.	+	.	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	intron	3590261	3590333	.	+	.	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	CDS	3590334	3591251	0.71	+	0	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	exon	3590334	3591251	.	+	.	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
Phchi.S4	AUGUSTUS	stop_codon	3591252	3591254	.	+	0	transcript_id "Phchi.S4G058400.t1"; gene_id "Phchi.S4G058400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4903.t1 is derived from g2073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13332019	13333312	.	-	.	Phchi.S1G206200
Phchi.S1	AUGUSTUS	transcript	13332019	13333312	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	stop_codon	13332016	13332018	.	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332019	13332087	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332019	13332087	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332088	13332180	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332181	13332291	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332181	13332291	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332292	13332369	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332370	13332463	1	-	1	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332370	13332463	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332464	13332533	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332534	13332598	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332534	13332598	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332599	13332681	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332682	13332714	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332682	13332714	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332715	13332795	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332796	13332825	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332796	13332825	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332826	13332904	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13332905	13332973	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13332905	13332973	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13332974	13333046	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13333047	13333153	1	-	2	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13333047	13333153	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	intron	13333154	13333239	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	CDS	13333240	13333312	1	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	exon	13333240	13333312	.	-	.	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
Phchi.S1	AUGUSTUS	start_codon	13333310	13333312	.	-	0	transcript_id "Phchi.S1G206200.t1"; gene_id "Phchi.S1G206200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2900.t1 is derived from g69.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	386017	393405	.	-	.	Phchi.S1G005900
Phchi.S1	AUGUSTUS	transcript	386017	393405	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	stop_codon	386014	386016	.	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	386017	386148	0.9	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	386017	386148	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	386149	386243	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	386244	386333	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	386244	386333	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	386334	386409	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	386410	386586	0.79	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	386410	386586	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	386587	386671	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	386672	386731	0.92	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	386672	386731	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	386732	386921	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	386922	386975	0.99	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	386922	386975	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	386976	387070	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	387071	387149	0.99	-	1	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	387071	387149	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	387150	387239	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	387240	387517	0.88	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	387240	387517	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	387518	387602	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	387603	387713	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	387603	387713	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	387714	387818	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	387819	387944	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	387819	387944	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	387945	388097	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	388098	388181	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	388098	388181	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	388182	388270	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	388271	388391	0.98	-	1	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	388271	388391	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	388392	388519	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	388520	388763	0.97	-	2	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	388520	388763	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	388764	388915	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	388916	389009	0.99	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	388916	389009	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	389010	389109	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	389110	389178	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	389110	389178	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	389179	389283	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	389284	389398	1	-	1	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	389284	389398	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	389399	389490	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	389491	389585	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	389491	389585	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	389586	389677	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	389678	389983	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	389678	389983	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	389984	390125	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	390126	390244	1	-	2	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	390126	390244	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	390245	390343	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	390344	390450	1	-	1	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	390344	390450	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	390451	390536	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	390537	390646	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	390537	390646	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	390647	390734	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	390735	390935	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	390735	390935	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	390936	391020	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	391021	391161	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	391021	391161	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	391162	391300	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	391301	391429	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	391301	391429	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	391430	391562	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	391563	391748	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	391563	391748	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	391749	391893	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	391894	391965	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	391894	391965	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	391966	392057	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	392058	392159	0.9	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	392058	392159	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	392160	392267	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	392268	392363	0.88	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	392268	392363	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	392364	392974	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	392975	393088	0.91	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	392975	393088	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	intron	393089	393240	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	CDS	393241	393405	1	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	exon	393241	393405	.	-	.	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
Phchi.S1	AUGUSTUS	start_codon	393403	393405	.	-	0	transcript_id "Phchi.S1G005900.t1"; gene_id "Phchi.S1G005900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4827.t1 is derived from g1997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13025563	13027149	.	+	.	Phchi.S1G198600
Phchi.S1	AUGUSTUS	transcript	13025563	13027149	.	+	.	transcript_id "Phchi.S1G198600.t1"; gene_id "Phchi.S1G198600"
Phchi.S1	AUGUSTUS	start_codon	13025563	13025565	.	+	0	transcript_id "Phchi.S1G198600.t1"; gene_id "Phchi.S1G198600"
Phchi.S1	AUGUSTUS	CDS	13025563	13027149	1	+	0	transcript_id "Phchi.S1G198600.t1"; gene_id "Phchi.S1G198600"
Phchi.S1	AUGUSTUS	exon	13025563	13027149	.	+	.	transcript_id "Phchi.S1G198600.t1"; gene_id "Phchi.S1G198600"
Phchi.S1	AUGUSTUS	stop_codon	13027150	13027152	.	+	0	transcript_id "Phchi.S1G198600.t1"; gene_id "Phchi.S1G198600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15422.t1 is derived from g13890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19012497	19012815	.	+	.	Phchi.S3G274100
Phchi.S3	AUGUSTUS	transcript	19012497	19012815	.	+	.	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	start_codon	19012497	19012499	.	+	0	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	CDS	19012497	19012685	0.22	+	0	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	exon	19012497	19012685	.	+	.	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	intron	19012686	19012773	.	+	.	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	CDS	19012774	19012815	0.9	+	0	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	exon	19012774	19012815	.	+	.	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
Phchi.S3	AUGUSTUS	stop_codon	19012816	19012818	.	+	0	transcript_id "Phchi.S3G274100.t1"; gene_id "Phchi.S3G274100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9010.t1 is derived from g6185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39132308	39133938	.	-	.	Phchi.S1G616900
Phchi.S1	AUGUSTUS	transcript	39132308	39133938	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	stop_codon	39132305	39132307	.	-	0	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	CDS	39132308	39132507	1	-	2	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	exon	39132308	39132507	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	intron	39132508	39132586	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	CDS	39132587	39132851	1	-	0	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	exon	39132587	39132851	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	intron	39132852	39132945	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	CDS	39132946	39133182	1	-	0	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	exon	39132946	39133182	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	intron	39133183	39133296	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	CDS	39133297	39133424	0.98	-	2	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	exon	39133297	39133424	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	intron	39133425	39133512	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	CDS	39133513	39133639	1	-	0	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	exon	39133513	39133639	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	intron	39133640	39133776	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	CDS	39133777	39133938	1	-	0	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	exon	39133777	39133938	.	-	.	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
Phchi.S1	AUGUSTUS	start_codon	39133936	39133938	.	-	0	transcript_id "Phchi.S1G616900.t1"; gene_id "Phchi.S1G616900"
# This transcript jg9699.t2 is derived from g6875.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9700.t1 is derived from g6876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43332631	43335698	.	+	.	Phchi.S1G685900
Phchi.S1	AUGUSTUS	transcript	43332631	43335698	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	start_codon	43332631	43332633	.	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43332631	43333019	0.9	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43332631	43333019	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	intron	43333020	43333145	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43333146	43333992	0.97	+	1	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43333146	43333992	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	intron	43333993	43334153	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43334154	43334396	1	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43334154	43334396	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	intron	43334397	43334541	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43334542	43334652	1	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43334542	43334652	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	intron	43334653	43334731	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43334732	43334788	1	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43334732	43334788	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	intron	43334789	43334894	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43334895	43335131	1	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43334895	43335131	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	intron	43335132	43335671	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	CDS	43335672	43335698	1	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	exon	43335672	43335698	.	+	.	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
Phchi.S1	AUGUSTUS	stop_codon	43335699	43335701	.	+	0	transcript_id "Phchi.S1G685900.t1"; gene_id "Phchi.S1G685900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5158.t1 is derived from g2328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15193279	15195493	.	-	.	Phchi.S1G231700
Phchi.S1	AUGUSTUS	transcript	15193279	15195493	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	stop_codon	15193276	15193278	.	-	0	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	CDS	15193279	15193350	0.31	-	0	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	exon	15193279	15193350	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	intron	15193351	15193453	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	CDS	15193454	15193677	0.15	-	2	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	exon	15193454	15193677	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	intron	15193678	15193805	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	CDS	15193806	15194832	0.15	-	0	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	exon	15193806	15194832	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	intron	15194833	15194954	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	CDS	15194955	15195226	0.59	-	2	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	exon	15194955	15195226	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	intron	15195227	15195312	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	CDS	15195313	15195493	0.71	-	0	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	exon	15195313	15195493	.	-	.	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
Phchi.S1	AUGUSTUS	start_codon	15195491	15195493	.	-	0	transcript_id "Phchi.S1G231700.t1"; gene_id "Phchi.S1G231700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1964.t1 is derived from g8884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4062595	4065957	.	+	.	Phchi.S5G057300
Phchi.S5	AUGUSTUS	transcript	4062595	4065957	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	start_codon	4062595	4062597	.	+	0	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	CDS	4062595	4062724	0.11	+	0	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	exon	4062595	4062724	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	intron	4062725	4063143	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	CDS	4063144	4063234	0.01	+	2	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	exon	4063144	4063234	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	intron	4063235	4063434	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	CDS	4063435	4065618	0.81	+	1	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	exon	4063435	4065618	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	intron	4065619	4065956	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	CDS	4065957	4065957	0.39	+	1	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	exon	4065957	4065957	.	+	.	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
Phchi.S5	AUGUSTUS	stop_codon	4065958	4065960	.	+	0	transcript_id "Phchi.S5G057300.t1"; gene_id "Phchi.S5G057300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7102.t1 is derived from g4274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26916256	26920364	.	-	.	Phchi.S1G426100
Phchi.S1	AUGUSTUS	transcript	26916256	26920364	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	stop_codon	26916253	26916255	.	-	0	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26916256	26916412	0.53	-	1	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26916256	26916412	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26916413	26916831	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26916832	26916995	1	-	0	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26916832	26916995	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26916996	26917128	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26917129	26917312	1	-	1	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26917129	26917312	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26917313	26917440	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26917441	26917531	1	-	2	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26917441	26917531	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26917532	26917630	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26917631	26917687	1	-	2	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26917631	26917687	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26917688	26917821	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26917822	26917968	1	-	2	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26917822	26917968	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26917969	26918095	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26918096	26918115	1	-	1	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26918096	26918115	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26918116	26918362	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26918363	26918508	1	-	0	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26918363	26918508	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26918509	26918686	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26918687	26918837	1	-	1	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26918687	26918837	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26918838	26918926	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26918927	26919156	1	-	0	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26918927	26919156	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	intron	26919157	26919314	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	CDS	26919315	26920364	0.85	-	0	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	exon	26919315	26920364	.	-	.	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
Phchi.S1	AUGUSTUS	start_codon	26920362	26920364	.	-	0	transcript_id "Phchi.S1G426100.t1"; gene_id "Phchi.S1G426100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg121.t1 is derived from g9903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	684378	689672	.	-	.	Phchi.S6G008000
Phchi.S6	AUGUSTUS	transcript	684378	689672	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	stop_codon	684375	684377	.	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	684378	684674	1	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	684378	684674	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	684675	684788	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	684789	684932	1	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	684789	684932	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	684933	685045	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	685046	685201	0.91	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	685046	685201	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	685202	685325	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	685326	685367	0.78	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	685326	685367	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	685368	685420	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	685421	685495	0.98	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	685421	685495	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	685496	685586	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	685587	685706	1	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	685587	685706	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	685707	685798	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	685799	686155	1	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	685799	686155	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	686156	686234	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	686235	687971	0.99	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	686235	687971	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	687972	688093	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	688094	688219	1	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	688094	688219	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	688220	688353	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	688354	688581	0.99	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	688354	688581	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	688582	688769	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	688770	688929	1	-	1	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	688770	688929	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	688930	689048	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	689049	689098	1	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	689049	689098	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	intron	689099	689210	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	CDS	689211	689672	0.97	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	exon	689211	689672	.	-	.	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
Phchi.S6	AUGUSTUS	start_codon	689670	689672	.	-	0	transcript_id "Phchi.S6G008000.t1"; gene_id "Phchi.S6G008000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12032.t1 is derived from g7707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	708734	709671	.	-	.	Phchi.S2G011200
Phchi.S2	AUGUSTUS	transcript	708734	709671	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	stop_codon	708731	708733	.	-	0	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	CDS	708734	708844	1	-	0	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	exon	708734	708844	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	intron	708845	709128	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	CDS	709129	709263	1	-	0	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	exon	709129	709263	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	intron	709264	709416	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	CDS	709417	709497	1	-	0	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	exon	709417	709497	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	intron	709498	709668	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	CDS	709669	709671	0.99	-	0	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	exon	709669	709671	.	-	.	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
Phchi.S2	AUGUSTUS	start_codon	709669	709671	.	-	0	transcript_id "Phchi.S2G011200.t1"; gene_id "Phchi.S2G011200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4753.t1 is derived from g1923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12644940	12645167	.	-	.	Phchi.S1G191200
Phchi.S1	AUGUSTUS	transcript	12644940	12645167	.	-	.	transcript_id "Phchi.S1G191200.t1"; gene_id "Phchi.S1G191200"
Phchi.S1	AUGUSTUS	stop_codon	12644937	12644939	.	-	0	transcript_id "Phchi.S1G191200.t1"; gene_id "Phchi.S1G191200"
Phchi.S1	AUGUSTUS	CDS	12644940	12645167	0.67	-	0	transcript_id "Phchi.S1G191200.t1"; gene_id "Phchi.S1G191200"
Phchi.S1	AUGUSTUS	exon	12644940	12645167	.	-	.	transcript_id "Phchi.S1G191200.t1"; gene_id "Phchi.S1G191200"
Phchi.S1	AUGUSTUS	start_codon	12645165	12645167	.	-	0	transcript_id "Phchi.S1G191200.t1"; gene_id "Phchi.S1G191200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg111.t1 is derived from g9893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	596046	598192	.	-	.	Phchi.S6G007000
Phchi.S6	AUGUSTUS	transcript	596046	598192	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	stop_codon	596043	596045	.	-	0	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	CDS	596046	596072	0.55	-	0	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	exon	596046	596072	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	intron	596073	596172	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	CDS	596173	596990	0.57	-	2	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	exon	596173	596990	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	intron	596991	597232	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	CDS	597233	597452	1	-	0	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	exon	597233	597452	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	intron	597453	597573	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	CDS	597574	597821	1	-	2	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	exon	597574	597821	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	intron	597822	598016	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	CDS	598017	598050	0.99	-	0	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	exon	598017	598050	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	intron	598051	598120	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	CDS	598121	598192	0.45	-	0	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	exon	598121	598192	.	-	.	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
Phchi.S6	AUGUSTUS	start_codon	598190	598192	.	-	0	transcript_id "Phchi.S6G007000.t1"; gene_id "Phchi.S6G007000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2042.t1 is derived from g8962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4568756	4570782	.	-	.	Phchi.S5G065100
Phchi.S5	AUGUSTUS	transcript	4568756	4570782	.	-	.	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	stop_codon	4568753	4568755	.	-	0	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	CDS	4568756	4568884	0.79	-	0	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	exon	4568756	4568884	.	-	.	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	intron	4568885	4568996	.	-	.	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	CDS	4568997	4569052	0.83	-	2	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	exon	4568997	4569052	.	-	.	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	intron	4569053	4569275	.	-	.	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	CDS	4569276	4570782	0.46	-	0	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	exon	4569276	4570782	.	-	.	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
Phchi.S5	AUGUSTUS	start_codon	4570780	4570782	.	-	0	transcript_id "Phchi.S5G065100.t1"; gene_id "Phchi.S5G065100"
# This transcript jg15558.t2 is derived from g14027.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15559.t1 is derived from g14028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19917244	19917902	.	-	.	Phchi.S3G287800
Phchi.S3	AUGUSTUS	transcript	19917244	19917902	.	-	.	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	stop_codon	19917241	19917243	.	-	0	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	CDS	19917244	19917465	0.37	-	0	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	exon	19917244	19917465	.	-	.	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	intron	19917466	19917635	.	-	.	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	CDS	19917636	19917902	0.58	-	0	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	exon	19917636	19917902	.	-	.	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
Phchi.S3	AUGUSTUS	start_codon	19917900	19917902	.	-	0	transcript_id "Phchi.S3G287800.t1"; gene_id "Phchi.S3G287800"
# This transcript jg10860.t2 is derived from g14910.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10860.t3 is derived from g14910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10860.t4 is derived from g14910.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10861.t1 is derived from g14911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2598809	2601095	.	+	.	Phchi.S4G044300
Phchi.S4	AUGUSTUS	transcript	2598809	2601095	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	start_codon	2598809	2598811	.	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2598809	2598958	1	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2598809	2598958	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2598959	2599048	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2599049	2599128	1	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2599049	2599128	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2599129	2599242	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2599243	2599367	1	+	1	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2599243	2599367	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2599368	2599468	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2599469	2599584	1	+	2	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2599469	2599584	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2599585	2599699	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2599700	2599906	0.9	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2599700	2599906	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2599907	2600017	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2600018	2600092	0.98	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2600018	2600092	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2600093	2600265	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2600266	2600366	1	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2600266	2600366	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2600367	2600503	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2600504	2600556	1	+	1	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2600504	2600556	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2600557	2600679	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2600680	2600775	0.62	+	2	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2600680	2600775	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	intron	2600776	2600976	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	CDS	2600977	2601095	1	+	2	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	exon	2600977	2601095	.	+	.	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
Phchi.S4	AUGUSTUS	stop_codon	2601096	2601098	.	+	0	transcript_id "Phchi.S4G044300.t1"; gene_id "Phchi.S4G044300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14493.t1 is derived from g12961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13132523	13134171	.	+	.	Phchi.S3G181200
Phchi.S3	AUGUSTUS	transcript	13132523	13134171	.	+	.	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	start_codon	13132523	13132525	.	+	0	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	CDS	13132523	13132576	0.8	+	0	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	exon	13132523	13132576	.	+	.	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	intron	13132577	13132689	.	+	.	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	CDS	13132690	13134171	0.61	+	0	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	exon	13132690	13134171	.	+	.	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
Phchi.S3	AUGUSTUS	stop_codon	13134172	13134174	.	+	0	transcript_id "Phchi.S3G181200.t1"; gene_id "Phchi.S3G181200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10559.t1 is derived from g14609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	980022	980773	.	-	.	Phchi.S4G014100
Phchi.S4	AUGUSTUS	transcript	980022	980773	.	-	.	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	stop_codon	980019	980021	.	-	0	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	CDS	980022	980198	0.98	-	0	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	exon	980022	980198	.	-	.	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	intron	980199	980310	.	-	.	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	CDS	980311	980424	0.7	-	0	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	exon	980311	980424	.	-	.	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	intron	980425	980566	.	-	.	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	CDS	980567	980773	0.44	-	0	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	exon	980567	980773	.	-	.	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
Phchi.S4	AUGUSTUS	start_codon	980771	980773	.	-	0	transcript_id "Phchi.S4G014100.t1"; gene_id "Phchi.S4G014100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10120.t1 is derived from g7296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45830836	45831681	.	-	.	Phchi.S1G727900
Phchi.S1	AUGUSTUS	transcript	45830836	45831681	.	-	.	transcript_id "Phchi.S1G727900.t1"; gene_id "Phchi.S1G727900"
Phchi.S1	AUGUSTUS	stop_codon	45830833	45830835	.	-	0	transcript_id "Phchi.S1G727900.t1"; gene_id "Phchi.S1G727900"
Phchi.S1	AUGUSTUS	CDS	45830836	45831681	0.92	-	0	transcript_id "Phchi.S1G727900.t1"; gene_id "Phchi.S1G727900"
Phchi.S1	AUGUSTUS	exon	45830836	45831681	.	-	.	transcript_id "Phchi.S1G727900.t1"; gene_id "Phchi.S1G727900"
Phchi.S1	AUGUSTUS	start_codon	45831679	45831681	.	-	0	transcript_id "Phchi.S1G727900.t1"; gene_id "Phchi.S1G727900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2888.t1 is derived from g57.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	306279	308240	.	+	.	Phchi.S1G004700
Phchi.S1	AUGUSTUS	transcript	306279	308240	.	+	.	transcript_id "Phchi.S1G004700.t1"; gene_id "Phchi.S1G004700"
Phchi.S1	AUGUSTUS	start_codon	306279	306281	.	+	0	transcript_id "Phchi.S1G004700.t1"; gene_id "Phchi.S1G004700"
Phchi.S1	AUGUSTUS	CDS	306279	308240	1	+	0	transcript_id "Phchi.S1G004700.t1"; gene_id "Phchi.S1G004700"
Phchi.S1	AUGUSTUS	exon	306279	308240	.	+	.	transcript_id "Phchi.S1G004700.t1"; gene_id "Phchi.S1G004700"
Phchi.S1	AUGUSTUS	stop_codon	308241	308243	.	+	0	transcript_id "Phchi.S1G004700.t1"; gene_id "Phchi.S1G004700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15328.t1 is derived from g13796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18402812	18404280	.	+	.	Phchi.S3G264700
Phchi.S3	AUGUSTUS	transcript	18402812	18404280	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	start_codon	18402812	18402814	.	+	0	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18402812	18402835	0.99	+	0	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18402812	18402835	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	intron	18402836	18402955	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18402956	18403021	0.86	+	0	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18402956	18403021	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	intron	18403022	18403124	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18403125	18403216	1	+	0	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18403125	18403216	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	intron	18403217	18403298	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18403299	18403399	1	+	1	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18403299	18403399	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	intron	18403400	18403537	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18403538	18403640	1	+	2	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18403538	18403640	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	intron	18403641	18403817	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18403818	18403909	1	+	1	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18403818	18403909	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	intron	18403910	18403996	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	CDS	18403997	18404280	1	+	2	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	exon	18403997	18404280	.	+	.	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
Phchi.S3	AUGUSTUS	stop_codon	18404281	18404283	.	+	0	transcript_id "Phchi.S3G264700.t1"; gene_id "Phchi.S3G264700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10820.t1 is derived from g14870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2276876	2279998	.	+	.	Phchi.S4G040200
Phchi.S4	AUGUSTUS	transcript	2276876	2279998	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	start_codon	2276876	2276878	.	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2276876	2277279	0.96	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2276876	2277279	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2277280	2277370	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2277371	2277644	1	+	1	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2277371	2277644	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2277645	2277743	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2277744	2277892	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2277744	2277892	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2277893	2277988	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2277989	2278442	1	+	1	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2277989	2278442	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2278443	2278569	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2278570	2278640	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2278570	2278640	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2278641	2278808	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2278809	2278890	1	+	1	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2278809	2278890	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2278891	2279026	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2279027	2279113	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2279027	2279113	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2279114	2279206	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2279207	2279290	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2279207	2279290	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2279291	2279368	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2279369	2279500	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2279369	2279500	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2279501	2279577	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2279578	2279700	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2279578	2279700	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	intron	2279701	2279779	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	CDS	2279780	2279998	1	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	exon	2279780	2279998	.	+	.	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
Phchi.S4	AUGUSTUS	stop_codon	2279999	2280001	.	+	0	transcript_id "Phchi.S4G040200.t1"; gene_id "Phchi.S4G040200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7639.t1 is derived from g4813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30363239	30363511	.	+	.	Phchi.S1G479800
Phchi.S1	AUGUSTUS	transcript	30363239	30363511	.	+	.	transcript_id "Phchi.S1G479800.t1"; gene_id "Phchi.S1G479800"
Phchi.S1	AUGUSTUS	start_codon	30363239	30363241	.	+	0	transcript_id "Phchi.S1G479800.t1"; gene_id "Phchi.S1G479800"
Phchi.S1	AUGUSTUS	CDS	30363239	30363511	0.7	+	0	transcript_id "Phchi.S1G479800.t1"; gene_id "Phchi.S1G479800"
Phchi.S1	AUGUSTUS	exon	30363239	30363511	.	+	.	transcript_id "Phchi.S1G479800.t1"; gene_id "Phchi.S1G479800"
Phchi.S1	AUGUSTUS	stop_codon	30363512	30363514	.	+	0	transcript_id "Phchi.S1G479800.t1"; gene_id "Phchi.S1G479800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15366.t1 is derived from g13834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18625782	18626537	.	+	.	Phchi.S3G268500
Phchi.S3	AUGUSTUS	transcript	18625782	18626537	.	+	.	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	start_codon	18625782	18625784	.	+	0	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	CDS	18625782	18625977	0.96	+	0	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	exon	18625782	18625977	.	+	.	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	intron	18625978	18626166	.	+	.	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	CDS	18626167	18626537	1	+	2	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	exon	18626167	18626537	.	+	.	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
Phchi.S3	AUGUSTUS	stop_codon	18626538	18626540	.	+	0	transcript_id "Phchi.S3G268500.t1"; gene_id "Phchi.S3G268500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7936.t1 is derived from g5110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31998738	32002714	.	-	.	Phchi.S1G509500
Phchi.S1	AUGUSTUS	transcript	31998738	32002714	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	stop_codon	31998735	31998737	.	-	0	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	CDS	31998738	31998851	0.99	-	0	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	exon	31998738	31998851	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	intron	31998852	31998951	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	CDS	31998952	31999514	0.99	-	2	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	exon	31998952	31999514	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	intron	31999515	31999616	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	CDS	31999617	31999789	0.25	-	1	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	exon	31999617	31999789	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	intron	31999790	31999950	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	CDS	31999951	32000155	0.29	-	2	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	exon	31999951	32000155	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	intron	32000156	32000308	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	CDS	32000309	32000956	0.61	-	2	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	exon	32000309	32000956	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	intron	32000957	32001042	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	CDS	32001043	32002714	0.6	-	0	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	exon	32001043	32002714	.	-	.	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
Phchi.S1	AUGUSTUS	start_codon	32002712	32002714	.	-	0	transcript_id "Phchi.S1G509500.t1"; gene_id "Phchi.S1G509500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13850.t1 is derived from g12317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9236591	9238050	.	+	.	Phchi.S3G116900
Phchi.S3	AUGUSTUS	transcript	9236591	9238050	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	start_codon	9236591	9236593	.	+	0	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	CDS	9236591	9236775	1	+	0	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	exon	9236591	9236775	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	intron	9236776	9236886	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	CDS	9236887	9237004	1	+	1	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	exon	9236887	9237004	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	intron	9237005	9237095	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	CDS	9237096	9237210	1	+	0	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	exon	9237096	9237210	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	intron	9237211	9237341	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	CDS	9237342	9237517	1	+	2	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	exon	9237342	9237517	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	intron	9237518	9237610	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	CDS	9237611	9237706	1	+	0	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	exon	9237611	9237706	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	intron	9237707	9237795	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	CDS	9237796	9238050	0.99	+	0	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	exon	9237796	9238050	.	+	.	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
Phchi.S3	AUGUSTUS	stop_codon	9238051	9238053	.	+	0	transcript_id "Phchi.S3G116900.t1"; gene_id "Phchi.S3G116900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12936.t1 is derived from g11401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3241255	3241585	.	-	.	Phchi.S3G025500
Phchi.S3	AUGUSTUS	transcript	3241255	3241585	.	-	.	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	stop_codon	3241252	3241254	.	-	0	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	CDS	3241255	3241418	0.72	-	2	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	exon	3241255	3241418	.	-	.	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	intron	3241419	3241512	.	-	.	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	CDS	3241513	3241585	0.67	-	0	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	exon	3241513	3241585	.	-	.	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
Phchi.S3	AUGUSTUS	start_codon	3241583	3241585	.	-	0	transcript_id "Phchi.S3G025500.t1"; gene_id "Phchi.S3G025500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11684.t1 is derived from g15735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7653598	7656035	.	+	.	Phchi.S4G126600
Phchi.S4	AUGUSTUS	transcript	7653598	7656035	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	start_codon	7653598	7653600	.	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7653598	7653680	0.52	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7653598	7653680	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7653681	7653785	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7653786	7653852	0.62	+	1	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7653786	7653852	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7653853	7654044	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7654045	7654118	1	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7654045	7654118	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7654119	7654216	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7654217	7654301	1	+	1	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7654217	7654301	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7654302	7654419	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7654420	7654475	0.98	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7654420	7654475	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7654476	7654589	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7654590	7654644	0.98	+	1	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7654590	7654644	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7654645	7654765	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7654766	7654813	1	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7654766	7654813	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7654814	7654991	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7654992	7655075	1	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7654992	7655075	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7655076	7655168	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7655169	7655285	1	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7655169	7655285	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7655286	7655379	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7655380	7655463	1	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7655380	7655463	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7655464	7655553	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7655554	7655597	0.72	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7655554	7655597	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7655598	7655833	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7655834	7655884	0.73	+	1	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7655834	7655884	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	intron	7655885	7655983	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	CDS	7655984	7656035	0.91	+	1	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	exon	7655984	7656035	.	+	.	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
Phchi.S4	AUGUSTUS	stop_codon	7656036	7656038	.	+	0	transcript_id "Phchi.S4G126600.t1"; gene_id "Phchi.S4G126600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10105.t1 is derived from g7281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45758668	45758990	.	+	.	Phchi.S1G726400
Phchi.S1	AUGUSTUS	transcript	45758668	45758990	.	+	.	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	start_codon	45758668	45758670	.	+	0	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	CDS	45758668	45758817	0.77	+	0	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	exon	45758668	45758817	.	+	.	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	intron	45758818	45758891	.	+	.	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	CDS	45758892	45758990	1	+	0	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	exon	45758892	45758990	.	+	.	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
Phchi.S1	AUGUSTUS	stop_codon	45758991	45758993	.	+	0	transcript_id "Phchi.S1G726400.t1"; gene_id "Phchi.S1G726400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13990.t1 is derived from g12457.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10134706	10136891	.	+	.	Phchi.S3G130900
Phchi.S3	AUGUSTUS	transcript	10134706	10136891	.	+	.	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	start_codon	10134706	10134708	.	+	0	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	CDS	10134706	10135128	0.4	+	0	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	exon	10134706	10135128	.	+	.	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	intron	10135129	10135262	.	+	.	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	CDS	10135263	10136891	0.47	+	0	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	exon	10135263	10136891	.	+	.	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	stop_codon	10136892	10136894	.	+	0	transcript_id "Phchi.S3G130900.t1"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	transcript	10135266	10136891	.	+	.	transcript_id "Phchi.S3G130900.t2"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	start_codon	10135266	10135268	.	+	0	transcript_id "Phchi.S3G130900.t2"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	CDS	10135266	10136891	0.79	+	0	transcript_id "Phchi.S3G130900.t2"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	exon	10135266	10136891	.	+	.	transcript_id "Phchi.S3G130900.t2"; gene_id "Phchi.S3G130900"
Phchi.S3	AUGUSTUS	stop_codon	10136892	10136894	.	+	0	transcript_id "Phchi.S3G130900.t2"; gene_id "Phchi.S3G130900"
# This transcript jg14215.t2 is derived from g12682.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14215.t3 is derived from g12682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14216.t1 is derived from g12683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11552468	11553335	.	+	.	Phchi.S3G153500
Phchi.S3	AUGUSTUS	transcript	11552468	11553335	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	start_codon	11552468	11552470	.	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	CDS	11552468	11552542	1	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	exon	11552468	11552542	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	intron	11552543	11552624	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	CDS	11552625	11552687	1	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	exon	11552625	11552687	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	intron	11552688	11552855	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	CDS	11552856	11552903	1	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	exon	11552856	11552903	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	intron	11552904	11553007	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	CDS	11553008	11553067	1	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	exon	11553008	11553067	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	intron	11553068	11553139	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	CDS	11553140	11553206	1	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	exon	11553140	11553206	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	intron	11553207	11553300	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	CDS	11553301	11553335	0.97	+	2	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	exon	11553301	11553335	.	+	.	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
Phchi.S3	AUGUSTUS	stop_codon	11553336	11553338	.	+	0	transcript_id "Phchi.S3G153500.t1"; gene_id "Phchi.S3G153500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1973.t1 is derived from g8893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4089336	4090109	.	-	.	Phchi.S5G058200
Phchi.S5	AUGUSTUS	transcript	4089336	4090109	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	stop_codon	4089333	4089335	.	-	0	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	CDS	4089336	4089497	0.98	-	0	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	exon	4089336	4089497	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	intron	4089498	4089666	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	CDS	4089667	4089749	1	-	2	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	exon	4089667	4089749	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	intron	4089750	4089878	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	CDS	4089879	4089960	1	-	0	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	exon	4089879	4089960	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	intron	4089961	4090049	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	CDS	4090050	4090109	0.96	-	0	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	exon	4090050	4090109	.	-	.	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
Phchi.S5	AUGUSTUS	start_codon	4090107	4090109	.	-	0	transcript_id "Phchi.S5G058200.t1"; gene_id "Phchi.S5G058200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5418.t1 is derived from g2588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16791735	16793249	.	-	.	Phchi.S1G257700
Phchi.S1	AUGUSTUS	transcript	16791735	16793249	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	stop_codon	16791732	16791734	.	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16791735	16791785	1	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16791735	16791785	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16791786	16791882	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16791883	16791972	1	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16791883	16791972	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16791973	16792052	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16792053	16792138	0.97	-	2	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16792053	16792138	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16792139	16792244	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16792245	16792361	1	-	2	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16792245	16792361	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16792362	16792497	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16792498	16792534	0.98	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16792498	16792534	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16792535	16792899	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16792900	16792960	0.75	-	1	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16792900	16792960	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16792961	16793064	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16793065	16793111	1	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16793065	16793111	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	intron	16793112	16793186	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	CDS	16793187	16793249	0.5	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	exon	16793187	16793249	.	-	.	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
Phchi.S1	AUGUSTUS	start_codon	16793247	16793249	.	-	0	transcript_id "Phchi.S1G257700.t1"; gene_id "Phchi.S1G257700"
# This transcript jg11302.t2 is derived from g15352.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11303.t1 is derived from g15353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5302388	5303193	.	+	.	Phchi.S4G088500
Phchi.S4	AUGUSTUS	transcript	5302388	5303193	.	+	.	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	start_codon	5302388	5302390	.	+	0	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	CDS	5302388	5302737	0.62	+	0	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	exon	5302388	5302737	.	+	.	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	intron	5302738	5302814	.	+	.	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	CDS	5302815	5303193	0.41	+	1	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	exon	5302815	5303193	.	+	.	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	stop_codon	5303194	5303196	.	+	0	transcript_id "Phchi.S4G088500.t1"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	transcript	5302576	5303193	.	+	.	transcript_id "Phchi.S4G088500.t2"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	start_codon	5302576	5302578	.	+	0	transcript_id "Phchi.S4G088500.t2"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	CDS	5302576	5303193	0.2	+	0	transcript_id "Phchi.S4G088500.t2"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	exon	5302576	5303193	.	+	.	transcript_id "Phchi.S4G088500.t2"; gene_id "Phchi.S4G088500"
Phchi.S4	AUGUSTUS	stop_codon	5303194	5303196	.	+	0	transcript_id "Phchi.S4G088500.t2"; gene_id "Phchi.S4G088500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3526.t1 is derived from g695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4229046	4233848	.	+	.	Phchi.S1G068500
Phchi.S1	AUGUSTUS	transcript	4229046	4233848	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	start_codon	4229046	4229048	.	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4229046	4229201	1	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4229046	4229201	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4229202	4229352	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4229353	4229786	0.98	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4229353	4229786	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4229787	4229877	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4229878	4230301	1	+	1	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4229878	4230301	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4230302	4230406	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4230407	4230742	0.99	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4230407	4230742	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4230743	4230831	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4230832	4231459	0.8	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4230832	4231459	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4231460	4231661	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4231662	4231827	0.78	+	2	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4231662	4231827	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4231828	4231935	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4231936	4232293	0.67	+	1	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4231936	4232293	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4232294	4232375	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4232376	4232486	1	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4232376	4232486	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4232487	4232635	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4232636	4233008	1	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4232636	4233008	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4233009	4233089	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4233090	4233306	1	+	2	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4233090	4233306	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4233307	4233398	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4233399	4233617	1	+	1	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4233399	4233617	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	intron	4233618	4233703	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	CDS	4233704	4233848	1	+	1	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	exon	4233704	4233848	.	+	.	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
Phchi.S1	AUGUSTUS	stop_codon	4233849	4233851	.	+	0	transcript_id "Phchi.S1G068500.t1"; gene_id "Phchi.S1G068500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1835.t1 is derived from g8755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3484981	3485958	.	+	.	Phchi.S5G044400
Phchi.S5	AUGUSTUS	transcript	3484981	3485958	.	+	.	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	start_codon	3484981	3484983	.	+	0	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	CDS	3484981	3485265	0.98	+	0	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	exon	3484981	3485265	.	+	.	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	intron	3485266	3485533	.	+	.	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	CDS	3485534	3485613	1	+	0	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	exon	3485534	3485613	.	+	.	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	intron	3485614	3485699	.	+	.	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	CDS	3485700	3485958	0.89	+	1	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	exon	3485700	3485958	.	+	.	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
Phchi.S5	AUGUSTUS	stop_codon	3485959	3485961	.	+	0	transcript_id "Phchi.S5G044400.t1"; gene_id "Phchi.S5G044400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11632.t1 is derived from g15683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7398388	7399902	.	-	.	Phchi.S4G121400
Phchi.S4	AUGUSTUS	transcript	7398388	7399902	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	stop_codon	7398385	7398387	.	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	CDS	7398388	7398451	1	-	1	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	exon	7398388	7398451	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	intron	7398452	7398549	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	CDS	7398550	7398614	1	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	exon	7398550	7398614	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	intron	7398615	7398754	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	CDS	7398755	7398856	1	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	exon	7398755	7398856	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	intron	7398857	7398934	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	CDS	7398935	7399141	1	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	exon	7398935	7399141	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	intron	7399142	7399252	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	CDS	7399253	7399573	0.94	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	exon	7399253	7399573	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	intron	7399574	7399683	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	CDS	7399684	7399902	0.56	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	exon	7399684	7399902	.	-	.	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
Phchi.S4	AUGUSTUS	start_codon	7399900	7399902	.	-	0	transcript_id "Phchi.S4G121400.t1"; gene_id "Phchi.S4G121400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8384.t1 is derived from g5559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35608300	35608712	.	+	.	Phchi.S1G554300
Phchi.S1	AUGUSTUS	transcript	35608300	35608712	.	+	.	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	start_codon	35608300	35608302	.	+	0	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	CDS	35608300	35608446	0.94	+	0	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	exon	35608300	35608446	.	+	.	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	intron	35608447	35608661	.	+	.	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	CDS	35608662	35608712	0.45	+	0	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	exon	35608662	35608712	.	+	.	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
Phchi.S1	AUGUSTUS	stop_codon	35608713	35608715	.	+	0	transcript_id "Phchi.S1G554300.t1"; gene_id "Phchi.S1G554300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6385.t1 is derived from g3557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22666665	22667965	.	+	.	Phchi.S1G354400
Phchi.S1	AUGUSTUS	transcript	22666665	22667965	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	start_codon	22666665	22666667	.	+	0	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	CDS	22666665	22666876	0.99	+	0	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	exon	22666665	22666876	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	intron	22666877	22667216	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	CDS	22667217	22667302	1	+	1	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	exon	22667217	22667302	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	intron	22667303	22667395	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	CDS	22667396	22667510	1	+	2	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	exon	22667396	22667510	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	intron	22667511	22667670	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	CDS	22667671	22667965	1	+	1	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	exon	22667671	22667965	.	+	.	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
Phchi.S1	AUGUSTUS	stop_codon	22667966	22667968	.	+	0	transcript_id "Phchi.S1G354400.t1"; gene_id "Phchi.S1G354400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8246.t1 is derived from g5421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34678734	34681022	.	-	.	Phchi.S1G540500
Phchi.S1	AUGUSTUS	transcript	34678734	34681022	.	-	.	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	stop_codon	34678731	34678733	.	-	0	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	CDS	34678734	34679567	0.26	-	0	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	exon	34678734	34679567	.	-	.	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	intron	34679568	34680041	.	-	.	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	CDS	34680042	34681022	0.2	-	0	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	exon	34680042	34681022	.	-	.	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
Phchi.S1	AUGUSTUS	start_codon	34681020	34681022	.	-	0	transcript_id "Phchi.S1G540500.t1"; gene_id "Phchi.S1G540500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg605.t1 is derived from g10387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4378942	4379617	.	-	.	Phchi.S6G056400
Phchi.S6	AUGUSTUS	transcript	4378942	4379617	.	-	.	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	stop_codon	4378939	4378941	.	-	0	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	CDS	4378942	4379100	0.93	-	0	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	exon	4378942	4379100	.	-	.	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	intron	4379101	4379188	.	-	.	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	CDS	4379189	4379311	0.66	-	0	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	exon	4379189	4379311	.	-	.	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	intron	4379312	4379554	.	-	.	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	CDS	4379555	4379617	0.12	-	0	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	exon	4379555	4379617	.	-	.	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
Phchi.S6	AUGUSTUS	start_codon	4379615	4379617	.	-	0	transcript_id "Phchi.S6G056400.t1"; gene_id "Phchi.S6G056400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4696.t1 is derived from g1866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12339070	12339375	.	-	.	Phchi.S1G185500
Phchi.S1	AUGUSTUS	transcript	12339070	12339375	.	-	.	transcript_id "Phchi.S1G185500.t1"; gene_id "Phchi.S1G185500"
Phchi.S1	AUGUSTUS	stop_codon	12339067	12339069	.	-	0	transcript_id "Phchi.S1G185500.t1"; gene_id "Phchi.S1G185500"
Phchi.S1	AUGUSTUS	CDS	12339070	12339375	0.39	-	0	transcript_id "Phchi.S1G185500.t1"; gene_id "Phchi.S1G185500"
Phchi.S1	AUGUSTUS	exon	12339070	12339375	.	-	.	transcript_id "Phchi.S1G185500.t1"; gene_id "Phchi.S1G185500"
Phchi.S1	AUGUSTUS	start_codon	12339373	12339375	.	-	0	transcript_id "Phchi.S1G185500.t1"; gene_id "Phchi.S1G185500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg547.t1 is derived from g10329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4007726	4009543	.	+	.	Phchi.S6G050600
Phchi.S6	AUGUSTUS	transcript	4007726	4009543	.	+	.	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	start_codon	4007726	4007728	.	+	0	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	CDS	4007726	4007991	0.88	+	0	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	exon	4007726	4007991	.	+	.	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	intron	4007992	4008102	.	+	.	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	CDS	4008103	4009543	0.18	+	1	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	exon	4008103	4009543	.	+	.	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
Phchi.S6	AUGUSTUS	stop_codon	4009544	4009546	.	+	0	transcript_id "Phchi.S6G050600.t1"; gene_id "Phchi.S6G050600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3023.t1 is derived from g192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1187013	1187431	.	-	.	Phchi.S1G018200
Phchi.S1	AUGUSTUS	transcript	1187013	1187431	.	-	.	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	stop_codon	1187010	1187012	.	-	0	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	CDS	1187013	1187039	0.68	-	0	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	exon	1187013	1187039	.	-	.	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	intron	1187040	1187134	.	-	.	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	CDS	1187135	1187140	0.68	-	0	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	exon	1187135	1187140	.	-	.	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	intron	1187141	1187227	.	-	.	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	CDS	1187228	1187431	0.61	-	0	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	exon	1187228	1187431	.	-	.	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
Phchi.S1	AUGUSTUS	start_codon	1187429	1187431	.	-	0	transcript_id "Phchi.S1G018200.t1"; gene_id "Phchi.S1G018200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14915.t1 is derived from g13383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15484051	15485035	.	+	.	Phchi.S3G223400
Phchi.S3	AUGUSTUS	transcript	15484051	15485035	.	+	.	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	start_codon	15484051	15484053	.	+	0	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	CDS	15484051	15484862	0.37	+	0	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	exon	15484051	15484862	.	+	.	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	intron	15484863	15484956	.	+	.	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	CDS	15484957	15485035	0.38	+	1	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	exon	15484957	15485035	.	+	.	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
Phchi.S3	AUGUSTUS	stop_codon	15485036	15485038	.	+	0	transcript_id "Phchi.S3G223400.t1"; gene_id "Phchi.S3G223400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1490.t1 is derived from g8409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1168147	1168587	.	-	.	Phchi.S5G009900
Phchi.S5	AUGUSTUS	transcript	1168147	1168587	.	-	.	transcript_id "Phchi.S5G009900.t1"; gene_id "Phchi.S5G009900"
Phchi.S5	AUGUSTUS	stop_codon	1168144	1168146	.	-	0	transcript_id "Phchi.S5G009900.t1"; gene_id "Phchi.S5G009900"
Phchi.S5	AUGUSTUS	CDS	1168147	1168587	0.69	-	0	transcript_id "Phchi.S5G009900.t1"; gene_id "Phchi.S5G009900"
Phchi.S5	AUGUSTUS	exon	1168147	1168587	.	-	.	transcript_id "Phchi.S5G009900.t1"; gene_id "Phchi.S5G009900"
Phchi.S5	AUGUSTUS	start_codon	1168585	1168587	.	-	0	transcript_id "Phchi.S5G009900.t1"; gene_id "Phchi.S5G009900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4588.t1 is derived from g1758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11218232	11219794	.	+	.	Phchi.S1G174700
Phchi.S1	AUGUSTUS	transcript	11218232	11219794	.	+	.	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	start_codon	11218232	11218234	.	+	0	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	CDS	11218232	11218540	0.3	+	0	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	exon	11218232	11218540	.	+	.	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	intron	11218541	11218663	.	+	.	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	CDS	11218664	11219794	0.64	+	0	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	exon	11218664	11219794	.	+	.	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
Phchi.S1	AUGUSTUS	stop_codon	11219795	11219797	.	+	0	transcript_id "Phchi.S1G174700.t1"; gene_id "Phchi.S1G174700"
# This transcript jg1398.t2 is derived from g8317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1399.t1 is derived from g8318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	127946	132740	.	-	.	Phchi.S5G000800
Phchi.S5	AUGUSTUS	transcript	127946	132740	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	stop_codon	127943	127945	.	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	127946	128044	0.99	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	127946	128044	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	128045	128138	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	128139	128342	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	128139	128342	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	128343	128473	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	128474	128887	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	128474	128887	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	128888	129003	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	129004	129154	1	-	1	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	129004	129154	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	129155	129293	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	129294	129435	1	-	2	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	129294	129435	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	129436	129667	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	129668	129833	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	129668	129833	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	129834	129923	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	129924	130136	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	129924	130136	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	130137	130320	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	130321	130454	1	-	2	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	130321	130454	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	130455	130545	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	130546	130593	1	-	2	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	130546	130593	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	130594	130724	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	130725	130851	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	130725	130851	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	130852	130932	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	130933	131071	1	-	1	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	130933	131071	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	131072	131148	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	131149	131275	1	-	2	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	131149	131275	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	131276	131358	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	131359	131470	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	131359	131470	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	131471	131593	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	131594	131674	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	131594	131674	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	131675	131772	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	131773	131920	1	-	1	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	131773	131920	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	131921	132074	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	132075	132198	1	-	2	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	132075	132198	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	intron	132199	132673	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	CDS	132674	132740	1	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	exon	132674	132740	.	-	.	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
Phchi.S5	AUGUSTUS	start_codon	132738	132740	.	-	0	transcript_id "Phchi.S5G000800.t1"; gene_id "Phchi.S5G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12155.t1 is derived from g7831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5021976	5022371	.	+	.	Phchi.S2G023500
Phchi.S2	AUGUSTUS	transcript	5021976	5022371	.	+	.	transcript_id "Phchi.S2G023500.t1"; gene_id "Phchi.S2G023500"
Phchi.S2	AUGUSTUS	start_codon	5021976	5021978	.	+	0	transcript_id "Phchi.S2G023500.t1"; gene_id "Phchi.S2G023500"
Phchi.S2	AUGUSTUS	CDS	5021976	5022371	0.63	+	0	transcript_id "Phchi.S2G023500.t1"; gene_id "Phchi.S2G023500"
Phchi.S2	AUGUSTUS	exon	5021976	5022371	.	+	.	transcript_id "Phchi.S2G023500.t1"; gene_id "Phchi.S2G023500"
Phchi.S2	AUGUSTUS	stop_codon	5022372	5022374	.	+	0	transcript_id "Phchi.S2G023500.t1"; gene_id "Phchi.S2G023500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7827.t1 is derived from g5001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31385136	31388058	.	-	.	Phchi.S1G498600
Phchi.S1	AUGUSTUS	transcript	31385136	31388058	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	stop_codon	31385133	31385135	.	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385136	31385153	0.53	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385136	31385153	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385154	31385311	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385312	31385410	0.53	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385312	31385410	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385411	31385491	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385492	31385584	1	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385492	31385584	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385585	31385672	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385673	31385793	1	-	1	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385673	31385793	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385794	31385968	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385969	31386111	1	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385969	31386111	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386112	31386241	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31386242	31386326	1	-	1	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31386242	31386326	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386327	31386506	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31386507	31386718	0.99	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31386507	31386718	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386719	31386877	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31386878	31386999	0.91	-	2	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31386878	31386999	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387000	31387111	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31387112	31387240	0.45	-	2	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31387112	31387240	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387241	31387434	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31387435	31387554	1	-	2	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31387435	31387554	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387555	31387633	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31387634	31387784	1	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31387634	31387784	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387785	31388004	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31388005	31388058	0.93	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31388005	31388058	.	-	.	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	start_codon	31388056	31388058	.	-	0	transcript_id "Phchi.S1G498600.t1"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	transcript	31385136	31388058	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	stop_codon	31385133	31385135	.	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385136	31385153	0.54	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385136	31385153	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385154	31385311	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385312	31385410	0.54	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385312	31385410	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385411	31385491	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385492	31385584	1	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385492	31385584	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385585	31385672	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385673	31385793	1	-	1	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385673	31385793	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385794	31385868	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385869	31385874	0.87	-	1	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385869	31385874	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31385875	31385968	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31385969	31386111	1	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31385969	31386111	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386112	31386241	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31386242	31386326	1	-	1	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31386242	31386326	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386327	31386506	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31386507	31386723	0.93	-	2	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31386507	31386723	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386724	31386877	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31386878	31386904	0.8	-	2	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31386878	31386904	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31386905	31387111	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31387112	31387240	0.38	-	2	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31387112	31387240	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387241	31387434	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31387435	31387554	0.99	-	2	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31387435	31387554	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387555	31387633	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31387634	31387784	1	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31387634	31387784	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	intron	31387785	31388004	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	CDS	31388005	31388058	0.97	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	exon	31388005	31388058	.	-	.	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
Phchi.S1	AUGUSTUS	start_codon	31388056	31388058	.	-	0	transcript_id "Phchi.S1G498600.t2"; gene_id "Phchi.S1G498600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7345.t1 is derived from g4517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28633051	28633613	.	+	.	Phchi.S1G450400
Phchi.S1	AUGUSTUS	transcript	28633051	28633613	.	+	.	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	start_codon	28633051	28633053	.	+	0	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	CDS	28633051	28633237	0.94	+	0	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	exon	28633051	28633237	.	+	.	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	intron	28633238	28633335	.	+	.	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	CDS	28633336	28633613	0.99	+	2	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	exon	28633336	28633613	.	+	.	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
Phchi.S1	AUGUSTUS	stop_codon	28633614	28633616	.	+	0	transcript_id "Phchi.S1G450400.t1"; gene_id "Phchi.S1G450400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10262.t1 is derived from g7438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46730477	46732629	.	-	.	Phchi.S1G742100
Phchi.S1	AUGUSTUS	transcript	46730477	46732629	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	stop_codon	46730474	46730476	.	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46730477	46730556	0.26	-	2	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46730477	46730556	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46730557	46730696	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46730697	46730916	0.85	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46730697	46730916	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46730917	46731021	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46731022	46731162	0.93	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46731022	46731162	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46731163	46731251	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46731252	46731359	0.99	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46731252	46731359	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46731360	46731460	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46731461	46731569	0.95	-	1	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46731461	46731569	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46731570	46731656	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46731657	46731799	1	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46731657	46731799	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46731800	46731912	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46731913	46732011	0.99	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46731913	46732011	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46732012	46732114	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46732115	46732240	1	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46732115	46732240	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	intron	46732241	46732446	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	CDS	46732447	46732629	0.4	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	exon	46732447	46732629	.	-	.	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
Phchi.S1	AUGUSTUS	start_codon	46732627	46732629	.	-	0	transcript_id "Phchi.S1G742100.t1"; gene_id "Phchi.S1G742100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5764.t1 is derived from g2934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18844974	18845417	.	-	.	Phchi.S1G292300
Phchi.S1	AUGUSTUS	transcript	18844974	18845417	.	-	.	transcript_id "Phchi.S1G292300.t1"; gene_id "Phchi.S1G292300"
Phchi.S1	AUGUSTUS	stop_codon	18844971	18844973	.	-	0	transcript_id "Phchi.S1G292300.t1"; gene_id "Phchi.S1G292300"
Phchi.S1	AUGUSTUS	CDS	18844974	18845417	0.46	-	0	transcript_id "Phchi.S1G292300.t1"; gene_id "Phchi.S1G292300"
Phchi.S1	AUGUSTUS	exon	18844974	18845417	.	-	.	transcript_id "Phchi.S1G292300.t1"; gene_id "Phchi.S1G292300"
Phchi.S1	AUGUSTUS	start_codon	18845415	18845417	.	-	0	transcript_id "Phchi.S1G292300.t1"; gene_id "Phchi.S1G292300"
# This transcript jg8438.t2 is derived from g5613.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8439.t1 is derived from g5614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35943124	35943846	.	+	.	Phchi.S1G559800
Phchi.S1	AUGUSTUS	transcript	35943124	35943846	.	+	.	transcript_id "Phchi.S1G559800.t1"; gene_id "Phchi.S1G559800"
Phchi.S1	AUGUSTUS	start_codon	35943124	35943126	.	+	0	transcript_id "Phchi.S1G559800.t1"; gene_id "Phchi.S1G559800"
Phchi.S1	AUGUSTUS	CDS	35943124	35943846	0.64	+	0	transcript_id "Phchi.S1G559800.t1"; gene_id "Phchi.S1G559800"
Phchi.S1	AUGUSTUS	exon	35943124	35943846	.	+	.	transcript_id "Phchi.S1G559800.t1"; gene_id "Phchi.S1G559800"
Phchi.S1	AUGUSTUS	stop_codon	35943847	35943849	.	+	0	transcript_id "Phchi.S1G559800.t1"; gene_id "Phchi.S1G559800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10176.t1 is derived from g7352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46138589	46142260	.	+	.	Phchi.S1G733500
Phchi.S1	AUGUSTUS	transcript	46138589	46142260	.	+	.	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	start_codon	46138589	46138591	.	+	0	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	CDS	46138589	46138593	0.04	+	0	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	exon	46138589	46138593	.	+	.	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	intron	46138594	46142118	.	+	.	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	CDS	46142119	46142260	0.01	+	1	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	exon	46142119	46142260	.	+	.	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
Phchi.S1	AUGUSTUS	stop_codon	46142261	46142263	.	+	0	transcript_id "Phchi.S1G733500.t1"; gene_id "Phchi.S1G733500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5250.t1 is derived from g2420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15858029	15859321	.	-	.	Phchi.S1G240900
Phchi.S1	AUGUSTUS	transcript	15858029	15859321	.	-	.	transcript_id "Phchi.S1G240900.t1"; gene_id "Phchi.S1G240900"
Phchi.S1	AUGUSTUS	stop_codon	15858026	15858028	.	-	0	transcript_id "Phchi.S1G240900.t1"; gene_id "Phchi.S1G240900"
Phchi.S1	AUGUSTUS	CDS	15858029	15859321	1	-	0	transcript_id "Phchi.S1G240900.t1"; gene_id "Phchi.S1G240900"
Phchi.S1	AUGUSTUS	exon	15858029	15859321	.	-	.	transcript_id "Phchi.S1G240900.t1"; gene_id "Phchi.S1G240900"
Phchi.S1	AUGUSTUS	start_codon	15859319	15859321	.	-	0	transcript_id "Phchi.S1G240900.t1"; gene_id "Phchi.S1G240900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14140.t1 is derived from g12607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11107882	11108815	.	-	.	Phchi.S3G145900
Phchi.S3	AUGUSTUS	transcript	11107882	11108815	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	stop_codon	11107879	11107881	.	-	0	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	CDS	11107882	11107916	1	-	2	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	exon	11107882	11107916	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	intron	11107917	11108011	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	CDS	11108012	11108080	1	-	2	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	exon	11108012	11108080	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	intron	11108081	11108166	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	CDS	11108167	11108268	1	-	2	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	exon	11108167	11108268	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	intron	11108269	11108347	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	CDS	11108348	11108453	1	-	0	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	exon	11108348	11108453	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	intron	11108454	11108794	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	CDS	11108795	11108815	1	-	0	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	exon	11108795	11108815	.	-	.	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
Phchi.S3	AUGUSTUS	start_codon	11108813	11108815	.	-	0	transcript_id "Phchi.S3G145900.t1"; gene_id "Phchi.S3G145900"
# This transcript jg4449.t2 is derived from g1619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4450.t1 is derived from g1620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10562055	10563220	.	-	.	Phchi.S1G160900
Phchi.S1	AUGUSTUS	transcript	10562055	10563220	.	-	.	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	stop_codon	10562052	10562054	.	-	0	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	CDS	10562055	10562718	0.74	-	1	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	exon	10562055	10562718	.	-	.	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	intron	10562719	10562806	.	-	.	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	CDS	10562807	10563093	0.43	-	0	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	exon	10562807	10563093	.	-	.	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	intron	10563094	10563166	.	-	.	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	CDS	10563167	10563220	0.4	-	0	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	exon	10563167	10563220	.	-	.	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
Phchi.S1	AUGUSTUS	start_codon	10563218	10563220	.	-	0	transcript_id "Phchi.S1G160900.t1"; gene_id "Phchi.S1G160900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg124.t1 is derived from g9906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	696255	697402	.	+	.	Phchi.S6G008300
Phchi.S6	AUGUSTUS	transcript	696255	697402	.	+	.	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	start_codon	696255	696257	.	+	0	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	CDS	696255	697276	0.49	+	0	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	exon	696255	697276	.	+	.	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	intron	697277	697383	.	+	.	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	CDS	697384	697402	0.46	+	1	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	exon	697384	697402	.	+	.	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
Phchi.S6	AUGUSTUS	stop_codon	697403	697405	.	+	0	transcript_id "Phchi.S6G008300.t1"; gene_id "Phchi.S6G008300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5265.t1 is derived from g2435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15949337	15953416	.	-	.	Phchi.S1G242400
Phchi.S1	AUGUSTUS	transcript	15949337	15953416	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	stop_codon	15949334	15949336	.	-	0	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	CDS	15949337	15949517	0.99	-	1	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	exon	15949337	15949517	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	intron	15949518	15949658	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	CDS	15949659	15950031	1	-	2	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	exon	15949659	15950031	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	intron	15950032	15950129	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	CDS	15950130	15951172	1	-	1	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	exon	15950130	15951172	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	intron	15951173	15951273	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	CDS	15951274	15953002	1	-	2	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	exon	15951274	15953002	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	intron	15953003	15953146	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	CDS	15953147	15953185	1	-	2	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	exon	15953147	15953185	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	intron	15953186	15953403	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	CDS	15953404	15953416	1	-	0	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	exon	15953404	15953416	.	-	.	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
Phchi.S1	AUGUSTUS	start_codon	15953414	15953416	.	-	0	transcript_id "Phchi.S1G242400.t1"; gene_id "Phchi.S1G242400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12816.t1 is derived from g11281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2487461	2488759	.	-	.	Phchi.S3G013500
Phchi.S3	AUGUSTUS	transcript	2487461	2488759	.	-	.	transcript_id "Phchi.S3G013500.t1"; gene_id "Phchi.S3G013500"
Phchi.S3	AUGUSTUS	stop_codon	2487458	2487460	.	-	0	transcript_id "Phchi.S3G013500.t1"; gene_id "Phchi.S3G013500"
Phchi.S3	AUGUSTUS	CDS	2487461	2488759	0.72	-	0	transcript_id "Phchi.S3G013500.t1"; gene_id "Phchi.S3G013500"
Phchi.S3	AUGUSTUS	exon	2487461	2488759	.	-	.	transcript_id "Phchi.S3G013500.t1"; gene_id "Phchi.S3G013500"
Phchi.S3	AUGUSTUS	start_codon	2488757	2488759	.	-	0	transcript_id "Phchi.S3G013500.t1"; gene_id "Phchi.S3G013500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8327.t1 is derived from g5502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35332986	35333939	.	-	.	Phchi.S1G548600
Phchi.S1	AUGUSTUS	transcript	35332986	35333939	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	stop_codon	35332983	35332985	.	-	0	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	CDS	35332986	35333043	1	-	1	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	exon	35332986	35333043	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	intron	35333044	35333129	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	CDS	35333130	35333274	1	-	2	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	exon	35333130	35333274	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	intron	35333275	35333358	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	CDS	35333359	35333489	1	-	1	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	exon	35333359	35333489	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	intron	35333490	35333796	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	CDS	35333797	35333939	1	-	0	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	exon	35333797	35333939	.	-	.	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
Phchi.S1	AUGUSTUS	start_codon	35333937	35333939	.	-	0	transcript_id "Phchi.S1G548600.t1"; gene_id "Phchi.S1G548600"
# This transcript jg1632.t2 is derived from g8551.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1633.t1 is derived from g8552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2107520	2114091	.	+	.	Phchi.S5G024200
Phchi.S5	AUGUSTUS	transcript	2107520	2114091	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	start_codon	2107520	2107522	.	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2107520	2107729	0.45	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2107520	2107729	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2107730	2107822	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2107823	2107912	0.97	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2107823	2107912	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2107913	2108138	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108139	2108208	0.95	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108139	2108208	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108209	2108295	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108296	2108366	1	+	2	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108296	2108366	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108367	2108542	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108543	2108626	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108543	2108626	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108627	2108764	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108765	2108842	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108765	2108842	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108843	2108987	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108988	2109059	0.98	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108988	2109059	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109060	2109194	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109195	2109361	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109195	2109361	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109362	2109505	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109506	2109581	1	+	1	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109506	2109581	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109582	2109714	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109715	2109770	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109715	2109770	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109771	2109876	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109877	2109919	1	+	1	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109877	2109919	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109920	2110018	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110019	2110102	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110019	2110102	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110103	2110187	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110188	2110271	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110188	2110271	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110272	2110423	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110424	2110477	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110424	2110477	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110478	2110629	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110630	2110695	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110630	2110695	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110696	2110825	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110826	2110921	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110826	2110921	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110922	2111004	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111005	2111118	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111005	2111118	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2111119	2111231	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111232	2111450	0.95	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111232	2111450	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2111451	2111644	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111645	2111794	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111645	2111794	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2111795	2111883	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111884	2112000	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111884	2112000	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112001	2112085	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112086	2112184	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112086	2112184	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112185	2112297	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112298	2112435	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112298	2112435	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112436	2112518	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112519	2112619	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112519	2112619	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112620	2112703	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112704	2112749	1	+	1	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112704	2112749	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112750	2112873	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112874	2112957	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112874	2112957	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112958	2113126	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113127	2113219	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113127	2113219	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113220	2113304	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113305	2113412	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113305	2113412	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113413	2113496	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113497	2113588	1	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113497	2113588	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113589	2113667	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113668	2113765	1	+	1	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113668	2113765	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113766	2113846	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113847	2114091	0.91	+	2	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113847	2114091	.	+	.	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	stop_codon	2114092	2114094	.	+	0	transcript_id "Phchi.S5G024200.t1"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	transcript	2107520	2114091	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	start_codon	2107520	2107522	.	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2107520	2107729	0.5	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2107520	2107729	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2107730	2107822	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2107823	2107912	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2107823	2107912	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2107913	2108000	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108001	2108023	0.96	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108001	2108023	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108024	2108098	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108099	2108208	0.81	+	1	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108099	2108208	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108209	2108295	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108296	2108366	1	+	2	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108296	2108366	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108367	2108542	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108543	2108626	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108543	2108626	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108627	2108764	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108765	2108842	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108765	2108842	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2108843	2108987	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108988	2109059	0.95	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108988	2109059	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109060	2109194	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109195	2109361	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109195	2109361	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109362	2109505	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109506	2109581	1	+	1	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109506	2109581	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109582	2109714	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109715	2109770	0.99	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109715	2109770	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109771	2109876	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2109877	2109919	0.99	+	1	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2109877	2109919	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2109920	2110018	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110019	2110102	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110019	2110102	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110103	2110187	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110188	2110271	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110188	2110271	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110272	2110423	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110424	2110477	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110424	2110477	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110478	2110629	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110630	2110695	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110630	2110695	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110696	2110825	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2110826	2110921	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2110826	2110921	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2110922	2111004	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111005	2111118	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111005	2111118	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2111119	2111231	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111232	2111450	0.98	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111232	2111450	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2111451	2111644	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111645	2111794	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111645	2111794	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2111795	2111883	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2111884	2112000	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2111884	2112000	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112001	2112085	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112086	2112184	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112086	2112184	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112185	2112297	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112298	2112435	0.99	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112298	2112435	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112436	2112518	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112519	2112619	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112519	2112619	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112620	2112703	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112704	2112749	1	+	1	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112704	2112749	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112750	2112873	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2112874	2112957	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2112874	2112957	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2112958	2113126	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113127	2113219	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113127	2113219	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113220	2113304	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113305	2113412	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113305	2113412	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113413	2113496	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113497	2113588	1	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113497	2113588	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113589	2113667	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113668	2113765	1	+	1	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113668	2113765	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2113766	2113846	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2113847	2114091	0.95	+	2	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2113847	2114091	.	+	.	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	stop_codon	2114092	2114094	.	+	0	transcript_id "Phchi.S5G024200.t2"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	transcript	2107520	2108073	.	+	.	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	start_codon	2107520	2107522	.	+	0	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2107520	2107729	0.41	+	0	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2107520	2107729	.	+	.	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2107730	2107822	.	+	.	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2107823	2107912	0.74	+	0	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2107823	2107912	.	+	.	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	intron	2107913	2108055	.	+	.	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	CDS	2108056	2108073	0.71	+	0	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	exon	2108056	2108073	.	+	.	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
Phchi.S5	AUGUSTUS	stop_codon	2108074	2108076	.	+	0	transcript_id "Phchi.S5G024200.t3"; gene_id "Phchi.S5G024200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4200.t1 is derived from g1369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8881487	8883540	.	+	.	Phchi.S1G135900
Phchi.S1	AUGUSTUS	transcript	8881487	8883540	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	start_codon	8881487	8881489	.	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8881487	8881771	0.7	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8881487	8881771	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8881772	8881971	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8881972	8882085	0.94	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8881972	8882085	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8882086	8882275	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8882276	8882484	1	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8882276	8882484	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8882485	8882606	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8882607	8882736	1	+	1	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8882607	8882736	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8882737	8882879	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8882880	8882939	1	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8882880	8882939	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8882940	8883047	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8883048	8883125	1	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8883048	8883125	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8883126	8883243	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8883244	8883335	0.8	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8883244	8883335	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	intron	8883336	8883446	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	CDS	8883447	8883540	0.72	+	1	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	exon	8883447	8883540	.	+	.	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
Phchi.S1	AUGUSTUS	stop_codon	8883541	8883543	.	+	0	transcript_id "Phchi.S1G135900.t1"; gene_id "Phchi.S1G135900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg275.t1 is derived from g10057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1981934	1985800	.	+	.	Phchi.S6G023400
Phchi.S6	AUGUSTUS	transcript	1981934	1985800	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	start_codon	1981934	1981936	.	+	0	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1981934	1982524	0.99	+	0	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1981934	1982524	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1982525	1982610	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1982611	1982761	1	+	0	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1982611	1982761	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1982762	1982851	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1982852	1983138	0.93	+	2	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1982852	1983138	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1983139	1983222	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1983223	1983460	0.78	+	0	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1983223	1983460	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1983461	1983549	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1983550	1983915	1	+	2	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1983550	1983915	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1983916	1984007	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1984008	1984093	0.52	+	2	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1984008	1984093	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1984094	1984370	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1984371	1984675	0.99	+	0	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1984371	1984675	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	intron	1984676	1984773	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	CDS	1984774	1985800	1	+	1	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	exon	1984774	1985800	.	+	.	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
Phchi.S6	AUGUSTUS	stop_codon	1985801	1985803	.	+	0	transcript_id "Phchi.S6G023400.t1"; gene_id "Phchi.S6G023400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9477.t1 is derived from g6653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41908989	41909931	.	-	.	Phchi.S1G663600
Phchi.S1	AUGUSTUS	transcript	41908989	41909931	.	-	.	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	stop_codon	41908986	41908988	.	-	0	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	CDS	41908989	41909095	0.09	-	2	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	exon	41908989	41909095	.	-	.	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	intron	41909096	41909678	.	-	.	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	CDS	41909679	41909931	0.66	-	0	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	exon	41909679	41909931	.	-	.	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
Phchi.S1	AUGUSTUS	start_codon	41909929	41909931	.	-	0	transcript_id "Phchi.S1G663600.t1"; gene_id "Phchi.S1G663600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1017.t1 is derived from g10800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7133153	7136442	.	+	.	Phchi.S6G097600
Phchi.S6	AUGUSTUS	transcript	7133153	7136442	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	start_codon	7133153	7133155	.	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7133153	7133351	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7133153	7133351	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7133352	7133583	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7133584	7133768	0.98	+	2	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7133584	7133768	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7133769	7133881	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7133882	7134064	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7133882	7134064	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7134065	7134164	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7134165	7134296	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7134165	7134296	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7134297	7134798	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7134799	7134984	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7134799	7134984	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7134985	7135089	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7135090	7135179	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7135090	7135179	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7135180	7135307	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7135308	7135391	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7135308	7135391	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7135392	7135485	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7135486	7135656	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7135486	7135656	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7135657	7135947	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7135948	7136217	0.99	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7135948	7136217	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	intron	7136218	7136331	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	CDS	7136332	7136442	1	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	exon	7136332	7136442	.	+	.	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
Phchi.S6	AUGUSTUS	stop_codon	7136443	7136445	.	+	0	transcript_id "Phchi.S6G097600.t1"; gene_id "Phchi.S6G097600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13536.t1 is derived from g12003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7406793	7409728	.	+	.	Phchi.S3G085500
Phchi.S3	AUGUSTUS	transcript	7406793	7409728	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	start_codon	7406793	7406795	.	+	0	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	CDS	7406793	7407091	1	+	0	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	exon	7406793	7407091	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	intron	7407092	7407235	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	CDS	7407236	7407469	1	+	1	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	exon	7407236	7407469	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	intron	7407470	7407550	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	CDS	7407551	7408888	1	+	1	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	exon	7407551	7408888	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	intron	7408889	7409013	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	CDS	7409014	7409728	1	+	1	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	exon	7409014	7409728	.	+	.	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
Phchi.S3	AUGUSTUS	stop_codon	7409729	7409731	.	+	0	transcript_id "Phchi.S3G085500.t1"; gene_id "Phchi.S3G085500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2877.t1 is derived from g46.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	233590	238450	.	+	.	Phchi.S1G003600
Phchi.S1	AUGUSTUS	transcript	233590	238450	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	start_codon	233590	233592	.	+	0	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	233590	233615	0.85	+	0	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	233590	233615	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	233616	233890	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	233891	233956	0.54	+	1	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	233891	233956	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	233957	234115	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	234116	234154	0.92	+	1	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	234116	234154	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	234155	234601	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	234602	234673	1	+	1	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	234602	234673	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	234674	234788	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	234789	235096	1	+	1	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	234789	235096	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	235097	235182	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	235183	235362	1	+	2	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	235183	235362	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	235363	235477	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	235478	235639	1	+	2	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	235478	235639	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	235640	235727	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	235728	235882	1	+	2	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	235728	235882	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	235883	235960	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	235961	236053	1	+	0	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	235961	236053	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	236054	236166	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	236167	236252	1	+	0	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	236167	236252	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	236253	236344	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	236345	236571	1	+	1	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	236345	236571	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	236572	238008	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	238009	238254	1	+	2	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	238009	238254	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	intron	238255	238349	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	CDS	238350	238450	0.91	+	2	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	exon	238350	238450	.	+	.	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
Phchi.S1	AUGUSTUS	stop_codon	238451	238453	.	+	0	transcript_id "Phchi.S1G003600.t1"; gene_id "Phchi.S1G003600"
# This transcript jg1123.t2 is derived from g10906.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1123.t3 is derived from g10906.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1124.t1 is derived from g10907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7849064	7851871	.	+	.	Phchi.S6G108300
Phchi.S6	AUGUSTUS	transcript	7849064	7851871	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	start_codon	7849064	7849066	.	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7849064	7849205	1	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7849064	7849205	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7849206	7849327	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7849328	7849419	1	+	2	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7849328	7849419	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7849420	7849530	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7849531	7849593	0.9	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7849531	7849593	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7849594	7849732	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7849733	7849831	1	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7849733	7849831	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7849832	7849929	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7849930	7850088	1	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7849930	7850088	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7850089	7850224	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7850225	7850296	1	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7850225	7850296	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7850297	7850376	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7850377	7850509	0.67	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7850377	7850509	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7850510	7850611	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7850612	7850676	1	+	2	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7850612	7850676	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7850677	7850812	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7850813	7850888	1	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7850813	7850888	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7850889	7850986	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7850987	7851088	0.99	+	2	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7850987	7851088	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7851089	7851190	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7851191	7851383	1	+	2	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7851191	7851383	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	intron	7851384	7851630	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	CDS	7851631	7851871	1	+	1	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	exon	7851631	7851871	.	+	.	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
Phchi.S6	AUGUSTUS	stop_codon	7851872	7851874	.	+	0	transcript_id "Phchi.S6G108300.t1"; gene_id "Phchi.S6G108300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4865.t1 is derived from g2035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13157167	13158036	.	-	.	Phchi.S1G202400
Phchi.S1	AUGUSTUS	transcript	13157167	13158036	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	stop_codon	13157164	13157166	.	-	0	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	CDS	13157167	13157421	0.66	-	0	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	exon	13157167	13157421	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	intron	13157422	13157512	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	CDS	13157513	13157590	1	-	0	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	exon	13157513	13157590	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	intron	13157591	13157687	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	CDS	13157688	13157758	1	-	2	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	exon	13157688	13157758	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	intron	13157759	13157828	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	CDS	13157829	13157939	1	-	2	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	exon	13157829	13157939	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	intron	13157940	13158020	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	CDS	13158021	13158036	1	-	0	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	exon	13158021	13158036	.	-	.	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
Phchi.S1	AUGUSTUS	start_codon	13158034	13158036	.	-	0	transcript_id "Phchi.S1G202400.t1"; gene_id "Phchi.S1G202400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6696.t1 is derived from g3868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24573512	24575317	.	+	.	Phchi.S1G385500
Phchi.S1	AUGUSTUS	transcript	24573512	24575317	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	start_codon	24573512	24573514	.	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24573512	24573619	1	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24573512	24573619	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24573620	24573708	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24573709	24573810	1	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24573709	24573810	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24573811	24573907	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24573908	24574017	1	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24573908	24574017	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24574018	24574133	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24574134	24574203	1	+	1	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24574134	24574203	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24574204	24574288	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24574289	24574366	1	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24574289	24574366	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24574367	24574485	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24574486	24574602	1	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24574486	24574602	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24574603	24574686	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24574687	24574781	1	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24574687	24574781	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24574782	24574865	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24574866	24574945	1	+	1	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24574866	24574945	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24574946	24575041	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24575042	24575101	1	+	2	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24575042	24575101	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	intron	24575102	24575192	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	CDS	24575193	24575317	1	+	2	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	exon	24575193	24575317	.	+	.	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
Phchi.S1	AUGUSTUS	stop_codon	24575318	24575320	.	+	0	transcript_id "Phchi.S1G385500.t1"; gene_id "Phchi.S1G385500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4024.t1 is derived from g1193.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7218542	7219283	.	+	.	Phchi.S1G118300
Phchi.S1	AUGUSTUS	transcript	7218542	7219283	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	start_codon	7218542	7218544	.	+	0	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7218542	7218667	0.63	+	0	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7218542	7218667	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	intron	7218668	7218813	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7218814	7218930	0.99	+	0	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7218814	7218930	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	intron	7218931	7219017	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7219018	7219104	1	+	0	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7219018	7219104	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	intron	7219105	7219196	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7219197	7219283	1	+	0	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7219197	7219283	.	+	.	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	stop_codon	7219284	7219286	.	+	0	transcript_id "Phchi.S1G118300.t1"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	transcript	7218542	7219283	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	start_codon	7218542	7218544	.	+	0	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7218542	7218676	0.48	+	0	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7218542	7218676	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	intron	7218677	7218813	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7218814	7218930	0.99	+	0	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7218814	7218930	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	intron	7218931	7219017	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7219018	7219104	0.99	+	0	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7219018	7219104	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	intron	7219105	7219196	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	CDS	7219197	7219283	0.99	+	0	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	exon	7219197	7219283	.	+	.	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
Phchi.S1	AUGUSTUS	stop_codon	7219284	7219286	.	+	0	transcript_id "Phchi.S1G118300.t2"; gene_id "Phchi.S1G118300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4799.t1 is derived from g1969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12881533	12883633	.	+	.	Phchi.S1G195800
Phchi.S1	AUGUSTUS	transcript	12881533	12883633	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	start_codon	12881533	12881535	.	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12881533	12882061	0.98	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12881533	12882061	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12882062	12882224	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12882225	12882409	1	+	2	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12882225	12882409	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12882410	12882517	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12882518	12882568	1	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12882518	12882568	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12882569	12882704	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12882705	12882796	1	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12882705	12882796	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12882797	12882892	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12882893	12882963	1	+	1	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12882893	12882963	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12882964	12883044	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12883045	12883100	1	+	2	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12883045	12883100	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12883101	12883269	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12883270	12883374	1	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12883270	12883374	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	intron	12883375	12883459	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	CDS	12883460	12883633	1	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	exon	12883460	12883633	.	+	.	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
Phchi.S1	AUGUSTUS	stop_codon	12883634	12883636	.	+	0	transcript_id "Phchi.S1G195800.t1"; gene_id "Phchi.S1G195800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8857.t1 is derived from g6032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38310690	38311408	.	+	.	Phchi.S1G601600
Phchi.S1	AUGUSTUS	transcript	38310690	38311408	.	+	.	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	start_codon	38310690	38310692	.	+	0	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	CDS	38310690	38310914	0.97	+	0	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	exon	38310690	38310914	.	+	.	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	intron	38310915	38311014	.	+	.	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	CDS	38311015	38311110	1	+	0	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	exon	38311015	38311110	.	+	.	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	intron	38311111	38311222	.	+	.	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	CDS	38311223	38311408	0.99	+	0	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	exon	38311223	38311408	.	+	.	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
Phchi.S1	AUGUSTUS	stop_codon	38311409	38311411	.	+	0	transcript_id "Phchi.S1G601600.t1"; gene_id "Phchi.S1G601600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15480.t1 is derived from g13948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19409104	19409980	.	+	.	Phchi.S3G279900
Phchi.S3	AUGUSTUS	transcript	19409104	19409980	.	+	.	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	start_codon	19409104	19409106	.	+	0	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	CDS	19409104	19409266	0.33	+	0	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	exon	19409104	19409266	.	+	.	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	intron	19409267	19409343	.	+	.	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	CDS	19409344	19409595	0.81	+	2	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	exon	19409344	19409595	.	+	.	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	intron	19409596	19409738	.	+	.	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	CDS	19409739	19409980	0.75	+	2	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	exon	19409739	19409980	.	+	.	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
Phchi.S3	AUGUSTUS	stop_codon	19409981	19409983	.	+	0	transcript_id "Phchi.S3G279900.t1"; gene_id "Phchi.S3G279900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6236.t1 is derived from g3408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21804217	21808292	.	-	.	Phchi.S1G339500
Phchi.S1	AUGUSTUS	transcript	21804217	21808292	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	stop_codon	21804214	21804216	.	-	0	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	CDS	21804217	21806495	0.87	-	2	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	exon	21804217	21806495	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	intron	21806496	21806669	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	CDS	21806670	21807072	1	-	0	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	exon	21806670	21807072	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	intron	21807073	21807233	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	CDS	21807234	21807337	1	-	2	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	exon	21807234	21807337	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	intron	21807338	21807519	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	CDS	21807520	21807772	1	-	0	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	exon	21807520	21807772	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	intron	21807773	21808061	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	CDS	21808062	21808292	1	-	0	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	exon	21808062	21808292	.	-	.	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
Phchi.S1	AUGUSTUS	start_codon	21808290	21808292	.	-	0	transcript_id "Phchi.S1G339500.t1"; gene_id "Phchi.S1G339500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg212.t1 is derived from g9994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1229453	1229767	.	+	.	Phchi.S6G017100
Phchi.S6	AUGUSTUS	transcript	1229453	1229767	.	+	.	transcript_id "Phchi.S6G017100.t1"; gene_id "Phchi.S6G017100"
Phchi.S6	AUGUSTUS	start_codon	1229453	1229455	.	+	0	transcript_id "Phchi.S6G017100.t1"; gene_id "Phchi.S6G017100"
Phchi.S6	AUGUSTUS	CDS	1229453	1229767	0.97	+	0	transcript_id "Phchi.S6G017100.t1"; gene_id "Phchi.S6G017100"
Phchi.S6	AUGUSTUS	exon	1229453	1229767	.	+	.	transcript_id "Phchi.S6G017100.t1"; gene_id "Phchi.S6G017100"
Phchi.S6	AUGUSTUS	stop_codon	1229768	1229770	.	+	0	transcript_id "Phchi.S6G017100.t1"; gene_id "Phchi.S6G017100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6245.t1 is derived from g3417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21842409	21845421	.	+	.	Phchi.S1G340400
Phchi.S1	AUGUSTUS	transcript	21842409	21845421	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	start_codon	21842409	21842411	.	+	0	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	CDS	21842409	21842420	1	+	0	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	exon	21842409	21842420	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	intron	21842421	21842566	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	CDS	21842567	21844864	0.75	+	0	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	exon	21842567	21844864	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	intron	21844865	21844975	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	CDS	21844976	21845001	0.58	+	0	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	exon	21844976	21845001	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	intron	21845002	21845076	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	CDS	21845077	21845223	0.62	+	1	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	exon	21845077	21845223	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	intron	21845224	21845357	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	CDS	21845358	21845421	0.94	+	1	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	exon	21845358	21845421	.	+	.	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
Phchi.S1	AUGUSTUS	stop_codon	21845422	21845424	.	+	0	transcript_id "Phchi.S1G340400.t1"; gene_id "Phchi.S1G340400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10530.t1 is derived from g14580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	843947	846032	.	-	.	Phchi.S4G011200
Phchi.S4	AUGUSTUS	transcript	843947	846032	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	stop_codon	843944	843946	.	-	0	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	843947	843958	0.95	-	0	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	843947	843958	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	843959	844036	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	844037	844167	1	-	2	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	844037	844167	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	844168	844330	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	844331	844599	1	-	1	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	844331	844599	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	844600	844735	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	844736	844997	1	-	2	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	844736	844997	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	844998	845153	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	845154	845266	1	-	1	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	845154	845266	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	845267	845412	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	845413	845447	1	-	0	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	845413	845447	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	845448	845568	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	845569	845676	1	-	0	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	845569	845676	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	intron	845677	845912	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	CDS	845913	846032	0.99	-	0	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	exon	845913	846032	.	-	.	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
Phchi.S4	AUGUSTUS	start_codon	846030	846032	.	-	0	transcript_id "Phchi.S4G011200.t1"; gene_id "Phchi.S4G011200"
# This transcript jg14684.t2 is derived from g13152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14685.t1 is derived from g13153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14159222	14160481	.	+	.	Phchi.S3G200400
Phchi.S3	AUGUSTUS	transcript	14159222	14160481	.	+	.	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	start_codon	14159222	14159224	.	+	0	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	CDS	14159222	14159963	0.6	+	0	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	exon	14159222	14159963	.	+	.	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	intron	14159964	14160088	.	+	.	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	CDS	14160089	14160262	1	+	2	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	exon	14160089	14160262	.	+	.	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	intron	14160263	14160347	.	+	.	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	CDS	14160348	14160481	1	+	2	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	exon	14160348	14160481	.	+	.	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
Phchi.S3	AUGUSTUS	stop_codon	14160482	14160484	.	+	0	transcript_id "Phchi.S3G200400.t1"; gene_id "Phchi.S3G200400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14537.t1 is derived from g13005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13385196	13388362	.	-	.	Phchi.S3G185600
Phchi.S3	AUGUSTUS	transcript	13385196	13388362	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	stop_codon	13385193	13385195	.	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13385196	13385297	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13385196	13385297	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13385298	13385392	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13385393	13385578	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13385393	13385578	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13385579	13385684	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13385685	13385852	0.97	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13385685	13385852	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13385853	13385988	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13385989	13386033	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13385989	13386033	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13386034	13386122	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13386123	13386296	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13386123	13386296	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13386297	13386391	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13386392	13386478	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13386392	13386478	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13386479	13386610	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13386611	13386772	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13386611	13386772	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13386773	13386939	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13386940	13387010	1	-	2	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13386940	13387010	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13387011	13387119	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13387120	13387259	0.86	-	1	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13387120	13387259	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13387260	13387400	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13387401	13387525	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13387401	13387525	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13387526	13387655	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13387656	13387790	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13387656	13387790	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13387791	13387911	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13387912	13388157	1	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13387912	13388157	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	intron	13388158	13388308	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	CDS	13388309	13388362	0.94	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	exon	13388309	13388362	.	-	.	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
Phchi.S3	AUGUSTUS	start_codon	13388360	13388362	.	-	0	transcript_id "Phchi.S3G185600.t1"; gene_id "Phchi.S3G185600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14664.t1 is derived from g13132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14024484	14025518	.	+	.	Phchi.S3G198300
Phchi.S3	AUGUSTUS	transcript	14024484	14025518	.	+	.	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	start_codon	14024484	14024486	.	+	0	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	CDS	14024484	14025059	0.66	+	0	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	exon	14024484	14025059	.	+	.	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	intron	14025060	14025305	.	+	.	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	CDS	14025306	14025518	1	+	0	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	exon	14025306	14025518	.	+	.	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
Phchi.S3	AUGUSTUS	stop_codon	14025519	14025521	.	+	0	transcript_id "Phchi.S3G198300.t1"; gene_id "Phchi.S3G198300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5768.t1 is derived from g2938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18873420	18874627	.	+	.	Phchi.S1G292700
Phchi.S1	AUGUSTUS	transcript	18873420	18874627	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	start_codon	18873420	18873422	.	+	0	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	CDS	18873420	18873630	0.45	+	0	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	exon	18873420	18873630	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	intron	18873631	18873727	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	CDS	18873728	18873918	1	+	2	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	exon	18873728	18873918	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	intron	18873919	18874039	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	CDS	18874040	18874085	1	+	0	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	exon	18874040	18874085	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	intron	18874086	18874176	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	CDS	18874177	18874259	1	+	2	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	exon	18874177	18874259	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	intron	18874260	18874352	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	CDS	18874353	18874469	1	+	0	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	exon	18874353	18874469	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	intron	18874470	18874558	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	CDS	18874559	18874627	1	+	0	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	exon	18874559	18874627	.	+	.	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
Phchi.S1	AUGUSTUS	stop_codon	18874628	18874630	.	+	0	transcript_id "Phchi.S1G292700.t1"; gene_id "Phchi.S1G292700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11218.t1 is derived from g15268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4836174	4836758	.	-	.	Phchi.S4G080000
Phchi.S4	AUGUSTUS	transcript	4836174	4836758	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	stop_codon	4836171	4836173	.	-	0	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	CDS	4836174	4836237	1	-	1	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	exon	4836174	4836237	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	intron	4836238	4836343	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	CDS	4836344	4836411	1	-	0	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	exon	4836344	4836411	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	intron	4836412	4836501	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	CDS	4836502	4836553	0.81	-	1	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	exon	4836502	4836553	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	intron	4836554	4836675	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	CDS	4836676	4836758	0.79	-	0	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	exon	4836676	4836758	.	-	.	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
Phchi.S4	AUGUSTUS	start_codon	4836756	4836758	.	-	0	transcript_id "Phchi.S4G080000.t1"; gene_id "Phchi.S4G080000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12655.t1 is derived from g14454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	17029	17585	.	-	.	Phchi.C12G000500
Phchi.C12	AUGUSTUS	transcript	17029	17585	.	-	.	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	stop_codon	17026	17028	.	-	0	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	CDS	17029	17142	1	-	0	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	exon	17029	17142	.	-	.	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	intron	17143	17224	.	-	.	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	CDS	17225	17299	0.7	-	0	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	exon	17225	17299	.	-	.	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	intron	17300	17477	.	-	.	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	CDS	17478	17585	0.68	-	0	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	exon	17478	17585	.	-	.	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
Phchi.C12	AUGUSTUS	start_codon	17583	17585	.	-	0	transcript_id "Phchi.C12G000500.t1"; gene_id "Phchi.C12G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14016.t1 is derived from g12483.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10322655	10327753	.	-	.	Phchi.S3G133500
Phchi.S3	AUGUSTUS	transcript	10322655	10327753	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	stop_codon	10322652	10322654	.	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10322655	10323863	0.93	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10322655	10323863	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10323864	10324050	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324051	10324167	1	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324051	10324167	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324168	10324262	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324263	10324396	0.93	-	2	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324263	10324396	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324397	10324503	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324504	10324573	0.92	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324504	10324573	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324574	10324683	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324684	10324779	1	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324684	10324779	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324780	10325151	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10325152	10325330	0.94	-	2	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10325152	10325330	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10325331	10325442	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10325443	10325598	1	-	2	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10325443	10325598	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10325599	10325790	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10325791	10326027	0.98	-	2	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10325791	10326027	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10326028	10326127	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10326128	10327135	0.73	-	2	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10326128	10327135	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10327136	10327716	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10327717	10327753	1	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10327717	10327753	.	-	.	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	start_codon	10327751	10327753	.	-	0	transcript_id "Phchi.S3G133500.t1"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	transcript	10322655	10327268	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	stop_codon	10322652	10322654	.	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10322655	10323863	0.97	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10322655	10323863	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10323864	10324050	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324051	10324167	1	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324051	10324167	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324168	10324262	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324263	10324396	0.96	-	2	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324263	10324396	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324397	10324503	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324504	10324573	0.9	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324504	10324573	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324574	10324683	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10324684	10324779	1	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10324684	10324779	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10324780	10325151	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10325152	10325330	0.95	-	2	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10325152	10325330	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10325331	10325442	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10325443	10325598	1	-	2	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10325443	10325598	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10325599	10325790	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10325791	10326027	0.94	-	2	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10325791	10326027	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10326028	10326127	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10326128	10327135	0.62	-	2	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10326128	10327135	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	intron	10327136	10327255	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	CDS	10327256	10327268	0.83	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	exon	10327256	10327268	.	-	.	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
Phchi.S3	AUGUSTUS	start_codon	10327266	10327268	.	-	0	transcript_id "Phchi.S3G133500.t2"; gene_id "Phchi.S3G133500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1574.t1 is derived from g8493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1830664	1831271	.	-	.	Phchi.S5G018300
Phchi.S5	AUGUSTUS	transcript	1830664	1831271	.	-	.	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	stop_codon	1830661	1830663	.	-	0	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	CDS	1830664	1831074	0.53	-	0	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	exon	1830664	1831074	.	-	.	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	intron	1831075	1831202	.	-	.	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	CDS	1831203	1831271	0.73	-	0	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	exon	1831203	1831271	.	-	.	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
Phchi.S5	AUGUSTUS	start_codon	1831269	1831271	.	-	0	transcript_id "Phchi.S5G018300.t1"; gene_id "Phchi.S5G018300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13783.t1 is derived from g12250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8879506	8882516	.	-	.	Phchi.S3G110200
Phchi.S3	AUGUSTUS	transcript	8879506	8882516	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	stop_codon	8879503	8879505	.	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8879506	8879532	1	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8879506	8879532	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8879533	8879616	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8879617	8879694	1	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8879617	8879694	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8879695	8879780	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8879781	8880276	0.48	-	1	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8879781	8880276	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8880277	8880383	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8880384	8880420	0.55	-	2	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8880384	8880420	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8880421	8880506	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8880507	8880627	1	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8880507	8880627	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8880628	8880874	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8880875	8880959	1	-	1	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8880875	8880959	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8880960	8881051	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8881052	8881110	1	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8881052	8881110	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8881111	8881202	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8881203	8881283	1	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8881203	8881283	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8881284	8881398	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8881399	8881471	1	-	1	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8881399	8881471	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8881472	8881642	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8881643	8881738	1	-	1	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8881643	8881738	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8881739	8881847	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8881848	8881921	0.99	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8881848	8881921	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8881922	8882050	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8882051	8882148	1	-	2	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8882051	8882148	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8882149	8882291	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8882292	8882373	1	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8882292	8882373	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	intron	8882374	8882453	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	CDS	8882454	8882516	0.98	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	exon	8882454	8882516	.	-	.	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
Phchi.S3	AUGUSTUS	start_codon	8882514	8882516	.	-	0	transcript_id "Phchi.S3G110200.t1"; gene_id "Phchi.S3G110200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12078.t1 is derived from g7753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2145057	2146553	.	+	.	Phchi.S2G015800
Phchi.S2	AUGUSTUS	transcript	2145057	2146553	.	+	.	transcript_id "Phchi.S2G015800.t1"; gene_id "Phchi.S2G015800"
Phchi.S2	AUGUSTUS	start_codon	2145057	2145059	.	+	0	transcript_id "Phchi.S2G015800.t1"; gene_id "Phchi.S2G015800"
Phchi.S2	AUGUSTUS	CDS	2145057	2146553	1	+	0	transcript_id "Phchi.S2G015800.t1"; gene_id "Phchi.S2G015800"
Phchi.S2	AUGUSTUS	exon	2145057	2146553	.	+	.	transcript_id "Phchi.S2G015800.t1"; gene_id "Phchi.S2G015800"
Phchi.S2	AUGUSTUS	stop_codon	2146554	2146556	.	+	0	transcript_id "Phchi.S2G015800.t1"; gene_id "Phchi.S2G015800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7443.t1 is derived from g4615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29152320	29152886	.	+	.	Phchi.S1G460200
Phchi.S1	AUGUSTUS	transcript	29152320	29152886	.	+	.	transcript_id "Phchi.S1G460200.t1"; gene_id "Phchi.S1G460200"
Phchi.S1	AUGUSTUS	start_codon	29152320	29152322	.	+	0	transcript_id "Phchi.S1G460200.t1"; gene_id "Phchi.S1G460200"
Phchi.S1	AUGUSTUS	CDS	29152320	29152886	0.74	+	0	transcript_id "Phchi.S1G460200.t1"; gene_id "Phchi.S1G460200"
Phchi.S1	AUGUSTUS	exon	29152320	29152886	.	+	.	transcript_id "Phchi.S1G460200.t1"; gene_id "Phchi.S1G460200"
Phchi.S1	AUGUSTUS	stop_codon	29152887	29152889	.	+	0	transcript_id "Phchi.S1G460200.t1"; gene_id "Phchi.S1G460200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11779.t1 is derived from g15831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8133714	8137637	.	+	.	Phchi.S4G136100
Phchi.S4	AUGUSTUS	transcript	8133714	8137637	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	start_codon	8133714	8133716	.	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8133714	8133798	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8133714	8133798	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8133799	8134316	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8134317	8134396	1	+	2	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8134317	8134396	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8134397	8134575	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8134576	8134644	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8134576	8134644	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8134645	8134850	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8134851	8134908	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8134851	8134908	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8134909	8135001	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8135002	8135054	0.99	+	2	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8135002	8135054	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8135055	8135179	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8135180	8135222	0.96	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8135180	8135222	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8135223	8135323	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8135324	8135382	1	+	2	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8135324	8135382	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8135383	8135503	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8135504	8135620	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8135504	8135620	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8135621	8135864	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8135865	8135967	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8135865	8135967	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8135968	8136075	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8136076	8136125	1	+	2	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8136076	8136125	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8136126	8136208	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8136209	8136337	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8136209	8136337	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8136338	8136467	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8136468	8136719	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8136468	8136719	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8136720	8136790	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8136791	8136870	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8136791	8136870	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8136871	8136976	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8136977	8137103	1	+	1	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8136977	8137103	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8137104	8137181	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8137182	8137325	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8137182	8137325	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	intron	8137326	8137454	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	CDS	8137455	8137637	1	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	exon	8137455	8137637	.	+	.	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
Phchi.S4	AUGUSTUS	stop_codon	8137638	8137640	.	+	0	transcript_id "Phchi.S4G136100.t1"; gene_id "Phchi.S4G136100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5262.t1 is derived from g2432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15909468	15909935	.	-	.	Phchi.S1G242100
Phchi.S1	AUGUSTUS	transcript	15909468	15909935	.	-	.	transcript_id "Phchi.S1G242100.t1"; gene_id "Phchi.S1G242100"
Phchi.S1	AUGUSTUS	stop_codon	15909465	15909467	.	-	0	transcript_id "Phchi.S1G242100.t1"; gene_id "Phchi.S1G242100"
Phchi.S1	AUGUSTUS	CDS	15909468	15909935	0.62	-	0	transcript_id "Phchi.S1G242100.t1"; gene_id "Phchi.S1G242100"
Phchi.S1	AUGUSTUS	exon	15909468	15909935	.	-	.	transcript_id "Phchi.S1G242100.t1"; gene_id "Phchi.S1G242100"
Phchi.S1	AUGUSTUS	start_codon	15909933	15909935	.	-	0	transcript_id "Phchi.S1G242100.t1"; gene_id "Phchi.S1G242100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg691.t1 is derived from g10473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4921628	4921963	.	+	.	Phchi.S6G065000
Phchi.S6	AUGUSTUS	transcript	4921628	4921963	.	+	.	transcript_id "Phchi.S6G065000.t1"; gene_id "Phchi.S6G065000"
Phchi.S6	AUGUSTUS	start_codon	4921628	4921630	.	+	0	transcript_id "Phchi.S6G065000.t1"; gene_id "Phchi.S6G065000"
Phchi.S6	AUGUSTUS	CDS	4921628	4921963	0.95	+	0	transcript_id "Phchi.S6G065000.t1"; gene_id "Phchi.S6G065000"
Phchi.S6	AUGUSTUS	exon	4921628	4921963	.	+	.	transcript_id "Phchi.S6G065000.t1"; gene_id "Phchi.S6G065000"
Phchi.S6	AUGUSTUS	stop_codon	4921964	4921966	.	+	0	transcript_id "Phchi.S6G065000.t1"; gene_id "Phchi.S6G065000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1303.t1 is derived from g11086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8916082	8916727	.	+	.	Phchi.S6G126200
Phchi.S6	AUGUSTUS	transcript	8916082	8916727	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	start_codon	8916082	8916084	.	+	0	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	CDS	8916082	8916111	0.44	+	0	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	exon	8916082	8916111	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	intron	8916112	8916206	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	CDS	8916207	8916287	0.62	+	0	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	exon	8916207	8916287	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	intron	8916288	8916479	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	CDS	8916480	8916537	0.97	+	0	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	exon	8916480	8916537	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	intron	8916538	8916692	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	CDS	8916693	8916727	0.98	+	2	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	exon	8916693	8916727	.	+	.	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
Phchi.S6	AUGUSTUS	stop_codon	8916728	8916730	.	+	0	transcript_id "Phchi.S6G126200.t1"; gene_id "Phchi.S6G126200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8915.t1 is derived from g6090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38658523	38659882	.	+	.	Phchi.S1G607400
Phchi.S1	AUGUSTUS	transcript	38658523	38659882	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	start_codon	38658523	38658525	.	+	0	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	CDS	38658523	38658534	0.94	+	0	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	exon	38658523	38658534	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	intron	38658535	38658746	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	CDS	38658747	38658942	1	+	0	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	exon	38658747	38658942	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	intron	38658943	38659272	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	CDS	38659273	38659448	1	+	2	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	exon	38659273	38659448	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	intron	38659449	38659649	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	CDS	38659650	38659793	0.66	+	0	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	exon	38659650	38659793	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	intron	38659794	38659879	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	CDS	38659880	38659882	0.66	+	0	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	exon	38659880	38659882	.	+	.	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
Phchi.S1	AUGUSTUS	stop_codon	38659883	38659885	.	+	0	transcript_id "Phchi.S1G607400.t1"; gene_id "Phchi.S1G607400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3988.t1 is derived from g1157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6882575	6883177	.	-	.	Phchi.S1G114700
Phchi.S1	AUGUSTUS	transcript	6882575	6883177	.	-	.	transcript_id "Phchi.S1G114700.t1"; gene_id "Phchi.S1G114700"
Phchi.S1	AUGUSTUS	stop_codon	6882572	6882574	.	-	0	transcript_id "Phchi.S1G114700.t1"; gene_id "Phchi.S1G114700"
Phchi.S1	AUGUSTUS	CDS	6882575	6883177	0.63	-	0	transcript_id "Phchi.S1G114700.t1"; gene_id "Phchi.S1G114700"
Phchi.S1	AUGUSTUS	exon	6882575	6883177	.	-	.	transcript_id "Phchi.S1G114700.t1"; gene_id "Phchi.S1G114700"
Phchi.S1	AUGUSTUS	start_codon	6883175	6883177	.	-	0	transcript_id "Phchi.S1G114700.t1"; gene_id "Phchi.S1G114700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12629.t1 is derived from g8306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37653316	37656978	.	-	.	Phchi.S2G070900
Phchi.S2	AUGUSTUS	transcript	37653316	37656978	.	-	.	transcript_id "Phchi.S2G070900.t1"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	stop_codon	37653313	37653315	.	-	0	transcript_id "Phchi.S2G070900.t1"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	CDS	37653316	37656978	0.75	-	0	transcript_id "Phchi.S2G070900.t1"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	exon	37653316	37656978	.	-	.	transcript_id "Phchi.S2G070900.t1"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	start_codon	37656976	37656978	.	-	0	transcript_id "Phchi.S2G070900.t1"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	transcript	37653316	37655115	.	-	.	transcript_id "Phchi.S2G070900.t2"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	stop_codon	37653313	37653315	.	-	0	transcript_id "Phchi.S2G070900.t2"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	CDS	37653316	37655115	0.39	-	0	transcript_id "Phchi.S2G070900.t2"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	exon	37653316	37655115	.	-	.	transcript_id "Phchi.S2G070900.t2"; gene_id "Phchi.S2G070900"
Phchi.S2	AUGUSTUS	start_codon	37655113	37655115	.	-	0	transcript_id "Phchi.S2G070900.t2"; gene_id "Phchi.S2G070900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1545.t1 is derived from g8464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1690875	1693710	.	+	.	Phchi.S5G015400
Phchi.S5	AUGUSTUS	transcript	1690875	1693710	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	start_codon	1690875	1690877	.	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1690875	1690938	0.98	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1690875	1690938	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1690939	1691180	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1691181	1691328	1	+	2	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1691181	1691328	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1691329	1691433	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1691434	1691518	0.77	+	1	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1691434	1691518	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1691519	1691621	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1691622	1691717	0.92	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1691622	1691717	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1691718	1691811	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1691812	1691877	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1691812	1691877	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1691878	1691957	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1691958	1692056	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1691958	1692056	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1692057	1692200	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1692201	1692314	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1692201	1692314	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1692315	1692410	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1692411	1692521	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1692411	1692521	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1692522	1692630	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1692631	1692693	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1692631	1692693	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1692694	1692791	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1692792	1692884	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1692792	1692884	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1692885	1693084	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1693085	1693198	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1693085	1693198	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1693199	1693282	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1693283	1693354	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1693283	1693354	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1693355	1693444	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1693445	1693510	1	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1693445	1693510	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	intron	1693511	1693596	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	CDS	1693597	1693710	0.99	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	exon	1693597	1693710	.	+	.	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
Phchi.S5	AUGUSTUS	stop_codon	1693711	1693713	.	+	0	transcript_id "Phchi.S5G015400.t1"; gene_id "Phchi.S5G015400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14465.t1 is derived from g12933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13002937	13004457	.	-	.	Phchi.S3G178400
Phchi.S3	AUGUSTUS	transcript	13002937	13004457	.	-	.	transcript_id "Phchi.S3G178400.t1"; gene_id "Phchi.S3G178400"
Phchi.S3	AUGUSTUS	stop_codon	13002934	13002936	.	-	0	transcript_id "Phchi.S3G178400.t1"; gene_id "Phchi.S3G178400"
Phchi.S3	AUGUSTUS	CDS	13002937	13004457	0.91	-	0	transcript_id "Phchi.S3G178400.t1"; gene_id "Phchi.S3G178400"
Phchi.S3	AUGUSTUS	exon	13002937	13004457	.	-	.	transcript_id "Phchi.S3G178400.t1"; gene_id "Phchi.S3G178400"
Phchi.S3	AUGUSTUS	start_codon	13004455	13004457	.	-	0	transcript_id "Phchi.S3G178400.t1"; gene_id "Phchi.S3G178400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6825.t1 is derived from g3997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25227673	25231789	.	+	.	Phchi.S1G398400
Phchi.S1	AUGUSTUS	transcript	25227673	25231789	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	start_codon	25227673	25227675	.	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25227673	25227778	0.97	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25227673	25227778	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25227779	25227937	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25227938	25228035	1	+	2	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25227938	25228035	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25228036	25228177	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25228178	25228269	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25228178	25228269	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25228270	25228378	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25228379	25228450	0.96	+	1	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25228379	25228450	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25228451	25228560	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25228561	25228657	1	+	1	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25228561	25228657	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25228658	25228808	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25228809	25229023	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25228809	25229023	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25229024	25229166	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25229167	25229234	1	+	1	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25229167	25229234	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25229235	25229333	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25229334	25229415	1	+	2	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25229334	25229415	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25229416	25229586	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25229587	25229752	1	+	1	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25229587	25229752	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25229753	25229913	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25229914	25229961	0.97	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25229914	25229961	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25229962	25230069	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25230070	25230160	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25230070	25230160	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25230161	25230238	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25230239	25230328	1	+	2	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25230239	25230328	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25230329	25230409	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25230410	25230489	1	+	2	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25230410	25230489	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25230490	25230655	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25230656	25230768	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25230656	25230768	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25230769	25230856	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25230857	25230884	1	+	1	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25230857	25230884	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25230885	25231042	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25231043	25231216	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25231043	25231216	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25231217	25231294	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25231295	25231369	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25231295	25231369	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25231370	25231455	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25231456	25231533	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25231456	25231533	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	intron	25231534	25231612	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	CDS	25231613	25231789	1	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	exon	25231613	25231789	.	+	.	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
Phchi.S1	AUGUSTUS	stop_codon	25231790	25231792	.	+	0	transcript_id "Phchi.S1G398400.t1"; gene_id "Phchi.S1G398400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2562.t1 is derived from g9482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7398786	7406079	.	-	.	Phchi.S5G117100
Phchi.S5	AUGUSTUS	transcript	7398786	7406079	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	stop_codon	7398783	7398785	.	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7398786	7398832	1	-	2	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7398786	7398832	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7398833	7398912	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7398913	7399099	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7398913	7399099	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7399100	7399185	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7399186	7399407	0.99	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7399186	7399407	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7399408	7399521	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7399522	7399694	0.92	-	2	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7399522	7399694	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7399695	7399793	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7399794	7400004	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7399794	7400004	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7400005	7400084	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7400085	7400212	1	-	2	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7400085	7400212	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7400213	7400307	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7400308	7400398	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7400308	7400398	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7400399	7400486	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7400487	7400630	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7400487	7400630	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7400631	7400747	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7400748	7400897	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7400748	7400897	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7400898	7401044	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7401045	7401188	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7401045	7401188	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7401189	7401278	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7401279	7401398	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7401279	7401398	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7401399	7401516	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7401517	7401619	1	-	1	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7401517	7401619	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7401620	7401708	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7401709	7401785	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7401709	7401785	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7401786	7401865	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7401866	7402036	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7401866	7402036	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7402037	7402117	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7402118	7402194	0.76	-	2	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7402118	7402194	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7402195	7402308	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7402309	7402433	0.45	-	1	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7402309	7402433	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7402434	7402558	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7402559	7402729	0.71	-	1	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7402559	7402729	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7402730	7402906	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7402907	7403118	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7402907	7403118	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7403119	7403226	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7403227	7403436	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7403227	7403436	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7403437	7403528	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7403529	7403625	0.97	-	1	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7403529	7403625	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7403626	7403744	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7403745	7403917	0.92	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7403745	7403917	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7403918	7404030	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7404031	7404170	0.65	-	2	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7404031	7404170	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7404171	7404293	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7404294	7404399	0.8	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7404294	7404399	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7404400	7404492	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7404493	7404562	1	-	1	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7404493	7404562	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7404563	7404659	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7404660	7404752	1	-	1	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7404660	7404752	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7404753	7404860	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7404861	7404931	0.99	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7404861	7404931	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7404932	7405117	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7405118	7405237	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7405118	7405237	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7405238	7405362	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7405363	7405440	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7405363	7405440	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7405441	7405572	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7405573	7405637	1	-	2	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7405573	7405637	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7405638	7405725	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7405726	7405798	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7405726	7405798	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	intron	7405799	7406022	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	CDS	7406023	7406079	1	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	exon	7406023	7406079	.	-	.	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
Phchi.S5	AUGUSTUS	start_codon	7406077	7406079	.	-	0	transcript_id "Phchi.S5G117100.t1"; gene_id "Phchi.S5G117100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6973.t1 is derived from g4145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26238575	26240821	.	-	.	Phchi.S1G413200
Phchi.S1	AUGUSTUS	transcript	26238575	26240821	.	-	.	transcript_id "Phchi.S1G413200.t1"; gene_id "Phchi.S1G413200"
Phchi.S1	AUGUSTUS	stop_codon	26238572	26238574	.	-	0	transcript_id "Phchi.S1G413200.t1"; gene_id "Phchi.S1G413200"
Phchi.S1	AUGUSTUS	CDS	26238575	26240821	0.99	-	0	transcript_id "Phchi.S1G413200.t1"; gene_id "Phchi.S1G413200"
Phchi.S1	AUGUSTUS	exon	26238575	26240821	.	-	.	transcript_id "Phchi.S1G413200.t1"; gene_id "Phchi.S1G413200"
Phchi.S1	AUGUSTUS	start_codon	26240819	26240821	.	-	0	transcript_id "Phchi.S1G413200.t1"; gene_id "Phchi.S1G413200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13751.t1 is derived from g12218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8691403	8694518	.	+	.	Phchi.S3G107000
Phchi.S3	AUGUSTUS	transcript	8691403	8694518	.	+	.	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	start_codon	8691403	8691405	.	+	0	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	CDS	8691403	8691718	0.41	+	0	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	exon	8691403	8691718	.	+	.	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	intron	8691719	8691883	.	+	.	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	CDS	8691884	8692950	0.78	+	2	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	exon	8691884	8692950	.	+	.	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	intron	8692951	8693114	.	+	.	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	CDS	8693115	8694518	0.76	+	0	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	exon	8693115	8694518	.	+	.	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
Phchi.S3	AUGUSTUS	stop_codon	8694519	8694521	.	+	0	transcript_id "Phchi.S3G107000.t1"; gene_id "Phchi.S3G107000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9646.t1 is derived from g6822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43048674	43049060	.	+	.	Phchi.S1G680500
Phchi.S1	AUGUSTUS	transcript	43048674	43049060	.	+	.	transcript_id "Phchi.S1G680500.t1"; gene_id "Phchi.S1G680500"
Phchi.S1	AUGUSTUS	start_codon	43048674	43048676	.	+	0	transcript_id "Phchi.S1G680500.t1"; gene_id "Phchi.S1G680500"
Phchi.S1	AUGUSTUS	CDS	43048674	43049060	0.95	+	0	transcript_id "Phchi.S1G680500.t1"; gene_id "Phchi.S1G680500"
Phchi.S1	AUGUSTUS	exon	43048674	43049060	.	+	.	transcript_id "Phchi.S1G680500.t1"; gene_id "Phchi.S1G680500"
Phchi.S1	AUGUSTUS	stop_codon	43049061	43049063	.	+	0	transcript_id "Phchi.S1G680500.t1"; gene_id "Phchi.S1G680500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11289.t1 is derived from g15339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5236686	5237094	.	-	.	Phchi.S4G087100
Phchi.S4	AUGUSTUS	transcript	5236686	5237094	.	-	.	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	stop_codon	5236683	5236685	.	-	0	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	CDS	5236686	5236811	0.54	-	0	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	exon	5236686	5236811	.	-	.	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	intron	5236812	5236953	.	-	.	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	CDS	5236954	5237094	0.65	-	0	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	exon	5236954	5237094	.	-	.	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
Phchi.S4	AUGUSTUS	start_codon	5237092	5237094	.	-	0	transcript_id "Phchi.S4G087100.t1"; gene_id "Phchi.S4G087100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3659.t1 is derived from g828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5004702	5006018	.	-	.	Phchi.S1G081800
Phchi.S1	AUGUSTUS	transcript	5004702	5006018	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	stop_codon	5004699	5004701	.	-	0	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	CDS	5004702	5004759	0.88	-	1	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	exon	5004702	5004759	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	intron	5004760	5004907	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	CDS	5004908	5005017	0.68	-	0	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	exon	5004908	5005017	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	intron	5005018	5005219	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	CDS	5005220	5005295	0.28	-	1	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	exon	5005220	5005295	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	intron	5005296	5005371	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	CDS	5005372	5005447	0.3	-	2	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	exon	5005372	5005447	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	intron	5005448	5005768	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	CDS	5005769	5006018	0.52	-	0	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	exon	5005769	5006018	.	-	.	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
Phchi.S1	AUGUSTUS	start_codon	5006016	5006018	.	-	0	transcript_id "Phchi.S1G081800.t1"; gene_id "Phchi.S1G081800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14466.t1 is derived from g12934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13004671	13010151	.	+	.	Phchi.S3G178500
Phchi.S3	AUGUSTUS	transcript	13004671	13010151	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	start_codon	13004671	13004673	.	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13004671	13005747	0.47	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13004671	13005747	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13005748	13006163	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006164	13006253	0.99	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006164	13006253	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006254	13006369	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006370	13006414	0.79	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006370	13006414	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006415	13006609	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006610	13006664	0.87	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006610	13006664	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006665	13006767	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006768	13006811	0.87	+	2	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006768	13006811	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006812	13006922	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006923	13007184	1	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006923	13007184	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13007185	13007273	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13007274	13007488	1	+	2	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13007274	13007488	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13007489	13007595	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13007596	13007847	0.76	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13007596	13007847	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13007848	13007977	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13007978	13008017	0.76	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13007978	13008017	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008018	13008078	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008079	13008155	0.69	+	2	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008079	13008155	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008156	13008238	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008239	13008286	1	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008239	13008286	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008287	13008381	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008382	13008573	0.53	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008382	13008573	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008574	13008746	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008747	13008892	0.58	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008747	13008892	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008893	13009059	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13009060	13009516	0.65	+	1	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13009060	13009516	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13009517	13009600	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13009601	13009747	0.42	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13009601	13009747	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13009748	13009839	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13009840	13010151	0.96	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13009840	13010151	.	+	.	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	stop_codon	13010152	13010154	.	+	0	transcript_id "Phchi.S3G178500.t1"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	transcript	13004671	13010151	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	start_codon	13004671	13004673	.	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13004671	13005747	0.51	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13004671	13005747	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13005748	13006163	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006164	13006253	0.99	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006164	13006253	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006254	13006424	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006425	13006469	0.46	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006425	13006469	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006470	13006609	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006610	13006664	0.49	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006610	13006664	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006665	13006767	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006768	13006811	0.48	+	2	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006768	13006811	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13006812	13006922	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13006923	13007184	0.94	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13006923	13007184	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13007185	13007273	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13007274	13007488	0.99	+	2	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13007274	13007488	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13007489	13007595	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13007596	13007847	0.77	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13007596	13007847	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13007848	13007977	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13007978	13008017	0.77	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13007978	13008017	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008018	13008078	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008079	13008155	0.7	+	2	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008079	13008155	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008156	13008238	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008239	13008286	1	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008239	13008286	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008287	13008381	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008382	13008573	0.51	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008382	13008573	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008574	13008746	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13008747	13008892	0.56	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13008747	13008892	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13008893	13009059	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13009060	13009516	0.67	+	1	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13009060	13009516	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13009517	13009600	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13009601	13009747	0.48	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13009601	13009747	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	intron	13009748	13009839	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	CDS	13009840	13010151	0.96	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	exon	13009840	13010151	.	+	.	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
Phchi.S3	AUGUSTUS	stop_codon	13010152	13010154	.	+	0	transcript_id "Phchi.S3G178500.t2"; gene_id "Phchi.S3G178500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12777.t1 is derived from g11242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2057839	2059038	.	-	.	Phchi.S3G009600
Phchi.S3	AUGUSTUS	transcript	2057839	2059038	.	-	.	transcript_id "Phchi.S3G009600.t1"; gene_id "Phchi.S3G009600"
Phchi.S3	AUGUSTUS	stop_codon	2057836	2057838	.	-	0	transcript_id "Phchi.S3G009600.t1"; gene_id "Phchi.S3G009600"
Phchi.S3	AUGUSTUS	CDS	2057839	2059038	0.87	-	0	transcript_id "Phchi.S3G009600.t1"; gene_id "Phchi.S3G009600"
Phchi.S3	AUGUSTUS	exon	2057839	2059038	.	-	.	transcript_id "Phchi.S3G009600.t1"; gene_id "Phchi.S3G009600"
Phchi.S3	AUGUSTUS	start_codon	2059036	2059038	.	-	0	transcript_id "Phchi.S3G009600.t1"; gene_id "Phchi.S3G009600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8987.t1 is derived from g6162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38985353	38987505	.	+	.	Phchi.S1G614600
Phchi.S1	AUGUSTUS	transcript	38985353	38987505	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	start_codon	38985353	38985355	.	+	0	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	CDS	38985353	38985443	0.52	+	0	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	exon	38985353	38985443	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	intron	38985444	38985546	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	CDS	38985547	38985764	0.87	+	2	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	exon	38985547	38985764	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	intron	38985765	38985889	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	CDS	38985890	38986290	0.7	+	0	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	exon	38985890	38986290	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	intron	38986291	38986394	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	CDS	38986395	38986565	0.68	+	1	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	exon	38986395	38986565	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	intron	38986566	38986643	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	CDS	38986644	38987505	0.91	+	1	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	exon	38986644	38987505	.	+	.	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
Phchi.S1	AUGUSTUS	stop_codon	38987506	38987508	.	+	0	transcript_id "Phchi.S1G614600.t1"; gene_id "Phchi.S1G614600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9525.t1 is derived from g6701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42272213	42273931	.	-	.	Phchi.S1G668400
Phchi.S1	AUGUSTUS	transcript	42272213	42273931	.	-	.	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	stop_codon	42272210	42272212	.	-	0	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	CDS	42272213	42273290	0.99	-	1	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	exon	42272213	42273290	.	-	.	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	intron	42273291	42273377	.	-	.	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	CDS	42273378	42273643	1	-	0	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	exon	42273378	42273643	.	-	.	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	intron	42273644	42273751	.	-	.	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	CDS	42273752	42273931	0.58	-	0	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	exon	42273752	42273931	.	-	.	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
Phchi.S1	AUGUSTUS	start_codon	42273929	42273931	.	-	0	transcript_id "Phchi.S1G668400.t1"; gene_id "Phchi.S1G668400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5829.t1 is derived from g2999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19149890	19151688	.	+	.	Phchi.S1G298800
Phchi.S1	AUGUSTUS	transcript	19149890	19151688	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	start_codon	19149890	19149892	.	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19149890	19149903	0.99	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19149890	19149903	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19149904	19149988	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19149989	19150083	0.99	+	1	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19149989	19150083	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19150084	19150172	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19150173	19150204	0.99	+	2	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19150173	19150204	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19150205	19150331	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19150332	19150407	0.99	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19150332	19150407	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19150408	19150494	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19150495	19150547	0.99	+	2	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19150495	19150547	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19150548	19150639	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19150640	19150644	0.99	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19150640	19150644	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19150645	19151054	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19151055	19151217	0.61	+	1	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19151055	19151217	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19151218	19151364	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19151365	19151514	1	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19151365	19151514	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	intron	19151515	19151604	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	CDS	19151605	19151688	1	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	exon	19151605	19151688	.	+	.	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
Phchi.S1	AUGUSTUS	stop_codon	19151689	19151691	.	+	0	transcript_id "Phchi.S1G298800.t1"; gene_id "Phchi.S1G298800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7888.t1 is derived from g5062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31765370	31766907	.	+	.	Phchi.S1G504700
Phchi.S1	AUGUSTUS	transcript	31765370	31766907	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	start_codon	31765370	31765372	.	+	0	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	CDS	31765370	31765658	1	+	0	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	exon	31765370	31765658	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	intron	31765659	31765863	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	CDS	31765864	31766069	1	+	2	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	exon	31765864	31766069	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	intron	31766070	31766235	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	CDS	31766236	31766331	1	+	0	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	exon	31766236	31766331	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	intron	31766332	31766469	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	CDS	31766470	31766543	1	+	0	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	exon	31766470	31766543	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	intron	31766544	31766648	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	CDS	31766649	31766907	1	+	1	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	exon	31766649	31766907	.	+	.	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
Phchi.S1	AUGUSTUS	stop_codon	31766908	31766910	.	+	0	transcript_id "Phchi.S1G504700.t1"; gene_id "Phchi.S1G504700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12710.t1 is derived from g11175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	689914	693076	.	-	.	Phchi.S3G002900
Phchi.S3	AUGUSTUS	transcript	689914	693076	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	stop_codon	689911	689913	.	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	689914	689967	1	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	689914	689967	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	689968	690067	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690068	690196	1	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690068	690196	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690197	690277	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690278	690348	0.53	-	2	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690278	690348	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690349	690522	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690523	690550	0.61	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690523	690550	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690551	690634	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690635	690754	0.99	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690635	690754	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690755	690850	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690851	690988	1	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690851	690988	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690989	691127	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691128	691209	1	-	1	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691128	691209	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691210	691302	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691303	691415	0.97	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691303	691415	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691416	691518	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691519	691601	0.86	-	2	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691519	691601	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691602	691687	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691688	691724	0.91	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691688	691724	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691725	691965	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691966	691982	0.92	-	2	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691966	691982	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691983	692292	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692293	692423	0.68	-	1	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692293	692423	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	692424	692543	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692544	692551	0.68	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692544	692551	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	692552	692719	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692720	692942	0.52	-	1	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692720	692942	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	692943	693044	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	693045	693076	0.93	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	693045	693076	.	-	.	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	start_codon	693074	693076	.	-	0	transcript_id "Phchi.S3G002900.t1"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	transcript	689914	692978	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	stop_codon	689911	689913	.	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	689914	689967	1	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	689914	689967	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	689968	690067	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690068	690196	1	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690068	690196	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690197	690277	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690278	690348	0.54	-	2	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690278	690348	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690349	690522	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690523	690550	0.49	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690523	690550	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690551	690634	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690635	690754	0.96	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690635	690754	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690755	690850	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	690851	690988	1	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	690851	690988	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	690989	691127	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691128	691209	1	-	1	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691128	691209	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691210	691302	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691303	691415	0.95	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691303	691415	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691416	691518	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691519	691601	0.81	-	2	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691519	691601	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691602	691687	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691688	691724	0.92	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691688	691724	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691725	691965	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	691966	691982	0.95	-	2	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	691966	691982	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	691983	692292	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692293	692423	0.62	-	1	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692293	692423	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	692424	692543	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692544	692551	0.62	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692544	692551	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	692552	692719	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692720	692873	0.52	-	1	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692720	692873	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	intron	692874	692973	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	CDS	692974	692978	0.42	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	exon	692974	692978	.	-	.	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
Phchi.S3	AUGUSTUS	start_codon	692976	692978	.	-	0	transcript_id "Phchi.S3G002900.t2"; gene_id "Phchi.S3G002900"
# This transcript jg8484.t2 is derived from g5659.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8485.t1 is derived from g5660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36152891	36155716	.	+	.	Phchi.S1G564400
Phchi.S1	AUGUSTUS	transcript	36152891	36155716	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	start_codon	36152891	36152893	.	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36152891	36153001	1	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36152891	36153001	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36153002	36153197	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36153198	36153323	1	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36153198	36153323	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36153324	36153466	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36153467	36153554	1	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36153467	36153554	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36153555	36153646	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36153647	36153759	0.62	+	2	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36153647	36153759	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36153760	36153835	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36153836	36154042	1	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36153836	36154042	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36154043	36154196	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36154197	36154360	1	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36154197	36154360	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36154361	36154584	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36154585	36154743	1	+	1	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36154585	36154743	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36154744	36154843	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36154844	36154924	1	+	1	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36154844	36154924	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36154925	36155036	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36155037	36155091	1	+	1	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36155037	36155091	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36155092	36155213	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36155214	36155323	0.91	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36155214	36155323	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36155324	36155533	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36155534	36155610	0.84	+	1	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36155534	36155610	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	intron	36155611	36155705	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	CDS	36155706	36155716	0.96	+	2	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	exon	36155706	36155716	.	+	.	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
Phchi.S1	AUGUSTUS	stop_codon	36155717	36155719	.	+	0	transcript_id "Phchi.S1G564400.t1"; gene_id "Phchi.S1G564400"
# This transcript jg7093.t2 is derived from g4265.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7094.t1 is derived from g4266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26882472	26884773	.	+	.	Phchi.S1G425300
Phchi.S1	AUGUSTUS	transcript	26882472	26884773	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	start_codon	26882472	26882474	.	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26882472	26882667	0.96	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26882472	26882667	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26882668	26883221	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26883222	26883427	1	+	2	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26883222	26883427	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26883428	26883646	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26883647	26883850	1	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26883647	26883850	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26883851	26883935	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26883936	26884046	0.99	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26883936	26884046	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26884047	26884150	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26884151	26884246	1	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26884151	26884246	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26884247	26884370	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26884371	26884416	1	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26884371	26884416	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26884417	26884515	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26884516	26884594	1	+	2	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26884516	26884594	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	intron	26884595	26884757	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	CDS	26884758	26884773	1	+	1	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	exon	26884758	26884773	.	+	.	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
Phchi.S1	AUGUSTUS	stop_codon	26884774	26884776	.	+	0	transcript_id "Phchi.S1G425300.t1"; gene_id "Phchi.S1G425300"
# This transcript jg14975.t2 is derived from g13443.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14976.t1 is derived from g13444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15811528	15814131	.	-	.	Phchi.S3G229500
Phchi.S3	AUGUSTUS	transcript	15811528	15814131	.	-	.	transcript_id "Phchi.S3G229500.t1"; gene_id "Phchi.S3G229500"
Phchi.S3	AUGUSTUS	stop_codon	15811525	15811527	.	-	0	transcript_id "Phchi.S3G229500.t1"; gene_id "Phchi.S3G229500"
Phchi.S3	AUGUSTUS	CDS	15811528	15814131	0.95	-	0	transcript_id "Phchi.S3G229500.t1"; gene_id "Phchi.S3G229500"
Phchi.S3	AUGUSTUS	exon	15811528	15814131	.	-	.	transcript_id "Phchi.S3G229500.t1"; gene_id "Phchi.S3G229500"
Phchi.S3	AUGUSTUS	start_codon	15814129	15814131	.	-	0	transcript_id "Phchi.S3G229500.t1"; gene_id "Phchi.S3G229500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6957.t1 is derived from g4129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26138691	26140900	.	-	.	Phchi.S1G411600
Phchi.S1	AUGUSTUS	transcript	26138691	26140900	.	-	.	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	stop_codon	26138688	26138690	.	-	0	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	CDS	26138691	26139405	0.98	-	1	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	exon	26138691	26139405	.	-	.	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	intron	26139406	26139512	.	-	.	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	CDS	26139513	26140900	0.87	-	0	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	exon	26139513	26140900	.	-	.	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
Phchi.S1	AUGUSTUS	start_codon	26140898	26140900	.	-	0	transcript_id "Phchi.S1G411600.t1"; gene_id "Phchi.S1G411600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6369.t1 is derived from g3541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22596140	22597644	.	-	.	Phchi.S1G352800
Phchi.S1	AUGUSTUS	transcript	22596140	22597644	.	-	.	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	stop_codon	22596137	22596139	.	-	0	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	CDS	22596140	22596553	0.26	-	0	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	exon	22596140	22596553	.	-	.	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	intron	22596554	22596621	.	-	.	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	CDS	22596622	22597160	0.44	-	2	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	exon	22596622	22597160	.	-	.	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	intron	22597161	22597637	.	-	.	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	CDS	22597638	22597644	0.52	-	0	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	exon	22597638	22597644	.	-	.	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
Phchi.S1	AUGUSTUS	start_codon	22597642	22597644	.	-	0	transcript_id "Phchi.S1G352800.t1"; gene_id "Phchi.S1G352800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16015.t1 is derived from g14418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C310	AUGUSTUS	gene	4093	5660	.	+	.	Phchi.C310G000200
Phchi.C310	AUGUSTUS	transcript	4093	5660	.	+	.	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	start_codon	4093	4095	.	+	0	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	CDS	4093	4609	0.51	+	0	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	exon	4093	4609	.	+	.	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	intron	4610	4755	.	+	.	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	CDS	4756	5660	0.99	+	2	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	exon	4756	5660	.	+	.	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
Phchi.C310	AUGUSTUS	stop_codon	5661	5663	.	+	0	transcript_id "Phchi.C310G000200.t1"; gene_id "Phchi.C310G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3979.t1 is derived from g1148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6844765	6846968	.	+	.	Phchi.S1G113800
Phchi.S1	AUGUSTUS	transcript	6844765	6846968	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	start_codon	6844765	6844767	.	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6844765	6844953	0.36	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6844765	6844953	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6844954	6845064	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6845065	6845277	0.94	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6845065	6845277	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6845278	6845374	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6845375	6845672	0.99	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6845375	6845672	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6845673	6845774	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6845775	6845842	0.98	+	2	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6845775	6845842	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6845843	6845969	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6845970	6846062	1	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6845970	6846062	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6846063	6846194	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6846195	6846236	1	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6846195	6846236	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6846237	6846332	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6846333	6846545	1	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6846333	6846545	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6846546	6846674	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6846675	6846802	1	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6846675	6846802	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	intron	6846803	6846946	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	CDS	6846947	6846968	1	+	1	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	exon	6846947	6846968	.	+	.	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
Phchi.S1	AUGUSTUS	stop_codon	6846969	6846971	.	+	0	transcript_id "Phchi.S1G113800.t1"; gene_id "Phchi.S1G113800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9850.t1 is derived from g7026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44075006	44075419	.	+	.	Phchi.S1G700900
Phchi.S1	AUGUSTUS	transcript	44075006	44075419	.	+	.	transcript_id "Phchi.S1G700900.t1"; gene_id "Phchi.S1G700900"
Phchi.S1	AUGUSTUS	start_codon	44075006	44075008	.	+	0	transcript_id "Phchi.S1G700900.t1"; gene_id "Phchi.S1G700900"
Phchi.S1	AUGUSTUS	CDS	44075006	44075419	0.52	+	0	transcript_id "Phchi.S1G700900.t1"; gene_id "Phchi.S1G700900"
Phchi.S1	AUGUSTUS	exon	44075006	44075419	.	+	.	transcript_id "Phchi.S1G700900.t1"; gene_id "Phchi.S1G700900"
Phchi.S1	AUGUSTUS	stop_codon	44075420	44075422	.	+	0	transcript_id "Phchi.S1G700900.t1"; gene_id "Phchi.S1G700900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6652.t1 is derived from g3824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24298575	24300690	.	-	.	Phchi.S1G381100
Phchi.S1	AUGUSTUS	transcript	24298575	24300690	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	stop_codon	24298572	24298574	.	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24298575	24298621	0.99	-	2	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24298575	24298621	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24298622	24298710	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24298711	24298767	0.77	-	2	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24298711	24298767	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24298768	24298818	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24298819	24298852	0.99	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24298819	24298852	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24298853	24298950	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24298951	24299075	1	-	2	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24298951	24299075	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24299076	24299282	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24299283	24299346	1	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24299283	24299346	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24299347	24299432	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24299433	24299573	1	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24299433	24299573	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24299574	24299699	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24299700	24299831	0.85	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24299700	24299831	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24299832	24300031	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24300032	24300133	1	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24300032	24300133	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	intron	24300134	24300219	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	CDS	24300220	24300690	1	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	exon	24300220	24300690	.	-	.	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
Phchi.S1	AUGUSTUS	start_codon	24300688	24300690	.	-	0	transcript_id "Phchi.S1G381100.t1"; gene_id "Phchi.S1G381100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1159.t1 is derived from g10942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8092155	8093309	.	+	.	Phchi.S6G111800
Phchi.S6	AUGUSTUS	transcript	8092155	8093309	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	start_codon	8092155	8092157	.	+	0	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	CDS	8092155	8092160	0.56	+	0	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	exon	8092155	8092160	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	intron	8092161	8092308	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	CDS	8092309	8092789	0.33	+	0	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	exon	8092309	8092789	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	intron	8092790	8093116	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	CDS	8093117	8093230	0.65	+	2	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	exon	8093117	8093230	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	intron	8093231	8093307	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	CDS	8093308	8093309	0.66	+	2	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	exon	8093308	8093309	.	+	.	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
Phchi.S6	AUGUSTUS	stop_codon	8093310	8093312	.	+	0	transcript_id "Phchi.S6G111800.t1"; gene_id "Phchi.S6G111800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15910.t1 is derived from g14380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22163622	22164339	.	+	.	Phchi.S3G322900
Phchi.S3	AUGUSTUS	transcript	22163622	22164339	.	+	.	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	start_codon	22163622	22163624	.	+	0	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	CDS	22163622	22163792	1	+	0	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	exon	22163622	22163792	.	+	.	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	intron	22163793	22163871	.	+	.	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	CDS	22163872	22164339	1	+	0	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	exon	22163872	22164339	.	+	.	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	stop_codon	22164340	22164342	.	+	0	transcript_id "Phchi.S3G322900.t1"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	transcript	22163622	22164339	.	+	.	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	start_codon	22163622	22163624	.	+	0	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	CDS	22163622	22163792	0.99	+	0	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	exon	22163622	22163792	.	+	.	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	intron	22163793	22163874	.	+	.	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	CDS	22163875	22164339	0.99	+	0	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	exon	22163875	22164339	.	+	.	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
Phchi.S3	AUGUSTUS	stop_codon	22164340	22164342	.	+	0	transcript_id "Phchi.S3G322900.t2"; gene_id "Phchi.S3G322900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2508.t1 is derived from g9428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7059935	7060667	.	-	.	Phchi.S5G111700
Phchi.S5	AUGUSTUS	transcript	7059935	7060667	.	-	.	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	stop_codon	7059932	7059934	.	-	0	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	CDS	7059935	7060111	0.3	-	0	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	exon	7059935	7060111	.	-	.	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	intron	7060112	7060437	.	-	.	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	CDS	7060438	7060498	0.68	-	1	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	exon	7060438	7060498	.	-	.	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	intron	7060499	7060626	.	-	.	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	CDS	7060627	7060667	0.61	-	0	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	exon	7060627	7060667	.	-	.	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
Phchi.S5	AUGUSTUS	start_codon	7060665	7060667	.	-	0	transcript_id "Phchi.S5G111700.t1"; gene_id "Phchi.S5G111700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6269.t1 is derived from g3441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21943418	21944990	.	-	.	Phchi.S1G342800
Phchi.S1	AUGUSTUS	transcript	21943418	21944990	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	stop_codon	21943415	21943417	.	-	0	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21943418	21943474	1	-	0	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21943418	21943474	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	intron	21943475	21943563	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21943564	21943632	1	-	0	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21943564	21943632	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	intron	21943633	21943760	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21943761	21943849	1	-	2	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21943761	21943849	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	intron	21943850	21944040	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21944041	21944137	1	-	0	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21944041	21944137	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	intron	21944138	21944232	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21944233	21944386	1	-	1	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21944233	21944386	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	intron	21944387	21944546	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21944547	21944661	1	-	2	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21944547	21944661	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	intron	21944662	21944875	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	CDS	21944876	21944990	1	-	0	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	exon	21944876	21944990	.	-	.	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
Phchi.S1	AUGUSTUS	start_codon	21944988	21944990	.	-	0	transcript_id "Phchi.S1G342800.t1"; gene_id "Phchi.S1G342800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10086.t1 is derived from g7262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45668037	45669015	.	-	.	Phchi.S1G724500
Phchi.S1	AUGUSTUS	transcript	45668037	45669015	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	stop_codon	45668034	45668036	.	-	0	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	CDS	45668037	45668224	1	-	2	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	exon	45668037	45668224	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	intron	45668225	45668369	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	CDS	45668370	45668445	1	-	0	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	exon	45668370	45668445	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	intron	45668446	45668573	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	CDS	45668574	45668879	1	-	0	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	exon	45668574	45668879	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	intron	45668880	45668997	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	CDS	45668998	45669015	1	-	0	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	exon	45668998	45669015	.	-	.	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
Phchi.S1	AUGUSTUS	start_codon	45669013	45669015	.	-	0	transcript_id "Phchi.S1G724500.t1"; gene_id "Phchi.S1G724500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8743.t1 is derived from g5918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37770328	37770609	.	+	.	Phchi.S1G590200
Phchi.S1	AUGUSTUS	transcript	37770328	37770609	.	+	.	transcript_id "Phchi.S1G590200.t1"; gene_id "Phchi.S1G590200"
Phchi.S1	AUGUSTUS	start_codon	37770328	37770330	.	+	0	transcript_id "Phchi.S1G590200.t1"; gene_id "Phchi.S1G590200"
Phchi.S1	AUGUSTUS	CDS	37770328	37770609	0.46	+	0	transcript_id "Phchi.S1G590200.t1"; gene_id "Phchi.S1G590200"
Phchi.S1	AUGUSTUS	exon	37770328	37770609	.	+	.	transcript_id "Phchi.S1G590200.t1"; gene_id "Phchi.S1G590200"
Phchi.S1	AUGUSTUS	stop_codon	37770610	37770612	.	+	0	transcript_id "Phchi.S1G590200.t1"; gene_id "Phchi.S1G590200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3557.t1 is derived from g726.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4465191	4465750	.	+	.	Phchi.S1G071600
Phchi.S1	AUGUSTUS	transcript	4465191	4465638	.	+	.	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	start_codon	4465191	4465193	.	+	0	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	CDS	4465191	4465198	0.87	+	0	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	exon	4465191	4465198	.	+	.	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	intron	4465199	4465333	.	+	.	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	CDS	4465334	4465511	0.87	+	1	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	exon	4465334	4465511	.	+	.	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	intron	4465512	4465590	.	+	.	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	CDS	4465591	4465638	1	+	0	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	exon	4465591	4465638	.	+	.	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	stop_codon	4465639	4465641	.	+	0	transcript_id "Phchi.S1G071600.t1"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	transcript	4465191	4465750	.	+	.	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	start_codon	4465191	4465193	.	+	0	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	CDS	4465191	4465198	0.83	+	0	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	exon	4465191	4465198	.	+	.	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	intron	4465199	4465333	.	+	.	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	CDS	4465334	4465511	0.83	+	1	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	exon	4465334	4465511	.	+	.	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	intron	4465512	4465594	.	+	.	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	CDS	4465595	4465750	0.97	+	0	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	exon	4465595	4465750	.	+	.	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
Phchi.S1	AUGUSTUS	stop_codon	4465751	4465753	.	+	0	transcript_id "Phchi.S1G071600.t2"; gene_id "Phchi.S1G071600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7585.t1 is derived from g4759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30160952	30162836	.	+	.	Phchi.S1G474400
Phchi.S1	AUGUSTUS	transcript	30160952	30162836	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	start_codon	30160952	30160954	.	+	0	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30160952	30161184	0.98	+	0	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30160952	30161184	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30161185	30161288	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30161289	30161351	1	+	1	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30161289	30161351	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30161352	30161427	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30161428	30161544	1	+	1	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30161428	30161544	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30161545	30161725	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30161726	30162002	1	+	1	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30161726	30162002	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30162003	30162121	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30162122	30162199	0.87	+	0	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30162122	30162199	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30162200	30162258	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30162259	30162279	1	+	0	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30162259	30162279	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30162280	30162375	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30162376	30162527	1	+	0	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30162376	30162527	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	intron	30162528	30162670	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	CDS	30162671	30162836	1	+	1	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	exon	30162671	30162836	.	+	.	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
Phchi.S1	AUGUSTUS	stop_codon	30162837	30162839	.	+	0	transcript_id "Phchi.S1G474400.t1"; gene_id "Phchi.S1G474400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11047.t1 is derived from g15097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3806057	3806671	.	-	.	Phchi.S4G062900
Phchi.S4	AUGUSTUS	transcript	3806057	3806671	.	-	.	transcript_id "Phchi.S4G062900.t1"; gene_id "Phchi.S4G062900"
Phchi.S4	AUGUSTUS	stop_codon	3806054	3806056	.	-	0	transcript_id "Phchi.S4G062900.t1"; gene_id "Phchi.S4G062900"
Phchi.S4	AUGUSTUS	CDS	3806057	3806671	0.99	-	0	transcript_id "Phchi.S4G062900.t1"; gene_id "Phchi.S4G062900"
Phchi.S4	AUGUSTUS	exon	3806057	3806671	.	-	.	transcript_id "Phchi.S4G062900.t1"; gene_id "Phchi.S4G062900"
Phchi.S4	AUGUSTUS	start_codon	3806669	3806671	.	-	0	transcript_id "Phchi.S4G062900.t1"; gene_id "Phchi.S4G062900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8462.t1 is derived from g5637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36053280	36054206	.	+	.	Phchi.S1G562100
Phchi.S1	AUGUSTUS	transcript	36053280	36054206	.	+	.	transcript_id "Phchi.S1G562100.t1"; gene_id "Phchi.S1G562100"
Phchi.S1	AUGUSTUS	start_codon	36053280	36053282	.	+	0	transcript_id "Phchi.S1G562100.t1"; gene_id "Phchi.S1G562100"
Phchi.S1	AUGUSTUS	CDS	36053280	36054206	0.72	+	0	transcript_id "Phchi.S1G562100.t1"; gene_id "Phchi.S1G562100"
Phchi.S1	AUGUSTUS	exon	36053280	36054206	.	+	.	transcript_id "Phchi.S1G562100.t1"; gene_id "Phchi.S1G562100"
Phchi.S1	AUGUSTUS	stop_codon	36054207	36054209	.	+	0	transcript_id "Phchi.S1G562100.t1"; gene_id "Phchi.S1G562100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1178.t1 is derived from g10961.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8312336	8315067	.	-	.	Phchi.S6G113700
Phchi.S6	AUGUSTUS	transcript	8312336	8315067	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	stop_codon	8312333	8312335	.	-	0	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8312336	8312966	0.98	-	1	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8312336	8312966	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8312967	8313069	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313070	8313135	1	-	1	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313070	8313135	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313136	8313289	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313290	8313332	1	-	2	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313290	8313332	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313333	8313471	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313472	8313540	1	-	2	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313472	8313540	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313541	8313632	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313633	8313752	1	-	2	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313633	8313752	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313753	8313959	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313960	8313999	1	-	0	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313960	8313999	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314000	8314188	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314189	8314504	1	-	1	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314189	8314504	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314505	8314589	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314590	8314630	1	-	0	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314590	8314630	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314631	8314728	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314729	8314800	1	-	0	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314729	8314800	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314801	8314911	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314912	8315067	0.91	-	0	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314912	8315067	.	-	.	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	start_codon	8315065	8315067	.	-	0	transcript_id "Phchi.S6G113700.t1"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	transcript	8312336	8315067	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	stop_codon	8312333	8312335	.	-	0	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8312336	8312966	0.98	-	1	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8312336	8312966	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8312967	8313069	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313070	8313135	1	-	1	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313070	8313135	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313136	8313289	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313290	8313332	1	-	2	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313290	8313332	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313333	8313471	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313472	8313540	1	-	2	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313472	8313540	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313541	8313632	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313633	8313752	1	-	2	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313633	8313752	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313753	8313853	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8313854	8313929	1	-	0	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8313854	8313929	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8313930	8314188	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314189	8314504	1	-	1	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314189	8314504	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314505	8314589	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314590	8314630	1	-	0	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314590	8314630	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314631	8314728	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314729	8314800	1	-	0	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314729	8314800	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	intron	8314801	8314911	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	CDS	8314912	8315067	0.82	-	0	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	exon	8314912	8315067	.	-	.	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
Phchi.S6	AUGUSTUS	start_codon	8315065	8315067	.	-	0	transcript_id "Phchi.S6G113700.t2"; gene_id "Phchi.S6G113700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13127.t1 is derived from g11592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4261506	4262533	.	+	.	Phchi.S3G044600
Phchi.S3	AUGUSTUS	transcript	4261506	4262533	.	+	.	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	start_codon	4261506	4261508	.	+	0	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	CDS	4261506	4261654	0.59	+	0	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	exon	4261506	4261654	.	+	.	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	intron	4261655	4262183	.	+	.	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	CDS	4262184	4262342	0.99	+	1	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	exon	4262184	4262342	.	+	.	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	intron	4262343	4262493	.	+	.	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	CDS	4262494	4262533	0.99	+	1	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	exon	4262494	4262533	.	+	.	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
Phchi.S3	AUGUSTUS	stop_codon	4262534	4262536	.	+	0	transcript_id "Phchi.S3G044600.t1"; gene_id "Phchi.S3G044600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9299.t1 is derived from g6474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40830555	40831853	.	-	.	Phchi.S1G645800
Phchi.S1	AUGUSTUS	transcript	40830555	40831853	.	-	.	transcript_id "Phchi.S1G645800.t1"; gene_id "Phchi.S1G645800"
Phchi.S1	AUGUSTUS	stop_codon	40830552	40830554	.	-	0	transcript_id "Phchi.S1G645800.t1"; gene_id "Phchi.S1G645800"
Phchi.S1	AUGUSTUS	CDS	40830555	40831853	0.94	-	0	transcript_id "Phchi.S1G645800.t1"; gene_id "Phchi.S1G645800"
Phchi.S1	AUGUSTUS	exon	40830555	40831853	.	-	.	transcript_id "Phchi.S1G645800.t1"; gene_id "Phchi.S1G645800"
Phchi.S1	AUGUSTUS	start_codon	40831851	40831853	.	-	0	transcript_id "Phchi.S1G645800.t1"; gene_id "Phchi.S1G645800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4522.t1 is derived from g1692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10938374	10940470	.	+	.	Phchi.S1G168100
Phchi.S1	AUGUSTUS	transcript	10938374	10940470	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	start_codon	10938374	10938376	.	+	0	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10938374	10938542	0.68	+	0	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10938374	10938542	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10938543	10938624	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10938625	10938724	0.61	+	2	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10938625	10938724	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10938725	10938825	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10938826	10939002	0.96	+	1	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10938826	10939002	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10939003	10939100	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10939101	10939219	0.38	+	1	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10939101	10939219	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10939220	10939322	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10939323	10939505	0.8	+	2	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10939323	10939505	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10939506	10939600	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10939601	10939698	1	+	2	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10939601	10939698	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10939699	10939812	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10939813	10939885	0.85	+	0	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10939813	10939885	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10939886	10940049	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10940050	10940197	0.66	+	2	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10940050	10940197	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	intron	10940198	10940283	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	CDS	10940284	10940470	0.86	+	1	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	exon	10940284	10940470	.	+	.	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
Phchi.S1	AUGUSTUS	stop_codon	10940471	10940473	.	+	0	transcript_id "Phchi.S1G168100.t1"; gene_id "Phchi.S1G168100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12493.t1 is derived from g8170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	29336822	29337223	.	-	.	Phchi.S2G057300
Phchi.S2	AUGUSTUS	transcript	29336822	29337223	.	-	.	transcript_id "Phchi.S2G057300.t1"; gene_id "Phchi.S2G057300"
Phchi.S2	AUGUSTUS	stop_codon	29336819	29336821	.	-	0	transcript_id "Phchi.S2G057300.t1"; gene_id "Phchi.S2G057300"
Phchi.S2	AUGUSTUS	CDS	29336822	29337223	0.94	-	0	transcript_id "Phchi.S2G057300.t1"; gene_id "Phchi.S2G057300"
Phchi.S2	AUGUSTUS	exon	29336822	29337223	.	-	.	transcript_id "Phchi.S2G057300.t1"; gene_id "Phchi.S2G057300"
Phchi.S2	AUGUSTUS	start_codon	29337221	29337223	.	-	0	transcript_id "Phchi.S2G057300.t1"; gene_id "Phchi.S2G057300"
# This transcript jg8205.t2 is derived from g5380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8206.t1 is derived from g5381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34433782	34434401	.	-	.	Phchi.S1G536500
Phchi.S1	AUGUSTUS	transcript	34433782	34434401	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	stop_codon	34433779	34433781	.	-	0	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	CDS	34433782	34433851	0.95	-	1	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	exon	34433782	34433851	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	intron	34433852	34434010	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	CDS	34434011	34434015	0.92	-	0	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	exon	34434011	34434015	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	intron	34434016	34434110	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	CDS	34434111	34434165	0.92	-	1	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	exon	34434111	34434165	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	intron	34434166	34434249	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	CDS	34434250	34434401	1	-	0	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	exon	34434250	34434401	.	-	.	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
Phchi.S1	AUGUSTUS	start_codon	34434399	34434401	.	-	0	transcript_id "Phchi.S1G536500.t1"; gene_id "Phchi.S1G536500"
# This transcript jg14839.t2 is derived from g13307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14840.t1 is derived from g13308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14954276	14956587	.	+	.	Phchi.S3G215900
Phchi.S3	AUGUSTUS	transcript	14954276	14956587	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	start_codon	14954276	14954278	.	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14954276	14954422	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14954276	14954422	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14954423	14954506	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14954507	14954609	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14954507	14954609	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14954610	14954714	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14954715	14954787	1	+	2	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14954715	14954787	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14954788	14954946	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14954947	14955012	1	+	1	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14954947	14955012	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14955013	14955097	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14955098	14955182	0.95	+	1	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14955098	14955182	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14955183	14955283	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14955284	14955445	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14955284	14955445	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14955446	14955634	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14955635	14955760	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14955635	14955760	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14955761	14955843	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14955844	14955969	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14955844	14955969	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14955970	14956045	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14956046	14956225	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14956046	14956225	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	intron	14956226	14956344	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	CDS	14956345	14956587	1	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	exon	14956345	14956587	.	+	.	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
Phchi.S3	AUGUSTUS	stop_codon	14956588	14956590	.	+	0	transcript_id "Phchi.S3G215900.t1"; gene_id "Phchi.S3G215900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1153.t1 is derived from g10936.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8040289	8043276	.	+	.	Phchi.S6G111200
Phchi.S6	AUGUSTUS	transcript	8040289	8043276	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	start_codon	8040289	8040291	.	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8040289	8040307	1	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8040289	8040307	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8040308	8040710	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8040711	8040973	1	+	2	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8040711	8040973	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8040974	8041094	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8041095	8041259	0.81	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8041095	8041259	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8041260	8041462	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8041463	8041695	0.89	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8041463	8041695	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8041696	8041872	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8041873	8041913	0.94	+	1	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8041873	8041913	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8041914	8042185	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8042186	8042198	0.96	+	2	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8042186	8042198	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8042199	8042333	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8042334	8042433	0.84	+	1	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8042334	8042433	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8042434	8042606	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8042607	8042762	0.99	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8042607	8042762	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8042763	8042849	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8042850	8042999	0.73	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8042850	8042999	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8043000	8043107	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8043108	8043146	0.28	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8043108	8043146	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8043147	8043234	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8043235	8043276	0.41	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8043235	8043276	.	+	.	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	stop_codon	8043277	8043279	.	+	0	transcript_id "Phchi.S6G111200.t1"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	transcript	8040289	8043276	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	start_codon	8040289	8040291	.	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8040289	8040307	1	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8040289	8040307	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8040308	8040710	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8040711	8040973	0.99	+	2	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8040711	8040973	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8040974	8041094	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8041095	8041259	0.93	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8041095	8041259	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8041260	8041753	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8041754	8041804	0.43	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8041754	8041804	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8041805	8041895	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8041896	8041913	0.35	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8041896	8041913	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8041914	8042684	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8042685	8042762	0.89	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8042685	8042762	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8042763	8042849	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8042850	8042999	0.77	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8042850	8042999	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8043000	8043107	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8043108	8043146	0.3	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8043108	8043146	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	intron	8043147	8043234	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	CDS	8043235	8043276	0.42	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	exon	8043235	8043276	.	+	.	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
Phchi.S6	AUGUSTUS	stop_codon	8043277	8043279	.	+	0	transcript_id "Phchi.S6G111200.t2"; gene_id "Phchi.S6G111200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13670.t1 is derived from g12137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8082579	8083330	.	-	.	Phchi.S3G098900
Phchi.S3	AUGUSTUS	transcript	8082579	8083330	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	stop_codon	8082576	8082578	.	-	0	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	CDS	8082579	8082689	0.86	-	0	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	exon	8082579	8082689	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	intron	8082690	8082772	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	CDS	8082773	8082907	1	-	0	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	exon	8082773	8082907	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	intron	8082908	8083006	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	CDS	8083007	8083064	1	-	1	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	exon	8083007	8083064	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	intron	8083065	8083154	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	CDS	8083155	8083330	0.49	-	0	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	exon	8083155	8083330	.	-	.	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
Phchi.S3	AUGUSTUS	start_codon	8083328	8083330	.	-	0	transcript_id "Phchi.S3G098900.t1"; gene_id "Phchi.S3G098900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15395.t1 is derived from g13863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18816464	18817060	.	-	.	Phchi.S3G271400
Phchi.S3	AUGUSTUS	transcript	18816464	18817060	.	-	.	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	stop_codon	18816461	18816463	.	-	0	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	CDS	18816464	18816489	0.99	-	2	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	exon	18816464	18816489	.	-	.	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	intron	18816490	18816579	.	-	.	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	CDS	18816580	18817060	0.45	-	0	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	exon	18816580	18817060	.	-	.	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
Phchi.S3	AUGUSTUS	start_codon	18817058	18817060	.	-	0	transcript_id "Phchi.S3G271400.t1"; gene_id "Phchi.S3G271400"
# This transcript jg13881.t2 is derived from g12348.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13882.t1 is derived from g12349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9448620	9450892	.	-	.	Phchi.S3G120100
Phchi.S3	AUGUSTUS	transcript	9448620	9450892	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	stop_codon	9448617	9448619	.	-	0	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	CDS	9448620	9449250	0.84	-	1	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	exon	9448620	9449250	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	intron	9449251	9449393	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	CDS	9449394	9449526	0.74	-	2	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	exon	9449394	9449526	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	intron	9449527	9449598	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	CDS	9449599	9449761	0.97	-	0	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	exon	9449599	9449761	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	intron	9449762	9450040	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	CDS	9450041	9450892	0.5	-	0	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	exon	9450041	9450892	.	-	.	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
Phchi.S3	AUGUSTUS	start_codon	9450890	9450892	.	-	0	transcript_id "Phchi.S3G120100.t1"; gene_id "Phchi.S3G120100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14697.t1 is derived from g13165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14207501	14210224	.	+	.	Phchi.S3G201600
Phchi.S3	AUGUSTUS	transcript	14207501	14210224	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	start_codon	14207501	14207503	.	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14207501	14207917	0.83	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14207501	14207917	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14207918	14208017	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14208018	14208134	1	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14208018	14208134	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14208135	14208266	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14208267	14208359	1	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14208267	14208359	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14208360	14208453	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14208454	14208516	1	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14208454	14208516	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14208517	14208607	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14208608	14208706	1	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14208608	14208706	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14208707	14208781	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14208782	14208858	1	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14208782	14208858	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14208859	14209138	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14209139	14209251	1	+	1	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14209139	14209251	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14209252	14209403	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14209404	14209492	1	+	2	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14209404	14209492	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14209493	14209625	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14209626	14209703	1	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14209626	14209703	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14209704	14209861	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14209862	14209936	0.99	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14209862	14209936	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	intron	14209937	14210044	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	CDS	14210045	14210224	0.97	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	exon	14210045	14210224	.	+	.	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
Phchi.S3	AUGUSTUS	stop_codon	14210225	14210227	.	+	0	transcript_id "Phchi.S3G201600.t1"; gene_id "Phchi.S3G201600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3498.t1 is derived from g667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4102617	4104209	.	-	.	Phchi.S1G065700
Phchi.S1	AUGUSTUS	transcript	4102617	4104209	.	-	.	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	stop_codon	4102614	4102616	.	-	0	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	CDS	4102617	4102931	1	-	0	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	exon	4102617	4102931	.	-	.	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	intron	4102932	4103021	.	-	.	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	CDS	4103022	4104209	0.47	-	0	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	exon	4103022	4104209	.	-	.	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
Phchi.S1	AUGUSTUS	start_codon	4104207	4104209	.	-	0	transcript_id "Phchi.S1G065700.t1"; gene_id "Phchi.S1G065700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15368.t1 is derived from g13836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18663966	18666763	.	+	.	Phchi.S3G268700
Phchi.S3	AUGUSTUS	transcript	18663966	18666763	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	start_codon	18663966	18663968	.	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18663966	18663976	0.97	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18663966	18663976	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18663977	18664131	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18664132	18664236	0.85	+	1	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18664132	18664236	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18664237	18664418	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18664419	18664503	0.98	+	1	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18664419	18664503	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18664504	18664596	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18664597	18664674	1	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18664597	18664674	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18664675	18664804	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18664805	18664996	1	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18664805	18664996	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18664997	18665121	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18665122	18665220	1	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18665122	18665220	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18665221	18665362	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18665363	18665431	1	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18665363	18665431	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18665432	18665557	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18665558	18665773	0.98	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18665558	18665773	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18665774	18665888	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18665889	18666029	0.97	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18665889	18666029	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18666030	18666135	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18666136	18666191	1	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18666136	18666191	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18666192	18666276	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18666277	18666343	1	+	1	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18666277	18666343	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18666344	18666465	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18666466	18666570	1	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18666466	18666570	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	intron	18666571	18666646	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	CDS	18666647	18666763	0.9	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	exon	18666647	18666763	.	+	.	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
Phchi.S3	AUGUSTUS	stop_codon	18666764	18666766	.	+	0	transcript_id "Phchi.S3G268700.t1"; gene_id "Phchi.S3G268700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2305.t1 is derived from g9225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5964115	5964646	.	+	.	Phchi.S5G091400
Phchi.S5	AUGUSTUS	transcript	5964115	5964646	.	+	.	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	start_codon	5964115	5964117	.	+	0	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	CDS	5964115	5964199	0.87	+	0	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	exon	5964115	5964199	.	+	.	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	intron	5964200	5964377	.	+	.	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	CDS	5964378	5964646	1	+	2	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	exon	5964378	5964646	.	+	.	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
Phchi.S5	AUGUSTUS	stop_codon	5964647	5964649	.	+	0	transcript_id "Phchi.S5G091400.t1"; gene_id "Phchi.S5G091400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15626.t1 is derived from g14095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20367546	20368760	.	-	.	Phchi.S3G294500
Phchi.S3	AUGUSTUS	transcript	20367546	20368760	.	-	.	transcript_id "Phchi.S3G294500.t1"; gene_id "Phchi.S3G294500"
Phchi.S3	AUGUSTUS	stop_codon	20367543	20367545	.	-	0	transcript_id "Phchi.S3G294500.t1"; gene_id "Phchi.S3G294500"
Phchi.S3	AUGUSTUS	CDS	20367546	20368760	0.74	-	0	transcript_id "Phchi.S3G294500.t1"; gene_id "Phchi.S3G294500"
Phchi.S3	AUGUSTUS	exon	20367546	20368760	.	-	.	transcript_id "Phchi.S3G294500.t1"; gene_id "Phchi.S3G294500"
Phchi.S3	AUGUSTUS	start_codon	20368758	20368760	.	-	0	transcript_id "Phchi.S3G294500.t1"; gene_id "Phchi.S3G294500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15116.t1 is derived from g13584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17157009	17158886	.	-	.	Phchi.S3G243500
Phchi.S3	AUGUSTUS	transcript	17157009	17158886	.	-	.	transcript_id "Phchi.S3G243500.t1"; gene_id "Phchi.S3G243500"
Phchi.S3	AUGUSTUS	stop_codon	17157006	17157008	.	-	0	transcript_id "Phchi.S3G243500.t1"; gene_id "Phchi.S3G243500"
Phchi.S3	AUGUSTUS	CDS	17157009	17158886	1	-	0	transcript_id "Phchi.S3G243500.t1"; gene_id "Phchi.S3G243500"
Phchi.S3	AUGUSTUS	exon	17157009	17158886	.	-	.	transcript_id "Phchi.S3G243500.t1"; gene_id "Phchi.S3G243500"
Phchi.S3	AUGUSTUS	start_codon	17158884	17158886	.	-	0	transcript_id "Phchi.S3G243500.t1"; gene_id "Phchi.S3G243500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14554.t1 is derived from g13022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13450236	13450735	.	-	.	Phchi.S3G187300
Phchi.S3	AUGUSTUS	transcript	13450236	13450735	.	-	.	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	stop_codon	13450233	13450235	.	-	0	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	CDS	13450236	13450249	0.99	-	2	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	exon	13450236	13450249	.	-	.	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	intron	13450250	13450533	.	-	.	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	CDS	13450534	13450735	0.92	-	0	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	exon	13450534	13450735	.	-	.	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
Phchi.S3	AUGUSTUS	start_codon	13450733	13450735	.	-	0	transcript_id "Phchi.S3G187300.t1"; gene_id "Phchi.S3G187300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14483.t1 is derived from g12951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13061347	13063073	.	+	.	Phchi.S3G180200
Phchi.S3	AUGUSTUS	transcript	13061347	13063073	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	start_codon	13061347	13061349	.	+	0	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13061347	13061409	0.92	+	0	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13061347	13061409	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13061410	13061524	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13061525	13061582	1	+	0	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13061525	13061582	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13061583	13061819	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13061820	13061912	1	+	2	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13061820	13061912	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13061913	13062002	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13062003	13062117	1	+	2	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13062003	13062117	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13062118	13062249	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13062250	13062297	1	+	1	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13062250	13062297	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13062298	13062461	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13062462	13062507	1	+	1	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13062462	13062507	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13062508	13062586	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13062587	13062657	1	+	0	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13062587	13062657	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13062658	13062750	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13062751	13062760	0.8	+	1	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13062751	13062760	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13062761	13062813	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13062814	13062826	0.86	+	0	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13062814	13062826	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	intron	13062827	13062999	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	CDS	13063000	13063073	0.83	+	2	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	exon	13063000	13063073	.	+	.	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
Phchi.S3	AUGUSTUS	stop_codon	13063074	13063076	.	+	0	transcript_id "Phchi.S3G180200.t1"; gene_id "Phchi.S3G180200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5307.t1 is derived from g2477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16215749	16217079	.	-	.	Phchi.S1G246600
Phchi.S1	AUGUSTUS	transcript	16215749	16217079	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	stop_codon	16215746	16215748	.	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16215749	16215866	1	-	1	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16215749	16215866	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	intron	16215867	16215951	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16215952	16216037	1	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16215952	16216037	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	intron	16216038	16216124	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16216125	16216181	1	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16216125	16216181	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	intron	16216182	16216275	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16216276	16216389	0.99	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16216276	16216389	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	intron	16216390	16216490	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16216491	16216541	1	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16216491	16216541	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	intron	16216542	16216631	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16216632	16216693	0.99	-	2	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16216632	16216693	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	intron	16216694	16216832	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	CDS	16216833	16217079	0.48	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	exon	16216833	16217079	.	-	.	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
Phchi.S1	AUGUSTUS	start_codon	16217077	16217079	.	-	0	transcript_id "Phchi.S1G246600.t1"; gene_id "Phchi.S1G246600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8629.t1 is derived from g5804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37152319	37154316	.	+	.	Phchi.S1G578800
Phchi.S1	AUGUSTUS	transcript	37152319	37154316	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	start_codon	37152319	37152321	.	+	0	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37152319	37152331	1	+	0	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37152319	37152331	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37152332	37152409	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37152410	37152581	1	+	2	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37152410	37152581	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37152582	37152667	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37152668	37152777	1	+	1	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37152668	37152777	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37152778	37152894	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37152895	37153076	1	+	2	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37152895	37153076	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37153077	37153169	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37153170	37153257	1	+	0	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37153170	37153257	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37153258	37153356	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37153357	37153442	1	+	2	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37153357	37153442	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37153443	37153540	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37153541	37153655	1	+	0	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37153541	37153655	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37153656	37153735	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37153736	37153883	1	+	2	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37153736	37153883	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37153884	37154009	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37154010	37154055	1	+	1	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37154010	37154055	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	intron	37154056	37154208	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	CDS	37154209	37154316	0.9	+	0	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	exon	37154209	37154316	.	+	.	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
Phchi.S1	AUGUSTUS	stop_codon	37154317	37154319	.	+	0	transcript_id "Phchi.S1G578800.t1"; gene_id "Phchi.S1G578800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4097.t1 is derived from g1266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7802470	7808081	.	-	.	Phchi.S1G125600
Phchi.S1	AUGUSTUS	transcript	7802470	7808081	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	stop_codon	7802467	7802469	.	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7802470	7802484	0.52	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7802470	7802484	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7802485	7802572	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7802573	7802580	0.52	-	2	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7802573	7802580	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7802581	7802681	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7802682	7802700	0.52	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7802682	7802700	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7802701	7802828	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7802829	7802900	0.52	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7802829	7802900	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7802901	7803043	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7803044	7803103	0.56	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7803044	7803103	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7803104	7803237	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7803238	7803472	0.56	-	1	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7803238	7803472	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7803473	7803560	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7803561	7803701	1	-	1	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7803561	7803701	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7803702	7803780	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7803781	7804005	0.98	-	1	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7803781	7804005	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7804006	7804155	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7804156	7804489	0.84	-	2	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7804156	7804489	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7804490	7804617	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7804618	7805619	0.24	-	2	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7804618	7805619	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7805620	7805706	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7805707	7805745	0.78	-	2	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7805707	7805745	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7805746	7805877	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7805878	7806046	1	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7805878	7806046	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7806047	7806216	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7806217	7806457	1	-	1	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7806217	7806457	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7806458	7806630	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7806631	7806841	0.82	-	2	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7806631	7806841	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7806842	7806952	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7806953	7807076	0.77	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7806953	7807076	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7807077	7807189	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7807190	7807384	0.41	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7807190	7807384	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7807385	7807489	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7807490	7807711	0.43	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7807490	7807711	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	intron	7807712	7807802	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	CDS	7807803	7808081	1	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	exon	7807803	7808081	.	-	.	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
Phchi.S1	AUGUSTUS	start_codon	7808079	7808081	.	-	0	transcript_id "Phchi.S1G125600.t1"; gene_id "Phchi.S1G125600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5770.t1 is derived from g2940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18877799	18878629	.	-	.	Phchi.S1G292900
Phchi.S1	AUGUSTUS	transcript	18877799	18878629	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	stop_codon	18877796	18877798	.	-	0	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	CDS	18877799	18877807	1	-	0	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	exon	18877799	18877807	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	intron	18877808	18878012	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	CDS	18878013	18878140	0.67	-	2	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	exon	18878013	18878140	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	intron	18878141	18878332	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	CDS	18878333	18878390	0.67	-	0	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	exon	18878333	18878390	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	intron	18878391	18878485	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	CDS	18878486	18878629	1	-	0	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	exon	18878486	18878629	.	-	.	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
Phchi.S1	AUGUSTUS	start_codon	18878627	18878629	.	-	0	transcript_id "Phchi.S1G292900.t1"; gene_id "Phchi.S1G292900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12906.t1 is derived from g11371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3085924	3089147	.	+	.	Phchi.S3G022500
Phchi.S3	AUGUSTUS	transcript	3085924	3089147	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	start_codon	3085924	3085926	.	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3085924	3086057	0.89	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3085924	3086057	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3086058	3086158	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3086159	3086183	1	+	1	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3086159	3086183	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3086184	3086267	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3086268	3086376	1	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3086268	3086376	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3086377	3086523	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3086524	3086593	1	+	2	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3086524	3086593	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3086594	3086726	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3086727	3086810	1	+	1	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3086727	3086810	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3086811	3086896	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3086897	3086981	1	+	1	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3086897	3086981	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3086982	3087073	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3087074	3087166	1	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3087074	3087166	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3087167	3087299	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3087300	3087363	1	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3087300	3087363	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3087364	3087446	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3087447	3087532	1	+	2	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3087447	3087532	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3087533	3087654	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3087655	3087756	1	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3087655	3087756	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3087757	3087893	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3087894	3087977	1	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3087894	3087977	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3087978	3088127	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3088128	3088188	1	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3088128	3088188	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3088189	3088283	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3088284	3088350	1	+	2	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3088284	3088350	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3088351	3088501	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3088502	3088579	1	+	1	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3088502	3088579	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3088580	3088665	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3088666	3088730	1	+	1	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3088666	3088730	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3088731	3088813	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3088814	3088891	1	+	2	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3088814	3088891	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	intron	3088892	3088977	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	CDS	3088978	3089147	0.99	+	2	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	exon	3088978	3089147	.	+	.	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
Phchi.S3	AUGUSTUS	stop_codon	3089148	3089150	.	+	0	transcript_id "Phchi.S3G022500.t1"; gene_id "Phchi.S3G022500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4284.t1 is derived from g1453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9401568	9402164	.	-	.	Phchi.S1G144300
Phchi.S1	AUGUSTUS	transcript	9401568	9402164	.	-	.	transcript_id "Phchi.S1G144300.t1"; gene_id "Phchi.S1G144300"
Phchi.S1	AUGUSTUS	stop_codon	9401565	9401567	.	-	0	transcript_id "Phchi.S1G144300.t1"; gene_id "Phchi.S1G144300"
Phchi.S1	AUGUSTUS	CDS	9401568	9402164	0.39	-	0	transcript_id "Phchi.S1G144300.t1"; gene_id "Phchi.S1G144300"
Phchi.S1	AUGUSTUS	exon	9401568	9402164	.	-	.	transcript_id "Phchi.S1G144300.t1"; gene_id "Phchi.S1G144300"
Phchi.S1	AUGUSTUS	start_codon	9402162	9402164	.	-	0	transcript_id "Phchi.S1G144300.t1"; gene_id "Phchi.S1G144300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9803.t1 is derived from g6979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43782024	43786057	.	-	.	Phchi.S1G696200
Phchi.S1	AUGUSTUS	transcript	43782024	43786057	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	stop_codon	43782021	43782023	.	-	0	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43782024	43782780	1	-	1	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43782024	43782780	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43782781	43782939	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43782940	43783206	1	-	1	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43782940	43783206	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43783207	43783306	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43783307	43783596	1	-	0	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43783307	43783596	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43783597	43783692	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43783693	43783800	1	-	0	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43783693	43783800	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43783801	43783903	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43783904	43783989	1	-	2	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43783904	43783989	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43783990	43784245	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43784246	43784446	0.88	-	2	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43784246	43784446	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43784447	43784566	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43784567	43784804	1	-	0	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43784567	43784804	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43784805	43784891	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43784892	43785190	1	-	2	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43784892	43785190	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43785191	43785285	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43785286	43785741	1	-	2	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43785286	43785741	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	intron	43785742	43785906	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	CDS	43785907	43786057	0.51	-	0	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	exon	43785907	43786057	.	-	.	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
Phchi.S1	AUGUSTUS	start_codon	43786055	43786057	.	-	0	transcript_id "Phchi.S1G696200.t1"; gene_id "Phchi.S1G696200"
# This transcript jg12718.t2 is derived from g11183.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12718.t3 is derived from g11183.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12719.t1 is derived from g11184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1098122	1098457	.	+	.	Phchi.S3G003800
Phchi.S3	AUGUSTUS	transcript	1098122	1098457	.	+	.	transcript_id "Phchi.S3G003800.t1"; gene_id "Phchi.S3G003800"
Phchi.S3	AUGUSTUS	start_codon	1098122	1098124	.	+	0	transcript_id "Phchi.S3G003800.t1"; gene_id "Phchi.S3G003800"
Phchi.S3	AUGUSTUS	CDS	1098122	1098457	0.55	+	0	transcript_id "Phchi.S3G003800.t1"; gene_id "Phchi.S3G003800"
Phchi.S3	AUGUSTUS	exon	1098122	1098457	.	+	.	transcript_id "Phchi.S3G003800.t1"; gene_id "Phchi.S3G003800"
Phchi.S3	AUGUSTUS	stop_codon	1098458	1098460	.	+	0	transcript_id "Phchi.S3G003800.t1"; gene_id "Phchi.S3G003800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8584.t1 is derived from g5759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36739161	36741596	.	-	.	Phchi.S1G574300
Phchi.S1	AUGUSTUS	transcript	36739161	36741596	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	stop_codon	36739158	36739160	.	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739161	36739283	0.99	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739161	36739283	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739284	36739376	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739377	36739520	1	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739377	36739520	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739521	36739648	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739649	36739756	1	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739649	36739756	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739757	36739851	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739852	36739918	1	-	1	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739852	36739918	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739919	36740015	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740016	36740168	0.92	-	1	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740016	36740168	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740169	36740277	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740278	36740426	0.92	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740278	36740426	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740427	36740566	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740567	36740656	1	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740567	36740656	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740657	36740849	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740850	36741596	1	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740850	36741596	.	-	.	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	start_codon	36741594	36741596	.	-	0	transcript_id "Phchi.S1G574300.t1"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	transcript	36739161	36741596	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	stop_codon	36739158	36739160	.	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739161	36739283	0.97	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739161	36739283	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739284	36739376	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739377	36739520	1	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739377	36739520	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739521	36739648	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739649	36739756	1	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739649	36739756	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739757	36739851	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36739852	36739918	1	-	1	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36739852	36739918	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36739919	36740015	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740016	36740168	0.9	-	1	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740016	36740168	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740169	36740277	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740278	36740426	0.81	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740278	36740426	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740427	36740566	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740567	36740583	0.67	-	2	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740567	36740583	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740584	36740675	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740676	36740694	0.65	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740676	36740694	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	intron	36740695	36740849	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	CDS	36740850	36741596	1	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	exon	36740850	36741596	.	-	.	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
Phchi.S1	AUGUSTUS	start_codon	36741594	36741596	.	-	0	transcript_id "Phchi.S1G574300.t2"; gene_id "Phchi.S1G574300"
# This transcript jg3236.t2 is derived from g405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3237.t1 is derived from g406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2396599	2397112	.	+	.	Phchi.S1G039600
Phchi.S1	AUGUSTUS	transcript	2396599	2397112	.	+	.	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	start_codon	2396599	2396601	.	+	0	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	CDS	2396599	2396745	0.95	+	0	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	exon	2396599	2396745	.	+	.	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	intron	2396746	2396844	.	+	.	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	CDS	2396845	2396960	1	+	0	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	exon	2396845	2396960	.	+	.	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	intron	2396961	2397060	.	+	.	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	CDS	2397061	2397112	0.87	+	1	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	exon	2397061	2397112	.	+	.	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
Phchi.S1	AUGUSTUS	stop_codon	2397113	2397115	.	+	0	transcript_id "Phchi.S1G039600.t1"; gene_id "Phchi.S1G039600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg13243.t1 is derived from g11708.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4888899	4893383	.	+	.	Phchi.S3G056200
Phchi.S3	AUGUSTUS	transcript	4891144	4893383	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	start_codon	4891144	4891146	.	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891144	4891221	0.88	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891144	4891221	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891222	4891298	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891299	4891379	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891299	4891379	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891380	4891473	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891474	4891542	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891474	4891542	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891543	4891662	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891663	4891740	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891663	4891740	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891741	4891814	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891815	4891842	0.81	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891815	4891842	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891843	4891952	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891953	4892026	0.48	+	2	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891953	4892026	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892027	4892125	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892126	4892224	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892126	4892224	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892225	4892372	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892373	4892441	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892373	4892441	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892442	4892535	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892536	4892601	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892536	4892601	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892602	4892874	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892875	4892984	1	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892875	4892984	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892985	4893070	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4893071	4893383	1	+	1	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4893071	4893383	.	+	.	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	stop_codon	4893384	4893386	.	+	0	transcript_id "Phchi.S3G056200.t1"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	transcript	4888899	4892752	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	start_codon	4888899	4888901	.	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4888899	4888910	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4888899	4888910	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4888911	4888987	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4888988	4889033	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4888988	4889033	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889034	4889129	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889130	4889221	0.99	+	2	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889130	4889221	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889222	4889333	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889334	4889399	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889334	4889399	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889400	4889481	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889482	4889553	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889482	4889553	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889554	4889662	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889663	4889735	0.69	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889663	4889735	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889736	4889851	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889852	4889889	1	+	2	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889852	4889889	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889890	4890039	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4890040	4890156	0.99	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4890040	4890156	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4890157	4891101	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891102	4891221	0.99	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891102	4891221	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891222	4891298	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891299	4891379	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891299	4891379	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891380	4891473	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891474	4891542	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891474	4891542	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891543	4891662	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891663	4891740	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891663	4891740	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891741	4891814	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891815	4891842	0.69	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891815	4891842	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4891843	4891952	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4891953	4892026	0.36	+	2	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4891953	4892026	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892027	4892125	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892126	4892224	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892126	4892224	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892225	4892372	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892373	4892441	1	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892373	4892441	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892442	4892535	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892536	4892601	0.98	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892536	4892601	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4892602	4892713	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4892714	4892752	0.34	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4892714	4892752	.	+	.	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	stop_codon	4892753	4892755	.	+	0	transcript_id "Phchi.S3G056200.t2"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	transcript	4888899	4890476	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	start_codon	4888899	4888901	.	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4888899	4888910	1	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4888899	4888910	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4888911	4888987	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4888988	4889033	1	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4888988	4889033	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889034	4889129	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889130	4889221	1	+	2	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889130	4889221	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889222	4889333	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889334	4889399	1	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889334	4889399	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889400	4889481	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889482	4889553	1	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889482	4889553	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889554	4889662	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889663	4889735	0.73	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889663	4889735	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889736	4889851	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4889852	4889889	1	+	2	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4889852	4889889	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4889890	4890039	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4890040	4890160	0.51	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4890040	4890160	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4890161	4890261	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4890262	4890266	0.51	+	2	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4890262	4890266	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	intron	4890267	4890410	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	CDS	4890411	4890476	0.94	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	exon	4890411	4890476	.	+	.	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
Phchi.S3	AUGUSTUS	stop_codon	4890477	4890479	.	+	0	transcript_id "Phchi.S3G056200.t3"; gene_id "Phchi.S3G056200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3248.t1 is derived from g417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2509380	2510003	.	-	.	Phchi.S1G040700
Phchi.S1	AUGUSTUS	transcript	2509380	2510003	.	-	.	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	stop_codon	2509377	2509379	.	-	0	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	CDS	2509380	2509448	0.96	-	0	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	exon	2509380	2509448	.	-	.	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	intron	2509449	2509530	.	-	.	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	CDS	2509531	2509702	0.68	-	1	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	exon	2509531	2509702	.	-	.	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	intron	2509703	2509881	.	-	.	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	CDS	2509882	2510003	0.38	-	0	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	exon	2509882	2510003	.	-	.	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
Phchi.S1	AUGUSTUS	start_codon	2510001	2510003	.	-	0	transcript_id "Phchi.S1G040700.t1"; gene_id "Phchi.S1G040700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10528.t1 is derived from g14578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	839856	841405	.	+	.	Phchi.S4G011000
Phchi.S4	AUGUSTUS	transcript	839856	841405	.	+	.	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	start_codon	839856	839858	.	+	0	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	CDS	839856	841065	0.73	+	0	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	exon	839856	841065	.	+	.	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	intron	841066	841148	.	+	.	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	CDS	841149	841405	0.93	+	2	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	exon	841149	841405	.	+	.	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
Phchi.S4	AUGUSTUS	stop_codon	841406	841408	.	+	0	transcript_id "Phchi.S4G011000.t1"; gene_id "Phchi.S4G011000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg944.t1 is derived from g10726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6605125	6606144	.	+	.	Phchi.S6G090300
Phchi.S6	AUGUSTUS	transcript	6605125	6606144	.	+	.	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	start_codon	6605125	6605127	.	+	0	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	CDS	6605125	6605345	0.54	+	0	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	exon	6605125	6605345	.	+	.	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	intron	6605346	6605522	.	+	.	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	CDS	6605523	6605638	0.67	+	1	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	exon	6605523	6605638	.	+	.	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	intron	6605639	6605872	.	+	.	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	CDS	6605873	6606144	0.62	+	2	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	exon	6605873	6606144	.	+	.	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
Phchi.S6	AUGUSTUS	stop_codon	6606145	6606147	.	+	0	transcript_id "Phchi.S6G090300.t1"; gene_id "Phchi.S6G090300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3446.t1 is derived from g615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3758834	3767100	.	-	.	Phchi.S1G060500
Phchi.S1	AUGUSTUS	transcript	3758834	3767100	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	stop_codon	3758831	3758833	.	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3758834	3759618	0.47	-	2	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3758834	3759618	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3759619	3759699	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3759700	3759934	1	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3759700	3759934	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3759935	3760065	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3760066	3760117	1	-	1	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3760066	3760117	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3760118	3760251	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3760252	3760430	0.99	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3760252	3760430	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3760431	3760514	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3760515	3761826	0.99	-	1	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3760515	3761826	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3761827	3761916	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3761917	3762426	0.99	-	1	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3761917	3762426	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3762427	3762537	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3762538	3762902	0.96	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3762538	3762902	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3762903	3762990	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3762991	3763198	1	-	1	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3762991	3763198	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3763199	3763277	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3763278	3763533	0.64	-	2	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3763278	3763533	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3763534	3763650	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3763651	3763978	0.99	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3763651	3763978	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3763979	3764112	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3764113	3764207	0.83	-	2	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3764113	3764207	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3764208	3764293	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3764294	3765155	0.59	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3764294	3765155	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3765156	3765251	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3765252	3765284	0.88	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3765252	3765284	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3765285	3765374	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3765375	3765477	0.86	-	1	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3765375	3765477	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3765478	3765609	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3765610	3765638	0.76	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3765610	3765638	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3765639	3765845	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3765846	3765920	1	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3765846	3765920	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3765921	3766020	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3766021	3766142	0.97	-	2	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3766021	3766142	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3766143	3766485	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3766486	3766626	0.78	-	2	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3766486	3766626	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	intron	3766627	3766733	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	CDS	3766734	3767100	0.85	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	exon	3766734	3767100	.	-	.	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
Phchi.S1	AUGUSTUS	start_codon	3767098	3767100	.	-	0	transcript_id "Phchi.S1G060500.t1"; gene_id "Phchi.S1G060500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6257.t1 is derived from g3429.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21900038	21902058	.	-	.	Phchi.S1G341600
Phchi.S1	AUGUSTUS	transcript	21900038	21902058	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	stop_codon	21900035	21900037	.	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21900038	21900154	0.81	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21900038	21900154	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21900155	21900258	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21900259	21900279	0.8	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21900259	21900279	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21900280	21900377	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21900378	21900497	0.93	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21900378	21900497	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21900498	21900603	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21900604	21900747	0.92	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21900604	21900747	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21900748	21900848	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21900849	21900900	1	-	1	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21900849	21900900	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21900901	21901002	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21901003	21901063	1	-	2	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21901003	21901063	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21901064	21901162	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21901163	21901310	1	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21901163	21901310	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21901311	21901518	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21901519	21901564	1	-	1	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21901519	21901564	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21901565	21901695	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21901696	21901781	1	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21901696	21901781	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	intron	21901782	21902010	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	CDS	21902011	21902058	1	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	exon	21902011	21902058	.	-	.	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
Phchi.S1	AUGUSTUS	start_codon	21902056	21902058	.	-	0	transcript_id "Phchi.S1G341600.t1"; gene_id "Phchi.S1G341600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13450.t1 is derived from g11917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6778678	6782999	.	-	.	Phchi.S3G076900
Phchi.S3	AUGUSTUS	transcript	6778678	6782999	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	stop_codon	6778675	6778677	.	-	0	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6778678	6779274	1	-	0	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6778678	6779274	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6779275	6779372	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6779373	6779422	1	-	2	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6779373	6779422	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6779423	6779516	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6779517	6779585	1	-	2	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6779517	6779585	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6779586	6779711	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6779712	6779838	1	-	0	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6779712	6779838	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6779839	6779960	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6779961	6780193	0.93	-	2	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6779961	6780193	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6780194	6780295	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6780296	6780591	0.99	-	1	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6780296	6780591	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6780592	6780697	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6780698	6780766	1	-	1	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6780698	6780766	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6780767	6780859	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6780860	6780880	1	-	1	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6780860	6780880	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6780881	6781012	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6781013	6781081	1	-	1	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6781013	6781081	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6781082	6781194	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6781195	6781309	1	-	2	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6781195	6781309	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6781310	6781419	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6781420	6781664	0.98	-	1	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6781420	6781664	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6781665	6781752	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6781753	6782025	1	-	1	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6781753	6782025	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6782026	6782130	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6782131	6782402	1	-	0	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6782131	6782402	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6782403	6782488	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6782489	6782772	1	-	2	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6782489	6782772	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	intron	6782773	6782866	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	CDS	6782867	6782999	0.62	-	0	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	exon	6782867	6782999	.	-	.	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
Phchi.S3	AUGUSTUS	start_codon	6782997	6782999	.	-	0	transcript_id "Phchi.S3G076900.t1"; gene_id "Phchi.S3G076900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15442.t1 is derived from g13910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19176548	19179266	.	+	.	Phchi.S3G276100
Phchi.S3	AUGUSTUS	transcript	19176548	19179266	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	start_codon	19176548	19176550	.	+	0	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19176548	19176566	0.56	+	0	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19176548	19176566	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19176567	19176768	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19176769	19176862	0.67	+	2	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19176769	19176862	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19176863	19177036	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19177037	19177177	0.89	+	1	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19177037	19177177	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19177178	19177267	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19177268	19177317	0.21	+	1	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19177268	19177317	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19177318	19177441	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19177442	19178019	0.13	+	2	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19177442	19178019	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19178020	19178207	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19178208	19178687	0.87	+	0	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19178208	19178687	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19178688	19178776	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19178777	19178826	0.94	+	0	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19178777	19178826	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19178827	19178885	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19178886	19178927	0.95	+	1	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19178886	19178927	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	intron	19178928	19179016	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	CDS	19179017	19179266	0.54	+	1	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	exon	19179017	19179266	.	+	.	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
Phchi.S3	AUGUSTUS	stop_codon	19179267	19179269	.	+	0	transcript_id "Phchi.S3G276100.t1"; gene_id "Phchi.S3G276100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15690.t1 is derived from g14159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20672188	20674940	.	-	.	Phchi.S3G300900
Phchi.S3	AUGUSTUS	transcript	20672188	20674940	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	stop_codon	20672185	20672187	.	-	0	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20672188	20672553	1	-	0	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20672188	20672553	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20672554	20672651	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20672652	20672801	1	-	0	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20672652	20672801	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20672802	20672933	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20672934	20673087	1	-	1	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20672934	20673087	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20673088	20673171	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20673172	20673243	0.97	-	1	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20673172	20673243	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20673244	20673350	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20673351	20673402	0.98	-	2	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20673351	20673402	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20673403	20673516	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20673517	20673575	0.99	-	1	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20673517	20673575	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20673576	20673714	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20673715	20673999	1	-	1	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20673715	20673999	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20674000	20674095	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20674096	20674277	1	-	0	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20674096	20674277	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20674278	20674363	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20674364	20674542	1	-	2	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20674364	20674542	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	intron	20674543	20674735	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	CDS	20674736	20674940	1	-	0	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	exon	20674736	20674940	.	-	.	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
Phchi.S3	AUGUSTUS	start_codon	20674938	20674940	.	-	0	transcript_id "Phchi.S3G300900.t1"; gene_id "Phchi.S3G300900"
# This transcript jg13436.t2 is derived from g11903.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13437.t1 is derived from g11904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6695312	6696244	.	-	.	Phchi.S3G075600
Phchi.S3	AUGUSTUS	transcript	6695312	6696244	.	-	.	transcript_id "Phchi.S3G075600.t1"; gene_id "Phchi.S3G075600"
Phchi.S3	AUGUSTUS	stop_codon	6695309	6695311	.	-	0	transcript_id "Phchi.S3G075600.t1"; gene_id "Phchi.S3G075600"
Phchi.S3	AUGUSTUS	CDS	6695312	6696244	0.94	-	0	transcript_id "Phchi.S3G075600.t1"; gene_id "Phchi.S3G075600"
Phchi.S3	AUGUSTUS	exon	6695312	6696244	.	-	.	transcript_id "Phchi.S3G075600.t1"; gene_id "Phchi.S3G075600"
Phchi.S3	AUGUSTUS	start_codon	6696242	6696244	.	-	0	transcript_id "Phchi.S3G075600.t1"; gene_id "Phchi.S3G075600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11102.t1 is derived from g15152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4137945	4138547	.	+	.	Phchi.S4G068400
Phchi.S4	AUGUSTUS	transcript	4137945	4138547	.	+	.	transcript_id "Phchi.S4G068400.t1"; gene_id "Phchi.S4G068400"
Phchi.S4	AUGUSTUS	start_codon	4137945	4137947	.	+	0	transcript_id "Phchi.S4G068400.t1"; gene_id "Phchi.S4G068400"
Phchi.S4	AUGUSTUS	CDS	4137945	4138547	0.61	+	0	transcript_id "Phchi.S4G068400.t1"; gene_id "Phchi.S4G068400"
Phchi.S4	AUGUSTUS	exon	4137945	4138547	.	+	.	transcript_id "Phchi.S4G068400.t1"; gene_id "Phchi.S4G068400"
Phchi.S4	AUGUSTUS	stop_codon	4138548	4138550	.	+	0	transcript_id "Phchi.S4G068400.t1"; gene_id "Phchi.S4G068400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10838.t1 is derived from g14888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2393049	2394296	.	+	.	Phchi.S4G042000
Phchi.S4	AUGUSTUS	transcript	2393049	2394296	.	+	.	transcript_id "Phchi.S4G042000.t1"; gene_id "Phchi.S4G042000"
Phchi.S4	AUGUSTUS	start_codon	2393049	2393051	.	+	0	transcript_id "Phchi.S4G042000.t1"; gene_id "Phchi.S4G042000"
Phchi.S4	AUGUSTUS	CDS	2393049	2394296	1	+	0	transcript_id "Phchi.S4G042000.t1"; gene_id "Phchi.S4G042000"
Phchi.S4	AUGUSTUS	exon	2393049	2394296	.	+	.	transcript_id "Phchi.S4G042000.t1"; gene_id "Phchi.S4G042000"
Phchi.S4	AUGUSTUS	stop_codon	2394297	2394299	.	+	0	transcript_id "Phchi.S4G042000.t1"; gene_id "Phchi.S4G042000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3640.t1 is derived from g809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4905528	4907020	.	-	.	Phchi.S1G079900
Phchi.S1	AUGUSTUS	transcript	4905528	4907020	.	-	.	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	stop_codon	4905525	4905527	.	-	0	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	CDS	4905528	4905549	1	-	1	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	exon	4905528	4905549	.	-	.	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	intron	4905550	4905641	.	-	.	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	CDS	4905642	4907020	1	-	0	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	exon	4905642	4907020	.	-	.	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
Phchi.S1	AUGUSTUS	start_codon	4907018	4907020	.	-	0	transcript_id "Phchi.S1G079900.t1"; gene_id "Phchi.S1G079900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8884.t1 is derived from g6059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38480696	38483205	.	-	.	Phchi.S1G604300
Phchi.S1	AUGUSTUS	transcript	38480696	38483205	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	stop_codon	38480693	38480695	.	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38480696	38480884	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38480696	38480884	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38480885	38480978	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38480979	38481091	1	-	2	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38480979	38481091	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38481092	38481188	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38481189	38481357	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38481189	38481357	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38481358	38481449	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38481450	38481548	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38481450	38481548	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38481549	38481691	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38481692	38481733	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38481692	38481733	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38481734	38481844	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38481845	38481934	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38481845	38481934	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38481935	38482021	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38482022	38482093	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38482022	38482093	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38482094	38482229	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38482230	38482463	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38482230	38482463	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38482464	38482583	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38482584	38482597	1	-	2	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38482584	38482597	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38482598	38482707	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38482708	38482810	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38482708	38482810	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	intron	38482811	38482932	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	CDS	38482933	38483205	1	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	exon	38482933	38483205	.	-	.	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
Phchi.S1	AUGUSTUS	start_codon	38483203	38483205	.	-	0	transcript_id "Phchi.S1G604300.t1"; gene_id "Phchi.S1G604300"
# This transcript jg3952.t2 is derived from g1121.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3953.t1 is derived from g1122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6642623	6642962	.	-	.	Phchi.S1G111200
Phchi.S1	AUGUSTUS	transcript	6642623	6642962	.	-	.	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	stop_codon	6642620	6642622	.	-	0	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	CDS	6642623	6642790	1	-	0	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	exon	6642623	6642790	.	-	.	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	intron	6642791	6642884	.	-	.	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	CDS	6642885	6642962	0.99	-	0	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	exon	6642885	6642962	.	-	.	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
Phchi.S1	AUGUSTUS	start_codon	6642960	6642962	.	-	0	transcript_id "Phchi.S1G111200.t1"; gene_id "Phchi.S1G111200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3181.t1 is derived from g350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2123035	2125695	.	+	.	Phchi.S1G034000
Phchi.S1	AUGUSTUS	transcript	2123035	2125695	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	start_codon	2123035	2123037	.	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2123035	2123082	1	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2123035	2123082	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2123083	2123288	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2123289	2123765	0.99	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2123289	2123765	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2123766	2123860	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2123861	2123935	0.93	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2123861	2123935	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2123936	2124028	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2124029	2124163	1	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2124029	2124163	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2124164	2124293	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2124294	2124443	0.56	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2124294	2124443	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2124444	2124562	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2124563	2124625	0.94	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2124563	2124625	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2124626	2124714	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2124715	2124897	1	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2124715	2124897	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2124898	2124991	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2124992	2125102	1	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2124992	2125102	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2125103	2125189	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2125190	2125303	1	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2125190	2125303	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	intron	2125304	2125401	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	CDS	2125402	2125695	1	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	exon	2125402	2125695	.	+	.	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
Phchi.S1	AUGUSTUS	stop_codon	2125696	2125698	.	+	0	transcript_id "Phchi.S1G034000.t1"; gene_id "Phchi.S1G034000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2630.t1 is derived from g9550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7849469	7849738	.	+	.	Phchi.S5G123900
Phchi.S5	AUGUSTUS	transcript	7849469	7849738	.	+	.	transcript_id "Phchi.S5G123900.t1"; gene_id "Phchi.S5G123900"
Phchi.S5	AUGUSTUS	start_codon	7849469	7849471	.	+	0	transcript_id "Phchi.S5G123900.t1"; gene_id "Phchi.S5G123900"
Phchi.S5	AUGUSTUS	CDS	7849469	7849738	0.87	+	0	transcript_id "Phchi.S5G123900.t1"; gene_id "Phchi.S5G123900"
Phchi.S5	AUGUSTUS	exon	7849469	7849738	.	+	.	transcript_id "Phchi.S5G123900.t1"; gene_id "Phchi.S5G123900"
Phchi.S5	AUGUSTUS	stop_codon	7849739	7849741	.	+	0	transcript_id "Phchi.S5G123900.t1"; gene_id "Phchi.S5G123900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2771.t1 is derived from g9691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8751751	8752879	.	+	.	Phchi.S5G138000
Phchi.S5	AUGUSTUS	transcript	8751751	8752879	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	start_codon	8751751	8751753	.	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8751751	8751783	0.92	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8751751	8751783	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	intron	8751784	8751958	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8751959	8752063	0.57	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8751959	8752063	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	intron	8752064	8752159	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8752160	8752207	1	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8752160	8752207	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	intron	8752208	8752302	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8752303	8752365	1	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8752303	8752365	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	intron	8752366	8752444	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8752445	8752498	1	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8752445	8752498	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	intron	8752499	8752594	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8752595	8752681	1	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8752595	8752681	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	intron	8752682	8752756	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	CDS	8752757	8752879	0.89	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	exon	8752757	8752879	.	+	.	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
Phchi.S5	AUGUSTUS	stop_codon	8752880	8752882	.	+	0	transcript_id "Phchi.S5G138000.t1"; gene_id "Phchi.S5G138000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9791.t1 is derived from g6967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43706875	43707781	.	-	.	Phchi.S1G695000
Phchi.S1	AUGUSTUS	transcript	43706875	43707781	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	stop_codon	43706872	43706874	.	-	0	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	CDS	43706875	43707213	1	-	0	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	exon	43706875	43707213	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	intron	43707214	43707326	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	CDS	43707327	43707390	1	-	1	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	exon	43707327	43707390	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	intron	43707391	43707513	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	CDS	43707514	43707629	1	-	0	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	exon	43707514	43707629	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	intron	43707630	43707769	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	CDS	43707770	43707781	1	-	0	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	exon	43707770	43707781	.	-	.	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
Phchi.S1	AUGUSTUS	start_codon	43707779	43707781	.	-	0	transcript_id "Phchi.S1G695000.t1"; gene_id "Phchi.S1G695000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3434.t1 is derived from g603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3627145	3627822	.	+	.	Phchi.S1G059300
Phchi.S1	AUGUSTUS	transcript	3627145	3627822	.	+	.	transcript_id "Phchi.S1G059300.t1"; gene_id "Phchi.S1G059300"
Phchi.S1	AUGUSTUS	start_codon	3627145	3627147	.	+	0	transcript_id "Phchi.S1G059300.t1"; gene_id "Phchi.S1G059300"
Phchi.S1	AUGUSTUS	CDS	3627145	3627822	0.99	+	0	transcript_id "Phchi.S1G059300.t1"; gene_id "Phchi.S1G059300"
Phchi.S1	AUGUSTUS	exon	3627145	3627822	.	+	.	transcript_id "Phchi.S1G059300.t1"; gene_id "Phchi.S1G059300"
Phchi.S1	AUGUSTUS	stop_codon	3627823	3627825	.	+	0	transcript_id "Phchi.S1G059300.t1"; gene_id "Phchi.S1G059300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4242.t1 is derived from g1411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9120462	9124579	.	+	.	Phchi.S1G140100
Phchi.S1	AUGUSTUS	transcript	9120462	9124579	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	start_codon	9120462	9120464	.	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9120462	9120686	0.76	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9120462	9120686	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9120687	9120788	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9120789	9120850	1	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9120789	9120850	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9120851	9120944	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9120945	9121065	0.97	+	1	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9120945	9121065	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9121066	9121144	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9121145	9121408	0.98	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9121145	9121408	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9121409	9121556	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9121557	9121797	0.98	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9121557	9121797	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9121798	9121892	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9121893	9121969	1	+	2	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9121893	9121969	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9121970	9122067	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9122068	9122238	1	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9122068	9122238	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9122239	9122327	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9122328	9122420	1	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9122328	9122420	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9122421	9122508	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9122509	9122658	1	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9122509	9122658	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9122659	9122768	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9122769	9122855	1	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9122769	9122855	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9122856	9122952	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9122953	9123117	1	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9122953	9123117	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9123118	9123233	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9123234	9123353	0.96	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9123234	9123353	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9123354	9123485	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9123486	9123688	0.96	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9123486	9123688	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9123689	9123776	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9123777	9123926	1	+	1	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9123777	9123926	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9123927	9124019	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9124020	9124167	1	+	1	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9124020	9124167	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9124168	9124272	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9124273	9124356	0.99	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9124273	9124356	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	intron	9124357	9124462	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	CDS	9124463	9124579	0.92	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	exon	9124463	9124579	.	+	.	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
Phchi.S1	AUGUSTUS	stop_codon	9124580	9124582	.	+	0	transcript_id "Phchi.S1G140100.t1"; gene_id "Phchi.S1G140100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13423.t1 is derived from g11890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6629353	6631379	.	+	.	Phchi.S3G074200
Phchi.S3	AUGUSTUS	transcript	6629353	6631379	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	start_codon	6629353	6629355	.	+	0	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6629353	6629417	1	+	0	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6629353	6629417	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	intron	6629418	6629505	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6629506	6629665	1	+	1	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6629506	6629665	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	intron	6629666	6630022	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6630023	6630139	0.74	+	0	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6630023	6630139	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	intron	6630140	6630260	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6630261	6630425	0.62	+	0	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6630261	6630425	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	intron	6630426	6630646	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6630647	6630956	0.89	+	0	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6630647	6630956	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	intron	6630957	6631055	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6631056	6631106	0.51	+	2	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6631056	6631106	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	intron	6631107	6631209	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	CDS	6631210	6631379	0.54	+	2	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	exon	6631210	6631379	.	+	.	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
Phchi.S3	AUGUSTUS	stop_codon	6631380	6631382	.	+	0	transcript_id "Phchi.S3G074200.t1"; gene_id "Phchi.S3G074200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8139.t1 is derived from g5314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33871831	33873023	.	-	.	Phchi.S1G529800
Phchi.S1	AUGUSTUS	transcript	33871831	33873023	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	stop_codon	33871828	33871830	.	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	CDS	33871831	33871959	1	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	exon	33871831	33871959	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	intron	33871960	33872029	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	CDS	33872030	33872149	1	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	exon	33872030	33872149	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	intron	33872150	33872233	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	CDS	33872234	33872311	1	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	exon	33872234	33872311	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	intron	33872312	33872400	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	CDS	33872401	33872505	1	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	exon	33872401	33872505	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	intron	33872506	33872609	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	CDS	33872610	33872705	1	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	exon	33872610	33872705	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	intron	33872706	33872786	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	CDS	33872787	33873023	0.97	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	exon	33872787	33873023	.	-	.	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
Phchi.S1	AUGUSTUS	start_codon	33873021	33873023	.	-	0	transcript_id "Phchi.S1G529800.t1"; gene_id "Phchi.S1G529800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8724.t1 is derived from g5899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37678599	37683070	.	-	.	Phchi.S1G588300
Phchi.S1	AUGUSTUS	transcript	37678599	37683070	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	stop_codon	37678596	37678598	.	-	0	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37678599	37678904	1	-	0	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37678599	37678904	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37678905	37678995	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37678996	37679137	1	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37678996	37679137	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37679138	37679223	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37679224	37679386	1	-	2	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37679224	37679386	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37679387	37679476	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37679477	37679545	1	-	2	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37679477	37679545	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37679546	37679647	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37679648	37679774	1	-	0	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37679648	37679774	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37679775	37679858	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37679859	37680121	0.82	-	2	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37679859	37680121	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37680122	37680235	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37680236	37680459	0.82	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37680236	37680459	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37680460	37680550	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37680551	37680622	1	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37680551	37680622	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37680623	37680694	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37680695	37680763	1	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37680695	37680763	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37680764	37680928	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37680929	37680997	1	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37680929	37680997	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37680998	37681083	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37681084	37681158	1	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37681084	37681158	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37681159	37681237	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37681238	37681355	1	-	2	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37681238	37681355	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37681356	37681443	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37681444	37681682	1	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37681444	37681682	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37681683	37681769	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37681770	37682036	0.99	-	1	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37681770	37682036	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37682037	37682127	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37682128	37682420	0.99	-	0	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37682128	37682420	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37682421	37682548	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37682549	37682862	0.99	-	2	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37682549	37682862	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	intron	37682863	37682985	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	CDS	37682986	37683070	0.98	-	0	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	exon	37682986	37683070	.	-	.	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
Phchi.S1	AUGUSTUS	start_codon	37683068	37683070	.	-	0	transcript_id "Phchi.S1G588300.t1"; gene_id "Phchi.S1G588300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8105.t1 is derived from g5280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33101102	33103745	.	+	.	Phchi.S1G526400
Phchi.S1	AUGUSTUS	transcript	33101102	33103745	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	start_codon	33101102	33101104	.	+	0	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	CDS	33101102	33101414	0.37	+	0	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	exon	33101102	33101414	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	intron	33101415	33101526	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	CDS	33101527	33101554	0.37	+	2	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	exon	33101527	33101554	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	intron	33101555	33101636	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	CDS	33101637	33102336	0.35	+	1	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	exon	33101637	33102336	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	intron	33102337	33102416	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	CDS	33102417	33103745	0.97	+	0	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	exon	33102417	33103745	.	+	.	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
Phchi.S1	AUGUSTUS	stop_codon	33103746	33103748	.	+	0	transcript_id "Phchi.S1G526400.t1"; gene_id "Phchi.S1G526400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7726.t1 is derived from g4900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30837865	30840316	.	+	.	Phchi.S1G488500
Phchi.S1	AUGUSTUS	transcript	30837865	30840316	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	start_codon	30837865	30837867	.	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30837865	30837954	0.77	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30837865	30837954	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30837955	30838355	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30838356	30838427	0.99	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30838356	30838427	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30838428	30838605	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30838606	30838731	1	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30838606	30838731	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30838732	30838891	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30838892	30838990	1	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30838892	30838990	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30838991	30839127	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839128	30839200	1	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839128	30839200	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30839201	30839346	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839347	30839432	1	+	2	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839347	30839432	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30839433	30839558	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839559	30839645	1	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839559	30839645	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30839646	30839949	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839950	30840009	1	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839950	30840009	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30840010	30840130	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30840131	30840316	0.99	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30840131	30840316	.	+	.	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	stop_codon	30840317	30840319	.	+	0	transcript_id "Phchi.S1G488500.t1"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	transcript	30837865	30840316	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	start_codon	30837865	30837867	.	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30837865	30837954	0.8	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30837865	30837954	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30837955	30838608	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30838609	30838731	0.96	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30838609	30838731	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30838732	30838891	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30838892	30838990	1	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30838892	30838990	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30838991	30839127	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839128	30839200	1	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839128	30839200	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30839201	30839346	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839347	30839432	1	+	2	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839347	30839432	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30839433	30839558	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839559	30839645	1	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839559	30839645	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30839646	30839949	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30839950	30840009	1	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30839950	30840009	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	intron	30840010	30840130	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	CDS	30840131	30840316	0.98	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	exon	30840131	30840316	.	+	.	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
Phchi.S1	AUGUSTUS	stop_codon	30840317	30840319	.	+	0	transcript_id "Phchi.S1G488500.t2"; gene_id "Phchi.S1G488500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13029.t1 is derived from g11494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3745151	3745734	.	-	.	Phchi.S3G034800
Phchi.S3	AUGUSTUS	transcript	3745151	3745734	.	-	.	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	stop_codon	3745148	3745150	.	-	0	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	CDS	3745151	3745183	0.94	-	0	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	exon	3745151	3745183	.	-	.	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	intron	3745184	3745334	.	-	.	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	CDS	3745335	3745349	0.82	-	0	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	exon	3745335	3745349	.	-	.	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	intron	3745350	3745554	.	-	.	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	CDS	3745555	3745734	0.58	-	0	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	exon	3745555	3745734	.	-	.	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
Phchi.S3	AUGUSTUS	start_codon	3745732	3745734	.	-	0	transcript_id "Phchi.S3G034800.t1"; gene_id "Phchi.S3G034800"
# This transcript jg6525.t2 is derived from g3697.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6526.t1 is derived from g3698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23485308	23488884	.	+	.	Phchi.S1G368500
Phchi.S1	AUGUSTUS	transcript	23485308	23488884	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	start_codon	23485308	23485310	.	+	0	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23485308	23485385	0.78	+	0	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23485308	23485385	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23485386	23485520	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23485521	23485595	0.64	+	0	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23485521	23485595	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23485596	23485673	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23485674	23485735	0.66	+	0	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23485674	23485735	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23485736	23485934	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23485935	23487187	0.8	+	1	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23485935	23487187	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23487188	23487264	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23487265	23488363	0.82	+	2	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23487265	23488363	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23488364	23488529	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23488530	23488650	0.63	+	1	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23488530	23488650	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23488651	23488731	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23488732	23488748	0.64	+	0	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23488732	23488748	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	intron	23488749	23488883	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	CDS	23488884	23488884	0.64	+	1	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	exon	23488884	23488884	.	+	.	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
Phchi.S1	AUGUSTUS	stop_codon	23488885	23488887	.	+	0	transcript_id "Phchi.S1G368500.t1"; gene_id "Phchi.S1G368500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1167.t1 is derived from g10950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8236898	8237899	.	-	.	Phchi.S6G112600
Phchi.S6	AUGUSTUS	transcript	8236898	8237899	.	-	.	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	stop_codon	8236895	8236897	.	-	0	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	CDS	8236898	8237273	0.42	-	1	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	exon	8236898	8237273	.	-	.	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	intron	8237274	8237539	.	-	.	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	CDS	8237540	8237567	0.82	-	2	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	exon	8237540	8237567	.	-	.	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	intron	8237568	8237835	.	-	.	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	CDS	8237836	8237899	0.37	-	0	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	exon	8237836	8237899	.	-	.	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
Phchi.S6	AUGUSTUS	start_codon	8237897	8237899	.	-	0	transcript_id "Phchi.S6G112600.t1"; gene_id "Phchi.S6G112600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7643.t1 is derived from g4817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30378105	30380140	.	-	.	Phchi.S1G480200
Phchi.S1	AUGUSTUS	transcript	30378105	30380140	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	stop_codon	30378102	30378104	.	-	0	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30378105	30378126	1	-	1	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30378105	30378126	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30378127	30378209	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30378210	30378321	1	-	2	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30378210	30378321	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30378322	30378469	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30378470	30378644	1	-	0	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30378470	30378644	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30378645	30378724	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30378725	30378772	0.85	-	0	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30378725	30378772	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30378773	30378873	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30378874	30379187	0.4	-	2	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30378874	30379187	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30379188	30379302	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30379303	30379331	0.5	-	1	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30379303	30379331	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30379332	30379574	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30379575	30379645	1	-	0	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30379575	30379645	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30379646	30379729	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30379730	30379842	0.74	-	2	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30379730	30379842	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	intron	30379843	30379923	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	CDS	30379924	30380140	0.62	-	0	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	exon	30379924	30380140	.	-	.	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
Phchi.S1	AUGUSTUS	start_codon	30380138	30380140	.	-	0	transcript_id "Phchi.S1G480200.t1"; gene_id "Phchi.S1G480200"
# This transcript jg12607.t2 is derived from g8284.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12607.t3 is derived from g8284.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12608.t1 is derived from g8285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37560197	37560966	.	-	.	Phchi.S2G068800
Phchi.S2	AUGUSTUS	transcript	37560197	37560966	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	stop_codon	37560194	37560196	.	-	0	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	CDS	37560197	37560327	0.86	-	2	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	exon	37560197	37560327	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	intron	37560328	37560557	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	CDS	37560558	37560634	0.9	-	1	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	exon	37560558	37560634	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	intron	37560635	37560713	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	CDS	37560714	37560812	0.67	-	1	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	exon	37560714	37560812	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	intron	37560813	37560889	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	CDS	37560890	37560966	0.79	-	0	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	exon	37560890	37560966	.	-	.	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
Phchi.S2	AUGUSTUS	start_codon	37560964	37560966	.	-	0	transcript_id "Phchi.S2G068800.t1"; gene_id "Phchi.S2G068800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13165.t1 is derived from g11630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4454601	4457230	.	-	.	Phchi.S3G048400
Phchi.S3	AUGUSTUS	transcript	4454601	4457230	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	stop_codon	4454598	4454600	.	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4454601	4455157	0.94	-	2	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4454601	4455157	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4455158	4455279	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4455280	4455337	0.98	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4455280	4455337	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4455338	4455445	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4455446	4455564	0.99	-	2	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4455446	4455564	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4455565	4455692	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4455693	4455912	1	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4455693	4455912	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4455913	4456043	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4456044	4456070	1	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4456044	4456070	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4456071	4456135	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4456136	4456161	0.64	-	2	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4456136	4456161	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4456162	4456311	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4456312	4456392	1	-	2	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4456312	4456392	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4456393	4456514	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4456515	4456566	1	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4456515	4456566	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	intron	4456567	4457110	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	CDS	4457111	4457230	1	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	exon	4457111	4457230	.	-	.	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
Phchi.S3	AUGUSTUS	start_codon	4457228	4457230	.	-	0	transcript_id "Phchi.S3G048400.t1"; gene_id "Phchi.S3G048400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10211.t1 is derived from g7387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46394522	46395775	.	+	.	Phchi.S1G737000
Phchi.S1	AUGUSTUS	transcript	46394522	46395775	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	start_codon	46394522	46394524	.	+	0	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	CDS	46394522	46394716	0.4	+	0	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	exon	46394522	46394716	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	intron	46394717	46394797	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	CDS	46394798	46394977	1	+	0	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	exon	46394798	46394977	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	intron	46394978	46395068	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	CDS	46395069	46395234	1	+	0	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	exon	46395069	46395234	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	intron	46395235	46395365	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	CDS	46395366	46395775	1	+	2	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	exon	46395366	46395775	.	+	.	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
Phchi.S1	AUGUSTUS	stop_codon	46395776	46395778	.	+	0	transcript_id "Phchi.S1G737000.t1"; gene_id "Phchi.S1G737000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg637.t1 is derived from g10419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4536914	4539293	.	-	.	Phchi.S6G059600
Phchi.S6	AUGUSTUS	transcript	4536914	4539293	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	stop_codon	4536911	4536913	.	-	0	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	CDS	4536914	4537276	0.96	-	0	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	exon	4536914	4537276	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	intron	4537277	4537370	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	CDS	4537371	4537571	1	-	0	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	exon	4537371	4537571	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	intron	4537572	4537670	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	CDS	4537671	4537943	1	-	0	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	exon	4537671	4537943	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	intron	4537944	4538039	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	CDS	4538040	4538275	1	-	2	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	exon	4538040	4538275	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	intron	4538276	4538380	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	CDS	4538381	4539293	0.94	-	0	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	exon	4538381	4539293	.	-	.	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
Phchi.S6	AUGUSTUS	start_codon	4539291	4539293	.	-	0	transcript_id "Phchi.S6G059600.t1"; gene_id "Phchi.S6G059600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13457.t1 is derived from g11924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6983017	6983670	.	+	.	Phchi.S3G077600
Phchi.S3	AUGUSTUS	transcript	6983017	6983670	.	+	.	transcript_id "Phchi.S3G077600.t1"; gene_id "Phchi.S3G077600"
Phchi.S3	AUGUSTUS	start_codon	6983017	6983019	.	+	0	transcript_id "Phchi.S3G077600.t1"; gene_id "Phchi.S3G077600"
Phchi.S3	AUGUSTUS	CDS	6983017	6983670	0.88	+	0	transcript_id "Phchi.S3G077600.t1"; gene_id "Phchi.S3G077600"
Phchi.S3	AUGUSTUS	exon	6983017	6983670	.	+	.	transcript_id "Phchi.S3G077600.t1"; gene_id "Phchi.S3G077600"
Phchi.S3	AUGUSTUS	stop_codon	6983671	6983673	.	+	0	transcript_id "Phchi.S3G077600.t1"; gene_id "Phchi.S3G077600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1376.t1 is derived from g11135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C13	AUGUSTUS	gene	61121	61567	.	+	.	Phchi.C13G000300
Phchi.C13	AUGUSTUS	transcript	61121	61567	.	+	.	transcript_id "Phchi.C13G000300.t1"; gene_id "Phchi.C13G000300"
Phchi.C13	AUGUSTUS	start_codon	61121	61123	.	+	0	transcript_id "Phchi.C13G000300.t1"; gene_id "Phchi.C13G000300"
Phchi.C13	AUGUSTUS	CDS	61121	61567	0.57	+	0	transcript_id "Phchi.C13G000300.t1"; gene_id "Phchi.C13G000300"
Phchi.C13	AUGUSTUS	exon	61121	61567	.	+	.	transcript_id "Phchi.C13G000300.t1"; gene_id "Phchi.C13G000300"
Phchi.C13	AUGUSTUS	stop_codon	61568	61570	.	+	0	transcript_id "Phchi.C13G000300.t1"; gene_id "Phchi.C13G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg739.t1 is derived from g10521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5258167	5259542	.	-	.	Phchi.S6G069800
Phchi.S6	AUGUSTUS	transcript	5258167	5259542	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	stop_codon	5258164	5258166	.	-	0	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	CDS	5258167	5258508	1	-	0	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	exon	5258167	5258508	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	intron	5258509	5258596	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	CDS	5258597	5258705	1	-	1	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	exon	5258597	5258705	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	intron	5258706	5258791	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	CDS	5258792	5258964	1	-	0	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	exon	5258792	5258964	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	intron	5258965	5259051	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	CDS	5259052	5259255	1	-	0	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	exon	5259052	5259255	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	intron	5259256	5259335	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	CDS	5259336	5259542	0.61	-	0	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	exon	5259336	5259542	.	-	.	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
Phchi.S6	AUGUSTUS	start_codon	5259540	5259542	.	-	0	transcript_id "Phchi.S6G069800.t1"; gene_id "Phchi.S6G069800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3475.t1 is derived from g644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3969868	3970263	.	-	.	Phchi.S1G063400
Phchi.S1	AUGUSTUS	transcript	3969868	3970263	.	-	.	transcript_id "Phchi.S1G063400.t1"; gene_id "Phchi.S1G063400"
Phchi.S1	AUGUSTUS	stop_codon	3969865	3969867	.	-	0	transcript_id "Phchi.S1G063400.t1"; gene_id "Phchi.S1G063400"
Phchi.S1	AUGUSTUS	CDS	3969868	3970263	0.8	-	0	transcript_id "Phchi.S1G063400.t1"; gene_id "Phchi.S1G063400"
Phchi.S1	AUGUSTUS	exon	3969868	3970263	.	-	.	transcript_id "Phchi.S1G063400.t1"; gene_id "Phchi.S1G063400"
Phchi.S1	AUGUSTUS	start_codon	3970261	3970263	.	-	0	transcript_id "Phchi.S1G063400.t1"; gene_id "Phchi.S1G063400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13948.t1 is derived from g12415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9859371	9861314	.	-	.	Phchi.S3G126700
Phchi.S3	AUGUSTUS	transcript	9859371	9861314	.	-	.	transcript_id "Phchi.S3G126700.t1"; gene_id "Phchi.S3G126700"
Phchi.S3	AUGUSTUS	stop_codon	9859368	9859370	.	-	0	transcript_id "Phchi.S3G126700.t1"; gene_id "Phchi.S3G126700"
Phchi.S3	AUGUSTUS	CDS	9859371	9861314	0.97	-	0	transcript_id "Phchi.S3G126700.t1"; gene_id "Phchi.S3G126700"
Phchi.S3	AUGUSTUS	exon	9859371	9861314	.	-	.	transcript_id "Phchi.S3G126700.t1"; gene_id "Phchi.S3G126700"
Phchi.S3	AUGUSTUS	start_codon	9861312	9861314	.	-	0	transcript_id "Phchi.S3G126700.t1"; gene_id "Phchi.S3G126700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg340.t1 is derived from g10122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2479677	2480933	.	+	.	Phchi.S6G029900
Phchi.S6	AUGUSTUS	transcript	2479677	2480933	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	start_codon	2479677	2479679	.	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2479677	2479746	1	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2479677	2479746	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	intron	2479747	2479831	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2479832	2479956	1	+	2	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2479832	2479956	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	intron	2479957	2480088	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2480089	2480185	1	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2480089	2480185	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	intron	2480186	2480299	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2480300	2480409	1	+	2	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2480300	2480409	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	intron	2480410	2480574	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2480575	2480649	1	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2480575	2480649	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	intron	2480650	2480741	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2480742	2480771	1	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2480742	2480771	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	intron	2480772	2480864	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	CDS	2480865	2480933	1	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	exon	2480865	2480933	.	+	.	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
Phchi.S6	AUGUSTUS	stop_codon	2480934	2480936	.	+	0	transcript_id "Phchi.S6G029900.t1"; gene_id "Phchi.S6G029900"
# This transcript jg3712.t2 is derived from g881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3712.t3 is derived from g881.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3713.t1 is derived from g882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5319826	5341531	.	-	.	Phchi.S1G087200
Phchi.S1	AUGUSTUS	transcript	5319826	5341531	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	stop_codon	5319823	5319825	.	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5319826	5320134	0.59	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5319826	5320134	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5320135	5320265	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5320266	5320377	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5320266	5320377	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5320378	5320455	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5320456	5320514	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5320456	5320514	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5320515	5320622	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5320623	5320943	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5320623	5320943	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5320944	5321045	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5321046	5321360	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5321046	5321360	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5321361	5321479	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5321480	5321638	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5321480	5321638	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5321639	5321714	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5321715	5321927	0.45	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5321715	5321927	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5321928	5322176	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5322177	5322398	0.99	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5322177	5322398	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5322399	5322530	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5322531	5322657	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5322531	5322657	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5322658	5322883	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5322884	5323026	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5322884	5323026	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5323027	5323134	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5323135	5323315	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5323135	5323315	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5323316	5323435	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5323436	5323975	0.98	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5323436	5323975	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5323976	5324080	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5324081	5324265	0.31	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5324081	5324265	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5324266	5324367	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5324368	5324523	0.27	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5324368	5324523	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5324524	5324633	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5324634	5324723	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5324634	5324723	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5324724	5324875	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5324876	5325323	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5324876	5325323	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5325324	5325422	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5325423	5325499	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5325423	5325499	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5325500	5325606	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5325607	5326066	0.5	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5325607	5326066	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5326067	5326365	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5326366	5326398	0.72	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5326366	5326398	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5326399	5326485	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5326486	5326549	0.47	-	2	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5326486	5326549	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5326550	5326781	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5326782	5326992	0.44	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5326782	5326992	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5326993	5327138	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5327139	5327305	1	-	2	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5327139	5327305	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5327306	5327386	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5327387	5327441	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5327387	5327441	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5327442	5327571	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5327572	5327778	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5327572	5327778	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5327779	5327853	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5327854	5328123	0.98	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5327854	5328123	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5328124	5328202	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5328203	5328383	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5328203	5328383	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5328384	5328545	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5328546	5328709	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5328546	5328709	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5328710	5328801	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5328802	5328960	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5328802	5328960	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5328961	5329068	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5329069	5329384	0.97	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5329069	5329384	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5329385	5329480	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5329481	5329757	0.47	-	2	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5329481	5329757	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5329758	5329834	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5329835	5329884	0.53	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5329835	5329884	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5329885	5329962	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5329963	5330277	0.81	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5329963	5330277	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5330278	5330385	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5330386	5330470	1	-	2	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5330386	5330470	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5330471	5330614	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5330615	5330910	0.95	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5330615	5330910	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5330911	5331009	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5331010	5331113	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5331010	5331113	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5331114	5331313	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5331314	5331529	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5331314	5331529	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5331530	5331673	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5331674	5332324	0.97	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5331674	5332324	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5332325	5332407	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5332408	5332716	0.99	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5332408	5332716	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5332717	5332854	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5332855	5332998	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5332855	5332998	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5332999	5333103	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5333104	5333212	0.99	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5333104	5333212	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5333213	5333407	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5333408	5333592	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5333408	5333592	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5333593	5333797	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5333798	5333911	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5333798	5333911	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5333912	5333992	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5333993	5334124	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5333993	5334124	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5334125	5334286	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5334287	5334616	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5334287	5334616	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5334617	5334751	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5334752	5335270	0.85	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5334752	5335270	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5335271	5335345	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5335346	5335417	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5335346	5335417	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5335418	5335583	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5335584	5335724	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5335584	5335724	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5335725	5335844	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5335845	5335943	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5335845	5335943	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5335944	5336031	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5336032	5336128	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5336032	5336128	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5336129	5336329	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5336330	5336364	0.97	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5336330	5336364	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5336365	5336445	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5336446	5336673	0.97	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5336446	5336673	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5336674	5336760	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5336761	5336991	0.98	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5336761	5336991	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5336992	5337103	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5337104	5337224	1	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5337104	5337224	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5337225	5337354	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5337355	5337422	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5337355	5337422	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5337423	5337537	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5337538	5337633	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5337538	5337633	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5337634	5337718	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5337719	5337832	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5337719	5337832	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5337833	5338023	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5338024	5338363	0.66	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5338024	5338363	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5338364	5338692	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5338693	5338851	0.64	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5338693	5338851	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5338852	5338964	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5338965	5339029	0.36	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5338965	5339029	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5339030	5339247	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5339248	5339448	0.62	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5339248	5339448	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5339449	5339576	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5339577	5339678	0.86	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5339577	5339678	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5339679	5339806	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5339807	5339924	0.9	-	1	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5339807	5339924	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5339925	5340013	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5340014	5340117	0.99	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5340014	5340117	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5340118	5340207	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5340208	5340264	1	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5340208	5340264	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5340265	5340472	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5340473	5340520	0.6	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5340473	5340520	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5340521	5340661	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5340662	5340757	0.68	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5340662	5340757	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5340758	5340900	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5340901	5341004	0.5	-	2	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5340901	5341004	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5341005	5341132	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5341133	5341214	0.78	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5341133	5341214	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	intron	5341215	5341516	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	CDS	5341517	5341531	0.51	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	exon	5341517	5341531	.	-	.	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
Phchi.S1	AUGUSTUS	start_codon	5341529	5341531	.	-	0	transcript_id "Phchi.S1G087200.t1"; gene_id "Phchi.S1G087200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3113.t1 is derived from g282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1777744	1778610	.	+	.	Phchi.S1G027200
Phchi.S1	AUGUSTUS	transcript	1777744	1778610	.	+	.	transcript_id "Phchi.S1G027200.t1"; gene_id "Phchi.S1G027200"
Phchi.S1	AUGUSTUS	start_codon	1777744	1777746	.	+	0	transcript_id "Phchi.S1G027200.t1"; gene_id "Phchi.S1G027200"
Phchi.S1	AUGUSTUS	CDS	1777744	1778610	1	+	0	transcript_id "Phchi.S1G027200.t1"; gene_id "Phchi.S1G027200"
Phchi.S1	AUGUSTUS	exon	1777744	1778610	.	+	.	transcript_id "Phchi.S1G027200.t1"; gene_id "Phchi.S1G027200"
Phchi.S1	AUGUSTUS	stop_codon	1778611	1778613	.	+	0	transcript_id "Phchi.S1G027200.t1"; gene_id "Phchi.S1G027200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13539.t1 is derived from g12006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7423505	7425038	.	+	.	Phchi.S3G085800
Phchi.S3	AUGUSTUS	transcript	7423505	7425038	.	+	.	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	start_codon	7423505	7423507	.	+	0	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	CDS	7423505	7424075	0.61	+	0	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	exon	7423505	7424075	.	+	.	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	intron	7424076	7424232	.	+	.	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	CDS	7424233	7424362	0.61	+	2	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	exon	7424233	7424362	.	+	.	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	intron	7424363	7424476	.	+	.	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	CDS	7424477	7425038	0.52	+	1	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	exon	7424477	7425038	.	+	.	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
Phchi.S3	AUGUSTUS	stop_codon	7425039	7425041	.	+	0	transcript_id "Phchi.S3G085800.t1"; gene_id "Phchi.S3G085800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15128.t1 is derived from g13596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17194911	17196668	.	-	.	Phchi.S3G244700
Phchi.S3	AUGUSTUS	transcript	17194911	17196668	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	stop_codon	17194908	17194910	.	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17194911	17195072	1	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17194911	17195072	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	intron	17195073	17195150	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17195151	17195248	1	-	2	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17195151	17195248	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	intron	17195249	17195362	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17195363	17195429	0.95	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17195363	17195429	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	intron	17195430	17195502	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17195503	17195631	0.67	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17195503	17195631	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	intron	17195632	17195738	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17195739	17195882	0.88	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17195739	17195882	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	intron	17195883	17195972	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17195973	17196146	0.98	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17195973	17196146	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	intron	17196147	17196347	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	CDS	17196348	17196668	0.76	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	exon	17196348	17196668	.	-	.	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
Phchi.S3	AUGUSTUS	start_codon	17196666	17196668	.	-	0	transcript_id "Phchi.S3G244700.t1"; gene_id "Phchi.S3G244700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11164.t1 is derived from g15214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4437828	4438715	.	-	.	Phchi.S4G074600
Phchi.S4	AUGUSTUS	transcript	4437828	4438715	.	-	.	transcript_id "Phchi.S4G074600.t1"; gene_id "Phchi.S4G074600"
Phchi.S4	AUGUSTUS	stop_codon	4437825	4437827	.	-	0	transcript_id "Phchi.S4G074600.t1"; gene_id "Phchi.S4G074600"
Phchi.S4	AUGUSTUS	CDS	4437828	4438715	0.94	-	0	transcript_id "Phchi.S4G074600.t1"; gene_id "Phchi.S4G074600"
Phchi.S4	AUGUSTUS	exon	4437828	4438715	.	-	.	transcript_id "Phchi.S4G074600.t1"; gene_id "Phchi.S4G074600"
Phchi.S4	AUGUSTUS	start_codon	4438713	4438715	.	-	0	transcript_id "Phchi.S4G074600.t1"; gene_id "Phchi.S4G074600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg205.t1 is derived from g9987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1139669	1140132	.	-	.	Phchi.S6G016400
Phchi.S6	AUGUSTUS	transcript	1139669	1140132	.	-	.	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	stop_codon	1139666	1139668	.	-	0	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	CDS	1139669	1139881	0.95	-	0	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	exon	1139669	1139881	.	-	.	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	intron	1139882	1140114	.	-	.	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	CDS	1140115	1140132	0.94	-	0	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	exon	1140115	1140132	.	-	.	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
Phchi.S6	AUGUSTUS	start_codon	1140130	1140132	.	-	0	transcript_id "Phchi.S6G016400.t1"; gene_id "Phchi.S6G016400"
# This transcript jg3414.t2 is derived from g583.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3415.t1 is derived from g584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3388944	3392633	.	-	.	Phchi.S1G057400
Phchi.S1	AUGUSTUS	transcript	3388944	3392633	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	stop_codon	3388941	3388943	.	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3388944	3389284	1	-	2	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3388944	3389284	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3389285	3389425	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3389426	3389436	1	-	1	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3389426	3389436	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3389437	3389513	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3389514	3389564	1	-	1	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3389514	3389564	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3389565	3389754	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3389755	3389790	0.93	-	1	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3389755	3389790	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3389791	3389961	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3389962	3390041	1	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3389962	3390041	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3390042	3390191	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3390192	3390410	1	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3390192	3390410	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3390411	3390543	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3390544	3390771	1	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3390544	3390771	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3390772	3390891	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3390892	3391035	1	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3390892	3391035	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3391036	3391145	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3391146	3391261	0.99	-	2	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3391146	3391261	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3391262	3391386	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3391387	3391733	1	-	1	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3391387	3391733	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3391734	3391851	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3391852	3391997	1	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3391852	3391997	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3391998	3392215	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3392216	3392371	1	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3392216	3392371	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	intron	3392372	3392462	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	CDS	3392463	3392633	0.39	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	exon	3392463	3392633	.	-	.	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
Phchi.S1	AUGUSTUS	start_codon	3392631	3392633	.	-	0	transcript_id "Phchi.S1G057400.t1"; gene_id "Phchi.S1G057400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13660.t1 is derived from g12127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8046509	8048206	.	+	.	Phchi.S3G097900
Phchi.S3	AUGUSTUS	transcript	8046509	8048206	.	+	.	transcript_id "Phchi.S3G097900.t1"; gene_id "Phchi.S3G097900"
Phchi.S3	AUGUSTUS	start_codon	8046509	8046511	.	+	0	transcript_id "Phchi.S3G097900.t1"; gene_id "Phchi.S3G097900"
Phchi.S3	AUGUSTUS	CDS	8046509	8048206	0.87	+	0	transcript_id "Phchi.S3G097900.t1"; gene_id "Phchi.S3G097900"
Phchi.S3	AUGUSTUS	exon	8046509	8048206	.	+	.	transcript_id "Phchi.S3G097900.t1"; gene_id "Phchi.S3G097900"
Phchi.S3	AUGUSTUS	stop_codon	8048207	8048209	.	+	0	transcript_id "Phchi.S3G097900.t1"; gene_id "Phchi.S3G097900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4716.t1 is derived from g1886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12439782	12444247	.	-	.	Phchi.S1G187500
Phchi.S1	AUGUSTUS	transcript	12439782	12444247	.	-	.	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	stop_codon	12439779	12439781	.	-	0	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	CDS	12439782	12442927	0.29	-	2	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	exon	12439782	12442927	.	-	.	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	intron	12442928	12443088	.	-	.	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	CDS	12443089	12444247	0.23	-	0	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	exon	12443089	12444247	.	-	.	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
Phchi.S1	AUGUSTUS	start_codon	12444245	12444247	.	-	0	transcript_id "Phchi.S1G187500.t1"; gene_id "Phchi.S1G187500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8356.t1 is derived from g5531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35475196	35477930	.	+	.	Phchi.S1G551500
Phchi.S1	AUGUSTUS	transcript	35475196	35477930	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	start_codon	35475196	35475198	.	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35475196	35475198	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35475196	35475198	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35475199	35475292	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35475293	35475409	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35475293	35475409	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35475410	35475491	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35475492	35475638	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35475492	35475638	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35475639	35475726	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35475727	35475822	0.5	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35475727	35475822	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35475823	35475995	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35475996	35476096	0.5	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35475996	35476096	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35476097	35476234	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35476235	35476481	0.9	+	1	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35476235	35476481	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35476482	35476783	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35476784	35476833	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35476784	35476833	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35476834	35476984	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35476985	35477045	1	+	1	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35476985	35477045	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35477046	35477180	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35477181	35477216	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35477181	35477216	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35477217	35477331	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35477332	35477382	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35477332	35477382	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35477383	35477481	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35477482	35477574	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35477482	35477574	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35477575	35477665	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35477666	35477769	1	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35477666	35477769	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	intron	35477770	35477902	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	CDS	35477903	35477930	1	+	1	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	exon	35477903	35477930	.	+	.	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
Phchi.S1	AUGUSTUS	stop_codon	35477931	35477933	.	+	0	transcript_id "Phchi.S1G551500.t1"; gene_id "Phchi.S1G551500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6772.t1 is derived from g3944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25006541	25007284	.	+	.	Phchi.S1G393100
Phchi.S1	AUGUSTUS	transcript	25006541	25007284	.	+	.	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	start_codon	25006541	25006543	.	+	0	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	CDS	25006541	25006874	0.5	+	0	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	exon	25006541	25006874	.	+	.	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	intron	25006875	25007095	.	+	.	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	CDS	25007096	25007139	0.51	+	2	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	exon	25007096	25007139	.	+	.	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	intron	25007140	25007278	.	+	.	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	CDS	25007279	25007284	0.94	+	0	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	exon	25007279	25007284	.	+	.	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
Phchi.S1	AUGUSTUS	stop_codon	25007285	25007287	.	+	0	transcript_id "Phchi.S1G393100.t1"; gene_id "Phchi.S1G393100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5349.t1 is derived from g2519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16427932	16428524	.	-	.	Phchi.S1G250800
Phchi.S1	AUGUSTUS	transcript	16427932	16428524	.	-	.	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	stop_codon	16427929	16427931	.	-	0	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	CDS	16427932	16428108	1	-	0	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	exon	16427932	16428108	.	-	.	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	intron	16428109	16428221	.	-	.	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	CDS	16428222	16428295	1	-	2	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	exon	16428222	16428295	.	-	.	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	intron	16428296	16428430	.	-	.	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	CDS	16428431	16428524	0.91	-	0	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	exon	16428431	16428524	.	-	.	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
Phchi.S1	AUGUSTUS	start_codon	16428522	16428524	.	-	0	transcript_id "Phchi.S1G250800.t1"; gene_id "Phchi.S1G250800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14663.t1 is derived from g13131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14011586	14015417	.	+	.	Phchi.S3G198200
Phchi.S3	AUGUSTUS	transcript	14011586	14015417	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	start_codon	14011586	14011588	.	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14011586	14011909	0.91	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14011586	14011909	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14011910	14012040	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14012041	14012134	0.99	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14012041	14012134	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14012135	14012304	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14012305	14012497	0.95	+	2	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14012305	14012497	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14012498	14012610	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14012611	14012845	0.92	+	1	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14012611	14012845	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14012846	14012985	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14012986	14013171	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14012986	14013171	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14013172	14013288	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14013289	14013375	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14013289	14013375	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14013376	14013498	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14013499	14013633	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14013499	14013633	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14013634	14013720	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14013721	14013837	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14013721	14013837	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14013838	14014010	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14014011	14014258	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14014011	14014258	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14014259	14014337	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14014338	14014415	1	+	1	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14014338	14014415	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14014416	14014513	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14014514	14014745	1	+	1	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14014514	14014745	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14014746	14014827	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14014828	14014926	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14014828	14014926	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14014927	14015021	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14015022	14015207	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14015022	14015207	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	intron	14015208	14015327	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	CDS	14015328	14015417	1	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	exon	14015328	14015417	.	+	.	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
Phchi.S3	AUGUSTUS	stop_codon	14015418	14015420	.	+	0	transcript_id "Phchi.S3G198200.t1"; gene_id "Phchi.S3G198200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13416.t1 is derived from g11882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6599943	6602216	.	-	.	Phchi.S3G073500
Phchi.S3	AUGUSTUS	transcript	6599943	6602216	.	-	.	transcript_id "Phchi.S3G073500.t1"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	stop_codon	6599940	6599942	.	-	0	transcript_id "Phchi.S3G073500.t1"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	CDS	6599943	6602216	1	-	0	transcript_id "Phchi.S3G073500.t1"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	exon	6599943	6602216	.	-	.	transcript_id "Phchi.S3G073500.t1"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	start_codon	6602214	6602216	.	-	0	transcript_id "Phchi.S3G073500.t1"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	transcript	6599943	6600815	.	-	.	transcript_id "Phchi.S3G073500.t2"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	stop_codon	6599940	6599942	.	-	0	transcript_id "Phchi.S3G073500.t2"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	CDS	6599943	6600815	0.99	-	0	transcript_id "Phchi.S3G073500.t2"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	exon	6599943	6600815	.	-	.	transcript_id "Phchi.S3G073500.t2"; gene_id "Phchi.S3G073500"
Phchi.S3	AUGUSTUS	start_codon	6600813	6600815	.	-	0	transcript_id "Phchi.S3G073500.t2"; gene_id "Phchi.S3G073500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6292.t1 is derived from g3464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22108435	22109871	.	+	.	Phchi.S1G345100
Phchi.S1	AUGUSTUS	transcript	22108435	22109871	.	+	.	transcript_id "Phchi.S1G345100.t1"; gene_id "Phchi.S1G345100"
Phchi.S1	AUGUSTUS	start_codon	22108435	22108437	.	+	0	transcript_id "Phchi.S1G345100.t1"; gene_id "Phchi.S1G345100"
Phchi.S1	AUGUSTUS	CDS	22108435	22109871	0.54	+	0	transcript_id "Phchi.S1G345100.t1"; gene_id "Phchi.S1G345100"
Phchi.S1	AUGUSTUS	exon	22108435	22109871	.	+	.	transcript_id "Phchi.S1G345100.t1"; gene_id "Phchi.S1G345100"
Phchi.S1	AUGUSTUS	stop_codon	22109872	22109874	.	+	0	transcript_id "Phchi.S1G345100.t1"; gene_id "Phchi.S1G345100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13229.t1 is derived from g11694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4789846	4790844	.	+	.	Phchi.S3G054800
Phchi.S3	AUGUSTUS	transcript	4789846	4790844	.	+	.	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	start_codon	4789846	4789848	.	+	0	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	CDS	4789846	4789922	0.97	+	0	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	exon	4789846	4789922	.	+	.	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	intron	4789923	4790087	.	+	.	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	CDS	4790088	4790844	1	+	1	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	exon	4790088	4790844	.	+	.	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
Phchi.S3	AUGUSTUS	stop_codon	4790845	4790847	.	+	0	transcript_id "Phchi.S3G054800.t1"; gene_id "Phchi.S3G054800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10739.t1 is derived from g14789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1865263	1865870	.	-	.	Phchi.S4G032100
Phchi.S4	AUGUSTUS	transcript	1865263	1865870	.	-	.	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	stop_codon	1865260	1865262	.	-	0	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	CDS	1865263	1865582	1	-	2	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	exon	1865263	1865582	.	-	.	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	intron	1865583	1865677	.	-	.	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	CDS	1865678	1865870	0.92	-	0	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	exon	1865678	1865870	.	-	.	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
Phchi.S4	AUGUSTUS	start_codon	1865868	1865870	.	-	0	transcript_id "Phchi.S4G032100.t1"; gene_id "Phchi.S4G032100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13324.t1 is derived from g11790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6101697	6103055	.	+	.	Phchi.S3G064300
Phchi.S3	AUGUSTUS	transcript	6101697	6103055	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	start_codon	6101697	6101699	.	+	0	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	CDS	6101697	6101876	1	+	0	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	exon	6101697	6101876	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	intron	6101877	6101981	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	CDS	6101982	6102122	1	+	0	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	exon	6101982	6102122	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	intron	6102123	6102260	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	CDS	6102261	6102489	1	+	0	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	exon	6102261	6102489	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	intron	6102490	6102605	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	CDS	6102606	6102809	1	+	2	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	exon	6102606	6102809	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	intron	6102810	6102894	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	CDS	6102895	6103055	1	+	2	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	exon	6102895	6103055	.	+	.	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
Phchi.S3	AUGUSTUS	stop_codon	6103056	6103058	.	+	0	transcript_id "Phchi.S3G064300.t1"; gene_id "Phchi.S3G064300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2005.t1 is derived from g8925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4411757	4412716	.	-	.	Phchi.S5G061400
Phchi.S5	AUGUSTUS	transcript	4411757	4412716	.	-	.	transcript_id "Phchi.S5G061400.t1"; gene_id "Phchi.S5G061400"
Phchi.S5	AUGUSTUS	stop_codon	4411754	4411756	.	-	0	transcript_id "Phchi.S5G061400.t1"; gene_id "Phchi.S5G061400"
Phchi.S5	AUGUSTUS	CDS	4411757	4412716	0.88	-	0	transcript_id "Phchi.S5G061400.t1"; gene_id "Phchi.S5G061400"
Phchi.S5	AUGUSTUS	exon	4411757	4412716	.	-	.	transcript_id "Phchi.S5G061400.t1"; gene_id "Phchi.S5G061400"
Phchi.S5	AUGUSTUS	start_codon	4412714	4412716	.	-	0	transcript_id "Phchi.S5G061400.t1"; gene_id "Phchi.S5G061400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13092.t1 is derived from g11557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4110769	4113386	.	+	.	Phchi.S3G041100
Phchi.S3	AUGUSTUS	transcript	4110769	4113386	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	start_codon	4110769	4110771	.	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4110769	4110985	0.97	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4110769	4110985	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4110986	4111091	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4111092	4111207	0.97	+	2	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4111092	4111207	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4111208	4111301	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4111302	4111466	1	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4111302	4111466	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4111467	4111566	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4111567	4111733	1	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4111567	4111733	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4111734	4111829	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4111830	4112051	1	+	1	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4111830	4112051	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4112052	4112141	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4112142	4112304	1	+	1	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4112142	4112304	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4112305	4112446	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4112447	4112686	1	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4112447	4112686	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4112687	4112799	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4112800	4112949	0.99	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4112800	4112949	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4112950	4113032	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4113033	4113162	1	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4113033	4113162	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	intron	4113163	4113243	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	CDS	4113244	4113386	0.99	+	2	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	exon	4113244	4113386	.	+	.	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
Phchi.S3	AUGUSTUS	stop_codon	4113387	4113389	.	+	0	transcript_id "Phchi.S3G041100.t1"; gene_id "Phchi.S3G041100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10393.t1 is derived from g7569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47520473	47521042	.	+	.	Phchi.S1G755200
Phchi.S1	AUGUSTUS	transcript	47520473	47521042	.	+	.	transcript_id "Phchi.S1G755200.t1"; gene_id "Phchi.S1G755200"
Phchi.S1	AUGUSTUS	start_codon	47520473	47520475	.	+	0	transcript_id "Phchi.S1G755200.t1"; gene_id "Phchi.S1G755200"
Phchi.S1	AUGUSTUS	CDS	47520473	47521042	0.94	+	0	transcript_id "Phchi.S1G755200.t1"; gene_id "Phchi.S1G755200"
Phchi.S1	AUGUSTUS	exon	47520473	47521042	.	+	.	transcript_id "Phchi.S1G755200.t1"; gene_id "Phchi.S1G755200"
Phchi.S1	AUGUSTUS	stop_codon	47521043	47521045	.	+	0	transcript_id "Phchi.S1G755200.t1"; gene_id "Phchi.S1G755200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2725.t1 is derived from g9645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8452413	8455422	.	+	.	Phchi.S5G133400
Phchi.S5	AUGUSTUS	transcript	8452413	8455422	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	start_codon	8452413	8452415	.	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8452413	8452611	0.48	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8452413	8452611	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8452612	8452695	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8452696	8452785	1	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8452696	8452785	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8452786	8452869	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8452870	8453004	0.29	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8452870	8453004	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8453005	8453194	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8453195	8453323	0.29	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8453195	8453323	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8453324	8453419	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8453420	8453500	1	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8453420	8453500	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8453501	8453597	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8453598	8453792	1	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8453598	8453792	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8453793	8453936	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8453937	8454023	1	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8453937	8454023	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8454024	8454133	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8454134	8454309	1	+	2	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8454134	8454309	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8454310	8454401	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8454402	8454527	1	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8454402	8454527	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8454528	8454614	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8454615	8454761	0.95	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8454615	8454761	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8454762	8454870	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8454871	8454998	1	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8454871	8454998	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8454999	8455096	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8455097	8455217	1	+	1	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8455097	8455217	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	intron	8455218	8455329	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	CDS	8455330	8455422	1	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	exon	8455330	8455422	.	+	.	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
Phchi.S5	AUGUSTUS	stop_codon	8455423	8455425	.	+	0	transcript_id "Phchi.S5G133400.t1"; gene_id "Phchi.S5G133400"
# This transcript jg12750.t2 is derived from g11215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12751.t1 is derived from g11216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1887161	1889753	.	+	.	Phchi.S3G007000
Phchi.S3	AUGUSTUS	transcript	1887161	1889753	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	start_codon	1887161	1887163	.	+	0	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1887161	1888118	0.52	+	0	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1887161	1888118	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	intron	1888119	1888214	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1888215	1888447	1	+	2	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1888215	1888447	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	intron	1888448	1888538	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1888539	1888665	1	+	0	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1888539	1888665	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	intron	1888666	1888759	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1888760	1888828	1	+	2	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1888760	1888828	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	intron	1888829	1888958	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1888959	1889148	1	+	2	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1888959	1889148	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	intron	1889149	1889250	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1889251	1889374	1	+	1	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1889251	1889374	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	intron	1889375	1889462	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	CDS	1889463	1889753	1	+	0	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	exon	1889463	1889753	.	+	.	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
Phchi.S3	AUGUSTUS	stop_codon	1889754	1889756	.	+	0	transcript_id "Phchi.S3G007000.t1"; gene_id "Phchi.S3G007000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2546.t1 is derived from g9466.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7267733	7269886	.	+	.	Phchi.S5G115500
Phchi.S5	AUGUSTUS	transcript	7269353	7269886	.	+	.	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	start_codon	7269353	7269355	.	+	0	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7269353	7269434	0.46	+	0	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7269353	7269434	.	+	.	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	intron	7269435	7269515	.	+	.	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7269516	7269886	0.95	+	2	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7269516	7269886	.	+	.	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	stop_codon	7269887	7269889	.	+	0	transcript_id "Phchi.S5G115500.t1"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	transcript	7267733	7269886	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	start_codon	7267733	7267735	.	+	0	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7267733	7268432	0.61	+	0	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7267733	7268432	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	intron	7268433	7268523	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7268524	7268856	0.46	+	2	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7268524	7268856	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	intron	7268857	7268958	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7268959	7269191	0.92	+	2	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7268959	7269191	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	intron	7269192	7269283	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7269284	7269434	1	+	0	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7269284	7269434	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	intron	7269435	7269515	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	CDS	7269516	7269886	0.9	+	2	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	exon	7269516	7269886	.	+	.	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
Phchi.S5	AUGUSTUS	stop_codon	7269887	7269889	.	+	0	transcript_id "Phchi.S5G115500.t2"; gene_id "Phchi.S5G115500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10644.t1 is derived from g14694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1394988	1397214	.	-	.	Phchi.S4G022600
Phchi.S4	AUGUSTUS	transcript	1394988	1397214	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	stop_codon	1394985	1394987	.	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1394988	1395158	0.97	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1394988	1395158	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1395159	1395442	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1395443	1395598	1	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1395443	1395598	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1395599	1395679	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1395680	1395763	1	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1395680	1395763	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1395764	1395918	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1395919	1396008	1	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1395919	1396008	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1396009	1396144	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1396145	1396182	1	-	2	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1396145	1396182	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1396183	1396328	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1396329	1396481	1	-	2	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1396329	1396481	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1396482	1396583	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1396584	1396689	0.96	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1396584	1396689	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1396690	1396780	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1396781	1396891	1	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1396781	1396891	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	intron	1396892	1397040	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	CDS	1397041	1397214	0.56	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	exon	1397041	1397214	.	-	.	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
Phchi.S4	AUGUSTUS	start_codon	1397212	1397214	.	-	0	transcript_id "Phchi.S4G022600.t1"; gene_id "Phchi.S4G022600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2780.t1 is derived from g9700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8844505	8845026	.	-	.	Phchi.S5G138900
Phchi.S5	AUGUSTUS	transcript	8844505	8845026	.	-	.	transcript_id "Phchi.S5G138900.t1"; gene_id "Phchi.S5G138900"
Phchi.S5	AUGUSTUS	stop_codon	8844502	8844504	.	-	0	transcript_id "Phchi.S5G138900.t1"; gene_id "Phchi.S5G138900"
Phchi.S5	AUGUSTUS	CDS	8844505	8845026	0.95	-	0	transcript_id "Phchi.S5G138900.t1"; gene_id "Phchi.S5G138900"
Phchi.S5	AUGUSTUS	exon	8844505	8845026	.	-	.	transcript_id "Phchi.S5G138900.t1"; gene_id "Phchi.S5G138900"
Phchi.S5	AUGUSTUS	start_codon	8845024	8845026	.	-	0	transcript_id "Phchi.S5G138900.t1"; gene_id "Phchi.S5G138900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1753.t1 is derived from g8673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2887174	2887971	.	+	.	Phchi.S5G036200
Phchi.S5	AUGUSTUS	transcript	2887174	2887971	.	+	.	transcript_id "Phchi.S5G036200.t1"; gene_id "Phchi.S5G036200"
Phchi.S5	AUGUSTUS	start_codon	2887174	2887176	.	+	0	transcript_id "Phchi.S5G036200.t1"; gene_id "Phchi.S5G036200"
Phchi.S5	AUGUSTUS	CDS	2887174	2887971	1	+	0	transcript_id "Phchi.S5G036200.t1"; gene_id "Phchi.S5G036200"
Phchi.S5	AUGUSTUS	exon	2887174	2887971	.	+	.	transcript_id "Phchi.S5G036200.t1"; gene_id "Phchi.S5G036200"
Phchi.S5	AUGUSTUS	stop_codon	2887972	2887974	.	+	0	transcript_id "Phchi.S5G036200.t1"; gene_id "Phchi.S5G036200"
# This transcript jg12748.t2 is derived from g11213.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12749.t1 is derived from g11214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1881817	1882781	.	+	.	Phchi.S3G006800
Phchi.S3	AUGUSTUS	transcript	1881817	1882781	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	start_codon	1881817	1881819	.	+	0	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	CDS	1881817	1881820	0.94	+	0	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	exon	1881817	1881820	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	intron	1881821	1881906	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	CDS	1881907	1881918	0.92	+	2	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	exon	1881907	1881918	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	intron	1881919	1882007	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	CDS	1882008	1882019	0.94	+	2	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	exon	1882008	1882019	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	intron	1882020	1882111	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	CDS	1882112	1882170	1	+	2	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	exon	1882112	1882170	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	intron	1882171	1882530	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	CDS	1882531	1882643	0.97	+	0	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	exon	1882531	1882643	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	intron	1882644	1882735	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	CDS	1882736	1882781	0.97	+	1	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	exon	1882736	1882781	.	+	.	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
Phchi.S3	AUGUSTUS	stop_codon	1882782	1882784	.	+	0	transcript_id "Phchi.S3G006800.t1"; gene_id "Phchi.S3G006800"
# This transcript jg8394.t2 is derived from g5569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8395.t1 is derived from g5570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35694542	35699363	.	-	.	Phchi.S1G555400
Phchi.S1	AUGUSTUS	transcript	35694542	35699363	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	stop_codon	35694539	35694541	.	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35694542	35694801	0.98	-	2	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35694542	35694801	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35694802	35694924	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35694925	35694985	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35694925	35694985	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35694986	35695077	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35695078	35695128	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35695078	35695128	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35695129	35695200	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35695201	35695272	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35695201	35695272	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35695273	35695369	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35695370	35695403	1	-	1	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35695370	35695403	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35695404	35695538	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35695539	35695624	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35695539	35695624	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35695625	35695724	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35695725	35695812	1	-	1	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35695725	35695812	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35695813	35695955	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35695956	35696059	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35695956	35696059	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35696060	35696208	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35696209	35696265	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35696209	35696265	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35696266	35696356	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35696357	35696436	1	-	2	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35696357	35696436	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35696437	35696534	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35696535	35696634	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35696535	35696634	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35696635	35696716	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35696717	35696775	1	-	2	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35696717	35696775	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35696776	35696945	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35696946	35697012	0.99	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35696946	35697012	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35697013	35697120	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35697121	35697198	0.99	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35697121	35697198	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35697199	35697296	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35697297	35697404	0.99	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35697297	35697404	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35697405	35697509	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35697510	35697554	0.99	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35697510	35697554	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35697555	35697952	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35697953	35698016	1	-	1	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35697953	35698016	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35698017	35698141	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35698142	35698215	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35698142	35698215	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35698216	35698312	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35698313	35698366	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35698313	35698366	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35698367	35698495	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35698496	35698693	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35698496	35698693	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35698694	35698943	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35698944	35698982	1	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35698944	35698982	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35698983	35699071	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35699072	35699177	0.96	-	1	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35699072	35699177	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	intron	35699178	35699280	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	CDS	35699281	35699363	0.97	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	exon	35699281	35699363	.	-	.	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
Phchi.S1	AUGUSTUS	start_codon	35699361	35699363	.	-	0	transcript_id "Phchi.S1G555400.t1"; gene_id "Phchi.S1G555400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15464.t1 is derived from g13932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19328270	19328941	.	-	.	Phchi.S3G278300
Phchi.S3	AUGUSTUS	transcript	19328270	19328941	.	-	.	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	stop_codon	19328267	19328269	.	-	0	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	CDS	19328270	19328455	0.62	-	0	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	exon	19328270	19328455	.	-	.	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	intron	19328456	19328674	.	-	.	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	CDS	19328675	19328941	0.65	-	0	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	exon	19328675	19328941	.	-	.	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
Phchi.S3	AUGUSTUS	start_codon	19328939	19328941	.	-	0	transcript_id "Phchi.S3G278300.t1"; gene_id "Phchi.S3G278300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5474.t1 is derived from g2644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17002091	17002654	.	-	.	Phchi.S1G263300
Phchi.S1	AUGUSTUS	transcript	17002091	17002654	.	-	.	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	stop_codon	17002088	17002090	.	-	0	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	CDS	17002091	17002173	0.69	-	2	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	exon	17002091	17002173	.	-	.	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	intron	17002174	17002497	.	-	.	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	CDS	17002498	17002654	0.52	-	0	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	exon	17002498	17002654	.	-	.	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
Phchi.S1	AUGUSTUS	start_codon	17002652	17002654	.	-	0	transcript_id "Phchi.S1G263300.t1"; gene_id "Phchi.S1G263300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4490.t1 is derived from g1660.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10780249	10783113	.	-	.	Phchi.S1G164900
Phchi.S1	AUGUSTUS	transcript	10780249	10783113	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	stop_codon	10780246	10780248	.	-	0	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	CDS	10780249	10781692	0.93	-	1	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	exon	10780249	10781692	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	intron	10781693	10781888	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	CDS	10781889	10782231	0.88	-	2	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	exon	10781889	10782231	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	intron	10782232	10782380	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	CDS	10782381	10782646	0.95	-	1	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	exon	10782381	10782646	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	intron	10782647	10782852	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	CDS	10782853	10782888	0.62	-	1	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	exon	10782853	10782888	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	intron	10782889	10783009	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	CDS	10783010	10783113	0.84	-	0	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	exon	10783010	10783113	.	-	.	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	start_codon	10783111	10783113	.	-	0	transcript_id "Phchi.S1G164900.t1"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	transcript	10780249	10781523	.	-	.	transcript_id "Phchi.S1G164900.t2"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	stop_codon	10780246	10780248	.	-	0	transcript_id "Phchi.S1G164900.t2"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	CDS	10780249	10781523	0.98	-	0	transcript_id "Phchi.S1G164900.t2"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	exon	10780249	10781523	.	-	.	transcript_id "Phchi.S1G164900.t2"; gene_id "Phchi.S1G164900"
Phchi.S1	AUGUSTUS	start_codon	10781521	10781523	.	-	0	transcript_id "Phchi.S1G164900.t2"; gene_id "Phchi.S1G164900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4238.t1 is derived from g1407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9061813	9062652	.	-	.	Phchi.S1G139700
Phchi.S1	AUGUSTUS	transcript	9061813	9062652	.	-	.	transcript_id "Phchi.S1G139700.t1"; gene_id "Phchi.S1G139700"
Phchi.S1	AUGUSTUS	stop_codon	9061810	9061812	.	-	0	transcript_id "Phchi.S1G139700.t1"; gene_id "Phchi.S1G139700"
Phchi.S1	AUGUSTUS	CDS	9061813	9062652	0.99	-	0	transcript_id "Phchi.S1G139700.t1"; gene_id "Phchi.S1G139700"
Phchi.S1	AUGUSTUS	exon	9061813	9062652	.	-	.	transcript_id "Phchi.S1G139700.t1"; gene_id "Phchi.S1G139700"
Phchi.S1	AUGUSTUS	start_codon	9062650	9062652	.	-	0	transcript_id "Phchi.S1G139700.t1"; gene_id "Phchi.S1G139700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3792.t1 is derived from g961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5765557	5766810	.	+	.	Phchi.S1G095100
Phchi.S1	AUGUSTUS	transcript	5765557	5766810	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	start_codon	5765557	5765559	.	+	0	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	CDS	5765557	5765621	0.63	+	0	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	exon	5765557	5765621	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	intron	5765622	5765698	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	CDS	5765699	5765737	0.84	+	1	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	exon	5765699	5765737	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	intron	5765738	5765832	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	CDS	5765833	5765990	0.19	+	1	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	exon	5765833	5765990	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	intron	5765991	5766064	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	CDS	5766065	5766810	0.21	+	2	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	exon	5766065	5766810	.	+	.	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
Phchi.S1	AUGUSTUS	stop_codon	5766811	5766813	.	+	0	transcript_id "Phchi.S1G095100.t1"; gene_id "Phchi.S1G095100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8790.t1 is derived from g5965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37969711	37971208	.	+	.	Phchi.S1G594900
Phchi.S1	AUGUSTUS	transcript	37969711	37971208	.	+	.	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	start_codon	37969711	37969713	.	+	0	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	CDS	37969711	37969863	1	+	0	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	exon	37969711	37969863	.	+	.	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	intron	37969864	37969961	.	+	.	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	CDS	37969962	37970786	0.67	+	0	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	exon	37969962	37970786	.	+	.	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	intron	37970787	37970872	.	+	.	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	CDS	37970873	37971208	1	+	0	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	exon	37970873	37971208	.	+	.	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
Phchi.S1	AUGUSTUS	stop_codon	37971209	37971211	.	+	0	transcript_id "Phchi.S1G594900.t1"; gene_id "Phchi.S1G594900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12479.t1 is derived from g8156.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28134825	28137968	.	-	.	Phchi.S2G055900
Phchi.S2	AUGUSTUS	transcript	28134825	28137968	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	stop_codon	28134822	28134824	.	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28134825	28134989	0.99	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28134825	28134989	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28134990	28135110	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135111	28135346	1	-	2	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135111	28135346	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135347	28135522	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135523	28135631	1	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135523	28135631	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135632	28135788	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135789	28135932	1	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135789	28135932	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135933	28136117	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136118	28136186	1	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136118	28136186	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136187	28136303	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136304	28136381	1	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136304	28136381	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136382	28136590	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136591	28136783	1	-	1	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136591	28136783	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136784	28136910	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136911	28136994	1	-	1	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136911	28136994	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136995	28137247	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137248	28137408	1	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137248	28137408	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137409	28137669	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137670	28137842	1	-	2	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137670	28137842	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137843	28137910	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137911	28137968	0.69	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137911	28137968	.	-	.	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	start_codon	28137966	28137968	.	-	0	transcript_id "Phchi.S2G055900.t1"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	transcript	28134825	28137968	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	stop_codon	28134822	28134824	.	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28134825	28134989	1	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28134825	28134989	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28134990	28135110	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135111	28135313	0.97	-	2	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135111	28135313	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135314	28135522	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135523	28135631	1	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135523	28135631	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135632	28135788	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135789	28135932	1	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135789	28135932	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135933	28136117	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136118	28136186	1	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136118	28136186	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136187	28136303	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136304	28136381	1	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136304	28136381	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136382	28136590	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136591	28136783	0.99	-	1	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136591	28136783	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136784	28136910	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136911	28136994	1	-	1	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136911	28136994	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136995	28137247	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137248	28137408	1	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137248	28137408	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137409	28137669	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137670	28137842	1	-	2	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137670	28137842	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137843	28137910	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137911	28137968	0.68	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137911	28137968	.	-	.	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	start_codon	28137966	28137968	.	-	0	transcript_id "Phchi.S2G055900.t2"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	transcript	28134825	28137968	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	stop_codon	28134822	28134824	.	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28134825	28134989	1	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28134825	28134989	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28134990	28135110	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135111	28135346	1	-	2	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135111	28135346	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135347	28135522	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135523	28135631	1	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135523	28135631	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135632	28135788	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28135789	28135932	1	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28135789	28135932	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28135933	28136117	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136118	28136186	1	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136118	28136186	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136187	28136303	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136304	28136381	1	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136304	28136381	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136382	28136590	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136591	28136783	1	-	1	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136591	28136783	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28136784	28136910	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28136911	28137009	0.85	-	1	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28136911	28137009	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137010	28137247	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137248	28137408	1	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137248	28137408	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137409	28137669	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137670	28137842	0.99	-	2	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137670	28137842	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	intron	28137843	28137910	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	CDS	28137911	28137968	0.62	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	exon	28137911	28137968	.	-	.	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
Phchi.S2	AUGUSTUS	start_codon	28137966	28137968	.	-	0	transcript_id "Phchi.S2G055900.t3"; gene_id "Phchi.S2G055900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14801.t1 is derived from g13269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14782561	14782812	.	-	.	Phchi.S3G212000
Phchi.S3	AUGUSTUS	transcript	14782561	14782812	.	-	.	transcript_id "Phchi.S3G212000.t1"; gene_id "Phchi.S3G212000"
Phchi.S3	AUGUSTUS	stop_codon	14782558	14782560	.	-	0	transcript_id "Phchi.S3G212000.t1"; gene_id "Phchi.S3G212000"
Phchi.S3	AUGUSTUS	CDS	14782561	14782812	0.61	-	0	transcript_id "Phchi.S3G212000.t1"; gene_id "Phchi.S3G212000"
Phchi.S3	AUGUSTUS	exon	14782561	14782812	.	-	.	transcript_id "Phchi.S3G212000.t1"; gene_id "Phchi.S3G212000"
Phchi.S3	AUGUSTUS	start_codon	14782810	14782812	.	-	0	transcript_id "Phchi.S3G212000.t1"; gene_id "Phchi.S3G212000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1847.t1 is derived from g8767.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3537781	3540343	.	-	.	Phchi.S5G045600
Phchi.S5	AUGUSTUS	transcript	3537781	3540343	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	stop_codon	3537778	3537780	.	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3537781	3538199	0.99	-	2	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3537781	3538199	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538200	3538274	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538275	3538362	1	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538275	3538362	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538363	3538442	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538443	3538504	1	-	2	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538443	3538504	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538505	3538801	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538802	3538898	1	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538802	3538898	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538899	3538973	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538974	3539006	1	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538974	3539006	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539007	3539113	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539114	3539219	1	-	1	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539114	3539219	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539220	3539366	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539367	3539458	0.96	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539367	3539458	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539459	3539565	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539566	3539672	0.95	-	2	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539566	3539672	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539673	3539763	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539764	3539811	0.95	-	2	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539764	3539811	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539812	3540051	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3540052	3540343	0.77	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3540052	3540343	.	-	.	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	start_codon	3540341	3540343	.	-	0	transcript_id "Phchi.S5G045600.t1"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	transcript	3537781	3540343	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	stop_codon	3537778	3537780	.	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3537781	3538199	0.99	-	2	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3537781	3538199	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538200	3538274	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538275	3538362	1	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538275	3538362	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538363	3538442	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538443	3538504	1	-	2	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538443	3538504	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538505	3538801	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538802	3538898	1	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538802	3538898	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3538899	3538973	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3538974	3539006	1	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3538974	3539006	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539007	3539113	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539114	3539219	1	-	1	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539114	3539219	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539220	3539366	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539367	3539458	0.97	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539367	3539458	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539459	3539565	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539566	3539652	0.95	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539566	3539652	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539653	3539763	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3539764	3539921	0.77	-	2	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3539764	3539921	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	intron	3539922	3540051	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	CDS	3540052	3540343	0.7	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	exon	3540052	3540343	.	-	.	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
Phchi.S5	AUGUSTUS	start_codon	3540341	3540343	.	-	0	transcript_id "Phchi.S5G045600.t2"; gene_id "Phchi.S5G045600"
# This transcript jg12982.t2 is derived from g11447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12983.t1 is derived from g11448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3448011	3448397	.	-	.	Phchi.S3G030200
Phchi.S3	AUGUSTUS	transcript	3448011	3448397	.	-	.	transcript_id "Phchi.S3G030200.t1"; gene_id "Phchi.S3G030200"
Phchi.S3	AUGUSTUS	stop_codon	3448008	3448010	.	-	0	transcript_id "Phchi.S3G030200.t1"; gene_id "Phchi.S3G030200"
Phchi.S3	AUGUSTUS	CDS	3448011	3448397	1	-	0	transcript_id "Phchi.S3G030200.t1"; gene_id "Phchi.S3G030200"
Phchi.S3	AUGUSTUS	exon	3448011	3448397	.	-	.	transcript_id "Phchi.S3G030200.t1"; gene_id "Phchi.S3G030200"
Phchi.S3	AUGUSTUS	start_codon	3448395	3448397	.	-	0	transcript_id "Phchi.S3G030200.t1"; gene_id "Phchi.S3G030200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15074.t1 is derived from g13542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16918527	16921049	.	-	.	Phchi.S3G239300
Phchi.S3	AUGUSTUS	transcript	16918527	16921049	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	stop_codon	16918524	16918526	.	-	0	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16918527	16918624	0.63	-	2	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16918527	16918624	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16918625	16918744	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16918745	16918792	0.81	-	2	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16918745	16918792	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16918793	16918950	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16918951	16919093	1	-	1	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16918951	16919093	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16919094	16919174	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16919175	16919379	1	-	2	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16919175	16919379	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16919380	16919491	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16919492	16919629	0.88	-	2	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16919492	16919629	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16919630	16919733	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16919734	16920010	1	-	0	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16919734	16920010	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16920011	16920184	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16920185	16920518	1	-	1	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16920185	16920518	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16920519	16920612	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16920613	16920701	1	-	0	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16920613	16920701	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	intron	16920702	16920908	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	CDS	16920909	16921049	0.92	-	0	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	exon	16920909	16921049	.	-	.	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
Phchi.S3	AUGUSTUS	start_codon	16921047	16921049	.	-	0	transcript_id "Phchi.S3G239300.t1"; gene_id "Phchi.S3G239300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10220.t1 is derived from g7396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46454167	46457863	.	-	.	Phchi.S1G737900
Phchi.S1	AUGUSTUS	transcript	46454167	46457863	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	stop_codon	46454164	46454166	.	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46454167	46454289	1	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46454167	46454289	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46454290	46454405	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46454406	46454463	1	-	1	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46454406	46454463	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46454464	46454547	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46454548	46454618	1	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46454548	46454618	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46454619	46454724	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46454725	46454801	0.88	-	2	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46454725	46454801	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46454802	46454885	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46454886	46454971	1	-	1	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46454886	46454971	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46454972	46455083	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46455084	46455143	1	-	1	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46455084	46455143	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46455144	46455261	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46455262	46455397	1	-	2	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46455262	46455397	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46455398	46455496	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46455497	46455567	1	-	1	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46455497	46455567	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46455568	46455691	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46455692	46455783	1	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46455692	46455783	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46455784	46455882	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46455883	46455980	1	-	2	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46455883	46455980	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46455981	46456165	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46456166	46456318	1	-	2	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46456166	46456318	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46456319	46456401	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46456402	46456573	1	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46456402	46456573	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46456574	46456761	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46456762	46457304	0.96	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46456762	46457304	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46457305	46457388	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46457389	46457470	1	-	1	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46457389	46457470	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	intron	46457471	46457672	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	CDS	46457673	46457863	0.95	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	exon	46457673	46457863	.	-	.	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
Phchi.S1	AUGUSTUS	start_codon	46457861	46457863	.	-	0	transcript_id "Phchi.S1G737900.t1"; gene_id "Phchi.S1G737900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6148.t1 is derived from g3319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21155876	21157618	.	-	.	Phchi.S1G330700
Phchi.S1	AUGUSTUS	transcript	21155876	21157618	.	-	.	transcript_id "Phchi.S1G330700.t1"; gene_id "Phchi.S1G330700"
Phchi.S1	AUGUSTUS	stop_codon	21155873	21155875	.	-	0	transcript_id "Phchi.S1G330700.t1"; gene_id "Phchi.S1G330700"
Phchi.S1	AUGUSTUS	CDS	21155876	21157618	1	-	0	transcript_id "Phchi.S1G330700.t1"; gene_id "Phchi.S1G330700"
Phchi.S1	AUGUSTUS	exon	21155876	21157618	.	-	.	transcript_id "Phchi.S1G330700.t1"; gene_id "Phchi.S1G330700"
Phchi.S1	AUGUSTUS	start_codon	21157616	21157618	.	-	0	transcript_id "Phchi.S1G330700.t1"; gene_id "Phchi.S1G330700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13601.t1 is derived from g12068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7648415	7649748	.	-	.	Phchi.S3G092000
Phchi.S3	AUGUSTUS	transcript	7648415	7649748	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	stop_codon	7648412	7648414	.	-	0	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	CDS	7648415	7648421	1	-	1	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	exon	7648415	7648421	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	intron	7648422	7648559	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	CDS	7648560	7648782	1	-	2	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	exon	7648560	7648782	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	intron	7648783	7648868	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	CDS	7648869	7649154	1	-	0	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	exon	7648869	7649154	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	intron	7649155	7649277	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	CDS	7649278	7649748	1	-	0	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	exon	7649278	7649748	.	-	.	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
Phchi.S3	AUGUSTUS	start_codon	7649746	7649748	.	-	0	transcript_id "Phchi.S3G092000.t1"; gene_id "Phchi.S3G092000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg423.t1 is derived from g10205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3004633	3006039	.	-	.	Phchi.S6G038200
Phchi.S6	AUGUSTUS	transcript	3004633	3006039	.	-	.	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	stop_codon	3004630	3004632	.	-	0	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	CDS	3004633	3004928	0.69	-	2	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	exon	3004633	3004928	.	-	.	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	intron	3004929	3005015	.	-	.	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	CDS	3005016	3006039	0.36	-	0	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	exon	3005016	3006039	.	-	.	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
Phchi.S6	AUGUSTUS	start_codon	3006037	3006039	.	-	0	transcript_id "Phchi.S6G038200.t1"; gene_id "Phchi.S6G038200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14168.t1 is derived from g12635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11248506	11249475	.	+	.	Phchi.S3G148700
Phchi.S3	AUGUSTUS	transcript	11248506	11249475	.	+	.	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	start_codon	11248506	11248508	.	+	0	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	CDS	11248506	11248838	1	+	0	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	exon	11248506	11248838	.	+	.	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	intron	11248839	11249015	.	+	.	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	CDS	11249016	11249138	1	+	0	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	exon	11249016	11249138	.	+	.	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	intron	11249139	11249226	.	+	.	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	CDS	11249227	11249475	0.49	+	0	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	exon	11249227	11249475	.	+	.	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
Phchi.S3	AUGUSTUS	stop_codon	11249476	11249478	.	+	0	transcript_id "Phchi.S3G148700.t1"; gene_id "Phchi.S3G148700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13160.t1 is derived from g11625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4444927	4446210	.	-	.	Phchi.S3G047900
Phchi.S3	AUGUSTUS	transcript	4444927	4446210	.	-	.	transcript_id "Phchi.S3G047900.t1"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	stop_codon	4444924	4444926	.	-	0	transcript_id "Phchi.S3G047900.t1"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	CDS	4444927	4446210	0.94	-	0	transcript_id "Phchi.S3G047900.t1"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	exon	4444927	4446210	.	-	.	transcript_id "Phchi.S3G047900.t1"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	start_codon	4446208	4446210	.	-	0	transcript_id "Phchi.S3G047900.t1"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	transcript	4444927	4445697	.	-	.	transcript_id "Phchi.S3G047900.t2"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	stop_codon	4444924	4444926	.	-	0	transcript_id "Phchi.S3G047900.t2"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	CDS	4444927	4445697	0.58	-	0	transcript_id "Phchi.S3G047900.t2"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	exon	4444927	4445697	.	-	.	transcript_id "Phchi.S3G047900.t2"; gene_id "Phchi.S3G047900"
Phchi.S3	AUGUSTUS	start_codon	4445695	4445697	.	-	0	transcript_id "Phchi.S3G047900.t2"; gene_id "Phchi.S3G047900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7836.t1 is derived from g5010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31460377	31460931	.	+	.	Phchi.S1G499500
Phchi.S1	AUGUSTUS	transcript	31460377	31460931	.	+	.	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	start_codon	31460377	31460379	.	+	0	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	CDS	31460377	31460379	0.86	+	0	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	exon	31460377	31460379	.	+	.	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	intron	31460380	31460715	.	+	.	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	CDS	31460716	31460931	0.68	+	0	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	exon	31460716	31460931	.	+	.	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
Phchi.S1	AUGUSTUS	stop_codon	31460932	31460934	.	+	0	transcript_id "Phchi.S1G499500.t1"; gene_id "Phchi.S1G499500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11674.t1 is derived from g15725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7604674	7605790	.	-	.	Phchi.S4G125600
Phchi.S4	AUGUSTUS	transcript	7604674	7605790	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	stop_codon	7604671	7604673	.	-	0	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	CDS	7604674	7605042	0.47	-	0	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	exon	7604674	7605042	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	intron	7605043	7605155	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	CDS	7605156	7605289	1	-	2	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	exon	7605156	7605289	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	intron	7605290	7605373	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	CDS	7605374	7605419	1	-	0	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	exon	7605374	7605419	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	intron	7605420	7605522	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	CDS	7605523	7605555	1	-	0	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	exon	7605523	7605555	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	intron	7605556	7605652	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	CDS	7605653	7605790	1	-	0	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	exon	7605653	7605790	.	-	.	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
Phchi.S4	AUGUSTUS	start_codon	7605788	7605790	.	-	0	transcript_id "Phchi.S4G125600.t1"; gene_id "Phchi.S4G125600"
# This transcript jg2293.t2 is derived from g9213.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2294.t1 is derived from g9214.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5912517	5918391	.	+	.	Phchi.S5G090300
Phchi.S5	AUGUSTUS	transcript	5912517	5918391	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	start_codon	5912517	5912519	.	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5912517	5912615	0.82	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5912517	5912615	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5912616	5912961	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5912962	5913070	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5912962	5913070	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913071	5913165	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913166	5913237	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913166	5913237	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913238	5913432	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913433	5913534	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913433	5913534	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913535	5913614	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913615	5913783	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913615	5913783	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913784	5913859	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913860	5913958	1	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913860	5913958	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913959	5914059	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914060	5914209	0.99	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914060	5914209	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914210	5914351	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914352	5914391	1	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914352	5914391	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914392	5914478	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914479	5914539	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914479	5914539	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914540	5914694	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914695	5914780	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914695	5914780	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914781	5914870	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914871	5914969	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914871	5914969	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914970	5915057	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915058	5915170	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915058	5915170	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915171	5915273	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915274	5915404	1	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915274	5915404	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915405	5915573	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915574	5915644	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915574	5915644	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915645	5915752	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915753	5915858	0.99	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915753	5915858	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915859	5915962	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915963	5916102	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915963	5916102	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916103	5916332	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5916333	5916491	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5916333	5916491	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916492	5916570	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5916571	5916671	0.97	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5916571	5916671	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916672	5916777	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5916778	5916941	1	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5916778	5916941	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916942	5917066	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917067	5917259	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917067	5917259	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917260	5917393	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917394	5917493	1	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917394	5917493	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917494	5917580	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917581	5917749	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917581	5917749	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917750	5917868	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917869	5917960	1	+	2	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917869	5917960	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917961	5918051	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5918052	5918128	1	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5918052	5918128	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5918129	5918222	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5918223	5918391	1	+	1	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5918223	5918391	.	+	.	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	stop_codon	5918392	5918394	.	+	0	transcript_id "Phchi.S5G090300.t1"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	transcript	5912517	5918391	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	start_codon	5912517	5912519	.	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5912517	5912615	0.8	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5912517	5912615	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5912616	5912961	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5912962	5913070	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5912962	5913070	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913071	5913165	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913166	5913237	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913166	5913237	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913238	5913432	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913433	5913534	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913433	5913534	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913535	5913614	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913615	5913783	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913615	5913783	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913784	5913859	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5913860	5913958	1	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5913860	5913958	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5913959	5914059	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914060	5914209	0.97	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914060	5914209	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914210	5914351	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914352	5914391	1	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914352	5914391	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914392	5914478	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914479	5914539	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914479	5914539	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914540	5914694	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914695	5914780	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914695	5914780	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914781	5914870	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5914871	5914969	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5914871	5914969	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5914970	5915057	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915058	5915170	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915058	5915170	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915171	5915273	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915274	5915404	1	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915274	5915404	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915405	5915576	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915577	5915644	0.98	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915577	5915644	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915645	5915752	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915753	5915858	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915753	5915858	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5915859	5915962	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5915963	5916102	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5915963	5916102	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916103	5916332	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5916333	5916491	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5916333	5916491	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916492	5916570	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5916571	5916671	0.96	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5916571	5916671	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916672	5916777	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5916778	5916941	1	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5916778	5916941	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5916942	5917066	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917067	5917259	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917067	5917259	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917260	5917393	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917394	5917493	1	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917394	5917493	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917494	5917580	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917581	5917749	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917581	5917749	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917750	5917868	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5917869	5917960	1	+	2	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5917869	5917960	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5917961	5918051	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5918052	5918128	1	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5918052	5918128	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	intron	5918129	5918222	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	CDS	5918223	5918391	1	+	1	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	exon	5918223	5918391	.	+	.	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
Phchi.S5	AUGUSTUS	stop_codon	5918392	5918394	.	+	0	transcript_id "Phchi.S5G090300.t2"; gene_id "Phchi.S5G090300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6449.t1 is derived from g3621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23071249	23071802	.	-	.	Phchi.S1G360800
Phchi.S1	AUGUSTUS	transcript	23071249	23071802	.	-	.	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	stop_codon	23071246	23071248	.	-	0	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	CDS	23071249	23071390	1	-	1	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	exon	23071249	23071390	.	-	.	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	intron	23071391	23071554	.	-	.	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	CDS	23071555	23071802	1	-	0	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	exon	23071555	23071802	.	-	.	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
Phchi.S1	AUGUSTUS	start_codon	23071800	23071802	.	-	0	transcript_id "Phchi.S1G360800.t1"; gene_id "Phchi.S1G360800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5526.t1 is derived from g2696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17416816	17417748	.	+	.	Phchi.S1G268500
Phchi.S1	AUGUSTUS	transcript	17416816	17417748	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	start_codon	17416816	17416818	.	+	0	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	CDS	17416816	17416895	0.58	+	0	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	exon	17416816	17416895	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	intron	17416896	17417029	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	CDS	17417030	17417192	0.59	+	1	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	exon	17417030	17417192	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	intron	17417193	17417281	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	CDS	17417282	17417348	1	+	0	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	exon	17417282	17417348	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	intron	17417349	17417485	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	CDS	17417486	17417748	0.73	+	2	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	exon	17417486	17417748	.	+	.	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
Phchi.S1	AUGUSTUS	stop_codon	17417749	17417751	.	+	0	transcript_id "Phchi.S1G268500.t1"; gene_id "Phchi.S1G268500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13832.t1 is derived from g12299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9104448	9106777	.	+	.	Phchi.S3G115100
Phchi.S3	AUGUSTUS	transcript	9104448	9106777	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	start_codon	9104448	9104450	.	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9104448	9104732	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9104448	9104732	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9104733	9104896	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9104897	9104975	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9104897	9104975	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9104976	9105223	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9105224	9105318	1	+	2	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9105224	9105318	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9105319	9105490	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9105491	9105595	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9105491	9105595	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9105596	9105721	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9105722	9105801	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9105722	9105801	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9105802	9105881	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9105882	9105972	1	+	1	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9105882	9105972	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9105973	9106069	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9106070	9106177	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9106070	9106177	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9106178	9106307	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9106308	9106394	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9106308	9106394	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9106395	9106485	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9106486	9106554	1	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9106486	9106554	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	intron	9106555	9106639	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	CDS	9106640	9106777	0.95	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	exon	9106640	9106777	.	+	.	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
Phchi.S3	AUGUSTUS	stop_codon	9106778	9106780	.	+	0	transcript_id "Phchi.S3G115100.t1"; gene_id "Phchi.S3G115100"
# This transcript jg5696.t2 is derived from g2866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5697.t1 is derived from g2867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18375901	18377187	.	-	.	Phchi.S1G285600
Phchi.S1	AUGUSTUS	transcript	18375901	18377187	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	stop_codon	18375898	18375900	.	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18375901	18375930	1	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18375901	18375930	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18375931	18376024	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18376025	18376133	1	-	1	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18376025	18376133	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18376134	18376267	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18376268	18376356	1	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18376268	18376356	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18376357	18376445	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18376446	18376490	1	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18376446	18376490	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18376491	18376576	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18376577	18376604	1	-	1	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18376577	18376604	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18376605	18376824	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18376825	18376832	1	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18376825	18376832	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18376833	18376929	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18376930	18376935	0.93	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18376930	18376935	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	intron	18376936	18377091	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	CDS	18377092	18377187	1	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	exon	18377092	18377187	.	-	.	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
Phchi.S1	AUGUSTUS	start_codon	18377185	18377187	.	-	0	transcript_id "Phchi.S1G285600.t1"; gene_id "Phchi.S1G285600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10018.t1 is derived from g7194.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45067700	45072066	.	+	.	Phchi.S1G717700
Phchi.S1	AUGUSTUS	transcript	45067700	45072066	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	start_codon	45067700	45067702	.	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45067700	45067736	0.61	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45067700	45067736	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45067737	45067977	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45067978	45068087	0.63	+	2	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45067978	45068087	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45068088	45068171	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45068172	45068280	0.95	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45068172	45068280	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45068281	45068370	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45068371	45068463	0.95	+	2	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45068371	45068463	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45068464	45068543	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45068544	45068630	0.69	+	2	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45068544	45068630	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45068631	45068756	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45068757	45068845	0.61	+	2	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45068757	45068845	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45068846	45069293	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45069294	45069431	1	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45069294	45069431	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45069432	45069515	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45069516	45069640	1	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45069516	45069640	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45069641	45069775	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45069776	45069836	1	+	1	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45069776	45069836	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45069837	45069911	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45069912	45070010	0.91	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45069912	45070010	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45070011	45070114	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45070115	45070213	0.35	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45070115	45070213	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45070214	45070325	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45070326	45070473	0.46	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45070326	45070473	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45070474	45070546	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45070547	45070707	0.84	+	2	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45070547	45070707	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45070708	45070841	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45070842	45071008	1	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45070842	45071008	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45071009	45071094	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45071095	45071266	0.99	+	1	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45071095	45071266	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45071267	45071361	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45071362	45071451	0.7	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45071362	45071451	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45071452	45071526	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45071527	45071699	0.7	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45071527	45071699	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45071700	45071782	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45071783	45071906	0.99	+	1	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45071783	45071906	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	intron	45071907	45071991	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	CDS	45071992	45072066	1	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	exon	45071992	45072066	.	+	.	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
Phchi.S1	AUGUSTUS	stop_codon	45072067	45072069	.	+	0	transcript_id "Phchi.S1G717700.t1"; gene_id "Phchi.S1G717700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14564.t1 is derived from g13032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13485014	13487107	.	+	.	Phchi.S3G188300
Phchi.S3	AUGUSTUS	transcript	13485014	13487107	.	+	.	transcript_id "Phchi.S3G188300.t1"; gene_id "Phchi.S3G188300"
Phchi.S3	AUGUSTUS	start_codon	13485014	13485016	.	+	0	transcript_id "Phchi.S3G188300.t1"; gene_id "Phchi.S3G188300"
Phchi.S3	AUGUSTUS	CDS	13485014	13487107	1	+	0	transcript_id "Phchi.S3G188300.t1"; gene_id "Phchi.S3G188300"
Phchi.S3	AUGUSTUS	exon	13485014	13487107	.	+	.	transcript_id "Phchi.S3G188300.t1"; gene_id "Phchi.S3G188300"
Phchi.S3	AUGUSTUS	stop_codon	13487108	13487110	.	+	0	transcript_id "Phchi.S3G188300.t1"; gene_id "Phchi.S3G188300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7976.t1 is derived from g5151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32198665	32201505	.	+	.	Phchi.S1G513500
Phchi.S1	AUGUSTUS	transcript	32198665	32201505	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	start_codon	32198665	32198667	.	+	0	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	CDS	32198665	32199418	1	+	0	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	exon	32198665	32199418	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	intron	32199419	32199552	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	CDS	32199553	32200470	1	+	2	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	exon	32199553	32200470	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	intron	32200471	32200647	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	CDS	32200648	32200778	0.99	+	2	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	exon	32200648	32200778	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	intron	32200779	32200881	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	CDS	32200882	32201505	1	+	0	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	exon	32200882	32201505	.	+	.	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
Phchi.S1	AUGUSTUS	stop_codon	32201506	32201508	.	+	0	transcript_id "Phchi.S1G513500.t1"; gene_id "Phchi.S1G513500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12269.t1 is derived from g7945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7397102	7397827	.	+	.	Phchi.S2G034900
Phchi.S2	AUGUSTUS	transcript	7397102	7397827	.	+	.	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	start_codon	7397102	7397104	.	+	0	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	CDS	7397102	7397366	0.98	+	0	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	exon	7397102	7397366	.	+	.	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	intron	7397367	7397522	.	+	.	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	CDS	7397523	7397827	0.55	+	2	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	exon	7397523	7397827	.	+	.	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
Phchi.S2	AUGUSTUS	stop_codon	7397828	7397830	.	+	0	transcript_id "Phchi.S2G034900.t1"; gene_id "Phchi.S2G034900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg571.t1 is derived from g10353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4148873	4149435	.	+	.	Phchi.S6G053000
Phchi.S6	AUGUSTUS	transcript	4148873	4149435	.	+	.	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	start_codon	4148873	4148875	.	+	0	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	CDS	4148873	4149229	0.42	+	0	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	exon	4148873	4149229	.	+	.	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	intron	4149230	4149309	.	+	.	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	CDS	4149310	4149435	1	+	0	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	exon	4149310	4149435	.	+	.	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
Phchi.S6	AUGUSTUS	stop_codon	4149436	4149438	.	+	0	transcript_id "Phchi.S6G053000.t1"; gene_id "Phchi.S6G053000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6513.t1 is derived from g3685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23411067	23412278	.	+	.	Phchi.S1G367200
Phchi.S1	AUGUSTUS	transcript	23411067	23412278	.	+	.	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	start_codon	23411067	23411069	.	+	0	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	CDS	23411067	23411278	0.94	+	0	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	exon	23411067	23411278	.	+	.	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	intron	23411279	23411428	.	+	.	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	CDS	23411429	23411543	0.93	+	1	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	exon	23411429	23411543	.	+	.	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	intron	23411544	23412260	.	+	.	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	CDS	23412261	23412278	0.97	+	0	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	exon	23412261	23412278	.	+	.	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
Phchi.S1	AUGUSTUS	stop_codon	23412279	23412281	.	+	0	transcript_id "Phchi.S1G367200.t1"; gene_id "Phchi.S1G367200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5607.t1 is derived from g2777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17860160	17861566	.	-	.	Phchi.S1G276600
Phchi.S1	AUGUSTUS	transcript	17860160	17861566	.	-	.	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	stop_codon	17860157	17860159	.	-	0	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	CDS	17860160	17860547	0.99	-	1	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	exon	17860160	17860547	.	-	.	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	intron	17860548	17860812	.	-	.	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	CDS	17860813	17860972	1	-	2	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	exon	17860813	17860972	.	-	.	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	intron	17860973	17861163	.	-	.	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	CDS	17861164	17861566	0.98	-	0	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	exon	17861164	17861566	.	-	.	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
Phchi.S1	AUGUSTUS	start_codon	17861564	17861566	.	-	0	transcript_id "Phchi.S1G276600.t1"; gene_id "Phchi.S1G276600"
# This transcript jg9074.t2 is derived from g6249.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9075.t1 is derived from g6250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39730090	39731461	.	+	.	Phchi.S1G623400
Phchi.S1	AUGUSTUS	transcript	39730090	39731461	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	start_codon	39730090	39730092	.	+	0	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	CDS	39730090	39730318	1	+	0	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	exon	39730090	39730318	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	intron	39730319	39730402	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	CDS	39730403	39730602	0.87	+	2	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	exon	39730403	39730602	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	intron	39730603	39730712	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	CDS	39730713	39730853	0.79	+	0	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	exon	39730713	39730853	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	intron	39730854	39731003	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	CDS	39731004	39731084	1	+	0	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	exon	39731004	39731084	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	intron	39731085	39731188	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	CDS	39731189	39731313	0.69	+	0	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	exon	39731189	39731313	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	intron	39731314	39731415	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	CDS	39731416	39731461	0.67	+	1	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	exon	39731416	39731461	.	+	.	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
Phchi.S1	AUGUSTUS	stop_codon	39731462	39731464	.	+	0	transcript_id "Phchi.S1G623400.t1"; gene_id "Phchi.S1G623400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2706.t1 is derived from g9626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8271330	8271864	.	-	.	Phchi.S5G131500
Phchi.S5	AUGUSTUS	transcript	8271330	8271864	.	-	.	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	stop_codon	8271327	8271329	.	-	0	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	CDS	8271330	8271426	0.25	-	1	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	exon	8271330	8271426	.	-	.	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	intron	8271427	8271604	.	-	.	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	CDS	8271605	8271864	0.53	-	0	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	exon	8271605	8271864	.	-	.	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
Phchi.S5	AUGUSTUS	start_codon	8271862	8271864	.	-	0	transcript_id "Phchi.S5G131500.t1"; gene_id "Phchi.S5G131500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6970.t1 is derived from g4142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26212616	26213280	.	-	.	Phchi.S1G412900
Phchi.S1	AUGUSTUS	transcript	26212616	26213280	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	stop_codon	26212613	26212615	.	-	0	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	CDS	26212616	26212705	0.99	-	0	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	exon	26212616	26212705	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	intron	26212706	26212803	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	CDS	26212804	26212923	0.9	-	0	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	exon	26212804	26212923	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	intron	26212924	26213064	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	CDS	26213065	26213073	0.76	-	0	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	exon	26213065	26213073	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	intron	26213074	26213259	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	CDS	26213260	26213280	0.47	-	0	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	exon	26213260	26213280	.	-	.	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
Phchi.S1	AUGUSTUS	start_codon	26213278	26213280	.	-	0	transcript_id "Phchi.S1G412900.t1"; gene_id "Phchi.S1G412900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10723.t1 is derived from g14773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1763980	1765460	.	+	.	Phchi.S4G030500
Phchi.S4	AUGUSTUS	transcript	1763980	1765460	.	+	.	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	start_codon	1763980	1763982	.	+	0	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	CDS	1763980	1764842	0.56	+	0	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	exon	1763980	1764842	.	+	.	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	intron	1764843	1765097	.	+	.	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	CDS	1765098	1765105	0.42	+	1	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	exon	1765098	1765105	.	+	.	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	intron	1765106	1765401	.	+	.	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	CDS	1765402	1765460	0.44	+	2	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	exon	1765402	1765460	.	+	.	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
Phchi.S4	AUGUSTUS	stop_codon	1765461	1765463	.	+	0	transcript_id "Phchi.S4G030500.t1"; gene_id "Phchi.S4G030500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9289.t1 is derived from g6464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40779890	40782612	.	-	.	Phchi.S1G644800
Phchi.S1	AUGUSTUS	transcript	40779890	40782612	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	stop_codon	40779887	40779889	.	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40779890	40780068	0.97	-	2	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40779890	40780068	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40780069	40780284	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40780285	40780390	0.69	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40780285	40780390	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40780391	40780587	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40780588	40780832	0.98	-	2	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40780588	40780832	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40780833	40780989	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40780990	40781067	1	-	2	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40780990	40781067	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40781068	40781156	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40781157	40781255	0.97	-	2	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40781157	40781255	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40781256	40781366	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40781367	40781385	1	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40781367	40781385	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40781386	40781510	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40781511	40781573	0.99	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40781511	40781573	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40781574	40781675	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40781676	40782004	0.83	-	2	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40781676	40782004	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40782005	40782171	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40782172	40782202	0.5	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40782172	40782202	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40782203	40782273	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40782274	40782314	0.5	-	2	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40782274	40782314	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40782315	40782447	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40782448	40782493	0.76	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40782448	40782493	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	intron	40782494	40782603	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	CDS	40782604	40782612	0.72	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	exon	40782604	40782612	.	-	.	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
Phchi.S1	AUGUSTUS	start_codon	40782610	40782612	.	-	0	transcript_id "Phchi.S1G644800.t1"; gene_id "Phchi.S1G644800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9983.t1 is derived from g7159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44781818	44784267	.	+	.	Phchi.S1G714200
Phchi.S1	AUGUSTUS	transcript	44781818	44784267	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	start_codon	44781818	44781820	.	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44781818	44781825	0.67	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44781818	44781825	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44781826	44781900	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44781901	44782024	0.67	+	1	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44781901	44782024	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44782025	44782119	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44782120	44782182	1	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44782120	44782182	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44782183	44782371	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44782372	44782452	1	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44782372	44782452	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44782453	44782550	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44782551	44782588	1	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44782551	44782588	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44782589	44782945	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44782946	44783108	1	+	1	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44782946	44783108	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44783109	44783243	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44783244	44783450	1	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44783244	44783450	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	intron	44783451	44783535	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	CDS	44783536	44784267	0.89	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	exon	44783536	44784267	.	+	.	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
Phchi.S1	AUGUSTUS	stop_codon	44784268	44784270	.	+	0	transcript_id "Phchi.S1G714200.t1"; gene_id "Phchi.S1G714200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10673.t1 is derived from g14723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1536329	1541254	.	-	.	Phchi.S4G025500
Phchi.S4	AUGUSTUS	transcript	1536329	1541254	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	stop_codon	1536326	1536328	.	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1536329	1536422	1	-	1	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1536329	1536422	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1536423	1536642	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1536643	1536762	1	-	1	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1536643	1536762	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1536763	1536989	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1536990	1537351	0.77	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1536990	1537351	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1537352	1537459	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1537460	1537712	0.83	-	1	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1537460	1537712	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1537713	1537835	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1537836	1537882	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1537836	1537882	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1537883	1538076	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1538077	1538145	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1538077	1538145	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1538146	1538226	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1538227	1538334	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1538227	1538334	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1538335	1538530	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1538531	1538584	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1538531	1538584	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1538585	1538682	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1538683	1538859	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1538683	1538859	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1538860	1538980	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1538981	1539065	1	-	1	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1538981	1539065	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1539066	1539216	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1539217	1539660	0.96	-	1	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1539217	1539660	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1539661	1539801	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1539802	1539905	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1539802	1539905	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1539906	1539981	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1539982	1540068	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1539982	1540068	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1540069	1540250	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1540251	1540335	1	-	1	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1540251	1540335	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1540336	1540544	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1540545	1540647	1	-	2	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1540545	1540647	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1540648	1540744	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1540745	1540829	1	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1540745	1540829	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	intron	1540830	1541095	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	CDS	1541096	1541254	0.97	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	exon	1541096	1541254	.	-	.	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
Phchi.S4	AUGUSTUS	start_codon	1541252	1541254	.	-	0	transcript_id "Phchi.S4G025500.t1"; gene_id "Phchi.S4G025500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg180.t1 is derived from g9962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1031260	1032424	.	+	.	Phchi.S6G013900
Phchi.S6	AUGUSTUS	transcript	1031260	1032424	.	+	.	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	start_codon	1031260	1031262	.	+	0	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	CDS	1031260	1031837	0.41	+	0	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	exon	1031260	1031837	.	+	.	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	intron	1031838	1032023	.	+	.	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	CDS	1032024	1032180	0.47	+	1	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	exon	1032024	1032180	.	+	.	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	intron	1032181	1032268	.	+	.	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	CDS	1032269	1032424	0.98	+	0	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	exon	1032269	1032424	.	+	.	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
Phchi.S6	AUGUSTUS	stop_codon	1032425	1032427	.	+	0	transcript_id "Phchi.S6G013900.t1"; gene_id "Phchi.S6G013900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4675.t1 is derived from g1845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11762015	11763361	.	-	.	Phchi.S1G183400
Phchi.S1	AUGUSTUS	transcript	11762015	11763361	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	stop_codon	11762012	11762014	.	-	0	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	CDS	11762015	11762575	1	-	0	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	exon	11762015	11762575	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	intron	11762576	11762665	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	CDS	11762666	11762857	1	-	0	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	exon	11762666	11762857	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	intron	11762858	11762959	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	CDS	11762960	11763192	0.96	-	2	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	exon	11762960	11763192	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	intron	11763193	11763276	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	CDS	11763277	11763361	0.31	-	0	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	exon	11763277	11763361	.	-	.	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
Phchi.S1	AUGUSTUS	start_codon	11763359	11763361	.	-	0	transcript_id "Phchi.S1G183400.t1"; gene_id "Phchi.S1G183400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6498.t1 is derived from g3670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23329438	23331180	.	-	.	Phchi.S1G365700
Phchi.S1	AUGUSTUS	transcript	23329438	23331180	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	stop_codon	23329435	23329437	.	-	0	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23329438	23329497	1	-	0	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23329438	23329497	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23329498	23329575	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23329576	23329685	1	-	2	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23329576	23329685	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23329686	23329769	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23329770	23329867	1	-	1	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23329770	23329867	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23329868	23329961	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23329962	23330048	0.99	-	1	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23329962	23330048	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23330049	23330165	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23330166	23330271	1	-	2	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23330166	23330271	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23330272	23330368	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23330369	23330453	1	-	0	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23330369	23330453	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23330454	23330540	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23330541	23330594	1	-	0	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23330541	23330594	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23330595	23330675	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23330676	23330785	1	-	2	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23330676	23330785	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23330786	23330880	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23330881	23330894	0.75	-	1	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23330881	23330894	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	intron	23330895	23330989	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	CDS	23330990	23331180	0.4	-	0	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	exon	23330990	23331180	.	-	.	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
Phchi.S1	AUGUSTUS	start_codon	23331178	23331180	.	-	0	transcript_id "Phchi.S1G365700.t1"; gene_id "Phchi.S1G365700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg254.t1 is derived from g10036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1728588	1729930	.	+	.	Phchi.S6G021300
Phchi.S6	AUGUSTUS	transcript	1728588	1729930	.	+	.	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	start_codon	1728588	1728590	.	+	0	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	CDS	1728588	1728982	1	+	0	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	exon	1728588	1728982	.	+	.	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	intron	1728983	1729067	.	+	.	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	CDS	1729068	1729641	0.94	+	1	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	exon	1729068	1729641	.	+	.	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	intron	1729642	1729720	.	+	.	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	CDS	1729721	1729930	0.95	+	0	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	exon	1729721	1729930	.	+	.	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
Phchi.S6	AUGUSTUS	stop_codon	1729931	1729933	.	+	0	transcript_id "Phchi.S6G021300.t1"; gene_id "Phchi.S6G021300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12652.t1 is derived from g14451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	1217	2821	.	+	.	Phchi.C12G000200
Phchi.C12	AUGUSTUS	transcript	1217	2821	.	+	.	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	start_codon	1217	1219	.	+	0	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	CDS	1217	1534	0.61	+	0	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	exon	1217	1534	.	+	.	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	intron	1535	1649	.	+	.	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	CDS	1650	1739	0.43	+	0	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	exon	1650	1739	.	+	.	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	intron	1740	1825	.	+	.	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	CDS	1826	2821	0.3	+	0	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	exon	1826	2821	.	+	.	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
Phchi.C12	AUGUSTUS	stop_codon	2822	2824	.	+	0	transcript_id "Phchi.C12G000200.t1"; gene_id "Phchi.C12G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10798.t1 is derived from g14848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2162598	2163458	.	+	.	Phchi.S4G038000
Phchi.S4	AUGUSTUS	transcript	2162598	2163458	.	+	.	transcript_id "Phchi.S4G038000.t1"; gene_id "Phchi.S4G038000"
Phchi.S4	AUGUSTUS	start_codon	2162598	2162600	.	+	0	transcript_id "Phchi.S4G038000.t1"; gene_id "Phchi.S4G038000"
Phchi.S4	AUGUSTUS	CDS	2162598	2163458	0.49	+	0	transcript_id "Phchi.S4G038000.t1"; gene_id "Phchi.S4G038000"
Phchi.S4	AUGUSTUS	exon	2162598	2163458	.	+	.	transcript_id "Phchi.S4G038000.t1"; gene_id "Phchi.S4G038000"
Phchi.S4	AUGUSTUS	stop_codon	2163459	2163461	.	+	0	transcript_id "Phchi.S4G038000.t1"; gene_id "Phchi.S4G038000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1238.t1 is derived from g11021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8550798	8552061	.	-	.	Phchi.S6G119700
Phchi.S6	AUGUSTUS	transcript	8550798	8552061	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	stop_codon	8550795	8550797	.	-	0	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	CDS	8550798	8551195	1	-	2	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	exon	8550798	8551195	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	intron	8551196	8551287	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	CDS	8551288	8551453	1	-	0	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	exon	8551288	8551453	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	intron	8551454	8551535	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	CDS	8551536	8551730	1	-	0	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	exon	8551536	8551730	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	intron	8551731	8551842	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	CDS	8551843	8552061	1	-	0	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	exon	8551843	8552061	.	-	.	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
Phchi.S6	AUGUSTUS	start_codon	8552059	8552061	.	-	0	transcript_id "Phchi.S6G119700.t1"; gene_id "Phchi.S6G119700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4891.t1 is derived from g2061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13267475	13268138	.	-	.	Phchi.S1G205000
Phchi.S1	AUGUSTUS	transcript	13267475	13268138	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	stop_codon	13267472	13267474	.	-	0	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	CDS	13267475	13267551	0.45	-	2	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	exon	13267475	13267551	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	intron	13267552	13267654	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	CDS	13267655	13267775	0.45	-	0	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	exon	13267655	13267775	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	intron	13267776	13267870	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	CDS	13267871	13267992	0.91	-	2	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	exon	13267871	13267992	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	intron	13267993	13268080	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	CDS	13268081	13268138	0.87	-	0	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	exon	13268081	13268138	.	-	.	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
Phchi.S1	AUGUSTUS	start_codon	13268136	13268138	.	-	0	transcript_id "Phchi.S1G205000.t1"; gene_id "Phchi.S1G205000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3277.t1 is derived from g446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2650303	2651270	.	+	.	Phchi.S1G043600
Phchi.S1	AUGUSTUS	transcript	2650303	2651270	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	start_codon	2650303	2650305	.	+	0	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	CDS	2650303	2650454	0.94	+	0	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	exon	2650303	2650454	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	intron	2650455	2650674	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	CDS	2650675	2650748	1	+	1	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	exon	2650675	2650748	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	intron	2650749	2650824	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	CDS	2650825	2650923	1	+	2	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	exon	2650825	2650923	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	intron	2650924	2651068	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	CDS	2651069	2651102	0.86	+	2	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	exon	2651069	2651102	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	intron	2651103	2651251	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	CDS	2651252	2651270	1	+	1	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	exon	2651252	2651270	.	+	.	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
Phchi.S1	AUGUSTUS	stop_codon	2651271	2651273	.	+	0	transcript_id "Phchi.S1G043600.t1"; gene_id "Phchi.S1G043600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4203.t1 is derived from g1372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8889425	8890141	.	+	.	Phchi.S1G136200
Phchi.S1	AUGUSTUS	transcript	8889425	8890141	.	+	.	transcript_id "Phchi.S1G136200.t1"; gene_id "Phchi.S1G136200"
Phchi.S1	AUGUSTUS	start_codon	8889425	8889427	.	+	0	transcript_id "Phchi.S1G136200.t1"; gene_id "Phchi.S1G136200"
Phchi.S1	AUGUSTUS	CDS	8889425	8890141	0.96	+	0	transcript_id "Phchi.S1G136200.t1"; gene_id "Phchi.S1G136200"
Phchi.S1	AUGUSTUS	exon	8889425	8890141	.	+	.	transcript_id "Phchi.S1G136200.t1"; gene_id "Phchi.S1G136200"
Phchi.S1	AUGUSTUS	stop_codon	8890142	8890144	.	+	0	transcript_id "Phchi.S1G136200.t1"; gene_id "Phchi.S1G136200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1129.t1 is derived from g10912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7865035	7866355	.	+	.	Phchi.S6G108800
Phchi.S6	AUGUSTUS	transcript	7865035	7866355	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	start_codon	7865035	7865037	.	+	0	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	CDS	7865035	7865120	0.89	+	0	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	exon	7865035	7865120	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	intron	7865121	7865295	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	CDS	7865296	7865446	1	+	1	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	exon	7865296	7865446	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	intron	7865447	7865576	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	CDS	7865577	7865643	1	+	0	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	exon	7865577	7865643	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	intron	7865644	7865770	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	CDS	7865771	7866005	1	+	2	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	exon	7865771	7866005	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	intron	7866006	7866147	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	CDS	7866148	7866355	0.99	+	1	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	exon	7866148	7866355	.	+	.	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
Phchi.S6	AUGUSTUS	stop_codon	7866356	7866358	.	+	0	transcript_id "Phchi.S6G108800.t1"; gene_id "Phchi.S6G108800"
# This transcript jg10325.t2 is derived from g7501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10325.t3 is derived from g7501.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10326.t1 is derived from g7502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47128000	47128821	.	-	.	Phchi.S1G748500
Phchi.S1	AUGUSTUS	transcript	47128000	47128821	.	-	.	transcript_id "Phchi.S1G748500.t1"; gene_id "Phchi.S1G748500"
Phchi.S1	AUGUSTUS	stop_codon	47127997	47127999	.	-	0	transcript_id "Phchi.S1G748500.t1"; gene_id "Phchi.S1G748500"
Phchi.S1	AUGUSTUS	CDS	47128000	47128821	0.7	-	0	transcript_id "Phchi.S1G748500.t1"; gene_id "Phchi.S1G748500"
Phchi.S1	AUGUSTUS	exon	47128000	47128821	.	-	.	transcript_id "Phchi.S1G748500.t1"; gene_id "Phchi.S1G748500"
Phchi.S1	AUGUSTUS	start_codon	47128819	47128821	.	-	0	transcript_id "Phchi.S1G748500.t1"; gene_id "Phchi.S1G748500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3821.t1 is derived from g990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5890525	5891294	.	+	.	Phchi.S1G098000
Phchi.S1	AUGUSTUS	transcript	5890525	5891294	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	start_codon	5890525	5890527	.	+	0	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	CDS	5890525	5890530	0.99	+	0	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	exon	5890525	5890530	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	intron	5890531	5890796	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	CDS	5890797	5890910	1	+	0	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	exon	5890797	5890910	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	intron	5890911	5890993	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	CDS	5890994	5891058	1	+	0	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	exon	5890994	5891058	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	intron	5891059	5891152	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	CDS	5891153	5891294	0.99	+	1	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	exon	5891153	5891294	.	+	.	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
Phchi.S1	AUGUSTUS	stop_codon	5891295	5891297	.	+	0	transcript_id "Phchi.S1G098000.t1"; gene_id "Phchi.S1G098000"
# This transcript jg14137.t2 is derived from g12604.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14138.t1 is derived from g12605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11104292	11106668	.	+	.	Phchi.S3G145700
Phchi.S3	AUGUSTUS	transcript	11104292	11106668	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	start_codon	11104292	11104294	.	+	0	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	CDS	11104292	11104515	0.96	+	0	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	exon	11104292	11104515	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	intron	11104516	11104619	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	CDS	11104620	11104697	1	+	1	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	exon	11104620	11104697	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	intron	11104698	11105886	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	CDS	11105887	11106051	1	+	1	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	exon	11105887	11106051	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	intron	11106052	11106140	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	CDS	11106141	11106193	0.56	+	1	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	exon	11106141	11106193	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	intron	11106194	11106300	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	CDS	11106301	11106367	0.52	+	2	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	exon	11106301	11106367	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	intron	11106368	11106460	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	CDS	11106461	11106668	0.53	+	1	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	exon	11106461	11106668	.	+	.	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
Phchi.S3	AUGUSTUS	stop_codon	11106669	11106671	.	+	0	transcript_id "Phchi.S3G145700.t1"; gene_id "Phchi.S3G145700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3079.t1 is derived from g248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1492460	1493332	.	+	.	Phchi.S1G023800
Phchi.S1	AUGUSTUS	transcript	1492460	1493332	.	+	.	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	start_codon	1492460	1492462	.	+	0	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	CDS	1492460	1492720	0.92	+	0	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	exon	1492460	1492720	.	+	.	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	intron	1492721	1492806	.	+	.	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	CDS	1492807	1493001	1	+	0	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	exon	1492807	1493001	.	+	.	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	intron	1493002	1493092	.	+	.	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	CDS	1493093	1493332	1	+	0	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	exon	1493093	1493332	.	+	.	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
Phchi.S1	AUGUSTUS	stop_codon	1493333	1493335	.	+	0	transcript_id "Phchi.S1G023800.t1"; gene_id "Phchi.S1G023800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3978.t1 is derived from g1147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6834497	6835829	.	+	.	Phchi.S1G113700
Phchi.S1	AUGUSTUS	transcript	6834497	6835829	.	+	.	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	start_codon	6834497	6834499	.	+	0	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	CDS	6834497	6834969	1	+	0	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	exon	6834497	6834969	.	+	.	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	intron	6834970	6835112	.	+	.	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	CDS	6835113	6835266	1	+	1	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	exon	6835113	6835266	.	+	.	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	intron	6835267	6835505	.	+	.	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	CDS	6835506	6835829	1	+	0	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	exon	6835506	6835829	.	+	.	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
Phchi.S1	AUGUSTUS	stop_codon	6835830	6835832	.	+	0	transcript_id "Phchi.S1G113700.t1"; gene_id "Phchi.S1G113700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13454.t1 is derived from g11921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6934715	6935193	.	+	.	Phchi.S3G077300
Phchi.S3	AUGUSTUS	transcript	6934715	6935193	.	+	.	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	start_codon	6934715	6934717	.	+	0	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	CDS	6934715	6934902	0.38	+	0	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	exon	6934715	6934902	.	+	.	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	intron	6934903	6935057	.	+	.	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	CDS	6935058	6935193	0.61	+	1	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	exon	6935058	6935193	.	+	.	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
Phchi.S3	AUGUSTUS	stop_codon	6935194	6935196	.	+	0	transcript_id "Phchi.S3G077300.t1"; gene_id "Phchi.S3G077300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7386.t1 is derived from g4558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28874454	28875520	.	-	.	Phchi.S1G454500
Phchi.S1	AUGUSTUS	transcript	28874454	28875520	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	stop_codon	28874451	28874453	.	-	0	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	CDS	28874454	28874650	1	-	2	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	exon	28874454	28874650	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	intron	28874651	28874866	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	CDS	28874867	28874944	1	-	2	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	exon	28874867	28874944	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	intron	28874945	28875042	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	CDS	28875043	28875053	1	-	1	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	exon	28875043	28875053	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	intron	28875054	28875197	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	CDS	28875198	28875278	1	-	1	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	exon	28875198	28875278	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	intron	28875279	28875419	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	CDS	28875420	28875520	0.84	-	0	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	exon	28875420	28875520	.	-	.	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
Phchi.S1	AUGUSTUS	start_codon	28875518	28875520	.	-	0	transcript_id "Phchi.S1G454500.t1"; gene_id "Phchi.S1G454500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10743.t1 is derived from g14793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1877876	1878663	.	+	.	Phchi.S4G032500
Phchi.S4	AUGUSTUS	transcript	1877876	1878663	.	+	.	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	start_codon	1877876	1877878	.	+	0	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	CDS	1877876	1878068	0.99	+	0	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	exon	1877876	1878068	.	+	.	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	intron	1878069	1878160	.	+	.	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	CDS	1878161	1878663	1	+	2	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	exon	1878161	1878663	.	+	.	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
Phchi.S4	AUGUSTUS	stop_codon	1878664	1878666	.	+	0	transcript_id "Phchi.S4G032500.t1"; gene_id "Phchi.S4G032500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12280.t1 is derived from g7956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8473938	8475059	.	-	.	Phchi.S2G036000
Phchi.S2	AUGUSTUS	transcript	8473938	8475059	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	stop_codon	8473935	8473937	.	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	CDS	8473938	8474156	0.6	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	exon	8473938	8474156	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	intron	8474157	8474234	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	CDS	8474235	8474402	0.49	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	exon	8474235	8474402	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	intron	8474403	8474555	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	CDS	8474556	8474591	0.57	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	exon	8474556	8474591	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	intron	8474592	8474668	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	CDS	8474669	8474839	0.99	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	exon	8474669	8474839	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	intron	8474840	8474984	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	CDS	8474985	8475059	0.98	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	exon	8474985	8475059	.	-	.	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
Phchi.S2	AUGUSTUS	start_codon	8475057	8475059	.	-	0	transcript_id "Phchi.S2G036000.t1"; gene_id "Phchi.S2G036000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8888.t1 is derived from g6063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38494928	38496659	.	+	.	Phchi.S1G604700
Phchi.S1	AUGUSTUS	transcript	38494928	38496659	.	+	.	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	start_codon	38494928	38494930	.	+	0	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	CDS	38494928	38495303	0.79	+	0	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	exon	38494928	38495303	.	+	.	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	intron	38495304	38495388	.	+	.	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	CDS	38495389	38496659	0.99	+	2	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	exon	38495389	38496659	.	+	.	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
Phchi.S1	AUGUSTUS	stop_codon	38496660	38496662	.	+	0	transcript_id "Phchi.S1G604700.t1"; gene_id "Phchi.S1G604700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13439.t1 is derived from g11906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6706683	6710214	.	-	.	Phchi.S3G075800
Phchi.S3	AUGUSTUS	transcript	6706683	6710214	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	stop_codon	6706680	6706682	.	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6706683	6706955	0.97	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6706683	6706955	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6706956	6707050	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707051	6707086	0.45	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707051	6707086	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6707087	6707285	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707286	6707474	1	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707286	6707474	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6707475	6707557	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707558	6707704	0.98	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707558	6707704	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6707705	6707817	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707818	6708045	0.9	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707818	6708045	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6708046	6708149	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6708150	6708338	0.97	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6708150	6708338	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6708339	6708494	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6708495	6708590	1	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6708495	6708590	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6708591	6708752	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6708753	6709208	0.95	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6708753	6709208	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709209	6709285	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709286	6709471	1	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709286	6709471	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709472	6709566	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709567	6709674	1	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709567	6709674	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709675	6709764	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709765	6709937	1	-	2	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709765	6709937	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709938	6710078	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6710079	6710214	1	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6710079	6710214	.	-	.	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	start_codon	6710212	6710214	.	-	0	transcript_id "Phchi.S3G075800.t1"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	transcript	6706683	6710214	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	stop_codon	6706680	6706682	.	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6706683	6706955	0.97	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6706683	6706955	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6706956	6707050	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707051	6707086	0.37	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707051	6707086	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6707087	6707285	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707286	6707474	0.99	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707286	6707474	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6707475	6707557	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707558	6707704	1	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707558	6707704	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6707705	6707817	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6707818	6708045	0.82	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6707818	6708045	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6708046	6708149	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6708150	6708338	0.94	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6708150	6708338	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6708339	6708494	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6708495	6708590	1	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6708495	6708590	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6708591	6708752	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6708753	6709089	1	-	1	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6708753	6709089	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709090	6709187	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709188	6709201	1	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709188	6709201	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709202	6709285	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709286	6709471	1	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709286	6709471	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709472	6709566	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709567	6709674	1	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709567	6709674	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709675	6709764	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6709765	6709937	1	-	2	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6709765	6709937	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	intron	6709938	6710078	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	CDS	6710079	6710214	0.98	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	exon	6710079	6710214	.	-	.	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
Phchi.S3	AUGUSTUS	start_codon	6710212	6710214	.	-	0	transcript_id "Phchi.S3G075800.t2"; gene_id "Phchi.S3G075800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12534.t1 is derived from g8211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33633770	33634255	.	-	.	Phchi.S2G061400
Phchi.S2	AUGUSTUS	transcript	33633770	33634255	.	-	.	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	stop_codon	33633767	33633769	.	-	0	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	CDS	33633770	33633973	0.56	-	0	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	exon	33633770	33633973	.	-	.	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	intron	33633974	33634060	.	-	.	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	CDS	33634061	33634123	1	-	0	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	exon	33634061	33634123	.	-	.	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	intron	33634124	33634207	.	-	.	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	CDS	33634208	33634255	1	-	0	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	exon	33634208	33634255	.	-	.	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
Phchi.S2	AUGUSTUS	start_codon	33634253	33634255	.	-	0	transcript_id "Phchi.S2G061400.t1"; gene_id "Phchi.S2G061400"
# This transcript jg14120.t2 is derived from g12587.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14120.t3 is derived from g12587.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14120.t4 is derived from g12587.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14121.t1 is derived from g12588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10979327	10981967	.	-	.	Phchi.S3G144000
Phchi.S3	AUGUSTUS	transcript	10979327	10981967	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	stop_codon	10979324	10979326	.	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10979327	10979773	1	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10979327	10979773	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10979774	10979874	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10979875	10980012	1	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10979875	10980012	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10980013	10980101	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10980102	10980309	0.99	-	1	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10980102	10980309	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10980310	10980411	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10980412	10980512	0.92	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10980412	10980512	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10980513	10980697	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10980698	10980793	1	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10980698	10980793	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10980794	10980901	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10980902	10980958	1	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10980902	10980958	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10980959	10981095	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10981096	10981353	1	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10981096	10981353	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	intron	10981354	10981580	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	CDS	10981581	10981967	0.54	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	exon	10981581	10981967	.	-	.	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
Phchi.S3	AUGUSTUS	start_codon	10981965	10981967	.	-	0	transcript_id "Phchi.S3G144000.t1"; gene_id "Phchi.S3G144000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg902.t1 is derived from g10684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6360063	6360520	.	-	.	Phchi.S6G086100
Phchi.S6	AUGUSTUS	transcript	6360063	6360520	.	-	.	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	stop_codon	6360060	6360062	.	-	0	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	CDS	6360063	6360068	0.74	-	0	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	exon	6360063	6360068	.	-	.	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	intron	6360069	6360166	.	-	.	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	CDS	6360167	6360429	0.74	-	2	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	exon	6360167	6360429	.	-	.	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	intron	6360430	6360507	.	-	.	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	CDS	6360508	6360520	1	-	0	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	exon	6360508	6360520	.	-	.	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
Phchi.S6	AUGUSTUS	start_codon	6360518	6360520	.	-	0	transcript_id "Phchi.S6G086100.t1"; gene_id "Phchi.S6G086100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13295.t1 is derived from g11761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5297562	5299180	.	+	.	Phchi.S3G061400
Phchi.S3	AUGUSTUS	transcript	5297562	5299180	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	start_codon	5297562	5297564	.	+	0	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5297562	5297709	1	+	0	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5297562	5297709	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	intron	5297710	5297830	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5297831	5297871	0.8	+	2	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5297831	5297871	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	intron	5297872	5298276	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5298277	5298436	0.74	+	0	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5298277	5298436	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	intron	5298437	5298527	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5298528	5298655	1	+	2	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5298528	5298655	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	intron	5298656	5298792	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5298793	5298862	0.57	+	0	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5298793	5298862	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	intron	5298863	5298958	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5298959	5298994	0.65	+	2	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5298959	5298994	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	intron	5298995	5299091	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	CDS	5299092	5299180	0.99	+	2	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	exon	5299092	5299180	.	+	.	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
Phchi.S3	AUGUSTUS	stop_codon	5299181	5299183	.	+	0	transcript_id "Phchi.S3G061400.t1"; gene_id "Phchi.S3G061400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11790.t1 is derived from g15842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8168744	8169666	.	-	.	Phchi.S4G137200
Phchi.S4	AUGUSTUS	transcript	8168744	8169666	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	stop_codon	8168741	8168743	.	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8168744	8168821	0.91	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8168744	8168821	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8168822	8168923	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8168924	8168971	0.99	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8168924	8168971	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8168972	8169063	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169064	8169144	0.99	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169064	8169144	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8169145	8169220	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169221	8169358	1	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169221	8169358	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8169359	8169445	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169446	8169481	1	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169446	8169481	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8169482	8169570	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169571	8169666	0.85	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169571	8169666	.	-	.	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	start_codon	8169664	8169666	.	-	0	transcript_id "Phchi.S4G137200.t1"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	transcript	8168744	8169666	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	stop_codon	8168741	8168743	.	-	0	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8168744	8168792	0.4	-	1	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8168744	8168792	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8168793	8168923	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8168924	8168971	0.42	-	1	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8168924	8168971	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8168972	8169055	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169056	8169144	1	-	0	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169056	8169144	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8169145	8169220	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169221	8169358	1	-	0	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169221	8169358	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8169359	8169445	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169446	8169481	1	-	0	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169446	8169481	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	intron	8169482	8169570	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	CDS	8169571	8169666	0.87	-	0	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	exon	8169571	8169666	.	-	.	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
Phchi.S4	AUGUSTUS	start_codon	8169664	8169666	.	-	0	transcript_id "Phchi.S4G137200.t2"; gene_id "Phchi.S4G137200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10189.t1 is derived from g7365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46227882	46229554	.	+	.	Phchi.S1G734800
Phchi.S1	AUGUSTUS	transcript	46227882	46229554	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	start_codon	46227882	46227884	.	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46227882	46228034	0.99	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46227882	46228034	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46228035	46228112	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46228113	46228188	0.99	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46228113	46228188	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46228189	46228289	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46228290	46228378	0.88	+	2	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46228290	46228378	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46228379	46228587	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46228588	46228677	1	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46228588	46228677	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46228678	46228945	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46228946	46229016	0.98	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46228946	46229016	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46229017	46229102	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46229103	46229235	1	+	1	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46229103	46229235	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46229236	46229340	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46229341	46229438	0.6	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46229341	46229438	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	intron	46229439	46229517	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	CDS	46229518	46229554	0.59	+	1	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	exon	46229518	46229554	.	+	.	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
Phchi.S1	AUGUSTUS	stop_codon	46229555	46229557	.	+	0	transcript_id "Phchi.S1G734800.t1"; gene_id "Phchi.S1G734800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10869.t1 is derived from g14920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2679311	2679801	.	-	.	Phchi.S4G045200
Phchi.S4	AUGUSTUS	transcript	2679311	2679801	.	-	.	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	stop_codon	2679308	2679310	.	-	0	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	CDS	2679311	2679324	1	-	2	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	exon	2679311	2679324	.	-	.	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	intron	2679325	2679498	.	-	.	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	CDS	2679499	2679572	1	-	1	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	exon	2679499	2679572	.	-	.	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	intron	2679573	2679661	.	-	.	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	CDS	2679662	2679801	0.98	-	0	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	exon	2679662	2679801	.	-	.	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
Phchi.S4	AUGUSTUS	start_codon	2679799	2679801	.	-	0	transcript_id "Phchi.S4G045200.t1"; gene_id "Phchi.S4G045200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5032.t1 is derived from g2202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14178209	14180904	.	+	.	Phchi.S1G219100
Phchi.S1	AUGUSTUS	transcript	14178209	14180904	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	start_codon	14178209	14178211	.	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14178209	14178411	0.61	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14178209	14178411	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14178412	14178513	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14178514	14178928	0.65	+	1	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14178514	14178928	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14178929	14179049	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14179050	14179199	1	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14179050	14179199	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14179200	14179291	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14179292	14179546	0.66	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14179292	14179546	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14179547	14179699	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14179700	14179786	0.67	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14179700	14179786	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14179787	14179878	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14179879	14179989	0.63	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14179879	14179989	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14179990	14180174	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14180175	14180309	0.63	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14180175	14180309	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14180310	14180453	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14180454	14180572	0.49	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14180454	14180572	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	intron	14180573	14180807	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	CDS	14180808	14180904	0.66	+	1	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	exon	14180808	14180904	.	+	.	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
Phchi.S1	AUGUSTUS	stop_codon	14180905	14180907	.	+	0	transcript_id "Phchi.S1G219100.t1"; gene_id "Phchi.S1G219100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2577.t1 is derived from g9497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7465423	7466217	.	-	.	Phchi.S5G118600
Phchi.S5	AUGUSTUS	transcript	7465423	7466217	.	-	.	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	stop_codon	7465420	7465422	.	-	0	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	CDS	7465423	7465926	1	-	0	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	exon	7465423	7465926	.	-	.	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	intron	7465927	7466073	.	-	.	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	CDS	7466074	7466217	0.94	-	0	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	exon	7466074	7466217	.	-	.	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
Phchi.S5	AUGUSTUS	start_codon	7466215	7466217	.	-	0	transcript_id "Phchi.S5G118600.t1"; gene_id "Phchi.S5G118600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7738.t1 is derived from g4912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30900848	30901396	.	-	.	Phchi.S1G489700
Phchi.S1	AUGUSTUS	transcript	30900848	30901396	.	-	.	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	stop_codon	30900845	30900847	.	-	0	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	CDS	30900848	30900963	0.93	-	2	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	exon	30900848	30900963	.	-	.	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	intron	30900964	30901174	.	-	.	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	CDS	30901175	30901268	0.93	-	0	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	exon	30901175	30901268	.	-	.	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	intron	30901269	30901366	.	-	.	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	CDS	30901367	30901396	0.39	-	0	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	exon	30901367	30901396	.	-	.	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
Phchi.S1	AUGUSTUS	start_codon	30901394	30901396	.	-	0	transcript_id "Phchi.S1G489700.t1"; gene_id "Phchi.S1G489700"
# This transcript jg12758.t2 is derived from g11223.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12759.t1 is derived from g11224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1935684	1936110	.	+	.	Phchi.S3G007800
Phchi.S3	AUGUSTUS	transcript	1935684	1936110	.	+	.	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	start_codon	1935684	1935686	.	+	0	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	CDS	1935684	1935851	0.84	+	0	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	exon	1935684	1935851	.	+	.	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	intron	1935852	1936065	.	+	.	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	CDS	1936066	1936110	1	+	0	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	exon	1936066	1936110	.	+	.	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
Phchi.S3	AUGUSTUS	stop_codon	1936111	1936113	.	+	0	transcript_id "Phchi.S3G007800.t1"; gene_id "Phchi.S3G007800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14314.t1 is derived from g12781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12062360	12066143	.	+	.	Phchi.S3G163300
Phchi.S3	AUGUSTUS	transcript	12062360	12066143	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	start_codon	12062360	12062362	.	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12062360	12062515	0.72	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12062360	12062515	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12062516	12062685	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12062686	12062930	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12062686	12062930	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12062931	12063054	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12063055	12063253	1	+	1	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12063055	12063253	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12063254	12063337	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12063338	12063385	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12063338	12063385	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12063386	12063515	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12063516	12063623	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12063516	12063623	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12063624	12063791	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12063792	12063980	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12063792	12063980	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12063981	12064077	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12064078	12064374	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12064078	12064374	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12064375	12064457	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12064458	12064559	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12064458	12064559	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12064560	12064650	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12064651	12064785	0.99	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12064651	12064785	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12064786	12064892	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12064893	12065117	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12064893	12065117	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12065118	12065237	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12065238	12065441	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12065238	12065441	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12065442	12065541	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12065542	12065712	1	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12065542	12065712	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12065713	12065844	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12065845	12065886	0.57	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12065845	12065886	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12065887	12065970	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12065971	12065993	0.89	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12065971	12065993	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	intron	12065994	12066118	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	CDS	12066119	12066143	0.95	+	1	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	exon	12066119	12066143	.	+	.	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
Phchi.S3	AUGUSTUS	stop_codon	12066144	12066146	.	+	0	transcript_id "Phchi.S3G163300.t1"; gene_id "Phchi.S3G163300"
# This transcript jg7656.t2 is derived from g4830.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7657.t1 is derived from g4831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30451731	30452393	.	+	.	Phchi.S1G481600
Phchi.S1	AUGUSTUS	transcript	30451731	30452393	.	+	.	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	start_codon	30451731	30451733	.	+	0	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	CDS	30451731	30451977	0.61	+	0	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	exon	30451731	30451977	.	+	.	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	intron	30451978	30452262	.	+	.	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	CDS	30452263	30452393	0.98	+	2	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	exon	30452263	30452393	.	+	.	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
Phchi.S1	AUGUSTUS	stop_codon	30452394	30452396	.	+	0	transcript_id "Phchi.S1G481600.t1"; gene_id "Phchi.S1G481600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11.t1 is derived from g9778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C265	AUGUSTUS	gene	894	2213	.	+	.	Phchi.C265G000200
Phchi.C265	AUGUSTUS	transcript	894	2213	.	+	.	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	start_codon	894	896	.	+	0	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	CDS	894	1011	0.45	+	0	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	exon	894	1011	.	+	.	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	intron	1012	1155	.	+	.	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	CDS	1156	1664	1	+	2	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	exon	1156	1664	.	+	.	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	intron	1665	1805	.	+	.	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	CDS	1806	2213	0.85	+	0	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	exon	1806	2213	.	+	.	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
Phchi.C265	AUGUSTUS	stop_codon	2214	2216	.	+	0	transcript_id "Phchi.C265G000200.t1"; gene_id "Phchi.C265G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13394.t1 is derived from g11860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6517869	6518324	.	-	.	Phchi.S3G071300
Phchi.S3	AUGUSTUS	transcript	6517869	6518324	.	-	.	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	stop_codon	6517866	6517868	.	-	0	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	CDS	6517869	6517920	1	-	1	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	exon	6517869	6517920	.	-	.	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	intron	6517921	6518004	.	-	.	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	CDS	6518005	6518107	0.98	-	2	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	exon	6518005	6518107	.	-	.	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	intron	6518108	6518218	.	-	.	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	CDS	6518219	6518324	0.64	-	0	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	exon	6518219	6518324	.	-	.	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
Phchi.S3	AUGUSTUS	start_codon	6518322	6518324	.	-	0	transcript_id "Phchi.S3G071300.t1"; gene_id "Phchi.S3G071300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12244.t1 is derived from g7920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6953013	6954105	.	-	.	Phchi.S2G032400
Phchi.S2	AUGUSTUS	transcript	6953013	6954105	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	stop_codon	6953010	6953012	.	-	0	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	CDS	6953013	6953072	0.73	-	0	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	exon	6953013	6953072	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	intron	6953073	6953227	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	CDS	6953228	6953483	0.63	-	1	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	exon	6953228	6953483	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	intron	6953484	6953704	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	CDS	6953705	6953750	0.43	-	2	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	exon	6953705	6953750	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	intron	6953751	6953837	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	CDS	6953838	6953892	0.38	-	0	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	exon	6953838	6953892	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	intron	6953893	6954066	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	CDS	6954067	6954105	0.55	-	0	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	exon	6954067	6954105	.	-	.	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
Phchi.S2	AUGUSTUS	start_codon	6954103	6954105	.	-	0	transcript_id "Phchi.S2G032400.t1"; gene_id "Phchi.S2G032400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11756.t1 is derived from g15808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8019196	8022412	.	-	.	Phchi.S4G133800
Phchi.S4	AUGUSTUS	transcript	8019196	8022412	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	stop_codon	8019193	8019195	.	-	0	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	CDS	8019196	8019759	0.99	-	0	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	exon	8019196	8019759	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	intron	8019760	8019882	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	CDS	8019883	8020569	0.97	-	0	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	exon	8019883	8020569	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	intron	8020570	8020666	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	CDS	8020667	8021511	1	-	2	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	exon	8020667	8021511	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	intron	8021512	8021724	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	CDS	8021725	8022412	0.96	-	0	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	exon	8021725	8022412	.	-	.	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
Phchi.S4	AUGUSTUS	start_codon	8022410	8022412	.	-	0	transcript_id "Phchi.S4G133800.t1"; gene_id "Phchi.S4G133800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5487.t1 is derived from g2657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17095973	17097883	.	-	.	Phchi.S1G264600
Phchi.S1	AUGUSTUS	transcript	17095973	17097883	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	stop_codon	17095970	17095972	.	-	0	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17095973	17096149	1	-	0	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17095973	17096149	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17096150	17096245	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17096246	17096399	1	-	1	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17096246	17096399	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17096400	17096511	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17096512	17096587	1	-	2	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17096512	17096587	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17096588	17096675	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17096676	17096780	0.95	-	2	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17096676	17096780	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17096781	17096890	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17096891	17097009	0.97	-	1	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17096891	17097009	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17097010	17097097	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17097098	17097131	0.78	-	2	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17097098	17097131	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17097132	17097238	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17097239	17097305	0.58	-	0	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17097239	17097305	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17097306	17097393	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17097394	17097422	1	-	2	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17097394	17097422	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17097423	17097518	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17097519	17097585	1	-	0	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17097519	17097585	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	intron	17097586	17097742	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	CDS	17097743	17097883	0.85	-	0	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	exon	17097743	17097883	.	-	.	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
Phchi.S1	AUGUSTUS	start_codon	17097881	17097883	.	-	0	transcript_id "Phchi.S1G264600.t1"; gene_id "Phchi.S1G264600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1994.t1 is derived from g8914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4342116	4344086	.	+	.	Phchi.S5G060300
Phchi.S5	AUGUSTUS	transcript	4342116	4344086	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	start_codon	4342116	4342118	.	+	0	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4342116	4342174	0.98	+	0	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4342116	4342174	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4342175	4342248	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4342249	4342290	0.99	+	1	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4342249	4342290	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4342291	4342441	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4342442	4342486	0.99	+	1	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4342442	4342486	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4342487	4342628	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4342629	4342673	0.65	+	1	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4342629	4342673	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4342674	4342726	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4342727	4342811	0.64	+	1	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4342727	4342811	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4342812	4342895	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4342896	4343195	0.89	+	0	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4342896	4343195	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4343196	4343572	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4343573	4343675	0.94	+	0	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4343573	4343675	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4343676	4343792	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4343793	4343860	0.98	+	2	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4343793	4343860	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	intron	4343861	4344044	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	CDS	4344045	4344086	0.98	+	0	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	exon	4344045	4344086	.	+	.	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
Phchi.S5	AUGUSTUS	stop_codon	4344087	4344089	.	+	0	transcript_id "Phchi.S5G060300.t1"; gene_id "Phchi.S5G060300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14598.t1 is derived from g13066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13660024	13661302	.	-	.	Phchi.S3G191700
Phchi.S3	AUGUSTUS	transcript	13660024	13661302	.	-	.	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	stop_codon	13660021	13660023	.	-	0	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	CDS	13660024	13660939	0.63	-	1	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	exon	13660024	13660939	.	-	.	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	intron	13660940	13661024	.	-	.	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	CDS	13661025	13661302	0.66	-	0	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	exon	13661025	13661302	.	-	.	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
Phchi.S3	AUGUSTUS	start_codon	13661300	13661302	.	-	0	transcript_id "Phchi.S3G191700.t1"; gene_id "Phchi.S3G191700"
# This transcript jg3606.t2 is derived from g775.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3606.t3 is derived from g775.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3607.t1 is derived from g776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4718300	4720748	.	+	.	Phchi.S1G076600
Phchi.S1	AUGUSTUS	transcript	4718300	4720748	.	+	.	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	start_codon	4718300	4718302	.	+	0	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	CDS	4718300	4718383	1	+	0	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	exon	4718300	4718383	.	+	.	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	intron	4718384	4718483	.	+	.	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	CDS	4718484	4720748	0.99	+	0	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	exon	4718484	4720748	.	+	.	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
Phchi.S1	AUGUSTUS	stop_codon	4720749	4720751	.	+	0	transcript_id "Phchi.S1G076600.t1"; gene_id "Phchi.S1G076600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4630.t1 is derived from g1800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11473326	11474455	.	+	.	Phchi.S1G178900
Phchi.S1	AUGUSTUS	transcript	11473326	11474455	.	+	.	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	start_codon	11473326	11473328	.	+	0	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	CDS	11473326	11473387	1	+	0	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	exon	11473326	11473387	.	+	.	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	intron	11473388	11473631	.	+	.	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	CDS	11473632	11473790	1	+	1	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	exon	11473632	11473790	.	+	.	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	intron	11473791	11473899	.	+	.	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	CDS	11473900	11474455	1	+	1	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	exon	11473900	11474455	.	+	.	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
Phchi.S1	AUGUSTUS	stop_codon	11474456	11474458	.	+	0	transcript_id "Phchi.S1G178900.t1"; gene_id "Phchi.S1G178900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3708.t1 is derived from g877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5257122	5258365	.	+	.	Phchi.S1G086700
Phchi.S1	AUGUSTUS	transcript	5257122	5257764	.	+	.	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	start_codon	5257122	5257124	.	+	0	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	CDS	5257122	5257422	0.95	+	0	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	exon	5257122	5257422	.	+	.	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	intron	5257423	5257492	.	+	.	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	CDS	5257493	5257764	0.99	+	2	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	exon	5257493	5257764	.	+	.	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	stop_codon	5257765	5257767	.	+	0	transcript_id "Phchi.S1G086700.t1"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	transcript	5257122	5258365	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	start_codon	5257122	5257124	.	+	0	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	CDS	5257122	5257422	0.97	+	0	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	exon	5257122	5257422	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	intron	5257423	5257492	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	CDS	5257493	5257709	0.8	+	2	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	exon	5257493	5257709	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	intron	5257710	5257801	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	CDS	5257802	5258075	0.87	+	1	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	exon	5257802	5258075	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	intron	5258076	5258194	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	CDS	5258195	5258365	1	+	0	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	exon	5258195	5258365	.	+	.	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
Phchi.S1	AUGUSTUS	stop_codon	5258366	5258368	.	+	0	transcript_id "Phchi.S1G086700.t2"; gene_id "Phchi.S1G086700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5619.t1 is derived from g2789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17916023	17917467	.	-	.	Phchi.S1G277800
Phchi.S1	AUGUSTUS	transcript	17916023	17917467	.	-	.	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	stop_codon	17916020	17916022	.	-	0	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	CDS	17916023	17916139	1	-	0	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	exon	17916023	17916139	.	-	.	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	intron	17916140	17916224	.	-	.	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	CDS	17916225	17916319	1	-	2	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	exon	17916225	17916319	.	-	.	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	intron	17916320	17917439	.	-	.	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	CDS	17917440	17917467	0.01	-	0	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	exon	17917440	17917467	.	-	.	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
Phchi.S1	AUGUSTUS	start_codon	17917465	17917467	.	-	0	transcript_id "Phchi.S1G277800.t1"; gene_id "Phchi.S1G277800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10601.t1 is derived from g14651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1154661	1157892	.	-	.	Phchi.S4G018300
Phchi.S4	AUGUSTUS	transcript	1154661	1157892	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	stop_codon	1154658	1154660	.	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1154661	1154906	1	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1154661	1154906	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1154907	1154995	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1154996	1155102	1	-	2	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1154996	1155102	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1155103	1155201	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1155202	1155359	1	-	1	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1155202	1155359	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1155360	1155512	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1155513	1155854	0.99	-	1	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1155513	1155854	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1155855	1156003	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1156004	1156096	1	-	1	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1156004	1156096	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1156097	1156251	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1156252	1156436	1	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1156252	1156436	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1156437	1156607	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1156608	1156835	1	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1156608	1156835	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1156836	1156924	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1156925	1157011	1	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1156925	1157011	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1157012	1157096	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1157097	1157198	1	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1157097	1157198	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1157199	1157302	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1157303	1157433	1	-	2	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1157303	1157433	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1157434	1157522	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1157523	1157646	1	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1157523	1157646	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	intron	1157647	1157730	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	CDS	1157731	1157892	0.42	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	exon	1157731	1157892	.	-	.	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
Phchi.S4	AUGUSTUS	start_codon	1157890	1157892	.	-	0	transcript_id "Phchi.S4G018300.t1"; gene_id "Phchi.S4G018300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12540.t1 is derived from g8217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33958991	33964422	.	-	.	Phchi.S2G062000
Phchi.S2	AUGUSTUS	transcript	33958991	33964422	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	stop_codon	33958988	33958990	.	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33958991	33959217	0.87	-	2	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33958991	33959217	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33959218	33959595	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33959596	33959687	1	-	1	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33959596	33959687	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33959688	33959765	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33959766	33959839	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33959766	33959839	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33959840	33960027	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33960028	33960093	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33960028	33960093	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33960094	33960192	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33960193	33960261	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33960193	33960261	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33960262	33960369	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33960370	33960629	0.78	-	2	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33960370	33960629	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33960630	33960822	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33960823	33960919	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33960823	33960919	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33960920	33961114	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33961115	33961159	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33961115	33961159	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33961160	33961303	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33961304	33961386	1	-	2	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33961304	33961386	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33961387	33961499	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33961500	33961560	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33961500	33961560	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33961561	33961798	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33961799	33962064	0.97	-	2	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33961799	33962064	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33962065	33962139	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33962140	33962389	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33962140	33962389	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33962390	33962479	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33962480	33962584	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33962480	33962584	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33962585	33962672	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33962673	33962778	1	-	1	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33962673	33962778	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33962779	33962916	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33962917	33962990	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33962917	33962990	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33962991	33963094	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33963095	33963252	1	-	2	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33963095	33963252	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33963253	33963389	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33963390	33963600	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33963390	33963600	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33963601	33963688	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33963689	33963996	1	-	2	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33963689	33963996	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33963997	33964077	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33964078	33964183	1	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33964078	33964183	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	intron	33964184	33964341	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	CDS	33964342	33964422	0.66	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	exon	33964342	33964422	.	-	.	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
Phchi.S2	AUGUSTUS	start_codon	33964420	33964422	.	-	0	transcript_id "Phchi.S2G062000.t1"; gene_id "Phchi.S2G062000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15256.t1 is derived from g13724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17931244	17937488	.	-	.	Phchi.S3G257500
Phchi.S3	AUGUSTUS	transcript	17931244	17937488	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	stop_codon	17931241	17931243	.	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17931244	17931523	0.93	-	1	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17931244	17931523	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17931524	17931594	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17931595	17931750	0.99	-	1	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17931595	17931750	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17931751	17931845	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17931846	17932077	1	-	2	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17931846	17932077	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17932078	17932160	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17932161	17932278	0.24	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17932161	17932278	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17932279	17932468	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17932469	17933943	0.17	-	2	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17932469	17933943	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17933944	17934060	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17934061	17934175	0.5	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17934061	17934175	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17934176	17934299	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17934300	17934407	0.98	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17934300	17934407	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17934408	17934490	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17934491	17934631	1	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17934491	17934631	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17934632	17934711	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17934712	17934855	0.98	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17934712	17934855	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17934856	17934942	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17934943	17934993	1	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17934943	17934993	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17934994	17935074	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17935075	17935149	1	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17935075	17935149	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17935150	17935278	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17935279	17935449	0.42	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17935279	17935449	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17935450	17935572	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17935573	17935863	0.44	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17935573	17935863	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17935864	17936022	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17936023	17936152	0.53	-	1	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17936023	17936152	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17936153	17936261	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17936262	17936557	0.37	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17936262	17936557	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	intron	17936558	17936636	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	CDS	17936637	17937488	0.94	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	exon	17936637	17937488	.	-	.	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
Phchi.S3	AUGUSTUS	start_codon	17937486	17937488	.	-	0	transcript_id "Phchi.S3G257500.t1"; gene_id "Phchi.S3G257500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6533.t1 is derived from g3705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23522327	23523038	.	+	.	Phchi.S1G369200
Phchi.S1	AUGUSTUS	transcript	23522327	23523038	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	start_codon	23522327	23522329	.	+	0	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	CDS	23522327	23522489	0.8	+	0	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	exon	23522327	23522489	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	intron	23522490	23522577	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	CDS	23522578	23522611	0.96	+	2	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	exon	23522578	23522611	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	intron	23522612	23522836	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	CDS	23522837	23522873	0.94	+	1	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	exon	23522837	23522873	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	intron	23522874	23523017	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	CDS	23523018	23523038	0.94	+	0	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	exon	23523018	23523038	.	+	.	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
Phchi.S1	AUGUSTUS	stop_codon	23523039	23523041	.	+	0	transcript_id "Phchi.S1G369200.t1"; gene_id "Phchi.S1G369200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2255.t1 is derived from g9175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5704293	5706561	.	-	.	Phchi.S5G086400
Phchi.S5	AUGUSTUS	transcript	5704293	5706561	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	stop_codon	5704290	5704292	.	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5704293	5704378	0.99	-	2	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5704293	5704378	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5704379	5704452	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5704453	5704561	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5704453	5704561	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5704562	5704687	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5704688	5704837	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5704688	5704837	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5704838	5704915	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5704916	5704993	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5704916	5704993	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5704994	5705189	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5705190	5705259	1	-	1	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5705190	5705259	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5705260	5705397	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5705398	5705474	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5705398	5705474	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5705475	5705548	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5705549	5705668	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5705549	5705668	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5705669	5705742	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5705743	5705820	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5705743	5705820	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5705821	5705937	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5705938	5706009	1	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5705938	5706009	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5706010	5706090	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5706091	5706362	0.7	-	2	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5706091	5706362	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	intron	5706363	5706482	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	CDS	5706483	5706561	0.99	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	exon	5706483	5706561	.	-	.	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
Phchi.S5	AUGUSTUS	start_codon	5706559	5706561	.	-	0	transcript_id "Phchi.S5G086400.t1"; gene_id "Phchi.S5G086400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13976.t1 is derived from g12443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10010426	10010950	.	+	.	Phchi.S3G129500
Phchi.S3	AUGUSTUS	transcript	10010426	10010950	.	+	.	transcript_id "Phchi.S3G129500.t1"; gene_id "Phchi.S3G129500"
Phchi.S3	AUGUSTUS	start_codon	10010426	10010428	.	+	0	transcript_id "Phchi.S3G129500.t1"; gene_id "Phchi.S3G129500"
Phchi.S3	AUGUSTUS	CDS	10010426	10010950	1	+	0	transcript_id "Phchi.S3G129500.t1"; gene_id "Phchi.S3G129500"
Phchi.S3	AUGUSTUS	exon	10010426	10010950	.	+	.	transcript_id "Phchi.S3G129500.t1"; gene_id "Phchi.S3G129500"
Phchi.S3	AUGUSTUS	stop_codon	10010951	10010953	.	+	0	transcript_id "Phchi.S3G129500.t1"; gene_id "Phchi.S3G129500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2134.t1 is derived from g9054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5011746	5014646	.	+	.	Phchi.S5G074300
Phchi.S5	AUGUSTUS	transcript	5011746	5014646	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	start_codon	5011746	5011748	.	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5011746	5011783	1	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5011746	5011783	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5011784	5012039	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5012040	5012142	0.68	+	1	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5012040	5012142	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5012143	5012353	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5012354	5012559	0.66	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5012354	5012559	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5012560	5012663	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5012664	5012844	0.99	+	1	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5012664	5012844	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5012845	5012962	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5012963	5013009	1	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5012963	5013009	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5013010	5013100	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5013101	5013308	1	+	1	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5013101	5013308	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5013309	5013384	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5013385	5013549	1	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5013385	5013549	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5013550	5013691	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5013692	5014025	1	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5013692	5014025	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5014026	5014103	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5014104	5014261	1	+	2	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5014104	5014261	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5014262	5014351	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5014352	5014379	0.98	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5014352	5014379	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	intron	5014380	5014470	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	CDS	5014471	5014646	0.99	+	2	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	exon	5014471	5014646	.	+	.	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
Phchi.S5	AUGUSTUS	stop_codon	5014647	5014649	.	+	0	transcript_id "Phchi.S5G074300.t1"; gene_id "Phchi.S5G074300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7563.t1 is derived from g4737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30052432	30053490	.	-	.	Phchi.S1G472200
Phchi.S1	AUGUSTUS	transcript	30052432	30053490	.	-	.	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	stop_codon	30052429	30052431	.	-	0	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	CDS	30052432	30052590	0.7	-	0	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	exon	30052432	30052590	.	-	.	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	intron	30052591	30052670	.	-	.	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	CDS	30052671	30053209	0.51	-	2	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	exon	30052671	30053209	.	-	.	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	intron	30053210	30053423	.	-	.	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	CDS	30053424	30053490	1	-	0	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	exon	30053424	30053490	.	-	.	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
Phchi.S1	AUGUSTUS	start_codon	30053488	30053490	.	-	0	transcript_id "Phchi.S1G472200.t1"; gene_id "Phchi.S1G472200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1723.t1 is derived from g8643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2719135	2720493	.	+	.	Phchi.S5G033200
Phchi.S5	AUGUSTUS	transcript	2719135	2720493	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	start_codon	2719135	2719137	.	+	0	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	CDS	2719135	2719330	1	+	0	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	exon	2719135	2719330	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	intron	2719331	2719462	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	CDS	2719463	2719547	1	+	2	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	exon	2719463	2719547	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	intron	2719548	2719642	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	CDS	2719643	2719693	1	+	1	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	exon	2719643	2719693	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	intron	2719694	2719779	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	CDS	2719780	2719900	1	+	1	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	exon	2719780	2719900	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	intron	2719901	2719998	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	CDS	2719999	2720145	1	+	0	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	exon	2719999	2720145	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	intron	2720146	2720238	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	CDS	2720239	2720493	0.96	+	0	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	exon	2720239	2720493	.	+	.	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
Phchi.S5	AUGUSTUS	stop_codon	2720494	2720496	.	+	0	transcript_id "Phchi.S5G033200.t1"; gene_id "Phchi.S5G033200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9038.t1 is derived from g6213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39240717	39242449	.	-	.	Phchi.S1G619700
Phchi.S1	AUGUSTUS	transcript	39240717	39242449	.	-	.	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	stop_codon	39240714	39240716	.	-	0	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	CDS	39240717	39240858	1	-	1	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	exon	39240717	39240858	.	-	.	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	intron	39240859	39240991	.	-	.	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	CDS	39240992	39241164	1	-	0	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	exon	39240992	39241164	.	-	.	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	intron	39241165	39241285	.	-	.	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	CDS	39241286	39242449	1	-	0	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	exon	39241286	39242449	.	-	.	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
Phchi.S1	AUGUSTUS	start_codon	39242447	39242449	.	-	0	transcript_id "Phchi.S1G619700.t1"; gene_id "Phchi.S1G619700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11637.t1 is derived from g15688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7409340	7410422	.	-	.	Phchi.S4G121900
Phchi.S4	AUGUSTUS	transcript	7409340	7410422	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	stop_codon	7409337	7409339	.	-	0	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	CDS	7409340	7409391	1	-	1	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	exon	7409340	7409391	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	intron	7409392	7409479	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	CDS	7409480	7409683	1	-	1	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	exon	7409480	7409683	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	intron	7409684	7409833	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	CDS	7409834	7409977	1	-	1	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	exon	7409834	7409977	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	intron	7409978	7410075	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	CDS	7410076	7410203	1	-	0	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	exon	7410076	7410203	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	intron	7410204	7410356	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	CDS	7410357	7410422	1	-	0	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	exon	7410357	7410422	.	-	.	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
Phchi.S4	AUGUSTUS	start_codon	7410420	7410422	.	-	0	transcript_id "Phchi.S4G121900.t1"; gene_id "Phchi.S4G121900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9008.t1 is derived from g6183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39126116	39126684	.	-	.	Phchi.S1G616700
Phchi.S1	AUGUSTUS	transcript	39126116	39126684	.	-	.	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	stop_codon	39126113	39126115	.	-	0	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	CDS	39126116	39126190	1	-	0	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	exon	39126116	39126190	.	-	.	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	intron	39126191	39126325	.	-	.	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	CDS	39126326	39126481	1	-	0	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	exon	39126326	39126481	.	-	.	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	intron	39126482	39126579	.	-	.	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	CDS	39126580	39126684	0.94	-	0	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	exon	39126580	39126684	.	-	.	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
Phchi.S1	AUGUSTUS	start_codon	39126682	39126684	.	-	0	transcript_id "Phchi.S1G616700.t1"; gene_id "Phchi.S1G616700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7192.t1 is derived from g4364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27484286	27495928	.	+	.	Phchi.S1G435100
Phchi.S1	AUGUSTUS	transcript	27484286	27495928	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	start_codon	27484286	27484288	.	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27484286	27484555	0.99	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27484286	27484555	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27484556	27484654	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27484655	27484844	1	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27484655	27484844	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27484845	27484995	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27484996	27485150	1	+	2	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27484996	27485150	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27485151	27485259	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27485260	27485328	1	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27485260	27485328	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27485329	27485482	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27485483	27485625	1	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27485483	27485625	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27485626	27485706	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27485707	27485770	1	+	1	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27485707	27485770	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27485771	27485927	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27485928	27486144	1	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27485928	27486144	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27486145	27486230	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27486231	27486443	0.94	+	2	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27486231	27486443	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27486444	27486558	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27486559	27489239	0.43	+	2	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27486559	27489239	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27489240	27489484	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27489485	27490579	0.89	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27489485	27490579	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27490580	27490683	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27490684	27491206	0.99	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27490684	27491206	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27491207	27491354	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27491355	27491993	1	+	2	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27491355	27491993	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27491994	27492067	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27492068	27492593	0.99	+	2	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27492068	27492593	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27492594	27492687	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27492688	27492946	1	+	1	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27492688	27492946	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27492947	27493138	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27493139	27493291	1	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27493139	27493291	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27493292	27493364	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27493365	27495220	0.55	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27493365	27495220	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	intron	27495221	27495324	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	CDS	27495325	27495928	0.55	+	1	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	exon	27495325	27495928	.	+	.	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
Phchi.S1	AUGUSTUS	stop_codon	27495929	27495931	.	+	0	transcript_id "Phchi.S1G435100.t1"; gene_id "Phchi.S1G435100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6254.t1 is derived from g3426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21885992	21886869	.	-	.	Phchi.S1G341300
Phchi.S1	AUGUSTUS	transcript	21885992	21886869	.	-	.	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	stop_codon	21885989	21885991	.	-	0	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	CDS	21885992	21886276	0.99	-	0	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	exon	21885992	21886276	.	-	.	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	intron	21886277	21886518	.	-	.	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	CDS	21886519	21886869	1	-	0	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	exon	21886519	21886869	.	-	.	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
Phchi.S1	AUGUSTUS	start_codon	21886867	21886869	.	-	0	transcript_id "Phchi.S1G341300.t1"; gene_id "Phchi.S1G341300"
# This transcript jg7591.t2 is derived from g4765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7592.t1 is derived from g4766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30185673	30186131	.	-	.	Phchi.S1G475100
Phchi.S1	AUGUSTUS	transcript	30185673	30186131	.	-	.	transcript_id "Phchi.S1G475100.t1"; gene_id "Phchi.S1G475100"
Phchi.S1	AUGUSTUS	stop_codon	30185670	30185672	.	-	0	transcript_id "Phchi.S1G475100.t1"; gene_id "Phchi.S1G475100"
Phchi.S1	AUGUSTUS	CDS	30185673	30186131	0.96	-	0	transcript_id "Phchi.S1G475100.t1"; gene_id "Phchi.S1G475100"
Phchi.S1	AUGUSTUS	exon	30185673	30186131	.	-	.	transcript_id "Phchi.S1G475100.t1"; gene_id "Phchi.S1G475100"
Phchi.S1	AUGUSTUS	start_codon	30186129	30186131	.	-	0	transcript_id "Phchi.S1G475100.t1"; gene_id "Phchi.S1G475100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15438.t1 is derived from g13906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19154481	19156150	.	+	.	Phchi.S3G275700
Phchi.S3	AUGUSTUS	transcript	19154481	19156150	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	start_codon	19154481	19154483	.	+	0	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	CDS	19154481	19155175	0.65	+	0	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	exon	19154481	19155175	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	intron	19155176	19155307	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	CDS	19155308	19155539	0.85	+	1	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	exon	19155308	19155539	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	intron	19155540	19155654	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	CDS	19155655	19155777	1	+	0	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	exon	19155655	19155777	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	intron	19155778	19155904	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	CDS	19155905	19156150	1	+	0	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	exon	19155905	19156150	.	+	.	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
Phchi.S3	AUGUSTUS	stop_codon	19156151	19156153	.	+	0	transcript_id "Phchi.S3G275700.t1"; gene_id "Phchi.S3G275700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg962.t1 is derived from g10744.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6665453	6667373	.	+	.	Phchi.S6G092100
Phchi.S6	AUGUSTUS	transcript	6665453	6667373	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	start_codon	6665453	6665455	.	+	0	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6665453	6666391	0.49	+	0	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6665453	6666391	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	intron	6666392	6666598	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6666599	6666628	0.98	+	0	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6666599	6666628	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	intron	6666629	6667014	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6667015	6667141	0.95	+	0	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6667015	6667141	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	intron	6667142	6667224	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6667225	6667373	0.56	+	2	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6667225	6667373	.	+	.	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	stop_codon	6667374	6667376	.	+	0	transcript_id "Phchi.S6G092100.t1"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	transcript	6666755	6667373	.	+	.	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	start_codon	6666755	6666757	.	+	0	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6666755	6666787	0.41	+	0	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6666755	6666787	.	+	.	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	intron	6666788	6667014	.	+	.	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6667015	6667141	0.89	+	0	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6667015	6667141	.	+	.	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	intron	6667142	6667224	.	+	.	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	CDS	6667225	6667373	0.56	+	2	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	exon	6667225	6667373	.	+	.	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
Phchi.S6	AUGUSTUS	stop_codon	6667374	6667376	.	+	0	transcript_id "Phchi.S6G092100.t2"; gene_id "Phchi.S6G092100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15979.t1 is derived from g8309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C157	AUGUSTUS	gene	1151	2311	.	+	.	Phchi.C157G000100
Phchi.C157	AUGUSTUS	transcript	1151	2311	.	+	.	transcript_id "Phchi.C157G000100.t1"; gene_id "Phchi.C157G000100"
Phchi.C157	AUGUSTUS	start_codon	1151	1153	.	+	0	transcript_id "Phchi.C157G000100.t1"; gene_id "Phchi.C157G000100"
Phchi.C157	AUGUSTUS	CDS	1151	2311	0.84	+	0	transcript_id "Phchi.C157G000100.t1"; gene_id "Phchi.C157G000100"
Phchi.C157	AUGUSTUS	exon	1151	2311	.	+	.	transcript_id "Phchi.C157G000100.t1"; gene_id "Phchi.C157G000100"
Phchi.C157	AUGUSTUS	stop_codon	2312	2314	.	+	0	transcript_id "Phchi.C157G000100.t1"; gene_id "Phchi.C157G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4499.t1 is derived from g1669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10823539	10825817	.	-	.	Phchi.S1G165800
Phchi.S1	AUGUSTUS	transcript	10823539	10825817	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	stop_codon	10823536	10823538	.	-	0	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10823539	10823617	1	-	1	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10823539	10823617	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10823618	10823729	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10823730	10823778	0.75	-	2	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10823730	10823778	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10823779	10823901	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10823902	10823943	1	-	2	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10823902	10823943	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10823944	10824041	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10824042	10824126	1	-	0	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10824042	10824126	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10824127	10824233	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10824234	10824522	1	-	1	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10824234	10824522	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10824523	10824611	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10824612	10824888	1	-	2	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10824612	10824888	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10824889	10825044	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10825045	10825124	1	-	1	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10825045	10825124	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10825125	10825290	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10825291	10825523	0.99	-	0	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10825291	10825523	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10825524	10825620	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10825621	10825697	0.89	-	2	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10825621	10825697	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	intron	10825698	10825804	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	CDS	10825805	10825817	0.98	-	0	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	exon	10825805	10825817	.	-	.	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
Phchi.S1	AUGUSTUS	start_codon	10825815	10825817	.	-	0	transcript_id "Phchi.S1G165800.t1"; gene_id "Phchi.S1G165800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11635.t1 is derived from g15686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7407208	7407669	.	-	.	Phchi.S4G121700
Phchi.S4	AUGUSTUS	transcript	7407208	7407669	.	-	.	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	stop_codon	7407205	7407207	.	-	0	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	CDS	7407208	7407225	1	-	0	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	exon	7407208	7407225	.	-	.	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	intron	7407226	7407390	.	-	.	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	CDS	7407391	7407669	1	-	0	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	exon	7407391	7407669	.	-	.	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
Phchi.S4	AUGUSTUS	start_codon	7407667	7407669	.	-	0	transcript_id "Phchi.S4G121700.t1"; gene_id "Phchi.S4G121700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13996.t1 is derived from g12463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10150790	10160508	.	+	.	Phchi.S3G131500
Phchi.S3	AUGUSTUS	transcript	10150790	10160508	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	start_codon	10150790	10150792	.	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10150790	10151273	0.59	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10150790	10151273	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10151274	10151419	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10151420	10152274	0.41	+	2	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10151420	10152274	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10152275	10152452	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10152453	10152515	1	+	2	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10152453	10152515	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10152516	10152614	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10152615	10154405	1	+	2	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10152615	10154405	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10154406	10154491	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10154492	10154699	0.99	+	2	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10154492	10154699	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10154700	10154798	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10154799	10154929	0.59	+	1	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10154799	10154929	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10154930	10155021	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10155022	10155521	0.35	+	2	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10155022	10155521	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10155522	10155670	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10155671	10155787	0.29	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10155671	10155787	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10155788	10155987	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10155988	10156127	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10155988	10156127	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10156128	10156212	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10156213	10156867	0.95	+	1	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10156213	10156867	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10156868	10156953	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10156954	10157058	0.94	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10156954	10157058	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10157059	10157193	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10157194	10157418	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10157194	10157418	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10157419	10157597	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10157598	10157780	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10157598	10157780	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10157781	10157905	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10157906	10158006	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10157906	10158006	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10158007	10158193	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10158194	10158293	1	+	1	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10158194	10158293	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10158294	10158457	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10158458	10158553	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10158458	10158553	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10158554	10158642	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10158643	10158810	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10158643	10158810	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10158811	10158929	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10158930	10159067	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10158930	10159067	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10159068	10159149	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10159150	10159203	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10159150	10159203	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10159204	10159326	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10159327	10159565	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10159327	10159565	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10159566	10159654	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10159655	10159763	1	+	1	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10159655	10159763	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10159764	10159846	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10159847	10160140	1	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10159847	10160140	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10160141	10160228	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10160229	10160325	0.66	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10160229	10160325	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	intron	10160326	10160446	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	CDS	10160447	10160508	0.66	+	2	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	exon	10160447	10160508	.	+	.	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
Phchi.S3	AUGUSTUS	stop_codon	10160509	10160511	.	+	0	transcript_id "Phchi.S3G131500.t1"; gene_id "Phchi.S3G131500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2866.t1 is derived from g35.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	176731	177349	.	-	.	Phchi.S1G002500
Phchi.S1	AUGUSTUS	transcript	176731	177349	.	-	.	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	stop_codon	176728	176730	.	-	0	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	CDS	176731	177095	0.68	-	2	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	exon	176731	177095	.	-	.	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	intron	177096	177240	.	-	.	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	CDS	177241	177349	0.62	-	0	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	exon	177241	177349	.	-	.	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
Phchi.S1	AUGUSTUS	start_codon	177347	177349	.	-	0	transcript_id "Phchi.S1G002500.t1"; gene_id "Phchi.S1G002500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11574.t1 is derived from g15625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7141511	7142871	.	+	.	Phchi.S4G115600
Phchi.S4	AUGUSTUS	transcript	7141511	7142871	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	start_codon	7141511	7141513	.	+	0	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	CDS	7141511	7141524	0.92	+	0	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	exon	7141511	7141524	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	intron	7141525	7141619	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	CDS	7141620	7141729	0.92	+	1	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	exon	7141620	7141729	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	intron	7141730	7141813	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	CDS	7141814	7142324	1	+	2	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	exon	7141814	7142324	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	intron	7142325	7142416	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	CDS	7142417	7142590	0.55	+	1	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	exon	7142417	7142590	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	intron	7142591	7142711	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	CDS	7142712	7142871	0.33	+	1	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	exon	7142712	7142871	.	+	.	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
Phchi.S4	AUGUSTUS	stop_codon	7142872	7142874	.	+	0	transcript_id "Phchi.S4G115600.t1"; gene_id "Phchi.S4G115600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6164.t1 is derived from g3335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21263487	21264278	.	+	.	Phchi.S1G332300
Phchi.S1	AUGUSTUS	transcript	21263487	21264278	.	+	.	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	start_codon	21263487	21263489	.	+	0	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	CDS	21263487	21263606	1	+	0	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	exon	21263487	21263606	.	+	.	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	intron	21263607	21263731	.	+	.	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	CDS	21263732	21263905	1	+	0	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	exon	21263732	21263905	.	+	.	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	intron	21263906	21263993	.	+	.	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	CDS	21263994	21264278	0.87	+	0	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	exon	21263994	21264278	.	+	.	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
Phchi.S1	AUGUSTUS	stop_codon	21264279	21264281	.	+	0	transcript_id "Phchi.S1G332300.t1"; gene_id "Phchi.S1G332300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7681.t1 is derived from g4855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30592212	30592982	.	+	.	Phchi.S1G484000
Phchi.S1	AUGUSTUS	transcript	30592212	30592982	.	+	.	transcript_id "Phchi.S1G484000.t1"; gene_id "Phchi.S1G484000"
Phchi.S1	AUGUSTUS	start_codon	30592212	30592214	.	+	0	transcript_id "Phchi.S1G484000.t1"; gene_id "Phchi.S1G484000"
Phchi.S1	AUGUSTUS	CDS	30592212	30592982	0.55	+	0	transcript_id "Phchi.S1G484000.t1"; gene_id "Phchi.S1G484000"
Phchi.S1	AUGUSTUS	exon	30592212	30592982	.	+	.	transcript_id "Phchi.S1G484000.t1"; gene_id "Phchi.S1G484000"
Phchi.S1	AUGUSTUS	stop_codon	30592983	30592985	.	+	0	transcript_id "Phchi.S1G484000.t1"; gene_id "Phchi.S1G484000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13731.t1 is derived from g12198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8579368	8579925	.	-	.	Phchi.S3G105000
Phchi.S3	AUGUSTUS	transcript	8579368	8579925	.	-	.	transcript_id "Phchi.S3G105000.t1"; gene_id "Phchi.S3G105000"
Phchi.S3	AUGUSTUS	stop_codon	8579365	8579367	.	-	0	transcript_id "Phchi.S3G105000.t1"; gene_id "Phchi.S3G105000"
Phchi.S3	AUGUSTUS	CDS	8579368	8579925	0.55	-	0	transcript_id "Phchi.S3G105000.t1"; gene_id "Phchi.S3G105000"
Phchi.S3	AUGUSTUS	exon	8579368	8579925	.	-	.	transcript_id "Phchi.S3G105000.t1"; gene_id "Phchi.S3G105000"
Phchi.S3	AUGUSTUS	start_codon	8579923	8579925	.	-	0	transcript_id "Phchi.S3G105000.t1"; gene_id "Phchi.S3G105000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5079.t1 is derived from g2249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14587977	14588573	.	-	.	Phchi.S1G223800
Phchi.S1	AUGUSTUS	transcript	14587977	14588573	.	-	.	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	stop_codon	14587974	14587976	.	-	0	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	CDS	14587977	14588293	0.93	-	2	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	exon	14587977	14588293	.	-	.	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	intron	14588294	14588371	.	-	.	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	CDS	14588372	14588573	0.58	-	0	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	exon	14588372	14588573	.	-	.	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
Phchi.S1	AUGUSTUS	start_codon	14588571	14588573	.	-	0	transcript_id "Phchi.S1G223800.t1"; gene_id "Phchi.S1G223800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7327.t1 is derived from g4499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28526609	28529412	.	-	.	Phchi.S1G448600
Phchi.S1	AUGUSTUS	transcript	28526609	28529412	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	stop_codon	28526606	28526608	.	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28526609	28526671	1	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28526609	28526671	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28526672	28526748	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28526749	28526853	1	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28526749	28526853	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28526854	28526946	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28526947	28526997	1	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28526947	28526997	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28526998	28527081	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527082	28527147	1	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527082	28527147	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527148	28527262	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527263	28527429	1	-	2	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527263	28527429	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527430	28527569	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527570	28527647	0.72	-	2	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527570	28527647	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527648	28527716	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527717	28527816	0.75	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527717	28527816	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527817	28527950	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527951	28528143	1	-	1	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527951	28528143	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28528144	28528331	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28528332	28528479	1	-	2	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28528332	28528479	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28528480	28528657	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28528658	28528731	1	-	1	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28528658	28528731	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28528732	28529281	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28529282	28529412	0.79	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28529282	28529412	.	-	.	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	start_codon	28529410	28529412	.	-	0	transcript_id "Phchi.S1G448600.t1"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	transcript	28526609	28529412	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	stop_codon	28526606	28526608	.	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28526609	28526671	1	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28526609	28526671	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28526672	28526748	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28526749	28526853	1	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28526749	28526853	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28526854	28526946	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28526947	28526997	1	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28526947	28526997	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28526998	28527081	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527082	28527147	1	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527082	28527147	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527148	28527262	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527263	28527429	1	-	2	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527263	28527429	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527430	28527569	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527570	28527647	0.64	-	2	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527570	28527647	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527648	28527716	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527717	28527816	0.67	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527717	28527816	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28527817	28527950	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28527951	28528143	1	-	1	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28527951	28528143	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28528144	28528331	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28528332	28528476	1	-	2	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28528332	28528476	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28528477	28528657	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28528658	28528731	1	-	1	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28528658	28528731	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	intron	28528732	28529281	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	CDS	28529282	28529412	0.8	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	exon	28529282	28529412	.	-	.	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
Phchi.S1	AUGUSTUS	start_codon	28529410	28529412	.	-	0	transcript_id "Phchi.S1G448600.t2"; gene_id "Phchi.S1G448600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg71.t1 is derived from g9853.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	351847	357903	.	-	.	Phchi.S6G003000
Phchi.S6	AUGUSTUS	transcript	351847	357903	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	stop_codon	351844	351846	.	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	351847	352132	0.95	-	1	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	351847	352132	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352133	352219	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352220	352297	1	-	1	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352220	352297	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352298	352377	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352378	352481	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352378	352481	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352482	352592	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352593	352707	1	-	1	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352593	352707	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352708	352795	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352796	352851	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352796	352851	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352852	352944	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352945	353109	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352945	353109	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353110	353232	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	353233	353313	0.89	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	353233	353313	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353314	353478	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	353479	353637	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	353479	353637	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353638	353785	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	353786	353926	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	353786	353926	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353927	354043	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354044	354112	0.83	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354044	354112	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354113	354224	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354225	354295	1	-	2	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354225	354295	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354296	354380	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354381	354504	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354381	354504	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354505	354616	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354617	354752	0.89	-	1	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354617	354752	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354753	354831	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354832	354859	1	-	2	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354832	354859	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354860	354981	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354982	354988	0.99	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354982	354988	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354989	355094	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355095	355215	0.98	-	1	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355095	355215	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355216	355308	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355309	355436	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355309	355436	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355437	355523	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355524	355610	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355524	355610	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355611	355741	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355742	355873	1	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355742	355873	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355874	355959	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355960	356312	0.45	-	2	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355960	356312	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356313	356459	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356460	356589	0.78	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356460	356589	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356590	356728	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356729	356772	0.82	-	2	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356729	356772	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356773	356860	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356861	356909	0.99	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356861	356909	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356910	356992	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356993	357442	0.99	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356993	357442	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	357443	357531	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	357532	357589	0.64	-	1	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	357532	357589	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	357590	357712	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	357713	357903	0.37	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	357713	357903	.	-	.	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	start_codon	357901	357903	.	-	0	transcript_id "Phchi.S6G003000.t1"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	transcript	351847	357903	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	stop_codon	351844	351846	.	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	351847	352132	0.99	-	1	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	351847	352132	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352133	352219	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352220	352297	1	-	1	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352220	352297	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352298	352377	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352378	352481	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352378	352481	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352482	352592	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352593	352707	1	-	1	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352593	352707	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352708	352795	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352796	352851	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352796	352851	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	352852	352944	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	352945	353109	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	352945	353109	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353110	353232	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	353233	353313	0.9	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	353233	353313	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353314	353478	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	353479	353637	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	353479	353637	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353638	353785	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	353786	353926	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	353786	353926	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	353927	354043	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354044	354112	0.82	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354044	354112	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354113	354224	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354225	354295	0.97	-	2	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354225	354295	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354296	354380	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354381	354504	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354381	354504	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354505	354616	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354617	354752	0.9	-	1	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354617	354752	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354753	354836	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	354837	354988	0.98	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	354837	354988	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	354989	355094	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355095	355215	1	-	1	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355095	355215	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355216	355308	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355309	355436	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355309	355436	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355437	355523	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355524	355610	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355524	355610	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355611	355741	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355742	355873	1	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355742	355873	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	355874	355959	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	355960	356312	0.4	-	2	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	355960	356312	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356313	356459	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356460	356589	0.68	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356460	356589	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356590	356728	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356729	356772	0.86	-	2	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356729	356772	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356773	356860	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356861	356909	0.99	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356861	356909	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	356910	356992	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	356993	357442	0.99	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	356993	357442	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	357443	357531	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	357532	357589	0.61	-	1	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	357532	357589	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	intron	357590	357712	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	CDS	357713	357903	0.36	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	exon	357713	357903	.	-	.	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
Phchi.S6	AUGUSTUS	start_codon	357901	357903	.	-	0	transcript_id "Phchi.S6G003000.t2"; gene_id "Phchi.S6G003000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14621.t1 is derived from g13089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13812081	13814185	.	+	.	Phchi.S3G194000
Phchi.S3	AUGUSTUS	transcript	13812081	13814185	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	start_codon	13812081	13812083	.	+	0	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13812081	13812217	1	+	0	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13812081	13812217	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13812218	13812300	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13812301	13812380	1	+	1	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13812301	13812380	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13812381	13812466	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13812467	13812541	1	+	2	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13812467	13812541	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13812542	13812629	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13812630	13812733	1	+	2	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13812630	13812733	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13812734	13812833	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13812834	13812990	1	+	0	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13812834	13812990	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13812991	13813161	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13813162	13813249	1	+	2	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13813162	13813249	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13813250	13813354	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13813355	13813427	1	+	1	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13813355	13813427	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13813428	13813508	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13813509	13813639	1	+	0	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13813509	13813639	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13813640	13813729	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13813730	13813798	0.96	+	1	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13813730	13813798	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13813799	13813890	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13813891	13813925	0.93	+	1	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13813891	13813925	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	intron	13813926	13814126	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	CDS	13814127	13814185	1	+	2	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	exon	13814127	13814185	.	+	.	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
Phchi.S3	AUGUSTUS	stop_codon	13814186	13814188	.	+	0	transcript_id "Phchi.S3G194000.t1"; gene_id "Phchi.S3G194000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8639.t1 is derived from g5814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37191685	37192818	.	+	.	Phchi.S1G579800
Phchi.S1	AUGUSTUS	transcript	37191685	37192818	.	+	.	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	start_codon	37191685	37191687	.	+	0	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	CDS	37191685	37191888	0.87	+	0	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	exon	37191685	37191888	.	+	.	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	intron	37191889	37191976	.	+	.	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	CDS	37191977	37192181	1	+	0	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	exon	37191977	37192181	.	+	.	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	intron	37192182	37192276	.	+	.	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	CDS	37192277	37192818	1	+	2	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	exon	37192277	37192818	.	+	.	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
Phchi.S1	AUGUSTUS	stop_codon	37192819	37192821	.	+	0	transcript_id "Phchi.S1G579800.t1"; gene_id "Phchi.S1G579800"
# This transcript jg11948.t2 is derived from g7623.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11949.t1 is derived from g7624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	162140	163774	.	-	.	Phchi.S2G002900
Phchi.S2	AUGUSTUS	transcript	162140	163774	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	stop_codon	162137	162139	.	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	162140	162281	1	-	1	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	162140	162281	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	intron	162282	162371	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	162372	162448	1	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	162372	162448	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	intron	162449	162557	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	162558	162767	0.97	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	162558	162767	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	intron	162768	162982	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	162983	163147	0.84	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	162983	163147	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	intron	163148	163212	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	163213	163292	1	-	2	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	163213	163292	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	intron	163293	163486	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	163487	163604	1	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	163487	163604	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	intron	163605	163699	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	CDS	163700	163774	0.99	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	exon	163700	163774	.	-	.	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
Phchi.S2	AUGUSTUS	start_codon	163772	163774	.	-	0	transcript_id "Phchi.S2G002900.t1"; gene_id "Phchi.S2G002900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15505.t1 is derived from g13974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19589639	19591143	.	-	.	Phchi.S3G282400
Phchi.S3	AUGUSTUS	transcript	19589639	19591143	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	stop_codon	19589636	19589638	.	-	0	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	CDS	19589639	19589838	0.77	-	2	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	exon	19589639	19589838	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	intron	19589839	19589980	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	CDS	19589981	19590087	1	-	1	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	exon	19589981	19590087	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	intron	19590088	19590286	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	CDS	19590287	19590551	0.59	-	2	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	exon	19590287	19590551	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	intron	19590552	19590649	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	CDS	19590650	19590762	0.58	-	1	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	exon	19590650	19590762	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	intron	19590763	19590928	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	CDS	19590929	19590985	0.67	-	1	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	exon	19590929	19590985	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	intron	19590986	19591138	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	CDS	19591139	19591143	0.9	-	0	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	exon	19591139	19591143	.	-	.	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
Phchi.S3	AUGUSTUS	start_codon	19591141	19591143	.	-	0	transcript_id "Phchi.S3G282400.t1"; gene_id "Phchi.S3G282400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4014.t1 is derived from g1183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7183859	7184230	.	+	.	Phchi.S1G117300
Phchi.S1	AUGUSTUS	transcript	7183859	7184230	.	+	.	transcript_id "Phchi.S1G117300.t1"; gene_id "Phchi.S1G117300"
Phchi.S1	AUGUSTUS	start_codon	7183859	7183861	.	+	0	transcript_id "Phchi.S1G117300.t1"; gene_id "Phchi.S1G117300"
Phchi.S1	AUGUSTUS	CDS	7183859	7184230	1	+	0	transcript_id "Phchi.S1G117300.t1"; gene_id "Phchi.S1G117300"
Phchi.S1	AUGUSTUS	exon	7183859	7184230	.	+	.	transcript_id "Phchi.S1G117300.t1"; gene_id "Phchi.S1G117300"
Phchi.S1	AUGUSTUS	stop_codon	7184231	7184233	.	+	0	transcript_id "Phchi.S1G117300.t1"; gene_id "Phchi.S1G117300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9952.t1 is derived from g7128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44635851	44636728	.	-	.	Phchi.S1G711100
Phchi.S1	AUGUSTUS	transcript	44635851	44636728	.	-	.	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	stop_codon	44635848	44635850	.	-	0	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	CDS	44635851	44636479	1	-	2	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	exon	44635851	44636479	.	-	.	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	intron	44636480	44636613	.	-	.	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	CDS	44636614	44636728	1	-	0	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	exon	44636614	44636728	.	-	.	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
Phchi.S1	AUGUSTUS	start_codon	44636726	44636728	.	-	0	transcript_id "Phchi.S1G711100.t1"; gene_id "Phchi.S1G711100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13305.t1 is derived from g11771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5608266	5609571	.	-	.	Phchi.S3G062400
Phchi.S3	AUGUSTUS	transcript	5608266	5609571	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	stop_codon	5608263	5608265	.	-	0	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	CDS	5608266	5608426	1	-	2	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	exon	5608266	5608426	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	intron	5608427	5608525	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	CDS	5608526	5608729	1	-	2	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	exon	5608526	5608729	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	intron	5608730	5608836	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	CDS	5608837	5609068	1	-	0	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	exon	5608837	5609068	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	intron	5609069	5609164	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	CDS	5609165	5609299	1	-	0	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	exon	5609165	5609299	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	intron	5609300	5609391	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	CDS	5609392	5609571	0.99	-	0	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	exon	5609392	5609571	.	-	.	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
Phchi.S3	AUGUSTUS	start_codon	5609569	5609571	.	-	0	transcript_id "Phchi.S3G062400.t1"; gene_id "Phchi.S3G062400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2044.t1 is derived from g8964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4572310	4572912	.	+	.	Phchi.S5G065300
Phchi.S5	AUGUSTUS	transcript	4572310	4572912	.	+	.	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	start_codon	4572310	4572312	.	+	0	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	CDS	4572310	4572758	0.87	+	0	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	exon	4572310	4572758	.	+	.	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	intron	4572759	4572842	.	+	.	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	CDS	4572843	4572912	0.98	+	1	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	exon	4572843	4572912	.	+	.	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
Phchi.S5	AUGUSTUS	stop_codon	4572913	4572915	.	+	0	transcript_id "Phchi.S5G065300.t1"; gene_id "Phchi.S5G065300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1586.t1 is derived from g8505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1892505	1896676	.	-	.	Phchi.S5G019500
Phchi.S5	AUGUSTUS	transcript	1892505	1896676	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	stop_codon	1892502	1892504	.	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1892505	1892804	0.55	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1892505	1892804	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1892805	1892889	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1892890	1892998	0.91	-	1	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1892890	1892998	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1892999	1893086	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893087	1893261	0.88	-	2	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893087	1893261	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893262	1893350	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893351	1893419	0.89	-	2	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893351	1893419	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893420	1893535	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893536	1893677	0.61	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893536	1893677	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893678	1893811	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893812	1893880	0.8	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893812	1893880	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893881	1894000	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894001	1894099	1	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894001	1894099	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894100	1894254	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894255	1894326	1	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894255	1894326	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894327	1894451	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894452	1894529	0.73	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894452	1894529	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894530	1894708	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894709	1894929	1	-	2	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894709	1894929	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894930	1895092	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1895093	1895105	1	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1895093	1895105	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1895106	1895172	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1895173	1895207	0.65	-	2	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1895173	1895207	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1895208	1895363	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1895364	1896456	0.98	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1895364	1896456	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1896457	1896544	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1896545	1896676	0.96	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1896545	1896676	.	-	.	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	start_codon	1896674	1896676	.	-	0	transcript_id "Phchi.S5G019500.t1"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	transcript	1892505	1896676	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	stop_codon	1892502	1892504	.	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1892505	1892804	0.63	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1892505	1892804	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1892805	1892889	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1892890	1892998	0.92	-	1	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1892890	1892998	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1892999	1893086	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893087	1893261	0.87	-	2	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893087	1893261	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893262	1893350	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893351	1893419	0.85	-	2	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893351	1893419	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893420	1893535	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893536	1893677	0.56	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893536	1893677	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893678	1893811	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1893812	1893880	0.79	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1893812	1893880	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1893881	1894000	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894001	1894099	1	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894001	1894099	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894100	1894254	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894255	1894309	0.85	-	1	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894255	1894309	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894310	1894502	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894503	1894526	0.85	-	1	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894503	1894526	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894527	1894623	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894624	1894648	0.54	-	2	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894624	1894648	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894649	1894833	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1894834	1894929	0.28	-	2	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1894834	1894929	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1894930	1895092	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1895093	1895105	1	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1895093	1895105	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1895106	1895172	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1895173	1895207	0.64	-	2	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1895173	1895207	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1895208	1895363	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1895364	1896456	0.94	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1895364	1896456	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	intron	1896457	1896544	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	CDS	1896545	1896676	0.98	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	exon	1896545	1896676	.	-	.	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
Phchi.S5	AUGUSTUS	start_codon	1896674	1896676	.	-	0	transcript_id "Phchi.S5G019500.t2"; gene_id "Phchi.S5G019500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10147.t1 is derived from g7323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45982078	45986819	.	-	.	Phchi.S1G730600
Phchi.S1	AUGUSTUS	transcript	45982078	45986819	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	stop_codon	45982075	45982077	.	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45982078	45982122	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45982078	45982122	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45982123	45982222	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45982223	45982328	0.89	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45982223	45982328	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45982329	45982438	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45982439	45982519	0.89	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45982439	45982519	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45982520	45982617	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45982618	45982754	0.98	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45982618	45982754	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45982755	45982829	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45982830	45982923	1	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45982830	45982923	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45982924	45983002	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45983003	45983076	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45983003	45983076	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45983077	45983168	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45983169	45983330	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45983169	45983330	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45983331	45983418	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45983419	45983478	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45983419	45983478	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45983479	45983576	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45983577	45983639	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45983577	45983639	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45983640	45983717	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45983718	45983841	1	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45983718	45983841	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45983842	45983927	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45983928	45983980	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45983928	45983980	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45983981	45984061	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45984062	45984157	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45984062	45984157	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45984158	45984239	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45984240	45984342	1	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45984240	45984342	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45984343	45984435	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45984436	45984584	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45984436	45984584	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45984585	45984677	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45984678	45984706	0.9	-	2	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45984678	45984706	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45984707	45984807	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45984808	45984988	0.96	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45984808	45984988	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45984989	45985075	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45985076	45985199	1	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45985076	45985199	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45985200	45985281	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45985282	45985429	1	-	2	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45985282	45985429	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45985430	45985532	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45985533	45985611	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45985533	45985611	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45985612	45985718	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45985719	45985778	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45985719	45985778	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45985779	45985870	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45985871	45985972	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45985871	45985972	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45985973	45986128	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45986129	45986237	1	-	1	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45986129	45986237	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45986238	45986328	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45986329	45986543	1	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45986329	45986543	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	intron	45986544	45986645	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	CDS	45986646	45986819	0.98	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	exon	45986646	45986819	.	-	.	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
Phchi.S1	AUGUSTUS	start_codon	45986817	45986819	.	-	0	transcript_id "Phchi.S1G730600.t1"; gene_id "Phchi.S1G730600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg102.t1 is derived from g9884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	514378	516609	.	+	.	Phchi.S6G006100
Phchi.S6	AUGUSTUS	transcript	514378	516609	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	start_codon	514378	514380	.	+	0	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	CDS	514378	515499	0.42	+	0	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	exon	514378	515499	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	intron	515500	515656	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	CDS	515657	515730	0.41	+	0	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	exon	515657	515730	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	intron	515731	515850	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	CDS	515851	515957	0.42	+	1	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	exon	515851	515957	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	intron	515958	516142	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	CDS	516143	516609	0.89	+	2	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	exon	516143	516609	.	+	.	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
Phchi.S6	AUGUSTUS	stop_codon	516610	516612	.	+	0	transcript_id "Phchi.S6G006100.t1"; gene_id "Phchi.S6G006100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6809.t1 is derived from g3981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25148943	25153087	.	-	.	Phchi.S1G396800
Phchi.S1	AUGUSTUS	transcript	25148943	25153087	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	stop_codon	25148940	25148942	.	-	0	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25148943	25149160	0.61	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25148943	25149160	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25149161	25149240	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25149241	25149321	0.93	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25149241	25149321	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25149322	25149461	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25149462	25149500	1	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25149462	25149500	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25149501	25149682	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25149683	25149866	0.98	-	0	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25149683	25149866	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25149867	25149971	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25149972	25150091	0.91	-	0	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25149972	25150091	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25150092	25150203	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25150204	25150333	1	-	1	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25150204	25150333	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25150334	25150422	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25150423	25150486	1	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25150423	25150486	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25150487	25150578	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25150579	25150669	1	-	0	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25150579	25150669	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25150670	25150943	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25150944	25151620	0.92	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25150944	25151620	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25151621	25151707	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25151708	25151926	1	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25151708	25151926	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25151927	25152080	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25152081	25152182	0.91	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25152081	25152182	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25152183	25152347	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25152348	25152497	0.91	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25152348	25152497	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25152498	25152608	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25152609	25152890	0.95	-	2	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25152609	25152890	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	intron	25152891	25153068	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	CDS	25153069	25153087	1	-	0	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	exon	25153069	25153087	.	-	.	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
Phchi.S1	AUGUSTUS	start_codon	25153085	25153087	.	-	0	transcript_id "Phchi.S1G396800.t1"; gene_id "Phchi.S1G396800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13778.t1 is derived from g12245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8863641	8868477	.	+	.	Phchi.S3G109700
Phchi.S3	AUGUSTUS	transcript	8863641	8868477	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	start_codon	8863641	8863643	.	+	0	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8863641	8863776	0.75	+	0	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8863641	8863776	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8863777	8863892	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8863893	8863976	0.78	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8863893	8863976	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8863977	8864073	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8864074	8864371	0.34	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8864074	8864371	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8864372	8864562	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8864563	8864595	0.34	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8864563	8864595	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8864596	8864753	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8864754	8865259	0.33	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8864754	8865259	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8865260	8865403	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8865404	8865527	1	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8865404	8865527	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8865528	8865618	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8865619	8865699	1	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8865619	8865699	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8865700	8865849	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8865850	8865921	1	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8865850	8865921	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8865922	8866071	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8866072	8866149	1	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8866072	8866149	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8866150	8866260	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8866261	8866329	1	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8866261	8866329	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8866330	8866452	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8866453	8866787	1	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8866453	8866787	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8866788	8866921	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8866922	8866966	1	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8866922	8866966	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8866967	8867049	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8867050	8867249	1	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8867050	8867249	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8867250	8867327	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8867328	8867454	1	+	0	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8867328	8867454	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8867455	8867575	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8867576	8867641	1	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8867576	8867641	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8867642	8867783	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8867784	8867976	1	+	2	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8867784	8867976	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8867977	8868056	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8868057	8868192	1	+	1	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8868057	8868192	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	intron	8868193	8868291	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	CDS	8868292	8868477	0.98	+	0	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	exon	8868292	8868477	.	+	.	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
Phchi.S3	AUGUSTUS	stop_codon	8868478	8868480	.	+	0	transcript_id "Phchi.S3G109700.t1"; gene_id "Phchi.S3G109700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5738.t1 is derived from g2908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18668110	18670654	.	-	.	Phchi.S1G289700
Phchi.S1	AUGUSTUS	transcript	18668110	18670654	.	-	.	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	stop_codon	18668107	18668109	.	-	0	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	CDS	18668110	18668994	1	-	0	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	exon	18668110	18668994	.	-	.	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	intron	18668995	18669139	.	-	.	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	CDS	18669140	18670654	0.98	-	0	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	exon	18669140	18670654	.	-	.	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
Phchi.S1	AUGUSTUS	start_codon	18670652	18670654	.	-	0	transcript_id "Phchi.S1G289700.t1"; gene_id "Phchi.S1G289700"
# This transcript jg5868.t2 is derived from g3038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5869.t1 is derived from g3039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19484779	19486659	.	+	.	Phchi.S1G302800
Phchi.S1	AUGUSTUS	transcript	19484779	19486659	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	start_codon	19484779	19484781	.	+	0	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19484779	19484788	1	+	0	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19484779	19484788	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19484789	19484931	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19484932	19485126	1	+	2	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19484932	19485126	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19485127	19485390	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19485391	19485455	0.62	+	2	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19485391	19485455	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19485456	19485599	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19485600	19485640	0.5	+	0	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19485600	19485640	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19485641	19485811	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19485812	19485867	0.61	+	1	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19485812	19485867	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19485868	19485950	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19485951	19486048	0.63	+	2	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19485951	19486048	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19486049	19486126	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19486127	19486184	0.92	+	0	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19486127	19486184	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19486185	19486418	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19486419	19486564	0.3	+	2	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19486419	19486564	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	intron	19486565	19486644	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	CDS	19486645	19486659	0.82	+	0	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	exon	19486645	19486659	.	+	.	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
Phchi.S1	AUGUSTUS	stop_codon	19486660	19486662	.	+	0	transcript_id "Phchi.S1G302800.t1"; gene_id "Phchi.S1G302800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14893.t1 is derived from g13361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15305811	15308513	.	-	.	Phchi.S3G221200
Phchi.S3	AUGUSTUS	transcript	15305811	15308513	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	stop_codon	15305808	15305810	.	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15305811	15305844	0.95	-	1	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15305811	15305844	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15305845	15306030	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15306031	15306152	0.95	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15306031	15306152	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15306153	15306325	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15306326	15306397	0.91	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15306326	15306397	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15306398	15306485	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15306486	15306694	0.76	-	2	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15306486	15306694	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15306695	15306801	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15306802	15307288	0.93	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15306802	15307288	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15307289	15307371	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15307372	15307669	1	-	1	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15307372	15307669	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15307670	15307752	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15307753	15307933	1	-	2	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15307753	15307933	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15307934	15308062	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15308063	15308339	1	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15308063	15308339	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	intron	15308340	15308426	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	CDS	15308427	15308513	1	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	exon	15308427	15308513	.	-	.	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
Phchi.S3	AUGUSTUS	start_codon	15308511	15308513	.	-	0	transcript_id "Phchi.S3G221200.t1"; gene_id "Phchi.S3G221200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5856.t1 is derived from g3026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19382670	19383063	.	-	.	Phchi.S1G301500
Phchi.S1	AUGUSTUS	transcript	19382670	19383063	.	-	.	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	stop_codon	19382667	19382669	.	-	0	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	CDS	19382670	19382816	0.64	-	0	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	exon	19382670	19382816	.	-	.	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	intron	19382817	19382895	.	-	.	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	CDS	19382896	19383063	0.64	-	0	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	exon	19382896	19383063	.	-	.	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
Phchi.S1	AUGUSTUS	start_codon	19383061	19383063	.	-	0	transcript_id "Phchi.S1G301500.t1"; gene_id "Phchi.S1G301500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12736.t1 is derived from g11201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1456787	1458379	.	+	.	Phchi.S3G005500
Phchi.S3	AUGUSTUS	transcript	1456787	1458379	.	+	.	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	start_codon	1456787	1456789	.	+	0	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	CDS	1456787	1457158	0.35	+	0	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	exon	1456787	1457158	.	+	.	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	intron	1457159	1457320	.	+	.	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	CDS	1457321	1458379	0.77	+	0	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	exon	1457321	1458379	.	+	.	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
Phchi.S3	AUGUSTUS	stop_codon	1458380	1458382	.	+	0	transcript_id "Phchi.S3G005500.t1"; gene_id "Phchi.S3G005500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12524.t1 is derived from g8201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32863198	32864061	.	-	.	Phchi.S2G060400
Phchi.S2	AUGUSTUS	transcript	32863198	32864061	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	stop_codon	32863195	32863197	.	-	0	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	CDS	32863198	32863289	1	-	2	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	exon	32863198	32863289	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	intron	32863290	32863371	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	CDS	32863372	32863549	0.78	-	0	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	exon	32863372	32863549	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	intron	32863550	32863636	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	CDS	32863637	32863854	0.76	-	2	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	exon	32863637	32863854	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	intron	32863855	32863940	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	CDS	32863941	32864061	0.64	-	0	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	exon	32863941	32864061	.	-	.	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
Phchi.S2	AUGUSTUS	start_codon	32864059	32864061	.	-	0	transcript_id "Phchi.S2G060400.t1"; gene_id "Phchi.S2G060400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3562.t1 is derived from g731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4496292	4497089	.	-	.	Phchi.S1G072100
Phchi.S1	AUGUSTUS	transcript	4496292	4497089	.	-	.	transcript_id "Phchi.S1G072100.t1"; gene_id "Phchi.S1G072100"
Phchi.S1	AUGUSTUS	stop_codon	4496289	4496291	.	-	0	transcript_id "Phchi.S1G072100.t1"; gene_id "Phchi.S1G072100"
Phchi.S1	AUGUSTUS	CDS	4496292	4497089	0.48	-	0	transcript_id "Phchi.S1G072100.t1"; gene_id "Phchi.S1G072100"
Phchi.S1	AUGUSTUS	exon	4496292	4497089	.	-	.	transcript_id "Phchi.S1G072100.t1"; gene_id "Phchi.S1G072100"
Phchi.S1	AUGUSTUS	start_codon	4497087	4497089	.	-	0	transcript_id "Phchi.S1G072100.t1"; gene_id "Phchi.S1G072100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3942.t1 is derived from g1111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6576921	6578876	.	-	.	Phchi.S1G110100
Phchi.S1	AUGUSTUS	transcript	6576921	6578876	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	stop_codon	6576918	6576920	.	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6576921	6577109	1	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6576921	6577109	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6577110	6577224	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6577225	6577395	0.98	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6577225	6577395	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6577396	6577485	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6577486	6577869	1	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6577486	6577869	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6577870	6577992	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6577993	6578109	1	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6577993	6578109	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6578110	6578187	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6578188	6578252	0.96	-	2	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6578188	6578252	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6578253	6578302	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6578303	6578313	0.96	-	1	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6578303	6578313	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6578314	6578453	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6578454	6578542	1	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6578454	6578542	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6578543	6578684	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6578685	6578690	1	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6578685	6578690	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	intron	6578691	6578783	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	CDS	6578784	6578876	0.47	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	exon	6578784	6578876	.	-	.	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
Phchi.S1	AUGUSTUS	start_codon	6578874	6578876	.	-	0	transcript_id "Phchi.S1G110100.t1"; gene_id "Phchi.S1G110100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5509.t1 is derived from g2679.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17165815	17166416	.	-	.	Phchi.S1G266800
Phchi.S1	AUGUSTUS	transcript	17165815	17166416	.	-	.	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	stop_codon	17165812	17165814	.	-	0	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	CDS	17165815	17165928	1	-	0	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	exon	17165815	17165928	.	-	.	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	intron	17165929	17165994	.	-	.	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	CDS	17165995	17166126	1	-	0	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	exon	17165995	17166126	.	-	.	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	intron	17166127	17166209	.	-	.	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	CDS	17166210	17166416	0.75	-	0	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	exon	17166210	17166416	.	-	.	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	start_codon	17166414	17166416	.	-	0	transcript_id "Phchi.S1G266800.t1"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	transcript	17165889	17166416	.	-	.	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	stop_codon	17165886	17165888	.	-	0	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	CDS	17165889	17165921	0.63	-	0	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	exon	17165889	17165921	.	-	.	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	intron	17165922	17165994	.	-	.	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	CDS	17165995	17166126	0.93	-	0	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	exon	17165995	17166126	.	-	.	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	intron	17166127	17166209	.	-	.	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	CDS	17166210	17166416	0.71	-	0	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	exon	17166210	17166416	.	-	.	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
Phchi.S1	AUGUSTUS	start_codon	17166414	17166416	.	-	0	transcript_id "Phchi.S1G266800.t2"; gene_id "Phchi.S1G266800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg461.t1 is derived from g10243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3243501	3245948	.	-	.	Phchi.S6G042000
Phchi.S6	AUGUSTUS	transcript	3243501	3245948	.	-	.	transcript_id "Phchi.S6G042000.t1"; gene_id "Phchi.S6G042000"
Phchi.S6	AUGUSTUS	stop_codon	3243498	3243500	.	-	0	transcript_id "Phchi.S6G042000.t1"; gene_id "Phchi.S6G042000"
Phchi.S6	AUGUSTUS	CDS	3243501	3245948	0.81	-	0	transcript_id "Phchi.S6G042000.t1"; gene_id "Phchi.S6G042000"
Phchi.S6	AUGUSTUS	exon	3243501	3245948	.	-	.	transcript_id "Phchi.S6G042000.t1"; gene_id "Phchi.S6G042000"
Phchi.S6	AUGUSTUS	start_codon	3245946	3245948	.	-	0	transcript_id "Phchi.S6G042000.t1"; gene_id "Phchi.S6G042000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14947.t1 is derived from g13415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15656898	15658918	.	+	.	Phchi.S3G226600
Phchi.S3	AUGUSTUS	transcript	15656898	15658918	.	+	.	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	start_codon	15656898	15656900	.	+	0	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	CDS	15656898	15657897	0.99	+	0	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	exon	15656898	15657897	.	+	.	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	intron	15657898	15658016	.	+	.	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	CDS	15658017	15658918	0.94	+	2	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	exon	15658017	15658918	.	+	.	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
Phchi.S3	AUGUSTUS	stop_codon	15658919	15658921	.	+	0	transcript_id "Phchi.S3G226600.t1"; gene_id "Phchi.S3G226600"
# This transcript jg3546.t2 is derived from g715.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3547.t1 is derived from g716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4408847	4409632	.	-	.	Phchi.S1G070600
Phchi.S1	AUGUSTUS	transcript	4408847	4409632	.	-	.	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	stop_codon	4408844	4408846	.	-	0	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	CDS	4408847	4409013	0.51	-	2	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	exon	4408847	4409013	.	-	.	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	intron	4409014	4409087	.	-	.	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	CDS	4409088	4409339	0.91	-	2	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	exon	4409088	4409339	.	-	.	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	intron	4409340	4409424	.	-	.	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	CDS	4409425	4409632	0.51	-	0	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	exon	4409425	4409632	.	-	.	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
Phchi.S1	AUGUSTUS	start_codon	4409630	4409632	.	-	0	transcript_id "Phchi.S1G070600.t1"; gene_id "Phchi.S1G070600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8212.t1 is derived from g5387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34442585	34445076	.	+	.	Phchi.S1G537100
Phchi.S1	AUGUSTUS	transcript	34442585	34445076	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	start_codon	34442585	34442587	.	+	0	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34442585	34442884	0.76	+	0	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34442585	34442884	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34442885	34443391	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34443392	34443503	1	+	0	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34443392	34443503	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34443504	34443600	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34443601	34443788	1	+	2	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34443601	34443788	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34443789	34443924	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34443925	34444002	1	+	0	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34443925	34444002	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34444003	34444187	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34444188	34444263	1	+	0	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34444188	34444263	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34444264	34444348	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34444349	34444456	1	+	2	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34444349	34444456	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34444457	34444592	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34444593	34444665	1	+	2	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34444593	34444665	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	intron	34444666	34445018	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	CDS	34445019	34445076	1	+	1	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	exon	34445019	34445076	.	+	.	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
Phchi.S1	AUGUSTUS	stop_codon	34445077	34445079	.	+	0	transcript_id "Phchi.S1G537100.t1"; gene_id "Phchi.S1G537100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2535.t1 is derived from g9455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7195642	7198698	.	-	.	Phchi.S5G114400
Phchi.S5	AUGUSTUS	transcript	7195642	7198698	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	stop_codon	7195639	7195641	.	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7195642	7196105	1	-	2	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7195642	7196105	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7196106	7196190	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7196191	7196356	1	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7196191	7196356	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7196357	7196453	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7196454	7196642	1	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7196454	7196642	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7196643	7196754	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7196755	7197000	0.52	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7196755	7197000	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7197001	7197180	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7197181	7197215	0.35	-	2	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7197181	7197215	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7197216	7197510	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7197511	7197605	0.29	-	1	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7197511	7197605	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7197606	7197826	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7197827	7197915	0.35	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7197827	7197915	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7197916	7198016	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7198017	7198127	0.98	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7198017	7198127	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7198128	7198211	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7198212	7198355	0.99	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7198212	7198355	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	intron	7198356	7198467	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	CDS	7198468	7198698	0.99	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	exon	7198468	7198698	.	-	.	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
Phchi.S5	AUGUSTUS	start_codon	7198696	7198698	.	-	0	transcript_id "Phchi.S5G114400.t1"; gene_id "Phchi.S5G114400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5098.t1 is derived from g2268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14728748	14729287	.	+	.	Phchi.S1G225700
Phchi.S1	AUGUSTUS	transcript	14728748	14729287	.	+	.	transcript_id "Phchi.S1G225700.t1"; gene_id "Phchi.S1G225700"
Phchi.S1	AUGUSTUS	start_codon	14728748	14728750	.	+	0	transcript_id "Phchi.S1G225700.t1"; gene_id "Phchi.S1G225700"
Phchi.S1	AUGUSTUS	CDS	14728748	14729287	0.85	+	0	transcript_id "Phchi.S1G225700.t1"; gene_id "Phchi.S1G225700"
Phchi.S1	AUGUSTUS	exon	14728748	14729287	.	+	.	transcript_id "Phchi.S1G225700.t1"; gene_id "Phchi.S1G225700"
Phchi.S1	AUGUSTUS	stop_codon	14729288	14729290	.	+	0	transcript_id "Phchi.S1G225700.t1"; gene_id "Phchi.S1G225700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg108.t1 is derived from g9890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	580201	582592	.	-	.	Phchi.S6G006700
Phchi.S6	AUGUSTUS	transcript	580201	582592	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	stop_codon	580198	580200	.	-	0	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	580201	580490	1	-	2	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	580201	580490	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	intron	580491	580587	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	580588	580753	0.99	-	0	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	580588	580753	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	intron	580754	580860	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	580861	581175	1	-	0	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	580861	581175	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	intron	581176	581275	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	581276	581573	1	-	1	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	581276	581573	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	intron	581574	581794	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	581795	581972	1	-	2	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	581795	581972	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	intron	581973	582109	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	582110	582383	1	-	0	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	582110	582383	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	intron	582384	582487	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	CDS	582488	582592	0.89	-	0	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	exon	582488	582592	.	-	.	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
Phchi.S6	AUGUSTUS	start_codon	582590	582592	.	-	0	transcript_id "Phchi.S6G006700.t1"; gene_id "Phchi.S6G006700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8952.t1 is derived from g6127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38833009	38836462	.	-	.	Phchi.S1G611100
Phchi.S1	AUGUSTUS	transcript	38833009	38836462	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	stop_codon	38833006	38833008	.	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38833009	38833196	0.99	-	2	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38833009	38833196	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38833197	38833260	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38833261	38833382	1	-	1	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38833261	38833382	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38833383	38833455	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38833456	38833541	1	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38833456	38833541	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38833542	38833636	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38833637	38833750	1	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38833637	38833750	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38833751	38833833	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38833834	38834206	1	-	1	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38833834	38834206	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38834207	38834299	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38834300	38834436	1	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38834300	38834436	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38834437	38834573	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38834574	38834682	1	-	1	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38834574	38834682	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38834683	38834784	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38834785	38834906	1	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38834785	38834906	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38834907	38834993	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38834994	38835100	1	-	2	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38834994	38835100	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38835101	38835203	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38835204	38835308	1	-	2	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38835204	38835308	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38835309	38835438	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38835439	38835594	1	-	2	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38835439	38835594	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38835595	38835679	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38835680	38835735	1	-	1	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38835680	38835735	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38835736	38835817	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38835818	38835869	1	-	2	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38835818	38835869	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	intron	38835870	38835975	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	CDS	38835976	38836462	0.81	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	exon	38835976	38836462	.	-	.	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
Phchi.S1	AUGUSTUS	start_codon	38836460	38836462	.	-	0	transcript_id "Phchi.S1G611100.t1"; gene_id "Phchi.S1G611100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10442.t1 is derived from g14491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	350558	351673	.	-	.	Phchi.S4G002400
Phchi.S4	AUGUSTUS	transcript	350558	351673	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	stop_codon	350555	350557	.	-	0	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	CDS	350558	350662	1	-	0	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	exon	350558	350662	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	intron	350663	350760	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	CDS	350761	350969	1	-	2	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	exon	350761	350969	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	intron	350970	351056	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	CDS	351057	351282	1	-	0	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	exon	351057	351282	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	intron	351283	351424	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	CDS	351425	351673	0.99	-	0	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	exon	351425	351673	.	-	.	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
Phchi.S4	AUGUSTUS	start_codon	351671	351673	.	-	0	transcript_id "Phchi.S4G002400.t1"; gene_id "Phchi.S4G002400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6577.t1 is derived from g3749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23830158	23832930	.	+	.	Phchi.S1G373600
Phchi.S1	AUGUSTUS	transcript	23830158	23832930	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	start_codon	23830158	23830160	.	+	0	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23830158	23830219	0.19	+	0	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23830158	23830219	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23830220	23830419	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23830420	23830772	0.15	+	1	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23830420	23830772	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23830773	23830978	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23830979	23831458	1	+	2	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23830979	23831458	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23831459	23831555	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23831556	23831620	0.19	+	2	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23831556	23831620	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23831621	23831826	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23831827	23832003	0.28	+	0	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23831827	23832003	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832004	23832100	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832101	23832200	0.61	+	0	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832101	23832200	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832201	23832392	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832393	23832475	0.63	+	2	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832393	23832475	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832476	23832658	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832659	23832734	0.36	+	0	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832659	23832734	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832735	23832817	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832818	23832930	0.52	+	2	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832818	23832930	.	+	.	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	stop_codon	23832931	23832933	.	+	0	transcript_id "Phchi.S1G373600.t1"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	transcript	23830158	23832930	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	start_codon	23830158	23830160	.	+	0	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23830158	23830219	0.26	+	0	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23830158	23830219	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23830220	23830419	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23830420	23830772	0.2	+	1	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23830420	23830772	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23830773	23830978	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23830979	23831458	1	+	2	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23830979	23831458	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23831459	23831546	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23831547	23831620	0.18	+	2	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23831547	23831620	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23831621	23831826	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23831827	23832003	0.34	+	0	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23831827	23832003	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832004	23832100	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832101	23832200	0.54	+	0	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832101	23832200	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832201	23832392	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832393	23832475	0.56	+	2	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832393	23832475	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832476	23832658	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832659	23832734	0.31	+	0	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832659	23832734	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	intron	23832735	23832817	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	CDS	23832818	23832930	0.48	+	2	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	exon	23832818	23832930	.	+	.	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
Phchi.S1	AUGUSTUS	stop_codon	23832931	23832933	.	+	0	transcript_id "Phchi.S1G373600.t2"; gene_id "Phchi.S1G373600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5413.t1 is derived from g2583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16746891	16750120	.	-	.	Phchi.S1G257200
Phchi.S1	AUGUSTUS	transcript	16746891	16750120	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	stop_codon	16746888	16746890	.	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16746891	16746991	0.75	-	2	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16746891	16746991	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16746992	16747077	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16747078	16747220	1	-	1	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16747078	16747220	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16747221	16747299	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16747300	16747364	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16747300	16747364	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16747365	16747451	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16747452	16747508	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16747452	16747508	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16747509	16747588	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16747589	16747664	1	-	1	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16747589	16747664	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16747665	16747737	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16747738	16747849	1	-	2	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16747738	16747849	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16747850	16747977	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16747978	16748062	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16747978	16748062	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16748063	16748256	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16748257	16748517	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16748257	16748517	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16748518	16748669	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16748670	16748777	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16748670	16748777	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16748778	16748866	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16748867	16748944	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16748867	16748944	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16748945	16749028	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16749029	16749133	1	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16749029	16749133	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16749134	16749211	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16749212	16749306	0.97	-	2	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16749212	16749306	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16749307	16749415	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16749416	16749477	0.98	-	1	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16749416	16749477	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	intron	16749478	16749590	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	CDS	16749591	16750120	0.95	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	exon	16749591	16750120	.	-	.	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
Phchi.S1	AUGUSTUS	start_codon	16750118	16750120	.	-	0	transcript_id "Phchi.S1G257200.t1"; gene_id "Phchi.S1G257200"
# This transcript jg11027.t2 is derived from g15077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11028.t1 is derived from g15078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3710159	3710923	.	-	.	Phchi.S4G061000
Phchi.S4	AUGUSTUS	transcript	3710159	3710923	.	-	.	transcript_id "Phchi.S4G061000.t1"; gene_id "Phchi.S4G061000"
Phchi.S4	AUGUSTUS	stop_codon	3710156	3710158	.	-	0	transcript_id "Phchi.S4G061000.t1"; gene_id "Phchi.S4G061000"
Phchi.S4	AUGUSTUS	CDS	3710159	3710923	0.68	-	0	transcript_id "Phchi.S4G061000.t1"; gene_id "Phchi.S4G061000"
Phchi.S4	AUGUSTUS	exon	3710159	3710923	.	-	.	transcript_id "Phchi.S4G061000.t1"; gene_id "Phchi.S4G061000"
Phchi.S4	AUGUSTUS	start_codon	3710921	3710923	.	-	0	transcript_id "Phchi.S4G061000.t1"; gene_id "Phchi.S4G061000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4940.t1 is derived from g2110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13666378	13668243	.	+	.	Phchi.S1G209900
Phchi.S1	AUGUSTUS	transcript	13666378	13668243	.	+	.	transcript_id "Phchi.S1G209900.t1"; gene_id "Phchi.S1G209900"
Phchi.S1	AUGUSTUS	start_codon	13666378	13666380	.	+	0	transcript_id "Phchi.S1G209900.t1"; gene_id "Phchi.S1G209900"
Phchi.S1	AUGUSTUS	CDS	13666378	13668243	1	+	0	transcript_id "Phchi.S1G209900.t1"; gene_id "Phchi.S1G209900"
Phchi.S1	AUGUSTUS	exon	13666378	13668243	.	+	.	transcript_id "Phchi.S1G209900.t1"; gene_id "Phchi.S1G209900"
Phchi.S1	AUGUSTUS	stop_codon	13668244	13668246	.	+	0	transcript_id "Phchi.S1G209900.t1"; gene_id "Phchi.S1G209900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4104.t1 is derived from g1273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7829923	7830825	.	-	.	Phchi.S1G126300
Phchi.S1	AUGUSTUS	transcript	7829923	7830825	.	-	.	transcript_id "Phchi.S1G126300.t1"; gene_id "Phchi.S1G126300"
Phchi.S1	AUGUSTUS	stop_codon	7829920	7829922	.	-	0	transcript_id "Phchi.S1G126300.t1"; gene_id "Phchi.S1G126300"
Phchi.S1	AUGUSTUS	CDS	7829923	7830825	0.57	-	0	transcript_id "Phchi.S1G126300.t1"; gene_id "Phchi.S1G126300"
Phchi.S1	AUGUSTUS	exon	7829923	7830825	.	-	.	transcript_id "Phchi.S1G126300.t1"; gene_id "Phchi.S1G126300"
Phchi.S1	AUGUSTUS	start_codon	7830823	7830825	.	-	0	transcript_id "Phchi.S1G126300.t1"; gene_id "Phchi.S1G126300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4333.t1 is derived from g1502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9823735	9826462	.	+	.	Phchi.S1G149200
Phchi.S1	AUGUSTUS	transcript	9823735	9826462	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	start_codon	9823735	9823737	.	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9823735	9823850	0.98	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9823735	9823850	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9823851	9823936	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9823937	9824345	0.99	+	1	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9823937	9824345	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9824346	9824456	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9824457	9824579	0.95	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9824457	9824579	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9824580	9824770	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9824771	9824994	1	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9824771	9824994	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9824995	9825103	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9825104	9825233	1	+	1	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9825104	9825233	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9825234	9825375	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9825376	9825438	1	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9825376	9825438	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9825439	9825571	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9825572	9825649	1	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9825572	9825649	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9825650	9825731	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9825732	9825823	0.96	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9825732	9825823	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9825824	9825932	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9825933	9825998	1	+	1	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9825933	9825998	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9825999	9826110	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9826111	9826264	0.96	+	1	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9826111	9826264	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	intron	9826265	9826366	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	CDS	9826367	9826462	0.96	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	exon	9826367	9826462	.	+	.	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
Phchi.S1	AUGUSTUS	stop_codon	9826463	9826465	.	+	0	transcript_id "Phchi.S1G149200.t1"; gene_id "Phchi.S1G149200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13874.t1 is derived from g12341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9422069	9424184	.	+	.	Phchi.S3G119300
Phchi.S3	AUGUSTUS	transcript	9422069	9424184	.	+	.	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	start_codon	9422069	9422071	.	+	0	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	CDS	9422069	9422103	0.84	+	0	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	exon	9422069	9422103	.	+	.	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	intron	9422104	9422187	.	+	.	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	CDS	9422188	9423167	0.9	+	1	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	exon	9422188	9423167	.	+	.	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	intron	9423168	9423624	.	+	.	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	CDS	9423625	9424184	1	+	2	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	exon	9423625	9424184	.	+	.	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
Phchi.S3	AUGUSTUS	stop_codon	9424185	9424187	.	+	0	transcript_id "Phchi.S3G119300.t1"; gene_id "Phchi.S3G119300"
# This transcript jg1218.t2 is derived from g11001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1219.t1 is derived from g11002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8449820	8450863	.	+	.	Phchi.S6G117800
Phchi.S6	AUGUSTUS	transcript	8449820	8450863	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	start_codon	8449820	8449822	.	+	0	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	CDS	8449820	8449840	0.97	+	0	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	exon	8449820	8449840	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	intron	8449841	8449917	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	CDS	8449918	8449992	1	+	0	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	exon	8449918	8449992	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	intron	8449993	8450165	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	CDS	8450166	8450270	1	+	0	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	exon	8450166	8450270	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	intron	8450271	8450390	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	CDS	8450391	8450469	1	+	0	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	exon	8450391	8450469	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	intron	8450470	8450561	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	CDS	8450562	8450615	0.98	+	2	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	exon	8450562	8450615	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	intron	8450616	8450813	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	CDS	8450814	8450863	1	+	2	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	exon	8450814	8450863	.	+	.	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
Phchi.S6	AUGUSTUS	stop_codon	8450864	8450866	.	+	0	transcript_id "Phchi.S6G117800.t1"; gene_id "Phchi.S6G117800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15192.t1 is derived from g13660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17492543	17493176	.	-	.	Phchi.S3G251100
Phchi.S3	AUGUSTUS	transcript	17492543	17493176	.	-	.	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	stop_codon	17492540	17492542	.	-	0	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	CDS	17492543	17492545	1	-	0	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	exon	17492543	17492545	.	-	.	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	intron	17492546	17492882	.	-	.	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	CDS	17492883	17493004	1	-	2	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	exon	17492883	17493004	.	-	.	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	intron	17493005	17493103	.	-	.	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	CDS	17493104	17493176	1	-	0	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	exon	17493104	17493176	.	-	.	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
Phchi.S3	AUGUSTUS	start_codon	17493174	17493176	.	-	0	transcript_id "Phchi.S3G251100.t1"; gene_id "Phchi.S3G251100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15159.t1 is derived from g13627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17315371	17316535	.	-	.	Phchi.S3G247800
Phchi.S3	AUGUSTUS	transcript	17315371	17316535	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	stop_codon	17315368	17315370	.	-	0	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	CDS	17315371	17315409	1	-	0	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	exon	17315371	17315409	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	intron	17315410	17315496	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	CDS	17315497	17315666	1	-	2	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	exon	17315497	17315666	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	intron	17315667	17315755	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	CDS	17315756	17315966	1	-	0	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	exon	17315756	17315966	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	intron	17315967	17316035	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	CDS	17316036	17316279	0.99	-	1	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	exon	17316036	17316279	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	intron	17316280	17316362	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	CDS	17316363	17316535	0.49	-	0	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	exon	17316363	17316535	.	-	.	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
Phchi.S3	AUGUSTUS	start_codon	17316533	17316535	.	-	0	transcript_id "Phchi.S3G247800.t1"; gene_id "Phchi.S3G247800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11947.t1 is derived from g7622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	155843	157209	.	-	.	Phchi.S2G002700
Phchi.S2	AUGUSTUS	transcript	155843	157209	.	-	.	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	stop_codon	155840	155842	.	-	0	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	CDS	155843	156067	0.92	-	0	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	exon	155843	156067	.	-	.	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	intron	156068	156369	.	-	.	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	CDS	156370	156585	1	-	0	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	exon	156370	156585	.	-	.	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	intron	156586	156909	.	-	.	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	CDS	156910	157209	0.96	-	0	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	exon	156910	157209	.	-	.	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
Phchi.S2	AUGUSTUS	start_codon	157207	157209	.	-	0	transcript_id "Phchi.S2G002700.t1"; gene_id "Phchi.S2G002700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12.t1 is derived from g9779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C265	AUGUSTUS	gene	2815	3292	.	+	.	Phchi.C265G000300
Phchi.C265	AUGUSTUS	transcript	2815	3292	.	+	.	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	start_codon	2815	2817	.	+	0	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	CDS	2815	2922	0.47	+	0	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	exon	2815	2922	.	+	.	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	intron	2923	3022	.	+	.	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	CDS	3023	3075	0.56	+	0	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	exon	3023	3075	.	+	.	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	intron	3076	3222	.	+	.	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	CDS	3223	3292	0.94	+	1	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	exon	3223	3292	.	+	.	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
Phchi.C265	AUGUSTUS	stop_codon	3293	3295	.	+	0	transcript_id "Phchi.C265G000300.t1"; gene_id "Phchi.C265G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2664.t1 is derived from g9584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8109860	8110800	.	-	.	Phchi.S5G127300
Phchi.S5	AUGUSTUS	transcript	8109860	8110800	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	stop_codon	8109857	8109859	.	-	0	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	CDS	8109860	8109976	0.71	-	0	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	exon	8109860	8109976	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	intron	8109977	8110168	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	CDS	8110169	8110327	0.58	-	0	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	exon	8110169	8110327	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	intron	8110328	8110462	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	CDS	8110463	8110592	0.26	-	1	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	exon	8110463	8110592	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	intron	8110593	8110717	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	CDS	8110718	8110800	0.24	-	0	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	exon	8110718	8110800	.	-	.	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
Phchi.S5	AUGUSTUS	start_codon	8110798	8110800	.	-	0	transcript_id "Phchi.S5G127300.t1"; gene_id "Phchi.S5G127300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11153.t1 is derived from g15203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4397443	4399058	.	-	.	Phchi.S4G073500
Phchi.S4	AUGUSTUS	transcript	4397443	4399058	.	-	.	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	stop_codon	4397440	4397442	.	-	0	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	CDS	4397443	4397891	0.93	-	2	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	exon	4397443	4397891	.	-	.	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	intron	4397892	4397971	.	-	.	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	CDS	4397972	4398137	1	-	0	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	exon	4397972	4398137	.	-	.	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	intron	4398138	4398230	.	-	.	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	CDS	4398231	4399058	1	-	0	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	exon	4398231	4399058	.	-	.	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
Phchi.S4	AUGUSTUS	start_codon	4399056	4399058	.	-	0	transcript_id "Phchi.S4G073500.t1"; gene_id "Phchi.S4G073500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6175.t1 is derived from g3346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21309531	21318158	.	+	.	Phchi.S1G333400
Phchi.S1	AUGUSTUS	transcript	21309531	21318158	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	start_codon	21309531	21309533	.	+	0	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	CDS	21309531	21309596	1	+	0	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	exon	21309531	21309596	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	intron	21309597	21309699	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	CDS	21309700	21310963	0.75	+	0	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	exon	21309700	21310963	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	intron	21310964	21311097	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	CDS	21311098	21311146	0.73	+	2	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	exon	21311098	21311146	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	intron	21311147	21311241	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	CDS	21311242	21311439	0.72	+	1	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	exon	21311242	21311439	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	intron	21311440	21311528	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	CDS	21311529	21317314	0.43	+	1	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	exon	21311529	21317314	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	intron	21317315	21317604	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	CDS	21317605	21318158	0.82	+	2	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	exon	21317605	21318158	.	+	.	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
Phchi.S1	AUGUSTUS	stop_codon	21318159	21318161	.	+	0	transcript_id "Phchi.S1G333400.t1"; gene_id "Phchi.S1G333400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14822.t1 is derived from g13290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14889744	14891636	.	+	.	Phchi.S3G214100
Phchi.S3	AUGUSTUS	transcript	14889744	14891636	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	start_codon	14889744	14889746	.	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14889744	14889854	1	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14889744	14889854	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14889855	14890000	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14890001	14890265	1	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14890001	14890265	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14890266	14890359	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14890360	14890493	1	+	2	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14890360	14890493	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14890494	14890588	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14890589	14890667	1	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14890589	14890667	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14890668	14890744	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14890745	14890836	1	+	2	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14890745	14890836	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14890837	14890928	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14890929	14891006	1	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14890929	14891006	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14891007	14891091	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14891092	14891154	1	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14891092	14891154	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14891155	14891231	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14891232	14891466	1	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14891232	14891466	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	intron	14891467	14891571	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	CDS	14891572	14891636	1	+	2	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	exon	14891572	14891636	.	+	.	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
Phchi.S3	AUGUSTUS	stop_codon	14891637	14891639	.	+	0	transcript_id "Phchi.S3G214100.t1"; gene_id "Phchi.S3G214100"
# This transcript jg7051.t2 is derived from g4223.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7052.t1 is derived from g4224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26628786	26629346	.	-	.	Phchi.S1G421100
Phchi.S1	AUGUSTUS	transcript	26628786	26629346	.	-	.	transcript_id "Phchi.S1G421100.t1"; gene_id "Phchi.S1G421100"
Phchi.S1	AUGUSTUS	stop_codon	26628783	26628785	.	-	0	transcript_id "Phchi.S1G421100.t1"; gene_id "Phchi.S1G421100"
Phchi.S1	AUGUSTUS	CDS	26628786	26629346	0.48	-	0	transcript_id "Phchi.S1G421100.t1"; gene_id "Phchi.S1G421100"
Phchi.S1	AUGUSTUS	exon	26628786	26629346	.	-	.	transcript_id "Phchi.S1G421100.t1"; gene_id "Phchi.S1G421100"
Phchi.S1	AUGUSTUS	start_codon	26629344	26629346	.	-	0	transcript_id "Phchi.S1G421100.t1"; gene_id "Phchi.S1G421100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg388.t1 is derived from g10170.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2845207	2846971	.	-	.	Phchi.S6G034700
Phchi.S6	AUGUSTUS	transcript	2845207	2846971	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	stop_codon	2845204	2845206	.	-	0	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845207	2845263	0.66	-	0	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845207	2845263	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845264	2845412	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845413	2845449	0.66	-	1	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845413	2845449	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845450	2845685	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845686	2845774	0.97	-	0	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845686	2845774	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845775	2845863	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845864	2845973	1	-	2	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845864	2845973	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845974	2846072	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846073	2846141	1	-	2	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846073	2846141	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2846142	2846229	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846230	2846320	1	-	0	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846230	2846320	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2846321	2846424	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846425	2846531	0.99	-	2	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846425	2846531	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2846532	2846670	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846671	2846971	0.61	-	0	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846671	2846971	.	-	.	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	start_codon	2846969	2846971	.	-	0	transcript_id "Phchi.S6G034700.t1"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	transcript	2845207	2846691	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	stop_codon	2845204	2845206	.	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845207	2845263	0.76	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845207	2845263	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845264	2845412	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845413	2845449	0.76	-	1	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845413	2845449	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845450	2845685	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845686	2845774	0.99	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845686	2845774	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845775	2845863	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2845864	2845973	1	-	2	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2845864	2845973	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2845974	2846072	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846073	2846141	1	-	2	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846073	2846141	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2846142	2846229	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846230	2846320	0.85	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846230	2846320	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2846321	2846424	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846425	2846583	0.64	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846425	2846583	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	intron	2846584	2846670	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	CDS	2846671	2846691	0.58	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	exon	2846671	2846691	.	-	.	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
Phchi.S6	AUGUSTUS	start_codon	2846689	2846691	.	-	0	transcript_id "Phchi.S6G034700.t2"; gene_id "Phchi.S6G034700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5011.t1 is derived from g2181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14024969	14028128	.	-	.	Phchi.S1G217000
Phchi.S1	AUGUSTUS	transcript	14024969	14028128	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	stop_codon	14024966	14024968	.	-	0	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	CDS	14024969	14026020	0.72	-	2	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	exon	14024969	14026020	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	intron	14026021	14026164	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	CDS	14026165	14026408	1	-	0	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	exon	14026165	14026408	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	intron	14026409	14026598	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	CDS	14026599	14027111	1	-	0	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	exon	14026599	14027111	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	intron	14027112	14027192	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	CDS	14027193	14028128	1	-	0	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	exon	14027193	14028128	.	-	.	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
Phchi.S1	AUGUSTUS	start_codon	14028126	14028128	.	-	0	transcript_id "Phchi.S1G217000.t1"; gene_id "Phchi.S1G217000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13659.t1 is derived from g12126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8045209	8046030	.	-	.	Phchi.S3G097800
Phchi.S3	AUGUSTUS	transcript	8045209	8046030	.	-	.	transcript_id "Phchi.S3G097800.t1"; gene_id "Phchi.S3G097800"
Phchi.S3	AUGUSTUS	stop_codon	8045206	8045208	.	-	0	transcript_id "Phchi.S3G097800.t1"; gene_id "Phchi.S3G097800"
Phchi.S3	AUGUSTUS	CDS	8045209	8046030	0.54	-	0	transcript_id "Phchi.S3G097800.t1"; gene_id "Phchi.S3G097800"
Phchi.S3	AUGUSTUS	exon	8045209	8046030	.	-	.	transcript_id "Phchi.S3G097800.t1"; gene_id "Phchi.S3G097800"
Phchi.S3	AUGUSTUS	start_codon	8046028	8046030	.	-	0	transcript_id "Phchi.S3G097800.t1"; gene_id "Phchi.S3G097800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14919.t1 is derived from g13387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15501027	15508685	.	-	.	Phchi.S3G223800
Phchi.S3	AUGUSTUS	transcript	15501027	15508685	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	stop_codon	15501024	15501026	.	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15501027	15501695	0.46	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15501027	15501695	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15501696	15501779	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15501780	15502331	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15501780	15502331	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15502332	15502411	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15502412	15502597	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15502412	15502597	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15502598	15502698	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15502699	15502764	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15502699	15502764	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15502765	15502945	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15502946	15503035	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15502946	15503035	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15503036	15503186	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15503187	15503450	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15503187	15503450	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15503451	15503557	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15503558	15503629	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15503558	15503629	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15503630	15503736	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15503737	15503790	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15503737	15503790	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15503791	15503883	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15503884	15503973	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15503884	15503973	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15503974	15504051	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15504052	15504207	0.99	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15504052	15504207	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15504208	15504331	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15504332	15504434	1	-	1	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15504332	15504434	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15504435	15504551	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15504552	15504643	0.99	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15504552	15504643	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15504644	15504810	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15504811	15504897	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15504811	15504897	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15504898	15504999	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15505000	15505188	0.99	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15505000	15505188	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15505189	15505310	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15505311	15505364	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15505311	15505364	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15505365	15505535	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15505536	15505592	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15505536	15505592	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15505593	15505672	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15505673	15505762	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15505673	15505762	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15505763	15505843	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15505844	15505909	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15505844	15505909	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15505910	15506028	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15506029	15506100	0.75	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15506029	15506100	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15506101	15506235	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15506236	15506355	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15506236	15506355	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15506356	15506504	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15506505	15506631	1	-	1	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15506505	15506631	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15506632	15506738	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15506739	15506851	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15506739	15506851	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15506852	15506939	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15506940	15507047	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15506940	15507047	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15507048	15507139	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15507140	15507208	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15507140	15507208	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15507209	15507298	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15507299	15507397	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15507299	15507397	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15507398	15507465	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15507466	15507650	1	-	2	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15507466	15507650	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15507651	15507729	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15507730	15507862	1	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15507730	15507862	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15507863	15507972	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15507973	15508020	0.99	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15507973	15508020	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15508021	15508125	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15508126	15508233	0.81	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15508126	15508233	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15508234	15508321	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15508322	15508386	1	-	2	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15508322	15508386	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	intron	15508387	15508618	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	CDS	15508619	15508685	0.67	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	exon	15508619	15508685	.	-	.	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
Phchi.S3	AUGUSTUS	start_codon	15508683	15508685	.	-	0	transcript_id "Phchi.S3G223800.t1"; gene_id "Phchi.S3G223800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg695.t1 is derived from g10477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4948077	4948640	.	+	.	Phchi.S6G065400
Phchi.S6	AUGUSTUS	transcript	4948077	4948640	.	+	.	transcript_id "Phchi.S6G065400.t1"; gene_id "Phchi.S6G065400"
Phchi.S6	AUGUSTUS	start_codon	4948077	4948079	.	+	0	transcript_id "Phchi.S6G065400.t1"; gene_id "Phchi.S6G065400"
Phchi.S6	AUGUSTUS	CDS	4948077	4948640	0.54	+	0	transcript_id "Phchi.S6G065400.t1"; gene_id "Phchi.S6G065400"
Phchi.S6	AUGUSTUS	exon	4948077	4948640	.	+	.	transcript_id "Phchi.S6G065400.t1"; gene_id "Phchi.S6G065400"
Phchi.S6	AUGUSTUS	stop_codon	4948641	4948643	.	+	0	transcript_id "Phchi.S6G065400.t1"; gene_id "Phchi.S6G065400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12640.t1 is derived from g9792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C183	AUGUSTUS	gene	27887	28228	.	+	.	Phchi.C183G000400
Phchi.C183	AUGUSTUS	transcript	27887	28228	.	+	.	transcript_id "Phchi.C183G000400.t1"; gene_id "Phchi.C183G000400"
Phchi.C183	AUGUSTUS	start_codon	27887	27889	.	+	0	transcript_id "Phchi.C183G000400.t1"; gene_id "Phchi.C183G000400"
Phchi.C183	AUGUSTUS	CDS	27887	28228	1	+	0	transcript_id "Phchi.C183G000400.t1"; gene_id "Phchi.C183G000400"
Phchi.C183	AUGUSTUS	exon	27887	28228	.	+	.	transcript_id "Phchi.C183G000400.t1"; gene_id "Phchi.C183G000400"
Phchi.C183	AUGUSTUS	stop_codon	28229	28231	.	+	0	transcript_id "Phchi.C183G000400.t1"; gene_id "Phchi.C183G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4405.t1 is derived from g1574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10254844	10256172	.	-	.	Phchi.S1G156400
Phchi.S1	AUGUSTUS	transcript	10254844	10256172	.	-	.	transcript_id "Phchi.S1G156400.t1"; gene_id "Phchi.S1G156400"
Phchi.S1	AUGUSTUS	stop_codon	10254841	10254843	.	-	0	transcript_id "Phchi.S1G156400.t1"; gene_id "Phchi.S1G156400"
Phchi.S1	AUGUSTUS	CDS	10254844	10256172	1	-	0	transcript_id "Phchi.S1G156400.t1"; gene_id "Phchi.S1G156400"
Phchi.S1	AUGUSTUS	exon	10254844	10256172	.	-	.	transcript_id "Phchi.S1G156400.t1"; gene_id "Phchi.S1G156400"
Phchi.S1	AUGUSTUS	start_codon	10256170	10256172	.	-	0	transcript_id "Phchi.S1G156400.t1"; gene_id "Phchi.S1G156400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12580.t1 is derived from g8257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35825838	35826583	.	-	.	Phchi.S2G066000
Phchi.S2	AUGUSTUS	transcript	35825838	35826583	.	-	.	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	stop_codon	35825835	35825837	.	-	0	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	CDS	35825838	35826211	0.96	-	2	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	exon	35825838	35826211	.	-	.	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	intron	35826212	35826309	.	-	.	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	CDS	35826310	35826583	0.93	-	0	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	exon	35826310	35826583	.	-	.	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
Phchi.S2	AUGUSTUS	start_codon	35826581	35826583	.	-	0	transcript_id "Phchi.S2G066000.t1"; gene_id "Phchi.S2G066000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11840.t1 is derived from g15892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8526221	8530267	.	-	.	Phchi.S4G142200
Phchi.S4	AUGUSTUS	transcript	8526221	8530267	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	stop_codon	8526218	8526220	.	-	0	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8526221	8526811	0.99	-	0	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8526221	8526811	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	intron	8526812	8526900	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8526901	8527333	0.97	-	1	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8526901	8527333	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	intron	8527334	8527453	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8527454	8528319	0.74	-	0	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8527454	8528319	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	intron	8528320	8528468	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8528469	8528757	0.4	-	1	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8528469	8528757	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	intron	8528758	8528879	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8528880	8529262	0.41	-	0	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8528880	8529262	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	intron	8529263	8529364	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8529365	8529582	1	-	2	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8529365	8529582	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	intron	8529583	8529837	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	CDS	8529838	8530267	0.49	-	0	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	exon	8529838	8530267	.	-	.	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
Phchi.S4	AUGUSTUS	start_codon	8530265	8530267	.	-	0	transcript_id "Phchi.S4G142200.t1"; gene_id "Phchi.S4G142200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5141.t1 is derived from g2311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15129497	15129913	.	-	.	Phchi.S1G230000
Phchi.S1	AUGUSTUS	transcript	15129497	15129913	.	-	.	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	stop_codon	15129494	15129496	.	-	0	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	CDS	15129497	15129725	0.78	-	1	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	exon	15129497	15129725	.	-	.	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	intron	15129726	15129815	.	-	.	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	CDS	15129816	15129913	0.78	-	0	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	exon	15129816	15129913	.	-	.	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
Phchi.S1	AUGUSTUS	start_codon	15129911	15129913	.	-	0	transcript_id "Phchi.S1G230000.t1"; gene_id "Phchi.S1G230000"
# This transcript jg2003.t2 is derived from g8923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2003.t3 is derived from g8923.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2004.t1 is derived from g8924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4409795	4410973	.	-	.	Phchi.S5G061300
Phchi.S5	AUGUSTUS	transcript	4409795	4410973	.	-	.	transcript_id "Phchi.S5G061300.t1"; gene_id "Phchi.S5G061300"
Phchi.S5	AUGUSTUS	stop_codon	4409792	4409794	.	-	0	transcript_id "Phchi.S5G061300.t1"; gene_id "Phchi.S5G061300"
Phchi.S5	AUGUSTUS	CDS	4409795	4410973	0.62	-	0	transcript_id "Phchi.S5G061300.t1"; gene_id "Phchi.S5G061300"
Phchi.S5	AUGUSTUS	exon	4409795	4410973	.	-	.	transcript_id "Phchi.S5G061300.t1"; gene_id "Phchi.S5G061300"
Phchi.S5	AUGUSTUS	start_codon	4410971	4410973	.	-	0	transcript_id "Phchi.S5G061300.t1"; gene_id "Phchi.S5G061300"
# This transcript jg2704.t2 is derived from g9624.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2705.t1 is derived from g9625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8264868	8266590	.	-	.	Phchi.S5G131400
Phchi.S5	AUGUSTUS	transcript	8264868	8266590	.	-	.	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	stop_codon	8264865	8264867	.	-	0	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	CDS	8264868	8265363	1	-	1	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	exon	8264868	8265363	.	-	.	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	intron	8265364	8265471	.	-	.	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	CDS	8265472	8266051	1	-	2	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	exon	8265472	8266051	.	-	.	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	intron	8266052	8266178	.	-	.	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	CDS	8266179	8266590	0.84	-	0	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	exon	8266179	8266590	.	-	.	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
Phchi.S5	AUGUSTUS	start_codon	8266588	8266590	.	-	0	transcript_id "Phchi.S5G131400.t1"; gene_id "Phchi.S5G131400"
# This transcript jg1426.t1 is derived from g8345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	794499	794834	.	-	.	Phchi.S5G003500
Phchi.S5	AUGUSTUS	transcript	794499	794834	.	-	.	transcript_id "Phchi.S5G003500.t1"; gene_id "Phchi.S5G003500"
Phchi.S5	AUGUSTUS	stop_codon	794496	794498	.	-	0	transcript_id "Phchi.S5G003500.t1"; gene_id "Phchi.S5G003500"
Phchi.S5	AUGUSTUS	CDS	794499	794834	0.3	-	0	transcript_id "Phchi.S5G003500.t1"; gene_id "Phchi.S5G003500"
Phchi.S5	AUGUSTUS	exon	794499	794834	.	-	.	transcript_id "Phchi.S5G003500.t1"; gene_id "Phchi.S5G003500"
Phchi.S5	AUGUSTUS	start_codon	794832	794834	.	-	0	transcript_id "Phchi.S5G003500.t1"; gene_id "Phchi.S5G003500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12815.t1 is derived from g11280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2484941	2487119	.	+	.	Phchi.S3G013400
Phchi.S3	AUGUSTUS	transcript	2484941	2487119	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	start_codon	2484941	2484943	.	+	0	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	CDS	2484941	2485410	0.78	+	0	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	exon	2484941	2485410	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	intron	2485411	2485653	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	CDS	2485654	2485978	0.44	+	1	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	exon	2485654	2485978	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	intron	2485979	2486084	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	CDS	2486085	2486374	0.85	+	0	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	exon	2486085	2486374	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	intron	2486375	2486478	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	CDS	2486479	2486834	1	+	1	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	exon	2486479	2486834	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	intron	2486835	2486928	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	CDS	2486929	2487119	0.99	+	2	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	exon	2486929	2487119	.	+	.	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
Phchi.S3	AUGUSTUS	stop_codon	2487120	2487122	.	+	0	transcript_id "Phchi.S3G013400.t1"; gene_id "Phchi.S3G013400"
# This transcript jg7703.t2 is derived from g4877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7703.t3 is derived from g4877.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7704.t1 is derived from g4878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30712875	30714238	.	+	.	Phchi.S1G486300
Phchi.S1	AUGUSTUS	transcript	30712875	30714238	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	start_codon	30712875	30712877	.	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30712875	30713033	1	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30712875	30713033	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30713034	30713140	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30713141	30713215	1	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30713141	30713215	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30713216	30713346	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30713347	30713435	1	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30713347	30713435	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30713436	30713508	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30713509	30713593	1	+	1	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30713509	30713593	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30713594	30713769	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30713770	30713851	1	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30713770	30713851	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30713852	30713919	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30713920	30713936	1	+	2	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30713920	30713936	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30713937	30714023	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30714024	30714078	1	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30714024	30714078	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	intron	30714079	30714236	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	CDS	30714237	30714238	1	+	2	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	exon	30714237	30714238	.	+	.	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
Phchi.S1	AUGUSTUS	stop_codon	30714239	30714241	.	+	0	transcript_id "Phchi.S1G486300.t1"; gene_id "Phchi.S1G486300"
# This transcript jg13434.t2 is derived from g11901.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13435.t1 is derived from g11902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6685792	6686747	.	+	.	Phchi.S3G075400
Phchi.S3	AUGUSTUS	transcript	6685792	6686747	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	start_codon	6685792	6685794	.	+	0	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6685792	6685815	1	+	0	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6685792	6685815	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6685816	6685900	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6685901	6685954	1	+	0	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6685901	6685954	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6685955	6686030	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686031	6686136	1	+	0	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686031	6686136	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6686137	6686242	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686243	6686249	1	+	2	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686243	6686249	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6686250	6686420	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686421	6686505	1	+	1	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686421	6686505	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6686506	6686636	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686637	6686747	1	+	0	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686637	6686747	.	+	.	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	stop_codon	6686748	6686750	.	+	0	transcript_id "Phchi.S3G075400.t1"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	transcript	6685792	6686747	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	start_codon	6685792	6685794	.	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6685792	6685815	1	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6685792	6685815	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6685816	6685900	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6685901	6685954	1	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6685901	6685954	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6685955	6686030	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686031	6686153	0.42	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686031	6686153	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6686154	6686324	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686325	6686329	0.89	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686325	6686329	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6686330	6686420	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686421	6686505	0.98	+	1	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686421	6686505	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	intron	6686506	6686636	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	CDS	6686637	6686747	1	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	exon	6686637	6686747	.	+	.	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
Phchi.S3	AUGUSTUS	stop_codon	6686748	6686750	.	+	0	transcript_id "Phchi.S3G075400.t2"; gene_id "Phchi.S3G075400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8180.t1 is derived from g5355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34320365	34322353	.	-	.	Phchi.S1G533900
Phchi.S1	AUGUSTUS	transcript	34320365	34322353	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	stop_codon	34320362	34320364	.	-	0	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	CDS	34320365	34320510	0.31	-	2	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	exon	34320365	34320510	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	intron	34320511	34320729	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	CDS	34320730	34320861	0.26	-	2	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	exon	34320730	34320861	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	intron	34320862	34321269	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	CDS	34321270	34321725	0.41	-	2	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	exon	34321270	34321725	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	intron	34321726	34321866	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	CDS	34321867	34322002	0.56	-	0	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	exon	34321867	34322002	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	intron	34322003	34322098	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	CDS	34322099	34322353	0.71	-	0	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	exon	34322099	34322353	.	-	.	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
Phchi.S1	AUGUSTUS	start_codon	34322351	34322353	.	-	0	transcript_id "Phchi.S1G533900.t1"; gene_id "Phchi.S1G533900"
# This transcript jg8387.t2 is derived from g5562.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8388.t1 is derived from g5563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35668233	35670584	.	+	.	Phchi.S1G554700
Phchi.S1	AUGUSTUS	transcript	35668233	35670584	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	start_codon	35668233	35668235	.	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35668233	35668442	1	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35668233	35668442	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35668443	35668635	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35668636	35668749	1	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35668636	35668749	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35668750	35668829	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35668830	35668963	1	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35668830	35668963	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35668964	35669204	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35669205	35669361	1	+	1	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35669205	35669361	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35669362	35669459	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35669460	35669671	1	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35669460	35669671	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35669672	35669805	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35669806	35669906	0.76	+	1	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35669806	35669906	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35669907	35670006	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35670007	35670260	1	+	2	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35670007	35670260	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	intron	35670261	35670338	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	CDS	35670339	35670584	0.58	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	exon	35670339	35670584	.	+	.	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
Phchi.S1	AUGUSTUS	stop_codon	35670585	35670587	.	+	0	transcript_id "Phchi.S1G554700.t1"; gene_id "Phchi.S1G554700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2057.t1 is derived from g8977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4634118	4635440	.	-	.	Phchi.S5G066600
Phchi.S5	AUGUSTUS	transcript	4634118	4635440	.	-	.	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	stop_codon	4634115	4634117	.	-	0	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	CDS	4634118	4634611	0.98	-	2	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	exon	4634118	4634611	.	-	.	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	intron	4634612	4634725	.	-	.	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	CDS	4634726	4635440	0.72	-	0	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	exon	4634726	4635440	.	-	.	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
Phchi.S5	AUGUSTUS	start_codon	4635438	4635440	.	-	0	transcript_id "Phchi.S5G066600.t1"; gene_id "Phchi.S5G066600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2605.t1 is derived from g9525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7746941	7747616	.	-	.	Phchi.S5G121400
Phchi.S5	AUGUSTUS	transcript	7746941	7747616	.	-	.	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	stop_codon	7746938	7746940	.	-	0	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	CDS	7746941	7747114	0.97	-	0	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	exon	7746941	7747114	.	-	.	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	intron	7747115	7747214	.	-	.	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	CDS	7747215	7747616	0.6	-	0	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	exon	7747215	7747616	.	-	.	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
Phchi.S5	AUGUSTUS	start_codon	7747614	7747616	.	-	0	transcript_id "Phchi.S5G121400.t1"; gene_id "Phchi.S5G121400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12352.t1 is derived from g8028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12501158	12501646	.	+	.	Phchi.S2G043200
Phchi.S2	AUGUSTUS	transcript	12501158	12501646	.	+	.	transcript_id "Phchi.S2G043200.t1"; gene_id "Phchi.S2G043200"
Phchi.S2	AUGUSTUS	start_codon	12501158	12501160	.	+	0	transcript_id "Phchi.S2G043200.t1"; gene_id "Phchi.S2G043200"
Phchi.S2	AUGUSTUS	CDS	12501158	12501646	0.76	+	0	transcript_id "Phchi.S2G043200.t1"; gene_id "Phchi.S2G043200"
Phchi.S2	AUGUSTUS	exon	12501158	12501646	.	+	.	transcript_id "Phchi.S2G043200.t1"; gene_id "Phchi.S2G043200"
Phchi.S2	AUGUSTUS	stop_codon	12501647	12501649	.	+	0	transcript_id "Phchi.S2G043200.t1"; gene_id "Phchi.S2G043200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3511.t1 is derived from g680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4144770	4146399	.	+	.	Phchi.S1G067000
Phchi.S1	AUGUSTUS	transcript	4144770	4146399	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	start_codon	4144770	4144772	.	+	0	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	CDS	4144770	4144809	0.99	+	0	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	exon	4144770	4144809	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	intron	4144810	4145054	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	CDS	4145055	4145187	1	+	2	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	exon	4145055	4145187	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	intron	4145188	4145556	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	CDS	4145557	4145684	0.71	+	1	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	exon	4145557	4145684	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	intron	4145685	4145828	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	CDS	4145829	4145952	1	+	2	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	exon	4145829	4145952	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	intron	4145953	4146287	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	CDS	4146288	4146399	1	+	1	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	exon	4146288	4146399	.	+	.	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
Phchi.S1	AUGUSTUS	stop_codon	4146400	4146402	.	+	0	transcript_id "Phchi.S1G067000.t1"; gene_id "Phchi.S1G067000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg446.t1 is derived from g10228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3124395	3127461	.	+	.	Phchi.S6G040500
Phchi.S6	AUGUSTUS	transcript	3124395	3127461	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	start_codon	3124395	3124397	.	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3124395	3124532	0.92	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3124395	3124532	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3124533	3124652	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3124653	3124710	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3124653	3124710	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3124711	3124832	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3124833	3125113	0.96	+	2	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3124833	3125113	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3125114	3125200	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3125201	3125314	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3125201	3125314	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3125315	3125393	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3125394	3125454	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3125394	3125454	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3125455	3125545	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3125546	3125634	1	+	2	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3125546	3125634	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3125635	3125726	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3125727	3125801	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3125727	3125801	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3125802	3125877	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3125878	3125963	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3125878	3125963	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3125964	3126062	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3126063	3126112	1	+	1	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3126063	3126112	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3126113	3126282	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3126283	3126323	1	+	2	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3126283	3126323	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3126324	3126413	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3126414	3126575	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3126414	3126575	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3126576	3126715	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3126716	3126751	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3126716	3126751	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3126752	3126871	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3126872	3126939	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3126872	3126939	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3126940	3127035	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3127036	3127096	1	+	1	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3127036	3127096	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	intron	3127097	3127188	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	CDS	3127189	3127461	1	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	exon	3127189	3127461	.	+	.	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
Phchi.S6	AUGUSTUS	stop_codon	3127462	3127464	.	+	0	transcript_id "Phchi.S6G040500.t1"; gene_id "Phchi.S6G040500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14670.t1 is derived from g13138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14110196	14111508	.	-	.	Phchi.S3G198900
Phchi.S3	AUGUSTUS	transcript	14110196	14111508	.	-	.	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	stop_codon	14110193	14110195	.	-	0	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	CDS	14110196	14111160	0.96	-	2	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	exon	14110196	14111160	.	-	.	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	intron	14111161	14111240	.	-	.	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	CDS	14111241	14111508	0.83	-	0	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	exon	14111241	14111508	.	-	.	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
Phchi.S3	AUGUSTUS	start_codon	14111506	14111508	.	-	0	transcript_id "Phchi.S3G198900.t1"; gene_id "Phchi.S3G198900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7634.t1 is derived from g4808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30332992	30335078	.	-	.	Phchi.S1G479300
Phchi.S1	AUGUSTUS	transcript	30332992	30335078	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	stop_codon	30332989	30332991	.	-	0	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30332992	30333038	0.99	-	2	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30332992	30333038	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30333039	30333134	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30333135	30333174	1	-	0	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30333135	30333174	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30333175	30333302	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30333303	30333375	1	-	1	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30333303	30333375	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30333376	30333452	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30333453	30333530	1	-	1	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30333453	30333530	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30333531	30333632	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30333633	30333669	1	-	2	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30333633	30333669	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30333670	30334103	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30334104	30334164	1	-	0	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30334104	30334164	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30334165	30334277	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30334278	30334562	1	-	0	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30334278	30334562	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	intron	30334563	30335021	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	CDS	30335022	30335078	1	-	0	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	exon	30335022	30335078	.	-	.	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
Phchi.S1	AUGUSTUS	start_codon	30335076	30335078	.	-	0	transcript_id "Phchi.S1G479300.t1"; gene_id "Phchi.S1G479300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9779.t1 is derived from g6955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43625916	43626944	.	-	.	Phchi.S1G693800
Phchi.S1	AUGUSTUS	transcript	43625916	43626374	.	-	.	transcript_id "Phchi.S1G693800.t1"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	stop_codon	43625913	43625915	.	-	0	transcript_id "Phchi.S1G693800.t1"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	CDS	43625916	43626374	0.64	-	0	transcript_id "Phchi.S1G693800.t1"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	exon	43625916	43626374	.	-	.	transcript_id "Phchi.S1G693800.t1"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	start_codon	43626372	43626374	.	-	0	transcript_id "Phchi.S1G693800.t1"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	transcript	43625916	43626944	.	-	.	transcript_id "Phchi.S1G693800.t2"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	stop_codon	43625913	43625915	.	-	0	transcript_id "Phchi.S1G693800.t2"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	CDS	43625916	43626944	0.57	-	0	transcript_id "Phchi.S1G693800.t2"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	exon	43625916	43626944	.	-	.	transcript_id "Phchi.S1G693800.t2"; gene_id "Phchi.S1G693800"
Phchi.S1	AUGUSTUS	start_codon	43626942	43626944	.	-	0	transcript_id "Phchi.S1G693800.t2"; gene_id "Phchi.S1G693800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4197.t1 is derived from g1366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8872553	8873392	.	-	.	Phchi.S1G135600
Phchi.S1	AUGUSTUS	transcript	8872553	8873392	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	stop_codon	8872550	8872552	.	-	0	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	CDS	8872553	8872688	0.89	-	1	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	exon	8872553	8872688	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	intron	8872689	8872907	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	CDS	8872908	8872963	0.66	-	0	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	exon	8872908	8872963	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	intron	8872964	8873062	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	CDS	8873063	8873084	1	-	1	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	exon	8873063	8873084	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	intron	8873085	8873223	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	CDS	8873224	8873302	0.91	-	2	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	exon	8873224	8873302	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	intron	8873303	8873379	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	CDS	8873380	8873392	0.98	-	0	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	exon	8873380	8873392	.	-	.	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
Phchi.S1	AUGUSTUS	start_codon	8873390	8873392	.	-	0	transcript_id "Phchi.S1G135600.t1"; gene_id "Phchi.S1G135600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15969.t1 is derived from g14402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C26	AUGUSTUS	gene	79372	86203	.	+	.	Phchi.C26G000100
Phchi.C26	AUGUSTUS	transcript	79372	86203	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	start_codon	79372	79374	.	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	79372	79611	0.84	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	79372	79611	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	79612	80304	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	80305	80501	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	80305	80501	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	80502	80699	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	80700	80853	1	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	80700	80853	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	80854	81035	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81036	81145	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81036	81145	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81146	81480	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81481	81550	1	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81481	81550	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81551	81680	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81681	81763	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81681	81763	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81764	81907	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81908	81980	1	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81908	81980	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81981	82104	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82105	82145	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82105	82145	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82146	82392	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82393	82515	1	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82393	82515	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82516	82607	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82608	82746	1	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82608	82746	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82747	82845	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82846	82960	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82846	82960	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82961	83221	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83222	83304	1	+	2	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83222	83304	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	83305	83491	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83492	83566	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83492	83566	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	83567	83678	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83679	83753	1	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83679	83753	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	83754	83998	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83999	84876	0.64	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83999	84876	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	84877	85038	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	85039	85368	1	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	85039	85368	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	85369	85447	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	85448	85923	0.96	+	1	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	85448	85923	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	85924	86135	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	86136	86203	0.98	+	2	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	86136	86203	.	+	.	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	stop_codon	86204	86206	.	+	0	transcript_id "Phchi.C26G000100.t1"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	transcript	79372	86203	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	start_codon	79372	79374	.	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	79372	79611	0.84	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	79372	79611	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	79612	80304	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	80305	80501	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	80305	80501	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	80502	80699	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	80700	80853	1	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	80700	80853	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	80854	81035	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81036	81145	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81036	81145	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81146	81480	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81481	81550	1	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81481	81550	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81551	81680	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81681	81763	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81681	81763	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81764	81901	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	81902	81980	1	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	81902	81980	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	81981	82104	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82105	82145	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82105	82145	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82146	82392	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82393	82515	1	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82393	82515	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82516	82607	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82608	82746	1	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82608	82746	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82747	82845	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	82846	82960	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	82846	82960	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	82961	83221	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83222	83304	1	+	2	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83222	83304	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	83305	83491	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83492	83566	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83492	83566	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	83567	83678	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83679	83753	1	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83679	83753	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	83754	83998	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	83999	84876	0.57	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	83999	84876	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	84877	85038	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	85039	85368	1	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	85039	85368	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	85369	85447	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	85448	85923	0.93	+	1	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	85448	85923	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	intron	85924	86135	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	CDS	86136	86203	0.93	+	2	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	exon	86136	86203	.	+	.	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
Phchi.C26	AUGUSTUS	stop_codon	86204	86206	.	+	0	transcript_id "Phchi.C26G000100.t2"; gene_id "Phchi.C26G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7752.t1 is derived from g4926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30957132	30957958	.	-	.	Phchi.S1G491100
Phchi.S1	AUGUSTUS	transcript	30957132	30957958	.	-	.	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	stop_codon	30957129	30957131	.	-	0	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	CDS	30957132	30957645	0.49	-	1	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	exon	30957132	30957645	.	-	.	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	intron	30957646	30957761	.	-	.	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	CDS	30957762	30957958	0.92	-	0	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	exon	30957762	30957958	.	-	.	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
Phchi.S1	AUGUSTUS	start_codon	30957956	30957958	.	-	0	transcript_id "Phchi.S1G491100.t1"; gene_id "Phchi.S1G491100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5009.t1 is derived from g2179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14016118	14019079	.	+	.	Phchi.S1G216800
Phchi.S1	AUGUSTUS	transcript	14016118	14019079	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	start_codon	14016118	14016120	.	+	0	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14016118	14016477	0.39	+	0	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14016118	14016477	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14016478	14016644	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14016645	14016888	1	+	0	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14016645	14016888	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14016889	14017018	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14017019	14017105	0.5	+	2	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14017019	14017105	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14017106	14017203	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14017204	14017538	0.89	+	2	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14017204	14017538	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14017539	14017735	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14017736	14017772	0.87	+	0	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14017736	14017772	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14017773	14017932	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14017933	14018007	0.47	+	2	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14017933	14018007	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14018008	14018199	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14018200	14018310	0.43	+	2	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14018200	14018310	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14018311	14018402	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14018403	14018603	0.88	+	2	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14018403	14018603	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	intron	14018604	14019026	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	CDS	14019027	14019079	0.88	+	2	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	exon	14019027	14019079	.	+	.	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
Phchi.S1	AUGUSTUS	stop_codon	14019080	14019082	.	+	0	transcript_id "Phchi.S1G216800.t1"; gene_id "Phchi.S1G216800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12440.t1 is derived from g8117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20415903	20416415	.	+	.	Phchi.S2G052000
Phchi.S2	AUGUSTUS	transcript	20415903	20416415	.	+	.	transcript_id "Phchi.S2G052000.t1"; gene_id "Phchi.S2G052000"
Phchi.S2	AUGUSTUS	start_codon	20415903	20415905	.	+	0	transcript_id "Phchi.S2G052000.t1"; gene_id "Phchi.S2G052000"
Phchi.S2	AUGUSTUS	CDS	20415903	20416415	0.89	+	0	transcript_id "Phchi.S2G052000.t1"; gene_id "Phchi.S2G052000"
Phchi.S2	AUGUSTUS	exon	20415903	20416415	.	+	.	transcript_id "Phchi.S2G052000.t1"; gene_id "Phchi.S2G052000"
Phchi.S2	AUGUSTUS	stop_codon	20416416	20416418	.	+	0	transcript_id "Phchi.S2G052000.t1"; gene_id "Phchi.S2G052000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3103.t1 is derived from g272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1761067	1761950	.	-	.	Phchi.S1G026200
Phchi.S1	AUGUSTUS	transcript	1761067	1761950	.	-	.	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	stop_codon	1761064	1761066	.	-	0	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	CDS	1761067	1761421	0.99	-	1	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	exon	1761067	1761421	.	-	.	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	intron	1761422	1761535	.	-	.	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	CDS	1761536	1761791	1	-	2	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	exon	1761536	1761791	.	-	.	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	intron	1761792	1761934	.	-	.	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	CDS	1761935	1761950	0.59	-	0	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	exon	1761935	1761950	.	-	.	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
Phchi.S1	AUGUSTUS	start_codon	1761948	1761950	.	-	0	transcript_id "Phchi.S1G026200.t1"; gene_id "Phchi.S1G026200"
# This transcript jg9492.t2 is derived from g6668.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9493.t1 is derived from g6669.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42014681	42018262	.	-	.	Phchi.S1G665200
Phchi.S1	AUGUSTUS	transcript	42014681	42018262	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	stop_codon	42014678	42014680	.	-	0	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42014681	42014777	1	-	1	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42014681	42014777	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42014778	42014864	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42014865	42014971	1	-	0	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42014865	42014971	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42014972	42015062	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015063	42015174	0.99	-	1	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015063	42015174	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015175	42015264	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015265	42015352	0.52	-	2	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015265	42015352	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015353	42015426	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015427	42015581	0.52	-	1	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015427	42015581	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015582	42015713	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015714	42015842	1	-	1	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015714	42015842	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015843	42015923	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015924	42016286	1	-	1	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015924	42016286	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42016287	42016469	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42016470	42018262	0.99	-	0	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42016470	42018262	.	-	.	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	start_codon	42018260	42018262	.	-	0	transcript_id "Phchi.S1G665200.t1"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	transcript	42014681	42018262	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	stop_codon	42014678	42014680	.	-	0	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42014681	42014780	0.98	-	1	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42014681	42014780	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42014781	42014864	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42014865	42014971	1	-	0	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42014865	42014971	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42014972	42015062	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015063	42015174	0.97	-	1	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015063	42015174	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015175	42015264	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015265	42015352	0.49	-	2	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015265	42015352	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015353	42015426	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015427	42015581	0.49	-	1	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015427	42015581	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015582	42015713	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015714	42015842	1	-	1	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015714	42015842	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42015843	42015923	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42015924	42016286	1	-	1	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42015924	42016286	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	intron	42016287	42016469	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	CDS	42016470	42018262	0.96	-	0	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	exon	42016470	42018262	.	-	.	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
Phchi.S1	AUGUSTUS	start_codon	42018260	42018262	.	-	0	transcript_id "Phchi.S1G665200.t2"; gene_id "Phchi.S1G665200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7499.t1 is derived from g4673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29677040	29677294	.	+	.	Phchi.S1G465800
Phchi.S1	AUGUSTUS	transcript	29677040	29677294	.	+	.	transcript_id "Phchi.S1G465800.t1"; gene_id "Phchi.S1G465800"
Phchi.S1	AUGUSTUS	start_codon	29677040	29677042	.	+	0	transcript_id "Phchi.S1G465800.t1"; gene_id "Phchi.S1G465800"
Phchi.S1	AUGUSTUS	CDS	29677040	29677294	0.68	+	0	transcript_id "Phchi.S1G465800.t1"; gene_id "Phchi.S1G465800"
Phchi.S1	AUGUSTUS	exon	29677040	29677294	.	+	.	transcript_id "Phchi.S1G465800.t1"; gene_id "Phchi.S1G465800"
Phchi.S1	AUGUSTUS	stop_codon	29677295	29677297	.	+	0	transcript_id "Phchi.S1G465800.t1"; gene_id "Phchi.S1G465800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13827.t1 is derived from g12294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9088284	9089462	.	+	.	Phchi.S3G114600
Phchi.S3	AUGUSTUS	transcript	9088284	9089462	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	start_codon	9088284	9088286	.	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	CDS	9088284	9088627	0.83	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	exon	9088284	9088627	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	intron	9088628	9088724	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	CDS	9088725	9088776	1	+	1	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	exon	9088725	9088776	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	intron	9088777	9088920	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	CDS	9088921	9088995	1	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	exon	9088921	9088995	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	intron	9088996	9089088	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	CDS	9089089	9089151	1	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	exon	9089089	9089151	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	intron	9089152	9089240	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	CDS	9089241	9089300	1	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	exon	9089241	9089300	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	intron	9089301	9089390	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	CDS	9089391	9089462	0.95	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	exon	9089391	9089462	.	+	.	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
Phchi.S3	AUGUSTUS	stop_codon	9089463	9089465	.	+	0	transcript_id "Phchi.S3G114600.t1"; gene_id "Phchi.S3G114600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10255.t1 is derived from g7431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46703779	46705356	.	+	.	Phchi.S1G741400
Phchi.S1	AUGUSTUS	transcript	46703779	46705356	.	+	.	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	start_codon	46703779	46703781	.	+	0	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	CDS	46703779	46704060	0.56	+	0	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	exon	46703779	46704060	.	+	.	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	intron	46704061	46704298	.	+	.	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	CDS	46704299	46704480	1	+	0	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	exon	46704299	46704480	.	+	.	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	intron	46704481	46704722	.	+	.	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	CDS	46704723	46705356	1	+	1	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	exon	46704723	46705356	.	+	.	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
Phchi.S1	AUGUSTUS	stop_codon	46705357	46705359	.	+	0	transcript_id "Phchi.S1G741400.t1"; gene_id "Phchi.S1G741400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7186.t1 is derived from g4358.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27451432	27456140	.	-	.	Phchi.S1G434500
Phchi.S1	AUGUSTUS	transcript	27451432	27456140	.	-	.	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	stop_codon	27451429	27451431	.	-	0	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	CDS	27451432	27455999	0.55	-	2	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	exon	27451432	27455999	.	-	.	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	intron	27456000	27456079	.	-	.	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	CDS	27456080	27456140	0.69	-	0	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	exon	27456080	27456140	.	-	.	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	start_codon	27456138	27456140	.	-	0	transcript_id "Phchi.S1G434500.t1"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	transcript	27451432	27453696	.	-	.	transcript_id "Phchi.S1G434500.t2"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	stop_codon	27451429	27451431	.	-	0	transcript_id "Phchi.S1G434500.t2"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	CDS	27451432	27453696	0.94	-	0	transcript_id "Phchi.S1G434500.t2"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	exon	27451432	27453696	.	-	.	transcript_id "Phchi.S1G434500.t2"; gene_id "Phchi.S1G434500"
Phchi.S1	AUGUSTUS	start_codon	27453694	27453696	.	-	0	transcript_id "Phchi.S1G434500.t2"; gene_id "Phchi.S1G434500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4.t1 is derived from g14426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C114	AUGUSTUS	gene	29592	30053	.	-	.	Phchi.C114G000100
Phchi.C114	AUGUSTUS	transcript	29592	30053	.	-	.	transcript_id "Phchi.C114G000100.t1"; gene_id "Phchi.C114G000100"
Phchi.C114	AUGUSTUS	stop_codon	29589	29591	.	-	0	transcript_id "Phchi.C114G000100.t1"; gene_id "Phchi.C114G000100"
Phchi.C114	AUGUSTUS	CDS	29592	30053	0.47	-	0	transcript_id "Phchi.C114G000100.t1"; gene_id "Phchi.C114G000100"
Phchi.C114	AUGUSTUS	exon	29592	30053	.	-	.	transcript_id "Phchi.C114G000100.t1"; gene_id "Phchi.C114G000100"
Phchi.C114	AUGUSTUS	start_codon	30051	30053	.	-	0	transcript_id "Phchi.C114G000100.t1"; gene_id "Phchi.C114G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14067.t1 is derived from g12534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10635182	10637503	.	-	.	Phchi.S3G138600
Phchi.S3	AUGUSTUS	transcript	10635182	10637503	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	stop_codon	10635179	10635181	.	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10635182	10635247	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10635182	10635247	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10635248	10635330	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10635331	10635390	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10635331	10635390	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10635391	10635520	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10635521	10635591	1	-	2	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10635521	10635591	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10635592	10635671	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10635672	10635699	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10635672	10635699	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10635700	10635828	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10635829	10635975	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10635829	10635975	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10635976	10636107	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10636108	10636362	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10636108	10636362	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10636363	10636565	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10636566	10636628	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10636566	10636628	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10636629	10636750	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10636751	10636861	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10636751	10636861	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10636862	10637018	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10637019	10637072	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10637019	10637072	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10637073	10637169	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10637170	10637358	1	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10637170	10637358	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	intron	10637359	10637437	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	CDS	10637438	10637503	0.59	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	exon	10637438	10637503	.	-	.	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
Phchi.S3	AUGUSTUS	start_codon	10637501	10637503	.	-	0	transcript_id "Phchi.S3G138600.t1"; gene_id "Phchi.S3G138600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4304.t1 is derived from g1473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9516599	9517547	.	+	.	Phchi.S1G146300
Phchi.S1	AUGUSTUS	transcript	9516599	9517547	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	start_codon	9516599	9516601	.	+	0	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	CDS	9516599	9516739	0.99	+	0	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	exon	9516599	9516739	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	intron	9516740	9516969	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	CDS	9516970	9517056	1	+	0	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	exon	9516970	9517056	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	intron	9517057	9517173	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	CDS	9517174	9517242	1	+	0	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	exon	9517174	9517242	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	intron	9517243	9517415	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	CDS	9517416	9517547	1	+	0	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	exon	9517416	9517547	.	+	.	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
Phchi.S1	AUGUSTUS	stop_codon	9517548	9517550	.	+	0	transcript_id "Phchi.S1G146300.t1"; gene_id "Phchi.S1G146300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9209.t1 is derived from g6384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40401516	40402184	.	+	.	Phchi.S1G636800
Phchi.S1	AUGUSTUS	transcript	40401516	40402184	.	+	.	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	start_codon	40401516	40401518	.	+	0	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	CDS	40401516	40401922	0.81	+	0	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	exon	40401516	40401922	.	+	.	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	intron	40401923	40402036	.	+	.	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	CDS	40402037	40402184	0.97	+	1	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	exon	40402037	40402184	.	+	.	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
Phchi.S1	AUGUSTUS	stop_codon	40402185	40402187	.	+	0	transcript_id "Phchi.S1G636800.t1"; gene_id "Phchi.S1G636800"
# This transcript jg1738.t2 is derived from g8658.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1739.t1 is derived from g8659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2786246	2787620	.	+	.	Phchi.S5G034800
Phchi.S5	AUGUSTUS	transcript	2786246	2787620	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	start_codon	2786246	2786248	.	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	CDS	2786246	2786443	1	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	exon	2786246	2786443	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	intron	2786444	2786575	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	CDS	2786576	2786797	1	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	exon	2786576	2786797	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	intron	2786798	2786893	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	CDS	2786894	2787013	1	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	exon	2786894	2787013	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	intron	2787014	2787113	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	CDS	2787114	2787386	1	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	exon	2787114	2787386	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	intron	2787387	2787467	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	CDS	2787468	2787620	0.99	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	exon	2787468	2787620	.	+	.	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
Phchi.S5	AUGUSTUS	stop_codon	2787621	2787623	.	+	0	transcript_id "Phchi.S5G034800.t1"; gene_id "Phchi.S5G034800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9082.t1 is derived from g6257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39763128	39764029	.	+	.	Phchi.S1G624100
Phchi.S1	AUGUSTUS	transcript	39763128	39764029	.	+	.	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	start_codon	39763128	39763130	.	+	0	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	CDS	39763128	39763726	0.66	+	0	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	exon	39763128	39763726	.	+	.	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	intron	39763727	39763983	.	+	.	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	CDS	39763984	39764029	0.71	+	1	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	exon	39763984	39764029	.	+	.	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
Phchi.S1	AUGUSTUS	stop_codon	39764030	39764032	.	+	0	transcript_id "Phchi.S1G624100.t1"; gene_id "Phchi.S1G624100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11939.t1 is derived from g7614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	124456	127561	.	-	.	Phchi.S2G001900
Phchi.S2	AUGUSTUS	transcript	124456	127561	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	stop_codon	124453	124455	.	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	124456	124566	1	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	124456	124566	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	124567	124645	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	124646	124722	1	-	2	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	124646	124722	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	124723	124814	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	124815	124936	1	-	1	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	124815	124936	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	124937	125030	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	125031	125212	1	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	125031	125212	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	125213	125308	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	125309	125419	1	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	125309	125419	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	125420	125563	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	125564	125611	1	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	125564	125611	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	125612	125818	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	125819	125958	1	-	2	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	125819	125958	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	125959	126402	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	126403	126540	1	-	2	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	126403	126540	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	126541	126734	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	126735	126879	1	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	126735	126879	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	126880	126962	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	126963	127032	0.85	-	1	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	126963	127032	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	127033	127150	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	127151	127257	0.88	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	127151	127257	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	intron	127258	127402	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	CDS	127403	127561	0.98	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	exon	127403	127561	.	-	.	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
Phchi.S2	AUGUSTUS	start_codon	127559	127561	.	-	0	transcript_id "Phchi.S2G001900.t1"; gene_id "Phchi.S2G001900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14759.t1 is derived from g13227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14575778	14576756	.	+	.	Phchi.S3G207800
Phchi.S3	AUGUSTUS	transcript	14575778	14576756	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	start_codon	14575778	14575780	.	+	0	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	CDS	14575778	14575860	0.94	+	0	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	exon	14575778	14575860	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	intron	14575861	14575948	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	CDS	14575949	14576049	1	+	1	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	exon	14575949	14576049	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	intron	14576050	14576205	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	CDS	14576206	14576296	0.9	+	2	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	exon	14576206	14576296	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	intron	14576297	14576397	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	CDS	14576398	14576497	1	+	1	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	exon	14576398	14576497	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	intron	14576498	14576633	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	CDS	14576634	14576756	1	+	0	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	exon	14576634	14576756	.	+	.	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
Phchi.S3	AUGUSTUS	stop_codon	14576757	14576759	.	+	0	transcript_id "Phchi.S3G207800.t1"; gene_id "Phchi.S3G207800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2700.t1 is derived from g9620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8250979	8251239	.	-	.	Phchi.S5G130900
Phchi.S5	AUGUSTUS	transcript	8250979	8251239	.	-	.	transcript_id "Phchi.S5G130900.t1"; gene_id "Phchi.S5G130900"
Phchi.S5	AUGUSTUS	stop_codon	8250976	8250978	.	-	0	transcript_id "Phchi.S5G130900.t1"; gene_id "Phchi.S5G130900"
Phchi.S5	AUGUSTUS	CDS	8250979	8251239	0.52	-	0	transcript_id "Phchi.S5G130900.t1"; gene_id "Phchi.S5G130900"
Phchi.S5	AUGUSTUS	exon	8250979	8251239	.	-	.	transcript_id "Phchi.S5G130900.t1"; gene_id "Phchi.S5G130900"
Phchi.S5	AUGUSTUS	start_codon	8251237	8251239	.	-	0	transcript_id "Phchi.S5G130900.t1"; gene_id "Phchi.S5G130900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13862.t1 is derived from g12329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9296601	9298926	.	-	.	Phchi.S3G118100
Phchi.S3	AUGUSTUS	transcript	9296601	9298926	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	stop_codon	9296598	9296600	.	-	0	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9296601	9296799	1	-	1	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9296601	9296799	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9296800	9296975	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9296976	9297064	1	-	0	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9296976	9297064	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9297065	9297153	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9297154	9297342	1	-	0	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9297154	9297342	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9297343	9297462	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9297463	9297839	0.99	-	2	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9297463	9297839	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9297840	9297937	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9297938	9298250	1	-	0	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9297938	9298250	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9298251	9298343	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9298344	9298524	1	-	1	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9298344	9298524	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9298525	9298614	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9298615	9298624	1	-	2	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9298615	9298624	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9298625	9298673	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9298674	9298693	1	-	1	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9298674	9298693	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9298694	9298785	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9298786	9298816	0.84	-	2	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9298786	9298816	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	intron	9298817	9298916	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	CDS	9298917	9298926	0.6	-	0	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	exon	9298917	9298926	.	-	.	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
Phchi.S3	AUGUSTUS	start_codon	9298924	9298926	.	-	0	transcript_id "Phchi.S3G118100.t1"; gene_id "Phchi.S3G118100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7902.t1 is derived from g5076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31815585	31818557	.	+	.	Phchi.S1G506100
Phchi.S1	AUGUSTUS	transcript	31815585	31818557	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	start_codon	31815585	31815587	.	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31815585	31815657	0.48	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31815585	31815657	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31815658	31815960	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31815961	31816132	0.74	+	2	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31815961	31816132	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31816133	31816255	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31816256	31816417	0.99	+	1	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31816256	31816417	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31816418	31816492	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31816493	31816544	0.99	+	1	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31816493	31816544	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31816545	31816632	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31816633	31816807	1	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31816633	31816807	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31816808	31816890	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31816891	31816973	0.74	+	2	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31816891	31816973	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31816974	31817251	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31817252	31817305	0.86	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31817252	31817305	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31817306	31817387	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31817388	31817468	1	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31817388	31817468	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31817469	31817540	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31817541	31817676	1	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31817541	31817676	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31817677	31817756	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31817757	31817864	1	+	2	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31817757	31817864	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31817865	31817954	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31817955	31818020	1	+	2	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31817955	31818020	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31818021	31818100	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31818101	31818351	0.81	+	2	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31818101	31818351	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	intron	31818352	31818422	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	CDS	31818423	31818557	0.79	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	exon	31818423	31818557	.	+	.	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
Phchi.S1	AUGUSTUS	stop_codon	31818558	31818560	.	+	0	transcript_id "Phchi.S1G506100.t1"; gene_id "Phchi.S1G506100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5230.t1 is derived from g2400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15742236	15742933	.	-	.	Phchi.S1G238900
Phchi.S1	AUGUSTUS	transcript	15742236	15742933	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	stop_codon	15742233	15742235	.	-	0	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	CDS	15742236	15742339	0.8	-	2	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	exon	15742236	15742339	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	intron	15742340	15742463	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	CDS	15742464	15742495	0.81	-	1	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	exon	15742464	15742495	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	intron	15742496	15742609	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	CDS	15742610	15742698	1	-	0	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	exon	15742610	15742698	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	intron	15742699	15742855	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	CDS	15742856	15742933	0.5	-	0	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	exon	15742856	15742933	.	-	.	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
Phchi.S1	AUGUSTUS	start_codon	15742931	15742933	.	-	0	transcript_id "Phchi.S1G238900.t1"; gene_id "Phchi.S1G238900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3594.t1 is derived from g763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4653328	4658438	.	+	.	Phchi.S1G075300
Phchi.S1	AUGUSTUS	transcript	4653328	4658438	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	start_codon	4653328	4653330	.	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4653328	4653366	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4653328	4653366	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4653367	4654074	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4654075	4654206	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4654075	4654206	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4654207	4654422	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4654423	4654660	0.99	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4654423	4654660	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4654661	4654755	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4654756	4654825	1	+	2	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4654756	4654825	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4654826	4654983	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4654984	4655253	0.99	+	1	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4654984	4655253	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4655254	4655405	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4655406	4656312	0.92	+	1	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4655406	4656312	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4656313	4656416	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4656417	4656533	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4656417	4656533	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4656534	4656694	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4656695	4656757	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4656695	4656757	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4656758	4656877	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4656878	4656985	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4656878	4656985	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4656986	4657089	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4657090	4657191	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4657090	4657191	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4657192	4657270	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4657271	4657338	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4657271	4657338	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4657339	4657420	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4657421	4657502	1	+	1	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4657421	4657502	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4657503	4657608	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4657609	4657725	1	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4657609	4657725	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4657726	4657808	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4657809	4657838	0.39	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4657809	4657838	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4657839	4658012	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4658013	4658218	0.32	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4658013	4658218	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	intron	4658219	4658407	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	CDS	4658408	4658438	0.56	+	1	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	exon	4658408	4658438	.	+	.	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
Phchi.S1	AUGUSTUS	stop_codon	4658439	4658441	.	+	0	transcript_id "Phchi.S1G075300.t1"; gene_id "Phchi.S1G075300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15737.t1 is derived from g14207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20963571	20964951	.	+	.	Phchi.S3G305600
Phchi.S3	AUGUSTUS	transcript	20963571	20964951	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	start_codon	20963571	20963573	.	+	0	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20963571	20963592	0.91	+	0	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20963571	20963592	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20963593	20963780	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20963781	20963907	1	+	2	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20963781	20963907	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20963908	20963982	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20963983	20964066	1	+	1	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20963983	20964066	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20964067	20964141	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20964142	20964181	0.99	+	1	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20964142	20964181	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20964182	20964288	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20964289	20964357	1	+	0	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20964289	20964357	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20964358	20964442	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20964443	20964517	1	+	0	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20964443	20964517	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20964518	20964680	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20964681	20964715	1	+	0	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20964681	20964715	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	intron	20964716	20964806	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	CDS	20964807	20964951	0.42	+	1	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	exon	20964807	20964951	.	+	.	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
Phchi.S3	AUGUSTUS	stop_codon	20964952	20964954	.	+	0	transcript_id "Phchi.S3G305600.t1"; gene_id "Phchi.S3G305600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3132.t1 is derived from g301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1886015	1888321	.	-	.	Phchi.S1G029100
Phchi.S1	AUGUSTUS	transcript	1886015	1888321	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	stop_codon	1886012	1886014	.	-	0	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	CDS	1886015	1886503	1	-	0	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	exon	1886015	1886503	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	intron	1886504	1886625	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	CDS	1886626	1886964	0.98	-	0	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	exon	1886626	1886964	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	intron	1886965	1887074	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	CDS	1887075	1887239	0.96	-	0	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	exon	1887075	1887239	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	intron	1887240	1887322	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	CDS	1887323	1887543	0.93	-	2	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	exon	1887323	1887543	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	intron	1887544	1887651	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	CDS	1887652	1888321	0.93	-	0	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	exon	1887652	1888321	.	-	.	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
Phchi.S1	AUGUSTUS	start_codon	1888319	1888321	.	-	0	transcript_id "Phchi.S1G029100.t1"; gene_id "Phchi.S1G029100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4435.t1 is derived from g1604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10490421	10491518	.	+	.	Phchi.S1G159400
Phchi.S1	AUGUSTUS	transcript	10490421	10491518	.	+	.	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	start_codon	10490421	10490423	.	+	0	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	CDS	10490421	10490893	0.52	+	0	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	exon	10490421	10490893	.	+	.	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	intron	10490894	10490972	.	+	.	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	CDS	10490973	10491172	0.98	+	1	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	exon	10490973	10491172	.	+	.	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	intron	10491173	10491369	.	+	.	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	CDS	10491370	10491518	0.97	+	2	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	exon	10491370	10491518	.	+	.	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
Phchi.S1	AUGUSTUS	stop_codon	10491519	10491521	.	+	0	transcript_id "Phchi.S1G159400.t1"; gene_id "Phchi.S1G159400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15419.t1 is derived from g13887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18995314	18997128	.	-	.	Phchi.S3G273800
Phchi.S3	AUGUSTUS	transcript	18995314	18997128	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	stop_codon	18995311	18995313	.	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18995314	18995358	1	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18995314	18995358	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	intron	18995359	18995472	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18995473	18995535	1	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18995473	18995535	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	intron	18995536	18995632	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18995633	18995963	1	-	1	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18995633	18995963	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	intron	18995964	18996057	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18996058	18996116	1	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18996058	18996116	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	intron	18996117	18996221	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18996222	18996446	0.98	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18996222	18996446	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	intron	18996447	18996704	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18996705	18996809	1	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18996705	18996809	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	intron	18996810	18996930	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	CDS	18996931	18997128	1	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	exon	18996931	18997128	.	-	.	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
Phchi.S3	AUGUSTUS	start_codon	18997126	18997128	.	-	0	transcript_id "Phchi.S3G273800.t1"; gene_id "Phchi.S3G273800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5417.t1 is derived from g2587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16784518	16786722	.	-	.	Phchi.S1G257600
Phchi.S1	AUGUSTUS	transcript	16784518	16786722	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	stop_codon	16784515	16784517	.	-	0	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	CDS	16784518	16785566	1	-	2	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	exon	16784518	16785566	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	intron	16785567	16785688	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	CDS	16785689	16785923	1	-	0	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	exon	16785689	16785923	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	intron	16785924	16786014	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	CDS	16786015	16786225	1	-	1	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	exon	16786015	16786225	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	intron	16786226	16786311	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	CDS	16786312	16786385	1	-	0	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	exon	16786312	16786385	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	intron	16786386	16786503	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	CDS	16786504	16786722	1	-	0	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	exon	16786504	16786722	.	-	.	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
Phchi.S1	AUGUSTUS	start_codon	16786720	16786722	.	-	0	transcript_id "Phchi.S1G257600.t1"; gene_id "Phchi.S1G257600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1221.t1 is derived from g11004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8454424	8456878	.	-	.	Phchi.S6G118000
Phchi.S6	AUGUSTUS	transcript	8454424	8456878	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	stop_codon	8454421	8454423	.	-	0	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8454424	8454627	0.76	-	0	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8454424	8454627	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8454628	8454712	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8454713	8454819	1	-	2	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8454713	8454819	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8454820	8454954	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8454955	8455033	1	-	0	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8454955	8455033	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8455034	8455153	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8455154	8455276	1	-	0	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8455154	8455276	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8455277	8455367	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8455368	8455516	0.87	-	2	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8455368	8455516	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8455517	8455810	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8455811	8455918	0.8	-	2	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8455811	8455918	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8455919	8456002	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8456003	8456019	0.77	-	1	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8456003	8456019	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8456020	8456103	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8456104	8456367	0.78	-	1	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8456104	8456367	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	intron	8456368	8456483	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	CDS	8456484	8456878	0.27	-	0	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	exon	8456484	8456878	.	-	.	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
Phchi.S6	AUGUSTUS	start_codon	8456876	8456878	.	-	0	transcript_id "Phchi.S6G118000.t1"; gene_id "Phchi.S6G118000"
# This transcript jg1528.t2 is derived from g8447.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1529.t1 is derived from g8448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1605693	1607453	.	-	.	Phchi.S5G013800
Phchi.S5	AUGUSTUS	transcript	1605693	1607453	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	stop_codon	1605690	1605692	.	-	0	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	CDS	1605693	1605732	1	-	1	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	exon	1605693	1605732	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	intron	1605733	1605860	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	CDS	1605861	1605949	1	-	0	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	exon	1605861	1605949	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	intron	1605950	1606029	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	CDS	1606030	1606099	1	-	1	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	exon	1606030	1606099	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	intron	1606100	1606247	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	CDS	1606248	1607032	0.87	-	0	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	exon	1606248	1607032	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	intron	1607033	1607193	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	CDS	1607194	1607324	0.72	-	2	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	exon	1607194	1607324	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	intron	1607325	1607407	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	CDS	1607408	1607453	0.69	-	0	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	exon	1607408	1607453	.	-	.	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
Phchi.S5	AUGUSTUS	start_codon	1607451	1607453	.	-	0	transcript_id "Phchi.S5G013800.t1"; gene_id "Phchi.S5G013800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11465.t1 is derived from g15515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6495645	6497158	.	-	.	Phchi.S4G104700
Phchi.S4	AUGUSTUS	transcript	6495645	6497158	.	-	.	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	stop_codon	6495642	6495644	.	-	0	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	CDS	6495645	6496904	0.99	-	0	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	exon	6495645	6496904	.	-	.	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	intron	6496905	6496996	.	-	.	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	CDS	6496997	6497158	0.57	-	0	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	exon	6496997	6497158	.	-	.	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
Phchi.S4	AUGUSTUS	start_codon	6497156	6497158	.	-	0	transcript_id "Phchi.S4G104700.t1"; gene_id "Phchi.S4G104700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10402.t1 is derived from g7578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47593181	47593825	.	+	.	Phchi.S1G756100
Phchi.S1	AUGUSTUS	transcript	47593181	47593825	.	+	.	transcript_id "Phchi.S1G756100.t1"; gene_id "Phchi.S1G756100"
Phchi.S1	AUGUSTUS	start_codon	47593181	47593183	.	+	0	transcript_id "Phchi.S1G756100.t1"; gene_id "Phchi.S1G756100"
Phchi.S1	AUGUSTUS	CDS	47593181	47593825	0.51	+	0	transcript_id "Phchi.S1G756100.t1"; gene_id "Phchi.S1G756100"
Phchi.S1	AUGUSTUS	exon	47593181	47593825	.	+	.	transcript_id "Phchi.S1G756100.t1"; gene_id "Phchi.S1G756100"
Phchi.S1	AUGUSTUS	stop_codon	47593826	47593828	.	+	0	transcript_id "Phchi.S1G756100.t1"; gene_id "Phchi.S1G756100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2978.t1 is derived from g147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	941285	945681	.	+	.	Phchi.S1G013700
Phchi.S1	AUGUSTUS	transcript	941285	945681	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	start_codon	941285	941287	.	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	941285	941524	0.79	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	941285	941524	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	941525	941643	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	941644	941742	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	941644	941742	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	941743	941895	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	941896	941945	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	941896	941945	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	941946	942041	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	942042	942162	0.97	+	1	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	942042	942162	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	942163	942271	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	942272	942358	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	942272	942358	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	942359	942514	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	942515	942586	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	942515	942586	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	942587	942709	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	942710	942775	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	942710	942775	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	942776	942879	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	942880	942939	0.97	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	942880	942939	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	942940	943033	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	943034	943081	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	943034	943081	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	943082	943192	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	943193	943241	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	943193	943241	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	943242	943365	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	943366	943478	1	+	2	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	943366	943478	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	943479	943603	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	943604	943686	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	943604	943686	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	943687	943810	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	943811	943950	1	+	1	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	943811	943950	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	943951	944026	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	944027	944132	1	+	2	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	944027	944132	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	944133	944209	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	944210	944300	1	+	1	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	944210	944300	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	944301	944392	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	944393	944479	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	944393	944479	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	944480	944567	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	944568	944696	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	944568	944696	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	944697	944791	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	944792	944898	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	944792	944898	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	944899	944992	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	944993	945095	1	+	1	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	944993	945095	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	intron	945096	945177	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	CDS	945178	945681	1	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	exon	945178	945681	.	+	.	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
Phchi.S1	AUGUSTUS	stop_codon	945682	945684	.	+	0	transcript_id "Phchi.S1G013700.t1"; gene_id "Phchi.S1G013700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13004.t1 is derived from g11469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3598990	3602609	.	+	.	Phchi.S3G032300
Phchi.S3	AUGUSTUS	transcript	3598990	3602609	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	start_codon	3598990	3598992	.	+	0	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3598990	3599485	0.97	+	0	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3598990	3599485	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3599486	3599576	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3599577	3599860	1	+	2	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3599577	3599860	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3599861	3599953	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3599954	3600191	1	+	0	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3599954	3600191	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3600192	3600271	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3600272	3600604	1	+	2	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3600272	3600604	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3600605	3600681	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3600682	3600767	1	+	2	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3600682	3600767	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3600768	3600895	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3600896	3601003	1	+	0	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3600896	3601003	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3601004	3601090	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3601091	3601395	1	+	0	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3601091	3601395	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3601396	3601486	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3601487	3601753	1	+	1	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3601487	3601753	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	intron	3601754	3601837	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	CDS	3601838	3602609	0.98	+	1	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	exon	3601838	3602609	.	+	.	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
Phchi.S3	AUGUSTUS	stop_codon	3602610	3602612	.	+	0	transcript_id "Phchi.S3G032300.t1"; gene_id "Phchi.S3G032300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6740.t1 is derived from g3912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24804005	24804532	.	-	.	Phchi.S1G389900
Phchi.S1	AUGUSTUS	transcript	24804005	24804532	.	-	.	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	stop_codon	24804002	24804004	.	-	0	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	CDS	24804005	24804275	0.99	-	1	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	exon	24804005	24804275	.	-	.	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	intron	24804276	24804356	.	-	.	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	CDS	24804357	24804532	0.52	-	0	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	exon	24804357	24804532	.	-	.	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
Phchi.S1	AUGUSTUS	start_codon	24804530	24804532	.	-	0	transcript_id "Phchi.S1G389900.t1"; gene_id "Phchi.S1G389900"
# This transcript jg9852.t2 is derived from g7028.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9853.t1 is derived from g7029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44093236	44094106	.	-	.	Phchi.S1G701200
Phchi.S1	AUGUSTUS	transcript	44093236	44094106	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	stop_codon	44093233	44093235	.	-	0	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	CDS	44093236	44093396	0.99	-	2	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	exon	44093236	44093396	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	intron	44093397	44093474	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	CDS	44093475	44093552	1	-	2	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	exon	44093475	44093552	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	intron	44093553	44093708	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	CDS	44093709	44093840	0.67	-	2	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	exon	44093709	44093840	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	intron	44093841	44094030	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	CDS	44094031	44094106	0.35	-	0	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	exon	44094031	44094106	.	-	.	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
Phchi.S1	AUGUSTUS	start_codon	44094104	44094106	.	-	0	transcript_id "Phchi.S1G701200.t1"; gene_id "Phchi.S1G701200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13875.t1 is derived from g12342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9425290	9428045	.	-	.	Phchi.S3G119400
Phchi.S3	AUGUSTUS	transcript	9425290	9428045	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	stop_codon	9425287	9425289	.	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9425290	9425571	0.99	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9425290	9425571	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9425572	9425646	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9425647	9425832	1	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9425647	9425832	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9425833	9425907	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9425908	9426067	1	-	1	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9425908	9426067	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9426068	9426194	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9426195	9427048	0.96	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9426195	9427048	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9427049	9427127	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9427128	9427240	0.98	-	2	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9427128	9427240	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9427241	9427334	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9427335	9427347	0.98	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9427335	9427347	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9427348	9427424	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9427425	9427565	0.94	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9427425	9427565	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9427566	9427657	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9427658	9427787	1	-	1	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9427658	9427787	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	intron	9427788	9427881	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	CDS	9427882	9428045	0.34	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	exon	9427882	9428045	.	-	.	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
Phchi.S3	AUGUSTUS	start_codon	9428043	9428045	.	-	0	transcript_id "Phchi.S3G119400.t1"; gene_id "Phchi.S3G119400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5431.t1 is derived from g2601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16839640	16840324	.	+	.	Phchi.S1G259000
Phchi.S1	AUGUSTUS	transcript	16839640	16840324	.	+	.	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	start_codon	16839640	16839642	.	+	0	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	CDS	16839640	16839972	0.34	+	0	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	exon	16839640	16839972	.	+	.	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	intron	16839973	16840155	.	+	.	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	CDS	16840156	16840236	1	+	0	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	exon	16840156	16840236	.	+	.	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	intron	16840237	16840321	.	+	.	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	CDS	16840322	16840324	1	+	0	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	exon	16840322	16840324	.	+	.	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
Phchi.S1	AUGUSTUS	stop_codon	16840325	16840327	.	+	0	transcript_id "Phchi.S1G259000.t1"; gene_id "Phchi.S1G259000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg27.t1 is derived from g15980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C121	AUGUSTUS	gene	34015	34425	.	+	.	Phchi.C121G000200
Phchi.C121	AUGUSTUS	transcript	34015	34425	.	+	.	transcript_id "Phchi.C121G000200.t1"; gene_id "Phchi.C121G000200"
Phchi.C121	AUGUSTUS	start_codon	34015	34017	.	+	0	transcript_id "Phchi.C121G000200.t1"; gene_id "Phchi.C121G000200"
Phchi.C121	AUGUSTUS	CDS	34015	34425	0.62	+	0	transcript_id "Phchi.C121G000200.t1"; gene_id "Phchi.C121G000200"
Phchi.C121	AUGUSTUS	exon	34015	34425	.	+	.	transcript_id "Phchi.C121G000200.t1"; gene_id "Phchi.C121G000200"
Phchi.C121	AUGUSTUS	stop_codon	34426	34428	.	+	0	transcript_id "Phchi.C121G000200.t1"; gene_id "Phchi.C121G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14382.t1 is derived from g12850.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12469548	12470578	.	+	.	Phchi.S3G170100
Phchi.S3	AUGUSTUS	transcript	12469548	12470578	.	+	.	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	start_codon	12469548	12469550	.	+	0	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	CDS	12469548	12470093	0.48	+	0	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	exon	12469548	12470093	.	+	.	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	intron	12470094	12470300	.	+	.	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	CDS	12470301	12470401	0.69	+	0	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	exon	12470301	12470401	.	+	.	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	intron	12470402	12470460	.	+	.	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	CDS	12470461	12470578	0.38	+	1	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	exon	12470461	12470578	.	+	.	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	stop_codon	12470579	12470581	.	+	0	transcript_id "Phchi.S3G170100.t1"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	transcript	12469548	12470177	.	+	.	transcript_id "Phchi.S3G170100.t2"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	start_codon	12469548	12469550	.	+	0	transcript_id "Phchi.S3G170100.t2"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	CDS	12469548	12470177	0.86	+	0	transcript_id "Phchi.S3G170100.t2"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	exon	12469548	12470177	.	+	.	transcript_id "Phchi.S3G170100.t2"; gene_id "Phchi.S3G170100"
Phchi.S3	AUGUSTUS	stop_codon	12470178	12470180	.	+	0	transcript_id "Phchi.S3G170100.t2"; gene_id "Phchi.S3G170100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3161.t1 is derived from g330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2022201	2022788	.	+	.	Phchi.S1G032000
Phchi.S1	AUGUSTUS	transcript	2022201	2022788	.	+	.	transcript_id "Phchi.S1G032000.t1"; gene_id "Phchi.S1G032000"
Phchi.S1	AUGUSTUS	start_codon	2022201	2022203	.	+	0	transcript_id "Phchi.S1G032000.t1"; gene_id "Phchi.S1G032000"
Phchi.S1	AUGUSTUS	CDS	2022201	2022788	1	+	0	transcript_id "Phchi.S1G032000.t1"; gene_id "Phchi.S1G032000"
Phchi.S1	AUGUSTUS	exon	2022201	2022788	.	+	.	transcript_id "Phchi.S1G032000.t1"; gene_id "Phchi.S1G032000"
Phchi.S1	AUGUSTUS	stop_codon	2022789	2022791	.	+	0	transcript_id "Phchi.S1G032000.t1"; gene_id "Phchi.S1G032000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg680.t1 is derived from g10462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4695482	4696306	.	-	.	Phchi.S6G063900
Phchi.S6	AUGUSTUS	transcript	4695482	4696306	.	-	.	transcript_id "Phchi.S6G063900.t1"; gene_id "Phchi.S6G063900"
Phchi.S6	AUGUSTUS	stop_codon	4695479	4695481	.	-	0	transcript_id "Phchi.S6G063900.t1"; gene_id "Phchi.S6G063900"
Phchi.S6	AUGUSTUS	CDS	4695482	4696306	0.4	-	0	transcript_id "Phchi.S6G063900.t1"; gene_id "Phchi.S6G063900"
Phchi.S6	AUGUSTUS	exon	4695482	4696306	.	-	.	transcript_id "Phchi.S6G063900.t1"; gene_id "Phchi.S6G063900"
Phchi.S6	AUGUSTUS	start_codon	4696304	4696306	.	-	0	transcript_id "Phchi.S6G063900.t1"; gene_id "Phchi.S6G063900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13277.t1 is derived from g11742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5119343	5119573	.	-	.	Phchi.S3G059600
Phchi.S3	AUGUSTUS	transcript	5119343	5119573	.	-	.	transcript_id "Phchi.S3G059600.t1"; gene_id "Phchi.S3G059600"
Phchi.S3	AUGUSTUS	stop_codon	5119340	5119342	.	-	0	transcript_id "Phchi.S3G059600.t1"; gene_id "Phchi.S3G059600"
Phchi.S3	AUGUSTUS	CDS	5119343	5119573	0.8	-	0	transcript_id "Phchi.S3G059600.t1"; gene_id "Phchi.S3G059600"
Phchi.S3	AUGUSTUS	exon	5119343	5119573	.	-	.	transcript_id "Phchi.S3G059600.t1"; gene_id "Phchi.S3G059600"
Phchi.S3	AUGUSTUS	start_codon	5119571	5119573	.	-	0	transcript_id "Phchi.S3G059600.t1"; gene_id "Phchi.S3G059600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9451.t1 is derived from g6627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41534064	41534870	.	-	.	Phchi.S1G661000
Phchi.S1	AUGUSTUS	transcript	41534064	41534870	.	-	.	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	stop_codon	41534061	41534063	.	-	0	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	CDS	41534064	41534156	0.39	-	0	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	exon	41534064	41534156	.	-	.	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	intron	41534157	41534247	.	-	.	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	CDS	41534248	41534419	0.64	-	1	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	exon	41534248	41534419	.	-	.	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	intron	41534420	41534526	.	-	.	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	CDS	41534527	41534870	0.87	-	0	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	exon	41534527	41534870	.	-	.	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
Phchi.S1	AUGUSTUS	start_codon	41534868	41534870	.	-	0	transcript_id "Phchi.S1G661000.t1"; gene_id "Phchi.S1G661000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg520.t1 is derived from g10302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3737254	3738825	.	-	.	Phchi.S6G047900
Phchi.S6	AUGUSTUS	transcript	3737254	3738825	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	stop_codon	3737251	3737253	.	-	0	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3737254	3737354	1	-	2	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3737254	3737354	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	intron	3737355	3737454	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3737455	3737526	1	-	2	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3737455	3737526	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	intron	3737527	3737674	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3737675	3737760	1	-	1	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3737675	3737760	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	intron	3737761	3737879	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3737880	3737966	0.87	-	1	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3737880	3737966	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	intron	3737967	3738074	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3738075	3738153	1	-	2	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3738075	3738153	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	intron	3738154	3738304	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3738305	3738345	1	-	1	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3738305	3738345	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	intron	3738346	3738667	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	CDS	3738668	3738825	1	-	0	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	exon	3738668	3738825	.	-	.	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
Phchi.S6	AUGUSTUS	start_codon	3738823	3738825	.	-	0	transcript_id "Phchi.S6G047900.t1"; gene_id "Phchi.S6G047900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7310.t1 is derived from g4482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28454858	28455718	.	+	.	Phchi.S1G446900
Phchi.S1	AUGUSTUS	transcript	28454858	28455718	.	+	.	transcript_id "Phchi.S1G446900.t1"; gene_id "Phchi.S1G446900"
Phchi.S1	AUGUSTUS	start_codon	28454858	28454860	.	+	0	transcript_id "Phchi.S1G446900.t1"; gene_id "Phchi.S1G446900"
Phchi.S1	AUGUSTUS	CDS	28454858	28455718	0.87	+	0	transcript_id "Phchi.S1G446900.t1"; gene_id "Phchi.S1G446900"
Phchi.S1	AUGUSTUS	exon	28454858	28455718	.	+	.	transcript_id "Phchi.S1G446900.t1"; gene_id "Phchi.S1G446900"
Phchi.S1	AUGUSTUS	stop_codon	28455719	28455721	.	+	0	transcript_id "Phchi.S1G446900.t1"; gene_id "Phchi.S1G446900"
# This transcript jg9653.t2 is derived from g6829.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9654.t1 is derived from g6830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43084046	43085459	.	-	.	Phchi.S1G681300
Phchi.S1	AUGUSTUS	transcript	43084046	43085459	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	stop_codon	43084043	43084045	.	-	0	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	CDS	43084046	43084291	0.77	-	0	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	exon	43084046	43084291	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	intron	43084292	43084481	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	CDS	43084482	43084586	0.26	-	0	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	exon	43084482	43084586	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	intron	43084587	43084768	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	CDS	43084769	43084892	0.76	-	1	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	exon	43084769	43084892	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	intron	43084893	43085049	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	CDS	43085050	43085459	0.37	-	0	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	exon	43085050	43085459	.	-	.	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
Phchi.S1	AUGUSTUS	start_codon	43085457	43085459	.	-	0	transcript_id "Phchi.S1G681300.t1"; gene_id "Phchi.S1G681300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14557.t1 is derived from g13025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13455990	13459198	.	+	.	Phchi.S3G187600
Phchi.S3	AUGUSTUS	transcript	13455990	13459198	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	start_codon	13455990	13455992	.	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13455990	13456002	1	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13455990	13456002	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13456003	13456095	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13456096	13456243	1	+	2	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13456096	13456243	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13456244	13456333	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13456334	13456469	1	+	1	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13456334	13456469	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13456470	13456608	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13456609	13456665	0.99	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13456609	13456665	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13456666	13456782	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13456783	13456878	0.99	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13456783	13456878	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13456879	13456969	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13456970	13457062	0.68	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13456970	13457062	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13457063	13457174	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13457175	13457365	0.7	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13457175	13457365	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13457366	13457480	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13457481	13457712	0.99	+	1	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13457481	13457712	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13457713	13457798	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13457799	13457909	1	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13457799	13457909	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13457910	13458119	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13458120	13458179	1	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13458120	13458179	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13458180	13458315	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13458316	13458678	1	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13458316	13458678	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13458679	13458761	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13458762	13459019	0.6	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13458762	13459019	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	intron	13459020	13459135	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	CDS	13459136	13459198	0.62	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	exon	13459136	13459198	.	+	.	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
Phchi.S3	AUGUSTUS	stop_codon	13459199	13459201	.	+	0	transcript_id "Phchi.S3G187600.t1"; gene_id "Phchi.S3G187600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1595.t1 is derived from g8514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1940667	1941766	.	+	.	Phchi.S5G020400
Phchi.S5	AUGUSTUS	transcript	1940667	1941766	.	+	.	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	start_codon	1940667	1940669	.	+	0	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	CDS	1940667	1941214	0.8	+	0	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	exon	1940667	1941214	.	+	.	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	intron	1941215	1941309	.	+	.	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	CDS	1941310	1941766	0.91	+	1	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	exon	1941310	1941766	.	+	.	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
Phchi.S5	AUGUSTUS	stop_codon	1941767	1941769	.	+	0	transcript_id "Phchi.S5G020400.t1"; gene_id "Phchi.S5G020400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7648.t1 is derived from g4822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30390665	30391836	.	-	.	Phchi.S1G480700
Phchi.S1	AUGUSTUS	transcript	30390665	30391836	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	stop_codon	30390662	30390664	.	-	0	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	CDS	30390665	30390692	1	-	1	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	exon	30390665	30390692	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	intron	30390693	30390772	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	CDS	30390773	30390806	0.99	-	2	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	exon	30390773	30390806	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	intron	30390807	30390876	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	CDS	30390877	30391217	0.56	-	1	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	exon	30390877	30391217	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	intron	30391218	30391438	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	CDS	30391439	30391836	0.4	-	0	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	exon	30391439	30391836	.	-	.	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
Phchi.S1	AUGUSTUS	start_codon	30391834	30391836	.	-	0	transcript_id "Phchi.S1G480700.t1"; gene_id "Phchi.S1G480700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3829.t1 is derived from g998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5914535	5915661	.	+	.	Phchi.S1G098800
Phchi.S1	AUGUSTUS	transcript	5914535	5915661	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	start_codon	5914535	5914537	.	+	0	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	CDS	5914535	5914789	0.89	+	0	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	exon	5914535	5914789	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	intron	5914790	5915020	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	CDS	5915021	5915101	1	+	0	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	exon	5915021	5915101	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	intron	5915102	5915242	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	CDS	5915243	5915359	0.93	+	0	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	exon	5915243	5915359	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	intron	5915360	5915499	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	CDS	5915500	5915534	0.62	+	0	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	exon	5915500	5915534	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	intron	5915535	5915627	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	CDS	5915628	5915661	1	+	1	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	exon	5915628	5915661	.	+	.	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
Phchi.S1	AUGUSTUS	stop_codon	5915662	5915664	.	+	0	transcript_id "Phchi.S1G098800.t1"; gene_id "Phchi.S1G098800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15391.t1 is derived from g13859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18810580	18812871	.	+	.	Phchi.S3G271000
Phchi.S3	AUGUSTUS	transcript	18810580	18812871	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	start_codon	18810580	18810582	.	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18810580	18810726	1	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18810580	18810726	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18810727	18810799	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18810800	18810933	1	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18810800	18810933	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18810934	18811051	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18811052	18811211	1	+	1	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18811052	18811211	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18811212	18811378	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18811379	18811565	1	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18811379	18811565	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18811566	18811688	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18811689	18811834	0.93	+	2	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18811689	18811834	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18811835	18811936	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18811937	18812009	0.99	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18811937	18812009	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18812010	18812098	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18812099	18812162	1	+	2	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18812099	18812162	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18812163	18812276	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18812277	18812376	1	+	1	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18812277	18812376	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18812377	18812455	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18812456	18812614	1	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18812456	18812614	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	intron	18812615	18812703	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	CDS	18812704	18812871	1	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	exon	18812704	18812871	.	+	.	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
Phchi.S3	AUGUSTUS	stop_codon	18812872	18812874	.	+	0	transcript_id "Phchi.S3G271000.t1"; gene_id "Phchi.S3G271000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7456.t1 is derived from g4628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29377139	29377432	.	-	.	Phchi.S1G461500
Phchi.S1	AUGUSTUS	transcript	29377139	29377432	.	-	.	transcript_id "Phchi.S1G461500.t1"; gene_id "Phchi.S1G461500"
Phchi.S1	AUGUSTUS	stop_codon	29377136	29377138	.	-	0	transcript_id "Phchi.S1G461500.t1"; gene_id "Phchi.S1G461500"
Phchi.S1	AUGUSTUS	CDS	29377139	29377432	0.97	-	0	transcript_id "Phchi.S1G461500.t1"; gene_id "Phchi.S1G461500"
Phchi.S1	AUGUSTUS	exon	29377139	29377432	.	-	.	transcript_id "Phchi.S1G461500.t1"; gene_id "Phchi.S1G461500"
Phchi.S1	AUGUSTUS	start_codon	29377430	29377432	.	-	0	transcript_id "Phchi.S1G461500.t1"; gene_id "Phchi.S1G461500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4555.t1 is derived from g1725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11095310	11098543	.	+	.	Phchi.S1G171400
Phchi.S1	AUGUSTUS	transcript	11095310	11098543	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	start_codon	11095310	11095312	.	+	0	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	CDS	11095310	11096302	0.96	+	0	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	exon	11095310	11096302	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	intron	11096303	11096426	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	CDS	11096427	11096673	1	+	0	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	exon	11096427	11096673	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	intron	11096674	11096785	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	CDS	11096786	11097097	1	+	2	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	exon	11096786	11097097	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	intron	11097098	11097215	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	CDS	11097216	11097910	1	+	2	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	exon	11097216	11097910	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	intron	11097911	11098000	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	CDS	11098001	11098543	0.99	+	0	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	exon	11098001	11098543	.	+	.	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
Phchi.S1	AUGUSTUS	stop_codon	11098544	11098546	.	+	0	transcript_id "Phchi.S1G171400.t1"; gene_id "Phchi.S1G171400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6317.t1 is derived from g3489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22236831	22238596	.	-	.	Phchi.S1G347600
Phchi.S1	AUGUSTUS	transcript	22236831	22238596	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	stop_codon	22236828	22236830	.	-	0	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	CDS	22236831	22236886	1	-	2	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	exon	22236831	22236886	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	intron	22236887	22236981	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	CDS	22236982	22237130	1	-	1	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	exon	22236982	22237130	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	intron	22237131	22237266	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	CDS	22237267	22237376	1	-	0	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	exon	22237267	22237376	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	intron	22237377	22237532	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	CDS	22237533	22237620	1	-	1	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	exon	22237533	22237620	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	intron	22237621	22237787	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	CDS	22237788	22238094	1	-	2	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	exon	22237788	22238094	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	intron	22238095	22238523	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	CDS	22238524	22238596	0.87	-	0	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	exon	22238524	22238596	.	-	.	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
Phchi.S1	AUGUSTUS	start_codon	22238594	22238596	.	-	0	transcript_id "Phchi.S1G347600.t1"; gene_id "Phchi.S1G347600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg378.t1 is derived from g10160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2720540	2722204	.	-	.	Phchi.S6G033700
Phchi.S6	AUGUSTUS	transcript	2720540	2722204	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	stop_codon	2720537	2720539	.	-	0	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	CDS	2720540	2720699	1	-	1	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	exon	2720540	2720699	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	intron	2720700	2720788	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	CDS	2720789	2720869	1	-	1	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	exon	2720789	2720869	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	intron	2720870	2721017	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	CDS	2721018	2721231	1	-	2	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	exon	2721018	2721231	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	intron	2721232	2721326	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	CDS	2721327	2721446	1	-	2	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	exon	2721327	2721446	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	intron	2721447	2721546	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	CDS	2721547	2722204	0.81	-	0	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	exon	2721547	2722204	.	-	.	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
Phchi.S6	AUGUSTUS	start_codon	2722202	2722204	.	-	0	transcript_id "Phchi.S6G033700.t1"; gene_id "Phchi.S6G033700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2578.t1 is derived from g9498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7467023	7467830	.	-	.	Phchi.S5G118700
Phchi.S5	AUGUSTUS	transcript	7467023	7467830	.	-	.	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	stop_codon	7467020	7467022	.	-	0	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	CDS	7467023	7467650	0.49	-	1	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	exon	7467023	7467650	.	-	.	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	intron	7467651	7467792	.	-	.	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	CDS	7467793	7467830	0.5	-	0	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	exon	7467793	7467830	.	-	.	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
Phchi.S5	AUGUSTUS	start_codon	7467828	7467830	.	-	0	transcript_id "Phchi.S5G118700.t1"; gene_id "Phchi.S5G118700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12838.t1 is derived from g11303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2636902	2637544	.	-	.	Phchi.S3G015700
Phchi.S3	AUGUSTUS	transcript	2636902	2637544	.	-	.	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	stop_codon	2636899	2636901	.	-	0	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	CDS	2636902	2637013	0.52	-	1	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	exon	2636902	2637013	.	-	.	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	intron	2637014	2637071	.	-	.	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	CDS	2637072	2637122	0.5	-	1	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	exon	2637072	2637122	.	-	.	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	intron	2637123	2637284	.	-	.	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	CDS	2637285	2637544	0.23	-	0	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	exon	2637285	2637544	.	-	.	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
Phchi.S3	AUGUSTUS	start_codon	2637542	2637544	.	-	0	transcript_id "Phchi.S3G015700.t1"; gene_id "Phchi.S3G015700"
# This transcript jg6126.t2 is derived from g3297.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6127.t1 is derived from g3298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21061434	21062279	.	+	.	Phchi.S1G328600
Phchi.S1	AUGUSTUS	transcript	21061434	21062279	.	+	.	transcript_id "Phchi.S1G328600.t1"; gene_id "Phchi.S1G328600"
Phchi.S1	AUGUSTUS	start_codon	21061434	21061436	.	+	0	transcript_id "Phchi.S1G328600.t1"; gene_id "Phchi.S1G328600"
Phchi.S1	AUGUSTUS	CDS	21061434	21062279	1	+	0	transcript_id "Phchi.S1G328600.t1"; gene_id "Phchi.S1G328600"
Phchi.S1	AUGUSTUS	exon	21061434	21062279	.	+	.	transcript_id "Phchi.S1G328600.t1"; gene_id "Phchi.S1G328600"
Phchi.S1	AUGUSTUS	stop_codon	21062280	21062282	.	+	0	transcript_id "Phchi.S1G328600.t1"; gene_id "Phchi.S1G328600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg213.t1 is derived from g9995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1303669	1305321	.	+	.	Phchi.S6G017200
Phchi.S6	AUGUSTUS	transcript	1303669	1305321	.	+	.	transcript_id "Phchi.S6G017200.t1"; gene_id "Phchi.S6G017200"
Phchi.S6	AUGUSTUS	start_codon	1303669	1303671	.	+	0	transcript_id "Phchi.S6G017200.t1"; gene_id "Phchi.S6G017200"
Phchi.S6	AUGUSTUS	CDS	1303669	1305321	0.58	+	0	transcript_id "Phchi.S6G017200.t1"; gene_id "Phchi.S6G017200"
Phchi.S6	AUGUSTUS	exon	1303669	1305321	.	+	.	transcript_id "Phchi.S6G017200.t1"; gene_id "Phchi.S6G017200"
Phchi.S6	AUGUSTUS	stop_codon	1305322	1305324	.	+	0	transcript_id "Phchi.S6G017200.t1"; gene_id "Phchi.S6G017200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3736.t1 is derived from g905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5449951	5450705	.	-	.	Phchi.S1G089500
Phchi.S1	AUGUSTUS	transcript	5449951	5450705	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	stop_codon	5449948	5449950	.	-	0	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	CDS	5449951	5449984	0.64	-	1	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	exon	5449951	5449984	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	intron	5449985	5450137	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	CDS	5450138	5450191	0.65	-	1	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	exon	5450138	5450191	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	intron	5450192	5450347	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	CDS	5450348	5450498	0.65	-	2	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	exon	5450348	5450498	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	intron	5450499	5450599	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	CDS	5450600	5450705	0.63	-	0	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	exon	5450600	5450705	.	-	.	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
Phchi.S1	AUGUSTUS	start_codon	5450703	5450705	.	-	0	transcript_id "Phchi.S1G089500.t1"; gene_id "Phchi.S1G089500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3317.t1 is derived from g486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2851704	2852846	.	-	.	Phchi.S1G047600
Phchi.S1	AUGUSTUS	transcript	2851704	2852846	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	stop_codon	2851701	2851703	.	-	0	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	CDS	2851704	2851743	0.7	-	1	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	exon	2851704	2851743	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	intron	2851744	2851831	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	CDS	2851832	2851849	0.7	-	1	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	exon	2851832	2851849	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	intron	2851850	2851936	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	CDS	2851937	2852330	0.7	-	2	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	exon	2851937	2852330	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	intron	2852331	2852433	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	CDS	2852434	2852482	1	-	0	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	exon	2852434	2852482	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	intron	2852483	2852699	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	CDS	2852700	2852846	0.98	-	0	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	exon	2852700	2852846	.	-	.	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
Phchi.S1	AUGUSTUS	start_codon	2852844	2852846	.	-	0	transcript_id "Phchi.S1G047600.t1"; gene_id "Phchi.S1G047600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5407.t1 is derived from g2577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16715177	16717974	.	+	.	Phchi.S1G256600
Phchi.S1	AUGUSTUS	transcript	16715177	16717974	.	+	.	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	start_codon	16715177	16715179	.	+	0	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	CDS	16715177	16717447	0.33	+	0	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	exon	16715177	16717447	.	+	.	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	intron	16717448	16717527	.	+	.	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	CDS	16717528	16717974	0.23	+	0	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	exon	16717528	16717974	.	+	.	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
Phchi.S1	AUGUSTUS	stop_codon	16717975	16717977	.	+	0	transcript_id "Phchi.S1G256600.t1"; gene_id "Phchi.S1G256600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14035.t1 is derived from g12502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10402520	10402867	.	+	.	Phchi.S3G135400
Phchi.S3	AUGUSTUS	transcript	10402520	10402867	.	+	.	transcript_id "Phchi.S3G135400.t1"; gene_id "Phchi.S3G135400"
Phchi.S3	AUGUSTUS	start_codon	10402520	10402522	.	+	0	transcript_id "Phchi.S3G135400.t1"; gene_id "Phchi.S3G135400"
Phchi.S3	AUGUSTUS	CDS	10402520	10402867	0.32	+	0	transcript_id "Phchi.S3G135400.t1"; gene_id "Phchi.S3G135400"
Phchi.S3	AUGUSTUS	exon	10402520	10402867	.	+	.	transcript_id "Phchi.S3G135400.t1"; gene_id "Phchi.S3G135400"
Phchi.S3	AUGUSTUS	stop_codon	10402868	10402870	.	+	0	transcript_id "Phchi.S3G135400.t1"; gene_id "Phchi.S3G135400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12168.t1 is derived from g7844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5308204	5309622	.	-	.	Phchi.S2G024800
Phchi.S2	AUGUSTUS	transcript	5308204	5309622	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	stop_codon	5308201	5308203	.	-	0	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	CDS	5308204	5308419	1	-	0	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	exon	5308204	5308419	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	intron	5308420	5308567	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	CDS	5308568	5308636	1	-	0	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	exon	5308568	5308636	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	intron	5308637	5308723	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	CDS	5308724	5308934	1	-	1	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	exon	5308724	5308934	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	intron	5308935	5309015	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	CDS	5309016	5309367	0.92	-	2	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	exon	5309016	5309367	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	intron	5309368	5309453	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	CDS	5309454	5309622	0.81	-	0	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	exon	5309454	5309622	.	-	.	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
Phchi.S2	AUGUSTUS	start_codon	5309620	5309622	.	-	0	transcript_id "Phchi.S2G024800.t1"; gene_id "Phchi.S2G024800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15686.t1 is derived from g14155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20661498	20663795	.	-	.	Phchi.S3G300500
Phchi.S3	AUGUSTUS	transcript	20661498	20663795	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	stop_codon	20661495	20661497	.	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20661498	20661698	1	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20661498	20661698	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20661699	20661783	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20661784	20662078	0.98	-	1	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20661784	20662078	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20662079	20662190	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20662191	20662303	0.96	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20662191	20662303	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20662304	20662387	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20662388	20662572	1	-	2	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20662388	20662572	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20662573	20662710	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20662711	20662858	1	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20662711	20662858	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20662859	20662961	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20662962	20663273	0.99	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20662962	20663273	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20663274	20663376	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20663377	20663481	0.99	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20663377	20663481	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	intron	20663482	20663609	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	CDS	20663610	20663795	0.76	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	exon	20663610	20663795	.	-	.	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
Phchi.S3	AUGUSTUS	start_codon	20663793	20663795	.	-	0	transcript_id "Phchi.S3G300500.t1"; gene_id "Phchi.S3G300500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg555.t1 is derived from g10337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4031466	4032508	.	+	.	Phchi.S6G051400
Phchi.S6	AUGUSTUS	transcript	4031466	4032508	.	+	.	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	start_codon	4031466	4031468	.	+	0	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	CDS	4031466	4032074	0.94	+	0	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	exon	4031466	4032074	.	+	.	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	intron	4032075	4032183	.	+	.	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	CDS	4032184	4032285	0.96	+	0	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	exon	4032184	4032285	.	+	.	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	intron	4032286	4032403	.	+	.	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	CDS	4032404	4032508	0.88	+	0	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	exon	4032404	4032508	.	+	.	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
Phchi.S6	AUGUSTUS	stop_codon	4032509	4032511	.	+	0	transcript_id "Phchi.S6G051400.t1"; gene_id "Phchi.S6G051400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15266.t1 is derived from g13734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18031874	18033137	.	+	.	Phchi.S3G258500
Phchi.S3	AUGUSTUS	transcript	18031874	18033137	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	start_codon	18031874	18031876	.	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18031874	18031915	0.94	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18031874	18031915	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18031916	18032041	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18032042	18032095	0.92	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18032042	18032095	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18032096	18032181	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18032182	18032226	0.93	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18032182	18032226	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18032227	18032326	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18032327	18032474	0.85	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18032327	18032474	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18032475	18032578	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18032579	18032708	0.99	+	2	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18032579	18032708	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18032709	18032778	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18032779	18032905	1	+	1	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18032779	18032905	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18032906	18032975	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18032976	18033004	1	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18032976	18033004	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	intron	18033005	18033091	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	CDS	18033092	18033137	0.92	+	1	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	exon	18033092	18033137	.	+	.	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
Phchi.S3	AUGUSTUS	stop_codon	18033138	18033140	.	+	0	transcript_id "Phchi.S3G258500.t1"; gene_id "Phchi.S3G258500"
# This transcript jg7866.t2 is derived from g5040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7867.t1 is derived from g5041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31620884	31621399	.	+	.	Phchi.S1G502600
Phchi.S1	AUGUSTUS	transcript	31620884	31621399	.	+	.	transcript_id "Phchi.S1G502600.t1"; gene_id "Phchi.S1G502600"
Phchi.S1	AUGUSTUS	start_codon	31620884	31620886	.	+	0	transcript_id "Phchi.S1G502600.t1"; gene_id "Phchi.S1G502600"
Phchi.S1	AUGUSTUS	CDS	31620884	31621399	0.96	+	0	transcript_id "Phchi.S1G502600.t1"; gene_id "Phchi.S1G502600"
Phchi.S1	AUGUSTUS	exon	31620884	31621399	.	+	.	transcript_id "Phchi.S1G502600.t1"; gene_id "Phchi.S1G502600"
Phchi.S1	AUGUSTUS	stop_codon	31621400	31621402	.	+	0	transcript_id "Phchi.S1G502600.t1"; gene_id "Phchi.S1G502600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9183.t1 is derived from g6358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40244516	40245283	.	+	.	Phchi.S1G634200
Phchi.S1	AUGUSTUS	transcript	40244516	40245283	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	start_codon	40244516	40244518	.	+	0	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	CDS	40244516	40244591	0.89	+	0	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	exon	40244516	40244591	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	intron	40244592	40244678	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	CDS	40244679	40244836	1	+	2	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	exon	40244679	40244836	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	intron	40244837	40244917	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	CDS	40244918	40245012	1	+	0	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	exon	40244918	40245012	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	intron	40245013	40245141	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	CDS	40245142	40245283	0.93	+	1	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	exon	40245142	40245283	.	+	.	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
Phchi.S1	AUGUSTUS	stop_codon	40245284	40245286	.	+	0	transcript_id "Phchi.S1G634200.t1"; gene_id "Phchi.S1G634200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7892.t1 is derived from g5066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31777639	31778901	.	+	.	Phchi.S1G505100
Phchi.S1	AUGUSTUS	transcript	31777639	31778901	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	start_codon	31777639	31777641	.	+	0	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	CDS	31777639	31778447	0.36	+	0	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	exon	31777639	31778447	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	intron	31778448	31778520	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	CDS	31778521	31778560	0.76	+	1	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	exon	31778521	31778560	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	intron	31778561	31778671	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	CDS	31778672	31778761	0.79	+	0	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	exon	31778672	31778761	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	intron	31778762	31778898	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	CDS	31778899	31778901	0.94	+	0	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	exon	31778899	31778901	.	+	.	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
Phchi.S1	AUGUSTUS	stop_codon	31778902	31778904	.	+	0	transcript_id "Phchi.S1G505100.t1"; gene_id "Phchi.S1G505100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11575.t1 is derived from g15626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7143469	7145716	.	+	.	Phchi.S4G115700
Phchi.S4	AUGUSTUS	transcript	7143469	7145716	.	+	.	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	start_codon	7143469	7143471	.	+	0	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	CDS	7143469	7145128	1	+	0	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	exon	7143469	7145128	.	+	.	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	intron	7145129	7145216	.	+	.	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	CDS	7145217	7145716	0.98	+	2	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	exon	7145217	7145716	.	+	.	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
Phchi.S4	AUGUSTUS	stop_codon	7145717	7145719	.	+	0	transcript_id "Phchi.S4G115700.t1"; gene_id "Phchi.S4G115700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4698.t1 is derived from g1868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12345330	12347728	.	-	.	Phchi.S1G185700
Phchi.S1	AUGUSTUS	transcript	12345330	12347728	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	stop_codon	12345327	12345329	.	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12345330	12345386	1	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12345330	12345386	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12345387	12345471	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12345472	12345549	1	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12345472	12345549	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12345550	12345620	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12345621	12345703	1	-	2	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12345621	12345703	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12345704	12345794	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12345795	12345855	1	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12345795	12345855	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12345856	12345926	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12345927	12346029	1	-	1	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12345927	12346029	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12346030	12346152	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12346153	12346211	1	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12346153	12346211	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12346212	12346319	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12346320	12346405	0.98	-	2	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12346320	12346405	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12346406	12346518	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12346519	12346630	0.87	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12346519	12346630	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12346631	12346718	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12346719	12346781	1	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12346719	12346781	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12346782	12346914	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12346915	12347007	1	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12346915	12347007	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12347008	12347131	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12347132	12347162	1	-	1	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12347132	12347162	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	intron	12347163	12347246	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	CDS	12347247	12347728	0.78	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	exon	12347247	12347728	.	-	.	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
Phchi.S1	AUGUSTUS	start_codon	12347726	12347728	.	-	0	transcript_id "Phchi.S1G185700.t1"; gene_id "Phchi.S1G185700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8534.t1 is derived from g5709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36526203	36528530	.	-	.	Phchi.S1G569300
Phchi.S1	AUGUSTUS	transcript	36526203	36528530	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	stop_codon	36526200	36526202	.	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	CDS	36526203	36526313	1	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	exon	36526203	36526313	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	intron	36526314	36526400	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	CDS	36526401	36526487	1	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	exon	36526401	36526487	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	intron	36526488	36526705	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	CDS	36526706	36526966	1	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	exon	36526706	36526966	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	intron	36526967	36527087	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	CDS	36527088	36527297	1	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	exon	36527088	36527297	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	intron	36527298	36527462	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	CDS	36527463	36528530	0.7	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	exon	36527463	36528530	.	-	.	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
Phchi.S1	AUGUSTUS	start_codon	36528528	36528530	.	-	0	transcript_id "Phchi.S1G569300.t1"; gene_id "Phchi.S1G569300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4233.t1 is derived from g1402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9038301	9040516	.	-	.	Phchi.S1G139200
Phchi.S1	AUGUSTUS	transcript	9038301	9040516	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	stop_codon	9038298	9038300	.	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9038301	9038344	0.63	-	2	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9038301	9038344	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9038345	9038506	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9038507	9038561	0.61	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9038507	9038561	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9038562	9038733	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9038734	9038832	0.28	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9038734	9038832	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9038833	9038917	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9038918	9039367	0.25	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9038918	9039367	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9039368	9039471	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9039472	9039552	0.99	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9039472	9039552	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9039553	9039706	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9039707	9039786	0.45	-	2	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9039707	9039786	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9039787	9040229	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9040230	9040254	0.61	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9040230	9040254	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	intron	9040255	9040498	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	CDS	9040499	9040516	0.97	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	exon	9040499	9040516	.	-	.	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
Phchi.S1	AUGUSTUS	start_codon	9040514	9040516	.	-	0	transcript_id "Phchi.S1G139200.t1"; gene_id "Phchi.S1G139200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5298.t1 is derived from g2468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16085478	16087817	.	-	.	Phchi.S1G245700
Phchi.S1	AUGUSTUS	transcript	16086118	16087817	.	-	.	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	stop_codon	16086115	16086117	.	-	0	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16086118	16086127	0.96	-	1	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16086118	16086127	.	-	.	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	intron	16086128	16086213	.	-	.	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16086214	16086506	0.39	-	0	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16086214	16086506	.	-	.	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	intron	16086507	16086689	.	-	.	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16086690	16087817	0.71	-	0	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16086690	16087817	.	-	.	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	start_codon	16087815	16087817	.	-	0	transcript_id "Phchi.S1G245700.t1"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	transcript	16086488	16087817	.	-	.	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	stop_codon	16086485	16086487	.	-	0	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16086488	16086557	0.48	-	1	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16086488	16086557	.	-	.	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	intron	16086558	16086663	.	-	.	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16086664	16087817	0.89	-	0	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16086664	16087817	.	-	.	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	start_codon	16087815	16087817	.	-	0	transcript_id "Phchi.S1G245700.t2"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	transcript	16085478	16087817	.	-	.	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	stop_codon	16085475	16085477	.	-	0	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16085478	16086527	0.42	-	0	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16085478	16086527	.	-	.	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	intron	16086528	16086689	.	-	.	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	CDS	16086690	16087817	0.82	-	0	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	exon	16086690	16087817	.	-	.	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
Phchi.S1	AUGUSTUS	start_codon	16087815	16087817	.	-	0	transcript_id "Phchi.S1G245700.t3"; gene_id "Phchi.S1G245700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4334.t1 is derived from g1503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9831212	9832544	.	-	.	Phchi.S1G149300
Phchi.S1	AUGUSTUS	transcript	9831212	9832544	.	-	.	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	stop_codon	9831209	9831211	.	-	0	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	CDS	9831212	9831832	0.45	-	0	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	exon	9831212	9831832	.	-	.	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	intron	9831833	9831932	.	-	.	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	CDS	9831933	9832544	0.65	-	0	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	exon	9831933	9832544	.	-	.	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
Phchi.S1	AUGUSTUS	start_codon	9832542	9832544	.	-	0	transcript_id "Phchi.S1G149300.t1"; gene_id "Phchi.S1G149300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2107.t1 is derived from g9027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4910367	4911749	.	+	.	Phchi.S5G071600
Phchi.S5	AUGUSTUS	transcript	4910367	4911749	.	+	.	transcript_id "Phchi.S5G071600.t1"; gene_id "Phchi.S5G071600"
Phchi.S5	AUGUSTUS	start_codon	4910367	4910369	.	+	0	transcript_id "Phchi.S5G071600.t1"; gene_id "Phchi.S5G071600"
Phchi.S5	AUGUSTUS	CDS	4910367	4911749	0.59	+	0	transcript_id "Phchi.S5G071600.t1"; gene_id "Phchi.S5G071600"
Phchi.S5	AUGUSTUS	exon	4910367	4911749	.	+	.	transcript_id "Phchi.S5G071600.t1"; gene_id "Phchi.S5G071600"
Phchi.S5	AUGUSTUS	stop_codon	4911750	4911752	.	+	0	transcript_id "Phchi.S5G071600.t1"; gene_id "Phchi.S5G071600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14757.t1 is derived from g13225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14566854	14568567	.	-	.	Phchi.S3G207600
Phchi.S3	AUGUSTUS	transcript	14566854	14568567	.	-	.	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	stop_codon	14566851	14566853	.	-	0	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	CDS	14566854	14566964	0.47	-	0	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	exon	14566854	14566964	.	-	.	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	intron	14566965	14567046	.	-	.	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	CDS	14567047	14568567	0.33	-	0	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	exon	14567047	14568567	.	-	.	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
Phchi.S3	AUGUSTUS	start_codon	14568565	14568567	.	-	0	transcript_id "Phchi.S3G207600.t1"; gene_id "Phchi.S3G207600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7421.t1 is derived from g4593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29067712	29068353	.	+	.	Phchi.S1G458000
Phchi.S1	AUGUSTUS	transcript	29067712	29068353	.	+	.	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	start_codon	29067712	29067714	.	+	0	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	CDS	29067712	29067904	0.52	+	0	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	exon	29067712	29067904	.	+	.	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	intron	29067905	29068112	.	+	.	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	CDS	29068113	29068173	0.55	+	2	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	exon	29068113	29068173	.	+	.	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	intron	29068174	29068265	.	+	.	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	CDS	29068266	29068353	0.72	+	1	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	exon	29068266	29068353	.	+	.	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	stop_codon	29068354	29068356	.	+	0	transcript_id "Phchi.S1G458000.t1"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	transcript	29067712	29068353	.	+	.	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	start_codon	29067712	29067714	.	+	0	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	CDS	29067712	29067904	0.22	+	0	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	exon	29067712	29067904	.	+	.	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	intron	29067905	29068112	.	+	.	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	CDS	29068113	29068179	0.21	+	2	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	exon	29068113	29068179	.	+	.	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	intron	29068180	29068265	.	+	.	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	CDS	29068266	29068353	0.58	+	1	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	exon	29068266	29068353	.	+	.	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
Phchi.S1	AUGUSTUS	stop_codon	29068354	29068356	.	+	0	transcript_id "Phchi.S1G458000.t2"; gene_id "Phchi.S1G458000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2323.t1 is derived from g9243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6179747	6182207	.	-	.	Phchi.S5G093200
Phchi.S5	AUGUSTUS	transcript	6179747	6182207	.	-	.	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	stop_codon	6179744	6179746	.	-	0	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	CDS	6179747	6179754	1	-	2	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	exon	6179747	6179754	.	-	.	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	intron	6179755	6179828	.	-	.	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	CDS	6179829	6179945	0.95	-	2	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	exon	6179829	6179945	.	-	.	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	intron	6179946	6180070	.	-	.	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	CDS	6180071	6182207	0.56	-	0	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	exon	6180071	6182207	.	-	.	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
Phchi.S5	AUGUSTUS	start_codon	6182205	6182207	.	-	0	transcript_id "Phchi.S5G093200.t1"; gene_id "Phchi.S5G093200"
# This transcript jg14113.t2 is derived from g12580.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14114.t1 is derived from g12581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10902588	10904232	.	-	.	Phchi.S3G143300
Phchi.S3	AUGUSTUS	transcript	10902588	10904232	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	stop_codon	10902585	10902587	.	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10902588	10902605	0.75	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10902588	10902605	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	intron	10902606	10902729	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10902730	10902817	1	-	1	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10902730	10902817	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	intron	10902818	10902897	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10902898	10903025	0.99	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10902898	10903025	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	intron	10903026	10903181	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10903182	10903313	0.95	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10903182	10903313	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	intron	10903314	10903411	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10903412	10903492	1	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10903412	10903492	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	intron	10903493	10903579	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10903580	10903738	1	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10903580	10903738	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	intron	10903739	10903902	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	CDS	10903903	10904232	0.65	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	exon	10903903	10904232	.	-	.	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
Phchi.S3	AUGUSTUS	start_codon	10904230	10904232	.	-	0	transcript_id "Phchi.S3G143300.t1"; gene_id "Phchi.S3G143300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7650.t1 is derived from g4824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30412009	30413949	.	+	.	Phchi.S1G480900
Phchi.S1	AUGUSTUS	transcript	30412009	30413949	.	+	.	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	start_codon	30412009	30412011	.	+	0	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	CDS	30412009	30412158	0.99	+	0	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	exon	30412009	30412158	.	+	.	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	intron	30412159	30412429	.	+	.	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	CDS	30412430	30412560	1	+	0	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	exon	30412430	30412560	.	+	.	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	intron	30412561	30412751	.	+	.	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	CDS	30412752	30413949	0.96	+	1	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	exon	30412752	30413949	.	+	.	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
Phchi.S1	AUGUSTUS	stop_codon	30413950	30413952	.	+	0	transcript_id "Phchi.S1G480900.t1"; gene_id "Phchi.S1G480900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15095.t1 is derived from g13563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16992571	16993986	.	-	.	Phchi.S3G241400
Phchi.S3	AUGUSTUS	transcript	16992571	16993986	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	stop_codon	16992568	16992570	.	-	0	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	CDS	16992571	16992702	1	-	0	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	exon	16992571	16992702	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	intron	16992703	16992784	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	CDS	16992785	16992911	0.97	-	1	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	exon	16992785	16992911	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	intron	16992912	16992995	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	CDS	16992996	16993060	0.88	-	0	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	exon	16992996	16993060	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	intron	16993061	16993231	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	CDS	16993232	16993419	0.86	-	2	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	exon	16993232	16993419	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	intron	16993420	16993501	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	CDS	16993502	16993661	1	-	0	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	exon	16993502	16993661	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	intron	16993662	16993761	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	CDS	16993762	16993986	0.58	-	0	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	exon	16993762	16993986	.	-	.	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
Phchi.S3	AUGUSTUS	start_codon	16993984	16993986	.	-	0	transcript_id "Phchi.S3G241400.t1"; gene_id "Phchi.S3G241400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8161.t1 is derived from g5336.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34228888	34233591	.	+	.	Phchi.S1G532000
Phchi.S1	AUGUSTUS	transcript	34228888	34233591	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	start_codon	34228888	34228890	.	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34228888	34229241	0.36	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34228888	34229241	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34229242	34229437	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34229438	34229539	1	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34229438	34229539	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34229540	34229776	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34229777	34229884	1	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34229777	34229884	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34229885	34229966	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34229967	34230047	1	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34229967	34230047	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34230048	34230176	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34230177	34230265	1	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34230177	34230265	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34230266	34230407	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34230408	34233591	0.82	+	1	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34230408	34233591	.	+	.	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	stop_codon	34233592	34233594	.	+	0	transcript_id "Phchi.S1G532000.t1"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	transcript	34228888	34233591	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	start_codon	34228888	34228890	.	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34228888	34229241	0.39	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34228888	34229241	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34229242	34229437	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34229438	34229539	1	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34229438	34229539	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34229540	34229776	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34229777	34229884	1	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34229777	34229884	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34229885	34229966	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34229967	34230047	1	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34229967	34230047	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34230048	34230176	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34230177	34230265	1	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34230177	34230265	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	intron	34230266	34230491	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	CDS	34230492	34233591	0.79	+	1	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	exon	34230492	34233591	.	+	.	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
Phchi.S1	AUGUSTUS	stop_codon	34233592	34233594	.	+	0	transcript_id "Phchi.S1G532000.t2"; gene_id "Phchi.S1G532000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15047.t1 is derived from g13515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16740211	16740951	.	-	.	Phchi.S3G236600
Phchi.S3	AUGUSTUS	transcript	16740211	16740951	.	-	.	transcript_id "Phchi.S3G236600.t1"; gene_id "Phchi.S3G236600"
Phchi.S3	AUGUSTUS	stop_codon	16740208	16740210	.	-	0	transcript_id "Phchi.S3G236600.t1"; gene_id "Phchi.S3G236600"
Phchi.S3	AUGUSTUS	CDS	16740211	16740951	0.63	-	0	transcript_id "Phchi.S3G236600.t1"; gene_id "Phchi.S3G236600"
Phchi.S3	AUGUSTUS	exon	16740211	16740951	.	-	.	transcript_id "Phchi.S3G236600.t1"; gene_id "Phchi.S3G236600"
Phchi.S3	AUGUSTUS	start_codon	16740949	16740951	.	-	0	transcript_id "Phchi.S3G236600.t1"; gene_id "Phchi.S3G236600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg584.t1 is derived from g10366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4293554	4295642	.	-	.	Phchi.S6G054300
Phchi.S6	AUGUSTUS	transcript	4293554	4295642	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	stop_codon	4293551	4293553	.	-	0	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	CDS	4293554	4293771	0.49	-	2	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	exon	4293554	4293771	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	intron	4293772	4293848	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	CDS	4293849	4293928	0.81	-	1	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	exon	4293849	4293928	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	intron	4293929	4293995	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	CDS	4293996	4294146	0.71	-	2	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	exon	4293996	4294146	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	intron	4294147	4294358	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	CDS	4294359	4294417	0.46	-	1	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	exon	4294359	4294417	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	intron	4294418	4294584	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	CDS	4294585	4295642	0.52	-	0	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	exon	4294585	4295642	.	-	.	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
Phchi.S6	AUGUSTUS	start_codon	4295640	4295642	.	-	0	transcript_id "Phchi.S6G054300.t1"; gene_id "Phchi.S6G054300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3054.t1 is derived from g223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1367106	1368745	.	-	.	Phchi.S1G021300
Phchi.S1	AUGUSTUS	transcript	1367106	1368745	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	stop_codon	1367103	1367105	.	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1367106	1367379	1	-	1	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1367106	1367379	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	intron	1367380	1367575	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1367576	1367646	1	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1367576	1367646	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	intron	1367647	1367774	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1367775	1367876	1	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1367775	1367876	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	intron	1367877	1367979	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1367980	1368048	1	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1367980	1368048	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	intron	1368049	1368141	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1368142	1368288	1	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1368142	1368288	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	intron	1368289	1368450	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1368451	1368513	1	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1368451	1368513	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	intron	1368514	1368613	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	CDS	1368614	1368745	0.91	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	exon	1368614	1368745	.	-	.	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
Phchi.S1	AUGUSTUS	start_codon	1368743	1368745	.	-	0	transcript_id "Phchi.S1G021300.t1"; gene_id "Phchi.S1G021300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg404.t1 is derived from g10186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2911553	2912588	.	-	.	Phchi.S6G036300
Phchi.S6	AUGUSTUS	transcript	2911553	2912588	.	-	.	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	stop_codon	2911550	2911552	.	-	0	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	CDS	2911553	2911643	0.55	-	1	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	exon	2911553	2911643	.	-	.	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	intron	2911644	2911741	.	-	.	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	CDS	2911742	2911799	0.39	-	2	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	exon	2911742	2911799	.	-	.	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	intron	2911800	2911891	.	-	.	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	CDS	2911892	2912588	0.39	-	0	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	exon	2911892	2912588	.	-	.	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
Phchi.S6	AUGUSTUS	start_codon	2912586	2912588	.	-	0	transcript_id "Phchi.S6G036300.t1"; gene_id "Phchi.S6G036300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8703.t1 is derived from g5878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37534130	37535919	.	-	.	Phchi.S1G586200
Phchi.S1	AUGUSTUS	transcript	37534130	37535919	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	stop_codon	37534127	37534129	.	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37534130	37534263	1	-	2	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37534130	37534263	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37534264	37534346	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37534347	37534470	1	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37534347	37534470	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37534471	37534557	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37534558	37534728	1	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37534558	37534728	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37534729	37534806	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37534807	37534923	1	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37534807	37534923	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37534924	37535009	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37535010	37535112	1	-	1	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37535010	37535112	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37535113	37535258	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37535259	37535425	1	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37535259	37535425	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37535426	37535500	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37535501	37535570	1	-	1	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37535501	37535570	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	intron	37535571	37535710	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	CDS	37535711	37535919	0.89	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	exon	37535711	37535919	.	-	.	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
Phchi.S1	AUGUSTUS	start_codon	37535917	37535919	.	-	0	transcript_id "Phchi.S1G586200.t1"; gene_id "Phchi.S1G586200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2276.t1 is derived from g9196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5834465	5835541	.	-	.	Phchi.S5G088500
Phchi.S5	AUGUSTUS	transcript	5834465	5835541	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	stop_codon	5834462	5834464	.	-	0	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	CDS	5834465	5834605	1	-	0	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	exon	5834465	5834605	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	intron	5834606	5834728	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	CDS	5834729	5834816	0.98	-	1	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	exon	5834729	5834816	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	intron	5834817	5834924	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	CDS	5834925	5835041	1	-	1	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	exon	5834925	5835041	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	intron	5835042	5835189	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	CDS	5835190	5835347	1	-	0	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	exon	5835190	5835347	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	intron	5835348	5835427	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	CDS	5835428	5835541	0.88	-	0	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	exon	5835428	5835541	.	-	.	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
Phchi.S5	AUGUSTUS	start_codon	5835539	5835541	.	-	0	transcript_id "Phchi.S5G088500.t1"; gene_id "Phchi.S5G088500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11642.t1 is derived from g15693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7430646	7434197	.	+	.	Phchi.S4G122400
Phchi.S4	AUGUSTUS	transcript	7430646	7434197	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	start_codon	7430646	7430648	.	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7430646	7431128	0.78	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7430646	7431128	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7431129	7431301	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7431302	7431371	0.96	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7431302	7431371	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7431372	7431508	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7431509	7431678	0.91	+	2	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7431509	7431678	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7431679	7431885	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7431886	7431957	0.56	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7431886	7431957	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7431958	7432120	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7432121	7432162	0.54	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7432121	7432162	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7432163	7432309	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7432310	7432372	1	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7432310	7432372	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7432373	7432452	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7432453	7432495	1	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7432453	7432495	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7432496	7432575	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7432576	7432756	0.83	+	2	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7432576	7432756	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7432757	7432862	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7432863	7433421	0.81	+	1	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7432863	7433421	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7433422	7433503	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7433504	7433602	0.99	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7433504	7433602	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	intron	7433603	7433675	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	CDS	7433676	7434197	0.66	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	exon	7433676	7434197	.	+	.	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
Phchi.S4	AUGUSTUS	stop_codon	7434198	7434200	.	+	0	transcript_id "Phchi.S4G122400.t1"; gene_id "Phchi.S4G122400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1331.t1 is derived from g11114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9058329	9058550	.	+	.	Phchi.S6G129000
Phchi.S6	AUGUSTUS	transcript	9058329	9058550	.	+	.	transcript_id "Phchi.S6G129000.t1"; gene_id "Phchi.S6G129000"
Phchi.S6	AUGUSTUS	start_codon	9058329	9058331	.	+	0	transcript_id "Phchi.S6G129000.t1"; gene_id "Phchi.S6G129000"
Phchi.S6	AUGUSTUS	CDS	9058329	9058550	0.48	+	0	transcript_id "Phchi.S6G129000.t1"; gene_id "Phchi.S6G129000"
Phchi.S6	AUGUSTUS	exon	9058329	9058550	.	+	.	transcript_id "Phchi.S6G129000.t1"; gene_id "Phchi.S6G129000"
Phchi.S6	AUGUSTUS	stop_codon	9058551	9058553	.	+	0	transcript_id "Phchi.S6G129000.t1"; gene_id "Phchi.S6G129000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13226.t1 is derived from g11691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4780960	4782834	.	-	.	Phchi.S3G054500
Phchi.S3	AUGUSTUS	transcript	4780960	4782834	.	-	.	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	stop_codon	4780957	4780959	.	-	0	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	CDS	4780960	4782359	0.95	-	2	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	exon	4780960	4782359	.	-	.	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	intron	4782360	4782629	.	-	.	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	CDS	4782630	4782834	0.9	-	0	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	exon	4782630	4782834	.	-	.	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
Phchi.S3	AUGUSTUS	start_codon	4782832	4782834	.	-	0	transcript_id "Phchi.S3G054500.t1"; gene_id "Phchi.S3G054500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11854.t1 is derived from g15906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8629789	8630788	.	+	.	Phchi.S4G143600
Phchi.S4	AUGUSTUS	transcript	8629789	8630788	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	start_codon	8629789	8629791	.	+	0	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	CDS	8629789	8630072	1	+	0	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	exon	8629789	8630072	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	intron	8630073	8630158	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	CDS	8630159	8630219	1	+	1	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	exon	8630159	8630219	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	intron	8630220	8630314	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	CDS	8630315	8630386	1	+	0	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	exon	8630315	8630386	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	intron	8630387	8630482	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	CDS	8630483	8630598	1	+	0	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	exon	8630483	8630598	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	intron	8630599	8630688	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	CDS	8630689	8630788	1	+	1	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	exon	8630689	8630788	.	+	.	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
Phchi.S4	AUGUSTUS	stop_codon	8630789	8630791	.	+	0	transcript_id "Phchi.S4G143600.t1"; gene_id "Phchi.S4G143600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2483.t1 is derived from g9403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6876041	6876552	.	-	.	Phchi.S5G109200
Phchi.S5	AUGUSTUS	transcript	6876041	6876552	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	stop_codon	6876038	6876040	.	-	0	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	CDS	6876041	6876109	1	-	0	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	exon	6876041	6876109	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	intron	6876110	6876199	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	CDS	6876200	6876290	0.8	-	1	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	exon	6876200	6876290	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	intron	6876291	6876372	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	CDS	6876373	6876442	0.93	-	2	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	exon	6876373	6876442	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	intron	6876443	6876521	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	CDS	6876522	6876552	1	-	0	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	exon	6876522	6876552	.	-	.	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
Phchi.S5	AUGUSTUS	start_codon	6876550	6876552	.	-	0	transcript_id "Phchi.S5G109200.t1"; gene_id "Phchi.S5G109200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1116.t1 is derived from g10899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7774229	7776625	.	+	.	Phchi.S6G107500
Phchi.S6	AUGUSTUS	transcript	7774229	7776625	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	start_codon	7774229	7774231	.	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774229	7774327	1	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774229	7774327	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774328	7774409	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774410	7774523	1	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774410	7774523	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774524	7774608	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774609	7774729	1	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774609	7774729	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774730	7774992	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774993	7775049	1	+	2	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774993	7775049	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775050	7775206	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775207	7775307	1	+	2	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775207	7775307	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775308	7775428	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775429	7775516	0.99	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775429	7775516	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775517	7775649	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775650	7775757	0.99	+	2	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775650	7775757	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775758	7775837	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775838	7775873	0.89	+	2	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775838	7775873	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775874	7775926	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775927	7775991	0.89	+	2	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775927	7775991	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775992	7776152	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7776153	7776224	1	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7776153	7776224	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7776225	7776305	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7776306	7776419	0.97	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7776306	7776419	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7776420	7776532	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7776533	7776625	0.98	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7776533	7776625	.	+	.	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	stop_codon	7776626	7776628	.	+	0	transcript_id "Phchi.S6G107500.t1"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	transcript	7774229	7776625	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	start_codon	7774229	7774231	.	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774229	7774327	1	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774229	7774327	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774328	7774409	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774410	7774523	1	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774410	7774523	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774524	7774618	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774619	7774627	1	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774619	7774627	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774628	7774707	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774708	7774729	1	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774708	7774729	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7774730	7774992	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7774993	7775049	1	+	2	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7774993	7775049	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775050	7775206	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775207	7775307	1	+	2	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775207	7775307	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775308	7775428	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775429	7775516	0.99	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775429	7775516	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775517	7775649	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775650	7775757	0.99	+	2	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775650	7775757	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775758	7775837	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775838	7775873	0.87	+	2	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775838	7775873	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775874	7775926	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7775927	7775991	0.87	+	2	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7775927	7775991	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7775992	7776152	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7776153	7776224	1	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7776153	7776224	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7776225	7776305	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7776306	7776419	0.97	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7776306	7776419	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	intron	7776420	7776532	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	CDS	7776533	7776625	0.99	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	exon	7776533	7776625	.	+	.	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
Phchi.S6	AUGUSTUS	stop_codon	7776626	7776628	.	+	0	transcript_id "Phchi.S6G107500.t2"; gene_id "Phchi.S6G107500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4687.t1 is derived from g1857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12098974	12099852	.	+	.	Phchi.S1G184600
Phchi.S1	AUGUSTUS	transcript	12098974	12099852	.	+	.	transcript_id "Phchi.S1G184600.t1"; gene_id "Phchi.S1G184600"
Phchi.S1	AUGUSTUS	start_codon	12098974	12098976	.	+	0	transcript_id "Phchi.S1G184600.t1"; gene_id "Phchi.S1G184600"
Phchi.S1	AUGUSTUS	CDS	12098974	12099852	0.46	+	0	transcript_id "Phchi.S1G184600.t1"; gene_id "Phchi.S1G184600"
Phchi.S1	AUGUSTUS	exon	12098974	12099852	.	+	.	transcript_id "Phchi.S1G184600.t1"; gene_id "Phchi.S1G184600"
Phchi.S1	AUGUSTUS	stop_codon	12099853	12099855	.	+	0	transcript_id "Phchi.S1G184600.t1"; gene_id "Phchi.S1G184600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5992.t1 is derived from g3163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20280792	20282450	.	-	.	Phchi.S1G315100
Phchi.S1	AUGUSTUS	transcript	20280792	20282450	.	-	.	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	stop_codon	20280789	20280791	.	-	0	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	CDS	20280792	20280814	1	-	2	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	exon	20280792	20280814	.	-	.	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	intron	20280815	20280982	.	-	.	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	CDS	20280983	20281052	1	-	0	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	exon	20280983	20281052	.	-	.	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	intron	20281053	20281313	.	-	.	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	CDS	20281314	20282450	1	-	0	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	exon	20281314	20282450	.	-	.	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
Phchi.S1	AUGUSTUS	start_codon	20282448	20282450	.	-	0	transcript_id "Phchi.S1G315100.t1"; gene_id "Phchi.S1G315100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8578.t1 is derived from g5753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36716463	36717929	.	-	.	Phchi.S1G573700
Phchi.S1	AUGUSTUS	transcript	36716463	36717929	.	-	.	transcript_id "Phchi.S1G573700.t1"; gene_id "Phchi.S1G573700"
Phchi.S1	AUGUSTUS	stop_codon	36716460	36716462	.	-	0	transcript_id "Phchi.S1G573700.t1"; gene_id "Phchi.S1G573700"
Phchi.S1	AUGUSTUS	CDS	36716463	36717929	0.83	-	0	transcript_id "Phchi.S1G573700.t1"; gene_id "Phchi.S1G573700"
Phchi.S1	AUGUSTUS	exon	36716463	36717929	.	-	.	transcript_id "Phchi.S1G573700.t1"; gene_id "Phchi.S1G573700"
Phchi.S1	AUGUSTUS	start_codon	36717927	36717929	.	-	0	transcript_id "Phchi.S1G573700.t1"; gene_id "Phchi.S1G573700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15162.t1 is derived from g13630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17325909	17326758	.	-	.	Phchi.S3G248100
Phchi.S3	AUGUSTUS	transcript	17325909	17326758	.	-	.	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	stop_codon	17325906	17325908	.	-	0	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	CDS	17325909	17326142	1	-	0	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	exon	17325909	17326142	.	-	.	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	intron	17326143	17326237	.	-	.	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	CDS	17326238	17326501	0.99	-	0	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	exon	17326238	17326501	.	-	.	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	intron	17326502	17326596	.	-	.	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	CDS	17326597	17326758	0.57	-	0	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	exon	17326597	17326758	.	-	.	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
Phchi.S3	AUGUSTUS	start_codon	17326756	17326758	.	-	0	transcript_id "Phchi.S3G248100.t1"; gene_id "Phchi.S3G248100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13917.t1 is derived from g12384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9647949	9649497	.	+	.	Phchi.S3G123600
Phchi.S3	AUGUSTUS	transcript	9647949	9649497	.	+	.	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	start_codon	9647949	9647951	.	+	0	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	CDS	9647949	9648155	1	+	0	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	exon	9647949	9648155	.	+	.	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	intron	9648156	9648774	.	+	.	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	CDS	9648775	9649497	1	+	0	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	exon	9648775	9649497	.	+	.	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
Phchi.S3	AUGUSTUS	stop_codon	9649498	9649500	.	+	0	transcript_id "Phchi.S3G123600.t1"; gene_id "Phchi.S3G123600"
# This transcript jg5995.t2 is derived from g3166.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5996.t1 is derived from g3167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20314256	20316127	.	-	.	Phchi.S1G315500
Phchi.S1	AUGUSTUS	transcript	20314256	20316127	.	-	.	transcript_id "Phchi.S1G315500.t1"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	stop_codon	20314253	20314255	.	-	0	transcript_id "Phchi.S1G315500.t1"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	CDS	20314256	20316127	0.98	-	0	transcript_id "Phchi.S1G315500.t1"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	exon	20314256	20316127	.	-	.	transcript_id "Phchi.S1G315500.t1"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	start_codon	20316125	20316127	.	-	0	transcript_id "Phchi.S1G315500.t1"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	transcript	20314256	20315257	.	-	.	transcript_id "Phchi.S1G315500.t2"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	stop_codon	20314253	20314255	.	-	0	transcript_id "Phchi.S1G315500.t2"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	CDS	20314256	20315257	0.83	-	0	transcript_id "Phchi.S1G315500.t2"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	exon	20314256	20315257	.	-	.	transcript_id "Phchi.S1G315500.t2"; gene_id "Phchi.S1G315500"
Phchi.S1	AUGUSTUS	start_codon	20315255	20315257	.	-	0	transcript_id "Phchi.S1G315500.t2"; gene_id "Phchi.S1G315500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11050.t1 is derived from g15100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3829821	3832550	.	+	.	Phchi.S4G063200
Phchi.S4	AUGUSTUS	transcript	3829821	3832550	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	start_codon	3829821	3829823	.	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3829821	3830015	0.84	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3829821	3830015	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3830016	3830118	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3830119	3830250	0.85	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3830119	3830250	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3830251	3830385	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3830386	3830638	0.99	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3830386	3830638	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3830639	3830737	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3830738	3830848	1	+	2	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3830738	3830848	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3830849	3831272	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3831273	3831391	1	+	2	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3831273	3831391	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3831392	3831520	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3831521	3831625	1	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3831521	3831625	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3831626	3831794	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3831795	3831997	1	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3831795	3831997	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3831998	3832134	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3832135	3832258	0.95	+	1	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3832135	3832258	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	intron	3832259	3832361	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	CDS	3832362	3832550	1	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	exon	3832362	3832550	.	+	.	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
Phchi.S4	AUGUSTUS	stop_codon	3832551	3832553	.	+	0	transcript_id "Phchi.S4G063200.t1"; gene_id "Phchi.S4G063200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8565.t1 is derived from g5740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36634550	36637452	.	+	.	Phchi.S1G572400
Phchi.S1	AUGUSTUS	transcript	36634550	36637452	.	+	.	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	start_codon	36634550	36634552	.	+	0	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	CDS	36634550	36634722	0.8	+	0	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	exon	36634550	36634722	.	+	.	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	intron	36634723	36634906	.	+	.	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	CDS	36634907	36637311	0.81	+	1	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	exon	36634907	36637311	.	+	.	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	intron	36637312	36637447	.	+	.	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	CDS	36637448	36637452	0.64	+	2	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	exon	36637448	36637452	.	+	.	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	stop_codon	36637453	36637455	.	+	0	transcript_id "Phchi.S1G572400.t1"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	transcript	36635025	36637452	.	+	.	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	start_codon	36635025	36635027	.	+	0	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	CDS	36635025	36637311	0.97	+	0	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	exon	36635025	36637311	.	+	.	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	intron	36637312	36637447	.	+	.	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	CDS	36637448	36637452	0.59	+	2	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	exon	36637448	36637452	.	+	.	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
Phchi.S1	AUGUSTUS	stop_codon	36637453	36637455	.	+	0	transcript_id "Phchi.S1G572400.t2"; gene_id "Phchi.S1G572400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7300.t1 is derived from g4472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28383799	28384823	.	+	.	Phchi.S1G445900
Phchi.S1	AUGUSTUS	transcript	28383799	28384823	.	+	.	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	start_codon	28383799	28383801	.	+	0	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	CDS	28383799	28383946	0.94	+	0	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	exon	28383799	28383946	.	+	.	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	intron	28383947	28384047	.	+	.	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	CDS	28384048	28384823	0.86	+	2	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	exon	28384048	28384823	.	+	.	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
Phchi.S1	AUGUSTUS	stop_codon	28384824	28384826	.	+	0	transcript_id "Phchi.S1G445900.t1"; gene_id "Phchi.S1G445900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8936.t1 is derived from g6111.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38749330	38752440	.	+	.	Phchi.S1G609500
Phchi.S1	AUGUSTUS	transcript	38749330	38752440	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	start_codon	38749330	38749332	.	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749330	38749341	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749330	38749341	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749342	38749498	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749499	38749615	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749499	38749615	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749616	38749742	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749743	38749801	0.98	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749743	38749801	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749802	38749916	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749917	38749976	0.98	+	1	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749917	38749976	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749977	38750068	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750069	38750122	1	+	1	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750069	38750122	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750123	38750256	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750257	38750305	1	+	1	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750257	38750305	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750306	38750405	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750406	38750453	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750406	38750453	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750454	38750541	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750542	38750607	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750542	38750607	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750608	38750730	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750731	38750781	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750731	38750781	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750782	38750875	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750876	38750995	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750876	38750995	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750996	38751181	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751182	38751266	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751182	38751266	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751267	38751355	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751356	38751434	1	+	2	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751356	38751434	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751435	38751525	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751526	38751640	1	+	1	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751526	38751640	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751641	38751726	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751727	38751783	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751727	38751783	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751784	38751913	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751914	38751960	1	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751914	38751960	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751961	38752053	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38752054	38752108	1	+	1	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38752054	38752108	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38752109	38752190	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38752191	38752273	0.64	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38752191	38752273	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38752274	38752382	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38752383	38752440	0.59	+	1	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38752383	38752440	.	+	.	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	stop_codon	38752441	38752443	.	+	0	transcript_id "Phchi.S1G609500.t1"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	transcript	38749330	38752440	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	start_codon	38749330	38749332	.	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749330	38749341	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749330	38749341	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749342	38749498	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749499	38749615	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749499	38749615	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749616	38749742	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749743	38749801	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749743	38749801	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749802	38749916	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38749917	38749976	1	+	1	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38749917	38749976	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38749977	38750068	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750069	38750122	1	+	1	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750069	38750122	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750123	38750256	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750257	38750305	1	+	1	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750257	38750305	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750306	38750405	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750406	38750453	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750406	38750453	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750454	38750541	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750542	38750607	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750542	38750607	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750608	38750730	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750731	38750781	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750731	38750781	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750782	38750875	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38750876	38750995	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38750876	38750995	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38750996	38751181	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751182	38751266	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751182	38751266	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751267	38751355	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751356	38751434	1	+	2	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751356	38751434	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751435	38751525	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751526	38751640	1	+	1	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751526	38751640	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751641	38751726	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751727	38751783	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751727	38751783	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751784	38751913	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38751914	38751960	1	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38751914	38751960	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38751961	38752053	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38752054	38752108	0.98	+	1	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38752054	38752108	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38752109	38752187	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38752188	38752273	0.4	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38752188	38752273	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	intron	38752274	38752382	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	CDS	38752383	38752440	0.54	+	1	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	exon	38752383	38752440	.	+	.	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
Phchi.S1	AUGUSTUS	stop_codon	38752441	38752443	.	+	0	transcript_id "Phchi.S1G609500.t2"; gene_id "Phchi.S1G609500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15732.t1 is derived from g14202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20950627	20955463	.	-	.	Phchi.S3G305100
Phchi.S3	AUGUSTUS	transcript	20950627	20955463	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	stop_codon	20950624	20950626	.	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20950627	20950719	0.99	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20950627	20950719	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20950720	20950835	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20950836	20951068	1	-	2	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20950836	20951068	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20951069	20951236	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20951237	20951370	1	-	1	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20951237	20951370	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20951371	20951463	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20951464	20951594	0.98	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20951464	20951594	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20951595	20951702	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20951703	20951762	1	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20951703	20951762	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20951763	20951868	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20951869	20952009	1	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20951869	20952009	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20952010	20952169	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20952170	20952670	1	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20952170	20952670	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20952671	20952754	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20952755	20952953	1	-	1	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20952755	20952953	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20952954	20953122	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20953123	20953220	1	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20953123	20953220	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20953221	20953436	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20953437	20953538	1	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20953437	20953538	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20953539	20953784	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20953785	20953994	0.4	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20953785	20953994	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20953995	20954192	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20954193	20954375	0.8	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20954193	20954375	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20954376	20954500	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20954501	20954893	0.98	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20954501	20954893	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20954894	20955021	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20955022	20955129	0.78	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20955022	20955129	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20955130	20955214	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20955215	20955289	0.97	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20955215	20955289	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	intron	20955290	20955376	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	CDS	20955377	20955463	0.77	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	exon	20955377	20955463	.	-	.	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
Phchi.S3	AUGUSTUS	start_codon	20955461	20955463	.	-	0	transcript_id "Phchi.S3G305100.t1"; gene_id "Phchi.S3G305100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7098.t1 is derived from g4270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26893898	26895286	.	-	.	Phchi.S1G425700
Phchi.S1	AUGUSTUS	transcript	26893898	26895286	.	-	.	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	stop_codon	26893895	26893897	.	-	0	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	CDS	26893898	26894681	0.84	-	1	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	exon	26893898	26894681	.	-	.	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	intron	26894682	26894767	.	-	.	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	CDS	26894768	26894826	0.98	-	0	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	exon	26894768	26894826	.	-	.	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	intron	26894827	26894908	.	-	.	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	CDS	26894909	26895286	1	-	0	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	exon	26894909	26895286	.	-	.	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
Phchi.S1	AUGUSTUS	start_codon	26895284	26895286	.	-	0	transcript_id "Phchi.S1G425700.t1"; gene_id "Phchi.S1G425700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg834.t1 is derived from g10616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5791354	5796183	.	-	.	Phchi.S6G079300
Phchi.S6	AUGUSTUS	transcript	5791354	5796183	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	stop_codon	5791351	5791353	.	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5791354	5791536	1	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5791354	5791536	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5791537	5791633	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5791634	5791777	1	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5791634	5791777	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5791778	5791872	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5791873	5792017	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5791873	5792017	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5792018	5792103	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5792104	5792243	1	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5792104	5792243	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5792244	5792318	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5792319	5792410	1	-	2	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5792319	5792410	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5792411	5792501	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5792502	5792553	1	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5792502	5792553	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5792554	5792626	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5792627	5792684	0.95	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5792627	5792684	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5792685	5792794	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5792795	5792912	0.61	-	2	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5792795	5792912	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5792913	5793020	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5793021	5793215	0.49	-	2	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5793021	5793215	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5793216	5793327	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5793328	5793399	0.61	-	2	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5793328	5793399	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5793400	5793486	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5793487	5793596	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5793487	5793596	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5793597	5793769	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5793770	5793823	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5793770	5793823	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5793824	5793925	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5793926	5793994	0.99	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5793926	5793994	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5793995	5794083	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5794084	5794155	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5794084	5794155	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5794156	5794281	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5794282	5794353	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5794282	5794353	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5794354	5794488	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5794489	5794560	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5794489	5794560	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5794561	5794642	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5794643	5794714	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5794643	5794714	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5794715	5794857	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5794858	5794929	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5794858	5794929	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5794930	5795029	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5795030	5795101	0.91	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5795030	5795101	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5795102	5795211	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5795212	5795283	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5795212	5795283	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5795284	5795417	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5795418	5795594	1	-	1	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5795418	5795594	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5795595	5795685	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5795686	5795809	1	-	2	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5795686	5795809	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5795810	5795905	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5795906	5795983	1	-	2	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5795906	5795983	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	intron	5795984	5796122	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	CDS	5796123	5796183	0.95	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	exon	5796123	5796183	.	-	.	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
Phchi.S6	AUGUSTUS	start_codon	5796181	5796183	.	-	0	transcript_id "Phchi.S6G079300.t1"; gene_id "Phchi.S6G079300"
# This transcript jg14302.t2 is derived from g12769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14303.t1 is derived from g12770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12018192	12021091	.	-	.	Phchi.S3G162200
Phchi.S3	AUGUSTUS	transcript	12018192	12021091	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	stop_codon	12018189	12018191	.	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12018192	12018318	1	-	1	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12018192	12018318	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12018319	12018402	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12018403	12018447	0.92	-	1	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12018403	12018447	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12018448	12018578	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12018579	12018659	1	-	1	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12018579	12018659	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12018660	12018750	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12018751	12018871	1	-	2	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12018751	12018871	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12018872	12018958	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12018959	12019053	0.99	-	1	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12018959	12019053	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12019054	12019155	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12019156	12019277	0.96	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12019156	12019277	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12019278	12019401	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12019402	12019539	1	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12019402	12019539	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12019540	12019615	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12019616	12019779	1	-	2	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12019616	12019779	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12019780	12019905	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12019906	12020026	0.8	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12019906	12020026	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12020027	12020170	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12020171	12020234	0.86	-	1	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12020171	12020234	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12020235	12020319	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12020320	12020465	1	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12020320	12020465	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12020466	12020582	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12020583	12020654	1	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12020583	12020654	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	intron	12020655	12020887	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	CDS	12020888	12021091	0.52	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	exon	12020888	12021091	.	-	.	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
Phchi.S3	AUGUSTUS	start_codon	12021089	12021091	.	-	0	transcript_id "Phchi.S3G162200.t1"; gene_id "Phchi.S3G162200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7058.t1 is derived from g4230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26656495	26658433	.	-	.	Phchi.S1G421700
Phchi.S1	AUGUSTUS	transcript	26656495	26658433	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	stop_codon	26656492	26656494	.	-	0	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26656495	26656555	1	-	1	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26656495	26656555	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	intron	26656556	26656772	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26656773	26657072	1	-	1	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26656773	26657072	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	intron	26657073	26657182	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26657183	26657418	1	-	0	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26657183	26657418	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	intron	26657419	26657502	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26657503	26657628	1	-	0	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26657503	26657628	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	intron	26657629	26657721	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26657722	26657830	1	-	1	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26657722	26657830	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	intron	26657831	26657915	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26657916	26658214	1	-	0	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26657916	26658214	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	intron	26658215	26658352	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	CDS	26658353	26658433	0.99	-	0	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	exon	26658353	26658433	.	-	.	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
Phchi.S1	AUGUSTUS	start_codon	26658431	26658433	.	-	0	transcript_id "Phchi.S1G421700.t1"; gene_id "Phchi.S1G421700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12732.t1 is derived from g11197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1428642	1433408	.	-	.	Phchi.S3G005100
Phchi.S3	AUGUSTUS	transcript	1428642	1433408	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	stop_codon	1428639	1428641	.	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1428642	1428642	0.94	-	1	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1428642	1428642	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1428643	1428765	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1428766	1428813	0.88	-	1	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1428766	1428813	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1428814	1429000	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1429001	1429311	0.53	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1429001	1429311	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1429312	1429402	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1429403	1430987	0.9	-	1	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1429403	1430987	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1430988	1431067	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1431068	1431469	0.98	-	1	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1431068	1431469	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1431470	1431588	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1431589	1431860	1	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1431589	1431860	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1431861	1432069	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1432070	1432192	1	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1432070	1432192	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1432193	1432314	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1432315	1432944	1	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1432315	1432944	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	intron	1432945	1433333	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	CDS	1433334	1433408	0.95	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	exon	1433334	1433408	.	-	.	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
Phchi.S3	AUGUSTUS	start_codon	1433406	1433408	.	-	0	transcript_id "Phchi.S3G005100.t1"; gene_id "Phchi.S3G005100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15075.t1 is derived from g13543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16922447	16932129	.	-	.	Phchi.S3G239400
Phchi.S3	AUGUSTUS	transcript	16922447	16932129	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	stop_codon	16922444	16922446	.	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16922447	16922516	1	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16922447	16922516	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16922517	16922674	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16922675	16922979	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16922675	16922979	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16922980	16923077	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16923078	16924222	0.66	-	2	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16923078	16924222	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16924223	16924335	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16924336	16924825	0.36	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16924336	16924825	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16924826	16924992	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16924993	16925073	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16924993	16925073	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16925074	16925166	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16925167	16925322	0.69	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16925167	16925322	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16925323	16925441	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16925442	16925546	0.84	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16925442	16925546	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16925547	16925638	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16925639	16926245	0.66	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16925639	16926245	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16926246	16926421	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16926422	16926600	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16926422	16926600	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16926601	16926708	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16926709	16926889	1	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16926709	16926889	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16926890	16927020	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16927021	16927124	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16927021	16927124	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16927125	16927223	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16927224	16927352	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16927224	16927352	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16927353	16927553	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16927554	16927650	1	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16927554	16927650	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16927651	16927774	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16927775	16927902	0.99	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16927775	16927902	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16927903	16928018	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16928019	16928078	0.99	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16928019	16928078	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16928079	16928159	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16928160	16928279	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16928160	16928279	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16928280	16928423	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16928424	16928504	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16928424	16928504	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16928505	16928668	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16928669	16928712	0.47	-	2	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16928669	16928712	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16928713	16928849	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16928850	16928913	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16928850	16928913	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16928914	16929006	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16929007	16929190	1	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16929007	16929190	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16929191	16929278	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16929279	16929359	1	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16929279	16929359	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16929360	16929536	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16929537	16929730	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16929537	16929730	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16929731	16929969	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16929970	16930045	1	-	1	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16929970	16930045	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16930046	16930150	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16930151	16930284	0.99	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16930151	16930284	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16930285	16930397	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16930398	16930466	0.89	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16930398	16930466	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16930467	16930578	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16930579	16930626	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16930579	16930626	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16930627	16930770	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16930771	16930845	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16930771	16930845	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16930846	16930925	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16930926	16931006	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16930926	16931006	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16931007	16931097	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16931098	16931160	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16931098	16931160	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16931161	16931307	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16931308	16931367	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16931308	16931367	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16931368	16931615	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16931616	16931657	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16931616	16931657	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16931658	16931757	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16931758	16931883	1	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16931758	16931883	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	intron	16931884	16931979	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	CDS	16931980	16932129	0.83	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	exon	16931980	16932129	.	-	.	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
Phchi.S3	AUGUSTUS	start_codon	16932127	16932129	.	-	0	transcript_id "Phchi.S3G239400.t1"; gene_id "Phchi.S3G239400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9867.t1 is derived from g7043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44142224	44146774	.	-	.	Phchi.S1G702600
Phchi.S1	AUGUSTUS	transcript	44142224	44146774	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	stop_codon	44142221	44142223	.	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44142224	44142316	0.8	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44142224	44142316	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44142317	44142407	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44142408	44143190	0.76	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44142408	44143190	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44143191	44143267	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44143268	44143336	0.99	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44143268	44143336	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44143337	44143443	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44143444	44143589	0.98	-	2	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44143444	44143589	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44143590	44143758	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44143759	44143928	1	-	1	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44143759	44143928	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44143929	44144014	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44144015	44144342	0.95	-	2	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44144015	44144342	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44144343	44144467	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44144468	44144605	0.99	-	2	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44144468	44144605	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44144606	44144709	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44144710	44144965	0.76	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44144710	44144965	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44144966	44145051	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44145052	44145230	0.9	-	2	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44145052	44145230	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44145231	44145340	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44145341	44145517	0.97	-	2	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44145341	44145517	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44145518	44145614	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44145615	44146269	0.69	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44145615	44146269	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	intron	44146270	44146360	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	CDS	44146361	44146774	0.41	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	exon	44146361	44146774	.	-	.	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
Phchi.S1	AUGUSTUS	start_codon	44146772	44146774	.	-	0	transcript_id "Phchi.S1G702600.t1"; gene_id "Phchi.S1G702600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14709.t1 is derived from g13177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14323598	14325199	.	-	.	Phchi.S3G202800
Phchi.S3	AUGUSTUS	transcript	14323598	14325199	.	-	.	transcript_id "Phchi.S3G202800.t1"; gene_id "Phchi.S3G202800"
Phchi.S3	AUGUSTUS	stop_codon	14323595	14323597	.	-	0	transcript_id "Phchi.S3G202800.t1"; gene_id "Phchi.S3G202800"
Phchi.S3	AUGUSTUS	CDS	14323598	14325199	0.75	-	0	transcript_id "Phchi.S3G202800.t1"; gene_id "Phchi.S3G202800"
Phchi.S3	AUGUSTUS	exon	14323598	14325199	.	-	.	transcript_id "Phchi.S3G202800.t1"; gene_id "Phchi.S3G202800"
Phchi.S3	AUGUSTUS	start_codon	14325197	14325199	.	-	0	transcript_id "Phchi.S3G202800.t1"; gene_id "Phchi.S3G202800"
# This transcript jg10360.t2 is derived from g7536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10361.t1 is derived from g7537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47346724	47351153	.	+	.	Phchi.S1G752000
Phchi.S1	AUGUSTUS	transcript	47346724	47351153	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	start_codon	47346724	47346726	.	+	0	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	CDS	47346724	47350374	1	+	0	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	exon	47346724	47350374	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	intron	47350375	47350473	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	CDS	47350474	47350696	0.99	+	0	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	exon	47350474	47350696	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	intron	47350697	47350810	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	CDS	47350811	47350920	0.81	+	2	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	exon	47350811	47350920	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	intron	47350921	47351051	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	CDS	47351052	47351153	0.77	+	0	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	exon	47351052	47351153	.	+	.	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
Phchi.S1	AUGUSTUS	stop_codon	47351154	47351156	.	+	0	transcript_id "Phchi.S1G752000.t1"; gene_id "Phchi.S1G752000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg720.t1 is derived from g10502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5123786	5124343	.	-	.	Phchi.S6G067900
Phchi.S6	AUGUSTUS	transcript	5123786	5124343	.	-	.	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	stop_codon	5123783	5123785	.	-	0	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	CDS	5123786	5123864	0.84	-	1	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	exon	5123786	5123864	.	-	.	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	intron	5123865	5124056	.	-	.	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	CDS	5124057	5124343	0.68	-	0	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	exon	5124057	5124343	.	-	.	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
Phchi.S6	AUGUSTUS	start_codon	5124341	5124343	.	-	0	transcript_id "Phchi.S6G067900.t1"; gene_id "Phchi.S6G067900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5531.t1 is derived from g2701.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17431283	17432702	.	+	.	Phchi.S1G269000
Phchi.S1	AUGUSTUS	transcript	17431283	17432702	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	start_codon	17431283	17431285	.	+	0	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431283	17431353	0.86	+	0	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431283	17431353	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17431354	17431432	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431433	17431536	1	+	1	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431433	17431536	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17431537	17431670	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431671	17431819	0.65	+	2	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431671	17431819	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17431820	17431924	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431925	17432048	0.71	+	0	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431925	17432048	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432049	17432144	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432145	17432239	1	+	2	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432145	17432239	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432240	17432333	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432334	17432406	0.42	+	0	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432334	17432406	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432407	17432520	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432521	17432602	0.77	+	2	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432521	17432602	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432603	17432698	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432699	17432702	0.73	+	1	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432699	17432702	.	+	.	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	stop_codon	17432703	17432705	.	+	0	transcript_id "Phchi.S1G269000.t1"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	transcript	17431283	17432702	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	start_codon	17431283	17431285	.	+	0	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431283	17431353	0.78	+	0	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431283	17431353	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17431354	17431432	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431433	17431536	1	+	1	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431433	17431536	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17431537	17431670	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431671	17431819	0.53	+	2	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431671	17431819	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17431820	17431924	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17431925	17432048	0.6	+	0	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17431925	17432048	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432049	17432144	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432145	17432239	1	+	2	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432145	17432239	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432240	17432333	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432334	17432406	0.35	+	0	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432334	17432406	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432407	17432520	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432521	17432602	0.65	+	2	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432521	17432602	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	intron	17432603	17432695	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	CDS	17432696	17432702	0.65	+	1	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	exon	17432696	17432702	.	+	.	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
Phchi.S1	AUGUSTUS	stop_codon	17432703	17432705	.	+	0	transcript_id "Phchi.S1G269000.t2"; gene_id "Phchi.S1G269000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9032.t1 is derived from g6207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39223677	39227042	.	+	.	Phchi.S1G619100
Phchi.S1	AUGUSTUS	transcript	39223677	39227042	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	start_codon	39223677	39223679	.	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39223677	39224034	0.99	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39223677	39224034	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39224035	39224319	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39224320	39224639	1	+	2	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39224320	39224639	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39224640	39224761	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39224762	39225241	1	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39224762	39225241	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39225242	39225330	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39225331	39225466	1	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39225331	39225466	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39225467	39225611	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39225612	39225787	1	+	2	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39225612	39225787	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39225788	39226189	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39226190	39226304	0.89	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39226190	39226304	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39226305	39226421	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39226422	39226519	0.42	+	2	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39226422	39226519	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39226520	39226710	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39226711	39226782	0.39	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39226711	39226782	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	intron	39226783	39226967	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	CDS	39226968	39227042	0.41	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	exon	39226968	39227042	.	+	.	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
Phchi.S1	AUGUSTUS	stop_codon	39227043	39227045	.	+	0	transcript_id "Phchi.S1G619100.t1"; gene_id "Phchi.S1G619100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7656.t1 is derived from g4830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30439146	30449885	.	+	.	Phchi.S1G481500
Phchi.S1	AUGUSTUS	transcript	30439146	30449885	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	start_codon	30439146	30439148	.	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30439146	30439496	0.64	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30439146	30439496	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30439497	30439619	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30439620	30439826	0.98	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30439620	30439826	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30439827	30440027	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440028	30440189	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440028	30440189	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440190	30440315	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440316	30440408	0.99	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440316	30440408	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440409	30440517	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440518	30440613	0.99	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440518	30440613	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440614	30440743	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440744	30440917	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440744	30440917	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440918	30441009	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441010	30441103	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441010	30441103	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441104	30441197	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441198	30441385	0.79	+	2	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441198	30441385	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441386	30441508	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441509	30441559	0.67	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441509	30441559	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441560	30441672	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441673	30441712	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441673	30441712	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441713	30441821	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441822	30441946	0.82	+	2	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441822	30441946	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441947	30442034	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442035	30442058	0.22	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442035	30442058	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442059	30442301	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442302	30442376	0.97	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442302	30442376	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442377	30442465	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442466	30442522	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442466	30442522	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442523	30442604	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442605	30442632	0.97	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442605	30442632	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442633	30442703	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442704	30442708	0.98	+	2	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442704	30442708	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442709	30442863	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442864	30442950	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442864	30442950	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442951	30443046	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443047	30443238	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443047	30443238	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30443239	30443426	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443427	30443615	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443427	30443615	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30443616	30443761	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443762	30443872	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443762	30443872	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30443873	30443968	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443969	30444061	0.79	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443969	30444061	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444062	30444172	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444173	30444343	0.99	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444173	30444343	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444344	30444534	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444535	30444612	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444535	30444612	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444613	30444698	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444699	30444821	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444699	30444821	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444822	30444981	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444982	30445248	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444982	30445248	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30445249	30445442	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30445443	30445780	0.88	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30445443	30445780	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30445781	30445892	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30445893	30446130	0.96	+	1	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30445893	30446130	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30446131	30446260	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30446261	30446595	0.97	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30446261	30446595	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30446596	30446723	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30446724	30446940	0.9	+	1	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30446724	30446940	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30446941	30447081	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30447082	30447264	0.92	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30447082	30447264	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30447265	30447380	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30447381	30447895	1	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30447381	30447895	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30447896	30447972	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30447973	30448057	0.97	+	1	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30447973	30448057	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30448058	30448163	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30448164	30448467	0.93	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30448164	30448467	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30448468	30448589	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30448590	30449564	0.56	+	2	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30448590	30449564	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30449565	30449669	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30449670	30449790	0.67	+	2	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30449670	30449790	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30449791	30449872	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30449873	30449885	0.87	+	1	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30449873	30449885	.	+	.	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	stop_codon	30449886	30449888	.	+	0	transcript_id "Phchi.S1G481500.t1"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	transcript	30439146	30449885	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	start_codon	30439146	30439148	.	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30439146	30439496	0.64	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30439146	30439496	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30439497	30439619	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30439620	30439826	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30439620	30439826	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30439827	30440027	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440028	30440189	0.99	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440028	30440189	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440190	30440315	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440316	30440408	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440316	30440408	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440409	30440517	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440518	30440613	0.97	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440518	30440613	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440614	30440743	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30440744	30440917	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30440744	30440917	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30440918	30441009	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441010	30441103	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441010	30441103	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441104	30441197	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441198	30441385	0.83	+	2	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441198	30441385	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441386	30441508	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441509	30441559	0.58	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441509	30441559	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441560	30441672	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441673	30441712	0.96	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441673	30441712	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441713	30441821	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30441822	30441946	0.76	+	2	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30441822	30441946	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30441947	30442034	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442035	30442058	0.23	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442035	30442058	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442059	30442301	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442302	30442376	0.91	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442302	30442376	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442377	30442465	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442466	30442522	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442466	30442522	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442523	30442604	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442605	30442632	0.94	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442605	30442632	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442633	30442703	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442704	30442708	0.95	+	2	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442704	30442708	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442709	30442863	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30442864	30442950	0.98	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30442864	30442950	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30442951	30443046	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443047	30443238	0.99	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443047	30443238	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30443239	30443426	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443427	30443615	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443427	30443615	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30443616	30443761	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443762	30443872	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443762	30443872	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30443873	30443968	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30443969	30444061	0.75	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30443969	30444061	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444062	30444172	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444173	30444343	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444173	30444343	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444344	30444534	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444535	30444612	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444535	30444612	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444613	30444698	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444699	30444821	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444699	30444821	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30444822	30444981	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30444982	30445248	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30444982	30445248	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30445249	30445442	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30445443	30445780	0.88	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30445443	30445780	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30445781	30445892	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30445893	30446130	0.93	+	1	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30445893	30446130	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30446131	30446260	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30446261	30446595	0.88	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30446261	30446595	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30446596	30446720	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30446721	30446940	0.64	+	1	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30446721	30446940	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30446941	30447081	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30447082	30447264	0.92	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30447082	30447264	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30447265	30447380	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30447381	30447895	1	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30447381	30447895	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30447896	30447972	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30447973	30448057	0.86	+	1	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30447973	30448057	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30448058	30448163	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30448164	30448467	0.81	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30448164	30448467	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30448468	30448589	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30448590	30449564	0.48	+	2	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30448590	30449564	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30449565	30449669	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30449670	30449790	0.61	+	2	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30449670	30449790	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	intron	30449791	30449872	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	CDS	30449873	30449885	0.86	+	1	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	exon	30449873	30449885	.	+	.	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
Phchi.S1	AUGUSTUS	stop_codon	30449886	30449888	.	+	0	transcript_id "Phchi.S1G481500.t2"; gene_id "Phchi.S1G481500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4313.t1 is derived from g1482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9582703	9583410	.	+	.	Phchi.S1G147200
Phchi.S1	AUGUSTUS	transcript	9582703	9583410	.	+	.	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	start_codon	9582703	9582705	.	+	0	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	CDS	9582703	9583281	0.82	+	0	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	exon	9582703	9583281	.	+	.	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	intron	9583282	9583377	.	+	.	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	CDS	9583378	9583410	0.84	+	0	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	exon	9583378	9583410	.	+	.	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
Phchi.S1	AUGUSTUS	stop_codon	9583411	9583413	.	+	0	transcript_id "Phchi.S1G147200.t1"; gene_id "Phchi.S1G147200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12919.t1 is derived from g11384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3166877	3167319	.	+	.	Phchi.S3G023800
Phchi.S3	AUGUSTUS	transcript	3166877	3167319	.	+	.	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	start_codon	3166877	3166879	.	+	0	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	CDS	3166877	3167011	0.98	+	0	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	exon	3166877	3167011	.	+	.	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	intron	3167012	3167190	.	+	.	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	CDS	3167191	3167319	0.46	+	0	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	exon	3167191	3167319	.	+	.	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
Phchi.S3	AUGUSTUS	stop_codon	3167320	3167322	.	+	0	transcript_id "Phchi.S3G023800.t1"; gene_id "Phchi.S3G023800"
# This transcript jg11435.t2 is derived from g15485.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11435.t3 is derived from g15485.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11436.t1 is derived from g15486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6370215	6372247	.	+	.	Phchi.S4G101800
Phchi.S4	AUGUSTUS	transcript	6370215	6372247	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	start_codon	6370215	6370217	.	+	0	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6370215	6370448	0.61	+	0	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6370215	6370448	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6370449	6370566	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6370567	6370760	1	+	0	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6370567	6370760	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6370761	6370964	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6370965	6371159	1	+	1	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6370965	6371159	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6371160	6371259	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6371260	6371321	1	+	1	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6371260	6371321	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6371322	6371408	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6371409	6371475	1	+	2	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6371409	6371475	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6371476	6371563	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6371564	6371682	1	+	1	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6371564	6371682	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6371683	6371806	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6371807	6371983	1	+	2	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6371807	6371983	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	intron	6371984	6372164	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	CDS	6372165	6372247	1	+	2	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	exon	6372165	6372247	.	+	.	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
Phchi.S4	AUGUSTUS	stop_codon	6372248	6372250	.	+	0	transcript_id "Phchi.S4G101800.t1"; gene_id "Phchi.S4G101800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7507.t1 is derived from g4681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29734266	29735558	.	+	.	Phchi.S1G466600
Phchi.S1	AUGUSTUS	transcript	29734266	29735558	.	+	.	transcript_id "Phchi.S1G466600.t1"; gene_id "Phchi.S1G466600"
Phchi.S1	AUGUSTUS	start_codon	29734266	29734268	.	+	0	transcript_id "Phchi.S1G466600.t1"; gene_id "Phchi.S1G466600"
Phchi.S1	AUGUSTUS	CDS	29734266	29735558	0.86	+	0	transcript_id "Phchi.S1G466600.t1"; gene_id "Phchi.S1G466600"
Phchi.S1	AUGUSTUS	exon	29734266	29735558	.	+	.	transcript_id "Phchi.S1G466600.t1"; gene_id "Phchi.S1G466600"
Phchi.S1	AUGUSTUS	stop_codon	29735559	29735561	.	+	0	transcript_id "Phchi.S1G466600.t1"; gene_id "Phchi.S1G466600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9655.t1 is derived from g6831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43089901	43094273	.	-	.	Phchi.S1G681400
Phchi.S1	AUGUSTUS	transcript	43089901	43094273	.	-	.	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	stop_codon	43089898	43089900	.	-	0	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	CDS	43089901	43091040	0.95	-	0	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	exon	43089901	43091040	.	-	.	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	intron	43091041	43091159	.	-	.	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	CDS	43091160	43092613	1	-	2	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	exon	43091160	43092613	.	-	.	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	intron	43092614	43092721	.	-	.	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	CDS	43092722	43094273	0.61	-	0	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	exon	43092722	43094273	.	-	.	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
Phchi.S1	AUGUSTUS	start_codon	43094271	43094273	.	-	0	transcript_id "Phchi.S1G681400.t1"; gene_id "Phchi.S1G681400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12790.t1 is derived from g11255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2385128	2385884	.	+	.	Phchi.S3G010900
Phchi.S3	AUGUSTUS	transcript	2385128	2385884	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	start_codon	2385128	2385130	.	+	0	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	CDS	2385128	2385152	1	+	0	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	exon	2385128	2385152	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	intron	2385153	2385240	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	CDS	2385241	2385444	0.99	+	2	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	exon	2385241	2385444	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	intron	2385445	2385567	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	CDS	2385568	2385713	0.81	+	2	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	exon	2385568	2385713	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	intron	2385714	2385812	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	CDS	2385813	2385884	0.81	+	0	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	exon	2385813	2385884	.	+	.	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
Phchi.S3	AUGUSTUS	stop_codon	2385885	2385887	.	+	0	transcript_id "Phchi.S3G010900.t1"; gene_id "Phchi.S3G010900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4378.t1 is derived from g1547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10141474	10144176	.	+	.	Phchi.S1G153700
Phchi.S1	AUGUSTUS	transcript	10141474	10144176	.	+	.	transcript_id "Phchi.S1G153700.t1"; gene_id "Phchi.S1G153700"
Phchi.S1	AUGUSTUS	start_codon	10141474	10141476	.	+	0	transcript_id "Phchi.S1G153700.t1"; gene_id "Phchi.S1G153700"
Phchi.S1	AUGUSTUS	CDS	10141474	10144176	0.61	+	0	transcript_id "Phchi.S1G153700.t1"; gene_id "Phchi.S1G153700"
Phchi.S1	AUGUSTUS	exon	10141474	10144176	.	+	.	transcript_id "Phchi.S1G153700.t1"; gene_id "Phchi.S1G153700"
Phchi.S1	AUGUSTUS	stop_codon	10144177	10144179	.	+	0	transcript_id "Phchi.S1G153700.t1"; gene_id "Phchi.S1G153700"
# This transcript jg250.t2 is derived from g10032.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg251.t1 is derived from g10033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1713256	1714239	.	-	.	Phchi.S6G021000
Phchi.S6	AUGUSTUS	transcript	1713256	1714239	.	-	.	transcript_id "Phchi.S6G021000.t1"; gene_id "Phchi.S6G021000"
Phchi.S6	AUGUSTUS	stop_codon	1713253	1713255	.	-	0	transcript_id "Phchi.S6G021000.t1"; gene_id "Phchi.S6G021000"
Phchi.S6	AUGUSTUS	CDS	1713256	1714239	0.99	-	0	transcript_id "Phchi.S6G021000.t1"; gene_id "Phchi.S6G021000"
Phchi.S6	AUGUSTUS	exon	1713256	1714239	.	-	.	transcript_id "Phchi.S6G021000.t1"; gene_id "Phchi.S6G021000"
Phchi.S6	AUGUSTUS	start_codon	1714237	1714239	.	-	0	transcript_id "Phchi.S6G021000.t1"; gene_id "Phchi.S6G021000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15597.t1 is derived from g14066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20194035	20195942	.	-	.	Phchi.S3G291600
Phchi.S3	AUGUSTUS	transcript	20194035	20195942	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	stop_codon	20194032	20194034	.	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20194035	20194133	1	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20194035	20194133	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	intron	20194134	20194216	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20194217	20194303	1	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20194217	20194303	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	intron	20194304	20194386	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20194387	20194497	1	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20194387	20194497	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	intron	20194498	20194612	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20194613	20194894	1	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20194613	20194894	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	intron	20194895	20194977	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20194978	20195058	1	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20194978	20195058	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	intron	20195059	20195144	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20195145	20195420	1	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20195145	20195420	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	intron	20195421	20195660	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	CDS	20195661	20195942	0.9	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	exon	20195661	20195942	.	-	.	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
Phchi.S3	AUGUSTUS	start_codon	20195940	20195942	.	-	0	transcript_id "Phchi.S3G291600.t1"; gene_id "Phchi.S3G291600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1437.t1 is derived from g8356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	846250	848422	.	+	.	Phchi.S5G004600
Phchi.S5	AUGUSTUS	transcript	846250	848422	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	start_codon	846250	846252	.	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	846250	846537	0.93	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	846250	846537	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	intron	846538	846620	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	846621	846836	1	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	846621	846836	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	intron	846837	846925	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	846926	847237	1	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	846926	847237	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	intron	847238	847323	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	847324	847588	1	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	847324	847588	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	intron	847589	847714	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	847715	847866	1	+	2	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	847715	847866	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	intron	847867	847955	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	847956	848156	1	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	847956	848156	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	intron	848157	848242	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	CDS	848243	848422	1	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	exon	848243	848422	.	+	.	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
Phchi.S5	AUGUSTUS	stop_codon	848423	848425	.	+	0	transcript_id "Phchi.S5G004600.t1"; gene_id "Phchi.S5G004600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4746.t1 is derived from g1916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12606944	12607708	.	-	.	Phchi.S1G190500
Phchi.S1	AUGUSTUS	transcript	12606944	12607708	.	-	.	transcript_id "Phchi.S1G190500.t1"; gene_id "Phchi.S1G190500"
Phchi.S1	AUGUSTUS	stop_codon	12606941	12606943	.	-	0	transcript_id "Phchi.S1G190500.t1"; gene_id "Phchi.S1G190500"
Phchi.S1	AUGUSTUS	CDS	12606944	12607708	0.55	-	0	transcript_id "Phchi.S1G190500.t1"; gene_id "Phchi.S1G190500"
Phchi.S1	AUGUSTUS	exon	12606944	12607708	.	-	.	transcript_id "Phchi.S1G190500.t1"; gene_id "Phchi.S1G190500"
Phchi.S1	AUGUSTUS	start_codon	12607706	12607708	.	-	0	transcript_id "Phchi.S1G190500.t1"; gene_id "Phchi.S1G190500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2617.t1 is derived from g9537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7796511	7798139	.	+	.	Phchi.S5G122600
Phchi.S5	AUGUSTUS	transcript	7796511	7798139	.	+	.	transcript_id "Phchi.S5G122600.t1"; gene_id "Phchi.S5G122600"
Phchi.S5	AUGUSTUS	start_codon	7796511	7796513	.	+	0	transcript_id "Phchi.S5G122600.t1"; gene_id "Phchi.S5G122600"
Phchi.S5	AUGUSTUS	CDS	7796511	7798139	1	+	0	transcript_id "Phchi.S5G122600.t1"; gene_id "Phchi.S5G122600"
Phchi.S5	AUGUSTUS	exon	7796511	7798139	.	+	.	transcript_id "Phchi.S5G122600.t1"; gene_id "Phchi.S5G122600"
Phchi.S5	AUGUSTUS	stop_codon	7798140	7798142	.	+	0	transcript_id "Phchi.S5G122600.t1"; gene_id "Phchi.S5G122600"
# This transcript jg10059.t2 is derived from g7235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10060.t1 is derived from g7236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45575373	45576525	.	+	.	Phchi.S1G721900
Phchi.S1	AUGUSTUS	transcript	45575373	45576525	.	+	.	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	start_codon	45575373	45575375	.	+	0	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	CDS	45575373	45575453	0.7	+	0	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	exon	45575373	45575453	.	+	.	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	intron	45575454	45575603	.	+	.	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	CDS	45575604	45575845	0.67	+	0	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	exon	45575604	45575845	.	+	.	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	intron	45575846	45576002	.	+	.	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	CDS	45576003	45576525	0.96	+	1	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	exon	45576003	45576525	.	+	.	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
Phchi.S1	AUGUSTUS	stop_codon	45576526	45576528	.	+	0	transcript_id "Phchi.S1G721900.t1"; gene_id "Phchi.S1G721900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12070.t1 is derived from g7745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2003204	2008239	.	+	.	Phchi.S2G015000
Phchi.S2	AUGUSTUS	transcript	2003204	2008239	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	start_codon	2003204	2003206	.	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2003204	2003257	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2003204	2003257	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2003258	2003349	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2003350	2003443	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2003350	2003443	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2003444	2003522	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2003523	2003885	0.99	+	2	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2003523	2003885	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2003886	2004065	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2004066	2004526	1	+	2	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2004066	2004526	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2004527	2004658	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2004659	2004817	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2004659	2004817	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2004818	2004941	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2004942	2005058	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2004942	2005058	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2005059	2005270	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2005271	2005422	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2005271	2005422	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2005423	2005589	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2005590	2005681	1	+	1	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2005590	2005681	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2005682	2005784	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2005785	2006015	0.71	+	2	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2005785	2006015	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2006016	2006105	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2006106	2006216	0.84	+	2	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2006106	2006216	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2006217	2006350	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2006351	2007062	0.63	+	2	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2006351	2007062	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2007063	2007182	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2007183	2007267	1	+	1	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2007183	2007267	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2007268	2007410	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2007411	2007479	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2007411	2007479	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2007480	2007742	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2007743	2007922	1	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2007743	2007922	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	intron	2007923	2008065	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	CDS	2008066	2008239	0.96	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	exon	2008066	2008239	.	+	.	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
Phchi.S2	AUGUSTUS	stop_codon	2008240	2008242	.	+	0	transcript_id "Phchi.S2G015000.t1"; gene_id "Phchi.S2G015000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5077.t1 is derived from g2247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14569121	14571377	.	+	.	Phchi.S1G223600
Phchi.S1	AUGUSTUS	transcript	14569121	14571377	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	start_codon	14569121	14569123	.	+	0	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	CDS	14569121	14569626	0.31	+	0	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	exon	14569121	14569626	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	intron	14569627	14569708	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	CDS	14569709	14570277	0.61	+	1	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	exon	14569709	14570277	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	intron	14570278	14570412	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	CDS	14570413	14570651	0.36	+	2	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	exon	14570413	14570651	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	intron	14570652	14570765	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	CDS	14570766	14570894	0.57	+	0	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	exon	14570766	14570894	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	intron	14570895	14571116	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	CDS	14571117	14571191	0.84	+	0	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	exon	14571117	14571191	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	intron	14571192	14571326	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	CDS	14571327	14571377	1	+	0	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	exon	14571327	14571377	.	+	.	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
Phchi.S1	AUGUSTUS	stop_codon	14571378	14571380	.	+	0	transcript_id "Phchi.S1G223600.t1"; gene_id "Phchi.S1G223600"
# This transcript jg1080.t2 is derived from g10863.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1081.t1 is derived from g10864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7505695	7508931	.	+	.	Phchi.S6G104000
Phchi.S6	AUGUSTUS	transcript	7505695	7508931	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	start_codon	7505695	7505697	.	+	0	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	CDS	7505695	7505828	0.47	+	0	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	exon	7505695	7505828	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	intron	7505829	7505883	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	CDS	7505884	7505984	0.86	+	1	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	exon	7505884	7505984	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	intron	7505985	7506139	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	CDS	7506140	7506291	1	+	2	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	exon	7506140	7506291	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	intron	7506292	7506456	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	CDS	7506457	7506531	1	+	0	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	exon	7506457	7506531	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	intron	7506532	7506671	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	CDS	7506672	7506743	1	+	0	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	exon	7506672	7506743	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	intron	7506744	7506954	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	CDS	7506955	7508931	1	+	0	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	exon	7506955	7508931	.	+	.	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
Phchi.S6	AUGUSTUS	stop_codon	7508932	7508934	.	+	0	transcript_id "Phchi.S6G104000.t1"; gene_id "Phchi.S6G104000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3989.t1 is derived from g1158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6883895	6885270	.	-	.	Phchi.S1G114800
Phchi.S1	AUGUSTUS	transcript	6883895	6885270	.	-	.	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	stop_codon	6883892	6883894	.	-	0	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	CDS	6883895	6884406	1	-	2	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	exon	6883895	6884406	.	-	.	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	intron	6884407	6884546	.	-	.	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	CDS	6884547	6885270	0.59	-	0	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	exon	6884547	6885270	.	-	.	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
Phchi.S1	AUGUSTUS	start_codon	6885268	6885270	.	-	0	transcript_id "Phchi.S1G114800.t1"; gene_id "Phchi.S1G114800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13180.t1 is derived from g11645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4553193	4555227	.	-	.	Phchi.S3G049900
Phchi.S3	AUGUSTUS	transcript	4553193	4555227	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	stop_codon	4553190	4553192	.	-	0	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4553193	4553259	1	-	1	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4553193	4553259	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4553260	4553336	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4553337	4553416	1	-	0	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4553337	4553416	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4553417	4553548	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4553549	4553594	1	-	1	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4553549	4553594	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4553595	4553689	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4553690	4553746	1	-	1	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4553690	4553746	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4553747	4553839	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4553840	4553898	1	-	0	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4553840	4553898	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4553899	4553977	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4553978	4554078	0.87	-	2	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4553978	4554078	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4554079	4554171	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4554172	4554293	0.91	-	1	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4554172	4554293	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4554294	4554509	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4554510	4554561	1	-	2	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4554510	4554561	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4554562	4554643	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4554644	4554739	1	-	2	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4554644	4554739	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4554740	4554816	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4554817	4555012	1	-	0	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4554817	4555012	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	intron	4555013	4555137	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	CDS	4555138	4555227	0.99	-	0	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	exon	4555138	4555227	.	-	.	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
Phchi.S3	AUGUSTUS	start_codon	4555225	4555227	.	-	0	transcript_id "Phchi.S3G049900.t1"; gene_id "Phchi.S3G049900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9879.t1 is derived from g7055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44215397	44215864	.	-	.	Phchi.S1G703800
Phchi.S1	AUGUSTUS	transcript	44215397	44215864	.	-	.	transcript_id "Phchi.S1G703800.t1"; gene_id "Phchi.S1G703800"
Phchi.S1	AUGUSTUS	stop_codon	44215394	44215396	.	-	0	transcript_id "Phchi.S1G703800.t1"; gene_id "Phchi.S1G703800"
Phchi.S1	AUGUSTUS	CDS	44215397	44215864	0.05	-	0	transcript_id "Phchi.S1G703800.t1"; gene_id "Phchi.S1G703800"
Phchi.S1	AUGUSTUS	exon	44215397	44215864	.	-	.	transcript_id "Phchi.S1G703800.t1"; gene_id "Phchi.S1G703800"
Phchi.S1	AUGUSTUS	start_codon	44215862	44215864	.	-	0	transcript_id "Phchi.S1G703800.t1"; gene_id "Phchi.S1G703800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9591.t1 is derived from g6767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42816898	42818092	.	-	.	Phchi.S1G675000
Phchi.S1	AUGUSTUS	transcript	42816898	42818092	.	-	.	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	stop_codon	42816895	42816897	.	-	0	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	CDS	42816898	42817028	0.56	-	2	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	exon	42816898	42817028	.	-	.	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	intron	42817029	42817218	.	-	.	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	CDS	42817219	42818092	0.29	-	0	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	exon	42817219	42818092	.	-	.	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
Phchi.S1	AUGUSTUS	start_codon	42818090	42818092	.	-	0	transcript_id "Phchi.S1G675000.t1"; gene_id "Phchi.S1G675000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg195.t1 is derived from g9977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1092460	1094278	.	-	.	Phchi.S6G015400
Phchi.S6	AUGUSTUS	transcript	1092460	1094278	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	stop_codon	1092457	1092459	.	-	0	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1092460	1092482	0.97	-	2	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1092460	1092482	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	intron	1092483	1092708	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1092709	1092803	0.98	-	1	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1092709	1092803	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	intron	1092804	1092967	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1092968	1093180	1	-	1	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1092968	1093180	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	intron	1093181	1093280	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1093281	1093381	1	-	0	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1093281	1093381	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	intron	1093382	1093464	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1093465	1093688	1	-	2	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1093465	1093688	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	intron	1093689	1093781	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1093782	1093850	1	-	2	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1093782	1093850	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	intron	1093851	1094019	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	CDS	1094020	1094278	0.97	-	0	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	exon	1094020	1094278	.	-	.	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
Phchi.S6	AUGUSTUS	start_codon	1094276	1094278	.	-	0	transcript_id "Phchi.S6G015400.t1"; gene_id "Phchi.S6G015400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1208.t1 is derived from g10991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8416775	8419570	.	+	.	Phchi.S6G116700
Phchi.S6	AUGUSTUS	transcript	8416775	8419570	.	+	.	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	start_codon	8416775	8416777	.	+	0	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	CDS	8416775	8417692	0.98	+	0	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	exon	8416775	8417692	.	+	.	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	intron	8417693	8418091	.	+	.	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	CDS	8418092	8419570	0.42	+	0	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	exon	8418092	8419570	.	+	.	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
Phchi.S6	AUGUSTUS	stop_codon	8419571	8419573	.	+	0	transcript_id "Phchi.S6G116700.t1"; gene_id "Phchi.S6G116700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2742.t1 is derived from g9662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8523869	8524456	.	-	.	Phchi.S5G135100
Phchi.S5	AUGUSTUS	transcript	8523869	8524456	.	-	.	transcript_id "Phchi.S5G135100.t1"; gene_id "Phchi.S5G135100"
Phchi.S5	AUGUSTUS	stop_codon	8523866	8523868	.	-	0	transcript_id "Phchi.S5G135100.t1"; gene_id "Phchi.S5G135100"
Phchi.S5	AUGUSTUS	CDS	8523869	8524456	0.81	-	0	transcript_id "Phchi.S5G135100.t1"; gene_id "Phchi.S5G135100"
Phchi.S5	AUGUSTUS	exon	8523869	8524456	.	-	.	transcript_id "Phchi.S5G135100.t1"; gene_id "Phchi.S5G135100"
Phchi.S5	AUGUSTUS	start_codon	8524454	8524456	.	-	0	transcript_id "Phchi.S5G135100.t1"; gene_id "Phchi.S5G135100"
# This transcript jg10493.t1 is derived from g14542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	685581	685997	.	+	.	Phchi.S4G007500
Phchi.S4	AUGUSTUS	transcript	685581	685997	.	+	.	transcript_id "Phchi.S4G007500.t1"; gene_id "Phchi.S4G007500"
Phchi.S4	AUGUSTUS	start_codon	685581	685583	.	+	0	transcript_id "Phchi.S4G007500.t1"; gene_id "Phchi.S4G007500"
Phchi.S4	AUGUSTUS	CDS	685581	685997	0.93	+	0	transcript_id "Phchi.S4G007500.t1"; gene_id "Phchi.S4G007500"
Phchi.S4	AUGUSTUS	exon	685581	685997	.	+	.	transcript_id "Phchi.S4G007500.t1"; gene_id "Phchi.S4G007500"
Phchi.S4	AUGUSTUS	stop_codon	685998	686000	.	+	0	transcript_id "Phchi.S4G007500.t1"; gene_id "Phchi.S4G007500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5171.t1 is derived from g2341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15302285	15305417	.	+	.	Phchi.S1G233000
Phchi.S1	AUGUSTUS	transcript	15302285	15305417	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	start_codon	15302285	15302287	.	+	0	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	CDS	15302285	15303822	0.65	+	0	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	exon	15302285	15303822	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	intron	15303823	15303941	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	CDS	15303942	15304167	0.56	+	1	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	exon	15303942	15304167	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	intron	15304168	15304270	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	CDS	15304271	15304514	0.48	+	0	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	exon	15304271	15304514	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	intron	15304515	15304605	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	CDS	15304606	15305417	1	+	2	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	exon	15304606	15305417	.	+	.	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
Phchi.S1	AUGUSTUS	stop_codon	15305418	15305420	.	+	0	transcript_id "Phchi.S1G233000.t1"; gene_id "Phchi.S1G233000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9659.t1 is derived from g6835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43113067	43115915	.	-	.	Phchi.S1G681800
Phchi.S1	AUGUSTUS	transcript	43113067	43115915	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	stop_codon	43113064	43113066	.	-	0	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	CDS	43113067	43115294	0.58	-	2	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	exon	43113067	43115294	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	intron	43115295	43115453	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	CDS	43115454	43115545	0.93	-	1	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	exon	43115454	43115545	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	intron	43115546	43115697	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	CDS	43115698	43115725	0.98	-	2	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	exon	43115698	43115725	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	intron	43115726	43115815	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	CDS	43115816	43115915	0.61	-	0	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	exon	43115816	43115915	.	-	.	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
Phchi.S1	AUGUSTUS	start_codon	43115913	43115915	.	-	0	transcript_id "Phchi.S1G681800.t1"; gene_id "Phchi.S1G681800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6646.t1 is derived from g3818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24260716	24263853	.	+	.	Phchi.S1G380500
Phchi.S1	AUGUSTUS	transcript	24260716	24263853	.	+	.	transcript_id "Phchi.S1G380500.t1"; gene_id "Phchi.S1G380500"
Phchi.S1	AUGUSTUS	start_codon	24260716	24260718	.	+	0	transcript_id "Phchi.S1G380500.t1"; gene_id "Phchi.S1G380500"
Phchi.S1	AUGUSTUS	CDS	24260716	24263853	1	+	0	transcript_id "Phchi.S1G380500.t1"; gene_id "Phchi.S1G380500"
Phchi.S1	AUGUSTUS	exon	24260716	24263853	.	+	.	transcript_id "Phchi.S1G380500.t1"; gene_id "Phchi.S1G380500"
Phchi.S1	AUGUSTUS	stop_codon	24263854	24263856	.	+	0	transcript_id "Phchi.S1G380500.t1"; gene_id "Phchi.S1G380500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12527.t1 is derived from g8204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32988587	32996152	.	+	.	Phchi.S2G060700
Phchi.S2	AUGUSTUS	transcript	32988587	32996152	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	start_codon	32988587	32988589	.	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32988587	32988676	0.98	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32988587	32988676	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32988677	32988766	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32988767	32988964	1	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32988767	32988964	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32988965	32989102	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32989103	32989250	1	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32989103	32989250	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32989251	32989511	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32989512	32989524	0.95	+	2	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32989512	32989524	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32989525	32989662	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32989663	32989732	0.92	+	1	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32989663	32989732	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32989733	32989855	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32989856	32992292	0.68	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32989856	32992292	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32992293	32992369	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32992370	32995788	0.72	+	2	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32992370	32995788	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32995789	32995933	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32995934	32996008	1	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32995934	32996008	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	intron	32996009	32996089	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	CDS	32996090	32996152	1	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	exon	32996090	32996152	.	+	.	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
Phchi.S2	AUGUSTUS	stop_codon	32996153	32996155	.	+	0	transcript_id "Phchi.S2G060700.t1"; gene_id "Phchi.S2G060700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6465.t1 is derived from g3637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23131925	23133906	.	-	.	Phchi.S1G362400
Phchi.S1	AUGUSTUS	transcript	23131925	23133906	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	stop_codon	23131922	23131924	.	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	CDS	23131925	23132227	1	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	exon	23131925	23132227	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	intron	23132228	23132343	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	CDS	23132344	23132496	1	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	exon	23132344	23132496	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	intron	23132497	23132677	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	CDS	23132678	23132770	1	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	exon	23132678	23132770	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	intron	23132771	23132862	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	CDS	23132863	23132968	0.98	-	1	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	exon	23132863	23132968	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	intron	23132969	23133104	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	CDS	23133105	23133355	0.96	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	exon	23133105	23133355	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	intron	23133356	23133450	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	CDS	23133451	23133906	0.8	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	exon	23133451	23133906	.	-	.	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
Phchi.S1	AUGUSTUS	start_codon	23133904	23133906	.	-	0	transcript_id "Phchi.S1G362400.t1"; gene_id "Phchi.S1G362400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1383.t1 is derived from g16016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	113	454	.	+	.	Phchi.C243G000100
Phchi.C243	AUGUSTUS	transcript	113	454	.	+	.	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
Phchi.C243	AUGUSTUS	CDS	113	262	0.4	+	1	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
Phchi.C243	AUGUSTUS	exon	113	262	.	+	.	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
Phchi.C243	AUGUSTUS	intron	263	435	.	+	.	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
Phchi.C243	AUGUSTUS	CDS	436	454	1	+	1	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
Phchi.C243	AUGUSTUS	exon	436	454	.	+	.	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
Phchi.C243	AUGUSTUS	stop_codon	455	457	.	+	0	transcript_id "Phchi.C243G000100.t1"; gene_id "Phchi.C243G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg912.t1 is derived from g10694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6407233	6409443	.	-	.	Phchi.S6G087100
Phchi.S6	AUGUSTUS	transcript	6407233	6409443	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	stop_codon	6407230	6407232	.	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6407233	6407243	1	-	2	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6407233	6407243	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6407244	6407318	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6407319	6407440	0.8	-	1	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6407319	6407440	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6407441	6407540	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6407541	6407625	0.8	-	2	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6407541	6407625	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6407626	6407718	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6407719	6407797	1	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6407719	6407797	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6407798	6407899	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6407900	6407995	0.98	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6407900	6407995	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6407996	6408102	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6408103	6408290	0.99	-	2	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6408103	6408290	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6408291	6408371	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6408372	6408435	1	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6408372	6408435	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6408436	6408546	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6408547	6408696	1	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6408547	6408696	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6408697	6408777	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6408778	6409096	1	-	1	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6408778	6409096	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	intron	6409097	6409177	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	CDS	6409178	6409443	1	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	exon	6409178	6409443	.	-	.	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
Phchi.S6	AUGUSTUS	start_codon	6409441	6409443	.	-	0	transcript_id "Phchi.S6G087100.t1"; gene_id "Phchi.S6G087100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1712.t1 is derived from g8632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2661803	2663011	.	-	.	Phchi.S5G032100
Phchi.S5	AUGUSTUS	transcript	2661803	2663011	.	-	.	transcript_id "Phchi.S5G032100.t1"; gene_id "Phchi.S5G032100"
Phchi.S5	AUGUSTUS	stop_codon	2661800	2661802	.	-	0	transcript_id "Phchi.S5G032100.t1"; gene_id "Phchi.S5G032100"
Phchi.S5	AUGUSTUS	CDS	2661803	2663011	0.94	-	0	transcript_id "Phchi.S5G032100.t1"; gene_id "Phchi.S5G032100"
Phchi.S5	AUGUSTUS	exon	2661803	2663011	.	-	.	transcript_id "Phchi.S5G032100.t1"; gene_id "Phchi.S5G032100"
Phchi.S5	AUGUSTUS	start_codon	2663009	2663011	.	-	0	transcript_id "Phchi.S5G032100.t1"; gene_id "Phchi.S5G032100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15697.t1 is derived from g14166.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20742064	20745420	.	-	.	Phchi.S3G301600
Phchi.S3	AUGUSTUS	transcript	20742209	20745420	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	stop_codon	20742206	20742208	.	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742209	20742496	0.8	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742209	20742496	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742497	20742574	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742575	20742643	1	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742575	20742643	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742644	20742729	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742730	20742797	1	-	2	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742730	20742797	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742798	20742889	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742890	20743010	1	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742890	20743010	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743011	20743136	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743137	20743259	1	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743137	20743259	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743260	20743390	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743391	20743585	1	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743391	20743585	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743586	20743674	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743675	20743803	1	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743675	20743803	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743804	20743909	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743910	20744081	1	-	1	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743910	20744081	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744082	20744252	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744253	20744382	1	-	2	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744253	20744382	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744383	20744456	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744457	20744621	0.98	-	2	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744457	20744621	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744622	20744816	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744817	20744978	0.98	-	2	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744817	20744978	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744979	20745068	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20745069	20745152	1	-	2	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20745069	20745152	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20745153	20745275	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20745276	20745420	0.62	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20745276	20745420	.	-	.	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	start_codon	20745418	20745420	.	-	0	transcript_id "Phchi.S3G301600.t1"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	transcript	20742209	20745420	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	stop_codon	20742206	20742208	.	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742209	20742496	0.75	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742209	20742496	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742497	20742574	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742575	20742643	1	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742575	20742643	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742644	20742729	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742730	20742797	1	-	2	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742730	20742797	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742798	20742889	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742890	20743010	1	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742890	20743010	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743011	20743136	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743137	20743259	1	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743137	20743259	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743260	20743390	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743391	20743585	1	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743391	20743585	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743586	20743674	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743675	20743803	1	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743675	20743803	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743804	20743909	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743910	20744081	0.99	-	1	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743910	20744081	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744082	20744252	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744253	20744382	1	-	2	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744253	20744382	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744383	20744456	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744457	20744621	0.98	-	2	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744457	20744621	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744622	20744828	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744829	20744978	0.98	-	2	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744829	20744978	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744979	20745068	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20745069	20745152	1	-	2	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20745069	20745152	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20745153	20745275	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20745276	20745420	0.67	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20745276	20745420	.	-	.	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	start_codon	20745418	20745420	.	-	0	transcript_id "Phchi.S3G301600.t2"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	transcript	20742064	20745420	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	stop_codon	20742061	20742063	.	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742064	20742129	0.76	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742064	20742129	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742130	20742320	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742321	20742496	0.76	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742321	20742496	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742497	20742574	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742575	20742643	0.78	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742575	20742643	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742644	20742719	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742720	20742797	0.76	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742720	20742797	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20742798	20742889	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20742890	20743010	0.87	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20742890	20743010	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743011	20743136	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743137	20743259	1	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743137	20743259	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743260	20743390	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743391	20743585	1	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743391	20743585	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743586	20743674	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743675	20743803	0.99	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743675	20743803	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20743804	20743909	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20743910	20744081	1	-	1	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20743910	20744081	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744082	20744252	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744253	20744382	1	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744253	20744382	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744383	20744456	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744457	20744621	1	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744457	20744621	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744622	20744828	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20744829	20744978	1	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20744829	20744978	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20744979	20745068	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20745069	20745152	1	-	2	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20745069	20745152	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	intron	20745153	20745275	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	CDS	20745276	20745420	0.59	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	exon	20745276	20745420	.	-	.	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
Phchi.S3	AUGUSTUS	start_codon	20745418	20745420	.	-	0	transcript_id "Phchi.S3G301600.t3"; gene_id "Phchi.S3G301600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15350.t1 is derived from g13818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18520038	18520595	.	+	.	Phchi.S3G266900
Phchi.S3	AUGUSTUS	transcript	18520038	18520595	.	+	.	transcript_id "Phchi.S3G266900.t1"; gene_id "Phchi.S3G266900"
Phchi.S3	AUGUSTUS	start_codon	18520038	18520040	.	+	0	transcript_id "Phchi.S3G266900.t1"; gene_id "Phchi.S3G266900"
Phchi.S3	AUGUSTUS	CDS	18520038	18520595	1	+	0	transcript_id "Phchi.S3G266900.t1"; gene_id "Phchi.S3G266900"
Phchi.S3	AUGUSTUS	exon	18520038	18520595	.	+	.	transcript_id "Phchi.S3G266900.t1"; gene_id "Phchi.S3G266900"
Phchi.S3	AUGUSTUS	stop_codon	18520596	18520598	.	+	0	transcript_id "Phchi.S3G266900.t1"; gene_id "Phchi.S3G266900"
# This transcript jg7254.t2 is derived from g4426.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7255.t1 is derived from g4427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27882296	27883094	.	-	.	Phchi.S1G441400
Phchi.S1	AUGUSTUS	transcript	27882296	27882899	.	-	.	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	stop_codon	27882293	27882295	.	-	0	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27882296	27882390	0.84	-	2	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27882296	27882390	.	-	.	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	intron	27882391	27882484	.	-	.	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27882485	27882776	0.99	-	0	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27882485	27882776	.	-	.	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	intron	27882777	27882875	.	-	.	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27882876	27882899	0.99	-	0	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27882876	27882899	.	-	.	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	start_codon	27882897	27882899	.	-	0	transcript_id "Phchi.S1G441400.t1"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	transcript	27882296	27883094	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	stop_codon	27882293	27882295	.	-	0	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27882296	27882390	0.87	-	2	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27882296	27882390	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	intron	27882391	27882484	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27882485	27882578	0.53	-	0	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27882485	27882578	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	intron	27882579	27882667	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27882668	27882776	0.61	-	1	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27882668	27882776	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	intron	27882777	27883050	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	CDS	27883051	27883094	0.5	-	0	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	exon	27883051	27883094	.	-	.	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
Phchi.S1	AUGUSTUS	start_codon	27883092	27883094	.	-	0	transcript_id "Phchi.S1G441400.t2"; gene_id "Phchi.S1G441400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1952.t1 is derived from g8872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3999407	4002762	.	-	.	Phchi.S5G056100
Phchi.S5	AUGUSTUS	transcript	3999407	4002762	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	stop_codon	3999404	3999406	.	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	3999407	4000057	0.99	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	3999407	4000057	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	intron	4000058	4000814	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	4000815	4000889	1	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	4000815	4000889	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	intron	4000890	4001062	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	4001063	4001248	1	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	4001063	4001248	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	intron	4001249	4001405	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	4001406	4001532	1	-	1	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	4001406	4001532	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	intron	4001533	4001642	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	4001643	4001806	1	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	4001643	4001806	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	intron	4001807	4001897	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	4001898	4001976	1	-	1	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	4001898	4001976	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	intron	4001977	4002247	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	CDS	4002248	4002762	0.6	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	exon	4002248	4002762	.	-	.	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
Phchi.S5	AUGUSTUS	start_codon	4002760	4002762	.	-	0	transcript_id "Phchi.S5G056100.t1"; gene_id "Phchi.S5G056100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2592.t1 is derived from g9512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7555689	7557393	.	+	.	Phchi.S5G120100
Phchi.S5	AUGUSTUS	transcript	7555689	7557393	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	start_codon	7555689	7555691	.	+	0	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	CDS	7555689	7555817	0.83	+	0	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	exon	7555689	7555817	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	intron	7555818	7555982	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	CDS	7555983	7556097	0.26	+	0	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	exon	7555983	7556097	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	intron	7556098	7556197	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	CDS	7556198	7556275	0.29	+	2	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	exon	7556198	7556275	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	intron	7556276	7556343	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	CDS	7556344	7556541	0.48	+	2	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	exon	7556344	7556541	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	intron	7556542	7556653	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	CDS	7556654	7557047	0.61	+	2	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	exon	7556654	7557047	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	intron	7557048	7557197	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	CDS	7557198	7557393	0.31	+	1	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	exon	7557198	7557393	.	+	.	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
Phchi.S5	AUGUSTUS	stop_codon	7557394	7557396	.	+	0	transcript_id "Phchi.S5G120100.t1"; gene_id "Phchi.S5G120100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12250.t1 is derived from g7926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7011304	7013501	.	+	.	Phchi.S2G033000
Phchi.S2	AUGUSTUS	transcript	7011304	7013501	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	start_codon	7011304	7011306	.	+	0	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7011304	7011446	0.38	+	0	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7011304	7011446	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7011447	7011557	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7011558	7012747	0.95	+	1	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7011558	7012747	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7012748	7012914	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7012915	7013256	1	+	2	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7012915	7013256	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7013257	7013352	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7013353	7013501	0.95	+	2	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7013353	7013501	.	+	.	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	stop_codon	7013502	7013504	.	+	0	transcript_id "Phchi.S2G033000.t1"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	transcript	7011309	7013501	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	start_codon	7011309	7011311	.	+	0	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7011309	7011446	0.58	+	0	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7011309	7011446	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7011447	7011537	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7011538	7012747	0.7	+	0	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7011538	7012747	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7012748	7012914	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7012915	7013256	1	+	2	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7012915	7013256	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7013257	7013352	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7013353	7013501	0.99	+	2	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7013353	7013501	.	+	.	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	stop_codon	7013502	7013504	.	+	0	transcript_id "Phchi.S2G033000.t2"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	transcript	7011309	7013501	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	start_codon	7011309	7011311	.	+	0	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7011309	7011446	0.43	+	0	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7011309	7011446	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7011447	7011537	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7011538	7012747	0.53	+	0	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7011538	7012747	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7012748	7012914	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7012915	7013256	1	+	2	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7012915	7013256	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	intron	7013257	7013349	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	CDS	7013350	7013501	0.95	+	2	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	exon	7013350	7013501	.	+	.	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
Phchi.S2	AUGUSTUS	stop_codon	7013502	7013504	.	+	0	transcript_id "Phchi.S2G033000.t3"; gene_id "Phchi.S2G033000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12125.t1 is derived from g7801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4005706	4008682	.	+	.	Phchi.S2G020500
Phchi.S2	AUGUSTUS	transcript	4005706	4008682	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	start_codon	4005706	4005708	.	+	0	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	CDS	4005706	4006324	0.99	+	0	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	exon	4005706	4006324	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	intron	4006325	4006498	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	CDS	4006499	4007657	0.76	+	2	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	exon	4006499	4007657	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	intron	4007658	4007762	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	CDS	4007763	4007891	0.99	+	1	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	exon	4007763	4007891	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	intron	4007892	4008020	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	CDS	4008021	4008043	1	+	1	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	exon	4008021	4008043	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	intron	4008044	4008143	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	CDS	4008144	4008682	0.98	+	2	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	exon	4008144	4008682	.	+	.	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
Phchi.S2	AUGUSTUS	stop_codon	4008683	4008685	.	+	0	transcript_id "Phchi.S2G020500.t1"; gene_id "Phchi.S2G020500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7914.t1 is derived from g5088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31886472	31886780	.	+	.	Phchi.S1G507300
Phchi.S1	AUGUSTUS	transcript	31886472	31886780	.	+	.	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	start_codon	31886472	31886474	.	+	0	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	CDS	31886472	31886554	0.9	+	0	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	exon	31886472	31886554	.	+	.	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	intron	31886555	31886650	.	+	.	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	CDS	31886651	31886780	0.99	+	1	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	exon	31886651	31886780	.	+	.	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
Phchi.S1	AUGUSTUS	stop_codon	31886781	31886783	.	+	0	transcript_id "Phchi.S1G507300.t1"; gene_id "Phchi.S1G507300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10270.t1 is derived from g7446.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46775114	46778530	.	-	.	Phchi.S1G742900
Phchi.S1	AUGUSTUS	transcript	46775114	46778530	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	stop_codon	46775111	46775113	.	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775114	46775165	0.98	-	1	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775114	46775165	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775166	46775652	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775653	46775741	1	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775653	46775741	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775742	46775825	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775826	46775859	1	-	1	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775826	46775859	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775860	46775928	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775929	46775975	0.57	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775929	46775975	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775976	46776089	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776090	46776224	1	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776090	46776224	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776225	46776317	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776318	46776467	0.99	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776318	46776467	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776468	46776573	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776574	46776607	0.99	-	1	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776574	46776607	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776608	46776701	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776702	46776778	1	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776702	46776778	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776779	46776860	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776861	46776936	1	-	1	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776861	46776936	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776937	46777023	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777024	46777157	1	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777024	46777157	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46777158	46777253	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777254	46777346	0.99	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777254	46777346	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46777347	46777461	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777462	46777607	0.69	-	2	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777462	46777607	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46777608	46777698	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777699	46778104	1	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777699	46778104	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46778105	46778242	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46778243	46778530	0.49	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46778243	46778530	.	-	.	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	start_codon	46778528	46778530	.	-	0	transcript_id "Phchi.S1G742900.t1"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	transcript	46775114	46778530	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	stop_codon	46775111	46775113	.	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775114	46775165	1	-	1	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775114	46775165	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775166	46775652	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775653	46775741	1	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775653	46775741	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775742	46775825	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775826	46775859	0.98	-	1	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775826	46775859	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775860	46775928	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46775929	46775975	0.58	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46775929	46775975	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46775976	46776089	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776090	46776224	0.98	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776090	46776224	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776225	46776317	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776318	46776467	1	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776318	46776467	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776468	46776573	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776574	46776607	0.99	-	1	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776574	46776607	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776608	46776701	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776702	46776778	1	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776702	46776778	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776779	46776860	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46776861	46776936	1	-	1	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46776861	46776936	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46776937	46777023	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777024	46777157	1	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777024	46777157	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46777158	46777253	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777254	46777346	1	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777254	46777346	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46777347	46777461	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777462	46777604	0.67	-	2	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777462	46777604	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46777605	46777698	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46777699	46778104	1	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46777699	46778104	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	intron	46778105	46778242	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	CDS	46778243	46778530	0.44	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	exon	46778243	46778530	.	-	.	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
Phchi.S1	AUGUSTUS	start_codon	46778528	46778530	.	-	0	transcript_id "Phchi.S1G742900.t2"; gene_id "Phchi.S1G742900"
# This transcript jg7611.t2 is derived from g4785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7612.t1 is derived from g4786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30255266	30259734	.	-	.	Phchi.S1G477100
Phchi.S1	AUGUSTUS	transcript	30255266	30259734	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	stop_codon	30255263	30255265	.	-	0	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30255266	30255592	0.98	-	0	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30255266	30255592	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30255593	30255691	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30255692	30256048	1	-	0	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30255692	30256048	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30256049	30256139	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30256140	30256290	1	-	1	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30256140	30256290	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30256291	30256383	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30256384	30256849	0.99	-	2	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30256384	30256849	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30256850	30256962	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30256963	30258457	0.72	-	0	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30256963	30258457	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30258458	30258657	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30258658	30259231	0.6	-	1	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30258658	30259231	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30259232	30259331	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30259332	30259457	0.41	-	1	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30259332	30259457	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	intron	30259458	30259630	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	CDS	30259631	30259734	0.4	-	0	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	exon	30259631	30259734	.	-	.	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
Phchi.S1	AUGUSTUS	start_codon	30259732	30259734	.	-	0	transcript_id "Phchi.S1G477100.t1"; gene_id "Phchi.S1G477100"
# This transcript jg988.t1 is derived from g10770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6895846	6897345	.	+	.	Phchi.S6G094600
Phchi.S6	AUGUSTUS	transcript	6895846	6897345	.	+	.	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	start_codon	6895846	6895848	.	+	0	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	CDS	6895846	6896113	0.36	+	0	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	exon	6895846	6896113	.	+	.	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	intron	6896114	6896233	.	+	.	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	CDS	6896234	6896574	0.89	+	2	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	exon	6896234	6896574	.	+	.	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	intron	6896575	6896724	.	+	.	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	CDS	6896725	6897345	0.7	+	0	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	exon	6896725	6897345	.	+	.	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
Phchi.S6	AUGUSTUS	stop_codon	6897346	6897348	.	+	0	transcript_id "Phchi.S6G094600.t1"; gene_id "Phchi.S6G094600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3899.t1 is derived from g1068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6310095	6313003	.	-	.	Phchi.S1G105800
Phchi.S1	AUGUSTUS	transcript	6310095	6313003	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	stop_codon	6310092	6310094	.	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6310095	6310322	0.63	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6310095	6310322	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6310323	6310427	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6310428	6310630	0.72	-	2	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6310428	6310630	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6310631	6310747	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6310748	6311315	0.96	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6310748	6311315	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6311316	6311415	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6311416	6311653	0.91	-	1	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6311416	6311653	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6311654	6311765	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6311766	6312037	0.99	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6311766	6312037	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6312038	6312163	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6312164	6312205	1	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6312164	6312205	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6312206	6312399	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6312400	6312442	0.91	-	1	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6312400	6312442	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6312443	6312550	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6312551	6312639	0.57	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6312551	6312639	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6312640	6312733	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6312734	6312760	0.97	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6312734	6312760	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	intron	6312761	6312928	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	CDS	6312929	6313003	0.37	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	exon	6312929	6313003	.	-	.	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
Phchi.S1	AUGUSTUS	start_codon	6313001	6313003	.	-	0	transcript_id "Phchi.S1G105800.t1"; gene_id "Phchi.S1G105800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14821.t1 is derived from g13289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14868481	14868711	.	+	.	Phchi.S3G214000
Phchi.S3	AUGUSTUS	transcript	14868481	14868711	.	+	.	transcript_id "Phchi.S3G214000.t1"; gene_id "Phchi.S3G214000"
Phchi.S3	AUGUSTUS	start_codon	14868481	14868483	.	+	0	transcript_id "Phchi.S3G214000.t1"; gene_id "Phchi.S3G214000"
Phchi.S3	AUGUSTUS	CDS	14868481	14868711	0.89	+	0	transcript_id "Phchi.S3G214000.t1"; gene_id "Phchi.S3G214000"
Phchi.S3	AUGUSTUS	exon	14868481	14868711	.	+	.	transcript_id "Phchi.S3G214000.t1"; gene_id "Phchi.S3G214000"
Phchi.S3	AUGUSTUS	stop_codon	14868712	14868714	.	+	0	transcript_id "Phchi.S3G214000.t1"; gene_id "Phchi.S3G214000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5331.t1 is derived from g2501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16323092	16327942	.	-	.	Phchi.S1G249000
Phchi.S1	AUGUSTUS	transcript	16323092	16327942	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	stop_codon	16323089	16323091	.	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16323092	16323138	0.6	-	2	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16323092	16323138	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16323139	16323311	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16323312	16323346	0.61	-	1	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16323312	16323346	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16323347	16323437	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16323438	16323754	0.62	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16323438	16323754	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16323755	16323845	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16323846	16324007	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16323846	16324007	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16324008	16324120	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16324121	16324210	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16324121	16324210	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16324211	16324298	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16324299	16324460	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16324299	16324460	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16324461	16324549	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16324550	16324651	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16324550	16324651	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16324652	16324726	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16324727	16324801	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16324727	16324801	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16324802	16324897	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16324898	16325042	1	-	1	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16324898	16325042	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16325043	16325118	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16325119	16325300	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16325119	16325300	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16325301	16325378	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16325379	16325513	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16325379	16325513	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16325514	16325654	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16325655	16325756	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16325655	16325756	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16325757	16325883	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16325884	16325997	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16325884	16325997	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16325998	16326079	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16326080	16326130	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16326080	16326130	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16326131	16326255	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16326256	16326324	0.99	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16326256	16326324	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16326325	16326433	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16326434	16326511	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16326434	16326511	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16326512	16326616	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16326617	16326718	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16326617	16326718	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16326719	16326878	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16326879	16326959	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16326879	16326959	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16326960	16327066	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16327067	16327168	1	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16327067	16327168	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16327169	16327309	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16327310	16327541	0.53	-	1	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16327310	16327541	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	intron	16327542	16327889	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	CDS	16327890	16327942	0.54	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	exon	16327890	16327942	.	-	.	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
Phchi.S1	AUGUSTUS	start_codon	16327940	16327942	.	-	0	transcript_id "Phchi.S1G249000.t1"; gene_id "Phchi.S1G249000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg731.t1 is derived from g10513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5207872	5209559	.	-	.	Phchi.S6G069000
Phchi.S6	AUGUSTUS	transcript	5207872	5209559	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	stop_codon	5207869	5207871	.	-	0	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	CDS	5207872	5208019	0.98	-	1	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	exon	5207872	5208019	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	intron	5208020	5208151	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	CDS	5208152	5208387	1	-	0	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	exon	5208152	5208387	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	intron	5208388	5208558	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	CDS	5208559	5208765	0.99	-	0	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	exon	5208559	5208765	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	intron	5208766	5208879	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	CDS	5208880	5209048	0.99	-	1	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	exon	5208880	5209048	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	intron	5209049	5209221	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	CDS	5209222	5209559	0.99	-	0	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	exon	5209222	5209559	.	-	.	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
Phchi.S6	AUGUSTUS	start_codon	5209557	5209559	.	-	0	transcript_id "Phchi.S6G069000.t1"; gene_id "Phchi.S6G069000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg640.t1 is derived from g10422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4553865	4556161	.	-	.	Phchi.S6G059900
Phchi.S6	AUGUSTUS	transcript	4553865	4556161	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	stop_codon	4553862	4553864	.	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4553865	4554146	0.97	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4553865	4554146	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4554147	4554248	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4554249	4554512	0.94	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4554249	4554512	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4554513	4554610	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4554611	4554739	0.56	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4554611	4554739	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4554740	4554830	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4554831	4554932	1	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4554831	4554932	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4554933	4555019	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4555020	4555095	1	-	1	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4555020	4555095	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4555096	4555219	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4555220	4555308	1	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4555220	4555308	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4555309	4555415	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4555416	4555610	1	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4555416	4555610	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4555611	4555703	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4555704	4555770	1	-	1	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4555704	4555770	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4555771	4555853	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4555854	4555906	1	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4555854	4555906	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	intron	4555907	4556005	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	CDS	4556006	4556161	0.91	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	exon	4556006	4556161	.	-	.	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
Phchi.S6	AUGUSTUS	start_codon	4556159	4556161	.	-	0	transcript_id "Phchi.S6G059900.t1"; gene_id "Phchi.S6G059900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5544.t1 is derived from g2714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17473653	17474342	.	+	.	Phchi.S1G270300
Phchi.S1	AUGUSTUS	transcript	17473653	17474342	.	+	.	transcript_id "Phchi.S1G270300.t1"; gene_id "Phchi.S1G270300"
Phchi.S1	AUGUSTUS	start_codon	17473653	17473655	.	+	0	transcript_id "Phchi.S1G270300.t1"; gene_id "Phchi.S1G270300"
Phchi.S1	AUGUSTUS	CDS	17473653	17474342	1	+	0	transcript_id "Phchi.S1G270300.t1"; gene_id "Phchi.S1G270300"
Phchi.S1	AUGUSTUS	exon	17473653	17474342	.	+	.	transcript_id "Phchi.S1G270300.t1"; gene_id "Phchi.S1G270300"
Phchi.S1	AUGUSTUS	stop_codon	17474343	17474345	.	+	0	transcript_id "Phchi.S1G270300.t1"; gene_id "Phchi.S1G270300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10038.t1 is derived from g7214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45197803	45198797	.	-	.	Phchi.S1G719700
Phchi.S1	AUGUSTUS	transcript	45197803	45198797	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	stop_codon	45197800	45197802	.	-	0	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	CDS	45197803	45197883	1	-	0	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	exon	45197803	45197883	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	intron	45197884	45197976	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	CDS	45197977	45198099	1	-	0	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	exon	45197977	45198099	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	intron	45198100	45198256	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	CDS	45198257	45198547	1	-	0	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	exon	45198257	45198547	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	intron	45198548	45198725	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	CDS	45198726	45198797	1	-	0	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	exon	45198726	45198797	.	-	.	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
Phchi.S1	AUGUSTUS	start_codon	45198795	45198797	.	-	0	transcript_id "Phchi.S1G719700.t1"; gene_id "Phchi.S1G719700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15924.t1 is derived from g14394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22244683	22246630	.	-	.	Phchi.S3G324300
Phchi.S3	AUGUSTUS	transcript	22244683	22246630	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	stop_codon	22244680	22244682	.	-	0	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22244683	22244840	0.99	-	2	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22244683	22244840	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22244841	22244964	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22244965	22245035	1	-	1	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22244965	22245035	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22245036	22245130	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22245131	22245294	1	-	0	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22245131	22245294	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22245295	22245394	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22245395	22245416	0.95	-	1	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22245395	22245416	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22245417	22245554	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22245555	22245794	0.95	-	1	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22245555	22245794	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22245795	22245905	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22245906	22246211	0.6	-	1	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22245906	22246211	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22246212	22246302	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22246303	22246313	0.7	-	0	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22246303	22246313	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	intron	22246314	22246573	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	CDS	22246574	22246630	0.55	-	0	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	exon	22246574	22246630	.	-	.	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
Phchi.S3	AUGUSTUS	start_codon	22246628	22246630	.	-	0	transcript_id "Phchi.S3G324300.t1"; gene_id "Phchi.S3G324300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10970.t1 is derived from g15020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3413269	3413742	.	-	.	Phchi.S4G055200
Phchi.S4	AUGUSTUS	transcript	3413269	3413742	.	-	.	transcript_id "Phchi.S4G055200.t1"; gene_id "Phchi.S4G055200"
Phchi.S4	AUGUSTUS	stop_codon	3413266	3413268	.	-	0	transcript_id "Phchi.S4G055200.t1"; gene_id "Phchi.S4G055200"
Phchi.S4	AUGUSTUS	CDS	3413269	3413742	0.99	-	0	transcript_id "Phchi.S4G055200.t1"; gene_id "Phchi.S4G055200"
Phchi.S4	AUGUSTUS	exon	3413269	3413742	.	-	.	transcript_id "Phchi.S4G055200.t1"; gene_id "Phchi.S4G055200"
Phchi.S4	AUGUSTUS	start_codon	3413740	3413742	.	-	0	transcript_id "Phchi.S4G055200.t1"; gene_id "Phchi.S4G055200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12880.t1 is derived from g11345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2901342	2903091	.	-	.	Phchi.S3G019900
Phchi.S3	AUGUSTUS	transcript	2901342	2903091	.	-	.	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	stop_codon	2901339	2901341	.	-	0	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	CDS	2901342	2902181	0.98	-	0	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	exon	2901342	2902181	.	-	.	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	intron	2902182	2902306	.	-	.	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	CDS	2902307	2902519	0.97	-	0	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	exon	2902307	2902519	.	-	.	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	intron	2902520	2902653	.	-	.	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	CDS	2902654	2903091	0.77	-	0	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	exon	2902654	2903091	.	-	.	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
Phchi.S3	AUGUSTUS	start_codon	2903089	2903091	.	-	0	transcript_id "Phchi.S3G019900.t1"; gene_id "Phchi.S3G019900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg384.t1 is derived from g10166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2784660	2785421	.	-	.	Phchi.S6G034300
Phchi.S6	AUGUSTUS	transcript	2784660	2785421	.	-	.	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	stop_codon	2784657	2784659	.	-	0	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	CDS	2784660	2784826	1	-	2	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	exon	2784660	2784826	.	-	.	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	intron	2784827	2784954	.	-	.	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	CDS	2784955	2785018	1	-	0	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	exon	2784955	2785018	.	-	.	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	intron	2785019	2785169	.	-	.	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	CDS	2785170	2785421	0.84	-	0	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	exon	2785170	2785421	.	-	.	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
Phchi.S6	AUGUSTUS	start_codon	2785419	2785421	.	-	0	transcript_id "Phchi.S6G034300.t1"; gene_id "Phchi.S6G034300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7586.t1 is derived from g4760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30163548	30166364	.	-	.	Phchi.S1G474500
Phchi.S1	AUGUSTUS	transcript	30163548	30166364	.	-	.	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	stop_codon	30163545	30163547	.	-	0	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	CDS	30163548	30165027	1	-	1	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	exon	30163548	30165027	.	-	.	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	intron	30165028	30165141	.	-	.	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	CDS	30165142	30166364	0.66	-	0	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	exon	30165142	30166364	.	-	.	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
Phchi.S1	AUGUSTUS	start_codon	30166362	30166364	.	-	0	transcript_id "Phchi.S1G474500.t1"; gene_id "Phchi.S1G474500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4075.t1 is derived from g1244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7647466	7648424	.	-	.	Phchi.S1G123400
Phchi.S1	AUGUSTUS	transcript	7647466	7648424	.	-	.	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	stop_codon	7647463	7647465	.	-	0	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	CDS	7647466	7647711	0.57	-	0	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	exon	7647466	7647711	.	-	.	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	intron	7647712	7647884	.	-	.	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	CDS	7647885	7647955	0.7	-	2	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	exon	7647885	7647955	.	-	.	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	intron	7647956	7648222	.	-	.	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	CDS	7648223	7648424	0.98	-	0	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	exon	7648223	7648424	.	-	.	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
Phchi.S1	AUGUSTUS	start_codon	7648422	7648424	.	-	0	transcript_id "Phchi.S1G123400.t1"; gene_id "Phchi.S1G123400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12187.t1 is derived from g7863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6312012	6314836	.	+	.	Phchi.S2G026700
Phchi.S2	AUGUSTUS	transcript	6312012	6314836	.	+	.	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	start_codon	6312012	6312014	.	+	0	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	CDS	6312012	6312289	0.03	+	0	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	exon	6312012	6312289	.	+	.	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	intron	6312290	6314751	.	+	.	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	CDS	6314752	6314836	0.02	+	1	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	exon	6314752	6314836	.	+	.	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
Phchi.S2	AUGUSTUS	stop_codon	6314837	6314839	.	+	0	transcript_id "Phchi.S2G026700.t1"; gene_id "Phchi.S2G026700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9240.t1 is derived from g6415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40554948	40556995	.	+	.	Phchi.S1G639900
Phchi.S1	AUGUSTUS	transcript	40554948	40556995	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	start_codon	40554948	40554950	.	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	CDS	40554948	40555277	0.75	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	exon	40554948	40555277	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	intron	40555278	40555371	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	CDS	40555372	40555587	0.9	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	exon	40555372	40555587	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	intron	40555588	40555665	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	CDS	40555666	40555959	0.99	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	exon	40555666	40555959	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	intron	40555960	40556039	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	CDS	40556040	40556426	1	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	exon	40556040	40556426	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	intron	40556427	40556520	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	CDS	40556521	40556721	1	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	exon	40556521	40556721	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	intron	40556722	40556803	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	CDS	40556804	40556995	0.99	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	exon	40556804	40556995	.	+	.	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
Phchi.S1	AUGUSTUS	stop_codon	40556996	40556998	.	+	0	transcript_id "Phchi.S1G639900.t1"; gene_id "Phchi.S1G639900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10773.t1 is derived from g14823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2049688	2051550	.	-	.	Phchi.S4G035500
Phchi.S4	AUGUSTUS	transcript	2049688	2051550	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	stop_codon	2049685	2049687	.	-	0	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	CDS	2049688	2049920	0.99	-	2	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	exon	2049688	2049920	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	intron	2049921	2050106	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	CDS	2050107	2050580	0.97	-	2	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	exon	2050107	2050580	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	intron	2050581	2050845	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	CDS	2050846	2051252	0.79	-	1	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	exon	2050846	2051252	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	intron	2051253	2051461	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	CDS	2051462	2051550	1	-	0	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	exon	2051462	2051550	.	-	.	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
Phchi.S4	AUGUSTUS	start_codon	2051548	2051550	.	-	0	transcript_id "Phchi.S4G035500.t1"; gene_id "Phchi.S4G035500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1077.t1 is derived from g10860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7479373	7481339	.	+	.	Phchi.S6G103600
Phchi.S6	AUGUSTUS	transcript	7479373	7481339	.	+	.	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	start_codon	7479373	7479375	.	+	0	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	CDS	7479373	7479594	0.56	+	0	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	exon	7479373	7479594	.	+	.	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	intron	7479595	7479884	.	+	.	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	CDS	7479885	7481339	0.73	+	0	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	exon	7479885	7481339	.	+	.	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
Phchi.S6	AUGUSTUS	stop_codon	7481340	7481342	.	+	0	transcript_id "Phchi.S6G103600.t1"; gene_id "Phchi.S6G103600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5234.t1 is derived from g2404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15780425	15786610	.	-	.	Phchi.S1G239300
Phchi.S1	AUGUSTUS	transcript	15780425	15786610	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	stop_codon	15780422	15780424	.	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15780425	15780484	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15780425	15780484	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15780485	15780838	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15780839	15780927	1	-	2	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15780839	15780927	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15780928	15781050	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15781051	15781082	1	-	1	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15781051	15781082	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15781083	15781196	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15781197	15781285	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15781197	15781285	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15781286	15781447	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15781448	15781627	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15781448	15781627	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15781628	15781719	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15781720	15781865	1	-	2	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15781720	15781865	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15781866	15781987	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15781988	15782152	1	-	2	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15781988	15782152	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15782153	15782264	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15782265	15782403	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15782265	15782403	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15782404	15782482	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15782483	15782560	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15782483	15782560	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15782561	15782646	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15782647	15782715	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15782647	15782715	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15782716	15782863	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15782864	15782983	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15782864	15782983	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15782984	15783106	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15783107	15783190	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15783107	15783190	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15783191	15783352	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15783353	15783424	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15783353	15783424	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15783425	15783563	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15783564	15783637	1	-	2	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15783564	15783637	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15783638	15783725	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15783726	15783780	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15783726	15783780	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15783781	15783857	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15783858	15783950	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15783858	15783950	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15783951	15784097	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15784098	15784175	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15784098	15784175	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15784176	15784295	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15784296	15784376	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15784296	15784376	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15784377	15784502	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15784503	15784622	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15784503	15784622	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15784623	15784760	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15784761	15784888	1	-	2	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15784761	15784888	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15784889	15785130	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15785131	15785242	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15785131	15785242	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15785243	15785359	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15785360	15785458	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15785360	15785458	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15785459	15785577	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15785578	15785652	1	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15785578	15785652	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	intron	15785653	15785782	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	CDS	15785783	15786610	0.75	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	exon	15785783	15786610	.	-	.	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
Phchi.S1	AUGUSTUS	start_codon	15786608	15786610	.	-	0	transcript_id "Phchi.S1G239300.t1"; gene_id "Phchi.S1G239300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9447.t1 is derived from g6623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41505060	41506742	.	-	.	Phchi.S1G660600
Phchi.S1	AUGUSTUS	transcript	41505060	41506742	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	stop_codon	41505057	41505059	.	-	0	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	CDS	41505060	41505707	0.59	-	0	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	exon	41505060	41505707	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	intron	41505708	41505790	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	CDS	41505791	41506183	0.55	-	0	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	exon	41505791	41506183	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	intron	41506184	41506265	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	CDS	41506266	41506321	1	-	2	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	exon	41506266	41506321	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	intron	41506322	41506405	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	CDS	41506406	41506510	1	-	2	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	exon	41506406	41506510	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	intron	41506511	41506595	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	CDS	41506596	41506623	0.87	-	0	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	exon	41506596	41506623	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	intron	41506624	41506703	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	CDS	41506704	41506742	0.33	-	0	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	exon	41506704	41506742	.	-	.	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
Phchi.S1	AUGUSTUS	start_codon	41506740	41506742	.	-	0	transcript_id "Phchi.S1G660600.t1"; gene_id "Phchi.S1G660600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15358.t1 is derived from g13826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18575867	18579855	.	-	.	Phchi.S3G267700
Phchi.S3	AUGUSTUS	transcript	18575867	18579855	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	stop_codon	18575864	18575866	.	-	0	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18575867	18576486	1	-	2	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18575867	18576486	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	intron	18576487	18576678	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18576679	18577306	0.99	-	0	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18576679	18577306	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	intron	18577307	18577426	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18577427	18577568	0.84	-	1	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18577427	18577568	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	intron	18577569	18577651	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18577652	18577712	0.51	-	2	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18577652	18577712	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	intron	18577713	18577944	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18577945	18579366	0.26	-	2	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18577945	18579366	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	intron	18579367	18579495	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18579496	18579631	0.41	-	0	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18579496	18579631	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	intron	18579632	18579711	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	CDS	18579712	18579855	0.3	-	0	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	exon	18579712	18579855	.	-	.	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
Phchi.S3	AUGUSTUS	start_codon	18579853	18579855	.	-	0	transcript_id "Phchi.S3G267700.t1"; gene_id "Phchi.S3G267700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13219.t1 is derived from g11684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4737621	4739591	.	-	.	Phchi.S3G053800
Phchi.S3	AUGUSTUS	transcript	4737621	4739591	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	stop_codon	4737618	4737620	.	-	0	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	CDS	4737621	4737626	0.99	-	0	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	exon	4737621	4737626	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	intron	4737627	4737712	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	CDS	4737713	4737981	0.98	-	2	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	exon	4737713	4737981	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	intron	4737982	4738108	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	CDS	4738109	4738339	1	-	2	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	exon	4738109	4738339	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	intron	4738340	4738466	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	CDS	4738467	4739107	0.98	-	1	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	exon	4738467	4739107	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	intron	4739108	4739211	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	CDS	4739212	4739383	1	-	2	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	exon	4739212	4739383	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	intron	4739384	4739464	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	CDS	4739465	4739591	0.8	-	0	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	exon	4739465	4739591	.	-	.	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
Phchi.S3	AUGUSTUS	start_codon	4739589	4739591	.	-	0	transcript_id "Phchi.S3G053800.t1"; gene_id "Phchi.S3G053800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15778.t1 is derived from g14248.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21296739	21298518	.	+	.	Phchi.S3G309700
Phchi.S3	AUGUSTUS	transcript	21296739	21298518	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	start_codon	21296739	21296741	.	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21296739	21296879	0.59	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21296739	21296879	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21296880	21297061	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297062	21297107	0.94	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297062	21297107	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297108	21297205	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297206	21297405	0.98	+	2	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297206	21297405	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297406	21297505	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297506	21297655	0.95	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297506	21297655	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297656	21297730	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297731	21297945	1	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297731	21297945	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297946	21298028	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21298029	21298287	1	+	1	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21298029	21298287	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21298288	21298386	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21298387	21298518	1	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21298387	21298518	.	+	.	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	stop_codon	21298519	21298521	.	+	0	transcript_id "Phchi.S3G309700.t1"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	transcript	21296739	21298518	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	start_codon	21296739	21296741	.	+	0	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21296739	21296808	0.55	+	0	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21296739	21296808	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21296809	21296920	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21296921	21297107	0.55	+	2	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21296921	21297107	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297108	21297200	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297201	21297405	0.82	+	1	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297201	21297405	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297406	21297505	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297506	21297655	1	+	0	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297506	21297655	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297656	21297730	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297731	21297945	1	+	0	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297731	21297945	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297946	21298028	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21298029	21298287	1	+	1	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21298029	21298287	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21298288	21298386	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21298387	21298518	1	+	0	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21298387	21298518	.	+	.	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	stop_codon	21298519	21298521	.	+	0	transcript_id "Phchi.S3G309700.t2"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	transcript	21296739	21298518	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	start_codon	21296739	21296741	.	+	0	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21296739	21296808	0.42	+	0	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21296739	21296808	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21296809	21296920	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21296921	21297107	0.44	+	2	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21296921	21297107	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297108	21297200	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297201	21297405	0.86	+	1	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297201	21297405	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297406	21297495	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297496	21297505	0.93	+	0	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297496	21297505	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297506	21297587	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297588	21297655	0.93	+	2	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297588	21297655	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297656	21297730	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21297731	21297945	1	+	0	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21297731	21297945	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21297946	21298028	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21298029	21298287	1	+	1	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21298029	21298287	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	intron	21298288	21298386	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	CDS	21298387	21298518	1	+	0	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	exon	21298387	21298518	.	+	.	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
Phchi.S3	AUGUSTUS	stop_codon	21298519	21298521	.	+	0	transcript_id "Phchi.S3G309700.t3"; gene_id "Phchi.S3G309700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3402.t1 is derived from g571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3358522	3363168	.	-	.	Phchi.S1G056100
Phchi.S1	AUGUSTUS	transcript	3358522	3363168	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	stop_codon	3358519	3358521	.	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3358522	3358604	1	-	2	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3358522	3358604	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3358605	3358687	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3358688	3358803	1	-	1	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3358688	3358803	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3358804	3358889	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3358890	3358904	0.67	-	1	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3358890	3358904	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3358905	3359014	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3359015	3359254	0.67	-	1	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3359015	3359254	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3359255	3359341	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3359342	3359476	1	-	1	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3359342	3359476	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3359477	3359649	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3359650	3359841	1	-	1	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3359650	3359841	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3359842	3359941	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3359942	3360015	1	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3359942	3360015	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3360016	3360107	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3360108	3360691	0.52	-	2	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3360108	3360691	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3360692	3360799	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3360800	3362492	0.48	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3360800	3362492	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3362493	3362624	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3362625	3362744	1	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3362625	3362744	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3362745	3362883	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3362884	3362991	1	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3362884	3362991	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	intron	3362992	3363078	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	CDS	3363079	3363168	0.99	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	exon	3363079	3363168	.	-	.	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
Phchi.S1	AUGUSTUS	start_codon	3363166	3363168	.	-	0	transcript_id "Phchi.S1G056100.t1"; gene_id "Phchi.S1G056100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14978.t1 is derived from g13446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15828843	15830659	.	-	.	Phchi.S3G229700
Phchi.S3	AUGUSTUS	transcript	15828843	15830659	.	-	.	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	stop_codon	15828840	15828842	.	-	0	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	CDS	15828843	15829019	1	-	0	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	exon	15828843	15829019	.	-	.	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	intron	15829020	15829195	.	-	.	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	CDS	15829196	15830659	0.93	-	0	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	exon	15829196	15830659	.	-	.	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
Phchi.S3	AUGUSTUS	start_codon	15830657	15830659	.	-	0	transcript_id "Phchi.S3G229700.t1"; gene_id "Phchi.S3G229700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9166.t1 is derived from g6341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40187952	40188873	.	+	.	Phchi.S1G632500
Phchi.S1	AUGUSTUS	transcript	40187952	40188873	.	+	.	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	start_codon	40187952	40187954	.	+	0	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	CDS	40187952	40187997	0.56	+	0	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	exon	40187952	40187997	.	+	.	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	intron	40187998	40188142	.	+	.	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	CDS	40188143	40188873	0.62	+	2	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	exon	40188143	40188873	.	+	.	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
Phchi.S1	AUGUSTUS	stop_codon	40188874	40188876	.	+	0	transcript_id "Phchi.S1G632500.t1"; gene_id "Phchi.S1G632500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14777.t1 is derived from g13245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14653110	14654262	.	+	.	Phchi.S3G209600
Phchi.S3	AUGUSTUS	transcript	14653110	14654262	.	+	.	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	start_codon	14653110	14653112	.	+	0	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	CDS	14653110	14653266	1	+	0	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	exon	14653110	14653266	.	+	.	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	intron	14653267	14653738	.	+	.	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	CDS	14653739	14654262	0.74	+	2	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	exon	14653739	14654262	.	+	.	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
Phchi.S3	AUGUSTUS	stop_codon	14654263	14654265	.	+	0	transcript_id "Phchi.S3G209600.t1"; gene_id "Phchi.S3G209600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15449.t1 is derived from g13917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19222030	19222656	.	+	.	Phchi.S3G276800
Phchi.S3	AUGUSTUS	transcript	19222030	19222656	.	+	.	transcript_id "Phchi.S3G276800.t1"; gene_id "Phchi.S3G276800"
Phchi.S3	AUGUSTUS	start_codon	19222030	19222032	.	+	0	transcript_id "Phchi.S3G276800.t1"; gene_id "Phchi.S3G276800"
Phchi.S3	AUGUSTUS	CDS	19222030	19222656	0.76	+	0	transcript_id "Phchi.S3G276800.t1"; gene_id "Phchi.S3G276800"
Phchi.S3	AUGUSTUS	exon	19222030	19222656	.	+	.	transcript_id "Phchi.S3G276800.t1"; gene_id "Phchi.S3G276800"
Phchi.S3	AUGUSTUS	stop_codon	19222657	19222659	.	+	0	transcript_id "Phchi.S3G276800.t1"; gene_id "Phchi.S3G276800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7943.t1 is derived from g5117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32034636	32041695	.	-	.	Phchi.S1G510200
Phchi.S1	AUGUSTUS	transcript	32034636	32041695	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	stop_codon	32034633	32034635	.	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32034636	32034821	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32034636	32034821	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32034822	32034904	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32034905	32034974	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32034905	32034974	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32034975	32035052	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32035053	32035249	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32035053	32035249	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32035250	32035342	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32035343	32035456	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32035343	32035456	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32035457	32035539	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32035540	32035617	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32035540	32035617	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32035618	32035720	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32035721	32035771	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32035721	32035771	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32035772	32035876	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32035877	32035984	0.95	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32035877	32035984	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32035985	32036078	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32036079	32036222	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32036079	32036222	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32036223	32036306	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32036307	32036438	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32036307	32036438	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32036439	32036514	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32036515	32036617	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32036515	32036617	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32036618	32036741	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32036742	32036806	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32036742	32036806	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32036807	32036899	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32036900	32036974	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32036900	32036974	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32036975	32037053	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32037054	32037125	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32037054	32037125	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32037126	32037244	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32037245	32037499	0.6	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32037245	32037499	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32037500	32037622	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32037623	32037698	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32037623	32037698	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32037699	32037789	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32037790	32037863	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32037790	32037863	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32037864	32037978	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32037979	32038086	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32037979	32038086	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32038087	32038283	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32038284	32038393	1	-	2	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32038284	32038393	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32038394	32038623	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32038624	32038686	1	-	2	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32038624	32038686	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32038687	32038767	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32038768	32038861	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32038768	32038861	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32038862	32039002	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32039003	32039138	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32039003	32039138	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32039139	32039218	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32039219	32039308	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32039219	32039308	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32039309	32039412	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32039413	32039524	1	-	2	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32039413	32039524	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32039525	32039623	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32039624	32039637	0.94	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32039624	32039637	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32039638	32039744	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32039745	32039806	0.94	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32039745	32039806	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32039807	32039996	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32039997	32040260	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32039997	32040260	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32040261	32040355	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32040356	32040451	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32040356	32040451	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32040452	32040535	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32040536	32040607	0.99	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32040536	32040607	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32040608	32040708	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32040709	32040751	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32040709	32040751	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32040752	32040847	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32040848	32040946	1	-	1	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32040848	32040946	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32040947	32041134	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32041135	32041243	1	-	2	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32041135	32041243	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32041244	32041411	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32041412	32041499	1	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32041412	32041499	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	intron	32041500	32041587	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	CDS	32041588	32041695	0.5	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	exon	32041588	32041695	.	-	.	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
Phchi.S1	AUGUSTUS	start_codon	32041693	32041695	.	-	0	transcript_id "Phchi.S1G510200.t1"; gene_id "Phchi.S1G510200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8631.t1 is derived from g5806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37160423	37166188	.	+	.	Phchi.S1G579000
Phchi.S1	AUGUSTUS	transcript	37160423	37166188	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	start_codon	37160423	37160425	.	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37160423	37161132	0.37	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37160423	37161132	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37161133	37161322	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37161323	37161752	1	+	1	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37161323	37161752	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37161753	37161951	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37161952	37162152	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37161952	37162152	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37162153	37162245	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37162246	37162539	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37162246	37162539	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37162540	37162696	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37162697	37162972	0.96	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37162697	37162972	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37162973	37163082	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37163083	37163163	0.91	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37163083	37163163	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37163164	37163270	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37163271	37163405	0.78	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37163271	37163405	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37163406	37163520	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37163521	37163650	0.98	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37163521	37163650	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37163651	37163778	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37163779	37163899	0.96	+	2	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37163779	37163899	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37163900	37164012	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37164013	37164214	1	+	1	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37164013	37164214	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37164215	37164337	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37164338	37164466	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37164338	37164466	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37164467	37164607	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37164608	37164790	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37164608	37164790	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37164791	37164901	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37164902	37165021	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37164902	37165021	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37165022	37165141	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37165142	37165327	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37165142	37165327	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37165328	37165413	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37165414	37165488	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37165414	37165488	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37165489	37165615	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37165616	37165675	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37165616	37165675	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37165676	37165778	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37165779	37165886	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37165779	37165886	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37165887	37165967	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37165968	37166048	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37165968	37166048	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	intron	37166049	37166125	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	CDS	37166126	37166188	1	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	exon	37166126	37166188	.	+	.	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
Phchi.S1	AUGUSTUS	stop_codon	37166189	37166191	.	+	0	transcript_id "Phchi.S1G579000.t1"; gene_id "Phchi.S1G579000"
# This transcript jg9800.t2 is derived from g6976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9801.t1 is derived from g6977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43778360	43779046	.	+	.	Phchi.S1G696000
Phchi.S1	AUGUSTUS	transcript	43778360	43779046	.	+	.	transcript_id "Phchi.S1G696000.t1"; gene_id "Phchi.S1G696000"
Phchi.S1	AUGUSTUS	start_codon	43778360	43778362	.	+	0	transcript_id "Phchi.S1G696000.t1"; gene_id "Phchi.S1G696000"
Phchi.S1	AUGUSTUS	CDS	43778360	43779046	0.71	+	0	transcript_id "Phchi.S1G696000.t1"; gene_id "Phchi.S1G696000"
Phchi.S1	AUGUSTUS	exon	43778360	43779046	.	+	.	transcript_id "Phchi.S1G696000.t1"; gene_id "Phchi.S1G696000"
Phchi.S1	AUGUSTUS	stop_codon	43779047	43779049	.	+	0	transcript_id "Phchi.S1G696000.t1"; gene_id "Phchi.S1G696000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7024.t1 is derived from g4196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26472312	26474132	.	-	.	Phchi.S1G418300
Phchi.S1	AUGUSTUS	transcript	26472312	26474132	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	stop_codon	26472309	26472311	.	-	0	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	CDS	26472312	26472731	0.6	-	0	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	exon	26472312	26472731	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	intron	26472732	26472804	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	CDS	26472805	26472845	0.96	-	2	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	exon	26472805	26472845	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	intron	26472846	26473420	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	CDS	26473421	26473456	0.97	-	2	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	exon	26473421	26473456	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	intron	26473457	26473600	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	CDS	26473601	26473645	0.79	-	2	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	exon	26473601	26473645	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	intron	26473646	26473747	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	CDS	26473748	26473768	0.59	-	2	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	exon	26473748	26473768	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	intron	26473769	26473936	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	CDS	26473937	26474132	0.31	-	0	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	exon	26473937	26474132	.	-	.	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
Phchi.S1	AUGUSTUS	start_codon	26474130	26474132	.	-	0	transcript_id "Phchi.S1G418300.t1"; gene_id "Phchi.S1G418300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14421.t1 is derived from g12889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12735318	12741868	.	+	.	Phchi.S3G174000
Phchi.S3	AUGUSTUS	transcript	12735318	12741868	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	start_codon	12735318	12735320	.	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735318	12735351	0.96	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735318	12735351	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735352	12735539	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735540	12735614	0.61	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735540	12735614	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735615	12735727	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735728	12735765	0.47	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735728	12735765	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735766	12735870	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735871	12735926	0.37	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735871	12735926	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735927	12736022	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12736023	12736071	0.41	+	1	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12736023	12736071	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12736072	12736452	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12736453	12736494	0.74	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12736453	12736494	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12736495	12736711	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12736712	12738136	0.95	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12736712	12738136	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12738137	12738265	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12738266	12738326	1	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12738266	12738326	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12738327	12738401	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12738402	12738661	1	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12738402	12738661	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12738662	12738745	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12738746	12739226	0.66	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12738746	12739226	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739227	12739321	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12739322	12739351	0.98	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12739322	12739351	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739352	12739442	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12739443	12739564	0.98	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12739443	12739564	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739565	12739694	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12739695	12739859	1	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12739695	12739859	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739860	12740014	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12740015	12740309	1	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12740015	12740309	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12740310	12740430	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12740431	12740645	1	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12740431	12740645	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12740646	12740813	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12740814	12741119	0.99	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12740814	12741119	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12741120	12741224	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12741225	12741288	1	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12741225	12741288	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12741289	12741392	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12741393	12741632	1	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12741393	12741632	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12741633	12741731	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12741732	12741868	1	+	2	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12741732	12741868	.	+	.	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	stop_codon	12741869	12741871	.	+	0	transcript_id "Phchi.S3G174000.t1"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	transcript	12735318	12741868	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	start_codon	12735318	12735320	.	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735318	12735351	0.96	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735318	12735351	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735352	12735539	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735540	12735614	0.71	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735540	12735614	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735615	12735727	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735728	12735765	0.43	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735728	12735765	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735766	12735870	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12735871	12735926	0.32	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12735871	12735926	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12735927	12736022	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12736023	12736071	0.37	+	1	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12736023	12736071	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12736072	12736452	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12736453	12736494	0.69	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12736453	12736494	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12736495	12736645	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12736646	12738136	0.91	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12736646	12738136	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12738137	12738265	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12738266	12738326	1	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12738266	12738326	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12738327	12738401	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12738402	12738661	1	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12738402	12738661	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12738662	12738745	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12738746	12739226	0.58	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12738746	12739226	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739227	12739321	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12739322	12739351	0.97	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12739322	12739351	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739352	12739442	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12739443	12739564	0.97	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12739443	12739564	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739565	12739694	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12739695	12739859	1	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12739695	12739859	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12739860	12740014	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12740015	12740309	1	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12740015	12740309	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12740310	12740430	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12740431	12740645	1	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12740431	12740645	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12740646	12740813	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12740814	12741119	0.97	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12740814	12741119	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12741120	12741224	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12741225	12741288	1	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12741225	12741288	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12741289	12741392	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12741393	12741632	1	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12741393	12741632	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	intron	12741633	12741731	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	CDS	12741732	12741868	1	+	2	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	exon	12741732	12741868	.	+	.	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
Phchi.S3	AUGUSTUS	stop_codon	12741869	12741871	.	+	0	transcript_id "Phchi.S3G174000.t2"; gene_id "Phchi.S3G174000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12895.t1 is derived from g11360.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3028939	3031477	.	-	.	Phchi.S3G021400
Phchi.S3	AUGUSTUS	transcript	3028939	3031477	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	stop_codon	3028936	3028938	.	-	0	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3028939	3028940	0.7	-	2	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3028939	3028940	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3028941	3029076	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3029077	3030854	0.59	-	1	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3029077	3030854	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3030855	3030955	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3030956	3031152	1	-	0	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3030956	3031152	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3031153	3031226	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3031227	3031288	1	-	2	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3031227	3031288	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3031289	3031365	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3031366	3031477	0.98	-	0	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3031366	3031477	.	-	.	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	start_codon	3031475	3031477	.	-	0	transcript_id "Phchi.S3G021400.t1"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	transcript	3028939	3031477	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	stop_codon	3028936	3028938	.	-	0	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3028939	3028940	0.63	-	2	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3028939	3028940	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3028941	3029076	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3029077	3030854	0.56	-	1	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3029077	3030854	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3030855	3030955	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3030956	3031152	1	-	0	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3030956	3031152	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3031153	3031226	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3031227	3031279	0.95	-	2	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3031227	3031279	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	intron	3031280	3031365	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	CDS	3031366	3031477	0.94	-	0	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	exon	3031366	3031477	.	-	.	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
Phchi.S3	AUGUSTUS	start_codon	3031475	3031477	.	-	0	transcript_id "Phchi.S3G021400.t2"; gene_id "Phchi.S3G021400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9820.t1 is derived from g6996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43945846	43946891	.	+	.	Phchi.S1G697900
Phchi.S1	AUGUSTUS	transcript	43945846	43946891	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	start_codon	43945846	43945848	.	+	0	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	CDS	43945846	43946082	0.52	+	0	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	exon	43945846	43946082	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	intron	43946083	43946165	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	CDS	43946166	43946217	1	+	0	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	exon	43946166	43946217	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	intron	43946218	43946365	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	CDS	43946366	43946765	0.83	+	2	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	exon	43946366	43946765	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	intron	43946766	43946857	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	CDS	43946858	43946891	0.5	+	1	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	exon	43946858	43946891	.	+	.	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
Phchi.S1	AUGUSTUS	stop_codon	43946892	43946894	.	+	0	transcript_id "Phchi.S1G697900.t1"; gene_id "Phchi.S1G697900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2344.t1 is derived from g9264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6264424	6265667	.	-	.	Phchi.S5G095300
Phchi.S5	AUGUSTUS	transcript	6264424	6265667	.	-	.	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	stop_codon	6264421	6264423	.	-	0	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	CDS	6264424	6264940	0.51	-	1	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	exon	6264424	6264940	.	-	.	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	intron	6264941	6265062	.	-	.	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	CDS	6265063	6265667	0.52	-	0	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	exon	6265063	6265667	.	-	.	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
Phchi.S5	AUGUSTUS	start_codon	6265665	6265667	.	-	0	transcript_id "Phchi.S5G095300.t1"; gene_id "Phchi.S5G095300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13107.t1 is derived from g11572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4180044	4181502	.	-	.	Phchi.S3G042600
Phchi.S3	AUGUSTUS	transcript	4180044	4181502	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	stop_codon	4180041	4180043	.	-	0	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4180044	4180081	1	-	2	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4180044	4180081	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	intron	4180082	4180164	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4180165	4180248	0.98	-	2	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4180165	4180248	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	intron	4180249	4180408	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4180409	4180483	0.59	-	2	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4180409	4180483	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	intron	4180484	4180583	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4180584	4180692	1	-	0	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4180584	4180692	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	intron	4180693	4180806	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4180807	4181096	1	-	2	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4180807	4181096	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	intron	4181097	4181187	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4181188	4181337	0.85	-	2	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4181188	4181337	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	intron	4181338	4181423	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	CDS	4181424	4181502	0.64	-	0	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	exon	4181424	4181502	.	-	.	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
Phchi.S3	AUGUSTUS	start_codon	4181500	4181502	.	-	0	transcript_id "Phchi.S3G042600.t1"; gene_id "Phchi.S3G042600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg897.t1 is derived from g10679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6351354	6352970	.	-	.	Phchi.S6G085600
Phchi.S6	AUGUSTUS	transcript	6351354	6352970	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	stop_codon	6351351	6351353	.	-	0	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	CDS	6351354	6351534	0.79	-	1	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	exon	6351354	6351534	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	intron	6351535	6351611	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	CDS	6351612	6351951	0.76	-	2	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	exon	6351612	6351951	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	intron	6351952	6352031	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	CDS	6352032	6352485	0.78	-	0	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	exon	6352032	6352485	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	intron	6352486	6352934	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	CDS	6352935	6352970	0.96	-	0	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	exon	6352935	6352970	.	-	.	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
Phchi.S6	AUGUSTUS	start_codon	6352968	6352970	.	-	0	transcript_id "Phchi.S6G085600.t1"; gene_id "Phchi.S6G085600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13928.t1 is derived from g12395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9738869	9742217	.	+	.	Phchi.S3G124700
Phchi.S3	AUGUSTUS	transcript	9738869	9742217	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	start_codon	9738869	9738871	.	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9738869	9739185	0.99	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9738869	9739185	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9739186	9739258	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9739259	9739338	1	+	1	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9739259	9739338	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9739339	9739436	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9739437	9739540	1	+	2	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9739437	9739540	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9739541	9739668	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9739669	9739736	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9739669	9739736	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9739737	9739822	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9739823	9739880	1	+	1	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9739823	9739880	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9739881	9739968	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9739969	9740085	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9739969	9740085	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9740086	9740210	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9740211	9740294	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9740211	9740294	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9740295	9740419	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9740420	9740524	0.95	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9740420	9740524	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9740525	9740633	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9740634	9740747	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9740634	9740747	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9740748	9740830	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9740831	9740962	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9740831	9740962	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9740963	9741053	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9741054	9741143	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9741054	9741143	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9741144	9741242	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9741243	9741332	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9741243	9741332	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9741333	9741428	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9741429	9741638	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9741429	9741638	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9741639	9741716	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9741717	9741827	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9741717	9741827	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9741828	9741910	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9741911	9741990	1	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9741911	9741990	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	intron	9741991	9742081	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	CDS	9742082	9742217	1	+	1	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	exon	9742082	9742217	.	+	.	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
Phchi.S3	AUGUSTUS	stop_codon	9742218	9742220	.	+	0	transcript_id "Phchi.S3G124700.t1"; gene_id "Phchi.S3G124700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5402.t1 is derived from g2572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16693162	16693798	.	-	.	Phchi.S1G256100
Phchi.S1	AUGUSTUS	transcript	16693162	16693798	.	-	.	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	stop_codon	16693159	16693161	.	-	0	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	CDS	16693162	16693431	0.96	-	0	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	exon	16693162	16693431	.	-	.	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	intron	16693432	16693648	.	-	.	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	CDS	16693649	16693798	0.54	-	0	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	exon	16693649	16693798	.	-	.	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
Phchi.S1	AUGUSTUS	start_codon	16693796	16693798	.	-	0	transcript_id "Phchi.S1G256100.t1"; gene_id "Phchi.S1G256100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg13791.t1 is derived from g12258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8901823	8904798	.	-	.	Phchi.S3G111000
Phchi.S3	AUGUSTUS	transcript	8901823	8904798	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	stop_codon	8901820	8901822	.	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901823	8901829	1	-	1	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901823	8901829	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901830	8901922	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901923	8901961	1	-	1	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901923	8901961	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901962	8902128	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902129	8902208	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902129	8902208	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902209	8902323	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902324	8902503	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902324	8902503	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902504	8902636	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902637	8902750	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902637	8902750	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902751	8902845	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902846	8902965	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902846	8902965	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902966	8903059	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903060	8903153	1	-	1	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903060	8903153	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903154	8903265	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903266	8903345	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903266	8903345	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903346	8903451	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903452	8903545	1	-	1	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903452	8903545	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903546	8903629	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903630	8903704	1	-	1	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903630	8903704	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903705	8903889	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903890	8903936	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903890	8903936	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903937	8904036	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904037	8904114	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904037	8904114	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904115	8904215	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904216	8904375	1	-	1	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904216	8904375	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904376	8904595	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904596	8904798	1	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904596	8904798	.	-	.	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	start_codon	8904796	8904798	.	-	0	transcript_id "Phchi.S3G111000.t1"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	transcript	8901823	8904798	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	stop_codon	8901820	8901822	.	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901823	8901829	1	-	1	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901823	8901829	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901830	8901922	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901923	8901961	1	-	1	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901923	8901961	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901962	8902128	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902129	8902208	1	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902129	8902208	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902209	8902323	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902324	8902503	1	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902324	8902503	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902504	8902636	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902637	8902750	1	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902637	8902750	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902751	8902845	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902846	8902965	1	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902846	8902965	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902966	8903059	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903060	8903153	1	-	1	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903060	8903153	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903154	8903265	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903266	8903345	1	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903266	8903345	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903346	8903451	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903452	8903545	1	-	1	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903452	8903545	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903546	8903629	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903630	8903730	0.98	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903630	8903730	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903731	8903889	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903890	8903940	0.98	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903890	8903940	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903941	8904036	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904037	8904114	0.98	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904037	8904114	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904115	8904215	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904216	8904375	1	-	1	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904216	8904375	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904376	8904595	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904596	8904798	1	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904596	8904798	.	-	.	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	start_codon	8904796	8904798	.	-	0	transcript_id "Phchi.S3G111000.t2"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	transcript	8901823	8904798	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	stop_codon	8901820	8901822	.	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901823	8901829	0.99	-	1	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901823	8901829	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901830	8901922	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901923	8901961	0.99	-	1	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901923	8901961	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901962	8902128	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902129	8902208	0.97	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902129	8902208	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902209	8902451	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902452	8902503	0.96	-	1	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902452	8902503	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902504	8902636	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902637	8902758	1	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902637	8902758	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902759	8902845	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902846	8902965	1	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902846	8902965	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902966	8903059	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903060	8903153	1	-	1	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903060	8903153	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903154	8903265	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903266	8903345	0.98	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903266	8903345	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903346	8903451	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903452	8903545	1	-	1	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903452	8903545	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903546	8903629	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903630	8903730	0.99	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903630	8903730	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903731	8903889	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903890	8903940	0.99	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903890	8903940	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903941	8904036	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904037	8904114	0.99	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904037	8904114	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904115	8904215	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904216	8904375	0.98	-	1	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904216	8904375	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904376	8904595	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904596	8904798	1	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904596	8904798	.	-	.	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	start_codon	8904796	8904798	.	-	0	transcript_id "Phchi.S3G111000.t3"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	transcript	8901823	8904798	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	stop_codon	8901820	8901822	.	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901823	8901829	0.99	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901823	8901829	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901830	8901922	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8901923	8901961	0.99	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8901923	8901961	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8901962	8902128	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902129	8902208	1	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902129	8902208	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902209	8902323	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902324	8902503	1	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902324	8902503	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902504	8902636	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902637	8902750	1	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902637	8902750	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902751	8902845	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8902846	8902965	1	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8902846	8902965	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8902966	8903059	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903060	8903153	1	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903060	8903153	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903154	8903265	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903266	8903345	0.97	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903266	8903345	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903346	8903451	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903452	8903545	0.97	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903452	8903545	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903546	8903629	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903630	8903704	0.97	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903630	8903704	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903705	8903889	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8903890	8903940	0.97	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8903890	8903940	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8903941	8904036	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904037	8904083	0.87	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904037	8904083	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904084	8904215	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904216	8904375	0.97	-	1	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904216	8904375	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	intron	8904376	8904595	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	CDS	8904596	8904798	0.99	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	exon	8904596	8904798	.	-	.	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
Phchi.S3	AUGUSTUS	start_codon	8904796	8904798	.	-	0	transcript_id "Phchi.S3G111000.t4"; gene_id "Phchi.S3G111000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5229.t1 is derived from g2399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15740538	15740855	.	-	.	Phchi.S1G238800
Phchi.S1	AUGUSTUS	transcript	15740538	15740855	.	-	.	transcript_id "Phchi.S1G238800.t1"; gene_id "Phchi.S1G238800"
Phchi.S1	AUGUSTUS	stop_codon	15740535	15740537	.	-	0	transcript_id "Phchi.S1G238800.t1"; gene_id "Phchi.S1G238800"
Phchi.S1	AUGUSTUS	CDS	15740538	15740855	0.59	-	0	transcript_id "Phchi.S1G238800.t1"; gene_id "Phchi.S1G238800"
Phchi.S1	AUGUSTUS	exon	15740538	15740855	.	-	.	transcript_id "Phchi.S1G238800.t1"; gene_id "Phchi.S1G238800"
Phchi.S1	AUGUSTUS	start_codon	15740853	15740855	.	-	0	transcript_id "Phchi.S1G238800.t1"; gene_id "Phchi.S1G238800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12941.t1 is derived from g11406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3257032	3257631	.	-	.	Phchi.S3G026000
Phchi.S3	AUGUSTUS	transcript	3257032	3257631	.	-	.	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	stop_codon	3257029	3257031	.	-	0	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	CDS	3257032	3257234	0.57	-	2	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	exon	3257032	3257234	.	-	.	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	intron	3257235	3257394	.	-	.	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	CDS	3257395	3257419	0.57	-	0	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	exon	3257395	3257419	.	-	.	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	intron	3257420	3257568	.	-	.	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	CDS	3257569	3257631	0.89	-	0	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	exon	3257569	3257631	.	-	.	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
Phchi.S3	AUGUSTUS	start_codon	3257629	3257631	.	-	0	transcript_id "Phchi.S3G026000.t1"; gene_id "Phchi.S3G026000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2092.t1 is derived from g9012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4838148	4838779	.	+	.	Phchi.S5G070100
Phchi.S5	AUGUSTUS	transcript	4838148	4838779	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	start_codon	4838148	4838150	.	+	0	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	CDS	4838148	4838221	0.99	+	0	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	exon	4838148	4838221	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	intron	4838222	4838308	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	CDS	4838309	4838395	1	+	1	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	exon	4838309	4838395	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	intron	4838396	4838537	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	CDS	4838538	4838617	1	+	1	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	exon	4838538	4838617	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	intron	4838618	4838759	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	CDS	4838760	4838779	1	+	2	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	exon	4838760	4838779	.	+	.	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
Phchi.S5	AUGUSTUS	stop_codon	4838780	4838782	.	+	0	transcript_id "Phchi.S5G070100.t1"; gene_id "Phchi.S5G070100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1107.t1 is derived from g10890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7655613	7657582	.	-	.	Phchi.S6G106600
Phchi.S6	AUGUSTUS	transcript	7655613	7657582	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	stop_codon	7655610	7655612	.	-	0	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	CDS	7655613	7655726	0.88	-	0	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	exon	7655613	7655726	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	intron	7655727	7655817	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	CDS	7655818	7655915	1	-	2	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	exon	7655818	7655915	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	intron	7655916	7656014	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	CDS	7656015	7656051	1	-	0	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	exon	7656015	7656051	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	intron	7656052	7656142	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	CDS	7656143	7657400	0.57	-	1	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	exon	7656143	7657400	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	intron	7657401	7657535	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	CDS	7657536	7657582	0.38	-	0	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	exon	7657536	7657582	.	-	.	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
Phchi.S6	AUGUSTUS	start_codon	7657580	7657582	.	-	0	transcript_id "Phchi.S6G106600.t1"; gene_id "Phchi.S6G106600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6110.t1 is derived from g3281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20982314	20983985	.	+	.	Phchi.S1G326900
Phchi.S1	AUGUSTUS	transcript	20982314	20983985	.	+	.	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	start_codon	20982314	20982316	.	+	0	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	CDS	20982314	20982519	0.97	+	0	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	exon	20982314	20982519	.	+	.	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	intron	20982520	20983891	.	+	.	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	CDS	20983892	20983985	0.01	+	1	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	exon	20983892	20983985	.	+	.	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
Phchi.S1	AUGUSTUS	stop_codon	20983986	20983988	.	+	0	transcript_id "Phchi.S1G326900.t1"; gene_id "Phchi.S1G326900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4368.t1 is derived from g1537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10097183	10099070	.	-	.	Phchi.S1G152700
Phchi.S1	AUGUSTUS	transcript	10097183	10099070	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	stop_codon	10097180	10097182	.	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10097183	10097482	0.17	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10097183	10097482	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	intron	10097483	10097621	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10097622	10097957	0.17	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10097622	10097957	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	intron	10097958	10098122	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10098123	10098170	0.29	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10098123	10098170	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	intron	10098171	10098252	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10098253	10098330	0.93	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10098253	10098330	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	intron	10098331	10098410	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10098411	10098497	0.99	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10098411	10098497	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	intron	10098498	10098599	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10098600	10098776	0.51	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10098600	10098776	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	intron	10098777	10098965	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	CDS	10098966	10099070	0.66	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	exon	10098966	10099070	.	-	.	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
Phchi.S1	AUGUSTUS	start_codon	10099068	10099070	.	-	0	transcript_id "Phchi.S1G152700.t1"; gene_id "Phchi.S1G152700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4012.t1 is derived from g1181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7145792	7152634	.	+	.	Phchi.S1G117100
Phchi.S1	AUGUSTUS	transcript	7145792	7152634	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	start_codon	7145792	7145794	.	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7145792	7146031	0.81	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7145792	7146031	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7146032	7146724	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7146725	7146921	1	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7146725	7146921	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7146922	7147119	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7147120	7147273	1	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7147120	7147273	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7147274	7147455	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7147456	7147565	1	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7147456	7147565	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7147566	7147900	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7147901	7147970	1	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7147901	7147970	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7147971	7148100	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148101	7148183	1	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148101	7148183	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148184	7148321	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148322	7148400	1	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148322	7148400	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148401	7148524	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148525	7148565	1	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148525	7148565	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148566	7148812	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148813	7148935	1	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148813	7148935	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148936	7149027	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149028	7149166	1	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149028	7149166	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149167	7149264	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149265	7149379	1	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149265	7149379	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149380	7149640	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149641	7149723	1	+	2	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149641	7149723	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149724	7149910	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149911	7149985	0.98	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149911	7149985	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149986	7150097	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7150098	7150172	1	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7150098	7150172	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7150173	7150417	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7150418	7151295	0.6	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7150418	7151295	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7151296	7151457	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7151458	7151787	1	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7151458	7151787	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7151788	7151866	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7151867	7152342	0.94	+	1	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7151867	7152342	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7152343	7152554	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7152555	7152634	0.94	+	2	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7152555	7152634	.	+	.	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	stop_codon	7152635	7152637	.	+	0	transcript_id "Phchi.S1G117100.t1"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	transcript	7145792	7152634	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	start_codon	7145792	7145794	.	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7145792	7146031	0.8	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7145792	7146031	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7146032	7146724	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7146725	7146921	1	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7146725	7146921	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7146922	7147119	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7147120	7147273	1	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7147120	7147273	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7147274	7147455	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7147456	7147565	1	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7147456	7147565	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7147566	7147900	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7147901	7147970	1	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7147901	7147970	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7147971	7148100	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148101	7148183	1	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148101	7148183	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148184	7148327	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148328	7148400	1	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148328	7148400	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148401	7148524	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148525	7148565	1	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148525	7148565	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148566	7148812	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7148813	7148935	1	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7148813	7148935	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7148936	7149027	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149028	7149166	1	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149028	7149166	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149167	7149264	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149265	7149379	1	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149265	7149379	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149380	7149640	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149641	7149723	1	+	2	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149641	7149723	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149724	7149910	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7149911	7149985	0.99	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7149911	7149985	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7149986	7150097	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7150098	7150172	1	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7150098	7150172	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7150173	7150417	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7150418	7151295	0.5	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7150418	7151295	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7151296	7151457	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7151458	7151787	1	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7151458	7151787	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7151788	7151866	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7151867	7152342	0.89	+	1	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7151867	7152342	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	intron	7152343	7152554	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	CDS	7152555	7152634	0.89	+	2	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	exon	7152555	7152634	.	+	.	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
Phchi.S1	AUGUSTUS	stop_codon	7152635	7152637	.	+	0	transcript_id "Phchi.S1G117100.t2"; gene_id "Phchi.S1G117100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7859.t1 is derived from g5033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31568223	31569248	.	-	.	Phchi.S1G501800
Phchi.S1	AUGUSTUS	transcript	31568223	31569248	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	stop_codon	31568220	31568222	.	-	0	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31568223	31568283	1	-	1	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31568223	31568283	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	intron	31568284	31568404	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31568405	31568449	1	-	1	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31568405	31568449	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	intron	31568450	31568528	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31568529	31568577	1	-	2	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31568529	31568577	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	intron	31568578	31568654	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31568655	31568721	1	-	0	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31568655	31568721	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	intron	31568722	31568812	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31568813	31568911	1	-	0	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31568813	31568911	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	intron	31568912	31568989	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31568990	31569100	0.84	-	0	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31568990	31569100	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	intron	31569101	31569200	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	CDS	31569201	31569248	0.83	-	0	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	exon	31569201	31569248	.	-	.	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
Phchi.S1	AUGUSTUS	start_codon	31569246	31569248	.	-	0	transcript_id "Phchi.S1G501800.t1"; gene_id "Phchi.S1G501800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8024.t1 is derived from g5199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32543269	32545112	.	-	.	Phchi.S1G518300
Phchi.S1	AUGUSTUS	transcript	32543269	32545112	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	stop_codon	32543266	32543268	.	-	0	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	CDS	32543269	32543455	1	-	1	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	exon	32543269	32543455	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	intron	32543456	32543531	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	CDS	32543532	32543658	1	-	2	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	exon	32543532	32543658	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	intron	32543659	32543748	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	CDS	32543749	32543899	1	-	0	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	exon	32543749	32543899	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	intron	32543900	32544055	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	CDS	32544056	32544304	1	-	0	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	exon	32544056	32544304	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	intron	32544305	32544400	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	CDS	32544401	32544806	0.66	-	1	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	exon	32544401	32544806	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	intron	32544807	32545095	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	CDS	32545096	32545112	0.64	-	0	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	exon	32545096	32545112	.	-	.	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
Phchi.S1	AUGUSTUS	start_codon	32545110	32545112	.	-	0	transcript_id "Phchi.S1G518300.t1"; gene_id "Phchi.S1G518300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8755.t1 is derived from g5930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37830027	37832190	.	+	.	Phchi.S1G591400
Phchi.S1	AUGUSTUS	transcript	37830027	37832190	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	start_codon	37830027	37830029	.	+	0	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	CDS	37830027	37830425	0.67	+	0	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	exon	37830027	37830425	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	intron	37830426	37830672	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	CDS	37830673	37830912	0.7	+	0	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	exon	37830673	37830912	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	intron	37830913	37831012	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	CDS	37831013	37831405	0.48	+	0	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	exon	37831013	37831405	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	intron	37831406	37831528	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	CDS	37831529	37831733	0.96	+	0	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	exon	37831529	37831733	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	intron	37831734	37831846	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	CDS	37831847	37832190	1	+	2	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	exon	37831847	37832190	.	+	.	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
Phchi.S1	AUGUSTUS	stop_codon	37832191	37832193	.	+	0	transcript_id "Phchi.S1G591400.t1"; gene_id "Phchi.S1G591400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6131.t1 is derived from g3302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21080135	21081721	.	+	.	Phchi.S1G329000
Phchi.S1	AUGUSTUS	transcript	21080135	21081721	.	+	.	transcript_id "Phchi.S1G329000.t1"; gene_id "Phchi.S1G329000"
Phchi.S1	AUGUSTUS	start_codon	21080135	21080137	.	+	0	transcript_id "Phchi.S1G329000.t1"; gene_id "Phchi.S1G329000"
Phchi.S1	AUGUSTUS	CDS	21080135	21081721	1	+	0	transcript_id "Phchi.S1G329000.t1"; gene_id "Phchi.S1G329000"
Phchi.S1	AUGUSTUS	exon	21080135	21081721	.	+	.	transcript_id "Phchi.S1G329000.t1"; gene_id "Phchi.S1G329000"
Phchi.S1	AUGUSTUS	stop_codon	21081722	21081724	.	+	0	transcript_id "Phchi.S1G329000.t1"; gene_id "Phchi.S1G329000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3012.t1 is derived from g181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1121430	1124156	.	+	.	Phchi.S1G017100
Phchi.S1	AUGUSTUS	transcript	1121430	1124156	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	start_codon	1121430	1121432	.	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1121430	1121519	0.99	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1121430	1121519	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1121520	1121606	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1121607	1121653	1	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1121607	1121653	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1121654	1121808	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1121809	1121865	1	+	1	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1121809	1121865	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1121866	1121950	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1121951	1122023	1	+	1	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1121951	1122023	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1122024	1122116	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1122117	1122172	1	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1122117	1122172	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1122173	1122270	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1122271	1122465	0.97	+	1	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1122271	1122465	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1122466	1122630	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1122631	1122758	0.93	+	1	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1122631	1122758	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1122759	1122840	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1122841	1122929	0.93	+	2	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1122841	1122929	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1122930	1123051	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1123052	1123200	0.96	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1123052	1123200	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1123201	1123331	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1123332	1123582	0.98	+	1	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1123332	1123582	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1123583	1123673	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1123674	1123828	1	+	2	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1123674	1123828	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	intron	1123829	1123919	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	CDS	1123920	1124156	1	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	exon	1123920	1124156	.	+	.	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
Phchi.S1	AUGUSTUS	stop_codon	1124157	1124159	.	+	0	transcript_id "Phchi.S1G017100.t1"; gene_id "Phchi.S1G017100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6655.t1 is derived from g3827.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24324428	24326098	.	+	.	Phchi.S1G381400
Phchi.S1	AUGUSTUS	transcript	24324428	24326098	.	+	.	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	start_codon	24324428	24324430	.	+	0	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	CDS	24324428	24325018	0.9	+	0	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	exon	24324428	24325018	.	+	.	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	intron	24325019	24325159	.	+	.	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	CDS	24325160	24326098	1	+	0	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	exon	24325160	24326098	.	+	.	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	stop_codon	24326099	24326101	.	+	0	transcript_id "Phchi.S1G381400.t1"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	transcript	24325196	24326098	.	+	.	transcript_id "Phchi.S1G381400.t2"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	start_codon	24325196	24325198	.	+	0	transcript_id "Phchi.S1G381400.t2"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	CDS	24325196	24326098	1	+	0	transcript_id "Phchi.S1G381400.t2"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	exon	24325196	24326098	.	+	.	transcript_id "Phchi.S1G381400.t2"; gene_id "Phchi.S1G381400"
Phchi.S1	AUGUSTUS	stop_codon	24326099	24326101	.	+	0	transcript_id "Phchi.S1G381400.t2"; gene_id "Phchi.S1G381400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13102.t1 is derived from g11567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4139358	4144152	.	-	.	Phchi.S3G042100
Phchi.S3	AUGUSTUS	transcript	4139358	4144152	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	stop_codon	4139355	4139357	.	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4139358	4139983	0.68	-	2	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4139358	4139983	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4139984	4140057	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4140058	4140131	0.68	-	1	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4140058	4140131	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4140132	4140299	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4140300	4140489	0.85	-	2	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4140300	4140489	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4140490	4140600	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4140601	4140730	0.77	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4140601	4140730	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4140731	4140907	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4140908	4141118	1	-	1	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4140908	4141118	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4141119	4141239	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4141240	4141349	1	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4141240	4141349	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4141350	4141442	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4141443	4142467	0.71	-	2	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4141443	4142467	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4142468	4142598	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4142599	4143009	0.46	-	2	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4142599	4143009	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4143010	4143242	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4143243	4143564	0.94	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4143243	4143564	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4143565	4143667	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4143668	4143877	0.98	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4143668	4143877	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	intron	4143878	4143993	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	CDS	4143994	4144152	0.43	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	exon	4143994	4144152	.	-	.	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
Phchi.S3	AUGUSTUS	start_codon	4144150	4144152	.	-	0	transcript_id "Phchi.S3G042100.t1"; gene_id "Phchi.S3G042100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6701.t1 is derived from g3873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24596703	24598116	.	+	.	Phchi.S1G386000
Phchi.S1	AUGUSTUS	transcript	24596703	24598116	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	start_codon	24596703	24596705	.	+	0	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	CDS	24596703	24596793	0.88	+	0	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	exon	24596703	24596793	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	intron	24596794	24596881	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	CDS	24596882	24597059	1	+	2	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	exon	24596882	24597059	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	intron	24597060	24597141	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	CDS	24597142	24597223	1	+	1	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	exon	24597142	24597223	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	intron	24597224	24597385	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	CDS	24597386	24597562	1	+	0	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	exon	24597386	24597562	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	intron	24597563	24597672	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	CDS	24597673	24597840	0.97	+	0	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	exon	24597673	24597840	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	intron	24597841	24597927	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	CDS	24597928	24598116	0.95	+	0	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	exon	24597928	24598116	.	+	.	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
Phchi.S1	AUGUSTUS	stop_codon	24598117	24598119	.	+	0	transcript_id "Phchi.S1G386000.t1"; gene_id "Phchi.S1G386000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9247.t1 is derived from g6422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40577679	40581125	.	-	.	Phchi.S1G640600
Phchi.S1	AUGUSTUS	transcript	40577679	40581125	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	stop_codon	40577676	40577678	.	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40577679	40577771	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40577679	40577771	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40577772	40577853	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40577854	40577969	1	-	2	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40577854	40577969	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40577970	40578043	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40578044	40578122	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40578044	40578122	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40578123	40578225	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40578226	40578316	0.87	-	1	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40578226	40578316	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40578317	40578400	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40578401	40578479	1	-	2	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40578401	40578479	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40578480	40578551	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40578552	40578639	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40578552	40578639	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40578640	40578721	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40578722	40578805	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40578722	40578805	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40578806	40578886	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40578887	40578934	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40578887	40578934	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40578935	40579013	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40579014	40579088	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40579014	40579088	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40579089	40579260	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40579261	40579337	1	-	2	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40579261	40579337	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40579338	40579479	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40579480	40579568	1	-	1	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40579480	40579568	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40579569	40579693	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40579694	40579732	1	-	1	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40579694	40579732	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40579733	40579811	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40579812	40579885	1	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40579812	40579885	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40579886	40579991	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40579992	40580084	0.97	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40579992	40580084	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40580085	40580163	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40580164	40580261	1	-	2	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40580164	40580261	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40580262	40580362	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40580363	40580435	0.95	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40580363	40580435	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40580436	40580550	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40580551	40580632	1	-	1	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40580551	40580632	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40580633	40580780	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40580781	40580885	1	-	1	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40580781	40580885	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	intron	40580886	40581111	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	CDS	40581112	40581125	0.99	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	exon	40581112	40581125	.	-	.	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
Phchi.S1	AUGUSTUS	start_codon	40581123	40581125	.	-	0	transcript_id "Phchi.S1G640600.t1"; gene_id "Phchi.S1G640600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1405.t1 is derived from g8324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	153613	155143	.	-	.	Phchi.S5G001400
Phchi.S5	AUGUSTUS	transcript	153613	155143	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	stop_codon	153610	153612	.	-	0	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	CDS	153613	153781	1	-	1	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	exon	153613	153781	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	intron	153782	153869	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	CDS	153870	154033	1	-	0	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	exon	153870	154033	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	intron	154034	154111	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	CDS	154112	154248	1	-	2	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	exon	154112	154248	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	intron	154249	154348	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	CDS	154349	154484	1	-	0	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	exon	154349	154484	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	intron	154485	154564	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	CDS	154565	154776	1	-	2	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	exon	154565	154776	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	intron	154777	154923	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	CDS	154924	155143	0.97	-	0	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	exon	154924	155143	.	-	.	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
Phchi.S5	AUGUSTUS	start_codon	155141	155143	.	-	0	transcript_id "Phchi.S5G001400.t1"; gene_id "Phchi.S5G001400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15067.t1 is derived from g13535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16854936	16861758	.	-	.	Phchi.S3G238600
Phchi.S3	AUGUSTUS	transcript	16854936	16861758	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	stop_codon	16854933	16854935	.	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16854936	16855202	0.8	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16854936	16855202	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16855203	16855320	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16855321	16855575	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16855321	16855575	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16855576	16855709	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16855710	16855881	1	-	1	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16855710	16855881	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16855882	16855989	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16855990	16856217	1	-	1	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16855990	16856217	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16856218	16856301	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16856302	16856435	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16856302	16856435	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16856436	16856549	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16856550	16856633	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16856550	16856633	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16856634	16856721	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16856722	16857012	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16856722	16857012	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16857013	16857108	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16857109	16857441	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16857109	16857441	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16857442	16857535	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16857536	16857696	1	-	2	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16857536	16857696	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16857697	16857842	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16857843	16858046	1	-	2	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16857843	16858046	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16858047	16858136	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16858137	16858296	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16858137	16858296	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16858297	16858384	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16858385	16858488	1	-	2	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16858385	16858488	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16858489	16858583	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16858584	16858744	1	-	1	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16858584	16858744	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16858745	16858886	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16858887	16859203	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16858887	16859203	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16859204	16859292	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16859293	16859574	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16859293	16859574	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16859575	16859657	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16859658	16859959	1	-	2	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16859658	16859959	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16859960	16860100	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16860101	16860191	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16860101	16860191	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16860192	16860276	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16860277	16860330	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16860277	16860330	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16860331	16860412	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16860413	16860489	1	-	2	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16860413	16860489	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16860490	16860606	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16860607	16860766	1	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16860607	16860766	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16860767	16860842	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16860843	16860927	1	-	1	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16860843	16860927	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16860928	16861014	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16861015	16861103	0.99	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16861015	16861103	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16861104	16861275	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16861276	16861336	0.99	-	1	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16861276	16861336	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	intron	16861337	16861426	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	CDS	16861427	16861758	0.93	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	exon	16861427	16861758	.	-	.	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
Phchi.S3	AUGUSTUS	start_codon	16861756	16861758	.	-	0	transcript_id "Phchi.S3G238600.t1"; gene_id "Phchi.S3G238600"
# This transcript jg12143.t2 is derived from g7819.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12144.t1 is derived from g7820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4841203	4843827	.	+	.	Phchi.S2G022400
Phchi.S2	AUGUSTUS	transcript	4841203	4843827	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	start_codon	4841203	4841205	.	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4841203	4841218	0.98	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4841203	4841218	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4841219	4841893	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4841894	4842054	1	+	2	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4841894	4842054	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4842055	4842304	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4842305	4842514	1	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4842305	4842514	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4842515	4842649	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4842650	4842798	1	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4842650	4842798	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4842799	4842928	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4842929	4843112	1	+	1	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4842929	4843112	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4843113	4843196	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4843197	4843289	1	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4843197	4843289	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4843290	4843379	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4843380	4843519	1	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4843380	4843519	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4843520	4843608	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4843609	4843704	1	+	1	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4843609	4843704	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	intron	4843705	4843826	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	CDS	4843827	4843827	1	+	1	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	exon	4843827	4843827	.	+	.	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
Phchi.S2	AUGUSTUS	stop_codon	4843828	4843830	.	+	0	transcript_id "Phchi.S2G022400.t1"; gene_id "Phchi.S2G022400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14090.t1 is derived from g12557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10798434	10799913	.	+	.	Phchi.S3G140900
Phchi.S3	AUGUSTUS	transcript	10798434	10799913	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	start_codon	10798434	10798436	.	+	0	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	CDS	10798434	10798441	1	+	0	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	exon	10798434	10798441	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	intron	10798442	10798620	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	CDS	10798621	10798663	0.81	+	1	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	exon	10798621	10798663	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	intron	10798664	10798774	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	CDS	10798775	10798816	1	+	0	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	exon	10798775	10798816	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	intron	10798817	10798904	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	CDS	10798905	10799187	0.91	+	0	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	exon	10798905	10799187	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	intron	10799188	10799350	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	CDS	10799351	10799913	0.92	+	2	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	exon	10799351	10799913	.	+	.	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
Phchi.S3	AUGUSTUS	stop_codon	10799914	10799916	.	+	0	transcript_id "Phchi.S3G140900.t1"; gene_id "Phchi.S3G140900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6899.t1 is derived from g4071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25896116	25897137	.	+	.	Phchi.S1G405800
Phchi.S1	AUGUSTUS	transcript	25896116	25897137	.	+	.	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	start_codon	25896116	25896118	.	+	0	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	CDS	25896116	25896443	0.81	+	0	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	exon	25896116	25896443	.	+	.	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	intron	25896444	25896532	.	+	.	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	CDS	25896533	25897137	0.83	+	2	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	exon	25896533	25897137	.	+	.	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
Phchi.S1	AUGUSTUS	stop_codon	25897138	25897140	.	+	0	transcript_id "Phchi.S1G405800.t1"; gene_id "Phchi.S1G405800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11297.t1 is derived from g15347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5287887	5289067	.	-	.	Phchi.S4G087900
Phchi.S4	AUGUSTUS	transcript	5287887	5289067	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	stop_codon	5287884	5287886	.	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5287887	5287958	1	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5287887	5287958	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	intron	5287959	5288036	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5288037	5288096	1	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5288037	5288096	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	intron	5288097	5288194	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5288195	5288344	1	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5288195	5288344	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	intron	5288345	5288434	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5288435	5288521	1	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5288435	5288521	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	intron	5288522	5288617	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5288618	5288688	1	-	2	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5288618	5288688	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	intron	5288689	5288784	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5288785	5288975	1	-	1	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5288785	5288975	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	intron	5288976	5289047	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	CDS	5289048	5289067	1	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	exon	5289048	5289067	.	-	.	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
Phchi.S4	AUGUSTUS	start_codon	5289065	5289067	.	-	0	transcript_id "Phchi.S4G087900.t1"; gene_id "Phchi.S4G087900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8589.t1 is derived from g5764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36778366	36778993	.	-	.	Phchi.S1G574800
Phchi.S1	AUGUSTUS	transcript	36778366	36778993	.	-	.	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	stop_codon	36778363	36778365	.	-	0	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	CDS	36778366	36778697	0.92	-	2	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	exon	36778366	36778697	.	-	.	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	intron	36778698	36778911	.	-	.	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	CDS	36778912	36778993	0.94	-	0	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	exon	36778912	36778993	.	-	.	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
Phchi.S1	AUGUSTUS	start_codon	36778991	36778993	.	-	0	transcript_id "Phchi.S1G574800.t1"; gene_id "Phchi.S1G574800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2923.t1 is derived from g92.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	578963	580520	.	-	.	Phchi.S1G008200
Phchi.S1	AUGUSTUS	transcript	578963	580520	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	stop_codon	578960	578962	.	-	0	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	578963	579044	1	-	1	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	578963	579044	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	intron	579045	579187	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	579188	579307	1	-	1	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	579188	579307	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	intron	579308	579489	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	579490	579721	1	-	2	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	579490	579721	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	intron	579722	579820	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	579821	580016	1	-	0	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	579821	580016	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	intron	580017	580116	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	580117	580229	1	-	2	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	580117	580229	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	intron	580230	580326	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	580327	580407	1	-	2	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	580327	580407	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	intron	580408	580489	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	CDS	580490	580520	1	-	0	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	exon	580490	580520	.	-	.	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
Phchi.S1	AUGUSTUS	start_codon	580518	580520	.	-	0	transcript_id "Phchi.S1G008200.t1"; gene_id "Phchi.S1G008200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8732.t1 is derived from g5907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37710962	37712481	.	-	.	Phchi.S1G589100
Phchi.S1	AUGUSTUS	transcript	37710962	37712481	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	stop_codon	37710959	37710961	.	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37710962	37711120	0.99	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37710962	37711120	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	intron	37711121	37711236	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37711237	37711443	0.86	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37711237	37711443	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	intron	37711444	37711545	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37711546	37711641	0.91	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37711546	37711641	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	intron	37711642	37711771	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37711772	37711849	1	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37711772	37711849	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	intron	37711850	37711941	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37711942	37712094	1	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37711942	37712094	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	intron	37712095	37712190	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37712191	37712305	0.91	-	1	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37712191	37712305	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	intron	37712306	37712380	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	CDS	37712381	37712481	0.19	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	exon	37712381	37712481	.	-	.	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
Phchi.S1	AUGUSTUS	start_codon	37712479	37712481	.	-	0	transcript_id "Phchi.S1G589100.t1"; gene_id "Phchi.S1G589100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1552.t1 is derived from g8471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1719649	1720692	.	-	.	Phchi.S5G016100
Phchi.S5	AUGUSTUS	transcript	1719649	1720692	.	-	.	transcript_id "Phchi.S5G016100.t1"; gene_id "Phchi.S5G016100"
Phchi.S5	AUGUSTUS	stop_codon	1719646	1719648	.	-	0	transcript_id "Phchi.S5G016100.t1"; gene_id "Phchi.S5G016100"
Phchi.S5	AUGUSTUS	CDS	1719649	1720692	0.9	-	0	transcript_id "Phchi.S5G016100.t1"; gene_id "Phchi.S5G016100"
Phchi.S5	AUGUSTUS	exon	1719649	1720692	.	-	.	transcript_id "Phchi.S5G016100.t1"; gene_id "Phchi.S5G016100"
Phchi.S5	AUGUSTUS	start_codon	1720690	1720692	.	-	0	transcript_id "Phchi.S5G016100.t1"; gene_id "Phchi.S5G016100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg705.t1 is derived from g10487.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4981007	4983422	.	-	.	Phchi.S6G066400
Phchi.S6	AUGUSTUS	transcript	4981007	4981697	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	stop_codon	4981004	4981006	.	-	0	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981007	4981133	1	-	1	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981007	4981133	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981134	4981214	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981215	4981311	1	-	2	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981215	4981311	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981312	4981411	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981412	4981493	1	-	0	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981412	4981493	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981494	4981583	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981584	4981697	0.96	-	0	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981584	4981697	.	-	.	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	start_codon	4981695	4981697	.	-	0	transcript_id "Phchi.S6G066400.t1"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	transcript	4982205	4983422	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	stop_codon	4982202	4982204	.	-	0	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982205	4982236	0.96	-	2	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982205	4982236	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4982237	4982371	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982372	4982467	1	-	2	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982372	4982467	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4982468	4982821	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982822	4983002	0.99	-	0	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982822	4983002	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4983003	4983118	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4983119	4983248	1	-	1	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4983119	4983248	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4983249	4983351	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4983352	4983422	1	-	0	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4983352	4983422	.	-	.	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	start_codon	4983420	4983422	.	-	0	transcript_id "Phchi.S6G066400.t2"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	transcript	4981007	4983422	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	stop_codon	4981004	4981006	.	-	0	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981007	4981133	1	-	1	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981007	4981133	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981134	4981214	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981215	4981311	1	-	2	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981215	4981311	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981312	4981411	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981412	4981493	1	-	0	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981412	4981493	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981494	4981583	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981584	4981709	1	-	0	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981584	4981709	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4981710	4981783	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4981784	4982001	1	-	2	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4981784	4982001	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4982002	4982086	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982087	4982101	1	-	2	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982087	4982101	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4982102	4982224	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982225	4982236	0.9	-	2	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982225	4982236	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4982237	4982371	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982372	4982467	0.99	-	2	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982372	4982467	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4982468	4982821	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4982822	4983002	0.99	-	0	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4982822	4983002	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4983003	4983118	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4983119	4983248	0.99	-	1	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4983119	4983248	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	intron	4983249	4983351	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	CDS	4983352	4983422	0.99	-	0	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	exon	4983352	4983422	.	-	.	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
Phchi.S6	AUGUSTUS	start_codon	4983420	4983422	.	-	0	transcript_id "Phchi.S6G066400.t3"; gene_id "Phchi.S6G066400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13237.t1 is derived from g11702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4860896	4862360	.	-	.	Phchi.S3G055600
Phchi.S3	AUGUSTUS	transcript	4860896	4862360	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	stop_codon	4860893	4860895	.	-	0	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	CDS	4860896	4860928	0.73	-	0	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	exon	4860896	4860928	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	intron	4860929	4861064	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	CDS	4861065	4861100	0.73	-	0	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	exon	4861065	4861100	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	intron	4861101	4861271	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	CDS	4861272	4862029	0.85	-	2	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	exon	4861272	4862029	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	intron	4862030	4862155	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	CDS	4862156	4862360	0.82	-	0	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	exon	4862156	4862360	.	-	.	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
Phchi.S3	AUGUSTUS	start_codon	4862358	4862360	.	-	0	transcript_id "Phchi.S3G055600.t1"; gene_id "Phchi.S3G055600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7451.t1 is derived from g4623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29275738	29277903	.	-	.	Phchi.S1G461000
Phchi.S1	AUGUSTUS	transcript	29275738	29277903	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	stop_codon	29275735	29275737	.	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29275738	29275777	0.99	-	1	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29275738	29275777	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29275778	29275954	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29275955	29275990	0.98	-	1	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29275955	29275990	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29275991	29276083	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29276084	29276169	0.91	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29276084	29276169	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29276170	29276272	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29276273	29276412	0.99	-	2	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29276273	29276412	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29276413	29276501	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29276502	29276575	0.93	-	1	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29276502	29276575	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29276576	29276801	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29276802	29276851	0.86	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29276802	29276851	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29276852	29276959	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29276960	29277157	1	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29276960	29277157	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29277158	29277276	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29277277	29277375	1	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29277277	29277375	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29277376	29277466	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29277467	29277650	1	-	1	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29277467	29277650	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	intron	29277651	29277739	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	CDS	29277740	29277903	1	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	exon	29277740	29277903	.	-	.	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
Phchi.S1	AUGUSTUS	start_codon	29277901	29277903	.	-	0	transcript_id "Phchi.S1G461000.t1"; gene_id "Phchi.S1G461000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2732.t1 is derived from g9652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8486770	8487894	.	+	.	Phchi.S5G134100
Phchi.S5	AUGUSTUS	transcript	8486770	8487894	.	+	.	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	start_codon	8486770	8486772	.	+	0	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	CDS	8486770	8487246	1	+	0	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	exon	8486770	8487246	.	+	.	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	intron	8487247	8487348	.	+	.	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	CDS	8487349	8487894	0.96	+	0	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	exon	8487349	8487894	.	+	.	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
Phchi.S5	AUGUSTUS	stop_codon	8487895	8487897	.	+	0	transcript_id "Phchi.S5G134100.t1"; gene_id "Phchi.S5G134100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg719.t1 is derived from g10501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5088958	5092552	.	+	.	Phchi.S6G067800
Phchi.S6	AUGUSTUS	transcript	5088958	5092552	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	start_codon	5088958	5088960	.	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5088958	5089012	0.28	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5088958	5089012	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5089013	5089161	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5089162	5089202	0.27	+	2	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5089162	5089202	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5089203	5089301	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5089302	5089508	1	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5089302	5089508	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5089509	5089589	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5089590	5089823	0.99	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5089590	5089823	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5089824	5089982	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5089983	5090157	0.36	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5089983	5090157	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5090158	5090231	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5090232	5091244	0.82	+	2	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5090232	5091244	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5091245	5091393	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5091394	5091510	0.62	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5091394	5091510	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5091511	5091608	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5091609	5091890	0.95	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5091609	5091890	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5091891	5091997	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5091998	5092219	0.88	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5091998	5092219	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	intron	5092220	5092543	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	CDS	5092544	5092552	0.27	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	exon	5092544	5092552	.	+	.	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
Phchi.S6	AUGUSTUS	stop_codon	5092553	5092555	.	+	0	transcript_id "Phchi.S6G067800.t1"; gene_id "Phchi.S6G067800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1950.t1 is derived from g8870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3961482	3964236	.	+	.	Phchi.S5G055900
Phchi.S5	AUGUSTUS	transcript	3961482	3964236	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	start_codon	3961482	3961484	.	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3961482	3962198	0.88	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3961482	3962198	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3962199	3962403	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3962404	3962586	1	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3962404	3962586	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3962587	3962728	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3962729	3962820	1	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3962729	3962820	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3962821	3962962	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3962963	3963022	1	+	1	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3962963	3963022	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3963023	3963211	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3963212	3963281	0.97	+	1	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3963212	3963281	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3963282	3963394	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3963395	3963598	1	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3963395	3963598	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3963599	3963679	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3963680	3964037	1	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3963680	3964037	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3964038	3964174	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3964175	3964236	0.99	+	2	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3964175	3964236	.	+	.	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	stop_codon	3964237	3964239	.	+	0	transcript_id "Phchi.S5G055900.t1"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	transcript	3961482	3963395	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	start_codon	3961482	3961484	.	+	0	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3961482	3962198	0.83	+	0	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3961482	3962198	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3962199	3962403	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3962404	3962586	1	+	0	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3962404	3962586	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3962587	3962728	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3962729	3962820	1	+	0	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3962729	3962820	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3962821	3962962	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3962963	3963022	0.99	+	1	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3962963	3963022	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	intron	3963023	3963394	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	CDS	3963395	3963395	0.94	+	1	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	exon	3963395	3963395	.	+	.	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
Phchi.S5	AUGUSTUS	stop_codon	3963396	3963398	.	+	0	transcript_id "Phchi.S5G055900.t2"; gene_id "Phchi.S5G055900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11908.t1 is derived from g15960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9249387	9255065	.	+	.	Phchi.S4G149000
Phchi.S4	AUGUSTUS	transcript	9249387	9255065	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	start_codon	9249387	9249389	.	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9249387	9249725	0.6	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9249387	9249725	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9249726	9249818	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9249819	9249952	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9249819	9249952	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9249953	9250053	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9250054	9250189	1	+	1	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9250054	9250189	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9250190	9250271	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9250272	9250460	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9250272	9250460	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9250461	9250657	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9250658	9250867	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9250658	9250867	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9250868	9250993	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9250994	9251149	0.82	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9250994	9251149	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9251150	9251257	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9251258	9251344	0.82	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9251258	9251344	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9251345	9251435	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9251436	9251559	0.93	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9251436	9251559	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9251560	9251668	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9251669	9251851	1	+	2	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9251669	9251851	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9251852	9251994	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9251995	9252133	1	+	2	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9251995	9252133	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9252134	9252219	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9252220	9252309	1	+	1	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9252220	9252309	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9252310	9252392	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9252393	9252477	1	+	1	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9252393	9252477	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9252478	9252555	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9252556	9252705	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9252556	9252705	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9252706	9252849	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9252850	9252893	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9252850	9252893	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9252894	9253008	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9253009	9253264	1	+	1	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9253009	9253264	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9253265	9253362	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9253363	9253548	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9253363	9253548	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9253549	9253632	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9253633	9253752	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9253633	9253752	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9253753	9253854	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9253855	9254307	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9253855	9254307	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9254308	9254395	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9254396	9254623	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9254396	9254623	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9254624	9254720	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9254721	9254810	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9254721	9254810	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	intron	9254811	9254894	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	CDS	9254895	9255065	1	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	exon	9254895	9255065	.	+	.	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
Phchi.S4	AUGUSTUS	stop_codon	9255066	9255068	.	+	0	transcript_id "Phchi.S4G149000.t1"; gene_id "Phchi.S4G149000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1046.t1 is derived from g10829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7277404	7278203	.	+	.	Phchi.S6G100500
Phchi.S6	AUGUSTUS	transcript	7277404	7278203	.	+	.	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	start_codon	7277404	7277406	.	+	0	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	CDS	7277404	7277662	0.84	+	0	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	exon	7277404	7277662	.	+	.	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	intron	7277663	7277784	.	+	.	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	CDS	7277785	7277843	0.76	+	2	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	exon	7277785	7277843	.	+	.	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	intron	7277844	7277963	.	+	.	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	CDS	7277964	7278203	0.76	+	0	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	exon	7277964	7278203	.	+	.	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
Phchi.S6	AUGUSTUS	stop_codon	7278204	7278206	.	+	0	transcript_id "Phchi.S6G100500.t1"; gene_id "Phchi.S6G100500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3672.t1 is derived from g841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5113922	5115238	.	-	.	Phchi.S1G083100
Phchi.S1	AUGUSTUS	transcript	5113922	5115238	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	stop_codon	5113919	5113921	.	-	0	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	CDS	5113922	5113979	0.88	-	1	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	exon	5113922	5113979	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	intron	5113980	5114127	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	CDS	5114128	5114237	0.72	-	0	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	exon	5114128	5114237	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	intron	5114238	5114439	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	CDS	5114440	5114515	0.22	-	1	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	exon	5114440	5114515	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	intron	5114516	5114591	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	CDS	5114592	5114667	0.3	-	2	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	exon	5114592	5114667	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	intron	5114668	5114988	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	CDS	5114989	5115238	0.46	-	0	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	exon	5114989	5115238	.	-	.	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
Phchi.S1	AUGUSTUS	start_codon	5115236	5115238	.	-	0	transcript_id "Phchi.S1G083100.t1"; gene_id "Phchi.S1G083100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8697.t1 is derived from g5872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37507298	37510583	.	-	.	Phchi.S1G585600
Phchi.S1	AUGUSTUS	transcript	37507298	37510583	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	stop_codon	37507295	37507297	.	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37507298	37507443	1	-	2	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37507298	37507443	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37507444	37507555	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37507556	37507663	1	-	2	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37507556	37507663	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37507664	37507753	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37507754	37507865	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37507754	37507865	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37507866	37507969	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37507970	37508047	0.97	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37507970	37508047	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37508048	37508162	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37508163	37508228	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37508163	37508228	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37508229	37508330	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37508331	37508435	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37508331	37508435	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37508436	37508547	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37508548	37508745	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37508548	37508745	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37508746	37508830	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37508831	37508923	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37508831	37508923	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37508924	37509042	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37509043	37509135	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37509043	37509135	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37509136	37509347	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37509348	37509472	1	-	2	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37509348	37509472	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37509473	37509596	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37509597	37509673	1	-	1	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37509597	37509673	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37509674	37509760	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37509761	37509882	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37509761	37509882	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37509883	37509979	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37509980	37510066	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37509980	37510066	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37510067	37510161	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37510162	37510227	1	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37510162	37510227	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	intron	37510228	37510472	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	CDS	37510473	37510583	0.72	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	exon	37510473	37510583	.	-	.	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
Phchi.S1	AUGUSTUS	start_codon	37510581	37510583	.	-	0	transcript_id "Phchi.S1G585600.t1"; gene_id "Phchi.S1G585600"
# This transcript jg2019.t2 is derived from g8939.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2020.t1 is derived from g8940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4477373	4478095	.	-	.	Phchi.S5G062900
Phchi.S5	AUGUSTUS	transcript	4477373	4478095	.	-	.	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	stop_codon	4477370	4477372	.	-	0	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	CDS	4477373	4477555	1	-	0	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	exon	4477373	4477555	.	-	.	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	intron	4477556	4477640	.	-	.	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	CDS	4477641	4477715	1	-	0	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	exon	4477641	4477715	.	-	.	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	intron	4477716	4477792	.	-	.	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	CDS	4477793	4478095	0.98	-	0	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	exon	4477793	4478095	.	-	.	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
Phchi.S5	AUGUSTUS	start_codon	4478093	4478095	.	-	0	transcript_id "Phchi.S5G062900.t1"; gene_id "Phchi.S5G062900"
# This transcript jg7720.t2 is derived from g4894.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7721.t1 is derived from g4895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30794550	30795026	.	+	.	Phchi.S1G488000
Phchi.S1	AUGUSTUS	transcript	30794550	30795026	.	+	.	transcript_id "Phchi.S1G488000.t1"; gene_id "Phchi.S1G488000"
Phchi.S1	AUGUSTUS	start_codon	30794550	30794552	.	+	0	transcript_id "Phchi.S1G488000.t1"; gene_id "Phchi.S1G488000"
Phchi.S1	AUGUSTUS	CDS	30794550	30795026	0.9	+	0	transcript_id "Phchi.S1G488000.t1"; gene_id "Phchi.S1G488000"
Phchi.S1	AUGUSTUS	exon	30794550	30795026	.	+	.	transcript_id "Phchi.S1G488000.t1"; gene_id "Phchi.S1G488000"
Phchi.S1	AUGUSTUS	stop_codon	30795027	30795029	.	+	0	transcript_id "Phchi.S1G488000.t1"; gene_id "Phchi.S1G488000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11161.t1 is derived from g15211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4428456	4428812	.	+	.	Phchi.S4G074300
Phchi.S4	AUGUSTUS	transcript	4428456	4428812	.	+	.	transcript_id "Phchi.S4G074300.t1"; gene_id "Phchi.S4G074300"
Phchi.S4	AUGUSTUS	start_codon	4428456	4428458	.	+	0	transcript_id "Phchi.S4G074300.t1"; gene_id "Phchi.S4G074300"
Phchi.S4	AUGUSTUS	CDS	4428456	4428812	0.98	+	0	transcript_id "Phchi.S4G074300.t1"; gene_id "Phchi.S4G074300"
Phchi.S4	AUGUSTUS	exon	4428456	4428812	.	+	.	transcript_id "Phchi.S4G074300.t1"; gene_id "Phchi.S4G074300"
Phchi.S4	AUGUSTUS	stop_codon	4428813	4428815	.	+	0	transcript_id "Phchi.S4G074300.t1"; gene_id "Phchi.S4G074300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6713.t1 is derived from g3885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24669890	24671530	.	+	.	Phchi.S1G387200
Phchi.S1	AUGUSTUS	transcript	24669890	24671530	.	+	.	transcript_id "Phchi.S1G387200.t1"; gene_id "Phchi.S1G387200"
Phchi.S1	AUGUSTUS	start_codon	24669890	24669892	.	+	0	transcript_id "Phchi.S1G387200.t1"; gene_id "Phchi.S1G387200"
Phchi.S1	AUGUSTUS	CDS	24669890	24671530	0.87	+	0	transcript_id "Phchi.S1G387200.t1"; gene_id "Phchi.S1G387200"
Phchi.S1	AUGUSTUS	exon	24669890	24671530	.	+	.	transcript_id "Phchi.S1G387200.t1"; gene_id "Phchi.S1G387200"
Phchi.S1	AUGUSTUS	stop_codon	24671531	24671533	.	+	0	transcript_id "Phchi.S1G387200.t1"; gene_id "Phchi.S1G387200"
# This transcript jg6064.t2 is derived from g3235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6065.t1 is derived from g3236.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20705420	20707168	.	-	.	Phchi.S1G322400
Phchi.S1	AUGUSTUS	transcript	20705420	20707168	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	stop_codon	20705417	20705419	.	-	0	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20705420	20705614	1	-	0	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20705420	20705614	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	intron	20705615	20705712	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20705713	20706011	1	-	2	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20705713	20706011	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	intron	20706012	20706102	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20706103	20706463	0.84	-	0	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20706103	20706463	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	intron	20706464	20706710	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20706711	20706822	0.81	-	1	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20706711	20706822	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	intron	20706823	20706911	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20706912	20707168	1	-	0	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20706912	20707168	.	-	.	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	start_codon	20707166	20707168	.	-	0	transcript_id "Phchi.S1G322400.t1"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	transcript	20706793	20707168	.	-	.	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	stop_codon	20706790	20706792	.	-	0	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20706793	20706822	0.52	-	0	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20706793	20706822	.	-	.	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	intron	20706823	20706952	.	-	.	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	CDS	20706953	20707168	0.52	-	0	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	exon	20706953	20707168	.	-	.	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
Phchi.S1	AUGUSTUS	start_codon	20707166	20707168	.	-	0	transcript_id "Phchi.S1G322400.t2"; gene_id "Phchi.S1G322400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14293.t1 is derived from g12760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11967638	11969031	.	+	.	Phchi.S3G161200
Phchi.S3	AUGUSTUS	transcript	11967638	11969031	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	start_codon	11967638	11967640	.	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11967638	11967760	0.29	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11967638	11967760	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	intron	11967761	11967954	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11967955	11968047	0.44	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11967955	11968047	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	intron	11968048	11968336	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11968337	11968366	0.72	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11968337	11968366	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	intron	11968367	11968546	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11968547	11968563	0.98	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11968547	11968563	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	intron	11968564	11968645	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11968646	11968733	0.98	+	1	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11968646	11968733	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	intron	11968734	11968861	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11968862	11968931	0.98	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11968862	11968931	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	intron	11968932	11969026	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	CDS	11969027	11969031	0.98	+	2	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	exon	11969027	11969031	.	+	.	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
Phchi.S3	AUGUSTUS	stop_codon	11969032	11969034	.	+	0	transcript_id "Phchi.S3G161200.t1"; gene_id "Phchi.S3G161200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13982.t1 is derived from g12449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10040494	10041797	.	+	.	Phchi.S3G130100
Phchi.S3	AUGUSTUS	transcript	10040494	10041797	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	start_codon	10040494	10040496	.	+	0	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	CDS	10040494	10040694	0.39	+	0	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	exon	10040494	10040694	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	intron	10040695	10040946	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	CDS	10040947	10041085	0.81	+	0	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	exon	10040947	10041085	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	intron	10041086	10041230	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	CDS	10041231	10041353	0.74	+	2	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	exon	10041231	10041353	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	intron	10041354	10041459	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	CDS	10041460	10041797	0.74	+	2	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	exon	10041460	10041797	.	+	.	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
Phchi.S3	AUGUSTUS	stop_codon	10041798	10041800	.	+	0	transcript_id "Phchi.S3G130100.t1"; gene_id "Phchi.S3G130100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13120.t1 is derived from g11585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4222136	4222695	.	-	.	Phchi.S3G043900
Phchi.S3	AUGUSTUS	transcript	4222136	4222695	.	-	.	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	stop_codon	4222133	4222135	.	-	0	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	CDS	4222136	4222403	0.85	-	1	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	exon	4222136	4222403	.	-	.	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	intron	4222404	4222564	.	-	.	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	CDS	4222565	4222695	0.62	-	0	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	exon	4222565	4222695	.	-	.	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
Phchi.S3	AUGUSTUS	start_codon	4222693	4222695	.	-	0	transcript_id "Phchi.S3G043900.t1"; gene_id "Phchi.S3G043900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11810.t1 is derived from g15862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8239690	8247219	.	-	.	Phchi.S4G139200
Phchi.S4	AUGUSTUS	transcript	8239690	8247219	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	stop_codon	8239687	8239689	.	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8239690	8239801	1	-	1	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8239690	8239801	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8239802	8239929	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8239930	8240150	1	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8239930	8240150	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8240151	8240241	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8240242	8240616	0.73	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8240242	8240616	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8240617	8240714	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8240715	8240793	1	-	1	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8240715	8240793	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8240794	8240893	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8240894	8241033	1	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8240894	8241033	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8241034	8241262	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8241263	8241581	1	-	1	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8241263	8241581	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8241582	8241664	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8241665	8241807	1	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8241665	8241807	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8241808	8241877	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8241878	8242078	0.99	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8241878	8242078	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8242079	8242158	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8242159	8242287	1	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8242159	8242287	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8242288	8242483	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8242484	8242762	1	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8242484	8242762	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8242763	8242854	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8242855	8243151	1	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8242855	8243151	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8243152	8243276	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8243277	8243995	0.93	-	2	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8243277	8243995	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8243996	8244184	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8244185	8245354	0.4	-	2	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8244185	8245354	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8245355	8245449	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8245450	8246470	0.98	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8245450	8246470	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8246471	8246550	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8246551	8246668	1	-	1	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8246551	8246668	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8246669	8247049	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8247050	8247219	0.94	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8247050	8247219	.	-	.	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	start_codon	8247217	8247219	.	-	0	transcript_id "Phchi.S4G139200.t1"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	transcript	8239690	8247219	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	stop_codon	8239687	8239689	.	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8239690	8239801	0.99	-	1	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8239690	8239801	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8239802	8239929	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8239930	8240150	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8239930	8240150	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8240151	8240241	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8240242	8240628	0.42	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8240242	8240628	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8240629	8240714	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8240715	8240793	0.98	-	1	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8240715	8240793	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8240794	8240893	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8240894	8241033	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8240894	8241033	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8241034	8241262	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8241263	8241581	1	-	1	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8241263	8241581	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8241582	8241664	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8241665	8241807	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8241665	8241807	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8241808	8241877	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8241878	8242078	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8241878	8242078	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8242079	8242158	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8242159	8242287	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8242159	8242287	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8242288	8242483	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8242484	8242762	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8242484	8242762	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8242763	8242854	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8242855	8243151	1	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8242855	8243151	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8243152	8243276	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8243277	8243995	0.88	-	2	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8243277	8243995	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8243996	8244184	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8244185	8245354	0.32	-	2	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8244185	8245354	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8245355	8245449	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8245450	8246470	0.98	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8245450	8246470	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8246471	8246550	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8246551	8246668	1	-	1	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8246551	8246668	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	intron	8246669	8247049	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	CDS	8247050	8247219	0.99	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	exon	8247050	8247219	.	-	.	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
Phchi.S4	AUGUSTUS	start_codon	8247217	8247219	.	-	0	transcript_id "Phchi.S4G139200.t2"; gene_id "Phchi.S4G139200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15039.t1 is derived from g13507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16699439	16706691	.	+	.	Phchi.S3G235800
Phchi.S3	AUGUSTUS	transcript	16699439	16706691	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	start_codon	16699439	16699441	.	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16699439	16699891	0.99	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16699439	16699891	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16699892	16700023	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16700024	16700164	0.99	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16700024	16700164	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16700165	16700250	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16700251	16700334	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16700251	16700334	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16700335	16700413	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16700414	16700539	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16700414	16700539	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16700540	16700636	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16700637	16700696	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16700637	16700696	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16700697	16700806	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16700807	16700860	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16700807	16700860	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16700861	16700949	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16700950	16701042	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16700950	16701042	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16701043	16701137	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16701138	16701233	0.99	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16701138	16701233	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16701234	16701336	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16701337	16701482	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16701337	16701482	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16701483	16701566	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16701567	16701716	1	+	1	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16701567	16701716	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16701717	16701795	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16701796	16701925	1	+	1	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16701796	16701925	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16701926	16702006	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16702007	16703285	0.87	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16702007	16703285	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16703286	16703463	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16703464	16704686	0.5	+	2	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16703464	16704686	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16704687	16704772	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16704773	16704871	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16704773	16704871	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16704872	16704963	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16704964	16705116	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16704964	16705116	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16705117	16705205	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16705206	16706204	1	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16705206	16706204	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	intron	16706205	16706286	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	CDS	16706287	16706691	0.86	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	exon	16706287	16706691	.	+	.	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
Phchi.S3	AUGUSTUS	stop_codon	16706692	16706694	.	+	0	transcript_id "Phchi.S3G235800.t1"; gene_id "Phchi.S3G235800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15816.t1 is derived from g14286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21526871	21530231	.	+	.	Phchi.S3G313500
Phchi.S3	AUGUSTUS	transcript	21526871	21530231	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	start_codon	21526871	21526873	.	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21526871	21527067	1	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21526871	21527067	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21527068	21527318	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21527319	21527638	1	+	1	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21527319	21527638	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21527639	21527739	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21527740	21527954	0.96	+	2	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21527740	21527954	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21527955	21528199	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21528200	21528223	1	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21528200	21528223	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21528224	21528341	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21528342	21528522	1	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21528342	21528522	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21528523	21528610	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21528611	21528830	1	+	2	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21528611	21528830	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21528831	21528931	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21528932	21529067	1	+	1	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21528932	21529067	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21529068	21529164	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21529165	21529184	1	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21529165	21529184	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21529185	21529284	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21529285	21529316	0.42	+	1	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21529285	21529316	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21529317	21529545	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21529546	21529589	0.42	+	2	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21529546	21529589	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21529590	21529882	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21529883	21529945	0.58	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21529883	21529945	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	intron	21529946	21530123	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	CDS	21530124	21530231	0.58	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	exon	21530124	21530231	.	+	.	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
Phchi.S3	AUGUSTUS	stop_codon	21530232	21530234	.	+	0	transcript_id "Phchi.S3G313500.t1"; gene_id "Phchi.S3G313500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10875.t1 is derived from g14925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2709693	2712746	.	+	.	Phchi.S4G045700
Phchi.S4	AUGUSTUS	transcript	2709693	2712746	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	start_codon	2709693	2709695	.	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2709693	2709848	0.91	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2709693	2709848	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2709849	2710033	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2710034	2710186	1	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2710034	2710186	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2710187	2710271	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2710272	2710323	1	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2710272	2710323	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2710324	2710418	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2710419	2710688	1	+	2	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2710419	2710688	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2710689	2710865	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2710866	2711077	1	+	2	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2710866	2711077	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2711078	2711157	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2711158	2711278	0.94	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2711158	2711278	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2711279	2711391	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2711392	2711479	1	+	2	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2711392	2711479	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2711480	2711567	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2711568	2711646	1	+	1	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2711568	2711646	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2711647	2711743	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2711744	2711831	1	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2711744	2711831	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2711832	2711936	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2711937	2711977	1	+	2	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2711937	2711977	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2711978	2712108	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2712109	2712161	1	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2712109	2712161	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2712162	2712265	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2712266	2712422	1	+	1	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2712266	2712422	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	intron	2712423	2712518	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	CDS	2712519	2712746	1	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	exon	2712519	2712746	.	+	.	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
Phchi.S4	AUGUSTUS	stop_codon	2712747	2712749	.	+	0	transcript_id "Phchi.S4G045700.t1"; gene_id "Phchi.S4G045700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4536.t1 is derived from g1706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11003113	11005035	.	-	.	Phchi.S1G169500
Phchi.S1	AUGUSTUS	transcript	11003113	11005035	.	-	.	transcript_id "Phchi.S1G169500.t1"; gene_id "Phchi.S1G169500"
Phchi.S1	AUGUSTUS	stop_codon	11003110	11003112	.	-	0	transcript_id "Phchi.S1G169500.t1"; gene_id "Phchi.S1G169500"
Phchi.S1	AUGUSTUS	CDS	11003113	11005035	1	-	0	transcript_id "Phchi.S1G169500.t1"; gene_id "Phchi.S1G169500"
Phchi.S1	AUGUSTUS	exon	11003113	11005035	.	-	.	transcript_id "Phchi.S1G169500.t1"; gene_id "Phchi.S1G169500"
Phchi.S1	AUGUSTUS	start_codon	11005033	11005035	.	-	0	transcript_id "Phchi.S1G169500.t1"; gene_id "Phchi.S1G169500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8394.t1 is derived from g5569.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35693244	35694244	.	+	.	Phchi.S1G555300
Phchi.S1	AUGUSTUS	transcript	35693244	35694244	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	start_codon	35693244	35693246	.	+	0	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693244	35693334	0.9	+	0	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693244	35693334	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693335	35693424	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693425	35693494	0.82	+	2	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693425	35693494	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693495	35693580	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693581	35693591	0.82	+	1	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693581	35693591	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693592	35693683	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693684	35693919	0.99	+	2	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693684	35693919	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693920	35694013	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35694014	35694244	0.99	+	0	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35694014	35694244	.	+	.	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	stop_codon	35694245	35694247	.	+	0	transcript_id "Phchi.S1G555300.t1"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	transcript	35693244	35694244	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	start_codon	35693244	35693246	.	+	0	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693244	35693334	0.87	+	0	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693244	35693334	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693335	35693424	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693425	35693574	0.44	+	2	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693425	35693574	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693575	35693683	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35693684	35693919	0.89	+	2	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35693684	35693919	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	intron	35693920	35694013	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	CDS	35694014	35694244	1	+	0	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	exon	35694014	35694244	.	+	.	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
Phchi.S1	AUGUSTUS	stop_codon	35694245	35694247	.	+	0	transcript_id "Phchi.S1G555300.t2"; gene_id "Phchi.S1G555300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15495.t1 is derived from g13964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19490951	19491538	.	-	.	Phchi.S3G281400
Phchi.S3	AUGUSTUS	transcript	19490951	19491538	.	-	.	transcript_id "Phchi.S3G281400.t1"; gene_id "Phchi.S3G281400"
Phchi.S3	AUGUSTUS	stop_codon	19490948	19490950	.	-	0	transcript_id "Phchi.S3G281400.t1"; gene_id "Phchi.S3G281400"
Phchi.S3	AUGUSTUS	CDS	19490951	19491538	0.38	-	0	transcript_id "Phchi.S3G281400.t1"; gene_id "Phchi.S3G281400"
Phchi.S3	AUGUSTUS	exon	19490951	19491538	.	-	.	transcript_id "Phchi.S3G281400.t1"; gene_id "Phchi.S3G281400"
Phchi.S3	AUGUSTUS	start_codon	19491536	19491538	.	-	0	transcript_id "Phchi.S3G281400.t1"; gene_id "Phchi.S3G281400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9768.t1 is derived from g6944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43595011	43597375	.	-	.	Phchi.S1G692700
Phchi.S1	AUGUSTUS	transcript	43595011	43597375	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	stop_codon	43595008	43595010	.	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	CDS	43595011	43595154	1	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	exon	43595011	43595154	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	intron	43595155	43595239	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	CDS	43595240	43595419	1	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	exon	43595240	43595419	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	intron	43595420	43595537	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	CDS	43595538	43595609	1	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	exon	43595538	43595609	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	intron	43595610	43595795	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	CDS	43595796	43596140	0.99	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	exon	43595796	43596140	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	intron	43596141	43596230	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	CDS	43596231	43596371	1	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	exon	43596231	43596371	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	intron	43596372	43596478	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	CDS	43596479	43597375	0.32	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	exon	43596479	43597375	.	-	.	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
Phchi.S1	AUGUSTUS	start_codon	43597373	43597375	.	-	0	transcript_id "Phchi.S1G692700.t1"; gene_id "Phchi.S1G692700"
# This transcript jg9452.t2 is derived from g6628.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9453.t1 is derived from g6629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41537712	41540489	.	-	.	Phchi.S1G661200
Phchi.S1	AUGUSTUS	transcript	41537712	41540489	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	stop_codon	41537709	41537711	.	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41537712	41537972	0.99	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41537712	41537972	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41537973	41538078	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41538079	41538408	1	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41538079	41538408	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41538409	41538515	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41538516	41538626	1	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41538516	41538626	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41538627	41538829	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41538830	41539044	1	-	2	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41538830	41539044	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41539045	41539219	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41539220	41539268	0.8	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41539220	41539268	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41539269	41539441	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41539442	41539851	0.45	-	2	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41539442	41539851	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41539852	41540007	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41540008	41540093	0.49	-	1	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41540008	41540093	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41540094	41540266	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41540267	41540280	0.8	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41540267	41540280	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	intron	41540281	41540459	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	CDS	41540460	41540489	0.89	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	exon	41540460	41540489	.	-	.	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
Phchi.S1	AUGUSTUS	start_codon	41540487	41540489	.	-	0	transcript_id "Phchi.S1G661200.t1"; gene_id "Phchi.S1G661200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1082.t1 is derived from g10865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7509177	7510307	.	-	.	Phchi.S6G104100
Phchi.S6	AUGUSTUS	transcript	7509177	7510307	.	-	.	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	stop_codon	7509174	7509176	.	-	0	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	CDS	7509177	7509800	1	-	0	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	exon	7509177	7509800	.	-	.	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	intron	7509801	7509897	.	-	.	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	CDS	7509898	7510062	0.59	-	0	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	exon	7509898	7510062	.	-	.	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	intron	7510063	7510133	.	-	.	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	CDS	7510134	7510307	0.78	-	0	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	exon	7510134	7510307	.	-	.	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
Phchi.S6	AUGUSTUS	start_codon	7510305	7510307	.	-	0	transcript_id "Phchi.S6G104100.t1"; gene_id "Phchi.S6G104100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13224.t1 is derived from g11689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4766626	4767554	.	+	.	Phchi.S3G054300
Phchi.S3	AUGUSTUS	transcript	4766626	4767554	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	start_codon	4766626	4766628	.	+	0	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	CDS	4766626	4766640	1	+	0	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	exon	4766626	4766640	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	intron	4766641	4766931	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	CDS	4766932	4767007	0.54	+	0	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	exon	4766932	4767007	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	intron	4767008	4767286	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	CDS	4767287	4767408	0.93	+	2	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	exon	4767287	4767408	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	intron	4767409	4767494	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	CDS	4767495	4767554	1	+	0	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	exon	4767495	4767554	.	+	.	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
Phchi.S3	AUGUSTUS	stop_codon	4767555	4767557	.	+	0	transcript_id "Phchi.S3G054300.t1"; gene_id "Phchi.S3G054300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6429.t1 is derived from g3601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22991931	22994079	.	-	.	Phchi.S1G358800
Phchi.S1	AUGUSTUS	transcript	22991931	22994079	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	stop_codon	22991928	22991930	.	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22991931	22992053	0.91	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22991931	22992053	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22992054	22992140	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22992141	22992247	1	-	2	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22992141	22992247	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22992248	22992340	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22992341	22992394	1	-	2	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22992341	22992394	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22992395	22992529	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22992530	22992596	0.95	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22992530	22992596	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22992597	22992714	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22992715	22992792	0.95	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22992715	22992792	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22992793	22992885	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22992886	22992921	1	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22992886	22992921	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22992922	22993002	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22993003	22993059	1	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22993003	22993059	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22993060	22993195	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22993196	22993281	1	-	2	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22993196	22993281	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22993282	22993363	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22993364	22993406	1	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22993364	22993406	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22993407	22993547	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22993548	22993645	1	-	2	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22993548	22993645	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22993646	22993728	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22993729	22993947	1	-	2	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22993729	22993947	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	intron	22993948	22994021	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	CDS	22994022	22994079	1	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	exon	22994022	22994079	.	-	.	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
Phchi.S1	AUGUSTUS	start_codon	22994077	22994079	.	-	0	transcript_id "Phchi.S1G358800.t1"; gene_id "Phchi.S1G358800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5318.t1 is derived from g2488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16264550	16265236	.	-	.	Phchi.S1G247700
Phchi.S1	AUGUSTUS	transcript	16264550	16265236	.	-	.	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	stop_codon	16264547	16264549	.	-	0	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	CDS	16264550	16264807	1	-	0	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	exon	16264550	16264807	.	-	.	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	intron	16264808	16265019	.	-	.	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	CDS	16265020	16265130	1	-	0	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	exon	16265020	16265130	.	-	.	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	intron	16265131	16265227	.	-	.	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	CDS	16265228	16265236	1	-	0	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	exon	16265228	16265236	.	-	.	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
Phchi.S1	AUGUSTUS	start_codon	16265234	16265236	.	-	0	transcript_id "Phchi.S1G247700.t1"; gene_id "Phchi.S1G247700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8358.t1 is derived from g5533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35480461	35482435	.	-	.	Phchi.S1G551700
Phchi.S1	AUGUSTUS	transcript	35480461	35482435	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	stop_codon	35480458	35480460	.	-	0	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	CDS	35480461	35480678	0.9	-	2	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	exon	35480461	35480678	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	intron	35480679	35480770	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	CDS	35480771	35480897	1	-	0	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	exon	35480771	35480897	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	intron	35480898	35481042	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	CDS	35481043	35481314	1	-	2	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	exon	35481043	35481314	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	intron	35481315	35481516	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	CDS	35481517	35481657	1	-	2	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	exon	35481517	35481657	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	intron	35481658	35481807	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	CDS	35481808	35482435	0.96	-	0	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	exon	35481808	35482435	.	-	.	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
Phchi.S1	AUGUSTUS	start_codon	35482433	35482435	.	-	0	transcript_id "Phchi.S1G551700.t1"; gene_id "Phchi.S1G551700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1965.t1 is derived from g8885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4066628	4067591	.	+	.	Phchi.S5G057400
Phchi.S5	AUGUSTUS	transcript	4066628	4067591	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	start_codon	4066628	4066630	.	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	CDS	4066628	4066630	0.96	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	exon	4066628	4066630	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	intron	4066631	4066721	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	CDS	4066722	4066811	1	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	exon	4066722	4066811	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	intron	4066812	4066926	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	CDS	4066927	4067055	1	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	exon	4066927	4067055	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	intron	4067056	4067181	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	CDS	4067182	4067364	1	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	exon	4067182	4067364	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	intron	4067365	4067435	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	CDS	4067436	4067591	0.63	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	exon	4067436	4067591	.	+	.	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
Phchi.S5	AUGUSTUS	stop_codon	4067592	4067594	.	+	0	transcript_id "Phchi.S5G057400.t1"; gene_id "Phchi.S5G057400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14860.t1 is derived from g13328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15090171	15091122	.	-	.	Phchi.S3G217900
Phchi.S3	AUGUSTUS	transcript	15090171	15091122	.	-	.	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	stop_codon	15090168	15090170	.	-	0	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090171	15090215	1	-	0	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090171	15090215	.	-	.	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	intron	15090216	15090303	.	-	.	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090304	15090465	1	-	0	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090304	15090465	.	-	.	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	intron	15090466	15090843	.	-	.	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090844	15091122	0.96	-	0	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090844	15091122	.	-	.	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	start_codon	15091120	15091122	.	-	0	transcript_id "Phchi.S3G217900.t1"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	transcript	15090171	15091122	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	stop_codon	15090168	15090170	.	-	0	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090171	15090215	1	-	0	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090171	15090215	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	intron	15090216	15090303	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090304	15090465	1	-	0	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090304	15090465	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	intron	15090466	15090607	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090608	15090657	0.64	-	2	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090608	15090657	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	intron	15090658	15090824	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	CDS	15090825	15091122	0.42	-	0	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	exon	15090825	15091122	.	-	.	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
Phchi.S3	AUGUSTUS	start_codon	15091120	15091122	.	-	0	transcript_id "Phchi.S3G217900.t2"; gene_id "Phchi.S3G217900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15061.t1 is derived from g13529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16791218	16798163	.	+	.	Phchi.S3G238000
Phchi.S3	AUGUSTUS	transcript	16791218	16798163	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	start_codon	16791218	16791220	.	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16791218	16791615	0.99	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16791218	16791615	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16791616	16791722	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16791723	16791843	0.99	+	1	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16791723	16791843	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16791844	16791925	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16791926	16792014	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16791926	16792014	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16792015	16792110	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16792111	16792195	1	+	1	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16792111	16792195	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16792196	16792302	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16792303	16792462	0.8	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16792303	16792462	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16792463	16792566	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16792567	16792643	0.87	+	2	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16792567	16792643	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16792644	16792781	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16792782	16792835	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16792782	16792835	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16792836	16792922	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16792923	16793013	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16792923	16793013	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16793014	16793129	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16793130	16793431	1	+	2	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16793130	16793431	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16793432	16793535	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16793536	16793817	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16793536	16793817	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16793818	16793955	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16793956	16794272	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16793956	16794272	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16794273	16794392	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16794393	16794553	1	+	1	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16794393	16794553	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16794554	16794673	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16794674	16794789	1	+	2	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16794674	16794789	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16794790	16794882	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16794883	16795036	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16794883	16795036	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16795037	16795144	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16795145	16795294	1	+	2	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16795145	16795294	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16795295	16795383	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16795384	16795568	1	+	2	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16795384	16795568	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16795569	16795662	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16795663	16795995	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16795663	16795995	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16795996	16796118	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16796119	16796409	0.99	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16796119	16796409	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16796410	16796517	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16796518	16796601	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16796518	16796601	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16796602	16796689	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16796690	16796823	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16796690	16796823	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16796824	16796905	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16796906	16796965	0.46	+	1	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16796906	16796965	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16796966	16797090	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16797091	16797132	0.91	+	1	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16797091	16797132	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16797133	16797256	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16797257	16797428	1	+	1	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16797257	16797428	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16797429	16797524	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16797525	16797779	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16797525	16797779	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	intron	16797780	16797896	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	CDS	16797897	16798163	1	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	exon	16797897	16798163	.	+	.	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
Phchi.S3	AUGUSTUS	stop_codon	16798164	16798166	.	+	0	transcript_id "Phchi.S3G238000.t1"; gene_id "Phchi.S3G238000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5231.t1 is derived from g2401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15750415	15750732	.	-	.	Phchi.S1G239000
Phchi.S1	AUGUSTUS	transcript	15750415	15750732	.	-	.	transcript_id "Phchi.S1G239000.t1"; gene_id "Phchi.S1G239000"
Phchi.S1	AUGUSTUS	stop_codon	15750412	15750414	.	-	0	transcript_id "Phchi.S1G239000.t1"; gene_id "Phchi.S1G239000"
Phchi.S1	AUGUSTUS	CDS	15750415	15750732	0.61	-	0	transcript_id "Phchi.S1G239000.t1"; gene_id "Phchi.S1G239000"
Phchi.S1	AUGUSTUS	exon	15750415	15750732	.	-	.	transcript_id "Phchi.S1G239000.t1"; gene_id "Phchi.S1G239000"
Phchi.S1	AUGUSTUS	start_codon	15750730	15750732	.	-	0	transcript_id "Phchi.S1G239000.t1"; gene_id "Phchi.S1G239000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10418.t1 is derived from g7594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47760786	47761783	.	+	.	Phchi.S1G757700
Phchi.S1	AUGUSTUS	transcript	47760786	47761783	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	start_codon	47760786	47760788	.	+	0	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	CDS	47760786	47760850	0.76	+	0	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	exon	47760786	47760850	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	intron	47760851	47760942	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	CDS	47760943	47760963	0.98	+	1	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	exon	47760943	47760963	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	intron	47760964	47761129	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	CDS	47761130	47761149	0.98	+	1	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	exon	47761130	47761149	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	intron	47761150	47761386	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	CDS	47761387	47761395	1	+	2	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	exon	47761387	47761395	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	intron	47761396	47761481	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	CDS	47761482	47761783	0.95	+	2	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	exon	47761482	47761783	.	+	.	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
Phchi.S1	AUGUSTUS	stop_codon	47761784	47761786	.	+	0	transcript_id "Phchi.S1G757700.t1"; gene_id "Phchi.S1G757700"
# This transcript jg104.t2 is derived from g9886.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg105.t1 is derived from g9887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	534336	535016	.	+	.	Phchi.S6G006400
Phchi.S6	AUGUSTUS	transcript	534336	535016	.	+	.	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	start_codon	534336	534338	.	+	0	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	CDS	534336	534371	0.31	+	0	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	exon	534336	534371	.	+	.	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	intron	534372	534468	.	+	.	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	CDS	534469	534612	1	+	0	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	exon	534469	534612	.	+	.	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	intron	534613	534962	.	+	.	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	CDS	534963	535016	1	+	0	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	exon	534963	535016	.	+	.	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
Phchi.S6	AUGUSTUS	stop_codon	535017	535019	.	+	0	transcript_id "Phchi.S6G006400.t1"; gene_id "Phchi.S6G006400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9185.t1 is derived from g6360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40247678	40249733	.	-	.	Phchi.S1G634400
Phchi.S1	AUGUSTUS	transcript	40247678	40249733	.	-	.	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	stop_codon	40247675	40247677	.	-	0	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	CDS	40247678	40247679	0.67	-	2	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	exon	40247678	40247679	.	-	.	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	intron	40247680	40247803	.	-	.	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	CDS	40247804	40249013	0.38	-	0	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	exon	40247804	40249013	.	-	.	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	intron	40249014	40249241	.	-	.	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	CDS	40249242	40249733	0.21	-	0	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	exon	40249242	40249733	.	-	.	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
Phchi.S1	AUGUSTUS	start_codon	40249731	40249733	.	-	0	transcript_id "Phchi.S1G634400.t1"; gene_id "Phchi.S1G634400"
# This transcript jg13429.t2 is derived from g11896.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13430.t1 is derived from g11897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6652841	6655747	.	+	.	Phchi.S3G074900
Phchi.S3	AUGUSTUS	transcript	6652841	6655747	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	start_codon	6652841	6652843	.	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6652841	6652977	0.31	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6652841	6652977	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6652978	6653195	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6653196	6653388	0.57	+	1	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6653196	6653388	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6653389	6653515	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6653516	6653671	0.75	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6653516	6653671	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6653672	6653758	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6653759	6654298	1	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6653759	6654298	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6654299	6654384	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6654385	6654465	1	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6654385	6654465	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6654466	6654536	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6654537	6654674	1	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6654537	6654674	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6654675	6654762	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6654763	6654878	1	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6654763	6654878	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6654879	6654962	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6654963	6655187	1	+	1	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6654963	6655187	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	intron	6655188	6655740	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	CDS	6655741	6655747	1	+	1	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	exon	6655741	6655747	.	+	.	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
Phchi.S3	AUGUSTUS	stop_codon	6655748	6655750	.	+	0	transcript_id "Phchi.S3G074900.t1"; gene_id "Phchi.S3G074900"
# This transcript jg15895.t2 is derived from g14365.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15896.t1 is derived from g14366.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22056796	22058643	.	-	.	Phchi.S3G321500
Phchi.S3	AUGUSTUS	transcript	22056796	22058643	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	stop_codon	22056793	22056795	.	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22056796	22056903	1	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22056796	22056903	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22056904	22056985	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22056986	22057110	1	-	2	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22056986	22057110	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057111	22057192	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057193	22057283	1	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057193	22057283	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057284	22057447	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057448	22057531	1	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057448	22057531	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057532	22057614	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057615	22057713	1	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057615	22057713	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057714	22057801	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057802	22057906	1	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057802	22057906	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057907	22058300	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22058301	22058454	1	-	1	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22058301	22058454	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22058455	22058605	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22058606	22058643	1	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22058606	22058643	.	-	.	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	start_codon	22058641	22058643	.	-	0	transcript_id "Phchi.S3G321500.t1"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	transcript	22056796	22058643	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	stop_codon	22056793	22056795	.	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22056796	22056903	1	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22056796	22056903	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22056904	22056985	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22056986	22057110	1	-	2	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22056986	22057110	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057111	22057192	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057193	22057283	1	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057193	22057283	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057284	22057429	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057430	22057531	0.98	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057430	22057531	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057532	22057614	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057615	22057713	1	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057615	22057713	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057714	22057801	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22057802	22057906	1	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22057802	22057906	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22057907	22058022	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22058023	22058166	0.96	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22058023	22058166	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22058167	22058300	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22058301	22058454	0.98	-	1	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22058301	22058454	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	intron	22058455	22058605	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	CDS	22058606	22058643	1	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	exon	22058606	22058643	.	-	.	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
Phchi.S3	AUGUSTUS	start_codon	22058641	22058643	.	-	0	transcript_id "Phchi.S3G321500.t2"; gene_id "Phchi.S3G321500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1222.t1 is derived from g11005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8457512	8459567	.	+	.	Phchi.S6G118100
Phchi.S6	AUGUSTUS	transcript	8457512	8459567	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	start_codon	8457512	8457514	.	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8457512	8457622	0.81	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8457512	8457622	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8457623	8457706	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8457707	8457799	1	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8457707	8457799	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8457800	8457964	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8457965	8458010	0.48	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8457965	8458010	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8458011	8458169	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8458170	8458189	0.3	+	2	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8458170	8458189	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8458190	8458412	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8458413	8458572	0.81	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8458413	8458572	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8458573	8458677	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8458678	8458781	0.77	+	2	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8458678	8458781	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8458782	8458894	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8458895	8459026	1	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8458895	8459026	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8459027	8459119	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8459120	8459276	1	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8459120	8459276	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	intron	8459277	8459448	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	CDS	8459449	8459567	1	+	2	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	exon	8459449	8459567	.	+	.	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
Phchi.S6	AUGUSTUS	stop_codon	8459568	8459570	.	+	0	transcript_id "Phchi.S6G118100.t1"; gene_id "Phchi.S6G118100"
# This transcript jg8381.t2 is derived from g5556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8382.t1 is derived from g5557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35599816	35600479	.	+	.	Phchi.S1G554100
Phchi.S1	AUGUSTUS	transcript	35599816	35600479	.	+	.	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	start_codon	35599816	35599818	.	+	0	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	CDS	35599816	35600163	0.73	+	0	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	exon	35599816	35600163	.	+	.	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	intron	35600164	35600410	.	+	.	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	CDS	35600411	35600479	1	+	0	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	exon	35600411	35600479	.	+	.	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
Phchi.S1	AUGUSTUS	stop_codon	35600480	35600482	.	+	0	transcript_id "Phchi.S1G554100.t1"; gene_id "Phchi.S1G554100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4764.t1 is derived from g1934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12710137	12710970	.	+	.	Phchi.S1G192300
Phchi.S1	AUGUSTUS	transcript	12710137	12710970	.	+	.	transcript_id "Phchi.S1G192300.t1"; gene_id "Phchi.S1G192300"
Phchi.S1	AUGUSTUS	start_codon	12710137	12710139	.	+	0	transcript_id "Phchi.S1G192300.t1"; gene_id "Phchi.S1G192300"
Phchi.S1	AUGUSTUS	CDS	12710137	12710970	0.96	+	0	transcript_id "Phchi.S1G192300.t1"; gene_id "Phchi.S1G192300"
Phchi.S1	AUGUSTUS	exon	12710137	12710970	.	+	.	transcript_id "Phchi.S1G192300.t1"; gene_id "Phchi.S1G192300"
Phchi.S1	AUGUSTUS	stop_codon	12710971	12710973	.	+	0	transcript_id "Phchi.S1G192300.t1"; gene_id "Phchi.S1G192300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11599.t1 is derived from g15650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7279662	7280447	.	+	.	Phchi.S4G118100
Phchi.S4	AUGUSTUS	transcript	7279662	7280447	.	+	.	transcript_id "Phchi.S4G118100.t1"; gene_id "Phchi.S4G118100"
Phchi.S4	AUGUSTUS	start_codon	7279662	7279664	.	+	0	transcript_id "Phchi.S4G118100.t1"; gene_id "Phchi.S4G118100"
Phchi.S4	AUGUSTUS	CDS	7279662	7280447	0.99	+	0	transcript_id "Phchi.S4G118100.t1"; gene_id "Phchi.S4G118100"
Phchi.S4	AUGUSTUS	exon	7279662	7280447	.	+	.	transcript_id "Phchi.S4G118100.t1"; gene_id "Phchi.S4G118100"
Phchi.S4	AUGUSTUS	stop_codon	7280448	7280450	.	+	0	transcript_id "Phchi.S4G118100.t1"; gene_id "Phchi.S4G118100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4553.t1 is derived from g1723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11088191	11089236	.	-	.	Phchi.S1G171200
Phchi.S1	AUGUSTUS	transcript	11088191	11089236	.	-	.	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	stop_codon	11088188	11088190	.	-	0	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	CDS	11088191	11088364	0.64	-	0	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	exon	11088191	11088364	.	-	.	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	intron	11088365	11088504	.	-	.	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	CDS	11088505	11089236	0.31	-	0	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	exon	11088505	11089236	.	-	.	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
Phchi.S1	AUGUSTUS	start_codon	11089234	11089236	.	-	0	transcript_id "Phchi.S1G171200.t1"; gene_id "Phchi.S1G171200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6976.t1 is derived from g4148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26245088	26248306	.	-	.	Phchi.S1G413500
Phchi.S1	AUGUSTUS	transcript	26245088	26248306	.	-	.	transcript_id "Phchi.S1G413500.t1"; gene_id "Phchi.S1G413500"
Phchi.S1	AUGUSTUS	stop_codon	26245085	26245087	.	-	0	transcript_id "Phchi.S1G413500.t1"; gene_id "Phchi.S1G413500"
Phchi.S1	AUGUSTUS	CDS	26245088	26248306	0.8	-	0	transcript_id "Phchi.S1G413500.t1"; gene_id "Phchi.S1G413500"
Phchi.S1	AUGUSTUS	exon	26245088	26248306	.	-	.	transcript_id "Phchi.S1G413500.t1"; gene_id "Phchi.S1G413500"
Phchi.S1	AUGUSTUS	start_codon	26248304	26248306	.	-	0	transcript_id "Phchi.S1G413500.t1"; gene_id "Phchi.S1G413500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2819.t1 is derived from g9739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9020028	9020935	.	+	.	Phchi.S5G142800
Phchi.S5	AUGUSTUS	transcript	9020028	9020935	.	+	.	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	start_codon	9020028	9020030	.	+	0	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	CDS	9020028	9020336	1	+	0	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	exon	9020028	9020336	.	+	.	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	intron	9020337	9020444	.	+	.	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	CDS	9020445	9020612	1	+	0	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	exon	9020445	9020612	.	+	.	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	intron	9020613	9020704	.	+	.	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	CDS	9020705	9020935	1	+	0	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	exon	9020705	9020935	.	+	.	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
Phchi.S5	AUGUSTUS	stop_codon	9020936	9020938	.	+	0	transcript_id "Phchi.S5G142800.t1"; gene_id "Phchi.S5G142800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4674.t1 is derived from g1844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11759850	11761236	.	-	.	Phchi.S1G183300
Phchi.S1	AUGUSTUS	transcript	11759850	11761236	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	stop_codon	11759847	11759849	.	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11759850	11759877	0.96	-	1	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11759850	11759877	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11759878	11759983	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11759984	11760063	0.97	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11759984	11760063	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11760064	11760168	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11760169	11760216	1	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11760169	11760216	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11760217	11760356	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11760357	11760405	1	-	1	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11760357	11760405	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11760406	11760494	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11760495	11760547	1	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11760495	11760547	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11760548	11760631	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11760632	11760727	1	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11760632	11760727	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11760728	11760799	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11760800	11760899	1	-	1	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11760800	11760899	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	intron	11760900	11760991	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	CDS	11760992	11761236	0.61	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	exon	11760992	11761236	.	-	.	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
Phchi.S1	AUGUSTUS	start_codon	11761234	11761236	.	-	0	transcript_id "Phchi.S1G183300.t1"; gene_id "Phchi.S1G183300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14262.t1 is derived from g12729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11810432	11811664	.	-	.	Phchi.S3G158100
Phchi.S3	AUGUSTUS	transcript	11810432	11811664	.	-	.	transcript_id "Phchi.S3G158100.t1"; gene_id "Phchi.S3G158100"
Phchi.S3	AUGUSTUS	stop_codon	11810429	11810431	.	-	0	transcript_id "Phchi.S3G158100.t1"; gene_id "Phchi.S3G158100"
Phchi.S3	AUGUSTUS	CDS	11810432	11811664	0.82	-	0	transcript_id "Phchi.S3G158100.t1"; gene_id "Phchi.S3G158100"
Phchi.S3	AUGUSTUS	exon	11810432	11811664	.	-	.	transcript_id "Phchi.S3G158100.t1"; gene_id "Phchi.S3G158100"
Phchi.S3	AUGUSTUS	start_codon	11811662	11811664	.	-	0	transcript_id "Phchi.S3G158100.t1"; gene_id "Phchi.S3G158100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3411.t1 is derived from g580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3380242	3381624	.	+	.	Phchi.S1G057000
Phchi.S1	AUGUSTUS	transcript	3380242	3380974	.	+	.	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	start_codon	3380242	3380244	.	+	0	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	CDS	3380242	3380853	0.73	+	0	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	exon	3380242	3380853	.	+	.	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	intron	3380854	3380950	.	+	.	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	CDS	3380951	3380974	1	+	0	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	exon	3380951	3380974	.	+	.	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	stop_codon	3380975	3380977	.	+	0	transcript_id "Phchi.S1G057000.t1"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	transcript	3380242	3381624	.	+	.	transcript_id "Phchi.S1G057000.t2"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	start_codon	3380242	3380244	.	+	0	transcript_id "Phchi.S1G057000.t2"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	CDS	3380242	3381624	0.43	+	0	transcript_id "Phchi.S1G057000.t2"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	exon	3380242	3381624	.	+	.	transcript_id "Phchi.S1G057000.t2"; gene_id "Phchi.S1G057000"
Phchi.S1	AUGUSTUS	stop_codon	3381625	3381627	.	+	0	transcript_id "Phchi.S1G057000.t2"; gene_id "Phchi.S1G057000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4537.t1 is derived from g1707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11005714	11007670	.	-	.	Phchi.S1G169600
Phchi.S1	AUGUSTUS	transcript	11005714	11007670	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	stop_codon	11005711	11005713	.	-	0	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	CDS	11005714	11006199	0.8	-	0	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	exon	11005714	11006199	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	intron	11006200	11006280	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	CDS	11006281	11006723	0.98	-	2	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	exon	11006281	11006723	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	intron	11006724	11006820	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	CDS	11006821	11007134	0.72	-	1	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	exon	11006821	11007134	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	intron	11007135	11007223	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	CDS	11007224	11007482	0.56	-	2	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	exon	11007224	11007482	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	intron	11007483	11007594	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	CDS	11007595	11007670	0.5	-	0	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	exon	11007595	11007670	.	-	.	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
Phchi.S1	AUGUSTUS	start_codon	11007668	11007670	.	-	0	transcript_id "Phchi.S1G169600.t1"; gene_id "Phchi.S1G169600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7778.t1 is derived from g4952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31180550	31181813	.	+	.	Phchi.S1G493700
Phchi.S1	AUGUSTUS	transcript	31180550	31181813	.	+	.	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	start_codon	31180550	31180552	.	+	0	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	CDS	31180550	31180687	0.89	+	0	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	exon	31180550	31180687	.	+	.	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	intron	31180688	31180779	.	+	.	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	CDS	31180780	31181095	0.81	+	0	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	exon	31180780	31181095	.	+	.	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	intron	31181096	31181400	.	+	.	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	CDS	31181401	31181813	0.39	+	2	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	exon	31181401	31181813	.	+	.	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
Phchi.S1	AUGUSTUS	stop_codon	31181814	31181816	.	+	0	transcript_id "Phchi.S1G493700.t1"; gene_id "Phchi.S1G493700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3462.t1 is derived from g631.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3880502	3882987	.	-	.	Phchi.S1G062100
Phchi.S1	AUGUSTUS	transcript	3880502	3882987	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	stop_codon	3880499	3880501	.	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3880502	3880517	0.83	-	1	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3880502	3880517	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3880518	3880615	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3880616	3880663	0.83	-	1	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3880616	3880663	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3880664	3880829	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3880830	3880858	0.83	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3880830	3880858	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3880859	3881296	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881297	3881362	0.88	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881297	3881362	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881363	3881458	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881459	3881545	1	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881459	3881545	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881546	3881636	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881637	3881729	1	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881637	3881729	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881730	3881808	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881809	3881881	1	-	1	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881809	3881881	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881882	3882004	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882005	3882096	1	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882005	3882096	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3882097	3882222	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882223	3882310	1	-	1	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882223	3882310	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3882311	3882525	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882526	3882650	0.82	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882526	3882650	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3882651	3882762	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882763	3882987	0.76	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882763	3882987	.	-	.	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	start_codon	3882985	3882987	.	-	0	transcript_id "Phchi.S1G062100.t1"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	transcript	3880502	3882987	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	stop_codon	3880499	3880501	.	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3880502	3880517	0.8	-	1	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3880502	3880517	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3880518	3880615	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3880616	3880663	0.8	-	1	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3880616	3880663	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3880664	3880829	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3880830	3880858	0.8	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3880830	3880858	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3880859	3881296	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881297	3881362	0.83	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881297	3881362	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881363	3881458	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881459	3881545	1	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881459	3881545	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881546	3881636	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881637	3881729	1	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881637	3881729	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881730	3881808	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3881809	3881881	1	-	1	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3881809	3881881	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3881882	3882004	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882005	3882096	1	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882005	3882096	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3882097	3882222	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882223	3882310	1	-	1	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882223	3882310	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3882311	3882409	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882410	3882512	0.53	-	2	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882410	3882512	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	intron	3882513	3882641	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	CDS	3882642	3882987	0.34	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	exon	3882642	3882987	.	-	.	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
Phchi.S1	AUGUSTUS	start_codon	3882985	3882987	.	-	0	transcript_id "Phchi.S1G062100.t2"; gene_id "Phchi.S1G062100"
# This transcript jg2389.t1 is derived from g9309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6456570	6456824	.	-	.	Phchi.S5G099800
Phchi.S5	AUGUSTUS	transcript	6456570	6456824	.	-	.	transcript_id "Phchi.S5G099800.t1"; gene_id "Phchi.S5G099800"
Phchi.S5	AUGUSTUS	stop_codon	6456567	6456569	.	-	0	transcript_id "Phchi.S5G099800.t1"; gene_id "Phchi.S5G099800"
Phchi.S5	AUGUSTUS	CDS	6456570	6456824	0.85	-	0	transcript_id "Phchi.S5G099800.t1"; gene_id "Phchi.S5G099800"
Phchi.S5	AUGUSTUS	exon	6456570	6456824	.	-	.	transcript_id "Phchi.S5G099800.t1"; gene_id "Phchi.S5G099800"
Phchi.S5	AUGUSTUS	start_codon	6456822	6456824	.	-	0	transcript_id "Phchi.S5G099800.t1"; gene_id "Phchi.S5G099800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13118.t1 is derived from g11583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4210707	4212193	.	+	.	Phchi.S3G043700
Phchi.S3	AUGUSTUS	transcript	4210707	4212193	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	start_codon	4210707	4210709	.	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4210707	4210761	0.97	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4210707	4210761	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4210762	4210985	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4210986	4211041	0.99	+	2	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4210986	4211041	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4211042	4211178	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4211179	4211253	0.82	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4211179	4211253	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4211254	4211345	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4211346	4211382	0.98	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4211346	4211382	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4211383	4211491	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4211492	4211589	1	+	2	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4211492	4211589	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4211590	4211679	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4211680	4211741	1	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4211680	4211741	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4211742	4211858	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4211859	4211982	1	+	1	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4211859	4211982	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	intron	4211983	4212076	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	CDS	4212077	4212193	1	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	exon	4212077	4212193	.	+	.	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
Phchi.S3	AUGUSTUS	stop_codon	4212194	4212196	.	+	0	transcript_id "Phchi.S3G043700.t1"; gene_id "Phchi.S3G043700"
# This transcript jg9080.t2 is derived from g6255.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9081.t1 is derived from g6256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39756696	39762493	.	-	.	Phchi.S1G624000
Phchi.S1	AUGUSTUS	transcript	39756696	39762493	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	stop_codon	39756693	39756695	.	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	CDS	39756696	39757112	0.96	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	exon	39756696	39757112	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	intron	39757113	39757232	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	CDS	39757233	39757373	0.6	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	exon	39757233	39757373	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	intron	39757374	39757494	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	CDS	39757495	39759930	0.87	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	exon	39757495	39759930	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	intron	39759931	39760049	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	CDS	39760050	39761849	0.96	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	exon	39760050	39761849	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	intron	39761850	39761974	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	CDS	39761975	39762493	0.84	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	exon	39761975	39762493	.	-	.	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
Phchi.S1	AUGUSTUS	start_codon	39762491	39762493	.	-	0	transcript_id "Phchi.S1G624000.t1"; gene_id "Phchi.S1G624000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2775.t1 is derived from g9695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8777112	8778871	.	+	.	Phchi.S5G138400
Phchi.S5	AUGUSTUS	transcript	8777112	8778871	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	start_codon	8777112	8777114	.	+	0	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	CDS	8777112	8777227	0.48	+	0	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	exon	8777112	8777227	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	intron	8777228	8777364	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	CDS	8777365	8777502	0.65	+	1	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	exon	8777365	8777502	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	intron	8777503	8777644	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	CDS	8777645	8778257	0.22	+	1	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	exon	8777645	8778257	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	intron	8778258	8778392	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	CDS	8778393	8778615	0.16	+	0	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	exon	8778393	8778615	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	intron	8778616	8778836	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	CDS	8778837	8778871	0.74	+	2	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	exon	8778837	8778871	.	+	.	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
Phchi.S5	AUGUSTUS	stop_codon	8778872	8778874	.	+	0	transcript_id "Phchi.S5G138400.t1"; gene_id "Phchi.S5G138400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9069.t1 is derived from g6244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39650629	39652613	.	+	.	Phchi.S1G622800
Phchi.S1	AUGUSTUS	transcript	39650629	39652613	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	start_codon	39650629	39650631	.	+	0	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	CDS	39650629	39651017	0.99	+	0	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	exon	39650629	39651017	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	intron	39651018	39651108	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	CDS	39651109	39651353	1	+	1	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	exon	39651109	39651353	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	intron	39651354	39651434	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	CDS	39651435	39651799	0.84	+	2	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	exon	39651435	39651799	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	intron	39651800	39651903	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	CDS	39651904	39652017	0.69	+	0	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	exon	39651904	39652017	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	intron	39652018	39652141	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	CDS	39652142	39652272	1	+	0	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	exon	39652142	39652272	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	intron	39652273	39652366	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	CDS	39652367	39652613	0.99	+	1	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	exon	39652367	39652613	.	+	.	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
Phchi.S1	AUGUSTUS	stop_codon	39652614	39652616	.	+	0	transcript_id "Phchi.S1G622800.t1"; gene_id "Phchi.S1G622800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15203.t1 is derived from g13671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17537324	17538832	.	+	.	Phchi.S3G252200
Phchi.S3	AUGUSTUS	transcript	17537324	17538832	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	start_codon	17537324	17537326	.	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17537324	17537444	0.76	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17537324	17537444	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	intron	17537445	17537556	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17537557	17537675	1	+	2	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17537557	17537675	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	intron	17537676	17537765	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17537766	17537918	1	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17537766	17537918	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	intron	17537919	17538053	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17538054	17538200	1	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17538054	17538200	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	intron	17538201	17538278	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17538279	17538431	1	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17538279	17538431	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	intron	17538432	17538506	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17538507	17538629	0.99	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17538507	17538629	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	intron	17538630	17538736	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	CDS	17538737	17538832	0.99	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	exon	17538737	17538832	.	+	.	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
Phchi.S3	AUGUSTUS	stop_codon	17538833	17538835	.	+	0	transcript_id "Phchi.S3G252200.t1"; gene_id "Phchi.S3G252200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14785.t1 is derived from g13253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14702882	14705145	.	+	.	Phchi.S3G210400
Phchi.S3	AUGUSTUS	transcript	14702882	14705145	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	start_codon	14702882	14702884	.	+	0	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	CDS	14702882	14703154	1	+	0	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	exon	14702882	14703154	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	intron	14703155	14703247	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	CDS	14703248	14703364	0.99	+	0	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	exon	14703248	14703364	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	intron	14703365	14703479	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	CDS	14703480	14703929	0.96	+	0	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	exon	14703480	14703929	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	intron	14703930	14704044	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	CDS	14704045	14705145	0.5	+	0	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	exon	14704045	14705145	.	+	.	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
Phchi.S3	AUGUSTUS	stop_codon	14705146	14705148	.	+	0	transcript_id "Phchi.S3G210400.t1"; gene_id "Phchi.S3G210400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8381.t1 is derived from g5556.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35598633	35599412	.	-	.	Phchi.S1G554000
Phchi.S1	AUGUSTUS	transcript	35598633	35599412	.	-	.	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	stop_codon	35598630	35598632	.	-	0	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	CDS	35598633	35598875	0.94	-	0	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	exon	35598633	35598875	.	-	.	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	intron	35598876	35598954	.	-	.	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	CDS	35598955	35599050	1	-	0	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	exon	35598955	35599050	.	-	.	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	intron	35599051	35599211	.	-	.	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	CDS	35599212	35599412	0.89	-	0	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	exon	35599212	35599412	.	-	.	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	start_codon	35599410	35599412	.	-	0	transcript_id "Phchi.S1G554000.t1"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	transcript	35598633	35599399	.	-	.	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	stop_codon	35598630	35598632	.	-	0	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	CDS	35598633	35598875	0.98	-	0	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	exon	35598633	35598875	.	-	.	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	intron	35598876	35598954	.	-	.	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	CDS	35598955	35599050	1	-	0	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	exon	35598955	35599050	.	-	.	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	intron	35599051	35599207	.	-	.	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	CDS	35599208	35599399	0.52	-	0	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	exon	35599208	35599399	.	-	.	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
Phchi.S1	AUGUSTUS	start_codon	35599397	35599399	.	-	0	transcript_id "Phchi.S1G554000.t2"; gene_id "Phchi.S1G554000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14513.t1 is derived from g12981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13244620	13247190	.	+	.	Phchi.S3G183200
Phchi.S3	AUGUSTUS	transcript	13244620	13247190	.	+	.	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	start_codon	13244620	13244622	.	+	0	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	CDS	13244620	13244795	0.16	+	0	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	exon	13244620	13244795	.	+	.	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	intron	13244796	13245078	.	+	.	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	CDS	13245079	13246132	0.64	+	1	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	exon	13245079	13246132	.	+	.	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	intron	13246133	13246278	.	+	.	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	CDS	13246279	13247190	0.63	+	0	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	exon	13246279	13247190	.	+	.	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
Phchi.S3	AUGUSTUS	stop_codon	13247191	13247193	.	+	0	transcript_id "Phchi.S3G183200.t1"; gene_id "Phchi.S3G183200"
# This transcript jg5457.t2 is derived from g2627.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5457.t3 is derived from g2627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5457.t4 is derived from g2627.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5458.t1 is derived from g2628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16944861	16950401	.	+	.	Phchi.S1G261700
Phchi.S1	AUGUSTUS	transcript	16944861	16950401	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	start_codon	16944861	16944863	.	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16944861	16944947	0.84	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16944861	16944947	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16944948	16945052	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16945053	16945113	0.83	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16945053	16945113	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16945114	16945222	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16945223	16945259	1	+	2	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16945223	16945259	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16945260	16945354	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16945355	16945485	1	+	1	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16945355	16945485	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16945486	16945648	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16945649	16945816	1	+	2	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16945649	16945816	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16945817	16945915	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16945916	16945997	1	+	2	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16945916	16945997	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16945998	16946089	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16946090	16946223	1	+	1	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16946090	16946223	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16946224	16946371	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16946372	16946511	1	+	2	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16946372	16946511	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16946512	16946595	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16946596	16946646	1	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16946596	16946646	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16946647	16946829	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16946830	16946912	1	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16946830	16946912	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16946913	16947046	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16947047	16947098	1	+	1	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16947047	16947098	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16947099	16947224	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16947225	16947360	1	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16947225	16947360	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16947361	16947461	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16947462	16947942	1	+	2	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16947462	16947942	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16947943	16948039	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16948040	16948366	1	+	1	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16948040	16948366	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16948367	16948472	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16948473	16948695	1	+	1	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16948473	16948695	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16948696	16948804	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16948805	16948875	1	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16948805	16948875	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16948876	16948951	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16948952	16949120	1	+	1	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16948952	16949120	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16949121	16949205	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16949206	16949326	1	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16949206	16949326	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16949327	16949472	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16949473	16950032	1	+	2	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16949473	16950032	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	intron	16950033	16950185	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	CDS	16950186	16950401	1	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	exon	16950186	16950401	.	+	.	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
Phchi.S1	AUGUSTUS	stop_codon	16950402	16950404	.	+	0	transcript_id "Phchi.S1G261700.t1"; gene_id "Phchi.S1G261700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1746.t1 is derived from g8666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2842178	2843174	.	-	.	Phchi.S5G035500
Phchi.S5	AUGUSTUS	transcript	2842178	2843174	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	stop_codon	2842175	2842177	.	-	0	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	CDS	2842178	2842426	0.98	-	0	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	exon	2842178	2842426	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	intron	2842427	2842506	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	CDS	2842507	2842596	1	-	0	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	exon	2842507	2842596	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	intron	2842597	2842672	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	CDS	2842673	2842851	1	-	2	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	exon	2842673	2842851	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	intron	2842852	2842931	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	CDS	2842932	2843074	1	-	1	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	exon	2842932	2843074	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	intron	2843075	2843160	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	CDS	2843161	2843174	1	-	0	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	exon	2843161	2843174	.	-	.	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
Phchi.S5	AUGUSTUS	start_codon	2843172	2843174	.	-	0	transcript_id "Phchi.S5G035500.t1"; gene_id "Phchi.S5G035500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15872.t1 is derived from g14342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21984470	21985929	.	-	.	Phchi.S3G319100
Phchi.S3	AUGUSTUS	transcript	21984470	21985929	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	stop_codon	21984467	21984469	.	-	0	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984470	21984472	0.99	-	0	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984470	21984472	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21984473	21984559	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984560	21984615	0.92	-	2	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984560	21984615	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21984616	21984707	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984708	21984730	0.92	-	1	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984708	21984730	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21984731	21984933	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984934	21985167	0.8	-	1	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984934	21985167	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21985168	21985291	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21985292	21985414	0.64	-	1	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21985292	21985414	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21985415	21985501	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21985502	21985929	0.7	-	0	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21985502	21985929	.	-	.	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	start_codon	21985927	21985929	.	-	0	transcript_id "Phchi.S3G319100.t1"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	transcript	21984470	21985929	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	stop_codon	21984467	21984469	.	-	0	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984470	21984472	0.99	-	0	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984470	21984472	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21984473	21984559	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984560	21984615	0.91	-	2	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984560	21984615	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21984616	21984707	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984708	21984742	0.92	-	1	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984708	21984742	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21984743	21984933	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21984934	21985167	0.76	-	1	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21984934	21985167	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21985168	21985291	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21985292	21985414	0.63	-	1	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21985292	21985414	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	intron	21985415	21985501	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	CDS	21985502	21985929	0.67	-	0	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	exon	21985502	21985929	.	-	.	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
Phchi.S3	AUGUSTUS	start_codon	21985927	21985929	.	-	0	transcript_id "Phchi.S3G319100.t2"; gene_id "Phchi.S3G319100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13583.t1 is derived from g12050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7575384	7575803	.	+	.	Phchi.S3G090200
Phchi.S3	AUGUSTUS	transcript	7575384	7575803	.	+	.	transcript_id "Phchi.S3G090200.t1"; gene_id "Phchi.S3G090200"
Phchi.S3	AUGUSTUS	start_codon	7575384	7575386	.	+	0	transcript_id "Phchi.S3G090200.t1"; gene_id "Phchi.S3G090200"
Phchi.S3	AUGUSTUS	CDS	7575384	7575803	0.98	+	0	transcript_id "Phchi.S3G090200.t1"; gene_id "Phchi.S3G090200"
Phchi.S3	AUGUSTUS	exon	7575384	7575803	.	+	.	transcript_id "Phchi.S3G090200.t1"; gene_id "Phchi.S3G090200"
Phchi.S3	AUGUSTUS	stop_codon	7575804	7575806	.	+	0	transcript_id "Phchi.S3G090200.t1"; gene_id "Phchi.S3G090200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12774.t1 is derived from g11239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1982603	1985509	.	+	.	Phchi.S3G009300
Phchi.S3	AUGUSTUS	transcript	1982603	1985509	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	start_codon	1982603	1982605	.	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1982603	1983662	0.94	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1982603	1983662	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	intron	1983663	1983854	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1983855	1984027	0.94	+	2	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1983855	1984027	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	intron	1984028	1984226	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1984227	1984298	1	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1984227	1984298	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	intron	1984299	1984387	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1984388	1984477	0.59	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1984388	1984477	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	intron	1984478	1984590	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1984591	1984851	0.98	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1984591	1984851	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	intron	1984852	1984946	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1984947	1985159	1	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1984947	1985159	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	intron	1985160	1985254	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	CDS	1985255	1985509	0.91	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	exon	1985255	1985509	.	+	.	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
Phchi.S3	AUGUSTUS	stop_codon	1985510	1985512	.	+	0	transcript_id "Phchi.S3G009300.t1"; gene_id "Phchi.S3G009300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8612.t1 is derived from g5787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36911538	36912848	.	-	.	Phchi.S1G577100
Phchi.S1	AUGUSTUS	transcript	36911538	36912848	.	-	.	transcript_id "Phchi.S1G577100.t1"; gene_id "Phchi.S1G577100"
Phchi.S1	AUGUSTUS	stop_codon	36911535	36911537	.	-	0	transcript_id "Phchi.S1G577100.t1"; gene_id "Phchi.S1G577100"
Phchi.S1	AUGUSTUS	CDS	36911538	36912848	0.84	-	0	transcript_id "Phchi.S1G577100.t1"; gene_id "Phchi.S1G577100"
Phchi.S1	AUGUSTUS	exon	36911538	36912848	.	-	.	transcript_id "Phchi.S1G577100.t1"; gene_id "Phchi.S1G577100"
Phchi.S1	AUGUSTUS	start_codon	36912846	36912848	.	-	0	transcript_id "Phchi.S1G577100.t1"; gene_id "Phchi.S1G577100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15056.t1 is derived from g13524.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16769296	16772527	.	-	.	Phchi.S3G237500
Phchi.S3	AUGUSTUS	transcript	16769296	16772527	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	stop_codon	16769293	16769295	.	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16769296	16769367	0.69	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16769296	16769367	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16769368	16769495	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16769496	16769588	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16769496	16769588	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16769589	16769715	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16769716	16769786	1	-	2	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16769716	16769786	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16769787	16769924	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16769925	16769994	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16769925	16769994	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16769995	16770092	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16770093	16770170	0.75	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16770093	16770170	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16770171	16770276	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16770277	16770364	0.61	-	1	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16770277	16770364	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16770365	16770538	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16770539	16770567	0.96	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16770539	16770567	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16770568	16771071	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16771072	16771173	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16771072	16771173	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16771174	16771258	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16771259	16771315	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16771259	16771315	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16771316	16771395	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16771396	16771518	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16771396	16771518	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16771519	16771633	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16771634	16771705	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16771634	16771705	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16771706	16771876	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16771877	16772017	1	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16771877	16772017	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16772018	16772201	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16772202	16772276	0.81	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16772202	16772276	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	intron	16772277	16772407	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	CDS	16772408	16772527	0.77	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	exon	16772408	16772527	.	-	.	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
Phchi.S3	AUGUSTUS	start_codon	16772525	16772527	.	-	0	transcript_id "Phchi.S3G237500.t1"; gene_id "Phchi.S3G237500"
# This transcript jg6990.t2 is derived from g4162.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6991.t1 is derived from g4163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26301703	26302467	.	-	.	Phchi.S1G415000
Phchi.S1	AUGUSTUS	transcript	26301703	26302467	.	-	.	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	stop_codon	26301700	26301702	.	-	0	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	CDS	26301703	26301851	1	-	2	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	exon	26301703	26301851	.	-	.	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	intron	26301852	26301971	.	-	.	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	CDS	26301972	26302014	1	-	0	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	exon	26301972	26302014	.	-	.	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	intron	26302015	26302101	.	-	.	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	CDS	26302102	26302467	1	-	0	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	exon	26302102	26302467	.	-	.	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
Phchi.S1	AUGUSTUS	start_codon	26302465	26302467	.	-	0	transcript_id "Phchi.S1G415000.t1"; gene_id "Phchi.S1G415000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8153.t1 is derived from g5328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34124337	34125461	.	+	.	Phchi.S1G531200
Phchi.S1	AUGUSTUS	transcript	34124337	34125461	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	start_codon	34124337	34124339	.	+	0	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	CDS	34124337	34124572	0.28	+	0	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	exon	34124337	34124572	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	intron	34124573	34124640	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	CDS	34124641	34124750	0.59	+	1	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	exon	34124641	34124750	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	intron	34124751	34124848	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	CDS	34124849	34124948	0.51	+	2	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	exon	34124849	34124948	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	intron	34124949	34125040	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	CDS	34125041	34125461	0.74	+	1	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	exon	34125041	34125461	.	+	.	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
Phchi.S1	AUGUSTUS	stop_codon	34125462	34125464	.	+	0	transcript_id "Phchi.S1G531200.t1"; gene_id "Phchi.S1G531200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6542.t1 is derived from g3714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23562219	23562666	.	+	.	Phchi.S1G370100
Phchi.S1	AUGUSTUS	transcript	23562219	23562666	.	+	.	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	start_codon	23562219	23562221	.	+	0	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	CDS	23562219	23562360	0.98	+	0	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	exon	23562219	23562360	.	+	.	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	intron	23562361	23562463	.	+	.	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	CDS	23562464	23562569	1	+	2	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	exon	23562464	23562569	.	+	.	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	intron	23562570	23562662	.	+	.	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	CDS	23562663	23562666	1	+	1	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	exon	23562663	23562666	.	+	.	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
Phchi.S1	AUGUSTUS	stop_codon	23562667	23562669	.	+	0	transcript_id "Phchi.S1G370100.t1"; gene_id "Phchi.S1G370100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7607.t1 is derived from g4781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30226987	30228375	.	-	.	Phchi.S1G476600
Phchi.S1	AUGUSTUS	transcript	30226987	30228375	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	stop_codon	30226984	30226986	.	-	0	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	CDS	30226987	30227093	1	-	2	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	exon	30226987	30227093	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	intron	30227094	30227171	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	CDS	30227172	30227279	1	-	2	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	exon	30227172	30227279	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	intron	30227280	30227378	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	CDS	30227379	30227658	0.4	-	0	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	exon	30227379	30227658	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	intron	30227659	30227765	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	CDS	30227766	30227825	1	-	0	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	exon	30227766	30227825	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	intron	30227826	30227922	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	CDS	30227923	30228056	1	-	2	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	exon	30227923	30228056	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	intron	30228057	30228140	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	CDS	30228141	30228375	1	-	0	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	exon	30228141	30228375	.	-	.	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
Phchi.S1	AUGUSTUS	start_codon	30228373	30228375	.	-	0	transcript_id "Phchi.S1G476600.t1"; gene_id "Phchi.S1G476600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6562.t1 is derived from g3734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23733267	23733952	.	+	.	Phchi.S1G372100
Phchi.S1	AUGUSTUS	transcript	23733267	23733952	.	+	.	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	start_codon	23733267	23733269	.	+	0	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	CDS	23733267	23733472	0.73	+	0	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	exon	23733267	23733472	.	+	.	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	intron	23733473	23733834	.	+	.	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	CDS	23733835	23733952	0.66	+	1	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	exon	23733835	23733952	.	+	.	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
Phchi.S1	AUGUSTUS	stop_codon	23733953	23733955	.	+	0	transcript_id "Phchi.S1G372100.t1"; gene_id "Phchi.S1G372100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5937.t1 is derived from g3108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19945886	19946860	.	-	.	Phchi.S1G309600
Phchi.S1	AUGUSTUS	transcript	19945886	19946860	.	-	.	transcript_id "Phchi.S1G309600.t1"; gene_id "Phchi.S1G309600"
Phchi.S1	AUGUSTUS	stop_codon	19945883	19945885	.	-	0	transcript_id "Phchi.S1G309600.t1"; gene_id "Phchi.S1G309600"
Phchi.S1	AUGUSTUS	CDS	19945886	19946860	1	-	0	transcript_id "Phchi.S1G309600.t1"; gene_id "Phchi.S1G309600"
Phchi.S1	AUGUSTUS	exon	19945886	19946860	.	-	.	transcript_id "Phchi.S1G309600.t1"; gene_id "Phchi.S1G309600"
Phchi.S1	AUGUSTUS	start_codon	19946858	19946860	.	-	0	transcript_id "Phchi.S1G309600.t1"; gene_id "Phchi.S1G309600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3494.t1 is derived from g663.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4042331	4044323	.	-	.	Phchi.S1G065300
Phchi.S1	AUGUSTUS	transcript	4042331	4044323	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	stop_codon	4042328	4042330	.	-	0	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4042331	4043255	0.98	-	1	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4042331	4043255	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043256	4043458	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4043459	4043482	0.97	-	1	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4043459	4043482	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043483	4043681	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4043682	4043763	0.98	-	2	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4043682	4043763	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043764	4043914	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4043915	4043921	0.98	-	0	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4043915	4043921	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043922	4044079	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4044080	4044127	1	-	0	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4044080	4044127	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4044128	4044212	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4044213	4044323	0.88	-	0	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4044213	4044323	.	-	.	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	start_codon	4044321	4044323	.	-	0	transcript_id "Phchi.S1G065300.t1"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	transcript	4042331	4044246	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	stop_codon	4042328	4042330	.	-	0	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4042331	4043255	0.62	-	1	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4042331	4043255	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043256	4043458	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4043459	4043482	0.61	-	1	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4043459	4043482	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043483	4043681	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4043682	4043763	0.61	-	2	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4043682	4043763	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043764	4043914	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4043915	4043921	0.61	-	0	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4043915	4043921	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4043922	4044079	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4044080	4044117	0.64	-	2	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4044080	4044117	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	intron	4044118	4044212	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	CDS	4044213	4044246	0.63	-	0	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	exon	4044213	4044246	.	-	.	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
Phchi.S1	AUGUSTUS	start_codon	4044244	4044246	.	-	0	transcript_id "Phchi.S1G065300.t2"; gene_id "Phchi.S1G065300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg846.t1 is derived from g10628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5875507	5876049	.	+	.	Phchi.S6G080500
Phchi.S6	AUGUSTUS	transcript	5875507	5876049	.	+	.	transcript_id "Phchi.S6G080500.t1"; gene_id "Phchi.S6G080500"
Phchi.S6	AUGUSTUS	start_codon	5875507	5875509	.	+	0	transcript_id "Phchi.S6G080500.t1"; gene_id "Phchi.S6G080500"
Phchi.S6	AUGUSTUS	CDS	5875507	5876049	0.97	+	0	transcript_id "Phchi.S6G080500.t1"; gene_id "Phchi.S6G080500"
Phchi.S6	AUGUSTUS	exon	5875507	5876049	.	+	.	transcript_id "Phchi.S6G080500.t1"; gene_id "Phchi.S6G080500"
Phchi.S6	AUGUSTUS	stop_codon	5876050	5876052	.	+	0	transcript_id "Phchi.S6G080500.t1"; gene_id "Phchi.S6G080500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1788.t1 is derived from g8708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3001867	3004030	.	+	.	Phchi.S5G039700
Phchi.S5	AUGUSTUS	transcript	3001867	3004030	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	start_codon	3001867	3001869	.	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3001867	3002053	0.81	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3001867	3002053	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002054	3002180	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002181	3002229	0.45	+	2	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002181	3002229	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002230	3002318	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002319	3002394	1	+	1	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002319	3002394	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002395	3002472	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002473	3002760	1	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002473	3002760	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002761	3002901	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002902	3003179	1	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002902	3003179	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3003180	3003290	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3003291	3003408	1	+	1	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3003291	3003408	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3003409	3003574	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3003575	3003733	1	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3003575	3003733	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3003734	3003871	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3003872	3004030	1	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3003872	3004030	.	+	.	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	stop_codon	3004031	3004033	.	+	0	transcript_id "Phchi.S5G039700.t1"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	transcript	3001867	3004030	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	start_codon	3001867	3001869	.	+	0	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3001867	3002053	0.85	+	0	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3001867	3002053	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002054	3002180	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002181	3002229	0.48	+	2	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002181	3002229	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002230	3002318	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002319	3002394	1	+	1	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002319	3002394	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002395	3002472	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002473	3002666	0.97	+	0	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002473	3002666	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002667	3002743	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002744	3002760	0.91	+	1	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002744	3002760	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3002761	3002917	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3002918	3003179	0.91	+	2	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3002918	3003179	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3003180	3003290	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3003291	3003408	1	+	1	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3003291	3003408	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3003409	3003574	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3003575	3003733	1	+	0	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3003575	3003733	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	intron	3003734	3003871	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	CDS	3003872	3004030	1	+	0	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	exon	3003872	3004030	.	+	.	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
Phchi.S5	AUGUSTUS	stop_codon	3004031	3004033	.	+	0	transcript_id "Phchi.S5G039700.t2"; gene_id "Phchi.S5G039700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14501.t1 is derived from g12969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13213453	13214828	.	-	.	Phchi.S3G182000
Phchi.S3	AUGUSTUS	transcript	13213453	13214828	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	stop_codon	13213450	13213452	.	-	0	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	CDS	13213453	13213574	0.79	-	2	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	exon	13213453	13213574	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	intron	13213575	13213661	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	CDS	13213662	13213920	1	-	0	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	exon	13213662	13213920	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	intron	13213921	13213993	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	CDS	13213994	13214233	0.91	-	0	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	exon	13213994	13214233	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	intron	13214234	13214334	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	CDS	13214335	13214456	0.85	-	2	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	exon	13214335	13214456	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	intron	13214457	13214581	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	CDS	13214582	13214828	0.97	-	0	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	exon	13214582	13214828	.	-	.	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
Phchi.S3	AUGUSTUS	start_codon	13214826	13214828	.	-	0	transcript_id "Phchi.S3G182000.t1"; gene_id "Phchi.S3G182000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6263.t1 is derived from g3435.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21923812	21925202	.	-	.	Phchi.S1G342200
Phchi.S1	AUGUSTUS	transcript	21923812	21925202	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	stop_codon	21923809	21923811	.	-	0	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21923812	21923870	1	-	2	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21923812	21923870	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21923871	21924061	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924062	21924091	0.61	-	2	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924062	21924091	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924092	21924289	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924290	21924496	0.63	-	2	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924290	21924496	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924497	21924588	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924589	21924634	0.29	-	0	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924589	21924634	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924635	21924778	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924779	21924961	0.34	-	0	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924779	21924961	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924962	21925103	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21925104	21925202	1	-	0	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21925104	21925202	.	-	.	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	start_codon	21925200	21925202	.	-	0	transcript_id "Phchi.S1G342200.t1"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	transcript	21923812	21925202	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	stop_codon	21923809	21923811	.	-	0	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21923812	21923870	0.98	-	2	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21923812	21923870	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21923871	21924031	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924032	21924061	0.41	-	2	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924032	21924061	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924062	21924289	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924290	21924496	0.57	-	2	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924290	21924496	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924497	21924588	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924589	21924634	0.32	-	0	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924589	21924634	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924635	21924778	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21924779	21924961	0.4	-	0	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21924779	21924961	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	intron	21924962	21925103	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	CDS	21925104	21925202	1	-	0	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	exon	21925104	21925202	.	-	.	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
Phchi.S1	AUGUSTUS	start_codon	21925200	21925202	.	-	0	transcript_id "Phchi.S1G342200.t2"; gene_id "Phchi.S1G342200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9467.t1 is derived from g6643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41602157	41602624	.	+	.	Phchi.S1G662600
Phchi.S1	AUGUSTUS	transcript	41602157	41602624	.	+	.	transcript_id "Phchi.S1G662600.t1"; gene_id "Phchi.S1G662600"
Phchi.S1	AUGUSTUS	start_codon	41602157	41602159	.	+	0	transcript_id "Phchi.S1G662600.t1"; gene_id "Phchi.S1G662600"
Phchi.S1	AUGUSTUS	CDS	41602157	41602624	0.95	+	0	transcript_id "Phchi.S1G662600.t1"; gene_id "Phchi.S1G662600"
Phchi.S1	AUGUSTUS	exon	41602157	41602624	.	+	.	transcript_id "Phchi.S1G662600.t1"; gene_id "Phchi.S1G662600"
Phchi.S1	AUGUSTUS	stop_codon	41602625	41602627	.	+	0	transcript_id "Phchi.S1G662600.t1"; gene_id "Phchi.S1G662600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2629.t1 is derived from g9549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7842768	7844730	.	+	.	Phchi.S5G123800
Phchi.S5	AUGUSTUS	transcript	7842768	7844730	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	start_codon	7842768	7842770	.	+	0	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7842768	7842826	0.68	+	0	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7842768	7842826	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	intron	7842827	7843006	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7843007	7843058	1	+	1	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7843007	7843058	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	intron	7843059	7843148	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7843149	7843374	1	+	0	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7843149	7843374	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	intron	7843375	7843534	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7843535	7843645	1	+	2	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7843535	7843645	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	intron	7843646	7843819	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7843820	7843978	1	+	2	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7843820	7843978	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	intron	7843979	7844072	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7844073	7844323	1	+	2	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7844073	7844323	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	intron	7844324	7844409	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	CDS	7844410	7844730	1	+	0	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	exon	7844410	7844730	.	+	.	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
Phchi.S5	AUGUSTUS	stop_codon	7844731	7844733	.	+	0	transcript_id "Phchi.S5G123800.t1"; gene_id "Phchi.S5G123800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9715.t1 is derived from g6891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43386103	43387835	.	+	.	Phchi.S1G687400
Phchi.S1	AUGUSTUS	transcript	43386103	43387835	.	+	.	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	start_codon	43386103	43386105	.	+	0	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	CDS	43386103	43387144	0.97	+	0	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	exon	43386103	43387144	.	+	.	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	intron	43387145	43387269	.	+	.	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	CDS	43387270	43387835	0.95	+	2	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	exon	43387270	43387835	.	+	.	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
Phchi.S1	AUGUSTUS	stop_codon	43387836	43387838	.	+	0	transcript_id "Phchi.S1G687400.t1"; gene_id "Phchi.S1G687400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2421.t1 is derived from g9341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6568361	6570205	.	+	.	Phchi.S5G103000
Phchi.S5	AUGUSTUS	transcript	6568361	6570205	.	+	.	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	start_codon	6568361	6568363	.	+	0	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	CDS	6568361	6568887	0.68	+	0	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	exon	6568361	6568887	.	+	.	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	intron	6568888	6569078	.	+	.	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	CDS	6569079	6569895	0.66	+	1	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	exon	6569079	6569895	.	+	.	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	intron	6569896	6570178	.	+	.	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	CDS	6570179	6570205	0.84	+	0	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	exon	6570179	6570205	.	+	.	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
Phchi.S5	AUGUSTUS	stop_codon	6570206	6570208	.	+	0	transcript_id "Phchi.S5G103000.t1"; gene_id "Phchi.S5G103000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12216.t1 is derived from g7892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6803212	6805150	.	+	.	Phchi.S2G029600
Phchi.S2	AUGUSTUS	transcript	6803212	6805150	.	+	.	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	start_codon	6803212	6803214	.	+	0	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	CDS	6803212	6803643	0.86	+	0	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	exon	6803212	6803643	.	+	.	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	intron	6803644	6803739	.	+	.	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	CDS	6803740	6804006	1	+	0	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	exon	6803740	6804006	.	+	.	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	intron	6804007	6804091	.	+	.	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	CDS	6804092	6805150	1	+	0	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	exon	6804092	6805150	.	+	.	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
Phchi.S2	AUGUSTUS	stop_codon	6805151	6805153	.	+	0	transcript_id "Phchi.S2G029600.t1"; gene_id "Phchi.S2G029600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7649.t1 is derived from g4823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30392090	30394314	.	-	.	Phchi.S1G480800
Phchi.S1	AUGUSTUS	transcript	30392090	30394314	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	stop_codon	30392087	30392089	.	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30392090	30392252	0.89	-	1	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30392090	30392252	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30392253	30392332	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30392333	30392391	1	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30392333	30392391	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30392392	30392481	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30392482	30392631	1	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30392482	30392631	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30392632	30392727	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30392728	30392819	0.7	-	2	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30392728	30392819	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30392820	30392958	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30392959	30393045	0.7	-	2	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30392959	30393045	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30393046	30393140	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30393141	30393147	0.7	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30393141	30393147	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30393148	30393227	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30393228	30393311	0.7	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30393228	30393311	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30393312	30393541	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30393542	30393601	1	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30393542	30393601	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30393602	30393742	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30393743	30393871	1	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30393743	30393871	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30393872	30393963	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30393964	30394047	1	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30393964	30394047	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	intron	30394048	30394176	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	CDS	30394177	30394314	0.99	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	exon	30394177	30394314	.	-	.	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
Phchi.S1	AUGUSTUS	start_codon	30394312	30394314	.	-	0	transcript_id "Phchi.S1G480800.t1"; gene_id "Phchi.S1G480800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4316.t1 is derived from g1485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9587798	9589049	.	-	.	Phchi.S1G147500
Phchi.S1	AUGUSTUS	transcript	9587798	9589049	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	stop_codon	9587795	9587797	.	-	0	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	CDS	9587798	9588096	0.78	-	2	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	exon	9587798	9588096	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	intron	9588097	9588240	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	CDS	9588241	9588308	0.32	-	1	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	exon	9588241	9588308	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	intron	9588309	9588467	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	CDS	9588468	9588589	0.36	-	0	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	exon	9588468	9588589	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	intron	9588590	9588899	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	CDS	9588900	9589049	0.46	-	0	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	exon	9588900	9589049	.	-	.	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
Phchi.S1	AUGUSTUS	start_codon	9589047	9589049	.	-	0	transcript_id "Phchi.S1G147500.t1"; gene_id "Phchi.S1G147500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14087.t1 is derived from g12554.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10791708	10792972	.	-	.	Phchi.S3G140600
Phchi.S3	AUGUSTUS	transcript	10791708	10792972	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	stop_codon	10791705	10791707	.	-	0	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10791708	10791822	1	-	1	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10791708	10791822	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10791823	10791913	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10791914	10792092	1	-	0	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10791914	10792092	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792093	10792189	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792190	10792261	1	-	0	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792190	10792261	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792262	10792356	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792357	10792515	1	-	0	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792357	10792515	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792516	10792628	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792629	10792692	1	-	1	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792629	10792692	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792693	10792787	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792788	10792972	0.92	-	0	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792788	10792972	.	-	.	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	start_codon	10792970	10792972	.	-	0	transcript_id "Phchi.S3G140600.t1"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	transcript	10791708	10792972	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	stop_codon	10791705	10791707	.	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10791708	10791822	1	-	1	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10791708	10791822	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10791823	10791913	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10791914	10792092	1	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10791914	10792092	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792093	10792189	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792190	10792261	1	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792190	10792261	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792262	10792356	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792357	10792515	0.98	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792357	10792515	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792516	10792628	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792629	10792697	0.99	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792629	10792697	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792698	10792787	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792788	10792828	0.99	-	2	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792788	10792828	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	intron	10792829	10792902	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	CDS	10792903	10792972	0.41	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	exon	10792903	10792972	.	-	.	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
Phchi.S3	AUGUSTUS	start_codon	10792970	10792972	.	-	0	transcript_id "Phchi.S3G140600.t2"; gene_id "Phchi.S3G140600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3856.t1 is derived from g1025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6053782	6054789	.	+	.	Phchi.S1G101500
Phchi.S1	AUGUSTUS	transcript	6053782	6054789	.	+	.	transcript_id "Phchi.S1G101500.t1"; gene_id "Phchi.S1G101500"
Phchi.S1	AUGUSTUS	start_codon	6053782	6053784	.	+	0	transcript_id "Phchi.S1G101500.t1"; gene_id "Phchi.S1G101500"
Phchi.S1	AUGUSTUS	CDS	6053782	6054789	0.72	+	0	transcript_id "Phchi.S1G101500.t1"; gene_id "Phchi.S1G101500"
Phchi.S1	AUGUSTUS	exon	6053782	6054789	.	+	.	transcript_id "Phchi.S1G101500.t1"; gene_id "Phchi.S1G101500"
Phchi.S1	AUGUSTUS	stop_codon	6054790	6054792	.	+	0	transcript_id "Phchi.S1G101500.t1"; gene_id "Phchi.S1G101500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2447.t1 is derived from g9367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6664970	6665960	.	-	.	Phchi.S5G105600
Phchi.S5	AUGUSTUS	transcript	6664970	6665960	.	-	.	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	stop_codon	6664967	6664969	.	-	0	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	CDS	6664970	6665151	0.97	-	2	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	exon	6664970	6665151	.	-	.	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	intron	6665152	6665241	.	-	.	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	CDS	6665242	6665380	1	-	0	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	exon	6665242	6665380	.	-	.	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	intron	6665381	6665489	.	-	.	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	CDS	6665490	6665960	0.97	-	0	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	exon	6665490	6665960	.	-	.	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
Phchi.S5	AUGUSTUS	start_codon	6665958	6665960	.	-	0	transcript_id "Phchi.S5G105600.t1"; gene_id "Phchi.S5G105600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3175.t1 is derived from g344.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2109388	2110834	.	-	.	Phchi.S1G033400
Phchi.S1	AUGUSTUS	transcript	2109388	2110834	.	-	.	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	stop_codon	2109385	2109387	.	-	0	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	CDS	2109388	2109549	1	-	0	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	exon	2109388	2109549	.	-	.	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	intron	2109550	2109802	.	-	.	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	CDS	2109803	2110640	1	-	1	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	exon	2109803	2110640	.	-	.	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	intron	2110641	2110802	.	-	.	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	CDS	2110803	2110834	0.98	-	0	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	exon	2110803	2110834	.	-	.	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	start_codon	2110832	2110834	.	-	0	transcript_id "Phchi.S1G033400.t1"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	transcript	2109388	2110763	.	-	.	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	stop_codon	2109385	2109387	.	-	0	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	CDS	2109388	2109549	1	-	0	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	exon	2109388	2109549	.	-	.	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	intron	2109550	2109802	.	-	.	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	CDS	2109803	2110640	0.97	-	1	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	exon	2109803	2110640	.	-	.	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	intron	2110641	2110707	.	-	.	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	CDS	2110708	2110763	0.97	-	0	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	exon	2110708	2110763	.	-	.	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
Phchi.S1	AUGUSTUS	start_codon	2110761	2110763	.	-	0	transcript_id "Phchi.S1G033400.t2"; gene_id "Phchi.S1G033400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8271.t1 is derived from g5446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35053902	35054684	.	-	.	Phchi.S1G543000
Phchi.S1	AUGUSTUS	transcript	35053902	35054684	.	-	.	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	stop_codon	35053899	35053901	.	-	0	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	CDS	35053902	35054360	1	-	0	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	exon	35053902	35054360	.	-	.	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	intron	35054361	35054453	.	-	.	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	CDS	35054454	35054684	0.97	-	0	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	exon	35054454	35054684	.	-	.	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
Phchi.S1	AUGUSTUS	start_codon	35054682	35054684	.	-	0	transcript_id "Phchi.S1G543000.t1"; gene_id "Phchi.S1G543000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3679.t1 is derived from g848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5150074	5150811	.	+	.	Phchi.S1G083800
Phchi.S1	AUGUSTUS	transcript	5150074	5150811	.	+	.	transcript_id "Phchi.S1G083800.t1"; gene_id "Phchi.S1G083800"
Phchi.S1	AUGUSTUS	start_codon	5150074	5150076	.	+	0	transcript_id "Phchi.S1G083800.t1"; gene_id "Phchi.S1G083800"
Phchi.S1	AUGUSTUS	CDS	5150074	5150811	0.96	+	0	transcript_id "Phchi.S1G083800.t1"; gene_id "Phchi.S1G083800"
Phchi.S1	AUGUSTUS	exon	5150074	5150811	.	+	.	transcript_id "Phchi.S1G083800.t1"; gene_id "Phchi.S1G083800"
Phchi.S1	AUGUSTUS	stop_codon	5150812	5150814	.	+	0	transcript_id "Phchi.S1G083800.t1"; gene_id "Phchi.S1G083800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6866.t1 is derived from g4038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25669944	25670935	.	+	.	Phchi.S1G402500
Phchi.S1	AUGUSTUS	transcript	25669944	25670935	.	+	.	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	start_codon	25669944	25669946	.	+	0	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	CDS	25669944	25670190	0.41	+	0	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	exon	25669944	25670190	.	+	.	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	intron	25670191	25670651	.	+	.	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	CDS	25670652	25670747	0.23	+	2	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	exon	25670652	25670747	.	+	.	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	intron	25670748	25670858	.	+	.	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	CDS	25670859	25670935	0.23	+	2	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	exon	25670859	25670935	.	+	.	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
Phchi.S1	AUGUSTUS	stop_codon	25670936	25670938	.	+	0	transcript_id "Phchi.S1G402500.t1"; gene_id "Phchi.S1G402500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10065.t1 is derived from g7241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45598362	45598792	.	+	.	Phchi.S1G722400
Phchi.S1	AUGUSTUS	transcript	45598362	45598792	.	+	.	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	start_codon	45598362	45598364	.	+	0	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	CDS	45598362	45598510	0.31	+	0	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	exon	45598362	45598510	.	+	.	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	intron	45598511	45598596	.	+	.	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	CDS	45598597	45598792	0.97	+	1	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	exon	45598597	45598792	.	+	.	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
Phchi.S1	AUGUSTUS	stop_codon	45598793	45598795	.	+	0	transcript_id "Phchi.S1G722400.t1"; gene_id "Phchi.S1G722400"
# This transcript jg1506.t2 is derived from g8425.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1507.t1 is derived from g8426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1284608	1287130	.	+	.	Phchi.S5G011600
Phchi.S5	AUGUSTUS	transcript	1284608	1287130	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	start_codon	1284608	1284610	.	+	0	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1284608	1285075	0.81	+	0	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1284608	1285075	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	intron	1285076	1285264	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1285265	1285428	1	+	0	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1285265	1285428	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	intron	1285429	1285623	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1285624	1285865	1	+	1	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1285624	1285865	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	intron	1285866	1285974	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1285975	1286082	1	+	2	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1285975	1286082	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	intron	1286083	1286318	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1286319	1286475	1	+	2	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1286319	1286475	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	intron	1286476	1286574	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1286575	1286793	0.98	+	1	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1286575	1286793	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	intron	1286794	1286877	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	CDS	1286878	1287130	0.98	+	1	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	exon	1286878	1287130	.	+	.	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
Phchi.S5	AUGUSTUS	stop_codon	1287131	1287133	.	+	0	transcript_id "Phchi.S5G011600.t1"; gene_id "Phchi.S5G011600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11269.t1 is derived from g15319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5099571	5100494	.	+	.	Phchi.S4G085100
Phchi.S4	AUGUSTUS	transcript	5099571	5100494	.	+	.	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	start_codon	5099571	5099573	.	+	0	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	CDS	5099571	5099671	0.91	+	0	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	exon	5099571	5099671	.	+	.	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	intron	5099672	5099907	.	+	.	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	CDS	5099908	5100077	0.94	+	1	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	exon	5099908	5100077	.	+	.	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	intron	5100078	5100429	.	+	.	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	CDS	5100430	5100494	1	+	2	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	exon	5100430	5100494	.	+	.	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
Phchi.S4	AUGUSTUS	stop_codon	5100495	5100497	.	+	0	transcript_id "Phchi.S4G085100.t1"; gene_id "Phchi.S4G085100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3524.t1 is derived from g693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4221986	4222465	.	-	.	Phchi.S1G068300
Phchi.S1	AUGUSTUS	transcript	4221986	4222465	.	-	.	transcript_id "Phchi.S1G068300.t1"; gene_id "Phchi.S1G068300"
Phchi.S1	AUGUSTUS	stop_codon	4221983	4221985	.	-	0	transcript_id "Phchi.S1G068300.t1"; gene_id "Phchi.S1G068300"
Phchi.S1	AUGUSTUS	CDS	4221986	4222465	0.1	-	0	transcript_id "Phchi.S1G068300.t1"; gene_id "Phchi.S1G068300"
Phchi.S1	AUGUSTUS	exon	4221986	4222465	.	-	.	transcript_id "Phchi.S1G068300.t1"; gene_id "Phchi.S1G068300"
Phchi.S1	AUGUSTUS	start_codon	4222463	4222465	.	-	0	transcript_id "Phchi.S1G068300.t1"; gene_id "Phchi.S1G068300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2296.t1 is derived from g9216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5920350	5922049	.	-	.	Phchi.S5G090500
Phchi.S5	AUGUSTUS	transcript	5920350	5922049	.	-	.	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	stop_codon	5920347	5920349	.	-	0	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	CDS	5920350	5920417	0.6	-	2	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	exon	5920350	5920417	.	-	.	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	intron	5920418	5920560	.	-	.	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	CDS	5920561	5922049	0.49	-	0	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	exon	5920561	5922049	.	-	.	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
Phchi.S5	AUGUSTUS	start_codon	5922047	5922049	.	-	0	transcript_id "Phchi.S5G090500.t1"; gene_id "Phchi.S5G090500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14149.t1 is derived from g12616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11169575	11170553	.	+	.	Phchi.S3G146800
Phchi.S3	AUGUSTUS	transcript	11169575	11170553	.	+	.	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	start_codon	11169575	11169577	.	+	0	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	CDS	11169575	11169748	0.95	+	0	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	exon	11169575	11169748	.	+	.	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	intron	11169749	11169929	.	+	.	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	CDS	11169930	11170118	1	+	0	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	exon	11169930	11170118	.	+	.	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	intron	11170119	11170232	.	+	.	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	CDS	11170233	11170553	1	+	0	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	exon	11170233	11170553	.	+	.	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
Phchi.S3	AUGUSTUS	stop_codon	11170554	11170556	.	+	0	transcript_id "Phchi.S3G146800.t1"; gene_id "Phchi.S3G146800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1823.t1 is derived from g8743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3321236	3322454	.	+	.	Phchi.S5G043200
Phchi.S5	AUGUSTUS	transcript	3321236	3322454	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	start_codon	3321236	3321238	.	+	0	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	CDS	3321236	3321673	1	+	0	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	exon	3321236	3321673	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	intron	3321674	3321860	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	CDS	3321861	3321899	0.84	+	0	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	exon	3321861	3321899	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	intron	3321900	3322070	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	CDS	3322071	3322155	0.88	+	0	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	exon	3322071	3322155	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	intron	3322156	3322365	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	CDS	3322366	3322454	0.5	+	2	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	exon	3322366	3322454	.	+	.	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
Phchi.S5	AUGUSTUS	stop_codon	3322455	3322457	.	+	0	transcript_id "Phchi.S5G043200.t1"; gene_id "Phchi.S5G043200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3673.t1 is derived from g842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5116502	5117743	.	+	.	Phchi.S1G083200
Phchi.S1	AUGUSTUS	transcript	5116502	5117743	.	+	.	transcript_id "Phchi.S1G083200.t1"; gene_id "Phchi.S1G083200"
Phchi.S1	AUGUSTUS	start_codon	5116502	5116504	.	+	0	transcript_id "Phchi.S1G083200.t1"; gene_id "Phchi.S1G083200"
Phchi.S1	AUGUSTUS	CDS	5116502	5117743	0.99	+	0	transcript_id "Phchi.S1G083200.t1"; gene_id "Phchi.S1G083200"
Phchi.S1	AUGUSTUS	exon	5116502	5117743	.	+	.	transcript_id "Phchi.S1G083200.t1"; gene_id "Phchi.S1G083200"
Phchi.S1	AUGUSTUS	stop_codon	5117744	5117746	.	+	0	transcript_id "Phchi.S1G083200.t1"; gene_id "Phchi.S1G083200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4158.t1 is derived from g1327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8679530	8680081	.	-	.	Phchi.S1G131700
Phchi.S1	AUGUSTUS	transcript	8679530	8680081	.	-	.	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	stop_codon	8679527	8679529	.	-	0	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	CDS	8679530	8679578	0.57	-	1	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	exon	8679530	8679578	.	-	.	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	intron	8679579	8679689	.	-	.	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	CDS	8679690	8680081	0.52	-	0	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	exon	8679690	8680081	.	-	.	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
Phchi.S1	AUGUSTUS	start_codon	8680079	8680081	.	-	0	transcript_id "Phchi.S1G131700.t1"; gene_id "Phchi.S1G131700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2222.t1 is derived from g9142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5507296	5510000	.	+	.	Phchi.S5G083100
Phchi.S5	AUGUSTUS	transcript	5507296	5510000	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	start_codon	5507296	5507298	.	+	0	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5507296	5507462	0.44	+	0	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5507296	5507462	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5507463	5507753	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5507754	5507948	0.49	+	1	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5507754	5507948	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5507949	5508185	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5508186	5508250	0.53	+	1	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5508186	5508250	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5508251	5508370	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5508371	5508603	0.89	+	2	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5508371	5508603	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5508604	5508708	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5508709	5508835	1	+	0	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5508709	5508835	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5508836	5508935	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5508936	5509004	1	+	2	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5508936	5509004	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5509005	5509104	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5509105	5509300	1	+	2	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5509105	5509300	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5509301	5509435	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5509436	5509553	1	+	1	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5509436	5509553	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5509554	5509639	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5509640	5509808	0.44	+	0	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5509640	5509808	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	intron	5509809	5509965	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	CDS	5509966	5510000	0.2	+	2	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	exon	5509966	5510000	.	+	.	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
Phchi.S5	AUGUSTUS	stop_codon	5510001	5510003	.	+	0	transcript_id "Phchi.S5G083100.t1"; gene_id "Phchi.S5G083100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2494.t1 is derived from g9414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6958266	6958824	.	-	.	Phchi.S5G110300
Phchi.S5	AUGUSTUS	transcript	6958266	6958824	.	-	.	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	stop_codon	6958263	6958265	.	-	0	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	CDS	6958266	6958587	0.43	-	1	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	exon	6958266	6958587	.	-	.	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	intron	6958588	6958762	.	-	.	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	CDS	6958763	6958824	0.57	-	0	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	exon	6958763	6958824	.	-	.	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
Phchi.S5	AUGUSTUS	start_codon	6958822	6958824	.	-	0	transcript_id "Phchi.S5G110300.t1"; gene_id "Phchi.S5G110300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2157.t1 is derived from g9077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5097641	5099017	.	+	.	Phchi.S5G076600
Phchi.S5	AUGUSTUS	transcript	5097641	5099017	.	+	.	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	start_codon	5097641	5097643	.	+	0	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	CDS	5097641	5097703	0.47	+	0	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	exon	5097641	5097703	.	+	.	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	intron	5097704	5097958	.	+	.	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	CDS	5097959	5098070	0.85	+	0	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	exon	5097959	5098070	.	+	.	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	intron	5098071	5098184	.	+	.	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	CDS	5098185	5099017	0.75	+	2	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	exon	5098185	5099017	.	+	.	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
Phchi.S5	AUGUSTUS	stop_codon	5099018	5099020	.	+	0	transcript_id "Phchi.S5G076600.t1"; gene_id "Phchi.S5G076600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12632.t1 is derived from g15981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C86	AUGUSTUS	gene	19434	20048	.	-	.	Phchi.C86G000100
Phchi.C86	AUGUSTUS	transcript	19434	20048	.	-	.	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	stop_codon	19431	19433	.	-	0	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	CDS	19434	19775	0.53	-	0	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	exon	19434	19775	.	-	.	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	intron	19776	19970	.	-	.	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	CDS	19971	20048	0.52	-	0	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	exon	19971	20048	.	-	.	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
Phchi.C86	AUGUSTUS	start_codon	20046	20048	.	-	0	transcript_id "Phchi.C86G000100.t1"; gene_id "Phchi.C86G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15455.t1 is derived from g13923.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19260308	19262147	.	-	.	Phchi.S3G277400
Phchi.S3	AUGUSTUS	transcript	19260308	19262147	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	stop_codon	19260305	19260307	.	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19260308	19260679	0.99	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19260308	19260679	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19260680	19260871	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19260872	19261012	1	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19260872	19261012	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261013	19261099	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261100	19261177	1	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261100	19261177	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261178	19261260	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261261	19261343	1	-	2	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261261	19261343	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261344	19261426	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261427	19261524	1	-	1	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261427	19261524	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261525	19261648	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261649	19261680	1	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261649	19261680	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261681	19262063	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19262064	19262147	1	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19262064	19262147	.	-	.	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	start_codon	19262145	19262147	.	-	0	transcript_id "Phchi.S3G277400.t1"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	transcript	19260666	19262147	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	stop_codon	19260663	19260665	.	-	0	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19260666	19260679	0.86	-	2	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19260666	19260679	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19260680	19260876	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19260877	19261012	0.95	-	0	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19260877	19261012	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261013	19261099	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261100	19261177	1	-	0	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261100	19261177	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261178	19261260	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261261	19261343	1	-	2	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261261	19261343	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261344	19261426	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261427	19261524	1	-	1	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261427	19261524	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261525	19261648	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19261649	19261680	1	-	0	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19261649	19261680	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	intron	19261681	19262063	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	CDS	19262064	19262147	0.99	-	0	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	exon	19262064	19262147	.	-	.	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
Phchi.S3	AUGUSTUS	start_codon	19262145	19262147	.	-	0	transcript_id "Phchi.S3G277400.t2"; gene_id "Phchi.S3G277400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7682.t1 is derived from g4856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30594895	30596300	.	-	.	Phchi.S1G484100
Phchi.S1	AUGUSTUS	transcript	30594895	30596300	.	-	.	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	stop_codon	30594892	30594894	.	-	0	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	CDS	30594895	30596125	0.62	-	1	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	exon	30594895	30596125	.	-	.	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	intron	30596126	30596220	.	-	.	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	CDS	30596221	30596300	0.64	-	0	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	exon	30596221	30596300	.	-	.	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
Phchi.S1	AUGUSTUS	start_codon	30596298	30596300	.	-	0	transcript_id "Phchi.S1G484100.t1"; gene_id "Phchi.S1G484100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8748.t1 is derived from g5923.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37781059	37782388	.	+	.	Phchi.S1G590700
Phchi.S1	AUGUSTUS	transcript	37781602	37782388	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	start_codon	37781602	37781604	.	+	0	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781602	37781847	0.89	+	0	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781602	37781847	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37781848	37781937	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781938	37782031	1	+	0	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781938	37782031	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37782032	37782115	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37782116	37782213	1	+	2	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37782116	37782213	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37782214	37782370	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37782371	37782388	0.97	+	0	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37782371	37782388	.	+	.	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	stop_codon	37782389	37782391	.	+	0	transcript_id "Phchi.S1G590700.t1"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	transcript	37781059	37782388	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	start_codon	37781059	37781061	.	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781059	37781096	0.93	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781059	37781096	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37781097	37781181	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781182	37781245	0.95	+	1	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781182	37781245	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37781246	37781363	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781364	37781501	0.96	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781364	37781501	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37781502	37781613	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781614	37781847	0.99	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781614	37781847	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37781848	37781937	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37781938	37782031	1	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37781938	37782031	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37782032	37782115	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37782116	37782213	1	+	2	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37782116	37782213	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	intron	37782214	37782370	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	CDS	37782371	37782388	0.97	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	exon	37782371	37782388	.	+	.	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
Phchi.S1	AUGUSTUS	stop_codon	37782389	37782391	.	+	0	transcript_id "Phchi.S1G590700.t2"; gene_id "Phchi.S1G590700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15948.t1 is derived from g14441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	15109	15741	.	-	.	Phchi.C116G000400
Phchi.C116	AUGUSTUS	transcript	15109	15741	.	-	.	transcript_id "Phchi.C116G000400.t1"; gene_id "Phchi.C116G000400"
Phchi.C116	AUGUSTUS	stop_codon	15106	15108	.	-	0	transcript_id "Phchi.C116G000400.t1"; gene_id "Phchi.C116G000400"
Phchi.C116	AUGUSTUS	CDS	15109	15741	0.51	-	0	transcript_id "Phchi.C116G000400.t1"; gene_id "Phchi.C116G000400"
Phchi.C116	AUGUSTUS	exon	15109	15741	.	-	.	transcript_id "Phchi.C116G000400.t1"; gene_id "Phchi.C116G000400"
Phchi.C116	AUGUSTUS	start_codon	15739	15741	.	-	0	transcript_id "Phchi.C116G000400.t1"; gene_id "Phchi.C116G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13851.t1 is derived from g12318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9241049	9242188	.	-	.	Phchi.S3G117000
Phchi.S3	AUGUSTUS	transcript	9241049	9242188	.	-	.	transcript_id "Phchi.S3G117000.t1"; gene_id "Phchi.S3G117000"
Phchi.S3	AUGUSTUS	stop_codon	9241046	9241048	.	-	0	transcript_id "Phchi.S3G117000.t1"; gene_id "Phchi.S3G117000"
Phchi.S3	AUGUSTUS	CDS	9241049	9242188	0.89	-	0	transcript_id "Phchi.S3G117000.t1"; gene_id "Phchi.S3G117000"
Phchi.S3	AUGUSTUS	exon	9241049	9242188	.	-	.	transcript_id "Phchi.S3G117000.t1"; gene_id "Phchi.S3G117000"
Phchi.S3	AUGUSTUS	start_codon	9242186	9242188	.	-	0	transcript_id "Phchi.S3G117000.t1"; gene_id "Phchi.S3G117000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5210.t1 is derived from g2380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15493946	15494617	.	+	.	Phchi.S1G236900
Phchi.S1	AUGUSTUS	transcript	15493946	15494617	.	+	.	transcript_id "Phchi.S1G236900.t1"; gene_id "Phchi.S1G236900"
Phchi.S1	AUGUSTUS	start_codon	15493946	15493948	.	+	0	transcript_id "Phchi.S1G236900.t1"; gene_id "Phchi.S1G236900"
Phchi.S1	AUGUSTUS	CDS	15493946	15494617	0.93	+	0	transcript_id "Phchi.S1G236900.t1"; gene_id "Phchi.S1G236900"
Phchi.S1	AUGUSTUS	exon	15493946	15494617	.	+	.	transcript_id "Phchi.S1G236900.t1"; gene_id "Phchi.S1G236900"
Phchi.S1	AUGUSTUS	stop_codon	15494618	15494620	.	+	0	transcript_id "Phchi.S1G236900.t1"; gene_id "Phchi.S1G236900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5640.t1 is derived from g2810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18016896	18019506	.	-	.	Phchi.S1G279900
Phchi.S1	AUGUSTUS	transcript	18016896	18019506	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	stop_codon	18016893	18016895	.	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18016896	18016982	0.54	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18016896	18016982	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18016983	18017101	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017102	18017326	0.72	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017102	18017326	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18017327	18017423	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017424	18017555	1	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017424	18017555	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18017556	18017698	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017699	18017861	1	-	1	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017699	18017861	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18017862	18017962	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017963	18018079	1	-	1	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017963	18018079	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18018080	18018245	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18018246	18018619	0.53	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18018246	18018619	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18018620	18018725	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18018726	18018910	0.17	-	2	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18018726	18018910	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18018911	18019087	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18019088	18019218	0.38	-	1	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18019088	18019218	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18019219	18019361	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18019362	18019386	0.74	-	2	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18019362	18019386	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18019387	18019499	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18019500	18019506	0.67	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18019500	18019506	.	-	.	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	start_codon	18019504	18019506	.	-	0	transcript_id "Phchi.S1G279900.t1"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	transcript	18016896	18019506	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	stop_codon	18016893	18016895	.	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18016896	18016982	0.45	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18016896	18016982	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18016983	18017101	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017102	18017326	0.59	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017102	18017326	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18017327	18017423	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017424	18017555	1	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017424	18017555	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18017556	18017698	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017699	18017861	1	-	1	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017699	18017861	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18017862	18017962	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18017963	18018079	1	-	1	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18017963	18018079	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18018080	18018245	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18018246	18018619	0.46	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18018246	18018619	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18018620	18018725	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18018726	18018910	0.13	-	2	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18018726	18018910	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18018911	18019087	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18019088	18019215	0.21	-	1	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18019088	18019215	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18019216	18019361	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18019362	18019386	0.44	-	2	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18019362	18019386	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	intron	18019387	18019499	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	CDS	18019500	18019506	0.39	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	exon	18019500	18019506	.	-	.	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
Phchi.S1	AUGUSTUS	start_codon	18019504	18019506	.	-	0	transcript_id "Phchi.S1G279900.t2"; gene_id "Phchi.S1G279900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14901.t1 is derived from g13369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15442973	15445302	.	+	.	Phchi.S3G222000
Phchi.S3	AUGUSTUS	transcript	15442973	15445302	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	start_codon	15442973	15442975	.	+	0	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	CDS	15442973	15443061	0.33	+	0	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	exon	15442973	15443061	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	intron	15443062	15443174	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	CDS	15443175	15444205	0.35	+	1	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	exon	15443175	15444205	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	intron	15444206	15444361	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	CDS	15444362	15444374	0.88	+	2	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	exon	15444362	15444374	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	intron	15444375	15444788	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	CDS	15444789	15445302	0.91	+	1	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	exon	15444789	15445302	.	+	.	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
Phchi.S3	AUGUSTUS	stop_codon	15445303	15445305	.	+	0	transcript_id "Phchi.S3G222000.t1"; gene_id "Phchi.S3G222000"
# This transcript jg428.t2 is derived from g10210.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg428.t3 is derived from g10210.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg429.t1 is derived from g10211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3043677	3044237	.	+	.	Phchi.S6G038800
Phchi.S6	AUGUSTUS	transcript	3043677	3044237	.	+	.	transcript_id "Phchi.S6G038800.t1"; gene_id "Phchi.S6G038800"
Phchi.S6	AUGUSTUS	start_codon	3043677	3043679	.	+	0	transcript_id "Phchi.S6G038800.t1"; gene_id "Phchi.S6G038800"
Phchi.S6	AUGUSTUS	CDS	3043677	3044237	1	+	0	transcript_id "Phchi.S6G038800.t1"; gene_id "Phchi.S6G038800"
Phchi.S6	AUGUSTUS	exon	3043677	3044237	.	+	.	transcript_id "Phchi.S6G038800.t1"; gene_id "Phchi.S6G038800"
Phchi.S6	AUGUSTUS	stop_codon	3044238	3044240	.	+	0	transcript_id "Phchi.S6G038800.t1"; gene_id "Phchi.S6G038800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4335.t1 is derived from g1504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9835613	9836377	.	-	.	Phchi.S1G149400
Phchi.S1	AUGUSTUS	transcript	9835613	9836377	.	-	.	transcript_id "Phchi.S1G149400.t1"; gene_id "Phchi.S1G149400"
Phchi.S1	AUGUSTUS	stop_codon	9835610	9835612	.	-	0	transcript_id "Phchi.S1G149400.t1"; gene_id "Phchi.S1G149400"
Phchi.S1	AUGUSTUS	CDS	9835613	9836377	1	-	0	transcript_id "Phchi.S1G149400.t1"; gene_id "Phchi.S1G149400"
Phchi.S1	AUGUSTUS	exon	9835613	9836377	.	-	.	transcript_id "Phchi.S1G149400.t1"; gene_id "Phchi.S1G149400"
Phchi.S1	AUGUSTUS	start_codon	9836375	9836377	.	-	0	transcript_id "Phchi.S1G149400.t1"; gene_id "Phchi.S1G149400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15239.t1 is derived from g13707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17873817	17875381	.	+	.	Phchi.S3G255800
Phchi.S3	AUGUSTUS	transcript	17873817	17875381	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	start_codon	17873817	17873819	.	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17873817	17873855	1	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17873817	17873855	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	intron	17873856	17874293	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17874294	17874371	1	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17874294	17874371	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	intron	17874372	17874471	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17874472	17874639	1	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17874472	17874639	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	intron	17874640	17874749	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17874750	17874798	1	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17874750	17874798	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	intron	17874799	17874926	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17874927	17875000	0.93	+	2	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17874927	17875000	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	intron	17875001	17875104	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17875105	17875198	0.97	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17875105	17875198	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	intron	17875199	17875286	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	CDS	17875287	17875381	0.99	+	2	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	exon	17875287	17875381	.	+	.	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
Phchi.S3	AUGUSTUS	stop_codon	17875382	17875384	.	+	0	transcript_id "Phchi.S3G255800.t1"; gene_id "Phchi.S3G255800"
# This transcript jg14496.t2 is derived from g12964.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14497.t1 is derived from g12965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13170106	13175727	.	+	.	Phchi.S3G181600
Phchi.S3	AUGUSTUS	transcript	13170106	13175727	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	start_codon	13170106	13170108	.	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13170106	13171196	0.6	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13170106	13171196	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13171197	13171285	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13171286	13171451	1	+	1	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13171286	13171451	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13171452	13171546	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13171547	13171602	1	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13171547	13171602	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13171603	13171690	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13171691	13171748	1	+	1	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13171691	13171748	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13171749	13171867	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13171868	13173634	1	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13171868	13173634	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13173635	13173734	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13173735	13173795	1	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13173735	13173795	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13173796	13173940	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13173941	13174236	1	+	2	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13173941	13174236	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13174237	13174318	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13174319	13174474	1	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13174319	13174474	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13174475	13174566	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13174567	13174835	1	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13174567	13174835	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13174836	13174931	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13174932	13175043	0.99	+	1	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13174932	13175043	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13175044	13175154	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13175155	13175412	0.99	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13175155	13175412	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13175413	13175503	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13175504	13175550	0.85	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13175504	13175550	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	intron	13175551	13175666	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	CDS	13175667	13175727	0.85	+	1	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	exon	13175667	13175727	.	+	.	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
Phchi.S3	AUGUSTUS	stop_codon	13175728	13175730	.	+	0	transcript_id "Phchi.S3G181600.t1"; gene_id "Phchi.S3G181600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8590.t1 is derived from g5765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36780498	36782629	.	-	.	Phchi.S1G574900
Phchi.S1	AUGUSTUS	transcript	36780498	36782629	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	stop_codon	36780495	36780497	.	-	0	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	CDS	36780498	36780545	0.95	-	0	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	exon	36780498	36780545	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	intron	36780546	36780642	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	CDS	36780643	36780940	1	-	1	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	exon	36780643	36780940	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	intron	36780941	36781048	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	CDS	36781049	36781441	1	-	1	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	exon	36781049	36781441	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	intron	36781442	36781541	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	CDS	36781542	36782629	0.98	-	0	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	exon	36781542	36782629	.	-	.	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
Phchi.S1	AUGUSTUS	start_codon	36782627	36782629	.	-	0	transcript_id "Phchi.S1G574900.t1"; gene_id "Phchi.S1G574900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13649.t1 is derived from g12116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8007415	8009800	.	+	.	Phchi.S3G096800
Phchi.S3	AUGUSTUS	transcript	8007415	8009800	.	+	.	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	start_codon	8007415	8007417	.	+	0	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	CDS	8007415	8007469	0.88	+	0	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	exon	8007415	8007469	.	+	.	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	intron	8007470	8007751	.	+	.	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	CDS	8007752	8007812	0.96	+	2	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	exon	8007752	8007812	.	+	.	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	intron	8007813	8007906	.	+	.	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	CDS	8007907	8009800	0.97	+	1	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	exon	8007907	8009800	.	+	.	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
Phchi.S3	AUGUSTUS	stop_codon	8009801	8009803	.	+	0	transcript_id "Phchi.S3G096800.t1"; gene_id "Phchi.S3G096800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8856.t1 is derived from g6031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38307946	38310518	.	+	.	Phchi.S1G601500
Phchi.S1	AUGUSTUS	transcript	38307946	38310518	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	start_codon	38307946	38307948	.	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38307946	38308018	0.67	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38307946	38308018	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38308019	38308131	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38308132	38308271	1	+	2	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38308132	38308271	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38308272	38308383	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38308384	38308596	0.99	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38308384	38308596	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38308597	38308709	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38308710	38308931	0.98	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38308710	38308931	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38308932	38309068	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38309069	38309185	1	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38309069	38309185	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38309186	38309305	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38309306	38309352	1	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38309306	38309352	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38309353	38309438	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38309439	38309515	1	+	1	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38309439	38309515	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38309516	38309615	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38309616	38309694	1	+	2	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38309616	38309694	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38309695	38309788	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38309789	38309858	1	+	1	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38309789	38309858	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38309859	38309955	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38309956	38310079	1	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38309956	38310079	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38310080	38310154	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38310155	38310204	1	+	2	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38310155	38310204	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	intron	38310205	38310281	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	CDS	38310282	38310518	0.84	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	exon	38310282	38310518	.	+	.	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
Phchi.S1	AUGUSTUS	stop_codon	38310519	38310521	.	+	0	transcript_id "Phchi.S1G601500.t1"; gene_id "Phchi.S1G601500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9553.t1 is derived from g6729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42425089	42425900	.	-	.	Phchi.S1G671200
Phchi.S1	AUGUSTUS	transcript	42425089	42425900	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	stop_codon	42424946	42424948	.	-	0	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	CDS	42425089	42425217	0.88	-	0	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	exon	42425089	42425217	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	intron	42425218	42425462	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	CDS	42425463	42425534	1	-	0	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	exon	42425463	42425534	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	intron	42425535	42425615	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	CDS	42425616	42425714	1	-	0	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	exon	42425616	42425714	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	intron	42425715	42425840	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	CDS	42425841	42425900	0.41	-	0	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	exon	42425841	42425900	.	-	.	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
Phchi.S1	AUGUSTUS	start_codon	42425898	42425900	.	-	0	transcript_id "Phchi.S1G671200.t1"; gene_id "Phchi.S1G671200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1695.t1 is derived from g8614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2552280	2554444	.	-	.	Phchi.S5G030400
Phchi.S5	AUGUSTUS	transcript	2552280	2554444	.	-	.	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	stop_codon	2552277	2552279	.	-	0	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	CDS	2552280	2553718	1	-	2	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	exon	2552280	2553718	.	-	.	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	intron	2553719	2554410	.	-	.	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	CDS	2554411	2554444	0.76	-	0	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	exon	2554411	2554444	.	-	.	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
Phchi.S5	AUGUSTUS	start_codon	2554442	2554444	.	-	0	transcript_id "Phchi.S5G030400.t1"; gene_id "Phchi.S5G030400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10540.t1 is derived from g14590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	877812	878081	.	+	.	Phchi.S4G012200
Phchi.S4	AUGUSTUS	transcript	877812	878081	.	+	.	transcript_id "Phchi.S4G012200.t1"; gene_id "Phchi.S4G012200"
Phchi.S4	AUGUSTUS	start_codon	877812	877814	.	+	0	transcript_id "Phchi.S4G012200.t1"; gene_id "Phchi.S4G012200"
Phchi.S4	AUGUSTUS	CDS	877812	878081	0.94	+	0	transcript_id "Phchi.S4G012200.t1"; gene_id "Phchi.S4G012200"
Phchi.S4	AUGUSTUS	exon	877812	878081	.	+	.	transcript_id "Phchi.S4G012200.t1"; gene_id "Phchi.S4G012200"
Phchi.S4	AUGUSTUS	stop_codon	878082	878084	.	+	0	transcript_id "Phchi.S4G012200.t1"; gene_id "Phchi.S4G012200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7835.t1 is derived from g5009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31446488	31448374	.	-	.	Phchi.S1G499400
Phchi.S1	AUGUSTUS	transcript	31446488	31448374	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	stop_codon	31446485	31446487	.	-	0	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	CDS	31446488	31446514	0.95	-	0	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	exon	31446488	31446514	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	intron	31446515	31446612	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	CDS	31446613	31446825	1	-	0	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	exon	31446613	31446825	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	intron	31446826	31446929	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	CDS	31446930	31447627	1	-	2	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	exon	31446930	31447627	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	intron	31447628	31447716	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	CDS	31447717	31448374	0.89	-	0	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	exon	31447717	31448374	.	-	.	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
Phchi.S1	AUGUSTUS	start_codon	31448372	31448374	.	-	0	transcript_id "Phchi.S1G499400.t1"; gene_id "Phchi.S1G499400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5104.t1 is derived from g2274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14765521	14771757	.	+	.	Phchi.S1G226300
Phchi.S1	AUGUSTUS	transcript	14765521	14771757	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	start_codon	14765521	14765523	.	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14765521	14765638	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14765521	14765638	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14765639	14766289	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14766290	14766369	1	+	2	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14766290	14766369	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14766370	14766484	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14766485	14766571	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14766485	14766571	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14766572	14766659	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14766660	14766710	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14766660	14766710	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14766711	14766831	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14766832	14766949	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14766832	14766949	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14766950	14767062	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14767063	14767119	1	+	2	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14767063	14767119	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14767120	14767203	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14767204	14767268	1	+	2	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14767204	14767268	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14767269	14767353	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14767354	14767437	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14767354	14767437	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14767438	14767522	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14767523	14767573	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14767523	14767573	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14767574	14767689	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14767690	14767752	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14767690	14767752	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14767753	14767855	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14767856	14767899	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14767856	14767899	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14767900	14768012	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14768013	14768082	1	+	1	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14768013	14768082	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14768083	14768170	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14768171	14768233	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14768171	14768233	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14768234	14768329	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14768330	14768419	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14768330	14768419	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14768420	14768559	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14768560	14768598	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14768560	14768598	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14768599	14768765	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14768766	14768915	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14768766	14768915	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14768916	14769013	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14769014	14769091	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14769014	14769091	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14769092	14769172	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14769173	14769258	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14769173	14769258	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14769259	14769370	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14769371	14769446	1	+	1	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14769371	14769446	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14769447	14769541	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14769542	14769622	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14769542	14769622	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14769623	14769704	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14769705	14769798	1	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14769705	14769798	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	intron	14769799	14769886	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	CDS	14769887	14771757	1	+	2	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	exon	14769887	14771757	.	+	.	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
Phchi.S1	AUGUSTUS	stop_codon	14771758	14771760	.	+	0	transcript_id "Phchi.S1G226300.t1"; gene_id "Phchi.S1G226300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11832.t1 is derived from g15884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8476647	8479597	.	-	.	Phchi.S4G141400
Phchi.S4	AUGUSTUS	transcript	8476647	8479597	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	stop_codon	8476644	8476646	.	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8476647	8476806	1	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8476647	8476806	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8476807	8476902	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8476903	8476991	1	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8476903	8476991	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8476992	8477082	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8477083	8477188	1	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8477083	8477188	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8477189	8477282	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8477283	8477347	1	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8477283	8477347	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8477348	8477494	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8477495	8477555	0.82	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8477495	8477555	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8477556	8477666	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8477667	8477752	0.99	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8477667	8477752	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8477753	8477922	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8477923	8478040	0.79	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8477923	8478040	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8478041	8478159	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8478160	8478255	0.82	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8478160	8478255	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8478256	8478340	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8478341	8478450	1	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8478341	8478450	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8478451	8478613	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8478614	8478683	1	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8478614	8478683	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8478684	8478778	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8478779	8478877	1	-	1	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8478779	8478877	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8478878	8478991	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8478992	8479019	1	-	2	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8478992	8479019	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8479020	8479161	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8479162	8479273	1	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8479162	8479273	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8479274	8479344	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8479345	8479434	1	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8479345	8479434	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	intron	8479435	8479531	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	CDS	8479532	8479597	1	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	exon	8479532	8479597	.	-	.	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
Phchi.S4	AUGUSTUS	start_codon	8479595	8479597	.	-	0	transcript_id "Phchi.S4G141400.t1"; gene_id "Phchi.S4G141400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8571.t1 is derived from g5746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36695766	36697743	.	-	.	Phchi.S1G573000
Phchi.S1	AUGUSTUS	transcript	36695766	36697743	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	stop_codon	36695763	36695765	.	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	CDS	36695766	36695936	1	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	exon	36695766	36695936	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	intron	36695937	36696033	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	CDS	36696034	36696165	1	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	exon	36696034	36696165	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	intron	36696166	36696237	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	CDS	36696238	36696348	1	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	exon	36696238	36696348	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	intron	36696349	36696505	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	CDS	36696506	36696751	0.99	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	exon	36696506	36696751	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	intron	36696752	36696861	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	CDS	36696862	36697087	0.99	-	1	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	exon	36696862	36697087	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	intron	36697088	36697288	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	CDS	36697289	36697743	0.98	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	exon	36697289	36697743	.	-	.	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
Phchi.S1	AUGUSTUS	start_codon	36697741	36697743	.	-	0	transcript_id "Phchi.S1G573000.t1"; gene_id "Phchi.S1G573000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7378.t1 is derived from g4550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28833817	28834298	.	-	.	Phchi.S1G453700
Phchi.S1	AUGUSTUS	transcript	28833817	28834298	.	-	.	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	stop_codon	28833814	28833816	.	-	0	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	CDS	28833817	28833960	0.98	-	0	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	exon	28833817	28833960	.	-	.	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	intron	28833961	28834109	.	-	.	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	CDS	28834110	28834298	0.98	-	0	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	exon	28834110	28834298	.	-	.	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
Phchi.S1	AUGUSTUS	start_codon	28834296	28834298	.	-	0	transcript_id "Phchi.S1G453700.t1"; gene_id "Phchi.S1G453700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15375.t1 is derived from g13843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18680705	18682742	.	-	.	Phchi.S3G269400
Phchi.S3	AUGUSTUS	transcript	18680705	18682742	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	stop_codon	18680702	18680704	.	-	0	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	CDS	18680705	18681268	1	-	0	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	exon	18680705	18681268	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	intron	18681269	18681370	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	CDS	18681371	18681661	1	-	0	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	exon	18681371	18681661	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	intron	18681662	18681753	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	CDS	18681754	18681897	0.97	-	0	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	exon	18681754	18681897	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	intron	18681898	18682262	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	CDS	18682263	18682308	0.84	-	1	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	exon	18682263	18682308	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	intron	18682309	18682719	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	CDS	18682720	18682742	0.61	-	0	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	exon	18682720	18682742	.	-	.	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
Phchi.S3	AUGUSTUS	start_codon	18682740	18682742	.	-	0	transcript_id "Phchi.S3G269400.t1"; gene_id "Phchi.S3G269400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15201.t1 is derived from g13669.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17533932	17534562	.	+	.	Phchi.S3G252000
Phchi.S3	AUGUSTUS	transcript	17533932	17534562	.	+	.	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	start_codon	17533932	17533934	.	+	0	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	CDS	17533932	17534086	0.97	+	0	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	exon	17533932	17534086	.	+	.	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	intron	17534087	17534222	.	+	.	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	CDS	17534223	17534267	1	+	1	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	exon	17534223	17534267	.	+	.	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	intron	17534268	17534408	.	+	.	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	CDS	17534409	17534562	0.85	+	1	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	exon	17534409	17534562	.	+	.	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	stop_codon	17534563	17534565	.	+	0	transcript_id "Phchi.S3G252000.t1"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	transcript	17533932	17534562	.	+	.	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	start_codon	17533932	17533934	.	+	0	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	CDS	17533932	17534086	1	+	0	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	exon	17533932	17534086	.	+	.	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	intron	17534087	17534222	.	+	.	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	CDS	17534223	17534303	0.64	+	1	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	exon	17534223	17534303	.	+	.	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	intron	17534304	17534408	.	+	.	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	CDS	17534409	17534562	0.76	+	1	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	exon	17534409	17534562	.	+	.	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
Phchi.S3	AUGUSTUS	stop_codon	17534563	17534565	.	+	0	transcript_id "Phchi.S3G252000.t2"; gene_id "Phchi.S3G252000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12665.t1 is derived from g9765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C100	AUGUSTUS	gene	25814	26326	.	-	.	Phchi.C100G000100
Phchi.C100	AUGUSTUS	transcript	25814	26326	.	-	.	transcript_id "Phchi.C100G000100.t1"; gene_id "Phchi.C100G000100"
Phchi.C100	AUGUSTUS	stop_codon	25811	25813	.	-	0	transcript_id "Phchi.C100G000100.t1"; gene_id "Phchi.C100G000100"
Phchi.C100	AUGUSTUS	CDS	25814	26326	0.36	-	0	transcript_id "Phchi.C100G000100.t1"; gene_id "Phchi.C100G000100"
Phchi.C100	AUGUSTUS	exon	25814	26326	.	-	.	transcript_id "Phchi.C100G000100.t1"; gene_id "Phchi.C100G000100"
Phchi.C100	AUGUSTUS	start_codon	26324	26326	.	-	0	transcript_id "Phchi.C100G000100.t1"; gene_id "Phchi.C100G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4936.t1 is derived from g2106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13655106	13656164	.	+	.	Phchi.S1G209500
Phchi.S1	AUGUSTUS	transcript	13655106	13656164	.	+	.	transcript_id "Phchi.S1G209500.t1"; gene_id "Phchi.S1G209500"
Phchi.S1	AUGUSTUS	start_codon	13655106	13655108	.	+	0	transcript_id "Phchi.S1G209500.t1"; gene_id "Phchi.S1G209500"
Phchi.S1	AUGUSTUS	CDS	13655106	13656164	0.62	+	0	transcript_id "Phchi.S1G209500.t1"; gene_id "Phchi.S1G209500"
Phchi.S1	AUGUSTUS	exon	13655106	13656164	.	+	.	transcript_id "Phchi.S1G209500.t1"; gene_id "Phchi.S1G209500"
Phchi.S1	AUGUSTUS	stop_codon	13656165	13656167	.	+	0	transcript_id "Phchi.S1G209500.t1"; gene_id "Phchi.S1G209500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15676.t1 is derived from g14145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20616999	20618575	.	-	.	Phchi.S3G299500
Phchi.S3	AUGUSTUS	transcript	20616999	20618575	.	-	.	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	stop_codon	20616996	20616998	.	-	0	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	CDS	20616999	20617565	0.87	-	0	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	exon	20616999	20617565	.	-	.	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	intron	20617566	20617709	.	-	.	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	CDS	20617710	20617880	0.92	-	0	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	exon	20617710	20617880	.	-	.	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	intron	20617881	20618089	.	-	.	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	CDS	20618090	20618575	1	-	0	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	exon	20618090	20618575	.	-	.	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
Phchi.S3	AUGUSTUS	start_codon	20618573	20618575	.	-	0	transcript_id "Phchi.S3G299500.t1"; gene_id "Phchi.S3G299500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6990.t1 is derived from g4162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26299654	26301363	.	-	.	Phchi.S1G414900
Phchi.S1	AUGUSTUS	transcript	26299654	26301363	.	-	.	transcript_id "Phchi.S1G414900.t1"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	stop_codon	26299651	26299653	.	-	0	transcript_id "Phchi.S1G414900.t1"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	CDS	26299654	26301363	0.63	-	0	transcript_id "Phchi.S1G414900.t1"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	exon	26299654	26301363	.	-	.	transcript_id "Phchi.S1G414900.t1"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	start_codon	26301361	26301363	.	-	0	transcript_id "Phchi.S1G414900.t1"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	transcript	26299654	26300580	.	-	.	transcript_id "Phchi.S1G414900.t2"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	stop_codon	26299651	26299653	.	-	0	transcript_id "Phchi.S1G414900.t2"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	CDS	26299654	26300580	0.55	-	0	transcript_id "Phchi.S1G414900.t2"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	exon	26299654	26300580	.	-	.	transcript_id "Phchi.S1G414900.t2"; gene_id "Phchi.S1G414900"
Phchi.S1	AUGUSTUS	start_codon	26300578	26300580	.	-	0	transcript_id "Phchi.S1G414900.t2"; gene_id "Phchi.S1G414900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7340.t1 is derived from g4512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28597321	28598724	.	+	.	Phchi.S1G449900
Phchi.S1	AUGUSTUS	transcript	28597321	28598724	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	start_codon	28597321	28597323	.	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28597321	28597587	0.39	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28597321	28597587	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28597588	28597664	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28597665	28597781	1	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28597665	28597781	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28597782	28597936	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28597937	28598032	0.52	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28597937	28598032	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28598033	28598136	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28598137	28598229	0.57	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28598137	28598229	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28598230	28598507	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28598508	28598630	1	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28598508	28598630	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28598631	28598703	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28598704	28598724	1	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28598704	28598724	.	+	.	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	stop_codon	28598725	28598727	.	+	0	transcript_id "Phchi.S1G449900.t1"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	transcript	28597321	28598724	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	start_codon	28597321	28597323	.	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28597321	28597587	0.42	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28597321	28597587	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28597588	28597664	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28597665	28597781	1	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28597665	28597781	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28597782	28597936	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28597937	28597980	0.56	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28597937	28597980	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28597981	28598136	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28598137	28598143	0.32	+	1	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28598137	28598143	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28598144	28598507	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28598508	28598630	0.93	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28598508	28598630	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	intron	28598631	28598703	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	CDS	28598704	28598724	0.98	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	exon	28598704	28598724	.	+	.	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
Phchi.S1	AUGUSTUS	stop_codon	28598725	28598727	.	+	0	transcript_id "Phchi.S1G449900.t2"; gene_id "Phchi.S1G449900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13133.t1 is derived from g11598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4307747	4310141	.	-	.	Phchi.S3G045200
Phchi.S3	AUGUSTUS	transcript	4307747	4310141	.	-	.	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	stop_codon	4307744	4307746	.	-	0	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	CDS	4307747	4309460	1	-	1	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	exon	4307747	4309460	.	-	.	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	intron	4309461	4309581	.	-	.	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	CDS	4309582	4309752	0.37	-	1	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	exon	4309582	4309752	.	-	.	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	intron	4309753	4309842	.	-	.	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	CDS	4309843	4310141	0.77	-	0	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	exon	4309843	4310141	.	-	.	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
Phchi.S3	AUGUSTUS	start_codon	4310139	4310141	.	-	0	transcript_id "Phchi.S3G045200.t1"; gene_id "Phchi.S3G045200"
# This transcript jg11893.t2 is derived from g15945.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11894.t1 is derived from g15946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9065914	9066972	.	+	.	Phchi.S4G147600
Phchi.S4	AUGUSTUS	transcript	9065914	9066972	.	+	.	transcript_id "Phchi.S4G147600.t1"; gene_id "Phchi.S4G147600"
Phchi.S4	AUGUSTUS	start_codon	9065914	9065916	.	+	0	transcript_id "Phchi.S4G147600.t1"; gene_id "Phchi.S4G147600"
Phchi.S4	AUGUSTUS	CDS	9065914	9066972	0.39	+	0	transcript_id "Phchi.S4G147600.t1"; gene_id "Phchi.S4G147600"
Phchi.S4	AUGUSTUS	exon	9065914	9066972	.	+	.	transcript_id "Phchi.S4G147600.t1"; gene_id "Phchi.S4G147600"
Phchi.S4	AUGUSTUS	stop_codon	9066973	9066975	.	+	0	transcript_id "Phchi.S4G147600.t1"; gene_id "Phchi.S4G147600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11919.t1 is derived from g15971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9314857	9316743	.	-	.	Phchi.S4G150100
Phchi.S4	AUGUSTUS	transcript	9314857	9316743	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	stop_codon	9314854	9314856	.	-	0	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	CDS	9314857	9314962	0.93	-	1	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	exon	9314857	9314962	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	intron	9314963	9315054	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	CDS	9315055	9315355	1	-	2	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	exon	9315055	9315355	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	intron	9315356	9315491	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	CDS	9315492	9315662	1	-	2	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	exon	9315492	9315662	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	intron	9315663	9315735	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	CDS	9315736	9316021	1	-	0	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	exon	9315736	9316021	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	intron	9316022	9316155	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	CDS	9316156	9316743	0.89	-	0	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	exon	9316156	9316743	.	-	.	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
Phchi.S4	AUGUSTUS	start_codon	9316741	9316743	.	-	0	transcript_id "Phchi.S4G150100.t1"; gene_id "Phchi.S4G150100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15281.t1 is derived from g13749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18147467	18150433	.	-	.	Phchi.S3G260000
Phchi.S3	AUGUSTUS	transcript	18147467	18150433	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	stop_codon	18147464	18147466	.	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18147467	18147607	0.71	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18147467	18147607	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18147608	18147858	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18147859	18148002	0.99	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18147859	18148002	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18148003	18148110	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18148111	18148202	0.99	-	2	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18148111	18148202	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18148203	18148283	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18148284	18148362	1	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18148284	18148362	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18148363	18148485	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18148486	18148552	1	-	1	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18148486	18148552	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18148553	18148663	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18148664	18148755	1	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18148664	18148755	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18148756	18148859	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18148860	18148976	0.85	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18148860	18148976	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18148977	18149095	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18149096	18149204	0.97	-	1	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18149096	18149204	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18149205	18149353	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18149354	18149463	1	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18149354	18149463	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18149464	18149582	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18149583	18149659	1	-	2	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18149583	18149659	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18149660	18149744	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18149745	18149826	1	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18149745	18149826	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18149827	18149951	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18149952	18150089	1	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18149952	18150089	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18150090	18150254	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18150255	18150318	0.38	-	1	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18150255	18150318	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	intron	18150319	18150371	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	CDS	18150372	18150433	0.7	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	exon	18150372	18150433	.	-	.	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
Phchi.S3	AUGUSTUS	start_codon	18150431	18150433	.	-	0	transcript_id "Phchi.S3G260000.t1"; gene_id "Phchi.S3G260000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12544.t1 is derived from g8221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34119690	34128344	.	-	.	Phchi.S2G062400
Phchi.S2	AUGUSTUS	transcript	34119690	34128344	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	stop_codon	34119687	34119689	.	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34119690	34119696	1	-	1	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34119690	34119696	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34119697	34119830	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34119831	34119919	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34119831	34119919	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34119920	34120344	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34120345	34120455	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34120345	34120455	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34120456	34120694	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34120695	34120937	0.98	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34120695	34120937	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34120938	34121173	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34121174	34121386	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34121174	34121386	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34121387	34121501	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34121502	34121568	1	-	1	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34121502	34121568	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34121569	34121659	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34121660	34121817	0.99	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34121660	34121817	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34121818	34121897	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34121898	34121991	1	-	1	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34121898	34121991	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34121992	34122349	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34122350	34122417	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34122350	34122417	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34122418	34122576	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34122577	34122768	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34122577	34122768	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34122769	34123271	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34123272	34123406	0.99	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34123272	34123406	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34123407	34123519	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34123520	34123607	1	-	1	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34123520	34123607	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34123608	34123861	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34123862	34123955	1	-	2	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34123862	34123955	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34123956	34124094	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34124095	34124158	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34124095	34124158	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34124159	34124480	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34124481	34124532	1	-	1	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34124481	34124532	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34124533	34125066	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34125067	34125170	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34125067	34125170	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34125171	34125262	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34125263	34125322	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34125263	34125322	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34125323	34125451	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34125452	34125535	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34125452	34125535	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34125536	34125616	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34125617	34125850	1	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34125617	34125850	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34125851	34126121	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34126122	34126577	0.76	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34126122	34126577	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34126578	34127285	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34127286	34127365	1	-	2	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34127286	34127365	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34127366	34127489	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34127490	34127777	0.61	-	2	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34127490	34127777	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	intron	34127778	34127971	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	CDS	34127972	34128344	0.86	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	exon	34127972	34128344	.	-	.	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
Phchi.S2	AUGUSTUS	start_codon	34128342	34128344	.	-	0	transcript_id "Phchi.S2G062400.t1"; gene_id "Phchi.S2G062400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15072.t1 is derived from g13540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16913351	16914593	.	+	.	Phchi.S3G239100
Phchi.S3	AUGUSTUS	transcript	16913351	16914593	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	start_codon	16913351	16913353	.	+	0	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	CDS	16913351	16913661	0.53	+	0	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	exon	16913351	16913661	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	intron	16913662	16913766	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	CDS	16913767	16914023	1	+	1	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	exon	16913767	16914023	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	intron	16914024	16914108	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	CDS	16914109	16914400	0.64	+	2	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	exon	16914109	16914400	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	intron	16914401	16914490	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	CDS	16914491	16914593	0.65	+	1	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	exon	16914491	16914593	.	+	.	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
Phchi.S3	AUGUSTUS	stop_codon	16914594	16914596	.	+	0	transcript_id "Phchi.S3G239100.t1"; gene_id "Phchi.S3G239100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13438.t1 is derived from g11905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6705288	6706156	.	-	.	Phchi.S3G075700
Phchi.S3	AUGUSTUS	transcript	6705288	6706156	.	-	.	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	stop_codon	6705285	6705287	.	-	0	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	CDS	6705288	6705705	0.29	-	1	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	exon	6705288	6705705	.	-	.	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	intron	6705706	6705755	.	-	.	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	CDS	6705756	6706156	0.04	-	0	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	exon	6705756	6706156	.	-	.	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
Phchi.S3	AUGUSTUS	start_codon	6706154	6706156	.	-	0	transcript_id "Phchi.S3G075700.t1"; gene_id "Phchi.S3G075700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3129.t1 is derived from g298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1875159	1875890	.	-	.	Phchi.S1G028800
Phchi.S1	AUGUSTUS	transcript	1875159	1875890	.	-	.	transcript_id "Phchi.S1G028800.t1"; gene_id "Phchi.S1G028800"
Phchi.S1	AUGUSTUS	stop_codon	1875156	1875158	.	-	0	transcript_id "Phchi.S1G028800.t1"; gene_id "Phchi.S1G028800"
Phchi.S1	AUGUSTUS	CDS	1875159	1875890	0.71	-	0	transcript_id "Phchi.S1G028800.t1"; gene_id "Phchi.S1G028800"
Phchi.S1	AUGUSTUS	exon	1875159	1875890	.	-	.	transcript_id "Phchi.S1G028800.t1"; gene_id "Phchi.S1G028800"
Phchi.S1	AUGUSTUS	start_codon	1875888	1875890	.	-	0	transcript_id "Phchi.S1G028800.t1"; gene_id "Phchi.S1G028800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8706.t1 is derived from g5881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37545395	37548126	.	-	.	Phchi.S1G586500
Phchi.S1	AUGUSTUS	transcript	37545395	37548126	.	-	.	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	stop_codon	37545392	37545394	.	-	0	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	CDS	37545395	37545416	0.52	-	1	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	exon	37545395	37545416	.	-	.	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	intron	37545417	37545508	.	-	.	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	CDS	37545509	37548126	0.3	-	0	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	exon	37545509	37548126	.	-	.	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
Phchi.S1	AUGUSTUS	start_codon	37548124	37548126	.	-	0	transcript_id "Phchi.S1G586500.t1"; gene_id "Phchi.S1G586500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10009.t1 is derived from g7185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45026776	45032150	.	-	.	Phchi.S1G716800
Phchi.S1	AUGUSTUS	transcript	45026776	45032150	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	stop_codon	45026773	45026775	.	-	0	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	CDS	45026776	45027915	1	-	0	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	exon	45026776	45027915	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	intron	45027916	45028031	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	CDS	45028032	45029527	1	-	2	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	exon	45028032	45029527	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	intron	45029528	45029635	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	CDS	45029636	45031220	0.79	-	0	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	exon	45029636	45031220	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	intron	45031221	45031670	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	CDS	45031671	45031828	0.83	-	2	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	exon	45031671	45031828	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	intron	45031829	45032032	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	CDS	45032033	45032150	0.77	-	0	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	exon	45032033	45032150	.	-	.	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
Phchi.S1	AUGUSTUS	start_codon	45032148	45032150	.	-	0	transcript_id "Phchi.S1G716800.t1"; gene_id "Phchi.S1G716800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4926.t1 is derived from g2096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13602397	13604089	.	+	.	Phchi.S1G208500
Phchi.S1	AUGUSTUS	transcript	13602397	13603984	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	start_codon	13602397	13602399	.	+	0	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602397	13602523	0.94	+	0	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602397	13602523	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13602524	13602610	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602611	13602681	1	+	2	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602611	13602681	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13602682	13602839	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602840	13602894	1	+	0	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602840	13602894	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13602895	13602989	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602990	13603084	1	+	2	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602990	13603084	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13603085	13603176	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13603177	13603846	1	+	0	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13603177	13603846	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13603847	13603982	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13603983	13603984	1	+	2	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13603983	13603984	.	+	.	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	stop_codon	13603985	13603987	.	+	0	transcript_id "Phchi.S1G208500.t1"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	transcript	13602397	13604089	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	start_codon	13602397	13602399	.	+	0	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602397	13602523	0.97	+	0	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602397	13602523	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13602524	13602610	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602611	13602681	1	+	2	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602611	13602681	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13602682	13602839	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602840	13602894	1	+	0	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602840	13602894	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13602895	13602989	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13602990	13603084	1	+	2	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13602990	13603084	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13603085	13603176	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13603177	13603846	1	+	0	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13603177	13603846	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	intron	13603847	13604045	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	CDS	13604046	13604089	0.93	+	2	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	exon	13604046	13604089	.	+	.	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
Phchi.S1	AUGUSTUS	stop_codon	13604090	13604092	.	+	0	transcript_id "Phchi.S1G208500.t2"; gene_id "Phchi.S1G208500"
# This transcript jg7189.t2 is derived from g4361.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7190.t1 is derived from g4362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27475473	27479977	.	+	.	Phchi.S1G434900
Phchi.S1	AUGUSTUS	transcript	27475473	27479977	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	start_codon	27475473	27475475	.	+	0	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	CDS	27475473	27476075	0.19	+	0	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	exon	27475473	27476075	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	intron	27476076	27476160	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	CDS	27476161	27476416	0.27	+	0	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	exon	27476161	27476416	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	intron	27476417	27476544	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	CDS	27476545	27479440	0.39	+	2	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	exon	27476545	27479440	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	intron	27479441	27479526	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	CDS	27479527	27479977	0.82	+	1	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	exon	27479527	27479977	.	+	.	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
Phchi.S1	AUGUSTUS	stop_codon	27479978	27479980	.	+	0	transcript_id "Phchi.S1G434900.t1"; gene_id "Phchi.S1G434900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5102.t1 is derived from g2272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14752675	14755573	.	+	.	Phchi.S1G226100
Phchi.S1	AUGUSTUS	transcript	14752675	14755573	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	start_codon	14752675	14752677	.	+	0	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14752675	14753473	0.92	+	0	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14752675	14753473	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	intron	14753474	14753563	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14753564	14753720	1	+	2	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14753564	14753720	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	intron	14753721	14753806	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14753807	14754322	0.59	+	1	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14753807	14754322	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	intron	14754323	14754599	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14754600	14754766	0.21	+	1	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14754600	14754766	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	intron	14754767	14754845	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14754846	14754924	0.5	+	2	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14754846	14754924	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	intron	14754925	14755093	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14755094	14755158	0.93	+	1	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14755094	14755158	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	intron	14755159	14755472	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	CDS	14755473	14755573	1	+	2	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	exon	14755473	14755573	.	+	.	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
Phchi.S1	AUGUSTUS	stop_codon	14755574	14755576	.	+	0	transcript_id "Phchi.S1G226100.t1"; gene_id "Phchi.S1G226100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12486.t1 is derived from g8163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28854545	28854874	.	+	.	Phchi.S2G056600
Phchi.S2	AUGUSTUS	transcript	28854545	28854874	.	+	.	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	start_codon	28854545	28854547	.	+	0	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	CDS	28854545	28854732	0.99	+	0	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	exon	28854545	28854732	.	+	.	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	intron	28854733	28854813	.	+	.	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	CDS	28854814	28854874	1	+	1	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	exon	28854814	28854874	.	+	.	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
Phchi.S2	AUGUSTUS	stop_codon	28854875	28854877	.	+	0	transcript_id "Phchi.S2G056600.t1"; gene_id "Phchi.S2G056600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4363.t1 is derived from g1532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10053179	10054009	.	-	.	Phchi.S1G152200
Phchi.S1	AUGUSTUS	transcript	10053179	10054009	.	-	.	transcript_id "Phchi.S1G152200.t1"; gene_id "Phchi.S1G152200"
Phchi.S1	AUGUSTUS	stop_codon	10053176	10053178	.	-	0	transcript_id "Phchi.S1G152200.t1"; gene_id "Phchi.S1G152200"
Phchi.S1	AUGUSTUS	CDS	10053179	10054009	0.84	-	0	transcript_id "Phchi.S1G152200.t1"; gene_id "Phchi.S1G152200"
Phchi.S1	AUGUSTUS	exon	10053179	10054009	.	-	.	transcript_id "Phchi.S1G152200.t1"; gene_id "Phchi.S1G152200"
Phchi.S1	AUGUSTUS	start_codon	10054007	10054009	.	-	0	transcript_id "Phchi.S1G152200.t1"; gene_id "Phchi.S1G152200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg89.t1 is derived from g9871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	459244	460928	.	+	.	Phchi.S6G004800
Phchi.S6	AUGUSTUS	transcript	459244	460928	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	start_codon	459244	459246	.	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	459244	459361	0.91	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	459244	459361	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	459362	459463	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	459464	459577	0.94	+	2	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	459464	459577	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	459578	459718	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	459719	459819	1	+	2	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	459719	459819	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	459820	459904	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	459905	459925	1	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	459905	459925	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	459926	460014	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	460015	460087	1	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	460015	460087	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	460088	460268	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	460269	460336	1	+	2	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	460269	460336	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	460337	460476	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	460477	460606	1	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	460477	460606	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	460607	460693	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	460694	460782	1	+	2	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	460694	460782	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	intron	460783	460910	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	CDS	460911	460928	1	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	exon	460911	460928	.	+	.	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
Phchi.S6	AUGUSTUS	stop_codon	460929	460931	.	+	0	transcript_id "Phchi.S6G004800.t1"; gene_id "Phchi.S6G004800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7088.t1 is derived from g4260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26852972	26855472	.	+	.	Phchi.S1G424700
Phchi.S1	AUGUSTUS	transcript	26852972	26855472	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	start_codon	26852972	26852974	.	+	0	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	CDS	26852972	26854883	0.82	+	0	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	exon	26852972	26854883	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	intron	26854884	26854978	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	CDS	26854979	26855083	0.85	+	2	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	exon	26854979	26855083	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	intron	26855084	26855173	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	CDS	26855174	26855229	0.57	+	2	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	exon	26855174	26855229	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	intron	26855230	26855310	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	CDS	26855311	26855472	0.93	+	0	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	exon	26855311	26855472	.	+	.	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
Phchi.S1	AUGUSTUS	stop_codon	26855473	26855475	.	+	0	transcript_id "Phchi.S1G424700.t1"; gene_id "Phchi.S1G424700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15733.t1 is derived from g14203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20955796	20957989	.	+	.	Phchi.S3G305200
Phchi.S3	AUGUSTUS	transcript	20955796	20957989	.	+	.	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	start_codon	20955796	20955798	.	+	0	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	CDS	20955796	20955915	0.38	+	0	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	exon	20955796	20955915	.	+	.	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	intron	20955916	20956106	.	+	.	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	CDS	20956107	20956175	0.85	+	0	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	exon	20956107	20956175	.	+	.	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	intron	20956176	20956516	.	+	.	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	CDS	20956517	20957989	0.93	+	0	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	exon	20956517	20957989	.	+	.	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
Phchi.S3	AUGUSTUS	stop_codon	20957990	20957992	.	+	0	transcript_id "Phchi.S3G305200.t1"; gene_id "Phchi.S3G305200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3561.t1 is derived from g730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4494568	4495736	.	+	.	Phchi.S1G072000
Phchi.S1	AUGUSTUS	transcript	4494568	4495736	.	+	.	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	start_codon	4494568	4494570	.	+	0	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	CDS	4494568	4494677	0.88	+	0	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	exon	4494568	4494677	.	+	.	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	intron	4494678	4494868	.	+	.	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	CDS	4494869	4495481	0.85	+	1	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	exon	4494869	4495481	.	+	.	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	intron	4495482	4495604	.	+	.	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	CDS	4495605	4495736	0.9	+	0	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	exon	4495605	4495736	.	+	.	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
Phchi.S1	AUGUSTUS	stop_codon	4495737	4495739	.	+	0	transcript_id "Phchi.S1G072000.t1"; gene_id "Phchi.S1G072000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5078.t1 is derived from g2248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14572923	14573643	.	-	.	Phchi.S1G223700
Phchi.S1	AUGUSTUS	transcript	14572923	14573643	.	-	.	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	stop_codon	14572920	14572922	.	-	0	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	CDS	14572923	14573233	0.9	-	2	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	exon	14572923	14573233	.	-	.	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	intron	14573234	14573347	.	-	.	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	CDS	14573348	14573527	0.57	-	2	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	exon	14573348	14573527	.	-	.	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	intron	14573528	14573627	.	-	.	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	CDS	14573628	14573643	1	-	0	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	exon	14573628	14573643	.	-	.	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
Phchi.S1	AUGUSTUS	start_codon	14573641	14573643	.	-	0	transcript_id "Phchi.S1G223700.t1"; gene_id "Phchi.S1G223700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15059.t1 is derived from g13527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16786919	16787724	.	-	.	Phchi.S3G237800
Phchi.S3	AUGUSTUS	transcript	16786919	16787724	.	-	.	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	stop_codon	16786916	16786918	.	-	0	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	CDS	16786919	16787359	0.73	-	0	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	exon	16786919	16787359	.	-	.	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	intron	16787360	16787430	.	-	.	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	CDS	16787431	16787724	0.66	-	0	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	exon	16787431	16787724	.	-	.	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
Phchi.S3	AUGUSTUS	start_codon	16787722	16787724	.	-	0	transcript_id "Phchi.S3G237800.t1"; gene_id "Phchi.S3G237800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5308.t1 is derived from g2478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16217905	16219961	.	-	.	Phchi.S1G246700
Phchi.S1	AUGUSTUS	transcript	16217905	16219961	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	stop_codon	16217902	16217904	.	-	0	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16217905	16218078	0.97	-	0	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16217905	16218078	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16218079	16218171	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16218172	16218248	1	-	2	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16218172	16218248	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16218249	16218517	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16218518	16218621	1	-	1	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16218518	16218621	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16218622	16218711	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16218712	16218763	1	-	2	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16218712	16218763	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16218764	16218896	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16218897	16218987	1	-	0	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16218897	16218987	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16218988	16219125	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16219126	16219200	1	-	0	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16219126	16219200	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16219201	16219282	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16219283	16219452	1	-	2	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16219283	16219452	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	intron	16219453	16219609	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	CDS	16219610	16219961	0.54	-	0	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	exon	16219610	16219961	.	-	.	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
Phchi.S1	AUGUSTUS	start_codon	16219959	16219961	.	-	0	transcript_id "Phchi.S1G246700.t1"; gene_id "Phchi.S1G246700"
# This transcript jg7198.t2 is derived from g4370.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7199.t1 is derived from g4371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27611986	27613053	.	+	.	Phchi.S1G435800
Phchi.S1	AUGUSTUS	transcript	27611986	27613053	.	+	.	transcript_id "Phchi.S1G435800.t1"; gene_id "Phchi.S1G435800"
Phchi.S1	AUGUSTUS	start_codon	27611986	27611988	.	+	0	transcript_id "Phchi.S1G435800.t1"; gene_id "Phchi.S1G435800"
Phchi.S1	AUGUSTUS	CDS	27611986	27613053	0.92	+	0	transcript_id "Phchi.S1G435800.t1"; gene_id "Phchi.S1G435800"
Phchi.S1	AUGUSTUS	exon	27611986	27613053	.	+	.	transcript_id "Phchi.S1G435800.t1"; gene_id "Phchi.S1G435800"
Phchi.S1	AUGUSTUS	stop_codon	27613054	27613056	.	+	0	transcript_id "Phchi.S1G435800.t1"; gene_id "Phchi.S1G435800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7232.t1 is derived from g4404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27751369	27754384	.	-	.	Phchi.S1G439100
Phchi.S1	AUGUSTUS	transcript	27751369	27754384	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	stop_codon	27751366	27751368	.	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27751369	27751464	1	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27751369	27751464	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27751465	27751560	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27751561	27751683	1	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27751561	27751683	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27751684	27751764	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27751765	27751906	1	-	1	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27751765	27751906	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27751907	27752019	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27752020	27752117	1	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27752020	27752117	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27752118	27752204	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27752205	27752267	0.95	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27752205	27752267	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27752268	27752421	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27752422	27752563	0.9	-	1	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27752422	27752563	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27752564	27752655	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27752656	27752759	1	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27752656	27752759	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27752760	27752839	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27752840	27753016	1	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27752840	27753016	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27753017	27753127	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27753128	27753190	0.71	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27753128	27753190	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27753191	27753329	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27753330	27753476	0.98	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27753330	27753476	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27753477	27753591	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27753592	27753754	0.86	-	1	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27753592	27753754	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27753755	27753859	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27753860	27753915	0.9	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27753860	27753915	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27753916	27754117	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27754118	27754185	0.98	-	2	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27754118	27754185	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	intron	27754186	27754362	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	CDS	27754363	27754384	0.58	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	exon	27754363	27754384	.	-	.	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
Phchi.S1	AUGUSTUS	start_codon	27754382	27754384	.	-	0	transcript_id "Phchi.S1G439100.t1"; gene_id "Phchi.S1G439100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2280.t1 is derived from g9200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5845772	5846370	.	+	.	Phchi.S5G088900
Phchi.S5	AUGUSTUS	transcript	5845772	5846370	.	+	.	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	start_codon	5845772	5845774	.	+	0	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	CDS	5845772	5845850	0.97	+	0	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	exon	5845772	5845850	.	+	.	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	intron	5845851	5845944	.	+	.	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	CDS	5845945	5846018	0.98	+	2	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	exon	5845945	5846018	.	+	.	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	intron	5846019	5846148	.	+	.	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	CDS	5846149	5846370	0.8	+	0	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	exon	5846149	5846370	.	+	.	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
Phchi.S5	AUGUSTUS	stop_codon	5846371	5846373	.	+	0	transcript_id "Phchi.S5G088900.t1"; gene_id "Phchi.S5G088900"
# This transcript jg201.t2 is derived from g9983.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg202.t1 is derived from g9984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1127575	1129309	.	+	.	Phchi.S6G016100
Phchi.S6	AUGUSTUS	transcript	1127575	1129309	.	+	.	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	start_codon	1127575	1127577	.	+	0	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	CDS	1127575	1128740	0.46	+	0	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	exon	1127575	1128740	.	+	.	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	intron	1128741	1128877	.	+	.	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	CDS	1128878	1128998	0.69	+	1	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	exon	1128878	1128998	.	+	.	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	intron	1128999	1129102	.	+	.	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	CDS	1129103	1129309	0.56	+	0	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	exon	1129103	1129309	.	+	.	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
Phchi.S6	AUGUSTUS	stop_codon	1129310	1129312	.	+	0	transcript_id "Phchi.S6G016100.t1"; gene_id "Phchi.S6G016100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6157.t1 is derived from g3328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21228563	21229854	.	+	.	Phchi.S1G331600
Phchi.S1	AUGUSTUS	transcript	21228563	21229854	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	start_codon	21228563	21228565	.	+	0	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	CDS	21228563	21228716	1	+	0	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	exon	21228563	21228716	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	intron	21228717	21228890	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	CDS	21228891	21229063	1	+	2	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	exon	21228891	21229063	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	intron	21229064	21229229	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	CDS	21229230	21229431	1	+	0	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	exon	21229230	21229431	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	intron	21229432	21229624	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	CDS	21229625	21229854	0.88	+	2	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	exon	21229625	21229854	.	+	.	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
Phchi.S1	AUGUSTUS	stop_codon	21229855	21229857	.	+	0	transcript_id "Phchi.S1G331600.t1"; gene_id "Phchi.S1G331600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1660.t1 is derived from g8579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2285861	2286874	.	-	.	Phchi.S5G026900
Phchi.S5	AUGUSTUS	transcript	2285861	2286874	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	stop_codon	2285858	2285860	.	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	CDS	2285861	2285902	1	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	exon	2285861	2285902	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	intron	2285903	2285982	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	CDS	2285983	2286027	1	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	exon	2285983	2286027	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	intron	2286028	2286125	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	CDS	2286126	2286194	1	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	exon	2286126	2286194	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	intron	2286195	2286275	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	CDS	2286276	2286364	1	-	2	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	exon	2286276	2286364	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	intron	2286365	2286521	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	CDS	2286522	2286585	1	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	exon	2286522	2286585	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	intron	2286586	2286679	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	CDS	2286680	2286874	0.32	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	exon	2286680	2286874	.	-	.	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
Phchi.S5	AUGUSTUS	start_codon	2286872	2286874	.	-	0	transcript_id "Phchi.S5G026900.t1"; gene_id "Phchi.S5G026900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6497.t1 is derived from g3669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23322533	23328931	.	-	.	Phchi.S1G365600
Phchi.S1	AUGUSTUS	transcript	23322533	23328931	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	stop_codon	23322530	23322532	.	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23322533	23322604	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23322533	23322604	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23322605	23322697	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23322698	23322814	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23322698	23322814	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23322815	23322903	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23322904	23323017	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23322904	23323017	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23323018	23323123	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23323124	23323249	0.99	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23323124	23323249	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23323250	23323381	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23323382	23323436	1	-	1	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23323382	23323436	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23323437	23323544	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23323545	23323630	0.99	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23323545	23323630	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23323631	23323743	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23323744	23323920	0.98	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23323744	23323920	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23323921	23324049	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23324050	23324124	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23324050	23324124	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23324125	23324213	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23324214	23324357	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23324214	23324357	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23324358	23324502	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23324503	23324571	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23324503	23324571	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23324572	23324644	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23324645	23324755	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23324645	23324755	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23324756	23324860	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23324861	23325018	1	-	2	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23324861	23325018	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23325019	23325241	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23325242	23325284	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23325242	23325284	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23325285	23325449	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23325450	23325603	0.91	-	1	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23325450	23325603	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23325604	23325953	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23325954	23325963	0.78	-	2	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23325954	23325963	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23325964	23326073	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23326074	23326158	0.82	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23326074	23326158	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23326159	23326258	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23326259	23326423	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23326259	23326423	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23326424	23326510	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23326511	23326670	1	-	1	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23326511	23326670	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23326671	23326838	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23326839	23326894	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23326839	23326894	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23326895	23327030	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23327031	23327102	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23327031	23327102	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23327103	23327207	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23327208	23327342	0.99	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23327208	23327342	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23327343	23327685	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23327686	23327754	0.64	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23327686	23327754	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23327755	23327856	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23327857	23327955	0.62	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23327857	23327955	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23327956	23328049	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23328050	23328185	1	-	1	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23328050	23328185	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23328186	23328272	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23328273	23328385	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23328273	23328385	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	intron	23328386	23328823	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	CDS	23328824	23328931	1	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	exon	23328824	23328931	.	-	.	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
Phchi.S1	AUGUSTUS	start_codon	23328929	23328931	.	-	0	transcript_id "Phchi.S1G365600.t1"; gene_id "Phchi.S1G365600"
# This transcript jg11504.t2 is derived from g15554.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11505.t1 is derived from g15555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6760590	6763536	.	+	.	Phchi.S4G108700
Phchi.S4	AUGUSTUS	transcript	6760590	6763536	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	start_codon	6760590	6760592	.	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6760590	6760927	0.9	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6760590	6760927	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6760928	6761138	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6761139	6761255	0.98	+	1	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6761139	6761255	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6761256	6761367	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6761368	6761464	1	+	1	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6761368	6761464	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6761465	6761600	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6761601	6761636	1	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6761601	6761636	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6761637	6761724	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6761725	6761912	1	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6761725	6761912	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6761913	6762032	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6762033	6762135	1	+	1	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6762033	6762135	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6762136	6762234	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6762235	6762416	1	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6762235	6762416	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6762417	6762501	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6762502	6762579	1	+	1	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6762502	6762579	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6762580	6762809	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6762810	6762912	1	+	1	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6762810	6762912	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6762913	6763001	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6763002	6763095	1	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6763002	6763095	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	intron	6763096	6763186	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	CDS	6763187	6763536	1	+	2	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	exon	6763187	6763536	.	+	.	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
Phchi.S4	AUGUSTUS	stop_codon	6763537	6763539	.	+	0	transcript_id "Phchi.S4G108700.t1"; gene_id "Phchi.S4G108700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14690.t1 is derived from g13158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14184238	14188040	.	-	.	Phchi.S3G200900
Phchi.S3	AUGUSTUS	transcript	14184238	14188040	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	stop_codon	14184235	14184237	.	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14184238	14184310	1	-	1	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14184238	14184310	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14184311	14184401	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14184402	14184486	1	-	2	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14184402	14184486	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14184487	14184577	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14184578	14184635	1	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14184578	14184635	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14184636	14184719	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14184720	14184886	1	-	2	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14184720	14184886	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14184887	14184961	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14184962	14185034	1	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14184962	14185034	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14185035	14185121	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14185122	14185220	1	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14185122	14185220	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14185221	14185308	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14185309	14185408	1	-	1	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14185309	14185408	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14185409	14185497	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14185498	14185587	0.99	-	1	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14185498	14185587	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14185588	14185695	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14185696	14185751	0.99	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14185696	14185751	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14185752	14185830	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14185831	14185928	1	-	2	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14185831	14185928	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14185929	14186054	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14186055	14186245	1	-	1	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14186055	14186245	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14186246	14186354	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14186355	14186475	1	-	2	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14186355	14186475	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14186476	14186596	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14186597	14186690	1	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14186597	14186690	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14186691	14186784	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14186785	14186880	1	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14186785	14186880	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14186881	14186993	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14186994	14187097	1	-	2	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14186994	14187097	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14187098	14187172	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14187173	14187309	1	-	1	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14187173	14187309	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14187310	14187457	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14187458	14187617	0.98	-	2	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14187458	14187617	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14187618	14187725	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14187726	14187897	0.78	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14187726	14187897	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	intron	14187898	14188037	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	CDS	14188038	14188040	1	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	exon	14188038	14188040	.	-	.	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
Phchi.S3	AUGUSTUS	start_codon	14188038	14188040	.	-	0	transcript_id "Phchi.S3G200900.t1"; gene_id "Phchi.S3G200900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg807.t1 is derived from g10589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5687982	5688728	.	-	.	Phchi.S6G076600
Phchi.S6	AUGUSTUS	transcript	5687982	5688728	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	stop_codon	5687979	5687981	.	-	0	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	CDS	5687982	5688061	0.76	-	2	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	exon	5687982	5688061	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	intron	5688062	5688186	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	CDS	5688187	5688284	1	-	1	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	exon	5688187	5688284	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	intron	5688285	5688476	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	CDS	5688477	5688577	1	-	0	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	exon	5688477	5688577	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	intron	5688578	5688719	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	CDS	5688720	5688728	0.55	-	0	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	exon	5688720	5688728	.	-	.	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
Phchi.S6	AUGUSTUS	start_codon	5688726	5688728	.	-	0	transcript_id "Phchi.S6G076600.t1"; gene_id "Phchi.S6G076600"
# This transcript jg1559.t2 is derived from g8478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1560.t1 is derived from g8479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1771326	1771655	.	-	.	Phchi.S5G016900
Phchi.S5	AUGUSTUS	transcript	1771326	1771655	.	-	.	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	stop_codon	1771323	1771325	.	-	0	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	CDS	1771326	1771459	0.99	-	2	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	exon	1771326	1771459	.	-	.	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	intron	1771460	1771549	.	-	.	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	CDS	1771550	1771655	0.93	-	0	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	exon	1771550	1771655	.	-	.	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
Phchi.S5	AUGUSTUS	start_codon	1771653	1771655	.	-	0	transcript_id "Phchi.S5G016900.t1"; gene_id "Phchi.S5G016900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg574.t1 is derived from g10356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4219813	4220439	.	+	.	Phchi.S6G053300
Phchi.S6	AUGUSTUS	transcript	4219813	4220439	.	+	.	transcript_id "Phchi.S6G053300.t1"; gene_id "Phchi.S6G053300"
Phchi.S6	AUGUSTUS	start_codon	4219813	4219815	.	+	0	transcript_id "Phchi.S6G053300.t1"; gene_id "Phchi.S6G053300"
Phchi.S6	AUGUSTUS	CDS	4219813	4220439	0.62	+	0	transcript_id "Phchi.S6G053300.t1"; gene_id "Phchi.S6G053300"
Phchi.S6	AUGUSTUS	exon	4219813	4220439	.	+	.	transcript_id "Phchi.S6G053300.t1"; gene_id "Phchi.S6G053300"
Phchi.S6	AUGUSTUS	stop_codon	4220440	4220442	.	+	0	transcript_id "Phchi.S6G053300.t1"; gene_id "Phchi.S6G053300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15374.t1 is derived from g13842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18678904	18680397	.	+	.	Phchi.S3G269300
Phchi.S3	AUGUSTUS	transcript	18678904	18680397	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	start_codon	18678904	18678906	.	+	0	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18678904	18679107	0.93	+	0	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18678904	18679107	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	intron	18679108	18679188	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18679189	18679309	1	+	0	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18679189	18679309	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	intron	18679310	18679490	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18679491	18679664	1	+	2	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18679491	18679664	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	intron	18679665	18679809	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18679810	18679856	1	+	2	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18679810	18679856	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	intron	18679857	18679943	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18679944	18680082	1	+	0	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18679944	18680082	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	intron	18680083	18680172	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18680173	18680239	1	+	2	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18680173	18680239	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	intron	18680240	18680354	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	CDS	18680355	18680397	1	+	1	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	exon	18680355	18680397	.	+	.	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
Phchi.S3	AUGUSTUS	stop_codon	18680398	18680400	.	+	0	transcript_id "Phchi.S3G269300.t1"; gene_id "Phchi.S3G269300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13183.t1 is derived from g11648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4574534	4576163	.	+	.	Phchi.S3G050200
Phchi.S3	AUGUSTUS	transcript	4574534	4576163	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	start_codon	4574534	4574536	.	+	0	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4574534	4574733	0.35	+	0	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4574534	4574733	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	intron	4574734	4574948	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4574949	4575045	1	+	1	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4574949	4575045	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	intron	4575046	4575156	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4575157	4575213	0.61	+	0	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4575157	4575213	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	intron	4575214	4575346	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4575347	4575468	1	+	0	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4575347	4575468	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	intron	4575469	4575580	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4575581	4575771	1	+	1	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4575581	4575771	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	intron	4575772	4575854	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4575855	4575911	0.91	+	2	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4575855	4575911	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	intron	4575912	4576014	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	CDS	4576015	4576163	0.91	+	2	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	exon	4576015	4576163	.	+	.	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
Phchi.S3	AUGUSTUS	stop_codon	4576164	4576166	.	+	0	transcript_id "Phchi.S3G050200.t1"; gene_id "Phchi.S3G050200"
# This transcript jg12828.t2 is derived from g11293.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12829.t1 is derived from g11294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2588556	2590209	.	+	.	Phchi.S3G014800
Phchi.S3	AUGUSTUS	transcript	2588556	2590209	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	start_codon	2588556	2588558	.	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2588556	2588607	0.99	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2588556	2588607	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2588608	2588705	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2588706	2588830	1	+	2	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2588706	2588830	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2588831	2588922	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2588923	2589117	1	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2588923	2589117	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589118	2589195	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589196	2589303	1	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589196	2589303	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589304	2589395	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589396	2589573	1	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589396	2589573	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589574	2589749	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589750	2589835	1	+	2	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589750	2589835	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589836	2589919	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589920	2589989	1	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589920	2589989	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589990	2590087	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2590088	2590209	0.99	+	2	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2590088	2590209	.	+	.	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	stop_codon	2590210	2590212	.	+	0	transcript_id "Phchi.S3G014800.t1"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	transcript	2588556	2590209	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	start_codon	2588556	2588558	.	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2588556	2588607	1	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2588556	2588607	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2588608	2588705	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2588706	2588830	1	+	2	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2588706	2588830	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2588831	2588922	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2588923	2589117	1	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2588923	2589117	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589118	2589195	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589196	2589303	1	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589196	2589303	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589304	2589395	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589396	2589573	1	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589396	2589573	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589574	2589752	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589753	2589835	0.91	+	2	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589753	2589835	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589836	2589919	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2589920	2589989	1	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2589920	2589989	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	intron	2589990	2590087	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	CDS	2590088	2590209	0.99	+	2	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	exon	2590088	2590209	.	+	.	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
Phchi.S3	AUGUSTUS	stop_codon	2590210	2590212	.	+	0	transcript_id "Phchi.S3G014800.t2"; gene_id "Phchi.S3G014800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9188.t1 is derived from g6363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40266358	40267250	.	+	.	Phchi.S1G634700
Phchi.S1	AUGUSTUS	transcript	40266358	40267250	.	+	.	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	start_codon	40266358	40266360	.	+	0	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	CDS	40266358	40266509	1	+	0	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	exon	40266358	40266509	.	+	.	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	intron	40266510	40266601	.	+	.	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	CDS	40266602	40267250	1	+	1	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	exon	40266602	40267250	.	+	.	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
Phchi.S1	AUGUSTUS	stop_codon	40267251	40267253	.	+	0	transcript_id "Phchi.S1G634700.t1"; gene_id "Phchi.S1G634700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15387.t1 is derived from g13855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18758652	18760836	.	+	.	Phchi.S3G270600
Phchi.S3	AUGUSTUS	transcript	18758652	18760836	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	start_codon	18758652	18758654	.	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18758652	18758881	0.99	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18758652	18758881	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18758882	18758967	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18758968	18759289	0.87	+	1	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18758968	18759289	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18759290	18759401	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18759402	18759551	0.91	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18759402	18759551	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18759552	18759649	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18759650	18759793	0.92	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18759650	18759793	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18759794	18759994	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18759995	18760081	1	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18759995	18760081	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760082	18760150	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760151	18760238	1	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760151	18760238	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760239	18760327	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760328	18760434	1	+	2	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760328	18760434	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760435	18760536	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760537	18760664	1	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760537	18760664	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760665	18760751	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760752	18760836	1	+	1	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760752	18760836	.	+	.	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	stop_codon	18760837	18760839	.	+	0	transcript_id "Phchi.S3G270600.t1"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	transcript	18758652	18760836	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	start_codon	18758652	18758654	.	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18758652	18758881	1	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18758652	18758881	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18758882	18758967	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18758968	18759289	0.88	+	1	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18758968	18759289	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18759290	18759401	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18759402	18759551	0.9	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18759402	18759551	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18759552	18759649	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18759650	18759793	0.9	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18759650	18759793	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18759794	18759994	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18759995	18760081	1	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18759995	18760081	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760082	18760159	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760160	18760238	0.97	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760160	18760238	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760239	18760327	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760328	18760434	1	+	2	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760328	18760434	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760435	18760536	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760537	18760664	1	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760537	18760664	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	intron	18760665	18760751	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	CDS	18760752	18760836	1	+	1	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	exon	18760752	18760836	.	+	.	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
Phchi.S3	AUGUSTUS	stop_codon	18760837	18760839	.	+	0	transcript_id "Phchi.S3G270600.t2"; gene_id "Phchi.S3G270600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14392.t1 is derived from g12860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12574256	12575761	.	-	.	Phchi.S3G171100
Phchi.S3	AUGUSTUS	transcript	12574256	12575761	.	-	.	transcript_id "Phchi.S3G171100.t1"; gene_id "Phchi.S3G171100"
Phchi.S3	AUGUSTUS	stop_codon	12574253	12574255	.	-	0	transcript_id "Phchi.S3G171100.t1"; gene_id "Phchi.S3G171100"
Phchi.S3	AUGUSTUS	CDS	12574256	12575761	1	-	0	transcript_id "Phchi.S3G171100.t1"; gene_id "Phchi.S3G171100"
Phchi.S3	AUGUSTUS	exon	12574256	12575761	.	-	.	transcript_id "Phchi.S3G171100.t1"; gene_id "Phchi.S3G171100"
Phchi.S3	AUGUSTUS	start_codon	12575759	12575761	.	-	0	transcript_id "Phchi.S3G171100.t1"; gene_id "Phchi.S3G171100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2452.t1 is derived from g9372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6702079	6703204	.	+	.	Phchi.S5G106100
Phchi.S5	AUGUSTUS	transcript	6702079	6703204	.	+	.	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	start_codon	6702079	6702081	.	+	0	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	CDS	6702079	6702422	0.5	+	0	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	exon	6702079	6702422	.	+	.	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	intron	6702423	6702748	.	+	.	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	CDS	6702749	6702841	0.71	+	1	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	exon	6702749	6702841	.	+	.	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	intron	6702842	6702936	.	+	.	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	CDS	6702937	6703204	0.59	+	1	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	exon	6702937	6703204	.	+	.	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
Phchi.S5	AUGUSTUS	stop_codon	6703205	6703207	.	+	0	transcript_id "Phchi.S5G106100.t1"; gene_id "Phchi.S5G106100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11244.t1 is derived from g15294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4986500	4987313	.	+	.	Phchi.S4G082600
Phchi.S4	AUGUSTUS	transcript	4986500	4987313	.	+	.	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	start_codon	4986500	4986502	.	+	0	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	CDS	4986500	4986706	0.94	+	0	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	exon	4986500	4986706	.	+	.	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	intron	4986707	4986837	.	+	.	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	CDS	4986838	4986956	0.32	+	0	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	exon	4986838	4986956	.	+	.	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	intron	4986957	4987042	.	+	.	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	CDS	4987043	4987313	0.12	+	1	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	exon	4987043	4987313	.	+	.	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
Phchi.S4	AUGUSTUS	stop_codon	4987314	4987316	.	+	0	transcript_id "Phchi.S4G082600.t1"; gene_id "Phchi.S4G082600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7724.t1 is derived from g4898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30820437	30823209	.	-	.	Phchi.S1G488300
Phchi.S1	AUGUSTUS	transcript	30820437	30823209	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	stop_codon	30820434	30820436	.	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	CDS	30820437	30821099	0.93	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	exon	30820437	30821099	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	intron	30821100	30821205	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	CDS	30821206	30821319	1	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	exon	30821206	30821319	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	intron	30821320	30821434	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	CDS	30821435	30821725	1	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	exon	30821435	30821725	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	intron	30821726	30821844	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	CDS	30821845	30822153	1	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	exon	30821845	30822153	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	intron	30822154	30822378	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	CDS	30822379	30823209	0.59	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	exon	30822379	30823209	.	-	.	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
Phchi.S1	AUGUSTUS	start_codon	30823207	30823209	.	-	0	transcript_id "Phchi.S1G488300.t1"; gene_id "Phchi.S1G488300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg715.t1 is derived from g10497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5047751	5050370	.	-	.	Phchi.S6G067400
Phchi.S6	AUGUSTUS	transcript	5047751	5050370	.	-	.	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	stop_codon	5047748	5047750	.	-	0	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	CDS	5047751	5048984	0.86	-	1	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	exon	5047751	5048984	.	-	.	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	intron	5048985	5049060	.	-	.	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	CDS	5049061	5050370	0.89	-	0	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	exon	5049061	5050370	.	-	.	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
Phchi.S6	AUGUSTUS	start_codon	5050368	5050370	.	-	0	transcript_id "Phchi.S6G067400.t1"; gene_id "Phchi.S6G067400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2846.t1 is derived from g15.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9452	9896	.	-	.	Phchi.S1G000500
Phchi.S1	AUGUSTUS	transcript	9452	9896	.	-	.	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	stop_codon	9449	9451	.	-	0	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	CDS	9452	9468	0.99	-	2	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	exon	9452	9468	.	-	.	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	intron	9469	9616	.	-	.	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	CDS	9617	9896	0.98	-	0	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	exon	9617	9896	.	-	.	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
Phchi.S1	AUGUSTUS	start_codon	9894	9896	.	-	0	transcript_id "Phchi.S1G000500.t1"; gene_id "Phchi.S1G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13694.t1 is derived from g12161.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8231385	8233953	.	-	.	Phchi.S3G101300
Phchi.S3	AUGUSTUS	transcript	8231385	8233953	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	stop_codon	8231382	8231384	.	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8231385	8231431	0.66	-	2	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8231385	8231431	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8231432	8231519	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8231520	8231598	0.99	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8231520	8231598	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8231599	8231895	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8231896	8231918	0.84	-	2	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8231896	8231918	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8231919	8232005	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8232006	8232119	0.95	-	2	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8232006	8232119	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8232120	8232221	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8232222	8232284	0.49	-	2	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8232222	8232284	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8232285	8232396	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8232397	8232520	0.4	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8232397	8232520	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8232521	8232616	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8232617	8232706	0.58	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8232617	8232706	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8232707	8233177	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8233178	8233270	0.52	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8233178	8233270	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	intron	8233271	8233410	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	CDS	8233411	8233953	0.63	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	exon	8233411	8233953	.	-	.	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
Phchi.S3	AUGUSTUS	start_codon	8233951	8233953	.	-	0	transcript_id "Phchi.S3G101300.t1"; gene_id "Phchi.S3G101300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6859.t1 is derived from g4031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25611573	25613289	.	-	.	Phchi.S1G401800
Phchi.S1	AUGUSTUS	transcript	25611573	25613289	.	-	.	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	stop_codon	25611570	25611572	.	-	0	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	CDS	25611573	25611779	0.97	-	0	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	exon	25611573	25611779	.	-	.	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	intron	25611780	25611900	.	-	.	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	CDS	25611901	25612437	1	-	0	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	exon	25611901	25612437	.	-	.	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	intron	25612438	25612575	.	-	.	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	CDS	25612576	25613289	1	-	0	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	exon	25612576	25613289	.	-	.	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
Phchi.S1	AUGUSTUS	start_codon	25613287	25613289	.	-	0	transcript_id "Phchi.S1G401800.t1"; gene_id "Phchi.S1G401800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg840.t1 is derived from g10622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5838681	5840606	.	-	.	Phchi.S6G079900
Phchi.S6	AUGUSTUS	transcript	5838681	5840606	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	stop_codon	5838678	5838680	.	-	0	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	CDS	5838681	5838801	0.93	-	1	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	exon	5838681	5838801	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	intron	5838802	5838929	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	CDS	5838930	5839275	0.86	-	2	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	exon	5838930	5839275	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	intron	5839276	5839386	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	CDS	5839387	5839523	0.99	-	1	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	exon	5839387	5839523	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	intron	5839524	5839617	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	CDS	5839618	5839821	1	-	1	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	exon	5839618	5839821	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	intron	5839822	5839899	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	CDS	5839900	5840207	0.99	-	0	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	exon	5839900	5840207	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	intron	5840208	5840294	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	CDS	5840295	5840606	0.76	-	0	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	exon	5840295	5840606	.	-	.	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
Phchi.S6	AUGUSTUS	start_codon	5840604	5840606	.	-	0	transcript_id "Phchi.S6G079900.t1"; gene_id "Phchi.S6G079900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2256.t1 is derived from g9176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5706895	5710057	.	+	.	Phchi.S5G086500
Phchi.S5	AUGUSTUS	transcript	5706895	5710057	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	start_codon	5706895	5706897	.	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5706895	5707109	0.94	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5706895	5707109	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5707110	5707200	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5707201	5707325	1	+	1	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5707201	5707325	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5707326	5707425	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5707426	5707550	1	+	2	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5707426	5707550	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5707551	5707642	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5707643	5707826	1	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5707643	5707826	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5707827	5707909	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5707910	5707993	1	+	2	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5707910	5707993	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5707994	5708079	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5708080	5708147	1	+	2	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5708080	5708147	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5708148	5708238	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5708239	5708784	1	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5708239	5708784	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5708785	5708873	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5708874	5708936	1	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5708874	5708936	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5708937	5709061	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5709062	5709127	0.91	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5709062	5709127	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5709128	5709240	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5709241	5709426	0.53	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5709241	5709426	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5709427	5709529	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5709530	5709586	1	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5709530	5709586	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5709587	5709666	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5709667	5709727	0.99	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5709667	5709727	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	intron	5709728	5709836	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	CDS	5709837	5710057	0.84	+	2	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	exon	5709837	5710057	.	+	.	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
Phchi.S5	AUGUSTUS	stop_codon	5710058	5710060	.	+	0	transcript_id "Phchi.S5G086500.t1"; gene_id "Phchi.S5G086500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13744.t1 is derived from g12211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8673963	8675816	.	-	.	Phchi.S3G106300
Phchi.S3	AUGUSTUS	transcript	8673963	8675816	.	-	.	transcript_id "Phchi.S3G106300.t1"; gene_id "Phchi.S3G106300"
Phchi.S3	AUGUSTUS	stop_codon	8673960	8673962	.	-	0	transcript_id "Phchi.S3G106300.t1"; gene_id "Phchi.S3G106300"
Phchi.S3	AUGUSTUS	CDS	8673963	8675816	1	-	0	transcript_id "Phchi.S3G106300.t1"; gene_id "Phchi.S3G106300"
Phchi.S3	AUGUSTUS	exon	8673963	8675816	.	-	.	transcript_id "Phchi.S3G106300.t1"; gene_id "Phchi.S3G106300"
Phchi.S3	AUGUSTUS	start_codon	8675814	8675816	.	-	0	transcript_id "Phchi.S3G106300.t1"; gene_id "Phchi.S3G106300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg232.t1 is derived from g10014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1585229	1587322	.	-	.	Phchi.S6G019100
Phchi.S6	AUGUSTUS	transcript	1585229	1586735	.	-	.	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	stop_codon	1585226	1585228	.	-	0	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1585229	1585816	0.93	-	0	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1585229	1585816	.	-	.	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	intron	1585817	1585925	.	-	.	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1585926	1586197	0.98	-	2	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1585926	1586197	.	-	.	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	intron	1586198	1586281	.	-	.	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1586282	1586735	0.71	-	0	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1586282	1586735	.	-	.	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	start_codon	1586733	1586735	.	-	0	transcript_id "Phchi.S6G019100.t1"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	transcript	1585229	1587322	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	stop_codon	1585226	1585228	.	-	0	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1585229	1585816	0.9	-	0	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1585229	1585816	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	intron	1585817	1585925	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1585926	1586197	0.97	-	2	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1585926	1586197	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	intron	1586198	1586281	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1586282	1586813	0.97	-	0	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1586282	1586813	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	intron	1586814	1586914	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	CDS	1586915	1587322	0.53	-	0	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	exon	1586915	1587322	.	-	.	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
Phchi.S6	AUGUSTUS	start_codon	1587320	1587322	.	-	0	transcript_id "Phchi.S6G019100.t2"; gene_id "Phchi.S6G019100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3472.t1 is derived from g641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3938158	3939856	.	+	.	Phchi.S1G063100
Phchi.S1	AUGUSTUS	transcript	3938158	3939856	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	start_codon	3938158	3938160	.	+	0	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	CDS	3938158	3938410	0.54	+	0	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	exon	3938158	3938410	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	intron	3938411	3938627	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	CDS	3938628	3938656	0.54	+	2	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	exon	3938628	3938656	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	intron	3938657	3938827	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	CDS	3938828	3939194	0.7	+	0	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	exon	3938828	3939194	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	intron	3939195	3939290	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	CDS	3939291	3939856	0.99	+	2	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	exon	3939291	3939856	.	+	.	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
Phchi.S1	AUGUSTUS	stop_codon	3939857	3939859	.	+	0	transcript_id "Phchi.S1G063100.t1"; gene_id "Phchi.S1G063100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11128.t1 is derived from g15178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4292204	4293682	.	-	.	Phchi.S4G071000
Phchi.S4	AUGUSTUS	transcript	4292204	4293682	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	stop_codon	4292201	4292203	.	-	0	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4292204	4292332	0.88	-	0	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4292204	4292332	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	intron	4292333	4292435	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4292436	4292489	0.88	-	0	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4292436	4292489	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	intron	4292490	4292583	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4292584	4292733	1	-	0	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4292584	4292733	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	intron	4292734	4292814	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4292815	4292908	1	-	1	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4292815	4292908	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	intron	4292909	4292995	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4292996	4293103	1	-	1	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4292996	4293103	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	intron	4293104	4293200	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4293201	4293333	1	-	2	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4293201	4293333	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	intron	4293334	4293411	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	CDS	4293412	4293682	0.56	-	0	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	exon	4293412	4293682	.	-	.	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
Phchi.S4	AUGUSTUS	start_codon	4293680	4293682	.	-	0	transcript_id "Phchi.S4G071000.t1"; gene_id "Phchi.S4G071000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15118.t1 is derived from g13586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17160901	17162703	.	-	.	Phchi.S3G243700
Phchi.S3	AUGUSTUS	transcript	17160901	17161677	.	-	.	transcript_id "Phchi.S3G243700.t1"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	stop_codon	17160898	17160900	.	-	0	transcript_id "Phchi.S3G243700.t1"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	CDS	17160901	17161677	0.64	-	0	transcript_id "Phchi.S3G243700.t1"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	exon	17160901	17161677	.	-	.	transcript_id "Phchi.S3G243700.t1"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	start_codon	17161675	17161677	.	-	0	transcript_id "Phchi.S3G243700.t1"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	transcript	17160901	17162703	.	-	.	transcript_id "Phchi.S3G243700.t2"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	stop_codon	17160898	17160900	.	-	0	transcript_id "Phchi.S3G243700.t2"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	CDS	17160901	17162703	0.57	-	0	transcript_id "Phchi.S3G243700.t2"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	exon	17160901	17162703	.	-	.	transcript_id "Phchi.S3G243700.t2"; gene_id "Phchi.S3G243700"
Phchi.S3	AUGUSTUS	start_codon	17162701	17162703	.	-	0	transcript_id "Phchi.S3G243700.t2"; gene_id "Phchi.S3G243700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11991.t1 is derived from g7666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	419106	422500	.	+	.	Phchi.S2G007100
Phchi.S2	AUGUSTUS	transcript	419106	422500	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	start_codon	419106	419108	.	+	0	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	419106	419709	1	+	0	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	419106	419709	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	419710	419810	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	419811	419991	0.55	+	2	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	419811	419991	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	419992	420123	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	420124	420927	0.54	+	1	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	420124	420927	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	420928	421057	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	421058	421156	0.99	+	1	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	421058	421156	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	421157	421273	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	421274	421489	1	+	1	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	421274	421489	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	421490	421631	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	421632	421770	0.97	+	1	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	421632	421770	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	421771	421887	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	421888	422133	0.98	+	0	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	421888	422133	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	422134	422215	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	422216	422335	0.82	+	0	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	422216	422335	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	intron	422336	422416	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	CDS	422417	422500	0.83	+	0	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	exon	422417	422500	.	+	.	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
Phchi.S2	AUGUSTUS	stop_codon	422501	422503	.	+	0	transcript_id "Phchi.S2G007100.t1"; gene_id "Phchi.S2G007100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10770.t1 is derived from g14820.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2017372	2018845	.	-	.	Phchi.S4G035200
Phchi.S4	AUGUSTUS	transcript	2017372	2018845	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	stop_codon	2017369	2017371	.	-	0	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017372	2017434	0.99	-	0	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017372	2017434	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2017435	2017515	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017516	2017673	1	-	2	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017516	2017673	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2017674	2017756	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017757	2017871	0.95	-	0	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017757	2017871	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2017872	2017972	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017973	2018044	0.34	-	0	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017973	2018044	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2018045	2018132	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2018133	2018175	1	-	1	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2018133	2018175	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2018176	2018259	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2018260	2018394	1	-	1	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2018260	2018394	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2018395	2018492	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2018493	2018845	1	-	0	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2018493	2018845	.	-	.	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	start_codon	2018843	2018845	.	-	0	transcript_id "Phchi.S4G035200.t1"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	transcript	2017372	2018845	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	stop_codon	2017369	2017371	.	-	0	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017372	2017434	1	-	0	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017372	2017434	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2017435	2017515	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017516	2017673	1	-	2	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017516	2017673	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2017674	2017756	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017757	2017846	0.85	-	2	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017757	2017846	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2017847	2017972	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2017973	2018026	0.41	-	2	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2017973	2018026	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2018027	2018132	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2018133	2018175	0.89	-	0	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2018133	2018175	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2018176	2018267	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2018268	2018394	0.91	-	1	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2018268	2018394	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	intron	2018395	2018492	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	CDS	2018493	2018845	0.99	-	0	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	exon	2018493	2018845	.	-	.	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
Phchi.S4	AUGUSTUS	start_codon	2018843	2018845	.	-	0	transcript_id "Phchi.S4G035200.t2"; gene_id "Phchi.S4G035200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1852.t1 is derived from g8772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3553600	3557102	.	-	.	Phchi.S5G046100
Phchi.S5	AUGUSTUS	transcript	3553600	3557102	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	stop_codon	3553597	3553599	.	-	0	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3553600	3554514	0.22	-	0	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3553600	3554514	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3554515	3554599	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3554600	3554714	1	-	1	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3554600	3554714	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3554715	3554843	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3554844	3555092	1	-	1	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3554844	3555092	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3555093	3555213	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3555214	3555308	0.93	-	0	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3555214	3555308	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3555309	3555427	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3555428	3555998	0.94	-	1	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3555428	3555998	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3555999	3556127	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3556128	3556239	1	-	2	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3556128	3556239	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3556240	3556344	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3556345	3556509	1	-	2	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3556345	3556509	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3556510	3556605	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3556606	3556709	1	-	1	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3556606	3556709	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3556710	3556821	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3556822	3556937	1	-	0	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3556822	3556937	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	intron	3556938	3557027	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	CDS	3557028	3557102	1	-	0	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	exon	3557028	3557102	.	-	.	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
Phchi.S5	AUGUSTUS	start_codon	3557100	3557102	.	-	0	transcript_id "Phchi.S5G046100.t1"; gene_id "Phchi.S5G046100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10151.t1 is derived from g7327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45999652	46000493	.	-	.	Phchi.S1G731000
Phchi.S1	AUGUSTUS	transcript	45999652	46000493	.	-	.	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	stop_codon	45999649	45999651	.	-	0	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	CDS	45999652	45999685	0.55	-	1	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	exon	45999652	45999685	.	-	.	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	intron	45999686	45999777	.	-	.	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	CDS	45999778	46000493	0.47	-	0	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	exon	45999778	46000493	.	-	.	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
Phchi.S1	AUGUSTUS	start_codon	46000491	46000493	.	-	0	transcript_id "Phchi.S1G731000.t1"; gene_id "Phchi.S1G731000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg304.t1 is derived from g10086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2155225	2155809	.	-	.	Phchi.S6G026300
Phchi.S6	AUGUSTUS	transcript	2155225	2155809	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	stop_codon	2155222	2155224	.	-	0	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	CDS	2155225	2155266	0.82	-	0	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	exon	2155225	2155266	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	intron	2155267	2155355	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	CDS	2155356	2155454	1	-	0	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	exon	2155356	2155454	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	intron	2155455	2155540	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	CDS	2155541	2155641	1	-	2	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	exon	2155541	2155641	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	intron	2155642	2155721	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	CDS	2155722	2155809	0.99	-	0	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	exon	2155722	2155809	.	-	.	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
Phchi.S6	AUGUSTUS	start_codon	2155807	2155809	.	-	0	transcript_id "Phchi.S6G026300.t1"; gene_id "Phchi.S6G026300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5828.t1 is derived from g2998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19149192	19149756	.	+	.	Phchi.S1G298700
Phchi.S1	AUGUSTUS	transcript	19149192	19149756	.	+	.	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	start_codon	19149192	19149194	.	+	0	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	CDS	19149192	19149420	0.57	+	0	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	exon	19149192	19149420	.	+	.	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	intron	19149421	19149676	.	+	.	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	CDS	19149677	19149756	0.66	+	2	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	exon	19149677	19149756	.	+	.	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
Phchi.S1	AUGUSTUS	stop_codon	19149757	19149759	.	+	0	transcript_id "Phchi.S1G298700.t1"; gene_id "Phchi.S1G298700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15525.t1 is derived from g13994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19724973	19726467	.	+	.	Phchi.S3G284400
Phchi.S3	AUGUSTUS	transcript	19724973	19726467	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	start_codon	19724973	19724975	.	+	0	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	CDS	19724973	19725218	0.34	+	0	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	exon	19724973	19725218	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	intron	19725219	19725346	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	CDS	19725347	19725514	1	+	0	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	exon	19725347	19725514	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	intron	19725515	19725614	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	CDS	19725615	19725708	1	+	0	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	exon	19725615	19725708	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	intron	19725709	19725797	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	CDS	19725798	19726052	0.99	+	2	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	exon	19725798	19726052	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	intron	19726053	19726174	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	CDS	19726175	19726467	0.98	+	2	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	exon	19726175	19726467	.	+	.	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
Phchi.S3	AUGUSTUS	stop_codon	19726468	19726470	.	+	0	transcript_id "Phchi.S3G284400.t1"; gene_id "Phchi.S3G284400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2836.t1 is derived from g9756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9104100	9105074	.	+	.	Phchi.S5G144500
Phchi.S5	AUGUSTUS	transcript	9104100	9105074	.	+	.	transcript_id "Phchi.S5G144500.t1"; gene_id "Phchi.S5G144500"
Phchi.S5	AUGUSTUS	start_codon	9104100	9104102	.	+	0	transcript_id "Phchi.S5G144500.t1"; gene_id "Phchi.S5G144500"
Phchi.S5	AUGUSTUS	CDS	9104100	9105074	0.63	+	0	transcript_id "Phchi.S5G144500.t1"; gene_id "Phchi.S5G144500"
Phchi.S5	AUGUSTUS	exon	9104100	9105074	.	+	.	transcript_id "Phchi.S5G144500.t1"; gene_id "Phchi.S5G144500"
Phchi.S5	AUGUSTUS	stop_codon	9105075	9105077	.	+	0	transcript_id "Phchi.S5G144500.t1"; gene_id "Phchi.S5G144500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3222.t1 is derived from g391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2330092	2331463	.	-	.	Phchi.S1G038100
Phchi.S1	AUGUSTUS	transcript	2330092	2331463	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	stop_codon	2330089	2330091	.	-	0	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	CDS	2330092	2330101	0.65	-	1	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	exon	2330092	2330101	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	intron	2330102	2330182	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	CDS	2330183	2330416	0.75	-	1	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	exon	2330183	2330416	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	intron	2330417	2330524	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	CDS	2330525	2330693	0.99	-	2	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	exon	2330525	2330693	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	intron	2330694	2330848	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	CDS	2330849	2330997	1	-	1	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	exon	2330849	2330997	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	intron	2330998	2331077	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	CDS	2331078	2331265	1	-	0	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	exon	2331078	2331265	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	intron	2331266	2331430	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	CDS	2331431	2331463	0.74	-	0	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	exon	2331431	2331463	.	-	.	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
Phchi.S1	AUGUSTUS	start_codon	2331461	2331463	.	-	0	transcript_id "Phchi.S1G038100.t1"; gene_id "Phchi.S1G038100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3367.t1 is derived from g536.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3189214	3193524	.	-	.	Phchi.S1G052600
Phchi.S1	AUGUSTUS	transcript	3189214	3193524	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	stop_codon	3189211	3189213	.	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3189214	3189303	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3189214	3189303	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3189304	3189545	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3189546	3189874	1	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3189546	3189874	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3189875	3189951	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3189952	3190060	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3189952	3190060	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190061	3190146	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190147	3190223	1	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190147	3190223	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190224	3190307	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190308	3190406	1	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190308	3190406	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190407	3190523	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190524	3190664	1	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190524	3190664	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190665	3190744	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190745	3190963	0.5	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190745	3190963	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190964	3191062	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191063	3191177	0.43	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191063	3191177	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191178	3191432	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191433	3191463	0.5	-	1	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191433	3191463	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191464	3191543	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191544	3191641	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191544	3191641	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191642	3191737	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191738	3191773	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191738	3191773	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191774	3191856	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191857	3191982	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191857	3191982	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191983	3192217	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192218	3192306	0.97	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192218	3192306	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3192307	3192427	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192428	3192549	1	-	1	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192428	3192549	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3192550	3192629	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192630	3192775	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192630	3192775	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3192776	3192923	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192924	3193150	1	-	2	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192924	3193150	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3193151	3193241	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3193242	3193368	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3193242	3193368	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3193369	3193464	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3193465	3193524	1	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3193465	3193524	.	-	.	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	start_codon	3193522	3193524	.	-	0	transcript_id "Phchi.S1G052600.t1"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	transcript	3189214	3193524	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	stop_codon	3189211	3189213	.	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3189214	3189303	0.99	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3189214	3189303	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3189304	3189545	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3189546	3189874	1	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3189546	3189874	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3189875	3189951	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3189952	3190060	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3189952	3190060	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190061	3190146	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190147	3190223	1	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190147	3190223	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190224	3190307	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190308	3190406	1	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190308	3190406	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190407	3190523	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190524	3190664	1	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190524	3190664	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190665	3190744	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3190745	3190963	0.48	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3190745	3190963	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3190964	3191062	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191063	3191177	0.36	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191063	3191177	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191178	3191432	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191433	3191463	0.46	-	1	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191433	3191463	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191464	3191543	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191544	3191641	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191544	3191641	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191642	3191737	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191738	3191773	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191738	3191773	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191774	3191856	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3191857	3191982	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3191857	3191982	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3191983	3192217	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192218	3192306	0.73	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192218	3192306	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3192307	3192427	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192428	3192549	1	-	1	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192428	3192549	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3192550	3192629	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192630	3192775	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192630	3192775	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3192776	3192923	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3192924	3193042	1	-	2	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3192924	3193042	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3193043	3193241	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3193242	3193368	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3193242	3193368	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	intron	3193369	3193464	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	CDS	3193465	3193524	1	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	exon	3193465	3193524	.	-	.	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
Phchi.S1	AUGUSTUS	start_codon	3193522	3193524	.	-	0	transcript_id "Phchi.S1G052600.t2"; gene_id "Phchi.S1G052600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7729.t1 is derived from g4903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30877252	30878177	.	-	.	Phchi.S1G488800
Phchi.S1	AUGUSTUS	transcript	30877252	30878177	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	stop_codon	30877249	30877251	.	-	0	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	CDS	30877252	30877384	1	-	1	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	exon	30877252	30877384	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	intron	30877385	30877484	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	CDS	30877485	30877550	1	-	1	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	exon	30877485	30877550	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	intron	30877551	30877639	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	CDS	30877640	30877752	0.81	-	0	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	exon	30877640	30877752	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	intron	30877753	30877859	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	CDS	30877860	30878177	0.99	-	0	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	exon	30877860	30878177	.	-	.	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
Phchi.S1	AUGUSTUS	start_codon	30878175	30878177	.	-	0	transcript_id "Phchi.S1G488800.t1"; gene_id "Phchi.S1G488800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg783.t1 is derived from g10565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5475844	5477849	.	-	.	Phchi.S6G074200
Phchi.S6	AUGUSTUS	transcript	5475844	5477849	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	stop_codon	5475841	5475843	.	-	0	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5475844	5475852	0.99	-	0	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5475844	5475852	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5475853	5476132	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5476133	5476203	0.99	-	2	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5476133	5476203	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5476204	5476484	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5476485	5476628	0.77	-	2	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5476485	5476628	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5476629	5476747	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5476748	5476817	0.82	-	0	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5476748	5476817	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5476818	5477019	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5477020	5477090	0.98	-	2	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5477020	5477090	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5477091	5477200	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5477201	5477398	1	-	2	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5477201	5477398	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5477399	5477537	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5477538	5477685	0.35	-	0	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5477538	5477685	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	intron	5477686	5477834	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	CDS	5477835	5477849	0.39	-	0	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	exon	5477835	5477849	.	-	.	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
Phchi.S6	AUGUSTUS	start_codon	5477847	5477849	.	-	0	transcript_id "Phchi.S6G074200.t1"; gene_id "Phchi.S6G074200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7801.t1 is derived from g4975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31253178	31254508	.	-	.	Phchi.S1G496000
Phchi.S1	AUGUSTUS	transcript	31253178	31254508	.	-	.	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	stop_codon	31253175	31253177	.	-	0	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	CDS	31253178	31253461	0.98	-	2	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	exon	31253178	31253461	.	-	.	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	intron	31253462	31253759	.	-	.	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	CDS	31253760	31254018	1	-	0	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	exon	31253760	31254018	.	-	.	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	intron	31254019	31254106	.	-	.	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	CDS	31254107	31254508	1	-	0	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	exon	31254107	31254508	.	-	.	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
Phchi.S1	AUGUSTUS	start_codon	31254506	31254508	.	-	0	transcript_id "Phchi.S1G496000.t1"; gene_id "Phchi.S1G496000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13813.t1 is derived from g12280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9037718	9038964	.	-	.	Phchi.S3G113200
Phchi.S3	AUGUSTUS	transcript	9037718	9038964	.	-	.	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	stop_codon	9037715	9037717	.	-	0	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	CDS	9037718	9038731	0.3	-	0	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	exon	9037718	9038731	.	-	.	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	intron	9038732	9038826	.	-	.	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	CDS	9038827	9038964	0.34	-	0	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	exon	9038827	9038964	.	-	.	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
Phchi.S3	AUGUSTUS	start_codon	9038962	9038964	.	-	0	transcript_id "Phchi.S3G113200.t1"; gene_id "Phchi.S3G113200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8372.t1 is derived from g5547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35560241	35560582	.	+	.	Phchi.S1G553100
Phchi.S1	AUGUSTUS	transcript	35560241	35560582	.	+	.	transcript_id "Phchi.S1G553100.t1"; gene_id "Phchi.S1G553100"
Phchi.S1	AUGUSTUS	start_codon	35560241	35560243	.	+	0	transcript_id "Phchi.S1G553100.t1"; gene_id "Phchi.S1G553100"
Phchi.S1	AUGUSTUS	CDS	35560241	35560582	1	+	0	transcript_id "Phchi.S1G553100.t1"; gene_id "Phchi.S1G553100"
Phchi.S1	AUGUSTUS	exon	35560241	35560582	.	+	.	transcript_id "Phchi.S1G553100.t1"; gene_id "Phchi.S1G553100"
Phchi.S1	AUGUSTUS	stop_codon	35560583	35560585	.	+	0	transcript_id "Phchi.S1G553100.t1"; gene_id "Phchi.S1G553100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4297.t1 is derived from g1466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9495811	9497206	.	-	.	Phchi.S1G145600
Phchi.S1	AUGUSTUS	transcript	9495811	9497206	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	stop_codon	9495808	9495810	.	-	0	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	CDS	9495811	9496233	1	-	0	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	exon	9495811	9496233	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	intron	9496234	9496314	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	CDS	9496315	9496463	0.74	-	2	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	exon	9496315	9496463	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	intron	9496464	9496864	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	CDS	9496865	9497018	0.66	-	0	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	exon	9496865	9497018	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	intron	9497019	9497110	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	CDS	9497111	9497206	0.42	-	0	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	exon	9497111	9497206	.	-	.	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
Phchi.S1	AUGUSTUS	start_codon	9497204	9497206	.	-	0	transcript_id "Phchi.S1G145600.t1"; gene_id "Phchi.S1G145600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2197.t1 is derived from g9117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5367522	5367971	.	+	.	Phchi.S5G080600
Phchi.S5	AUGUSTUS	transcript	5367522	5367971	.	+	.	transcript_id "Phchi.S5G080600.t1"; gene_id "Phchi.S5G080600"
Phchi.S5	AUGUSTUS	start_codon	5367522	5367524	.	+	0	transcript_id "Phchi.S5G080600.t1"; gene_id "Phchi.S5G080600"
Phchi.S5	AUGUSTUS	CDS	5367522	5367971	0.6	+	0	transcript_id "Phchi.S5G080600.t1"; gene_id "Phchi.S5G080600"
Phchi.S5	AUGUSTUS	exon	5367522	5367971	.	+	.	transcript_id "Phchi.S5G080600.t1"; gene_id "Phchi.S5G080600"
Phchi.S5	AUGUSTUS	stop_codon	5367972	5367974	.	+	0	transcript_id "Phchi.S5G080600.t1"; gene_id "Phchi.S5G080600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg13993.t1 is derived from g12460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10140701	10142476	.	+	.	Phchi.S3G131200
Phchi.S3	AUGUSTUS	transcript	10140701	10142476	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	start_codon	10140701	10140703	.	+	0	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10140701	10140940	0.99	+	0	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10140701	10140940	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10140941	10141089	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141090	10141199	1	+	0	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141090	10141199	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141200	10141295	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141296	10141416	1	+	1	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141296	10141416	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141417	10141487	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141488	10141583	1	+	0	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141488	10141583	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141584	10141664	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141665	10142050	0.99	+	0	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141665	10142050	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10142051	10142249	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10142250	10142323	1	+	1	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10142250	10142323	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10142324	10142408	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10142409	10142476	1	+	2	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10142409	10142476	.	+	.	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	stop_codon	10142477	10142479	.	+	0	transcript_id "Phchi.S3G131200.t1"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	transcript	10140701	10142227	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	start_codon	10140701	10140703	.	+	0	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10140701	10140940	0.99	+	0	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10140701	10140940	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10140941	10141089	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141090	10141199	1	+	0	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141090	10141199	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141200	10141295	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141296	10141416	1	+	1	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141296	10141416	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141417	10141487	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141488	10141583	1	+	0	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141488	10141583	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141584	10141664	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141665	10142050	0.97	+	0	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141665	10142050	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10142051	10142220	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10142221	10142227	1	+	1	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10142221	10142227	.	+	.	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	stop_codon	10142228	10142230	.	+	0	transcript_id "Phchi.S3G131200.t2"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	transcript	10140701	10142476	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	start_codon	10140701	10140703	.	+	0	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10140701	10140940	1	+	0	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10140701	10140940	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10140941	10141089	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141090	10141199	1	+	0	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141090	10141199	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141200	10141295	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141296	10141416	1	+	1	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141296	10141416	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141417	10141487	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141488	10141583	1	+	0	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141488	10141583	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10141584	10141664	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10141665	10142050	0.92	+	0	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10141665	10142050	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10142051	10142252	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10142253	10142323	0.98	+	1	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10142253	10142323	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	intron	10142324	10142408	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	CDS	10142409	10142476	0.98	+	2	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	exon	10142409	10142476	.	+	.	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
Phchi.S3	AUGUSTUS	stop_codon	10142477	10142479	.	+	0	transcript_id "Phchi.S3G131200.t3"; gene_id "Phchi.S3G131200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8701.t1 is derived from g5876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37530048	37531022	.	+	.	Phchi.S1G586000
Phchi.S1	AUGUSTUS	transcript	37530048	37531022	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	start_codon	37530048	37530050	.	+	0	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	CDS	37530048	37530188	1	+	0	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	exon	37530048	37530188	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	intron	37530189	37530281	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	CDS	37530282	37530545	0.68	+	0	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	exon	37530282	37530545	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	intron	37530546	37530648	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	CDS	37530649	37530656	0.62	+	0	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	exon	37530649	37530656	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	intron	37530657	37530729	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	CDS	37530730	37530801	1	+	1	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	exon	37530730	37530801	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	intron	37530802	37530886	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	CDS	37530887	37531022	1	+	1	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	exon	37530887	37531022	.	+	.	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
Phchi.S1	AUGUSTUS	stop_codon	37531023	37531025	.	+	0	transcript_id "Phchi.S1G586000.t1"; gene_id "Phchi.S1G586000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14084.t1 is derived from g12551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10777527	10778832	.	-	.	Phchi.S3G140300
Phchi.S3	AUGUSTUS	transcript	10777527	10778832	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	stop_codon	10777524	10777526	.	-	0	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	CDS	10777527	10777592	1	-	0	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	exon	10777527	10777592	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	intron	10777593	10777664	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	CDS	10777665	10777769	1	-	0	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	exon	10777665	10777769	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	intron	10777770	10777852	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	CDS	10777853	10778274	1	-	2	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	exon	10777853	10778274	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	intron	10778275	10778483	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	CDS	10778484	10778832	0.98	-	0	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	exon	10778484	10778832	.	-	.	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
Phchi.S3	AUGUSTUS	start_codon	10778830	10778832	.	-	0	transcript_id "Phchi.S3G140300.t1"; gene_id "Phchi.S3G140300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5923.t1 is derived from g3094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19882610	19885719	.	-	.	Phchi.S1G308200
Phchi.S1	AUGUSTUS	transcript	19882610	19885719	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	stop_codon	19882607	19882609	.	-	0	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	CDS	19882610	19883107	1	-	0	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	exon	19882610	19883107	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	intron	19883108	19883236	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	CDS	19883237	19883411	1	-	1	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	exon	19883237	19883411	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	intron	19883412	19883534	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	CDS	19883535	19884026	0.95	-	1	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	exon	19883535	19884026	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	intron	19884027	19884187	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	CDS	19884188	19885719	0.94	-	0	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	exon	19884188	19885719	.	-	.	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
Phchi.S1	AUGUSTUS	start_codon	19885717	19885719	.	-	0	transcript_id "Phchi.S1G308200.t1"; gene_id "Phchi.S1G308200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13773.t1 is derived from g12240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8841289	8845779	.	+	.	Phchi.S3G109200
Phchi.S3	AUGUSTUS	transcript	8841289	8845779	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	start_codon	8841289	8841291	.	+	0	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8841289	8841370	1	+	0	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8841289	8841370	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8841371	8841582	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8841583	8842156	1	+	2	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8841583	8842156	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8842157	8842362	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8842363	8842841	0.98	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8842363	8842841	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8842842	8842940	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8842941	8843067	1	+	2	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8842941	8843067	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8843068	8843187	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8843188	8843259	1	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8843188	8843259	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8843260	8843357	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8843358	8843426	1	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8843358	8843426	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8843427	8843512	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8843513	8843584	1	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8843513	8843584	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8843585	8843699	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8843700	8843771	0.71	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8843700	8843771	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8843772	8843925	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8843926	8844149	0.8	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8843926	8844149	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8844150	8844258	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8844259	8844458	1	+	2	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8844259	8844458	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8844459	8844576	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8844577	8844709	1	+	0	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8844577	8844709	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8844710	8844820	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8844821	8844892	0.98	+	2	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8844821	8844892	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8844893	8845051	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8845052	8845075	0.84	+	2	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8845052	8845075	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8845076	8845203	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8845204	8845246	0.61	+	2	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8845204	8845246	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8845247	8845349	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8845350	8845485	0.99	+	1	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8845350	8845485	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	intron	8845486	8845575	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	CDS	8845576	8845779	0.99	+	0	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	exon	8845576	8845779	.	+	.	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
Phchi.S3	AUGUSTUS	stop_codon	8845780	8845782	.	+	0	transcript_id "Phchi.S3G109200.t1"; gene_id "Phchi.S3G109200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2523.t1 is derived from g9443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7130001	7132114	.	+	.	Phchi.S5G113200
Phchi.S5	AUGUSTUS	transcript	7130001	7132114	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	start_codon	7130001	7130003	.	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7130001	7130060	0.26	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7130001	7130060	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	intron	7130061	7130295	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7130296	7130544	0.35	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7130296	7130544	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	intron	7130545	7130620	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7130621	7130698	1	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7130621	7130698	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	intron	7130699	7130841	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7130842	7130940	1	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7130842	7130940	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	intron	7130941	7131087	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7131088	7131280	1	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7131088	7131280	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	intron	7131281	7131354	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7131355	7131776	0.89	+	2	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7131355	7131776	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	intron	7131777	7131871	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	CDS	7131872	7132114	0.93	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	exon	7131872	7132114	.	+	.	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
Phchi.S5	AUGUSTUS	stop_codon	7132115	7132117	.	+	0	transcript_id "Phchi.S5G113200.t1"; gene_id "Phchi.S5G113200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7993.t1 is derived from g5168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32313140	32313778	.	-	.	Phchi.S1G515200
Phchi.S1	AUGUSTUS	transcript	32313140	32313778	.	-	.	transcript_id "Phchi.S1G515200.t1"; gene_id "Phchi.S1G515200"
Phchi.S1	AUGUSTUS	stop_codon	32313137	32313139	.	-	0	transcript_id "Phchi.S1G515200.t1"; gene_id "Phchi.S1G515200"
Phchi.S1	AUGUSTUS	CDS	32313140	32313778	0.82	-	0	transcript_id "Phchi.S1G515200.t1"; gene_id "Phchi.S1G515200"
Phchi.S1	AUGUSTUS	exon	32313140	32313778	.	-	.	transcript_id "Phchi.S1G515200.t1"; gene_id "Phchi.S1G515200"
Phchi.S1	AUGUSTUS	start_codon	32313776	32313778	.	-	0	transcript_id "Phchi.S1G515200.t1"; gene_id "Phchi.S1G515200"
# This transcript jg6679.t2 is derived from g3851.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6680.t1 is derived from g3852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24467149	24468314	.	-	.	Phchi.S1G383900
Phchi.S1	AUGUSTUS	transcript	24467149	24468314	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	stop_codon	24467146	24467148	.	-	0	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	CDS	24467149	24467221	0.67	-	1	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	exon	24467149	24467221	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	intron	24467222	24467297	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	CDS	24467298	24467351	0.55	-	1	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	exon	24467298	24467351	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	intron	24467352	24467458	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	CDS	24467459	24467514	0.57	-	0	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	exon	24467459	24467514	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	intron	24467515	24467645	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	CDS	24467646	24467731	1	-	2	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	exon	24467646	24467731	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	intron	24467732	24467813	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	CDS	24467814	24467946	1	-	0	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	exon	24467814	24467946	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	intron	24467947	24468029	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	CDS	24468030	24468314	1	-	0	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	exon	24468030	24468314	.	-	.	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
Phchi.S1	AUGUSTUS	start_codon	24468312	24468314	.	-	0	transcript_id "Phchi.S1G383900.t1"; gene_id "Phchi.S1G383900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2798.t1 is derived from g9718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8935841	8937859	.	+	.	Phchi.S5G140700
Phchi.S5	AUGUSTUS	transcript	8935841	8937859	.	+	.	transcript_id "Phchi.S5G140700.t1"; gene_id "Phchi.S5G140700"
Phchi.S5	AUGUSTUS	start_codon	8935841	8935843	.	+	0	transcript_id "Phchi.S5G140700.t1"; gene_id "Phchi.S5G140700"
Phchi.S5	AUGUSTUS	CDS	8935841	8937859	0.91	+	0	transcript_id "Phchi.S5G140700.t1"; gene_id "Phchi.S5G140700"
Phchi.S5	AUGUSTUS	exon	8935841	8937859	.	+	.	transcript_id "Phchi.S5G140700.t1"; gene_id "Phchi.S5G140700"
Phchi.S5	AUGUSTUS	stop_codon	8937860	8937862	.	+	0	transcript_id "Phchi.S5G140700.t1"; gene_id "Phchi.S5G140700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4551.t1 is derived from g1721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11071616	11074334	.	-	.	Phchi.S1G171000
Phchi.S1	AUGUSTUS	transcript	11071616	11074334	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	stop_codon	11071613	11071615	.	-	0	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11071616	11071881	0.5	-	2	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11071616	11071881	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11071882	11072081	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11072082	11072277	0.33	-	0	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11072082	11072277	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11072278	11072365	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11072366	11072489	0.73	-	1	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11072366	11072489	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11072490	11072581	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11072582	11072669	0.91	-	2	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11072582	11072669	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11072670	11072754	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11072755	11073015	0.97	-	2	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11072755	11073015	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11073016	11073201	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11073202	11073388	0.95	-	0	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11073202	11073388	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11073389	11073517	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11073518	11073667	0.96	-	0	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11073518	11073667	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11073668	11073751	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11073752	11074152	0.56	-	2	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11073752	11074152	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	intron	11074153	11074285	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	CDS	11074286	11074334	0.88	-	0	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	exon	11074286	11074334	.	-	.	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
Phchi.S1	AUGUSTUS	start_codon	11074332	11074334	.	-	0	transcript_id "Phchi.S1G171000.t1"; gene_id "Phchi.S1G171000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4076.t1 is derived from g1245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7649703	7653051	.	-	.	Phchi.S1G123500
Phchi.S1	AUGUSTUS	transcript	7649703	7653051	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	stop_codon	7649700	7649702	.	-	0	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7649703	7649884	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7649703	7649884	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7649885	7649977	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7649978	7650027	0.67	-	1	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7649978	7650027	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7650028	7650146	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7650147	7650152	0.84	-	1	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7650147	7650152	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7650153	7650237	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7650238	7650422	1	-	0	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7650238	7650422	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7650423	7650507	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7650508	7650560	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7650508	7650560	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7650561	7650655	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7650656	7650811	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7650656	7650811	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7650812	7650914	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7650915	7651052	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7650915	7651052	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7651053	7651155	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7651156	7651221	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7651156	7651221	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7651222	7651315	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7651316	7651395	1	-	1	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7651316	7651395	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7651396	7651477	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7651478	7651642	0.99	-	1	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7651478	7651642	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7651643	7651744	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7651745	7651884	0.98	-	0	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7651745	7651884	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7651885	7651983	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7651984	7652135	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7651984	7652135	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7652136	7652238	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7652239	7652399	0.98	-	1	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7652239	7652399	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7652400	7652495	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7652496	7652587	1	-	0	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7652496	7652587	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7652588	7652676	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7652677	7652756	1	-	2	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7652677	7652756	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	intron	7652757	7652837	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	CDS	7652838	7653051	0.97	-	0	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	exon	7652838	7653051	.	-	.	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
Phchi.S1	AUGUSTUS	start_codon	7653049	7653051	.	-	0	transcript_id "Phchi.S1G123500.t1"; gene_id "Phchi.S1G123500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14838.t1 is derived from g13306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14943288	14951370	.	+	.	Phchi.S3G215700
Phchi.S3	AUGUSTUS	transcript	14943288	14951370	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	start_codon	14943288	14943290	.	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14943288	14943624	0.99	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14943288	14943624	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14943625	14943742	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14943743	14943979	1	+	2	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14943743	14943979	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14943980	14944067	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14944068	14944636	1	+	2	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14944068	14944636	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14944637	14944762	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14944763	14944936	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14944763	14944936	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14944937	14945086	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14945087	14945170	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14945087	14945170	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14945171	14945304	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14945305	14945379	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14945305	14945379	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14945380	14945490	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14945491	14945555	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14945491	14945555	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14945556	14945718	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14945719	14945809	1	+	1	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14945719	14945809	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14945810	14945913	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14945914	14946102	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14945914	14946102	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14946103	14946240	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14946241	14946404	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14946241	14946404	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14946405	14946526	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14946527	14946641	0.97	+	1	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14946527	14946641	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14946642	14946744	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14946745	14946924	0.98	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14946745	14946924	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14946925	14947013	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14947014	14947127	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14947014	14947127	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14947128	14947221	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14947222	14947341	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14947222	14947341	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14947342	14947503	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14947504	14947824	0.99	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14947504	14947824	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14947825	14947940	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14947941	14948033	0.99	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14947941	14948033	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14948034	14948129	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14948130	14948251	0.99	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14948130	14948251	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14948252	14948354	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14948355	14948427	1	+	1	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14948355	14948427	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14948428	14948578	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14948579	14948635	0.97	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14948579	14948635	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14948636	14948744	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14948745	14948837	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14948745	14948837	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14948838	14948944	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14948945	14949070	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14948945	14949070	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14949071	14949160	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14949161	14949258	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14949161	14949258	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14949259	14949344	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14949345	14949390	1	+	1	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14949345	14949390	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14949391	14949540	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14949541	14949654	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14949541	14949654	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14949655	14949744	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14949745	14949828	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14949745	14949828	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14949829	14949917	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14949918	14950031	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14949918	14950031	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14950032	14950113	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14950114	14950203	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14950114	14950203	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14950204	14950282	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14950283	14950365	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14950283	14950365	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14950366	14950454	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14950455	14950650	1	+	1	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14950455	14950650	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14950651	14950719	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14950720	14950773	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14950720	14950773	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14950774	14950867	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14950868	14950987	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14950868	14950987	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14950988	14951070	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14951071	14951145	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14951071	14951145	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	intron	14951146	14951220	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	CDS	14951221	14951370	1	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	exon	14951221	14951370	.	+	.	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
Phchi.S3	AUGUSTUS	stop_codon	14951371	14951373	.	+	0	transcript_id "Phchi.S3G215700.t1"; gene_id "Phchi.S3G215700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12167.t1 is derived from g7843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5306927	5307945	.	+	.	Phchi.S2G024700
Phchi.S2	AUGUSTUS	transcript	5306927	5307945	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	start_codon	5306927	5306929	.	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5306927	5306953	1	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5306927	5306953	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	intron	5306954	5307087	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5307088	5307153	1	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5307088	5307153	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	intron	5307154	5307237	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5307238	5307291	1	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5307238	5307291	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	intron	5307292	5307393	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5307394	5307447	1	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5307394	5307447	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	intron	5307448	5307596	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5307597	5307650	1	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5307597	5307650	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	intron	5307651	5307737	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5307738	5307803	0.68	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5307738	5307803	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	intron	5307804	5307912	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	CDS	5307913	5307945	0.68	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	exon	5307913	5307945	.	+	.	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
Phchi.S2	AUGUSTUS	stop_codon	5307946	5307948	.	+	0	transcript_id "Phchi.S2G024700.t1"; gene_id "Phchi.S2G024700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6030.t1 is derived from g3201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20510899	20512230	.	+	.	Phchi.S1G318900
Phchi.S1	AUGUSTUS	transcript	20510899	20512230	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	start_codon	20510899	20510901	.	+	0	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	CDS	20510899	20510941	0.65	+	0	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	exon	20510899	20510941	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	intron	20510942	20511214	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	CDS	20511215	20511358	1	+	2	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	exon	20511215	20511358	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	intron	20511359	20511438	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	CDS	20511439	20511476	1	+	2	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	exon	20511439	20511476	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	intron	20511477	20511577	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	CDS	20511578	20511628	1	+	0	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	exon	20511578	20511628	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	intron	20511629	20511731	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	CDS	20511732	20511957	0.5	+	0	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	exon	20511732	20511957	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	intron	20511958	20512051	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	CDS	20512052	20512230	0.5	+	2	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	exon	20512052	20512230	.	+	.	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
Phchi.S1	AUGUSTUS	stop_codon	20512231	20512233	.	+	0	transcript_id "Phchi.S1G318900.t1"; gene_id "Phchi.S1G318900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12360.t1 is derived from g8036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12717725	12720574	.	-	.	Phchi.S2G044000
Phchi.S2	AUGUSTUS	transcript	12717725	12720574	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	stop_codon	12717722	12717724	.	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12717725	12717825	0.39	-	2	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12717725	12717825	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12717826	12717924	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12717925	12717951	0.34	-	2	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12717925	12717951	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12717952	12718173	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12718174	12718507	0.56	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12718174	12718507	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12718508	12718717	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12718718	12718804	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12718718	12718804	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12718805	12718976	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12718977	12719082	1	-	1	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12718977	12719082	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12719083	12719262	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12719263	12719354	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12719263	12719354	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12719355	12719471	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12719472	12719582	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12719472	12719582	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12719583	12719707	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12719708	12719842	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12719708	12719842	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12719843	12720000	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12720001	12720087	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12720001	12720087	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12720088	12720180	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12720181	12720348	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12720181	12720348	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	intron	12720349	12720439	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	CDS	12720440	12720574	1	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	exon	12720440	12720574	.	-	.	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
Phchi.S2	AUGUSTUS	start_codon	12720572	12720574	.	-	0	transcript_id "Phchi.S2G044000.t1"; gene_id "Phchi.S2G044000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4487.t1 is derived from g1657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10768149	10770586	.	+	.	Phchi.S1G164600
Phchi.S1	AUGUSTUS	transcript	10768149	10770586	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	start_codon	10768149	10768151	.	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10768149	10768274	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10768149	10768274	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10768275	10768371	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10768372	10768429	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10768372	10768429	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10768430	10768526	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10768527	10768646	1	+	2	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10768527	10768646	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10768647	10768767	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10768768	10768850	1	+	2	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10768768	10768850	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10768851	10768950	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10768951	10768957	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10768951	10768957	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10768958	10769019	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10769020	10769026	1	+	2	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10769020	10769026	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10769027	10769191	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10769192	10769282	1	+	1	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10769192	10769282	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10769283	10769429	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10769430	10769483	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10769430	10769483	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10769484	10769580	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10769581	10769676	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10769581	10769676	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10769677	10769783	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10769784	10769873	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10769784	10769873	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10769874	10769996	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10769997	10770048	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10769997	10770048	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10770049	10770126	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10770127	10770188	1	+	2	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10770127	10770188	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10770189	10770277	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10770278	10770358	1	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10770278	10770358	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	intron	10770359	10770445	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	CDS	10770446	10770586	0.93	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	exon	10770446	10770586	.	+	.	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
Phchi.S1	AUGUSTUS	stop_codon	10770587	10770589	.	+	0	transcript_id "Phchi.S1G164600.t1"; gene_id "Phchi.S1G164600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5343.t1 is derived from g2513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16375913	16381650	.	-	.	Phchi.S1G250200
Phchi.S1	AUGUSTUS	transcript	16375913	16381650	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	stop_codon	16375910	16375912	.	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16375913	16376062	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16375913	16376062	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16376063	16376157	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16376158	16376361	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16376158	16376361	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16376362	16376458	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16376459	16376707	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16376459	16376707	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16376708	16376791	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16376792	16377025	0.39	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16376792	16377025	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16377026	16377138	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16377139	16377378	0.71	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16377139	16377378	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16377379	16377456	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16377457	16377675	0.95	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16377457	16377675	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16377676	16377807	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16377808	16377878	0.96	-	2	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16377808	16377878	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16377879	16378030	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16378031	16378394	0.52	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16378031	16378394	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16378395	16378520	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16378521	16378729	0.96	-	2	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16378521	16378729	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16378730	16378847	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16378848	16379064	0.96	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16378848	16379064	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16379065	16379179	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16379180	16379520	0.95	-	2	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16379180	16379520	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16379521	16379603	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16379604	16379699	0.98	-	2	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16379604	16379699	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16379700	16379826	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16379827	16380073	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16379827	16380073	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16380074	16380261	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16380262	16380472	1	-	1	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16380262	16380472	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16380473	16380571	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16380572	16380762	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16380572	16380762	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16380763	16380909	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16380910	16381028	1	-	2	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16380910	16381028	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16381029	16381151	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16381152	16381242	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16381152	16381242	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16381243	16381338	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16381339	16381485	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16381339	16381485	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	intron	16381486	16381623	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	CDS	16381624	16381650	1	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	exon	16381624	16381650	.	-	.	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
Phchi.S1	AUGUSTUS	start_codon	16381648	16381650	.	-	0	transcript_id "Phchi.S1G250200.t1"; gene_id "Phchi.S1G250200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10845.t1 is derived from g14895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2448117	2449364	.	+	.	Phchi.S4G042700
Phchi.S4	AUGUSTUS	transcript	2448117	2449364	.	+	.	transcript_id "Phchi.S4G042700.t1"; gene_id "Phchi.S4G042700"
Phchi.S4	AUGUSTUS	start_codon	2448117	2448119	.	+	0	transcript_id "Phchi.S4G042700.t1"; gene_id "Phchi.S4G042700"
Phchi.S4	AUGUSTUS	CDS	2448117	2449364	1	+	0	transcript_id "Phchi.S4G042700.t1"; gene_id "Phchi.S4G042700"
Phchi.S4	AUGUSTUS	exon	2448117	2449364	.	+	.	transcript_id "Phchi.S4G042700.t1"; gene_id "Phchi.S4G042700"
Phchi.S4	AUGUSTUS	stop_codon	2449365	2449367	.	+	0	transcript_id "Phchi.S4G042700.t1"; gene_id "Phchi.S4G042700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7196.t1 is derived from g4368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27598680	27600791	.	-	.	Phchi.S1G435500
Phchi.S1	AUGUSTUS	transcript	27598680	27600791	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	stop_codon	27598677	27598679	.	-	0	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	CDS	27598680	27599312	1	-	0	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	exon	27598680	27599312	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	intron	27599313	27599402	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	CDS	27599403	27599602	1	-	2	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	exon	27599403	27599602	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	intron	27599603	27599737	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	CDS	27599738	27599807	1	-	0	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	exon	27599738	27599807	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	intron	27599808	27599892	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	CDS	27599893	27600043	1	-	1	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	exon	27599893	27600043	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	intron	27600044	27600134	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	CDS	27600135	27600368	1	-	1	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	exon	27600135	27600368	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	intron	27600369	27600477	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	CDS	27600478	27600791	1	-	0	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	exon	27600478	27600791	.	-	.	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
Phchi.S1	AUGUSTUS	start_codon	27600789	27600791	.	-	0	transcript_id "Phchi.S1G435500.t1"; gene_id "Phchi.S1G435500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10991.t1 is derived from g15041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3552494	3553873	.	-	.	Phchi.S4G057300
Phchi.S4	AUGUSTUS	transcript	3552494	3553873	.	-	.	transcript_id "Phchi.S4G057300.t1"; gene_id "Phchi.S4G057300"
Phchi.S4	AUGUSTUS	stop_codon	3552491	3552493	.	-	0	transcript_id "Phchi.S4G057300.t1"; gene_id "Phchi.S4G057300"
Phchi.S4	AUGUSTUS	CDS	3552494	3553873	0.76	-	0	transcript_id "Phchi.S4G057300.t1"; gene_id "Phchi.S4G057300"
Phchi.S4	AUGUSTUS	exon	3552494	3553873	.	-	.	transcript_id "Phchi.S4G057300.t1"; gene_id "Phchi.S4G057300"
Phchi.S4	AUGUSTUS	start_codon	3553871	3553873	.	-	0	transcript_id "Phchi.S4G057300.t1"; gene_id "Phchi.S4G057300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1123.t1 is derived from g10906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7843444	7848345	.	+	.	Phchi.S6G108200
Phchi.S6	AUGUSTUS	transcript	7845577	7848345	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	start_codon	7845577	7845579	.	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845577	7845603	0.97	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845577	7845603	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845604	7845787	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845788	7845886	0.99	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845788	7845886	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845887	7846016	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846017	7846223	0.99	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846017	7846223	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846224	7846343	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846344	7846403	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846344	7846403	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846404	7846502	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846503	7846610	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846503	7846610	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846611	7846694	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846695	7846910	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846695	7846910	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846911	7847000	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847001	7847105	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847001	7847105	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847106	7847242	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847243	7847356	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847243	7847356	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847357	7847502	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847503	7847634	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847503	7847634	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847635	7847717	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847718	7847861	0.98	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847718	7847861	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847862	7847982	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847983	7848082	1	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847983	7848082	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7848083	7848168	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7848169	7848198	1	+	2	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7848169	7848198	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7848199	7848277	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7848278	7848345	1	+	2	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7848278	7848345	.	+	.	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	stop_codon	7848346	7848348	.	+	0	transcript_id "Phchi.S6G108200.t1"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	transcript	7843444	7848345	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	start_codon	7843444	7843446	.	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7843444	7844912	0.38	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7843444	7844912	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7844913	7845100	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845101	7845143	0.81	+	1	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845101	7845143	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845144	7845452	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845453	7845596	0.96	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845453	7845596	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845597	7845787	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845788	7845886	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845788	7845886	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845887	7846016	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846017	7846223	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846017	7846223	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846224	7846343	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846344	7846403	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846344	7846403	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846404	7846502	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846503	7846610	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846503	7846610	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846611	7846694	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846695	7846910	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846695	7846910	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846911	7847000	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847001	7847105	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847001	7847105	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847106	7847242	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847243	7847356	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847243	7847356	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847357	7847502	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847503	7847634	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847503	7847634	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847635	7847717	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847718	7847861	0.91	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847718	7847861	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847862	7847982	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847983	7848082	1	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847983	7848082	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7848083	7848168	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7848169	7848198	1	+	2	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7848169	7848198	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7848199	7848277	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7848278	7848345	1	+	2	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7848278	7848345	.	+	.	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	stop_codon	7848346	7848348	.	+	0	transcript_id "Phchi.S6G108200.t2"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	transcript	7843444	7848311	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	start_codon	7843444	7843446	.	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7843444	7844912	0.28	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7843444	7844912	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7844913	7845100	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845101	7845143	0.7	+	1	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845101	7845143	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845144	7845452	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845453	7845596	0.94	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845453	7845596	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845597	7845787	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7845788	7845886	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7845788	7845886	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7845887	7846016	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846017	7846223	0.99	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846017	7846223	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846224	7846343	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846344	7846403	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846344	7846403	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846404	7846502	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846503	7846610	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846503	7846610	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846611	7846694	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7846695	7846910	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7846695	7846910	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7846911	7847000	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847001	7847105	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847001	7847105	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847106	7847242	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847243	7847356	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847243	7847356	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847357	7847502	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847503	7847634	1	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847503	7847634	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847635	7847717	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847718	7847861	0.93	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847718	7847861	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7847862	7847982	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7847983	7848082	0.99	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7847983	7848082	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7848083	7848168	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7848169	7848202	0.98	+	2	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7848169	7848202	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	intron	7848203	7848277	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	CDS	7848278	7848311	0.98	+	1	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	exon	7848278	7848311	.	+	.	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
Phchi.S6	AUGUSTUS	stop_codon	7848312	7848314	.	+	0	transcript_id "Phchi.S6G108200.t3"; gene_id "Phchi.S6G108200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg958.t1 is derived from g10740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6654306	6656138	.	-	.	Phchi.S6G091700
Phchi.S6	AUGUSTUS	transcript	6654306	6656138	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	stop_codon	6654303	6654305	.	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6654306	6654467	0.93	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6654306	6654467	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6654468	6654569	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6654570	6654683	0.92	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6654570	6654683	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6654684	6654791	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6654792	6654873	1	-	1	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6654792	6654873	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6654874	6654962	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6654963	6655022	1	-	1	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6654963	6655022	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6655023	6655170	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6655171	6655256	1	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6655171	6655256	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6655257	6655348	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6655349	6655443	1	-	2	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6655349	6655443	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6655444	6655583	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6655584	6655632	1	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6655584	6655632	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6655633	6655750	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6655751	6655815	1	-	2	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6655751	6655815	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	intron	6655816	6655951	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	CDS	6655952	6656138	1	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	exon	6655952	6656138	.	-	.	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
Phchi.S6	AUGUSTUS	start_codon	6656136	6656138	.	-	0	transcript_id "Phchi.S6G091700.t1"; gene_id "Phchi.S6G091700"
# This transcript jg15433.t2 is derived from g13901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15433.t3 is derived from g13901.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15434.t1 is derived from g13902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19079554	19079888	.	-	.	Phchi.S3G275300
Phchi.S3	AUGUSTUS	transcript	19079554	19079888	.	-	.	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	stop_codon	19079551	19079553	.	-	0	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	CDS	19079554	19079669	0.59	-	2	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	exon	19079554	19079669	.	-	.	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	intron	19079670	19079764	.	-	.	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	CDS	19079765	19079888	0.98	-	0	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	exon	19079765	19079888	.	-	.	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
Phchi.S3	AUGUSTUS	start_codon	19079886	19079888	.	-	0	transcript_id "Phchi.S3G275300.t1"; gene_id "Phchi.S3G275300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15601.t1 is derived from g14070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20218980	20223001	.	+	.	Phchi.S3G292000
Phchi.S3	AUGUSTUS	transcript	20218980	20223001	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	start_codon	20218980	20218982	.	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20218980	20219309	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20218980	20219309	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20219310	20219391	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20219392	20219814	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20219392	20219814	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20219815	20219907	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20219908	20220243	0.71	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20219908	20220243	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20220244	20220338	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20220339	20220425	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20220339	20220425	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20220426	20220508	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20220509	20220703	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20220509	20220703	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20220704	20220813	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20220814	20221277	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20220814	20221277	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20221278	20221372	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20221373	20221642	0.59	+	1	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20221373	20221642	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20221643	20221872	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20221873	20221940	0.58	+	1	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20221873	20221940	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20221941	20222100	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20222101	20222156	1	+	2	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20222101	20222156	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20222157	20222246	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20222247	20222377	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20222247	20222377	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20222378	20222516	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20222517	20222652	1	+	1	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20222517	20222652	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20222653	20222763	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20222764	20222892	1	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20222764	20222892	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	intron	20222893	20222980	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	CDS	20222981	20223001	0.99	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	exon	20222981	20223001	.	+	.	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
Phchi.S3	AUGUSTUS	stop_codon	20223002	20223004	.	+	0	transcript_id "Phchi.S3G292000.t1"; gene_id "Phchi.S3G292000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6078.t1 is derived from g3249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20821858	20822636	.	-	.	Phchi.S1G323700
Phchi.S1	AUGUSTUS	transcript	20821858	20822636	.	-	.	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	stop_codon	20821855	20821857	.	-	0	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	CDS	20821858	20822255	0.46	-	2	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	exon	20821858	20822255	.	-	.	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	intron	20822256	20822401	.	-	.	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	CDS	20822402	20822636	0.29	-	0	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	exon	20822402	20822636	.	-	.	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
Phchi.S1	AUGUSTUS	start_codon	20822634	20822636	.	-	0	transcript_id "Phchi.S1G323700.t1"; gene_id "Phchi.S1G323700"
# This transcript jg3359.t2 is derived from g528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3360.t1 is derived from g529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3143026	3145656	.	+	.	Phchi.S1G051900
Phchi.S1	AUGUSTUS	transcript	3143026	3145656	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	start_codon	3143026	3143028	.	+	0	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3143026	3143103	0.98	+	0	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3143026	3143103	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3143104	3143210	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3143211	3143302	0.53	+	0	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3143211	3143302	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3143303	3143427	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3143428	3144261	0.47	+	1	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3143428	3144261	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3144262	3144388	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3144389	3144438	0.87	+	1	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3144389	3144438	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3144439	3144548	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3144549	3144655	0.85	+	2	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3144549	3144655	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3144656	3144850	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3144851	3145048	0.99	+	0	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3144851	3145048	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3145049	3145166	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3145167	3145306	1	+	0	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3145167	3145306	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	intron	3145307	3145394	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	CDS	3145395	3145656	1	+	1	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	exon	3145395	3145656	.	+	.	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
Phchi.S1	AUGUSTUS	stop_codon	3145657	3145659	.	+	0	transcript_id "Phchi.S1G051900.t1"; gene_id "Phchi.S1G051900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15333.t1 is derived from g13801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18432785	18433966	.	-	.	Phchi.S3G265200
Phchi.S3	AUGUSTUS	transcript	18432785	18433966	.	-	.	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	stop_codon	18432782	18432784	.	-	0	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	CDS	18432785	18432852	0.99	-	2	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	exon	18432785	18432852	.	-	.	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	intron	18432853	18432953	.	-	.	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	CDS	18432954	18433236	0.99	-	0	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	exon	18432954	18433236	.	-	.	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	intron	18433237	18433321	.	-	.	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	CDS	18433322	18433966	0.98	-	0	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	exon	18433322	18433966	.	-	.	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
Phchi.S3	AUGUSTUS	start_codon	18433964	18433966	.	-	0	transcript_id "Phchi.S3G265200.t1"; gene_id "Phchi.S3G265200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4658.t1 is derived from g1828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11666036	11669412	.	+	.	Phchi.S1G181700
Phchi.S1	AUGUSTUS	transcript	11666036	11669412	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	start_codon	11666036	11666038	.	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11666036	11666132	0.86	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11666036	11666132	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11666133	11666253	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11666254	11666313	0.8	+	2	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11666254	11666313	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11666314	11666394	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11666395	11666436	0.43	+	2	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11666395	11666436	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11666437	11666506	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11666507	11666514	0.49	+	2	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11666507	11666514	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11666515	11666653	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11666654	11666765	0.8	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11666654	11666765	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11666766	11666892	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11666893	11666975	1	+	2	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11666893	11666975	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11666976	11667180	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11667181	11667246	1	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11667181	11667246	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11667247	11667382	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11667383	11667483	1	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11667383	11667483	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11667484	11667612	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11667613	11667731	1	+	1	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11667613	11667731	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11667732	11667955	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11667956	11667996	1	+	2	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11667956	11667996	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11667997	11668123	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11668124	11668212	1	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11668124	11668212	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11668213	11668330	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11668331	11668511	1	+	1	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11668331	11668511	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11668512	11668594	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11668595	11668711	0.99	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11668595	11668711	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11668712	11668818	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11668819	11668863	0.98	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11668819	11668863	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11668864	11669006	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11669007	11669111	1	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11669007	11669111	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	intron	11669112	11669256	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	CDS	11669257	11669412	1	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	exon	11669257	11669412	.	+	.	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
Phchi.S1	AUGUSTUS	stop_codon	11669413	11669415	.	+	0	transcript_id "Phchi.S1G181700.t1"; gene_id "Phchi.S1G181700"
# This transcript jg8099.t2 is derived from g5274.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8100.t1 is derived from g5275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32995464	32997634	.	+	.	Phchi.S1G525900
Phchi.S1	AUGUSTUS	transcript	32995464	32997634	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	start_codon	32995464	32995466	.	+	0	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32995464	32995590	0.83	+	0	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32995464	32995590	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32995591	32995646	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32995647	32995698	1	+	2	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32995647	32995698	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32995699	32995963	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32995964	32996093	1	+	1	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32995964	32996093	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32996094	32996405	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32996406	32996543	1	+	0	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32996406	32996543	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32996544	32996702	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32996703	32996817	0.64	+	0	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32996703	32996817	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32996818	32996929	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32996930	32997036	0.6	+	2	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32996930	32997036	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32997037	32997176	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32997177	32997360	1	+	0	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32997177	32997360	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	intron	32997361	32997464	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	CDS	32997465	32997634	1	+	2	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	exon	32997465	32997634	.	+	.	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
Phchi.S1	AUGUSTUS	stop_codon	32997635	32997637	.	+	0	transcript_id "Phchi.S1G525900.t1"; gene_id "Phchi.S1G525900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9134.t1 is derived from g6309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40027622	40028141	.	+	.	Phchi.S1G629300
Phchi.S1	AUGUSTUS	transcript	40027622	40028141	.	+	.	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	start_codon	40027622	40027624	.	+	0	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	CDS	40027622	40027787	1	+	0	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	exon	40027622	40027787	.	+	.	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	intron	40027788	40027916	.	+	.	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	CDS	40027917	40028005	1	+	2	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	exon	40027917	40028005	.	+	.	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	intron	40028006	40028090	.	+	.	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	CDS	40028091	40028141	1	+	0	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	exon	40028091	40028141	.	+	.	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
Phchi.S1	AUGUSTUS	stop_codon	40028142	40028144	.	+	0	transcript_id "Phchi.S1G629300.t1"; gene_id "Phchi.S1G629300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14151.t1 is derived from g12618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11173048	11175569	.	+	.	Phchi.S3G147000
Phchi.S3	AUGUSTUS	transcript	11173048	11175569	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	start_codon	11173048	11173050	.	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11173048	11173095	1	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11173048	11173095	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11173096	11173270	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11173271	11173310	1	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11173271	11173310	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11173311	11173393	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11173394	11173497	1	+	2	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11173394	11173497	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11173498	11173578	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11173579	11173660	1	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11173579	11173660	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11173661	11173739	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11173740	11173909	1	+	2	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11173740	11173909	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11173910	11173988	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11173989	11174050	1	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11173989	11174050	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11174051	11174241	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11174242	11174386	1	+	1	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11174242	11174386	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11174387	11174480	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11174481	11174699	1	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11174481	11174699	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11174700	11174854	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11174855	11175036	1	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11174855	11175036	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11175037	11175158	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11175159	11175334	0.99	+	1	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11175159	11175334	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	intron	11175335	11175414	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	CDS	11175415	11175569	0.8	+	2	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	exon	11175415	11175569	.	+	.	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
Phchi.S3	AUGUSTUS	stop_codon	11175570	11175572	.	+	0	transcript_id "Phchi.S3G147000.t1"; gene_id "Phchi.S3G147000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14281.t1 is derived from g12748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11905952	11907415	.	+	.	Phchi.S3G160000
Phchi.S3	AUGUSTUS	transcript	11905952	11907415	.	+	.	transcript_id "Phchi.S3G160000.t1"; gene_id "Phchi.S3G160000"
Phchi.S3	AUGUSTUS	start_codon	11905952	11905954	.	+	0	transcript_id "Phchi.S3G160000.t1"; gene_id "Phchi.S3G160000"
Phchi.S3	AUGUSTUS	CDS	11905952	11907415	0.73	+	0	transcript_id "Phchi.S3G160000.t1"; gene_id "Phchi.S3G160000"
Phchi.S3	AUGUSTUS	exon	11905952	11907415	.	+	.	transcript_id "Phchi.S3G160000.t1"; gene_id "Phchi.S3G160000"
Phchi.S3	AUGUSTUS	stop_codon	11907416	11907418	.	+	0	transcript_id "Phchi.S3G160000.t1"; gene_id "Phchi.S3G160000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13944.t1 is derived from g12411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9839474	9843196	.	+	.	Phchi.S3G126300
Phchi.S3	AUGUSTUS	transcript	9839474	9843196	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	start_codon	9839474	9839476	.	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9839474	9839565	0.99	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9839474	9839565	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9839566	9839708	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9839709	9839786	0.96	+	1	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9839709	9839786	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9839787	9839911	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9839912	9839981	0.96	+	1	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9839912	9839981	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9839982	9840069	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9840070	9840128	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9840070	9840128	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9840129	9840315	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9840316	9840338	1	+	1	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9840316	9840338	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9840339	9840429	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9840430	9840547	1	+	2	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9840430	9840547	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9840548	9840645	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9840646	9840709	1	+	1	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9840646	9840709	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9840710	9840804	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9840805	9840867	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9840805	9840867	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9840868	9840946	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9840947	9841027	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9840947	9841027	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9841028	9841134	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9841135	9841227	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9841135	9841227	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9841228	9841310	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9841311	9841386	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9841311	9841386	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9841387	9841470	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9841471	9841519	1	+	2	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9841471	9841519	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9841520	9841610	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9841611	9841650	1	+	1	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9841611	9841650	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9841651	9841727	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9841728	9842054	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9841728	9842054	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9842055	9842132	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9842133	9842299	0.8	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9842133	9842299	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9842300	9842579	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9842580	9842694	0.8	+	1	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9842580	9842694	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9842695	9842913	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9842914	9843037	1	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9842914	9843037	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	intron	9843038	9843122	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	CDS	9843123	9843196	0.78	+	2	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	exon	9843123	9843196	.	+	.	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
Phchi.S3	AUGUSTUS	stop_codon	9843197	9843199	.	+	0	transcript_id "Phchi.S3G126300.t1"; gene_id "Phchi.S3G126300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7438.t1 is derived from g4610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29118493	29119557	.	-	.	Phchi.S1G459700
Phchi.S1	AUGUSTUS	transcript	29118493	29119557	.	-	.	transcript_id "Phchi.S1G459700.t1"; gene_id "Phchi.S1G459700"
Phchi.S1	AUGUSTUS	stop_codon	29118490	29118492	.	-	0	transcript_id "Phchi.S1G459700.t1"; gene_id "Phchi.S1G459700"
Phchi.S1	AUGUSTUS	CDS	29118493	29119557	0.84	-	0	transcript_id "Phchi.S1G459700.t1"; gene_id "Phchi.S1G459700"
Phchi.S1	AUGUSTUS	exon	29118493	29119557	.	-	.	transcript_id "Phchi.S1G459700.t1"; gene_id "Phchi.S1G459700"
Phchi.S1	AUGUSTUS	start_codon	29119555	29119557	.	-	0	transcript_id "Phchi.S1G459700.t1"; gene_id "Phchi.S1G459700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3537.t1 is derived from g706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4353297	4353714	.	-	.	Phchi.S1G069600
Phchi.S1	AUGUSTUS	transcript	4353297	4353714	.	-	.	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	stop_codon	4353294	4353296	.	-	0	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	CDS	4353297	4353458	0.94	-	0	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	exon	4353297	4353458	.	-	.	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	intron	4353459	4353564	.	-	.	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	CDS	4353565	4353714	0.6	-	0	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	exon	4353565	4353714	.	-	.	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
Phchi.S1	AUGUSTUS	start_codon	4353712	4353714	.	-	0	transcript_id "Phchi.S1G069600.t1"; gene_id "Phchi.S1G069600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4054.t1 is derived from g1223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7553914	7555635	.	+	.	Phchi.S1G121300
Phchi.S1	AUGUSTUS	transcript	7553914	7555635	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	start_codon	7553914	7553916	.	+	0	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7553914	7553985	0.98	+	0	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7553914	7553985	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7553986	7554111	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7554112	7554256	0.98	+	0	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7554112	7554256	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7554257	7554346	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7554347	7554457	1	+	2	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7554347	7554457	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7554458	7554545	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7554546	7554637	1	+	2	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7554546	7554637	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7554638	7554712	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7554713	7554807	1	+	0	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7554713	7554807	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7554808	7554885	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7554886	7554999	1	+	1	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7554886	7554999	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7555000	7555088	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7555089	7555218	1	+	1	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7555089	7555218	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7555219	7555303	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7555304	7555428	1	+	0	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7555304	7555428	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	intron	7555429	7555514	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	CDS	7555515	7555635	1	+	1	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	exon	7555515	7555635	.	+	.	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
Phchi.S1	AUGUSTUS	stop_codon	7555636	7555638	.	+	0	transcript_id "Phchi.S1G121300.t1"; gene_id "Phchi.S1G121300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg17.t1 is derived from g16027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C11	AUGUSTUS	gene	11527	12078	.	+	.	Phchi.C11G000100
Phchi.C11	AUGUSTUS	transcript	11527	12078	.	+	.	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	start_codon	11527	11529	.	+	0	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	CDS	11527	11634	0.7	+	0	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	exon	11527	11634	.	+	.	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	intron	11635	11763	.	+	.	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	CDS	11764	12078	0.43	+	0	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	exon	11764	12078	.	+	.	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
Phchi.C11	AUGUSTUS	stop_codon	12079	12081	.	+	0	transcript_id "Phchi.C11G000100.t1"; gene_id "Phchi.C11G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15567.t1 is derived from g14036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20021411	20024228	.	+	.	Phchi.S3G288600
Phchi.S3	AUGUSTUS	transcript	20021411	20024228	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	start_codon	20021411	20021413	.	+	0	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20021411	20021781	0.71	+	0	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20021411	20021781	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20021782	20021924	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20021925	20022713	0.99	+	1	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20021925	20022713	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20022714	20022784	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20022785	20022924	0.99	+	1	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20022785	20022924	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20022925	20023046	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20023047	20023290	0.99	+	2	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20023047	20023290	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20023291	20023416	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20023417	20023502	1	+	1	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20023417	20023502	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20023503	20023691	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20023692	20023849	1	+	2	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20023692	20023849	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20023850	20023994	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20023995	20024071	1	+	0	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20023995	20024071	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	intron	20024072	20024164	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	CDS	20024165	20024228	1	+	1	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	exon	20024165	20024228	.	+	.	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
Phchi.S3	AUGUSTUS	stop_codon	20024229	20024231	.	+	0	transcript_id "Phchi.S3G288600.t1"; gene_id "Phchi.S3G288600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6777.t1 is derived from g3949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25044233	25045821	.	-	.	Phchi.S1G393600
Phchi.S1	AUGUSTUS	transcript	25044233	25045821	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	stop_codon	25044230	25044232	.	-	0	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	CDS	25044233	25044469	1	-	0	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	exon	25044233	25044469	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	intron	25044470	25044550	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	CDS	25044551	25044846	1	-	2	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	exon	25044551	25044846	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	intron	25044847	25044942	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	CDS	25044943	25045181	1	-	1	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	exon	25044943	25045181	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	intron	25045182	25045363	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	CDS	25045364	25045821	0.97	-	0	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	exon	25045364	25045821	.	-	.	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
Phchi.S1	AUGUSTUS	start_codon	25045819	25045821	.	-	0	transcript_id "Phchi.S1G393600.t1"; gene_id "Phchi.S1G393600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13204.t1 is derived from g11669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4655422	4658727	.	+	.	Phchi.S3G052300
Phchi.S3	AUGUSTUS	transcript	4655422	4658727	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	start_codon	4655422	4655424	.	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4655422	4655498	0.91	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4655422	4655498	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4655499	4655587	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4655588	4655606	0.93	+	1	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4655588	4655606	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4655607	4655685	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4655686	4655700	0.78	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4655686	4655700	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4655701	4655810	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4655811	4655840	0.66	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4655811	4655840	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4655841	4655982	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4655983	4656002	0.98	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4655983	4656002	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4656003	4656105	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4656106	4656177	0.98	+	1	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4656106	4656177	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4656178	4656295	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4656296	4656524	0.99	+	1	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4656296	4656524	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4656525	4656682	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4656683	4656804	1	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4656683	4656804	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4656805	4656892	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4656893	4656953	1	+	1	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4656893	4656953	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4656954	4657084	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4657085	4657225	0.84	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4657085	4657225	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4657226	4657329	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4657330	4657437	1	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4657330	4657437	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4657438	4657506	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4657507	4657735	0.99	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4657507	4657735	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4657736	4657853	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4657854	4658102	0.98	+	2	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4657854	4658102	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4658103	4658321	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4658322	4658427	1	+	2	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4658322	4658427	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4658428	4658507	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4658508	4658578	1	+	1	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4658508	4658578	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	intron	4658579	4658665	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	CDS	4658666	4658727	1	+	2	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	exon	4658666	4658727	.	+	.	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
Phchi.S3	AUGUSTUS	stop_codon	4658728	4658730	.	+	0	transcript_id "Phchi.S3G052300.t1"; gene_id "Phchi.S3G052300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4664.t1 is derived from g1834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11704015	11704485	.	-	.	Phchi.S1G182300
Phchi.S1	AUGUSTUS	transcript	11704015	11704485	.	-	.	transcript_id "Phchi.S1G182300.t1"; gene_id "Phchi.S1G182300"
Phchi.S1	AUGUSTUS	stop_codon	11704012	11704014	.	-	0	transcript_id "Phchi.S1G182300.t1"; gene_id "Phchi.S1G182300"
Phchi.S1	AUGUSTUS	CDS	11704015	11704485	0.76	-	0	transcript_id "Phchi.S1G182300.t1"; gene_id "Phchi.S1G182300"
Phchi.S1	AUGUSTUS	exon	11704015	11704485	.	-	.	transcript_id "Phchi.S1G182300.t1"; gene_id "Phchi.S1G182300"
Phchi.S1	AUGUSTUS	start_codon	11704483	11704485	.	-	0	transcript_id "Phchi.S1G182300.t1"; gene_id "Phchi.S1G182300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13613.t1 is derived from g12080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7690181	7693326	.	+	.	Phchi.S3G093200
Phchi.S3	AUGUSTUS	transcript	7690181	7693326	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	start_codon	7690181	7690183	.	+	0	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	CDS	7690181	7691259	0.95	+	0	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	exon	7690181	7691259	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	intron	7691260	7691327	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	CDS	7691328	7691405	0.95	+	1	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	exon	7691328	7691405	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	intron	7691406	7691489	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	CDS	7691490	7691524	0.85	+	1	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	exon	7691490	7691524	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	intron	7691525	7691702	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	CDS	7691703	7691768	0.34	+	2	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	exon	7691703	7691768	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	intron	7691769	7691887	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	CDS	7691888	7693326	0.4	+	2	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	exon	7691888	7693326	.	+	.	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
Phchi.S3	AUGUSTUS	stop_codon	7693327	7693329	.	+	0	transcript_id "Phchi.S3G093200.t1"; gene_id "Phchi.S3G093200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg927.t1 is derived from g10709.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6479706	6481992	.	-	.	Phchi.S6G088600
Phchi.S6	AUGUSTUS	transcript	6479706	6481992	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	stop_codon	6479703	6479705	.	-	0	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6479706	6479774	0.89	-	0	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6479706	6479774	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6479775	6479875	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6479876	6480066	0.89	-	2	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6479876	6480066	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6480067	6480159	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6480160	6480333	1	-	2	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6480160	6480333	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6480334	6480431	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6480432	6480579	1	-	0	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6480432	6480579	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6480580	6480691	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6480692	6481330	0.99	-	0	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6480692	6481330	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6481331	6481421	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6481422	6481621	1	-	2	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6481422	6481621	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6481622	6481718	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6481719	6481992	0.98	-	0	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6481719	6481992	.	-	.	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	start_codon	6481990	6481992	.	-	0	transcript_id "Phchi.S6G088600.t1"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	transcript	6479706	6481992	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	stop_codon	6479703	6479705	.	-	0	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6479706	6479774	0.91	-	0	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6479706	6479774	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6479775	6479875	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6479876	6480012	0.9	-	2	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6479876	6480012	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6480013	6480159	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6480160	6480333	1	-	2	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6480160	6480333	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6480334	6480431	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6480432	6480579	0.97	-	0	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6480432	6480579	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6480580	6480691	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6480692	6481330	0.98	-	0	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6480692	6481330	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6481331	6481421	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6481422	6481621	1	-	2	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6481422	6481621	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	intron	6481622	6481718	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	CDS	6481719	6481992	0.96	-	0	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	exon	6481719	6481992	.	-	.	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
Phchi.S6	AUGUSTUS	start_codon	6481990	6481992	.	-	0	transcript_id "Phchi.S6G088600.t2"; gene_id "Phchi.S6G088600"
# This transcript jg9132.t2 is derived from g6307.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9133.t1 is derived from g6308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40025046	40027333	.	+	.	Phchi.S1G629200
Phchi.S1	AUGUSTUS	transcript	40025046	40027333	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	start_codon	40025046	40025048	.	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40025046	40025104	0.99	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40025046	40025104	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40025105	40025185	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40025186	40025281	1	+	1	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40025186	40025281	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40025282	40025451	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40025452	40025533	1	+	1	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40025452	40025533	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40025534	40025626	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40025627	40025648	1	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40025627	40025648	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40025649	40025697	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40025698	40025710	1	+	2	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40025698	40025710	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40025711	40025802	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40025803	40025866	1	+	1	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40025803	40025866	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40025867	40026008	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40026009	40026055	1	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40026009	40026055	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40026056	40026154	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40026155	40026209	1	+	1	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40026155	40026209	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40026210	40026321	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40026322	40026360	1	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40026322	40026360	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40026361	40026439	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40026440	40026635	1	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40026440	40026635	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40026636	40026766	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40026767	40026836	1	+	2	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40026767	40026836	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40026837	40026909	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40026910	40026966	1	+	1	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40026910	40026966	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	intron	40026967	40027065	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	CDS	40027066	40027333	0.95	+	1	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	exon	40027066	40027333	.	+	.	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
Phchi.S1	AUGUSTUS	stop_codon	40027334	40027336	.	+	0	transcript_id "Phchi.S1G629200.t1"; gene_id "Phchi.S1G629200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4853.t1 is derived from g2023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13110636	13111783	.	+	.	Phchi.S1G201200
Phchi.S1	AUGUSTUS	transcript	13110636	13111783	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	start_codon	13110636	13110638	.	+	0	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	CDS	13110636	13110802	0.68	+	0	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	exon	13110636	13110802	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	intron	13110803	13111129	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	CDS	13111130	13111215	1	+	1	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	exon	13111130	13111215	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	intron	13111216	13111299	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	CDS	13111300	13111457	1	+	2	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	exon	13111300	13111457	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	intron	13111458	13111548	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	CDS	13111549	13111650	1	+	0	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	exon	13111549	13111650	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	intron	13111651	13111741	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	CDS	13111742	13111783	1	+	0	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	exon	13111742	13111783	.	+	.	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
Phchi.S1	AUGUSTUS	stop_codon	13111784	13111786	.	+	0	transcript_id "Phchi.S1G201200.t1"; gene_id "Phchi.S1G201200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8957.t1 is derived from g6132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38844915	38845445	.	+	.	Phchi.S1G611600
Phchi.S1	AUGUSTUS	transcript	38844915	38845445	.	+	.	transcript_id "Phchi.S1G611600.t1"; gene_id "Phchi.S1G611600"
Phchi.S1	AUGUSTUS	start_codon	38844915	38844917	.	+	0	transcript_id "Phchi.S1G611600.t1"; gene_id "Phchi.S1G611600"
Phchi.S1	AUGUSTUS	CDS	38844915	38845445	0.55	+	0	transcript_id "Phchi.S1G611600.t1"; gene_id "Phchi.S1G611600"
Phchi.S1	AUGUSTUS	exon	38844915	38845445	.	+	.	transcript_id "Phchi.S1G611600.t1"; gene_id "Phchi.S1G611600"
Phchi.S1	AUGUSTUS	stop_codon	38845446	38845448	.	+	0	transcript_id "Phchi.S1G611600.t1"; gene_id "Phchi.S1G611600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2065.t1 is derived from g8985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4674801	4675346	.	-	.	Phchi.S5G067400
Phchi.S5	AUGUSTUS	transcript	4674801	4675346	.	-	.	transcript_id "Phchi.S5G067400.t1"; gene_id "Phchi.S5G067400"
Phchi.S5	AUGUSTUS	stop_codon	4674798	4674800	.	-	0	transcript_id "Phchi.S5G067400.t1"; gene_id "Phchi.S5G067400"
Phchi.S5	AUGUSTUS	CDS	4674801	4675346	0.48	-	0	transcript_id "Phchi.S5G067400.t1"; gene_id "Phchi.S5G067400"
Phchi.S5	AUGUSTUS	exon	4674801	4675346	.	-	.	transcript_id "Phchi.S5G067400.t1"; gene_id "Phchi.S5G067400"
Phchi.S5	AUGUSTUS	start_codon	4675344	4675346	.	-	0	transcript_id "Phchi.S5G067400.t1"; gene_id "Phchi.S5G067400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4303.t1 is derived from g1472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9515176	9516107	.	-	.	Phchi.S1G146200
Phchi.S1	AUGUSTUS	transcript	9515176	9516107	.	-	.	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	stop_codon	9515173	9515175	.	-	0	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	CDS	9515176	9515309	1	-	2	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	exon	9515176	9515309	.	-	.	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	intron	9515310	9515461	.	-	.	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	CDS	9515462	9515680	1	-	2	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	exon	9515462	9515680	.	-	.	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	intron	9515681	9515896	.	-	.	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	CDS	9515897	9516107	0.47	-	0	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	exon	9515897	9516107	.	-	.	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
Phchi.S1	AUGUSTUS	start_codon	9516105	9516107	.	-	0	transcript_id "Phchi.S1G146200.t1"; gene_id "Phchi.S1G146200"
# This transcript jg10524.t2 is derived from g14574.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10525.t1 is derived from g14575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	833720	835108	.	+	.	Phchi.S4G010700
Phchi.S4	AUGUSTUS	transcript	833720	835108	.	+	.	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	start_codon	833720	833722	.	+	0	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	CDS	833720	834348	1	+	0	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	exon	833720	834348	.	+	.	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	intron	834349	834436	.	+	.	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	CDS	834437	834604	1	+	1	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	exon	834437	834604	.	+	.	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	intron	834605	834705	.	+	.	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	CDS	834706	835108	1	+	1	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	exon	834706	835108	.	+	.	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
Phchi.S4	AUGUSTUS	stop_codon	835109	835111	.	+	0	transcript_id "Phchi.S4G010700.t1"; gene_id "Phchi.S4G010700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10737.t1 is derived from g14787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1845568	1847017	.	-	.	Phchi.S4G031900
Phchi.S4	AUGUSTUS	transcript	1845568	1847017	.	-	.	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	stop_codon	1845565	1845567	.	-	0	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	CDS	1845568	1845758	0.49	-	2	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	exon	1845568	1845758	.	-	.	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	intron	1845759	1845846	.	-	.	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	CDS	1845847	1845952	0.39	-	0	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	exon	1845847	1845952	.	-	.	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	intron	1845953	1846090	.	-	.	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	CDS	1846091	1847017	0.93	-	0	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	exon	1846091	1847017	.	-	.	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
Phchi.S4	AUGUSTUS	start_codon	1847015	1847017	.	-	0	transcript_id "Phchi.S4G031900.t1"; gene_id "Phchi.S4G031900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7719.t1 is derived from g4893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30790027	30790553	.	-	.	Phchi.S1G487800
Phchi.S1	AUGUSTUS	transcript	30790027	30790553	.	-	.	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	stop_codon	30790024	30790026	.	-	0	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	CDS	30790027	30790164	0.98	-	0	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	exon	30790027	30790164	.	-	.	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	intron	30790165	30790262	.	-	.	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	CDS	30790263	30790313	1	-	0	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	exon	30790263	30790313	.	-	.	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	intron	30790314	30790463	.	-	.	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	CDS	30790464	30790553	0.88	-	0	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	exon	30790464	30790553	.	-	.	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
Phchi.S1	AUGUSTUS	start_codon	30790551	30790553	.	-	0	transcript_id "Phchi.S1G487800.t1"; gene_id "Phchi.S1G487800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9089.t1 is derived from g6264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39798052	39798860	.	-	.	Phchi.S1G624800
Phchi.S1	AUGUSTUS	transcript	39798052	39798860	.	-	.	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	stop_codon	39798049	39798051	.	-	0	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	CDS	39798052	39798153	0.6	-	0	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	exon	39798052	39798153	.	-	.	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	intron	39798154	39798290	.	-	.	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	CDS	39798291	39798860	0.31	-	0	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	exon	39798291	39798860	.	-	.	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
Phchi.S1	AUGUSTUS	start_codon	39798858	39798860	.	-	0	transcript_id "Phchi.S1G624800.t1"; gene_id "Phchi.S1G624800"
# This transcript jg8331.t2 is derived from g5506.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8332.t1 is derived from g5507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35342957	35343484	.	-	.	Phchi.S1G549100
Phchi.S1	AUGUSTUS	transcript	35342957	35343484	.	-	.	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	stop_codon	35342954	35342956	.	-	0	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	CDS	35342957	35342963	1	-	1	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	exon	35342957	35342963	.	-	.	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	intron	35342964	35343053	.	-	.	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	CDS	35343054	35343126	0.8	-	2	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	exon	35343054	35343126	.	-	.	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	intron	35343127	35343282	.	-	.	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	CDS	35343283	35343484	0.64	-	0	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	exon	35343283	35343484	.	-	.	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
Phchi.S1	AUGUSTUS	start_codon	35343482	35343484	.	-	0	transcript_id "Phchi.S1G549100.t1"; gene_id "Phchi.S1G549100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5916.t1 is derived from g3087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19859827	19860445	.	+	.	Phchi.S1G307500
Phchi.S1	AUGUSTUS	transcript	19859827	19860445	.	+	.	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	start_codon	19859827	19859829	.	+	0	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	CDS	19859827	19860338	0.37	+	0	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	exon	19859827	19860338	.	+	.	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	intron	19860339	19860423	.	+	.	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	CDS	19860424	19860445	0.19	+	1	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	exon	19860424	19860445	.	+	.	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
Phchi.S1	AUGUSTUS	stop_codon	19860446	19860448	.	+	0	transcript_id "Phchi.S1G307500.t1"; gene_id "Phchi.S1G307500"
# This transcript jg15520.t2 is derived from g13989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15521.t1 is derived from g13990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19707364	19708116	.	-	.	Phchi.S3G284000
Phchi.S3	AUGUSTUS	transcript	19707364	19708116	.	-	.	transcript_id "Phchi.S3G284000.t1"; gene_id "Phchi.S3G284000"
Phchi.S3	AUGUSTUS	stop_codon	19707361	19707363	.	-	0	transcript_id "Phchi.S3G284000.t1"; gene_id "Phchi.S3G284000"
Phchi.S3	AUGUSTUS	CDS	19707364	19708116	0.93	-	0	transcript_id "Phchi.S3G284000.t1"; gene_id "Phchi.S3G284000"
Phchi.S3	AUGUSTUS	exon	19707364	19708116	.	-	.	transcript_id "Phchi.S3G284000.t1"; gene_id "Phchi.S3G284000"
Phchi.S3	AUGUSTUS	start_codon	19708114	19708116	.	-	0	transcript_id "Phchi.S3G284000.t1"; gene_id "Phchi.S3G284000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10278.t1 is derived from g7454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46794404	46796773	.	+	.	Phchi.S1G743700
Phchi.S1	AUGUSTUS	transcript	46794404	46796773	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	start_codon	46794404	46794406	.	+	0	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	CDS	46794404	46794426	0.3	+	0	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	exon	46794404	46794426	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	intron	46794427	46794576	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	CDS	46794577	46795181	0.58	+	1	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	exon	46794577	46795181	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	intron	46795182	46795259	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	CDS	46795260	46795319	1	+	2	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	exon	46795260	46795319	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	intron	46795320	46795397	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	CDS	46795398	46795547	1	+	2	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	exon	46795398	46795547	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	intron	46795548	46795646	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	CDS	46795647	46795846	0.92	+	2	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	exon	46795647	46795846	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	intron	46795847	46795951	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	CDS	46795952	46796773	1	+	0	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	exon	46795952	46796773	.	+	.	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
Phchi.S1	AUGUSTUS	stop_codon	46796774	46796776	.	+	0	transcript_id "Phchi.S1G743700.t1"; gene_id "Phchi.S1G743700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3319.t1 is derived from g488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2876052	2877448	.	+	.	Phchi.S1G047800
Phchi.S1	AUGUSTUS	transcript	2876052	2877448	.	+	.	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	start_codon	2876052	2876054	.	+	0	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	CDS	2876052	2877277	0.29	+	0	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	exon	2876052	2877277	.	+	.	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	intron	2877278	2877429	.	+	.	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	CDS	2877430	2877448	0.48	+	1	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	exon	2877430	2877448	.	+	.	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
Phchi.S1	AUGUSTUS	stop_codon	2877449	2877451	.	+	0	transcript_id "Phchi.S1G047800.t1"; gene_id "Phchi.S1G047800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15114.t1 is derived from g13582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17154440	17155297	.	+	.	Phchi.S3G243300
Phchi.S3	AUGUSTUS	transcript	17154440	17155297	.	+	.	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	start_codon	17154440	17154442	.	+	0	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	CDS	17154440	17154994	0.55	+	0	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	exon	17154440	17154994	.	+	.	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	intron	17154995	17155063	.	+	.	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	CDS	17155064	17155297	0.87	+	0	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	exon	17155064	17155297	.	+	.	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
Phchi.S3	AUGUSTUS	stop_codon	17155298	17155300	.	+	0	transcript_id "Phchi.S3G243300.t1"; gene_id "Phchi.S3G243300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14242.t1 is derived from g12709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11706642	11708616	.	-	.	Phchi.S3G156100
Phchi.S3	AUGUSTUS	transcript	11706642	11708616	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	stop_codon	11706639	11706641	.	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11706642	11707109	1	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11706642	11707109	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	intron	11707110	11707204	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11707205	11707294	1	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11707205	11707294	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	intron	11707295	11707453	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11707454	11707536	1	-	2	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11707454	11707536	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	intron	11707537	11707631	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11707632	11707725	1	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11707632	11707725	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	intron	11707726	11707815	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11707816	11707938	0.94	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11707816	11707938	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	intron	11707939	11708040	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11708041	11708315	0.91	-	2	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11708041	11708315	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	intron	11708316	11708489	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	CDS	11708490	11708616	0.85	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	exon	11708490	11708616	.	-	.	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
Phchi.S3	AUGUSTUS	start_codon	11708614	11708616	.	-	0	transcript_id "Phchi.S3G156100.t1"; gene_id "Phchi.S3G156100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11683.t1 is derived from g15734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7651253	7652182	.	+	.	Phchi.S4G126500
Phchi.S4	AUGUSTUS	transcript	7651253	7652182	.	+	.	transcript_id "Phchi.S4G126500.t1"; gene_id "Phchi.S4G126500"
Phchi.S4	AUGUSTUS	start_codon	7651253	7651255	.	+	0	transcript_id "Phchi.S4G126500.t1"; gene_id "Phchi.S4G126500"
Phchi.S4	AUGUSTUS	CDS	7651253	7652182	0.94	+	0	transcript_id "Phchi.S4G126500.t1"; gene_id "Phchi.S4G126500"
Phchi.S4	AUGUSTUS	exon	7651253	7652182	.	+	.	transcript_id "Phchi.S4G126500.t1"; gene_id "Phchi.S4G126500"
Phchi.S4	AUGUSTUS	stop_codon	7652183	7652185	.	+	0	transcript_id "Phchi.S4G126500.t1"; gene_id "Phchi.S4G126500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12470.t1 is derived from g8147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	25848955	25849371	.	-	.	Phchi.S2G055000
Phchi.S2	AUGUSTUS	transcript	25848955	25849371	.	-	.	transcript_id "Phchi.S2G055000.t1"; gene_id "Phchi.S2G055000"
Phchi.S2	AUGUSTUS	stop_codon	25848952	25848954	.	-	0	transcript_id "Phchi.S2G055000.t1"; gene_id "Phchi.S2G055000"
Phchi.S2	AUGUSTUS	CDS	25848955	25849371	0.78	-	0	transcript_id "Phchi.S2G055000.t1"; gene_id "Phchi.S2G055000"
Phchi.S2	AUGUSTUS	exon	25848955	25849371	.	-	.	transcript_id "Phchi.S2G055000.t1"; gene_id "Phchi.S2G055000"
Phchi.S2	AUGUSTUS	start_codon	25849369	25849371	.	-	0	transcript_id "Phchi.S2G055000.t1"; gene_id "Phchi.S2G055000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12227.t1 is derived from g7903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6839022	6842128	.	+	.	Phchi.S2G030700
Phchi.S2	AUGUSTUS	transcript	6839022	6842128	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	start_codon	6839022	6839024	.	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6839022	6839174	0.56	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6839022	6839174	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6839175	6839313	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6839314	6839377	0.72	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6839314	6839377	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6839378	6839460	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6839461	6839746	0.74	+	2	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6839461	6839746	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6839747	6839829	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6839830	6840071	0.99	+	1	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6839830	6840071	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6840072	6840181	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6840182	6840282	1	+	2	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6840182	6840282	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6840283	6840451	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6840452	6840640	1	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6840452	6840640	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6840641	6840753	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6840754	6840849	1	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6840754	6840849	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6840850	6841472	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6841473	6841598	1	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6841473	6841598	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	intron	6841599	6842119	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	CDS	6842120	6842128	1	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	exon	6842120	6842128	.	+	.	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
Phchi.S2	AUGUSTUS	stop_codon	6842129	6842131	.	+	0	transcript_id "Phchi.S2G030700.t1"; gene_id "Phchi.S2G030700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4585.t1 is derived from g1755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11212406	11212719	.	+	.	Phchi.S1G174400
Phchi.S1	AUGUSTUS	transcript	11212406	11212719	.	+	.	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	start_codon	11212406	11212408	.	+	0	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	CDS	11212406	11212546	0.53	+	0	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	exon	11212406	11212546	.	+	.	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	intron	11212547	11212641	.	+	.	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	CDS	11212642	11212719	0.55	+	0	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	exon	11212642	11212719	.	+	.	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
Phchi.S1	AUGUSTUS	stop_codon	11212720	11212722	.	+	0	transcript_id "Phchi.S1G174400.t1"; gene_id "Phchi.S1G174400"
# This transcript jg6993.t2 is derived from g4165.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6993.t3 is derived from g4165.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6993.t4 is derived from g4165.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6994.t1 is derived from g4166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26308571	26308974	.	-	.	Phchi.S1G415300
Phchi.S1	AUGUSTUS	transcript	26308571	26308974	.	-	.	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	stop_codon	26308568	26308570	.	-	0	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	CDS	26308571	26308572	0.38	-	2	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	exon	26308571	26308572	.	-	.	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	intron	26308573	26308718	.	-	.	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	CDS	26308719	26308974	0.38	-	0	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	exon	26308719	26308974	.	-	.	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
Phchi.S1	AUGUSTUS	start_codon	26308972	26308974	.	-	0	transcript_id "Phchi.S1G415300.t1"; gene_id "Phchi.S1G415300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7845.t1 is derived from g5019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31506223	31506724	.	+	.	Phchi.S1G500400
Phchi.S1	AUGUSTUS	transcript	31506223	31506724	.	+	.	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	start_codon	31506223	31506225	.	+	0	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	CDS	31506223	31506540	0.6	+	0	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	exon	31506223	31506540	.	+	.	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	intron	31506541	31506631	.	+	.	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	CDS	31506632	31506724	0.78	+	0	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	exon	31506632	31506724	.	+	.	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	stop_codon	31506725	31506727	.	+	0	transcript_id "Phchi.S1G500400.t1"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	transcript	31506223	31506594	.	+	.	transcript_id "Phchi.S1G500400.t2"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	start_codon	31506223	31506225	.	+	0	transcript_id "Phchi.S1G500400.t2"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	CDS	31506223	31506594	0.53	+	0	transcript_id "Phchi.S1G500400.t2"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	exon	31506223	31506594	.	+	.	transcript_id "Phchi.S1G500400.t2"; gene_id "Phchi.S1G500400"
Phchi.S1	AUGUSTUS	stop_codon	31506595	31506597	.	+	0	transcript_id "Phchi.S1G500400.t2"; gene_id "Phchi.S1G500400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3311.t1 is derived from g480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2786754	2787410	.	-	.	Phchi.S1G047000
Phchi.S1	AUGUSTUS	transcript	2786754	2787410	.	-	.	transcript_id "Phchi.S1G047000.t1"; gene_id "Phchi.S1G047000"
Phchi.S1	AUGUSTUS	stop_codon	2786751	2786753	.	-	0	transcript_id "Phchi.S1G047000.t1"; gene_id "Phchi.S1G047000"
Phchi.S1	AUGUSTUS	CDS	2786754	2787410	0.94	-	0	transcript_id "Phchi.S1G047000.t1"; gene_id "Phchi.S1G047000"
Phchi.S1	AUGUSTUS	exon	2786754	2787410	.	-	.	transcript_id "Phchi.S1G047000.t1"; gene_id "Phchi.S1G047000"
Phchi.S1	AUGUSTUS	start_codon	2787408	2787410	.	-	0	transcript_id "Phchi.S1G047000.t1"; gene_id "Phchi.S1G047000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7233.t1 is derived from g4405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27755056	27755673	.	-	.	Phchi.S1G439200
Phchi.S1	AUGUSTUS	transcript	27755056	27755673	.	-	.	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	stop_codon	27755053	27755055	.	-	0	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	CDS	27755056	27755360	1	-	2	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	exon	27755056	27755360	.	-	.	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	intron	27755361	27755465	.	-	.	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	CDS	27755466	27755673	0.66	-	0	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	exon	27755466	27755673	.	-	.	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
Phchi.S1	AUGUSTUS	start_codon	27755671	27755673	.	-	0	transcript_id "Phchi.S1G439200.t1"; gene_id "Phchi.S1G439200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2349.t1 is derived from g9269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6302218	6305343	.	-	.	Phchi.S5G095800
Phchi.S5	AUGUSTUS	transcript	6302218	6305343	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	stop_codon	6302215	6302217	.	-	0	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6302218	6302531	1	-	2	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6302218	6302531	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6302532	6302631	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6302632	6302866	1	-	0	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6302632	6302866	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6302867	6303022	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6303023	6303266	1	-	1	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6303023	6303266	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6303267	6303357	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6303358	6303479	1	-	0	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6303358	6303479	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6303480	6303598	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6303599	6303792	1	-	2	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6303599	6303792	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6303793	6303913	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6303914	6304004	1	-	0	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6303914	6304004	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6304005	6304090	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6304091	6304317	1	-	2	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6304091	6304317	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6304318	6304430	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6304431	6304991	1	-	2	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6304431	6304991	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	intron	6304992	6305261	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	CDS	6305262	6305343	1	-	0	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	exon	6305262	6305343	.	-	.	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
Phchi.S5	AUGUSTUS	start_codon	6305341	6305343	.	-	0	transcript_id "Phchi.S5G095800.t1"; gene_id "Phchi.S5G095800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11450.t1 is derived from g15500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6422956	6423963	.	-	.	Phchi.S4G103200
Phchi.S4	AUGUSTUS	transcript	6422956	6423963	.	-	.	transcript_id "Phchi.S4G103200.t1"; gene_id "Phchi.S4G103200"
Phchi.S4	AUGUSTUS	stop_codon	6422953	6422955	.	-	0	transcript_id "Phchi.S4G103200.t1"; gene_id "Phchi.S4G103200"
Phchi.S4	AUGUSTUS	CDS	6422956	6423963	0.34	-	0	transcript_id "Phchi.S4G103200.t1"; gene_id "Phchi.S4G103200"
Phchi.S4	AUGUSTUS	exon	6422956	6423963	.	-	.	transcript_id "Phchi.S4G103200.t1"; gene_id "Phchi.S4G103200"
Phchi.S4	AUGUSTUS	start_codon	6423961	6423963	.	-	0	transcript_id "Phchi.S4G103200.t1"; gene_id "Phchi.S4G103200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13318.t1 is derived from g11784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6088123	6088422	.	-	.	Phchi.S3G063700
Phchi.S3	AUGUSTUS	transcript	6088123	6088422	.	-	.	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	stop_codon	6088120	6088122	.	-	0	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	CDS	6088123	6088125	0.89	-	0	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	exon	6088123	6088125	.	-	.	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	intron	6088126	6088218	.	-	.	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	CDS	6088219	6088422	0.26	-	0	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	exon	6088219	6088422	.	-	.	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
Phchi.S3	AUGUSTUS	start_codon	6088420	6088422	.	-	0	transcript_id "Phchi.S3G063700.t1"; gene_id "Phchi.S3G063700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13559.t1 is derived from g12026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7491526	7492466	.	+	.	Phchi.S3G087800
Phchi.S3	AUGUSTUS	transcript	7491526	7492466	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	start_codon	7491526	7491528	.	+	0	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	CDS	7491526	7491578	0.54	+	0	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	exon	7491526	7491578	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	intron	7491579	7491800	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	CDS	7491801	7491816	0.52	+	1	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	exon	7491801	7491816	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	intron	7491817	7492058	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	CDS	7492059	7492263	0.97	+	0	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	exon	7492059	7492263	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	intron	7492264	7492452	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	CDS	7492453	7492466	0.87	+	2	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	exon	7492453	7492466	.	+	.	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
Phchi.S3	AUGUSTUS	stop_codon	7492467	7492469	.	+	0	transcript_id "Phchi.S3G087800.t1"; gene_id "Phchi.S3G087800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10131.t1 is derived from g7307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45877626	45877886	.	+	.	Phchi.S1G729000
Phchi.S1	AUGUSTUS	transcript	45877626	45877886	.	+	.	transcript_id "Phchi.S1G729000.t1"; gene_id "Phchi.S1G729000"
Phchi.S1	AUGUSTUS	start_codon	45877626	45877628	.	+	0	transcript_id "Phchi.S1G729000.t1"; gene_id "Phchi.S1G729000"
Phchi.S1	AUGUSTUS	CDS	45877626	45877886	1	+	0	transcript_id "Phchi.S1G729000.t1"; gene_id "Phchi.S1G729000"
Phchi.S1	AUGUSTUS	exon	45877626	45877886	.	+	.	transcript_id "Phchi.S1G729000.t1"; gene_id "Phchi.S1G729000"
Phchi.S1	AUGUSTUS	stop_codon	45877887	45877889	.	+	0	transcript_id "Phchi.S1G729000.t1"; gene_id "Phchi.S1G729000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10384.t1 is derived from g7560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47488061	47489427	.	-	.	Phchi.S1G754300
Phchi.S1	AUGUSTUS	transcript	47488061	47489427	.	-	.	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	stop_codon	47488058	47488060	.	-	0	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	CDS	47488061	47488214	0.99	-	1	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	exon	47488061	47488214	.	-	.	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	intron	47488215	47488289	.	-	.	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	CDS	47488290	47488513	1	-	0	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	exon	47488290	47488513	.	-	.	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	intron	47488514	47488638	.	-	.	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	CDS	47488639	47489427	0.74	-	0	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	exon	47488639	47489427	.	-	.	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
Phchi.S1	AUGUSTUS	start_codon	47489425	47489427	.	-	0	transcript_id "Phchi.S1G754300.t1"; gene_id "Phchi.S1G754300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10157.t1 is derived from g7333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46026105	46031214	.	+	.	Phchi.S1G731600
Phchi.S1	AUGUSTUS	transcript	46026105	46031214	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	start_codon	46026105	46026107	.	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46026105	46026188	0.68	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46026105	46026188	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46026189	46026273	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46026274	46027205	0.71	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46026274	46027205	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46027206	46027401	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46027402	46027438	1	+	1	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46027402	46027438	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46027439	46027525	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46027526	46027756	1	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46027526	46027756	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46027757	46027838	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46027839	46027932	0.98	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46027839	46027932	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46027933	46028043	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46028044	46028112	1	+	2	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46028044	46028112	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46028113	46028226	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46028227	46028358	1	+	2	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46028227	46028358	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46028359	46028436	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46028437	46028570	1	+	2	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46028437	46028570	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46028571	46028714	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46028715	46028759	1	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46028715	46028759	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46028760	46028860	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46028861	46029211	1	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46028861	46029211	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46029212	46029355	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46029356	46029458	1	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46029356	46029458	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46029459	46029591	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46029592	46029704	0.9	+	2	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46029592	46029704	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46029705	46029823	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46029824	46030444	0.88	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46029824	46030444	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46030445	46030607	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46030608	46030718	1	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46030608	46030718	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	intron	46030719	46030836	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	CDS	46030837	46031214	0.51	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	exon	46030837	46031214	.	+	.	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
Phchi.S1	AUGUSTUS	stop_codon	46031215	46031217	.	+	0	transcript_id "Phchi.S1G731600.t1"; gene_id "Phchi.S1G731600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14394.t1 is derived from g12862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12590201	12594466	.	+	.	Phchi.S3G171300
Phchi.S3	AUGUSTUS	transcript	12590201	12594466	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	start_codon	12590201	12590203	.	+	0	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12590201	12590363	0.96	+	0	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12590201	12590363	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12590364	12590476	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12590477	12590757	0.33	+	2	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12590477	12590757	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12590758	12590877	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12590878	12591134	0.59	+	0	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12590878	12591134	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12591135	12591260	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12591261	12591509	0.98	+	1	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12591261	12591509	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12591510	12591608	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12591609	12591829	1	+	1	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12591609	12591829	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12591830	12591938	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12591939	12592053	1	+	2	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12591939	12592053	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12592054	12592141	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12592142	12592255	0.84	+	1	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12592142	12592255	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12592256	12592512	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12592513	12592581	0.88	+	1	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12592513	12592581	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12592582	12592677	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12592678	12592910	1	+	1	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12592678	12592910	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12592911	12592994	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12592995	12593281	1	+	2	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12592995	12593281	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12593282	12593355	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12593356	12593482	1	+	0	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12593356	12593482	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12593483	12593558	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12593559	12593627	1	+	2	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12593559	12593627	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12593628	12593702	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12593703	12593889	1	+	2	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12593703	12593889	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12593890	12593982	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12593983	12594121	1	+	1	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12593983	12594121	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	intron	12594122	12594205	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	CDS	12594206	12594466	1	+	0	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	exon	12594206	12594466	.	+	.	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
Phchi.S3	AUGUSTUS	stop_codon	12594467	12594469	.	+	0	transcript_id "Phchi.S3G171300.t1"; gene_id "Phchi.S3G171300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6984.t1 is derived from g4156.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26266984	26272611	.	+	.	Phchi.S1G414300
Phchi.S1	AUGUSTUS	transcript	26268118	26272611	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	start_codon	26268118	26268120	.	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268118	26268208	0.71	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268118	26268208	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268209	26268347	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268348	26268400	1	+	2	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268348	26268400	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268401	26268487	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268488	26268555	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268488	26268555	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268556	26268710	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268711	26268786	1	+	1	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268711	26268786	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268787	26268870	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268871	26268954	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268871	26268954	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268955	26269101	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269102	26269250	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269102	26269250	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269251	26269350	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269351	26269468	1	+	1	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269351	26269468	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269469	26269545	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269546	26269662	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269546	26269662	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269663	26269739	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269740	26269957	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269740	26269957	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269958	26270108	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270109	26270198	1	+	1	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270109	26270198	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270199	26270281	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270282	26270393	1	+	1	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270282	26270393	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270394	26270516	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270517	26270630	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270517	26270630	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270631	26270797	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270798	26270935	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270798	26270935	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270936	26271074	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271075	26271125	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271075	26271125	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26271126	26271239	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271240	26271352	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271240	26271352	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26271353	26271469	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271470	26271617	1	+	1	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271470	26271617	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26271618	26271707	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271708	26271812	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271708	26271812	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26271813	26271897	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271898	26272002	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271898	26272002	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26272003	26272081	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26272082	26272154	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26272082	26272154	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26272155	26272232	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26272233	26272399	1	+	2	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26272233	26272399	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26272400	26272485	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26272486	26272611	1	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26272486	26272611	.	+	.	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	stop_codon	26272612	26272614	.	+	0	transcript_id "Phchi.S1G414300.t1"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	transcript	26266984	26271680	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	start_codon	26266984	26266986	.	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26266984	26267053	0.71	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26266984	26267053	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267054	26267124	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267125	26267206	0.79	+	2	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267125	26267206	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267207	26267309	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267310	26267436	1	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267310	26267436	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267437	26267543	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267544	26267627	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267544	26267627	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267628	26267733	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267734	26267828	0.96	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267734	26267828	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267829	26267950	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267951	26268042	0.95	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267951	26268042	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268043	26268154	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268155	26268208	0.99	+	2	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268155	26268208	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268209	26268347	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268348	26268400	1	+	2	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268348	26268400	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268401	26268487	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268488	26268555	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268488	26268555	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268556	26268710	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268711	26268786	1	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268711	26268786	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268787	26268870	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26268871	26268954	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26268871	26268954	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26268955	26269101	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269102	26269250	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269102	26269250	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269251	26269350	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269351	26269468	1	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269351	26269468	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269469	26269545	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269546	26269662	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269546	26269662	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269663	26269739	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26269740	26269957	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26269740	26269957	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26269958	26270108	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270109	26270198	1	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270109	26270198	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270199	26270281	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270282	26270393	1	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270282	26270393	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270394	26270516	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270517	26270630	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270517	26270630	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270631	26270797	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26270798	26270935	1	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26270798	26270935	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26270936	26271074	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271075	26271125	0.97	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271075	26271125	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26271126	26271239	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271240	26271352	0.97	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271240	26271352	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26271353	26271469	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26271470	26271680	1	+	1	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26271470	26271680	.	+	.	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	stop_codon	26271681	26271683	.	+	0	transcript_id "Phchi.S1G414300.t2"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	transcript	26266984	26267985	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	start_codon	26266984	26266986	.	+	0	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26266984	26267053	0.73	+	0	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26266984	26267053	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267054	26267124	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267125	26267206	0.76	+	2	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267125	26267206	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267207	26267309	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267310	26267436	1	+	1	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267310	26267436	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267437	26267543	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267544	26267627	1	+	0	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267544	26267627	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267628	26267733	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267734	26267851	1	+	0	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267734	26267851	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	intron	26267852	26267950	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	CDS	26267951	26267985	0.86	+	2	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	exon	26267951	26267985	.	+	.	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
Phchi.S1	AUGUSTUS	stop_codon	26267986	26267988	.	+	0	transcript_id "Phchi.S1G414300.t3"; gene_id "Phchi.S1G414300"
# This transcript jg11421.t2 is derived from g15471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11422.t1 is derived from g15472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6263073	6264326	.	+	.	Phchi.S4G100400
Phchi.S4	AUGUSTUS	transcript	6263073	6264326	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	start_codon	6263073	6263075	.	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	CDS	6263073	6263234	1	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	exon	6263073	6263234	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	intron	6263235	6263309	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	CDS	6263310	6263366	0.93	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	exon	6263310	6263366	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	intron	6263367	6263473	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	CDS	6263474	6263536	1	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	exon	6263474	6263536	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	intron	6263537	6263622	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	CDS	6263623	6263725	1	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	exon	6263623	6263725	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	intron	6263726	6263807	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	CDS	6263808	6263905	1	+	2	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	exon	6263808	6263905	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	intron	6263906	6263999	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	CDS	6264000	6264326	0.82	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	exon	6264000	6264326	.	+	.	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
Phchi.S4	AUGUSTUS	stop_codon	6264327	6264329	.	+	0	transcript_id "Phchi.S4G100400.t1"; gene_id "Phchi.S4G100400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2518.t1 is derived from g9438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7108938	7110146	.	-	.	Phchi.S5G112700
Phchi.S5	AUGUSTUS	transcript	7108938	7110146	.	-	.	transcript_id "Phchi.S5G112700.t1"; gene_id "Phchi.S5G112700"
Phchi.S5	AUGUSTUS	stop_codon	7108935	7108937	.	-	0	transcript_id "Phchi.S5G112700.t1"; gene_id "Phchi.S5G112700"
Phchi.S5	AUGUSTUS	CDS	7108938	7110146	0.59	-	0	transcript_id "Phchi.S5G112700.t1"; gene_id "Phchi.S5G112700"
Phchi.S5	AUGUSTUS	exon	7108938	7110146	.	-	.	transcript_id "Phchi.S5G112700.t1"; gene_id "Phchi.S5G112700"
Phchi.S5	AUGUSTUS	start_codon	7110144	7110146	.	-	0	transcript_id "Phchi.S5G112700.t1"; gene_id "Phchi.S5G112700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3014.t1 is derived from g183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1127136	1130761	.	-	.	Phchi.S1G017300
Phchi.S1	AUGUSTUS	transcript	1127136	1130761	.	-	.	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	stop_codon	1127133	1127135	.	-	0	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	CDS	1127136	1130504	0.95	-	0	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	exon	1127136	1130504	.	-	.	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	intron	1130505	1130599	.	-	.	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	CDS	1130600	1130761	0.91	-	0	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	exon	1130600	1130761	.	-	.	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
Phchi.S1	AUGUSTUS	start_codon	1130759	1130761	.	-	0	transcript_id "Phchi.S1G017300.t1"; gene_id "Phchi.S1G017300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10004.t1 is derived from g7180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45005303	45005808	.	-	.	Phchi.S1G716300
Phchi.S1	AUGUSTUS	transcript	45005303	45005808	.	-	.	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	stop_codon	45005300	45005302	.	-	0	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	CDS	45005303	45005399	0.7	-	1	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	exon	45005303	45005399	.	-	.	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	intron	45005400	45005506	.	-	.	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	CDS	45005507	45005808	0.62	-	0	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	exon	45005507	45005808	.	-	.	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
Phchi.S1	AUGUSTUS	start_codon	45005806	45005808	.	-	0	transcript_id "Phchi.S1G716300.t1"; gene_id "Phchi.S1G716300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2970.t1 is derived from g139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	894725	896640	.	+	.	Phchi.S1G012900
Phchi.S1	AUGUSTUS	transcript	894725	896640	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	start_codon	894725	894727	.	+	0	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	894725	894842	1	+	0	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	894725	894842	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	intron	894843	894937	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	894938	895533	0.98	+	2	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	894938	895533	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	intron	895534	895612	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	895613	895809	1	+	0	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	895613	895809	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	intron	895810	895954	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	895955	895997	1	+	1	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	895955	895997	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	intron	895998	896215	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	896216	896307	0.96	+	0	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	896216	896307	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	intron	896308	896390	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	896391	896430	0.95	+	1	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	896391	896430	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	intron	896431	896592	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	CDS	896593	896640	1	+	0	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	exon	896593	896640	.	+	.	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
Phchi.S1	AUGUSTUS	stop_codon	896641	896643	.	+	0	transcript_id "Phchi.S1G012900.t1"; gene_id "Phchi.S1G012900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13231.t1 is derived from g11696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4800247	4802248	.	+	.	Phchi.S3G055000
Phchi.S3	AUGUSTUS	transcript	4800247	4802248	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	start_codon	4800247	4800249	.	+	0	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4800247	4800434	0.92	+	0	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4800247	4800434	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4800435	4800632	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4800633	4800695	1	+	1	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4800633	4800695	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4800696	4800838	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4800839	4800955	1	+	1	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4800839	4800955	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4800956	4801050	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4801051	4801342	0.89	+	1	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4801051	4801342	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4801343	4801448	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4801449	4801610	0.84	+	0	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4801449	4801610	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4801611	4801712	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4801713	4801864	0.98	+	0	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4801713	4801864	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4801865	4801956	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4801957	4802110	1	+	1	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4801957	4802110	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	intron	4802111	4802197	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	CDS	4802198	4802248	1	+	0	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	exon	4802198	4802248	.	+	.	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
Phchi.S3	AUGUSTUS	stop_codon	4802249	4802251	.	+	0	transcript_id "Phchi.S3G055000.t1"; gene_id "Phchi.S3G055000"
# This transcript jg12829.t2 is derived from g11294.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12830.t1 is derived from g11295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2591136	2593015	.	-	.	Phchi.S3G014900
Phchi.S3	AUGUSTUS	transcript	2591136	2593015	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	stop_codon	2591133	2591135	.	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	CDS	2591136	2591261	0.99	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	exon	2591136	2591261	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	intron	2591262	2591329	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	CDS	2591330	2591587	1	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	exon	2591330	2591587	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	intron	2591588	2591708	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	CDS	2591709	2591796	1	-	1	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	exon	2591709	2591796	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	intron	2591797	2591879	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	CDS	2591880	2591962	1	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	exon	2591880	2591962	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	intron	2591963	2592066	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	CDS	2592067	2592150	0.64	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	exon	2592067	2592150	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	intron	2592151	2592229	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	CDS	2592230	2593015	0.55	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	exon	2592230	2593015	.	-	.	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
Phchi.S3	AUGUSTUS	start_codon	2593013	2593015	.	-	0	transcript_id "Phchi.S3G014900.t1"; gene_id "Phchi.S3G014900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11112.t1 is derived from g15162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4208900	4218190	.	-	.	Phchi.S4G069400
Phchi.S4	AUGUSTUS	transcript	4208900	4218190	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	stop_codon	4208897	4208899	.	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4208900	4209065	1	-	1	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4208900	4209065	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4209066	4209163	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4209164	4209537	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4209164	4209537	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4209538	4209640	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4209641	4210780	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4209641	4210780	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4210781	4210875	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4210876	4211075	1	-	2	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4210876	4211075	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4211076	4211339	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4211340	4211440	1	-	1	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4211340	4211440	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4211441	4211527	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4211528	4212144	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4211528	4212144	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4212145	4212328	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4212329	4212424	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4212329	4212424	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4212425	4212584	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4212585	4212737	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4212585	4212737	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4212738	4212897	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4212898	4213080	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4212898	4213080	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4213081	4213180	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4213181	4213331	1	-	1	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4213181	4213331	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4213332	4213425	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4213426	4213508	0.94	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4213426	4213508	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4213509	4213603	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4213604	4213646	0.94	-	1	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4213604	4213646	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4213647	4213840	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4213841	4214001	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4213841	4214001	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4214002	4214485	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4214486	4214608	0.96	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4214486	4214608	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4214609	4214717	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4214718	4214890	0.99	-	2	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4214718	4214890	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4214891	4214986	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4214987	4215206	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4214987	4215206	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4215207	4215666	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4215667	4216061	1	-	2	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4215667	4216061	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4216062	4216134	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4216135	4216345	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4216135	4216345	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4216346	4216446	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4216447	4216560	1	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4216447	4216560	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	intron	4216561	4216720	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	CDS	4216721	4218190	0.54	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	exon	4216721	4218190	.	-	.	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
Phchi.S4	AUGUSTUS	start_codon	4218188	4218190	.	-	0	transcript_id "Phchi.S4G069400.t1"; gene_id "Phchi.S4G069400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12347.t1 is derived from g8023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12340157	12340471	.	-	.	Phchi.S2G042700
Phchi.S2	AUGUSTUS	transcript	12340157	12340471	.	-	.	transcript_id "Phchi.S2G042700.t1"; gene_id "Phchi.S2G042700"
Phchi.S2	AUGUSTUS	stop_codon	12340154	12340156	.	-	0	transcript_id "Phchi.S2G042700.t1"; gene_id "Phchi.S2G042700"
Phchi.S2	AUGUSTUS	CDS	12340157	12340471	0.69	-	0	transcript_id "Phchi.S2G042700.t1"; gene_id "Phchi.S2G042700"
Phchi.S2	AUGUSTUS	exon	12340157	12340471	.	-	.	transcript_id "Phchi.S2G042700.t1"; gene_id "Phchi.S2G042700"
Phchi.S2	AUGUSTUS	start_codon	12340469	12340471	.	-	0	transcript_id "Phchi.S2G042700.t1"; gene_id "Phchi.S2G042700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15560.t1 is derived from g14029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19920013	19920654	.	+	.	Phchi.S3G287900
Phchi.S3	AUGUSTUS	transcript	19920013	19920654	.	+	.	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	start_codon	19920013	19920015	.	+	0	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	CDS	19920013	19920121	0.94	+	0	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	exon	19920013	19920121	.	+	.	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	intron	19920122	19920321	.	+	.	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	CDS	19920322	19920455	1	+	2	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	exon	19920322	19920455	.	+	.	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	intron	19920456	19920642	.	+	.	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	CDS	19920643	19920654	1	+	0	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	exon	19920643	19920654	.	+	.	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
Phchi.S3	AUGUSTUS	stop_codon	19920655	19920657	.	+	0	transcript_id "Phchi.S3G287900.t1"; gene_id "Phchi.S3G287900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1100.t1 is derived from g10883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7599363	7600440	.	+	.	Phchi.S6G105900
Phchi.S6	AUGUSTUS	transcript	7599363	7600440	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	start_codon	7599363	7599365	.	+	0	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	CDS	7599363	7599464	0.53	+	0	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	exon	7599363	7599464	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	intron	7599465	7599552	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	CDS	7599553	7599602	0.5	+	0	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	exon	7599553	7599602	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	intron	7599603	7599722	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	CDS	7599723	7599756	0.73	+	1	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	exon	7599723	7599756	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	intron	7599757	7600095	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	CDS	7600096	7600199	0.95	+	0	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	exon	7600096	7600199	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	intron	7600200	7600364	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	CDS	7600365	7600440	0.93	+	1	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	exon	7600365	7600440	.	+	.	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
Phchi.S6	AUGUSTUS	stop_codon	7600441	7600443	.	+	0	transcript_id "Phchi.S6G105900.t1"; gene_id "Phchi.S6G105900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3298.t1 is derived from g467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2730718	2731844	.	+	.	Phchi.S1G045700
Phchi.S1	AUGUSTUS	transcript	2730718	2731844	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	start_codon	2730718	2730720	.	+	0	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	CDS	2730718	2731071	0.54	+	0	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	exon	2730718	2731071	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	intron	2731072	2731144	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	CDS	2731145	2731178	0.83	+	0	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	exon	2731145	2731178	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	intron	2731179	2731318	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	CDS	2731319	2731397	0.96	+	2	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	exon	2731319	2731397	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	intron	2731398	2731483	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	CDS	2731484	2731844	1	+	1	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	exon	2731484	2731844	.	+	.	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
Phchi.S1	AUGUSTUS	stop_codon	2731845	2731847	.	+	0	transcript_id "Phchi.S1G045700.t1"; gene_id "Phchi.S1G045700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15526.t1 is derived from g13995.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19726609	19727260	.	-	.	Phchi.S3G284500
Phchi.S3	AUGUSTUS	transcript	19726609	19727260	.	-	.	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	stop_codon	19726606	19726608	.	-	0	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	CDS	19726609	19726980	0.59	-	0	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	exon	19726609	19726980	.	-	.	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	intron	19726981	19727128	.	-	.	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	CDS	19727129	19727260	0.87	-	0	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	exon	19727129	19727260	.	-	.	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	start_codon	19727258	19727260	.	-	0	transcript_id "Phchi.S3G284500.t1"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	transcript	19726609	19727260	.	-	.	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	stop_codon	19726606	19726608	.	-	0	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	CDS	19726609	19726983	0.55	-	0	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	exon	19726609	19726983	.	-	.	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	intron	19726984	19727128	.	-	.	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	CDS	19727129	19727260	0.74	-	0	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	exon	19727129	19727260	.	-	.	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
Phchi.S3	AUGUSTUS	start_codon	19727258	19727260	.	-	0	transcript_id "Phchi.S3G284500.t2"; gene_id "Phchi.S3G284500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14479.t1 is derived from g12947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13049373	13051125	.	+	.	Phchi.S3G179800
Phchi.S3	AUGUSTUS	transcript	13049373	13051125	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	start_codon	13049373	13049375	.	+	0	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	CDS	13049373	13050639	0.53	+	0	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	exon	13049373	13050639	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	intron	13050640	13050742	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	CDS	13050743	13050754	0.56	+	2	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	exon	13050743	13050754	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	intron	13050755	13050836	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	CDS	13050837	13051003	1	+	2	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	exon	13050837	13051003	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	intron	13051004	13051083	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	CDS	13051084	13051125	0.84	+	0	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	exon	13051084	13051125	.	+	.	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
Phchi.S3	AUGUSTUS	stop_codon	13051126	13051128	.	+	0	transcript_id "Phchi.S3G179800.t1"; gene_id "Phchi.S3G179800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg405.t1 is derived from g10187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2912627	2913574	.	-	.	Phchi.S6G036400
Phchi.S6	AUGUSTUS	transcript	2912627	2913574	.	-	.	transcript_id "Phchi.S6G036400.t1"; gene_id "Phchi.S6G036400"
Phchi.S6	AUGUSTUS	stop_codon	2912624	2912626	.	-	0	transcript_id "Phchi.S6G036400.t1"; gene_id "Phchi.S6G036400"
Phchi.S6	AUGUSTUS	CDS	2912627	2913574	0.69	-	0	transcript_id "Phchi.S6G036400.t1"; gene_id "Phchi.S6G036400"
Phchi.S6	AUGUSTUS	exon	2912627	2913574	.	-	.	transcript_id "Phchi.S6G036400.t1"; gene_id "Phchi.S6G036400"
Phchi.S6	AUGUSTUS	start_codon	2913572	2913574	.	-	0	transcript_id "Phchi.S6G036400.t1"; gene_id "Phchi.S6G036400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4783.t1 is derived from g1953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12798356	12801098	.	+	.	Phchi.S1G194200
Phchi.S1	AUGUSTUS	transcript	12798356	12801098	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	start_codon	12798356	12798358	.	+	0	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12798356	12798434	0.48	+	0	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12798356	12798434	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12798435	12798518	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12798519	12798781	1	+	2	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12798519	12798781	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12798782	12798917	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12798918	12799037	0.99	+	0	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12798918	12799037	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12799038	12799155	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12799156	12799298	0.96	+	0	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12799156	12799298	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12799299	12799458	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12799459	12799707	1	+	1	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12799459	12799707	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12799708	12799860	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12799861	12800300	1	+	1	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12799861	12800300	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12800301	12800484	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12800485	12800660	1	+	2	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12800485	12800660	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12800661	12800734	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12800735	12800831	0.99	+	0	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12800735	12800831	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	intron	12800832	12800940	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	CDS	12800941	12801098	0.81	+	2	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	exon	12800941	12801098	.	+	.	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
Phchi.S1	AUGUSTUS	stop_codon	12801099	12801101	.	+	0	transcript_id "Phchi.S1G194200.t1"; gene_id "Phchi.S1G194200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12248.t1 is derived from g7924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7006506	7008329	.	+	.	Phchi.S2G032800
Phchi.S2	AUGUSTUS	transcript	7006506	7008329	.	+	.	transcript_id "Phchi.S2G032800.t1"; gene_id "Phchi.S2G032800"
Phchi.S2	AUGUSTUS	start_codon	7006506	7006508	.	+	0	transcript_id "Phchi.S2G032800.t1"; gene_id "Phchi.S2G032800"
Phchi.S2	AUGUSTUS	CDS	7006506	7008329	0.85	+	0	transcript_id "Phchi.S2G032800.t1"; gene_id "Phchi.S2G032800"
Phchi.S2	AUGUSTUS	exon	7006506	7008329	.	+	.	transcript_id "Phchi.S2G032800.t1"; gene_id "Phchi.S2G032800"
Phchi.S2	AUGUSTUS	stop_codon	7008330	7008332	.	+	0	transcript_id "Phchi.S2G032800.t1"; gene_id "Phchi.S2G032800"
# This transcript jg11257.t2 is derived from g15307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11258.t1 is derived from g15308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5049385	5052702	.	+	.	Phchi.S4G084000
Phchi.S4	AUGUSTUS	transcript	5050207	5052702	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	start_codon	5050207	5050209	.	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5050207	5050225	0.96	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5050207	5050225	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5050226	5050551	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5050552	5050667	1	+	2	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5050552	5050667	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5050668	5050835	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5050836	5050954	1	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5050836	5050954	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5050955	5051103	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051104	5051167	1	+	1	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051104	5051167	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051168	5051244	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051245	5051315	1	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051245	5051315	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051316	5051407	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051408	5051466	1	+	1	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051408	5051466	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051467	5051646	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051647	5051806	1	+	2	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051647	5051806	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051807	5051929	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051930	5051949	0.99	+	1	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051930	5051949	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051950	5052056	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052057	5052103	1	+	2	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052057	5052103	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5052104	5052177	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052178	5052258	1	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052178	5052258	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5052259	5052345	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052346	5052435	1	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052346	5052435	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5052436	5052579	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052580	5052702	0.99	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052580	5052702	.	+	.	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	stop_codon	5052703	5052705	.	+	0	transcript_id "Phchi.S4G084000.t1"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	transcript	5049385	5052702	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	start_codon	5049385	5049387	.	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5049385	5049409	0.66	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5049385	5049409	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5049410	5050551	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5050552	5050667	0.87	+	2	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5050552	5050667	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5050668	5050835	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5050836	5050954	1	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5050836	5050954	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5050955	5051103	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051104	5051167	1	+	1	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051104	5051167	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051168	5051244	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051245	5051315	1	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051245	5051315	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051316	5051407	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051408	5051466	1	+	1	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051408	5051466	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051467	5051646	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051647	5051806	1	+	2	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051647	5051806	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051807	5051929	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5051930	5051949	0.98	+	1	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5051930	5051949	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5051950	5052056	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052057	5052103	1	+	2	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052057	5052103	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5052104	5052177	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052178	5052258	1	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052178	5052258	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5052259	5052345	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052346	5052435	1	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052346	5052435	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	intron	5052436	5052579	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	CDS	5052580	5052702	0.98	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	exon	5052580	5052702	.	+	.	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
Phchi.S4	AUGUSTUS	stop_codon	5052703	5052705	.	+	0	transcript_id "Phchi.S4G084000.t2"; gene_id "Phchi.S4G084000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14446.t1 is derived from g12914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12870340	12871560	.	-	.	Phchi.S3G176500
Phchi.S3	AUGUSTUS	transcript	12870340	12871560	.	-	.	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	stop_codon	12870337	12870339	.	-	0	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	CDS	12870340	12871125	0.52	-	0	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	exon	12870340	12871125	.	-	.	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	intron	12871126	12871222	.	-	.	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	CDS	12871223	12871274	1	-	1	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	exon	12871223	12871274	.	-	.	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	intron	12871275	12871549	.	-	.	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	CDS	12871550	12871560	0.53	-	0	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	exon	12871550	12871560	.	-	.	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
Phchi.S3	AUGUSTUS	start_codon	12871558	12871560	.	-	0	transcript_id "Phchi.S3G176500.t1"; gene_id "Phchi.S3G176500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10111.t1 is derived from g7287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45781532	45783338	.	+	.	Phchi.S1G727000
Phchi.S1	AUGUSTUS	transcript	45781532	45783338	.	+	.	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	start_codon	45781532	45781534	.	+	0	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	CDS	45781532	45781753	1	+	0	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	exon	45781532	45781753	.	+	.	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	intron	45781754	45782120	.	+	.	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	CDS	45782121	45783338	1	+	0	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	exon	45782121	45783338	.	+	.	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
Phchi.S1	AUGUSTUS	stop_codon	45783339	45783341	.	+	0	transcript_id "Phchi.S1G727000.t1"; gene_id "Phchi.S1G727000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1663.t1 is derived from g8582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2291403	2293525	.	+	.	Phchi.S5G027200
Phchi.S5	AUGUSTUS	transcript	2291403	2293525	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	start_codon	2291403	2291405	.	+	0	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2291403	2291532	1	+	0	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2291403	2291532	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	intron	2291533	2291665	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2291666	2291825	1	+	2	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2291666	2291825	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	intron	2291826	2291912	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2291913	2292034	1	+	1	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2291913	2292034	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	intron	2292035	2292123	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2292124	2292214	1	+	2	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2292124	2292214	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	intron	2292215	2292361	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2292362	2292491	1	+	1	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2292362	2292491	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	intron	2292492	2292642	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2292643	2292812	1	+	0	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2292643	2292812	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	intron	2292813	2292963	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	CDS	2292964	2293525	0.99	+	1	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	exon	2292964	2293525	.	+	.	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
Phchi.S5	AUGUSTUS	stop_codon	2293526	2293528	.	+	0	transcript_id "Phchi.S5G027200.t1"; gene_id "Phchi.S5G027200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8695.t1 is derived from g5870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37502645	37504209	.	-	.	Phchi.S1G585400
Phchi.S1	AUGUSTUS	transcript	37502645	37504209	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	stop_codon	37502642	37502644	.	-	0	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37502645	37502670	1	-	2	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37502645	37502670	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	intron	37502671	37502783	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37502784	37503087	1	-	0	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37502784	37503087	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	intron	37503088	37503217	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37503218	37503266	1	-	1	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37503218	37503266	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	intron	37503267	37503422	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37503423	37503494	1	-	1	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37503423	37503494	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	intron	37503495	37503624	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37503625	37503748	1	-	2	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37503625	37503748	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	intron	37503749	37503858	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37503859	37503963	1	-	2	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37503859	37503963	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	intron	37503964	37504166	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	CDS	37504167	37504209	1	-	0	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	exon	37504167	37504209	.	-	.	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
Phchi.S1	AUGUSTUS	start_codon	37504207	37504209	.	-	0	transcript_id "Phchi.S1G585400.t1"; gene_id "Phchi.S1G585400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6204.t1 is derived from g3375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21465853	21466782	.	+	.	Phchi.S1G336300
Phchi.S1	AUGUSTUS	transcript	21465853	21466782	.	+	.	transcript_id "Phchi.S1G336300.t1"; gene_id "Phchi.S1G336300"
Phchi.S1	AUGUSTUS	start_codon	21465853	21465855	.	+	0	transcript_id "Phchi.S1G336300.t1"; gene_id "Phchi.S1G336300"
Phchi.S1	AUGUSTUS	CDS	21465853	21466782	0.6	+	0	transcript_id "Phchi.S1G336300.t1"; gene_id "Phchi.S1G336300"
Phchi.S1	AUGUSTUS	exon	21465853	21466782	.	+	.	transcript_id "Phchi.S1G336300.t1"; gene_id "Phchi.S1G336300"
Phchi.S1	AUGUSTUS	stop_codon	21466783	21466785	.	+	0	transcript_id "Phchi.S1G336300.t1"; gene_id "Phchi.S1G336300"
# This transcript jg3185.t2 is derived from g354.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3186.t1 is derived from g355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2139156	2139690	.	-	.	Phchi.S1G034500
Phchi.S1	AUGUSTUS	transcript	2139156	2139690	.	-	.	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	stop_codon	2139153	2139155	.	-	0	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	CDS	2139156	2139225	0.84	-	1	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	exon	2139156	2139225	.	-	.	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	intron	2139226	2139532	.	-	.	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	CDS	2139533	2139690	0.58	-	0	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	exon	2139533	2139690	.	-	.	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
Phchi.S1	AUGUSTUS	start_codon	2139688	2139690	.	-	0	transcript_id "Phchi.S1G034500.t1"; gene_id "Phchi.S1G034500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5135.t1 is derived from g2305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15084729	15087203	.	-	.	Phchi.S1G229400
Phchi.S1	AUGUSTUS	transcript	15084729	15087203	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	stop_codon	15084726	15084728	.	-	0	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15084729	15085709	0.96	-	0	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15084729	15085709	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	intron	15085710	15085813	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15085814	15086072	0.79	-	1	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15085814	15086072	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	intron	15086073	15086146	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15086147	15086277	0.98	-	0	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15086147	15086277	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	intron	15086278	15086410	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15086411	15086550	1	-	2	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15086411	15086550	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	intron	15086551	15086625	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15086626	15086682	0.96	-	2	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15086626	15086682	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	intron	15086683	15086854	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15086855	15086985	0.95	-	1	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15086855	15086985	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	intron	15086986	15087183	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	CDS	15087184	15087203	0.84	-	0	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	exon	15087184	15087203	.	-	.	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
Phchi.S1	AUGUSTUS	start_codon	15087201	15087203	.	-	0	transcript_id "Phchi.S1G229400.t1"; gene_id "Phchi.S1G229400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13348.t1 is derived from g11814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6235516	6236518	.	-	.	Phchi.S3G066700
Phchi.S3	AUGUSTUS	transcript	6235516	6236518	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	stop_codon	6235513	6235515	.	-	0	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	CDS	6235516	6235628	1	-	2	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	exon	6235516	6235628	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	intron	6235629	6235721	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	CDS	6235722	6235835	1	-	2	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	exon	6235722	6235835	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	intron	6235836	6236040	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	CDS	6236041	6236167	1	-	0	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	exon	6236041	6236167	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	intron	6236168	6236305	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	CDS	6236306	6236518	0.83	-	0	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	exon	6236306	6236518	.	-	.	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
Phchi.S3	AUGUSTUS	start_codon	6236516	6236518	.	-	0	transcript_id "Phchi.S3G066700.t1"; gene_id "Phchi.S3G066700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10701.t1 is derived from g14751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1673447	1673773	.	+	.	Phchi.S4G028300
Phchi.S4	AUGUSTUS	transcript	1673447	1673773	.	+	.	transcript_id "Phchi.S4G028300.t1"; gene_id "Phchi.S4G028300"
Phchi.S4	AUGUSTUS	start_codon	1673447	1673449	.	+	0	transcript_id "Phchi.S4G028300.t1"; gene_id "Phchi.S4G028300"
Phchi.S4	AUGUSTUS	CDS	1673447	1673773	0.75	+	0	transcript_id "Phchi.S4G028300.t1"; gene_id "Phchi.S4G028300"
Phchi.S4	AUGUSTUS	exon	1673447	1673773	.	+	.	transcript_id "Phchi.S4G028300.t1"; gene_id "Phchi.S4G028300"
Phchi.S4	AUGUSTUS	stop_codon	1673774	1673776	.	+	0	transcript_id "Phchi.S4G028300.t1"; gene_id "Phchi.S4G028300"
# This transcript jg1393.t2 is derived from g8312.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1394.t1 is derived from g8313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	17799	22567	.	+	.	Phchi.S5G000300
Phchi.S5	AUGUSTUS	transcript	17799	22567	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	start_codon	17799	17801	.	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	17799	17868	0.56	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	17799	17868	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	17869	18006	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18007	18066	1	+	2	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18007	18066	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	18067	18460	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18461	18522	0.85	+	2	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18461	18522	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	18523	18600	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18601	18678	0.85	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18601	18678	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	18679	18956	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18957	19034	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18957	19034	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	19035	19319	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	19320	19354	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	19320	19354	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	19355	19514	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	19515	19620	1	+	1	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	19515	19620	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	19621	19755	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	19756	19959	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	19756	19959	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	19960	20129	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	20130	20258	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	20130	20258	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	20259	20649	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	20650	20743	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	20650	20743	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	20744	21289	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	21290	21357	1	+	2	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	21290	21357	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	21358	21437	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	21438	21512	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	21438	21512	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	21513	21765	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	21766	21836	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	21766	21836	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	21837	22287	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	22288	22348	1	+	1	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	22288	22348	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	22349	22483	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	22484	22567	1	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	22484	22567	.	+	.	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	stop_codon	22568	22570	.	+	0	transcript_id "Phchi.S5G000300.t1"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	transcript	17799	19532	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	start_codon	17799	17801	.	+	0	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	17799	17868	0.54	+	0	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	17799	17868	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	17869	18006	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18007	18066	1	+	2	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18007	18066	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	18067	18460	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18461	18522	0.91	+	2	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18461	18522	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	18523	18600	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18601	18678	0.91	+	0	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18601	18678	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	18679	18956	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	18957	19034	1	+	0	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	18957	19034	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	intron	19035	19514	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	CDS	19515	19532	1	+	0	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	exon	19515	19532	.	+	.	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
Phchi.S5	AUGUSTUS	stop_codon	19533	19535	.	+	0	transcript_id "Phchi.S5G000300.t2"; gene_id "Phchi.S5G000300"
# This transcript jg9847.t2 is derived from g7023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9848.t1 is derived from g7024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44070418	44072510	.	+	.	Phchi.S1G700700
Phchi.S1	AUGUSTUS	transcript	44070418	44072510	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	start_codon	44070418	44070420	.	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44070418	44070991	0.75	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44070418	44070991	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	intron	44070992	44071091	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44071092	44071186	1	+	2	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44071092	44071186	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	intron	44071187	44071282	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44071283	44071444	1	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44071283	44071444	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	intron	44071445	44071540	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44071541	44071713	1	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44071541	44071713	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	intron	44071714	44071812	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44071813	44071921	1	+	1	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44071813	44071921	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	intron	44071922	44072035	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44072036	44072194	0.68	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44072036	44072194	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	intron	44072195	44072315	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	CDS	44072316	44072510	0.99	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	exon	44072316	44072510	.	+	.	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
Phchi.S1	AUGUSTUS	stop_codon	44072511	44072513	.	+	0	transcript_id "Phchi.S1G700700.t1"; gene_id "Phchi.S1G700700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11260.t1 is derived from g15310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5060826	5061899	.	-	.	Phchi.S4G084200
Phchi.S4	AUGUSTUS	transcript	5060826	5061899	.	-	.	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	stop_codon	5060823	5060825	.	-	0	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	CDS	5060826	5061259	0.91	-	2	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	exon	5060826	5061259	.	-	.	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	intron	5061260	5061463	.	-	.	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	CDS	5061464	5061899	0.71	-	0	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	exon	5061464	5061899	.	-	.	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
Phchi.S4	AUGUSTUS	start_codon	5061897	5061899	.	-	0	transcript_id "Phchi.S4G084200.t1"; gene_id "Phchi.S4G084200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1298.t1 is derived from g11081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8897713	8898687	.	+	.	Phchi.S6G125700
Phchi.S6	AUGUSTUS	transcript	8897713	8898687	.	+	.	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	start_codon	8897713	8897715	.	+	0	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	CDS	8897713	8897866	1	+	0	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	exon	8897713	8897866	.	+	.	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	intron	8897867	8898043	.	+	.	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	CDS	8898044	8898687	1	+	2	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	exon	8898044	8898687	.	+	.	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
Phchi.S6	AUGUSTUS	stop_codon	8898688	8898690	.	+	0	transcript_id "Phchi.S6G125700.t1"; gene_id "Phchi.S6G125700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2279.t1 is derived from g9199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5841424	5844421	.	-	.	Phchi.S5G088800
Phchi.S5	AUGUSTUS	transcript	5841424	5844421	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	stop_codon	5841421	5841423	.	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5841424	5841448	0.82	-	1	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5841424	5841448	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5841449	5841579	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5841580	5841636	0.8	-	1	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5841580	5841636	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5841637	5841714	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5841715	5841778	0.81	-	2	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5841715	5841778	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5841779	5841896	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5841897	5841946	0.96	-	1	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5841897	5841946	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5841947	5842032	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5842033	5842160	1	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5842033	5842160	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5842161	5842250	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5842251	5842356	1	-	1	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5842251	5842356	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5842357	5842469	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5842470	5842549	0.92	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5842470	5842549	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5842550	5842659	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5842660	5842757	1	-	2	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5842660	5842757	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5842758	5842873	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5842874	5842987	0.98	-	2	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5842874	5842987	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5842988	5843091	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5843092	5843238	0.96	-	2	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5843092	5843238	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5843239	5843344	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5843345	5843429	0.89	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5843345	5843429	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5843430	5843575	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5843576	5843890	1	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5843576	5843890	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5843891	5844058	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5844059	5844084	0.6	-	2	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5844059	5844084	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	intron	5844085	5844294	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	CDS	5844295	5844421	0.95	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	exon	5844295	5844421	.	-	.	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
Phchi.S5	AUGUSTUS	start_codon	5844419	5844421	.	-	0	transcript_id "Phchi.S5G088800.t1"; gene_id "Phchi.S5G088800"
# This transcript jg11533.t2 is derived from g15583.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11534.t1 is derived from g15584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6949482	6950834	.	-	.	Phchi.S4G111600
Phchi.S4	AUGUSTUS	transcript	6949482	6950834	.	-	.	transcript_id "Phchi.S4G111600.t1"; gene_id "Phchi.S4G111600"
Phchi.S4	AUGUSTUS	stop_codon	6949479	6949481	.	-	0	transcript_id "Phchi.S4G111600.t1"; gene_id "Phchi.S4G111600"
Phchi.S4	AUGUSTUS	CDS	6949482	6950834	0.96	-	0	transcript_id "Phchi.S4G111600.t1"; gene_id "Phchi.S4G111600"
Phchi.S4	AUGUSTUS	exon	6949482	6950834	.	-	.	transcript_id "Phchi.S4G111600.t1"; gene_id "Phchi.S4G111600"
Phchi.S4	AUGUSTUS	start_codon	6950832	6950834	.	-	0	transcript_id "Phchi.S4G111600.t1"; gene_id "Phchi.S4G111600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1933.t1 is derived from g8853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3900160	3901776	.	+	.	Phchi.S5G054200
Phchi.S5	AUGUSTUS	transcript	3900160	3901776	.	+	.	transcript_id "Phchi.S5G054200.t1"; gene_id "Phchi.S5G054200"
Phchi.S5	AUGUSTUS	start_codon	3900160	3900162	.	+	0	transcript_id "Phchi.S5G054200.t1"; gene_id "Phchi.S5G054200"
Phchi.S5	AUGUSTUS	CDS	3900160	3901776	0.86	+	0	transcript_id "Phchi.S5G054200.t1"; gene_id "Phchi.S5G054200"
Phchi.S5	AUGUSTUS	exon	3900160	3901776	.	+	.	transcript_id "Phchi.S5G054200.t1"; gene_id "Phchi.S5G054200"
Phchi.S5	AUGUSTUS	stop_codon	3901777	3901779	.	+	0	transcript_id "Phchi.S5G054200.t1"; gene_id "Phchi.S5G054200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15620.t1 is derived from g14089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20328159	20333217	.	-	.	Phchi.S3G293900
Phchi.S3	AUGUSTUS	transcript	20328159	20333217	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	stop_codon	20328156	20328158	.	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20328159	20328239	1	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20328159	20328239	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20328240	20328331	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20328332	20328421	1	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20328332	20328421	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20328422	20328502	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20328503	20328619	1	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20328503	20328619	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20328620	20328706	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20328707	20328814	1	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20328707	20328814	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20328815	20328942	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20328943	20329035	1	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20328943	20329035	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20329036	20329122	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20329123	20329293	1	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20329123	20329293	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20329294	20329381	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20329382	20329442	0.81	-	1	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20329382	20329442	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20329443	20329525	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20329526	20329633	0.81	-	1	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20329526	20329633	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20329634	20329755	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20329756	20330001	1	-	1	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20329756	20330001	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20330002	20330139	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20330140	20330474	0.66	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20330140	20330474	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20330475	20330595	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20330596	20331567	0.98	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20330596	20331567	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20331568	20331719	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20331720	20332357	0.94	-	2	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20331720	20332357	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20332358	20332523	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20332524	20332764	0.91	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20332524	20332764	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20332765	20332870	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20332871	20332993	0.95	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20332871	20332993	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	intron	20332994	20333190	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	CDS	20333191	20333217	0.98	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	exon	20333191	20333217	.	-	.	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
Phchi.S3	AUGUSTUS	start_codon	20333215	20333217	.	-	0	transcript_id "Phchi.S3G293900.t1"; gene_id "Phchi.S3G293900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3693.t1 is derived from g862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5216327	5216764	.	-	.	Phchi.S1G085200
Phchi.S1	AUGUSTUS	transcript	5216327	5216764	.	-	.	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	stop_codon	5216324	5216326	.	-	0	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	CDS	5216327	5216560	0.92	-	0	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	exon	5216327	5216560	.	-	.	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	intron	5216561	5216656	.	-	.	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	CDS	5216657	5216764	0.63	-	0	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	exon	5216657	5216764	.	-	.	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
Phchi.S1	AUGUSTUS	start_codon	5216762	5216764	.	-	0	transcript_id "Phchi.S1G085200.t1"; gene_id "Phchi.S1G085200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4999.t1 is derived from g2169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13950571	13953960	.	+	.	Phchi.S1G215800
Phchi.S1	AUGUSTUS	transcript	13950571	13953960	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	start_codon	13950571	13950573	.	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13950571	13950804	0.55	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13950571	13950804	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13950805	13950961	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13950962	13951087	0.57	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13950962	13951087	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13951088	13951175	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13951176	13951442	1	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13951176	13951442	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13951443	13951542	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13951543	13951570	0.92	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13951543	13951570	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13951571	13951695	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13951696	13951889	0.65	+	2	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13951696	13951889	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13951890	13952038	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13952039	13953588	0.8	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13952039	13953588	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13953589	13953677	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13953678	13953795	0.53	+	1	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13953678	13953795	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	intron	13953796	13953885	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	CDS	13953886	13953960	0.53	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	exon	13953886	13953960	.	+	.	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
Phchi.S1	AUGUSTUS	stop_codon	13953961	13953963	.	+	0	transcript_id "Phchi.S1G215800.t1"; gene_id "Phchi.S1G215800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6682.t1 is derived from g3854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24493295	24496376	.	-	.	Phchi.S1G384100
Phchi.S1	AUGUSTUS	transcript	24493295	24496376	.	-	.	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	stop_codon	24493292	24493294	.	-	0	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	CDS	24493295	24493960	0.98	-	0	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	exon	24493295	24493960	.	-	.	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	intron	24493961	24494037	.	-	.	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	CDS	24494038	24494425	0.52	-	1	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	exon	24494038	24494425	.	-	.	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	intron	24494426	24494505	.	-	.	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	CDS	24494506	24496376	0.51	-	0	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	exon	24494506	24496376	.	-	.	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
Phchi.S1	AUGUSTUS	start_codon	24496374	24496376	.	-	0	transcript_id "Phchi.S1G384100.t1"; gene_id "Phchi.S1G384100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5013.t1 is derived from g2183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14038929	14041431	.	-	.	Phchi.S1G217200
Phchi.S1	AUGUSTUS	transcript	14038929	14041431	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	stop_codon	14038926	14038928	.	-	0	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	CDS	14038929	14039545	0.77	-	2	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	exon	14038929	14039545	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	intron	14039546	14039687	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	CDS	14039688	14039931	1	-	0	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	exon	14039688	14039931	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	intron	14039932	14040118	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	CDS	14040119	14040406	1	-	0	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	exon	14040119	14040406	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	intron	14040407	14040486	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	CDS	14040487	14041431	1	-	0	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	exon	14040487	14041431	.	-	.	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
Phchi.S1	AUGUSTUS	start_codon	14041429	14041431	.	-	0	transcript_id "Phchi.S1G217200.t1"; gene_id "Phchi.S1G217200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1854.t1 is derived from g8774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3562755	3565305	.	-	.	Phchi.S5G046300
Phchi.S5	AUGUSTUS	transcript	3562755	3565305	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	stop_codon	3562752	3562754	.	-	0	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	CDS	3562755	3562860	0.27	-	1	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	exon	3562755	3562860	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	intron	3562861	3562974	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	CDS	3562975	3563918	0.36	-	0	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	exon	3562975	3563918	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	intron	3563919	3564042	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	CDS	3564043	3564954	0.99	-	0	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	exon	3564043	3564954	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	intron	3564955	3565089	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	CDS	3565090	3565305	1	-	0	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	exon	3565090	3565305	.	-	.	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
Phchi.S5	AUGUSTUS	start_codon	3565303	3565305	.	-	0	transcript_id "Phchi.S5G046300.t1"; gene_id "Phchi.S5G046300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2530.t1 is derived from g9450.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7175619	7179795	.	+	.	Phchi.S5G113900
Phchi.S5	AUGUSTUS	transcript	7175619	7178261	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	start_codon	7175619	7175621	.	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7175619	7175967	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7175619	7175967	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7175968	7176045	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176046	7176207	1	+	2	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176046	7176207	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7176208	7176300	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176301	7176473	0.99	+	2	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176301	7176473	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7176474	7176573	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176574	7176729	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176574	7176729	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7176730	7176809	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176810	7177013	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176810	7177013	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177014	7177085	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177086	7177199	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177086	7177199	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177200	7177282	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177283	7177375	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177283	7177375	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177376	7177458	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177459	7177548	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177459	7177548	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177549	7177627	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177628	7177701	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177628	7177701	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177702	7177794	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177795	7177869	1	+	1	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177795	7177869	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177870	7177948	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177949	7178042	1	+	1	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177949	7178042	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178043	7178115	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178116	7178173	1	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178116	7178173	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178174	7178244	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178245	7178261	0.99	+	2	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178245	7178261	.	+	.	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	stop_codon	7178262	7178264	.	+	0	transcript_id "Phchi.S5G113900.t1"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	transcript	7175619	7179795	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	start_codon	7175619	7175621	.	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7175619	7175967	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7175619	7175967	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7175968	7176045	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176046	7176207	0.99	+	2	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176046	7176207	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7176208	7176300	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176301	7176473	0.99	+	2	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176301	7176473	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7176474	7176573	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176574	7176729	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176574	7176729	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7176730	7176809	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7176810	7177013	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7176810	7177013	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177014	7177085	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177086	7177199	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177086	7177199	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177200	7177282	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177283	7177375	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177283	7177375	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177376	7177458	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177459	7177548	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177459	7177548	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177549	7177627	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177628	7177701	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177628	7177701	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177702	7177794	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177795	7177869	1	+	1	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177795	7177869	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7177870	7177948	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7177949	7178042	1	+	1	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7177949	7178042	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178043	7178115	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178116	7178173	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178116	7178173	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178174	7178371	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178372	7178475	1	+	2	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178372	7178475	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178476	7178558	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178559	7178681	1	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178559	7178681	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178682	7178766	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178767	7179795	0.89	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178767	7179795	.	+	.	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	stop_codon	7179796	7179798	.	+	0	transcript_id "Phchi.S5G113900.t2"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	transcript	7178359	7179795	.	+	.	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	start_codon	7178359	7178361	.	+	0	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178359	7178475	0.99	+	0	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178359	7178475	.	+	.	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178476	7178558	.	+	.	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178559	7178681	1	+	0	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178559	7178681	.	+	.	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	intron	7178682	7178766	.	+	.	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	CDS	7178767	7179795	0.87	+	0	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	exon	7178767	7179795	.	+	.	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
Phchi.S5	AUGUSTUS	stop_codon	7179796	7179798	.	+	0	transcript_id "Phchi.S5G113900.t3"; gene_id "Phchi.S5G113900"
# This transcript jg15780.t2 is derived from g14250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15781.t1 is derived from g14251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21316279	21317241	.	-	.	Phchi.S3G310000
Phchi.S3	AUGUSTUS	transcript	21316279	21317241	.	-	.	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	stop_codon	21316276	21316278	.	-	0	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	CDS	21316279	21316361	1	-	2	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	exon	21316279	21316361	.	-	.	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	intron	21316362	21316455	.	-	.	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	CDS	21316456	21316666	1	-	0	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	exon	21316456	21316666	.	-	.	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	intron	21316667	21316764	.	-	.	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	CDS	21316765	21317241	0.94	-	0	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	exon	21316765	21317241	.	-	.	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
Phchi.S3	AUGUSTUS	start_codon	21317239	21317241	.	-	0	transcript_id "Phchi.S3G310000.t1"; gene_id "Phchi.S3G310000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12392.t1 is derived from g8069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	16467868	16468321	.	+	.	Phchi.S2G047200
Phchi.S2	AUGUSTUS	transcript	16467868	16468321	.	+	.	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	start_codon	16467868	16467870	.	+	0	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	CDS	16467868	16468074	0.54	+	0	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	exon	16467868	16468074	.	+	.	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	intron	16468075	16468195	.	+	.	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	CDS	16468196	16468321	0.86	+	0	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	exon	16468196	16468321	.	+	.	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
Phchi.S2	AUGUSTUS	stop_codon	16468322	16468324	.	+	0	transcript_id "Phchi.S2G047200.t1"; gene_id "Phchi.S2G047200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4951.t1 is derived from g2121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13697793	13699679	.	-	.	Phchi.S1G211000
Phchi.S1	AUGUSTUS	transcript	13697793	13699679	.	-	.	transcript_id "Phchi.S1G211000.t1"; gene_id "Phchi.S1G211000"
Phchi.S1	AUGUSTUS	stop_codon	13697790	13697792	.	-	0	transcript_id "Phchi.S1G211000.t1"; gene_id "Phchi.S1G211000"
Phchi.S1	AUGUSTUS	CDS	13697793	13699679	0.12	-	0	transcript_id "Phchi.S1G211000.t1"; gene_id "Phchi.S1G211000"
Phchi.S1	AUGUSTUS	exon	13697793	13699679	.	-	.	transcript_id "Phchi.S1G211000.t1"; gene_id "Phchi.S1G211000"
Phchi.S1	AUGUSTUS	start_codon	13699677	13699679	.	-	0	transcript_id "Phchi.S1G211000.t1"; gene_id "Phchi.S1G211000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg300.t1 is derived from g10082.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2119192	2121560	.	-	.	Phchi.S6G025900
Phchi.S6	AUGUSTUS	transcript	2119295	2121560	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	stop_codon	2119292	2119294	.	-	0	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119295	2119327	0.95	-	0	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119295	2119327	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119328	2119416	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119417	2119423	0.95	-	1	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119417	2119423	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119424	2119519	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119520	2119541	0.95	-	2	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119520	2119541	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119542	2119674	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119675	2119807	0.96	-	0	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119675	2119807	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119808	2119901	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119902	2121560	0.82	-	0	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119902	2121560	.	-	.	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	start_codon	2121558	2121560	.	-	0	transcript_id "Phchi.S6G025900.t1"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	transcript	2119192	2121560	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	stop_codon	2119189	2119191	.	-	0	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119192	2119327	0.92	-	1	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119192	2119327	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119328	2119416	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119417	2119423	0.92	-	2	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119417	2119423	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119424	2119519	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119520	2119541	0.91	-	0	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119520	2119541	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119542	2119639	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119640	2119807	0.92	-	0	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119640	2119807	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	intron	2119808	2119901	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	CDS	2119902	2121560	0.77	-	0	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	exon	2119902	2121560	.	-	.	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
Phchi.S6	AUGUSTUS	start_codon	2121558	2121560	.	-	0	transcript_id "Phchi.S6G025900.t2"; gene_id "Phchi.S6G025900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2984.t1 is derived from g153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	975510	980596	.	+	.	Phchi.S1G014300
Phchi.S1	AUGUSTUS	transcript	975510	980596	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	start_codon	975510	975512	.	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	975510	976090	0.77	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	975510	976090	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	976091	976291	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	976292	976436	1	+	1	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	976292	976436	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	976437	976525	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	976526	976582	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	976526	976582	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	976583	976705	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	976706	976825	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	976706	976825	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	976826	976925	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	976926	977030	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	976926	977030	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	977031	977123	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	977124	977341	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	977124	977341	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	977342	977433	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	977434	977500	0.99	+	1	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	977434	977500	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	977501	977607	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	977608	977762	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	977608	977762	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	977763	977847	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	977848	978001	0.98	+	1	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	977848	978001	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	978002	978105	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	978106	978112	0.98	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	978106	978112	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	978113	978246	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	978247	978440	0.98	+	2	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	978247	978440	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	978441	978611	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	978612	978691	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	978612	978691	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	978692	978769	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	978770	978832	1	+	1	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	978770	978832	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	978833	978926	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	978927	979008	1	+	1	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	978927	979008	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	979009	979109	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	979110	979187	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	979110	979187	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	979188	979268	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	979269	979364	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	979269	979364	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	979365	979438	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	979439	979611	0.99	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	979439	979611	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	979612	979724	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	979725	979905	1	+	1	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	979725	979905	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	979906	979998	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	979999	980076	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	979999	980076	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	980077	980157	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	980158	980289	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	980158	980289	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	intron	980290	980383	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	CDS	980384	980596	1	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	exon	980384	980596	.	+	.	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
Phchi.S1	AUGUSTUS	stop_codon	980597	980599	.	+	0	transcript_id "Phchi.S1G014300.t1"; gene_id "Phchi.S1G014300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4271.t1 is derived from g1440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9334327	9335554	.	+	.	Phchi.S1G143000
Phchi.S1	AUGUSTUS	transcript	9334327	9335554	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	start_codon	9334327	9334329	.	+	0	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	CDS	9334327	9334524	0.86	+	0	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	exon	9334327	9334524	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	intron	9334525	9334608	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	CDS	9334609	9334771	0.26	+	0	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	exon	9334609	9334771	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	intron	9334772	9335110	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	CDS	9335111	9335258	0.2	+	2	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	exon	9335111	9335258	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	intron	9335259	9335496	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	CDS	9335497	9335554	0.76	+	1	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	exon	9335497	9335554	.	+	.	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
Phchi.S1	AUGUSTUS	stop_codon	9335555	9335557	.	+	0	transcript_id "Phchi.S1G143000.t1"; gene_id "Phchi.S1G143000"
# This transcript jg7575.t2 is derived from g4749.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7576.t1 is derived from g4750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30113714	30114160	.	+	.	Phchi.S1G473500
Phchi.S1	AUGUSTUS	transcript	30113714	30114160	.	+	.	transcript_id "Phchi.S1G473500.t1"; gene_id "Phchi.S1G473500"
Phchi.S1	AUGUSTUS	start_codon	30113714	30113716	.	+	0	transcript_id "Phchi.S1G473500.t1"; gene_id "Phchi.S1G473500"
Phchi.S1	AUGUSTUS	CDS	30113714	30114160	0.77	+	0	transcript_id "Phchi.S1G473500.t1"; gene_id "Phchi.S1G473500"
Phchi.S1	AUGUSTUS	exon	30113714	30114160	.	+	.	transcript_id "Phchi.S1G473500.t1"; gene_id "Phchi.S1G473500"
Phchi.S1	AUGUSTUS	stop_codon	30114161	30114163	.	+	0	transcript_id "Phchi.S1G473500.t1"; gene_id "Phchi.S1G473500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6581.t1 is derived from g3753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23843373	23847729	.	+	.	Phchi.S1G374000
Phchi.S1	AUGUSTUS	transcript	23843373	23847729	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	start_codon	23843373	23843375	.	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23843373	23843534	0.89	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23843373	23843534	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23843535	23843634	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23843635	23843856	1	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23843635	23843856	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23843857	23843941	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23843942	23844180	1	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23843942	23844180	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23844181	23844265	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23844266	23844791	1	+	1	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23844266	23844791	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23844792	23844903	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23844904	23845177	0.98	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23844904	23845177	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23845178	23845267	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23845268	23845928	0.91	+	2	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23845268	23845928	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23845929	23846074	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23846075	23846303	0.99	+	1	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23846075	23846303	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23846304	23846382	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23846383	23846649	0.76	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23846383	23846649	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23846650	23846732	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23846733	23846993	0.98	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23846733	23846993	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	intron	23846994	23847090	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	CDS	23847091	23847729	1	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	exon	23847091	23847729	.	+	.	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
Phchi.S1	AUGUSTUS	stop_codon	23847730	23847732	.	+	0	transcript_id "Phchi.S1G374000.t1"; gene_id "Phchi.S1G374000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg14723.t1 is derived from g13191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14366024	14372694	.	-	.	Phchi.S3G204200
Phchi.S3	AUGUSTUS	transcript	14366024	14367654	.	-	.	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	stop_codon	14366021	14366023	.	-	0	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14366024	14366742	0.99	-	2	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14366024	14366742	.	-	.	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	intron	14366743	14366843	.	-	.	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14366844	14367654	0.92	-	0	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14366844	14367654	.	-	.	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	start_codon	14367652	14367654	.	-	0	transcript_id "Phchi.S3G204200.t1"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	transcript	14368217	14372694	.	-	.	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	stop_codon	14368214	14368216	.	-	0	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14368217	14368245	1	-	2	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14368217	14368245	.	-	.	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	intron	14368246	14368340	.	-	.	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14368341	14372694	0.87	-	0	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14368341	14372694	.	-	.	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	start_codon	14372692	14372694	.	-	0	transcript_id "Phchi.S3G204200.t2"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	transcript	14366024	14372694	.	-	.	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	stop_codon	14366021	14366023	.	-	0	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14366024	14366742	0.99	-	2	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14366024	14366742	.	-	.	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	intron	14366743	14366843	.	-	.	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14366844	14372694	0.83	-	0	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14366844	14372694	.	-	.	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	start_codon	14372692	14372694	.	-	0	transcript_id "Phchi.S3G204200.t3"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	transcript	14368889	14372694	.	-	.	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	stop_codon	14368886	14368888	.	-	0	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14368889	14368898	0.41	-	1	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14368889	14368898	.	-	.	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	intron	14368899	14369011	.	-	.	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	CDS	14369012	14372694	0.3	-	0	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	exon	14369012	14372694	.	-	.	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
Phchi.S3	AUGUSTUS	start_codon	14372692	14372694	.	-	0	transcript_id "Phchi.S3G204200.t4"; gene_id "Phchi.S3G204200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9840.t1 is derived from g7016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44021704	44022189	.	-	.	Phchi.S1G699900
Phchi.S1	AUGUSTUS	transcript	44021704	44022189	.	-	.	transcript_id "Phchi.S1G699900.t1"; gene_id "Phchi.S1G699900"
Phchi.S1	AUGUSTUS	stop_codon	44021701	44021703	.	-	0	transcript_id "Phchi.S1G699900.t1"; gene_id "Phchi.S1G699900"
Phchi.S1	AUGUSTUS	CDS	44021704	44022189	0.95	-	0	transcript_id "Phchi.S1G699900.t1"; gene_id "Phchi.S1G699900"
Phchi.S1	AUGUSTUS	exon	44021704	44022189	.	-	.	transcript_id "Phchi.S1G699900.t1"; gene_id "Phchi.S1G699900"
Phchi.S1	AUGUSTUS	start_codon	44022187	44022189	.	-	0	transcript_id "Phchi.S1G699900.t1"; gene_id "Phchi.S1G699900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7878.t1 is derived from g5052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31684237	31685813	.	-	.	Phchi.S1G503700
Phchi.S1	AUGUSTUS	transcript	31684237	31685813	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	stop_codon	31684234	31684236	.	-	0	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31684237	31684240	1	-	1	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31684237	31684240	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	intron	31684241	31684339	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31684340	31684397	1	-	2	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31684340	31684397	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	intron	31684398	31684501	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31684502	31684690	1	-	2	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31684502	31684690	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	intron	31684691	31684893	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31684894	31684993	0.99	-	0	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31684894	31684993	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	intron	31684994	31685102	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31685103	31685224	0.98	-	2	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31685103	31685224	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	intron	31685225	31685371	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31685372	31685459	1	-	0	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31685372	31685459	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	intron	31685460	31685588	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	CDS	31685589	31685813	1	-	0	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	exon	31685589	31685813	.	-	.	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
Phchi.S1	AUGUSTUS	start_codon	31685811	31685813	.	-	0	transcript_id "Phchi.S1G503700.t1"; gene_id "Phchi.S1G503700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5980.t1 is derived from g3151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20216739	20218405	.	+	.	Phchi.S1G313900
Phchi.S1	AUGUSTUS	transcript	20216739	20218405	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	start_codon	20216739	20216741	.	+	0	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20216739	20216852	1	+	0	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20216739	20216852	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20216853	20216965	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20216966	20217041	1	+	0	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20216966	20217041	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20217042	20217307	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20217308	20217381	1	+	2	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20217308	20217381	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20217382	20217518	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20217519	20217589	1	+	0	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20217519	20217589	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20217590	20217728	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20217729	20217752	0.94	+	1	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20217729	20217752	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20217753	20217846	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20217847	20217902	0.87	+	1	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20217847	20217902	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20217903	20218077	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20218078	20218144	0.86	+	2	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20218078	20218144	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20218145	20218226	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20218227	20218237	0.98	+	1	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20218227	20218237	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	intron	20218238	20218397	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	CDS	20218398	20218405	0.98	+	2	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	exon	20218398	20218405	.	+	.	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
Phchi.S1	AUGUSTUS	stop_codon	20218406	20218408	.	+	0	transcript_id "Phchi.S1G313900.t1"; gene_id "Phchi.S1G313900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1095.t1 is derived from g10878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7588362	7589970	.	+	.	Phchi.S6G105400
Phchi.S6	AUGUSTUS	transcript	7588362	7589970	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	start_codon	7588362	7588364	.	+	0	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	CDS	7588362	7588432	0.23	+	0	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	exon	7588362	7588432	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	intron	7588433	7588515	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	CDS	7588516	7588543	0.32	+	1	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	exon	7588516	7588543	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	intron	7588544	7588697	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	CDS	7588698	7589538	0.22	+	0	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	exon	7588698	7589538	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	intron	7589539	7589711	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	CDS	7589712	7589725	0.8	+	2	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	exon	7589712	7589725	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	intron	7589726	7589886	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	CDS	7589887	7589970	0.78	+	0	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	exon	7589887	7589970	.	+	.	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
Phchi.S6	AUGUSTUS	stop_codon	7589971	7589973	.	+	0	transcript_id "Phchi.S6G105400.t1"; gene_id "Phchi.S6G105400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6980.t1 is derived from g4152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26255639	26256259	.	-	.	Phchi.S1G413900
Phchi.S1	AUGUSTUS	transcript	26255639	26256259	.	-	.	transcript_id "Phchi.S1G413900.t1"; gene_id "Phchi.S1G413900"
Phchi.S1	AUGUSTUS	stop_codon	26255636	26255638	.	-	0	transcript_id "Phchi.S1G413900.t1"; gene_id "Phchi.S1G413900"
Phchi.S1	AUGUSTUS	CDS	26255639	26256259	0.7	-	0	transcript_id "Phchi.S1G413900.t1"; gene_id "Phchi.S1G413900"
Phchi.S1	AUGUSTUS	exon	26255639	26256259	.	-	.	transcript_id "Phchi.S1G413900.t1"; gene_id "Phchi.S1G413900"
Phchi.S1	AUGUSTUS	start_codon	26256257	26256259	.	-	0	transcript_id "Phchi.S1G413900.t1"; gene_id "Phchi.S1G413900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14914.t1 is derived from g13382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15480212	15482974	.	-	.	Phchi.S3G223300
Phchi.S3	AUGUSTUS	transcript	15480212	15482974	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	stop_codon	15480209	15480211	.	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15480212	15480535	0.83	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15480212	15480535	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15480536	15480637	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15480638	15480822	0.87	-	2	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15480638	15480822	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15480823	15480909	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15480910	15481048	1	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15480910	15481048	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15481049	15481168	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15481169	15481223	1	-	1	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15481169	15481223	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15481224	15481308	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15481309	15481376	1	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15481309	15481376	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15481377	15481470	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15481471	15481767	1	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15481471	15481767	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15481768	15481867	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15481868	15481942	1	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15481868	15481942	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15481943	15482023	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15482024	15482117	1	-	1	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15482024	15482117	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15482118	15482206	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15482207	15482284	1	-	1	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15482207	15482284	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15482285	15482394	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15482395	15482543	0.98	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15482395	15482543	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15482544	15482623	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15482624	15482776	1	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15482624	15482776	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	intron	15482777	15482860	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	CDS	15482861	15482974	1	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	exon	15482861	15482974	.	-	.	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
Phchi.S3	AUGUSTUS	start_codon	15482972	15482974	.	-	0	transcript_id "Phchi.S3G223300.t1"; gene_id "Phchi.S3G223300"
# This transcript jg14876.t2 is derived from g13344.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14877.t1 is derived from g13345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15245907	15247251	.	+	.	Phchi.S3G219600
Phchi.S3	AUGUSTUS	transcript	15245907	15247251	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	start_codon	15245907	15245909	.	+	0	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	CDS	15245907	15245909	1	+	0	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	exon	15245907	15245909	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	intron	15245910	15246056	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	CDS	15246057	15246227	1	+	0	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	exon	15246057	15246227	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	intron	15246228	15246364	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	CDS	15246365	15246469	0.94	+	0	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	exon	15246365	15246469	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	intron	15246470	15246582	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	CDS	15246583	15246734	1	+	0	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	exon	15246583	15246734	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	intron	15246735	15246878	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	CDS	15246879	15247251	0.99	+	1	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	exon	15246879	15247251	.	+	.	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
Phchi.S3	AUGUSTUS	stop_codon	15247252	15247254	.	+	0	transcript_id "Phchi.S3G219600.t1"; gene_id "Phchi.S3G219600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5416.t1 is derived from g2586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16777470	16781601	.	-	.	Phchi.S1G257500
Phchi.S1	AUGUSTUS	transcript	16777470	16781601	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	stop_codon	16777467	16777469	.	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16777470	16777637	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16777470	16777637	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16777638	16777715	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16777716	16777781	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16777716	16777781	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16777782	16777878	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16777879	16777935	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16777879	16777935	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16777936	16778010	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16778011	16778067	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16778011	16778067	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16778068	16778148	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16778149	16778283	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16778149	16778283	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16778284	16778394	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16778395	16778484	0.61	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16778395	16778484	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16778485	16778592	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16778593	16778741	1	-	2	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16778593	16778741	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16778742	16778861	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16778862	16779141	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16778862	16779141	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16779142	16779267	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16779268	16779330	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16779268	16779330	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16779331	16779478	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16779479	16779607	0.67	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16779479	16779607	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16779608	16779717	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16779718	16779768	0.65	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16779718	16779768	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16779769	16779879	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16779880	16779980	1	-	2	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16779880	16779980	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16779981	16780099	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16780100	16780190	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16780100	16780190	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16780191	16780386	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16780387	16780488	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16780387	16780488	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16780489	16780572	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16780573	16780596	1	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16780573	16780596	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16780597	16780703	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16780704	16780891	1	-	2	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16780704	16780891	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	intron	16780892	16781096	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	CDS	16781097	16781601	0.8	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	exon	16781097	16781601	.	-	.	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
Phchi.S1	AUGUSTUS	start_codon	16781599	16781601	.	-	0	transcript_id "Phchi.S1G257500.t1"; gene_id "Phchi.S1G257500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4858.t1 is derived from g2028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13124690	13125860	.	+	.	Phchi.S1G201700
Phchi.S1	AUGUSTUS	transcript	13124690	13125860	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	start_codon	13124690	13124692	.	+	0	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13124690	13124803	0.81	+	0	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13124690	13124803	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	intron	13124804	13124872	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13124873	13124952	1	+	0	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13124873	13124952	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	intron	13124953	13125040	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13125041	13125111	1	+	1	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13125041	13125111	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	intron	13125112	13125252	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13125253	13125323	1	+	2	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13125253	13125323	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	intron	13125324	13125445	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13125446	13125527	1	+	0	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13125446	13125527	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	intron	13125528	13125645	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13125646	13125695	1	+	2	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13125646	13125695	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	intron	13125696	13125785	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	CDS	13125786	13125860	1	+	0	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	exon	13125786	13125860	.	+	.	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
Phchi.S1	AUGUSTUS	stop_codon	13125861	13125863	.	+	0	transcript_id "Phchi.S1G201700.t1"; gene_id "Phchi.S1G201700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12463.t1 is derived from g8140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24577102	24577689	.	+	.	Phchi.S2G054300
Phchi.S2	AUGUSTUS	transcript	24577102	24577689	.	+	.	transcript_id "Phchi.S2G054300.t1"; gene_id "Phchi.S2G054300"
Phchi.S2	AUGUSTUS	start_codon	24577102	24577104	.	+	0	transcript_id "Phchi.S2G054300.t1"; gene_id "Phchi.S2G054300"
Phchi.S2	AUGUSTUS	CDS	24577102	24577689	0.85	+	0	transcript_id "Phchi.S2G054300.t1"; gene_id "Phchi.S2G054300"
Phchi.S2	AUGUSTUS	exon	24577102	24577689	.	+	.	transcript_id "Phchi.S2G054300.t1"; gene_id "Phchi.S2G054300"
Phchi.S2	AUGUSTUS	stop_codon	24577690	24577692	.	+	0	transcript_id "Phchi.S2G054300.t1"; gene_id "Phchi.S2G054300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9573.t1 is derived from g6749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42725159	42728382	.	-	.	Phchi.S1G673200
Phchi.S1	AUGUSTUS	transcript	42725159	42728382	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	stop_codon	42725156	42725158	.	-	0	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	CDS	42725159	42726616	0.91	-	0	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	exon	42725159	42726616	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	intron	42726617	42726734	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	CDS	42726735	42727441	0.35	-	2	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	exon	42726735	42727441	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	intron	42727442	42727584	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	CDS	42727585	42727816	0.17	-	0	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	exon	42727585	42727816	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	intron	42727817	42727908	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	CDS	42727909	42728382	0.65	-	0	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	exon	42727909	42728382	.	-	.	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
Phchi.S1	AUGUSTUS	start_codon	42728380	42728382	.	-	0	transcript_id "Phchi.S1G673200.t1"; gene_id "Phchi.S1G673200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15647.t1 is derived from g14116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20470192	20471835	.	-	.	Phchi.S3G296600
Phchi.S3	AUGUSTUS	transcript	20470192	20471835	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	stop_codon	20470189	20470191	.	-	0	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	CDS	20470192	20470428	0.61	-	0	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	exon	20470192	20470428	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	intron	20470429	20470588	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	CDS	20470589	20470734	1	-	2	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	exon	20470589	20470734	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	intron	20470735	20470860	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	CDS	20470861	20471034	1	-	2	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	exon	20470861	20471034	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	intron	20471035	20471132	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	CDS	20471133	20471291	1	-	2	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	exon	20471133	20471291	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	intron	20471292	20471750	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	CDS	20471751	20471835	0.99	-	0	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	exon	20471751	20471835	.	-	.	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
Phchi.S3	AUGUSTUS	start_codon	20471833	20471835	.	-	0	transcript_id "Phchi.S3G296600.t1"; gene_id "Phchi.S3G296600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13424.t1 is derived from g11891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6631822	6632894	.	-	.	Phchi.S3G074300
Phchi.S3	AUGUSTUS	transcript	6631822	6632894	.	-	.	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	stop_codon	6631819	6631821	.	-	0	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	CDS	6631822	6632385	1	-	0	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	exon	6631822	6632385	.	-	.	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	intron	6632386	6632471	.	-	.	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	CDS	6632472	6632894	0.44	-	0	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	exon	6632472	6632894	.	-	.	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
Phchi.S3	AUGUSTUS	start_codon	6632892	6632894	.	-	0	transcript_id "Phchi.S3G074300.t1"; gene_id "Phchi.S3G074300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10246.t1 is derived from g7422.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46575781	46583107	.	+	.	Phchi.S1G740500
Phchi.S1	AUGUSTUS	transcript	46575781	46583107	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	start_codon	46575781	46575783	.	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46575781	46576805	0.81	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46575781	46576805	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46576806	46577037	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577038	46577076	0.98	+	1	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577038	46577076	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577077	46577162	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577163	46577346	1	+	1	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577163	46577346	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577347	46577456	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577457	46577720	0.62	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577457	46577720	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577721	46577842	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577843	46577954	0.59	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577843	46577954	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577955	46578079	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46578080	46578252	0.74	+	2	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46578080	46578252	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46578253	46578372	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46578373	46579042	0.99	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46578373	46579042	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579043	46579128	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579129	46579193	1	+	2	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579129	46579193	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579194	46579279	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579280	46579381	1	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579280	46579381	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579382	46579526	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579527	46579669	1	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579527	46579669	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579670	46579805	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579806	46579861	1	+	1	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579806	46579861	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579862	46579975	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579976	46580649	0.77	+	2	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579976	46580649	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46580650	46580738	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46580739	46580938	1	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46580739	46580938	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46580939	46581043	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46581044	46581317	0.97	+	1	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46581044	46581317	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46581318	46581462	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46581463	46581708	1	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46581463	46581708	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46581709	46581851	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46581852	46581961	1	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46581852	46581961	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46581962	46582047	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46582048	46582360	1	+	1	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46582048	46582360	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46582361	46582441	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46582442	46582930	0.93	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46582442	46582930	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46582931	46583023	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46583024	46583107	0.65	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46583024	46583107	.	+	.	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	stop_codon	46583108	46583110	.	+	0	transcript_id "Phchi.S1G740500.t1"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	transcript	46575781	46583107	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	start_codon	46575781	46575783	.	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46575781	46576861	0.75	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46575781	46576861	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46576862	46577037	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577038	46577076	0.92	+	2	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577038	46577076	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577077	46577167	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577168	46577346	0.92	+	2	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577168	46577346	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577347	46577456	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577457	46577720	0.53	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577457	46577720	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577721	46577842	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46577843	46577954	0.51	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46577843	46577954	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46577955	46578079	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46578080	46578252	0.82	+	2	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46578080	46578252	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46578253	46578372	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46578373	46579042	0.94	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46578373	46579042	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579043	46579128	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579129	46579193	1	+	2	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579129	46579193	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579194	46579279	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579280	46579381	1	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579280	46579381	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579382	46579526	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579527	46579669	1	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579527	46579669	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579670	46579805	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579806	46579861	1	+	1	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579806	46579861	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46579862	46579975	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46579976	46580649	0.71	+	2	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46579976	46580649	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46580650	46580738	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46580739	46580938	0.99	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46580739	46580938	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46580939	46581043	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46581044	46581317	0.97	+	1	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46581044	46581317	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46581318	46581462	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46581463	46581708	1	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46581463	46581708	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46581709	46581851	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46581852	46581961	1	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46581852	46581961	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46581962	46582047	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46582048	46582360	1	+	1	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46582048	46582360	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46582361	46582441	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46582442	46582930	0.95	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46582442	46582930	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	intron	46582931	46583023	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	CDS	46583024	46583107	0.79	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	exon	46583024	46583107	.	+	.	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
Phchi.S1	AUGUSTUS	stop_codon	46583108	46583110	.	+	0	transcript_id "Phchi.S1G740500.t2"; gene_id "Phchi.S1G740500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5849.t1 is derived from g3019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19328453	19329888	.	+	.	Phchi.S1G300800
Phchi.S1	AUGUSTUS	transcript	19328453	19329888	.	+	.	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	start_codon	19328453	19328455	.	+	0	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	CDS	19328453	19328471	1	+	0	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	exon	19328453	19328471	.	+	.	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	intron	19328472	19328542	.	+	.	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	CDS	19328543	19329888	0.76	+	2	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	exon	19328543	19329888	.	+	.	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
Phchi.S1	AUGUSTUS	stop_codon	19329889	19329891	.	+	0	transcript_id "Phchi.S1G300800.t1"; gene_id "Phchi.S1G300800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6544.t1 is derived from g3716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23565731	23568282	.	+	.	Phchi.S1G370300
Phchi.S1	AUGUSTUS	transcript	23565731	23568282	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	start_codon	23565731	23565733	.	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23565731	23565991	0.68	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23565731	23565991	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23565992	23566072	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23566073	23566154	1	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23566073	23566154	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23566155	23566294	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23566295	23566430	1	+	2	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23566295	23566430	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23566431	23566522	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23566523	23566795	0.95	+	1	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23566523	23566795	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23566796	23566894	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23566895	23567048	1	+	1	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23566895	23567048	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23567049	23567137	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23567138	23567377	1	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23567138	23567377	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23567378	23567462	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23567463	23567595	1	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23567463	23567595	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23567596	23567675	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23567676	23567857	1	+	2	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23567676	23567857	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23567858	23567950	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23567951	23568038	1	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23567951	23568038	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	intron	23568039	23568151	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	CDS	23568152	23568282	0.99	+	2	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	exon	23568152	23568282	.	+	.	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
Phchi.S1	AUGUSTUS	stop_codon	23568283	23568285	.	+	0	transcript_id "Phchi.S1G370300.t1"; gene_id "Phchi.S1G370300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2010.t1 is derived from g8930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4445523	4447256	.	-	.	Phchi.S5G061900
Phchi.S5	AUGUSTUS	transcript	4445523	4447256	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	stop_codon	4445520	4445522	.	-	0	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	CDS	4445523	4446193	0.99	-	2	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	exon	4445523	4446193	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	intron	4446194	4446289	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	CDS	4446290	4446559	1	-	2	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	exon	4446290	4446559	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	intron	4446560	4446649	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	CDS	4446650	4447055	1	-	0	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	exon	4446650	4447055	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	intron	4447056	4447187	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	CDS	4447188	4447256	0.71	-	0	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	exon	4447188	4447256	.	-	.	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
Phchi.S5	AUGUSTUS	start_codon	4447254	4447256	.	-	0	transcript_id "Phchi.S5G061900.t1"; gene_id "Phchi.S5G061900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11042.t1 is derived from g15092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3792508	3793230	.	+	.	Phchi.S4G062400
Phchi.S4	AUGUSTUS	transcript	3792508	3793230	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	start_codon	3792508	3792510	.	+	0	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	CDS	3792508	3792601	0.96	+	0	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	exon	3792508	3792601	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	intron	3792602	3792779	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	CDS	3792780	3792937	1	+	2	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	exon	3792780	3792937	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	intron	3792938	3793018	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	CDS	3793019	3793066	1	+	0	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	exon	3793019	3793066	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	intron	3793067	3793164	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	CDS	3793165	3793230	1	+	0	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	exon	3793165	3793230	.	+	.	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
Phchi.S4	AUGUSTUS	stop_codon	3793231	3793233	.	+	0	transcript_id "Phchi.S4G062400.t1"; gene_id "Phchi.S4G062400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg999.t1 is derived from g10782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6974543	6977139	.	-	.	Phchi.S6G095800
Phchi.S6	AUGUSTUS	transcript	6974543	6977139	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	stop_codon	6974540	6974542	.	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6974543	6974710	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6974543	6974710	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6974711	6974801	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6974802	6974990	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6974802	6974990	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6974991	6975089	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6975090	6975140	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6975090	6975140	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6975141	6975230	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6975231	6975350	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6975231	6975350	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6975351	6975430	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6975431	6975502	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6975431	6975502	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6975503	6975594	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6975595	6975687	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6975595	6975687	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6975688	6975778	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6975779	6975879	1	-	2	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6975779	6975879	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6975880	6975998	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6975999	6976079	1	-	2	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6975999	6976079	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6976080	6976227	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6976228	6976426	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6976228	6976426	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6976427	6976513	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6976514	6976609	1	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6976514	6976609	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6976610	6976716	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6976717	6976926	0.99	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6976717	6976926	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	intron	6976927	6977052	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	CDS	6977053	6977139	0.45	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	exon	6977053	6977139	.	-	.	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
Phchi.S6	AUGUSTUS	start_codon	6977137	6977139	.	-	0	transcript_id "Phchi.S6G095800.t1"; gene_id "Phchi.S6G095800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg19.t1 is derived from g16029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C11	AUGUSTUS	gene	39705	40522	.	-	.	Phchi.C11G000300
Phchi.C11	AUGUSTUS	transcript	39705	40522	.	-	.	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	stop_codon	39702	39704	.	-	0	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	CDS	39705	39999	0.71	-	1	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	exon	39705	39999	.	-	.	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	intron	40000	40268	.	-	.	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	CDS	40269	40522	0.47	-	0	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	exon	40269	40522	.	-	.	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
Phchi.C11	AUGUSTUS	start_codon	40520	40522	.	-	0	transcript_id "Phchi.C11G000300.t1"; gene_id "Phchi.C11G000300"
# This transcript jg12707.t2 is derived from g11172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12707.t3 is derived from g11172.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12708.t1 is derived from g11173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	674065	674462	.	-	.	Phchi.S3G002700
Phchi.S3	AUGUSTUS	transcript	674065	674462	.	-	.	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	stop_codon	674062	674064	.	-	0	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	CDS	674065	674240	0.9	-	2	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	exon	674065	674240	.	-	.	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	intron	674241	674395	.	-	.	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	CDS	674396	674462	0.97	-	0	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	exon	674396	674462	.	-	.	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
Phchi.S3	AUGUSTUS	start_codon	674460	674462	.	-	0	transcript_id "Phchi.S3G002700.t1"; gene_id "Phchi.S3G002700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8764.t1 is derived from g5939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37862593	37863246	.	+	.	Phchi.S1G592300
Phchi.S1	AUGUSTUS	transcript	37862593	37863246	.	+	.	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	start_codon	37862593	37862595	.	+	0	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	CDS	37862593	37862948	0.75	+	0	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	exon	37862593	37862948	.	+	.	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	intron	37862949	37863022	.	+	.	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	CDS	37863023	37863093	0.94	+	1	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	exon	37863023	37863093	.	+	.	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	intron	37863094	37863184	.	+	.	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	CDS	37863185	37863246	0.98	+	2	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	exon	37863185	37863246	.	+	.	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
Phchi.S1	AUGUSTUS	stop_codon	37863247	37863249	.	+	0	transcript_id "Phchi.S1G592300.t1"; gene_id "Phchi.S1G592300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6475.t1 is derived from g3647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23188775	23189878	.	-	.	Phchi.S1G363400
Phchi.S1	AUGUSTUS	transcript	23188775	23189878	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	stop_codon	23188772	23188774	.	-	0	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	CDS	23188775	23189089	1	-	0	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	exon	23188775	23189089	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	intron	23189090	23189180	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	CDS	23189181	23189343	1	-	1	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	exon	23189181	23189343	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	intron	23189344	23189434	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	CDS	23189435	23189538	0.53	-	0	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	exon	23189435	23189538	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	intron	23189539	23189644	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	CDS	23189645	23189878	0.98	-	0	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	exon	23189645	23189878	.	-	.	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
Phchi.S1	AUGUSTUS	start_codon	23189876	23189878	.	-	0	transcript_id "Phchi.S1G363400.t1"; gene_id "Phchi.S1G363400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14558.t1 is derived from g13026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13461961	13463519	.	+	.	Phchi.S3G187700
Phchi.S3	AUGUSTUS	transcript	13461961	13463519	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	start_codon	13461961	13461963	.	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13461961	13462047	0.98	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13461961	13462047	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13462048	13462164	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13462165	13462199	1	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13462165	13462199	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13462200	13462305	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13462306	13462439	1	+	1	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13462306	13462439	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13462440	13462531	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13462532	13462671	1	+	2	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13462532	13462671	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13462672	13462794	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13462795	13462863	1	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13462795	13462863	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13462864	13462953	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13462954	13463074	1	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13462954	13463074	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13463075	13463165	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13463166	13463228	1	+	2	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13463166	13463228	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13463229	13463312	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13463313	13463356	1	+	2	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13463313	13463356	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	intron	13463357	13463447	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	CDS	13463448	13463519	0.8	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	exon	13463448	13463519	.	+	.	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
Phchi.S3	AUGUSTUS	stop_codon	13463520	13463522	.	+	0	transcript_id "Phchi.S3G187700.t1"; gene_id "Phchi.S3G187700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15352.t1 is derived from g13820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18558595	18559758	.	+	.	Phchi.S3G267100
Phchi.S3	AUGUSTUS	transcript	18558595	18559758	.	+	.	transcript_id "Phchi.S3G267100.t1"; gene_id "Phchi.S3G267100"
Phchi.S3	AUGUSTUS	start_codon	18558595	18558597	.	+	0	transcript_id "Phchi.S3G267100.t1"; gene_id "Phchi.S3G267100"
Phchi.S3	AUGUSTUS	CDS	18558595	18559758	0.48	+	0	transcript_id "Phchi.S3G267100.t1"; gene_id "Phchi.S3G267100"
Phchi.S3	AUGUSTUS	exon	18558595	18559758	.	+	.	transcript_id "Phchi.S3G267100.t1"; gene_id "Phchi.S3G267100"
Phchi.S3	AUGUSTUS	stop_codon	18559759	18559761	.	+	0	transcript_id "Phchi.S3G267100.t1"; gene_id "Phchi.S3G267100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8419.t1 is derived from g5594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35870019	35871647	.	+	.	Phchi.S1G557800
Phchi.S1	AUGUSTUS	transcript	35870019	35871647	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	start_codon	35870019	35870021	.	+	0	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	CDS	35870019	35870130	0.51	+	0	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	exon	35870019	35870130	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	intron	35870131	35870395	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	CDS	35870396	35870628	1	+	2	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	exon	35870396	35870628	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	intron	35870629	35871015	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	CDS	35871016	35871127	1	+	0	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	exon	35871016	35871127	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	intron	35871128	35871498	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	CDS	35871499	35871647	1	+	2	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	exon	35871499	35871647	.	+	.	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
Phchi.S1	AUGUSTUS	stop_codon	35871648	35871650	.	+	0	transcript_id "Phchi.S1G557800.t1"; gene_id "Phchi.S1G557800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5010.t1 is derived from g2180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14019284	14023508	.	+	.	Phchi.S1G216900
Phchi.S1	AUGUSTUS	transcript	14019284	14023508	.	+	.	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	start_codon	14019284	14019286	.	+	0	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	CDS	14019284	14020784	0.99	+	0	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	exon	14019284	14020784	.	+	.	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	intron	14020785	14020897	.	+	.	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	CDS	14020898	14022288	0.99	+	2	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	exon	14020898	14022288	.	+	.	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	intron	14022289	14022410	.	+	.	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	CDS	14022411	14023508	1	+	0	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	exon	14022411	14023508	.	+	.	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
Phchi.S1	AUGUSTUS	stop_codon	14023509	14023511	.	+	0	transcript_id "Phchi.S1G216900.t1"; gene_id "Phchi.S1G216900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2124.t1 is derived from g9044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4971516	4972790	.	+	.	Phchi.S5G073300
Phchi.S5	AUGUSTUS	transcript	4971516	4972790	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	start_codon	4971516	4971518	.	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4971516	4971518	1	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4971516	4971518	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	intron	4971519	4971643	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4971644	4971680	1	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4971644	4971680	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	intron	4971681	4971795	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4971796	4971836	1	+	2	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4971796	4971836	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	intron	4971837	4971996	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4971997	4972227	1	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4971997	4972227	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	intron	4972228	4972376	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4972377	4972479	1	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4972377	4972479	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	intron	4972480	4972562	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4972563	4972630	1	+	2	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4972563	4972630	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	intron	4972631	4972724	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	CDS	4972725	4972790	1	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	exon	4972725	4972790	.	+	.	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
Phchi.S5	AUGUSTUS	stop_codon	4972791	4972793	.	+	0	transcript_id "Phchi.S5G073300.t1"; gene_id "Phchi.S5G073300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9458.t1 is derived from g6634.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41564219	41564864	.	-	.	Phchi.S1G661700
Phchi.S1	AUGUSTUS	transcript	41564388	41564864	.	-	.	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	stop_codon	41564385	41564387	.	-	0	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	CDS	41564388	41564435	0.97	-	0	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	exon	41564388	41564435	.	-	.	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	intron	41564436	41564663	.	-	.	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	CDS	41564664	41564864	0.91	-	0	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	exon	41564664	41564864	.	-	.	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	start_codon	41564862	41564864	.	-	0	transcript_id "Phchi.S1G661700.t1"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	transcript	41564219	41564864	.	-	.	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	stop_codon	41564216	41564218	.	-	0	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	CDS	41564219	41564435	0.41	-	1	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	exon	41564219	41564435	.	-	.	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	intron	41564436	41564512	.	-	.	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	CDS	41564513	41564538	1	-	0	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	exon	41564513	41564538	.	-	.	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	intron	41564539	41564663	.	-	.	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	CDS	41564664	41564864	0.97	-	0	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	exon	41564664	41564864	.	-	.	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
Phchi.S1	AUGUSTUS	start_codon	41564862	41564864	.	-	0	transcript_id "Phchi.S1G661700.t2"; gene_id "Phchi.S1G661700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14377.t1 is derived from g12844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12449209	12449806	.	+	.	Phchi.S3G169600
Phchi.S3	AUGUSTUS	transcript	12449209	12449806	.	+	.	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	start_codon	12449209	12449211	.	+	0	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	CDS	12449209	12449418	0.97	+	0	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	exon	12449209	12449418	.	+	.	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	intron	12449419	12449554	.	+	.	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	CDS	12449555	12449806	1	+	0	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	exon	12449555	12449806	.	+	.	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
Phchi.S3	AUGUSTUS	stop_codon	12449807	12449809	.	+	0	transcript_id "Phchi.S3G169600.t1"; gene_id "Phchi.S3G169600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4318.t1 is derived from g1487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9602682	9603341	.	+	.	Phchi.S1G147700
Phchi.S1	AUGUSTUS	transcript	9602682	9603341	.	+	.	transcript_id "Phchi.S1G147700.t1"; gene_id "Phchi.S1G147700"
Phchi.S1	AUGUSTUS	start_codon	9602682	9602684	.	+	0	transcript_id "Phchi.S1G147700.t1"; gene_id "Phchi.S1G147700"
Phchi.S1	AUGUSTUS	CDS	9602682	9603341	1	+	0	transcript_id "Phchi.S1G147700.t1"; gene_id "Phchi.S1G147700"
Phchi.S1	AUGUSTUS	exon	9602682	9603341	.	+	.	transcript_id "Phchi.S1G147700.t1"; gene_id "Phchi.S1G147700"
Phchi.S1	AUGUSTUS	stop_codon	9603342	9603344	.	+	0	transcript_id "Phchi.S1G147700.t1"; gene_id "Phchi.S1G147700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10622.t1 is derived from g14672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1278048	1280925	.	-	.	Phchi.S4G020400
Phchi.S4	AUGUSTUS	transcript	1278048	1280353	.	-	.	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	stop_codon	1278045	1278047	.	-	0	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1278048	1279096	0.71	-	2	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1278048	1279096	.	-	.	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	intron	1279097	1279197	.	-	.	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1279198	1280353	0.77	-	0	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1279198	1280353	.	-	.	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	start_codon	1280351	1280353	.	-	0	transcript_id "Phchi.S4G020400.t1"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	transcript	1278048	1280679	.	-	.	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	stop_codon	1278045	1278047	.	-	0	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1278048	1279096	0.78	-	2	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1278048	1279096	.	-	.	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	intron	1279097	1279197	.	-	.	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1279198	1280396	0.25	-	1	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1279198	1280396	.	-	.	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	intron	1280397	1280491	.	-	.	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1280492	1280679	0.27	-	0	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1280492	1280679	.	-	.	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	start_codon	1280677	1280679	.	-	0	transcript_id "Phchi.S4G020400.t2"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	transcript	1278048	1280925	.	-	.	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	stop_codon	1278045	1278047	.	-	0	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1278048	1279096	0.79	-	2	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1278048	1279096	.	-	.	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	intron	1279097	1279197	.	-	.	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1279198	1280396	0.23	-	1	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1279198	1280396	.	-	.	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	intron	1280397	1280491	.	-	.	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	CDS	1280492	1280925	0.25	-	0	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	exon	1280492	1280925	.	-	.	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
Phchi.S4	AUGUSTUS	start_codon	1280923	1280925	.	-	0	transcript_id "Phchi.S4G020400.t3"; gene_id "Phchi.S4G020400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9170.t1 is derived from g6345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40198364	40198990	.	+	.	Phchi.S1G632900
Phchi.S1	AUGUSTUS	transcript	40198364	40198990	.	+	.	transcript_id "Phchi.S1G632900.t1"; gene_id "Phchi.S1G632900"
Phchi.S1	AUGUSTUS	start_codon	40198364	40198366	.	+	0	transcript_id "Phchi.S1G632900.t1"; gene_id "Phchi.S1G632900"
Phchi.S1	AUGUSTUS	CDS	40198364	40198990	1	+	0	transcript_id "Phchi.S1G632900.t1"; gene_id "Phchi.S1G632900"
Phchi.S1	AUGUSTUS	exon	40198364	40198990	.	+	.	transcript_id "Phchi.S1G632900.t1"; gene_id "Phchi.S1G632900"
Phchi.S1	AUGUSTUS	stop_codon	40198991	40198993	.	+	0	transcript_id "Phchi.S1G632900.t1"; gene_id "Phchi.S1G632900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4348.t1 is derived from g1517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9907134	9910852	.	-	.	Phchi.S1G150700
Phchi.S1	AUGUSTUS	transcript	9907134	9910852	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	stop_codon	9907131	9907133	.	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9907134	9907983	0.99	-	1	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9907134	9907983	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9907984	9908074	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9908075	9908248	1	-	1	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9908075	9908248	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9908249	9908354	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9908355	9908397	1	-	2	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9908355	9908397	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9908398	9908567	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9908568	9908691	1	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9908568	9908691	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9908692	9908811	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9908812	9908904	1	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9908812	9908904	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9908905	9909005	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9909006	9909186	1	-	1	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9909006	9909186	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9909187	9909267	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9909268	9909374	1	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9909268	9909374	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9909375	9909631	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9909632	9909713	1	-	1	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9909632	9909713	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9909714	9909840	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9909841	9909878	1	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9909841	9909878	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9909879	9909958	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9909959	9910045	1	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9909959	9910045	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9910046	9910271	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9910272	9910382	1	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9910272	9910382	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	intron	9910383	9910579	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	CDS	9910580	9910852	0.73	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	exon	9910580	9910852	.	-	.	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
Phchi.S1	AUGUSTUS	start_codon	9910850	9910852	.	-	0	transcript_id "Phchi.S1G150700.t1"; gene_id "Phchi.S1G150700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8257.t1 is derived from g5432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34746403	34746725	.	+	.	Phchi.S1G541600
Phchi.S1	AUGUSTUS	transcript	34746403	34746725	.	+	.	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	start_codon	34746403	34746405	.	+	0	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	CDS	34746403	34746552	0.53	+	0	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	exon	34746403	34746552	.	+	.	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	intron	34746553	34746638	.	+	.	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	CDS	34746639	34746725	0.45	+	0	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	exon	34746639	34746725	.	+	.	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
Phchi.S1	AUGUSTUS	stop_codon	34746726	34746728	.	+	0	transcript_id "Phchi.S1G541600.t1"; gene_id "Phchi.S1G541600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15960.t1 is derived from g11143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	38025	42689	.	-	.	Phchi.C91G000700
Phchi.C91	AUGUSTUS	transcript	38025	42689	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	stop_codon	38022	38024	.	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	38025	38084	0.8	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	38025	38084	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	38085	38312	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	38313	38417	0.98	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	38313	38417	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	38418	38589	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	38590	38730	1	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	38590	38730	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	38731	38891	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	38892	39176	1	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	38892	39176	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	39177	39301	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	39302	39385	1	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	39302	39385	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	39386	39484	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	39485	39623	0.99	-	1	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	39485	39623	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	39624	39732	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	39733	39896	0.86	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	39733	39896	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	39897	40068	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	40069	40935	0.99	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	40069	40935	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	40936	41113	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	41114	42004	0.44	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	41114	42004	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	42005	42111	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	42112	42346	0.38	-	1	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	42112	42346	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	intron	42347	42453	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	CDS	42454	42689	0.95	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	exon	42454	42689	.	-	.	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
Phchi.C91	AUGUSTUS	start_codon	42687	42689	.	-	0	transcript_id "Phchi.C91G000700.t1"; gene_id "Phchi.C91G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3037.t1 is derived from g206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1264283	1264758	.	-	.	Phchi.S1G019600
Phchi.S1	AUGUSTUS	transcript	1264283	1264758	.	-	.	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	stop_codon	1264280	1264282	.	-	0	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	CDS	1264283	1264643	0.66	-	1	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	exon	1264283	1264643	.	-	.	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	intron	1264644	1264723	.	-	.	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	CDS	1264724	1264758	0.94	-	0	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	exon	1264724	1264758	.	-	.	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
Phchi.S1	AUGUSTUS	start_codon	1264756	1264758	.	-	0	transcript_id "Phchi.S1G019600.t1"; gene_id "Phchi.S1G019600"
# This transcript jg2246.t2 is derived from g9166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2247.t1 is derived from g9167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5648382	5650705	.	+	.	Phchi.S5G085600
Phchi.S5	AUGUSTUS	transcript	5648382	5650705	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	start_codon	5648382	5648384	.	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5648382	5648506	0.3	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5648382	5648506	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5648507	5648699	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5648700	5648817	0.99	+	1	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5648700	5648817	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5648818	5648923	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5648924	5649046	1	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5648924	5649046	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649047	5649159	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649160	5649294	1	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649160	5649294	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649295	5649443	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649444	5649542	1	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649444	5649542	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649543	5649640	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649641	5649756	0.61	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649641	5649756	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649757	5649836	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649837	5649943	0.84	+	1	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649837	5649943	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649944	5650025	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650026	5650249	0.9	+	2	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650026	5650249	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5650250	5650336	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650337	5650423	1	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650337	5650423	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5650424	5650514	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650515	5650612	1	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650515	5650612	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5650613	5650704	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650705	5650705	1	+	1	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650705	5650705	.	+	.	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	stop_codon	5650706	5650708	.	+	0	transcript_id "Phchi.S5G085600.t1"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	transcript	5648382	5650705	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	start_codon	5648382	5648384	.	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5648382	5648506	0.22	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5648382	5648506	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5648507	5648699	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5648700	5648806	0.41	+	1	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5648700	5648806	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5648807	5648923	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5648924	5649046	0.59	+	2	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5648924	5649046	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649047	5649241	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649242	5649294	0.78	+	2	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649242	5649294	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649295	5649443	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649444	5649542	1	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649444	5649542	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649543	5649640	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649641	5649756	0.66	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649641	5649756	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649757	5649836	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5649837	5649943	0.86	+	1	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5649837	5649943	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5649944	5650025	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650026	5650249	0.91	+	2	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650026	5650249	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5650250	5650336	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650337	5650423	1	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650337	5650423	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5650424	5650514	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650515	5650612	1	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650515	5650612	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	intron	5650613	5650704	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	CDS	5650705	5650705	1	+	1	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	exon	5650705	5650705	.	+	.	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
Phchi.S5	AUGUSTUS	stop_codon	5650706	5650708	.	+	0	transcript_id "Phchi.S5G085600.t2"; gene_id "Phchi.S5G085600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2388.t1 is derived from g9308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6456383	6458296	.	+	.	Phchi.S5G099700
Phchi.S5	AUGUSTUS	transcript	6456383	6458296	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	start_codon	6456383	6456385	.	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6456383	6456529	0.94	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6456383	6456529	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	intron	6456530	6456618	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6456619	6457290	1	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6456619	6457290	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	intron	6457291	6457422	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6457423	6457503	0.49	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6457423	6457503	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	intron	6457504	6457574	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6457575	6457589	0.49	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6457575	6457589	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	intron	6457590	6457714	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6457715	6457906	0.9	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6457715	6457906	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	intron	6457907	6458042	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6458043	6458111	0.89	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6458043	6458111	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	intron	6458112	6458215	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	CDS	6458216	6458296	0.89	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	exon	6458216	6458296	.	+	.	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
Phchi.S5	AUGUSTUS	stop_codon	6458297	6458299	.	+	0	transcript_id "Phchi.S5G099700.t1"; gene_id "Phchi.S5G099700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11580.t1 is derived from g15631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7190172	7191392	.	-	.	Phchi.S4G116200
Phchi.S4	AUGUSTUS	transcript	7190172	7191392	.	-	.	transcript_id "Phchi.S4G116200.t1"; gene_id "Phchi.S4G116200"
Phchi.S4	AUGUSTUS	stop_codon	7190169	7190171	.	-	0	transcript_id "Phchi.S4G116200.t1"; gene_id "Phchi.S4G116200"
Phchi.S4	AUGUSTUS	CDS	7190172	7191392	0.66	-	0	transcript_id "Phchi.S4G116200.t1"; gene_id "Phchi.S4G116200"
Phchi.S4	AUGUSTUS	exon	7190172	7191392	.	-	.	transcript_id "Phchi.S4G116200.t1"; gene_id "Phchi.S4G116200"
Phchi.S4	AUGUSTUS	start_codon	7191390	7191392	.	-	0	transcript_id "Phchi.S4G116200.t1"; gene_id "Phchi.S4G116200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10312.t1 is derived from g7488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47080459	47082216	.	+	.	Phchi.S1G747100
Phchi.S1	AUGUSTUS	transcript	47080459	47082216	.	+	.	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	start_codon	47080459	47080461	.	+	0	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	CDS	47080459	47080580	0.44	+	0	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	exon	47080459	47080580	.	+	.	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	intron	47080581	47080680	.	+	.	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	CDS	47080681	47081917	0.47	+	1	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	exon	47080681	47081917	.	+	.	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	intron	47081918	47082144	.	+	.	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	CDS	47082145	47082216	0.34	+	0	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	exon	47082145	47082216	.	+	.	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
Phchi.S1	AUGUSTUS	stop_codon	47082217	47082219	.	+	0	transcript_id "Phchi.S1G747100.t1"; gene_id "Phchi.S1G747100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11882.t1 is derived from g15934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8965886	8967675	.	+	.	Phchi.S4G146400
Phchi.S4	AUGUSTUS	transcript	8965886	8967675	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	start_codon	8965886	8965888	.	+	0	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	CDS	8965886	8966151	0.95	+	0	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	exon	8965886	8966151	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	intron	8966152	8966285	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	CDS	8966286	8966451	0.95	+	1	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	exon	8966286	8966451	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	intron	8966452	8966615	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	CDS	8966616	8966695	1	+	0	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	exon	8966616	8966695	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	intron	8966696	8966800	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	CDS	8966801	8967237	0.99	+	1	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	exon	8966801	8967237	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	intron	8967238	8967361	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	CDS	8967362	8967675	0.96	+	2	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	exon	8967362	8967675	.	+	.	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
Phchi.S4	AUGUSTUS	stop_codon	8967676	8967678	.	+	0	transcript_id "Phchi.S4G146400.t1"; gene_id "Phchi.S4G146400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14136.t1 is derived from g12603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11081681	11082975	.	-	.	Phchi.S3G145500
Phchi.S3	AUGUSTUS	transcript	11081681	11082975	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	stop_codon	11081678	11081680	.	-	0	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	CDS	11081681	11082000	0.96	-	2	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	exon	11081681	11082000	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	intron	11082001	11082090	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	CDS	11082091	11082142	1	-	0	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	exon	11082091	11082142	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	intron	11082143	11082226	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	CDS	11082227	11082391	0.99	-	0	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	exon	11082227	11082391	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	intron	11082392	11082470	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	CDS	11082471	11082723	0.37	-	1	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	exon	11082471	11082723	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	intron	11082724	11082805	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	CDS	11082806	11082975	0.37	-	0	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	exon	11082806	11082975	.	-	.	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
Phchi.S3	AUGUSTUS	start_codon	11082973	11082975	.	-	0	transcript_id "Phchi.S3G145500.t1"; gene_id "Phchi.S3G145500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2758.t1 is derived from g9678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8701091	8702235	.	+	.	Phchi.S5G136700
Phchi.S5	AUGUSTUS	transcript	8701091	8702235	.	+	.	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	start_codon	8701091	8701093	.	+	0	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	CDS	8701091	8701724	0.98	+	0	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	exon	8701091	8701724	.	+	.	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	intron	8701725	8701811	.	+	.	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	CDS	8701812	8701946	1	+	2	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	exon	8701812	8701946	.	+	.	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	intron	8701947	8702089	.	+	.	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	CDS	8702090	8702235	0.98	+	2	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	exon	8702090	8702235	.	+	.	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
Phchi.S5	AUGUSTUS	stop_codon	8702236	8702238	.	+	0	transcript_id "Phchi.S5G136700.t1"; gene_id "Phchi.S5G136700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15132.t1 is derived from g13600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17204381	17206104	.	+	.	Phchi.S3G245100
Phchi.S3	AUGUSTUS	transcript	17204381	17206104	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	start_codon	17204381	17204383	.	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17204381	17204407	0.44	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17204381	17204407	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17204408	17204507	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17204508	17204513	0.8	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17204508	17204513	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17204514	17204680	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17204681	17204721	0.8	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17204681	17204721	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17204722	17204825	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17204826	17205050	0.77	+	1	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17204826	17205050	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17205051	17205178	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17205179	17205275	1	+	1	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17205179	17205275	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17205276	17205452	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17205453	17205542	1	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17205453	17205542	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17205543	17205624	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17205625	17205690	1	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17205625	17205690	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17205691	17205773	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17205774	17205842	1	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17205774	17205842	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	intron	17205843	17205969	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	CDS	17205970	17206104	1	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	exon	17205970	17206104	.	+	.	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
Phchi.S3	AUGUSTUS	stop_codon	17206105	17206107	.	+	0	transcript_id "Phchi.S3G245100.t1"; gene_id "Phchi.S3G245100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6732.t1 is derived from g3904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24779386	24781305	.	+	.	Phchi.S1G389100
Phchi.S1	AUGUSTUS	transcript	24779386	24781305	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	start_codon	24779386	24779388	.	+	0	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	CDS	24779386	24780401	0.09	+	0	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	exon	24779386	24780401	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	intron	24780402	24780591	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	CDS	24780592	24780761	0.71	+	1	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	exon	24780592	24780761	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	intron	24780762	24780835	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	CDS	24780836	24781007	0.76	+	2	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	exon	24780836	24781007	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	intron	24781008	24781223	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	CDS	24781224	24781305	0.6	+	1	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	exon	24781224	24781305	.	+	.	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
Phchi.S1	AUGUSTUS	stop_codon	24781306	24781308	.	+	0	transcript_id "Phchi.S1G389100.t1"; gene_id "Phchi.S1G389100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10299.t1 is derived from g7475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46993531	46997251	.	+	.	Phchi.S1G745800
Phchi.S1	AUGUSTUS	transcript	46993531	46997251	.	+	.	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	start_codon	46993531	46993533	.	+	0	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	CDS	46993531	46995889	0.78	+	0	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	exon	46993531	46995889	.	+	.	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	intron	46995890	46996026	.	+	.	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	CDS	46996027	46996283	0.59	+	2	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	exon	46996027	46996283	.	+	.	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	intron	46996284	46996396	.	+	.	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	CDS	46996397	46997251	0.59	+	0	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	exon	46996397	46997251	.	+	.	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
Phchi.S1	AUGUSTUS	stop_codon	46997252	46997254	.	+	0	transcript_id "Phchi.S1G745800.t1"; gene_id "Phchi.S1G745800"
# This transcript jg10716.t2 is derived from g14766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10717.t1 is derived from g14767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1741748	1742474	.	+	.	Phchi.S4G029900
Phchi.S4	AUGUSTUS	transcript	1741748	1742474	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	start_codon	1741748	1741750	.	+	0	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	CDS	1741748	1741880	0.74	+	0	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	exon	1741748	1741880	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	intron	1741881	1741967	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	CDS	1741968	1742037	1	+	2	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	exon	1741968	1742037	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	intron	1742038	1742117	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	CDS	1742118	1742223	1	+	1	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	exon	1742118	1742223	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	intron	1742224	1742312	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	CDS	1742313	1742474	0.87	+	0	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	exon	1742313	1742474	.	+	.	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
Phchi.S4	AUGUSTUS	stop_codon	1742475	1742477	.	+	0	transcript_id "Phchi.S4G029900.t1"; gene_id "Phchi.S4G029900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9503.t1 is derived from g6679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42081570	42084421	.	+	.	Phchi.S1G666200
Phchi.S1	AUGUSTUS	transcript	42081570	42084421	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	start_codon	42081570	42081572	.	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42081570	42081664	1	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42081570	42081664	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42081665	42081758	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42081759	42081809	1	+	1	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42081759	42081809	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42081810	42081988	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42081989	42082174	0.95	+	1	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42081989	42082174	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082175	42082278	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082279	42082354	1	+	1	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082279	42082354	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082355	42082467	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082468	42082515	1	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082468	42082515	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082516	42082609	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082610	42082654	1	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082610	42082654	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082655	42082728	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082729	42082828	1	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082729	42082828	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082829	42083002	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083003	42083054	1	+	2	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083003	42083054	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083055	42083177	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083178	42083219	1	+	1	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083178	42083219	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083220	42083326	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083327	42083388	1	+	1	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083327	42083388	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083389	42083527	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083528	42083626	1	+	2	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083528	42083626	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083627	42083708	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083709	42083782	1	+	2	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083709	42083782	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083783	42083866	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083867	42083936	1	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083867	42083936	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083937	42084022	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42084023	42084088	1	+	2	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42084023	42084088	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42084089	42084171	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42084172	42084260	1	+	2	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42084172	42084260	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42084261	42084349	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42084350	42084421	1	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42084350	42084421	.	+	.	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	stop_codon	42084422	42084424	.	+	0	transcript_id "Phchi.S1G666200.t1"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	transcript	42081641	42084421	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	start_codon	42081641	42081643	.	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42081641	42081664	0.32	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42081641	42081664	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42081665	42081758	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42081759	42081809	0.71	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42081759	42081809	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42081810	42081995	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42081996	42082174	0.71	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42081996	42082174	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082175	42082278	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082279	42082354	1	+	1	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082279	42082354	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082355	42082467	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082468	42082515	1	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082468	42082515	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082516	42082609	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082610	42082654	1	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082610	42082654	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082655	42082728	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42082729	42082828	1	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42082729	42082828	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42082829	42083002	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083003	42083054	1	+	2	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083003	42083054	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083055	42083177	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083178	42083219	1	+	1	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083178	42083219	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083220	42083326	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083327	42083388	1	+	1	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083327	42083388	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083389	42083527	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083528	42083626	1	+	2	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083528	42083626	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083627	42083708	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083709	42083782	1	+	2	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083709	42083782	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083783	42083866	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42083867	42083936	1	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42083867	42083936	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42083937	42084022	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42084023	42084088	1	+	2	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42084023	42084088	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42084089	42084171	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42084172	42084260	1	+	2	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42084172	42084260	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	intron	42084261	42084349	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	CDS	42084350	42084421	1	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	exon	42084350	42084421	.	+	.	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
Phchi.S1	AUGUSTUS	stop_codon	42084422	42084424	.	+	0	transcript_id "Phchi.S1G666200.t2"; gene_id "Phchi.S1G666200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8725.t1 is derived from g5900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37684160	37685932	.	+	.	Phchi.S1G588400
Phchi.S1	AUGUSTUS	transcript	37684160	37685932	.	+	.	transcript_id "Phchi.S1G588400.t1"; gene_id "Phchi.S1G588400"
Phchi.S1	AUGUSTUS	start_codon	37684160	37684162	.	+	0	transcript_id "Phchi.S1G588400.t1"; gene_id "Phchi.S1G588400"
Phchi.S1	AUGUSTUS	CDS	37684160	37685932	0.85	+	0	transcript_id "Phchi.S1G588400.t1"; gene_id "Phchi.S1G588400"
Phchi.S1	AUGUSTUS	exon	37684160	37685932	.	+	.	transcript_id "Phchi.S1G588400.t1"; gene_id "Phchi.S1G588400"
Phchi.S1	AUGUSTUS	stop_codon	37685933	37685935	.	+	0	transcript_id "Phchi.S1G588400.t1"; gene_id "Phchi.S1G588400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13709.t1 is derived from g12176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8307265	8310897	.	-	.	Phchi.S3G102800
Phchi.S3	AUGUSTUS	transcript	8307265	8310897	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	stop_codon	8307262	8307264	.	-	0	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	CDS	8307265	8308903	0.31	-	1	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	exon	8307265	8308903	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	intron	8308904	8309001	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	CDS	8309002	8309020	0.46	-	2	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	exon	8309002	8309020	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	intron	8309021	8309234	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	CDS	8309235	8310014	0.77	-	2	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	exon	8309235	8310014	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	intron	8310015	8310163	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	CDS	8310164	8310338	0.99	-	0	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	exon	8310164	8310338	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	intron	8310339	8310433	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	CDS	8310434	8310589	0.91	-	0	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	exon	8310434	8310589	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	intron	8310590	8310744	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	CDS	8310745	8310897	0.92	-	0	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	exon	8310745	8310897	.	-	.	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
Phchi.S3	AUGUSTUS	start_codon	8310895	8310897	.	-	0	transcript_id "Phchi.S3G102800.t1"; gene_id "Phchi.S3G102800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14454.t1 is derived from g12922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12939471	12943045	.	+	.	Phchi.S3G177300
Phchi.S3	AUGUSTUS	transcript	12939471	12943045	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	start_codon	12939471	12939473	.	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12939471	12939571	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12939471	12939571	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12939572	12939868	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12939869	12939914	1	+	1	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12939869	12939914	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12939915	12940019	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12940020	12940195	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12940020	12940195	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12940196	12940275	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12940276	12940393	1	+	1	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12940276	12940393	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12940394	12940514	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12940515	12940597	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12940515	12940597	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12940598	12940719	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12940720	12940779	1	+	1	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12940720	12940779	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12940780	12940903	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12940904	12940984	0.58	+	1	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12940904	12940984	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12940985	12941079	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12941080	12941169	0.96	+	1	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12941080	12941169	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12941170	12941335	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12941336	12941432	1	+	1	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12941336	12941432	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12941433	12941632	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12941633	12941683	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12941633	12941683	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12941684	12941776	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12941777	12941857	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12941777	12941857	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12941858	12941975	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12941976	12942047	0.99	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12941976	12942047	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12942048	12942158	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12942159	12942221	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12942159	12942221	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12942222	12942312	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12942313	12942465	0.94	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12942313	12942465	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12942466	12942570	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12942571	12942628	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12942571	12942628	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12942629	12942757	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12942758	12942831	1	+	2	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12942758	12942831	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	intron	12942832	12942961	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	CDS	12942962	12943045	1	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	exon	12942962	12943045	.	+	.	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
Phchi.S3	AUGUSTUS	stop_codon	12943046	12943048	.	+	0	transcript_id "Phchi.S3G177300.t1"; gene_id "Phchi.S3G177300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1911.t1 is derived from g8831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3825496	3828310	.	-	.	Phchi.S5G052000
Phchi.S5	AUGUSTUS	transcript	3825496	3828310	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	stop_codon	3825493	3825495	.	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3825496	3825803	0.87	-	2	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3825496	3825803	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3825804	3825904	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3825905	3826027	0.87	-	2	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3825905	3826027	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3826028	3826116	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3826117	3826468	1	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3826117	3826468	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3826469	3826546	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3826547	3826707	1	-	2	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3826547	3826707	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3826708	3826785	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3826786	3826912	0.81	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3826786	3826912	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3826913	3827028	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3827029	3827193	0.92	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3827029	3827193	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3827194	3827288	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3827289	3827378	1	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3827289	3827378	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3827379	3827472	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3827473	3827673	0.96	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3827473	3827673	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3827674	3827775	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3827776	3827988	0.96	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3827776	3827988	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	intron	3827989	3828079	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	CDS	3828080	3828310	0.84	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	exon	3828080	3828310	.	-	.	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
Phchi.S5	AUGUSTUS	start_codon	3828308	3828310	.	-	0	transcript_id "Phchi.S5G052000.t1"; gene_id "Phchi.S5G052000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9734.t1 is derived from g6910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43446881	43448587	.	+	.	Phchi.S1G689300
Phchi.S1	AUGUSTUS	transcript	43446881	43448587	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	start_codon	43446881	43446883	.	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43446881	43447342	0.58	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43446881	43447342	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	intron	43447343	43447470	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43447471	43447701	1	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43447471	43447701	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	intron	43447702	43447782	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43447783	43447794	0.39	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43447783	43447794	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	intron	43447795	43447913	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43447914	43447940	0.4	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43447914	43447940	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	intron	43447941	43448032	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43448033	43448185	1	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43448033	43448185	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	intron	43448186	43448270	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43448271	43448354	0.97	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43448271	43448354	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	intron	43448355	43448455	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	CDS	43448456	43448587	0.95	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	exon	43448456	43448587	.	+	.	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
Phchi.S1	AUGUSTUS	stop_codon	43448588	43448590	.	+	0	transcript_id "Phchi.S1G689300.t1"; gene_id "Phchi.S1G689300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3506.t1 is derived from g675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4123973	4124320	.	+	.	Phchi.S1G066500
Phchi.S1	AUGUSTUS	transcript	4123973	4124320	.	+	.	transcript_id "Phchi.S1G066500.t1"; gene_id "Phchi.S1G066500"
Phchi.S1	AUGUSTUS	start_codon	4123973	4123975	.	+	0	transcript_id "Phchi.S1G066500.t1"; gene_id "Phchi.S1G066500"
Phchi.S1	AUGUSTUS	CDS	4123973	4124320	0.49	+	0	transcript_id "Phchi.S1G066500.t1"; gene_id "Phchi.S1G066500"
Phchi.S1	AUGUSTUS	exon	4123973	4124320	.	+	.	transcript_id "Phchi.S1G066500.t1"; gene_id "Phchi.S1G066500"
Phchi.S1	AUGUSTUS	stop_codon	4124321	4124323	.	+	0	transcript_id "Phchi.S1G066500.t1"; gene_id "Phchi.S1G066500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15004.t1 is derived from g13472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16312969	16313328	.	-	.	Phchi.S3G232300
Phchi.S3	AUGUSTUS	transcript	16312969	16313328	.	-	.	transcript_id "Phchi.S3G232300.t1"; gene_id "Phchi.S3G232300"
Phchi.S3	AUGUSTUS	stop_codon	16312966	16312968	.	-	0	transcript_id "Phchi.S3G232300.t1"; gene_id "Phchi.S3G232300"
Phchi.S3	AUGUSTUS	CDS	16312969	16313328	0.94	-	0	transcript_id "Phchi.S3G232300.t1"; gene_id "Phchi.S3G232300"
Phchi.S3	AUGUSTUS	exon	16312969	16313328	.	-	.	transcript_id "Phchi.S3G232300.t1"; gene_id "Phchi.S3G232300"
Phchi.S3	AUGUSTUS	start_codon	16313326	16313328	.	-	0	transcript_id "Phchi.S3G232300.t1"; gene_id "Phchi.S3G232300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6283.t1 is derived from g3455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22079419	22081674	.	-	.	Phchi.S1G344200
Phchi.S1	AUGUSTUS	transcript	22079419	22081674	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	stop_codon	22079416	22079418	.	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22079419	22079590	1	-	1	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22079419	22079590	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22079591	22079745	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22079746	22079789	1	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22079746	22079789	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22079790	22079915	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22079916	22079984	1	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22079916	22079984	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22079985	22080076	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22080077	22080136	1	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22080077	22080136	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22080137	22080249	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22080250	22080630	0.8	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22080250	22080630	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22080631	22080725	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22080726	22080744	0.97	-	1	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22080726	22080744	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22080745	22080896	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22080897	22081068	1	-	2	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22080897	22081068	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	intron	22081069	22081442	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	CDS	22081443	22081674	0.33	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	exon	22081443	22081674	.	-	.	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
Phchi.S1	AUGUSTUS	start_codon	22081672	22081674	.	-	0	transcript_id "Phchi.S1G344200.t1"; gene_id "Phchi.S1G344200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12231.t1 is derived from g7907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6875743	6879498	.	-	.	Phchi.S2G031100
Phchi.S2	AUGUSTUS	transcript	6875743	6879498	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	stop_codon	6875740	6875742	.	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6875743	6875807	0.95	-	2	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6875743	6875807	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6875808	6876132	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6876133	6876460	1	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6876133	6876460	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6876461	6876690	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6876691	6876772	1	-	1	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6876691	6876772	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6876773	6877180	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6877181	6877311	1	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6877181	6877311	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6877312	6877390	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6877391	6877489	1	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6877391	6877489	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6877490	6877652	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6877653	6877808	1	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6877653	6877808	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6877809	6878071	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6878072	6878146	1	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6878072	6878146	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6878147	6878316	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6878317	6878499	1	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6878317	6878499	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6878500	6878636	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6878637	6878787	1	-	1	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6878637	6878787	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	intron	6878788	6879409	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	CDS	6879410	6879498	0.85	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	exon	6879410	6879498	.	-	.	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
Phchi.S2	AUGUSTUS	start_codon	6879496	6879498	.	-	0	transcript_id "Phchi.S2G031100.t1"; gene_id "Phchi.S2G031100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2553.t1 is derived from g9473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7316094	7317011	.	-	.	Phchi.S5G116200
Phchi.S5	AUGUSTUS	transcript	7316094	7317011	.	-	.	transcript_id "Phchi.S5G116200.t1"; gene_id "Phchi.S5G116200"
Phchi.S5	AUGUSTUS	stop_codon	7316091	7316093	.	-	0	transcript_id "Phchi.S5G116200.t1"; gene_id "Phchi.S5G116200"
Phchi.S5	AUGUSTUS	CDS	7316094	7317011	0.99	-	0	transcript_id "Phchi.S5G116200.t1"; gene_id "Phchi.S5G116200"
Phchi.S5	AUGUSTUS	exon	7316094	7317011	.	-	.	transcript_id "Phchi.S5G116200.t1"; gene_id "Phchi.S5G116200"
Phchi.S5	AUGUSTUS	start_codon	7317009	7317011	.	-	0	transcript_id "Phchi.S5G116200.t1"; gene_id "Phchi.S5G116200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2381.t1 is derived from g9301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6426385	6427182	.	-	.	Phchi.S5G099000
Phchi.S5	AUGUSTUS	transcript	6426385	6427182	.	-	.	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	stop_codon	6426382	6426384	.	-	0	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	CDS	6426385	6426408	1	-	0	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	exon	6426385	6426408	.	-	.	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	intron	6426409	6426740	.	-	.	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	CDS	6426741	6426973	1	-	2	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	exon	6426741	6426973	.	-	.	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	intron	6426974	6427094	.	-	.	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	CDS	6427095	6427182	1	-	0	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	exon	6427095	6427182	.	-	.	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
Phchi.S5	AUGUSTUS	start_codon	6427180	6427182	.	-	0	transcript_id "Phchi.S5G099000.t1"; gene_id "Phchi.S5G099000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15891.t1 is derived from g14361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22045055	22046686	.	-	.	Phchi.S3G321000
Phchi.S3	AUGUSTUS	transcript	22045055	22046686	.	-	.	transcript_id "Phchi.S3G321000.t1"; gene_id "Phchi.S3G321000"
Phchi.S3	AUGUSTUS	stop_codon	22045052	22045054	.	-	0	transcript_id "Phchi.S3G321000.t1"; gene_id "Phchi.S3G321000"
Phchi.S3	AUGUSTUS	CDS	22045055	22046686	0.68	-	0	transcript_id "Phchi.S3G321000.t1"; gene_id "Phchi.S3G321000"
Phchi.S3	AUGUSTUS	exon	22045055	22046686	.	-	.	transcript_id "Phchi.S3G321000.t1"; gene_id "Phchi.S3G321000"
Phchi.S3	AUGUSTUS	start_codon	22046684	22046686	.	-	0	transcript_id "Phchi.S3G321000.t1"; gene_id "Phchi.S3G321000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10422.t1 is derived from g14471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	149993	150557	.	-	.	Phchi.S4G000400
Phchi.S4	AUGUSTUS	transcript	149993	150557	.	-	.	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	stop_codon	149990	149992	.	-	0	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	CDS	149993	150122	0.55	-	1	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	exon	149993	150122	.	-	.	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	intron	150123	150216	.	-	.	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	CDS	150217	150557	0.42	-	0	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	exon	150217	150557	.	-	.	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
Phchi.S4	AUGUSTUS	start_codon	150555	150557	.	-	0	transcript_id "Phchi.S4G000400.t1"; gene_id "Phchi.S4G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5803.t1 is derived from g2973.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19027859	19028514	.	-	.	Phchi.S1G296200
Phchi.S1	AUGUSTUS	transcript	19027859	19028514	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	stop_codon	19027856	19027858	.	-	0	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19027859	19028020	0.85	-	0	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19027859	19028020	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	intron	19028021	19028100	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19028101	19028240	0.97	-	2	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19028101	19028240	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	intron	19028241	19028308	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19028309	19028410	1	-	2	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19028309	19028410	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	intron	19028411	19028495	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19028496	19028514	0.99	-	0	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19028496	19028514	.	-	.	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	start_codon	19028512	19028514	.	-	0	transcript_id "Phchi.S1G296200.t1"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	transcript	19027859	19028514	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	stop_codon	19027856	19027858	.	-	0	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19027859	19028020	0.76	-	0	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19027859	19028020	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	intron	19028021	19028100	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19028101	19028234	1	-	2	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19028101	19028234	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	intron	19028235	19028308	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19028309	19028410	1	-	2	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19028309	19028410	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	intron	19028411	19028495	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	CDS	19028496	19028514	1	-	0	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	exon	19028496	19028514	.	-	.	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
Phchi.S1	AUGUSTUS	start_codon	19028512	19028514	.	-	0	transcript_id "Phchi.S1G296200.t2"; gene_id "Phchi.S1G296200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3061.t1 is derived from g230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1396847	1399720	.	+	.	Phchi.S1G022000
Phchi.S1	AUGUSTUS	transcript	1396847	1399720	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	start_codon	1396847	1396849	.	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	CDS	1396847	1396987	0.78	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	exon	1396847	1396987	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	intron	1396988	1397139	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	CDS	1397140	1397454	0.95	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	exon	1397140	1397454	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	intron	1397455	1397568	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	CDS	1397569	1397913	0.89	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	exon	1397569	1397913	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	intron	1397914	1398128	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	CDS	1398129	1398260	1	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	exon	1398129	1398260	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	intron	1398261	1398378	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	CDS	1398379	1399268	1	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	exon	1398379	1399268	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	intron	1399269	1399524	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	CDS	1399525	1399720	0.85	+	1	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	exon	1399525	1399720	.	+	.	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
Phchi.S1	AUGUSTUS	stop_codon	1399721	1399723	.	+	0	transcript_id "Phchi.S1G022000.t1"; gene_id "Phchi.S1G022000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15727.t1 is derived from g14197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20908647	20909982	.	+	.	Phchi.S3G304600
Phchi.S3	AUGUSTUS	transcript	20908647	20909982	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	start_codon	20908647	20908649	.	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	CDS	20908647	20908705	0.51	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	exon	20908647	20908705	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	intron	20908706	20908863	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	CDS	20908864	20908969	1	+	1	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	exon	20908864	20908969	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	intron	20908970	20909077	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	CDS	20909078	20909215	0.95	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	exon	20909078	20909215	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	intron	20909216	20909289	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	CDS	20909290	20909475	1	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	exon	20909290	20909475	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	intron	20909476	20909588	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	CDS	20909589	20909789	1	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	exon	20909589	20909789	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	intron	20909790	20909883	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	CDS	20909884	20909982	0.99	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	exon	20909884	20909982	.	+	.	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
Phchi.S3	AUGUSTUS	stop_codon	20909983	20909985	.	+	0	transcript_id "Phchi.S3G304600.t1"; gene_id "Phchi.S3G304600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8946.t1 is derived from g6121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38796336	38800235	.	+	.	Phchi.S1G610500
Phchi.S1	AUGUSTUS	transcript	38796336	38800235	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	start_codon	38796336	38796338	.	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38796336	38796482	0.43	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38796336	38796482	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38796483	38796667	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38796668	38796850	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38796668	38796850	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38796851	38796927	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38796928	38797020	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38796928	38797020	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38797021	38797118	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38797119	38797271	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38797119	38797271	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38797272	38797352	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38797353	38797444	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38797353	38797444	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38797445	38797538	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38797539	38797680	1	+	1	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38797539	38797680	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38797681	38797786	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38797787	38797894	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38797787	38797894	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38797895	38798044	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38798045	38798130	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38798045	38798130	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38798131	38798221	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38798222	38798293	1	+	1	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38798222	38798293	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38798294	38798380	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38798381	38798513	0.94	+	1	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38798381	38798513	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38798514	38798619	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38798620	38798706	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38798620	38798706	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38798707	38798849	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38798850	38798942	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38798850	38798942	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38798943	38799039	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38799040	38799198	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38799040	38799198	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38799199	38799294	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38799295	38799378	0.52	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38799295	38799378	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38799379	38799458	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38799459	38799538	0.52	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38799459	38799538	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38799539	38799696	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38799697	38799717	0.52	+	1	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38799697	38799717	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38799718	38799780	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38799781	38799898	1	+	1	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38799781	38799898	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	intron	38799899	38799980	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	CDS	38799981	38800235	1	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	exon	38799981	38800235	.	+	.	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
Phchi.S1	AUGUSTUS	stop_codon	38800236	38800238	.	+	0	transcript_id "Phchi.S1G610500.t1"; gene_id "Phchi.S1G610500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14252.t1 is derived from g12719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11757921	11764806	.	-	.	Phchi.S3G157100
Phchi.S3	AUGUSTUS	transcript	11757921	11764806	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	stop_codon	11757918	11757920	.	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11757921	11758052	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11757921	11758052	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11758053	11758368	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11758369	11758467	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11758369	11758467	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11758468	11758579	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11758580	11758677	1	-	2	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11758580	11758677	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11758678	11758751	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11758752	11758842	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11758752	11758842	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11758843	11758944	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11758945	11759176	0.96	-	1	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11758945	11759176	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11759177	11759309	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11759310	11759362	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11759310	11759362	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11759363	11759460	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11759461	11759940	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11759461	11759940	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11759941	11760015	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11760016	11760177	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11760016	11760177	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11760178	11760267	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11760268	11760415	1	-	1	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11760268	11760415	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11760416	11760518	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11760519	11760658	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11760519	11760658	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11760659	11760876	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11760877	11761133	1	-	2	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11760877	11761133	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11761134	11761210	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11761211	11761293	0.97	-	1	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11761211	11761293	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11761294	11761395	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11761396	11761532	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11761396	11761532	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11761533	11761631	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11761632	11761697	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11761632	11761697	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11761698	11761797	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11761798	11762001	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11761798	11762001	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11762002	11762085	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11762086	11762249	1	-	2	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11762086	11762249	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11762250	11762361	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11762362	11762595	1	-	2	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11762362	11762595	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11762596	11762676	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11762677	11762777	1	-	1	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11762677	11762777	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11762778	11762864	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11762865	11763061	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11762865	11763061	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11763062	11763138	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11763139	11763292	0.94	-	1	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11763139	11763292	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11763293	11763408	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11763409	11763835	0.83	-	2	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11763409	11763835	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	intron	11763836	11764163	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	CDS	11764164	11764806	1	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	exon	11764164	11764806	.	-	.	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
Phchi.S3	AUGUSTUS	start_codon	11764804	11764806	.	-	0	transcript_id "Phchi.S3G157100.t1"; gene_id "Phchi.S3G157100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10083.t1 is derived from g7259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45662026	45662877	.	-	.	Phchi.S1G724200
Phchi.S1	AUGUSTUS	transcript	45662026	45662877	.	-	.	transcript_id "Phchi.S1G724200.t1"; gene_id "Phchi.S1G724200"
Phchi.S1	AUGUSTUS	stop_codon	45662023	45662025	.	-	0	transcript_id "Phchi.S1G724200.t1"; gene_id "Phchi.S1G724200"
Phchi.S1	AUGUSTUS	CDS	45662026	45662877	0.96	-	0	transcript_id "Phchi.S1G724200.t1"; gene_id "Phchi.S1G724200"
Phchi.S1	AUGUSTUS	exon	45662026	45662877	.	-	.	transcript_id "Phchi.S1G724200.t1"; gene_id "Phchi.S1G724200"
Phchi.S1	AUGUSTUS	start_codon	45662875	45662877	.	-	0	transcript_id "Phchi.S1G724200.t1"; gene_id "Phchi.S1G724200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13632.t1 is derived from g12099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7839053	7840267	.	-	.	Phchi.S3G095100
Phchi.S3	AUGUSTUS	transcript	7839053	7840267	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	stop_codon	7839050	7839052	.	-	0	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	CDS	7839053	7839246	0.51	-	2	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	exon	7839053	7839246	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	intron	7839247	7839439	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	CDS	7839440	7839584	1	-	0	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	exon	7839440	7839584	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	intron	7839585	7839717	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	CDS	7839718	7839957	0.99	-	0	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	exon	7839718	7839957	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	intron	7839958	7840114	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	CDS	7840115	7840267	0.99	-	0	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	exon	7840115	7840267	.	-	.	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
Phchi.S3	AUGUSTUS	start_codon	7840265	7840267	.	-	0	transcript_id "Phchi.S3G095100.t1"; gene_id "Phchi.S3G095100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg925.t1 is derived from g10707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6473930	6475672	.	-	.	Phchi.S6G088400
Phchi.S6	AUGUSTUS	transcript	6473930	6475672	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	stop_codon	6473927	6473929	.	-	0	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	CDS	6473930	6474330	0.97	-	2	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	exon	6473930	6474330	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	intron	6474331	6474455	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	CDS	6474456	6474708	0.99	-	0	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	exon	6474456	6474708	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	intron	6474709	6474806	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	CDS	6474807	6475012	1	-	2	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	exon	6474807	6475012	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	intron	6475013	6475092	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	CDS	6475093	6475672	0.84	-	0	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	exon	6475093	6475672	.	-	.	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
Phchi.S6	AUGUSTUS	start_codon	6475670	6475672	.	-	0	transcript_id "Phchi.S6G088400.t1"; gene_id "Phchi.S6G088400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2986.t1 is derived from g155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	991819	995371	.	+	.	Phchi.S1G014500
Phchi.S1	AUGUSTUS	transcript	991819	995371	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	start_codon	991819	991821	.	+	0	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	991819	991862	0.71	+	0	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	991819	991862	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	991863	991961	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	991962	992061	0.91	+	1	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	991962	992061	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	992062	992245	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	992246	992623	0.59	+	0	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	992246	992623	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	992624	992707	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	992708	992973	1	+	0	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	992708	992973	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	992974	993135	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	993136	993204	1	+	1	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	993136	993204	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	993205	993291	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	993292	993384	0.82	+	1	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	993292	993384	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	993385	993463	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	993464	993516	1	+	1	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	993464	993516	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	993517	993610	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	993611	993686	1	+	2	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	993611	993686	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	intron	993687	993771	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	CDS	993772	995371	0.78	+	1	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	exon	993772	995371	.	+	.	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
Phchi.S1	AUGUSTUS	stop_codon	995372	995374	.	+	0	transcript_id "Phchi.S1G014500.t1"; gene_id "Phchi.S1G014500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15469.t1 is derived from g13937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19344308	19344796	.	+	.	Phchi.S3G278800
Phchi.S3	AUGUSTUS	transcript	19344308	19344796	.	+	.	transcript_id "Phchi.S3G278800.t1"; gene_id "Phchi.S3G278800"
Phchi.S3	AUGUSTUS	start_codon	19344308	19344310	.	+	0	transcript_id "Phchi.S3G278800.t1"; gene_id "Phchi.S3G278800"
Phchi.S3	AUGUSTUS	CDS	19344308	19344796	0.4	+	0	transcript_id "Phchi.S3G278800.t1"; gene_id "Phchi.S3G278800"
Phchi.S3	AUGUSTUS	exon	19344308	19344796	.	+	.	transcript_id "Phchi.S3G278800.t1"; gene_id "Phchi.S3G278800"
Phchi.S3	AUGUSTUS	stop_codon	19344797	19344799	.	+	0	transcript_id "Phchi.S3G278800.t1"; gene_id "Phchi.S3G278800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11866.t1 is derived from g15918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8859541	8859951	.	-	.	Phchi.S4G144800
Phchi.S4	AUGUSTUS	transcript	8859541	8859951	.	-	.	transcript_id "Phchi.S4G144800.t1"; gene_id "Phchi.S4G144800"
Phchi.S4	AUGUSTUS	stop_codon	8859538	8859540	.	-	0	transcript_id "Phchi.S4G144800.t1"; gene_id "Phchi.S4G144800"
Phchi.S4	AUGUSTUS	CDS	8859541	8859951	0.84	-	0	transcript_id "Phchi.S4G144800.t1"; gene_id "Phchi.S4G144800"
Phchi.S4	AUGUSTUS	exon	8859541	8859951	.	-	.	transcript_id "Phchi.S4G144800.t1"; gene_id "Phchi.S4G144800"
Phchi.S4	AUGUSTUS	start_codon	8859949	8859951	.	-	0	transcript_id "Phchi.S4G144800.t1"; gene_id "Phchi.S4G144800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10006.t1 is derived from g7182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45011972	45012528	.	+	.	Phchi.S1G716500
Phchi.S1	AUGUSTUS	transcript	45011972	45012528	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	start_codon	45011972	45011974	.	+	0	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	CDS	45011972	45011995	0.29	+	0	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	exon	45011972	45011995	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	intron	45011996	45012074	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	CDS	45012075	45012079	0.97	+	0	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	exon	45012075	45012079	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	intron	45012080	45012217	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	CDS	45012218	45012332	0.97	+	1	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	exon	45012218	45012332	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	intron	45012333	45012414	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	CDS	45012415	45012528	1	+	0	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	exon	45012415	45012528	.	+	.	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
Phchi.S1	AUGUSTUS	stop_codon	45012529	45012531	.	+	0	transcript_id "Phchi.S1G716500.t1"; gene_id "Phchi.S1G716500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5623.t1 is derived from g2793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17923357	17927298	.	-	.	Phchi.S1G278200
Phchi.S1	AUGUSTUS	transcript	17923357	17927298	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	stop_codon	17923354	17923356	.	-	0	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17923357	17923612	1	-	1	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17923357	17923612	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	intron	17923613	17923716	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17923717	17923919	1	-	0	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17923717	17923919	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	intron	17923920	17924029	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17924030	17924323	1	-	0	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17924030	17924323	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	intron	17924324	17924412	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17924413	17924536	1	-	1	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17924413	17924536	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	intron	17924537	17924630	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17924631	17924945	1	-	1	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17924631	17924945	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	intron	17924946	17925031	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17925032	17925608	1	-	2	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17925032	17925608	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	intron	17925609	17925716	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	CDS	17925717	17927298	0.98	-	0	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	exon	17925717	17927298	.	-	.	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
Phchi.S1	AUGUSTUS	start_codon	17927296	17927298	.	-	0	transcript_id "Phchi.S1G278200.t1"; gene_id "Phchi.S1G278200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg567.t1 is derived from g10349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4082351	4084668	.	+	.	Phchi.S6G052600
Phchi.S6	AUGUSTUS	transcript	4082351	4084668	.	+	.	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	start_codon	4082351	4082353	.	+	0	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	CDS	4082351	4083945	0.86	+	0	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	exon	4082351	4083945	.	+	.	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	intron	4083946	4084082	.	+	.	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	CDS	4084083	4084668	0.87	+	1	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	exon	4084083	4084668	.	+	.	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
Phchi.S6	AUGUSTUS	stop_codon	4084669	4084671	.	+	0	transcript_id "Phchi.S6G052600.t1"; gene_id "Phchi.S6G052600"
# This transcript jg3747.t2 is derived from g916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3747.t3 is derived from g916.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3748.t1 is derived from g917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5480102	5483988	.	-	.	Phchi.S1G090700
Phchi.S1	AUGUSTUS	transcript	5480102	5483988	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	stop_codon	5480099	5480101	.	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5480102	5480340	0.91	-	2	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5480102	5480340	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5480341	5480477	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5480478	5480625	1	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5480478	5480625	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5480626	5480707	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5480708	5480899	0.93	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5480708	5480899	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5480900	5481102	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5481103	5481388	0.93	-	1	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5481103	5481388	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5481389	5481575	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5481576	5481727	0.99	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5481576	5481727	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5481728	5481835	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5481836	5481883	0.99	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5481836	5481883	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5481884	5482010	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5482011	5482120	0.67	-	2	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5482011	5482120	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5482121	5482240	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5482241	5482426	0.35	-	2	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5482241	5482426	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5482427	5482535	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5482536	5482642	0.56	-	1	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5482536	5482642	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5482643	5482749	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5482750	5483293	0.82	-	2	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5482750	5483293	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5483294	5483413	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5483414	5483571	1	-	1	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5483414	5483571	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5483572	5483661	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5483662	5483713	1	-	2	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5483662	5483713	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	intron	5483714	5483825	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	CDS	5483826	5483988	0.97	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	exon	5483826	5483988	.	-	.	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
Phchi.S1	AUGUSTUS	start_codon	5483986	5483988	.	-	0	transcript_id "Phchi.S1G090700.t1"; gene_id "Phchi.S1G090700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14593.t1 is derived from g13061.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13620976	13622312	.	+	.	Phchi.S3G191200
Phchi.S3	AUGUSTUS	transcript	13620976	13622312	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	start_codon	13620976	13620978	.	+	0	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13620976	13621059	0.98	+	0	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13620976	13621059	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621060	13621147	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621148	13621257	1	+	0	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621148	13621257	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621258	13621356	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621357	13621362	0.88	+	1	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621357	13621362	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621363	13621497	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621498	13621568	0.55	+	1	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621498	13621568	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621569	13621784	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621785	13621805	0.94	+	2	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621785	13621805	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621806	13621938	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621939	13621990	0.93	+	2	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621939	13621990	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621991	13622209	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13622210	13622312	0.97	+	1	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13622210	13622312	.	+	.	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	stop_codon	13622313	13622315	.	+	0	transcript_id "Phchi.S3G191200.t1"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	transcript	13620976	13622312	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	start_codon	13620976	13620978	.	+	0	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13620976	13621059	1	+	0	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13620976	13621059	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621060	13621147	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621148	13621257	1	+	0	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621148	13621257	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621258	13621356	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621357	13621362	0.88	+	1	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621357	13621362	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621363	13621497	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621498	13621568	0.55	+	1	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621498	13621568	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621569	13621649	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621650	13621772	0.51	+	2	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621650	13621772	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621773	13621938	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13621939	13621990	0.94	+	2	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13621939	13621990	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	intron	13621991	13622209	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	CDS	13622210	13622312	1	+	1	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	exon	13622210	13622312	.	+	.	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
Phchi.S3	AUGUSTUS	stop_codon	13622313	13622315	.	+	0	transcript_id "Phchi.S3G191200.t2"; gene_id "Phchi.S3G191200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13695.t1 is derived from g12162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8240076	8243953	.	+	.	Phchi.S3G101400
Phchi.S3	AUGUSTUS	transcript	8240076	8243953	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	start_codon	8240076	8240078	.	+	0	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8240076	8240109	0.98	+	0	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8240076	8240109	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8240110	8240339	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8240340	8240504	1	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8240340	8240504	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8240505	8240992	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8240993	8241036	1	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8240993	8241036	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8241037	8241130	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8241131	8241240	1	+	0	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8241131	8241240	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8241241	8241356	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8241357	8241394	1	+	1	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8241357	8241394	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8241395	8241604	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8241605	8241682	1	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8241605	8241682	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8241683	8241817	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8241818	8241871	1	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8241818	8241871	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8241872	8241967	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8241968	8242069	0.99	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8241968	8242069	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8242070	8242170	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8242171	8242259	1	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8242171	8242259	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8242260	8242364	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8242365	8242468	1	+	0	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8242365	8242468	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8242469	8242581	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8242582	8242650	1	+	1	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8242582	8242650	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8242651	8242745	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8242746	8242861	1	+	1	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8242746	8242861	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8242862	8242959	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8242960	8242994	0.99	+	2	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8242960	8242994	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8242995	8243100	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8243101	8243243	1	+	0	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8243101	8243243	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8243244	8243332	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8243333	8243455	1	+	1	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8243333	8243455	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8243456	8243585	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8243586	8243681	1	+	1	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8243586	8243681	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	intron	8243682	8243946	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	CDS	8243947	8243953	1	+	1	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	exon	8243947	8243953	.	+	.	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
Phchi.S3	AUGUSTUS	stop_codon	8243954	8243956	.	+	0	transcript_id "Phchi.S3G101400.t1"; gene_id "Phchi.S3G101400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14951.t1 is derived from g13419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15674411	15676015	.	+	.	Phchi.S3G227000
Phchi.S3	AUGUSTUS	transcript	15674411	15676015	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	start_codon	15674411	15674413	.	+	0	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	CDS	15674411	15674419	0.81	+	0	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	exon	15674411	15674419	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	intron	15674420	15674561	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	CDS	15674562	15674598	0.69	+	0	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	exon	15674562	15674598	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	intron	15674599	15675035	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	CDS	15675036	15675069	0.61	+	2	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	exon	15675036	15675069	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	intron	15675070	15675229	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	CDS	15675230	15675898	0.27	+	1	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	exon	15675230	15675898	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	intron	15675899	15675981	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	CDS	15675982	15676015	0.48	+	1	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	exon	15675982	15676015	.	+	.	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
Phchi.S3	AUGUSTUS	stop_codon	15676016	15676018	.	+	0	transcript_id "Phchi.S3G227000.t1"; gene_id "Phchi.S3G227000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6007.t1 is derived from g3178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20376745	20378711	.	+	.	Phchi.S1G316600
Phchi.S1	AUGUSTUS	transcript	20376745	20378711	.	+	.	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	start_codon	20376745	20376747	.	+	0	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	CDS	20376745	20377749	0.92	+	0	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	exon	20376745	20377749	.	+	.	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	intron	20377750	20377835	.	+	.	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	CDS	20377836	20378711	0.99	+	0	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	exon	20377836	20378711	.	+	.	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
Phchi.S1	AUGUSTUS	stop_codon	20378712	20378714	.	+	0	transcript_id "Phchi.S1G316600.t1"; gene_id "Phchi.S1G316600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13691.t1 is derived from g12158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8224273	8224920	.	-	.	Phchi.S3G101000
Phchi.S3	AUGUSTUS	transcript	8224273	8224920	.	-	.	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	stop_codon	8224270	8224272	.	-	0	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	CDS	8224273	8224478	1	-	2	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	exon	8224273	8224478	.	-	.	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	intron	8224479	8224568	.	-	.	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	CDS	8224569	8224626	1	-	0	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	exon	8224569	8224626	.	-	.	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	intron	8224627	8224710	.	-	.	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	CDS	8224711	8224920	0.76	-	0	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	exon	8224711	8224920	.	-	.	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
Phchi.S3	AUGUSTUS	start_codon	8224918	8224920	.	-	0	transcript_id "Phchi.S3G101000.t1"; gene_id "Phchi.S3G101000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11879.t1 is derived from g15931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8954657	8956116	.	+	.	Phchi.S4G146100
Phchi.S4	AUGUSTUS	transcript	8954657	8956116	.	+	.	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	start_codon	8954657	8954659	.	+	0	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	CDS	8954657	8954714	0.65	+	0	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	exon	8954657	8954714	.	+	.	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	intron	8954715	8954830	.	+	.	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	CDS	8954831	8955823	0.82	+	2	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	exon	8954831	8955823	.	+	.	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	intron	8955824	8955925	.	+	.	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	CDS	8955926	8956116	0.95	+	2	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	exon	8955926	8956116	.	+	.	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
Phchi.S4	AUGUSTUS	stop_codon	8956117	8956119	.	+	0	transcript_id "Phchi.S4G146100.t1"; gene_id "Phchi.S4G146100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14639.t1 is derived from g13107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13884190	13884798	.	-	.	Phchi.S3G195800
Phchi.S3	AUGUSTUS	transcript	13884190	13884798	.	-	.	transcript_id "Phchi.S3G195800.t1"; gene_id "Phchi.S3G195800"
Phchi.S3	AUGUSTUS	stop_codon	13884187	13884189	.	-	0	transcript_id "Phchi.S3G195800.t1"; gene_id "Phchi.S3G195800"
Phchi.S3	AUGUSTUS	CDS	13884190	13884798	0.76	-	0	transcript_id "Phchi.S3G195800.t1"; gene_id "Phchi.S3G195800"
Phchi.S3	AUGUSTUS	exon	13884190	13884798	.	-	.	transcript_id "Phchi.S3G195800.t1"; gene_id "Phchi.S3G195800"
Phchi.S3	AUGUSTUS	start_codon	13884796	13884798	.	-	0	transcript_id "Phchi.S3G195800.t1"; gene_id "Phchi.S3G195800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10517.t1 is derived from g14567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	797011	797809	.	-	.	Phchi.S4G009900
Phchi.S4	AUGUSTUS	transcript	797011	797809	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	stop_codon	797008	797010	.	-	0	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	CDS	797011	797097	1	-	0	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	exon	797011	797097	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	intron	797098	797234	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	CDS	797235	797284	0.93	-	2	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	exon	797235	797284	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	intron	797285	797344	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	CDS	797345	797385	0.93	-	1	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	exon	797345	797385	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	intron	797386	797468	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	CDS	797469	797499	0.99	-	2	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	exon	797469	797499	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	intron	797500	797564	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	CDS	797565	797577	1	-	0	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	exon	797565	797577	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	intron	797578	797719	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	CDS	797720	797809	1	-	0	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	exon	797720	797809	.	-	.	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
Phchi.S4	AUGUSTUS	start_codon	797807	797809	.	-	0	transcript_id "Phchi.S4G009900.t1"; gene_id "Phchi.S4G009900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10283.t1 is derived from g7459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46810708	46811718	.	-	.	Phchi.S1G744200
Phchi.S1	AUGUSTUS	transcript	46810708	46811718	.	-	.	transcript_id "Phchi.S1G744200.t1"; gene_id "Phchi.S1G744200"
Phchi.S1	AUGUSTUS	stop_codon	46810705	46810707	.	-	0	transcript_id "Phchi.S1G744200.t1"; gene_id "Phchi.S1G744200"
Phchi.S1	AUGUSTUS	CDS	46810708	46811718	0.92	-	0	transcript_id "Phchi.S1G744200.t1"; gene_id "Phchi.S1G744200"
Phchi.S1	AUGUSTUS	exon	46810708	46811718	.	-	.	transcript_id "Phchi.S1G744200.t1"; gene_id "Phchi.S1G744200"
Phchi.S1	AUGUSTUS	start_codon	46811716	46811718	.	-	0	transcript_id "Phchi.S1G744200.t1"; gene_id "Phchi.S1G744200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7594.t1 is derived from g4768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30188333	30189567	.	+	.	Phchi.S1G475300
Phchi.S1	AUGUSTUS	transcript	30188333	30189567	.	+	.	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	start_codon	30188333	30188335	.	+	0	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	CDS	30188333	30188936	1	+	0	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	exon	30188333	30188936	.	+	.	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	intron	30188937	30189028	.	+	.	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	CDS	30189029	30189148	0.89	+	2	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	exon	30189029	30189148	.	+	.	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	intron	30189149	30189259	.	+	.	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	CDS	30189260	30189567	0.89	+	2	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	exon	30189260	30189567	.	+	.	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
Phchi.S1	AUGUSTUS	stop_codon	30189568	30189570	.	+	0	transcript_id "Phchi.S1G475300.t1"; gene_id "Phchi.S1G475300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14444.t1 is derived from g12912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12856567	12861026	.	-	.	Phchi.S3G176300
Phchi.S3	AUGUSTUS	transcript	12856567	12861026	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	stop_codon	12856564	12856566	.	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12856567	12856760	0.93	-	2	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12856567	12856760	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12856761	12856839	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12856840	12856931	1	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12856840	12856931	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12856932	12857056	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12857057	12857151	1	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12857057	12857151	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12857152	12857328	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12857329	12857461	1	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12857329	12857461	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12857462	12857551	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12857552	12857635	1	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12857552	12857635	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12857636	12857791	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12857792	12857891	1	-	2	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12857792	12857891	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12857892	12857974	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12857975	12858038	1	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12857975	12858038	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12858039	12858159	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12858160	12858240	1	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12858160	12858240	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12858241	12858343	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12858344	12858400	0.93	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12858344	12858400	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12858401	12858571	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12858572	12858762	0.93	-	2	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12858572	12858762	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12858763	12858880	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12858881	12858972	0.92	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12858881	12858972	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12858973	12859097	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12859098	12859120	0.92	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12859098	12859120	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12859121	12859234	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12859235	12859424	0.96	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12859235	12859424	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12859425	12859515	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12859516	12859626	1	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12859516	12859626	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12859627	12859718	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12859719	12859795	0.88	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12859719	12859795	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12859796	12859885	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12859886	12859938	0.88	-	2	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12859886	12859938	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12859939	12860137	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12860138	12860766	0.62	-	1	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12860138	12860766	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12860767	12860907	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12860908	12860927	0.65	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12860908	12860927	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	intron	12860928	12861023	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	CDS	12861024	12861026	1	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	exon	12861024	12861026	.	-	.	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
Phchi.S3	AUGUSTUS	start_codon	12861024	12861026	.	-	0	transcript_id "Phchi.S3G176300.t1"; gene_id "Phchi.S3G176300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15400.t1 is derived from g13868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18822498	18823435	.	+	.	Phchi.S3G271900
Phchi.S3	AUGUSTUS	transcript	18822498	18823435	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	start_codon	18822498	18822500	.	+	0	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18822498	18822558	1	+	0	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18822498	18822558	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	intron	18822559	18822638	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18822639	18822701	1	+	2	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18822639	18822701	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	intron	18822702	18822785	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18822786	18822842	1	+	2	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18822786	18822842	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	intron	18822843	18822914	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18822915	18822988	1	+	2	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18822915	18822988	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	intron	18822989	18823070	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18823071	18823132	1	+	0	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18823071	18823132	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	intron	18823133	18823221	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18823222	18823270	1	+	1	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18823222	18823270	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	intron	18823271	18823348	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	CDS	18823349	18823435	1	+	0	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	exon	18823349	18823435	.	+	.	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
Phchi.S3	AUGUSTUS	stop_codon	18823436	18823438	.	+	0	transcript_id "Phchi.S3G271900.t1"; gene_id "Phchi.S3G271900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg798.t1 is derived from g10580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5664786	5665710	.	-	.	Phchi.S6G075700
Phchi.S6	AUGUSTUS	transcript	5664786	5665710	.	-	.	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	stop_codon	5664783	5664785	.	-	0	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	CDS	5664786	5665010	0.85	-	0	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	exon	5664786	5665010	.	-	.	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	intron	5665011	5665100	.	-	.	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	CDS	5665101	5665286	1	-	0	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	exon	5665101	5665286	.	-	.	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	intron	5665287	5665383	.	-	.	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	CDS	5665384	5665710	0.78	-	0	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	exon	5665384	5665710	.	-	.	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
Phchi.S6	AUGUSTUS	start_codon	5665708	5665710	.	-	0	transcript_id "Phchi.S6G075700.t1"; gene_id "Phchi.S6G075700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9429.t1 is derived from g6605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41429369	41430726	.	+	.	Phchi.S1G658800
Phchi.S1	AUGUSTUS	transcript	41429369	41430726	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	start_codon	41429369	41429371	.	+	0	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	CDS	41429369	41429379	1	+	0	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	exon	41429369	41429379	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	intron	41429380	41429568	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	CDS	41429569	41429610	1	+	1	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	exon	41429569	41429610	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	intron	41429611	41429793	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	CDS	41429794	41430328	0.99	+	1	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	exon	41429794	41430328	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	intron	41430329	41430429	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	CDS	41430430	41430726	0.87	+	0	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	exon	41430430	41430726	.	+	.	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
Phchi.S1	AUGUSTUS	stop_codon	41430727	41430729	.	+	0	transcript_id "Phchi.S1G658800.t1"; gene_id "Phchi.S1G658800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5725.t1 is derived from g2895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18570443	18571786	.	-	.	Phchi.S1G288400
Phchi.S1	AUGUSTUS	transcript	18570443	18571786	.	-	.	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	stop_codon	18570440	18570442	.	-	0	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	CDS	18570443	18570897	0.99	-	2	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	exon	18570443	18570897	.	-	.	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	intron	18570898	18571003	.	-	.	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	CDS	18571004	18571349	1	-	0	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	exon	18571004	18571349	.	-	.	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	intron	18571350	18571471	.	-	.	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	CDS	18571472	18571786	0.86	-	0	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	exon	18571472	18571786	.	-	.	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
Phchi.S1	AUGUSTUS	start_codon	18571784	18571786	.	-	0	transcript_id "Phchi.S1G288400.t1"; gene_id "Phchi.S1G288400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8249.t1 is derived from g5424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34685495	34686514	.	-	.	Phchi.S1G540800
Phchi.S1	AUGUSTUS	transcript	34685495	34686514	.	-	.	transcript_id "Phchi.S1G540800.t1"; gene_id "Phchi.S1G540800"
Phchi.S1	AUGUSTUS	stop_codon	34685492	34685494	.	-	0	transcript_id "Phchi.S1G540800.t1"; gene_id "Phchi.S1G540800"
Phchi.S1	AUGUSTUS	CDS	34685495	34686514	0.5	-	0	transcript_id "Phchi.S1G540800.t1"; gene_id "Phchi.S1G540800"
Phchi.S1	AUGUSTUS	exon	34685495	34686514	.	-	.	transcript_id "Phchi.S1G540800.t1"; gene_id "Phchi.S1G540800"
Phchi.S1	AUGUSTUS	start_codon	34686512	34686514	.	-	0	transcript_id "Phchi.S1G540800.t1"; gene_id "Phchi.S1G540800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13286.t1 is derived from g11752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5185912	5186943	.	-	.	Phchi.S3G060500
Phchi.S3	AUGUSTUS	transcript	5185912	5186943	.	-	.	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	stop_codon	5185909	5185911	.	-	0	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	CDS	5185912	5186535	0.83	-	0	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	exon	5185912	5186535	.	-	.	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	intron	5186536	5186697	.	-	.	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	CDS	5186698	5186943	0.81	-	0	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	exon	5186698	5186943	.	-	.	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
Phchi.S3	AUGUSTUS	start_codon	5186941	5186943	.	-	0	transcript_id "Phchi.S3G060500.t1"; gene_id "Phchi.S3G060500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12147.t1 is derived from g7823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4903270	4904166	.	-	.	Phchi.S2G022700
Phchi.S2	AUGUSTUS	transcript	4903270	4904166	.	-	.	transcript_id "Phchi.S2G022700.t1"; gene_id "Phchi.S2G022700"
Phchi.S2	AUGUSTUS	stop_codon	4903267	4903269	.	-	0	transcript_id "Phchi.S2G022700.t1"; gene_id "Phchi.S2G022700"
Phchi.S2	AUGUSTUS	CDS	4903270	4904166	1	-	0	transcript_id "Phchi.S2G022700.t1"; gene_id "Phchi.S2G022700"
Phchi.S2	AUGUSTUS	exon	4903270	4904166	.	-	.	transcript_id "Phchi.S2G022700.t1"; gene_id "Phchi.S2G022700"
Phchi.S2	AUGUSTUS	start_codon	4904164	4904166	.	-	0	transcript_id "Phchi.S2G022700.t1"; gene_id "Phchi.S2G022700"
# This transcript jg12191.t2 is derived from g7867.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12192.t1 is derived from g7868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6500602	6503607	.	+	.	Phchi.S2G027200
Phchi.S2	AUGUSTUS	transcript	6500602	6503607	.	+	.	transcript_id "Phchi.S2G027200.t1"; gene_id "Phchi.S2G027200"
Phchi.S2	AUGUSTUS	start_codon	6500602	6500604	.	+	0	transcript_id "Phchi.S2G027200.t1"; gene_id "Phchi.S2G027200"
Phchi.S2	AUGUSTUS	CDS	6500602	6503607	0.67	+	0	transcript_id "Phchi.S2G027200.t1"; gene_id "Phchi.S2G027200"
Phchi.S2	AUGUSTUS	exon	6500602	6503607	.	+	.	transcript_id "Phchi.S2G027200.t1"; gene_id "Phchi.S2G027200"
Phchi.S2	AUGUSTUS	stop_codon	6503608	6503610	.	+	0	transcript_id "Phchi.S2G027200.t1"; gene_id "Phchi.S2G027200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11435.t1 is derived from g15485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6363585	6370070	.	-	.	Phchi.S4G101700
Phchi.S4	AUGUSTUS	transcript	6363585	6370070	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	stop_codon	6363582	6363584	.	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6363585	6363690	1	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6363585	6363690	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6363691	6363779	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6363780	6363981	1	-	2	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6363780	6363981	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6363982	6364073	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364074	6364688	1	-	2	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364074	6364688	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6364689	6364805	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364806	6364891	0.98	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364806	6364891	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6364892	6364980	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364981	6365061	1	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364981	6365061	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6365062	6365180	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6365181	6365765	0.73	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6365181	6365765	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6365766	6365851	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6365852	6366108	0.92	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6365852	6366108	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366109	6366224	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366225	6366317	0.99	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366225	6366317	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366318	6366411	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366412	6366479	0.99	-	2	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366412	6366479	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366480	6366598	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366599	6366620	0.98	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366599	6366620	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366621	6366890	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366891	6366923	1	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366891	6366923	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366924	6367025	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367026	6367209	0.55	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367026	6367209	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6367210	6367314	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367315	6367689	0.49	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367315	6367689	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6367690	6367826	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367827	6368033	1	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367827	6368033	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368034	6368240	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368241	6368323	1	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368241	6368323	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368324	6368532	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368533	6368668	0.98	-	1	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368533	6368668	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368669	6368780	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368781	6369016	0.89	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368781	6369016	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369017	6369136	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369137	6369219	1	-	2	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369137	6369219	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369220	6369300	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369301	6369439	1	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369301	6369439	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369440	6369525	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369526	6369821	0.92	-	2	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369526	6369821	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369822	6369970	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369971	6370070	0.85	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369971	6370070	.	-	.	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	start_codon	6370068	6370070	.	-	0	transcript_id "Phchi.S4G101700.t1"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	transcript	6363585	6370070	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	stop_codon	6363582	6363584	.	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6363585	6363690	1	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6363585	6363690	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6363691	6363779	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6363780	6363981	1	-	2	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6363780	6363981	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6363982	6364073	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364074	6364688	0.97	-	2	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364074	6364688	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6364689	6364805	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364806	6364891	0.98	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364806	6364891	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6364892	6364980	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364981	6365061	1	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364981	6365061	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6365062	6365180	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6365181	6365765	0.72	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6365181	6365765	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6365766	6365851	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6365852	6366108	0.9	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6365852	6366108	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366109	6366224	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366225	6366317	1	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366225	6366317	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366318	6366411	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366412	6366479	1	-	2	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366412	6366479	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366480	6366598	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366599	6366620	0.96	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366599	6366620	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366621	6366890	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366891	6366923	0.98	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366891	6366923	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366924	6367025	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367026	6367209	0.49	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367026	6367209	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6367210	6367314	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367315	6367689	0.47	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367315	6367689	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6367690	6367826	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367827	6368033	1	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367827	6368033	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368034	6368240	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368241	6368323	1	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368241	6368323	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368324	6368532	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368533	6368668	0.96	-	1	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368533	6368668	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368669	6369136	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369137	6369215	0.98	-	2	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369137	6369215	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369216	6369300	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369301	6369439	1	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369301	6369439	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369440	6369525	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369526	6369821	0.88	-	2	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369526	6369821	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369822	6369970	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369971	6370070	0.78	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369971	6370070	.	-	.	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	start_codon	6370068	6370070	.	-	0	transcript_id "Phchi.S4G101700.t2"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	transcript	6363585	6370070	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	stop_codon	6363582	6363584	.	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6363585	6363690	1	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6363585	6363690	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6363691	6363779	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6363780	6363981	1	-	2	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6363780	6363981	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6363982	6364073	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364074	6364688	1	-	2	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364074	6364688	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6364689	6364805	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364806	6364891	0.97	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364806	6364891	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6364892	6364980	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6364981	6365061	1	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6364981	6365061	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6365062	6365180	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6365181	6365765	0.73	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6365181	6365765	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6365766	6365851	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6365852	6366108	0.88	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6365852	6366108	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366109	6366224	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366225	6366317	0.99	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366225	6366317	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366318	6366411	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366412	6366479	1	-	2	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366412	6366479	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366480	6366598	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366599	6366620	0.97	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366599	6366620	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366621	6366890	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6366891	6366923	1	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6366891	6366923	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6366924	6367025	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367026	6367209	0.39	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367026	6367209	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6367210	6367314	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367315	6367689	0.34	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367315	6367689	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6367690	6367826	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6367827	6368033	1	-	1	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6367827	6368033	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368034	6368532	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368533	6368668	0.81	-	2	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368533	6368668	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368669	6368780	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368781	6368796	0.95	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368781	6368796	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6368797	6368917	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6368918	6369016	0.95	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6368918	6369016	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369017	6369136	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369137	6369219	1	-	2	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369137	6369219	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369220	6369300	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369301	6369439	1	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369301	6369439	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369440	6369525	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369526	6369821	0.94	-	2	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369526	6369821	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	intron	6369822	6369970	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	CDS	6369971	6370070	0.91	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	exon	6369971	6370070	.	-	.	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
Phchi.S4	AUGUSTUS	start_codon	6370068	6370070	.	-	0	transcript_id "Phchi.S4G101700.t3"; gene_id "Phchi.S4G101700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10221.t1 is derived from g7397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46458215	46462858	.	-	.	Phchi.S1G738000
Phchi.S1	AUGUSTUS	transcript	46458215	46462858	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	stop_codon	46458212	46458214	.	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46458215	46458406	0.95	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46458215	46458406	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46458407	46458478	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46458479	46458638	1	-	1	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46458479	46458638	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46458639	46458709	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46458710	46458868	1	-	1	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46458710	46458868	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46458869	46458949	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46458950	46459107	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46458950	46459107	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46459108	46459194	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46459195	46459374	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46459195	46459374	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46459375	46459467	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46459468	46459585	1	-	1	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46459468	46459585	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46459586	46459685	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46459686	46459790	1	-	1	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46459686	46459790	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46459791	46459912	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46459913	46460007	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46459913	46460007	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46460008	46460080	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46460081	46460158	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46460081	46460158	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46460159	46460299	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46460300	46460365	0.98	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46460300	46460365	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46460366	46460445	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46460446	46460574	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46460446	46460574	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46460575	46460703	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46460704	46460832	0.86	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46460704	46460832	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46460833	46460926	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46460927	46461094	0.72	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46460927	46461094	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46461095	46461173	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46461174	46461245	0.91	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46461174	46461245	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46461246	46461368	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46461369	46461551	0.93	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46461369	46461551	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46461552	46461624	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46461625	46461732	0.98	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46461625	46461732	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46461733	46461859	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46461860	46461913	0.93	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46461860	46461913	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46461914	46462022	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46462023	46462241	0.99	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46462023	46462241	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46462242	46462328	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46462329	46462413	1	-	1	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46462329	46462413	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46462414	46462495	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46462496	46462752	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46462496	46462752	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	intron	46462753	46462831	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	CDS	46462832	46462858	1	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	exon	46462832	46462858	.	-	.	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
Phchi.S1	AUGUSTUS	start_codon	46462856	46462858	.	-	0	transcript_id "Phchi.S1G738000.t1"; gene_id "Phchi.S1G738000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4045.t1 is derived from g1214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7380823	7382513	.	-	.	Phchi.S1G120400
Phchi.S1	AUGUSTUS	transcript	7380922	7382513	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	stop_codon	7380919	7380921	.	-	0	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7380922	7380933	0.91	-	0	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7380922	7380933	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7380934	7381029	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381030	7381130	0.92	-	2	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381030	7381130	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7381131	7381404	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381405	7381597	0.83	-	0	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381405	7381597	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7381598	7381699	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381700	7381798	1	-	0	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381700	7381798	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7381799	7381950	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381951	7382120	0.87	-	2	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381951	7382120	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7382121	7382228	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7382229	7382290	0.94	-	1	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7382229	7382290	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7382291	7382385	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7382386	7382513	0.43	-	0	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7382386	7382513	.	-	.	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	start_codon	7382511	7382513	.	-	0	transcript_id "Phchi.S1G120400.t1"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	transcript	7380823	7382513	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	stop_codon	7380820	7380822	.	-	0	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7380823	7380918	0.79	-	0	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7380823	7380918	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7380919	7381029	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381030	7381130	0.68	-	2	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381030	7381130	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7381131	7381404	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381405	7381597	0.62	-	0	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381405	7381597	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7381598	7381699	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381700	7381798	1	-	0	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381700	7381798	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7381799	7381950	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7381951	7382120	0.84	-	2	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7381951	7382120	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7382121	7382228	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7382229	7382290	0.89	-	1	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7382229	7382290	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	intron	7382291	7382385	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	CDS	7382386	7382513	0.42	-	0	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	exon	7382386	7382513	.	-	.	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
Phchi.S1	AUGUSTUS	start_codon	7382511	7382513	.	-	0	transcript_id "Phchi.S1G120400.t2"; gene_id "Phchi.S1G120400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15600.t1 is derived from g14069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20217631	20218340	.	+	.	Phchi.S3G291900
Phchi.S3	AUGUSTUS	transcript	20217631	20218340	.	+	.	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	start_codon	20217631	20217633	.	+	0	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	CDS	20217631	20217857	0.58	+	0	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	exon	20217631	20217857	.	+	.	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	intron	20217858	20217976	.	+	.	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	CDS	20217977	20218340	0.63	+	1	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	exon	20217977	20218340	.	+	.	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
Phchi.S3	AUGUSTUS	stop_codon	20218341	20218343	.	+	0	transcript_id "Phchi.S3G291900.t1"; gene_id "Phchi.S3G291900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3770.t1 is derived from g939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5618398	5619347	.	-	.	Phchi.S1G092900
Phchi.S1	AUGUSTUS	transcript	5618398	5619347	.	-	.	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	stop_codon	5618395	5618397	.	-	0	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	CDS	5618398	5618478	1	-	0	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	exon	5618398	5618478	.	-	.	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	intron	5618479	5618591	.	-	.	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	CDS	5618592	5619347	0.84	-	0	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	exon	5618592	5619347	.	-	.	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
Phchi.S1	AUGUSTUS	start_codon	5619345	5619347	.	-	0	transcript_id "Phchi.S1G092900.t1"; gene_id "Phchi.S1G092900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4513.t1 is derived from g1683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10899640	10902580	.	-	.	Phchi.S1G167200
Phchi.S1	AUGUSTUS	transcript	10899640	10902580	.	-	.	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	stop_codon	10899637	10899639	.	-	0	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	CDS	10899640	10902289	0.77	-	1	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	exon	10899640	10902289	.	-	.	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	intron	10902290	10902383	.	-	.	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	CDS	10902384	10902580	0.73	-	0	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	exon	10902384	10902580	.	-	.	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
Phchi.S1	AUGUSTUS	start_codon	10902578	10902580	.	-	0	transcript_id "Phchi.S1G167200.t1"; gene_id "Phchi.S1G167200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4921.t1 is derived from g2091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13567556	13568071	.	-	.	Phchi.S1G208000
Phchi.S1	AUGUSTUS	transcript	13567556	13568071	.	-	.	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	stop_codon	13567553	13567555	.	-	0	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	CDS	13567556	13567595	0.6	-	1	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	exon	13567556	13567595	.	-	.	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	intron	13567596	13567685	.	-	.	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	CDS	13567686	13567770	0.6	-	2	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	exon	13567686	13567770	.	-	.	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	intron	13567771	13567905	.	-	.	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	CDS	13567906	13568071	0.36	-	0	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	exon	13567906	13568071	.	-	.	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
Phchi.S1	AUGUSTUS	start_codon	13568069	13568071	.	-	0	transcript_id "Phchi.S1G208000.t1"; gene_id "Phchi.S1G208000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2816.t1 is derived from g9736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8995962	8997663	.	-	.	Phchi.S5G142500
Phchi.S5	AUGUSTUS	transcript	8995962	8997663	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	stop_codon	8995959	8995961	.	-	0	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8995962	8996022	0.86	-	1	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8995962	8996022	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8996023	8996133	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8996134	8996214	0.97	-	1	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8996134	8996214	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8996215	8996308	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8996309	8996378	1	-	2	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8996309	8996378	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8996379	8996509	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8996510	8996547	1	-	1	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8996510	8996547	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8996548	8996646	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8996647	8996721	0.96	-	1	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8996647	8996721	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8996722	8996831	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8996832	8996912	1	-	1	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8996832	8996912	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8996913	8996991	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8996992	8997135	1	-	1	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8996992	8997135	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8997136	8997217	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8997218	8997419	1	-	2	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8997218	8997419	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	intron	8997420	8997497	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	CDS	8997498	8997663	1	-	0	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	exon	8997498	8997663	.	-	.	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
Phchi.S5	AUGUSTUS	start_codon	8997661	8997663	.	-	0	transcript_id "Phchi.S5G142500.t1"; gene_id "Phchi.S5G142500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4869.t1 is derived from g2039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13165481	13175140	.	-	.	Phchi.S1G202800
Phchi.S1	AUGUSTUS	transcript	13165481	13175140	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	stop_codon	13165478	13165480	.	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13165481	13165748	1	-	1	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13165481	13165748	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13165749	13165834	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13165835	13165919	1	-	2	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13165835	13165919	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13165920	13166015	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13166016	13166388	0.99	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13166016	13166388	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13166389	13166478	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13166479	13166838	1	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13166479	13166838	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13166839	13166946	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13166947	13167105	0.97	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13166947	13167105	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13167106	13167213	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13167214	13167417	0.99	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13167214	13167417	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13167418	13167501	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13167502	13167705	1	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13167502	13167705	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13167706	13167805	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13167806	13168036	1	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13167806	13168036	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13168037	13168159	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13168160	13171696	1	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13168160	13171696	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13171697	13171793	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13171794	13171933	1	-	2	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13171794	13171933	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13171934	13172022	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13172023	13172587	1	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13172023	13172587	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13172588	13172786	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13172787	13173627	0.99	-	1	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13172787	13173627	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13173628	13173750	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13173751	13174711	0.99	-	2	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13173751	13174711	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	intron	13174712	13174806	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	CDS	13174807	13175140	0.88	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	exon	13174807	13175140	.	-	.	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
Phchi.S1	AUGUSTUS	start_codon	13175138	13175140	.	-	0	transcript_id "Phchi.S1G202800.t1"; gene_id "Phchi.S1G202800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6821.t1 is derived from g3993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25218201	25219782	.	+	.	Phchi.S1G398000
Phchi.S1	AUGUSTUS	transcript	25218201	25219782	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	start_codon	25218201	25218203	.	+	0	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25218201	25218295	0.92	+	0	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25218201	25218295	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	intron	25218296	25218386	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25218387	25218404	0.5	+	1	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25218387	25218404	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	intron	25218405	25218578	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25218579	25218918	0.52	+	1	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25218579	25218918	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	intron	25218919	25219097	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25219098	25219189	1	+	0	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25219098	25219189	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	intron	25219190	25219307	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25219308	25219365	1	+	1	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25219308	25219365	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	intron	25219366	25219456	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25219457	25219522	1	+	0	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25219457	25219522	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	intron	25219523	25219650	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	CDS	25219651	25219782	0.97	+	0	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	exon	25219651	25219782	.	+	.	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
Phchi.S1	AUGUSTUS	stop_codon	25219783	25219785	.	+	0	transcript_id "Phchi.S1G398000.t1"; gene_id "Phchi.S1G398000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2202.t1 is derived from g9122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5407738	5408834	.	+	.	Phchi.S5G081100
Phchi.S5	AUGUSTUS	transcript	5407738	5408834	.	+	.	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	start_codon	5407738	5407740	.	+	0	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	CDS	5407738	5407812	0.55	+	0	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	exon	5407738	5407812	.	+	.	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	intron	5407813	5407964	.	+	.	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	CDS	5407965	5408175	1	+	0	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	exon	5407965	5408175	.	+	.	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	intron	5408176	5408277	.	+	.	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	CDS	5408278	5408834	0.25	+	2	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	exon	5408278	5408834	.	+	.	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
Phchi.S5	AUGUSTUS	stop_codon	5408835	5408837	.	+	0	transcript_id "Phchi.S5G081100.t1"; gene_id "Phchi.S5G081100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6122.t1 is derived from g3293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21030463	21031324	.	+	.	Phchi.S1G328100
Phchi.S1	AUGUSTUS	transcript	21030463	21031324	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	start_codon	21030463	21030465	.	+	0	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	CDS	21030463	21030609	0.53	+	0	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	exon	21030463	21030609	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	intron	21030610	21030709	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	CDS	21030710	21030880	1	+	0	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	exon	21030710	21030880	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	intron	21030881	21030975	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	CDS	21030976	21031140	1	+	0	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	exon	21030976	21031140	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	intron	21031141	21031222	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	CDS	21031223	21031324	0.98	+	0	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	exon	21031223	21031324	.	+	.	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
Phchi.S1	AUGUSTUS	stop_codon	21031325	21031327	.	+	0	transcript_id "Phchi.S1G328100.t1"; gene_id "Phchi.S1G328100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3397.t1 is derived from g566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3334068	3335347	.	+	.	Phchi.S1G055600
Phchi.S1	AUGUSTUS	transcript	3334068	3335347	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	start_codon	3334068	3334070	.	+	0	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	CDS	3334068	3334148	0.97	+	0	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	exon	3334068	3334148	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	intron	3334149	3334624	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	CDS	3334625	3334766	1	+	0	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	exon	3334625	3334766	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	intron	3334767	3334887	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	CDS	3334888	3335012	1	+	2	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	exon	3334888	3335012	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	intron	3335013	3335093	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	CDS	3335094	3335157	1	+	0	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	exon	3335094	3335157	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	intron	3335158	3335264	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	CDS	3335265	3335347	0.69	+	2	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	exon	3335265	3335347	.	+	.	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
Phchi.S1	AUGUSTUS	stop_codon	3335348	3335350	.	+	0	transcript_id "Phchi.S1G055600.t1"; gene_id "Phchi.S1G055600"
# This transcript jg6566.t2 is derived from g3738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6567.t1 is derived from g3739.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23741318	23743982	.	+	.	Phchi.S1G372600
Phchi.S1	AUGUSTUS	transcript	23741318	23743982	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	start_codon	23741318	23741320	.	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741318	23741391	0.99	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741318	23741391	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741392	23741471	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741472	23741571	1	+	1	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741472	23741571	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741572	23741655	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741656	23741733	1	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741656	23741733	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741734	23741818	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741819	23741917	1	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741819	23741917	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741918	23742011	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742012	23742064	1	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742012	23742064	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742065	23742169	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742170	23742264	1	+	1	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742170	23742264	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742265	23742462	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742463	23742554	1	+	2	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742463	23742554	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742555	23742718	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742719	23742787	1	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742719	23742787	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742788	23742870	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742871	23742966	1	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742871	23742966	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742967	23743055	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23743056	23743128	0.85	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23743056	23743128	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23743129	23743459	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23743460	23743601	0.96	+	2	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23743460	23743601	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23743602	23743675	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23743676	23743982	0.93	+	1	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23743676	23743982	.	+	.	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	stop_codon	23743983	23743985	.	+	0	transcript_id "Phchi.S1G372600.t1"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	transcript	23741318	23743982	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	start_codon	23741318	23741320	.	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741318	23741391	1	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741318	23741391	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741392	23741471	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741472	23741571	1	+	1	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741472	23741571	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741572	23741655	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741656	23741733	1	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741656	23741733	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741734	23741818	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23741819	23741917	1	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23741819	23741917	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23741918	23742011	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742012	23742064	1	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742012	23742064	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742065	23742169	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742170	23742264	1	+	1	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742170	23742264	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742265	23742462	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742463	23742554	1	+	2	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742463	23742554	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742555	23742718	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742719	23742787	1	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742719	23742787	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742788	23742876	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23742877	23742966	1	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23742877	23742966	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23742967	23743055	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23743056	23743128	0.84	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23743056	23743128	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23743129	23743459	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23743460	23743601	0.95	+	2	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23743460	23743601	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	intron	23743602	23743675	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	CDS	23743676	23743982	0.96	+	1	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	exon	23743676	23743982	.	+	.	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
Phchi.S1	AUGUSTUS	stop_codon	23743983	23743985	.	+	0	transcript_id "Phchi.S1G372600.t2"; gene_id "Phchi.S1G372600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3233.t1 is derived from g402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2374041	2379030	.	-	.	Phchi.S1G039200
Phchi.S1	AUGUSTUS	transcript	2374041	2379030	.	-	.	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	stop_codon	2374038	2374040	.	-	0	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	CDS	2374041	2374911	0.57	-	1	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	exon	2374041	2374911	.	-	.	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	intron	2374912	2374988	.	-	.	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	CDS	2374989	2378551	0.46	-	0	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	exon	2374989	2378551	.	-	.	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	intron	2378552	2378757	.	-	.	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	CDS	2378758	2379030	0.29	-	0	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	exon	2378758	2379030	.	-	.	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
Phchi.S1	AUGUSTUS	start_codon	2379028	2379030	.	-	0	transcript_id "Phchi.S1G039200.t1"; gene_id "Phchi.S1G039200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5118.t1 is derived from g2288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14815298	14817599	.	+	.	Phchi.S1G227700
Phchi.S1	AUGUSTUS	transcript	14815298	14817599	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	start_codon	14815298	14815300	.	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14815298	14815696	0.98	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14815298	14815696	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14815697	14815787	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14815788	14815898	1	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14815788	14815898	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14815899	14815987	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14815988	14816049	0.86	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14815988	14816049	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14816050	14816141	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14816142	14816483	0.87	+	1	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14816142	14816483	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14816484	14816659	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14816660	14816828	1	+	1	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14816660	14816828	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14816829	14816904	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14816905	14817144	1	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14816905	14817144	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14817145	14817240	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14817241	14817375	1	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14817241	14817375	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	intron	14817376	14817473	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	CDS	14817474	14817599	1	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	exon	14817474	14817599	.	+	.	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
Phchi.S1	AUGUSTUS	stop_codon	14817600	14817602	.	+	0	transcript_id "Phchi.S1G227700.t1"; gene_id "Phchi.S1G227700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5382.t1 is derived from g2552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16614292	16615362	.	-	.	Phchi.S1G254100
Phchi.S1	AUGUSTUS	transcript	16614292	16615362	.	-	.	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	stop_codon	16614289	16614291	.	-	0	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	CDS	16614292	16614450	0.99	-	0	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	exon	16614292	16614450	.	-	.	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	intron	16614451	16614630	.	-	.	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	CDS	16614631	16615362	1	-	0	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	exon	16614631	16615362	.	-	.	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
Phchi.S1	AUGUSTUS	start_codon	16615360	16615362	.	-	0	transcript_id "Phchi.S1G254100.t1"; gene_id "Phchi.S1G254100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13268.t1 is derived from g11733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4989387	4989887	.	+	.	Phchi.S3G058700
Phchi.S3	AUGUSTUS	transcript	4989387	4989887	.	+	.	transcript_id "Phchi.S3G058700.t1"; gene_id "Phchi.S3G058700"
Phchi.S3	AUGUSTUS	start_codon	4989387	4989389	.	+	0	transcript_id "Phchi.S3G058700.t1"; gene_id "Phchi.S3G058700"
Phchi.S3	AUGUSTUS	CDS	4989387	4989887	0.65	+	0	transcript_id "Phchi.S3G058700.t1"; gene_id "Phchi.S3G058700"
Phchi.S3	AUGUSTUS	exon	4989387	4989887	.	+	.	transcript_id "Phchi.S3G058700.t1"; gene_id "Phchi.S3G058700"
Phchi.S3	AUGUSTUS	stop_codon	4989888	4989890	.	+	0	transcript_id "Phchi.S3G058700.t1"; gene_id "Phchi.S3G058700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8679.t1 is derived from g5854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37399028	37400018	.	+	.	Phchi.S1G583800
Phchi.S1	AUGUSTUS	transcript	37399028	37400018	.	+	.	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	start_codon	37399028	37399030	.	+	0	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	CDS	37399028	37399292	0.36	+	0	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	exon	37399028	37399292	.	+	.	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	intron	37399293	37399478	.	+	.	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	CDS	37399479	37399706	0.61	+	2	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	exon	37399479	37399706	.	+	.	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	intron	37399707	37400016	.	+	.	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	CDS	37400017	37400018	1	+	2	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	exon	37400017	37400018	.	+	.	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
Phchi.S1	AUGUSTUS	stop_codon	37400019	37400021	.	+	0	transcript_id "Phchi.S1G583800.t1"; gene_id "Phchi.S1G583800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7640.t1 is derived from g4814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30370529	30372602	.	-	.	Phchi.S1G479900
Phchi.S1	AUGUSTUS	transcript	30370529	30372602	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	stop_codon	30370526	30370528	.	-	0	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30370529	30370711	0.84	-	0	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30370529	30370711	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30370712	30370794	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30370795	30371011	1	-	1	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30370795	30371011	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30371012	30371099	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30371100	30371222	1	-	1	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30371100	30371222	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30371223	30371324	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30371325	30371439	0.88	-	2	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30371325	30371439	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30371440	30371572	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30371573	30371625	1	-	1	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30371573	30371625	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30371626	30371717	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30371718	30371890	1	-	0	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30371718	30371890	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30371891	30372039	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30372040	30372116	0.7	-	2	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30372040	30372116	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30372117	30372247	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30372248	30372282	0.69	-	1	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30372248	30372282	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	intron	30372283	30372483	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	CDS	30372484	30372602	0.64	-	0	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	exon	30372484	30372602	.	-	.	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
Phchi.S1	AUGUSTUS	start_codon	30372600	30372602	.	-	0	transcript_id "Phchi.S1G479900.t1"; gene_id "Phchi.S1G479900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12883.t1 is derived from g11348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2929182	2930829	.	-	.	Phchi.S3G020200
Phchi.S3	AUGUSTUS	transcript	2929182	2930829	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	stop_codon	2929179	2929181	.	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929182	2929234	0.92	-	2	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929182	2929234	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929235	2929321	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929322	2929422	0.81	-	1	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929322	2929422	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929423	2929499	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929500	2929594	1	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929500	2929594	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929595	2929678	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929679	2929798	1	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929679	2929798	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929799	2929894	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929895	2930032	1	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929895	2930032	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930033	2930171	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930172	2930253	1	-	1	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930172	2930253	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930254	2930353	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930354	2930466	1	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930354	2930466	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930467	2930569	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930570	2930652	1	-	2	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930570	2930652	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930653	2930813	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930814	2930829	1	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930814	2930829	.	-	.	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	start_codon	2930827	2930829	.	-	0	transcript_id "Phchi.S3G020200.t1"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	transcript	2929182	2930829	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	stop_codon	2929179	2929181	.	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929182	2929234	0.88	-	2	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929182	2929234	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929235	2929321	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929322	2929422	0.77	-	1	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929322	2929422	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929423	2929499	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929500	2929594	0.98	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929500	2929594	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929595	2929678	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929679	2929798	1	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929679	2929798	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929799	2929894	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929895	2930032	1	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929895	2930032	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930033	2930171	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930172	2930253	1	-	1	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930172	2930253	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930254	2930353	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930354	2930482	0.94	-	1	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930354	2930482	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930483	2930569	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930570	2930652	0.94	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930570	2930652	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930653	2930742	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930743	2930829	0.55	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930743	2930829	.	-	.	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	start_codon	2930827	2930829	.	-	0	transcript_id "Phchi.S3G020200.t2"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	transcript	2929182	2930829	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	stop_codon	2929179	2929181	.	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929182	2929234	0.92	-	2	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929182	2929234	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929235	2929321	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929322	2929422	0.88	-	1	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929322	2929422	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929423	2929570	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929571	2929611	0.67	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929571	2929611	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929612	2929678	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929679	2929798	1	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929679	2929798	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2929799	2929894	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2929895	2930032	1	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2929895	2930032	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930033	2930171	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930172	2930253	1	-	1	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930172	2930253	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930254	2930353	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930354	2930482	0.91	-	1	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930354	2930482	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930483	2930569	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930570	2930652	0.91	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930570	2930652	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	intron	2930653	2930742	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	CDS	2930743	2930829	0.62	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	exon	2930743	2930829	.	-	.	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
Phchi.S3	AUGUSTUS	start_codon	2930827	2930829	.	-	0	transcript_id "Phchi.S3G020200.t3"; gene_id "Phchi.S3G020200"
# This transcript jg1117.t2 is derived from g10900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1118.t1 is derived from g10901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7788369	7790791	.	-	.	Phchi.S6G107700
Phchi.S6	AUGUSTUS	transcript	7788369	7790791	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	stop_codon	7788366	7788368	.	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7788369	7788404	1	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7788369	7788404	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7788405	7788548	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7788549	7788560	1	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7788549	7788560	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7788561	7788652	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7788653	7788928	0.99	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7788653	7788928	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7788929	7789013	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7789014	7789106	0.97	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7789014	7789106	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7789107	7789218	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7789219	7789351	0.56	-	1	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7789219	7789351	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7789352	7789464	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7789465	7789611	1	-	1	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7789465	7789611	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7789612	7789708	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7789709	7789875	1	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7789709	7789875	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7789876	7790004	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7790005	7790109	1	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7790005	7790109	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7790110	7790470	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7790471	7790526	0.85	-	2	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7790471	7790526	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	intron	7790527	7790754	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	CDS	7790755	7790791	0.67	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	exon	7790755	7790791	.	-	.	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
Phchi.S6	AUGUSTUS	start_codon	7790789	7790791	.	-	0	transcript_id "Phchi.S6G107700.t1"; gene_id "Phchi.S6G107700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7091.t1 is derived from g4263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26863989	26866330	.	-	.	Phchi.S1G425000
Phchi.S1	AUGUSTUS	transcript	26863989	26866330	.	-	.	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	stop_codon	26863986	26863988	.	-	0	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	CDS	26863989	26864198	1	-	0	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	exon	26863989	26864198	.	-	.	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	intron	26864199	26864282	.	-	.	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	CDS	26864283	26864750	1	-	0	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	exon	26864283	26864750	.	-	.	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	intron	26864751	26864833	.	-	.	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	CDS	26864834	26866330	1	-	0	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	exon	26864834	26866330	.	-	.	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
Phchi.S1	AUGUSTUS	start_codon	26866328	26866330	.	-	0	transcript_id "Phchi.S1G425000.t1"; gene_id "Phchi.S1G425000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1533.t1 is derived from g8452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1627932	1630083	.	+	.	Phchi.S5G014200
Phchi.S5	AUGUSTUS	transcript	1627932	1630083	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	start_codon	1627932	1627934	.	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1627932	1628114	0.78	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1627932	1628114	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1628115	1628219	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1628220	1628435	0.8	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1628220	1628435	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1628436	1628517	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1628518	1628595	1	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1628518	1628595	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1628596	1628747	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1628748	1628972	1	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1628748	1628972	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1628973	1629128	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1629129	1629230	1	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1629129	1629230	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1629231	1629311	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1629312	1629370	1	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1629312	1629370	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1629371	1629696	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1629697	1629847	1	+	1	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1629697	1629847	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	intron	1629848	1629930	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	CDS	1629931	1630083	0.8	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	exon	1629931	1630083	.	+	.	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
Phchi.S5	AUGUSTUS	stop_codon	1630084	1630086	.	+	0	transcript_id "Phchi.S5G014200.t1"; gene_id "Phchi.S5G014200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1523.t1 is derived from g8442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1536483	1538094	.	-	.	Phchi.S5G013200
Phchi.S5	AUGUSTUS	transcript	1536483	1538094	.	-	.	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	stop_codon	1536480	1536482	.	-	0	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	CDS	1536483	1537229	1	-	0	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	exon	1536483	1537229	.	-	.	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	intron	1537230	1537325	.	-	.	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	CDS	1537326	1537612	0.99	-	2	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	exon	1537326	1537612	.	-	.	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	intron	1537613	1537784	.	-	.	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	CDS	1537785	1538094	0.98	-	0	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	exon	1537785	1538094	.	-	.	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
Phchi.S5	AUGUSTUS	start_codon	1538092	1538094	.	-	0	transcript_id "Phchi.S5G013200.t1"; gene_id "Phchi.S5G013200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11681.t1 is derived from g15732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7646785	7650297	.	-	.	Phchi.S4G126300
Phchi.S4	AUGUSTUS	transcript	7646785	7650297	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	stop_codon	7646491	7646493	.	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7646785	7646848	1	-	1	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7646785	7646848	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7646849	7647661	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7647662	7647715	1	-	1	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7647662	7647715	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7647716	7647893	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7647894	7648029	1	-	2	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7647894	7648029	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7648030	7648123	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7648124	7648182	1	-	1	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7648124	7648182	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7648183	7648299	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7648300	7648438	1	-	2	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7648300	7648438	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7648439	7648568	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7648569	7648645	1	-	1	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7648569	7648645	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7648646	7648768	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7648769	7648908	1	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7648769	7648908	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7648909	7649075	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7649076	7649139	1	-	1	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7649076	7649139	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7649140	7649226	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7649227	7649324	1	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7649227	7649324	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7649325	7649463	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7649464	7649589	1	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7649464	7649589	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7649590	7649753	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7649754	7649842	1	-	2	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7649754	7649842	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7649843	7649975	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7649976	7650105	1	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7649976	7650105	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	intron	7650106	7650210	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	CDS	7650211	7650297	0.94	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	exon	7650211	7650297	.	-	.	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
Phchi.S4	AUGUSTUS	start_codon	7650295	7650297	.	-	0	transcript_id "Phchi.S4G126300.t1"; gene_id "Phchi.S4G126300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg120.t1 is derived from g9902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	681536	682792	.	+	.	Phchi.S6G007900
Phchi.S6	AUGUSTUS	transcript	681536	682792	.	+	.	transcript_id "Phchi.S6G007900.t1"; gene_id "Phchi.S6G007900"
Phchi.S6	AUGUSTUS	start_codon	681536	681538	.	+	0	transcript_id "Phchi.S6G007900.t1"; gene_id "Phchi.S6G007900"
Phchi.S6	AUGUSTUS	CDS	681536	682792	0.79	+	0	transcript_id "Phchi.S6G007900.t1"; gene_id "Phchi.S6G007900"
Phchi.S6	AUGUSTUS	exon	681536	682792	.	+	.	transcript_id "Phchi.S6G007900.t1"; gene_id "Phchi.S6G007900"
Phchi.S6	AUGUSTUS	stop_codon	682793	682795	.	+	0	transcript_id "Phchi.S6G007900.t1"; gene_id "Phchi.S6G007900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12604.t1 is derived from g8281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37471738	37472713	.	-	.	Phchi.S2G068400
Phchi.S2	AUGUSTUS	transcript	37471738	37472713	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	stop_codon	37471735	37471737	.	-	0	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37471738	37471770	0.91	-	0	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37471738	37471770	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37471771	37472032	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472033	37472150	0.92	-	1	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472033	37472150	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37472151	37472224	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472225	37472336	0.87	-	2	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472225	37472336	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37472337	37472438	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472439	37472515	1	-	1	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472439	37472515	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37472516	37472609	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472610	37472713	0.55	-	0	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472610	37472713	.	-	.	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	start_codon	37472711	37472713	.	-	0	transcript_id "Phchi.S2G068400.t1"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	transcript	37472024	37472713	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	stop_codon	37472021	37472023	.	-	0	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472024	37472150	0.88	-	1	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472024	37472150	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37472151	37472224	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472225	37472336	0.87	-	2	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472225	37472336	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37472337	37472438	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472439	37472515	0.99	-	1	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472439	37472515	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	intron	37472516	37472609	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	CDS	37472610	37472713	0.61	-	0	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	exon	37472610	37472713	.	-	.	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
Phchi.S2	AUGUSTUS	start_codon	37472711	37472713	.	-	0	transcript_id "Phchi.S2G068400.t2"; gene_id "Phchi.S2G068400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10830.t1 is derived from g14880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2327935	2329812	.	+	.	Phchi.S4G041200
Phchi.S4	AUGUSTUS	transcript	2327935	2329812	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	start_codon	2327935	2327937	.	+	0	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	CDS	2327935	2328267	0.46	+	0	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	exon	2327935	2328267	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	intron	2328268	2328366	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	CDS	2328367	2328629	0.99	+	0	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	exon	2328367	2328629	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	intron	2328630	2328761	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	CDS	2328762	2328879	1	+	1	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	exon	2328762	2328879	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	intron	2328880	2328977	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	CDS	2328978	2329186	1	+	0	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	exon	2328978	2329186	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	intron	2329187	2329346	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	CDS	2329347	2329812	1	+	1	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	exon	2329347	2329812	.	+	.	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
Phchi.S4	AUGUSTUS	stop_codon	2329813	2329815	.	+	0	transcript_id "Phchi.S4G041200.t1"; gene_id "Phchi.S4G041200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3188.t1 is derived from g357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2144535	2148731	.	+	.	Phchi.S1G034700
Phchi.S1	AUGUSTUS	transcript	2144535	2148731	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	start_codon	2144535	2144537	.	+	0	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	CDS	2144535	2147377	0.76	+	0	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	exon	2144535	2147377	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	intron	2147378	2147482	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	CDS	2147483	2147574	0.86	+	1	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	exon	2147483	2147574	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	intron	2147575	2147653	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	CDS	2147654	2147807	0.26	+	2	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	exon	2147654	2147807	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	intron	2147808	2147936	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	CDS	2147937	2148007	0.36	+	1	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	exon	2147937	2148007	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	intron	2148008	2148169	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	CDS	2148170	2148310	0.96	+	2	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	exon	2148170	2148310	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	intron	2148311	2148507	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	CDS	2148508	2148731	0.98	+	2	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	exon	2148508	2148731	.	+	.	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
Phchi.S1	AUGUSTUS	stop_codon	2148732	2148734	.	+	0	transcript_id "Phchi.S1G034700.t1"; gene_id "Phchi.S1G034700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11212.t1 is derived from g15262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4801227	4804388	.	-	.	Phchi.S4G079400
Phchi.S4	AUGUSTUS	transcript	4801227	4804388	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	stop_codon	4801224	4801226	.	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4801227	4801301	0.94	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4801227	4801301	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4801302	4801402	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4801403	4801515	0.94	-	2	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4801403	4801515	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4801516	4801594	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4801595	4801703	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4801595	4801703	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4801704	4801837	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4801838	4801936	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4801838	4801936	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4801937	4802040	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4802041	4802175	0.93	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4802041	4802175	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4802176	4802284	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4802285	4802459	0.95	-	1	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4802285	4802459	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4802460	4802568	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4802569	4802627	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4802569	4802627	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4802628	4802773	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4802774	4802890	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4802774	4802890	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4802891	4803014	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4803015	4803116	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4803015	4803116	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4803117	4803221	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4803222	4803297	1	-	1	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4803222	4803297	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4803298	4803379	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4803380	4803441	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4803380	4803441	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4803442	4803528	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4803529	4803684	0.65	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4803529	4803684	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4803685	4803779	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4803780	4803899	1	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4803780	4803899	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4803900	4803989	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4803990	4804137	0.98	-	1	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4803990	4804137	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	intron	4804138	4804257	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	CDS	4804258	4804388	0.97	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	exon	4804258	4804388	.	-	.	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
Phchi.S4	AUGUSTUS	start_codon	4804386	4804388	.	-	0	transcript_id "Phchi.S4G079400.t1"; gene_id "Phchi.S4G079400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7805.t1 is derived from g4979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31265927	31267054	.	-	.	Phchi.S1G496400
Phchi.S1	AUGUSTUS	transcript	31265927	31267054	.	-	.	transcript_id "Phchi.S1G496400.t1"; gene_id "Phchi.S1G496400"
Phchi.S1	AUGUSTUS	stop_codon	31265924	31265926	.	-	0	transcript_id "Phchi.S1G496400.t1"; gene_id "Phchi.S1G496400"
Phchi.S1	AUGUSTUS	CDS	31265927	31267054	0.68	-	0	transcript_id "Phchi.S1G496400.t1"; gene_id "Phchi.S1G496400"
Phchi.S1	AUGUSTUS	exon	31265927	31267054	.	-	.	transcript_id "Phchi.S1G496400.t1"; gene_id "Phchi.S1G496400"
Phchi.S1	AUGUSTUS	start_codon	31267052	31267054	.	-	0	transcript_id "Phchi.S1G496400.t1"; gene_id "Phchi.S1G496400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3481.t1 is derived from g650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3999327	3999821	.	-	.	Phchi.S1G064000
Phchi.S1	AUGUSTUS	transcript	3999327	3999821	.	-	.	transcript_id "Phchi.S1G064000.t1"; gene_id "Phchi.S1G064000"
Phchi.S1	AUGUSTUS	stop_codon	3999324	3999326	.	-	0	transcript_id "Phchi.S1G064000.t1"; gene_id "Phchi.S1G064000"
Phchi.S1	AUGUSTUS	CDS	3999327	3999821	0.29	-	0	transcript_id "Phchi.S1G064000.t1"; gene_id "Phchi.S1G064000"
Phchi.S1	AUGUSTUS	exon	3999327	3999821	.	-	.	transcript_id "Phchi.S1G064000.t1"; gene_id "Phchi.S1G064000"
Phchi.S1	AUGUSTUS	start_codon	3999819	3999821	.	-	0	transcript_id "Phchi.S1G064000.t1"; gene_id "Phchi.S1G064000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11478.t1 is derived from g15528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6565846	6566578	.	-	.	Phchi.S4G106000
Phchi.S4	AUGUSTUS	transcript	6565846	6566578	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	stop_codon	6565843	6565845	.	-	0	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	CDS	6565846	6565953	0.65	-	0	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	exon	6565846	6565953	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	intron	6565954	6566112	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	CDS	6566113	6566170	0.85	-	1	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	exon	6566113	6566170	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	intron	6566171	6566251	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	CDS	6566252	6566275	0.85	-	1	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	exon	6566252	6566275	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	intron	6566276	6566561	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	CDS	6566562	6566578	1	-	0	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	exon	6566562	6566578	.	-	.	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
Phchi.S4	AUGUSTUS	start_codon	6566576	6566578	.	-	0	transcript_id "Phchi.S4G106000.t1"; gene_id "Phchi.S4G106000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1133.t1 is derived from g10916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7875332	7876427	.	+	.	Phchi.S6G109200
Phchi.S6	AUGUSTUS	transcript	7875332	7876427	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	start_codon	7875332	7875334	.	+	0	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	CDS	7875332	7875681	0.68	+	0	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	exon	7875332	7875681	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	intron	7875682	7875798	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	CDS	7875799	7875886	1	+	1	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	exon	7875799	7875886	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	intron	7875887	7875972	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	CDS	7875973	7876100	1	+	0	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	exon	7875973	7876100	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	intron	7876101	7876230	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	CDS	7876231	7876289	0.75	+	1	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	exon	7876231	7876289	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	intron	7876290	7876386	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	CDS	7876387	7876427	0.48	+	2	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	exon	7876387	7876427	.	+	.	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
Phchi.S6	AUGUSTUS	stop_codon	7876428	7876430	.	+	0	transcript_id "Phchi.S6G109200.t1"; gene_id "Phchi.S6G109200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3848.t1 is derived from g1017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6021807	6025204	.	-	.	Phchi.S1G100700
Phchi.S1	AUGUSTUS	transcript	6021807	6025204	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	stop_codon	6021804	6021806	.	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6021807	6022112	0.92	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6021807	6022112	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6022113	6022198	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6022199	6022987	0.96	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6022199	6022987	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6022988	6023090	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6023091	6023177	1	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6023091	6023177	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6023178	6023312	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6023313	6023447	0.95	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6023313	6023447	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6023448	6023555	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6023556	6023735	1	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6023556	6023735	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6023736	6023899	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6023900	6023971	1	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6023900	6023971	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6023972	6024197	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6024198	6024380	1	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6024198	6024380	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6024381	6024477	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6024478	6024632	1	-	2	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6024478	6024632	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	intron	6024633	6024720	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	CDS	6024721	6025204	0.31	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	exon	6024721	6025204	.	-	.	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
Phchi.S1	AUGUSTUS	start_codon	6025202	6025204	.	-	0	transcript_id "Phchi.S1G100700.t1"; gene_id "Phchi.S1G100700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13150.t1 is derived from g11615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4406986	4407381	.	+	.	Phchi.S3G046900
Phchi.S3	AUGUSTUS	transcript	4406986	4407381	.	+	.	transcript_id "Phchi.S3G046900.t1"; gene_id "Phchi.S3G046900"
Phchi.S3	AUGUSTUS	start_codon	4406986	4406988	.	+	0	transcript_id "Phchi.S3G046900.t1"; gene_id "Phchi.S3G046900"
Phchi.S3	AUGUSTUS	CDS	4406986	4407381	0.48	+	0	transcript_id "Phchi.S3G046900.t1"; gene_id "Phchi.S3G046900"
Phchi.S3	AUGUSTUS	exon	4406986	4407381	.	+	.	transcript_id "Phchi.S3G046900.t1"; gene_id "Phchi.S3G046900"
Phchi.S3	AUGUSTUS	stop_codon	4407382	4407384	.	+	0	transcript_id "Phchi.S3G046900.t1"; gene_id "Phchi.S3G046900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14547.t1 is derived from g13015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13420855	13423059	.	+	.	Phchi.S3G186600
Phchi.S3	AUGUSTUS	transcript	13420855	13423059	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	start_codon	13420855	13420857	.	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13420855	13421160	0.66	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13420855	13421160	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	intron	13421161	13421293	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13421294	13421410	1	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13421294	13421410	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	intron	13421411	13421560	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13421561	13421649	0.79	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13421561	13421649	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	intron	13421650	13421735	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13421736	13421772	0.96	+	1	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13421736	13421772	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	intron	13421773	13422405	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13422406	13422546	1	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13422406	13422546	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	intron	13422547	13422674	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13422675	13422754	0.88	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13422675	13422754	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	intron	13422755	13422968	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	CDS	13422969	13423059	0.43	+	1	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	exon	13422969	13423059	.	+	.	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
Phchi.S3	AUGUSTUS	stop_codon	13423060	13423062	.	+	0	transcript_id "Phchi.S3G186600.t1"; gene_id "Phchi.S3G186600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg591.t1 is derived from g10373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4323248	4326529	.	-	.	Phchi.S6G055000
Phchi.S6	AUGUSTUS	transcript	4323248	4326529	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	stop_codon	4323245	4323247	.	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	CDS	4323248	4323565	0.82	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	exon	4323248	4323565	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	intron	4323566	4323644	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	CDS	4323645	4324115	1	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	exon	4323645	4324115	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	intron	4324116	4324227	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	CDS	4324228	4324344	0.99	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	exon	4324228	4324344	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	intron	4324345	4324442	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	CDS	4324443	4324499	0.85	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	exon	4324443	4324499	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	intron	4324500	4324652	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	CDS	4324653	4324751	0.45	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	exon	4324653	4324751	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	intron	4324752	4324864	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	CDS	4324865	4326529	0.42	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	exon	4324865	4326529	.	-	.	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
Phchi.S6	AUGUSTUS	start_codon	4326527	4326529	.	-	0	transcript_id "Phchi.S6G055000.t1"; gene_id "Phchi.S6G055000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10968.t1 is derived from g15018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3406026	3406797	.	+	.	Phchi.S4G055000
Phchi.S4	AUGUSTUS	transcript	3406026	3406797	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	start_codon	3406026	3406028	.	+	0	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	CDS	3406026	3406028	0.75	+	0	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	exon	3406026	3406028	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	intron	3406029	3406186	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	CDS	3406187	3406260	0.42	+	0	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	exon	3406187	3406260	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	intron	3406261	3406322	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	CDS	3406323	3406451	0.73	+	1	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	exon	3406323	3406451	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	intron	3406452	3406649	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	CDS	3406650	3406797	1	+	1	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	exon	3406650	3406797	.	+	.	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
Phchi.S4	AUGUSTUS	stop_codon	3406798	3406800	.	+	0	transcript_id "Phchi.S4G055000.t1"; gene_id "Phchi.S4G055000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3785.t1 is derived from g954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5712830	5713389	.	-	.	Phchi.S1G094400
Phchi.S1	AUGUSTUS	transcript	5712830	5713348	.	-	.	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	stop_codon	5712827	5712829	.	-	0	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	CDS	5712830	5712946	0.99	-	0	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	exon	5712830	5712946	.	-	.	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	intron	5712947	5713088	.	-	.	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	CDS	5713089	5713154	0.99	-	0	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	exon	5713089	5713154	.	-	.	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	intron	5713155	5713225	.	-	.	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	CDS	5713226	5713348	0.76	-	0	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	exon	5713226	5713348	.	-	.	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	start_codon	5713346	5713348	.	-	0	transcript_id "Phchi.S1G094400.t1"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	transcript	5712830	5713389	.	-	.	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	stop_codon	5712827	5712829	.	-	0	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	CDS	5712830	5712946	0.6	-	0	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	exon	5712830	5712946	.	-	.	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	intron	5712947	5713088	.	-	.	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	CDS	5713089	5713154	0.6	-	0	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	exon	5713089	5713154	.	-	.	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	intron	5713155	5713368	.	-	.	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	CDS	5713369	5713389	0.21	-	0	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	exon	5713369	5713389	.	-	.	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
Phchi.S1	AUGUSTUS	start_codon	5713387	5713389	.	-	0	transcript_id "Phchi.S1G094400.t2"; gene_id "Phchi.S1G094400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9718.t1 is derived from g6894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43392699	43393550	.	+	.	Phchi.S1G687700
Phchi.S1	AUGUSTUS	transcript	43392699	43393550	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	start_codon	43392699	43392701	.	+	0	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	CDS	43392699	43392701	1	+	0	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	exon	43392699	43392701	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	intron	43392702	43392801	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	CDS	43392802	43392882	1	+	0	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	exon	43392802	43392882	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	intron	43392883	43393015	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	CDS	43393016	43393150	1	+	0	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	exon	43393016	43393150	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	intron	43393151	43393439	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	CDS	43393440	43393550	1	+	0	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	exon	43393440	43393550	.	+	.	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
Phchi.S1	AUGUSTUS	stop_codon	43393551	43393553	.	+	0	transcript_id "Phchi.S1G687700.t1"; gene_id "Phchi.S1G687700"
# This transcript jg2229.t2 is derived from g9149.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2230.t1 is derived from g9150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5561856	5563322	.	-	.	Phchi.S5G083900
Phchi.S5	AUGUSTUS	transcript	5561856	5563322	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	stop_codon	5561853	5561855	.	-	0	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	CDS	5561856	5562626	1	-	0	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	exon	5561856	5562626	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	intron	5562627	5562816	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	CDS	5562817	5562919	1	-	1	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	exon	5562817	5562919	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	intron	5562920	5563003	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	CDS	5563004	5563050	1	-	0	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	exon	5563004	5563050	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	intron	5563051	5563174	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	CDS	5563175	5563221	1	-	2	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	exon	5563175	5563221	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	intron	5563222	5563291	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	CDS	5563292	5563322	1	-	0	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	exon	5563292	5563322	.	-	.	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
Phchi.S5	AUGUSTUS	start_codon	5563320	5563322	.	-	0	transcript_id "Phchi.S5G083900.t1"; gene_id "Phchi.S5G083900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5090.t1 is derived from g2260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14702208	14703741	.	-	.	Phchi.S1G224900
Phchi.S1	AUGUSTUS	transcript	14702208	14703741	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	stop_codon	14702205	14702207	.	-	0	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	CDS	14702208	14702410	0.84	-	2	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	exon	14702208	14702410	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	intron	14702411	14702510	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	CDS	14702511	14702738	1	-	2	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	exon	14702511	14702738	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	intron	14702739	14702874	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	CDS	14702875	14703030	1	-	2	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	exon	14702875	14703030	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	intron	14703031	14703296	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	CDS	14703297	14703741	0.92	-	0	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	exon	14703297	14703741	.	-	.	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
Phchi.S1	AUGUSTUS	start_codon	14703739	14703741	.	-	0	transcript_id "Phchi.S1G224900.t1"; gene_id "Phchi.S1G224900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10818.t1 is derived from g14868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2255772	2256954	.	-	.	Phchi.S4G040000
Phchi.S4	AUGUSTUS	transcript	2255772	2256954	.	-	.	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	stop_codon	2255769	2255771	.	-	0	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	CDS	2255772	2256310	0.7	-	2	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	exon	2255772	2256310	.	-	.	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	intron	2256311	2256420	.	-	.	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	CDS	2256421	2256568	0.74	-	0	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	exon	2256421	2256568	.	-	.	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	intron	2256569	2256663	.	-	.	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	CDS	2256664	2256954	0.56	-	0	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	exon	2256664	2256954	.	-	.	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
Phchi.S4	AUGUSTUS	start_codon	2256952	2256954	.	-	0	transcript_id "Phchi.S4G040000.t1"; gene_id "Phchi.S4G040000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg80.t1 is derived from g9862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	411467	414959	.	+	.	Phchi.S6G003900
Phchi.S6	AUGUSTUS	transcript	411467	414959	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	start_codon	411467	411469	.	+	0	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	CDS	411467	412172	0.62	+	0	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	exon	411467	412172	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	intron	412173	412333	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	CDS	412334	413733	0.96	+	2	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	exon	412334	413733	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	intron	413734	413823	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	CDS	413824	414512	0.54	+	0	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	exon	413824	414512	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	intron	414513	414583	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	CDS	414584	414959	0.53	+	1	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	exon	414584	414959	.	+	.	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
Phchi.S6	AUGUSTUS	stop_codon	414960	414962	.	+	0	transcript_id "Phchi.S6G003900.t1"; gene_id "Phchi.S6G003900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9073.t1 is derived from g6248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39721946	39724038	.	+	.	Phchi.S1G623200
Phchi.S1	AUGUSTUS	transcript	39721946	39724038	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	start_codon	39721946	39721948	.	+	0	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	CDS	39721946	39722095	1	+	0	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	exon	39721946	39722095	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	intron	39722096	39722182	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	CDS	39722183	39722386	0.64	+	0	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	exon	39722183	39722386	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	intron	39722387	39722494	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	CDS	39722495	39722949	0.6	+	0	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	exon	39722495	39722949	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	intron	39722950	39723240	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	CDS	39723241	39723719	0.32	+	1	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	exon	39723241	39723719	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	intron	39723720	39724012	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	CDS	39724013	39724038	0.61	+	2	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	exon	39724013	39724038	.	+	.	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
Phchi.S1	AUGUSTUS	stop_codon	39724039	39724041	.	+	0	transcript_id "Phchi.S1G623200.t1"; gene_id "Phchi.S1G623200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12110.t1 is derived from g7786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3568214	3570186	.	-	.	Phchi.S2G019000
Phchi.S2	AUGUSTUS	transcript	3568214	3570186	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	stop_codon	3568211	3568213	.	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3568214	3568306	0.97	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3568214	3568306	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3568307	3568473	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3568474	3568558	1	-	1	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3568474	3568558	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3568559	3568734	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3568735	3568826	1	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3568735	3568826	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3568827	3569178	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569179	3569289	1	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569179	3569289	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569290	3569381	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569382	3569456	1	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569382	3569456	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569457	3569600	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569601	3569699	1	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569601	3569699	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569700	3569777	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569778	3569985	1	-	1	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569778	3569985	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569986	3570067	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3570068	3570186	1	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3570068	3570186	.	-	.	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	start_codon	3570184	3570186	.	-	0	transcript_id "Phchi.S2G019000.t1"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	transcript	3569276	3570186	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	stop_codon	3569273	3569275	.	-	0	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569276	3569289	0.58	-	2	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569276	3569289	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569290	3569381	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569382	3569502	0.58	-	0	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569382	3569502	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569503	3569600	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569601	3569699	1	-	0	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569601	3569699	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569700	3569777	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3569778	3569985	1	-	1	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3569778	3569985	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	intron	3569986	3570067	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	CDS	3570068	3570186	1	-	0	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	exon	3570068	3570186	.	-	.	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
Phchi.S2	AUGUSTUS	start_codon	3570184	3570186	.	-	0	transcript_id "Phchi.S2G019000.t2"; gene_id "Phchi.S2G019000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1241.t1 is derived from g11024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8559325	8562739	.	-	.	Phchi.S6G120000
Phchi.S6	AUGUSTUS	transcript	8559325	8562739	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	stop_codon	8559322	8559324	.	-	0	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8559325	8560372	0.97	-	1	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8559325	8560372	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8560373	8560544	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8560545	8560670	0.99	-	1	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8560545	8560670	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8560671	8560780	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8560781	8561006	1	-	2	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8560781	8561006	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8561007	8561104	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8561105	8561207	1	-	0	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8561105	8561207	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8561208	8561308	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8561309	8561346	1	-	2	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8561309	8561346	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8561347	8561433	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8561434	8561472	1	-	2	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8561434	8561472	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8561473	8561966	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8561967	8562470	1	-	2	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8561967	8562470	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	intron	8562471	8562687	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	CDS	8562688	8562739	0.76	-	0	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	exon	8562688	8562739	.	-	.	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
Phchi.S6	AUGUSTUS	start_codon	8562737	8562739	.	-	0	transcript_id "Phchi.S6G120000.t1"; gene_id "Phchi.S6G120000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10667.t1 is derived from g14717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1506475	1508697	.	+	.	Phchi.S4G024900
Phchi.S4	AUGUSTUS	transcript	1506475	1508697	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	start_codon	1506475	1506477	.	+	0	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	CDS	1506475	1506565	0.53	+	0	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	exon	1506475	1506565	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	intron	1506566	1506691	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	CDS	1506692	1506865	1	+	2	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	exon	1506692	1506865	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	intron	1506866	1506954	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	CDS	1506955	1507235	1	+	2	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	exon	1506955	1507235	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	intron	1507236	1507393	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	CDS	1507394	1507694	1	+	0	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	exon	1507394	1507694	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	intron	1507695	1507843	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	CDS	1507844	1508113	1	+	2	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	exon	1507844	1508113	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	intron	1508114	1508245	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	CDS	1508246	1508697	1	+	2	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	exon	1508246	1508697	.	+	.	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
Phchi.S4	AUGUSTUS	stop_codon	1508698	1508700	.	+	0	transcript_id "Phchi.S4G024900.t1"; gene_id "Phchi.S4G024900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11604.t1 is derived from g15655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7298526	7299832	.	+	.	Phchi.S4G118600
Phchi.S4	AUGUSTUS	transcript	7298526	7299832	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	start_codon	7298526	7298528	.	+	0	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7298526	7298749	1	+	0	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7298526	7298749	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7298750	7298917	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7298918	7299152	1	+	1	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7298918	7299152	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7299153	7299228	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7299229	7299447	1	+	0	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7299229	7299447	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7299448	7299551	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7299552	7299577	1	+	0	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7299552	7299577	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7299578	7299663	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7299664	7299832	1	+	1	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7299664	7299832	.	+	.	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	stop_codon	7299833	7299835	.	+	0	transcript_id "Phchi.S4G118600.t1"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	transcript	7298526	7299832	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	start_codon	7298526	7298528	.	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7298526	7298549	0.88	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7298526	7298549	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7298550	7298695	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7298696	7298749	0.91	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7298696	7298749	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7298750	7298897	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7298898	7299152	0.98	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7298898	7299152	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7299153	7299228	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7299229	7299447	1	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7299229	7299447	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7299448	7299551	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7299552	7299577	1	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7299552	7299577	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	intron	7299578	7299663	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	CDS	7299664	7299832	1	+	1	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	exon	7299664	7299832	.	+	.	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
Phchi.S4	AUGUSTUS	stop_codon	7299833	7299835	.	+	0	transcript_id "Phchi.S4G118600.t2"; gene_id "Phchi.S4G118600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13072.t1 is derived from g11537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4025219	4026221	.	+	.	Phchi.S3G039100
Phchi.S3	AUGUSTUS	transcript	4025219	4026221	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	start_codon	4025219	4025221	.	+	0	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	CDS	4025219	4025325	0.98	+	0	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	exon	4025219	4025325	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	intron	4025326	4025415	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	CDS	4025416	4025494	1	+	1	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	exon	4025416	4025494	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	intron	4025495	4025638	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	CDS	4025639	4025728	1	+	0	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	exon	4025639	4025728	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	intron	4025729	4025817	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	CDS	4025818	4025911	1	+	0	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	exon	4025818	4025911	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	intron	4025912	4026007	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	CDS	4026008	4026055	1	+	2	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	exon	4026008	4026055	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	intron	4026056	4026141	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	CDS	4026142	4026221	1	+	2	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	exon	4026142	4026221	.	+	.	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
Phchi.S3	AUGUSTUS	stop_codon	4026222	4026224	.	+	0	transcript_id "Phchi.S3G039100.t1"; gene_id "Phchi.S3G039100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4678.t1 is derived from g1848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11792249	11793635	.	-	.	Phchi.S1G183700
Phchi.S1	AUGUSTUS	transcript	11792249	11793635	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	stop_codon	11792246	11792248	.	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11792249	11792276	0.98	-	1	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11792249	11792276	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11792277	11792382	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11792383	11792462	0.99	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11792383	11792462	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11792463	11792567	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11792568	11792615	1	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11792568	11792615	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11792616	11792755	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11792756	11792804	1	-	1	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11792756	11792804	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11792805	11792893	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11792894	11792946	1	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11792894	11792946	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11792947	11793030	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11793031	11793126	1	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11793031	11793126	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11793127	11793198	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11793199	11793298	1	-	1	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11793199	11793298	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	intron	11793299	11793390	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	CDS	11793391	11793635	0.63	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	exon	11793391	11793635	.	-	.	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
Phchi.S1	AUGUSTUS	start_codon	11793633	11793635	.	-	0	transcript_id "Phchi.S1G183700.t1"; gene_id "Phchi.S1G183700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10973.t1 is derived from g15023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3424104	3424827	.	+	.	Phchi.S4G055500
Phchi.S4	AUGUSTUS	transcript	3424104	3424827	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	start_codon	3424104	3424106	.	+	0	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	CDS	3424104	3424175	0.81	+	0	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	exon	3424104	3424175	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	intron	3424176	3424386	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	CDS	3424387	3424498	0.96	+	0	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	exon	3424387	3424498	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	intron	3424499	3424616	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	CDS	3424617	3424626	0.99	+	2	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	exon	3424617	3424626	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	intron	3424627	3424796	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	CDS	3424797	3424827	0.99	+	1	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	exon	3424797	3424827	.	+	.	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
Phchi.S4	AUGUSTUS	stop_codon	3424828	3424830	.	+	0	transcript_id "Phchi.S4G055500.t1"; gene_id "Phchi.S4G055500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1421.t1 is derived from g8340.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	775781	780243	.	-	.	Phchi.S5G003000
Phchi.S5	AUGUSTUS	transcript	775781	780188	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	stop_codon	775778	775780	.	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	775781	776214	1	-	2	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	775781	776214	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776215	776312	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776313	776537	1	-	2	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776313	776537	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776538	776625	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776626	776907	0.97	-	2	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776626	776907	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776908	776979	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776980	777232	0.9	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776980	777232	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777233	777329	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777330	777422	1	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777330	777422	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777423	777641	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777642	777800	1	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777642	777800	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777801	777899	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777900	778077	0.5	-	1	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777900	778077	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778078	778223	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778224	778285	0.91	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778224	778285	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778286	778375	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778376	778386	0.65	-	2	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778376	778386	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778387	778481	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778482	778556	0.87	-	2	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778482	778556	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778557	778751	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778752	778797	0.98	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778752	778797	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778798	778877	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778878	778961	1	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778878	778961	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778962	779108	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779109	779376	0.83	-	1	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779109	779376	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779377	779654	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779655	779741	0.98	-	1	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779655	779741	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779742	779843	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779844	780061	0.67	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779844	780061	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	780062	780137	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	780138	780188	0.67	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	780138	780188	.	-	.	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	start_codon	780186	780188	.	-	0	transcript_id "Phchi.S5G003000.t1"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	transcript	775781	780243	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	stop_codon	775778	775780	.	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	775781	776214	1	-	2	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	775781	776214	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776215	776312	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776313	776537	1	-	2	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776313	776537	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776538	776625	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776626	776907	0.97	-	2	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776626	776907	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776908	776979	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776980	777232	0.92	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776980	777232	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777233	777329	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777330	777422	1	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777330	777422	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777423	777641	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777642	777800	1	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777642	777800	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777801	777899	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777900	778077	0.55	-	1	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777900	778077	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778078	778223	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778224	778285	0.91	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778224	778285	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778286	778375	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778376	778386	0.66	-	2	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778376	778386	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778387	778481	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778482	778556	0.85	-	2	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778482	778556	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778557	778751	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778752	778797	0.99	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778752	778797	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778798	778877	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778878	778961	1	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778878	778961	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778962	779108	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779109	779376	0.74	-	1	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779109	779376	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779377	779488	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779489	779580	0.32	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779489	779580	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779581	779654	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779655	779741	0.78	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779655	779741	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779742	779843	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779844	780061	0.77	-	2	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779844	780061	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	780062	780137	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	780138	780243	0.8	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	780138	780243	.	-	.	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	start_codon	780241	780243	.	-	0	transcript_id "Phchi.S5G003000.t2"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	transcript	775781	780243	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	stop_codon	775778	775780	.	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	775781	776214	1	-	2	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	775781	776214	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776215	776312	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776313	776537	1	-	2	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776313	776537	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776538	776625	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776626	776907	0.96	-	2	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776626	776907	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	776908	776979	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	776980	777232	0.92	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	776980	777232	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777233	777329	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777330	777422	1	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777330	777422	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777423	777641	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777642	777800	1	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777642	777800	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	777801	777899	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	777900	778077	0.48	-	1	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	777900	778077	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778078	778223	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778224	778285	0.89	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778224	778285	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778286	778375	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778376	778552	0.81	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778376	778552	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778553	778751	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778752	778797	1	-	1	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778752	778797	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778798	778877	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	778878	778933	1	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	778878	778933	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	778934	779108	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779109	779376	0.73	-	1	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779109	779376	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779377	779488	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779489	779580	0.3	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779489	779580	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779581	779654	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779655	779741	0.65	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779655	779741	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	779742	779843	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	779844	780061	0.65	-	2	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	779844	780061	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	intron	780062	780137	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	CDS	780138	780243	0.71	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	exon	780138	780243	.	-	.	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
Phchi.S5	AUGUSTUS	start_codon	780241	780243	.	-	0	transcript_id "Phchi.S5G003000.t3"; gene_id "Phchi.S5G003000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2082.t1 is derived from g9002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4767511	4768685	.	+	.	Phchi.S5G069100
Phchi.S5	AUGUSTUS	transcript	4767511	4768685	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	start_codon	4767511	4767513	.	+	0	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	CDS	4767511	4767747	0.79	+	0	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	exon	4767511	4767747	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	intron	4767748	4767858	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	CDS	4767859	4768047	1	+	0	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	exon	4767859	4768047	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	intron	4768048	4768138	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	CDS	4768139	4768302	1	+	0	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	exon	4768139	4768302	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	intron	4768303	4768387	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	CDS	4768388	4768685	1	+	1	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	exon	4768388	4768685	.	+	.	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
Phchi.S5	AUGUSTUS	stop_codon	4768686	4768688	.	+	0	transcript_id "Phchi.S5G069100.t1"; gene_id "Phchi.S5G069100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3295.t1 is derived from g464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2717060	2718967	.	-	.	Phchi.S1G045400
Phchi.S1	AUGUSTUS	transcript	2717060	2718967	.	-	.	transcript_id "Phchi.S1G045400.t1"; gene_id "Phchi.S1G045400"
Phchi.S1	AUGUSTUS	stop_codon	2717057	2717059	.	-	0	transcript_id "Phchi.S1G045400.t1"; gene_id "Phchi.S1G045400"
Phchi.S1	AUGUSTUS	CDS	2717060	2718967	0.51	-	0	transcript_id "Phchi.S1G045400.t1"; gene_id "Phchi.S1G045400"
Phchi.S1	AUGUSTUS	exon	2717060	2718967	.	-	.	transcript_id "Phchi.S1G045400.t1"; gene_id "Phchi.S1G045400"
Phchi.S1	AUGUSTUS	start_codon	2718965	2718967	.	-	0	transcript_id "Phchi.S1G045400.t1"; gene_id "Phchi.S1G045400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7879.t1 is derived from g5053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31737320	31737658	.	+	.	Phchi.S1G503800
Phchi.S1	AUGUSTUS	transcript	31737320	31737658	.	+	.	transcript_id "Phchi.S1G503800.t1"; gene_id "Phchi.S1G503800"
Phchi.S1	AUGUSTUS	start_codon	31737320	31737322	.	+	0	transcript_id "Phchi.S1G503800.t1"; gene_id "Phchi.S1G503800"
Phchi.S1	AUGUSTUS	CDS	31737320	31737658	1	+	0	transcript_id "Phchi.S1G503800.t1"; gene_id "Phchi.S1G503800"
Phchi.S1	AUGUSTUS	exon	31737320	31737658	.	+	.	transcript_id "Phchi.S1G503800.t1"; gene_id "Phchi.S1G503800"
Phchi.S1	AUGUSTUS	stop_codon	31737659	31737661	.	+	0	transcript_id "Phchi.S1G503800.t1"; gene_id "Phchi.S1G503800"
# This transcript jg12911.t2 is derived from g11376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12911.t3 is derived from g11376.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12912.t1 is derived from g11377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3108809	3110779	.	+	.	Phchi.S3G023100
Phchi.S3	AUGUSTUS	transcript	3108809	3110779	.	+	.	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	start_codon	3108809	3108811	.	+	0	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	CDS	3108809	3109061	0.87	+	0	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	exon	3108809	3109061	.	+	.	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	intron	3109062	3109172	.	+	.	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	CDS	3109173	3110779	0.98	+	2	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	exon	3109173	3110779	.	+	.	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
Phchi.S3	AUGUSTUS	stop_codon	3110780	3110782	.	+	0	transcript_id "Phchi.S3G023100.t1"; gene_id "Phchi.S3G023100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6969.t1 is derived from g4141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26210996	26212279	.	-	.	Phchi.S1G412800
Phchi.S1	AUGUSTUS	transcript	26210996	26212279	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	stop_codon	26210993	26210995	.	-	0	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	CDS	26210996	26211130	0.99	-	0	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	exon	26210996	26211130	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	intron	26211131	26211230	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	CDS	26211231	26211369	1	-	1	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	exon	26211231	26211369	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	intron	26211370	26211463	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	CDS	26211464	26211526	1	-	1	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	exon	26211464	26211526	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	intron	26211527	26211766	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	CDS	26211767	26211812	0.42	-	2	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	exon	26211767	26211812	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	intron	26211813	26212016	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	CDS	26212017	26212140	0.98	-	0	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	exon	26212017	26212140	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	intron	26212141	26212267	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	CDS	26212268	26212279	0.94	-	0	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	exon	26212268	26212279	.	-	.	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
Phchi.S1	AUGUSTUS	start_codon	26212277	26212279	.	-	0	transcript_id "Phchi.S1G412800.t1"; gene_id "Phchi.S1G412800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2103.t1 is derived from g9023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4881725	4884752	.	-	.	Phchi.S5G071200
Phchi.S5	AUGUSTUS	transcript	4881725	4884752	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	stop_codon	4881722	4881724	.	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4881725	4882102	1	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4881725	4882102	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4882103	4882186	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4882187	4882345	1	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4882187	4882345	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4882346	4882439	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4882440	4882861	0.7	-	2	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4882440	4882861	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4882862	4883008	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4883009	4883280	0.76	-	1	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4883009	4883280	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4883281	4883373	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4883374	4883546	1	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4883374	4883546	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4883547	4883670	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4883671	4883937	0.81	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4883671	4883937	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4883938	4884042	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4884043	4884485	0.73	-	2	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4884043	4884485	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	intron	4884486	4884589	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	CDS	4884590	4884752	0.9	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	exon	4884590	4884752	.	-	.	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
Phchi.S5	AUGUSTUS	start_codon	4884750	4884752	.	-	0	transcript_id "Phchi.S5G071200.t1"; gene_id "Phchi.S5G071200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5227.t1 is derived from g2397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15720746	15721063	.	-	.	Phchi.S1G238600
Phchi.S1	AUGUSTUS	transcript	15720746	15721063	.	-	.	transcript_id "Phchi.S1G238600.t1"; gene_id "Phchi.S1G238600"
Phchi.S1	AUGUSTUS	stop_codon	15720743	15720745	.	-	0	transcript_id "Phchi.S1G238600.t1"; gene_id "Phchi.S1G238600"
Phchi.S1	AUGUSTUS	CDS	15720746	15721063	0.66	-	0	transcript_id "Phchi.S1G238600.t1"; gene_id "Phchi.S1G238600"
Phchi.S1	AUGUSTUS	exon	15720746	15721063	.	-	.	transcript_id "Phchi.S1G238600.t1"; gene_id "Phchi.S1G238600"
Phchi.S1	AUGUSTUS	start_codon	15721061	15721063	.	-	0	transcript_id "Phchi.S1G238600.t1"; gene_id "Phchi.S1G238600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11561.t1 is derived from g15612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7059474	7059995	.	-	.	Phchi.S4G114300
Phchi.S4	AUGUSTUS	transcript	7059474	7059995	.	-	.	transcript_id "Phchi.S4G114300.t1"; gene_id "Phchi.S4G114300"
Phchi.S4	AUGUSTUS	stop_codon	7059471	7059473	.	-	0	transcript_id "Phchi.S4G114300.t1"; gene_id "Phchi.S4G114300"
Phchi.S4	AUGUSTUS	CDS	7059474	7059995	0.71	-	0	transcript_id "Phchi.S4G114300.t1"; gene_id "Phchi.S4G114300"
Phchi.S4	AUGUSTUS	exon	7059474	7059995	.	-	.	transcript_id "Phchi.S4G114300.t1"; gene_id "Phchi.S4G114300"
Phchi.S4	AUGUSTUS	start_codon	7059993	7059995	.	-	0	transcript_id "Phchi.S4G114300.t1"; gene_id "Phchi.S4G114300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8769.t1 is derived from g5944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37887109	37888843	.	-	.	Phchi.S1G592800
Phchi.S1	AUGUSTUS	transcript	37887109	37888843	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	stop_codon	37887106	37887108	.	-	0	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	CDS	37887109	37887390	0.72	-	0	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	exon	37887109	37887390	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	intron	37887391	37887468	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	CDS	37887469	37887567	1	-	0	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	exon	37887469	37887567	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	intron	37887568	37887686	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	CDS	37887687	37887741	1	-	1	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	exon	37887687	37887741	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	intron	37887742	37887862	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	CDS	37887863	37888122	1	-	0	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	exon	37887863	37888122	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	intron	37888123	37888438	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	CDS	37888439	37888843	0.55	-	0	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	exon	37888439	37888843	.	-	.	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
Phchi.S1	AUGUSTUS	start_codon	37888841	37888843	.	-	0	transcript_id "Phchi.S1G592800.t1"; gene_id "Phchi.S1G592800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg437.t1 is derived from g10219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3074598	3077490	.	+	.	Phchi.S6G039600
Phchi.S6	AUGUSTUS	transcript	3074598	3077490	.	+	.	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	start_codon	3074598	3074600	.	+	0	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	CDS	3074598	3074806	0.81	+	0	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	exon	3074598	3074806	.	+	.	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	intron	3074807	3074952	.	+	.	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	CDS	3074953	3076639	0.36	+	1	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	exon	3074953	3076639	.	+	.	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	intron	3076640	3076776	.	+	.	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	CDS	3076777	3077490	0.67	+	0	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	exon	3076777	3077490	.	+	.	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
Phchi.S6	AUGUSTUS	stop_codon	3077491	3077493	.	+	0	transcript_id "Phchi.S6G039600.t1"; gene_id "Phchi.S6G039600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6597.t1 is derived from g3769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23927095	23928191	.	+	.	Phchi.S1G375600
Phchi.S1	AUGUSTUS	transcript	23927095	23928191	.	+	.	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	start_codon	23927095	23927097	.	+	0	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	CDS	23927095	23927255	0.82	+	0	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	exon	23927095	23927255	.	+	.	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	intron	23927256	23927365	.	+	.	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	CDS	23927366	23928191	0.67	+	1	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	exon	23927366	23928191	.	+	.	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
Phchi.S1	AUGUSTUS	stop_codon	23928192	23928194	.	+	0	transcript_id "Phchi.S1G375600.t1"; gene_id "Phchi.S1G375600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3256.t1 is derived from g425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2531292	2531857	.	+	.	Phchi.S1G041500
Phchi.S1	AUGUSTUS	transcript	2531292	2531857	.	+	.	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	start_codon	2531292	2531294	.	+	0	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	CDS	2531292	2531649	0.79	+	0	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	exon	2531292	2531649	.	+	.	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	intron	2531650	2531741	.	+	.	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	CDS	2531742	2531857	0.94	+	2	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	exon	2531742	2531857	.	+	.	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
Phchi.S1	AUGUSTUS	stop_codon	2531858	2531860	.	+	0	transcript_id "Phchi.S1G041500.t1"; gene_id "Phchi.S1G041500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg203.t1 is derived from g9985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1129882	1131581	.	+	.	Phchi.S6G016200
Phchi.S6	AUGUSTUS	transcript	1129882	1131581	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	start_codon	1129882	1129884	.	+	0	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	CDS	1129882	1130204	0.47	+	0	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	exon	1129882	1130204	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	intron	1130205	1130347	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	CDS	1130348	1130525	0.38	+	1	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	exon	1130348	1130525	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	intron	1130526	1130704	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	CDS	1130705	1130884	0.46	+	0	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	exon	1130705	1130884	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	intron	1130885	1131045	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	CDS	1131046	1131476	0.71	+	0	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	exon	1131046	1131476	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	intron	1131477	1131568	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	CDS	1131569	1131581	0.99	+	1	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	exon	1131569	1131581	.	+	.	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
Phchi.S6	AUGUSTUS	stop_codon	1131582	1131584	.	+	0	transcript_id "Phchi.S6G016200.t1"; gene_id "Phchi.S6G016200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1311.t1 is derived from g11094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8947392	8948369	.	+	.	Phchi.S6G127000
Phchi.S6	AUGUSTUS	transcript	8947392	8948369	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	start_codon	8947392	8947394	.	+	0	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	CDS	8947392	8947450	0.85	+	0	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	exon	8947392	8947450	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	intron	8947451	8947533	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	CDS	8947534	8947551	0.84	+	1	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	exon	8947534	8947551	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	intron	8947552	8947655	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	CDS	8947656	8947827	0.31	+	1	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	exon	8947656	8947827	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	intron	8947828	8947964	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	CDS	8947965	8948369	0.3	+	0	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	exon	8947965	8948369	.	+	.	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
Phchi.S6	AUGUSTUS	stop_codon	8948370	8948372	.	+	0	transcript_id "Phchi.S6G127000.t1"; gene_id "Phchi.S6G127000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12724.t1 is derived from g11189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1188504	1191300	.	+	.	Phchi.S3G004300
Phchi.S3	AUGUSTUS	transcript	1188504	1191300	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	start_codon	1188504	1188506	.	+	0	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	CDS	1188504	1188737	0.22	+	0	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	exon	1188504	1188737	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	intron	1188738	1189046	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	CDS	1189047	1189086	0.99	+	0	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	exon	1189047	1189086	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	intron	1189087	1189361	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	CDS	1189362	1190879	0.79	+	2	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	exon	1189362	1190879	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	intron	1190880	1190995	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	CDS	1190996	1191300	0.52	+	2	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	exon	1190996	1191300	.	+	.	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
Phchi.S3	AUGUSTUS	stop_codon	1191301	1191303	.	+	0	transcript_id "Phchi.S3G004300.t1"; gene_id "Phchi.S3G004300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1912.t1 is derived from g8832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3833478	3834107	.	-	.	Phchi.S5G052100
Phchi.S5	AUGUSTUS	transcript	3833478	3834107	.	-	.	transcript_id "Phchi.S5G052100.t1"; gene_id "Phchi.S5G052100"
Phchi.S5	AUGUSTUS	stop_codon	3833475	3833477	.	-	0	transcript_id "Phchi.S5G052100.t1"; gene_id "Phchi.S5G052100"
Phchi.S5	AUGUSTUS	CDS	3833478	3834107	0.53	-	0	transcript_id "Phchi.S5G052100.t1"; gene_id "Phchi.S5G052100"
Phchi.S5	AUGUSTUS	exon	3833478	3834107	.	-	.	transcript_id "Phchi.S5G052100.t1"; gene_id "Phchi.S5G052100"
Phchi.S5	AUGUSTUS	start_codon	3834105	3834107	.	-	0	transcript_id "Phchi.S5G052100.t1"; gene_id "Phchi.S5G052100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg110.t1 is derived from g9892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	590888	592388	.	-	.	Phchi.S6G006900
Phchi.S6	AUGUSTUS	transcript	590888	592388	.	-	.	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	stop_codon	590885	590887	.	-	0	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	CDS	590888	591558	1	-	2	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	exon	590888	591558	.	-	.	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	intron	591559	591634	.	-	.	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	CDS	591635	591904	1	-	2	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	exon	591635	591904	.	-	.	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	intron	591905	591994	.	-	.	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	CDS	591995	592388	1	-	0	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	exon	591995	592388	.	-	.	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
Phchi.S6	AUGUSTUS	start_codon	592386	592388	.	-	0	transcript_id "Phchi.S6G006900.t1"; gene_id "Phchi.S6G006900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5880.t1 is derived from g3050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19565321	19568747	.	-	.	Phchi.S1G303900
Phchi.S1	AUGUSTUS	transcript	19565321	19568747	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	stop_codon	19565318	19565320	.	-	0	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19565321	19565794	0.94	-	0	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19565321	19565794	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19565795	19565892	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19565893	19566019	1	-	1	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19565893	19566019	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566020	19566108	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566109	19566400	1	-	2	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566109	19566400	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566401	19566499	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566500	19566618	1	-	1	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566500	19566618	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566619	19566701	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566702	19566754	1	-	0	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566702	19566754	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566755	19566857	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566858	19567368	0.95	-	1	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566858	19567368	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19567369	19567478	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19567479	19567750	0.97	-	0	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19567479	19567750	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19567751	19567848	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19567849	19567891	0.73	-	1	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19567849	19567891	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19567892	19568175	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19568176	19568358	0.45	-	1	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19568176	19568358	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19568359	19568549	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19568550	19568631	0.5	-	2	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19568550	19568631	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19568632	19568728	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19568729	19568747	0.53	-	0	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19568729	19568747	.	-	.	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	start_codon	19568745	19568747	.	-	0	transcript_id "Phchi.S1G303900.t1"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	transcript	19565321	19568747	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	stop_codon	19565318	19565320	.	-	0	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19565321	19565794	1	-	0	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19565321	19565794	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19565795	19565892	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19565893	19566019	1	-	1	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19565893	19566019	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566020	19566108	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566109	19566400	1	-	2	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566109	19566400	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566401	19566499	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566500	19566618	1	-	1	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566500	19566618	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566619	19566701	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566702	19566754	1	-	0	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566702	19566754	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19566755	19566857	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19566858	19567368	0.94	-	1	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19566858	19567368	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19567369	19567478	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19567479	19567759	0.96	-	0	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19567479	19567759	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19567760	19567848	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19567849	19567891	0.62	-	1	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19567849	19567891	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19567892	19568175	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19568176	19568358	0.45	-	1	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19568176	19568358	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19568359	19568549	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19568550	19568631	0.43	-	2	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19568550	19568631	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	intron	19568632	19568728	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	CDS	19568729	19568747	0.49	-	0	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	exon	19568729	19568747	.	-	.	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
Phchi.S1	AUGUSTUS	start_codon	19568745	19568747	.	-	0	transcript_id "Phchi.S1G303900.t2"; gene_id "Phchi.S1G303900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg188.t1 is derived from g9970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1069271	1074167	.	+	.	Phchi.S6G014700
Phchi.S6	AUGUSTUS	transcript	1069271	1074167	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	start_codon	1069271	1069273	.	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1069271	1069552	0.99	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1069271	1069552	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1069553	1069627	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1069628	1069981	0.82	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1069628	1069981	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1069982	1070092	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070093	1070212	0.76	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070093	1070212	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070213	1070309	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070310	1070431	0.98	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070310	1070431	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070432	1070557	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070558	1070630	1	+	1	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070558	1070630	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070631	1070701	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070702	1070818	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070702	1070818	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070819	1070908	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070909	1070992	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070909	1070992	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070993	1071083	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071084	1071263	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071084	1071263	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071264	1071369	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071370	1071498	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071370	1071498	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071499	1071624	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071625	1071699	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071625	1071699	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071700	1071793	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071794	1071883	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071794	1071883	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071884	1071975	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071976	1072080	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071976	1072080	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072081	1072184	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072185	1072219	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072185	1072219	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072220	1072319	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072320	1072449	0.9	+	1	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072320	1072449	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072450	1072565	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072566	1072618	0.98	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072566	1072618	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072619	1072769	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072770	1072863	1	+	1	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072770	1072863	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072864	1072955	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072956	1072994	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072956	1072994	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072995	1073081	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073082	1073160	1	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073082	1073160	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073161	1073249	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073250	1073321	1	+	2	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073250	1073321	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073322	1073401	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073402	1073479	1	+	2	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073402	1073479	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073480	1073589	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073590	1073769	1	+	2	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073590	1073769	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073770	1073845	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073846	1073963	1	+	2	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073846	1073963	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073964	1074061	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1074062	1074167	1	+	1	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1074062	1074167	.	+	.	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	stop_codon	1074168	1074170	.	+	0	transcript_id "Phchi.S6G014700.t1"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	transcript	1069271	1074167	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	start_codon	1069271	1069273	.	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1069271	1069552	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1069271	1069552	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1069553	1069627	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1069628	1069981	0.77	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1069628	1069981	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1069982	1070092	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070093	1070212	0.85	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070093	1070212	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070213	1070309	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070310	1070327	0.78	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070310	1070327	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070328	1070413	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070414	1070472	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070414	1070472	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070473	1070557	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070558	1070630	1	+	1	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070558	1070630	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070631	1070701	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070702	1070818	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070702	1070818	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070819	1070908	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1070909	1070992	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1070909	1070992	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1070993	1071083	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071084	1071263	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071084	1071263	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071264	1071369	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071370	1071498	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071370	1071498	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071499	1071624	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071625	1071699	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071625	1071699	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071700	1071793	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071794	1071883	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071794	1071883	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1071884	1071975	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1071976	1072080	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1071976	1072080	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072081	1072184	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072185	1072219	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072185	1072219	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072220	1072319	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072320	1072449	0.89	+	1	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072320	1072449	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072450	1072565	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072566	1072618	0.94	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072566	1072618	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072619	1072769	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072770	1072863	1	+	1	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072770	1072863	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072864	1072955	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1072956	1072994	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1072956	1072994	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1072995	1073081	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073082	1073160	1	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073082	1073160	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073161	1073249	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073250	1073321	1	+	2	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073250	1073321	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073322	1073401	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073402	1073479	1	+	2	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073402	1073479	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073480	1073589	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073590	1073769	1	+	2	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073590	1073769	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073770	1073845	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1073846	1073963	1	+	2	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1073846	1073963	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	intron	1073964	1074061	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	CDS	1074062	1074167	1	+	1	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	exon	1074062	1074167	.	+	.	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
Phchi.S6	AUGUSTUS	stop_codon	1074168	1074170	.	+	0	transcript_id "Phchi.S6G014700.t2"; gene_id "Phchi.S6G014700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14371.t1 is derived from g12838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12404586	12407928	.	-	.	Phchi.S3G169000
Phchi.S3	AUGUSTUS	transcript	12404586	12407928	.	-	.	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	stop_codon	12404583	12404585	.	-	0	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	CDS	12404586	12405320	0.76	-	0	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	exon	12404586	12405320	.	-	.	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	intron	12405321	12405403	.	-	.	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	CDS	12405404	12407260	0.7	-	0	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	exon	12405404	12407260	.	-	.	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	intron	12407261	12407397	.	-	.	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	CDS	12407398	12407928	0.98	-	0	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	exon	12407398	12407928	.	-	.	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
Phchi.S3	AUGUSTUS	start_codon	12407926	12407928	.	-	0	transcript_id "Phchi.S3G169000.t1"; gene_id "Phchi.S3G169000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9092.t1 is derived from g6267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39811401	39812070	.	+	.	Phchi.S1G625100
Phchi.S1	AUGUSTUS	transcript	39811401	39812070	.	+	.	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	start_codon	39811401	39811403	.	+	0	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	CDS	39811401	39811589	0.81	+	0	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	exon	39811401	39811589	.	+	.	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	intron	39811590	39811671	.	+	.	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	CDS	39811672	39811782	1	+	0	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	exon	39811672	39811782	.	+	.	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	intron	39811783	39811875	.	+	.	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	CDS	39811876	39812070	1	+	0	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	exon	39811876	39812070	.	+	.	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
Phchi.S1	AUGUSTUS	stop_codon	39812071	39812073	.	+	0	transcript_id "Phchi.S1G625100.t1"; gene_id "Phchi.S1G625100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14618.t1 is derived from g13086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13805619	13806889	.	-	.	Phchi.S3G193700
Phchi.S3	AUGUSTUS	transcript	13805619	13806889	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	stop_codon	13805616	13805618	.	-	0	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	CDS	13805619	13805824	1	-	2	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	exon	13805619	13805824	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	intron	13805825	13805919	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	CDS	13805920	13806012	1	-	2	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	exon	13805920	13806012	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	intron	13806013	13806132	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	CDS	13806133	13806294	1	-	2	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	exon	13806133	13806294	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	intron	13806295	13806381	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	CDS	13806382	13806397	1	-	0	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	exon	13806382	13806397	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	intron	13806398	13806481	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	CDS	13806482	13806615	0.99	-	2	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	exon	13806482	13806615	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	intron	13806616	13806741	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	CDS	13806742	13806889	1	-	0	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	exon	13806742	13806889	.	-	.	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
Phchi.S3	AUGUSTUS	start_codon	13806887	13806889	.	-	0	transcript_id "Phchi.S3G193700.t1"; gene_id "Phchi.S3G193700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14402.t1 is derived from g12870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12667101	12667956	.	+	.	Phchi.S3G172100
Phchi.S3	AUGUSTUS	transcript	12667101	12667956	.	+	.	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	start_codon	12667101	12667103	.	+	0	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	CDS	12667101	12667176	0.93	+	0	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	exon	12667101	12667176	.	+	.	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	intron	12667177	12667392	.	+	.	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	CDS	12667393	12667678	1	+	2	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	exon	12667393	12667678	.	+	.	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	intron	12667679	12667829	.	+	.	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	CDS	12667830	12667956	0.98	+	1	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	exon	12667830	12667956	.	+	.	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
Phchi.S3	AUGUSTUS	stop_codon	12667957	12667959	.	+	0	transcript_id "Phchi.S3G172100.t1"; gene_id "Phchi.S3G172100"
# This transcript jg15802.t2 is derived from g14272.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15803.t1 is derived from g14273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21464687	21466000	.	-	.	Phchi.S3G312200
Phchi.S3	AUGUSTUS	transcript	21464687	21466000	.	-	.	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	stop_codon	21464684	21464686	.	-	0	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	CDS	21464687	21464800	0.41	-	0	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	exon	21464687	21464800	.	-	.	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	intron	21464801	21464974	.	-	.	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	CDS	21464975	21466000	0.64	-	0	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	exon	21464975	21466000	.	-	.	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
Phchi.S3	AUGUSTUS	start_codon	21465998	21466000	.	-	0	transcript_id "Phchi.S3G312200.t1"; gene_id "Phchi.S3G312200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6872.t1 is derived from g4044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25748956	25752155	.	-	.	Phchi.S1G403100
Phchi.S1	AUGUSTUS	transcript	25748956	25752155	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	stop_codon	25748953	25748955	.	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25748956	25749043	0.91	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25748956	25749043	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25749044	25749203	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25749204	25749245	0.68	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25749204	25749245	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25749246	25749510	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25749511	25749584	0.88	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25749511	25749584	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25749585	25749684	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25749685	25749748	1	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25749685	25749748	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25749749	25749912	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25749913	25750019	1	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25749913	25750019	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25750020	25750107	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25750108	25750199	1	-	2	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25750108	25750199	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25750200	25750279	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25750280	25750362	1	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25750280	25750362	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25750363	25750452	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25750453	25750519	1	-	2	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25750453	25750519	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25750520	25750601	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25750602	25750680	1	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25750602	25750680	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25750681	25750838	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25750839	25750909	1	-	2	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25750839	25750909	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25750910	25750999	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25751000	25751283	1	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25751000	25751283	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25751284	25751355	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25751356	25751412	1	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25751356	25751412	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25751413	25751506	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25751507	25751638	1	-	1	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25751507	25751638	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25751639	25751717	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25751718	25751754	0.98	-	2	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25751718	25751754	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25751755	25751841	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25751842	25751854	0.98	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25751842	25751854	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	intron	25751855	25752047	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	CDS	25752048	25752155	0.72	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	exon	25752048	25752155	.	-	.	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
Phchi.S1	AUGUSTUS	start_codon	25752153	25752155	.	-	0	transcript_id "Phchi.S1G403100.t1"; gene_id "Phchi.S1G403100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3398.t1 is derived from g567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3335626	3340733	.	-	.	Phchi.S1G055700
Phchi.S1	AUGUSTUS	transcript	3335626	3340733	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	stop_codon	3335623	3335625	.	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3335626	3335718	0.9	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3335626	3335718	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3335719	3335789	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3335790	3335861	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3335790	3335861	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3335862	3335954	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3335955	3336152	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3335955	3336152	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3336153	3336248	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3336249	3336332	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3336249	3336332	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3336333	3336443	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3336444	3336596	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3336444	3336596	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3336597	3336748	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3336749	3336895	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3336749	3336895	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3336896	3337007	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3337008	3337071	0.99	-	1	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3337008	3337071	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3337072	3337183	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3337184	3337300	1	-	1	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3337184	3337300	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3337301	3337376	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3337377	3337459	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3337377	3337459	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3337460	3337600	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3337601	3337649	1	-	1	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3337601	3337649	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3337650	3337875	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3337876	3337920	1	-	1	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3337876	3337920	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3337921	3338099	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3338100	3338311	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3338100	3338311	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3338312	3338432	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3338433	3338625	1	-	1	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3338433	3338625	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3338626	3338781	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3338782	3338894	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3338782	3338894	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3338895	3339039	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3339040	3339171	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3339040	3339171	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3339172	3339258	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3339259	3339352	1	-	1	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3339259	3339352	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3339353	3339459	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3339460	3339554	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3339460	3339554	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3339555	3339643	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3339644	3339763	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3339644	3339763	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3339764	3339852	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3339853	3339969	1	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3339853	3339969	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3339970	3340094	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3340095	3340135	1	-	2	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3340095	3340135	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3340136	3340271	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3340272	3340478	1	-	2	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3340272	3340478	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	intron	3340479	3340564	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	CDS	3340565	3340733	0.98	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	exon	3340565	3340733	.	-	.	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
Phchi.S1	AUGUSTUS	start_codon	3340731	3340733	.	-	0	transcript_id "Phchi.S1G055700.t1"; gene_id "Phchi.S1G055700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3271.t1 is derived from g440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2638845	2640185	.	-	.	Phchi.S1G043000
Phchi.S1	AUGUSTUS	transcript	2638845	2640185	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	stop_codon	2638842	2638844	.	-	0	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	CDS	2638845	2639108	1	-	0	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	exon	2638845	2639108	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	intron	2639109	2639201	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	CDS	2639202	2639348	1	-	0	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	exon	2639202	2639348	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	intron	2639349	2639445	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	CDS	2639446	2639729	1	-	2	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	exon	2639446	2639729	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	intron	2639730	2639827	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	CDS	2639828	2640185	0.68	-	0	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	exon	2639828	2640185	.	-	.	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
Phchi.S1	AUGUSTUS	start_codon	2640183	2640185	.	-	0	transcript_id "Phchi.S1G043000.t1"; gene_id "Phchi.S1G043000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3425.t1 is derived from g594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3579221	3581611	.	-	.	Phchi.S1G058400
Phchi.S1	AUGUSTUS	transcript	3579221	3581611	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	stop_codon	3579218	3579220	.	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3579221	3579242	1	-	1	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3579221	3579242	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	intron	3579243	3579334	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3579335	3579720	0.89	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3579335	3579720	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	intron	3579721	3579882	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3579883	3580230	0.91	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3579883	3580230	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	intron	3580231	3580413	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3580414	3581013	0.36	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3580414	3581013	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	intron	3581014	3581091	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3581092	3581119	1	-	1	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3581092	3581119	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	intron	3581120	3581281	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3581282	3581445	1	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3581282	3581445	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	intron	3581446	3581518	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	CDS	3581519	3581611	0.74	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	exon	3581519	3581611	.	-	.	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
Phchi.S1	AUGUSTUS	start_codon	3581609	3581611	.	-	0	transcript_id "Phchi.S1G058400.t1"; gene_id "Phchi.S1G058400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15138.t1 is derived from g13606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17235583	17237930	.	-	.	Phchi.S3G245700
Phchi.S3	AUGUSTUS	transcript	17235583	17237930	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	stop_codon	17235580	17235582	.	-	0	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	CDS	17235583	17235678	0.38	-	0	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	exon	17235583	17235678	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	intron	17235679	17235797	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	CDS	17235798	17236087	0.69	-	2	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	exon	17235798	17236087	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	intron	17236088	17236179	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	CDS	17236180	17236312	1	-	0	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	exon	17236180	17236312	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	intron	17236313	17236436	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	CDS	17236437	17237930	0.91	-	0	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	exon	17236437	17237930	.	-	.	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
Phchi.S3	AUGUSTUS	start_codon	17237928	17237930	.	-	0	transcript_id "Phchi.S3G245700.t1"; gene_id "Phchi.S3G245700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15140.t1 is derived from g13608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17245655	17246620	.	-	.	Phchi.S3G245900
Phchi.S3	AUGUSTUS	transcript	17245655	17246620	.	-	.	transcript_id "Phchi.S3G245900.t1"; gene_id "Phchi.S3G245900"
Phchi.S3	AUGUSTUS	stop_codon	17245652	17245654	.	-	0	transcript_id "Phchi.S3G245900.t1"; gene_id "Phchi.S3G245900"
Phchi.S3	AUGUSTUS	CDS	17245655	17246620	0.81	-	0	transcript_id "Phchi.S3G245900.t1"; gene_id "Phchi.S3G245900"
Phchi.S3	AUGUSTUS	exon	17245655	17246620	.	-	.	transcript_id "Phchi.S3G245900.t1"; gene_id "Phchi.S3G245900"
Phchi.S3	AUGUSTUS	start_codon	17246618	17246620	.	-	0	transcript_id "Phchi.S3G245900.t1"; gene_id "Phchi.S3G245900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1710.t1 is derived from g8630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2645012	2646517	.	+	.	Phchi.S5G031900
Phchi.S5	AUGUSTUS	transcript	2645012	2646517	.	+	.	transcript_id "Phchi.S5G031900.t1"; gene_id "Phchi.S5G031900"
Phchi.S5	AUGUSTUS	start_codon	2645012	2645014	.	+	0	transcript_id "Phchi.S5G031900.t1"; gene_id "Phchi.S5G031900"
Phchi.S5	AUGUSTUS	CDS	2645012	2646517	0.81	+	0	transcript_id "Phchi.S5G031900.t1"; gene_id "Phchi.S5G031900"
Phchi.S5	AUGUSTUS	exon	2645012	2646517	.	+	.	transcript_id "Phchi.S5G031900.t1"; gene_id "Phchi.S5G031900"
Phchi.S5	AUGUSTUS	stop_codon	2646518	2646520	.	+	0	transcript_id "Phchi.S5G031900.t1"; gene_id "Phchi.S5G031900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4945.t1 is derived from g2115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13679170	13680879	.	+	.	Phchi.S1G210400
Phchi.S1	AUGUSTUS	transcript	13679170	13680879	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	start_codon	13679170	13679172	.	+	0	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	CDS	13679170	13679298	1	+	0	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	exon	13679170	13679298	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	intron	13679299	13679369	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	CDS	13679370	13680295	1	+	0	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	exon	13679370	13680295	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	intron	13680296	13680385	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	CDS	13680386	13680721	0.7	+	1	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	exon	13680386	13680721	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	intron	13680722	13680824	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	CDS	13680825	13680879	0.69	+	1	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	exon	13680825	13680879	.	+	.	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
Phchi.S1	AUGUSTUS	stop_codon	13680880	13680882	.	+	0	transcript_id "Phchi.S1G210400.t1"; gene_id "Phchi.S1G210400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11439.t1 is derived from g15489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6381861	6383330	.	+	.	Phchi.S4G102100
Phchi.S4	AUGUSTUS	transcript	6382308	6383330	.	+	.	transcript_id "Phchi.S4G102100.t1"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	start_codon	6382308	6382310	.	+	0	transcript_id "Phchi.S4G102100.t1"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	CDS	6382308	6383330	0.68	+	0	transcript_id "Phchi.S4G102100.t1"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	exon	6382308	6383330	.	+	.	transcript_id "Phchi.S4G102100.t1"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	stop_codon	6383331	6383333	.	+	0	transcript_id "Phchi.S4G102100.t1"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	transcript	6381861	6383330	.	+	.	transcript_id "Phchi.S4G102100.t2"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	start_codon	6381861	6381863	.	+	0	transcript_id "Phchi.S4G102100.t2"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	CDS	6381861	6383330	0.51	+	0	transcript_id "Phchi.S4G102100.t2"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	exon	6381861	6383330	.	+	.	transcript_id "Phchi.S4G102100.t2"; gene_id "Phchi.S4G102100"
Phchi.S4	AUGUSTUS	stop_codon	6383331	6383333	.	+	0	transcript_id "Phchi.S4G102100.t2"; gene_id "Phchi.S4G102100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10816.t1 is derived from g14866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2249431	2250837	.	+	.	Phchi.S4G039800
Phchi.S4	AUGUSTUS	transcript	2249431	2250837	.	+	.	transcript_id "Phchi.S4G039800.t1"; gene_id "Phchi.S4G039800"
Phchi.S4	AUGUSTUS	start_codon	2249431	2249433	.	+	0	transcript_id "Phchi.S4G039800.t1"; gene_id "Phchi.S4G039800"
Phchi.S4	AUGUSTUS	CDS	2249431	2250837	0.99	+	0	transcript_id "Phchi.S4G039800.t1"; gene_id "Phchi.S4G039800"
Phchi.S4	AUGUSTUS	exon	2249431	2250837	.	+	.	transcript_id "Phchi.S4G039800.t1"; gene_id "Phchi.S4G039800"
Phchi.S4	AUGUSTUS	stop_codon	2250838	2250840	.	+	0	transcript_id "Phchi.S4G039800.t1"; gene_id "Phchi.S4G039800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12451.t1 is derived from g8128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23329773	23330324	.	-	.	Phchi.S2G053100
Phchi.S2	AUGUSTUS	transcript	23329773	23330324	.	-	.	transcript_id "Phchi.S2G053100.t1"; gene_id "Phchi.S2G053100"
Phchi.S2	AUGUSTUS	stop_codon	23329770	23329772	.	-	0	transcript_id "Phchi.S2G053100.t1"; gene_id "Phchi.S2G053100"
Phchi.S2	AUGUSTUS	CDS	23329773	23330324	0.92	-	0	transcript_id "Phchi.S2G053100.t1"; gene_id "Phchi.S2G053100"
Phchi.S2	AUGUSTUS	exon	23329773	23330324	.	-	.	transcript_id "Phchi.S2G053100.t1"; gene_id "Phchi.S2G053100"
Phchi.S2	AUGUSTUS	start_codon	23330322	23330324	.	-	0	transcript_id "Phchi.S2G053100.t1"; gene_id "Phchi.S2G053100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7273.t1 is derived from g4445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28079158	28082515	.	+	.	Phchi.S1G443200
Phchi.S1	AUGUSTUS	transcript	28079158	28082515	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	start_codon	28079158	28079160	.	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28079158	28079369	0.79	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28079158	28079369	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28079370	28079459	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28079460	28079821	0.97	+	1	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28079460	28079821	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28079822	28079936	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28079937	28080082	1	+	2	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28079937	28080082	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080083	28080204	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080205	28080388	1	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080205	28080388	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080389	28080524	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080525	28080607	1	+	2	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080525	28080607	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080608	28080712	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080713	28080826	1	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080713	28080826	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080827	28080908	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080909	28081265	0.99	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080909	28081265	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28081266	28081343	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28081344	28081505	0.86	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28081344	28081505	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28081506	28081663	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28081664	28081936	0.5	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28081664	28081936	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28081937	28082026	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28082027	28082145	1	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28082027	28082145	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28082146	28082278	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28082279	28082381	0.85	+	1	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28082279	28082381	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28082382	28082467	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28082468	28082515	0.86	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28082468	28082515	.	+	.	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	stop_codon	28082516	28082518	.	+	0	transcript_id "Phchi.S1G443200.t1"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	transcript	28079158	28082515	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	start_codon	28079158	28079160	.	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28079158	28079369	0.79	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28079158	28079369	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28079370	28079459	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28079460	28079821	0.97	+	1	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28079460	28079821	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28079822	28079936	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28079937	28080082	1	+	2	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28079937	28080082	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080083	28080204	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080205	28080388	1	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080205	28080388	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080389	28080524	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080525	28080607	1	+	2	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080525	28080607	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080608	28080712	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080713	28080826	1	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080713	28080826	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28080827	28080908	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28080909	28081265	1	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28080909	28081265	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28081266	28081343	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28081344	28081505	0.92	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28081344	28081505	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28081506	28081663	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28081664	28081936	0.52	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28081664	28081936	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28081937	28082026	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28082027	28082145	1	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28082027	28082145	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28082146	28082278	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28082279	28082381	0.76	+	1	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28082279	28082381	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	intron	28082382	28082476	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	CDS	28082477	28082515	0.77	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	exon	28082477	28082515	.	+	.	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
Phchi.S1	AUGUSTUS	stop_codon	28082516	28082518	.	+	0	transcript_id "Phchi.S1G443200.t2"; gene_id "Phchi.S1G443200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15073.t1 is derived from g13541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16914944	16918013	.	-	.	Phchi.S3G239200
Phchi.S3	AUGUSTUS	transcript	16914944	16918013	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	stop_codon	16914941	16914943	.	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16914944	16914985	1	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16914944	16914985	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16914986	16915056	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16915057	16915113	1	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16915057	16915113	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16915114	16915206	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16915207	16915283	1	-	2	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16915207	16915283	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16915284	16915365	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16915366	16915441	1	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16915366	16915441	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16915442	16915520	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16915521	16915653	1	-	1	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16915521	16915653	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16915654	16915756	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16915757	16915798	0.99	-	1	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16915757	16915798	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16915799	16915922	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16915923	16916008	0.99	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16915923	16916008	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16916009	16916100	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16916101	16916160	1	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16916101	16916160	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16916161	16916253	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16916254	16916348	1	-	2	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16916254	16916348	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16916349	16916463	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16916464	16916515	1	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16916464	16916515	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16916516	16916612	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16916613	16916694	1	-	1	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16916613	16916694	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16916695	16916836	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16916837	16916896	1	-	1	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16916837	16916896	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16916897	16916986	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16916987	16917130	1	-	1	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16916987	16917130	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16917131	16917216	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16917217	16917297	1	-	1	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16917217	16917297	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16917298	16917454	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16917455	16917531	1	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16917455	16917531	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16917532	16917672	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16917673	16917756	0.9	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16917673	16917756	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	intron	16917757	16917863	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	CDS	16917864	16918013	0.79	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	exon	16917864	16918013	.	-	.	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
Phchi.S3	AUGUSTUS	start_codon	16918011	16918013	.	-	0	transcript_id "Phchi.S3G239200.t1"; gene_id "Phchi.S3G239200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14681.t1 is derived from g13149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14145805	14146658	.	-	.	Phchi.S3G200000
Phchi.S3	AUGUSTUS	transcript	14145805	14146658	.	-	.	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	stop_codon	14145802	14145804	.	-	0	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	CDS	14145805	14146235	0.84	-	2	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	exon	14145805	14146235	.	-	.	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	intron	14146236	14146363	.	-	.	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	CDS	14146364	14146658	0.84	-	0	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	exon	14146364	14146658	.	-	.	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
Phchi.S3	AUGUSTUS	start_codon	14146656	14146658	.	-	0	transcript_id "Phchi.S3G200000.t1"; gene_id "Phchi.S3G200000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3482.t1 is derived from g651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4007792	4008200	.	-	.	Phchi.S1G064100
Phchi.S1	AUGUSTUS	transcript	4007792	4008200	.	-	.	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	stop_codon	4007789	4007791	.	-	0	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	CDS	4007792	4007862	1	-	2	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	exon	4007792	4007862	.	-	.	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	intron	4007863	4008019	.	-	.	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	CDS	4008020	4008200	0.62	-	0	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	exon	4008020	4008200	.	-	.	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
Phchi.S1	AUGUSTUS	start_codon	4008198	4008200	.	-	0	transcript_id "Phchi.S1G064100.t1"; gene_id "Phchi.S1G064100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7282.t1 is derived from g4454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28130934	28133288	.	+	.	Phchi.S1G444100
Phchi.S1	AUGUSTUS	transcript	28130934	28133288	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	start_codon	28130934	28130936	.	+	0	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28130934	28131612	0.63	+	0	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28130934	28131612	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28131613	28131796	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28131797	28131909	1	+	2	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28131797	28131909	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28131910	28132039	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28132040	28132147	1	+	0	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28132040	28132147	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28132148	28132228	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28132229	28132283	0.99	+	0	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28132229	28132283	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28132284	28132395	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28132396	28132581	0.99	+	2	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28132396	28132581	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28132582	28132671	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28132672	28132766	0.99	+	2	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28132672	28132766	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28132767	28132868	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28132869	28133065	0.49	+	0	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28132869	28133065	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	intron	28133066	28133188	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	CDS	28133189	28133288	0.95	+	1	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	exon	28133189	28133288	.	+	.	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
Phchi.S1	AUGUSTUS	stop_codon	28133289	28133291	.	+	0	transcript_id "Phchi.S1G444100.t1"; gene_id "Phchi.S1G444100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12740.t1 is derived from g11205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1465167	1467040	.	+	.	Phchi.S3G005900
Phchi.S3	AUGUSTUS	transcript	1465167	1467040	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	start_codon	1465167	1465169	.	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465167	1465529	0.84	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465167	1465529	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465530	1465604	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465605	1465682	1	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465605	1465682	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465683	1465778	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465779	1465820	1	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465779	1465820	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465821	1465903	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465904	1466009	0.99	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465904	1466009	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466010	1466113	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466114	1466178	0.99	+	2	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466114	1466178	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466179	1466287	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466288	1466332	0.62	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466288	1466332	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466333	1466437	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466438	1466545	1	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466438	1466545	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466546	1466643	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466644	1466731	1	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466644	1466731	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466732	1466824	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466825	1466871	1	+	2	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466825	1466871	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466872	1466962	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466963	1467040	0.98	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466963	1467040	.	+	.	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	stop_codon	1467041	1467043	.	+	0	transcript_id "Phchi.S3G005900.t1"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	transcript	1465167	1467040	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	start_codon	1465167	1465169	.	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465167	1465529	0.75	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465167	1465529	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465530	1465604	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465605	1465682	1	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465605	1465682	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465683	1465778	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465779	1465820	1	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465779	1465820	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465821	1465919	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1465920	1465972	0.55	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1465920	1465972	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1465973	1466045	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466046	1466178	0.53	+	1	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466046	1466178	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466179	1466287	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466288	1466332	0.48	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466288	1466332	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466333	1466437	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466438	1466545	1	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466438	1466545	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466546	1466643	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466644	1466731	1	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466644	1466731	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466732	1466824	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466825	1466871	1	+	2	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466825	1466871	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	intron	1466872	1466962	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	CDS	1466963	1467040	0.97	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	exon	1466963	1467040	.	+	.	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
Phchi.S3	AUGUSTUS	stop_codon	1467041	1467043	.	+	0	transcript_id "Phchi.S3G005900.t2"; gene_id "Phchi.S3G005900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12977.t1 is derived from g11442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3409868	3413776	.	+	.	Phchi.S3G029600
Phchi.S3	AUGUSTUS	transcript	3409868	3413776	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	start_codon	3409868	3409870	.	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3409868	3409942	0.4	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3409868	3409942	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3409943	3410040	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3410041	3410068	0.65	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3410041	3410068	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3410069	3410215	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3410216	3410297	0.43	+	2	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3410216	3410297	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3410298	3410539	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3410540	3411015	0.52	+	1	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3410540	3411015	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3411016	3411177	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3411178	3411272	1	+	2	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3411178	3411272	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3411273	3411375	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3411376	3411484	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3411376	3411484	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3411485	3411660	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3411661	3411716	1	+	2	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3411661	3411716	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3411717	3411861	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3411862	3411917	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3411862	3411917	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3411918	3412014	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3412015	3412153	1	+	1	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3412015	3412153	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3412154	3412289	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3412290	3412427	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3412290	3412427	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3412428	3412540	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3412541	3412609	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3412541	3412609	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3412610	3412700	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3412701	3412811	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3412701	3412811	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3412812	3412983	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3412984	3413112	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3412984	3413112	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3413113	3413205	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3413206	3413283	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3413206	3413283	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3413284	3413387	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3413388	3413459	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3413388	3413459	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3413460	3413546	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3413547	3413609	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3413547	3413609	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	intron	3413610	3413683	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	CDS	3413684	3413776	1	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	exon	3413684	3413776	.	+	.	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
Phchi.S3	AUGUSTUS	stop_codon	3413777	3413779	.	+	0	transcript_id "Phchi.S3G029600.t1"; gene_id "Phchi.S3G029600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7436.t1 is derived from g4608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29104933	29113482	.	+	.	Phchi.S1G459500
Phchi.S1	AUGUSTUS	transcript	29104933	29113482	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	start_codon	29104933	29104935	.	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29104933	29105008	0.44	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29104933	29105008	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29105009	29105088	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29105089	29106079	0.89	+	2	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29105089	29106079	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29106080	29106185	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29106186	29107124	0.95	+	1	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29106186	29107124	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29107125	29107231	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29107232	29107586	0.87	+	1	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29107232	29107586	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29107587	29107797	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29107798	29108020	0.99	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29107798	29108020	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29108021	29108285	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29108286	29108956	1	+	2	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29108286	29108956	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29108957	29109090	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29109091	29109729	0.99	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29109091	29109729	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29109730	29109907	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29109908	29109991	0.98	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29109908	29109991	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29109992	29110135	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29110136	29110246	0.46	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29110136	29110246	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29110247	29110378	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29110379	29110711	0.94	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29110379	29110711	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29110712	29110828	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29110829	29110927	0.98	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29110829	29110927	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29110928	29111095	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29111096	29111294	0.39	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29111096	29111294	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29111295	29111488	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29111489	29111631	0.76	+	2	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29111489	29111631	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29111632	29111751	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29111752	29112168	0.54	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29111752	29112168	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29112169	29112395	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29112396	29112702	0.55	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29112396	29112702	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29112703	29112803	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29112804	29113347	0.26	+	2	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29112804	29113347	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	intron	29113348	29113457	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	CDS	29113458	29113482	0.57	+	1	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	exon	29113458	29113482	.	+	.	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
Phchi.S1	AUGUSTUS	stop_codon	29113483	29113485	.	+	0	transcript_id "Phchi.S1G459500.t1"; gene_id "Phchi.S1G459500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10148.t1 is derived from g7324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45988991	45990367	.	-	.	Phchi.S1G730700
Phchi.S1	AUGUSTUS	transcript	45988991	45990367	.	-	.	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	stop_codon	45988988	45988990	.	-	0	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	CDS	45988991	45990022	0.99	-	0	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	exon	45988991	45990022	.	-	.	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	intron	45990023	45990118	.	-	.	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	CDS	45990119	45990367	0.38	-	0	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	exon	45990119	45990367	.	-	.	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
Phchi.S1	AUGUSTUS	start_codon	45990365	45990367	.	-	0	transcript_id "Phchi.S1G730700.t1"; gene_id "Phchi.S1G730700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15383.t1 is derived from g13851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18728348	18733010	.	+	.	Phchi.S3G270200
Phchi.S3	AUGUSTUS	transcript	18728348	18733010	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	start_codon	18728348	18728350	.	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18728348	18729127	0.55	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18728348	18729127	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18729128	18729225	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18729226	18729524	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18729226	18729524	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18729525	18729650	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18729651	18729795	1	+	1	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18729651	18729795	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18729796	18729974	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18729975	18730078	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18729975	18730078	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18730079	18730215	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18730216	18730412	1	+	1	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18730216	18730412	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18730413	18730609	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18730610	18731125	1	+	2	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18730610	18731125	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18731126	18731259	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18731260	18731300	1	+	2	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18731260	18731300	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18731301	18731479	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18731480	18731548	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18731480	18731548	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18731549	18731659	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18731660	18731760	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18731660	18731760	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18731761	18731847	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18731848	18731932	0.98	+	1	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18731848	18731932	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18731933	18732043	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18732044	18732142	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18732044	18732142	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18732143	18732282	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18732283	18732351	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18732283	18732351	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18732352	18732449	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18732450	18732581	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18732450	18732581	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18732582	18732659	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18732660	18732754	1	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18732660	18732754	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	intron	18732755	18732910	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	CDS	18732911	18733010	1	+	1	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	exon	18732911	18733010	.	+	.	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
Phchi.S3	AUGUSTUS	stop_codon	18733011	18733013	.	+	0	transcript_id "Phchi.S3G270200.t1"; gene_id "Phchi.S3G270200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3003.t1 is derived from g172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1085626	1087213	.	-	.	Phchi.S1G016200
Phchi.S1	AUGUSTUS	transcript	1085626	1087213	.	-	.	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	stop_codon	1085623	1085625	.	-	0	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	CDS	1085626	1085848	0.61	-	1	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	exon	1085626	1085848	.	-	.	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	intron	1085849	1086343	.	-	.	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	CDS	1086344	1086551	0.96	-	2	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	exon	1086344	1086551	.	-	.	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	intron	1086552	1086798	.	-	.	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	CDS	1086799	1087213	0.4	-	0	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	exon	1086799	1087213	.	-	.	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
Phchi.S1	AUGUSTUS	start_codon	1087211	1087213	.	-	0	transcript_id "Phchi.S1G016200.t1"; gene_id "Phchi.S1G016200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10487.t1 is derived from g14536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	665374	671083	.	+	.	Phchi.S4G006900
Phchi.S4	AUGUSTUS	transcript	665374	671083	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	start_codon	665374	665376	.	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	665374	665499	0.5	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	665374	665499	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	665500	665576	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	665577	665848	0.99	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	665577	665848	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	665849	665924	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	665925	666171	1	+	1	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	665925	666171	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	666172	666241	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	666242	666355	1	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	666242	666355	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	666356	666444	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	666445	666493	0.99	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	666445	666493	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	666494	666696	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	666697	666871	0.99	+	2	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	666697	666871	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	666872	666959	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	666960	667200	1	+	1	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	666960	667200	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	667201	667301	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	667302	667393	0.66	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	667302	667393	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	667394	667483	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	667484	667616	0.28	+	1	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	667484	667616	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	667617	667726	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	667727	667876	0.83	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	667727	667876	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	667877	667969	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	667970	668197	1	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	667970	668197	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	668198	668333	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	668334	668874	0.7	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	668334	668874	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	668875	669007	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	669008	669198	1	+	2	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	669008	669198	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	669199	669292	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	669293	669412	1	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	669293	669412	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	669413	669482	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	669483	669598	1	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	669483	669598	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	669599	669690	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	669691	669871	1	+	1	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	669691	669871	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	669872	669952	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	669953	670111	1	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	669953	670111	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	670112	670221	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	670222	670686	1	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	670222	670686	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	intron	670687	670762	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	CDS	670763	671083	0.83	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	exon	670763	671083	.	+	.	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
Phchi.S4	AUGUSTUS	stop_codon	671084	671086	.	+	0	transcript_id "Phchi.S4G006900.t1"; gene_id "Phchi.S4G006900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7071.t1 is derived from g4243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26741648	26744032	.	+	.	Phchi.S1G423000
Phchi.S1	AUGUSTUS	transcript	26741648	26744032	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	start_codon	26741648	26741650	.	+	0	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	CDS	26741648	26743489	0.53	+	0	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	exon	26741648	26743489	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	intron	26743490	26743577	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	CDS	26743578	26743623	0.98	+	0	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	exon	26743578	26743623	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	intron	26743624	26743723	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	CDS	26743724	26743740	0.79	+	2	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	exon	26743724	26743740	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	intron	26743741	26743882	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	CDS	26743883	26744032	0.76	+	0	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	exon	26743883	26744032	.	+	.	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
Phchi.S1	AUGUSTUS	stop_codon	26744033	26744035	.	+	0	transcript_id "Phchi.S1G423000.t1"; gene_id "Phchi.S1G423000"
# This transcript jg11551.t2 is derived from g15602.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11552.t1 is derived from g15603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7010410	7012392	.	+	.	Phchi.S4G113400
Phchi.S4	AUGUSTUS	transcript	7010410	7012392	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	start_codon	7010410	7010412	.	+	0	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	CDS	7010410	7010574	0.38	+	0	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	exon	7010410	7010574	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	intron	7010575	7010648	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	CDS	7010649	7011117	0.32	+	0	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	exon	7010649	7011117	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	intron	7011118	7011323	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	CDS	7011324	7011534	0.33	+	2	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	exon	7011324	7011534	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	intron	7011535	7011670	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	CDS	7011671	7011692	0.79	+	1	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	exon	7011671	7011692	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	intron	7011693	7012125	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	CDS	7012126	7012217	1	+	0	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	exon	7012126	7012217	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	intron	7012218	7012361	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	CDS	7012362	7012392	0.99	+	1	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	exon	7012362	7012392	.	+	.	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
Phchi.S4	AUGUSTUS	stop_codon	7012393	7012395	.	+	0	transcript_id "Phchi.S4G113400.t1"; gene_id "Phchi.S4G113400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15650.t1 is derived from g14119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20487747	20487995	.	+	.	Phchi.S3G296900
Phchi.S3	AUGUSTUS	transcript	20487747	20487995	.	+	.	transcript_id "Phchi.S3G296900.t1"; gene_id "Phchi.S3G296900"
Phchi.S3	AUGUSTUS	start_codon	20487747	20487749	.	+	0	transcript_id "Phchi.S3G296900.t1"; gene_id "Phchi.S3G296900"
Phchi.S3	AUGUSTUS	CDS	20487747	20487995	0.62	+	0	transcript_id "Phchi.S3G296900.t1"; gene_id "Phchi.S3G296900"
Phchi.S3	AUGUSTUS	exon	20487747	20487995	.	+	.	transcript_id "Phchi.S3G296900.t1"; gene_id "Phchi.S3G296900"
Phchi.S3	AUGUSTUS	stop_codon	20487996	20487998	.	+	0	transcript_id "Phchi.S3G296900.t1"; gene_id "Phchi.S3G296900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7049.t1 is derived from g4221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26618098	26618601	.	-	.	Phchi.S1G420800
Phchi.S1	AUGUSTUS	transcript	26618098	26618601	.	-	.	transcript_id "Phchi.S1G420800.t1"; gene_id "Phchi.S1G420800"
Phchi.S1	AUGUSTUS	stop_codon	26618095	26618097	.	-	0	transcript_id "Phchi.S1G420800.t1"; gene_id "Phchi.S1G420800"
Phchi.S1	AUGUSTUS	CDS	26618098	26618601	0.81	-	0	transcript_id "Phchi.S1G420800.t1"; gene_id "Phchi.S1G420800"
Phchi.S1	AUGUSTUS	exon	26618098	26618601	.	-	.	transcript_id "Phchi.S1G420800.t1"; gene_id "Phchi.S1G420800"
Phchi.S1	AUGUSTUS	start_codon	26618599	26618601	.	-	0	transcript_id "Phchi.S1G420800.t1"; gene_id "Phchi.S1G420800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14784.t1 is derived from g13252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14688109	14696411	.	+	.	Phchi.S3G210300
Phchi.S3	AUGUSTUS	transcript	14688109	14696411	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	start_codon	14688109	14688111	.	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14688109	14688152	0.4	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14688109	14688152	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14688153	14688299	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14688300	14688516	1	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14688300	14688516	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14688517	14688658	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14688659	14688715	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14688659	14688715	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14688716	14688944	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14688945	14689040	0.58	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14688945	14689040	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14689041	14689146	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14689147	14689239	0.62	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14689147	14689239	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14689240	14689325	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14689326	14689513	0.99	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14689326	14689513	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14689514	14689624	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14689625	14689859	0.97	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14689625	14689859	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14689860	14689961	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14689962	14690066	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14689962	14690066	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14690067	14690205	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14690206	14690307	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14690206	14690307	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14690308	14690397	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14690398	14691162	0.99	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14690398	14691162	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14691163	14691417	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14691418	14691659	0.93	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14691418	14691659	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14691660	14691769	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14691770	14691842	0.98	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14691770	14691842	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14691843	14691956	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14691957	14692169	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14691957	14692169	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14692170	14692261	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14692262	14692381	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14692262	14692381	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14692382	14692477	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14692478	14692638	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14692478	14692638	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14692639	14692746	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14692747	14692888	1	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14692747	14692888	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14692889	14692986	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14692987	14693139	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14692987	14693139	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14693140	14693330	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14693331	14693386	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14693331	14693386	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14693387	14693529	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14693530	14693808	0.27	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14693530	14693808	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14693809	14693938	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14693939	14694069	0.86	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14693939	14694069	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14694070	14694152	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14694153	14694214	1	+	2	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14694153	14694214	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14694215	14694322	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14694323	14694555	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14694323	14694555	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14694556	14694643	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14694644	14694847	1	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14694644	14694847	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14694848	14694934	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14694935	14695013	1	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14694935	14695013	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14695014	14695138	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14695139	14695404	1	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14695139	14695404	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	intron	14695405	14695492	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	CDS	14695493	14696411	1	+	1	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	exon	14695493	14696411	.	+	.	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
Phchi.S3	AUGUSTUS	stop_codon	14696412	14696414	.	+	0	transcript_id "Phchi.S3G210300.t1"; gene_id "Phchi.S3G210300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6640.t1 is derived from g3812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24209868	24212282	.	+	.	Phchi.S1G379900
Phchi.S1	AUGUSTUS	transcript	24209868	24212282	.	+	.	transcript_id "Phchi.S1G379900.t1"; gene_id "Phchi.S1G379900"
Phchi.S1	AUGUSTUS	start_codon	24209868	24209870	.	+	0	transcript_id "Phchi.S1G379900.t1"; gene_id "Phchi.S1G379900"
Phchi.S1	AUGUSTUS	CDS	24209868	24212282	0.87	+	0	transcript_id "Phchi.S1G379900.t1"; gene_id "Phchi.S1G379900"
Phchi.S1	AUGUSTUS	exon	24209868	24212282	.	+	.	transcript_id "Phchi.S1G379900.t1"; gene_id "Phchi.S1G379900"
Phchi.S1	AUGUSTUS	stop_codon	24212283	24212285	.	+	0	transcript_id "Phchi.S1G379900.t1"; gene_id "Phchi.S1G379900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11423.t1 is derived from g15473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6272924	6273522	.	+	.	Phchi.S4G100500
Phchi.S4	AUGUSTUS	transcript	6272924	6273522	.	+	.	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	start_codon	6272924	6272926	.	+	0	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	CDS	6272924	6273155	0.47	+	0	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	exon	6272924	6273155	.	+	.	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	intron	6273156	6273298	.	+	.	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	CDS	6273299	6273522	0.52	+	2	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	exon	6273299	6273522	.	+	.	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
Phchi.S4	AUGUSTUS	stop_codon	6273523	6273525	.	+	0	transcript_id "Phchi.S4G100500.t1"; gene_id "Phchi.S4G100500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13155.t1 is derived from g11620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4427748	4430690	.	-	.	Phchi.S3G047400
Phchi.S3	AUGUSTUS	transcript	4427748	4430690	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	stop_codon	4427745	4427747	.	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4427748	4427814	1	-	1	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4427748	4427814	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4427815	4427905	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4427906	4428112	1	-	1	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4427906	4428112	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4428113	4428194	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4428195	4428274	1	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4428195	4428274	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4428275	4428358	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4428359	4428440	1	-	1	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4428359	4428440	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4428441	4428544	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4428545	4428609	0.99	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4428545	4428609	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4428610	4428697	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4428698	4429177	0.97	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4428698	4429177	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4429178	4429254	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4429255	4429433	0.21	-	2	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4429255	4429433	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4429434	4429682	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4429683	4429763	0.32	-	2	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4429683	4429763	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4429764	4429850	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4429851	4429941	0.85	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4429851	4429941	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4429942	4430061	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4430062	4430151	1	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4430062	4430151	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4430152	4430230	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4430231	4430311	1	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4430231	4430311	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4430312	4430380	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4430381	4430434	1	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4430381	4430434	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4430435	4430522	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4430523	4430561	1	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4430523	4430561	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	intron	4430562	4430645	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	CDS	4430646	4430690	0.77	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	exon	4430646	4430690	.	-	.	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
Phchi.S3	AUGUSTUS	start_codon	4430688	4430690	.	-	0	transcript_id "Phchi.S3G047400.t1"; gene_id "Phchi.S3G047400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15342.t1 is derived from g13810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18467081	18467591	.	+	.	Phchi.S3G266100
Phchi.S3	AUGUSTUS	transcript	18467081	18467591	.	+	.	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	start_codon	18467081	18467083	.	+	0	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	CDS	18467081	18467448	0.35	+	0	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	exon	18467081	18467448	.	+	.	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	intron	18467449	18467578	.	+	.	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	CDS	18467579	18467591	0.56	+	1	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	exon	18467579	18467591	.	+	.	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
Phchi.S3	AUGUSTUS	stop_codon	18467592	18467594	.	+	0	transcript_id "Phchi.S3G266100.t1"; gene_id "Phchi.S3G266100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4471.t1 is derived from g1641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10675512	10677636	.	+	.	Phchi.S1G163000
Phchi.S1	AUGUSTUS	transcript	10675512	10677636	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	start_codon	10675512	10675514	.	+	0	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	CDS	10675512	10675801	1	+	0	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	exon	10675512	10675801	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	intron	10675802	10675920	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	CDS	10675921	10676022	1	+	1	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	exon	10675921	10676022	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	intron	10676023	10676162	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	CDS	10676163	10676983	1	+	1	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	exon	10676163	10676983	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	intron	10676984	10677061	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	CDS	10677062	10677636	0.99	+	2	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	exon	10677062	10677636	.	+	.	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
Phchi.S1	AUGUSTUS	stop_codon	10677637	10677639	.	+	0	transcript_id "Phchi.S1G163000.t1"; gene_id "Phchi.S1G163000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12806.t1 is derived from g11271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2467888	2468340	.	+	.	Phchi.S3G012500
Phchi.S3	AUGUSTUS	transcript	2467888	2468340	.	+	.	transcript_id "Phchi.S3G012500.t1"; gene_id "Phchi.S3G012500"
Phchi.S3	AUGUSTUS	start_codon	2467888	2467890	.	+	0	transcript_id "Phchi.S3G012500.t1"; gene_id "Phchi.S3G012500"
Phchi.S3	AUGUSTUS	CDS	2467888	2468340	0.5	+	0	transcript_id "Phchi.S3G012500.t1"; gene_id "Phchi.S3G012500"
Phchi.S3	AUGUSTUS	exon	2467888	2468340	.	+	.	transcript_id "Phchi.S3G012500.t1"; gene_id "Phchi.S3G012500"
Phchi.S3	AUGUSTUS	stop_codon	2468341	2468343	.	+	0	transcript_id "Phchi.S3G012500.t1"; gene_id "Phchi.S3G012500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3617.t1 is derived from g786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4776235	4776909	.	-	.	Phchi.S1G077600
Phchi.S1	AUGUSTUS	transcript	4776235	4776909	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	stop_codon	4776232	4776234	.	-	0	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	CDS	4776235	4776345	1	-	0	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	exon	4776235	4776345	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	intron	4776346	4776426	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	CDS	4776427	4776488	1	-	2	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	exon	4776427	4776488	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	intron	4776489	4776580	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	CDS	4776581	4776692	1	-	0	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	exon	4776581	4776692	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	intron	4776693	4776789	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	CDS	4776790	4776909	0.88	-	0	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	exon	4776790	4776909	.	-	.	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
Phchi.S1	AUGUSTUS	start_codon	4776907	4776909	.	-	0	transcript_id "Phchi.S1G077600.t1"; gene_id "Phchi.S1G077600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12548.t1 is derived from g8225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34389189	34391376	.	-	.	Phchi.S2G062800
Phchi.S2	AUGUSTUS	transcript	34389189	34391376	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	stop_codon	34389186	34389188	.	-	0	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34389189	34389261	1	-	1	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34389189	34389261	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34389262	34389393	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34389394	34389515	1	-	0	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34389394	34389515	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34389516	34389755	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34389756	34389872	1	-	0	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34389756	34389872	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34389873	34389987	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34389988	34390110	0.98	-	0	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34389988	34390110	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34390111	34390217	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34390218	34390345	0.99	-	2	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34390218	34390345	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34390346	34390572	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34390573	34390692	1	-	2	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34390573	34390692	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34390693	34390895	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34390896	34391048	1	-	2	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34390896	34391048	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	intron	34391049	34391231	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	CDS	34391232	34391376	0.64	-	0	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	exon	34391232	34391376	.	-	.	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
Phchi.S2	AUGUSTUS	start_codon	34391374	34391376	.	-	0	transcript_id "Phchi.S2G062800.t1"; gene_id "Phchi.S2G062800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9956.t1 is derived from g7132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44653689	44656130	.	-	.	Phchi.S1G711500
Phchi.S1	AUGUSTUS	transcript	44653689	44656130	.	-	.	transcript_id "Phchi.S1G711500.t1"; gene_id "Phchi.S1G711500"
Phchi.S1	AUGUSTUS	stop_codon	44653686	44653688	.	-	0	transcript_id "Phchi.S1G711500.t1"; gene_id "Phchi.S1G711500"
Phchi.S1	AUGUSTUS	CDS	44653689	44656130	0.91	-	0	transcript_id "Phchi.S1G711500.t1"; gene_id "Phchi.S1G711500"
Phchi.S1	AUGUSTUS	exon	44653689	44656130	.	-	.	transcript_id "Phchi.S1G711500.t1"; gene_id "Phchi.S1G711500"
Phchi.S1	AUGUSTUS	start_codon	44656128	44656130	.	-	0	transcript_id "Phchi.S1G711500.t1"; gene_id "Phchi.S1G711500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5101.t1 is derived from g2271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14745375	14750861	.	+	.	Phchi.S1G226000
Phchi.S1	AUGUSTUS	transcript	14745375	14750861	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	start_codon	14745375	14745377	.	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14745375	14745888	0.98	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14745375	14745888	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14745889	14745975	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14745976	14746094	1	+	2	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14745976	14746094	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14746095	14746172	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14746173	14746337	0.93	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14746173	14746337	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14746338	14746459	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14746460	14746534	0.89	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14746460	14746534	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14746535	14746668	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14746669	14746719	0.79	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14746669	14746719	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14746720	14746814	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14746815	14746910	0.99	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14746815	14746910	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14746911	14747037	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14747038	14747100	1	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14747038	14747100	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14747101	14747221	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14747222	14747260	0.99	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14747222	14747260	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14747261	14747354	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14747355	14747459	0.65	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14747355	14747459	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14747460	14747781	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14747782	14747847	0.63	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14747782	14747847	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14747848	14747986	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14747987	14748049	1	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14747987	14748049	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14748050	14748191	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14748192	14748245	1	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14748192	14748245	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14748246	14748326	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14748327	14748437	1	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14748327	14748437	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14748438	14748544	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14748545	14748745	0.85	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14748545	14748745	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14748746	14748822	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14748823	14748917	0.99	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14748823	14748917	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14748918	14749032	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14749033	14749102	0.96	+	1	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14749033	14749102	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14749103	14749253	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14749254	14749319	0.79	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14749254	14749319	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14749320	14749430	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14749431	14749522	1	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14749431	14749522	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14749523	14749623	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14749624	14749693	1	+	1	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14749624	14749693	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14749694	14749764	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14749765	14749832	1	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14749765	14749832	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14749833	14749911	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14749912	14750038	0.99	+	1	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14749912	14750038	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14750039	14750126	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14750127	14750659	0.9	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14750127	14750659	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	intron	14750660	14750779	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	CDS	14750780	14750861	0.9	+	1	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	exon	14750780	14750861	.	+	.	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
Phchi.S1	AUGUSTUS	stop_codon	14750862	14750864	.	+	0	transcript_id "Phchi.S1G226000.t1"; gene_id "Phchi.S1G226000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7203.t1 is derived from g4375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27624699	27626049	.	+	.	Phchi.S1G436200
Phchi.S1	AUGUSTUS	transcript	27624699	27626049	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	start_codon	27624699	27624701	.	+	0	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	CDS	27624699	27624739	0.57	+	0	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	exon	27624699	27624739	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	intron	27624740	27624829	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	CDS	27624830	27624962	0.98	+	1	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	exon	27624830	27624962	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	intron	27624963	27625143	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	CDS	27625144	27625594	0.97	+	0	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	exon	27625144	27625594	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	intron	27625595	27625738	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	CDS	27625739	27625848	1	+	2	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	exon	27625739	27625848	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	intron	27625849	27626025	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	CDS	27626026	27626049	1	+	0	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	exon	27626026	27626049	.	+	.	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
Phchi.S1	AUGUSTUS	stop_codon	27626050	27626052	.	+	0	transcript_id "Phchi.S1G436200.t1"; gene_id "Phchi.S1G436200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3471.t1 is derived from g640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3930512	3932216	.	+	.	Phchi.S1G063000
Phchi.S1	AUGUSTUS	transcript	3930512	3932216	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	start_codon	3930512	3930514	.	+	0	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	CDS	3930512	3930764	0.46	+	0	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	exon	3930512	3930764	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	intron	3930765	3930981	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	CDS	3930982	3931010	0.51	+	2	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	exon	3930982	3931010	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	intron	3931011	3931181	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	CDS	3931182	3931554	0.69	+	0	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	exon	3931182	3931554	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	intron	3931555	3931650	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	CDS	3931651	3932216	0.97	+	2	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	exon	3931651	3932216	.	+	.	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
Phchi.S1	AUGUSTUS	stop_codon	3932217	3932219	.	+	0	transcript_id "Phchi.S1G063000.t1"; gene_id "Phchi.S1G063000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3488.t1 is derived from g657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4023629	4024727	.	+	.	Phchi.S1G064700
Phchi.S1	AUGUSTUS	transcript	4023629	4024727	.	+	.	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	start_codon	4023629	4023631	.	+	0	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	CDS	4023629	4023778	0.5	+	0	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	exon	4023629	4023778	.	+	.	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	intron	4023779	4023912	.	+	.	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	CDS	4023913	4024504	0.43	+	0	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	exon	4023913	4024504	.	+	.	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	intron	4024505	4024608	.	+	.	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	CDS	4024609	4024727	0.44	+	2	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	exon	4024609	4024727	.	+	.	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
Phchi.S1	AUGUSTUS	stop_codon	4024728	4024730	.	+	0	transcript_id "Phchi.S1G064700.t1"; gene_id "Phchi.S1G064700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5475.t1 is derived from g2645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17025771	17028066	.	-	.	Phchi.S1G263400
Phchi.S1	AUGUSTUS	transcript	17025771	17028066	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	stop_codon	17025768	17025770	.	-	0	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	CDS	17025771	17026080	1	-	1	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	exon	17025771	17026080	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	intron	17026081	17026170	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	CDS	17026171	17026304	1	-	0	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	exon	17026171	17026304	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	intron	17026305	17026493	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	CDS	17026494	17026530	1	-	1	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	exon	17026494	17026530	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	intron	17026531	17026688	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	CDS	17026689	17027091	0.63	-	2	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	exon	17026689	17027091	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	intron	17027092	17027181	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	CDS	17027182	17027893	0.59	-	0	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	exon	17027182	17027893	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	intron	17027894	17027964	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	CDS	17027965	17028066	0.93	-	0	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	exon	17027965	17028066	.	-	.	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
Phchi.S1	AUGUSTUS	start_codon	17028064	17028066	.	-	0	transcript_id "Phchi.S1G263400.t1"; gene_id "Phchi.S1G263400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7762.t1 is derived from g4936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31158062	31159162	.	+	.	Phchi.S1G492100
Phchi.S1	AUGUSTUS	transcript	31158062	31159162	.	+	.	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	start_codon	31158062	31158064	.	+	0	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	CDS	31158062	31158371	0.51	+	0	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	exon	31158062	31158371	.	+	.	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	intron	31158372	31158663	.	+	.	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	CDS	31158664	31158902	0.09	+	2	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	exon	31158664	31158902	.	+	.	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	intron	31158903	31159021	.	+	.	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	CDS	31159022	31159162	0.2	+	0	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	exon	31159022	31159162	.	+	.	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
Phchi.S1	AUGUSTUS	stop_codon	31159163	31159165	.	+	0	transcript_id "Phchi.S1G492100.t1"; gene_id "Phchi.S1G492100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8508.t1 is derived from g5683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36373715	36374612	.	+	.	Phchi.S1G566700
Phchi.S1	AUGUSTUS	transcript	36373715	36374612	.	+	.	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	start_codon	36373715	36373717	.	+	0	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	CDS	36373715	36374154	1	+	0	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	exon	36373715	36374154	.	+	.	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	intron	36374155	36374269	.	+	.	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	CDS	36374270	36374612	1	+	1	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	exon	36374270	36374612	.	+	.	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
Phchi.S1	AUGUSTUS	stop_codon	36374613	36374615	.	+	0	transcript_id "Phchi.S1G566700.t1"; gene_id "Phchi.S1G566700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12375.t1 is derived from g8051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14073579	14075265	.	+	.	Phchi.S2G045500
Phchi.S2	AUGUSTUS	transcript	14073579	14075265	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	start_codon	14073579	14073581	.	+	0	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14073579	14073732	0.75	+	0	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14073579	14073732	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14073733	14073831	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14073832	14073858	0.81	+	2	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14073832	14073858	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14073859	14073930	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14073931	14073957	0.78	+	2	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14073931	14073957	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14073958	14074280	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14074281	14074296	0.51	+	2	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14074281	14074296	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14074297	14074727	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14074728	14074765	0.61	+	1	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14074728	14074765	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14074766	14074861	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14074862	14075014	0.55	+	2	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14074862	14075014	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14075015	14075112	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14075113	14075123	0.97	+	2	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14075113	14075123	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	intron	14075124	14075223	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	CDS	14075224	14075265	0.97	+	0	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	exon	14075224	14075265	.	+	.	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
Phchi.S2	AUGUSTUS	stop_codon	14075266	14075268	.	+	0	transcript_id "Phchi.S2G045500.t1"; gene_id "Phchi.S2G045500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5042.t1 is derived from g2212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14223664	14225527	.	-	.	Phchi.S1G220100
Phchi.S1	AUGUSTUS	transcript	14223664	14225527	.	-	.	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	stop_codon	14223661	14223663	.	-	0	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	CDS	14223664	14223685	1	-	1	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	exon	14223664	14223685	.	-	.	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	intron	14223686	14223911	.	-	.	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	CDS	14223912	14225527	0.5	-	0	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	exon	14223912	14225527	.	-	.	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
Phchi.S1	AUGUSTUS	start_codon	14225525	14225527	.	-	0	transcript_id "Phchi.S1G220100.t1"; gene_id "Phchi.S1G220100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12545.t1 is derived from g8222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34224019	34227991	.	+	.	Phchi.S2G062500
Phchi.S2	AUGUSTUS	transcript	34224019	34227991	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	start_codon	34224019	34224021	.	+	0	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34224019	34224303	0.58	+	0	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34224019	34224303	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34224304	34224526	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34224527	34224588	1	+	0	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34224527	34224588	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34224589	34224830	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34224831	34224926	0.97	+	1	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34224831	34224926	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34224927	34225033	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34225034	34225152	0.84	+	1	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34225034	34225152	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34225153	34225283	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34225284	34226953	0.8	+	2	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34225284	34226953	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34226954	34227064	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34227065	34227991	0.94	+	0	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34227065	34227991	.	+	.	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	stop_codon	34227992	34227994	.	+	0	transcript_id "Phchi.S2G062500.t1"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	transcript	34224130	34227991	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	start_codon	34224130	34224132	.	+	0	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34224130	34224354	0.6	+	0	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34224130	34224354	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34224355	34224526	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34224527	34224588	1	+	0	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34224527	34224588	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34224589	34224830	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34224831	34224926	0.98	+	1	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34224831	34224926	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34224927	34225033	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34225034	34225152	0.8	+	1	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34225034	34225152	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34225153	34225283	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34225284	34226953	0.78	+	2	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34225284	34226953	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	intron	34226954	34227064	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	CDS	34227065	34227991	0.95	+	0	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	exon	34227065	34227991	.	+	.	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
Phchi.S2	AUGUSTUS	stop_codon	34227992	34227994	.	+	0	transcript_id "Phchi.S2G062500.t2"; gene_id "Phchi.S2G062500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13329.t1 is derived from g11795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6128038	6129141	.	+	.	Phchi.S3G064800
Phchi.S3	AUGUSTUS	transcript	6128038	6129141	.	+	.	transcript_id "Phchi.S3G064800.t1"; gene_id "Phchi.S3G064800"
Phchi.S3	AUGUSTUS	start_codon	6128038	6128040	.	+	0	transcript_id "Phchi.S3G064800.t1"; gene_id "Phchi.S3G064800"
Phchi.S3	AUGUSTUS	CDS	6128038	6129141	0.9	+	0	transcript_id "Phchi.S3G064800.t1"; gene_id "Phchi.S3G064800"
Phchi.S3	AUGUSTUS	exon	6128038	6129141	.	+	.	transcript_id "Phchi.S3G064800.t1"; gene_id "Phchi.S3G064800"
Phchi.S3	AUGUSTUS	stop_codon	6129142	6129144	.	+	0	transcript_id "Phchi.S3G064800.t1"; gene_id "Phchi.S3G064800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5099.t1 is derived from g2269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14729984	14734120	.	-	.	Phchi.S1G225800
Phchi.S1	AUGUSTUS	transcript	14729984	14734120	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	stop_codon	14729981	14729983	.	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14729984	14730017	1	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14729984	14730017	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14730018	14730103	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14730104	14730193	1	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14730104	14730193	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14730194	14730326	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14730327	14730415	1	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14730327	14730415	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14730416	14730497	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14730498	14730576	1	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14730498	14730576	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14730577	14730665	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14730666	14730727	1	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14730666	14730727	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14730728	14730828	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14730829	14730906	1	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14730829	14730906	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14730907	14731014	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14731015	14731059	1	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14731015	14731059	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14731060	14731229	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14731230	14731298	1	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14731230	14731298	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14731299	14731386	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14731387	14731507	0.95	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14731387	14731507	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14731508	14731615	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14731616	14731689	0.62	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14731616	14731689	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14731690	14731771	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14731772	14731896	1	-	2	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14731772	14731896	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14731897	14731985	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14731986	14732064	0.37	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14731986	14732064	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14732065	14732182	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14732183	14732233	0.33	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14732183	14732233	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14732234	14732336	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14732337	14732448	0.22	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14732337	14732448	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14732449	14732582	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14732583	14732704	0.71	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14732583	14732704	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14732705	14732798	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14732799	14732928	1	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14732799	14732928	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14732929	14733043	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14733044	14733450	0.92	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14733044	14733450	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14733451	14733675	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14733676	14733841	0.23	-	1	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14733676	14733841	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	intron	14733842	14733983	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	CDS	14733984	14734120	0.61	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	exon	14733984	14734120	.	-	.	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
Phchi.S1	AUGUSTUS	start_codon	14734118	14734120	.	-	0	transcript_id "Phchi.S1G225800.t1"; gene_id "Phchi.S1G225800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2253.t1 is derived from g9173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5698685	5699620	.	+	.	Phchi.S5G086200
Phchi.S5	AUGUSTUS	transcript	5698685	5699620	.	+	.	transcript_id "Phchi.S5G086200.t1"; gene_id "Phchi.S5G086200"
Phchi.S5	AUGUSTUS	start_codon	5698685	5698687	.	+	0	transcript_id "Phchi.S5G086200.t1"; gene_id "Phchi.S5G086200"
Phchi.S5	AUGUSTUS	CDS	5698685	5699620	0.39	+	0	transcript_id "Phchi.S5G086200.t1"; gene_id "Phchi.S5G086200"
Phchi.S5	AUGUSTUS	exon	5698685	5699620	.	+	.	transcript_id "Phchi.S5G086200.t1"; gene_id "Phchi.S5G086200"
Phchi.S5	AUGUSTUS	stop_codon	5699621	5699623	.	+	0	transcript_id "Phchi.S5G086200.t1"; gene_id "Phchi.S5G086200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12495.t1 is derived from g8172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30080761	30087915	.	+	.	Phchi.S2G057500
Phchi.S2	AUGUSTUS	transcript	30080761	30087915	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	start_codon	30080761	30080763	.	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30080761	30081095	0.8	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30080761	30081095	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081096	30081200	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081201	30081321	1	+	1	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081201	30081321	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081322	30081399	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081400	30081488	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081400	30081488	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081489	30081644	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081645	30081729	1	+	1	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081645	30081729	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081730	30081873	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081874	30082033	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081874	30082033	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082034	30082130	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082131	30082207	1	+	2	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082131	30082207	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082208	30082302	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082303	30082447	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082303	30082447	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082448	30082644	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082645	30082850	0.99	+	2	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082645	30082850	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082851	30082920	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082921	30082944	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082921	30082944	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082945	30083026	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30083027	30083308	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30083027	30083308	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30083309	30083440	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30083441	30083757	0.96	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30083441	30083757	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30083758	30083860	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30083861	30084021	1	+	1	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30083861	30084021	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084022	30084274	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30084275	30084378	1	+	2	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30084275	30084378	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084379	30084452	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30084453	30084609	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30084453	30084609	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084610	30084739	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30084740	30084862	1	+	2	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30084740	30084862	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084863	30085077	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30085078	30085265	1	+	2	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30085078	30085265	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30085266	30085356	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30085357	30085689	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30085357	30085689	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30085690	30085783	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30085784	30086074	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30085784	30086074	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086075	30086157	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086158	30086241	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086158	30086241	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086242	30086370	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086371	30086504	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086371	30086504	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086505	30086596	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086597	30086771	0.78	+	1	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086597	30086771	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086772	30086968	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086969	30087139	0.9	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086969	30087139	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30087140	30087217	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30087218	30087305	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30087218	30087305	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30087306	30087406	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30087407	30087573	1	+	2	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30087407	30087573	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30087574	30087651	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30087652	30087915	1	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30087652	30087915	.	+	.	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	stop_codon	30087916	30087918	.	+	0	transcript_id "Phchi.S2G057500.t1"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	transcript	30080761	30087915	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	start_codon	30080761	30080763	.	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30080761	30081095	0.83	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30080761	30081095	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081096	30081200	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081201	30081321	1	+	1	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081201	30081321	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081322	30081399	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081400	30081488	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081400	30081488	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081489	30081644	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081645	30081729	1	+	1	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081645	30081729	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30081730	30081873	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30081874	30082033	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30081874	30082033	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082034	30082130	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082131	30082207	1	+	2	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082131	30082207	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082208	30082302	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082303	30082447	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082303	30082447	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082448	30082644	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082645	30082850	1	+	2	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082645	30082850	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082851	30082920	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30082921	30082944	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30082921	30082944	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30082945	30083026	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30083027	30083308	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30083027	30083308	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30083309	30083440	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30083441	30083757	0.96	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30083441	30083757	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30083758	30083860	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30083861	30084021	1	+	1	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30083861	30084021	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084022	30084274	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30084275	30084378	1	+	2	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30084275	30084378	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084379	30084452	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30084453	30084609	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30084453	30084609	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084610	30084739	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30084740	30084862	1	+	2	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30084740	30084862	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30084863	30085086	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30085087	30085265	1	+	2	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30085087	30085265	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30085266	30085356	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30085357	30085689	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30085357	30085689	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30085690	30085783	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30085784	30086074	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30085784	30086074	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086075	30086157	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086158	30086241	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086158	30086241	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086242	30086370	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086371	30086504	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086371	30086504	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086505	30086596	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086597	30086771	0.77	+	1	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086597	30086771	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30086772	30086968	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30086969	30087139	0.89	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30086969	30087139	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30087140	30087217	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30087218	30087305	1	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30087218	30087305	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30087306	30087406	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30087407	30087573	1	+	2	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30087407	30087573	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	intron	30087574	30087651	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	CDS	30087652	30087915	0.99	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	exon	30087652	30087915	.	+	.	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
Phchi.S2	AUGUSTUS	stop_codon	30087916	30087918	.	+	0	transcript_id "Phchi.S2G057500.t2"; gene_id "Phchi.S2G057500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8406.t1 is derived from g5581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35808756	35811046	.	+	.	Phchi.S1G556500
Phchi.S1	AUGUSTUS	transcript	35808756	35811046	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	start_codon	35808756	35808758	.	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35808756	35808800	0.82	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35808756	35808800	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35808801	35808890	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35808891	35808967	0.88	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35808891	35808967	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35808968	35809080	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35809081	35809181	0.94	+	1	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35809081	35809181	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35809182	35809265	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35809266	35809336	1	+	2	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35809266	35809336	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35809337	35809522	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35809523	35809585	0.99	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35809523	35809585	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35809586	35809707	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35809708	35809716	1	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35809708	35809716	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35809717	35810176	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35810177	35810221	1	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35810177	35810221	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35810222	35810314	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35810315	35810380	1	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35810315	35810380	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35810381	35810493	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35810494	35810541	1	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35810494	35810541	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35810542	35810624	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35810625	35810720	0.85	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35810625	35810720	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35810721	35810822	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35810823	35810864	0.86	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35810823	35810864	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	intron	35810865	35810992	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	CDS	35810993	35811046	0.81	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	exon	35810993	35811046	.	+	.	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
Phchi.S1	AUGUSTUS	stop_codon	35811047	35811049	.	+	0	transcript_id "Phchi.S1G556500.t1"; gene_id "Phchi.S1G556500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9236.t1 is derived from g6411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40541032	40543227	.	+	.	Phchi.S1G639500
Phchi.S1	AUGUSTUS	transcript	40541032	40543227	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	start_codon	40541032	40541034	.	+	0	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	CDS	40541032	40541148	0.68	+	0	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	exon	40541032	40541148	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	intron	40541149	40541245	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	CDS	40541246	40541678	0.52	+	0	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	exon	40541246	40541678	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	intron	40541679	40541767	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	CDS	40541768	40541847	1	+	2	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	exon	40541768	40541847	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	intron	40541848	40541948	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	CDS	40541949	40543009	0.63	+	0	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	exon	40541949	40543009	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	intron	40543010	40543118	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	CDS	40543119	40543227	0.72	+	1	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	exon	40543119	40543227	.	+	.	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
Phchi.S1	AUGUSTUS	stop_codon	40543228	40543230	.	+	0	transcript_id "Phchi.S1G639500.t1"; gene_id "Phchi.S1G639500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11474.t1 is derived from g15524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6529494	6530768	.	-	.	Phchi.S4G105600
Phchi.S4	AUGUSTUS	transcript	6529494	6530768	.	-	.	transcript_id "Phchi.S4G105600.t1"; gene_id "Phchi.S4G105600"
Phchi.S4	AUGUSTUS	stop_codon	6529491	6529493	.	-	0	transcript_id "Phchi.S4G105600.t1"; gene_id "Phchi.S4G105600"
Phchi.S4	AUGUSTUS	CDS	6529494	6530768	0.54	-	0	transcript_id "Phchi.S4G105600.t1"; gene_id "Phchi.S4G105600"
Phchi.S4	AUGUSTUS	exon	6529494	6530768	.	-	.	transcript_id "Phchi.S4G105600.t1"; gene_id "Phchi.S4G105600"
Phchi.S4	AUGUSTUS	start_codon	6530766	6530768	.	-	0	transcript_id "Phchi.S4G105600.t1"; gene_id "Phchi.S4G105600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg875.t1 is derived from g10657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6077636	6079642	.	+	.	Phchi.S6G083400
Phchi.S6	AUGUSTUS	transcript	6077636	6079642	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	start_codon	6077636	6077638	.	+	0	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	CDS	6077636	6077822	0.74	+	0	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	exon	6077636	6077822	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	intron	6077823	6077949	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	CDS	6077950	6078248	1	+	2	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	exon	6077950	6078248	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	intron	6078249	6078359	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	CDS	6078360	6078734	0.87	+	0	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	exon	6078360	6078734	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	intron	6078735	6078817	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	CDS	6078818	6079642	0.63	+	0	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	exon	6078818	6079642	.	+	.	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
Phchi.S6	AUGUSTUS	stop_codon	6079643	6079645	.	+	0	transcript_id "Phchi.S6G083400.t1"; gene_id "Phchi.S6G083400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11284.t1 is derived from g15334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5193895	5196015	.	+	.	Phchi.S4G086600
Phchi.S4	AUGUSTUS	transcript	5193895	5196015	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	start_codon	5193895	5193897	.	+	0	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	CDS	5193895	5194416	1	+	0	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	exon	5193895	5194416	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	intron	5194417	5194551	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	CDS	5194552	5194698	0.99	+	0	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	exon	5194552	5194698	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	intron	5194699	5194840	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	CDS	5194841	5194981	0.54	+	0	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	exon	5194841	5194981	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	intron	5194982	5195133	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	CDS	5195134	5196015	1	+	0	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	exon	5195134	5196015	.	+	.	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
Phchi.S4	AUGUSTUS	stop_codon	5196016	5196018	.	+	0	transcript_id "Phchi.S4G086600.t1"; gene_id "Phchi.S4G086600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11618.t1 is derived from g15669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7343135	7344721	.	-	.	Phchi.S4G120000
Phchi.S4	AUGUSTUS	transcript	7343135	7344721	.	-	.	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	stop_codon	7343132	7343134	.	-	0	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	CDS	7343135	7343796	1	-	2	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	exon	7343135	7343796	.	-	.	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	intron	7343797	7343929	.	-	.	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	CDS	7343930	7344458	0.76	-	0	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	exon	7343930	7344458	.	-	.	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	intron	7344459	7344568	.	-	.	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	CDS	7344569	7344721	0.26	-	0	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	exon	7344569	7344721	.	-	.	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
Phchi.S4	AUGUSTUS	start_codon	7344719	7344721	.	-	0	transcript_id "Phchi.S4G120000.t1"; gene_id "Phchi.S4G120000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4546.t1 is derived from g1716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11058302	11059939	.	-	.	Phchi.S1G170500
Phchi.S1	AUGUSTUS	transcript	11058302	11059939	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	stop_codon	11058299	11058301	.	-	0	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	CDS	11058302	11058431	0.89	-	1	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	exon	11058302	11058431	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	intron	11058432	11058533	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	CDS	11058534	11058621	0.98	-	2	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	exon	11058534	11058621	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	intron	11058622	11058706	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	CDS	11058707	11059048	1	-	2	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	exon	11058707	11059048	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	intron	11059049	11059134	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	CDS	11059135	11059321	0.94	-	0	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	exon	11059135	11059321	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	intron	11059322	11059450	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	CDS	11059451	11059603	0.34	-	0	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	exon	11059451	11059603	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	intron	11059604	11059810	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	CDS	11059811	11059939	0.61	-	0	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	exon	11059811	11059939	.	-	.	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
Phchi.S1	AUGUSTUS	start_codon	11059937	11059939	.	-	0	transcript_id "Phchi.S1G170500.t1"; gene_id "Phchi.S1G170500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg954.t1 is derived from g10736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6638178	6639899	.	+	.	Phchi.S6G091300
Phchi.S6	AUGUSTUS	transcript	6638178	6639899	.	+	.	transcript_id "Phchi.S6G091300.t1"; gene_id "Phchi.S6G091300"
Phchi.S6	AUGUSTUS	start_codon	6638178	6638180	.	+	0	transcript_id "Phchi.S6G091300.t1"; gene_id "Phchi.S6G091300"
Phchi.S6	AUGUSTUS	CDS	6638178	6639899	0.98	+	0	transcript_id "Phchi.S6G091300.t1"; gene_id "Phchi.S6G091300"
Phchi.S6	AUGUSTUS	exon	6638178	6639899	.	+	.	transcript_id "Phchi.S6G091300.t1"; gene_id "Phchi.S6G091300"
Phchi.S6	AUGUSTUS	stop_codon	6639900	6639902	.	+	0	transcript_id "Phchi.S6G091300.t1"; gene_id "Phchi.S6G091300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7124.t1 is derived from g4296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27078801	27080027	.	+	.	Phchi.S1G428300
Phchi.S1	AUGUSTUS	transcript	27078801	27080027	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	start_codon	27078801	27078803	.	+	0	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	CDS	27078801	27079007	0.99	+	0	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	exon	27078801	27079007	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	intron	27079008	27079096	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	CDS	27079097	27079420	0.93	+	0	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	exon	27079097	27079420	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	intron	27079421	27079497	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	CDS	27079498	27079657	1	+	0	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	exon	27079498	27079657	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	intron	27079658	27079761	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	CDS	27079762	27080027	1	+	2	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	exon	27079762	27080027	.	+	.	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
Phchi.S1	AUGUSTUS	stop_codon	27080028	27080030	.	+	0	transcript_id "Phchi.S1G428300.t1"; gene_id "Phchi.S1G428300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg831.t1 is derived from g10613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5773841	5776708	.	-	.	Phchi.S6G079000
Phchi.S6	AUGUSTUS	transcript	5776017	5776708	.	-	.	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	stop_codon	5776014	5776016	.	-	0	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5776017	5776221	1	-	1	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5776017	5776221	.	-	.	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5776222	5776305	.	-	.	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5776306	5776414	1	-	2	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5776306	5776414	.	-	.	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5776415	5776509	.	-	.	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5776510	5776708	0.95	-	0	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5776510	5776708	.	-	.	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	start_codon	5776706	5776708	.	-	0	transcript_id "Phchi.S6G079000.t1"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	transcript	5773841	5776708	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	stop_codon	5773838	5773840	.	-	0	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5773841	5774004	0.71	-	2	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5773841	5774004	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5774005	5774091	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5774092	5774786	0.7	-	1	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5774092	5774786	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5774787	5774860	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5774861	5775105	0.85	-	0	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5774861	5775105	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5775106	5775240	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5775241	5775570	0.77	-	0	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5775241	5775570	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5775571	5775652	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5775653	5775893	0.81	-	1	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5775653	5775893	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5775894	5776017	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5776018	5776221	0.81	-	1	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5776018	5776221	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5776222	5776305	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5776306	5776414	1	-	2	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5776306	5776414	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5776415	5776509	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5776510	5776708	0.95	-	0	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5776510	5776708	.	-	.	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	start_codon	5776706	5776708	.	-	0	transcript_id "Phchi.S6G079000.t2"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	transcript	5773841	5775835	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	stop_codon	5773838	5773840	.	-	0	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5773841	5774004	0.68	-	2	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5773841	5774004	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5774005	5774091	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5774092	5774786	0.67	-	1	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5774092	5774786	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5774787	5774860	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5774861	5775105	0.86	-	0	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5774861	5775105	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5775106	5775240	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5775241	5775570	0.72	-	0	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5775241	5775570	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	intron	5775571	5775652	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	CDS	5775653	5775835	0.77	-	0	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	exon	5775653	5775835	.	-	.	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
Phchi.S6	AUGUSTUS	start_codon	5775833	5775835	.	-	0	transcript_id "Phchi.S6G079000.t3"; gene_id "Phchi.S6G079000"
# This transcript jg12368.t2 is derived from g8045.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12368.t3 is derived from g8045.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12370.t1 is derived from g8046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13094039	13094497	.	+	.	Phchi.S2G045000
Phchi.S2	AUGUSTUS	transcript	13094039	13094497	.	+	.	transcript_id "Phchi.S2G045000.t1"; gene_id "Phchi.S2G045000"
Phchi.S2	AUGUSTUS	start_codon	13094039	13094041	.	+	0	transcript_id "Phchi.S2G045000.t1"; gene_id "Phchi.S2G045000"
Phchi.S2	AUGUSTUS	CDS	13094039	13094497	0.59	+	0	transcript_id "Phchi.S2G045000.t1"; gene_id "Phchi.S2G045000"
Phchi.S2	AUGUSTUS	exon	13094039	13094497	.	+	.	transcript_id "Phchi.S2G045000.t1"; gene_id "Phchi.S2G045000"
Phchi.S2	AUGUSTUS	stop_codon	13094498	13094500	.	+	0	transcript_id "Phchi.S2G045000.t1"; gene_id "Phchi.S2G045000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg474.t1 is derived from g10256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3336849	3338117	.	+	.	Phchi.S6G043300
Phchi.S6	AUGUSTUS	transcript	3336849	3338117	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	start_codon	3336849	3336851	.	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3336849	3336902	0.54	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3336849	3336902	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	intron	3336903	3336991	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3336992	3337105	0.79	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3336992	3337105	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	intron	3337106	3337247	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3337248	3337298	0.86	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3337248	3337298	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	intron	3337299	3337395	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3337396	3337518	0.94	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3337396	3337518	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	intron	3337519	3337584	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3337585	3337704	1	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3337585	3337704	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	intron	3337705	3337805	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3337806	3337964	1	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3337806	3337964	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	intron	3337965	3338045	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	CDS	3338046	3338117	1	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	exon	3338046	3338117	.	+	.	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
Phchi.S6	AUGUSTUS	stop_codon	3338118	3338120	.	+	0	transcript_id "Phchi.S6G043300.t1"; gene_id "Phchi.S6G043300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7651.t1 is derived from g4825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30418560	30423376	.	+	.	Phchi.S1G481000
Phchi.S1	AUGUSTUS	transcript	30418560	30423376	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	start_codon	30418560	30418562	.	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30418560	30418691	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30418560	30418691	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30418692	30418908	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30418909	30419212	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30418909	30419212	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30419213	30419379	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30419380	30419468	1	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30419380	30419468	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30419469	30419585	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30419586	30419736	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30419586	30419736	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30419737	30419889	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30419890	30420018	1	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30419890	30420018	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30420019	30420124	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30420125	30420249	0.96	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30420125	30420249	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30420250	30420331	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30420332	30420487	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30420332	30420487	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30420488	30420594	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30420595	30420757	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30420595	30420757	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30420758	30420889	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30420890	30421015	1	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30420890	30421015	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30421016	30421118	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30421119	30421202	1	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30421119	30421202	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30421203	30421323	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30421324	30421709	1	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30421324	30421709	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30421710	30421816	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30421817	30422017	0.99	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30421817	30422017	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30422018	30422133	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30422134	30422243	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30422134	30422243	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30422244	30422329	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30422330	30422414	1	+	1	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30422330	30422414	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30422415	30422521	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30422522	30422644	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30422522	30422644	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30422645	30422717	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30422718	30422823	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30422718	30422823	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30422824	30422902	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30422903	30422991	1	+	2	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30422903	30422991	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	intron	30422992	30423079	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	CDS	30423080	30423376	1	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	exon	30423080	30423376	.	+	.	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
Phchi.S1	AUGUSTUS	stop_codon	30423377	30423379	.	+	0	transcript_id "Phchi.S1G481000.t1"; gene_id "Phchi.S1G481000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg373.t1 is derived from g10155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2698286	2698678	.	+	.	Phchi.S6G033200
Phchi.S6	AUGUSTUS	transcript	2698286	2698678	.	+	.	transcript_id "Phchi.S6G033200.t1"; gene_id "Phchi.S6G033200"
Phchi.S6	AUGUSTUS	start_codon	2698286	2698288	.	+	0	transcript_id "Phchi.S6G033200.t1"; gene_id "Phchi.S6G033200"
Phchi.S6	AUGUSTUS	CDS	2698286	2698678	0.99	+	0	transcript_id "Phchi.S6G033200.t1"; gene_id "Phchi.S6G033200"
Phchi.S6	AUGUSTUS	exon	2698286	2698678	.	+	.	transcript_id "Phchi.S6G033200.t1"; gene_id "Phchi.S6G033200"
Phchi.S6	AUGUSTUS	stop_codon	2698679	2698681	.	+	0	transcript_id "Phchi.S6G033200.t1"; gene_id "Phchi.S6G033200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14367.t1 is derived from g12834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12381127	12383097	.	+	.	Phchi.S3G168600
Phchi.S3	AUGUSTUS	transcript	12381127	12383097	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	start_codon	12381127	12381129	.	+	0	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	CDS	12381127	12381469	1	+	0	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	exon	12381127	12381469	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	intron	12381470	12381552	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	CDS	12381553	12381867	1	+	2	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	exon	12381553	12381867	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	intron	12381868	12381941	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	CDS	12381942	12382285	1	+	2	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	exon	12381942	12382285	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	intron	12382286	12382392	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	CDS	12382393	12382621	1	+	0	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	exon	12382393	12382621	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	intron	12382622	12382714	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	CDS	12382715	12383097	1	+	2	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	exon	12382715	12383097	.	+	.	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
Phchi.S3	AUGUSTUS	stop_codon	12383098	12383100	.	+	0	transcript_id "Phchi.S3G168600.t1"; gene_id "Phchi.S3G168600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14013.t1 is derived from g12480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10307359	10308252	.	+	.	Phchi.S3G133200
Phchi.S3	AUGUSTUS	transcript	10307359	10308252	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	start_codon	10307359	10307361	.	+	0	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	CDS	10307359	10307402	0.71	+	0	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	exon	10307359	10307402	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	intron	10307403	10307471	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	CDS	10307472	10307604	1	+	1	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	exon	10307472	10307604	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	intron	10307605	10307685	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	CDS	10307686	10307726	1	+	0	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	exon	10307686	10307726	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	intron	10307727	10307840	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	CDS	10307841	10307896	1	+	1	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	exon	10307841	10307896	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	intron	10307897	10308029	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	CDS	10308030	10308087	1	+	2	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	exon	10308030	10308087	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	intron	10308088	10308173	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	CDS	10308174	10308252	1	+	1	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	exon	10308174	10308252	.	+	.	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
Phchi.S3	AUGUSTUS	stop_codon	10308253	10308255	.	+	0	transcript_id "Phchi.S3G133200.t1"; gene_id "Phchi.S3G133200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13911.t1 is derived from g12378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9633851	9634231	.	+	.	Phchi.S3G123000
Phchi.S3	AUGUSTUS	transcript	9633851	9634231	.	+	.	transcript_id "Phchi.S3G123000.t1"; gene_id "Phchi.S3G123000"
Phchi.S3	AUGUSTUS	start_codon	9633851	9633853	.	+	0	transcript_id "Phchi.S3G123000.t1"; gene_id "Phchi.S3G123000"
Phchi.S3	AUGUSTUS	CDS	9633851	9634231	1	+	0	transcript_id "Phchi.S3G123000.t1"; gene_id "Phchi.S3G123000"
Phchi.S3	AUGUSTUS	exon	9633851	9634231	.	+	.	transcript_id "Phchi.S3G123000.t1"; gene_id "Phchi.S3G123000"
Phchi.S3	AUGUSTUS	stop_codon	9634232	9634234	.	+	0	transcript_id "Phchi.S3G123000.t1"; gene_id "Phchi.S3G123000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3162.t1 is derived from g331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2032493	2034020	.	+	.	Phchi.S1G032100
Phchi.S1	AUGUSTUS	transcript	2032493	2034020	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	start_codon	2032493	2032495	.	+	0	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	CDS	2032493	2032553	0.85	+	0	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	exon	2032493	2032553	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	intron	2032554	2032665	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	CDS	2032666	2032884	0.85	+	2	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	exon	2032666	2032884	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	intron	2032885	2033012	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	CDS	2033013	2033305	1	+	2	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	exon	2033013	2033305	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	intron	2033306	2033383	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	CDS	2033384	2033687	0.84	+	0	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	exon	2033384	2033687	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	intron	2033688	2033790	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	CDS	2033791	2034020	0.68	+	2	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	exon	2033791	2034020	.	+	.	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
Phchi.S1	AUGUSTUS	stop_codon	2034021	2034023	.	+	0	transcript_id "Phchi.S1G032100.t1"; gene_id "Phchi.S1G032100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2213.t1 is derived from g9133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5439117	5440410	.	+	.	Phchi.S5G082200
Phchi.S5	AUGUSTUS	transcript	5439117	5440410	.	+	.	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	start_codon	5439117	5439119	.	+	0	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	CDS	5439117	5439333	0.99	+	0	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	exon	5439117	5439333	.	+	.	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	intron	5439334	5439452	.	+	.	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	CDS	5439453	5439890	0.92	+	2	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	exon	5439453	5439890	.	+	.	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	intron	5439891	5439994	.	+	.	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	CDS	5439995	5440410	0.9	+	2	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	exon	5439995	5440410	.	+	.	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
Phchi.S5	AUGUSTUS	stop_codon	5440411	5440413	.	+	0	transcript_id "Phchi.S5G082200.t1"; gene_id "Phchi.S5G082200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3082.t1 is derived from g251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1549577	1550201	.	+	.	Phchi.S1G024100
Phchi.S1	AUGUSTUS	transcript	1549577	1550201	.	+	.	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	start_codon	1549577	1549579	.	+	0	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	CDS	1549577	1549726	0.34	+	0	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	exon	1549577	1549726	.	+	.	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	intron	1549727	1549814	.	+	.	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	CDS	1549815	1550201	0.25	+	0	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	exon	1549815	1550201	.	+	.	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
Phchi.S1	AUGUSTUS	stop_codon	1550202	1550204	.	+	0	transcript_id "Phchi.S1G024100.t1"; gene_id "Phchi.S1G024100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14659.t1 is derived from g13127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13996413	14001154	.	-	.	Phchi.S3G197800
Phchi.S3	AUGUSTUS	transcript	13996413	14001154	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	stop_codon	13996410	13996412	.	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996413	13996658	0.96	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996413	13996658	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996659	13996764	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996765	13996872	0.44	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996765	13996872	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996873	13996949	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996950	13996990	0.53	-	2	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996950	13996990	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996991	13997081	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997082	13997203	0.32	-	1	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997082	13997203	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997204	13997289	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997290	13997320	0.44	-	2	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997290	13997320	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997321	13997416	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997417	13997469	0.96	-	1	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997417	13997469	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997470	13997575	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997576	13998098	0.86	-	2	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997576	13998098	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998099	13998213	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998214	13998322	1	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998214	13998322	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998323	13998456	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998457	13998682	1	-	1	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998457	13998682	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998683	13998764	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998765	13998886	1	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998765	13998886	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998887	13998981	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998982	13999098	1	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998982	13999098	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13999099	13999399	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13999400	14000602	0.66	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13999400	14000602	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	14000603	14000788	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	14000789	14001154	0.93	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	14000789	14001154	.	-	.	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	start_codon	14001152	14001154	.	-	0	transcript_id "Phchi.S3G197800.t1"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	transcript	13996413	14001154	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	stop_codon	13996410	13996412	.	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996413	13996658	0.96	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996413	13996658	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996659	13996764	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996765	13996872	0.47	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996765	13996872	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996873	13996949	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996950	13996990	0.58	-	2	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996950	13996990	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996991	13997081	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997082	13997203	0.34	-	1	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997082	13997203	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997204	13997289	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997290	13997320	0.42	-	2	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997290	13997320	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997321	13997416	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997417	13997469	0.88	-	1	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997417	13997469	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997470	13997575	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997576	13998098	0.87	-	2	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997576	13998098	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998099	13998213	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998214	13998322	1	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998214	13998322	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998323	13998456	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998457	13998682	1	-	1	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998457	13998682	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998683	13998764	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998765	13998886	1	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998765	13998886	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998887	13998981	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998982	13999098	0.99	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998982	13999098	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13999099	13999352	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13999353	13999399	0.98	-	2	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13999353	13999399	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13999400	13999584	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13999585	14000602	0.3	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13999585	14000602	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	14000603	14000788	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	14000789	14001154	0.97	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	14000789	14001154	.	-	.	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	start_codon	14001152	14001154	.	-	0	transcript_id "Phchi.S3G197800.t2"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	transcript	13996413	14001154	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	stop_codon	13996410	13996412	.	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996413	13996658	0.92	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996413	13996658	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996659	13996764	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996765	13996872	0.56	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996765	13996872	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996873	13996949	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13996950	13996990	0.63	-	2	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13996950	13996990	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13996991	13997081	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997082	13997203	0.31	-	1	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997082	13997203	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997204	13997289	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997290	13997320	0.3	-	2	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997290	13997320	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997321	13997416	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997417	13997469	0.87	-	1	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997417	13997469	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13997470	13997575	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13997576	13998098	0.86	-	2	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13997576	13998098	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998099	13998213	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998214	13998252	0.62	-	2	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998214	13998252	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998253	13998322	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998323	13998356	0.98	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998323	13998356	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998357	13998456	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998457	13998682	0.99	-	1	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998457	13998682	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998683	13998764	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998765	13998886	1	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998765	13998886	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13998887	13998981	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13998982	13999098	1	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13998982	13999098	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	13999099	13999399	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	13999400	14000602	0.56	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	13999400	14000602	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	intron	14000603	14000788	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	CDS	14000789	14001154	0.96	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	exon	14000789	14001154	.	-	.	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
Phchi.S3	AUGUSTUS	start_codon	14001152	14001154	.	-	0	transcript_id "Phchi.S3G197800.t3"; gene_id "Phchi.S3G197800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7619.t1 is derived from g4793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30298402	30298881	.	-	.	Phchi.S1G477800
Phchi.S1	AUGUSTUS	transcript	30298402	30298881	.	-	.	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	stop_codon	30298399	30298401	.	-	0	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	CDS	30298402	30298605	1	-	0	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	exon	30298402	30298605	.	-	.	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	intron	30298606	30298704	.	-	.	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	CDS	30298705	30298881	1	-	0	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	exon	30298705	30298881	.	-	.	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
Phchi.S1	AUGUSTUS	start_codon	30298879	30298881	.	-	0	transcript_id "Phchi.S1G477800.t1"; gene_id "Phchi.S1G477800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg785.t1 is derived from g10567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5480621	5482260	.	+	.	Phchi.S6G074400
Phchi.S6	AUGUSTUS	transcript	5480621	5482260	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	start_codon	5480621	5480623	.	+	0	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	CDS	5480621	5481012	0.83	+	0	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	exon	5480621	5481012	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	intron	5481013	5481126	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	CDS	5481127	5481298	1	+	1	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	exon	5481127	5481298	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	intron	5481299	5481381	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	CDS	5481382	5481393	1	+	0	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	exon	5481382	5481393	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	intron	5481394	5481488	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	CDS	5481489	5481587	1	+	0	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	exon	5481489	5481587	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	intron	5481588	5481734	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	CDS	5481735	5481982	1	+	0	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	exon	5481735	5481982	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	intron	5481983	5482112	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	CDS	5482113	5482260	1	+	1	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	exon	5482113	5482260	.	+	.	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
Phchi.S6	AUGUSTUS	stop_codon	5482261	5482263	.	+	0	transcript_id "Phchi.S6G074400.t1"; gene_id "Phchi.S6G074400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg74.t1 is derived from g9856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	371254	371769	.	+	.	Phchi.S6G003300
Phchi.S6	AUGUSTUS	transcript	371254	371769	.	+	.	transcript_id "Phchi.S6G003300.t1"; gene_id "Phchi.S6G003300"
Phchi.S6	AUGUSTUS	start_codon	371254	371256	.	+	0	transcript_id "Phchi.S6G003300.t1"; gene_id "Phchi.S6G003300"
Phchi.S6	AUGUSTUS	CDS	371254	371769	0.43	+	0	transcript_id "Phchi.S6G003300.t1"; gene_id "Phchi.S6G003300"
Phchi.S6	AUGUSTUS	exon	371254	371769	.	+	.	transcript_id "Phchi.S6G003300.t1"; gene_id "Phchi.S6G003300"
Phchi.S6	AUGUSTUS	stop_codon	371770	371772	.	+	0	transcript_id "Phchi.S6G003300.t1"; gene_id "Phchi.S6G003300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11641.t1 is derived from g15692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7424019	7427218	.	+	.	Phchi.S4G122300
Phchi.S4	AUGUSTUS	transcript	7424019	7427218	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	start_codon	7424019	7424021	.	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7424019	7424037	0.47	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7424019	7424037	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7424038	7424688	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7424689	7424917	1	+	2	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7424689	7424917	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7424918	7425018	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7425019	7425136	0.98	+	1	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7425019	7425136	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7425137	7425255	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7425256	7425633	0.85	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7425256	7425633	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7425634	7425745	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7425746	7425832	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7425746	7425832	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7425833	7425991	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7425992	7426076	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7425992	7426076	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7426077	7426175	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7426176	7426246	1	+	2	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7426176	7426246	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7426247	7426342	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7426343	7426407	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7426343	7426407	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7426408	7426485	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7426486	7426558	1	+	1	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7426486	7426558	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7426559	7426651	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7426652	7426717	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7426652	7426717	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7426718	7426834	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7426835	7426858	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7426835	7426858	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7426859	7426940	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7426941	7427012	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7426941	7427012	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	intron	7427013	7427107	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	CDS	7427108	7427218	1	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	exon	7427108	7427218	.	+	.	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
Phchi.S4	AUGUSTUS	stop_codon	7427219	7427221	.	+	0	transcript_id "Phchi.S4G122300.t1"; gene_id "Phchi.S4G122300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7019.t1 is derived from g4191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26416891	26417230	.	-	.	Phchi.S1G417800
Phchi.S1	AUGUSTUS	transcript	26416891	26417230	.	-	.	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	stop_codon	26416888	26416890	.	-	0	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	CDS	26416891	26416988	0.46	-	2	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	exon	26416891	26416988	.	-	.	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	intron	26416989	26417073	.	-	.	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	CDS	26417074	26417230	0.51	-	0	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	exon	26417074	26417230	.	-	.	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
Phchi.S1	AUGUSTUS	start_codon	26417228	26417230	.	-	0	transcript_id "Phchi.S1G417800.t1"; gene_id "Phchi.S1G417800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15641.t1 is derived from g14110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20434050	20441066	.	-	.	Phchi.S3G296000
Phchi.S3	AUGUSTUS	transcript	20434050	20441066	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	stop_codon	20434047	20434049	.	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20434050	20434453	0.58	-	2	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20434050	20434453	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20434454	20434532	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20434533	20434942	1	-	1	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20434533	20434942	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20434943	20435027	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20435028	20435179	0.66	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20435028	20435179	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20435180	20435451	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20435452	20435580	0.69	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20435452	20435580	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20435581	20435693	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20435694	20435723	0.68	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20435694	20435723	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20435724	20435910	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20435911	20436005	0.72	-	2	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20435911	20436005	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20436006	20436158	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20436159	20436612	0.64	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20436159	20436612	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20436613	20436704	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20436705	20438096	0.99	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20436705	20438096	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20438097	20438199	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20438200	20439225	0.98	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20438200	20439225	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20439226	20439384	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20439385	20439726	1	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20439385	20439726	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20439727	20439823	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20439824	20440395	1	-	2	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20439824	20440395	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20440396	20440505	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20440506	20440667	0.89	-	2	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20440506	20440667	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	intron	20440668	20440780	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	CDS	20440781	20441066	0.97	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	exon	20440781	20441066	.	-	.	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
Phchi.S3	AUGUSTUS	start_codon	20441064	20441066	.	-	0	transcript_id "Phchi.S3G296000.t1"; gene_id "Phchi.S3G296000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg184.t1 is derived from g9966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1061577	1062888	.	-	.	Phchi.S6G014300
Phchi.S6	AUGUSTUS	transcript	1061577	1062888	.	-	.	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	stop_codon	1061574	1061576	.	-	0	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	CDS	1061577	1061627	0.74	-	0	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	exon	1061577	1061627	.	-	.	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	intron	1061628	1061721	.	-	.	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	CDS	1061722	1062888	0.62	-	0	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	exon	1061722	1062888	.	-	.	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
Phchi.S6	AUGUSTUS	start_codon	1062886	1062888	.	-	0	transcript_id "Phchi.S6G014300.t1"; gene_id "Phchi.S6G014300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13481.t1 is derived from g11948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7093588	7094423	.	+	.	Phchi.S3G080000
Phchi.S3	AUGUSTUS	transcript	7093588	7094423	.	+	.	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	start_codon	7093588	7093590	.	+	0	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	CDS	7093588	7093872	1	+	0	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	exon	7093588	7093872	.	+	.	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	intron	7093873	7094022	.	+	.	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	CDS	7094023	7094127	1	+	0	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	exon	7094023	7094127	.	+	.	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	intron	7094128	7094243	.	+	.	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	CDS	7094244	7094423	1	+	0	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	exon	7094244	7094423	.	+	.	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
Phchi.S3	AUGUSTUS	stop_codon	7094424	7094426	.	+	0	transcript_id "Phchi.S3G080000.t1"; gene_id "Phchi.S3G080000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13060.t1 is derived from g11525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3953884	3956215	.	+	.	Phchi.S3G037900
Phchi.S3	AUGUSTUS	transcript	3953884	3956215	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	start_codon	3953884	3953886	.	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3953884	3954161	0.7	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3953884	3954161	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3954162	3954250	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3954251	3954578	1	+	1	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3954251	3954578	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3954579	3954704	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3954705	3954854	0.95	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3954705	3954854	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3954855	3954958	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3954959	3955219	0.83	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3954959	3955219	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3955220	3955349	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3955350	3955433	1	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3955350	3955433	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3955434	3955546	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3955547	3955666	0.92	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3955547	3955666	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3955667	3955929	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3955930	3956051	0.96	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3955930	3956051	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	intron	3956052	3956127	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	CDS	3956128	3956215	1	+	1	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	exon	3956128	3956215	.	+	.	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
Phchi.S3	AUGUSTUS	stop_codon	3956216	3956218	.	+	0	transcript_id "Phchi.S3G037900.t1"; gene_id "Phchi.S3G037900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg450.t1 is derived from g10232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3138605	3141076	.	-	.	Phchi.S6G040900
Phchi.S6	AUGUSTUS	transcript	3138605	3141076	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	stop_codon	3138602	3138604	.	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3138605	3138769	1	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3138605	3138769	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3138770	3138858	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3138859	3139005	1	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3138859	3139005	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139006	3139078	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139079	3139138	1	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139079	3139138	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139139	3139271	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139272	3139378	1	-	2	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139272	3139378	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139379	3139504	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139505	3139597	1	-	2	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139505	3139597	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139598	3139713	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139714	3139786	1	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139714	3139786	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139787	3139926	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139927	3140024	0.98	-	2	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139927	3140024	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140025	3140248	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140249	3140283	0.94	-	1	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140249	3140283	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140284	3140374	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140375	3140586	0.85	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140375	3140586	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140587	3140755	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140756	3141076	0.99	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140756	3141076	.	-	.	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	start_codon	3141074	3141076	.	-	0	transcript_id "Phchi.S6G040900.t1"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	transcript	3138605	3141076	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	stop_codon	3138602	3138604	.	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3138605	3138769	1	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3138605	3138769	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3138770	3138858	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3138859	3139005	1	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3138859	3139005	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139006	3139078	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139079	3139138	1	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139079	3139138	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139139	3139271	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139272	3139378	1	-	2	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139272	3139378	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139379	3139504	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139505	3139597	1	-	2	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139505	3139597	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139598	3139713	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139714	3139786	1	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139714	3139786	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139787	3139926	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139927	3139968	0.81	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139927	3139968	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139969	3140142	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140143	3140283	0.87	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140143	3140283	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140284	3140415	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140416	3140586	0.95	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140416	3140586	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140587	3140755	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140756	3141076	1	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140756	3141076	.	-	.	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	start_codon	3141074	3141076	.	-	0	transcript_id "Phchi.S6G040900.t2"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	transcript	3138605	3141076	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	stop_codon	3138602	3138604	.	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3138605	3138769	1	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3138605	3138769	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3138770	3138858	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3138859	3139005	1	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3138859	3139005	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139006	3139078	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139079	3139138	1	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139079	3139138	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139139	3139271	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139272	3139378	1	-	2	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139272	3139378	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139379	3139504	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139505	3139597	1	-	2	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139505	3139597	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139598	3139713	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139714	3139786	1	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139714	3139786	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139787	3139926	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3139927	3139968	0.7	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3139927	3139968	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3139969	3140142	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140143	3140283	0.85	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140143	3140283	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140284	3140415	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140416	3140471	0.97	-	2	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140416	3140471	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140472	3140566	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140567	3140606	0.76	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140567	3140606	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	intron	3140607	3140755	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	CDS	3140756	3141076	0.98	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	exon	3140756	3141076	.	-	.	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
Phchi.S6	AUGUSTUS	start_codon	3141074	3141076	.	-	0	transcript_id "Phchi.S6G040900.t3"; gene_id "Phchi.S6G040900"
# This transcript jg11805.t2 is derived from g15857.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11806.t1 is derived from g15858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8223243	8223787	.	-	.	Phchi.S4G138800
Phchi.S4	AUGUSTUS	transcript	8223243	8223787	.	-	.	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	stop_codon	8223240	8223242	.	-	0	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	CDS	8223243	8223297	0.98	-	1	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	exon	8223243	8223297	.	-	.	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	intron	8223298	8223460	.	-	.	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	CDS	8223461	8223540	1	-	0	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	exon	8223461	8223540	.	-	.	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	intron	8223541	8223652	.	-	.	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	CDS	8223653	8223787	0.78	-	0	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	exon	8223653	8223787	.	-	.	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
Phchi.S4	AUGUSTUS	start_codon	8223785	8223787	.	-	0	transcript_id "Phchi.S4G138800.t1"; gene_id "Phchi.S4G138800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11107.t1 is derived from g15157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4171141	4173006	.	+	.	Phchi.S4G068900
Phchi.S4	AUGUSTUS	transcript	4171141	4173006	.	+	.	transcript_id "Phchi.S4G068900.t1"; gene_id "Phchi.S4G068900"
Phchi.S4	AUGUSTUS	start_codon	4171141	4171143	.	+	0	transcript_id "Phchi.S4G068900.t1"; gene_id "Phchi.S4G068900"
Phchi.S4	AUGUSTUS	CDS	4171141	4173006	0.3	+	0	transcript_id "Phchi.S4G068900.t1"; gene_id "Phchi.S4G068900"
Phchi.S4	AUGUSTUS	exon	4171141	4173006	.	+	.	transcript_id "Phchi.S4G068900.t1"; gene_id "Phchi.S4G068900"
Phchi.S4	AUGUSTUS	stop_codon	4173007	4173009	.	+	0	transcript_id "Phchi.S4G068900.t1"; gene_id "Phchi.S4G068900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11025.t1 is derived from g15075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3701672	3702795	.	+	.	Phchi.S4G060700
Phchi.S4	AUGUSTUS	transcript	3701672	3702795	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	start_codon	3701672	3701674	.	+	0	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	CDS	3701672	3701676	1	+	0	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	exon	3701672	3701676	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	intron	3701677	3701839	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	CDS	3701840	3701976	1	+	1	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	exon	3701840	3701976	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	intron	3701977	3702081	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	CDS	3702082	3702376	0.85	+	2	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	exon	3702082	3702376	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	intron	3702377	3702491	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	CDS	3702492	3702795	0.85	+	1	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	exon	3702492	3702795	.	+	.	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
Phchi.S4	AUGUSTUS	stop_codon	3702796	3702798	.	+	0	transcript_id "Phchi.S4G060700.t1"; gene_id "Phchi.S4G060700"
# This transcript jg4791.t2 is derived from g1961.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4792.t1 is derived from g1962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12826020	12827753	.	-	.	Phchi.S1G195100
Phchi.S1	AUGUSTUS	transcript	12826020	12827753	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	stop_codon	12826017	12826019	.	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12826020	12826118	0.47	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12826020	12826118	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12826119	12826236	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12826237	12826302	0.51	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12826237	12826302	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12826303	12826383	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12826384	12826503	1	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12826384	12826503	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12826504	12826581	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12826582	12826728	0.96	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12826582	12826728	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12826729	12826812	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12826813	12826852	0.96	-	1	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12826813	12826852	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12826853	12826975	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12826976	12827154	1	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12826976	12827154	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12827155	12827229	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12827230	12827377	1	-	1	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12827230	12827377	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12827378	12827457	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12827458	12827570	1	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12827458	12827570	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	intron	12827571	12827663	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	CDS	12827664	12827753	0.96	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	exon	12827664	12827753	.	-	.	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
Phchi.S1	AUGUSTUS	start_codon	12827751	12827753	.	-	0	transcript_id "Phchi.S1G195100.t1"; gene_id "Phchi.S1G195100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg564.t1 is derived from g10346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4065467	4066708	.	-	.	Phchi.S6G052300
Phchi.S6	AUGUSTUS	transcript	4065467	4066708	.	-	.	transcript_id "Phchi.S6G052300.t1"; gene_id "Phchi.S6G052300"
Phchi.S6	AUGUSTUS	stop_codon	4065464	4065466	.	-	0	transcript_id "Phchi.S6G052300.t1"; gene_id "Phchi.S6G052300"
Phchi.S6	AUGUSTUS	CDS	4065467	4066708	0.68	-	0	transcript_id "Phchi.S6G052300.t1"; gene_id "Phchi.S6G052300"
Phchi.S6	AUGUSTUS	exon	4065467	4066708	.	-	.	transcript_id "Phchi.S6G052300.t1"; gene_id "Phchi.S6G052300"
Phchi.S6	AUGUSTUS	start_codon	4066706	4066708	.	-	0	transcript_id "Phchi.S6G052300.t1"; gene_id "Phchi.S6G052300"
# This transcript jg12987.t2 is derived from g11452.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12988.t1 is derived from g11453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3486570	3487175	.	+	.	Phchi.S3G030700
Phchi.S3	AUGUSTUS	transcript	3486570	3487175	.	+	.	transcript_id "Phchi.S3G030700.t1"; gene_id "Phchi.S3G030700"
Phchi.S3	AUGUSTUS	start_codon	3486570	3486572	.	+	0	transcript_id "Phchi.S3G030700.t1"; gene_id "Phchi.S3G030700"
Phchi.S3	AUGUSTUS	CDS	3486570	3487175	1	+	0	transcript_id "Phchi.S3G030700.t1"; gene_id "Phchi.S3G030700"
Phchi.S3	AUGUSTUS	exon	3486570	3487175	.	+	.	transcript_id "Phchi.S3G030700.t1"; gene_id "Phchi.S3G030700"
Phchi.S3	AUGUSTUS	stop_codon	3487176	3487178	.	+	0	transcript_id "Phchi.S3G030700.t1"; gene_id "Phchi.S3G030700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10672.t1 is derived from g14722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1531220	1535416	.	-	.	Phchi.S4G025400
Phchi.S4	AUGUSTUS	transcript	1531220	1535416	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	stop_codon	1531217	1531219	.	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1531220	1531390	0.97	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1531220	1531390	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1531391	1531471	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1531472	1531646	1	-	1	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1531472	1531646	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1531647	1531733	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1531734	1531828	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1531734	1531828	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1531829	1532009	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1532010	1532148	1	-	1	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1532010	1532148	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1532149	1532271	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1532272	1532363	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1532272	1532363	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1532364	1532493	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1532494	1532566	1	-	1	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1532494	1532566	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1532567	1532692	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1532693	1532778	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1532693	1532778	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1532779	1532861	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1532862	1532977	1	-	2	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1532862	1532977	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1532978	1533071	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1533072	1533250	0.64	-	1	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1533072	1533250	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1533251	1533374	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1533375	1533460	0.99	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1533375	1533460	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1533461	1533670	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1533671	1533773	1	-	1	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1533671	1533773	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1533774	1533844	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1533845	1533951	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1533845	1533951	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1533952	1534045	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1534046	1534110	1	-	2	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1534046	1534110	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1534111	1534189	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1534190	1534241	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1534190	1534241	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1534242	1534435	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1534436	1534573	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1534436	1534573	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1534574	1534653	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1534654	1534759	0.99	-	1	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1534654	1534759	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1534760	1534862	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1534863	1534960	1	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1534863	1534960	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1534961	1535184	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1535185	1535237	1	-	2	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1535185	1535237	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	intron	1535238	1535325	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	CDS	1535326	1535416	0.57	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	exon	1535326	1535416	.	-	.	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
Phchi.S4	AUGUSTUS	start_codon	1535414	1535416	.	-	0	transcript_id "Phchi.S4G025400.t1"; gene_id "Phchi.S4G025400"
# This transcript jg10622.t2 is derived from g14672.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10622.t3 is derived from g14672.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10623.t1 is derived from g14673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1283657	1283983	.	-	.	Phchi.S4G020500
Phchi.S4	AUGUSTUS	transcript	1283657	1283983	.	-	.	transcript_id "Phchi.S4G020500.t1"; gene_id "Phchi.S4G020500"
Phchi.S4	AUGUSTUS	stop_codon	1283654	1283656	.	-	0	transcript_id "Phchi.S4G020500.t1"; gene_id "Phchi.S4G020500"
Phchi.S4	AUGUSTUS	CDS	1283657	1283983	0.77	-	0	transcript_id "Phchi.S4G020500.t1"; gene_id "Phchi.S4G020500"
Phchi.S4	AUGUSTUS	exon	1283657	1283983	.	-	.	transcript_id "Phchi.S4G020500.t1"; gene_id "Phchi.S4G020500"
Phchi.S4	AUGUSTUS	start_codon	1283981	1283983	.	-	0	transcript_id "Phchi.S4G020500.t1"; gene_id "Phchi.S4G020500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11448.t1 is derived from g15498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6404539	6406786	.	+	.	Phchi.S4G103000
Phchi.S4	AUGUSTUS	transcript	6404539	6406786	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	start_codon	6404539	6404541	.	+	0	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	CDS	6404539	6404650	0.62	+	0	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	exon	6404539	6404650	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	intron	6404651	6404806	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	CDS	6404807	6405024	0.99	+	2	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	exon	6404807	6405024	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	intron	6405025	6405117	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	CDS	6405118	6405548	0.57	+	0	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	exon	6405118	6405548	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	intron	6405549	6405653	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	CDS	6405654	6405824	0.98	+	1	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	exon	6405654	6405824	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	intron	6405825	6405912	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	CDS	6405913	6406786	1	+	1	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	exon	6405913	6406786	.	+	.	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
Phchi.S4	AUGUSTUS	stop_codon	6406787	6406789	.	+	0	transcript_id "Phchi.S4G103000.t1"; gene_id "Phchi.S4G103000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9045.t1 is derived from g6220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39345671	39346207	.	-	.	Phchi.S1G620400
Phchi.S1	AUGUSTUS	transcript	39345671	39346207	.	-	.	transcript_id "Phchi.S1G620400.t1"; gene_id "Phchi.S1G620400"
Phchi.S1	AUGUSTUS	stop_codon	39345668	39345670	.	-	0	transcript_id "Phchi.S1G620400.t1"; gene_id "Phchi.S1G620400"
Phchi.S1	AUGUSTUS	CDS	39345671	39346207	0.89	-	0	transcript_id "Phchi.S1G620400.t1"; gene_id "Phchi.S1G620400"
Phchi.S1	AUGUSTUS	exon	39345671	39346207	.	-	.	transcript_id "Phchi.S1G620400.t1"; gene_id "Phchi.S1G620400"
Phchi.S1	AUGUSTUS	start_codon	39346205	39346207	.	-	0	transcript_id "Phchi.S1G620400.t1"; gene_id "Phchi.S1G620400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3159.t1 is derived from g328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2019491	2021340	.	+	.	Phchi.S1G031800
Phchi.S1	AUGUSTUS	transcript	2019491	2021340	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	start_codon	2019491	2019493	.	+	0	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	CDS	2019491	2019710	0.38	+	0	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	exon	2019491	2019710	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	intron	2019711	2019980	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	CDS	2019981	2020888	1	+	2	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	exon	2019981	2020888	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	intron	2020889	2020964	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	CDS	2020965	2021021	1	+	0	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	exon	2020965	2021021	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	intron	2021022	2021094	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	CDS	2021095	2021340	1	+	0	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	exon	2021095	2021340	.	+	.	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
Phchi.S1	AUGUSTUS	stop_codon	2021341	2021343	.	+	0	transcript_id "Phchi.S1G031800.t1"; gene_id "Phchi.S1G031800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3746.t1 is derived from g915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5474045	5477353	.	-	.	Phchi.S1G090500
Phchi.S1	AUGUSTUS	transcript	5474045	5477353	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	stop_codon	5474042	5474044	.	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5474045	5474422	0.98	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5474045	5474422	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5474423	5474503	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5474504	5474563	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5474504	5474563	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5474564	5474827	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5474828	5474905	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5474828	5474905	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5474906	5475038	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5475039	5475113	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5475039	5475113	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5475114	5475191	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5475192	5475227	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5475192	5475227	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5475228	5475336	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5475337	5475399	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5475337	5475399	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5475400	5475567	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5475568	5475651	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5475568	5475651	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5475652	5475784	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5475785	5475874	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5475785	5475874	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5475875	5475977	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5475978	5476115	1	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5475978	5476115	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5476116	5476259	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5476260	5476534	0.99	-	2	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5476260	5476534	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	intron	5476535	5476656	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	CDS	5476657	5477353	0.46	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	exon	5476657	5477353	.	-	.	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
Phchi.S1	AUGUSTUS	start_codon	5477351	5477353	.	-	0	transcript_id "Phchi.S1G090500.t1"; gene_id "Phchi.S1G090500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg4448.t1 is derived from g1617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10555820	10558683	.	-	.	Phchi.S1G160700
Phchi.S1	AUGUSTUS	transcript	10555820	10558683	.	-	.	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	stop_codon	10555817	10555819	.	-	0	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10555820	10556787	0.86	-	2	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10555820	10556787	.	-	.	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10556788	10556970	.	-	.	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556971	10557633	0.67	-	2	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556971	10557633	.	-	.	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10557634	10557743	.	-	.	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10557744	10558683	0.46	-	0	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10557744	10558683	.	-	.	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	start_codon	10558681	10558683	.	-	0	transcript_id "Phchi.S1G160700.t1"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	transcript	10555820	10558182	.	-	.	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	stop_codon	10555817	10555819	.	-	0	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10555820	10556787	0.87	-	2	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10555820	10556787	.	-	.	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10556788	10556970	.	-	.	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556971	10557633	0.69	-	2	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556971	10557633	.	-	.	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10557634	10557743	.	-	.	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10557744	10558182	0.39	-	0	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10557744	10558182	.	-	.	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	start_codon	10558180	10558182	.	-	0	transcript_id "Phchi.S1G160700.t2"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	transcript	10556346	10558683	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	stop_codon	10556343	10556345	.	-	0	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556346	10556362	0.61	-	2	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556346	10556362	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10556363	10556448	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556449	10556787	0.55	-	2	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556449	10556787	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10556788	10556970	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556971	10557633	0.77	-	2	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556971	10557633	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10557634	10557743	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10557744	10558683	0.43	-	0	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10557744	10558683	.	-	.	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	start_codon	10558681	10558683	.	-	0	transcript_id "Phchi.S1G160700.t3"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	transcript	10556346	10558182	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	stop_codon	10556343	10556345	.	-	0	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556346	10556362	0.66	-	2	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556346	10556362	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10556363	10556448	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556449	10556787	0.58	-	2	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556449	10556787	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10556788	10556970	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10556971	10557633	0.76	-	2	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10556971	10557633	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	intron	10557634	10557743	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	CDS	10557744	10558182	0.31	-	0	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	exon	10557744	10558182	.	-	.	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
Phchi.S1	AUGUSTUS	start_codon	10558180	10558182	.	-	0	transcript_id "Phchi.S1G160700.t4"; gene_id "Phchi.S1G160700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8051.t1 is derived from g5226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32717257	32720513	.	+	.	Phchi.S1G521000
Phchi.S1	AUGUSTUS	transcript	32717257	32720513	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	start_codon	32717257	32717259	.	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32717257	32717281	1	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32717257	32717281	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32717282	32717405	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32717406	32717583	1	+	2	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32717406	32717583	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32717584	32717716	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32717717	32717789	0.96	+	1	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32717717	32717789	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32717790	32717890	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32717891	32718008	1	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32717891	32718008	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32718009	32718140	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32718141	32718214	1	+	2	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32718141	32718214	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32718215	32718293	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32718294	32718430	1	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32718294	32718430	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32718431	32718534	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32718535	32718598	1	+	1	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32718535	32718598	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32718599	32718699	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32718700	32718765	1	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32718700	32718765	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32718766	32718857	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32718858	32718927	1	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32718858	32718927	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32718928	32719022	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32719023	32719127	1	+	2	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32719023	32719127	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32719128	32719222	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32719223	32719364	1	+	2	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32719223	32719364	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32719365	32719507	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32719508	32719604	1	+	1	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32719508	32719604	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	intron	32719605	32719688	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	CDS	32719689	32720513	0.79	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	exon	32719689	32720513	.	+	.	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
Phchi.S1	AUGUSTUS	stop_codon	32720514	32720516	.	+	0	transcript_id "Phchi.S1G521000.t1"; gene_id "Phchi.S1G521000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1585.t1 is derived from g8504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1890720	1891869	.	+	.	Phchi.S5G019400
Phchi.S5	AUGUSTUS	transcript	1890720	1891869	.	+	.	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	start_codon	1890720	1890722	.	+	0	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	CDS	1890720	1890995	0.99	+	0	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	exon	1890720	1890995	.	+	.	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	intron	1890996	1891092	.	+	.	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	CDS	1891093	1891869	1	+	0	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	exon	1891093	1891869	.	+	.	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
Phchi.S5	AUGUSTUS	stop_codon	1891870	1891872	.	+	0	transcript_id "Phchi.S5G019400.t1"; gene_id "Phchi.S5G019400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1957.t1 is derived from g8877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4018541	4020690	.	-	.	Phchi.S5G056600
Phchi.S5	AUGUSTUS	transcript	4018541	4020690	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	stop_codon	4018538	4018540	.	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	CDS	4018541	4018666	1	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	exon	4018541	4018666	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	intron	4018667	4018738	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	CDS	4018739	4019014	1	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	exon	4018739	4019014	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	intron	4019015	4019161	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	CDS	4019162	4019323	1	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	exon	4019162	4019323	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	intron	4019324	4019588	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	CDS	4019589	4020103	0.53	-	2	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	exon	4019589	4020103	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	intron	4020104	4020312	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	CDS	4020313	4020364	0.58	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	exon	4020313	4020364	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	intron	4020365	4020555	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	CDS	4020556	4020690	0.64	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	exon	4020556	4020690	.	-	.	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
Phchi.S5	AUGUSTUS	start_codon	4020688	4020690	.	-	0	transcript_id "Phchi.S5G056600.t1"; gene_id "Phchi.S5G056600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1732.t1 is derived from g8652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2754937	2755499	.	-	.	Phchi.S5G034100
Phchi.S5	AUGUSTUS	transcript	2754937	2755499	.	-	.	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	stop_codon	2754934	2754936	.	-	0	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	CDS	2754937	2754998	0.96	-	2	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	exon	2754937	2754998	.	-	.	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	intron	2754999	2755147	.	-	.	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	CDS	2755148	2755324	0.99	-	2	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	exon	2755148	2755324	.	-	.	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	intron	2755325	2755426	.	-	.	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	CDS	2755427	2755499	0.98	-	0	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	exon	2755427	2755499	.	-	.	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
Phchi.S5	AUGUSTUS	start_codon	2755497	2755499	.	-	0	transcript_id "Phchi.S5G034100.t1"; gene_id "Phchi.S5G034100"
# This transcript jg11704.t2 is derived from g15755.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11705.t1 is derived from g15756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7769579	7772278	.	+	.	Phchi.S4G128700
Phchi.S4	AUGUSTUS	transcript	7769579	7772278	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	start_codon	7769579	7769581	.	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7769579	7769676	0.89	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7769579	7769676	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7769677	7769837	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7769838	7769928	1	+	1	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7769838	7769928	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7769929	7770045	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7770046	7770108	1	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7770046	7770108	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7770109	7770243	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7770244	7770310	1	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7770244	7770310	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7770311	7770449	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7770450	7770553	1	+	2	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7770450	7770553	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7770554	7770639	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7770640	7770766	1	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7770640	7770766	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7770767	7770840	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7770841	7771673	1	+	2	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7770841	7771673	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	intron	7771674	7771768	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	CDS	7771769	7772278	1	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	exon	7771769	7772278	.	+	.	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
Phchi.S4	AUGUSTUS	stop_codon	7772279	7772281	.	+	0	transcript_id "Phchi.S4G128700.t1"; gene_id "Phchi.S4G128700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10039.t1 is derived from g7215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45205185	45208570	.	-	.	Phchi.S1G719800
Phchi.S1	AUGUSTUS	transcript	45205185	45208570	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	stop_codon	45205182	45205184	.	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45205185	45205188	1	-	1	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45205185	45205188	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45205189	45205269	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45205270	45205364	1	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45205270	45205364	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45205365	45205476	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45205477	45205586	1	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45205477	45205586	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45205587	45205684	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45205685	45205729	1	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45205685	45205729	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45205730	45205809	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45205810	45205819	1	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45205810	45205819	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45205820	45205910	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45205911	45205977	1	-	1	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45205911	45205977	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45205978	45206074	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45206075	45206156	1	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45206075	45206156	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45206157	45206245	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45206246	45206327	1	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45206246	45206327	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45206328	45206423	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45206424	45206500	1	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45206424	45206500	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45206501	45206582	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45206583	45206666	1	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45206583	45206666	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45206667	45206751	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45206752	45206821	1	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45206752	45206821	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45206822	45206975	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45206976	45207064	1	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45206976	45207064	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45207065	45207180	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45207181	45207882	0.96	-	2	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45207181	45207882	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	intron	45207883	45208278	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	CDS	45208279	45208570	0.96	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	exon	45208279	45208570	.	-	.	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
Phchi.S1	AUGUSTUS	start_codon	45208568	45208570	.	-	0	transcript_id "Phchi.S1G719800.t1"; gene_id "Phchi.S1G719800"
# This transcript jg8125.t2 is derived from g5300.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8126.t1 is derived from g5301.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33618813	33622980	.	-	.	Phchi.S1G528500
Phchi.S1	AUGUSTUS	transcript	33618813	33622980	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	stop_codon	33618810	33618812	.	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33618813	33618888	1	-	1	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33618813	33618888	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33618889	33619017	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619018	33619112	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619018	33619112	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619113	33619248	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619249	33619314	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619249	33619314	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619315	33619407	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619408	33619632	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619408	33619632	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619633	33619864	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619865	33619974	1	-	2	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619865	33619974	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619975	33620137	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620138	33620222	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620138	33620222	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620223	33620414	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620415	33620497	0.51	-	2	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620415	33620497	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620498	33620607	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620608	33620664	0.98	-	2	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620608	33620664	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620665	33620805	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620806	33620941	0.98	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620806	33620941	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620942	33621273	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33621274	33621429	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33621274	33621429	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33621430	33621564	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33621565	33621687	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33621565	33621687	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33621688	33621831	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33621832	33622062	0.99	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33621832	33622062	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33622063	33622190	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33622191	33622387	1	-	2	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33622191	33622387	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33622388	33622540	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33622541	33622775	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33622541	33622775	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33622776	33622857	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33622858	33622980	1	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33622858	33622980	.	-	.	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	start_codon	33622978	33622980	.	-	0	transcript_id "Phchi.S1G528500.t1"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	transcript	33618813	33622980	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	stop_codon	33618810	33618812	.	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33618813	33618888	1	-	1	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33618813	33618888	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33618889	33619017	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619018	33619112	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619018	33619112	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619113	33619248	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619249	33619314	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619249	33619314	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619315	33619407	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619408	33619632	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619408	33619632	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619633	33619864	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33619865	33619974	1	-	2	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33619865	33619974	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33619975	33620137	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620138	33620222	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620138	33620222	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620223	33620414	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620415	33620664	0.62	-	1	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620415	33620664	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620665	33620771	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33620772	33620941	0.62	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33620772	33620941	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33620942	33621273	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33621274	33621429	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33621274	33621429	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33621430	33621564	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33621565	33621687	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33621565	33621687	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33621688	33621831	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33621832	33622062	0.99	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33621832	33622062	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33622063	33622190	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33622191	33622387	1	-	2	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33622191	33622387	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33622388	33622540	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33622541	33622775	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33622541	33622775	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	intron	33622776	33622857	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	CDS	33622858	33622980	1	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	exon	33622858	33622980	.	-	.	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
Phchi.S1	AUGUSTUS	start_codon	33622978	33622980	.	-	0	transcript_id "Phchi.S1G528500.t2"; gene_id "Phchi.S1G528500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7430.t1 is derived from g4602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29092665	29093925	.	+	.	Phchi.S1G458900
Phchi.S1	AUGUSTUS	transcript	29092665	29093925	.	+	.	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	start_codon	29092665	29092667	.	+	0	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	CDS	29092665	29093753	0.16	+	0	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	exon	29092665	29093753	.	+	.	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	intron	29093754	29093838	.	+	.	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	CDS	29093839	29093925	0.33	+	0	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	exon	29093839	29093925	.	+	.	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
Phchi.S1	AUGUSTUS	stop_codon	29093926	29093928	.	+	0	transcript_id "Phchi.S1G458900.t1"; gene_id "Phchi.S1G458900"
# This transcript jg4323.t2 is derived from g1492.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4323.t3 is derived from g1492.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4324.t1 is derived from g1493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9784091	9785533	.	-	.	Phchi.S1G148300
Phchi.S1	AUGUSTUS	transcript	9784091	9785533	.	-	.	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	stop_codon	9784088	9784090	.	-	0	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	CDS	9784091	9784815	0.8	-	2	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	exon	9784091	9784815	.	-	.	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	intron	9784816	9784893	.	-	.	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	CDS	9784894	9785248	0.97	-	0	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	exon	9784894	9785248	.	-	.	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	intron	9785249	9785392	.	-	.	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	CDS	9785393	9785533	0.65	-	0	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	exon	9785393	9785533	.	-	.	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
Phchi.S1	AUGUSTUS	start_codon	9785531	9785533	.	-	0	transcript_id "Phchi.S1G148300.t1"; gene_id "Phchi.S1G148300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6844.t1 is derived from g4016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25512636	25515846	.	-	.	Phchi.S1G400300
Phchi.S1	AUGUSTUS	transcript	25512636	25515846	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	stop_codon	25512633	25512635	.	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25512636	25512846	0.99	-	1	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25512636	25512846	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25512847	25512937	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25512938	25513046	1	-	2	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25512938	25513046	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25513047	25513144	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25513145	25513247	1	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25513145	25513247	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25513248	25513399	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25513400	25513431	1	-	2	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25513400	25513431	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25513432	25513527	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25513528	25513748	1	-	1	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25513528	25513748	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25513749	25513860	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25513861	25513976	1	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25513861	25513976	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25513977	25514146	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25514147	25514396	1	-	1	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25514147	25514396	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25514397	25514545	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25514546	25514633	1	-	2	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25514546	25514633	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25514634	25514741	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25514742	25514813	1	-	2	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25514742	25514813	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25514814	25514928	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25514929	25515004	1	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25514929	25515004	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25515005	25515105	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25515106	25515164	0.95	-	2	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25515106	25515164	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25515165	25515263	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25515264	25515330	1	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25515264	25515330	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25515331	25515428	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25515429	25515650	1	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25515429	25515650	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	intron	25515651	25515807	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	CDS	25515808	25515846	1	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	exon	25515808	25515846	.	-	.	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
Phchi.S1	AUGUSTUS	start_codon	25515844	25515846	.	-	0	transcript_id "Phchi.S1G400300.t1"; gene_id "Phchi.S1G400300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2100.t1 is derived from g9020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4871623	4873116	.	+	.	Phchi.S5G070900
Phchi.S5	AUGUSTUS	transcript	4871623	4873116	.	+	.	transcript_id "Phchi.S5G070900.t1"; gene_id "Phchi.S5G070900"
Phchi.S5	AUGUSTUS	start_codon	4871623	4871625	.	+	0	transcript_id "Phchi.S5G070900.t1"; gene_id "Phchi.S5G070900"
Phchi.S5	AUGUSTUS	CDS	4871623	4873116	1	+	0	transcript_id "Phchi.S5G070900.t1"; gene_id "Phchi.S5G070900"
Phchi.S5	AUGUSTUS	exon	4871623	4873116	.	+	.	transcript_id "Phchi.S5G070900.t1"; gene_id "Phchi.S5G070900"
Phchi.S5	AUGUSTUS	stop_codon	4873117	4873119	.	+	0	transcript_id "Phchi.S5G070900.t1"; gene_id "Phchi.S5G070900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1493.t1 is derived from g8412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1188991	1192030	.	-	.	Phchi.S5G010200
Phchi.S5	AUGUSTUS	transcript	1188991	1192030	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	stop_codon	1188988	1188990	.	-	0	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1188991	1189166	0.99	-	2	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1188991	1189166	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1189167	1189253	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1189254	1189402	0.99	-	1	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1189254	1189402	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1189403	1189958	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1189959	1189987	0.99	-	0	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1189959	1189987	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1189988	1190080	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1190081	1190119	0.69	-	0	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1190081	1190119	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1190120	1190301	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1190302	1190353	0.54	-	1	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1190302	1190353	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1190354	1190502	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1190503	1190535	0.59	-	1	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1190503	1190535	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1190536	1190713	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1190714	1190784	0.6	-	0	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1190714	1190784	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1190785	1190881	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1190882	1191119	1	-	1	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1190882	1191119	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1191120	1191213	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1191214	1191396	1	-	1	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1191214	1191396	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1191397	1191551	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1191552	1191642	1	-	2	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1191552	1191642	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	intron	1191643	1191801	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	CDS	1191802	1192030	1	-	0	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	exon	1191802	1192030	.	-	.	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
Phchi.S5	AUGUSTUS	start_codon	1192028	1192030	.	-	0	transcript_id "Phchi.S5G010200.t1"; gene_id "Phchi.S5G010200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11299.t1 is derived from g15349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5291538	5292493	.	+	.	Phchi.S4G088100
Phchi.S4	AUGUSTUS	transcript	5291538	5292493	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	start_codon	5291538	5291540	.	+	0	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	CDS	5291538	5291727	0.71	+	0	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	exon	5291538	5291727	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	intron	5291728	5291850	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	CDS	5291851	5291874	0.81	+	2	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	exon	5291851	5291874	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	intron	5291875	5292025	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	CDS	5292026	5292080	0.75	+	2	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	exon	5292026	5292080	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	intron	5292081	5292185	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	CDS	5292186	5292224	0.79	+	1	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	exon	5292186	5292224	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	intron	5292225	5292414	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	CDS	5292415	5292493	0.81	+	1	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	exon	5292415	5292493	.	+	.	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
Phchi.S4	AUGUSTUS	stop_codon	5292494	5292496	.	+	0	transcript_id "Phchi.S4G088100.t1"; gene_id "Phchi.S4G088100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg872.t1 is derived from g10654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6037118	6041781	.	+	.	Phchi.S6G083100
Phchi.S6	AUGUSTUS	transcript	6037118	6041781	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	start_codon	6037118	6037120	.	+	0	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	CDS	6037118	6037274	1	+	0	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	exon	6037118	6037274	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	intron	6037275	6037363	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	CDS	6037364	6037434	0.99	+	2	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	exon	6037364	6037434	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	intron	6037435	6037543	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	CDS	6037544	6040657	0.99	+	0	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	exon	6037544	6040657	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	intron	6040658	6040745	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	CDS	6040746	6040977	1	+	0	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	exon	6040746	6040977	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	intron	6040978	6041059	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	CDS	6041060	6041781	0.61	+	2	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	exon	6041060	6041781	.	+	.	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
Phchi.S6	AUGUSTUS	stop_codon	6041782	6041784	.	+	0	transcript_id "Phchi.S6G083100.t1"; gene_id "Phchi.S6G083100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7405.t1 is derived from g4577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28974552	28976929	.	+	.	Phchi.S1G456400
Phchi.S1	AUGUSTUS	transcript	28974552	28976929	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	start_codon	28974552	28974554	.	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28974552	28974788	0.67	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28974552	28974788	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28974789	28974890	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28974891	28975103	1	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28974891	28975103	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28975104	28975303	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28975304	28975501	1	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28975304	28975501	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28975502	28975626	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28975627	28975722	1	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28975627	28975722	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28975723	28975840	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28975841	28976005	1	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28975841	28976005	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28976006	28976098	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28976099	28976204	0.99	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28976099	28976204	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28976205	28976310	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28976311	28976474	1	+	2	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28976311	28976474	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	intron	28976475	28976611	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	CDS	28976612	28976929	0.97	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	exon	28976612	28976929	.	+	.	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
Phchi.S1	AUGUSTUS	stop_codon	28976930	28976932	.	+	0	transcript_id "Phchi.S1G456400.t1"; gene_id "Phchi.S1G456400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15487.t1 is derived from g13956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19444452	19446281	.	+	.	Phchi.S3G280600
Phchi.S3	AUGUSTUS	transcript	19444452	19446281	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	start_codon	19444452	19444454	.	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19444452	19444542	1	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19444452	19444542	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19444543	19444691	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19444692	19444853	1	+	2	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19444692	19444853	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19444854	19445021	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19445022	19445072	1	+	2	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19445022	19445072	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19445073	19445177	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19445178	19445266	1	+	2	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19445178	19445266	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19445267	19445504	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19445505	19445582	1	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19445505	19445582	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19445583	19445687	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19445688	19445891	1	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19445688	19445891	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19445892	19446031	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19446032	19446109	0.99	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19446032	19446109	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	intron	19446110	19446215	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	CDS	19446216	19446281	1	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	exon	19446216	19446281	.	+	.	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
Phchi.S3	AUGUSTUS	stop_codon	19446282	19446284	.	+	0	transcript_id "Phchi.S3G280600.t1"; gene_id "Phchi.S3G280600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10290.t1 is derived from g7466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46837323	46839385	.	+	.	Phchi.S1G744900
Phchi.S1	AUGUSTUS	transcript	46837323	46839385	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	start_codon	46837323	46837325	.	+	0	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46837323	46837381	0.96	+	0	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46837323	46837381	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46837382	46837473	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46837474	46837533	1	+	1	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46837474	46837533	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46837534	46837687	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46837688	46837863	1	+	1	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46837688	46837863	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46837864	46837960	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46837961	46838015	1	+	2	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46837961	46838015	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46838016	46838120	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46838121	46838262	1	+	1	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46838121	46838262	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46838263	46838342	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46838343	46838438	0.84	+	0	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46838343	46838438	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46838439	46838561	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46838562	46838814	0.68	+	0	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46838562	46838814	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46838815	46839016	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46839017	46839079	0.86	+	2	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46839017	46839079	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46839080	46839183	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46839184	46839220	0.52	+	2	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46839184	46839220	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	intron	46839221	46839321	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	CDS	46839322	46839385	0.94	+	1	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	exon	46839322	46839385	.	+	.	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
Phchi.S1	AUGUSTUS	stop_codon	46839386	46839388	.	+	0	transcript_id "Phchi.S1G744900.t1"; gene_id "Phchi.S1G744900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12454.t1 is derived from g8131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23561992	23564558	.	-	.	Phchi.S2G053400
Phchi.S2	AUGUSTUS	transcript	23561992	23564558	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	stop_codon	23561989	23561991	.	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23561992	23562079	0.99	-	1	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23561992	23562079	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23562080	23562198	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23562199	23562277	1	-	2	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23562199	23562277	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23562278	23562363	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23562364	23562460	1	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23562364	23562460	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23562461	23562661	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23562662	23562850	1	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23562662	23562850	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23562851	23562926	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23562927	23563019	1	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23562927	23563019	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23563020	23563205	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23563206	23563721	0.98	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23563206	23563721	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23563722	23563843	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23563844	23563942	0.98	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23563844	23563942	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23563943	23564046	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23564047	23564117	0.98	-	2	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23564047	23564117	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23564118	23564286	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23564287	23564378	0.98	-	1	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23564287	23564378	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	intron	23564379	23564553	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	CDS	23564554	23564558	0.88	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	exon	23564554	23564558	.	-	.	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
Phchi.S2	AUGUSTUS	start_codon	23564556	23564558	.	-	0	transcript_id "Phchi.S2G053400.t1"; gene_id "Phchi.S2G053400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3228.t1 is derived from g397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2357768	2358445	.	+	.	Phchi.S1G038700
Phchi.S1	AUGUSTUS	transcript	2357768	2358445	.	+	.	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	start_codon	2357768	2357770	.	+	0	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	CDS	2357768	2357899	0.68	+	0	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	exon	2357768	2357899	.	+	.	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	intron	2357900	2358162	.	+	.	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	CDS	2358163	2358250	1	+	0	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	exon	2358163	2358250	.	+	.	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	intron	2358251	2358341	.	+	.	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	CDS	2358342	2358445	0.98	+	2	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	exon	2358342	2358445	.	+	.	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
Phchi.S1	AUGUSTUS	stop_codon	2358446	2358448	.	+	0	transcript_id "Phchi.S1G038700.t1"; gene_id "Phchi.S1G038700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13956.t1 is derived from g12423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9915246	9916076	.	-	.	Phchi.S3G127500
Phchi.S3	AUGUSTUS	transcript	9915246	9916076	.	-	.	transcript_id "Phchi.S3G127500.t1"; gene_id "Phchi.S3G127500"
Phchi.S3	AUGUSTUS	stop_codon	9915243	9915245	.	-	0	transcript_id "Phchi.S3G127500.t1"; gene_id "Phchi.S3G127500"
Phchi.S3	AUGUSTUS	CDS	9915246	9916076	0.88	-	0	transcript_id "Phchi.S3G127500.t1"; gene_id "Phchi.S3G127500"
Phchi.S3	AUGUSTUS	exon	9915246	9916076	.	-	.	transcript_id "Phchi.S3G127500.t1"; gene_id "Phchi.S3G127500"
Phchi.S3	AUGUSTUS	start_codon	9916074	9916076	.	-	0	transcript_id "Phchi.S3G127500.t1"; gene_id "Phchi.S3G127500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2744.t1 is derived from g9664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8577568	8578155	.	-	.	Phchi.S5G135300
Phchi.S5	AUGUSTUS	transcript	8577568	8578155	.	-	.	transcript_id "Phchi.S5G135300.t1"; gene_id "Phchi.S5G135300"
Phchi.S5	AUGUSTUS	stop_codon	8577565	8577567	.	-	0	transcript_id "Phchi.S5G135300.t1"; gene_id "Phchi.S5G135300"
Phchi.S5	AUGUSTUS	CDS	8577568	8578155	0.83	-	0	transcript_id "Phchi.S5G135300.t1"; gene_id "Phchi.S5G135300"
Phchi.S5	AUGUSTUS	exon	8577568	8578155	.	-	.	transcript_id "Phchi.S5G135300.t1"; gene_id "Phchi.S5G135300"
Phchi.S5	AUGUSTUS	start_codon	8578153	8578155	.	-	0	transcript_id "Phchi.S5G135300.t1"; gene_id "Phchi.S5G135300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1489.t1 is derived from g8408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1157945	1158607	.	-	.	Phchi.S5G009800
Phchi.S5	AUGUSTUS	transcript	1157945	1158607	.	-	.	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	stop_codon	1157942	1157944	.	-	0	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	CDS	1157945	1158264	0.97	-	2	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	exon	1157945	1158264	.	-	.	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	intron	1158265	1158342	.	-	.	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	CDS	1158343	1158607	0.87	-	0	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	exon	1158343	1158607	.	-	.	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
Phchi.S5	AUGUSTUS	start_codon	1158605	1158607	.	-	0	transcript_id "Phchi.S5G009800.t1"; gene_id "Phchi.S5G009800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15103.t1 is derived from g13571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17073182	17074598	.	-	.	Phchi.S3G242200
Phchi.S3	AUGUSTUS	transcript	17073182	17074598	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	stop_codon	17073179	17073181	.	-	0	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	CDS	17073182	17073454	1	-	0	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	exon	17073182	17073454	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	intron	17073455	17073549	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	CDS	17073550	17073877	1	-	1	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	exon	17073550	17073877	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	intron	17073878	17073970	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	CDS	17073971	17074333	0.59	-	1	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	exon	17073971	17074333	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	intron	17074334	17074467	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	CDS	17074468	17074598	0.47	-	0	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	exon	17074468	17074598	.	-	.	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
Phchi.S3	AUGUSTUS	start_codon	17074596	17074598	.	-	0	transcript_id "Phchi.S3G242200.t1"; gene_id "Phchi.S3G242200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11678.t1 is derived from g15729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7638604	7640040	.	+	.	Phchi.S4G126000
Phchi.S4	AUGUSTUS	transcript	7638604	7640040	.	+	.	transcript_id "Phchi.S4G126000.t1"; gene_id "Phchi.S4G126000"
Phchi.S4	AUGUSTUS	start_codon	7638604	7638606	.	+	0	transcript_id "Phchi.S4G126000.t1"; gene_id "Phchi.S4G126000"
Phchi.S4	AUGUSTUS	CDS	7638604	7640040	0.87	+	0	transcript_id "Phchi.S4G126000.t1"; gene_id "Phchi.S4G126000"
Phchi.S4	AUGUSTUS	exon	7638604	7640040	.	+	.	transcript_id "Phchi.S4G126000.t1"; gene_id "Phchi.S4G126000"
Phchi.S4	AUGUSTUS	stop_codon	7640041	7640043	.	+	0	transcript_id "Phchi.S4G126000.t1"; gene_id "Phchi.S4G126000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10686.t1 is derived from g14736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1582117	1583219	.	+	.	Phchi.S4G026800
Phchi.S4	AUGUSTUS	transcript	1582117	1583219	.	+	.	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	start_codon	1582117	1582119	.	+	0	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	CDS	1582117	1582926	0.89	+	0	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	exon	1582117	1582926	.	+	.	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	intron	1582927	1583162	.	+	.	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	CDS	1583163	1583219	0.6	+	0	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	exon	1583163	1583219	.	+	.	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
Phchi.S4	AUGUSTUS	stop_codon	1583220	1583222	.	+	0	transcript_id "Phchi.S4G026800.t1"; gene_id "Phchi.S4G026800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12071.t1 is derived from g7746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2063567	2067100	.	-	.	Phchi.S2G015100
Phchi.S2	AUGUSTUS	transcript	2063567	2067100	.	-	.	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	stop_codon	2063564	2063566	.	-	0	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	CDS	2063567	2063629	0.99	-	0	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	exon	2063567	2063629	.	-	.	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	intron	2063630	2063727	.	-	.	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	CDS	2063728	2064086	1	-	2	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	exon	2063728	2064086	.	-	.	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	intron	2064087	2064168	.	-	.	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	CDS	2064169	2067100	0.7	-	0	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	exon	2064169	2067100	.	-	.	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
Phchi.S2	AUGUSTUS	start_codon	2067098	2067100	.	-	0	transcript_id "Phchi.S2G015100.t1"; gene_id "Phchi.S2G015100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8633.t1 is derived from g5808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37170301	37171004	.	+	.	Phchi.S1G579200
Phchi.S1	AUGUSTUS	transcript	37170301	37171004	.	+	.	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	start_codon	37170301	37170303	.	+	0	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	CDS	37170301	37170713	0.97	+	0	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	exon	37170301	37170713	.	+	.	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	intron	37170714	37170820	.	+	.	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	CDS	37170821	37171004	0.55	+	1	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	exon	37170821	37171004	.	+	.	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
Phchi.S1	AUGUSTUS	stop_codon	37171005	37171007	.	+	0	transcript_id "Phchi.S1G579200.t1"; gene_id "Phchi.S1G579200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8670.t1 is derived from g5845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37361748	37365663	.	-	.	Phchi.S1G582900
Phchi.S1	AUGUSTUS	transcript	37361748	37365663	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	stop_codon	37361745	37361747	.	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37361748	37362116	0.99	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37361748	37362116	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37362117	37362216	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37362217	37362537	0.99	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37362217	37362537	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37362538	37362627	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37362628	37362729	1	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37362628	37362729	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37362730	37362831	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37362832	37362915	1	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37362832	37362915	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37362916	37363020	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37363021	37363078	1	-	1	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37363021	37363078	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37363079	37363247	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37363248	37363345	0.98	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37363248	37363345	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37363346	37363448	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37363449	37363556	0.84	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37363449	37363556	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37363557	37363661	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37363662	37363799	0.91	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37363662	37363799	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37363800	37363902	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37363903	37363962	0.92	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37363903	37363962	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37363963	37364070	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37364071	37364472	0.34	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37364071	37364472	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37364473	37364573	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37364574	37364759	0.86	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37364574	37364759	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37364760	37364850	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37364851	37365002	1	-	2	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37364851	37365002	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	intron	37365003	37365095	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	CDS	37365096	37365663	0.96	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	exon	37365096	37365663	.	-	.	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
Phchi.S1	AUGUSTUS	start_codon	37365661	37365663	.	-	0	transcript_id "Phchi.S1G582900.t1"; gene_id "Phchi.S1G582900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11147.t1 is derived from g15197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4379699	4380841	.	+	.	Phchi.S4G072900
Phchi.S4	AUGUSTUS	transcript	4379699	4380841	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	start_codon	4379699	4379701	.	+	0	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	CDS	4379699	4379863	0.99	+	0	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	exon	4379699	4379863	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	intron	4379864	4379938	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	CDS	4379939	4380041	1	+	0	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	exon	4379939	4380041	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	intron	4380042	4380124	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	CDS	4380125	4380181	0.99	+	2	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	exon	4380125	4380181	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	intron	4380182	4380292	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	CDS	4380293	4380370	0.99	+	2	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	exon	4380293	4380370	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	intron	4380371	4380488	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	CDS	4380489	4380841	0.98	+	2	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	exon	4380489	4380841	.	+	.	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
Phchi.S4	AUGUSTUS	stop_codon	4380842	4380844	.	+	0	transcript_id "Phchi.S4G072900.t1"; gene_id "Phchi.S4G072900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12584.t1 is derived from g8261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35998596	36002170	.	+	.	Phchi.S2G066400
Phchi.S2	AUGUSTUS	transcript	35998596	36002170	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	start_codon	35998596	35998598	.	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35998596	35998686	1	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35998596	35998686	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35998687	35998834	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35998835	35998907	1	+	2	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35998835	35998907	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35998908	35998987	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35998988	35999089	1	+	1	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35998988	35999089	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35999090	35999173	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35999174	35999204	1	+	1	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35999174	35999204	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35999205	35999369	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35999370	35999426	0.71	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35999370	35999426	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35999427	35999587	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35999588	35999647	0.7	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35999588	35999647	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35999648	35999868	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	35999869	35999991	0.83	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	35999869	35999991	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	35999992	36000168	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36000169	36000273	0.99	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36000169	36000273	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36000274	36000379	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36000380	36000426	0.99	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36000380	36000426	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36000427	36000635	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36000636	36000689	0.45	+	1	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36000636	36000689	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36000690	36000914	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36000915	36001017	0.55	+	1	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36000915	36001017	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36001018	36001115	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36001116	36001178	1	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36001116	36001178	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36001179	36001267	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36001268	36001348	1	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36001268	36001348	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36001349	36001498	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36001499	36001562	1	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36001499	36001562	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	intron	36001563	36001688	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	CDS	36001689	36002170	1	+	2	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	exon	36001689	36002170	.	+	.	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
Phchi.S2	AUGUSTUS	stop_codon	36002171	36002173	.	+	0	transcript_id "Phchi.S2G066400.t1"; gene_id "Phchi.S2G066400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2814.t1 is derived from g9734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8991519	8993240	.	-	.	Phchi.S5G142300
Phchi.S5	AUGUSTUS	transcript	8991519	8993240	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	stop_codon	8991516	8991518	.	-	0	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8991519	8991623	1	-	0	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8991519	8991623	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8991624	8991709	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8991710	8991797	1	-	1	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8991710	8991797	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8991798	8991874	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8991875	8991994	1	-	1	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8991875	8991994	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8991995	8992095	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8992096	8992172	1	-	0	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8992096	8992172	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8992173	8992249	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8992250	8992440	1	-	2	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8992250	8992440	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8992441	8992522	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8992523	8992693	1	-	2	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8992523	8992693	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8992694	8992766	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8992767	8992915	1	-	1	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8992767	8992915	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	intron	8992916	8992995	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	CDS	8992996	8993240	0.99	-	0	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	exon	8992996	8993240	.	-	.	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
Phchi.S5	AUGUSTUS	start_codon	8993238	8993240	.	-	0	transcript_id "Phchi.S5G142300.t1"; gene_id "Phchi.S5G142300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2450.t1 is derived from g9370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6674213	6674807	.	+	.	Phchi.S5G105900
Phchi.S5	AUGUSTUS	transcript	6674213	6674807	.	+	.	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	start_codon	6674213	6674215	.	+	0	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	CDS	6674213	6674241	0.84	+	0	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	exon	6674213	6674241	.	+	.	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	intron	6674242	6674385	.	+	.	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	CDS	6674386	6674426	0.65	+	1	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	exon	6674386	6674426	.	+	.	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	intron	6674427	6674559	.	+	.	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	CDS	6674560	6674807	0.77	+	2	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	exon	6674560	6674807	.	+	.	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
Phchi.S5	AUGUSTUS	stop_codon	6674808	6674810	.	+	0	transcript_id "Phchi.S5G105900.t1"; gene_id "Phchi.S5G105900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15324.t1 is derived from g13792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18388788	18390859	.	+	.	Phchi.S3G264300
Phchi.S3	AUGUSTUS	transcript	18388788	18390859	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	start_codon	18388788	18388790	.	+	0	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18388788	18388874	0.89	+	0	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18388788	18388874	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18388875	18388980	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18388981	18389067	0.99	+	0	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18388981	18389067	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18389068	18389177	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18389178	18389265	0.73	+	0	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18389178	18389265	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18389266	18389361	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18389362	18389488	0.97	+	2	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18389362	18389488	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18389489	18389580	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18389581	18389609	0.91	+	1	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18389581	18389609	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18389610	18389826	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18389827	18390068	0.73	+	2	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18389827	18390068	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18390069	18390558	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18390559	18390646	0.91	+	0	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18390559	18390646	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	intron	18390647	18390779	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	CDS	18390780	18390859	0.86	+	2	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	exon	18390780	18390859	.	+	.	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
Phchi.S3	AUGUSTUS	stop_codon	18390860	18390862	.	+	0	transcript_id "Phchi.S3G264300.t1"; gene_id "Phchi.S3G264300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16004.t1 is derived from g14428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	12556	13227	.	+	.	Phchi.C10G000200
Phchi.C10	AUGUSTUS	transcript	12556	13227	.	+	.	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	start_codon	12556	12558	.	+	0	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	CDS	12556	12616	0.79	+	0	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	exon	12556	12616	.	+	.	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	intron	12617	12754	.	+	.	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	CDS	12755	13227	0.54	+	2	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	exon	12755	13227	.	+	.	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
Phchi.C10	AUGUSTUS	stop_codon	13228	13230	.	+	0	transcript_id "Phchi.C10G000200.t1"; gene_id "Phchi.C10G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9357.t1 is derived from g6533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41149802	41151721	.	-	.	Phchi.S1G651600
Phchi.S1	AUGUSTUS	transcript	41149802	41151721	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	stop_codon	41149799	41149801	.	-	0	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	CDS	41149802	41149836	0.98	-	2	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	exon	41149802	41149836	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	intron	41149837	41149962	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	CDS	41149963	41150002	0.61	-	0	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	exon	41149963	41150002	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	intron	41150003	41150159	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	CDS	41150160	41150898	0.36	-	1	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	exon	41150160	41150898	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	intron	41150899	41151072	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	CDS	41151073	41151136	1	-	2	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	exon	41151073	41151136	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	intron	41151137	41151612	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	CDS	41151613	41151721	1	-	0	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	exon	41151613	41151721	.	-	.	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
Phchi.S1	AUGUSTUS	start_codon	41151719	41151721	.	-	0	transcript_id "Phchi.S1G651600.t1"; gene_id "Phchi.S1G651600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2913.t1 is derived from g82.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	459982	463826	.	+	.	Phchi.S1G007200
Phchi.S1	AUGUSTUS	transcript	459982	463826	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	start_codon	459982	459984	.	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	459982	460146	1	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	459982	460146	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	460147	460242	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	460243	460383	1	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	460243	460383	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	460384	460465	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	460466	460577	1	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	460466	460577	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	460578	460652	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	460653	460875	1	+	2	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	460653	460875	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	460876	461015	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	461016	461176	1	+	1	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	461016	461176	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	461177	461293	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	461294	461548	0.76	+	2	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	461294	461548	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	461549	461664	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	461665	461760	1	+	2	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	461665	461760	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	461761	461862	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	461863	462015	1	+	2	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	461863	462015	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	462016	462195	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	462196	462266	1	+	2	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	462196	462266	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	462267	462400	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	462401	462519	1	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	462401	462519	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	462520	462618	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	462619	462748	1	+	1	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	462619	462748	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	462749	462842	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	462843	462888	1	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	462843	462888	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	462889	462974	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	462975	463119	1	+	2	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	462975	463119	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	463120	463197	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	463198	463363	1	+	1	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	463198	463363	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	463364	463442	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	463443	463613	1	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	463443	463613	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	intron	463614	463703	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	CDS	463704	463826	0.99	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	exon	463704	463826	.	+	.	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
Phchi.S1	AUGUSTUS	stop_codon	463827	463829	.	+	0	transcript_id "Phchi.S1G007200.t1"; gene_id "Phchi.S1G007200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6105.t1 is derived from g3276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20969035	20970746	.	-	.	Phchi.S1G326400
Phchi.S1	AUGUSTUS	transcript	20969035	20970746	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	stop_codon	20969032	20969034	.	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	CDS	20969035	20969269	0.63	-	1	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	exon	20969035	20969269	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	intron	20969270	20969356	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	CDS	20969357	20969517	1	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	exon	20969357	20969517	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	intron	20969518	20969679	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	CDS	20969680	20969796	1	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	exon	20969680	20969796	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	intron	20969797	20969940	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	CDS	20969941	20970129	0.8	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	exon	20969941	20970129	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	intron	20970130	20970232	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	CDS	20970233	20970382	0.86	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	exon	20970233	20970382	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	intron	20970383	20970539	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	CDS	20970540	20970746	1	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	exon	20970540	20970746	.	-	.	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
Phchi.S1	AUGUSTUS	start_codon	20970744	20970746	.	-	0	transcript_id "Phchi.S1G326400.t1"; gene_id "Phchi.S1G326400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg455.t1 is derived from g10237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3184373	3186560	.	+	.	Phchi.S6G041400
Phchi.S6	AUGUSTUS	transcript	3184373	3186560	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	start_codon	3184373	3184375	.	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3184373	3184466	1	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3184373	3184466	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3184467	3184586	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3184587	3184706	1	+	2	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3184587	3184706	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3184707	3184810	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3184811	3184947	1	+	2	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3184811	3184947	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3184948	3185071	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3185072	3185233	1	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3185072	3185233	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3185234	3185322	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3185323	3185409	1	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3185323	3185409	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3185410	3185522	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3185523	3185609	1	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3185523	3185609	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3185610	3185773	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3185774	3185911	0.97	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3185774	3185911	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3185912	3186016	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3186017	3186208	0.98	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3186017	3186208	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3186209	3186295	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3186296	3186394	1	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3186296	3186394	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	intron	3186395	3186488	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	CDS	3186489	3186560	1	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	exon	3186489	3186560	.	+	.	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
Phchi.S6	AUGUSTUS	stop_codon	3186561	3186563	.	+	0	transcript_id "Phchi.S6G041400.t1"; gene_id "Phchi.S6G041400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14508.t1 is derived from g12976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13228531	13228752	.	-	.	Phchi.S3G182700
Phchi.S3	AUGUSTUS	transcript	13228531	13228752	.	-	.	transcript_id "Phchi.S3G182700.t1"; gene_id "Phchi.S3G182700"
Phchi.S3	AUGUSTUS	stop_codon	13228528	13228530	.	-	0	transcript_id "Phchi.S3G182700.t1"; gene_id "Phchi.S3G182700"
Phchi.S3	AUGUSTUS	CDS	13228531	13228752	0.67	-	0	transcript_id "Phchi.S3G182700.t1"; gene_id "Phchi.S3G182700"
Phchi.S3	AUGUSTUS	exon	13228531	13228752	.	-	.	transcript_id "Phchi.S3G182700.t1"; gene_id "Phchi.S3G182700"
Phchi.S3	AUGUSTUS	start_codon	13228750	13228752	.	-	0	transcript_id "Phchi.S3G182700.t1"; gene_id "Phchi.S3G182700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4828.t1 is derived from g1998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13027781	13029353	.	-	.	Phchi.S1G198700
Phchi.S1	AUGUSTUS	transcript	13027781	13029353	.	-	.	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	stop_codon	13027778	13027780	.	-	0	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	CDS	13027781	13027783	0.81	-	0	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	exon	13027781	13027783	.	-	.	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	intron	13027784	13027958	.	-	.	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	CDS	13027959	13029353	0.55	-	0	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	exon	13027959	13029353	.	-	.	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
Phchi.S1	AUGUSTUS	start_codon	13029351	13029353	.	-	0	transcript_id "Phchi.S1G198700.t1"; gene_id "Phchi.S1G198700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg178.t1 is derived from g9960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1025809	1028744	.	-	.	Phchi.S6G013700
Phchi.S6	AUGUSTUS	transcript	1025809	1028744	.	-	.	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	stop_codon	1025806	1025808	.	-	0	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	CDS	1025809	1027670	0.01	-	2	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	exon	1025809	1027670	.	-	.	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	intron	1027671	1028455	.	-	.	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	CDS	1028456	1028744	0.01	-	0	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	exon	1028456	1028744	.	-	.	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
Phchi.S6	AUGUSTUS	start_codon	1028742	1028744	.	-	0	transcript_id "Phchi.S6G013700.t1"; gene_id "Phchi.S6G013700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7772.t1 is derived from g4946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31172539	31173545	.	+	.	Phchi.S1G493100
Phchi.S1	AUGUSTUS	transcript	31172539	31173545	.	+	.	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	start_codon	31172539	31172541	.	+	0	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	CDS	31172539	31172636	0.95	+	0	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	exon	31172539	31172636	.	+	.	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	intron	31172637	31172781	.	+	.	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	CDS	31172782	31173091	0.45	+	1	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	exon	31172782	31173091	.	+	.	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	intron	31173092	31173188	.	+	.	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	CDS	31173189	31173545	0.59	+	0	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	exon	31173189	31173545	.	+	.	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
Phchi.S1	AUGUSTUS	stop_codon	31173546	31173548	.	+	0	transcript_id "Phchi.S1G493100.t1"; gene_id "Phchi.S1G493100"
# This transcript jg12923.t2 is derived from g11388.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12924.t1 is derived from g11389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3180092	3181224	.	-	.	Phchi.S3G024300
Phchi.S3	AUGUSTUS	transcript	3180092	3181224	.	-	.	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	stop_codon	3180089	3180091	.	-	0	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	CDS	3180092	3180229	1	-	0	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	exon	3180092	3180229	.	-	.	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	intron	3180230	3180319	.	-	.	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	CDS	3180320	3181098	1	-	2	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	exon	3180320	3181098	.	-	.	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	intron	3181099	3181178	.	-	.	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	CDS	3181179	3181224	1	-	0	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	exon	3181179	3181224	.	-	.	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
Phchi.S3	AUGUSTUS	start_codon	3181222	3181224	.	-	0	transcript_id "Phchi.S3G024300.t1"; gene_id "Phchi.S3G024300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5170.t1 is derived from g2340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15300902	15302211	.	+	.	Phchi.S1G232900
Phchi.S1	AUGUSTUS	transcript	15300902	15302211	.	+	.	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	start_codon	15300902	15300904	.	+	0	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	CDS	15300902	15301055	0.59	+	0	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	exon	15300902	15301055	.	+	.	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	intron	15301056	15301197	.	+	.	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	CDS	15301198	15301262	1	+	2	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	exon	15301198	15301262	.	+	.	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	intron	15301263	15301356	.	+	.	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	CDS	15301357	15302211	0.89	+	0	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	exon	15301357	15302211	.	+	.	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
Phchi.S1	AUGUSTUS	stop_codon	15302212	15302214	.	+	0	transcript_id "Phchi.S1G232900.t1"; gene_id "Phchi.S1G232900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12327.t1 is derived from g8003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10984258	10986707	.	+	.	Phchi.S2G040700
Phchi.S2	AUGUSTUS	transcript	10984258	10986707	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	start_codon	10984258	10984260	.	+	0	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10984258	10984339	0.95	+	0	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10984258	10984339	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10984340	10984428	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10984429	10984750	0.99	+	2	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10984429	10984750	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10984751	10984848	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10984849	10984925	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10984849	10984925	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10984926	10985052	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10985053	10985122	1	+	2	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10985053	10985122	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10985123	10985215	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10985216	10985296	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10985216	10985296	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10985297	10985374	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10985375	10985449	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10985375	10985449	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10985450	10985526	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10985527	10985589	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10985527	10985589	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10985590	10985752	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10985753	10985896	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10985753	10985896	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10985897	10985988	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10985989	10986054	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10985989	10986054	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10986055	10986158	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10986159	10986302	0.95	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10986159	10986302	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10986303	10986390	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10986391	10986481	1	+	1	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10986391	10986481	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	intron	10986482	10986557	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	CDS	10986558	10986707	0.99	+	0	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	exon	10986558	10986707	.	+	.	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
Phchi.S2	AUGUSTUS	stop_codon	10986708	10986710	.	+	0	transcript_id "Phchi.S2G040700.t1"; gene_id "Phchi.S2G040700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12940.t1 is derived from g11405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3256017	3256616	.	-	.	Phchi.S3G025900
Phchi.S3	AUGUSTUS	transcript	3256017	3256616	.	-	.	transcript_id "Phchi.S3G025900.t1"; gene_id "Phchi.S3G025900"
Phchi.S3	AUGUSTUS	stop_codon	3256014	3256016	.	-	0	transcript_id "Phchi.S3G025900.t1"; gene_id "Phchi.S3G025900"
Phchi.S3	AUGUSTUS	CDS	3256017	3256616	0.97	-	0	transcript_id "Phchi.S3G025900.t1"; gene_id "Phchi.S3G025900"
Phchi.S3	AUGUSTUS	exon	3256017	3256616	.	-	.	transcript_id "Phchi.S3G025900.t1"; gene_id "Phchi.S3G025900"
Phchi.S3	AUGUSTUS	start_codon	3256614	3256616	.	-	0	transcript_id "Phchi.S3G025900.t1"; gene_id "Phchi.S3G025900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9300.t1 is derived from g6475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40838126	40840164	.	-	.	Phchi.S1G645900
Phchi.S1	AUGUSTUS	transcript	40838126	40839724	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	stop_codon	40838123	40838125	.	-	0	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40838126	40838305	0.68	-	0	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40838126	40838305	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40838306	40838406	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40838407	40838607	0.67	-	0	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40838407	40838607	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40838608	40838723	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40838724	40839077	0.98	-	0	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40838724	40839077	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40839078	40839163	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40839164	40839368	0.99	-	1	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40839164	40839368	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40839369	40839548	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40839549	40839724	0.81	-	0	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40839549	40839724	.	-	.	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	start_codon	40839722	40839724	.	-	0	transcript_id "Phchi.S1G645900.t1"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	transcript	40838126	40840164	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	stop_codon	40838123	40838125	.	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40838126	40838305	0.58	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40838126	40838305	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40838306	40838406	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40838407	40838607	0.57	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40838407	40838607	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40838608	40838723	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40838724	40839077	1	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40838724	40839077	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40839078	40839163	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40839164	40839460	1	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40839164	40839460	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40839461	40839548	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40839549	40839764	0.95	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40839549	40839764	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	intron	40839765	40839876	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	CDS	40839877	40840164	0.48	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	exon	40839877	40840164	.	-	.	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
Phchi.S1	AUGUSTUS	start_codon	40840162	40840164	.	-	0	transcript_id "Phchi.S1G645900.t2"; gene_id "Phchi.S1G645900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4358.t1 is derived from g1527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9987213	9989298	.	-	.	Phchi.S1G151700
Phchi.S1	AUGUSTUS	transcript	9987213	9989298	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	stop_codon	9987210	9987212	.	-	0	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	CDS	9987213	9987515	0.58	-	0	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	exon	9987213	9987515	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	intron	9987516	9987642	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	CDS	9987643	9987820	0.48	-	1	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	exon	9987643	9987820	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	intron	9987821	9987944	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	CDS	9987945	9988208	0.47	-	1	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	exon	9987945	9988208	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	intron	9988209	9988319	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	CDS	9988320	9988570	0.55	-	0	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	exon	9988320	9988570	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	intron	9988571	9988710	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	CDS	9988711	9989298	0.7	-	0	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	exon	9988711	9989298	.	-	.	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
Phchi.S1	AUGUSTUS	start_codon	9989296	9989298	.	-	0	transcript_id "Phchi.S1G151700.t1"; gene_id "Phchi.S1G151700"
# This transcript jg9395.t2 is derived from g6571.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9396.t1 is derived from g6572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41318665	41319446	.	+	.	Phchi.S1G655500
Phchi.S1	AUGUSTUS	transcript	41318665	41319446	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	start_codon	41318665	41318667	.	+	0	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	CDS	41318665	41318788	0.45	+	0	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	exon	41318665	41318788	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	intron	41318789	41318931	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	CDS	41318932	41318955	0.96	+	2	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	exon	41318932	41318955	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	intron	41318956	41319059	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	CDS	41319060	41319092	0.96	+	2	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	exon	41319060	41319092	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	intron	41319093	41319375	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	CDS	41319376	41319446	0.96	+	2	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	exon	41319376	41319446	.	+	.	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
Phchi.S1	AUGUSTUS	stop_codon	41319447	41319449	.	+	0	transcript_id "Phchi.S1G655500.t1"; gene_id "Phchi.S1G655500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7527.t1 is derived from g4701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29889529	29892072	.	-	.	Phchi.S1G468600
Phchi.S1	AUGUSTUS	transcript	29889529	29892072	.	-	.	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	stop_codon	29889526	29889528	.	-	0	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	CDS	29889529	29890250	1	-	2	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	exon	29889529	29890250	.	-	.	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	intron	29890251	29890400	.	-	.	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	CDS	29890401	29892072	0.94	-	0	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	exon	29890401	29892072	.	-	.	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
Phchi.S1	AUGUSTUS	start_codon	29892070	29892072	.	-	0	transcript_id "Phchi.S1G468600.t1"; gene_id "Phchi.S1G468600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg878.t1 is derived from g10660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6206985	6209035	.	-	.	Phchi.S6G083700
Phchi.S6	AUGUSTUS	transcript	6206985	6209035	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	stop_codon	6206982	6206984	.	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6206985	6207386	1	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6206985	6207386	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6207387	6207453	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6207454	6207579	1	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6207454	6207579	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6207580	6207671	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6207672	6207702	1	-	1	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6207672	6207702	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6207703	6207788	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6207789	6207856	1	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6207789	6207856	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6207857	6207955	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6207956	6208173	1	-	2	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6207956	6208173	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6208174	6208256	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6208257	6208376	0.99	-	2	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6208257	6208376	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6208377	6208479	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6208480	6208612	0.88	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6208480	6208612	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	intron	6208613	6208732	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	CDS	6208733	6209035	0.99	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	exon	6208733	6209035	.	-	.	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
Phchi.S6	AUGUSTUS	start_codon	6209033	6209035	.	-	0	transcript_id "Phchi.S6G083700.t1"; gene_id "Phchi.S6G083700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3568.t1 is derived from g737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4546059	4546733	.	+	.	Phchi.S1G072700
Phchi.S1	AUGUSTUS	transcript	4546059	4546733	.	+	.	transcript_id "Phchi.S1G072700.t1"; gene_id "Phchi.S1G072700"
Phchi.S1	AUGUSTUS	start_codon	4546059	4546061	.	+	0	transcript_id "Phchi.S1G072700.t1"; gene_id "Phchi.S1G072700"
Phchi.S1	AUGUSTUS	CDS	4546059	4546733	0.77	+	0	transcript_id "Phchi.S1G072700.t1"; gene_id "Phchi.S1G072700"
Phchi.S1	AUGUSTUS	exon	4546059	4546733	.	+	.	transcript_id "Phchi.S1G072700.t1"; gene_id "Phchi.S1G072700"
Phchi.S1	AUGUSTUS	stop_codon	4546734	4546736	.	+	0	transcript_id "Phchi.S1G072700.t1"; gene_id "Phchi.S1G072700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7226.t1 is derived from g4398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27711687	27713343	.	-	.	Phchi.S1G438500
Phchi.S1	AUGUSTUS	transcript	27711687	27713343	.	-	.	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	stop_codon	27711684	27711686	.	-	0	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	CDS	27711687	27712348	0.38	-	2	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	exon	27711687	27712348	.	-	.	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	intron	27712349	27712442	.	-	.	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	CDS	27712443	27713343	0.23	-	0	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	exon	27712443	27713343	.	-	.	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
Phchi.S1	AUGUSTUS	start_codon	27713341	27713343	.	-	0	transcript_id "Phchi.S1G438500.t1"; gene_id "Phchi.S1G438500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9439.t1 is derived from g6615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41458443	41460746	.	+	.	Phchi.S1G659800
Phchi.S1	AUGUSTUS	transcript	41458443	41459961	.	+	.	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	start_codon	41458443	41458445	.	+	0	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	CDS	41458443	41459805	0.57	+	0	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	exon	41458443	41459805	.	+	.	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	intron	41459806	41459944	.	+	.	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	CDS	41459945	41459961	0.96	+	2	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	exon	41459945	41459961	.	+	.	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	stop_codon	41459962	41459964	.	+	0	transcript_id "Phchi.S1G659800.t1"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	transcript	41458443	41460746	.	+	.	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	start_codon	41458443	41458445	.	+	0	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	CDS	41458443	41460220	0.53	+	0	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	exon	41458443	41460220	.	+	.	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	intron	41460221	41460568	.	+	.	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	CDS	41460569	41460746	0.96	+	1	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	exon	41460569	41460746	.	+	.	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
Phchi.S1	AUGUSTUS	stop_codon	41460747	41460749	.	+	0	transcript_id "Phchi.S1G659800.t2"; gene_id "Phchi.S1G659800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4287.t1 is derived from g1456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9420916	9421695	.	+	.	Phchi.S1G144600
Phchi.S1	AUGUSTUS	transcript	9420916	9421695	.	+	.	transcript_id "Phchi.S1G144600.t1"; gene_id "Phchi.S1G144600"
Phchi.S1	AUGUSTUS	start_codon	9420916	9420918	.	+	0	transcript_id "Phchi.S1G144600.t1"; gene_id "Phchi.S1G144600"
Phchi.S1	AUGUSTUS	CDS	9420916	9421695	0.38	+	0	transcript_id "Phchi.S1G144600.t1"; gene_id "Phchi.S1G144600"
Phchi.S1	AUGUSTUS	exon	9420916	9421695	.	+	.	transcript_id "Phchi.S1G144600.t1"; gene_id "Phchi.S1G144600"
Phchi.S1	AUGUSTUS	stop_codon	9421696	9421698	.	+	0	transcript_id "Phchi.S1G144600.t1"; gene_id "Phchi.S1G144600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6101.t1 is derived from g3272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20953415	20954486	.	+	.	Phchi.S1G326000
Phchi.S1	AUGUSTUS	transcript	20953415	20954486	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	start_codon	20953415	20953417	.	+	0	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	CDS	20953415	20953511	0.49	+	0	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	exon	20953415	20953511	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	intron	20953512	20953720	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	CDS	20953721	20953769	0.59	+	2	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	exon	20953721	20953769	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	intron	20953770	20954093	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	CDS	20954094	20954178	0.77	+	1	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	exon	20954094	20954178	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	intron	20954179	20954369	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	CDS	20954370	20954486	0.23	+	0	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	exon	20954370	20954486	.	+	.	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
Phchi.S1	AUGUSTUS	stop_codon	20954487	20954489	.	+	0	transcript_id "Phchi.S1G326000.t1"; gene_id "Phchi.S1G326000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4178.t1 is derived from g1347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8777915	8778420	.	+	.	Phchi.S1G133700
Phchi.S1	AUGUSTUS	transcript	8777915	8778420	.	+	.	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	start_codon	8777915	8777917	.	+	0	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	CDS	8777915	8778136	0.46	+	0	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	exon	8777915	8778136	.	+	.	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	intron	8778137	8778411	.	+	.	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	CDS	8778412	8778420	1	+	0	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	exon	8778412	8778420	.	+	.	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
Phchi.S1	AUGUSTUS	stop_codon	8778421	8778423	.	+	0	transcript_id "Phchi.S1G133700.t1"; gene_id "Phchi.S1G133700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 6 different transcripts
# This transcript jg15376.t1 is derived from g13844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18683408	18686283	.	+	.	Phchi.S3G269500
Phchi.S3	AUGUSTUS	transcript	18685729	18686283	.	+	.	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	start_codon	18685729	18685731	.	+	0	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685729	18686031	1	+	0	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685729	18686031	.	+	.	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18686032	18686118	.	+	.	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18686119	18686283	0.91	+	0	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18686119	18686283	.	+	.	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	stop_codon	18686284	18686286	.	+	0	transcript_id "Phchi.S3G269500.t1"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	transcript	18684737	18686283	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	start_codon	18684737	18684739	.	+	0	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18684737	18684977	0.75	+	0	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18684737	18684977	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684978	18685074	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685075	18685344	1	+	2	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685075	18685344	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18685345	18685423	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685424	18686031	1	+	2	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685424	18686031	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18686032	18686118	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18686119	18686283	0.83	+	0	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18686119	18686283	.	+	.	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	stop_codon	18686284	18686286	.	+	0	transcript_id "Phchi.S3G269500.t2"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	transcript	18683408	18686283	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	start_codon	18683408	18683410	.	+	0	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18683408	18683639	0.41	+	0	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18683408	18683639	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18683640	18683718	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18683719	18684247	0.99	+	2	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18683719	18684247	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684248	18684356	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18684357	18684535	1	+	1	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18684357	18684535	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684536	18684641	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18684642	18684977	0.87	+	2	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18684642	18684977	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684978	18685074	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685075	18685344	1	+	2	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685075	18685344	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18685345	18685423	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685424	18686031	1	+	2	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685424	18686031	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18686032	18686118	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18686119	18686283	0.91	+	0	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18686119	18686283	.	+	.	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	stop_codon	18686284	18686286	.	+	0	transcript_id "Phchi.S3G269500.t3"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	transcript	18684644	18686283	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	start_codon	18684644	18684646	.	+	0	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18684644	18684977	0.44	+	0	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18684644	18684977	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684978	18685074	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685075	18685344	0.99	+	2	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685075	18685344	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18685345	18685423	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685424	18686031	0.99	+	2	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685424	18686031	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18686032	18686118	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18686119	18686283	0.81	+	0	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18686119	18686283	.	+	.	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	stop_codon	18686284	18686286	.	+	0	transcript_id "Phchi.S3G269500.t4"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	transcript	18683408	18685030	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	start_codon	18683408	18683410	.	+	0	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18683408	18683639	0.41	+	0	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18683408	18683639	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18683640	18683718	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18683719	18684247	0.96	+	2	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18683719	18684247	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684248	18684356	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18684357	18684535	1	+	1	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18684357	18684535	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18684536	18684641	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18684642	18685030	0.92	+	2	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18684642	18685030	.	+	.	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	stop_codon	18685031	18685033	.	+	0	transcript_id "Phchi.S3G269500.t5"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	transcript	18685462	18686283	.	+	.	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	start_codon	18685462	18685464	.	+	0	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18685462	18686031	0.81	+	0	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18685462	18686031	.	+	.	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	intron	18686032	18686118	.	+	.	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	CDS	18686119	18686283	0.86	+	0	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	exon	18686119	18686283	.	+	.	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
Phchi.S3	AUGUSTUS	stop_codon	18686284	18686286	.	+	0	transcript_id "Phchi.S3G269500.t6"; gene_id "Phchi.S3G269500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5112.t1 is derived from g2282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14787535	14789323	.	-	.	Phchi.S1G227100
Phchi.S1	AUGUSTUS	transcript	14787535	14789323	.	-	.	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	stop_codon	14787532	14787534	.	-	0	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	CDS	14787535	14788470	0.94	-	0	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	exon	14787535	14788470	.	-	.	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	intron	14788471	14788551	.	-	.	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	CDS	14788552	14789030	0.84	-	2	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	exon	14788552	14789030	.	-	.	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	intron	14789031	14789130	.	-	.	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	CDS	14789131	14789323	0.98	-	0	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	exon	14789131	14789323	.	-	.	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
Phchi.S1	AUGUSTUS	start_codon	14789321	14789323	.	-	0	transcript_id "Phchi.S1G227100.t1"; gene_id "Phchi.S1G227100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13895.t1 is derived from g12362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9504431	9505156	.	+	.	Phchi.S3G121400
Phchi.S3	AUGUSTUS	transcript	9504431	9505156	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	start_codon	9504431	9504433	.	+	0	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	CDS	9504431	9504460	0.3	+	0	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	exon	9504431	9504460	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	intron	9504461	9504611	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	CDS	9504612	9504715	1	+	0	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	exon	9504612	9504715	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	intron	9504716	9504860	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	CDS	9504861	9504958	1	+	1	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	exon	9504861	9504958	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	intron	9504959	9505079	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	CDS	9505080	9505156	0.98	+	2	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	exon	9505080	9505156	.	+	.	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
Phchi.S3	AUGUSTUS	stop_codon	9505157	9505159	.	+	0	transcript_id "Phchi.S3G121400.t1"; gene_id "Phchi.S3G121400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15121.t1 is derived from g13589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17167977	17168858	.	+	.	Phchi.S3G244000
Phchi.S3	AUGUSTUS	transcript	17167977	17168858	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	start_codon	17167977	17167979	.	+	0	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	CDS	17167977	17168006	0.38	+	0	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	exon	17167977	17168006	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	intron	17168007	17168179	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	CDS	17168180	17168284	0.26	+	0	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	exon	17168180	17168284	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	intron	17168285	17168371	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	CDS	17168372	17168441	0.67	+	0	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	exon	17168372	17168441	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	intron	17168442	17168589	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	CDS	17168590	17168858	0.6	+	2	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	exon	17168590	17168858	.	+	.	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
Phchi.S3	AUGUSTUS	stop_codon	17168859	17168861	.	+	0	transcript_id "Phchi.S3G244000.t1"; gene_id "Phchi.S3G244000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13057.t1 is derived from g11522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3932754	3934541	.	+	.	Phchi.S3G037600
Phchi.S3	AUGUSTUS	transcript	3932754	3934541	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	start_codon	3932754	3932756	.	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	CDS	3932754	3933031	0.84	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	exon	3932754	3933031	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	intron	3933032	3933122	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	CDS	3933123	3933450	1	+	1	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	exon	3933123	3933450	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	intron	3933451	3933576	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	CDS	3933577	3933726	0.95	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	exon	3933577	3933726	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	intron	3933727	3933830	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	CDS	3933831	3934091	0.86	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	exon	3933831	3934091	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	intron	3934092	3934221	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	CDS	3934222	3934305	1	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	exon	3934222	3934305	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	intron	3934306	3934418	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	CDS	3934419	3934541	0.62	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	exon	3934419	3934541	.	+	.	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
Phchi.S3	AUGUSTUS	stop_codon	3934542	3934544	.	+	0	transcript_id "Phchi.S3G037600.t1"; gene_id "Phchi.S3G037600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4099.t1 is derived from g1268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7817624	7818837	.	+	.	Phchi.S1G125800
Phchi.S1	AUGUSTUS	transcript	7817624	7818837	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	start_codon	7817624	7817626	.	+	0	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7817624	7817629	1	+	0	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7817624	7817629	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	intron	7817630	7817715	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7817716	7817897	1	+	0	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7817716	7817897	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	intron	7817898	7818008	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7818009	7818116	1	+	1	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7818009	7818116	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	intron	7818117	7818204	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7818205	7818294	1	+	1	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7818205	7818294	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	intron	7818295	7818401	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7818402	7818486	1	+	1	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7818402	7818486	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	intron	7818487	7818585	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7818586	7818680	0.95	+	0	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7818586	7818680	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	intron	7818681	7818791	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	CDS	7818792	7818837	0.93	+	1	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	exon	7818792	7818837	.	+	.	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
Phchi.S1	AUGUSTUS	stop_codon	7818838	7818840	.	+	0	transcript_id "Phchi.S1G125800.t1"; gene_id "Phchi.S1G125800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg696.t1 is derived from g10478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4950479	4950781	.	+	.	Phchi.S6G065500
Phchi.S6	AUGUSTUS	transcript	4950479	4950781	.	+	.	transcript_id "Phchi.S6G065500.t1"; gene_id "Phchi.S6G065500"
Phchi.S6	AUGUSTUS	start_codon	4950479	4950481	.	+	0	transcript_id "Phchi.S6G065500.t1"; gene_id "Phchi.S6G065500"
Phchi.S6	AUGUSTUS	CDS	4950479	4950781	0.88	+	0	transcript_id "Phchi.S6G065500.t1"; gene_id "Phchi.S6G065500"
Phchi.S6	AUGUSTUS	exon	4950479	4950781	.	+	.	transcript_id "Phchi.S6G065500.t1"; gene_id "Phchi.S6G065500"
Phchi.S6	AUGUSTUS	stop_codon	4950782	4950784	.	+	0	transcript_id "Phchi.S6G065500.t1"; gene_id "Phchi.S6G065500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3413.t1 is derived from g582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3384806	3385744	.	-	.	Phchi.S1G057200
Phchi.S1	AUGUSTUS	transcript	3384806	3385744	.	-	.	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	stop_codon	3384803	3384805	.	-	0	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	CDS	3384806	3385285	0.79	-	0	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	exon	3384806	3385285	.	-	.	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	intron	3385286	3385375	.	-	.	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	CDS	3385376	3385486	0.89	-	0	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	exon	3385376	3385486	.	-	.	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	intron	3385487	3385642	.	-	.	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	CDS	3385643	3385744	0.53	-	0	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	exon	3385643	3385744	.	-	.	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
Phchi.S1	AUGUSTUS	start_codon	3385742	3385744	.	-	0	transcript_id "Phchi.S1G057200.t1"; gene_id "Phchi.S1G057200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11378.t1 is derived from g15428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5966184	5966471	.	-	.	Phchi.S4G096000
Phchi.S4	AUGUSTUS	transcript	5966184	5966471	.	-	.	transcript_id "Phchi.S4G096000.t1"; gene_id "Phchi.S4G096000"
Phchi.S4	AUGUSTUS	stop_codon	5966181	5966183	.	-	0	transcript_id "Phchi.S4G096000.t1"; gene_id "Phchi.S4G096000"
Phchi.S4	AUGUSTUS	CDS	5966184	5966471	0.95	-	0	transcript_id "Phchi.S4G096000.t1"; gene_id "Phchi.S4G096000"
Phchi.S4	AUGUSTUS	exon	5966184	5966471	.	-	.	transcript_id "Phchi.S4G096000.t1"; gene_id "Phchi.S4G096000"
Phchi.S4	AUGUSTUS	start_codon	5966469	5966471	.	-	0	transcript_id "Phchi.S4G096000.t1"; gene_id "Phchi.S4G096000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13546.t1 is derived from g12013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7440047	7441551	.	-	.	Phchi.S3G086500
Phchi.S3	AUGUSTUS	transcript	7440047	7441551	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	stop_codon	7440044	7440046	.	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7440047	7440229	1	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7440047	7440229	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	intron	7440230	7440317	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7440318	7440392	1	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7440318	7440392	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	intron	7440393	7440482	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7440483	7440581	1	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7440483	7440581	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	intron	7440582	7440661	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7440662	7440861	1	-	2	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7440662	7440861	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	intron	7440862	7441030	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7441031	7441078	1	-	2	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7441031	7441078	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	intron	7441079	7441211	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7441212	7441329	1	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7441212	7441329	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	intron	7441330	7441407	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	CDS	7441408	7441551	0.94	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	exon	7441408	7441551	.	-	.	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
Phchi.S3	AUGUSTUS	start_codon	7441549	7441551	.	-	0	transcript_id "Phchi.S3G086500.t1"; gene_id "Phchi.S3G086500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10088.t1 is derived from g7264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45687438	45688076	.	+	.	Phchi.S1G724700
Phchi.S1	AUGUSTUS	transcript	45687438	45688076	.	+	.	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	start_codon	45687438	45687440	.	+	0	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	CDS	45687438	45687512	0.46	+	0	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	exon	45687438	45687512	.	+	.	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	intron	45687513	45687671	.	+	.	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	CDS	45687672	45687994	0.47	+	0	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	exon	45687672	45687994	.	+	.	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	intron	45687995	45688075	.	+	.	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	CDS	45688076	45688076	0.95	+	1	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	exon	45688076	45688076	.	+	.	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
Phchi.S1	AUGUSTUS	stop_codon	45688077	45688079	.	+	0	transcript_id "Phchi.S1G724700.t1"; gene_id "Phchi.S1G724700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg994.t1 is derived from g10777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6954298	6955529	.	-	.	Phchi.S6G095300
Phchi.S6	AUGUSTUS	transcript	6954298	6955529	.	-	.	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	stop_codon	6954295	6954297	.	-	0	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	CDS	6954298	6954596	0.66	-	2	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	exon	6954298	6954596	.	-	.	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	intron	6954597	6954859	.	-	.	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	CDS	6954860	6954872	0.52	-	0	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	exon	6954860	6954872	.	-	.	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	intron	6954873	6954995	.	-	.	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	CDS	6954996	6955529	0.83	-	0	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	exon	6954996	6955529	.	-	.	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
Phchi.S6	AUGUSTUS	start_codon	6955527	6955529	.	-	0	transcript_id "Phchi.S6G095300.t1"; gene_id "Phchi.S6G095300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3265.t1 is derived from g434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2611117	2613027	.	+	.	Phchi.S1G042400
Phchi.S1	AUGUSTUS	transcript	2611117	2613027	.	+	.	transcript_id "Phchi.S1G042400.t1"; gene_id "Phchi.S1G042400"
Phchi.S1	AUGUSTUS	start_codon	2611117	2611119	.	+	0	transcript_id "Phchi.S1G042400.t1"; gene_id "Phchi.S1G042400"
Phchi.S1	AUGUSTUS	CDS	2611117	2613027	0.63	+	0	transcript_id "Phchi.S1G042400.t1"; gene_id "Phchi.S1G042400"
Phchi.S1	AUGUSTUS	exon	2611117	2613027	.	+	.	transcript_id "Phchi.S1G042400.t1"; gene_id "Phchi.S1G042400"
Phchi.S1	AUGUSTUS	stop_codon	2613028	2613030	.	+	0	transcript_id "Phchi.S1G042400.t1"; gene_id "Phchi.S1G042400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9107.t1 is derived from g6282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39853149	39854288	.	-	.	Phchi.S1G626600
Phchi.S1	AUGUSTUS	transcript	39853149	39854288	.	-	.	transcript_id "Phchi.S1G626600.t1"; gene_id "Phchi.S1G626600"
Phchi.S1	AUGUSTUS	stop_codon	39853146	39853148	.	-	0	transcript_id "Phchi.S1G626600.t1"; gene_id "Phchi.S1G626600"
Phchi.S1	AUGUSTUS	CDS	39853149	39854288	0.49	-	0	transcript_id "Phchi.S1G626600.t1"; gene_id "Phchi.S1G626600"
Phchi.S1	AUGUSTUS	exon	39853149	39854288	.	-	.	transcript_id "Phchi.S1G626600.t1"; gene_id "Phchi.S1G626600"
Phchi.S1	AUGUSTUS	start_codon	39854286	39854288	.	-	0	transcript_id "Phchi.S1G626600.t1"; gene_id "Phchi.S1G626600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1197.t1 is derived from g10980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8379336	8379967	.	+	.	Phchi.S6G115600
Phchi.S6	AUGUSTUS	transcript	8379336	8379967	.	+	.	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	start_codon	8379336	8379338	.	+	0	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	CDS	8379336	8379475	0.61	+	0	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	exon	8379336	8379475	.	+	.	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	intron	8379476	8379588	.	+	.	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	CDS	8379589	8379679	0.99	+	1	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	exon	8379589	8379679	.	+	.	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	intron	8379680	8379802	.	+	.	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	CDS	8379803	8379967	0.99	+	0	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	exon	8379803	8379967	.	+	.	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
Phchi.S6	AUGUSTUS	stop_codon	8379968	8379970	.	+	0	transcript_id "Phchi.S6G115600.t1"; gene_id "Phchi.S6G115600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5886.t1 is derived from g3056.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19583593	19587465	.	-	.	Phchi.S1G304500
Phchi.S1	AUGUSTUS	transcript	19583593	19587465	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	stop_codon	19583590	19583592	.	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19583593	19584333	1	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19583593	19584333	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19584334	19584450	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19584451	19584552	1	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19584451	19584552	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19584553	19584656	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19584657	19584749	1	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19584657	19584749	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19584750	19584908	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19584909	19585046	1	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19584909	19585046	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585047	19585177	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585178	19585265	1	-	1	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585178	19585265	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585266	19585347	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585348	19585436	1	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585348	19585436	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585437	19585573	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585574	19585639	1	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585574	19585639	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585640	19585741	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585742	19585856	1	-	1	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585742	19585856	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585857	19585954	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585955	19586432	0.99	-	2	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585955	19586432	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19586433	19586775	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19586776	19586836	0.96	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19586776	19586836	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19586837	19587071	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19587072	19587123	0.98	-	1	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19587072	19587123	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19587124	19587301	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19587302	19587465	0.98	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19587302	19587465	.	-	.	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	start_codon	19587463	19587465	.	-	0	transcript_id "Phchi.S1G304500.t1"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	transcript	19583593	19586648	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	stop_codon	19583590	19583592	.	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19583593	19584333	1	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19583593	19584333	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19584334	19584450	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19584451	19584552	1	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19584451	19584552	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19584553	19584656	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19584657	19584749	0.99	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19584657	19584749	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19584750	19584908	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19584909	19585046	1	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19584909	19585046	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585047	19585177	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585178	19585265	1	-	1	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585178	19585265	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585266	19585347	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585348	19585436	1	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585348	19585436	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585437	19585573	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585574	19585639	1	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585574	19585639	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585640	19585741	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585742	19585856	1	-	1	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585742	19585856	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19585857	19585954	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19585955	19586298	0.66	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19585955	19586298	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19586299	19586365	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19586366	19586432	0.81	-	1	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19586366	19586432	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	intron	19586433	19586580	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	CDS	19586581	19586648	0.31	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	exon	19586581	19586648	.	-	.	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
Phchi.S1	AUGUSTUS	start_codon	19586646	19586648	.	-	0	transcript_id "Phchi.S1G304500.t2"; gene_id "Phchi.S1G304500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4349.t1 is derived from g1518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9913363	9915764	.	-	.	Phchi.S1G150800
Phchi.S1	AUGUSTUS	transcript	9913363	9915764	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	stop_codon	9913360	9913362	.	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9913363	9913596	0.99	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9913363	9913596	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9913597	9913678	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9913679	9913828	1	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9913679	9913828	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9913829	9913908	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9913909	9913999	1	-	1	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9913909	9913999	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9914000	9914073	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9914074	9914243	1	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9914074	9914243	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9914244	9914348	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9914349	9914453	1	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9914349	9914453	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9914454	9914567	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9914568	9914683	1	-	2	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9914568	9914683	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9914684	9914764	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9914765	9914834	0.93	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9914765	9914834	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9914835	9914920	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9914921	9914970	0.57	-	2	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9914921	9914970	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9914971	9915082	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9915083	9915179	1	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9915083	9915179	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9915180	9915290	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9915291	9915359	1	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9915291	9915359	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	intron	9915360	9915536	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	CDS	9915537	9915764	0.98	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	exon	9915537	9915764	.	-	.	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
Phchi.S1	AUGUSTUS	start_codon	9915762	9915764	.	-	0	transcript_id "Phchi.S1G150800.t1"; gene_id "Phchi.S1G150800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13089.t1 is derived from g11554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4102809	4103522	.	+	.	Phchi.S3G040800
Phchi.S3	AUGUSTUS	transcript	4102809	4103522	.	+	.	transcript_id "Phchi.S3G040800.t1"; gene_id "Phchi.S3G040800"
Phchi.S3	AUGUSTUS	start_codon	4102809	4102811	.	+	0	transcript_id "Phchi.S3G040800.t1"; gene_id "Phchi.S3G040800"
Phchi.S3	AUGUSTUS	CDS	4102809	4103522	0.91	+	0	transcript_id "Phchi.S3G040800.t1"; gene_id "Phchi.S3G040800"
Phchi.S3	AUGUSTUS	exon	4102809	4103522	.	+	.	transcript_id "Phchi.S3G040800.t1"; gene_id "Phchi.S3G040800"
Phchi.S3	AUGUSTUS	stop_codon	4103523	4103525	.	+	0	transcript_id "Phchi.S3G040800.t1"; gene_id "Phchi.S3G040800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14006.t1 is derived from g12473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10253294	10254974	.	+	.	Phchi.S3G132500
Phchi.S3	AUGUSTUS	transcript	10253294	10254974	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	start_codon	10253294	10253296	.	+	0	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	CDS	10253294	10253517	0.82	+	0	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	exon	10253294	10253517	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	intron	10253518	10253610	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	CDS	10253611	10253754	1	+	1	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	exon	10253611	10253754	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	intron	10253755	10253871	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	CDS	10253872	10254002	1	+	1	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	exon	10253872	10254002	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	intron	10254003	10254079	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	CDS	10254080	10254259	1	+	2	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	exon	10254080	10254259	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	intron	10254260	10254345	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	CDS	10254346	10254974	1	+	2	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	exon	10254346	10254974	.	+	.	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
Phchi.S3	AUGUSTUS	stop_codon	10254975	10254977	.	+	0	transcript_id "Phchi.S3G132500.t1"; gene_id "Phchi.S3G132500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11984.t1 is derived from g7659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	352955	354289	.	+	.	Phchi.S2G006400
Phchi.S2	AUGUSTUS	transcript	352955	354289	.	+	.	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	start_codon	352955	352957	.	+	0	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	CDS	352955	353206	0.59	+	0	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	exon	352955	353206	.	+	.	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	intron	353207	353299	.	+	.	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	CDS	353300	354289	0.94	+	0	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	exon	353300	354289	.	+	.	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
Phchi.S2	AUGUSTUS	stop_codon	354290	354292	.	+	0	transcript_id "Phchi.S2G006400.t1"; gene_id "Phchi.S2G006400"
# This transcript jg300.t2 is derived from g10082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg301.t1 is derived from g10083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2129285	2130180	.	+	.	Phchi.S6G026000
Phchi.S6	AUGUSTUS	transcript	2129285	2130180	.	+	.	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	start_codon	2129285	2129287	.	+	0	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	CDS	2129285	2129345	0.44	+	0	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	exon	2129285	2129345	.	+	.	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	intron	2129346	2129566	.	+	.	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	CDS	2129567	2129844	0.43	+	2	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	exon	2129567	2129844	.	+	.	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	intron	2129845	2129928	.	+	.	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	CDS	2129929	2130180	0.48	+	0	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	exon	2129929	2130180	.	+	.	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
Phchi.S6	AUGUSTUS	stop_codon	2130181	2130183	.	+	0	transcript_id "Phchi.S6G026000.t1"; gene_id "Phchi.S6G026000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1223.t1 is derived from g11006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8460376	8460962	.	-	.	Phchi.S6G118200
Phchi.S6	AUGUSTUS	transcript	8460376	8460962	.	-	.	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	stop_codon	8460373	8460375	.	-	0	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	CDS	8460376	8460647	1	-	2	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	exon	8460376	8460647	.	-	.	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	intron	8460648	8460733	.	-	.	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	CDS	8460734	8460962	0.31	-	0	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	exon	8460734	8460962	.	-	.	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
Phchi.S6	AUGUSTUS	start_codon	8460960	8460962	.	-	0	transcript_id "Phchi.S6G118200.t1"; gene_id "Phchi.S6G118200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14081.t1 is derived from g12548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10698324	10699989	.	-	.	Phchi.S3G140000
Phchi.S3	AUGUSTUS	transcript	10698324	10699989	.	-	.	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	stop_codon	10698321	10698323	.	-	0	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	CDS	10698324	10698773	1	-	0	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	exon	10698324	10698773	.	-	.	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	intron	10698774	10698927	.	-	.	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	CDS	10698928	10699989	0.52	-	0	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	exon	10698928	10699989	.	-	.	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
Phchi.S3	AUGUSTUS	start_codon	10699987	10699989	.	-	0	transcript_id "Phchi.S3G140000.t1"; gene_id "Phchi.S3G140000"
# This transcript jg1139.t1 is derived from g10922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7891703	7892146	.	+	.	Phchi.S6G109800
Phchi.S6	AUGUSTUS	transcript	7891703	7892146	.	+	.	transcript_id "Phchi.S6G109800.t1"; gene_id "Phchi.S6G109800"
Phchi.S6	AUGUSTUS	start_codon	7891703	7891705	.	+	0	transcript_id "Phchi.S6G109800.t1"; gene_id "Phchi.S6G109800"
Phchi.S6	AUGUSTUS	CDS	7891703	7892146	0.92	+	0	transcript_id "Phchi.S6G109800.t1"; gene_id "Phchi.S6G109800"
Phchi.S6	AUGUSTUS	exon	7891703	7892146	.	+	.	transcript_id "Phchi.S6G109800.t1"; gene_id "Phchi.S6G109800"
Phchi.S6	AUGUSTUS	stop_codon	7892147	7892149	.	+	0	transcript_id "Phchi.S6G109800.t1"; gene_id "Phchi.S6G109800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5732.t1 is derived from g2902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18593465	18595613	.	-	.	Phchi.S1G289100
Phchi.S1	AUGUSTUS	transcript	18593465	18595613	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	stop_codon	18593462	18593464	.	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18593465	18593539	1	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18593465	18593539	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18593540	18593618	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18593619	18593759	1	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18593619	18593759	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18593760	18593835	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18593836	18593955	1	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18593836	18593955	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18593956	18594054	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18594055	18594142	1	-	1	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18594055	18594142	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18594143	18594237	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18594238	18594356	1	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18594238	18594356	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18594357	18594429	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18594430	18594446	1	-	2	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18594430	18594446	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18594447	18594538	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18594539	18594620	0.98	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18594539	18594620	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18594621	18594781	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18594782	18594973	0.86	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18594782	18594973	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18594974	18595084	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18595085	18595309	0.83	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18595085	18595309	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	intron	18595310	18595496	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	CDS	18595497	18595613	1	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	exon	18595497	18595613	.	-	.	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
Phchi.S1	AUGUSTUS	start_codon	18595611	18595613	.	-	0	transcript_id "Phchi.S1G289100.t1"; gene_id "Phchi.S1G289100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2193.t1 is derived from g9113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5326231	5326884	.	-	.	Phchi.S5G080200
Phchi.S5	AUGUSTUS	transcript	5326231	5326884	.	-	.	transcript_id "Phchi.S5G080200.t1"; gene_id "Phchi.S5G080200"
Phchi.S5	AUGUSTUS	stop_codon	5326228	5326230	.	-	0	transcript_id "Phchi.S5G080200.t1"; gene_id "Phchi.S5G080200"
Phchi.S5	AUGUSTUS	CDS	5326231	5326884	0.77	-	0	transcript_id "Phchi.S5G080200.t1"; gene_id "Phchi.S5G080200"
Phchi.S5	AUGUSTUS	exon	5326231	5326884	.	-	.	transcript_id "Phchi.S5G080200.t1"; gene_id "Phchi.S5G080200"
Phchi.S5	AUGUSTUS	start_codon	5326882	5326884	.	-	0	transcript_id "Phchi.S5G080200.t1"; gene_id "Phchi.S5G080200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1570.t1 is derived from g8489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1801247	1802803	.	-	.	Phchi.S5G017900
Phchi.S5	AUGUSTUS	transcript	1801247	1802803	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	stop_codon	1801244	1801246	.	-	0	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1801247	1801299	1	-	2	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1801247	1801299	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	intron	1801300	1801385	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1801386	1801468	0.99	-	1	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1801386	1801468	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	intron	1801469	1801612	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1801613	1801724	0.99	-	2	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1801613	1801724	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	intron	1801725	1801824	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1801825	1801990	0.64	-	0	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1801825	1801990	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	intron	1801991	1802134	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1802135	1802165	0.64	-	1	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1802135	1802165	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	intron	1802166	1802227	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1802228	1802256	0.64	-	0	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1802228	1802256	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	intron	1802257	1802338	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	CDS	1802339	1802803	0.81	-	0	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	exon	1802339	1802803	.	-	.	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
Phchi.S5	AUGUSTUS	start_codon	1802801	1802803	.	-	0	transcript_id "Phchi.S5G017900.t1"; gene_id "Phchi.S5G017900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13222.t1 is derived from g11687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4762803	4765591	.	-	.	Phchi.S3G054100
Phchi.S3	AUGUSTUS	transcript	4762803	4765591	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	stop_codon	4762800	4762802	.	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4762803	4762864	1	-	2	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4762803	4762864	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4762865	4762955	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4762956	4763049	1	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4762956	4763049	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4763050	4763129	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4763130	4763348	1	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4763130	4763348	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4763349	4763430	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4763431	4763715	1	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4763431	4763715	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4763716	4763840	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4763841	4763993	0.99	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4763841	4763993	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4763994	4764099	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4764100	4764222	0.98	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4764100	4764222	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4764223	4764327	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4764328	4764394	1	-	1	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4764328	4764394	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4764395	4764632	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4764633	4764820	1	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4764633	4764820	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4764821	4764911	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4764912	4765028	1	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4764912	4765028	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4765029	4765112	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4765113	4765205	1	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4765113	4765205	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4765206	4765286	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4765287	4765316	0.71	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4765287	4765316	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	intron	4765317	4765408	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	CDS	4765409	4765591	0.61	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	exon	4765409	4765591	.	-	.	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
Phchi.S3	AUGUSTUS	start_codon	4765589	4765591	.	-	0	transcript_id "Phchi.S3G054100.t1"; gene_id "Phchi.S3G054100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8134.t1 is derived from g5309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33753236	33754049	.	-	.	Phchi.S1G529300
Phchi.S1	AUGUSTUS	transcript	33753236	33754049	.	-	.	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	stop_codon	33753233	33753235	.	-	0	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	CDS	33753236	33753241	0.98	-	0	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	exon	33753236	33753241	.	-	.	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	intron	33753242	33753392	.	-	.	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	CDS	33753393	33754049	0.86	-	0	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	exon	33753393	33754049	.	-	.	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
Phchi.S1	AUGUSTUS	start_codon	33754047	33754049	.	-	0	transcript_id "Phchi.S1G529300.t1"; gene_id "Phchi.S1G529300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg868.t1 is derived from g10650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5997403	5998304	.	+	.	Phchi.S6G082700
Phchi.S6	AUGUSTUS	transcript	5997403	5998304	.	+	.	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	start_codon	5997403	5997405	.	+	0	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	CDS	5997403	5997733	0.63	+	0	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	exon	5997403	5997733	.	+	.	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	intron	5997734	5997852	.	+	.	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	CDS	5997853	5998304	0.73	+	2	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	exon	5997853	5998304	.	+	.	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
Phchi.S6	AUGUSTUS	stop_codon	5998305	5998307	.	+	0	transcript_id "Phchi.S6G082700.t1"; gene_id "Phchi.S6G082700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14995.t1 is derived from g13463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16172480	16174819	.	-	.	Phchi.S3G231400
Phchi.S3	AUGUSTUS	transcript	16172480	16174819	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	stop_codon	16172477	16172479	.	-	0	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	CDS	16172480	16172500	1	-	0	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	exon	16172480	16172500	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	intron	16172501	16172655	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	CDS	16172656	16172978	0.73	-	2	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	exon	16172656	16172978	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	intron	16172979	16173067	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	CDS	16173068	16173751	0.78	-	2	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	exon	16173068	16173751	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	intron	16173752	16173878	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	CDS	16173879	16174119	1	-	0	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	exon	16173879	16174119	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	intron	16174120	16174240	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	CDS	16174241	16174819	1	-	0	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	exon	16174241	16174819	.	-	.	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
Phchi.S3	AUGUSTUS	start_codon	16174817	16174819	.	-	0	transcript_id "Phchi.S3G231400.t1"; gene_id "Phchi.S3G231400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3435.t1 is derived from g604.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3630478	3632039	.	+	.	Phchi.S1G059400
Phchi.S1	AUGUSTUS	transcript	3630478	3632039	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	start_codon	3630478	3630480	.	+	0	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3630478	3630569	0.84	+	0	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3630478	3630569	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	intron	3630570	3630666	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3630667	3630684	1	+	1	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3630667	3630684	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	intron	3630685	3630813	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3630814	3631044	0.72	+	1	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3630814	3631044	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	intron	3631045	3631258	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3631259	3631348	0.89	+	1	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3631259	3631348	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	intron	3631349	3631442	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3631443	3631692	0.7	+	1	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3631443	3631692	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	intron	3631693	3631786	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3631787	3631837	0.56	+	0	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3631787	3631837	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	intron	3631838	3631949	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	CDS	3631950	3632039	0.3	+	0	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	exon	3631950	3632039	.	+	.	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
Phchi.S1	AUGUSTUS	stop_codon	3632040	3632042	.	+	0	transcript_id "Phchi.S1G059400.t1"; gene_id "Phchi.S1G059400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7261.t1 is derived from g4433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27908763	27909949	.	+	.	Phchi.S1G442000
Phchi.S1	AUGUSTUS	transcript	27908763	27909949	.	+	.	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	start_codon	27908763	27908765	.	+	0	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	CDS	27908763	27909600	0.53	+	0	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	exon	27908763	27909600	.	+	.	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	intron	27909601	27909710	.	+	.	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	CDS	27909711	27909949	0.72	+	2	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	exon	27909711	27909949	.	+	.	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
Phchi.S1	AUGUSTUS	stop_codon	27909950	27909952	.	+	0	transcript_id "Phchi.S1G442000.t1"; gene_id "Phchi.S1G442000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3171.t1 is derived from g340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2088589	2090259	.	-	.	Phchi.S1G033000
Phchi.S1	AUGUSTUS	transcript	2088589	2090259	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	stop_codon	2088586	2088588	.	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	CDS	2088589	2088864	0.91	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	exon	2088589	2088864	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	intron	2088865	2088951	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	CDS	2088952	2089221	1	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	exon	2088952	2089221	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	intron	2089222	2089301	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	CDS	2089302	2089392	1	-	1	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	exon	2089302	2089392	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	intron	2089393	2089497	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	CDS	2089498	2089607	1	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	exon	2089498	2089607	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	intron	2089608	2089702	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	CDS	2089703	2089972	1	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	exon	2089703	2089972	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	intron	2089973	2090097	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	CDS	2090098	2090259	0.61	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	exon	2090098	2090259	.	-	.	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
Phchi.S1	AUGUSTUS	start_codon	2090257	2090259	.	-	0	transcript_id "Phchi.S1G033000.t1"; gene_id "Phchi.S1G033000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9371.t1 is derived from g6547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41204971	41205511	.	+	.	Phchi.S1G653000
Phchi.S1	AUGUSTUS	transcript	41204971	41205511	.	+	.	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	start_codon	41204971	41204973	.	+	0	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	CDS	41204971	41205002	0.82	+	0	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	exon	41204971	41205002	.	+	.	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	intron	41205003	41205096	.	+	.	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	CDS	41205097	41205511	0.93	+	1	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	exon	41205097	41205511	.	+	.	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
Phchi.S1	AUGUSTUS	stop_codon	41205512	41205514	.	+	0	transcript_id "Phchi.S1G653000.t1"; gene_id "Phchi.S1G653000"
# This transcript jg15087.t2 is derived from g13555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15088.t1 is derived from g13556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16965245	16965824	.	-	.	Phchi.S3G240700
Phchi.S3	AUGUSTUS	transcript	16965245	16965824	.	-	.	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	stop_codon	16965242	16965244	.	-	0	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	CDS	16965245	16965394	0.99	-	0	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	exon	16965245	16965394	.	-	.	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	intron	16965395	16965555	.	-	.	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	CDS	16965556	16965615	0.83	-	0	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	exon	16965556	16965615	.	-	.	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	intron	16965616	16965704	.	-	.	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	CDS	16965705	16965824	0.99	-	0	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	exon	16965705	16965824	.	-	.	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
Phchi.S3	AUGUSTUS	start_codon	16965822	16965824	.	-	0	transcript_id "Phchi.S3G240700.t1"; gene_id "Phchi.S3G240700"
# This transcript jg13680.t2 is derived from g12147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13681.t1 is derived from g12148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8185537	8186778	.	-	.	Phchi.S3G100000
Phchi.S3	AUGUSTUS	transcript	8185537	8186778	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	stop_codon	8185534	8185536	.	-	0	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8185537	8185657	0.91	-	1	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8185537	8185657	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8185658	8185727	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8185728	8185840	1	-	0	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8185728	8185840	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8185841	8185919	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8185920	8185970	1	-	0	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8185920	8185970	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8185971	8186085	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8186086	8186129	1	-	2	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8186086	8186129	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8186130	8186251	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8186252	8186330	1	-	0	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8186252	8186330	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8186331	8186426	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8186427	8186467	1	-	2	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8186427	8186467	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8186468	8186553	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8186554	8186652	1	-	2	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8186554	8186652	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	intron	8186653	8186732	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	CDS	8186733	8186778	0.76	-	0	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	exon	8186733	8186778	.	-	.	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
Phchi.S3	AUGUSTUS	start_codon	8186776	8186778	.	-	0	transcript_id "Phchi.S3G100000.t1"; gene_id "Phchi.S3G100000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10245.t1 is derived from g7421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46574756	46575568	.	+	.	Phchi.S1G740400
Phchi.S1	AUGUSTUS	transcript	46574756	46575568	.	+	.	transcript_id "Phchi.S1G740400.t1"; gene_id "Phchi.S1G740400"
Phchi.S1	AUGUSTUS	start_codon	46574756	46574758	.	+	0	transcript_id "Phchi.S1G740400.t1"; gene_id "Phchi.S1G740400"
Phchi.S1	AUGUSTUS	CDS	46574756	46575568	0.38	+	0	transcript_id "Phchi.S1G740400.t1"; gene_id "Phchi.S1G740400"
Phchi.S1	AUGUSTUS	exon	46574756	46575568	.	+	.	transcript_id "Phchi.S1G740400.t1"; gene_id "Phchi.S1G740400"
Phchi.S1	AUGUSTUS	stop_codon	46575569	46575571	.	+	0	transcript_id "Phchi.S1G740400.t1"; gene_id "Phchi.S1G740400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13084.t1 is derived from g11549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4086184	4086821	.	+	.	Phchi.S3G040300
Phchi.S3	AUGUSTUS	transcript	4086184	4086821	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	start_codon	4086184	4086186	.	+	0	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	CDS	4086184	4086256	0.84	+	0	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	exon	4086184	4086256	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	intron	4086257	4086364	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	CDS	4086365	4086465	0.88	+	2	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	exon	4086365	4086465	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	intron	4086466	4086611	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	CDS	4086612	4086709	0.98	+	0	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	exon	4086612	4086709	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	intron	4086710	4086793	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	CDS	4086794	4086821	0.98	+	1	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	exon	4086794	4086821	.	+	.	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
Phchi.S3	AUGUSTUS	stop_codon	4086822	4086824	.	+	0	transcript_id "Phchi.S3G040300.t1"; gene_id "Phchi.S3G040300"
# This transcript jg3531.t2 is derived from g700.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3532.t1 is derived from g701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4257324	4259485	.	-	.	Phchi.S1G069100
Phchi.S1	AUGUSTUS	transcript	4257324	4259485	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	stop_codon	4257321	4257323	.	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4257324	4257719	0.85	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4257324	4257719	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	intron	4257720	4257831	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4257832	4258092	0.85	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4257832	4258092	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	intron	4258093	4258166	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4258167	4258352	1	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4258167	4258352	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	intron	4258353	4258482	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4258483	4258719	1	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4258483	4258719	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	intron	4258720	4258830	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4258831	4258890	1	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4258831	4258890	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	intron	4258891	4259136	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4259137	4259282	0.93	-	2	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4259137	4259282	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	intron	4259283	4259385	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	CDS	4259386	4259485	0.96	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	exon	4259386	4259485	.	-	.	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
Phchi.S1	AUGUSTUS	start_codon	4259483	4259485	.	-	0	transcript_id "Phchi.S1G069100.t1"; gene_id "Phchi.S1G069100"
# This transcript jg8126.t2 is derived from g5301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8127.t1 is derived from g5302.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33623546	33628581	.	+	.	Phchi.S1G528600
Phchi.S1	AUGUSTUS	transcript	33623546	33628581	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	start_codon	33623546	33623548	.	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33623546	33623609	0.47	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33623546	33623609	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33623610	33623711	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33623712	33623770	0.52	+	2	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33623712	33623770	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33623771	33623999	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33624000	33624081	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33624000	33624081	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33624082	33624333	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33624334	33624412	1	+	2	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33624334	33624412	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33624413	33624588	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33624589	33624639	1	+	1	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33624589	33624639	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33624640	33624732	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33624733	33624829	1	+	1	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33624733	33624829	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33624830	33624996	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33624997	33625029	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33624997	33625029	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33625030	33625154	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33625155	33625283	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33625155	33625283	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33625284	33625418	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33625419	33625610	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33625419	33625610	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33625611	33625707	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33625708	33625791	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33625708	33625791	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33625792	33625874	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33625875	33625970	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33625875	33625970	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33625971	33626068	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33626069	33626145	0.92	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33626069	33626145	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33626146	33626273	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33626274	33626327	0.98	+	1	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33626274	33626327	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33626328	33626472	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33626473	33626569	1	+	1	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33626473	33626569	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33626570	33626836	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33626837	33626962	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33626837	33626962	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33626963	33627066	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33627067	33627162	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33627067	33627162	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33627163	33627355	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33627356	33627469	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33627356	33627469	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33627470	33627620	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33627621	33627698	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33627621	33627698	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33627699	33627793	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33627794	33627999	1	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33627794	33627999	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33628000	33628103	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33628104	33628182	1	+	1	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33628104	33628182	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33628183	33628341	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33628342	33628431	0.94	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33628342	33628431	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	intron	33628432	33628542	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	CDS	33628543	33628581	0.97	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	exon	33628543	33628581	.	+	.	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
Phchi.S1	AUGUSTUS	stop_codon	33628582	33628584	.	+	0	transcript_id "Phchi.S1G528600.t1"; gene_id "Phchi.S1G528600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9206.t1 is derived from g6381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40385085	40386664	.	-	.	Phchi.S1G636500
Phchi.S1	AUGUSTUS	transcript	40385085	40386664	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	stop_codon	40385082	40385084	.	-	0	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	CDS	40385085	40385089	0.54	-	2	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	exon	40385085	40385089	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	intron	40385090	40385168	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	CDS	40385169	40385730	0.35	-	0	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	exon	40385169	40385730	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	intron	40385731	40385892	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	CDS	40385893	40386327	0.32	-	0	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	exon	40385893	40386327	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	intron	40386328	40386541	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	CDS	40386542	40386664	0.62	-	0	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	exon	40386542	40386664	.	-	.	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
Phchi.S1	AUGUSTUS	start_codon	40386662	40386664	.	-	0	transcript_id "Phchi.S1G636500.t1"; gene_id "Phchi.S1G636500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7994.t1 is derived from g5169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32339683	32343392	.	+	.	Phchi.S1G515300
Phchi.S1	AUGUSTUS	transcript	32339683	32343392	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	start_codon	32339683	32339685	.	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32339683	32339709	0.52	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32339683	32339709	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32339710	32339802	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32339803	32340264	0.96	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32339803	32340264	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32340265	32340376	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32340377	32340427	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32340377	32340427	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32340428	32340512	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32340513	32340548	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32340513	32340548	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32340549	32340678	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32340679	32340733	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32340679	32340733	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32340734	32340901	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32340902	32341032	1	+	2	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32340902	32341032	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32341033	32341131	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32341132	32341311	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32341132	32341311	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32341312	32341402	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32341403	32341495	0.99	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32341403	32341495	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32341496	32341610	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32341611	32341709	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32341611	32341709	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32341710	32341799	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32341800	32341846	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32341800	32341846	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32341847	32341926	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32341927	32342015	1	+	1	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32341927	32342015	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32342016	32342198	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32342199	32342361	1	+	2	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32342199	32342361	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32342362	32342486	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32342487	32342595	1	+	1	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32342487	32342595	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32342596	32342689	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32342690	32342866	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32342690	32342866	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32342867	32342965	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32342966	32343187	1	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32342966	32343187	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	intron	32343188	32343299	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	CDS	32343300	32343392	0.99	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	exon	32343300	32343392	.	+	.	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
Phchi.S1	AUGUSTUS	stop_codon	32343393	32343395	.	+	0	transcript_id "Phchi.S1G515300.t1"; gene_id "Phchi.S1G515300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3962.t1 is derived from g1131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6745769	6746038	.	+	.	Phchi.S1G112100
Phchi.S1	AUGUSTUS	transcript	6745769	6746038	.	+	.	transcript_id "Phchi.S1G112100.t1"; gene_id "Phchi.S1G112100"
Phchi.S1	AUGUSTUS	start_codon	6745769	6745771	.	+	0	transcript_id "Phchi.S1G112100.t1"; gene_id "Phchi.S1G112100"
Phchi.S1	AUGUSTUS	CDS	6745769	6746038	0.6	+	0	transcript_id "Phchi.S1G112100.t1"; gene_id "Phchi.S1G112100"
Phchi.S1	AUGUSTUS	exon	6745769	6746038	.	+	.	transcript_id "Phchi.S1G112100.t1"; gene_id "Phchi.S1G112100"
Phchi.S1	AUGUSTUS	stop_codon	6746039	6746041	.	+	0	transcript_id "Phchi.S1G112100.t1"; gene_id "Phchi.S1G112100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8320.t1 is derived from g5495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35267760	35269359	.	-	.	Phchi.S1G547900
Phchi.S1	AUGUSTUS	transcript	35267760	35269359	.	-	.	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	stop_codon	35267757	35267759	.	-	0	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	CDS	35267760	35268132	0.9	-	1	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	exon	35267760	35268132	.	-	.	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	intron	35268133	35268321	.	-	.	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	CDS	35268322	35269019	0.95	-	0	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	exon	35268322	35269019	.	-	.	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	intron	35269020	35269116	.	-	.	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	CDS	35269117	35269359	0.31	-	0	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	exon	35269117	35269359	.	-	.	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
Phchi.S1	AUGUSTUS	start_codon	35269357	35269359	.	-	0	transcript_id "Phchi.S1G547900.t1"; gene_id "Phchi.S1G547900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7885.t1 is derived from g5059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31754198	31760013	.	+	.	Phchi.S1G504400
Phchi.S1	AUGUSTUS	transcript	31754198	31760013	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	start_codon	31754198	31754200	.	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31754198	31754284	0.21	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31754198	31754284	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31754285	31754445	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31754446	31754775	0.75	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31754446	31754775	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31754776	31754889	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31754890	31754983	0.84	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31754890	31754983	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31754984	31755119	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31755120	31755652	0.67	+	2	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31755120	31755652	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31755653	31755758	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31755759	31755866	1	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31755759	31755866	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31755867	31756168	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31756169	31756362	0.96	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31756169	31756362	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31756363	31756475	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31756476	31756608	0.96	+	1	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31756476	31756608	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31756609	31756747	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31756748	31756791	0.56	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31756748	31756791	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31756792	31756926	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31756927	31757126	0.55	+	1	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31756927	31757126	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31757127	31757268	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31757269	31757759	1	+	2	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31757269	31757759	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31757760	31757847	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31757848	31758027	1	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31757848	31758027	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31758028	31758170	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31758171	31758329	1	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31758171	31758329	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31758330	31758413	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31758414	31758488	1	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31758414	31758488	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31758489	31758611	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31758612	31758890	1	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31758612	31758890	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31758891	31759056	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31759057	31759275	1	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31759057	31759275	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	intron	31759276	31759362	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	CDS	31759363	31760013	0.99	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	exon	31759363	31760013	.	+	.	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
Phchi.S1	AUGUSTUS	stop_codon	31760014	31760016	.	+	0	transcript_id "Phchi.S1G504400.t1"; gene_id "Phchi.S1G504400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1372.t1 is derived from g14416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C47	AUGUSTUS	gene	8959	9791	.	-	.	Phchi.C47G000100
Phchi.C47	AUGUSTUS	transcript	8959	9791	.	-	.	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	stop_codon	8956	8958	.	-	0	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	CDS	8959	9388	0.17	-	1	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	exon	8959	9388	.	-	.	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	intron	9389	9502	.	-	.	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	CDS	9503	9620	0.22	-	2	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	exon	9503	9620	.	-	.	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	intron	9621	9721	.	-	.	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	CDS	9722	9791	0.76	-	0	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	exon	9722	9791	.	-	.	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
Phchi.C47	AUGUSTUS	start_codon	9789	9791	.	-	0	transcript_id "Phchi.C47G000100.t1"; gene_id "Phchi.C47G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7219.t1 is derived from g4391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27687539	27688259	.	-	.	Phchi.S1G437800
Phchi.S1	AUGUSTUS	transcript	27687539	27688259	.	-	.	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	stop_codon	27687536	27687538	.	-	0	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	CDS	27687539	27687663	0.88	-	2	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	exon	27687539	27687663	.	-	.	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	intron	27687664	27687969	.	-	.	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	CDS	27687970	27688111	0.63	-	0	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	exon	27687970	27688111	.	-	.	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	intron	27688112	27688217	.	-	.	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	CDS	27688218	27688259	0.63	-	0	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	exon	27688218	27688259	.	-	.	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
Phchi.S1	AUGUSTUS	start_codon	27688257	27688259	.	-	0	transcript_id "Phchi.S1G437800.t1"; gene_id "Phchi.S1G437800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4897.t1 is derived from g2067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13298831	13299882	.	-	.	Phchi.S1G205600
Phchi.S1	AUGUSTUS	transcript	13298831	13299882	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	stop_codon	13298828	13298830	.	-	0	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	CDS	13298831	13298938	1	-	0	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	exon	13298831	13298938	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	intron	13298939	13299030	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	CDS	13299031	13299313	1	-	1	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	exon	13299031	13299313	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	intron	13299314	13299403	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	CDS	13299404	13299603	1	-	0	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	exon	13299404	13299603	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	intron	13299604	13299687	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	CDS	13299688	13299882	1	-	0	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	exon	13299688	13299882	.	-	.	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
Phchi.S1	AUGUSTUS	start_codon	13299880	13299882	.	-	0	transcript_id "Phchi.S1G205600.t1"; gene_id "Phchi.S1G205600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12734.t1 is derived from g11199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1446021	1446583	.	-	.	Phchi.S3G005300
Phchi.S3	AUGUSTUS	transcript	1446021	1446583	.	-	.	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	stop_codon	1446018	1446020	.	-	0	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	CDS	1446021	1446029	0.56	-	0	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	exon	1446021	1446029	.	-	.	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	intron	1446030	1446162	.	-	.	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	CDS	1446163	1446391	0.53	-	1	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	exon	1446163	1446391	.	-	.	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	intron	1446392	1446482	.	-	.	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	CDS	1446483	1446583	0.85	-	0	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	exon	1446483	1446583	.	-	.	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
Phchi.S3	AUGUSTUS	start_codon	1446581	1446583	.	-	0	transcript_id "Phchi.S3G005300.t1"; gene_id "Phchi.S3G005300"
# This transcript jg15455.t2 is derived from g13923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15456.t1 is derived from g13924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19272157	19279758	.	-	.	Phchi.S3G277500
Phchi.S3	AUGUSTUS	transcript	19272157	19279758	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	stop_codon	19272154	19272156	.	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19272157	19272327	0.92	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19272157	19272327	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19272328	19272411	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19272412	19272554	1	-	2	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19272412	19272554	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19272555	19272627	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19272628	19272729	1	-	2	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19272628	19272729	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19272730	19272800	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19272801	19272904	1	-	1	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19272801	19272904	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19272905	19272988	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19272989	19273077	1	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19272989	19273077	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19273078	19273180	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19273181	19274635	0.87	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19273181	19274635	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19274636	19274727	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19274728	19275000	1	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19274728	19275000	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19275001	19275086	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19275087	19277636	1	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19275087	19277636	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19277637	19277772	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19277773	19277922	1	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19277773	19277922	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19277923	19278012	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19278013	19278066	1	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19278013	19278066	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19278067	19278151	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19278152	19278275	1	-	1	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19278152	19278275	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19278276	19278420	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19278421	19278485	1	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19278421	19278485	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19278486	19278661	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19278662	19278850	0.51	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19278662	19278850	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19278851	19279196	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19279197	19279294	0.67	-	2	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19279197	19279294	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19279295	19279477	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19279478	19279580	0.84	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19279478	19279580	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	intron	19279581	19279743	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	CDS	19279744	19279758	0.84	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	exon	19279744	19279758	.	-	.	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
Phchi.S3	AUGUSTUS	start_codon	19279756	19279758	.	-	0	transcript_id "Phchi.S3G277500.t1"; gene_id "Phchi.S3G277500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg975.t1 is derived from g10758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6747608	6755961	.	+	.	Phchi.S6G093400
Phchi.S6	AUGUSTUS	transcript	6747608	6755961	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	start_codon	6747608	6747610	.	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6747608	6747934	0.75	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6747608	6747934	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6747935	6748059	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748060	6748327	0.75	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748060	6748327	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6748328	6748525	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748526	6751054	0.97	+	2	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748526	6751054	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751055	6751178	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751179	6751263	0.89	+	2	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751179	6751263	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751264	6751369	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751370	6751420	0.98	+	1	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751370	6751420	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751421	6751561	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751562	6751634	1	+	1	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751562	6751634	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751635	6751743	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751744	6751901	0.85	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751744	6751901	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751902	6752352	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752353	6752362	1	+	1	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752353	6752362	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752363	6752677	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752678	6752737	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752678	6752737	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752738	6752881	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752882	6753094	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752882	6753094	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753095	6753206	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753207	6753491	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753207	6753491	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753492	6753807	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753808	6753963	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753808	6753963	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753964	6754042	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754043	6754148	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754043	6754148	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754149	6754298	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754299	6754419	1	+	2	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754299	6754419	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754420	6754513	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754514	6754641	1	+	1	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754514	6754641	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754642	6754736	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754737	6754876	1	+	2	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754737	6754876	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754877	6755090	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755091	6755159	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755091	6755159	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755160	6755339	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755340	6755475	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755340	6755475	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755476	6755581	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755582	6755644	1	+	2	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755582	6755644	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755645	6755733	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755734	6755777	1	+	2	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755734	6755777	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755778	6755877	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755878	6755961	1	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755878	6755961	.	+	.	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	stop_codon	6755962	6755964	.	+	0	transcript_id "Phchi.S6G093400.t1"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	transcript	6747608	6755961	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	start_codon	6747608	6747610	.	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6747608	6747934	0.72	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6747608	6747934	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6747935	6748059	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748060	6748327	0.72	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748060	6748327	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6748328	6748525	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748526	6751054	0.99	+	2	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748526	6751054	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751055	6751178	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751179	6751263	0.79	+	2	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751179	6751263	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751264	6751369	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751370	6751420	0.97	+	1	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751370	6751420	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751421	6751561	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751562	6751634	1	+	1	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751562	6751634	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751635	6751743	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751744	6751901	0.83	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751744	6751901	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751902	6752352	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752353	6752362	1	+	1	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752353	6752362	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752363	6752677	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752678	6752737	1	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752678	6752737	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752738	6752881	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752882	6753094	1	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752882	6753094	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753095	6753206	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753207	6753491	1	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753207	6753491	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753492	6753807	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753808	6753963	0.66	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753808	6753963	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753964	6754081	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754082	6754148	0.7	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754082	6754148	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754149	6754298	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754299	6754419	1	+	2	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754299	6754419	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754420	6754513	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754514	6754641	1	+	1	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754514	6754641	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754642	6754736	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754737	6754876	1	+	2	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754737	6754876	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754877	6755090	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755091	6755159	1	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755091	6755159	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755160	6755339	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755340	6755475	0.99	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755340	6755475	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755476	6755581	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755582	6755644	0.99	+	2	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755582	6755644	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755645	6755733	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755734	6755777	1	+	2	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755734	6755777	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755778	6755877	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755878	6755961	1	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755878	6755961	.	+	.	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	stop_codon	6755962	6755964	.	+	0	transcript_id "Phchi.S6G093400.t2"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	transcript	6747608	6755961	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	start_codon	6747608	6747610	.	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6747608	6747934	0.68	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6747608	6747934	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6747935	6748059	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748060	6748327	0.68	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748060	6748327	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6748328	6748525	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748526	6751054	1	+	2	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748526	6751054	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751055	6751178	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751179	6751263	0.84	+	2	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751179	6751263	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751264	6751369	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751370	6751420	0.98	+	1	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751370	6751420	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751421	6751561	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751562	6751634	1	+	1	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751562	6751634	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751635	6751743	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751744	6751901	0.85	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751744	6751901	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751902	6752352	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752353	6752362	1	+	1	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752353	6752362	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752363	6752677	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752678	6752737	1	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752678	6752737	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752738	6752881	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752882	6753094	1	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752882	6753094	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753095	6753206	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753207	6753491	0.75	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753207	6753491	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753492	6753776	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753777	6753823	0.61	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753777	6753823	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753824	6753905	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753906	6753963	0.67	+	1	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753906	6753963	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753964	6754042	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754043	6754148	0.74	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754043	6754148	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754149	6754298	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754299	6754419	1	+	2	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754299	6754419	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754420	6754513	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754514	6754641	1	+	1	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754514	6754641	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754642	6754736	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754737	6754876	1	+	2	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754737	6754876	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754877	6755090	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755091	6755159	1	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755091	6755159	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755160	6755339	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755340	6755475	1	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755340	6755475	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755476	6755581	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755582	6755644	1	+	2	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755582	6755644	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755645	6755733	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755734	6755777	1	+	2	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755734	6755777	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755778	6755877	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755878	6755961	1	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755878	6755961	.	+	.	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	stop_codon	6755962	6755964	.	+	0	transcript_id "Phchi.S6G093400.t3"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	transcript	6747608	6755961	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	start_codon	6747608	6747610	.	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6747608	6747934	0.75	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6747608	6747934	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6747935	6748059	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748060	6748327	0.73	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748060	6748327	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6748328	6748525	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6748526	6751054	0.99	+	2	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6748526	6751054	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751055	6751178	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751179	6751263	0.85	+	2	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751179	6751263	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751264	6751369	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751370	6751420	0.99	+	1	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751370	6751420	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751421	6751561	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751562	6751634	0.98	+	1	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751562	6751634	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751635	6751743	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6751744	6751893	0.48	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6751744	6751893	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6751894	6752240	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752241	6752362	0.5	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752241	6752362	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752363	6752579	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752580	6752631	0.28	+	1	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752580	6752631	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752632	6752713	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752714	6752737	0.28	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752714	6752737	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6752738	6752881	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6752882	6753094	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6752882	6753094	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753095	6753206	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753207	6753491	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753207	6753491	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753492	6753807	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6753808	6753963	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6753808	6753963	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6753964	6754042	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754043	6754148	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754043	6754148	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754149	6754298	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754299	6754419	1	+	2	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754299	6754419	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754420	6754513	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754514	6754641	1	+	1	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754514	6754641	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754642	6754736	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6754737	6754876	1	+	2	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6754737	6754876	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6754877	6755090	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755091	6755159	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755091	6755159	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755160	6755339	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755340	6755475	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755340	6755475	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755476	6755581	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755582	6755644	1	+	2	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755582	6755644	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755645	6755733	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755734	6755777	1	+	2	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755734	6755777	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	intron	6755778	6755877	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	CDS	6755878	6755961	1	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	exon	6755878	6755961	.	+	.	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
Phchi.S6	AUGUSTUS	stop_codon	6755962	6755964	.	+	0	transcript_id "Phchi.S6G093400.t4"; gene_id "Phchi.S6G093400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg328.t1 is derived from g10110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2278457	2280424	.	+	.	Phchi.S6G028700
Phchi.S6	AUGUSTUS	transcript	2278457	2280424	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	start_codon	2278457	2278459	.	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2278457	2278690	0.95	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2278457	2278690	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2278691	2278769	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2278770	2278784	0.95	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2278770	2278784	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2278785	2278870	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2278871	2278934	0.78	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2278871	2278934	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2278935	2279063	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2279064	2279249	1	+	2	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2279064	2279249	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2279250	2279351	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2279352	2279554	1	+	2	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2279352	2279554	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2279555	2279661	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2279662	2279813	1	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2279662	2279813	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2279814	2279945	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2279946	2280192	1	+	1	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2279946	2280192	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	intron	2280193	2280313	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	CDS	2280314	2280424	0.99	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	exon	2280314	2280424	.	+	.	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
Phchi.S6	AUGUSTUS	stop_codon	2280425	2280427	.	+	0	transcript_id "Phchi.S6G028700.t1"; gene_id "Phchi.S6G028700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9998.t1 is derived from g7174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44920091	44921191	.	+	.	Phchi.S1G715700
Phchi.S1	AUGUSTUS	transcript	44920091	44921191	.	+	.	transcript_id "Phchi.S1G715700.t1"; gene_id "Phchi.S1G715700"
Phchi.S1	AUGUSTUS	start_codon	44920091	44920093	.	+	0	transcript_id "Phchi.S1G715700.t1"; gene_id "Phchi.S1G715700"
Phchi.S1	AUGUSTUS	CDS	44920091	44921191	0.5	+	0	transcript_id "Phchi.S1G715700.t1"; gene_id "Phchi.S1G715700"
Phchi.S1	AUGUSTUS	exon	44920091	44921191	.	+	.	transcript_id "Phchi.S1G715700.t1"; gene_id "Phchi.S1G715700"
Phchi.S1	AUGUSTUS	stop_codon	44921192	44921194	.	+	0	transcript_id "Phchi.S1G715700.t1"; gene_id "Phchi.S1G715700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4259.t1 is derived from g1428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9207961	9208865	.	+	.	Phchi.S1G141800
Phchi.S1	AUGUSTUS	transcript	9207961	9208865	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	start_codon	9207961	9207963	.	+	0	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	CDS	9207961	9208072	0.84	+	0	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	exon	9207961	9208072	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	intron	9208073	9208164	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	CDS	9208165	9208331	0.9	+	2	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	exon	9208165	9208331	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	intron	9208332	9208587	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	CDS	9208588	9208701	0.88	+	0	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	exon	9208588	9208701	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	intron	9208702	9208835	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	CDS	9208836	9208865	0.72	+	0	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	exon	9208836	9208865	.	+	.	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
Phchi.S1	AUGUSTUS	stop_codon	9208866	9208868	.	+	0	transcript_id "Phchi.S1G141800.t1"; gene_id "Phchi.S1G141800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3905.t1 is derived from g1074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6369806	6370258	.	+	.	Phchi.S1G106400
Phchi.S1	AUGUSTUS	transcript	6369806	6370258	.	+	.	transcript_id "Phchi.S1G106400.t1"; gene_id "Phchi.S1G106400"
Phchi.S1	AUGUSTUS	start_codon	6369806	6369808	.	+	0	transcript_id "Phchi.S1G106400.t1"; gene_id "Phchi.S1G106400"
Phchi.S1	AUGUSTUS	CDS	6369806	6370258	0.6	+	0	transcript_id "Phchi.S1G106400.t1"; gene_id "Phchi.S1G106400"
Phchi.S1	AUGUSTUS	exon	6369806	6370258	.	+	.	transcript_id "Phchi.S1G106400.t1"; gene_id "Phchi.S1G106400"
Phchi.S1	AUGUSTUS	stop_codon	6370259	6370261	.	+	0	transcript_id "Phchi.S1G106400.t1"; gene_id "Phchi.S1G106400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15658.t1 is derived from g14127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20521110	20521577	.	+	.	Phchi.S3G297700
Phchi.S3	AUGUSTUS	transcript	20521110	20521577	.	+	.	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	start_codon	20521110	20521112	.	+	0	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	CDS	20521110	20521363	0.78	+	0	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	exon	20521110	20521363	.	+	.	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	intron	20521364	20521522	.	+	.	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	CDS	20521523	20521577	0.63	+	1	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	exon	20521523	20521577	.	+	.	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
Phchi.S3	AUGUSTUS	stop_codon	20521578	20521580	.	+	0	transcript_id "Phchi.S3G297700.t1"; gene_id "Phchi.S3G297700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11770.t1 is derived from g15822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8100886	8103777	.	+	.	Phchi.S4G135200
Phchi.S4	AUGUSTUS	transcript	8100886	8103777	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	start_codon	8100886	8100888	.	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8100886	8100931	0.95	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8100886	8100931	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8100932	8101029	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8101030	8101034	0.51	+	2	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8101030	8101034	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8101035	8101152	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8101153	8101601	0.65	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8101153	8101601	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8101602	8101689	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8101690	8101805	1	+	1	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8101690	8101805	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8101806	8101901	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8101902	8102782	1	+	2	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8101902	8102782	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8102783	8102875	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8102876	8103055	1	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8102876	8103055	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8103056	8103149	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8103150	8103316	1	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8103150	8103316	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8103317	8103399	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8103400	8103523	1	+	1	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8103400	8103523	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	intron	8103524	8103624	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	CDS	8103625	8103777	0.99	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	exon	8103625	8103777	.	+	.	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
Phchi.S4	AUGUSTUS	stop_codon	8103778	8103780	.	+	0	transcript_id "Phchi.S4G135200.t1"; gene_id "Phchi.S4G135200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8338.t1 is derived from g5513.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35386511	35388327	.	-	.	Phchi.S1G549700
Phchi.S1	AUGUSTUS	transcript	35386511	35388327	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	stop_codon	35386508	35386510	.	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35386511	35386582	1	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35386511	35386582	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35386583	35386668	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35386669	35386710	1	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35386669	35386710	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35386711	35386806	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35386807	35386911	1	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35386807	35386911	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35386912	35386999	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387000	35387047	1	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387000	35387047	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387048	35387141	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387142	35387252	1	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387142	35387252	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387253	35387349	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387350	35387469	1	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387350	35387469	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387470	35387553	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387554	35387659	1	-	1	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387554	35387659	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387660	35387827	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387828	35388327	0.95	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387828	35388327	.	-	.	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	start_codon	35388325	35388327	.	-	0	transcript_id "Phchi.S1G549700.t1"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	transcript	35386511	35387986	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	stop_codon	35386508	35386510	.	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35386511	35386582	1	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35386511	35386582	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35386583	35386668	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35386669	35386710	1	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35386669	35386710	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35386711	35386806	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35386807	35386911	1	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35386807	35386911	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35386912	35386999	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387000	35387047	1	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387000	35387047	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387048	35387141	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387142	35387252	1	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387142	35387252	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387253	35387349	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387350	35387469	1	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387350	35387469	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387470	35387553	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387554	35387659	1	-	1	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387554	35387659	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	intron	35387660	35387795	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	CDS	35387796	35387986	0.83	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	exon	35387796	35387986	.	-	.	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
Phchi.S1	AUGUSTUS	start_codon	35387984	35387986	.	-	0	transcript_id "Phchi.S1G549700.t2"; gene_id "Phchi.S1G549700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11019.t1 is derived from g15069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3658064	3659047	.	-	.	Phchi.S4G060100
Phchi.S4	AUGUSTUS	transcript	3658064	3659047	.	-	.	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	stop_codon	3658061	3658063	.	-	0	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	CDS	3658064	3658370	0.99	-	1	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	exon	3658064	3658370	.	-	.	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	intron	3658371	3658497	.	-	.	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	CDS	3658498	3658669	0.68	-	2	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	exon	3658498	3658669	.	-	.	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	intron	3658670	3658890	.	-	.	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	CDS	3658891	3659047	0.86	-	0	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	exon	3658891	3659047	.	-	.	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
Phchi.S4	AUGUSTUS	start_codon	3659045	3659047	.	-	0	transcript_id "Phchi.S4G060100.t1"; gene_id "Phchi.S4G060100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11034.t1 is derived from g15084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3737814	3739629	.	-	.	Phchi.S4G061600
Phchi.S4	AUGUSTUS	transcript	3737814	3739629	.	-	.	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	stop_codon	3737811	3737813	.	-	0	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	CDS	3737814	3737983	0.31	-	2	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	exon	3737814	3737983	.	-	.	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	intron	3737984	3738158	.	-	.	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	CDS	3738159	3739399	0.48	-	1	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	exon	3738159	3739399	.	-	.	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	intron	3739400	3739504	.	-	.	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	CDS	3739505	3739629	0.99	-	0	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	exon	3739505	3739629	.	-	.	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
Phchi.S4	AUGUSTUS	start_codon	3739627	3739629	.	-	0	transcript_id "Phchi.S4G061600.t1"; gene_id "Phchi.S4G061600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13702.t1 is derived from g12169.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8275970	8279954	.	+	.	Phchi.S3G102100
Phchi.S3	AUGUSTUS	transcript	8275970	8279954	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	start_codon	8275970	8275972	.	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8275970	8276314	0.96	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8275970	8276314	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8276315	8276403	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8276404	8276439	0.97	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8276404	8276439	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8276440	8276601	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8276602	8276700	0.97	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8276602	8276700	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8276701	8276796	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8276797	8276863	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8276797	8276863	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8276864	8276956	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8276957	8277141	1	+	2	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8276957	8277141	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8277142	8277237	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8277238	8277477	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8277238	8277477	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8277478	8277617	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8277618	8277701	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8277618	8277701	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8277702	8277800	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8277801	8277848	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8277801	8277848	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8277849	8277943	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8277944	8278008	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8277944	8278008	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8278009	8278139	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8278140	8278188	1	+	1	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8278140	8278188	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8278189	8278294	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8278295	8278523	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8278295	8278523	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8278524	8278594	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8278595	8278716	1	+	2	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8278595	8278716	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8278717	8278846	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8278847	8278927	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8278847	8278927	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8278928	8279022	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8279023	8279097	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8279023	8279097	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8279098	8279187	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8279188	8279411	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8279188	8279411	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8279412	8279517	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8279518	8279668	1	+	1	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8279518	8279668	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	intron	8279669	8279762	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	CDS	8279763	8279954	1	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	exon	8279763	8279954	.	+	.	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
Phchi.S3	AUGUSTUS	stop_codon	8279955	8279957	.	+	0	transcript_id "Phchi.S3G102100.t1"; gene_id "Phchi.S3G102100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4286.t1 is derived from g1455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9419246	9420102	.	-	.	Phchi.S1G144500
Phchi.S1	AUGUSTUS	transcript	9419246	9420102	.	-	.	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	stop_codon	9419243	9419245	.	-	0	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	CDS	9419246	9419613	0.44	-	2	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	exon	9419246	9419613	.	-	.	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	intron	9419614	9420014	.	-	.	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	CDS	9420015	9420102	0.04	-	0	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	exon	9420015	9420102	.	-	.	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
Phchi.S1	AUGUSTUS	start_codon	9420100	9420102	.	-	0	transcript_id "Phchi.S1G144500.t1"; gene_id "Phchi.S1G144500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9886.t1 is derived from g7062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44261636	44268435	.	-	.	Phchi.S1G704500
Phchi.S1	AUGUSTUS	transcript	44261636	44263484	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	stop_codon	44261633	44261635	.	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44261636	44261872	0.98	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44261636	44261872	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44261873	44261949	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44261950	44262065	1	-	2	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44261950	44262065	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262066	44262147	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262148	44262284	1	-	1	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262148	44262284	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262285	44262373	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262374	44262537	1	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262374	44262537	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262538	44262603	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262604	44262684	1	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262604	44262684	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262685	44262813	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262814	44262993	1	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262814	44262993	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262994	44263092	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263093	44263198	0.69	-	1	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263093	44263198	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263199	44263299	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263300	44263484	0.61	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263300	44263484	.	-	.	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	start_codon	44263482	44263484	.	-	0	transcript_id "Phchi.S1G704500.t1"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	transcript	44261636	44268435	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	stop_codon	44261633	44261635	.	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44261636	44261872	0.99	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44261636	44261872	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44261873	44261949	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44261950	44262065	1	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44261950	44262065	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262066	44262147	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262148	44262284	1	-	1	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262148	44262284	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262285	44262373	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262374	44262537	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262374	44262537	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262538	44262603	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262604	44262684	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262604	44262684	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262685	44262813	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262814	44262993	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262814	44262993	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262994	44263092	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263093	44263208	0.92	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263093	44263208	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263209	44263299	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263300	44263321	0.8	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263300	44263321	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263322	44263466	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263467	44263569	0.24	-	1	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263467	44263569	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263570	44263645	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263646	44263705	0.25	-	1	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263646	44263705	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263706	44263804	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263805	44263841	0.41	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263805	44263841	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263842	44263930	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263931	44263953	0.38	-	1	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263931	44263953	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263954	44264063	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264064	44264149	0.82	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264064	44264149	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264150	44264235	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264236	44264298	0.84	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264236	44264298	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264299	44264400	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264401	44264582	0.87	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264401	44264582	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264583	44264683	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264684	44264975	0.99	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264684	44264975	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264976	44265170	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44265171	44265485	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44265171	44265485	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44265486	44265656	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44265657	44265919	1	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44265657	44265919	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44265920	44266003	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266004	44266144	1	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266004	44266144	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44266145	44266218	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266219	44266472	0.97	-	1	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266219	44266472	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44266473	44266575	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266576	44266655	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266576	44266655	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44266656	44266735	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266736	44267052	0.94	-	2	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266736	44267052	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267053	44267178	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44267179	44267366	0.98	-	1	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44267179	44267366	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267367	44267487	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44267488	44267603	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44267488	44267603	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267604	44267787	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44267788	44267910	1	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44267788	44267910	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267911	44268006	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44268007	44268435	0.99	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44268007	44268435	.	-	.	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	start_codon	44268433	44268435	.	-	0	transcript_id "Phchi.S1G704500.t2"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	transcript	44261636	44268435	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	stop_codon	44261633	44261635	.	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44261636	44261872	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44261636	44261872	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44261873	44261949	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44261950	44262065	1	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44261950	44262065	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262066	44262147	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262148	44262284	1	-	1	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262148	44262284	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262285	44262424	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262425	44262537	0.99	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262425	44262537	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262538	44262603	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262604	44262684	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262604	44262684	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262685	44262813	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44262814	44262993	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44262814	44262993	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44262994	44263092	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263093	44263208	0.93	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263093	44263208	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263209	44263299	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263300	44263321	0.8	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263300	44263321	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263322	44263466	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263467	44263569	0.18	-	1	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263467	44263569	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263570	44263645	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263646	44263705	0.22	-	1	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263646	44263705	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263706	44263804	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263805	44263841	0.48	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263805	44263841	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263842	44263930	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44263931	44263953	0.41	-	1	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44263931	44263953	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44263954	44264063	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264064	44264149	0.8	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264064	44264149	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264150	44264235	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264236	44264298	0.83	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264236	44264298	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264299	44264400	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264401	44264582	0.93	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264401	44264582	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264583	44264683	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44264684	44264975	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44264684	44264975	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44264976	44265170	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44265171	44265485	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44265171	44265485	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44265486	44265656	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44265657	44265919	1	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44265657	44265919	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44265920	44266003	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266004	44266144	1	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266004	44266144	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44266145	44266218	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266219	44266472	0.98	-	1	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266219	44266472	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44266473	44266575	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266576	44266655	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266576	44266655	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44266656	44266735	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44266736	44267052	0.97	-	2	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44266736	44267052	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267053	44267178	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44267179	44267366	0.96	-	1	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44267179	44267366	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267367	44267487	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44267488	44267603	0.99	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44267488	44267603	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267604	44267787	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44267788	44267910	1	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44267788	44267910	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	intron	44267911	44268006	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	CDS	44268007	44268435	0.98	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	exon	44268007	44268435	.	-	.	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
Phchi.S1	AUGUSTUS	start_codon	44268433	44268435	.	-	0	transcript_id "Phchi.S1G704500.t3"; gene_id "Phchi.S1G704500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3961.t1 is derived from g1130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6742338	6742775	.	-	.	Phchi.S1G112000
Phchi.S1	AUGUSTUS	transcript	6742338	6742775	.	-	.	transcript_id "Phchi.S1G112000.t1"; gene_id "Phchi.S1G112000"
Phchi.S1	AUGUSTUS	stop_codon	6742335	6742337	.	-	0	transcript_id "Phchi.S1G112000.t1"; gene_id "Phchi.S1G112000"
Phchi.S1	AUGUSTUS	CDS	6742338	6742775	0.83	-	0	transcript_id "Phchi.S1G112000.t1"; gene_id "Phchi.S1G112000"
Phchi.S1	AUGUSTUS	exon	6742338	6742775	.	-	.	transcript_id "Phchi.S1G112000.t1"; gene_id "Phchi.S1G112000"
Phchi.S1	AUGUSTUS	start_codon	6742773	6742775	.	-	0	transcript_id "Phchi.S1G112000.t1"; gene_id "Phchi.S1G112000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3315.t1 is derived from g484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2807150	2808119	.	-	.	Phchi.S1G047400
Phchi.S1	AUGUSTUS	transcript	2807150	2808119	.	-	.	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	stop_codon	2807147	2807149	.	-	0	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	CDS	2807150	2807608	0.96	-	0	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	exon	2807150	2807608	.	-	.	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	intron	2807609	2807972	.	-	.	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	CDS	2807973	2808119	0.93	-	0	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	exon	2807973	2808119	.	-	.	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
Phchi.S1	AUGUSTUS	start_codon	2808117	2808119	.	-	0	transcript_id "Phchi.S1G047400.t1"; gene_id "Phchi.S1G047400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3565.t1 is derived from g734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4501448	4502034	.	-	.	Phchi.S1G072400
Phchi.S1	AUGUSTUS	transcript	4501448	4502034	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	stop_codon	4501445	4501447	.	-	0	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	CDS	4501448	4501532	1	-	1	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	exon	4501448	4501532	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	intron	4501533	4501615	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	CDS	4501616	4501716	1	-	0	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	exon	4501616	4501716	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	intron	4501717	4501819	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	CDS	4501820	4501872	1	-	2	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	exon	4501820	4501872	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	intron	4501873	4501958	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	CDS	4501959	4502034	1	-	0	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	exon	4501959	4502034	.	-	.	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
Phchi.S1	AUGUSTUS	start_codon	4502032	4502034	.	-	0	transcript_id "Phchi.S1G072400.t1"; gene_id "Phchi.S1G072400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4468.t1 is derived from g1638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10645616	10647740	.	+	.	Phchi.S1G162700
Phchi.S1	AUGUSTUS	transcript	10645616	10647740	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	start_codon	10645616	10645618	.	+	0	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	CDS	10645616	10645905	1	+	0	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	exon	10645616	10645905	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	intron	10645906	10646024	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	CDS	10646025	10646126	1	+	1	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	exon	10646025	10646126	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	intron	10646127	10646266	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	CDS	10646267	10647087	0.99	+	1	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	exon	10646267	10647087	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	intron	10647088	10647165	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	CDS	10647166	10647740	0.85	+	2	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	exon	10647166	10647740	.	+	.	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
Phchi.S1	AUGUSTUS	stop_codon	10647741	10647743	.	+	0	transcript_id "Phchi.S1G162700.t1"; gene_id "Phchi.S1G162700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4914.t1 is derived from g2084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13448842	13449883	.	+	.	Phchi.S1G207300
Phchi.S1	AUGUSTUS	transcript	13448842	13449883	.	+	.	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	start_codon	13448842	13448844	.	+	0	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	CDS	13448842	13449024	0.93	+	0	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	exon	13448842	13449024	.	+	.	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	intron	13449025	13449122	.	+	.	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	CDS	13449123	13449499	0.41	+	0	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	exon	13449123	13449499	.	+	.	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	intron	13449500	13449846	.	+	.	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	CDS	13449847	13449883	0.41	+	1	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	exon	13449847	13449883	.	+	.	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
Phchi.S1	AUGUSTUS	stop_codon	13449884	13449886	.	+	0	transcript_id "Phchi.S1G207300.t1"; gene_id "Phchi.S1G207300"
# This transcript jg490.t2 is derived from g10272.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg491.t1 is derived from g10273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3420671	3421813	.	+	.	Phchi.S6G045000
Phchi.S6	AUGUSTUS	transcript	3420671	3421813	.	+	.	transcript_id "Phchi.S6G045000.t1"; gene_id "Phchi.S6G045000"
Phchi.S6	AUGUSTUS	start_codon	3420671	3420673	.	+	0	transcript_id "Phchi.S6G045000.t1"; gene_id "Phchi.S6G045000"
Phchi.S6	AUGUSTUS	CDS	3420671	3421813	0.93	+	0	transcript_id "Phchi.S6G045000.t1"; gene_id "Phchi.S6G045000"
Phchi.S6	AUGUSTUS	exon	3420671	3421813	.	+	.	transcript_id "Phchi.S6G045000.t1"; gene_id "Phchi.S6G045000"
Phchi.S6	AUGUSTUS	stop_codon	3421814	3421816	.	+	0	transcript_id "Phchi.S6G045000.t1"; gene_id "Phchi.S6G045000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8855.t1 is derived from g6030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38292862	38295964	.	+	.	Phchi.S1G601400
Phchi.S1	AUGUSTUS	transcript	38292862	38295964	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	start_codon	38292862	38292864	.	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38292862	38293098	0.71	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38292862	38293098	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38293099	38293269	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38293270	38293344	1	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38293270	38293344	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38293345	38293420	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38293421	38293496	1	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38293421	38293496	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38293497	38293595	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38293596	38293674	1	+	2	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38293596	38293674	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38293675	38293761	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38293762	38293896	1	+	1	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38293762	38293896	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38293897	38294044	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38294045	38294109	1	+	1	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38294045	38294109	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38294110	38294215	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38294216	38294343	1	+	2	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38294216	38294343	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38294344	38294468	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38294469	38294722	1	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38294469	38294722	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38294723	38294818	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38294819	38294852	1	+	1	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38294819	38294852	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38294853	38294938	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38294939	38295426	0.35	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38294939	38295426	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38295427	38295633	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38295634	38295681	0.98	+	1	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38295634	38295681	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38295682	38295759	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38295760	38295862	1	+	1	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38295760	38295862	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	intron	38295863	38295955	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	CDS	38295956	38295964	1	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	exon	38295956	38295964	.	+	.	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
Phchi.S1	AUGUSTUS	stop_codon	38295965	38295967	.	+	0	transcript_id "Phchi.S1G601400.t1"; gene_id "Phchi.S1G601400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12699.t1 is derived from g11164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	618396	620534	.	-	.	Phchi.S3G001800
Phchi.S3	AUGUSTUS	transcript	618396	620534	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	stop_codon	618393	618395	.	-	0	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	618396	618522	0.47	-	1	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	618396	618522	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	intron	618523	618619	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	618620	618815	0.49	-	2	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	618620	618815	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	intron	618816	618943	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	618944	619224	1	-	1	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	618944	619224	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	intron	619225	619311	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	619312	619480	1	-	2	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	619312	619480	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	intron	619481	619605	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	619606	620065	0.99	-	0	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	619606	620065	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	intron	620066	620203	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	620204	620283	1	-	2	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	620204	620283	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	intron	620284	620455	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	CDS	620456	620534	0.97	-	0	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	exon	620456	620534	.	-	.	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
Phchi.S3	AUGUSTUS	start_codon	620532	620534	.	-	0	transcript_id "Phchi.S3G001800.t1"; gene_id "Phchi.S3G001800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3609.t1 is derived from g778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4731460	4733738	.	-	.	Phchi.S1G076800
Phchi.S1	AUGUSTUS	transcript	4731460	4733738	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	stop_codon	4731457	4731459	.	-	0	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	CDS	4731460	4731581	0.56	-	2	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	exon	4731460	4731581	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	intron	4731582	4731678	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	CDS	4731679	4731730	0.49	-	0	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	exon	4731679	4731730	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	intron	4731731	4731854	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	CDS	4731855	4731900	0.64	-	1	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	exon	4731855	4731900	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	intron	4731901	4732096	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	CDS	4732097	4732161	0.86	-	0	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	exon	4732097	4732161	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	intron	4732162	4732349	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	CDS	4732350	4733738	0.88	-	0	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	exon	4732350	4733738	.	-	.	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
Phchi.S1	AUGUSTUS	start_codon	4733736	4733738	.	-	0	transcript_id "Phchi.S1G076800.t1"; gene_id "Phchi.S1G076800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6995.t1 is derived from g4167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26310054	26312637	.	-	.	Phchi.S1G415400
Phchi.S1	AUGUSTUS	transcript	26310054	26312637	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	stop_codon	26310051	26310053	.	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26310054	26310134	0.87	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26310054	26310134	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26310135	26310221	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26310222	26310335	1	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26310222	26310335	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26310336	26310417	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26310418	26310696	1	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26310418	26310696	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26310697	26310787	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26310788	26311881	0.54	-	2	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26310788	26311881	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26311882	26311952	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26311953	26311958	0.71	-	2	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26311953	26311958	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26311959	26312107	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26312108	26312155	0.98	-	2	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26312108	26312155	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26312156	26312336	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26312337	26312397	0.91	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26312337	26312397	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	intron	26312398	26312598	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	CDS	26312599	26312637	0.35	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	exon	26312599	26312637	.	-	.	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
Phchi.S1	AUGUSTUS	start_codon	26312635	26312637	.	-	0	transcript_id "Phchi.S1G415400.t1"; gene_id "Phchi.S1G415400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3241.t1 is derived from g410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2403697	2404988	.	-	.	Phchi.S1G040000
Phchi.S1	AUGUSTUS	transcript	2403697	2404988	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	stop_codon	2403694	2403696	.	-	0	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2403697	2403909	0.74	-	0	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2403697	2403909	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	intron	2403910	2404004	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2404005	2404103	1	-	0	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2404005	2404103	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	intron	2404104	2404188	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2404189	2404269	1	-	0	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2404189	2404269	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	intron	2404270	2404359	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2404360	2404451	1	-	2	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2404360	2404451	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	intron	2404452	2404610	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2404611	2404658	1	-	2	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2404611	2404658	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	intron	2404659	2404744	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2404745	2404858	1	-	2	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2404745	2404858	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	intron	2404859	2404942	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	CDS	2404943	2404988	0.6	-	0	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	exon	2404943	2404988	.	-	.	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
Phchi.S1	AUGUSTUS	start_codon	2404986	2404988	.	-	0	transcript_id "Phchi.S1G040000.t1"; gene_id "Phchi.S1G040000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4066.t1 is derived from g1235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7615348	7619247	.	-	.	Phchi.S1G122500
Phchi.S1	AUGUSTUS	transcript	7615348	7619247	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	stop_codon	7615345	7615347	.	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7615348	7615638	0.78	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7615348	7615638	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7615639	7615740	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7615741	7616397	0.38	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7615741	7616397	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7616398	7616581	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7616582	7616797	0.85	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7616582	7616797	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7616798	7616904	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7616905	7617012	0.96	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7616905	7617012	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7617013	7617120	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7617121	7617524	0.64	-	2	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7617121	7617524	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7617525	7617634	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7617635	7617969	0.95	-	1	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7617635	7617969	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7617970	7618079	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7618080	7619128	0.7	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7618080	7619128	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	intron	7619129	7619217	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	CDS	7619218	7619247	0.57	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	exon	7619218	7619247	.	-	.	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
Phchi.S1	AUGUSTUS	start_codon	7619245	7619247	.	-	0	transcript_id "Phchi.S1G122500.t1"; gene_id "Phchi.S1G122500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9598.t1 is derived from g6774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42880449	42881349	.	-	.	Phchi.S1G675700
Phchi.S1	AUGUSTUS	transcript	42880449	42881349	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	stop_codon	42880446	42880448	.	-	0	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	CDS	42880449	42880457	1	-	0	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	exon	42880449	42880457	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	intron	42880458	42880591	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	CDS	42880592	42880633	1	-	0	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	exon	42880592	42880633	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	intron	42880634	42880825	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	CDS	42880826	42880862	1	-	1	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	exon	42880826	42880862	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	intron	42880863	42880954	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	CDS	42880955	42881015	0.98	-	2	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	exon	42880955	42881015	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	intron	42881016	42881291	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	CDS	42881292	42881349	1	-	0	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	exon	42881292	42881349	.	-	.	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
Phchi.S1	AUGUSTUS	start_codon	42881347	42881349	.	-	0	transcript_id "Phchi.S1G675700.t1"; gene_id "Phchi.S1G675700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11581.t1 is derived from g15632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7191863	7193605	.	-	.	Phchi.S4G116300
Phchi.S4	AUGUSTUS	transcript	7191863	7193605	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	stop_codon	7191860	7191862	.	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	CDS	7191863	7192042	0.36	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	exon	7191863	7192042	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	intron	7192043	7192155	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	CDS	7192156	7193217	0.5	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	exon	7192156	7193217	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	intron	7193218	7193308	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	CDS	7193309	7193407	1	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	exon	7193309	7193407	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	intron	7193408	7193493	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	CDS	7193494	7193511	0.99	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	exon	7193494	7193511	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	intron	7193512	7193602	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	CDS	7193603	7193605	0.97	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	exon	7193603	7193605	.	-	.	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
Phchi.S4	AUGUSTUS	start_codon	7193603	7193605	.	-	0	transcript_id "Phchi.S4G116300.t1"; gene_id "Phchi.S4G116300"
# This transcript jg14447.t2 is derived from g12915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14448.t1 is derived from g12916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12885554	12886845	.	+	.	Phchi.S3G176700
Phchi.S3	AUGUSTUS	transcript	12885554	12886845	.	+	.	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	start_codon	12885554	12885556	.	+	0	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	CDS	12885554	12886695	0.53	+	0	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	exon	12885554	12886695	.	+	.	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	intron	12886696	12886817	.	+	.	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	CDS	12886818	12886845	0.64	+	1	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	exon	12886818	12886845	.	+	.	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
Phchi.S3	AUGUSTUS	stop_codon	12886846	12886848	.	+	0	transcript_id "Phchi.S3G176700.t1"; gene_id "Phchi.S3G176700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9456.t1 is derived from g6632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41558945	41561341	.	-	.	Phchi.S1G661500
Phchi.S1	AUGUSTUS	transcript	41558945	41561341	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	stop_codon	41558942	41558944	.	-	0	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	CDS	41558945	41559592	0.97	-	0	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	exon	41558945	41559592	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	intron	41559593	41559698	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	CDS	41559699	41560718	0.91	-	0	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	exon	41559699	41560718	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	intron	41560719	41560802	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	CDS	41560803	41560946	0.86	-	0	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	exon	41560803	41560946	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	intron	41560947	41561320	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	CDS	41561321	41561341	0.59	-	0	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	exon	41561321	41561341	.	-	.	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
Phchi.S1	AUGUSTUS	start_codon	41561339	41561341	.	-	0	transcript_id "Phchi.S1G661500.t1"; gene_id "Phchi.S1G661500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8038.t1 is derived from g5213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32615657	32624270	.	-	.	Phchi.S1G519700
Phchi.S1	AUGUSTUS	transcript	32615657	32624270	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	stop_codon	32615654	32615656	.	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32615657	32616025	0.88	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32615657	32616025	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32616026	32616135	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32616136	32616192	1	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32616136	32616192	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32616193	32616324	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32616325	32617421	0.28	-	2	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32616325	32617421	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32617422	32617527	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32617528	32618014	0.61	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32617528	32618014	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32618015	32618136	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32618137	32618643	1	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32618137	32618643	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32618644	32618739	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32618740	32619027	0.93	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32618740	32619027	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32619028	32619319	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32619320	32619412	0.38	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32619320	32619412	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32619413	32619571	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32619572	32619736	1	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32619572	32619736	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32619737	32619915	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32619916	32620144	1	-	1	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32619916	32620144	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32620145	32620299	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32620300	32620453	0.58	-	2	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32620300	32620453	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32620454	32620698	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32620699	32620845	0.32	-	2	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32620699	32620845	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32620846	32621085	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32621086	32621268	0.78	-	2	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32621086	32621268	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32621269	32621409	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32621410	32622590	0.26	-	1	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32621410	32622590	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32622591	32622679	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32622680	32622971	0.34	-	2	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32622680	32622971	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32622972	32623136	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32623137	32623844	0.71	-	2	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32623137	32623844	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	intron	32623845	32623933	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	CDS	32623934	32624270	0.79	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	exon	32623934	32624270	.	-	.	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
Phchi.S1	AUGUSTUS	start_codon	32624268	32624270	.	-	0	transcript_id "Phchi.S1G519700.t1"; gene_id "Phchi.S1G519700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9200.t1 is derived from g6375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40338019	40340677	.	+	.	Phchi.S1G635900
Phchi.S1	AUGUSTUS	transcript	40338019	40340677	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	start_codon	40338019	40338021	.	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40338019	40338032	0.98	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40338019	40338032	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40338033	40338339	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40338340	40338412	1	+	1	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40338340	40338412	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40338413	40338771	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40338772	40338819	1	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40338772	40338819	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40338820	40338951	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40338952	40338999	1	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40338952	40338999	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40339000	40339363	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40339364	40339435	1	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40339364	40339435	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40339436	40339523	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40339524	40339679	1	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40339524	40339679	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40339680	40339829	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40339830	40339933	1	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40339830	40339933	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40339934	40340013	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40340014	40340039	1	+	1	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40340014	40340039	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40340040	40340091	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40340092	40340108	1	+	2	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40340092	40340108	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	intron	40340109	40340515	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	CDS	40340516	40340677	0.97	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	exon	40340516	40340677	.	+	.	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
Phchi.S1	AUGUSTUS	stop_codon	40340678	40340680	.	+	0	transcript_id "Phchi.S1G635900.t1"; gene_id "Phchi.S1G635900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1134.t1 is derived from g10917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7877134	7878881	.	+	.	Phchi.S6G109300
Phchi.S6	AUGUSTUS	transcript	7877134	7878881	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	start_codon	7877134	7877136	.	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	CDS	7877134	7877376	0.42	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	exon	7877134	7877376	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	intron	7877377	7877485	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	CDS	7877486	7877596	1	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	exon	7877486	7877596	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	intron	7877597	7877839	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	CDS	7877840	7878215	0.6	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	exon	7877840	7878215	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	intron	7878216	7878328	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	CDS	7878329	7878447	0.82	+	2	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	exon	7878329	7878447	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	intron	7878448	7878583	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	CDS	7878584	7878634	0.78	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	exon	7878584	7878634	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	intron	7878635	7878713	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	CDS	7878714	7878881	0.75	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	exon	7878714	7878881	.	+	.	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
Phchi.S6	AUGUSTUS	stop_codon	7878882	7878884	.	+	0	transcript_id "Phchi.S6G109300.t1"; gene_id "Phchi.S6G109300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10082.t1 is derived from g7258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45656883	45658736	.	-	.	Phchi.S1G724100
Phchi.S1	AUGUSTUS	transcript	45656883	45658736	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	stop_codon	45656880	45656882	.	-	0	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45656883	45657003	0.58	-	1	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45656883	45657003	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	intron	45657004	45657150	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45657151	45657199	0.75	-	2	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45657151	45657199	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	intron	45657200	45657337	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45657338	45657438	1	-	1	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45657338	45657438	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	intron	45657439	45657577	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45657578	45657628	0.76	-	1	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45657578	45657628	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	intron	45657629	45657817	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45657818	45657884	0.74	-	2	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45657818	45657884	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	intron	45657885	45658039	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45658040	45658148	0.24	-	0	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45658040	45658148	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	intron	45658149	45658271	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	CDS	45658272	45658736	0.41	-	0	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	exon	45658272	45658736	.	-	.	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
Phchi.S1	AUGUSTUS	start_codon	45658734	45658736	.	-	0	transcript_id "Phchi.S1G724100.t1"; gene_id "Phchi.S1G724100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13567.t1 is derived from g12034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7530687	7531607	.	-	.	Phchi.S3G088600
Phchi.S3	AUGUSTUS	transcript	7530687	7531607	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	stop_codon	7530684	7530686	.	-	0	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	CDS	7530687	7530792	1	-	1	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	exon	7530687	7530792	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	intron	7530793	7530866	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	CDS	7530867	7530985	1	-	0	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	exon	7530867	7530985	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	intron	7530986	7531085	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	CDS	7531086	7531207	1	-	2	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	exon	7531086	7531207	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	intron	7531208	7531289	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	CDS	7531290	7531498	1	-	1	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	exon	7531290	7531498	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	intron	7531499	7531590	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	CDS	7531591	7531607	0.65	-	0	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	exon	7531591	7531607	.	-	.	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
Phchi.S3	AUGUSTUS	start_codon	7531605	7531607	.	-	0	transcript_id "Phchi.S3G088600.t1"; gene_id "Phchi.S3G088600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6760.t1 is derived from g3932.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24917253	24918613	.	+	.	Phchi.S1G391900
Phchi.S1	AUGUSTUS	transcript	24917253	24918613	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	start_codon	24917253	24917255	.	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917253	24917307	1	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917253	24917307	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24917308	24917403	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917404	24917528	1	+	2	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917404	24917528	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24917529	24917619	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917620	24917847	1	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917620	24917847	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24917848	24917931	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917932	24918018	1	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917932	24918018	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24918019	24918173	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24918174	24918263	1	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24918174	24918263	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24918264	24918338	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24918339	24918422	1	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24918339	24918422	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24918423	24918496	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24918497	24918613	1	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24918497	24918613	.	+	.	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	stop_codon	24918614	24918616	.	+	0	transcript_id "Phchi.S1G391900.t1"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	transcript	24917253	24918613	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	start_codon	24917253	24917255	.	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917253	24917307	1	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917253	24917307	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24917308	24917403	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917404	24917528	1	+	2	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917404	24917528	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24917529	24917616	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917617	24917847	0.99	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917617	24917847	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24917848	24917931	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24917932	24918018	1	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24917932	24918018	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24918019	24918173	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24918174	24918263	1	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24918174	24918263	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24918264	24918338	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24918339	24918422	1	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24918339	24918422	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	intron	24918423	24918496	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	CDS	24918497	24918613	1	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	exon	24918497	24918613	.	+	.	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
Phchi.S1	AUGUSTUS	stop_codon	24918614	24918616	.	+	0	transcript_id "Phchi.S1G391900.t2"; gene_id "Phchi.S1G391900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4119.t1 is derived from g1288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8356167	8357038	.	+	.	Phchi.S1G127800
Phchi.S1	AUGUSTUS	transcript	8356167	8357038	.	+	.	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	start_codon	8356167	8356169	.	+	0	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	CDS	8356167	8356623	0.66	+	0	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	exon	8356167	8356623	.	+	.	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	intron	8356624	8356742	.	+	.	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	CDS	8356743	8357038	0.8	+	2	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	exon	8356743	8357038	.	+	.	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
Phchi.S1	AUGUSTUS	stop_codon	8357039	8357041	.	+	0	transcript_id "Phchi.S1G127800.t1"; gene_id "Phchi.S1G127800"
# This transcript jg1476.t2 is derived from g8395.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1477.t1 is derived from g8396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1116217	1116890	.	+	.	Phchi.S5G008600
Phchi.S5	AUGUSTUS	transcript	1116217	1116890	.	+	.	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	start_codon	1116217	1116219	.	+	0	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	CDS	1116217	1116295	1	+	0	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	exon	1116217	1116295	.	+	.	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	intron	1116296	1116434	.	+	.	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	CDS	1116435	1116536	1	+	2	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	exon	1116435	1116536	.	+	.	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	intron	1116537	1116744	.	+	.	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	CDS	1116745	1116890	0.62	+	2	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	exon	1116745	1116890	.	+	.	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
Phchi.S5	AUGUSTUS	stop_codon	1116891	1116893	.	+	0	transcript_id "Phchi.S5G008600.t1"; gene_id "Phchi.S5G008600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2463.t1 is derived from g9383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6781328	6784051	.	-	.	Phchi.S5G107200
Phchi.S5	AUGUSTUS	transcript	6781328	6784051	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	stop_codon	6781325	6781327	.	-	0	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6781328	6782168	0.97	-	1	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6781328	6782168	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6782169	6782255	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6782256	6782469	1	-	2	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6782256	6782469	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6782470	6782591	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6782592	6782924	1	-	2	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6782592	6782924	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6782925	6783012	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6783013	6783087	1	-	2	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6783013	6783087	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6783088	6783171	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6783172	6783368	0.74	-	1	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6783172	6783368	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6783369	6783466	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6783467	6783611	0.33	-	2	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6783467	6783611	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6783612	6783689	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6783690	6783773	0.4	-	2	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6783690	6783773	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	intron	6783774	6783990	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	CDS	6783991	6784051	0.39	-	0	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	exon	6783991	6784051	.	-	.	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
Phchi.S5	AUGUSTUS	start_codon	6784049	6784051	.	-	0	transcript_id "Phchi.S5G107200.t1"; gene_id "Phchi.S5G107200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3993.t1 is derived from g1162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6895513	6896781	.	-	.	Phchi.S1G115200
Phchi.S1	AUGUSTUS	transcript	6895513	6896781	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	stop_codon	6895510	6895512	.	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6895513	6895569	1	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6895513	6895569	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	intron	6895570	6895662	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6895663	6895768	1	-	1	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6895663	6895768	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	intron	6895769	6895854	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6895855	6895943	1	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6895855	6895943	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	intron	6895944	6896023	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6896024	6896152	1	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6896024	6896152	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	intron	6896153	6896277	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6896278	6896378	1	-	2	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6896278	6896378	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	intron	6896379	6896454	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6896455	6896662	1	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6896455	6896662	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	intron	6896663	6896748	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	CDS	6896749	6896781	1	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	exon	6896749	6896781	.	-	.	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
Phchi.S1	AUGUSTUS	start_codon	6896779	6896781	.	-	0	transcript_id "Phchi.S1G115200.t1"; gene_id "Phchi.S1G115200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1953.t1 is derived from g8873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4003052	4005170	.	+	.	Phchi.S5G056200
Phchi.S5	AUGUSTUS	transcript	4003052	4005170	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	start_codon	4003052	4003054	.	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003052	4003117	0.92	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003052	4003117	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003118	4003212	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003213	4003222	0.99	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003213	4003222	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003223	4003305	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003306	4003398	0.97	+	2	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003306	4003398	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003399	4003506	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003507	4003599	0.98	+	2	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003507	4003599	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003600	4003713	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003714	4003784	0.93	+	2	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003714	4003784	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003785	4003889	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003890	4003958	0.97	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003890	4003958	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003959	4004601	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4004602	4004800	0.99	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4004602	4004800	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4004801	4004960	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4004961	4005007	0.75	+	2	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4004961	4005007	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4005008	4005107	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4005108	4005170	0.75	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4005108	4005170	.	+	.	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	stop_codon	4005171	4005173	.	+	0	transcript_id "Phchi.S5G056200.t1"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	transcript	4003052	4005170	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	start_codon	4003052	4003054	.	+	0	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003052	4003117	0.94	+	0	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003052	4003117	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003118	4003212	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003213	4003222	0.99	+	0	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003213	4003222	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003223	4003305	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003306	4003398	0.99	+	2	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003306	4003398	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003399	4003506	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003507	4003599	1	+	2	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003507	4003599	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003600	4003713	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003714	4003784	0.82	+	2	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003714	4003784	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003785	4003889	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4003890	4003958	0.96	+	0	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4003890	4003958	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4003959	4004601	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4004602	4004800	0.94	+	0	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4004602	4004800	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4004801	4004912	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4004913	4004960	0.45	+	2	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4004913	4004960	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	intron	4004961	4005114	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	CDS	4005115	4005170	0.65	+	2	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	exon	4005115	4005170	.	+	.	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
Phchi.S5	AUGUSTUS	stop_codon	4005171	4005173	.	+	0	transcript_id "Phchi.S5G056200.t2"; gene_id "Phchi.S5G056200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15152.t1 is derived from g13620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17280242	17280942	.	-	.	Phchi.S3G247100
Phchi.S3	AUGUSTUS	transcript	17280242	17280942	.	-	.	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	stop_codon	17280239	17280241	.	-	0	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	CDS	17280242	17280441	1	-	2	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	exon	17280242	17280441	.	-	.	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	intron	17280442	17280548	.	-	.	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	CDS	17280549	17280942	0.96	-	0	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	exon	17280549	17280942	.	-	.	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
Phchi.S3	AUGUSTUS	start_codon	17280940	17280942	.	-	0	transcript_id "Phchi.S3G247100.t1"; gene_id "Phchi.S3G247100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5007.t1 is derived from g2177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14005605	14008221	.	-	.	Phchi.S1G216600
Phchi.S1	AUGUSTUS	transcript	14005605	14008221	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	stop_codon	14005602	14005604	.	-	0	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14005605	14005712	1	-	0	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14005605	14005712	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14005713	14005790	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14005791	14006008	1	-	2	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14005791	14006008	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14006009	14006103	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14006104	14006247	1	-	2	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14006104	14006247	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14006248	14006344	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14006345	14006441	1	-	0	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14006345	14006441	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14006442	14006569	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14006570	14006664	1	-	2	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14006570	14006664	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14006665	14006739	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14006740	14006831	1	-	1	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14006740	14006831	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14006832	14006976	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14006977	14007122	1	-	0	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14006977	14007122	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14007123	14007317	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14007318	14007417	1	-	1	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14007318	14007417	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14007418	14007558	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14007559	14007663	1	-	1	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14007559	14007663	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14007664	14007849	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14007850	14007886	1	-	2	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14007850	14007886	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	intron	14007887	14008073	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	CDS	14008074	14008221	0.98	-	0	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	exon	14008074	14008221	.	-	.	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
Phchi.S1	AUGUSTUS	start_codon	14008219	14008221	.	-	0	transcript_id "Phchi.S1G216600.t1"; gene_id "Phchi.S1G216600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6903.t1 is derived from g4075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25907182	25908475	.	-	.	Phchi.S1G406200
Phchi.S1	AUGUSTUS	transcript	25907182	25908475	.	-	.	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	stop_codon	25907179	25907181	.	-	0	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	CDS	25907182	25907418	0.28	-	0	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	exon	25907182	25907418	.	-	.	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	intron	25907419	25907553	.	-	.	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	CDS	25907554	25907649	0.28	-	0	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	exon	25907554	25907649	.	-	.	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	intron	25907650	25907986	.	-	.	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	CDS	25907987	25908475	0.25	-	0	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	exon	25907987	25908475	.	-	.	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
Phchi.S1	AUGUSTUS	start_codon	25908473	25908475	.	-	0	transcript_id "Phchi.S1G406200.t1"; gene_id "Phchi.S1G406200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5103.t1 is derived from g2273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14757353	14758316	.	-	.	Phchi.S1G226200
Phchi.S1	AUGUSTUS	transcript	14757353	14758316	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	stop_codon	14757350	14757352	.	-	0	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	CDS	14757353	14757399	0.99	-	2	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	exon	14757353	14757399	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	intron	14757400	14757561	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	CDS	14757562	14757662	1	-	1	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	exon	14757562	14757662	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	intron	14757663	14757817	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	CDS	14757818	14757898	0.75	-	1	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	exon	14757818	14757898	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	intron	14757899	14758251	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	CDS	14758252	14758316	0.8	-	0	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	exon	14758252	14758316	.	-	.	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
Phchi.S1	AUGUSTUS	start_codon	14758314	14758316	.	-	0	transcript_id "Phchi.S1G226200.t1"; gene_id "Phchi.S1G226200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7595.t1 is derived from g4769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30191465	30194048	.	-	.	Phchi.S1G475400
Phchi.S1	AUGUSTUS	transcript	30191465	30194048	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	stop_codon	30191462	30191464	.	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30191465	30192094	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30191465	30192094	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30192095	30192175	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30192176	30192256	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30192176	30192256	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30192257	30192351	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30192352	30192411	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30192352	30192411	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30192412	30192526	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30192527	30192751	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30192527	30192751	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30192752	30192863	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30192864	30192949	1	-	2	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30192864	30192949	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30192950	30193042	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30193043	30193058	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30193043	30193058	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30193059	30193141	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30193142	30193259	1	-	1	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30193142	30193259	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30193260	30193351	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30193352	30193731	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30193352	30193731	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	intron	30193732	30193817	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	CDS	30193818	30194048	1	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	exon	30193818	30194048	.	-	.	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
Phchi.S1	AUGUSTUS	start_codon	30194046	30194048	.	-	0	transcript_id "Phchi.S1G475400.t1"; gene_id "Phchi.S1G475400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5392.t1 is derived from g2562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16647536	16649509	.	-	.	Phchi.S1G255100
Phchi.S1	AUGUSTUS	transcript	16647536	16649509	.	-	.	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	stop_codon	16647533	16647535	.	-	0	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	CDS	16647536	16647978	0.5	-	2	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	exon	16647536	16647978	.	-	.	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	intron	16647979	16648071	.	-	.	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	CDS	16648072	16649509	0.82	-	0	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	exon	16648072	16649509	.	-	.	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
Phchi.S1	AUGUSTUS	start_codon	16649507	16649509	.	-	0	transcript_id "Phchi.S1G255100.t1"; gene_id "Phchi.S1G255100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12188.t1 is derived from g7864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6315775	6318747	.	-	.	Phchi.S2G026800
Phchi.S2	AUGUSTUS	transcript	6315775	6318747	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	stop_codon	6315772	6315774	.	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6315775	6315895	1	-	1	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6315775	6315895	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6315896	6316054	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316055	6316164	1	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316055	6316164	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316165	6316239	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316240	6316326	0.82	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316240	6316326	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316327	6316404	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316405	6316522	0.93	-	1	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316405	6316522	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316523	6316641	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316642	6316697	0.84	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316642	6316697	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316698	6316804	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316805	6316939	0.97	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316805	6316939	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316940	6317015	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317016	6317063	1	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317016	6317063	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317064	6317154	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317155	6317220	0.99	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317155	6317220	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317221	6317332	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317333	6317386	0.99	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317333	6317386	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317387	6317535	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317536	6317637	0.99	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317536	6317637	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317638	6317742	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317743	6317814	0.97	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317743	6317814	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317815	6317908	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317909	6318030	1	-	2	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317909	6318030	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6318031	6318128	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6318129	6318235	1	-	1	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6318129	6318235	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6318236	6318430	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6318431	6318747	0.59	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6318431	6318747	.	-	.	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	start_codon	6318745	6318747	.	-	0	transcript_id "Phchi.S2G026800.t1"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	transcript	6315775	6318747	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	stop_codon	6315772	6315774	.	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6315775	6315895	1	-	1	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6315775	6315895	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6315896	6316054	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316055	6316164	1	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316055	6316164	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316165	6316239	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316240	6316326	0.75	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316240	6316326	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316327	6316404	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316405	6316522	0.91	-	1	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316405	6316522	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316523	6316641	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316642	6316697	0.87	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316642	6316697	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316698	6316804	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6316805	6316939	0.99	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6316805	6316939	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6316940	6317015	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317016	6317063	1	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317016	6317063	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317064	6317154	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317155	6317220	1	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317155	6317220	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317221	6317361	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317362	6317394	1	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317362	6317394	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317395	6317535	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317536	6317637	0.97	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317536	6317637	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317638	6317742	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317743	6317814	0.94	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317743	6317814	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6317815	6317908	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6317909	6318030	1	-	2	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6317909	6318030	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6318031	6318128	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6318129	6318235	1	-	1	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6318129	6318235	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	intron	6318236	6318430	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	CDS	6318431	6318747	0.4	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	exon	6318431	6318747	.	-	.	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
Phchi.S2	AUGUSTUS	start_codon	6318745	6318747	.	-	0	transcript_id "Phchi.S2G026800.t2"; gene_id "Phchi.S2G026800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg67.t1 is derived from g9849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	333361	334199	.	+	.	Phchi.S6G002600
Phchi.S6	AUGUSTUS	transcript	333361	334199	.	+	.	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	start_codon	333361	333363	.	+	0	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	CDS	333361	333448	0.9	+	0	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	exon	333361	333448	.	+	.	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	intron	333449	333540	.	+	.	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	CDS	333541	334199	0.93	+	2	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	exon	333541	334199	.	+	.	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
Phchi.S6	AUGUSTUS	stop_codon	334200	334202	.	+	0	transcript_id "Phchi.S6G002600.t1"; gene_id "Phchi.S6G002600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8298.t1 is derived from g5473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35144398	35145454	.	-	.	Phchi.S1G545700
Phchi.S1	AUGUSTUS	transcript	35144398	35145454	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	stop_codon	35144395	35144397	.	-	0	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	CDS	35144398	35144495	1	-	2	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	exon	35144398	35144495	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	intron	35144496	35144590	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	CDS	35144591	35144737	1	-	2	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	exon	35144591	35144737	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	intron	35144738	35144828	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	CDS	35144829	35144889	1	-	0	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	exon	35144829	35144889	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	intron	35144890	35144976	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	CDS	35144977	35145041	1	-	2	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	exon	35144977	35145041	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	intron	35145042	35145189	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	CDS	35145190	35145454	0.6	-	0	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	exon	35145190	35145454	.	-	.	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
Phchi.S1	AUGUSTUS	start_codon	35145452	35145454	.	-	0	transcript_id "Phchi.S1G545700.t1"; gene_id "Phchi.S1G545700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1300.t1 is derived from g11083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8900721	8901949	.	-	.	Phchi.S6G125900
Phchi.S6	AUGUSTUS	transcript	8900721	8901949	.	-	.	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	stop_codon	8900718	8900720	.	-	0	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	CDS	8900721	8900749	0.4	-	2	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	exon	8900721	8900749	.	-	.	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	intron	8900750	8900846	.	-	.	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	CDS	8900847	8901741	0.37	-	0	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	exon	8900847	8901741	.	-	.	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	intron	8901742	8901829	.	-	.	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	CDS	8901830	8901949	0.74	-	0	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	exon	8901830	8901949	.	-	.	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
Phchi.S6	AUGUSTUS	start_codon	8901947	8901949	.	-	0	transcript_id "Phchi.S6G125900.t1"; gene_id "Phchi.S6G125900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10940.t1 is derived from g14990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3192008	3192593	.	-	.	Phchi.S4G052200
Phchi.S4	AUGUSTUS	transcript	3192008	3192593	.	-	.	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	stop_codon	3192005	3192007	.	-	0	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	CDS	3192008	3192144	0.79	-	2	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	exon	3192008	3192144	.	-	.	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	intron	3192145	3192233	.	-	.	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	CDS	3192234	3192333	1	-	0	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	exon	3192234	3192333	.	-	.	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	intron	3192334	3192419	.	-	.	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	CDS	3192420	3192593	0.96	-	0	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	exon	3192420	3192593	.	-	.	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
Phchi.S4	AUGUSTUS	start_codon	3192591	3192593	.	-	0	transcript_id "Phchi.S4G052200.t1"; gene_id "Phchi.S4G052200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8380.t1 is derived from g5555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35597553	35598374	.	+	.	Phchi.S1G553900
Phchi.S1	AUGUSTUS	transcript	35597553	35598374	.	+	.	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	start_codon	35597553	35597555	.	+	0	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	CDS	35597553	35597782	0.86	+	0	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	exon	35597553	35597782	.	+	.	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	intron	35597783	35597902	.	+	.	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	CDS	35597903	35598374	0.95	+	1	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	exon	35597903	35598374	.	+	.	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
Phchi.S1	AUGUSTUS	stop_codon	35598375	35598377	.	+	0	transcript_id "Phchi.S1G553900.t1"; gene_id "Phchi.S1G553900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4047.t1 is derived from g1216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7495909	7496405	.	+	.	Phchi.S1G120600
Phchi.S1	AUGUSTUS	transcript	7495909	7496405	.	+	.	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	start_codon	7495909	7495911	.	+	0	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	CDS	7495909	7496052	0.61	+	0	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	exon	7495909	7496052	.	+	.	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	intron	7496053	7496183	.	+	.	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	CDS	7496184	7496405	0.43	+	0	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	exon	7496184	7496405	.	+	.	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
Phchi.S1	AUGUSTUS	stop_codon	7496406	7496408	.	+	0	transcript_id "Phchi.S1G120600.t1"; gene_id "Phchi.S1G120600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg643.t1 is derived from g10425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4562768	4565829	.	-	.	Phchi.S6G060200
Phchi.S6	AUGUSTUS	transcript	4562768	4565829	.	-	.	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	stop_codon	4562765	4562767	.	-	0	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	CDS	4562768	4564214	0.54	-	1	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	exon	4562768	4564214	.	-	.	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	intron	4564215	4564303	.	-	.	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	CDS	4564304	4565399	0.5	-	2	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	exon	4564304	4565399	.	-	.	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	intron	4565400	4565666	.	-	.	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	CDS	4565667	4565829	0.95	-	0	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	exon	4565667	4565829	.	-	.	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
Phchi.S6	AUGUSTUS	start_codon	4565827	4565829	.	-	0	transcript_id "Phchi.S6G060200.t1"; gene_id "Phchi.S6G060200"
# This transcript jg10770.t2 is derived from g14820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10771.t1 is derived from g14821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2025385	2026657	.	-	.	Phchi.S4G035300
Phchi.S4	AUGUSTUS	transcript	2025385	2026657	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	stop_codon	2025382	2025384	.	-	0	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	CDS	2025385	2025597	0.98	-	0	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	exon	2025385	2025597	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	intron	2025598	2025682	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	CDS	2025683	2025785	1	-	1	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	exon	2025683	2025785	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	intron	2025786	2025876	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	CDS	2025877	2025956	1	-	0	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	exon	2025877	2025956	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	intron	2025957	2026076	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	CDS	2026077	2026134	1	-	1	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	exon	2026077	2026134	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	intron	2026135	2026241	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	CDS	2026242	2026318	0.45	-	0	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	exon	2026242	2026318	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	intron	2026319	2026465	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	CDS	2026466	2026657	1	-	0	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	exon	2026466	2026657	.	-	.	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
Phchi.S4	AUGUSTUS	start_codon	2026655	2026657	.	-	0	transcript_id "Phchi.S4G035300.t1"; gene_id "Phchi.S4G035300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9479.t1 is derived from g6655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41951436	41952045	.	-	.	Phchi.S1G663800
Phchi.S1	AUGUSTUS	transcript	41951436	41952045	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	stop_codon	41951433	41951435	.	-	0	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	CDS	41951436	41951473	0.57	-	2	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	exon	41951436	41951473	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	intron	41951474	41951585	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	CDS	41951586	41951661	0.56	-	0	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	exon	41951586	41951661	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	intron	41951662	41951764	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	CDS	41951765	41951905	0.96	-	0	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	exon	41951765	41951905	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	intron	41951906	41952015	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	CDS	41952016	41952045	0.57	-	0	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	exon	41952016	41952045	.	-	.	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
Phchi.S1	AUGUSTUS	start_codon	41952043	41952045	.	-	0	transcript_id "Phchi.S1G663800.t1"; gene_id "Phchi.S1G663800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9380.t1 is derived from g6556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41248663	41251253	.	+	.	Phchi.S1G653900
Phchi.S1	AUGUSTUS	transcript	41248663	41251253	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	start_codon	41248663	41248665	.	+	0	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	CDS	41248663	41248788	0.67	+	0	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	exon	41248663	41248788	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	intron	41248789	41248874	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	CDS	41248875	41249041	0.52	+	0	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	exon	41248875	41249041	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	intron	41249042	41249154	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	CDS	41249155	41250052	0.55	+	1	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	exon	41249155	41250052	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	intron	41250053	41250189	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	CDS	41250190	41250449	1	+	0	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	exon	41250190	41250449	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	intron	41250450	41250543	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	CDS	41250544	41250662	1	+	1	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	exon	41250544	41250662	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	intron	41250663	41250747	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	CDS	41250748	41251253	0.99	+	2	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	exon	41250748	41251253	.	+	.	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
Phchi.S1	AUGUSTUS	stop_codon	41251254	41251256	.	+	0	transcript_id "Phchi.S1G653900.t1"; gene_id "Phchi.S1G653900"
# This transcript jg11785.t2 is derived from g15837.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11786.t1 is derived from g15838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8152509	8152905	.	-	.	Phchi.S4G136800
Phchi.S4	AUGUSTUS	transcript	8152509	8152905	.	-	.	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	stop_codon	8152506	8152508	.	-	0	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	CDS	8152509	8152663	0.81	-	2	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	exon	8152509	8152663	.	-	.	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	intron	8152664	8152832	.	-	.	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	CDS	8152833	8152905	0.42	-	0	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	exon	8152833	8152905	.	-	.	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
Phchi.S4	AUGUSTUS	start_codon	8152903	8152905	.	-	0	transcript_id "Phchi.S4G136800.t1"; gene_id "Phchi.S4G136800"
# This transcript jg8470.t2 is derived from g5645.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8471.t1 is derived from g5646.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36106488	36107523	.	-	.	Phchi.S1G563000
Phchi.S1	AUGUSTUS	transcript	36106488	36107523	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	stop_codon	36106485	36106487	.	-	0	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36106488	36106580	0.66	-	0	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36106488	36106580	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36106581	36106667	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36106668	36106899	1	-	1	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36106668	36106899	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36106900	36106990	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36106991	36107179	0.96	-	1	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36106991	36107179	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36107180	36107283	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36107284	36107384	0.99	-	0	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36107284	36107384	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36107385	36107508	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36107509	36107523	0.68	-	0	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36107509	36107523	.	-	.	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	start_codon	36107521	36107523	.	-	0	transcript_id "Phchi.S1G563000.t1"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	transcript	36106488	36107523	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	stop_codon	36106485	36106487	.	-	0	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36106488	36106580	0.66	-	0	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36106488	36106580	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36106581	36106667	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36106668	36106902	0.69	-	1	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36106668	36106902	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36106903	36106990	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36106991	36107179	0.97	-	1	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36106991	36107179	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36107180	36107283	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36107284	36107384	0.98	-	0	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36107284	36107384	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	intron	36107385	36107508	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	CDS	36107509	36107523	0.55	-	0	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	exon	36107509	36107523	.	-	.	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
Phchi.S1	AUGUSTUS	start_codon	36107521	36107523	.	-	0	transcript_id "Phchi.S1G563000.t2"; gene_id "Phchi.S1G563000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3530.t1 is derived from g699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4240014	4240352	.	-	.	Phchi.S1G068900
Phchi.S1	AUGUSTUS	transcript	4240014	4240352	.	-	.	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	stop_codon	4240011	4240013	.	-	0	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	CDS	4240014	4240109	1	-	0	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	exon	4240014	4240109	.	-	.	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	intron	4240110	4240190	.	-	.	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	CDS	4240191	4240352	0.88	-	0	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	exon	4240191	4240352	.	-	.	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
Phchi.S1	AUGUSTUS	start_codon	4240350	4240352	.	-	0	transcript_id "Phchi.S1G068900.t1"; gene_id "Phchi.S1G068900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14201.t1 is derived from g12668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11453848	11455375	.	+	.	Phchi.S3G152000
Phchi.S3	AUGUSTUS	transcript	11453848	11455375	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	start_codon	11453848	11453850	.	+	0	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11453848	11453861	0.45	+	0	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11453848	11453861	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11453862	11454061	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11454062	11454127	0.39	+	1	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11454062	11454127	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11454128	11454215	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11454216	11454294	0.39	+	1	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11454216	11454294	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11454295	11454391	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11454392	11454512	1	+	0	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11454392	11454512	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11454513	11454601	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11454602	11454698	1	+	2	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11454602	11454698	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11454699	11454831	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11454832	11454871	1	+	1	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11454832	11454871	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11454872	11454992	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11454993	11455076	1	+	0	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11454993	11455076	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	intron	11455077	11455213	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	CDS	11455214	11455375	0.99	+	0	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	exon	11455214	11455375	.	+	.	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
Phchi.S3	AUGUSTUS	stop_codon	11455376	11455378	.	+	0	transcript_id "Phchi.S3G152000.t1"; gene_id "Phchi.S3G152000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5020.t1 is derived from g2190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14089316	14089893	.	-	.	Phchi.S1G217900
Phchi.S1	AUGUSTUS	transcript	14089316	14089893	.	-	.	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	stop_codon	14089313	14089315	.	-	0	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	CDS	14089316	14089382	0.82	-	1	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	exon	14089316	14089382	.	-	.	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	intron	14089383	14089501	.	-	.	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	CDS	14089502	14089893	0.43	-	0	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	exon	14089502	14089893	.	-	.	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
Phchi.S1	AUGUSTUS	start_codon	14089891	14089893	.	-	0	transcript_id "Phchi.S1G217900.t1"; gene_id "Phchi.S1G217900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13338.t1 is derived from g11804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6147718	6150555	.	-	.	Phchi.S3G065700
Phchi.S3	AUGUSTUS	transcript	6147718	6150555	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	stop_codon	6147715	6147717	.	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6147718	6147762	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6147718	6147762	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6147763	6147847	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6147848	6147931	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6147848	6147931	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6147932	6148077	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6148078	6148182	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6148078	6148182	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6148183	6148321	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6148322	6148447	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6148322	6148447	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6148448	6148554	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6148555	6148626	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6148555	6148626	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6148627	6148726	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6148727	6148802	1	-	1	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6148727	6148802	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6148803	6148966	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6148967	6149008	1	-	1	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6148967	6149008	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6149009	6149125	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6149126	6149181	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6149126	6149181	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6149182	6149296	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6149297	6149410	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6149297	6149410	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6149411	6149483	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6149484	6149534	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6149484	6149534	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6149535	6149637	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6149638	6149760	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6149638	6149760	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6149761	6149840	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6149841	6149977	1	-	2	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6149841	6149977	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6149978	6150146	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6150147	6150257	1	-	2	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6150147	6150257	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	intron	6150258	6150392	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	CDS	6150393	6150555	1	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	exon	6150393	6150555	.	-	.	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
Phchi.S3	AUGUSTUS	start_codon	6150553	6150555	.	-	0	transcript_id "Phchi.S3G065700.t1"; gene_id "Phchi.S3G065700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8614.t1 is derived from g5789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36915376	36917666	.	-	.	Phchi.S1G577300
Phchi.S1	AUGUSTUS	transcript	36915376	36917666	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	stop_codon	36915373	36915375	.	-	0	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36915376	36915674	0.81	-	2	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36915376	36915674	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	intron	36915675	36915812	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36915813	36915978	1	-	0	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36915813	36915978	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	intron	36915979	36916098	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36916099	36916419	1	-	0	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36916099	36916419	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	intron	36916420	36916530	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36916531	36916777	0.3	-	1	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36916531	36916777	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	intron	36916778	36916931	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36916932	36917112	0.8	-	2	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36916932	36917112	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	intron	36917113	36917201	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36917202	36917475	1	-	0	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36917202	36917475	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	intron	36917476	36917555	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	CDS	36917556	36917666	1	-	0	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	exon	36917556	36917666	.	-	.	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
Phchi.S1	AUGUSTUS	start_codon	36917664	36917666	.	-	0	transcript_id "Phchi.S1G577300.t1"; gene_id "Phchi.S1G577300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1996.t1 is derived from g8916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4353227	4355728	.	+	.	Phchi.S5G060500
Phchi.S5	AUGUSTUS	transcript	4353227	4355728	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	start_codon	4353227	4353229	.	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4353227	4353589	0.94	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4353227	4353589	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4353590	4353738	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4353739	4353895	1	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4353739	4353895	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4353896	4354052	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354053	4354227	1	+	2	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354053	4354227	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354228	4354454	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354455	4354570	1	+	1	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354455	4354570	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354571	4354687	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354688	4354747	1	+	2	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354688	4354747	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354748	4354825	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354826	4354976	1	+	2	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354826	4354976	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354977	4355119	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355120	4355186	1	+	1	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355120	4355186	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4355187	4355269	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355270	4355341	1	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355270	4355341	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4355342	4355430	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355431	4355496	1	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355431	4355496	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4355497	4355578	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355579	4355728	0.96	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355579	4355728	.	+	.	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	stop_codon	4355729	4355731	.	+	0	transcript_id "Phchi.S5G060500.t1"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	transcript	4353227	4355728	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	start_codon	4353227	4353229	.	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4353227	4353589	0.95	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4353227	4353589	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4353590	4353738	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4353739	4353895	1	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4353739	4353895	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4353896	4354052	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354053	4354096	0.88	+	2	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354053	4354096	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354097	4354193	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354194	4354227	1	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354194	4354227	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354228	4354411	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354412	4354570	1	+	2	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354412	4354570	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354571	4354687	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354688	4354747	1	+	2	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354688	4354747	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354748	4354825	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4354826	4354976	1	+	2	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4354826	4354976	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4354977	4355119	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355120	4355186	1	+	1	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355120	4355186	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4355187	4355269	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355270	4355341	1	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355270	4355341	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4355342	4355430	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355431	4355496	1	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355431	4355496	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	intron	4355497	4355578	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	CDS	4355579	4355728	0.97	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	exon	4355579	4355728	.	+	.	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
Phchi.S5	AUGUSTUS	stop_codon	4355729	4355731	.	+	0	transcript_id "Phchi.S5G060500.t2"; gene_id "Phchi.S5G060500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8539.t1 is derived from g5714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36542234	36544026	.	+	.	Phchi.S1G569800
Phchi.S1	AUGUSTUS	transcript	36542234	36544026	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	start_codon	36542234	36542236	.	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36542234	36542336	0.97	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36542234	36542336	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36542337	36542484	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36542485	36542603	0.96	+	2	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36542485	36542603	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36542604	36542747	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36542748	36542798	0.63	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36542748	36542798	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36542799	36542895	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36542896	36542972	1	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36542896	36542972	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36542973	36543052	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36543053	36543140	1	+	1	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36543053	36543140	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36543141	36543236	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36543237	36543515	0.92	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36543237	36543515	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36543516	36543615	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36543616	36543864	1	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36543616	36543864	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	intron	36543865	36543951	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	CDS	36543952	36544026	1	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	exon	36543952	36544026	.	+	.	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
Phchi.S1	AUGUSTUS	stop_codon	36544027	36544029	.	+	0	transcript_id "Phchi.S1G569800.t1"; gene_id "Phchi.S1G569800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5924.t1 is derived from g3095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19886105	19887504	.	+	.	Phchi.S1G308300
Phchi.S1	AUGUSTUS	transcript	19886105	19887504	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	start_codon	19886105	19886107	.	+	0	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19886105	19886240	1	+	0	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19886105	19886240	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	intron	19886241	19886320	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19886321	19886459	1	+	2	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19886321	19886459	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	intron	19886460	19886631	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19886632	19886745	1	+	1	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19886632	19886745	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	intron	19886746	19886858	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19886859	19886984	1	+	1	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19886859	19886984	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	intron	19886985	19887072	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19887073	19887124	1	+	1	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19887073	19887124	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	intron	19887125	19887224	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19887225	19887406	1	+	0	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19887225	19887406	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	intron	19887407	19887497	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	CDS	19887498	19887504	1	+	1	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	exon	19887498	19887504	.	+	.	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
Phchi.S1	AUGUSTUS	stop_codon	19887505	19887507	.	+	0	transcript_id "Phchi.S1G308300.t1"; gene_id "Phchi.S1G308300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11514.t1 is derived from g15564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6855877	6857762	.	+	.	Phchi.S4G109600
Phchi.S4	AUGUSTUS	transcript	6855877	6857762	.	+	.	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	start_codon	6855877	6855879	.	+	0	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	CDS	6855877	6856200	0.67	+	0	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	exon	6855877	6856200	.	+	.	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	intron	6856201	6856316	.	+	.	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	CDS	6856317	6857762	0.98	+	0	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	exon	6856317	6857762	.	+	.	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
Phchi.S4	AUGUSTUS	stop_codon	6857763	6857765	.	+	0	transcript_id "Phchi.S4G109600.t1"; gene_id "Phchi.S4G109600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5643.t1 is derived from g2813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18028874	18030871	.	-	.	Phchi.S1G280200
Phchi.S1	AUGUSTUS	transcript	18028874	18030871	.	-	.	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	stop_codon	18028871	18028873	.	-	0	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	CDS	18028874	18030211	1	-	0	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	exon	18028874	18030211	.	-	.	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	intron	18030212	18030289	.	-	.	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	CDS	18030290	18030871	0.99	-	0	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	exon	18030290	18030871	.	-	.	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
Phchi.S1	AUGUSTUS	start_codon	18030869	18030871	.	-	0	transcript_id "Phchi.S1G280200.t1"; gene_id "Phchi.S1G280200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10156.t1 is derived from g7332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46020165	46024867	.	+	.	Phchi.S1G731500
Phchi.S1	AUGUSTUS	transcript	46020165	46024867	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	start_codon	46020165	46020167	.	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46020165	46020536	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46020165	46020536	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46020537	46020621	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46020622	46021320	0.97	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46020622	46021320	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46021321	46021407	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46021408	46021651	0.99	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46021408	46021651	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46021652	46021807	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46021808	46021949	1	+	2	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46021808	46021949	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46021950	46022036	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46022037	46022301	1	+	1	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46022037	46022301	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46022302	46022407	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46022408	46022617	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46022408	46022617	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46022618	46022847	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46022848	46023117	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46022848	46023117	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46023118	46023201	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46023202	46023273	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46023202	46023273	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46023274	46023350	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46023351	46023437	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46023351	46023437	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46023438	46023545	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46023546	46023668	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46023546	46023668	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46023669	46023782	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46023783	46023893	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46023783	46023893	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46023894	46023990	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46023991	46024029	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46023991	46024029	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46024030	46024131	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46024132	46024253	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46024132	46024253	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46024254	46024345	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46024346	46024490	1	+	1	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46024346	46024490	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46024491	46024573	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46024574	46024666	1	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46024574	46024666	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	intron	46024667	46024756	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	CDS	46024757	46024867	0.98	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	exon	46024757	46024867	.	+	.	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
Phchi.S1	AUGUSTUS	stop_codon	46024868	46024870	.	+	0	transcript_id "Phchi.S1G731500.t1"; gene_id "Phchi.S1G731500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8275.t1 is derived from g5450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35063168	35065423	.	+	.	Phchi.S1G543400
Phchi.S1	AUGUSTUS	transcript	35063168	35065423	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	start_codon	35063168	35063170	.	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35063168	35063275	0.97	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35063168	35063275	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35063276	35063446	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35063447	35063569	1	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35063447	35063569	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35063570	35063641	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35063642	35063728	1	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35063642	35063728	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35063729	35063897	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35063898	35064002	1	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35063898	35064002	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35064003	35064142	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35064143	35064304	1	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35064143	35064304	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35064305	35064450	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35064451	35064486	1	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35064451	35064486	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35064487	35064602	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35064603	35064671	0.88	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35064603	35064671	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35064672	35064793	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35064794	35065062	1	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35064794	35065062	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	intron	35065063	35065194	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	CDS	35065195	35065423	0.83	+	1	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	exon	35065195	35065423	.	+	.	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
Phchi.S1	AUGUSTUS	stop_codon	35065424	35065426	.	+	0	transcript_id "Phchi.S1G543400.t1"; gene_id "Phchi.S1G543400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2924.t1 is derived from g93.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	580646	582374	.	+	.	Phchi.S1G008300
Phchi.S1	AUGUSTUS	transcript	580646	582374	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	start_codon	580646	580648	.	+	0	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	580646	580817	1	+	0	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	580646	580817	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	580818	580896	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	580897	580946	1	+	2	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	580897	580946	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	580947	581034	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	581035	581104	1	+	0	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	581035	581104	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	581105	581182	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	581183	581288	1	+	2	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	581183	581288	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	581289	581508	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	581509	581575	1	+	1	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	581509	581575	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	581576	581658	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	581659	581734	1	+	0	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	581659	581734	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	581735	581864	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	581865	582208	1	+	2	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	581865	582208	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	intron	582209	582305	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	CDS	582306	582374	1	+	0	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	exon	582306	582374	.	+	.	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
Phchi.S1	AUGUSTUS	stop_codon	582375	582377	.	+	0	transcript_id "Phchi.S1G008300.t1"; gene_id "Phchi.S1G008300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6284.t1 is derived from g3456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22082438	22084512	.	+	.	Phchi.S1G344300
Phchi.S1	AUGUSTUS	transcript	22082438	22084512	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	start_codon	22082438	22082440	.	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22082438	22082546	0.54	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22082438	22082546	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22082547	22082704	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22082705	22082781	1	+	2	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22082705	22082781	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22082782	22082929	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22082930	22083130	1	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22082930	22083130	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22083131	22083218	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22083219	22083296	1	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22083219	22083296	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22083297	22083395	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22083396	22083523	1	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22083396	22083523	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22083524	22083674	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22083675	22083741	1	+	1	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22083675	22083741	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22083742	22083838	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22083839	22083948	1	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22083839	22083948	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22083949	22084111	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22084112	22084235	0.92	+	1	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22084112	22084235	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	intron	22084236	22084389	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	CDS	22084390	22084512	0.92	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	exon	22084390	22084512	.	+	.	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
Phchi.S1	AUGUSTUS	stop_codon	22084513	22084515	.	+	0	transcript_id "Phchi.S1G344300.t1"; gene_id "Phchi.S1G344300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5781.t1 is derived from g2951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18922387	18924897	.	+	.	Phchi.S1G294000
Phchi.S1	AUGUSTUS	transcript	18922387	18924897	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	start_codon	18922387	18922389	.	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18922387	18922534	0.84	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18922387	18922534	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18922535	18922699	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18922700	18923058	0.29	+	2	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18922700	18923058	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18923059	18923167	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18923168	18923347	1	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18923168	18923347	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18923348	18923476	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18923477	18923626	0.51	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18923477	18923626	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18923627	18923718	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18923719	18923898	1	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18923719	18923898	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18923899	18923989	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18923990	18924124	0.74	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18923990	18924124	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18924125	18924231	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18924232	18924348	1	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18924232	18924348	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18924349	18924451	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18924452	18924655	1	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18924452	18924655	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	intron	18924656	18924750	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	CDS	18924751	18924897	0.99	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	exon	18924751	18924897	.	+	.	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
Phchi.S1	AUGUSTUS	stop_codon	18924898	18924900	.	+	0	transcript_id "Phchi.S1G294000.t1"; gene_id "Phchi.S1G294000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3983.t1 is derived from g1152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6860450	6861832	.	-	.	Phchi.S1G114200
Phchi.S1	AUGUSTUS	transcript	6860450	6861832	.	-	.	transcript_id "Phchi.S1G114200.t1"; gene_id "Phchi.S1G114200"
Phchi.S1	AUGUSTUS	stop_codon	6860447	6860449	.	-	0	transcript_id "Phchi.S1G114200.t1"; gene_id "Phchi.S1G114200"
Phchi.S1	AUGUSTUS	CDS	6860450	6861832	0.96	-	0	transcript_id "Phchi.S1G114200.t1"; gene_id "Phchi.S1G114200"
Phchi.S1	AUGUSTUS	exon	6860450	6861832	.	-	.	transcript_id "Phchi.S1G114200.t1"; gene_id "Phchi.S1G114200"
Phchi.S1	AUGUSTUS	start_codon	6861830	6861832	.	-	0	transcript_id "Phchi.S1G114200.t1"; gene_id "Phchi.S1G114200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5012.t1 is derived from g2182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14028986	14030900	.	+	.	Phchi.S1G217100
Phchi.S1	AUGUSTUS	transcript	14028986	14030900	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	start_codon	14028986	14028988	.	+	0	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	CDS	14028986	14029525	1	+	0	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	exon	14028986	14029525	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	intron	14029526	14029808	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	CDS	14029809	14030055	1	+	0	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	exon	14029809	14030055	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	intron	14030056	14030213	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	CDS	14030214	14030578	0.88	+	2	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	exon	14030214	14030578	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	intron	14030579	14030669	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	CDS	14030670	14030724	0.88	+	0	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	exon	14030670	14030724	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	intron	14030725	14030850	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	CDS	14030851	14030900	0.88	+	2	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	exon	14030851	14030900	.	+	.	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
Phchi.S1	AUGUSTUS	stop_codon	14030901	14030903	.	+	0	transcript_id "Phchi.S1G217100.t1"; gene_id "Phchi.S1G217100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2942.t1 is derived from g111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	694570	695805	.	-	.	Phchi.S1G010100
Phchi.S1	AUGUSTUS	transcript	694570	695805	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	stop_codon	694567	694569	.	-	0	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	CDS	694570	694833	1	-	0	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	exon	694570	694833	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	intron	694834	694964	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	CDS	694965	695109	1	-	1	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	exon	694965	695109	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	intron	695110	695295	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	CDS	695296	695356	1	-	2	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	exon	695296	695356	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	intron	695357	695513	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	CDS	695514	695805	1	-	0	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	exon	695514	695805	.	-	.	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
Phchi.S1	AUGUSTUS	start_codon	695803	695805	.	-	0	transcript_id "Phchi.S1G010100.t1"; gene_id "Phchi.S1G010100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10467.t1 is derived from g14516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	533656	537024	.	-	.	Phchi.S4G004900
Phchi.S4	AUGUSTUS	transcript	533656	537024	.	-	.	transcript_id "Phchi.S4G004900.t1"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	stop_codon	533653	533655	.	-	0	transcript_id "Phchi.S4G004900.t1"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	CDS	533656	537024	0.77	-	0	transcript_id "Phchi.S4G004900.t1"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	exon	533656	537024	.	-	.	transcript_id "Phchi.S4G004900.t1"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	start_codon	537022	537024	.	-	0	transcript_id "Phchi.S4G004900.t1"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	transcript	533656	536193	.	-	.	transcript_id "Phchi.S4G004900.t2"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	stop_codon	533653	533655	.	-	0	transcript_id "Phchi.S4G004900.t2"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	CDS	533656	536193	0.52	-	0	transcript_id "Phchi.S4G004900.t2"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	exon	533656	536193	.	-	.	transcript_id "Phchi.S4G004900.t2"; gene_id "Phchi.S4G004900"
Phchi.S4	AUGUSTUS	start_codon	536191	536193	.	-	0	transcript_id "Phchi.S4G004900.t2"; gene_id "Phchi.S4G004900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15199.t1 is derived from g13667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17528052	17531514	.	+	.	Phchi.S3G251800
Phchi.S3	AUGUSTUS	transcript	17528052	17531514	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	start_codon	17528052	17528054	.	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17528052	17528295	0.61	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17528052	17528295	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17528296	17528441	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17528442	17529605	0.79	+	2	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17528442	17529605	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17529606	17529787	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17529788	17529925	1	+	2	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17529788	17529925	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17529926	17530008	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17530009	17530099	1	+	2	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17530009	17530099	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17530100	17530269	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17530270	17530348	1	+	1	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17530270	17530348	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17530349	17530470	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17530471	17530593	1	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17530471	17530593	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17530594	17530697	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17530698	17530775	1	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17530698	17530775	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17530776	17530861	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17530862	17530965	1	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17530862	17530965	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17530966	17531068	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17531069	17531156	1	+	1	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17531069	17531156	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17531157	17531243	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17531244	17531342	1	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17531244	17531342	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	intron	17531343	17531427	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	CDS	17531428	17531514	1	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	exon	17531428	17531514	.	+	.	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
Phchi.S3	AUGUSTUS	stop_codon	17531515	17531517	.	+	0	transcript_id "Phchi.S3G251800.t1"; gene_id "Phchi.S3G251800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1635.t1 is derived from g8554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2124941	2125462	.	-	.	Phchi.S5G024400
Phchi.S5	AUGUSTUS	transcript	2124941	2125462	.	-	.	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	stop_codon	2124938	2124940	.	-	0	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	CDS	2124941	2125054	0.86	-	0	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	exon	2124941	2125054	.	-	.	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	intron	2125055	2125156	.	-	.	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	CDS	2125157	2125211	0.97	-	1	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	exon	2125157	2125211	.	-	.	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	intron	2125212	2125304	.	-	.	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	CDS	2125305	2125462	0.96	-	0	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	exon	2125305	2125462	.	-	.	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
Phchi.S5	AUGUSTUS	start_codon	2125460	2125462	.	-	0	transcript_id "Phchi.S5G024400.t1"; gene_id "Phchi.S5G024400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg527.t1 is derived from g10309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3781886	3784905	.	-	.	Phchi.S6G048600
Phchi.S6	AUGUSTUS	transcript	3781886	3784905	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	stop_codon	3781883	3781885	.	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3781886	3782007	1	-	2	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3781886	3782007	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3782008	3782096	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3782097	3782137	1	-	1	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3782097	3782137	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3782138	3782225	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3782226	3782314	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3782226	3782314	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3782315	3782401	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3782402	3782446	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3782402	3782446	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3782447	3782548	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3782549	3782656	0.98	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3782549	3782656	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3782657	3782742	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3782743	3782828	1	-	2	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3782743	3782828	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3782829	3782922	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3782923	3783010	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3782923	3783010	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3783011	3783091	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3783092	3783292	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3783092	3783292	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3783293	3783379	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3783380	3783455	1	-	1	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3783380	3783455	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3783456	3783545	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3783546	3783595	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3783546	3783595	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3783596	3783678	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3783679	3783741	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3783679	3783741	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3783742	3783845	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3783846	3783899	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3783846	3783899	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3783900	3784023	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3784024	3784126	0.95	-	1	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3784024	3784126	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3784127	3784236	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3784237	3784339	0.95	-	2	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3784237	3784339	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3784340	3784428	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3784429	3784489	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3784429	3784489	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3784490	3784581	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3784582	3784622	1	-	2	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3784582	3784622	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	intron	3784623	3784757	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	CDS	3784758	3784905	1	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	exon	3784758	3784905	.	-	.	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
Phchi.S6	AUGUSTUS	start_codon	3784903	3784905	.	-	0	transcript_id "Phchi.S6G048600.t1"; gene_id "Phchi.S6G048600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg516.t1 is derived from g10298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3697608	3699530	.	-	.	Phchi.S6G047500
Phchi.S6	AUGUSTUS	transcript	3697608	3699530	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	stop_codon	3697605	3697607	.	-	0	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3697608	3697769	0.36	-	0	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3697608	3697769	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	intron	3697770	3697988	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3697989	3698069	0.54	-	0	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3697989	3698069	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	intron	3698070	3698166	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3698167	3698484	0.95	-	0	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3698167	3698484	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	intron	3698485	3698640	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3698641	3698815	0.81	-	1	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3698641	3698815	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	intron	3698816	3698919	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3698920	3699070	0.57	-	2	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3698920	3699070	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	intron	3699071	3699178	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3699179	3699294	1	-	1	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3699179	3699294	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	intron	3699295	3699396	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	CDS	3699397	3699530	0.94	-	0	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	exon	3699397	3699530	.	-	.	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
Phchi.S6	AUGUSTUS	start_codon	3699528	3699530	.	-	0	transcript_id "Phchi.S6G047500.t1"; gene_id "Phchi.S6G047500"
# This transcript jg14161.t2 is derived from g12629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14162.t1 is derived from g12628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11222998	11224445	.	-	.	Phchi.S3G148000
Phchi.S3	AUGUSTUS	transcript	11222998	11224445	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	stop_codon	11222995	11222997	.	-	0	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11222998	11223454	0.6	-	1	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11222998	11223454	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	intron	11223455	11223657	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11223658	11223703	0.4	-	2	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11223658	11223703	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	intron	11223704	11224105	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11224106	11224244	0.35	-	0	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11224106	11224244	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	intron	11224245	11224421	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11224422	11224445	0.35	-	0	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11224422	11224445	.	-	.	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	start_codon	11224443	11224445	.	-	0	transcript_id "Phchi.S3G148000.t1"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	transcript	11222998	11224222	.	-	.	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	stop_codon	11222995	11222997	.	-	0	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11222998	11223454	0.35	-	1	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11222998	11223454	.	-	.	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	intron	11223455	11223575	.	-	.	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11223576	11223703	0.35	-	0	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11223576	11223703	.	-	.	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	intron	11223704	11224105	.	-	.	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	CDS	11224106	11224222	0.36	-	0	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	exon	11224106	11224222	.	-	.	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
Phchi.S3	AUGUSTUS	start_codon	11224220	11224222	.	-	0	transcript_id "Phchi.S3G148000.t2"; gene_id "Phchi.S3G148000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3084.t1 is derived from g253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1553960	1554372	.	+	.	Phchi.S1G024300
Phchi.S1	AUGUSTUS	transcript	1553960	1554372	.	+	.	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	start_codon	1553960	1553962	.	+	0	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	CDS	1553960	1554156	0.29	+	0	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	exon	1553960	1554156	.	+	.	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	intron	1554157	1554332	.	+	.	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	CDS	1554333	1554372	0.58	+	1	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	exon	1554333	1554372	.	+	.	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
Phchi.S1	AUGUSTUS	stop_codon	1554373	1554375	.	+	0	transcript_id "Phchi.S1G024300.t1"; gene_id "Phchi.S1G024300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9875.t1 is derived from g7051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44204741	44205052	.	+	.	Phchi.S1G703400
Phchi.S1	AUGUSTUS	transcript	44204741	44205052	.	+	.	transcript_id "Phchi.S1G703400.t1"; gene_id "Phchi.S1G703400"
Phchi.S1	AUGUSTUS	start_codon	44204741	44204743	.	+	0	transcript_id "Phchi.S1G703400.t1"; gene_id "Phchi.S1G703400"
Phchi.S1	AUGUSTUS	CDS	44204741	44205052	0.79	+	0	transcript_id "Phchi.S1G703400.t1"; gene_id "Phchi.S1G703400"
Phchi.S1	AUGUSTUS	exon	44204741	44205052	.	+	.	transcript_id "Phchi.S1G703400.t1"; gene_id "Phchi.S1G703400"
Phchi.S1	AUGUSTUS	stop_codon	44205053	44205055	.	+	0	transcript_id "Phchi.S1G703400.t1"; gene_id "Phchi.S1G703400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1151.t1 is derived from g10934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8029896	8034217	.	+	.	Phchi.S6G111000
Phchi.S6	AUGUSTUS	transcript	8029896	8034217	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	start_codon	8029896	8029898	.	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8029896	8029941	0.86	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8029896	8029941	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8029942	8030037	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8030038	8030586	0.99	+	2	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8030038	8030586	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8030587	8030754	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8030755	8030885	0.99	+	2	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8030755	8030885	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8030886	8030983	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8030984	8031172	0.99	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8030984	8031172	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8031173	8031258	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8031259	8032004	0.53	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8031259	8032004	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8032005	8032124	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8032125	8032569	0.9	+	1	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8032125	8032569	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8032570	8032656	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8032657	8032752	1	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8032657	8032752	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8032753	8032844	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8032845	8032937	1	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8032845	8032937	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8032938	8033066	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8033067	8033261	1	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8033067	8033261	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8033262	8033380	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8033381	8033473	1	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8033381	8033473	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8033474	8033558	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8033559	8033771	0.94	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8033559	8033771	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8033772	8033881	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8033882	8033971	1	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8033882	8033971	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	intron	8033972	8034058	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	CDS	8034059	8034217	0.98	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	exon	8034059	8034217	.	+	.	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
Phchi.S6	AUGUSTUS	stop_codon	8034218	8034220	.	+	0	transcript_id "Phchi.S6G111000.t1"; gene_id "Phchi.S6G111000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2108.t1 is derived from g9028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4912995	4914155	.	-	.	Phchi.S5G071700
Phchi.S5	AUGUSTUS	transcript	4912995	4914155	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	stop_codon	4912992	4912994	.	-	0	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	CDS	4912995	4913105	0.99	-	0	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	exon	4912995	4913105	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	intron	4913106	4913283	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	CDS	4913284	4913446	1	-	1	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	exon	4913284	4913446	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	intron	4913447	4913544	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	CDS	4913545	4913616	0.77	-	1	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	exon	4913545	4913616	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	intron	4913617	4913723	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	CDS	4913724	4913761	1	-	0	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	exon	4913724	4913761	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	intron	4913762	4913921	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	CDS	4913922	4914155	0.73	-	0	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	exon	4913922	4914155	.	-	.	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
Phchi.S5	AUGUSTUS	start_codon	4914153	4914155	.	-	0	transcript_id "Phchi.S5G071700.t1"; gene_id "Phchi.S5G071700"
# This transcript jg10995.t2 is derived from g15045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10996.t1 is derived from g15046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3570714	3572369	.	+	.	Phchi.S4G057800
Phchi.S4	AUGUSTUS	transcript	3570714	3572369	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	start_codon	3570714	3570716	.	+	0	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3570714	3570952	0.99	+	0	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3570714	3570952	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3570953	3571039	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3571040	3571164	1	+	1	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3571040	3571164	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3571165	3571238	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3571239	3571305	1	+	2	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3571239	3571305	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3571306	3571435	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3571436	3571625	1	+	1	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3571436	3571625	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3571626	3571723	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3571724	3571862	1	+	0	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3571724	3571862	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3571863	3571948	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3571949	3572059	1	+	2	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3571949	3572059	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3572060	3572141	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3572142	3572255	0.94	+	2	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3572142	3572255	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	intron	3572256	3572334	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	CDS	3572335	3572369	0.94	+	2	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	exon	3572335	3572369	.	+	.	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
Phchi.S4	AUGUSTUS	stop_codon	3572370	3572372	.	+	0	transcript_id "Phchi.S4G057800.t1"; gene_id "Phchi.S4G057800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9834.t1 is derived from g7010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44003031	44005761	.	+	.	Phchi.S1G699300
Phchi.S1	AUGUSTUS	transcript	44003031	44005761	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	start_codon	44003031	44003033	.	+	0	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	CDS	44003031	44004061	0.55	+	0	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	exon	44003031	44004061	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	intron	44004062	44004237	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	CDS	44004238	44004439	1	+	1	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	exon	44004238	44004439	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	intron	44004440	44004711	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	CDS	44004712	44004915	1	+	0	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	exon	44004712	44004915	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	intron	44004916	44005056	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	CDS	44005057	44005143	1	+	0	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	exon	44005057	44005143	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	intron	44005144	44005239	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	CDS	44005240	44005761	0.85	+	0	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	exon	44005240	44005761	.	+	.	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
Phchi.S1	AUGUSTUS	stop_codon	44005762	44005764	.	+	0	transcript_id "Phchi.S1G699300.t1"; gene_id "Phchi.S1G699300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4817.t1 is derived from g1987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12974921	12975664	.	-	.	Phchi.S1G197600
Phchi.S1	AUGUSTUS	transcript	12974921	12975664	.	-	.	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	stop_codon	12974918	12974920	.	-	0	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	CDS	12974921	12974928	1	-	2	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	exon	12974921	12974928	.	-	.	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	intron	12974929	12975319	.	-	.	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	CDS	12975320	12975532	1	-	2	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	exon	12975320	12975532	.	-	.	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	intron	12975533	12975624	.	-	.	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	CDS	12975625	12975664	1	-	0	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	exon	12975625	12975664	.	-	.	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
Phchi.S1	AUGUSTUS	start_codon	12975662	12975664	.	-	0	transcript_id "Phchi.S1G197600.t1"; gene_id "Phchi.S1G197600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8172.t1 is derived from g5347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34271194	34275875	.	+	.	Phchi.S1G533100
Phchi.S1	AUGUSTUS	transcript	34271194	34275875	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	start_codon	34271194	34271196	.	+	0	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34271194	34271404	0.89	+	0	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34271194	34271404	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	intron	34271405	34271504	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34271505	34272319	0.99	+	2	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34271505	34272319	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	intron	34272320	34272908	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34272909	34273878	0.73	+	0	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34272909	34273878	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	intron	34273879	34274019	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34274020	34274499	0.64	+	2	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34274020	34274499	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	intron	34274500	34274596	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34274597	34274706	1	+	2	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34274597	34274706	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	intron	34274707	34274825	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34274826	34274973	1	+	0	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34274826	34274973	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	intron	34274974	34275189	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	CDS	34275190	34275875	0.46	+	2	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	exon	34275190	34275875	.	+	.	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
Phchi.S1	AUGUSTUS	stop_codon	34275876	34275878	.	+	0	transcript_id "Phchi.S1G533100.t1"; gene_id "Phchi.S1G533100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14181.t1 is derived from g12648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11321221	11322797	.	-	.	Phchi.S3G150000
Phchi.S3	AUGUSTUS	transcript	11321221	11322797	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	stop_codon	11321218	11321220	.	-	0	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11321221	11321335	0.96	-	1	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11321221	11321335	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	intron	11321336	11321466	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11321467	11321589	1	-	1	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11321467	11321589	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	intron	11321590	11321749	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11321750	11321880	1	-	0	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11321750	11321880	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	intron	11321881	11321969	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11321970	11322045	1	-	1	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11321970	11322045	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	intron	11322046	11322198	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11322199	11322368	1	-	0	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11322199	11322368	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	intron	11322369	11322483	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11322484	11322651	0.94	-	0	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11322484	11322651	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	intron	11322652	11322788	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	CDS	11322789	11322797	0.93	-	0	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	exon	11322789	11322797	.	-	.	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
Phchi.S3	AUGUSTUS	start_codon	11322795	11322797	.	-	0	transcript_id "Phchi.S3G150000.t1"; gene_id "Phchi.S3G150000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13808.t1 is derived from g12275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9014004	9015727	.	-	.	Phchi.S3G112700
Phchi.S3	AUGUSTUS	transcript	9014004	9015727	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	stop_codon	9014001	9014003	.	-	0	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	CDS	9014004	9014459	0.59	-	0	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	exon	9014004	9014459	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	intron	9014460	9014623	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	CDS	9014624	9015085	0.56	-	0	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	exon	9014624	9015085	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	intron	9015086	9015167	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	CDS	9015168	9015274	0.71	-	2	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	exon	9015168	9015274	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	intron	9015275	9015471	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	CDS	9015472	9015727	0.6	-	0	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	exon	9015472	9015727	.	-	.	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
Phchi.S3	AUGUSTUS	start_codon	9015725	9015727	.	-	0	transcript_id "Phchi.S3G112700.t1"; gene_id "Phchi.S3G112700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6602.t1 is derived from g3774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23943646	23944496	.	+	.	Phchi.S1G376100
Phchi.S1	AUGUSTUS	transcript	23943646	23944496	.	+	.	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	start_codon	23943646	23943648	.	+	0	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	CDS	23943646	23943683	0.89	+	0	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	exon	23943646	23943683	.	+	.	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	intron	23943684	23943769	.	+	.	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	CDS	23943770	23944496	0.68	+	1	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	exon	23943770	23944496	.	+	.	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
Phchi.S1	AUGUSTUS	stop_codon	23944497	23944499	.	+	0	transcript_id "Phchi.S1G376100.t1"; gene_id "Phchi.S1G376100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13485.t1 is derived from g11952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7123269	7126052	.	+	.	Phchi.S3G080400
Phchi.S3	AUGUSTUS	transcript	7123269	7126052	.	+	.	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	start_codon	7123269	7123271	.	+	0	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	CDS	7123269	7123271	1	+	0	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	exon	7123269	7123271	.	+	.	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	intron	7123272	7123425	.	+	.	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	CDS	7123426	7123513	1	+	0	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	exon	7123426	7123513	.	+	.	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	intron	7123514	7123614	.	+	.	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	CDS	7123615	7126052	1	+	2	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	exon	7123615	7126052	.	+	.	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
Phchi.S3	AUGUSTUS	stop_codon	7126053	7126055	.	+	0	transcript_id "Phchi.S3G080400.t1"; gene_id "Phchi.S3G080400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7390.t1 is derived from g4562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28892937	28895123	.	+	.	Phchi.S1G454900
Phchi.S1	AUGUSTUS	transcript	28892937	28895123	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	start_codon	28892937	28892939	.	+	0	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	CDS	28892937	28893036	0.47	+	0	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	exon	28892937	28893036	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	intron	28893037	28893200	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	CDS	28893201	28893481	0.62	+	2	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	exon	28893201	28893481	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	intron	28893482	28893582	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	CDS	28893583	28894382	0.62	+	0	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	exon	28893583	28894382	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	intron	28894383	28894615	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	CDS	28894616	28894700	0.77	+	1	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	exon	28894616	28894700	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	intron	28894701	28894784	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	CDS	28894785	28895123	0.56	+	0	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	exon	28894785	28895123	.	+	.	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
Phchi.S1	AUGUSTUS	stop_codon	28895124	28895126	.	+	0	transcript_id "Phchi.S1G454900.t1"; gene_id "Phchi.S1G454900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6340.t1 is derived from g3512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22409544	22412472	.	-	.	Phchi.S1G349900
Phchi.S1	AUGUSTUS	transcript	22409544	22412472	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	stop_codon	22409541	22409543	.	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22409544	22409874	0.99	-	1	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22409544	22409874	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22409875	22409972	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22409973	22410193	1	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22409973	22410193	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22410194	22410278	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22410279	22410385	1	-	2	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22410279	22410385	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22410386	22410477	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22410478	22410544	0.96	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22410478	22410544	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22410545	22410618	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22410619	22411068	0.8	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22410619	22411068	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22411069	22411259	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22411260	22411335	0.51	-	1	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22411260	22411335	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22411336	22411430	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22411431	22411441	0.51	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22411431	22411441	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22411442	22411574	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22411575	22411739	1	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22411575	22411739	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22411740	22411920	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22411921	22412359	0.96	-	1	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22411921	22412359	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	intron	22412360	22412458	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	CDS	22412459	22412472	0.59	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	exon	22412459	22412472	.	-	.	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
Phchi.S1	AUGUSTUS	start_codon	22412470	22412472	.	-	0	transcript_id "Phchi.S1G349900.t1"; gene_id "Phchi.S1G349900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8734.t1 is derived from g5909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37714976	37717100	.	-	.	Phchi.S1G589300
Phchi.S1	AUGUSTUS	transcript	37714976	37717100	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	stop_codon	37714973	37714975	.	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37714976	37715133	1	-	2	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37714976	37715133	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37715134	37715229	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37715230	37715284	1	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37715230	37715284	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37715285	37715374	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37715375	37715439	1	-	2	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37715375	37715439	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37715440	37715508	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37715509	37715612	1	-	1	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37715509	37715612	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37715613	37715707	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37715708	37715772	0.88	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37715708	37715772	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37715773	37715873	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37715874	37715972	0.88	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37715874	37715972	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37715973	37716072	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37716073	37716181	1	-	1	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37716073	37716181	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37716182	37716287	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37716288	37716344	1	-	1	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37716288	37716344	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37716345	37716462	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37716463	37716660	1	-	1	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37716463	37716660	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37716661	37716754	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37716755	37716854	1	-	2	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37716755	37716854	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37716855	37716935	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37716936	37717026	1	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37716936	37717026	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	intron	37717027	37717097	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	CDS	37717098	37717100	1	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	exon	37717098	37717100	.	-	.	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
Phchi.S1	AUGUSTUS	start_codon	37717098	37717100	.	-	0	transcript_id "Phchi.S1G589300.t1"; gene_id "Phchi.S1G589300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5432.t1 is derived from g2602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16840599	16842013	.	-	.	Phchi.S1G259100
Phchi.S1	AUGUSTUS	transcript	16840599	16842013	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	stop_codon	16840596	16840598	.	-	0	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16840599	16840767	1	-	1	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16840599	16840767	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	intron	16840768	16840848	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16840849	16840895	1	-	0	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16840849	16840895	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	intron	16840896	16840979	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16840980	16841055	1	-	1	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16840980	16841055	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	intron	16841056	16841142	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16841143	16841338	1	-	2	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16841143	16841338	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	intron	16841339	16841431	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16841432	16841612	1	-	0	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16841432	16841612	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	intron	16841613	16841743	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16841744	16841843	1	-	1	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16841744	16841843	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	intron	16841844	16841921	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	CDS	16841922	16842013	0.68	-	0	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	exon	16841922	16842013	.	-	.	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
Phchi.S1	AUGUSTUS	start_codon	16842011	16842013	.	-	0	transcript_id "Phchi.S1G259100.t1"; gene_id "Phchi.S1G259100"
# This transcript jg12201.t2 is derived from g7877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12202.t1 is derived from g7878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6718679	6719134	.	-	.	Phchi.S2G028200
Phchi.S2	AUGUSTUS	transcript	6718679	6719134	.	-	.	transcript_id "Phchi.S2G028200.t1"; gene_id "Phchi.S2G028200"
Phchi.S2	AUGUSTUS	stop_codon	6718676	6718678	.	-	0	transcript_id "Phchi.S2G028200.t1"; gene_id "Phchi.S2G028200"
Phchi.S2	AUGUSTUS	CDS	6718679	6719134	1	-	0	transcript_id "Phchi.S2G028200.t1"; gene_id "Phchi.S2G028200"
Phchi.S2	AUGUSTUS	exon	6718679	6719134	.	-	.	transcript_id "Phchi.S2G028200.t1"; gene_id "Phchi.S2G028200"
Phchi.S2	AUGUSTUS	start_codon	6719132	6719134	.	-	0	transcript_id "Phchi.S2G028200.t1"; gene_id "Phchi.S2G028200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14616.t1 is derived from g13084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13793617	13795280	.	-	.	Phchi.S3G193500
Phchi.S3	AUGUSTUS	transcript	13793617	13795280	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	stop_codon	13793614	13793616	.	-	0	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	CDS	13793617	13793641	0.74	-	1	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	exon	13793617	13793641	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	intron	13793642	13793785	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	CDS	13793786	13793871	1	-	0	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	exon	13793786	13793871	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	intron	13793872	13793951	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	CDS	13793952	13794005	1	-	0	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	exon	13793952	13794005	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	intron	13794006	13794142	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	CDS	13794143	13794240	1	-	2	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	exon	13794143	13794240	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	intron	13794241	13794322	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	CDS	13794323	13794400	1	-	2	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	exon	13794323	13794400	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	intron	13794401	13794535	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	CDS	13794536	13795280	0.99	-	0	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	exon	13794536	13795280	.	-	.	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
Phchi.S3	AUGUSTUS	start_codon	13795278	13795280	.	-	0	transcript_id "Phchi.S3G193500.t1"; gene_id "Phchi.S3G193500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9253.t1 is derived from g6428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40601206	40605461	.	+	.	Phchi.S1G641200
Phchi.S1	AUGUSTUS	transcript	40601206	40605461	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	start_codon	40601206	40601208	.	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40601206	40601588	0.58	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40601206	40601588	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40601589	40601748	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40601749	40601842	1	+	1	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40601749	40601842	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40601843	40602049	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40602050	40602160	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40602050	40602160	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40602161	40602267	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40602268	40602351	0.92	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40602268	40602351	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40602352	40602459	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40602460	40602531	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40602460	40602531	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40602532	40602660	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40602661	40602717	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40602661	40602717	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40602718	40602960	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40602961	40603080	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40602961	40603080	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40603081	40603201	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40603202	40603402	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40603202	40603402	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40603403	40603497	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40603498	40603608	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40603498	40603608	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40603609	40603685	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40603686	40603723	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40603686	40603723	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40603724	40603867	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40603868	40604024	1	+	1	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40603868	40604024	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40604025	40604151	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40604152	40604256	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40604152	40604256	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40604257	40604328	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40604329	40604385	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40604329	40604385	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40604386	40604492	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40604493	40604636	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40604493	40604636	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40604637	40604738	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40604739	40604809	0.99	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40604739	40604809	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40604810	40604915	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40604916	40605027	0.99	+	1	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40604916	40605027	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40605028	40605111	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40605112	40605168	1	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40605112	40605168	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	intron	40605169	40605263	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	CDS	40605264	40605461	0.98	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	exon	40605264	40605461	.	+	.	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
Phchi.S1	AUGUSTUS	stop_codon	40605462	40605464	.	+	0	transcript_id "Phchi.S1G641200.t1"; gene_id "Phchi.S1G641200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7996.t1 is derived from g5171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32346028	32347089	.	-	.	Phchi.S1G515500
Phchi.S1	AUGUSTUS	transcript	32346028	32347089	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	stop_codon	32346025	32346027	.	-	0	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	CDS	32346028	32346028	1	-	1	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	exon	32346028	32346028	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	intron	32346029	32346112	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	CDS	32346113	32346334	1	-	1	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	exon	32346113	32346334	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	intron	32346335	32346427	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	CDS	32346428	32346692	1	-	2	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	exon	32346428	32346692	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	intron	32346693	32346770	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	CDS	32346771	32347089	0.98	-	0	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	exon	32346771	32347089	.	-	.	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
Phchi.S1	AUGUSTUS	start_codon	32347087	32347089	.	-	0	transcript_id "Phchi.S1G515500.t1"; gene_id "Phchi.S1G515500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8700.t1 is derived from g5875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37523450	37529455	.	-	.	Phchi.S1G585900
Phchi.S1	AUGUSTUS	transcript	37523450	37529455	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	stop_codon	37523447	37523449	.	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37523450	37524528	1	-	2	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37523450	37524528	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37524529	37524633	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37524634	37524760	0.98	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37524634	37524760	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37524761	37524851	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37524852	37524968	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37524852	37524968	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37524969	37525042	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37525043	37525154	1	-	1	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37525043	37525154	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37525155	37525266	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37525267	37525427	0.99	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37525267	37525427	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37525428	37525516	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37525517	37525588	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37525517	37525588	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37525589	37525698	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37525699	37525764	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37525699	37525764	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37525765	37525859	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37525860	37525988	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37525860	37525988	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37525989	37526083	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37526084	37526192	1	-	1	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37526084	37526192	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37526193	37526290	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37526291	37526370	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37526291	37526370	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37526371	37526577	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37526578	37526703	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37526578	37526703	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37526704	37526805	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37526806	37526856	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37526806	37526856	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37526857	37526939	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37526940	37527122	0.97	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37526940	37527122	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37527123	37527242	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37527243	37527329	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37527243	37527329	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37527330	37527508	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37527509	37527619	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37527509	37527619	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37527620	37527717	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37527718	37527822	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37527718	37527822	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37527823	37527917	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37527918	37528089	1	-	1	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37527918	37528089	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37528090	37528176	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37528177	37528349	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37528177	37528349	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37528350	37528445	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37528446	37528518	1	-	1	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37528446	37528518	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37528519	37528629	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37528630	37528853	0.92	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37528630	37528853	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37528854	37528982	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37528983	37529078	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37528983	37529078	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	intron	37529079	37529209	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	CDS	37529210	37529455	1	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	exon	37529210	37529455	.	-	.	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
Phchi.S1	AUGUSTUS	start_codon	37529453	37529455	.	-	0	transcript_id "Phchi.S1G585900.t1"; gene_id "Phchi.S1G585900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5208.t1 is derived from g2378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15474730	15476044	.	-	.	Phchi.S1G236700
Phchi.S1	AUGUSTUS	transcript	15474730	15476044	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	stop_codon	15474727	15474729	.	-	0	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	CDS	15474730	15474771	0.36	-	0	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	exon	15474730	15474771	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	intron	15474772	15474865	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	CDS	15474866	15475072	0.44	-	0	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	exon	15474866	15475072	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	intron	15475073	15475163	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	CDS	15475164	15475601	0.46	-	0	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	exon	15475164	15475601	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	intron	15475602	15475723	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	CDS	15475724	15476044	0.4	-	0	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	exon	15475724	15476044	.	-	.	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
Phchi.S1	AUGUSTUS	start_codon	15476042	15476044	.	-	0	transcript_id "Phchi.S1G236700.t1"; gene_id "Phchi.S1G236700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4998.t1 is derived from g2168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13944796	13947022	.	+	.	Phchi.S1G215700
Phchi.S1	AUGUSTUS	transcript	13944796	13947022	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	start_codon	13944796	13944798	.	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13944796	13944906	0.84	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13944796	13944906	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13944907	13945003	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13945004	13945060	1	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13945004	13945060	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13945061	13945153	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13945154	13945216	1	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13945154	13945216	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13945217	13945300	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13945301	13945372	1	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13945301	13945372	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13945373	13945458	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13945459	13945548	1	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13945459	13945548	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13945549	13945715	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13945716	13945770	0.99	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13945716	13945770	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13945771	13945858	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13945859	13945951	0.99	+	2	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13945859	13945951	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13945952	13946037	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13946038	13946115	0.85	+	2	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13946038	13946115	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13946116	13946395	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13946396	13946443	0.98	+	2	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13946396	13946443	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13946444	13946585	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13946586	13946651	1	+	2	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13946586	13946651	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13946652	13946743	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13946744	13946784	1	+	2	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13946744	13946784	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13946785	13946871	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13946872	13946928	1	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13946872	13946928	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	intron	13946929	13947007	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	CDS	13947008	13947022	1	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	exon	13947008	13947022	.	+	.	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
Phchi.S1	AUGUSTUS	stop_codon	13947023	13947025	.	+	0	transcript_id "Phchi.S1G215700.t1"; gene_id "Phchi.S1G215700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11737.t1 is derived from g15789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7919050	7928543	.	-	.	Phchi.S4G131900
Phchi.S4	AUGUSTUS	transcript	7919050	7928543	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	stop_codon	7919047	7919049	.	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7919050	7919241	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7919050	7919241	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7919242	7919318	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7919319	7919474	0.95	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7919319	7919474	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7919475	7919566	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7919567	7919637	0.95	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7919567	7919637	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7919638	7919743	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7919744	7919887	0.93	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7919744	7919887	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7919888	7920017	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7920018	7920258	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7920018	7920258	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7920259	7920345	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7920346	7920414	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7920346	7920414	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7920415	7920529	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7920530	7920635	0.99	-	1	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7920530	7920635	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7920636	7920740	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7920741	7920880	0.99	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7920741	7920880	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7920881	7921072	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7921073	7921219	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7921073	7921219	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7921220	7921316	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7921317	7921367	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7921317	7921367	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7921368	7921474	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7921475	7921549	0.74	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7921475	7921549	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7921550	7921638	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7921639	7921746	0.95	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7921639	7921746	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7921747	7921851	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7921852	7921899	0.94	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7921852	7921899	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7921900	7921984	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7921985	7922146	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7921985	7922146	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7922147	7922225	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7922226	7922326	1	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7922226	7922326	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7922327	7922399	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7922400	7922547	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7922400	7922547	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7922548	7922638	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7922639	7922806	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7922639	7922806	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7922807	7922897	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7922898	7923021	1	-	1	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7922898	7923021	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7923022	7923184	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7923185	7923324	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7923185	7923324	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7923325	7923460	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7923461	7923718	0.98	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7923461	7923718	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7923719	7923814	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7923815	7923949	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7923815	7923949	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7923950	7924030	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7924031	7924186	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7924031	7924186	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7924187	7924295	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7924296	7924469	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7924296	7924469	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7924470	7924635	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7924636	7924889	1	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7924636	7924889	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7924890	7925182	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7925183	7925296	1	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7925183	7925296	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7925297	7925379	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7925380	7925666	1	-	1	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7925380	7925666	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7925667	7925755	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7925756	7925837	1	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7925756	7925837	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7925838	7925980	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7925981	7926115	1	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7925981	7926115	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7926116	7926211	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7926212	7926250	0.91	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7926212	7926250	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7926251	7926326	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7926327	7926786	0.87	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7926327	7926786	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7926787	7926907	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7926908	7927121	0.97	-	1	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7926908	7927121	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7927122	7927245	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7927246	7927721	0.82	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7927246	7927721	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7927722	7927855	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7927856	7927950	1	-	2	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7927856	7927950	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7927951	7928026	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7928027	7928111	1	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7928027	7928111	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	intron	7928112	7928369	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	CDS	7928370	7928543	0.78	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	exon	7928370	7928543	.	-	.	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
Phchi.S4	AUGUSTUS	start_codon	7928541	7928543	.	-	0	transcript_id "Phchi.S4G131900.t1"; gene_id "Phchi.S4G131900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12294.t1 is derived from g7970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8961910	8963273	.	-	.	Phchi.S2G037400
Phchi.S2	AUGUSTUS	transcript	8961910	8963273	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	stop_codon	8961907	8961909	.	-	0	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8961910	8961934	0.99	-	1	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8961910	8961934	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	intron	8961935	8962027	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8962028	8962090	1	-	1	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8962028	8962090	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	intron	8962091	8962254	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8962255	8962403	1	-	0	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8962255	8962403	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	intron	8962404	8962516	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8962517	8962643	0.99	-	1	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8962517	8962643	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	intron	8962644	8962739	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8962740	8962858	1	-	0	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8962740	8962858	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	intron	8962859	8962998	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8962999	8963024	0.39	-	2	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8962999	8963024	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	intron	8963025	8963098	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	CDS	8963099	8963273	0.39	-	0	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	exon	8963099	8963273	.	-	.	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
Phchi.S2	AUGUSTUS	start_codon	8963271	8963273	.	-	0	transcript_id "Phchi.S2G037400.t1"; gene_id "Phchi.S2G037400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6643.t1 is derived from g3815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24222727	24223131	.	-	.	Phchi.S1G380200
Phchi.S1	AUGUSTUS	transcript	24222727	24223131	.	-	.	transcript_id "Phchi.S1G380200.t1"; gene_id "Phchi.S1G380200"
Phchi.S1	AUGUSTUS	stop_codon	24222724	24222726	.	-	0	transcript_id "Phchi.S1G380200.t1"; gene_id "Phchi.S1G380200"
Phchi.S1	AUGUSTUS	CDS	24222727	24223131	0.36	-	0	transcript_id "Phchi.S1G380200.t1"; gene_id "Phchi.S1G380200"
Phchi.S1	AUGUSTUS	exon	24222727	24223131	.	-	.	transcript_id "Phchi.S1G380200.t1"; gene_id "Phchi.S1G380200"
Phchi.S1	AUGUSTUS	start_codon	24223129	24223131	.	-	0	transcript_id "Phchi.S1G380200.t1"; gene_id "Phchi.S1G380200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12528.t1 is derived from g8205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32996871	32998026	.	-	.	Phchi.S2G060800
Phchi.S2	AUGUSTUS	transcript	32996871	32998026	.	-	.	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	stop_codon	32996868	32996870	.	-	0	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	CDS	32996871	32996972	1	-	0	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	exon	32996871	32996972	.	-	.	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	intron	32996973	32997228	.	-	.	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	CDS	32997229	32997308	1	-	2	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	exon	32997229	32997308	.	-	.	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	intron	32997309	32997914	.	-	.	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	CDS	32997915	32998026	0.94	-	0	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	exon	32997915	32998026	.	-	.	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
Phchi.S2	AUGUSTUS	start_codon	32998024	32998026	.	-	0	transcript_id "Phchi.S2G060800.t1"; gene_id "Phchi.S2G060800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3895.t1 is derived from g1064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6281733	6283828	.	-	.	Phchi.S1G105400
Phchi.S1	AUGUSTUS	transcript	6281733	6283828	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	stop_codon	6281730	6281732	.	-	0	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	CDS	6281733	6282633	0.64	-	1	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	exon	6281733	6282633	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	intron	6282634	6282802	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	CDS	6282803	6283065	0.91	-	0	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	exon	6282803	6283065	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	intron	6283066	6283146	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	CDS	6283147	6283273	1	-	1	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	exon	6283147	6283273	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	intron	6283274	6283397	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	CDS	6283398	6283567	0.87	-	0	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	exon	6283398	6283567	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	intron	6283568	6283666	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	CDS	6283667	6283828	1	-	0	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	exon	6283667	6283828	.	-	.	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
Phchi.S1	AUGUSTUS	start_codon	6283826	6283828	.	-	0	transcript_id "Phchi.S1G105400.t1"; gene_id "Phchi.S1G105400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14341.t1 is derived from g12808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12306227	12307748	.	-	.	Phchi.S3G166000
Phchi.S3	AUGUSTUS	transcript	12306227	12307748	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	stop_codon	12306224	12306226	.	-	0	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	CDS	12306227	12306685	0.99	-	0	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	exon	12306227	12306685	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	intron	12306686	12306787	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	CDS	12306788	12306951	1	-	2	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	exon	12306788	12306951	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	intron	12306952	12307048	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	CDS	12307049	12307133	1	-	0	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	exon	12307049	12307133	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	intron	12307134	12307215	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	CDS	12307216	12307347	0.97	-	0	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	exon	12307216	12307347	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	intron	12307348	12307451	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	CDS	12307452	12307748	0.54	-	0	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	exon	12307452	12307748	.	-	.	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
Phchi.S3	AUGUSTUS	start_codon	12307746	12307748	.	-	0	transcript_id "Phchi.S3G166000.t1"; gene_id "Phchi.S3G166000"
# This transcript jg3716.t2 is derived from g885.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3717.t1 is derived from g886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5353378	5354580	.	+	.	Phchi.S1G087600
Phchi.S1	AUGUSTUS	transcript	5353378	5354580	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	start_codon	5353378	5353380	.	+	0	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	CDS	5353378	5353579	0.95	+	0	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	exon	5353378	5353579	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	intron	5353580	5353689	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	CDS	5353690	5353772	1	+	2	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	exon	5353690	5353772	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	intron	5353773	5353943	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	CDS	5353944	5354156	1	+	0	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	exon	5353944	5354156	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	intron	5354157	5354231	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	CDS	5354232	5354341	1	+	0	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	exon	5354232	5354341	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	intron	5354342	5354426	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	CDS	5354427	5354580	1	+	1	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	exon	5354427	5354580	.	+	.	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
Phchi.S1	AUGUSTUS	stop_codon	5354581	5354583	.	+	0	transcript_id "Phchi.S1G087600.t1"; gene_id "Phchi.S1G087600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14325.t1 is derived from g12792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12097330	12097921	.	+	.	Phchi.S3G164400
Phchi.S3	AUGUSTUS	transcript	12097330	12097921	.	+	.	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	start_codon	12097330	12097332	.	+	0	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	CDS	12097330	12097478	0.88	+	0	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	exon	12097330	12097478	.	+	.	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	intron	12097479	12097567	.	+	.	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	CDS	12097568	12097658	1	+	1	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	exon	12097568	12097658	.	+	.	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	intron	12097659	12097753	.	+	.	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	CDS	12097754	12097921	0.99	+	0	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	exon	12097754	12097921	.	+	.	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
Phchi.S3	AUGUSTUS	stop_codon	12097922	12097924	.	+	0	transcript_id "Phchi.S3G164400.t1"; gene_id "Phchi.S3G164400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4714.t1 is derived from g1884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12434773	12435521	.	-	.	Phchi.S1G187300
Phchi.S1	AUGUSTUS	transcript	12434773	12435521	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	stop_codon	12434770	12434772	.	-	0	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	CDS	12434773	12434824	0.53	-	1	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	exon	12434773	12434824	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	intron	12434825	12434976	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	CDS	12434977	12435133	0.41	-	2	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	exon	12434977	12435133	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	intron	12435134	12435231	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	CDS	12435232	12435360	0.88	-	2	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	exon	12435232	12435360	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	intron	12435361	12435457	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	CDS	12435458	12435521	0.57	-	0	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	exon	12435458	12435521	.	-	.	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
Phchi.S1	AUGUSTUS	start_codon	12435519	12435521	.	-	0	transcript_id "Phchi.S1G187300.t1"; gene_id "Phchi.S1G187300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg586.t1 is derived from g10368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4308987	4311479	.	-	.	Phchi.S6G054500
Phchi.S6	AUGUSTUS	transcript	4308987	4311479	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	stop_codon	4308984	4308986	.	-	0	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	CDS	4308987	4310447	1	-	0	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	exon	4308987	4310447	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	intron	4310448	4310529	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	CDS	4310530	4310747	1	-	2	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	exon	4310530	4310747	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	intron	4310748	4310900	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	CDS	4310901	4311121	0.73	-	1	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	exon	4310901	4311121	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	intron	4311122	4311213	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	CDS	4311214	4311256	0.84	-	2	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	exon	4311214	4311256	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	intron	4311257	4311412	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	CDS	4311413	4311479	0.89	-	0	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	exon	4311413	4311479	.	-	.	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
Phchi.S6	AUGUSTUS	start_codon	4311477	4311479	.	-	0	transcript_id "Phchi.S6G054500.t1"; gene_id "Phchi.S6G054500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11444.t1 is derived from g15494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6394257	6395681	.	+	.	Phchi.S4G102600
Phchi.S4	AUGUSTUS	transcript	6394257	6395681	.	+	.	transcript_id "Phchi.S4G102600.t1"; gene_id "Phchi.S4G102600"
Phchi.S4	AUGUSTUS	start_codon	6394257	6394259	.	+	0	transcript_id "Phchi.S4G102600.t1"; gene_id "Phchi.S4G102600"
Phchi.S4	AUGUSTUS	CDS	6394257	6395681	1	+	0	transcript_id "Phchi.S4G102600.t1"; gene_id "Phchi.S4G102600"
Phchi.S4	AUGUSTUS	exon	6394257	6395681	.	+	.	transcript_id "Phchi.S4G102600.t1"; gene_id "Phchi.S4G102600"
Phchi.S4	AUGUSTUS	stop_codon	6395682	6395684	.	+	0	transcript_id "Phchi.S4G102600.t1"; gene_id "Phchi.S4G102600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6314.t1 is derived from g3486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22225237	22226760	.	-	.	Phchi.S1G347300
Phchi.S1	AUGUSTUS	transcript	22225237	22226760	.	-	.	transcript_id "Phchi.S1G347300.t1"; gene_id "Phchi.S1G347300"
Phchi.S1	AUGUSTUS	stop_codon	22225234	22225236	.	-	0	transcript_id "Phchi.S1G347300.t1"; gene_id "Phchi.S1G347300"
Phchi.S1	AUGUSTUS	CDS	22225237	22226760	0.6	-	0	transcript_id "Phchi.S1G347300.t1"; gene_id "Phchi.S1G347300"
Phchi.S1	AUGUSTUS	exon	22225237	22226760	.	-	.	transcript_id "Phchi.S1G347300.t1"; gene_id "Phchi.S1G347300"
Phchi.S1	AUGUSTUS	start_codon	22226758	22226760	.	-	0	transcript_id "Phchi.S1G347300.t1"; gene_id "Phchi.S1G347300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg464.t1 is derived from g10246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3263774	3265998	.	-	.	Phchi.S6G042300
Phchi.S6	AUGUSTUS	transcript	3263774	3265998	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	stop_codon	3263771	3263773	.	-	0	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	CDS	3263774	3265306	1	-	0	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	exon	3263774	3265306	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	intron	3265307	3265393	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	CDS	3265394	3265473	1	-	2	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	exon	3265394	3265473	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	intron	3265474	3265564	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	CDS	3265565	3265907	1	-	0	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	exon	3265565	3265907	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	intron	3265908	3265995	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	CDS	3265996	3265998	1	-	0	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	exon	3265996	3265998	.	-	.	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
Phchi.S6	AUGUSTUS	start_codon	3265996	3265998	.	-	0	transcript_id "Phchi.S6G042300.t1"; gene_id "Phchi.S6G042300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7183.t1 is derived from g4355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27443745	27444842	.	+	.	Phchi.S1G434200
Phchi.S1	AUGUSTUS	transcript	27443745	27444842	.	+	.	transcript_id "Phchi.S1G434200.t1"; gene_id "Phchi.S1G434200"
Phchi.S1	AUGUSTUS	start_codon	27443745	27443747	.	+	0	transcript_id "Phchi.S1G434200.t1"; gene_id "Phchi.S1G434200"
Phchi.S1	AUGUSTUS	CDS	27443745	27444842	0.85	+	0	transcript_id "Phchi.S1G434200.t1"; gene_id "Phchi.S1G434200"
Phchi.S1	AUGUSTUS	exon	27443745	27444842	.	+	.	transcript_id "Phchi.S1G434200.t1"; gene_id "Phchi.S1G434200"
Phchi.S1	AUGUSTUS	stop_codon	27444843	27444845	.	+	0	transcript_id "Phchi.S1G434200.t1"; gene_id "Phchi.S1G434200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg44.t1 is derived from g9826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	46596	47402	.	+	.	Phchi.S6G000300
Phchi.S6	AUGUSTUS	transcript	46596	47402	.	+	.	transcript_id "Phchi.S6G000300.t1"; gene_id "Phchi.S6G000300"
Phchi.S6	AUGUSTUS	start_codon	46596	46598	.	+	0	transcript_id "Phchi.S6G000300.t1"; gene_id "Phchi.S6G000300"
Phchi.S6	AUGUSTUS	CDS	46596	47402	0.97	+	0	transcript_id "Phchi.S6G000300.t1"; gene_id "Phchi.S6G000300"
Phchi.S6	AUGUSTUS	exon	46596	47402	.	+	.	transcript_id "Phchi.S6G000300.t1"; gene_id "Phchi.S6G000300"
Phchi.S6	AUGUSTUS	stop_codon	47403	47405	.	+	0	transcript_id "Phchi.S6G000300.t1"; gene_id "Phchi.S6G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9285.t1 is derived from g6460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40761658	40762593	.	-	.	Phchi.S1G644400
Phchi.S1	AUGUSTUS	transcript	40761658	40762593	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	stop_codon	40761655	40761657	.	-	0	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	CDS	40761658	40761884	1	-	2	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	exon	40761658	40761884	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	intron	40761885	40761980	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	CDS	40761981	40762168	0.98	-	1	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	exon	40761981	40762168	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	intron	40762169	40762285	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	CDS	40762286	40762414	1	-	1	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	exon	40762286	40762414	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	intron	40762415	40762510	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	CDS	40762511	40762593	0.82	-	0	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	exon	40762511	40762593	.	-	.	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
Phchi.S1	AUGUSTUS	start_codon	40762591	40762593	.	-	0	transcript_id "Phchi.S1G644400.t1"; gene_id "Phchi.S1G644400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14613.t1 is derived from g13081.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13753403	13755083	.	+	.	Phchi.S3G193200
Phchi.S3	AUGUSTUS	transcript	13753403	13755083	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	start_codon	13753403	13753405	.	+	0	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13753403	13753533	1	+	0	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13753403	13753533	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13753534	13753620	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13753621	13753722	1	+	1	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13753621	13753722	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13753723	13753824	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13753825	13753942	1	+	1	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13753825	13753942	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13753943	13754072	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754073	13754165	1	+	0	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754073	13754165	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754166	13754249	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754250	13754295	1	+	0	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754250	13754295	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754296	13754417	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754418	13754490	1	+	2	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754418	13754490	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754491	13754583	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754584	13754618	1	+	1	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754584	13754618	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754619	13754704	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754705	13754793	1	+	2	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754705	13754793	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754794	13754876	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754877	13755083	1	+	0	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754877	13755083	.	+	.	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	stop_codon	13755084	13755086	.	+	0	transcript_id "Phchi.S3G193200.t1"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	transcript	13753403	13755083	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	start_codon	13753403	13753405	.	+	0	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13753403	13753533	1	+	0	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13753403	13753533	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13753534	13753629	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13753630	13753722	0.99	+	1	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13753630	13753722	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13753723	13753824	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13753825	13753942	1	+	1	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13753825	13753942	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13753943	13754072	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754073	13754165	1	+	0	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754073	13754165	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754166	13754249	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754250	13754295	1	+	0	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754250	13754295	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754296	13754417	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754418	13754490	1	+	2	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754418	13754490	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754491	13754583	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754584	13754618	1	+	1	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754584	13754618	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754619	13754704	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754705	13754793	1	+	2	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754705	13754793	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	intron	13754794	13754876	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	CDS	13754877	13755083	1	+	0	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	exon	13754877	13755083	.	+	.	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
Phchi.S3	AUGUSTUS	stop_codon	13755084	13755086	.	+	0	transcript_id "Phchi.S3G193200.t2"; gene_id "Phchi.S3G193200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15908.t1 is derived from g14378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22153412	22154130	.	-	.	Phchi.S3G322700
Phchi.S3	AUGUSTUS	transcript	22153412	22154130	.	-	.	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	stop_codon	22153409	22153411	.	-	0	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	CDS	22153412	22153919	0.59	-	1	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	exon	22153412	22153919	.	-	.	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	intron	22153920	22153996	.	-	.	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	CDS	22153997	22154130	0.57	-	0	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	exon	22153997	22154130	.	-	.	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
Phchi.S3	AUGUSTUS	start_codon	22154128	22154130	.	-	0	transcript_id "Phchi.S3G322700.t1"; gene_id "Phchi.S3G322700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1090.t1 is derived from g10873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7529995	7530674	.	-	.	Phchi.S6G104900
Phchi.S6	AUGUSTUS	transcript	7529995	7530674	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	stop_codon	7529992	7529994	.	-	0	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	CDS	7529995	7530056	0.84	-	2	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	exon	7529995	7530056	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	intron	7530057	7530294	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	CDS	7530295	7530350	0.66	-	1	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	exon	7530295	7530350	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	intron	7530351	7530439	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	CDS	7530440	7530510	1	-	0	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	exon	7530440	7530510	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	intron	7530511	7530647	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	CDS	7530648	7530674	0.72	-	0	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	exon	7530648	7530674	.	-	.	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
Phchi.S6	AUGUSTUS	start_codon	7530672	7530674	.	-	0	transcript_id "Phchi.S6G104900.t1"; gene_id "Phchi.S6G104900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14286.t1 is derived from g12753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11920055	11922078	.	+	.	Phchi.S3G160500
Phchi.S3	AUGUSTUS	transcript	11920055	11922078	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	start_codon	11920055	11920057	.	+	0	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	CDS	11920055	11920157	0.99	+	0	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	exon	11920055	11920157	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	intron	11920158	11920302	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	CDS	11920303	11920471	0.33	+	2	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	exon	11920303	11920471	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	intron	11920472	11920576	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	CDS	11920577	11920618	0.31	+	1	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	exon	11920577	11920618	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	intron	11920619	11920874	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	CDS	11920875	11921835	0.33	+	1	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	exon	11920875	11921835	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	intron	11921836	11922045	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	CDS	11922046	11922078	1	+	0	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	exon	11922046	11922078	.	+	.	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
Phchi.S3	AUGUSTUS	stop_codon	11922079	11922081	.	+	0	transcript_id "Phchi.S3G160500.t1"; gene_id "Phchi.S3G160500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2251.t1 is derived from g9171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5691964	5694513	.	+	.	Phchi.S5G086000
Phchi.S5	AUGUSTUS	transcript	5691964	5694513	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	start_codon	5691964	5691966	.	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5691964	5692066	0.99	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5691964	5692066	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5692067	5692221	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5692222	5692454	1	+	2	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5692222	5692454	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5692455	5692623	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5692624	5692707	1	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5692624	5692707	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5692708	5692858	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5692859	5693073	0.98	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5692859	5693073	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5693074	5693175	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5693176	5693254	1	+	1	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5693176	5693254	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5693255	5693389	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5693390	5693559	1	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5693390	5693559	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5693560	5693678	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5693679	5693865	0.97	+	1	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5693679	5693865	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5693866	5693957	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5693958	5694035	1	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5693958	5694035	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5694036	5694120	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5694121	5694145	0.83	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5694121	5694145	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5694146	5694271	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5694272	5694349	0.67	+	2	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5694272	5694349	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	intron	5694350	5694421	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	CDS	5694422	5694513	0.95	+	2	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	exon	5694422	5694513	.	+	.	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
Phchi.S5	AUGUSTUS	stop_codon	5694514	5694516	.	+	0	transcript_id "Phchi.S5G086000.t1"; gene_id "Phchi.S5G086000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg770.t1 is derived from g10552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5438026	5439309	.	+	.	Phchi.S6G072900
Phchi.S6	AUGUSTUS	transcript	5438026	5439309	.	+	.	transcript_id "Phchi.S6G072900.t1"; gene_id "Phchi.S6G072900"
Phchi.S6	AUGUSTUS	start_codon	5438026	5438028	.	+	0	transcript_id "Phchi.S6G072900.t1"; gene_id "Phchi.S6G072900"
Phchi.S6	AUGUSTUS	CDS	5438026	5439309	1	+	0	transcript_id "Phchi.S6G072900.t1"; gene_id "Phchi.S6G072900"
Phchi.S6	AUGUSTUS	exon	5438026	5439309	.	+	.	transcript_id "Phchi.S6G072900.t1"; gene_id "Phchi.S6G072900"
Phchi.S6	AUGUSTUS	stop_codon	5439310	5439312	.	+	0	transcript_id "Phchi.S6G072900.t1"; gene_id "Phchi.S6G072900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3515.t1 is derived from g684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4157255	4159265	.	+	.	Phchi.S1G067400
Phchi.S1	AUGUSTUS	transcript	4157255	4159265	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	start_codon	4157255	4157257	.	+	0	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	CDS	4157255	4157340	0.41	+	0	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	exon	4157255	4157340	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	intron	4157341	4157477	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	CDS	4157478	4157545	0.61	+	1	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	exon	4157478	4157545	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	intron	4157546	4158186	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	CDS	4158187	4158311	1	+	2	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	exon	4158187	4158311	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	intron	4158312	4158571	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	CDS	4158572	4158747	0.98	+	0	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	exon	4158572	4158747	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	intron	4158748	4158853	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	CDS	4158854	4159265	0.5	+	1	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	exon	4158854	4159265	.	+	.	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
Phchi.S1	AUGUSTUS	stop_codon	4159266	4159268	.	+	0	transcript_id "Phchi.S1G067400.t1"; gene_id "Phchi.S1G067400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15370.t1 is derived from g13838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18670761	18673227	.	-	.	Phchi.S3G268900
Phchi.S3	AUGUSTUS	transcript	18670761	18673227	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	stop_codon	18670758	18670760	.	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18670761	18670941	1	-	1	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18670761	18670941	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18670942	18671051	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18671052	18671110	1	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18671052	18671110	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18671111	18671207	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18671208	18671337	1	-	1	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18671208	18671337	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18671338	18671427	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18671428	18671492	1	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18671428	18671492	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18671493	18671610	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18671611	18671796	1	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18671611	18671796	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18671797	18671900	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18671901	18672494	0.98	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18671901	18672494	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18672495	18672579	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18672580	18672859	0.62	-	1	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18672580	18672859	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	intron	18672860	18673036	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	CDS	18673037	18673227	0.43	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	exon	18673037	18673227	.	-	.	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
Phchi.S3	AUGUSTUS	start_codon	18673225	18673227	.	-	0	transcript_id "Phchi.S3G268900.t1"; gene_id "Phchi.S3G268900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10205.t1 is derived from g7381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46377613	46378917	.	+	.	Phchi.S1G736400
Phchi.S1	AUGUSTUS	transcript	46377613	46378917	.	+	.	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	start_codon	46377613	46377615	.	+	0	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	CDS	46377613	46377627	0.58	+	0	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	exon	46377613	46377627	.	+	.	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	intron	46377628	46377754	.	+	.	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	CDS	46377755	46378511	0.41	+	0	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	exon	46377755	46378511	.	+	.	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	intron	46378512	46378600	.	+	.	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	CDS	46378601	46378917	0.65	+	2	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	exon	46378601	46378917	.	+	.	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
Phchi.S1	AUGUSTUS	stop_codon	46378918	46378920	.	+	0	transcript_id "Phchi.S1G736400.t1"; gene_id "Phchi.S1G736400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11200.t1 is derived from g15250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4657875	4659013	.	-	.	Phchi.S4G078200
Phchi.S4	AUGUSTUS	transcript	4657875	4659013	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	stop_codon	4657872	4657874	.	-	0	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	CDS	4657875	4657993	1	-	2	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	exon	4657875	4657993	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	intron	4657994	4658065	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	CDS	4658066	4658154	1	-	1	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	exon	4658066	4658154	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	intron	4658155	4658249	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	CDS	4658250	4658415	1	-	2	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	exon	4658250	4658415	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	intron	4658416	4658515	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	CDS	4658516	4658576	1	-	0	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	exon	4658516	4658576	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	intron	4658577	4658673	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	CDS	4658674	4658810	1	-	2	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	exon	4658674	4658810	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	intron	4658811	4658967	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	CDS	4658968	4659013	1	-	0	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	exon	4658968	4659013	.	-	.	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
Phchi.S4	AUGUSTUS	start_codon	4659011	4659013	.	-	0	transcript_id "Phchi.S4G078200.t1"; gene_id "Phchi.S4G078200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2665.t1 is derived from g9585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8112267	8113503	.	+	.	Phchi.S5G127400
Phchi.S5	AUGUSTUS	transcript	8112267	8113503	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	start_codon	8112267	8112269	.	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8112267	8112377	1	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8112267	8112377	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	intron	8112378	8112463	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8112464	8112613	1	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8112464	8112613	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	intron	8112614	8112709	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8112710	8112801	1	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8112710	8112801	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	intron	8112802	8112888	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8112889	8112965	0.98	+	1	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8112889	8112965	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	intron	8112966	8113048	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8113049	8113074	0.99	+	2	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8113049	8113074	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	intron	8113075	8113190	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8113191	8113346	1	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8113191	8113346	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	intron	8113347	8113446	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	CDS	8113447	8113503	0.97	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	exon	8113447	8113503	.	+	.	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
Phchi.S5	AUGUSTUS	stop_codon	8113504	8113506	.	+	0	transcript_id "Phchi.S5G127400.t1"; gene_id "Phchi.S5G127400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11636.t1 is derived from g15687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7408307	7408831	.	+	.	Phchi.S4G121800
Phchi.S4	AUGUSTUS	transcript	7408307	7408831	.	+	.	transcript_id "Phchi.S4G121800.t1"; gene_id "Phchi.S4G121800"
Phchi.S4	AUGUSTUS	start_codon	7408307	7408309	.	+	0	transcript_id "Phchi.S4G121800.t1"; gene_id "Phchi.S4G121800"
Phchi.S4	AUGUSTUS	CDS	7408307	7408831	0.96	+	0	transcript_id "Phchi.S4G121800.t1"; gene_id "Phchi.S4G121800"
Phchi.S4	AUGUSTUS	exon	7408307	7408831	.	+	.	transcript_id "Phchi.S4G121800.t1"; gene_id "Phchi.S4G121800"
Phchi.S4	AUGUSTUS	stop_codon	7408832	7408834	.	+	0	transcript_id "Phchi.S4G121800.t1"; gene_id "Phchi.S4G121800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15672.t1 is derived from g14141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20601495	20602331	.	+	.	Phchi.S3G299100
Phchi.S3	AUGUSTUS	transcript	20601495	20602331	.	+	.	transcript_id "Phchi.S3G299100.t1"; gene_id "Phchi.S3G299100"
Phchi.S3	AUGUSTUS	start_codon	20601495	20601497	.	+	0	transcript_id "Phchi.S3G299100.t1"; gene_id "Phchi.S3G299100"
Phchi.S3	AUGUSTUS	CDS	20601495	20602331	1	+	0	transcript_id "Phchi.S3G299100.t1"; gene_id "Phchi.S3G299100"
Phchi.S3	AUGUSTUS	exon	20601495	20602331	.	+	.	transcript_id "Phchi.S3G299100.t1"; gene_id "Phchi.S3G299100"
Phchi.S3	AUGUSTUS	stop_codon	20602332	20602334	.	+	0	transcript_id "Phchi.S3G299100.t1"; gene_id "Phchi.S3G299100"
# This transcript jg1976.t2 is derived from g8896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1977.t1 is derived from g8897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4106918	4108265	.	+	.	Phchi.S5G058600
Phchi.S5	AUGUSTUS	transcript	4106918	4108265	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	start_codon	4106918	4106920	.	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	CDS	4106918	4107142	0.52	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	exon	4106918	4107142	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	intron	4107143	4107235	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	CDS	4107236	4107328	1	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	exon	4107236	4107328	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	intron	4107329	4107542	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	CDS	4107543	4107635	1	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	exon	4107543	4107635	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	intron	4107636	4107721	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	CDS	4107722	4107820	1	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	exon	4107722	4107820	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	intron	4107821	4107917	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	CDS	4107918	4107974	1	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	exon	4107918	4107974	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	intron	4107975	4108067	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	CDS	4108068	4108265	0.99	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	exon	4108068	4108265	.	+	.	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
Phchi.S5	AUGUSTUS	stop_codon	4108266	4108268	.	+	0	transcript_id "Phchi.S5G058600.t1"; gene_id "Phchi.S5G058600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10814.t1 is derived from g14864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2227684	2228650	.	+	.	Phchi.S4G039600
Phchi.S4	AUGUSTUS	transcript	2227684	2228650	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	start_codon	2227684	2227686	.	+	0	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	CDS	2227684	2227751	0.99	+	0	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	exon	2227684	2227751	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	intron	2227752	2227850	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	CDS	2227851	2227906	1	+	1	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	exon	2227851	2227906	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	intron	2227907	2228078	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	CDS	2228079	2228275	0.99	+	2	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	exon	2228079	2228275	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	intron	2228276	2228376	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	CDS	2228377	2228473	0.65	+	0	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	exon	2228377	2228473	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	intron	2228474	2228567	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	CDS	2228568	2228650	0.71	+	2	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	exon	2228568	2228650	.	+	.	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
Phchi.S4	AUGUSTUS	stop_codon	2228651	2228653	.	+	0	transcript_id "Phchi.S4G039600.t1"; gene_id "Phchi.S4G039600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3107.t1 is derived from g276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1767022	1767450	.	-	.	Phchi.S1G026600
Phchi.S1	AUGUSTUS	transcript	1767022	1767450	.	-	.	transcript_id "Phchi.S1G026600.t1"; gene_id "Phchi.S1G026600"
Phchi.S1	AUGUSTUS	stop_codon	1767019	1767021	.	-	0	transcript_id "Phchi.S1G026600.t1"; gene_id "Phchi.S1G026600"
Phchi.S1	AUGUSTUS	CDS	1767022	1767450	0.9	-	0	transcript_id "Phchi.S1G026600.t1"; gene_id "Phchi.S1G026600"
Phchi.S1	AUGUSTUS	exon	1767022	1767450	.	-	.	transcript_id "Phchi.S1G026600.t1"; gene_id "Phchi.S1G026600"
Phchi.S1	AUGUSTUS	start_codon	1767448	1767450	.	-	0	transcript_id "Phchi.S1G026600.t1"; gene_id "Phchi.S1G026600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15775.t1 is derived from g14245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21288962	21291530	.	+	.	Phchi.S3G309400
Phchi.S3	AUGUSTUS	transcript	21288962	21291530	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	start_codon	21288962	21288964	.	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21288962	21288970	0.28	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21288962	21288970	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21288971	21289255	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21289256	21289315	0.56	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21289256	21289315	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21289316	21289407	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21289408	21289524	1	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21289408	21289524	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21289525	21289639	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21289640	21289709	0.99	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21289640	21289709	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21289710	21289821	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21289822	21289970	1	+	2	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21289822	21289970	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21289971	21290203	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21290204	21290305	1	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21290204	21290305	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21290306	21290401	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21290402	21290606	1	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21290402	21290606	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21290607	21290783	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21290784	21290842	1	+	2	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21290784	21290842	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21290843	21290926	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21290927	21291106	1	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21290927	21291106	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21291107	21291217	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21291218	21291292	1	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21291218	21291292	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	intron	21291293	21291407	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	CDS	21291408	21291530	0.97	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	exon	21291408	21291530	.	+	.	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
Phchi.S3	AUGUSTUS	stop_codon	21291531	21291533	.	+	0	transcript_id "Phchi.S3G309400.t1"; gene_id "Phchi.S3G309400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9759.t1 is derived from g6935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43537006	43537542	.	+	.	Phchi.S1G691800
Phchi.S1	AUGUSTUS	transcript	43537006	43537542	.	+	.	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	start_codon	43537006	43537008	.	+	0	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	CDS	43537006	43537119	1	+	0	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	exon	43537006	43537119	.	+	.	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	intron	43537120	43537205	.	+	.	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	CDS	43537206	43537247	1	+	0	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	exon	43537206	43537247	.	+	.	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	intron	43537248	43537413	.	+	.	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	CDS	43537414	43537542	0.87	+	0	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	exon	43537414	43537542	.	+	.	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
Phchi.S1	AUGUSTUS	stop_codon	43537543	43537545	.	+	0	transcript_id "Phchi.S1G691800.t1"; gene_id "Phchi.S1G691800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg168.t1 is derived from g9950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	969900	974171	.	+	.	Phchi.S6G012700
Phchi.S6	AUGUSTUS	transcript	969900	974171	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	start_codon	969900	969902	.	+	0	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	CDS	969900	971427	0.73	+	0	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	exon	969900	971427	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	intron	971428	971575	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	CDS	971576	971928	0.72	+	2	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	exon	971576	971928	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	intron	971929	972049	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	CDS	972050	972919	0.73	+	0	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	exon	972050	972919	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	intron	972920	973037	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	CDS	973038	974171	0.71	+	0	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	exon	973038	974171	.	+	.	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
Phchi.S6	AUGUSTUS	stop_codon	974172	974174	.	+	0	transcript_id "Phchi.S6G012700.t1"; gene_id "Phchi.S6G012700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9818.t1 is derived from g6994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43929454	43933886	.	-	.	Phchi.S1G697700
Phchi.S1	AUGUSTUS	transcript	43929454	43933886	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	stop_codon	43929451	43929453	.	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43929454	43929559	0.99	-	1	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43929454	43929559	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43929560	43929658	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43929659	43930001	0.85	-	2	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43929659	43930001	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43930002	43930325	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43930326	43930576	1	-	1	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43930326	43930576	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43930577	43930673	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43930674	43930771	1	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43930674	43930771	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43930772	43930880	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43930881	43931017	1	-	2	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43930881	43931017	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43931018	43931097	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43931098	43931276	1	-	1	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43931098	43931276	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43931277	43931352	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43931353	43931507	1	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43931353	43931507	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43931508	43931597	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43931598	43931703	1	-	1	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43931598	43931703	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43931704	43931807	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43931808	43931899	0.99	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43931808	43931899	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43931900	43932048	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43932049	43932170	1	-	2	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43932049	43932170	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43932171	43932331	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43932332	43932432	1	-	1	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43932332	43932432	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43932433	43932504	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43932505	43932724	0.79	-	2	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43932505	43932724	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43932725	43932839	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43932840	43932981	1	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43932840	43932981	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43932982	43933152	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43933153	43933470	0.53	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43933153	43933470	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43933471	43933734	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43933735	43933741	0.95	-	1	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43933735	43933741	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	intron	43933742	43933824	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	CDS	43933825	43933886	0.97	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	exon	43933825	43933886	.	-	.	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
Phchi.S1	AUGUSTUS	start_codon	43933884	43933886	.	-	0	transcript_id "Phchi.S1G697700.t1"; gene_id "Phchi.S1G697700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8836.t1 is derived from g6011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38216026	38216280	.	+	.	Phchi.S1G599500
Phchi.S1	AUGUSTUS	transcript	38216026	38216280	.	+	.	transcript_id "Phchi.S1G599500.t1"; gene_id "Phchi.S1G599500"
Phchi.S1	AUGUSTUS	start_codon	38216026	38216028	.	+	0	transcript_id "Phchi.S1G599500.t1"; gene_id "Phchi.S1G599500"
Phchi.S1	AUGUSTUS	CDS	38216026	38216280	0.56	+	0	transcript_id "Phchi.S1G599500.t1"; gene_id "Phchi.S1G599500"
Phchi.S1	AUGUSTUS	exon	38216026	38216280	.	+	.	transcript_id "Phchi.S1G599500.t1"; gene_id "Phchi.S1G599500"
Phchi.S1	AUGUSTUS	stop_codon	38216281	38216283	.	+	0	transcript_id "Phchi.S1G599500.t1"; gene_id "Phchi.S1G599500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16014.t1 is derived from g14417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C310	AUGUSTUS	gene	1909	2800	.	-	.	Phchi.C310G000100
Phchi.C310	AUGUSTUS	transcript	1909	2800	.	-	.	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	stop_codon	1906	1908	.	-	0	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	CDS	1909	2196	1	-	0	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	exon	1909	2196	.	-	.	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	intron	2197	2297	.	-	.	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	CDS	2298	2374	0.71	-	2	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	exon	2298	2374	.	-	.	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	intron	2375	2577	.	-	.	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	CDS	2578	2800	0.44	-	0	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	exon	2578	2800	.	-	.	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
Phchi.C310	AUGUSTUS	start_codon	2798	2800	.	-	0	transcript_id "Phchi.C310G000100.t1"; gene_id "Phchi.C310G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8493.t1 is derived from g5668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36246702	36247066	.	+	.	Phchi.S1G565200
Phchi.S1	AUGUSTUS	transcript	36246702	36247066	.	+	.	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	start_codon	36246702	36246704	.	+	0	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	CDS	36246702	36246937	0.37	+	0	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	exon	36246702	36246937	.	+	.	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	intron	36246938	36247035	.	+	.	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	CDS	36247036	36247066	0.98	+	1	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	exon	36247036	36247066	.	+	.	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
Phchi.S1	AUGUSTUS	stop_codon	36247067	36247069	.	+	0	transcript_id "Phchi.S1G565200.t1"; gene_id "Phchi.S1G565200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14650.t1 is derived from g13118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13947070	13950602	.	-	.	Phchi.S3G196900
Phchi.S3	AUGUSTUS	transcript	13947070	13950602	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	stop_codon	13947067	13947069	.	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947070	13947234	0.9	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947070	13947234	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947235	13947321	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947322	13947408	1	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947322	13947408	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947409	13947505	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947506	13947625	1	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947506	13947625	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947626	13947727	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947728	13947826	1	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947728	13947826	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947827	13947904	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947905	13948018	0.87	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947905	13948018	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948019	13948129	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948130	13948183	0.87	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948130	13948183	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948184	13948261	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948262	13948356	1	-	2	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948262	13948356	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948357	13948505	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948506	13948641	1	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948506	13948641	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948642	13948764	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948765	13949087	0.99	-	2	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948765	13949087	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13949088	13949244	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13949245	13949350	1	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13949245	13949350	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13949351	13949480	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13949481	13949686	1	-	2	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13949481	13949686	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13949687	13949918	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13949919	13950359	1	-	2	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13949919	13950359	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13950360	13950457	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13950458	13950602	0.96	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13950458	13950602	.	-	.	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	start_codon	13950600	13950602	.	-	0	transcript_id "Phchi.S3G196900.t1"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	transcript	13947070	13950602	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	stop_codon	13947067	13947069	.	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947070	13947234	0.93	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947070	13947234	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947235	13947321	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947322	13947408	1	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947322	13947408	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947409	13947505	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947506	13947625	1	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947506	13947625	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947626	13947727	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947728	13947826	1	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947728	13947826	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13947827	13947904	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13947905	13948018	0.75	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13947905	13948018	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948019	13948129	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948130	13948183	0.75	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948130	13948183	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948184	13948261	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948262	13948356	1	-	2	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948262	13948356	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948357	13948505	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948506	13948641	1	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948506	13948641	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13948642	13948764	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13948765	13949021	1	-	2	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13948765	13949021	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13949022	13949244	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13949245	13949350	1	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13949245	13949350	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13949351	13949480	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13949481	13949686	1	-	2	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13949481	13949686	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13949687	13949918	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13949919	13950359	1	-	2	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13949919	13950359	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	intron	13950360	13950457	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	CDS	13950458	13950602	0.99	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	exon	13950458	13950602	.	-	.	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
Phchi.S3	AUGUSTUS	start_codon	13950600	13950602	.	-	0	transcript_id "Phchi.S3G196900.t2"; gene_id "Phchi.S3G196900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg649.t1 is derived from g10431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4577896	4579999	.	-	.	Phchi.S6G060800
Phchi.S6	AUGUSTUS	transcript	4577896	4579999	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	stop_codon	4577893	4577895	.	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4577896	4578096	1	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4577896	4578096	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4578097	4578181	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4578182	4578322	1	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4578182	4578322	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4578323	4578404	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4578405	4578605	1	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4578405	4578605	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4578606	4578688	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4578689	4578778	1	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4578689	4578778	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4578779	4578876	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4578877	4579050	1	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4578877	4579050	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4579051	4579137	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4579138	4579287	1	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4579138	4579287	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4579288	4579446	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4579447	4579647	0.99	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4579447	4579647	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	intron	4579648	4579759	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	CDS	4579760	4579999	0.58	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	exon	4579760	4579999	.	-	.	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
Phchi.S6	AUGUSTUS	start_codon	4579997	4579999	.	-	0	transcript_id "Phchi.S6G060800.t1"; gene_id "Phchi.S6G060800"
# This transcript jg14688.t2 is derived from g13156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14689.t1 is derived from g13157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14181997	14183694	.	-	.	Phchi.S3G200800
Phchi.S3	AUGUSTUS	transcript	14181997	14183694	.	-	.	transcript_id "Phchi.S3G200800.t1"; gene_id "Phchi.S3G200800"
Phchi.S3	AUGUSTUS	stop_codon	14181994	14181996	.	-	0	transcript_id "Phchi.S3G200800.t1"; gene_id "Phchi.S3G200800"
Phchi.S3	AUGUSTUS	CDS	14181997	14183694	1	-	0	transcript_id "Phchi.S3G200800.t1"; gene_id "Phchi.S3G200800"
Phchi.S3	AUGUSTUS	exon	14181997	14183694	.	-	.	transcript_id "Phchi.S3G200800.t1"; gene_id "Phchi.S3G200800"
Phchi.S3	AUGUSTUS	start_codon	14183692	14183694	.	-	0	transcript_id "Phchi.S3G200800.t1"; gene_id "Phchi.S3G200800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4863.t1 is derived from g2033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13154668	13155321	.	-	.	Phchi.S1G202200
Phchi.S1	AUGUSTUS	transcript	13154668	13155321	.	-	.	transcript_id "Phchi.S1G202200.t1"; gene_id "Phchi.S1G202200"
Phchi.S1	AUGUSTUS	stop_codon	13154665	13154667	.	-	0	transcript_id "Phchi.S1G202200.t1"; gene_id "Phchi.S1G202200"
Phchi.S1	AUGUSTUS	CDS	13154668	13155321	0.87	-	0	transcript_id "Phchi.S1G202200.t1"; gene_id "Phchi.S1G202200"
Phchi.S1	AUGUSTUS	exon	13154668	13155321	.	-	.	transcript_id "Phchi.S1G202200.t1"; gene_id "Phchi.S1G202200"
Phchi.S1	AUGUSTUS	start_codon	13155319	13155321	.	-	0	transcript_id "Phchi.S1G202200.t1"; gene_id "Phchi.S1G202200"
# This transcript jg8922.t2 is derived from g6097.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8923.t1 is derived from g6098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38685129	38686089	.	-	.	Phchi.S1G608200
Phchi.S1	AUGUSTUS	transcript	38685129	38686089	.	-	.	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	stop_codon	38685126	38685128	.	-	0	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	CDS	38685129	38685657	0.94	-	1	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	exon	38685129	38685657	.	-	.	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	intron	38685658	38685742	.	-	.	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	CDS	38685743	38686089	0.9	-	0	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	exon	38685743	38686089	.	-	.	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
Phchi.S1	AUGUSTUS	start_codon	38686087	38686089	.	-	0	transcript_id "Phchi.S1G608200.t1"; gene_id "Phchi.S1G608200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2926.t1 is derived from g95.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	584458	588715	.	-	.	Phchi.S1G008500
Phchi.S1	AUGUSTUS	transcript	584458	588715	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	stop_codon	584455	584457	.	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	584458	584472	1	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	584458	584472	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	584473	584567	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	584568	584652	0.55	-	1	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	584568	584652	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	584653	584779	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	584780	584922	0.88	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	584780	584922	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	584923	585047	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585048	585067	0.95	-	2	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585048	585067	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585068	585225	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585226	585274	0.97	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585226	585274	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585275	585370	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585371	585414	1	-	2	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585371	585414	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585415	585566	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585567	585630	1	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585567	585630	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585631	585734	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585735	585968	0.96	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585735	585968	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585969	586047	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586048	586191	1	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586048	586191	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	586192	586479	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586480	586857	1	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586480	586857	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	586858	586945	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586946	587021	1	-	1	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586946	587021	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587022	587171	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587172	587271	0.98	-	2	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587172	587271	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587272	587374	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587375	587408	0.98	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587375	587408	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587409	587513	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587514	587598	0.95	-	1	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587514	587598	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587599	587710	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587711	587775	0.95	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587711	587775	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587776	587885	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587886	587984	0.99	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587886	587984	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587985	588123	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	588124	588189	1	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	588124	588189	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	588190	588463	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	588464	588715	1	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	588464	588715	.	-	.	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	start_codon	588713	588715	.	-	0	transcript_id "Phchi.S1G008500.t1"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	transcript	584458	588715	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	stop_codon	584455	584457	.	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	584458	584472	0.98	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	584458	584472	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	584473	584567	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	584568	584652	0.61	-	1	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	584568	584652	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	584653	584779	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	584780	584922	0.87	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	584780	584922	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	584923	585047	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585048	585067	0.94	-	2	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585048	585067	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585068	585225	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585226	585274	0.96	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585226	585274	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585275	585370	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585371	585414	1	-	2	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585371	585414	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585415	585566	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585567	585630	1	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585567	585630	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585631	585734	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	585735	585968	0.98	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	585735	585968	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	585969	586047	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586048	586191	0.99	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586048	586191	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	586192	586337	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586338	586348	0.93	-	2	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586338	586348	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	586349	586649	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586650	586857	0.69	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586650	586857	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	586858	586945	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	586946	587021	1	-	1	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	586946	587021	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587022	587171	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587172	587271	0.98	-	2	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587172	587271	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587272	587374	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587375	587408	0.97	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587375	587408	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587409	587513	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587514	587598	0.95	-	1	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587514	587598	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587599	587710	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587711	587775	0.93	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587711	587775	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587776	587885	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	587886	587984	0.99	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	587886	587984	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	587985	588123	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	588124	588189	1	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	588124	588189	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	intron	588190	588463	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	CDS	588464	588715	1	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	exon	588464	588715	.	-	.	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
Phchi.S1	AUGUSTUS	start_codon	588713	588715	.	-	0	transcript_id "Phchi.S1G008500.t2"; gene_id "Phchi.S1G008500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8152.t1 is derived from g5327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34117419	34123615	.	-	.	Phchi.S1G531100
Phchi.S1	AUGUSTUS	transcript	34117419	34123615	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	stop_codon	34117416	34117418	.	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34117419	34117511	0.99	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34117419	34117511	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34117512	34117648	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34117649	34117675	0.65	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34117649	34117675	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34117676	34117797	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34117798	34117817	0.99	-	2	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34117798	34117817	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34117818	34117998	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34117999	34118052	1	-	2	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34117999	34118052	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34118053	34118665	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34118666	34118747	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34118666	34118747	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34118748	34119245	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34119246	34119293	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34119246	34119293	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34119294	34119378	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34119379	34119492	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34119379	34119492	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34119493	34119707	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34119708	34119839	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34119708	34119839	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34119840	34120110	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34120111	34120195	1	-	1	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34120111	34120195	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34120196	34120303	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34120304	34120383	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34120304	34120383	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34120384	34120893	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34120894	34121140	1	-	1	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34120894	34121140	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34121141	34121873	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34121874	34122115	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34121874	34122115	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34122116	34122425	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34122426	34122509	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34122426	34122509	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34122510	34122678	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34122679	34122853	1	-	1	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34122679	34122853	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	intron	34122854	34123358	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	CDS	34123359	34123615	1	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	exon	34123359	34123615	.	-	.	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
Phchi.S1	AUGUSTUS	start_codon	34123613	34123615	.	-	0	transcript_id "Phchi.S1G531100.t1"; gene_id "Phchi.S1G531100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11873.t1 is derived from g15925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8940827	8942859	.	+	.	Phchi.S4G145500
Phchi.S4	AUGUSTUS	transcript	8940827	8942859	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	start_codon	8940827	8940829	.	+	0	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	CDS	8940827	8941006	1	+	0	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	exon	8940827	8941006	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	intron	8941007	8941128	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	CDS	8941129	8941238	1	+	0	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	exon	8941129	8941238	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	intron	8941239	8941580	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	CDS	8941581	8941676	1	+	1	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	exon	8941581	8941676	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	intron	8941677	8941784	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	CDS	8941785	8942041	0.91	+	1	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	exon	8941785	8942041	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	intron	8942042	8942151	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	CDS	8942152	8942372	0.93	+	2	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	exon	8942152	8942372	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	intron	8942373	8942490	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	CDS	8942491	8942859	1	+	0	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	exon	8942491	8942859	.	+	.	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
Phchi.S4	AUGUSTUS	stop_codon	8942860	8942862	.	+	0	transcript_id "Phchi.S4G145500.t1"; gene_id "Phchi.S4G145500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1497.t1 is derived from g8416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1204529	1206894	.	+	.	Phchi.S5G010600
Phchi.S5	AUGUSTUS	transcript	1204529	1206894	.	+	.	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	start_codon	1204529	1204531	.	+	0	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	CDS	1204529	1205291	0.6	+	0	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	exon	1204529	1205291	.	+	.	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	intron	1205292	1205378	.	+	.	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	CDS	1205379	1205561	1	+	2	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	exon	1205379	1205561	.	+	.	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	intron	1205562	1205662	.	+	.	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	CDS	1205663	1206894	1	+	2	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	exon	1205663	1206894	.	+	.	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
Phchi.S5	AUGUSTUS	stop_codon	1206895	1206897	.	+	0	transcript_id "Phchi.S5G010600.t1"; gene_id "Phchi.S5G010600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10401.t1 is derived from g7577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47568716	47569436	.	+	.	Phchi.S1G756000
Phchi.S1	AUGUSTUS	transcript	47568716	47569436	.	+	.	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	start_codon	47568716	47568718	.	+	0	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	CDS	47568716	47568955	0.23	+	0	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	exon	47568716	47568955	.	+	.	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	intron	47568956	47569034	.	+	.	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	CDS	47569035	47569436	0.66	+	0	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	exon	47569035	47569436	.	+	.	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
Phchi.S1	AUGUSTUS	stop_codon	47569437	47569439	.	+	0	transcript_id "Phchi.S1G756000.t1"; gene_id "Phchi.S1G756000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2073.t1 is derived from g8993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4718028	4718698	.	-	.	Phchi.S5G068200
Phchi.S5	AUGUSTUS	transcript	4718028	4718698	.	-	.	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	stop_codon	4718025	4718027	.	-	0	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	CDS	4718028	4718103	0.76	-	1	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	exon	4718028	4718103	.	-	.	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	intron	4718104	4718219	.	-	.	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	CDS	4718220	4718698	0.39	-	0	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	exon	4718220	4718698	.	-	.	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
Phchi.S5	AUGUSTUS	start_codon	4718696	4718698	.	-	0	transcript_id "Phchi.S5G068200.t1"; gene_id "Phchi.S5G068200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1143.t1 is derived from g10926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7974240	7974464	.	-	.	Phchi.S6G110200
Phchi.S6	AUGUSTUS	transcript	7974240	7974464	.	-	.	transcript_id "Phchi.S6G110200.t1"; gene_id "Phchi.S6G110200"
Phchi.S6	AUGUSTUS	stop_codon	7974237	7974239	.	-	0	transcript_id "Phchi.S6G110200.t1"; gene_id "Phchi.S6G110200"
Phchi.S6	AUGUSTUS	CDS	7974240	7974464	0.94	-	0	transcript_id "Phchi.S6G110200.t1"; gene_id "Phchi.S6G110200"
Phchi.S6	AUGUSTUS	exon	7974240	7974464	.	-	.	transcript_id "Phchi.S6G110200.t1"; gene_id "Phchi.S6G110200"
Phchi.S6	AUGUSTUS	start_codon	7974462	7974464	.	-	0	transcript_id "Phchi.S6G110200.t1"; gene_id "Phchi.S6G110200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11199.t1 is derived from g15249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4656596	4657452	.	-	.	Phchi.S4G078100
Phchi.S4	AUGUSTUS	transcript	4656596	4657452	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	stop_codon	4656593	4656595	.	-	0	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	CDS	4656596	4656668	1	-	1	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	exon	4656596	4656668	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	intron	4656669	4656748	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	CDS	4656749	4656821	1	-	2	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	exon	4656749	4656821	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	intron	4656822	4656909	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	CDS	4656910	4657125	1	-	2	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	exon	4656910	4657125	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	intron	4657126	4657194	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	CDS	4657195	4657270	1	-	0	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	exon	4657195	4657270	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	intron	4657271	4657341	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	CDS	4657342	4657452	1	-	0	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	exon	4657342	4657452	.	-	.	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
Phchi.S4	AUGUSTUS	start_codon	4657450	4657452	.	-	0	transcript_id "Phchi.S4G078100.t1"; gene_id "Phchi.S4G078100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4547.t1 is derived from g1717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11060514	11060906	.	-	.	Phchi.S1G170600
Phchi.S1	AUGUSTUS	transcript	11060514	11060906	.	-	.	transcript_id "Phchi.S1G170600.t1"; gene_id "Phchi.S1G170600"
Phchi.S1	AUGUSTUS	stop_codon	11060511	11060513	.	-	0	transcript_id "Phchi.S1G170600.t1"; gene_id "Phchi.S1G170600"
Phchi.S1	AUGUSTUS	CDS	11060514	11060906	0.48	-	0	transcript_id "Phchi.S1G170600.t1"; gene_id "Phchi.S1G170600"
Phchi.S1	AUGUSTUS	exon	11060514	11060906	.	-	.	transcript_id "Phchi.S1G170600.t1"; gene_id "Phchi.S1G170600"
Phchi.S1	AUGUSTUS	start_codon	11060904	11060906	.	-	0	transcript_id "Phchi.S1G170600.t1"; gene_id "Phchi.S1G170600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9636.t1 is derived from g6812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43005776	43007988	.	+	.	Phchi.S1G679500
Phchi.S1	AUGUSTUS	transcript	43005776	43007988	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	start_codon	43005776	43005778	.	+	0	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	CDS	43005776	43006825	0.32	+	0	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	exon	43005776	43006825	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	intron	43006826	43006975	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	CDS	43006976	43007060	0.88	+	0	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	exon	43006976	43007060	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	intron	43007061	43007322	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	CDS	43007323	43007351	0.95	+	2	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	exon	43007323	43007351	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	intron	43007352	43007560	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	CDS	43007561	43007642	0.95	+	0	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	exon	43007561	43007642	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	intron	43007643	43007765	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	CDS	43007766	43007803	0.81	+	2	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	exon	43007766	43007803	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	intron	43007804	43007895	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	CDS	43007896	43007988	0.55	+	0	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	exon	43007896	43007988	.	+	.	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
Phchi.S1	AUGUSTUS	stop_codon	43007989	43007991	.	+	0	transcript_id "Phchi.S1G679500.t1"; gene_id "Phchi.S1G679500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7690.t1 is derived from g4864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30636511	30637140	.	+	.	Phchi.S1G484900
Phchi.S1	AUGUSTUS	transcript	30636511	30637140	.	+	.	transcript_id "Phchi.S1G484900.t1"; gene_id "Phchi.S1G484900"
Phchi.S1	AUGUSTUS	start_codon	30636511	30636513	.	+	0	transcript_id "Phchi.S1G484900.t1"; gene_id "Phchi.S1G484900"
Phchi.S1	AUGUSTUS	CDS	30636511	30637140	0.65	+	0	transcript_id "Phchi.S1G484900.t1"; gene_id "Phchi.S1G484900"
Phchi.S1	AUGUSTUS	exon	30636511	30637140	.	+	.	transcript_id "Phchi.S1G484900.t1"; gene_id "Phchi.S1G484900"
Phchi.S1	AUGUSTUS	stop_codon	30637141	30637143	.	+	0	transcript_id "Phchi.S1G484900.t1"; gene_id "Phchi.S1G484900"
# This transcript jg14856.t2 is derived from g13324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14857.t1 is derived from g13325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15080432	15083002	.	+	.	Phchi.S3G217600
Phchi.S3	AUGUSTUS	transcript	15080432	15083002	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	start_codon	15080432	15080434	.	+	0	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	CDS	15080432	15080758	0.48	+	0	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	exon	15080432	15080758	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	intron	15080759	15080848	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	CDS	15080849	15081004	1	+	0	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	exon	15080849	15081004	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	intron	15081005	15081090	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	CDS	15081091	15081795	1	+	0	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	exon	15081091	15081795	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	intron	15081796	15081913	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	CDS	15081914	15083002	1	+	0	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	exon	15081914	15083002	.	+	.	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
Phchi.S3	AUGUSTUS	stop_codon	15083003	15083005	.	+	0	transcript_id "Phchi.S3G217600.t1"; gene_id "Phchi.S3G217600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7960.t1 is derived from g5135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32106181	32109230	.	-	.	Phchi.S1G511900
Phchi.S1	AUGUSTUS	transcript	32106181	32109230	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	stop_codon	32106178	32106180	.	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32106181	32106330	1	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32106181	32106330	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32106331	32106415	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32106416	32106479	1	-	1	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32106416	32106479	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32106480	32106565	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32106566	32106906	1	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32106566	32106906	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32106907	32106998	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32106999	32107215	1	-	1	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32106999	32107215	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32107216	32107306	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32107307	32107437	1	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32107307	32107437	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32107438	32107514	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32107515	32107631	1	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32107515	32107631	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32107632	32107706	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32107707	32107857	1	-	1	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32107707	32107857	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32107858	32107952	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32107953	32108146	0.87	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32107953	32108146	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32108147	32108263	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32108264	32108368	0.87	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32108264	32108368	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32108369	32108454	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32108455	32109094	0.94	-	1	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32108455	32109094	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	intron	32109095	32109189	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	CDS	32109190	32109230	0.87	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	exon	32109190	32109230	.	-	.	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
Phchi.S1	AUGUSTUS	start_codon	32109228	32109230	.	-	0	transcript_id "Phchi.S1G511900.t1"; gene_id "Phchi.S1G511900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6737.t1 is derived from g3909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24796592	24799136	.	-	.	Phchi.S1G389600
Phchi.S1	AUGUSTUS	transcript	24796592	24799136	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	stop_codon	24796589	24796591	.	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24796592	24796666	0.81	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24796592	24796666	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24796667	24796773	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24796774	24796945	0.87	-	1	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24796774	24796945	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24796946	24797027	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24797028	24797152	1	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24797028	24797152	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24797153	24797240	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24797241	24797306	1	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24797241	24797306	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24797307	24797419	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24797420	24797521	1	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24797420	24797521	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24797522	24797596	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24797597	24797649	1	-	2	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24797597	24797649	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24797650	24797735	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24797736	24797793	1	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24797736	24797793	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24797794	24797994	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24797995	24798093	0.87	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24797995	24798093	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24798094	24798184	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24798185	24798245	0.69	-	1	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24798185	24798245	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24798246	24798337	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24798338	24798348	0.76	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24798338	24798348	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24798349	24798542	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24798543	24798569	1	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24798543	24798569	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24798570	24798774	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24798775	24798794	1	-	2	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24798775	24798794	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24798795	24798896	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24798897	24798927	1	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24798897	24798927	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	intron	24798928	24799070	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	CDS	24799071	24799136	0.59	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	exon	24799071	24799136	.	-	.	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
Phchi.S1	AUGUSTUS	start_codon	24799134	24799136	.	-	0	transcript_id "Phchi.S1G389600.t1"; gene_id "Phchi.S1G389600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7935.t1 is derived from g5109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31996923	31998184	.	+	.	Phchi.S1G509400
Phchi.S1	AUGUSTUS	transcript	31996923	31998184	.	+	.	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	start_codon	31996923	31996925	.	+	0	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	CDS	31996923	31997690	0.59	+	0	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	exon	31996923	31997690	.	+	.	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	intron	31997691	31997782	.	+	.	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	CDS	31997783	31998184	0.72	+	0	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	exon	31997783	31998184	.	+	.	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
Phchi.S1	AUGUSTUS	stop_codon	31998185	31998187	.	+	0	transcript_id "Phchi.S1G509400.t1"; gene_id "Phchi.S1G509400"
# This transcript jg3785.t2 is derived from g954.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3786.t1 is derived from g955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5720289	5720733	.	-	.	Phchi.S1G094500
Phchi.S1	AUGUSTUS	transcript	5720289	5720733	.	-	.	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	stop_codon	5720286	5720288	.	-	0	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	CDS	5720289	5720435	1	-	0	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	exon	5720289	5720435	.	-	.	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	intron	5720436	5720523	.	-	.	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	CDS	5720524	5720733	0.99	-	0	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	exon	5720524	5720733	.	-	.	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
Phchi.S1	AUGUSTUS	start_codon	5720731	5720733	.	-	0	transcript_id "Phchi.S1G094500.t1"; gene_id "Phchi.S1G094500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15122.t1 is derived from g13590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17168885	17169409	.	+	.	Phchi.S3G244100
Phchi.S3	AUGUSTUS	transcript	17168885	17169409	.	+	.	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	start_codon	17168885	17168887	.	+	0	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	CDS	17168885	17169157	0.99	+	0	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	exon	17168885	17169157	.	+	.	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	intron	17169158	17169283	.	+	.	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	CDS	17169284	17169409	0.95	+	0	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	exon	17169284	17169409	.	+	.	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
Phchi.S3	AUGUSTUS	stop_codon	17169410	17169412	.	+	0	transcript_id "Phchi.S3G244100.t1"; gene_id "Phchi.S3G244100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4430.t1 is derived from g1599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10452585	10453293	.	-	.	Phchi.S1G158900
Phchi.S1	AUGUSTUS	transcript	10452585	10453293	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	stop_codon	10452582	10452584	.	-	0	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	CDS	10452585	10452669	1	-	1	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	exon	10452585	10452669	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	intron	10452670	10452809	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	CDS	10452810	10452864	0.71	-	2	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	exon	10452810	10452864	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	intron	10452865	10452986	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	CDS	10452987	10453043	0.69	-	2	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	exon	10452987	10453043	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	intron	10453044	10453115	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	CDS	10453116	10453293	0.81	-	0	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	exon	10453116	10453293	.	-	.	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
Phchi.S1	AUGUSTUS	start_codon	10453291	10453293	.	-	0	transcript_id "Phchi.S1G158900.t1"; gene_id "Phchi.S1G158900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9034.t1 is derived from g6209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39232581	39234059	.	-	.	Phchi.S1G619300
Phchi.S1	AUGUSTUS	transcript	39232581	39234059	.	-	.	transcript_id "Phchi.S1G619300.t1"; gene_id "Phchi.S1G619300"
Phchi.S1	AUGUSTUS	stop_codon	39232578	39232580	.	-	0	transcript_id "Phchi.S1G619300.t1"; gene_id "Phchi.S1G619300"
Phchi.S1	AUGUSTUS	CDS	39232581	39234059	0.45	-	0	transcript_id "Phchi.S1G619300.t1"; gene_id "Phchi.S1G619300"
Phchi.S1	AUGUSTUS	exon	39232581	39234059	.	-	.	transcript_id "Phchi.S1G619300.t1"; gene_id "Phchi.S1G619300"
Phchi.S1	AUGUSTUS	start_codon	39234057	39234059	.	-	0	transcript_id "Phchi.S1G619300.t1"; gene_id "Phchi.S1G619300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12791.t1 is derived from g11256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2391253	2392877	.	-	.	Phchi.S3G011000
Phchi.S3	AUGUSTUS	transcript	2391253	2392877	.	-	.	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	stop_codon	2391250	2391252	.	-	0	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	CDS	2391253	2392565	0.29	-	2	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	exon	2391253	2392565	.	-	.	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	intron	2392566	2392639	.	-	.	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	CDS	2392640	2392877	0.18	-	0	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	exon	2392640	2392877	.	-	.	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
Phchi.S3	AUGUSTUS	start_codon	2392875	2392877	.	-	0	transcript_id "Phchi.S3G011000.t1"; gene_id "Phchi.S3G011000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1683.t1 is derived from g8602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2488387	2488947	.	-	.	Phchi.S5G029200
Phchi.S5	AUGUSTUS	transcript	2488387	2488947	.	-	.	transcript_id "Phchi.S5G029200.t1"; gene_id "Phchi.S5G029200"
Phchi.S5	AUGUSTUS	stop_codon	2488384	2488386	.	-	0	transcript_id "Phchi.S5G029200.t1"; gene_id "Phchi.S5G029200"
Phchi.S5	AUGUSTUS	CDS	2488387	2488947	0.66	-	0	transcript_id "Phchi.S5G029200.t1"; gene_id "Phchi.S5G029200"
Phchi.S5	AUGUSTUS	exon	2488387	2488947	.	-	.	transcript_id "Phchi.S5G029200.t1"; gene_id "Phchi.S5G029200"
Phchi.S5	AUGUSTUS	start_codon	2488945	2488947	.	-	0	transcript_id "Phchi.S5G029200.t1"; gene_id "Phchi.S5G029200"
# This transcript jg4719.t1 is derived from g1888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12454128	12454973	.	-	.	Phchi.S1G187700
Phchi.S1	AUGUSTUS	transcript	12454128	12454973	.	-	.	transcript_id "Phchi.S1G187700.t1"; gene_id "Phchi.S1G187700"
Phchi.S1	AUGUSTUS	stop_codon	12454125	12454127	.	-	0	transcript_id "Phchi.S1G187700.t1"; gene_id "Phchi.S1G187700"
Phchi.S1	AUGUSTUS	CDS	12454128	12454973	0.86	-	0	transcript_id "Phchi.S1G187700.t1"; gene_id "Phchi.S1G187700"
Phchi.S1	AUGUSTUS	exon	12454128	12454973	.	-	.	transcript_id "Phchi.S1G187700.t1"; gene_id "Phchi.S1G187700"
Phchi.S1	AUGUSTUS	start_codon	12454971	12454973	.	-	0	transcript_id "Phchi.S1G187700.t1"; gene_id "Phchi.S1G187700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13.t1 is derived from g9780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C265	AUGUSTUS	gene	3839	6387	.	-	.	Phchi.C265G000400
Phchi.C265	AUGUSTUS	transcript	3839	6387	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	stop_codon	3836	3838	.	-	0	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	CDS	3839	4762	0.86	-	0	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	exon	3839	4762	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	intron	4763	4884	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	CDS	4885	5076	0.71	-	0	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	exon	4885	5076	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	intron	5077	5208	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	CDS	5209	5354	0.28	-	2	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	exon	5209	5354	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	intron	5355	5483	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	CDS	5484	6387	0.54	-	0	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	exon	5484	6387	.	-	.	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
Phchi.C265	AUGUSTUS	start_codon	6385	6387	.	-	0	transcript_id "Phchi.C265G000400.t1"; gene_id "Phchi.C265G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8603.t1 is derived from g5778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36857667	36858110	.	+	.	Phchi.S1G576200
Phchi.S1	AUGUSTUS	transcript	36857667	36858110	.	+	.	transcript_id "Phchi.S1G576200.t1"; gene_id "Phchi.S1G576200"
Phchi.S1	AUGUSTUS	start_codon	36857667	36857669	.	+	0	transcript_id "Phchi.S1G576200.t1"; gene_id "Phchi.S1G576200"
Phchi.S1	AUGUSTUS	CDS	36857667	36858110	0.46	+	0	transcript_id "Phchi.S1G576200.t1"; gene_id "Phchi.S1G576200"
Phchi.S1	AUGUSTUS	exon	36857667	36858110	.	+	.	transcript_id "Phchi.S1G576200.t1"; gene_id "Phchi.S1G576200"
Phchi.S1	AUGUSTUS	stop_codon	36858111	36858113	.	+	0	transcript_id "Phchi.S1G576200.t1"; gene_id "Phchi.S1G576200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1984.t1 is derived from g8904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4245753	4247522	.	+	.	Phchi.S5G059300
Phchi.S5	AUGUSTUS	transcript	4245753	4247522	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	start_codon	4245753	4245755	.	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4245753	4245923	1	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4245753	4245923	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4245924	4246074	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246075	4246155	1	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246075	4246155	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246156	4246229	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246230	4246297	1	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246230	4246297	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246298	4246402	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246403	4246487	1	+	1	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246403	4246487	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246488	4246593	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246594	4246702	1	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246594	4246702	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246703	4246797	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246798	4246886	1	+	2	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246798	4246886	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246887	4246983	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246984	4247048	1	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246984	4247048	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4247049	4247137	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4247138	4247219	1	+	1	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4247138	4247219	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4247220	4247414	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4247415	4247522	1	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4247415	4247522	.	+	.	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	stop_codon	4247523	4247525	.	+	0	transcript_id "Phchi.S5G059300.t1"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	transcript	4245753	4247522	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	start_codon	4245753	4245755	.	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4245753	4245923	0.98	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4245753	4245923	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4245924	4246074	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246075	4246155	0.98	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246075	4246155	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246156	4246236	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246237	4246247	0.99	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246237	4246247	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246248	4246342	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246343	4246487	0.63	+	1	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246343	4246487	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246488	4246593	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246594	4246702	1	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246594	4246702	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246703	4246797	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246798	4246886	1	+	2	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246798	4246886	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4246887	4246983	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4246984	4247048	1	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4246984	4247048	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4247049	4247137	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4247138	4247219	1	+	1	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4247138	4247219	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	intron	4247220	4247414	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	CDS	4247415	4247522	0.99	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	exon	4247415	4247522	.	+	.	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
Phchi.S5	AUGUSTUS	stop_codon	4247523	4247525	.	+	0	transcript_id "Phchi.S5G059300.t2"; gene_id "Phchi.S5G059300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14634.t1 is derived from g13102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13854685	13854991	.	-	.	Phchi.S3G195300
Phchi.S3	AUGUSTUS	transcript	13854685	13854991	.	-	.	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	stop_codon	13854682	13854684	.	-	0	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	CDS	13854685	13854799	0.72	-	1	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	exon	13854685	13854799	.	-	.	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	intron	13854800	13854899	.	-	.	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	CDS	13854900	13854991	0.98	-	0	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	exon	13854900	13854991	.	-	.	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
Phchi.S3	AUGUSTUS	start_codon	13854989	13854991	.	-	0	transcript_id "Phchi.S3G195300.t1"; gene_id "Phchi.S3G195300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14981.t1 is derived from g13449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15860194	15862359	.	+	.	Phchi.S3G230000
Phchi.S3	AUGUSTUS	transcript	15860194	15862359	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	start_codon	15860194	15860196	.	+	0	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15860194	15860389	0.7	+	0	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15860194	15860389	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15860390	15860537	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15860538	15860713	0.98	+	2	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15860538	15860713	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15860714	15860826	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15860827	15860957	0.54	+	0	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15860827	15860957	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15860958	15861122	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15861123	15861243	0.48	+	1	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15861123	15861243	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15861244	15861329	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15861330	15861392	0.39	+	0	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15861330	15861392	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15861393	15861509	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15861510	15861756	0.76	+	0	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15861510	15861756	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15861757	15861875	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15861876	15861963	0.55	+	2	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15861876	15861963	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	intron	15861964	15862067	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	CDS	15862068	15862359	1	+	1	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	exon	15862068	15862359	.	+	.	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
Phchi.S3	AUGUSTUS	stop_codon	15862360	15862362	.	+	0	transcript_id "Phchi.S3G230000.t1"; gene_id "Phchi.S3G230000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg87.t1 is derived from g9869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	446181	448833	.	+	.	Phchi.S6G004600
Phchi.S6	AUGUSTUS	transcript	446181	448833	.	+	.	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	start_codon	446181	446183	.	+	0	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	CDS	446181	447951	0.88	+	0	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	exon	446181	447951	.	+	.	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	intron	447952	448052	.	+	.	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	CDS	448053	448494	0.49	+	2	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	exon	448053	448494	.	+	.	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	intron	448495	448814	.	+	.	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	CDS	448815	448833	0.28	+	1	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	exon	448815	448833	.	+	.	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
Phchi.S6	AUGUSTUS	stop_codon	448834	448836	.	+	0	transcript_id "Phchi.S6G004600.t1"; gene_id "Phchi.S6G004600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12739.t1 is derived from g11204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1462388	1464712	.	+	.	Phchi.S3G005800
Phchi.S3	AUGUSTUS	transcript	1462388	1464712	.	+	.	transcript_id "Phchi.S3G005800.t1"; gene_id "Phchi.S3G005800"
Phchi.S3	AUGUSTUS	start_codon	1462388	1462390	.	+	0	transcript_id "Phchi.S3G005800.t1"; gene_id "Phchi.S3G005800"
Phchi.S3	AUGUSTUS	CDS	1462388	1464712	0.99	+	0	transcript_id "Phchi.S3G005800.t1"; gene_id "Phchi.S3G005800"
Phchi.S3	AUGUSTUS	exon	1462388	1464712	.	+	.	transcript_id "Phchi.S3G005800.t1"; gene_id "Phchi.S3G005800"
Phchi.S3	AUGUSTUS	stop_codon	1464713	1464715	.	+	0	transcript_id "Phchi.S3G005800.t1"; gene_id "Phchi.S3G005800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg578.t1 is derived from g10360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4256861	4258783	.	+	.	Phchi.S6G053700
Phchi.S6	AUGUSTUS	transcript	4256861	4258783	.	+	.	transcript_id "Phchi.S6G053700.t1"; gene_id "Phchi.S6G053700"
Phchi.S6	AUGUSTUS	start_codon	4256861	4256863	.	+	0	transcript_id "Phchi.S6G053700.t1"; gene_id "Phchi.S6G053700"
Phchi.S6	AUGUSTUS	CDS	4256861	4258783	0.62	+	0	transcript_id "Phchi.S6G053700.t1"; gene_id "Phchi.S6G053700"
Phchi.S6	AUGUSTUS	exon	4256861	4258783	.	+	.	transcript_id "Phchi.S6G053700.t1"; gene_id "Phchi.S6G053700"
Phchi.S6	AUGUSTUS	stop_codon	4258784	4258786	.	+	0	transcript_id "Phchi.S6G053700.t1"; gene_id "Phchi.S6G053700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9351.t1 is derived from g6527.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41093954	41096548	.	-	.	Phchi.S1G651000
Phchi.S1	AUGUSTUS	transcript	41093954	41096548	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	stop_codon	41093951	41093953	.	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41093954	41094065	0.95	-	1	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41093954	41094065	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094066	41094168	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094169	41094233	1	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094169	41094233	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094234	41094368	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094369	41094389	1	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094369	41094389	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094390	41094503	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094504	41094575	1	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094504	41094575	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094576	41094671	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094672	41094782	1	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094672	41094782	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094783	41094942	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094943	41095016	1	-	2	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094943	41095016	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095017	41095179	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095180	41095276	1	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095180	41095276	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095277	41095418	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095419	41095511	0.79	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095419	41095511	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095512	41095659	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095660	41095695	0.79	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095660	41095695	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095696	41095871	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095872	41095948	1	-	2	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095872	41095948	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095949	41096034	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41096035	41096220	0.93	-	2	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41096035	41096220	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41096221	41096313	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41096314	41096548	0.4	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41096314	41096548	.	-	.	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	start_codon	41096546	41096548	.	-	0	transcript_id "Phchi.S1G651000.t1"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	transcript	41093954	41096548	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	stop_codon	41093951	41093953	.	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41093954	41094065	0.97	-	1	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41093954	41094065	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094066	41094168	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094169	41094233	0.99	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094169	41094233	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094234	41094368	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094369	41094389	1	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094369	41094389	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094390	41094503	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094504	41094575	1	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094504	41094575	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094576	41094671	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094672	41094782	1	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094672	41094782	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094783	41094942	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094943	41095016	1	-	2	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094943	41095016	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095017	41095179	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095180	41095245	1	-	2	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095180	41095245	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095246	41095418	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095419	41095432	0.61	-	1	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095419	41095432	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095433	41095618	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095619	41095695	0.95	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095619	41095695	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095696	41095871	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095872	41095948	1	-	2	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095872	41095948	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095949	41096034	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41096035	41096220	0.9	-	2	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41096035	41096220	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41096221	41096313	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41096314	41096548	0.48	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41096314	41096548	.	-	.	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	start_codon	41096546	41096548	.	-	0	transcript_id "Phchi.S1G651000.t2"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	transcript	41093954	41096548	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	stop_codon	41093951	41093953	.	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41093954	41094065	0.96	-	1	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41093954	41094065	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094066	41094168	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094169	41094233	1	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094169	41094233	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094234	41094368	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094369	41094389	1	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094369	41094389	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094390	41094503	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094504	41094575	1	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094504	41094575	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094576	41094671	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094672	41094782	1	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094672	41094782	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41094783	41094942	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41094943	41095016	1	-	2	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41094943	41095016	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095017	41095179	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095180	41095196	0.94	-	1	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095180	41095196	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095197	41095276	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095277	41095329	0.94	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095277	41095329	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095330	41095418	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095419	41095511	0.73	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095419	41095511	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095512	41095659	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095660	41095695	0.73	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095660	41095695	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095696	41095871	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41095872	41095948	1	-	2	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41095872	41095948	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41095949	41096034	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41096035	41096220	0.86	-	2	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41096035	41096220	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	intron	41096221	41096313	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	CDS	41096314	41096548	0.49	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	exon	41096314	41096548	.	-	.	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
Phchi.S1	AUGUSTUS	start_codon	41096546	41096548	.	-	0	transcript_id "Phchi.S1G651000.t3"; gene_id "Phchi.S1G651000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7204.t1 is derived from g4376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27626786	27627622	.	+	.	Phchi.S1G436300
Phchi.S1	AUGUSTUS	transcript	27626786	27627622	.	+	.	transcript_id "Phchi.S1G436300.t1"; gene_id "Phchi.S1G436300"
Phchi.S1	AUGUSTUS	start_codon	27626786	27626788	.	+	0	transcript_id "Phchi.S1G436300.t1"; gene_id "Phchi.S1G436300"
Phchi.S1	AUGUSTUS	CDS	27626786	27627622	0.91	+	0	transcript_id "Phchi.S1G436300.t1"; gene_id "Phchi.S1G436300"
Phchi.S1	AUGUSTUS	exon	27626786	27627622	.	+	.	transcript_id "Phchi.S1G436300.t1"; gene_id "Phchi.S1G436300"
Phchi.S1	AUGUSTUS	stop_codon	27627623	27627625	.	+	0	transcript_id "Phchi.S1G436300.t1"; gene_id "Phchi.S1G436300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14882.t1 is derived from g13350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15265936	15267172	.	-	.	Phchi.S3G220100
Phchi.S3	AUGUSTUS	transcript	15265936	15267172	.	-	.	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	stop_codon	15265933	15265935	.	-	0	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	CDS	15265936	15266714	1	-	2	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	exon	15265936	15266714	.	-	.	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	intron	15266715	15266844	.	-	.	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	CDS	15266845	15267172	0.83	-	0	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	exon	15266845	15267172	.	-	.	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
Phchi.S3	AUGUSTUS	start_codon	15267170	15267172	.	-	0	transcript_id "Phchi.S3G220100.t1"; gene_id "Phchi.S3G220100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8234.t1 is derived from g5409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34570394	34572315	.	-	.	Phchi.S1G539300
Phchi.S1	AUGUSTUS	transcript	34570394	34572315	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	stop_codon	34570391	34570393	.	-	0	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34570394	34570407	0.93	-	2	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34570394	34570407	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	intron	34570408	34570618	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34570619	34570631	0.91	-	0	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34570619	34570631	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	intron	34570632	34570813	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34570814	34570990	0.96	-	0	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34570814	34570990	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	intron	34570991	34571084	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34571085	34571177	1	-	0	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34571085	34571177	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	intron	34571178	34571279	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34571280	34571647	0.74	-	2	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34571280	34571647	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	intron	34571648	34571729	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34571730	34571948	1	-	2	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34571730	34571948	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	intron	34571949	34572299	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	CDS	34572300	34572315	1	-	0	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	exon	34572300	34572315	.	-	.	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
Phchi.S1	AUGUSTUS	start_codon	34572313	34572315	.	-	0	transcript_id "Phchi.S1G539300.t1"; gene_id "Phchi.S1G539300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7118.t1 is derived from g4290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27060433	27061781	.	-	.	Phchi.S1G427700
Phchi.S1	AUGUSTUS	transcript	27060433	27061781	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	stop_codon	27060430	27060432	.	-	0	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	CDS	27060433	27060450	0.68	-	0	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	exon	27060433	27060450	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	intron	27060451	27060554	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	CDS	27060555	27060636	0.84	-	1	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	exon	27060555	27060636	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	intron	27060637	27060729	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	CDS	27060730	27060800	1	-	0	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	exon	27060730	27060800	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	intron	27060801	27060905	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	CDS	27060906	27061039	0.97	-	2	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	exon	27060906	27061039	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	intron	27061040	27061138	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	CDS	27061139	27061214	1	-	0	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	exon	27061139	27061214	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	intron	27061215	27061304	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	CDS	27061305	27061781	0.52	-	0	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	exon	27061305	27061781	.	-	.	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
Phchi.S1	AUGUSTUS	start_codon	27061779	27061781	.	-	0	transcript_id "Phchi.S1G427700.t1"; gene_id "Phchi.S1G427700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13890.t1 is derived from g12357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9476271	9480579	.	+	.	Phchi.S3G120900
Phchi.S3	AUGUSTUS	transcript	9476271	9480579	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	start_codon	9476271	9476273	.	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9476271	9477654	0.99	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9476271	9477654	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9477655	9477834	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9477835	9478226	1	+	2	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9477835	9478226	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9478227	9478376	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9478377	9478913	1	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9478377	9478913	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9478914	9479014	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9479015	9479371	0.99	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9479015	9479371	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9479372	9479571	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9479572	9479795	1	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9479572	9479795	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9479796	9479905	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9479906	9479972	1	+	1	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9479906	9479972	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9479973	9480055	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9480056	9480252	1	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9480056	9480252	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	intron	9480253	9480368	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	CDS	9480369	9480579	1	+	1	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	exon	9480369	9480579	.	+	.	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
Phchi.S3	AUGUSTUS	stop_codon	9480580	9480582	.	+	0	transcript_id "Phchi.S3G120900.t1"; gene_id "Phchi.S3G120900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10854.t1 is derived from g14904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2551128	2551883	.	-	.	Phchi.S4G043600
Phchi.S4	AUGUSTUS	transcript	2551128	2551883	.	-	.	transcript_id "Phchi.S4G043600.t1"; gene_id "Phchi.S4G043600"
Phchi.S4	AUGUSTUS	stop_codon	2551125	2551127	.	-	0	transcript_id "Phchi.S4G043600.t1"; gene_id "Phchi.S4G043600"
Phchi.S4	AUGUSTUS	CDS	2551128	2551883	0.51	-	0	transcript_id "Phchi.S4G043600.t1"; gene_id "Phchi.S4G043600"
Phchi.S4	AUGUSTUS	exon	2551128	2551883	.	-	.	transcript_id "Phchi.S4G043600.t1"; gene_id "Phchi.S4G043600"
Phchi.S4	AUGUSTUS	start_codon	2551881	2551883	.	-	0	transcript_id "Phchi.S4G043600.t1"; gene_id "Phchi.S4G043600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11467.t1 is derived from g15517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6504562	6506155	.	+	.	Phchi.S4G104900
Phchi.S4	AUGUSTUS	transcript	6504562	6506155	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	start_codon	6504562	6504564	.	+	0	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6504562	6504895	0.95	+	0	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6504562	6504895	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	intron	6504896	6505002	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6505003	6505289	0.32	+	2	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6505003	6505289	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	intron	6505290	6505435	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6505436	6505534	0.51	+	0	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6505436	6505534	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	intron	6505535	6505633	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6505634	6505727	0.98	+	0	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6505634	6505727	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	intron	6505728	6505813	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6505814	6505863	0.68	+	2	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6505814	6505863	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	intron	6505864	6505976	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6505977	6505983	0.67	+	0	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6505977	6505983	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	intron	6505984	6506054	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	CDS	6506055	6506155	0.64	+	2	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	exon	6506055	6506155	.	+	.	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
Phchi.S4	AUGUSTUS	stop_codon	6506156	6506158	.	+	0	transcript_id "Phchi.S4G104900.t1"; gene_id "Phchi.S4G104900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3136.t1 is derived from g305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1928925	1929902	.	+	.	Phchi.S1G029500
Phchi.S1	AUGUSTUS	transcript	1928925	1929902	.	+	.	transcript_id "Phchi.S1G029500.t1"; gene_id "Phchi.S1G029500"
Phchi.S1	AUGUSTUS	start_codon	1928925	1928927	.	+	0	transcript_id "Phchi.S1G029500.t1"; gene_id "Phchi.S1G029500"
Phchi.S1	AUGUSTUS	CDS	1928925	1929902	0.73	+	0	transcript_id "Phchi.S1G029500.t1"; gene_id "Phchi.S1G029500"
Phchi.S1	AUGUSTUS	exon	1928925	1929902	.	+	.	transcript_id "Phchi.S1G029500.t1"; gene_id "Phchi.S1G029500"
Phchi.S1	AUGUSTUS	stop_codon	1929903	1929905	.	+	0	transcript_id "Phchi.S1G029500.t1"; gene_id "Phchi.S1G029500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15401.t1 is derived from g13869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18823665	18824296	.	-	.	Phchi.S3G272000
Phchi.S3	AUGUSTUS	transcript	18823665	18824296	.	-	.	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	stop_codon	18823662	18823664	.	-	0	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	CDS	18823665	18823892	1	-	0	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	exon	18823665	18823892	.	-	.	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	intron	18823893	18824095	.	-	.	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	CDS	18824096	18824296	0.81	-	0	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	exon	18824096	18824296	.	-	.	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
Phchi.S3	AUGUSTUS	start_codon	18824294	18824296	.	-	0	transcript_id "Phchi.S3G272000.t1"; gene_id "Phchi.S3G272000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14968.t1 is derived from g13436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15788621	15790832	.	+	.	Phchi.S3G228700
Phchi.S3	AUGUSTUS	transcript	15788621	15790832	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	start_codon	15788621	15788623	.	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15788621	15788661	0.53	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15788621	15788661	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15788662	15788793	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15788794	15788925	1	+	1	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15788794	15788925	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15788926	15789134	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15789135	15789231	1	+	1	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15789135	15789231	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15789232	15789367	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15789368	15789478	1	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15789368	15789478	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15789479	15789572	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15789573	15789641	1	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15789573	15789641	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15789642	15789726	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15789727	15789798	1	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15789727	15789798	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15789799	15789922	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15789923	15789973	1	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15789923	15789973	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15789974	15790058	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15790059	15790152	1	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15790059	15790152	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15790153	15790286	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15790287	15790319	1	+	2	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15790287	15790319	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15790320	15790396	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15790397	15790464	1	+	2	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15790397	15790464	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15790465	15790614	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15790615	15790745	1	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15790615	15790745	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	intron	15790746	15790831	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	CDS	15790832	15790832	1	+	1	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	exon	15790832	15790832	.	+	.	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
Phchi.S3	AUGUSTUS	stop_codon	15790833	15790835	.	+	0	transcript_id "Phchi.S3G228700.t1"; gene_id "Phchi.S3G228700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8222.t1 is derived from g5397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34533124	34538628	.	-	.	Phchi.S1G538100
Phchi.S1	AUGUSTUS	transcript	34533124	34537093	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	stop_codon	34533121	34533123	.	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533124	34533165	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533124	34533165	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533166	34533244	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533245	34533299	1	-	1	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533245	34533299	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533300	34533393	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533394	34533479	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533394	34533479	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533480	34533568	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533569	34533673	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533569	34533673	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533674	34533770	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533771	34533851	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533771	34533851	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533852	34534012	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534013	34534120	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534013	34534120	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534121	34534242	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534243	34534320	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534243	34534320	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534321	34534410	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534411	34534512	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534411	34534512	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534513	34534635	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534636	34534704	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534636	34534704	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534705	34534891	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534892	34535029	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534892	34535029	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535030	34535277	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535278	34535380	0.8	-	1	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535278	34535380	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535381	34535482	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535483	34535584	0.99	-	1	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535483	34535584	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535585	34535692	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535693	34535783	0.99	-	2	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535693	34535783	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535784	34535864	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535865	34535972	1	-	2	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535865	34535972	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535973	34536069	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536070	34536145	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536070	34536145	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536146	34536259	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536260	34536349	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536260	34536349	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536350	34536548	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536549	34536671	1	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536549	34536671	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536672	34536991	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536992	34537093	0.59	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536992	34537093	.	-	.	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	start_codon	34537091	34537093	.	-	0	transcript_id "Phchi.S1G538100.t1"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	transcript	34533124	34538628	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	stop_codon	34533121	34533123	.	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533124	34533165	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533124	34533165	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533166	34533244	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533245	34533299	1	-	1	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533245	34533299	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533300	34533393	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533394	34533479	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533394	34533479	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533480	34533568	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533569	34533673	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533569	34533673	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533674	34533770	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533771	34533851	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533771	34533851	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533852	34534012	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534013	34534120	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534013	34534120	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534121	34534242	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534243	34534320	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534243	34534320	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534321	34534410	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534411	34534512	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534411	34534512	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534513	34534635	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534636	34534704	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534636	34534704	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534705	34534891	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534892	34535029	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534892	34535029	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535030	34535277	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535278	34535380	0.86	-	1	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535278	34535380	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535381	34535482	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535483	34535584	0.97	-	1	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535483	34535584	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535585	34535692	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535693	34535783	0.98	-	2	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535693	34535783	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535784	34535864	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535865	34535972	1	-	2	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535865	34535972	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535973	34536069	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536070	34536145	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536070	34536145	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536146	34536259	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536260	34536349	1	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536260	34536349	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536350	34536548	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536549	34536594	0.35	-	1	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536549	34536594	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536595	34536689	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536690	34536720	0.34	-	2	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536690	34536720	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536721	34536991	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536992	34537708	0.44	-	2	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536992	34537708	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34537709	34537819	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34537820	34537884	0.98	-	1	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34537820	34537884	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34537885	34538113	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34538114	34538185	0.99	-	1	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34538114	34538185	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34538186	34538290	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34538291	34538628	0.51	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34538291	34538628	.	-	.	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	start_codon	34538626	34538628	.	-	0	transcript_id "Phchi.S1G538100.t2"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	transcript	34533124	34538628	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	stop_codon	34533121	34533123	.	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533124	34533165	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533124	34533165	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533166	34533244	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533245	34533299	1	-	1	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533245	34533299	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533300	34533393	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533394	34533479	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533394	34533479	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533480	34533568	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533569	34533673	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533569	34533673	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533674	34533770	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34533771	34533851	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34533771	34533851	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34533852	34534012	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534013	34534120	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534013	34534120	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534121	34534242	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534243	34534320	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534243	34534320	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534321	34534410	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534411	34534512	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534411	34534512	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534513	34534635	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534636	34534704	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534636	34534704	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34534705	34534891	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34534892	34535029	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34534892	34535029	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535030	34535277	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535278	34535380	0.79	-	1	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535278	34535380	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535381	34535482	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535483	34535584	0.98	-	1	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535483	34535584	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535585	34535692	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535693	34535783	0.97	-	2	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535693	34535783	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535784	34535864	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34535865	34535972	1	-	2	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34535865	34535972	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34535973	34536069	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536070	34536145	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536070	34536145	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536146	34536259	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536260	34536349	1	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536260	34536349	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536350	34536548	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536549	34536594	0.44	-	1	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536549	34536594	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536595	34536689	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536690	34536720	0.44	-	2	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536690	34536720	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34536721	34536991	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34536992	34537708	0.35	-	2	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34536992	34537708	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34537709	34537819	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34537820	34537884	0.97	-	1	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34537820	34537884	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34537885	34537969	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34537970	34538040	0.67	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34537970	34538040	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34538041	34538127	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34538128	34538185	0.61	-	1	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34538128	34538185	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	intron	34538186	34538290	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	CDS	34538291	34538628	0.52	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	exon	34538291	34538628	.	-	.	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
Phchi.S1	AUGUSTUS	start_codon	34538626	34538628	.	-	0	transcript_id "Phchi.S1G538100.t3"; gene_id "Phchi.S1G538100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9679.t1 is derived from g6855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43251095	43251975	.	+	.	Phchi.S1G683800
Phchi.S1	AUGUSTUS	transcript	43251095	43251975	.	+	.	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	start_codon	43251095	43251097	.	+	0	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	CDS	43251095	43251226	0.45	+	0	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	exon	43251095	43251226	.	+	.	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	intron	43251227	43251354	.	+	.	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	CDS	43251355	43251975	1	+	0	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	exon	43251355	43251975	.	+	.	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
Phchi.S1	AUGUSTUS	stop_codon	43251976	43251978	.	+	0	transcript_id "Phchi.S1G683800.t1"; gene_id "Phchi.S1G683800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3305.t1 is derived from g474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2756866	2758299	.	-	.	Phchi.S1G046400
Phchi.S1	AUGUSTUS	transcript	2756866	2758299	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	stop_codon	2756863	2756865	.	-	0	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2756866	2756965	0.68	-	1	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2756866	2756965	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	intron	2756966	2757138	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2757139	2757192	0.64	-	1	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2757139	2757192	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	intron	2757193	2757278	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2757279	2757386	0.99	-	1	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2757279	2757386	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	intron	2757387	2757487	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2757488	2757564	0.81	-	0	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2757488	2757564	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	intron	2757565	2757745	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2757746	2757838	1	-	0	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2757746	2757838	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	intron	2757839	2757936	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2757937	2757997	1	-	1	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2757937	2757997	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	intron	2757998	2758156	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	CDS	2758157	2758299	0.82	-	0	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	exon	2758157	2758299	.	-	.	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
Phchi.S1	AUGUSTUS	start_codon	2758297	2758299	.	-	0	transcript_id "Phchi.S1G046400.t1"; gene_id "Phchi.S1G046400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2828.t1 is derived from g9748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9080640	9083562	.	-	.	Phchi.S5G143700
Phchi.S5	AUGUSTUS	transcript	9080640	9083562	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	stop_codon	9080637	9080639	.	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9080640	9080726	0.9	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9080640	9080726	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9080727	9080812	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9080813	9080881	1	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9080813	9080881	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9080882	9080977	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9080978	9081043	1	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9080978	9081043	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9081044	9081226	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9081227	9081233	1	-	1	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9081227	9081233	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9081234	9081375	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9081376	9081559	1	-	2	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9081376	9081559	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9081560	9081645	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9081646	9081693	1	-	2	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9081646	9081693	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9081694	9081824	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9081825	9081933	0.94	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9081825	9081933	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9081934	9082047	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9082048	9082208	1	-	2	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9082048	9082208	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9082209	9082418	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9082419	9082805	0.72	-	2	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9082419	9082805	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9082806	9082966	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9082967	9083068	0.9	-	2	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9082967	9083068	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9083069	9083186	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9083187	9083238	0.99	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9083187	9083238	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9083239	9083310	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9083311	9083358	0.94	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9083311	9083358	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	intron	9083359	9083433	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	CDS	9083434	9083562	0.99	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	exon	9083434	9083562	.	-	.	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
Phchi.S5	AUGUSTUS	start_codon	9083560	9083562	.	-	0	transcript_id "Phchi.S5G143700.t1"; gene_id "Phchi.S5G143700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10358.t1 is derived from g7534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47334421	47334870	.	-	.	Phchi.S1G751700
Phchi.S1	AUGUSTUS	transcript	47334421	47334870	.	-	.	transcript_id "Phchi.S1G751700.t1"; gene_id "Phchi.S1G751700"
Phchi.S1	AUGUSTUS	stop_codon	47334418	47334420	.	-	0	transcript_id "Phchi.S1G751700.t1"; gene_id "Phchi.S1G751700"
Phchi.S1	AUGUSTUS	CDS	47334421	47334870	0.67	-	0	transcript_id "Phchi.S1G751700.t1"; gene_id "Phchi.S1G751700"
Phchi.S1	AUGUSTUS	exon	47334421	47334870	.	-	.	transcript_id "Phchi.S1G751700.t1"; gene_id "Phchi.S1G751700"
Phchi.S1	AUGUSTUS	start_codon	47334868	47334870	.	-	0	transcript_id "Phchi.S1G751700.t1"; gene_id "Phchi.S1G751700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15661.t1 is derived from g14130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20551289	20553992	.	-	.	Phchi.S3G298000
Phchi.S3	AUGUSTUS	transcript	20551289	20553992	.	-	.	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	stop_codon	20551286	20551288	.	-	0	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	CDS	20551289	20552711	0.58	-	1	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	exon	20551289	20552711	.	-	.	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	intron	20552712	20552804	.	-	.	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	CDS	20552805	20553816	1	-	2	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	exon	20552805	20553816	.	-	.	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	intron	20553817	20553886	.	-	.	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	CDS	20553887	20553992	0.87	-	0	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	exon	20553887	20553992	.	-	.	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
Phchi.S3	AUGUSTUS	start_codon	20553990	20553992	.	-	0	transcript_id "Phchi.S3G298000.t1"; gene_id "Phchi.S3G298000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12990.t1 is derived from g11455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3495981	3496292	.	+	.	Phchi.S3G030900
Phchi.S3	AUGUSTUS	transcript	3495981	3496292	.	+	.	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	start_codon	3495981	3495983	.	+	0	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	CDS	3495981	3496074	0.94	+	0	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	exon	3495981	3496074	.	+	.	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	intron	3496075	3496152	.	+	.	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	CDS	3496153	3496292	0.64	+	2	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	exon	3496153	3496292	.	+	.	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
Phchi.S3	AUGUSTUS	stop_codon	3496293	3496295	.	+	0	transcript_id "Phchi.S3G030900.t1"; gene_id "Phchi.S3G030900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1504.t1 is derived from g8423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1264597	1269487	.	+	.	Phchi.S5G011300
Phchi.S5	AUGUSTUS	transcript	1264597	1269487	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	start_codon	1264597	1264599	.	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1264597	1264681	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1264597	1264681	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1264682	1264767	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1264768	1264853	1	+	2	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1264768	1264853	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1264854	1264928	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1264929	1265006	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1264929	1265006	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1265007	1265096	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1265097	1265276	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1265097	1265276	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1265277	1265402	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1265403	1265453	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1265403	1265453	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1265454	1265560	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1265561	1265692	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1265561	1265692	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1265693	1265771	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1265772	1265897	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1265772	1265897	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1265898	1265986	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1265987	1266064	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1265987	1266064	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1266065	1266145	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1266146	1266238	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1266146	1266238	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1266239	1266491	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1266492	1266617	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1266492	1266617	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1266618	1266710	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1266711	1266794	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1266711	1266794	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1266795	1266909	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1266910	1267005	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1266910	1267005	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1267006	1267438	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1267439	1267651	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1267439	1267651	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1267652	1267732	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1267733	1267808	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1267733	1267808	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1267809	1267904	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1267905	1268008	1	+	2	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1267905	1268008	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1268009	1268162	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1268163	1268422	0.99	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1268163	1268422	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1268423	1268526	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1268527	1268613	1	+	1	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1268527	1268613	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1268614	1268733	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1268734	1268961	1	+	1	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1268734	1268961	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1268962	1269059	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1269060	1269138	1	+	1	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1269060	1269138	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1269139	1269235	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1269236	1269299	1	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1269236	1269299	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	intron	1269300	1269389	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	CDS	1269390	1269487	0.98	+	2	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	exon	1269390	1269487	.	+	.	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
Phchi.S5	AUGUSTUS	stop_codon	1269488	1269490	.	+	0	transcript_id "Phchi.S5G011300.t1"; gene_id "Phchi.S5G011300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13492.t1 is derived from g11959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7152771	7153868	.	-	.	Phchi.S3G081100
Phchi.S3	AUGUSTUS	transcript	7152771	7153868	.	-	.	transcript_id "Phchi.S3G081100.t1"; gene_id "Phchi.S3G081100"
Phchi.S3	AUGUSTUS	stop_codon	7152768	7152770	.	-	0	transcript_id "Phchi.S3G081100.t1"; gene_id "Phchi.S3G081100"
Phchi.S3	AUGUSTUS	CDS	7152771	7153868	0.81	-	0	transcript_id "Phchi.S3G081100.t1"; gene_id "Phchi.S3G081100"
Phchi.S3	AUGUSTUS	exon	7152771	7153868	.	-	.	transcript_id "Phchi.S3G081100.t1"; gene_id "Phchi.S3G081100"
Phchi.S3	AUGUSTUS	start_codon	7153866	7153868	.	-	0	transcript_id "Phchi.S3G081100.t1"; gene_id "Phchi.S3G081100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11114.t1 is derived from g15164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4221543	4224128	.	+	.	Phchi.S4G069600
Phchi.S4	AUGUSTUS	transcript	4221543	4224128	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	start_codon	4221543	4221545	.	+	0	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	CDS	4221543	4221674	0.93	+	0	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	exon	4221543	4221674	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	intron	4221675	4221776	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	CDS	4221777	4221874	0.95	+	0	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	exon	4221777	4221874	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	intron	4221875	4222002	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	CDS	4222003	4222048	1	+	1	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	exon	4222003	4222048	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	intron	4222049	4222199	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	CDS	4222200	4222349	1	+	0	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	exon	4222200	4222349	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	intron	4222350	4222472	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	CDS	4222473	4224128	1	+	0	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	exon	4222473	4224128	.	+	.	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
Phchi.S4	AUGUSTUS	stop_codon	4224129	4224131	.	+	0	transcript_id "Phchi.S4G069600.t1"; gene_id "Phchi.S4G069600"
# This transcript jg15915.t2 is derived from g14385.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15915.t3 is derived from g14385.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15915.t4 is derived from g14385.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15916.t1 is derived from g14386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22196552	22199079	.	-	.	Phchi.S3G323500
Phchi.S3	AUGUSTUS	transcript	22196552	22199079	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	stop_codon	22196549	22196551	.	-	0	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22196552	22196668	1	-	0	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22196552	22196668	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22196669	22196753	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22196754	22196828	1	-	0	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22196754	22196828	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22196829	22196921	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22196922	22197028	1	-	2	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22196922	22197028	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22197029	22197220	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22197221	22197303	0.44	-	1	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22197221	22197303	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22197304	22197402	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22197403	22197412	0.44	-	2	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22197403	22197412	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22197413	22197494	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22197495	22198038	0.41	-	0	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22197495	22198038	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22198039	22198212	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22198213	22198286	1	-	2	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22198213	22198286	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22198287	22198413	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22198414	22198476	1	-	2	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22198414	22198476	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22198477	22198559	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22198560	22198664	1	-	2	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22198560	22198664	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22198665	22198743	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22198744	22198832	1	-	1	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22198744	22198832	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	intron	22198833	22198963	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	CDS	22198964	22199079	0.89	-	0	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	exon	22198964	22199079	.	-	.	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
Phchi.S3	AUGUSTUS	start_codon	22199077	22199079	.	-	0	transcript_id "Phchi.S3G323500.t1"; gene_id "Phchi.S3G323500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14843.t1 is derived from g13311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14961517	14963464	.	+	.	Phchi.S3G216200
Phchi.S3	AUGUSTUS	transcript	14961517	14963464	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	start_codon	14961517	14961519	.	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14961517	14961828	0.59	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14961517	14961828	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14961829	14961927	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14961928	14962152	0.96	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14961928	14962152	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14962153	14962281	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14962282	14962353	1	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14962282	14962353	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14962354	14962441	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14962442	14962493	1	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14962442	14962493	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14962494	14962579	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14962580	14962683	1	+	2	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14962580	14962683	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14962684	14962770	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14962771	14962832	0.98	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14962771	14962832	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14962833	14962927	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14962928	14962991	0.98	+	1	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14962928	14962991	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14962992	14963173	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14963174	14963281	1	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14963174	14963281	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	intron	14963282	14963377	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	CDS	14963378	14963464	0.67	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	exon	14963378	14963464	.	+	.	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
Phchi.S3	AUGUSTUS	stop_codon	14963465	14963467	.	+	0	transcript_id "Phchi.S3G216200.t1"; gene_id "Phchi.S3G216200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg286.t1 is derived from g10068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2027928	2030070	.	+	.	Phchi.S6G024500
Phchi.S6	AUGUSTUS	transcript	2027928	2030070	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	start_codon	2027928	2027930	.	+	0	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2027928	2028002	0.99	+	0	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2027928	2028002	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	intron	2028003	2028075	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2028076	2028349	0.51	+	0	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2028076	2028349	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	intron	2028350	2028439	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2028440	2028620	0.5	+	2	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2028440	2028620	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	intron	2028621	2028730	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2028731	2029046	0.95	+	1	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2028731	2029046	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	intron	2029047	2029146	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2029147	2029458	1	+	0	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2029147	2029458	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	intron	2029459	2029549	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2029550	2029715	1	+	0	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2029550	2029715	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	intron	2029716	2029792	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	CDS	2029793	2030070	1	+	2	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	exon	2029793	2030070	.	+	.	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
Phchi.S6	AUGUSTUS	stop_codon	2030071	2030073	.	+	0	transcript_id "Phchi.S6G024500.t1"; gene_id "Phchi.S6G024500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2730.t1 is derived from g9650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8476207	8478148	.	+	.	Phchi.S5G133900
Phchi.S5	AUGUSTUS	transcript	8476207	8478148	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	start_codon	8476207	8476209	.	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8476207	8476560	1	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8476207	8476560	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	intron	8476561	8476649	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8476650	8476762	1	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8476650	8476762	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	intron	8476763	8476858	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8476859	8477042	1	+	1	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8476859	8477042	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	intron	8477043	8477131	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8477132	8477232	1	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8477132	8477232	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	intron	8477233	8477319	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8477320	8477527	1	+	1	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8477320	8477527	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	intron	8477528	8477621	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8477622	8477876	1	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8477622	8477876	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	intron	8477877	8477962	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	CDS	8477963	8478148	0.99	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	exon	8477963	8478148	.	+	.	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
Phchi.S5	AUGUSTUS	stop_codon	8478149	8478151	.	+	0	transcript_id "Phchi.S5G133900.t1"; gene_id "Phchi.S5G133900"
# This transcript jg4901.t2 is derived from g2071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4902.t1 is derived from g2072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13328825	13331794	.	-	.	Phchi.S1G206100
Phchi.S1	AUGUSTUS	transcript	13328825	13331794	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	stop_codon	13328822	13328824	.	-	0	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	CDS	13328825	13329098	0.96	-	1	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	exon	13328825	13329098	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	intron	13329099	13329208	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	CDS	13329209	13329316	1	-	1	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	exon	13329209	13329316	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	intron	13329317	13329429	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	CDS	13329430	13329586	1	-	2	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	exon	13329430	13329586	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	intron	13329587	13329669	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	CDS	13329670	13329743	1	-	1	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	exon	13329670	13329743	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	intron	13329744	13329848	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	CDS	13329849	13330486	0.99	-	0	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	exon	13329849	13330486	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	intron	13330487	13330573	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	CDS	13330574	13331794	0.97	-	0	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	exon	13330574	13331794	.	-	.	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
Phchi.S1	AUGUSTUS	start_codon	13331792	13331794	.	-	0	transcript_id "Phchi.S1G206100.t1"; gene_id "Phchi.S1G206100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1483.t1 is derived from g8402.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1142750	1145899	.	+	.	Phchi.S5G009200
Phchi.S5	AUGUSTUS	transcript	1142750	1145899	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	start_codon	1142750	1142752	.	+	0	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1142750	1144147	0.57	+	0	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1142750	1144147	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	intron	1144148	1144363	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1144364	1144479	1	+	0	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1144364	1144479	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	intron	1144480	1144560	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1144561	1145720	1	+	1	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1144561	1145720	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	intron	1145721	1145804	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1145805	1145899	1	+	2	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1145805	1145899	.	+	.	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	stop_codon	1145900	1145902	.	+	0	transcript_id "Phchi.S5G009200.t1"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	transcript	1142750	1145899	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	start_codon	1142750	1142752	.	+	0	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1142750	1144147	0.56	+	0	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1142750	1144147	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	intron	1144148	1144363	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1144364	1144479	1	+	0	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1144364	1144479	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	intron	1144480	1144560	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1144561	1145720	1	+	1	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1144561	1145720	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	intron	1145721	1145801	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	CDS	1145802	1145899	1	+	2	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	exon	1145802	1145899	.	+	.	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
Phchi.S5	AUGUSTUS	stop_codon	1145900	1145902	.	+	0	transcript_id "Phchi.S5G009200.t2"; gene_id "Phchi.S5G009200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15338.t1 is derived from g13806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18454107	18454715	.	+	.	Phchi.S3G265700
Phchi.S3	AUGUSTUS	transcript	18454107	18454715	.	+	.	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	start_codon	18454107	18454109	.	+	0	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	CDS	18454107	18454348	0.88	+	0	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	exon	18454107	18454348	.	+	.	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	intron	18454349	18454705	.	+	.	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	CDS	18454706	18454715	1	+	1	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	exon	18454706	18454715	.	+	.	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
Phchi.S3	AUGUSTUS	stop_codon	18454716	18454718	.	+	0	transcript_id "Phchi.S3G265700.t1"; gene_id "Phchi.S3G265700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8787.t1 is derived from g5962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37949639	37954930	.	+	.	Phchi.S1G594600
Phchi.S1	AUGUSTUS	transcript	37949639	37954930	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	start_codon	37949639	37949641	.	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37949639	37949857	0.62	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37949639	37949857	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37949858	37949969	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37949970	37950024	0.96	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37949970	37950024	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37950025	37950111	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37950112	37950181	0.99	+	2	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37950112	37950181	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37950182	37950318	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37950319	37951602	0.99	+	1	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37950319	37951602	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37951603	37951755	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37951756	37952248	0.46	+	1	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37951756	37952248	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37952249	37952401	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37952402	37953626	0.84	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37952402	37953626	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37953627	37953908	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37953909	37954151	0.79	+	2	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37953909	37954151	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37954152	37954292	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37954293	37954350	0.8	+	2	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37954293	37954350	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37954351	37954480	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37954481	37954550	1	+	1	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37954481	37954550	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37954551	37954816	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37954817	37954840	0.52	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37954817	37954840	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	intron	37954841	37954927	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	CDS	37954928	37954930	1	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	exon	37954928	37954930	.	+	.	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
Phchi.S1	AUGUSTUS	stop_codon	37954931	37954933	.	+	0	transcript_id "Phchi.S1G594600.t1"; gene_id "Phchi.S1G594600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13836.t1 is derived from g12303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9132845	9134064	.	-	.	Phchi.S3G115500
Phchi.S3	AUGUSTUS	transcript	9132845	9134064	.	-	.	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	stop_codon	9132842	9132844	.	-	0	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	CDS	9132845	9133293	0.61	-	2	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	exon	9132845	9133293	.	-	.	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	intron	9133294	9133375	.	-	.	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	CDS	9133376	9133916	0.19	-	0	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	exon	9133376	9133916	.	-	.	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	intron	9133917	9133986	.	-	.	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	CDS	9133987	9134064	0.46	-	0	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	exon	9133987	9134064	.	-	.	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
Phchi.S3	AUGUSTUS	start_codon	9134062	9134064	.	-	0	transcript_id "Phchi.S3G115500.t1"; gene_id "Phchi.S3G115500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1728.t1 is derived from g8648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2736479	2739072	.	-	.	Phchi.S5G033700
Phchi.S5	AUGUSTUS	transcript	2736479	2739072	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	stop_codon	2736476	2736478	.	-	0	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2736479	2736572	0.99	-	1	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2736479	2736572	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2736573	2736653	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2736654	2736753	0.98	-	2	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2736654	2736753	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2736754	2736862	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2736863	2736930	1	-	1	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2736863	2736930	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2736931	2737009	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2737010	2737169	0.91	-	2	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2737010	2737169	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2737170	2737304	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2737305	2737491	1	-	0	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2737305	2737491	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2737492	2737706	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2737707	2738039	1	-	0	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2737707	2738039	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2738040	2738175	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2738176	2738413	0.97	-	1	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2738176	2738413	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	intron	2738414	2738539	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	CDS	2738540	2739072	0.96	-	0	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	exon	2738540	2739072	.	-	.	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
Phchi.S5	AUGUSTUS	start_codon	2739070	2739072	.	-	0	transcript_id "Phchi.S5G033700.t1"; gene_id "Phchi.S5G033700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4373.t1 is derived from g1542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10114211	10117915	.	+	.	Phchi.S1G153200
Phchi.S1	AUGUSTUS	transcript	10114211	10117915	.	+	.	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	start_codon	10114211	10114213	.	+	0	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	CDS	10114211	10117197	0.65	+	0	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	exon	10114211	10117197	.	+	.	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	intron	10117198	10117284	.	+	.	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	CDS	10117285	10117610	0.79	+	1	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	exon	10117285	10117610	.	+	.	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	intron	10117611	10117697	.	+	.	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	CDS	10117698	10117915	0.97	+	2	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	exon	10117698	10117915	.	+	.	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
Phchi.S1	AUGUSTUS	stop_codon	10117916	10117918	.	+	0	transcript_id "Phchi.S1G153200.t1"; gene_id "Phchi.S1G153200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15396.t1 is derived from g13864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18817322	18817627	.	+	.	Phchi.S3G271500
Phchi.S3	AUGUSTUS	transcript	18817322	18817627	.	+	.	transcript_id "Phchi.S3G271500.t1"; gene_id "Phchi.S3G271500"
Phchi.S3	AUGUSTUS	start_codon	18817322	18817324	.	+	0	transcript_id "Phchi.S3G271500.t1"; gene_id "Phchi.S3G271500"
Phchi.S3	AUGUSTUS	CDS	18817322	18817627	0.6	+	0	transcript_id "Phchi.S3G271500.t1"; gene_id "Phchi.S3G271500"
Phchi.S3	AUGUSTUS	exon	18817322	18817627	.	+	.	transcript_id "Phchi.S3G271500.t1"; gene_id "Phchi.S3G271500"
Phchi.S3	AUGUSTUS	stop_codon	18817628	18817630	.	+	0	transcript_id "Phchi.S3G271500.t1"; gene_id "Phchi.S3G271500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8593.t1 is derived from g5768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36797323	36797958	.	-	.	Phchi.S1G575200
Phchi.S1	AUGUSTUS	transcript	36797323	36797958	.	-	.	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	stop_codon	36797320	36797322	.	-	0	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	CDS	36797323	36797417	0.94	-	2	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	exon	36797323	36797417	.	-	.	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	intron	36797418	36797753	.	-	.	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	CDS	36797754	36797810	0.94	-	2	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	exon	36797754	36797810	.	-	.	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	intron	36797811	36797903	.	-	.	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	CDS	36797904	36797958	0.68	-	0	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	exon	36797904	36797958	.	-	.	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
Phchi.S1	AUGUSTUS	start_codon	36797956	36797958	.	-	0	transcript_id "Phchi.S1G575200.t1"; gene_id "Phchi.S1G575200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15076.t1 is derived from g13544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16932354	16933384	.	+	.	Phchi.S3G239500
Phchi.S3	AUGUSTUS	transcript	16932354	16933384	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	start_codon	16932354	16932356	.	+	0	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	CDS	16932354	16932380	0.91	+	0	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	exon	16932354	16932380	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	intron	16932381	16932492	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	CDS	16932493	16932601	1	+	0	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	exon	16932493	16932601	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	intron	16932602	16932681	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	CDS	16932682	16932771	0.39	+	2	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	exon	16932682	16932771	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	intron	16932772	16932869	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	CDS	16932870	16932961	0.74	+	2	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	exon	16932870	16932961	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	intron	16932962	16933077	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	CDS	16933078	16933176	1	+	0	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	exon	16933078	16933176	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	intron	16933177	16933270	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	CDS	16933271	16933384	1	+	0	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	exon	16933271	16933384	.	+	.	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
Phchi.S3	AUGUSTUS	stop_codon	16933385	16933387	.	+	0	transcript_id "Phchi.S3G239500.t1"; gene_id "Phchi.S3G239500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12836.t1 is derived from g11301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2616724	2617366	.	-	.	Phchi.S3G015500
Phchi.S3	AUGUSTUS	transcript	2616724	2617366	.	-	.	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	stop_codon	2616721	2616723	.	-	0	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	CDS	2616724	2616960	0.54	-	0	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	exon	2616724	2616960	.	-	.	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	intron	2616961	2617066	.	-	.	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	CDS	2617067	2617366	0.71	-	0	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	exon	2617067	2617366	.	-	.	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
Phchi.S3	AUGUSTUS	start_codon	2617364	2617366	.	-	0	transcript_id "Phchi.S3G015500.t1"; gene_id "Phchi.S3G015500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13961.t1 is derived from g12428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9938287	9940655	.	-	.	Phchi.S3G128000
Phchi.S3	AUGUSTUS	transcript	9938287	9940655	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	stop_codon	9938284	9938286	.	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9938287	9938700	0.83	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9938287	9938700	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9938701	9938783	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9938784	9938862	1	-	1	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9938784	9938862	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9938863	9938989	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9938990	9939142	1	-	1	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9938990	9939142	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9939143	9939272	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9939273	9939445	1	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9939273	9939445	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9939446	9939693	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9939694	9939881	0.45	-	2	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9939694	9939881	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9939882	9940009	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9940010	9940034	0.43	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9940010	9940034	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9940035	9940162	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9940163	9940216	0.43	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9940163	9940216	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	intron	9940217	9940337	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	CDS	9940338	9940655	0.98	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	exon	9940338	9940655	.	-	.	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
Phchi.S3	AUGUSTUS	start_codon	9940653	9940655	.	-	0	transcript_id "Phchi.S3G128000.t1"; gene_id "Phchi.S3G128000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg682.t1 is derived from g10464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4749488	4750552	.	-	.	Phchi.S6G064100
Phchi.S6	AUGUSTUS	transcript	4749488	4750552	.	-	.	transcript_id "Phchi.S6G064100.t1"; gene_id "Phchi.S6G064100"
Phchi.S6	AUGUSTUS	stop_codon	4749485	4749487	.	-	0	transcript_id "Phchi.S6G064100.t1"; gene_id "Phchi.S6G064100"
Phchi.S6	AUGUSTUS	CDS	4749488	4750552	0.64	-	0	transcript_id "Phchi.S6G064100.t1"; gene_id "Phchi.S6G064100"
Phchi.S6	AUGUSTUS	exon	4749488	4750552	.	-	.	transcript_id "Phchi.S6G064100.t1"; gene_id "Phchi.S6G064100"
Phchi.S6	AUGUSTUS	start_codon	4750550	4750552	.	-	0	transcript_id "Phchi.S6G064100.t1"; gene_id "Phchi.S6G064100"
# This transcript jg145.t2 is derived from g9927.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg146.t1 is derived from g9928.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	798658	799598	.	+	.	Phchi.S6G010500
Phchi.S6	AUGUSTUS	transcript	798663	799598	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	start_codon	798663	798665	.	+	0	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	798663	798784	1	+	0	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	798663	798784	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	798785	798855	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	798856	798934	1	+	1	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	798856	798934	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	798935	799064	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	799065	799246	0.89	+	0	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	799065	799246	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	799247	799360	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	799361	799483	0.9	+	1	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	799361	799483	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	799484	799570	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	799571	799598	1	+	1	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	799571	799598	.	+	.	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	stop_codon	799599	799601	.	+	0	transcript_id "Phchi.S6G010500.t1"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	transcript	798658	799598	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	start_codon	798658	798660	.	+	0	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	798658	798680	0.99	+	0	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	798658	798680	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	798681	798855	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	798856	798934	0.99	+	1	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	798856	798934	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	798935	799064	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	799065	799246	0.82	+	0	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	799065	799246	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	799247	799360	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	799361	799483	0.84	+	1	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	799361	799483	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	intron	799484	799570	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	CDS	799571	799598	1	+	1	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	exon	799571	799598	.	+	.	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
Phchi.S6	AUGUSTUS	stop_codon	799599	799601	.	+	0	transcript_id "Phchi.S6G010500.t2"; gene_id "Phchi.S6G010500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7311.t1 is derived from g4483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28455948	28459319	.	+	.	Phchi.S1G447000
Phchi.S1	AUGUSTUS	transcript	28455948	28459319	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	start_codon	28455948	28455950	.	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28455948	28456037	0.99	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28455948	28456037	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28456038	28456131	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28456132	28456456	1	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28456132	28456456	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28456457	28456537	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28456538	28456728	1	+	2	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28456538	28456728	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28456729	28456910	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28456911	28457420	0.95	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28456911	28457420	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28457421	28457518	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28457519	28457654	1	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28457519	28457654	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28457655	28457776	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28457777	28457909	0.82	+	2	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28457777	28457909	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28457910	28458004	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28458005	28458041	0.88	+	1	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28458005	28458041	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28458042	28458218	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28458219	28458421	1	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28458219	28458421	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28458422	28458502	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28458503	28458602	1	+	1	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28458503	28458602	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28458603	28458873	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28458874	28458990	1	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28458874	28458990	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28458991	28459096	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28459097	28459153	1	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28459097	28459153	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	intron	28459154	28459223	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	CDS	28459224	28459319	0.96	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	exon	28459224	28459319	.	+	.	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
Phchi.S1	AUGUSTUS	stop_codon	28459320	28459322	.	+	0	transcript_id "Phchi.S1G447000.t1"; gene_id "Phchi.S1G447000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7664.t1 is derived from g4838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30493728	30494837	.	-	.	Phchi.S1G482300
Phchi.S1	AUGUSTUS	transcript	30493728	30494837	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	stop_codon	30493725	30493727	.	-	0	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	CDS	30493728	30493821	0.99	-	1	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	exon	30493728	30493821	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	intron	30493822	30493903	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	CDS	30493904	30494083	1	-	1	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	exon	30493904	30494083	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	intron	30494084	30494157	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	CDS	30494158	30494233	1	-	2	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	exon	30494158	30494233	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	intron	30494234	30494368	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	CDS	30494369	30494480	1	-	0	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	exon	30494369	30494480	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	intron	30494481	30494609	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	CDS	30494610	30494837	0.4	-	0	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	exon	30494610	30494837	.	-	.	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
Phchi.S1	AUGUSTUS	start_codon	30494835	30494837	.	-	0	transcript_id "Phchi.S1G482300.t1"; gene_id "Phchi.S1G482300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3664.t1 is derived from g833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5040270	5040608	.	-	.	Phchi.S1G082300
Phchi.S1	AUGUSTUS	transcript	5040270	5040608	.	-	.	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	stop_codon	5040267	5040269	.	-	0	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	CDS	5040270	5040384	0.88	-	1	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	exon	5040270	5040384	.	-	.	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	intron	5040385	5040492	.	-	.	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	CDS	5040493	5040608	0.9	-	0	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	exon	5040493	5040608	.	-	.	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
Phchi.S1	AUGUSTUS	start_codon	5040606	5040608	.	-	0	transcript_id "Phchi.S1G082300.t1"; gene_id "Phchi.S1G082300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6366.t1 is derived from g3538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22586898	22588133	.	+	.	Phchi.S1G352500
Phchi.S1	AUGUSTUS	transcript	22586898	22588133	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	start_codon	22586898	22586900	.	+	0	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	CDS	22586898	22587002	0.58	+	0	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	exon	22586898	22587002	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	intron	22587003	22587075	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	CDS	22587076	22587163	0.69	+	0	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	exon	22587076	22587163	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	intron	22587164	22587245	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	CDS	22587246	22587306	0.89	+	2	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	exon	22587246	22587306	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	intron	22587307	22587732	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	CDS	22587733	22587899	0.56	+	1	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	exon	22587733	22587899	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	intron	22587900	22588062	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	CDS	22588063	22588133	0.72	+	2	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	exon	22588063	22588133	.	+	.	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
Phchi.S1	AUGUSTUS	stop_codon	22588134	22588136	.	+	0	transcript_id "Phchi.S1G352500.t1"; gene_id "Phchi.S1G352500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5152.t1 is derived from g2322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15171378	15173185	.	-	.	Phchi.S1G231100
Phchi.S1	AUGUSTUS	transcript	15171378	15173185	.	-	.	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	stop_codon	15171375	15171377	.	-	0	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	CDS	15171378	15173008	0.66	-	2	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	exon	15171378	15173008	.	-	.	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	intron	15173009	15173103	.	-	.	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	CDS	15173104	15173185	0.65	-	0	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	exon	15173104	15173185	.	-	.	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
Phchi.S1	AUGUSTUS	start_codon	15173183	15173185	.	-	0	transcript_id "Phchi.S1G231100.t1"; gene_id "Phchi.S1G231100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9508.t1 is derived from g6684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42116978	42118147	.	+	.	Phchi.S1G666700
Phchi.S1	AUGUSTUS	transcript	42116978	42118147	.	+	.	transcript_id "Phchi.S1G666700.t1"; gene_id "Phchi.S1G666700"
Phchi.S1	AUGUSTUS	start_codon	42116978	42116980	.	+	0	transcript_id "Phchi.S1G666700.t1"; gene_id "Phchi.S1G666700"
Phchi.S1	AUGUSTUS	CDS	42116978	42118147	0.57	+	0	transcript_id "Phchi.S1G666700.t1"; gene_id "Phchi.S1G666700"
Phchi.S1	AUGUSTUS	exon	42116978	42118147	.	+	.	transcript_id "Phchi.S1G666700.t1"; gene_id "Phchi.S1G666700"
Phchi.S1	AUGUSTUS	stop_codon	42118148	42118150	.	+	0	transcript_id "Phchi.S1G666700.t1"; gene_id "Phchi.S1G666700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4330.t1 is derived from g1499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9814821	9816396	.	-	.	Phchi.S1G148900
Phchi.S1	AUGUSTUS	transcript	9814821	9816396	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	stop_codon	9814818	9814820	.	-	0	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	CDS	9814821	9814989	0.99	-	1	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	exon	9814821	9814989	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	intron	9814990	9815065	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	CDS	9815066	9815252	1	-	2	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	exon	9815066	9815252	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	intron	9815253	9815337	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	CDS	9815338	9815500	1	-	0	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	exon	9815338	9815500	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	intron	9815501	9815591	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	CDS	9815592	9815780	1	-	0	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	exon	9815592	9815780	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	intron	9815781	9815920	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	CDS	9815921	9816090	1	-	2	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	exon	9815921	9816090	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	intron	9816091	9816284	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	CDS	9816285	9816396	1	-	0	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	exon	9816285	9816396	.	-	.	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
Phchi.S1	AUGUSTUS	start_codon	9816394	9816396	.	-	0	transcript_id "Phchi.S1G148900.t1"; gene_id "Phchi.S1G148900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12899.t1 is derived from g11364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3068581	3070758	.	-	.	Phchi.S3G021800
Phchi.S3	AUGUSTUS	transcript	3068581	3070758	.	-	.	transcript_id "Phchi.S3G021800.t1"; gene_id "Phchi.S3G021800"
Phchi.S3	AUGUSTUS	stop_codon	3068578	3068580	.	-	0	transcript_id "Phchi.S3G021800.t1"; gene_id "Phchi.S3G021800"
Phchi.S3	AUGUSTUS	CDS	3068581	3070758	1	-	0	transcript_id "Phchi.S3G021800.t1"; gene_id "Phchi.S3G021800"
Phchi.S3	AUGUSTUS	exon	3068581	3070758	.	-	.	transcript_id "Phchi.S3G021800.t1"; gene_id "Phchi.S3G021800"
Phchi.S3	AUGUSTUS	start_codon	3070756	3070758	.	-	0	transcript_id "Phchi.S3G021800.t1"; gene_id "Phchi.S3G021800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12120.t1 is derived from g7796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3795457	3796881	.	-	.	Phchi.S2G020000
Phchi.S2	AUGUSTUS	transcript	3795457	3796881	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	stop_codon	3795454	3795456	.	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3795457	3795512	1	-	2	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3795457	3795512	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3795513	3795713	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3795714	3795790	1	-	1	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3795714	3795790	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3795791	3795889	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3795890	3795906	1	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3795890	3795906	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3795907	3796001	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3796002	3796052	1	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3796002	3796052	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3796053	3796179	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3796180	3796193	1	-	2	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3796180	3796193	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3796194	3796274	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3796275	3796342	1	-	1	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3796275	3796342	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3796343	3796435	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3796436	3796482	0.78	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3796436	3796482	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3796483	3796558	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3796559	3796570	0.78	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3796559	3796570	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	intron	3796571	3796773	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	CDS	3796774	3796881	0.87	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	exon	3796774	3796881	.	-	.	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
Phchi.S2	AUGUSTUS	start_codon	3796879	3796881	.	-	0	transcript_id "Phchi.S2G020000.t1"; gene_id "Phchi.S2G020000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3697.t1 is derived from g866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5227234	5228364	.	-	.	Phchi.S1G085600
Phchi.S1	AUGUSTUS	transcript	5227234	5228364	.	-	.	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	stop_codon	5227231	5227233	.	-	0	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	CDS	5227234	5227535	0.73	-	2	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	exon	5227234	5227535	.	-	.	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	intron	5227536	5227712	.	-	.	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	CDS	5227713	5228364	0.73	-	0	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	exon	5227713	5228364	.	-	.	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
Phchi.S1	AUGUSTUS	start_codon	5228362	5228364	.	-	0	transcript_id "Phchi.S1G085600.t1"; gene_id "Phchi.S1G085600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15481.t1 is derived from g13949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19413879	19415378	.	+	.	Phchi.S3G280000
Phchi.S3	AUGUSTUS	transcript	19413879	19415378	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	start_codon	19413879	19413881	.	+	0	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19413879	19413957	0.95	+	0	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19413879	19413957	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	intron	19413958	19414051	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19414052	19414128	1	+	2	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19414052	19414128	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	intron	19414129	19414477	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19414478	19414531	1	+	0	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19414478	19414531	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	intron	19414532	19414653	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19414654	19414710	1	+	0	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19414654	19414710	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	intron	19414711	19414800	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19414801	19414913	1	+	0	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19414801	19414913	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	intron	19414914	19415002	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19415003	19415082	1	+	1	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19415003	19415082	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	intron	19415083	19415172	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	CDS	19415173	19415378	1	+	2	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	exon	19415173	19415378	.	+	.	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
Phchi.S3	AUGUSTUS	stop_codon	19415379	19415381	.	+	0	transcript_id "Phchi.S3G280000.t1"; gene_id "Phchi.S3G280000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9118.t1 is derived from g6293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39913118	39914184	.	+	.	Phchi.S1G627700
Phchi.S1	AUGUSTUS	transcript	39913118	39914184	.	+	.	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	start_codon	39913118	39913120	.	+	0	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	CDS	39913118	39913411	0.95	+	0	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	exon	39913118	39913411	.	+	.	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	intron	39913412	39913499	.	+	.	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	CDS	39913500	39913826	0.38	+	0	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	exon	39913500	39913826	.	+	.	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	intron	39913827	39913923	.	+	.	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	CDS	39913924	39914184	0.48	+	0	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	exon	39913924	39914184	.	+	.	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
Phchi.S1	AUGUSTUS	stop_codon	39914185	39914187	.	+	0	transcript_id "Phchi.S1G627700.t1"; gene_id "Phchi.S1G627700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11104.t1 is derived from g15154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4147604	4149681	.	-	.	Phchi.S4G068600
Phchi.S4	AUGUSTUS	transcript	4147604	4149681	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	stop_codon	4147601	4147603	.	-	0	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	CDS	4147604	4148849	0.2	-	1	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	exon	4147604	4148849	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	intron	4148850	4148951	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	CDS	4148952	4149052	1	-	0	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	exon	4148952	4149052	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	intron	4149053	4149142	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	CDS	4149143	4149261	1	-	2	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	exon	4149143	4149261	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	intron	4149262	4149434	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	CDS	4149435	4149681	0.98	-	0	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	exon	4149435	4149681	.	-	.	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
Phchi.S4	AUGUSTUS	start_codon	4149679	4149681	.	-	0	transcript_id "Phchi.S4G068600.t1"; gene_id "Phchi.S4G068600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4539.t1 is derived from g1709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11011446	11012814	.	-	.	Phchi.S1G169800
Phchi.S1	AUGUSTUS	transcript	11011446	11012814	.	-	.	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	stop_codon	11011443	11011445	.	-	0	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	CDS	11011446	11012446	0.28	-	2	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	exon	11011446	11012446	.	-	.	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	intron	11012447	11012573	.	-	.	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	CDS	11012574	11012814	0.86	-	0	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	exon	11012574	11012814	.	-	.	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
Phchi.S1	AUGUSTUS	start_codon	11012812	11012814	.	-	0	transcript_id "Phchi.S1G169800.t1"; gene_id "Phchi.S1G169800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7458.t1 is derived from g4630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29381845	29384061	.	-	.	Phchi.S1G461700
Phchi.S1	AUGUSTUS	transcript	29381845	29384061	.	-	.	transcript_id "Phchi.S1G461700.t1"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	stop_codon	29381842	29381844	.	-	0	transcript_id "Phchi.S1G461700.t1"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	CDS	29381845	29384061	1	-	0	transcript_id "Phchi.S1G461700.t1"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	exon	29381845	29384061	.	-	.	transcript_id "Phchi.S1G461700.t1"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	start_codon	29384059	29384061	.	-	0	transcript_id "Phchi.S1G461700.t1"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	transcript	29381845	29383791	.	-	.	transcript_id "Phchi.S1G461700.t2"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	stop_codon	29381842	29381844	.	-	0	transcript_id "Phchi.S1G461700.t2"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	CDS	29381845	29383791	0.52	-	0	transcript_id "Phchi.S1G461700.t2"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	exon	29381845	29383791	.	-	.	transcript_id "Phchi.S1G461700.t2"; gene_id "Phchi.S1G461700"
Phchi.S1	AUGUSTUS	start_codon	29383789	29383791	.	-	0	transcript_id "Phchi.S1G461700.t2"; gene_id "Phchi.S1G461700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6258.t1 is derived from g3430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21902426	21904107	.	+	.	Phchi.S1G341700
Phchi.S1	AUGUSTUS	transcript	21902426	21904107	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	start_codon	21902426	21902428	.	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21902426	21902513	1	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21902426	21902513	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21902514	21902667	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21902668	21902774	1	+	2	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21902668	21902774	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21902775	21902866	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21902867	21902926	1	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21902867	21902926	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21902927	21903133	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21903134	21903242	1	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21903134	21903242	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21903243	21903326	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21903327	21903379	1	+	2	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21903327	21903379	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21903380	21903590	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21903591	21903671	1	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21903591	21903671	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21903672	21903851	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21903852	21903964	1	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21903852	21903964	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	intron	21903965	21904046	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	CDS	21904047	21904107	0.83	+	1	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	exon	21904047	21904107	.	+	.	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
Phchi.S1	AUGUSTUS	stop_codon	21904108	21904110	.	+	0	transcript_id "Phchi.S1G341700.t1"; gene_id "Phchi.S1G341700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2423.t1 is derived from g9343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6578094	6579868	.	+	.	Phchi.S5G103200
Phchi.S5	AUGUSTUS	transcript	6578094	6579868	.	+	.	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	start_codon	6578094	6578096	.	+	0	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	CDS	6578094	6578928	0.7	+	0	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	exon	6578094	6578928	.	+	.	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	intron	6578929	6579113	.	+	.	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	CDS	6579114	6579868	0.94	+	2	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	exon	6579114	6579868	.	+	.	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
Phchi.S5	AUGUSTUS	stop_codon	6579869	6579871	.	+	0	transcript_id "Phchi.S5G103200.t1"; gene_id "Phchi.S5G103200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3771.t1 is derived from g940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5620221	5621110	.	+	.	Phchi.S1G093000
Phchi.S1	AUGUSTUS	transcript	5620221	5621110	.	+	.	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	start_codon	5620221	5620223	.	+	0	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	CDS	5620221	5620913	0.59	+	0	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	exon	5620221	5620913	.	+	.	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	intron	5620914	5621047	.	+	.	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	CDS	5621048	5621110	0.99	+	0	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	exon	5621048	5621110	.	+	.	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
Phchi.S1	AUGUSTUS	stop_codon	5621111	5621113	.	+	0	transcript_id "Phchi.S1G093000.t1"; gene_id "Phchi.S1G093000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12206.t1 is derived from g7882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6732863	6736223	.	+	.	Phchi.S2G028600
Phchi.S2	AUGUSTUS	transcript	6732863	6736223	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	start_codon	6732863	6732865	.	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6732863	6734476	0.98	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6732863	6734476	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	intron	6734477	6734571	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6734572	6734661	1	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6734572	6734661	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	intron	6734662	6734752	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6734753	6734821	1	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6734753	6734821	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	intron	6734822	6734903	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6734904	6735044	1	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6734904	6735044	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	intron	6735045	6735155	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6735156	6735204	1	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6735156	6735204	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	intron	6735205	6735297	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6735298	6735401	0.99	+	2	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6735298	6735401	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	intron	6735402	6735506	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	CDS	6735507	6736223	0.97	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	exon	6735507	6736223	.	+	.	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
Phchi.S2	AUGUSTUS	stop_codon	6736224	6736226	.	+	0	transcript_id "Phchi.S2G028600.t1"; gene_id "Phchi.S2G028600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg979.t1 is derived from g10762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6827154	6828725	.	-	.	Phchi.S6G093800
Phchi.S6	AUGUSTUS	transcript	6827154	6828725	.	-	.	transcript_id "Phchi.S6G093800.t1"; gene_id "Phchi.S6G093800"
Phchi.S6	AUGUSTUS	stop_codon	6827151	6827153	.	-	0	transcript_id "Phchi.S6G093800.t1"; gene_id "Phchi.S6G093800"
Phchi.S6	AUGUSTUS	CDS	6827154	6828725	0.94	-	0	transcript_id "Phchi.S6G093800.t1"; gene_id "Phchi.S6G093800"
Phchi.S6	AUGUSTUS	exon	6827154	6828725	.	-	.	transcript_id "Phchi.S6G093800.t1"; gene_id "Phchi.S6G093800"
Phchi.S6	AUGUSTUS	start_codon	6828723	6828725	.	-	0	transcript_id "Phchi.S6G093800.t1"; gene_id "Phchi.S6G093800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10238.t1 is derived from g7414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46515622	46516030	.	+	.	Phchi.S1G739700
Phchi.S1	AUGUSTUS	transcript	46515622	46516030	.	+	.	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	start_codon	46515622	46515624	.	+	0	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	CDS	46515622	46515839	1	+	0	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	exon	46515622	46515839	.	+	.	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	intron	46515840	46516029	.	+	.	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	CDS	46516030	46516030	1	+	1	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	exon	46516030	46516030	.	+	.	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
Phchi.S1	AUGUSTUS	stop_codon	46516031	46516033	.	+	0	transcript_id "Phchi.S1G739700.t1"; gene_id "Phchi.S1G739700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1735.t1 is derived from g8655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2777704	2778775	.	+	.	Phchi.S5G034400
Phchi.S5	AUGUSTUS	transcript	2777704	2778775	.	+	.	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	start_codon	2777704	2777706	.	+	0	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	CDS	2777704	2778373	0.61	+	0	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	exon	2777704	2778373	.	+	.	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	intron	2778374	2778554	.	+	.	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	CDS	2778555	2778585	1	+	2	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	exon	2778555	2778585	.	+	.	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	intron	2778586	2778768	.	+	.	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	CDS	2778769	2778775	1	+	1	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	exon	2778769	2778775	.	+	.	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
Phchi.S5	AUGUSTUS	stop_codon	2778776	2778778	.	+	0	transcript_id "Phchi.S5G034400.t1"; gene_id "Phchi.S5G034400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13825.t1 is derived from g12292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9082498	9084531	.	-	.	Phchi.S3G114400
Phchi.S3	AUGUSTUS	transcript	9082498	9084531	.	-	.	transcript_id "Phchi.S3G114400.t1"; gene_id "Phchi.S3G114400"
Phchi.S3	AUGUSTUS	stop_codon	9082495	9082497	.	-	0	transcript_id "Phchi.S3G114400.t1"; gene_id "Phchi.S3G114400"
Phchi.S3	AUGUSTUS	CDS	9082498	9084531	0.74	-	0	transcript_id "Phchi.S3G114400.t1"; gene_id "Phchi.S3G114400"
Phchi.S3	AUGUSTUS	exon	9082498	9084531	.	-	.	transcript_id "Phchi.S3G114400.t1"; gene_id "Phchi.S3G114400"
Phchi.S3	AUGUSTUS	start_codon	9084529	9084531	.	-	0	transcript_id "Phchi.S3G114400.t1"; gene_id "Phchi.S3G114400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11220.t1 is derived from g15270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4846867	4847613	.	+	.	Phchi.S4G080200
Phchi.S4	AUGUSTUS	transcript	4846867	4847613	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	start_codon	4846867	4846869	.	+	0	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	CDS	4846867	4846919	0.81	+	0	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	exon	4846867	4846919	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	intron	4846920	4847023	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	CDS	4847024	4847113	1	+	1	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	exon	4847024	4847113	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	intron	4847114	4847206	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	CDS	4847207	4847285	0.99	+	1	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	exon	4847207	4847285	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	intron	4847286	4847391	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	CDS	4847392	4847487	0.66	+	0	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	exon	4847392	4847487	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	intron	4847488	4847580	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	CDS	4847581	4847613	0.65	+	0	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	exon	4847581	4847613	.	+	.	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
Phchi.S4	AUGUSTUS	stop_codon	4847614	4847616	.	+	0	transcript_id "Phchi.S4G080200.t1"; gene_id "Phchi.S4G080200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1510.t1 is derived from g8429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1296936	1298075	.	-	.	Phchi.S5G011900
Phchi.S5	AUGUSTUS	transcript	1296936	1298075	.	-	.	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	stop_codon	1296933	1296935	.	-	0	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	CDS	1296936	1297593	1	-	1	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	exon	1296936	1297593	.	-	.	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	intron	1297594	1297686	.	-	.	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	CDS	1297687	1298075	0.74	-	0	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	exon	1297687	1298075	.	-	.	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
Phchi.S5	AUGUSTUS	start_codon	1298073	1298075	.	-	0	transcript_id "Phchi.S5G011900.t1"; gene_id "Phchi.S5G011900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15903.t1 is derived from g14373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22074337	22080386	.	-	.	Phchi.S3G322200
Phchi.S3	AUGUSTUS	transcript	22074337	22080386	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	stop_codon	22074334	22074336	.	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22074337	22074884	0.97	-	2	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22074337	22074884	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22074885	22074961	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22074962	22075064	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22074962	22075064	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075065	22075185	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075186	22075242	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075186	22075242	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075243	22075362	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075363	22075467	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075363	22075467	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075468	22075555	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075556	22075891	0.9	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075556	22075891	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075892	22075992	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075993	22076192	0.71	-	2	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075993	22076192	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076193	22076387	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076388	22076543	0.72	-	2	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076388	22076543	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076544	22076672	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076673	22076709	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076673	22076709	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076710	22076925	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076926	22077034	1	-	1	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076926	22077034	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22077035	22077383	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22077384	22077511	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22077384	22077511	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22077512	22077898	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22077899	22078069	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22077899	22078069	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22078070	22078648	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22078649	22078888	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22078649	22078888	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22078889	22078992	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22078993	22079170	1	-	1	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22078993	22079170	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079171	22079299	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079300	22079490	1	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079300	22079490	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079491	22079600	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079601	22079743	1	-	2	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079601	22079743	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079744	22079959	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079960	22080386	0.96	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079960	22080386	.	-	.	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	start_codon	22080384	22080386	.	-	0	transcript_id "Phchi.S3G322200.t1"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	transcript	22074337	22080386	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	stop_codon	22074334	22074336	.	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22074337	22074884	1	-	2	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22074337	22074884	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22074885	22074961	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22074962	22075064	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22074962	22075064	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075065	22075185	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075186	22075242	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075186	22075242	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075243	22075362	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075363	22075467	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075363	22075467	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075468	22075555	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075556	22075891	0.94	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075556	22075891	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075892	22075992	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075993	22076192	0.47	-	2	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075993	22076192	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076193	22076387	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076388	22076543	0.75	-	2	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076388	22076543	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076544	22076672	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076673	22076709	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076673	22076709	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076710	22076925	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076926	22077061	1	-	1	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076926	22077061	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22077062	22077383	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22077384	22077511	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22077384	22077511	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22077512	22077898	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22077899	22078069	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22077899	22078069	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22078070	22078648	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22078649	22078888	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22078649	22078888	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22078889	22078992	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22078993	22079170	1	-	1	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22078993	22079170	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079171	22079299	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079300	22079490	1	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079300	22079490	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079491	22079600	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079601	22079743	1	-	2	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079601	22079743	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079744	22079959	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079960	22080386	0.97	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079960	22080386	.	-	.	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	start_codon	22080384	22080386	.	-	0	transcript_id "Phchi.S3G322200.t2"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	transcript	22074337	22080386	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	stop_codon	22074334	22074336	.	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22074337	22074884	0.96	-	2	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22074337	22074884	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22074885	22074961	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22074962	22075064	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22074962	22075064	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075065	22075185	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075186	22075242	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075186	22075242	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075243	22075362	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075363	22075467	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075363	22075467	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075468	22075555	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075556	22075891	0.92	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075556	22075891	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22075892	22075992	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22075993	22076231	0.58	-	2	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22075993	22076231	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076232	22076387	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076388	22076543	0.62	-	2	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076388	22076543	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076544	22076672	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076673	22076709	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076673	22076709	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22076710	22076925	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22076926	22077034	1	-	1	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22076926	22077034	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22077035	22077383	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22077384	22077511	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22077384	22077511	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22077512	22077898	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22077899	22078069	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22077899	22078069	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22078070	22078648	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22078649	22078888	0.96	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22078649	22078888	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22078889	22078992	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22078993	22079170	0.96	-	1	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22078993	22079170	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079171	22079299	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079300	22079490	1	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079300	22079490	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079491	22079600	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079601	22079743	1	-	2	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079601	22079743	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	intron	22079744	22079959	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	CDS	22079960	22080386	0.97	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	exon	22079960	22080386	.	-	.	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
Phchi.S3	AUGUSTUS	start_codon	22080384	22080386	.	-	0	transcript_id "Phchi.S3G322200.t3"; gene_id "Phchi.S3G322200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3160.t1 is derived from g329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2021524	2022101	.	-	.	Phchi.S1G031900
Phchi.S1	AUGUSTUS	transcript	2021524	2022101	.	-	.	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	stop_codon	2021521	2021523	.	-	0	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	CDS	2021524	2021597	0.99	-	2	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	exon	2021524	2021597	.	-	.	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	intron	2021598	2021675	.	-	.	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	CDS	2021676	2021805	1	-	0	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	exon	2021676	2021805	.	-	.	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	intron	2021806	2021891	.	-	.	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	CDS	2021892	2022101	1	-	0	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	exon	2021892	2022101	.	-	.	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
Phchi.S1	AUGUSTUS	start_codon	2022099	2022101	.	-	0	transcript_id "Phchi.S1G031900.t1"; gene_id "Phchi.S1G031900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11307.t1 is derived from g15357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5308409	5310731	.	+	.	Phchi.S4G088900
Phchi.S4	AUGUSTUS	transcript	5308409	5310731	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	start_codon	5308409	5308411	.	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5308409	5308755	0.75	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5308409	5308755	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5308756	5308835	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5308836	5308890	1	+	1	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5308836	5308890	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5308891	5308969	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5308970	5309134	0.91	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5308970	5309134	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5309135	5309215	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5309216	5309406	1	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5309216	5309406	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5309407	5309501	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5309502	5309762	1	+	1	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5309502	5309762	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5309763	5309857	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5309858	5309960	1	+	1	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5309858	5309960	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5309961	5310067	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5310068	5310153	1	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5310068	5310153	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5310154	5310243	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5310244	5310391	1	+	1	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5310244	5310391	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	intron	5310392	5310626	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	CDS	5310627	5310731	0.9	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	exon	5310627	5310731	.	+	.	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
Phchi.S4	AUGUSTUS	stop_codon	5310732	5310734	.	+	0	transcript_id "Phchi.S4G088900.t1"; gene_id "Phchi.S4G088900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3794.t1 is derived from g963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5769239	5771014	.	+	.	Phchi.S1G095300
Phchi.S1	AUGUSTUS	transcript	5769239	5771014	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	start_codon	5769239	5769241	.	+	0	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	CDS	5769239	5769437	0.95	+	0	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	exon	5769239	5769437	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	intron	5769438	5769518	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	CDS	5769519	5769667	1	+	2	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	exon	5769519	5769667	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	intron	5769668	5769808	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	CDS	5769809	5769936	1	+	0	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	exon	5769809	5769936	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	intron	5769937	5770030	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	CDS	5770031	5770134	1	+	1	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	exon	5770031	5770134	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	intron	5770135	5770239	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	CDS	5770240	5770367	0.99	+	2	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	exon	5770240	5770367	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	intron	5770368	5770468	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	CDS	5770469	5771014	1	+	0	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	exon	5770469	5771014	.	+	.	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
Phchi.S1	AUGUSTUS	stop_codon	5771015	5771017	.	+	0	transcript_id "Phchi.S1G095300.t1"; gene_id "Phchi.S1G095300"
# This transcript jg9313.t2 is derived from g6488.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9314.t1 is derived from g6489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40908591	40912577	.	+	.	Phchi.S1G647300
Phchi.S1	AUGUSTUS	transcript	40908591	40912118	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	start_codon	40908591	40908593	.	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40908591	40908806	0.93	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40908591	40908806	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40908807	40908981	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40908982	40909051	1	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40908982	40909051	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909052	40909165	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909166	40909284	0.99	+	2	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909166	40909284	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909285	40909415	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909416	40909548	1	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909416	40909548	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909549	40909661	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909662	40909762	1	+	2	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909662	40909762	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909763	40909861	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909862	40909953	1	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909862	40909953	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909954	40910056	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40910057	40910161	0.99	+	1	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40910057	40910161	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40910162	40910245	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40910246	40910524	0.86	+	1	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40910246	40910524	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40910525	40910618	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40910619	40910751	1	+	1	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40910619	40910751	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40910752	40911040	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911041	40911154	1	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911041	40911154	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911155	40911351	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911352	40911422	1	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911352	40911422	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911423	40911594	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911595	40911728	1	+	1	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911595	40911728	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911729	40911810	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911811	40911893	1	+	2	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911811	40911893	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911894	40911995	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911996	40912118	0.9	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911996	40912118	.	+	.	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	stop_codon	40912119	40912121	.	+	0	transcript_id "Phchi.S1G647300.t1"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	transcript	40909709	40912577	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	start_codon	40909709	40909711	.	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909709	40909762	0.54	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909709	40909762	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909763	40909861	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909862	40909953	1	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909862	40909953	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909954	40910056	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40910057	40910161	1	+	1	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40910057	40910161	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40910162	40910245	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40910246	40910524	0.8	+	1	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40910246	40910524	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40910525	40910618	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40910619	40910751	1	+	1	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40910619	40910751	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40910752	40911040	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911041	40911154	1	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911041	40911154	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911155	40911351	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911352	40911422	1	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911352	40911422	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911423	40911594	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911595	40911728	1	+	1	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911595	40911728	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911729	40911810	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911811	40911893	1	+	2	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911811	40911893	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40911894	40911995	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40911996	40912103	1	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40911996	40912103	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40912104	40912194	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40912195	40912353	0.89	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40912195	40912353	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40912354	40912463	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40912464	40912577	0.81	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40912464	40912577	.	+	.	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	stop_codon	40912578	40912580	.	+	0	transcript_id "Phchi.S1G647300.t2"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	transcript	40908591	40909662	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	start_codon	40908591	40908593	.	+	0	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40908591	40908806	0.93	+	0	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40908591	40908806	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40908807	40908981	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40908982	40909051	0.99	+	0	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40908982	40909051	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909052	40909165	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909166	40909284	0.99	+	2	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909166	40909284	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909285	40909415	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909416	40909548	1	+	0	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909416	40909548	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	intron	40909549	40909639	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	CDS	40909640	40909662	0.59	+	2	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	exon	40909640	40909662	.	+	.	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
Phchi.S1	AUGUSTUS	stop_codon	40909663	40909665	.	+	0	transcript_id "Phchi.S1G647300.t3"; gene_id "Phchi.S1G647300"
# This transcript jg5831.t2 is derived from g3001.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5832.t1 is derived from g3002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19168000	19168755	.	-	.	Phchi.S1G299100
Phchi.S1	AUGUSTUS	transcript	19168000	19168755	.	-	.	transcript_id "Phchi.S1G299100.t1"; gene_id "Phchi.S1G299100"
Phchi.S1	AUGUSTUS	stop_codon	19167997	19167999	.	-	0	transcript_id "Phchi.S1G299100.t1"; gene_id "Phchi.S1G299100"
Phchi.S1	AUGUSTUS	CDS	19168000	19168755	0.81	-	0	transcript_id "Phchi.S1G299100.t1"; gene_id "Phchi.S1G299100"
Phchi.S1	AUGUSTUS	exon	19168000	19168755	.	-	.	transcript_id "Phchi.S1G299100.t1"; gene_id "Phchi.S1G299100"
Phchi.S1	AUGUSTUS	start_codon	19168753	19168755	.	-	0	transcript_id "Phchi.S1G299100.t1"; gene_id "Phchi.S1G299100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7958.t1 is derived from g5133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32093739	32101451	.	-	.	Phchi.S1G511700
Phchi.S1	AUGUSTUS	transcript	32093739	32101451	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	stop_codon	32093736	32093738	.	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32093739	32093850	1	-	1	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32093739	32093850	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32093851	32094000	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32094001	32094362	0.98	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32094001	32094362	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32094363	32094515	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32094516	32094701	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32094516	32094701	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32094702	32094928	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32094929	32095102	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32094929	32095102	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32095103	32095199	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32095200	32095331	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32095200	32095331	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32095332	32095417	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32095418	32095612	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32095418	32095612	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32095613	32095690	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32095691	32095768	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32095691	32095768	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32095769	32095923	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32095924	32095989	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32095924	32095989	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32095990	32096072	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32096073	32096153	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32096073	32096153	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32096154	32096266	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32096267	32097033	0.9	-	2	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32096267	32097033	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32097034	32097130	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32097131	32097330	1	-	1	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32097131	32097330	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32097331	32097424	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32097425	32097519	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32097425	32097519	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32097520	32097659	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32097660	32097797	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32097660	32097797	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32097798	32097963	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32097964	32098041	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32097964	32098041	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32098042	32098139	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32098140	32098268	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32098140	32098268	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32098269	32098348	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32098349	32098489	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32098349	32098489	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32098490	32098751	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32098752	32098883	0.99	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32098752	32098883	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32098884	32098994	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32098995	32099046	0.99	-	1	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32098995	32099046	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32099047	32099197	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32099198	32099329	0.97	-	1	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32099198	32099329	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32099330	32099454	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32099455	32099507	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32099455	32099507	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32099508	32099611	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32099612	32099707	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32099612	32099707	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32099708	32099890	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32099891	32100036	1	-	2	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32099891	32100036	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32100037	32100332	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32100333	32100468	1	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32100333	32100468	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32100469	32100558	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32100559	32100712	1	-	1	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32100559	32100712	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32100713	32100869	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32100870	32101016	1	-	1	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32100870	32101016	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	intron	32101017	32101188	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	CDS	32101189	32101451	0.98	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	exon	32101189	32101451	.	-	.	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
Phchi.S1	AUGUSTUS	start_codon	32101449	32101451	.	-	0	transcript_id "Phchi.S1G511700.t1"; gene_id "Phchi.S1G511700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13575.t1 is derived from g12042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7554012	7555504	.	+	.	Phchi.S3G089400
Phchi.S3	AUGUSTUS	transcript	7554012	7555504	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	start_codon	7554012	7554014	.	+	0	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	CDS	7554012	7554219	0.99	+	0	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	exon	7554012	7554219	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	intron	7554220	7554314	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	CDS	7554315	7554514	1	+	2	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	exon	7554315	7554514	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	intron	7554515	7554598	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	CDS	7554599	7554889	1	+	0	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	exon	7554599	7554889	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	intron	7554890	7555004	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	CDS	7555005	7555158	0.73	+	0	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	exon	7555005	7555158	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	intron	7555159	7555286	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	CDS	7555287	7555504	0.74	+	2	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	exon	7555287	7555504	.	+	.	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
Phchi.S3	AUGUSTUS	stop_codon	7555505	7555507	.	+	0	transcript_id "Phchi.S3G089400.t1"; gene_id "Phchi.S3G089400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2985.t1 is derived from g154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	988024	990120	.	+	.	Phchi.S1G014400
Phchi.S1	AUGUSTUS	transcript	988024	990120	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	start_codon	988024	988026	.	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	988024	988134	0.99	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	988024	988134	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	988135	988333	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	988334	988534	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	988334	988534	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	988535	988703	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	988704	988946	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	988704	988946	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	988947	989036	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	989037	989084	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	989037	989084	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	989085	989210	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	989211	989267	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	989211	989267	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	989268	989353	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	989354	989455	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	989354	989455	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	989456	989571	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	989572	989637	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	989572	989637	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	989638	989814	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	989815	989916	1	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	989815	989916	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	intron	989917	990006	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	CDS	990007	990120	0.99	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	exon	990007	990120	.	+	.	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
Phchi.S1	AUGUSTUS	stop_codon	990121	990123	.	+	0	transcript_id "Phchi.S1G014400.t1"; gene_id "Phchi.S1G014400"
# This transcript jg11481.t2 is derived from g15531.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11482.t1 is derived from g15532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6588285	6589525	.	+	.	Phchi.S4G106400
Phchi.S4	AUGUSTUS	transcript	6588285	6589525	.	+	.	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	start_codon	6588285	6588287	.	+	0	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	CDS	6588285	6588707	1	+	0	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	exon	6588285	6588707	.	+	.	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	intron	6588708	6588844	.	+	.	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	CDS	6588845	6589525	1	+	0	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	exon	6588845	6589525	.	+	.	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
Phchi.S4	AUGUSTUS	stop_codon	6589526	6589528	.	+	0	transcript_id "Phchi.S4G106400.t1"; gene_id "Phchi.S4G106400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10410.t1 is derived from g7586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47704894	47705372	.	-	.	Phchi.S1G756900
Phchi.S1	AUGUSTUS	transcript	47704894	47705372	.	-	.	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	stop_codon	47704891	47704893	.	-	0	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	CDS	47704894	47704979	0.59	-	2	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	exon	47704894	47704979	.	-	.	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	intron	47704980	47705119	.	-	.	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	CDS	47705120	47705372	0.45	-	0	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	exon	47705120	47705372	.	-	.	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
Phchi.S1	AUGUSTUS	start_codon	47705370	47705372	.	-	0	transcript_id "Phchi.S1G756900.t1"; gene_id "Phchi.S1G756900"
# This transcript jg12435.t2 is derived from g8112.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12436.t1 is derived from g8113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19840202	19840754	.	+	.	Phchi.S2G051600
Phchi.S2	AUGUSTUS	transcript	19840202	19840754	.	+	.	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	start_codon	19840202	19840204	.	+	0	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	CDS	19840202	19840421	0.89	+	0	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	exon	19840202	19840421	.	+	.	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	intron	19840422	19840521	.	+	.	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	CDS	19840522	19840754	1	+	2	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	exon	19840522	19840754	.	+	.	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
Phchi.S2	AUGUSTUS	stop_codon	19840755	19840757	.	+	0	transcript_id "Phchi.S2G051600.t1"; gene_id "Phchi.S2G051600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7042.t1 is derived from g4214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26553072	26555345	.	+	.	Phchi.S1G420100
Phchi.S1	AUGUSTUS	transcript	26553072	26555345	.	+	.	transcript_id "Phchi.S1G420100.t1"; gene_id "Phchi.S1G420100"
Phchi.S1	AUGUSTUS	start_codon	26553072	26553074	.	+	0	transcript_id "Phchi.S1G420100.t1"; gene_id "Phchi.S1G420100"
Phchi.S1	AUGUSTUS	CDS	26553072	26555345	0.71	+	0	transcript_id "Phchi.S1G420100.t1"; gene_id "Phchi.S1G420100"
Phchi.S1	AUGUSTUS	exon	26553072	26555345	.	+	.	transcript_id "Phchi.S1G420100.t1"; gene_id "Phchi.S1G420100"
Phchi.S1	AUGUSTUS	stop_codon	26555346	26555348	.	+	0	transcript_id "Phchi.S1G420100.t1"; gene_id "Phchi.S1G420100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14260.t1 is derived from g12727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11790390	11791661	.	-	.	Phchi.S3G157900
Phchi.S3	AUGUSTUS	transcript	11790390	11791661	.	-	.	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	stop_codon	11790387	11790389	.	-	0	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	CDS	11790390	11790685	0.8	-	2	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	exon	11790390	11790685	.	-	.	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	intron	11790686	11790780	.	-	.	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	CDS	11790781	11791000	1	-	0	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	exon	11790781	11791000	.	-	.	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	intron	11791001	11791175	.	-	.	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	CDS	11791176	11791661	0.84	-	0	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	exon	11791176	11791661	.	-	.	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
Phchi.S3	AUGUSTUS	start_codon	11791659	11791661	.	-	0	transcript_id "Phchi.S3G157900.t1"; gene_id "Phchi.S3G157900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1991.t1 is derived from g8911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4337130	4337580	.	+	.	Phchi.S5G060000
Phchi.S5	AUGUSTUS	transcript	4337130	4337580	.	+	.	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	start_codon	4337130	4337132	.	+	0	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	CDS	4337130	4337411	0.79	+	0	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	exon	4337130	4337411	.	+	.	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	intron	4337412	4337496	.	+	.	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	CDS	4337497	4337580	1	+	0	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	exon	4337497	4337580	.	+	.	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
Phchi.S5	AUGUSTUS	stop_codon	4337581	4337583	.	+	0	transcript_id "Phchi.S5G060000.t1"; gene_id "Phchi.S5G060000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9757.t1 is derived from g6933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43531219	43532774	.	-	.	Phchi.S1G691600
Phchi.S1	AUGUSTUS	transcript	43531219	43532774	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	stop_codon	43531216	43531218	.	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	CDS	43531219	43531488	1	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	exon	43531219	43531488	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	intron	43531489	43531575	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	CDS	43531576	43531743	1	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	exon	43531576	43531743	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	intron	43531744	43531839	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	CDS	43531840	43531971	1	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	exon	43531840	43531971	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	intron	43531972	43532060	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	CDS	43532061	43532146	0.97	-	2	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	exon	43532061	43532146	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	intron	43532147	43532268	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	CDS	43532269	43532461	1	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	exon	43532269	43532461	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	intron	43532462	43532585	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	CDS	43532586	43532774	0.92	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	exon	43532586	43532774	.	-	.	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
Phchi.S1	AUGUSTUS	start_codon	43532772	43532774	.	-	0	transcript_id "Phchi.S1G691600.t1"; gene_id "Phchi.S1G691600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13723.t1 is derived from g12190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8547405	8548916	.	+	.	Phchi.S3G104200
Phchi.S3	AUGUSTUS	transcript	8547405	8548916	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	start_codon	8547405	8547407	.	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8547405	8547425	1	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8547405	8547425	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	intron	8547426	8547507	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8547508	8547597	1	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8547508	8547597	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	intron	8547598	8547698	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8547699	8547821	0.98	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8547699	8547821	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	intron	8547822	8547923	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8547924	8548091	1	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8547924	8548091	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	intron	8548092	8548304	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8548305	8548385	1	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8548305	8548385	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	intron	8548386	8548484	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8548485	8548596	1	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8548485	8548596	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	intron	8548597	8548815	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	CDS	8548816	8548916	0.99	+	2	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	exon	8548816	8548916	.	+	.	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
Phchi.S3	AUGUSTUS	stop_codon	8548917	8548919	.	+	0	transcript_id "Phchi.S3G104200.t1"; gene_id "Phchi.S3G104200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8144.t1 is derived from g5319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34063242	34064354	.	-	.	Phchi.S1G530300
Phchi.S1	AUGUSTUS	transcript	34063242	34064354	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	stop_codon	34063239	34063241	.	-	0	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	CDS	34063242	34063342	0.44	-	2	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	exon	34063242	34063342	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	intron	34063343	34063448	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	CDS	34063449	34063561	0.49	-	1	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	exon	34063449	34063561	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	intron	34063562	34063754	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	CDS	34063755	34063927	0.16	-	0	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	exon	34063755	34063927	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	intron	34063928	34064124	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	CDS	34064125	34064175	0.7	-	0	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	exon	34064125	34064175	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	intron	34064176	34064273	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	CDS	34064274	34064354	0.66	-	0	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	exon	34064274	34064354	.	-	.	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
Phchi.S1	AUGUSTUS	start_codon	34064352	34064354	.	-	0	transcript_id "Phchi.S1G530300.t1"; gene_id "Phchi.S1G530300"
# This transcript jg6202.t2 is derived from g3373.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6203.t1 is derived from g3374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21463397	21464408	.	+	.	Phchi.S1G336200
Phchi.S1	AUGUSTUS	transcript	21463397	21464408	.	+	.	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	start_codon	21463397	21463399	.	+	0	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	CDS	21463397	21463619	0.52	+	0	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	exon	21463397	21463619	.	+	.	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	intron	21463620	21463788	.	+	.	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	CDS	21463789	21464408	1	+	2	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	exon	21463789	21464408	.	+	.	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
Phchi.S1	AUGUSTUS	stop_codon	21464409	21464411	.	+	0	transcript_id "Phchi.S1G336200.t1"; gene_id "Phchi.S1G336200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7291.t1 is derived from g4463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28361307	28362953	.	-	.	Phchi.S1G445000
Phchi.S1	AUGUSTUS	transcript	28361307	28362953	.	-	.	transcript_id "Phchi.S1G445000.t1"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	stop_codon	28361304	28361306	.	-	0	transcript_id "Phchi.S1G445000.t1"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	CDS	28361307	28362953	0.83	-	0	transcript_id "Phchi.S1G445000.t1"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	exon	28361307	28362953	.	-	.	transcript_id "Phchi.S1G445000.t1"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	start_codon	28362951	28362953	.	-	0	transcript_id "Phchi.S1G445000.t1"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	transcript	28361307	28362842	.	-	.	transcript_id "Phchi.S1G445000.t2"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	stop_codon	28361304	28361306	.	-	0	transcript_id "Phchi.S1G445000.t2"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	CDS	28361307	28362842	0.51	-	0	transcript_id "Phchi.S1G445000.t2"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	exon	28361307	28362842	.	-	.	transcript_id "Phchi.S1G445000.t2"; gene_id "Phchi.S1G445000"
Phchi.S1	AUGUSTUS	start_codon	28362840	28362842	.	-	0	transcript_id "Phchi.S1G445000.t2"; gene_id "Phchi.S1G445000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9501.t1 is derived from g6677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42074073	42075229	.	-	.	Phchi.S1G666000
Phchi.S1	AUGUSTUS	transcript	42074073	42075229	.	-	.	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	stop_codon	42074070	42074072	.	-	0	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	CDS	42074073	42074959	0.55	-	2	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	exon	42074073	42074959	.	-	.	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	intron	42074960	42075078	.	-	.	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	CDS	42075079	42075229	0.71	-	0	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	exon	42075079	42075229	.	-	.	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
Phchi.S1	AUGUSTUS	start_codon	42075227	42075229	.	-	0	transcript_id "Phchi.S1G666000.t1"; gene_id "Phchi.S1G666000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4685.t1 is derived from g1855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12045988	12047157	.	+	.	Phchi.S1G184400
Phchi.S1	AUGUSTUS	transcript	12045988	12047157	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	start_codon	12045988	12045990	.	+	0	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	CDS	12045988	12046231	0.48	+	0	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	exon	12045988	12046231	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	intron	12046232	12046303	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	CDS	12046304	12046404	0.24	+	2	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	exon	12046304	12046404	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	intron	12046405	12046722	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	CDS	12046723	12046933	0.27	+	0	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	exon	12046723	12046933	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	intron	12046934	12047077	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	CDS	12047078	12047157	1	+	2	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	exon	12047078	12047157	.	+	.	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
Phchi.S1	AUGUSTUS	stop_codon	12047158	12047160	.	+	0	transcript_id "Phchi.S1G184400.t1"; gene_id "Phchi.S1G184400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2480.t1 is derived from g9400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6867446	6870851	.	-	.	Phchi.S5G108900
Phchi.S5	AUGUSTUS	transcript	6867446	6870851	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	stop_codon	6867443	6867445	.	-	0	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	CDS	6867446	6867879	0.9	-	2	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	exon	6867446	6867879	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	intron	6867880	6867995	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	CDS	6867996	6868564	0.87	-	1	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	exon	6867996	6868564	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	intron	6868565	6868757	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	CDS	6868758	6869707	0.86	-	0	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	exon	6868758	6869707	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	intron	6869708	6869822	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	CDS	6869823	6870851	0.52	-	0	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	exon	6869823	6870851	.	-	.	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
Phchi.S5	AUGUSTUS	start_codon	6870849	6870851	.	-	0	transcript_id "Phchi.S5G108900.t1"; gene_id "Phchi.S5G108900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10162.t1 is derived from g7338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46049681	46050892	.	-	.	Phchi.S1G732100
Phchi.S1	AUGUSTUS	transcript	46049681	46050892	.	-	.	transcript_id "Phchi.S1G732100.t1"; gene_id "Phchi.S1G732100"
Phchi.S1	AUGUSTUS	stop_codon	46049678	46049680	.	-	0	transcript_id "Phchi.S1G732100.t1"; gene_id "Phchi.S1G732100"
Phchi.S1	AUGUSTUS	CDS	46049681	46050892	0.5	-	0	transcript_id "Phchi.S1G732100.t1"; gene_id "Phchi.S1G732100"
Phchi.S1	AUGUSTUS	exon	46049681	46050892	.	-	.	transcript_id "Phchi.S1G732100.t1"; gene_id "Phchi.S1G732100"
Phchi.S1	AUGUSTUS	start_codon	46050890	46050892	.	-	0	transcript_id "Phchi.S1G732100.t1"; gene_id "Phchi.S1G732100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5442.t1 is derived from g2612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16889527	16890979	.	+	.	Phchi.S1G260100
Phchi.S1	AUGUSTUS	transcript	16889527	16890979	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	start_codon	16889527	16889529	.	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889527	16889561	1	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889527	16889561	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889562	16889652	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889653	16889727	1	+	1	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889653	16889727	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889728	16889864	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889865	16889946	1	+	1	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889865	16889946	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889947	16890121	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890122	16890151	1	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890122	16890151	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890152	16890236	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890237	16890322	0.98	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890237	16890322	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890323	16890438	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890439	16890514	0.98	+	1	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890439	16890514	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890515	16890614	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890615	16890734	0.97	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890615	16890734	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890735	16890823	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890824	16890835	0.68	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890824	16890835	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890836	16890931	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890932	16890979	0.71	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890932	16890979	.	+	.	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	stop_codon	16890980	16890982	.	+	0	transcript_id "Phchi.S1G260100.t1"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	transcript	16889527	16890979	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	start_codon	16889527	16889529	.	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889527	16889561	0.98	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889527	16889561	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889562	16889652	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889653	16889727	0.98	+	1	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889653	16889727	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889728	16889864	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889865	16889906	0.98	+	1	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889865	16889906	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889907	16889965	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16889966	16889978	1	+	1	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16889966	16889978	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16889979	16890121	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890122	16890151	1	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890122	16890151	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890152	16890236	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890237	16890322	0.97	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890237	16890322	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890323	16890438	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890439	16890514	0.97	+	1	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890439	16890514	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890515	16890614	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890615	16890734	0.97	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890615	16890734	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890735	16890823	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890824	16890835	0.59	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890824	16890835	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	intron	16890836	16890931	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	CDS	16890932	16890979	0.63	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	exon	16890932	16890979	.	+	.	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
Phchi.S1	AUGUSTUS	stop_codon	16890980	16890982	.	+	0	transcript_id "Phchi.S1G260100.t2"; gene_id "Phchi.S1G260100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3320.t1 is derived from g489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2879518	2880306	.	+	.	Phchi.S1G047900
Phchi.S1	AUGUSTUS	transcript	2879518	2880306	.	+	.	transcript_id "Phchi.S1G047900.t1"; gene_id "Phchi.S1G047900"
Phchi.S1	AUGUSTUS	start_codon	2879518	2879520	.	+	0	transcript_id "Phchi.S1G047900.t1"; gene_id "Phchi.S1G047900"
Phchi.S1	AUGUSTUS	CDS	2879518	2880306	0.59	+	0	transcript_id "Phchi.S1G047900.t1"; gene_id "Phchi.S1G047900"
Phchi.S1	AUGUSTUS	exon	2879518	2880306	.	+	.	transcript_id "Phchi.S1G047900.t1"; gene_id "Phchi.S1G047900"
Phchi.S1	AUGUSTUS	stop_codon	2880307	2880309	.	+	0	transcript_id "Phchi.S1G047900.t1"; gene_id "Phchi.S1G047900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14767.t1 is derived from g13235.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14594464	14598615	.	+	.	Phchi.S3G208600
Phchi.S3	AUGUSTUS	transcript	14594464	14598615	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	start_codon	14594464	14594466	.	+	0	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14594464	14594536	0.98	+	0	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14594464	14594536	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14594537	14594727	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14594728	14594841	1	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14594728	14594841	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14594842	14594927	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14594928	14595023	1	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14594928	14595023	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14595024	14595112	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14595113	14595352	1	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14595113	14595352	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14595353	14595627	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14595628	14595735	0.89	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14595628	14595735	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14595736	14595933	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14595934	14596076	0.99	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14595934	14596076	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14596077	14596510	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14596511	14596991	1	+	0	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14596511	14596991	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14596992	14597150	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14597151	14597261	1	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14597151	14597261	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14597262	14597388	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14597389	14597490	1	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14597389	14597490	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14597491	14597604	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14597605	14597662	1	+	2	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14597605	14597662	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14597663	14597790	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14597791	14597859	1	+	1	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14597791	14597859	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14597860	14598050	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14598051	14598138	1	+	1	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14598051	14598138	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14598139	14598257	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14598258	14598319	1	+	0	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14598258	14598319	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14598320	14598400	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14598401	14598452	0.8	+	1	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14598401	14598452	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	intron	14598453	14598558	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	CDS	14598559	14598615	0.8	+	0	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	exon	14598559	14598615	.	+	.	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
Phchi.S3	AUGUSTUS	stop_codon	14598616	14598618	.	+	0	transcript_id "Phchi.S3G208600.t1"; gene_id "Phchi.S3G208600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10222.t1 is derived from g7398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46463078	46465465	.	+	.	Phchi.S1G738100
Phchi.S1	AUGUSTUS	transcript	46463078	46465465	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	start_codon	46463078	46463080	.	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46463078	46463288	0.83	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46463078	46463288	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46463289	46463404	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46463405	46463502	0.97	+	2	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46463405	46463502	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46463503	46463602	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46463603	46463662	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46463603	46463662	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46463663	46463778	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46463779	46463892	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46463779	46463892	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46463893	46464029	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46464030	46464095	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46464030	46464095	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46464096	46464174	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46464175	46464282	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46464175	46464282	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46464283	46464363	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46464364	46464447	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46464364	46464447	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46464448	46464582	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46464583	46464683	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46464583	46464683	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46464684	46464769	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46464770	46464789	0.64	+	1	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46464770	46464789	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46464790	46464926	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46464927	46465078	0.38	+	2	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46464927	46465078	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46465079	46465160	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46465161	46465283	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46465161	46465283	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	intron	46465284	46465372	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	CDS	46465373	46465465	1	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	exon	46465373	46465465	.	+	.	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
Phchi.S1	AUGUSTUS	stop_codon	46465466	46465468	.	+	0	transcript_id "Phchi.S1G738100.t1"; gene_id "Phchi.S1G738100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14468.t1 is derived from g12936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13021349	13022652	.	+	.	Phchi.S3G178700
Phchi.S3	AUGUSTUS	transcript	13021349	13022652	.	+	.	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	start_codon	13021349	13021351	.	+	0	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	CDS	13021349	13021966	0.97	+	0	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	exon	13021349	13021966	.	+	.	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	intron	13021967	13022081	.	+	.	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	CDS	13022082	13022267	1	+	0	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	exon	13022082	13022267	.	+	.	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	intron	13022268	13022364	.	+	.	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	CDS	13022365	13022652	1	+	0	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	exon	13022365	13022652	.	+	.	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
Phchi.S3	AUGUSTUS	stop_codon	13022653	13022655	.	+	0	transcript_id "Phchi.S3G178700.t1"; gene_id "Phchi.S3G178700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3391.t1 is derived from g560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3317506	3320971	.	-	.	Phchi.S1G055000
Phchi.S1	AUGUSTUS	transcript	3317506	3320971	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	stop_codon	3317503	3317505	.	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3317506	3318286	0.84	-	1	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3317506	3318286	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3318287	3318381	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3318382	3318542	0.79	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3318382	3318542	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3318543	3318680	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3318681	3318767	1	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3318681	3318767	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3318768	3318851	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3318852	3318920	1	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3318852	3318920	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3318921	3319021	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3319022	3319132	1	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3319022	3319132	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3319133	3319215	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3319216	3319378	1	-	1	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3319216	3319378	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3319379	3319502	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3319503	3319913	1	-	1	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3319503	3319913	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	intron	3319914	3320576	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	CDS	3320577	3320971	0.98	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	exon	3320577	3320971	.	-	.	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
Phchi.S1	AUGUSTUS	start_codon	3320969	3320971	.	-	0	transcript_id "Phchi.S1G055000.t1"; gene_id "Phchi.S1G055000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13935.t1 is derived from g12402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9800859	9804018	.	-	.	Phchi.S3G125400
Phchi.S3	AUGUSTUS	transcript	9800859	9804018	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	stop_codon	9800856	9800858	.	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9800859	9800973	1	-	1	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9800859	9800973	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9800974	9801090	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9801091	9801191	1	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9801091	9801191	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9801192	9801276	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9801277	9801387	1	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9801277	9801387	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9801388	9801538	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9801539	9801662	1	-	1	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9801539	9801662	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9801663	9801743	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9801744	9801772	1	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9801744	9801772	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9801773	9801853	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9801854	9801926	1	-	1	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9801854	9801926	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9801927	9802040	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9802041	9802130	1	-	1	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9802041	9802130	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9802131	9802248	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9802249	9802349	1	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9802249	9802349	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9802350	9802450	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9802451	9802645	1	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9802451	9802645	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9802646	9802781	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9802782	9802936	0.56	-	2	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9802782	9802936	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9802937	9803062	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9803063	9803195	0.56	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9803063	9803195	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9803196	9803281	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9803282	9803485	0.92	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9803282	9803485	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9803486	9803592	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9803593	9803710	1	-	1	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9803593	9803710	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	intron	9803711	9803863	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	CDS	9803864	9804018	0.92	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	exon	9803864	9804018	.	-	.	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
Phchi.S3	AUGUSTUS	start_codon	9804016	9804018	.	-	0	transcript_id "Phchi.S3G125400.t1"; gene_id "Phchi.S3G125400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4639.t1 is derived from g1809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11556076	11558306	.	-	.	Phchi.S1G179800
Phchi.S1	AUGUSTUS	transcript	11556076	11558306	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	stop_codon	11556073	11556075	.	-	0	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	CDS	11556076	11557035	1	-	0	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	exon	11556076	11557035	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	intron	11557036	11557156	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	CDS	11557157	11557570	0.93	-	0	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	exon	11557157	11557570	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	intron	11557571	11557677	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	CDS	11557678	11557770	1	-	0	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	exon	11557678	11557770	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	intron	11557771	11558054	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	CDS	11558055	11558306	0.99	-	0	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	exon	11558055	11558306	.	-	.	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
Phchi.S1	AUGUSTUS	start_codon	11558304	11558306	.	-	0	transcript_id "Phchi.S1G179800.t1"; gene_id "Phchi.S1G179800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14905.t1 is derived from g13373.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15454501	15456211	.	-	.	Phchi.S3G222400
Phchi.S3	AUGUSTUS	transcript	15454501	15456211	.	-	.	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	stop_codon	15454498	15454500	.	-	0	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	CDS	15454501	15455543	0.94	-	2	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	exon	15454501	15455543	.	-	.	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	intron	15455544	15455622	.	-	.	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	CDS	15455623	15456211	0.4	-	0	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	exon	15455623	15456211	.	-	.	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	start_codon	15456209	15456211	.	-	0	transcript_id "Phchi.S3G222400.t1"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	transcript	15455208	15456211	.	-	.	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	stop_codon	15455205	15455207	.	-	0	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	CDS	15455208	15455224	0.89	-	2	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	exon	15455208	15455224	.	-	.	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	intron	15455225	15455324	.	-	.	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	CDS	15455325	15455543	0.89	-	2	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	exon	15455325	15455543	.	-	.	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	intron	15455544	15455622	.	-	.	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	CDS	15455623	15456211	0.31	-	0	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	exon	15455623	15456211	.	-	.	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
Phchi.S3	AUGUSTUS	start_codon	15456209	15456211	.	-	0	transcript_id "Phchi.S3G222400.t2"; gene_id "Phchi.S3G222400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15568.t1 is derived from g14037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20026399	20027796	.	-	.	Phchi.S3G288700
Phchi.S3	AUGUSTUS	transcript	20026399	20027796	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	stop_codon	20026396	20026398	.	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	CDS	20026399	20026875	1	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	exon	20026399	20026875	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	intron	20026876	20026953	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	CDS	20026954	20027043	1	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	exon	20026954	20027043	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	intron	20027044	20027147	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	CDS	20027148	20027252	1	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	exon	20027148	20027252	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	intron	20027253	20027406	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	CDS	20027407	20027550	1	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	exon	20027407	20027550	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	intron	20027551	20027643	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	CDS	20027644	20027796	0.63	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	exon	20027644	20027796	.	-	.	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
Phchi.S3	AUGUSTUS	start_codon	20027794	20027796	.	-	0	transcript_id "Phchi.S3G288700.t1"; gene_id "Phchi.S3G288700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11062.t1 is derived from g15112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3940369	3943293	.	+	.	Phchi.S4G064400
Phchi.S4	AUGUSTUS	transcript	3940369	3943293	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	start_codon	3940369	3940371	.	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3940369	3940395	1	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3940369	3940395	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3940396	3940483	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3940484	3940564	1	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3940484	3940564	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3940565	3940640	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3940641	3940746	0.31	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3940641	3940746	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3940747	3940836	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3940837	3940904	0.26	+	2	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3940837	3940904	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3940905	3941062	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3941063	3941254	0.4	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3941063	3941254	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3941255	3941337	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3941338	3941478	0.88	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3941338	3941478	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3941479	3941567	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3941568	3941657	0.88	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3941568	3941657	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3941658	3941739	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3941740	3941808	0.78	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3941740	3941808	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3941809	3942202	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3942203	3942211	0.83	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3942203	3942211	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3942212	3942290	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3942291	3942369	0.86	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3942291	3942369	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	intron	3942370	3942739	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	CDS	3942740	3943293	0.54	+	2	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	exon	3942740	3943293	.	+	.	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
Phchi.S4	AUGUSTUS	stop_codon	3943294	3943296	.	+	0	transcript_id "Phchi.S4G064400.t1"; gene_id "Phchi.S4G064400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7078.t1 is derived from g4250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26789937	26792030	.	+	.	Phchi.S1G423700
Phchi.S1	AUGUSTUS	transcript	26789937	26792030	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	start_codon	26789937	26789939	.	+	0	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26789937	26790093	0.53	+	0	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26789937	26790093	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	intron	26790094	26790166	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26790167	26790397	1	+	2	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26790167	26790397	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	intron	26790398	26790501	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26790502	26790599	1	+	2	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26790502	26790599	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	intron	26790600	26790688	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26790689	26790875	1	+	0	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26790689	26790875	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	intron	26790876	26791110	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26791111	26791241	1	+	2	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26791111	26791241	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	intron	26791242	26791343	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26791344	26791565	1	+	0	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26791344	26791565	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	intron	26791566	26791652	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	CDS	26791653	26792030	1	+	0	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	exon	26791653	26792030	.	+	.	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
Phchi.S1	AUGUSTUS	stop_codon	26792031	26792033	.	+	0	transcript_id "Phchi.S1G423700.t1"; gene_id "Phchi.S1G423700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6960.t1 is derived from g4132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26145368	26147497	.	+	.	Phchi.S1G411900
Phchi.S1	AUGUSTUS	transcript	26145368	26147497	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	start_codon	26145368	26145370	.	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26145368	26145481	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26145368	26145481	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26145482	26145609	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26145610	26145678	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26145610	26145678	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26145679	26145751	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26145752	26145882	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26145752	26145882	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26145883	26145973	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26145974	26146073	1	+	1	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26145974	26146073	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26146074	26146167	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26146168	26146235	0.99	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26146168	26146235	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26146236	26146344	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26146345	26146486	0.99	+	1	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26146345	26146486	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26146487	26146609	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26146610	26146726	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26146610	26146726	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26146727	26146818	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26146819	26146944	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26146819	26146944	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26146945	26147063	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26147064	26147147	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26147064	26147147	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26147148	26147235	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26147236	26147315	1	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26147236	26147315	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	intron	26147316	26147397	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	CDS	26147398	26147497	1	+	1	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	exon	26147398	26147497	.	+	.	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
Phchi.S1	AUGUSTUS	stop_codon	26147498	26147500	.	+	0	transcript_id "Phchi.S1G411900.t1"; gene_id "Phchi.S1G411900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8461.t1 is derived from g5636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36050892	36052769	.	+	.	Phchi.S1G562000
Phchi.S1	AUGUSTUS	transcript	36050892	36052769	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	start_codon	36050892	36050894	.	+	0	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36050892	36050894	0.96	+	0	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36050892	36050894	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36050895	36051450	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36051451	36051523	1	+	0	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36051451	36051523	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36051524	36051636	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36051637	36051693	1	+	2	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36051637	36051693	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36051694	36051776	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36051777	36051894	1	+	2	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36051777	36051894	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36051895	36051996	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36051997	36052086	1	+	1	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36051997	36052086	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36052087	36052260	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36052261	36052440	1	+	1	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36052261	36052440	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36052441	36052544	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36052545	36052622	1	+	1	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36052545	36052622	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	intron	36052623	36052699	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	CDS	36052700	36052769	1	+	1	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	exon	36052700	36052769	.	+	.	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
Phchi.S1	AUGUSTUS	stop_codon	36052770	36052772	.	+	0	transcript_id "Phchi.S1G562000.t1"; gene_id "Phchi.S1G562000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5906.t1 is derived from g3076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19717483	19722243	.	-	.	Phchi.S1G306500
Phchi.S1	AUGUSTUS	transcript	19717483	19722243	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	stop_codon	19717480	19717482	.	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19717483	19717521	1	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19717483	19717521	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19717522	19717601	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19717602	19717880	1	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19717602	19717880	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19717881	19717997	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19717998	19718601	1	-	1	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19717998	19718601	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19718602	19718774	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19718775	19719175	0.74	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19718775	19719175	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19719176	19719254	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19719255	19719446	0.67	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19719255	19719446	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19719447	19719550	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19719551	19720012	0.79	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19719551	19720012	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19720013	19720291	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19720292	19720554	1	-	2	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19720292	19720554	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19720555	19720818	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19720819	19721140	1	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19720819	19721140	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19721141	19721320	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19721321	19721366	1	-	1	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19721321	19721366	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19721367	19721518	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19721519	19721607	1	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19721519	19721607	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19721608	19721823	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19721824	19721939	1	-	2	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19721824	19721939	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	intron	19721940	19722146	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	CDS	19722147	19722243	0.71	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	exon	19722147	19722243	.	-	.	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
Phchi.S1	AUGUSTUS	start_codon	19722241	19722243	.	-	0	transcript_id "Phchi.S1G306500.t1"; gene_id "Phchi.S1G306500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6040.t1 is derived from g3211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20587418	20588313	.	-	.	Phchi.S1G319900
Phchi.S1	AUGUSTUS	transcript	20587418	20588313	.	-	.	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	stop_codon	20587415	20587417	.	-	0	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	CDS	20587418	20588071	0.92	-	0	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	exon	20587418	20588071	.	-	.	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	intron	20588072	20588226	.	-	.	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	CDS	20588227	20588313	0.9	-	0	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	exon	20588227	20588313	.	-	.	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
Phchi.S1	AUGUSTUS	start_codon	20588311	20588313	.	-	0	transcript_id "Phchi.S1G319900.t1"; gene_id "Phchi.S1G319900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12854.t1 is derived from g11319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2731647	2732133	.	-	.	Phchi.S3G017300
Phchi.S3	AUGUSTUS	transcript	2731647	2732133	.	-	.	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	stop_codon	2731644	2731646	.	-	0	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	CDS	2731647	2731701	0.98	-	1	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	exon	2731647	2731701	.	-	.	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	intron	2731702	2731783	.	-	.	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	CDS	2731784	2731917	0.93	-	0	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	exon	2731784	2731917	.	-	.	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	intron	2731918	2732007	.	-	.	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	CDS	2732008	2732133	0.51	-	0	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	exon	2732008	2732133	.	-	.	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
Phchi.S3	AUGUSTUS	start_codon	2732131	2732133	.	-	0	transcript_id "Phchi.S3G017300.t1"; gene_id "Phchi.S3G017300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15104.t1 is derived from g13572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17098250	17100420	.	+	.	Phchi.S3G242300
Phchi.S3	AUGUSTUS	transcript	17098250	17100420	.	+	.	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	start_codon	17098250	17098252	.	+	0	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	CDS	17098250	17099663	0.98	+	0	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	exon	17098250	17099663	.	+	.	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	intron	17099664	17099770	.	+	.	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	CDS	17099771	17100420	0.68	+	2	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	exon	17099771	17100420	.	+	.	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
Phchi.S3	AUGUSTUS	stop_codon	17100421	17100423	.	+	0	transcript_id "Phchi.S3G242300.t1"; gene_id "Phchi.S3G242300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11673.t1 is derived from g15724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7602681	7604039	.	-	.	Phchi.S4G125500
Phchi.S4	AUGUSTUS	transcript	7602681	7604039	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	stop_codon	7602678	7602680	.	-	0	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7602681	7602755	0.75	-	0	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7602681	7602755	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7602756	7602852	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7602853	7602928	1	-	1	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7602853	7602928	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7602929	7603006	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7603007	7603072	1	-	1	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7603007	7603072	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7603073	7603158	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7603159	7603212	1	-	1	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7603159	7603212	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7603213	7603307	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7603308	7603403	1	-	1	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7603308	7603403	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7603404	7603546	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7603547	7603598	1	-	2	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7603547	7603598	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7603599	7603684	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7603685	7603727	1	-	0	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7603685	7603727	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	intron	7603728	7603802	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	CDS	7603803	7604039	0.45	-	0	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	exon	7603803	7604039	.	-	.	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
Phchi.S4	AUGUSTUS	start_codon	7604037	7604039	.	-	0	transcript_id "Phchi.S4G125500.t1"; gene_id "Phchi.S4G125500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13587.t1 is derived from g12054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7592167	7592723	.	-	.	Phchi.S3G090600
Phchi.S3	AUGUSTUS	transcript	7592167	7592723	.	-	.	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	stop_codon	7592164	7592166	.	-	0	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	CDS	7592167	7592392	0.52	-	1	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	exon	7592167	7592392	.	-	.	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	intron	7592393	7592493	.	-	.	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	CDS	7592494	7592723	0.54	-	0	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	exon	7592494	7592723	.	-	.	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
Phchi.S3	AUGUSTUS	start_codon	7592721	7592723	.	-	0	transcript_id "Phchi.S3G090600.t1"; gene_id "Phchi.S3G090600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11014.t1 is derived from g15064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3640873	3642686	.	-	.	Phchi.S4G059600
Phchi.S4	AUGUSTUS	transcript	3640873	3642686	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	stop_codon	3640870	3640872	.	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3640873	3641068	0.86	-	1	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3640873	3641068	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3641069	3641172	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3641173	3641240	1	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3641173	3641240	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3641241	3641324	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3641325	3641453	1	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3641325	3641453	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3641454	3641571	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3641572	3641714	1	-	2	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3641572	3641714	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3641715	3641825	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3641826	3641957	1	-	2	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3641826	3641957	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3641958	3642085	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3642086	3642242	0.97	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3642086	3642242	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3642243	3642347	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3642348	3642545	0.9	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3642348	3642545	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	intron	3642546	3642629	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	CDS	3642630	3642686	1	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	exon	3642630	3642686	.	-	.	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
Phchi.S4	AUGUSTUS	start_codon	3642684	3642686	.	-	0	transcript_id "Phchi.S4G059600.t1"; gene_id "Phchi.S4G059600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg187.t1 is derived from g9969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1068341	1069182	.	-	.	Phchi.S6G014600
Phchi.S6	AUGUSTUS	transcript	1068341	1069182	.	-	.	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	stop_codon	1068338	1068340	.	-	0	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	CDS	1068341	1068734	0.95	-	1	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	exon	1068341	1068734	.	-	.	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	intron	1068735	1068915	.	-	.	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	CDS	1068916	1068963	0.75	-	1	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	exon	1068916	1068963	.	-	.	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	intron	1068964	1069090	.	-	.	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	CDS	1069091	1069182	0.5	-	0	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	exon	1069091	1069182	.	-	.	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
Phchi.S6	AUGUSTUS	start_codon	1069180	1069182	.	-	0	transcript_id "Phchi.S6G014600.t1"; gene_id "Phchi.S6G014600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2395.t1 is derived from g9315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6471858	6474579	.	-	.	Phchi.S5G100400
Phchi.S5	AUGUSTUS	transcript	6471858	6474579	.	-	.	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	stop_codon	6471855	6471857	.	-	0	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	CDS	6471858	6472028	0.88	-	0	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	exon	6471858	6472028	.	-	.	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	intron	6472029	6472140	.	-	.	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	CDS	6472141	6472235	0.8	-	2	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	exon	6472141	6472235	.	-	.	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	intron	6472236	6474368	.	-	.	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	CDS	6474369	6474579	0.12	-	0	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	exon	6474369	6474579	.	-	.	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
Phchi.S5	AUGUSTUS	start_codon	6474577	6474579	.	-	0	transcript_id "Phchi.S5G100400.t1"; gene_id "Phchi.S5G100400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10330.t1 is derived from g7506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47206629	47207192	.	+	.	Phchi.S1G748900
Phchi.S1	AUGUSTUS	transcript	47206629	47207192	.	+	.	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	start_codon	47206629	47206631	.	+	0	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	CDS	47206629	47206719	1	+	0	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	exon	47206629	47206719	.	+	.	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	intron	47206720	47206803	.	+	.	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	CDS	47206804	47206871	1	+	2	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	exon	47206804	47206871	.	+	.	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	intron	47206872	47206997	.	+	.	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	CDS	47206998	47207192	1	+	0	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	exon	47206998	47207192	.	+	.	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
Phchi.S1	AUGUSTUS	stop_codon	47207193	47207195	.	+	0	transcript_id "Phchi.S1G748900.t1"; gene_id "Phchi.S1G748900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6297.t1 is derived from g3469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22157990	22158674	.	+	.	Phchi.S1G345600
Phchi.S1	AUGUSTUS	transcript	22157990	22158674	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	start_codon	22157990	22157992	.	+	0	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	CDS	22157990	22158104	1	+	0	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	exon	22157990	22158104	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	intron	22158105	22158288	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	CDS	22158289	22158356	0.89	+	2	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	exon	22158289	22158356	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	intron	22158357	22158462	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	CDS	22158463	22158537	1	+	0	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	exon	22158463	22158537	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	intron	22158538	22158617	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	CDS	22158618	22158674	1	+	0	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	exon	22158618	22158674	.	+	.	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
Phchi.S1	AUGUSTUS	stop_codon	22158675	22158677	.	+	0	transcript_id "Phchi.S1G345600.t1"; gene_id "Phchi.S1G345600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15012.t1 is derived from g13480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16483058	16483490	.	-	.	Phchi.S3G233100
Phchi.S3	AUGUSTUS	transcript	16483058	16483490	.	-	.	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	stop_codon	16483055	16483057	.	-	0	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	CDS	16483058	16483114	1	-	0	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	exon	16483058	16483114	.	-	.	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	intron	16483115	16483262	.	-	.	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	CDS	16483263	16483490	0.99	-	0	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	exon	16483263	16483490	.	-	.	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
Phchi.S3	AUGUSTUS	start_codon	16483488	16483490	.	-	0	transcript_id "Phchi.S3G233100.t1"; gene_id "Phchi.S3G233100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg436.t1 is derived from g10218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3071070	3072916	.	-	.	Phchi.S6G039500
Phchi.S6	AUGUSTUS	transcript	3071070	3072916	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	stop_codon	3071067	3071069	.	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3071070	3071132	1	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3071070	3071132	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3071133	3071222	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3071223	3071298	1	-	1	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3071223	3071298	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3071299	3071372	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3071373	3071498	1	-	1	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3071373	3071498	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3071499	3071584	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3071585	3071652	1	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3071585	3071652	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3071653	3071738	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3071739	3071822	1	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3071739	3071822	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3071823	3071906	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3071907	3071955	1	-	1	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3071907	3071955	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3071956	3072060	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3072061	3072108	1	-	1	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3072061	3072108	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3072109	3072197	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3072198	3072253	1	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3072198	3072253	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3072254	3072345	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3072346	3072400	1	-	1	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3072346	3072400	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3072401	3072592	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3072593	3072620	0.65	-	2	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3072593	3072620	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3072621	3072696	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3072697	3072764	0.5	-	1	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3072697	3072764	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	intron	3072765	3072851	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	CDS	3072852	3072916	0.34	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	exon	3072852	3072916	.	-	.	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
Phchi.S6	AUGUSTUS	start_codon	3072914	3072916	.	-	0	transcript_id "Phchi.S6G039500.t1"; gene_id "Phchi.S6G039500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9593.t1 is derived from g6769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42853533	42855608	.	-	.	Phchi.S1G675200
Phchi.S1	AUGUSTUS	transcript	42853533	42855608	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	stop_codon	42853530	42853532	.	-	0	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	CDS	42853533	42853871	0.98	-	0	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	exon	42853533	42853871	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	intron	42853872	42853953	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	CDS	42853954	42854103	1	-	0	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	exon	42853954	42854103	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	intron	42854104	42854212	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	CDS	42854213	42854360	0.99	-	1	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	exon	42854213	42854360	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	intron	42854361	42854466	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	CDS	42854467	42854543	0.99	-	0	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	exon	42854467	42854543	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	intron	42854544	42854618	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	CDS	42854619	42854779	1	-	2	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	exon	42854619	42854779	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	intron	42854780	42854860	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	CDS	42854861	42855608	0.44	-	0	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	exon	42854861	42855608	.	-	.	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
Phchi.S1	AUGUSTUS	start_codon	42855606	42855608	.	-	0	transcript_id "Phchi.S1G675200.t1"; gene_id "Phchi.S1G675200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1562.t1 is derived from g8481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1773813	1774097	.	-	.	Phchi.S5G017100
Phchi.S5	AUGUSTUS	transcript	1773813	1774097	.	-	.	transcript_id "Phchi.S5G017100.t1"; gene_id "Phchi.S5G017100"
Phchi.S5	AUGUSTUS	stop_codon	1773810	1773812	.	-	0	transcript_id "Phchi.S5G017100.t1"; gene_id "Phchi.S5G017100"
Phchi.S5	AUGUSTUS	CDS	1773813	1774097	1	-	0	transcript_id "Phchi.S5G017100.t1"; gene_id "Phchi.S5G017100"
Phchi.S5	AUGUSTUS	exon	1773813	1774097	.	-	.	transcript_id "Phchi.S5G017100.t1"; gene_id "Phchi.S5G017100"
Phchi.S5	AUGUSTUS	start_codon	1774095	1774097	.	-	0	transcript_id "Phchi.S5G017100.t1"; gene_id "Phchi.S5G017100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1846.t1 is derived from g8766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3535812	3537203	.	-	.	Phchi.S5G045500
Phchi.S5	AUGUSTUS	transcript	3535812	3537203	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	stop_codon	3535809	3535811	.	-	0	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	CDS	3535812	3535891	0.98	-	2	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	exon	3535812	3535891	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	intron	3535892	3536063	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	CDS	3536064	3536114	1	-	2	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	exon	3536064	3536114	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	intron	3536115	3536217	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	CDS	3536218	3536352	0.98	-	2	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	exon	3536218	3536352	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	intron	3536353	3536433	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	CDS	3536434	3536788	1	-	0	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	exon	3536434	3536788	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	intron	3536789	3537149	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	CDS	3537150	3537203	1	-	0	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	exon	3537150	3537203	.	-	.	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
Phchi.S5	AUGUSTUS	start_codon	3537201	3537203	.	-	0	transcript_id "Phchi.S5G045500.t1"; gene_id "Phchi.S5G045500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2171.t1 is derived from g9091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5157587	5159190	.	-	.	Phchi.S5G078000
Phchi.S5	AUGUSTUS	transcript	5157587	5159190	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	stop_codon	5157584	5157586	.	-	0	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	CDS	5157587	5158480	1	-	0	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	exon	5157587	5158480	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	intron	5158481	5158562	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	CDS	5158563	5158680	1	-	1	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	exon	5158563	5158680	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	intron	5158681	5158770	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	CDS	5158771	5158897	1	-	2	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	exon	5158771	5158897	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	intron	5158898	5158965	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	CDS	5158966	5159034	1	-	2	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	exon	5158966	5159034	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	intron	5159035	5159123	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	CDS	5159124	5159190	0.99	-	0	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	exon	5159124	5159190	.	-	.	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
Phchi.S5	AUGUSTUS	start_codon	5159188	5159190	.	-	0	transcript_id "Phchi.S5G078000.t1"; gene_id "Phchi.S5G078000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14620.t1 is derived from g13088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13807690	13811612	.	-	.	Phchi.S3G193900
Phchi.S3	AUGUSTUS	transcript	13807690	13811612	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	stop_codon	13807687	13807689	.	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13807690	13808103	1	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13807690	13808103	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13808104	13808183	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13808184	13808315	1	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13808184	13808315	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13808316	13808417	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13808418	13808534	0.99	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13808418	13808534	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13808535	13808654	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13808655	13808803	0.99	-	2	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13808655	13808803	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13808804	13808898	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13808899	13809794	0.93	-	1	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13808899	13809794	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13809795	13809943	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13809944	13810303	0.95	-	1	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13809944	13810303	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13810304	13810413	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13810414	13810865	0.96	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13810414	13810865	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13810866	13811178	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13811179	13811280	1	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13811179	13811280	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	intron	13811281	13811366	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	CDS	13811367	13811612	0.99	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	exon	13811367	13811612	.	-	.	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
Phchi.S3	AUGUSTUS	start_codon	13811610	13811612	.	-	0	transcript_id "Phchi.S3G193900.t1"; gene_id "Phchi.S3G193900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7267.t1 is derived from g4439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27974074	27983454	.	-	.	Phchi.S1G442600
Phchi.S1	AUGUSTUS	transcript	27974074	27983454	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	stop_codon	27974071	27974073	.	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27974074	27974206	1	-	1	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27974074	27974206	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27974207	27974320	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27974321	27974465	1	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27974321	27974465	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27974466	27974556	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27974557	27975226	0.97	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27974557	27975226	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27975227	27975335	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27975336	27975494	0.95	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27975336	27975494	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27975495	27975773	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27975774	27976178	0.94	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27975774	27976178	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27976179	27976275	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27976276	27977640	0.73	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27976276	27977640	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27977641	27977747	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27977748	27977783	0.76	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27977748	27977783	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27977784	27977933	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27977934	27978916	0.93	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27977934	27978916	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27978917	27978997	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27978998	27980551	0.83	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27978998	27980551	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27980552	27980643	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27980644	27980877	1	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27980644	27980877	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27980878	27980975	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27980976	27981149	1	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27980976	27981149	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27981150	27981239	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27981240	27981368	1	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27981240	27981368	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27981369	27981451	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27981452	27981632	0.99	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27981452	27981632	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27981633	27981735	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27981736	27981942	0.59	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27981736	27981942	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27981943	27982047	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27982048	27982132	1	-	1	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27982048	27982132	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27982133	27982268	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27982269	27982375	1	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27982269	27982375	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27982376	27982467	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27982468	27982651	1	-	1	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27982468	27982651	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27982652	27982745	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27982746	27982911	1	-	2	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27982746	27982911	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27982912	27983083	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27983084	27983214	0.96	-	1	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27983084	27983214	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	intron	27983215	27983326	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	CDS	27983327	27983454	0.48	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	exon	27983327	27983454	.	-	.	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
Phchi.S1	AUGUSTUS	start_codon	27983452	27983454	.	-	0	transcript_id "Phchi.S1G442600.t1"; gene_id "Phchi.S1G442600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1336.t1 is derived from g11119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9089016	9093676	.	-	.	Phchi.S6G129500
Phchi.S6	AUGUSTUS	transcript	9089016	9093676	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	stop_codon	9089013	9089015	.	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9089016	9089060	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9089016	9089060	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9089061	9089139	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9089140	9089328	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9089140	9089328	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9089329	9089416	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9089417	9089522	1	-	1	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9089417	9089522	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9089523	9089655	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9089656	9089786	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9089656	9089786	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9089787	9089872	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9089873	9089954	0.83	-	1	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9089873	9089954	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9089955	9090065	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9090066	9090113	0.83	-	1	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9090066	9090113	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9090114	9090211	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9090212	9090372	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9090212	9090372	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9090373	9090459	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9090460	9090567	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9090460	9090567	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9090568	9090666	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9090667	9090726	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9090667	9090726	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9090727	9090815	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9090816	9090872	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9090816	9090872	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9090873	9091006	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9091007	9091126	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9091007	9091126	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9091127	9091233	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9091234	9091377	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9091234	9091377	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9091378	9091560	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9091561	9091705	1	-	1	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9091561	9091705	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9091706	9091958	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9091959	9092060	1	-	1	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9091959	9092060	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9092061	9092223	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9092224	9092291	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9092224	9092291	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9092292	9092517	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9092518	9092613	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9092518	9092613	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9092614	9092699	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9092700	9092839	1	-	2	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9092700	9092839	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9092840	9092970	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9092971	9093183	1	-	2	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9092971	9093183	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9093184	9093275	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9093276	9093468	1	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9093276	9093468	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	intron	9093469	9093589	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	CDS	9093590	9093676	0.99	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	exon	9093590	9093676	.	-	.	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
Phchi.S6	AUGUSTUS	start_codon	9093674	9093676	.	-	0	transcript_id "Phchi.S6G129500.t1"; gene_id "Phchi.S6G129500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13426.t1 is derived from g11893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6637924	6639812	.	-	.	Phchi.S3G074500
Phchi.S3	AUGUSTUS	transcript	6637924	6639812	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	stop_codon	6637921	6637923	.	-	0	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6637924	6638024	0.99	-	2	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6637924	6638024	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6638025	6638115	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6638116	6638218	1	-	0	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6638116	6638218	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6638219	6638317	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6638318	6638421	1	-	2	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6638318	6638421	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6638422	6638527	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6638528	6638628	1	-	1	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6638528	6638628	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6638629	6638708	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6638709	6638808	1	-	2	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6638709	6638808	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6638809	6638887	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6638888	6638958	0.58	-	1	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6638888	6638958	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6638959	6639080	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6639081	6639285	0.55	-	2	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6639081	6639285	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6639286	6639414	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6639415	6639615	0.84	-	2	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6639415	6639615	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	intron	6639616	6639694	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	CDS	6639695	6639812	0.54	-	0	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	exon	6639695	6639812	.	-	.	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
Phchi.S3	AUGUSTUS	start_codon	6639810	6639812	.	-	0	transcript_id "Phchi.S3G074500.t1"; gene_id "Phchi.S3G074500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8992.t1 is derived from g6167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39023078	39024947	.	+	.	Phchi.S1G615100
Phchi.S1	AUGUSTUS	transcript	39023078	39024947	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	start_codon	39023078	39023080	.	+	0	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	CDS	39023078	39023442	0.75	+	0	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	exon	39023078	39023442	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	intron	39023443	39023578	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	CDS	39023579	39023624	0.89	+	1	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	exon	39023579	39023624	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	intron	39023625	39023893	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	CDS	39023894	39024062	0.38	+	0	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	exon	39023894	39024062	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	intron	39024063	39024169	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	CDS	39024170	39024410	0.59	+	2	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	exon	39024170	39024410	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	intron	39024411	39024493	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	CDS	39024494	39024947	0.69	+	1	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	exon	39024494	39024947	.	+	.	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
Phchi.S1	AUGUSTUS	stop_codon	39024948	39024950	.	+	0	transcript_id "Phchi.S1G615100.t1"; gene_id "Phchi.S1G615100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3294.t1 is derived from g463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2713468	2716488	.	+	.	Phchi.S1G045300
Phchi.S1	AUGUSTUS	transcript	2713468	2716488	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	start_codon	2713468	2713470	.	+	0	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2713468	2714277	0.72	+	0	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2713468	2714277	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	intron	2714278	2714410	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2714411	2714962	0.94	+	0	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2714411	2714962	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	intron	2714963	2715071	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2715072	2715369	0.67	+	0	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2715072	2715369	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	intron	2715370	2715645	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2715646	2715715	0.45	+	2	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2715646	2715715	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	intron	2715716	2715849	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2715850	2715893	0.96	+	1	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2715850	2715893	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	intron	2715894	2716033	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2716034	2716153	0.98	+	2	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2716034	2716153	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	intron	2716154	2716432	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	CDS	2716433	2716488	0.98	+	2	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	exon	2716433	2716488	.	+	.	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
Phchi.S1	AUGUSTUS	stop_codon	2716489	2716491	.	+	0	transcript_id "Phchi.S1G045300.t1"; gene_id "Phchi.S1G045300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2588.t1 is derived from g9508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7524151	7526144	.	-	.	Phchi.S5G119700
Phchi.S5	AUGUSTUS	transcript	7524151	7526144	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	stop_codon	7524148	7524150	.	-	0	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	CDS	7524151	7524399	0.94	-	0	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	exon	7524151	7524399	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	intron	7524400	7524495	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	CDS	7524496	7524741	1	-	0	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	exon	7524496	7524741	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	intron	7524742	7524841	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	CDS	7524842	7525118	1	-	1	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	exon	7524842	7525118	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	intron	7525119	7525231	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	CDS	7525232	7525506	1	-	0	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	exon	7525232	7525506	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	intron	7525507	7525601	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	CDS	7525602	7526144	0.93	-	0	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	exon	7525602	7526144	.	-	.	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
Phchi.S5	AUGUSTUS	start_codon	7526142	7526144	.	-	0	transcript_id "Phchi.S5G119700.t1"; gene_id "Phchi.S5G119700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6156.t1 is derived from g3327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21226088	21227380	.	-	.	Phchi.S1G331500
Phchi.S1	AUGUSTUS	transcript	21226088	21227380	.	-	.	transcript_id "Phchi.S1G331500.t1"; gene_id "Phchi.S1G331500"
Phchi.S1	AUGUSTUS	stop_codon	21226085	21226087	.	-	0	transcript_id "Phchi.S1G331500.t1"; gene_id "Phchi.S1G331500"
Phchi.S1	AUGUSTUS	CDS	21226088	21227380	0.87	-	0	transcript_id "Phchi.S1G331500.t1"; gene_id "Phchi.S1G331500"
Phchi.S1	AUGUSTUS	exon	21226088	21227380	.	-	.	transcript_id "Phchi.S1G331500.t1"; gene_id "Phchi.S1G331500"
Phchi.S1	AUGUSTUS	start_codon	21227378	21227380	.	-	0	transcript_id "Phchi.S1G331500.t1"; gene_id "Phchi.S1G331500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13699.t1 is derived from g12166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8254226	8255689	.	+	.	Phchi.S3G101800
Phchi.S3	AUGUSTUS	transcript	8254226	8255689	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	start_codon	8254226	8254228	.	+	0	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	CDS	8254226	8254646	0.55	+	0	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	exon	8254226	8254646	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	intron	8254647	8254726	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	CDS	8254727	8254861	1	+	2	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	exon	8254727	8254861	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	intron	8254862	8254942	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	CDS	8254943	8255115	1	+	2	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	exon	8254943	8255115	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	intron	8255116	8255196	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	CDS	8255197	8255322	1	+	0	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	exon	8255197	8255322	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	intron	8255323	8255395	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	CDS	8255396	8255512	1	+	0	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	exon	8255396	8255512	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	intron	8255513	8255596	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	CDS	8255597	8255689	1	+	0	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	exon	8255597	8255689	.	+	.	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
Phchi.S3	AUGUSTUS	stop_codon	8255690	8255692	.	+	0	transcript_id "Phchi.S3G101800.t1"; gene_id "Phchi.S3G101800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13514.t1 is derived from g11981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7264081	7266725	.	-	.	Phchi.S3G083300
Phchi.S3	AUGUSTUS	transcript	7264081	7266725	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	stop_codon	7264078	7264080	.	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7264081	7264218	0.24	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7264081	7264218	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7264219	7264309	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7264310	7264459	1	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7264310	7264459	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7264460	7264542	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7264543	7264747	1	-	1	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7264543	7264747	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7264748	7264864	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7264865	7264916	1	-	2	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7264865	7264916	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7264917	7265008	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7265009	7265234	1	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7265009	7265234	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7265235	7265310	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7265311	7265452	1	-	1	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7265311	7265452	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7265453	7265572	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7265573	7265679	1	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7265573	7265679	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7265680	7265876	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7265877	7265975	1	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7265877	7265975	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7265976	7266065	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7266066	7266244	1	-	2	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7266066	7266244	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7266245	7266368	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7266369	7266480	1	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7266369	7266480	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	intron	7266481	7266617	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	CDS	7266618	7266725	1	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	exon	7266618	7266725	.	-	.	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
Phchi.S3	AUGUSTUS	start_codon	7266723	7266725	.	-	0	transcript_id "Phchi.S3G083300.t1"; gene_id "Phchi.S3G083300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6992.t1 is derived from g4164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26302701	26303722	.	+	.	Phchi.S1G415100
Phchi.S1	AUGUSTUS	transcript	26302701	26303722	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	start_codon	26302701	26302703	.	+	0	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	CDS	26302701	26302842	0.95	+	0	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	exon	26302701	26302842	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	intron	26302843	26302922	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	CDS	26302923	26303056	0.94	+	2	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	exon	26302923	26303056	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	intron	26303057	26303157	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	CDS	26303158	26303407	0.94	+	0	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	exon	26303158	26303407	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	intron	26303408	26303498	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	CDS	26303499	26303722	0.96	+	2	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	exon	26303499	26303722	.	+	.	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
Phchi.S1	AUGUSTUS	stop_codon	26303723	26303725	.	+	0	transcript_id "Phchi.S1G415100.t1"; gene_id "Phchi.S1G415100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11420.t1 is derived from g15470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6257840	6258592	.	-	.	Phchi.S4G100200
Phchi.S4	AUGUSTUS	transcript	6257840	6258592	.	-	.	transcript_id "Phchi.S4G100200.t1"; gene_id "Phchi.S4G100200"
Phchi.S4	AUGUSTUS	stop_codon	6257837	6257839	.	-	0	transcript_id "Phchi.S4G100200.t1"; gene_id "Phchi.S4G100200"
Phchi.S4	AUGUSTUS	CDS	6257840	6258592	0.97	-	0	transcript_id "Phchi.S4G100200.t1"; gene_id "Phchi.S4G100200"
Phchi.S4	AUGUSTUS	exon	6257840	6258592	.	-	.	transcript_id "Phchi.S4G100200.t1"; gene_id "Phchi.S4G100200"
Phchi.S4	AUGUSTUS	start_codon	6258590	6258592	.	-	0	transcript_id "Phchi.S4G100200.t1"; gene_id "Phchi.S4G100200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4958.t1 is derived from g2128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13741834	13742103	.	-	.	Phchi.S1G211700
Phchi.S1	AUGUSTUS	transcript	13741834	13742103	.	-	.	transcript_id "Phchi.S1G211700.t1"; gene_id "Phchi.S1G211700"
Phchi.S1	AUGUSTUS	stop_codon	13741831	13741833	.	-	0	transcript_id "Phchi.S1G211700.t1"; gene_id "Phchi.S1G211700"
Phchi.S1	AUGUSTUS	CDS	13741834	13742103	0.88	-	0	transcript_id "Phchi.S1G211700.t1"; gene_id "Phchi.S1G211700"
Phchi.S1	AUGUSTUS	exon	13741834	13742103	.	-	.	transcript_id "Phchi.S1G211700.t1"; gene_id "Phchi.S1G211700"
Phchi.S1	AUGUSTUS	start_codon	13742101	13742103	.	-	0	transcript_id "Phchi.S1G211700.t1"; gene_id "Phchi.S1G211700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13570.t1 is derived from g12037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7541427	7542686	.	-	.	Phchi.S3G088900
Phchi.S3	AUGUSTUS	transcript	7541427	7542686	.	-	.	transcript_id "Phchi.S3G088900.t1"; gene_id "Phchi.S3G088900"
Phchi.S3	AUGUSTUS	stop_codon	7541424	7541426	.	-	0	transcript_id "Phchi.S3G088900.t1"; gene_id "Phchi.S3G088900"
Phchi.S3	AUGUSTUS	CDS	7541427	7542686	0.91	-	0	transcript_id "Phchi.S3G088900.t1"; gene_id "Phchi.S3G088900"
Phchi.S3	AUGUSTUS	exon	7541427	7542686	.	-	.	transcript_id "Phchi.S3G088900.t1"; gene_id "Phchi.S3G088900"
Phchi.S3	AUGUSTUS	start_codon	7542684	7542686	.	-	0	transcript_id "Phchi.S3G088900.t1"; gene_id "Phchi.S3G088900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4155.t1 is derived from g1324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8664644	8669336	.	-	.	Phchi.S1G131400
Phchi.S1	AUGUSTUS	transcript	8664644	8669336	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	stop_codon	8664641	8664643	.	-	0	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8664644	8664671	1	-	1	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8664644	8664671	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8664672	8664770	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8664771	8664860	1	-	1	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8664771	8664860	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8664861	8665003	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8665004	8665026	0.94	-	0	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8665004	8665026	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8665027	8665151	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8665152	8665217	0.7	-	0	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8665152	8665217	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8665218	8665559	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8665560	8666728	0.61	-	2	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8665560	8666728	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8666729	8666824	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8666825	8666947	1	-	2	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8666825	8666947	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8666948	8667186	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8667187	8667505	1	-	0	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8667187	8667505	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8667506	8667600	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8667601	8668058	1	-	2	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8667601	8668058	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	intron	8668059	8668327	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	CDS	8668328	8669336	0.37	-	0	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	exon	8668328	8669336	.	-	.	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
Phchi.S1	AUGUSTUS	start_codon	8669334	8669336	.	-	0	transcript_id "Phchi.S1G131400.t1"; gene_id "Phchi.S1G131400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3665.t1 is derived from g834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5069213	5069698	.	+	.	Phchi.S1G082400
Phchi.S1	AUGUSTUS	transcript	5069213	5069698	.	+	.	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	start_codon	5069213	5069215	.	+	0	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	CDS	5069213	5069328	0.91	+	0	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	exon	5069213	5069328	.	+	.	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	intron	5069329	5069436	.	+	.	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	CDS	5069437	5069698	0.92	+	1	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	exon	5069437	5069698	.	+	.	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
Phchi.S1	AUGUSTUS	stop_codon	5069699	5069701	.	+	0	transcript_id "Phchi.S1G082400.t1"; gene_id "Phchi.S1G082400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14321.t1 is derived from g12788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12084487	12085544	.	+	.	Phchi.S3G164000
Phchi.S3	AUGUSTUS	transcript	12084487	12085544	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	start_codon	12084487	12084489	.	+	0	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	CDS	12084487	12084644	0.84	+	0	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	exon	12084487	12084644	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	intron	12084645	12084754	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	CDS	12084755	12084847	0.68	+	1	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	exon	12084755	12084847	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	intron	12084848	12084965	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	CDS	12084966	12085033	0.75	+	1	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	exon	12084966	12085033	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	intron	12085034	12085168	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	CDS	12085169	12085261	0.72	+	2	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	exon	12085169	12085261	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	intron	12085262	12085377	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	CDS	12085378	12085544	0.77	+	2	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	exon	12085378	12085544	.	+	.	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
Phchi.S3	AUGUSTUS	stop_codon	12085545	12085547	.	+	0	transcript_id "Phchi.S3G164000.t1"; gene_id "Phchi.S3G164000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10924.t1 is derived from g14974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2982928	2985949	.	-	.	Phchi.S4G050600
Phchi.S4	AUGUSTUS	transcript	2982928	2985949	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	stop_codon	2982925	2982927	.	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2982928	2982951	0.96	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2982928	2982951	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2982952	2983161	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2983162	2983381	0.96	-	1	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2983162	2983381	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2983382	2983553	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2983554	2983703	1	-	1	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2983554	2983703	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2983704	2983784	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2983785	2983847	1	-	1	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2983785	2983847	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2983848	2983934	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2983935	2984020	0.9	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2983935	2984020	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2984021	2984137	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2984138	2984162	0.9	-	1	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2984138	2984162	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2984163	2984248	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2984249	2984295	0.94	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2984249	2984295	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2984296	2984384	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2984385	2984433	1	-	1	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2984385	2984433	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2984434	2984523	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2984524	2984648	1	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2984524	2984648	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2984649	2984720	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2984721	2984891	1	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2984721	2984891	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2984892	2984993	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2984994	2985391	0.99	-	2	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2984994	2985391	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2985392	2985460	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2985461	2985514	0.5	-	2	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2985461	2985514	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2985515	2985624	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2985625	2985684	0.89	-	2	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2985625	2985684	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2985685	2985784	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2985785	2985801	0.97	-	1	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2985785	2985801	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	intron	2985802	2985908	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	CDS	2985909	2985949	0.78	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	exon	2985909	2985949	.	-	.	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
Phchi.S4	AUGUSTUS	start_codon	2985947	2985949	.	-	0	transcript_id "Phchi.S4G050600.t1"; gene_id "Phchi.S4G050600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14031.t1 is derived from g12498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10376366	10379491	.	-	.	Phchi.S3G135000
Phchi.S3	AUGUSTUS	transcript	10376366	10379491	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	stop_codon	10376363	10376365	.	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10376366	10376376	1	-	2	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10376366	10376376	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10376377	10376469	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10376470	10376596	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10376470	10376596	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10376597	10376681	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10376682	10376774	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10376682	10376774	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10376775	10376856	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10376857	10376949	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10376857	10376949	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10376950	10377055	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10377056	10377160	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10377056	10377160	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10377161	10377272	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10377273	10377344	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10377273	10377344	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10377345	10377477	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10377478	10377555	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10377478	10377555	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10377556	10377645	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10377646	10377815	1	-	2	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10377646	10377815	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10377816	10377902	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10377903	10378137	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10377903	10378137	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10378138	10378221	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10378222	10378464	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10378222	10378464	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10378465	10378558	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10378559	10378654	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10378559	10378654	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10378655	10378772	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10378773	10378910	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10378773	10378910	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10378911	10379005	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10379006	10379131	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10379006	10379131	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	intron	10379132	10379254	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	CDS	10379255	10379491	1	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	exon	10379255	10379491	.	-	.	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
Phchi.S3	AUGUSTUS	start_codon	10379489	10379491	.	-	0	transcript_id "Phchi.S3G135000.t1"; gene_id "Phchi.S3G135000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13860.t1 is derived from g12327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9290251	9292388	.	-	.	Phchi.S3G117900
Phchi.S3	AUGUSTUS	transcript	9290251	9292388	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	stop_codon	9290248	9290250	.	-	0	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9290251	9290399	0.83	-	2	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9290251	9290399	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9290400	9290499	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9290500	9290570	0.99	-	1	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9290500	9290570	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9290571	9290675	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9290676	9290792	0.99	-	1	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9290676	9290792	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9290793	9290901	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9290902	9291025	1	-	2	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9290902	9291025	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9291026	9291151	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9291152	9291224	1	-	0	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9291152	9291224	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9291225	9291429	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9291430	9291523	1	-	1	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9291430	9291523	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9291524	9291606	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9291607	9291698	1	-	0	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9291607	9291698	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9291699	9291779	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9291780	9291924	1	-	1	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9291780	9291924	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9291925	9291997	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9291998	9292092	1	-	0	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9291998	9292092	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	intron	9292093	9292181	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	CDS	9292182	9292388	0.99	-	0	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	exon	9292182	9292388	.	-	.	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
Phchi.S3	AUGUSTUS	start_codon	9292386	9292388	.	-	0	transcript_id "Phchi.S3G117900.t1"; gene_id "Phchi.S3G117900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9971.t1 is derived from g7147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44713721	44714968	.	-	.	Phchi.S1G713000
Phchi.S1	AUGUSTUS	transcript	44713721	44714968	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	stop_codon	44713718	44713720	.	-	0	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	CDS	44713721	44713721	0.46	-	1	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	exon	44713721	44713721	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	intron	44713722	44713816	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	CDS	44713817	44714061	0.42	-	0	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	exon	44713817	44714061	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	intron	44714062	44714242	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	CDS	44714243	44714380	0.62	-	0	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	exon	44714243	44714380	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	intron	44714381	44714609	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	CDS	44714610	44714746	0.49	-	2	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	exon	44714610	44714746	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	intron	44714747	44714931	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	CDS	44714932	44714968	0.66	-	0	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	exon	44714932	44714968	.	-	.	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
Phchi.S1	AUGUSTUS	start_codon	44714966	44714968	.	-	0	transcript_id "Phchi.S1G713000.t1"; gene_id "Phchi.S1G713000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12765.t1 is derived from g11230.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1948948	1950831	.	-	.	Phchi.S3G008400
Phchi.S3	AUGUSTUS	transcript	1948948	1949874	.	-	.	transcript_id "Phchi.S3G008400.t1"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	stop_codon	1948945	1948947	.	-	0	transcript_id "Phchi.S3G008400.t1"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	CDS	1948948	1949874	1	-	0	transcript_id "Phchi.S3G008400.t1"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	exon	1948948	1949874	.	-	.	transcript_id "Phchi.S3G008400.t1"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	start_codon	1949872	1949874	.	-	0	transcript_id "Phchi.S3G008400.t1"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	transcript	1948948	1950831	.	-	.	transcript_id "Phchi.S3G008400.t2"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	stop_codon	1948945	1948947	.	-	0	transcript_id "Phchi.S3G008400.t2"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	CDS	1948948	1950831	1	-	0	transcript_id "Phchi.S3G008400.t2"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	exon	1948948	1950831	.	-	.	transcript_id "Phchi.S3G008400.t2"; gene_id "Phchi.S3G008400"
Phchi.S3	AUGUSTUS	start_codon	1950829	1950831	.	-	0	transcript_id "Phchi.S3G008400.t2"; gene_id "Phchi.S3G008400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9111.t1 is derived from g6286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39879687	39881674	.	-	.	Phchi.S1G627000
Phchi.S1	AUGUSTUS	transcript	39879687	39881674	.	-	.	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	stop_codon	39879684	39879686	.	-	0	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	CDS	39879687	39879917	0.93	-	0	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	exon	39879687	39879917	.	-	.	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	intron	39879918	39880033	.	-	.	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	CDS	39880034	39881674	0.62	-	0	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	exon	39880034	39881674	.	-	.	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
Phchi.S1	AUGUSTUS	start_codon	39881672	39881674	.	-	0	transcript_id "Phchi.S1G627000.t1"; gene_id "Phchi.S1G627000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1468.t1 is derived from g8387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1082784	1083880	.	+	.	Phchi.S5G007700
Phchi.S5	AUGUSTUS	transcript	1082784	1083880	.	+	.	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	start_codon	1082784	1082786	.	+	0	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	CDS	1082784	1083287	0.68	+	0	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	exon	1082784	1083287	.	+	.	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	intron	1083288	1083376	.	+	.	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	CDS	1083377	1083880	1	+	0	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	exon	1083377	1083880	.	+	.	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
Phchi.S5	AUGUSTUS	stop_codon	1083881	1083883	.	+	0	transcript_id "Phchi.S5G007700.t1"; gene_id "Phchi.S5G007700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7793.t1 is derived from g4967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31202388	31202870	.	+	.	Phchi.S1G495200
Phchi.S1	AUGUSTUS	transcript	31202388	31202870	.	+	.	transcript_id "Phchi.S1G495200.t1"; gene_id "Phchi.S1G495200"
Phchi.S1	AUGUSTUS	start_codon	31202388	31202390	.	+	0	transcript_id "Phchi.S1G495200.t1"; gene_id "Phchi.S1G495200"
Phchi.S1	AUGUSTUS	CDS	31202388	31202870	0.61	+	0	transcript_id "Phchi.S1G495200.t1"; gene_id "Phchi.S1G495200"
Phchi.S1	AUGUSTUS	exon	31202388	31202870	.	+	.	transcript_id "Phchi.S1G495200.t1"; gene_id "Phchi.S1G495200"
Phchi.S1	AUGUSTUS	stop_codon	31202871	31202873	.	+	0	transcript_id "Phchi.S1G495200.t1"; gene_id "Phchi.S1G495200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9474.t1 is derived from g6650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41721386	41726035	.	-	.	Phchi.S1G663300
Phchi.S1	AUGUSTUS	transcript	41721386	41726035	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	stop_codon	41721383	41721385	.	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41721386	41722984	0.42	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41721386	41722984	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41722985	41723076	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41723077	41723614	0.74	-	1	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41723077	41723614	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41723615	41723746	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41723747	41724132	0.99	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41723747	41724132	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41724133	41724282	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41724283	41724461	0.66	-	2	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41724283	41724461	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41724462	41724536	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41724537	41725203	1	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41724537	41725203	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41725204	41725299	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41725300	41725563	0.91	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41725300	41725563	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41725564	41725667	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41725668	41725848	0.64	-	1	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41725668	41725848	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	intron	41725849	41726000	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	CDS	41726001	41726035	0.32	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	exon	41726001	41726035	.	-	.	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
Phchi.S1	AUGUSTUS	start_codon	41726033	41726035	.	-	0	transcript_id "Phchi.S1G663300.t1"; gene_id "Phchi.S1G663300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2380.t1 is derived from g9300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6425573	6426063	.	+	.	Phchi.S5G098900
Phchi.S5	AUGUSTUS	transcript	6425573	6426063	.	+	.	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	start_codon	6425573	6425575	.	+	0	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	CDS	6425573	6425828	1	+	0	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	exon	6425573	6425828	.	+	.	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	intron	6425829	6425902	.	+	.	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	CDS	6425903	6426063	0.53	+	2	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	exon	6425903	6426063	.	+	.	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
Phchi.S5	AUGUSTUS	stop_codon	6426064	6426066	.	+	0	transcript_id "Phchi.S5G098900.t1"; gene_id "Phchi.S5G098900"
# This transcript jg5635.t2 is derived from g2805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5636.t1 is derived from g2806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17986446	17987983	.	+	.	Phchi.S1G279500
Phchi.S1	AUGUSTUS	transcript	17986446	17987983	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	start_codon	17986446	17986448	.	+	0	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	CDS	17986446	17986467	0.73	+	0	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	exon	17986446	17986467	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	intron	17986468	17986619	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	CDS	17986620	17986929	1	+	2	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	exon	17986620	17986929	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	intron	17986930	17987024	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	CDS	17987025	17987417	0.99	+	1	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	exon	17987025	17987417	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	intron	17987418	17987540	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	CDS	17987541	17987618	1	+	1	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	exon	17987541	17987618	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	intron	17987619	17987706	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	CDS	17987707	17987983	1	+	1	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	exon	17987707	17987983	.	+	.	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
Phchi.S1	AUGUSTUS	stop_codon	17987984	17987986	.	+	0	transcript_id "Phchi.S1G279500.t1"; gene_id "Phchi.S1G279500"
# This transcript jg8498.t2 is derived from g5673.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8499.t1 is derived from g5674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36318862	36319788	.	-	.	Phchi.S1G565800
Phchi.S1	AUGUSTUS	transcript	36318862	36319788	.	-	.	transcript_id "Phchi.S1G565800.t1"; gene_id "Phchi.S1G565800"
Phchi.S1	AUGUSTUS	stop_codon	36318859	36318861	.	-	0	transcript_id "Phchi.S1G565800.t1"; gene_id "Phchi.S1G565800"
Phchi.S1	AUGUSTUS	CDS	36318862	36319788	0.95	-	0	transcript_id "Phchi.S1G565800.t1"; gene_id "Phchi.S1G565800"
Phchi.S1	AUGUSTUS	exon	36318862	36319788	.	-	.	transcript_id "Phchi.S1G565800.t1"; gene_id "Phchi.S1G565800"
Phchi.S1	AUGUSTUS	start_codon	36319786	36319788	.	-	0	transcript_id "Phchi.S1G565800.t1"; gene_id "Phchi.S1G565800"
# This transcript jg5247.t2 is derived from g2417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5248.t1 is derived from g2418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15853295	15855361	.	+	.	Phchi.S1G240700
Phchi.S1	AUGUSTUS	transcript	15853295	15855361	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	start_codon	15853295	15853297	.	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15853295	15853712	0.47	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15853295	15853712	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15853713	15853790	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15853791	15853936	1	+	2	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15853791	15853936	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15853937	15854033	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15854034	15854174	1	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15854034	15854174	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15854175	15854266	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15854267	15854380	1	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15854267	15854380	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15854381	15854503	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15854504	15854629	0.96	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15854504	15854629	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15854630	15854738	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15854739	15854837	1	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15854739	15854837	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15854838	15854917	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15854918	15855019	0.98	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15854918	15855019	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15855020	15855124	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15855125	15855205	0.98	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15855125	15855205	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	intron	15855206	15855280	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	CDS	15855281	15855361	0.92	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	exon	15855281	15855361	.	+	.	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
Phchi.S1	AUGUSTUS	stop_codon	15855362	15855364	.	+	0	transcript_id "Phchi.S1G240700.t1"; gene_id "Phchi.S1G240700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13045.t1 is derived from g11510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3865079	3865408	.	-	.	Phchi.S3G036400
Phchi.S3	AUGUSTUS	transcript	3865079	3865408	.	-	.	transcript_id "Phchi.S3G036400.t1"; gene_id "Phchi.S3G036400"
Phchi.S3	AUGUSTUS	stop_codon	3865076	3865078	.	-	0	transcript_id "Phchi.S3G036400.t1"; gene_id "Phchi.S3G036400"
Phchi.S3	AUGUSTUS	CDS	3865079	3865408	0.79	-	0	transcript_id "Phchi.S3G036400.t1"; gene_id "Phchi.S3G036400"
Phchi.S3	AUGUSTUS	exon	3865079	3865408	.	-	.	transcript_id "Phchi.S3G036400.t1"; gene_id "Phchi.S3G036400"
Phchi.S3	AUGUSTUS	start_codon	3865406	3865408	.	-	0	transcript_id "Phchi.S3G036400.t1"; gene_id "Phchi.S3G036400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2427.t1 is derived from g9347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6595701	6597302	.	-	.	Phchi.S5G103600
Phchi.S5	AUGUSTUS	transcript	6595701	6597302	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	stop_codon	6595698	6595700	.	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6595701	6595814	0.99	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6595701	6595814	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	intron	6595815	6595912	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6595913	6596035	1	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6595913	6596035	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	intron	6596036	6596124	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6596125	6596256	0.81	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6596125	6596256	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	intron	6596257	6596497	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6596498	6596578	0.99	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6596498	6596578	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	intron	6596579	6596678	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6596679	6596762	1	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6596679	6596762	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	intron	6596763	6596860	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6596861	6596972	1	-	1	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6596861	6596972	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	intron	6596973	6597138	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	CDS	6597139	6597302	1	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	exon	6597139	6597302	.	-	.	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
Phchi.S5	AUGUSTUS	start_codon	6597300	6597302	.	-	0	transcript_id "Phchi.S5G103600.t1"; gene_id "Phchi.S5G103600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3112.t1 is derived from g281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1777137	1777679	.	+	.	Phchi.S1G027100
Phchi.S1	AUGUSTUS	transcript	1777137	1777679	.	+	.	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	start_codon	1777137	1777139	.	+	0	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	CDS	1777137	1777349	0.98	+	0	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	exon	1777137	1777349	.	+	.	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	intron	1777350	1777637	.	+	.	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	CDS	1777638	1777679	1	+	0	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	exon	1777638	1777679	.	+	.	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
Phchi.S1	AUGUSTUS	stop_codon	1777680	1777682	.	+	0	transcript_id "Phchi.S1G027100.t1"; gene_id "Phchi.S1G027100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12602.t1 is derived from g8279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37412898	37417048	.	-	.	Phchi.S2G068200
Phchi.S2	AUGUSTUS	transcript	37412898	37417048	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	stop_codon	37412895	37412897	.	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37412898	37412999	0.98	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37412898	37412999	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37413000	37413115	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37413116	37413446	0.28	-	1	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37413116	37413446	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37413447	37413718	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37413719	37413750	0.77	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37413719	37413750	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37413751	37413943	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37413944	37414202	0.78	-	1	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37413944	37414202	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37414203	37414397	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37414398	37414863	1	-	2	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37414398	37414863	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37414864	37415002	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37415003	37415150	0.62	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37415003	37415150	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37415151	37415460	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37415461	37415490	0.53	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37415461	37415490	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37415491	37415579	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37415580	37415615	0.53	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37415580	37415615	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37415616	37415817	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37415818	37415951	1	-	2	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37415818	37415951	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37415952	37416064	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37416065	37416226	1	-	2	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37416065	37416226	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	intron	37416227	37416699	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	CDS	37416700	37417048	0.56	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	exon	37416700	37417048	.	-	.	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
Phchi.S2	AUGUSTUS	start_codon	37417046	37417048	.	-	0	transcript_id "Phchi.S2G068200.t1"; gene_id "Phchi.S2G068200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2377.t1 is derived from g9297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6411516	6414049	.	+	.	Phchi.S5G098600
Phchi.S5	AUGUSTUS	transcript	6411516	6414049	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	start_codon	6411516	6411518	.	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6411516	6411579	0.65	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6411516	6411579	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6411580	6411833	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6411834	6411869	0.98	+	2	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6411834	6411869	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6411870	6411959	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6411960	6412069	1	+	2	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6411960	6412069	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6412070	6412155	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6412156	6412278	1	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6412156	6412278	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6412279	6412425	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6412426	6412513	1	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6412426	6412513	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6412514	6412666	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6412667	6412741	1	+	2	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6412667	6412741	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6412742	6412861	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6412862	6412947	1	+	2	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6412862	6412947	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6412948	6413071	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6413072	6413212	1	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6413072	6413212	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6413213	6413320	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6413321	6413390	0.6	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6413321	6413390	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6413391	6413553	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6413554	6413881	1	+	2	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6413554	6413881	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	intron	6413882	6413973	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	CDS	6413974	6414049	1	+	1	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	exon	6413974	6414049	.	+	.	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
Phchi.S5	AUGUSTUS	stop_codon	6414050	6414052	.	+	0	transcript_id "Phchi.S5G098600.t1"; gene_id "Phchi.S5G098600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14399.t1 is derived from g12867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12626036	12627205	.	+	.	Phchi.S3G171800
Phchi.S3	AUGUSTUS	transcript	12626036	12627205	.	+	.	transcript_id "Phchi.S3G171800.t1"; gene_id "Phchi.S3G171800"
Phchi.S3	AUGUSTUS	start_codon	12626036	12626038	.	+	0	transcript_id "Phchi.S3G171800.t1"; gene_id "Phchi.S3G171800"
Phchi.S3	AUGUSTUS	CDS	12626036	12627205	0.73	+	0	transcript_id "Phchi.S3G171800.t1"; gene_id "Phchi.S3G171800"
Phchi.S3	AUGUSTUS	exon	12626036	12627205	.	+	.	transcript_id "Phchi.S3G171800.t1"; gene_id "Phchi.S3G171800"
Phchi.S3	AUGUSTUS	stop_codon	12627206	12627208	.	+	0	transcript_id "Phchi.S3G171800.t1"; gene_id "Phchi.S3G171800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10024.t1 is derived from g7200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45140279	45142164	.	-	.	Phchi.S1G718300
Phchi.S1	AUGUSTUS	transcript	45140279	45142164	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	stop_codon	45140276	45140278	.	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45140279	45140339	1	-	1	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45140279	45140339	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45140340	45140428	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45140429	45140544	1	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45140429	45140544	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45140545	45140627	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45140628	45140702	1	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45140628	45140702	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45140703	45140797	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45140798	45140920	1	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45140798	45140920	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45140921	45141003	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45141004	45141136	1	-	1	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45141004	45141136	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45141137	45141214	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45141215	45141345	1	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45141215	45141345	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45141346	45141425	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45141426	45141661	1	-	2	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45141426	45141661	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	intron	45141662	45141740	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	CDS	45141741	45142164	0.97	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	exon	45141741	45142164	.	-	.	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
Phchi.S1	AUGUSTUS	start_codon	45142162	45142164	.	-	0	transcript_id "Phchi.S1G718300.t1"; gene_id "Phchi.S1G718300"
# This transcript jg11841.t2 is derived from g15893.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11842.t1 is derived from g15894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8535690	8538536	.	+	.	Phchi.S4G142400
Phchi.S4	AUGUSTUS	transcript	8535690	8538536	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	start_codon	8535690	8535692	.	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8535690	8535716	0.9	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8535690	8535716	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8535717	8535901	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8535902	8535953	0.84	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8535902	8535953	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8535954	8536173	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8536174	8536844	0.87	+	2	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8536174	8536844	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8536845	8536946	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8536947	8537200	0.92	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8536947	8537200	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8537201	8537367	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8537368	8537514	0.74	+	1	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8537368	8537514	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8537515	8537614	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8537615	8537891	0.92	+	1	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8537615	8537891	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8537892	8538057	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8538058	8538162	1	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8538058	8538162	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	intron	8538163	8538524	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	CDS	8538525	8538536	0.97	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	exon	8538525	8538536	.	+	.	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
Phchi.S4	AUGUSTUS	stop_codon	8538537	8538539	.	+	0	transcript_id "Phchi.S4G142400.t1"; gene_id "Phchi.S4G142400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg497.t1 is derived from g10279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3448877	3450496	.	+	.	Phchi.S6G045600
Phchi.S6	AUGUSTUS	transcript	3448877	3450266	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	start_codon	3448877	3448879	.	+	0	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3448877	3448909	0.51	+	0	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3448877	3448909	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3448910	3449041	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3449042	3449303	0.51	+	0	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3449042	3449303	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3449304	3449546	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3449547	3449741	1	+	2	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3449547	3449741	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3449742	3449833	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3449834	3449963	1	+	2	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3449834	3449963	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3449964	3450241	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3450242	3450266	1	+	1	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3450242	3450266	.	+	.	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	stop_codon	3450267	3450269	.	+	0	transcript_id "Phchi.S6G045600.t1"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	transcript	3448877	3450496	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	start_codon	3448877	3448879	.	+	0	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3448877	3448909	0.42	+	0	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3448877	3448909	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3448910	3449041	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3449042	3449303	0.42	+	0	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3449042	3449303	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3449304	3449546	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3449547	3449741	1	+	2	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3449547	3449741	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3449742	3449833	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3449834	3449963	1	+	2	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3449834	3449963	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	intron	3449964	3450462	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	CDS	3450463	3450496	1	+	1	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	exon	3450463	3450496	.	+	.	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
Phchi.S6	AUGUSTUS	stop_codon	3450497	3450499	.	+	0	transcript_id "Phchi.S6G045600.t2"; gene_id "Phchi.S6G045600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg892.t1 is derived from g10674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6328501	6331159	.	-	.	Phchi.S6G085100
Phchi.S6	AUGUSTUS	transcript	6328501	6331159	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	stop_codon	6328498	6328500	.	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	CDS	6328501	6328529	0.89	-	2	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	exon	6328501	6328529	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	intron	6328530	6328617	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	CDS	6328618	6328843	0.41	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	exon	6328618	6328843	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	intron	6328844	6328926	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	CDS	6328927	6329904	0.98	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	exon	6328927	6329904	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	intron	6329905	6330032	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	CDS	6330033	6330068	1	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	exon	6330033	6330068	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	intron	6330069	6330223	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	CDS	6330224	6330283	1	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	exon	6330224	6330283	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	intron	6330284	6330382	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	CDS	6330383	6331159	0.57	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	exon	6330383	6331159	.	-	.	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
Phchi.S6	AUGUSTUS	start_codon	6331157	6331159	.	-	0	transcript_id "Phchi.S6G085100.t1"; gene_id "Phchi.S6G085100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg39.t1 is derived from g9799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C67	AUGUSTUS	gene	27040	28164	.	+	.	Phchi.C67G000500
Phchi.C67	AUGUSTUS	transcript	27040	28164	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	start_codon	27040	27042	.	+	0	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	27040	27042	1	+	0	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	27040	27042	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	intron	27043	27254	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	27255	27313	1	+	0	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	27255	27313	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	intron	27314	27416	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	27417	27476	0.93	+	1	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	27417	27476	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	intron	27477	27632	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	27633	27652	0.92	+	1	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	27633	27652	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	intron	27653	27745	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	27746	27814	0.92	+	2	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	27746	27814	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	intron	27815	27959	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	27960	27983	0.79	+	2	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	27960	27983	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	intron	27984	28105	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	CDS	28106	28164	0.79	+	2	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	exon	28106	28164	.	+	.	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
Phchi.C67	AUGUSTUS	stop_codon	28165	28167	.	+	0	transcript_id "Phchi.C67G000500.t1"; gene_id "Phchi.C67G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5943.t1 is derived from g3114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19961053	19962219	.	-	.	Phchi.S1G310200
Phchi.S1	AUGUSTUS	transcript	19961053	19962219	.	-	.	transcript_id "Phchi.S1G310200.t1"; gene_id "Phchi.S1G310200"
Phchi.S1	AUGUSTUS	stop_codon	19961050	19961052	.	-	0	transcript_id "Phchi.S1G310200.t1"; gene_id "Phchi.S1G310200"
Phchi.S1	AUGUSTUS	CDS	19961053	19962219	0.98	-	0	transcript_id "Phchi.S1G310200.t1"; gene_id "Phchi.S1G310200"
Phchi.S1	AUGUSTUS	exon	19961053	19962219	.	-	.	transcript_id "Phchi.S1G310200.t1"; gene_id "Phchi.S1G310200"
Phchi.S1	AUGUSTUS	start_codon	19962217	19962219	.	-	0	transcript_id "Phchi.S1G310200.t1"; gene_id "Phchi.S1G310200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15845.t1 is derived from g14315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21792538	21793215	.	+	.	Phchi.S3G316400
Phchi.S3	AUGUSTUS	transcript	21792538	21793215	.	+	.	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	start_codon	21792538	21792540	.	+	0	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	CDS	21792538	21792609	0.43	+	0	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	exon	21792538	21792609	.	+	.	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	intron	21792610	21792693	.	+	.	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	CDS	21792694	21792799	1	+	0	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	exon	21792694	21792799	.	+	.	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	intron	21792800	21792895	.	+	.	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	CDS	21792896	21793215	0.98	+	2	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	exon	21792896	21793215	.	+	.	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
Phchi.S3	AUGUSTUS	stop_codon	21793216	21793218	.	+	0	transcript_id "Phchi.S3G316400.t1"; gene_id "Phchi.S3G316400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1856.t1 is derived from g8776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3568639	3571207	.	+	.	Phchi.S5G046500
Phchi.S5	AUGUSTUS	transcript	3568639	3571207	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	start_codon	3568639	3568641	.	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3568639	3568777	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3568639	3568777	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3568778	3569052	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3569053	3569090	0.52	+	2	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3569053	3569090	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3569091	3569242	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3569243	3569326	0.98	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3569243	3569326	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3569327	3569419	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3569420	3569500	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3569420	3569500	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3569501	3569587	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3569588	3569668	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3569588	3569668	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3569669	3569841	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3569842	3569883	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3569842	3569883	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3569884	3570078	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3570079	3570258	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3570079	3570258	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3570259	3570349	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3570350	3570417	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3570350	3570417	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3570418	3570507	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3570508	3570559	1	+	1	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3570508	3570559	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3570560	3570664	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3570665	3570718	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3570665	3570718	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3570719	3570801	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3570802	3570894	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3570802	3570894	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3570895	3570967	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3570968	3571034	1	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3570968	3571034	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	intron	3571035	3571118	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	CDS	3571119	3571207	1	+	2	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	exon	3571119	3571207	.	+	.	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
Phchi.S5	AUGUSTUS	stop_codon	3571208	3571210	.	+	0	transcript_id "Phchi.S5G046500.t1"; gene_id "Phchi.S5G046500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1319.t1 is derived from g11102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9007641	9009361	.	-	.	Phchi.S6G127800
Phchi.S6	AUGUSTUS	transcript	9007641	9009361	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	stop_codon	9007638	9007640	.	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9007641	9007745	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9007641	9007745	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9007746	9007835	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9007836	9007901	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9007836	9007901	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9007902	9007982	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9007983	9008060	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9007983	9008060	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9008061	9008145	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9008146	9008192	1	-	2	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9008146	9008192	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9008193	9008283	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9008284	9008389	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9008284	9008389	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9008390	9008488	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9008489	9008566	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9008489	9008566	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9008567	9008654	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9008655	9008771	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9008655	9008771	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9008772	9008926	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9008927	9008992	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9008927	9008992	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9008993	9009089	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9009090	9009143	1	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9009090	9009143	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	intron	9009144	9009262	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	CDS	9009263	9009361	0.95	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	exon	9009263	9009361	.	-	.	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
Phchi.S6	AUGUSTUS	start_codon	9009359	9009361	.	-	0	transcript_id "Phchi.S6G127800.t1"; gene_id "Phchi.S6G127800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5961.t1 is derived from g3132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20093724	20097253	.	+	.	Phchi.S1G312000
Phchi.S1	AUGUSTUS	transcript	20093724	20097253	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	start_codon	20093724	20093726	.	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20093724	20094203	0.97	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20093724	20094203	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20094204	20094286	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20094287	20094334	0.98	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20094287	20094334	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20094335	20094438	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20094439	20094594	0.86	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20094439	20094594	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20094595	20094704	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20094705	20094751	1	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20094705	20094751	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20094752	20094851	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20094852	20095008	0.99	+	1	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20094852	20095008	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20095009	20095111	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20095112	20095173	1	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20095112	20095173	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20095174	20095261	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20095262	20095445	1	+	1	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20095262	20095445	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20095446	20095544	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20095545	20095634	1	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20095545	20095634	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20095635	20095748	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20095749	20095888	0.8	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20095749	20095888	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20095889	20095977	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20095978	20096107	0.81	+	1	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20095978	20096107	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	intron	20096108	20096218	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	CDS	20096219	20097253	0.73	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	exon	20096219	20097253	.	+	.	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
Phchi.S1	AUGUSTUS	stop_codon	20097254	20097256	.	+	0	transcript_id "Phchi.S1G312000.t1"; gene_id "Phchi.S1G312000"
# This transcript jg14039.t2 is derived from g12506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14040.t1 is derived from g12507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10418949	10420022	.	-	.	Phchi.S3G135900
Phchi.S3	AUGUSTUS	transcript	10418949	10420022	.	-	.	transcript_id "Phchi.S3G135900.t1"; gene_id "Phchi.S3G135900"
Phchi.S3	AUGUSTUS	stop_codon	10418946	10418948	.	-	0	transcript_id "Phchi.S3G135900.t1"; gene_id "Phchi.S3G135900"
Phchi.S3	AUGUSTUS	CDS	10418949	10420022	0.83	-	0	transcript_id "Phchi.S3G135900.t1"; gene_id "Phchi.S3G135900"
Phchi.S3	AUGUSTUS	exon	10418949	10420022	.	-	.	transcript_id "Phchi.S3G135900.t1"; gene_id "Phchi.S3G135900"
Phchi.S3	AUGUSTUS	start_codon	10420020	10420022	.	-	0	transcript_id "Phchi.S3G135900.t1"; gene_id "Phchi.S3G135900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13059.t1 is derived from g11524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3951741	3952717	.	+	.	Phchi.S3G037800
Phchi.S3	AUGUSTUS	transcript	3951741	3952717	.	+	.	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	start_codon	3951741	3951743	.	+	0	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	CDS	3951741	3952091	0.26	+	0	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	exon	3951741	3952091	.	+	.	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	intron	3952092	3952168	.	+	.	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	CDS	3952169	3952717	1	+	0	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	exon	3952169	3952717	.	+	.	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
Phchi.S3	AUGUSTUS	stop_codon	3952718	3952720	.	+	0	transcript_id "Phchi.S3G037800.t1"; gene_id "Phchi.S3G037800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1690.t1 is derived from g8609.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2512128	2514973	.	+	.	Phchi.S5G029900
Phchi.S5	AUGUSTUS	transcript	2512177	2514973	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	start_codon	2512177	2512179	.	+	0	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2512177	2512182	0.99	+	0	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2512177	2512182	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2512183	2512356	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2512357	2512740	1	+	0	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2512357	2512740	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2512741	2512827	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2512828	2513113	0.91	+	0	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2512828	2513113	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2513114	2513192	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2513193	2514160	0.88	+	2	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2513193	2514160	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2514161	2514415	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2514416	2514973	0.88	+	0	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2514416	2514973	.	+	.	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	stop_codon	2514974	2514976	.	+	0	transcript_id "Phchi.S5G029900.t1"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	transcript	2512128	2514973	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	start_codon	2512128	2512130	.	+	0	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2512128	2512182	0.77	+	0	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2512128	2512182	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2512183	2512348	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2512349	2512740	1	+	2	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2512349	2512740	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2512741	2512827	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2512828	2513113	0.86	+	0	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2512828	2513113	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2513114	2513192	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2513193	2514160	0.82	+	2	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2513193	2514160	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	intron	2514161	2514415	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	CDS	2514416	2514973	0.89	+	0	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	exon	2514416	2514973	.	+	.	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
Phchi.S5	AUGUSTUS	stop_codon	2514974	2514976	.	+	0	transcript_id "Phchi.S5G029900.t2"; gene_id "Phchi.S5G029900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5667.t1 is derived from g2837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18203588	18204171	.	-	.	Phchi.S1G282600
Phchi.S1	AUGUSTUS	transcript	18203588	18204171	.	-	.	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	stop_codon	18203585	18203587	.	-	0	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	CDS	18203588	18203747	1	-	1	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	exon	18203588	18203747	.	-	.	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	intron	18203748	18203844	.	-	.	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	CDS	18203845	18203890	1	-	2	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	exon	18203845	18203890	.	-	.	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	intron	18203891	18204035	.	-	.	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	CDS	18204036	18204171	0.93	-	0	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	exon	18204036	18204171	.	-	.	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
Phchi.S1	AUGUSTUS	start_codon	18204169	18204171	.	-	0	transcript_id "Phchi.S1G282600.t1"; gene_id "Phchi.S1G282600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14029.t1 is derived from g12496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10369997	10370494	.	+	.	Phchi.S3G134800
Phchi.S3	AUGUSTUS	transcript	10369997	10370494	.	+	.	transcript_id "Phchi.S3G134800.t1"; gene_id "Phchi.S3G134800"
Phchi.S3	AUGUSTUS	start_codon	10369997	10369999	.	+	0	transcript_id "Phchi.S3G134800.t1"; gene_id "Phchi.S3G134800"
Phchi.S3	AUGUSTUS	CDS	10369997	10370494	0.52	+	0	transcript_id "Phchi.S3G134800.t1"; gene_id "Phchi.S3G134800"
Phchi.S3	AUGUSTUS	exon	10369997	10370494	.	+	.	transcript_id "Phchi.S3G134800.t1"; gene_id "Phchi.S3G134800"
Phchi.S3	AUGUSTUS	stop_codon	10370495	10370497	.	+	0	transcript_id "Phchi.S3G134800.t1"; gene_id "Phchi.S3G134800"
# This transcript jg4711.t2 is derived from g1881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4712.t1 is derived from g1882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12430612	12431236	.	-	.	Phchi.S1G187100
Phchi.S1	AUGUSTUS	transcript	12430612	12431236	.	-	.	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	stop_codon	12430609	12430611	.	-	0	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	CDS	12430612	12430880	0.98	-	2	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	exon	12430612	12430880	.	-	.	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	intron	12430881	12431025	.	-	.	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	CDS	12431026	12431236	1	-	0	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	exon	12431026	12431236	.	-	.	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
Phchi.S1	AUGUSTUS	start_codon	12431234	12431236	.	-	0	transcript_id "Phchi.S1G187100.t1"; gene_id "Phchi.S1G187100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10759.t1 is derived from g14809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1985534	1986524	.	-	.	Phchi.S4G034100
Phchi.S4	AUGUSTUS	transcript	1985534	1986524	.	-	.	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	stop_codon	1985531	1985533	.	-	0	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	CDS	1985534	1985786	0.66	-	1	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	exon	1985534	1985786	.	-	.	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	intron	1985787	1986495	.	-	.	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	CDS	1986496	1986524	0.97	-	0	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	exon	1986496	1986524	.	-	.	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
Phchi.S4	AUGUSTUS	start_codon	1986522	1986524	.	-	0	transcript_id "Phchi.S4G034100.t1"; gene_id "Phchi.S4G034100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8329.t1 is derived from g5504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35336539	35338048	.	-	.	Phchi.S1G548800
Phchi.S1	AUGUSTUS	transcript	35336539	35338048	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	stop_codon	35336536	35336538	.	-	0	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	CDS	35336539	35337030	0.91	-	0	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	exon	35336539	35337030	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	intron	35337031	35337124	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	CDS	35337125	35337345	1	-	2	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	exon	35337125	35337345	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	intron	35337346	35337414	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	CDS	35337415	35337712	0.99	-	0	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	exon	35337415	35337712	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	intron	35337713	35337802	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	CDS	35337803	35338048	1	-	0	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	exon	35337803	35338048	.	-	.	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
Phchi.S1	AUGUSTUS	start_codon	35338046	35338048	.	-	0	transcript_id "Phchi.S1G548800.t1"; gene_id "Phchi.S1G548800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1020.t1 is derived from g10803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7146309	7147815	.	-	.	Phchi.S6G097900
Phchi.S6	AUGUSTUS	transcript	7146309	7147815	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	stop_codon	7146306	7146308	.	-	0	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	CDS	7146309	7146497	0.08	-	0	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	exon	7146309	7146497	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	intron	7146498	7146585	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	CDS	7146586	7146720	1	-	0	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	exon	7146586	7146720	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	intron	7146721	7146844	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	CDS	7146845	7147027	0.68	-	0	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	exon	7146845	7147027	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	intron	7147028	7147119	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	CDS	7147120	7147310	0.79	-	2	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	exon	7147120	7147310	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	intron	7147311	7147466	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	CDS	7147467	7147815	0.51	-	0	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	exon	7147467	7147815	.	-	.	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
Phchi.S6	AUGUSTUS	start_codon	7147813	7147815	.	-	0	transcript_id "Phchi.S6G097900.t1"; gene_id "Phchi.S6G097900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1870.t1 is derived from g8790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3630517	3632155	.	+	.	Phchi.S5G047900
Phchi.S5	AUGUSTUS	transcript	3630517	3632155	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	start_codon	3630517	3630519	.	+	0	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	CDS	3630517	3630787	1	+	0	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	exon	3630517	3630787	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	intron	3630788	3630878	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	CDS	3630879	3631102	0.98	+	2	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	exon	3630879	3631102	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	intron	3631103	3631178	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	CDS	3631179	3631707	0.55	+	0	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	exon	3631179	3631707	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	intron	3631708	3631802	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	CDS	3631803	3632155	1	+	2	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	exon	3631803	3632155	.	+	.	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
Phchi.S5	AUGUSTUS	stop_codon	3632156	3632158	.	+	0	transcript_id "Phchi.S5G047900.t1"; gene_id "Phchi.S5G047900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6530.t1 is derived from g3702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23509271	23511267	.	+	.	Phchi.S1G368900
Phchi.S1	AUGUSTUS	transcript	23509271	23511267	.	+	.	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	start_codon	23509271	23509273	.	+	0	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	CDS	23509271	23511141	0.78	+	0	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	exon	23509271	23511141	.	+	.	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	intron	23511142	23511233	.	+	.	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	CDS	23511234	23511267	0.76	+	1	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	exon	23511234	23511267	.	+	.	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
Phchi.S1	AUGUSTUS	stop_codon	23511268	23511270	.	+	0	transcript_id "Phchi.S1G368900.t1"; gene_id "Phchi.S1G368900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg779.t1 is derived from g10561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5467225	5469262	.	-	.	Phchi.S6G073800
Phchi.S6	AUGUSTUS	transcript	5467225	5469262	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	stop_codon	5467222	5467224	.	-	0	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	CDS	5467225	5467231	0.39	-	1	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	exon	5467225	5467231	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	intron	5467232	5467299	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	CDS	5467300	5467846	0.39	-	2	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	exon	5467300	5467846	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	intron	5467847	5467971	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	CDS	5467972	5468954	0.98	-	1	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	exon	5467972	5468954	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	intron	5468955	5469128	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	CDS	5469129	5469262	1	-	0	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	exon	5469129	5469262	.	-	.	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
Phchi.S6	AUGUSTUS	start_codon	5469260	5469262	.	-	0	transcript_id "Phchi.S6G073800.t1"; gene_id "Phchi.S6G073800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5483.t1 is derived from g2653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17065440	17066686	.	-	.	Phchi.S1G264200
Phchi.S1	AUGUSTUS	transcript	17065440	17066686	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	stop_codon	17065437	17065439	.	-	0	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	CDS	17065440	17065469	0.72	-	0	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	exon	17065440	17065469	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	intron	17065470	17065628	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	CDS	17065629	17065643	0.79	-	0	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	exon	17065629	17065643	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	intron	17065644	17065734	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	CDS	17065735	17065821	0.78	-	0	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	exon	17065735	17065821	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	intron	17065822	17065992	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	CDS	17065993	17066008	0.73	-	1	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	exon	17065993	17066008	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	intron	17066009	17066151	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	CDS	17066152	17066224	0.73	-	2	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	exon	17066152	17066224	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	intron	17066225	17066376	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	CDS	17066377	17066686	0.49	-	0	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	exon	17066377	17066686	.	-	.	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
Phchi.S1	AUGUSTUS	start_codon	17066684	17066686	.	-	0	transcript_id "Phchi.S1G264200.t1"; gene_id "Phchi.S1G264200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9078.t1 is derived from g6253.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39739175	39742751	.	+	.	Phchi.S1G623700
Phchi.S1	AUGUSTUS	transcript	39739175	39742751	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	start_codon	39739175	39739177	.	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39739175	39739400	0.29	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39739175	39739400	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39739401	39739771	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39739772	39740229	1	+	2	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39739772	39740229	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39740230	39740336	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39740337	39740558	1	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39740337	39740558	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39740559	39740691	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39740692	39740886	1	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39740692	39740886	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39740887	39741044	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39741045	39741119	1	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39741045	39741119	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39741120	39741336	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39741337	39741406	1	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39741337	39741406	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39741407	39741564	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39741565	39742751	0.38	+	2	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39741565	39742751	.	+	.	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	stop_codon	39742752	39742754	.	+	0	transcript_id "Phchi.S1G623700.t1"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	transcript	39739175	39742751	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	start_codon	39739175	39739177	.	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39739175	39739400	0.29	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39739175	39739400	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39739401	39739771	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39739772	39740229	1	+	2	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39739772	39740229	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39740230	39740336	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39740337	39740558	1	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39740337	39740558	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39740559	39740691	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39740692	39740886	1	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39740692	39740886	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39740887	39741044	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39741045	39741119	1	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39741045	39741119	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39741120	39741336	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39741337	39741406	1	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39741337	39741406	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	intron	39741407	39741558	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	CDS	39741559	39742751	0.38	+	2	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	exon	39741559	39742751	.	+	.	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
Phchi.S1	AUGUSTUS	stop_codon	39742752	39742754	.	+	0	transcript_id "Phchi.S1G623700.t2"; gene_id "Phchi.S1G623700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg666.t1 is derived from g10448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4642123	4643399	.	-	.	Phchi.S6G062500
Phchi.S6	AUGUSTUS	transcript	4642123	4643399	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	stop_codon	4642120	4642122	.	-	0	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	CDS	4642123	4642328	0.76	-	2	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	exon	4642123	4642328	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	intron	4642329	4642438	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	CDS	4642439	4643010	0.33	-	1	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	exon	4642439	4643010	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	intron	4643011	4643164	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	CDS	4643165	4643260	0.45	-	1	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	exon	4643165	4643260	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	intron	4643261	4643334	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	CDS	4643335	4643399	0.37	-	0	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	exon	4643335	4643399	.	-	.	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
Phchi.S6	AUGUSTUS	start_codon	4643397	4643399	.	-	0	transcript_id "Phchi.S6G062500.t1"; gene_id "Phchi.S6G062500"
# This transcript jg14971.t2 is derived from g13439.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14972.t1 is derived from g13440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15799185	15803999	.	-	.	Phchi.S3G229100
Phchi.S3	AUGUSTUS	transcript	15799185	15803999	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	stop_codon	15799182	15799184	.	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15799185	15799268	0.79	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15799185	15799268	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15799269	15799374	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15799375	15799534	0.89	-	1	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15799375	15799534	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15799535	15799677	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15799678	15799829	1	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15799678	15799829	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15799830	15799924	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15799925	15800102	1	-	1	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15799925	15800102	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15800103	15800202	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15800203	15800432	0.98	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15800203	15800432	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15800433	15800537	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15800538	15801963	0.82	-	1	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15800538	15801963	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15801964	15802057	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15802058	15802194	1	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15802058	15802194	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15802195	15802338	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15802339	15802448	0.92	-	2	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15802339	15802448	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15802449	15802706	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15802707	15803082	0.92	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15802707	15803082	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	intron	15803083	15803369	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	CDS	15803370	15803999	0.95	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	exon	15803370	15803999	.	-	.	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
Phchi.S3	AUGUSTUS	start_codon	15803997	15803999	.	-	0	transcript_id "Phchi.S3G229100.t1"; gene_id "Phchi.S3G229100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13846.t1 is derived from g12313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9208744	9209091	.	-	.	Phchi.S3G116500
Phchi.S3	AUGUSTUS	transcript	9208744	9209091	.	-	.	transcript_id "Phchi.S3G116500.t1"; gene_id "Phchi.S3G116500"
Phchi.S3	AUGUSTUS	stop_codon	9208741	9208743	.	-	0	transcript_id "Phchi.S3G116500.t1"; gene_id "Phchi.S3G116500"
Phchi.S3	AUGUSTUS	CDS	9208744	9209091	0.66	-	0	transcript_id "Phchi.S3G116500.t1"; gene_id "Phchi.S3G116500"
Phchi.S3	AUGUSTUS	exon	9208744	9209091	.	-	.	transcript_id "Phchi.S3G116500.t1"; gene_id "Phchi.S3G116500"
Phchi.S3	AUGUSTUS	start_codon	9209089	9209091	.	-	0	transcript_id "Phchi.S3G116500.t1"; gene_id "Phchi.S3G116500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4509.t1 is derived from g1679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10884566	10887341	.	+	.	Phchi.S1G166800
Phchi.S1	AUGUSTUS	transcript	10884566	10887341	.	+	.	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	start_codon	10884566	10884568	.	+	0	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	CDS	10884566	10886306	0.86	+	0	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	exon	10884566	10886306	.	+	.	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	intron	10886307	10886400	.	+	.	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	CDS	10886401	10886520	1	+	2	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	exon	10886401	10886520	.	+	.	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	intron	10886521	10886598	.	+	.	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	CDS	10886599	10887341	0.84	+	2	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	exon	10886599	10887341	.	+	.	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
Phchi.S1	AUGUSTUS	stop_codon	10887342	10887344	.	+	0	transcript_id "Phchi.S1G166800.t1"; gene_id "Phchi.S1G166800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2225.t1 is derived from g9145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5531722	5533492	.	+	.	Phchi.S5G083400
Phchi.S5	AUGUSTUS	transcript	5531722	5533492	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	start_codon	5531722	5531724	.	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5531722	5532126	1	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5531722	5532126	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	intron	5532127	5532209	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5532210	5532391	0.99	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5532210	5532391	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	intron	5532392	5532485	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5532486	5532576	1	+	1	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5532486	5532576	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	intron	5532577	5532655	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5532656	5532813	1	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5532656	5532813	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	intron	5532814	5532893	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5532894	5533065	1	+	1	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5532894	5533065	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	intron	5533066	5533173	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5533174	5533284	0.99	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5533174	5533284	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	intron	5533285	5533411	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	CDS	5533412	5533492	0.97	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	exon	5533412	5533492	.	+	.	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
Phchi.S5	AUGUSTUS	stop_codon	5533493	5533495	.	+	0	transcript_id "Phchi.S5G083400.t1"; gene_id "Phchi.S5G083400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9496.t1 is derived from g6672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42047002	42048977	.	+	.	Phchi.S1G665500
Phchi.S1	AUGUSTUS	transcript	42047002	42048977	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	start_codon	42047002	42047004	.	+	0	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	CDS	42047002	42047593	0.63	+	0	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	exon	42047002	42047593	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	intron	42047594	42047727	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	CDS	42047728	42048092	0.53	+	2	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	exon	42047728	42048092	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	intron	42048093	42048176	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	CDS	42048177	42048439	0.84	+	0	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	exon	42048177	42048439	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	intron	42048440	42048523	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	CDS	42048524	42048658	0.99	+	1	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	exon	42048524	42048658	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	intron	42048659	42048814	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	CDS	42048815	42048977	0.37	+	1	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	exon	42048815	42048977	.	+	.	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
Phchi.S1	AUGUSTUS	stop_codon	42048978	42048980	.	+	0	transcript_id "Phchi.S1G665500.t1"; gene_id "Phchi.S1G665500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4427.t1 is derived from g1596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10442145	10444246	.	-	.	Phchi.S1G158600
Phchi.S1	AUGUSTUS	transcript	10442145	10444246	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	stop_codon	10442142	10442144	.	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10442145	10442390	0.75	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10442145	10442390	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10442391	10442472	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10442473	10442598	1	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10442473	10442598	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10442599	10442698	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10442699	10442751	1	-	2	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10442699	10442751	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10442752	10442840	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10442841	10442932	1	-	1	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10442841	10442932	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10442933	10443021	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10443022	10443074	1	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10443022	10443074	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10443075	10443227	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10443228	10443300	1	-	1	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10443228	10443300	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10443301	10443411	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10443412	10443579	1	-	1	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10443412	10443579	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10443580	10443716	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10443717	10443811	1	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10443717	10443811	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10443812	10443900	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10443901	10443994	1	-	1	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10443901	10443994	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	intron	10443995	10444094	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	CDS	10444095	10444246	0.94	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	exon	10444095	10444246	.	-	.	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
Phchi.S1	AUGUSTUS	start_codon	10444244	10444246	.	-	0	transcript_id "Phchi.S1G158600.t1"; gene_id "Phchi.S1G158600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3523.t1 is derived from g692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4204704	4205818	.	-	.	Phchi.S1G068200
Phchi.S1	AUGUSTUS	transcript	4204704	4205818	.	-	.	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	stop_codon	4204701	4204703	.	-	0	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	CDS	4204704	4204825	0.47	-	2	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	exon	4204704	4204825	.	-	.	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	intron	4204826	4204979	.	-	.	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	CDS	4204980	4205559	0.54	-	0	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	exon	4204980	4205559	.	-	.	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	intron	4205560	4205653	.	-	.	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	CDS	4205654	4205818	0.91	-	0	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	exon	4205654	4205818	.	-	.	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
Phchi.S1	AUGUSTUS	start_codon	4205816	4205818	.	-	0	transcript_id "Phchi.S1G068200.t1"; gene_id "Phchi.S1G068200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9641.t1 is derived from g6817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43032316	43032702	.	+	.	Phchi.S1G680000
Phchi.S1	AUGUSTUS	transcript	43032316	43032702	.	+	.	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	start_codon	43032316	43032318	.	+	0	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	CDS	43032316	43032348	0.79	+	0	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	exon	43032316	43032348	.	+	.	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	intron	43032349	43032435	.	+	.	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	CDS	43032436	43032611	0.78	+	0	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	exon	43032436	43032611	.	+	.	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	intron	43032612	43032698	.	+	.	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	CDS	43032699	43032702	0.78	+	1	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	exon	43032699	43032702	.	+	.	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
Phchi.S1	AUGUSTUS	stop_codon	43032703	43032705	.	+	0	transcript_id "Phchi.S1G680000.t1"; gene_id "Phchi.S1G680000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2231.t1 is derived from g9151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5563663	5564846	.	+	.	Phchi.S5G084000
Phchi.S5	AUGUSTUS	transcript	5563663	5564846	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	start_codon	5563663	5563665	.	+	0	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	CDS	5563663	5563815	0.84	+	0	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	exon	5563663	5563815	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	intron	5563816	5563927	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	CDS	5563928	5563961	0.96	+	0	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	exon	5563928	5563961	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	intron	5563962	5564114	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	CDS	5564115	5564124	1	+	2	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	exon	5564115	5564124	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	intron	5564125	5564224	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	CDS	5564225	5564846	0.99	+	1	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	exon	5564225	5564846	.	+	.	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
Phchi.S5	AUGUSTUS	stop_codon	5564847	5564849	.	+	0	transcript_id "Phchi.S5G084000.t1"; gene_id "Phchi.S5G084000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13316.t1 is derived from g11782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5963352	5966166	.	+	.	Phchi.S3G063500
Phchi.S3	AUGUSTUS	transcript	5963352	5966166	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	start_codon	5963352	5963354	.	+	0	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5963352	5964331	0.47	+	0	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5963352	5964331	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	intron	5964332	5964416	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5964417	5964520	0.93	+	1	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5964417	5964520	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	intron	5964521	5964612	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5964613	5964961	1	+	2	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5964613	5964961	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	intron	5964962	5965090	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5965091	5965189	1	+	1	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5965091	5965189	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	intron	5965190	5965277	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5965278	5965505	1	+	1	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5965278	5965505	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	intron	5965506	5965595	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5965596	5965734	1	+	1	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5965596	5965734	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	intron	5965735	5965824	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	CDS	5965825	5966166	0.82	+	0	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	exon	5965825	5966166	.	+	.	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
Phchi.S3	AUGUSTUS	stop_codon	5966167	5966169	.	+	0	transcript_id "Phchi.S3G063500.t1"; gene_id "Phchi.S3G063500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1272.t1 is derived from g11055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8768549	8770657	.	-	.	Phchi.S6G123100
Phchi.S6	AUGUSTUS	transcript	8768549	8770657	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	stop_codon	8768546	8768548	.	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8768549	8768618	0.87	-	1	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8768549	8768618	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	intron	8768619	8768710	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8768711	8768835	0.86	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8768711	8768835	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	intron	8768836	8768916	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8768917	8768970	0.38	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8768917	8768970	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	intron	8768971	8769058	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8769059	8769199	0.14	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8769059	8769199	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	intron	8769200	8769681	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8769682	8769786	0.28	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8769682	8769786	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	intron	8769787	8769906	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8769907	8770113	0.65	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8769907	8770113	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	intron	8770114	8770192	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	CDS	8770193	8770657	0.45	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	exon	8770193	8770657	.	-	.	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
Phchi.S6	AUGUSTUS	start_codon	8770655	8770657	.	-	0	transcript_id "Phchi.S6G123100.t1"; gene_id "Phchi.S6G123100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2387.t1 is derived from g9307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6454560	6456195	.	-	.	Phchi.S5G099600
Phchi.S5	AUGUSTUS	transcript	6454560	6456195	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	stop_codon	6454557	6454559	.	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	CDS	6454560	6454673	1	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	exon	6454560	6454673	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	intron	6454674	6454765	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	CDS	6454766	6454855	1	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	exon	6454766	6454855	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	intron	6454856	6454938	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	CDS	6454939	6455058	1	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	exon	6454939	6455058	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	intron	6455059	6455237	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	CDS	6455238	6455342	1	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	exon	6455238	6455342	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	intron	6455343	6455515	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	CDS	6455516	6455584	1	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	exon	6455516	6455584	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	intron	6455585	6455664	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	CDS	6455665	6456195	0.98	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	exon	6455665	6456195	.	-	.	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
Phchi.S5	AUGUSTUS	start_codon	6456193	6456195	.	-	0	transcript_id "Phchi.S5G099600.t1"; gene_id "Phchi.S5G099600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11646.t1 is derived from g15697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7445950	7447505	.	+	.	Phchi.S4G122800
Phchi.S4	AUGUSTUS	transcript	7445950	7447505	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	start_codon	7445950	7445952	.	+	0	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7445950	7446005	1	+	0	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7445950	7446005	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	intron	7446006	7446138	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7446139	7446216	0.99	+	1	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7446139	7446216	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	intron	7446217	7446318	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7446319	7446367	0.84	+	1	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7446319	7446367	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	intron	7446368	7446485	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7446486	7446570	0.53	+	0	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7446486	7446570	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	intron	7446571	7446694	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7446695	7446747	1	+	2	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7446695	7446747	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	intron	7446748	7446825	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7446826	7446888	0.98	+	0	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7446826	7446888	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	intron	7446889	7447001	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	CDS	7447002	7447505	0.85	+	0	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	exon	7447002	7447505	.	+	.	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
Phchi.S4	AUGUSTUS	stop_codon	7447506	7447508	.	+	0	transcript_id "Phchi.S4G122800.t1"; gene_id "Phchi.S4G122800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8164.t1 is derived from g5339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34244084	34244344	.	-	.	Phchi.S1G532300
Phchi.S1	AUGUSTUS	transcript	34244084	34244344	.	-	.	transcript_id "Phchi.S1G532300.t1"; gene_id "Phchi.S1G532300"
Phchi.S1	AUGUSTUS	stop_codon	34244081	34244083	.	-	0	transcript_id "Phchi.S1G532300.t1"; gene_id "Phchi.S1G532300"
Phchi.S1	AUGUSTUS	CDS	34244084	34244344	0.49	-	0	transcript_id "Phchi.S1G532300.t1"; gene_id "Phchi.S1G532300"
Phchi.S1	AUGUSTUS	exon	34244084	34244344	.	-	.	transcript_id "Phchi.S1G532300.t1"; gene_id "Phchi.S1G532300"
Phchi.S1	AUGUSTUS	start_codon	34244342	34244344	.	-	0	transcript_id "Phchi.S1G532300.t1"; gene_id "Phchi.S1G532300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2275.t1 is derived from g9195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5826622	5828296	.	-	.	Phchi.S5G088400
Phchi.S5	AUGUSTUS	transcript	5826622	5828296	.	-	.	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	stop_codon	5826619	5826621	.	-	0	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	CDS	5826622	5828148	0.82	-	0	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	exon	5826622	5828148	.	-	.	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	intron	5828149	5828251	.	-	.	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	CDS	5828252	5828296	0.89	-	0	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	exon	5828252	5828296	.	-	.	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
Phchi.S5	AUGUSTUS	start_codon	5828294	5828296	.	-	0	transcript_id "Phchi.S5G088400.t1"; gene_id "Phchi.S5G088400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9638.t1 is derived from g6814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43017736	43019106	.	-	.	Phchi.S1G679700
Phchi.S1	AUGUSTUS	transcript	43017736	43019106	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	stop_codon	43017733	43017735	.	-	0	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	CDS	43017736	43018529	1	-	2	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	exon	43017736	43018529	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	intron	43018530	43018662	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	CDS	43018663	43018757	1	-	1	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	exon	43018663	43018757	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	intron	43018758	43018899	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	CDS	43018900	43018972	1	-	2	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	exon	43018900	43018972	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	intron	43018973	43019057	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	CDS	43019058	43019106	1	-	0	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	exon	43019058	43019106	.	-	.	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
Phchi.S1	AUGUSTUS	start_codon	43019104	43019106	.	-	0	transcript_id "Phchi.S1G679700.t1"; gene_id "Phchi.S1G679700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12314.t1 is derived from g7990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10417897	10419047	.	+	.	Phchi.S2G039400
Phchi.S2	AUGUSTUS	transcript	10417897	10419047	.	+	.	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	start_codon	10417897	10417899	.	+	0	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	CDS	10417897	10418531	0.68	+	0	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	exon	10417897	10418531	.	+	.	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	intron	10418532	10418725	.	+	.	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	CDS	10418726	10419047	0.71	+	1	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	exon	10418726	10419047	.	+	.	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
Phchi.S2	AUGUSTUS	stop_codon	10419048	10419050	.	+	0	transcript_id "Phchi.S2G039400.t1"; gene_id "Phchi.S2G039400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10583.t1 is derived from g14633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1059820	1060164	.	+	.	Phchi.S4G016500
Phchi.S4	AUGUSTUS	transcript	1059820	1060164	.	+	.	transcript_id "Phchi.S4G016500.t1"; gene_id "Phchi.S4G016500"
Phchi.S4	AUGUSTUS	start_codon	1059820	1059822	.	+	0	transcript_id "Phchi.S4G016500.t1"; gene_id "Phchi.S4G016500"
Phchi.S4	AUGUSTUS	CDS	1059820	1060164	0.92	+	0	transcript_id "Phchi.S4G016500.t1"; gene_id "Phchi.S4G016500"
Phchi.S4	AUGUSTUS	exon	1059820	1060164	.	+	.	transcript_id "Phchi.S4G016500.t1"; gene_id "Phchi.S4G016500"
Phchi.S4	AUGUSTUS	stop_codon	1060165	1060167	.	+	0	transcript_id "Phchi.S4G016500.t1"; gene_id "Phchi.S4G016500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg755.t1 is derived from g10537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5351332	5353151	.	+	.	Phchi.S6G071400
Phchi.S6	AUGUSTUS	transcript	5351332	5353151	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	start_codon	5351332	5351334	.	+	0	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	CDS	5351332	5351628	0.98	+	0	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	exon	5351332	5351628	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	intron	5351629	5351722	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	CDS	5351723	5351868	1	+	0	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	exon	5351723	5351868	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	intron	5351869	5351954	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	CDS	5351955	5352231	1	+	1	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	exon	5351955	5352231	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	intron	5352232	5352313	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	CDS	5352314	5352586	1	+	0	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	exon	5352314	5352586	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	intron	5352587	5352671	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	CDS	5352672	5353151	0.99	+	0	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	exon	5352672	5353151	.	+	.	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
Phchi.S6	AUGUSTUS	stop_codon	5353152	5353154	.	+	0	transcript_id "Phchi.S6G071400.t1"; gene_id "Phchi.S6G071400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7839.t1 is derived from g5013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31470550	31472166	.	-	.	Phchi.S1G499800
Phchi.S1	AUGUSTUS	transcript	31470550	31472166	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	stop_codon	31470547	31470549	.	-	0	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	CDS	31470550	31470810	1	-	0	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	exon	31470550	31470810	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	intron	31470811	31470903	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	CDS	31470904	31471038	1	-	0	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	exon	31470904	31471038	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	intron	31471039	31471112	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	CDS	31471113	31471233	1	-	1	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	exon	31471113	31471233	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	intron	31471234	31471320	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	CDS	31471321	31471461	1	-	1	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	exon	31471321	31471461	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	intron	31471462	31471533	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	CDS	31471534	31471711	1	-	2	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	exon	31471534	31471711	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	intron	31471712	31471796	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	CDS	31471797	31472166	0.96	-	0	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	exon	31471797	31472166	.	-	.	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
Phchi.S1	AUGUSTUS	start_codon	31472164	31472166	.	-	0	transcript_id "Phchi.S1G499800.t1"; gene_id "Phchi.S1G499800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7143.t1 is derived from g4315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27154851	27155443	.	-	.	Phchi.S1G430200
Phchi.S1	AUGUSTUS	transcript	27154851	27155443	.	-	.	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	stop_codon	27154848	27154850	.	-	0	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	CDS	27154851	27154933	1	-	2	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	exon	27154851	27154933	.	-	.	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	intron	27154934	27155157	.	-	.	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	CDS	27155158	27155443	1	-	0	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	exon	27155158	27155443	.	-	.	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
Phchi.S1	AUGUSTUS	start_codon	27155441	27155443	.	-	0	transcript_id "Phchi.S1G430200.t1"; gene_id "Phchi.S1G430200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1548.t1 is derived from g8467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1700950	1703784	.	+	.	Phchi.S5G015700
Phchi.S5	AUGUSTUS	transcript	1701811	1703784	.	+	.	transcript_id "Phchi.S5G015700.t1"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	start_codon	1701811	1701813	.	+	0	transcript_id "Phchi.S5G015700.t1"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	CDS	1701811	1703784	0.97	+	0	transcript_id "Phchi.S5G015700.t1"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	exon	1701811	1703784	.	+	.	transcript_id "Phchi.S5G015700.t1"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	stop_codon	1703785	1703787	.	+	0	transcript_id "Phchi.S5G015700.t1"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	transcript	1700950	1703784	.	+	.	transcript_id "Phchi.S5G015700.t2"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	start_codon	1700950	1700952	.	+	0	transcript_id "Phchi.S5G015700.t2"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	CDS	1700950	1703784	0.73	+	0	transcript_id "Phchi.S5G015700.t2"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	exon	1700950	1703784	.	+	.	transcript_id "Phchi.S5G015700.t2"; gene_id "Phchi.S5G015700"
Phchi.S5	AUGUSTUS	stop_codon	1703785	1703787	.	+	0	transcript_id "Phchi.S5G015700.t2"; gene_id "Phchi.S5G015700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3030.t1 is derived from g199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1238452	1242180	.	-	.	Phchi.S1G018900
Phchi.S1	AUGUSTUS	transcript	1238452	1242180	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	stop_codon	1238449	1238451	.	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	CDS	1238452	1238679	0.84	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	exon	1238452	1238679	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	intron	1238680	1238776	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	CDS	1238777	1239778	0.95	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	exon	1238777	1239778	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	intron	1239779	1239888	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	CDS	1239889	1240041	1	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	exon	1239889	1240041	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	intron	1240042	1240153	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	CDS	1240154	1240252	0.95	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	exon	1240154	1240252	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	intron	1240253	1240332	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	CDS	1240333	1242180	0.65	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	exon	1240333	1242180	.	-	.	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
Phchi.S1	AUGUSTUS	start_codon	1242178	1242180	.	-	0	transcript_id "Phchi.S1G018900.t1"; gene_id "Phchi.S1G018900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12747.t1 is derived from g11212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1768590	1769831	.	+	.	Phchi.S3G006600
Phchi.S3	AUGUSTUS	transcript	1768590	1769583	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	start_codon	1768590	1768592	.	+	0	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1768590	1768650	0.68	+	0	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1768590	1768650	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1768651	1768737	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1768738	1768810	0.73	+	2	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1768738	1768810	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1768811	1769031	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769032	1769091	1	+	1	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769032	1769091	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1769092	1769317	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769318	1769455	1	+	1	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769318	1769455	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1769456	1769540	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769541	1769583	0.99	+	1	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769541	1769583	.	+	.	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	stop_codon	1769584	1769586	.	+	0	transcript_id "Phchi.S3G006600.t1"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	transcript	1768590	1769831	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	start_codon	1768590	1768592	.	+	0	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1768590	1768650	0.59	+	0	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1768590	1768650	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1768651	1768737	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1768738	1768810	0.68	+	2	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1768738	1768810	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1768811	1769031	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769032	1769091	0.99	+	1	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769032	1769091	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1769092	1769322	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769323	1769455	0.99	+	1	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769323	1769455	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1769456	1769540	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769541	1769672	0.98	+	0	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769541	1769672	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	intron	1769673	1769756	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	CDS	1769757	1769831	1	+	0	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	exon	1769757	1769831	.	+	.	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
Phchi.S3	AUGUSTUS	stop_codon	1769832	1769834	.	+	0	transcript_id "Phchi.S3G006600.t2"; gene_id "Phchi.S3G006600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6881.t1 is derived from g4053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25806256	25807229	.	-	.	Phchi.S1G404000
Phchi.S1	AUGUSTUS	transcript	25806256	25807229	.	-	.	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	stop_codon	25806253	25806255	.	-	0	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	CDS	25806256	25806497	0.45	-	2	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	exon	25806256	25806497	.	-	.	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	intron	25806498	25806661	.	-	.	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	CDS	25806662	25807229	0.72	-	0	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	exon	25806662	25807229	.	-	.	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
Phchi.S1	AUGUSTUS	start_codon	25807227	25807229	.	-	0	transcript_id "Phchi.S1G404000.t1"; gene_id "Phchi.S1G404000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8693.t1 is derived from g5868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37461983	37463139	.	+	.	Phchi.S1G585200
Phchi.S1	AUGUSTUS	transcript	37461983	37463139	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	start_codon	37461983	37461985	.	+	0	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	CDS	37461983	37462167	0.97	+	0	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	exon	37461983	37462167	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	intron	37462168	37462281	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	CDS	37462282	37462642	0.98	+	1	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	exon	37462282	37462642	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	intron	37462643	37462748	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	CDS	37462749	37462817	1	+	0	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	exon	37462749	37462817	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	intron	37462818	37462900	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	CDS	37462901	37462951	1	+	0	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	exon	37462901	37462951	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	intron	37462952	37463031	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	CDS	37463032	37463139	1	+	0	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	exon	37463032	37463139	.	+	.	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
Phchi.S1	AUGUSTUS	stop_codon	37463140	37463142	.	+	0	transcript_id "Phchi.S1G585200.t1"; gene_id "Phchi.S1G585200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4650.t1 is derived from g1820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11632424	11638792	.	+	.	Phchi.S1G180900
Phchi.S1	AUGUSTUS	transcript	11632424	11638792	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	start_codon	11632424	11632426	.	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11632424	11635761	0.83	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11632424	11635761	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11635762	11636039	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11636040	11636279	0.99	+	1	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11636040	11636279	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11636280	11636422	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11636423	11636555	1	+	1	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11636423	11636555	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11636556	11636653	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11636654	11636806	1	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11636654	11636806	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11636807	11636925	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11636926	11637161	1	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11636926	11637161	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11637162	11637276	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11637277	11637349	1	+	1	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11637277	11637349	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11637350	11637425	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11637426	11637632	1	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11637426	11637632	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11637633	11637765	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11637766	11638010	1	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11637766	11638010	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11638011	11638121	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11638122	11638203	0.65	+	1	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11638122	11638203	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11638204	11638304	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11638305	11638442	0.99	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11638305	11638442	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	intron	11638443	11638522	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	CDS	11638523	11638792	1	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	exon	11638523	11638792	.	+	.	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
Phchi.S1	AUGUSTUS	stop_codon	11638793	11638795	.	+	0	transcript_id "Phchi.S1G180900.t1"; gene_id "Phchi.S1G180900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg709.t1 is derived from g10491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5015669	5016690	.	+	.	Phchi.S6G066800
Phchi.S6	AUGUSTUS	transcript	5015669	5016690	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	start_codon	5015669	5015671	.	+	0	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	CDS	5015669	5015838	0.66	+	0	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	exon	5015669	5015838	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	intron	5015839	5015950	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	CDS	5015951	5016020	0.88	+	1	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	exon	5015951	5016020	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	intron	5016021	5016122	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	CDS	5016123	5016248	0.55	+	0	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	exon	5016123	5016248	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	intron	5016249	5016333	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	CDS	5016334	5016343	0.56	+	0	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	exon	5016334	5016343	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	intron	5016344	5016437	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	CDS	5016438	5016472	0.45	+	2	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	exon	5016438	5016472	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	intron	5016473	5016624	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	CDS	5016625	5016690	0.45	+	0	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	exon	5016625	5016690	.	+	.	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
Phchi.S6	AUGUSTUS	stop_codon	5016691	5016693	.	+	0	transcript_id "Phchi.S6G066800.t1"; gene_id "Phchi.S6G066800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg891.t1 is derived from g10673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6317398	6318617	.	-	.	Phchi.S6G085000
Phchi.S6	AUGUSTUS	transcript	6317398	6318617	.	-	.	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	stop_codon	6317395	6317397	.	-	0	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	CDS	6317398	6317856	0.99	-	0	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	exon	6317398	6317856	.	-	.	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	intron	6317857	6317942	.	-	.	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	CDS	6317943	6318617	0.99	-	0	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	exon	6317943	6318617	.	-	.	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
Phchi.S6	AUGUSTUS	start_codon	6318615	6318617	.	-	0	transcript_id "Phchi.S6G085000.t1"; gene_id "Phchi.S6G085000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6691.t1 is derived from g3863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24544394	24544828	.	-	.	Phchi.S1G385000
Phchi.S1	AUGUSTUS	transcript	24544394	24544828	.	-	.	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	stop_codon	24544391	24544393	.	-	0	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	CDS	24544394	24544436	0.64	-	1	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	exon	24544394	24544436	.	-	.	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	intron	24544437	24544604	.	-	.	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	CDS	24544605	24544828	0.43	-	0	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	exon	24544605	24544828	.	-	.	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
Phchi.S1	AUGUSTUS	start_codon	24544826	24544828	.	-	0	transcript_id "Phchi.S1G385000.t1"; gene_id "Phchi.S1G385000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9442.t1 is derived from g6618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41490168	41490689	.	+	.	Phchi.S1G660100
Phchi.S1	AUGUSTUS	transcript	41490168	41490689	.	+	.	transcript_id "Phchi.S1G660100.t1"; gene_id "Phchi.S1G660100"
Phchi.S1	AUGUSTUS	start_codon	41490168	41490170	.	+	0	transcript_id "Phchi.S1G660100.t1"; gene_id "Phchi.S1G660100"
Phchi.S1	AUGUSTUS	CDS	41490168	41490689	0.97	+	0	transcript_id "Phchi.S1G660100.t1"; gene_id "Phchi.S1G660100"
Phchi.S1	AUGUSTUS	exon	41490168	41490689	.	+	.	transcript_id "Phchi.S1G660100.t1"; gene_id "Phchi.S1G660100"
Phchi.S1	AUGUSTUS	stop_codon	41490690	41490692	.	+	0	transcript_id "Phchi.S1G660100.t1"; gene_id "Phchi.S1G660100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1220.t1 is derived from g11003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8452039	8453376	.	+	.	Phchi.S6G117900
Phchi.S6	AUGUSTUS	transcript	8452039	8453376	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	start_codon	8452039	8452041	.	+	0	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	CDS	8452039	8452148	1	+	0	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	exon	8452039	8452148	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	intron	8452149	8452248	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	CDS	8452249	8452342	1	+	1	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	exon	8452249	8452342	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	intron	8452343	8452432	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	CDS	8452433	8452555	1	+	0	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	exon	8452433	8452555	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	intron	8452556	8452632	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	CDS	8452633	8452730	0.65	+	0	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	exon	8452633	8452730	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	intron	8452731	8452901	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	CDS	8452902	8453376	0.58	+	1	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	exon	8452902	8453376	.	+	.	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
Phchi.S6	AUGUSTUS	stop_codon	8453377	8453379	.	+	0	transcript_id "Phchi.S6G117900.t1"; gene_id "Phchi.S6G117900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3661.t1 is derived from g830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5036085	5036504	.	-	.	Phchi.S1G082000
Phchi.S1	AUGUSTUS	transcript	5036085	5036504	.	-	.	transcript_id "Phchi.S1G082000.t1"; gene_id "Phchi.S1G082000"
Phchi.S1	AUGUSTUS	stop_codon	5036082	5036084	.	-	0	transcript_id "Phchi.S1G082000.t1"; gene_id "Phchi.S1G082000"
Phchi.S1	AUGUSTUS	CDS	5036085	5036504	1	-	0	transcript_id "Phchi.S1G082000.t1"; gene_id "Phchi.S1G082000"
Phchi.S1	AUGUSTUS	exon	5036085	5036504	.	-	.	transcript_id "Phchi.S1G082000.t1"; gene_id "Phchi.S1G082000"
Phchi.S1	AUGUSTUS	start_codon	5036502	5036504	.	-	0	transcript_id "Phchi.S1G082000.t1"; gene_id "Phchi.S1G082000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11783.t1 is derived from g15835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8147421	8147783	.	+	.	Phchi.S4G136500
Phchi.S4	AUGUSTUS	transcript	8147421	8147783	.	+	.	transcript_id "Phchi.S4G136500.t1"; gene_id "Phchi.S4G136500"
Phchi.S4	AUGUSTUS	start_codon	8147421	8147423	.	+	0	transcript_id "Phchi.S4G136500.t1"; gene_id "Phchi.S4G136500"
Phchi.S4	AUGUSTUS	CDS	8147421	8147783	0.49	+	0	transcript_id "Phchi.S4G136500.t1"; gene_id "Phchi.S4G136500"
Phchi.S4	AUGUSTUS	exon	8147421	8147783	.	+	.	transcript_id "Phchi.S4G136500.t1"; gene_id "Phchi.S4G136500"
Phchi.S4	AUGUSTUS	stop_codon	8147784	8147786	.	+	0	transcript_id "Phchi.S4G136500.t1"; gene_id "Phchi.S4G136500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8390.t1 is derived from g5565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35672726	35673990	.	+	.	Phchi.S1G554900
Phchi.S1	AUGUSTUS	transcript	35672726	35673990	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	start_codon	35672726	35672728	.	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	CDS	35672726	35672962	0.93	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	exon	35672726	35672962	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	intron	35672963	35673109	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	CDS	35673110	35673229	1	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	exon	35673110	35673229	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	intron	35673230	35673393	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	CDS	35673394	35673471	1	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	exon	35673394	35673471	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	intron	35673472	35673573	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	CDS	35673574	35673663	0.99	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	exon	35673574	35673663	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	intron	35673664	35673765	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	CDS	35673766	35673819	1	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	exon	35673766	35673819	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	intron	35673820	35673912	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	CDS	35673913	35673990	1	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	exon	35673913	35673990	.	+	.	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
Phchi.S1	AUGUSTUS	stop_codon	35673991	35673993	.	+	0	transcript_id "Phchi.S1G554900.t1"; gene_id "Phchi.S1G554900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14807.t1 is derived from g13275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14803343	14804806	.	+	.	Phchi.S3G212600
Phchi.S3	AUGUSTUS	transcript	14803343	14804806	.	+	.	transcript_id "Phchi.S3G212600.t1"; gene_id "Phchi.S3G212600"
Phchi.S3	AUGUSTUS	start_codon	14803343	14803345	.	+	0	transcript_id "Phchi.S3G212600.t1"; gene_id "Phchi.S3G212600"
Phchi.S3	AUGUSTUS	CDS	14803343	14804806	0.9	+	0	transcript_id "Phchi.S3G212600.t1"; gene_id "Phchi.S3G212600"
Phchi.S3	AUGUSTUS	exon	14803343	14804806	.	+	.	transcript_id "Phchi.S3G212600.t1"; gene_id "Phchi.S3G212600"
Phchi.S3	AUGUSTUS	stop_codon	14804807	14804809	.	+	0	transcript_id "Phchi.S3G212600.t1"; gene_id "Phchi.S3G212600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13998.t1 is derived from g12465.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10172318	10178984	.	-	.	Phchi.S3G131700
Phchi.S3	AUGUSTUS	transcript	10172758	10178984	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	stop_codon	10172755	10172757	.	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10172758	10172769	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10172758	10172769	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10172770	10172860	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10172861	10173089	0.99	-	1	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10172861	10173089	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10173090	10173193	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10173194	10173477	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10173194	10173477	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10173478	10173558	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10173559	10173813	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10173559	10173813	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10173814	10173904	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10173905	10174069	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10173905	10174069	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10174070	10174257	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10174258	10174524	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10174258	10174524	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10174525	10174602	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10174603	10174800	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10174603	10174800	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10174801	10174959	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10174960	10175094	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10174960	10175094	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10175095	10175174	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10175175	10175277	1	-	1	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10175175	10175277	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10175278	10175472	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10175473	10175675	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10175473	10175675	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10175676	10175890	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10175891	10176052	0.96	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10175891	10176052	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10176053	10176163	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10176164	10176734	1	-	1	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10176164	10176734	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10176735	10176900	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10176901	10177155	1	-	1	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10176901	10177155	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10177156	10177303	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10177304	10177578	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10177304	10177578	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10177579	10177690	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10177691	10177784	0.89	-	1	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10177691	10177784	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10177785	10178009	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10178010	10178170	1	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10178010	10178170	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10178171	10178351	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10178352	10178984	0.78	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10178352	10178984	.	-	.	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	start_codon	10178982	10178984	.	-	0	transcript_id "Phchi.S3G131700.t1"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	transcript	10172318	10178984	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	stop_codon	10172315	10172317	.	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10172318	10172566	0.69	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10172318	10172566	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10172567	10172860	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10172861	10173089	1	-	1	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10172861	10173089	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10173090	10173193	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10173194	10173477	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10173194	10173477	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10173478	10173558	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10173559	10173813	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10173559	10173813	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10173814	10173904	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10173905	10174069	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10173905	10174069	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10174070	10174257	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10174258	10174524	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10174258	10174524	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10174525	10174602	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10174603	10174800	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10174603	10174800	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10174801	10174959	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10174960	10175094	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10174960	10175094	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10175095	10175174	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10175175	10175277	1	-	1	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10175175	10175277	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10175278	10175472	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10175473	10175675	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10175473	10175675	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10175676	10175890	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10175891	10176052	0.94	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10175891	10176052	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10176053	10176163	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10176164	10176734	0.98	-	1	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10176164	10176734	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10176735	10176900	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10176901	10177155	1	-	1	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10176901	10177155	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10177156	10177303	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10177304	10177578	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10177304	10177578	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10177579	10177690	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10177691	10177784	0.92	-	1	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10177691	10177784	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10177785	10178009	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10178010	10178170	1	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10178010	10178170	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	intron	10178171	10178351	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	CDS	10178352	10178984	0.71	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	exon	10178352	10178984	.	-	.	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
Phchi.S3	AUGUSTUS	start_codon	10178982	10178984	.	-	0	transcript_id "Phchi.S3G131700.t2"; gene_id "Phchi.S3G131700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9931.t1 is derived from g7107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44530682	44531260	.	+	.	Phchi.S1G709000
Phchi.S1	AUGUSTUS	transcript	44530682	44531260	.	+	.	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	start_codon	44530682	44530684	.	+	0	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	CDS	44530682	44530834	1	+	0	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	exon	44530682	44530834	.	+	.	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	intron	44530835	44530964	.	+	.	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	CDS	44530965	44531051	1	+	0	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	exon	44530965	44531051	.	+	.	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	intron	44531052	44531149	.	+	.	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	CDS	44531150	44531260	1	+	0	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	exon	44531150	44531260	.	+	.	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
Phchi.S1	AUGUSTUS	stop_codon	44531261	44531263	.	+	0	transcript_id "Phchi.S1G709000.t1"; gene_id "Phchi.S1G709000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6818.t1 is derived from g3990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25191953	25192689	.	+	.	Phchi.S1G397700
Phchi.S1	AUGUSTUS	transcript	25191953	25192689	.	+	.	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	start_codon	25191953	25191955	.	+	0	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	CDS	25191953	25192066	0.98	+	0	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	exon	25191953	25192066	.	+	.	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	intron	25192067	25192141	.	+	.	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	CDS	25192142	25192341	1	+	0	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	exon	25192142	25192341	.	+	.	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	intron	25192342	25192421	.	+	.	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	CDS	25192422	25192689	1	+	1	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	exon	25192422	25192689	.	+	.	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
Phchi.S1	AUGUSTUS	stop_codon	25192690	25192692	.	+	0	transcript_id "Phchi.S1G397700.t1"; gene_id "Phchi.S1G397700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6546.t1 is derived from g3718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23572368	23572715	.	-	.	Phchi.S1G370500
Phchi.S1	AUGUSTUS	transcript	23572368	23572715	.	-	.	transcript_id "Phchi.S1G370500.t1"; gene_id "Phchi.S1G370500"
Phchi.S1	AUGUSTUS	stop_codon	23572365	23572367	.	-	0	transcript_id "Phchi.S1G370500.t1"; gene_id "Phchi.S1G370500"
Phchi.S1	AUGUSTUS	CDS	23572368	23572715	0.85	-	0	transcript_id "Phchi.S1G370500.t1"; gene_id "Phchi.S1G370500"
Phchi.S1	AUGUSTUS	exon	23572368	23572715	.	-	.	transcript_id "Phchi.S1G370500.t1"; gene_id "Phchi.S1G370500"
Phchi.S1	AUGUSTUS	start_codon	23572713	23572715	.	-	0	transcript_id "Phchi.S1G370500.t1"; gene_id "Phchi.S1G370500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg412.t1 is derived from g10194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2950604	2953348	.	-	.	Phchi.S6G037100
Phchi.S6	AUGUSTUS	transcript	2950604	2953348	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	stop_codon	2950601	2950603	.	-	0	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	CDS	2950604	2950613	0.68	-	1	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	exon	2950604	2950613	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	intron	2950614	2950804	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	CDS	2950805	2952726	0.66	-	0	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	exon	2950805	2952726	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	intron	2952727	2952810	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	CDS	2952811	2952948	0.88	-	0	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	exon	2952811	2952948	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	intron	2952949	2953060	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	CDS	2953061	2953348	0.49	-	0	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	exon	2953061	2953348	.	-	.	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
Phchi.S6	AUGUSTUS	start_codon	2953346	2953348	.	-	0	transcript_id "Phchi.S6G037100.t1"; gene_id "Phchi.S6G037100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4964.t1 is derived from g2134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13782894	13785441	.	-	.	Phchi.S1G212300
Phchi.S1	AUGUSTUS	transcript	13782894	13785441	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	stop_codon	13782891	13782893	.	-	0	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	CDS	13782894	13783519	1	-	2	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	exon	13782894	13783519	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	intron	13783520	13783653	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	CDS	13783654	13783792	0.84	-	0	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	exon	13783654	13783792	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	intron	13783793	13783932	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	CDS	13783933	13784878	0.7	-	1	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	exon	13783933	13784878	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	intron	13784879	13785169	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	CDS	13785170	13785441	0.53	-	0	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	exon	13785170	13785441	.	-	.	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
Phchi.S1	AUGUSTUS	start_codon	13785439	13785441	.	-	0	transcript_id "Phchi.S1G212300.t1"; gene_id "Phchi.S1G212300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2358.t1 is derived from g9278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6331050	6332645	.	-	.	Phchi.S5G096700
Phchi.S5	AUGUSTUS	transcript	6331050	6332645	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	stop_codon	6331047	6331049	.	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6331050	6331076	0.44	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6331050	6331076	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	intron	6331077	6331160	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6331161	6331231	0.46	-	2	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6331161	6331231	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	intron	6331232	6331323	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6331324	6331510	0.76	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6331324	6331510	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	intron	6331511	6331600	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6331601	6331845	1	-	2	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6331601	6331845	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	intron	6331846	6332010	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6332011	6332152	1	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6332011	6332152	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	intron	6332153	6332250	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6332251	6332475	1	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6332251	6332475	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	intron	6332476	6332567	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	CDS	6332568	6332645	1	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	exon	6332568	6332645	.	-	.	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
Phchi.S5	AUGUSTUS	start_codon	6332643	6332645	.	-	0	transcript_id "Phchi.S5G096700.t1"; gene_id "Phchi.S5G096700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5796.t1 is derived from g2966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18990052	18991035	.	+	.	Phchi.S1G295500
Phchi.S1	AUGUSTUS	transcript	18990052	18991035	.	+	.	transcript_id "Phchi.S1G295500.t1"; gene_id "Phchi.S1G295500"
Phchi.S1	AUGUSTUS	start_codon	18990052	18990054	.	+	0	transcript_id "Phchi.S1G295500.t1"; gene_id "Phchi.S1G295500"
Phchi.S1	AUGUSTUS	CDS	18990052	18991035	1	+	0	transcript_id "Phchi.S1G295500.t1"; gene_id "Phchi.S1G295500"
Phchi.S1	AUGUSTUS	exon	18990052	18991035	.	+	.	transcript_id "Phchi.S1G295500.t1"; gene_id "Phchi.S1G295500"
Phchi.S1	AUGUSTUS	stop_codon	18991036	18991038	.	+	0	transcript_id "Phchi.S1G295500.t1"; gene_id "Phchi.S1G295500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14234.t1 is derived from g12701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11680706	11681321	.	-	.	Phchi.S3G155300
Phchi.S3	AUGUSTUS	transcript	11680706	11681321	.	-	.	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	stop_codon	11680703	11680705	.	-	0	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	CDS	11680706	11680772	0.29	-	1	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	exon	11680706	11680772	.	-	.	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	intron	11680773	11680860	.	-	.	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	CDS	11680861	11681023	0.52	-	2	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	exon	11680861	11681023	.	-	.	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	intron	11681024	11681281	.	-	.	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	CDS	11681282	11681321	0.99	-	0	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	exon	11681282	11681321	.	-	.	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
Phchi.S3	AUGUSTUS	start_codon	11681319	11681321	.	-	0	transcript_id "Phchi.S3G155300.t1"; gene_id "Phchi.S3G155300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7564.t1 is derived from g4738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30054174	30055809	.	-	.	Phchi.S1G472300
Phchi.S1	AUGUSTUS	transcript	30054174	30055809	.	-	.	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	stop_codon	30054171	30054173	.	-	0	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30054174	30054761	0.96	-	0	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30054174	30054761	.	-	.	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	intron	30054762	30055057	.	-	.	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30055058	30055311	1	-	2	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30055058	30055311	.	-	.	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	intron	30055312	30055604	.	-	.	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30055605	30055809	0.98	-	0	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30055605	30055809	.	-	.	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	start_codon	30055807	30055809	.	-	0	transcript_id "Phchi.S1G472300.t1"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	transcript	30054174	30055809	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	stop_codon	30054171	30054173	.	-	0	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30054174	30054761	0.96	-	0	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30054174	30054761	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	intron	30054762	30055057	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30055058	30055245	0.83	-	2	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30055058	30055245	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	intron	30055246	30055369	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30055370	30055462	0.94	-	2	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30055370	30055462	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	intron	30055463	30055604	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	CDS	30055605	30055809	0.96	-	0	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	exon	30055605	30055809	.	-	.	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
Phchi.S1	AUGUSTUS	start_codon	30055807	30055809	.	-	0	transcript_id "Phchi.S1G472300.t2"; gene_id "Phchi.S1G472300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12241.t1 is derived from g7917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6940356	6943149	.	+	.	Phchi.S2G032100
Phchi.S2	AUGUSTUS	transcript	6940356	6943149	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	start_codon	6940356	6940358	.	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6940356	6940400	1	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6940356	6940400	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	intron	6940401	6940902	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6940903	6940962	0.87	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6940903	6940962	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	intron	6940963	6941042	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6941043	6941056	0.95	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6941043	6941056	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	intron	6941057	6941882	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6941883	6941953	1	+	1	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6941883	6941953	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	intron	6941954	6942039	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6942040	6942299	1	+	2	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6942040	6942299	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	intron	6942300	6942716	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6942717	6942794	1	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6942717	6942794	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	intron	6942795	6942915	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	CDS	6942916	6943149	0.77	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	exon	6942916	6943149	.	+	.	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
Phchi.S2	AUGUSTUS	stop_codon	6943150	6943152	.	+	0	transcript_id "Phchi.S2G032100.t1"; gene_id "Phchi.S2G032100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14070.t1 is derived from g12537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10650883	10653814	.	-	.	Phchi.S3G138900
Phchi.S3	AUGUSTUS	transcript	10650883	10653814	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	stop_codon	10650880	10650882	.	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10650883	10650897	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10650883	10650897	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10650898	10650990	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10650991	10651065	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10650991	10651065	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10651066	10651155	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10651156	10651496	1	-	2	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10651156	10651496	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10651497	10651600	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10651601	10651697	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10651601	10651697	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10651698	10651789	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10651790	10651870	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10651790	10651870	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10651871	10652020	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10652021	10652098	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10652021	10652098	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10652099	10652168	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10652169	10652220	0.78	-	1	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10652169	10652220	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10652221	10652387	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10652388	10652437	0.61	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10652388	10652437	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10652438	10652516	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10652517	10652618	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10652517	10652618	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10652619	10652707	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10652708	10652785	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10652708	10652785	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10652786	10652950	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10652951	10653217	1	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10652951	10653217	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10653218	10653303	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10653304	10653403	0.96	-	1	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10653304	10653403	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	intron	10653404	10653506	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	CDS	10653507	10653814	0.87	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	exon	10653507	10653814	.	-	.	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
Phchi.S3	AUGUSTUS	start_codon	10653812	10653814	.	-	0	transcript_id "Phchi.S3G138900.t1"; gene_id "Phchi.S3G138900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10421.t1 is derived from g14470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	143816	144160	.	-	.	Phchi.S4G000300
Phchi.S4	AUGUSTUS	transcript	143816	144160	.	-	.	transcript_id "Phchi.S4G000300.t1"; gene_id "Phchi.S4G000300"
Phchi.S4	AUGUSTUS	stop_codon	143813	143815	.	-	0	transcript_id "Phchi.S4G000300.t1"; gene_id "Phchi.S4G000300"
Phchi.S4	AUGUSTUS	CDS	143816	144160	0.72	-	0	transcript_id "Phchi.S4G000300.t1"; gene_id "Phchi.S4G000300"
Phchi.S4	AUGUSTUS	exon	143816	144160	.	-	.	transcript_id "Phchi.S4G000300.t1"; gene_id "Phchi.S4G000300"
Phchi.S4	AUGUSTUS	start_codon	144158	144160	.	-	0	transcript_id "Phchi.S4G000300.t1"; gene_id "Phchi.S4G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10978.t1 is derived from g15028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3494954	3498712	.	-	.	Phchi.S4G056000
Phchi.S4	AUGUSTUS	transcript	3494954	3498712	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	stop_codon	3494951	3494953	.	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3494954	3495337	1	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3494954	3495337	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3495338	3495424	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3495425	3495858	0.79	-	2	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3495425	3495858	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3495859	3495972	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3495973	3496254	0.74	-	2	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3495973	3496254	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3496255	3496375	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3496376	3496616	1	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3496376	3496616	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3496617	3496705	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3496706	3497209	1	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3496706	3497209	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3497210	3497359	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3497360	3497497	1	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3497360	3497497	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3497498	3497633	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3497634	3497856	0.78	-	1	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3497634	3497856	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	intron	3497857	3497951	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	CDS	3497952	3498712	0.78	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	exon	3497952	3498712	.	-	.	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
Phchi.S4	AUGUSTUS	start_codon	3498710	3498712	.	-	0	transcript_id "Phchi.S4G056000.t1"; gene_id "Phchi.S4G056000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13617.t1 is derived from g12084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7772358	7773470	.	+	.	Phchi.S3G093600
Phchi.S3	AUGUSTUS	transcript	7772358	7773470	.	+	.	transcript_id "Phchi.S3G093600.t1"; gene_id "Phchi.S3G093600"
Phchi.S3	AUGUSTUS	start_codon	7772358	7772360	.	+	0	transcript_id "Phchi.S3G093600.t1"; gene_id "Phchi.S3G093600"
Phchi.S3	AUGUSTUS	CDS	7772358	7773470	0.77	+	0	transcript_id "Phchi.S3G093600.t1"; gene_id "Phchi.S3G093600"
Phchi.S3	AUGUSTUS	exon	7772358	7773470	.	+	.	transcript_id "Phchi.S3G093600.t1"; gene_id "Phchi.S3G093600"
Phchi.S3	AUGUSTUS	stop_codon	7773471	7773473	.	+	0	transcript_id "Phchi.S3G093600.t1"; gene_id "Phchi.S3G093600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4885.t1 is derived from g2055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13213169	13220247	.	+	.	Phchi.S1G204400
Phchi.S1	AUGUSTUS	transcript	13213169	13220247	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	start_codon	13213169	13213171	.	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13213169	13213264	1	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13213169	13213264	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13213265	13213346	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13213347	13213465	1	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13213347	13213465	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13213466	13213626	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13213627	13213672	0.56	+	1	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13213627	13213672	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13213673	13213783	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13213784	13213856	0.56	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13213784	13213856	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13213857	13214020	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13214021	13214078	1	+	2	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13214021	13214078	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13214079	13214195	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13214196	13214291	0.99	+	1	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13214196	13214291	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13214292	13214467	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13214468	13214588	0.96	+	1	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13214468	13214588	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13214589	13214690	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13214691	13214957	0.96	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13214691	13214957	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13214958	13215150	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13215151	13215252	1	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13215151	13215252	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13215253	13215416	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13215417	13216002	1	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13215417	13216002	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13216003	13216093	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13216094	13216725	0.98	+	2	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13216094	13216725	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13216726	13216831	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13216832	13217028	0.97	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13216832	13217028	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13217029	13217133	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13217134	13217356	0.88	+	1	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13217134	13217356	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13217357	13217460	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13217461	13217580	0.96	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13217461	13217580	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13217581	13217663	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13217664	13218182	0.68	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13217664	13218182	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13218183	13218315	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13218316	13218438	0.83	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13218316	13218438	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	intron	13218439	13218543	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	CDS	13218544	13220247	0.9	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	exon	13218544	13220247	.	+	.	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
Phchi.S1	AUGUSTUS	stop_codon	13220248	13220250	.	+	0	transcript_id "Phchi.S1G204400.t1"; gene_id "Phchi.S1G204400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13036.t1 is derived from g11501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3826509	3828138	.	-	.	Phchi.S3G035500
Phchi.S3	AUGUSTUS	transcript	3826509	3828138	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	stop_codon	3826506	3826508	.	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3826509	3826599	1	-	1	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3826509	3826599	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	intron	3826600	3826733	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3826734	3826813	1	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3826734	3826813	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	intron	3826814	3826930	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3826931	3827047	0.72	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3826931	3827047	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	intron	3827048	3827190	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3827191	3827326	0.97	-	1	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3827191	3827326	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	intron	3827327	3827457	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3827458	3827609	1	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3827458	3827609	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	intron	3827610	3827703	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3827704	3827793	1	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3827704	3827793	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	intron	3827794	3827976	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	CDS	3827977	3828138	1	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	exon	3827977	3828138	.	-	.	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
Phchi.S3	AUGUSTUS	start_codon	3828136	3828138	.	-	0	transcript_id "Phchi.S3G035500.t1"; gene_id "Phchi.S3G035500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6573.t1 is derived from g3745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23790246	23794328	.	-	.	Phchi.S1G373200
Phchi.S1	AUGUSTUS	transcript	23790246	23794328	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	stop_codon	23790243	23790245	.	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23790246	23790258	0.96	-	1	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23790246	23790258	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23790259	23790347	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23790348	23790598	0.85	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23790348	23790598	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23790599	23790678	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23790679	23790975	0.86	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23790679	23790975	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23790976	23791054	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23791055	23791099	0.94	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23791055	23791099	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23791100	23791188	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23791189	23791761	0.99	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23791189	23791761	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23791762	23791870	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23791871	23792353	1	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23791871	23792353	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23792354	23792470	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23792471	23792683	1	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23792471	23792683	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23792684	23792800	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23792801	23792823	0.88	-	2	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23792801	23792823	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23792824	23792924	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23792925	23793089	0.87	-	2	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23792925	23793089	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23793090	23793218	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23793219	23793358	1	-	1	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23793219	23793358	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23793359	23793458	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23793459	23793687	0.91	-	2	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23793459	23793687	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23793688	23793796	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23793797	23793977	0.95	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23793797	23793977	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	intron	23793978	23794139	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	CDS	23794140	23794328	0.98	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	exon	23794140	23794328	.	-	.	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
Phchi.S1	AUGUSTUS	start_codon	23794326	23794328	.	-	0	transcript_id "Phchi.S1G373200.t1"; gene_id "Phchi.S1G373200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1536.t1 is derived from g8455.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1662166	1665335	.	+	.	Phchi.S5G014500
Phchi.S5	AUGUSTUS	transcript	1662166	1665335	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	start_codon	1662166	1662168	.	+	0	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1662166	1662451	0.86	+	0	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1662166	1662451	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1662452	1662916	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1662917	1663201	1	+	2	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1662917	1663201	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1663202	1663368	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1663369	1663588	1	+	2	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1663369	1663588	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1663589	1663725	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1663726	1663835	1	+	1	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1663726	1663835	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1663836	1663971	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1663972	1664027	0.82	+	2	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1663972	1664027	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664028	1664091	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664092	1664166	0.82	+	0	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664092	1664166	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664167	1664283	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664284	1664387	1	+	0	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664284	1664387	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664388	1664514	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664515	1664702	1	+	1	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664515	1664702	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664703	1664790	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664791	1664990	1	+	2	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664791	1664990	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664991	1665110	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1665111	1665335	0.81	+	0	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1665111	1665335	.	+	.	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	stop_codon	1665336	1665338	.	+	0	transcript_id "Phchi.S5G014500.t1"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	transcript	1662166	1665335	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	start_codon	1662166	1662168	.	+	0	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1662166	1662451	0.85	+	0	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1662166	1662451	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1662452	1662907	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1662908	1663201	1	+	2	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1662908	1663201	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1663202	1663368	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1663369	1663588	1	+	2	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1663369	1663588	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1663589	1663725	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1663726	1663835	1	+	1	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1663726	1663835	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1663836	1663971	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1663972	1664027	0.69	+	2	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1663972	1664027	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664028	1664091	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664092	1664166	0.69	+	0	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664092	1664166	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664167	1664283	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664284	1664387	1	+	0	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664284	1664387	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664388	1664514	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664515	1664702	1	+	1	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664515	1664702	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664703	1664790	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1664791	1664990	1	+	2	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1664791	1664990	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	intron	1664991	1665110	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	CDS	1665111	1665335	0.79	+	0	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	exon	1665111	1665335	.	+	.	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
Phchi.S5	AUGUSTUS	stop_codon	1665336	1665338	.	+	0	transcript_id "Phchi.S5G014500.t2"; gene_id "Phchi.S5G014500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11598.t1 is derived from g15649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7273508	7278668	.	-	.	Phchi.S4G118000
Phchi.S4	AUGUSTUS	transcript	7273508	7278668	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	stop_codon	7273505	7273507	.	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7273508	7273675	1	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7273508	7273675	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7273676	7273776	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7273777	7273867	0.97	-	1	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7273777	7273867	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7273868	7273960	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7273961	7274037	1	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7273961	7274037	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7274038	7274802	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7274803	7274855	0.89	-	2	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7274803	7274855	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7274856	7275302	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7275303	7275612	0.38	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7275303	7275612	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7275613	7275738	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7275739	7277550	0.99	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7275739	7277550	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7277551	7277645	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7277646	7277960	1	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7277646	7277960	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7277961	7278198	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7278199	7278372	1	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7278199	7278372	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	intron	7278373	7278449	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	CDS	7278450	7278668	0.99	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	exon	7278450	7278668	.	-	.	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
Phchi.S4	AUGUSTUS	start_codon	7278666	7278668	.	-	0	transcript_id "Phchi.S4G118000.t1"; gene_id "Phchi.S4G118000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8058.t1 is derived from g5233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32736315	32741218	.	+	.	Phchi.S1G521700
Phchi.S1	AUGUSTUS	transcript	32736315	32741218	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	start_codon	32736315	32736317	.	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32736315	32736324	0.96	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32736315	32736324	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32736325	32736411	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32736412	32736556	0.96	+	2	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32736412	32736556	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32736557	32736680	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32736681	32736759	1	+	1	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32736681	32736759	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32736760	32736895	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32736896	32736997	1	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32736896	32736997	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32736998	32737081	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32737082	32737165	1	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32737082	32737165	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32737166	32737334	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32737335	32737445	1	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32737335	32737445	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32737446	32737572	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32737573	32737932	0.6	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32737573	32737932	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32737933	32738034	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32738035	32738221	0.97	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32738035	32738221	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32738222	32738316	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32738317	32738952	0.86	+	2	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32738317	32738952	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32738953	32739052	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32739053	32739327	0.67	+	2	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32739053	32739327	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32739328	32739442	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32739443	32739494	1	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32739443	32739494	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32739495	32739618	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32739619	32739739	1	+	2	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32739619	32739739	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32739740	32739839	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32739840	32739964	1	+	1	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32739840	32739964	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32739965	32740051	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32740052	32740197	0.94	+	2	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32740052	32740197	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32740198	32740302	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32740303	32740398	0.94	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32740303	32740398	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32740399	32740521	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32740522	32740607	1	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32740522	32740607	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32740608	32740724	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32740725	32740800	1	+	1	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32740725	32740800	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	intron	32740801	32740894	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	CDS	32740895	32741218	0.64	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	exon	32740895	32741218	.	+	.	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
Phchi.S1	AUGUSTUS	stop_codon	32741219	32741221	.	+	0	transcript_id "Phchi.S1G521700.t1"; gene_id "Phchi.S1G521700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7956.t1 is derived from g5131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32091168	32092310	.	-	.	Phchi.S1G511500
Phchi.S1	AUGUSTUS	transcript	32091168	32092310	.	-	.	transcript_id "Phchi.S1G511500.t1"; gene_id "Phchi.S1G511500"
Phchi.S1	AUGUSTUS	stop_codon	32091165	32091167	.	-	0	transcript_id "Phchi.S1G511500.t1"; gene_id "Phchi.S1G511500"
Phchi.S1	AUGUSTUS	CDS	32091168	32092310	0.61	-	0	transcript_id "Phchi.S1G511500.t1"; gene_id "Phchi.S1G511500"
Phchi.S1	AUGUSTUS	exon	32091168	32092310	.	-	.	transcript_id "Phchi.S1G511500.t1"; gene_id "Phchi.S1G511500"
Phchi.S1	AUGUSTUS	start_codon	32092308	32092310	.	-	0	transcript_id "Phchi.S1G511500.t1"; gene_id "Phchi.S1G511500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15071.t1 is derived from g13539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16910739	16912162	.	+	.	Phchi.S3G239000
Phchi.S3	AUGUSTUS	transcript	16910739	16912162	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	start_codon	16910739	16910741	.	+	0	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	CDS	16910739	16911049	0.61	+	0	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	exon	16910739	16911049	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	intron	16911050	16911129	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	CDS	16911130	16911380	1	+	1	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	exon	16911130	16911380	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	intron	16911381	16911489	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	CDS	16911490	16911782	0.99	+	2	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	exon	16911490	16911782	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	intron	16911783	16911907	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	CDS	16911908	16912162	1	+	0	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	exon	16911908	16912162	.	+	.	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
Phchi.S3	AUGUSTUS	stop_codon	16912163	16912165	.	+	0	transcript_id "Phchi.S3G239000.t1"; gene_id "Phchi.S3G239000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6842.t1 is derived from g4014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25508785	25511075	.	+	.	Phchi.S1G400100
Phchi.S1	AUGUSTUS	transcript	25508785	25511075	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	start_codon	25508785	25508787	.	+	0	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25508785	25509051	0.49	+	0	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25508785	25509051	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	intron	25509052	25509327	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25509328	25509495	1	+	0	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25509328	25509495	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	intron	25509496	25509640	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25509641	25509902	1	+	0	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25509641	25509902	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	intron	25509903	25510039	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25510040	25510351	1	+	2	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25510040	25510351	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	intron	25510352	25510427	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25510428	25510625	0.7	+	2	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25510428	25510625	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	intron	25510626	25510738	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25510739	25510833	0.34	+	2	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25510739	25510833	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	intron	25510834	25510991	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	CDS	25510992	25511075	1	+	0	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	exon	25510992	25511075	.	+	.	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
Phchi.S1	AUGUSTUS	stop_codon	25511076	25511078	.	+	0	transcript_id "Phchi.S1G400100.t1"; gene_id "Phchi.S1G400100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg33.t1 is derived from g15993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C27	AUGUSTUS	gene	22342	22734	.	-	.	Phchi.C27G000100
Phchi.C27	AUGUSTUS	transcript	22342	22734	.	-	.	transcript_id "Phchi.C27G000100.t1"; gene_id "Phchi.C27G000100"
Phchi.C27	AUGUSTUS	stop_codon	22339	22341	.	-	0	transcript_id "Phchi.C27G000100.t1"; gene_id "Phchi.C27G000100"
Phchi.C27	AUGUSTUS	CDS	22342	22734	0.47	-	0	transcript_id "Phchi.C27G000100.t1"; gene_id "Phchi.C27G000100"
Phchi.C27	AUGUSTUS	exon	22342	22734	.	-	.	transcript_id "Phchi.C27G000100.t1"; gene_id "Phchi.C27G000100"
Phchi.C27	AUGUSTUS	start_codon	22732	22734	.	-	0	transcript_id "Phchi.C27G000100.t1"; gene_id "Phchi.C27G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg678.t1 is derived from g10460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4676218	4677281	.	+	.	Phchi.S6G063700
Phchi.S6	AUGUSTUS	transcript	4676218	4677281	.	+	.	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	start_codon	4676218	4676220	.	+	0	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	CDS	4676218	4676736	0.4	+	0	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	exon	4676218	4676736	.	+	.	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	intron	4676737	4676819	.	+	.	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	CDS	4676820	4677281	0.86	+	0	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	exon	4676820	4677281	.	+	.	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
Phchi.S6	AUGUSTUS	stop_codon	4677282	4677284	.	+	0	transcript_id "Phchi.S6G063700.t1"; gene_id "Phchi.S6G063700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2890.t1 is derived from g59.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	338455	340702	.	-	.	Phchi.S1G004900
Phchi.S1	AUGUSTUS	transcript	338455	340702	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	stop_codon	338452	338454	.	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	338455	338589	0.92	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	338455	338589	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	338590	338674	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	338675	338745	1	-	2	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	338675	338745	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	338746	338824	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	338825	338933	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	338825	338933	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	338934	339046	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	339047	339109	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	339047	339109	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	339110	339218	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	339219	339269	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	339219	339269	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	339270	339396	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	339397	339461	1	-	2	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	339397	339461	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	339462	339565	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	339566	339704	0.99	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	339566	339704	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	339705	339831	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	339832	339888	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	339832	339888	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	339889	339992	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	339993	340100	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	339993	340100	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	340101	340184	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	340185	340256	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	340185	340256	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	340257	340369	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	340370	340438	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	340370	340438	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	intron	340439	340570	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	CDS	340571	340702	1	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	exon	340571	340702	.	-	.	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
Phchi.S1	AUGUSTUS	start_codon	340700	340702	.	-	0	transcript_id "Phchi.S1G004900.t1"; gene_id "Phchi.S1G004900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8786.t1 is derived from g5961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37949037	37949453	.	-	.	Phchi.S1G594500
Phchi.S1	AUGUSTUS	transcript	37949037	37949453	.	-	.	transcript_id "Phchi.S1G594500.t1"; gene_id "Phchi.S1G594500"
Phchi.S1	AUGUSTUS	stop_codon	37949034	37949036	.	-	0	transcript_id "Phchi.S1G594500.t1"; gene_id "Phchi.S1G594500"
Phchi.S1	AUGUSTUS	CDS	37949037	37949453	1	-	0	transcript_id "Phchi.S1G594500.t1"; gene_id "Phchi.S1G594500"
Phchi.S1	AUGUSTUS	exon	37949037	37949453	.	-	.	transcript_id "Phchi.S1G594500.t1"; gene_id "Phchi.S1G594500"
Phchi.S1	AUGUSTUS	start_codon	37949451	37949453	.	-	0	transcript_id "Phchi.S1G594500.t1"; gene_id "Phchi.S1G594500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12876.t1 is derived from g11341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2857433	2858536	.	-	.	Phchi.S3G019500
Phchi.S3	AUGUSTUS	transcript	2857433	2858536	.	-	.	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	stop_codon	2857430	2857432	.	-	0	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	CDS	2857433	2858429	1	-	1	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	exon	2857433	2858429	.	-	.	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	intron	2858430	2858513	.	-	.	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	CDS	2858514	2858536	0.95	-	0	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	exon	2858514	2858536	.	-	.	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
Phchi.S3	AUGUSTUS	start_codon	2858534	2858536	.	-	0	transcript_id "Phchi.S3G019500.t1"; gene_id "Phchi.S3G019500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3941.t1 is derived from g1110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6576213	6576585	.	+	.	Phchi.S1G110000
Phchi.S1	AUGUSTUS	transcript	6576213	6576585	.	+	.	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	start_codon	6576213	6576215	.	+	0	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	CDS	6576213	6576273	0.71	+	0	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	exon	6576213	6576273	.	+	.	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	intron	6576274	6576371	.	+	.	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	CDS	6576372	6576488	0.75	+	2	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	exon	6576372	6576488	.	+	.	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	intron	6576489	6576559	.	+	.	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	CDS	6576560	6576585	0.99	+	2	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	exon	6576560	6576585	.	+	.	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
Phchi.S1	AUGUSTUS	stop_codon	6576586	6576588	.	+	0	transcript_id "Phchi.S1G110000.t1"; gene_id "Phchi.S1G110000"
# This transcript jg14346.t2 is derived from g12813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14347.t1 is derived from g12814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12320695	12321536	.	-	.	Phchi.S3G166600
Phchi.S3	AUGUSTUS	transcript	12320695	12321536	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	stop_codon	12320692	12320694	.	-	0	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	CDS	12320695	12320808	1	-	0	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	exon	12320695	12320808	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	intron	12320809	12320912	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	CDS	12320913	12321017	0.98	-	0	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	exon	12320913	12321017	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	intron	12321018	12321242	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	CDS	12321243	12321317	1	-	0	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	exon	12321243	12321317	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	intron	12321318	12321405	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	CDS	12321406	12321433	1	-	1	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	exon	12321406	12321433	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	intron	12321434	12321525	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	CDS	12321526	12321536	0.86	-	0	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	exon	12321526	12321536	.	-	.	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
Phchi.S3	AUGUSTUS	start_codon	12321534	12321536	.	-	0	transcript_id "Phchi.S3G166600.t1"; gene_id "Phchi.S3G166600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12173.t1 is derived from g7849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5921826	5925445	.	+	.	Phchi.S2G025300
Phchi.S2	AUGUSTUS	transcript	5921826	5925445	.	+	.	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	start_codon	5921826	5921828	.	+	0	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	CDS	5921826	5921893	0.01	+	0	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	exon	5921826	5921893	.	+	.	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	intron	5921894	5925318	.	+	.	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	CDS	5925319	5925445	0.07	+	1	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	exon	5925319	5925445	.	+	.	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
Phchi.S2	AUGUSTUS	stop_codon	5925446	5925448	.	+	0	transcript_id "Phchi.S2G025300.t1"; gene_id "Phchi.S2G025300"
# This transcript jg4101.t2 is derived from g1270.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4101.t3 is derived from g1270.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4102.t1 is derived from g1271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7823767	7825402	.	-	.	Phchi.S1G126100
Phchi.S1	AUGUSTUS	transcript	7823767	7825402	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	stop_codon	7823764	7823766	.	-	0	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	CDS	7823767	7823943	0.86	-	0	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	exon	7823767	7823943	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	intron	7823944	7824111	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	CDS	7824112	7824361	1	-	1	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	exon	7824112	7824361	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	intron	7824362	7824562	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	CDS	7824563	7824871	0.45	-	1	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	exon	7824563	7824871	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	intron	7824872	7825013	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	CDS	7825014	7825402	0.54	-	0	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	exon	7825014	7825402	.	-	.	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
Phchi.S1	AUGUSTUS	start_codon	7825400	7825402	.	-	0	transcript_id "Phchi.S1G126100.t1"; gene_id "Phchi.S1G126100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4790.t1 is derived from g1960.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12823589	12824377	.	-	.	Phchi.S1G194900
Phchi.S1	AUGUSTUS	transcript	12823589	12824377	.	-	.	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	stop_codon	12823586	12823588	.	-	0	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	CDS	12823589	12823834	0.98	-	0	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	exon	12823589	12823834	.	-	.	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	intron	12823835	12823941	.	-	.	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	CDS	12823942	12824097	1	-	0	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	exon	12823942	12824097	.	-	.	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	intron	12824098	12824185	.	-	.	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	CDS	12824186	12824377	0.67	-	0	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	exon	12824186	12824377	.	-	.	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	start_codon	12824375	12824377	.	-	0	transcript_id "Phchi.S1G194900.t1"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	transcript	12823589	12824238	.	-	.	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	stop_codon	12823586	12823588	.	-	0	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	CDS	12823589	12823834	0.99	-	0	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	exon	12823589	12823834	.	-	.	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	intron	12823835	12823941	.	-	.	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	CDS	12823942	12824097	0.96	-	0	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	exon	12823942	12824097	.	-	.	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	intron	12824098	12824181	.	-	.	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	CDS	12824182	12824238	0.76	-	0	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	exon	12824182	12824238	.	-	.	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
Phchi.S1	AUGUSTUS	start_codon	12824236	12824238	.	-	0	transcript_id "Phchi.S1G194900.t2"; gene_id "Phchi.S1G194900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4227.t1 is derived from g1396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9010702	9012623	.	+	.	Phchi.S1G138600
Phchi.S1	AUGUSTUS	transcript	9010702	9012623	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	start_codon	9010702	9010704	.	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9010702	9010928	1	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9010702	9010928	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9010929	9011090	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9011091	9011204	1	+	1	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9011091	9011204	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9011205	9011472	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9011473	9011568	1	+	1	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9011473	9011568	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9011569	9011680	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9011681	9011723	1	+	1	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9011681	9011723	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9011724	9011809	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9011810	9011965	1	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9011810	9011965	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9011966	9012062	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9012063	9012143	1	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9012063	9012143	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9012144	9012241	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9012242	9012349	1	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9012242	9012349	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	intron	9012350	9012461	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	CDS	9012462	9012623	1	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	exon	9012462	9012623	.	+	.	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
Phchi.S1	AUGUSTUS	stop_codon	9012624	9012626	.	+	0	transcript_id "Phchi.S1G138600.t1"; gene_id "Phchi.S1G138600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12214.t1 is derived from g7890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6798023	6798764	.	-	.	Phchi.S2G029400
Phchi.S2	AUGUSTUS	transcript	6798023	6798723	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	stop_codon	6798020	6798022	.	-	0	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798023	6798256	1	-	0	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798023	6798256	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	intron	6798257	6798353	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798354	6798445	1	-	2	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798354	6798445	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	intron	6798446	6798611	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798612	6798646	1	-	1	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798612	6798646	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	intron	6798647	6798718	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798719	6798723	1	-	0	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798719	6798723	.	-	.	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	start_codon	6798721	6798723	.	-	0	transcript_id "Phchi.S2G029400.t1"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	transcript	6798023	6798764	.	-	.	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	stop_codon	6798020	6798022	.	-	0	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798023	6798256	1	-	0	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798023	6798256	.	-	.	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	intron	6798257	6798353	.	-	.	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798354	6798445	1	-	2	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798354	6798445	.	-	.	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	intron	6798446	6798718	.	-	.	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	CDS	6798719	6798764	1	-	0	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	exon	6798719	6798764	.	-	.	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
Phchi.S2	AUGUSTUS	start_codon	6798762	6798764	.	-	0	transcript_id "Phchi.S2G029400.t2"; gene_id "Phchi.S2G029400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13214.t1 is derived from g11679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4721667	4724552	.	-	.	Phchi.S3G053300
Phchi.S3	AUGUSTUS	transcript	4721667	4724552	.	-	.	transcript_id "Phchi.S3G053300.t1"; gene_id "Phchi.S3G053300"
Phchi.S3	AUGUSTUS	stop_codon	4721664	4721666	.	-	0	transcript_id "Phchi.S3G053300.t1"; gene_id "Phchi.S3G053300"
Phchi.S3	AUGUSTUS	CDS	4721667	4724552	0.83	-	0	transcript_id "Phchi.S3G053300.t1"; gene_id "Phchi.S3G053300"
Phchi.S3	AUGUSTUS	exon	4721667	4724552	.	-	.	transcript_id "Phchi.S3G053300.t1"; gene_id "Phchi.S3G053300"
Phchi.S3	AUGUSTUS	start_codon	4724550	4724552	.	-	0	transcript_id "Phchi.S3G053300.t1"; gene_id "Phchi.S3G053300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1344.t1 is derived from g11127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9120416	9121269	.	-	.	Phchi.S6G130300
Phchi.S6	AUGUSTUS	transcript	9120416	9121269	.	-	.	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	stop_codon	9120413	9120415	.	-	0	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	CDS	9120416	9120805	0.71	-	0	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	exon	9120416	9120805	.	-	.	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	intron	9120806	9120924	.	-	.	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	CDS	9120925	9121269	0.62	-	0	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	exon	9120925	9121269	.	-	.	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
Phchi.S6	AUGUSTUS	start_codon	9121267	9121269	.	-	0	transcript_id "Phchi.S6G130300.t1"; gene_id "Phchi.S6G130300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7733.t1 is derived from g4907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30885868	30887211	.	+	.	Phchi.S1G489200
Phchi.S1	AUGUSTUS	transcript	30885868	30887211	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	start_codon	30885868	30885870	.	+	0	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30885868	30886185	0.38	+	0	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30885868	30886185	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	intron	30886186	30886292	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30886293	30886359	0.71	+	0	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30886293	30886359	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	intron	30886360	30886431	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30886432	30886483	1	+	2	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30886432	30886483	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	intron	30886484	30886620	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30886621	30886703	1	+	1	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30886621	30886703	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	intron	30886704	30886799	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30886800	30886894	1	+	2	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30886800	30886894	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	intron	30886895	30886961	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30886962	30887007	1	+	0	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30886962	30887007	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	intron	30887008	30887128	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	CDS	30887129	30887211	0.79	+	2	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	exon	30887129	30887211	.	+	.	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
Phchi.S1	AUGUSTUS	stop_codon	30887212	30887214	.	+	0	transcript_id "Phchi.S1G489200.t1"; gene_id "Phchi.S1G489200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1315.t1 is derived from g11098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8965671	8966982	.	-	.	Phchi.S6G127400
Phchi.S6	AUGUSTUS	transcript	8965671	8966982	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	stop_codon	8965668	8965670	.	-	0	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	CDS	8965671	8965901	1	-	0	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	exon	8965671	8965901	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	intron	8965902	8966001	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	CDS	8966002	8966088	1	-	0	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	exon	8966002	8966088	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	intron	8966089	8966163	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	CDS	8966164	8966513	0.83	-	2	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	exon	8966164	8966513	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	intron	8966514	8966705	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	CDS	8966706	8966982	1	-	0	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	exon	8966706	8966982	.	-	.	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
Phchi.S6	AUGUSTUS	start_codon	8966980	8966982	.	-	0	transcript_id "Phchi.S6G127400.t1"; gene_id "Phchi.S6G127400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5243.t1 is derived from g2413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15840036	15842162	.	-	.	Phchi.S1G240200
Phchi.S1	AUGUSTUS	transcript	15840036	15842162	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	stop_codon	15840033	15840035	.	-	0	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	CDS	15840036	15840661	0.99	-	2	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	exon	15840036	15840661	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	intron	15840662	15840764	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	CDS	15840765	15840978	0.35	-	0	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	exon	15840765	15840978	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	intron	15840979	15841133	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	CDS	15841134	15841566	0.2	-	1	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	exon	15841134	15841566	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	intron	15841567	15841645	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	CDS	15841646	15841747	1	-	1	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	exon	15841646	15841747	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	intron	15841748	15841836	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	CDS	15841837	15842162	1	-	0	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	exon	15841837	15842162	.	-	.	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
Phchi.S1	AUGUSTUS	start_codon	15842160	15842162	.	-	0	transcript_id "Phchi.S1G240200.t1"; gene_id "Phchi.S1G240200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14795.t1 is derived from g13263.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14746522	14748015	.	-	.	Phchi.S3G211400
Phchi.S3	AUGUSTUS	transcript	14746902	14748015	.	-	.	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	stop_codon	14746899	14746901	.	-	0	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	CDS	14746902	14746938	0.69	-	1	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	exon	14746902	14746938	.	-	.	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	intron	14746939	14747218	.	-	.	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	CDS	14747219	14748015	0.83	-	0	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	exon	14747219	14748015	.	-	.	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	start_codon	14748013	14748015	.	-	0	transcript_id "Phchi.S3G211400.t1"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	transcript	14746522	14748015	.	-	.	transcript_id "Phchi.S3G211400.t2"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	stop_codon	14746519	14746521	.	-	0	transcript_id "Phchi.S3G211400.t2"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	CDS	14746522	14748015	0.91	-	0	transcript_id "Phchi.S3G211400.t2"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	exon	14746522	14748015	.	-	.	transcript_id "Phchi.S3G211400.t2"; gene_id "Phchi.S3G211400"
Phchi.S3	AUGUSTUS	start_codon	14748013	14748015	.	-	0	transcript_id "Phchi.S3G211400.t2"; gene_id "Phchi.S3G211400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13822.t1 is derived from g12289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9074419	9077143	.	+	.	Phchi.S3G114100
Phchi.S3	AUGUSTUS	transcript	9074419	9077143	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	start_codon	9074419	9074421	.	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9074419	9074487	1	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9074419	9074487	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	intron	9074488	9075087	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9075088	9075206	1	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9075088	9075206	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	intron	9075207	9075302	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9075303	9075732	1	+	1	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9075303	9075732	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	intron	9075733	9075842	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9075843	9076106	1	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9075843	9076106	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	intron	9076107	9076220	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9076221	9076346	1	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9076221	9076346	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	intron	9076347	9076472	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9076473	9076583	1	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9076473	9076583	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	intron	9076584	9077038	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	CDS	9077039	9077143	1	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	exon	9077039	9077143	.	+	.	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
Phchi.S3	AUGUSTUS	stop_codon	9077144	9077146	.	+	0	transcript_id "Phchi.S3G114100.t1"; gene_id "Phchi.S3G114100"
# This transcript jg8595.t2 is derived from g5770.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8596.t1 is derived from g5771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36825785	36827136	.	-	.	Phchi.S1G575500
Phchi.S1	AUGUSTUS	transcript	36825785	36827136	.	-	.	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	stop_codon	36825782	36825784	.	-	0	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	CDS	36825785	36826369	0.44	-	0	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	exon	36825785	36826369	.	-	.	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	intron	36826370	36826497	.	-	.	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	CDS	36826498	36827136	0.34	-	0	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	exon	36826498	36827136	.	-	.	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
Phchi.S1	AUGUSTUS	start_codon	36827134	36827136	.	-	0	transcript_id "Phchi.S1G575500.t1"; gene_id "Phchi.S1G575500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9896.t1 is derived from g7072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44324663	44325317	.	-	.	Phchi.S1G705500
Phchi.S1	AUGUSTUS	transcript	44324663	44325317	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	stop_codon	44324660	44324662	.	-	0	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	CDS	44324663	44324778	0.64	-	2	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	exon	44324663	44324778	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	intron	44324779	44324879	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	CDS	44324880	44324947	0.87	-	1	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	exon	44324880	44324947	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	intron	44324948	44325146	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	CDS	44325147	44325165	0.84	-	2	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	exon	44325147	44325165	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	intron	44325166	44325298	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	CDS	44325299	44325317	0.96	-	0	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	exon	44325299	44325317	.	-	.	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
Phchi.S1	AUGUSTUS	start_codon	44325315	44325317	.	-	0	transcript_id "Phchi.S1G705500.t1"; gene_id "Phchi.S1G705500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8228.t1 is derived from g5403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34550671	34552605	.	-	.	Phchi.S1G538700
Phchi.S1	AUGUSTUS	transcript	34550671	34552605	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	stop_codon	34550668	34550670	.	-	0	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34550671	34550926	1	-	1	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34550671	34550926	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34550927	34551004	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34551005	34551145	1	-	1	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34551005	34551145	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34551146	34551266	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34551267	34551401	1	-	1	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34551267	34551401	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34551402	34551485	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34551486	34551525	1	-	2	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34551486	34551525	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34551526	34551690	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34551691	34551772	1	-	0	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34551691	34551772	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34551773	34551847	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34551848	34551929	1	-	1	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34551848	34551929	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34551930	34552024	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34552025	34552129	1	-	1	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34552025	34552129	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	intron	34552130	34552282	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	CDS	34552283	34552605	0.98	-	0	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	exon	34552283	34552605	.	-	.	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
Phchi.S1	AUGUSTUS	start_codon	34552603	34552605	.	-	0	transcript_id "Phchi.S1G538700.t1"; gene_id "Phchi.S1G538700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6764.t1 is derived from g3936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24924279	24927448	.	-	.	Phchi.S1G392300
Phchi.S1	AUGUSTUS	transcript	24924279	24927448	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	stop_codon	24924276	24924278	.	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24924279	24925053	0.77	-	1	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24924279	24925053	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24925054	24925129	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24925130	24925230	0.76	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24925130	24925230	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24925231	24925381	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24925382	24925432	1	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24925382	24925432	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24925433	24925538	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24925539	24925676	0.98	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24925539	24925676	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24925677	24925789	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24925790	24925855	0.99	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24925790	24925855	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24925856	24926099	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24926100	24926180	1	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24926100	24926180	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24926181	24926314	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24926315	24927037	0.84	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24926315	24927037	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24927038	24927258	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24927259	24927263	0.96	-	2	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24927259	24927263	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	intron	24927264	24927381	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	CDS	24927382	24927448	0.93	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	exon	24927382	24927448	.	-	.	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
Phchi.S1	AUGUSTUS	start_codon	24927446	24927448	.	-	0	transcript_id "Phchi.S1G392300.t1"; gene_id "Phchi.S1G392300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8044.t1 is derived from g5219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32650806	32652456	.	-	.	Phchi.S1G520300
Phchi.S1	AUGUSTUS	transcript	32650806	32652456	.	-	.	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	stop_codon	32650803	32650805	.	-	0	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	CDS	32650806	32651240	0.43	-	0	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	exon	32650806	32651240	.	-	.	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	intron	32651241	32651334	.	-	.	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	CDS	32651335	32652456	0.63	-	0	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	exon	32651335	32652456	.	-	.	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
Phchi.S1	AUGUSTUS	start_codon	32652454	32652456	.	-	0	transcript_id "Phchi.S1G520300.t1"; gene_id "Phchi.S1G520300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4821.t1 is derived from g1991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13003849	13004754	.	-	.	Phchi.S1G198000
Phchi.S1	AUGUSTUS	transcript	13003849	13004754	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	stop_codon	13003846	13003848	.	-	0	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	CDS	13003849	13004306	1	-	2	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	exon	13003849	13004306	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	intron	13004307	13004382	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	CDS	13004383	13004415	0.99	-	2	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	exon	13004383	13004415	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	intron	13004416	13004525	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	CDS	13004526	13004636	1	-	2	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	exon	13004526	13004636	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	intron	13004637	13004714	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	CDS	13004715	13004754	0.74	-	0	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	exon	13004715	13004754	.	-	.	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
Phchi.S1	AUGUSTUS	start_codon	13004752	13004754	.	-	0	transcript_id "Phchi.S1G198000.t1"; gene_id "Phchi.S1G198000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12412.t1 is derived from g8089.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18506687	18511890	.	-	.	Phchi.S2G049200
Phchi.S2	AUGUSTUS	transcript	18506687	18511890	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	stop_codon	18506684	18506686	.	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18506687	18506956	0.82	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18506687	18506956	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18506957	18507054	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507055	18507126	0.99	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507055	18507126	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507127	18507227	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507228	18507338	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507228	18507338	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507339	18507486	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507487	18507564	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507487	18507564	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507565	18507705	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507706	18507863	1	-	2	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507706	18507863	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507864	18507962	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507963	18508071	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507963	18508071	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508072	18508269	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508270	18508353	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508270	18508353	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508354	18508515	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508516	18508692	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508516	18508692	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508693	18508785	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508786	18508911	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508786	18508911	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508912	18508991	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508992	18509214	1	-	1	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508992	18509214	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509215	18509381	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509382	18509471	1	-	1	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509382	18509471	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509472	18509610	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509611	18509670	1	-	1	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509611	18509670	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509671	18509762	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509763	18509826	1	-	2	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509763	18509826	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509827	18509917	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509918	18509969	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509918	18509969	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509970	18510056	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18510057	18510113	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18510057	18510113	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18510114	18510202	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18510203	18510335	1	-	1	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18510203	18510335	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18510336	18510572	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18510573	18510901	0.89	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18510573	18510901	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18510902	18511054	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18511055	18511162	1	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18511055	18511162	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18511163	18511258	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18511259	18511529	0.96	-	1	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18511259	18511529	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18511530	18511759	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18511760	18511890	0.54	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18511760	18511890	.	-	.	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	start_codon	18511888	18511890	.	-	0	transcript_id "Phchi.S2G049200.t1"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	transcript	18506687	18511890	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	stop_codon	18506684	18506686	.	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18506687	18506956	0.79	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18506687	18506956	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18506957	18507054	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507055	18507126	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507055	18507126	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507127	18507227	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507228	18507338	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507228	18507338	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507339	18507486	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507487	18507564	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507487	18507564	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507565	18507705	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507706	18507863	1	-	2	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507706	18507863	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18507864	18507962	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18507963	18508071	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18507963	18508071	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508072	18508269	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508270	18508353	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508270	18508353	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508354	18508515	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508516	18508692	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508516	18508692	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508693	18508785	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508786	18508911	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508786	18508911	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18508912	18508991	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18508992	18509214	1	-	1	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18508992	18509214	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509215	18509381	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509382	18509471	1	-	1	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509382	18509471	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509472	18509610	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509611	18509673	1	-	1	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509611	18509673	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509674	18509762	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509763	18509826	1	-	2	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509763	18509826	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509827	18509917	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18509918	18509969	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18509918	18509969	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18509970	18510056	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18510057	18510113	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18510057	18510113	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18510114	18510202	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18510203	18510335	1	-	1	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18510203	18510335	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18510336	18510572	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18510573	18510901	0.85	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18510573	18510901	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18510902	18511054	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18511055	18511162	1	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18511055	18511162	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18511163	18511258	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18511259	18511529	0.92	-	1	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18511259	18511529	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	intron	18511530	18511759	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	CDS	18511760	18511890	0.48	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	exon	18511760	18511890	.	-	.	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
Phchi.S2	AUGUSTUS	start_codon	18511888	18511890	.	-	0	transcript_id "Phchi.S2G049200.t2"; gene_id "Phchi.S2G049200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12442.t1 is derived from g8119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20572384	20572885	.	+	.	Phchi.S2G052200
Phchi.S2	AUGUSTUS	transcript	20572384	20572885	.	+	.	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	start_codon	20572384	20572386	.	+	0	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	CDS	20572384	20572572	0.97	+	0	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	exon	20572384	20572572	.	+	.	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	intron	20572573	20572792	.	+	.	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	CDS	20572793	20572885	0.96	+	0	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	exon	20572793	20572885	.	+	.	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
Phchi.S2	AUGUSTUS	stop_codon	20572886	20572888	.	+	0	transcript_id "Phchi.S2G052200.t1"; gene_id "Phchi.S2G052200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8975.t1 is derived from g6150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38934250	38935689	.	+	.	Phchi.S1G613400
Phchi.S1	AUGUSTUS	transcript	38934250	38935689	.	+	.	transcript_id "Phchi.S1G613400.t1"; gene_id "Phchi.S1G613400"
Phchi.S1	AUGUSTUS	start_codon	38934250	38934252	.	+	0	transcript_id "Phchi.S1G613400.t1"; gene_id "Phchi.S1G613400"
Phchi.S1	AUGUSTUS	CDS	38934250	38935689	1	+	0	transcript_id "Phchi.S1G613400.t1"; gene_id "Phchi.S1G613400"
Phchi.S1	AUGUSTUS	exon	38934250	38935689	.	+	.	transcript_id "Phchi.S1G613400.t1"; gene_id "Phchi.S1G613400"
Phchi.S1	AUGUSTUS	stop_codon	38935690	38935692	.	+	0	transcript_id "Phchi.S1G613400.t1"; gene_id "Phchi.S1G613400"
# This transcript jg9838.t2 is derived from g7014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9839.t1 is derived from g7015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44019189	44020790	.	-	.	Phchi.S1G699800
Phchi.S1	AUGUSTUS	transcript	44019189	44020790	.	-	.	transcript_id "Phchi.S1G699800.t1"; gene_id "Phchi.S1G699800"
Phchi.S1	AUGUSTUS	stop_codon	44019186	44019188	.	-	0	transcript_id "Phchi.S1G699800.t1"; gene_id "Phchi.S1G699800"
Phchi.S1	AUGUSTUS	CDS	44019189	44020790	1	-	0	transcript_id "Phchi.S1G699800.t1"; gene_id "Phchi.S1G699800"
Phchi.S1	AUGUSTUS	exon	44019189	44020790	.	-	.	transcript_id "Phchi.S1G699800.t1"; gene_id "Phchi.S1G699800"
Phchi.S1	AUGUSTUS	start_codon	44020788	44020790	.	-	0	transcript_id "Phchi.S1G699800.t1"; gene_id "Phchi.S1G699800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5140.t1 is derived from g2310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15123556	15128815	.	+	.	Phchi.S1G229900
Phchi.S1	AUGUSTUS	transcript	15123556	15128815	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	start_codon	15123556	15123558	.	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15123556	15124248	0.93	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15123556	15124248	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15124249	15124360	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15124361	15124435	0.96	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15124361	15124435	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15124436	15124546	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15124547	15124770	0.98	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15124547	15124770	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15124771	15124913	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15124914	15125076	1	+	1	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15124914	15125076	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15125077	15125164	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15125165	15125293	1	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15125165	15125293	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15125294	15125379	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15125380	15126212	1	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15125380	15126212	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15126213	15126302	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15126303	15126477	0.6	+	1	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15126303	15126477	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15126478	15126797	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15126798	15126875	0.33	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15126798	15126875	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15126876	15126957	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15126958	15127015	1	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15126958	15127015	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15127016	15127184	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15127185	15127437	0.99	+	2	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15127185	15127437	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15127438	15127583	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15127584	15127924	0.91	+	1	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15127584	15127924	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15127925	15128060	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15128061	15128344	0.97	+	2	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15128061	15128344	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15128345	15128430	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15128431	15128498	1	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15128431	15128498	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15128499	15128594	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15128595	15128656	1	+	1	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15128595	15128656	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	intron	15128657	15128756	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	CDS	15128757	15128815	1	+	2	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	exon	15128757	15128815	.	+	.	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
Phchi.S1	AUGUSTUS	stop_codon	15128816	15128818	.	+	0	transcript_id "Phchi.S1G229900.t1"; gene_id "Phchi.S1G229900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9194.t1 is derived from g6369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40290980	40291945	.	-	.	Phchi.S1G635300
Phchi.S1	AUGUSTUS	transcript	40290980	40291945	.	-	.	transcript_id "Phchi.S1G635300.t1"; gene_id "Phchi.S1G635300"
Phchi.S1	AUGUSTUS	stop_codon	40290977	40290979	.	-	0	transcript_id "Phchi.S1G635300.t1"; gene_id "Phchi.S1G635300"
Phchi.S1	AUGUSTUS	CDS	40290980	40291945	0.45	-	0	transcript_id "Phchi.S1G635300.t1"; gene_id "Phchi.S1G635300"
Phchi.S1	AUGUSTUS	exon	40290980	40291945	.	-	.	transcript_id "Phchi.S1G635300.t1"; gene_id "Phchi.S1G635300"
Phchi.S1	AUGUSTUS	start_codon	40291943	40291945	.	-	0	transcript_id "Phchi.S1G635300.t1"; gene_id "Phchi.S1G635300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6072.t1 is derived from g3243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20738359	20739092	.	+	.	Phchi.S1G323100
Phchi.S1	AUGUSTUS	transcript	20738359	20739092	.	+	.	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	start_codon	20738359	20738361	.	+	0	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	CDS	20738359	20738439	1	+	0	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	exon	20738359	20738439	.	+	.	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	intron	20738440	20738764	.	+	.	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	CDS	20738765	20738896	1	+	0	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	exon	20738765	20738896	.	+	.	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	intron	20738897	20738969	.	+	.	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	CDS	20738970	20739092	1	+	0	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	exon	20738970	20739092	.	+	.	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
Phchi.S1	AUGUSTUS	stop_codon	20739093	20739095	.	+	0	transcript_id "Phchi.S1G323100.t1"; gene_id "Phchi.S1G323100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12613.t1 is derived from g8290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37576495	37577856	.	-	.	Phchi.S2G069300
Phchi.S2	AUGUSTUS	transcript	37576495	37577856	.	-	.	transcript_id "Phchi.S2G069300.t1"; gene_id "Phchi.S2G069300"
Phchi.S2	AUGUSTUS	stop_codon	37576492	37576494	.	-	0	transcript_id "Phchi.S2G069300.t1"; gene_id "Phchi.S2G069300"
Phchi.S2	AUGUSTUS	CDS	37576495	37577856	0.61	-	0	transcript_id "Phchi.S2G069300.t1"; gene_id "Phchi.S2G069300"
Phchi.S2	AUGUSTUS	exon	37576495	37577856	.	-	.	transcript_id "Phchi.S2G069300.t1"; gene_id "Phchi.S2G069300"
Phchi.S2	AUGUSTUS	start_codon	37577854	37577856	.	-	0	transcript_id "Phchi.S2G069300.t1"; gene_id "Phchi.S2G069300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12942.t1 is derived from g11407.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3258038	3259566	.	-	.	Phchi.S3G026100
Phchi.S3	AUGUSTUS	transcript	3258038	3259566	.	-	.	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	stop_codon	3258035	3258037	.	-	0	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	CDS	3258038	3258849	0.72	-	2	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	exon	3258038	3258849	.	-	.	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	intron	3258850	3258980	.	-	.	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	CDS	3258981	3259311	0.44	-	0	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	exon	3258981	3259311	.	-	.	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	intron	3259312	3259398	.	-	.	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	CDS	3259399	3259566	0.44	-	0	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	exon	3259399	3259566	.	-	.	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	start_codon	3259564	3259566	.	-	0	transcript_id "Phchi.S3G026100.t1"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	transcript	3258038	3258376	.	-	.	transcript_id "Phchi.S3G026100.t2"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	stop_codon	3258035	3258037	.	-	0	transcript_id "Phchi.S3G026100.t2"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	CDS	3258038	3258376	0.57	-	0	transcript_id "Phchi.S3G026100.t2"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	exon	3258038	3258376	.	-	.	transcript_id "Phchi.S3G026100.t2"; gene_id "Phchi.S3G026100"
Phchi.S3	AUGUSTUS	start_codon	3258374	3258376	.	-	0	transcript_id "Phchi.S3G026100.t2"; gene_id "Phchi.S3G026100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13466.t1 is derived from g11933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7022743	7024465	.	+	.	Phchi.S3G078500
Phchi.S3	AUGUSTUS	transcript	7022743	7024465	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	start_codon	7022743	7022745	.	+	0	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7022743	7022869	0.6	+	0	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7022743	7022869	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	intron	7022870	7022965	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7022966	7023162	1	+	2	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7022966	7023162	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	intron	7023163	7023284	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7023285	7023358	1	+	0	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7023285	7023358	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	intron	7023359	7023446	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7023447	7023499	1	+	1	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7023447	7023499	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	intron	7023500	7023606	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7023607	7023758	0.97	+	2	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7023607	7023758	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	intron	7023759	7023866	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7023867	7024070	1	+	0	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7023867	7024070	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	intron	7024071	7024216	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	CDS	7024217	7024465	1	+	0	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	exon	7024217	7024465	.	+	.	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
Phchi.S3	AUGUSTUS	stop_codon	7024466	7024468	.	+	0	transcript_id "Phchi.S3G078500.t1"; gene_id "Phchi.S3G078500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12024.t1 is derived from g7699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	619834	620886	.	-	.	Phchi.S2G010400
Phchi.S2	AUGUSTUS	transcript	619834	620886	.	-	.	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	stop_codon	619831	619833	.	-	0	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	CDS	619834	619908	1	-	0	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	exon	619834	619908	.	-	.	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	intron	619909	620004	.	-	.	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	CDS	620005	620886	0.99	-	0	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	exon	620005	620886	.	-	.	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
Phchi.S2	AUGUSTUS	start_codon	620884	620886	.	-	0	transcript_id "Phchi.S2G010400.t1"; gene_id "Phchi.S2G010400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13599.t1 is derived from g12066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7643308	7644452	.	+	.	Phchi.S3G091800
Phchi.S3	AUGUSTUS	transcript	7643308	7644452	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	start_codon	7643308	7643310	.	+	0	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	CDS	7643308	7643416	1	+	0	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	exon	7643308	7643416	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	intron	7643417	7643560	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	CDS	7643561	7643639	1	+	2	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	exon	7643561	7643639	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	intron	7643640	7643847	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	CDS	7643848	7644196	1	+	1	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	exon	7643848	7644196	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	intron	7644197	7644350	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	CDS	7644351	7644452	1	+	0	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	exon	7644351	7644452	.	+	.	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
Phchi.S3	AUGUSTUS	stop_codon	7644453	7644455	.	+	0	transcript_id "Phchi.S3G091800.t1"; gene_id "Phchi.S3G091800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10466.t1 is derived from g14515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	530162	530985	.	+	.	Phchi.S4G004800
Phchi.S4	AUGUSTUS	transcript	530162	530985	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	start_codon	530162	530164	.	+	0	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	CDS	530162	530215	0.66	+	0	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	exon	530162	530215	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	intron	530216	530304	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	CDS	530305	530421	1	+	0	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	exon	530305	530421	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	intron	530422	530509	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	CDS	530510	530580	1	+	0	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	exon	530510	530580	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	intron	530581	530678	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	CDS	530679	530985	0.42	+	1	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	exon	530679	530985	.	+	.	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
Phchi.S4	AUGUSTUS	stop_codon	530986	530988	.	+	0	transcript_id "Phchi.S4G004800.t1"; gene_id "Phchi.S4G004800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15484.t1 is derived from g13953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19433275	19434123	.	+	.	Phchi.S3G280300
Phchi.S3	AUGUSTUS	transcript	19433275	19434123	.	+	.	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	start_codon	19433275	19433277	.	+	0	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	CDS	19433275	19433445	0.48	+	0	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	exon	19433275	19433445	.	+	.	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	intron	19433446	19433878	.	+	.	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	CDS	19433879	19434011	0.73	+	0	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	exon	19433879	19434011	.	+	.	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	intron	19434012	19434103	.	+	.	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	CDS	19434104	19434123	0.73	+	2	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	exon	19434104	19434123	.	+	.	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
Phchi.S3	AUGUSTUS	stop_codon	19434124	19434126	.	+	0	transcript_id "Phchi.S3G280300.t1"; gene_id "Phchi.S3G280300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg848.t1 is derived from g10630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5893347	5894263	.	-	.	Phchi.S6G080700
Phchi.S6	AUGUSTUS	transcript	5893347	5894263	.	-	.	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	stop_codon	5893344	5893346	.	-	0	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	CDS	5893347	5893958	0.69	-	0	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	exon	5893347	5893958	.	-	.	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	intron	5893959	5894056	.	-	.	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	CDS	5894057	5894263	0.67	-	0	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	exon	5894057	5894263	.	-	.	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
Phchi.S6	AUGUSTUS	start_codon	5894261	5894263	.	-	0	transcript_id "Phchi.S6G080700.t1"; gene_id "Phchi.S6G080700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14974.t1 is derived from g13442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15807168	15807524	.	-	.	Phchi.S3G229300
Phchi.S3	AUGUSTUS	transcript	15807168	15807524	.	-	.	transcript_id "Phchi.S3G229300.t1"; gene_id "Phchi.S3G229300"
Phchi.S3	AUGUSTUS	stop_codon	15807165	15807167	.	-	0	transcript_id "Phchi.S3G229300.t1"; gene_id "Phchi.S3G229300"
Phchi.S3	AUGUSTUS	CDS	15807168	15807524	0.93	-	0	transcript_id "Phchi.S3G229300.t1"; gene_id "Phchi.S3G229300"
Phchi.S3	AUGUSTUS	exon	15807168	15807524	.	-	.	transcript_id "Phchi.S3G229300.t1"; gene_id "Phchi.S3G229300"
Phchi.S3	AUGUSTUS	start_codon	15807522	15807524	.	-	0	transcript_id "Phchi.S3G229300.t1"; gene_id "Phchi.S3G229300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12686.t1 is derived from g11151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	225759	227419	.	-	.	Phchi.S3G000500
Phchi.S3	AUGUSTUS	transcript	225759	227419	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	stop_codon	225756	225758	.	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	225759	225811	0.59	-	2	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	225759	225811	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	225812	225898	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	225899	225999	0.57	-	1	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	225899	225999	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226000	226076	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226077	226171	0.66	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226077	226171	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226172	226255	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226256	226375	1	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226256	226375	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226376	226471	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226472	226609	1	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226472	226609	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226610	226749	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226750	226831	1	-	1	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226750	226831	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226832	226931	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226932	227044	1	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226932	227044	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	227045	227147	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	227148	227230	1	-	2	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	227148	227230	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	227231	227403	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	227404	227419	1	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	227404	227419	.	-	.	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	start_codon	227417	227419	.	-	0	transcript_id "Phchi.S3G000500.t1"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	transcript	225759	227419	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	stop_codon	225756	225758	.	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	225759	225811	0.74	-	2	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	225759	225811	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	225812	225898	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	225899	225999	0.66	-	1	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	225899	225999	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226000	226147	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226148	226188	0.59	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226148	226188	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226189	226255	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226256	226375	1	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226256	226375	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226376	226471	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226472	226609	1	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226472	226609	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226610	226749	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226750	226831	1	-	1	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226750	226831	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226832	226931	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226932	227044	1	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226932	227044	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	227045	227147	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	227148	227230	1	-	2	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	227148	227230	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	227231	227403	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	227404	227419	0.99	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	227404	227419	.	-	.	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	start_codon	227417	227419	.	-	0	transcript_id "Phchi.S3G000500.t2"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	transcript	225759	227335	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	stop_codon	225756	225758	.	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	225759	225811	0.56	-	2	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	225759	225811	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	225812	225898	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	225899	225999	0.47	-	1	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	225899	225999	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226000	226076	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226077	226171	0.65	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226077	226171	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226172	226255	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226256	226375	1	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226256	226375	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226376	226471	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226472	226609	1	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226472	226609	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226610	226749	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226750	226831	1	-	1	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226750	226831	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	226832	226931	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	226932	227060	0.99	-	1	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	226932	227060	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	227061	227147	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	227148	227230	0.99	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	227148	227230	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	intron	227231	227320	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	CDS	227321	227335	0.5	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	exon	227321	227335	.	-	.	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
Phchi.S3	AUGUSTUS	start_codon	227333	227335	.	-	0	transcript_id "Phchi.S3G000500.t3"; gene_id "Phchi.S3G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7974.t1 is derived from g5149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32194465	32194842	.	+	.	Phchi.S1G513300
Phchi.S1	AUGUSTUS	transcript	32194465	32194842	.	+	.	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	start_codon	32194465	32194467	.	+	0	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	CDS	32194465	32194590	0.66	+	0	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	exon	32194465	32194590	.	+	.	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	intron	32194591	32194686	.	+	.	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	CDS	32194687	32194842	0.98	+	0	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	exon	32194687	32194842	.	+	.	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
Phchi.S1	AUGUSTUS	stop_codon	32194843	32194845	.	+	0	transcript_id "Phchi.S1G513300.t1"; gene_id "Phchi.S1G513300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14853.t1 is derived from g13321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15071004	15073215	.	+	.	Phchi.S3G217200
Phchi.S3	AUGUSTUS	transcript	15071004	15073215	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	start_codon	15071004	15071006	.	+	0	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	CDS	15071004	15071198	0.71	+	0	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	exon	15071004	15071198	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	intron	15071199	15071271	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	CDS	15071272	15072572	0.7	+	0	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	exon	15071272	15072572	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	intron	15072573	15072853	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	CDS	15072854	15072923	0.7	+	1	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	exon	15072854	15072923	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	intron	15072924	15073062	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	CDS	15073063	15073215	0.72	+	0	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	exon	15073063	15073215	.	+	.	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
Phchi.S3	AUGUSTUS	stop_codon	15073216	15073218	.	+	0	transcript_id "Phchi.S3G217200.t1"; gene_id "Phchi.S3G217200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6941.t1 is derived from g4113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26078147	26078848	.	-	.	Phchi.S1G410000
Phchi.S1	AUGUSTUS	transcript	26078147	26078848	.	-	.	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	stop_codon	26078144	26078146	.	-	0	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	CDS	26078147	26078275	0.99	-	0	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	exon	26078147	26078275	.	-	.	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	intron	26078276	26078363	.	-	.	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	CDS	26078364	26078706	0.98	-	1	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	exon	26078364	26078706	.	-	.	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	intron	26078707	26078786	.	-	.	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	CDS	26078787	26078848	1	-	0	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	exon	26078787	26078848	.	-	.	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
Phchi.S1	AUGUSTUS	start_codon	26078846	26078848	.	-	0	transcript_id "Phchi.S1G410000.t1"; gene_id "Phchi.S1G410000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2445.t1 is derived from g9365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6659891	6660967	.	-	.	Phchi.S5G105400
Phchi.S5	AUGUSTUS	transcript	6659891	6660967	.	-	.	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	stop_codon	6659888	6659890	.	-	0	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	CDS	6659891	6660517	1	-	0	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	exon	6659891	6660517	.	-	.	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	intron	6660518	6660628	.	-	.	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	CDS	6660629	6660967	1	-	0	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	exon	6660629	6660967	.	-	.	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
Phchi.S5	AUGUSTUS	start_codon	6660965	6660967	.	-	0	transcript_id "Phchi.S5G105400.t1"; gene_id "Phchi.S5G105400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13787.t1 is derived from g12254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8891348	8891893	.	-	.	Phchi.S3G110600
Phchi.S3	AUGUSTUS	transcript	8891348	8891893	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	stop_codon	8891345	8891347	.	-	0	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	CDS	8891348	8891473	0.94	-	0	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	exon	8891348	8891473	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	intron	8891474	8891553	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	CDS	8891554	8891630	0.97	-	2	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	exon	8891554	8891630	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	intron	8891631	8891714	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	CDS	8891715	8891793	0.94	-	0	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	exon	8891715	8891793	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	intron	8891794	8891878	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	CDS	8891879	8891893	0.86	-	0	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	exon	8891879	8891893	.	-	.	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
Phchi.S3	AUGUSTUS	start_codon	8891891	8891893	.	-	0	transcript_id "Phchi.S3G110600.t1"; gene_id "Phchi.S3G110600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7973.t1 is derived from g5148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32193367	32194357	.	+	.	Phchi.S1G513200
Phchi.S1	AUGUSTUS	transcript	32193367	32194357	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	start_codon	32193367	32193369	.	+	0	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	CDS	32193367	32193754	0.89	+	0	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	exon	32193367	32193754	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	intron	32193755	32193841	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	CDS	32193842	32193926	1	+	2	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	exon	32193842	32193926	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	intron	32193927	32194046	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	CDS	32194047	32194216	1	+	1	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	exon	32194047	32194216	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	intron	32194217	32194313	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	CDS	32194314	32194357	1	+	2	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	exon	32194314	32194357	.	+	.	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
Phchi.S1	AUGUSTUS	stop_codon	32194358	32194360	.	+	0	transcript_id "Phchi.S1G513200.t1"; gene_id "Phchi.S1G513200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3348.t1 is derived from g517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3056087	3056821	.	+	.	Phchi.S1G050700
Phchi.S1	AUGUSTUS	transcript	3056087	3056821	.	+	.	transcript_id "Phchi.S1G050700.t1"; gene_id "Phchi.S1G050700"
Phchi.S1	AUGUSTUS	start_codon	3056087	3056089	.	+	0	transcript_id "Phchi.S1G050700.t1"; gene_id "Phchi.S1G050700"
Phchi.S1	AUGUSTUS	CDS	3056087	3056821	0.71	+	0	transcript_id "Phchi.S1G050700.t1"; gene_id "Phchi.S1G050700"
Phchi.S1	AUGUSTUS	exon	3056087	3056821	.	+	.	transcript_id "Phchi.S1G050700.t1"; gene_id "Phchi.S1G050700"
Phchi.S1	AUGUSTUS	stop_codon	3056822	3056824	.	+	0	transcript_id "Phchi.S1G050700.t1"; gene_id "Phchi.S1G050700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg406.t1 is derived from g10188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2916917	2922119	.	+	.	Phchi.S6G036500
Phchi.S6	AUGUSTUS	transcript	2916917	2922119	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	start_codon	2916917	2916919	.	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2916917	2916921	0.97	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2916917	2916921	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2916922	2917181	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917182	2917240	0.36	+	1	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917182	2917240	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2917241	2917347	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917348	2917371	0.66	+	2	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917348	2917371	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2917372	2917519	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917520	2917612	0.91	+	2	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917520	2917612	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2917613	2917782	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917783	2918231	0.93	+	2	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917783	2918231	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2918232	2918413	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2918414	2919662	0.29	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2918414	2919662	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2919663	2920092	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920093	2920281	0.55	+	2	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920093	2920281	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2920282	2920428	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920429	2920565	0.72	+	2	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920429	2920565	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2920566	2920725	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920726	2920860	1	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920726	2920860	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2920861	2920960	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920961	2921032	1	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920961	2921032	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2921033	2921124	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2921125	2921319	0.9	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2921125	2921319	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2921320	2921421	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2921422	2921587	0.9	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2921422	2921587	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2921588	2921712	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2921713	2922119	1	+	2	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2921713	2922119	.	+	.	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	stop_codon	2922120	2922122	.	+	0	transcript_id "Phchi.S6G036500.t1"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	transcript	2916917	2922119	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	start_codon	2916917	2916919	.	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2916917	2916921	0.95	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2916917	2916921	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2916922	2917181	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917182	2917240	0.37	+	1	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917182	2917240	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2917241	2917347	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917348	2917371	0.74	+	2	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917348	2917371	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2917372	2917519	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917520	2917612	0.91	+	2	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917520	2917612	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2917613	2917782	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2917783	2918231	0.94	+	2	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2917783	2918231	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2918232	2918413	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2918414	2919662	0.18	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2918414	2919662	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2919663	2920092	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920093	2920281	0.4	+	2	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920093	2920281	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2920282	2920428	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920429	2920565	0.75	+	2	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920429	2920565	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2920566	2920725	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920726	2920752	1	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920726	2920752	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2920753	2920960	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2920961	2921032	0.87	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2920961	2921032	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2921033	2921124	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2921125	2921319	0.87	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2921125	2921319	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2921320	2921421	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2921422	2921587	0.87	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2921422	2921587	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	intron	2921588	2921712	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	CDS	2921713	2922119	1	+	2	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	exon	2921713	2922119	.	+	.	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
Phchi.S6	AUGUSTUS	stop_codon	2922120	2922122	.	+	0	transcript_id "Phchi.S6G036500.t2"; gene_id "Phchi.S6G036500"
# This transcript jg6775.t2 is derived from g3947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6776.t1 is derived from g3948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25024702	25025960	.	+	.	Phchi.S1G393500
Phchi.S1	AUGUSTUS	transcript	25024702	25025960	.	+	.	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	start_codon	25024702	25024704	.	+	0	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	CDS	25024702	25025810	0.82	+	0	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	exon	25024702	25025810	.	+	.	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	intron	25025811	25025959	.	+	.	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	CDS	25025960	25025960	0.76	+	1	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	exon	25025960	25025960	.	+	.	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
Phchi.S1	AUGUSTUS	stop_codon	25025961	25025963	.	+	0	transcript_id "Phchi.S1G393500.t1"; gene_id "Phchi.S1G393500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14668.t1 is derived from g13136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14099752	14107419	.	+	.	Phchi.S3G198700
Phchi.S3	AUGUSTUS	transcript	14099752	14107419	.	+	.	transcript_id "Phchi.S3G198700.t1"; gene_id "Phchi.S3G198700"
Phchi.S3	AUGUSTUS	start_codon	14099752	14099754	.	+	0	transcript_id "Phchi.S3G198700.t1"; gene_id "Phchi.S3G198700"
Phchi.S3	AUGUSTUS	CDS	14099752	14107419	1	+	0	transcript_id "Phchi.S3G198700.t1"; gene_id "Phchi.S3G198700"
Phchi.S3	AUGUSTUS	exon	14099752	14107419	.	+	.	transcript_id "Phchi.S3G198700.t1"; gene_id "Phchi.S3G198700"
Phchi.S3	AUGUSTUS	stop_codon	14107420	14107422	.	+	0	transcript_id "Phchi.S3G198700.t1"; gene_id "Phchi.S3G198700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11819.t1 is derived from g15871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8391455	8392801	.	+	.	Phchi.S4G140100
Phchi.S4	AUGUSTUS	transcript	8391455	8392801	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	start_codon	8391455	8391457	.	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	CDS	8391455	8391664	0.85	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	exon	8391455	8391664	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	intron	8391665	8391738	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	CDS	8391739	8391873	0.99	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	exon	8391739	8391873	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	intron	8391874	8391974	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	CDS	8391975	8392265	0.86	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	exon	8391975	8392265	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	intron	8392266	8392355	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	CDS	8392356	8392562	1	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	exon	8392356	8392562	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	intron	8392563	8392777	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	CDS	8392778	8392801	1	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	exon	8392778	8392801	.	+	.	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
Phchi.S4	AUGUSTUS	stop_codon	8392802	8392804	.	+	0	transcript_id "Phchi.S4G140100.t1"; gene_id "Phchi.S4G140100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7810.t1 is derived from g4984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31300072	31301722	.	-	.	Phchi.S1G496900
Phchi.S1	AUGUSTUS	transcript	31300072	31301722	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	stop_codon	31300069	31300071	.	-	0	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	CDS	31300072	31300080	0.98	-	0	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	exon	31300072	31300080	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	intron	31300081	31300543	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	CDS	31300544	31300757	0.98	-	1	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	exon	31300544	31300757	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	intron	31300758	31301038	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	CDS	31301039	31301143	1	-	1	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	exon	31301039	31301143	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	intron	31301144	31301292	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	CDS	31301293	31301414	1	-	0	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	exon	31301293	31301414	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	intron	31301415	31301512	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	CDS	31301513	31301722	0.26	-	0	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	exon	31301513	31301722	.	-	.	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
Phchi.S1	AUGUSTUS	start_codon	31301720	31301722	.	-	0	transcript_id "Phchi.S1G496900.t1"; gene_id "Phchi.S1G496900"
# This transcript jg15850.t2 is derived from g14320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15851.t1 is derived from g14321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21815324	21818915	.	+	.	Phchi.S3G317000
Phchi.S3	AUGUSTUS	transcript	21815324	21818915	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	start_codon	21815324	21815326	.	+	0	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21815324	21815532	0.74	+	0	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21815324	21815532	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21815533	21815631	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21815632	21815810	0.64	+	1	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21815632	21815810	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21815811	21816074	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21816075	21816344	0.2	+	2	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21816075	21816344	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21816345	21816512	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21816513	21817331	0.22	+	2	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21816513	21817331	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21817332	21817541	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21817542	21817707	0.24	+	2	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21817542	21817707	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21817708	21818214	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21818215	21818344	0.99	+	1	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21818215	21818344	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21818345	21818587	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21818588	21818692	1	+	0	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21818588	21818692	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	intron	21818693	21818840	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	CDS	21818841	21818915	1	+	0	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	exon	21818841	21818915	.	+	.	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
Phchi.S3	AUGUSTUS	stop_codon	21818916	21818918	.	+	0	transcript_id "Phchi.S3G317000.t1"; gene_id "Phchi.S3G317000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6768.t1 is derived from g3940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24978284	24981573	.	-	.	Phchi.S1G392700
Phchi.S1	AUGUSTUS	transcript	24978284	24981573	.	-	.	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	stop_codon	24978281	24978283	.	-	0	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	CDS	24978284	24979758	0.99	-	2	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	exon	24978284	24979758	.	-	.	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	intron	24979759	24979901	.	-	.	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	CDS	24979902	24980193	1	-	0	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	exon	24979902	24980193	.	-	.	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	intron	24980194	24980361	.	-	.	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	CDS	24980362	24981573	0.42	-	0	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	exon	24980362	24981573	.	-	.	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
Phchi.S1	AUGUSTUS	start_codon	24981571	24981573	.	-	0	transcript_id "Phchi.S1G392700.t1"; gene_id "Phchi.S1G392700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9891.t1 is derived from g7067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44300222	44303212	.	-	.	Phchi.S1G705000
Phchi.S1	AUGUSTUS	transcript	44300222	44303212	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	stop_codon	44300219	44300221	.	-	0	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44300222	44300589	1	-	2	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44300222	44300589	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44300590	44300702	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44300703	44300803	1	-	1	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44300703	44300803	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44300804	44300911	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44300912	44301053	0.99	-	2	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44300912	44301053	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44301054	44301172	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44301173	44301282	0.97	-	1	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44301173	44301282	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44301283	44301441	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44301442	44301514	1	-	2	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44301442	44301514	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44301515	44301614	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44301615	44301711	1	-	0	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44301615	44301711	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44301712	44301850	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44301851	44302116	0.96	-	2	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44301851	44302116	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44302117	44302262	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44302263	44302366	1	-	1	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44302263	44302366	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44302367	44302545	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44302546	44302621	1	-	2	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44302546	44302621	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44302622	44302711	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44302712	44302738	1	-	2	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44302712	44302738	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44302739	44302896	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44302897	44303008	1	-	0	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44302897	44303008	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	intron	44303009	44303098	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	CDS	44303099	44303212	1	-	0	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	exon	44303099	44303212	.	-	.	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
Phchi.S1	AUGUSTUS	start_codon	44303210	44303212	.	-	0	transcript_id "Phchi.S1G705000.t1"; gene_id "Phchi.S1G705000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3591.t1 is derived from g761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4647678	4648519	.	+	.	Phchi.S1G075100
Phchi.S1	AUGUSTUS	transcript	4647678	4648519	.	+	.	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	start_codon	4647678	4647680	.	+	0	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	CDS	4647678	4647726	0.7	+	0	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	exon	4647678	4647726	.	+	.	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	intron	4647727	4647794	.	+	.	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	CDS	4647795	4648519	0.67	+	2	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	exon	4647795	4648519	.	+	.	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
Phchi.S1	AUGUSTUS	stop_codon	4648520	4648522	.	+	0	transcript_id "Phchi.S1G075100.t1"; gene_id "Phchi.S1G075100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1927.t1 is derived from g8847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3876982	3878887	.	-	.	Phchi.S5G053600
Phchi.S5	AUGUSTUS	transcript	3876982	3878887	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	stop_codon	3876979	3876981	.	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3876982	3877190	0.99	-	2	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3876982	3877190	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3877191	3877319	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3877320	3877419	1	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3877320	3877419	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3877420	3877496	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3877497	3877599	1	-	1	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3877497	3877599	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3877600	3877721	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3877722	3877856	1	-	1	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3877722	3877856	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3877857	3878171	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3878172	3878199	0.99	-	2	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3878172	3878199	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3878200	3878309	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3878310	3878322	1	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3878310	3878322	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3878323	3878410	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3878411	3878467	1	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3878411	3878467	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3878468	3878601	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3878602	3878676	1	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3878602	3878676	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	intron	3878677	3878812	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	CDS	3878813	3878887	1	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	exon	3878813	3878887	.	-	.	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
Phchi.S5	AUGUSTUS	start_codon	3878885	3878887	.	-	0	transcript_id "Phchi.S5G053600.t1"; gene_id "Phchi.S5G053600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12841.t1 is derived from g11306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2649340	2652345	.	+	.	Phchi.S3G016000
Phchi.S3	AUGUSTUS	transcript	2649340	2652345	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	start_codon	2649340	2649342	.	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2649340	2649513	0.81	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2649340	2649513	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2649514	2649620	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2649621	2649676	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2649621	2649676	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2649677	2649775	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2649776	2649828	1	+	1	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2649776	2649828	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2649829	2649982	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2649983	2650109	1	+	2	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2649983	2650109	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2650110	2650304	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2650305	2650416	1	+	1	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2650305	2650416	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2650417	2650505	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2650506	2650576	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2650506	2650576	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2650577	2650741	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2650742	2650811	1	+	1	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2650742	2650811	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2650812	2650904	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2650905	2650967	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2650905	2650967	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2650968	2651088	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2651089	2651160	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2651089	2651160	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2651161	2651334	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2651335	2651448	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2651335	2651448	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2651449	2651528	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2651529	2651603	0.98	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2651529	2651603	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2651604	2651713	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2651714	2651833	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2651714	2651833	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2651834	2651932	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2651933	2652049	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2651933	2652049	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2652050	2652131	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2652132	2652188	1	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2652132	2652188	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	intron	2652189	2652282	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	CDS	2652283	2652345	0.56	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	exon	2652283	2652345	.	+	.	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
Phchi.S3	AUGUSTUS	stop_codon	2652346	2652348	.	+	0	transcript_id "Phchi.S3G016000.t1"; gene_id "Phchi.S3G016000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14481.t1 is derived from g12949.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13058159	13060097	.	-	.	Phchi.S3G180000
Phchi.S3	AUGUSTUS	transcript	13058159	13060097	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	stop_codon	13058156	13058158	.	-	0	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	CDS	13058159	13058629	0.99	-	0	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	exon	13058159	13058629	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	intron	13058630	13058767	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	CDS	13058768	13058914	1	-	0	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	exon	13058768	13058914	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	intron	13058915	13059052	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	CDS	13059053	13059158	1	-	1	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	exon	13059053	13059158	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	intron	13059159	13059381	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	CDS	13059382	13059420	0.56	-	1	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	exon	13059382	13059420	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	intron	13059421	13059512	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	CDS	13059513	13059660	1	-	2	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	exon	13059513	13059660	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	intron	13059661	13059862	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	CDS	13059863	13060097	1	-	0	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	exon	13059863	13060097	.	-	.	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
Phchi.S3	AUGUSTUS	start_codon	13060095	13060097	.	-	0	transcript_id "Phchi.S3G180000.t1"; gene_id "Phchi.S3G180000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5397.t1 is derived from g2567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16677623	16681406	.	+	.	Phchi.S1G255600
Phchi.S1	AUGUSTUS	transcript	16677623	16681406	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	start_codon	16677623	16677625	.	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16677623	16677637	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16677623	16677637	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16677638	16677811	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16677812	16677988	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16677812	16677988	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16677989	16678135	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16678136	16678223	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16678136	16678223	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16678224	16678311	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16678312	16678419	1	+	2	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16678312	16678419	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16678420	16678505	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16678506	16678590	1	+	2	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16678506	16678590	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16678591	16678724	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16678725	16678779	1	+	1	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16678725	16678779	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16678780	16678857	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16678858	16679247	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16678858	16679247	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16679248	16679512	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16679513	16679593	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16679513	16679593	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16679594	16679762	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16679763	16679822	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16679763	16679822	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16679823	16679912	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16679913	16680011	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16679913	16680011	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16680012	16680127	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16680128	16680238	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16680128	16680238	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16680239	16680322	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16680323	16680394	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16680323	16680394	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16680395	16680474	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16680475	16680591	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16680475	16680591	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16680592	16680685	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16680686	16680835	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16680686	16680835	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16680836	16680923	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16680924	16681024	1	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16680924	16681024	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	intron	16681025	16681105	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	CDS	16681106	16681406	1	+	1	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	exon	16681106	16681406	.	+	.	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
Phchi.S1	AUGUSTUS	stop_codon	16681407	16681409	.	+	0	transcript_id "Phchi.S1G255600.t1"; gene_id "Phchi.S1G255600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5986.t1 is derived from g3157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20267107	20267448	.	+	.	Phchi.S1G314500
Phchi.S1	AUGUSTUS	transcript	20267107	20267448	.	+	.	transcript_id "Phchi.S1G314500.t1"; gene_id "Phchi.S1G314500"
Phchi.S1	AUGUSTUS	start_codon	20267107	20267109	.	+	0	transcript_id "Phchi.S1G314500.t1"; gene_id "Phchi.S1G314500"
Phchi.S1	AUGUSTUS	CDS	20267107	20267448	0.93	+	0	transcript_id "Phchi.S1G314500.t1"; gene_id "Phchi.S1G314500"
Phchi.S1	AUGUSTUS	exon	20267107	20267448	.	+	.	transcript_id "Phchi.S1G314500.t1"; gene_id "Phchi.S1G314500"
Phchi.S1	AUGUSTUS	stop_codon	20267449	20267451	.	+	0	transcript_id "Phchi.S1G314500.t1"; gene_id "Phchi.S1G314500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15249.t1 is derived from g13717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17898884	17899598	.	-	.	Phchi.S3G256800
Phchi.S3	AUGUSTUS	transcript	17898884	17899598	.	-	.	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	stop_codon	17898881	17898883	.	-	0	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	CDS	17898884	17899062	1	-	2	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	exon	17898884	17899062	.	-	.	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	intron	17899063	17899147	.	-	.	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	CDS	17899148	17899598	0.7	-	0	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	exon	17899148	17899598	.	-	.	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
Phchi.S3	AUGUSTUS	start_codon	17899596	17899598	.	-	0	transcript_id "Phchi.S3G256800.t1"; gene_id "Phchi.S3G256800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2521.t1 is derived from g9441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7119803	7122025	.	+	.	Phchi.S5G113000
Phchi.S5	AUGUSTUS	transcript	7119803	7122025	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	start_codon	7119803	7119805	.	+	0	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	CDS	7119803	7120103	0.76	+	0	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	exon	7119803	7120103	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	intron	7120104	7120197	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	CDS	7120198	7120915	1	+	2	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	exon	7120198	7120915	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	intron	7120916	7121032	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	CDS	7121033	7121399	0.95	+	1	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	exon	7121033	7121399	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	intron	7121400	7121568	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	CDS	7121569	7121611	0.48	+	0	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	exon	7121569	7121611	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	intron	7121612	7121729	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	CDS	7121730	7121844	0.96	+	2	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	exon	7121730	7121844	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	intron	7121845	7121931	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	CDS	7121932	7122025	0.96	+	1	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	exon	7121932	7122025	.	+	.	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
Phchi.S5	AUGUSTUS	stop_codon	7122026	7122028	.	+	0	transcript_id "Phchi.S5G113000.t1"; gene_id "Phchi.S5G113000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8746.t1 is derived from g5921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37776118	37777063	.	+	.	Phchi.S1G590500
Phchi.S1	AUGUSTUS	transcript	37776118	37777063	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	start_codon	37776118	37776120	.	+	0	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	CDS	37776118	37776195	0.84	+	0	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	exon	37776118	37776195	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	intron	37776196	37776281	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	CDS	37776282	37776373	0.83	+	0	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	exon	37776282	37776373	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	intron	37776374	37776488	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	CDS	37776489	37776601	0.42	+	1	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	exon	37776489	37776601	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	intron	37776602	37776711	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	CDS	37776712	37776901	0.36	+	2	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	exon	37776712	37776901	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	intron	37776902	37777023	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	CDS	37777024	37777063	0.79	+	1	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	exon	37777024	37777063	.	+	.	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
Phchi.S1	AUGUSTUS	stop_codon	37777064	37777066	.	+	0	transcript_id "Phchi.S1G590500.t1"; gene_id "Phchi.S1G590500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15552.t1 is derived from g14021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19886763	19889013	.	-	.	Phchi.S3G287100
Phchi.S3	AUGUSTUS	transcript	19886763	19889013	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	stop_codon	19886760	19886762	.	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19886763	19886818	0.99	-	2	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19886763	19886818	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19886819	19886901	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19886902	19886947	0.99	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19886902	19886947	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19886948	19887058	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19887059	19887133	1	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19887059	19887133	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19887134	19887213	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19887214	19887283	1	-	1	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19887214	19887283	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19887284	19887400	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19887401	19887499	1	-	1	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19887401	19887499	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19887500	19887629	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19887630	19887766	0.82	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19887630	19887766	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19887767	19887873	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19887874	19888055	0.88	-	2	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19887874	19888055	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19888056	19888170	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19888171	19888339	0.96	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19888171	19888339	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19888340	19888438	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19888439	19888471	1	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19888439	19888471	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19888472	19888645	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19888646	19888756	1	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19888646	19888756	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	intron	19888757	19888929	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	CDS	19888930	19889013	0.99	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	exon	19888930	19889013	.	-	.	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
Phchi.S3	AUGUSTUS	start_codon	19889011	19889013	.	-	0	transcript_id "Phchi.S3G287100.t1"; gene_id "Phchi.S3G287100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6220.t1 is derived from g3392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21508570	21509349	.	+	.	Phchi.S1G337900
Phchi.S1	AUGUSTUS	transcript	21508570	21509349	.	+	.	transcript_id "Phchi.S1G337900.t1"; gene_id "Phchi.S1G337900"
Phchi.S1	AUGUSTUS	start_codon	21508570	21508572	.	+	0	transcript_id "Phchi.S1G337900.t1"; gene_id "Phchi.S1G337900"
Phchi.S1	AUGUSTUS	CDS	21508570	21509349	0.98	+	0	transcript_id "Phchi.S1G337900.t1"; gene_id "Phchi.S1G337900"
Phchi.S1	AUGUSTUS	exon	21508570	21509349	.	+	.	transcript_id "Phchi.S1G337900.t1"; gene_id "Phchi.S1G337900"
Phchi.S1	AUGUSTUS	stop_codon	21509350	21509352	.	+	0	transcript_id "Phchi.S1G337900.t1"; gene_id "Phchi.S1G337900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5219.t1 is derived from g2389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15547581	15551618	.	-	.	Phchi.S1G237800
Phchi.S1	AUGUSTUS	transcript	15547581	15551618	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	stop_codon	15547578	15547580	.	-	0	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	CDS	15547581	15547892	0.99	-	0	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	exon	15547581	15547892	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	intron	15547893	15547979	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	CDS	15547980	15549397	1	-	2	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	exon	15547980	15549397	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	intron	15549398	15549714	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	CDS	15549715	15549931	1	-	0	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	exon	15549715	15549931	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	intron	15549932	15550047	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	CDS	15550048	15550151	1	-	2	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	exon	15550048	15550151	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	intron	15550152	15550251	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	CDS	15550252	15551320	1	-	0	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	exon	15550252	15551320	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	intron	15551321	15551414	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	CDS	15551415	15551618	1	-	0	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	exon	15551415	15551618	.	-	.	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
Phchi.S1	AUGUSTUS	start_codon	15551616	15551618	.	-	0	transcript_id "Phchi.S1G237800.t1"; gene_id "Phchi.S1G237800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg137.t1 is derived from g9919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	761952	764383	.	+	.	Phchi.S6G009600
Phchi.S6	AUGUSTUS	transcript	761952	764383	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	start_codon	761952	761954	.	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	761952	762251	1	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	761952	762251	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	762252	762472	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	762473	762571	1	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	762473	762571	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	762572	762652	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	762653	762905	0.99	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	762653	762905	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	762906	763010	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	763011	763121	0.85	+	2	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	763011	763121	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	763122	763222	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	763223	763359	0.84	+	2	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	763223	763359	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	763360	763498	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	763499	763612	1	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	763499	763612	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	763613	763699	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	763700	763896	1	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	763700	763896	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	763897	763990	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	763991	764143	1	+	1	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	763991	764143	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	intron	764144	764232	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	CDS	764233	764383	0.76	+	1	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	exon	764233	764383	.	+	.	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
Phchi.S6	AUGUSTUS	stop_codon	764384	764386	.	+	0	transcript_id "Phchi.S6G009600.t1"; gene_id "Phchi.S6G009600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11634.t1 is derived from g15685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7404185	7407158	.	-	.	Phchi.S4G121600
Phchi.S4	AUGUSTUS	transcript	7404185	7407158	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	stop_codon	7404182	7404184	.	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7404185	7404265	0.99	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7404185	7404265	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7404266	7404396	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7404397	7404565	1	-	1	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7404397	7404565	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7404566	7404657	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7404658	7404913	1	-	2	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7404658	7404913	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7404914	7405055	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7405056	7405170	1	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7405056	7405170	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7405171	7405295	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7405296	7405546	0.96	-	2	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7405296	7405546	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7405547	7405692	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7405693	7406053	1	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7405693	7406053	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7406054	7406148	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7406149	7406316	1	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7406149	7406316	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7406317	7406528	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7406529	7406674	1	-	2	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7406529	7406674	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7406675	7406803	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7406804	7406933	1	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7406804	7406933	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	intron	7406934	7407053	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	CDS	7407054	7407158	1	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	exon	7407054	7407158	.	-	.	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
Phchi.S4	AUGUSTUS	start_codon	7407156	7407158	.	-	0	transcript_id "Phchi.S4G121600.t1"; gene_id "Phchi.S4G121600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3650.t1 is derived from g819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4967135	4968842	.	-	.	Phchi.S1G080900
Phchi.S1	AUGUSTUS	transcript	4967135	4968842	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	stop_codon	4967132	4967134	.	-	0	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	CDS	4967135	4967149	1	-	0	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	exon	4967135	4967149	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	intron	4967150	4967532	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	CDS	4967533	4968051	1	-	0	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	exon	4967533	4968051	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	intron	4968052	4968152	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	CDS	4968153	4968262	0.97	-	2	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	exon	4968153	4968262	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	intron	4968263	4968340	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	CDS	4968341	4968438	1	-	1	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	exon	4968341	4968438	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	intron	4968439	4968810	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	CDS	4968811	4968842	0.99	-	0	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	exon	4968811	4968842	.	-	.	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
Phchi.S1	AUGUSTUS	start_codon	4968840	4968842	.	-	0	transcript_id "Phchi.S1G080900.t1"; gene_id "Phchi.S1G080900"
# This transcript jg855.t2 is derived from g10637.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg856.t1 is derived from g10638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5953882	5955366	.	+	.	Phchi.S6G081500
Phchi.S6	AUGUSTUS	transcript	5953882	5955366	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	start_codon	5953882	5953884	.	+	0	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5953882	5954281	1	+	0	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5953882	5954281	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	intron	5954282	5954379	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5954380	5954477	1	+	2	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5954380	5954477	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	intron	5954478	5954587	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5954588	5954638	1	+	0	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5954588	5954638	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	intron	5954639	5954731	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5954732	5954762	0.9	+	0	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5954732	5954762	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	intron	5954763	5954951	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5954952	5955007	0.97	+	2	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5954952	5955007	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	intron	5955008	5955081	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5955082	5955170	1	+	0	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5955082	5955170	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	intron	5955171	5955257	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	CDS	5955258	5955366	1	+	1	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	exon	5955258	5955366	.	+	.	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
Phchi.S6	AUGUSTUS	stop_codon	5955367	5955369	.	+	0	transcript_id "Phchi.S6G081500.t1"; gene_id "Phchi.S6G081500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14112.t1 is derived from g12579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10900768	10901170	.	+	.	Phchi.S3G143100
Phchi.S3	AUGUSTUS	transcript	10900768	10901170	.	+	.	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	start_codon	10900768	10900770	.	+	0	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	CDS	10900768	10901059	0.77	+	0	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	exon	10900768	10901059	.	+	.	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	intron	10901060	10901129	.	+	.	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	CDS	10901130	10901170	0.99	+	2	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	exon	10901130	10901170	.	+	.	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
Phchi.S3	AUGUSTUS	stop_codon	10901171	10901173	.	+	0	transcript_id "Phchi.S3G143100.t1"; gene_id "Phchi.S3G143100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11021.t1 is derived from g15071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3666968	3667839	.	-	.	Phchi.S4G060300
Phchi.S4	AUGUSTUS	transcript	3666968	3667839	.	-	.	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	stop_codon	3666965	3666967	.	-	0	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	CDS	3666968	3667273	0.75	-	0	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	exon	3666968	3667273	.	-	.	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	intron	3667274	3667392	.	-	.	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	CDS	3667393	3667667	0.52	-	2	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	exon	3667393	3667667	.	-	.	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	intron	3667668	3667760	.	-	.	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	CDS	3667761	3667839	1	-	0	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	exon	3667761	3667839	.	-	.	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
Phchi.S4	AUGUSTUS	start_codon	3667837	3667839	.	-	0	transcript_id "Phchi.S4G060300.t1"; gene_id "Phchi.S4G060300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg495.t1 is derived from g10277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3440908	3444914	.	-	.	Phchi.S6G045400
Phchi.S6	AUGUSTUS	transcript	3440908	3444914	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	stop_codon	3440905	3440907	.	-	0	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	CDS	3440908	3442905	0.79	-	0	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	exon	3440908	3442905	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	intron	3442906	3443036	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	CDS	3443037	3443317	0.72	-	2	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	exon	3443037	3443317	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	intron	3443318	3443485	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	CDS	3443486	3444264	0.39	-	1	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	exon	3443486	3444264	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	intron	3444265	3444387	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	CDS	3444388	3444495	0.75	-	1	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	exon	3444388	3444495	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	intron	3444496	3444602	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	CDS	3444603	3444684	1	-	2	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	exon	3444603	3444684	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	intron	3444685	3444775	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	CDS	3444776	3444914	1	-	0	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	exon	3444776	3444914	.	-	.	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
Phchi.S6	AUGUSTUS	start_codon	3444912	3444914	.	-	0	transcript_id "Phchi.S6G045400.t1"; gene_id "Phchi.S6G045400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15754.t1 is derived from g14224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21077535	21078499	.	+	.	Phchi.S3G307300
Phchi.S3	AUGUSTUS	transcript	21077535	21078499	.	+	.	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	start_codon	21077535	21077537	.	+	0	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	CDS	21077535	21077857	0.53	+	0	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	exon	21077535	21077857	.	+	.	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	intron	21077858	21077980	.	+	.	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	CDS	21077981	21078190	0.95	+	1	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	exon	21077981	21078190	.	+	.	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	intron	21078191	21078423	.	+	.	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	CDS	21078424	21078499	1	+	1	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	exon	21078424	21078499	.	+	.	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
Phchi.S3	AUGUSTUS	stop_codon	21078500	21078502	.	+	0	transcript_id "Phchi.S3G307300.t1"; gene_id "Phchi.S3G307300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7294.t1 is derived from g4466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28368904	28371047	.	-	.	Phchi.S1G445300
Phchi.S1	AUGUSTUS	transcript	28368904	28371047	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	stop_codon	28368901	28368903	.	-	0	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	CDS	28368904	28369204	1	-	1	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	exon	28368904	28369204	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	intron	28369205	28369316	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	CDS	28369317	28369707	1	-	2	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	exon	28369317	28369707	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	intron	28369708	28369805	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	CDS	28369806	28370532	1	-	0	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	exon	28369806	28370532	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	intron	28370533	28370639	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	CDS	28370640	28371047	0.99	-	0	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	exon	28370640	28371047	.	-	.	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
Phchi.S1	AUGUSTUS	start_codon	28371045	28371047	.	-	0	transcript_id "Phchi.S1G445300.t1"; gene_id "Phchi.S1G445300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13740.t1 is derived from g12207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8663973	8664473	.	-	.	Phchi.S3G105900
Phchi.S3	AUGUSTUS	transcript	8663973	8664473	.	-	.	transcript_id "Phchi.S3G105900.t1"; gene_id "Phchi.S3G105900"
Phchi.S3	AUGUSTUS	stop_codon	8663970	8663972	.	-	0	transcript_id "Phchi.S3G105900.t1"; gene_id "Phchi.S3G105900"
Phchi.S3	AUGUSTUS	CDS	8663973	8664473	0.54	-	0	transcript_id "Phchi.S3G105900.t1"; gene_id "Phchi.S3G105900"
Phchi.S3	AUGUSTUS	exon	8663973	8664473	.	-	.	transcript_id "Phchi.S3G105900.t1"; gene_id "Phchi.S3G105900"
Phchi.S3	AUGUSTUS	start_codon	8664471	8664473	.	-	0	transcript_id "Phchi.S3G105900.t1"; gene_id "Phchi.S3G105900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11702.t1 is derived from g15753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7765137	7766103	.	-	.	Phchi.S4G128400
Phchi.S4	AUGUSTUS	transcript	7765137	7766103	.	-	.	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	stop_codon	7765134	7765136	.	-	0	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	CDS	7765137	7765215	1	-	1	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	exon	7765137	7765215	.	-	.	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	intron	7765216	7765876	.	-	.	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	CDS	7765877	7766103	0.89	-	0	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	exon	7765877	7766103	.	-	.	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
Phchi.S4	AUGUSTUS	start_codon	7766101	7766103	.	-	0	transcript_id "Phchi.S4G128400.t1"; gene_id "Phchi.S4G128400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14808.t1 is derived from g13276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14807827	14808962	.	-	.	Phchi.S3G212700
Phchi.S3	AUGUSTUS	transcript	14807827	14808962	.	-	.	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	stop_codon	14807824	14807826	.	-	0	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	CDS	14807827	14808283	0.6	-	1	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	exon	14807827	14808283	.	-	.	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	intron	14808284	14808567	.	-	.	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	CDS	14808568	14808962	0.34	-	0	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	exon	14808568	14808962	.	-	.	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
Phchi.S3	AUGUSTUS	start_codon	14808960	14808962	.	-	0	transcript_id "Phchi.S3G212700.t1"; gene_id "Phchi.S3G212700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3269.t1 is derived from g438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2632670	2636026	.	+	.	Phchi.S1G042800
Phchi.S1	AUGUSTUS	transcript	2632670	2636026	.	+	.	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	start_codon	2632670	2632672	.	+	0	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	CDS	2632670	2634337	0.77	+	0	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	exon	2632670	2634337	.	+	.	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	intron	2634338	2634442	.	+	.	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	CDS	2634443	2635134	1	+	0	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	exon	2634443	2635134	.	+	.	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	intron	2635135	2635995	.	+	.	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	CDS	2635996	2636026	1	+	1	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	exon	2635996	2636026	.	+	.	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
Phchi.S1	AUGUSTUS	stop_codon	2636027	2636029	.	+	0	transcript_id "Phchi.S1G042800.t1"; gene_id "Phchi.S1G042800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10828.t1 is derived from g14878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2317412	2318603	.	+	.	Phchi.S4G041000
Phchi.S4	AUGUSTUS	transcript	2317412	2318603	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	start_codon	2317412	2317414	.	+	0	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	CDS	2317412	2317431	0.81	+	0	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	exon	2317412	2317431	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	intron	2317432	2317516	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	CDS	2317517	2317775	0.88	+	1	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	exon	2317517	2317775	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	intron	2317776	2317877	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	CDS	2317878	2318051	0.72	+	0	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	exon	2317878	2318051	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	intron	2318052	2318173	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	CDS	2318174	2318268	0.58	+	0	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	exon	2318174	2318268	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	intron	2318269	2318383	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	CDS	2318384	2318603	0.2	+	1	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	exon	2318384	2318603	.	+	.	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
Phchi.S4	AUGUSTUS	stop_codon	2318604	2318606	.	+	0	transcript_id "Phchi.S4G041000.t1"; gene_id "Phchi.S4G041000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11668.t1 is derived from g15719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7590621	7592512	.	-	.	Phchi.S4G125000
Phchi.S4	AUGUSTUS	transcript	7590621	7592512	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	stop_codon	7590618	7590620	.	-	0	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	CDS	7590621	7590860	0.97	-	0	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	exon	7590621	7590860	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	intron	7590861	7590976	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	CDS	7590977	7591056	0.97	-	2	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	exon	7590977	7591056	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	intron	7591057	7591175	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	CDS	7591176	7591422	0.76	-	0	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	exon	7591176	7591422	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	intron	7591423	7591549	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	CDS	7591550	7591671	1	-	2	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	exon	7591550	7591671	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	intron	7591672	7591893	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	CDS	7591894	7591951	1	-	0	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	exon	7591894	7591951	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	intron	7591952	7592188	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	CDS	7592189	7592512	0.42	-	0	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	exon	7592189	7592512	.	-	.	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
Phchi.S4	AUGUSTUS	start_codon	7592510	7592512	.	-	0	transcript_id "Phchi.S4G125000.t1"; gene_id "Phchi.S4G125000"
# This transcript jg7373.t2 is derived from g4545.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7374.t1 is derived from g4546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28819827	28820834	.	-	.	Phchi.S1G453300
Phchi.S1	AUGUSTUS	transcript	28819827	28820834	.	-	.	transcript_id "Phchi.S1G453300.t1"; gene_id "Phchi.S1G453300"
Phchi.S1	AUGUSTUS	stop_codon	28819824	28819826	.	-	0	transcript_id "Phchi.S1G453300.t1"; gene_id "Phchi.S1G453300"
Phchi.S1	AUGUSTUS	CDS	28819827	28820834	0.97	-	0	transcript_id "Phchi.S1G453300.t1"; gene_id "Phchi.S1G453300"
Phchi.S1	AUGUSTUS	exon	28819827	28820834	.	-	.	transcript_id "Phchi.S1G453300.t1"; gene_id "Phchi.S1G453300"
Phchi.S1	AUGUSTUS	start_codon	28820832	28820834	.	-	0	transcript_id "Phchi.S1G453300.t1"; gene_id "Phchi.S1G453300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1243.t1 is derived from g11026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8601702	8604579	.	-	.	Phchi.S6G120200
Phchi.S6	AUGUSTUS	transcript	8601702	8604579	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	stop_codon	8601699	8601701	.	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8601702	8601800	1	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8601702	8601800	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8601801	8601884	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8601885	8601950	1	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8601885	8601950	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8601951	8602051	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8602052	8602152	0.98	-	2	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8602052	8602152	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8602153	8602310	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8602311	8602371	1	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8602311	8602371	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8602372	8602463	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8602464	8602547	1	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8602464	8602547	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8602548	8602688	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8602689	8602725	1	-	1	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8602689	8602725	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8602726	8602800	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8602801	8602875	1	-	1	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8602801	8602875	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8602876	8602987	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8602988	8603078	1	-	2	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8602988	8603078	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8603079	8603790	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8603791	8604002	0.59	-	1	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8603791	8604002	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8604003	8604155	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8604156	8604229	0.79	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8604156	8604229	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8604230	8604373	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8604374	8604479	0.78	-	1	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8604374	8604479	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	intron	8604480	8604559	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	CDS	8604560	8604579	0.57	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	exon	8604560	8604579	.	-	.	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
Phchi.S6	AUGUSTUS	start_codon	8604577	8604579	.	-	0	transcript_id "Phchi.S6G120200.t1"; gene_id "Phchi.S6G120200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15961.t1 is derived from g11144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	45614	46530	.	+	.	Phchi.C91G000800
Phchi.C91	AUGUSTUS	transcript	45614	46530	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	start_codon	45614	45616	.	+	0	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	CDS	45614	45827	0.29	+	0	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	exon	45614	45827	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	intron	45828	45922	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	CDS	45923	45985	0.59	+	2	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	exon	45923	45985	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	intron	45986	46072	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	CDS	46073	46276	0.66	+	2	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	exon	46073	46276	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	intron	46277	46387	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	CDS	46388	46530	0.98	+	2	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	exon	46388	46530	.	+	.	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
Phchi.C91	AUGUSTUS	stop_codon	46531	46533	.	+	0	transcript_id "Phchi.C91G000800.t1"; gene_id "Phchi.C91G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg51.t1 is derived from g9833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	106072	106711	.	-	.	Phchi.S6G001000
Phchi.S6	AUGUSTUS	transcript	106072	106711	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	stop_codon	106069	106071	.	-	0	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	CDS	106072	106150	1	-	1	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	exon	106072	106150	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	intron	106151	106273	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	CDS	106274	106299	0.85	-	0	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	exon	106274	106299	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	intron	106300	106377	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	CDS	106378	106444	1	-	1	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	exon	106378	106444	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	intron	106445	106622	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	CDS	106623	106711	0.88	-	0	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	exon	106623	106711	.	-	.	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
Phchi.S6	AUGUSTUS	start_codon	106709	106711	.	-	0	transcript_id "Phchi.S6G001000.t1"; gene_id "Phchi.S6G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12913.t1 is derived from g11378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3111187	3112509	.	+	.	Phchi.S3G023200
Phchi.S3	AUGUSTUS	transcript	3111187	3112509	.	+	.	transcript_id "Phchi.S3G023200.t1"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	start_codon	3111187	3111189	.	+	0	transcript_id "Phchi.S3G023200.t1"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	CDS	3111187	3112509	1	+	0	transcript_id "Phchi.S3G023200.t1"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	exon	3111187	3112509	.	+	.	transcript_id "Phchi.S3G023200.t1"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	stop_codon	3112510	3112512	.	+	0	transcript_id "Phchi.S3G023200.t1"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	transcript	3112015	3112509	.	+	.	transcript_id "Phchi.S3G023200.t2"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	start_codon	3112015	3112017	.	+	0	transcript_id "Phchi.S3G023200.t2"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	CDS	3112015	3112509	0.71	+	0	transcript_id "Phchi.S3G023200.t2"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	exon	3112015	3112509	.	+	.	transcript_id "Phchi.S3G023200.t2"; gene_id "Phchi.S3G023200"
Phchi.S3	AUGUSTUS	stop_codon	3112510	3112512	.	+	0	transcript_id "Phchi.S3G023200.t2"; gene_id "Phchi.S3G023200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7391.t1 is derived from g4563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28896261	28897975	.	-	.	Phchi.S1G455000
Phchi.S1	AUGUSTUS	transcript	28896261	28897975	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	stop_codon	28896258	28896260	.	-	0	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	CDS	28896261	28896452	1	-	0	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	exon	28896261	28896452	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	intron	28896453	28896546	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	CDS	28896547	28896679	1	-	1	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	exon	28896547	28896679	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	intron	28896680	28896832	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	CDS	28896833	28896936	1	-	0	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	exon	28896833	28896936	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	intron	28896937	28897043	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	CDS	28897044	28897674	0.98	-	1	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	exon	28897044	28897674	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	intron	28897675	28897796	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	CDS	28897797	28897975	0.98	-	0	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	exon	28897797	28897975	.	-	.	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
Phchi.S1	AUGUSTUS	start_codon	28897973	28897975	.	-	0	transcript_id "Phchi.S1G455000.t1"; gene_id "Phchi.S1G455000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12979.t1 is derived from g11444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3419912	3425079	.	-	.	Phchi.S3G029800
Phchi.S3	AUGUSTUS	transcript	3419912	3425079	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	stop_codon	3419909	3419911	.	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3419912	3420118	0.92	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3419912	3420118	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3420119	3420196	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3420197	3420337	1	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3420197	3420337	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3420338	3420425	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3420426	3420567	1	-	1	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3420426	3420567	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3420568	3420736	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3420737	3422288	1	-	2	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3420737	3422288	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3422289	3422400	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3422401	3422733	1	-	2	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3422401	3422733	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3422734	3422885	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3422886	3423033	0.58	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3422886	3423033	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3423034	3423083	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3423084	3423157	1	-	2	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3423084	3423157	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3423158	3423318	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3423319	3423568	1	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3423319	3423568	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3423569	3423648	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3423649	3423726	1	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3423649	3423726	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3423727	3423812	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3423813	3424385	0.85	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3423813	3424385	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	intron	3424386	3424497	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	CDS	3424498	3425079	0.53	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	exon	3424498	3425079	.	-	.	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
Phchi.S3	AUGUSTUS	start_codon	3425077	3425079	.	-	0	transcript_id "Phchi.S3G029800.t1"; gene_id "Phchi.S3G029800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7476.t1 is derived from g4649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29546107	29546325	.	-	.	Phchi.S1G463500
Phchi.S1	AUGUSTUS	transcript	29546107	29546325	.	-	.	transcript_id "Phchi.S1G463500.t1"; gene_id "Phchi.S1G463500"
Phchi.S1	AUGUSTUS	stop_codon	29546104	29546106	.	-	0	transcript_id "Phchi.S1G463500.t1"; gene_id "Phchi.S1G463500"
Phchi.S1	AUGUSTUS	CDS	29546107	29546325	1	-	0	transcript_id "Phchi.S1G463500.t1"; gene_id "Phchi.S1G463500"
Phchi.S1	AUGUSTUS	exon	29546107	29546325	.	-	.	transcript_id "Phchi.S1G463500.t1"; gene_id "Phchi.S1G463500"
Phchi.S1	AUGUSTUS	start_codon	29546323	29546325	.	-	0	transcript_id "Phchi.S1G463500.t1"; gene_id "Phchi.S1G463500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3580.t1 is derived from g749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4600482	4601330	.	-	.	Phchi.S1G073900
Phchi.S1	AUGUSTUS	transcript	4600482	4601330	.	-	.	transcript_id "Phchi.S1G073900.t1"; gene_id "Phchi.S1G073900"
Phchi.S1	AUGUSTUS	stop_codon	4600479	4600481	.	-	0	transcript_id "Phchi.S1G073900.t1"; gene_id "Phchi.S1G073900"
Phchi.S1	AUGUSTUS	CDS	4600482	4601330	1	-	0	transcript_id "Phchi.S1G073900.t1"; gene_id "Phchi.S1G073900"
Phchi.S1	AUGUSTUS	exon	4600482	4601330	.	-	.	transcript_id "Phchi.S1G073900.t1"; gene_id "Phchi.S1G073900"
Phchi.S1	AUGUSTUS	start_codon	4601328	4601330	.	-	0	transcript_id "Phchi.S1G073900.t1"; gene_id "Phchi.S1G073900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4768.t1 is derived from g1938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12741356	12742653	.	-	.	Phchi.S1G192700
Phchi.S1	AUGUSTUS	transcript	12741356	12742653	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	stop_codon	12741353	12741355	.	-	0	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	CDS	12741356	12741482	0.99	-	1	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	exon	12741356	12741482	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	intron	12741483	12741628	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	CDS	12741629	12741662	1	-	2	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	exon	12741629	12741662	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	intron	12741663	12741817	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	CDS	12741818	12741904	0.94	-	2	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	exon	12741818	12741904	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	intron	12741905	12742008	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	CDS	12742009	12742191	1	-	2	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	exon	12742009	12742191	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	intron	12742192	12742526	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	CDS	12742527	12742653	1	-	0	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	exon	12742527	12742653	.	-	.	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
Phchi.S1	AUGUSTUS	start_codon	12742651	12742653	.	-	0	transcript_id "Phchi.S1G192700.t1"; gene_id "Phchi.S1G192700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5962.t1 is derived from g3133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20097697	20098486	.	-	.	Phchi.S1G312100
Phchi.S1	AUGUSTUS	transcript	20097697	20098486	.	-	.	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	stop_codon	20097694	20097696	.	-	0	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	CDS	20097697	20097851	0.93	-	2	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	exon	20097697	20097851	.	-	.	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	intron	20097852	20097978	.	-	.	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	CDS	20097979	20098486	0.93	-	0	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	exon	20097979	20098486	.	-	.	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
Phchi.S1	AUGUSTUS	start_codon	20098484	20098486	.	-	0	transcript_id "Phchi.S1G312100.t1"; gene_id "Phchi.S1G312100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4341.t1 is derived from g1510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9858313	9858792	.	+	.	Phchi.S1G150000
Phchi.S1	AUGUSTUS	transcript	9858313	9858792	.	+	.	transcript_id "Phchi.S1G150000.t1"; gene_id "Phchi.S1G150000"
Phchi.S1	AUGUSTUS	start_codon	9858313	9858315	.	+	0	transcript_id "Phchi.S1G150000.t1"; gene_id "Phchi.S1G150000"
Phchi.S1	AUGUSTUS	CDS	9858313	9858792	0.6	+	0	transcript_id "Phchi.S1G150000.t1"; gene_id "Phchi.S1G150000"
Phchi.S1	AUGUSTUS	exon	9858313	9858792	.	+	.	transcript_id "Phchi.S1G150000.t1"; gene_id "Phchi.S1G150000"
Phchi.S1	AUGUSTUS	stop_codon	9858793	9858795	.	+	0	transcript_id "Phchi.S1G150000.t1"; gene_id "Phchi.S1G150000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3940.t1 is derived from g1109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6573474	6575319	.	+	.	Phchi.S1G109900
Phchi.S1	AUGUSTUS	transcript	6573474	6575319	.	+	.	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	start_codon	6573474	6573476	.	+	0	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	CDS	6573474	6573570	1	+	0	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	exon	6573474	6573570	.	+	.	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	intron	6573571	6573670	.	+	.	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	CDS	6573671	6575319	1	+	2	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	exon	6573671	6575319	.	+	.	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
Phchi.S1	AUGUSTUS	stop_codon	6575320	6575322	.	+	0	transcript_id "Phchi.S1G109900.t1"; gene_id "Phchi.S1G109900"
# This transcript jg7811.t2 is derived from g4985.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7812.t1 is derived from g4986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31309124	31312079	.	+	.	Phchi.S1G497100
Phchi.S1	AUGUSTUS	transcript	31309124	31312079	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	start_codon	31309124	31309126	.	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31309124	31309426	0.91	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31309124	31309426	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31309427	31309526	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31309527	31309610	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31309527	31309610	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31309611	31309705	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31309706	31309834	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31309706	31309834	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31309835	31309917	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31309918	31310006	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31309918	31310006	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31310007	31310093	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31310094	31310274	1	+	1	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31310094	31310274	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31310275	31310376	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31310377	31310467	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31310377	31310467	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31310468	31310595	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31310596	31310750	0.82	+	2	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31310596	31310750	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31310751	31310858	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31310859	31310951	0.93	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31310859	31310951	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31310952	31311061	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31311062	31311154	0.98	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31311062	31311154	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31311155	31311274	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31311275	31311355	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31311275	31311355	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31311356	31311459	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31311460	31311609	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31311460	31311609	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31311610	31311727	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31311728	31311823	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31311728	31311823	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	intron	31311824	31311962	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	CDS	31311963	31312079	1	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	exon	31311963	31312079	.	+	.	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
Phchi.S1	AUGUSTUS	stop_codon	31312080	31312082	.	+	0	transcript_id "Phchi.S1G497100.t1"; gene_id "Phchi.S1G497100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8345.t1 is derived from g5520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35410014	35420378	.	+	.	Phchi.S1G550400
Phchi.S1	AUGUSTUS	transcript	35410014	35420378	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	start_codon	35410014	35410016	.	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410014	35410088	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410014	35410088	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410089	35410175	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410176	35410264	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410176	35410264	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410265	35410346	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410347	35410470	1	+	1	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410347	35410470	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410471	35410557	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410558	35411787	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410558	35411787	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35411788	35411886	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35411887	35412261	0.89	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35411887	35412261	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412262	35412377	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412378	35412461	0.64	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412378	35412461	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412462	35412551	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412552	35412740	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412552	35412740	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412741	35412898	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412899	35413037	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412899	35413037	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413038	35413138	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413139	35413320	0.91	+	2	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413139	35413320	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413321	35413431	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413432	35413517	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413432	35413517	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413518	35413617	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413618	35413666	1	+	1	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413618	35413666	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413667	35413760	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413761	35413818	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413761	35413818	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413819	35413900	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413901	35414397	1	+	2	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413901	35414397	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414398	35414522	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414523	35414622	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414523	35414622	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414623	35414711	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414712	35414845	1	+	2	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414712	35414845	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414846	35414983	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414984	35415051	0.99	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414984	35415051	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415052	35415180	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415181	35415415	0.93	+	1	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415181	35415415	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415416	35415505	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415506	35415694	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415506	35415694	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415695	35415801	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415802	35415957	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415802	35415957	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415958	35416140	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416141	35416194	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416141	35416194	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416195	35416292	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416293	35416495	0.99	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416293	35416495	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416496	35416662	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416663	35416735	1	+	1	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416663	35416735	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416736	35416832	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416833	35417200	1	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416833	35417200	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417201	35417324	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417325	35417505	1	+	1	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417325	35417505	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417506	35417659	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417660	35417689	0.73	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417660	35417689	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417690	35417782	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417783	35419374	0.6	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417783	35419374	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35419375	35419964	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35419965	35420014	0.83	+	1	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35419965	35420014	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35420015	35420189	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35420190	35420261	0.97	+	2	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35420190	35420261	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35420262	35420343	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35420344	35420378	0.96	+	2	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35420344	35420378	.	+	.	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	stop_codon	35420379	35420381	.	+	0	transcript_id "Phchi.S1G550400.t1"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	transcript	35410014	35420378	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	start_codon	35410014	35410016	.	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410014	35410088	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410014	35410088	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410089	35410175	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410176	35410264	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410176	35410264	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410265	35410346	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410347	35410470	1	+	1	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410347	35410470	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410471	35410557	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410558	35411787	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410558	35411787	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35411788	35411886	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35411887	35412261	0.96	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35411887	35412261	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412262	35412377	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412378	35412461	0.63	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412378	35412461	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412462	35412551	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412552	35412740	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412552	35412740	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412741	35412898	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412899	35413037	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412899	35413037	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413038	35413138	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413139	35413320	0.91	+	2	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413139	35413320	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413321	35413431	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413432	35413517	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413432	35413517	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413518	35413617	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413618	35413666	1	+	1	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413618	35413666	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413667	35413760	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413761	35413818	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413761	35413818	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413819	35413900	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413901	35414397	1	+	2	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413901	35414397	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414398	35414522	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414523	35414622	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414523	35414622	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414623	35414711	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414712	35414845	1	+	2	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414712	35414845	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414846	35414983	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414984	35415051	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414984	35415051	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415052	35415206	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415207	35415241	0.8	+	1	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415207	35415241	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415242	35415386	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415387	35415415	0.56	+	2	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415387	35415415	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415416	35415505	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415506	35415694	0.85	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415506	35415694	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415695	35415801	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415802	35415957	0.93	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415802	35415957	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415958	35416140	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416141	35416194	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416141	35416194	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416195	35416292	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416293	35416495	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416293	35416495	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416496	35416662	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416663	35416735	1	+	1	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416663	35416735	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416736	35416832	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416833	35417200	1	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416833	35417200	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417201	35417324	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417325	35417505	1	+	1	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417325	35417505	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417506	35417659	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417660	35417689	0.75	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417660	35417689	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417690	35417782	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417783	35419374	0.63	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417783	35419374	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35419375	35419964	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35419965	35420014	0.88	+	1	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35419965	35420014	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35420015	35420189	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35420190	35420261	0.98	+	2	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35420190	35420261	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35420262	35420343	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35420344	35420378	0.98	+	2	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35420344	35420378	.	+	.	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	stop_codon	35420379	35420381	.	+	0	transcript_id "Phchi.S1G550400.t2"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	transcript	35410014	35420378	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	start_codon	35410014	35410016	.	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410014	35410088	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410014	35410088	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410089	35410175	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410176	35410264	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410176	35410264	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410265	35410346	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410347	35410470	1	+	1	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410347	35410470	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35410471	35410557	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35410558	35411787	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35410558	35411787	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35411788	35411886	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35411887	35412261	0.92	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35411887	35412261	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412262	35412377	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412378	35412461	0.57	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412378	35412461	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412462	35412554	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412555	35412740	0.98	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412555	35412740	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35412741	35412898	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35412899	35413037	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35412899	35413037	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413038	35413138	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413139	35413320	0.89	+	2	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413139	35413320	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413321	35413431	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413432	35413517	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413432	35413517	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413518	35413617	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413618	35413666	1	+	1	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413618	35413666	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413667	35413760	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413761	35413818	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413761	35413818	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35413819	35413900	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35413901	35414397	1	+	2	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35413901	35414397	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414398	35414522	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414523	35414622	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414523	35414622	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414623	35414711	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414712	35414845	1	+	2	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414712	35414845	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35414846	35414983	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35414984	35415051	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35414984	35415051	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415052	35415206	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415207	35415241	0.72	+	1	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415207	35415241	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415242	35415386	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415387	35415415	0.58	+	2	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415387	35415415	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415416	35415505	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415506	35415694	0.83	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415506	35415694	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415695	35415801	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35415802	35415957	0.93	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35415802	35415957	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35415958	35416140	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416141	35416194	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416141	35416194	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416195	35416292	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416293	35416495	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416293	35416495	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416496	35416662	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416663	35416735	1	+	1	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416663	35416735	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35416736	35416832	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35416833	35417200	1	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35416833	35417200	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417201	35417324	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417325	35417505	1	+	1	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417325	35417505	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417506	35417659	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417660	35417689	0.64	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417660	35417689	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35417690	35417782	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35417783	35419374	0.52	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35417783	35419374	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35419375	35419964	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35419965	35420014	0.84	+	1	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35419965	35420014	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35420015	35420189	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35420190	35420261	0.97	+	2	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35420190	35420261	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	intron	35420262	35420343	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	CDS	35420344	35420378	0.97	+	2	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	exon	35420344	35420378	.	+	.	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
Phchi.S1	AUGUSTUS	stop_codon	35420379	35420381	.	+	0	transcript_id "Phchi.S1G550400.t3"; gene_id "Phchi.S1G550400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7715.t1 is derived from g4889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30774656	30777499	.	+	.	Phchi.S1G487400
Phchi.S1	AUGUSTUS	transcript	30774656	30777499	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	start_codon	30774656	30774658	.	+	0	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30774656	30775604	0.79	+	0	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30774656	30775604	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	intron	30775605	30775754	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30775755	30775856	0.58	+	2	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30775755	30775856	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	intron	30775857	30776026	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30776027	30776292	0.91	+	2	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30776027	30776292	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	intron	30776293	30776425	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30776426	30776597	1	+	0	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30776426	30776597	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	intron	30776598	30776664	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30776665	30776747	0.97	+	2	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30776665	30776747	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	intron	30776748	30776848	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30776849	30777109	0.91	+	0	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30776849	30777109	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	intron	30777110	30777205	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	CDS	30777206	30777499	1	+	0	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	exon	30777206	30777499	.	+	.	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
Phchi.S1	AUGUSTUS	stop_codon	30777500	30777502	.	+	0	transcript_id "Phchi.S1G487400.t1"; gene_id "Phchi.S1G487400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12937.t1 is derived from g11402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3241959	3247869	.	+	.	Phchi.S3G025600
Phchi.S3	AUGUSTUS	transcript	3241959	3247869	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	start_codon	3241959	3241961	.	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3241959	3242519	0.6	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3241959	3242519	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3242520	3242617	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3242618	3243161	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3242618	3243161	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3243162	3243289	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3243290	3243541	0.99	+	2	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3243290	3243541	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3243542	3243651	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3243652	3243743	1	+	2	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3243652	3243743	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3243744	3243864	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3243865	3244074	0.99	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3243865	3244074	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3244075	3244163	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3244164	3244355	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3244164	3244355	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3244356	3244446	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3244447	3244686	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3244447	3244686	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3244687	3244797	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3244798	3245046	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3244798	3245046	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3245047	3245153	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3245154	3245210	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3245154	3245210	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3245211	3245330	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3245331	3245465	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3245331	3245465	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3245466	3245612	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3245613	3245681	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3245613	3245681	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3245682	3245797	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3245798	3245911	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3245798	3245911	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3245912	3245993	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3245994	3246158	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3245994	3246158	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3246159	3246304	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3246305	3246433	0.99	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3246305	3246433	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3246434	3246536	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3246537	3246638	0.99	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3246537	3246638	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3246639	3246752	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3246753	3246847	1	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3246753	3246847	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3246848	3246959	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3246960	3247085	1	+	1	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3246960	3247085	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	intron	3247086	3247226	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	CDS	3247227	3247869	1	+	1	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	exon	3247227	3247869	.	+	.	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
Phchi.S3	AUGUSTUS	stop_codon	3247870	3247872	.	+	0	transcript_id "Phchi.S3G025600.t1"; gene_id "Phchi.S3G025600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4266.t1 is derived from g1435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9291096	9292927	.	-	.	Phchi.S1G142500
Phchi.S1	AUGUSTUS	transcript	9291096	9292927	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	stop_codon	9291093	9291095	.	-	0	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	CDS	9291096	9291115	0.72	-	2	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	exon	9291096	9291115	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	intron	9291116	9291253	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	CDS	9291254	9291317	0.72	-	0	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	exon	9291254	9291317	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	intron	9291318	9291581	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	CDS	9291582	9291830	0.44	-	0	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	exon	9291582	9291830	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	intron	9291831	9291940	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	CDS	9291941	9292005	1	-	2	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	exon	9291941	9292005	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	intron	9292006	9292092	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	CDS	9292093	9292539	1	-	2	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	exon	9292093	9292539	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	intron	9292540	9292680	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	CDS	9292681	9292927	0.93	-	0	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	exon	9292681	9292927	.	-	.	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
Phchi.S1	AUGUSTUS	start_codon	9292925	9292927	.	-	0	transcript_id "Phchi.S1G142500.t1"; gene_id "Phchi.S1G142500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15040.t1 is derived from g13508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16707168	16710854	.	-	.	Phchi.S3G235900
Phchi.S3	AUGUSTUS	transcript	16707168	16710854	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	stop_codon	16707165	16707167	.	-	0	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16707168	16708031	0.9	-	0	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16707168	16708031	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16708032	16708451	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16708452	16708694	0.58	-	0	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16708452	16708694	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16708695	16708988	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16708989	16709380	0.52	-	2	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16708989	16709380	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16709381	16709509	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16709510	16709761	0.47	-	2	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16709510	16709761	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16709762	16710115	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16710116	16710207	0.91	-	1	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16710116	16710207	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16710208	16710349	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16710350	16710486	0.91	-	0	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16710350	16710486	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16710487	16710580	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16710581	16710645	0.71	-	2	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16710581	16710645	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	intron	16710646	16710730	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	CDS	16710731	16710854	0.88	-	0	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	exon	16710731	16710854	.	-	.	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
Phchi.S3	AUGUSTUS	start_codon	16710852	16710854	.	-	0	transcript_id "Phchi.S3G235900.t1"; gene_id "Phchi.S3G235900"
# This transcript jg14593.t2 is derived from g13061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14594.t1 is derived from g13062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13622538	13623599	.	-	.	Phchi.S3G191300
Phchi.S3	AUGUSTUS	transcript	13622538	13623599	.	-	.	transcript_id "Phchi.S3G191300.t1"; gene_id "Phchi.S3G191300"
Phchi.S3	AUGUSTUS	stop_codon	13622535	13622537	.	-	0	transcript_id "Phchi.S3G191300.t1"; gene_id "Phchi.S3G191300"
Phchi.S3	AUGUSTUS	CDS	13622538	13623599	0.79	-	0	transcript_id "Phchi.S3G191300.t1"; gene_id "Phchi.S3G191300"
Phchi.S3	AUGUSTUS	exon	13622538	13623599	.	-	.	transcript_id "Phchi.S3G191300.t1"; gene_id "Phchi.S3G191300"
Phchi.S3	AUGUSTUS	start_codon	13623597	13623599	.	-	0	transcript_id "Phchi.S3G191300.t1"; gene_id "Phchi.S3G191300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5606.t1 is derived from g2776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17855861	17859456	.	+	.	Phchi.S1G276500
Phchi.S1	AUGUSTUS	transcript	17855861	17859456	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	start_codon	17855861	17855863	.	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17855861	17856331	0.99	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17855861	17856331	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17856332	17856414	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17856415	17856582	1	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17856415	17856582	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17856583	17856696	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17856697	17856825	1	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17856697	17856825	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17856826	17856931	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17856932	17857090	0.55	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17856932	17857090	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17857091	17857241	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17857242	17857313	0.35	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17857242	17857313	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17857314	17857546	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17857547	17857639	0.76	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17857547	17857639	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17857640	17857729	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17857730	17857846	1	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17857730	17857846	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17857847	17857971	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17857972	17858046	1	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17857972	17858046	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	intron	17858047	17858139	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	CDS	17858140	17859456	1	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	exon	17858140	17859456	.	+	.	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
Phchi.S1	AUGUSTUS	stop_codon	17859457	17859459	.	+	0	transcript_id "Phchi.S1G276500.t1"; gene_id "Phchi.S1G276500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg761.t1 is derived from g10543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5372622	5373430	.	+	.	Phchi.S6G072000
Phchi.S6	AUGUSTUS	transcript	5372622	5373430	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	start_codon	5372622	5372624	.	+	0	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	CDS	5372622	5372650	0.63	+	0	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	exon	5372622	5372650	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	intron	5372651	5372900	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	CDS	5372901	5372992	0.63	+	1	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	exon	5372901	5372992	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	intron	5372993	5373123	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	CDS	5373124	5373242	1	+	2	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	exon	5373124	5373242	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	intron	5373243	5373325	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	CDS	5373326	5373430	0.95	+	0	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	exon	5373326	5373430	.	+	.	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
Phchi.S6	AUGUSTUS	stop_codon	5373431	5373433	.	+	0	transcript_id "Phchi.S6G072000.t1"; gene_id "Phchi.S6G072000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9381.t1 is derived from g6557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41251587	41254136	.	-	.	Phchi.S1G654000
Phchi.S1	AUGUSTUS	transcript	41251587	41254136	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	stop_codon	41251584	41251586	.	-	0	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	CDS	41251587	41252433	1	-	1	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	exon	41251587	41252433	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	intron	41252434	41252544	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	CDS	41252545	41252768	1	-	0	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	exon	41252545	41252768	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	intron	41252769	41252859	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	CDS	41252860	41253059	1	-	2	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	exon	41252860	41253059	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	intron	41253060	41253304	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	CDS	41253305	41253650	0.99	-	0	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	exon	41253305	41253650	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	intron	41253651	41253932	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	CDS	41253933	41254136	0.85	-	0	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	exon	41253933	41254136	.	-	.	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
Phchi.S1	AUGUSTUS	start_codon	41254134	41254136	.	-	0	transcript_id "Phchi.S1G654000.t1"; gene_id "Phchi.S1G654000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14846.t1 is derived from g13314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15039199	15039847	.	+	.	Phchi.S3G216500
Phchi.S3	AUGUSTUS	transcript	15039199	15039847	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	start_codon	15039199	15039201	.	+	0	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	CDS	15039199	15039247	1	+	0	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	exon	15039199	15039247	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	intron	15039248	15039330	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	CDS	15039331	15039386	0.96	+	2	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	exon	15039331	15039386	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	intron	15039387	15039496	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	CDS	15039497	15039565	0.96	+	0	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	exon	15039497	15039565	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	intron	15039566	15039667	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	CDS	15039668	15039847	0.98	+	0	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	exon	15039668	15039847	.	+	.	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
Phchi.S3	AUGUSTUS	stop_codon	15039848	15039850	.	+	0	transcript_id "Phchi.S3G216500.t1"; gene_id "Phchi.S3G216500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3275.t1 is derived from g444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2646402	2646836	.	+	.	Phchi.S1G043400
Phchi.S1	AUGUSTUS	transcript	2646402	2646836	.	+	.	transcript_id "Phchi.S1G043400.t1"; gene_id "Phchi.S1G043400"
Phchi.S1	AUGUSTUS	start_codon	2646402	2646404	.	+	0	transcript_id "Phchi.S1G043400.t1"; gene_id "Phchi.S1G043400"
Phchi.S1	AUGUSTUS	CDS	2646402	2646836	0.99	+	0	transcript_id "Phchi.S1G043400.t1"; gene_id "Phchi.S1G043400"
Phchi.S1	AUGUSTUS	exon	2646402	2646836	.	+	.	transcript_id "Phchi.S1G043400.t1"; gene_id "Phchi.S1G043400"
Phchi.S1	AUGUSTUS	stop_codon	2646837	2646839	.	+	0	transcript_id "Phchi.S1G043400.t1"; gene_id "Phchi.S1G043400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15614.t1 is derived from g14083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20298150	20299336	.	-	.	Phchi.S3G293300
Phchi.S3	AUGUSTUS	transcript	20298150	20299336	.	-	.	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	stop_codon	20298147	20298149	.	-	0	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	CDS	20298150	20298442	0.92	-	2	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	exon	20298150	20298442	.	-	.	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	intron	20298443	20298535	.	-	.	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	CDS	20298536	20298683	0.99	-	0	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	exon	20298536	20298683	.	-	.	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	intron	20298684	20298826	.	-	.	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	CDS	20298827	20299336	0.98	-	0	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	exon	20298827	20299336	.	-	.	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
Phchi.S3	AUGUSTUS	start_codon	20299334	20299336	.	-	0	transcript_id "Phchi.S3G293300.t1"; gene_id "Phchi.S3G293300"
# This transcript jg7113.t2 is derived from g4285.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7114.t1 is derived from g4286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27045579	27048450	.	-	.	Phchi.S1G427300
Phchi.S1	AUGUSTUS	transcript	27045579	27048450	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	stop_codon	27045576	27045578	.	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27045579	27045785	0.93	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27045579	27045785	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27045786	27045860	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27045861	27045987	1	-	1	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27045861	27045987	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27045988	27046128	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27046129	27046256	1	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27046129	27046256	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27046257	27046336	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27046337	27046378	0.97	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27046337	27046378	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27046379	27046490	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27046491	27046529	0.92	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27046491	27046529	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27046530	27046621	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27046622	27046714	0.96	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27046622	27046714	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27046715	27046804	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27046805	27046900	0.73	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27046805	27046900	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27046901	27046996	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27046997	27047101	1	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27046997	27047101	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27047102	27047369	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27047370	27047546	1	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27047370	27047546	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27047547	27047640	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27047641	27047716	1	-	1	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27047641	27047716	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27047717	27047805	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27047806	27047885	1	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27047806	27047885	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27047886	27047964	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27047965	27048060	1	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27047965	27048060	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	intron	27048061	27048144	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	CDS	27048145	27048450	0.96	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	exon	27048145	27048450	.	-	.	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
Phchi.S1	AUGUSTUS	start_codon	27048448	27048450	.	-	0	transcript_id "Phchi.S1G427300.t1"; gene_id "Phchi.S1G427300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13283.t1 is derived from g11749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5178014	5179296	.	+	.	Phchi.S3G060200
Phchi.S3	AUGUSTUS	transcript	5178014	5179296	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	start_codon	5178014	5178016	.	+	0	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	CDS	5178014	5178096	0.59	+	0	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	exon	5178014	5178096	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	intron	5178097	5178362	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	CDS	5178363	5178403	0.38	+	1	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	exon	5178363	5178403	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	intron	5178404	5178742	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	CDS	5178743	5178769	0.41	+	2	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	exon	5178743	5178769	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	intron	5178770	5178940	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	CDS	5178941	5179009	0.5	+	2	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	exon	5178941	5179009	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	intron	5179010	5179249	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	CDS	5179250	5179296	0.5	+	2	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	exon	5179250	5179296	.	+	.	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
Phchi.S3	AUGUSTUS	stop_codon	5179297	5179299	.	+	0	transcript_id "Phchi.S3G060200.t1"; gene_id "Phchi.S3G060200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15544.t1 is derived from g14013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19794423	19798419	.	+	.	Phchi.S3G286300
Phchi.S3	AUGUSTUS	transcript	19794423	19798419	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	start_codon	19794423	19794425	.	+	0	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19794423	19796821	0.44	+	0	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19794423	19796821	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	intron	19796822	19796946	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19796947	19797016	0.7	+	1	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19796947	19797016	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	intron	19797017	19797346	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19797347	19797530	0.97	+	0	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19797347	19797530	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	intron	19797531	19797656	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19797657	19797809	1	+	2	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19797657	19797809	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	intron	19797810	19797947	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19797948	19798073	1	+	2	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19797948	19798073	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	intron	19798074	19798178	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19798179	19798231	1	+	2	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19798179	19798231	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	intron	19798232	19798314	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	CDS	19798315	19798419	0.72	+	0	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	exon	19798315	19798419	.	+	.	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
Phchi.S3	AUGUSTUS	stop_codon	19798420	19798422	.	+	0	transcript_id "Phchi.S3G286300.t1"; gene_id "Phchi.S3G286300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2561.t1 is derived from g9481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7396652	7398577	.	+	.	Phchi.S5G117000
Phchi.S5	AUGUSTUS	transcript	7396652	7398577	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	start_codon	7396652	7396654	.	+	0	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	CDS	7396652	7397094	0.39	+	0	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	exon	7396652	7397094	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	intron	7397095	7397176	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	CDS	7397177	7397462	0.88	+	1	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	exon	7397177	7397462	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	intron	7397463	7397532	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	CDS	7397533	7397733	0.97	+	0	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	exon	7397533	7397733	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	intron	7397734	7397829	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	CDS	7397830	7398078	1	+	0	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	exon	7397830	7398078	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	intron	7398079	7398181	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	CDS	7398182	7398577	1	+	0	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	exon	7398182	7398577	.	+	.	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
Phchi.S5	AUGUSTUS	stop_codon	7398578	7398580	.	+	0	transcript_id "Phchi.S5G117000.t1"; gene_id "Phchi.S5G117000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg998.t1 is derived from g10781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6972150	6974464	.	+	.	Phchi.S6G095700
Phchi.S6	AUGUSTUS	transcript	6972150	6974464	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	start_codon	6972150	6972152	.	+	0	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	CDS	6972150	6973128	0.86	+	0	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	exon	6972150	6973128	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	intron	6973129	6973261	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	CDS	6973262	6973585	1	+	2	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	exon	6973262	6973585	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	intron	6973586	6973680	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	CDS	6973681	6973781	0.7	+	2	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	exon	6973681	6973781	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	intron	6973782	6973936	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	CDS	6973937	6974464	0.7	+	0	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	exon	6973937	6974464	.	+	.	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
Phchi.S6	AUGUSTUS	stop_codon	6974465	6974467	.	+	0	transcript_id "Phchi.S6G095700.t1"; gene_id "Phchi.S6G095700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10337.t1 is derived from g7513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47238349	47238669	.	+	.	Phchi.S1G749600
Phchi.S1	AUGUSTUS	transcript	47238349	47238669	.	+	.	transcript_id "Phchi.S1G749600.t1"; gene_id "Phchi.S1G749600"
Phchi.S1	AUGUSTUS	start_codon	47238349	47238351	.	+	0	transcript_id "Phchi.S1G749600.t1"; gene_id "Phchi.S1G749600"
Phchi.S1	AUGUSTUS	CDS	47238349	47238669	0.91	+	0	transcript_id "Phchi.S1G749600.t1"; gene_id "Phchi.S1G749600"
Phchi.S1	AUGUSTUS	exon	47238349	47238669	.	+	.	transcript_id "Phchi.S1G749600.t1"; gene_id "Phchi.S1G749600"
Phchi.S1	AUGUSTUS	stop_codon	47238670	47238672	.	+	0	transcript_id "Phchi.S1G749600.t1"; gene_id "Phchi.S1G749600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1894.t1 is derived from g8814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3756114	3756495	.	+	.	Phchi.S5G050300
Phchi.S5	AUGUSTUS	transcript	3756114	3756495	.	+	.	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	start_codon	3756114	3756116	.	+	0	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	CDS	3756114	3756201	0.73	+	0	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	exon	3756114	3756201	.	+	.	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	intron	3756202	3756313	.	+	.	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	CDS	3756314	3756495	0.74	+	2	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	exon	3756314	3756495	.	+	.	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
Phchi.S5	AUGUSTUS	stop_codon	3756496	3756498	.	+	0	transcript_id "Phchi.S5G050300.t1"; gene_id "Phchi.S5G050300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14364.t1 is derived from g12831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12371434	12372452	.	+	.	Phchi.S3G168300
Phchi.S3	AUGUSTUS	transcript	12371434	12372452	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	start_codon	12371434	12371436	.	+	0	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	CDS	12371434	12371547	0.93	+	0	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	exon	12371434	12371547	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	intron	12371548	12371627	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	CDS	12371628	12371785	1	+	0	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	exon	12371628	12371785	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	intron	12371786	12371877	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	CDS	12371878	12371994	1	+	1	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	exon	12371878	12371994	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	intron	12371995	12372104	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	CDS	12372105	12372192	1	+	1	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	exon	12372105	12372192	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	intron	12372193	12372311	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	CDS	12372312	12372452	1	+	0	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	exon	12372312	12372452	.	+	.	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
Phchi.S3	AUGUSTUS	stop_codon	12372453	12372455	.	+	0	transcript_id "Phchi.S3G168300.t1"; gene_id "Phchi.S3G168300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1790.t1 is derived from g8710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3026754	3029854	.	-	.	Phchi.S5G039900
Phchi.S5	AUGUSTUS	transcript	3026754	3029854	.	-	.	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	stop_codon	3026751	3026753	.	-	0	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	CDS	3026754	3028889	0.97	-	0	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	exon	3026754	3028889	.	-	.	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	intron	3028890	3029038	.	-	.	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	CDS	3029039	3029854	0.92	-	0	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	exon	3029039	3029854	.	-	.	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
Phchi.S5	AUGUSTUS	start_codon	3029852	3029854	.	-	0	transcript_id "Phchi.S5G039900.t1"; gene_id "Phchi.S5G039900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4305.t1 is derived from g1474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9523141	9525383	.	+	.	Phchi.S1G146400
Phchi.S1	AUGUSTUS	transcript	9523141	9525383	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	start_codon	9523141	9523143	.	+	0	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	CDS	9523141	9523429	0.6	+	0	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	exon	9523141	9523429	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	intron	9523430	9523551	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	CDS	9523552	9523769	0.8	+	2	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	exon	9523552	9523769	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	intron	9523770	9523886	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	CDS	9523887	9524479	0.81	+	0	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	exon	9523887	9524479	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	intron	9524480	9524575	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	CDS	9524576	9525383	0.89	+	1	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	exon	9524576	9525383	.	+	.	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
Phchi.S1	AUGUSTUS	stop_codon	9525384	9525386	.	+	0	transcript_id "Phchi.S1G146400.t1"; gene_id "Phchi.S1G146400"
# This transcript jg8727.t2 is derived from g5902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8728.t1 is derived from g5903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37697646	37699658	.	-	.	Phchi.S1G588700
Phchi.S1	AUGUSTUS	transcript	37697646	37699658	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	stop_codon	37697643	37697645	.	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	CDS	37697646	37698794	1	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	exon	37697646	37698794	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	intron	37698795	37698882	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	CDS	37698883	37698945	1	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	exon	37698883	37698945	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	intron	37698946	37699040	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	CDS	37699041	37699123	1	-	2	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	exon	37699041	37699123	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	intron	37699124	37699245	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	CDS	37699246	37699354	0.99	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	exon	37699246	37699354	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	intron	37699355	37699425	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	CDS	37699426	37699524	1	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	exon	37699426	37699524	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	intron	37699525	37699610	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	CDS	37699611	37699658	1	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	exon	37699611	37699658	.	-	.	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
Phchi.S1	AUGUSTUS	start_codon	37699656	37699658	.	-	0	transcript_id "Phchi.S1G588700.t1"; gene_id "Phchi.S1G588700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1024.t1 is derived from g10807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7169351	7170553	.	-	.	Phchi.S6G098300
Phchi.S6	AUGUSTUS	transcript	7169351	7170553	.	-	.	transcript_id "Phchi.S6G098300.t1"; gene_id "Phchi.S6G098300"
Phchi.S6	AUGUSTUS	stop_codon	7169348	7169350	.	-	0	transcript_id "Phchi.S6G098300.t1"; gene_id "Phchi.S6G098300"
Phchi.S6	AUGUSTUS	CDS	7169351	7170553	0.72	-	0	transcript_id "Phchi.S6G098300.t1"; gene_id "Phchi.S6G098300"
Phchi.S6	AUGUSTUS	exon	7169351	7170553	.	-	.	transcript_id "Phchi.S6G098300.t1"; gene_id "Phchi.S6G098300"
Phchi.S6	AUGUSTUS	start_codon	7170551	7170553	.	-	0	transcript_id "Phchi.S6G098300.t1"; gene_id "Phchi.S6G098300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6870.t1 is derived from g4042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25698803	25699831	.	-	.	Phchi.S1G402900
Phchi.S1	AUGUSTUS	transcript	25698803	25699831	.	-	.	transcript_id "Phchi.S1G402900.t1"; gene_id "Phchi.S1G402900"
Phchi.S1	AUGUSTUS	stop_codon	25698800	25698802	.	-	0	transcript_id "Phchi.S1G402900.t1"; gene_id "Phchi.S1G402900"
Phchi.S1	AUGUSTUS	CDS	25698803	25699831	0.59	-	0	transcript_id "Phchi.S1G402900.t1"; gene_id "Phchi.S1G402900"
Phchi.S1	AUGUSTUS	exon	25698803	25699831	.	-	.	transcript_id "Phchi.S1G402900.t1"; gene_id "Phchi.S1G402900"
Phchi.S1	AUGUSTUS	start_codon	25699829	25699831	.	-	0	transcript_id "Phchi.S1G402900.t1"; gene_id "Phchi.S1G402900"
# This transcript jg10909.t2 is derived from g14959.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10910.t1 is derived from g14960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2887975	2890142	.	+	.	Phchi.S4G049200
Phchi.S4	AUGUSTUS	transcript	2887975	2890142	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	start_codon	2887975	2887977	.	+	0	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2887975	2888095	0.93	+	0	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2887975	2888095	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888096	2888183	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888184	2888235	1	+	2	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888184	2888235	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888236	2888360	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888361	2888431	1	+	1	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888361	2888431	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888432	2888548	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888549	2888676	0.98	+	2	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888549	2888676	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888677	2888781	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888782	2888864	1	+	0	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888782	2888864	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888865	2888955	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888956	2889061	1	+	1	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888956	2889061	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889062	2889204	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889205	2889609	0.63	+	0	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889205	2889609	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889610	2889696	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889697	2889824	1	+	0	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889697	2889824	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889825	2889967	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889968	2890142	0.91	+	1	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889968	2890142	.	+	.	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	stop_codon	2890143	2890145	.	+	0	transcript_id "Phchi.S4G049200.t1"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	transcript	2887975	2890142	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	start_codon	2887975	2887977	.	+	0	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2887975	2888095	0.95	+	0	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2887975	2888095	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888096	2888183	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888184	2888235	1	+	2	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888184	2888235	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888236	2888360	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888361	2888431	0.99	+	1	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888361	2888431	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888432	2888548	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888549	2888676	0.96	+	2	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888549	2888676	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888677	2888781	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888782	2888864	1	+	0	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888782	2888864	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2888865	2888955	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2888956	2889051	1	+	1	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2888956	2889051	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889052	2889204	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889205	2889236	0.93	+	1	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889205	2889236	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889237	2889385	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889386	2889609	0.41	+	2	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889386	2889609	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889610	2889696	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889697	2889824	1	+	0	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889697	2889824	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	intron	2889825	2889967	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	CDS	2889968	2890142	0.88	+	1	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	exon	2889968	2890142	.	+	.	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
Phchi.S4	AUGUSTUS	stop_codon	2890143	2890145	.	+	0	transcript_id "Phchi.S4G049200.t2"; gene_id "Phchi.S4G049200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12716.t1 is derived from g11181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	878031	878384	.	-	.	Phchi.S3G003500
Phchi.S3	AUGUSTUS	transcript	878031	878384	.	-	.	transcript_id "Phchi.S3G003500.t1"; gene_id "Phchi.S3G003500"
Phchi.S3	AUGUSTUS	stop_codon	878028	878030	.	-	0	transcript_id "Phchi.S3G003500.t1"; gene_id "Phchi.S3G003500"
Phchi.S3	AUGUSTUS	CDS	878031	878384	0.35	-	0	transcript_id "Phchi.S3G003500.t1"; gene_id "Phchi.S3G003500"
Phchi.S3	AUGUSTUS	exon	878031	878384	.	-	.	transcript_id "Phchi.S3G003500.t1"; gene_id "Phchi.S3G003500"
Phchi.S3	AUGUSTUS	start_codon	878382	878384	.	-	0	transcript_id "Phchi.S3G003500.t1"; gene_id "Phchi.S3G003500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13633.t1 is derived from g12100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7841200	7842056	.	+	.	Phchi.S3G095200
Phchi.S3	AUGUSTUS	transcript	7841200	7842056	.	+	.	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	start_codon	7841200	7841202	.	+	0	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	CDS	7841200	7841523	0.64	+	0	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	exon	7841200	7841523	.	+	.	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	intron	7841524	7841618	.	+	.	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	CDS	7841619	7841792	1	+	0	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	exon	7841619	7841792	.	+	.	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	intron	7841793	7841894	.	+	.	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	CDS	7841895	7842056	1	+	0	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	exon	7841895	7842056	.	+	.	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
Phchi.S3	AUGUSTUS	stop_codon	7842057	7842059	.	+	0	transcript_id "Phchi.S3G095200.t1"; gene_id "Phchi.S3G095200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8007.t1 is derived from g5182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32419240	32422880	.	-	.	Phchi.S1G516600
Phchi.S1	AUGUSTUS	transcript	32419240	32422880	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	stop_codon	32419237	32419239	.	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32419240	32419384	0.63	-	1	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32419240	32419384	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32419385	32419471	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32419472	32419524	0.66	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32419472	32419524	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32419525	32419604	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32419605	32419675	0.81	-	2	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32419605	32419675	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32419676	32419760	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32419761	32419891	1	-	1	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32419761	32419891	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32419892	32419976	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32419977	32420038	1	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32419977	32420038	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32420039	32420122	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32420123	32420215	1	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32420123	32420215	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32420216	32420334	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32420335	32420461	0.59	-	1	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32420335	32420461	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32420462	32420543	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32420544	32420647	0.96	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32420544	32420647	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32420648	32420739	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32420740	32420863	0.75	-	1	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32420740	32420863	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32420864	32420964	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32420965	32421448	0.7	-	2	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32420965	32421448	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32421449	32421540	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32421541	32422146	0.52	-	2	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32421541	32422146	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32422147	32422399	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32422400	32422491	0.3	-	1	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32422400	32422491	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32422492	32422610	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32422611	32422758	0.65	-	2	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32422611	32422758	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	intron	32422759	32422840	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	CDS	32422841	32422880	0.69	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	exon	32422841	32422880	.	-	.	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
Phchi.S1	AUGUSTUS	start_codon	32422878	32422880	.	-	0	transcript_id "Phchi.S1G516600.t1"; gene_id "Phchi.S1G516600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13537.t1 is derived from g12004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7409774	7410331	.	-	.	Phchi.S3G085600
Phchi.S3	AUGUSTUS	transcript	7409774	7410331	.	-	.	transcript_id "Phchi.S3G085600.t1"; gene_id "Phchi.S3G085600"
Phchi.S3	AUGUSTUS	stop_codon	7409771	7409773	.	-	0	transcript_id "Phchi.S3G085600.t1"; gene_id "Phchi.S3G085600"
Phchi.S3	AUGUSTUS	CDS	7409774	7410331	0.99	-	0	transcript_id "Phchi.S3G085600.t1"; gene_id "Phchi.S3G085600"
Phchi.S3	AUGUSTUS	exon	7409774	7410331	.	-	.	transcript_id "Phchi.S3G085600.t1"; gene_id "Phchi.S3G085600"
Phchi.S3	AUGUSTUS	start_codon	7410329	7410331	.	-	0	transcript_id "Phchi.S3G085600.t1"; gene_id "Phchi.S3G085600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13829.t1 is derived from g12296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9093378	9095924	.	-	.	Phchi.S3G114800
Phchi.S3	AUGUSTUS	transcript	9093378	9095924	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	stop_codon	9093375	9093377	.	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093378	9093395	0.62	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093378	9093395	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093396	9093492	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093493	9093543	0.62	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093493	9093543	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093544	9093643	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093644	9093668	0.55	-	1	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093644	9093668	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093669	9093762	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093763	9093832	0.56	-	2	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093763	9093832	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093833	9094349	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9094350	9094456	0.49	-	1	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9094350	9094456	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9094457	9094629	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9094630	9094666	0.51	-	2	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9094630	9094666	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9094667	9094746	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9094747	9094862	0.8	-	1	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9094747	9094862	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9094863	9095057	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9095058	9095184	0.8	-	2	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9095058	9095184	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9095185	9095286	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9095287	9095368	1	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9095287	9095368	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9095369	9095464	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9095465	9095551	1	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9095465	9095551	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9095552	9095678	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9095679	9095924	1	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9095679	9095924	.	-	.	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	start_codon	9095922	9095924	.	-	0	transcript_id "Phchi.S3G114800.t1"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	transcript	9093378	9094116	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	stop_codon	9093375	9093377	.	-	0	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093378	9093395	0.7	-	0	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093378	9093395	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093396	9093492	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093493	9093543	0.7	-	0	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093493	9093543	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093544	9093643	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9093644	9093832	0.88	-	0	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9093644	9093832	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	intron	9093833	9094035	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	CDS	9094036	9094116	0.31	-	0	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	exon	9094036	9094116	.	-	.	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
Phchi.S3	AUGUSTUS	start_codon	9094114	9094116	.	-	0	transcript_id "Phchi.S3G114800.t2"; gene_id "Phchi.S3G114800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7720.t1 is derived from g4894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30790862	30793333	.	+	.	Phchi.S1G487900
Phchi.S1	AUGUSTUS	transcript	30790862	30793333	.	+	.	transcript_id "Phchi.S1G487900.t1"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	start_codon	30790862	30790864	.	+	0	transcript_id "Phchi.S1G487900.t1"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	CDS	30790862	30793333	0.65	+	0	transcript_id "Phchi.S1G487900.t1"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	exon	30790862	30793333	.	+	.	transcript_id "Phchi.S1G487900.t1"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	stop_codon	30793334	30793336	.	+	0	transcript_id "Phchi.S1G487900.t1"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	transcript	30791132	30793333	.	+	.	transcript_id "Phchi.S1G487900.t2"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	start_codon	30791132	30791134	.	+	0	transcript_id "Phchi.S1G487900.t2"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	CDS	30791132	30793333	0.58	+	0	transcript_id "Phchi.S1G487900.t2"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	exon	30791132	30793333	.	+	.	transcript_id "Phchi.S1G487900.t2"; gene_id "Phchi.S1G487900"
Phchi.S1	AUGUSTUS	stop_codon	30793334	30793336	.	+	0	transcript_id "Phchi.S1G487900.t2"; gene_id "Phchi.S1G487900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4232.t1 is derived from g1401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9037029	9038074	.	-	.	Phchi.S1G139100
Phchi.S1	AUGUSTUS	transcript	9037029	9038074	.	-	.	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	stop_codon	9037026	9037028	.	-	0	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	CDS	9037029	9037127	0.89	-	0	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	exon	9037029	9037127	.	-	.	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	intron	9037128	9037225	.	-	.	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	CDS	9037226	9038074	0.91	-	0	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	exon	9037226	9038074	.	-	.	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
Phchi.S1	AUGUSTUS	start_codon	9038072	9038074	.	-	0	transcript_id "Phchi.S1G139100.t1"; gene_id "Phchi.S1G139100"
# This transcript jg397.t2 is derived from g10179.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg398.t1 is derived from g10180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2879818	2881258	.	-	.	Phchi.S6G035700
Phchi.S6	AUGUSTUS	transcript	2879818	2881258	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	stop_codon	2879815	2879817	.	-	0	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2879818	2879970	1	-	0	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2879818	2879970	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	intron	2879971	2880055	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2880056	2880134	1	-	1	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2880056	2880134	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	intron	2880135	2880286	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2880287	2880382	1	-	1	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2880287	2880382	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	intron	2880383	2880564	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2880565	2880725	0.98	-	0	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2880565	2880725	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	intron	2880726	2880842	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2880843	2880917	0.98	-	0	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2880843	2880917	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	intron	2880918	2881006	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2881007	2881088	1	-	1	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2881007	2881088	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	intron	2881089	2881175	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	CDS	2881176	2881258	0.99	-	0	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	exon	2881176	2881258	.	-	.	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
Phchi.S6	AUGUSTUS	start_codon	2881256	2881258	.	-	0	transcript_id "Phchi.S6G035700.t1"; gene_id "Phchi.S6G035700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15974.t1 is derived from g9817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C54	AUGUSTUS	gene	38022	38393	.	+	.	Phchi.C54G000100
Phchi.C54	AUGUSTUS	transcript	38022	38393	.	+	.	transcript_id "Phchi.C54G000100.t1"; gene_id "Phchi.C54G000100"
Phchi.C54	AUGUSTUS	start_codon	38022	38024	.	+	0	transcript_id "Phchi.C54G000100.t1"; gene_id "Phchi.C54G000100"
Phchi.C54	AUGUSTUS	CDS	38022	38393	0.85	+	0	transcript_id "Phchi.C54G000100.t1"; gene_id "Phchi.C54G000100"
Phchi.C54	AUGUSTUS	exon	38022	38393	.	+	.	transcript_id "Phchi.C54G000100.t1"; gene_id "Phchi.C54G000100"
Phchi.C54	AUGUSTUS	stop_codon	38394	38396	.	+	0	transcript_id "Phchi.C54G000100.t1"; gene_id "Phchi.C54G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5785.t1 is derived from g2955.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18948921	18950219	.	+	.	Phchi.S1G294400
Phchi.S1	AUGUSTUS	transcript	18948921	18950219	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	start_codon	18948921	18948923	.	+	0	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18948921	18949207	0.87	+	0	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18948921	18949207	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	intron	18949208	18949455	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18949456	18949534	1	+	1	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18949456	18949534	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	intron	18949535	18949613	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18949614	18949872	0.19	+	0	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18949614	18949872	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	intron	18949873	18949965	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18949966	18950219	0.69	+	2	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18949966	18950219	.	+	.	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	stop_codon	18950220	18950222	.	+	0	transcript_id "Phchi.S1G294400.t1"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	transcript	18948921	18950219	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	start_codon	18948921	18948923	.	+	0	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18948921	18949293	0.84	+	0	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18948921	18949293	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	intron	18949294	18949445	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18949446	18949534	1	+	2	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18949446	18949534	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	intron	18949535	18949613	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18949614	18949872	0.17	+	0	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18949614	18949872	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	intron	18949873	18949965	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	CDS	18949966	18950219	0.53	+	2	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	exon	18949966	18950219	.	+	.	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
Phchi.S1	AUGUSTUS	stop_codon	18950220	18950222	.	+	0	transcript_id "Phchi.S1G294400.t2"; gene_id "Phchi.S1G294400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5492.t1 is derived from g2662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17113453	17118053	.	+	.	Phchi.S1G265100
Phchi.S1	AUGUSTUS	transcript	17113453	17118053	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	start_codon	17113453	17113455	.	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17113453	17113463	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17113453	17113463	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17113464	17113565	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17113566	17113656	1	+	1	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17113566	17113656	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17113657	17113729	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17113730	17113804	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17113730	17113804	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17113805	17113965	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17113966	17114096	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17113966	17114096	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17114097	17114171	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17114172	17114265	0.95	+	1	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17114172	17114265	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17114266	17114349	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17114350	17114448	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17114350	17114448	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17114449	17114551	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17114552	17114650	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17114552	17114650	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17114651	17114733	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17114734	17114789	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17114734	17114789	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17114790	17114956	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17114957	17115043	1	+	1	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17114957	17115043	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17115044	17115141	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17115142	17115206	1	+	1	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17115142	17115206	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17115207	17115290	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17115291	17115653	1	+	2	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17115291	17115653	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17115654	17115761	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17115762	17115976	1	+	2	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17115762	17115976	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17115977	17116060	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17116061	17116338	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17116061	17116338	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17116339	17116415	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17116416	17116567	1	+	1	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17116416	17116567	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17116568	17116674	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17116675	17116727	0.96	+	2	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17116675	17116727	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17116728	17116797	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17116798	17116920	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17116798	17116920	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17116921	17116998	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17116999	17117163	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17116999	17117163	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17117164	17117242	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17117243	17117395	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17117243	17117395	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17117396	17117478	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17117479	17117727	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17117479	17117727	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17117728	17117807	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17117808	17117897	0.99	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17117808	17117897	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	intron	17117898	17117993	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	CDS	17117994	17118053	1	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	exon	17117994	17118053	.	+	.	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
Phchi.S1	AUGUSTUS	stop_codon	17118054	17118056	.	+	0	transcript_id "Phchi.S1G265100.t1"; gene_id "Phchi.S1G265100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15770.t1 is derived from g14240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21273338	21275516	.	-	.	Phchi.S3G308900
Phchi.S3	AUGUSTUS	transcript	21273338	21275516	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	stop_codon	21273335	21273337	.	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21273338	21273523	0.91	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21273338	21273523	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21273524	21273623	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21273624	21273713	1	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21273624	21273713	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21273714	21273809	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21273810	21273926	1	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21273810	21273926	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21273927	21274031	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21274032	21274253	0.98	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21274032	21274253	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21274254	21274347	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21274348	21274408	1	-	1	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21274348	21274408	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21274409	21274541	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21274542	21274596	1	-	2	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21274542	21274596	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21274597	21274682	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21274683	21274773	1	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21274683	21274773	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21274774	21274861	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21274862	21274948	1	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21274862	21274948	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21274949	21275094	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21275095	21275253	1	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21275095	21275253	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	intron	21275254	21275345	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	CDS	21275346	21275516	0.97	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	exon	21275346	21275516	.	-	.	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
Phchi.S3	AUGUSTUS	start_codon	21275514	21275516	.	-	0	transcript_id "Phchi.S3G308900.t1"; gene_id "Phchi.S3G308900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5406.t1 is derived from g2576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16711707	16713930	.	+	.	Phchi.S1G256500
Phchi.S1	AUGUSTUS	transcript	16711707	16713930	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	start_codon	16711707	16711709	.	+	0	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	CDS	16711707	16711981	1	+	0	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	exon	16711707	16711981	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	intron	16711982	16712123	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	CDS	16712124	16712460	1	+	1	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	exon	16712124	16712460	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	intron	16712461	16712603	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	CDS	16712604	16713349	0.96	+	0	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	exon	16712604	16713349	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	intron	16713350	16713476	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	CDS	16713477	16713930	1	+	1	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	exon	16713477	16713930	.	+	.	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
Phchi.S1	AUGUSTUS	stop_codon	16713931	16713933	.	+	0	transcript_id "Phchi.S1G256500.t1"; gene_id "Phchi.S1G256500"
# This transcript jg14491.t2 is derived from g12959.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14492.t1 is derived from g12960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13125191	13126844	.	-	.	Phchi.S3G181100
Phchi.S3	AUGUSTUS	transcript	13125191	13126844	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	stop_codon	13125188	13125190	.	-	0	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13125191	13125211	1	-	0	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13125191	13125211	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	intron	13125212	13125557	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13125558	13125590	1	-	0	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13125558	13125590	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	intron	13125591	13125724	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13125725	13125857	1	-	1	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13125725	13125857	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	intron	13125858	13125956	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13125957	13126046	1	-	1	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13125957	13126046	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	intron	13126047	13126126	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13126127	13126216	1	-	1	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13126127	13126216	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	intron	13126217	13126355	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13126356	13126633	1	-	0	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13126356	13126633	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	intron	13126634	13126718	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	CDS	13126719	13126844	0.99	-	0	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	exon	13126719	13126844	.	-	.	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
Phchi.S3	AUGUSTUS	start_codon	13126842	13126844	.	-	0	transcript_id "Phchi.S3G181100.t1"; gene_id "Phchi.S3G181100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12566.t1 is derived from g8243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35446276	35446563	.	-	.	Phchi.S2G064600
Phchi.S2	AUGUSTUS	transcript	35446276	35446563	.	-	.	transcript_id "Phchi.S2G064600.t1"; gene_id "Phchi.S2G064600"
Phchi.S2	AUGUSTUS	stop_codon	35446273	35446275	.	-	0	transcript_id "Phchi.S2G064600.t1"; gene_id "Phchi.S2G064600"
Phchi.S2	AUGUSTUS	CDS	35446276	35446563	0.77	-	0	transcript_id "Phchi.S2G064600.t1"; gene_id "Phchi.S2G064600"
Phchi.S2	AUGUSTUS	exon	35446276	35446563	.	-	.	transcript_id "Phchi.S2G064600.t1"; gene_id "Phchi.S2G064600"
Phchi.S2	AUGUSTUS	start_codon	35446561	35446563	.	-	0	transcript_id "Phchi.S2G064600.t1"; gene_id "Phchi.S2G064600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2412.t1 is derived from g9332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6536918	6539297	.	+	.	Phchi.S5G102100
Phchi.S5	AUGUSTUS	transcript	6536918	6539297	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	start_codon	6536918	6536920	.	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6536918	6536932	1	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6536918	6536932	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6536933	6537322	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6537323	6537529	1	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6537323	6537529	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6537530	6537692	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6537693	6537777	1	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6537693	6537777	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6537778	6537868	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6537869	6538009	0.86	+	2	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6537869	6538009	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6538010	6538112	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6538113	6538226	0.98	+	2	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6538113	6538226	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6538227	6538349	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6538350	6538447	1	+	2	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6538350	6538447	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6538448	6538549	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6538550	6538623	1	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6538550	6538623	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6538624	6538750	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6538751	6538856	1	+	1	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6538751	6538856	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6538857	6538930	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6538931	6539058	1	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6538931	6539058	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	intron	6539059	6539188	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	CDS	6539189	6539297	0.99	+	1	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	exon	6539189	6539297	.	+	.	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
Phchi.S5	AUGUSTUS	stop_codon	6539298	6539300	.	+	0	transcript_id "Phchi.S5G102100.t1"; gene_id "Phchi.S5G102100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1401.t1 is derived from g8320.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	137464	143730	.	-	.	Phchi.S5G001000
Phchi.S5	AUGUSTUS	transcript	137464	143730	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	stop_codon	137461	137463	.	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137464	137538	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137464	137538	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	137539	137634	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137635	137697	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137635	137697	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	137698	137769	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137770	137886	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137770	137886	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	137887	137971	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137972	138049	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137972	138049	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138050	138137	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138138	138273	1	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138138	138273	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138274	138460	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138461	138573	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138461	138573	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138574	138658	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138659	138700	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138659	138700	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138701	138854	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138855	138914	0.89	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138855	138914	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138915	139030	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139031	139088	0.85	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139031	139088	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139089	139235	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139236	139270	0.51	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139236	139270	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139271	139353	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139354	139450	0.69	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139354	139450	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139451	139536	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139537	139649	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139537	139649	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139650	139778	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139779	139958	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139779	139958	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139959	140074	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140075	140128	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140075	140128	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	140129	140214	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140215	140389	1	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140215	140389	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	140390	140481	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140482	140639	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140482	140639	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	140640	140810	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140811	141006	1	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140811	141006	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	141007	141221	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	141222	141301	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	141222	141301	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	141302	141386	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	141387	141446	0.99	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	141387	141446	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	141447	141568	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	141569	142007	0.68	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	141569	142007	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	142008	142162	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	142163	142584	0.97	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	142163	142584	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	142585	142704	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	142705	142786	1	-	1	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	142705	142786	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	142787	142880	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	142881	143029	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	142881	143029	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	143030	143205	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	143206	143313	1	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	143206	143313	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	143314	143583	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	143584	143730	0.66	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	143584	143730	.	-	.	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	start_codon	143728	143730	.	-	0	transcript_id "Phchi.S5G001000.t1"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	transcript	137464	143730	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	stop_codon	137461	137463	.	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137464	137538	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137464	137538	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	137539	137634	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137635	137697	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137635	137697	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	137698	137769	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137770	137886	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137770	137886	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	137887	137971	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	137972	138049	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	137972	138049	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138050	138137	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138138	138273	1	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138138	138273	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138274	138460	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138461	138573	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138461	138573	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138574	138658	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138659	138700	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138659	138700	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138701	138854	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	138855	138914	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	138855	138914	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	138915	139030	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139031	139088	1	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139031	139088	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139089	139239	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139240	139303	0.71	-	2	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139240	139303	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139304	139430	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139431	139450	0.28	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139431	139450	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139451	139536	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139537	139649	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139537	139649	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139650	139778	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	139779	139958	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	139779	139958	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	139959	140074	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140075	140128	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140075	140128	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	140129	140214	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140215	140389	1	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140215	140389	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	140390	140481	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140482	140639	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140482	140639	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	140640	140810	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	140811	141006	1	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	140811	141006	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	141007	141221	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	141222	141301	0.99	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	141222	141301	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	141302	141386	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	141387	141446	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	141387	141446	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	141447	141568	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	141569	142007	0.71	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	141569	142007	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	142008	142162	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	142163	142584	0.93	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	142163	142584	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	142585	142704	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	142705	142786	1	-	1	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	142705	142786	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	142787	142880	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	142881	143029	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	142881	143029	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	143030	143205	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	143206	143313	1	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	143206	143313	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	intron	143314	143583	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	CDS	143584	143730	0.65	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	exon	143584	143730	.	-	.	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
Phchi.S5	AUGUSTUS	start_codon	143728	143730	.	-	0	transcript_id "Phchi.S5G001000.t2"; gene_id "Phchi.S5G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12152.t1 is derived from g7828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4963367	4963609	.	-	.	Phchi.S2G023200
Phchi.S2	AUGUSTUS	transcript	4963367	4963609	.	-	.	transcript_id "Phchi.S2G023200.t1"; gene_id "Phchi.S2G023200"
Phchi.S2	AUGUSTUS	stop_codon	4963364	4963366	.	-	0	transcript_id "Phchi.S2G023200.t1"; gene_id "Phchi.S2G023200"
Phchi.S2	AUGUSTUS	CDS	4963367	4963609	0.61	-	0	transcript_id "Phchi.S2G023200.t1"; gene_id "Phchi.S2G023200"
Phchi.S2	AUGUSTUS	exon	4963367	4963609	.	-	.	transcript_id "Phchi.S2G023200.t1"; gene_id "Phchi.S2G023200"
Phchi.S2	AUGUSTUS	start_codon	4963607	4963609	.	-	0	transcript_id "Phchi.S2G023200.t1"; gene_id "Phchi.S2G023200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4506.t1 is derived from g1676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10873357	10875007	.	+	.	Phchi.S1G166500
Phchi.S1	AUGUSTUS	transcript	10873357	10875007	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	start_codon	10873357	10873359	.	+	0	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	CDS	10873357	10874313	0.54	+	0	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	exon	10873357	10874313	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	intron	10874314	10874408	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	CDS	10874409	10874453	0.88	+	0	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	exon	10874409	10874453	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	intron	10874454	10874685	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	CDS	10874686	10874749	0.78	+	0	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	exon	10874686	10874749	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	intron	10874750	10874819	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	CDS	10874820	10874886	0.85	+	2	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	exon	10874820	10874886	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	intron	10874887	10874973	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	CDS	10874974	10875007	0.84	+	1	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	exon	10874974	10875007	.	+	.	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
Phchi.S1	AUGUSTUS	stop_codon	10875008	10875010	.	+	0	transcript_id "Phchi.S1G166500.t1"; gene_id "Phchi.S1G166500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9851.t1 is derived from g7027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44086743	44087263	.	-	.	Phchi.S1G701000
Phchi.S1	AUGUSTUS	transcript	44086743	44087263	.	-	.	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	stop_codon	44086740	44086742	.	-	0	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	CDS	44086743	44086941	0.99	-	1	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	exon	44086743	44086941	.	-	.	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	intron	44086942	44087028	.	-	.	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	CDS	44087029	44087104	1	-	2	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	exon	44087029	44087104	.	-	.	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	intron	44087105	44087259	.	-	.	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	CDS	44087260	44087263	1	-	0	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	exon	44087260	44087263	.	-	.	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
Phchi.S1	AUGUSTUS	start_codon	44087261	44087263	.	-	0	transcript_id "Phchi.S1G701000.t1"; gene_id "Phchi.S1G701000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5726.t1 is derived from g2896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18572496	18572975	.	-	.	Phchi.S1G288500
Phchi.S1	AUGUSTUS	transcript	18572496	18572975	.	-	.	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	stop_codon	18572493	18572495	.	-	0	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	CDS	18572496	18572592	0.72	-	1	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	exon	18572496	18572592	.	-	.	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	intron	18572593	18572791	.	-	.	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	CDS	18572792	18572825	0.72	-	2	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	exon	18572792	18572825	.	-	.	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	intron	18572826	18572902	.	-	.	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	CDS	18572903	18572975	0.69	-	0	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	exon	18572903	18572975	.	-	.	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
Phchi.S1	AUGUSTUS	start_codon	18572973	18572975	.	-	0	transcript_id "Phchi.S1G288500.t1"; gene_id "Phchi.S1G288500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7535.t1 is derived from g4709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29942402	29943985	.	-	.	Phchi.S1G469400
Phchi.S1	AUGUSTUS	transcript	29942402	29943985	.	-	.	transcript_id "Phchi.S1G469400.t1"; gene_id "Phchi.S1G469400"
Phchi.S1	AUGUSTUS	stop_codon	29942399	29942401	.	-	0	transcript_id "Phchi.S1G469400.t1"; gene_id "Phchi.S1G469400"
Phchi.S1	AUGUSTUS	CDS	29942402	29943985	0.99	-	0	transcript_id "Phchi.S1G469400.t1"; gene_id "Phchi.S1G469400"
Phchi.S1	AUGUSTUS	exon	29942402	29943985	.	-	.	transcript_id "Phchi.S1G469400.t1"; gene_id "Phchi.S1G469400"
Phchi.S1	AUGUSTUS	start_codon	29943983	29943985	.	-	0	transcript_id "Phchi.S1G469400.t1"; gene_id "Phchi.S1G469400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4623.t1 is derived from g1793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11449059	11449496	.	+	.	Phchi.S1G178200
Phchi.S1	AUGUSTUS	transcript	11449059	11449496	.	+	.	transcript_id "Phchi.S1G178200.t1"; gene_id "Phchi.S1G178200"
Phchi.S1	AUGUSTUS	start_codon	11449059	11449061	.	+	0	transcript_id "Phchi.S1G178200.t1"; gene_id "Phchi.S1G178200"
Phchi.S1	AUGUSTUS	CDS	11449059	11449496	0.69	+	0	transcript_id "Phchi.S1G178200.t1"; gene_id "Phchi.S1G178200"
Phchi.S1	AUGUSTUS	exon	11449059	11449496	.	+	.	transcript_id "Phchi.S1G178200.t1"; gene_id "Phchi.S1G178200"
Phchi.S1	AUGUSTUS	stop_codon	11449497	11449499	.	+	0	transcript_id "Phchi.S1G178200.t1"; gene_id "Phchi.S1G178200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10909.t1 is derived from g14959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2880121	2882929	.	-	.	Phchi.S4G049100
Phchi.S4	AUGUSTUS	transcript	2880121	2882929	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	stop_codon	2880118	2880120	.	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880121	2880195	1	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880121	2880195	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880196	2880268	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880269	2880320	1	-	1	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880269	2880320	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880321	2880422	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880423	2880490	1	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880423	2880490	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880491	2880599	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880600	2880695	0.68	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880600	2880695	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880696	2880847	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880848	2880948	1	-	2	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880848	2880948	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880949	2881070	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881071	2881141	0.98	-	1	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881071	2881141	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881142	2881247	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881248	2881353	1	-	2	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881248	2881353	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881354	2881436	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881437	2881505	1	-	2	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881437	2881505	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881506	2881636	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881637	2881698	1	-	1	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881637	2881698	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881699	2881904	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881905	2881977	1	-	2	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881905	2881977	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881978	2882075	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882076	2882128	1	-	1	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882076	2882128	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882129	2882246	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882247	2882300	1	-	1	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882247	2882300	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882301	2882396	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882397	2882446	1	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882397	2882446	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882447	2882540	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882541	2882618	1	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882541	2882618	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882619	2882776	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882777	2882820	1	-	2	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882777	2882820	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882821	2882913	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882914	2882929	1	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882914	2882929	.	-	.	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	start_codon	2882927	2882929	.	-	0	transcript_id "Phchi.S4G049100.t1"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	transcript	2880121	2882929	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	stop_codon	2880118	2880120	.	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880121	2880195	1	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880121	2880195	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880196	2880268	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880269	2880320	1	-	1	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880269	2880320	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880321	2880422	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880423	2880490	1	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880423	2880490	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880491	2880599	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880600	2880695	0.71	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880600	2880695	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880696	2880847	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2880848	2880948	1	-	2	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2880848	2880948	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2880949	2881070	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881071	2881141	0.96	-	1	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881071	2881141	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881142	2881247	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881248	2881353	1	-	2	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881248	2881353	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881354	2881436	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881437	2881505	1	-	2	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881437	2881505	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881506	2881636	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881637	2881698	1	-	1	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881637	2881698	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881699	2881904	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2881905	2881977	1	-	2	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2881905	2881977	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2881978	2882075	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882076	2882128	1	-	1	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882076	2882128	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882129	2882246	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882247	2882300	1	-	1	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882247	2882300	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882301	2882396	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882397	2882446	1	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882397	2882446	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882447	2882540	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882541	2882618	1	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882541	2882618	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882619	2882776	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882777	2882829	0.83	-	2	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882777	2882829	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	intron	2882830	2882913	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	CDS	2882914	2882929	0.83	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	exon	2882914	2882929	.	-	.	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
Phchi.S4	AUGUSTUS	start_codon	2882927	2882929	.	-	0	transcript_id "Phchi.S4G049100.t2"; gene_id "Phchi.S4G049100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5419.t1 is derived from g2589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16793449	16794588	.	-	.	Phchi.S1G257800
Phchi.S1	AUGUSTUS	transcript	16793449	16794588	.	-	.	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	stop_codon	16793446	16793448	.	-	0	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	CDS	16793449	16793462	0.81	-	2	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	exon	16793449	16793462	.	-	.	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	intron	16793463	16793636	.	-	.	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	CDS	16793637	16794414	0.99	-	0	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	exon	16793637	16794414	.	-	.	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	intron	16794415	16794495	.	-	.	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	CDS	16794496	16794588	0.65	-	0	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	exon	16794496	16794588	.	-	.	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
Phchi.S1	AUGUSTUS	start_codon	16794586	16794588	.	-	0	transcript_id "Phchi.S1G257800.t1"; gene_id "Phchi.S1G257800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5682.t1 is derived from g2852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18302892	18307915	.	-	.	Phchi.S1G284100
Phchi.S1	AUGUSTUS	transcript	18302892	18307915	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	stop_codon	18302889	18302891	.	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18302892	18302989	0.98	-	2	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18302892	18302989	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18302990	18303087	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18303088	18303119	0.79	-	1	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18303088	18303119	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18303120	18303197	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18303198	18303230	0.87	-	1	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18303198	18303230	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18303231	18303350	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18303351	18303434	1	-	1	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18303351	18303434	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18303435	18303565	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18303566	18303915	0.91	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18303566	18303915	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18303916	18304029	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18304030	18304192	0.83	-	1	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18304030	18304192	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18304193	18304330	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18304331	18305145	0.97	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18304331	18305145	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18305146	18305342	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18305343	18305510	1	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18305343	18305510	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18305511	18305606	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18305607	18305684	1	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18305607	18305684	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18305685	18305773	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18305774	18305875	1	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18305774	18305875	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18305876	18305992	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18305993	18306196	0.94	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18305993	18306196	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18306197	18306378	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18306379	18306558	1	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18306379	18306558	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18306559	18306653	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18306654	18306854	0.98	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18306654	18306854	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18306855	18306935	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18306936	18306976	0.82	-	2	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18306936	18306976	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18306977	18307112	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18307113	18307167	0.77	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18307113	18307167	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	intron	18307168	18307672	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	CDS	18307673	18307915	0.25	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	exon	18307673	18307915	.	-	.	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
Phchi.S1	AUGUSTUS	start_codon	18307913	18307915	.	-	0	transcript_id "Phchi.S1G284100.t1"; gene_id "Phchi.S1G284100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8944.t1 is derived from g6119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38790341	38791147	.	-	.	Phchi.S1G610300
Phchi.S1	AUGUSTUS	transcript	38790341	38791147	.	-	.	transcript_id "Phchi.S1G610300.t1"; gene_id "Phchi.S1G610300"
Phchi.S1	AUGUSTUS	stop_codon	38790338	38790340	.	-	0	transcript_id "Phchi.S1G610300.t1"; gene_id "Phchi.S1G610300"
Phchi.S1	AUGUSTUS	CDS	38790341	38791147	0.83	-	0	transcript_id "Phchi.S1G610300.t1"; gene_id "Phchi.S1G610300"
Phchi.S1	AUGUSTUS	exon	38790341	38791147	.	-	.	transcript_id "Phchi.S1G610300.t1"; gene_id "Phchi.S1G610300"
Phchi.S1	AUGUSTUS	start_codon	38791145	38791147	.	-	0	transcript_id "Phchi.S1G610300.t1"; gene_id "Phchi.S1G610300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10683.t1 is derived from g14733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1569478	1570343	.	-	.	Phchi.S4G026500
Phchi.S4	AUGUSTUS	transcript	1569478	1570343	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	stop_codon	1569475	1569477	.	-	0	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	CDS	1569478	1569529	0.74	-	1	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	exon	1569478	1569529	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	intron	1569530	1569717	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	CDS	1569718	1569814	0.75	-	2	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	exon	1569718	1569814	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	intron	1569815	1569977	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	CDS	1569978	1570045	1	-	1	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	exon	1569978	1570045	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	intron	1570046	1570335	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	CDS	1570336	1570343	1	-	0	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	exon	1570336	1570343	.	-	.	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
Phchi.S4	AUGUSTUS	start_codon	1570341	1570343	.	-	0	transcript_id "Phchi.S4G026500.t1"; gene_id "Phchi.S4G026500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1086.t1 is derived from g10869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7522490	7523785	.	+	.	Phchi.S6G104500
Phchi.S6	AUGUSTUS	transcript	7522490	7523785	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	start_codon	7522490	7522492	.	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7522490	7522567	0.68	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7522490	7522567	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	intron	7522568	7522668	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7522669	7522751	1	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7522669	7522751	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	intron	7522752	7522855	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7522856	7522910	0.97	+	1	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7522856	7522910	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	intron	7522911	7523067	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7523068	7523109	0.97	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7523068	7523109	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	intron	7523110	7523210	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7523211	7523288	0.82	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7523211	7523288	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	intron	7523289	7523441	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7523442	7523564	1	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7523442	7523564	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	intron	7523565	7523653	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	CDS	7523654	7523785	0.98	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	exon	7523654	7523785	.	+	.	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
Phchi.S6	AUGUSTUS	stop_codon	7523786	7523788	.	+	0	transcript_id "Phchi.S6G104500.t1"; gene_id "Phchi.S6G104500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5225.t1 is derived from g2395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15619546	15619863	.	-	.	Phchi.S1G238400
Phchi.S1	AUGUSTUS	transcript	15619546	15619863	.	-	.	transcript_id "Phchi.S1G238400.t1"; gene_id "Phchi.S1G238400"
Phchi.S1	AUGUSTUS	stop_codon	15619543	15619545	.	-	0	transcript_id "Phchi.S1G238400.t1"; gene_id "Phchi.S1G238400"
Phchi.S1	AUGUSTUS	CDS	15619546	15619863	0.55	-	0	transcript_id "Phchi.S1G238400.t1"; gene_id "Phchi.S1G238400"
Phchi.S1	AUGUSTUS	exon	15619546	15619863	.	-	.	transcript_id "Phchi.S1G238400.t1"; gene_id "Phchi.S1G238400"
Phchi.S1	AUGUSTUS	start_codon	15619861	15619863	.	-	0	transcript_id "Phchi.S1G238400.t1"; gene_id "Phchi.S1G238400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2677.t1 is derived from g9597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8153488	8154294	.	+	.	Phchi.S5G128600
Phchi.S5	AUGUSTUS	transcript	8153488	8154294	.	+	.	transcript_id "Phchi.S5G128600.t1"; gene_id "Phchi.S5G128600"
Phchi.S5	AUGUSTUS	start_codon	8153488	8153490	.	+	0	transcript_id "Phchi.S5G128600.t1"; gene_id "Phchi.S5G128600"
Phchi.S5	AUGUSTUS	CDS	8153488	8154294	1	+	0	transcript_id "Phchi.S5G128600.t1"; gene_id "Phchi.S5G128600"
Phchi.S5	AUGUSTUS	exon	8153488	8154294	.	+	.	transcript_id "Phchi.S5G128600.t1"; gene_id "Phchi.S5G128600"
Phchi.S5	AUGUSTUS	stop_codon	8154295	8154297	.	+	0	transcript_id "Phchi.S5G128600.t1"; gene_id "Phchi.S5G128600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10941.t1 is derived from g14991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3193182	3195560	.	-	.	Phchi.S4G052300
Phchi.S4	AUGUSTUS	transcript	3193182	3194786	.	-	.	transcript_id "Phchi.S4G052300.t1"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	stop_codon	3193179	3193181	.	-	0	transcript_id "Phchi.S4G052300.t1"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	CDS	3193182	3194786	0.99	-	0	transcript_id "Phchi.S4G052300.t1"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	exon	3193182	3194786	.	-	.	transcript_id "Phchi.S4G052300.t1"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	start_codon	3194784	3194786	.	-	0	transcript_id "Phchi.S4G052300.t1"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	transcript	3193182	3195560	.	-	.	transcript_id "Phchi.S4G052300.t2"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	stop_codon	3193179	3193181	.	-	0	transcript_id "Phchi.S4G052300.t2"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	CDS	3193182	3195560	0.75	-	0	transcript_id "Phchi.S4G052300.t2"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	exon	3193182	3195560	.	-	.	transcript_id "Phchi.S4G052300.t2"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	start_codon	3195558	3195560	.	-	0	transcript_id "Phchi.S4G052300.t2"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	transcript	3193182	3194705	.	-	.	transcript_id "Phchi.S4G052300.t3"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	stop_codon	3193179	3193181	.	-	0	transcript_id "Phchi.S4G052300.t3"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	CDS	3193182	3194705	0.68	-	0	transcript_id "Phchi.S4G052300.t3"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	exon	3193182	3194705	.	-	.	transcript_id "Phchi.S4G052300.t3"; gene_id "Phchi.S4G052300"
Phchi.S4	AUGUSTUS	start_codon	3194703	3194705	.	-	0	transcript_id "Phchi.S4G052300.t3"; gene_id "Phchi.S4G052300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10122.t1 is derived from g7298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45836848	45838646	.	-	.	Phchi.S1G728100
Phchi.S1	AUGUSTUS	transcript	45836848	45838646	.	-	.	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	stop_codon	45836845	45836847	.	-	0	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	CDS	45836848	45838258	0.97	-	1	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	exon	45836848	45838258	.	-	.	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	intron	45838259	45838605	.	-	.	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	CDS	45838606	45838646	0.94	-	0	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	exon	45838606	45838646	.	-	.	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
Phchi.S1	AUGUSTUS	start_codon	45838644	45838646	.	-	0	transcript_id "Phchi.S1G728100.t1"; gene_id "Phchi.S1G728100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12281.t1 is derived from g7957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8475123	8476434	.	-	.	Phchi.S2G036100
Phchi.S2	AUGUSTUS	transcript	8475123	8476434	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	stop_codon	8475120	8475122	.	-	0	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	CDS	8475123	8475211	0.99	-	2	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	exon	8475123	8475211	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	intron	8475212	8475304	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	CDS	8475305	8475432	0.99	-	1	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	exon	8475305	8475432	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	intron	8475433	8475560	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	CDS	8475561	8475643	0.95	-	0	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	exon	8475561	8475643	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	intron	8475644	8475896	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	CDS	8475897	8476023	0.56	-	1	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	exon	8475897	8476023	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	intron	8476024	8476112	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	CDS	8476113	8476153	0.69	-	0	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	exon	8476113	8476153	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	intron	8476154	8476248	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	CDS	8476249	8476434	0.79	-	0	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	exon	8476249	8476434	.	-	.	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
Phchi.S2	AUGUSTUS	start_codon	8476432	8476434	.	-	0	transcript_id "Phchi.S2G036100.t1"; gene_id "Phchi.S2G036100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8667.t1 is derived from g5842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37355531	37356411	.	-	.	Phchi.S1G582600
Phchi.S1	AUGUSTUS	transcript	37355531	37356411	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	stop_codon	37355528	37355530	.	-	0	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	CDS	37355531	37355624	0.83	-	1	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	exon	37355531	37355624	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	intron	37355625	37355718	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	CDS	37355719	37355801	0.83	-	0	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	exon	37355719	37355801	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	intron	37355802	37355899	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	CDS	37355900	37356023	1	-	1	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	exon	37355900	37356023	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	intron	37356024	37356124	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	CDS	37356125	37356411	0.9	-	0	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	exon	37356125	37356411	.	-	.	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
Phchi.S1	AUGUSTUS	start_codon	37356409	37356411	.	-	0	transcript_id "Phchi.S1G582600.t1"; gene_id "Phchi.S1G582600"
# This transcript jg1844.t2 is derived from g8764.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1845.t1 is derived from g8765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3533082	3533600	.	-	.	Phchi.S5G045400
Phchi.S5	AUGUSTUS	transcript	3533082	3533600	.	-	.	transcript_id "Phchi.S5G045400.t1"; gene_id "Phchi.S5G045400"
Phchi.S5	AUGUSTUS	stop_codon	3533079	3533081	.	-	0	transcript_id "Phchi.S5G045400.t1"; gene_id "Phchi.S5G045400"
Phchi.S5	AUGUSTUS	CDS	3533082	3533600	1	-	0	transcript_id "Phchi.S5G045400.t1"; gene_id "Phchi.S5G045400"
Phchi.S5	AUGUSTUS	exon	3533082	3533600	.	-	.	transcript_id "Phchi.S5G045400.t1"; gene_id "Phchi.S5G045400"
Phchi.S5	AUGUSTUS	start_codon	3533598	3533600	.	-	0	transcript_id "Phchi.S5G045400.t1"; gene_id "Phchi.S5G045400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg752.t1 is derived from g10534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5337084	5338193	.	+	.	Phchi.S6G071100
Phchi.S6	AUGUSTUS	transcript	5337084	5338193	.	+	.	transcript_id "Phchi.S6G071100.t1"; gene_id "Phchi.S6G071100"
Phchi.S6	AUGUSTUS	start_codon	5337084	5337086	.	+	0	transcript_id "Phchi.S6G071100.t1"; gene_id "Phchi.S6G071100"
Phchi.S6	AUGUSTUS	CDS	5337084	5338193	0.47	+	0	transcript_id "Phchi.S6G071100.t1"; gene_id "Phchi.S6G071100"
Phchi.S6	AUGUSTUS	exon	5337084	5338193	.	+	.	transcript_id "Phchi.S6G071100.t1"; gene_id "Phchi.S6G071100"
Phchi.S6	AUGUSTUS	stop_codon	5338194	5338196	.	+	0	transcript_id "Phchi.S6G071100.t1"; gene_id "Phchi.S6G071100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2040.t1 is derived from g8960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4559826	4561253	.	-	.	Phchi.S5G064900
Phchi.S5	AUGUSTUS	transcript	4559826	4561253	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	stop_codon	4559823	4559825	.	-	0	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	CDS	4559826	4559976	0.98	-	1	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	exon	4559826	4559976	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	intron	4559977	4560064	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	CDS	4560065	4560118	1	-	1	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	exon	4560065	4560118	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	intron	4560119	4560308	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	CDS	4560309	4560616	1	-	0	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	exon	4560309	4560616	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	intron	4560617	4560691	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	CDS	4560692	4560841	1	-	0	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	exon	4560692	4560841	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	intron	4560842	4560914	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	CDS	4560915	4561024	1	-	2	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	exon	4560915	4561024	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	intron	4561025	4561105	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	CDS	4561106	4561253	0.46	-	0	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	exon	4561106	4561253	.	-	.	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
Phchi.S5	AUGUSTUS	start_codon	4561251	4561253	.	-	0	transcript_id "Phchi.S5G064900.t1"; gene_id "Phchi.S5G064900"
# This transcript jg11952.t2 is derived from g7627.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11953.t1 is derived from g7628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	179431	181501	.	+	.	Phchi.S2G003300
Phchi.S2	AUGUSTUS	transcript	179431	181501	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	start_codon	179431	179433	.	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	179431	179718	1	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	179431	179718	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	179719	179790	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	179791	179982	1	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	179791	179982	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	179983	180051	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	180052	180146	1	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	180052	180146	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	180147	180246	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	180247	180367	1	+	1	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	180247	180367	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	180368	180456	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	180457	180536	1	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	180457	180536	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	180537	180627	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	180628	180690	1	+	1	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	180628	180690	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	180691	180791	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	180792	180907	1	+	1	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	180792	180907	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	180908	180998	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	180999	181048	0.96	+	2	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	180999	181048	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	181049	181127	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	181128	181205	0.9	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	181128	181205	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	intron	181206	181294	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	CDS	181295	181501	1	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	exon	181295	181501	.	+	.	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
Phchi.S2	AUGUSTUS	stop_codon	181502	181504	.	+	0	transcript_id "Phchi.S2G003300.t1"; gene_id "Phchi.S2G003300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15776.t1 is derived from g14246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21292358	21293122	.	-	.	Phchi.S3G309500
Phchi.S3	AUGUSTUS	transcript	21292358	21293122	.	-	.	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	stop_codon	21292355	21292357	.	-	0	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	CDS	21292358	21292872	1	-	2	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	exon	21292358	21292872	.	-	.	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	intron	21292873	21292962	.	-	.	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	CDS	21292963	21293122	0.47	-	0	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	exon	21292963	21293122	.	-	.	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
Phchi.S3	AUGUSTUS	start_codon	21293120	21293122	.	-	0	transcript_id "Phchi.S3G309500.t1"; gene_id "Phchi.S3G309500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15426.t1 is derived from g13894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19031418	19041024	.	+	.	Phchi.S3G274500
Phchi.S3	AUGUSTUS	transcript	19031418	19041024	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	start_codon	19031418	19031420	.	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19031418	19031420	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19031418	19031420	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19031421	19031638	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19031639	19031767	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19031639	19031767	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19031768	19031880	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19031881	19032024	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19031881	19032024	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19032025	19032181	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19032182	19032327	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19032182	19032327	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19032328	19032408	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19032409	19032565	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19032409	19032565	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19032566	19032736	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19032737	19032795	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19032737	19032795	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19032796	19032951	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19032952	19033108	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19032952	19033108	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19033109	19033194	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19033195	19033344	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19033195	19033344	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19033345	19033442	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19033443	19033579	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19033443	19033579	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19033580	19033757	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19033758	19033904	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19033758	19033904	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19033905	19034040	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19034041	19034142	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19034041	19034142	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19034143	19034325	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19034326	19034383	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19034326	19034383	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19034384	19034495	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19034496	19034597	0.88	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19034496	19034597	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19034598	19034863	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19034864	19034901	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19034864	19034901	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19034902	19035157	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19035158	19035284	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19035158	19035284	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19035285	19035374	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19035375	19035545	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19035375	19035545	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19035546	19035731	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19035732	19035863	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19035732	19035863	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19035864	19036033	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19036034	19036143	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19036034	19036143	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19036144	19036294	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19036295	19036355	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19036295	19036355	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19036356	19036518	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19036519	19036696	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19036519	19036696	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19036697	19036774	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19036775	19036980	1	+	2	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19036775	19036980	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19036981	19037072	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19037073	19037192	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19037073	19037192	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19037193	19037272	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19037273	19037370	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19037273	19037370	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19037371	19037461	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19037462	19037482	0.9	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19037462	19037482	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19037483	19037568	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19037569	19037671	0.9	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19037569	19037671	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19037672	19037841	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19037842	19037981	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19037842	19037981	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19037982	19038094	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19038095	19038209	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19038095	19038209	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19038210	19038376	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19038377	19038430	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19038377	19038430	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19038431	19038513	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19038514	19038603	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19038514	19038603	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19038604	19038728	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19038729	19038899	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19038729	19038899	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19038900	19039016	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19039017	19039169	0.99	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19039017	19039169	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19039170	19039270	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19039271	19039477	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19039271	19039477	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19039478	19039629	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19039630	19039773	0.99	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19039630	19039773	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19039774	19039879	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19039880	19039950	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19039880	19039950	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19039951	19040037	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19040038	19040137	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19040038	19040137	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19040138	19040265	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19040266	19040322	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19040266	19040322	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19040323	19040413	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19040414	19040470	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19040414	19040470	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19040471	19040569	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19040570	19040650	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19040570	19040650	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19040651	19040735	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19040736	19040818	1	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19040736	19040818	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	intron	19040819	19040903	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	CDS	19040904	19041024	1	+	1	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	exon	19040904	19041024	.	+	.	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
Phchi.S3	AUGUSTUS	stop_codon	19041025	19041027	.	+	0	transcript_id "Phchi.S3G274500.t1"; gene_id "Phchi.S3G274500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12898.t1 is derived from g11363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3066549	3067908	.	+	.	Phchi.S3G021700
Phchi.S3	AUGUSTUS	transcript	3066549	3067908	.	+	.	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	start_codon	3066549	3066551	.	+	0	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	CDS	3066549	3066733	0.71	+	0	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	exon	3066549	3066733	.	+	.	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	intron	3066734	3066814	.	+	.	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	CDS	3066815	3066959	1	+	1	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	exon	3066815	3066959	.	+	.	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	intron	3066960	3067197	.	+	.	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	CDS	3067198	3067908	1	+	0	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	exon	3067198	3067908	.	+	.	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
Phchi.S3	AUGUSTUS	stop_codon	3067909	3067911	.	+	0	transcript_id "Phchi.S3G021700.t1"; gene_id "Phchi.S3G021700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9793.t1 is derived from g6969.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43719276	43719925	.	-	.	Phchi.S1G695200
Phchi.S1	AUGUSTUS	transcript	43719276	43719925	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	stop_codon	43719273	43719275	.	-	0	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719276	43719356	0.74	-	0	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719276	43719356	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	intron	43719357	43719554	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719555	43719669	0.95	-	1	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719555	43719669	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	intron	43719670	43719757	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719758	43719774	0.95	-	0	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719758	43719774	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	intron	43719775	43719859	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719860	43719925	0.7	-	0	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719860	43719925	.	-	.	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	start_codon	43719923	43719925	.	-	0	transcript_id "Phchi.S1G695200.t1"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	transcript	43719276	43719925	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	stop_codon	43719273	43719275	.	-	0	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719276	43719356	0.6	-	0	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719276	43719356	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	intron	43719357	43719512	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719513	43719669	0.85	-	1	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719513	43719669	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	intron	43719670	43719757	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719758	43719774	0.84	-	0	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719758	43719774	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	intron	43719775	43719859	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	CDS	43719860	43719925	0.61	-	0	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	exon	43719860	43719925	.	-	.	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
Phchi.S1	AUGUSTUS	start_codon	43719923	43719925	.	-	0	transcript_id "Phchi.S1G695200.t2"; gene_id "Phchi.S1G695200"
# This transcript jg4459.t2 is derived from g1629.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4459.t3 is derived from g1629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4460.t1 is derived from g1630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10596281	10596771	.	-	.	Phchi.S1G161900
Phchi.S1	AUGUSTUS	transcript	10596281	10596771	.	-	.	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	stop_codon	10596278	10596280	.	-	0	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	CDS	10596281	10596414	0.8	-	2	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	exon	10596281	10596414	.	-	.	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	intron	10596415	10596503	.	-	.	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	CDS	10596504	10596771	0.81	-	0	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	exon	10596504	10596771	.	-	.	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
Phchi.S1	AUGUSTUS	start_codon	10596769	10596771	.	-	0	transcript_id "Phchi.S1G161900.t1"; gene_id "Phchi.S1G161900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12072.t1 is derived from g7747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2067340	2068464	.	-	.	Phchi.S2G015200
Phchi.S2	AUGUSTUS	transcript	2067854	2068464	.	-	.	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	stop_codon	2067851	2067853	.	-	0	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	CDS	2067854	2067908	0.99	-	1	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	exon	2067854	2067908	.	-	.	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	intron	2067909	2068033	.	-	.	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	CDS	2068034	2068464	0.99	-	0	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	exon	2068034	2068464	.	-	.	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	start_codon	2068462	2068464	.	-	0	transcript_id "Phchi.S2G015200.t1"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	transcript	2067340	2068464	.	-	.	transcript_id "Phchi.S2G015200.t2"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	stop_codon	2067337	2067339	.	-	0	transcript_id "Phchi.S2G015200.t2"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	CDS	2067340	2068464	0.83	-	0	transcript_id "Phchi.S2G015200.t2"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	exon	2067340	2068464	.	-	.	transcript_id "Phchi.S2G015200.t2"; gene_id "Phchi.S2G015200"
Phchi.S2	AUGUSTUS	start_codon	2068462	2068464	.	-	0	transcript_id "Phchi.S2G015200.t2"; gene_id "Phchi.S2G015200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg559.t1 is derived from g10341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4041734	4043307	.	+	.	Phchi.S6G051800
Phchi.S6	AUGUSTUS	transcript	4041734	4043307	.	+	.	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	start_codon	4041734	4041736	.	+	0	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	CDS	4041734	4042094	0.35	+	0	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	exon	4041734	4042094	.	+	.	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	intron	4042095	4042347	.	+	.	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	CDS	4042348	4042574	0.64	+	2	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	exon	4042348	4042574	.	+	.	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	intron	4042575	4042794	.	+	.	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	CDS	4042795	4043307	1	+	0	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	exon	4042795	4043307	.	+	.	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
Phchi.S6	AUGUSTUS	stop_codon	4043308	4043310	.	+	0	transcript_id "Phchi.S6G051800.t1"; gene_id "Phchi.S6G051800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4911.t1 is derived from g2081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13356925	13357503	.	+	.	Phchi.S1G207000
Phchi.S1	AUGUSTUS	transcript	13356925	13357503	.	+	.	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	start_codon	13356925	13356927	.	+	0	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	CDS	13356925	13357248	0.8	+	0	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	exon	13356925	13357248	.	+	.	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	intron	13357249	13357338	.	+	.	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	CDS	13357339	13357503	0.99	+	0	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	exon	13357339	13357503	.	+	.	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
Phchi.S1	AUGUSTUS	stop_codon	13357504	13357506	.	+	0	transcript_id "Phchi.S1G207000.t1"; gene_id "Phchi.S1G207000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7020.t1 is derived from g4192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26426912	26427172	.	+	.	Phchi.S1G417900
Phchi.S1	AUGUSTUS	transcript	26426912	26427172	.	+	.	transcript_id "Phchi.S1G417900.t1"; gene_id "Phchi.S1G417900"
Phchi.S1	AUGUSTUS	start_codon	26426912	26426914	.	+	0	transcript_id "Phchi.S1G417900.t1"; gene_id "Phchi.S1G417900"
Phchi.S1	AUGUSTUS	CDS	26426912	26427172	0.52	+	0	transcript_id "Phchi.S1G417900.t1"; gene_id "Phchi.S1G417900"
Phchi.S1	AUGUSTUS	exon	26426912	26427172	.	+	.	transcript_id "Phchi.S1G417900.t1"; gene_id "Phchi.S1G417900"
Phchi.S1	AUGUSTUS	stop_codon	26427173	26427175	.	+	0	transcript_id "Phchi.S1G417900.t1"; gene_id "Phchi.S1G417900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1654.t1 is derived from g8573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2242900	2243843	.	-	.	Phchi.S5G026300
Phchi.S5	AUGUSTUS	transcript	2242900	2243843	.	-	.	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	stop_codon	2242897	2242899	.	-	0	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	CDS	2242900	2243552	0.99	-	2	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	exon	2242900	2243552	.	-	.	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	intron	2243553	2243662	.	-	.	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	CDS	2243663	2243843	0.93	-	0	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	exon	2243663	2243843	.	-	.	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
Phchi.S5	AUGUSTUS	start_codon	2243841	2243843	.	-	0	transcript_id "Phchi.S5G026300.t1"; gene_id "Phchi.S5G026300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14961.t1 is derived from g13429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15772730	15773590	.	-	.	Phchi.S3G228000
Phchi.S3	AUGUSTUS	transcript	15772730	15773590	.	-	.	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	stop_codon	15772727	15772729	.	-	0	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	CDS	15772730	15772963	1	-	0	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	exon	15772730	15772963	.	-	.	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	intron	15772964	15773074	.	-	.	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	CDS	15773075	15773197	1	-	0	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	exon	15773075	15773197	.	-	.	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	intron	15773198	15773317	.	-	.	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	CDS	15773318	15773590	0.99	-	0	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	exon	15773318	15773590	.	-	.	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
Phchi.S3	AUGUSTUS	start_codon	15773588	15773590	.	-	0	transcript_id "Phchi.S3G228000.t1"; gene_id "Phchi.S3G228000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13706.t1 is derived from g12173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8288824	8290241	.	+	.	Phchi.S3G102500
Phchi.S3	AUGUSTUS	transcript	8288824	8290241	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	start_codon	8288824	8288826	.	+	0	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8288824	8288953	0.98	+	0	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8288824	8288953	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8288954	8289038	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8289039	8289103	1	+	2	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8289039	8289103	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8289104	8289233	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8289234	8289297	1	+	0	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8289234	8289297	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8289298	8289425	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8289426	8289435	1	+	2	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8289426	8289435	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8289436	8289557	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8289558	8289589	1	+	1	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8289558	8289589	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8289590	8289695	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8289696	8289808	1	+	2	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8289696	8289808	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8289809	8289961	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8289962	8290038	1	+	0	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8289962	8290038	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	intron	8290039	8290132	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	CDS	8290133	8290241	1	+	1	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	exon	8290133	8290241	.	+	.	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
Phchi.S3	AUGUSTUS	stop_codon	8290242	8290244	.	+	0	transcript_id "Phchi.S3G102500.t1"; gene_id "Phchi.S3G102500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9037.t1 is derived from g6212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39237994	39239301	.	-	.	Phchi.S1G619600
Phchi.S1	AUGUSTUS	transcript	39237994	39239301	.	-	.	transcript_id "Phchi.S1G619600.t1"; gene_id "Phchi.S1G619600"
Phchi.S1	AUGUSTUS	stop_codon	39237991	39237993	.	-	0	transcript_id "Phchi.S1G619600.t1"; gene_id "Phchi.S1G619600"
Phchi.S1	AUGUSTUS	CDS	39237994	39239301	0.99	-	0	transcript_id "Phchi.S1G619600.t1"; gene_id "Phchi.S1G619600"
Phchi.S1	AUGUSTUS	exon	39237994	39239301	.	-	.	transcript_id "Phchi.S1G619600.t1"; gene_id "Phchi.S1G619600"
Phchi.S1	AUGUSTUS	start_codon	39239299	39239301	.	-	0	transcript_id "Phchi.S1G619600.t1"; gene_id "Phchi.S1G619600"
# This transcript jg12284.t2 is derived from g7960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12285.t1 is derived from g7961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8753130	8755355	.	-	.	Phchi.S2G036500
Phchi.S2	AUGUSTUS	transcript	8753130	8755355	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	stop_codon	8753127	8753129	.	-	0	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	CDS	8753130	8753248	1	-	2	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	exon	8753130	8753248	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	intron	8753249	8753347	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	CDS	8753348	8753404	1	-	2	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	exon	8753348	8753404	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	intron	8753405	8754114	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	CDS	8754115	8754193	1	-	0	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	exon	8754115	8754193	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	intron	8754194	8754312	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	CDS	8754313	8754552	1	-	0	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	exon	8754313	8754552	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	intron	8754553	8754872	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	CDS	8754873	8754977	1	-	0	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	exon	8754873	8754977	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	intron	8754978	8755061	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	CDS	8755062	8755355	1	-	0	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	exon	8755062	8755355	.	-	.	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
Phchi.S2	AUGUSTUS	start_codon	8755353	8755355	.	-	0	transcript_id "Phchi.S2G036500.t1"; gene_id "Phchi.S2G036500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5238.t1 is derived from g2408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15799451	15803318	.	+	.	Phchi.S1G239700
Phchi.S1	AUGUSTUS	transcript	15799451	15803318	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	start_codon	15799451	15799453	.	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15799451	15799635	0.48	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15799451	15799635	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15799636	15799750	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15799751	15799861	1	+	1	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15799751	15799861	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15799862	15799959	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15799960	15800042	1	+	1	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15799960	15800042	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15800043	15800192	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15800193	15800310	1	+	2	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15800193	15800310	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15800311	15800395	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15800396	15800538	1	+	1	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15800396	15800538	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15800539	15800632	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15800633	15800682	0.97	+	2	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15800633	15800682	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15800683	15800823	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15800824	15801177	0.97	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15800824	15801177	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15801178	15801291	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15801292	15801362	1	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15801292	15801362	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15801363	15801488	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15801489	15801745	1	+	1	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15801489	15801745	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15801746	15801841	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15801842	15802023	1	+	2	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15801842	15802023	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15802024	15802151	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15802152	15802435	1	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15802152	15802435	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15802436	15802524	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15802525	15802642	1	+	1	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15802525	15802642	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15802643	15802734	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15802735	15802911	1	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15802735	15802911	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	intron	15802912	15802997	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	CDS	15802998	15803318	0.56	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	exon	15802998	15803318	.	+	.	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
Phchi.S1	AUGUSTUS	stop_codon	15803319	15803321	.	+	0	transcript_id "Phchi.S1G239700.t1"; gene_id "Phchi.S1G239700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10316.t1 is derived from g7492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47088180	47090053	.	+	.	Phchi.S1G747500
Phchi.S1	AUGUSTUS	transcript	47088180	47090053	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	start_codon	47088180	47088182	.	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47088180	47088385	0.99	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47088180	47088385	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47088386	47088481	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47088482	47088605	0.99	+	1	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47088482	47088605	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47088606	47088714	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47088715	47088832	0.99	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47088715	47088832	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47088833	47088962	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47088963	47089099	0.99	+	2	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47088963	47089099	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47089100	47089200	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47089201	47089302	1	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47089201	47089302	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47089303	47089441	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47089442	47089534	1	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47089442	47089534	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47089535	47089615	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47089616	47089691	0.66	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47089616	47089691	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	intron	47089692	47089793	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	CDS	47089794	47090053	0.74	+	2	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	exon	47089794	47090053	.	+	.	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
Phchi.S1	AUGUSTUS	stop_codon	47090054	47090056	.	+	0	transcript_id "Phchi.S1G747500.t1"; gene_id "Phchi.S1G747500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1757.t1 is derived from g8677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2900062	2905066	.	+	.	Phchi.S5G036600
Phchi.S5	AUGUSTUS	transcript	2900062	2905066	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	start_codon	2900062	2900064	.	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2900062	2900235	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2900062	2900235	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2900236	2900324	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2900325	2900468	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2900325	2900468	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2900469	2900566	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2900567	2900674	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2900567	2900674	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2900675	2900847	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2900848	2900943	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2900848	2900943	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2900944	2901056	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2901057	2901190	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2901057	2901190	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2901191	2901323	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2901324	2901384	1	+	1	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2901324	2901384	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2901385	2901527	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2901528	2901694	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2901528	2901694	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2901695	2901858	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2901859	2901964	1	+	1	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2901859	2901964	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2901965	2902210	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2902211	2902288	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2902211	2902288	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2902289	2902393	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2902394	2902455	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2902394	2902455	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2902456	2902534	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2902535	2902607	1	+	1	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2902535	2902607	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2902608	2902739	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2902740	2902805	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2902740	2902805	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2902806	2902945	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2902946	2903089	0.95	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2902946	2903089	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2903090	2903196	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2903197	2903257	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2903197	2903257	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2903258	2903367	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2903368	2903475	0.86	+	2	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2903368	2903475	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2903476	2903600	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2903601	2903655	1	+	2	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2903601	2903655	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2903656	2903767	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2903768	2903936	0.99	+	1	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2903768	2903936	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2903937	2904040	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2904041	2904105	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2904041	2904105	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2904106	2904248	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2904249	2904339	1	+	1	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2904249	2904339	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2904340	2904423	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2904424	2904507	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2904424	2904507	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2904508	2904665	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2904666	2904758	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2904666	2904758	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2904759	2904855	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2904856	2904884	1	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2904856	2904884	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	intron	2904885	2904978	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	CDS	2904979	2905066	1	+	1	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	exon	2904979	2905066	.	+	.	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
Phchi.S5	AUGUSTUS	stop_codon	2905067	2905069	.	+	0	transcript_id "Phchi.S5G036600.t1"; gene_id "Phchi.S5G036600"
# This transcript jg7512.t2 is derived from g4686.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7513.t1 is derived from g4687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29790830	29792253	.	+	.	Phchi.S1G467200
Phchi.S1	AUGUSTUS	transcript	29790830	29792253	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	start_codon	29790830	29790832	.	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	CDS	29790830	29791135	0.96	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	exon	29790830	29791135	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	intron	29791136	29791389	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	CDS	29791390	29791500	0.98	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	exon	29791390	29791500	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	intron	29791501	29791620	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	CDS	29791621	29791731	0.99	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	exon	29791621	29791731	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	intron	29791732	29791991	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	CDS	29791992	29792150	0.85	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	exon	29791992	29792150	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	intron	29792151	29792238	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	CDS	29792239	29792253	0.85	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	exon	29792239	29792253	.	+	.	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
Phchi.S1	AUGUSTUS	stop_codon	29792254	29792256	.	+	0	transcript_id "Phchi.S1G467200.t1"; gene_id "Phchi.S1G467200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15535.t1 is derived from g14004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19756435	19757411	.	+	.	Phchi.S3G285400
Phchi.S3	AUGUSTUS	transcript	19756435	19757411	.	+	.	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	start_codon	19756435	19756437	.	+	0	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	CDS	19756435	19756674	0.96	+	0	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	exon	19756435	19756674	.	+	.	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	intron	19756675	19756927	.	+	.	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	CDS	19756928	19757165	1	+	0	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	exon	19756928	19757165	.	+	.	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	intron	19757166	19757271	.	+	.	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	CDS	19757272	19757411	0.99	+	2	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	exon	19757272	19757411	.	+	.	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
Phchi.S3	AUGUSTUS	stop_codon	19757412	19757414	.	+	0	transcript_id "Phchi.S3G285400.t1"; gene_id "Phchi.S3G285400"
# This transcript jg7722.t2 is derived from g4896.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7723.t1 is derived from g4897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30816649	30817584	.	+	.	Phchi.S1G488200
Phchi.S1	AUGUSTUS	transcript	30816649	30817584	.	+	.	transcript_id "Phchi.S1G488200.t1"; gene_id "Phchi.S1G488200"
Phchi.S1	AUGUSTUS	start_codon	30816649	30816651	.	+	0	transcript_id "Phchi.S1G488200.t1"; gene_id "Phchi.S1G488200"
Phchi.S1	AUGUSTUS	CDS	30816649	30817584	0.41	+	0	transcript_id "Phchi.S1G488200.t1"; gene_id "Phchi.S1G488200"
Phchi.S1	AUGUSTUS	exon	30816649	30817584	.	+	.	transcript_id "Phchi.S1G488200.t1"; gene_id "Phchi.S1G488200"
Phchi.S1	AUGUSTUS	stop_codon	30817585	30817587	.	+	0	transcript_id "Phchi.S1G488200.t1"; gene_id "Phchi.S1G488200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14979.t1 is derived from g13447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15856903	15857967	.	+	.	Phchi.S3G229800
Phchi.S3	AUGUSTUS	transcript	15856903	15857967	.	+	.	transcript_id "Phchi.S3G229800.t1"; gene_id "Phchi.S3G229800"
Phchi.S3	AUGUSTUS	start_codon	15856903	15856905	.	+	0	transcript_id "Phchi.S3G229800.t1"; gene_id "Phchi.S3G229800"
Phchi.S3	AUGUSTUS	CDS	15856903	15857967	0.75	+	0	transcript_id "Phchi.S3G229800.t1"; gene_id "Phchi.S3G229800"
Phchi.S3	AUGUSTUS	exon	15856903	15857967	.	+	.	transcript_id "Phchi.S3G229800.t1"; gene_id "Phchi.S3G229800"
Phchi.S3	AUGUSTUS	stop_codon	15857968	15857970	.	+	0	transcript_id "Phchi.S3G229800.t1"; gene_id "Phchi.S3G229800"
# This transcript jg8345.t2 is derived from g5520.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8345.t3 is derived from g5520.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8346.t1 is derived from g5521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35428304	35433974	.	+	.	Phchi.S1G550500
Phchi.S1	AUGUSTUS	transcript	35428304	35433974	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	start_codon	35428304	35428306	.	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35428304	35428484	0.95	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35428304	35428484	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35428485	35428691	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35428692	35429379	0.96	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35428692	35429379	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35429380	35429535	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35429536	35429617	1	+	1	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35429536	35429617	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35429618	35429749	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35429750	35429837	1	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35429750	35429837	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35429838	35430088	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35430089	35430279	0.99	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35430089	35430279	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35430280	35430385	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35430386	35430518	0.8	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35430386	35430518	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35430519	35430614	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35430615	35430751	1	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35430615	35430751	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35430752	35430926	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35430927	35431001	1	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35430927	35431001	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35431002	35431080	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35431081	35431197	0.79	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35431081	35431197	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35431198	35431304	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35431305	35431868	0.81	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35431305	35431868	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35431869	35432499	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35432500	35432614	1	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35432500	35432614	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35432615	35432746	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35432747	35432884	1	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35432747	35432884	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35432885	35432967	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35432968	35433034	1	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35432968	35433034	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35433035	35433130	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35433131	35433240	1	+	1	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35433131	35433240	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35433241	35433371	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35433372	35433415	0.83	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35433372	35433415	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35433416	35433546	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35433547	35433554	0.86	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35433547	35433554	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35433555	35433648	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35433649	35433707	0.86	+	1	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35433649	35433707	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	intron	35433708	35433897	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	CDS	35433898	35433974	0.83	+	2	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	exon	35433898	35433974	.	+	.	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
Phchi.S1	AUGUSTUS	stop_codon	35433975	35433977	.	+	0	transcript_id "Phchi.S1G550500.t1"; gene_id "Phchi.S1G550500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1266.t1 is derived from g11049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8716464	8717822	.	+	.	Phchi.S6G122500
Phchi.S6	AUGUSTUS	transcript	8716464	8717822	.	+	.	transcript_id "Phchi.S6G122500.t1"; gene_id "Phchi.S6G122500"
Phchi.S6	AUGUSTUS	start_codon	8716464	8716466	.	+	0	transcript_id "Phchi.S6G122500.t1"; gene_id "Phchi.S6G122500"
Phchi.S6	AUGUSTUS	CDS	8716464	8717822	0.37	+	0	transcript_id "Phchi.S6G122500.t1"; gene_id "Phchi.S6G122500"
Phchi.S6	AUGUSTUS	exon	8716464	8717822	.	+	.	transcript_id "Phchi.S6G122500.t1"; gene_id "Phchi.S6G122500"
Phchi.S6	AUGUSTUS	stop_codon	8717823	8717825	.	+	0	transcript_id "Phchi.S6G122500.t1"; gene_id "Phchi.S6G122500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg99.t1 is derived from g9881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	505828	506485	.	+	.	Phchi.S6G005800
Phchi.S6	AUGUSTUS	transcript	505828	506485	.	+	.	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	start_codon	505828	505830	.	+	0	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	CDS	505828	505873	0.62	+	0	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	exon	505828	505873	.	+	.	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	intron	505874	506252	.	+	.	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	CDS	506253	506485	0.51	+	2	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	exon	506253	506485	.	+	.	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
Phchi.S6	AUGUSTUS	stop_codon	506486	506488	.	+	0	transcript_id "Phchi.S6G005800.t1"; gene_id "Phchi.S6G005800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14894.t1 is derived from g13362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15317939	15318307	.	+	.	Phchi.S3G221300
Phchi.S3	AUGUSTUS	transcript	15317939	15318307	.	+	.	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	start_codon	15317939	15317941	.	+	0	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	CDS	15317939	15318016	1	+	0	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	exon	15317939	15318016	.	+	.	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	intron	15318017	15318103	.	+	.	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	CDS	15318104	15318307	1	+	0	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	exon	15318104	15318307	.	+	.	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
Phchi.S3	AUGUSTUS	stop_codon	15318308	15318310	.	+	0	transcript_id "Phchi.S3G221300.t1"; gene_id "Phchi.S3G221300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1408.t1 is derived from g8327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	183519	188124	.	-	.	Phchi.S5G001700
Phchi.S5	AUGUSTUS	transcript	183519	188124	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	stop_codon	183516	183518	.	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	183519	183606	0.91	-	1	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	183519	183606	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	183607	183703	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	183704	183888	0.93	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	183704	183888	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	183889	183977	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	183978	184145	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	183978	184145	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	184146	184233	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	184234	184374	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	184234	184374	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	184375	184443	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	184444	184662	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	184444	184662	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	184663	184818	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	184819	184935	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	184819	184935	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	184936	185050	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	185051	185147	1	-	1	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	185051	185147	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	185148	185241	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	185242	185333	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	185242	185333	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	185334	185431	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	185432	185494	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	185432	185494	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	185495	185590	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	185591	185650	0.94	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	185591	185650	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	185651	185768	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	185769	185933	0.76	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	185769	185933	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	185934	186171	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	186172	186357	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	186172	186357	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	186358	186446	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	186447	186737	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	186447	186737	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	186738	186820	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	186821	186964	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	186821	186964	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	186965	187051	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	187052	187732	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	187052	187732	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	intron	187733	187806	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	CDS	187807	188124	1	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	exon	187807	188124	.	-	.	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
Phchi.S5	AUGUSTUS	start_codon	188122	188124	.	-	0	transcript_id "Phchi.S5G001700.t1"; gene_id "Phchi.S5G001700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12564.t1 is derived from g8241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35294411	35297015	.	+	.	Phchi.S2G064400
Phchi.S2	AUGUSTUS	transcript	35294411	35297015	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	start_codon	35294411	35294413	.	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35294411	35294431	0.53	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35294411	35294431	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35294432	35294516	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35294517	35294682	1	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35294517	35294682	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35294683	35294875	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35294876	35294997	1	+	2	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35294876	35294997	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35294998	35295125	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35295126	35295263	1	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35295126	35295263	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35295264	35295347	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35295348	35295481	1	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35295348	35295481	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35295482	35295649	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35295650	35295712	1	+	1	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35295650	35295712	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35295713	35295830	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35295831	35295894	1	+	1	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35295831	35295894	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35295895	35296042	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35296043	35296178	1	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35296043	35296178	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35296179	35296261	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35296262	35296335	1	+	2	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35296262	35296335	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35296336	35296426	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35296427	35296521	1	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35296427	35296521	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35296522	35296642	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35296643	35296674	1	+	1	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35296643	35296674	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	intron	35296675	35296788	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	CDS	35296789	35297015	0.98	+	2	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	exon	35296789	35297015	.	+	.	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
Phchi.S2	AUGUSTUS	stop_codon	35297016	35297018	.	+	0	transcript_id "Phchi.S2G064400.t1"; gene_id "Phchi.S2G064400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5333.t1 is derived from g2503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16337879	16338562	.	+	.	Phchi.S1G249200
Phchi.S1	AUGUSTUS	transcript	16337879	16338562	.	+	.	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	start_codon	16337879	16337881	.	+	0	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	CDS	16337879	16337998	0.72	+	0	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	exon	16337879	16337998	.	+	.	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	intron	16337999	16338090	.	+	.	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	CDS	16338091	16338198	1	+	0	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	exon	16338091	16338198	.	+	.	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	intron	16338199	16338361	.	+	.	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	CDS	16338362	16338562	0.78	+	0	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	exon	16338362	16338562	.	+	.	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
Phchi.S1	AUGUSTUS	stop_codon	16338563	16338565	.	+	0	transcript_id "Phchi.S1G249200.t1"; gene_id "Phchi.S1G249200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4950.t1 is derived from g2120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13694641	13695538	.	-	.	Phchi.S1G210900
Phchi.S1	AUGUSTUS	transcript	13694641	13695538	.	-	.	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	stop_codon	13694638	13694640	.	-	0	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	CDS	13694641	13694673	0.21	-	0	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	exon	13694641	13694673	.	-	.	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	intron	13694674	13694788	.	-	.	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	CDS	13694789	13695538	0.31	-	0	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	exon	13694789	13695538	.	-	.	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
Phchi.S1	AUGUSTUS	start_codon	13695536	13695538	.	-	0	transcript_id "Phchi.S1G210900.t1"; gene_id "Phchi.S1G210900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9432.t1 is derived from g6608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41434525	41436917	.	+	.	Phchi.S1G659100
Phchi.S1	AUGUSTUS	transcript	41434525	41436917	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	start_codon	41434525	41434527	.	+	0	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41434525	41434678	0.45	+	0	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41434525	41434678	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41434679	41435154	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41435155	41435331	1	+	2	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41435155	41435331	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41435332	41435414	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41435415	41435505	1	+	2	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41435415	41435505	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41435506	41435588	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41435589	41435628	1	+	1	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41435589	41435628	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41435629	41435809	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41435810	41435930	1	+	0	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41435810	41435930	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41435931	41436060	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41436061	41436152	1	+	2	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41436061	41436152	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41436153	41436253	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41436254	41436350	1	+	0	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41436254	41436350	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41436351	41436446	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41436447	41436688	0.98	+	2	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41436447	41436688	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	intron	41436689	41436794	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	CDS	41436795	41436917	0.97	+	0	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	exon	41436795	41436917	.	+	.	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
Phchi.S1	AUGUSTUS	stop_codon	41436918	41436920	.	+	0	transcript_id "Phchi.S1G659100.t1"; gene_id "Phchi.S1G659100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4957.t1 is derived from g2127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13732048	13736498	.	-	.	Phchi.S1G211600
Phchi.S1	AUGUSTUS	transcript	13732048	13736498	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	stop_codon	13732045	13732047	.	-	0	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13732048	13732257	1	-	0	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13732048	13732257	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13732258	13732416	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13732417	13732534	1	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13732417	13732534	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13732535	13732640	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13732641	13732830	0.98	-	2	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13732641	13732830	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13732831	13732925	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13732926	13732991	1	-	2	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13732926	13732991	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13732992	13733067	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13733068	13733194	1	-	0	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13733068	13733194	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13733195	13733283	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13733284	13733483	1	-	2	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13733284	13733483	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13733484	13733615	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13733616	13733836	0.34	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13733616	13733836	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13733837	13733945	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13733946	13734011	0.65	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13733946	13734011	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13734012	13734204	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13734205	13734267	1	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13734205	13734267	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13734268	13734402	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13734403	13734474	1	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13734403	13734474	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13734475	13734569	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13734570	13734644	0.99	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13734570	13734644	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13734645	13734750	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13734751	13734880	1	-	2	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13734751	13734880	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13734881	13734981	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13734982	13735211	1	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13734982	13735211	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13735212	13735293	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13735294	13735545	1	-	1	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13735294	13735545	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13735546	13735653	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13735654	13735922	1	-	0	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13735654	13735922	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13735923	13736014	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13736015	13736328	0.99	-	2	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13736015	13736328	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	intron	13736329	13736422	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	CDS	13736423	13736498	1	-	0	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	exon	13736423	13736498	.	-	.	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
Phchi.S1	AUGUSTUS	start_codon	13736496	13736498	.	-	0	transcript_id "Phchi.S1G211600.t1"; gene_id "Phchi.S1G211600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11772.t1 is derived from g15824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8106687	8109952	.	-	.	Phchi.S4G135400
Phchi.S4	AUGUSTUS	transcript	8106687	8109952	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	stop_codon	8106684	8106686	.	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8106687	8106922	1	-	2	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8106687	8106922	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8106923	8107013	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8107014	8107086	1	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8107014	8107086	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8107087	8107179	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8107180	8107367	0.71	-	2	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8107180	8107367	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8107368	8107450	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8107451	8107631	0.67	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8107451	8107631	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8107632	8107747	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8107748	8107975	0.99	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8107748	8107975	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8107976	8108187	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8108188	8108254	1	-	1	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8108188	8108254	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8108255	8108371	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8108372	8108472	1	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8108372	8108472	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8108473	8108608	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8108609	8108734	0.98	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8108609	8108734	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8108735	8108844	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8108845	8109004	0.99	-	1	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8108845	8109004	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8109005	8109112	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8109113	8109198	0.81	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8109113	8109198	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8109199	8109287	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8109288	8109408	1	-	1	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8109288	8109408	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	intron	8109409	8109494	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	CDS	8109495	8109952	0.99	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	exon	8109495	8109952	.	-	.	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
Phchi.S4	AUGUSTUS	start_codon	8109950	8109952	.	-	0	transcript_id "Phchi.S4G135400.t1"; gene_id "Phchi.S4G135400"
# This transcript jg15917.t2 is derived from g14387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15918.t1 is derived from g14388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22203656	22204558	.	+	.	Phchi.S3G323700
Phchi.S3	AUGUSTUS	transcript	22203656	22204558	.	+	.	transcript_id "Phchi.S3G323700.t1"; gene_id "Phchi.S3G323700"
Phchi.S3	AUGUSTUS	start_codon	22203656	22203658	.	+	0	transcript_id "Phchi.S3G323700.t1"; gene_id "Phchi.S3G323700"
Phchi.S3	AUGUSTUS	CDS	22203656	22204558	1	+	0	transcript_id "Phchi.S3G323700.t1"; gene_id "Phchi.S3G323700"
Phchi.S3	AUGUSTUS	exon	22203656	22204558	.	+	.	transcript_id "Phchi.S3G323700.t1"; gene_id "Phchi.S3G323700"
Phchi.S3	AUGUSTUS	stop_codon	22204559	22204561	.	+	0	transcript_id "Phchi.S3G323700.t1"; gene_id "Phchi.S3G323700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15355.t1 is derived from g13823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18564857	18566342	.	-	.	Phchi.S3G267400
Phchi.S3	AUGUSTUS	transcript	18564857	18566342	.	-	.	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	stop_codon	18564854	18564856	.	-	0	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	CDS	18564857	18564867	1	-	2	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	exon	18564857	18564867	.	-	.	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	intron	18564868	18565235	.	-	.	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	CDS	18565236	18565443	0.86	-	0	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	exon	18565236	18565443	.	-	.	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	intron	18565444	18565499	.	-	.	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	CDS	18565500	18566342	0.41	-	0	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	exon	18565500	18566342	.	-	.	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
Phchi.S3	AUGUSTUS	start_codon	18566340	18566342	.	-	0	transcript_id "Phchi.S3G267400.t1"; gene_id "Phchi.S3G267400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15189.t1 is derived from g13657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17480123	17481205	.	-	.	Phchi.S3G250800
Phchi.S3	AUGUSTUS	transcript	17480123	17481205	.	-	.	transcript_id "Phchi.S3G250800.t1"; gene_id "Phchi.S3G250800"
Phchi.S3	AUGUSTUS	stop_codon	17480120	17480122	.	-	0	transcript_id "Phchi.S3G250800.t1"; gene_id "Phchi.S3G250800"
Phchi.S3	AUGUSTUS	CDS	17480123	17481205	0.27	-	0	transcript_id "Phchi.S3G250800.t1"; gene_id "Phchi.S3G250800"
Phchi.S3	AUGUSTUS	exon	17480123	17481205	.	-	.	transcript_id "Phchi.S3G250800.t1"; gene_id "Phchi.S3G250800"
Phchi.S3	AUGUSTUS	start_codon	17481203	17481205	.	-	0	transcript_id "Phchi.S3G250800.t1"; gene_id "Phchi.S3G250800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11178.t1 is derived from g15228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4514142	4515050	.	+	.	Phchi.S4G076000
Phchi.S4	AUGUSTUS	transcript	4514142	4515050	.	+	.	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	start_codon	4514142	4514144	.	+	0	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	CDS	4514142	4514581	1	+	0	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	exon	4514142	4514581	.	+	.	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	intron	4514582	4514707	.	+	.	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	CDS	4514708	4515050	1	+	1	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	exon	4514708	4515050	.	+	.	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
Phchi.S4	AUGUSTUS	stop_codon	4515051	4515053	.	+	0	transcript_id "Phchi.S4G076000.t1"; gene_id "Phchi.S4G076000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8165.t1 is derived from g5340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34245144	34247013	.	+	.	Phchi.S1G532400
Phchi.S1	AUGUSTUS	transcript	34245144	34247013	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	start_codon	34245144	34245146	.	+	0	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34245144	34245914	0.8	+	0	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34245144	34245914	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	intron	34245915	34246036	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34246037	34246170	0.87	+	0	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34246037	34246170	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	intron	34246171	34246274	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34246275	34246388	1	+	1	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34246275	34246388	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	intron	34246389	34246480	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34246481	34246649	1	+	1	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34246481	34246649	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	intron	34246650	34246738	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34246739	34246807	1	+	0	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34246739	34246807	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	intron	34246808	34246891	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34246892	34246931	0.32	+	0	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34246892	34246931	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	intron	34246932	34246981	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	CDS	34246982	34247013	0.32	+	2	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	exon	34246982	34247013	.	+	.	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
Phchi.S1	AUGUSTUS	stop_codon	34247014	34247016	.	+	0	transcript_id "Phchi.S1G532400.t1"; gene_id "Phchi.S1G532400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg613.t1 is derived from g10395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4405281	4405727	.	-	.	Phchi.S6G057200
Phchi.S6	AUGUSTUS	transcript	4405281	4405727	.	-	.	transcript_id "Phchi.S6G057200.t1"; gene_id "Phchi.S6G057200"
Phchi.S6	AUGUSTUS	stop_codon	4405278	4405280	.	-	0	transcript_id "Phchi.S6G057200.t1"; gene_id "Phchi.S6G057200"
Phchi.S6	AUGUSTUS	CDS	4405281	4405727	0.58	-	0	transcript_id "Phchi.S6G057200.t1"; gene_id "Phchi.S6G057200"
Phchi.S6	AUGUSTUS	exon	4405281	4405727	.	-	.	transcript_id "Phchi.S6G057200.t1"; gene_id "Phchi.S6G057200"
Phchi.S6	AUGUSTUS	start_codon	4405725	4405727	.	-	0	transcript_id "Phchi.S6G057200.t1"; gene_id "Phchi.S6G057200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14684.t1 is derived from g13152.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14157474	14158781	.	+	.	Phchi.S3G200300
Phchi.S3	AUGUSTUS	transcript	14157474	14158781	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	start_codon	14157474	14157476	.	+	0	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14157474	14157505	0.46	+	0	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14157474	14157505	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14157506	14157758	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14157759	14157817	0.69	+	1	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14157759	14157817	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14157818	14157990	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14157991	14158082	0.68	+	2	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14157991	14158082	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14158083	14158152	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14158153	14158240	1	+	0	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14158153	14158240	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14158241	14158457	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14158458	14158581	0.44	+	2	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14158458	14158581	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14158582	14158666	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14158667	14158781	0.34	+	1	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14158667	14158781	.	+	.	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	stop_codon	14158782	14158784	.	+	0	transcript_id "Phchi.S3G200300.t1"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	transcript	14157474	14158626	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	start_codon	14157474	14157476	.	+	0	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14157474	14157505	0.55	+	0	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14157474	14157505	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14157506	14157758	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14157759	14157817	0.61	+	1	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14157759	14157817	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14157818	14157990	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14157991	14158082	0.62	+	2	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14157991	14158082	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14158083	14158152	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14158153	14158216	0.71	+	0	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14158153	14158216	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	intron	14158217	14158615	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	CDS	14158616	14158626	0.49	+	2	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	exon	14158616	14158626	.	+	.	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
Phchi.S3	AUGUSTUS	stop_codon	14158627	14158629	.	+	0	transcript_id "Phchi.S3G200300.t2"; gene_id "Phchi.S3G200300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6299.t1 is derived from g3471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22161961	22163226	.	-	.	Phchi.S1G345800
Phchi.S1	AUGUSTUS	transcript	22161961	22163226	.	-	.	transcript_id "Phchi.S1G345800.t1"; gene_id "Phchi.S1G345800"
Phchi.S1	AUGUSTUS	stop_codon	22161958	22161960	.	-	0	transcript_id "Phchi.S1G345800.t1"; gene_id "Phchi.S1G345800"
Phchi.S1	AUGUSTUS	CDS	22161961	22163226	1	-	0	transcript_id "Phchi.S1G345800.t1"; gene_id "Phchi.S1G345800"
Phchi.S1	AUGUSTUS	exon	22161961	22163226	.	-	.	transcript_id "Phchi.S1G345800.t1"; gene_id "Phchi.S1G345800"
Phchi.S1	AUGUSTUS	start_codon	22163224	22163226	.	-	0	transcript_id "Phchi.S1G345800.t1"; gene_id "Phchi.S1G345800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16005.t1 is derived from g14429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	99709	100047	.	+	.	Phchi.C10G000300
Phchi.C10	AUGUSTUS	transcript	99709	100047	.	+	.	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	start_codon	99709	99711	.	+	0	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	CDS	99709	99824	0.85	+	0	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	exon	99709	99824	.	+	.	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	intron	99825	99932	.	+	.	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	CDS	99933	100047	0.81	+	1	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	exon	99933	100047	.	+	.	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
Phchi.C10	AUGUSTUS	stop_codon	100048	100050	.	+	0	transcript_id "Phchi.C10G000300.t1"; gene_id "Phchi.C10G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6462.t1 is derived from g3634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23127617	23128891	.	+	.	Phchi.S1G362100
Phchi.S1	AUGUSTUS	transcript	23127617	23128891	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	start_codon	23127617	23127619	.	+	0	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	CDS	23127617	23127886	0.82	+	0	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	exon	23127617	23127886	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	intron	23127887	23127967	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	CDS	23127968	23128278	1	+	0	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	exon	23127968	23128278	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	intron	23128279	23128367	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	CDS	23128368	23128617	1	+	1	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	exon	23128368	23128617	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	intron	23128618	23128708	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	CDS	23128709	23128891	0.97	+	0	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	exon	23128709	23128891	.	+	.	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
Phchi.S1	AUGUSTUS	stop_codon	23128892	23128894	.	+	0	transcript_id "Phchi.S1G362100.t1"; gene_id "Phchi.S1G362100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1234.t1 is derived from g11017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8539464	8540153	.	+	.	Phchi.S6G119300
Phchi.S6	AUGUSTUS	transcript	8539464	8540153	.	+	.	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	start_codon	8539464	8539466	.	+	0	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	CDS	8539464	8539542	0.64	+	0	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	exon	8539464	8539542	.	+	.	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	intron	8539543	8539632	.	+	.	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	CDS	8539633	8539872	1	+	2	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	exon	8539633	8539872	.	+	.	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	intron	8539873	8539953	.	+	.	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	CDS	8539954	8540153	1	+	2	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	exon	8539954	8540153	.	+	.	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
Phchi.S6	AUGUSTUS	stop_codon	8540154	8540156	.	+	0	transcript_id "Phchi.S6G119300.t1"; gene_id "Phchi.S6G119300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14941.t1 is derived from g13409.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15642384	15646549	.	+	.	Phchi.S3G226000
Phchi.S3	AUGUSTUS	transcript	15642384	15646549	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	start_codon	15642384	15642386	.	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15642384	15642731	0.52	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15642384	15642731	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15642732	15642825	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15642826	15642870	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15642826	15642870	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15642871	15642957	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15642958	15642996	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15642958	15642996	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15642997	15643133	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643134	15643167	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643134	15643167	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643168	15643241	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643242	15643342	1	+	2	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643242	15643342	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643343	15643427	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643428	15643580	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643428	15643580	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643581	15643661	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643662	15643697	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643662	15643697	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643698	15643797	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643798	15643841	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643798	15643841	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643842	15643965	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643966	15644056	1	+	1	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643966	15644056	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644057	15644139	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644140	15644181	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644140	15644181	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644182	15644263	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644264	15644372	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644264	15644372	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644373	15644446	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644447	15644561	1	+	2	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644447	15644561	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644562	15644647	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644648	15644697	1	+	1	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644648	15644697	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644698	15644783	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644784	15644862	0.98	+	2	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644784	15644862	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644863	15645129	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645130	15645271	0.91	+	1	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645130	15645271	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645272	15645362	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645363	15645407	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645363	15645407	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645408	15645526	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645527	15645649	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645527	15645649	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645650	15645747	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645748	15645789	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645748	15645789	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645790	15645865	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645866	15646042	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645866	15646042	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15646043	15646131	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15646132	15646260	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15646132	15646260	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15646261	15646340	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15646341	15646454	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15646341	15646454	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15646455	15646537	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15646538	15646549	1	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15646538	15646549	.	+	.	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	stop_codon	15646550	15646552	.	+	0	transcript_id "Phchi.S3G226000.t1"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	transcript	15642384	15646549	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	start_codon	15642384	15642386	.	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15642384	15642731	0.45	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15642384	15642731	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15642732	15642825	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15642826	15642870	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15642826	15642870	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15642871	15642957	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15642958	15642996	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15642958	15642996	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15642997	15643171	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643172	15643342	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643172	15643342	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643343	15643427	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643428	15643580	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643428	15643580	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643581	15643661	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643662	15643697	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643662	15643697	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643698	15643797	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643798	15643841	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643798	15643841	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15643842	15643965	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15643966	15644056	1	+	1	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15643966	15644056	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644057	15644139	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644140	15644181	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644140	15644181	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644182	15644263	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644264	15644372	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644264	15644372	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644373	15644446	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644447	15644561	1	+	2	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644447	15644561	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644562	15644647	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644648	15644697	1	+	1	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644648	15644697	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644698	15644783	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15644784	15644862	0.98	+	2	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15644784	15644862	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15644863	15645129	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645130	15645271	0.94	+	1	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645130	15645271	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645272	15645362	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645363	15645407	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645363	15645407	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645408	15645526	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645527	15645649	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645527	15645649	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645650	15645747	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645748	15645789	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645748	15645789	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15645790	15645865	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15645866	15646042	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15645866	15646042	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15646043	15646131	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15646132	15646260	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15646132	15646260	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15646261	15646340	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15646341	15646454	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15646341	15646454	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	intron	15646455	15646537	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	CDS	15646538	15646549	1	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	exon	15646538	15646549	.	+	.	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
Phchi.S3	AUGUSTUS	stop_codon	15646550	15646552	.	+	0	transcript_id "Phchi.S3G226000.t2"; gene_id "Phchi.S3G226000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9385.t1 is derived from g6561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41270029	41272335	.	-	.	Phchi.S1G654400
Phchi.S1	AUGUSTUS	transcript	41270029	41272335	.	-	.	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	stop_codon	41270026	41270028	.	-	0	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	CDS	41270029	41270322	0.39	-	0	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	exon	41270029	41270322	.	-	.	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	intron	41270323	41270411	.	-	.	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	CDS	41270412	41271781	0.31	-	2	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	exon	41270412	41271781	.	-	.	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	intron	41271782	41271920	.	-	.	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	CDS	41271921	41272335	0.43	-	0	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	exon	41271921	41272335	.	-	.	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
Phchi.S1	AUGUSTUS	start_codon	41272333	41272335	.	-	0	transcript_id "Phchi.S1G654400.t1"; gene_id "Phchi.S1G654400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3223.t1 is derived from g392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2331635	2334290	.	-	.	Phchi.S1G038200
Phchi.S1	AUGUSTUS	transcript	2331635	2334290	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	stop_codon	2331632	2331634	.	-	0	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2331635	2331814	0.67	-	0	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2331635	2331814	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	intron	2331815	2332005	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2332006	2332067	0.78	-	2	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2332006	2332067	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	intron	2332068	2332162	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2332163	2332173	0.78	-	1	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2332163	2332173	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	intron	2332174	2332335	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2332336	2332398	0.98	-	1	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2332336	2332398	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	intron	2332399	2332505	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2332506	2332608	0.79	-	2	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2332506	2332608	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	intron	2332609	2332754	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2332755	2333691	0.99	-	0	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2332755	2333691	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	intron	2333692	2334131	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	CDS	2334132	2334290	0.67	-	0	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	exon	2334132	2334290	.	-	.	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
Phchi.S1	AUGUSTUS	start_codon	2334288	2334290	.	-	0	transcript_id "Phchi.S1G038200.t1"; gene_id "Phchi.S1G038200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12373.t1 is derived from g8049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14049932	14050683	.	+	.	Phchi.S2G045300
Phchi.S2	AUGUSTUS	transcript	14049932	14050683	.	+	.	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	start_codon	14049932	14049934	.	+	0	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	CDS	14049932	14050286	0.8	+	0	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	exon	14049932	14050286	.	+	.	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	intron	14050287	14050498	.	+	.	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	CDS	14050499	14050683	0.66	+	2	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	exon	14050499	14050683	.	+	.	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
Phchi.S2	AUGUSTUS	stop_codon	14050684	14050686	.	+	0	transcript_id "Phchi.S2G045300.t1"; gene_id "Phchi.S2G045300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9739.t1 is derived from g6915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43460700	43462158	.	+	.	Phchi.S1G689800
Phchi.S1	AUGUSTUS	transcript	43460700	43462158	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	start_codon	43460700	43460702	.	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43460700	43460738	0.25	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43460700	43460738	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	intron	43460739	43460861	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43460862	43460948	1	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43460862	43460948	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	intron	43460949	43461047	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43461048	43461157	1	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43461048	43461157	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	intron	43461158	43461277	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43461278	43461501	0.98	+	1	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43461278	43461501	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	intron	43461502	43461587	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43461588	43461655	1	+	2	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43461588	43461655	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	intron	43461656	43461748	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43461749	43461862	1	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43461749	43461862	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	intron	43461863	43461957	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	CDS	43461958	43462158	0.96	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	exon	43461958	43462158	.	+	.	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
Phchi.S1	AUGUSTUS	stop_codon	43462159	43462161	.	+	0	transcript_id "Phchi.S1G689800.t1"; gene_id "Phchi.S1G689800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4177.t1 is derived from g1346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8775237	8777540	.	+	.	Phchi.S1G133600
Phchi.S1	AUGUSTUS	transcript	8775237	8777540	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	start_codon	8775237	8775239	.	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	CDS	8775237	8775710	0.59	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	exon	8775237	8775710	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	intron	8775711	8775821	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	CDS	8775822	8775983	0.59	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	exon	8775822	8775983	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	intron	8775984	8776100	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	CDS	8776101	8776505	1	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	exon	8776101	8776505	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	intron	8776506	8776601	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	CDS	8776602	8776769	1	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	exon	8776602	8776769	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	intron	8776770	8776896	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	CDS	8776897	8777091	1	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	exon	8776897	8777091	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	intron	8777092	8777192	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	CDS	8777193	8777540	0.97	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	exon	8777193	8777540	.	+	.	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
Phchi.S1	AUGUSTUS	stop_codon	8777541	8777543	.	+	0	transcript_id "Phchi.S1G133600.t1"; gene_id "Phchi.S1G133600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6700.t1 is derived from g3872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24595472	24596369	.	-	.	Phchi.S1G385900
Phchi.S1	AUGUSTUS	transcript	24595472	24596369	.	-	.	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	stop_codon	24595469	24595471	.	-	0	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	CDS	24595472	24596118	1	-	2	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	exon	24595472	24596118	.	-	.	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	intron	24596119	24596266	.	-	.	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	CDS	24596267	24596369	0.95	-	0	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	exon	24596267	24596369	.	-	.	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
Phchi.S1	AUGUSTUS	start_codon	24596367	24596369	.	-	0	transcript_id "Phchi.S1G385900.t1"; gene_id "Phchi.S1G385900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13250.t1 is derived from g11715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4923480	4923911	.	-	.	Phchi.S3G056900
Phchi.S3	AUGUSTUS	transcript	4923480	4923911	.	-	.	transcript_id "Phchi.S3G056900.t1"; gene_id "Phchi.S3G056900"
Phchi.S3	AUGUSTUS	stop_codon	4923477	4923479	.	-	0	transcript_id "Phchi.S3G056900.t1"; gene_id "Phchi.S3G056900"
Phchi.S3	AUGUSTUS	CDS	4923480	4923911	0.98	-	0	transcript_id "Phchi.S3G056900.t1"; gene_id "Phchi.S3G056900"
Phchi.S3	AUGUSTUS	exon	4923480	4923911	.	-	.	transcript_id "Phchi.S3G056900.t1"; gene_id "Phchi.S3G056900"
Phchi.S3	AUGUSTUS	start_codon	4923909	4923911	.	-	0	transcript_id "Phchi.S3G056900.t1"; gene_id "Phchi.S3G056900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10912.t1 is derived from g14962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2901385	2901879	.	+	.	Phchi.S4G049400
Phchi.S4	AUGUSTUS	transcript	2901385	2901879	.	+	.	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	start_codon	2901385	2901387	.	+	0	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	CDS	2901385	2901771	0.6	+	0	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	exon	2901385	2901771	.	+	.	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	intron	2901772	2901861	.	+	.	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	CDS	2901862	2901879	0.44	+	0	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	exon	2901862	2901879	.	+	.	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
Phchi.S4	AUGUSTUS	stop_codon	2901880	2901882	.	+	0	transcript_id "Phchi.S4G049400.t1"; gene_id "Phchi.S4G049400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4180.t1 is derived from g1349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8786069	8786705	.	+	.	Phchi.S1G133900
Phchi.S1	AUGUSTUS	transcript	8786069	8786705	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	start_codon	8786069	8786071	.	+	0	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	CDS	8786069	8786112	0.85	+	0	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	exon	8786069	8786112	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	intron	8786113	8786189	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	CDS	8786190	8786259	0.84	+	1	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	exon	8786190	8786259	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	intron	8786260	8786338	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	CDS	8786339	8786482	1	+	0	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	exon	8786339	8786482	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	intron	8786483	8786561	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	CDS	8786562	8786705	1	+	0	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	exon	8786562	8786705	.	+	.	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
Phchi.S1	AUGUSTUS	stop_codon	8786706	8786708	.	+	0	transcript_id "Phchi.S1G133900.t1"; gene_id "Phchi.S1G133900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11051.t1 is derived from g15101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3832570	3833646	.	-	.	Phchi.S4G063300
Phchi.S4	AUGUSTUS	transcript	3832570	3833646	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	stop_codon	3832567	3832569	.	-	0	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	CDS	3832570	3832648	0.65	-	1	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	exon	3832570	3832648	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	intron	3832649	3832827	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	CDS	3832828	3833105	0.63	-	0	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	exon	3832828	3833105	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	intron	3833106	3833237	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	CDS	3833238	3833435	0.8	-	0	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	exon	3833238	3833435	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	intron	3833436	3833550	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	CDS	3833551	3833646	0.58	-	0	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	exon	3833551	3833646	.	-	.	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
Phchi.S4	AUGUSTUS	start_codon	3833644	3833646	.	-	0	transcript_id "Phchi.S4G063300.t1"; gene_id "Phchi.S4G063300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9554.t1 is derived from g6730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42426217	42426982	.	-	.	Phchi.S1G671300
Phchi.S1	AUGUSTUS	transcript	42426217	42426982	.	-	.	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	stop_codon	42426214	42426216	.	-	0	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	CDS	42426217	42426282	1	-	0	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	exon	42426217	42426282	.	-	.	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	intron	42426283	42426619	.	-	.	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	CDS	42426620	42426982	0.94	-	0	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	exon	42426620	42426982	.	-	.	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
Phchi.S1	AUGUSTUS	start_codon	42426980	42426982	.	-	0	transcript_id "Phchi.S1G671300.t1"; gene_id "Phchi.S1G671300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12567.t1 is derived from g8244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35474020	35477604	.	-	.	Phchi.S2G064700
Phchi.S2	AUGUSTUS	transcript	35474020	35477604	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	stop_codon	35474017	35474019	.	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35474020	35474066	0.84	-	2	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35474020	35474066	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35474067	35474164	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35474165	35474276	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35474165	35474276	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35474277	35474450	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35474451	35474549	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35474451	35474549	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35474550	35474669	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35474670	35474873	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35474670	35474873	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35474874	35475154	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35475155	35475295	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35475155	35475295	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35475296	35475421	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35475422	35475526	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35475422	35475526	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35475527	35475609	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35475610	35476050	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35475610	35476050	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35476051	35476364	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35476365	35476505	1	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35476365	35476505	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35476506	35477028	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35477029	35477243	1	-	2	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35477029	35477243	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	intron	35477244	35477378	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	CDS	35477379	35477604	0.66	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	exon	35477379	35477604	.	-	.	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
Phchi.S2	AUGUSTUS	start_codon	35477602	35477604	.	-	0	transcript_id "Phchi.S2G064700.t1"; gene_id "Phchi.S2G064700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11729.t1 is derived from g15781.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7894933	7896194	.	-	.	Phchi.S4G131100
Phchi.S4	AUGUSTUS	transcript	7894933	7896194	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	stop_codon	7894930	7894932	.	-	0	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7894933	7895040	1	-	0	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7894933	7895040	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895041	7895133	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7895134	7895269	1	-	1	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7895134	7895269	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895270	7895351	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7895352	7895479	0.91	-	0	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7895352	7895479	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895480	7895585	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7895586	7895985	1	-	1	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7895586	7895985	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895986	7896177	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7896178	7896194	1	-	0	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7896178	7896194	.	-	.	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	start_codon	7896192	7896194	.	-	0	transcript_id "Phchi.S4G131100.t1"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	transcript	7894933	7896088	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	stop_codon	7894930	7894932	.	-	0	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7894933	7895040	1	-	0	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7894933	7895040	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895041	7895133	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7895134	7895269	1	-	1	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7895134	7895269	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895270	7895351	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7895352	7895479	0.9	-	0	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7895352	7895479	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895480	7895585	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7895586	7895985	0.99	-	1	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7895586	7895985	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	intron	7895986	7896083	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	CDS	7896084	7896088	0.57	-	0	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	exon	7896084	7896088	.	-	.	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
Phchi.S4	AUGUSTUS	start_codon	7896086	7896088	.	-	0	transcript_id "Phchi.S4G131100.t2"; gene_id "Phchi.S4G131100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10620.t1 is derived from g14670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1272145	1272477	.	-	.	Phchi.S4G020200
Phchi.S4	AUGUSTUS	transcript	1272145	1272477	.	-	.	transcript_id "Phchi.S4G020200.t1"; gene_id "Phchi.S4G020200"
Phchi.S4	AUGUSTUS	stop_codon	1272142	1272144	.	-	0	transcript_id "Phchi.S4G020200.t1"; gene_id "Phchi.S4G020200"
Phchi.S4	AUGUSTUS	CDS	1272145	1272477	0.31	-	0	transcript_id "Phchi.S4G020200.t1"; gene_id "Phchi.S4G020200"
Phchi.S4	AUGUSTUS	exon	1272145	1272477	.	-	.	transcript_id "Phchi.S4G020200.t1"; gene_id "Phchi.S4G020200"
Phchi.S4	AUGUSTUS	start_codon	1272475	1272477	.	-	0	transcript_id "Phchi.S4G020200.t1"; gene_id "Phchi.S4G020200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6780.t1 is derived from g3952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25059365	25059949	.	+	.	Phchi.S1G393900
Phchi.S1	AUGUSTUS	transcript	25059365	25059949	.	+	.	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	start_codon	25059365	25059367	.	+	0	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	CDS	25059365	25059572	0.75	+	0	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	exon	25059365	25059572	.	+	.	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	intron	25059573	25059677	.	+	.	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	CDS	25059678	25059949	0.8	+	2	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	exon	25059678	25059949	.	+	.	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
Phchi.S1	AUGUSTUS	stop_codon	25059950	25059952	.	+	0	transcript_id "Phchi.S1G393900.t1"; gene_id "Phchi.S1G393900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1514.t1 is derived from g8433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1371079	1371303	.	-	.	Phchi.S5G012300
Phchi.S5	AUGUSTUS	transcript	1371079	1371303	.	-	.	transcript_id "Phchi.S5G012300.t1"; gene_id "Phchi.S5G012300"
Phchi.S5	AUGUSTUS	stop_codon	1371076	1371078	.	-	0	transcript_id "Phchi.S5G012300.t1"; gene_id "Phchi.S5G012300"
Phchi.S5	AUGUSTUS	CDS	1371079	1371303	0.71	-	0	transcript_id "Phchi.S5G012300.t1"; gene_id "Phchi.S5G012300"
Phchi.S5	AUGUSTUS	exon	1371079	1371303	.	-	.	transcript_id "Phchi.S5G012300.t1"; gene_id "Phchi.S5G012300"
Phchi.S5	AUGUSTUS	start_codon	1371301	1371303	.	-	0	transcript_id "Phchi.S5G012300.t1"; gene_id "Phchi.S5G012300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11621.t1 is derived from g15672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7354912	7358611	.	+	.	Phchi.S4G120300
Phchi.S4	AUGUSTUS	transcript	7354912	7358611	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	start_codon	7354912	7354914	.	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7354912	7355133	0.7	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7354912	7355133	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7355134	7355321	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7355322	7355566	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7355322	7355566	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7355567	7355746	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7355747	7355819	1	+	1	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7355747	7355819	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7355820	7356009	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7356010	7356051	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7356010	7356051	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7356052	7356172	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7356173	7356235	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7356173	7356235	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7356236	7356338	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7356339	7356388	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7356339	7356388	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7356389	7356514	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7356515	7356542	1	+	1	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7356515	7356542	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7356543	7356620	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7356621	7356698	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7356621	7356698	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7356699	7356877	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7356878	7356988	0.99	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7356878	7356988	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7356989	7357073	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7357074	7357161	0.48	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7357074	7357161	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7357162	7357245	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7357246	7357371	1	+	2	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7357246	7357371	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7357372	7357485	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7357486	7357607	1	+	2	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7357486	7357607	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7357608	7357735	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7357736	7357805	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7357736	7357805	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7357806	7357904	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7357905	7357946	1	+	2	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7357905	7357946	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7357947	7358107	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7358108	7358148	1	+	2	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7358108	7358148	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7358149	7358273	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7358274	7358400	1	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7358274	7358400	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	intron	7358401	7358492	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	CDS	7358493	7358611	0.95	+	2	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	exon	7358493	7358611	.	+	.	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
Phchi.S4	AUGUSTUS	stop_codon	7358612	7358614	.	+	0	transcript_id "Phchi.S4G120300.t1"; gene_id "Phchi.S4G120300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9114.t1 is derived from g6289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39887857	39889882	.	-	.	Phchi.S1G627300
Phchi.S1	AUGUSTUS	transcript	39887857	39889882	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	stop_codon	39887854	39887856	.	-	0	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	CDS	39887857	39888064	1	-	1	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	exon	39887857	39888064	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	intron	39888065	39888234	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	CDS	39888235	39888368	0.4	-	0	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	exon	39888235	39888368	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	intron	39888369	39888473	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	CDS	39888474	39888634	0.01	-	2	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	exon	39888474	39888634	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	intron	39888635	39889308	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	CDS	39889309	39889882	0.02	-	0	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	exon	39889309	39889882	.	-	.	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
Phchi.S1	AUGUSTUS	start_codon	39889880	39889882	.	-	0	transcript_id "Phchi.S1G627300.t1"; gene_id "Phchi.S1G627300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8242.t1 is derived from g5417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34640309	34641395	.	+	.	Phchi.S1G540100
Phchi.S1	AUGUSTUS	transcript	34640309	34641395	.	+	.	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	start_codon	34640309	34640311	.	+	0	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	CDS	34640309	34640768	0.26	+	0	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	exon	34640309	34640768	.	+	.	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	intron	34640769	34640879	.	+	.	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	CDS	34640880	34641085	0.59	+	2	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	exon	34640880	34641085	.	+	.	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	intron	34641086	34641353	.	+	.	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	CDS	34641354	34641395	0.75	+	0	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	exon	34641354	34641395	.	+	.	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
Phchi.S1	AUGUSTUS	stop_codon	34641396	34641398	.	+	0	transcript_id "Phchi.S1G540100.t1"; gene_id "Phchi.S1G540100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6801.t1 is derived from g3973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25123307	25123837	.	-	.	Phchi.S1G396000
Phchi.S1	AUGUSTUS	transcript	25123307	25123837	.	-	.	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	stop_codon	25123304	25123306	.	-	0	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	CDS	25123307	25123336	1	-	0	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	exon	25123307	25123336	.	-	.	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	intron	25123337	25123545	.	-	.	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	CDS	25123546	25123552	1	-	1	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	exon	25123546	25123552	.	-	.	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	intron	25123553	25123661	.	-	.	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	CDS	25123662	25123837	0.66	-	0	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	exon	25123662	25123837	.	-	.	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
Phchi.S1	AUGUSTUS	start_codon	25123835	25123837	.	-	0	transcript_id "Phchi.S1G396000.t1"; gene_id "Phchi.S1G396000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5295.t1 is derived from g2465.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16051318	16051652	.	-	.	Phchi.S1G245400
Phchi.S1	AUGUSTUS	transcript	16051318	16051652	.	-	.	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	stop_codon	16051315	16051317	.	-	0	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	CDS	16051318	16051418	1	-	2	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	exon	16051318	16051418	.	-	.	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	intron	16051419	16051507	.	-	.	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	CDS	16051508	16051652	0.91	-	0	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	exon	16051508	16051652	.	-	.	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	start_codon	16051650	16051652	.	-	0	transcript_id "Phchi.S1G245400.t1"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	transcript	16051335	16051652	.	-	.	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	stop_codon	16051332	16051334	.	-	0	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	CDS	16051335	16051402	0.9	-	2	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	exon	16051335	16051402	.	-	.	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	intron	16051403	16051507	.	-	.	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	CDS	16051508	16051652	0.84	-	0	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	exon	16051508	16051652	.	-	.	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
Phchi.S1	AUGUSTUS	start_codon	16051650	16051652	.	-	0	transcript_id "Phchi.S1G245400.t2"; gene_id "Phchi.S1G245400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15553.t1 is derived from g14022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19889370	19889718	.	+	.	Phchi.S3G287200
Phchi.S3	AUGUSTUS	transcript	19889370	19889718	.	+	.	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	start_codon	19889370	19889372	.	+	0	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	CDS	19889370	19889522	0.98	+	0	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	exon	19889370	19889522	.	+	.	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	intron	19889523	19889664	.	+	.	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	CDS	19889665	19889718	1	+	0	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	exon	19889665	19889718	.	+	.	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
Phchi.S3	AUGUSTUS	stop_codon	19889719	19889721	.	+	0	transcript_id "Phchi.S3G287200.t1"; gene_id "Phchi.S3G287200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11940.t1 is derived from g7615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	128345	134639	.	+	.	Phchi.S2G002000
Phchi.S2	AUGUSTUS	transcript	128345	134639	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	start_codon	128345	128347	.	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128345	128500	0.8	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128345	128500	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128501	128619	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128620	128684	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128620	128684	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128685	128819	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128820	128907	1	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128820	128907	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128908	129065	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129066	129127	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129066	129127	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129128	129226	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129227	129365	1	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129227	129365	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129366	129457	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129458	129540	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129458	129540	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129541	129778	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129779	129868	1	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129779	129868	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129869	129975	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129976	130048	0.93	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129976	130048	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130049	130187	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130188	130250	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130188	130250	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130251	130628	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130629	130736	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130629	130736	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130737	130935	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130936	131021	0.79	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130936	131021	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131022	131139	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131140	131191	0.72	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131140	131191	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131192	131318	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131319	131487	0.74	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131319	131487	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131488	131690	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131691	131943	1	+	2	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131691	131943	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131944	132137	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132138	132207	1	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132138	132207	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	132208	132417	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132418	132636	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132418	132636	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	132637	132759	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132760	133005	1	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132760	133005	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133006	133150	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133151	133453	0.4	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133151	133453	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133454	133545	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133546	133665	0.91	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133546	133665	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133666	134132	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	134133	134335	0.47	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	134133	134335	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	134336	134425	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	134426	134639	0.3	+	1	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	134426	134639	.	+	.	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	stop_codon	134640	134642	.	+	0	transcript_id "Phchi.S2G002000.t1"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	transcript	128345	134639	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	start_codon	128345	128347	.	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128345	128500	0.79	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128345	128500	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128501	128619	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128620	128684	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128620	128684	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128685	128819	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128820	128907	1	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128820	128907	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128908	129065	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129066	129127	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129066	129127	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129128	129226	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129227	129365	1	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129227	129365	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129366	129457	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129458	129540	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129458	129540	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129541	129778	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129779	129868	1	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129779	129868	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129869	129975	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129976	130048	0.9	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129976	130048	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130049	130187	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130188	130250	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130188	130250	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130251	130628	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130629	130736	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130629	130736	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130737	130935	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130936	131021	0.85	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130936	131021	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131022	131139	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131140	131191	0.59	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131140	131191	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131192	131318	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131319	131487	0.73	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131319	131487	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131488	131690	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131691	131943	1	+	2	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131691	131943	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131944	132137	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132138	132207	1	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132138	132207	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	132208	132417	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132418	132636	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132418	132636	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	132637	132759	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132760	133005	1	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132760	133005	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133006	133150	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133151	133453	0.37	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133151	133453	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133454	133545	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133546	133717	0.76	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133546	133717	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133718	133865	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133866	133930	0.54	+	2	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133866	133930	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133931	134132	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	134133	134335	0.39	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	134133	134335	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	134336	134425	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	134426	134639	0.26	+	1	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	134426	134639	.	+	.	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	stop_codon	134640	134642	.	+	0	transcript_id "Phchi.S2G002000.t2"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	transcript	128345	134639	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	start_codon	128345	128347	.	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128345	128500	0.72	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128345	128500	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128501	128619	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128620	128684	1	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128620	128684	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128685	128819	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	128820	128907	1	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	128820	128907	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	128908	129065	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129066	129127	1	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129066	129127	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129128	129226	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129227	129365	1	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129227	129365	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129366	129457	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129458	129540	1	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129458	129540	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129541	129778	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129779	129868	1	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129779	129868	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	129869	129975	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	129976	130048	0.92	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	129976	130048	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130049	130187	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130188	130250	1	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130188	130250	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130251	130628	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130629	130736	1	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130629	130736	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	130737	130935	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	130936	131021	0.76	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	130936	131021	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131022	131139	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131140	131191	0.69	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131140	131191	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131192	131318	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131319	131487	0.71	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131319	131487	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131488	131690	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131691	131809	0.83	+	2	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131691	131809	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131810	131993	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	131994	131998	0.83	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	131994	131998	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	131999	132137	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132138	132207	0.85	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132138	132207	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	132208	132417	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132418	132636	0.86	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132418	132636	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	132637	132759	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	132760	133005	1	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	132760	133005	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133006	133150	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133151	133453	0.33	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133151	133453	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133454	133545	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	133546	133665	0.81	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	133546	133665	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	133666	134132	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	134133	134335	0.38	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	134133	134335	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	intron	134336	134425	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	CDS	134426	134639	0.18	+	1	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	exon	134426	134639	.	+	.	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
Phchi.S2	AUGUSTUS	stop_codon	134640	134642	.	+	0	transcript_id "Phchi.S2G002000.t3"; gene_id "Phchi.S2G002000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3647.t1 is derived from g816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4931680	4933940	.	+	.	Phchi.S1G080600
Phchi.S1	AUGUSTUS	transcript	4931680	4933940	.	+	.	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	start_codon	4931680	4931682	.	+	0	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	CDS	4931680	4933093	0.37	+	0	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	exon	4931680	4933093	.	+	.	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	intron	4933094	4933650	.	+	.	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	CDS	4933651	4933782	0.22	+	2	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	exon	4933651	4933782	.	+	.	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	intron	4933783	4933863	.	+	.	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	CDS	4933864	4933940	0.27	+	2	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	exon	4933864	4933940	.	+	.	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
Phchi.S1	AUGUSTUS	stop_codon	4933941	4933943	.	+	0	transcript_id "Phchi.S1G080600.t1"; gene_id "Phchi.S1G080600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8026.t1 is derived from g5201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32548310	32551001	.	-	.	Phchi.S1G518500
Phchi.S1	AUGUSTUS	transcript	32548310	32551001	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	stop_codon	32548307	32548309	.	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32548310	32548445	0.86	-	1	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32548310	32548445	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32548446	32548539	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32548540	32548640	1	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32548540	32548640	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32548641	32548761	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32548762	32548884	1	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32548762	32548884	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32548885	32548979	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32548980	32549094	1	-	1	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32548980	32549094	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32549095	32549193	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32549194	32549278	1	-	2	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32549194	32549278	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32549279	32549395	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32549396	32549436	0.99	-	1	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32549396	32549436	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32549437	32549536	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32549537	32549583	1	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32549537	32549583	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32549584	32549680	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32549681	32549755	1	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32549681	32549755	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32549756	32549879	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32549880	32549939	0.99	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32549880	32549939	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32549940	32550134	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32550135	32550188	0.97	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32550135	32550188	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32550189	32550311	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32550312	32550369	0.33	-	1	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32550312	32550369	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	intron	32550370	32550828	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	CDS	32550829	32551001	0.32	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	exon	32550829	32551001	.	-	.	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
Phchi.S1	AUGUSTUS	start_codon	32550999	32551001	.	-	0	transcript_id "Phchi.S1G518500.t1"; gene_id "Phchi.S1G518500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5821.t1 is derived from g2991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19108801	19110768	.	-	.	Phchi.S1G298000
Phchi.S1	AUGUSTUS	transcript	19108801	19110768	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	stop_codon	19108798	19108800	.	-	0	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	CDS	19108801	19109134	1	-	1	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	exon	19108801	19109134	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	intron	19109135	19109296	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	CDS	19109297	19109556	0.99	-	0	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	exon	19109297	19109556	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	intron	19109557	19109660	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	CDS	19109661	19110540	1	-	1	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	exon	19109661	19110540	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	intron	19110541	19110613	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	CDS	19110614	19110768	0.74	-	0	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	exon	19110614	19110768	.	-	.	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
Phchi.S1	AUGUSTUS	start_codon	19110766	19110768	.	-	0	transcript_id "Phchi.S1G298000.t1"; gene_id "Phchi.S1G298000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg668.t1 is derived from g10450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4647440	4648677	.	+	.	Phchi.S6G062700
Phchi.S6	AUGUSTUS	transcript	4647440	4648677	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	start_codon	4647440	4647442	.	+	0	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	CDS	4647440	4647646	1	+	0	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	exon	4647440	4647646	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	intron	4647647	4647742	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	CDS	4647743	4648063	1	+	0	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	exon	4647743	4648063	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	intron	4648064	4648151	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	CDS	4648152	4648311	1	+	0	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	exon	4648152	4648311	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	intron	4648312	4648402	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	CDS	4648403	4648677	1	+	2	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	exon	4648403	4648677	.	+	.	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
Phchi.S6	AUGUSTUS	stop_codon	4648678	4648680	.	+	0	transcript_id "Phchi.S6G062700.t1"; gene_id "Phchi.S6G062700"
# This transcript jg15467.t2 is derived from g13935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15468.t1 is derived from g13936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19342349	19344153	.	+	.	Phchi.S3G278700
Phchi.S3	AUGUSTUS	transcript	19342349	19344153	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	start_codon	19342349	19342351	.	+	0	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	CDS	19342349	19342361	1	+	0	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	exon	19342349	19342361	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	intron	19342362	19342539	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	CDS	19342540	19342687	0.81	+	2	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	exon	19342540	19342687	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	intron	19342688	19342812	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	CDS	19342813	19343275	0.62	+	1	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	exon	19342813	19343275	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	intron	19343276	19343460	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	CDS	19343461	19344153	0.94	+	0	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	exon	19343461	19344153	.	+	.	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
Phchi.S3	AUGUSTUS	stop_codon	19344154	19344156	.	+	0	transcript_id "Phchi.S3G278700.t1"; gene_id "Phchi.S3G278700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3009.t1 is derived from g178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1115056	1116249	.	-	.	Phchi.S1G016800
Phchi.S1	AUGUSTUS	transcript	1115056	1116249	.	-	.	transcript_id "Phchi.S1G016800.t1"; gene_id "Phchi.S1G016800"
Phchi.S1	AUGUSTUS	stop_codon	1115053	1115055	.	-	0	transcript_id "Phchi.S1G016800.t1"; gene_id "Phchi.S1G016800"
Phchi.S1	AUGUSTUS	CDS	1115056	1116249	0.99	-	0	transcript_id "Phchi.S1G016800.t1"; gene_id "Phchi.S1G016800"
Phchi.S1	AUGUSTUS	exon	1115056	1116249	.	-	.	transcript_id "Phchi.S1G016800.t1"; gene_id "Phchi.S1G016800"
Phchi.S1	AUGUSTUS	start_codon	1116247	1116249	.	-	0	transcript_id "Phchi.S1G016800.t1"; gene_id "Phchi.S1G016800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9015.t1 is derived from g6190.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39152552	39154734	.	-	.	Phchi.S1G617400
Phchi.S1	AUGUSTUS	transcript	39152552	39154734	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	stop_codon	39152549	39152551	.	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39152552	39152563	0.91	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39152552	39152563	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39152564	39152669	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39152670	39152741	0.91	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39152670	39152741	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39152742	39152847	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39152848	39152925	0.73	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39152848	39152925	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39152926	39153105	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153106	39153211	0.86	-	1	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153106	39153211	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39153212	39153315	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153316	39153444	0.92	-	1	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153316	39153444	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39153445	39153717	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153718	39153792	0.99	-	1	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153718	39153792	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39153793	39153973	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153974	39154060	0.99	-	1	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153974	39154060	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39154061	39154125	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39154126	39154133	0.99	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39154126	39154133	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39154134	39154308	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39154309	39154734	0.77	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39154309	39154734	.	-	.	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	start_codon	39154732	39154734	.	-	0	transcript_id "Phchi.S1G617400.t1"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	transcript	39152552	39154734	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	stop_codon	39152549	39152551	.	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39152552	39152563	0.87	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39152552	39152563	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39152564	39152669	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39152670	39152741	0.87	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39152670	39152741	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39152742	39152847	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39152848	39152925	0.75	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39152848	39152925	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39152926	39153105	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153106	39153211	0.89	-	1	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153106	39153211	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39153212	39153315	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153316	39153444	0.92	-	1	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153316	39153444	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39153445	39153717	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153718	39153851	1	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153718	39153851	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39153852	39153973	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39153974	39154060	0.99	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39153974	39154060	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	intron	39154061	39154308	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	CDS	39154309	39154734	0.78	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	exon	39154309	39154734	.	-	.	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
Phchi.S1	AUGUSTUS	start_codon	39154732	39154734	.	-	0	transcript_id "Phchi.S1G617400.t2"; gene_id "Phchi.S1G617400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8509.t1 is derived from g5684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36381550	36382059	.	-	.	Phchi.S1G566800
Phchi.S1	AUGUSTUS	transcript	36381550	36382059	.	-	.	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	stop_codon	36381547	36381549	.	-	0	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	CDS	36381550	36381910	0.9	-	1	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	exon	36381550	36381910	.	-	.	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	intron	36381911	36381994	.	-	.	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	CDS	36381995	36382059	0.93	-	0	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	exon	36381995	36382059	.	-	.	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
Phchi.S1	AUGUSTUS	start_codon	36382057	36382059	.	-	0	transcript_id "Phchi.S1G566800.t1"; gene_id "Phchi.S1G566800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10107.t1 is derived from g7283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45762161	45763209	.	+	.	Phchi.S1G726600
Phchi.S1	AUGUSTUS	transcript	45762161	45763209	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	start_codon	45762161	45762163	.	+	0	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	CDS	45762161	45762249	0.9	+	0	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	exon	45762161	45762249	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	intron	45762250	45762433	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	CDS	45762434	45762504	1	+	1	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	exon	45762434	45762504	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	intron	45762505	45762588	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	CDS	45762589	45762694	1	+	2	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	exon	45762589	45762694	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	intron	45762695	45762788	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	CDS	45762789	45762921	0.99	+	1	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	exon	45762789	45762921	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	intron	45762922	45763026	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	CDS	45763027	45763209	0.8	+	0	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	exon	45763027	45763209	.	+	.	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
Phchi.S1	AUGUSTUS	stop_codon	45763210	45763212	.	+	0	transcript_id "Phchi.S1G726600.t1"; gene_id "Phchi.S1G726600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7111.t1 is derived from g4283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27034932	27036832	.	+	.	Phchi.S1G427000
Phchi.S1	AUGUSTUS	transcript	27034932	27036832	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	start_codon	27034932	27034934	.	+	0	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27034932	27035121	1	+	0	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27034932	27035121	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27035122	27035205	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27035206	27035260	1	+	2	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27035206	27035260	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27035261	27035402	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27035403	27035492	1	+	1	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27035403	27035492	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27035493	27035597	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27035598	27036691	0.99	+	1	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27035598	27036691	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27036692	27036776	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27036777	27036832	1	+	2	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27036777	27036832	.	+	.	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	stop_codon	27036833	27036835	.	+	0	transcript_id "Phchi.S1G427000.t1"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	transcript	27034932	27036832	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	start_codon	27034932	27034934	.	+	0	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27034932	27035121	1	+	0	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27034932	27035121	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27035122	27035205	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27035206	27035260	0.98	+	2	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27035206	27035260	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27035261	27035343	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27035344	27035469	0.2	+	1	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27035344	27035469	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27035470	27035597	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27035598	27036691	0.63	+	1	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27035598	27036691	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	intron	27036692	27036776	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	CDS	27036777	27036832	1	+	2	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	exon	27036777	27036832	.	+	.	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
Phchi.S1	AUGUSTUS	stop_codon	27036833	27036835	.	+	0	transcript_id "Phchi.S1G427000.t2"; gene_id "Phchi.S1G427000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15565.t1 is derived from g14034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19966280	19975336	.	+	.	Phchi.S3G288400
Phchi.S3	AUGUSTUS	transcript	19966280	19975336	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	start_codon	19966280	19966282	.	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19966280	19966375	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19966280	19966375	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19966376	19966468	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19966469	19966585	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19966469	19966585	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19966586	19966727	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19966728	19966820	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19966728	19966820	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19966821	19966963	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19966964	19967055	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19966964	19967055	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19967056	19967173	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19967174	19967315	1	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19967174	19967315	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19967316	19967405	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19967406	19967540	0.98	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19967406	19967540	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19967541	19967657	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19967658	19967734	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19967658	19967734	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19967735	19967896	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19967897	19967975	1	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19967897	19967975	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19967976	19968085	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19968086	19968199	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19968086	19968199	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19968200	19968350	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19968351	19968471	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19968351	19968471	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19968472	19968566	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19968567	19968690	0.44	+	2	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19968567	19968690	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19968691	19968793	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19968794	19968899	0.38	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19968794	19968899	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19968900	19968995	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19968996	19969042	0.69	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19968996	19969042	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19969043	19969126	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19969127	19969159	0.69	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19969127	19969159	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19969160	19969399	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19969400	19969460	1	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19969400	19969460	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19969461	19969608	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19969609	19969696	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19969609	19969696	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19969697	19969788	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19969789	19969832	1	+	2	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19969789	19969832	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19969833	19969986	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19969987	19970073	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19969987	19970073	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19970074	19970189	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19970190	19970284	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19970190	19970284	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19970285	19970418	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19970419	19970509	1	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19970419	19970509	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19970510	19970591	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19970592	19970683	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19970592	19970683	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19970684	19970768	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19970769	19970862	1	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19970769	19970862	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19970863	19970960	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19970961	19971293	0.88	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19970961	19971293	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19971294	19971397	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19971398	19971700	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19971398	19971700	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19971701	19971803	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19971804	19971936	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19971804	19971936	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19971937	19972011	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19972012	19972171	1	+	2	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19972012	19972171	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19972172	19972367	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19972368	19972893	0.98	+	1	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19972368	19972893	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19972894	19973150	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19973151	19973516	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19973151	19973516	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19973517	19973682	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19973683	19974192	0.96	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19973683	19974192	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19974193	19974293	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19974294	19975016	0.78	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19974294	19975016	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	intron	19975017	19975105	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	CDS	19975106	19975336	1	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	exon	19975106	19975336	.	+	.	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
Phchi.S3	AUGUSTUS	stop_codon	19975337	19975339	.	+	0	transcript_id "Phchi.S3G288400.t1"; gene_id "Phchi.S3G288400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9258.t1 is derived from g6433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40621385	40622125	.	-	.	Phchi.S1G641700
Phchi.S1	AUGUSTUS	transcript	40621385	40622125	.	-	.	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	stop_codon	40621382	40621384	.	-	0	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	CDS	40621385	40621474	0.98	-	0	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	exon	40621385	40621474	.	-	.	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	intron	40621475	40621621	.	-	.	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	CDS	40621622	40621682	0.94	-	1	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	exon	40621622	40621682	.	-	.	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	intron	40621683	40621925	.	-	.	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	CDS	40621926	40622125	0.74	-	0	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	exon	40621926	40622125	.	-	.	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
Phchi.S1	AUGUSTUS	start_codon	40622123	40622125	.	-	0	transcript_id "Phchi.S1G641700.t1"; gene_id "Phchi.S1G641700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12089.t1 is derived from g7764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2185975	2187784	.	+	.	Phchi.S2G016900
Phchi.S2	AUGUSTUS	transcript	2185975	2187784	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	start_codon	2185975	2185977	.	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2185975	2186031	1	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2185975	2186031	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2186032	2186122	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2186123	2186249	1	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2186123	2186249	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2186250	2186349	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2186350	2186383	0.42	+	2	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2186350	2186383	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2186384	2186483	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2186484	2186604	0.41	+	1	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2186484	2186604	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2186605	2186681	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2186682	2186777	1	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2186682	2186777	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2186778	2186883	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2186884	2186934	1	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2186884	2186934	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2186935	2187078	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2187079	2187531	0.97	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2187079	2187531	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	intron	2187532	2187625	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	CDS	2187626	2187784	1	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	exon	2187626	2187784	.	+	.	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
Phchi.S2	AUGUSTUS	stop_codon	2187785	2187787	.	+	0	transcript_id "Phchi.S2G016900.t1"; gene_id "Phchi.S2G016900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5479.t1 is derived from g2649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17050473	17052424	.	+	.	Phchi.S1G263800
Phchi.S1	AUGUSTUS	transcript	17050473	17052424	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	start_codon	17050473	17050475	.	+	0	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17050473	17050806	0.72	+	0	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17050473	17050806	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17050807	17050986	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17050987	17051402	1	+	2	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17050987	17051402	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051403	17051618	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17051619	17051764	1	+	0	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17051619	17051764	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051765	17051868	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17051869	17051929	1	+	1	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17051869	17051929	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051930	17052025	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17052026	17052146	0.65	+	0	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17052026	17052146	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17052147	17052227	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17052228	17052424	0.47	+	2	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17052228	17052424	.	+	.	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	stop_codon	17052425	17052427	.	+	0	transcript_id "Phchi.S1G263800.t1"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	transcript	17050473	17052424	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	start_codon	17050473	17050475	.	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17050473	17050760	0.73	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17050473	17050760	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17050761	17050986	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17050987	17051028	0.77	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17050987	17051028	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051029	17051159	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17051160	17051402	0.54	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17051160	17051402	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051403	17051618	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17051619	17051764	1	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17051619	17051764	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051765	17051868	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17051869	17051929	1	+	1	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17051869	17051929	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17051930	17052025	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17052026	17052146	0.69	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17052026	17052146	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	intron	17052147	17052227	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	CDS	17052228	17052424	0.52	+	2	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	exon	17052228	17052424	.	+	.	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
Phchi.S1	AUGUSTUS	stop_codon	17052425	17052427	.	+	0	transcript_id "Phchi.S1G263800.t2"; gene_id "Phchi.S1G263800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15725.t1 is derived from g14195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20904923	20906120	.	-	.	Phchi.S3G304400
Phchi.S3	AUGUSTUS	transcript	20904923	20906120	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	stop_codon	20904920	20904922	.	-	0	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	CDS	20904923	20905348	0.77	-	0	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	exon	20904923	20905348	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	intron	20905349	20905462	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	CDS	20905463	20905642	1	-	0	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	exon	20905463	20905642	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	intron	20905643	20905729	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	CDS	20905730	20905988	1	-	1	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	exon	20905730	20905988	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	intron	20905989	20906106	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	CDS	20906107	20906120	0.82	-	0	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	exon	20906107	20906120	.	-	.	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
Phchi.S3	AUGUSTUS	start_codon	20906118	20906120	.	-	0	transcript_id "Phchi.S3G304400.t1"; gene_id "Phchi.S3G304400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5214.t1 is derived from g2384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15507873	15508765	.	+	.	Phchi.S1G237300
Phchi.S1	AUGUSTUS	transcript	15507873	15508765	.	+	.	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	start_codon	15507873	15507875	.	+	0	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	CDS	15507873	15508615	0.92	+	0	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	exon	15507873	15508615	.	+	.	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	intron	15508616	15508749	.	+	.	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	CDS	15508750	15508765	0.93	+	1	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	exon	15508750	15508765	.	+	.	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
Phchi.S1	AUGUSTUS	stop_codon	15508766	15508768	.	+	0	transcript_id "Phchi.S1G237300.t1"; gene_id "Phchi.S1G237300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6023.t1 is derived from g3194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20487251	20489051	.	+	.	Phchi.S1G318200
Phchi.S1	AUGUSTUS	transcript	20487251	20489051	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	start_codon	20487251	20487253	.	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	CDS	20487251	20487406	0.92	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	exon	20487251	20487406	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	intron	20487407	20487496	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	CDS	20487497	20487697	1	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	exon	20487497	20487697	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	intron	20487698	20487796	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	CDS	20487797	20487874	1	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	exon	20487797	20487874	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	intron	20487875	20487993	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	CDS	20487994	20488366	0.81	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	exon	20487994	20488366	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	intron	20488367	20488485	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	CDS	20488486	20488652	0.92	+	2	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	exon	20488486	20488652	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	intron	20488653	20488730	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	CDS	20488731	20489051	0.92	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	exon	20488731	20489051	.	+	.	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
Phchi.S1	AUGUSTUS	stop_codon	20489052	20489054	.	+	0	transcript_id "Phchi.S1G318200.t1"; gene_id "Phchi.S1G318200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13519.t1 is derived from g11986.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7280157	7286355	.	-	.	Phchi.S3G083800
Phchi.S3	AUGUSTUS	transcript	7280157	7286355	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	stop_codon	7280154	7280156	.	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7280157	7280272	0.62	-	2	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7280157	7280272	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7280273	7280739	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7280740	7280917	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7280740	7280917	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7280918	7281003	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7281004	7281078	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7281004	7281078	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7281079	7281171	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7281172	7281339	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7281172	7281339	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7281340	7281421	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7281422	7281479	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7281422	7281479	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7281480	7281584	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7281585	7281862	0.98	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7281585	7281862	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7281863	7281963	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7281964	7282035	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7281964	7282035	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7282036	7282112	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7282113	7282179	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7282113	7282179	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7282180	7282272	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7282273	7282317	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7282273	7282317	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7282318	7282486	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7282487	7282728	0.97	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7282487	7282728	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7282729	7282833	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7282834	7282956	0.98	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7282834	7282956	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7282957	7283061	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7283062	7283136	0.87	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7283062	7283136	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7283137	7283214	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7283215	7283277	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7283215	7283277	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7283278	7283398	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7283399	7283481	1	-	2	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7283399	7283481	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7283482	7283572	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7283573	7283615	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7283573	7283615	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7283616	7283756	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7283757	7283918	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7283757	7283918	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7283919	7284070	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7284071	7284152	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7284071	7284152	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7284153	7284271	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7284272	7284342	0.82	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7284272	7284342	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7284343	7284502	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7284503	7284602	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7284503	7284602	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7284603	7284676	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7284677	7284877	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7284677	7284877	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7284878	7285036	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7285037	7285122	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7285037	7285122	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7285123	7285283	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7285284	7285358	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7285284	7285358	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7285359	7285455	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7285456	7285548	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7285456	7285548	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7285549	7285697	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7285698	7285802	0.99	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7285698	7285802	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7285803	7285893	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7285894	7285920	0.7	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7285894	7285920	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7285921	7286100	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7286101	7286179	1	-	1	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7286101	7286179	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	intron	7286180	7286329	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	CDS	7286330	7286355	1	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	exon	7286330	7286355	.	-	.	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
Phchi.S3	AUGUSTUS	start_codon	7286353	7286355	.	-	0	transcript_id "Phchi.S3G083800.t1"; gene_id "Phchi.S3G083800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12136.t1 is derived from g7812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4554861	4555326	.	-	.	Phchi.S2G021600
Phchi.S2	AUGUSTUS	transcript	4554861	4555326	.	-	.	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	stop_codon	4554858	4554860	.	-	0	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	CDS	4554861	4554992	0.72	-	0	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	exon	4554861	4554992	.	-	.	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	intron	4554993	4555185	.	-	.	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	CDS	4555186	4555326	0.53	-	0	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	exon	4555186	4555326	.	-	.	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
Phchi.S2	AUGUSTUS	start_codon	4555324	4555326	.	-	0	transcript_id "Phchi.S2G021600.t1"; gene_id "Phchi.S2G021600"
# This transcript jg2135.t2 is derived from g9055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2136.t1 is derived from g9056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5016484	5018090	.	+	.	Phchi.S5G074500
Phchi.S5	AUGUSTUS	transcript	5016484	5018090	.	+	.	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	start_codon	5016484	5016486	.	+	0	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	CDS	5016484	5017466	0.66	+	0	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	exon	5016484	5017466	.	+	.	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	intron	5017467	5017624	.	+	.	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	CDS	5017625	5018090	0.62	+	1	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	exon	5017625	5018090	.	+	.	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
Phchi.S5	AUGUSTUS	stop_codon	5018091	5018093	.	+	0	transcript_id "Phchi.S5G074500.t1"; gene_id "Phchi.S5G074500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14602.t1 is derived from g13070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13694131	13695153	.	-	.	Phchi.S3G192100
Phchi.S3	AUGUSTUS	transcript	13694131	13695153	.	-	.	transcript_id "Phchi.S3G192100.t1"; gene_id "Phchi.S3G192100"
Phchi.S3	AUGUSTUS	stop_codon	13694128	13694130	.	-	0	transcript_id "Phchi.S3G192100.t1"; gene_id "Phchi.S3G192100"
Phchi.S3	AUGUSTUS	CDS	13694131	13695153	0.99	-	0	transcript_id "Phchi.S3G192100.t1"; gene_id "Phchi.S3G192100"
Phchi.S3	AUGUSTUS	exon	13694131	13695153	.	-	.	transcript_id "Phchi.S3G192100.t1"; gene_id "Phchi.S3G192100"
Phchi.S3	AUGUSTUS	start_codon	13695151	13695153	.	-	0	transcript_id "Phchi.S3G192100.t1"; gene_id "Phchi.S3G192100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13140.t1 is derived from g11605.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4357744	4360888	.	-	.	Phchi.S3G045900
Phchi.S3	AUGUSTUS	transcript	4357744	4360888	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	stop_codon	4357741	4357743	.	-	0	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4357744	4357894	1	-	1	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4357744	4357894	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4357895	4357973	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4357974	4358103	0.99	-	2	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4357974	4358103	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358104	4358206	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4358207	4358384	1	-	0	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4358207	4358384	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358385	4358480	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4358481	4358590	1	-	2	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4358481	4358590	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358591	4358773	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4358774	4358889	1	-	1	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4358774	4358889	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358890	4359020	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4359021	4359282	1	-	2	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4359021	4359282	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4359283	4359475	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4359476	4359791	0.98	-	0	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4359476	4359791	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4359792	4360331	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4360332	4360467	0.89	-	1	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4360332	4360467	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4360468	4360594	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4360595	4360729	0.8	-	1	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4360595	4360729	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4360730	4360862	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4360863	4360888	0.87	-	0	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4360863	4360888	.	-	.	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	start_codon	4360886	4360888	.	-	0	transcript_id "Phchi.S3G045900.t1"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	transcript	4357744	4359923	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	stop_codon	4357741	4357743	.	-	0	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4357744	4357894	1	-	1	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4357744	4357894	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4357895	4357973	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4357974	4358103	0.99	-	2	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4357974	4358103	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358104	4358206	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4358207	4358384	1	-	0	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4358207	4358384	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358385	4358480	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4358481	4358590	1	-	2	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4358481	4358590	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358591	4358773	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4358774	4358889	1	-	1	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4358774	4358889	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4358890	4359020	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4359021	4359282	1	-	2	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4359021	4359282	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4359283	4359475	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4359476	4359791	0.93	-	0	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4359476	4359791	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	intron	4359792	4359890	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	CDS	4359891	4359923	0.18	-	0	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	exon	4359891	4359923	.	-	.	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
Phchi.S3	AUGUSTUS	start_codon	4359921	4359923	.	-	0	transcript_id "Phchi.S3G045900.t2"; gene_id "Phchi.S3G045900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15811.t1 is derived from g14281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21508384	21512530	.	+	.	Phchi.S3G313000
Phchi.S3	AUGUSTUS	transcript	21508384	21512530	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	start_codon	21508384	21508386	.	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21508384	21508533	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21508384	21508533	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21508534	21508621	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21508622	21508779	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21508622	21508779	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21508780	21508866	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21508867	21508957	1	+	1	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21508867	21508957	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21508958	21509061	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21509062	21509181	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21509062	21509181	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21509182	21509319	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21509320	21509388	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21509320	21509388	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21509389	21509462	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21509463	21509554	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21509463	21509554	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21509555	21509640	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21509641	21509743	1	+	1	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21509641	21509743	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21509744	21509811	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21509812	21509919	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21509812	21509919	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21509920	21510018	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21510019	21510081	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21510019	21510081	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21510082	21510215	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21510216	21510287	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21510216	21510287	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21510288	21510364	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21510365	21510439	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21510365	21510439	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21510440	21510532	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21510533	21510595	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21510533	21510595	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21510596	21510680	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21510681	21510744	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21510681	21510744	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21510745	21510833	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21510834	21510949	0.95	+	2	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21510834	21510949	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21510950	21511048	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21511049	21511162	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21511049	21511162	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21511163	21511282	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21511283	21511363	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21511283	21511363	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21511364	21511459	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21511460	21511540	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21511460	21511540	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21511541	21511681	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21511682	21511902	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21511682	21511902	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21511903	21511989	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21511990	21512110	1	+	1	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21511990	21512110	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21512111	21512203	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21512204	21512407	1	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21512204	21512407	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	intron	21512408	21512494	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	CDS	21512495	21512530	0.87	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	exon	21512495	21512530	.	+	.	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
Phchi.S3	AUGUSTUS	stop_codon	21512531	21512533	.	+	0	transcript_id "Phchi.S3G313000.t1"; gene_id "Phchi.S3G313000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15952.t1 is derived from g14445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	31872	32627	.	-	.	Phchi.C116G000800
Phchi.C116	AUGUSTUS	transcript	31872	32627	.	-	.	transcript_id "Phchi.C116G000800.t1"; gene_id "Phchi.C116G000800"
Phchi.C116	AUGUSTUS	stop_codon	31869	31871	.	-	0	transcript_id "Phchi.C116G000800.t1"; gene_id "Phchi.C116G000800"
Phchi.C116	AUGUSTUS	CDS	31872	32627	0.51	-	0	transcript_id "Phchi.C116G000800.t1"; gene_id "Phchi.C116G000800"
Phchi.C116	AUGUSTUS	exon	31872	32627	.	-	.	transcript_id "Phchi.C116G000800.t1"; gene_id "Phchi.C116G000800"
Phchi.C116	AUGUSTUS	start_codon	32625	32627	.	-	0	transcript_id "Phchi.C116G000800.t1"; gene_id "Phchi.C116G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10757.t1 is derived from g14807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1962043	1962972	.	-	.	Phchi.S4G033900
Phchi.S4	AUGUSTUS	transcript	1962043	1962972	.	-	.	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	stop_codon	1962040	1962042	.	-	0	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	CDS	1962043	1962348	1	-	0	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	exon	1962043	1962348	.	-	.	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	intron	1962349	1962420	.	-	.	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	CDS	1962421	1962972	1	-	0	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	exon	1962421	1962972	.	-	.	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
Phchi.S4	AUGUSTUS	start_codon	1962970	1962972	.	-	0	transcript_id "Phchi.S4G033900.t1"; gene_id "Phchi.S4G033900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8918.t1 is derived from g6093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38666226	38668345	.	+	.	Phchi.S1G607700
Phchi.S1	AUGUSTUS	transcript	38666226	38668345	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	start_codon	38666226	38666228	.	+	0	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	CDS	38666226	38666426	0.16	+	0	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	exon	38666226	38666426	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	intron	38666427	38666528	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	CDS	38666529	38666605	0.79	+	0	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	exon	38666529	38666605	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	intron	38666606	38666882	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	CDS	38666883	38667146	0.64	+	1	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	exon	38666883	38667146	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	intron	38667147	38667254	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	CDS	38667255	38667644	0.97	+	1	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	exon	38667255	38667644	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	intron	38667645	38667743	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	CDS	38667744	38667902	0.98	+	1	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	exon	38667744	38667902	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	intron	38667903	38668011	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	CDS	38668012	38668345	0.99	+	1	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	exon	38668012	38668345	.	+	.	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
Phchi.S1	AUGUSTUS	stop_codon	38668346	38668348	.	+	0	transcript_id "Phchi.S1G607700.t1"; gene_id "Phchi.S1G607700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11816.t1 is derived from g15868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8371842	8372423	.	-	.	Phchi.S4G139800
Phchi.S4	AUGUSTUS	transcript	8371842	8372423	.	-	.	transcript_id "Phchi.S4G139800.t1"; gene_id "Phchi.S4G139800"
Phchi.S4	AUGUSTUS	stop_codon	8371839	8371841	.	-	0	transcript_id "Phchi.S4G139800.t1"; gene_id "Phchi.S4G139800"
Phchi.S4	AUGUSTUS	CDS	8371842	8372423	0.71	-	0	transcript_id "Phchi.S4G139800.t1"; gene_id "Phchi.S4G139800"
Phchi.S4	AUGUSTUS	exon	8371842	8372423	.	-	.	transcript_id "Phchi.S4G139800.t1"; gene_id "Phchi.S4G139800"
Phchi.S4	AUGUSTUS	start_codon	8372421	8372423	.	-	0	transcript_id "Phchi.S4G139800.t1"; gene_id "Phchi.S4G139800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2918.t1 is derived from g87.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	563343	566107	.	-	.	Phchi.S1G007700
Phchi.S1	AUGUSTUS	transcript	563343	566107	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	stop_codon	563340	563342	.	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	563343	563455	0.99	-	2	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	563343	563455	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	563456	563603	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	563604	563679	1	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	563604	563679	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	563680	563773	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	563774	563832	0.99	-	2	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	563774	563832	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	563833	563936	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	563937	564001	0.69	-	1	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	563937	564001	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	564002	564167	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	564168	564220	1	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	564168	564220	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	564221	564347	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	564348	564431	1	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	564348	564431	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	564432	564615	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	564616	564668	1	-	2	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	564616	564668	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	564669	564914	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	564915	564992	1	-	2	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	564915	564992	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	564993	565180	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	565181	565247	1	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	565181	565247	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	intron	565248	565723	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	CDS	565724	566107	1	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	exon	565724	566107	.	-	.	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
Phchi.S1	AUGUSTUS	start_codon	566105	566107	.	-	0	transcript_id "Phchi.S1G007700.t1"; gene_id "Phchi.S1G007700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15890.t1 is derived from g14360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22041337	22042439	.	-	.	Phchi.S3G320900
Phchi.S3	AUGUSTUS	transcript	22041337	22042439	.	-	.	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	stop_codon	22041334	22041336	.	-	0	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	CDS	22041337	22041368	0.98	-	2	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	exon	22041337	22041368	.	-	.	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	intron	22041369	22041777	.	-	.	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	CDS	22041778	22041870	0.38	-	2	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	exon	22041778	22041870	.	-	.	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	intron	22041871	22041949	.	-	.	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	CDS	22041950	22042439	0.52	-	0	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	exon	22041950	22042439	.	-	.	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
Phchi.S3	AUGUSTUS	start_codon	22042437	22042439	.	-	0	transcript_id "Phchi.S3G320900.t1"; gene_id "Phchi.S3G320900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15085.t1 is derived from g13553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16949315	16953140	.	+	.	Phchi.S3G240400
Phchi.S3	AUGUSTUS	transcript	16949315	16953140	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	start_codon	16949315	16949317	.	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16949315	16949377	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16949315	16949377	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16949378	16949874	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16949875	16949940	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16949875	16949940	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16949941	16950059	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16950060	16950095	0.96	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16950060	16950095	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16950096	16950198	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16950199	16950273	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16950199	16950273	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16950274	16950358	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16950359	16950483	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16950359	16950483	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16950484	16950583	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16950584	16950683	1	+	1	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16950584	16950683	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16950684	16950774	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16950775	16950946	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16950775	16950946	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16950947	16951045	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16951046	16951164	1	+	2	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16951046	16951164	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16951165	16951240	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16951241	16951351	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16951241	16951351	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16951352	16951460	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16951461	16951605	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16951461	16951605	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16951606	16951685	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16951686	16951818	1	+	2	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16951686	16951818	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16951819	16951914	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16951915	16951993	1	+	1	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16951915	16951993	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16951994	16952132	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16952133	16952198	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16952133	16952198	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16952199	16952281	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16952282	16952389	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16952282	16952389	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16952390	16952463	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16952464	16952571	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16952464	16952571	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	intron	16952572	16952660	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	CDS	16952661	16953140	1	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	exon	16952661	16953140	.	+	.	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
Phchi.S3	AUGUSTUS	stop_codon	16953141	16953143	.	+	0	transcript_id "Phchi.S3G240400.t1"; gene_id "Phchi.S3G240400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5444.t1 is derived from g2614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16894447	16895389	.	-	.	Phchi.S1G260300
Phchi.S1	AUGUSTUS	transcript	16894447	16895389	.	-	.	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	stop_codon	16894444	16894446	.	-	0	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	CDS	16894447	16894486	0.99	-	1	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	exon	16894447	16894486	.	-	.	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	intron	16894487	16894634	.	-	.	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	CDS	16894635	16895389	0.95	-	0	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	exon	16894635	16895389	.	-	.	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
Phchi.S1	AUGUSTUS	start_codon	16895387	16895389	.	-	0	transcript_id "Phchi.S1G260300.t1"; gene_id "Phchi.S1G260300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8335.t1 is derived from g5510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35377096	35378176	.	+	.	Phchi.S1G549400
Phchi.S1	AUGUSTUS	transcript	35377096	35378176	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	start_codon	35377096	35377098	.	+	0	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	CDS	35377096	35377192	1	+	0	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	exon	35377096	35377192	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	intron	35377193	35377326	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	CDS	35377327	35377412	1	+	2	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	exon	35377327	35377412	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	intron	35377413	35377509	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	CDS	35377510	35377628	1	+	0	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	exon	35377510	35377628	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	intron	35377629	35377722	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	CDS	35377723	35377909	1	+	1	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	exon	35377723	35377909	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	intron	35377910	35378005	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	CDS	35378006	35378176	1	+	0	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	exon	35378006	35378176	.	+	.	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
Phchi.S1	AUGUSTUS	stop_codon	35378177	35378179	.	+	0	transcript_id "Phchi.S1G549400.t1"; gene_id "Phchi.S1G549400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10687.t1 is derived from g14737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1583446	1584450	.	+	.	Phchi.S4G026900
Phchi.S4	AUGUSTUS	transcript	1583446	1584450	.	+	.	transcript_id "Phchi.S4G026900.t1"; gene_id "Phchi.S4G026900"
Phchi.S4	AUGUSTUS	start_codon	1583446	1583448	.	+	0	transcript_id "Phchi.S4G026900.t1"; gene_id "Phchi.S4G026900"
Phchi.S4	AUGUSTUS	CDS	1583446	1584450	0.98	+	0	transcript_id "Phchi.S4G026900.t1"; gene_id "Phchi.S4G026900"
Phchi.S4	AUGUSTUS	exon	1583446	1584450	.	+	.	transcript_id "Phchi.S4G026900.t1"; gene_id "Phchi.S4G026900"
Phchi.S4	AUGUSTUS	stop_codon	1584451	1584453	.	+	0	transcript_id "Phchi.S4G026900.t1"; gene_id "Phchi.S4G026900"
# This transcript jg456.t2 is derived from g10238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg457.t1 is derived from g10239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3198496	3201056	.	-	.	Phchi.S6G041600
Phchi.S6	AUGUSTUS	transcript	3198496	3201056	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	stop_codon	3198493	3198495	.	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3198496	3198618	0.93	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3198496	3198618	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3198619	3198734	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3198735	3198899	1	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3198735	3198899	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3198900	3199033	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3199034	3199132	1	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3199034	3199132	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3199133	3199346	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3199347	3199421	1	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3199347	3199421	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3199422	3199576	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3199577	3199645	1	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3199577	3199645	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3199646	3199781	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3199782	3199980	1	-	1	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3199782	3199980	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3199981	3200114	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3200115	3200220	1	-	2	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3200115	3200220	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	intron	3200221	3200578	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	CDS	3200579	3201056	1	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	exon	3200579	3201056	.	-	.	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
Phchi.S6	AUGUSTUS	start_codon	3201054	3201056	.	-	0	transcript_id "Phchi.S6G041600.t1"; gene_id "Phchi.S6G041600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg131.t1 is derived from g9913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	712528	713459	.	+	.	Phchi.S6G009000
Phchi.S6	AUGUSTUS	transcript	712528	713459	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	start_codon	712528	712530	.	+	0	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	CDS	712528	712588	0.97	+	0	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	exon	712528	712588	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	intron	712589	712706	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	CDS	712707	712890	1	+	2	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	exon	712707	712890	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	intron	712891	713057	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	CDS	713058	713205	1	+	1	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	exon	713058	713205	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	intron	713206	713285	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	CDS	713286	713459	1	+	0	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	exon	713286	713459	.	+	.	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
Phchi.S6	AUGUSTUS	stop_codon	713460	713462	.	+	0	transcript_id "Phchi.S6G009000.t1"; gene_id "Phchi.S6G009000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg648.t1 is derived from g10430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4576488	4577626	.	+	.	Phchi.S6G060700
Phchi.S6	AUGUSTUS	transcript	4576488	4577626	.	+	.	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	start_codon	4576488	4576490	.	+	0	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	CDS	4576488	4577433	0.66	+	0	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	exon	4576488	4577433	.	+	.	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	intron	4577434	4577510	.	+	.	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	CDS	4577511	4577626	1	+	2	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	exon	4577511	4577626	.	+	.	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
Phchi.S6	AUGUSTUS	stop_codon	4577627	4577629	.	+	0	transcript_id "Phchi.S6G060700.t1"; gene_id "Phchi.S6G060700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1065.t1 is derived from g10848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7406186	7406788	.	+	.	Phchi.S6G102400
Phchi.S6	AUGUSTUS	transcript	7406186	7406788	.	+	.	transcript_id "Phchi.S6G102400.t1"; gene_id "Phchi.S6G102400"
Phchi.S6	AUGUSTUS	start_codon	7406186	7406188	.	+	0	transcript_id "Phchi.S6G102400.t1"; gene_id "Phchi.S6G102400"
Phchi.S6	AUGUSTUS	CDS	7406186	7406788	0.65	+	0	transcript_id "Phchi.S6G102400.t1"; gene_id "Phchi.S6G102400"
Phchi.S6	AUGUSTUS	exon	7406186	7406788	.	+	.	transcript_id "Phchi.S6G102400.t1"; gene_id "Phchi.S6G102400"
Phchi.S6	AUGUSTUS	stop_codon	7406789	7406791	.	+	0	transcript_id "Phchi.S6G102400.t1"; gene_id "Phchi.S6G102400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15156.t1 is derived from g13624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17298124	17299335	.	-	.	Phchi.S3G247500
Phchi.S3	AUGUSTUS	transcript	17298124	17299335	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	stop_codon	17298121	17298123	.	-	0	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	CDS	17298124	17298258	1	-	0	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	exon	17298124	17298258	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	intron	17298259	17298349	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	CDS	17298350	17298438	1	-	2	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	exon	17298350	17298438	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	intron	17298439	17298529	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	CDS	17298530	17298692	1	-	0	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	exon	17298530	17298692	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	intron	17298693	17298782	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	CDS	17298783	17298982	1	-	2	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	exon	17298783	17298982	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	intron	17298983	17299067	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	CDS	17299068	17299335	1	-	0	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	exon	17299068	17299335	.	-	.	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
Phchi.S3	AUGUSTUS	start_codon	17299333	17299335	.	-	0	transcript_id "Phchi.S3G247500.t1"; gene_id "Phchi.S3G247500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10140.t1 is derived from g7316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45954217	45958536	.	-	.	Phchi.S1G729900
Phchi.S1	AUGUSTUS	transcript	45954217	45958536	.	-	.	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	stop_codon	45954214	45954216	.	-	0	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	CDS	45954217	45955350	0.86	-	0	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	exon	45954217	45955350	.	-	.	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	intron	45955351	45955463	.	-	.	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	CDS	45955464	45956935	0.89	-	2	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	exon	45955464	45956935	.	-	.	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	intron	45956936	45957077	.	-	.	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	CDS	45957078	45958536	0.86	-	0	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	exon	45957078	45958536	.	-	.	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
Phchi.S1	AUGUSTUS	start_codon	45958534	45958536	.	-	0	transcript_id "Phchi.S1G729900.t1"; gene_id "Phchi.S1G729900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7014.t1 is derived from g4186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26405815	26407552	.	-	.	Phchi.S1G417300
Phchi.S1	AUGUSTUS	transcript	26405815	26407552	.	-	.	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	stop_codon	26405812	26405814	.	-	0	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	CDS	26405815	26406235	0.99	-	1	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	exon	26405815	26406235	.	-	.	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	intron	26406236	26406398	.	-	.	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	CDS	26406399	26406700	0.99	-	0	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	exon	26406399	26406700	.	-	.	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	intron	26406701	26406793	.	-	.	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	CDS	26406794	26407552	0.96	-	0	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	exon	26406794	26407552	.	-	.	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
Phchi.S1	AUGUSTUS	start_codon	26407550	26407552	.	-	0	transcript_id "Phchi.S1G417300.t1"; gene_id "Phchi.S1G417300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2416.t1 is derived from g9336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6545687	6546806	.	+	.	Phchi.S5G102500
Phchi.S5	AUGUSTUS	transcript	6545687	6546806	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	start_codon	6545687	6545689	.	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6545687	6545773	0.99	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6545687	6545773	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	intron	6545774	6545848	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6545849	6545898	1	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6545849	6545898	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	intron	6545899	6545977	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6545978	6546035	1	+	1	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6545978	6546035	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	intron	6546036	6546137	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6546138	6546170	1	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6546138	6546170	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	intron	6546171	6546263	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6546264	6546394	0.5	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6546264	6546394	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	intron	6546395	6546465	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6546466	6546634	0.5	+	1	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6546466	6546634	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	intron	6546635	6546713	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	CDS	6546714	6546806	0.97	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	exon	6546714	6546806	.	+	.	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
Phchi.S5	AUGUSTUS	stop_codon	6546807	6546809	.	+	0	transcript_id "Phchi.S5G102500.t1"; gene_id "Phchi.S5G102500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2817.t1 is derived from g9737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8997999	8999796	.	-	.	Phchi.S5G142600
Phchi.S5	AUGUSTUS	transcript	8997999	8999796	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	stop_codon	8997996	8997998	.	-	0	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8997999	8998296	1	-	1	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8997999	8998296	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	intron	8998297	8998381	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8998382	8998545	1	-	0	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8998382	8998545	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	intron	8998546	8998654	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8998655	8998930	0.99	-	0	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8998655	8998930	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	intron	8998931	8999024	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8999025	8999059	1	-	2	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8999025	8999059	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	intron	8999060	8999130	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8999131	8999296	0.99	-	0	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8999131	8999296	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	intron	8999297	8999385	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8999386	8999558	1	-	2	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8999386	8999558	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	intron	8999559	8999636	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	CDS	8999637	8999796	1	-	0	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	exon	8999637	8999796	.	-	.	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
Phchi.S5	AUGUSTUS	start_codon	8999794	8999796	.	-	0	transcript_id "Phchi.S5G142600.t1"; gene_id "Phchi.S5G142600"
# This transcript jg10805.t2 is derived from g14855.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10806.t1 is derived from g14856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2192188	2193998	.	+	.	Phchi.S4G038800
Phchi.S4	AUGUSTUS	transcript	2192188	2193998	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	start_codon	2192188	2192190	.	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2192188	2192352	0.98	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2192188	2192352	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2192353	2192429	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2192430	2192587	1	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2192430	2192587	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2192588	2192661	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2192662	2192747	1	+	1	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2192662	2192747	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2192748	2192871	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2192872	2192903	1	+	2	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2192872	2192903	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2192904	2192984	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2192985	2193146	1	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2192985	2193146	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2193147	2193229	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2193230	2193302	0.96	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2193230	2193302	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2193303	2193410	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2193411	2193511	0.85	+	2	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2193411	2193511	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2193512	2193621	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2193622	2193714	0.91	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2193622	2193714	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2193715	2193797	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2193798	2193844	1	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2193798	2193844	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	intron	2193845	2193925	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	CDS	2193926	2193998	1	+	1	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	exon	2193926	2193998	.	+	.	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
Phchi.S4	AUGUSTUS	stop_codon	2193999	2194001	.	+	0	transcript_id "Phchi.S4G038800.t1"; gene_id "Phchi.S4G038800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3779.t1 is derived from g948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5655014	5658916	.	+	.	Phchi.S1G093800
Phchi.S1	AUGUSTUS	transcript	5655014	5658916	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	start_codon	5655014	5655016	.	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5655014	5655073	0.95	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5655014	5655073	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5655074	5655290	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5655291	5655343	0.81	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5655291	5655343	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5655344	5655429	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5655430	5655517	0.75	+	1	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5655430	5655517	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5655518	5655671	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5655672	5655917	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5655672	5655917	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5655918	5656009	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5656010	5656177	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5656010	5656177	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5656178	5656322	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5656323	5656373	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5656323	5656373	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5656374	5656486	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5656487	5656621	0.99	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5656487	5656621	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5656622	5656728	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5656729	5656752	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5656729	5656752	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5656753	5656912	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5656913	5657024	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5656913	5657024	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5657025	5657128	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5657129	5657257	0.91	+	2	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5657129	5657257	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5657258	5657351	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5657352	5657401	0.96	+	2	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5657352	5657401	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5657402	5657505	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5657506	5657664	0.95	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5657506	5657664	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5657665	5657763	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5657764	5657859	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5657764	5657859	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5657860	5657941	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5657942	5658057	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5657942	5658057	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5658058	5658195	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5658196	5658319	1	+	1	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5658196	5658319	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5658320	5658398	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5658399	5658512	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5658399	5658512	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5658513	5658621	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5658622	5658702	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5658622	5658702	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	intron	5658703	5658814	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	CDS	5658815	5658916	1	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	exon	5658815	5658916	.	+	.	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
Phchi.S1	AUGUSTUS	stop_codon	5658917	5658919	.	+	0	transcript_id "Phchi.S1G093800.t1"; gene_id "Phchi.S1G093800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8747.t1 is derived from g5922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37779732	37780906	.	-	.	Phchi.S1G590600
Phchi.S1	AUGUSTUS	transcript	37779732	37780906	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	stop_codon	37779729	37779731	.	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	CDS	37779732	37779752	1	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	exon	37779732	37779752	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	intron	37779753	37779841	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	CDS	37779842	37779904	1	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	exon	37779842	37779904	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	intron	37779905	37780047	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	CDS	37780048	37780120	1	-	1	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	exon	37780048	37780120	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	intron	37780121	37780221	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	CDS	37780222	37780313	1	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	exon	37780222	37780313	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	intron	37780314	37780460	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	CDS	37780461	37780712	0.95	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	exon	37780461	37780712	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	intron	37780713	37780879	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	CDS	37780880	37780906	1	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	exon	37780880	37780906	.	-	.	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
Phchi.S1	AUGUSTUS	start_codon	37780904	37780906	.	-	0	transcript_id "Phchi.S1G590600.t1"; gene_id "Phchi.S1G590600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8262.t1 is derived from g5437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34979004	34981856	.	-	.	Phchi.S1G542100
Phchi.S1	AUGUSTUS	transcript	34979004	34981856	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	stop_codon	34979001	34979003	.	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979004	34979019	1	-	1	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979004	34979019	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979020	34979093	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979094	34979104	1	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979094	34979104	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979105	34979167	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979168	34979221	1	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979168	34979221	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979222	34979315	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979316	34979412	1	-	1	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979316	34979412	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979413	34979488	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979489	34979553	1	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979489	34979553	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979554	34979688	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979689	34979748	1	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979689	34979748	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979749	34979870	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34979871	34979941	1	-	2	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34979871	34979941	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34979942	34980030	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34980031	34980090	1	-	2	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34980031	34980090	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34980091	34980208	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34980209	34980308	1	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34980209	34980308	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34980309	34980449	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34980450	34980528	1	-	1	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34980450	34980528	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34980529	34980615	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34980616	34980690	1	-	1	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34980616	34980690	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34980691	34980888	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34980889	34981013	1	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34980889	34981013	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34981014	34981172	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34981173	34981231	1	-	2	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34981173	34981231	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34981232	34981357	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34981358	34981436	0.78	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34981358	34981436	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	intron	34981437	34981649	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	CDS	34981650	34981856	0.9	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	exon	34981650	34981856	.	-	.	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
Phchi.S1	AUGUSTUS	start_codon	34981854	34981856	.	-	0	transcript_id "Phchi.S1G542100.t1"; gene_id "Phchi.S1G542100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7587.t1 is derived from g4761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30167274	30167727	.	+	.	Phchi.S1G474600
Phchi.S1	AUGUSTUS	transcript	30167274	30167727	.	+	.	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	start_codon	30167274	30167276	.	+	0	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	CDS	30167274	30167475	0.96	+	0	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	exon	30167274	30167475	.	+	.	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	intron	30167476	30167566	.	+	.	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	CDS	30167567	30167588	0.96	+	2	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	exon	30167567	30167588	.	+	.	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	intron	30167589	30167687	.	+	.	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	CDS	30167688	30167727	0.9	+	1	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	exon	30167688	30167727	.	+	.	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
Phchi.S1	AUGUSTUS	stop_codon	30167728	30167730	.	+	0	transcript_id "Phchi.S1G474600.t1"; gene_id "Phchi.S1G474600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10352.t1 is derived from g7528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47321542	47323301	.	+	.	Phchi.S1G751100
Phchi.S1	AUGUSTUS	transcript	47321542	47323301	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	start_codon	47321542	47321544	.	+	0	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47321542	47321677	1	+	0	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47321542	47321677	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47321678	47321788	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47321789	47321964	1	+	2	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47321789	47321964	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47321965	47322054	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47322055	47322240	0.9	+	0	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47322055	47322240	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47322241	47322345	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47322346	47322415	1	+	0	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47322346	47322415	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47322416	47322504	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47322505	47322699	1	+	2	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47322505	47322699	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47322700	47322801	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47322802	47322818	1	+	2	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47322802	47322818	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47322819	47322933	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47322934	47322944	1	+	0	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47322934	47322944	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47322945	47323016	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47323017	47323090	1	+	1	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47323017	47323090	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	intron	47323091	47323179	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	CDS	47323180	47323301	0.96	+	2	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	exon	47323180	47323301	.	+	.	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
Phchi.S1	AUGUSTUS	stop_codon	47323302	47323304	.	+	0	transcript_id "Phchi.S1G751100.t1"; gene_id "Phchi.S1G751100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9574.t1 is derived from g6750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42729486	42734147	.	-	.	Phchi.S1G673300
Phchi.S1	AUGUSTUS	transcript	42729486	42734147	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	stop_codon	42729483	42729485	.	-	0	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	CDS	42729486	42729537	0.61	-	1	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	exon	42729486	42729537	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	intron	42729538	42729624	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	CDS	42729625	42729724	0.51	-	2	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	exon	42729625	42729724	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	intron	42729725	42729829	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	CDS	42729830	42731009	0.3	-	0	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	exon	42729830	42731009	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	intron	42731010	42731181	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	CDS	42731182	42732414	0.75	-	0	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	exon	42731182	42732414	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	intron	42732415	42732568	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	CDS	42732569	42732679	1	-	0	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	exon	42732569	42732679	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	intron	42732680	42732809	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	CDS	42732810	42734147	0.77	-	0	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	exon	42732810	42734147	.	-	.	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
Phchi.S1	AUGUSTUS	start_codon	42734145	42734147	.	-	0	transcript_id "Phchi.S1G673300.t1"; gene_id "Phchi.S1G673300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11985.t1 is derived from g7660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	356284	357833	.	-	.	Phchi.S2G006500
Phchi.S2	AUGUSTUS	transcript	356284	357833	.	-	.	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	stop_codon	356281	356283	.	-	0	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	CDS	356284	356558	0.13	-	2	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	exon	356284	356558	.	-	.	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	intron	356559	357715	.	-	.	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	CDS	357716	357833	0.01	-	0	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	exon	357716	357833	.	-	.	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
Phchi.S2	AUGUSTUS	start_codon	357831	357833	.	-	0	transcript_id "Phchi.S2G006500.t1"; gene_id "Phchi.S2G006500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10541.t1 is derived from g14591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	878597	880791	.	+	.	Phchi.S4G012300
Phchi.S4	AUGUSTUS	transcript	878597	880791	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	start_codon	878597	878599	.	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	878597	878650	0.96	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	878597	878650	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	878651	878795	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	878796	878909	0.8	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	878796	878909	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	878910	879157	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	879158	879387	0.44	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	879158	879387	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	879388	879533	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	879534	879615	1	+	1	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	879534	879615	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	879616	879760	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	879761	879818	1	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	879761	879818	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	879819	879977	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	879978	880075	1	+	2	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	879978	880075	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	880076	880165	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	880166	880261	1	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	880166	880261	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	880262	880354	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	880355	880425	1	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	880355	880425	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	880426	880519	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	880520	880590	1	+	1	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	880520	880590	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	intron	880591	880747	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	CDS	880748	880791	1	+	2	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	exon	880748	880791	.	+	.	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
Phchi.S4	AUGUSTUS	stop_codon	880792	880794	.	+	0	transcript_id "Phchi.S4G012300.t1"; gene_id "Phchi.S4G012300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11622.t1 is derived from g15673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7359644	7361370	.	+	.	Phchi.S4G120400
Phchi.S4	AUGUSTUS	transcript	7359644	7361370	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	start_codon	7359644	7359646	.	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7359644	7359746	0.98	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7359644	7359746	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7359747	7359940	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7359941	7359990	1	+	2	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7359941	7359990	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7359991	7360091	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7360092	7360184	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7360092	7360184	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7360185	7360255	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7360256	7360297	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7360256	7360297	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7360298	7360437	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7360438	7360500	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7360438	7360500	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7360501	7360630	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7360631	7360768	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7360631	7360768	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7360769	7360864	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7360865	7360978	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7360865	7360978	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7360979	7361069	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7361070	7361144	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7361070	7361144	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	intron	7361145	7361235	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	CDS	7361236	7361370	1	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	exon	7361236	7361370	.	+	.	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
Phchi.S4	AUGUSTUS	stop_codon	7361371	7361373	.	+	0	transcript_id "Phchi.S4G120400.t1"; gene_id "Phchi.S4G120400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12203.t1 is derived from g7879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6719339	6723033	.	+	.	Phchi.S2G028300
Phchi.S2	AUGUSTUS	transcript	6719339	6723033	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	start_codon	6719339	6719341	.	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6719339	6719412	0.68	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6719339	6719412	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6719413	6719495	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6719496	6719562	1	+	1	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6719496	6719562	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6719563	6719684	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6719685	6719935	1	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6719685	6719935	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6719936	6720029	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6720030	6721599	0.77	+	1	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6720030	6721599	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6721600	6721724	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6721725	6722255	1	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6721725	6722255	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6722256	6722345	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6722346	6722540	0.75	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6722346	6722540	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6722541	6722640	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6722641	6722676	0.52	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6722641	6722676	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6722677	6722803	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6722804	6722866	0.8	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6722804	6722866	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	intron	6722867	6722952	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	CDS	6722953	6723033	0.99	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	exon	6722953	6723033	.	+	.	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
Phchi.S2	AUGUSTUS	stop_codon	6723034	6723036	.	+	0	transcript_id "Phchi.S2G028300.t1"; gene_id "Phchi.S2G028300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13360.t1 is derived from g11826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6329672	6330006	.	-	.	Phchi.S3G067900
Phchi.S3	AUGUSTUS	transcript	6329672	6330006	.	-	.	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	stop_codon	6329669	6329671	.	-	0	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	CDS	6329672	6329764	0.89	-	0	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	exon	6329672	6329764	.	-	.	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	intron	6329765	6329847	.	-	.	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	CDS	6329848	6330006	0.85	-	0	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	exon	6329848	6330006	.	-	.	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
Phchi.S3	AUGUSTUS	start_codon	6330004	6330006	.	-	0	transcript_id "Phchi.S3G067900.t1"; gene_id "Phchi.S3G067900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8398.t1 is derived from g5573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35744967	35745746	.	-	.	Phchi.S1G555700
Phchi.S1	AUGUSTUS	transcript	35744967	35745746	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	stop_codon	35744964	35744966	.	-	0	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	CDS	35744967	35745005	0.99	-	0	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	exon	35744967	35745005	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	intron	35745006	35745100	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	CDS	35745101	35745246	1	-	2	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	exon	35745101	35745246	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	intron	35745247	35745404	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	CDS	35745405	35745518	0.52	-	2	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	exon	35745405	35745518	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	intron	35745519	35745691	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	CDS	35745692	35745746	0.31	-	0	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	exon	35745692	35745746	.	-	.	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
Phchi.S1	AUGUSTUS	start_codon	35745744	35745746	.	-	0	transcript_id "Phchi.S1G555700.t1"; gene_id "Phchi.S1G555700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12228.t1 is derived from g7904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6847899	6850695	.	-	.	Phchi.S2G030800
Phchi.S2	AUGUSTUS	transcript	6847899	6850695	.	-	.	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	stop_codon	6847896	6847898	.	-	0	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	CDS	6847899	6848228	1	-	0	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	exon	6847899	6848228	.	-	.	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	intron	6848229	6848318	.	-	.	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	CDS	6848319	6848592	0.98	-	1	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	exon	6848319	6848592	.	-	.	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	intron	6848593	6848728	.	-	.	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	CDS	6848729	6850695	0.84	-	0	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	exon	6848729	6850695	.	-	.	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
Phchi.S2	AUGUSTUS	start_codon	6850693	6850695	.	-	0	transcript_id "Phchi.S2G030800.t1"; gene_id "Phchi.S2G030800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5520.t1 is derived from g2690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17203697	17204323	.	+	.	Phchi.S1G267900
Phchi.S1	AUGUSTUS	transcript	17203697	17204323	.	+	.	transcript_id "Phchi.S1G267900.t1"; gene_id "Phchi.S1G267900"
Phchi.S1	AUGUSTUS	start_codon	17203697	17203699	.	+	0	transcript_id "Phchi.S1G267900.t1"; gene_id "Phchi.S1G267900"
Phchi.S1	AUGUSTUS	CDS	17203697	17204323	0.49	+	0	transcript_id "Phchi.S1G267900.t1"; gene_id "Phchi.S1G267900"
Phchi.S1	AUGUSTUS	exon	17203697	17204323	.	+	.	transcript_id "Phchi.S1G267900.t1"; gene_id "Phchi.S1G267900"
Phchi.S1	AUGUSTUS	stop_codon	17204324	17204326	.	+	0	transcript_id "Phchi.S1G267900.t1"; gene_id "Phchi.S1G267900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14471.t1 is derived from g12939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13026431	13027792	.	-	.	Phchi.S3G179000
Phchi.S3	AUGUSTUS	transcript	13026431	13027792	.	-	.	transcript_id "Phchi.S3G179000.t1"; gene_id "Phchi.S3G179000"
Phchi.S3	AUGUSTUS	stop_codon	13026428	13026430	.	-	0	transcript_id "Phchi.S3G179000.t1"; gene_id "Phchi.S3G179000"
Phchi.S3	AUGUSTUS	CDS	13026431	13027792	1	-	0	transcript_id "Phchi.S3G179000.t1"; gene_id "Phchi.S3G179000"
Phchi.S3	AUGUSTUS	exon	13026431	13027792	.	-	.	transcript_id "Phchi.S3G179000.t1"; gene_id "Phchi.S3G179000"
Phchi.S3	AUGUSTUS	start_codon	13027790	13027792	.	-	0	transcript_id "Phchi.S3G179000.t1"; gene_id "Phchi.S3G179000"
# This transcript jg9070.t2 is derived from g6245.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9071.t1 is derived from g6246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39658216	39659444	.	+	.	Phchi.S1G623000
Phchi.S1	AUGUSTUS	transcript	39658216	39659444	.	+	.	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	start_codon	39658216	39658218	.	+	0	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	CDS	39658216	39659356	0.56	+	0	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	exon	39658216	39659356	.	+	.	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	intron	39659357	39659439	.	+	.	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	CDS	39659440	39659444	0.5	+	2	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	exon	39659440	39659444	.	+	.	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
Phchi.S1	AUGUSTUS	stop_codon	39659445	39659447	.	+	0	transcript_id "Phchi.S1G623000.t1"; gene_id "Phchi.S1G623000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7416.t1 is derived from g4588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29038867	29040759	.	-	.	Phchi.S1G457500
Phchi.S1	AUGUSTUS	transcript	29038867	29040759	.	-	.	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	stop_codon	29038864	29038866	.	-	0	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	CDS	29038867	29039673	1	-	0	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	exon	29038867	29039673	.	-	.	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	intron	29039674	29039761	.	-	.	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	CDS	29039762	29040223	0.98	-	0	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	exon	29039762	29040223	.	-	.	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	intron	29040224	29040492	.	-	.	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	CDS	29040493	29040759	1	-	0	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	exon	29040493	29040759	.	-	.	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
Phchi.S1	AUGUSTUS	start_codon	29040757	29040759	.	-	0	transcript_id "Phchi.S1G457500.t1"; gene_id "Phchi.S1G457500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12309.t1 is derived from g7985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10072574	10076979	.	+	.	Phchi.S2G038900
Phchi.S2	AUGUSTUS	transcript	10072574	10076979	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	start_codon	10072574	10072576	.	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10072574	10072818	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10072574	10072818	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10072819	10073371	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10073372	10073546	1	+	1	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10073372	10073546	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10073547	10073642	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10073643	10073726	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10073643	10073726	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10073727	10074125	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10074126	10074367	0.84	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10074126	10074367	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10074368	10074761	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10074762	10075002	1	+	1	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10074762	10075002	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075003	10075418	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10075419	10075498	0.99	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10075419	10075498	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075499	10075605	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10075606	10075690	0.99	+	1	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10075606	10075690	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075691	10075834	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10075835	10075966	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10075835	10075966	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075967	10076080	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076081	10076194	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076081	10076194	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076195	10076317	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076318	10076365	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076318	10076365	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076366	10076495	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076496	10076580	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076496	10076580	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076581	10076705	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076706	10076758	1	+	2	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076706	10076758	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076759	10076940	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076941	10076979	1	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076941	10076979	.	+	.	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	stop_codon	10076980	10076982	.	+	0	transcript_id "Phchi.S2G038900.t1"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	transcript	10072574	10076979	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	start_codon	10072574	10072576	.	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10072574	10072818	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10072574	10072818	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10072819	10073371	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10073372	10073546	1	+	1	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10073372	10073546	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10073547	10073642	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10073643	10073726	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10073643	10073726	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10073727	10074125	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10074126	10074304	0.89	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10074126	10074304	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10074305	10074432	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10074433	10074486	0.87	+	1	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10074433	10074486	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10074487	10074761	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10074762	10075002	1	+	1	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10074762	10075002	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075003	10075418	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10075419	10075498	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10075419	10075498	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075499	10075605	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10075606	10075690	1	+	1	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10075606	10075690	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075691	10075834	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10075835	10075966	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10075835	10075966	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10075967	10076080	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076081	10076194	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076081	10076194	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076195	10076317	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076318	10076365	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076318	10076365	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076366	10076495	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076496	10076580	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076496	10076580	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076581	10076705	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076706	10076758	1	+	2	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076706	10076758	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	intron	10076759	10076940	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	CDS	10076941	10076979	1	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	exon	10076941	10076979	.	+	.	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
Phchi.S2	AUGUSTUS	stop_codon	10076980	10076982	.	+	0	transcript_id "Phchi.S2G038900.t2"; gene_id "Phchi.S2G038900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9309.t1 is derived from g6484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40894482	40896234	.	-	.	Phchi.S1G646800
Phchi.S1	AUGUSTUS	transcript	40894482	40896234	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	stop_codon	40894479	40894481	.	-	0	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	CDS	40894482	40894728	1	-	1	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	exon	40894482	40894728	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	intron	40894729	40894815	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	CDS	40894816	40895033	1	-	0	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	exon	40894816	40895033	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	intron	40895034	40895119	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	CDS	40895120	40895611	0.9	-	0	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	exon	40895120	40895611	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	intron	40895612	40895736	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	CDS	40895737	40896234	0.86	-	0	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	exon	40895737	40896234	.	-	.	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
Phchi.S1	AUGUSTUS	start_codon	40896232	40896234	.	-	0	transcript_id "Phchi.S1G646800.t1"; gene_id "Phchi.S1G646800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1444.t1 is derived from g8363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	917807	919206	.	+	.	Phchi.S5G005300
Phchi.S5	AUGUSTUS	transcript	917807	919206	.	+	.	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	start_codon	917807	917809	.	+	0	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	CDS	917807	917987	1	+	0	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	exon	917807	917987	.	+	.	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	intron	917988	918072	.	+	.	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	CDS	918073	918122	1	+	2	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	exon	918073	918122	.	+	.	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	intron	918123	918204	.	+	.	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	CDS	918205	919206	0.99	+	0	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	exon	918205	919206	.	+	.	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
Phchi.S5	AUGUSTUS	stop_codon	919207	919209	.	+	0	transcript_id "Phchi.S5G005300.t1"; gene_id "Phchi.S5G005300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5151.t1 is derived from g2321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15170210	15171152	.	-	.	Phchi.S1G231000
Phchi.S1	AUGUSTUS	transcript	15170210	15171152	.	-	.	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	stop_codon	15170207	15170209	.	-	0	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	CDS	15170210	15170306	1	-	1	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	exon	15170210	15170306	.	-	.	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	intron	15170307	15170388	.	-	.	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	CDS	15170389	15171152	0.65	-	0	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	exon	15170389	15171152	.	-	.	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
Phchi.S1	AUGUSTUS	start_codon	15171150	15171152	.	-	0	transcript_id "Phchi.S1G231000.t1"; gene_id "Phchi.S1G231000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12814.t1 is derived from g11279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2482840	2484351	.	-	.	Phchi.S3G013300
Phchi.S3	AUGUSTUS	transcript	2482840	2484351	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	stop_codon	2482837	2482839	.	-	0	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	CDS	2482840	2483105	0.92	-	2	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	exon	2482840	2483105	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	intron	2483106	2483203	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	CDS	2483204	2483447	1	-	0	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	exon	2483204	2483447	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	intron	2483448	2483631	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	CDS	2483632	2483751	1	-	0	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	exon	2483632	2483751	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	intron	2483752	2483877	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	CDS	2483878	2484351	0.8	-	0	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	exon	2483878	2484351	.	-	.	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
Phchi.S3	AUGUSTUS	start_codon	2484349	2484351	.	-	0	transcript_id "Phchi.S3G013300.t1"; gene_id "Phchi.S3G013300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1850.t1 is derived from g8770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3550225	3551387	.	-	.	Phchi.S5G045900
Phchi.S5	AUGUSTUS	transcript	3550225	3551387	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	stop_codon	3550222	3550224	.	-	0	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	CDS	3550225	3550317	0.73	-	0	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	exon	3550225	3550317	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	intron	3550318	3550415	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	CDS	3550416	3550960	0.95	-	2	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	exon	3550416	3550960	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	intron	3550961	3551043	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	CDS	3551044	3551200	1	-	0	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	exon	3551044	3551200	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	intron	3551201	3551279	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	CDS	3551280	3551387	0.75	-	0	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	exon	3551280	3551387	.	-	.	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
Phchi.S5	AUGUSTUS	start_codon	3551385	3551387	.	-	0	transcript_id "Phchi.S5G045900.t1"; gene_id "Phchi.S5G045900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7705.t1 is derived from g4879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30714387	30716008	.	-	.	Phchi.S1G486400
Phchi.S1	AUGUSTUS	transcript	30714387	30716008	.	-	.	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	stop_codon	30714384	30714386	.	-	0	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	CDS	30714387	30714997	0.99	-	2	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	exon	30714387	30714997	.	-	.	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	intron	30714998	30715098	.	-	.	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	CDS	30715099	30716008	0.8	-	0	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	exon	30715099	30716008	.	-	.	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
Phchi.S1	AUGUSTUS	start_codon	30716006	30716008	.	-	0	transcript_id "Phchi.S1G486400.t1"; gene_id "Phchi.S1G486400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12008.t1 is derived from g7683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	509769	511043	.	+	.	Phchi.S2G008800
Phchi.S2	AUGUSTUS	transcript	509769	511043	.	+	.	transcript_id "Phchi.S2G008800.t1"; gene_id "Phchi.S2G008800"
Phchi.S2	AUGUSTUS	start_codon	509769	509771	.	+	0	transcript_id "Phchi.S2G008800.t1"; gene_id "Phchi.S2G008800"
Phchi.S2	AUGUSTUS	CDS	509769	511043	0.68	+	0	transcript_id "Phchi.S2G008800.t1"; gene_id "Phchi.S2G008800"
Phchi.S2	AUGUSTUS	exon	509769	511043	.	+	.	transcript_id "Phchi.S2G008800.t1"; gene_id "Phchi.S2G008800"
Phchi.S2	AUGUSTUS	stop_codon	511044	511046	.	+	0	transcript_id "Phchi.S2G008800.t1"; gene_id "Phchi.S2G008800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9995.t1 is derived from g7171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44912149	44912861	.	-	.	Phchi.S1G715400
Phchi.S1	AUGUSTUS	transcript	44912149	44912861	.	-	.	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	stop_codon	44912146	44912148	.	-	0	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	CDS	44912149	44912443	0.48	-	1	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	exon	44912149	44912443	.	-	.	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	intron	44912444	44912715	.	-	.	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	CDS	44912716	44912861	0.57	-	0	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	exon	44912716	44912861	.	-	.	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
Phchi.S1	AUGUSTUS	start_codon	44912859	44912861	.	-	0	transcript_id "Phchi.S1G715400.t1"; gene_id "Phchi.S1G715400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9907.t1 is derived from g7083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44384522	44388340	.	-	.	Phchi.S1G706600
Phchi.S1	AUGUSTUS	transcript	44384522	44388340	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	stop_codon	44384519	44384521	.	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44384522	44385312	0.86	-	2	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44384522	44385312	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385313	44385386	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385387	44385476	1	-	2	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385387	44385476	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385477	44385555	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385556	44385670	1	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385556	44385670	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385671	44385823	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385824	44386017	1	-	2	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385824	44386017	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386018	44386150	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386151	44386361	1	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386151	44386361	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386362	44386515	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386516	44386591	1	-	1	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386516	44386591	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386592	44386700	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386701	44386735	0.89	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386701	44386735	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386736	44386823	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386824	44386919	1	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386824	44386919	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386920	44387090	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387091	44387162	1	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387091	44387162	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44387163	44387252	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387253	44387450	1	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387253	44387450	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44387451	44387525	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387526	44387728	1	-	2	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387526	44387728	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44387729	44387799	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387800	44388340	0.57	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387800	44388340	.	-	.	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	start_codon	44388338	44388340	.	-	0	transcript_id "Phchi.S1G706600.t1"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	transcript	44384522	44388340	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	stop_codon	44384519	44384521	.	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44384522	44385312	0.87	-	2	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44384522	44385312	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385313	44385386	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385387	44385476	1	-	2	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385387	44385476	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385477	44385555	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385556	44385665	0.91	-	1	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385556	44385665	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385666	44385823	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385824	44385841	0.91	-	1	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385824	44385841	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44385842	44385944	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44385945	44386017	0.91	-	2	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44385945	44386017	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386018	44386150	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386151	44386361	1	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386151	44386361	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386362	44386515	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386516	44386591	0.97	-	1	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386516	44386591	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386592	44386700	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386701	44386735	0.83	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386701	44386735	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386736	44386823	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44386824	44386919	1	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44386824	44386919	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44386920	44387090	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387091	44387162	1	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387091	44387162	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44387163	44387252	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387253	44387450	1	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387253	44387450	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44387451	44387525	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387526	44387728	1	-	2	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387526	44387728	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	intron	44387729	44387799	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	CDS	44387800	44388340	0.52	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	exon	44387800	44388340	.	-	.	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
Phchi.S1	AUGUSTUS	start_codon	44388338	44388340	.	-	0	transcript_id "Phchi.S1G706600.t2"; gene_id "Phchi.S1G706600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15329.t1 is derived from g13797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18423729	18425456	.	+	.	Phchi.S3G264800
Phchi.S3	AUGUSTUS	transcript	18423729	18425456	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	start_codon	18423729	18423731	.	+	0	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	CDS	18423729	18424301	0.97	+	0	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	exon	18423729	18424301	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	intron	18424302	18424435	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	CDS	18424436	18424480	0.52	+	0	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	exon	18424436	18424480	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	intron	18424481	18424571	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	CDS	18424572	18424658	0.44	+	0	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	exon	18424572	18424658	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	intron	18424659	18424869	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	CDS	18424870	18424901	0.74	+	0	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	exon	18424870	18424901	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	intron	18424902	18425395	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	CDS	18425396	18425456	0.46	+	1	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	exon	18425396	18425456	.	+	.	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
Phchi.S3	AUGUSTUS	stop_codon	18425457	18425459	.	+	0	transcript_id "Phchi.S3G264800.t1"; gene_id "Phchi.S3G264800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2026.t1 is derived from g8946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4500334	4505356	.	+	.	Phchi.S5G063500
Phchi.S5	AUGUSTUS	transcript	4500334	4505356	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	start_codon	4500334	4500336	.	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4500334	4500417	0.72	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4500334	4500417	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4500418	4500540	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4500541	4500604	0.88	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4500541	4500604	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4500605	4500689	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4500690	4500787	1	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4500690	4500787	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4500788	4500908	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4500909	4501080	1	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4500909	4501080	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4501081	4501271	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4501272	4501384	0.99	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4501272	4501384	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4501385	4501485	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4501486	4501822	0.99	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4501486	4501822	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4501823	4501942	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4501943	4502037	1	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4501943	4502037	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4502038	4502116	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4502117	4502250	1	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4502117	4502250	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4502251	4502392	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4502393	4502449	1	+	1	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4502393	4502449	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4502450	4502533	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4502534	4502611	1	+	1	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4502534	4502611	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4502612	4502708	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4502709	4502775	1	+	1	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4502709	4502775	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4502776	4502867	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4502868	4502909	1	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4502868	4502909	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4502910	4502999	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4503000	4503080	1	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4503000	4503080	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4503081	4503164	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4503165	4503366	1	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4503165	4503366	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4503367	4503450	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4503451	4503508	1	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4503451	4503508	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4503509	4503681	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4503682	4503804	1	+	1	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4503682	4503804	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4503805	4503929	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4503930	4504018	0.99	+	1	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4503930	4504018	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4504019	4504121	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4504122	4504214	0.99	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4504122	4504214	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4504215	4504311	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4504312	4504476	1	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4504312	4504476	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4504477	4504630	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4504631	4504764	1	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4504631	4504764	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4504765	4504926	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4504927	4505056	1	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4504927	4505056	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	intron	4505057	4505171	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	CDS	4505172	4505356	1	+	2	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	exon	4505172	4505356	.	+	.	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
Phchi.S5	AUGUSTUS	stop_codon	4505357	4505359	.	+	0	transcript_id "Phchi.S5G063500.t1"; gene_id "Phchi.S5G063500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12757.t1 is derived from g11222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1911197	1911563	.	-	.	Phchi.S3G007600
Phchi.S3	AUGUSTUS	transcript	1911197	1911563	.	-	.	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	stop_codon	1911194	1911196	.	-	0	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	CDS	1911197	1911316	0.96	-	0	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	exon	1911197	1911316	.	-	.	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	intron	1911317	1911407	.	-	.	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	CDS	1911408	1911563	0.8	-	0	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	exon	1911408	1911563	.	-	.	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
Phchi.S3	AUGUSTUS	start_codon	1911561	1911563	.	-	0	transcript_id "Phchi.S3G007600.t1"; gene_id "Phchi.S3G007600"
# This transcript jg8338.t2 is derived from g5513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8339.t1 is derived from g5514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35399649	35400866	.	-	.	Phchi.S1G549800
Phchi.S1	AUGUSTUS	transcript	35399649	35400866	.	-	.	transcript_id "Phchi.S1G549800.t1"; gene_id "Phchi.S1G549800"
Phchi.S1	AUGUSTUS	stop_codon	35399646	35399648	.	-	0	transcript_id "Phchi.S1G549800.t1"; gene_id "Phchi.S1G549800"
Phchi.S1	AUGUSTUS	CDS	35399649	35400866	1	-	0	transcript_id "Phchi.S1G549800.t1"; gene_id "Phchi.S1G549800"
Phchi.S1	AUGUSTUS	exon	35399649	35400866	.	-	.	transcript_id "Phchi.S1G549800.t1"; gene_id "Phchi.S1G549800"
Phchi.S1	AUGUSTUS	start_codon	35400864	35400866	.	-	0	transcript_id "Phchi.S1G549800.t1"; gene_id "Phchi.S1G549800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8402.t1 is derived from g5577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35791943	35793610	.	+	.	Phchi.S1G556100
Phchi.S1	AUGUSTUS	transcript	35791943	35793610	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	start_codon	35791943	35791945	.	+	0	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	CDS	35791943	35792463	0.54	+	0	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	exon	35791943	35792463	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	intron	35792464	35792571	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	CDS	35792572	35792805	0.96	+	1	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	exon	35792572	35792805	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	intron	35792806	35792902	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	CDS	35792903	35792981	0.94	+	1	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	exon	35792903	35792981	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	intron	35792982	35793090	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	CDS	35793091	35793175	0.94	+	0	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	exon	35793091	35793175	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	intron	35793176	35793295	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	CDS	35793296	35793342	0.99	+	2	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	exon	35793296	35793342	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	intron	35793343	35793433	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	CDS	35793434	35793610	1	+	0	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	exon	35793434	35793610	.	+	.	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
Phchi.S1	AUGUSTUS	stop_codon	35793611	35793613	.	+	0	transcript_id "Phchi.S1G556100.t1"; gene_id "Phchi.S1G556100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14093.t1 is derived from g12560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10821309	10822584	.	-	.	Phchi.S3G141200
Phchi.S3	AUGUSTUS	transcript	10821309	10822584	.	-	.	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	stop_codon	10821306	10821308	.	-	0	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	CDS	10821309	10821707	0.32	-	0	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	exon	10821309	10821707	.	-	.	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	intron	10821708	10821906	.	-	.	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	CDS	10821907	10822584	0.43	-	0	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	exon	10821907	10822584	.	-	.	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
Phchi.S3	AUGUSTUS	start_codon	10822582	10822584	.	-	0	transcript_id "Phchi.S3G141200.t1"; gene_id "Phchi.S3G141200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4656.t1 is derived from g1826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11657584	11659270	.	+	.	Phchi.S1G181500
Phchi.S1	AUGUSTUS	transcript	11657584	11659270	.	+	.	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	start_codon	11657584	11657586	.	+	0	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	CDS	11657584	11658378	0.43	+	0	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	exon	11657584	11658378	.	+	.	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	intron	11658379	11658480	.	+	.	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	CDS	11658481	11658788	0.99	+	0	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	exon	11658481	11658788	.	+	.	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	intron	11658789	11658906	.	+	.	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	CDS	11658907	11659270	1	+	1	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	exon	11658907	11659270	.	+	.	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
Phchi.S1	AUGUSTUS	stop_codon	11659271	11659273	.	+	0	transcript_id "Phchi.S1G181500.t1"; gene_id "Phchi.S1G181500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4669.t1 is derived from g1839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11727220	11727983	.	+	.	Phchi.S1G182800
Phchi.S1	AUGUSTUS	transcript	11727220	11727983	.	+	.	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	start_codon	11727220	11727222	.	+	0	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	CDS	11727220	11727260	0.67	+	0	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	exon	11727220	11727260	.	+	.	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	intron	11727261	11727334	.	+	.	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	CDS	11727335	11727983	0.34	+	1	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	exon	11727335	11727983	.	+	.	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
Phchi.S1	AUGUSTUS	stop_codon	11727984	11727986	.	+	0	transcript_id "Phchi.S1G182800.t1"; gene_id "Phchi.S1G182800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14716.t1 is derived from g13184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14346148	14346471	.	-	.	Phchi.S3G203500
Phchi.S3	AUGUSTUS	transcript	14346148	14346471	.	-	.	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	stop_codon	14346145	14346147	.	-	0	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	CDS	14346148	14346201	0.95	-	0	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	exon	14346148	14346201	.	-	.	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	intron	14346202	14346291	.	-	.	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	CDS	14346292	14346471	1	-	0	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	exon	14346292	14346471	.	-	.	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
Phchi.S3	AUGUSTUS	start_codon	14346469	14346471	.	-	0	transcript_id "Phchi.S3G203500.t1"; gene_id "Phchi.S3G203500"
# This transcript jg13540.t2 is derived from g12007.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13541.t1 is derived from g12008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7429303	7430851	.	+	.	Phchi.S3G086000
Phchi.S3	AUGUSTUS	transcript	7429303	7430851	.	+	.	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	start_codon	7429303	7429305	.	+	0	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7429303	7429440	0.63	+	0	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7429303	7429440	.	+	.	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	intron	7429441	7429524	.	+	.	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7429525	7430466	0.97	+	0	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7429525	7430466	.	+	.	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	intron	7430467	7430698	.	+	.	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7430699	7430851	1	+	0	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7430699	7430851	.	+	.	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	stop_codon	7430852	7430854	.	+	0	transcript_id "Phchi.S3G086000.t1"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	transcript	7429303	7430851	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	start_codon	7429303	7429305	.	+	0	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7429303	7429440	0.6	+	0	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7429303	7429440	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	intron	7429441	7429524	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7429525	7430466	0.98	+	0	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7429525	7430466	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	intron	7430467	7430556	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7430557	7430561	0.53	+	0	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7430557	7430561	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	intron	7430562	7430643	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	CDS	7430644	7430851	0.53	+	1	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	exon	7430644	7430851	.	+	.	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
Phchi.S3	AUGUSTUS	stop_codon	7430852	7430854	.	+	0	transcript_id "Phchi.S3G086000.t2"; gene_id "Phchi.S3G086000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9215.t1 is derived from g6390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40456797	40458052	.	+	.	Phchi.S1G637400
Phchi.S1	AUGUSTUS	transcript	40456797	40458052	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	start_codon	40456797	40456799	.	+	0	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	CDS	40456797	40456896	0.58	+	0	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	exon	40456797	40456896	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	intron	40456897	40456994	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	CDS	40456995	40457383	0.99	+	2	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	exon	40456995	40457383	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	intron	40457384	40457464	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	CDS	40457465	40457634	1	+	0	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	exon	40457465	40457634	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	intron	40457635	40457925	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	CDS	40457926	40458052	1	+	1	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	exon	40457926	40458052	.	+	.	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
Phchi.S1	AUGUSTUS	stop_codon	40458053	40458055	.	+	0	transcript_id "Phchi.S1G637400.t1"; gene_id "Phchi.S1G637400"
# This transcript jg12303.t2 is derived from g7979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12303.t3 is derived from g7979.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12304.t1 is derived from g7980.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9878681	9883661	.	+	.	Phchi.S2G038400
Phchi.S2	AUGUSTUS	transcript	9878681	9882056	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	start_codon	9878681	9878683	.	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9878681	9878732	0.81	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9878681	9878732	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9878733	9878962	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9878963	9879072	1	+	2	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9878963	9879072	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879073	9879273	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879274	9879331	1	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879274	9879331	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879332	9879650	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879651	9879853	1	+	2	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879651	9879853	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879854	9879998	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879999	9880128	1	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879999	9880128	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880129	9880445	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9880446	9880523	1	+	2	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9880446	9880523	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880524	9880625	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9880626	9880773	0.97	+	2	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9880626	9880773	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880774	9881014	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881015	9881127	1	+	1	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881015	9881127	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881128	9881195	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881196	9881271	1	+	2	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881196	9881271	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881272	9881382	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881383	9881454	0.99	+	1	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881383	9881454	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881455	9881544	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881545	9881596	1	+	1	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881545	9881596	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881597	9881714	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881715	9881804	1	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881715	9881804	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881805	9881975	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881976	9882056	1	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881976	9882056	.	+	.	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	stop_codon	9882195	9882197	.	+	0	transcript_id "Phchi.S2G038400.t1"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	transcript	9878681	9883661	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	start_codon	9878681	9878683	.	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9878681	9878732	0.79	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9878681	9878732	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9878733	9878962	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9878963	9879072	1	+	2	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9878963	9879072	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879073	9879273	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879274	9879331	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879274	9879331	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879332	9879647	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879648	9879853	0.97	+	2	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879648	9879853	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879854	9879998	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879999	9880128	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879999	9880128	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880129	9880445	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9880446	9880523	1	+	2	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9880446	9880523	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880524	9880625	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9880626	9880773	0.97	+	2	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9880626	9880773	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880774	9881014	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881015	9881127	1	+	1	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881015	9881127	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881128	9881195	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881196	9881271	1	+	2	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881196	9881271	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881272	9881382	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881383	9881454	0.95	+	1	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881383	9881454	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881455	9881544	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881545	9881596	1	+	1	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881545	9881596	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881597	9881714	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881715	9881804	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881715	9881804	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881805	9881975	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881976	9882056	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881976	9882056	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882057	9882389	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882390	9882493	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882390	9882493	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882494	9882607	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882608	9882700	1	+	1	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882608	9882700	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882701	9882830	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882831	9882899	1	+	1	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882831	9882899	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882900	9882989	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882990	9883054	0.89	+	1	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882990	9883054	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9883055	9883162	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9883163	9883224	0.89	+	2	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9883163	9883224	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9883225	9883441	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9883442	9883537	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9883442	9883537	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9883538	9883607	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9883608	9883661	1	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9883608	9883661	.	+	.	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	stop_codon	9883662	9883664	.	+	0	transcript_id "Phchi.S2G038400.t2"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	transcript	9878681	9883661	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	start_codon	9878681	9878683	.	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9878681	9878732	0.77	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9878681	9878732	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9878733	9878962	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9878963	9879072	1	+	2	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9878963	9879072	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879073	9879273	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879274	9879331	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879274	9879331	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879332	9879650	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879651	9879853	1	+	2	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879651	9879853	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9879854	9879998	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9879999	9880128	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9879999	9880128	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880129	9880445	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9880446	9880523	1	+	2	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9880446	9880523	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880524	9880625	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9880626	9880773	0.98	+	2	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9880626	9880773	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9880774	9881014	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881015	9881127	1	+	1	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881015	9881127	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881128	9881195	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881196	9881271	1	+	2	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881196	9881271	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881272	9881382	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881383	9881454	1	+	1	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881383	9881454	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881455	9881544	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881545	9881596	1	+	1	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881545	9881596	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881597	9881714	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881715	9881804	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881715	9881804	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9881805	9881975	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9881976	9882056	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9881976	9882056	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882057	9882389	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882390	9882493	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882390	9882493	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882494	9882607	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882608	9882700	0.99	+	1	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882608	9882700	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882701	9882830	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882831	9882899	1	+	1	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882831	9882899	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9882900	9882989	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9882990	9883054	0.84	+	1	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9882990	9883054	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9883055	9883162	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9883163	9883224	0.84	+	2	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9883163	9883224	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9883225	9883441	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9883442	9883537	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9883442	9883537	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	intron	9883538	9883607	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	CDS	9883608	9883661	1	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	exon	9883608	9883661	.	+	.	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
Phchi.S2	AUGUSTUS	stop_codon	9883662	9883664	.	+	0	transcript_id "Phchi.S2G038400.t3"; gene_id "Phchi.S2G038400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2650.t1 is derived from g9570.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7998277	8002784	.	+	.	Phchi.S5G125900
Phchi.S5	AUGUSTUS	transcript	7998277	8002784	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	start_codon	7998277	7998279	.	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998277	7998428	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998277	7998428	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998429	7998593	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998594	7998675	1	+	1	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998594	7998675	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998676	7998761	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998762	7998905	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998762	7998905	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998906	7998981	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998982	7999151	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998982	7999151	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999152	7999710	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7999711	7999978	1	+	1	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7999711	7999978	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999979	8000054	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8000055	8000484	0.97	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8000055	8000484	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8000485	8000692	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8000693	8000778	0.97	+	2	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8000693	8000778	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8000779	8001075	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001076	8001117	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001076	8001117	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001118	8001206	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001207	8001213	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001207	8001213	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001214	8001395	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001396	8001400	1	+	2	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001396	8001400	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001401	8001479	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001480	8001564	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001480	8001564	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001565	8002027	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002028	8002087	0.87	+	2	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002028	8002087	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8002088	8002499	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002500	8002573	0.85	+	2	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002500	8002573	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8002574	8002775	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002776	8002784	1	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002776	8002784	.	+	.	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	stop_codon	8002785	8002787	.	+	0	transcript_id "Phchi.S5G125900.t1"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	transcript	7998277	8002784	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	start_codon	7998277	7998279	.	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998277	7998428	1	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998277	7998428	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998429	7998593	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998594	7998675	1	+	1	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998594	7998675	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998676	7998761	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998762	7998905	1	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998762	7998905	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998906	7998981	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998982	7999151	1	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998982	7999151	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999152	7999710	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7999711	7999978	1	+	1	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7999711	7999978	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999979	8000054	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8000055	8000484	1	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8000055	8000484	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8000485	8001075	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001076	8001117	0.92	+	2	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001076	8001117	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001118	8001206	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001207	8001271	0.92	+	2	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001207	8001271	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001272	8001391	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001392	8001400	0.92	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001392	8001400	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001401	8001479	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001480	8001564	1	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001480	8001564	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001565	8002027	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002028	8002087	0.88	+	2	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002028	8002087	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8002088	8002499	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002500	8002573	0.8	+	2	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002500	8002573	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8002574	8002775	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002776	8002784	1	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002776	8002784	.	+	.	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	stop_codon	8002785	8002787	.	+	0	transcript_id "Phchi.S5G125900.t2"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	transcript	7998277	8002784	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	start_codon	7998277	7998279	.	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998277	7998428	1	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998277	7998428	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998429	7998593	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998594	7998675	1	+	1	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998594	7998675	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998676	7998761	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998762	7998905	1	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998762	7998905	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7998906	7998981	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7998982	7999151	1	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7998982	7999151	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999152	7999270	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7999271	7999397	0.86	+	1	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7999271	7999397	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999398	7999710	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7999711	7999742	0.71	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7999711	7999742	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999743	7999887	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	7999888	7999978	0.55	+	1	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	7999888	7999978	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	7999979	8000054	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8000055	8000484	0.99	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8000055	8000484	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8000485	8001075	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001076	8001117	0.87	+	2	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001076	8001117	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001118	8001206	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001207	8001271	0.87	+	2	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001207	8001271	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001272	8001391	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001392	8001400	0.87	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001392	8001400	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001401	8001479	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8001480	8001564	1	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8001480	8001564	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8001565	8002027	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002028	8002087	0.83	+	2	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002028	8002087	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8002088	8002499	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002500	8002573	0.84	+	2	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002500	8002573	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	intron	8002574	8002775	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	CDS	8002776	8002784	1	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	exon	8002776	8002784	.	+	.	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
Phchi.S5	AUGUSTUS	stop_codon	8002785	8002787	.	+	0	transcript_id "Phchi.S5G125900.t3"; gene_id "Phchi.S5G125900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2805.t1 is derived from g9725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8963382	8964003	.	-	.	Phchi.S5G141400
Phchi.S5	AUGUSTUS	transcript	8963382	8964003	.	-	.	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	stop_codon	8963379	8963381	.	-	0	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	CDS	8963382	8963745	0.79	-	1	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	exon	8963382	8963745	.	-	.	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	intron	8963746	8963932	.	-	.	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	CDS	8963933	8964003	0.88	-	0	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	exon	8963933	8964003	.	-	.	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
Phchi.S5	AUGUSTUS	start_codon	8964001	8964003	.	-	0	transcript_id "Phchi.S5G141400.t1"; gene_id "Phchi.S5G141400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10242.t1 is derived from g7418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46565288	46567122	.	-	.	Phchi.S1G740100
Phchi.S1	AUGUSTUS	transcript	46565288	46567122	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	stop_codon	46565285	46565287	.	-	0	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	CDS	46565288	46565562	0.98	-	2	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	exon	46565288	46565562	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	intron	46565563	46565662	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	CDS	46565663	46566452	0.85	-	0	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	exon	46565663	46566452	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	intron	46566453	46566628	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	CDS	46566629	46566727	1	-	0	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	exon	46566629	46566727	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	intron	46566728	46566867	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	CDS	46566868	46567122	0.95	-	0	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	exon	46566868	46567122	.	-	.	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
Phchi.S1	AUGUSTUS	start_codon	46567120	46567122	.	-	0	transcript_id "Phchi.S1G740100.t1"; gene_id "Phchi.S1G740100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8896.t1 is derived from g6071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38540054	38544149	.	+	.	Phchi.S1G605500
Phchi.S1	AUGUSTUS	transcript	38540054	38544149	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	start_codon	38540054	38540056	.	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38540054	38540240	0.68	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38540054	38540240	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38540241	38540553	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38540554	38540667	0.65	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38540554	38540667	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38540668	38540756	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38540757	38540888	0.46	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38540757	38540888	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38540889	38540975	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38540976	38541056	1	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38540976	38541056	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38541057	38541197	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38541198	38541286	1	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38541198	38541286	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38541287	38541418	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38541419	38541507	0.33	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38541419	38541507	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38541508	38541621	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38541622	38541703	0.7	+	1	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38541622	38541703	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38541704	38541953	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38541954	38542013	1	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38541954	38542013	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38542014	38542190	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38542191	38542293	1	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38542191	38542293	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38542294	38542436	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38542437	38542532	0.35	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38542437	38542532	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38542533	38542636	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38542637	38542778	0.47	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38542637	38542778	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38542779	38542886	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38542887	38543412	0.39	+	1	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38542887	38543412	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38543413	38543503	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38543504	38543609	0.89	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38543504	38543609	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38543610	38543833	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38543834	38543889	0.93	+	2	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38543834	38543889	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	intron	38543890	38544107	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	CDS	38544108	38544149	0.93	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	exon	38544108	38544149	.	+	.	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
Phchi.S1	AUGUSTUS	stop_codon	38544150	38544152	.	+	0	transcript_id "Phchi.S1G605500.t1"; gene_id "Phchi.S1G605500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6044.t1 is derived from g3215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20605759	20606235	.	+	.	Phchi.S1G320300
Phchi.S1	AUGUSTUS	transcript	20605759	20606235	.	+	.	transcript_id "Phchi.S1G320300.t1"; gene_id "Phchi.S1G320300"
Phchi.S1	AUGUSTUS	start_codon	20605759	20605761	.	+	0	transcript_id "Phchi.S1G320300.t1"; gene_id "Phchi.S1G320300"
Phchi.S1	AUGUSTUS	CDS	20605759	20606235	0.54	+	0	transcript_id "Phchi.S1G320300.t1"; gene_id "Phchi.S1G320300"
Phchi.S1	AUGUSTUS	exon	20605759	20606235	.	+	.	transcript_id "Phchi.S1G320300.t1"; gene_id "Phchi.S1G320300"
Phchi.S1	AUGUSTUS	stop_codon	20606236	20606238	.	+	0	transcript_id "Phchi.S1G320300.t1"; gene_id "Phchi.S1G320300"
# This transcript jg9439.t2 is derived from g6615.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9440.t1 is derived from g6616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41484159	41486549	.	+	.	Phchi.S1G659900
Phchi.S1	AUGUSTUS	transcript	41484159	41486549	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	start_codon	41484159	41484161	.	+	0	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	CDS	41484159	41485529	0.98	+	0	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	exon	41484159	41485529	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	intron	41485530	41485609	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	CDS	41485610	41485742	0.98	+	0	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	exon	41485610	41485742	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	intron	41485743	41485838	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	CDS	41485839	41486015	0.98	+	2	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	exon	41485839	41486015	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	intron	41486016	41486115	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	CDS	41486116	41486217	1	+	2	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	exon	41486116	41486217	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	intron	41486218	41486307	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	CDS	41486308	41486549	0.96	+	2	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	exon	41486308	41486549	.	+	.	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
Phchi.S1	AUGUSTUS	stop_codon	41486550	41486552	.	+	0	transcript_id "Phchi.S1G659900.t1"; gene_id "Phchi.S1G659900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7525.t1 is derived from g4699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29885386	29885853	.	+	.	Phchi.S1G468400
Phchi.S1	AUGUSTUS	transcript	29885386	29885853	.	+	.	transcript_id "Phchi.S1G468400.t1"; gene_id "Phchi.S1G468400"
Phchi.S1	AUGUSTUS	start_codon	29885386	29885388	.	+	0	transcript_id "Phchi.S1G468400.t1"; gene_id "Phchi.S1G468400"
Phchi.S1	AUGUSTUS	CDS	29885386	29885853	0.99	+	0	transcript_id "Phchi.S1G468400.t1"; gene_id "Phchi.S1G468400"
Phchi.S1	AUGUSTUS	exon	29885386	29885853	.	+	.	transcript_id "Phchi.S1G468400.t1"; gene_id "Phchi.S1G468400"
Phchi.S1	AUGUSTUS	stop_codon	29885854	29885856	.	+	0	transcript_id "Phchi.S1G468400.t1"; gene_id "Phchi.S1G468400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15623.t1 is derived from g14092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20346720	20348638	.	+	.	Phchi.S3G294200
Phchi.S3	AUGUSTUS	transcript	20346720	20348638	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	start_codon	20346720	20346722	.	+	0	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	CDS	20346720	20346919	1	+	0	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	exon	20346720	20346919	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	intron	20346920	20346996	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	CDS	20346997	20347302	0.68	+	1	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	exon	20346997	20347302	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	intron	20347303	20347406	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	CDS	20347407	20347619	1	+	1	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	exon	20347407	20347619	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	intron	20347620	20347732	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	CDS	20347733	20347860	0.69	+	1	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	exon	20347733	20347860	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	intron	20347861	20347956	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	CDS	20347957	20347986	0.69	+	2	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	exon	20347957	20347986	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	intron	20347987	20348561	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	CDS	20348562	20348638	0.95	+	2	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	exon	20348562	20348638	.	+	.	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
Phchi.S3	AUGUSTUS	stop_codon	20348639	20348641	.	+	0	transcript_id "Phchi.S3G294200.t1"; gene_id "Phchi.S3G294200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11974.t1 is derived from g7649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	256868	257656	.	+	.	Phchi.S2G005400
Phchi.S2	AUGUSTUS	transcript	256868	257656	.	+	.	transcript_id "Phchi.S2G005400.t1"; gene_id "Phchi.S2G005400"
Phchi.S2	AUGUSTUS	start_codon	256868	256870	.	+	0	transcript_id "Phchi.S2G005400.t1"; gene_id "Phchi.S2G005400"
Phchi.S2	AUGUSTUS	CDS	256868	257656	0.94	+	0	transcript_id "Phchi.S2G005400.t1"; gene_id "Phchi.S2G005400"
Phchi.S2	AUGUSTUS	exon	256868	257656	.	+	.	transcript_id "Phchi.S2G005400.t1"; gene_id "Phchi.S2G005400"
Phchi.S2	AUGUSTUS	stop_codon	257657	257659	.	+	0	transcript_id "Phchi.S2G005400.t1"; gene_id "Phchi.S2G005400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5763.t1 is derived from g2933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18842061	18844195	.	+	.	Phchi.S1G292200
Phchi.S1	AUGUSTUS	transcript	18842061	18844195	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	start_codon	18842061	18842063	.	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18842061	18842513	0.83	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18842061	18842513	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18842514	18842691	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18842692	18842814	1	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18842692	18842814	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18842815	18842903	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18842904	18843056	1	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18842904	18843056	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18843057	18843156	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18843157	18843242	1	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18843157	18843242	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18843243	18843334	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18843335	18843419	1	+	1	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18843335	18843419	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18843420	18843505	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18843506	18843625	1	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18843506	18843625	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18843626	18843723	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18843724	18843792	1	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18843724	18843792	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18843793	18843883	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18843884	18844013	1	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18843884	18844013	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	intron	18844014	18844109	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	CDS	18844110	18844195	1	+	2	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	exon	18844110	18844195	.	+	.	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
Phchi.S1	AUGUSTUS	stop_codon	18844196	18844198	.	+	0	transcript_id "Phchi.S1G292200.t1"; gene_id "Phchi.S1G292200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14291.t1 is derived from g12758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11962791	11966069	.	+	.	Phchi.S3G161000
Phchi.S3	AUGUSTUS	transcript	11962791	11966069	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	start_codon	11962791	11962793	.	+	0	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11962791	11963103	0.93	+	0	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11962791	11963103	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11963104	11963218	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11963219	11963655	1	+	2	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11963219	11963655	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11963656	11963757	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11963758	11964129	0.99	+	0	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11963758	11964129	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11964130	11964297	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11964298	11964731	0.99	+	0	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11964298	11964731	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11964732	11964820	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11964821	11964922	1	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11964821	11964922	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11964923	11964998	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11964999	11965103	1	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11964999	11965103	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11965104	11965197	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11965198	11965290	1	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11965198	11965290	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11965291	11965395	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11965396	11965494	1	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11965396	11965494	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11965495	11965583	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11965584	11965685	1	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11965584	11965685	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11965686	11965764	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11965765	11965869	1	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11965765	11965869	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	intron	11965870	11965969	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	CDS	11965970	11966069	0.75	+	1	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	exon	11965970	11966069	.	+	.	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
Phchi.S3	AUGUSTUS	stop_codon	11966070	11966072	.	+	0	transcript_id "Phchi.S3G161000.t1"; gene_id "Phchi.S3G161000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14318.t1 is derived from g12785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12071074	12074491	.	-	.	Phchi.S3G163700
Phchi.S3	AUGUSTUS	transcript	12071074	12074491	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	stop_codon	12071071	12071073	.	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12071074	12071187	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12071074	12071187	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12071188	12071287	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12071288	12071372	1	-	1	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12071288	12071372	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12071373	12071456	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12071457	12071542	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12071457	12071542	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12071543	12071629	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12071630	12071948	0.99	-	1	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12071630	12071948	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12071949	12072042	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12072043	12072149	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12072043	12072149	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12072150	12072278	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12072279	12072311	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12072279	12072311	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12072312	12072408	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12072409	12072501	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12072409	12072501	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12072502	12072668	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12072669	12072759	1	-	1	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12072669	12072759	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12072760	12072906	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12072907	12072959	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12072907	12072959	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12072960	12073062	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12073063	12073144	0.98	-	1	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12073063	12073144	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12073145	12073231	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12073232	12073284	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12073232	12073284	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12073285	12073390	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12073391	12073456	1	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12073391	12073456	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12073457	12073588	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12073589	12073755	1	-	2	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12073589	12073755	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	intron	12073756	12074037	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	CDS	12074038	12074491	0.64	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	exon	12074038	12074491	.	-	.	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
Phchi.S3	AUGUSTUS	start_codon	12074489	12074491	.	-	0	transcript_id "Phchi.S3G163700.t1"; gene_id "Phchi.S3G163700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8016.t1 is derived from g5191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32484690	32486872	.	+	.	Phchi.S1G517500
Phchi.S1	AUGUSTUS	transcript	32484690	32486872	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	start_codon	32484690	32484692	.	+	0	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32484690	32485013	0.99	+	0	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32484690	32485013	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32485014	32485288	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32485289	32485841	0.89	+	0	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32485289	32485841	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32485842	32485934	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32485935	32486148	1	+	2	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32485935	32486148	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32486149	32486317	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32486318	32486429	0.98	+	1	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32486318	32486429	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32486430	32486830	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32486831	32486872	0.98	+	0	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32486831	32486872	.	+	.	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	stop_codon	32486873	32486875	.	+	0	transcript_id "Phchi.S1G517500.t1"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	transcript	32484690	32486872	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	start_codon	32484690	32484692	.	+	0	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32484690	32485013	1	+	0	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32484690	32485013	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32485014	32485288	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32485289	32485841	0.86	+	0	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32485289	32485841	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32485842	32485934	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32485935	32486148	1	+	2	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32485935	32486148	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32486149	32486317	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32486318	32486433	0.89	+	1	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32486318	32486433	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32486434	32486521	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32486522	32486571	0.88	+	2	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32486522	32486571	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	intron	32486572	32486830	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	CDS	32486831	32486872	0.94	+	0	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	exon	32486831	32486872	.	+	.	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
Phchi.S1	AUGUSTUS	stop_codon	32486873	32486875	.	+	0	transcript_id "Phchi.S1G517500.t2"; gene_id "Phchi.S1G517500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13810.t1 is derived from g12277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9027717	9029081	.	+	.	Phchi.S3G112900
Phchi.S3	AUGUSTUS	transcript	9027717	9029081	.	+	.	transcript_id "Phchi.S3G112900.t1"; gene_id "Phchi.S3G112900"
Phchi.S3	AUGUSTUS	start_codon	9027717	9027719	.	+	0	transcript_id "Phchi.S3G112900.t1"; gene_id "Phchi.S3G112900"
Phchi.S3	AUGUSTUS	CDS	9027717	9029081	0.71	+	0	transcript_id "Phchi.S3G112900.t1"; gene_id "Phchi.S3G112900"
Phchi.S3	AUGUSTUS	exon	9027717	9029081	.	+	.	transcript_id "Phchi.S3G112900.t1"; gene_id "Phchi.S3G112900"
Phchi.S3	AUGUSTUS	stop_codon	9029082	9029084	.	+	0	transcript_id "Phchi.S3G112900.t1"; gene_id "Phchi.S3G112900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9219.t1 is derived from g6394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40464143	40464709	.	+	.	Phchi.S1G637800
Phchi.S1	AUGUSTUS	transcript	40464143	40464709	.	+	.	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	start_codon	40464143	40464145	.	+	0	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	CDS	40464143	40464349	0.86	+	0	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	exon	40464143	40464349	.	+	.	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	intron	40464350	40464583	.	+	.	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	CDS	40464584	40464709	1	+	0	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	exon	40464584	40464709	.	+	.	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
Phchi.S1	AUGUSTUS	stop_codon	40464710	40464712	.	+	0	transcript_id "Phchi.S1G637800.t1"; gene_id "Phchi.S1G637800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8897.t1 is derived from g6072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38544456	38545432	.	-	.	Phchi.S1G605600
Phchi.S1	AUGUSTUS	transcript	38544456	38545042	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	stop_codon	38544453	38544455	.	-	0	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544456	38544524	0.54	-	0	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544456	38544524	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38544525	38544610	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544611	38544675	0.54	-	2	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544611	38544675	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38544676	38544820	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544821	38544832	0.54	-	2	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544821	38544832	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38544833	38544978	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544979	38545042	1	-	0	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544979	38545042	.	-	.	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	start_codon	38545040	38545042	.	-	0	transcript_id "Phchi.S1G605600.t1"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	transcript	38544456	38545432	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	stop_codon	38544453	38544455	.	-	0	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544456	38544524	0.56	-	0	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544456	38544524	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38544525	38544610	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544611	38544675	0.53	-	2	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544611	38544675	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38544676	38544820	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38544821	38544832	0.53	-	2	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38544821	38544832	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38544833	38545098	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38545099	38545120	0.76	-	0	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38545099	38545120	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	intron	38545121	38545240	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	CDS	38545241	38545432	0.74	-	0	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	exon	38545241	38545432	.	-	.	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
Phchi.S1	AUGUSTUS	start_codon	38545430	38545432	.	-	0	transcript_id "Phchi.S1G605600.t2"; gene_id "Phchi.S1G605600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5657.t1 is derived from g2827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18158453	18160355	.	+	.	Phchi.S1G281600
Phchi.S1	AUGUSTUS	transcript	18158453	18160355	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	start_codon	18158453	18158455	.	+	0	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	CDS	18158453	18159699	0.68	+	0	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	exon	18158453	18159699	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	intron	18159700	18159808	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	CDS	18159809	18159868	0.7	+	1	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	exon	18159809	18159868	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	intron	18159869	18159976	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	CDS	18159977	18160142	0.8	+	1	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	exon	18159977	18160142	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	intron	18160143	18160223	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	CDS	18160224	18160355	0.98	+	0	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	exon	18160224	18160355	.	+	.	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
Phchi.S1	AUGUSTUS	stop_codon	18160356	18160358	.	+	0	transcript_id "Phchi.S1G281600.t1"; gene_id "Phchi.S1G281600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5365.t1 is derived from g2535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16512325	16512978	.	+	.	Phchi.S1G252400
Phchi.S1	AUGUSTUS	transcript	16512325	16512978	.	+	.	transcript_id "Phchi.S1G252400.t1"; gene_id "Phchi.S1G252400"
Phchi.S1	AUGUSTUS	start_codon	16512325	16512327	.	+	0	transcript_id "Phchi.S1G252400.t1"; gene_id "Phchi.S1G252400"
Phchi.S1	AUGUSTUS	CDS	16512325	16512978	0.94	+	0	transcript_id "Phchi.S1G252400.t1"; gene_id "Phchi.S1G252400"
Phchi.S1	AUGUSTUS	exon	16512325	16512978	.	+	.	transcript_id "Phchi.S1G252400.t1"; gene_id "Phchi.S1G252400"
Phchi.S1	AUGUSTUS	stop_codon	16512979	16512981	.	+	0	transcript_id "Phchi.S1G252400.t1"; gene_id "Phchi.S1G252400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9661.t1 is derived from g6837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43117858	43119648	.	+	.	Phchi.S1G682000
Phchi.S1	AUGUSTUS	transcript	43117858	43119648	.	+	.	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	start_codon	43117858	43117860	.	+	0	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	CDS	43117858	43118104	0.93	+	0	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	exon	43117858	43118104	.	+	.	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	intron	43118105	43118199	.	+	.	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	CDS	43118200	43118994	0.56	+	2	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	exon	43118200	43118994	.	+	.	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	intron	43118995	43119142	.	+	.	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	CDS	43119143	43119648	0.63	+	2	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	exon	43119143	43119648	.	+	.	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
Phchi.S1	AUGUSTUS	stop_codon	43119649	43119651	.	+	0	transcript_id "Phchi.S1G682000.t1"; gene_id "Phchi.S1G682000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1555.t1 is derived from g8474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1753850	1754595	.	-	.	Phchi.S5G016400
Phchi.S5	AUGUSTUS	transcript	1753850	1754595	.	-	.	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	stop_codon	1753847	1753849	.	-	0	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	CDS	1753850	1754295	1	-	2	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	exon	1753850	1754295	.	-	.	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	intron	1754296	1754396	.	-	.	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	CDS	1754397	1754595	0.97	-	0	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	exon	1754397	1754595	.	-	.	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
Phchi.S5	AUGUSTUS	start_codon	1754593	1754595	.	-	0	transcript_id "Phchi.S5G016400.t1"; gene_id "Phchi.S5G016400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3656.t1 is derived from g825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5000484	5000921	.	+	.	Phchi.S1G081500
Phchi.S1	AUGUSTUS	transcript	5000484	5000921	.	+	.	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	start_codon	5000484	5000486	.	+	0	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	CDS	5000484	5000608	0.86	+	0	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	exon	5000484	5000608	.	+	.	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	intron	5000609	5000701	.	+	.	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	CDS	5000702	5000921	0.87	+	1	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	exon	5000702	5000921	.	+	.	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
Phchi.S1	AUGUSTUS	stop_codon	5000922	5000924	.	+	0	transcript_id "Phchi.S1G081500.t1"; gene_id "Phchi.S1G081500"
# This transcript jg12693.t2 is derived from g11158.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12693.t3 is derived from g11158.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12694.t1 is derived from g11159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	581572	582297	.	-	.	Phchi.S3G001300
Phchi.S3	AUGUSTUS	transcript	581572	582297	.	-	.	transcript_id "Phchi.S3G001300.t1"; gene_id "Phchi.S3G001300"
Phchi.S3	AUGUSTUS	stop_codon	581569	581571	.	-	0	transcript_id "Phchi.S3G001300.t1"; gene_id "Phchi.S3G001300"
Phchi.S3	AUGUSTUS	CDS	581572	582297	0.67	-	0	transcript_id "Phchi.S3G001300.t1"; gene_id "Phchi.S3G001300"
Phchi.S3	AUGUSTUS	exon	581572	582297	.	-	.	transcript_id "Phchi.S3G001300.t1"; gene_id "Phchi.S3G001300"
Phchi.S3	AUGUSTUS	start_codon	582295	582297	.	-	0	transcript_id "Phchi.S3G001300.t1"; gene_id "Phchi.S3G001300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10272.t1 is derived from g7448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46783254	46785332	.	+	.	Phchi.S1G743100
Phchi.S1	AUGUSTUS	transcript	46783254	46785332	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	start_codon	46783254	46783256	.	+	0	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	CDS	46783254	46784449	1	+	0	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	exon	46783254	46784449	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	intron	46784450	46784553	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	CDS	46784554	46784591	1	+	1	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	exon	46784554	46784591	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	intron	46784592	46784859	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	CDS	46784860	46784928	1	+	2	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	exon	46784860	46784928	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	intron	46784929	46785070	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	CDS	46785071	46785118	1	+	2	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	exon	46785071	46785118	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	intron	46785119	46785189	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	CDS	46785190	46785332	0.62	+	2	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	exon	46785190	46785332	.	+	.	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
Phchi.S1	AUGUSTUS	stop_codon	46785333	46785335	.	+	0	transcript_id "Phchi.S1G743100.t1"; gene_id "Phchi.S1G743100"
# This transcript jg15513.t2 is derived from g13982.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15514.t1 is derived from g13983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19630705	19635204	.	+	.	Phchi.S3G283300
Phchi.S3	AUGUSTUS	transcript	19630705	19635204	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	start_codon	19630705	19630707	.	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19630705	19630803	0.77	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19630705	19630803	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19630804	19631023	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19631024	19631082	1	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19631024	19631082	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19631083	19631390	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19631391	19631484	1	+	1	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19631391	19631484	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19631485	19631610	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19631611	19631748	1	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19631611	19631748	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19631749	19631902	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19631903	19632127	1	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19631903	19632127	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19632128	19632269	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19632270	19633261	1	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19632270	19633261	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19633262	19633434	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19633435	19633649	1	+	1	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19633435	19633649	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19633650	19633788	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19633789	19633947	0.69	+	2	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19633789	19633947	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19633948	19634372	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19634373	19634450	0.4	+	2	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19634373	19634450	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19634451	19634781	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19634782	19634973	0.54	+	2	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19634782	19634973	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	intron	19634974	19635151	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	CDS	19635152	19635204	0.73	+	2	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	exon	19635152	19635204	.	+	.	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
Phchi.S3	AUGUSTUS	stop_codon	19635205	19635207	.	+	0	transcript_id "Phchi.S3G283300.t1"; gene_id "Phchi.S3G283300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8082.t1 is derived from g5257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32869919	32870998	.	+	.	Phchi.S1G524100
Phchi.S1	AUGUSTUS	transcript	32869919	32870998	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	start_codon	32869919	32869921	.	+	0	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	CDS	32869919	32870000	1	+	0	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	exon	32869919	32870000	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	intron	32870001	32870209	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	CDS	32870210	32870388	1	+	2	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	exon	32870210	32870388	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	intron	32870389	32870513	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	CDS	32870514	32870588	1	+	0	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	exon	32870514	32870588	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	intron	32870589	32870751	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	CDS	32870752	32870827	0.94	+	0	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	exon	32870752	32870827	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	intron	32870828	32870945	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	CDS	32870946	32870998	0.94	+	2	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	exon	32870946	32870998	.	+	.	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
Phchi.S1	AUGUSTUS	stop_codon	32870999	32871001	.	+	0	transcript_id "Phchi.S1G524100.t1"; gene_id "Phchi.S1G524100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3913.t1 is derived from g1082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6413449	6414254	.	+	.	Phchi.S1G107200
Phchi.S1	AUGUSTUS	transcript	6413449	6414254	.	+	.	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	start_codon	6413449	6413451	.	+	0	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	CDS	6413449	6413711	0.59	+	0	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	exon	6413449	6413711	.	+	.	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	intron	6413712	6413851	.	+	.	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	CDS	6413852	6414254	0.76	+	1	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	exon	6413852	6414254	.	+	.	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
Phchi.S1	AUGUSTUS	stop_codon	6414255	6414257	.	+	0	transcript_id "Phchi.S1G107200.t1"; gene_id "Phchi.S1G107200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2674.t1 is derived from g9594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8142689	8144864	.	-	.	Phchi.S5G128300
Phchi.S5	AUGUSTUS	transcript	8142689	8144864	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	stop_codon	8142686	8142688	.	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	CDS	8142689	8142868	0.39	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	exon	8142689	8142868	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	intron	8142869	8143098	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	CDS	8143099	8143299	0.72	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	exon	8143099	8143299	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	intron	8143300	8143406	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	CDS	8143407	8143772	1	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	exon	8143407	8143772	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	intron	8143773	8143877	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	CDS	8143878	8144156	1	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	exon	8143878	8144156	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	intron	8144157	8144252	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	CDS	8144253	8144468	1	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	exon	8144253	8144468	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	intron	8144469	8144567	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	CDS	8144568	8144864	0.5	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	exon	8144568	8144864	.	-	.	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
Phchi.S5	AUGUSTUS	start_codon	8144862	8144864	.	-	0	transcript_id "Phchi.S5G128300.t1"; gene_id "Phchi.S5G128300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3431.t1 is derived from g600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3606014	3606706	.	-	.	Phchi.S1G059000
Phchi.S1	AUGUSTUS	transcript	3606014	3606706	.	-	.	transcript_id "Phchi.S1G059000.t1"; gene_id "Phchi.S1G059000"
Phchi.S1	AUGUSTUS	stop_codon	3606011	3606013	.	-	0	transcript_id "Phchi.S1G059000.t1"; gene_id "Phchi.S1G059000"
Phchi.S1	AUGUSTUS	CDS	3606014	3606706	0.65	-	0	transcript_id "Phchi.S1G059000.t1"; gene_id "Phchi.S1G059000"
Phchi.S1	AUGUSTUS	exon	3606014	3606706	.	-	.	transcript_id "Phchi.S1G059000.t1"; gene_id "Phchi.S1G059000"
Phchi.S1	AUGUSTUS	start_codon	3606704	3606706	.	-	0	transcript_id "Phchi.S1G059000.t1"; gene_id "Phchi.S1G059000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10794.t1 is derived from g14844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2144850	2147599	.	+	.	Phchi.S4G037600
Phchi.S4	AUGUSTUS	transcript	2144850	2147599	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	start_codon	2144850	2144852	.	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2144850	2144852	1	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2144850	2144852	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2144853	2144943	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2144944	2144983	1	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2144944	2144983	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2144984	2145138	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2145139	2145362	1	+	2	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2145139	2145362	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2145363	2145553	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2145554	2145796	1	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2145554	2145796	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2145797	2145954	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2145955	2146081	1	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2145955	2146081	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2146082	2146169	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2146170	2146285	0.48	+	2	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2146170	2146285	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2146286	2146425	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2146426	2146479	0.59	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2146426	2146479	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2146480	2146573	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2146574	2146757	1	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2146574	2146757	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2146758	2146883	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2146884	2147037	1	+	2	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2146884	2147037	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2147038	2147127	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2147128	2147190	1	+	1	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2147128	2147190	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2147191	2147305	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2147306	2147402	0.75	+	1	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2147306	2147402	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	intron	2147403	2147506	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	CDS	2147507	2147599	0.73	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	exon	2147507	2147599	.	+	.	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
Phchi.S4	AUGUSTUS	stop_codon	2147600	2147602	.	+	0	transcript_id "Phchi.S4G037600.t1"; gene_id "Phchi.S4G037600"
# This transcript jg2161.t2 is derived from g9081.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2162.t1 is derived from g9082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5131915	5132780	.	-	.	Phchi.S5G077100
Phchi.S5	AUGUSTUS	transcript	5131915	5132780	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	stop_codon	5131912	5131914	.	-	0	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	CDS	5131915	5131998	0.72	-	0	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	exon	5131915	5131998	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	intron	5131999	5132095	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	CDS	5132096	5132189	0.7	-	1	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	exon	5132096	5132189	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	intron	5132190	5132280	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	CDS	5132281	5132342	0.82	-	0	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	exon	5132281	5132342	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	intron	5132343	5132433	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	CDS	5132434	5132487	0.99	-	0	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	exon	5132434	5132487	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	intron	5132488	5132624	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	CDS	5132625	5132780	0.55	-	0	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	exon	5132625	5132780	.	-	.	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
Phchi.S5	AUGUSTUS	start_codon	5132778	5132780	.	-	0	transcript_id "Phchi.S5G077100.t1"; gene_id "Phchi.S5G077100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6849.t1 is derived from g4021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25540651	25545312	.	-	.	Phchi.S1G400800
Phchi.S1	AUGUSTUS	transcript	25540651	25545312	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	stop_codon	25540648	25540650	.	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25540651	25540866	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25540651	25540866	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25540867	25540997	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25540998	25541084	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25540998	25541084	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25541085	25541167	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25541168	25541290	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25541168	25541290	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25541291	25541389	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25541390	25541755	0.96	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25541390	25541755	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25541756	25541901	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25541902	25541986	1	-	1	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25541902	25541986	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25541987	25542066	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25542067	25542125	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25542067	25542125	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25542126	25542228	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25542229	25542282	0.98	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25542229	25542282	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25542283	25542447	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25542448	25542540	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25542448	25542540	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25542541	25542659	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25542660	25542767	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25542660	25542767	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25542768	25542862	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25542863	25542960	1	-	2	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25542863	25542960	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25542961	25543042	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25543043	25543148	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25543043	25543148	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25543149	25543238	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25543239	25543359	1	-	1	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25543239	25543359	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25543360	25543459	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25543460	25543510	1	-	1	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25543460	25543510	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25543511	25543644	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25543645	25543730	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25543645	25543730	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25543731	25543909	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25543910	25543945	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25543910	25543945	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25543946	25544077	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25544078	25544278	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25544078	25544278	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25544279	25544409	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25544410	25544598	1	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25544410	25544598	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25544599	25544755	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25544756	25544892	1	-	2	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25544756	25544892	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25544893	25544997	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25544998	25545148	0.98	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25544998	25545148	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	intron	25545149	25545225	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	CDS	25545226	25545312	0.79	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	exon	25545226	25545312	.	-	.	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
Phchi.S1	AUGUSTUS	start_codon	25545310	25545312	.	-	0	transcript_id "Phchi.S1G400800.t1"; gene_id "Phchi.S1G400800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15980.t1 is derived from g8310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C157	AUGUSTUS	gene	4684	5424	.	+	.	Phchi.C157G000200
Phchi.C157	AUGUSTUS	transcript	4684	5424	.	+	.	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	start_codon	4684	4686	.	+	0	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	CDS	4684	4727	0.45	+	0	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	exon	4684	4727	.	+	.	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	intron	4728	4878	.	+	.	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	CDS	4879	5123	0.69	+	1	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	exon	4879	5123	.	+	.	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	intron	5124	5284	.	+	.	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	CDS	5285	5424	1	+	2	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	exon	5285	5424	.	+	.	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
Phchi.C157	AUGUSTUS	stop_codon	5425	5427	.	+	0	transcript_id "Phchi.C157G000200.t1"; gene_id "Phchi.C157G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8609.t1 is derived from g5784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36903657	36905722	.	-	.	Phchi.S1G576800
Phchi.S1	AUGUSTUS	transcript	36903657	36905722	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	stop_codon	36903654	36903656	.	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36903657	36903866	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36903657	36903866	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	intron	36903867	36903957	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36903958	36904116	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36903958	36904116	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	intron	36904117	36904210	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36904211	36904528	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36904211	36904528	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	intron	36904529	36904618	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36904619	36904879	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36904619	36904879	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	intron	36904880	36904963	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36904964	36905041	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36904964	36905041	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	intron	36905042	36905140	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36905141	36905374	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36905141	36905374	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	intron	36905375	36905494	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	CDS	36905495	36905722	1	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	exon	36905495	36905722	.	-	.	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
Phchi.S1	AUGUSTUS	start_codon	36905720	36905722	.	-	0	transcript_id "Phchi.S1G576800.t1"; gene_id "Phchi.S1G576800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1404.t1 is derived from g8323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	152448	153508	.	+	.	Phchi.S5G001300
Phchi.S5	AUGUSTUS	transcript	152448	153508	.	+	.	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	start_codon	152448	152450	.	+	0	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	CDS	152448	153083	0.28	+	0	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	exon	152448	153083	.	+	.	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	intron	153084	153208	.	+	.	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	CDS	153209	153508	0.81	+	0	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	exon	153209	153508	.	+	.	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
Phchi.S5	AUGUSTUS	stop_codon	153509	153511	.	+	0	transcript_id "Phchi.S5G001300.t1"; gene_id "Phchi.S5G001300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11804.t1 is derived from g15856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8215889	8217518	.	-	.	Phchi.S4G138600
Phchi.S4	AUGUSTUS	transcript	8215889	8217518	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	stop_codon	8215886	8215888	.	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8215889	8215916	1	-	1	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8215889	8215916	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8215917	8216058	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8216059	8216150	1	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8216059	8216150	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8216151	8216274	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8216275	8216299	1	-	1	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8216275	8216299	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8216300	8216438	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8216439	8216490	1	-	2	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8216439	8216490	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8216491	8216646	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8216647	8216704	1	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8216647	8216704	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8216705	8216807	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8216808	8216880	1	-	1	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8216808	8216880	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8216881	8217031	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8217032	8217111	1	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8217032	8217111	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8217112	8217213	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8217214	8217240	0.98	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8217214	8217240	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	intron	8217241	8217404	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	CDS	8217405	8217518	0.99	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	exon	8217405	8217518	.	-	.	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
Phchi.S4	AUGUSTUS	start_codon	8217516	8217518	.	-	0	transcript_id "Phchi.S4G138600.t1"; gene_id "Phchi.S4G138600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2481.t1 is derived from g9401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6871632	6872012	.	-	.	Phchi.S5G109000
Phchi.S5	AUGUSTUS	transcript	6871632	6872012	.	-	.	transcript_id "Phchi.S5G109000.t1"; gene_id "Phchi.S5G109000"
Phchi.S5	AUGUSTUS	stop_codon	6871629	6871631	.	-	0	transcript_id "Phchi.S5G109000.t1"; gene_id "Phchi.S5G109000"
Phchi.S5	AUGUSTUS	CDS	6871632	6872012	0.96	-	0	transcript_id "Phchi.S5G109000.t1"; gene_id "Phchi.S5G109000"
Phchi.S5	AUGUSTUS	exon	6871632	6872012	.	-	.	transcript_id "Phchi.S5G109000.t1"; gene_id "Phchi.S5G109000"
Phchi.S5	AUGUSTUS	start_codon	6872010	6872012	.	-	0	transcript_id "Phchi.S5G109000.t1"; gene_id "Phchi.S5G109000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2404.t1 is derived from g9324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6498291	6498500	.	-	.	Phchi.S5G101300
Phchi.S5	AUGUSTUS	transcript	6498291	6498500	.	-	.	transcript_id "Phchi.S5G101300.t1"; gene_id "Phchi.S5G101300"
Phchi.S5	AUGUSTUS	stop_codon	6498288	6498290	.	-	0	transcript_id "Phchi.S5G101300.t1"; gene_id "Phchi.S5G101300"
Phchi.S5	AUGUSTUS	CDS	6498291	6498500	0.49	-	0	transcript_id "Phchi.S5G101300.t1"; gene_id "Phchi.S5G101300"
Phchi.S5	AUGUSTUS	exon	6498291	6498500	.	-	.	transcript_id "Phchi.S5G101300.t1"; gene_id "Phchi.S5G101300"
Phchi.S5	AUGUSTUS	start_codon	6498498	6498500	.	-	0	transcript_id "Phchi.S5G101300.t1"; gene_id "Phchi.S5G101300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3303.t1 is derived from g472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2747408	2749755	.	+	.	Phchi.S1G046200
Phchi.S1	AUGUSTUS	transcript	2747408	2749755	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	start_codon	2747408	2747410	.	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747408	2747477	0.96	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747408	2747477	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2747478	2747597	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747598	2747606	1	+	2	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747598	2747606	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2747607	2747826	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747827	2747879	1	+	2	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747827	2747879	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2747880	2747943	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747944	2748156	0.99	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747944	2748156	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748157	2748247	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748248	2748377	1	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748248	2748377	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748378	2748467	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748468	2748610	1	+	2	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748468	2748610	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748611	2748699	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748700	2748835	1	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748700	2748835	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748836	2748938	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748939	2749053	1	+	2	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748939	2749053	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2749054	2749152	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2749153	2749303	1	+	1	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2749153	2749303	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2749304	2749428	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2749429	2749755	0.98	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2749429	2749755	.	+	.	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	stop_codon	2749756	2749758	.	+	0	transcript_id "Phchi.S1G046200.t1"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	transcript	2747408	2749755	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	start_codon	2747408	2747410	.	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747408	2747477	0.95	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747408	2747477	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2747478	2747597	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747598	2747606	1	+	2	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747598	2747606	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2747607	2747826	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747827	2747879	1	+	2	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747827	2747879	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2747880	2747952	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2747953	2748156	1	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2747953	2748156	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748157	2748247	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748248	2748377	1	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748248	2748377	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748378	2748467	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748468	2748610	1	+	2	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748468	2748610	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748611	2748699	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748700	2748835	1	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748700	2748835	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2748836	2748938	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2748939	2749053	1	+	2	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2748939	2749053	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2749054	2749152	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2749153	2749303	1	+	1	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2749153	2749303	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	intron	2749304	2749428	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	CDS	2749429	2749755	0.94	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	exon	2749429	2749755	.	+	.	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
Phchi.S1	AUGUSTUS	stop_codon	2749756	2749758	.	+	0	transcript_id "Phchi.S1G046200.t2"; gene_id "Phchi.S1G046200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7169.t1 is derived from g4341.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27364064	27368985	.	-	.	Phchi.S1G432800
Phchi.S1	AUGUSTUS	transcript	27364064	27368985	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	stop_codon	27364061	27364063	.	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27364064	27364486	0.85	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27364064	27364486	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27364487	27364600	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27364601	27364798	0.87	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27364601	27364798	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27364799	27364928	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27364929	27365029	1	-	2	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27364929	27365029	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27365030	27365117	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27365118	27366165	0.99	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27365118	27366165	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27366166	27366273	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27366274	27366648	0.99	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27366274	27366648	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27366649	27366750	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27366751	27366912	1	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27366751	27366912	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27366913	27367115	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27367116	27367340	0.99	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27367116	27367340	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27367341	27367552	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27367553	27367728	0.99	-	2	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27367553	27367728	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27367729	27367862	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27367863	27368094	0.71	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27367863	27368094	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27368095	27368188	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27368189	27368266	1	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27368189	27368266	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27368267	27368355	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27368356	27368427	1	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27368356	27368427	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27368428	27368664	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27368665	27368985	1	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27368665	27368985	.	-	.	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	start_codon	27368983	27368985	.	-	0	transcript_id "Phchi.S1G432800.t1"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	transcript	27364064	27368985	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	stop_codon	27364061	27364063	.	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27364064	27364486	0.78	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27364064	27364486	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27364487	27364600	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27364601	27364798	0.84	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27364601	27364798	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27364799	27364928	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27364929	27365029	1	-	2	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27364929	27365029	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27365030	27365117	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27365118	27366165	0.98	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27365118	27366165	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27366166	27366273	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27366274	27366648	0.99	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27366274	27366648	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27366649	27366750	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27366751	27366912	1	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27366751	27366912	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27366913	27367115	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27367116	27367340	1	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27367116	27367340	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27367341	27367552	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27367553	27367728	0.98	-	2	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27367553	27367728	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27367729	27367862	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27367863	27368094	0.64	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27367863	27368094	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27368095	27368188	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27368189	27368266	1	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27368189	27368266	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27368267	27368355	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27368356	27368427	1	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27368356	27368427	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	intron	27368428	27368751	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	CDS	27368752	27368985	0.87	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	exon	27368752	27368985	.	-	.	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
Phchi.S1	AUGUSTUS	start_codon	27368983	27368985	.	-	0	transcript_id "Phchi.S1G432800.t2"; gene_id "Phchi.S1G432800"
# This transcript jg7308.t2 is derived from g4480.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7309.t1 is derived from g4481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28451062	28452215	.	-	.	Phchi.S1G446800
Phchi.S1	AUGUSTUS	transcript	28451062	28452215	.	-	.	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	stop_codon	28451059	28451061	.	-	0	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	CDS	28451062	28451352	0.69	-	0	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	exon	28451062	28451352	.	-	.	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	intron	28451353	28451432	.	-	.	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	CDS	28451433	28452215	0.84	-	0	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	exon	28451433	28452215	.	-	.	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
Phchi.S1	AUGUSTUS	start_codon	28452213	28452215	.	-	0	transcript_id "Phchi.S1G446800.t1"; gene_id "Phchi.S1G446800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11956.t1 is derived from g7631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	186918	188125	.	-	.	Phchi.S2G003600
Phchi.S2	AUGUSTUS	transcript	186918	188125	.	-	.	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	stop_codon	186915	186917	.	-	0	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	CDS	186918	186951	0.35	-	1	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	exon	186918	186951	.	-	.	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	intron	186952	187043	.	-	.	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	CDS	187044	188125	0.35	-	0	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	exon	187044	188125	.	-	.	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
Phchi.S2	AUGUSTUS	start_codon	188123	188125	.	-	0	transcript_id "Phchi.S2G003600.t1"; gene_id "Phchi.S2G003600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6126.t1 is derived from g3297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21059235	21061322	.	-	.	Phchi.S1G328500
Phchi.S1	AUGUSTUS	transcript	21059235	21061322	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	stop_codon	21059232	21059234	.	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059235	21059362	1	-	2	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059235	21059362	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059363	21059446	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059447	21059516	1	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059447	21059516	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059517	21059601	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059602	21059769	1	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059602	21059769	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059770	21059855	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059856	21059945	1	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059856	21059945	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059946	21060047	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060048	21060188	0.98	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060048	21060188	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060189	21060291	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060292	21060360	0.84	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060292	21060360	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060361	21060451	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060452	21060550	0.99	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060452	21060550	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060551	21060683	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060684	21060850	0.99	-	2	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060684	21060850	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060851	21060942	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060943	21061050	0.88	-	2	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060943	21061050	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21061051	21061145	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21061146	21061154	0.89	-	2	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21061146	21061154	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21061155	21061252	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21061253	21061322	0.92	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21061253	21061322	.	-	.	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	start_codon	21061320	21061322	.	-	0	transcript_id "Phchi.S1G328500.t1"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	transcript	21059235	21061322	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	stop_codon	21059232	21059234	.	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059235	21059362	1	-	2	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059235	21059362	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059363	21059446	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059447	21059516	1	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059447	21059516	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059517	21059601	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059602	21059769	1	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059602	21059769	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059770	21059855	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21059856	21059945	1	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21059856	21059945	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21059946	21060047	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060048	21060075	0.79	-	1	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060048	21060075	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060076	21060194	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060195	21060217	0.43	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060195	21060217	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060218	21060291	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060292	21060360	1	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060292	21060360	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060361	21060451	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060452	21060550	1	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060452	21060550	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060551	21060683	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060684	21060850	1	-	2	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060684	21060850	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21060851	21060942	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21060943	21061050	0.94	-	2	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21060943	21061050	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21061051	21061145	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21061146	21061154	0.94	-	2	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21061146	21061154	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	intron	21061155	21061252	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	CDS	21061253	21061322	0.94	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	exon	21061253	21061322	.	-	.	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
Phchi.S1	AUGUSTUS	start_codon	21061320	21061322	.	-	0	transcript_id "Phchi.S1G328500.t2"; gene_id "Phchi.S1G328500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5582.t1 is derived from g2752.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17738275	17739416	.	+	.	Phchi.S1G274100
Phchi.S1	AUGUSTUS	transcript	17738275	17739416	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	start_codon	17738275	17738277	.	+	0	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738275	17738326	1	+	0	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738275	17738326	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17738327	17738442	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738443	17738546	0.99	+	2	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738443	17738546	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17738547	17738629	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738630	17738749	0.76	+	0	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738630	17738749	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17738750	17738913	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738914	17739233	0.96	+	0	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738914	17739233	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17739234	17739352	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17739353	17739416	0.99	+	1	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17739353	17739416	.	+	.	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	stop_codon	17739417	17739419	.	+	0	transcript_id "Phchi.S1G274100.t1"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	transcript	17738275	17739416	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	start_codon	17738275	17738277	.	+	0	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738275	17738326	1	+	0	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738275	17738326	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17738327	17738442	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738443	17738531	0.36	+	2	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738443	17738531	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17738532	17738607	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738608	17738634	0.56	+	0	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738608	17738634	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17738635	17738913	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17738914	17739233	1	+	0	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17738914	17739233	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	intron	17739234	17739352	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	CDS	17739353	17739416	1	+	1	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	exon	17739353	17739416	.	+	.	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
Phchi.S1	AUGUSTUS	stop_codon	17739417	17739419	.	+	0	transcript_id "Phchi.S1G274100.t2"; gene_id "Phchi.S1G274100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12047.t1 is derived from g7722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1008391	1010705	.	-	.	Phchi.S2G012700
Phchi.S2	AUGUSTUS	transcript	1008391	1010705	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	stop_codon	1008388	1008390	.	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008391	1008393	0.84	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008391	1008393	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008394	1008473	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008474	1008532	0.83	-	2	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008474	1008532	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008533	1008640	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008641	1008732	0.86	-	1	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008641	1008732	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008733	1008805	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008806	1008930	1	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008806	1008930	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008931	1009207	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009208	1009291	0.99	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009208	1009291	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009292	1009397	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009398	1009463	1	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009398	1009463	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009464	1009567	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009568	1009624	1	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009568	1009624	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009625	1009789	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009790	1009866	1	-	2	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009790	1009866	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009867	1010015	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1010016	1010186	1	-	2	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1010016	1010186	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1010187	1010539	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1010540	1010705	0.92	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1010540	1010705	.	-	.	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	start_codon	1010703	1010705	.	-	0	transcript_id "Phchi.S2G012700.t1"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	transcript	1008391	1010705	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	stop_codon	1008388	1008390	.	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008391	1008393	0.81	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008391	1008393	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008394	1008473	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008474	1008532	0.81	-	2	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008474	1008532	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008533	1008640	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008641	1008732	0.84	-	1	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008641	1008732	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008733	1008805	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1008806	1008930	1	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1008806	1008930	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1008931	1009207	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009208	1009291	1	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009208	1009291	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009292	1009397	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009398	1009463	1	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009398	1009463	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009464	1009567	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009568	1009624	1	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009568	1009624	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009625	1009816	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1009817	1009866	1	-	2	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1009817	1009866	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1009867	1010015	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1010016	1010186	1	-	2	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1010016	1010186	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	intron	1010187	1010539	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	CDS	1010540	1010705	0.95	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	exon	1010540	1010705	.	-	.	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
Phchi.S2	AUGUSTUS	start_codon	1010703	1010705	.	-	0	transcript_id "Phchi.S2G012700.t2"; gene_id "Phchi.S2G012700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10378.t1 is derived from g7554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47453305	47454496	.	+	.	Phchi.S1G753700
Phchi.S1	AUGUSTUS	transcript	47453305	47454496	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	start_codon	47453305	47453307	.	+	0	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	CDS	47453305	47453394	0.75	+	0	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	exon	47453305	47453394	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	intron	47453395	47453471	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	CDS	47453472	47453610	0.99	+	0	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	exon	47453472	47453610	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	intron	47453611	47453707	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	CDS	47453708	47453720	0.98	+	2	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	exon	47453708	47453720	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	intron	47453721	47453820	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	CDS	47453821	47453873	0.98	+	1	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	exon	47453821	47453873	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	intron	47453874	47454093	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	CDS	47454094	47454333	0.86	+	2	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	exon	47454094	47454333	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	intron	47454334	47454464	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	CDS	47454465	47454496	0.86	+	2	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	exon	47454465	47454496	.	+	.	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
Phchi.S1	AUGUSTUS	stop_codon	47454497	47454499	.	+	0	transcript_id "Phchi.S1G753700.t1"; gene_id "Phchi.S1G753700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12211.t1 is derived from g7887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6763522	6764430	.	-	.	Phchi.S2G029100
Phchi.S2	AUGUSTUS	transcript	6763522	6764430	.	-	.	transcript_id "Phchi.S2G029100.t1"; gene_id "Phchi.S2G029100"
Phchi.S2	AUGUSTUS	stop_codon	6763519	6763521	.	-	0	transcript_id "Phchi.S2G029100.t1"; gene_id "Phchi.S2G029100"
Phchi.S2	AUGUSTUS	CDS	6763522	6764430	0.67	-	0	transcript_id "Phchi.S2G029100.t1"; gene_id "Phchi.S2G029100"
Phchi.S2	AUGUSTUS	exon	6763522	6764430	.	-	.	transcript_id "Phchi.S2G029100.t1"; gene_id "Phchi.S2G029100"
Phchi.S2	AUGUSTUS	start_codon	6764428	6764430	.	-	0	transcript_id "Phchi.S2G029100.t1"; gene_id "Phchi.S2G029100"
# This transcript jg5085.t2 is derived from g2255.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5086.t1 is derived from g2256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14606983	14607819	.	-	.	Phchi.S1G224500
Phchi.S1	AUGUSTUS	transcript	14606983	14607819	.	-	.	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	stop_codon	14606980	14606982	.	-	0	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	CDS	14606983	14607648	0.73	-	0	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	exon	14606983	14607648	.	-	.	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	intron	14607649	14607789	.	-	.	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	CDS	14607790	14607819	0.54	-	0	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	exon	14607790	14607819	.	-	.	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
Phchi.S1	AUGUSTUS	start_codon	14607817	14607819	.	-	0	transcript_id "Phchi.S1G224500.t1"; gene_id "Phchi.S1G224500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15949.t1 is derived from g14442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	21036	21719	.	-	.	Phchi.C116G000500
Phchi.C116	AUGUSTUS	transcript	21036	21719	.	-	.	transcript_id "Phchi.C116G000500.t1"; gene_id "Phchi.C116G000500"
Phchi.C116	AUGUSTUS	stop_codon	21033	21035	.	-	0	transcript_id "Phchi.C116G000500.t1"; gene_id "Phchi.C116G000500"
Phchi.C116	AUGUSTUS	CDS	21036	21719	1	-	0	transcript_id "Phchi.C116G000500.t1"; gene_id "Phchi.C116G000500"
Phchi.C116	AUGUSTUS	exon	21036	21719	.	-	.	transcript_id "Phchi.C116G000500.t1"; gene_id "Phchi.C116G000500"
Phchi.C116	AUGUSTUS	start_codon	21717	21719	.	-	0	transcript_id "Phchi.C116G000500.t1"; gene_id "Phchi.C116G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8841.t1 is derived from g6016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38230041	38231384	.	-	.	Phchi.S1G600000
Phchi.S1	AUGUSTUS	transcript	38230041	38231384	.	-	.	transcript_id "Phchi.S1G600000.t1"; gene_id "Phchi.S1G600000"
Phchi.S1	AUGUSTUS	stop_codon	38230038	38230040	.	-	0	transcript_id "Phchi.S1G600000.t1"; gene_id "Phchi.S1G600000"
Phchi.S1	AUGUSTUS	CDS	38230041	38231384	0.99	-	0	transcript_id "Phchi.S1G600000.t1"; gene_id "Phchi.S1G600000"
Phchi.S1	AUGUSTUS	exon	38230041	38231384	.	-	.	transcript_id "Phchi.S1G600000.t1"; gene_id "Phchi.S1G600000"
Phchi.S1	AUGUSTUS	start_codon	38231382	38231384	.	-	0	transcript_id "Phchi.S1G600000.t1"; gene_id "Phchi.S1G600000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8801.t1 is derived from g5976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38053311	38055577	.	-	.	Phchi.S1G596000
Phchi.S1	AUGUSTUS	transcript	38053311	38055577	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	stop_codon	38053308	38053310	.	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38053311	38053520	1	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38053311	38053520	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38053521	38053610	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38053611	38053714	1	-	2	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38053611	38053714	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38053715	38053851	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38053852	38054011	1	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38053852	38054011	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38054012	38054105	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38054106	38054277	1	-	1	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38054106	38054277	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38054278	38054394	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38054395	38054475	1	-	1	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38054395	38054475	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38054476	38054562	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38054563	38054710	1	-	2	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38054563	38054710	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38054711	38054870	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38054871	38054955	0.55	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38054871	38054955	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38054956	38055086	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38055087	38055299	0.52	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38055087	38055299	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	intron	38055300	38055403	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	CDS	38055404	38055577	0.66	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	exon	38055404	38055577	.	-	.	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
Phchi.S1	AUGUSTUS	start_codon	38055575	38055577	.	-	0	transcript_id "Phchi.S1G596000.t1"; gene_id "Phchi.S1G596000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2071.t1 is derived from g8991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4715029	4715810	.	+	.	Phchi.S5G068000
Phchi.S5	AUGUSTUS	transcript	4715029	4715810	.	+	.	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	start_codon	4715029	4715031	.	+	0	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	CDS	4715029	4715453	0.94	+	0	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	exon	4715029	4715453	.	+	.	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	intron	4715454	4715782	.	+	.	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	CDS	4715783	4715810	0.97	+	1	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	exon	4715783	4715810	.	+	.	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
Phchi.S5	AUGUSTUS	stop_codon	4715811	4715813	.	+	0	transcript_id "Phchi.S5G068000.t1"; gene_id "Phchi.S5G068000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12956.t1 is derived from g11421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3300500	3301154	.	+	.	Phchi.S3G027500
Phchi.S3	AUGUSTUS	transcript	3300500	3301154	.	+	.	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	start_codon	3300500	3300502	.	+	0	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	CDS	3300500	3300996	0.69	+	0	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	exon	3300500	3300996	.	+	.	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	intron	3300997	3301102	.	+	.	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	CDS	3301103	3301154	0.49	+	1	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	exon	3301103	3301154	.	+	.	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
Phchi.S3	AUGUSTUS	stop_codon	3301155	3301157	.	+	0	transcript_id "Phchi.S3G027500.t1"; gene_id "Phchi.S3G027500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1030.t1 is derived from g10813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7213813	7214843	.	-	.	Phchi.S6G098900
Phchi.S6	AUGUSTUS	transcript	7213813	7214843	.	-	.	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	stop_codon	7213810	7213812	.	-	0	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	CDS	7213813	7214097	0.2	-	0	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	exon	7213813	7214097	.	-	.	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	intron	7214098	7214396	.	-	.	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	CDS	7214397	7214843	0.36	-	0	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	exon	7214397	7214843	.	-	.	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
Phchi.S6	AUGUSTUS	start_codon	7214841	7214843	.	-	0	transcript_id "Phchi.S6G098900.t1"; gene_id "Phchi.S6G098900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2718.t1 is derived from g9638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8353907	8355618	.	+	.	Phchi.S5G132700
Phchi.S5	AUGUSTUS	transcript	8353907	8355618	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	start_codon	8353907	8353909	.	+	0	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	CDS	8353907	8354084	0.26	+	0	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	exon	8353907	8354084	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	intron	8354085	8354200	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	CDS	8354201	8354385	1	+	2	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	exon	8354201	8354385	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	intron	8354386	8354458	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	CDS	8354459	8354944	0.92	+	0	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	exon	8354459	8354944	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	intron	8354945	8355033	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	CDS	8355034	8355251	1	+	0	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	exon	8355034	8355251	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	intron	8355252	8355380	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	CDS	8355381	8355618	1	+	1	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	exon	8355381	8355618	.	+	.	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
Phchi.S5	AUGUSTUS	stop_codon	8355619	8355621	.	+	0	transcript_id "Phchi.S5G132700.t1"; gene_id "Phchi.S5G132700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9044.t1 is derived from g6219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39289277	39289954	.	+	.	Phchi.S1G620300
Phchi.S1	AUGUSTUS	transcript	39289277	39289954	.	+	.	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	start_codon	39289277	39289279	.	+	0	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	CDS	39289277	39289292	0.2	+	0	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	exon	39289277	39289292	.	+	.	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	intron	39289293	39289415	.	+	.	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	CDS	39289416	39289637	1	+	2	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	exon	39289416	39289637	.	+	.	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	intron	39289638	39289760	.	+	.	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	CDS	39289761	39289954	1	+	2	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	exon	39289761	39289954	.	+	.	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
Phchi.S1	AUGUSTUS	stop_codon	39289955	39289957	.	+	0	transcript_id "Phchi.S1G620300.t1"; gene_id "Phchi.S1G620300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3208.t1 is derived from g377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2240524	2241723	.	-	.	Phchi.S1G036700
Phchi.S1	AUGUSTUS	transcript	2240524	2241723	.	-	.	transcript_id "Phchi.S1G036700.t1"; gene_id "Phchi.S1G036700"
Phchi.S1	AUGUSTUS	stop_codon	2240521	2240523	.	-	0	transcript_id "Phchi.S1G036700.t1"; gene_id "Phchi.S1G036700"
Phchi.S1	AUGUSTUS	CDS	2240524	2241723	0.75	-	0	transcript_id "Phchi.S1G036700.t1"; gene_id "Phchi.S1G036700"
Phchi.S1	AUGUSTUS	exon	2240524	2241723	.	-	.	transcript_id "Phchi.S1G036700.t1"; gene_id "Phchi.S1G036700"
Phchi.S1	AUGUSTUS	start_codon	2241721	2241723	.	-	0	transcript_id "Phchi.S1G036700.t1"; gene_id "Phchi.S1G036700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7182.t1 is derived from g4354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27440807	27442152	.	+	.	Phchi.S1G434100
Phchi.S1	AUGUSTUS	transcript	27440807	27442152	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	start_codon	27440807	27440809	.	+	0	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	CDS	27440807	27441060	0.52	+	0	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	exon	27440807	27441060	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	intron	27441061	27441200	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	CDS	27441201	27441419	0.9	+	1	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	exon	27441201	27441419	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	intron	27441420	27441507	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	CDS	27441508	27441608	0.94	+	1	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	exon	27441508	27441608	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	intron	27441609	27441766	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	CDS	27441767	27442152	0.12	+	2	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	exon	27441767	27442152	.	+	.	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
Phchi.S1	AUGUSTUS	stop_codon	27442153	27442155	.	+	0	transcript_id "Phchi.S1G434100.t1"; gene_id "Phchi.S1G434100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2373.t1 is derived from g9293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6397216	6398539	.	-	.	Phchi.S5G098200
Phchi.S5	AUGUSTUS	transcript	6397216	6398539	.	-	.	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	stop_codon	6397213	6397215	.	-	0	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	CDS	6397216	6397512	0.99	-	0	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	exon	6397216	6397512	.	-	.	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	intron	6397513	6397617	.	-	.	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	CDS	6397618	6397682	1	-	2	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	exon	6397618	6397682	.	-	.	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	intron	6397683	6397794	.	-	.	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	CDS	6397795	6398539	0.89	-	0	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	exon	6397795	6398539	.	-	.	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
Phchi.S5	AUGUSTUS	start_codon	6398537	6398539	.	-	0	transcript_id "Phchi.S5G098200.t1"; gene_id "Phchi.S5G098200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg732.t1 is derived from g10514.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5214798	5215722	.	-	.	Phchi.S6G069100
Phchi.S6	AUGUSTUS	transcript	5215248	5215722	.	-	.	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	stop_codon	5215245	5215247	.	-	0	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	CDS	5215248	5215344	0.94	-	1	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	exon	5215248	5215344	.	-	.	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	intron	5215345	5215426	.	-	.	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	CDS	5215427	5215722	0.96	-	0	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	exon	5215427	5215722	.	-	.	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	start_codon	5215720	5215722	.	-	0	transcript_id "Phchi.S6G069100.t1"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	transcript	5214798	5215722	.	-	.	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	stop_codon	5214795	5214797	.	-	0	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	CDS	5214798	5214816	0.94	-	1	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	exon	5214798	5214816	.	-	.	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	intron	5214817	5215426	.	-	.	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	CDS	5215427	5215722	0.97	-	0	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	exon	5215427	5215722	.	-	.	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
Phchi.S6	AUGUSTUS	start_codon	5215720	5215722	.	-	0	transcript_id "Phchi.S6G069100.t2"; gene_id "Phchi.S6G069100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4731.t1 is derived from g1901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12511579	12513801	.	+	.	Phchi.S1G189000
Phchi.S1	AUGUSTUS	transcript	12511579	12513801	.	+	.	transcript_id "Phchi.S1G189000.t1"; gene_id "Phchi.S1G189000"
Phchi.S1	AUGUSTUS	start_codon	12511579	12511581	.	+	0	transcript_id "Phchi.S1G189000.t1"; gene_id "Phchi.S1G189000"
Phchi.S1	AUGUSTUS	CDS	12511579	12513801	1	+	0	transcript_id "Phchi.S1G189000.t1"; gene_id "Phchi.S1G189000"
Phchi.S1	AUGUSTUS	exon	12511579	12513801	.	+	.	transcript_id "Phchi.S1G189000.t1"; gene_id "Phchi.S1G189000"
Phchi.S1	AUGUSTUS	stop_codon	12513802	12513804	.	+	0	transcript_id "Phchi.S1G189000.t1"; gene_id "Phchi.S1G189000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2554.t1 is derived from g9474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7324978	7327829	.	+	.	Phchi.S5G116300
Phchi.S5	AUGUSTUS	transcript	7324978	7327829	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	start_codon	7324978	7324980	.	+	0	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7324978	7325199	0.69	+	0	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7324978	7325199	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7325200	7325291	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7325292	7325399	0.78	+	0	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7325292	7325399	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7325400	7325523	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7325524	7325574	0.91	+	0	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7325524	7325574	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7325575	7325661	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7325662	7327460	0.91	+	0	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7325662	7327460	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7327461	7327780	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7327781	7327829	0.98	+	1	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7327781	7327829	.	+	.	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	stop_codon	7327830	7327832	.	+	0	transcript_id "Phchi.S5G116300.t1"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	transcript	7324978	7327574	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	start_codon	7324978	7324980	.	+	0	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7324978	7325199	0.69	+	0	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7324978	7325199	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7325200	7325291	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7325292	7325399	0.72	+	0	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7325292	7325399	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7325400	7325523	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7325524	7325574	0.82	+	0	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7325524	7325574	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7325575	7325661	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7325662	7327460	0.68	+	0	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7325662	7327460	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	intron	7327461	7327567	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	CDS	7327568	7327574	0.43	+	1	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	exon	7327568	7327574	.	+	.	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
Phchi.S5	AUGUSTUS	stop_codon	7327575	7327577	.	+	0	transcript_id "Phchi.S5G116300.t2"; gene_id "Phchi.S5G116300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2325.t1 is derived from g9245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6188681	6190224	.	-	.	Phchi.S5G093400
Phchi.S5	AUGUSTUS	transcript	6188681	6190224	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	stop_codon	6188678	6188680	.	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6188681	6188895	0.95	-	2	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6188681	6188895	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	intron	6188896	6189001	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6189002	6189140	0.93	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6189002	6189140	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	intron	6189141	6189241	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6189242	6189454	0.94	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6189242	6189454	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	intron	6189455	6189585	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6189586	6189690	1	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6189586	6189690	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	intron	6189691	6189781	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6189782	6189813	0.74	-	2	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6189782	6189813	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	intron	6189814	6189910	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6189911	6190028	0.8	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6189911	6190028	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	intron	6190029	6190170	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	CDS	6190171	6190224	0.74	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	exon	6190171	6190224	.	-	.	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
Phchi.S5	AUGUSTUS	start_codon	6190222	6190224	.	-	0	transcript_id "Phchi.S5G093400.t1"; gene_id "Phchi.S5G093400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15336.t1 is derived from g13804.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18448544	18451498	.	-	.	Phchi.S3G265500
Phchi.S3	AUGUSTUS	transcript	18448544	18451498	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	stop_codon	18448541	18448543	.	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18448544	18448777	1	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18448544	18448777	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18448778	18448852	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18448853	18449317	0.98	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18448853	18449317	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449318	18449397	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449398	18449487	1	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449398	18449487	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449488	18449587	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449588	18449660	1	-	1	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449588	18449660	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449661	18449832	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449833	18449889	1	-	1	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449833	18449889	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449890	18449977	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449978	18450042	1	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449978	18450042	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450043	18450173	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450174	18450225	1	-	1	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450174	18450225	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450226	18450362	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450363	18450416	1	-	1	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450363	18450416	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450417	18450529	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450530	18450612	1	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450530	18450612	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450613	18450704	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450705	18450740	1	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450705	18450740	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450741	18450998	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450999	18451017	0.99	-	1	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450999	18451017	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18451018	18451067	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18451068	18451104	0.99	-	2	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18451068	18451104	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18451105	18451199	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18451200	18451285	1	-	1	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18451200	18451285	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18451286	18451451	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18451452	18451498	0.66	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18451452	18451498	.	-	.	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	start_codon	18451496	18451498	.	-	0	transcript_id "Phchi.S3G265500.t1"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	transcript	18448544	18451485	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	stop_codon	18448541	18448543	.	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18448544	18448777	1	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18448544	18448777	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18448778	18448852	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18448853	18449317	0.95	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18448853	18449317	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449318	18449397	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449398	18449487	1	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449398	18449487	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449488	18449587	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449588	18449660	1	-	1	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449588	18449660	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449661	18449832	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449833	18449889	1	-	1	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449833	18449889	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18449890	18449977	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18449978	18450042	1	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18449978	18450042	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450043	18450173	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450174	18450225	1	-	1	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450174	18450225	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450226	18450362	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450363	18450416	1	-	1	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450363	18450416	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450417	18450529	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450530	18450612	1	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450530	18450612	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450613	18450704	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18450705	18450740	1	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18450705	18450740	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18450741	18451199	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18451200	18451285	0.56	-	2	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18451200	18451285	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	intron	18451286	18451451	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	CDS	18451452	18451485	0.56	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	exon	18451452	18451485	.	-	.	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
Phchi.S3	AUGUSTUS	start_codon	18451483	18451485	.	-	0	transcript_id "Phchi.S3G265500.t2"; gene_id "Phchi.S3G265500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9153.t1 is derived from g6328.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40114300	40115654	.	-	.	Phchi.S1G631200
Phchi.S1	AUGUSTUS	transcript	40114300	40115654	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	stop_codon	40114297	40114299	.	-	0	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40114300	40114542	0.96	-	0	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40114300	40114542	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40114543	40114639	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40114640	40114750	1	-	0	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40114640	40114750	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40114751	40114960	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40114961	40115039	0.95	-	1	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40114961	40115039	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40115040	40115200	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40115201	40115303	0.77	-	2	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40115201	40115303	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40115304	40115374	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40115375	40115654	0.71	-	0	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40115375	40115654	.	-	.	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	start_codon	40115652	40115654	.	-	0	transcript_id "Phchi.S1G631200.t1"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	transcript	40114300	40115654	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	stop_codon	40114297	40114299	.	-	0	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40114300	40114542	0.95	-	0	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40114300	40114542	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40114543	40114639	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40114640	40114750	0.98	-	0	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40114640	40114750	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40114751	40114824	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40114825	40115039	0.8	-	2	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40114825	40115039	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40115040	40115188	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40115189	40115200	0.9	-	2	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40115189	40115200	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40115201	40115311	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40115312	40115332	0.8	-	2	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40115312	40115332	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	intron	40115333	40115419	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	CDS	40115420	40115654	0.9	-	0	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	exon	40115420	40115654	.	-	.	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
Phchi.S1	AUGUSTUS	start_codon	40115652	40115654	.	-	0	transcript_id "Phchi.S1G631200.t2"; gene_id "Phchi.S1G631200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14496.t1 is derived from g12964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13156898	13158188	.	-	.	Phchi.S3G181500
Phchi.S3	AUGUSTUS	transcript	13156898	13158188	.	-	.	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	stop_codon	13156895	13156897	.	-	0	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	CDS	13156898	13157514	1	-	2	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	exon	13156898	13157514	.	-	.	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	intron	13157515	13157715	.	-	.	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	CDS	13157716	13157851	1	-	0	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	exon	13157716	13157851	.	-	.	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	intron	13157852	13158104	.	-	.	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	CDS	13158105	13158188	0.98	-	0	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	exon	13158105	13158188	.	-	.	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	start_codon	13158186	13158188	.	-	0	transcript_id "Phchi.S3G181500.t1"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	transcript	13156898	13158188	.	-	.	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	stop_codon	13156895	13156897	.	-	0	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	CDS	13156898	13157514	1	-	2	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	exon	13156898	13157514	.	-	.	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	intron	13157515	13157715	.	-	.	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	CDS	13157716	13157842	1	-	0	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	exon	13157716	13157842	.	-	.	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	intron	13157843	13158104	.	-	.	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	CDS	13158105	13158188	0.97	-	0	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	exon	13158105	13158188	.	-	.	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
Phchi.S3	AUGUSTUS	start_codon	13158186	13158188	.	-	0	transcript_id "Phchi.S3G181500.t2"; gene_id "Phchi.S3G181500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10663.t1 is derived from g14713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1495279	1496146	.	-	.	Phchi.S4G024500
Phchi.S4	AUGUSTUS	transcript	1495279	1496146	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	stop_codon	1495276	1495278	.	-	0	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	CDS	1495279	1495410	0.7	-	0	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	exon	1495279	1495410	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	intron	1495411	1495491	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	CDS	1495492	1495599	0.85	-	0	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	exon	1495492	1495599	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	intron	1495600	1495683	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	CDS	1495684	1495757	1	-	2	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	exon	1495684	1495757	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	intron	1495758	1495847	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	CDS	1495848	1495943	1	-	2	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	exon	1495848	1495943	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	intron	1495944	1496037	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	CDS	1496038	1496146	0.99	-	0	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	exon	1496038	1496146	.	-	.	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
Phchi.S4	AUGUSTUS	start_codon	1496144	1496146	.	-	0	transcript_id "Phchi.S4G024500.t1"; gene_id "Phchi.S4G024500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1269.t1 is derived from g11052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8749190	8751205	.	-	.	Phchi.S6G122800
Phchi.S6	AUGUSTUS	transcript	8749190	8751205	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	stop_codon	8749187	8749189	.	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8749190	8749193	0.84	-	1	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8749190	8749193	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8749194	8749283	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8749284	8749392	0.84	-	2	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8749284	8749392	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8749393	8749479	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8749480	8749613	0.84	-	1	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8749480	8749613	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8749614	8749719	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8749720	8749798	0.96	-	2	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8749720	8749798	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8749799	8749887	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8749888	8749957	1	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8749888	8749957	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8749958	8750096	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8750097	8750141	0.65	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8750097	8750141	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8750142	8750308	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8750309	8750364	0.84	-	2	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8750309	8750364	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8750365	8750509	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8750510	8750603	1	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8750510	8750603	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8750604	8750682	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8750683	8750772	1	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8750683	8750772	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8750773	8750894	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8750895	8750926	1	-	2	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8750895	8750926	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	intron	8750927	8751012	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	CDS	8751013	8751205	0.54	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	exon	8751013	8751205	.	-	.	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
Phchi.S6	AUGUSTUS	start_codon	8751203	8751205	.	-	0	transcript_id "Phchi.S6G122800.t1"; gene_id "Phchi.S6G122800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8276.t1 is derived from g5451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35065917	35066631	.	-	.	Phchi.S1G543500
Phchi.S1	AUGUSTUS	transcript	35065917	35066631	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	stop_codon	35065914	35065916	.	-	0	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	CDS	35065917	35065989	1	-	1	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	exon	35065917	35065989	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	intron	35065990	35066060	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	CDS	35066061	35066125	1	-	0	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	exon	35066061	35066125	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	intron	35066126	35066265	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	CDS	35066266	35066303	1	-	2	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	exon	35066266	35066303	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	intron	35066304	35066413	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	CDS	35066414	35066501	1	-	0	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	exon	35066414	35066501	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	intron	35066502	35066625	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	CDS	35066626	35066631	1	-	0	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	exon	35066626	35066631	.	-	.	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
Phchi.S1	AUGUSTUS	start_codon	35066629	35066631	.	-	0	transcript_id "Phchi.S1G543500.t1"; gene_id "Phchi.S1G543500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8050.t1 is derived from g5225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32716303	32716821	.	-	.	Phchi.S1G520900
Phchi.S1	AUGUSTUS	transcript	32716303	32716821	.	-	.	transcript_id "Phchi.S1G520900.t1"; gene_id "Phchi.S1G520900"
Phchi.S1	AUGUSTUS	stop_codon	32716300	32716302	.	-	0	transcript_id "Phchi.S1G520900.t1"; gene_id "Phchi.S1G520900"
Phchi.S1	AUGUSTUS	CDS	32716303	32716821	0.89	-	0	transcript_id "Phchi.S1G520900.t1"; gene_id "Phchi.S1G520900"
Phchi.S1	AUGUSTUS	exon	32716303	32716821	.	-	.	transcript_id "Phchi.S1G520900.t1"; gene_id "Phchi.S1G520900"
Phchi.S1	AUGUSTUS	start_codon	32716819	32716821	.	-	0	transcript_id "Phchi.S1G520900.t1"; gene_id "Phchi.S1G520900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6209.t1 is derived from g3380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21475438	21476000	.	-	.	Phchi.S1G336800
Phchi.S1	AUGUSTUS	transcript	21475438	21476000	.	-	.	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	stop_codon	21475435	21475437	.	-	0	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	CDS	21475438	21475459	0.96	-	1	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	exon	21475438	21475459	.	-	.	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	intron	21475460	21475668	.	-	.	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	CDS	21475669	21475853	0.96	-	0	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	exon	21475669	21475853	.	-	.	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	intron	21475854	21475991	.	-	.	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	CDS	21475992	21476000	0.85	-	0	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	exon	21475992	21476000	.	-	.	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
Phchi.S1	AUGUSTUS	start_codon	21475998	21476000	.	-	0	transcript_id "Phchi.S1G336800.t1"; gene_id "Phchi.S1G336800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12882.t1 is derived from g11347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2906355	2909445	.	+	.	Phchi.S3G020100
Phchi.S3	AUGUSTUS	transcript	2906355	2909445	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	start_codon	2906355	2906357	.	+	0	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	CDS	2906355	2907882	0.53	+	0	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	exon	2906355	2907882	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	intron	2907883	2908073	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	CDS	2908074	2908517	0.74	+	2	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	exon	2908074	2908517	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	intron	2908518	2908722	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	CDS	2908723	2908784	0.58	+	2	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	exon	2908723	2908784	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	intron	2908785	2909019	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	CDS	2909020	2909045	0.66	+	0	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	exon	2909020	2909045	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	intron	2909046	2909135	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	CDS	2909136	2909219	0.49	+	1	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	exon	2909136	2909219	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	intron	2909220	2909387	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	CDS	2909388	2909445	0.66	+	1	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	exon	2909388	2909445	.	+	.	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
Phchi.S3	AUGUSTUS	stop_codon	2909446	2909448	.	+	0	transcript_id "Phchi.S3G020100.t1"; gene_id "Phchi.S3G020100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9694.t1 is derived from g6870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43310184	43312945	.	-	.	Phchi.S1G685300
Phchi.S1	AUGUSTUS	transcript	43310184	43312945	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	stop_codon	43310181	43310183	.	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43310184	43310345	0.45	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43310184	43310345	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43310346	43310463	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43310464	43310535	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43310464	43310535	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43310536	43310618	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43310619	43310701	1	-	2	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43310619	43310701	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43310702	43310795	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43310796	43310856	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43310796	43310856	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43310857	43310974	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43310975	43311051	1	-	2	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43310975	43311051	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43311052	43311136	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43311137	43311203	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43311137	43311203	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43311204	43311369	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43311370	43311403	1	-	1	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43311370	43311403	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43311404	43311493	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43311494	43311574	1	-	1	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43311494	43311574	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43311575	43311651	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43311652	43311803	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43311652	43311803	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43311804	43311932	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43311933	43312019	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43311933	43312019	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43312020	43312152	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43312153	43312224	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43312153	43312224	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43312225	43312318	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43312319	43312423	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43312319	43312423	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43312424	43312510	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43312511	43312645	0.99	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43312511	43312645	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43312646	43312728	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43312729	43312739	1	-	2	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43312729	43312739	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	intron	43312740	43312818	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	CDS	43312819	43312945	1	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	exon	43312819	43312945	.	-	.	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
Phchi.S1	AUGUSTUS	start_codon	43312943	43312945	.	-	0	transcript_id "Phchi.S1G685300.t1"; gene_id "Phchi.S1G685300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4183.t1 is derived from g1352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8797104	8800672	.	+	.	Phchi.S1G134200
Phchi.S1	AUGUSTUS	transcript	8797104	8800672	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	start_codon	8797104	8797106	.	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8797104	8797246	0.96	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8797104	8797246	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8797247	8797442	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8797443	8797941	0.95	+	1	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8797443	8797941	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8797942	8798162	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798163	8798250	0.9	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798163	8798250	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798251	8798426	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798427	8798564	0.9	+	2	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798427	8798564	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798565	8798699	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798700	8798762	1	+	2	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798700	8798762	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798763	8798856	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798857	8798978	0.76	+	2	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798857	8798978	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798979	8799080	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8799081	8799461	1	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8799081	8799461	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8799462	8799556	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8799557	8799657	1	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8799557	8799657	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8799658	8799839	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8799840	8799921	1	+	1	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8799840	8799921	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8799922	8800061	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8800062	8800104	0.99	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8800062	8800104	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8800105	8800185	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8800186	8800300	1	+	2	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8800186	8800300	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8800301	8800605	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8800606	8800672	1	+	1	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8800606	8800672	.	+	.	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	stop_codon	8800673	8800675	.	+	0	transcript_id "Phchi.S1G134200.t1"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	transcript	8797104	8800672	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	start_codon	8797104	8797106	.	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8797104	8797246	1	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8797104	8797246	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8797247	8797442	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8797443	8797899	0.84	+	1	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8797443	8797899	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8797900	8797979	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8797980	8797991	1	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8797980	8797991	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8797992	8798162	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798163	8798250	0.9	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798163	8798250	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798251	8798426	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798427	8798564	0.9	+	2	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798427	8798564	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798565	8798699	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798700	8798762	1	+	2	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798700	8798762	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798763	8798856	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8798857	8798978	0.79	+	2	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8798857	8798978	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8798979	8799080	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8799081	8799461	0.99	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8799081	8799461	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8799462	8799556	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8799557	8799657	1	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8799557	8799657	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8799658	8799839	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8799840	8799921	0.96	+	1	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8799840	8799921	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8799922	8800061	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8800062	8800104	0.96	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8800062	8800104	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8800105	8800185	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8800186	8800300	1	+	2	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8800186	8800300	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	intron	8800301	8800605	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	CDS	8800606	8800672	1	+	1	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	exon	8800606	8800672	.	+	.	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
Phchi.S1	AUGUSTUS	stop_codon	8800673	8800675	.	+	0	transcript_id "Phchi.S1G134200.t2"; gene_id "Phchi.S1G134200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15522.t1 is derived from g13991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19709057	19710809	.	-	.	Phchi.S3G284100
Phchi.S3	AUGUSTUS	transcript	19709057	19710809	.	-	.	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	stop_codon	19709054	19709056	.	-	0	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	CDS	19709057	19709314	0.78	-	0	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	exon	19709057	19709314	.	-	.	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	intron	19709315	19709420	.	-	.	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	CDS	19709421	19709665	0.75	-	2	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	exon	19709421	19709665	.	-	.	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	intron	19709666	19709824	.	-	.	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	CDS	19709825	19710809	0.83	-	0	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	exon	19709825	19710809	.	-	.	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
Phchi.S3	AUGUSTUS	start_codon	19710807	19710809	.	-	0	transcript_id "Phchi.S3G284100.t1"; gene_id "Phchi.S3G284100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12226.t1 is derived from g7902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6836156	6838474	.	-	.	Phchi.S2G030600
Phchi.S2	AUGUSTUS	transcript	6836156	6838474	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	stop_codon	6836153	6836155	.	-	0	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	CDS	6836156	6836371	1	-	0	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	exon	6836156	6836371	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	intron	6836372	6836456	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	CDS	6836457	6836529	1	-	1	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	exon	6836457	6836529	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	intron	6836530	6836643	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	CDS	6836644	6836693	1	-	0	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	exon	6836644	6836693	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	intron	6836694	6836883	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	CDS	6836884	6837925	0.78	-	1	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	exon	6836884	6837925	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	intron	6837926	6838122	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	CDS	6838123	6838222	0.98	-	2	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	exon	6838123	6838222	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	intron	6838223	6838335	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	CDS	6838336	6838474	0.98	-	0	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	exon	6838336	6838474	.	-	.	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
Phchi.S2	AUGUSTUS	start_codon	6838472	6838474	.	-	0	transcript_id "Phchi.S2G030600.t1"; gene_id "Phchi.S2G030600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg314.t1 is derived from g10096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2230888	2231145	.	-	.	Phchi.S6G027300
Phchi.S6	AUGUSTUS	transcript	2230888	2231145	.	-	.	transcript_id "Phchi.S6G027300.t1"; gene_id "Phchi.S6G027300"
Phchi.S6	AUGUSTUS	stop_codon	2230885	2230887	.	-	0	transcript_id "Phchi.S6G027300.t1"; gene_id "Phchi.S6G027300"
Phchi.S6	AUGUSTUS	CDS	2230888	2231145	0.74	-	0	transcript_id "Phchi.S6G027300.t1"; gene_id "Phchi.S6G027300"
Phchi.S6	AUGUSTUS	exon	2230888	2231145	.	-	.	transcript_id "Phchi.S6G027300.t1"; gene_id "Phchi.S6G027300"
Phchi.S6	AUGUSTUS	start_codon	2231143	2231145	.	-	0	transcript_id "Phchi.S6G027300.t1"; gene_id "Phchi.S6G027300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6390.t1 is derived from g3562.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22703494	22705499	.	-	.	Phchi.S1G354900
Phchi.S1	AUGUSTUS	transcript	22703494	22705499	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	stop_codon	22703491	22703493	.	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22703494	22703619	0.99	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22703494	22703619	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22703620	22703716	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22703717	22703851	1	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22703717	22703851	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22703852	22703961	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22703962	22704003	1	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22703962	22704003	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22704004	22704096	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22704097	22704156	1	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22704097	22704156	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22704157	22704257	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22704258	22704404	1	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22704258	22704404	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22704405	22704533	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22704534	22704615	1	-	1	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22704534	22704615	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22704616	22704707	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22704708	22704764	1	-	1	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22704708	22704764	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22704765	22705012	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22705013	22705198	0.91	-	1	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22705013	22705198	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	intron	22705199	22705299	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	CDS	22705300	22705499	1	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	exon	22705300	22705499	.	-	.	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
Phchi.S1	AUGUSTUS	start_codon	22705497	22705499	.	-	0	transcript_id "Phchi.S1G354900.t1"; gene_id "Phchi.S1G354900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg966.t1 is derived from g10748.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6706984	6709744	.	+	.	Phchi.S6G092500
Phchi.S6	AUGUSTUS	transcript	6706984	6709744	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	start_codon	6706984	6706986	.	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6706984	6707175	0.49	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6706984	6707175	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6707176	6707283	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6707284	6707338	0.29	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6707284	6707338	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6707339	6707477	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6707478	6707482	0.56	+	2	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6707478	6707482	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6707483	6707681	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6707682	6707819	0.71	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6707682	6707819	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6707820	6707911	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6707912	6708373	1	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6707912	6708373	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6708374	6708529	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6708530	6708686	1	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6708530	6708686	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6708687	6708824	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6708825	6709103	0.83	+	2	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6708825	6709103	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6709104	6709330	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6709331	6709410	1	+	2	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6709331	6709410	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6709411	6709505	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6709506	6709603	1	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6709506	6709603	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	intron	6709604	6709743	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	CDS	6709744	6709744	1	+	1	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	exon	6709744	6709744	.	+	.	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
Phchi.S6	AUGUSTUS	stop_codon	6709745	6709747	.	+	0	transcript_id "Phchi.S6G092500.t1"; gene_id "Phchi.S6G092500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12272.t1 is derived from g7948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7402096	7404630	.	+	.	Phchi.S2G035200
Phchi.S2	AUGUSTUS	transcript	7402096	7404630	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	start_codon	7402096	7402098	.	+	0	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	CDS	7402096	7402509	0.95	+	0	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	exon	7402096	7402509	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	intron	7402510	7402607	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	CDS	7402608	7403678	0.99	+	0	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	exon	7402608	7403678	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	intron	7403679	7403800	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	CDS	7403801	7403950	1	+	0	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	exon	7403801	7403950	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	intron	7403951	7404198	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	CDS	7404199	7404630	1	+	0	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	exon	7404199	7404630	.	+	.	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
Phchi.S2	AUGUSTUS	stop_codon	7404631	7404633	.	+	0	transcript_id "Phchi.S2G035200.t1"; gene_id "Phchi.S2G035200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9901.t1 is derived from g7077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44333797	44335549	.	-	.	Phchi.S1G706000
Phchi.S1	AUGUSTUS	transcript	44333797	44335549	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	stop_codon	44333794	44333796	.	-	0	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	CDS	44333797	44333814	0.53	-	0	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	exon	44333797	44333814	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	intron	44333815	44333906	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	CDS	44333907	44335094	0.59	-	0	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	exon	44333907	44335094	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	intron	44335095	44335249	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	CDS	44335250	44335372	0.95	-	0	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	exon	44335250	44335372	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	intron	44335373	44335459	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	CDS	44335460	44335549	1	-	0	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	exon	44335460	44335549	.	-	.	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
Phchi.S1	AUGUSTUS	start_codon	44335547	44335549	.	-	0	transcript_id "Phchi.S1G706000.t1"; gene_id "Phchi.S1G706000"
# This transcript jg13174.t2 is derived from g11639.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13175.t1 is derived from g11640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4502828	4503810	.	-	.	Phchi.S3G049400
Phchi.S3	AUGUSTUS	transcript	4502828	4503810	.	-	.	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	stop_codon	4502825	4502827	.	-	0	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	CDS	4502828	4502880	0.66	-	2	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	exon	4502828	4502880	.	-	.	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	intron	4502881	4503034	.	-	.	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	CDS	4503035	4503047	0.62	-	0	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	exon	4503035	4503047	.	-	.	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	intron	4503048	4503111	.	-	.	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	CDS	4503112	4503810	0.41	-	0	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	exon	4503112	4503810	.	-	.	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
Phchi.S3	AUGUSTUS	start_codon	4503808	4503810	.	-	0	transcript_id "Phchi.S3G049400.t1"; gene_id "Phchi.S3G049400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10574.t1 is derived from g14624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1029310	1036503	.	+	.	Phchi.S4G015600
Phchi.S4	AUGUSTUS	transcript	1029310	1036503	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	start_codon	1029310	1029312	.	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1029310	1029459	0.98	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1029310	1029459	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1029460	1029839	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1029840	1029968	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1029840	1029968	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1029969	1030089	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1030090	1030161	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1030090	1030161	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1030162	1031028	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1031029	1031099	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1031029	1031099	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1031100	1031205	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1031206	1031305	1	+	1	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1031206	1031305	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1031306	1031390	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1031391	1031489	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1031391	1031489	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1031490	1031618	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1031619	1031745	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1031619	1031745	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1031746	1031908	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1031909	1032042	1	+	2	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1031909	1032042	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1032043	1032125	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1032126	1032185	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1032126	1032185	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1032186	1032301	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1032302	1032540	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1032302	1032540	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1032541	1032700	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1032701	1033133	0.69	+	1	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1032701	1033133	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1033134	1033344	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1033345	1033668	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1033345	1033668	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1033669	1033757	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1033758	1034369	0.76	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1033758	1034369	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1034370	1034472	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1034473	1034649	0.98	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1034473	1034649	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1034650	1034759	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1034760	1034990	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1034760	1034990	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1034991	1035082	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1035083	1035366	1	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1035083	1035366	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1035367	1035578	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1035579	1035881	1	+	1	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1035579	1035881	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1035882	1035963	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1035964	1036086	1	+	1	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1035964	1036086	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1036087	1036178	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1036179	1036297	0.43	+	1	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1036179	1036297	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1036298	1036348	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1036349	1036359	0.51	+	2	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1036349	1036359	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	intron	1036360	1036440	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	CDS	1036441	1036503	0.6	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	exon	1036441	1036503	.	+	.	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
Phchi.S4	AUGUSTUS	stop_codon	1036504	1036506	.	+	0	transcript_id "Phchi.S4G015600.t1"; gene_id "Phchi.S4G015600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6491.t1 is derived from g3663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23271376	23273935	.	+	.	Phchi.S1G365000
Phchi.S1	AUGUSTUS	transcript	23271376	23273935	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	start_codon	23271376	23271378	.	+	0	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23271376	23271623	1	+	0	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23271376	23271623	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23271624	23271712	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23271713	23271830	1	+	1	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23271713	23271830	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23271831	23271961	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23271962	23272066	1	+	0	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23271962	23272066	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23272067	23272198	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23272199	23272545	1	+	0	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23272199	23272545	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23272546	23272638	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23272639	23272920	0.96	+	1	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23272639	23272920	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23272921	23273065	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23273066	23273321	1	+	1	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23273066	23273321	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23273322	23273437	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23273438	23273589	0.97	+	0	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23273438	23273589	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	intron	23273590	23273673	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	CDS	23273674	23273935	0.99	+	1	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	exon	23273674	23273935	.	+	.	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
Phchi.S1	AUGUSTUS	stop_codon	23273936	23273938	.	+	0	transcript_id "Phchi.S1G365000.t1"; gene_id "Phchi.S1G365000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13616.t1 is derived from g12083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7768779	7769998	.	-	.	Phchi.S3G093500
Phchi.S3	AUGUSTUS	transcript	7768779	7769998	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	stop_codon	7768776	7768778	.	-	0	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	CDS	7768779	7768983	1	-	1	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	exon	7768779	7768983	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	intron	7768984	7769097	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	CDS	7769098	7769159	1	-	0	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	exon	7769098	7769159	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	intron	7769160	7769274	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	CDS	7769275	7769469	1	-	0	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	exon	7769275	7769469	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	intron	7769470	7769585	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	CDS	7769586	7769786	0.4	-	0	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	exon	7769586	7769786	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	intron	7769787	7769878	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	CDS	7769879	7769998	0.61	-	0	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	exon	7769879	7769998	.	-	.	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
Phchi.S3	AUGUSTUS	start_codon	7769996	7769998	.	-	0	transcript_id "Phchi.S3G093500.t1"; gene_id "Phchi.S3G093500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4868.t1 is derived from g2038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13164886	13165350	.	+	.	Phchi.S1G202700
Phchi.S1	AUGUSTUS	transcript	13164886	13165350	.	+	.	transcript_id "Phchi.S1G202700.t1"; gene_id "Phchi.S1G202700"
Phchi.S1	AUGUSTUS	start_codon	13164886	13164888	.	+	0	transcript_id "Phchi.S1G202700.t1"; gene_id "Phchi.S1G202700"
Phchi.S1	AUGUSTUS	CDS	13164886	13165350	0.28	+	0	transcript_id "Phchi.S1G202700.t1"; gene_id "Phchi.S1G202700"
Phchi.S1	AUGUSTUS	exon	13164886	13165350	.	+	.	transcript_id "Phchi.S1G202700.t1"; gene_id "Phchi.S1G202700"
Phchi.S1	AUGUSTUS	stop_codon	13165351	13165353	.	+	0	transcript_id "Phchi.S1G202700.t1"; gene_id "Phchi.S1G202700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11185.t1 is derived from g15235.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4539825	4541954	.	-	.	Phchi.S4G076700
Phchi.S4	AUGUSTUS	transcript	4539825	4541954	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	stop_codon	4539822	4539824	.	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4539825	4539968	0.98	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4539825	4539968	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	intron	4539969	4540110	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4540111	4540242	0.91	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4540111	4540242	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	intron	4540243	4540378	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4540379	4540492	1	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4540379	4540492	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	intron	4540493	4540581	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4540582	4540680	1	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4540582	4540680	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	intron	4540681	4540773	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4540774	4541208	0.91	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4540774	4541208	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	intron	4541209	4541313	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4541314	4541564	0.88	-	2	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4541314	4541564	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	intron	4541565	4541740	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	CDS	4541741	4541954	0.6	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	exon	4541741	4541954	.	-	.	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
Phchi.S4	AUGUSTUS	start_codon	4541952	4541954	.	-	0	transcript_id "Phchi.S4G076700.t1"; gene_id "Phchi.S4G076700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6085.t1 is derived from g3256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20874041	20875439	.	+	.	Phchi.S1G324400
Phchi.S1	AUGUSTUS	transcript	20874041	20875439	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	start_codon	20874041	20874043	.	+	0	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	CDS	20874041	20874101	0.73	+	0	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	exon	20874041	20874101	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	intron	20874102	20874234	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	CDS	20874235	20874545	0.97	+	2	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	exon	20874235	20874545	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	intron	20874546	20874648	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	CDS	20874649	20874885	0.98	+	0	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	exon	20874649	20874885	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	intron	20874886	20874986	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	CDS	20874987	20875154	0.6	+	0	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	exon	20874987	20875154	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	intron	20875155	20875271	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	CDS	20875272	20875439	1	+	0	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	exon	20875272	20875439	.	+	.	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
Phchi.S1	AUGUSTUS	stop_codon	20875440	20875442	.	+	0	transcript_id "Phchi.S1G324400.t1"; gene_id "Phchi.S1G324400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3809.t1 is derived from g978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5825641	5827740	.	-	.	Phchi.S1G096800
Phchi.S1	AUGUSTUS	transcript	5825641	5827740	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	stop_codon	5825638	5825640	.	-	0	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	CDS	5825641	5826508	0.43	-	1	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	exon	5825641	5826508	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	intron	5826509	5826919	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	CDS	5826920	5827015	0.27	-	1	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	exon	5826920	5827015	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	intron	5827016	5827465	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	CDS	5827466	5827524	0.82	-	0	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	exon	5827466	5827524	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	intron	5827525	5827599	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	CDS	5827600	5827740	1	-	0	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	exon	5827600	5827740	.	-	.	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
Phchi.S1	AUGUSTUS	start_codon	5827738	5827740	.	-	0	transcript_id "Phchi.S1G096800.t1"; gene_id "Phchi.S1G096800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2788.t1 is derived from g9708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8866365	8870466	.	-	.	Phchi.S5G139700
Phchi.S5	AUGUSTUS	transcript	8866365	8870466	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	stop_codon	8866362	8866364	.	-	0	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	CDS	8866365	8867116	0.33	-	2	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	exon	8866365	8867116	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	intron	8867117	8867292	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	CDS	8867293	8869308	0.57	-	2	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	exon	8867293	8869308	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	intron	8869309	8869548	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	CDS	8869549	8870043	0.99	-	2	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	exon	8869549	8870043	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	intron	8870044	8870258	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	CDS	8870259	8870466	1	-	0	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	exon	8870259	8870466	.	-	.	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
Phchi.S5	AUGUSTUS	start_codon	8870464	8870466	.	-	0	transcript_id "Phchi.S5G139700.t1"; gene_id "Phchi.S5G139700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11009.t1 is derived from g15059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3614528	3617194	.	-	.	Phchi.S4G059100
Phchi.S4	AUGUSTUS	transcript	3614528	3617194	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	stop_codon	3614525	3614527	.	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3614528	3614803	1	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3614528	3614803	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	intron	3614804	3614928	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3614929	3615021	1	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3614929	3615021	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	intron	3615022	3615115	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3615116	3615160	1	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3615116	3615160	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	intron	3615161	3615304	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3615305	3615376	1	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3615305	3615376	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	intron	3615377	3615453	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3615454	3615606	1	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3615454	3615606	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	intron	3615607	3615701	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3615702	3616318	0.98	-	2	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3615702	3616318	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	intron	3616319	3616533	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	CDS	3616534	3617194	0.46	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	exon	3616534	3617194	.	-	.	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
Phchi.S4	AUGUSTUS	start_codon	3617192	3617194	.	-	0	transcript_id "Phchi.S4G059100.t1"; gene_id "Phchi.S4G059100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11413.t1 is derived from g15463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6244607	6245874	.	+	.	Phchi.S4G099500
Phchi.S4	AUGUSTUS	transcript	6244607	6245874	.	+	.	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	start_codon	6244607	6244609	.	+	0	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	CDS	6244607	6244880	0.83	+	0	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	exon	6244607	6244880	.	+	.	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	intron	6244881	6245014	.	+	.	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	CDS	6245015	6245874	0.31	+	2	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	exon	6245015	6245874	.	+	.	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
Phchi.S4	AUGUSTUS	stop_codon	6245875	6245877	.	+	0	transcript_id "Phchi.S4G099500.t1"; gene_id "Phchi.S4G099500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3545.t1 is derived from g714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4386802	4388582	.	-	.	Phchi.S1G070400
Phchi.S1	AUGUSTUS	transcript	4387756	4388582	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	stop_codon	4387753	4387755	.	-	0	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4387756	4387834	0.52	-	1	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4387756	4387834	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4387835	4387951	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4387952	4388130	0.69	-	0	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4387952	4388130	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4388131	4388289	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4388290	4388342	1	-	2	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4388290	4388342	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4388343	4388482	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4388483	4388582	0.99	-	0	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4388483	4388582	.	-	.	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	start_codon	4388580	4388582	.	-	0	transcript_id "Phchi.S1G070400.t1"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	transcript	4386802	4388582	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	stop_codon	4386799	4386801	.	-	0	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4386802	4387490	0.4	-	2	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4386802	4387490	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4387491	4387708	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4387709	4387834	0.4	-	2	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4387709	4387834	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4387835	4388089	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4388090	4388150	0.5	-	0	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4388090	4388150	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4388151	4388289	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4388290	4388342	0.84	-	2	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4388290	4388342	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	intron	4388343	4388482	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	CDS	4388483	4388582	0.84	-	0	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	exon	4388483	4388582	.	-	.	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
Phchi.S1	AUGUSTUS	start_codon	4388580	4388582	.	-	0	transcript_id "Phchi.S1G070400.t2"; gene_id "Phchi.S1G070400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1928.t1 is derived from g8848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3879224	3879891	.	+	.	Phchi.S5G053700
Phchi.S5	AUGUSTUS	transcript	3879224	3879891	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	start_codon	3879224	3879226	.	+	0	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	CDS	3879224	3879274	0.99	+	0	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	exon	3879224	3879274	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	intron	3879275	3879433	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	CDS	3879434	3879497	0.9	+	0	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	exon	3879434	3879497	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	intron	3879498	3879625	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	CDS	3879626	3879719	0.99	+	2	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	exon	3879626	3879719	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	intron	3879720	3879884	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	CDS	3879885	3879891	0.82	+	1	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	exon	3879885	3879891	.	+	.	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
Phchi.S5	AUGUSTUS	stop_codon	3879892	3879894	.	+	0	transcript_id "Phchi.S5G053700.t1"; gene_id "Phchi.S5G053700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15529.t1 is derived from g13998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19733741	19736247	.	-	.	Phchi.S3G284800
Phchi.S3	AUGUSTUS	transcript	19733741	19736247	.	-	.	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	stop_codon	19733738	19733740	.	-	0	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	CDS	19733741	19735912	1	-	0	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	exon	19733741	19735912	.	-	.	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	intron	19735913	19735997	.	-	.	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	CDS	19735998	19736078	0.99	-	0	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	exon	19735998	19736078	.	-	.	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	intron	19736079	19736166	.	-	.	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	CDS	19736167	19736247	0.38	-	0	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	exon	19736167	19736247	.	-	.	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
Phchi.S3	AUGUSTUS	start_codon	19736245	19736247	.	-	0	transcript_id "Phchi.S3G284800.t1"; gene_id "Phchi.S3G284800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15994.t1 is derived from g16026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C69	AUGUSTUS	gene	53234	55153	.	+	.	Phchi.C69G000200
Phchi.C69	AUGUSTUS	transcript	53234	55153	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	start_codon	53234	53236	.	+	0	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	CDS	53234	53386	0.94	+	0	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	exon	53234	53386	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	intron	53387	53571	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	CDS	53572	53812	1	+	0	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	exon	53572	53812	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	intron	53813	54110	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	CDS	54111	54627	0.78	+	2	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	exon	54111	54627	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	intron	54628	54735	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	CDS	54736	55153	0.69	+	1	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	exon	54736	55153	.	+	.	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
Phchi.C69	AUGUSTUS	stop_codon	55154	55156	.	+	0	transcript_id "Phchi.C69G000200.t1"; gene_id "Phchi.C69G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10768.t1 is derived from g14818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2014334	2015722	.	+	.	Phchi.S4G035000
Phchi.S4	AUGUSTUS	transcript	2015108	2015722	.	+	.	transcript_id "Phchi.S4G035000.t1"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	start_codon	2015108	2015110	.	+	0	transcript_id "Phchi.S4G035000.t1"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	CDS	2015108	2015722	0.84	+	0	transcript_id "Phchi.S4G035000.t1"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	exon	2015108	2015722	.	+	.	transcript_id "Phchi.S4G035000.t1"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	stop_codon	2015723	2015725	.	+	0	transcript_id "Phchi.S4G035000.t1"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	transcript	2014334	2015722	.	+	.	transcript_id "Phchi.S4G035000.t2"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	start_codon	2014334	2014336	.	+	0	transcript_id "Phchi.S4G035000.t2"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	CDS	2014334	2015722	0.29	+	0	transcript_id "Phchi.S4G035000.t2"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	exon	2014334	2015722	.	+	.	transcript_id "Phchi.S4G035000.t2"; gene_id "Phchi.S4G035000"
Phchi.S4	AUGUSTUS	stop_codon	2015723	2015725	.	+	0	transcript_id "Phchi.S4G035000.t2"; gene_id "Phchi.S4G035000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15461.t1 is derived from g13929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19294294	19299328	.	-	.	Phchi.S3G278000
Phchi.S3	AUGUSTUS	transcript	19294294	19299328	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	stop_codon	19294291	19294293	.	-	0	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19294294	19294456	1	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19294294	19294456	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19294457	19294550	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19294551	19294678	1	-	0	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19294551	19294678	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19294679	19294767	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19294768	19295057	1	-	2	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19294768	19295057	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19295058	19295156	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19295157	19295305	0.86	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19295157	19295305	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19295306	19295410	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19295411	19295711	0.99	-	2	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19295411	19295711	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19295712	19295838	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19295839	19296020	0.98	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19295839	19296020	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19296021	19296132	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19296133	19296429	0.98	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19296133	19296429	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19296430	19296538	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19296539	19297455	0.98	-	0	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19296539	19297455	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19297456	19297569	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19297570	19297643	0.98	-	2	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19297570	19297643	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19297644	19297726	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19297727	19297761	1	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19297727	19297761	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19297762	19297912	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19297913	19298059	1	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19297913	19298059	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19298060	19298266	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19298267	19298330	1	-	2	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19298267	19298330	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19298331	19298429	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19298430	19298702	1	-	2	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19298430	19298702	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19298703	19298801	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19298802	19298875	1	-	1	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19298802	19298875	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	intron	19298876	19298960	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	CDS	19298961	19299328	0.98	-	0	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	exon	19298961	19299328	.	-	.	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
Phchi.S3	AUGUSTUS	start_codon	19299326	19299328	.	-	0	transcript_id "Phchi.S3G278000.t1"; gene_id "Phchi.S3G278000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg35.t1 is derived from g9795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C67	AUGUSTUS	gene	5110	6483	.	-	.	Phchi.C67G000100
Phchi.C67	AUGUSTUS	transcript	5110	6483	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	stop_codon	5107	5109	.	-	0	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	5110	5174	0.58	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	5110	5174	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	5175	5283	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	5284	5373	0.57	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	5284	5373	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	5374	5553	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	5554	5622	0.63	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	5554	5622	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	5623	5744	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	5745	5768	0.99	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	5745	5768	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	5769	5913	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	5914	5982	0.92	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	5914	5982	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	5983	6080	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	6081	6098	0.65	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	6081	6098	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	6099	6256	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	6257	6316	0.49	-	2	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	6257	6316	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	intron	6317	6419	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	CDS	6420	6483	0.67	-	0	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	exon	6420	6483	.	-	.	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
Phchi.C67	AUGUSTUS	start_codon	6481	6483	.	-	0	transcript_id "Phchi.C67G000100.t1"; gene_id "Phchi.C67G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7293.t1 is derived from g4465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28365801	28368134	.	+	.	Phchi.S1G445200
Phchi.S1	AUGUSTUS	transcript	28365801	28368134	.	+	.	transcript_id "Phchi.S1G445200.t1"; gene_id "Phchi.S1G445200"
Phchi.S1	AUGUSTUS	start_codon	28365801	28365803	.	+	0	transcript_id "Phchi.S1G445200.t1"; gene_id "Phchi.S1G445200"
Phchi.S1	AUGUSTUS	CDS	28365801	28368134	0.9	+	0	transcript_id "Phchi.S1G445200.t1"; gene_id "Phchi.S1G445200"
Phchi.S1	AUGUSTUS	exon	28365801	28368134	.	+	.	transcript_id "Phchi.S1G445200.t1"; gene_id "Phchi.S1G445200"
Phchi.S1	AUGUSTUS	stop_codon	28368135	28368137	.	+	0	transcript_id "Phchi.S1G445200.t1"; gene_id "Phchi.S1G445200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5186.t1 is derived from g2356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15382141	15382671	.	-	.	Phchi.S1G234500
Phchi.S1	AUGUSTUS	transcript	15382141	15382671	.	-	.	transcript_id "Phchi.S1G234500.t1"; gene_id "Phchi.S1G234500"
Phchi.S1	AUGUSTUS	stop_codon	15382138	15382140	.	-	0	transcript_id "Phchi.S1G234500.t1"; gene_id "Phchi.S1G234500"
Phchi.S1	AUGUSTUS	CDS	15382141	15382671	0.94	-	0	transcript_id "Phchi.S1G234500.t1"; gene_id "Phchi.S1G234500"
Phchi.S1	AUGUSTUS	exon	15382141	15382671	.	-	.	transcript_id "Phchi.S1G234500.t1"; gene_id "Phchi.S1G234500"
Phchi.S1	AUGUSTUS	start_codon	15382669	15382671	.	-	0	transcript_id "Phchi.S1G234500.t1"; gene_id "Phchi.S1G234500"
# This transcript jg6735.t2 is derived from g3907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6736.t1 is derived from g3908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24795192	24795984	.	-	.	Phchi.S1G389500
Phchi.S1	AUGUSTUS	transcript	24795192	24795984	.	-	.	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	stop_codon	24795189	24795191	.	-	0	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	CDS	24795192	24795220	0.41	-	2	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	exon	24795192	24795220	.	-	.	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	intron	24795221	24795335	.	-	.	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	CDS	24795336	24795984	0.71	-	0	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	exon	24795336	24795984	.	-	.	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
Phchi.S1	AUGUSTUS	start_codon	24795982	24795984	.	-	0	transcript_id "Phchi.S1G389500.t1"; gene_id "Phchi.S1G389500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12916.t1 is derived from g11381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3120535	3126434	.	-	.	Phchi.S3G023500
Phchi.S3	AUGUSTUS	transcript	3120535	3126434	.	-	.	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	stop_codon	3120532	3120534	.	-	0	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	CDS	3120535	3125126	0.78	-	2	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	exon	3120535	3125126	.	-	.	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	intron	3125127	3125212	.	-	.	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	CDS	3125213	3126434	0.32	-	0	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	exon	3125213	3126434	.	-	.	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
Phchi.S3	AUGUSTUS	start_codon	3126432	3126434	.	-	0	transcript_id "Phchi.S3G023500.t1"; gene_id "Phchi.S3G023500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13743.t1 is derived from g12210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8669462	8670891	.	-	.	Phchi.S3G106200
Phchi.S3	AUGUSTUS	transcript	8669462	8670891	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	stop_codon	8669459	8669461	.	-	0	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	CDS	8669462	8669583	0.85	-	2	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	exon	8669462	8669583	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	intron	8669584	8669670	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	CDS	8669671	8669712	0.86	-	2	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	exon	8669671	8669712	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	intron	8669713	8670014	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	CDS	8670015	8670523	0.64	-	1	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	exon	8670015	8670523	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	intron	8670524	8670617	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	CDS	8670618	8670648	0.66	-	2	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	exon	8670618	8670648	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	intron	8670649	8670776	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	CDS	8670777	8670891	0.98	-	0	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	exon	8670777	8670891	.	-	.	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
Phchi.S3	AUGUSTUS	start_codon	8670889	8670891	.	-	0	transcript_id "Phchi.S3G106200.t1"; gene_id "Phchi.S3G106200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9764.t1 is derived from g6940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43588279	43589884	.	-	.	Phchi.S1G692300
Phchi.S1	AUGUSTUS	transcript	43588279	43589884	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	stop_codon	43588276	43588278	.	-	0	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43588279	43588341	1	-	0	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43588279	43588341	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43588342	43588515	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43588516	43588554	1	-	0	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43588516	43588554	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43588555	43588736	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43588737	43588951	1	-	2	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43588737	43588951	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43588952	43589048	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43589049	43589222	1	-	2	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43589049	43589222	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43589223	43589370	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43589371	43589466	1	-	2	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43589371	43589466	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43589467	43589724	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43589725	43589884	0.54	-	0	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43589725	43589884	.	-	.	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	start_codon	43589882	43589884	.	-	0	transcript_id "Phchi.S1G692300.t1"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	transcript	43588279	43589750	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	stop_codon	43588276	43588278	.	-	0	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43588279	43588341	1	-	0	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43588279	43588341	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43588342	43588515	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43588516	43588554	1	-	0	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43588516	43588554	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43588555	43588736	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43588737	43588951	1	-	2	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43588737	43588951	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43588952	43589048	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43589049	43589222	1	-	2	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43589049	43589222	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43589223	43589395	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43589396	43589466	1	-	1	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43589396	43589466	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	intron	43589467	43589724	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	CDS	43589725	43589750	0.5	-	0	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	exon	43589725	43589750	.	-	.	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
Phchi.S1	AUGUSTUS	start_codon	43589748	43589750	.	-	0	transcript_id "Phchi.S1G692300.t2"; gene_id "Phchi.S1G692300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8214.t1 is derived from g5389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34452283	34453409	.	+	.	Phchi.S1G537300
Phchi.S1	AUGUSTUS	transcript	34452283	34453409	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	start_codon	34452283	34452285	.	+	0	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	CDS	34452283	34452330	1	+	0	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	exon	34452283	34452330	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	intron	34452331	34452449	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	CDS	34452450	34452542	1	+	0	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	exon	34452450	34452542	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	intron	34452543	34452619	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	CDS	34452620	34452737	1	+	0	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	exon	34452620	34452737	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	intron	34452738	34453091	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	CDS	34453092	34453150	1	+	2	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	exon	34453092	34453150	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	intron	34453151	34453271	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	CDS	34453272	34453409	1	+	0	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	exon	34453272	34453409	.	+	.	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
Phchi.S1	AUGUSTUS	stop_codon	34453410	34453412	.	+	0	transcript_id "Phchi.S1G537300.t1"; gene_id "Phchi.S1G537300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11318.t1 is derived from g15368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5336706	5337616	.	+	.	Phchi.S4G090000
Phchi.S4	AUGUSTUS	transcript	5336706	5337616	.	+	.	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	start_codon	5336706	5336708	.	+	0	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	CDS	5336706	5336915	0.49	+	0	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	exon	5336706	5336915	.	+	.	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	intron	5336916	5337002	.	+	.	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	CDS	5337003	5337241	0.91	+	0	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	exon	5337003	5337241	.	+	.	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	intron	5337242	5337345	.	+	.	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	CDS	5337346	5337616	0.7	+	1	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	exon	5337346	5337616	.	+	.	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
Phchi.S4	AUGUSTUS	stop_codon	5337617	5337619	.	+	0	transcript_id "Phchi.S4G090000.t1"; gene_id "Phchi.S4G090000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8548.t1 is derived from g5723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36575617	36578055	.	-	.	Phchi.S1G570700
Phchi.S1	AUGUSTUS	transcript	36575617	36578055	.	-	.	transcript_id "Phchi.S1G570700.t1"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	stop_codon	36575614	36575616	.	-	0	transcript_id "Phchi.S1G570700.t1"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	CDS	36575617	36578055	0.87	-	0	transcript_id "Phchi.S1G570700.t1"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	exon	36575617	36578055	.	-	.	transcript_id "Phchi.S1G570700.t1"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	start_codon	36578053	36578055	.	-	0	transcript_id "Phchi.S1G570700.t1"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	transcript	36575617	36577350	.	-	.	transcript_id "Phchi.S1G570700.t2"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	stop_codon	36575614	36575616	.	-	0	transcript_id "Phchi.S1G570700.t2"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	CDS	36575617	36577350	0.46	-	0	transcript_id "Phchi.S1G570700.t2"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	exon	36575617	36577350	.	-	.	transcript_id "Phchi.S1G570700.t2"; gene_id "Phchi.S1G570700"
Phchi.S1	AUGUSTUS	start_codon	36577348	36577350	.	-	0	transcript_id "Phchi.S1G570700.t2"; gene_id "Phchi.S1G570700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12809.t1 is derived from g11274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2473696	2474413	.	+	.	Phchi.S3G012800
Phchi.S3	AUGUSTUS	transcript	2473696	2474413	.	+	.	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	start_codon	2473696	2473698	.	+	0	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	CDS	2473696	2473776	0.57	+	0	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	exon	2473696	2473776	.	+	.	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	intron	2473777	2474072	.	+	.	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	CDS	2474073	2474216	1	+	0	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	exon	2474073	2474216	.	+	.	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	intron	2474217	2474335	.	+	.	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	CDS	2474336	2474413	1	+	0	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	exon	2474336	2474413	.	+	.	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
Phchi.S3	AUGUSTUS	stop_codon	2474414	2474416	.	+	0	transcript_id "Phchi.S3G012800.t1"; gene_id "Phchi.S3G012800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13579.t1 is derived from g12046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7562762	7564217	.	-	.	Phchi.S3G089800
Phchi.S3	AUGUSTUS	transcript	7562762	7564217	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	stop_codon	7562759	7562761	.	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7562762	7562819	1	-	1	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7562762	7562819	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7562820	7562903	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7562904	7562962	1	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7562904	7562962	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7562963	7563057	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7563058	7563198	0.93	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7563058	7563198	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7563199	7563301	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7563302	7563437	0.93	-	1	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7563302	7563437	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7563438	7563522	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7563523	7563599	1	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7563523	7563599	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7563600	7563676	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7563677	7563808	1	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7563677	7563808	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7563809	7563957	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7563958	7564041	0.84	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7563958	7564041	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	intron	7564042	7564124	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	CDS	7564125	7564217	0.33	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	exon	7564125	7564217	.	-	.	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
Phchi.S3	AUGUSTUS	start_codon	7564215	7564217	.	-	0	transcript_id "Phchi.S3G089800.t1"; gene_id "Phchi.S3G089800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8205.t1 is derived from g5380.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34431014	34432060	.	-	.	Phchi.S1G536400
Phchi.S1	AUGUSTUS	transcript	34431014	34432060	.	-	.	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	stop_codon	34431011	34431013	.	-	0	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	CDS	34431014	34431069	1	-	2	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	exon	34431014	34431069	.	-	.	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	intron	34431070	34431447	.	-	.	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	CDS	34431448	34431618	1	-	2	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	exon	34431448	34431618	.	-	.	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	intron	34431619	34431930	.	-	.	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	CDS	34431931	34432060	1	-	0	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	exon	34431931	34432060	.	-	.	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	start_codon	34432058	34432060	.	-	0	transcript_id "Phchi.S1G536400.t1"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	transcript	34431014	34432060	.	-	.	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	stop_codon	34431011	34431013	.	-	0	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	CDS	34431014	34431066	0.99	-	2	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	exon	34431014	34431066	.	-	.	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	intron	34431067	34431447	.	-	.	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	CDS	34431448	34431618	1	-	2	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	exon	34431448	34431618	.	-	.	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	intron	34431619	34431930	.	-	.	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	CDS	34431931	34432060	1	-	0	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	exon	34431931	34432060	.	-	.	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
Phchi.S1	AUGUSTUS	start_codon	34432058	34432060	.	-	0	transcript_id "Phchi.S1G536400.t2"; gene_id "Phchi.S1G536400"
# This transcript jg7162.t1 is derived from g4333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27340845	27341496	.	+	.	Phchi.S1G432000
Phchi.S1	AUGUSTUS	transcript	27340845	27341496	.	+	.	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	start_codon	27340845	27340847	.	+	0	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	CDS	27340845	27340972	0.76	+	0	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	exon	27340845	27340972	.	+	.	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	intron	27340973	27341129	.	+	.	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	CDS	27341130	27341496	0.77	+	1	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	exon	27341130	27341496	.	+	.	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
Phchi.S1	AUGUSTUS	stop_codon	27341497	27341499	.	+	0	transcript_id "Phchi.S1G432000.t1"; gene_id "Phchi.S1G432000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5488.t1 is derived from g2658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17099062	17101040	.	+	.	Phchi.S1G264700
Phchi.S1	AUGUSTUS	transcript	17099062	17101040	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	start_codon	17099062	17099064	.	+	0	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	CDS	17099062	17099343	0.94	+	0	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	exon	17099062	17099343	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	intron	17099344	17099454	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	CDS	17099455	17100213	0.96	+	0	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	exon	17099455	17100213	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	intron	17100214	17100389	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	CDS	17100390	17100738	0.99	+	0	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	exon	17100390	17100738	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	intron	17100739	17100858	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	CDS	17100859	17101040	1	+	2	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	exon	17100859	17101040	.	+	.	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
Phchi.S1	AUGUSTUS	stop_codon	17101041	17101043	.	+	0	transcript_id "Phchi.S1G264700.t1"; gene_id "Phchi.S1G264700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11771.t1 is derived from g15823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8103919	8106546	.	+	.	Phchi.S4G135300
Phchi.S4	AUGUSTUS	transcript	8103919	8106546	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	start_codon	8103919	8103921	.	+	0	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8103919	8104225	0.82	+	0	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8103919	8104225	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8104226	8104330	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8104331	8104473	1	+	2	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8104331	8104473	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8104474	8104589	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8104590	8104697	1	+	0	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8104590	8104697	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8104698	8104798	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8104799	8105022	1	+	0	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8104799	8105022	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8105023	8105103	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8105104	8105145	1	+	1	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8105104	8105145	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8105146	8105236	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8105237	8105324	1	+	1	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8105237	8105324	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8105325	8105412	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8105413	8105546	1	+	0	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8105413	8105546	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8105547	8105722	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8105723	8105811	1	+	1	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8105723	8105811	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8105812	8105904	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8105905	8106055	1	+	2	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8105905	8106055	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8106056	8106146	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8106147	8106215	1	+	1	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8106147	8106215	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	intron	8106216	8106317	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	CDS	8106318	8106546	0.99	+	1	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	exon	8106318	8106546	.	+	.	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
Phchi.S4	AUGUSTUS	stop_codon	8106547	8106549	.	+	0	transcript_id "Phchi.S4G135300.t1"; gene_id "Phchi.S4G135300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1132.t1 is derived from g10915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7874081	7874853	.	+	.	Phchi.S6G109100
Phchi.S6	AUGUSTUS	transcript	7874081	7874853	.	+	.	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	start_codon	7874081	7874083	.	+	0	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	CDS	7874081	7874141	0.92	+	0	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	exon	7874081	7874141	.	+	.	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	intron	7874142	7874268	.	+	.	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	CDS	7874269	7874503	1	+	2	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	exon	7874269	7874503	.	+	.	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	intron	7874504	7874645	.	+	.	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	CDS	7874646	7874853	1	+	1	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	exon	7874646	7874853	.	+	.	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
Phchi.S6	AUGUSTUS	stop_codon	7874854	7874856	.	+	0	transcript_id "Phchi.S6G109100.t1"; gene_id "Phchi.S6G109100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9841.t1 is derived from g7017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44023221	44024087	.	-	.	Phchi.S1G700000
Phchi.S1	AUGUSTUS	transcript	44023221	44024087	.	-	.	transcript_id "Phchi.S1G700000.t1"; gene_id "Phchi.S1G700000"
Phchi.S1	AUGUSTUS	stop_codon	44023218	44023220	.	-	0	transcript_id "Phchi.S1G700000.t1"; gene_id "Phchi.S1G700000"
Phchi.S1	AUGUSTUS	CDS	44023221	44024087	0.78	-	0	transcript_id "Phchi.S1G700000.t1"; gene_id "Phchi.S1G700000"
Phchi.S1	AUGUSTUS	exon	44023221	44024087	.	-	.	transcript_id "Phchi.S1G700000.t1"; gene_id "Phchi.S1G700000"
Phchi.S1	AUGUSTUS	start_codon	44024085	44024087	.	-	0	transcript_id "Phchi.S1G700000.t1"; gene_id "Phchi.S1G700000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11657.t1 is derived from g15708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7535046	7539395	.	-	.	Phchi.S4G123900
Phchi.S4	AUGUSTUS	transcript	7535046	7539395	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	stop_codon	7535043	7535045	.	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7535046	7535074	0.82	-	2	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7535046	7535074	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7535075	7535215	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7535216	7535249	0.82	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7535216	7535249	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7535250	7535331	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7535332	7535403	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7535332	7535403	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7535404	7535482	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7535483	7535554	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7535483	7535554	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7535555	7535636	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7535637	7535858	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7535637	7535858	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7535859	7535994	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7535995	7536180	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7535995	7536180	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7536181	7536271	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7536272	7536358	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7536272	7536358	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7536359	7536490	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7536491	7536523	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7536491	7536523	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7536524	7536722	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7536723	7536817	1	-	2	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7536723	7536817	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7536818	7536894	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7536895	7536979	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7536895	7536979	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7536980	7537075	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7537076	7537162	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7537076	7537162	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7537163	7537295	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7537296	7537392	1	-	1	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7537296	7537392	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7537393	7537537	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7537538	7537626	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7537538	7537626	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7537627	7537759	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7537760	7537849	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7537760	7537849	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7537850	7537934	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7537935	7538063	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7537935	7538063	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7538064	7538153	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7538154	7538228	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7538154	7538228	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7538229	7538325	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7538326	7538415	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7538326	7538415	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7538416	7538497	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7538498	7538557	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7538498	7538557	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7538558	7538675	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7538676	7538801	1	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7538676	7538801	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7538802	7538939	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7538940	7539051	1	-	1	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7538940	7539051	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	intron	7539052	7539150	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	CDS	7539151	7539395	0.88	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	exon	7539151	7539395	.	-	.	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
Phchi.S4	AUGUSTUS	start_codon	7539393	7539395	.	-	0	transcript_id "Phchi.S4G123900.t1"; gene_id "Phchi.S4G123900"
# This transcript jg9549.t1 is derived from g6725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42415045	42419780	.	+	.	Phchi.S1G670800
Phchi.S1	AUGUSTUS	transcript	42415045	42419780	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42415045	42416337	0.54	+	1	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42415045	42416337	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42416338	42416419	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42416420	42416555	1	+	1	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42416420	42416555	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42416556	42416655	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42416656	42416820	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42416656	42416820	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42416821	42416986	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42416987	42417274	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42416987	42417274	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42417275	42417368	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42417369	42417502	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42417369	42417502	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42417503	42417630	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42417631	42417733	1	+	1	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42417631	42417733	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42417734	42417840	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42417841	42417963	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42417841	42417963	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42417964	42418089	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42418090	42418245	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42418090	42418245	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42418246	42418330	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42418331	42418388	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42418331	42418388	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42418389	42418470	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42418471	42418606	0.98	+	2	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42418471	42418606	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42418607	42418707	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42418708	42418883	0.93	+	1	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42418708	42418883	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42418884	42418998	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42418999	42419072	1	+	2	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42418999	42419072	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42419073	42419179	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42419180	42419275	1	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42419180	42419275	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42419276	42419369	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42419370	42419446	0.94	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42419370	42419446	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42419447	42419549	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42419550	42419633	0.93	+	1	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42419550	42419633	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	intron	42419634	42419719	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	CDS	42419720	42419780	1	+	1	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	exon	42419720	42419780	.	+	.	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
Phchi.S1	AUGUSTUS	stop_codon	42419781	42419783	.	+	0	transcript_id "Phchi.S1G670800.t1"; gene_id "Phchi.S1G670800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5485.t1 is derived from g2655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17077802	17079007	.	-	.	Phchi.S1G264400
Phchi.S1	AUGUSTUS	transcript	17077802	17079007	.	-	.	transcript_id "Phchi.S1G264400.t1"; gene_id "Phchi.S1G264400"
Phchi.S1	AUGUSTUS	stop_codon	17077799	17077801	.	-	0	transcript_id "Phchi.S1G264400.t1"; gene_id "Phchi.S1G264400"
Phchi.S1	AUGUSTUS	CDS	17077802	17079007	0.6	-	0	transcript_id "Phchi.S1G264400.t1"; gene_id "Phchi.S1G264400"
Phchi.S1	AUGUSTUS	exon	17077802	17079007	.	-	.	transcript_id "Phchi.S1G264400.t1"; gene_id "Phchi.S1G264400"
Phchi.S1	AUGUSTUS	start_codon	17079005	17079007	.	-	0	transcript_id "Phchi.S1G264400.t1"; gene_id "Phchi.S1G264400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15330.t1 is derived from g13798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18425541	18428063	.	+	.	Phchi.S3G264900
Phchi.S3	AUGUSTUS	transcript	18425541	18428063	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	start_codon	18425541	18425543	.	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18425541	18425714	0.79	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18425541	18425714	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18425715	18425884	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18425885	18425935	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18425885	18425935	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18425936	18426083	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18426084	18426167	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18426084	18426167	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18426168	18426257	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18426258	18426332	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18426258	18426332	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18426333	18426456	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18426457	18426510	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18426457	18426510	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18426511	18426602	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18426603	18426701	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18426603	18426701	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18426702	18426896	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18426897	18426935	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18426897	18426935	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18426936	18427021	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18427022	18427144	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18427022	18427144	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18427145	18427225	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18427226	18427303	1	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18427226	18427303	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18427304	18427429	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18427430	18427521	0.97	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18427430	18427521	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18427522	18427630	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18427631	18427678	0.97	+	1	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18427631	18427678	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18427679	18427771	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18427772	18427861	1	+	1	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18427772	18427861	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	intron	18427862	18427948	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	CDS	18427949	18428063	1	+	1	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	exon	18427949	18428063	.	+	.	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
Phchi.S3	AUGUSTUS	stop_codon	18428064	18428066	.	+	0	transcript_id "Phchi.S3G264900.t1"; gene_id "Phchi.S3G264900"
# This transcript jg4344.t2 is derived from g1513.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4345.t1 is derived from g1514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9873740	9875334	.	-	.	Phchi.S1G150400
Phchi.S1	AUGUSTUS	transcript	9873740	9875334	.	-	.	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	stop_codon	9873737	9873739	.	-	0	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	CDS	9873740	9873934	0.97	-	0	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	exon	9873740	9873934	.	-	.	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	intron	9873935	9874008	.	-	.	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	CDS	9874009	9875334	1	-	0	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	exon	9874009	9875334	.	-	.	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
Phchi.S1	AUGUSTUS	start_codon	9875332	9875334	.	-	0	transcript_id "Phchi.S1G150400.t1"; gene_id "Phchi.S1G150400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7368.t1 is derived from g4540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28797781	28798187	.	-	.	Phchi.S1G452700
Phchi.S1	AUGUSTUS	transcript	28797781	28798187	.	-	.	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	stop_codon	28797778	28797780	.	-	0	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	CDS	28797781	28798003	0.99	-	1	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	exon	28797781	28798003	.	-	.	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	intron	28798004	28798137	.	-	.	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	CDS	28798138	28798187	0.94	-	0	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	exon	28798138	28798187	.	-	.	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
Phchi.S1	AUGUSTUS	start_codon	28798185	28798187	.	-	0	transcript_id "Phchi.S1G452700.t1"; gene_id "Phchi.S1G452700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2901.t1 is derived from g70.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	397351	398109	.	+	.	Phchi.S1G006000
Phchi.S1	AUGUSTUS	transcript	397351	398109	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	start_codon	397351	397353	.	+	0	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	CDS	397351	397364	1	+	0	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	exon	397351	397364	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	intron	397365	397436	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	CDS	397437	397616	0.98	+	1	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	exon	397437	397616	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	intron	397617	397723	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	CDS	397724	397771	1	+	1	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	exon	397724	397771	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	intron	397772	397848	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	CDS	397849	397904	0.96	+	1	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	exon	397849	397904	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	intron	397905	397993	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	CDS	397994	398109	0.95	+	2	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	exon	397994	398109	.	+	.	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
Phchi.S1	AUGUSTUS	stop_codon	398110	398112	.	+	0	transcript_id "Phchi.S1G006000.t1"; gene_id "Phchi.S1G006000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11105.t1 is derived from g15155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4150083	4152899	.	-	.	Phchi.S4G068700
Phchi.S4	AUGUSTUS	transcript	4150083	4152899	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	stop_codon	4150080	4150082	.	-	0	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	CDS	4150083	4150786	1	-	2	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	exon	4150083	4150786	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	intron	4150787	4150870	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	CDS	4150871	4151017	1	-	2	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	exon	4150871	4151017	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	intron	4151018	4151105	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	CDS	4151106	4152669	0.99	-	0	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	exon	4151106	4152669	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	intron	4152670	4152848	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	CDS	4152849	4152899	0.6	-	0	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	exon	4152849	4152899	.	-	.	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
Phchi.S4	AUGUSTUS	start_codon	4152897	4152899	.	-	0	transcript_id "Phchi.S4G068700.t1"; gene_id "Phchi.S4G068700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3674.t1 is derived from g843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5140621	5141970	.	-	.	Phchi.S1G083300
Phchi.S1	AUGUSTUS	transcript	5140621	5141970	.	-	.	transcript_id "Phchi.S1G083300.t1"; gene_id "Phchi.S1G083300"
Phchi.S1	AUGUSTUS	stop_codon	5140618	5140620	.	-	0	transcript_id "Phchi.S1G083300.t1"; gene_id "Phchi.S1G083300"
Phchi.S1	AUGUSTUS	CDS	5140621	5141970	0.89	-	0	transcript_id "Phchi.S1G083300.t1"; gene_id "Phchi.S1G083300"
Phchi.S1	AUGUSTUS	exon	5140621	5141970	.	-	.	transcript_id "Phchi.S1G083300.t1"; gene_id "Phchi.S1G083300"
Phchi.S1	AUGUSTUS	start_codon	5141968	5141970	.	-	0	transcript_id "Phchi.S1G083300.t1"; gene_id "Phchi.S1G083300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3378.t1 is derived from g547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3247697	3249309	.	-	.	Phchi.S1G053700
Phchi.S1	AUGUSTUS	transcript	3247697	3249309	.	-	.	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	stop_codon	3247694	3247696	.	-	0	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	CDS	3247697	3248041	0.98	-	0	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	exon	3247697	3248041	.	-	.	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	intron	3248042	3248112	.	-	.	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	CDS	3248113	3249309	0.77	-	0	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	exon	3248113	3249309	.	-	.	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
Phchi.S1	AUGUSTUS	start_codon	3249307	3249309	.	-	0	transcript_id "Phchi.S1G053700.t1"; gene_id "Phchi.S1G053700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15824.t1 is derived from g14294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21592040	21592666	.	+	.	Phchi.S3G314300
Phchi.S3	AUGUSTUS	transcript	21592040	21592666	.	+	.	transcript_id "Phchi.S3G314300.t1"; gene_id "Phchi.S3G314300"
Phchi.S3	AUGUSTUS	start_codon	21592040	21592042	.	+	0	transcript_id "Phchi.S3G314300.t1"; gene_id "Phchi.S3G314300"
Phchi.S3	AUGUSTUS	CDS	21592040	21592666	0.71	+	0	transcript_id "Phchi.S3G314300.t1"; gene_id "Phchi.S3G314300"
Phchi.S3	AUGUSTUS	exon	21592040	21592666	.	+	.	transcript_id "Phchi.S3G314300.t1"; gene_id "Phchi.S3G314300"
Phchi.S3	AUGUSTUS	stop_codon	21592667	21592669	.	+	0	transcript_id "Phchi.S3G314300.t1"; gene_id "Phchi.S3G314300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1512.t1 is derived from g8431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1327134	1329370	.	+	.	Phchi.S5G012100
Phchi.S5	AUGUSTUS	transcript	1327134	1329370	.	+	.	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	start_codon	1327134	1327136	.	+	0	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	CDS	1327134	1328830	0.21	+	0	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	exon	1327134	1328830	.	+	.	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	intron	1328831	1328922	.	+	.	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	CDS	1328923	1329370	0.21	+	1	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	exon	1328923	1329370	.	+	.	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
Phchi.S5	AUGUSTUS	stop_codon	1329371	1329373	.	+	0	transcript_id "Phchi.S5G012100.t1"; gene_id "Phchi.S5G012100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13031.t1 is derived from g11496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3789359	3790935	.	-	.	Phchi.S3G035000
Phchi.S3	AUGUSTUS	transcript	3789359	3790935	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	stop_codon	3789356	3789358	.	-	0	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	CDS	3789359	3789385	0.81	-	0	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	exon	3789359	3789385	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	intron	3789386	3789527	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	CDS	3789528	3789548	0.54	-	0	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	exon	3789528	3789548	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	intron	3789549	3789789	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	CDS	3789790	3789899	0.54	-	2	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	exon	3789790	3789899	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	intron	3789900	3789976	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	CDS	3789977	3789996	0.69	-	1	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	exon	3789977	3789996	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	intron	3789997	3790073	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	CDS	3790074	3790136	0.68	-	1	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	exon	3790074	3790136	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	intron	3790137	3790333	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	CDS	3790334	3790935	0.71	-	0	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	exon	3790334	3790935	.	-	.	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
Phchi.S3	AUGUSTUS	start_codon	3790933	3790935	.	-	0	transcript_id "Phchi.S3G035000.t1"; gene_id "Phchi.S3G035000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10114.t1 is derived from g7290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45797149	45797451	.	-	.	Phchi.S1G727300
Phchi.S1	AUGUSTUS	transcript	45797149	45797451	.	-	.	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	stop_codon	45797146	45797148	.	-	0	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	CDS	45797149	45797238	0.98	-	0	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	exon	45797149	45797238	.	-	.	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	intron	45797239	45797334	.	-	.	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	CDS	45797335	45797451	0.65	-	0	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	exon	45797335	45797451	.	-	.	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
Phchi.S1	AUGUSTUS	start_codon	45797449	45797451	.	-	0	transcript_id "Phchi.S1G727300.t1"; gene_id "Phchi.S1G727300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10597.t1 is derived from g14647.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1131128	1133664	.	-	.	Phchi.S4G017900
Phchi.S4	AUGUSTUS	transcript	1131128	1133664	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	stop_codon	1131125	1131127	.	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1131128	1131694	1	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1131128	1131694	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1131695	1131796	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1131797	1131877	1	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1131797	1131877	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1131878	1132055	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132056	1132130	1	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132056	1132130	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132131	1132267	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132268	1132318	1	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132268	1132318	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132319	1132450	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132451	1132546	0.99	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132451	1132546	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132547	1132661	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132662	1132745	0.98	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132662	1132745	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132746	1132862	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132863	1132941	1	-	1	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132863	1132941	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132942	1133015	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133016	1133117	1	-	1	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133016	1133117	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133118	1133210	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133211	1133328	1	-	2	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133211	1133328	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133329	1133412	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133413	1133511	1	-	2	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133413	1133511	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133512	1133615	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133616	1133664	0.78	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133616	1133664	.	-	.	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	start_codon	1133662	1133664	.	-	0	transcript_id "Phchi.S4G017900.t1"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	transcript	1131128	1133636	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	stop_codon	1131125	1131127	.	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1131128	1131694	0.99	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1131128	1131694	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1131695	1131796	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1131797	1131877	0.99	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1131797	1131877	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1131878	1132055	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132056	1132130	1	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132056	1132130	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132131	1132267	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132268	1132318	1	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132268	1132318	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132319	1132450	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132451	1132546	0.98	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132451	1132546	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132547	1132661	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132662	1132745	0.96	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132662	1132745	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132746	1132862	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132863	1132941	1	-	1	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132863	1132941	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132942	1133015	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133016	1133117	1	-	1	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133016	1133117	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133118	1133210	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133211	1133328	1	-	2	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133211	1133328	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133329	1133408	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133409	1133511	0.89	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133409	1133511	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133512	1133615	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133616	1133636	0.8	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133616	1133636	.	-	.	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	start_codon	1133634	1133636	.	-	0	transcript_id "Phchi.S4G017900.t2"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	transcript	1132883	1133664	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	stop_codon	1132880	1132882	.	-	0	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1132883	1132925	0.96	-	1	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1132883	1132925	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1132926	1133015	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133016	1133117	1	-	1	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133016	1133117	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133118	1133210	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133211	1133328	1	-	2	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133211	1133328	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133329	1133412	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133413	1133511	0.99	-	2	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133413	1133511	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	intron	1133512	1133615	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	CDS	1133616	1133664	0.66	-	0	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	exon	1133616	1133664	.	-	.	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
Phchi.S4	AUGUSTUS	start_codon	1133662	1133664	.	-	0	transcript_id "Phchi.S4G017900.t3"; gene_id "Phchi.S4G017900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1645.t1 is derived from g8564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2175644	2179260	.	-	.	Phchi.S5G025400
Phchi.S5	AUGUSTUS	transcript	2175644	2179260	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	stop_codon	2175641	2175643	.	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2175644	2176006	0.98	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2175644	2176006	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	intron	2176007	2176102	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2176103	2176438	0.97	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2176103	2176438	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	intron	2176439	2176709	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2176710	2176988	1	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2176710	2176988	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	intron	2176989	2177240	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2177241	2177360	1	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2177241	2177360	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	intron	2177361	2177737	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2177738	2177800	1	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2177738	2177800	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	intron	2177801	2177895	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2177896	2178047	1	-	2	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2177896	2178047	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	intron	2178048	2179097	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	CDS	2179098	2179260	1	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	exon	2179098	2179260	.	-	.	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
Phchi.S5	AUGUSTUS	start_codon	2179258	2179260	.	-	0	transcript_id "Phchi.S5G025400.t1"; gene_id "Phchi.S5G025400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7463.t1 is derived from g4636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29401758	29403331	.	-	.	Phchi.S1G462200
Phchi.S1	AUGUSTUS	transcript	29401758	29403331	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	stop_codon	29401755	29401757	.	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29401758	29401846	1	-	2	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29401758	29401846	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29401847	29401939	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29401940	29402021	1	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29401940	29402021	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29402022	29402118	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29402119	29402169	1	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29402119	29402169	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29402170	29402250	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29402251	29402415	1	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29402251	29402415	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29402416	29402499	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29402500	29402589	1	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29402500	29402589	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29402590	29402677	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29402678	29402763	1	-	2	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29402678	29402763	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29402764	29402875	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29402876	29402987	1	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29402876	29402987	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	intron	29402988	29403187	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	CDS	29403188	29403331	1	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	exon	29403188	29403331	.	-	.	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
Phchi.S1	AUGUSTUS	start_codon	29403329	29403331	.	-	0	transcript_id "Phchi.S1G462200.t1"; gene_id "Phchi.S1G462200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11443.t1 is derived from g15493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6392352	6394028	.	+	.	Phchi.S4G102500
Phchi.S4	AUGUSTUS	transcript	6392352	6394028	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	start_codon	6392352	6392354	.	+	0	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6392352	6392391	0.98	+	0	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6392352	6392391	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6392392	6392498	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6392499	6392576	1	+	2	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6392499	6392576	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6392577	6392664	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6392665	6392766	1	+	2	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6392665	6392766	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6392767	6392908	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6392909	6392985	1	+	2	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6392909	6392985	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6392986	6393082	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6393083	6393212	1	+	0	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6393083	6393212	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6393213	6393296	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6393297	6393361	1	+	2	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6393297	6393361	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6393362	6393423	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6393424	6393496	1	+	0	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6393424	6393496	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6393497	6393583	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6393584	6393659	1	+	2	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6393584	6393659	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6393660	6393752	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6393753	6393834	1	+	1	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6393753	6393834	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	intron	6393835	6393911	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	CDS	6393912	6394028	1	+	0	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	exon	6393912	6394028	.	+	.	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
Phchi.S4	AUGUSTUS	stop_codon	6394029	6394031	.	+	0	transcript_id "Phchi.S4G102500.t1"; gene_id "Phchi.S4G102500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2727.t1 is derived from g9647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8460035	8461330	.	-	.	Phchi.S5G133600
Phchi.S5	AUGUSTUS	transcript	8460035	8461330	.	-	.	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	stop_codon	8460032	8460034	.	-	0	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	CDS	8460035	8460411	0.97	-	2	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	exon	8460035	8460411	.	-	.	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	intron	8460412	8460493	.	-	.	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	CDS	8460494	8460541	0.71	-	2	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	exon	8460494	8460541	.	-	.	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	intron	8460542	8460639	.	-	.	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	CDS	8460640	8461330	0.71	-	0	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	exon	8460640	8461330	.	-	.	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
Phchi.S5	AUGUSTUS	start_codon	8461328	8461330	.	-	0	transcript_id "Phchi.S5G133600.t1"; gene_id "Phchi.S5G133600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3543.t1 is derived from g712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4370481	4370954	.	-	.	Phchi.S1G070200
Phchi.S1	AUGUSTUS	transcript	4370481	4370954	.	-	.	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	stop_codon	4370478	4370480	.	-	0	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	CDS	4370481	4370718	0.98	-	1	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	exon	4370481	4370718	.	-	.	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	intron	4370719	4370835	.	-	.	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	CDS	4370836	4370954	0.97	-	0	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	exon	4370836	4370954	.	-	.	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
Phchi.S1	AUGUSTUS	start_codon	4370952	4370954	.	-	0	transcript_id "Phchi.S1G070200.t1"; gene_id "Phchi.S1G070200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10670.t1 is derived from g14720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1521737	1523079	.	+	.	Phchi.S4G025200
Phchi.S4	AUGUSTUS	transcript	1521737	1523079	.	+	.	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	start_codon	1521737	1521739	.	+	0	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	CDS	1521737	1522041	0.41	+	0	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	exon	1521737	1522041	.	+	.	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	intron	1522042	1522365	.	+	.	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	CDS	1522366	1522965	0.18	+	1	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	exon	1522366	1522965	.	+	.	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	intron	1522966	1523057	.	+	.	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	CDS	1523058	1523079	0.34	+	1	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	exon	1523058	1523079	.	+	.	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
Phchi.S4	AUGUSTUS	stop_codon	1523080	1523082	.	+	0	transcript_id "Phchi.S4G025200.t1"; gene_id "Phchi.S4G025200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11761.t1 is derived from g15813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8040401	8041074	.	+	.	Phchi.S4G134300
Phchi.S4	AUGUSTUS	transcript	8040401	8041074	.	+	.	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	start_codon	8040401	8040403	.	+	0	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	CDS	8040401	8040726	0.21	+	0	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	exon	8040401	8040726	.	+	.	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	intron	8040727	8040824	.	+	.	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	CDS	8040825	8041074	0.75	+	1	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	exon	8040825	8041074	.	+	.	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
Phchi.S4	AUGUSTUS	stop_codon	8041075	8041077	.	+	0	transcript_id "Phchi.S4G134300.t1"; gene_id "Phchi.S4G134300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1327.t1 is derived from g11110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9045707	9046570	.	+	.	Phchi.S6G128600
Phchi.S6	AUGUSTUS	transcript	9045707	9046570	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	start_codon	9045707	9045709	.	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	CDS	9045707	9045769	0.91	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	exon	9045707	9045769	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	intron	9045770	9045877	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	CDS	9045878	9045958	0.94	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	exon	9045878	9045958	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	intron	9045959	9046051	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	CDS	9046052	9046153	1	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	exon	9046052	9046153	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	intron	9046154	9046266	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	CDS	9046267	9046341	1	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	exon	9046267	9046341	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	intron	9046342	9046498	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	CDS	9046499	9046570	1	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	exon	9046499	9046570	.	+	.	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
Phchi.S6	AUGUSTUS	stop_codon	9046571	9046573	.	+	0	transcript_id "Phchi.S6G128600.t1"; gene_id "Phchi.S6G128600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2048.t1 is derived from g8968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4582937	4584391	.	+	.	Phchi.S5G065700
Phchi.S5	AUGUSTUS	transcript	4582937	4584391	.	+	.	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	start_codon	4582937	4582939	.	+	0	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	CDS	4582937	4584103	0.77	+	0	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	exon	4582937	4584103	.	+	.	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	intron	4584104	4584268	.	+	.	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	CDS	4584269	4584391	0.83	+	0	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	exon	4584269	4584391	.	+	.	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
Phchi.S5	AUGUSTUS	stop_codon	4584392	4584394	.	+	0	transcript_id "Phchi.S5G065700.t1"; gene_id "Phchi.S5G065700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1096.t1 is derived from g10879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7590933	7593222	.	-	.	Phchi.S6G105500
Phchi.S6	AUGUSTUS	transcript	7590933	7593222	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	stop_codon	7590930	7590932	.	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7590933	7591014	1	-	1	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7590933	7591014	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7591015	7591099	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7591100	7591224	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7591100	7591224	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7591225	7591337	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7591338	7591400	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7591338	7591400	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7591401	7591587	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7591588	7591638	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7591588	7591638	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7591639	7591843	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7591844	7591915	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7591844	7591915	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7591916	7592186	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7592187	7592294	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7592187	7592294	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7592295	7592432	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7592433	7592537	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7592433	7592537	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7592538	7592673	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7592674	7592703	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7592674	7592703	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7592704	7592825	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7592826	7592882	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7592826	7592882	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7592883	7592966	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7592967	7593028	1	-	2	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7592967	7593028	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	intron	7593029	7593149	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	CDS	7593150	7593222	1	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	exon	7593150	7593222	.	-	.	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
Phchi.S6	AUGUSTUS	start_codon	7593220	7593222	.	-	0	transcript_id "Phchi.S6G105500.t1"; gene_id "Phchi.S6G105500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6351.t1 is derived from g3523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22448821	22451073	.	+	.	Phchi.S1G351000
Phchi.S1	AUGUSTUS	transcript	22448821	22451073	.	+	.	transcript_id "Phchi.S1G351000.t1"; gene_id "Phchi.S1G351000"
Phchi.S1	AUGUSTUS	start_codon	22448821	22448823	.	+	0	transcript_id "Phchi.S1G351000.t1"; gene_id "Phchi.S1G351000"
Phchi.S1	AUGUSTUS	CDS	22448821	22451073	0.66	+	0	transcript_id "Phchi.S1G351000.t1"; gene_id "Phchi.S1G351000"
Phchi.S1	AUGUSTUS	exon	22448821	22451073	.	+	.	transcript_id "Phchi.S1G351000.t1"; gene_id "Phchi.S1G351000"
Phchi.S1	AUGUSTUS	stop_codon	22451074	22451076	.	+	0	transcript_id "Phchi.S1G351000.t1"; gene_id "Phchi.S1G351000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1071.t1 is derived from g10854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7432180	7433343	.	-	.	Phchi.S6G103000
Phchi.S6	AUGUSTUS	transcript	7432180	7433343	.	-	.	transcript_id "Phchi.S6G103000.t1"; gene_id "Phchi.S6G103000"
Phchi.S6	AUGUSTUS	stop_codon	7432177	7432179	.	-	0	transcript_id "Phchi.S6G103000.t1"; gene_id "Phchi.S6G103000"
Phchi.S6	AUGUSTUS	CDS	7432180	7433343	0.78	-	0	transcript_id "Phchi.S6G103000.t1"; gene_id "Phchi.S6G103000"
Phchi.S6	AUGUSTUS	exon	7432180	7433343	.	-	.	transcript_id "Phchi.S6G103000.t1"; gene_id "Phchi.S6G103000"
Phchi.S6	AUGUSTUS	start_codon	7433341	7433343	.	-	0	transcript_id "Phchi.S6G103000.t1"; gene_id "Phchi.S6G103000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3540.t1 is derived from g709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4360595	4361296	.	-	.	Phchi.S1G069900
Phchi.S1	AUGUSTUS	transcript	4360595	4361296	.	-	.	transcript_id "Phchi.S1G069900.t1"; gene_id "Phchi.S1G069900"
Phchi.S1	AUGUSTUS	stop_codon	4360592	4360594	.	-	0	transcript_id "Phchi.S1G069900.t1"; gene_id "Phchi.S1G069900"
Phchi.S1	AUGUSTUS	CDS	4360595	4361296	0.83	-	0	transcript_id "Phchi.S1G069900.t1"; gene_id "Phchi.S1G069900"
Phchi.S1	AUGUSTUS	exon	4360595	4361296	.	-	.	transcript_id "Phchi.S1G069900.t1"; gene_id "Phchi.S1G069900"
Phchi.S1	AUGUSTUS	start_codon	4361294	4361296	.	-	0	transcript_id "Phchi.S1G069900.t1"; gene_id "Phchi.S1G069900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7145.t1 is derived from g4317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27166967	27171219	.	+	.	Phchi.S1G430400
Phchi.S1	AUGUSTUS	transcript	27166967	27171219	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	start_codon	27166967	27166969	.	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27166967	27167385	0.99	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27166967	27167385	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27167386	27167471	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27167472	27168110	0.98	+	1	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27167472	27168110	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27168111	27168204	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27168205	27168490	1	+	1	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27168205	27168490	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27168491	27168580	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27168581	27168691	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27168581	27168691	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27168692	27168793	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27168794	27168916	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27168794	27168916	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27168917	27168999	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27169000	27169110	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27169000	27169110	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27169111	27169205	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27169206	27169255	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27169206	27169255	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27169256	27169339	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27169340	27169415	0.75	+	1	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27169340	27169415	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27169416	27169520	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27169521	27169688	0.82	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27169521	27169688	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27169689	27169759	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27169760	27169828	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27169760	27169828	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27169829	27169899	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27169900	27170022	0.99	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27169900	27170022	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27170023	27170145	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27170146	27170219	0.95	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27170146	27170219	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27170220	27170321	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27170322	27170394	0.99	+	1	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27170322	27170394	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27170395	27170486	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27170487	27170588	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27170487	27170588	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27170589	27170660	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27170661	27170769	1	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27170661	27170769	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27170770	27170853	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27170854	27170938	0.59	+	2	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27170854	27170938	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	intron	27170939	27171041	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	CDS	27171042	27171219	0.57	+	1	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	exon	27171042	27171219	.	+	.	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
Phchi.S1	AUGUSTUS	stop_codon	27171220	27171222	.	+	0	transcript_id "Phchi.S1G430400.t1"; gene_id "Phchi.S1G430400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8085.t1 is derived from g5260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32875641	32881994	.	-	.	Phchi.S1G524400
Phchi.S1	AUGUSTUS	transcript	32875641	32881994	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	stop_codon	32875638	32875640	.	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32875641	32877121	0.77	-	2	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32875641	32877121	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32877122	32877216	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32877217	32877355	1	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32877217	32877355	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32877356	32877456	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32877457	32877687	1	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32877457	32877687	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32877688	32877832	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32877833	32878042	0.96	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32877833	32878042	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878043	32878149	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32878150	32878365	0.97	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32878150	32878365	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878366	32878516	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32878517	32878621	1	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32878517	32878621	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878622	32878712	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32878713	32878893	0.99	-	1	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32878713	32878893	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878894	32879012	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879013	32879102	0.99	-	1	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879013	32879102	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879103	32879202	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879203	32879636	0.94	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879203	32879636	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879637	32879733	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879734	32879759	1	-	2	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879734	32879759	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879760	32879904	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879905	32880100	1	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879905	32880100	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32880101	32880185	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32880186	32880439	1	-	2	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32880186	32880439	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32880440	32880587	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32880588	32881266	0.95	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32880588	32881266	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32881267	32881344	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32881345	32881737	1	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32881345	32881737	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32881738	32881841	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32881842	32881994	0.99	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32881842	32881994	.	-	.	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	start_codon	32881992	32881994	.	-	0	transcript_id "Phchi.S1G524400.t1"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	transcript	32875641	32881994	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	stop_codon	32875638	32875640	.	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32875641	32877121	0.68	-	2	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32875641	32877121	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32877122	32877216	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32877217	32877355	1	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32877217	32877355	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32877356	32877456	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32877457	32877687	1	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32877457	32877687	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32877688	32877832	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32877833	32878042	0.98	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32877833	32878042	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878043	32878149	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32878150	32878365	0.95	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32878150	32878365	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878366	32878516	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32878517	32878621	1	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32878517	32878621	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878622	32878712	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32878713	32878893	1	-	1	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32878713	32878893	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32878894	32879012	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879013	32879102	1	-	1	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879013	32879102	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879103	32879202	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879203	32879636	0.93	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879203	32879636	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879637	32879733	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879734	32879759	1	-	2	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879734	32879759	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879760	32879904	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32879905	32879988	0.94	-	2	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32879905	32879988	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32879989	32880088	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32880089	32880100	0.94	-	2	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32880089	32880100	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32880101	32880298	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32880299	32880439	0.98	-	2	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32880299	32880439	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32880440	32880587	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32880588	32881266	0.99	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32880588	32881266	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32881267	32881344	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32881345	32881737	0.99	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32881345	32881737	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	intron	32881738	32881841	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	CDS	32881842	32881994	1	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	exon	32881842	32881994	.	-	.	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
Phchi.S1	AUGUSTUS	start_codon	32881992	32881994	.	-	0	transcript_id "Phchi.S1G524400.t2"; gene_id "Phchi.S1G524400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12793.t1 is derived from g11258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2414330	2415883	.	-	.	Phchi.S3G011200
Phchi.S3	AUGUSTUS	transcript	2414330	2415883	.	-	.	transcript_id "Phchi.S3G011200.t1"; gene_id "Phchi.S3G011200"
Phchi.S3	AUGUSTUS	stop_codon	2414327	2414329	.	-	0	transcript_id "Phchi.S3G011200.t1"; gene_id "Phchi.S3G011200"
Phchi.S3	AUGUSTUS	CDS	2414330	2415883	0.79	-	0	transcript_id "Phchi.S3G011200.t1"; gene_id "Phchi.S3G011200"
Phchi.S3	AUGUSTUS	exon	2414330	2415883	.	-	.	transcript_id "Phchi.S3G011200.t1"; gene_id "Phchi.S3G011200"
Phchi.S3	AUGUSTUS	start_codon	2415881	2415883	.	-	0	transcript_id "Phchi.S3G011200.t1"; gene_id "Phchi.S3G011200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7635.t1 is derived from g4809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30337303	30338181	.	-	.	Phchi.S1G479400
Phchi.S1	AUGUSTUS	transcript	30337303	30338181	.	-	.	transcript_id "Phchi.S1G479400.t1"; gene_id "Phchi.S1G479400"
Phchi.S1	AUGUSTUS	stop_codon	30337300	30337302	.	-	0	transcript_id "Phchi.S1G479400.t1"; gene_id "Phchi.S1G479400"
Phchi.S1	AUGUSTUS	CDS	30337303	30338181	0.42	-	0	transcript_id "Phchi.S1G479400.t1"; gene_id "Phchi.S1G479400"
Phchi.S1	AUGUSTUS	exon	30337303	30338181	.	-	.	transcript_id "Phchi.S1G479400.t1"; gene_id "Phchi.S1G479400"
Phchi.S1	AUGUSTUS	start_codon	30338179	30338181	.	-	0	transcript_id "Phchi.S1G479400.t1"; gene_id "Phchi.S1G479400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7706.t1 is derived from g4880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30716809	30718427	.	-	.	Phchi.S1G486500
Phchi.S1	AUGUSTUS	transcript	30716809	30718427	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	stop_codon	30716806	30716808	.	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	CDS	30716809	30717093	0.91	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	exon	30716809	30717093	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	intron	30717094	30717175	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	CDS	30717176	30717301	1	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	exon	30717176	30717301	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	intron	30717302	30717389	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	CDS	30717390	30717521	1	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	exon	30717390	30717521	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	intron	30717522	30717603	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	CDS	30717604	30717689	1	-	2	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	exon	30717604	30717689	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	intron	30717690	30717938	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	CDS	30717939	30718131	1	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	exon	30717939	30718131	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	intron	30718132	30718244	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	CDS	30718245	30718427	0.94	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	exon	30718245	30718427	.	-	.	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
Phchi.S1	AUGUSTUS	start_codon	30718425	30718427	.	-	0	transcript_id "Phchi.S1G486500.t1"; gene_id "Phchi.S1G486500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4681.t1 is derived from g1851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11824318	11826589	.	+	.	Phchi.S1G184000
Phchi.S1	AUGUSTUS	transcript	11824318	11826589	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	start_codon	11824318	11824320	.	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11824318	11824479	0.92	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11824318	11824479	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11824480	11824564	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11824565	11825039	0.47	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11824565	11825039	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825040	11825132	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11825133	11825257	1	+	2	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11825133	11825257	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825258	11825342	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11825343	11825560	0.99	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11825343	11825560	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825561	11825645	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11825646	11825884	0.93	+	1	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11825646	11825884	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825885	11826000	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11826001	11826200	1	+	2	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11826001	11826200	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11826201	11826315	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11826316	11826441	1	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11826316	11826441	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11826442	11826508	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11826509	11826589	1	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11826509	11826589	.	+	.	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	stop_codon	11826590	11826592	.	+	0	transcript_id "Phchi.S1G184000.t1"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	transcript	11824995	11826589	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	start_codon	11824995	11824997	.	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11824995	11825039	0.99	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11824995	11825039	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825040	11825132	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11825133	11825210	0.95	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11825133	11825210	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825211	11825342	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11825343	11825560	0.62	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11825343	11825560	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825561	11825645	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11825646	11825884	0.88	+	1	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11825646	11825884	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11825885	11826000	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11826001	11826200	1	+	2	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11826001	11826200	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11826201	11826315	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11826316	11826441	1	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11826316	11826441	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	intron	11826442	11826508	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	CDS	11826509	11826589	1	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	exon	11826509	11826589	.	+	.	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
Phchi.S1	AUGUSTUS	stop_codon	11826590	11826592	.	+	0	transcript_id "Phchi.S1G184000.t2"; gene_id "Phchi.S1G184000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2012.t1 is derived from g8932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4449230	4451641	.	+	.	Phchi.S5G062100
Phchi.S5	AUGUSTUS	transcript	4449230	4451641	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	start_codon	4449230	4449232	.	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4449230	4449319	1	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4449230	4449319	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4449320	4449441	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4449442	4449951	0.84	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4449442	4449951	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4449952	4450059	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450060	4450152	0.98	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450060	4450152	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450153	4450273	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450274	4450381	1	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450274	4450381	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450382	4450486	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450487	4450600	1	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450487	4450600	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450601	4450719	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450720	4450812	1	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450720	4450812	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450813	4450978	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450979	4451122	0.97	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450979	4451122	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4451123	4451223	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4451224	4451331	1	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4451224	4451331	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4451332	4451417	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4451418	4451469	1	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4451418	4451469	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4451470	4451615	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4451616	4451641	1	+	2	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4451616	4451641	.	+	.	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	stop_codon	4451642	4451644	.	+	0	transcript_id "Phchi.S5G062100.t1"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	transcript	4449230	4451641	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	start_codon	4449230	4449232	.	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4449230	4449319	1	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4449230	4449319	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4449320	4449441	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4449442	4449951	0.85	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4449442	4449951	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4449952	4450059	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450060	4450152	0.96	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450060	4450152	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450153	4450273	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450274	4450381	1	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450274	4450381	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450382	4450486	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450487	4450600	0.99	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450487	4450600	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450601	4450719	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450720	4450774	0.48	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450720	4450774	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450775	4450861	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450862	4450890	0.91	+	2	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450862	4450890	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4450891	4450978	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4450979	4451122	1	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4450979	4451122	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4451123	4451223	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4451224	4451331	1	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4451224	4451331	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4451332	4451417	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4451418	4451469	1	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4451418	4451469	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	intron	4451470	4451615	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	CDS	4451616	4451641	1	+	2	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	exon	4451616	4451641	.	+	.	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
Phchi.S5	AUGUSTUS	stop_codon	4451642	4451644	.	+	0	transcript_id "Phchi.S5G062100.t2"; gene_id "Phchi.S5G062100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10139.t1 is derived from g7315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45949404	45949661	.	+	.	Phchi.S1G729800
Phchi.S1	AUGUSTUS	transcript	45949404	45949661	.	+	.	transcript_id "Phchi.S1G729800.t1"; gene_id "Phchi.S1G729800"
Phchi.S1	AUGUSTUS	start_codon	45949404	45949406	.	+	0	transcript_id "Phchi.S1G729800.t1"; gene_id "Phchi.S1G729800"
Phchi.S1	AUGUSTUS	CDS	45949404	45949661	1	+	0	transcript_id "Phchi.S1G729800.t1"; gene_id "Phchi.S1G729800"
Phchi.S1	AUGUSTUS	exon	45949404	45949661	.	+	.	transcript_id "Phchi.S1G729800.t1"; gene_id "Phchi.S1G729800"
Phchi.S1	AUGUSTUS	stop_codon	45949662	45949664	.	+	0	transcript_id "Phchi.S1G729800.t1"; gene_id "Phchi.S1G729800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg651.t1 is derived from g10433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4582301	4584816	.	-	.	Phchi.S6G061000
Phchi.S6	AUGUSTUS	transcript	4582301	4584816	.	-	.	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	stop_codon	4582298	4582300	.	-	0	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	CDS	4582301	4582310	0.97	-	1	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	exon	4582301	4582310	.	-	.	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	intron	4582311	4582537	.	-	.	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	CDS	4582538	4584816	0.78	-	0	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	exon	4582538	4584816	.	-	.	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
Phchi.S6	AUGUSTUS	start_codon	4584814	4584816	.	-	0	transcript_id "Phchi.S6G061000.t1"; gene_id "Phchi.S6G061000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3658.t1 is derived from g827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5003123	5003859	.	+	.	Phchi.S1G081700
Phchi.S1	AUGUSTUS	transcript	5003123	5003859	.	+	.	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	start_codon	5003123	5003125	.	+	0	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	CDS	5003123	5003230	0.76	+	0	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	exon	5003123	5003230	.	+	.	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	intron	5003231	5003372	.	+	.	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	CDS	5003373	5003506	0.98	+	0	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	exon	5003373	5003506	.	+	.	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	intron	5003507	5003633	.	+	.	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	CDS	5003634	5003859	0.99	+	1	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	exon	5003634	5003859	.	+	.	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
Phchi.S1	AUGUSTUS	stop_codon	5003860	5003862	.	+	0	transcript_id "Phchi.S1G081700.t1"; gene_id "Phchi.S1G081700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10606.t1 is derived from g14656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1164659	1167137	.	+	.	Phchi.S4G018800
Phchi.S4	AUGUSTUS	transcript	1164659	1167137	.	+	.	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	start_codon	1164659	1164661	.	+	0	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	CDS	1164659	1164869	0.9	+	0	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	exon	1164659	1164869	.	+	.	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	intron	1164870	1164949	.	+	.	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	CDS	1164950	1166163	0.91	+	2	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	exon	1164950	1166163	.	+	.	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	intron	1166164	1166255	.	+	.	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	CDS	1166256	1167137	0.66	+	0	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	exon	1166256	1167137	.	+	.	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
Phchi.S4	AUGUSTUS	stop_codon	1167138	1167140	.	+	0	transcript_id "Phchi.S4G018800.t1"; gene_id "Phchi.S4G018800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14748.t1 is derived from g13216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14526690	14529965	.	+	.	Phchi.S3G206700
Phchi.S3	AUGUSTUS	transcript	14526690	14529965	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	start_codon	14526690	14526692	.	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14526690	14526984	0.63	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14526690	14526984	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14526985	14527067	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14527068	14527183	1	+	2	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14527068	14527183	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14527184	14527288	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14527289	14527411	1	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14527289	14527411	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14527412	14527491	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14527492	14527677	1	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14527492	14527677	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14527678	14527764	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14527765	14527980	1	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14527765	14527980	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14527981	14528087	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14528088	14528305	1	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14528088	14528305	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14528306	14528388	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14528389	14528464	1	+	1	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14528389	14528464	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14528465	14528561	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14528562	14528651	1	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14528562	14528651	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	intron	14528652	14528777	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	CDS	14528778	14529965	1	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	exon	14528778	14529965	.	+	.	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
Phchi.S3	AUGUSTUS	stop_codon	14529966	14529968	.	+	0	transcript_id "Phchi.S3G206700.t1"; gene_id "Phchi.S3G206700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12743.t1 is derived from g11208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1549937	1550546	.	+	.	Phchi.S3G006200
Phchi.S3	AUGUSTUS	transcript	1549937	1550546	.	+	.	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	start_codon	1549937	1549939	.	+	0	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	CDS	1549937	1550087	0.88	+	0	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	exon	1549937	1550087	.	+	.	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	intron	1550088	1550200	.	+	.	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	CDS	1550201	1550293	0.84	+	2	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	exon	1550201	1550293	.	+	.	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	intron	1550294	1550379	.	+	.	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	CDS	1550380	1550546	0.38	+	2	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	exon	1550380	1550546	.	+	.	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
Phchi.S3	AUGUSTUS	stop_codon	1550547	1550549	.	+	0	transcript_id "Phchi.S3G006200.t1"; gene_id "Phchi.S3G006200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3258.t1 is derived from g427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2543365	2547097	.	+	.	Phchi.S1G041700
Phchi.S1	AUGUSTUS	transcript	2543365	2547097	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	start_codon	2543365	2543367	.	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2543365	2543556	0.62	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2543365	2543556	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2543557	2543633	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2543634	2543849	0.99	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2543634	2543849	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2543850	2543939	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2543940	2544085	1	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2543940	2544085	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2544086	2544188	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2544189	2544267	1	+	1	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2544189	2544267	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2544268	2544347	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2544348	2544417	1	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2544348	2544417	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2544418	2544604	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2544605	2544849	0.92	+	2	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2544605	2544849	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2544850	2545023	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2545024	2546161	0.77	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2545024	2546161	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2546162	2546239	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2546240	2546334	1	+	2	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2546240	2546334	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2546335	2546424	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2546425	2546928	0.97	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2546425	2546928	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	intron	2546929	2547022	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	CDS	2547023	2547097	0.98	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	exon	2547023	2547097	.	+	.	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
Phchi.S1	AUGUSTUS	stop_codon	2547098	2547100	.	+	0	transcript_id "Phchi.S1G041700.t1"; gene_id "Phchi.S1G041700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10051.t1 is derived from g7227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45443805	45445340	.	-	.	Phchi.S1G721000
Phchi.S1	AUGUSTUS	transcript	45443805	45445340	.	-	.	transcript_id "Phchi.S1G721000.t1"; gene_id "Phchi.S1G721000"
Phchi.S1	AUGUSTUS	stop_codon	45443802	45443804	.	-	0	transcript_id "Phchi.S1G721000.t1"; gene_id "Phchi.S1G721000"
Phchi.S1	AUGUSTUS	CDS	45443805	45445340	0.21	-	0	transcript_id "Phchi.S1G721000.t1"; gene_id "Phchi.S1G721000"
Phchi.S1	AUGUSTUS	exon	45443805	45445340	.	-	.	transcript_id "Phchi.S1G721000.t1"; gene_id "Phchi.S1G721000"
Phchi.S1	AUGUSTUS	start_codon	45445338	45445340	.	-	0	transcript_id "Phchi.S1G721000.t1"; gene_id "Phchi.S1G721000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg78.t1 is derived from g9860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	406224	407847	.	+	.	Phchi.S6G003700
Phchi.S6	AUGUSTUS	transcript	406224	407847	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	start_codon	406224	406226	.	+	0	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	CDS	406224	406267	0.85	+	0	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	exon	406224	406267	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	intron	406268	406381	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	CDS	406382	406461	0.98	+	1	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	exon	406382	406461	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	intron	406462	406628	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	CDS	406629	407022	0.78	+	2	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	exon	406629	407022	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	intron	407023	407120	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	CDS	407121	407448	0.98	+	1	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	exon	407121	407448	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	intron	407449	407538	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	CDS	407539	407847	1	+	0	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	exon	407539	407847	.	+	.	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
Phchi.S6	AUGUSTUS	stop_codon	407848	407850	.	+	0	transcript_id "Phchi.S6G003700.t1"; gene_id "Phchi.S6G003700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2729.t1 is derived from g9649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8468122	8469686	.	-	.	Phchi.S5G133800
Phchi.S5	AUGUSTUS	transcript	8468122	8469686	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	stop_codon	8468119	8468121	.	-	0	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8468122	8468246	1	-	2	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8468122	8468246	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	intron	8468247	8468332	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8468333	8468433	1	-	1	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8468333	8468433	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	intron	8468434	8468517	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8468518	8468621	1	-	0	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8468518	8468621	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	intron	8468622	8468750	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8468751	8468885	1	-	0	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8468751	8468885	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	intron	8468886	8469013	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8469014	8469120	1	-	2	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8469014	8469120	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	intron	8469121	8469308	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8469309	8469438	1	-	0	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8469309	8469438	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	intron	8469439	8469563	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	CDS	8469564	8469686	0.91	-	0	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	exon	8469564	8469686	.	-	.	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
Phchi.S5	AUGUSTUS	start_codon	8469684	8469686	.	-	0	transcript_id "Phchi.S5G133800.t1"; gene_id "Phchi.S5G133800"
# This transcript jg10240.t2 is derived from g7416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10241.t1 is derived from g7417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46552916	46557984	.	+	.	Phchi.S1G740000
Phchi.S1	AUGUSTUS	transcript	46552916	46557984	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	start_codon	46552916	46552918	.	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46552916	46553044	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46552916	46553044	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46553045	46553135	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46553136	46553199	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46553136	46553199	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46553200	46553468	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46553469	46553573	1	+	2	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46553469	46553573	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46553574	46553726	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46553727	46553828	1	+	2	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46553727	46553828	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46553829	46554004	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46554005	46554055	1	+	2	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46554005	46554055	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46554056	46554136	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46554137	46554198	1	+	2	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46554137	46554198	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46554199	46554300	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46554301	46554391	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46554301	46554391	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46554392	46554849	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46554850	46554914	1	+	2	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46554850	46554914	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46554915	46555007	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46555008	46555202	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46555008	46555202	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46555203	46555295	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46555296	46555415	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46555296	46555415	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46555416	46555642	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46555643	46555713	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46555643	46555713	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46555714	46555870	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46555871	46556096	1	+	1	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46555871	46556096	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46556097	46556253	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46556254	46556304	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46556254	46556304	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46556305	46556461	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46556462	46556690	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46556462	46556690	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46556691	46556858	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46556859	46556998	1	+	2	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46556859	46556998	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46556999	46557105	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46557106	46557230	1	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46557106	46557230	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46557231	46557311	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46557312	46557408	0.46	+	1	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46557312	46557408	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46557409	46557659	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46557660	46557692	0.28	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46557660	46557692	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46557693	46557784	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46557785	46557814	0.99	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46557785	46557814	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	intron	46557815	46557897	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	CDS	46557898	46557984	0.99	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	exon	46557898	46557984	.	+	.	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
Phchi.S1	AUGUSTUS	stop_codon	46557985	46557987	.	+	0	transcript_id "Phchi.S1G740000.t1"; gene_id "Phchi.S1G740000"
# This transcript jg13244.t2 is derived from g11709.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13245.t1 is derived from g11710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4895962	4896282	.	+	.	Phchi.S3G056400
Phchi.S3	AUGUSTUS	transcript	4895962	4896282	.	+	.	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	start_codon	4895962	4895964	.	+	0	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	CDS	4895962	4896151	1	+	0	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	exon	4895962	4896151	.	+	.	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	intron	4896152	4896247	.	+	.	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	CDS	4896248	4896282	1	+	2	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	exon	4896248	4896282	.	+	.	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
Phchi.S3	AUGUSTUS	stop_codon	4896283	4896285	.	+	0	transcript_id "Phchi.S3G056400.t1"; gene_id "Phchi.S3G056400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12727.t1 is derived from g11192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1416534	1418591	.	+	.	Phchi.S3G004600
Phchi.S3	AUGUSTUS	transcript	1416534	1418591	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	start_codon	1416534	1416536	.	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1416534	1416620	1	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1416534	1416620	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1416621	1416742	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1416743	1416843	1	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1416743	1416843	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1416844	1416930	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1416931	1417031	1	+	1	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1416931	1417031	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1417032	1417114	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1417115	1417181	1	+	2	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1417115	1417181	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1417182	1417373	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1417374	1417473	1	+	1	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1417374	1417473	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1417474	1417645	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1417646	1417762	1	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1417646	1417762	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1417763	1417853	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1417854	1417991	1	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1417854	1417991	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1417992	1418093	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1418094	1418178	1	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1418094	1418178	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1418179	1418260	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1418261	1418310	1	+	2	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1418261	1418310	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	intron	1418311	1418387	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	CDS	1418388	1418591	1	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	exon	1418388	1418591	.	+	.	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
Phchi.S3	AUGUSTUS	stop_codon	1418592	1418594	.	+	0	transcript_id "Phchi.S3G004600.t1"; gene_id "Phchi.S3G004600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10334.t1 is derived from g7510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47226165	47228256	.	-	.	Phchi.S1G749300
Phchi.S1	AUGUSTUS	transcript	47226165	47228256	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	stop_codon	47226162	47226164	.	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47226165	47226562	1	-	2	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47226165	47226562	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47226563	47226645	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47226646	47226700	0.94	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47226646	47226700	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47226701	47226861	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47226862	47226930	0.97	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47226862	47226930	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47226931	47227004	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47227005	47227109	1	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47227005	47227109	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47227110	47227182	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47227183	47227308	1	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47227183	47227308	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47227309	47227377	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47227378	47227501	1	-	1	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47227378	47227501	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47227502	47227635	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47227636	47227689	1	-	1	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47227636	47227689	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47227690	47227877	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47227878	47228081	0.82	-	1	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47227878	47228081	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	intron	47228082	47228173	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	CDS	47228174	47228256	1	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	exon	47228174	47228256	.	-	.	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
Phchi.S1	AUGUSTUS	start_codon	47228254	47228256	.	-	0	transcript_id "Phchi.S1G749300.t1"; gene_id "Phchi.S1G749300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2621.t1 is derived from g9541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7803872	7806647	.	+	.	Phchi.S5G123000
Phchi.S5	AUGUSTUS	transcript	7803872	7806647	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	start_codon	7803872	7803874	.	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7803872	7804099	0.72	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7803872	7804099	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7804100	7804198	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7804199	7804616	0.85	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7804199	7804616	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7804617	7804868	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7804869	7804909	0.99	+	2	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7804869	7804909	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7804910	7805004	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7805005	7805067	1	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7805005	7805067	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7805068	7805163	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7805164	7805238	1	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7805164	7805238	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7805239	7805342	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7805343	7805563	1	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7805343	7805563	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7805564	7805649	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7805650	7805722	1	+	1	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7805650	7805722	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7805723	7805804	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7805805	7806089	1	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7805805	7806089	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7806090	7806182	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7806183	7806326	1	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7806183	7806326	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7806327	7806415	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7806416	7806466	1	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7806416	7806466	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	intron	7806467	7806566	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	CDS	7806567	7806647	0.97	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	exon	7806567	7806647	.	+	.	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
Phchi.S5	AUGUSTUS	stop_codon	7806648	7806650	.	+	0	transcript_id "Phchi.S5G123000.t1"; gene_id "Phchi.S5G123000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11365.t1 is derived from g15415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5785923	5789011	.	+	.	Phchi.S4G094700
Phchi.S4	AUGUSTUS	transcript	5785923	5789011	.	+	.	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	start_codon	5785923	5785925	.	+	0	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	CDS	5785923	5786303	0.24	+	0	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	exon	5785923	5786303	.	+	.	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	intron	5786304	5786585	.	+	.	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	CDS	5786586	5788798	0.06	+	0	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	exon	5786586	5788798	.	+	.	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	intron	5788799	5789004	.	+	.	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	CDS	5789005	5789011	0.4	+	1	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	exon	5789005	5789011	.	+	.	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
Phchi.S4	AUGUSTUS	stop_codon	5789012	5789014	.	+	0	transcript_id "Phchi.S4G094700.t1"; gene_id "Phchi.S4G094700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13725.t1 is derived from g12192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8549694	8550350	.	+	.	Phchi.S3G104400
Phchi.S3	AUGUSTUS	transcript	8549694	8550350	.	+	.	transcript_id "Phchi.S3G104400.t1"; gene_id "Phchi.S3G104400"
Phchi.S3	AUGUSTUS	start_codon	8549694	8549696	.	+	0	transcript_id "Phchi.S3G104400.t1"; gene_id "Phchi.S3G104400"
Phchi.S3	AUGUSTUS	CDS	8549694	8550350	1	+	0	transcript_id "Phchi.S3G104400.t1"; gene_id "Phchi.S3G104400"
Phchi.S3	AUGUSTUS	exon	8549694	8550350	.	+	.	transcript_id "Phchi.S3G104400.t1"; gene_id "Phchi.S3G104400"
Phchi.S3	AUGUSTUS	stop_codon	8550351	8550353	.	+	0	transcript_id "Phchi.S3G104400.t1"; gene_id "Phchi.S3G104400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12326.t1 is derived from g8002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10979783	10983516	.	+	.	Phchi.S2G040600
Phchi.S2	AUGUSTUS	transcript	10979783	10983516	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	start_codon	10979783	10979785	.	+	0	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	CDS	10979783	10981341	0.45	+	0	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	exon	10979783	10981341	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	intron	10981342	10981463	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	CDS	10981464	10981831	0.54	+	1	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	exon	10981464	10981831	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	intron	10981832	10981938	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	CDS	10981939	10982761	0.98	+	2	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	exon	10981939	10982761	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	intron	10982762	10982876	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	CDS	10982877	10983170	0.98	+	1	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	exon	10982877	10983170	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	intron	10983171	10983296	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	CDS	10983297	10983516	1	+	1	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	exon	10983297	10983516	.	+	.	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
Phchi.S2	AUGUSTUS	stop_codon	10983517	10983519	.	+	0	transcript_id "Phchi.S2G040600.t1"; gene_id "Phchi.S2G040600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4216.t1 is derived from g1385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8963558	8964549	.	-	.	Phchi.S1G137500
Phchi.S1	AUGUSTUS	transcript	8963558	8964549	.	-	.	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	stop_codon	8963555	8963557	.	-	0	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	CDS	8963558	8964132	0.25	-	2	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	exon	8963558	8964132	.	-	.	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	intron	8964133	8964413	.	-	.	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	CDS	8964414	8964549	0.71	-	0	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	exon	8964414	8964549	.	-	.	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
Phchi.S1	AUGUSTUS	start_codon	8964547	8964549	.	-	0	transcript_id "Phchi.S1G137500.t1"; gene_id "Phchi.S1G137500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10138.t1 is derived from g7314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45945089	45946172	.	+	.	Phchi.S1G729700
Phchi.S1	AUGUSTUS	transcript	45945089	45946172	.	+	.	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	start_codon	45945089	45945091	.	+	0	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	CDS	45945089	45945268	0.81	+	0	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	exon	45945089	45945268	.	+	.	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	intron	45945269	45945365	.	+	.	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	CDS	45945366	45945495	0.93	+	0	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	exon	45945366	45945495	.	+	.	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	intron	45945496	45945627	.	+	.	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	CDS	45945628	45946172	0.67	+	2	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	exon	45945628	45946172	.	+	.	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
Phchi.S1	AUGUSTUS	stop_codon	45946173	45946175	.	+	0	transcript_id "Phchi.S1G729700.t1"; gene_id "Phchi.S1G729700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg923.t1 is derived from g10705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6459973	6463724	.	+	.	Phchi.S6G088200
Phchi.S6	AUGUSTUS	transcript	6459973	6463724	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	start_codon	6459973	6459975	.	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6459973	6460581	0.63	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6459973	6460581	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6460582	6460663	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6460664	6460753	0.73	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6460664	6460753	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6460754	6461066	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6461067	6461489	0.73	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6461067	6461489	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6461490	6461583	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6461584	6461715	1	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6461584	6461715	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6461716	6461865	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6461866	6462118	0.97	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6461866	6462118	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6462119	6462215	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6462216	6462326	1	+	2	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6462216	6462326	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6462327	6462417	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6462418	6462536	1	+	2	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6462418	6462536	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6462537	6462688	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6462689	6462793	1	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6462689	6462793	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6462794	6462940	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6462941	6463143	1	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6462941	6463143	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6463144	6463274	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6463275	6463398	1	+	1	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6463275	6463398	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	intron	6463399	6463535	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	CDS	6463536	6463724	1	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	exon	6463536	6463724	.	+	.	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
Phchi.S6	AUGUSTUS	stop_codon	6463725	6463727	.	+	0	transcript_id "Phchi.S6G088200.t1"; gene_id "Phchi.S6G088200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10470.t1 is derived from g14519.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	543816	547585	.	-	.	Phchi.S4G005200
Phchi.S4	AUGUSTUS	transcript	543816	547585	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	stop_codon	543813	543815	.	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	543816	544059	1	-	1	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	543816	544059	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	544060	544134	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	544135	545467	0.99	-	2	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	544135	545467	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	545468	545561	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	545562	545926	0.99	-	1	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	545562	545926	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	545927	546017	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546018	546078	1	-	2	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546018	546078	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546079	546311	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546312	546330	1	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546312	546330	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546331	546446	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546447	546572	0.95	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546447	546572	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546573	546657	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546658	546780	0.97	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546658	546780	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546781	546867	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546868	546974	1	-	2	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546868	546974	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546975	547061	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	547062	547158	1	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	547062	547158	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	547159	547257	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	547258	547375	1	-	1	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	547258	547375	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	547376	547457	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	547458	547585	0.53	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	547458	547585	.	-	.	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	start_codon	547583	547585	.	-	0	transcript_id "Phchi.S4G005200.t1"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	transcript	543816	547585	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	stop_codon	543813	543815	.	-	0	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	543816	544059	0.99	-	1	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	543816	544059	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	544060	544134	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	544135	545467	0.97	-	2	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	544135	545467	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	545468	545561	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	545562	545926	1	-	1	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	545562	545926	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	545927	546017	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546018	546078	1	-	2	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546018	546078	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546079	546311	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546312	546330	1	-	0	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546312	546330	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546331	546446	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546447	546599	0.96	-	0	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546447	546599	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546600	546867	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	546868	546974	1	-	2	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	546868	546974	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	546975	547061	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	547062	547158	1	-	0	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	547062	547158	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	547159	547257	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	547258	547375	1	-	1	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	547258	547375	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	intron	547376	547457	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	CDS	547458	547585	0.51	-	0	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	exon	547458	547585	.	-	.	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
Phchi.S4	AUGUSTUS	start_codon	547583	547585	.	-	0	transcript_id "Phchi.S4G005200.t2"; gene_id "Phchi.S4G005200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3163.t1 is derived from g332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2034568	2036263	.	-	.	Phchi.S1G032200
Phchi.S1	AUGUSTUS	transcript	2034568	2036263	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	stop_codon	2034565	2034567	.	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2034568	2034819	0.36	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2034568	2034819	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2034820	2034905	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2034906	2035039	0.99	-	2	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2034906	2035039	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035040	2035143	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035144	2035240	0.98	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035144	2035240	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035241	2035322	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035323	2035393	0.57	-	2	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035323	2035393	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035394	2035514	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035515	2035656	0.82	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035515	2035656	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035657	2035747	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035748	2035825	1	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035748	2035825	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035826	2035921	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035922	2036026	1	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035922	2036026	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2036027	2036107	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2036108	2036263	0.85	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2036108	2036263	.	-	.	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	start_codon	2036261	2036263	.	-	0	transcript_id "Phchi.S1G032200.t1"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	transcript	2034568	2036263	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	stop_codon	2034565	2034567	.	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2034568	2034822	0.45	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2034568	2034822	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2034823	2034905	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2034906	2035039	1	-	2	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2034906	2035039	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035040	2035143	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035144	2035240	1	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035144	2035240	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035241	2035322	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035323	2035393	0.5	-	2	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035323	2035393	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035394	2035514	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035515	2035656	0.79	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035515	2035656	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035657	2035747	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035748	2035825	1	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035748	2035825	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2035826	2035921	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2035922	2036026	1	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2035922	2036026	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	intron	2036027	2036107	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	CDS	2036108	2036263	0.81	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	exon	2036108	2036263	.	-	.	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
Phchi.S1	AUGUSTUS	start_codon	2036261	2036263	.	-	0	transcript_id "Phchi.S1G032200.t2"; gene_id "Phchi.S1G032200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12532.t1 is derived from g8209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33570153	33571862	.	-	.	Phchi.S2G061200
Phchi.S2	AUGUSTUS	transcript	33570312	33571862	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	stop_codon	33570309	33570311	.	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570312	33570446	1	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570312	33570446	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33570447	33570529	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570530	33570594	1	-	2	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570530	33570594	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33570595	33570686	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570687	33570762	1	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570687	33570762	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33570763	33570865	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570866	33571030	1	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570866	33571030	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33571031	33571111	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33571112	33571348	0.79	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33571112	33571348	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33571349	33571542	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33571543	33571659	0.68	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33571543	33571659	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33571660	33571766	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33571767	33571862	0.57	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33571767	33571862	.	-	.	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	start_codon	33571860	33571862	.	-	0	transcript_id "Phchi.S2G061200.t1"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	transcript	33570153	33571862	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	stop_codon	33570150	33570152	.	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570153	33570215	1	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570153	33570215	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33570216	33570529	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570530	33570594	1	-	2	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570530	33570594	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33570595	33570686	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570687	33570762	1	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570687	33570762	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33570763	33570865	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33570866	33571030	1	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33570866	33571030	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33571031	33571111	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33571112	33571348	0.79	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33571112	33571348	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33571349	33571542	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33571543	33571659	0.54	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33571543	33571659	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	intron	33571660	33571766	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	CDS	33571767	33571862	0.39	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	exon	33571767	33571862	.	-	.	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
Phchi.S2	AUGUSTUS	start_codon	33571860	33571862	.	-	0	transcript_id "Phchi.S2G061200.t2"; gene_id "Phchi.S2G061200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2268.t1 is derived from g9188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5776571	5780727	.	+	.	Phchi.S5G087700
Phchi.S5	AUGUSTUS	transcript	5776571	5780727	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	start_codon	5776571	5776573	.	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5776571	5777502	1	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5776571	5777502	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5777503	5777664	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5777665	5777835	1	+	1	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5777665	5777835	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5777836	5777994	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5777995	5778256	1	+	1	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5777995	5778256	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5778257	5778347	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5778348	5778437	0.55	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5778348	5778437	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5778438	5778552	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5778553	5778673	1	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5778553	5778673	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5778674	5778764	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5778765	5778919	1	+	2	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5778765	5778919	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5778920	5779009	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5779010	5779104	1	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5779010	5779104	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5779105	5779198	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5779199	5779317	1	+	1	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5779199	5779317	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5779318	5779404	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5779405	5779560	1	+	2	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5779405	5779560	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5779561	5779663	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5779664	5779797	0.89	+	2	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5779664	5779797	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5779798	5779887	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5779888	5780083	0.78	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5779888	5780083	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5780084	5780191	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5780192	5780271	0.92	+	2	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5780192	5780271	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5780272	5780355	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5780356	5780468	1	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5780356	5780468	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	intron	5780469	5780549	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	CDS	5780550	5780727	0.99	+	1	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	exon	5780550	5780727	.	+	.	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
Phchi.S5	AUGUSTUS	stop_codon	5780728	5780730	.	+	0	transcript_id "Phchi.S5G087700.t1"; gene_id "Phchi.S5G087700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2960.t1 is derived from g129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	793769	800737	.	+	.	Phchi.S1G011900
Phchi.S1	AUGUSTUS	transcript	793769	800737	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	start_codon	793769	793771	.	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	793769	794009	0.93	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	793769	794009	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	794010	794166	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	794167	794465	1	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	794167	794465	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	794466	794580	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	794581	794807	0.53	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	794581	794807	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	794808	794936	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	794937	795059	0.52	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	794937	795059	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	795060	795148	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	795149	795190	0.53	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	795149	795190	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	795191	795295	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	795296	795537	0.94	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	795296	795537	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	795538	795711	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	795712	795832	0.98	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	795712	795832	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	795833	795958	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	795959	796027	0.99	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	795959	796027	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	796028	796294	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	796295	796363	0.91	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	796295	796363	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	796364	796483	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	796484	796740	1	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	796484	796740	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	796741	796845	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	796846	797057	1	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	796846	797057	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	797058	797243	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	797244	797370	0.95	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	797244	797370	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	797371	797472	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	797473	797541	0.95	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	797473	797541	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	797542	797652	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	797653	797702	0.98	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	797653	797702	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	797703	797819	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	797820	798430	0.71	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	797820	798430	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	798431	798624	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	798625	798734	0.69	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	798625	798734	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	798735	798820	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	798821	798985	0.73	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	798821	798985	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	798986	799075	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	799076	799661	0.92	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	799076	799661	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	799662	799759	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	799760	799884	0.35	+	1	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	799760	799884	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	799885	800471	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	800472	800569	0.46	+	2	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	800472	800569	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	intron	800570	800662	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	CDS	800663	800737	0.34	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	exon	800663	800737	.	+	.	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
Phchi.S1	AUGUSTUS	stop_codon	800738	800740	.	+	0	transcript_id "Phchi.S1G011900.t1"; gene_id "Phchi.S1G011900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12949.t1 is derived from g11414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3282211	3284658	.	+	.	Phchi.S3G026800
Phchi.S3	AUGUSTUS	transcript	3282211	3284658	.	+	.	transcript_id "Phchi.S3G026800.t1"; gene_id "Phchi.S3G026800"
Phchi.S3	AUGUSTUS	start_codon	3282211	3282213	.	+	0	transcript_id "Phchi.S3G026800.t1"; gene_id "Phchi.S3G026800"
Phchi.S3	AUGUSTUS	CDS	3282211	3284658	0.42	+	0	transcript_id "Phchi.S3G026800.t1"; gene_id "Phchi.S3G026800"
Phchi.S3	AUGUSTUS	exon	3282211	3284658	.	+	.	transcript_id "Phchi.S3G026800.t1"; gene_id "Phchi.S3G026800"
Phchi.S3	AUGUSTUS	stop_codon	3284659	3284661	.	+	0	transcript_id "Phchi.S3G026800.t1"; gene_id "Phchi.S3G026800"
# This transcript jg11445.t2 is derived from g15495.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11446.t1 is derived from g15496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6397236	6399139	.	+	.	Phchi.S4G102800
Phchi.S4	AUGUSTUS	transcript	6397236	6399139	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	start_codon	6397236	6397238	.	+	0	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6397236	6397518	0.91	+	0	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6397236	6397518	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	intron	6397519	6397600	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6397601	6397770	1	+	2	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6397601	6397770	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	intron	6397771	6397852	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6397853	6398051	1	+	0	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6397853	6398051	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	intron	6398052	6398137	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6398138	6398319	1	+	2	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6398138	6398319	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	intron	6398320	6398447	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6398448	6398598	1	+	0	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6398448	6398598	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	intron	6398599	6398676	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6398677	6398810	0.99	+	2	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6398677	6398810	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	intron	6398811	6398911	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	CDS	6398912	6399139	0.99	+	0	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	exon	6398912	6399139	.	+	.	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
Phchi.S4	AUGUSTUS	stop_codon	6399140	6399142	.	+	0	transcript_id "Phchi.S4G102800.t1"; gene_id "Phchi.S4G102800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2043.t1 is derived from g8963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4570971	4571827	.	-	.	Phchi.S5G065200
Phchi.S5	AUGUSTUS	transcript	4570971	4571827	.	-	.	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	stop_codon	4570968	4570970	.	-	0	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	CDS	4570971	4571090	0.83	-	0	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	exon	4570971	4571090	.	-	.	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	intron	4571091	4571319	.	-	.	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	CDS	4571320	4571584	0.88	-	1	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	exon	4571320	4571584	.	-	.	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	intron	4571585	4571672	.	-	.	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	CDS	4571673	4571827	0.79	-	0	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	exon	4571673	4571827	.	-	.	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
Phchi.S5	AUGUSTUS	start_codon	4571825	4571827	.	-	0	transcript_id "Phchi.S5G065200.t1"; gene_id "Phchi.S5G065200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7171.t1 is derived from g4343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27387381	27391018	.	-	.	Phchi.S1G433000
Phchi.S1	AUGUSTUS	transcript	27387381	27391018	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	stop_codon	27387378	27387380	.	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27387381	27387416	0.88	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27387381	27387416	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27387417	27387582	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27387583	27387664	0.69	-	1	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27387583	27387664	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27387665	27387750	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27387751	27388142	0.5	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27387751	27388142	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27388143	27388252	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27388253	27388480	0.99	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27388253	27388480	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27388481	27388596	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27388597	27389364	1	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27388597	27389364	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27389365	27389511	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27389512	27389586	0.98	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27389512	27389586	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27389587	27389723	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27389724	27389993	0.84	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27389724	27389993	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27389994	27390103	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27390104	27390237	1	-	2	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27390104	27390237	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27390238	27390334	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27390335	27390406	1	-	2	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27390335	27390406	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27390407	27390509	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27390510	27390831	0.98	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27390510	27390831	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	intron	27390832	27390967	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	CDS	27390968	27391018	1	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	exon	27390968	27391018	.	-	.	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
Phchi.S1	AUGUSTUS	start_codon	27391016	27391018	.	-	0	transcript_id "Phchi.S1G433000.t1"; gene_id "Phchi.S1G433000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3577.t1 is derived from g746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4593273	4596707	.	+	.	Phchi.S1G073600
Phchi.S1	AUGUSTUS	transcript	4593273	4596707	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	start_codon	4593273	4593275	.	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4593273	4593669	0.59	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4593273	4593669	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4593670	4593946	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4593947	4594061	1	+	2	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4593947	4594061	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4594062	4594244	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4594245	4594302	1	+	1	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4594245	4594302	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4594303	4594447	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4594448	4594465	1	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4594448	4594465	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4594466	4594634	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4594635	4594923	0.99	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4594635	4594923	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4594924	4595080	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4595081	4595205	1	+	2	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4595081	4595205	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4595206	4595286	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4595287	4595347	1	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4595287	4595347	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4595348	4595487	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4595488	4595566	1	+	2	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4595488	4595566	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4595567	4595803	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4595804	4595844	1	+	1	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4595804	4595844	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4595845	4595931	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4595932	4595977	1	+	2	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4595932	4595977	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4595978	4596076	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4596077	4596171	1	+	1	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4596077	4596171	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4596172	4596290	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4596291	4596394	1	+	2	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4596291	4596394	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4596395	4596516	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4596517	4596564	1	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4596517	4596564	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	intron	4596565	4596647	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	CDS	4596648	4596707	0.95	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	exon	4596648	4596707	.	+	.	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
Phchi.S1	AUGUSTUS	stop_codon	4596708	4596710	.	+	0	transcript_id "Phchi.S1G073600.t1"; gene_id "Phchi.S1G073600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9372.t1 is derived from g6548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41213752	41217313	.	-	.	Phchi.S1G653100
Phchi.S1	AUGUSTUS	transcript	41213752	41217313	.	-	.	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	stop_codon	41213749	41213751	.	-	0	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	CDS	41213752	41214770	0.76	-	2	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	exon	41213752	41214770	.	-	.	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	intron	41214771	41214910	.	-	.	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	CDS	41214911	41215910	0.44	-	0	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	exon	41214911	41215910	.	-	.	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	intron	41215911	41216026	.	-	.	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	CDS	41216027	41217313	0.48	-	0	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	exon	41216027	41217313	.	-	.	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
Phchi.S1	AUGUSTUS	start_codon	41217311	41217313	.	-	0	transcript_id "Phchi.S1G653100.t1"; gene_id "Phchi.S1G653100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1345.t1 is derived from g11128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9121850	9122960	.	+	.	Phchi.S6G130400
Phchi.S6	AUGUSTUS	transcript	9121850	9122960	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	start_codon	9121850	9121852	.	+	0	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	CDS	9121850	9121948	0.94	+	0	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	exon	9121850	9121948	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	intron	9121949	9122036	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	CDS	9122037	9122197	1	+	0	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	exon	9122037	9122197	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	intron	9122198	9122314	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	CDS	9122315	9122455	1	+	1	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	exon	9122315	9122455	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	intron	9122456	9122536	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	CDS	9122537	9122960	1	+	1	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	exon	9122537	9122960	.	+	.	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
Phchi.S6	AUGUSTUS	stop_codon	9122961	9122963	.	+	0	transcript_id "Phchi.S6G130400.t1"; gene_id "Phchi.S6G130400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5398.t1 is derived from g2568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16682131	16686024	.	-	.	Phchi.S1G255700
Phchi.S1	AUGUSTUS	transcript	16682131	16686024	.	-	.	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	stop_codon	16682128	16682130	.	-	0	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	CDS	16682131	16682366	1	-	2	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	exon	16682131	16682366	.	-	.	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	intron	16682367	16683737	.	-	.	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	CDS	16683738	16683897	1	-	0	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	exon	16683738	16683897	.	-	.	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	intron	16683898	16685505	.	-	.	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	CDS	16685506	16686024	0.02	-	0	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	exon	16685506	16686024	.	-	.	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
Phchi.S1	AUGUSTUS	start_codon	16686022	16686024	.	-	0	transcript_id "Phchi.S1G255700.t1"; gene_id "Phchi.S1G255700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14656.t1 is derived from g13124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13990757	13991636	.	+	.	Phchi.S3G197500
Phchi.S3	AUGUSTUS	transcript	13990757	13991636	.	+	.	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	start_codon	13990757	13990759	.	+	0	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	CDS	13990757	13990841	1	+	0	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	exon	13990757	13990841	.	+	.	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	intron	13990842	13990971	.	+	.	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	CDS	13990972	13991117	1	+	2	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	exon	13990972	13991117	.	+	.	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	intron	13991118	13991567	.	+	.	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	CDS	13991568	13991636	0.99	+	0	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	exon	13991568	13991636	.	+	.	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
Phchi.S3	AUGUSTUS	stop_codon	13991637	13991639	.	+	0	transcript_id "Phchi.S3G197500.t1"; gene_id "Phchi.S3G197500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2728.t1 is derived from g9648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8466904	8467634	.	+	.	Phchi.S5G133700
Phchi.S5	AUGUSTUS	transcript	8466904	8467634	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	start_codon	8466904	8466906	.	+	0	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	CDS	8466904	8467036	1	+	0	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	exon	8466904	8467036	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	intron	8467037	8467137	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	CDS	8467138	8467207	1	+	2	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	exon	8467138	8467207	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	intron	8467208	8467282	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	CDS	8467283	8467388	1	+	1	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	exon	8467283	8467388	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	intron	8467389	8467472	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	CDS	8467473	8467634	0.67	+	0	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	exon	8467473	8467634	.	+	.	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
Phchi.S5	AUGUSTUS	stop_codon	8467635	8467637	.	+	0	transcript_id "Phchi.S5G133700.t1"; gene_id "Phchi.S5G133700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7834.t1 is derived from g5008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31432906	31435216	.	+	.	Phchi.S1G499300
Phchi.S1	AUGUSTUS	transcript	31432906	31435216	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	start_codon	31432906	31432908	.	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31432906	31432936	0.98	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31432906	31432936	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31432937	31433456	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31433457	31433501	1	+	2	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31433457	31433501	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31433502	31433699	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31433700	31433734	1	+	2	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31433700	31433734	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31433735	31433823	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31433824	31433874	1	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31433824	31433874	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31433875	31433969	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31433970	31434074	1	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31433970	31434074	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31434075	31434244	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31434245	31434316	1	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31434245	31434316	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31434317	31434426	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31434427	31434498	1	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31434427	31434498	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31434499	31434666	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31434667	31434767	0.98	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31434667	31434767	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31434768	31434852	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31434853	31434888	0.98	+	1	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31434853	31434888	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31434889	31435029	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31435030	31435088	1	+	1	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31435030	31435088	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	intron	31435089	31435187	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	CDS	31435188	31435216	1	+	2	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	exon	31435188	31435216	.	+	.	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
Phchi.S1	AUGUSTUS	stop_codon	31435217	31435219	.	+	0	transcript_id "Phchi.S1G499300.t1"; gene_id "Phchi.S1G499300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14749.t1 is derived from g13217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14530371	14533338	.	-	.	Phchi.S3G206800
Phchi.S3	AUGUSTUS	transcript	14530371	14533338	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	stop_codon	14530368	14530370	.	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14530371	14531504	0.97	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14530371	14531504	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14531505	14531616	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14531617	14531706	0.98	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14531617	14531706	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14531707	14531809	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14531810	14531885	1	-	1	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14531810	14531885	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14531886	14531980	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14531981	14532198	0.85	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14531981	14532198	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14532199	14532306	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14532307	14532516	0.85	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14532307	14532516	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14532517	14532608	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14532609	14532794	1	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14532609	14532794	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14532795	14532878	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14532879	14533000	1	-	2	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14532879	14533000	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	intron	14533001	14533112	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	CDS	14533113	14533338	0.99	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	exon	14533113	14533338	.	-	.	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
Phchi.S3	AUGUSTUS	start_codon	14533336	14533338	.	-	0	transcript_id "Phchi.S3G206800.t1"; gene_id "Phchi.S3G206800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6424.t1 is derived from g3596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22936561	22937459	.	+	.	Phchi.S1G358300
Phchi.S1	AUGUSTUS	transcript	22936561	22937459	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	start_codon	22936561	22936563	.	+	0	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	CDS	22936561	22936618	1	+	0	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	exon	22936561	22936618	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	intron	22936619	22936692	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	CDS	22936693	22936911	1	+	2	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	exon	22936693	22936911	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	intron	22936912	22936994	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	CDS	22936995	22937092	1	+	2	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	exon	22936995	22937092	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	intron	22937093	22937233	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	CDS	22937234	22937276	0.6	+	0	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	exon	22937234	22937276	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	intron	22937277	22937358	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	CDS	22937359	22937459	1	+	2	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	exon	22937359	22937459	.	+	.	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
Phchi.S1	AUGUSTUS	stop_codon	22937460	22937462	.	+	0	transcript_id "Phchi.S1G358300.t1"; gene_id "Phchi.S1G358300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10328.t1 is derived from g7504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47200466	47202220	.	-	.	Phchi.S1G748700
Phchi.S1	AUGUSTUS	transcript	47200466	47202220	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	stop_codon	47200463	47200465	.	-	0	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	CDS	47200466	47200619	0.96	-	1	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	exon	47200466	47200619	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	intron	47200620	47200846	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	CDS	47200847	47201050	1	-	1	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	exon	47200847	47201050	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	intron	47201051	47201135	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	CDS	47201136	47201329	1	-	0	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	exon	47201136	47201329	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	intron	47201330	47201563	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	CDS	47201564	47201814	1	-	2	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	exon	47201564	47201814	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	intron	47201815	47201952	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	CDS	47201953	47202220	0.95	-	0	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	exon	47201953	47202220	.	-	.	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
Phchi.S1	AUGUSTUS	start_codon	47202218	47202220	.	-	0	transcript_id "Phchi.S1G748700.t1"; gene_id "Phchi.S1G748700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1264.t1 is derived from g11047.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8709647	8710509	.	-	.	Phchi.S6G122300
Phchi.S6	AUGUSTUS	transcript	8709647	8710509	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	stop_codon	8709644	8709646	.	-	0	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8709647	8709766	1	-	0	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8709647	8709766	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8709767	8709860	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8709861	8709962	1	-	0	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8709861	8709962	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8709963	8710048	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8710049	8710085	1	-	1	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8710049	8710085	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8710086	8710262	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8710263	8710354	0.99	-	0	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8710263	8710354	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8710355	8710431	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8710432	8710509	0.99	-	0	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8710432	8710509	.	-	.	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	start_codon	8710507	8710509	.	-	0	transcript_id "Phchi.S6G122300.t1"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	transcript	8709647	8710448	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	stop_codon	8709644	8709646	.	-	0	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8709647	8709766	1	-	0	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8709647	8709766	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8709767	8709860	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8709861	8709962	1	-	0	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8709861	8709962	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8709963	8710048	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8710049	8710085	1	-	1	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8710049	8710085	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8710086	8710186	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8710187	8710354	0.98	-	1	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8710187	8710354	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	intron	8710355	8710431	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	CDS	8710432	8710448	1	-	0	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	exon	8710432	8710448	.	-	.	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
Phchi.S6	AUGUSTUS	start_codon	8710446	8710448	.	-	0	transcript_id "Phchi.S6G122300.t2"; gene_id "Phchi.S6G122300"
# This transcript jg146.t2 is derived from g9928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg147.t1 is derived from g9929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	829242	833021	.	+	.	Phchi.S6G010600
Phchi.S6	AUGUSTUS	transcript	829242	833021	.	+	.	transcript_id "Phchi.S6G010600.t1"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	start_codon	829242	829244	.	+	0	transcript_id "Phchi.S6G010600.t1"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	CDS	829242	833021	0.99	+	0	transcript_id "Phchi.S6G010600.t1"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	exon	829242	833021	.	+	.	transcript_id "Phchi.S6G010600.t1"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	stop_codon	833022	833024	.	+	0	transcript_id "Phchi.S6G010600.t1"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	transcript	830523	833021	.	+	.	transcript_id "Phchi.S6G010600.t2"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	start_codon	830523	830525	.	+	0	transcript_id "Phchi.S6G010600.t2"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	CDS	830523	833021	0.97	+	0	transcript_id "Phchi.S6G010600.t2"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	exon	830523	833021	.	+	.	transcript_id "Phchi.S6G010600.t2"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	stop_codon	833022	833024	.	+	0	transcript_id "Phchi.S6G010600.t2"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	transcript	830184	833021	.	+	.	transcript_id "Phchi.S6G010600.t3"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	start_codon	830184	830186	.	+	0	transcript_id "Phchi.S6G010600.t3"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	CDS	830184	833021	0.47	+	0	transcript_id "Phchi.S6G010600.t3"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	exon	830184	833021	.	+	.	transcript_id "Phchi.S6G010600.t3"; gene_id "Phchi.S6G010600"
Phchi.S6	AUGUSTUS	stop_codon	833022	833024	.	+	0	transcript_id "Phchi.S6G010600.t3"; gene_id "Phchi.S6G010600"
# This transcript jg406.t2 is derived from g10188.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg407.t1 is derived from g10189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2937417	2938752	.	+	.	Phchi.S6G036600
Phchi.S6	AUGUSTUS	transcript	2937417	2938752	.	+	.	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	start_codon	2937417	2937419	.	+	0	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	CDS	2937417	2938440	0.87	+	0	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	exon	2937417	2938440	.	+	.	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	intron	2938441	2938565	.	+	.	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	CDS	2938566	2938634	0.82	+	2	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	exon	2938566	2938634	.	+	.	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	intron	2938635	2938720	.	+	.	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	CDS	2938721	2938752	1	+	2	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	exon	2938721	2938752	.	+	.	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
Phchi.S6	AUGUSTUS	stop_codon	2938753	2938755	.	+	0	transcript_id "Phchi.S6G036600.t1"; gene_id "Phchi.S6G036600"
# This transcript jg4756.t2 is derived from g1926.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4757.t1 is derived from g1927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12668106	12668630	.	+	.	Phchi.S1G191600
Phchi.S1	AUGUSTUS	transcript	12668106	12668630	.	+	.	transcript_id "Phchi.S1G191600.t1"; gene_id "Phchi.S1G191600"
Phchi.S1	AUGUSTUS	start_codon	12668106	12668108	.	+	0	transcript_id "Phchi.S1G191600.t1"; gene_id "Phchi.S1G191600"
Phchi.S1	AUGUSTUS	CDS	12668106	12668630	0.75	+	0	transcript_id "Phchi.S1G191600.t1"; gene_id "Phchi.S1G191600"
Phchi.S1	AUGUSTUS	exon	12668106	12668630	.	+	.	transcript_id "Phchi.S1G191600.t1"; gene_id "Phchi.S1G191600"
Phchi.S1	AUGUSTUS	stop_codon	12668631	12668633	.	+	0	transcript_id "Phchi.S1G191600.t1"; gene_id "Phchi.S1G191600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10345.t1 is derived from g7521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47272378	47273078	.	-	.	Phchi.S1G750400
Phchi.S1	AUGUSTUS	transcript	47272378	47273078	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	stop_codon	47272375	47272377	.	-	0	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	CDS	47272378	47272399	1	-	1	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	exon	47272378	47272399	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	intron	47272400	47272491	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	CDS	47272492	47272510	0.6	-	2	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	exon	47272492	47272510	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	intron	47272511	47272711	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	CDS	47272712	47272795	0.49	-	2	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	exon	47272712	47272795	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	intron	47272796	47272963	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	CDS	47272964	47273078	1	-	0	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	exon	47272964	47273078	.	-	.	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
Phchi.S1	AUGUSTUS	start_codon	47273076	47273078	.	-	0	transcript_id "Phchi.S1G750400.t1"; gene_id "Phchi.S1G750400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14629.t1 is derived from g13097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13836234	13838556	.	-	.	Phchi.S3G194800
Phchi.S3	AUGUSTUS	transcript	13836234	13838556	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	stop_codon	13836231	13836233	.	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13836234	13836263	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13836234	13836263	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13836264	13836388	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13836389	13836471	1	-	2	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13836389	13836471	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13836472	13836552	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13836553	13836646	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13836553	13836646	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13836647	13836759	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13836760	13836894	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13836760	13836894	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13836895	13836999	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13837000	13837032	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13837000	13837032	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13837033	13837112	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13837113	13837207	1	-	2	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13837113	13837207	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13837208	13837314	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13837315	13837360	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13837315	13837360	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13837361	13837500	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13837501	13837581	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13837501	13837581	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13837582	13837669	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13837670	13837723	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13837670	13837723	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13837724	13837812	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13837813	13837955	1	-	2	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13837813	13837955	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13837956	13838099	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13838100	13838319	1	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13838100	13838319	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	intron	13838320	13838538	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	CDS	13838539	13838556	0.61	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	exon	13838539	13838556	.	-	.	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
Phchi.S3	AUGUSTUS	start_codon	13838554	13838556	.	-	0	transcript_id "Phchi.S3G194800.t1"; gene_id "Phchi.S3G194800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3548.t1 is derived from g717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4426033	4427016	.	-	.	Phchi.S1G070700
Phchi.S1	AUGUSTUS	transcript	4426033	4427016	.	-	.	transcript_id "Phchi.S1G070700.t1"; gene_id "Phchi.S1G070700"
Phchi.S1	AUGUSTUS	stop_codon	4426030	4426032	.	-	0	transcript_id "Phchi.S1G070700.t1"; gene_id "Phchi.S1G070700"
Phchi.S1	AUGUSTUS	CDS	4426033	4427016	0.74	-	0	transcript_id "Phchi.S1G070700.t1"; gene_id "Phchi.S1G070700"
Phchi.S1	AUGUSTUS	exon	4426033	4427016	.	-	.	transcript_id "Phchi.S1G070700.t1"; gene_id "Phchi.S1G070700"
Phchi.S1	AUGUSTUS	start_codon	4427014	4427016	.	-	0	transcript_id "Phchi.S1G070700.t1"; gene_id "Phchi.S1G070700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6103.t1 is derived from g3274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20956792	20958787	.	-	.	Phchi.S1G326200
Phchi.S1	AUGUSTUS	transcript	20956792	20958787	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	stop_codon	20956789	20956791	.	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	CDS	20956792	20957304	0.99	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	exon	20956792	20957304	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	intron	20957305	20957438	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	CDS	20957439	20957789	1	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	exon	20957439	20957789	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	intron	20957790	20957931	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	CDS	20957932	20957986	1	-	1	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	exon	20957932	20957986	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	intron	20957987	20958073	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	CDS	20958074	20958210	1	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	exon	20958074	20958210	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	intron	20958211	20958293	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	CDS	20958294	20958497	1	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	exon	20958294	20958497	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	intron	20958498	20958586	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	CDS	20958587	20958787	1	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	exon	20958587	20958787	.	-	.	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
Phchi.S1	AUGUSTUS	start_codon	20958785	20958787	.	-	0	transcript_id "Phchi.S1G326200.t1"; gene_id "Phchi.S1G326200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5275.t1 is derived from g2445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15998716	16000644	.	-	.	Phchi.S1G243400
Phchi.S1	AUGUSTUS	transcript	15998716	16000644	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	stop_codon	15998638	15998640	.	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15998716	15998742	0.9	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15998716	15998742	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15998743	15998884	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15998885	15998893	0.47	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15998885	15998893	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15998894	15999024	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15999025	15999031	0.47	-	1	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15999025	15999031	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15999032	15999191	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15999192	15999297	0.63	-	2	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15999192	15999297	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15999298	15999384	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15999385	15999426	0.63	-	2	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15999385	15999426	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15999427	15999566	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15999567	15999581	0.63	-	2	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15999567	15999581	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15999582	15999779	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15999780	15999792	0.63	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15999780	15999792	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15999793	15999878	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	15999879	15999963	1	-	1	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	15999879	15999963	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	15999964	16000085	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	16000086	16000225	0.87	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	16000086	16000225	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	intron	16000226	16000527	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	CDS	16000528	16000644	0.67	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	exon	16000528	16000644	.	-	.	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
Phchi.S1	AUGUSTUS	start_codon	16000642	16000644	.	-	0	transcript_id "Phchi.S1G243400.t1"; gene_id "Phchi.S1G243400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2165.t1 is derived from g9085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5137998	5139829	.	-	.	Phchi.S5G077400
Phchi.S5	AUGUSTUS	transcript	5137998	5139829	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	stop_codon	5137995	5137997	.	-	0	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	CDS	5137998	5138306	1	-	0	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	exon	5137998	5138306	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	intron	5138307	5138393	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	CDS	5138394	5138533	1	-	2	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	exon	5138394	5138533	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	intron	5138534	5138742	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	CDS	5138743	5138948	1	-	1	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	exon	5138743	5138948	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	intron	5138949	5139050	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	CDS	5139051	5139157	1	-	0	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	exon	5139051	5139157	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	intron	5139158	5139251	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	CDS	5139252	5139431	0.98	-	0	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	exon	5139252	5139431	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	intron	5139432	5139538	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	CDS	5139539	5139829	0.84	-	0	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	exon	5139539	5139829	.	-	.	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
Phchi.S5	AUGUSTUS	start_codon	5139827	5139829	.	-	0	transcript_id "Phchi.S5G077400.t1"; gene_id "Phchi.S5G077400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3369.t1 is derived from g538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3195412	3200130	.	-	.	Phchi.S1G052800
Phchi.S1	AUGUSTUS	transcript	3195412	3200130	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	stop_codon	3195409	3195411	.	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3195412	3195555	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3195412	3195555	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3195556	3195635	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3195636	3195695	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3195636	3195695	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3195696	3195780	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3195781	3195861	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3195781	3195861	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3195862	3195949	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3195950	3196099	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3195950	3196099	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3196100	3196256	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3196257	3196415	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3196257	3196415	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3196416	3196556	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3196557	3196646	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3196557	3196646	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3196647	3196752	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3196753	3196827	0.96	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3196753	3196827	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3196828	3196913	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3196914	3196961	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3196914	3196961	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3196962	3197034	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3197035	3197161	1	-	1	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3197035	3197161	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3197162	3197242	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3197243	3197352	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3197243	3197352	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3197353	3197496	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3197497	3197556	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3197497	3197556	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3197557	3197685	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3197686	3197753	0.99	-	2	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3197686	3197753	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3197754	3197856	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3197857	3197959	0.81	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3197857	3197959	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3197960	3198053	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3198054	3198101	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3198054	3198101	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3198102	3198189	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3198190	3198250	1	-	1	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3198190	3198250	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3198251	3198326	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3198327	3198413	1	-	1	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3198327	3198413	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3198414	3198548	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3198549	3198621	1	-	2	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3198549	3198621	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3198622	3198702	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3198703	3198796	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3198703	3198796	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3198797	3198892	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3198893	3199009	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3198893	3199009	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3199010	3199147	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3199148	3199225	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3199148	3199225	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3199226	3199338	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3199339	3199491	1	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3199339	3199491	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3199492	3199607	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3199608	3199820	0.74	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3199608	3199820	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	intron	3199821	3199944	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	CDS	3199945	3200130	0.45	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	exon	3199945	3200130	.	-	.	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
Phchi.S1	AUGUSTUS	start_codon	3200128	3200130	.	-	0	transcript_id "Phchi.S1G052800.t1"; gene_id "Phchi.S1G052800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9672.t1 is derived from g6848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43223708	43224962	.	-	.	Phchi.S1G683100
Phchi.S1	AUGUSTUS	transcript	43223708	43224962	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	stop_codon	43223705	43223707	.	-	0	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	CDS	43223708	43223923	0.98	-	0	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	exon	43223708	43223923	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	intron	43223924	43224020	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	CDS	43224021	43224086	1	-	0	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	exon	43224021	43224086	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	intron	43224087	43224205	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	CDS	43224206	43224278	0.98	-	1	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	exon	43224206	43224278	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	intron	43224279	43224409	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	CDS	43224410	43224545	0.99	-	2	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	exon	43224410	43224545	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	intron	43224546	43224626	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	CDS	43224627	43224688	1	-	1	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	exon	43224627	43224688	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	intron	43224689	43224774	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	CDS	43224775	43224962	0.92	-	0	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	exon	43224775	43224962	.	-	.	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
Phchi.S1	AUGUSTUS	start_codon	43224960	43224962	.	-	0	transcript_id "Phchi.S1G683100.t1"; gene_id "Phchi.S1G683100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4649.t1 is derived from g1819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11630929	11632094	.	-	.	Phchi.S1G180800
Phchi.S1	AUGUSTUS	transcript	11630929	11632094	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	stop_codon	11630926	11630928	.	-	0	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	CDS	11630929	11631003	1	-	0	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	exon	11630929	11631003	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	intron	11631004	11631128	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	CDS	11631129	11631210	1	-	1	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	exon	11631129	11631210	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	intron	11631211	11631316	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	CDS	11631317	11631499	1	-	1	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	exon	11631317	11631499	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	intron	11631500	11631619	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	CDS	11631620	11631938	1	-	2	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	exon	11631620	11631938	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	intron	11631939	11632084	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	CDS	11632085	11632094	1	-	0	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	exon	11632085	11632094	.	-	.	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
Phchi.S1	AUGUSTUS	start_codon	11632092	11632094	.	-	0	transcript_id "Phchi.S1G180800.t1"; gene_id "Phchi.S1G180800"
# This transcript jg10809.t2 is derived from g14859.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10810.t1 is derived from g14860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2204687	2205892	.	+	.	Phchi.S4G039200
Phchi.S4	AUGUSTUS	transcript	2204687	2205892	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	start_codon	2204687	2204689	.	+	0	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	CDS	2204687	2204975	1	+	0	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	exon	2204687	2204975	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	intron	2204976	2205076	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	CDS	2205077	2205231	1	+	2	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	exon	2205077	2205231	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	intron	2205232	2205387	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	CDS	2205388	2205549	1	+	0	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	exon	2205388	2205549	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	intron	2205550	2205666	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	CDS	2205667	2205782	1	+	0	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	exon	2205667	2205782	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	intron	2205783	2205861	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	CDS	2205862	2205892	1	+	1	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	exon	2205862	2205892	.	+	.	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
Phchi.S4	AUGUSTUS	stop_codon	2205893	2205895	.	+	0	transcript_id "Phchi.S4G039200.t1"; gene_id "Phchi.S4G039200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7572.t1 is derived from g4746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30089926	30097241	.	-	.	Phchi.S1G473100
Phchi.S1	AUGUSTUS	transcript	30089926	30097241	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	stop_codon	30089923	30089925	.	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30089926	30090039	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30089926	30090039	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30090040	30090158	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30090159	30090281	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30090159	30090281	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30090282	30090386	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30090387	30090482	0.99	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30090387	30090482	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30090483	30090567	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30090568	30090615	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30090568	30090615	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30090616	30090716	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30090717	30090815	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30090717	30090815	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30090816	30090890	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30090891	30090929	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30090891	30090929	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30090930	30091044	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30091045	30091146	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30091045	30091146	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30091147	30091233	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30091234	30091356	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30091234	30091356	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30091357	30091431	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30091432	30091693	0.93	-	1	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30091432	30091693	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30091694	30091846	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30091847	30092080	0.93	-	1	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30091847	30092080	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30092081	30092168	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30092169	30092215	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30092169	30092215	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30092216	30092324	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30092325	30092422	1	-	2	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30092325	30092422	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30092423	30092529	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30092530	30092575	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30092530	30092575	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30092576	30092673	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30092674	30092736	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30092674	30092736	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30092737	30092819	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30092820	30092913	1	-	1	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30092820	30092913	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30092914	30092999	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30093000	30093102	1	-	2	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30093000	30093102	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30093103	30093322	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30093323	30093395	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30093323	30093395	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30093396	30093544	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30093545	30093769	0.97	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30093545	30093769	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30093770	30093906	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30093907	30094254	0.81	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30093907	30094254	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30094255	30094335	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30094336	30094401	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30094336	30094401	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30094402	30094482	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30094483	30094632	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30094483	30094632	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30094633	30094743	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30094744	30094914	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30094744	30094914	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30094915	30095065	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30095066	30095116	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30095066	30095116	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30095117	30095228	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30095229	30095381	0.99	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30095229	30095381	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30095382	30095457	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30095458	30095529	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30095458	30095529	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30095530	30095650	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30095651	30095806	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30095651	30095806	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30095807	30095939	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30095940	30096164	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30095940	30096164	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30096165	30096286	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30096287	30096387	1	-	2	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30096287	30096387	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	intron	30096388	30096781	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	CDS	30096782	30097241	1	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	exon	30096782	30097241	.	-	.	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
Phchi.S1	AUGUSTUS	start_codon	30097239	30097241	.	-	0	transcript_id "Phchi.S1G473100.t1"; gene_id "Phchi.S1G473100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15406.t1 is derived from g13874.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18845792	18849590	.	+	.	Phchi.S3G272500
Phchi.S3	AUGUSTUS	transcript	18845792	18849590	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	start_codon	18845792	18845794	.	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18845792	18845861	0.97	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18845792	18845861	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18845862	18846644	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18846645	18846708	0.96	+	2	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18846645	18846708	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18846709	18846963	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18846964	18847107	0.93	+	1	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18846964	18847107	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847108	18847256	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18847257	18847296	1	+	1	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18847257	18847296	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847297	18847610	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18847611	18847663	1	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18847611	18847663	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847664	18847808	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18847809	18847854	1	+	1	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18847809	18847854	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847855	18848004	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848005	18848118	1	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848005	18848118	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848119	18848325	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848326	18848442	0.95	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848326	18848442	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848443	18848532	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848533	18848602	0.73	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848533	18848602	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848603	18848828	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848829	18848968	0.99	+	2	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848829	18848968	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848969	18849149	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18849150	18849200	1	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18849150	18849200	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18849201	18849299	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18849300	18849392	1	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18849300	18849392	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18849393	18849488	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18849489	18849590	0.99	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18849489	18849590	.	+	.	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	stop_codon	18849591	18849593	.	+	0	transcript_id "Phchi.S3G272500.t1"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	transcript	18845792	18849590	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	start_codon	18845792	18845794	.	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18845792	18845861	0.87	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18845792	18845861	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18845862	18846644	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18846645	18846708	0.95	+	2	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18846645	18846708	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18846709	18846963	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18846964	18847107	0.9	+	1	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18846964	18847107	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847108	18847256	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18847257	18847296	1	+	1	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18847257	18847296	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847297	18847610	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18847611	18847663	1	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18847611	18847663	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847664	18847808	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18847809	18847854	1	+	1	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18847809	18847854	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18847855	18848004	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848005	18848118	1	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848005	18848118	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848119	18848325	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848326	18848442	0.99	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848326	18848442	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848443	18848532	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848533	18848602	0.73	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848533	18848602	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848603	18848690	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18848691	18848968	1	+	2	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18848691	18848968	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18848969	18849149	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18849150	18849200	1	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18849150	18849200	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18849201	18849299	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18849300	18849392	1	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18849300	18849392	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	intron	18849393	18849488	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	CDS	18849489	18849590	1	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	exon	18849489	18849590	.	+	.	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
Phchi.S3	AUGUSTUS	stop_codon	18849591	18849593	.	+	0	transcript_id "Phchi.S3G272500.t2"; gene_id "Phchi.S3G272500"
# This transcript jg15118.t2 is derived from g13586.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15119.t1 is derived from g13587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17162729	17163613	.	-	.	Phchi.S3G243800
Phchi.S3	AUGUSTUS	transcript	17162729	17163613	.	-	.	transcript_id "Phchi.S3G243800.t1"; gene_id "Phchi.S3G243800"
Phchi.S3	AUGUSTUS	stop_codon	17162726	17162728	.	-	0	transcript_id "Phchi.S3G243800.t1"; gene_id "Phchi.S3G243800"
Phchi.S3	AUGUSTUS	CDS	17162729	17163613	0.51	-	0	transcript_id "Phchi.S3G243800.t1"; gene_id "Phchi.S3G243800"
Phchi.S3	AUGUSTUS	exon	17162729	17163613	.	-	.	transcript_id "Phchi.S3G243800.t1"; gene_id "Phchi.S3G243800"
Phchi.S3	AUGUSTUS	start_codon	17163611	17163613	.	-	0	transcript_id "Phchi.S3G243800.t1"; gene_id "Phchi.S3G243800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12531.t1 is derived from g8208.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33384183	33386906	.	+	.	Phchi.S2G061100
Phchi.S2	AUGUSTUS	transcript	33384183	33386906	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	start_codon	33384183	33384185	.	+	0	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33384183	33384499	0.86	+	0	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33384183	33384499	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33384500	33384885	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33384886	33384900	0.99	+	1	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33384886	33384900	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33384901	33385128	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33385129	33385207	1	+	1	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33385129	33385207	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33385208	33385445	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33385446	33385605	0.98	+	0	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33385446	33385605	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33385606	33385717	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33385718	33385843	1	+	2	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33385718	33385843	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33385844	33385956	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33385957	33386165	0.82	+	2	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33385957	33386165	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33386166	33386239	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33386240	33386365	0.64	+	0	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33386240	33386365	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	intron	33386366	33386504	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	CDS	33386505	33386906	1	+	0	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	exon	33386505	33386906	.	+	.	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
Phchi.S2	AUGUSTUS	stop_codon	33386907	33386909	.	+	0	transcript_id "Phchi.S2G061100.t1"; gene_id "Phchi.S2G061100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13847.t1 is derived from g12314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9212100	9212910	.	-	.	Phchi.S3G116600
Phchi.S3	AUGUSTUS	transcript	9212100	9212910	.	-	.	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	stop_codon	9212097	9212099	.	-	0	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	CDS	9212100	9212249	0.98	-	0	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	exon	9212100	9212249	.	-	.	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	intron	9212250	9212337	.	-	.	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	CDS	9212338	9212494	1	-	1	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	exon	9212338	9212494	.	-	.	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	intron	9212495	9212854	.	-	.	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	CDS	9212855	9212910	1	-	0	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	exon	9212855	9212910	.	-	.	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
Phchi.S3	AUGUSTUS	start_codon	9212908	9212910	.	-	0	transcript_id "Phchi.S3G116600.t1"; gene_id "Phchi.S3G116600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11831.t1 is derived from g15883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8473598	8475574	.	-	.	Phchi.S4G141300
Phchi.S4	AUGUSTUS	transcript	8473598	8475574	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	stop_codon	8473595	8473597	.	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8473598	8473855	1	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8473598	8473855	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	intron	8473856	8474068	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8474069	8474122	1	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8474069	8474122	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	intron	8474123	8474219	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8474220	8474314	1	-	2	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8474220	8474314	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	intron	8474315	8474418	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8474419	8474516	0.98	-	1	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8474419	8474516	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	intron	8474517	8474636	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8474637	8474911	0.89	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8474637	8474911	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	intron	8474912	8475020	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8475021	8475149	0.88	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8475021	8475149	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	intron	8475150	8475256	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	CDS	8475257	8475574	0.49	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	exon	8475257	8475574	.	-	.	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
Phchi.S4	AUGUSTUS	start_codon	8475572	8475574	.	-	0	transcript_id "Phchi.S4G141300.t1"; gene_id "Phchi.S4G141300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8404.t1 is derived from g5579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35796522	35800685	.	-	.	Phchi.S1G556300
Phchi.S1	AUGUSTUS	transcript	35796522	35800685	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	stop_codon	35796519	35796521	.	-	0	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	CDS	35796522	35797637	0.86	-	0	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	exon	35796522	35797637	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	intron	35797638	35797747	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	CDS	35797748	35798093	1	-	1	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	exon	35797748	35798093	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	intron	35798094	35799967	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	CDS	35799968	35800097	1	-	2	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	exon	35799968	35800097	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	intron	35800098	35800552	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	CDS	35800553	35800685	1	-	0	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	exon	35800553	35800685	.	-	.	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
Phchi.S1	AUGUSTUS	start_codon	35800683	35800685	.	-	0	transcript_id "Phchi.S1G556300.t1"; gene_id "Phchi.S1G556300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10546.t1 is derived from g14596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	906464	908850	.	+	.	Phchi.S4G012800
Phchi.S4	AUGUSTUS	transcript	906464	908850	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	start_codon	906464	906466	.	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	906464	906701	1	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	906464	906701	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	906702	906780	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	906781	907187	1	+	2	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	906781	907187	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	907188	907265	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	907266	907442	0.93	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	907266	907442	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	907443	907554	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	907555	907779	0.93	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	907555	907779	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	907780	907876	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	907877	908053	1	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	907877	908053	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	908054	908141	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	908142	908387	0.99	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	908142	908387	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	908388	908470	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	908471	908560	1	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	908471	908560	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	intron	908561	908679	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	CDS	908680	908850	1	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	exon	908680	908850	.	+	.	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
Phchi.S4	AUGUSTUS	stop_codon	908851	908853	.	+	0	transcript_id "Phchi.S4G012800.t1"; gene_id "Phchi.S4G012800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13130.t1 is derived from g11595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4266626	4269708	.	-	.	Phchi.S3G044900
Phchi.S3	AUGUSTUS	transcript	4266626	4269708	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	stop_codon	4266623	4266625	.	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4266626	4266720	1	-	2	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4266626	4266720	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4266721	4266813	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4266814	4266985	0.99	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4266814	4266985	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4266986	4267099	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4267100	4267253	1	-	1	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4267100	4267253	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4267254	4267366	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4267367	4267485	0.97	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4267367	4267485	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4267486	4267563	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4267564	4267672	1	-	1	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4267564	4267672	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4267673	4267764	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4267765	4267875	1	-	1	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4267765	4267875	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4267876	4267963	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4267964	4268091	1	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4267964	4268091	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4268092	4268205	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4268206	4268334	1	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4268206	4268334	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4268335	4268453	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4268454	4268501	1	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4268454	4268501	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4268502	4268638	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4268639	4268833	1	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4268639	4268833	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4268834	4268956	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4268957	4269085	1	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4268957	4269085	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4269086	4269168	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4269169	4269370	1	-	1	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4269169	4269370	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4269371	4269456	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4269457	4269503	0.87	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4269457	4269503	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	intron	4269504	4269609	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	CDS	4269610	4269708	0.87	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	exon	4269610	4269708	.	-	.	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
Phchi.S3	AUGUSTUS	start_codon	4269706	4269708	.	-	0	transcript_id "Phchi.S3G044900.t1"; gene_id "Phchi.S3G044900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7074.t1 is derived from g4246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26763600	26767447	.	+	.	Phchi.S1G423300
Phchi.S1	AUGUSTUS	transcript	26763600	26767447	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	start_codon	26763600	26763602	.	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26763600	26763824	0.63	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26763600	26763824	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26763825	26763944	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26763945	26763991	1	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26763945	26763991	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26763992	26764116	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26764117	26764156	1	+	1	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26764117	26764156	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26764157	26764267	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26764268	26764333	1	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26764268	26764333	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26764334	26764430	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26764431	26764568	1	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26764431	26764568	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26764569	26764747	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26764748	26764906	1	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26764748	26764906	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26764907	26765013	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26765014	26765067	0.99	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26765014	26765067	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26765068	26765144	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26765145	26765213	0.98	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26765145	26765213	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26765214	26765323	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26765324	26765453	1	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26765324	26765453	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26765454	26765569	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26765570	26765610	0.76	+	2	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26765570	26765610	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26765611	26765700	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26765701	26765928	0.79	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26765701	26765928	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26765929	26766049	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26766050	26766098	0.97	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26766050	26766098	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26766099	26766199	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26766200	26766354	0.86	+	2	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26766200	26766354	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26766355	26766460	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26766461	26766676	0.94	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26766461	26766676	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26766677	26766760	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26766761	26766957	0.84	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26766761	26766957	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26766958	26767123	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26767124	26767162	0.2	+	1	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26767124	26767162	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	intron	26767163	26767317	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	CDS	26767318	26767447	0.6	+	1	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	exon	26767318	26767447	.	+	.	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
Phchi.S1	AUGUSTUS	stop_codon	26767448	26767450	.	+	0	transcript_id "Phchi.S1G423300.t1"; gene_id "Phchi.S1G423300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3890.t1 is derived from g1059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6228300	6230510	.	+	.	Phchi.S1G104900
Phchi.S1	AUGUSTUS	transcript	6228300	6230510	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	start_codon	6228300	6228302	.	+	0	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	CDS	6228300	6228402	1	+	0	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	exon	6228300	6228402	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	intron	6228403	6228786	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	CDS	6228787	6228914	0.7	+	2	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	exon	6228787	6228914	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	intron	6228915	6228985	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	CDS	6228986	6230299	0.59	+	0	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	exon	6228986	6230299	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	intron	6230300	6230435	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	CDS	6230436	6230510	1	+	0	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	exon	6230436	6230510	.	+	.	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
Phchi.S1	AUGUSTUS	stop_codon	6230511	6230513	.	+	0	transcript_id "Phchi.S1G104900.t1"; gene_id "Phchi.S1G104900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5131.t1 is derived from g2301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15056455	15057818	.	-	.	Phchi.S1G229000
Phchi.S1	AUGUSTUS	transcript	15056455	15057818	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	stop_codon	15056452	15056454	.	-	0	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15056455	15056488	1	-	1	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15056455	15056488	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15056489	15056662	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15056663	15056735	1	-	2	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15056663	15056735	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15056736	15056847	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15056848	15056931	1	-	2	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15056848	15056931	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15056932	15057041	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15057042	15057120	1	-	0	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15057042	15057120	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15057121	15057242	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15057243	15057380	1	-	0	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15057243	15057380	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15057381	15057468	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15057469	15057542	0.99	-	2	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15057469	15057542	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15057543	15057629	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15057630	15057646	0.61	-	1	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15057630	15057646	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	intron	15057647	15057789	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	CDS	15057790	15057818	0.57	-	0	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	exon	15057790	15057818	.	-	.	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
Phchi.S1	AUGUSTUS	start_codon	15057816	15057818	.	-	0	transcript_id "Phchi.S1G229000.t1"; gene_id "Phchi.S1G229000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1553.t1 is derived from g8472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1720892	1723259	.	+	.	Phchi.S5G016200
Phchi.S5	AUGUSTUS	transcript	1720892	1723259	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	start_codon	1720892	1720894	.	+	0	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1720892	1721188	0.99	+	0	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1720892	1721188	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	intron	1721189	1721319	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1721320	1721564	1	+	0	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1721320	1721564	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	intron	1721565	1721759	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1721760	1721844	1	+	1	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1721760	1721844	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	intron	1721845	1721917	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1721918	1722487	1	+	0	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1721918	1722487	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	intron	1722488	1722569	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1722570	1722741	1	+	0	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1722570	1722741	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	intron	1722742	1722903	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1722904	1723075	1	+	2	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1722904	1723075	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	intron	1723076	1723168	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	CDS	1723169	1723259	1	+	1	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	exon	1723169	1723259	.	+	.	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
Phchi.S5	AUGUSTUS	stop_codon	1723260	1723262	.	+	0	transcript_id "Phchi.S5G016200.t1"; gene_id "Phchi.S5G016200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10260.t1 is derived from g7436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46721967	46723479	.	+	.	Phchi.S1G741900
Phchi.S1	AUGUSTUS	transcript	46721967	46723479	.	+	.	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	start_codon	46721967	46721969	.	+	0	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	CDS	46721967	46722105	0.34	+	0	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	exon	46721967	46722105	.	+	.	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	intron	46722106	46722360	.	+	.	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	CDS	46722361	46723115	0.26	+	2	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	exon	46722361	46723115	.	+	.	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	intron	46723116	46723446	.	+	.	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	CDS	46723447	46723479	0.95	+	0	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	exon	46723447	46723479	.	+	.	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
Phchi.S1	AUGUSTUS	stop_codon	46723480	46723482	.	+	0	transcript_id "Phchi.S1G741900.t1"; gene_id "Phchi.S1G741900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg701.t1 is derived from g10483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4972312	4974656	.	-	.	Phchi.S6G066000
Phchi.S6	AUGUSTUS	transcript	4972312	4974656	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	stop_codon	4972309	4972311	.	-	0	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4972312	4972487	1	-	2	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4972312	4972487	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	intron	4972488	4972577	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4972578	4973391	0.86	-	0	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4972578	4973391	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	intron	4973392	4973476	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4973477	4973655	0.4	-	2	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4973477	4973655	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	intron	4973656	4973705	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4973706	4973972	0.51	-	2	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4973706	4973972	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	intron	4973973	4974115	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4974116	4974196	0.78	-	2	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4974116	4974196	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	intron	4974197	4974295	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4974296	4974412	1	-	2	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4974296	4974412	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	intron	4974413	4974499	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	CDS	4974500	4974656	0.55	-	0	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	exon	4974500	4974656	.	-	.	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
Phchi.S6	AUGUSTUS	start_codon	4974654	4974656	.	-	0	transcript_id "Phchi.S6G066000.t1"; gene_id "Phchi.S6G066000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5461.t1 is derived from g2631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16954139	16955218	.	+	.	Phchi.S1G262000
Phchi.S1	AUGUSTUS	transcript	16954139	16955218	.	+	.	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	start_codon	16954139	16954141	.	+	0	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	CDS	16954139	16954747	0.84	+	0	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	exon	16954139	16954747	.	+	.	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	intron	16954748	16954839	.	+	.	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	CDS	16954840	16955053	1	+	0	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	exon	16954840	16955053	.	+	.	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	intron	16955054	16955135	.	+	.	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	CDS	16955136	16955218	1	+	2	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	exon	16955136	16955218	.	+	.	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
Phchi.S1	AUGUSTUS	stop_codon	16955219	16955221	.	+	0	transcript_id "Phchi.S1G262000.t1"; gene_id "Phchi.S1G262000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13480.t1 is derived from g11947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7090686	7093165	.	+	.	Phchi.S3G079900
Phchi.S3	AUGUSTUS	transcript	7090686	7093165	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	start_codon	7090686	7090688	.	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7090686	7090886	0.8	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7090686	7090886	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7090887	7090977	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7090978	7091247	0.98	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7090978	7091247	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7091248	7091337	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7091338	7091427	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7091338	7091427	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7091428	7091511	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7091512	7091607	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7091512	7091607	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7091608	7091787	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7091788	7091898	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7091788	7091898	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7091899	7091983	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7091984	7092033	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7091984	7092033	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7092034	7092118	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7092119	7092221	0.96	+	1	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7092119	7092221	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7092222	7092334	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7092335	7092388	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7092335	7092388	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7092389	7092535	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7092536	7092694	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7092536	7092694	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7092695	7092819	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7092820	7092942	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7092820	7092942	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7092943	7093032	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7093033	7093081	1	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7093033	7093081	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	intron	7093082	7093160	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	CDS	7093161	7093165	1	+	2	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	exon	7093161	7093165	.	+	.	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
Phchi.S3	AUGUSTUS	stop_codon	7093166	7093168	.	+	0	transcript_id "Phchi.S3G079900.t1"; gene_id "Phchi.S3G079900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13056.t1 is derived from g11521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3929722	3931475	.	-	.	Phchi.S3G037500
Phchi.S3	AUGUSTUS	transcript	3929722	3931475	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	stop_codon	3929719	3929721	.	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3929722	3929797	1	-	1	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3929722	3929797	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3929798	3929877	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3929878	3929988	1	-	1	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3929878	3929988	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3929989	3930082	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3930083	3930165	1	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3930083	3930165	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3930166	3930291	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3930292	3930345	0.98	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3930292	3930345	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3930346	3930428	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3930429	3930515	0.97	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3930429	3930515	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3930516	3930612	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3930613	3930696	0.96	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3930613	3930696	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3930697	3930790	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3930791	3930982	0.88	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3930791	3930982	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3930983	3931156	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3931157	3931279	0.54	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3931157	3931279	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	intron	3931280	3931385	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	CDS	3931386	3931475	0.44	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	exon	3931386	3931475	.	-	.	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
Phchi.S3	AUGUSTUS	start_codon	3931473	3931475	.	-	0	transcript_id "Phchi.S3G037500.t1"; gene_id "Phchi.S3G037500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5597.t1 is derived from g2767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17819535	17822697	.	+	.	Phchi.S1G275600
Phchi.S1	AUGUSTUS	transcript	17819535	17822697	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	start_codon	17819535	17819537	.	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17819535	17819676	0.92	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17819535	17819676	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17819677	17819751	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17819752	17820035	1	+	2	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17819752	17820035	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17820036	17820115	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17820116	17820189	1	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17820116	17820189	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17820190	17820280	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17820281	17820375	0.98	+	1	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17820281	17820375	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17820376	17820490	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17820491	17820588	0.98	+	2	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17820491	17820588	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17820589	17820743	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17820744	17820827	1	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17820744	17820827	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17820828	17820952	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17820953	17821033	1	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17820953	17821033	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17821034	17821306	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17821307	17821420	1	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17821307	17821420	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17821421	17821550	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17821551	17821646	1	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17821551	17821646	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17821647	17821736	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17821737	17821816	1	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17821737	17821816	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17821817	17821958	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17821959	17822041	1	+	1	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17821959	17822041	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	intron	17822042	17822185	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	CDS	17822186	17822697	0.98	+	2	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	exon	17822186	17822697	.	+	.	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
Phchi.S1	AUGUSTUS	stop_codon	17822698	17822700	.	+	0	transcript_id "Phchi.S1G275600.t1"; gene_id "Phchi.S1G275600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3795.t1 is derived from g964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5781418	5783903	.	-	.	Phchi.S1G095400
Phchi.S1	AUGUSTUS	transcript	5781418	5783903	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	stop_codon	5781415	5781417	.	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5781418	5781978	1	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5781418	5781978	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	intron	5781979	5782071	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5782072	5782431	1	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5782072	5782431	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	intron	5782432	5782529	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5782530	5782811	0.99	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5782530	5782811	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	intron	5782812	5782911	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5782912	5782986	0.85	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5782912	5782986	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	intron	5782987	5783087	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5783088	5783242	0.9	-	2	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5783088	5783242	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	intron	5783243	5783362	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5783363	5783479	0.97	-	2	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5783363	5783479	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	intron	5783480	5783590	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	CDS	5783591	5783903	0.98	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	exon	5783591	5783903	.	-	.	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
Phchi.S1	AUGUSTUS	start_codon	5783901	5783903	.	-	0	transcript_id "Phchi.S1G095400.t1"; gene_id "Phchi.S1G095400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7978.t1 is derived from g5153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32203661	32204795	.	-	.	Phchi.S1G513700
Phchi.S1	AUGUSTUS	transcript	32203661	32204795	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	stop_codon	32203658	32203660	.	-	0	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	CDS	32203661	32203750	0.25	-	0	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	exon	32203661	32203750	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	intron	32203751	32203987	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	CDS	32203988	32204093	0.67	-	1	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	exon	32203988	32204093	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	intron	32204094	32204203	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	CDS	32204204	32204354	0.56	-	2	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	exon	32204204	32204354	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	intron	32204355	32204719	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	CDS	32204720	32204795	0.97	-	0	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	exon	32204720	32204795	.	-	.	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
Phchi.S1	AUGUSTUS	start_codon	32204793	32204795	.	-	0	transcript_id "Phchi.S1G513700.t1"; gene_id "Phchi.S1G513700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3909.t1 is derived from g1078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6397194	6398873	.	-	.	Phchi.S1G106800
Phchi.S1	AUGUSTUS	transcript	6397194	6398873	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	stop_codon	6397191	6397193	.	-	0	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6397194	6397423	0.82	-	2	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6397194	6397423	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6397424	6397520	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6397521	6397625	1	-	2	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6397521	6397625	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6397626	6397721	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6397722	6397756	0.98	-	1	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6397722	6397756	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6397757	6397839	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6397840	6397851	0.98	-	1	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6397840	6397851	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6397852	6397949	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6397950	6398016	0.98	-	2	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6397950	6398016	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6398017	6398148	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6398149	6398220	1	-	2	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6398149	6398220	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6398221	6398376	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6398377	6398472	1	-	2	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6398377	6398472	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6398473	6398596	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6398597	6398711	1	-	0	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6398597	6398711	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	intron	6398712	6398834	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	CDS	6398835	6398873	1	-	0	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	exon	6398835	6398873	.	-	.	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
Phchi.S1	AUGUSTUS	start_codon	6398871	6398873	.	-	0	transcript_id "Phchi.S1G106800.t1"; gene_id "Phchi.S1G106800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3587.t1 is derived from g756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4622099	4622763	.	+	.	Phchi.S1G074600
Phchi.S1	AUGUSTUS	transcript	4622099	4622763	.	+	.	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	start_codon	4622099	4622101	.	+	0	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	CDS	4622099	4622134	0.4	+	0	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	exon	4622099	4622134	.	+	.	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	intron	4622135	4622217	.	+	.	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	CDS	4622218	4622352	0.89	+	0	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	exon	4622218	4622352	.	+	.	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	intron	4622353	4622460	.	+	.	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	CDS	4622461	4622763	0.83	+	0	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	exon	4622461	4622763	.	+	.	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
Phchi.S1	AUGUSTUS	stop_codon	4622764	4622766	.	+	0	transcript_id "Phchi.S1G074600.t1"; gene_id "Phchi.S1G074600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10641.t1 is derived from g14691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1379382	1380784	.	+	.	Phchi.S4G022300
Phchi.S4	AUGUSTUS	transcript	1379382	1380784	.	+	.	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	start_codon	1379382	1379384	.	+	0	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	CDS	1379382	1379390	0.86	+	0	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	exon	1379382	1379390	.	+	.	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	intron	1379391	1380021	.	+	.	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	CDS	1380022	1380472	0.98	+	0	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	exon	1380022	1380472	.	+	.	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	intron	1380473	1380584	.	+	.	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	CDS	1380585	1380784	0.95	+	2	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	exon	1380585	1380784	.	+	.	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
Phchi.S4	AUGUSTUS	stop_codon	1380785	1380787	.	+	0	transcript_id "Phchi.S4G022300.t1"; gene_id "Phchi.S4G022300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7259.t1 is derived from g4431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27899406	27902763	.	+	.	Phchi.S1G441800
Phchi.S1	AUGUSTUS	transcript	27899406	27902763	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	start_codon	27899406	27899408	.	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27899406	27899699	0.96	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27899406	27899699	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27899700	27899813	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27899814	27899906	0.99	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27899814	27899906	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27899907	27900011	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27900012	27900332	0.63	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27900012	27900332	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27900333	27900475	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27900476	27900541	0.6	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27900476	27900541	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27900542	27900903	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27900904	27901168	0.72	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27900904	27901168	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27901169	27901274	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27901275	27901444	0.7	+	2	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27901275	27901444	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27901445	27901524	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27901525	27901700	1	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27901525	27901700	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27901701	27901839	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27901840	27901948	0.99	+	1	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27901840	27901948	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	intron	27901949	27902049	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	CDS	27902050	27902763	1	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	exon	27902050	27902763	.	+	.	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
Phchi.S1	AUGUSTUS	stop_codon	27902764	27902766	.	+	0	transcript_id "Phchi.S1G441800.t1"; gene_id "Phchi.S1G441800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12595.t1 is derived from g8272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36932077	36932757	.	-	.	Phchi.S2G067500
Phchi.S2	AUGUSTUS	transcript	36932077	36932757	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	stop_codon	36932074	36932076	.	-	0	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932077	36932111	0.99	-	2	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932077	36932111	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932112	36932184	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932185	36932236	0.99	-	0	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932185	36932236	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932237	36932310	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932311	36932468	0.99	-	2	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932311	36932468	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932469	36932550	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932551	36932614	1	-	0	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932551	36932614	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932615	36932712	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932713	36932757	0.85	-	0	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932713	36932757	.	-	.	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	start_codon	36932755	36932757	.	-	0	transcript_id "Phchi.S2G067500.t1"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	transcript	36932077	36932757	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	stop_codon	36932074	36932076	.	-	0	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932077	36932111	1	-	2	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932077	36932111	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932112	36932184	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932185	36932225	0.73	-	1	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932185	36932225	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932226	36932310	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932311	36932354	0.71	-	0	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932311	36932354	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932355	36932433	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932434	36932468	0.71	-	2	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932434	36932468	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932469	36932550	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932551	36932614	0.94	-	0	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932551	36932614	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	intron	36932615	36932712	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	CDS	36932713	36932757	0.76	-	0	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	exon	36932713	36932757	.	-	.	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
Phchi.S2	AUGUSTUS	start_codon	36932755	36932757	.	-	0	transcript_id "Phchi.S2G067500.t2"; gene_id "Phchi.S2G067500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13947.t1 is derived from g12414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9858824	9859194	.	+	.	Phchi.S3G126600
Phchi.S3	AUGUSTUS	transcript	9858824	9859194	.	+	.	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	start_codon	9858824	9858826	.	+	0	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	CDS	9858824	9859010	0.94	+	0	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	exon	9858824	9859010	.	+	.	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	intron	9859011	9859153	.	+	.	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	CDS	9859154	9859194	0.94	+	2	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	exon	9859154	9859194	.	+	.	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
Phchi.S3	AUGUSTUS	stop_codon	9859195	9859197	.	+	0	transcript_id "Phchi.S3G126600.t1"; gene_id "Phchi.S3G126600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6757.t1 is derived from g3929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24905832	24908785	.	-	.	Phchi.S1G391600
Phchi.S1	AUGUSTUS	transcript	24905832	24908785	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	stop_codon	24905829	24905831	.	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24905832	24905884	0.8	-	2	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24905832	24905884	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24905885	24906018	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906019	24906082	0.75	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906019	24906082	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906083	24906174	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906175	24906187	0.75	-	1	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906175	24906187	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906188	24906327	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906328	24906396	0.59	-	1	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906328	24906396	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906397	24906834	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906835	24906975	0.23	-	1	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906835	24906975	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906976	24907093	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907094	24907275	0.51	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907094	24907275	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24907276	24907374	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907375	24907479	1	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907375	24907479	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24907480	24907649	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907650	24907840	1	-	2	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907650	24907840	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24907841	24907969	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907970	24908065	1	-	2	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907970	24908065	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24908066	24908330	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24908331	24908371	0.22	-	1	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24908331	24908371	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24908372	24908499	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24908500	24908531	0.44	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24908500	24908531	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24908532	24908689	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24908690	24908785	0.77	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24908690	24908785	.	-	.	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	start_codon	24908783	24908785	.	-	0	transcript_id "Phchi.S1G391600.t1"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	transcript	24905832	24908785	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	stop_codon	24905829	24905831	.	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24905832	24905884	0.82	-	2	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24905832	24905884	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24905885	24906018	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906019	24906082	0.72	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906019	24906082	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906083	24906174	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906175	24906187	0.72	-	1	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906175	24906187	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906188	24906327	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906328	24906396	0.51	-	1	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906328	24906396	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906397	24906834	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24906835	24906975	0.26	-	1	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24906835	24906975	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24906976	24907093	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907094	24907275	0.42	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907094	24907275	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24907276	24907374	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907375	24907479	1	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907375	24907479	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24907480	24907649	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907650	24907840	1	-	2	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907650	24907840	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24907841	24907969	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24907970	24908029	1	-	2	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24907970	24908029	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24908030	24908330	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24908331	24908371	0.26	-	1	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24908331	24908371	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24908372	24908499	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24908500	24908531	0.49	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24908500	24908531	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	intron	24908532	24908689	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	CDS	24908690	24908785	0.71	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	exon	24908690	24908785	.	-	.	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
Phchi.S1	AUGUSTUS	start_codon	24908783	24908785	.	-	0	transcript_id "Phchi.S1G391600.t2"; gene_id "Phchi.S1G391600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8646.t1 is derived from g5821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37224167	37229405	.	-	.	Phchi.S1G580500
Phchi.S1	AUGUSTUS	transcript	37224167	37229405	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	stop_codon	37224164	37224166	.	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37224167	37224256	0.88	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37224167	37224256	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37224257	37224432	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37224433	37225296	0.88	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37224433	37225296	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37225297	37225392	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37225393	37225473	0.98	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37225393	37225473	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37225474	37225569	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37225570	37225662	0.98	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37225570	37225662	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37225663	37225762	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37225763	37225869	0.93	-	2	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37225763	37225869	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37225870	37225978	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37225979	37226081	0.96	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37225979	37226081	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37226082	37226178	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37226179	37226355	1	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37226179	37226355	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37226356	37226447	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37226448	37226523	1	-	1	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37226448	37226523	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37226524	37226629	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37226630	37226714	1	-	2	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37226630	37226714	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37226715	37226861	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37226862	37227056	1	-	2	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37226862	37227056	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37227057	37227186	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37227187	37227350	0.74	-	1	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37227187	37227350	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37227351	37227674	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37227675	37227768	0.91	-	2	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37227675	37227768	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37227769	37228077	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37228078	37228314	1	-	2	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37228078	37228314	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37228315	37228644	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37228645	37228729	1	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37228645	37228729	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37228730	37228846	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37228847	37228993	1	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37228847	37228993	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	intron	37228994	37229084	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	CDS	37229085	37229405	0.95	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	exon	37229085	37229405	.	-	.	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
Phchi.S1	AUGUSTUS	start_codon	37229403	37229405	.	-	0	transcript_id "Phchi.S1G580500.t1"; gene_id "Phchi.S1G580500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3621.t1 is derived from g790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4804530	4806546	.	+	.	Phchi.S1G078000
Phchi.S1	AUGUSTUS	transcript	4804530	4806546	.	+	.	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	start_codon	4804530	4804532	.	+	0	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	CDS	4804530	4805709	0.96	+	0	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	exon	4804530	4805709	.	+	.	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	intron	4805710	4805809	.	+	.	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	CDS	4805810	4806546	0.98	+	2	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	exon	4805810	4806546	.	+	.	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
Phchi.S1	AUGUSTUS	stop_codon	4806547	4806549	.	+	0	transcript_id "Phchi.S1G078000.t1"; gene_id "Phchi.S1G078000"
# This transcript jg15540.t2 is derived from g14009.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15541.t1 is derived from g14010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19781289	19783152	.	+	.	Phchi.S3G286000
Phchi.S3	AUGUSTUS	transcript	19781289	19783152	.	+	.	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	start_codon	19781289	19781291	.	+	0	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	CDS	19781289	19781322	0.99	+	0	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	exon	19781289	19781322	.	+	.	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	intron	19781323	19781412	.	+	.	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	CDS	19781413	19781511	0.78	+	2	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	exon	19781413	19781511	.	+	.	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	intron	19781512	19781626	.	+	.	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	CDS	19781627	19783152	0.76	+	2	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	exon	19781627	19783152	.	+	.	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
Phchi.S3	AUGUSTUS	stop_codon	19783153	19783155	.	+	0	transcript_id "Phchi.S3G286000.t1"; gene_id "Phchi.S3G286000"
# This transcript jg4007.t2 is derived from g1176.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4008.t1 is derived from g1177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6998959	6999408	.	+	.	Phchi.S1G116700
Phchi.S1	AUGUSTUS	transcript	6998959	6999408	.	+	.	transcript_id "Phchi.S1G116700.t1"; gene_id "Phchi.S1G116700"
Phchi.S1	AUGUSTUS	start_codon	6998959	6998961	.	+	0	transcript_id "Phchi.S1G116700.t1"; gene_id "Phchi.S1G116700"
Phchi.S1	AUGUSTUS	CDS	6998959	6999408	0.74	+	0	transcript_id "Phchi.S1G116700.t1"; gene_id "Phchi.S1G116700"
Phchi.S1	AUGUSTUS	exon	6998959	6999408	.	+	.	transcript_id "Phchi.S1G116700.t1"; gene_id "Phchi.S1G116700"
Phchi.S1	AUGUSTUS	stop_codon	6999409	6999411	.	+	0	transcript_id "Phchi.S1G116700.t1"; gene_id "Phchi.S1G116700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13503.t1 is derived from g11970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7202860	7204479	.	-	.	Phchi.S3G082200
Phchi.S3	AUGUSTUS	transcript	7202860	7204479	.	-	.	transcript_id "Phchi.S3G082200.t1"; gene_id "Phchi.S3G082200"
Phchi.S3	AUGUSTUS	stop_codon	7202857	7202859	.	-	0	transcript_id "Phchi.S3G082200.t1"; gene_id "Phchi.S3G082200"
Phchi.S3	AUGUSTUS	CDS	7202860	7204479	0.66	-	0	transcript_id "Phchi.S3G082200.t1"; gene_id "Phchi.S3G082200"
Phchi.S3	AUGUSTUS	exon	7202860	7204479	.	-	.	transcript_id "Phchi.S3G082200.t1"; gene_id "Phchi.S3G082200"
Phchi.S3	AUGUSTUS	start_codon	7204477	7204479	.	-	0	transcript_id "Phchi.S3G082200.t1"; gene_id "Phchi.S3G082200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4181.t1 is derived from g1350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8786902	8788538	.	-	.	Phchi.S1G134000
Phchi.S1	AUGUSTUS	transcript	8786902	8788538	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	stop_codon	8786899	8786901	.	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8786902	8786997	1	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8786902	8786997	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	intron	8786998	8787078	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8787079	8787233	1	-	2	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8787079	8787233	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	intron	8787234	8787319	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8787320	8787483	1	-	1	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8787320	8787483	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	intron	8787484	8787585	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8787586	8787707	1	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8787586	8787707	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	intron	8787708	8787890	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8787891	8788106	1	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8787891	8788106	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	intron	8788107	8788200	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8788201	8788356	1	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8788201	8788356	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	intron	8788357	8788442	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	CDS	8788443	8788538	0.63	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	exon	8788443	8788538	.	-	.	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
Phchi.S1	AUGUSTUS	start_codon	8788536	8788538	.	-	0	transcript_id "Phchi.S1G134000.t1"; gene_id "Phchi.S1G134000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2176.t1 is derived from g9096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5227025	5232053	.	-	.	Phchi.S5G078500
Phchi.S5	AUGUSTUS	transcript	5227025	5232053	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	stop_codon	5227022	5227024	.	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5227025	5227271	0.93	-	1	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5227025	5227271	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5227272	5227370	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5227371	5227465	1	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5227371	5227465	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5227466	5227556	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5227557	5227598	1	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5227557	5227598	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5227599	5227671	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5227672	5227839	0.99	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5227672	5227839	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5227840	5227943	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5227944	5228128	0.95	-	2	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5227944	5228128	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5228129	5228247	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5228248	5228470	1	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5228248	5228470	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5228471	5228599	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5228600	5228893	0.99	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5228600	5228893	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5228894	5228976	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5228977	5229147	1	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5228977	5229147	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5229148	5229240	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5229241	5229602	0.7	-	2	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5229241	5229602	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5229603	5229707	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5229708	5229847	0.98	-	1	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5229708	5229847	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5229848	5229939	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5229940	5230351	0.59	-	2	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5229940	5230351	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5230352	5230434	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5230435	5230505	0.44	-	1	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5230435	5230505	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5230506	5230654	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5230655	5230769	0.44	-	2	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5230655	5230769	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5230770	5230919	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5230920	5231061	1	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5230920	5231061	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5231062	5231180	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5231181	5231285	1	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5231181	5231285	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5231286	5231361	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5231362	5231483	1	-	2	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5231362	5231483	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5231484	5231594	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5231595	5231637	0.63	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5231595	5231637	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	intron	5231638	5231861	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	CDS	5231862	5232053	0.96	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	exon	5231862	5232053	.	-	.	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
Phchi.S5	AUGUSTUS	start_codon	5232051	5232053	.	-	0	transcript_id "Phchi.S5G078500.t1"; gene_id "Phchi.S5G078500"
# This transcript jg14661.t2 is derived from g13129.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14662.t1 is derived from g13130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14008661	14009473	.	+	.	Phchi.S3G198100
Phchi.S3	AUGUSTUS	transcript	14008661	14009473	.	+	.	transcript_id "Phchi.S3G198100.t1"; gene_id "Phchi.S3G198100"
Phchi.S3	AUGUSTUS	start_codon	14008661	14008663	.	+	0	transcript_id "Phchi.S3G198100.t1"; gene_id "Phchi.S3G198100"
Phchi.S3	AUGUSTUS	CDS	14008661	14009473	1	+	0	transcript_id "Phchi.S3G198100.t1"; gene_id "Phchi.S3G198100"
Phchi.S3	AUGUSTUS	exon	14008661	14009473	.	+	.	transcript_id "Phchi.S3G198100.t1"; gene_id "Phchi.S3G198100"
Phchi.S3	AUGUSTUS	stop_codon	14009474	14009476	.	+	0	transcript_id "Phchi.S3G198100.t1"; gene_id "Phchi.S3G198100"
# This transcript jg1604.t2 is derived from g8523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1605.t1 is derived from g8524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1989929	1992275	.	+	.	Phchi.S5G021400
Phchi.S5	AUGUSTUS	transcript	1989929	1992275	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	start_codon	1989929	1989931	.	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1989929	1990087	0.98	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1989929	1990087	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1990088	1990181	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1990182	1990266	1	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1990182	1990266	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1990267	1990356	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1990357	1990571	1	+	2	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1990357	1990571	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1990572	1990658	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1990659	1990741	1	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1990659	1990741	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1990742	1990901	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1990902	1990947	1	+	1	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1990902	1990947	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1990948	1991176	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1991177	1991233	1	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1991177	1991233	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1991234	1991356	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1991357	1991411	1	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1991357	1991411	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1991412	1991500	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1991501	1991583	1	+	2	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1991501	1991583	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1991584	1991703	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1991704	1991767	1	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1991704	1991767	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1991768	1991861	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1991862	1991995	0.84	+	2	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1991862	1991995	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	intron	1991996	1992107	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	CDS	1992108	1992275	0.76	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	exon	1992108	1992275	.	+	.	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
Phchi.S5	AUGUSTUS	stop_codon	1992276	1992278	.	+	0	transcript_id "Phchi.S5G021400.t1"; gene_id "Phchi.S5G021400"
# This transcript jg14099.t2 is derived from g12566.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14100.t1 is derived from g12567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10838112	10841779	.	+	.	Phchi.S3G141900
Phchi.S3	AUGUSTUS	transcript	10838112	10841779	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	start_codon	10838112	10838114	.	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10838112	10838504	0.94	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10838112	10838504	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10838505	10838592	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10838593	10838736	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10838593	10838736	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10838737	10838854	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10838855	10838964	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10838855	10838964	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10838965	10839061	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10839062	10839173	1	+	1	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10839062	10839173	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10839174	10839266	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10839267	10839338	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10839267	10839338	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10839339	10839430	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10839431	10839522	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10839431	10839522	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10839523	10839609	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10839610	10839730	1	+	1	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10839610	10839730	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10839731	10839841	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10839842	10839964	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10839842	10839964	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10839965	10840251	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10840252	10840447	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10840252	10840447	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10840448	10840587	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10840588	10840775	1	+	2	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10840588	10840775	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10840776	10840898	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10840899	10840970	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10840899	10840970	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10840971	10841049	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10841050	10841148	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10841050	10841148	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10841149	10841261	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10841262	10841342	1	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10841262	10841342	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10841343	10841424	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10841425	10841482	0.91	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10841425	10841482	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	intron	10841483	10841585	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	CDS	10841586	10841779	1	+	2	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	exon	10841586	10841779	.	+	.	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
Phchi.S3	AUGUSTUS	stop_codon	10841780	10841782	.	+	0	transcript_id "Phchi.S3G141900.t1"; gene_id "Phchi.S3G141900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10365.t1 is derived from g7541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47400395	47401283	.	-	.	Phchi.S1G752400
Phchi.S1	AUGUSTUS	transcript	47400910	47401283	.	-	.	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	stop_codon	47400907	47400909	.	-	0	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47400910	47400927	0.61	-	0	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47400910	47400927	.	-	.	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	intron	47400928	47401018	.	-	.	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47401019	47401075	0.61	-	0	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47401019	47401075	.	-	.	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	intron	47401076	47401154	.	-	.	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47401155	47401283	0.61	-	0	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47401155	47401283	.	-	.	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	start_codon	47401281	47401283	.	-	0	transcript_id "Phchi.S1G752400.t1"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	transcript	47400395	47401283	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	stop_codon	47400392	47400394	.	-	0	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47400395	47400485	0.52	-	1	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47400395	47400485	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	intron	47400486	47400608	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47400609	47400683	0.33	-	1	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47400609	47400683	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	intron	47400684	47400813	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47400814	47400927	0.26	-	1	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47400814	47400927	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	intron	47400928	47401018	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47401019	47401095	0.81	-	0	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47401019	47401095	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	intron	47401096	47401154	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	CDS	47401155	47401283	0.81	-	0	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	exon	47401155	47401283	.	-	.	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
Phchi.S1	AUGUSTUS	start_codon	47401281	47401283	.	-	0	transcript_id "Phchi.S1G752400.t2"; gene_id "Phchi.S1G752400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2911.t1 is derived from g80.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	451082	451568	.	+	.	Phchi.S1G007000
Phchi.S1	AUGUSTUS	transcript	451082	451568	.	+	.	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	start_codon	451082	451084	.	+	0	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	CDS	451082	451167	0.99	+	0	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	exon	451082	451167	.	+	.	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	intron	451168	451258	.	+	.	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	CDS	451259	451315	0.99	+	1	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	exon	451259	451315	.	+	.	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	intron	451316	451405	.	+	.	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	CDS	451406	451568	0.51	+	1	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	exon	451406	451568	.	+	.	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
Phchi.S1	AUGUSTUS	stop_codon	451569	451571	.	+	0	transcript_id "Phchi.S1G007000.t1"; gene_id "Phchi.S1G007000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15967.t1 is derived from g16006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	25098	27431	.	-	.	Phchi.C133G000600
Phchi.C133	AUGUSTUS	transcript	25098	27431	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	stop_codon	25095	25097	.	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	25098	25185	1	-	1	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	25098	25185	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	25186	25261	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	25262	25383	1	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	25262	25383	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	25384	25488	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	25489	25595	1	-	2	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	25489	25595	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	25596	25687	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	25688	25766	1	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	25688	25766	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	25767	25879	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	25880	25963	1	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	25880	25963	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	25964	26093	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	26094	26354	0.78	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	26094	26354	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	26355	26458	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	26459	26608	0.99	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	26459	26608	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	26609	26734	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	26735	27062	1	-	1	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	26735	27062	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	intron	27063	27153	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	CDS	27154	27431	0.72	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	exon	27154	27431	.	-	.	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
Phchi.C133	AUGUSTUS	start_codon	27429	27431	.	-	0	transcript_id "Phchi.C133G000600.t1"; gene_id "Phchi.C133G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2999.t1 is derived from g168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1078052	1079753	.	-	.	Phchi.S1G015800
Phchi.S1	AUGUSTUS	transcript	1078052	1079753	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	stop_codon	1078049	1078051	.	-	0	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1078052	1078341	0.94	-	2	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1078052	1078341	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	intron	1078342	1078458	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1078459	1078628	0.99	-	1	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1078459	1078628	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	intron	1078629	1078707	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1078708	1078816	1	-	2	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1078708	1078816	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	intron	1078817	1078905	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1078906	1079099	1	-	1	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1078906	1079099	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	intron	1079100	1079219	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1079220	1079407	1	-	0	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1079220	1079407	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	intron	1079408	1079489	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1079490	1079582	1	-	0	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1079490	1079582	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	intron	1079583	1079681	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	CDS	1079682	1079753	0.58	-	0	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	exon	1079682	1079753	.	-	.	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
Phchi.S1	AUGUSTUS	start_codon	1079751	1079753	.	-	0	transcript_id "Phchi.S1G015800.t1"; gene_id "Phchi.S1G015800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12459.t1 is derived from g8136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24353318	24353923	.	+	.	Phchi.S2G053900
Phchi.S2	AUGUSTUS	transcript	24353318	24353923	.	+	.	transcript_id "Phchi.S2G053900.t1"; gene_id "Phchi.S2G053900"
Phchi.S2	AUGUSTUS	start_codon	24353318	24353320	.	+	0	transcript_id "Phchi.S2G053900.t1"; gene_id "Phchi.S2G053900"
Phchi.S2	AUGUSTUS	CDS	24353318	24353923	0.98	+	0	transcript_id "Phchi.S2G053900.t1"; gene_id "Phchi.S2G053900"
Phchi.S2	AUGUSTUS	exon	24353318	24353923	.	+	.	transcript_id "Phchi.S2G053900.t1"; gene_id "Phchi.S2G053900"
Phchi.S2	AUGUSTUS	stop_codon	24353924	24353926	.	+	0	transcript_id "Phchi.S2G053900.t1"; gene_id "Phchi.S2G053900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14570.t1 is derived from g13038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13538355	13538957	.	+	.	Phchi.S3G188900
Phchi.S3	AUGUSTUS	transcript	13538355	13538957	.	+	.	transcript_id "Phchi.S3G188900.t1"; gene_id "Phchi.S3G188900"
Phchi.S3	AUGUSTUS	start_codon	13538355	13538357	.	+	0	transcript_id "Phchi.S3G188900.t1"; gene_id "Phchi.S3G188900"
Phchi.S3	AUGUSTUS	CDS	13538355	13538957	0.47	+	0	transcript_id "Phchi.S3G188900.t1"; gene_id "Phchi.S3G188900"
Phchi.S3	AUGUSTUS	exon	13538355	13538957	.	+	.	transcript_id "Phchi.S3G188900.t1"; gene_id "Phchi.S3G188900"
Phchi.S3	AUGUSTUS	stop_codon	13538958	13538960	.	+	0	transcript_id "Phchi.S3G188900.t1"; gene_id "Phchi.S3G188900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14832.t1 is derived from g13300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14919757	14921227	.	-	.	Phchi.S3G215100
Phchi.S3	AUGUSTUS	transcript	14919757	14921227	.	-	.	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	stop_codon	14919754	14919756	.	-	0	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	CDS	14919757	14920323	1	-	0	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	exon	14919757	14920323	.	-	.	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	intron	14920324	14920444	.	-	.	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	CDS	14920445	14920970	1	-	1	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	exon	14920445	14920970	.	-	.	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	intron	14920971	14921045	.	-	.	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	CDS	14921046	14921227	0.97	-	0	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	exon	14921046	14921227	.	-	.	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
Phchi.S3	AUGUSTUS	start_codon	14921225	14921227	.	-	0	transcript_id "Phchi.S3G215100.t1"; gene_id "Phchi.S3G215100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7439.t1 is derived from g4611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29123460	29127016	.	+	.	Phchi.S1G459800
Phchi.S1	AUGUSTUS	transcript	29123460	29127016	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	start_codon	29123460	29123462	.	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29123460	29123826	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29123460	29123826	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29123827	29124041	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29124042	29124156	1	+	2	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29124042	29124156	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29124157	29124339	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29124340	29124535	1	+	1	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29124340	29124535	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29124536	29124686	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29124687	29124800	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29124687	29124800	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29124801	29124940	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29124941	29125111	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29124941	29125111	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29125112	29125216	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29125217	29125411	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29125217	29125411	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29125412	29125503	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29125504	29125626	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29125504	29125626	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29125627	29125819	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29125820	29125941	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29125820	29125941	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29125942	29126049	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29126050	29126088	1	+	1	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29126050	29126088	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29126089	29126173	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29126174	29126300	1	+	1	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29126174	29126300	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29126301	29126387	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29126388	29126663	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29126388	29126663	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	intron	29126664	29126776	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	CDS	29126777	29127016	1	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	exon	29126777	29127016	.	+	.	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
Phchi.S1	AUGUSTUS	stop_codon	29127017	29127019	.	+	0	transcript_id "Phchi.S1G459800.t1"; gene_id "Phchi.S1G459800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5650.t1 is derived from g2820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18058900	18059500	.	+	.	Phchi.S1G280900
Phchi.S1	AUGUSTUS	transcript	18058900	18059500	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	start_codon	18058900	18058902	.	+	0	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	CDS	18058900	18058910	0.55	+	0	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	exon	18058900	18058910	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	intron	18058911	18059075	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	CDS	18059076	18059198	0.24	+	1	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	exon	18059076	18059198	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	intron	18059199	18059309	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	CDS	18059310	18059344	0.32	+	1	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	exon	18059310	18059344	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	intron	18059345	18059438	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	CDS	18059439	18059500	0.44	+	2	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	exon	18059439	18059500	.	+	.	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
Phchi.S1	AUGUSTUS	stop_codon	18059501	18059503	.	+	0	transcript_id "Phchi.S1G280900.t1"; gene_id "Phchi.S1G280900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1440.t1 is derived from g8359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	862047	863129	.	+	.	Phchi.S5G004900
Phchi.S5	AUGUSTUS	transcript	862047	863129	.	+	.	transcript_id "Phchi.S5G004900.t1"; gene_id "Phchi.S5G004900"
Phchi.S5	AUGUSTUS	start_codon	862047	862049	.	+	0	transcript_id "Phchi.S5G004900.t1"; gene_id "Phchi.S5G004900"
Phchi.S5	AUGUSTUS	CDS	862047	863129	0.88	+	0	transcript_id "Phchi.S5G004900.t1"; gene_id "Phchi.S5G004900"
Phchi.S5	AUGUSTUS	exon	862047	863129	.	+	.	transcript_id "Phchi.S5G004900.t1"; gene_id "Phchi.S5G004900"
Phchi.S5	AUGUSTUS	stop_codon	863130	863132	.	+	0	transcript_id "Phchi.S5G004900.t1"; gene_id "Phchi.S5G004900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12420.t1 is derived from g8097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19338897	19343041	.	+	.	Phchi.S2G050000
Phchi.S2	AUGUSTUS	transcript	19338897	19343041	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	start_codon	19338897	19338899	.	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19338897	19338999	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19338897	19338999	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19339000	19339082	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19339083	19339177	1	+	2	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19339083	19339177	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19339178	19339263	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19339264	19339377	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19339264	19339377	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19339378	19339785	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19339786	19339890	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19339786	19339890	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19339891	19339985	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19339986	19340057	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19339986	19340057	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19340058	19340321	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19340322	19340434	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19340322	19340434	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19340435	19340547	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19340548	19340682	1	+	1	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19340548	19340682	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19340683	19340805	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19340806	19340874	1	+	1	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19340806	19340874	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19340875	19341327	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19341328	19341427	1	+	1	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19341328	19341427	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19341428	19341692	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19341693	19341764	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19341693	19341764	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19341765	19341882	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19341883	19341983	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19341883	19341983	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19341984	19342211	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19342212	19342329	1	+	1	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19342212	19342329	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19342330	19342474	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19342475	19342534	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19342475	19342534	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19342535	19342662	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19342663	19342773	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19342663	19342773	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	intron	19342774	19342939	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	CDS	19342940	19343041	1	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	exon	19342940	19343041	.	+	.	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
Phchi.S2	AUGUSTUS	stop_codon	19343042	19343044	.	+	0	transcript_id "Phchi.S2G050000.t1"; gene_id "Phchi.S2G050000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9392.t1 is derived from g6568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41311095	41312648	.	+	.	Phchi.S1G655100
Phchi.S1	AUGUSTUS	transcript	41311095	41312648	.	+	.	transcript_id "Phchi.S1G655100.t1"; gene_id "Phchi.S1G655100"
Phchi.S1	AUGUSTUS	start_codon	41311095	41311097	.	+	0	transcript_id "Phchi.S1G655100.t1"; gene_id "Phchi.S1G655100"
Phchi.S1	AUGUSTUS	CDS	41311095	41312648	1	+	0	transcript_id "Phchi.S1G655100.t1"; gene_id "Phchi.S1G655100"
Phchi.S1	AUGUSTUS	exon	41311095	41312648	.	+	.	transcript_id "Phchi.S1G655100.t1"; gene_id "Phchi.S1G655100"
Phchi.S1	AUGUSTUS	stop_codon	41312649	41312651	.	+	0	transcript_id "Phchi.S1G655100.t1"; gene_id "Phchi.S1G655100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14215.t1 is derived from g12682.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11545741	11551286	.	-	.	Phchi.S3G153400
Phchi.S3	AUGUSTUS	transcript	11545741	11551286	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	stop_codon	11545738	11545740	.	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11545741	11545806	1	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11545741	11545806	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11545807	11545889	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11545890	11545944	1	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11545890	11545944	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11545945	11546037	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546038	11546120	1	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546038	11546120	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546121	11546246	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546247	11546322	1	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546247	11546322	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546323	11546509	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546510	11546653	1	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546510	11546653	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546654	11546850	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546851	11546934	1	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546851	11546934	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546935	11547019	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547020	11547094	1	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547020	11547094	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547095	11547188	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547189	11547261	1	-	2	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547189	11547261	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547262	11547343	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547344	11547401	1	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547344	11547401	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547402	11547483	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547484	11547522	1	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547484	11547522	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547523	11547635	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547636	11548112	0.37	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547636	11548112	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548113	11548293	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548294	11548510	1	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548294	11548510	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548511	11548599	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548600	11548837	1	-	2	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548600	11548837	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548838	11548957	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548958	11549144	1	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548958	11549144	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11549145	11549571	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11549572	11549702	1	-	2	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11549572	11549702	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11549703	11549834	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11549835	11550346	0.99	-	1	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11549835	11550346	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550347	11550475	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11550476	11550731	1	-	2	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11550476	11550731	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550732	11550801	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11550802	11550946	1	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11550802	11550946	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550947	11551031	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11551032	11551286	0.34	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11551032	11551286	.	-	.	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	start_codon	11551284	11551286	.	-	0	transcript_id "Phchi.S3G153400.t1"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	transcript	11545741	11551286	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	stop_codon	11545738	11545740	.	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11545741	11545806	1	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11545741	11545806	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11545807	11545889	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11545890	11545944	1	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11545890	11545944	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11545945	11546037	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546038	11546120	1	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546038	11546120	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546121	11546246	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546247	11546322	1	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546247	11546322	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546323	11546509	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546510	11546653	1	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546510	11546653	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546654	11546850	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546851	11546934	1	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546851	11546934	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546935	11547019	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547020	11547094	1	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547020	11547094	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547095	11547188	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547189	11547261	1	-	2	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547189	11547261	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547262	11547343	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547344	11547401	1	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547344	11547401	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547402	11547551	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547552	11547688	0.54	-	2	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547552	11547688	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547689	11547853	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547854	11548112	0.46	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547854	11548112	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548113	11548293	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548294	11548510	1	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548294	11548510	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548511	11548599	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548600	11548837	1	-	2	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548600	11548837	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548838	11548957	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548958	11549144	1	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548958	11549144	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11549145	11549571	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11549572	11549702	1	-	2	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11549572	11549702	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11549703	11549834	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11549835	11550346	0.99	-	1	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11549835	11550346	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550347	11550475	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11550476	11550731	1	-	2	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11550476	11550731	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550732	11550801	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11550802	11550946	1	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11550802	11550946	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550947	11551031	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11551032	11551286	0.31	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11551032	11551286	.	-	.	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	start_codon	11551284	11551286	.	-	0	transcript_id "Phchi.S3G153400.t2"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	transcript	11545741	11551286	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	stop_codon	11545738	11545740	.	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11545741	11545806	1	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11545741	11545806	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11545807	11545889	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11545890	11545944	1	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11545890	11545944	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11545945	11546037	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546038	11546120	1	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546038	11546120	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546121	11546246	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546247	11546322	1	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546247	11546322	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546323	11546509	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546510	11546653	1	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546510	11546653	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546654	11546850	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11546851	11546934	1	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11546851	11546934	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11546935	11547019	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547020	11547094	1	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547020	11547094	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547095	11547188	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547189	11547261	1	-	2	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547189	11547261	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547262	11547343	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547344	11547401	1	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547344	11547401	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547402	11547551	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547552	11547688	0.52	-	2	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547552	11547688	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11547689	11547853	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11547854	11548112	0.36	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11547854	11548112	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548113	11548293	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548294	11548510	0.99	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548294	11548510	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548511	11548599	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548600	11548837	1	-	2	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548600	11548837	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11548838	11548957	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11548958	11549144	1	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11548958	11549144	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11549145	11549571	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11549572	11549702	1	-	2	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11549572	11549702	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11549703	11549834	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11549835	11550346	0.99	-	1	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11549835	11550346	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550347	11550475	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11550476	11550731	1	-	2	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11550476	11550731	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550732	11550813	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11550814	11550946	1	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11550814	11550946	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	intron	11550947	11551031	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	CDS	11551032	11551286	0.44	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	exon	11551032	11551286	.	-	.	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
Phchi.S3	AUGUSTUS	start_codon	11551284	11551286	.	-	0	transcript_id "Phchi.S3G153400.t3"; gene_id "Phchi.S3G153400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13768.t1 is derived from g12235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8825006	8829611	.	+	.	Phchi.S3G108700
Phchi.S3	AUGUSTUS	transcript	8825006	8829611	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	start_codon	8825006	8825008	.	+	0	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8825006	8825220	0.64	+	0	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8825006	8825220	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8825221	8825345	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8825346	8825404	0.65	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8825346	8825404	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8825405	8825490	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8825491	8825985	1	+	2	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8825491	8825985	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8825986	8826059	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8826060	8826147	1	+	2	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8826060	8826147	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8826148	8826244	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8826245	8826768	0.99	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8826245	8826768	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8826769	8826859	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8826860	8826992	1	+	2	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8826860	8826992	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8826993	8827170	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8827171	8827242	1	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8827171	8827242	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8827243	8827396	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8827397	8827471	1	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8827397	8827471	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8827472	8827579	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8827580	8827651	0.99	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8827580	8827651	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8827652	8827753	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8827754	8827923	0.77	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8827754	8827923	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8827924	8828016	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8828017	8828201	0.99	+	2	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8828017	8828201	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8828202	8828357	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8828358	8828484	0.94	+	0	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8828358	8828484	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8828485	8828580	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8828581	8828649	1	+	2	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8828581	8828649	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8828650	8828761	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8828762	8828957	0.95	+	2	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8828762	8828957	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8828958	8829052	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8829053	8829185	1	+	1	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8829053	8829185	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	intron	8829186	8829272	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	CDS	8829273	8829611	0.98	+	0	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	exon	8829273	8829611	.	+	.	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
Phchi.S3	AUGUSTUS	stop_codon	8829612	8829614	.	+	0	transcript_id "Phchi.S3G108700.t1"; gene_id "Phchi.S3G108700"
# This transcript jg7564.t2 is derived from g4738.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7565.t1 is derived from g4739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30056774	30061131	.	-	.	Phchi.S1G472400
Phchi.S1	AUGUSTUS	transcript	30056774	30061131	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	stop_codon	30056771	30056773	.	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30056774	30056894	1	-	1	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30056774	30056894	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30056895	30056989	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30056990	30057336	0.82	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30056990	30057336	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30057337	30057600	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30057601	30057727	0.9	-	1	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30057601	30057727	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30057728	30057837	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30057838	30058090	1	-	2	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30057838	30058090	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30058091	30058209	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30058210	30058543	1	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30058210	30058543	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30058544	30058629	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30058630	30059150	0.3	-	2	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30058630	30059150	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30059151	30059344	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30059345	30059621	0.39	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30059345	30059621	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30059622	30059748	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30059749	30059844	0.99	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30059749	30059844	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30059845	30059936	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30059937	30060593	1	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30059937	30060593	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30060594	30060708	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30060709	30060805	0.47	-	1	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30060709	30060805	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30060806	30060905	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30060906	30060957	0.43	-	2	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30060906	30060957	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30060958	30061049	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30061050	30061131	0.5	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30061050	30061131	.	-	.	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	start_codon	30061129	30061131	.	-	0	transcript_id "Phchi.S1G472400.t1"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	transcript	30056774	30061131	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	stop_codon	30056771	30056773	.	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30056774	30056894	1	-	1	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30056774	30056894	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30056895	30056989	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30056990	30057336	0.77	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30056990	30057336	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30057337	30057600	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30057601	30057727	0.89	-	1	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30057601	30057727	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30057728	30057837	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30057838	30058090	0.98	-	2	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30057838	30058090	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30058091	30058209	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30058210	30058314	0.55	-	2	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30058210	30058314	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30058315	30058532	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30058533	30058548	0.58	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30058533	30058548	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30058549	30058629	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30058630	30059150	0.32	-	2	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30058630	30059150	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30059151	30059344	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30059345	30059621	0.35	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30059345	30059621	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30059622	30059748	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30059749	30059844	0.99	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30059749	30059844	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30059845	30059936	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30059937	30060593	0.98	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30059937	30060593	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30060594	30060708	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30060709	30060805	0.55	-	1	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30060709	30060805	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30060806	30060905	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30060906	30060957	0.51	-	2	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30060906	30060957	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	intron	30060958	30061049	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	CDS	30061050	30061131	0.59	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	exon	30061050	30061131	.	-	.	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
Phchi.S1	AUGUSTUS	start_codon	30061129	30061131	.	-	0	transcript_id "Phchi.S1G472400.t2"; gene_id "Phchi.S1G472400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4550.t1 is derived from g1720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11069240	11071290	.	-	.	Phchi.S1G170900
Phchi.S1	AUGUSTUS	transcript	11069240	11071290	.	-	.	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	stop_codon	11069237	11069239	.	-	0	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	CDS	11069240	11069358	0.54	-	2	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	exon	11069240	11069358	.	-	.	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	intron	11069359	11069436	.	-	.	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	CDS	11069437	11069565	0.57	-	2	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	exon	11069437	11069565	.	-	.	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	intron	11069566	11069660	.	-	.	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	CDS	11069661	11071290	0.73	-	0	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	exon	11069661	11071290	.	-	.	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
Phchi.S1	AUGUSTUS	start_codon	11071288	11071290	.	-	0	transcript_id "Phchi.S1G170900.t1"; gene_id "Phchi.S1G170900"
# This transcript jg13913.t2 is derived from g12380.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13913.t3 is derived from g12380.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13914.t1 is derived from g12381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9639117	9640333	.	+	.	Phchi.S3G123300
Phchi.S3	AUGUSTUS	transcript	9639117	9640333	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	start_codon	9639117	9639119	.	+	0	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	CDS	9639117	9639269	0.57	+	0	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	exon	9639117	9639269	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	intron	9639270	9639444	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	CDS	9639445	9639638	1	+	0	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	exon	9639445	9639638	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	intron	9639639	9639757	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	CDS	9639758	9640094	0.99	+	1	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	exon	9639758	9640094	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	intron	9640095	9640168	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	CDS	9640169	9640247	1	+	0	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	exon	9640169	9640247	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	intron	9640248	9640322	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	CDS	9640323	9640333	1	+	2	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	exon	9640323	9640333	.	+	.	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
Phchi.S3	AUGUSTUS	stop_codon	9640334	9640336	.	+	0	transcript_id "Phchi.S3G123300.t1"; gene_id "Phchi.S3G123300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9846.t1 is derived from g7022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44061290	44061544	.	-	.	Phchi.S1G700500
Phchi.S1	AUGUSTUS	transcript	44061290	44061544	.	-	.	transcript_id "Phchi.S1G700500.t1"; gene_id "Phchi.S1G700500"
Phchi.S1	AUGUSTUS	stop_codon	44061287	44061289	.	-	0	transcript_id "Phchi.S1G700500.t1"; gene_id "Phchi.S1G700500"
Phchi.S1	AUGUSTUS	CDS	44061290	44061544	0.78	-	0	transcript_id "Phchi.S1G700500.t1"; gene_id "Phchi.S1G700500"
Phchi.S1	AUGUSTUS	exon	44061290	44061544	.	-	.	transcript_id "Phchi.S1G700500.t1"; gene_id "Phchi.S1G700500"
Phchi.S1	AUGUSTUS	start_codon	44061542	44061544	.	-	0	transcript_id "Phchi.S1G700500.t1"; gene_id "Phchi.S1G700500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11294.t1 is derived from g15344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5276275	5277010	.	-	.	Phchi.S4G087600
Phchi.S4	AUGUSTUS	transcript	5276275	5277010	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	stop_codon	5276272	5276274	.	-	0	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	CDS	5276275	5276320	0.9	-	1	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	exon	5276275	5276320	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	intron	5276321	5276424	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	CDS	5276425	5276484	0.9	-	1	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	exon	5276425	5276484	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	intron	5276485	5276602	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	CDS	5276603	5276727	0.98	-	0	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	exon	5276603	5276727	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	intron	5276728	5276869	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	CDS	5276870	5277010	0.73	-	0	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	exon	5276870	5277010	.	-	.	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
Phchi.S4	AUGUSTUS	start_codon	5277008	5277010	.	-	0	transcript_id "Phchi.S4G087600.t1"; gene_id "Phchi.S4G087600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9098.t1 is derived from g6273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39823729	39825109	.	-	.	Phchi.S1G625700
Phchi.S1	AUGUSTUS	transcript	39823729	39825109	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	stop_codon	39823726	39823728	.	-	0	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	CDS	39823729	39824036	1	-	2	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	exon	39823729	39824036	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	intron	39824037	39824233	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	CDS	39824234	39824319	1	-	1	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	exon	39824234	39824319	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	intron	39824320	39824545	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	CDS	39824546	39824555	0.87	-	2	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	exon	39824546	39824555	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	intron	39824556	39824652	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	CDS	39824653	39824681	1	-	1	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	exon	39824653	39824681	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	intron	39824682	39824819	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	CDS	39824820	39824887	0.72	-	0	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	exon	39824820	39824887	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	intron	39824888	39825031	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	CDS	39825032	39825109	0.6	-	0	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	exon	39825032	39825109	.	-	.	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
Phchi.S1	AUGUSTUS	start_codon	39825107	39825109	.	-	0	transcript_id "Phchi.S1G625700.t1"; gene_id "Phchi.S1G625700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1872.t1 is derived from g8792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3634440	3637130	.	+	.	Phchi.S5G048100
Phchi.S5	AUGUSTUS	transcript	3634440	3637130	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	start_codon	3634440	3634442	.	+	0	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3634440	3634644	0.77	+	0	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3634440	3634644	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	intron	3634645	3634891	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3634892	3635243	0.75	+	2	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3634892	3635243	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	intron	3635244	3635321	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3635322	3635424	1	+	1	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3635322	3635424	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	intron	3635425	3635504	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3635505	3635823	0.46	+	0	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3635505	3635823	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	intron	3635824	3636014	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3636015	3636566	0.8	+	2	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3636015	3636566	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	intron	3636567	3636648	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3636649	3636707	0.9	+	2	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3636649	3636707	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	intron	3636708	3637025	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	CDS	3637026	3637130	0.91	+	0	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	exon	3637026	3637130	.	+	.	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
Phchi.S5	AUGUSTUS	stop_codon	3637131	3637133	.	+	0	transcript_id "Phchi.S5G048100.t1"; gene_id "Phchi.S5G048100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10947.t1 is derived from g14997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3225065	3227971	.	+	.	Phchi.S4G052900
Phchi.S4	AUGUSTUS	transcript	3225065	3227971	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	start_codon	3225065	3225067	.	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3225065	3225286	0.88	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3225065	3225286	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3225287	3225391	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3225392	3225482	1	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3225392	3225482	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3225483	3225574	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3225575	3225702	0.87	+	2	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3225575	3225702	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3225703	3225812	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3225813	3225935	1	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3225813	3225935	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3225936	3226099	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3226100	3226188	1	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3226100	3226188	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3226189	3226305	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3226306	3226426	1	+	1	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3226306	3226426	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3226427	3226509	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3226510	3226601	0.97	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3226510	3226601	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3226602	3226719	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3226720	3226873	1	+	1	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3226720	3226873	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3226874	3227051	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3227052	3227303	1	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3227052	3227303	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3227304	3227383	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3227384	3227580	1	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3227384	3227580	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	intron	3227581	3227682	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	CDS	3227683	3227971	0.99	+	1	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	exon	3227683	3227971	.	+	.	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
Phchi.S4	AUGUSTUS	stop_codon	3227972	3227974	.	+	0	transcript_id "Phchi.S4G052900.t1"; gene_id "Phchi.S4G052900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4010.t1 is derived from g1179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7057592	7058647	.	-	.	Phchi.S1G116900
Phchi.S1	AUGUSTUS	transcript	7057592	7058647	.	-	.	transcript_id "Phchi.S1G116900.t1"; gene_id "Phchi.S1G116900"
Phchi.S1	AUGUSTUS	stop_codon	7057589	7057591	.	-	0	transcript_id "Phchi.S1G116900.t1"; gene_id "Phchi.S1G116900"
Phchi.S1	AUGUSTUS	CDS	7057592	7058647	0.81	-	0	transcript_id "Phchi.S1G116900.t1"; gene_id "Phchi.S1G116900"
Phchi.S1	AUGUSTUS	exon	7057592	7058647	.	-	.	transcript_id "Phchi.S1G116900.t1"; gene_id "Phchi.S1G116900"
Phchi.S1	AUGUSTUS	start_codon	7058645	7058647	.	-	0	transcript_id "Phchi.S1G116900.t1"; gene_id "Phchi.S1G116900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg509.t1 is derived from g10291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3523104	3523560	.	+	.	Phchi.S6G046800
Phchi.S6	AUGUSTUS	transcript	3523104	3523560	.	+	.	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	start_codon	3523104	3523106	.	+	0	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	CDS	3523104	3523250	0.95	+	0	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	exon	3523104	3523250	.	+	.	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	intron	3523251	3523389	.	+	.	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	CDS	3523390	3523560	1	+	0	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	exon	3523390	3523560	.	+	.	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
Phchi.S6	AUGUSTUS	stop_codon	3523561	3523563	.	+	0	transcript_id "Phchi.S6G046800.t1"; gene_id "Phchi.S6G046800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9249.t1 is derived from g6424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40586838	40587954	.	-	.	Phchi.S1G640800
Phchi.S1	AUGUSTUS	transcript	40586838	40587954	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	stop_codon	40586835	40586837	.	-	0	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	CDS	40586838	40586898	1	-	1	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	exon	40586838	40586898	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	intron	40586899	40586985	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	CDS	40586986	40587068	1	-	0	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	exon	40586986	40587068	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	intron	40587069	40587394	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	CDS	40587395	40587483	1	-	2	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	exon	40587395	40587483	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	intron	40587484	40587590	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	CDS	40587591	40587630	1	-	0	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	exon	40587591	40587630	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	intron	40587631	40587771	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	CDS	40587772	40587954	0.64	-	0	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	exon	40587772	40587954	.	-	.	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
Phchi.S1	AUGUSTUS	start_codon	40587952	40587954	.	-	0	transcript_id "Phchi.S1G640800.t1"; gene_id "Phchi.S1G640800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5185.t1 is derived from g2355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15378176	15381473	.	+	.	Phchi.S1G234400
Phchi.S1	AUGUSTUS	transcript	15378176	15381473	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	start_codon	15378176	15378178	.	+	0	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15378176	15378305	1	+	0	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15378176	15378305	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15378306	15378394	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15378395	15378474	1	+	2	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15378395	15378474	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15378475	15378548	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15378549	15378604	1	+	0	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15378549	15378604	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15378605	15378682	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15378683	15380688	0.93	+	1	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15378683	15380688	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15380689	15380761	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15380762	15380852	0.96	+	2	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15380762	15380852	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15380853	15381006	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15381007	15381089	1	+	1	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15381007	15381089	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15381090	15381351	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15381352	15381395	0.99	+	2	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15381352	15381395	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	intron	15381396	15381470	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	CDS	15381471	15381473	0.99	+	0	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	exon	15381471	15381473	.	+	.	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
Phchi.S1	AUGUSTUS	stop_codon	15381474	15381476	.	+	0	transcript_id "Phchi.S1G234400.t1"; gene_id "Phchi.S1G234400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg196.t1 is derived from g9978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1109093	1110079	.	-	.	Phchi.S6G015500
Phchi.S6	AUGUSTUS	transcript	1109093	1110079	.	-	.	transcript_id "Phchi.S6G015500.t1"; gene_id "Phchi.S6G015500"
Phchi.S6	AUGUSTUS	stop_codon	1109090	1109092	.	-	0	transcript_id "Phchi.S6G015500.t1"; gene_id "Phchi.S6G015500"
Phchi.S6	AUGUSTUS	CDS	1109093	1110079	0.64	-	0	transcript_id "Phchi.S6G015500.t1"; gene_id "Phchi.S6G015500"
Phchi.S6	AUGUSTUS	exon	1109093	1110079	.	-	.	transcript_id "Phchi.S6G015500.t1"; gene_id "Phchi.S6G015500"
Phchi.S6	AUGUSTUS	start_codon	1110077	1110079	.	-	0	transcript_id "Phchi.S6G015500.t1"; gene_id "Phchi.S6G015500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1329.t1 is derived from g11112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9052158	9054157	.	+	.	Phchi.S6G128800
Phchi.S6	AUGUSTUS	transcript	9052158	9054157	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	start_codon	9052158	9052160	.	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9052158	9052409	0.96	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9052158	9052409	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9052410	9052517	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9052518	9052810	0.64	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9052518	9052810	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9052811	9052933	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9052934	9052988	1	+	1	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9052934	9052988	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9052989	9053081	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9053082	9053162	1	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9053082	9053162	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9053163	9053252	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9053253	9053349	1	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9053253	9053349	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9053350	9053491	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9053492	9053559	1	+	2	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9053492	9053559	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9053560	9053648	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9053649	9053747	1	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9053649	9053747	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9053748	9053867	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9053868	9053909	0.97	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9053868	9053909	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	intron	9053910	9054010	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	CDS	9054011	9054157	0.97	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	exon	9054011	9054157	.	+	.	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
Phchi.S6	AUGUSTUS	stop_codon	9054158	9054160	.	+	0	transcript_id "Phchi.S6G128800.t1"; gene_id "Phchi.S6G128800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7816.t1 is derived from g4990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31341392	31343983	.	-	.	Phchi.S1G497500
Phchi.S1	AUGUSTUS	transcript	31341392	31343983	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	stop_codon	31341389	31341391	.	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31341392	31341550	1	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31341392	31341550	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31341551	31341640	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31341641	31341799	1	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31341641	31341799	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31341800	31341892	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31341893	31341988	1	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31341893	31341988	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31341989	31342080	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31342081	31342273	1	-	1	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31342081	31342273	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31342274	31342506	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31342507	31342928	1	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31342507	31342928	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31342929	31343030	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31343031	31343234	0.94	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31343031	31343234	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31343235	31343336	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31343337	31343487	0.99	-	1	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31343337	31343487	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31343488	31343565	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31343566	31343693	1	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31343566	31343693	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	intron	31343694	31343794	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	CDS	31343795	31343983	1	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	exon	31343795	31343983	.	-	.	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
Phchi.S1	AUGUSTUS	start_codon	31343981	31343983	.	-	0	transcript_id "Phchi.S1G497500.t1"; gene_id "Phchi.S1G497500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3381.t1 is derived from g550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3261154	3263125	.	-	.	Phchi.S1G054000
Phchi.S1	AUGUSTUS	transcript	3261154	3263125	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	stop_codon	3261151	3261153	.	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3261154	3261498	0.59	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3261154	3261498	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	intron	3261499	3261605	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3261606	3261658	0.65	-	2	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3261606	3261658	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	intron	3261659	3261770	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3261771	3261828	0.36	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3261771	3261828	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	intron	3261829	3262011	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3262012	3262092	0.91	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3262012	3262092	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	intron	3262093	3262196	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3262197	3262442	0.93	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3262197	3262442	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	intron	3262443	3262530	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3262531	3262649	1	-	2	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3262531	3262649	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	intron	3262650	3262947	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	CDS	3262948	3263125	1	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	exon	3262948	3263125	.	-	.	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
Phchi.S1	AUGUSTUS	start_codon	3263123	3263125	.	-	0	transcript_id "Phchi.S1G054000.t1"; gene_id "Phchi.S1G054000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5975.t1 is derived from g3146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20187046	20187900	.	-	.	Phchi.S1G313400
Phchi.S1	AUGUSTUS	transcript	20187046	20187900	.	-	.	transcript_id "Phchi.S1G313400.t1"; gene_id "Phchi.S1G313400"
Phchi.S1	AUGUSTUS	stop_codon	20187043	20187045	.	-	0	transcript_id "Phchi.S1G313400.t1"; gene_id "Phchi.S1G313400"
Phchi.S1	AUGUSTUS	CDS	20187046	20187900	0.98	-	0	transcript_id "Phchi.S1G313400.t1"; gene_id "Phchi.S1G313400"
Phchi.S1	AUGUSTUS	exon	20187046	20187900	.	-	.	transcript_id "Phchi.S1G313400.t1"; gene_id "Phchi.S1G313400"
Phchi.S1	AUGUSTUS	start_codon	20187898	20187900	.	-	0	transcript_id "Phchi.S1G313400.t1"; gene_id "Phchi.S1G313400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2807.t1 is derived from g9727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8967606	8968746	.	-	.	Phchi.S5G141600
Phchi.S5	AUGUSTUS	transcript	8967606	8968746	.	-	.	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	stop_codon	8967603	8967605	.	-	0	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	CDS	8967606	8967633	0.73	-	1	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	exon	8967606	8967633	.	-	.	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	intron	8967634	8967731	.	-	.	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	CDS	8967732	8967850	0.75	-	0	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	exon	8967732	8967850	.	-	.	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	intron	8967851	8968068	.	-	.	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	CDS	8968069	8968746	1	-	0	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	exon	8968069	8968746	.	-	.	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
Phchi.S5	AUGUSTUS	start_codon	8968744	8968746	.	-	0	transcript_id "Phchi.S5G141600.t1"; gene_id "Phchi.S5G141600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13676.t1 is derived from g12143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8101218	8109713	.	+	.	Phchi.S3G099500
Phchi.S3	AUGUSTUS	transcript	8101218	8109713	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	start_codon	8101218	8101220	.	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8101218	8101334	0.87	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8101218	8101334	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8101335	8101738	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8101739	8101801	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8101739	8101801	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8101802	8102012	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8102013	8102070	0.92	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8102013	8102070	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8102071	8102172	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8102173	8102421	1	+	2	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8102173	8102421	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8102422	8102813	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8102814	8102884	1	+	2	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8102814	8102884	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8102885	8103120	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8103121	8103211	0.64	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8103121	8103211	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8103212	8103430	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8103431	8103898	0.46	+	2	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8103431	8103898	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8103899	8104093	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8104094	8104601	0.48	+	2	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8104094	8104601	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8104602	8104699	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8104700	8104905	1	+	1	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8104700	8104905	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8104906	8105059	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8105060	8105297	1	+	2	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8105060	8105297	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8105298	8105376	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8105377	8105716	1	+	1	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8105377	8105716	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8105717	8105968	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8105969	8106178	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8105969	8106178	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8106179	8106297	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8106298	8106390	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8106298	8106390	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8106391	8106569	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8106570	8106776	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8106570	8106776	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8106777	8106961	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8106962	8107168	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8106962	8107168	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8107169	8107302	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8107303	8107780	0.99	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8107303	8107780	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8107781	8108096	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8108097	8108323	1	+	2	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8108097	8108323	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8108324	8108400	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8108401	8108541	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8108401	8108541	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8108542	8108719	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8108720	8108794	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8108720	8108794	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	intron	8108795	8108900	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	CDS	8108901	8109713	1	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	exon	8108901	8109713	.	+	.	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
Phchi.S3	AUGUSTUS	stop_codon	8109714	8109716	.	+	0	transcript_id "Phchi.S3G099500.t1"; gene_id "Phchi.S3G099500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15245.t1 is derived from g13713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17885453	17887305	.	+	.	Phchi.S3G256400
Phchi.S3	AUGUSTUS	transcript	17885453	17887305	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	start_codon	17885453	17885455	.	+	0	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	CDS	17885453	17886652	0.27	+	0	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	exon	17885453	17886652	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	intron	17886653	17886785	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	CDS	17886786	17886842	0.4	+	0	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	exon	17886786	17886842	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	intron	17886843	17886922	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	CDS	17886923	17886952	0.77	+	0	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	exon	17886923	17886952	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	intron	17886953	17887050	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	CDS	17887051	17887202	1	+	0	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	exon	17887051	17887202	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	intron	17887203	17887295	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	CDS	17887296	17887305	1	+	1	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	exon	17887296	17887305	.	+	.	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
Phchi.S3	AUGUSTUS	stop_codon	17887306	17887308	.	+	0	transcript_id "Phchi.S3G256400.t1"; gene_id "Phchi.S3G256400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3695.t1 is derived from g864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5218959	5219396	.	-	.	Phchi.S1G085400
Phchi.S1	AUGUSTUS	transcript	5218959	5219396	.	-	.	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	stop_codon	5218956	5218958	.	-	0	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	CDS	5218959	5219178	0.87	-	1	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	exon	5218959	5219178	.	-	.	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	intron	5219179	5219271	.	-	.	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	CDS	5219272	5219396	0.78	-	0	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	exon	5219272	5219396	.	-	.	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
Phchi.S1	AUGUSTUS	start_codon	5219394	5219396	.	-	0	transcript_id "Phchi.S1G085400.t1"; gene_id "Phchi.S1G085400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7359.t1 is derived from g4531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28763782	28765214	.	-	.	Phchi.S1G451800
Phchi.S1	AUGUSTUS	transcript	28763782	28765214	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	stop_codon	28763779	28763781	.	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28763782	28763886	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28763782	28763886	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28763887	28763982	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28763983	28764006	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28763983	28764006	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28764007	28764095	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28764096	28764122	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28764096	28764122	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28764123	28764242	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28764243	28764310	1	-	2	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28764243	28764310	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28764311	28764395	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28764396	28764567	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28764396	28764567	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28764568	28764665	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28764666	28764854	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28764666	28764854	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28764855	28764936	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28764937	28765020	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28764937	28765020	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	intron	28765021	28765103	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	CDS	28765104	28765214	1	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	exon	28765104	28765214	.	-	.	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
Phchi.S1	AUGUSTUS	start_codon	28765212	28765214	.	-	0	transcript_id "Phchi.S1G451800.t1"; gene_id "Phchi.S1G451800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1267.t1 is derived from g11050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8719099	8720237	.	-	.	Phchi.S6G122600
Phchi.S6	AUGUSTUS	transcript	8719099	8720237	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	stop_codon	8719096	8719098	.	-	0	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	CDS	8719099	8719155	0.9	-	0	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	exon	8719099	8719155	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	intron	8719156	8719314	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	CDS	8719315	8719372	1	-	1	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	exon	8719315	8719372	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	intron	8719373	8719522	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	CDS	8719523	8719695	1	-	0	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	exon	8719523	8719695	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	intron	8719696	8719782	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	CDS	8719783	8719838	1	-	2	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	exon	8719783	8719838	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	intron	8719839	8720227	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	CDS	8720228	8720237	0.76	-	0	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	exon	8720228	8720237	.	-	.	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
Phchi.S6	AUGUSTUS	start_codon	8720235	8720237	.	-	0	transcript_id "Phchi.S6G122600.t1"; gene_id "Phchi.S6G122600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3749.t1 is derived from g918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5484430	5487738	.	-	.	Phchi.S1G090800
Phchi.S1	AUGUSTUS	transcript	5484430	5487738	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	stop_codon	5484427	5484429	.	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5484430	5484443	1	-	2	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5484430	5484443	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5484444	5484577	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5484578	5484676	0.95	-	2	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5484578	5484676	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5484677	5484892	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5484893	5485133	0.77	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5484893	5485133	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5485134	5485233	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5485234	5485341	1	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5485234	5485341	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5485342	5485463	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5485464	5485523	1	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5485464	5485523	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5485524	5485639	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5485640	5485715	1	-	1	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5485640	5485715	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5485716	5485869	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5485870	5486027	1	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5485870	5486027	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5486028	5486176	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5486177	5486239	0.95	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5486177	5486239	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5486240	5486346	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5486347	5486422	1	-	1	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5486347	5486422	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	intron	5486423	5486521	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	CDS	5486522	5487738	1	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	exon	5486522	5487738	.	-	.	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
Phchi.S1	AUGUSTUS	start_codon	5487736	5487738	.	-	0	transcript_id "Phchi.S1G090800.t1"; gene_id "Phchi.S1G090800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12707.t1 is derived from g11172.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	671849	673509	.	-	.	Phchi.S3G002600
Phchi.S3	AUGUSTUS	transcript	671849	673509	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	stop_codon	671846	671848	.	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	671849	671901	0.53	-	2	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	671849	671901	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	671902	671988	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	671989	672089	0.47	-	1	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	671989	672089	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672090	672166	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672167	672261	0.61	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672167	672261	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672262	672345	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672346	672465	1	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672346	672465	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672466	672561	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672562	672699	1	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672562	672699	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672700	672839	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672840	672921	1	-	1	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672840	672921	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672922	673021	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673022	673134	1	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673022	673134	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	673135	673237	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673238	673320	1	-	2	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673238	673320	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	673321	673493	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673494	673509	1	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673494	673509	.	-	.	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	start_codon	673507	673509	.	-	0	transcript_id "Phchi.S3G002600.t1"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	transcript	671849	673509	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	stop_codon	671846	671848	.	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	671849	671901	0.71	-	2	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	671849	671901	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	671902	671988	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	671989	672089	0.63	-	1	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	671989	672089	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672090	672237	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672238	672278	0.57	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672238	672278	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672279	672345	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672346	672465	1	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672346	672465	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672466	672561	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672562	672699	1	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672562	672699	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672700	672839	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672840	672921	1	-	1	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672840	672921	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672922	673021	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673022	673134	1	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673022	673134	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	673135	673237	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673238	673320	1	-	2	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673238	673320	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	673321	673493	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673494	673509	0.99	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673494	673509	.	-	.	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	start_codon	673507	673509	.	-	0	transcript_id "Phchi.S3G002600.t2"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	transcript	671849	673425	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	stop_codon	671846	671848	.	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	671849	671901	0.51	-	2	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	671849	671901	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	671902	671988	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	671989	672089	0.48	-	1	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	671989	672089	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672090	672166	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672167	672261	0.56	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672167	672261	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672262	672345	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672346	672465	1	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672346	672465	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672466	672561	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672562	672699	1	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672562	672699	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672700	672839	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	672840	672921	1	-	1	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	672840	672921	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	672922	673021	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673022	673150	0.98	-	1	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673022	673150	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	673151	673237	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673238	673320	0.98	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673238	673320	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	intron	673321	673410	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	CDS	673411	673425	0.44	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	exon	673411	673425	.	-	.	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
Phchi.S3	AUGUSTUS	start_codon	673423	673425	.	-	0	transcript_id "Phchi.S3G002600.t3"; gene_id "Phchi.S3G002600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10696.t1 is derived from g14746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1639446	1639958	.	-	.	Phchi.S4G027800
Phchi.S4	AUGUSTUS	transcript	1639446	1639958	.	-	.	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	stop_codon	1639443	1639445	.	-	0	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	CDS	1639446	1639799	0.62	-	0	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	exon	1639446	1639799	.	-	.	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	intron	1639800	1639949	.	-	.	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	CDS	1639950	1639958	0.61	-	0	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	exon	1639950	1639958	.	-	.	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
Phchi.S4	AUGUSTUS	start_codon	1639956	1639958	.	-	0	transcript_id "Phchi.S4G027800.t1"; gene_id "Phchi.S4G027800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9164.t1 is derived from g6339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40177674	40182118	.	-	.	Phchi.S1G632300
Phchi.S1	AUGUSTUS	transcript	40177674	40182118	.	-	.	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	stop_codon	40177671	40177673	.	-	0	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	CDS	40177674	40181631	1	-	1	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	exon	40177674	40181631	.	-	.	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	intron	40181632	40181713	.	-	.	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	CDS	40181714	40181877	1	-	0	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	exon	40181714	40181877	.	-	.	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	intron	40181878	40181968	.	-	.	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	CDS	40181969	40182118	0.74	-	0	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	exon	40181969	40182118	.	-	.	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
Phchi.S1	AUGUSTUS	start_codon	40182116	40182118	.	-	0	transcript_id "Phchi.S1G632300.t1"; gene_id "Phchi.S1G632300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8114.t1 is derived from g5289.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33228451	33231233	.	-	.	Phchi.S1G527300
Phchi.S1	AUGUSTUS	transcript	33228451	33231233	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	stop_codon	33228448	33228450	.	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33228451	33228507	0.84	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33228451	33228507	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	intron	33228508	33228748	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33228749	33229261	1	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33228749	33229261	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	intron	33229262	33229517	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33229518	33229606	0.68	-	2	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33229518	33229606	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	intron	33229607	33229701	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33229702	33229777	0.72	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33229702	33229777	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	intron	33229778	33229882	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33229883	33229942	0.99	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33229883	33229942	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	intron	33229943	33230035	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33230036	33230137	1	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33230036	33230137	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	intron	33230138	33230663	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	CDS	33230664	33231233	1	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	exon	33230664	33231233	.	-	.	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
Phchi.S1	AUGUSTUS	start_codon	33231231	33231233	.	-	0	transcript_id "Phchi.S1G527300.t1"; gene_id "Phchi.S1G527300"
# This transcript jg5634.t2 is derived from g2804.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5634.t3 is derived from g2804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5635.t1 is derived from g2805.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17985074	17986377	.	+	.	Phchi.S1G279400
Phchi.S1	AUGUSTUS	transcript	17985283	17986377	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	start_codon	17985283	17985285	.	+	0	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17985283	17985343	0.99	+	0	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17985283	17985343	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	intron	17985344	17985493	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17985494	17985735	0.83	+	2	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17985494	17985735	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	intron	17985736	17985917	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17985918	17986133	0.73	+	0	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17985918	17986133	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	intron	17986134	17986257	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17986258	17986377	0.94	+	0	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17986258	17986377	.	+	.	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	stop_codon	17986378	17986380	.	+	0	transcript_id "Phchi.S1G279400.t1"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	transcript	17985074	17986377	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	start_codon	17985074	17985076	.	+	0	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17985074	17985095	0.67	+	0	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17985074	17985095	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	intron	17985096	17985493	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17985494	17985735	0.62	+	2	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17985494	17985735	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	intron	17985736	17985917	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17985918	17986133	0.64	+	0	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17985918	17986133	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	intron	17986134	17986257	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	CDS	17986258	17986377	0.83	+	0	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	exon	17986258	17986377	.	+	.	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
Phchi.S1	AUGUSTUS	stop_codon	17986378	17986380	.	+	0	transcript_id "Phchi.S1G279400.t2"; gene_id "Phchi.S1G279400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7210.t1 is derived from g4382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27646103	27651077	.	+	.	Phchi.S1G436900
Phchi.S1	AUGUSTUS	transcript	27646103	27651077	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	start_codon	27646103	27646105	.	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27646103	27647012	0.61	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27646103	27647012	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27647013	27647143	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27647144	27647290	0.88	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27647144	27647290	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27647291	27647567	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27647568	27647761	1	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27647568	27647761	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27647762	27647945	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27647946	27648188	1	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27647946	27648188	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27648189	27648282	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27648283	27648394	1	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27648283	27648394	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27648395	27648647	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27648648	27648818	1	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27648648	27648818	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27648819	27648912	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27648913	27648976	1	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27648913	27648976	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27648977	27649097	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27649098	27649161	1	+	1	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27649098	27649161	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27649162	27649325	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27649326	27649503	1	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27649326	27649503	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27649504	27649576	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27649577	27649707	1	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27649577	27649707	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27649708	27649893	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27649894	27649999	1	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27649894	27649999	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27650000	27650165	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27650166	27650245	1	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27650166	27650245	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27650246	27650348	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27650349	27650396	1	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27650349	27650396	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27650397	27650525	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27650526	27650675	1	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27650526	27650675	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27650676	27650757	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27650758	27650806	0.72	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27650758	27650806	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27650807	27650897	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27650898	27650962	0.72	+	2	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27650898	27650962	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	intron	27650963	27651047	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	CDS	27651048	27651077	0.73	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	exon	27651048	27651077	.	+	.	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
Phchi.S1	AUGUSTUS	stop_codon	27651078	27651080	.	+	0	transcript_id "Phchi.S1G436900.t1"; gene_id "Phchi.S1G436900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14342.t1 is derived from g12809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12307905	12309885	.	+	.	Phchi.S3G166100
Phchi.S3	AUGUSTUS	transcript	12307905	12309885	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	start_codon	12307905	12307907	.	+	0	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	CDS	12307905	12308024	0.43	+	0	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	exon	12307905	12308024	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	intron	12308025	12308107	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	CDS	12308108	12309503	0.38	+	0	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	exon	12308108	12309503	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	intron	12309504	12309661	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	CDS	12309662	12309693	0.38	+	2	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	exon	12309662	12309693	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	intron	12309694	12309831	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	CDS	12309832	12309885	0.35	+	0	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	exon	12309832	12309885	.	+	.	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
Phchi.S3	AUGUSTUS	stop_codon	12309886	12309888	.	+	0	transcript_id "Phchi.S3G166100.t1"; gene_id "Phchi.S3G166100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8081.t1 is derived from g5256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32869289	32869850	.	-	.	Phchi.S1G524000
Phchi.S1	AUGUSTUS	transcript	32869289	32869850	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	stop_codon	32869286	32869288	.	-	0	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	CDS	32869289	32869292	1	-	1	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	exon	32869289	32869292	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	intron	32869293	32869369	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	CDS	32869370	32869447	1	-	1	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	exon	32869370	32869447	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	intron	32869448	32869523	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	CDS	32869524	32869605	0.98	-	2	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	exon	32869524	32869605	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	intron	32869606	32869693	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	CDS	32869694	32869850	0.6	-	0	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	exon	32869694	32869850	.	-	.	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
Phchi.S1	AUGUSTUS	start_codon	32869848	32869850	.	-	0	transcript_id "Phchi.S1G524000.t1"; gene_id "Phchi.S1G524000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5137.t1 is derived from g2307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15111675	15113119	.	-	.	Phchi.S1G229600
Phchi.S1	AUGUSTUS	transcript	15111675	15113119	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	stop_codon	15111672	15111674	.	-	0	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	CDS	15111675	15111927	0.43	-	1	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	exon	15111675	15111927	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	intron	15111928	15112001	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	CDS	15112002	15112549	0.64	-	0	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	exon	15112002	15112549	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	intron	15112550	15112643	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	CDS	15112644	15112668	0.82	-	1	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	exon	15112644	15112668	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	intron	15112669	15112808	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	CDS	15112809	15112852	0.71	-	0	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	exon	15112809	15112852	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	intron	15112853	15113050	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	CDS	15113051	15113119	0.78	-	0	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	exon	15113051	15113119	.	-	.	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
Phchi.S1	AUGUSTUS	start_codon	15113117	15113119	.	-	0	transcript_id "Phchi.S1G229600.t1"; gene_id "Phchi.S1G229600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg69.t1 is derived from g9851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	336140	336481	.	-	.	Phchi.S6G002800
Phchi.S6	AUGUSTUS	transcript	336140	336481	.	-	.	transcript_id "Phchi.S6G002800.t1"; gene_id "Phchi.S6G002800"
Phchi.S6	AUGUSTUS	stop_codon	336137	336139	.	-	0	transcript_id "Phchi.S6G002800.t1"; gene_id "Phchi.S6G002800"
Phchi.S6	AUGUSTUS	CDS	336140	336481	0.6	-	0	transcript_id "Phchi.S6G002800.t1"; gene_id "Phchi.S6G002800"
Phchi.S6	AUGUSTUS	exon	336140	336481	.	-	.	transcript_id "Phchi.S6G002800.t1"; gene_id "Phchi.S6G002800"
Phchi.S6	AUGUSTUS	start_codon	336479	336481	.	-	0	transcript_id "Phchi.S6G002800.t1"; gene_id "Phchi.S6G002800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12750.t1 is derived from g11215.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1884449	1886496	.	-	.	Phchi.S3G006900
Phchi.S3	AUGUSTUS	transcript	1884449	1886496	.	-	.	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	stop_codon	1884446	1884448	.	-	0	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	CDS	1884449	1885405	0.95	-	0	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	exon	1884449	1885405	.	-	.	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	intron	1885406	1885701	.	-	.	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	CDS	1885702	1886496	0.88	-	0	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	exon	1885702	1886496	.	-	.	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	start_codon	1886494	1886496	.	-	0	transcript_id "Phchi.S3G006900.t1"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	transcript	1884449	1885291	.	-	.	transcript_id "Phchi.S3G006900.t2"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	stop_codon	1884446	1884448	.	-	0	transcript_id "Phchi.S3G006900.t2"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	CDS	1884449	1885291	1	-	0	transcript_id "Phchi.S3G006900.t2"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	exon	1884449	1885291	.	-	.	transcript_id "Phchi.S3G006900.t2"; gene_id "Phchi.S3G006900"
Phchi.S3	AUGUSTUS	start_codon	1885289	1885291	.	-	0	transcript_id "Phchi.S3G006900.t2"; gene_id "Phchi.S3G006900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15077.t1 is derived from g13545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16934161	16935954	.	+	.	Phchi.S3G239600
Phchi.S3	AUGUSTUS	transcript	16934161	16935954	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	start_codon	16934161	16934163	.	+	0	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16934161	16934174	1	+	0	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16934161	16934174	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	intron	16934175	16934398	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16934399	16934498	1	+	1	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16934399	16934498	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	intron	16934499	16934568	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16934569	16934593	0.77	+	0	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16934569	16934593	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	intron	16934594	16934758	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16934759	16934790	0.97	+	2	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16934759	16934790	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	intron	16934791	16934897	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16934898	16934972	1	+	0	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16934898	16934972	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	intron	16934973	16935043	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16935044	16935461	0.97	+	0	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16935044	16935461	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	intron	16935462	16935559	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	CDS	16935560	16935954	0.93	+	2	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	exon	16935560	16935954	.	+	.	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
Phchi.S3	AUGUSTUS	stop_codon	16935955	16935957	.	+	0	transcript_id "Phchi.S3G239600.t1"; gene_id "Phchi.S3G239600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3817.t1 is derived from g986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5878689	5881118	.	-	.	Phchi.S1G097600
Phchi.S1	AUGUSTUS	transcript	5878689	5881118	.	-	.	transcript_id "Phchi.S1G097600.t1"; gene_id "Phchi.S1G097600"
Phchi.S1	AUGUSTUS	stop_codon	5878686	5878688	.	-	0	transcript_id "Phchi.S1G097600.t1"; gene_id "Phchi.S1G097600"
Phchi.S1	AUGUSTUS	CDS	5878689	5881118	0.72	-	0	transcript_id "Phchi.S1G097600.t1"; gene_id "Phchi.S1G097600"
Phchi.S1	AUGUSTUS	exon	5878689	5881118	.	-	.	transcript_id "Phchi.S1G097600.t1"; gene_id "Phchi.S1G097600"
Phchi.S1	AUGUSTUS	start_codon	5881116	5881118	.	-	0	transcript_id "Phchi.S1G097600.t1"; gene_id "Phchi.S1G097600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1656.t1 is derived from g8575.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2254274	2259234	.	+	.	Phchi.S5G026500
Phchi.S5	AUGUSTUS	transcript	2254274	2259234	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	start_codon	2254274	2254276	.	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2254274	2254402	1	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2254274	2254402	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2254403	2254508	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2254509	2254624	1	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2254509	2254624	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2254625	2254841	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2254842	2255004	0.9	+	1	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2254842	2255004	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2255005	2255131	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2255132	2255272	1	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2255132	2255272	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2255273	2255441	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2255442	2255632	1	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2255442	2255632	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2255633	2255759	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2255760	2256144	1	+	1	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2255760	2256144	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256145	2256254	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2256255	2256407	0.95	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2256255	2256407	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256408	2256580	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2256581	2256613	0.97	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2256581	2256613	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256614	2256725	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2256726	2257121	0.89	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2256726	2257121	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2257122	2257211	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2257212	2257364	0.98	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2257212	2257364	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2257365	2257465	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2257466	2257764	0.99	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2257466	2257764	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2257765	2257874	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2257875	2258019	0.96	+	1	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2257875	2258019	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2258020	2258101	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2258102	2258278	0.83	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2258102	2258278	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2258279	2258663	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2258664	2258840	0.81	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2258664	2258840	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2258841	2258922	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2258923	2259234	0.91	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2258923	2259234	.	+	.	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	stop_codon	2259235	2259237	.	+	0	transcript_id "Phchi.S5G026500.t1"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	transcript	2254274	2257225	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	start_codon	2254274	2254276	.	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2254274	2254402	0.99	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2254274	2254402	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2254403	2254508	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2254509	2254624	0.99	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2254509	2254624	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2254625	2254841	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2254842	2255004	0.96	+	1	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2254842	2255004	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2255005	2255131	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2255132	2255272	1	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2255132	2255272	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2255273	2255441	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2255442	2255632	1	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2255442	2255632	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2255633	2255759	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2255760	2256144	0.97	+	1	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2255760	2256144	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256145	2256254	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2256255	2256407	0.6	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2256255	2256407	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256408	2256580	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2256581	2256613	0.62	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2256581	2256613	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256614	2256725	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2256726	2256921	0.54	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2256726	2256921	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	intron	2256922	2257211	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	CDS	2257212	2257225	0.53	+	2	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	exon	2257212	2257225	.	+	.	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
Phchi.S5	AUGUSTUS	stop_codon	2257226	2257228	.	+	0	transcript_id "Phchi.S5G026500.t2"; gene_id "Phchi.S5G026500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9946.t1 is derived from g7122.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44616540	44618468	.	+	.	Phchi.S1G710500
Phchi.S1	AUGUSTUS	transcript	44616540	44618468	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	start_codon	44616540	44616542	.	+	0	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44616540	44617238	0.97	+	0	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44616540	44617238	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	intron	44617239	44617319	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44617320	44617545	1	+	0	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44617320	44617545	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	intron	44617546	44617627	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44617628	44617665	1	+	2	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44617628	44617665	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	intron	44617666	44617835	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44617836	44618468	1	+	0	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44617836	44618468	.	+	.	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	stop_codon	44618469	44618471	.	+	0	transcript_id "Phchi.S1G710500.t1"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	transcript	44616540	44618468	.	+	.	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	start_codon	44616540	44616542	.	+	0	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44616540	44617238	0.95	+	0	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44616540	44617238	.	+	.	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	intron	44617239	44617319	.	+	.	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44617320	44617715	0.36	+	0	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44617320	44617715	.	+	.	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	intron	44617716	44617835	.	+	.	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	CDS	44617836	44618468	0.84	+	0	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	exon	44617836	44618468	.	+	.	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
Phchi.S1	AUGUSTUS	stop_codon	44618469	44618471	.	+	0	transcript_id "Phchi.S1G710500.t2"; gene_id "Phchi.S1G710500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15433.t1 is derived from g13901.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19073591	19078297	.	+	.	Phchi.S3G275200
Phchi.S3	AUGUSTUS	transcript	19073591	19078286	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	start_codon	19073591	19073593	.	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073591	19073597	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073591	19073597	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073598	19073732	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073733	19073767	1	+	2	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073733	19073767	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073768	19073848	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073849	19073912	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073849	19073912	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073913	19074099	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074100	19074174	1	+	2	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074100	19074174	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074175	19074307	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074308	19074360	1	+	2	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074308	19074360	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074361	19074595	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074596	19074669	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074596	19074669	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074670	19074755	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074756	19074837	1	+	1	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074756	19074837	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074838	19074958	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074959	19075020	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074959	19075020	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075021	19075262	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075263	19075338	1	+	1	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075263	19075338	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075339	19075480	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075481	19075555	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075481	19075555	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075556	19075638	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075639	19075710	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075639	19075710	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075711	19075892	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075893	19075976	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075893	19075976	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075977	19076107	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076108	19076176	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076108	19076176	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076177	19076353	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076354	19076431	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076354	19076431	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076432	19076550	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076551	19076639	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076551	19076639	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076640	19076731	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076732	19076828	1	+	1	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076732	19076828	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076829	19076917	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076918	19076971	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076918	19076971	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076972	19077066	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077067	19077162	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077067	19077162	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077163	19077287	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077288	19077476	0.99	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077288	19077476	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077477	19077590	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077591	19077668	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077591	19077668	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077669	19077763	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077764	19077808	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077764	19077808	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077809	19077908	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077909	19078001	1	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077909	19078001	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19078002	19078262	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19078263	19078286	0.99	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19078263	19078286	.	+	.	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	stop_codon	19078287	19078289	.	+	0	transcript_id "Phchi.S3G275200.t1"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	transcript	19073591	19078187	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	start_codon	19073591	19073593	.	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073591	19073597	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073591	19073597	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073598	19073732	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073733	19073767	1	+	2	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073733	19073767	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073768	19073848	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073849	19073912	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073849	19073912	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073913	19074099	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074100	19074174	1	+	2	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074100	19074174	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074175	19074307	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074308	19074360	1	+	2	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074308	19074360	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074361	19074595	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074596	19074669	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074596	19074669	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074670	19074755	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074756	19074837	1	+	1	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074756	19074837	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074838	19074958	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074959	19075020	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074959	19075020	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075021	19075262	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075263	19075338	1	+	1	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075263	19075338	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075339	19075480	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075481	19075555	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075481	19075555	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075556	19075638	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075639	19075710	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075639	19075710	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075711	19075892	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075893	19075976	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075893	19075976	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075977	19076107	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076108	19076176	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076108	19076176	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076177	19076353	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076354	19076431	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076354	19076431	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076432	19076550	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076551	19076639	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076551	19076639	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076640	19076731	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076732	19076828	1	+	1	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076732	19076828	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076829	19076917	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076918	19076971	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076918	19076971	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076972	19077066	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077067	19077162	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077067	19077162	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077163	19077287	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077288	19077476	0.99	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077288	19077476	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077477	19077590	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077591	19077668	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077591	19077668	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077669	19077763	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077764	19077808	1	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077764	19077808	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077809	19077908	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077909	19078001	0.88	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077909	19078001	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19078002	19078112	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19078113	19078187	0.52	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19078113	19078187	.	+	.	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	stop_codon	19078188	19078190	.	+	0	transcript_id "Phchi.S3G275200.t2"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	transcript	19073591	19078297	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	start_codon	19073591	19073593	.	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073591	19073597	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073591	19073597	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073598	19073732	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073733	19073767	1	+	2	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073733	19073767	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073768	19073848	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19073849	19073912	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19073849	19073912	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19073913	19074099	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074100	19074174	1	+	2	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074100	19074174	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074175	19074307	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074308	19074360	1	+	2	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074308	19074360	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074361	19074595	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074596	19074669	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074596	19074669	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074670	19074755	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074756	19074837	1	+	1	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074756	19074837	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19074838	19074958	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19074959	19075020	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19074959	19075020	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075021	19075262	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075263	19075338	1	+	1	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075263	19075338	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075339	19075480	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075481	19075555	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075481	19075555	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075556	19075638	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075639	19075710	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075639	19075710	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075711	19075892	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19075893	19075976	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19075893	19075976	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19075977	19076107	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076108	19076176	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076108	19076176	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076177	19076353	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076354	19076431	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076354	19076431	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076432	19076550	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076551	19076639	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076551	19076639	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076640	19076731	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076732	19076828	1	+	1	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076732	19076828	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076829	19076917	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19076918	19076971	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19076918	19076971	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19076972	19077066	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077067	19077162	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077067	19077162	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077163	19077287	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077288	19077476	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077288	19077476	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077477	19077590	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077591	19077668	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077591	19077668	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077669	19077763	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077764	19077808	1	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077764	19077808	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19077809	19077908	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19077909	19078001	0.95	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19077909	19078001	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	intron	19078002	19078255	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	CDS	19078256	19078297	0.39	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	exon	19078256	19078297	.	+	.	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
Phchi.S3	AUGUSTUS	stop_codon	19078298	19078300	.	+	0	transcript_id "Phchi.S3G275200.t3"; gene_id "Phchi.S3G275200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2515.t1 is derived from g9435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7088364	7090407	.	+	.	Phchi.S5G112400
Phchi.S5	AUGUSTUS	transcript	7088364	7090407	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	start_codon	7088364	7088366	.	+	0	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	CDS	7088364	7088682	1	+	0	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	exon	7088364	7088682	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	intron	7088683	7088812	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	CDS	7088813	7089124	1	+	2	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	exon	7088813	7089124	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	intron	7089125	7089222	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	CDS	7089223	7089536	1	+	2	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	exon	7089223	7089536	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	intron	7089537	7089633	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	CDS	7089634	7089844	1	+	0	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	exon	7089634	7089844	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	intron	7089845	7089986	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	CDS	7089987	7090114	0.22	+	2	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	exon	7089987	7090114	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	intron	7090115	7090218	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	CDS	7090219	7090407	0.18	+	0	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	exon	7090219	7090407	.	+	.	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
Phchi.S5	AUGUSTUS	stop_codon	7090408	7090410	.	+	0	transcript_id "Phchi.S5G112400.t1"; gene_id "Phchi.S5G112400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9930.t1 is derived from g7106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44527015	44530060	.	-	.	Phchi.S1G708900
Phchi.S1	AUGUSTUS	transcript	44527015	44530060	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	stop_codon	44527012	44527014	.	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44527015	44527143	0.76	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44527015	44527143	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44527144	44527234	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44527235	44527358	1	-	1	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44527235	44527358	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44527359	44527458	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44527459	44527556	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44527459	44527556	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44527557	44527659	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44527660	44527719	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44527660	44527719	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44527720	44527816	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44527817	44527877	1	-	1	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44527817	44527877	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44527878	44527972	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44527973	44528046	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44527973	44528046	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44528047	44528122	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44528123	44528198	1	-	1	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44528123	44528198	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44528199	44528360	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44528361	44528480	1	-	1	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44528361	44528480	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44528481	44528627	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44528628	44528737	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44528628	44528737	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44528738	44528888	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44528889	44528951	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44528889	44528951	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44528952	44529040	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44529041	44529145	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44529041	44529145	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44529146	44529312	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44529313	44529398	1	-	2	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44529313	44529398	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44529399	44529504	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44529505	44529685	1	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44529505	44529685	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	intron	44529686	44529799	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	CDS	44529800	44530060	0.59	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	exon	44529800	44530060	.	-	.	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
Phchi.S1	AUGUSTUS	start_codon	44530058	44530060	.	-	0	transcript_id "Phchi.S1G708900.t1"; gene_id "Phchi.S1G708900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9927.t1 is derived from g7103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44513187	44517171	.	+	.	Phchi.S1G708600
Phchi.S1	AUGUSTUS	transcript	44513187	44517171	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	start_codon	44513187	44513189	.	+	0	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	CDS	44513187	44513651	0.38	+	0	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	exon	44513187	44513651	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	intron	44513652	44513740	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	CDS	44513741	44514701	0.18	+	0	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	exon	44513741	44514701	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	intron	44514702	44514852	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	CDS	44514853	44516303	0.92	+	2	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	exon	44514853	44516303	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	intron	44516304	44516400	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	CDS	44516401	44517171	0.26	+	0	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	exon	44516401	44517171	.	+	.	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
Phchi.S1	AUGUSTUS	stop_codon	44517172	44517174	.	+	0	transcript_id "Phchi.S1G708600.t1"; gene_id "Phchi.S1G708600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8408.t1 is derived from g5583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35819277	35819828	.	+	.	Phchi.S1G556700
Phchi.S1	AUGUSTUS	transcript	35819277	35819828	.	+	.	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	start_codon	35819277	35819279	.	+	0	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	CDS	35819277	35819545	1	+	0	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	exon	35819277	35819545	.	+	.	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	intron	35819546	35819683	.	+	.	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	CDS	35819684	35819828	1	+	1	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	exon	35819684	35819828	.	+	.	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
Phchi.S1	AUGUSTUS	stop_codon	35819829	35819831	.	+	0	transcript_id "Phchi.S1G556700.t1"; gene_id "Phchi.S1G556700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg341.t1 is derived from g10123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2482574	2483653	.	-	.	Phchi.S6G030000
Phchi.S6	AUGUSTUS	transcript	2482574	2483653	.	-	.	transcript_id "Phchi.S6G030000.t1"; gene_id "Phchi.S6G030000"
Phchi.S6	AUGUSTUS	stop_codon	2482571	2482573	.	-	0	transcript_id "Phchi.S6G030000.t1"; gene_id "Phchi.S6G030000"
Phchi.S6	AUGUSTUS	CDS	2482574	2483653	0.58	-	0	transcript_id "Phchi.S6G030000.t1"; gene_id "Phchi.S6G030000"
Phchi.S6	AUGUSTUS	exon	2482574	2483653	.	-	.	transcript_id "Phchi.S6G030000.t1"; gene_id "Phchi.S6G030000"
Phchi.S6	AUGUSTUS	start_codon	2483651	2483653	.	-	0	transcript_id "Phchi.S6G030000.t1"; gene_id "Phchi.S6G030000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13902.t1 is derived from g12369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9592234	9595099	.	+	.	Phchi.S3G122100
Phchi.S3	AUGUSTUS	transcript	9592234	9595099	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	start_codon	9592234	9592236	.	+	0	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	CDS	9592234	9592504	0.68	+	0	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	exon	9592234	9592504	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	intron	9592505	9592708	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	CDS	9592709	9592890	1	+	2	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	exon	9592709	9592890	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	intron	9592891	9592985	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	CDS	9592986	9593258	1	+	0	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	exon	9592986	9593258	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	intron	9593259	9593406	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	CDS	9593407	9594248	0.95	+	0	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	exon	9593407	9594248	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	intron	9594249	9594352	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	CDS	9594353	9594608	1	+	1	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	exon	9594353	9594608	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	intron	9594609	9594691	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	CDS	9594692	9595099	1	+	0	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	exon	9594692	9595099	.	+	.	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
Phchi.S3	AUGUSTUS	stop_codon	9595100	9595102	.	+	0	transcript_id "Phchi.S3G122100.t1"; gene_id "Phchi.S3G122100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5491.t1 is derived from g2661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17106522	17108945	.	+	.	Phchi.S1G265000
Phchi.S1	AUGUSTUS	transcript	17106522	17108945	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	start_codon	17106522	17106524	.	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17106522	17106731	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17106522	17106731	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17106732	17106812	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17106813	17106881	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17106813	17106881	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17106882	17106969	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17106970	17107038	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17106970	17107038	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17107039	17107141	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17107142	17107282	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17107142	17107282	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17107283	17107377	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17107378	17107494	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17107378	17107494	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17107495	17107582	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17107583	17107652	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17107583	17107652	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17107653	17107741	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17107742	17107833	1	+	2	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17107742	17107833	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17107834	17107915	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17107916	17108047	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17107916	17108047	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17108048	17108130	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17108131	17108229	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17108131	17108229	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17108230	17108320	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17108321	17108419	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17108321	17108419	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17108420	17108507	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17108508	17108590	1	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17108508	17108590	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	intron	17108591	17108878	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	CDS	17108879	17108945	0.94	+	1	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	exon	17108879	17108945	.	+	.	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
Phchi.S1	AUGUSTUS	stop_codon	17108946	17108948	.	+	0	transcript_id "Phchi.S1G265000.t1"; gene_id "Phchi.S1G265000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15301.t1 is derived from g13769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18296708	18297826	.	-	.	Phchi.S3G262000
Phchi.S3	AUGUSTUS	transcript	18296708	18297826	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	stop_codon	18296705	18296707	.	-	0	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	CDS	18296708	18296992	0.8	-	0	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	exon	18296708	18296992	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	intron	18296993	18297158	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	CDS	18297159	18297242	0.46	-	0	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	exon	18297159	18297242	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	intron	18297243	18297335	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	CDS	18297336	18297479	1	-	0	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	exon	18297336	18297479	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	intron	18297480	18297598	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	CDS	18297599	18297826	0.79	-	0	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	exon	18297599	18297826	.	-	.	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
Phchi.S3	AUGUSTUS	start_codon	18297824	18297826	.	-	0	transcript_id "Phchi.S3G262000.t1"; gene_id "Phchi.S3G262000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9561.t1 is derived from g6737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42668519	42671706	.	+	.	Phchi.S1G672000
Phchi.S1	AUGUSTUS	transcript	42668519	42671706	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	start_codon	42668519	42668521	.	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42668519	42668629	0.98	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42668519	42668629	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42668630	42668708	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42668709	42668874	1	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42668709	42668874	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42668875	42669080	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42669081	42669256	1	+	2	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42669081	42669256	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42669257	42669421	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42669422	42669589	1	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42669422	42669589	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42669590	42669739	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42669740	42669901	1	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42669740	42669901	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42669902	42670001	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42670002	42670063	1	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42670002	42670063	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42670064	42670419	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42670420	42670555	1	+	1	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42670420	42670555	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42670556	42670729	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42670730	42670824	1	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42670730	42670824	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42670825	42670913	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42670914	42671029	1	+	1	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42670914	42671029	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42671030	42671146	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42671147	42671276	1	+	2	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42671147	42671276	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42671277	42671372	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42671373	42671427	1	+	1	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42671373	42671427	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	intron	42671428	42671511	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	CDS	42671512	42671706	0.24	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	exon	42671512	42671706	.	+	.	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
Phchi.S1	AUGUSTUS	stop_codon	42671707	42671709	.	+	0	transcript_id "Phchi.S1G672000.t1"; gene_id "Phchi.S1G672000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14089.t1 is derived from g12556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10795394	10796952	.	-	.	Phchi.S3G140800
Phchi.S3	AUGUSTUS	transcript	10795394	10796952	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	stop_codon	10795391	10795393	.	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10795394	10795457	0.84	-	1	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10795394	10795457	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10795458	10795544	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10795545	10795588	0.86	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10795545	10795588	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10795589	10795664	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10795665	10795691	0.86	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10795665	10795691	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10795692	10795790	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10795791	10795871	1	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10795791	10795871	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10795872	10796009	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10796010	10796156	0.76	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10796010	10796156	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10796157	10796258	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10796259	10796358	0.98	-	1	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10796259	10796358	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10796359	10796461	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10796462	10796488	1	-	1	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10796462	10796488	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	intron	10796489	10796899	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	CDS	10796900	10796952	1	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	exon	10796900	10796952	.	-	.	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
Phchi.S3	AUGUSTUS	start_codon	10796950	10796952	.	-	0	transcript_id "Phchi.S3G140800.t1"; gene_id "Phchi.S3G140800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10789.t1 is derived from g14839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2120776	2121695	.	-	.	Phchi.S4G037100
Phchi.S4	AUGUSTUS	transcript	2120776	2121695	.	-	.	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	stop_codon	2120773	2120775	.	-	0	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	CDS	2120776	2121429	0.78	-	0	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	exon	2120776	2121429	.	-	.	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	intron	2121430	2121524	.	-	.	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	CDS	2121525	2121695	0.7	-	0	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	exon	2121525	2121695	.	-	.	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
Phchi.S4	AUGUSTUS	start_codon	2121693	2121695	.	-	0	transcript_id "Phchi.S4G037100.t1"; gene_id "Phchi.S4G037100"
# This transcript jg1602.t2 is derived from g8521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1602.t3 is derived from g8521.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1603.t1 is derived from g8522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1978739	1981559	.	-	.	Phchi.S5G021200
Phchi.S5	AUGUSTUS	transcript	1978739	1981559	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	stop_codon	1978736	1978738	.	-	0	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1978739	1979030	0.82	-	1	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1978739	1979030	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1979031	1979120	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1979121	1979250	1	-	2	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1979121	1979250	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1979251	1979345	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1979346	1979562	1	-	0	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1979346	1979562	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1979563	1979642	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1979643	1979779	1	-	2	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1979643	1979779	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1979780	1979879	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1979880	1979968	1	-	1	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1979880	1979968	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1979969	1980162	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1980163	1980395	0.99	-	0	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1980163	1980395	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1980396	1980506	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1980507	1980682	0.89	-	2	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1980507	1980682	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1980683	1980875	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1980876	1981331	1	-	2	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1980876	1981331	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	intron	1981332	1981552	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	CDS	1981553	1981559	1	-	0	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	exon	1981553	1981559	.	-	.	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
Phchi.S5	AUGUSTUS	start_codon	1981557	1981559	.	-	0	transcript_id "Phchi.S5G021200.t1"; gene_id "Phchi.S5G021200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9957.t1 is derived from g7133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44657830	44658467	.	-	.	Phchi.S1G711600
Phchi.S1	AUGUSTUS	transcript	44657830	44658467	.	-	.	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	stop_codon	44657827	44657829	.	-	0	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	CDS	44657830	44658026	0.98	-	2	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	exon	44657830	44658026	.	-	.	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	intron	44658027	44658184	.	-	.	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	CDS	44658185	44658467	0.94	-	0	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	exon	44658185	44658467	.	-	.	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
Phchi.S1	AUGUSTUS	start_codon	44658465	44658467	.	-	0	transcript_id "Phchi.S1G711600.t1"; gene_id "Phchi.S1G711600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6316.t1 is derived from g3488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22228245	22230879	.	-	.	Phchi.S1G347500
Phchi.S1	AUGUSTUS	transcript	22228245	22230879	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	stop_codon	22228242	22228244	.	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22228245	22228397	0.39	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22228245	22228397	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22228398	22228465	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22228466	22228599	1	-	2	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22228466	22228599	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22228600	22228771	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22228772	22229030	0.99	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22228772	22229030	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22229031	22229134	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22229135	22229223	1	-	2	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22229135	22229223	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22229224	22229321	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22229322	22229472	1	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22229322	22229472	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22229473	22229600	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22229601	22229741	1	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22229601	22229741	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22229742	22229846	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22229847	22229966	1	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22229847	22229966	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22229967	22230088	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22230089	22230260	1	-	1	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22230089	22230260	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22230261	22230533	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22230534	22230696	0.33	-	2	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22230534	22230696	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	intron	22230697	22230770	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	CDS	22230771	22230879	0.46	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	exon	22230771	22230879	.	-	.	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
Phchi.S1	AUGUSTUS	start_codon	22230877	22230879	.	-	0	transcript_id "Phchi.S1G347500.t1"; gene_id "Phchi.S1G347500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2678.t1 is derived from g9598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8162401	8167152	.	-	.	Phchi.S5G128700
Phchi.S5	AUGUSTUS	transcript	8162401	8167152	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	stop_codon	8162398	8162400	.	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8162401	8163075	0.99	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8162401	8163075	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8163076	8163160	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8163161	8163346	1	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8163161	8163346	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8163347	8163467	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8163468	8163584	1	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8163468	8163584	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8163585	8163684	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8163685	8163750	0.98	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8163685	8163750	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8163751	8163859	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8163860	8163951	1	-	2	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8163860	8163951	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8163952	8164032	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8164033	8164096	0.99	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8164033	8164096	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8164097	8164209	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8164210	8164288	1	-	1	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8164210	8164288	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8164289	8164417	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8164418	8164557	1	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8164418	8164557	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8164558	8164676	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8164677	8164758	1	-	1	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8164677	8164758	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8164759	8164941	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8164942	8165045	0.76	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8164942	8165045	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8165046	8165147	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8165148	8165225	0.76	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8165148	8165225	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8165226	8165499	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8165500	8165593	1	-	1	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8165500	8165593	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8165594	8165781	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8165782	8165879	1	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8165782	8165879	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8165880	8166082	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8166083	8166273	0.45	-	2	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8166083	8166273	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8166274	8166551	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8166552	8166764	0.15	-	2	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8166552	8166764	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8166765	8166886	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8166887	8166964	0.63	-	2	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8166887	8166964	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	intron	8166965	8167127	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	CDS	8167128	8167152	0.37	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	exon	8167128	8167152	.	-	.	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
Phchi.S5	AUGUSTUS	start_codon	8167150	8167152	.	-	0	transcript_id "Phchi.S5G128700.t1"; gene_id "Phchi.S5G128700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1863.t1 is derived from g8783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3586408	3591056	.	-	.	Phchi.S5G047200
Phchi.S5	AUGUSTUS	transcript	3586408	3591056	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	stop_codon	3586405	3586407	.	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3586408	3586705	1	-	1	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3586408	3586705	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3586706	3586797	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3586798	3587164	0.99	-	2	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3586798	3587164	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3587165	3587242	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3587243	3587273	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3587243	3587273	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3587274	3587385	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3587386	3587489	0.62	-	2	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3587386	3587489	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3587490	3587625	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3587626	3587732	1	-	1	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3587626	3587732	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3587733	3587815	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3587816	3588286	0.99	-	1	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3587816	3588286	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3588287	3588366	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3588367	3588449	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3588367	3588449	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3588450	3588533	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3588534	3588602	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3588534	3588602	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3588603	3588760	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3588761	3589078	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3588761	3589078	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3589079	3589265	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3589266	3589315	1	-	2	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3589266	3589315	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3589316	3589412	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3589413	3589666	1	-	1	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3589413	3589666	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3589667	3589744	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3589745	3589860	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3589745	3589860	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3589861	3589951	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3589952	3589990	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3589952	3589990	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3589991	3590186	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3590187	3590261	1	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3590187	3590261	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	intron	3590262	3590372	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	CDS	3590373	3591056	0.76	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	exon	3590373	3591056	.	-	.	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
Phchi.S5	AUGUSTUS	start_codon	3591054	3591056	.	-	0	transcript_id "Phchi.S5G047200.t1"; gene_id "Phchi.S5G047200"
# This transcript jg12674.t2 is derived from g14408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12675.t1 is derived from g14409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	16751	17541	.	+	.	Phchi.C62G000600
Phchi.C62	AUGUSTUS	transcript	16751	17541	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	start_codon	16751	16753	.	+	0	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	CDS	16751	16761	0.49	+	0	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	exon	16751	16761	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	intron	16762	16848	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	CDS	16849	16942	0.58	+	1	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	exon	16849	16942	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	intron	16943	17039	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	CDS	17040	17130	0.94	+	0	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	exon	17040	17130	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	intron	17131	17235	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	CDS	17236	17364	0.94	+	2	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	exon	17236	17364	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	intron	17365	17455	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	CDS	17456	17541	0.99	+	2	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	exon	17456	17541	.	+	.	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
Phchi.C62	AUGUSTUS	stop_codon	17542	17544	.	+	0	transcript_id "Phchi.C62G000600.t1"; gene_id "Phchi.C62G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10735.t1 is derived from g14785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1834759	1837416	.	+	.	Phchi.S4G031700
Phchi.S4	AUGUSTUS	transcript	1834759	1837416	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	start_codon	1834759	1834761	.	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1834759	1834929	0.94	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1834759	1834929	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1834930	1835034	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1835035	1835099	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1835035	1835099	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1835100	1835196	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1835197	1835295	1	+	1	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1835197	1835295	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1835296	1835422	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1835423	1835555	1	+	1	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1835423	1835555	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1835556	1835681	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1835682	1835744	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1835682	1835744	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1835745	1835846	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1835847	1835906	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1835847	1835906	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1835907	1836059	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1836060	1836182	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1836060	1836182	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1836183	1836269	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1836270	1836341	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1836270	1836341	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1836342	1836490	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1836491	1836628	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1836491	1836628	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1836629	1836781	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1836782	1836946	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1836782	1836946	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1836947	1837036	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1837037	1837198	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1837037	1837198	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	intron	1837199	1837278	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	CDS	1837279	1837416	1	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	exon	1837279	1837416	.	+	.	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
Phchi.S4	AUGUSTUS	stop_codon	1837417	1837419	.	+	0	transcript_id "Phchi.S4G031700.t1"; gene_id "Phchi.S4G031700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11343.t1 is derived from g15393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5659882	5660966	.	-	.	Phchi.S4G092500
Phchi.S4	AUGUSTUS	transcript	5659882	5660966	.	-	.	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	stop_codon	5659879	5659881	.	-	0	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	CDS	5659882	5660556	0.99	-	0	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	exon	5659882	5660556	.	-	.	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	intron	5660557	5660648	.	-	.	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	CDS	5660649	5660966	1	-	0	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	exon	5660649	5660966	.	-	.	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
Phchi.S4	AUGUSTUS	start_codon	5660964	5660966	.	-	0	transcript_id "Phchi.S4G092500.t1"; gene_id "Phchi.S4G092500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12787.t1 is derived from g11252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2192652	2193943	.	-	.	Phchi.S3G010600
Phchi.S3	AUGUSTUS	transcript	2192652	2193943	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	stop_codon	2192649	2192651	.	-	0	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	CDS	2192652	2192766	0.98	-	1	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	exon	2192652	2192766	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	intron	2192767	2193102	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	CDS	2193103	2193224	1	-	0	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	exon	2193103	2193224	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	intron	2193225	2193305	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	CDS	2193306	2193324	1	-	1	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	exon	2193306	2193324	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	intron	2193325	2193409	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	CDS	2193410	2193547	0.99	-	1	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	exon	2193410	2193547	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	intron	2193548	2193624	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	CDS	2193625	2193696	0.97	-	1	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	exon	2193625	2193696	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	intron	2193697	2193878	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	CDS	2193879	2193943	0.83	-	0	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	exon	2193879	2193943	.	-	.	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
Phchi.S3	AUGUSTUS	start_codon	2193941	2193943	.	-	0	transcript_id "Phchi.S3G010600.t1"; gene_id "Phchi.S3G010600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14924.t1 is derived from g13392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15542775	15544099	.	+	.	Phchi.S3G224300
Phchi.S3	AUGUSTUS	transcript	15542775	15544099	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	start_codon	15542775	15542777	.	+	0	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	CDS	15542775	15543138	0.61	+	0	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	exon	15542775	15543138	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	intron	15543139	15543346	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	CDS	15543347	15543475	0.9	+	2	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	exon	15543347	15543475	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	intron	15543476	15543606	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	CDS	15543607	15543706	0.79	+	2	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	exon	15543607	15543706	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	intron	15543707	15543819	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	CDS	15543820	15543902	0.93	+	1	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	exon	15543820	15543902	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	intron	15543903	15543983	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	CDS	15543984	15544099	1	+	2	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	exon	15543984	15544099	.	+	.	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
Phchi.S3	AUGUSTUS	stop_codon	15544100	15544102	.	+	0	transcript_id "Phchi.S3G224300.t1"; gene_id "Phchi.S3G224300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3738.t1 is derived from g907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5454624	5456911	.	+	.	Phchi.S1G089700
Phchi.S1	AUGUSTUS	transcript	5454624	5456911	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	start_codon	5454624	5454626	.	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5454624	5455034	0.93	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5454624	5455034	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	intron	5455035	5455207	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5455208	5455471	1	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5455208	5455471	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	intron	5455472	5455558	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5455559	5455675	1	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5455559	5455675	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	intron	5455676	5455762	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5455763	5455938	1	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5455763	5455938	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	intron	5455939	5456027	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5456028	5456319	1	+	1	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5456028	5456319	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	intron	5456320	5456419	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5456420	5456584	1	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5456420	5456584	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	intron	5456585	5456668	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	CDS	5456669	5456911	0.78	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	exon	5456669	5456911	.	+	.	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
Phchi.S1	AUGUSTUS	stop_codon	5456912	5456914	.	+	0	transcript_id "Phchi.S1G089700.t1"; gene_id "Phchi.S1G089700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13011.t1 is derived from g11476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3623601	3629809	.	+	.	Phchi.S3G033000
Phchi.S3	AUGUSTUS	transcript	3623601	3629809	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	start_codon	3623601	3623603	.	+	0	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	CDS	3623601	3625374	0.54	+	0	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	exon	3623601	3625374	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	intron	3625375	3625514	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	CDS	3625515	3625707	0.37	+	2	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	exon	3625515	3625707	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	intron	3625708	3625853	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	CDS	3625854	3626743	0.44	+	1	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	exon	3625854	3626743	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	intron	3626744	3626838	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	CDS	3626839	3629081	0.24	+	2	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	exon	3626839	3629081	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	intron	3629082	3629170	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	CDS	3629171	3629809	0.47	+	0	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	exon	3629171	3629809	.	+	.	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
Phchi.S3	AUGUSTUS	stop_codon	3629810	3629812	.	+	0	transcript_id "Phchi.S3G033000.t1"; gene_id "Phchi.S3G033000"
# This transcript jg662.t2 is derived from g10444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg663.t1 is derived from g10445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4631456	4633086	.	+	.	Phchi.S6G062200
Phchi.S6	AUGUSTUS	transcript	4631456	4633086	.	+	.	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	start_codon	4631456	4631458	.	+	0	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	CDS	4631456	4631752	0.66	+	0	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	exon	4631456	4631752	.	+	.	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	intron	4631753	4631877	.	+	.	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	CDS	4631878	4633086	0.99	+	0	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	exon	4631878	4633086	.	+	.	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
Phchi.S6	AUGUSTUS	stop_codon	4633087	4633089	.	+	0	transcript_id "Phchi.S6G062200.t1"; gene_id "Phchi.S6G062200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2164.t1 is derived from g9084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5136025	5137306	.	-	.	Phchi.S5G077300
Phchi.S5	AUGUSTUS	transcript	5136025	5137306	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	stop_codon	5136022	5136024	.	-	0	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	CDS	5136025	5136247	0.99	-	1	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	exon	5136025	5136247	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	intron	5136248	5136370	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	CDS	5136371	5136730	1	-	1	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	exon	5136371	5136730	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	intron	5136731	5136875	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	CDS	5136876	5136927	0.79	-	2	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	exon	5136876	5136927	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	intron	5136928	5137028	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	CDS	5137029	5137147	0.61	-	1	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	exon	5137029	5137147	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	intron	5137148	5137229	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	CDS	5137230	5137306	0.58	-	0	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	exon	5137230	5137306	.	-	.	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
Phchi.S5	AUGUSTUS	start_codon	5137304	5137306	.	-	0	transcript_id "Phchi.S5G077300.t1"; gene_id "Phchi.S5G077300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg887.t1 is derived from g10669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6284300	6285676	.	-	.	Phchi.S6G084600
Phchi.S6	AUGUSTUS	transcript	6284300	6285676	.	-	.	transcript_id "Phchi.S6G084600.t1"; gene_id "Phchi.S6G084600"
Phchi.S6	AUGUSTUS	stop_codon	6284297	6284299	.	-	0	transcript_id "Phchi.S6G084600.t1"; gene_id "Phchi.S6G084600"
Phchi.S6	AUGUSTUS	CDS	6284300	6285676	0.56	-	0	transcript_id "Phchi.S6G084600.t1"; gene_id "Phchi.S6G084600"
Phchi.S6	AUGUSTUS	exon	6284300	6285676	.	-	.	transcript_id "Phchi.S6G084600.t1"; gene_id "Phchi.S6G084600"
Phchi.S6	AUGUSTUS	start_codon	6285674	6285676	.	-	0	transcript_id "Phchi.S6G084600.t1"; gene_id "Phchi.S6G084600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10741.t1 is derived from g14791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1870964	1871647	.	+	.	Phchi.S4G032300
Phchi.S4	AUGUSTUS	transcript	1870964	1871647	.	+	.	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	start_codon	1870964	1870966	.	+	0	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	CDS	1870964	1871258	1	+	0	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	exon	1870964	1871258	.	+	.	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	intron	1871259	1871350	.	+	.	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	CDS	1871351	1871405	1	+	2	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	exon	1871351	1871405	.	+	.	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	intron	1871406	1871496	.	+	.	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	CDS	1871497	1871647	1	+	1	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	exon	1871497	1871647	.	+	.	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
Phchi.S4	AUGUSTUS	stop_codon	1871648	1871650	.	+	0	transcript_id "Phchi.S4G032300.t1"; gene_id "Phchi.S4G032300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13196.t1 is derived from g11661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4636928	4637916	.	+	.	Phchi.S3G051500
Phchi.S3	AUGUSTUS	transcript	4636928	4637916	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	start_codon	4636928	4636930	.	+	0	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	CDS	4636928	4636930	0.96	+	0	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	exon	4636928	4636930	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	intron	4636931	4637021	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	CDS	4637022	4637120	0.96	+	0	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	exon	4637022	4637120	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	intron	4637121	4637226	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	CDS	4637227	4637361	0.94	+	0	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	exon	4637227	4637361	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	intron	4637362	4637451	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	CDS	4637452	4637916	0.99	+	0	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	exon	4637452	4637916	.	+	.	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
Phchi.S3	AUGUSTUS	stop_codon	4637917	4637919	.	+	0	transcript_id "Phchi.S3G051500.t1"; gene_id "Phchi.S3G051500"
# This transcript jg11749.t2 is derived from g15801.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11750.t1 is derived from g15802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8003369	8004624	.	+	.	Phchi.S4G133200
Phchi.S4	AUGUSTUS	transcript	8003369	8004624	.	+	.	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	start_codon	8003369	8003371	.	+	0	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	CDS	8003369	8003852	0.43	+	0	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	exon	8003369	8003852	.	+	.	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	intron	8003853	8003955	.	+	.	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	CDS	8003956	8004181	0.46	+	2	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	exon	8003956	8004181	.	+	.	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	intron	8004182	8004608	.	+	.	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	CDS	8004609	8004624	0.56	+	1	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	exon	8004609	8004624	.	+	.	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
Phchi.S4	AUGUSTUS	stop_codon	8004625	8004627	.	+	0	transcript_id "Phchi.S4G133200.t1"; gene_id "Phchi.S4G133200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1708.t1 is derived from g8628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2642678	2644203	.	-	.	Phchi.S5G031700
Phchi.S5	AUGUSTUS	transcript	2642678	2644203	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	stop_codon	2642675	2642677	.	-	0	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	CDS	2642678	2642780	0.61	-	1	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	exon	2642678	2642780	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	intron	2642781	2642876	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	CDS	2642877	2643069	0.5	-	2	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	exon	2642877	2643069	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	intron	2643070	2643140	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	CDS	2643141	2643327	0.92	-	0	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	exon	2643141	2643327	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	intron	2643328	2643415	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	CDS	2643416	2643802	0.6	-	0	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	exon	2643416	2643802	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	intron	2643803	2643924	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	CDS	2643925	2644203	1	-	0	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	exon	2643925	2644203	.	-	.	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
Phchi.S5	AUGUSTUS	start_codon	2644201	2644203	.	-	0	transcript_id "Phchi.S5G031700.t1"; gene_id "Phchi.S5G031700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13094.t1 is derived from g11559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4128326	4128936	.	+	.	Phchi.S3G041300
Phchi.S3	AUGUSTUS	transcript	4128326	4128936	.	+	.	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	start_codon	4128326	4128328	.	+	0	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	CDS	4128326	4128445	1	+	0	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	exon	4128326	4128445	.	+	.	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	intron	4128446	4128549	.	+	.	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	CDS	4128550	4128936	1	+	0	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	exon	4128550	4128936	.	+	.	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
Phchi.S3	AUGUSTUS	stop_codon	4128937	4128939	.	+	0	transcript_id "Phchi.S3G041300.t1"; gene_id "Phchi.S3G041300"
# This transcript jg1353.t2 is derived from g14420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1354.t1 is derived from g14421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C23	AUGUSTUS	gene	57201	57768	.	-	.	Phchi.C23G000300
Phchi.C23	AUGUSTUS	transcript	57201	57768	.	-	.	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	stop_codon	57198	57200	.	-	0	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	CDS	57201	57325	0.61	-	2	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	exon	57201	57325	.	-	.	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	intron	57326	57411	.	-	.	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	CDS	57412	57504	0.64	-	2	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	exon	57412	57504	.	-	.	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	intron	57505	57617	.	-	.	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	CDS	57618	57768	0.71	-	0	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	exon	57618	57768	.	-	.	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
Phchi.C23	AUGUSTUS	start_codon	57766	57768	.	-	0	transcript_id "Phchi.C23G000300.t1"; gene_id "Phchi.C23G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11331.t1 is derived from g15381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5602752	5603303	.	-	.	Phchi.S4G091300
Phchi.S4	AUGUSTUS	transcript	5602752	5603303	.	-	.	transcript_id "Phchi.S4G091300.t1"; gene_id "Phchi.S4G091300"
Phchi.S4	AUGUSTUS	stop_codon	5602749	5602751	.	-	0	transcript_id "Phchi.S4G091300.t1"; gene_id "Phchi.S4G091300"
Phchi.S4	AUGUSTUS	CDS	5602752	5603303	0.37	-	0	transcript_id "Phchi.S4G091300.t1"; gene_id "Phchi.S4G091300"
Phchi.S4	AUGUSTUS	exon	5602752	5603303	.	-	.	transcript_id "Phchi.S4G091300.t1"; gene_id "Phchi.S4G091300"
Phchi.S4	AUGUSTUS	start_codon	5603301	5603303	.	-	0	transcript_id "Phchi.S4G091300.t1"; gene_id "Phchi.S4G091300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3419.t1 is derived from g588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3511833	3514152	.	+	.	Phchi.S1G057800
Phchi.S1	AUGUSTUS	transcript	3511833	3514152	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	start_codon	3511833	3511835	.	+	0	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3511833	3511942	0.42	+	0	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3511833	3511942	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3511943	3512163	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3512164	3512237	0.26	+	1	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3512164	3512237	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3512238	3512442	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3512443	3512489	0.22	+	2	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3512443	3512489	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3512490	3512581	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3512582	3512726	0.38	+	0	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3512582	3512726	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3512727	3512833	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3512834	3512974	0.42	+	2	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3512834	3512974	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3512975	3513327	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3513328	3513449	0.52	+	2	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3513328	3513449	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3513450	3513552	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3513553	3513627	0.63	+	0	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3513553	3513627	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3513628	3513834	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3513835	3513863	0.75	+	0	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3513835	3513863	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	intron	3513864	3514118	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	CDS	3514119	3514152	0.7	+	1	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	exon	3514119	3514152	.	+	.	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
Phchi.S1	AUGUSTUS	stop_codon	3514153	3514155	.	+	0	transcript_id "Phchi.S1G057800.t1"; gene_id "Phchi.S1G057800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8318.t1 is derived from g5493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35260973	35261731	.	-	.	Phchi.S1G547700
Phchi.S1	AUGUSTUS	transcript	35260973	35261731	.	-	.	transcript_id "Phchi.S1G547700.t1"; gene_id "Phchi.S1G547700"
Phchi.S1	AUGUSTUS	stop_codon	35260970	35260972	.	-	0	transcript_id "Phchi.S1G547700.t1"; gene_id "Phchi.S1G547700"
Phchi.S1	AUGUSTUS	CDS	35260973	35261731	0.8	-	0	transcript_id "Phchi.S1G547700.t1"; gene_id "Phchi.S1G547700"
Phchi.S1	AUGUSTUS	exon	35260973	35261731	.	-	.	transcript_id "Phchi.S1G547700.t1"; gene_id "Phchi.S1G547700"
Phchi.S1	AUGUSTUS	start_codon	35261729	35261731	.	-	0	transcript_id "Phchi.S1G547700.t1"; gene_id "Phchi.S1G547700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3943.t1 is derived from g1112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6579591	6581401	.	+	.	Phchi.S1G110200
Phchi.S1	AUGUSTUS	transcript	6579591	6581401	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	start_codon	6579591	6579593	.	+	0	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	CDS	6579591	6579650	0.78	+	0	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	exon	6579591	6579650	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	intron	6579651	6580161	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	CDS	6580162	6580339	1	+	0	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	exon	6580162	6580339	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	intron	6580340	6580488	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	CDS	6580489	6580669	1	+	2	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	exon	6580489	6580669	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	intron	6580670	6580779	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	CDS	6580780	6580921	1	+	1	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	exon	6580780	6580921	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	intron	6580922	6581027	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	CDS	6581028	6581097	0.99	+	0	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	exon	6581028	6581097	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	intron	6581098	6581237	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	CDS	6581238	6581401	1	+	2	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	exon	6581238	6581401	.	+	.	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
Phchi.S1	AUGUSTUS	stop_codon	6581402	6581404	.	+	0	transcript_id "Phchi.S1G110200.t1"; gene_id "Phchi.S1G110200"
# This transcript jg15533.t2 is derived from g14002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15534.t1 is derived from g14003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19750294	19756005	.	-	.	Phchi.S3G285300
Phchi.S3	AUGUSTUS	transcript	19750294	19756005	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	stop_codon	19750291	19750293	.	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19750294	19750635	1	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19750294	19750635	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19750636	19750763	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19750764	19753340	0.93	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19750764	19753340	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19753341	19753485	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19753486	19753560	1	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19753486	19753560	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19753561	19753663	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19753664	19753861	1	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19753664	19753861	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19753862	19753956	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19753957	19754208	1	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19753957	19754208	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19754209	19754288	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19754289	19754895	0.91	-	1	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19754289	19754895	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19754896	19754983	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19754984	19755176	1	-	2	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19754984	19755176	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19755177	19755460	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19755461	19755576	1	-	1	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19755461	19755576	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	intron	19755577	19755757	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	CDS	19755758	19756005	0.41	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	exon	19755758	19756005	.	-	.	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
Phchi.S3	AUGUSTUS	start_codon	19756003	19756005	.	-	0	transcript_id "Phchi.S3G285300.t1"; gene_id "Phchi.S3G285300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1860.t1 is derived from g8780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3578543	3578815	.	+	.	Phchi.S5G046900
Phchi.S5	AUGUSTUS	transcript	3578543	3578815	.	+	.	transcript_id "Phchi.S5G046900.t1"; gene_id "Phchi.S5G046900"
Phchi.S5	AUGUSTUS	start_codon	3578543	3578545	.	+	0	transcript_id "Phchi.S5G046900.t1"; gene_id "Phchi.S5G046900"
Phchi.S5	AUGUSTUS	CDS	3578543	3578815	0.35	+	0	transcript_id "Phchi.S5G046900.t1"; gene_id "Phchi.S5G046900"
Phchi.S5	AUGUSTUS	exon	3578543	3578815	.	+	.	transcript_id "Phchi.S5G046900.t1"; gene_id "Phchi.S5G046900"
Phchi.S5	AUGUSTUS	stop_codon	3578816	3578818	.	+	0	transcript_id "Phchi.S5G046900.t1"; gene_id "Phchi.S5G046900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14579.t1 is derived from g13047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13562611	13563545	.	+	.	Phchi.S3G189800
Phchi.S3	AUGUSTUS	transcript	13562611	13563545	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	start_codon	13562611	13562613	.	+	0	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	CDS	13562611	13562615	0.99	+	0	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	exon	13562611	13562615	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	intron	13562616	13562708	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	CDS	13562709	13562928	1	+	1	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	exon	13562709	13562928	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	intron	13562929	13563015	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	CDS	13563016	13563387	0.99	+	0	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	exon	13563016	13563387	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	intron	13563388	13563494	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	CDS	13563495	13563545	0.99	+	0	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	exon	13563495	13563545	.	+	.	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
Phchi.S3	AUGUSTUS	stop_codon	13563546	13563548	.	+	0	transcript_id "Phchi.S3G189800.t1"; gene_id "Phchi.S3G189800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2883.t1 is derived from g52.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	265013	266569	.	-	.	Phchi.S1G004200
Phchi.S1	AUGUSTUS	transcript	265013	266569	.	-	.	transcript_id "Phchi.S1G004200.t1"; gene_id "Phchi.S1G004200"
Phchi.S1	AUGUSTUS	stop_codon	265010	265012	.	-	0	transcript_id "Phchi.S1G004200.t1"; gene_id "Phchi.S1G004200"
Phchi.S1	AUGUSTUS	CDS	265013	266569	1	-	0	transcript_id "Phchi.S1G004200.t1"; gene_id "Phchi.S1G004200"
Phchi.S1	AUGUSTUS	exon	265013	266569	.	-	.	transcript_id "Phchi.S1G004200.t1"; gene_id "Phchi.S1G004200"
Phchi.S1	AUGUSTUS	start_codon	266567	266569	.	-	0	transcript_id "Phchi.S1G004200.t1"; gene_id "Phchi.S1G004200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6132.t1 is derived from g3303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21084722	21091543	.	+	.	Phchi.S1G329100
Phchi.S1	AUGUSTUS	transcript	21084722	21091543	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	start_codon	21084722	21084724	.	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21084722	21084856	0.56	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21084722	21084856	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21084857	21084955	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21084956	21085016	0.99	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21084956	21085016	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21085017	21085099	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21085100	21085443	0.99	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21085100	21085443	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21085444	21085541	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21085542	21085699	0.92	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21085542	21085699	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21085700	21085788	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21085789	21087067	0.94	+	1	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21085789	21087067	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21087068	21087177	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21087178	21087253	0.78	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21087178	21087253	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21087254	21087375	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21087376	21087488	0.23	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21087376	21087488	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21087489	21087582	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21087583	21087672	0.26	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21087583	21087672	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21087673	21087949	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21087950	21088051	0.57	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21087950	21088051	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21088052	21088169	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21088170	21088439	0.58	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21088170	21088439	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21088440	21088529	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21088530	21088803	0.96	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21088530	21088803	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21088804	21088929	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21088930	21089021	0.92	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21088930	21089021	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21089022	21089148	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21089149	21089277	0.41	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21089149	21089277	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21089278	21089392	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21089393	21089498	0.34	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21089393	21089498	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21089499	21089584	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21089585	21089757	0.97	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21089585	21089757	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21089758	21089842	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21089843	21089978	0.87	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21089843	21089978	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21089979	21090116	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21090117	21090194	0.71	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21090117	21090194	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21090195	21090280	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21090281	21090452	0.98	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21090281	21090452	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21090453	21090580	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21090581	21090698	1	+	1	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21090581	21090698	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21090699	21090795	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21090796	21091195	1	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21090796	21091195	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	intron	21091196	21091280	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	CDS	21091281	21091543	0.93	+	2	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	exon	21091281	21091543	.	+	.	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
Phchi.S1	AUGUSTUS	stop_codon	21091544	21091546	.	+	0	transcript_id "Phchi.S1G329100.t1"; gene_id "Phchi.S1G329100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8489.t1 is derived from g5664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36226367	36228518	.	+	.	Phchi.S1G564800
Phchi.S1	AUGUSTUS	transcript	36226367	36228518	.	+	.	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	start_codon	36226367	36226369	.	+	0	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	CDS	36226367	36226910	0.99	+	0	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	exon	36226367	36226910	.	+	.	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	intron	36226911	36227082	.	+	.	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	CDS	36227083	36228518	0.91	+	2	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	exon	36227083	36228518	.	+	.	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
Phchi.S1	AUGUSTUS	stop_codon	36228519	36228521	.	+	0	transcript_id "Phchi.S1G564800.t1"; gene_id "Phchi.S1G564800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1446.t1 is derived from g8365.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	927338	928411	.	-	.	Phchi.S5G005500
Phchi.S5	AUGUSTUS	transcript	927338	928257	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	stop_codon	927335	927337	.	-	0	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	927338	927617	0.98	-	1	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	927338	927617	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	intron	927618	927736	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	927737	927885	1	-	0	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	927737	927885	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	intron	927886	927974	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	927975	928142	0.92	-	0	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	927975	928142	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	intron	928143	928230	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	928231	928257	0.91	-	0	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	928231	928257	.	-	.	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	start_codon	928255	928257	.	-	0	transcript_id "Phchi.S5G005500.t1"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	transcript	927338	928411	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	stop_codon	927335	927337	.	-	0	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	927338	927617	0.97	-	1	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	927338	927617	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	intron	927618	927736	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	927737	927885	1	-	0	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	927737	927885	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	intron	927886	927974	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	927975	928142	0.89	-	0	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	927975	928142	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	intron	928143	928408	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	CDS	928409	928411	0.85	-	0	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	exon	928409	928411	.	-	.	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
Phchi.S5	AUGUSTUS	start_codon	928409	928411	.	-	0	transcript_id "Phchi.S5G005500.t2"; gene_id "Phchi.S5G005500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg390.t1 is derived from g10172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2848580	2849245	.	-	.	Phchi.S6G034900
Phchi.S6	AUGUSTUS	transcript	2848580	2849245	.	-	.	transcript_id "Phchi.S6G034900.t1"; gene_id "Phchi.S6G034900"
Phchi.S6	AUGUSTUS	stop_codon	2848577	2848579	.	-	0	transcript_id "Phchi.S6G034900.t1"; gene_id "Phchi.S6G034900"
Phchi.S6	AUGUSTUS	CDS	2848580	2849245	0.95	-	0	transcript_id "Phchi.S6G034900.t1"; gene_id "Phchi.S6G034900"
Phchi.S6	AUGUSTUS	exon	2848580	2849245	.	-	.	transcript_id "Phchi.S6G034900.t1"; gene_id "Phchi.S6G034900"
Phchi.S6	AUGUSTUS	start_codon	2849243	2849245	.	-	0	transcript_id "Phchi.S6G034900.t1"; gene_id "Phchi.S6G034900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3696.t1 is derived from g865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5220886	5221533	.	+	.	Phchi.S1G085500
Phchi.S1	AUGUSTUS	transcript	5220886	5221533	.	+	.	transcript_id "Phchi.S1G085500.t1"; gene_id "Phchi.S1G085500"
Phchi.S1	AUGUSTUS	start_codon	5220886	5220888	.	+	0	transcript_id "Phchi.S1G085500.t1"; gene_id "Phchi.S1G085500"
Phchi.S1	AUGUSTUS	CDS	5220886	5221533	0.93	+	0	transcript_id "Phchi.S1G085500.t1"; gene_id "Phchi.S1G085500"
Phchi.S1	AUGUSTUS	exon	5220886	5221533	.	+	.	transcript_id "Phchi.S1G085500.t1"; gene_id "Phchi.S1G085500"
Phchi.S1	AUGUSTUS	stop_codon	5221534	5221536	.	+	0	transcript_id "Phchi.S1G085500.t1"; gene_id "Phchi.S1G085500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6934.t1 is derived from g4106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26049714	26051266	.	+	.	Phchi.S1G409300
Phchi.S1	AUGUSTUS	transcript	26049714	26051266	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	start_codon	26049714	26049716	.	+	0	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26049714	26049826	1	+	0	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26049714	26049826	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26049827	26049923	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26049924	26050051	1	+	1	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26049924	26050051	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26050052	26050141	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26050142	26050245	0.99	+	2	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26050142	26050245	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26050246	26050368	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26050369	26050456	1	+	0	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26050369	26050456	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26050457	26050542	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26050543	26050604	1	+	2	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26050543	26050604	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26050605	26050743	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26050744	26050892	1	+	0	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26050744	26050892	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26050893	26051096	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26051097	26051108	1	+	1	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26051097	26051108	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	intron	26051109	26051253	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	CDS	26051254	26051266	1	+	1	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	exon	26051254	26051266	.	+	.	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
Phchi.S1	AUGUSTUS	stop_codon	26051267	26051269	.	+	0	transcript_id "Phchi.S1G409300.t1"; gene_id "Phchi.S1G409300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14960.t1 is derived from g13428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15771132	15772077	.	+	.	Phchi.S3G227900
Phchi.S3	AUGUSTUS	transcript	15771132	15772077	.	+	.	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	start_codon	15771132	15771134	.	+	0	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	CDS	15771132	15771402	0.59	+	0	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	exon	15771132	15771402	.	+	.	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	intron	15771403	15771556	.	+	.	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	CDS	15771557	15771650	0.99	+	2	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	exon	15771557	15771650	.	+	.	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	intron	15771651	15771773	.	+	.	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	CDS	15771774	15772077	0.99	+	1	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	exon	15771774	15772077	.	+	.	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
Phchi.S3	AUGUSTUS	stop_codon	15772078	15772080	.	+	0	transcript_id "Phchi.S3G227900.t1"; gene_id "Phchi.S3G227900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7769.t1 is derived from g4943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31169428	31169898	.	+	.	Phchi.S1G492800
Phchi.S1	AUGUSTUS	transcript	31169428	31169898	.	+	.	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	start_codon	31169428	31169430	.	+	0	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	CDS	31169428	31169532	0.98	+	0	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	exon	31169428	31169532	.	+	.	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	intron	31169533	31169658	.	+	.	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	CDS	31169659	31169898	0.75	+	0	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	exon	31169659	31169898	.	+	.	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
Phchi.S1	AUGUSTUS	stop_codon	31169899	31169901	.	+	0	transcript_id "Phchi.S1G492800.t1"; gene_id "Phchi.S1G492800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5124.t1 is derived from g2294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15005390	15005788	.	+	.	Phchi.S1G228300
Phchi.S1	AUGUSTUS	transcript	15005390	15005788	.	+	.	transcript_id "Phchi.S1G228300.t1"; gene_id "Phchi.S1G228300"
Phchi.S1	AUGUSTUS	start_codon	15005390	15005392	.	+	0	transcript_id "Phchi.S1G228300.t1"; gene_id "Phchi.S1G228300"
Phchi.S1	AUGUSTUS	CDS	15005390	15005788	0.98	+	0	transcript_id "Phchi.S1G228300.t1"; gene_id "Phchi.S1G228300"
Phchi.S1	AUGUSTUS	exon	15005390	15005788	.	+	.	transcript_id "Phchi.S1G228300.t1"; gene_id "Phchi.S1G228300"
Phchi.S1	AUGUSTUS	stop_codon	15005789	15005791	.	+	0	transcript_id "Phchi.S1G228300.t1"; gene_id "Phchi.S1G228300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12547.t1 is derived from g8224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34311441	34312038	.	+	.	Phchi.S2G062700
Phchi.S2	AUGUSTUS	transcript	34311441	34312038	.	+	.	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	start_codon	34311441	34311443	.	+	0	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	CDS	34311441	34311461	0.45	+	0	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	exon	34311441	34311461	.	+	.	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	intron	34311462	34311605	.	+	.	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	CDS	34311606	34311722	0.62	+	0	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	exon	34311606	34311722	.	+	.	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	intron	34311723	34311870	.	+	.	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	CDS	34311871	34312038	0.69	+	0	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	exon	34311871	34312038	.	+	.	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
Phchi.S2	AUGUSTUS	stop_codon	34312039	34312041	.	+	0	transcript_id "Phchi.S2G062700.t1"; gene_id "Phchi.S2G062700"
# This transcript jg2893.t2 is derived from g62.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2894.t1 is derived from g63.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	371516	372851	.	-	.	Phchi.S1G005300
Phchi.S1	AUGUSTUS	transcript	371516	372851	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	stop_codon	371513	371515	.	-	0	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	CDS	371516	371571	0.46	-	2	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	exon	371516	371571	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	intron	371572	371724	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	CDS	371725	371911	0.87	-	0	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	exon	371725	371911	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	intron	371912	371999	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	CDS	372000	372319	0.62	-	2	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	exon	372000	372319	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	intron	372320	372586	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	CDS	372587	372851	0.56	-	0	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	exon	372587	372851	.	-	.	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
Phchi.S1	AUGUSTUS	start_codon	372849	372851	.	-	0	transcript_id "Phchi.S1G005300.t1"; gene_id "Phchi.S1G005300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10491.t1 is derived from g14540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	678892	680043	.	+	.	Phchi.S4G007300
Phchi.S4	AUGUSTUS	transcript	678892	680043	.	+	.	transcript_id "Phchi.S4G007300.t1"; gene_id "Phchi.S4G007300"
Phchi.S4	AUGUSTUS	start_codon	678892	678894	.	+	0	transcript_id "Phchi.S4G007300.t1"; gene_id "Phchi.S4G007300"
Phchi.S4	AUGUSTUS	CDS	678892	680043	0.72	+	0	transcript_id "Phchi.S4G007300.t1"; gene_id "Phchi.S4G007300"
Phchi.S4	AUGUSTUS	exon	678892	680043	.	+	.	transcript_id "Phchi.S4G007300.t1"; gene_id "Phchi.S4G007300"
Phchi.S4	AUGUSTUS	stop_codon	680044	680046	.	+	0	transcript_id "Phchi.S4G007300.t1"; gene_id "Phchi.S4G007300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10658.t1 is derived from g14708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1458691	1459224	.	-	.	Phchi.S4G024000
Phchi.S4	AUGUSTUS	transcript	1458691	1459224	.	-	.	transcript_id "Phchi.S4G024000.t1"; gene_id "Phchi.S4G024000"
Phchi.S4	AUGUSTUS	stop_codon	1458688	1458690	.	-	0	transcript_id "Phchi.S4G024000.t1"; gene_id "Phchi.S4G024000"
Phchi.S4	AUGUSTUS	CDS	1458691	1459224	0.85	-	0	transcript_id "Phchi.S4G024000.t1"; gene_id "Phchi.S4G024000"
Phchi.S4	AUGUSTUS	exon	1458691	1459224	.	-	.	transcript_id "Phchi.S4G024000.t1"; gene_id "Phchi.S4G024000"
Phchi.S4	AUGUSTUS	start_codon	1459222	1459224	.	-	0	transcript_id "Phchi.S4G024000.t1"; gene_id "Phchi.S4G024000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13645.t1 is derived from g12112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7995034	7997767	.	-	.	Phchi.S3G096400
Phchi.S3	AUGUSTUS	transcript	7995034	7997767	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	stop_codon	7995031	7995033	.	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7995034	7995037	0.95	-	1	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7995034	7995037	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7995038	7995135	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7995136	7995246	0.95	-	1	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7995136	7995246	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7995247	7995366	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7995367	7995830	1	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7995367	7995830	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7995831	7995921	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7995922	7996098	1	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7995922	7996098	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7996099	7996198	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7996199	7996282	1	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7996199	7996282	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7996283	7996409	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7996410	7996457	1	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7996410	7996457	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7996458	7996601	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7996602	7996727	1	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7996602	7996727	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7996728	7996865	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7996866	7997267	1	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7996866	7997267	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	intron	7997268	7997419	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	CDS	7997420	7997767	0.82	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	exon	7997420	7997767	.	-	.	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
Phchi.S3	AUGUSTUS	start_codon	7997765	7997767	.	-	0	transcript_id "Phchi.S3G096400.t1"; gene_id "Phchi.S3G096400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8532.t1 is derived from g5707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36520043	36522566	.	-	.	Phchi.S1G569100
Phchi.S1	AUGUSTUS	transcript	36520043	36522566	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	stop_codon	36520040	36520042	.	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36520043	36520121	1	-	1	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36520043	36520121	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36520122	36520219	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36520220	36520329	1	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36520220	36520329	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36520330	36520435	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36520436	36520618	1	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36520436	36520618	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36520619	36520723	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36520724	36520897	1	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36520724	36520897	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36520898	36521045	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36521046	36521206	0.99	-	2	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36521046	36521206	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36521207	36521299	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36521300	36521381	1	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36521300	36521381	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36521382	36521480	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36521481	36521513	1	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36521481	36521513	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36521514	36521589	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36521590	36521828	0.97	-	2	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36521590	36521828	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36521829	36521931	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36521932	36522108	1	-	2	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36521932	36522108	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36522109	36522226	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36522227	36522371	0.75	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36522227	36522371	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	intron	36522372	36522479	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	CDS	36522480	36522566	0.28	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	exon	36522480	36522566	.	-	.	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
Phchi.S1	AUGUSTUS	start_codon	36522564	36522566	.	-	0	transcript_id "Phchi.S1G569100.t1"; gene_id "Phchi.S1G569100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12159.t1 is derived from g7835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5072153	5073154	.	+	.	Phchi.S2G023900
Phchi.S2	AUGUSTUS	transcript	5072153	5073154	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	start_codon	5072153	5072155	.	+	0	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	CDS	5072153	5072178	1	+	0	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	exon	5072153	5072178	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	intron	5072179	5072265	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	CDS	5072266	5072359	0.98	+	1	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	exon	5072266	5072359	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	intron	5072360	5072454	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	CDS	5072455	5072726	0.99	+	0	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	exon	5072455	5072726	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	intron	5072727	5072807	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	CDS	5072808	5072992	1	+	1	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	exon	5072808	5072992	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	intron	5072993	5073074	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	CDS	5073075	5073154	1	+	2	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	exon	5073075	5073154	.	+	.	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
Phchi.S2	AUGUSTUS	stop_codon	5073155	5073157	.	+	0	transcript_id "Phchi.S2G023900.t1"; gene_id "Phchi.S2G023900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7661.t1 is derived from g4835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30480188	30484255	.	+	.	Phchi.S1G482000
Phchi.S1	AUGUSTUS	transcript	30480188	30484255	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	start_codon	30480188	30480190	.	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30480188	30481552	0.64	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30480188	30481552	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30481553	30481648	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30481649	30481754	1	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30481649	30481754	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30481755	30481968	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30481969	30482090	1	+	2	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30481969	30482090	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30482091	30482207	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30482208	30482486	0.99	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30482208	30482486	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30482487	30482589	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30482590	30482973	1	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30482590	30482973	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30482974	30483110	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30483111	30483220	1	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30483111	30483220	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30483221	30483342	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30483343	30483571	1	+	1	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30483343	30483571	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	intron	30483572	30483685	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	CDS	30483686	30484255	0.98	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	exon	30483686	30484255	.	+	.	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
Phchi.S1	AUGUSTUS	stop_codon	30484256	30484258	.	+	0	transcript_id "Phchi.S1G482000.t1"; gene_id "Phchi.S1G482000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9128.t1 is derived from g6303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39992442	39993779	.	-	.	Phchi.S1G628700
Phchi.S1	AUGUSTUS	transcript	39992442	39993779	.	-	.	transcript_id "Phchi.S1G628700.t1"; gene_id "Phchi.S1G628700"
Phchi.S1	AUGUSTUS	stop_codon	39992439	39992441	.	-	0	transcript_id "Phchi.S1G628700.t1"; gene_id "Phchi.S1G628700"
Phchi.S1	AUGUSTUS	CDS	39992442	39993779	0.99	-	0	transcript_id "Phchi.S1G628700.t1"; gene_id "Phchi.S1G628700"
Phchi.S1	AUGUSTUS	exon	39992442	39993779	.	-	.	transcript_id "Phchi.S1G628700.t1"; gene_id "Phchi.S1G628700"
Phchi.S1	AUGUSTUS	start_codon	39993777	39993779	.	-	0	transcript_id "Phchi.S1G628700.t1"; gene_id "Phchi.S1G628700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9096.t1 is derived from g6271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39821406	39822311	.	-	.	Phchi.S1G625500
Phchi.S1	AUGUSTUS	transcript	39821406	39822311	.	-	.	transcript_id "Phchi.S1G625500.t1"; gene_id "Phchi.S1G625500"
Phchi.S1	AUGUSTUS	stop_codon	39821403	39821405	.	-	0	transcript_id "Phchi.S1G625500.t1"; gene_id "Phchi.S1G625500"
Phchi.S1	AUGUSTUS	CDS	39821406	39822311	0.96	-	0	transcript_id "Phchi.S1G625500.t1"; gene_id "Phchi.S1G625500"
Phchi.S1	AUGUSTUS	exon	39821406	39822311	.	-	.	transcript_id "Phchi.S1G625500.t1"; gene_id "Phchi.S1G625500"
Phchi.S1	AUGUSTUS	start_codon	39822309	39822311	.	-	0	transcript_id "Phchi.S1G625500.t1"; gene_id "Phchi.S1G625500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15942.t1 is derived from g4.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C101	AUGUSTUS	gene	25933	28172	.	-	.	Phchi.C101G000100
Phchi.C101	AUGUSTUS	transcript	25933	28172	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	stop_codon	25930	25932	.	-	0	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	25933	26180	0.99	-	2	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	25933	26180	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	26181	26318	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	26319	26484	1	-	0	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	26319	26484	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	26485	26604	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	26605	26925	1	-	0	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	26605	26925	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	26926	27036	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	27037	27151	0.91	-	1	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	27037	27151	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	27152	27314	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	27315	27332	0.94	-	1	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	27315	27332	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	27333	27437	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	27438	27618	0.99	-	2	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	27438	27618	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	27619	27707	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	27708	27981	1	-	0	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	27708	27981	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	intron	27982	28061	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	CDS	28062	28172	0.93	-	0	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	exon	28062	28172	.	-	.	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
Phchi.C101	AUGUSTUS	start_codon	28170	28172	.	-	0	transcript_id "Phchi.C101G000100.t1"; gene_id "Phchi.C101G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3912.t1 is derived from g1081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6411637	6412365	.	-	.	Phchi.S1G107100
Phchi.S1	AUGUSTUS	transcript	6411637	6412365	.	-	.	transcript_id "Phchi.S1G107100.t1"; gene_id "Phchi.S1G107100"
Phchi.S1	AUGUSTUS	stop_codon	6411634	6411636	.	-	0	transcript_id "Phchi.S1G107100.t1"; gene_id "Phchi.S1G107100"
Phchi.S1	AUGUSTUS	CDS	6411637	6412365	1	-	0	transcript_id "Phchi.S1G107100.t1"; gene_id "Phchi.S1G107100"
Phchi.S1	AUGUSTUS	exon	6411637	6412365	.	-	.	transcript_id "Phchi.S1G107100.t1"; gene_id "Phchi.S1G107100"
Phchi.S1	AUGUSTUS	start_codon	6412363	6412365	.	-	0	transcript_id "Phchi.S1G107100.t1"; gene_id "Phchi.S1G107100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15619.t1 is derived from g14088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20321633	20322133	.	-	.	Phchi.S3G293800
Phchi.S3	AUGUSTUS	transcript	20321633	20322133	.	-	.	transcript_id "Phchi.S3G293800.t1"; gene_id "Phchi.S3G293800"
Phchi.S3	AUGUSTUS	stop_codon	20321630	20321632	.	-	0	transcript_id "Phchi.S3G293800.t1"; gene_id "Phchi.S3G293800"
Phchi.S3	AUGUSTUS	CDS	20321633	20322133	0.81	-	0	transcript_id "Phchi.S3G293800.t1"; gene_id "Phchi.S3G293800"
Phchi.S3	AUGUSTUS	exon	20321633	20322133	.	-	.	transcript_id "Phchi.S3G293800.t1"; gene_id "Phchi.S3G293800"
Phchi.S3	AUGUSTUS	start_codon	20322131	20322133	.	-	0	transcript_id "Phchi.S3G293800.t1"; gene_id "Phchi.S3G293800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg997.t1 is derived from g10780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6969458	6971150	.	+	.	Phchi.S6G095600
Phchi.S6	AUGUSTUS	transcript	6969458	6971150	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	start_codon	6969458	6969460	.	+	0	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	CDS	6969458	6969904	0.81	+	0	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	exon	6969458	6969904	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	intron	6969905	6970002	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	CDS	6970003	6970222	0.87	+	0	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	exon	6970003	6970222	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	intron	6970223	6970331	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	CDS	6970332	6970629	0.59	+	2	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	exon	6970332	6970629	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	intron	6970630	6970754	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	CDS	6970755	6970789	1	+	1	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	exon	6970755	6970789	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	intron	6970790	6970884	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	CDS	6970885	6971150	1	+	2	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	exon	6970885	6971150	.	+	.	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
Phchi.S6	AUGUSTUS	stop_codon	6971151	6971153	.	+	0	transcript_id "Phchi.S6G095600.t1"; gene_id "Phchi.S6G095600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2841.t1 is derived from g9766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C152	AUGUSTUS	gene	11914	12258	.	+	.	Phchi.C152G000100
Phchi.C152	AUGUSTUS	transcript	11914	12258	.	+	.	transcript_id "Phchi.C152G000100.t1"; gene_id "Phchi.C152G000100"
Phchi.C152	AUGUSTUS	start_codon	11914	11916	.	+	0	transcript_id "Phchi.C152G000100.t1"; gene_id "Phchi.C152G000100"
Phchi.C152	AUGUSTUS	CDS	11914	12258	0.98	+	0	transcript_id "Phchi.C152G000100.t1"; gene_id "Phchi.C152G000100"
Phchi.C152	AUGUSTUS	exon	11914	12258	.	+	.	transcript_id "Phchi.C152G000100.t1"; gene_id "Phchi.C152G000100"
Phchi.C152	AUGUSTUS	stop_codon	12259	12261	.	+	0	transcript_id "Phchi.C152G000100.t1"; gene_id "Phchi.C152G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7460.t1 is derived from g4633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29388396	29392529	.	-	.	Phchi.S1G461900
Phchi.S1	AUGUSTUS	transcript	29388396	29392529	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	stop_codon	29388393	29388395	.	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29388396	29388466	0.68	-	2	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29388396	29388466	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29388467	29388561	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29388562	29388703	0.99	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29388562	29388703	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29388704	29388813	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29388814	29388918	0.94	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29388814	29388918	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29388919	29389026	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29389027	29389101	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29389027	29389101	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29389102	29389223	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29389224	29389285	1	-	2	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29389224	29389285	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29389286	29389422	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29389423	29389507	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29389423	29389507	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29389508	29389624	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29389625	29389708	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29389625	29389708	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29389709	29389791	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29389792	29389848	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29389792	29389848	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29389849	29389942	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29389943	29390113	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29389943	29390113	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29390114	29390235	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29390236	29390327	1	-	2	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29390236	29390327	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29390328	29390484	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29390485	29390539	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29390485	29390539	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29390540	29390662	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29390663	29390756	1	-	1	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29390663	29390756	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29390757	29390871	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29390872	29390965	1	-	2	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29390872	29390965	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29390966	29391062	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29391063	29391150	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29391063	29391150	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29391151	29391278	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29391279	29391404	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29391279	29391404	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29391405	29391491	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29391492	29391635	1	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29391492	29391635	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29391636	29391750	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29391751	29392142	0.48	-	2	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29391751	29392142	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	intron	29392143	29392216	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	CDS	29392217	29392529	0.47	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	exon	29392217	29392529	.	-	.	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
Phchi.S1	AUGUSTUS	start_codon	29392527	29392529	.	-	0	transcript_id "Phchi.S1G461900.t1"; gene_id "Phchi.S1G461900"
# This transcript jg12984.t2 is derived from g11449.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12985.t1 is derived from g11450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3453503	3455093	.	-	.	Phchi.S3G030400
Phchi.S3	AUGUSTUS	transcript	3453503	3455093	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	stop_codon	3453500	3453502	.	-	0	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	CDS	3453503	3453796	0.96	-	0	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	exon	3453503	3453796	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	intron	3453797	3453890	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	CDS	3453891	3454084	1	-	2	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	exon	3453891	3454084	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	intron	3454085	3454176	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	CDS	3454177	3454258	1	-	0	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	exon	3454177	3454258	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	intron	3454259	3454350	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	CDS	3454351	3454614	1	-	0	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	exon	3454351	3454614	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	intron	3454615	3454729	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	CDS	3454730	3454904	1	-	1	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	exon	3454730	3454904	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	intron	3454905	3455022	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	CDS	3455023	3455093	0.73	-	0	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	exon	3455023	3455093	.	-	.	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
Phchi.S3	AUGUSTUS	start_codon	3455091	3455093	.	-	0	transcript_id "Phchi.S3G030400.t1"; gene_id "Phchi.S3G030400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8634.t1 is derived from g5809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37171581	37172661	.	-	.	Phchi.S1G579300
Phchi.S1	AUGUSTUS	transcript	37171581	37172661	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	stop_codon	37171578	37171580	.	-	0	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	CDS	37171581	37171773	0.99	-	1	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	exon	37171581	37171773	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	intron	37171774	37171934	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	CDS	37171935	37172130	1	-	2	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	exon	37171935	37172130	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	intron	37172131	37172214	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	CDS	37172215	37172257	1	-	0	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	exon	37172215	37172257	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	intron	37172258	37172398	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	CDS	37172399	37172506	1	-	0	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	exon	37172399	37172506	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	intron	37172507	37172646	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	CDS	37172647	37172661	0.99	-	0	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	exon	37172647	37172661	.	-	.	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
Phchi.S1	AUGUSTUS	start_codon	37172659	37172661	.	-	0	transcript_id "Phchi.S1G579300.t1"; gene_id "Phchi.S1G579300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13894.t1 is derived from g12361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9502216	9502997	.	+	.	Phchi.S3G121300
Phchi.S3	AUGUSTUS	transcript	9502216	9502997	.	+	.	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	start_codon	9502216	9502218	.	+	0	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	CDS	9502216	9502326	0.99	+	0	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	exon	9502216	9502326	.	+	.	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	intron	9502327	9502664	.	+	.	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	CDS	9502665	9502781	0.99	+	0	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	exon	9502665	9502781	.	+	.	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	intron	9502782	9502919	.	+	.	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	CDS	9502920	9502997	0.99	+	0	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	exon	9502920	9502997	.	+	.	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
Phchi.S3	AUGUSTUS	stop_codon	9502998	9503000	.	+	0	transcript_id "Phchi.S3G121300.t1"; gene_id "Phchi.S3G121300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12786.t1 is derived from g11251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2191298	2192486	.	+	.	Phchi.S3G010500
Phchi.S3	AUGUSTUS	transcript	2191298	2192486	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	start_codon	2191298	2191300	.	+	0	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	CDS	2191298	2191729	0.15	+	0	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	exon	2191298	2191729	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	intron	2191730	2191876	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	CDS	2191877	2191961	1	+	0	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	exon	2191877	2191961	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	intron	2191962	2192105	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	CDS	2192106	2192201	1	+	2	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	exon	2192106	2192201	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	intron	2192202	2192343	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	CDS	2192344	2192486	1	+	2	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	exon	2192344	2192486	.	+	.	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
Phchi.S3	AUGUSTUS	stop_codon	2192487	2192489	.	+	0	transcript_id "Phchi.S3G010500.t1"; gene_id "Phchi.S3G010500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10643.t1 is derived from g14693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1392284	1394452	.	-	.	Phchi.S4G022500
Phchi.S4	AUGUSTUS	transcript	1392284	1394452	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	stop_codon	1392281	1392283	.	-	0	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1392284	1392439	1	-	0	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1392284	1392439	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1392440	1392522	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1392523	1392742	1	-	1	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1392523	1392742	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1392743	1392826	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1392827	1392955	1	-	1	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1392827	1392955	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1392956	1393034	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1393035	1393195	1	-	0	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1393035	1393195	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1393196	1393269	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1393270	1393360	1	-	1	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1393270	1393360	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1393361	1393440	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1393441	1393489	1	-	2	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1393441	1393489	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1393490	1393586	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1393587	1393674	1	-	0	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1393587	1393674	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1393675	1393778	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1393779	1393965	0.83	-	1	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1393779	1393965	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1393966	1394050	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1394051	1394230	1	-	1	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1394051	1394230	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	intron	1394231	1394306	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	CDS	1394307	1394452	0.71	-	0	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	exon	1394307	1394452	.	-	.	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
Phchi.S4	AUGUSTUS	start_codon	1394450	1394452	.	-	0	transcript_id "Phchi.S4G022500.t1"; gene_id "Phchi.S4G022500"
# This transcript jg15263.t2 is derived from g13731.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15264.t1 is derived from g13732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18019410	18020499	.	+	.	Phchi.S3G258300
Phchi.S3	AUGUSTUS	transcript	18019410	18020499	.	+	.	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	start_codon	18019410	18019412	.	+	0	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	CDS	18019410	18020080	0.94	+	0	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	exon	18019410	18020080	.	+	.	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	intron	18020081	18020189	.	+	.	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	CDS	18020190	18020499	1	+	1	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	exon	18020190	18020499	.	+	.	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
Phchi.S3	AUGUSTUS	stop_codon	18020500	18020502	.	+	0	transcript_id "Phchi.S3G258300.t1"; gene_id "Phchi.S3G258300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4274.t1 is derived from g1443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9339686	9341799	.	-	.	Phchi.S1G143300
Phchi.S1	AUGUSTUS	transcript	9339686	9341799	.	-	.	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	stop_codon	9339683	9339685	.	-	0	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	CDS	9339686	9340074	1	-	2	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	exon	9339686	9340074	.	-	.	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	intron	9340075	9340220	.	-	.	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	CDS	9340221	9341799	0.55	-	0	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	exon	9340221	9341799	.	-	.	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
Phchi.S1	AUGUSTUS	start_codon	9341797	9341799	.	-	0	transcript_id "Phchi.S1G143300.t1"; gene_id "Phchi.S1G143300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5999.t1 is derived from g3170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20326377	20327083	.	+	.	Phchi.S1G315800
Phchi.S1	AUGUSTUS	transcript	20326377	20327083	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	start_codon	20326377	20326379	.	+	0	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	CDS	20326377	20326392	1	+	0	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	exon	20326377	20326392	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	intron	20326393	20326478	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	CDS	20326479	20326505	0.48	+	2	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	exon	20326479	20326505	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	intron	20326506	20326592	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	CDS	20326593	20326670	0.48	+	2	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	exon	20326593	20326670	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	intron	20326671	20326761	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	CDS	20326762	20326830	0.72	+	2	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	exon	20326762	20326830	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	intron	20326831	20326910	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	CDS	20326911	20327083	0.4	+	2	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	exon	20326911	20327083	.	+	.	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
Phchi.S1	AUGUSTUS	stop_codon	20327084	20327086	.	+	0	transcript_id "Phchi.S1G315800.t1"; gene_id "Phchi.S1G315800"
# This transcript jg15795.t2 is derived from g14265.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15796.t1 is derived from g14266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21373902	21379328	.	-	.	Phchi.S3G311500
Phchi.S3	AUGUSTUS	transcript	21373902	21379328	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	stop_codon	21373899	21373901	.	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21373902	21373988	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21373902	21373988	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21373989	21374074	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21374075	21374137	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21374075	21374137	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21374138	21374215	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21374216	21374275	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21374216	21374275	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21374276	21374361	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21374362	21374424	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21374362	21374424	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21374425	21374505	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21374506	21374556	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21374506	21374556	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21374557	21374625	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21374626	21374719	1	-	1	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21374626	21374719	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21374720	21374811	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21374812	21375041	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21374812	21375041	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21375042	21375127	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21375128	21375184	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21375128	21375184	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21375185	21375259	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21375260	21375346	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21375260	21375346	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21375347	21375419	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21375420	21375494	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21375420	21375494	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21375495	21375595	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21375596	21375634	0.82	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21375596	21375634	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21375635	21375726	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21375727	21375945	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21375727	21375945	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21375946	21376024	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21376025	21376102	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21376025	21376102	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21376103	21376195	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21376196	21376246	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21376196	21376246	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21376247	21376333	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21376334	21376400	1	-	1	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21376334	21376400	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21376401	21376538	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21376539	21376639	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21376539	21376639	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21376640	21376715	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21376716	21376829	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21376716	21376829	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21376830	21376902	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21376903	21376986	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21376903	21376986	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21376987	21377239	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21377240	21377362	0.78	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21377240	21377362	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21377363	21377463	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21377464	21377589	0.78	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21377464	21377589	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21377590	21377763	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21377764	21377838	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21377764	21377838	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21377839	21377951	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21377952	21378085	0.98	-	2	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21377952	21378085	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21378086	21378162	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21378163	21378268	1	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21378163	21378268	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21378269	21378367	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21378368	21378424	0.73	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21378368	21378424	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21378425	21378572	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21378573	21378786	0.73	-	1	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21378573	21378786	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21378787	21378863	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21378864	21378925	0.73	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21378864	21378925	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21378926	21379093	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21379094	21379135	0.78	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21379094	21379135	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	intron	21379136	21379217	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	CDS	21379218	21379328	0.73	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	exon	21379218	21379328	.	-	.	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
Phchi.S3	AUGUSTUS	start_codon	21379326	21379328	.	-	0	transcript_id "Phchi.S3G311500.t1"; gene_id "Phchi.S3G311500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9173.t1 is derived from g6348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40211713	40212072	.	-	.	Phchi.S1G633200
Phchi.S1	AUGUSTUS	transcript	40211713	40212072	.	-	.	transcript_id "Phchi.S1G633200.t1"; gene_id "Phchi.S1G633200"
Phchi.S1	AUGUSTUS	stop_codon	40211710	40211712	.	-	0	transcript_id "Phchi.S1G633200.t1"; gene_id "Phchi.S1G633200"
Phchi.S1	AUGUSTUS	CDS	40211713	40212072	0.58	-	0	transcript_id "Phchi.S1G633200.t1"; gene_id "Phchi.S1G633200"
Phchi.S1	AUGUSTUS	exon	40211713	40212072	.	-	.	transcript_id "Phchi.S1G633200.t1"; gene_id "Phchi.S1G633200"
Phchi.S1	AUGUSTUS	start_codon	40212070	40212072	.	-	0	transcript_id "Phchi.S1G633200.t1"; gene_id "Phchi.S1G633200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14779.t1 is derived from g13247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14659543	14660047	.	+	.	Phchi.S3G209800
Phchi.S3	AUGUSTUS	transcript	14659543	14660047	.	+	.	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	start_codon	14659543	14659545	.	+	0	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	CDS	14659543	14659609	0.94	+	0	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	exon	14659543	14659609	.	+	.	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	intron	14659610	14659757	.	+	.	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	CDS	14659758	14659833	1	+	2	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	exon	14659758	14659833	.	+	.	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	intron	14659834	14659923	.	+	.	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	CDS	14659924	14660047	1	+	1	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	exon	14659924	14660047	.	+	.	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
Phchi.S3	AUGUSTUS	stop_codon	14660048	14660050	.	+	0	transcript_id "Phchi.S3G209800.t1"; gene_id "Phchi.S3G209800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4469.t1 is derived from g1639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10648073	10648441	.	+	.	Phchi.S1G162800
Phchi.S1	AUGUSTUS	transcript	10648073	10648441	.	+	.	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	start_codon	10648073	10648075	.	+	0	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	CDS	10648073	10648083	0.41	+	0	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	exon	10648073	10648083	.	+	.	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	intron	10648084	10648162	.	+	.	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	CDS	10648163	10648240	0.87	+	1	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	exon	10648163	10648240	.	+	.	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	intron	10648241	10648329	.	+	.	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	CDS	10648330	10648441	0.87	+	1	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	exon	10648330	10648441	.	+	.	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
Phchi.S1	AUGUSTUS	stop_codon	10648442	10648444	.	+	0	transcript_id "Phchi.S1G162800.t1"; gene_id "Phchi.S1G162800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11913.t1 is derived from g15965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9275467	9276615	.	-	.	Phchi.S4G149500
Phchi.S4	AUGUSTUS	transcript	9275467	9276615	.	-	.	transcript_id "Phchi.S4G149500.t1"; gene_id "Phchi.S4G149500"
Phchi.S4	AUGUSTUS	stop_codon	9275464	9275466	.	-	0	transcript_id "Phchi.S4G149500.t1"; gene_id "Phchi.S4G149500"
Phchi.S4	AUGUSTUS	CDS	9275467	9276615	0.79	-	0	transcript_id "Phchi.S4G149500.t1"; gene_id "Phchi.S4G149500"
Phchi.S4	AUGUSTUS	exon	9275467	9276615	.	-	.	transcript_id "Phchi.S4G149500.t1"; gene_id "Phchi.S4G149500"
Phchi.S4	AUGUSTUS	start_codon	9276613	9276615	.	-	0	transcript_id "Phchi.S4G149500.t1"; gene_id "Phchi.S4G149500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11054.t1 is derived from g15104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3862768	3865942	.	+	.	Phchi.S4G063600
Phchi.S4	AUGUSTUS	transcript	3862768	3865942	.	+	.	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	start_codon	3862768	3862770	.	+	0	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	CDS	3862768	3863582	0.81	+	0	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	exon	3862768	3863582	.	+	.	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	intron	3863583	3863674	.	+	.	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	CDS	3863675	3865320	0.64	+	1	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	exon	3863675	3865320	.	+	.	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	intron	3865321	3865421	.	+	.	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	CDS	3865422	3865942	0.55	+	2	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	exon	3865422	3865942	.	+	.	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
Phchi.S4	AUGUSTUS	stop_codon	3865943	3865945	.	+	0	transcript_id "Phchi.S4G063600.t1"; gene_id "Phchi.S4G063600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9842.t1 is derived from g7018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44029874	44032932	.	-	.	Phchi.S1G700100
Phchi.S1	AUGUSTUS	transcript	44029874	44032932	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	stop_codon	44029871	44029873	.	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44029874	44029925	1	-	1	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44029874	44029925	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44029926	44030033	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44030034	44030181	1	-	2	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44030034	44030181	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44030182	44030279	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44030280	44030744	1	-	2	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44030280	44030744	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44030745	44030838	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44030839	44031020	1	-	1	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44030839	44031020	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031021	44031128	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031129	44031214	1	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031129	44031214	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031215	44031362	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031363	44031509	1	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031363	44031509	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031510	44031607	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031608	44031775	1	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031608	44031775	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031776	44031976	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031977	44032116	1	-	2	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031977	44032116	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032117	44032211	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032212	44032262	1	-	2	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032212	44032262	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032263	44032406	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032407	44032496	1	-	2	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032407	44032496	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032497	44032591	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032592	44032661	1	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032592	44032661	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032662	44032755	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032756	44032932	0.93	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032756	44032932	.	-	.	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	start_codon	44032930	44032932	.	-	0	transcript_id "Phchi.S1G700100.t1"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	transcript	44029874	44032932	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	stop_codon	44029871	44029873	.	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44029874	44029925	0.98	-	1	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44029874	44029925	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44029926	44030033	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44030034	44030181	0.98	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44030034	44030181	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44030182	44030279	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44030280	44030744	1	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44030280	44030744	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44030745	44030838	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44030839	44031020	1	-	1	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44030839	44031020	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031021	44031128	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031129	44031214	1	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031129	44031214	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031215	44031362	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031363	44031509	1	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031363	44031509	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031510	44031607	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031608	44031654	0.84	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031608	44031654	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031655	44031751	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031752	44031775	0.83	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031752	44031775	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031776	44031872	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44031873	44031975	0.52	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44031873	44031975	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44031976	44032063	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032064	44032116	0.52	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032064	44032116	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032117	44032211	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032212	44032262	1	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032212	44032262	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032263	44032406	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032407	44032496	1	-	2	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032407	44032496	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032497	44032591	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032592	44032661	1	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032592	44032661	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	intron	44032662	44032755	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	CDS	44032756	44032932	0.9	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	exon	44032756	44032932	.	-	.	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
Phchi.S1	AUGUSTUS	start_codon	44032930	44032932	.	-	0	transcript_id "Phchi.S1G700100.t2"; gene_id "Phchi.S1G700100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9232.t1 is derived from g6407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40522545	40523323	.	-	.	Phchi.S1G639100
Phchi.S1	AUGUSTUS	transcript	40522545	40523323	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	stop_codon	40522542	40522544	.	-	0	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	CDS	40522545	40522634	0.87	-	0	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	exon	40522545	40522634	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	intron	40522635	40522730	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	CDS	40522731	40522775	0.89	-	0	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	exon	40522731	40522775	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	intron	40522776	40522884	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	CDS	40522885	40522989	0.86	-	0	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	exon	40522885	40522989	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	intron	40522990	40523143	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	CDS	40523144	40523178	0.71	-	2	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	exon	40523144	40523178	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	intron	40523179	40523283	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	CDS	40523284	40523323	0.46	-	0	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	exon	40523284	40523323	.	-	.	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
Phchi.S1	AUGUSTUS	start_codon	40523321	40523323	.	-	0	transcript_id "Phchi.S1G639100.t1"; gene_id "Phchi.S1G639100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1643.t1 is derived from g8562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2171112	2172386	.	-	.	Phchi.S5G025200
Phchi.S5	AUGUSTUS	transcript	2171112	2172386	.	-	.	transcript_id "Phchi.S5G025200.t1"; gene_id "Phchi.S5G025200"
Phchi.S5	AUGUSTUS	stop_codon	2171109	2171111	.	-	0	transcript_id "Phchi.S5G025200.t1"; gene_id "Phchi.S5G025200"
Phchi.S5	AUGUSTUS	CDS	2171112	2172386	0.99	-	0	transcript_id "Phchi.S5G025200.t1"; gene_id "Phchi.S5G025200"
Phchi.S5	AUGUSTUS	exon	2171112	2172386	.	-	.	transcript_id "Phchi.S5G025200.t1"; gene_id "Phchi.S5G025200"
Phchi.S5	AUGUSTUS	start_codon	2172384	2172386	.	-	0	transcript_id "Phchi.S5G025200.t1"; gene_id "Phchi.S5G025200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7850.t1 is derived from g5024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31519877	31522727	.	-	.	Phchi.S1G500900
Phchi.S1	AUGUSTUS	transcript	31519877	31522727	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	stop_codon	31519874	31519876	.	-	0	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31519877	31520038	0.99	-	0	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31519877	31520038	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31520039	31520117	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31520118	31520209	1	-	2	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31520118	31520209	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31520210	31520280	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31520281	31520356	1	-	0	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31520281	31520356	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31520357	31520529	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31520530	31520608	0.95	-	1	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31520530	31520608	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31520609	31520709	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31520710	31520856	0.8	-	1	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31520710	31520856	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31520857	31520996	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31520997	31521102	1	-	2	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31520997	31521102	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31521103	31521187	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31521188	31521334	1	-	2	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31521188	31521334	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31521335	31521444	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31521445	31521509	1	-	1	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31521445	31521509	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31521510	31521613	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31521614	31521817	0.99	-	1	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31521614	31521817	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31521818	31521952	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31521953	31521988	1	-	1	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31521953	31521988	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31521989	31522264	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31522265	31522415	1	-	2	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31522265	31522415	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	intron	31522416	31522510	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	CDS	31522511	31522727	0.46	-	0	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	exon	31522511	31522727	.	-	.	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
Phchi.S1	AUGUSTUS	start_codon	31522725	31522727	.	-	0	transcript_id "Phchi.S1G500900.t1"; gene_id "Phchi.S1G500900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14071.t1 is derived from g12538.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10654833	10658756	.	-	.	Phchi.S3G139000
Phchi.S3	AUGUSTUS	transcript	10654833	10658756	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	stop_codon	10654830	10654832	.	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10654833	10655004	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10654833	10655004	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655005	10655142	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655143	10655321	1	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655143	10655321	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655322	10655475	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655476	10655627	1	-	2	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655476	10655627	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655628	10655795	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655796	10655859	1	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655796	10655859	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655860	10655948	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655949	10656108	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655949	10656108	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656109	10656261	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656262	10656385	1	-	2	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656262	10656385	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656386	10656471	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656472	10656564	1	-	2	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656472	10656564	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656565	10656674	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656675	10656889	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656675	10656889	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656890	10656981	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656982	10657068	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656982	10657068	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657069	10657206	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657207	10657219	1	-	2	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657207	10657219	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657220	10657291	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657292	10657319	1	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657292	10657319	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657320	10657438	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657439	10657555	0.99	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657439	10657555	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657556	10657665	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657666	10657718	0.98	-	2	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657666	10657718	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657719	10657828	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657829	10658046	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657829	10658046	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10658047	10658185	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10658186	10658290	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10658186	10658290	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10658291	10658365	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10658366	10658458	1	-	1	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10658366	10658458	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10658459	10658538	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10658539	10658756	0.74	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10658539	10658756	.	-	.	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	start_codon	10658754	10658756	.	-	0	transcript_id "Phchi.S3G139000.t1"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	transcript	10654833	10658756	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	stop_codon	10654830	10654832	.	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10654833	10655004	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10654833	10655004	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655005	10655142	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655143	10655321	1	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655143	10655321	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655322	10655475	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655476	10655627	1	-	2	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655476	10655627	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655628	10655795	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655796	10655859	1	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655796	10655859	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10655860	10655948	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10655949	10656108	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10655949	10656108	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656109	10656261	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656262	10656385	1	-	2	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656262	10656385	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656386	10656471	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656472	10656564	1	-	2	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656472	10656564	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656565	10656674	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656675	10656889	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656675	10656889	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10656890	10656981	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10656982	10657068	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10656982	10657068	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657069	10657227	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657228	10657319	1	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657228	10657319	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657320	10657438	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657439	10657555	0.98	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657439	10657555	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657556	10657665	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657666	10657718	0.98	-	2	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657666	10657718	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10657719	10657828	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10657829	10658046	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10657829	10658046	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10658047	10658185	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10658186	10658290	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10658186	10658290	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10658291	10658365	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10658366	10658458	1	-	1	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10658366	10658458	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	intron	10658459	10658538	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	CDS	10658539	10658756	0.69	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	exon	10658539	10658756	.	-	.	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
Phchi.S3	AUGUSTUS	start_codon	10658754	10658756	.	-	0	transcript_id "Phchi.S3G139000.t2"; gene_id "Phchi.S3G139000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg259.t1 is derived from g10041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1748272	1751929	.	-	.	Phchi.S6G021800
Phchi.S6	AUGUSTUS	transcript	1748272	1751929	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	stop_codon	1748269	1748271	.	-	0	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1748272	1748933	0.45	-	2	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1748272	1748933	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1748934	1749184	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1749185	1749225	0.63	-	1	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1749185	1749225	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1749226	1749370	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1749371	1749587	0.9	-	2	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1749371	1749587	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1749588	1749849	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1749850	1749892	0.98	-	0	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1749850	1749892	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1749893	1750098	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1750099	1750280	0.68	-	2	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1750099	1750280	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1750281	1750415	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1750416	1750982	0.9	-	2	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1750416	1750982	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1750983	1751122	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1751123	1751162	1	-	0	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1751123	1751162	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1751163	1751340	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1751341	1751587	1	-	1	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1751341	1751587	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	intron	1751588	1751729	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	CDS	1751730	1751929	0.94	-	0	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	exon	1751730	1751929	.	-	.	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
Phchi.S6	AUGUSTUS	start_codon	1751927	1751929	.	-	0	transcript_id "Phchi.S6G021800.t1"; gene_id "Phchi.S6G021800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12514.t1 is derived from g8191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32436887	32445661	.	-	.	Phchi.S2G059400
Phchi.S2	AUGUSTUS	transcript	32436887	32445661	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	stop_codon	32436884	32436886	.	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32436887	32437042	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32436887	32437042	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32437043	32437153	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32437154	32437228	0.99	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32437154	32437228	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32437229	32437323	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32437324	32437380	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32437324	32437380	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32437381	32437488	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32437489	32437665	0.99	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32437489	32437665	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32437666	32437773	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32437774	32437840	1	-	1	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32437774	32437840	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32437841	32438012	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32438013	32438071	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32438013	32438071	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32438072	32438221	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32438222	32438275	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32438222	32438275	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32438276	32438843	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32438844	32438993	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32438844	32438993	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32438994	32439273	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32439274	32439483	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32439274	32439483	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32439484	32439636	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32439637	32439765	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32439637	32439765	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32439766	32440044	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32440045	32440149	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32440045	32440149	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32440150	32440238	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32440239	32440328	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32440239	32440328	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32440329	32441283	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32441284	32441349	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32441284	32441349	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32441350	32441588	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32441589	32441657	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32441589	32441657	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32441658	32442058	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32442059	32442178	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32442059	32442178	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32442179	32442269	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32442270	32442329	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32442270	32442329	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32442330	32442587	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32442588	32442724	1	-	2	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32442588	32442724	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32442725	32442903	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32442904	32442994	1	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32442904	32442994	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32442995	32443084	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32443085	32443250	1	-	1	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32443085	32443250	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32443251	32443740	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32443741	32443807	1	-	2	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32443741	32443807	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32443808	32443951	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32443952	32445423	0.51	-	1	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32443952	32445423	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	intron	32445424	32445641	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	CDS	32445642	32445661	0.56	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	exon	32445642	32445661	.	-	.	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
Phchi.S2	AUGUSTUS	start_codon	32445659	32445661	.	-	0	transcript_id "Phchi.S2G059400.t1"; gene_id "Phchi.S2G059400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9774.t1 is derived from g6950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43619275	43619869	.	+	.	Phchi.S1G693300
Phchi.S1	AUGUSTUS	transcript	43619275	43619869	.	+	.	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	start_codon	43619275	43619277	.	+	0	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	CDS	43619275	43619386	0.63	+	0	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	exon	43619275	43619386	.	+	.	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	intron	43619387	43619477	.	+	.	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	CDS	43619478	43619869	0.66	+	2	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	exon	43619478	43619869	.	+	.	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
Phchi.S1	AUGUSTUS	stop_codon	43619870	43619872	.	+	0	transcript_id "Phchi.S1G693300.t1"; gene_id "Phchi.S1G693300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4353.t1 is derived from g1522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9929477	9930222	.	-	.	Phchi.S1G151200
Phchi.S1	AUGUSTUS	transcript	9929477	9930222	.	-	.	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	stop_codon	9929474	9929476	.	-	0	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	CDS	9929477	9929754	0.85	-	2	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	exon	9929477	9929754	.	-	.	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	intron	9929755	9929847	.	-	.	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	CDS	9929848	9929966	0.95	-	1	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	exon	9929848	9929966	.	-	.	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	intron	9929967	9930037	.	-	.	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	CDS	9930038	9930222	0.3	-	0	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	exon	9930038	9930222	.	-	.	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
Phchi.S1	AUGUSTUS	start_codon	9930220	9930222	.	-	0	transcript_id "Phchi.S1G151200.t1"; gene_id "Phchi.S1G151200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9228.t1 is derived from g6403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40512809	40513009	.	-	.	Phchi.S1G638700
Phchi.S1	AUGUSTUS	transcript	40512809	40513009	.	-	.	transcript_id "Phchi.S1G638700.t1"; gene_id "Phchi.S1G638700"
Phchi.S1	AUGUSTUS	stop_codon	40512806	40512808	.	-	0	transcript_id "Phchi.S1G638700.t1"; gene_id "Phchi.S1G638700"
Phchi.S1	AUGUSTUS	CDS	40512809	40513009	0.36	-	0	transcript_id "Phchi.S1G638700.t1"; gene_id "Phchi.S1G638700"
Phchi.S1	AUGUSTUS	exon	40512809	40513009	.	-	.	transcript_id "Phchi.S1G638700.t1"; gene_id "Phchi.S1G638700"
Phchi.S1	AUGUSTUS	start_codon	40513007	40513009	.	-	0	transcript_id "Phchi.S1G638700.t1"; gene_id "Phchi.S1G638700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1943.t1 is derived from g8863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3934433	3936323	.	-	.	Phchi.S5G055200
Phchi.S5	AUGUSTUS	transcript	3934433	3936323	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	stop_codon	3934430	3934432	.	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3934433	3934450	1	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3934433	3934450	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3934451	3934539	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3934540	3934659	1	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3934540	3934659	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3934660	3934774	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3934775	3935236	0.86	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3934775	3935236	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3935237	3935329	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3935330	3935382	1	-	2	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3935330	3935382	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3935383	3935479	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3935480	3935645	1	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3935480	3935645	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3935646	3935785	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3935786	3935877	1	-	2	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3935786	3935877	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3935878	3935957	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3935958	3936099	1	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3935958	3936099	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	intron	3936100	3936260	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	CDS	3936261	3936323	0.46	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	exon	3936261	3936323	.	-	.	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
Phchi.S5	AUGUSTUS	start_codon	3936321	3936323	.	-	0	transcript_id "Phchi.S5G055200.t1"; gene_id "Phchi.S5G055200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15302.t1 is derived from g13770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18298513	18302449	.	+	.	Phchi.S3G262100
Phchi.S3	AUGUSTUS	transcript	18298513	18302449	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	start_codon	18298513	18298515	.	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	CDS	18298513	18298566	1	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	exon	18298513	18298566	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	intron	18298567	18298651	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	CDS	18298652	18298840	1	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	exon	18298652	18298840	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	intron	18298841	18298938	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	CDS	18298939	18299169	1	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	exon	18298939	18299169	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	intron	18299170	18299272	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	CDS	18299273	18299386	1	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	exon	18299273	18299386	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	intron	18299387	18299615	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	CDS	18299616	18300788	1	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	exon	18299616	18300788	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	intron	18300789	18300943	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	CDS	18300944	18302449	0.99	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	exon	18300944	18302449	.	+	.	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
Phchi.S3	AUGUSTUS	stop_codon	18302450	18302452	.	+	0	transcript_id "Phchi.S3G262100.t1"; gene_id "Phchi.S3G262100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5649.t1 is derived from g2819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18054167	18056109	.	-	.	Phchi.S1G280800
Phchi.S1	AUGUSTUS	transcript	18054167	18056109	.	-	.	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	stop_codon	18054164	18054166	.	-	0	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	CDS	18054167	18055202	0.98	-	1	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	exon	18054167	18055202	.	-	.	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	intron	18055203	18055518	.	-	.	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	CDS	18055519	18055688	1	-	0	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	exon	18055519	18055688	.	-	.	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	intron	18055689	18055911	.	-	.	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	CDS	18055912	18056109	1	-	0	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	exon	18055912	18056109	.	-	.	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
Phchi.S1	AUGUSTUS	start_codon	18056107	18056109	.	-	0	transcript_id "Phchi.S1G280800.t1"; gene_id "Phchi.S1G280800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4504.t1 is derived from g1674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10866739	10868405	.	+	.	Phchi.S1G166300
Phchi.S1	AUGUSTUS	transcript	10866739	10868405	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	start_codon	10866739	10866741	.	+	0	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	CDS	10866739	10867137	0.75	+	0	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	exon	10866739	10867137	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	intron	10867138	10867250	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	CDS	10867251	10867267	0.76	+	0	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	exon	10867251	10867267	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	intron	10867268	10867359	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	CDS	10867360	10867483	0.56	+	1	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	exon	10867360	10867483	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	intron	10867484	10868006	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	CDS	10868007	10868114	0.98	+	0	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	exon	10868007	10868114	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	intron	10868115	10868210	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	CDS	10868211	10868405	0.96	+	0	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	exon	10868211	10868405	.	+	.	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
Phchi.S1	AUGUSTUS	stop_codon	10868406	10868408	.	+	0	transcript_id "Phchi.S1G166300.t1"; gene_id "Phchi.S1G166300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15564.t1 is derived from g14033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19933431	19934334	.	+	.	Phchi.S3G288300
Phchi.S3	AUGUSTUS	transcript	19933431	19934334	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	start_codon	19933431	19933433	.	+	0	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	CDS	19933431	19933582	0.88	+	0	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	exon	19933431	19933582	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	intron	19933583	19933707	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	CDS	19933708	19933825	0.73	+	1	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	exon	19933708	19933825	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	intron	19933826	19933928	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	CDS	19933929	19933992	1	+	0	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	exon	19933929	19933992	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	intron	19933993	19934090	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	CDS	19934091	19934197	1	+	2	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	exon	19934091	19934197	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	intron	19934198	19934274	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	CDS	19934275	19934334	1	+	0	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	exon	19934275	19934334	.	+	.	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
Phchi.S3	AUGUSTUS	stop_codon	19934335	19934337	.	+	0	transcript_id "Phchi.S3G288300.t1"; gene_id "Phchi.S3G288300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3922.t1 is derived from g1091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6435537	6437891	.	-	.	Phchi.S1G108100
Phchi.S1	AUGUSTUS	transcript	6435537	6437594	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	stop_codon	6435534	6435536	.	-	0	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6435537	6435637	0.86	-	2	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6435537	6435637	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	intron	6435638	6435803	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6435804	6435972	0.45	-	0	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6435804	6435972	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	intron	6435973	6436141	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6436142	6436279	0.84	-	0	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6436142	6436279	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	intron	6436280	6436473	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6436474	6436581	0.9	-	0	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6436474	6436581	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	intron	6436582	6436660	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6436661	6436781	0.5	-	1	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6436661	6436781	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	intron	6436782	6436890	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6436891	6436960	0.4	-	2	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6436891	6436960	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	intron	6436961	6437125	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6437126	6437594	0.32	-	0	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6437126	6437594	.	-	.	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	start_codon	6437592	6437594	.	-	0	transcript_id "Phchi.S1G108100.t1"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	transcript	6437109	6437891	.	-	.	transcript_id "Phchi.S1G108100.t2"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	stop_codon	6437106	6437108	.	-	0	transcript_id "Phchi.S1G108100.t2"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	CDS	6437109	6437891	0.29	-	0	transcript_id "Phchi.S1G108100.t2"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	exon	6437109	6437891	.	-	.	transcript_id "Phchi.S1G108100.t2"; gene_id "Phchi.S1G108100"
Phchi.S1	AUGUSTUS	start_codon	6437889	6437891	.	-	0	transcript_id "Phchi.S1G108100.t2"; gene_id "Phchi.S1G108100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5904.t1 is derived from g3074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19680764	19682649	.	-	.	Phchi.S1G306300
Phchi.S1	AUGUSTUS	transcript	19680764	19682649	.	-	.	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	stop_codon	19680761	19680763	.	-	0	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	CDS	19680764	19682095	0.27	-	0	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	exon	19680764	19682095	.	-	.	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	intron	19682096	19682286	.	-	.	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	CDS	19682287	19682649	0.09	-	0	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	exon	19682287	19682649	.	-	.	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
Phchi.S1	AUGUSTUS	start_codon	19682647	19682649	.	-	0	transcript_id "Phchi.S1G306300.t1"; gene_id "Phchi.S1G306300"
# This transcript jg11553.t2 is derived from g15604.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11554.t1 is derived from g15605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7015724	7016488	.	-	.	Phchi.S4G113600
Phchi.S4	AUGUSTUS	transcript	7015724	7016488	.	-	.	transcript_id "Phchi.S4G113600.t1"; gene_id "Phchi.S4G113600"
Phchi.S4	AUGUSTUS	stop_codon	7015721	7015723	.	-	0	transcript_id "Phchi.S4G113600.t1"; gene_id "Phchi.S4G113600"
Phchi.S4	AUGUSTUS	CDS	7015724	7016488	0.36	-	0	transcript_id "Phchi.S4G113600.t1"; gene_id "Phchi.S4G113600"
Phchi.S4	AUGUSTUS	exon	7015724	7016488	.	-	.	transcript_id "Phchi.S4G113600.t1"; gene_id "Phchi.S4G113600"
Phchi.S4	AUGUSTUS	start_codon	7016486	7016488	.	-	0	transcript_id "Phchi.S4G113600.t1"; gene_id "Phchi.S4G113600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7931.t1 is derived from g5105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31967695	31968253	.	+	.	Phchi.S1G509000
Phchi.S1	AUGUSTUS	transcript	31967695	31968253	.	+	.	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	start_codon	31967695	31967697	.	+	0	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	CDS	31967695	31967743	0.99	+	0	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	exon	31967695	31967743	.	+	.	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	intron	31967744	31967889	.	+	.	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	CDS	31967890	31968012	1	+	2	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	exon	31967890	31968012	.	+	.	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	intron	31968013	31968101	.	+	.	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	CDS	31968102	31968253	0.95	+	2	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	exon	31968102	31968253	.	+	.	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
Phchi.S1	AUGUSTUS	stop_codon	31968254	31968256	.	+	0	transcript_id "Phchi.S1G509000.t1"; gene_id "Phchi.S1G509000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13157.t1 is derived from g11622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4437405	4438709	.	+	.	Phchi.S3G047600
Phchi.S3	AUGUSTUS	transcript	4437405	4438709	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	start_codon	4437405	4437407	.	+	0	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4437405	4437485	0.93	+	0	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4437405	4437485	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	intron	4437486	4437565	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4437566	4437723	1	+	0	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4437566	4437723	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	intron	4437724	4437825	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4437826	4437891	1	+	1	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4437826	4437891	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	intron	4437892	4437974	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4437975	4438049	1	+	1	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4437975	4438049	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	intron	4438050	4438131	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4438132	4438261	1	+	1	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4438132	4438261	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	intron	4438262	4438351	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4438352	4438480	1	+	0	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4438352	4438480	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	intron	4438481	4438562	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	CDS	4438563	4438709	1	+	0	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	exon	4438563	4438709	.	+	.	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
Phchi.S3	AUGUSTUS	stop_codon	4438710	4438712	.	+	0	transcript_id "Phchi.S3G047600.t1"; gene_id "Phchi.S3G047600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14101.t1 is derived from g12568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10842277	10843149	.	-	.	Phchi.S3G142000
Phchi.S3	AUGUSTUS	transcript	10842277	10843149	.	-	.	transcript_id "Phchi.S3G142000.t1"; gene_id "Phchi.S3G142000"
Phchi.S3	AUGUSTUS	stop_codon	10842274	10842276	.	-	0	transcript_id "Phchi.S3G142000.t1"; gene_id "Phchi.S3G142000"
Phchi.S3	AUGUSTUS	CDS	10842277	10843149	0.81	-	0	transcript_id "Phchi.S3G142000.t1"; gene_id "Phchi.S3G142000"
Phchi.S3	AUGUSTUS	exon	10842277	10843149	.	-	.	transcript_id "Phchi.S3G142000.t1"; gene_id "Phchi.S3G142000"
Phchi.S3	AUGUSTUS	start_codon	10843147	10843149	.	-	0	transcript_id "Phchi.S3G142000.t1"; gene_id "Phchi.S3G142000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10056.t1 is derived from g7232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45538437	45542515	.	+	.	Phchi.S1G721500
Phchi.S1	AUGUSTUS	transcript	45538437	45542515	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	start_codon	45538437	45538439	.	+	0	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	CDS	45538437	45539655	0.12	+	0	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	exon	45538437	45539655	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	intron	45539656	45539800	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	CDS	45539801	45539900	0.39	+	2	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	exon	45539801	45539900	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	intron	45539901	45540079	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	CDS	45540080	45541259	0.39	+	1	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	exon	45540080	45541259	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	intron	45541260	45541375	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	CDS	45541376	45542515	0.99	+	0	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	exon	45541376	45542515	.	+	.	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
Phchi.S1	AUGUSTUS	stop_codon	45542516	45542518	.	+	0	transcript_id "Phchi.S1G721500.t1"; gene_id "Phchi.S1G721500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9910.t1 is derived from g7086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44396284	44396988	.	-	.	Phchi.S1G706900
Phchi.S1	AUGUSTUS	transcript	44396284	44396988	.	-	.	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	stop_codon	44396281	44396283	.	-	0	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	CDS	44396284	44396674	0.99	-	1	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	exon	44396284	44396674	.	-	.	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	intron	44396675	44396761	.	-	.	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	CDS	44396762	44396988	0.58	-	0	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	exon	44396762	44396988	.	-	.	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
Phchi.S1	AUGUSTUS	start_codon	44396986	44396988	.	-	0	transcript_id "Phchi.S1G706900.t1"; gene_id "Phchi.S1G706900"
# This transcript jg9764.t2 is derived from g6940.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9765.t1 is derived from g6941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43591338	43592372	.	+	.	Phchi.S1G692400
Phchi.S1	AUGUSTUS	transcript	43591338	43592372	.	+	.	transcript_id "Phchi.S1G692400.t1"; gene_id "Phchi.S1G692400"
Phchi.S1	AUGUSTUS	start_codon	43591338	43591340	.	+	0	transcript_id "Phchi.S1G692400.t1"; gene_id "Phchi.S1G692400"
Phchi.S1	AUGUSTUS	CDS	43591338	43592372	1	+	0	transcript_id "Phchi.S1G692400.t1"; gene_id "Phchi.S1G692400"
Phchi.S1	AUGUSTUS	exon	43591338	43592372	.	+	.	transcript_id "Phchi.S1G692400.t1"; gene_id "Phchi.S1G692400"
Phchi.S1	AUGUSTUS	stop_codon	43592373	43592375	.	+	0	transcript_id "Phchi.S1G692400.t1"; gene_id "Phchi.S1G692400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12097.t1 is derived from g7772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2693372	2696164	.	-	.	Phchi.S2G017700
Phchi.S2	AUGUSTUS	transcript	2693372	2696164	.	-	.	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	stop_codon	2693369	2693371	.	-	0	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	CDS	2693372	2694951	0.79	-	2	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	exon	2693372	2694951	.	-	.	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	intron	2694952	2695047	.	-	.	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	CDS	2695048	2695815	0.81	-	2	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	exon	2695048	2695815	.	-	.	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	intron	2695816	2695956	.	-	.	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	CDS	2695957	2696164	0.97	-	0	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	exon	2695957	2696164	.	-	.	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
Phchi.S2	AUGUSTUS	start_codon	2696162	2696164	.	-	0	transcript_id "Phchi.S2G017700.t1"; gene_id "Phchi.S2G017700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10603.t1 is derived from g14653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1158990	1159890	.	+	.	Phchi.S4G018500
Phchi.S4	AUGUSTUS	transcript	1158990	1159890	.	+	.	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	start_codon	1158990	1158992	.	+	0	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	CDS	1158990	1159138	0.95	+	0	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	exon	1158990	1159138	.	+	.	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	intron	1159139	1159217	.	+	.	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	CDS	1159218	1159890	0.83	+	1	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	exon	1159218	1159890	.	+	.	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
Phchi.S4	AUGUSTUS	stop_codon	1159891	1159893	.	+	0	transcript_id "Phchi.S4G018500.t1"; gene_id "Phchi.S4G018500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10567.t1 is derived from g14617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1004673	1006916	.	+	.	Phchi.S4G014900
Phchi.S4	AUGUSTUS	transcript	1004673	1006916	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	start_codon	1004673	1004675	.	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1004673	1004816	0.69	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1004673	1004816	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1004817	1004903	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1004904	1005044	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1004904	1005044	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1005045	1005177	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1005178	1005226	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1005178	1005226	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1005227	1005318	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1005319	1005336	1	+	2	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1005319	1005336	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1005337	1005487	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1005488	1005606	1	+	2	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1005488	1005606	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1005607	1005693	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1005694	1005807	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1005694	1005807	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1005808	1005888	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1005889	1005939	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1005889	1005939	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1005940	1006023	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1006024	1006112	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1006024	1006112	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1006113	1006226	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1006227	1006287	1	+	1	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1006227	1006287	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1006288	1006369	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1006370	1006447	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1006370	1006447	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1006448	1006544	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1006545	1006652	1	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1006545	1006652	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	intron	1006653	1006769	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	CDS	1006770	1006916	0.95	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	exon	1006770	1006916	.	+	.	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
Phchi.S4	AUGUSTUS	stop_codon	1006917	1006919	.	+	0	transcript_id "Phchi.S4G014900.t1"; gene_id "Phchi.S4G014900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5244.t1 is derived from g2414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15842709	15843263	.	-	.	Phchi.S1G240300
Phchi.S1	AUGUSTUS	transcript	15842709	15843263	.	-	.	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	stop_codon	15842706	15842708	.	-	0	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	CDS	15842709	15842748	0.97	-	1	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	exon	15842709	15842748	.	-	.	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	intron	15842749	15842903	.	-	.	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	CDS	15842904	15842981	0.97	-	1	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	exon	15842904	15842981	.	-	.	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	intron	15842982	15843165	.	-	.	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	CDS	15843166	15843263	0.41	-	0	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	exon	15843166	15843263	.	-	.	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
Phchi.S1	AUGUSTUS	start_codon	15843261	15843263	.	-	0	transcript_id "Phchi.S1G240300.t1"; gene_id "Phchi.S1G240300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5794.t1 is derived from g2964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18978591	18979565	.	-	.	Phchi.S1G295300
Phchi.S1	AUGUSTUS	transcript	18978591	18979430	.	-	.	transcript_id "Phchi.S1G295300.t1"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	stop_codon	18978588	18978590	.	-	0	transcript_id "Phchi.S1G295300.t1"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	CDS	18978591	18979430	1	-	0	transcript_id "Phchi.S1G295300.t1"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	exon	18978591	18979430	.	-	.	transcript_id "Phchi.S1G295300.t1"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	start_codon	18979428	18979430	.	-	0	transcript_id "Phchi.S1G295300.t1"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	transcript	18978591	18979565	.	-	.	transcript_id "Phchi.S1G295300.t2"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	stop_codon	18978588	18978590	.	-	0	transcript_id "Phchi.S1G295300.t2"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	CDS	18978591	18979565	1	-	0	transcript_id "Phchi.S1G295300.t2"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	exon	18978591	18979565	.	-	.	transcript_id "Phchi.S1G295300.t2"; gene_id "Phchi.S1G295300"
Phchi.S1	AUGUSTUS	start_codon	18979563	18979565	.	-	0	transcript_id "Phchi.S1G295300.t2"; gene_id "Phchi.S1G295300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14622.t1 is derived from g13090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13814449	13819756	.	+	.	Phchi.S3G194100
Phchi.S3	AUGUSTUS	transcript	13814449	13819756	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	start_codon	13814449	13814451	.	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13814449	13814535	1	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13814449	13814535	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13814536	13814759	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13814760	13814870	0.57	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13814760	13814870	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13814871	13814949	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13814950	13815004	1	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13814950	13815004	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13815005	13815130	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13815131	13815273	1	+	2	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13815131	13815273	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13815274	13815436	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13815437	13815720	1	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13815437	13815720	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13815721	13815922	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13815923	13815981	1	+	1	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13815923	13815981	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13815982	13816157	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13816158	13816398	1	+	2	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13816158	13816398	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13816399	13816549	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13816550	13816700	1	+	1	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13816550	13816700	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13816701	13816843	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13816844	13817050	1	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13816844	13817050	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13817051	13817140	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13817141	13818598	0.63	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13817141	13818598	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13818599	13818683	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13818684	13818752	1	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13818684	13818752	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13818753	13818904	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13818905	13819123	1	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13818905	13819123	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13819124	13819267	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13819268	13819363	0.7	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13819268	13819363	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	intron	13819364	13819471	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	CDS	13819472	13819756	0.99	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	exon	13819472	13819756	.	+	.	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
Phchi.S3	AUGUSTUS	stop_codon	13819757	13819759	.	+	0	transcript_id "Phchi.S3G194100.t1"; gene_id "Phchi.S3G194100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3625.t1 is derived from g794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4827176	4830534	.	+	.	Phchi.S1G078400
Phchi.S1	AUGUSTUS	transcript	4827176	4830534	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	start_codon	4827176	4827178	.	+	0	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4827176	4827290	0.93	+	0	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4827176	4827290	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	intron	4827291	4827403	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4827404	4827471	1	+	2	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4827404	4827471	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	intron	4827472	4827592	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4827593	4828568	0.98	+	0	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4827593	4828568	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	intron	4828569	4828827	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4828828	4828929	1	+	2	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4828828	4828929	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	intron	4828930	4829022	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4829023	4829128	1	+	2	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4829023	4829128	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	intron	4829129	4829319	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4829320	4829459	0.86	+	1	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4829320	4829459	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	intron	4829460	4829551	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	CDS	4829552	4830534	0.8	+	2	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	exon	4829552	4830534	.	+	.	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
Phchi.S1	AUGUSTUS	stop_codon	4830535	4830537	.	+	0	transcript_id "Phchi.S1G078400.t1"; gene_id "Phchi.S1G078400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2995.t1 is derived from g164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1052805	1054090	.	+	.	Phchi.S1G015400
Phchi.S1	AUGUSTUS	transcript	1052805	1054090	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	start_codon	1052805	1052807	.	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	CDS	1052805	1052887	0.99	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	exon	1052805	1052887	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	intron	1052888	1053016	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	CDS	1053017	1053131	0.73	+	1	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	exon	1053017	1053131	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	intron	1053132	1053336	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	CDS	1053337	1053474	0.52	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	exon	1053337	1053474	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	intron	1053475	1053633	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	CDS	1053634	1053720	1	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	exon	1053634	1053720	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	intron	1053721	1053807	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	CDS	1053808	1053942	1	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	exon	1053808	1053942	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	intron	1053943	1054024	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	CDS	1054025	1054090	1	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	exon	1054025	1054090	.	+	.	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
Phchi.S1	AUGUSTUS	stop_codon	1054091	1054093	.	+	0	transcript_id "Phchi.S1G015400.t1"; gene_id "Phchi.S1G015400"
# This transcript jg9280.t2 is derived from g6455.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9281.t1 is derived from g6456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40744570	40745208	.	+	.	Phchi.S1G644000
Phchi.S1	AUGUSTUS	transcript	40744570	40745208	.	+	.	transcript_id "Phchi.S1G644000.t1"; gene_id "Phchi.S1G644000"
Phchi.S1	AUGUSTUS	start_codon	40744570	40744572	.	+	0	transcript_id "Phchi.S1G644000.t1"; gene_id "Phchi.S1G644000"
Phchi.S1	AUGUSTUS	CDS	40744570	40745208	0.97	+	0	transcript_id "Phchi.S1G644000.t1"; gene_id "Phchi.S1G644000"
Phchi.S1	AUGUSTUS	exon	40744570	40745208	.	+	.	transcript_id "Phchi.S1G644000.t1"; gene_id "Phchi.S1G644000"
Phchi.S1	AUGUSTUS	stop_codon	40745209	40745211	.	+	0	transcript_id "Phchi.S1G644000.t1"; gene_id "Phchi.S1G644000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6529.t1 is derived from g3701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23503369	23508910	.	-	.	Phchi.S1G368800
Phchi.S1	AUGUSTUS	transcript	23503369	23508910	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	stop_codon	23503366	23503368	.	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23503369	23503864	1	-	1	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23503369	23503864	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23503865	23503945	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23503946	23504133	1	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23503946	23504133	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23504134	23504229	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23504230	23504421	1	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23504230	23504421	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23504422	23504509	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23504510	23504656	1	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23504510	23504656	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23504657	23504847	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23504848	23504913	0.39	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23504848	23504913	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23504914	23505014	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23505015	23505215	0.37	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23505015	23505215	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23505216	23505346	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23505347	23505478	1	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23505347	23505478	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23505479	23505602	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23505603	23505665	0.61	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23505603	23505665	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23505666	23505766	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23505767	23505867	1	-	2	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23505767	23505867	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23505868	23506112	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23506113	23506347	0.91	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23506113	23506347	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23506348	23506473	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23506474	23506576	1	-	1	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23506474	23506576	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23506577	23506685	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23506686	23506765	0.96	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23506686	23506765	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23506766	23507206	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23507207	23507247	0.88	-	2	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23507207	23507247	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23507248	23507410	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23507411	23507438	0.83	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23507411	23507438	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23507439	23507772	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23507773	23507898	0.96	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23507773	23507898	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23507899	23508026	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23508027	23508194	1	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23508027	23508194	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	intron	23508195	23508370	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	CDS	23508371	23508910	1	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	exon	23508371	23508910	.	-	.	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
Phchi.S1	AUGUSTUS	start_codon	23508908	23508910	.	-	0	transcript_id "Phchi.S1G368800.t1"; gene_id "Phchi.S1G368800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5114.t1 is derived from g2284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14798646	14799978	.	-	.	Phchi.S1G227300
Phchi.S1	AUGUSTUS	transcript	14798646	14799978	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	stop_codon	14798643	14798645	.	-	0	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	CDS	14798646	14798681	0.24	-	0	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	exon	14798646	14798681	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	intron	14798682	14798789	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	CDS	14798790	14798907	0.46	-	1	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	exon	14798790	14798907	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	intron	14798908	14799008	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	CDS	14799009	14799129	0.89	-	2	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	exon	14799009	14799129	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	intron	14799130	14799251	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	CDS	14799252	14799309	0.63	-	0	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	exon	14799252	14799309	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	intron	14799310	14799449	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	CDS	14799450	14799562	0.63	-	2	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	exon	14799450	14799562	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	intron	14799563	14799692	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	CDS	14799693	14799978	0.32	-	0	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	exon	14799693	14799978	.	-	.	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
Phchi.S1	AUGUSTUS	start_codon	14799976	14799978	.	-	0	transcript_id "Phchi.S1G227300.t1"; gene_id "Phchi.S1G227300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2903.t1 is derived from g72.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	399347	399804	.	-	.	Phchi.S1G006200
Phchi.S1	AUGUSTUS	transcript	399347	399804	.	-	.	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	stop_codon	399344	399346	.	-	0	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	CDS	399347	399371	0.83	-	1	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	exon	399347	399371	.	-	.	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	intron	399372	399452	.	-	.	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	CDS	399453	399621	0.92	-	2	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	exon	399453	399621	.	-	.	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	intron	399622	399713	.	-	.	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	CDS	399714	399804	0.86	-	0	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	exon	399714	399804	.	-	.	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
Phchi.S1	AUGUSTUS	start_codon	399802	399804	.	-	0	transcript_id "Phchi.S1G006200.t1"; gene_id "Phchi.S1G006200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg223.t1 is derived from g10005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1492638	1493576	.	-	.	Phchi.S6G018200
Phchi.S6	AUGUSTUS	transcript	1492638	1493576	.	-	.	transcript_id "Phchi.S6G018200.t1"; gene_id "Phchi.S6G018200"
Phchi.S6	AUGUSTUS	stop_codon	1492635	1492637	.	-	0	transcript_id "Phchi.S6G018200.t1"; gene_id "Phchi.S6G018200"
Phchi.S6	AUGUSTUS	CDS	1492638	1493576	0.93	-	0	transcript_id "Phchi.S6G018200.t1"; gene_id "Phchi.S6G018200"
Phchi.S6	AUGUSTUS	exon	1492638	1493576	.	-	.	transcript_id "Phchi.S6G018200.t1"; gene_id "Phchi.S6G018200"
Phchi.S6	AUGUSTUS	start_codon	1493574	1493576	.	-	0	transcript_id "Phchi.S6G018200.t1"; gene_id "Phchi.S6G018200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7789.t1 is derived from g4963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31196051	31197243	.	+	.	Phchi.S1G494800
Phchi.S1	AUGUSTUS	transcript	31196051	31197243	.	+	.	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	start_codon	31196051	31196053	.	+	0	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	CDS	31196051	31196612	0.83	+	0	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	exon	31196051	31196612	.	+	.	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	intron	31196613	31196740	.	+	.	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	CDS	31196741	31197243	0.49	+	2	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	exon	31196741	31197243	.	+	.	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
Phchi.S1	AUGUSTUS	stop_codon	31197244	31197246	.	+	0	transcript_id "Phchi.S1G494800.t1"; gene_id "Phchi.S1G494800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2366.t1 is derived from g9286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6368607	6370457	.	+	.	Phchi.S5G097500
Phchi.S5	AUGUSTUS	transcript	6368607	6370457	.	+	.	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	start_codon	6368607	6368609	.	+	0	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	CDS	6368607	6368857	0.92	+	0	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	exon	6368607	6368857	.	+	.	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	intron	6368858	6369002	.	+	.	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	CDS	6369003	6369700	0.54	+	1	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	exon	6369003	6369700	.	+	.	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	intron	6369701	6369810	.	+	.	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	CDS	6369811	6370457	0.38	+	2	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	exon	6369811	6370457	.	+	.	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
Phchi.S5	AUGUSTUS	stop_codon	6370458	6370460	.	+	0	transcript_id "Phchi.S5G097500.t1"; gene_id "Phchi.S5G097500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5165.t1 is derived from g2335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15235925	15236679	.	+	.	Phchi.S1G232400
Phchi.S1	AUGUSTUS	transcript	15235925	15236679	.	+	.	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	start_codon	15235925	15235927	.	+	0	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	CDS	15235925	15235984	0.42	+	0	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	exon	15235925	15235984	.	+	.	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	intron	15235985	15236076	.	+	.	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	CDS	15236077	15236248	0.95	+	0	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	exon	15236077	15236248	.	+	.	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	intron	15236249	15236515	.	+	.	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	CDS	15236516	15236679	0.94	+	2	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	exon	15236516	15236679	.	+	.	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
Phchi.S1	AUGUSTUS	stop_codon	15236680	15236682	.	+	0	transcript_id "Phchi.S1G232400.t1"; gene_id "Phchi.S1G232400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8348.t1 is derived from g5523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35437917	35438312	.	+	.	Phchi.S1G550700
Phchi.S1	AUGUSTUS	transcript	35437917	35438312	.	+	.	transcript_id "Phchi.S1G550700.t1"; gene_id "Phchi.S1G550700"
Phchi.S1	AUGUSTUS	start_codon	35437917	35437919	.	+	0	transcript_id "Phchi.S1G550700.t1"; gene_id "Phchi.S1G550700"
Phchi.S1	AUGUSTUS	CDS	35437917	35438312	0.62	+	0	transcript_id "Phchi.S1G550700.t1"; gene_id "Phchi.S1G550700"
Phchi.S1	AUGUSTUS	exon	35437917	35438312	.	+	.	transcript_id "Phchi.S1G550700.t1"; gene_id "Phchi.S1G550700"
Phchi.S1	AUGUSTUS	stop_codon	35438313	35438315	.	+	0	transcript_id "Phchi.S1G550700.t1"; gene_id "Phchi.S1G550700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6968.t1 is derived from g4140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26166597	26166970	.	-	.	Phchi.S1G412700
Phchi.S1	AUGUSTUS	transcript	26166597	26166970	.	-	.	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	stop_codon	26166594	26166596	.	-	0	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	CDS	26166597	26166729	1	-	1	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	exon	26166597	26166729	.	-	.	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	intron	26166730	26166893	.	-	.	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	CDS	26166894	26166970	0.88	-	0	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	exon	26166894	26166970	.	-	.	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
Phchi.S1	AUGUSTUS	start_codon	26166968	26166970	.	-	0	transcript_id "Phchi.S1G412700.t1"; gene_id "Phchi.S1G412700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5581.t1 is derived from g2751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17715277	17723652	.	+	.	Phchi.S1G274000
Phchi.S1	AUGUSTUS	transcript	17715277	17723652	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	start_codon	17715277	17715279	.	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17715277	17715321	0.97	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17715277	17715321	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17715322	17715464	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17715465	17715669	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17715465	17715669	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17715670	17715772	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17715773	17715858	1	+	2	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17715773	17715858	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17715859	17715983	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17715984	17716062	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17715984	17716062	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17716063	17716175	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17716176	17716303	1	+	2	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17716176	17716303	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17716304	17716389	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17716390	17716488	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17716390	17716488	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17716489	17716622	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17716623	17716731	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17716623	17716731	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17716732	17716817	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17716818	17716897	1	+	2	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17716818	17716897	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17716898	17717159	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17717160	17717387	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17717160	17717387	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17717388	17717473	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17717474	17717539	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17717474	17717539	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17717540	17717678	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17717679	17717795	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17717679	17717795	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17717796	17717934	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17717935	17718132	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17717935	17718132	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17718133	17718209	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17718210	17718326	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17718210	17718326	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17718327	17718407	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17718408	17718467	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17718408	17718467	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17718468	17718564	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17718565	17718651	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17718565	17718651	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17718652	17718816	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17718817	17718900	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17718817	17718900	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17718901	17718984	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17718985	17719119	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17718985	17719119	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17719120	17719323	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17719324	17719386	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17719324	17719386	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17719387	17719466	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17719467	17719571	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17719467	17719571	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17719572	17719652	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17719653	17719765	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17719653	17719765	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17719766	17719849	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17719850	17720102	1	+	1	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17719850	17720102	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17720103	17720246	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17720247	17720383	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17720247	17720383	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17720384	17720481	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17720482	17720760	1	+	1	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17720482	17720760	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17720761	17720856	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17720857	17721859	1	+	1	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17720857	17721859	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17721860	17721946	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17721947	17722432	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17721947	17722432	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17722433	17722539	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17722540	17722710	0.95	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17722540	17722710	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17722711	17722821	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17722822	17722894	0.55	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17722822	17722894	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17722895	17722947	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17722948	17723006	0.56	+	2	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17722948	17723006	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17723007	17723101	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17723102	17723224	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17723102	17723224	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17723225	17723312	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17723313	17723423	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17723313	17723423	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	intron	17723424	17723514	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	CDS	17723515	17723652	1	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	exon	17723515	17723652	.	+	.	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
Phchi.S1	AUGUSTUS	stop_codon	17723653	17723655	.	+	0	transcript_id "Phchi.S1G274000.t1"; gene_id "Phchi.S1G274000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8638.t1 is derived from g5813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37187720	37189783	.	+	.	Phchi.S1G579700
Phchi.S1	AUGUSTUS	transcript	37187720	37189783	.	+	.	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	start_codon	37187720	37187722	.	+	0	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	CDS	37187720	37189013	0.64	+	0	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	exon	37187720	37189013	.	+	.	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	intron	37189014	37189136	.	+	.	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	CDS	37189137	37189783	1	+	2	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	exon	37189137	37189783	.	+	.	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
Phchi.S1	AUGUSTUS	stop_codon	37189784	37189786	.	+	0	transcript_id "Phchi.S1G579700.t1"; gene_id "Phchi.S1G579700"
# This transcript jg6349.t2 is derived from g3521.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6350.t1 is derived from g3522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22445681	22448199	.	+	.	Phchi.S1G350900
Phchi.S1	AUGUSTUS	transcript	22445681	22448199	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	start_codon	22445681	22445683	.	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22445681	22445785	1	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22445681	22445785	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22445786	22445870	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22445871	22445955	1	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22445871	22445955	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22445956	22446220	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22446221	22446359	1	+	2	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22446221	22446359	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22446360	22446468	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22446469	22446517	1	+	1	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22446469	22446517	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22446518	22446707	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22446708	22446890	1	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22446708	22446890	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22446891	22446980	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22446981	22447055	1	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22446981	22447055	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22447056	22447163	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22447164	22447349	1	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22447164	22447349	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22447350	22447437	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22447438	22447526	0.95	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22447438	22447526	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	intron	22447527	22447637	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	CDS	22447638	22448199	1	+	1	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	exon	22447638	22448199	.	+	.	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
Phchi.S1	AUGUSTUS	stop_codon	22448200	22448202	.	+	0	transcript_id "Phchi.S1G350900.t1"; gene_id "Phchi.S1G350900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8261.t1 is derived from g5436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34976890	34978400	.	-	.	Phchi.S1G542000
Phchi.S1	AUGUSTUS	transcript	34976890	34978400	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	stop_codon	34976887	34976889	.	-	0	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	CDS	34976890	34976932	0.73	-	1	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	exon	34976890	34976932	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	intron	34976933	34977024	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	CDS	34977025	34977139	0.62	-	2	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	exon	34977025	34977139	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	intron	34977140	34977331	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	CDS	34977332	34977582	0.88	-	1	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	exon	34977332	34977582	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	intron	34977583	34977732	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	CDS	34977733	34977902	0.99	-	0	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	exon	34977733	34977902	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	intron	34977903	34977988	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	CDS	34977989	34978059	1	-	2	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	exon	34977989	34978059	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	intron	34978060	34978132	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	CDS	34978133	34978400	0.61	-	0	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	exon	34978133	34978400	.	-	.	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
Phchi.S1	AUGUSTUS	start_codon	34978398	34978400	.	-	0	transcript_id "Phchi.S1G542000.t1"; gene_id "Phchi.S1G542000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3266.t1 is derived from g435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2619609	2619998	.	-	.	Phchi.S1G042500
Phchi.S1	AUGUSTUS	transcript	2619609	2619998	.	-	.	transcript_id "Phchi.S1G042500.t1"; gene_id "Phchi.S1G042500"
Phchi.S1	AUGUSTUS	stop_codon	2619606	2619608	.	-	0	transcript_id "Phchi.S1G042500.t1"; gene_id "Phchi.S1G042500"
Phchi.S1	AUGUSTUS	CDS	2619609	2619998	0.4	-	0	transcript_id "Phchi.S1G042500.t1"; gene_id "Phchi.S1G042500"
Phchi.S1	AUGUSTUS	exon	2619609	2619998	.	-	.	transcript_id "Phchi.S1G042500.t1"; gene_id "Phchi.S1G042500"
Phchi.S1	AUGUSTUS	start_codon	2619996	2619998	.	-	0	transcript_id "Phchi.S1G042500.t1"; gene_id "Phchi.S1G042500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9199.t1 is derived from g6374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40323663	40327568	.	+	.	Phchi.S1G635800
Phchi.S1	AUGUSTUS	transcript	40323663	40327568	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	start_codon	40323663	40323665	.	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40323663	40323710	0.86	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40323663	40323710	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40323711	40323784	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40323785	40324836	0.93	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40323785	40324836	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40324837	40324928	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40324929	40325263	0.97	+	1	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40324929	40325263	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40325264	40325347	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40325348	40325748	0.56	+	2	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40325348	40325748	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40325749	40325854	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40325855	40325965	1	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40325855	40325965	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40325966	40326073	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40326074	40326286	1	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40326074	40326286	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40326287	40326449	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40326450	40327148	0.99	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40326450	40327148	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	intron	40327149	40327274	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	CDS	40327275	40327568	1	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	exon	40327275	40327568	.	+	.	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
Phchi.S1	AUGUSTUS	stop_codon	40327569	40327571	.	+	0	transcript_id "Phchi.S1G635800.t1"; gene_id "Phchi.S1G635800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8513.t1 is derived from g5688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36391237	36393048	.	+	.	Phchi.S1G567200
Phchi.S1	AUGUSTUS	transcript	36391237	36393048	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	start_codon	36391237	36391239	.	+	0	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	CDS	36391237	36391453	0.21	+	0	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	exon	36391237	36391453	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	intron	36391454	36391554	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	CDS	36391555	36391834	0.35	+	2	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	exon	36391555	36391834	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	intron	36391835	36391936	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	CDS	36391937	36392342	1	+	1	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	exon	36391937	36392342	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	intron	36392343	36392429	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	CDS	36392430	36392690	1	+	0	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	exon	36392430	36392690	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	intron	36392691	36392771	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	CDS	36392772	36392858	1	+	0	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	exon	36392772	36392858	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	intron	36392859	36392931	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	CDS	36392932	36393048	1	+	0	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	exon	36392932	36393048	.	+	.	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
Phchi.S1	AUGUSTUS	stop_codon	36393049	36393051	.	+	0	transcript_id "Phchi.S1G567200.t1"; gene_id "Phchi.S1G567200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3101.t1 is derived from g270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1757025	1758930	.	+	.	Phchi.S1G026000
Phchi.S1	AUGUSTUS	transcript	1757025	1758930	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	start_codon	1757025	1757027	.	+	0	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1757025	1757681	0.56	+	0	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1757025	1757681	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	intron	1757682	1757766	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1757767	1757844	1	+	0	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1757767	1757844	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	intron	1757845	1757992	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1757993	1758135	1	+	0	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1757993	1758135	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	intron	1758136	1758202	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1758203	1758273	1	+	1	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1758203	1758273	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	intron	1758274	1758460	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1758461	1758568	1	+	2	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1758461	1758568	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	intron	1758569	1758661	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1758662	1758754	1	+	2	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1758662	1758754	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	intron	1758755	1758850	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	CDS	1758851	1758930	1	+	2	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	exon	1758851	1758930	.	+	.	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
Phchi.S1	AUGUSTUS	stop_codon	1758931	1758933	.	+	0	transcript_id "Phchi.S1G026000.t1"; gene_id "Phchi.S1G026000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8870.t1 is derived from g6045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38390132	38390482	.	+	.	Phchi.S1G602900
Phchi.S1	AUGUSTUS	transcript	38390132	38390482	.	+	.	transcript_id "Phchi.S1G602900.t1"; gene_id "Phchi.S1G602900"
Phchi.S1	AUGUSTUS	start_codon	38390132	38390134	.	+	0	transcript_id "Phchi.S1G602900.t1"; gene_id "Phchi.S1G602900"
Phchi.S1	AUGUSTUS	CDS	38390132	38390482	0.34	+	0	transcript_id "Phchi.S1G602900.t1"; gene_id "Phchi.S1G602900"
Phchi.S1	AUGUSTUS	exon	38390132	38390482	.	+	.	transcript_id "Phchi.S1G602900.t1"; gene_id "Phchi.S1G602900"
Phchi.S1	AUGUSTUS	stop_codon	38390483	38390485	.	+	0	transcript_id "Phchi.S1G602900.t1"; gene_id "Phchi.S1G602900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6199.t1 is derived from g3370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21448186	21450103	.	+	.	Phchi.S1G335800
Phchi.S1	AUGUSTUS	transcript	21448186	21450103	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	start_codon	21448186	21448188	.	+	0	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	CDS	21448186	21448392	1	+	0	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	exon	21448186	21448392	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	intron	21448393	21448580	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	CDS	21448581	21448688	0.44	+	0	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	exon	21448581	21448688	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	intron	21448689	21448771	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	CDS	21448772	21448809	0.32	+	0	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	exon	21448772	21448809	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	intron	21448810	21448915	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	CDS	21448916	21449025	0.69	+	1	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	exon	21448916	21449025	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	intron	21449026	21449147	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	CDS	21449148	21450103	0.89	+	2	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	exon	21449148	21450103	.	+	.	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
Phchi.S1	AUGUSTUS	stop_codon	21450104	21450106	.	+	0	transcript_id "Phchi.S1G335800.t1"; gene_id "Phchi.S1G335800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2235.t1 is derived from g9155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5584858	5586822	.	+	.	Phchi.S5G084400
Phchi.S5	AUGUSTUS	transcript	5584858	5586822	.	+	.	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	start_codon	5584858	5584860	.	+	0	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	CDS	5584858	5585560	0.89	+	0	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	exon	5584858	5585560	.	+	.	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	intron	5585561	5585625	.	+	.	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	CDS	5585626	5585670	0.9	+	2	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	exon	5585626	5585670	.	+	.	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	intron	5585671	5585923	.	+	.	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	CDS	5585924	5586822	0.86	+	2	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	exon	5585924	5586822	.	+	.	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
Phchi.S5	AUGUSTUS	stop_codon	5586823	5586825	.	+	0	transcript_id "Phchi.S5G084400.t1"; gene_id "Phchi.S5G084400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5075.t1 is derived from g2245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14559078	14560558	.	+	.	Phchi.S1G223400
Phchi.S1	AUGUSTUS	transcript	14559078	14560558	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	start_codon	14559078	14559080	.	+	0	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	CDS	14559078	14559171	1	+	0	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	exon	14559078	14559171	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	intron	14559172	14559267	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	CDS	14559268	14559377	1	+	2	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	exon	14559268	14559377	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	intron	14559378	14559470	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	CDS	14559471	14559517	1	+	0	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	exon	14559471	14559517	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	intron	14559518	14559588	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	CDS	14559589	14560558	0.99	+	1	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	exon	14559589	14560558	.	+	.	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
Phchi.S1	AUGUSTUS	stop_codon	14560559	14560561	.	+	0	transcript_id "Phchi.S1G223400.t1"; gene_id "Phchi.S1G223400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg596.t1 is derived from g10378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4339177	4339992	.	+	.	Phchi.S6G055500
Phchi.S6	AUGUSTUS	transcript	4339177	4339992	.	+	.	transcript_id "Phchi.S6G055500.t1"; gene_id "Phchi.S6G055500"
Phchi.S6	AUGUSTUS	start_codon	4339177	4339179	.	+	0	transcript_id "Phchi.S6G055500.t1"; gene_id "Phchi.S6G055500"
Phchi.S6	AUGUSTUS	CDS	4339177	4339992	0.74	+	0	transcript_id "Phchi.S6G055500.t1"; gene_id "Phchi.S6G055500"
Phchi.S6	AUGUSTUS	exon	4339177	4339992	.	+	.	transcript_id "Phchi.S6G055500.t1"; gene_id "Phchi.S6G055500"
Phchi.S6	AUGUSTUS	stop_codon	4339993	4339995	.	+	0	transcript_id "Phchi.S6G055500.t1"; gene_id "Phchi.S6G055500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5436.t1 is derived from g2606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16862080	16862393	.	+	.	Phchi.S1G259500
Phchi.S1	AUGUSTUS	transcript	16862080	16862393	.	+	.	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	start_codon	16862080	16862082	.	+	0	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	CDS	16862080	16862176	0.85	+	0	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	exon	16862080	16862176	.	+	.	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	intron	16862177	16862274	.	+	.	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	CDS	16862275	16862393	0.97	+	2	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	exon	16862275	16862393	.	+	.	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
Phchi.S1	AUGUSTUS	stop_codon	16862394	16862396	.	+	0	transcript_id "Phchi.S1G259500.t1"; gene_id "Phchi.S1G259500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2375.t1 is derived from g9295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6405528	6406695	.	+	.	Phchi.S5G098400
Phchi.S5	AUGUSTUS	transcript	6405528	6406695	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	start_codon	6405528	6405530	.	+	0	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	CDS	6405528	6405578	0.49	+	0	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	exon	6405528	6405578	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	intron	6405579	6405783	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	CDS	6405784	6405958	0.54	+	0	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	exon	6405784	6405958	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	intron	6405959	6406061	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	CDS	6406062	6406592	0.7	+	2	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	exon	6406062	6406592	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	intron	6406593	6406693	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	CDS	6406694	6406695	0.91	+	2	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	exon	6406694	6406695	.	+	.	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
Phchi.S5	AUGUSTUS	stop_codon	6406696	6406698	.	+	0	transcript_id "Phchi.S5G098400.t1"; gene_id "Phchi.S5G098400"
# This transcript jg9458.t2 is derived from g6634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9459.t1 is derived from g6635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41565658	41567407	.	+	.	Phchi.S1G661800
Phchi.S1	AUGUSTUS	transcript	41565658	41567407	.	+	.	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	start_codon	41565658	41565660	.	+	0	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	CDS	41565658	41566347	0.55	+	0	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	exon	41565658	41566347	.	+	.	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	intron	41566348	41566426	.	+	.	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	CDS	41566427	41567407	0.53	+	0	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	exon	41566427	41567407	.	+	.	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
Phchi.S1	AUGUSTUS	stop_codon	41567408	41567410	.	+	0	transcript_id "Phchi.S1G661800.t1"; gene_id "Phchi.S1G661800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3239.t1 is derived from g408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2400169	2400805	.	+	.	Phchi.S1G039800
Phchi.S1	AUGUSTUS	transcript	2400169	2400805	.	+	.	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	start_codon	2400169	2400171	.	+	0	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	CDS	2400169	2400247	0.75	+	0	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	exon	2400169	2400247	.	+	.	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	intron	2400248	2400350	.	+	.	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	CDS	2400351	2400476	0.94	+	2	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	exon	2400351	2400476	.	+	.	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	intron	2400477	2400572	.	+	.	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	CDS	2400573	2400805	0.75	+	2	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	exon	2400573	2400805	.	+	.	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
Phchi.S1	AUGUSTUS	stop_codon	2400806	2400808	.	+	0	transcript_id "Phchi.S1G039800.t1"; gene_id "Phchi.S1G039800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4204.t1 is derived from g1373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8898725	8901295	.	-	.	Phchi.S1G136300
Phchi.S1	AUGUSTUS	transcript	8898725	8901295	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	stop_codon	8898722	8898724	.	-	0	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	CDS	8898725	8898836	1	-	1	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	exon	8898725	8898836	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	intron	8898837	8898962	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	CDS	8898963	8900044	0.99	-	0	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	exon	8898963	8900044	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	intron	8900045	8900117	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	CDS	8900118	8900151	0.91	-	1	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	exon	8900118	8900151	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	intron	8900152	8900287	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	CDS	8900288	8900933	0.93	-	2	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	exon	8900288	8900933	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	intron	8900934	8901021	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	CDS	8901022	8901295	0.86	-	0	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	exon	8901022	8901295	.	-	.	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
Phchi.S1	AUGUSTUS	start_codon	8901293	8901295	.	-	0	transcript_id "Phchi.S1G136300.t1"; gene_id "Phchi.S1G136300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9325.t1 is derived from g6500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40947094	40949056	.	-	.	Phchi.S1G648400
Phchi.S1	AUGUSTUS	transcript	40947094	40949056	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	stop_codon	40947091	40947093	.	-	0	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	CDS	40947094	40947170	0.96	-	2	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	exon	40947094	40947170	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	intron	40947171	40947265	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	CDS	40947266	40947361	0.92	-	2	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	exon	40947266	40947361	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	intron	40947362	40947465	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	CDS	40947466	40948366	0.93	-	0	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	exon	40947466	40948366	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	intron	40948367	40948461	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	CDS	40948462	40948641	1	-	0	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	exon	40948462	40948641	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	intron	40948642	40948729	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	CDS	40948730	40949056	0.86	-	0	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	exon	40948730	40949056	.	-	.	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
Phchi.S1	AUGUSTUS	start_codon	40949054	40949056	.	-	0	transcript_id "Phchi.S1G648400.t1"; gene_id "Phchi.S1G648400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg626.t1 is derived from g10408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4459727	4460857	.	+	.	Phchi.S6G058500
Phchi.S6	AUGUSTUS	transcript	4459727	4460857	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	start_codon	4459727	4459729	.	+	0	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	CDS	4459727	4460069	1	+	0	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	exon	4459727	4460069	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	intron	4460070	4460248	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	CDS	4460249	4460320	1	+	2	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	exon	4460249	4460320	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	intron	4460321	4460397	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	CDS	4460398	4460407	0.98	+	2	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	exon	4460398	4460407	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	intron	4460408	4460484	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	CDS	4460485	4460857	0.98	+	1	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	exon	4460485	4460857	.	+	.	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
Phchi.S6	AUGUSTUS	stop_codon	4460858	4460860	.	+	0	transcript_id "Phchi.S6G058500.t1"; gene_id "Phchi.S6G058500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15716.t1 is derived from g14186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20850640	20850963	.	+	.	Phchi.S3G303500
Phchi.S3	AUGUSTUS	transcript	20850640	20850963	.	+	.	transcript_id "Phchi.S3G303500.t1"; gene_id "Phchi.S3G303500"
Phchi.S3	AUGUSTUS	start_codon	20850640	20850642	.	+	0	transcript_id "Phchi.S3G303500.t1"; gene_id "Phchi.S3G303500"
Phchi.S3	AUGUSTUS	CDS	20850640	20850963	0.68	+	0	transcript_id "Phchi.S3G303500.t1"; gene_id "Phchi.S3G303500"
Phchi.S3	AUGUSTUS	exon	20850640	20850963	.	+	.	transcript_id "Phchi.S3G303500.t1"; gene_id "Phchi.S3G303500"
Phchi.S3	AUGUSTUS	stop_codon	20850964	20850966	.	+	0	transcript_id "Phchi.S3G303500.t1"; gene_id "Phchi.S3G303500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14247.t1 is derived from g12714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11746056	11747696	.	-	.	Phchi.S3G156600
Phchi.S3	AUGUSTUS	transcript	11746056	11747696	.	-	.	transcript_id "Phchi.S3G156600.t1"; gene_id "Phchi.S3G156600"
Phchi.S3	AUGUSTUS	stop_codon	11746053	11746055	.	-	0	transcript_id "Phchi.S3G156600.t1"; gene_id "Phchi.S3G156600"
Phchi.S3	AUGUSTUS	CDS	11746056	11747696	0.96	-	0	transcript_id "Phchi.S3G156600.t1"; gene_id "Phchi.S3G156600"
Phchi.S3	AUGUSTUS	exon	11746056	11747696	.	-	.	transcript_id "Phchi.S3G156600.t1"; gene_id "Phchi.S3G156600"
Phchi.S3	AUGUSTUS	start_codon	11747694	11747696	.	-	0	transcript_id "Phchi.S3G156600.t1"; gene_id "Phchi.S3G156600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4963.t1 is derived from g2133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13780262	13780486	.	-	.	Phchi.S1G212200
Phchi.S1	AUGUSTUS	transcript	13780262	13780486	.	-	.	transcript_id "Phchi.S1G212200.t1"; gene_id "Phchi.S1G212200"
Phchi.S1	AUGUSTUS	stop_codon	13780259	13780261	.	-	0	transcript_id "Phchi.S1G212200.t1"; gene_id "Phchi.S1G212200"
Phchi.S1	AUGUSTUS	CDS	13780262	13780486	0.81	-	0	transcript_id "Phchi.S1G212200.t1"; gene_id "Phchi.S1G212200"
Phchi.S1	AUGUSTUS	exon	13780262	13780486	.	-	.	transcript_id "Phchi.S1G212200.t1"; gene_id "Phchi.S1G212200"
Phchi.S1	AUGUSTUS	start_codon	13780484	13780486	.	-	0	transcript_id "Phchi.S1G212200.t1"; gene_id "Phchi.S1G212200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2514.t1 is derived from g9434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7084945	7086536	.	+	.	Phchi.S5G112300
Phchi.S5	AUGUSTUS	transcript	7084945	7086536	.	+	.	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	start_codon	7084945	7084947	.	+	0	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	CDS	7084945	7085493	0.3	+	0	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	exon	7084945	7085493	.	+	.	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	intron	7085494	7085609	.	+	.	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	CDS	7085610	7086536	0.45	+	0	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	exon	7085610	7086536	.	+	.	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
Phchi.S5	AUGUSTUS	stop_codon	7086537	7086539	.	+	0	transcript_id "Phchi.S5G112300.t1"; gene_id "Phchi.S5G112300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4325.t1 is derived from g1494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9787424	9787895	.	-	.	Phchi.S1G148400
Phchi.S1	AUGUSTUS	transcript	9787424	9787895	.	-	.	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	stop_codon	9787421	9787423	.	-	0	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	CDS	9787424	9787443	0.51	-	2	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	exon	9787424	9787443	.	-	.	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	intron	9787444	9787612	.	-	.	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	CDS	9787613	9787895	0.62	-	0	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	exon	9787613	9787895	.	-	.	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
Phchi.S1	AUGUSTUS	start_codon	9787893	9787895	.	-	0	transcript_id "Phchi.S1G148400.t1"; gene_id "Phchi.S1G148400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9816.t1 is derived from g6992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43921906	43922178	.	+	.	Phchi.S1G697500
Phchi.S1	AUGUSTUS	transcript	43921906	43922178	.	+	.	transcript_id "Phchi.S1G697500.t1"; gene_id "Phchi.S1G697500"
Phchi.S1	AUGUSTUS	start_codon	43921906	43921908	.	+	0	transcript_id "Phchi.S1G697500.t1"; gene_id "Phchi.S1G697500"
Phchi.S1	AUGUSTUS	CDS	43921906	43922178	0.85	+	0	transcript_id "Phchi.S1G697500.t1"; gene_id "Phchi.S1G697500"
Phchi.S1	AUGUSTUS	exon	43921906	43922178	.	+	.	transcript_id "Phchi.S1G697500.t1"; gene_id "Phchi.S1G697500"
Phchi.S1	AUGUSTUS	stop_codon	43922179	43922181	.	+	0	transcript_id "Phchi.S1G697500.t1"; gene_id "Phchi.S1G697500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14401.t1 is derived from g12869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12636793	12637101	.	+	.	Phchi.S3G172000
Phchi.S3	AUGUSTUS	transcript	12636793	12637101	.	+	.	transcript_id "Phchi.S3G172000.t1"; gene_id "Phchi.S3G172000"
Phchi.S3	AUGUSTUS	start_codon	12636793	12636795	.	+	0	transcript_id "Phchi.S3G172000.t1"; gene_id "Phchi.S3G172000"
Phchi.S3	AUGUSTUS	CDS	12636793	12637101	0.63	+	0	transcript_id "Phchi.S3G172000.t1"; gene_id "Phchi.S3G172000"
Phchi.S3	AUGUSTUS	exon	12636793	12637101	.	+	.	transcript_id "Phchi.S3G172000.t1"; gene_id "Phchi.S3G172000"
Phchi.S3	AUGUSTUS	stop_codon	12637102	12637104	.	+	0	transcript_id "Phchi.S3G172000.t1"; gene_id "Phchi.S3G172000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg13194.t1 is derived from g11659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4630007	4634446	.	-	.	Phchi.S3G051300
Phchi.S3	AUGUSTUS	transcript	4630007	4634446	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	stop_codon	4630004	4630006	.	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630007	4630196	1	-	1	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630007	4630196	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630197	4630336	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630337	4630470	1	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630337	4630470	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630471	4630629	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630630	4630833	1	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630630	4630833	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630834	4630923	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630924	4631262	1	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630924	4631262	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4631263	4631347	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4631348	4631813	1	-	1	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4631348	4631813	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4631814	4631953	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4631954	4632122	1	-	2	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4631954	4632122	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632123	4632260	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632261	4632418	1	-	1	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632261	4632418	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632419	4632694	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632695	4632772	1	-	1	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632695	4632772	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632773	4632904	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632905	4632977	1	-	2	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632905	4632977	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632978	4633104	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633105	4633165	1	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633105	4633165	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633166	4633254	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633255	4633472	1	-	2	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633255	4633472	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633473	4633708	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633709	4633880	1	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633709	4633880	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633881	4633984	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633985	4634446	0.99	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633985	4634446	.	-	.	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	start_codon	4634444	4634446	.	-	0	transcript_id "Phchi.S3G051300.t1"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	transcript	4630007	4634446	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	stop_codon	4630004	4630006	.	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630007	4630196	0.99	-	1	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630007	4630196	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630197	4630336	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630337	4630470	1	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630337	4630470	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630471	4630629	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630630	4630833	1	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630630	4630833	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630834	4630923	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630924	4631262	1	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630924	4631262	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4631263	4631347	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4631348	4631813	1	-	1	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4631348	4631813	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4631814	4631953	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4631954	4632122	1	-	2	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4631954	4632122	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632123	4632260	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632261	4632418	1	-	1	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632261	4632418	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632419	4632694	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632695	4632772	1	-	1	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632695	4632772	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632773	4632904	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632905	4632977	1	-	2	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632905	4632977	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632978	4633104	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633105	4633165	1	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633105	4633165	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633166	4633254	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633255	4633354	0.85	-	1	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633255	4633354	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633355	4633528	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633529	4633541	0.85	-	2	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633529	4633541	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633542	4633708	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633709	4633880	1	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633709	4633880	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633881	4633984	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633985	4634446	1	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633985	4634446	.	-	.	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	start_codon	4634444	4634446	.	-	0	transcript_id "Phchi.S3G051300.t2"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	transcript	4630007	4634446	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	stop_codon	4630004	4630006	.	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630007	4630196	1	-	1	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630007	4630196	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630197	4630336	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630337	4630470	1	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630337	4630470	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630471	4630629	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630630	4630833	1	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630630	4630833	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4630834	4630923	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4630924	4631262	1	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4630924	4631262	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4631263	4631347	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4631348	4631813	1	-	1	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4631348	4631813	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4631814	4631953	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4631954	4632122	1	-	2	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4631954	4632122	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632123	4632260	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632261	4632418	1	-	1	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632261	4632418	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632419	4632694	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632695	4632772	1	-	1	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632695	4632772	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632773	4632904	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4632905	4632977	1	-	2	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4632905	4632977	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4632978	4633254	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633255	4633331	0.56	-	1	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633255	4633331	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633332	4633528	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633529	4633541	0.67	-	2	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633529	4633541	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633542	4633708	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633709	4633880	1	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633709	4633880	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	intron	4633881	4633984	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	CDS	4633985	4634446	0.99	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	exon	4633985	4634446	.	-	.	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
Phchi.S3	AUGUSTUS	start_codon	4634444	4634446	.	-	0	transcript_id "Phchi.S3G051300.t3"; gene_id "Phchi.S3G051300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4762.t1 is derived from g1932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12694445	12695046	.	-	.	Phchi.S1G192100
Phchi.S1	AUGUSTUS	transcript	12694445	12695046	.	-	.	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	stop_codon	12694442	12694444	.	-	0	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	CDS	12694445	12694746	0.87	-	2	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	exon	12694445	12694746	.	-	.	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	intron	12694747	12694846	.	-	.	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	CDS	12694847	12694885	0.45	-	2	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	exon	12694847	12694885	.	-	.	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	intron	12694886	12694982	.	-	.	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	CDS	12694983	12695046	0.69	-	0	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	exon	12694983	12695046	.	-	.	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
Phchi.S1	AUGUSTUS	start_codon	12695044	12695046	.	-	0	transcript_id "Phchi.S1G192100.t1"; gene_id "Phchi.S1G192100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12695.t1 is derived from g11160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	598840	599721	.	-	.	Phchi.S3G001400
Phchi.S3	AUGUSTUS	transcript	598840	599721	.	-	.	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	stop_codon	598837	598839	.	-	0	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	CDS	598840	598870	0.73	-	1	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	exon	598840	598870	.	-	.	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	intron	598871	599245	.	-	.	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	CDS	599246	599302	0.54	-	1	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	exon	599246	599302	.	-	.	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	intron	599303	599536	.	-	.	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	CDS	599537	599721	0.86	-	0	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	exon	599537	599721	.	-	.	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
Phchi.S3	AUGUSTUS	start_codon	599719	599721	.	-	0	transcript_id "Phchi.S3G001400.t1"; gene_id "Phchi.S3G001400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4916.t1 is derived from g2086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13463961	13465171	.	-	.	Phchi.S1G207500
Phchi.S1	AUGUSTUS	transcript	13463961	13465171	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	stop_codon	13463958	13463960	.	-	0	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	CDS	13463961	13464230	0.98	-	0	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	exon	13463961	13464230	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	intron	13464231	13464328	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	CDS	13464329	13464443	1	-	1	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	exon	13464329	13464443	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	intron	13464444	13464536	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	CDS	13464537	13464595	1	-	0	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	exon	13464537	13464595	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	intron	13464596	13464684	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	CDS	13464685	13464753	1	-	0	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	exon	13464685	13464753	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	intron	13464754	13464834	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	CDS	13464835	13464949	1	-	1	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	exon	13464835	13464949	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	intron	13464950	13465028	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	CDS	13465029	13465171	0.63	-	0	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	exon	13465029	13465171	.	-	.	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
Phchi.S1	AUGUSTUS	start_codon	13465169	13465171	.	-	0	transcript_id "Phchi.S1G207500.t1"; gene_id "Phchi.S1G207500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15443.t1 is derived from g13911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19180538	19183757	.	+	.	Phchi.S3G276200
Phchi.S3	AUGUSTUS	transcript	19180538	19183757	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	start_codon	19180538	19180540	.	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19180538	19180750	0.96	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19180538	19180750	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19180751	19180834	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19180835	19180897	0.99	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19180835	19180897	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19180898	19181024	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19181025	19181113	1	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19181025	19181113	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19181114	19181196	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19181197	19181248	1	+	1	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19181197	19181248	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19181249	19181345	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19181346	19181392	1	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19181346	19181392	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19181393	19181484	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19181485	19181548	1	+	1	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19181485	19181548	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19181549	19181680	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19181681	19181749	1	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19181681	19181749	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19181750	19181830	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19181831	19181953	1	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19181831	19181953	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19181954	19182039	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19182040	19182126	1	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19182040	19182126	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19182127	19182211	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19182212	19182332	1	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19182212	19182332	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19182333	19182416	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19182417	19182554	1	+	2	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19182417	19182554	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19182555	19182688	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19182689	19182778	1	+	2	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19182689	19182778	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19182779	19182858	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19182859	19183634	1	+	2	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19182859	19183634	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	intron	19183635	19183721	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	CDS	19183722	19183757	0.67	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	exon	19183722	19183757	.	+	.	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
Phchi.S3	AUGUSTUS	stop_codon	19183758	19183760	.	+	0	transcript_id "Phchi.S3G276200.t1"; gene_id "Phchi.S3G276200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10371.t1 is derived from g7547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47411627	47412799	.	-	.	Phchi.S1G753000
Phchi.S1	AUGUSTUS	transcript	47411627	47412799	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	stop_codon	47411624	47411626	.	-	0	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	CDS	47411627	47411627	0.89	-	1	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	exon	47411627	47411627	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	intron	47411628	47411765	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	CDS	47411766	47411800	0.88	-	0	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	exon	47411766	47411800	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	intron	47411801	47411921	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	CDS	47411922	47411940	0.83	-	1	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	exon	47411922	47411940	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	intron	47411941	47412150	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	CDS	47412151	47412316	1	-	2	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	exon	47412151	47412316	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	intron	47412317	47412397	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	CDS	47412398	47412523	0.95	-	2	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	exon	47412398	47412523	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	intron	47412524	47412756	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	CDS	47412757	47412799	0.95	-	0	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	exon	47412757	47412799	.	-	.	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
Phchi.S1	AUGUSTUS	start_codon	47412797	47412799	.	-	0	transcript_id "Phchi.S1G753000.t1"; gene_id "Phchi.S1G753000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg392.t1 is derived from g10174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2861234	2861894	.	-	.	Phchi.S6G035100
Phchi.S6	AUGUSTUS	transcript	2861234	2861894	.	-	.	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	stop_codon	2861231	2861233	.	-	0	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	CDS	2861234	2861251	0.81	-	0	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	exon	2861234	2861251	.	-	.	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	intron	2861252	2861321	.	-	.	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	CDS	2861322	2861894	0.89	-	0	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	exon	2861322	2861894	.	-	.	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
Phchi.S6	AUGUSTUS	start_codon	2861892	2861894	.	-	0	transcript_id "Phchi.S6G035100.t1"; gene_id "Phchi.S6G035100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7394.t1 is derived from g4566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28923987	28925404	.	-	.	Phchi.S1G455300
Phchi.S1	AUGUSTUS	transcript	28923987	28925404	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	stop_codon	28923984	28923986	.	-	0	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	CDS	28923987	28924262	0.97	-	0	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	exon	28923987	28924262	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	intron	28924263	28924356	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	CDS	28924357	28924486	1	-	1	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	exon	28924357	28924486	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	intron	28924487	28924574	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	CDS	28924575	28924678	1	-	0	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	exon	28924575	28924678	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	intron	28924679	28924761	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	CDS	28924762	28924919	0.76	-	2	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	exon	28924762	28924919	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	intron	28924920	28925071	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	CDS	28925072	28925263	0.69	-	2	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	exon	28925072	28925263	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	intron	28925264	28925352	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	CDS	28925353	28925404	0.48	-	0	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	exon	28925353	28925404	.	-	.	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
Phchi.S1	AUGUSTUS	start_codon	28925402	28925404	.	-	0	transcript_id "Phchi.S1G455300.t1"; gene_id "Phchi.S1G455300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5449.t1 is derived from g2619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16910205	16911783	.	+	.	Phchi.S1G260800
Phchi.S1	AUGUSTUS	transcript	16910205	16911783	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	start_codon	16910205	16910207	.	+	0	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16910205	16910428	0.84	+	0	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16910205	16910428	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16910429	16910559	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16910560	16910619	0.96	+	1	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16910560	16910619	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16910620	16910728	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16910729	16910798	0.95	+	1	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16910729	16910798	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16910799	16910908	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16910909	16910964	0.89	+	0	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16910909	16910964	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16910965	16911062	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16911063	16911138	1	+	1	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16911063	16911138	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16911139	16911237	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16911238	16911274	1	+	0	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16911238	16911274	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16911275	16911393	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16911394	16911508	1	+	2	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16911394	16911508	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	intron	16911509	16911629	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	CDS	16911630	16911783	0.99	+	1	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	exon	16911630	16911783	.	+	.	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
Phchi.S1	AUGUSTUS	stop_codon	16911784	16911786	.	+	0	transcript_id "Phchi.S1G260800.t1"; gene_id "Phchi.S1G260800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4973.t1 is derived from g2143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13830111	13832478	.	+	.	Phchi.S1G213200
Phchi.S1	AUGUSTUS	transcript	13830111	13832478	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	start_codon	13830111	13830113	.	+	0	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830111	13830331	0.6	+	0	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830111	13830331	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13830332	13830417	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830418	13830552	1	+	1	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830418	13830552	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13830553	13830648	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830649	13830903	1	+	1	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830649	13830903	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13830904	13830990	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830991	13831072	0.99	+	1	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830991	13831072	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831073	13831181	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831182	13831297	1	+	0	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831182	13831297	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831298	13831417	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831418	13831472	0.99	+	1	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831418	13831472	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831473	13831758	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831759	13831870	1	+	0	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831759	13831870	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831871	13831961	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831962	13832131	1	+	2	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831962	13832131	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13832132	13832214	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13832215	13832478	1	+	0	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13832215	13832478	.	+	.	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	stop_codon	13832479	13832481	.	+	0	transcript_id "Phchi.S1G213200.t1"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	transcript	13830111	13832478	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	start_codon	13830111	13830113	.	+	0	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830111	13830331	0.41	+	0	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830111	13830331	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13830332	13830417	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830418	13830552	1	+	1	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830418	13830552	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13830553	13830648	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830649	13830903	1	+	1	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830649	13830903	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13830904	13830990	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13830991	13831072	1	+	1	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13830991	13831072	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831073	13831181	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831182	13831297	0.98	+	0	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831182	13831297	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831298	13831521	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831522	13831549	0.73	+	1	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831522	13831549	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831550	13831758	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831759	13831870	0.93	+	0	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831759	13831870	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13831871	13831961	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13831962	13832131	1	+	2	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13831962	13832131	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	intron	13832132	13832214	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	CDS	13832215	13832478	1	+	0	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	exon	13832215	13832478	.	+	.	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
Phchi.S1	AUGUSTUS	stop_codon	13832479	13832481	.	+	0	transcript_id "Phchi.S1G213200.t2"; gene_id "Phchi.S1G213200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15323.t1 is derived from g13791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18385918	18387866	.	-	.	Phchi.S3G264200
Phchi.S3	AUGUSTUS	transcript	18385918	18387866	.	-	.	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	stop_codon	18385915	18385917	.	-	0	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	CDS	18385918	18386712	0.93	-	0	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	exon	18385918	18386712	.	-	.	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	intron	18386713	18386816	.	-	.	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	CDS	18386817	18387866	0.62	-	0	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	exon	18386817	18387866	.	-	.	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
Phchi.S3	AUGUSTUS	start_codon	18387864	18387866	.	-	0	transcript_id "Phchi.S3G264200.t1"; gene_id "Phchi.S3G264200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9614.t1 is derived from g6790.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42935609	42937017	.	-	.	Phchi.S1G677300
Phchi.S1	AUGUSTUS	transcript	42935609	42937017	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	stop_codon	42935606	42935608	.	-	0	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42935609	42935835	1	-	2	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42935609	42935835	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42935836	42935910	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42935911	42935980	1	-	0	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42935911	42935980	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42935981	42936063	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42936064	42936181	0.9	-	1	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42936064	42936181	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42936182	42936416	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42936417	42936521	0.91	-	1	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42936417	42936521	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42936522	42936688	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42936689	42937017	1	-	0	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42936689	42937017	.	-	.	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	start_codon	42937015	42937017	.	-	0	transcript_id "Phchi.S1G677300.t1"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	transcript	42935609	42937017	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	stop_codon	42935606	42935608	.	-	0	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42935609	42935817	0.99	-	2	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42935609	42935817	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42935818	42935910	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42935911	42935980	1	-	0	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42935911	42935980	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42935981	42936063	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42936064	42936181	0.83	-	1	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42936064	42936181	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42936182	42936416	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42936417	42936521	0.84	-	1	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42936417	42936521	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	intron	42936522	42936688	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	CDS	42936689	42937017	1	-	0	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	exon	42936689	42937017	.	-	.	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
Phchi.S1	AUGUSTUS	start_codon	42937015	42937017	.	-	0	transcript_id "Phchi.S1G677300.t2"; gene_id "Phchi.S1G677300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14761.t1 is derived from g13229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14580502	14582206	.	+	.	Phchi.S3G208000
Phchi.S3	AUGUSTUS	transcript	14580502	14582206	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	start_codon	14580502	14580504	.	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14580502	14580662	1	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14580502	14580662	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	intron	14580663	14580745	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14580746	14580851	1	+	1	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14580746	14580851	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	intron	14580852	14580934	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14580935	14581180	1	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14580935	14581180	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	intron	14581181	14581308	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14581309	14581419	1	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14581309	14581419	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	intron	14581420	14581505	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14581506	14581664	1	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14581506	14581664	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	intron	14581665	14581782	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14581783	14581926	0.98	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14581783	14581926	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	intron	14581927	14582020	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	CDS	14582021	14582206	0.99	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	exon	14582021	14582206	.	+	.	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
Phchi.S3	AUGUSTUS	stop_codon	14582207	14582209	.	+	0	transcript_id "Phchi.S3G208000.t1"; gene_id "Phchi.S3G208000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12967.t1 is derived from g11432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3364043	3366326	.	+	.	Phchi.S3G028600
Phchi.S3	AUGUSTUS	transcript	3364043	3366326	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	start_codon	3364043	3364045	.	+	0	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3364043	3364182	1	+	0	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3364043	3364182	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3364183	3364300	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3364301	3364425	1	+	1	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3364301	3364425	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3364426	3364525	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3364526	3364620	1	+	2	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3364526	3364620	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3364621	3364714	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3364715	3364920	1	+	0	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3364715	3364920	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3364921	3365067	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3365068	3365256	1	+	1	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3365068	3365256	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3365257	3365368	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3365369	3365575	1	+	1	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3365369	3365575	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3365576	3365660	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3365661	3365814	1	+	1	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3365661	3365814	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3365815	3365901	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3365902	3365965	1	+	0	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3365902	3365965	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3365966	3366042	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3366043	3366126	1	+	2	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3366043	3366126	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	intron	3366127	3366252	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	CDS	3366253	3366326	1	+	2	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	exon	3366253	3366326	.	+	.	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
Phchi.S3	AUGUSTUS	stop_codon	3366327	3366329	.	+	0	transcript_id "Phchi.S3G028600.t1"; gene_id "Phchi.S3G028600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10961.t1 is derived from g15011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3310297	3311646	.	-	.	Phchi.S4G054300
Phchi.S4	AUGUSTUS	transcript	3310297	3311646	.	-	.	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	stop_codon	3310294	3310296	.	-	0	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	CDS	3310297	3311093	0.99	-	2	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	exon	3310297	3311093	.	-	.	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	intron	3311094	3311570	.	-	.	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	CDS	3311571	3311646	0.94	-	0	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	exon	3311571	3311646	.	-	.	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
Phchi.S4	AUGUSTUS	start_codon	3311644	3311646	.	-	0	transcript_id "Phchi.S4G054300.t1"; gene_id "Phchi.S4G054300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9132.t1 is derived from g6307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40022211	40024202	.	-	.	Phchi.S1G629100
Phchi.S1	AUGUSTUS	transcript	40022211	40024202	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	stop_codon	40022208	40022210	.	-	0	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40022211	40022222	1	-	0	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40022211	40022222	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40022223	40022740	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40022741	40022823	1	-	2	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40022741	40022823	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40022824	40023051	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023052	40023117	1	-	2	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023052	40023117	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023118	40023200	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023201	40023250	1	-	1	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023201	40023250	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023251	40023363	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023364	40023448	1	-	2	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023364	40023448	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023449	40023558	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023559	40023661	1	-	0	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023559	40023661	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023662	40023795	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023796	40023876	1	-	0	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023796	40023876	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023877	40024184	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40024185	40024202	1	-	0	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40024185	40024202	.	-	.	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	start_codon	40024200	40024202	.	-	0	transcript_id "Phchi.S1G629100.t1"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	transcript	40022211	40024202	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	stop_codon	40022208	40022210	.	-	0	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40022211	40022222	1	-	0	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40022211	40022222	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40022223	40022740	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40022741	40022805	1	-	2	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40022741	40022805	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40022806	40023051	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023052	40023117	1	-	2	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023052	40023117	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023118	40023200	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023201	40023250	1	-	1	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023201	40023250	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023251	40023363	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023364	40023448	1	-	2	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023364	40023448	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023449	40023558	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023559	40023661	1	-	0	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023559	40023661	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023662	40023795	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40023796	40023876	1	-	0	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40023796	40023876	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	intron	40023877	40024184	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	CDS	40024185	40024202	1	-	0	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	exon	40024185	40024202	.	-	.	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
Phchi.S1	AUGUSTUS	start_codon	40024200	40024202	.	-	0	transcript_id "Phchi.S1G629100.t2"; gene_id "Phchi.S1G629100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9175.t1 is derived from g6350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40225153	40227229	.	+	.	Phchi.S1G633400
Phchi.S1	AUGUSTUS	transcript	40225153	40227229	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	start_codon	40225153	40225155	.	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40225153	40225177	0.73	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40225153	40225177	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40225178	40225321	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40225322	40225356	1	+	2	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40225322	40225356	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40225357	40225460	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40225461	40225559	1	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40225461	40225559	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40225560	40225702	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40225703	40225836	1	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40225703	40225836	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40225837	40225930	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40225931	40226131	0.93	+	1	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40225931	40226131	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40226132	40226252	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40226253	40226394	0.93	+	1	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40226253	40226394	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40226395	40226483	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40226484	40226568	1	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40226484	40226568	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40226569	40226662	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40226663	40226780	1	+	2	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40226663	40226780	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40226781	40226859	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40226860	40226938	1	+	1	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40226860	40226938	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40226939	40227013	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40227014	40227088	1	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40227014	40227088	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	intron	40227089	40227166	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	CDS	40227167	40227229	1	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	exon	40227167	40227229	.	+	.	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
Phchi.S1	AUGUSTUS	stop_codon	40227230	40227232	.	+	0	transcript_id "Phchi.S1G633400.t1"; gene_id "Phchi.S1G633400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15231.t1 is derived from g13699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17845598	17847001	.	+	.	Phchi.S3G255000
Phchi.S3	AUGUSTUS	transcript	17845598	17847001	.	+	.	transcript_id "Phchi.S3G255000.t1"; gene_id "Phchi.S3G255000"
Phchi.S3	AUGUSTUS	start_codon	17845598	17845600	.	+	0	transcript_id "Phchi.S3G255000.t1"; gene_id "Phchi.S3G255000"
Phchi.S3	AUGUSTUS	CDS	17845598	17847001	0.46	+	0	transcript_id "Phchi.S3G255000.t1"; gene_id "Phchi.S3G255000"
Phchi.S3	AUGUSTUS	exon	17845598	17847001	.	+	.	transcript_id "Phchi.S3G255000.t1"; gene_id "Phchi.S3G255000"
Phchi.S3	AUGUSTUS	stop_codon	17847002	17847004	.	+	0	transcript_id "Phchi.S3G255000.t1"; gene_id "Phchi.S3G255000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg569.t1 is derived from g10351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4101763	4102230	.	-	.	Phchi.S6G052800
Phchi.S6	AUGUSTUS	transcript	4101763	4102230	.	-	.	transcript_id "Phchi.S6G052800.t1"; gene_id "Phchi.S6G052800"
Phchi.S6	AUGUSTUS	stop_codon	4101760	4101762	.	-	0	transcript_id "Phchi.S6G052800.t1"; gene_id "Phchi.S6G052800"
Phchi.S6	AUGUSTUS	CDS	4101763	4102230	0.89	-	0	transcript_id "Phchi.S6G052800.t1"; gene_id "Phchi.S6G052800"
Phchi.S6	AUGUSTUS	exon	4101763	4102230	.	-	.	transcript_id "Phchi.S6G052800.t1"; gene_id "Phchi.S6G052800"
Phchi.S6	AUGUSTUS	start_codon	4102228	4102230	.	-	0	transcript_id "Phchi.S6G052800.t1"; gene_id "Phchi.S6G052800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg369.t1 is derived from g10151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2683721	2684551	.	+	.	Phchi.S6G032800
Phchi.S6	AUGUSTUS	transcript	2683721	2684551	.	+	.	transcript_id "Phchi.S6G032800.t1"; gene_id "Phchi.S6G032800"
Phchi.S6	AUGUSTUS	start_codon	2683721	2683723	.	+	0	transcript_id "Phchi.S6G032800.t1"; gene_id "Phchi.S6G032800"
Phchi.S6	AUGUSTUS	CDS	2683721	2684551	0.69	+	0	transcript_id "Phchi.S6G032800.t1"; gene_id "Phchi.S6G032800"
Phchi.S6	AUGUSTUS	exon	2683721	2684551	.	+	.	transcript_id "Phchi.S6G032800.t1"; gene_id "Phchi.S6G032800"
Phchi.S6	AUGUSTUS	stop_codon	2684552	2684554	.	+	0	transcript_id "Phchi.S6G032800.t1"; gene_id "Phchi.S6G032800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7119.t1 is derived from g4291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27061994	27063458	.	+	.	Phchi.S1G427800
Phchi.S1	AUGUSTUS	transcript	27061994	27063458	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	start_codon	27061994	27061996	.	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27061994	27062062	1	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27061994	27062062	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	intron	27062063	27062141	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27062142	27062252	0.97	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27062142	27062252	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	intron	27062253	27062360	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27062361	27062636	0.98	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27062361	27062636	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	intron	27062637	27062715	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27062716	27062855	1	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27062716	27062855	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	intron	27062856	27062938	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27062939	27063062	1	+	1	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27062939	27063062	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	intron	27063063	27063143	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27063144	27063284	1	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27063144	27063284	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	intron	27063285	27063368	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	CDS	27063369	27063458	1	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	exon	27063369	27063458	.	+	.	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
Phchi.S1	AUGUSTUS	stop_codon	27063459	27063461	.	+	0	transcript_id "Phchi.S1G427800.t1"; gene_id "Phchi.S1G427800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12268.t1 is derived from g7944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7395343	7397003	.	-	.	Phchi.S2G034800
Phchi.S2	AUGUSTUS	transcript	7395343	7397003	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	stop_codon	7395340	7395342	.	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7395343	7395392	1	-	2	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7395343	7395392	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7395393	7395465	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7395466	7395511	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7395466	7395511	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7395512	7395582	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7395583	7395663	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7395583	7395663	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7395664	7395762	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7395763	7395816	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7395763	7395816	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7395817	7395914	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7395915	7395998	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7395915	7395998	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7395999	7396131	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7396132	7396218	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7396132	7396218	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7396219	7396452	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7396453	7396555	1	-	1	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7396453	7396555	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7396556	7396639	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7396640	7396686	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7396640	7396686	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	intron	7396687	7396766	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	CDS	7396767	7397003	1	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	exon	7396767	7397003	.	-	.	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
Phchi.S2	AUGUSTUS	start_codon	7397001	7397003	.	-	0	transcript_id "Phchi.S2G034800.t1"; gene_id "Phchi.S2G034800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15865.t1 is derived from g14335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21933250	21934537	.	-	.	Phchi.S3G318400
Phchi.S3	AUGUSTUS	transcript	21933250	21934537	.	-	.	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	stop_codon	21933247	21933249	.	-	0	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	CDS	21933250	21933313	0.54	-	1	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	exon	21933250	21933313	.	-	.	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	intron	21933314	21933573	.	-	.	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	CDS	21933574	21933698	0.59	-	0	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	exon	21933574	21933698	.	-	.	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	intron	21933699	21933856	.	-	.	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	CDS	21933857	21934537	0.97	-	0	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	exon	21933857	21934537	.	-	.	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
Phchi.S3	AUGUSTUS	start_codon	21934535	21934537	.	-	0	transcript_id "Phchi.S3G318400.t1"; gene_id "Phchi.S3G318400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10937.t1 is derived from g14987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3180006	3183753	.	-	.	Phchi.S4G051900
Phchi.S4	AUGUSTUS	transcript	3180006	3183753	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	stop_codon	3180003	3180005	.	-	0	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3180006	3180946	1	-	2	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3180006	3180946	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3180947	3181044	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3181045	3181177	1	-	0	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3181045	3181177	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3181178	3181308	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3181309	3181498	1	-	1	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3181309	3181498	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3181499	3181608	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3181609	3181743	1	-	1	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3181609	3181743	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3181744	3181912	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3181913	3182010	1	-	0	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3181913	3182010	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3182011	3182228	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3182229	3182398	1	-	2	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3182229	3182398	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3182399	3182685	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3182686	3183137	1	-	1	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3182686	3183137	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3183138	3183413	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3183414	3183440	0.82	-	1	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3183414	3183440	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3183441	3183508	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3183509	3183553	0.83	-	1	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3183509	3183553	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	intron	3183554	3183724	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	CDS	3183725	3183753	0.83	-	0	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	exon	3183725	3183753	.	-	.	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
Phchi.S4	AUGUSTUS	start_codon	3183751	3183753	.	-	0	transcript_id "Phchi.S4G051900.t1"; gene_id "Phchi.S4G051900"
# This transcript jg2055.t2 is derived from g8975.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2056.t1 is derived from g8976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4632425	4633680	.	+	.	Phchi.S5G066500
Phchi.S5	AUGUSTUS	transcript	4632425	4633680	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	start_codon	4632425	4632427	.	+	0	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	CDS	4632425	4632636	0.67	+	0	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	exon	4632425	4632636	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	intron	4632637	4632726	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	CDS	4632727	4632859	1	+	1	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	exon	4632727	4632859	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	intron	4632860	4632963	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	CDS	4632964	4633076	1	+	0	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	exon	4632964	4633076	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	intron	4633077	4633174	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	CDS	4633175	4633279	1	+	1	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	exon	4633175	4633279	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	intron	4633280	4633360	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	CDS	4633361	4633449	1	+	1	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	exon	4633361	4633449	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	intron	4633450	4633540	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	CDS	4633541	4633680	1	+	2	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	exon	4633541	4633680	.	+	.	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
Phchi.S5	AUGUSTUS	stop_codon	4633681	4633683	.	+	0	transcript_id "Phchi.S5G066500.t1"; gene_id "Phchi.S5G066500"
# This transcript jg13793.t2 is derived from g12260.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13794.t1 is derived from g12261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8917153	8920011	.	-	.	Phchi.S3G111300
Phchi.S3	AUGUSTUS	transcript	8917153	8920011	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	stop_codon	8917150	8917152	.	-	0	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8917153	8917162	1	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8917153	8917162	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8917163	8917262	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8917263	8917412	1	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8917263	8917412	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8917413	8917541	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8917542	8917693	1	-	0	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8917542	8917693	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8917694	8917799	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8917800	8917958	1	-	0	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8917800	8917958	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8917959	8918043	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8918044	8918323	0.99	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8918044	8918323	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8918324	8918446	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8918447	8918563	1	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8918447	8918563	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8918564	8918656	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8918657	8918719	1	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8918657	8918719	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8918720	8918835	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8918836	8919057	0.76	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8918836	8919057	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8919058	8919173	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8919174	8919251	0.6	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8919174	8919251	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8919252	8919357	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8919358	8919546	0.29	-	1	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8919358	8919546	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	intron	8919547	8919715	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	CDS	8919716	8920011	0.37	-	0	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	exon	8919716	8920011	.	-	.	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
Phchi.S3	AUGUSTUS	start_codon	8920009	8920011	.	-	0	transcript_id "Phchi.S3G111300.t1"; gene_id "Phchi.S3G111300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13037.t1 is derived from g11502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3828576	3830389	.	-	.	Phchi.S3G035600
Phchi.S3	AUGUSTUS	transcript	3828576	3830389	.	-	.	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	stop_codon	3828573	3828575	.	-	0	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	CDS	3828576	3829579	1	-	2	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	exon	3828576	3829579	.	-	.	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	intron	3829580	3829727	.	-	.	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	CDS	3829728	3829859	1	-	2	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	exon	3829728	3829859	.	-	.	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	intron	3829860	3829941	.	-	.	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	CDS	3829942	3830389	0.64	-	0	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	exon	3829942	3830389	.	-	.	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
Phchi.S3	AUGUSTUS	start_codon	3830387	3830389	.	-	0	transcript_id "Phchi.S3G035600.t1"; gene_id "Phchi.S3G035600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10618.t1 is derived from g14668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1260224	1265325	.	+	.	Phchi.S4G020000
Phchi.S4	AUGUSTUS	transcript	1260224	1265325	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	start_codon	1260224	1260226	.	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1260224	1260226	0.36	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1260224	1260226	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1260227	1260342	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1260343	1260613	0.62	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1260343	1260613	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1260614	1260712	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1260713	1260912	1	+	2	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1260713	1260912	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1260913	1260987	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1260988	1261197	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1260988	1261197	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1261198	1261287	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1261288	1261401	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1261288	1261401	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1261402	1261490	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1261491	1261601	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1261491	1261601	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1261602	1261675	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1261676	1261840	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1261676	1261840	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1261841	1261933	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1261934	1262119	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1261934	1262119	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1262120	1262201	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1262202	1262276	0.48	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1262202	1262276	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1262277	1262462	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1262463	1262596	0.9	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1262463	1262596	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1262597	1262685	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1262686	1262854	1	+	1	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1262686	1262854	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1262855	1262945	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1262946	1263134	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1262946	1263134	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1263135	1263216	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1263217	1263403	1	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1263217	1263403	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1263404	1263479	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1263480	1263529	1	+	2	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1263480	1263529	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1263530	1263606	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1263607	1263946	0.58	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1263607	1263946	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1263947	1264092	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1264093	1264290	0.31	+	2	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1264093	1264290	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1264291	1264377	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1264378	1264518	1	+	2	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1264378	1264518	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	intron	1264519	1264600	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	CDS	1264601	1265325	1	+	2	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	exon	1264601	1265325	.	+	.	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
Phchi.S4	AUGUSTUS	stop_codon	1265326	1265328	.	+	0	transcript_id "Phchi.S4G020000.t1"; gene_id "Phchi.S4G020000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2558.t1 is derived from g9478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7355031	7355294	.	+	.	Phchi.S5G116700
Phchi.S5	AUGUSTUS	transcript	7355031	7355294	.	+	.	transcript_id "Phchi.S5G116700.t1"; gene_id "Phchi.S5G116700"
Phchi.S5	AUGUSTUS	start_codon	7355031	7355033	.	+	0	transcript_id "Phchi.S5G116700.t1"; gene_id "Phchi.S5G116700"
Phchi.S5	AUGUSTUS	CDS	7355031	7355294	0.37	+	0	transcript_id "Phchi.S5G116700.t1"; gene_id "Phchi.S5G116700"
Phchi.S5	AUGUSTUS	exon	7355031	7355294	.	+	.	transcript_id "Phchi.S5G116700.t1"; gene_id "Phchi.S5G116700"
Phchi.S5	AUGUSTUS	stop_codon	7355295	7355297	.	+	0	transcript_id "Phchi.S5G116700.t1"; gene_id "Phchi.S5G116700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11715.t1 is derived from g15766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7804365	7810094	.	-	.	Phchi.S4G129700
Phchi.S4	AUGUSTUS	transcript	7804365	7810094	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	stop_codon	7804362	7804364	.	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7804365	7804589	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7804365	7804589	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7804590	7804662	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7804663	7804902	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7804663	7804902	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7804903	7805148	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7805149	7805220	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7805149	7805220	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7805221	7805319	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7805320	7805586	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7805320	7805586	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7805587	7805686	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7805687	7805911	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7805687	7805911	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7805912	7806007	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7806008	7806115	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7806008	7806115	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7806116	7806235	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7806236	7806337	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7806236	7806337	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7806338	7806421	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7806422	7806517	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7806422	7806517	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7806518	7806599	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7806600	7806758	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7806600	7806758	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7806759	7806858	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7806859	7806939	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7806859	7806939	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7806940	7807062	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7807063	7807326	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7807063	7807326	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7807327	7807439	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7807440	7807532	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7807440	7807532	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7807533	7807622	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7807623	7807691	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7807623	7807691	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7807692	7807784	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7807785	7807877	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7807785	7807877	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7807878	7807960	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7807961	7808061	1	-	2	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7807961	7808061	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7808062	7808206	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7808207	7808291	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7808207	7808291	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7808292	7808388	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7808389	7808603	1	-	2	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7808389	7808603	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7808604	7808714	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7808715	7808778	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7808715	7808778	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7808779	7808880	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7808881	7808997	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7808881	7808997	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7808998	7809085	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7809086	7809139	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7809086	7809139	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7809140	7809217	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7809218	7809318	1	-	2	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7809218	7809318	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7809319	7809456	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7809457	7809651	1	-	2	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7809457	7809651	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7809652	7809777	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7809778	7809844	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7809778	7809844	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	intron	7809845	7809953	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	CDS	7809954	7810094	1	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	exon	7809954	7810094	.	-	.	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
Phchi.S4	AUGUSTUS	start_codon	7810092	7810094	.	-	0	transcript_id "Phchi.S4G129700.t1"; gene_id "Phchi.S4G129700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8010.t1 is derived from g5185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32467165	32470272	.	-	.	Phchi.S1G516900
Phchi.S1	AUGUSTUS	transcript	32467165	32470272	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	stop_codon	32467162	32467164	.	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32467165	32467259	1	-	2	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32467165	32467259	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32467260	32467355	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32467356	32467434	1	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32467356	32467434	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32467435	32467596	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32467597	32467738	1	-	1	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32467597	32467738	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32467739	32467952	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32467953	32468026	1	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32467953	32468026	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32468027	32468127	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32468128	32468226	0.98	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32468128	32468226	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32468227	32468303	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32468304	32468441	0.88	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32468304	32468441	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32468442	32468586	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32468587	32468644	0.84	-	1	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32468587	32468644	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32468645	32468843	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32468844	32468989	0.98	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32468844	32468989	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32468990	32469097	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32469098	32469154	1	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32469098	32469154	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32469155	32469305	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32469306	32469389	1	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32469306	32469389	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32469390	32469560	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32469561	32469671	1	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32469561	32469671	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	intron	32469672	32470122	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	CDS	32470123	32470272	0.99	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	exon	32470123	32470272	.	-	.	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
Phchi.S1	AUGUSTUS	start_codon	32470270	32470272	.	-	0	transcript_id "Phchi.S1G516900.t1"; gene_id "Phchi.S1G516900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6505.t1 is derived from g3677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23360091	23360855	.	+	.	Phchi.S1G366400
Phchi.S1	AUGUSTUS	transcript	23360091	23360855	.	+	.	transcript_id "Phchi.S1G366400.t1"; gene_id "Phchi.S1G366400"
Phchi.S1	AUGUSTUS	start_codon	23360091	23360093	.	+	0	transcript_id "Phchi.S1G366400.t1"; gene_id "Phchi.S1G366400"
Phchi.S1	AUGUSTUS	CDS	23360091	23360855	0.98	+	0	transcript_id "Phchi.S1G366400.t1"; gene_id "Phchi.S1G366400"
Phchi.S1	AUGUSTUS	exon	23360091	23360855	.	+	.	transcript_id "Phchi.S1G366400.t1"; gene_id "Phchi.S1G366400"
Phchi.S1	AUGUSTUS	stop_codon	23360856	23360858	.	+	0	transcript_id "Phchi.S1G366400.t1"; gene_id "Phchi.S1G366400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1743.t1 is derived from g8663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2834686	2835191	.	+	.	Phchi.S5G035200
Phchi.S5	AUGUSTUS	transcript	2834686	2835191	.	+	.	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	start_codon	2834686	2834688	.	+	0	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	CDS	2834686	2834688	1	+	0	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	exon	2834686	2834688	.	+	.	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	intron	2834689	2834816	.	+	.	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	CDS	2834817	2834975	1	+	0	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	exon	2834817	2834975	.	+	.	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	intron	2834976	2835074	.	+	.	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	CDS	2835075	2835191	1	+	0	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	exon	2835075	2835191	.	+	.	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
Phchi.S5	AUGUSTUS	stop_codon	2835192	2835194	.	+	0	transcript_id "Phchi.S5G035200.t1"; gene_id "Phchi.S5G035200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8031.t1 is derived from g5206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32563499	32564067	.	+	.	Phchi.S1G519000
Phchi.S1	AUGUSTUS	transcript	32563499	32564067	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	start_codon	32563499	32563501	.	+	0	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	CDS	32563499	32563581	0.57	+	0	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	exon	32563499	32563581	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	intron	32563582	32563647	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	CDS	32563648	32563806	1	+	1	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	exon	32563648	32563806	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	intron	32563807	32563887	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	CDS	32563888	32563964	1	+	1	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	exon	32563888	32563964	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	intron	32563965	32564044	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	CDS	32564045	32564067	1	+	2	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	exon	32564045	32564067	.	+	.	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
Phchi.S1	AUGUSTUS	stop_codon	32564068	32564070	.	+	0	transcript_id "Phchi.S1G519000.t1"; gene_id "Phchi.S1G519000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7023.t1 is derived from g4195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26469173	26470801	.	-	.	Phchi.S1G418200
Phchi.S1	AUGUSTUS	transcript	26469173	26470801	.	-	.	transcript_id "Phchi.S1G418200.t1"; gene_id "Phchi.S1G418200"
Phchi.S1	AUGUSTUS	stop_codon	26469170	26469172	.	-	0	transcript_id "Phchi.S1G418200.t1"; gene_id "Phchi.S1G418200"
Phchi.S1	AUGUSTUS	CDS	26469173	26470801	0.98	-	0	transcript_id "Phchi.S1G418200.t1"; gene_id "Phchi.S1G418200"
Phchi.S1	AUGUSTUS	exon	26469173	26470801	.	-	.	transcript_id "Phchi.S1G418200.t1"; gene_id "Phchi.S1G418200"
Phchi.S1	AUGUSTUS	start_codon	26470799	26470801	.	-	0	transcript_id "Phchi.S1G418200.t1"; gene_id "Phchi.S1G418200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6185.t1 is derived from g3356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21370937	21374367	.	-	.	Phchi.S1G334400
Phchi.S1	AUGUSTUS	transcript	21370937	21374367	.	-	.	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	stop_codon	21370934	21370936	.	-	0	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	CDS	21370937	21372096	0.04	-	2	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	exon	21370937	21372096	.	-	.	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	intron	21372097	21373979	.	-	.	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	CDS	21373980	21374367	0.07	-	0	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	exon	21373980	21374367	.	-	.	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
Phchi.S1	AUGUSTUS	start_codon	21374365	21374367	.	-	0	transcript_id "Phchi.S1G334400.t1"; gene_id "Phchi.S1G334400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12485.t1 is derived from g8162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28827123	28827566	.	+	.	Phchi.S2G056500
Phchi.S2	AUGUSTUS	transcript	28827123	28827566	.	+	.	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	start_codon	28827123	28827125	.	+	0	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	CDS	28827123	28827311	0.97	+	0	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	exon	28827123	28827311	.	+	.	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	intron	28827312	28827461	.	+	.	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	CDS	28827462	28827566	0.73	+	0	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	exon	28827462	28827566	.	+	.	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
Phchi.S2	AUGUSTUS	stop_codon	28827567	28827569	.	+	0	transcript_id "Phchi.S2G056500.t1"; gene_id "Phchi.S2G056500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15605.t1 is derived from g14074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20250730	20252708	.	-	.	Phchi.S3G292400
Phchi.S3	AUGUSTUS	transcript	20250730	20252708	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	stop_codon	20250727	20250729	.	-	0	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20250730	20250898	0.97	-	1	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20250730	20250898	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20250899	20251003	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251004	20251221	0.98	-	0	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251004	20251221	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20251222	20251411	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251412	20251619	1	-	1	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251412	20251619	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20251620	20251710	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251711	20251801	1	-	2	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251711	20251801	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20251802	20251885	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251886	20252030	1	-	0	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251886	20252030	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20252031	20252134	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20252135	20252336	0.86	-	1	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20252135	20252336	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20252337	20252448	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20252449	20252708	0.89	-	0	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20252449	20252708	.	-	.	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	start_codon	20252706	20252708	.	-	0	transcript_id "Phchi.S3G292400.t1"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	transcript	20250730	20252708	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	stop_codon	20250727	20250729	.	-	0	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20250730	20250898	0.98	-	1	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20250730	20250898	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20250899	20251003	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251004	20251221	0.95	-	0	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251004	20251221	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20251222	20251411	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251412	20251619	1	-	1	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251412	20251619	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20251620	20251710	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251711	20251801	0.97	-	2	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251711	20251801	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20251802	20251885	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20251886	20252030	0.88	-	0	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20251886	20252030	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20252031	20252171	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20252172	20252177	0.7	-	0	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20252172	20252177	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20252178	20252269	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20252270	20252336	0.64	-	1	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20252270	20252336	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	intron	20252337	20252448	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	CDS	20252449	20252708	0.95	-	0	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	exon	20252449	20252708	.	-	.	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
Phchi.S3	AUGUSTUS	start_codon	20252706	20252708	.	-	0	transcript_id "Phchi.S3G292400.t2"; gene_id "Phchi.S3G292400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11903.t1 is derived from g15955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9214040	9216341	.	-	.	Phchi.S4G148500
Phchi.S4	AUGUSTUS	transcript	9214040	9216341	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	stop_codon	9214037	9214039	.	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9214040	9214300	0.62	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9214040	9214300	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	intron	9214301	9214431	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9214432	9214572	0.41	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9214432	9214572	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	intron	9214573	9214687	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9214688	9214972	1	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9214688	9214972	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	intron	9214973	9215095	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9215096	9215380	0.98	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9215096	9215380	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	intron	9215381	9215487	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9215488	9215874	1	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9215488	9215874	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	intron	9215875	9215974	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9215975	9216158	0.98	-	1	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9215975	9216158	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	intron	9216159	9216279	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	CDS	9216280	9216341	0.92	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	exon	9216280	9216341	.	-	.	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
Phchi.S4	AUGUSTUS	start_codon	9216339	9216341	.	-	0	transcript_id "Phchi.S4G148500.t1"; gene_id "Phchi.S4G148500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3906.t1 is derived from g1075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6391407	6392538	.	-	.	Phchi.S1G106500
Phchi.S1	AUGUSTUS	transcript	6391407	6392538	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	stop_codon	6391404	6391406	.	-	0	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	CDS	6391407	6391529	0.99	-	0	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	exon	6391407	6391529	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	intron	6391530	6391624	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	CDS	6391625	6391771	1	-	0	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	exon	6391625	6391771	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	intron	6391772	6391864	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	CDS	6391865	6392051	1	-	1	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	exon	6391865	6392051	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	intron	6392052	6392132	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	CDS	6392133	6392230	1	-	0	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	exon	6392133	6392230	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	intron	6392231	6392319	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	CDS	6392320	6392538	0.99	-	0	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	exon	6392320	6392538	.	-	.	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
Phchi.S1	AUGUSTUS	start_codon	6392536	6392538	.	-	0	transcript_id "Phchi.S1G106500.t1"; gene_id "Phchi.S1G106500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8637.t1 is derived from g5812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37187102	37187662	.	+	.	Phchi.S1G579600
Phchi.S1	AUGUSTUS	transcript	37187102	37187662	.	+	.	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	start_codon	37187102	37187104	.	+	0	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	CDS	37187102	37187358	0.63	+	0	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	exon	37187102	37187358	.	+	.	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	intron	37187359	37187553	.	+	.	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	CDS	37187554	37187662	0.64	+	1	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	exon	37187554	37187662	.	+	.	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
Phchi.S1	AUGUSTUS	stop_codon	37187663	37187665	.	+	0	transcript_id "Phchi.S1G579600.t1"; gene_id "Phchi.S1G579600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10186.t1 is derived from g7362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46213106	46213908	.	-	.	Phchi.S1G734500
Phchi.S1	AUGUSTUS	transcript	46213106	46213908	.	-	.	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	stop_codon	46213103	46213105	.	-	0	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	CDS	46213106	46213145	1	-	1	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	exon	46213106	46213145	.	-	.	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	intron	46213146	46213233	.	-	.	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	CDS	46213234	46213404	0.78	-	1	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	exon	46213234	46213404	.	-	.	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	intron	46213405	46213612	.	-	.	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	CDS	46213613	46213908	0.88	-	0	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	exon	46213613	46213908	.	-	.	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
Phchi.S1	AUGUSTUS	start_codon	46213906	46213908	.	-	0	transcript_id "Phchi.S1G734500.t1"; gene_id "Phchi.S1G734500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15837.t1 is derived from g14307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21681491	21683993	.	+	.	Phchi.S3G315600
Phchi.S3	AUGUSTUS	transcript	21681491	21683993	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	start_codon	21681491	21681493	.	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21681491	21681935	0.68	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21681491	21681935	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21681936	21682070	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21682071	21682282	1	+	2	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21682071	21682282	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21682283	21682402	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21682403	21682684	1	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21682403	21682684	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21682685	21682783	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21682784	21682906	1	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21682784	21682906	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21682907	21683086	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21683087	21683246	1	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21683087	21683246	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21683247	21683347	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21683348	21683643	0.99	+	2	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21683348	21683643	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21683644	21683746	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21683747	21683783	1	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21683747	21683783	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	intron	21683784	21683862	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	CDS	21683863	21683993	1	+	2	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	exon	21683863	21683993	.	+	.	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
Phchi.S3	AUGUSTUS	stop_codon	21683994	21683996	.	+	0	transcript_id "Phchi.S3G315600.t1"; gene_id "Phchi.S3G315600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6820.t1 is derived from g3992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25214687	25216108	.	+	.	Phchi.S1G397900
Phchi.S1	AUGUSTUS	transcript	25214687	25216108	.	+	.	transcript_id "Phchi.S1G397900.t1"; gene_id "Phchi.S1G397900"
Phchi.S1	AUGUSTUS	start_codon	25214687	25214689	.	+	0	transcript_id "Phchi.S1G397900.t1"; gene_id "Phchi.S1G397900"
Phchi.S1	AUGUSTUS	CDS	25214687	25216108	0.82	+	0	transcript_id "Phchi.S1G397900.t1"; gene_id "Phchi.S1G397900"
Phchi.S1	AUGUSTUS	exon	25214687	25216108	.	+	.	transcript_id "Phchi.S1G397900.t1"; gene_id "Phchi.S1G397900"
Phchi.S1	AUGUSTUS	stop_codon	25216109	25216111	.	+	0	transcript_id "Phchi.S1G397900.t1"; gene_id "Phchi.S1G397900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6063.t1 is derived from g3234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20694822	20697962	.	-	.	Phchi.S1G322200
Phchi.S1	AUGUSTUS	transcript	20694822	20697962	.	-	.	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	stop_codon	20694819	20694821	.	-	0	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	CDS	20694822	20694947	1	-	0	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	exon	20694822	20694947	.	-	.	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	intron	20694948	20695245	.	-	.	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	CDS	20695246	20695417	1	-	1	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	exon	20695246	20695417	.	-	.	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	intron	20695418	20697828	.	-	.	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	CDS	20697829	20697962	0.03	-	0	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	exon	20697829	20697962	.	-	.	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
Phchi.S1	AUGUSTUS	start_codon	20697960	20697962	.	-	0	transcript_id "Phchi.S1G322200.t1"; gene_id "Phchi.S1G322200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5190.t1 is derived from g2360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15402716	15405584	.	+	.	Phchi.S1G234900
Phchi.S1	AUGUSTUS	transcript	15402716	15405584	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	start_codon	15402716	15402718	.	+	0	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	CDS	15402716	15403058	0.32	+	0	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	exon	15402716	15403058	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	intron	15403059	15403243	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	CDS	15403244	15403461	0.98	+	2	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	exon	15403244	15403461	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	intron	15403462	15403607	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	CDS	15403608	15403910	0.97	+	0	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	exon	15403608	15403910	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	intron	15403911	15404044	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	CDS	15404045	15404307	0.88	+	0	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	exon	15404045	15404307	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	intron	15404308	15404398	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	CDS	15404399	15404813	0.96	+	1	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	exon	15404399	15404813	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	intron	15404814	15404948	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	CDS	15404949	15405584	0.96	+	0	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	exon	15404949	15405584	.	+	.	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
Phchi.S1	AUGUSTUS	stop_codon	15405585	15405587	.	+	0	transcript_id "Phchi.S1G234900.t1"; gene_id "Phchi.S1G234900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9341.t1 is derived from g6516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41023651	41024603	.	+	.	Phchi.S1G650000
Phchi.S1	AUGUSTUS	transcript	41023651	41024603	.	+	.	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	start_codon	41023651	41023653	.	+	0	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	CDS	41023651	41024118	0.51	+	0	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	exon	41023651	41024118	.	+	.	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	intron	41024119	41024402	.	+	.	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	CDS	41024403	41024603	0.83	+	0	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	exon	41024403	41024603	.	+	.	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
Phchi.S1	AUGUSTUS	stop_codon	41024604	41024606	.	+	0	transcript_id "Phchi.S1G650000.t1"; gene_id "Phchi.S1G650000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg579.t1 is derived from g10361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4259406	4260647	.	-	.	Phchi.S6G053800
Phchi.S6	AUGUSTUS	transcript	4259406	4260647	.	-	.	transcript_id "Phchi.S6G053800.t1"; gene_id "Phchi.S6G053800"
Phchi.S6	AUGUSTUS	stop_codon	4259403	4259405	.	-	0	transcript_id "Phchi.S6G053800.t1"; gene_id "Phchi.S6G053800"
Phchi.S6	AUGUSTUS	CDS	4259406	4260647	0.87	-	0	transcript_id "Phchi.S6G053800.t1"; gene_id "Phchi.S6G053800"
Phchi.S6	AUGUSTUS	exon	4259406	4260647	.	-	.	transcript_id "Phchi.S6G053800.t1"; gene_id "Phchi.S6G053800"
Phchi.S6	AUGUSTUS	start_codon	4260645	4260647	.	-	0	transcript_id "Phchi.S6G053800.t1"; gene_id "Phchi.S6G053800"
# This transcript jg8376.t2 is derived from g5551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8376.t3 is derived from g5551.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8377.t1 is derived from g5552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35591111	35594459	.	+	.	Phchi.S1G553600
Phchi.S1	AUGUSTUS	transcript	35591111	35594459	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	start_codon	35591111	35591113	.	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35591111	35591187	1	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35591111	35591187	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35591188	35591273	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35591274	35591340	1	+	1	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35591274	35591340	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35591341	35591543	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35591544	35591658	1	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35591544	35591658	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35591659	35591756	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35591757	35591867	0.65	+	2	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35591757	35591867	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35591868	35591948	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35591949	35592036	0.98	+	2	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35591949	35592036	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35592037	35592142	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35592143	35592247	1	+	1	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35592143	35592247	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35592248	35592340	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35592341	35592908	1	+	1	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35592341	35592908	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35592909	35592999	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35593000	35593187	1	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35593000	35593187	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35593188	35593293	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35593294	35593402	0.57	+	1	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35593294	35593402	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35593403	35593529	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35593530	35593678	1	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35593530	35593678	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35593679	35593777	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35593778	35593922	0.5	+	1	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35593778	35593922	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35593923	35594148	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35594149	35594319	0.55	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35594149	35594319	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	intron	35594320	35594429	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	CDS	35594430	35594459	0.62	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	exon	35594430	35594459	.	+	.	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
Phchi.S1	AUGUSTUS	stop_codon	35594460	35594462	.	+	0	transcript_id "Phchi.S1G553600.t1"; gene_id "Phchi.S1G553600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9725.t1 is derived from g6901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43408708	43410877	.	-	.	Phchi.S1G688400
Phchi.S1	AUGUSTUS	transcript	43408708	43410877	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	stop_codon	43408705	43408707	.	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43408708	43408754	0.97	-	2	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43408708	43408754	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	intron	43408755	43408851	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43408852	43408924	1	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43408852	43408924	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	intron	43408925	43409012	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43409013	43409075	1	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43409013	43409075	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	intron	43409076	43409180	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43409181	43409281	0.8	-	2	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43409181	43409281	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	intron	43409282	43409382	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43409383	43409569	1	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43409383	43409569	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	intron	43409570	43409654	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43409655	43410695	0.84	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43409655	43410695	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	intron	43410696	43410814	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	CDS	43410815	43410877	0.79	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	exon	43410815	43410877	.	-	.	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
Phchi.S1	AUGUSTUS	start_codon	43410875	43410877	.	-	0	transcript_id "Phchi.S1G688400.t1"; gene_id "Phchi.S1G688400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11688.t1 is derived from g15739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7686114	7688647	.	-	.	Phchi.S4G127000
Phchi.S4	AUGUSTUS	transcript	7686114	7688647	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	stop_codon	7686111	7686113	.	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7686114	7686203	0.98	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7686114	7686203	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7686204	7686316	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7686317	7686409	0.99	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7686317	7686409	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7686410	7686560	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7686561	7686680	0.99	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7686561	7686680	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7686681	7686781	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7686782	7686868	0.99	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7686782	7686868	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7686869	7686945	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7686946	7687167	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7686946	7687167	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7687168	7687258	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7687259	7687336	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7687259	7687336	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7687337	7687469	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7687470	7687619	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7687470	7687619	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7687620	7687703	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7687704	7687817	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7687704	7687817	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7687818	7687920	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7687921	7687983	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7687921	7687983	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7687984	7688076	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7688077	7688187	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7688077	7688187	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7688188	7688307	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7688308	7688421	1	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7688308	7688421	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	intron	7688422	7688623	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	CDS	7688624	7688647	0.95	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	exon	7688624	7688647	.	-	.	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
Phchi.S4	AUGUSTUS	start_codon	7688645	7688647	.	-	0	transcript_id "Phchi.S4G127000.t1"; gene_id "Phchi.S4G127000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7860.t1 is derived from g5034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31569347	31569677	.	+	.	Phchi.S1G501900
Phchi.S1	AUGUSTUS	transcript	31569347	31569677	.	+	.	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	start_codon	31569347	31569349	.	+	0	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	CDS	31569347	31569350	0.98	+	0	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	exon	31569347	31569350	.	+	.	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	intron	31569351	31569450	.	+	.	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	CDS	31569451	31569677	0.67	+	2	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	exon	31569451	31569677	.	+	.	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
Phchi.S1	AUGUSTUS	stop_codon	31569678	31569680	.	+	0	transcript_id "Phchi.S1G501900.t1"; gene_id "Phchi.S1G501900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4120.t1 is derived from g1289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8357355	8359142	.	-	.	Phchi.S1G127900
Phchi.S1	AUGUSTUS	transcript	8357355	8359142	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	stop_codon	8357352	8357354	.	-	0	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	CDS	8357355	8357666	1	-	0	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	exon	8357355	8357666	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	intron	8357667	8357743	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	CDS	8357744	8358029	0.99	-	1	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	exon	8357744	8358029	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	intron	8358030	8358251	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	CDS	8358252	8358463	1	-	0	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	exon	8358252	8358463	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	intron	8358464	8358554	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	CDS	8358555	8358811	1	-	2	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	exon	8358555	8358811	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	intron	8358812	8359132	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	CDS	8359133	8359142	1	-	0	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	exon	8359133	8359142	.	-	.	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
Phchi.S1	AUGUSTUS	start_codon	8359140	8359142	.	-	0	transcript_id "Phchi.S1G127900.t1"; gene_id "Phchi.S1G127900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8371.t1 is derived from g5546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35552976	35557474	.	-	.	Phchi.S1G553000
Phchi.S1	AUGUSTUS	transcript	35552976	35557474	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	stop_codon	35552973	35552975	.	-	0	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35552976	35552983	0.99	-	2	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35552976	35552983	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35552984	35553123	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35553124	35553415	1	-	0	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35553124	35553415	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35553416	35553502	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35553503	35553620	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35553503	35553620	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35553621	35553712	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35553713	35553853	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35553713	35553853	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35553854	35553926	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35553927	35553972	1	-	2	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35553927	35553972	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35553973	35554042	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35554043	35554108	1	-	2	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35554043	35554108	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35554109	35554197	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35554198	35554327	1	-	0	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35554198	35554327	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35554328	35554403	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35554404	35554618	1	-	2	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35554404	35554618	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35554619	35554757	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35554758	35554990	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35554758	35554990	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35554991	35555089	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35555090	35555164	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35555090	35555164	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35555165	35555244	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35555245	35555313	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35555245	35555313	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35555314	35555401	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35555402	35555473	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35555402	35555473	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35555474	35555550	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35555551	35555677	1	-	2	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35555551	35555677	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35555678	35555772	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35555773	35556017	1	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35555773	35556017	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35556018	35556131	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35556132	35556380	0.99	-	1	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35556132	35556380	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35556381	35556499	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35556500	35556777	1	-	0	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35556500	35556777	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35556778	35556860	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35556861	35557162	0.91	-	2	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35556861	35557162	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	intron	35557163	35557257	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	CDS	35557258	35557474	0.67	-	0	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	exon	35557258	35557474	.	-	.	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
Phchi.S1	AUGUSTUS	start_codon	35557472	35557474	.	-	0	transcript_id "Phchi.S1G553000.t1"; gene_id "Phchi.S1G553000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14511.t1 is derived from g12979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13239310	13240681	.	-	.	Phchi.S3G183000
Phchi.S3	AUGUSTUS	transcript	13239310	13240681	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	stop_codon	13239307	13239309	.	-	0	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	CDS	13239310	13239607	0.81	-	1	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	exon	13239310	13239607	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	intron	13239608	13239706	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	CDS	13239707	13239825	1	-	0	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	exon	13239707	13239825	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	intron	13239826	13239908	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	CDS	13239909	13240050	1	-	1	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	exon	13239909	13240050	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	intron	13240051	13240136	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	CDS	13240137	13240681	0.96	-	0	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	exon	13240137	13240681	.	-	.	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
Phchi.S3	AUGUSTUS	start_codon	13240679	13240681	.	-	0	transcript_id "Phchi.S3G183000.t1"; gene_id "Phchi.S3G183000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13327.t1 is derived from g11793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6115159	6116894	.	-	.	Phchi.S3G064600
Phchi.S3	AUGUSTUS	transcript	6115159	6116894	.	-	.	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	stop_codon	6115156	6115158	.	-	0	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	CDS	6115159	6115648	0.99	-	1	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	exon	6115159	6115648	.	-	.	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	intron	6115649	6115719	.	-	.	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	CDS	6115720	6116894	0.93	-	0	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	exon	6115720	6116894	.	-	.	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
Phchi.S3	AUGUSTUS	start_codon	6116892	6116894	.	-	0	transcript_id "Phchi.S3G064600.t1"; gene_id "Phchi.S3G064600"
# This transcript jg13507.t2 is derived from g11974.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13508.t1 is derived from g11975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7230154	7231824	.	+	.	Phchi.S3G082700
Phchi.S3	AUGUSTUS	transcript	7230154	7231824	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	start_codon	7230154	7230156	.	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	CDS	7230154	7230303	0.67	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	exon	7230154	7230303	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	intron	7230304	7230419	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	CDS	7230420	7230866	1	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	exon	7230420	7230866	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	intron	7230867	7230947	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	CDS	7230948	7231028	1	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	exon	7230948	7231028	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	intron	7231029	7231141	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	CDS	7231142	7231338	1	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	exon	7231142	7231338	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	intron	7231339	7231417	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	CDS	7231418	7231517	1	+	1	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	exon	7231418	7231517	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	intron	7231518	7231641	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	CDS	7231642	7231824	1	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	exon	7231642	7231824	.	+	.	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
Phchi.S3	AUGUSTUS	stop_codon	7231825	7231827	.	+	0	transcript_id "Phchi.S3G082700.t1"; gene_id "Phchi.S3G082700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12989.t1 is derived from g11454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3493564	3495492	.	-	.	Phchi.S3G030800
Phchi.S3	AUGUSTUS	transcript	3493564	3495492	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	stop_codon	3493561	3493563	.	-	0	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3493564	3493679	1	-	2	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3493564	3493679	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3493680	3493767	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3493768	3494111	1	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3493768	3494111	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3494112	3494213	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3494214	3494285	0.87	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3494214	3494285	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3494286	3494408	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3494409	3494480	1	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3494409	3494480	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3494481	3494558	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3494559	3494630	1	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3494559	3494630	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3494631	3494740	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3494741	3494812	1	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3494741	3494812	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3494813	3494950	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3494951	3495022	1	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3494951	3495022	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3495023	3495133	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3495134	3495199	1	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3495134	3495199	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3495200	3495289	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3495290	3495370	0.95	-	1	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3495290	3495370	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	intron	3495371	3495451	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	CDS	3495452	3495492	0.72	-	0	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	exon	3495452	3495492	.	-	.	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
Phchi.S3	AUGUSTUS	start_codon	3495490	3495492	.	-	0	transcript_id "Phchi.S3G030800.t1"; gene_id "Phchi.S3G030800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7304.t1 is derived from g4476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28405413	28410046	.	+	.	Phchi.S1G446300
Phchi.S1	AUGUSTUS	transcript	28405413	28410046	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	start_codon	28405413	28405415	.	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28405413	28405460	0.68	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28405413	28405460	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28405461	28405639	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28405640	28405678	0.76	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28405640	28405678	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28405679	28405921	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28405922	28408620	0.47	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28405922	28408620	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28408621	28408742	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28408743	28408860	0.41	+	1	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28408743	28408860	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28408861	28408966	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28408967	28409398	0.53	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28408967	28409398	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28409399	28409494	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28409495	28409531	0.73	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28409495	28409531	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28409532	28409662	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28409663	28409676	0.89	+	2	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28409663	28409676	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	intron	28409677	28409920	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	CDS	28409921	28410046	0.81	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	exon	28409921	28410046	.	+	.	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
Phchi.S1	AUGUSTUS	stop_codon	28410047	28410049	.	+	0	transcript_id "Phchi.S1G446300.t1"; gene_id "Phchi.S1G446300"
# This transcript jg4544.t2 is derived from g1714.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4545.t1 is derived from g1715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11036108	11039342	.	+	.	Phchi.S1G170400
Phchi.S1	AUGUSTUS	transcript	11036108	11039342	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	start_codon	11036108	11036110	.	+	0	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	CDS	11036108	11037100	0.99	+	0	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	exon	11036108	11037100	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	intron	11037101	11037224	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	CDS	11037225	11037471	1	+	0	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	exon	11037225	11037471	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	intron	11037472	11037583	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	CDS	11037584	11037895	1	+	2	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	exon	11037584	11037895	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	intron	11037896	11038013	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	CDS	11038014	11038708	0.98	+	2	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	exon	11038014	11038708	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	intron	11038709	11038799	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	CDS	11038800	11039342	1	+	0	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	exon	11038800	11039342	.	+	.	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
Phchi.S1	AUGUSTUS	stop_codon	11039343	11039345	.	+	0	transcript_id "Phchi.S1G170400.t1"; gene_id "Phchi.S1G170400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2965.t1 is derived from g134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	860674	861185	.	+	.	Phchi.S1G012400
Phchi.S1	AUGUSTUS	transcript	860674	861185	.	+	.	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	start_codon	860674	860676	.	+	0	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	CDS	860674	860957	0.96	+	0	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	exon	860674	860957	.	+	.	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	intron	860958	861100	.	+	.	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	CDS	861101	861185	0.97	+	1	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	exon	861101	861185	.	+	.	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
Phchi.S1	AUGUSTUS	stop_codon	861186	861188	.	+	0	transcript_id "Phchi.S1G012400.t1"; gene_id "Phchi.S1G012400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3939.t1 is derived from g1108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6570096	6573292	.	-	.	Phchi.S1G109800
Phchi.S1	AUGUSTUS	transcript	6570096	6573292	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	stop_codon	6570093	6570095	.	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6570096	6570212	1	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6570096	6570212	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6570213	6570300	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6570301	6570411	1	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6570301	6570411	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6570412	6570539	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6570540	6570646	1	-	2	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6570540	6570646	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6570647	6570724	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6570725	6570831	1	-	1	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6570725	6570831	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6570832	6570915	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6570916	6571000	1	-	2	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6570916	6571000	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6571001	6571151	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6571152	6571311	1	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6571152	6571311	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6571312	6571450	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6571451	6571504	1	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6571451	6571504	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6571505	6571587	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6571588	6571648	1	-	1	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6571588	6571648	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6571649	6571748	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6571749	6571818	1	-	2	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6571749	6571818	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6571819	6571910	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6571911	6571995	1	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6571911	6571995	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6571996	6572136	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6572137	6572235	1	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6572137	6572235	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6572236	6572341	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6572342	6572465	0.96	-	1	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6572342	6572465	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6572466	6572619	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6572620	6572707	0.9	-	2	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6572620	6572707	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6572708	6572986	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6572987	6573090	0.28	-	1	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6572987	6573090	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	intron	6573091	6573266	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	CDS	6573267	6573292	0.28	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	exon	6573267	6573292	.	-	.	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
Phchi.S1	AUGUSTUS	start_codon	6573290	6573292	.	-	0	transcript_id "Phchi.S1G109800.t1"; gene_id "Phchi.S1G109800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15585.t1 is derived from g14054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20133358	20134051	.	+	.	Phchi.S3G290400
Phchi.S3	AUGUSTUS	transcript	20133358	20134051	.	+	.	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	start_codon	20133358	20133360	.	+	0	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	CDS	20133358	20133558	0.94	+	0	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	exon	20133358	20133558	.	+	.	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	intron	20133559	20133676	.	+	.	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	CDS	20133677	20134051	0.95	+	0	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	exon	20133677	20134051	.	+	.	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
Phchi.S3	AUGUSTUS	stop_codon	20134052	20134054	.	+	0	transcript_id "Phchi.S3G290400.t1"; gene_id "Phchi.S3G290400"
# This transcript jg1178.t2 is derived from g10961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1179.t1 is derived from g10962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8315389	8316471	.	-	.	Phchi.S6G113800
Phchi.S6	AUGUSTUS	transcript	8315886	8316471	.	-	.	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	stop_codon	8315883	8315885	.	-	0	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	CDS	8315886	8315894	0.88	-	0	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	exon	8315886	8315894	.	-	.	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	intron	8315895	8315976	.	-	.	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	CDS	8315977	8316471	0.58	-	0	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	exon	8315977	8316471	.	-	.	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	start_codon	8316469	8316471	.	-	0	transcript_id "Phchi.S6G113800.t1"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	transcript	8315389	8316471	.	-	.	transcript_id "Phchi.S6G113800.t2"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	stop_codon	8315386	8315388	.	-	0	transcript_id "Phchi.S6G113800.t2"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	CDS	8315389	8316471	0.74	-	0	transcript_id "Phchi.S6G113800.t2"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	exon	8315389	8316471	.	-	.	transcript_id "Phchi.S6G113800.t2"; gene_id "Phchi.S6G113800"
Phchi.S6	AUGUSTUS	start_codon	8316469	8316471	.	-	0	transcript_id "Phchi.S6G113800.t2"; gene_id "Phchi.S6G113800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3773.t1 is derived from g942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5637054	5637802	.	-	.	Phchi.S1G093200
Phchi.S1	AUGUSTUS	transcript	5637054	5637802	.	-	.	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	stop_codon	5637051	5637053	.	-	0	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	CDS	5637054	5637146	0.91	-	0	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	exon	5637054	5637146	.	-	.	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	intron	5637147	5637331	.	-	.	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	CDS	5637332	5637486	0.47	-	2	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	exon	5637332	5637486	.	-	.	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	intron	5637487	5637723	.	-	.	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	CDS	5637724	5637802	0.27	-	0	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	exon	5637724	5637802	.	-	.	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
Phchi.S1	AUGUSTUS	start_codon	5637800	5637802	.	-	0	transcript_id "Phchi.S1G093200.t1"; gene_id "Phchi.S1G093200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg238.t1 is derived from g10020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1625585	1626508	.	-	.	Phchi.S6G019700
Phchi.S6	AUGUSTUS	transcript	1625585	1626508	.	-	.	transcript_id "Phchi.S6G019700.t1"; gene_id "Phchi.S6G019700"
Phchi.S6	AUGUSTUS	stop_codon	1625582	1625584	.	-	0	transcript_id "Phchi.S6G019700.t1"; gene_id "Phchi.S6G019700"
Phchi.S6	AUGUSTUS	CDS	1625585	1626508	1	-	0	transcript_id "Phchi.S6G019700.t1"; gene_id "Phchi.S6G019700"
Phchi.S6	AUGUSTUS	exon	1625585	1626508	.	-	.	transcript_id "Phchi.S6G019700.t1"; gene_id "Phchi.S6G019700"
Phchi.S6	AUGUSTUS	start_codon	1626506	1626508	.	-	0	transcript_id "Phchi.S6G019700.t1"; gene_id "Phchi.S6G019700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13220.t1 is derived from g11685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4741600	4743686	.	+	.	Phchi.S3G053900
Phchi.S3	AUGUSTUS	transcript	4741600	4743686	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	start_codon	4741600	4741602	.	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4741600	4741707	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4741600	4741707	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4741708	4741795	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4741796	4741894	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4741796	4741894	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4741895	4741980	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4741981	4742109	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4741981	4742109	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4742110	4742196	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4742197	4742256	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4742197	4742256	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4742257	4742449	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4742450	4742620	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4742450	4742620	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4742621	4742728	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4742729	4742816	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4742729	4742816	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4742817	4742943	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4742944	4743035	1	+	2	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4742944	4743035	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4743036	4743162	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4743163	4743312	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4743163	4743312	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4743313	4743389	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4743390	4743448	1	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4743390	4743448	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	intron	4743449	4743568	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	CDS	4743569	4743686	1	+	1	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	exon	4743569	4743686	.	+	.	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
Phchi.S3	AUGUSTUS	stop_codon	4743687	4743689	.	+	0	transcript_id "Phchi.S3G053900.t1"; gene_id "Phchi.S3G053900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3486.t1 is derived from g655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4014061	4014456	.	-	.	Phchi.S1G064500
Phchi.S1	AUGUSTUS	transcript	4014061	4014456	.	-	.	transcript_id "Phchi.S1G064500.t1"; gene_id "Phchi.S1G064500"
Phchi.S1	AUGUSTUS	stop_codon	4014058	4014060	.	-	0	transcript_id "Phchi.S1G064500.t1"; gene_id "Phchi.S1G064500"
Phchi.S1	AUGUSTUS	CDS	4014061	4014456	0.78	-	0	transcript_id "Phchi.S1G064500.t1"; gene_id "Phchi.S1G064500"
Phchi.S1	AUGUSTUS	exon	4014061	4014456	.	-	.	transcript_id "Phchi.S1G064500.t1"; gene_id "Phchi.S1G064500"
Phchi.S1	AUGUSTUS	start_codon	4014454	4014456	.	-	0	transcript_id "Phchi.S1G064500.t1"; gene_id "Phchi.S1G064500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7305.t1 is derived from g4477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28422784	28423122	.	+	.	Phchi.S1G446400
Phchi.S1	AUGUSTUS	transcript	28422784	28423122	.	+	.	transcript_id "Phchi.S1G446400.t1"; gene_id "Phchi.S1G446400"
Phchi.S1	AUGUSTUS	start_codon	28422784	28422786	.	+	0	transcript_id "Phchi.S1G446400.t1"; gene_id "Phchi.S1G446400"
Phchi.S1	AUGUSTUS	CDS	28422784	28423122	1	+	0	transcript_id "Phchi.S1G446400.t1"; gene_id "Phchi.S1G446400"
Phchi.S1	AUGUSTUS	exon	28422784	28423122	.	+	.	transcript_id "Phchi.S1G446400.t1"; gene_id "Phchi.S1G446400"
Phchi.S1	AUGUSTUS	stop_codon	28423123	28423125	.	+	0	transcript_id "Phchi.S1G446400.t1"; gene_id "Phchi.S1G446400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9572.t1 is derived from g6748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42724085	42724910	.	+	.	Phchi.S1G673100
Phchi.S1	AUGUSTUS	transcript	42724085	42724910	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	start_codon	42724085	42724087	.	+	0	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	CDS	42724085	42724114	1	+	0	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	exon	42724085	42724114	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	intron	42724115	42724210	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	CDS	42724211	42724325	1	+	0	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	exon	42724211	42724325	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	intron	42724326	42724448	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	CDS	42724449	42724563	0.99	+	2	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	exon	42724449	42724563	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	intron	42724564	42724643	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	CDS	42724644	42724761	1	+	1	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	exon	42724644	42724761	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	intron	42724762	42724850	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	CDS	42724851	42724910	1	+	0	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	exon	42724851	42724910	.	+	.	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
Phchi.S1	AUGUSTUS	stop_codon	42724911	42724913	.	+	0	transcript_id "Phchi.S1G673100.t1"; gene_id "Phchi.S1G673100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7453.t1 is derived from g4625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29366600	29368677	.	+	.	Phchi.S1G461200
Phchi.S1	AUGUSTUS	transcript	29366600	29368677	.	+	.	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	start_codon	29366600	29366602	.	+	0	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	CDS	29366600	29367814	0.63	+	0	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	exon	29366600	29367814	.	+	.	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	intron	29367815	29367903	.	+	.	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	CDS	29367904	29368677	0.53	+	0	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	exon	29367904	29368677	.	+	.	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
Phchi.S1	AUGUSTUS	stop_codon	29368678	29368680	.	+	0	transcript_id "Phchi.S1G461200.t1"; gene_id "Phchi.S1G461200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3108.t1 is derived from g277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1767534	1768151	.	-	.	Phchi.S1G026700
Phchi.S1	AUGUSTUS	transcript	1767534	1768151	.	-	.	transcript_id "Phchi.S1G026700.t1"; gene_id "Phchi.S1G026700"
Phchi.S1	AUGUSTUS	stop_codon	1767531	1767533	.	-	0	transcript_id "Phchi.S1G026700.t1"; gene_id "Phchi.S1G026700"
Phchi.S1	AUGUSTUS	CDS	1767534	1768151	0.49	-	0	transcript_id "Phchi.S1G026700.t1"; gene_id "Phchi.S1G026700"
Phchi.S1	AUGUSTUS	exon	1767534	1768151	.	-	.	transcript_id "Phchi.S1G026700.t1"; gene_id "Phchi.S1G026700"
Phchi.S1	AUGUSTUS	start_codon	1768149	1768151	.	-	0	transcript_id "Phchi.S1G026700.t1"; gene_id "Phchi.S1G026700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8899.t1 is derived from g6074.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38547538	38550461	.	+	.	Phchi.S1G605800
Phchi.S1	AUGUSTUS	transcript	38547538	38550461	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	start_codon	38547538	38547540	.	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38547538	38547738	0.94	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38547538	38547738	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38547739	38547945	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38547946	38548072	1	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38547946	38548072	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38548073	38548343	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38548344	38548688	1	+	2	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38548344	38548688	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38548689	38548845	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38548846	38549011	1	+	2	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38548846	38549011	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549012	38549250	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549251	38549377	1	+	1	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549251	38549377	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549378	38549550	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549551	38549616	1	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549551	38549616	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549617	38549771	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549772	38549816	1	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549772	38549816	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549817	38549899	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549900	38549944	1	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549900	38549944	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549945	38550042	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38550043	38550258	1	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38550043	38550258	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38550259	38550341	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38550342	38550461	0.98	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38550342	38550461	.	+	.	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	stop_codon	38550462	38550464	.	+	0	transcript_id "Phchi.S1G605800.t1"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	transcript	38547538	38550461	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	start_codon	38547538	38547540	.	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38547538	38547738	0.92	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38547538	38547738	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38547739	38547945	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38547946	38548072	1	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38547946	38548072	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38548073	38548155	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38548156	38548233	0.91	+	2	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38548156	38548233	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38548234	38548343	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38548344	38548688	0.95	+	2	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38548344	38548688	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38548689	38548845	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38548846	38549011	1	+	2	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38548846	38549011	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549012	38549250	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549251	38549377	1	+	1	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549251	38549377	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549378	38549550	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549551	38549616	1	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549551	38549616	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549617	38549771	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549772	38549816	1	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549772	38549816	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549817	38549902	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38549903	38549944	1	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38549903	38549944	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38549945	38550042	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38550043	38550258	1	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38550043	38550258	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	intron	38550259	38550341	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	CDS	38550342	38550461	1	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	exon	38550342	38550461	.	+	.	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
Phchi.S1	AUGUSTUS	stop_codon	38550462	38550464	.	+	0	transcript_id "Phchi.S1G605800.t2"; gene_id "Phchi.S1G605800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13393.t1 is derived from g11859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6516063	6516813	.	-	.	Phchi.S3G071200
Phchi.S3	AUGUSTUS	transcript	6516063	6516813	.	-	.	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	stop_codon	6516060	6516062	.	-	0	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	CDS	6516063	6516286	0.76	-	2	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	exon	6516063	6516286	.	-	.	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	intron	6516287	6516364	.	-	.	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	CDS	6516365	6516461	0.76	-	0	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	exon	6516365	6516461	.	-	.	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	intron	6516462	6516573	.	-	.	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	CDS	6516574	6516813	0.77	-	0	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	exon	6516574	6516813	.	-	.	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
Phchi.S3	AUGUSTUS	start_codon	6516811	6516813	.	-	0	transcript_id "Phchi.S3G071200.t1"; gene_id "Phchi.S3G071200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8654.t1 is derived from g5829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37254095	37256168	.	-	.	Phchi.S1G581300
Phchi.S1	AUGUSTUS	transcript	37254095	37256168	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	stop_codon	37254092	37254094	.	-	0	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	CDS	37254095	37254353	1	-	1	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	exon	37254095	37254353	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	intron	37254354	37254449	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	CDS	37254450	37254817	1	-	0	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	exon	37254450	37254817	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	intron	37254818	37254949	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	CDS	37254950	37255243	1	-	0	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	exon	37254950	37255243	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	intron	37255244	37255392	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	CDS	37255393	37255651	1	-	1	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	exon	37255393	37255651	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	intron	37255652	37255779	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	CDS	37255780	37256168	1	-	0	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	exon	37255780	37256168	.	-	.	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
Phchi.S1	AUGUSTUS	start_codon	37256166	37256168	.	-	0	transcript_id "Phchi.S1G581300.t1"; gene_id "Phchi.S1G581300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6183.t1 is derived from g3354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21336804	21338311	.	-	.	Phchi.S1G334200
Phchi.S1	AUGUSTUS	transcript	21336804	21338311	.	-	.	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	stop_codon	21336801	21336803	.	-	0	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	CDS	21336804	21337529	0.54	-	0	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	exon	21336804	21337529	.	-	.	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	intron	21337530	21337660	.	-	.	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	CDS	21337661	21338311	0.23	-	0	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	exon	21337661	21338311	.	-	.	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
Phchi.S1	AUGUSTUS	start_codon	21338309	21338311	.	-	0	transcript_id "Phchi.S1G334200.t1"; gene_id "Phchi.S1G334200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5080.t1 is derived from g2250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14589181	14589777	.	+	.	Phchi.S1G223900
Phchi.S1	AUGUSTUS	transcript	14589181	14589777	.	+	.	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	start_codon	14589181	14589183	.	+	0	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	CDS	14589181	14589382	0.37	+	0	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	exon	14589181	14589382	.	+	.	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	intron	14589383	14589460	.	+	.	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	CDS	14589461	14589777	0.92	+	2	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	exon	14589461	14589777	.	+	.	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
Phchi.S1	AUGUSTUS	stop_codon	14589778	14589780	.	+	0	transcript_id "Phchi.S1G223900.t1"; gene_id "Phchi.S1G223900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15902.t1 is derived from g14372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22072278	22074043	.	-	.	Phchi.S3G322100
Phchi.S3	AUGUSTUS	transcript	22072278	22074043	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	stop_codon	22072275	22072277	.	-	0	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22072278	22072312	0.98	-	2	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22072278	22072312	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22072313	22072396	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22072397	22072494	1	-	1	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22072397	22072494	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22072495	22072604	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22072605	22072678	1	-	0	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22072605	22072678	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22072679	22072809	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22072810	22072851	1	-	0	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22072810	22072851	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22072852	22072997	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22072998	22073056	1	-	2	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22072998	22073056	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22073057	22073412	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22073413	22073499	1	-	2	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22073413	22073499	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22073500	22073668	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22073669	22073696	1	-	0	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22073669	22073696	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	intron	22073697	22073995	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	CDS	22073996	22074043	0.97	-	0	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	exon	22073996	22074043	.	-	.	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
Phchi.S3	AUGUSTUS	start_codon	22074041	22074043	.	-	0	transcript_id "Phchi.S3G322100.t1"; gene_id "Phchi.S3G322100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4201.t1 is derived from g1370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8884684	8886143	.	+	.	Phchi.S1G136000
Phchi.S1	AUGUSTUS	transcript	8884684	8886143	.	+	.	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	start_codon	8884684	8884686	.	+	0	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	CDS	8884684	8885298	0.51	+	0	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	exon	8884684	8885298	.	+	.	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	intron	8885299	8885375	.	+	.	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	CDS	8885376	8886143	0.53	+	0	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	exon	8885376	8886143	.	+	.	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
Phchi.S1	AUGUSTUS	stop_codon	8886144	8886146	.	+	0	transcript_id "Phchi.S1G136000.t1"; gene_id "Phchi.S1G136000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6305.t1 is derived from g3477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22176793	22177474	.	+	.	Phchi.S1G346400
Phchi.S1	AUGUSTUS	transcript	22176793	22177474	.	+	.	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	start_codon	22176793	22176795	.	+	0	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	CDS	22176793	22176924	0.63	+	0	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	exon	22176793	22176924	.	+	.	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	intron	22176925	22177125	.	+	.	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	CDS	22177126	22177164	1	+	0	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	exon	22177126	22177164	.	+	.	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	intron	22177165	22177285	.	+	.	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	CDS	22177286	22177474	1	+	0	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	exon	22177286	22177474	.	+	.	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
Phchi.S1	AUGUSTUS	stop_codon	22177475	22177477	.	+	0	transcript_id "Phchi.S1G346400.t1"; gene_id "Phchi.S1G346400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8845.t1 is derived from g6020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38256157	38257135	.	-	.	Phchi.S1G600400
Phchi.S1	AUGUSTUS	transcript	38256157	38257135	.	-	.	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	stop_codon	38256154	38256156	.	-	0	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	CDS	38256157	38256204	0.94	-	0	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	exon	38256157	38256204	.	-	.	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	intron	38256205	38256427	.	-	.	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	CDS	38256428	38257135	0.45	-	0	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	exon	38256428	38257135	.	-	.	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
Phchi.S1	AUGUSTUS	start_codon	38257133	38257135	.	-	0	transcript_id "Phchi.S1G600400.t1"; gene_id "Phchi.S1G600400"
# This transcript jg14474.t2 is derived from g12942.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14474.t3 is derived from g12942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14475.t1 is derived from g12943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13038868	13042880	.	+	.	Phchi.S3G179400
Phchi.S3	AUGUSTUS	transcript	13038868	13041065	.	+	.	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	start_codon	13038868	13038870	.	+	0	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13038868	13039813	0.69	+	0	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13038868	13039813	.	+	.	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13039814	13039929	.	+	.	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13039930	13041065	0.55	+	2	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13039930	13041065	.	+	.	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	stop_codon	13041066	13041068	.	+	0	transcript_id "Phchi.S3G179400.t1"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	transcript	13038868	13042880	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	start_codon	13038868	13038870	.	+	0	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13038868	13039813	0.63	+	0	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13038868	13039813	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13039814	13039929	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13039930	13040708	0.38	+	2	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13039930	13040708	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13040709	13040908	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13040909	13042154	0.17	+	0	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13040909	13042154	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13042155	13042246	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13042247	13042381	0.26	+	2	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13042247	13042381	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13042382	13042485	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13042486	13042880	0.2	+	2	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13042486	13042880	.	+	.	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	stop_codon	13042881	13042883	.	+	0	transcript_id "Phchi.S3G179400.t2"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	transcript	13041008	13042880	.	+	.	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	start_codon	13041008	13041010	.	+	0	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13041008	13042154	0.41	+	0	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13041008	13042154	.	+	.	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13042155	13042246	.	+	.	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13042247	13042381	0.37	+	2	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13042247	13042381	.	+	.	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	intron	13042382	13042485	.	+	.	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	CDS	13042486	13042880	0.11	+	2	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	exon	13042486	13042880	.	+	.	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
Phchi.S3	AUGUSTUS	stop_codon	13042881	13042883	.	+	0	transcript_id "Phchi.S3G179400.t3"; gene_id "Phchi.S3G179400"
# This transcript jg3592.t1 is derived from g760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4647463	4647735	.	-	.	Phchi.S1G075000
Phchi.S1	AUGUSTUS	transcript	4647463	4647735	.	-	.	transcript_id "Phchi.S1G075000.t1"; gene_id "Phchi.S1G075000"
Phchi.S1	AUGUSTUS	stop_codon	4647460	4647462	.	-	0	transcript_id "Phchi.S1G075000.t1"; gene_id "Phchi.S1G075000"
Phchi.S1	AUGUSTUS	CDS	4647463	4647735	0.43	-	0	transcript_id "Phchi.S1G075000.t1"; gene_id "Phchi.S1G075000"
Phchi.S1	AUGUSTUS	exon	4647463	4647735	.	-	.	transcript_id "Phchi.S1G075000.t1"; gene_id "Phchi.S1G075000"
Phchi.S1	AUGUSTUS	start_codon	4647733	4647735	.	-	0	transcript_id "Phchi.S1G075000.t1"; gene_id "Phchi.S1G075000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4933.t1 is derived from g2103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13636943	13637516	.	-	.	Phchi.S1G209200
Phchi.S1	AUGUSTUS	transcript	13636943	13637516	.	-	.	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	stop_codon	13636940	13636942	.	-	0	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	CDS	13636943	13637059	0.99	-	0	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	exon	13636943	13637059	.	-	.	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	intron	13637060	13637273	.	-	.	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	CDS	13637274	13637516	0.29	-	0	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	exon	13637274	13637516	.	-	.	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
Phchi.S1	AUGUSTUS	start_codon	13637514	13637516	.	-	0	transcript_id "Phchi.S1G209200.t1"; gene_id "Phchi.S1G209200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4972.t1 is derived from g2142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13829478	13830005	.	-	.	Phchi.S1G213100
Phchi.S1	AUGUSTUS	transcript	13829478	13830005	.	-	.	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	stop_codon	13829475	13829477	.	-	0	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	CDS	13829478	13829871	0.94	-	1	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	exon	13829478	13829871	.	-	.	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	intron	13829872	13829964	.	-	.	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	CDS	13829965	13830005	0.85	-	0	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	exon	13829965	13830005	.	-	.	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
Phchi.S1	AUGUSTUS	start_codon	13830003	13830005	.	-	0	transcript_id "Phchi.S1G213100.t1"; gene_id "Phchi.S1G213100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11481.t1 is derived from g15531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6584814	6586933	.	+	.	Phchi.S4G106300
Phchi.S4	AUGUSTUS	transcript	6584814	6586933	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	start_codon	6584814	6584816	.	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6584814	6585001	0.99	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6584814	6585001	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6585002	6585309	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6585310	6585445	1	+	1	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6585310	6585445	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6585446	6585613	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6585614	6585741	1	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6585614	6585741	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6585742	6585871	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6585872	6586019	0.98	+	1	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6585872	6586019	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6586020	6586138	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6586139	6586244	1	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6586139	6586244	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6586245	6586338	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6586339	6586415	0.98	+	2	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6586339	6586415	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6586416	6586521	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6586522	6586557	0.98	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6586522	6586557	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6586558	6586634	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6586635	6586744	1	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6586635	6586744	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6586745	6586878	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6586879	6586933	1	+	1	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6586879	6586933	.	+	.	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	stop_codon	6586934	6586936	.	+	0	transcript_id "Phchi.S4G106300.t1"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	transcript	6584814	6585620	.	+	.	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	start_codon	6584814	6584816	.	+	0	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6584814	6585001	1	+	0	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6584814	6585001	.	+	.	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6585002	6585309	.	+	.	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6585310	6585435	0.98	+	1	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6585310	6585435	.	+	.	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	intron	6585436	6585613	.	+	.	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	CDS	6585614	6585620	0.98	+	1	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	exon	6585614	6585620	.	+	.	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
Phchi.S4	AUGUSTUS	stop_codon	6585621	6585623	.	+	0	transcript_id "Phchi.S4G106300.t2"; gene_id "Phchi.S4G106300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1502.t1 is derived from g8421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1228093	1232994	.	-	.	Phchi.S5G011100
Phchi.S5	AUGUSTUS	transcript	1228093	1232994	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	stop_codon	1228090	1228092	.	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1228093	1228113	0.92	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1228093	1228113	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1228114	1228377	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1228378	1229136	0.88	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1228378	1229136	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1229137	1229229	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1229230	1229958	0.99	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1229230	1229958	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1229959	1230095	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1230096	1230401	0.85	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1230096	1230401	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1230402	1230477	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1230478	1230837	0.78	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1230478	1230837	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1230838	1230919	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1230920	1231009	1	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1230920	1231009	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231010	1231112	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231113	1231231	1	-	2	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231113	1231231	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231232	1231572	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231573	1231650	1	-	2	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231573	1231650	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231651	1231736	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231737	1232040	1	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231737	1232040	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1232041	1232247	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1232248	1232438	1	-	2	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1232248	1232438	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1232439	1232564	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1232565	1232994	1	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1232565	1232994	.	-	.	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	start_codon	1232992	1232994	.	-	0	transcript_id "Phchi.S5G011100.t1"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	transcript	1228093	1232994	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	stop_codon	1228090	1228092	.	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1228093	1228113	0.91	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1228093	1228113	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1228114	1228377	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1228378	1229136	0.92	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1228378	1229136	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1229137	1229229	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1229230	1229958	1	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1229230	1229958	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1229959	1230095	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1230096	1230401	0.86	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1230096	1230401	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1230402	1230477	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1230478	1230837	0.73	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1230478	1230837	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1230838	1230919	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1230920	1231009	1	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1230920	1231009	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231010	1231112	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231113	1231231	1	-	2	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231113	1231231	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231232	1231483	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231484	1231497	0.53	-	1	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231484	1231497	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231498	1231586	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231587	1231650	0.95	-	2	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231587	1231650	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1231651	1231736	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1231737	1232040	1	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1231737	1232040	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1232041	1232247	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1232248	1232438	1	-	2	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1232248	1232438	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	intron	1232439	1232564	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	CDS	1232565	1232994	0.98	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	exon	1232565	1232994	.	-	.	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
Phchi.S5	AUGUSTUS	start_codon	1232992	1232994	.	-	0	transcript_id "Phchi.S5G011100.t2"; gene_id "Phchi.S5G011100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11036.t1 is derived from g15086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3758552	3763709	.	-	.	Phchi.S4G061800
Phchi.S4	AUGUSTUS	transcript	3758552	3763709	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	stop_codon	3758549	3758551	.	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3758552	3758823	0.9	-	2	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3758552	3758823	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3758824	3759126	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3759127	3761221	0.16	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3759127	3761221	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3761222	3761388	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3761389	3761487	0.31	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3761389	3761487	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3761488	3761693	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3761694	3761963	0.39	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3761694	3761963	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3761964	3762058	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3762059	3762148	1	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3762059	3762148	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3762149	3762281	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3762282	3762356	1	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3762282	3762356	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3762357	3762462	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3762463	3762522	0.99	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3762463	3762522	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3762523	3762638	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3762639	3762731	0.99	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3762639	3762731	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3762732	3762829	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3762830	3762857	0.82	-	1	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3762830	3762857	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3762858	3763138	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3763139	3763239	0.96	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3763139	3763239	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3763240	3763319	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3763320	3763438	1	-	2	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3763320	3763438	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	intron	3763439	3763639	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	CDS	3763640	3763709	0.81	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	exon	3763640	3763709	.	-	.	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
Phchi.S4	AUGUSTUS	start_codon	3763707	3763709	.	-	0	transcript_id "Phchi.S4G061800.t1"; gene_id "Phchi.S4G061800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7728.t1 is derived from g4902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30860433	30862244	.	-	.	Phchi.S1G488700
Phchi.S1	AUGUSTUS	transcript	30860433	30862244	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	stop_codon	30860430	30860432	.	-	0	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	CDS	30860433	30860489	1	-	0	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	exon	30860433	30860489	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	intron	30860490	30860571	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	CDS	30860572	30860713	1	-	1	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	exon	30860572	30860713	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	intron	30860714	30860856	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	CDS	30860857	30861077	1	-	0	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	exon	30860857	30861077	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	intron	30861078	30861231	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	CDS	30861232	30861579	1	-	0	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	exon	30861232	30861579	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	intron	30861580	30861667	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	CDS	30861668	30861852	1	-	2	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	exon	30861668	30861852	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	intron	30861853	30861994	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	CDS	30861995	30862244	1	-	0	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	exon	30861995	30862244	.	-	.	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
Phchi.S1	AUGUSTUS	start_codon	30862242	30862244	.	-	0	transcript_id "Phchi.S1G488700.t1"; gene_id "Phchi.S1G488700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3681.t1 is derived from g850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5158481	5159829	.	-	.	Phchi.S1G084000
Phchi.S1	AUGUSTUS	transcript	5158481	5159829	.	-	.	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	stop_codon	5158478	5158480	.	-	0	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	CDS	5158481	5158684	0.92	-	0	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	exon	5158481	5158684	.	-	.	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	intron	5158685	5158794	.	-	.	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	CDS	5158795	5159829	0.48	-	0	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	exon	5158795	5159829	.	-	.	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
Phchi.S1	AUGUSTUS	start_codon	5159827	5159829	.	-	0	transcript_id "Phchi.S1G084000.t1"; gene_id "Phchi.S1G084000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2692.t1 is derived from g9612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8229220	8230040	.	-	.	Phchi.S5G130100
Phchi.S5	AUGUSTUS	transcript	8229220	8230040	.	-	.	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	stop_codon	8229217	8229219	.	-	0	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	CDS	8229220	8229340	0.62	-	1	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	exon	8229220	8229340	.	-	.	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	intron	8229341	8229486	.	-	.	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	CDS	8229487	8230040	0.54	-	0	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	exon	8229487	8230040	.	-	.	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
Phchi.S5	AUGUSTUS	start_codon	8230038	8230040	.	-	0	transcript_id "Phchi.S5G130100.t1"; gene_id "Phchi.S5G130100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15274.t1 is derived from g13742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18062700	18068454	.	+	.	Phchi.S3G259300
Phchi.S3	AUGUSTUS	transcript	18062700	18068454	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	start_codon	18062700	18062702	.	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18062700	18062822	0.86	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18062700	18062822	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18062823	18062922	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18062923	18063020	0.92	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18062923	18063020	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063021	18063103	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063104	18063244	1	+	1	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063104	18063244	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063245	18063333	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063334	18063436	1	+	1	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063334	18063436	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063437	18063662	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063663	18063676	0.99	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063663	18063676	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063677	18063731	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063732	18063750	0.77	+	1	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063732	18063750	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063751	18063839	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063840	18064235	0.96	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063840	18064235	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18064236	18064527	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18064528	18064686	1	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18064528	18064686	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18064687	18064771	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18064772	18065008	0.89	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18064772	18065008	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18065009	18065161	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18065162	18065428	0.93	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18065162	18065428	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18065429	18065509	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18065510	18066240	0.92	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18065510	18066240	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18066241	18066314	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18066315	18066952	0.91	+	1	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18066315	18066952	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18066953	18067095	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067096	18067151	1	+	2	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067096	18067151	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067152	18067417	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067418	18067492	1	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067418	18067492	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067493	18067564	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067565	18067714	0.87	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067565	18067714	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067715	18067838	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067839	18067910	1	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067839	18067910	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067911	18067997	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067998	18068066	1	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067998	18068066	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18068067	18068148	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18068149	18068243	1	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18068149	18068243	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18068244	18068324	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18068325	18068454	0.99	+	1	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18068325	18068454	.	+	.	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	stop_codon	18068455	18068457	.	+	0	transcript_id "Phchi.S3G259300.t1"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	transcript	18062700	18068454	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	start_codon	18062700	18062702	.	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18062700	18062822	0.86	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18062700	18062822	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18062823	18062922	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18062923	18063020	0.88	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18062923	18063020	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063021	18063103	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063104	18063244	1	+	1	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063104	18063244	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063245	18063333	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063334	18063436	1	+	1	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063334	18063436	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063437	18063662	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063663	18063676	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063663	18063676	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063677	18063731	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063732	18063750	0.79	+	1	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063732	18063750	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18063751	18063839	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18063840	18064235	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18063840	18064235	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18064236	18064527	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18064528	18064686	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18064528	18064686	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18064687	18064771	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18064772	18065008	0.92	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18064772	18065008	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18065009	18065161	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18065162	18065428	0.91	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18065162	18065428	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18065429	18065509	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18065510	18066240	0.9	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18065510	18066240	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18066241	18066314	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18066315	18066952	0.88	+	1	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18066315	18066952	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18066953	18067095	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067096	18067151	1	+	2	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067096	18067151	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067152	18067417	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067418	18067492	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067418	18067492	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067493	18067573	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067574	18067714	0.73	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067574	18067714	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067715	18067838	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067839	18067910	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067839	18067910	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18067911	18067997	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18067998	18068066	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18067998	18068066	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18068067	18068148	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18068149	18068243	1	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18068149	18068243	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	intron	18068244	18068324	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	CDS	18068325	18068454	1	+	1	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	exon	18068325	18068454	.	+	.	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
Phchi.S3	AUGUSTUS	stop_codon	18068455	18068457	.	+	0	transcript_id "Phchi.S3G259300.t2"; gene_id "Phchi.S3G259300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11778.t1 is derived from g15830.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8123074	8127156	.	+	.	Phchi.S4G136000
Phchi.S4	AUGUSTUS	transcript	8123074	8127156	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	start_codon	8123074	8123076	.	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8123074	8123169	0.45	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8123074	8123169	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8123170	8123893	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8123894	8124007	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8123894	8124007	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8124008	8124349	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8124350	8124523	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8124350	8124523	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8124524	8124721	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8124722	8124814	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8124722	8124814	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8124815	8124885	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8124886	8124978	0.99	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8124886	8124978	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8124979	8125114	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8125115	8125198	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8125115	8125198	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8125199	8125341	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8125342	8125397	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8125342	8125397	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8125398	8125565	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8125566	8125659	1	+	1	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8125566	8125659	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8125660	8125774	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8125775	8125887	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8125775	8125887	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8125888	8125955	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8125956	8126028	1	+	1	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8125956	8126028	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8126029	8126124	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8126125	8126205	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8126125	8126205	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8126206	8126335	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8126336	8126422	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8126336	8126422	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8126423	8126509	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8126510	8126614	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8126510	8126614	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8126615	8126703	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8126704	8126810	1	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8126704	8126810	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8126811	8126912	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8126913	8126973	1	+	1	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8126913	8126973	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	intron	8126974	8127057	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	CDS	8127058	8127156	0.99	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	exon	8127058	8127156	.	+	.	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
Phchi.S4	AUGUSTUS	stop_codon	8127157	8127159	.	+	0	transcript_id "Phchi.S4G136000.t1"; gene_id "Phchi.S4G136000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9093.t1 is derived from g6268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39812290	39814199	.	-	.	Phchi.S1G625200
Phchi.S1	AUGUSTUS	transcript	39812290	39814199	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	stop_codon	39812287	39812289	.	-	0	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39812290	39812414	0.94	-	2	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39812290	39812414	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39812415	39812540	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39812541	39812612	1	-	2	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39812541	39812612	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39812613	39812742	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39812743	39812922	1	-	2	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39812743	39812922	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39812923	39813022	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39813023	39813089	1	-	0	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39813023	39813089	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39813090	39813218	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39813219	39813345	1	-	1	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39813219	39813345	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39813346	39813466	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39813467	39813522	1	-	0	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39813467	39813522	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39813523	39813664	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39813665	39813790	1	-	0	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39813665	39813790	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39813791	39813887	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39813888	39814054	1	-	2	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39813888	39814054	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	intron	39814055	39814144	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	CDS	39814145	39814199	1	-	0	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	exon	39814145	39814199	.	-	.	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
Phchi.S1	AUGUSTUS	start_codon	39814197	39814199	.	-	0	transcript_id "Phchi.S1G625200.t1"; gene_id "Phchi.S1G625200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3321.t1 is derived from g490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2888046	2888351	.	+	.	Phchi.S1G048000
Phchi.S1	AUGUSTUS	transcript	2888046	2888351	.	+	.	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	start_codon	2888046	2888048	.	+	0	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	CDS	2888046	2888159	0.99	+	0	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	exon	2888046	2888159	.	+	.	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	intron	2888160	2888243	.	+	.	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	CDS	2888244	2888351	1	+	0	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	exon	2888244	2888351	.	+	.	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
Phchi.S1	AUGUSTUS	stop_codon	2888352	2888354	.	+	0	transcript_id "Phchi.S1G048000.t1"; gene_id "Phchi.S1G048000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5521.t1 is derived from g2691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17205014	17207646	.	-	.	Phchi.S1G268000
Phchi.S1	AUGUSTUS	transcript	17205014	17207646	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	stop_codon	17205011	17205013	.	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17205014	17205412	0.76	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17205014	17205412	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17205413	17205500	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17205501	17205599	1	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17205501	17205599	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17205600	17205697	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17205698	17205889	1	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17205698	17205889	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17205890	17205976	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17205977	17206050	1	-	2	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17205977	17206050	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17206051	17206140	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17206141	17206350	0.97	-	2	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17206141	17206350	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17206351	17206463	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17206464	17206605	0.99	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17206464	17206605	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17206606	17206755	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17206756	17206822	1	-	1	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17206756	17206822	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17206823	17206897	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17206898	17207034	1	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17206898	17207034	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17207035	17207133	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17207134	17207179	1	-	1	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17207134	17207179	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17207180	17207260	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17207261	17207356	0.97	-	1	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17207261	17207356	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	intron	17207357	17207533	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	CDS	17207534	17207646	0.96	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	exon	17207534	17207646	.	-	.	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
Phchi.S1	AUGUSTUS	start_codon	17207644	17207646	.	-	0	transcript_id "Phchi.S1G268000.t1"; gene_id "Phchi.S1G268000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11233.t1 is derived from g15283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4926313	4928060	.	-	.	Phchi.S4G081500
Phchi.S4	AUGUSTUS	transcript	4926313	4928060	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	stop_codon	4926310	4926312	.	-	0	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	CDS	4926313	4926879	0.58	-	0	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	exon	4926313	4926879	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	intron	4926880	4927117	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	CDS	4927118	4927421	1	-	1	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	exon	4927118	4927421	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	intron	4927422	4927544	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	CDS	4927545	4927672	0.79	-	0	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	exon	4927545	4927672	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	intron	4927673	4927759	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	CDS	4927760	4927777	0.86	-	0	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	exon	4927760	4927777	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	intron	4927778	4927943	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	CDS	4927944	4928060	0.8	-	0	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	exon	4927944	4928060	.	-	.	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
Phchi.S4	AUGUSTUS	start_codon	4928058	4928060	.	-	0	transcript_id "Phchi.S4G081500.t1"; gene_id "Phchi.S4G081500"
# This transcript jg2261.t2 is derived from g9181.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2262.t1 is derived from g9182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5723669	5724259	.	-	.	Phchi.S5G087100
Phchi.S5	AUGUSTUS	transcript	5723669	5724259	.	-	.	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	stop_codon	5723666	5723668	.	-	0	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	CDS	5723669	5723838	0.99	-	2	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	exon	5723669	5723838	.	-	.	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	intron	5723839	5724012	.	-	.	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	CDS	5724013	5724259	0.65	-	0	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	exon	5724013	5724259	.	-	.	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
Phchi.S5	AUGUSTUS	start_codon	5724257	5724259	.	-	0	transcript_id "Phchi.S5G087100.t1"; gene_id "Phchi.S5G087100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5399.t1 is derived from g2569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16686065	16688128	.	-	.	Phchi.S1G255800
Phchi.S1	AUGUSTUS	transcript	16686065	16688128	.	-	.	transcript_id "Phchi.S1G255800.t1"; gene_id "Phchi.S1G255800"
Phchi.S1	AUGUSTUS	stop_codon	16686062	16686064	.	-	0	transcript_id "Phchi.S1G255800.t1"; gene_id "Phchi.S1G255800"
Phchi.S1	AUGUSTUS	CDS	16686065	16688128	0.6	-	0	transcript_id "Phchi.S1G255800.t1"; gene_id "Phchi.S1G255800"
Phchi.S1	AUGUSTUS	exon	16686065	16688128	.	-	.	transcript_id "Phchi.S1G255800.t1"; gene_id "Phchi.S1G255800"
Phchi.S1	AUGUSTUS	start_codon	16688126	16688128	.	-	0	transcript_id "Phchi.S1G255800.t1"; gene_id "Phchi.S1G255800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5822.t1 is derived from g2992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19118636	19120557	.	+	.	Phchi.S1G298100
Phchi.S1	AUGUSTUS	transcript	19118636	19120557	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	start_codon	19118636	19118638	.	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19118636	19118926	0.91	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19118636	19118926	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19118927	19119008	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19119009	19119076	1	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19119009	19119076	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19119077	19119176	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19119177	19119273	1	+	1	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19119177	19119273	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19119274	19119382	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19119383	19119514	1	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19119383	19119514	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19119515	19119607	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19119608	19119716	1	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19119608	19119716	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19119717	19119834	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19119835	19119979	1	+	2	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19119835	19119979	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19119980	19120082	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19120083	19120125	0.99	+	1	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19120083	19120125	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19120126	19120218	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19120219	19120248	0.95	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19120219	19120248	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19120249	19120361	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19120362	19120394	0.92	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19120362	19120394	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	intron	19120395	19120476	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	CDS	19120477	19120557	1	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	exon	19120477	19120557	.	+	.	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
Phchi.S1	AUGUSTUS	stop_codon	19120558	19120560	.	+	0	transcript_id "Phchi.S1G298100.t1"; gene_id "Phchi.S1G298100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12501.t1 is derived from g8178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30850345	30850890	.	-	.	Phchi.S2G058100
Phchi.S2	AUGUSTUS	transcript	30850345	30850890	.	-	.	transcript_id "Phchi.S2G058100.t1"; gene_id "Phchi.S2G058100"
Phchi.S2	AUGUSTUS	stop_codon	30850342	30850344	.	-	0	transcript_id "Phchi.S2G058100.t1"; gene_id "Phchi.S2G058100"
Phchi.S2	AUGUSTUS	CDS	30850345	30850890	0.54	-	0	transcript_id "Phchi.S2G058100.t1"; gene_id "Phchi.S2G058100"
Phchi.S2	AUGUSTUS	exon	30850345	30850890	.	-	.	transcript_id "Phchi.S2G058100.t1"; gene_id "Phchi.S2G058100"
Phchi.S2	AUGUSTUS	start_codon	30850888	30850890	.	-	0	transcript_id "Phchi.S2G058100.t1"; gene_id "Phchi.S2G058100"
# This transcript jg12383.t2 is derived from g8059.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12383.t3 is derived from g8059.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12384.t1 is derived from g8061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15321247	15321621	.	+	.	Phchi.S2G046400
Phchi.S2	AUGUSTUS	transcript	15321247	15321621	.	+	.	transcript_id "Phchi.S2G046400.t1"; gene_id "Phchi.S2G046400"
Phchi.S2	AUGUSTUS	start_codon	15321247	15321249	.	+	0	transcript_id "Phchi.S2G046400.t1"; gene_id "Phchi.S2G046400"
Phchi.S2	AUGUSTUS	CDS	15321247	15321621	0.37	+	0	transcript_id "Phchi.S2G046400.t1"; gene_id "Phchi.S2G046400"
Phchi.S2	AUGUSTUS	exon	15321247	15321621	.	+	.	transcript_id "Phchi.S2G046400.t1"; gene_id "Phchi.S2G046400"
Phchi.S2	AUGUSTUS	stop_codon	15321622	15321624	.	+	0	transcript_id "Phchi.S2G046400.t1"; gene_id "Phchi.S2G046400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15259.t1 is derived from g13727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17960594	17961349	.	+	.	Phchi.S3G257800
Phchi.S3	AUGUSTUS	transcript	17960594	17961349	.	+	.	transcript_id "Phchi.S3G257800.t1"; gene_id "Phchi.S3G257800"
Phchi.S3	AUGUSTUS	start_codon	17960594	17960596	.	+	0	transcript_id "Phchi.S3G257800.t1"; gene_id "Phchi.S3G257800"
Phchi.S3	AUGUSTUS	CDS	17960594	17961349	0.62	+	0	transcript_id "Phchi.S3G257800.t1"; gene_id "Phchi.S3G257800"
Phchi.S3	AUGUSTUS	exon	17960594	17961349	.	+	.	transcript_id "Phchi.S3G257800.t1"; gene_id "Phchi.S3G257800"
Phchi.S3	AUGUSTUS	stop_codon	17961350	17961352	.	+	0	transcript_id "Phchi.S3G257800.t1"; gene_id "Phchi.S3G257800"
# This transcript jg12755.t2 is derived from g11220.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12756.t1 is derived from g11221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1906476	1907156	.	+	.	Phchi.S3G007500
Phchi.S3	AUGUSTUS	transcript	1906476	1907156	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	start_codon	1906476	1906478	.	+	0	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	CDS	1906476	1906491	0.94	+	0	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	exon	1906476	1906491	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	intron	1906492	1906673	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	CDS	1906674	1906679	0.88	+	2	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	exon	1906674	1906679	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	intron	1906680	1906790	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	CDS	1906791	1906907	0.86	+	2	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	exon	1906791	1906907	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	intron	1906908	1907088	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	CDS	1907089	1907156	1	+	2	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	exon	1907089	1907156	.	+	.	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
Phchi.S3	AUGUSTUS	stop_codon	1907157	1907159	.	+	0	transcript_id "Phchi.S3G007500.t1"; gene_id "Phchi.S3G007500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14171.t1 is derived from g12638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11259327	11260089	.	-	.	Phchi.S3G149000
Phchi.S3	AUGUSTUS	transcript	11259327	11260089	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	stop_codon	11259324	11259326	.	-	0	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	CDS	11259327	11259375	0.7	-	1	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	exon	11259327	11259375	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	intron	11259376	11259448	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	CDS	11259449	11259526	0.66	-	1	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	exon	11259449	11259526	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	intron	11259527	11259789	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	CDS	11259790	11259838	0.99	-	2	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	exon	11259790	11259838	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	intron	11259839	11259956	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	CDS	11259957	11260089	0.81	-	0	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	exon	11259957	11260089	.	-	.	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
Phchi.S3	AUGUSTUS	start_codon	11260087	11260089	.	-	0	transcript_id "Phchi.S3G149000.t1"; gene_id "Phchi.S3G149000"
# This transcript jg5996.t2 is derived from g3167.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5997.t1 is derived from g3168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20320023	20321494	.	-	.	Phchi.S1G315600
Phchi.S1	AUGUSTUS	transcript	20320023	20321494	.	-	.	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	stop_codon	20320020	20320022	.	-	0	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	CDS	20320023	20320117	0.18	-	2	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	exon	20320023	20320117	.	-	.	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	intron	20320118	20320422	.	-	.	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	CDS	20320423	20321494	0.12	-	0	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	exon	20320423	20321494	.	-	.	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
Phchi.S1	AUGUSTUS	start_codon	20321492	20321494	.	-	0	transcript_id "Phchi.S1G315600.t1"; gene_id "Phchi.S1G315600"
# This transcript jg5422.t2 is derived from g2592.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5423.t1 is derived from g2593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16804914	16807791	.	-	.	Phchi.S1G258200
Phchi.S1	AUGUSTUS	transcript	16804914	16807791	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	stop_codon	16804911	16804913	.	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16804914	16804992	1	-	1	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16804914	16804992	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16804993	16805091	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16805092	16805144	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16805092	16805144	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16805145	16805221	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16805222	16805284	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16805222	16805284	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16805285	16805464	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16805465	16805539	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16805465	16805539	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16805540	16805640	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16805641	16805703	0.95	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16805641	16805703	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16805704	16805779	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16805780	16805869	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16805780	16805869	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16805870	16805987	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16805988	16806244	0.62	-	2	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16805988	16806244	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16806245	16806343	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16806344	16806354	0.62	-	1	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16806344	16806354	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16806355	16806480	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16806481	16806527	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16806481	16806527	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16806528	16806611	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16806612	16806887	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16806612	16806887	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16806888	16807003	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16807004	16807079	1	-	1	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16807004	16807079	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16807080	16807246	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16807247	16807311	1	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16807247	16807311	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	intron	16807312	16807677	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	CDS	16807678	16807791	0.99	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	exon	16807678	16807791	.	-	.	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
Phchi.S1	AUGUSTUS	start_codon	16807789	16807791	.	-	0	transcript_id "Phchi.S1G258200.t1"; gene_id "Phchi.S1G258200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8491.t1 is derived from g5666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36233498	36237036	.	+	.	Phchi.S1G565000
Phchi.S1	AUGUSTUS	transcript	36233498	36237036	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	start_codon	36233498	36233500	.	+	0	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	CDS	36233498	36233770	0.83	+	0	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	exon	36233498	36233770	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	intron	36233771	36233870	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	CDS	36233871	36234175	0.51	+	0	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	exon	36233871	36234175	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	intron	36234176	36234338	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	CDS	36234339	36235143	1	+	1	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	exon	36234339	36235143	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	intron	36235144	36235260	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	CDS	36235261	36237036	0.99	+	0	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	exon	36235261	36237036	.	+	.	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
Phchi.S1	AUGUSTUS	stop_codon	36237037	36237039	.	+	0	transcript_id "Phchi.S1G565000.t1"; gene_id "Phchi.S1G565000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6788.t1 is derived from g3960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25088983	25090568	.	+	.	Phchi.S1G394700
Phchi.S1	AUGUSTUS	transcript	25088983	25090568	.	+	.	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	start_codon	25088983	25088985	.	+	0	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	CDS	25088983	25089356	0.93	+	0	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	exon	25088983	25089356	.	+	.	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	intron	25089357	25089449	.	+	.	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	CDS	25089450	25089543	0.99	+	1	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	exon	25089450	25089543	.	+	.	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	intron	25089544	25089632	.	+	.	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	CDS	25089633	25090568	0.92	+	0	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	exon	25089633	25090568	.	+	.	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
Phchi.S1	AUGUSTUS	stop_codon	25090569	25090571	.	+	0	transcript_id "Phchi.S1G394700.t1"; gene_id "Phchi.S1G394700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2153.t1 is derived from g9073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5087546	5089799	.	-	.	Phchi.S5G076200
Phchi.S5	AUGUSTUS	transcript	5087546	5089799	.	-	.	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	stop_codon	5087543	5087545	.	-	0	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	CDS	5087546	5088922	0.99	-	0	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	exon	5087546	5088922	.	-	.	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	intron	5088923	5089064	.	-	.	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	CDS	5089065	5089337	1	-	0	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	exon	5089065	5089337	.	-	.	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	intron	5089338	5089547	.	-	.	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	CDS	5089548	5089799	0.92	-	0	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	exon	5089548	5089799	.	-	.	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
Phchi.S5	AUGUSTUS	start_codon	5089797	5089799	.	-	0	transcript_id "Phchi.S5G076200.t1"; gene_id "Phchi.S5G076200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7284.t1 is derived from g4456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28136276	28137307	.	-	.	Phchi.S1G444300
Phchi.S1	AUGUSTUS	transcript	28136276	28137307	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	stop_codon	28136273	28136275	.	-	0	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	CDS	28136276	28136298	0.97	-	2	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	exon	28136276	28136298	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	intron	28136299	28136433	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	CDS	28136434	28136490	0.97	-	2	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	exon	28136434	28136490	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	intron	28136491	28136613	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	CDS	28136614	28136691	0.9	-	2	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	exon	28136614	28136691	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	intron	28136692	28136813	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	CDS	28136814	28136859	0.91	-	0	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	exon	28136814	28136859	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	intron	28136860	28136982	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	CDS	28136983	28137092	1	-	2	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	exon	28136983	28137092	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	intron	28137093	28137162	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	CDS	28137163	28137307	1	-	0	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	exon	28137163	28137307	.	-	.	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
Phchi.S1	AUGUSTUS	start_codon	28137305	28137307	.	-	0	transcript_id "Phchi.S1G444300.t1"; gene_id "Phchi.S1G444300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6593.t1 is derived from g3765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23908184	23908688	.	+	.	Phchi.S1G375200
Phchi.S1	AUGUSTUS	transcript	23908184	23908688	.	+	.	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	start_codon	23908184	23908186	.	+	0	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	CDS	23908184	23908372	1	+	0	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	exon	23908184	23908372	.	+	.	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	intron	23908373	23908469	.	+	.	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	CDS	23908470	23908583	0.82	+	0	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	exon	23908470	23908583	.	+	.	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	intron	23908584	23908667	.	+	.	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	CDS	23908668	23908688	0.78	+	0	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	exon	23908668	23908688	.	+	.	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
Phchi.S1	AUGUSTUS	stop_codon	23908689	23908691	.	+	0	transcript_id "Phchi.S1G375200.t1"; gene_id "Phchi.S1G375200"
# This transcript jg12057.t2 is derived from g7732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12058.t1 is derived from g7733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1185016	1194596	.	+	.	Phchi.S2G013800
Phchi.S2	AUGUSTUS	transcript	1185016	1194596	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	start_codon	1185016	1185018	.	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1185016	1186200	0.97	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1185016	1186200	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1186201	1186324	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1186325	1186396	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1186325	1186396	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1186397	1186582	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1186583	1186648	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1186583	1186648	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1186649	1186743	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1186744	1186815	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1186744	1186815	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1186816	1186883	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1186884	1186949	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1186884	1186949	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1186950	1187178	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1187179	1187241	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1187179	1187241	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1187242	1187344	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1187345	1187410	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1187345	1187410	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1187411	1187600	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1187601	1187700	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1187601	1187700	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1187701	1187825	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1187826	1187927	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1187826	1187927	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1187928	1188035	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1188036	1188268	0.87	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1188036	1188268	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1188269	1188376	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1188377	1188491	0.95	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1188377	1188491	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1188492	1188588	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1188589	1188709	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1188589	1188709	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1188710	1188785	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1188786	1188961	1	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1188786	1188961	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1188962	1189034	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1189035	1189170	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1189035	1189170	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1189171	1189304	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1189305	1189384	0.39	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1189305	1189384	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1189385	1189468	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1189469	1189516	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1189469	1189516	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1189517	1189732	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1189733	1189908	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1189733	1189908	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1189909	1190040	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1190041	1190158	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1190041	1190158	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1190159	1190285	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1190286	1190413	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1190286	1190413	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1190414	1190530	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1190531	1190696	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1190531	1190696	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1190697	1190824	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1190825	1190943	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1190825	1190943	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1190944	1191037	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1191038	1191206	0.95	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1191038	1191206	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1191207	1191295	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1191296	1191307	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1191296	1191307	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1191308	1191363	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1191364	1191379	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1191364	1191379	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1191380	1191460	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1191461	1191534	1	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1191461	1191534	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1191535	1191625	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1191626	1191745	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1191626	1191745	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1191746	1191837	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1191838	1192015	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1191838	1192015	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1192016	1192100	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1192101	1192222	1	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1192101	1192222	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1192223	1192320	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1192321	1192387	0.67	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1192321	1192387	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1192388	1192515	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1192516	1192527	0.38	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1192516	1192527	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1192528	1192621	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1192622	1192695	1	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1192622	1192695	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1192696	1192918	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1192919	1193057	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1192919	1193057	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1193058	1193149	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1193150	1193325	1	+	1	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1193150	1193325	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1193326	1193438	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1193439	1193594	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1193439	1193594	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1193595	1193728	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1193729	1193860	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1193729	1193860	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1193861	1193947	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1193948	1194006	1	+	2	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1193948	1194006	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1194007	1194106	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1194107	1194139	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1194107	1194139	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1194140	1194218	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1194219	1194356	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1194219	1194356	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	intron	1194357	1194428	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	CDS	1194429	1194596	1	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	exon	1194429	1194596	.	+	.	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
Phchi.S2	AUGUSTUS	stop_codon	1194597	1194599	.	+	0	transcript_id "Phchi.S2G013800.t1"; gene_id "Phchi.S2G013800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9143.t1 is derived from g6318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40063583	40064542	.	-	.	Phchi.S1G630200
Phchi.S1	AUGUSTUS	transcript	40063583	40064542	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	stop_codon	40063580	40063582	.	-	0	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	CDS	40063583	40063685	0.99	-	1	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	exon	40063583	40063685	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	intron	40063686	40063810	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	CDS	40063811	40063944	1	-	0	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	exon	40063811	40063944	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	intron	40063945	40064029	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	CDS	40064030	40064116	1	-	0	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	exon	40064030	40064116	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	intron	40064117	40064206	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	CDS	40064207	40064542	1	-	0	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	exon	40064207	40064542	.	-	.	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
Phchi.S1	AUGUSTUS	start_codon	40064540	40064542	.	-	0	transcript_id "Phchi.S1G630200.t1"; gene_id "Phchi.S1G630200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9024.t1 is derived from g6199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39192519	39194673	.	-	.	Phchi.S1G618300
Phchi.S1	AUGUSTUS	transcript	39192519	39194673	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	stop_codon	39192516	39192518	.	-	0	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	CDS	39192519	39192629	0.91	-	0	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	exon	39192519	39192629	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	intron	39192630	39192720	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	CDS	39192721	39192756	0.96	-	0	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	exon	39192721	39192756	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	intron	39192757	39192847	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	CDS	39192848	39193548	0.5	-	2	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	exon	39192848	39193548	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	intron	39193549	39193712	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	CDS	39193713	39194673	0.98	-	0	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	exon	39193713	39194673	.	-	.	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
Phchi.S1	AUGUSTUS	start_codon	39194671	39194673	.	-	0	transcript_id "Phchi.S1G618300.t1"; gene_id "Phchi.S1G618300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11456.t1 is derived from g15506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6454366	6455373	.	-	.	Phchi.S4G103800
Phchi.S4	AUGUSTUS	transcript	6454366	6455373	.	-	.	transcript_id "Phchi.S4G103800.t1"; gene_id "Phchi.S4G103800"
Phchi.S4	AUGUSTUS	stop_codon	6454363	6454365	.	-	0	transcript_id "Phchi.S4G103800.t1"; gene_id "Phchi.S4G103800"
Phchi.S4	AUGUSTUS	CDS	6454366	6455373	0.36	-	0	transcript_id "Phchi.S4G103800.t1"; gene_id "Phchi.S4G103800"
Phchi.S4	AUGUSTUS	exon	6454366	6455373	.	-	.	transcript_id "Phchi.S4G103800.t1"; gene_id "Phchi.S4G103800"
Phchi.S4	AUGUSTUS	start_codon	6455371	6455373	.	-	0	transcript_id "Phchi.S4G103800.t1"; gene_id "Phchi.S4G103800"
# This transcript jg6786.t1 is derived from g3958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25082502	25082753	.	+	.	Phchi.S1G394500
Phchi.S1	AUGUSTUS	transcript	25082502	25082753	.	+	.	transcript_id "Phchi.S1G394500.t1"; gene_id "Phchi.S1G394500"
Phchi.S1	AUGUSTUS	start_codon	25082502	25082504	.	+	0	transcript_id "Phchi.S1G394500.t1"; gene_id "Phchi.S1G394500"
Phchi.S1	AUGUSTUS	CDS	25082502	25082753	0.17	+	0	transcript_id "Phchi.S1G394500.t1"; gene_id "Phchi.S1G394500"
Phchi.S1	AUGUSTUS	exon	25082502	25082753	.	+	.	transcript_id "Phchi.S1G394500.t1"; gene_id "Phchi.S1G394500"
Phchi.S1	AUGUSTUS	stop_codon	25082754	25082756	.	+	0	transcript_id "Phchi.S1G394500.t1"; gene_id "Phchi.S1G394500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13900.t1 is derived from g12367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9541561	9542075	.	+	.	Phchi.S3G121900
Phchi.S3	AUGUSTUS	transcript	9541561	9542075	.	+	.	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	start_codon	9541561	9541563	.	+	0	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	CDS	9541561	9541609	0.43	+	0	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	exon	9541561	9541609	.	+	.	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	intron	9541610	9541686	.	+	.	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	CDS	9541687	9542075	0.5	+	2	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	exon	9541687	9542075	.	+	.	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
Phchi.S3	AUGUSTUS	stop_codon	9542076	9542078	.	+	0	transcript_id "Phchi.S3G121900.t1"; gene_id "Phchi.S3G121900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5123.t1 is derived from g2293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14832264	14833874	.	-	.	Phchi.S1G228200
Phchi.S1	AUGUSTUS	transcript	14832264	14833874	.	-	.	transcript_id "Phchi.S1G228200.t1"; gene_id "Phchi.S1G228200"
Phchi.S1	AUGUSTUS	stop_codon	14832261	14832263	.	-	0	transcript_id "Phchi.S1G228200.t1"; gene_id "Phchi.S1G228200"
Phchi.S1	AUGUSTUS	CDS	14832264	14833874	0.82	-	0	transcript_id "Phchi.S1G228200.t1"; gene_id "Phchi.S1G228200"
Phchi.S1	AUGUSTUS	exon	14832264	14833874	.	-	.	transcript_id "Phchi.S1G228200.t1"; gene_id "Phchi.S1G228200"
Phchi.S1	AUGUSTUS	start_codon	14833872	14833874	.	-	0	transcript_id "Phchi.S1G228200.t1"; gene_id "Phchi.S1G228200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9117.t1 is derived from g6292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39903857	39906164	.	+	.	Phchi.S1G627600
Phchi.S1	AUGUSTUS	transcript	39903857	39906164	.	+	.	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	start_codon	39903857	39903859	.	+	0	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	CDS	39903857	39905954	0.18	+	0	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	exon	39903857	39905954	.	+	.	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	intron	39905955	39906153	.	+	.	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	CDS	39906154	39906164	0.52	+	2	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	exon	39906154	39906164	.	+	.	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
Phchi.S1	AUGUSTUS	stop_codon	39906165	39906167	.	+	0	transcript_id "Phchi.S1G627600.t1"; gene_id "Phchi.S1G627600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13261.t1 is derived from g11726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4966800	4968712	.	+	.	Phchi.S3G058000
Phchi.S3	AUGUSTUS	transcript	4966800	4968712	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	start_codon	4966800	4966802	.	+	0	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4966800	4966984	0.98	+	0	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4966800	4966984	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4966985	4967088	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4967089	4967151	0.99	+	1	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4967089	4967151	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4967152	4967256	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4967257	4967373	1	+	1	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4967257	4967373	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4967374	4967506	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4967507	4967804	1	+	1	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4967507	4967804	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4967805	4967894	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4967895	4968053	1	+	0	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4967895	4968053	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4968054	4968165	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4968166	4968317	1	+	0	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4968166	4968317	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4968318	4968405	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4968406	4968574	1	+	1	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4968406	4968574	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	intron	4968575	4968670	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	CDS	4968671	4968712	1	+	0	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	exon	4968671	4968712	.	+	.	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
Phchi.S3	AUGUSTUS	stop_codon	4968713	4968715	.	+	0	transcript_id "Phchi.S3G058000.t1"; gene_id "Phchi.S3G058000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15869.t1 is derived from g14339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21973383	21978758	.	-	.	Phchi.S3G318800
Phchi.S3	AUGUSTUS	transcript	21973383	21978758	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	stop_codon	21973380	21973382	.	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21973383	21973922	0.93	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21973383	21973922	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21973923	21974063	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21974064	21974162	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21974064	21974162	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21974163	21974254	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21974255	21974385	0.87	-	2	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21974255	21974385	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21974386	21974488	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21974489	21974576	0.98	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21974489	21974576	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21974577	21974725	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21974726	21974851	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21974726	21974851	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21974852	21974994	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21974995	21975174	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21974995	21975174	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21975175	21975356	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21975357	21975474	1	-	1	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21975357	21975474	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21975475	21975713	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21975714	21975901	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21975714	21975901	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21975902	21975982	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21975983	21976083	1	-	2	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21975983	21976083	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21976084	21976232	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21976233	21976281	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21976233	21976281	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21976282	21976422	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21976423	21976511	1	-	2	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21976423	21976511	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21976512	21976650	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21976651	21976801	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21976651	21976801	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21976802	21976945	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21976946	21977047	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21976946	21977047	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21977048	21977183	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21977184	21977298	1	-	1	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21977184	21977298	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21977299	21977392	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21977393	21977781	1	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21977393	21977781	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21977782	21977930	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21977931	21978031	1	-	2	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21977931	21978031	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	intron	21978032	21978169	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	CDS	21978170	21978758	0.56	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	exon	21978170	21978758	.	-	.	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
Phchi.S3	AUGUSTUS	start_codon	21978756	21978758	.	-	0	transcript_id "Phchi.S3G318800.t1"; gene_id "Phchi.S3G318800"
# This transcript jg1652.t2 is derived from g8571.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1653.t1 is derived from g8572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2240789	2242159	.	-	.	Phchi.S5G026200
Phchi.S5	AUGUSTUS	transcript	2240789	2242159	.	-	.	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	stop_codon	2240786	2240788	.	-	0	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	CDS	2240789	2241670	1	-	0	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	exon	2240789	2241670	.	-	.	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	intron	2241671	2241745	.	-	.	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	CDS	2241746	2242159	0.99	-	0	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	exon	2241746	2242159	.	-	.	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
Phchi.S5	AUGUSTUS	start_codon	2242157	2242159	.	-	0	transcript_id "Phchi.S5G026200.t1"; gene_id "Phchi.S5G026200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14251.t1 is derived from g12718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11756824	11757621	.	+	.	Phchi.S3G157000
Phchi.S3	AUGUSTUS	transcript	11756824	11757621	.	+	.	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	start_codon	11756824	11756826	.	+	0	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	CDS	11756824	11757067	1	+	0	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	exon	11756824	11757067	.	+	.	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	intron	11757068	11757133	.	+	.	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	CDS	11757134	11757621	1	+	2	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	exon	11757134	11757621	.	+	.	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
Phchi.S3	AUGUSTUS	stop_codon	11757622	11757624	.	+	0	transcript_id "Phchi.S3G157000.t1"; gene_id "Phchi.S3G157000"
# This transcript jg8688.t2 is derived from g5863.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8689.t1 is derived from g5864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37453506	37455338	.	+	.	Phchi.S1G584800
Phchi.S1	AUGUSTUS	transcript	37453506	37455338	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	start_codon	37453506	37453508	.	+	0	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	CDS	37453506	37453710	0.72	+	0	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	exon	37453506	37453710	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	intron	37453711	37453789	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	CDS	37453790	37453866	0.96	+	2	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	exon	37453790	37453866	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	intron	37453867	37453978	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	CDS	37453979	37454332	0.2	+	0	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	exon	37453979	37454332	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	intron	37454333	37454674	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	CDS	37454675	37455174	0.36	+	0	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	exon	37454675	37455174	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	intron	37455175	37455328	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	CDS	37455329	37455338	0.74	+	1	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	exon	37455329	37455338	.	+	.	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
Phchi.S1	AUGUSTUS	stop_codon	37455339	37455341	.	+	0	transcript_id "Phchi.S1G584800.t1"; gene_id "Phchi.S1G584800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1297.t1 is derived from g11080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8895328	8897191	.	+	.	Phchi.S6G125600
Phchi.S6	AUGUSTUS	transcript	8895328	8897191	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	start_codon	8895328	8895330	.	+	0	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	CDS	8895328	8896016	0.55	+	0	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	exon	8895328	8896016	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	intron	8896017	8896105	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	CDS	8896106	8896644	0.41	+	1	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	exon	8896106	8896644	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	intron	8896645	8896793	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	CDS	8896794	8896813	0.6	+	2	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	exon	8896794	8896813	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	intron	8896814	8896969	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	CDS	8896970	8897019	0.95	+	0	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	exon	8896970	8897019	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	intron	8897020	8897166	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	CDS	8897167	8897191	1	+	1	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	exon	8897167	8897191	.	+	.	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
Phchi.S6	AUGUSTUS	stop_codon	8897192	8897194	.	+	0	transcript_id "Phchi.S6G125600.t1"; gene_id "Phchi.S6G125600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5800.t1 is derived from g2970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19010845	19011997	.	-	.	Phchi.S1G295900
Phchi.S1	AUGUSTUS	transcript	19010845	19011997	.	-	.	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	stop_codon	19010842	19010844	.	-	0	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	CDS	19010845	19011081	1	-	0	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	exon	19010845	19011081	.	-	.	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	intron	19011082	19011199	.	-	.	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	CDS	19011200	19011997	1	-	0	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	exon	19011200	19011997	.	-	.	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
Phchi.S1	AUGUSTUS	start_codon	19011995	19011997	.	-	0	transcript_id "Phchi.S1G295900.t1"; gene_id "Phchi.S1G295900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3279.t1 is derived from g448.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2653106	2655266	.	+	.	Phchi.S1G043800
Phchi.S1	AUGUSTUS	transcript	2653106	2655266	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	start_codon	2653106	2653108	.	+	0	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2653106	2653442	0.99	+	0	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2653106	2653442	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2653443	2654107	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654108	2654183	1	+	2	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654108	2654183	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2654184	2654362	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654363	2654469	1	+	1	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654363	2654469	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2654470	2654658	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654659	2654708	1	+	2	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654659	2654708	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2654709	2654981	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654982	2655064	1	+	0	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654982	2655064	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2655065	2655154	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2655155	2655266	0.99	+	1	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2655155	2655266	.	+	.	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	stop_codon	2655267	2655269	.	+	0	transcript_id "Phchi.S1G043800.t1"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	transcript	2653106	2655266	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	start_codon	2653106	2653108	.	+	0	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2653106	2653442	0.95	+	0	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2653106	2653442	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2653443	2654107	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654108	2654183	1	+	2	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654108	2654183	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2654184	2654362	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654363	2654469	1	+	1	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654363	2654469	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2654470	2654658	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654659	2654708	1	+	2	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654659	2654708	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2654709	2654978	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2654979	2655064	1	+	0	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2654979	2655064	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	intron	2655065	2655154	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	CDS	2655155	2655266	1	+	1	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	exon	2655155	2655266	.	+	.	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
Phchi.S1	AUGUSTUS	stop_codon	2655267	2655269	.	+	0	transcript_id "Phchi.S1G043800.t2"; gene_id "Phchi.S1G043800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13785.t1 is derived from g12252.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8885715	8887795	.	-	.	Phchi.S3G110400
Phchi.S3	AUGUSTUS	transcript	8887059	8887795	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	stop_codon	8887056	8887058	.	-	0	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887059	8887059	1	-	1	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887059	8887059	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8887060	8887201	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887202	8887296	1	-	0	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887202	8887296	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8887297	8887388	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887389	8887502	1	-	0	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887389	8887502	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8887503	8887591	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887592	8887795	1	-	0	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887592	8887795	.	-	.	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	start_codon	8887793	8887795	.	-	0	transcript_id "Phchi.S3G110400.t1"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	transcript	8885715	8887795	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	stop_codon	8885712	8885714	.	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8885715	8886035	1	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8885715	8886035	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8886036	8886150	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8886151	8886461	0.99	-	2	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8886151	8886461	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8886462	8886569	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8886570	8886648	0.99	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8886570	8886648	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8886649	8886744	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8886745	8886818	1	-	2	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8886745	8886818	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8886819	8886902	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8886903	8887009	1	-	1	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8886903	8887009	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8887010	8887201	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887202	8887296	1	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887202	8887296	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8887297	8887388	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887389	8887502	1	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887389	8887502	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	intron	8887503	8887591	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	CDS	8887592	8887795	1	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	exon	8887592	8887795	.	-	.	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
Phchi.S3	AUGUSTUS	start_codon	8887793	8887795	.	-	0	transcript_id "Phchi.S3G110400.t2"; gene_id "Phchi.S3G110400"
# This transcript jg12896.t2 is derived from g11361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12897.t1 is derived from g11362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3059244	3060828	.	-	.	Phchi.S3G021600
Phchi.S3	AUGUSTUS	transcript	3059244	3060828	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	stop_codon	3059241	3059243	.	-	0	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	CDS	3059244	3059252	0.99	-	0	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	exon	3059244	3059252	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	intron	3059253	3059343	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	CDS	3059344	3060068	0.43	-	2	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	exon	3059344	3060068	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	intron	3060069	3060344	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	CDS	3060345	3060385	0.99	-	1	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	exon	3060345	3060385	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	intron	3060386	3060694	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	CDS	3060695	3060726	0.8	-	0	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	exon	3060695	3060726	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	intron	3060727	3060804	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	CDS	3060805	3060828	0.79	-	0	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	exon	3060805	3060828	.	-	.	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
Phchi.S3	AUGUSTUS	start_codon	3060826	3060828	.	-	0	transcript_id "Phchi.S3G021600.t1"; gene_id "Phchi.S3G021600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6875.t1 is derived from g4047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25756684	25760233	.	-	.	Phchi.S1G403400
Phchi.S1	AUGUSTUS	transcript	25756684	25760233	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	stop_codon	25756681	25756683	.	-	0	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25756684	25757234	0.98	-	2	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25756684	25757234	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25757235	25757325	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25757326	25757726	0.6	-	1	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25757326	25757726	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25757727	25757818	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25757819	25758040	0.58	-	1	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25757819	25758040	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25758041	25758129	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25758130	25758227	0.94	-	0	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25758130	25758227	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25758228	25758311	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25758312	25758676	0.98	-	2	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25758312	25758676	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25758677	25758758	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25758759	25758940	0.77	-	1	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25758759	25758940	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25758941	25759035	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25759036	25759147	0.95	-	2	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25759036	25759147	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25759148	25759274	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25759275	25759427	0.95	-	2	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25759275	25759427	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25759428	25759575	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25759576	25759676	0.98	-	1	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25759576	25759676	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25759677	25759864	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25759865	25759962	0.98	-	0	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25759865	25759962	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	intron	25759963	25760080	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	CDS	25760081	25760233	0.95	-	0	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	exon	25760081	25760233	.	-	.	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
Phchi.S1	AUGUSTUS	start_codon	25760231	25760233	.	-	0	transcript_id "Phchi.S1G403400.t1"; gene_id "Phchi.S1G403400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6587.t1 is derived from g3759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23888677	23889958	.	+	.	Phchi.S1G374600
Phchi.S1	AUGUSTUS	transcript	23888677	23889958	.	+	.	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	start_codon	23888677	23888679	.	+	0	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	CDS	23888677	23889162	0.98	+	0	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	exon	23888677	23889162	.	+	.	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	intron	23889163	23889334	.	+	.	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	CDS	23889335	23889958	0.98	+	0	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	exon	23889335	23889958	.	+	.	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
Phchi.S1	AUGUSTUS	stop_codon	23889959	23889961	.	+	0	transcript_id "Phchi.S1G374600.t1"; gene_id "Phchi.S1G374600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7645.t1 is derived from g4819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30383702	30386034	.	+	.	Phchi.S1G480400
Phchi.S1	AUGUSTUS	transcript	30383702	30386034	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	start_codon	30383702	30383704	.	+	0	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30383702	30383711	1	+	0	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30383702	30383711	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30383712	30383861	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30383862	30384432	1	+	2	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30383862	30384432	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30384433	30384505	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30384506	30384687	1	+	1	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30384506	30384687	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30384688	30384775	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30384776	30384950	1	+	2	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30384776	30384950	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30384951	30385053	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30385054	30385256	0.99	+	1	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30385054	30385256	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30385257	30385357	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30385358	30385483	0.99	+	2	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30385358	30385483	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30385484	30385590	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30385591	30385724	1	+	2	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30385591	30385724	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	intron	30385725	30385806	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	CDS	30385807	30386034	0.91	+	0	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	exon	30385807	30386034	.	+	.	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
Phchi.S1	AUGUSTUS	stop_codon	30386035	30386037	.	+	0	transcript_id "Phchi.S1G480400.t1"; gene_id "Phchi.S1G480400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6518.t1 is derived from g3690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23428844	23432275	.	-	.	Phchi.S1G367700
Phchi.S1	AUGUSTUS	transcript	23428844	23432275	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	stop_codon	23428841	23428843	.	-	0	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23428844	23428900	0.42	-	0	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23428844	23428900	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23428901	23429035	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23429036	23429079	0.45	-	2	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23429036	23429079	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23429080	23429257	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23429258	23429303	0.36	-	0	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23429258	23429303	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23429304	23429556	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23429557	23429653	0.36	-	1	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23429557	23429653	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23429654	23429747	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23429748	23429783	0.25	-	1	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23429748	23429783	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23429784	23430056	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23430057	23430273	0.13	-	2	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23430057	23430273	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23430274	23430369	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23430370	23430969	0.26	-	2	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23430370	23430969	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23430970	23431110	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23431111	23431191	0.91	-	2	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23431111	23431191	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23431192	23431425	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23431426	23431533	0.83	-	2	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23431426	23431533	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	intron	23431534	23431782	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	CDS	23431783	23432275	0.38	-	0	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	exon	23431783	23432275	.	-	.	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
Phchi.S1	AUGUSTUS	start_codon	23432273	23432275	.	-	0	transcript_id "Phchi.S1G367700.t1"; gene_id "Phchi.S1G367700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5215.t1 is derived from g2385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15513549	15515617	.	-	.	Phchi.S1G237400
Phchi.S1	AUGUSTUS	transcript	15513549	15515617	.	-	.	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	stop_codon	15513546	15513548	.	-	0	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	CDS	15513549	15514392	0.61	-	1	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	exon	15513549	15514392	.	-	.	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	intron	15514393	15514596	.	-	.	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	CDS	15514597	15515489	0.18	-	0	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	exon	15514597	15515489	.	-	.	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	intron	15515490	15515599	.	-	.	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	CDS	15515600	15515617	0.54	-	0	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	exon	15515600	15515617	.	-	.	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
Phchi.S1	AUGUSTUS	start_codon	15515615	15515617	.	-	0	transcript_id "Phchi.S1G237400.t1"; gene_id "Phchi.S1G237400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7262.t1 is derived from g4434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27910535	27912784	.	-	.	Phchi.S1G442100
Phchi.S1	AUGUSTUS	transcript	27910535	27912784	.	-	.	transcript_id "Phchi.S1G442100.t1"; gene_id "Phchi.S1G442100"
Phchi.S1	AUGUSTUS	stop_codon	27910532	27910534	.	-	0	transcript_id "Phchi.S1G442100.t1"; gene_id "Phchi.S1G442100"
Phchi.S1	AUGUSTUS	CDS	27910535	27912784	0.86	-	0	transcript_id "Phchi.S1G442100.t1"; gene_id "Phchi.S1G442100"
Phchi.S1	AUGUSTUS	exon	27910535	27912784	.	-	.	transcript_id "Phchi.S1G442100.t1"; gene_id "Phchi.S1G442100"
Phchi.S1	AUGUSTUS	start_codon	27912782	27912784	.	-	0	transcript_id "Phchi.S1G442100.t1"; gene_id "Phchi.S1G442100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4058.t1 is derived from g1227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7574683	7575171	.	-	.	Phchi.S1G121700
Phchi.S1	AUGUSTUS	transcript	7574683	7575171	.	-	.	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	stop_codon	7574680	7574682	.	-	0	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	CDS	7574683	7574845	0.54	-	1	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	exon	7574683	7574845	.	-	.	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	intron	7574846	7574986	.	-	.	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	CDS	7574987	7575171	0.53	-	0	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	exon	7574987	7575171	.	-	.	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
Phchi.S1	AUGUSTUS	start_codon	7575169	7575171	.	-	0	transcript_id "Phchi.S1G121700.t1"; gene_id "Phchi.S1G121700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9717.t1 is derived from g6893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43389982	43390803	.	-	.	Phchi.S1G687600
Phchi.S1	AUGUSTUS	transcript	43389982	43390803	.	-	.	transcript_id "Phchi.S1G687600.t1"; gene_id "Phchi.S1G687600"
Phchi.S1	AUGUSTUS	stop_codon	43389979	43389981	.	-	0	transcript_id "Phchi.S1G687600.t1"; gene_id "Phchi.S1G687600"
Phchi.S1	AUGUSTUS	CDS	43389982	43390803	0.41	-	0	transcript_id "Phchi.S1G687600.t1"; gene_id "Phchi.S1G687600"
Phchi.S1	AUGUSTUS	exon	43389982	43390803	.	-	.	transcript_id "Phchi.S1G687600.t1"; gene_id "Phchi.S1G687600"
Phchi.S1	AUGUSTUS	start_codon	43390801	43390803	.	-	0	transcript_id "Phchi.S1G687600.t1"; gene_id "Phchi.S1G687600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1242.t1 is derived from g11025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8596894	8597398	.	-	.	Phchi.S6G120100
Phchi.S6	AUGUSTUS	transcript	8596894	8597398	.	-	.	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	stop_codon	8596891	8596893	.	-	0	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	CDS	8596894	8596994	1	-	2	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	exon	8596894	8596994	.	-	.	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	intron	8596995	8597136	.	-	.	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	CDS	8597137	8597398	0.99	-	0	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	exon	8597137	8597398	.	-	.	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
Phchi.S6	AUGUSTUS	start_codon	8597396	8597398	.	-	0	transcript_id "Phchi.S6G120100.t1"; gene_id "Phchi.S6G120100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7040.t1 is derived from g4212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26546729	26547742	.	+	.	Phchi.S1G419900
Phchi.S1	AUGUSTUS	transcript	26546729	26547742	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	start_codon	26546729	26546731	.	+	0	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	CDS	26546729	26546796	0.94	+	0	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	exon	26546729	26546796	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	intron	26546797	26546921	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	CDS	26546922	26546982	0.94	+	1	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	exon	26546922	26546982	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	intron	26546983	26547129	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	CDS	26547130	26547199	0.48	+	0	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	exon	26547130	26547199	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	intron	26547200	26547324	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	CDS	26547325	26547381	0.81	+	2	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	exon	26547325	26547381	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	intron	26547382	26547467	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	CDS	26547468	26547742	0.24	+	2	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	exon	26547468	26547742	.	+	.	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
Phchi.S1	AUGUSTUS	stop_codon	26547743	26547745	.	+	0	transcript_id "Phchi.S1G419900.t1"; gene_id "Phchi.S1G419900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14514.t1 is derived from g12982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13256741	13263059	.	-	.	Phchi.S3G183300
Phchi.S3	AUGUSTUS	transcript	13256741	13263059	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	stop_codon	13256738	13256740	.	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13256741	13256945	0.83	-	1	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13256741	13256945	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13256946	13257043	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257044	13257135	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257044	13257135	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257136	13257224	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257225	13257373	0.99	-	2	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257225	13257373	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257374	13257482	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257483	13257581	0.99	-	2	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257483	13257581	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257582	13257715	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257716	13257878	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257716	13257878	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257879	13258037	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13258038	13258109	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13258038	13258109	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13258110	13258254	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13258255	13258353	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13258255	13258353	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13258354	13258471	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13258472	13259188	0.98	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13258472	13259188	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13259189	13259380	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13259381	13259485	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13259381	13259485	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13259486	13259734	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13259735	13259852	1	-	1	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13259735	13259852	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13259853	13259981	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13259982	13260047	1	-	1	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13259982	13260047	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260048	13260229	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260230	13260366	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260230	13260366	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260367	13260475	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260476	13260530	0.96	-	1	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260476	13260530	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260531	13260641	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260642	13260703	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260642	13260703	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260704	13260792	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260793	13260849	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260793	13260849	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260850	13260935	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260936	13261100	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260936	13261100	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261101	13261300	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13261301	13261384	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13261301	13261384	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261385	13261597	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13261598	13261837	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13261598	13261837	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261838	13262006	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13262007	13262069	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13262007	13262069	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13262070	13262307	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13262308	13262475	1	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13262308	13262475	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13262476	13262612	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13262613	13263059	0.3	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13262613	13263059	.	-	.	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	start_codon	13263057	13263059	.	-	0	transcript_id "Phchi.S3G183300.t1"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	transcript	13256741	13263059	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	stop_codon	13256738	13256740	.	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13256741	13256945	0.86	-	1	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13256741	13256945	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13256946	13257043	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257044	13257135	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257044	13257135	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257136	13257224	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257225	13257373	0.99	-	2	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257225	13257373	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257374	13257482	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257483	13257581	0.98	-	2	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257483	13257581	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257582	13257715	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13257716	13257878	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13257716	13257878	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13257879	13258037	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13258038	13258109	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13258038	13258109	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13258110	13258254	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13258255	13258353	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13258255	13258353	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13258354	13258471	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13258472	13259188	0.98	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13258472	13259188	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13259189	13259380	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13259381	13259485	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13259381	13259485	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13259486	13259734	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13259735	13259852	1	-	1	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13259735	13259852	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13259853	13259981	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13259982	13260047	1	-	1	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13259982	13260047	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260048	13260229	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260230	13260366	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260230	13260366	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260367	13260475	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260476	13260530	0.93	-	1	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260476	13260530	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260531	13260641	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260642	13260703	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260642	13260703	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260704	13260792	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260793	13260849	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260793	13260849	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13260850	13260935	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13260936	13261100	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13260936	13261100	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261101	13261300	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13261301	13261412	0.97	-	1	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13261301	13261412	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261413	13261597	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13261598	13261616	0.97	-	2	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13261598	13261616	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261617	13261713	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13261714	13261837	0.88	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13261714	13261837	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13261838	13262006	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13262007	13262069	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13262007	13262069	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13262070	13262307	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13262308	13262475	1	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13262308	13262475	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	intron	13262476	13262612	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	CDS	13262613	13263059	0.4	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	exon	13262613	13263059	.	-	.	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
Phchi.S3	AUGUSTUS	start_codon	13263057	13263059	.	-	0	transcript_id "Phchi.S3G183300.t2"; gene_id "Phchi.S3G183300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14806.t1 is derived from g13274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14799255	14801011	.	-	.	Phchi.S3G212500
Phchi.S3	AUGUSTUS	transcript	14799255	14801011	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	stop_codon	14799252	14799254	.	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14799255	14799359	0.96	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14799255	14799359	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14799360	14799454	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14799455	14799535	1	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14799455	14799535	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14799536	14799716	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14799717	14799866	1	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14799717	14799866	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14799867	14799959	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14799960	14800009	1	-	2	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14799960	14800009	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14800010	14800091	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14800092	14800140	1	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14800092	14800140	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14800141	14800264	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14800265	14800342	1	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14800265	14800342	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14800343	14800429	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14800430	14800508	0.98	-	1	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14800430	14800508	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14800509	14800610	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14800611	14800700	0.98	-	1	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14800611	14800700	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	intron	14800701	14800787	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	CDS	14800788	14801011	0.43	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	exon	14800788	14801011	.	-	.	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
Phchi.S3	AUGUSTUS	start_codon	14801009	14801011	.	-	0	transcript_id "Phchi.S3G212500.t1"; gene_id "Phchi.S3G212500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8671.t1 is derived from g5846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37366445	37368298	.	-	.	Phchi.S1G583000
Phchi.S1	AUGUSTUS	transcript	37366445	37368298	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	stop_codon	37366442	37366444	.	-	0	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	CDS	37366445	37366846	1	-	0	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	exon	37366445	37366846	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	intron	37366847	37366938	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	CDS	37366939	37367217	1	-	0	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	exon	37366939	37367217	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	intron	37367218	37367312	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	CDS	37367313	37367612	1	-	0	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	exon	37367313	37367612	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	intron	37367613	37367698	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	CDS	37367699	37367865	1	-	2	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	exon	37367699	37367865	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	intron	37367866	37367979	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	CDS	37367980	37368298	0.97	-	0	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	exon	37367980	37368298	.	-	.	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
Phchi.S1	AUGUSTUS	start_codon	37368296	37368298	.	-	0	transcript_id "Phchi.S1G583000.t1"; gene_id "Phchi.S1G583000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13607.t1 is derived from g12074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7676536	7678830	.	-	.	Phchi.S3G092600
Phchi.S3	AUGUSTUS	transcript	7676536	7678830	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	stop_codon	7676533	7676535	.	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7676536	7676568	0.89	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7676536	7676568	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7676569	7676767	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7676768	7676886	1	-	2	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7676768	7676886	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7676887	7676964	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7676965	7677155	1	-	1	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7676965	7677155	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677156	7677278	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677279	7677388	1	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677279	7677388	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677389	7677488	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677489	7677545	1	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677489	7677545	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677546	7677623	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677624	7677747	1	-	1	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677624	7677747	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677748	7677839	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677840	7677901	1	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677840	7677901	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677902	7677988	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677989	7678075	1	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677989	7678075	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7678076	7678171	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7678172	7678256	1	-	1	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7678172	7678256	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7678257	7678348	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7678349	7678830	0.95	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7678349	7678830	.	-	.	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	start_codon	7678828	7678830	.	-	0	transcript_id "Phchi.S3G092600.t1"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	transcript	7676536	7678830	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	stop_codon	7676533	7676535	.	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7676536	7676568	0.79	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7676536	7676568	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7676569	7676767	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7676768	7676886	1	-	2	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7676768	7676886	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7676887	7676964	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7676965	7677155	1	-	1	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7676965	7677155	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677156	7677278	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677279	7677388	1	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677279	7677388	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677389	7677488	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677489	7677545	1	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677489	7677545	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677546	7677623	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677624	7677747	1	-	1	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677624	7677747	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677748	7677839	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677840	7677901	1	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677840	7677901	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7677902	7677988	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7677989	7678078	1	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7677989	7678078	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7678079	7678171	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7678172	7678256	1	-	1	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7678172	7678256	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	intron	7678257	7678348	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	CDS	7678349	7678830	0.95	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	exon	7678349	7678830	.	-	.	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
Phchi.S3	AUGUSTUS	start_codon	7678828	7678830	.	-	0	transcript_id "Phchi.S3G092600.t2"; gene_id "Phchi.S3G092600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6381.t1 is derived from g3553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22653253	22655080	.	+	.	Phchi.S1G354000
Phchi.S1	AUGUSTUS	transcript	22653253	22655080	.	+	.	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	start_codon	22653253	22653255	.	+	0	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	CDS	22653253	22653671	1	+	0	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	exon	22653253	22653671	.	+	.	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	intron	22653672	22653766	.	+	.	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	CDS	22653767	22654306	0.72	+	1	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	exon	22653767	22654306	.	+	.	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	intron	22654307	22654449	.	+	.	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	CDS	22654450	22655080	0.72	+	1	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	exon	22654450	22655080	.	+	.	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
Phchi.S1	AUGUSTUS	stop_codon	22655081	22655083	.	+	0	transcript_id "Phchi.S1G354000.t1"; gene_id "Phchi.S1G354000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15799.t1 is derived from g14269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21427105	21427534	.	+	.	Phchi.S3G311800
Phchi.S3	AUGUSTUS	transcript	21427105	21427534	.	+	.	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	start_codon	21427105	21427107	.	+	0	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	CDS	21427105	21427219	0.71	+	0	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	exon	21427105	21427219	.	+	.	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	intron	21427220	21427376	.	+	.	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	CDS	21427377	21427534	0.55	+	2	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	exon	21427377	21427534	.	+	.	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
Phchi.S3	AUGUSTUS	stop_codon	21427535	21427537	.	+	0	transcript_id "Phchi.S3G311800.t1"; gene_id "Phchi.S3G311800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9776.t1 is derived from g6952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43622805	43623437	.	-	.	Phchi.S1G693500
Phchi.S1	AUGUSTUS	transcript	43622805	43623437	.	-	.	transcript_id "Phchi.S1G693500.t1"; gene_id "Phchi.S1G693500"
Phchi.S1	AUGUSTUS	stop_codon	43622802	43622804	.	-	0	transcript_id "Phchi.S1G693500.t1"; gene_id "Phchi.S1G693500"
Phchi.S1	AUGUSTUS	CDS	43622805	43623437	0.93	-	0	transcript_id "Phchi.S1G693500.t1"; gene_id "Phchi.S1G693500"
Phchi.S1	AUGUSTUS	exon	43622805	43623437	.	-	.	transcript_id "Phchi.S1G693500.t1"; gene_id "Phchi.S1G693500"
Phchi.S1	AUGUSTUS	start_codon	43623435	43623437	.	-	0	transcript_id "Phchi.S1G693500.t1"; gene_id "Phchi.S1G693500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11325.t1 is derived from g15375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5377152	5378250	.	-	.	Phchi.S4G090700
Phchi.S4	AUGUSTUS	transcript	5377152	5378250	.	-	.	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	stop_codon	5377149	5377151	.	-	0	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	CDS	5377152	5377880	0.8	-	0	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	exon	5377152	5377880	.	-	.	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	intron	5377881	5377993	.	-	.	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	CDS	5377994	5378037	0.95	-	2	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	exon	5377994	5378037	.	-	.	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	intron	5378038	5378132	.	-	.	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	CDS	5378133	5378250	0.92	-	0	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	exon	5378133	5378250	.	-	.	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
Phchi.S4	AUGUSTUS	start_codon	5378248	5378250	.	-	0	transcript_id "Phchi.S4G090700.t1"; gene_id "Phchi.S4G090700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6104.t1 is derived from g3275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20965038	20968514	.	-	.	Phchi.S1G326300
Phchi.S1	AUGUSTUS	transcript	20965038	20968514	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	stop_codon	20965035	20965037	.	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20965038	20965286	0.67	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20965038	20965286	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20965287	20965368	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20965369	20965421	0.7	-	2	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20965369	20965421	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20965422	20965510	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20965511	20965649	1	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20965511	20965649	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20965650	20965739	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20965740	20965892	0.99	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20965740	20965892	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20965893	20965998	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20965999	20966174	0.91	-	2	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20965999	20966174	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20966175	20966263	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20966264	20966412	1	-	1	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20966264	20966412	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20966413	20966506	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20966507	20967081	1	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20966507	20967081	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20967082	20967157	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20967158	20967598	1	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20967158	20967598	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20967599	20967728	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20967729	20968028	1	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20967729	20968028	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20968029	20968158	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20968159	20968258	1	-	1	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20968159	20968258	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	intron	20968259	20968353	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	CDS	20968354	20968514	0.63	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	exon	20968354	20968514	.	-	.	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
Phchi.S1	AUGUSTUS	start_codon	20968512	20968514	.	-	0	transcript_id "Phchi.S1G326300.t1"; gene_id "Phchi.S1G326300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14086.t1 is derived from g12553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10789434	10791509	.	+	.	Phchi.S3G140500
Phchi.S3	AUGUSTUS	transcript	10789434	10791509	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	start_codon	10789434	10789436	.	+	0	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	CDS	10789434	10789740	0.61	+	0	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	exon	10789434	10789740	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	intron	10789741	10789838	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	CDS	10789839	10789958	0.95	+	2	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	exon	10789839	10789958	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	intron	10789959	10790066	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	CDS	10790067	10790767	1	+	2	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	exon	10790067	10790767	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	intron	10790768	10790861	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	CDS	10790862	10791509	0.95	+	0	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	exon	10790862	10791509	.	+	.	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
Phchi.S3	AUGUSTUS	stop_codon	10791510	10791512	.	+	0	transcript_id "Phchi.S3G140500.t1"; gene_id "Phchi.S3G140500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3443.t1 is derived from g612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3752063	3752946	.	-	.	Phchi.S1G060200
Phchi.S1	AUGUSTUS	transcript	3752063	3752946	.	-	.	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	stop_codon	3752060	3752062	.	-	0	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	CDS	3752063	3752748	0.91	-	2	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	exon	3752063	3752748	.	-	.	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	intron	3752749	3752846	.	-	.	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	CDS	3752847	3752946	0.27	-	0	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	exon	3752847	3752946	.	-	.	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
Phchi.S1	AUGUSTUS	start_codon	3752944	3752946	.	-	0	transcript_id "Phchi.S1G060200.t1"; gene_id "Phchi.S1G060200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5789.t1 is derived from g2959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18965048	18966357	.	-	.	Phchi.S1G294800
Phchi.S1	AUGUSTUS	transcript	18965048	18966357	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	stop_codon	18965045	18965047	.	-	0	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	CDS	18965048	18965112	0.73	-	2	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	exon	18965048	18965112	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	intron	18965113	18965189	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	CDS	18965190	18965337	0.73	-	0	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	exon	18965190	18965337	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	intron	18965338	18965545	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	CDS	18965546	18965860	0.85	-	0	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	exon	18965546	18965860	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	intron	18965861	18965956	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	CDS	18965957	18966093	0.87	-	2	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	exon	18965957	18966093	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	intron	18966094	18966176	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	CDS	18966177	18966357	0.75	-	0	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	exon	18966177	18966357	.	-	.	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
Phchi.S1	AUGUSTUS	start_codon	18966355	18966357	.	-	0	transcript_id "Phchi.S1G294800.t1"; gene_id "Phchi.S1G294800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11701.t1 is derived from g15752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7763400	7764474	.	-	.	Phchi.S4G128300
Phchi.S4	AUGUSTUS	transcript	7763400	7764474	.	-	.	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	stop_codon	7763397	7763399	.	-	0	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	CDS	7763400	7763627	1	-	0	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	exon	7763400	7763627	.	-	.	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	intron	7763628	7764258	.	-	.	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	CDS	7764259	7764474	0.85	-	0	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	exon	7764259	7764474	.	-	.	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
Phchi.S4	AUGUSTUS	start_codon	7764472	7764474	.	-	0	transcript_id "Phchi.S4G128300.t1"; gene_id "Phchi.S4G128300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14491.t1 is derived from g12959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13122359	13125059	.	-	.	Phchi.S3G181000
Phchi.S3	AUGUSTUS	transcript	13122359	13125059	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	stop_codon	13122356	13122358	.	-	0	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13122359	13122600	0.44	-	2	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13122359	13122600	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13122601	13122684	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13122685	13122989	1	-	1	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13122685	13122989	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13122990	13123218	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13123219	13123437	1	-	1	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13123219	13123437	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13123438	13123578	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13123579	13123972	0.98	-	2	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13123579	13123972	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13123973	13124099	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13124100	13124280	0.99	-	0	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13124100	13124280	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13124281	13124462	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13124463	13124615	1	-	0	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13124463	13124615	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13124616	13124699	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13124700	13124828	1	-	0	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13124700	13124828	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13124829	13125023	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13125024	13125059	0.72	-	0	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13125024	13125059	.	-	.	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	start_codon	13125057	13125059	.	-	0	transcript_id "Phchi.S3G181000.t1"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	transcript	13122359	13125059	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	stop_codon	13122356	13122358	.	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13122359	13122600	0.44	-	2	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13122359	13122600	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13122601	13122684	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13122685	13122843	0.56	-	2	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13122685	13122843	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13122844	13122916	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13122917	13122989	0.91	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13122917	13122989	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13122990	13123226	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13123227	13123437	1	-	1	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13123227	13123437	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13123438	13123578	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13123579	13123972	0.97	-	2	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13123579	13123972	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13123973	13124099	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13124100	13124280	1	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13124100	13124280	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13124281	13124462	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13124463	13124615	1	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13124463	13124615	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13124616	13124699	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13124700	13124828	1	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13124700	13124828	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	intron	13124829	13125023	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	CDS	13125024	13125059	0.69	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	exon	13125024	13125059	.	-	.	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
Phchi.S3	AUGUSTUS	start_codon	13125057	13125059	.	-	0	transcript_id "Phchi.S3G181000.t2"; gene_id "Phchi.S3G181000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12864.t1 is derived from g11329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2814364	2815562	.	+	.	Phchi.S3G018300
Phchi.S3	AUGUSTUS	transcript	2814364	2815562	.	+	.	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	start_codon	2814364	2814366	.	+	0	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	CDS	2814364	2814904	0.55	+	0	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	exon	2814364	2814904	.	+	.	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	intron	2814905	2815135	.	+	.	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	CDS	2815136	2815426	0.16	+	2	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	exon	2815136	2815426	.	+	.	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	intron	2815427	2815518	.	+	.	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	CDS	2815519	2815562	0.23	+	2	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	exon	2815519	2815562	.	+	.	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
Phchi.S3	AUGUSTUS	stop_codon	2815563	2815565	.	+	0	transcript_id "Phchi.S3G018300.t1"; gene_id "Phchi.S3G018300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2548.t1 is derived from g9468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7272551	7274020	.	+	.	Phchi.S5G115700
Phchi.S5	AUGUSTUS	transcript	7272551	7274020	.	+	.	transcript_id "Phchi.S5G115700.t1"; gene_id "Phchi.S5G115700"
Phchi.S5	AUGUSTUS	start_codon	7272551	7272553	.	+	0	transcript_id "Phchi.S5G115700.t1"; gene_id "Phchi.S5G115700"
Phchi.S5	AUGUSTUS	CDS	7272551	7274020	0.33	+	0	transcript_id "Phchi.S5G115700.t1"; gene_id "Phchi.S5G115700"
Phchi.S5	AUGUSTUS	exon	7272551	7274020	.	+	.	transcript_id "Phchi.S5G115700.t1"; gene_id "Phchi.S5G115700"
Phchi.S5	AUGUSTUS	stop_codon	7274021	7274023	.	+	0	transcript_id "Phchi.S5G115700.t1"; gene_id "Phchi.S5G115700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13970.t1 is derived from g12437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9996821	9998860	.	+	.	Phchi.S3G128900
Phchi.S3	AUGUSTUS	transcript	9996821	9998860	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	start_codon	9996821	9996823	.	+	0	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	CDS	9996821	9996972	0.31	+	0	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	exon	9996821	9996972	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	intron	9996973	9997191	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	CDS	9997192	9997369	0.36	+	1	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	exon	9997192	9997369	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	intron	9997370	9997462	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	CDS	9997463	9997609	0.55	+	0	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	exon	9997463	9997609	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	intron	9997610	9997684	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	CDS	9997685	9998860	0.5	+	0	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	exon	9997685	9998860	.	+	.	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
Phchi.S3	AUGUSTUS	stop_codon	9998861	9998863	.	+	0	transcript_id "Phchi.S3G128900.t1"; gene_id "Phchi.S3G128900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8221.t1 is derived from g5396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34531477	34532982	.	+	.	Phchi.S1G538000
Phchi.S1	AUGUSTUS	transcript	34531477	34532982	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	start_codon	34531477	34531479	.	+	0	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	CDS	34531477	34531722	0.63	+	0	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	exon	34531477	34531722	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	intron	34531723	34531922	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	CDS	34531923	34532015	0.98	+	0	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	exon	34531923	34532015	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	intron	34532016	34532158	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	CDS	34532159	34532468	0.55	+	0	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	exon	34532159	34532468	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	intron	34532469	34532575	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	CDS	34532576	34532982	0.99	+	2	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	exon	34532576	34532982	.	+	.	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
Phchi.S1	AUGUSTUS	stop_codon	34532983	34532985	.	+	0	transcript_id "Phchi.S1G538000.t1"; gene_id "Phchi.S1G538000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13809.t1 is derived from g12276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9020308	9021428	.	-	.	Phchi.S3G112800
Phchi.S3	AUGUSTUS	transcript	9020308	9021428	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	stop_codon	9020305	9020307	.	-	0	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	CDS	9020308	9020721	1	-	0	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	exon	9020308	9020721	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	intron	9020722	9020871	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	CDS	9020872	9020978	1	-	2	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	exon	9020872	9020978	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	intron	9020979	9021071	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	CDS	9021072	9021140	1	-	2	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	exon	9021072	9021140	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	intron	9021141	9021286	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	CDS	9021287	9021428	1	-	0	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	exon	9021287	9021428	.	-	.	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
Phchi.S3	AUGUSTUS	start_codon	9021426	9021428	.	-	0	transcript_id "Phchi.S3G112800.t1"; gene_id "Phchi.S3G112800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5305.t1 is derived from g2475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16170944	16175401	.	+	.	Phchi.S1G246400
Phchi.S1	AUGUSTUS	transcript	16170944	16175401	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	start_codon	16170944	16170946	.	+	0	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16170944	16171037	0.5	+	0	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16170944	16171037	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16171038	16171135	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16171136	16171449	1	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16171136	16171449	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16171450	16171528	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16171529	16171788	1	+	0	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16171529	16171788	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16171789	16171897	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16171898	16172158	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16171898	16172158	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16172159	16172243	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16172244	16172467	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16172244	16172467	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16172468	16172576	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16172577	16172703	1	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16172577	16172703	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16172704	16172808	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16172809	16172883	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16172809	16172883	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16172884	16172975	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16172976	16173047	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16172976	16173047	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16173048	16173165	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16173166	16173228	0.99	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16173166	16173228	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16173229	16173378	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16173379	16173444	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16173379	16173444	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16173445	16173535	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16173536	16173765	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16173536	16173765	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16173766	16173899	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16173900	16173938	1	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16173900	16173938	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16173939	16174057	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16174058	16174126	0.85	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16174058	16174126	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16174127	16174221	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16174222	16174347	1	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16174222	16174347	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16174348	16174442	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16174443	16174508	1	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16174443	16174508	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16174509	16174588	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16174589	16174634	1	+	2	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16174589	16174634	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16174635	16174717	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16174718	16174864	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16174718	16174864	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16174865	16174950	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16174951	16175089	1	+	1	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16174951	16175089	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	intron	16175090	16175179	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	CDS	16175180	16175401	1	+	0	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	exon	16175180	16175401	.	+	.	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
Phchi.S1	AUGUSTUS	stop_codon	16175402	16175404	.	+	0	transcript_id "Phchi.S1G246400.t1"; gene_id "Phchi.S1G246400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1528.t1 is derived from g8447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1599517	1604975	.	+	.	Phchi.S5G013700
Phchi.S5	AUGUSTUS	transcript	1599830	1604975	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	start_codon	1599830	1599832	.	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1599830	1600561	0.51	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1599830	1600561	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1600562	1601015	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601016	1601104	1	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601016	1601104	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601105	1601266	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601267	1601352	1	+	1	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601267	1601352	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601353	1601444	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601445	1601607	1	+	2	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601445	1601607	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601608	1601732	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601733	1601856	1	+	1	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601733	1601856	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601857	1601942	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601943	1602100	1	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601943	1602100	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602101	1602292	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1602293	1602377	1	+	1	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1602293	1602377	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602378	1602512	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1602513	1602725	1	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1602513	1602725	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602726	1602841	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1602842	1602903	1	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1602842	1602903	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602904	1603036	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1603037	1604975	1	+	1	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1603037	1604975	.	+	.	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	stop_codon	1604976	1604978	.	+	0	transcript_id "Phchi.S5G013700.t1"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	transcript	1599517	1604975	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	start_codon	1599517	1599519	.	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1599517	1599794	0.7	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1599517	1599794	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1599795	1599906	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1599907	1600216	0.42	+	1	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1599907	1600216	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1600217	1600301	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1600302	1600342	0.73	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1600302	1600342	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1600343	1600493	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1600494	1600561	0.91	+	1	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1600494	1600561	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1600562	1600707	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1600708	1600793	0.99	+	2	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1600708	1600793	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1600794	1601015	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601016	1601104	1	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601016	1601104	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601105	1601266	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601267	1601352	1	+	1	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601267	1601352	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601353	1601444	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601445	1601607	1	+	2	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601445	1601607	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601608	1601732	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601733	1601856	1	+	1	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601733	1601856	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1601857	1601942	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1601943	1602100	1	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1601943	1602100	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602101	1602292	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1602293	1602377	1	+	1	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1602293	1602377	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602378	1602512	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1602513	1602725	1	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1602513	1602725	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602726	1602841	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1602842	1602903	1	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1602842	1602903	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	intron	1602904	1603036	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	CDS	1603037	1604975	1	+	1	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	exon	1603037	1604975	.	+	.	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
Phchi.S5	AUGUSTUS	stop_codon	1604976	1604978	.	+	0	transcript_id "Phchi.S5G013700.t2"; gene_id "Phchi.S5G013700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14606.t1 is derived from g13074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13730055	13732142	.	+	.	Phchi.S3G192500
Phchi.S3	AUGUSTUS	transcript	13730055	13732142	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	start_codon	13730055	13730057	.	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13730055	13730132	0.99	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13730055	13730132	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13730133	13730271	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13730272	13730343	0.96	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13730272	13730343	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13730344	13730455	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13730456	13730545	1	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13730456	13730545	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13730546	13730803	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13730804	13730846	1	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13730804	13730846	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13730847	13730954	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13730955	13731061	1	+	2	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13730955	13731061	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13731062	13731159	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13731160	13731255	1	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13731160	13731255	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13731256	13731479	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13731480	13731670	1	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13731480	13731670	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13731671	13731792	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13731793	13731862	1	+	1	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13731793	13731862	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	intron	13731863	13731983	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	CDS	13731984	13732142	0.99	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	exon	13731984	13732142	.	+	.	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
Phchi.S3	AUGUSTUS	stop_codon	13732143	13732145	.	+	0	transcript_id "Phchi.S3G192500.t1"; gene_id "Phchi.S3G192500"
# This transcript jg6885.t2 is derived from g4057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6886.t1 is derived from g4058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25826844	25828243	.	+	.	Phchi.S1G404500
Phchi.S1	AUGUSTUS	transcript	25826844	25828243	.	+	.	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	start_codon	25826844	25826846	.	+	0	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	CDS	25826844	25826957	0.48	+	0	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	exon	25826844	25826957	.	+	.	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	intron	25826958	25827101	.	+	.	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	CDS	25827102	25827203	0.72	+	0	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	exon	25827102	25827203	.	+	.	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	intron	25827204	25827295	.	+	.	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	CDS	25827296	25828243	1	+	0	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	exon	25827296	25828243	.	+	.	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
Phchi.S1	AUGUSTUS	stop_codon	25828244	25828246	.	+	0	transcript_id "Phchi.S1G404500.t1"; gene_id "Phchi.S1G404500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3892.t1 is derived from g1061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6273041	6274441	.	-	.	Phchi.S1G105100
Phchi.S1	AUGUSTUS	transcript	6273041	6274441	.	-	.	transcript_id "Phchi.S1G105100.t1"; gene_id "Phchi.S1G105100"
Phchi.S1	AUGUSTUS	stop_codon	6273038	6273040	.	-	0	transcript_id "Phchi.S1G105100.t1"; gene_id "Phchi.S1G105100"
Phchi.S1	AUGUSTUS	CDS	6273041	6274441	0.96	-	0	transcript_id "Phchi.S1G105100.t1"; gene_id "Phchi.S1G105100"
Phchi.S1	AUGUSTUS	exon	6273041	6274441	.	-	.	transcript_id "Phchi.S1G105100.t1"; gene_id "Phchi.S1G105100"
Phchi.S1	AUGUSTUS	start_codon	6274439	6274441	.	-	0	transcript_id "Phchi.S1G105100.t1"; gene_id "Phchi.S1G105100"
# This transcript jg8268.t2 is derived from g5443.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8269.t1 is derived from g5444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35046411	35048169	.	+	.	Phchi.S1G542800
Phchi.S1	AUGUSTUS	transcript	35046411	35048169	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	start_codon	35046411	35046413	.	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	CDS	35046411	35046752	0.97	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	exon	35046411	35046752	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	intron	35046753	35046828	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	CDS	35046829	35047182	0.98	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	exon	35046829	35047182	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	intron	35047183	35047260	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	CDS	35047261	35047842	0.83	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	exon	35047261	35047842	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	intron	35047843	35047931	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	CDS	35047932	35047955	0.82	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	exon	35047932	35047955	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	intron	35047956	35048097	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	CDS	35048098	35048169	0.57	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	exon	35048098	35048169	.	+	.	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
Phchi.S1	AUGUSTUS	stop_codon	35048170	35048172	.	+	0	transcript_id "Phchi.S1G542800.t1"; gene_id "Phchi.S1G542800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14555.t1 is derived from g13023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13451336	13453929	.	+	.	Phchi.S3G187400
Phchi.S3	AUGUSTUS	transcript	13451336	13453929	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	start_codon	13451336	13451338	.	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13451336	13451814	0.95	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13451336	13451814	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13451815	13452007	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13452008	13452136	1	+	1	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13452008	13452136	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13452137	13452318	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13452319	13452421	1	+	1	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13452319	13452421	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13452422	13452539	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13452540	13452650	1	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13452540	13452650	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13452651	13452750	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13452751	13452830	1	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13452751	13452830	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13452831	13452928	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13452929	13452982	1	+	1	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13452929	13452982	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13452983	13453083	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13453084	13453200	1	+	1	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13453084	13453200	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13453201	13453403	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13453404	13453458	1	+	1	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13453404	13453458	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13453459	13453542	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13453543	13453575	1	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13453543	13453575	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13453576	13453716	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13453717	13453763	1	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13453717	13453763	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	intron	13453764	13453856	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	CDS	13453857	13453929	1	+	1	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	exon	13453857	13453929	.	+	.	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
Phchi.S3	AUGUSTUS	stop_codon	13453930	13453932	.	+	0	transcript_id "Phchi.S3G187400.t1"; gene_id "Phchi.S3G187400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6223.t1 is derived from g3395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21759660	21762379	.	+	.	Phchi.S1G338200
Phchi.S1	AUGUSTUS	transcript	21759660	21762379	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	start_codon	21759660	21759662	.	+	0	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	CDS	21759660	21759704	0.77	+	0	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	exon	21759660	21759704	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	intron	21759705	21759854	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	CDS	21759855	21759962	0.91	+	0	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	exon	21759855	21759962	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	intron	21759963	21760043	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	CDS	21760044	21760123	1	+	0	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	exon	21760044	21760123	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	intron	21760124	21760203	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	CDS	21760204	21760286	0.6	+	1	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	exon	21760204	21760286	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	intron	21760287	21760503	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	CDS	21760504	21760727	0.42	+	2	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	exon	21760504	21760727	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	intron	21760728	21760834	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	CDS	21760835	21762379	0.79	+	0	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	exon	21760835	21762379	.	+	.	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
Phchi.S1	AUGUSTUS	stop_codon	21762380	21762382	.	+	0	transcript_id "Phchi.S1G338200.t1"; gene_id "Phchi.S1G338200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12477.t1 is derived from g8154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	27487242	27490923	.	-	.	Phchi.S2G055700
Phchi.S2	AUGUSTUS	transcript	27487242	27490923	.	-	.	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	stop_codon	27487239	27487241	.	-	0	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	CDS	27487242	27487421	0.99	-	0	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	exon	27487242	27487421	.	-	.	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	intron	27487422	27489799	.	-	.	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	CDS	27489800	27489866	0.72	-	1	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	exon	27489800	27489866	.	-	.	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	intron	27489867	27490888	.	-	.	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	CDS	27490889	27490923	0.01	-	0	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	exon	27490889	27490923	.	-	.	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
Phchi.S2	AUGUSTUS	start_codon	27490921	27490923	.	-	0	transcript_id "Phchi.S2G055700.t1"; gene_id "Phchi.S2G055700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2141.t1 is derived from g9061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5033170	5036275	.	+	.	Phchi.S5G075000
Phchi.S5	AUGUSTUS	transcript	5033170	5036275	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	start_codon	5033170	5033172	.	+	0	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5033170	5033284	0.95	+	0	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5033170	5033284	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5033285	5033362	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5033363	5033442	1	+	2	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5033363	5033442	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5033443	5033515	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5033516	5033628	1	+	0	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5033516	5033628	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5033629	5033713	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5033714	5033771	0.68	+	1	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5033714	5033771	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5033772	5033906	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5033907	5034303	0.92	+	0	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5033907	5034303	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5034304	5034792	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5034793	5035804	0.63	+	2	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5034793	5035804	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5035805	5035893	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5035894	5035933	0.65	+	1	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5035894	5035933	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5035934	5036077	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5036078	5036168	1	+	0	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5036078	5036168	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	intron	5036169	5036258	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	CDS	5036259	5036275	1	+	2	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	exon	5036259	5036275	.	+	.	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
Phchi.S5	AUGUSTUS	stop_codon	5036276	5036278	.	+	0	transcript_id "Phchi.S5G075000.t1"; gene_id "Phchi.S5G075000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12839.t1 is derived from g11304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2643200	2644512	.	+	.	Phchi.S3G015800
Phchi.S3	AUGUSTUS	transcript	2643200	2644512	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	start_codon	2643200	2643202	.	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	CDS	2643200	2643421	0.99	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	exon	2643200	2643421	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	intron	2643422	2643563	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	CDS	2643564	2643647	1	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	exon	2643564	2643647	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	intron	2643648	2643740	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	CDS	2643741	2643806	1	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	exon	2643741	2643806	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	intron	2643807	2643926	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	CDS	2643927	2643989	1	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	exon	2643927	2643989	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	intron	2643990	2644113	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	CDS	2644114	2644354	0.99	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	exon	2644114	2644354	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	intron	2644355	2644444	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	CDS	2644445	2644512	0.99	+	2	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	exon	2644445	2644512	.	+	.	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
Phchi.S3	AUGUSTUS	stop_codon	2644513	2644515	.	+	0	transcript_id "Phchi.S3G015800.t1"; gene_id "Phchi.S3G015800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6108.t1 is derived from g3279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20977498	20978702	.	+	.	Phchi.S1G326700
Phchi.S1	AUGUSTUS	transcript	20977498	20978702	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	start_codon	20977498	20977500	.	+	0	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	CDS	20977498	20977720	0.35	+	0	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	exon	20977498	20977720	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	intron	20977721	20977826	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	CDS	20977827	20977878	0.35	+	2	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	exon	20977827	20977878	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	intron	20977879	20978063	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	CDS	20978064	20978504	0.46	+	1	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	exon	20978064	20978504	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	intron	20978505	20978701	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	CDS	20978702	20978702	1	+	1	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	exon	20978702	20978702	.	+	.	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
Phchi.S1	AUGUSTUS	stop_codon	20978703	20978705	.	+	0	transcript_id "Phchi.S1G326700.t1"; gene_id "Phchi.S1G326700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10382.t1 is derived from g7558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47482847	47484842	.	+	.	Phchi.S1G754100
Phchi.S1	AUGUSTUS	transcript	47482847	47484842	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	start_codon	47482847	47482849	.	+	0	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	CDS	47482847	47483110	0.75	+	0	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	exon	47482847	47483110	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	intron	47483111	47483250	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	CDS	47483251	47483811	0.46	+	0	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	exon	47483251	47483811	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	intron	47483812	47483940	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	CDS	47483941	47484136	0.1	+	0	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	exon	47483941	47484136	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	intron	47484137	47484265	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	CDS	47484266	47484696	0.18	+	2	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	exon	47484266	47484696	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	intron	47484697	47484836	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	CDS	47484837	47484842	0.45	+	0	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	exon	47484837	47484842	.	+	.	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
Phchi.S1	AUGUSTUS	stop_codon	47484843	47484845	.	+	0	transcript_id "Phchi.S1G754100.t1"; gene_id "Phchi.S1G754100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2869.t1 is derived from g38.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	196885	198281	.	+	.	Phchi.S1G002800
Phchi.S1	AUGUSTUS	transcript	196885	198281	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	start_codon	196885	196887	.	+	0	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	196885	196952	0.35	+	0	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	196885	196952	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	intron	196953	197109	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	197110	197115	0.44	+	1	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	197110	197115	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	intron	197116	197194	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	197195	197208	0.44	+	1	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	197195	197208	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	intron	197209	197478	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	197479	197628	1	+	2	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	197479	197628	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	intron	197629	197747	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	197748	197845	0.97	+	2	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	197748	197845	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	intron	197846	197948	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	197949	198023	0.98	+	0	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	197949	198023	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	intron	198024	198263	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	CDS	198264	198281	0.98	+	0	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	exon	198264	198281	.	+	.	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
Phchi.S1	AUGUSTUS	stop_codon	198282	198284	.	+	0	transcript_id "Phchi.S1G002800.t1"; gene_id "Phchi.S1G002800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3226.t1 is derived from g395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2353435	2354441	.	-	.	Phchi.S1G038500
Phchi.S1	AUGUSTUS	transcript	2353435	2354441	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	stop_codon	2353432	2353434	.	-	0	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	CDS	2353435	2353566	0.57	-	0	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	exon	2353435	2353566	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	intron	2353567	2353677	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	CDS	2353678	2353803	0.96	-	0	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	exon	2353678	2353803	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	intron	2353804	2353997	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	CDS	2353998	2354051	1	-	0	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	exon	2353998	2354051	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	intron	2354052	2354192	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	CDS	2354193	2354441	1	-	0	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	exon	2354193	2354441	.	-	.	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
Phchi.S1	AUGUSTUS	start_codon	2354439	2354441	.	-	0	transcript_id "Phchi.S1G038500.t1"; gene_id "Phchi.S1G038500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8032.t1 is derived from g5207.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32564214	32565227	.	-	.	Phchi.S1G519100
Phchi.S1	AUGUSTUS	transcript	32564214	32565227	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	stop_codon	32564211	32564213	.	-	0	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564214	32564339	1	-	0	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564214	32564339	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564340	32564417	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564418	32564584	1	-	2	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564418	32564584	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564585	32564680	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564681	32564739	1	-	1	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564681	32564739	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564740	32564827	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564828	32564907	1	-	0	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564828	32564907	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564908	32564981	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564982	32565227	0.49	-	0	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564982	32565227	.	-	.	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	start_codon	32565225	32565227	.	-	0	transcript_id "Phchi.S1G519100.t1"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	transcript	32564214	32565227	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	stop_codon	32564211	32564213	.	-	0	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564214	32564339	1	-	0	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564214	32564339	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564340	32564417	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564418	32564584	1	-	2	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564418	32564584	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564585	32564680	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564681	32564739	1	-	1	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564681	32564739	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564740	32564830	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564831	32564907	0.55	-	0	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564831	32564907	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	intron	32564908	32564981	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	CDS	32564982	32565227	0.48	-	0	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	exon	32564982	32565227	.	-	.	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
Phchi.S1	AUGUSTUS	start_codon	32565225	32565227	.	-	0	transcript_id "Phchi.S1G519100.t2"; gene_id "Phchi.S1G519100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6490.t1 is derived from g3662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23269864	23270217	.	+	.	Phchi.S1G364900
Phchi.S1	AUGUSTUS	transcript	23269864	23270217	.	+	.	transcript_id "Phchi.S1G364900.t1"; gene_id "Phchi.S1G364900"
Phchi.S1	AUGUSTUS	start_codon	23269864	23269866	.	+	0	transcript_id "Phchi.S1G364900.t1"; gene_id "Phchi.S1G364900"
Phchi.S1	AUGUSTUS	CDS	23269864	23270217	0.36	+	0	transcript_id "Phchi.S1G364900.t1"; gene_id "Phchi.S1G364900"
Phchi.S1	AUGUSTUS	exon	23269864	23270217	.	+	.	transcript_id "Phchi.S1G364900.t1"; gene_id "Phchi.S1G364900"
Phchi.S1	AUGUSTUS	stop_codon	23270218	23270220	.	+	0	transcript_id "Phchi.S1G364900.t1"; gene_id "Phchi.S1G364900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12927.t1 is derived from g11392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3183062	3187379	.	-	.	Phchi.S3G024600
Phchi.S3	AUGUSTUS	transcript	3183062	3187379	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	stop_codon	3183059	3183061	.	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3183062	3183174	1	-	2	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3183062	3183174	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3183175	3183254	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3183255	3183361	0.67	-	1	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3183255	3183361	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3183362	3183558	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3183559	3183627	0.67	-	1	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3183559	3183627	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3183628	3183773	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3183774	3184019	0.8	-	1	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3183774	3184019	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3184020	3184180	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3184181	3184295	0.68	-	2	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3184181	3184295	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3184296	3184414	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3184415	3184495	0.72	-	2	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3184415	3184495	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3184496	3184581	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3184582	3184629	1	-	2	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3184582	3184629	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3184630	3184718	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3184719	3185183	0.52	-	2	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3184719	3185183	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3185184	3185281	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3185282	3185375	0.97	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3185282	3185375	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3185376	3185491	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3185492	3186076	0.84	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3185492	3186076	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3186077	3186181	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3186182	3186241	1	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3186182	3186241	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3186242	3186340	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3186341	3186445	1	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3186341	3186445	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3186446	3186620	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3186621	3186806	1	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3186621	3186806	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3186807	3186894	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3186895	3187026	1	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3186895	3187026	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3187027	3187116	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3187117	3187187	1	-	2	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3187117	3187187	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	intron	3187188	3187279	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	CDS	3187280	3187379	0.77	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	exon	3187280	3187379	.	-	.	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
Phchi.S3	AUGUSTUS	start_codon	3187377	3187379	.	-	0	transcript_id "Phchi.S3G024600.t1"; gene_id "Phchi.S3G024600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12036.t1 is derived from g7711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	785979	791231	.	-	.	Phchi.S2G011600
Phchi.S2	AUGUSTUS	transcript	785979	791231	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	stop_codon	785976	785978	.	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	785979	786095	1	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	785979	786095	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	786096	786174	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	786175	786273	1	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	786175	786273	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	786274	786371	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	786372	786473	1	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	786372	786473	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	786474	786556	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	786557	786640	1	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	786557	786640	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	786641	786762	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	786763	786850	1	-	1	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	786763	786850	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	786851	786937	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	786938	787014	1	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	786938	787014	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	787015	787317	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	787318	787359	1	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	787318	787359	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	787360	787452	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	787453	788583	0.7	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	787453	788583	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	788584	788720	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	788721	789436	0.63	-	2	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	788721	789436	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	789437	789516	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	789517	789784	0.57	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	789517	789784	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	789785	790088	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	790089	791070	0.87	-	1	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	790089	791070	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	intron	791071	791157	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	CDS	791158	791231	0.67	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	exon	791158	791231	.	-	.	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
Phchi.S2	AUGUSTUS	start_codon	791229	791231	.	-	0	transcript_id "Phchi.S2G011600.t1"; gene_id "Phchi.S2G011600"
# This transcript jg8939.t2 is derived from g6114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8940.t1 is derived from g6115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38766252	38769052	.	-	.	Phchi.S1G609900
Phchi.S1	AUGUSTUS	transcript	38766252	38769052	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	stop_codon	38766249	38766251	.	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38766252	38766252	0.67	-	1	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38766252	38766252	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38766253	38766346	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38766347	38766580	0.62	-	1	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38766347	38766580	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38766581	38766671	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38766672	38766871	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38766672	38766871	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38766872	38766965	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38766966	38767127	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38766966	38767127	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38767128	38767217	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38767218	38767355	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38767218	38767355	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38767356	38767437	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38767438	38767644	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38767438	38767644	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38767645	38767835	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38767836	38767949	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38767836	38767949	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38767950	38768033	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38768034	38768120	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38768034	38768120	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38768121	38768258	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38768259	38768369	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38768259	38768369	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38768370	38768453	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38768454	38768510	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38768454	38768510	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	intron	38768511	38768674	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	CDS	38768675	38769052	1	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	exon	38768675	38769052	.	-	.	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
Phchi.S1	AUGUSTUS	start_codon	38769050	38769052	.	-	0	transcript_id "Phchi.S1G609900.t1"; gene_id "Phchi.S1G609900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14829.t1 is derived from g13297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14914768	14916439	.	+	.	Phchi.S3G214800
Phchi.S3	AUGUSTUS	transcript	14914768	14916439	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	start_codon	14914768	14914770	.	+	0	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	CDS	14914768	14914816	0.83	+	0	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	exon	14914768	14914816	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	intron	14914817	14914945	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	CDS	14914946	14915113	1	+	2	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	exon	14914946	14915113	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	intron	14915114	14915301	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	CDS	14915302	14915564	1	+	2	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	exon	14915302	14915564	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	intron	14915565	14915703	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	CDS	14915704	14915992	1	+	0	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	exon	14915704	14915992	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	intron	14915993	14916080	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	CDS	14916081	14916439	0.9	+	2	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	exon	14916081	14916439	.	+	.	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
Phchi.S3	AUGUSTUS	stop_codon	14916440	14916442	.	+	0	transcript_id "Phchi.S3G214800.t1"; gene_id "Phchi.S3G214800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9541.t1 is derived from g6717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42396429	42397802	.	+	.	Phchi.S1G670000
Phchi.S1	AUGUSTUS	transcript	42396429	42397802	.	+	.	transcript_id "Phchi.S1G670000.t1"; gene_id "Phchi.S1G670000"
Phchi.S1	AUGUSTUS	start_codon	42396429	42396431	.	+	0	transcript_id "Phchi.S1G670000.t1"; gene_id "Phchi.S1G670000"
Phchi.S1	AUGUSTUS	CDS	42396429	42397802	0.89	+	0	transcript_id "Phchi.S1G670000.t1"; gene_id "Phchi.S1G670000"
Phchi.S1	AUGUSTUS	exon	42396429	42397802	.	+	.	transcript_id "Phchi.S1G670000.t1"; gene_id "Phchi.S1G670000"
Phchi.S1	AUGUSTUS	stop_codon	42397803	42397805	.	+	0	transcript_id "Phchi.S1G670000.t1"; gene_id "Phchi.S1G670000"
# This transcript jg11722.t2 is derived from g15774.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11723.t1 is derived from g15775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7844991	7846781	.	-	.	Phchi.S4G130500
Phchi.S4	AUGUSTUS	transcript	7844991	7846781	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	stop_codon	7844988	7844990	.	-	0	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	CDS	7844991	7845089	1	-	0	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	exon	7844991	7845089	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	intron	7845090	7845191	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	CDS	7845192	7845592	1	-	2	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	exon	7845192	7845592	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	intron	7845593	7845697	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	CDS	7845698	7845942	1	-	1	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	exon	7845698	7845942	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	intron	7845943	7846088	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	CDS	7846089	7846390	1	-	0	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	exon	7846089	7846390	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	intron	7846391	7846516	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	CDS	7846517	7846627	1	-	0	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	exon	7846517	7846627	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	intron	7846628	7846712	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	CDS	7846713	7846781	1	-	0	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	exon	7846713	7846781	.	-	.	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
Phchi.S4	AUGUSTUS	start_codon	7846779	7846781	.	-	0	transcript_id "Phchi.S4G130500.t1"; gene_id "Phchi.S4G130500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15382.t1 is derived from g13850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18726075	18726872	.	+	.	Phchi.S3G270100
Phchi.S3	AUGUSTUS	transcript	18726075	18726872	.	+	.	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	start_codon	18726075	18726077	.	+	0	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	CDS	18726075	18726373	0.23	+	0	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	exon	18726075	18726373	.	+	.	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	intron	18726374	18726844	.	+	.	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	CDS	18726845	18726872	0.8	+	1	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	exon	18726845	18726872	.	+	.	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
Phchi.S3	AUGUSTUS	stop_codon	18726873	18726875	.	+	0	transcript_id "Phchi.S3G270100.t1"; gene_id "Phchi.S3G270100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5019.t1 is derived from g2189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14087508	14089211	.	+	.	Phchi.S1G217800
Phchi.S1	AUGUSTUS	transcript	14087508	14089211	.	+	.	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	start_codon	14087508	14087510	.	+	0	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	CDS	14087508	14088047	1	+	0	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	exon	14087508	14088047	.	+	.	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	intron	14088048	14088322	.	+	.	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	CDS	14088323	14088569	1	+	0	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	exon	14088323	14088569	.	+	.	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	intron	14088570	14088732	.	+	.	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	CDS	14088733	14089211	0.93	+	2	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	exon	14088733	14089211	.	+	.	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
Phchi.S1	AUGUSTUS	stop_codon	14089212	14089214	.	+	0	transcript_id "Phchi.S1G217800.t1"; gene_id "Phchi.S1G217800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14267.t1 is derived from g12734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11861548	11862379	.	+	.	Phchi.S3G158600
Phchi.S3	AUGUSTUS	transcript	11861548	11862379	.	+	.	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	start_codon	11861548	11861550	.	+	0	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	CDS	11861548	11861991	0.77	+	0	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	exon	11861548	11861991	.	+	.	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	intron	11861992	11862064	.	+	.	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	CDS	11862065	11862379	0.86	+	0	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	exon	11862065	11862379	.	+	.	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
Phchi.S3	AUGUSTUS	stop_codon	11862380	11862382	.	+	0	transcript_id "Phchi.S3G158600.t1"; gene_id "Phchi.S3G158600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4432.t1 is derived from g1601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10476360	10476890	.	-	.	Phchi.S1G159100
Phchi.S1	AUGUSTUS	transcript	10476360	10476890	.	-	.	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	stop_codon	10476357	10476359	.	-	0	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	CDS	10476360	10476363	0.49	-	1	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	exon	10476360	10476363	.	-	.	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	intron	10476364	10476483	.	-	.	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	CDS	10476484	10476890	0.42	-	0	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	exon	10476484	10476890	.	-	.	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
Phchi.S1	AUGUSTUS	start_codon	10476888	10476890	.	-	0	transcript_id "Phchi.S1G159100.t1"; gene_id "Phchi.S1G159100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11227.t1 is derived from g15277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4896244	4896804	.	-	.	Phchi.S4G080900
Phchi.S4	AUGUSTUS	transcript	4896244	4896804	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	stop_codon	4896241	4896243	.	-	0	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	CDS	4896244	4896283	1	-	1	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	exon	4896244	4896283	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	intron	4896284	4896389	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	CDS	4896390	4896457	1	-	0	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	exon	4896390	4896457	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	intron	4896458	4896547	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	CDS	4896548	4896599	0.85	-	1	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	exon	4896548	4896599	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	intron	4896600	4896721	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	CDS	4896722	4896804	0.82	-	0	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	exon	4896722	4896804	.	-	.	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
Phchi.S4	AUGUSTUS	start_codon	4896802	4896804	.	-	0	transcript_id "Phchi.S4G080900.t1"; gene_id "Phchi.S4G080900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8704.t1 is derived from g5879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37537913	37538286	.	+	.	Phchi.S1G586300
Phchi.S1	AUGUSTUS	transcript	37537913	37538286	.	+	.	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	start_codon	37537913	37537915	.	+	0	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	CDS	37537913	37537970	1	+	0	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	exon	37537913	37537970	.	+	.	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	intron	37537971	37538044	.	+	.	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	CDS	37538045	37538286	0.18	+	2	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	exon	37538045	37538286	.	+	.	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
Phchi.S1	AUGUSTUS	stop_codon	37538287	37538289	.	+	0	transcript_id "Phchi.S1G586300.t1"; gene_id "Phchi.S1G586300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1547.t1 is derived from g8466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1694809	1700710	.	+	.	Phchi.S5G015600
Phchi.S5	AUGUSTUS	transcript	1694809	1700710	.	+	.	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	start_codon	1694809	1694811	.	+	0	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	CDS	1694809	1695837	0.44	+	0	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	exon	1694809	1695837	.	+	.	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	intron	1695838	1695926	.	+	.	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	CDS	1695927	1697401	0.22	+	0	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	exon	1695927	1697401	.	+	.	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	intron	1697402	1697604	.	+	.	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	CDS	1697605	1700710	0.91	+	1	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	exon	1697605	1700710	.	+	.	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
Phchi.S5	AUGUSTUS	stop_codon	1700711	1700713	.	+	0	transcript_id "Phchi.S5G015600.t1"; gene_id "Phchi.S5G015600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg414.t1 is derived from g10196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2955092	2956060	.	-	.	Phchi.S6G037300
Phchi.S6	AUGUSTUS	transcript	2955092	2956060	.	-	.	transcript_id "Phchi.S6G037300.t1"; gene_id "Phchi.S6G037300"
Phchi.S6	AUGUSTUS	stop_codon	2955089	2955091	.	-	0	transcript_id "Phchi.S6G037300.t1"; gene_id "Phchi.S6G037300"
Phchi.S6	AUGUSTUS	CDS	2955092	2956060	0.92	-	0	transcript_id "Phchi.S6G037300.t1"; gene_id "Phchi.S6G037300"
Phchi.S6	AUGUSTUS	exon	2955092	2956060	.	-	.	transcript_id "Phchi.S6G037300.t1"; gene_id "Phchi.S6G037300"
Phchi.S6	AUGUSTUS	start_codon	2956058	2956060	.	-	0	transcript_id "Phchi.S6G037300.t1"; gene_id "Phchi.S6G037300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10412.t1 is derived from g7588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47725289	47725874	.	-	.	Phchi.S1G757100
Phchi.S1	AUGUSTUS	transcript	47725289	47725874	.	-	.	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	stop_codon	47725286	47725288	.	-	0	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	CDS	47725289	47725312	0.98	-	0	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	exon	47725289	47725312	.	-	.	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	intron	47725313	47725694	.	-	.	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	CDS	47725695	47725874	0.61	-	0	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	exon	47725695	47725874	.	-	.	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
Phchi.S1	AUGUSTUS	start_codon	47725872	47725874	.	-	0	transcript_id "Phchi.S1G757100.t1"; gene_id "Phchi.S1G757100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12679.t1 is derived from g14413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	23208	23524	.	+	.	Phchi.C62G001000
Phchi.C62	AUGUSTUS	transcript	23208	23524	.	+	.	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	start_codon	23208	23210	.	+	0	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	CDS	23208	23405	0.74	+	0	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	exon	23208	23405	.	+	.	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	intron	23406	23497	.	+	.	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	CDS	23498	23524	0.96	+	0	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	exon	23498	23524	.	+	.	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
Phchi.C62	AUGUSTUS	stop_codon	23525	23527	.	+	0	transcript_id "Phchi.C62G001000.t1"; gene_id "Phchi.C62G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2943.t1 is derived from g112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	696574	698940	.	-	.	Phchi.S1G010200
Phchi.S1	AUGUSTUS	transcript	696574	698940	.	-	.	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	stop_codon	696571	696573	.	-	0	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	CDS	696574	696960	1	-	0	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	exon	696574	696960	.	-	.	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	intron	696961	697092	.	-	.	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	CDS	697093	698940	0.34	-	0	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	exon	697093	698940	.	-	.	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
Phchi.S1	AUGUSTUS	start_codon	698938	698940	.	-	0	transcript_id "Phchi.S1G010200.t1"; gene_id "Phchi.S1G010200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg77.t1 is derived from g9859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	393351	394375	.	-	.	Phchi.S6G003600
Phchi.S6	AUGUSTUS	transcript	393351	394375	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	stop_codon	393348	393350	.	-	0	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	CDS	393351	393556	0.94	-	2	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	exon	393351	393556	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	intron	393557	393694	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	CDS	393695	393748	1	-	2	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	exon	393695	393748	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	intron	393749	393955	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	CDS	393956	394174	0.53	-	2	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	exon	393956	394174	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	intron	394175	394317	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	CDS	394318	394375	0.92	-	0	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	exon	394318	394375	.	-	.	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
Phchi.S6	AUGUSTUS	start_codon	394373	394375	.	-	0	transcript_id "Phchi.S6G003600.t1"; gene_id "Phchi.S6G003600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg673.t1 is derived from g10455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4654662	4656315	.	+	.	Phchi.S6G063200
Phchi.S6	AUGUSTUS	transcript	4654662	4656315	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	start_codon	4654662	4654664	.	+	0	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4654662	4654790	0.81	+	0	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4654662	4654790	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	intron	4654791	4654874	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4654875	4654995	1	+	0	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4654875	4654995	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	intron	4654996	4655096	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4655097	4655162	1	+	2	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4655097	4655162	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	intron	4655163	4655245	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4655246	4655377	0.96	+	2	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4655246	4655377	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	intron	4655378	4655479	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4655480	4655532	0.91	+	2	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4655480	4655532	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	intron	4655533	4655616	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4655617	4656010	0.4	+	0	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4655617	4656010	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	intron	4656011	4656103	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	CDS	4656104	4656315	1	+	2	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	exon	4656104	4656315	.	+	.	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
Phchi.S6	AUGUSTUS	stop_codon	4656316	4656318	.	+	0	transcript_id "Phchi.S6G063200.t1"; gene_id "Phchi.S6G063200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8822.t1 is derived from g5997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38139952	38145397	.	+	.	Phchi.S1G598100
Phchi.S1	AUGUSTUS	transcript	38139952	38145397	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	start_codon	38139952	38139954	.	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38139952	38140059	0.86	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38139952	38140059	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38140060	38140210	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38140211	38140642	0.65	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38140211	38140642	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38140643	38140784	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38140785	38140991	1	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38140785	38140991	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38140992	38141141	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38141142	38141324	1	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38141142	38141324	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38141325	38141417	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38141418	38141500	0.95	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38141418	38141500	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38141501	38141611	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38141612	38141671	1	+	1	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38141612	38141671	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38141672	38141865	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38141866	38142157	0.99	+	1	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38141866	38142157	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38142158	38142241	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38142242	38142528	0.98	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38142242	38142528	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38142529	38142626	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38142627	38143498	1	+	1	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38142627	38143498	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38143499	38143603	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38143604	38144557	0.98	+	2	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38143604	38144557	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38144558	38144682	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38144683	38144840	0.77	+	2	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38144683	38144840	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38144841	38144928	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38144929	38145062	1	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38144929	38145062	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38145063	38145145	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38145146	38145223	1	+	1	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38145146	38145223	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	intron	38145224	38145384	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	CDS	38145385	38145397	0.5	+	1	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	exon	38145385	38145397	.	+	.	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
Phchi.S1	AUGUSTUS	stop_codon	38145398	38145400	.	+	0	transcript_id "Phchi.S1G598100.t1"; gene_id "Phchi.S1G598100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15236.t1 is derived from g13704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17865474	17867287	.	-	.	Phchi.S3G255500
Phchi.S3	AUGUSTUS	transcript	17865474	17867287	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	stop_codon	17865471	17865473	.	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17865474	17865593	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17865474	17865593	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17865594	17865691	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17865692	17865775	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17865692	17865775	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17865776	17865858	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17865859	17865912	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17865859	17865912	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17865913	17865995	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17865996	17866069	1	-	2	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17865996	17866069	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17866070	17866187	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17866188	17866284	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17866188	17866284	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17866285	17866401	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17866402	17866461	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17866402	17866461	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17866462	17866591	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17866592	17866714	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17866592	17866714	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17866715	17866805	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17866806	17866907	1	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17866806	17866907	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	intron	17866908	17866993	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	CDS	17866994	17867287	0.56	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	exon	17866994	17867287	.	-	.	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
Phchi.S3	AUGUSTUS	start_codon	17867285	17867287	.	-	0	transcript_id "Phchi.S3G255500.t1"; gene_id "Phchi.S3G255500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg741.t1 is derived from g10523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5281867	5282594	.	-	.	Phchi.S6G070000
Phchi.S6	AUGUSTUS	transcript	5281867	5282594	.	-	.	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	stop_codon	5281864	5281866	.	-	0	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	CDS	5281867	5282249	0.3	-	2	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	exon	5281867	5282249	.	-	.	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	intron	5282250	5282407	.	-	.	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	CDS	5282408	5282594	0.3	-	0	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	exon	5282408	5282594	.	-	.	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
Phchi.S6	AUGUSTUS	start_codon	5282592	5282594	.	-	0	transcript_id "Phchi.S6G070000.t1"; gene_id "Phchi.S6G070000"
# This transcript jg2844.t2 is derived from g13.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2845.t1 is derived from g14.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8057	9419	.	-	.	Phchi.S1G000400
Phchi.S1	AUGUSTUS	transcript	8057	9419	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	stop_codon	8054	8056	.	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	8057	8243	0.38	-	1	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	8057	8243	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	intron	8244	8363	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	8364	8437	0.99	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	8364	8437	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	intron	8438	8575	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	8576	8657	1	-	1	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	8576	8657	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	intron	8658	8756	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	8757	8848	1	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	8757	8848	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	intron	8849	8940	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	8941	9018	1	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	8941	9018	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	intron	9019	9108	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	9109	9228	1	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	9109	9228	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	intron	9229	9380	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	CDS	9381	9419	0.99	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	exon	9381	9419	.	-	.	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
Phchi.S1	AUGUSTUS	start_codon	9417	9419	.	-	0	transcript_id "Phchi.S1G000400.t1"; gene_id "Phchi.S1G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15978.t1 is derived from g9821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C54	AUGUSTUS	gene	58110	63470	.	+	.	Phchi.C54G000500
Phchi.C54	AUGUSTUS	transcript	58110	63470	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	start_codon	58110	58112	.	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	58110	58331	0.86	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	58110	58331	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	58332	58419	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	58420	58513	0.92	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	58420	58513	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	58514	58620	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	58621	58681	0.92	+	2	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	58621	58681	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	58682	58781	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	58782	58835	0.69	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	58782	58835	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	58836	58980	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	58981	59017	0.56	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	58981	59017	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	59018	59142	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	59143	59223	0.83	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	59143	59223	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	59224	59427	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	59428	59495	1	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	59428	59495	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	59496	59588	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	59589	59660	1	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	59589	59660	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	59661	59747	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	59748	59816	1	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	59748	59816	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	59817	59936	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	59937	60169	0.98	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	59937	60169	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	60170	60274	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	60275	60486	1	+	2	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	60275	60486	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	60487	60687	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	60688	60814	0.99	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	60688	60814	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	60815	60916	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	60917	60985	1	+	2	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	60917	60985	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	60986	61105	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	61106	61155	1	+	2	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	61106	61155	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	61156	61284	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	61285	61559	0.31	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	61285	61559	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	61560	61687	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	61688	61894	0.46	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	61688	61894	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	61895	62085	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	62086	62114	0.91	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	62086	62114	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	62115	62288	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	62289	62453	0.91	+	2	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	62289	62453	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	62454	62543	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	62544	62758	0.92	+	2	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	62544	62758	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	62759	62880	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	62881	63128	0.82	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	62881	63128	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	intron	63129	63226	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	CDS	63227	63470	1	+	1	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	exon	63227	63470	.	+	.	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
Phchi.C54	AUGUSTUS	stop_codon	63471	63473	.	+	0	transcript_id "Phchi.C54G000500.t1"; gene_id "Phchi.C54G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7854.t1 is derived from g5028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31530364	31540840	.	+	.	Phchi.S1G501300
Phchi.S1	AUGUSTUS	transcript	31530364	31540840	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	start_codon	31530364	31530366	.	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31530364	31530468	0.95	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31530364	31530468	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31530469	31530626	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31530627	31530695	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31530627	31530695	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31530696	31530745	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31530746	31530811	0.89	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31530746	31530811	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31530812	31531071	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531072	31531161	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531072	31531161	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531162	31531254	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531255	31531328	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531255	31531328	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531329	31531529	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531530	31531685	0.91	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531530	31531685	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531686	31531805	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531806	31531932	0.91	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531806	31531932	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531933	31532028	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532029	31532084	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532029	31532084	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532085	31532262	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532263	31532317	1	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532263	31532317	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532318	31532406	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532407	31532463	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532407	31532463	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532464	31532566	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532567	31532626	0.97	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532567	31532626	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532627	31532727	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532728	31532829	0.69	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532728	31532829	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532830	31532942	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532943	31533023	0.69	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532943	31533023	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533024	31533115	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533116	31533168	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533116	31533168	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533169	31533384	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533385	31533454	0.98	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533385	31533454	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533455	31533569	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533570	31533633	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533570	31533633	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533634	31533805	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533806	31533954	1	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533806	31533954	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533955	31534121	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534122	31534261	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534122	31534261	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534262	31534342	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534343	31534400	1	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534343	31534400	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534401	31534492	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534493	31534590	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534493	31534590	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534591	31534711	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534712	31534805	0.96	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534712	31534805	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534806	31534907	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534908	31534973	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534908	31534973	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534974	31535066	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535067	31535126	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535067	31535126	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535127	31535264	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535265	31535351	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535265	31535351	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535352	31535456	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535457	31535682	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535457	31535682	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535683	31535898	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535899	31535942	1	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535899	31535942	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535943	31536044	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536045	31536183	0.6	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536045	31536183	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536184	31536267	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536268	31536356	0.8	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536268	31536356	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536357	31536441	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536442	31536494	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536442	31536494	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536495	31536635	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536636	31536684	1	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536636	31536684	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536685	31536781	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536782	31536840	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536782	31536840	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536841	31536929	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536930	31537069	0.99	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536930	31537069	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537070	31537174	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537175	31537377	0.96	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537175	31537377	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537378	31537488	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537489	31537617	0.96	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537489	31537617	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537618	31537792	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537793	31537878	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537793	31537878	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537879	31537955	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537956	31538071	1	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537956	31538071	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538072	31538156	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538157	31538269	1	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538157	31538269	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538270	31538409	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538410	31538533	1	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538410	31538533	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538534	31538633	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538634	31538755	1	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538634	31538755	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538756	31538852	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538853	31539036	0.73	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538853	31539036	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31539037	31539173	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31539174	31539366	0.77	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31539174	31539366	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31539367	31539482	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31539483	31539822	1	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31539483	31539822	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31539823	31539959	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31539960	31540099	0.98	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31539960	31540099	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31540100	31540213	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31540214	31540335	1	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31540214	31540335	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31540336	31540418	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31540419	31540680	1	+	2	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31540419	31540680	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31540681	31540758	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31540759	31540840	0.62	+	1	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31540759	31540840	.	+	.	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	stop_codon	31540841	31540843	.	+	0	transcript_id "Phchi.S1G501300.t1"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	transcript	31530364	31540840	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	start_codon	31530364	31530366	.	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31530364	31530468	0.94	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31530364	31530468	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31530469	31530626	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31530627	31530695	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31530627	31530695	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31530696	31530745	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31530746	31530811	0.95	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31530746	31530811	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31530812	31531071	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531072	31531161	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531072	31531161	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531162	31531254	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531255	31531357	0.91	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531255	31531357	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531358	31531529	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531530	31531557	0.61	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531530	31531557	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531558	31531805	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31531806	31531932	0.36	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31531806	31531932	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31531933	31532028	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532029	31532084	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532029	31532084	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532085	31532262	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532263	31532317	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532263	31532317	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532318	31532406	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532407	31532463	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532407	31532463	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532464	31532727	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532728	31532829	0.66	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532728	31532829	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31532830	31532942	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31532943	31533023	0.66	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31532943	31533023	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533024	31533115	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533116	31533168	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533116	31533168	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533169	31533384	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533385	31533454	0.95	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533385	31533454	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533455	31533569	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533570	31533633	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533570	31533633	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533634	31533805	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31533806	31533954	1	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31533806	31533954	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31533955	31534121	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534122	31534261	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534122	31534261	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534262	31534342	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534343	31534400	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534343	31534400	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534401	31534492	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534493	31534590	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534493	31534590	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534591	31534711	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534712	31534805	0.98	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534712	31534805	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534806	31534907	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31534908	31534973	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31534908	31534973	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31534974	31535066	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535067	31535126	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535067	31535126	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535127	31535264	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535265	31535351	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535265	31535351	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535352	31535456	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535457	31535682	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535457	31535682	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535683	31535898	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31535899	31535942	1	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31535899	31535942	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31535943	31536044	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536045	31536183	0.63	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536045	31536183	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536184	31536267	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536268	31536356	0.77	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536268	31536356	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536357	31536441	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536442	31536494	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536442	31536494	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536495	31536635	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536636	31536684	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536636	31536684	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536685	31536781	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536782	31536840	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536782	31536840	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31536841	31536929	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31536930	31537069	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31536930	31537069	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537070	31537174	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537175	31537377	0.97	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537175	31537377	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537378	31537488	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537489	31537617	0.95	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537489	31537617	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537618	31537792	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537793	31537878	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537793	31537878	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31537879	31537955	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31537956	31538071	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31537956	31538071	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538072	31538156	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538157	31538269	1	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538157	31538269	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538270	31538409	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538410	31538533	1	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538410	31538533	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538534	31538633	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538634	31538755	1	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538634	31538755	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31538756	31538852	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31538853	31539036	0.75	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31538853	31539036	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31539037	31539173	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31539174	31539366	0.8	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31539174	31539366	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31539367	31539482	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31539483	31539822	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31539483	31539822	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31539823	31539959	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31539960	31540099	0.97	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31539960	31540099	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31540100	31540213	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31540214	31540335	1	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31540214	31540335	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31540336	31540418	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31540419	31540680	1	+	2	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31540419	31540680	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	intron	31540681	31540758	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	CDS	31540759	31540840	0.6	+	1	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	exon	31540759	31540840	.	+	.	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
Phchi.S1	AUGUSTUS	stop_codon	31540841	31540843	.	+	0	transcript_id "Phchi.S1G501300.t2"; gene_id "Phchi.S1G501300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14587.t1 is derived from g13055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13594557	13595572	.	+	.	Phchi.S3G190600
Phchi.S3	AUGUSTUS	transcript	13594557	13595572	.	+	.	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	start_codon	13594557	13594559	.	+	0	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	CDS	13594557	13595065	0.3	+	0	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	exon	13594557	13595065	.	+	.	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	intron	13595066	13595151	.	+	.	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	CDS	13595152	13595572	0.37	+	1	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	exon	13595152	13595572	.	+	.	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
Phchi.S3	AUGUSTUS	stop_codon	13595573	13595575	.	+	0	transcript_id "Phchi.S3G190600.t1"; gene_id "Phchi.S3G190600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6232.t1 is derived from g3404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21788712	21790030	.	+	.	Phchi.S1G339100
Phchi.S1	AUGUSTUS	transcript	21788712	21790030	.	+	.	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	start_codon	21788712	21788714	.	+	0	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	CDS	21788712	21789423	0.96	+	0	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	exon	21788712	21789423	.	+	.	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	intron	21789424	21789545	.	+	.	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	CDS	21789546	21790030	0.93	+	2	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	exon	21789546	21790030	.	+	.	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
Phchi.S1	AUGUSTUS	stop_codon	21790031	21790033	.	+	0	transcript_id "Phchi.S1G339100.t1"; gene_id "Phchi.S1G339100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10922.t1 is derived from g14972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2979023	2980051	.	+	.	Phchi.S4G050400
Phchi.S4	AUGUSTUS	transcript	2979023	2980051	.	+	.	transcript_id "Phchi.S4G050400.t1"; gene_id "Phchi.S4G050400"
Phchi.S4	AUGUSTUS	start_codon	2979023	2979025	.	+	0	transcript_id "Phchi.S4G050400.t1"; gene_id "Phchi.S4G050400"
Phchi.S4	AUGUSTUS	CDS	2979023	2980051	1	+	0	transcript_id "Phchi.S4G050400.t1"; gene_id "Phchi.S4G050400"
Phchi.S4	AUGUSTUS	exon	2979023	2980051	.	+	.	transcript_id "Phchi.S4G050400.t1"; gene_id "Phchi.S4G050400"
Phchi.S4	AUGUSTUS	stop_codon	2980052	2980054	.	+	0	transcript_id "Phchi.S4G050400.t1"; gene_id "Phchi.S4G050400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7955.t1 is derived from g5130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32088552	32090619	.	+	.	Phchi.S1G511400
Phchi.S1	AUGUSTUS	transcript	32088552	32090619	.	+	.	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	start_codon	32088552	32088554	.	+	0	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	CDS	32088552	32088768	0.92	+	0	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	exon	32088552	32088768	.	+	.	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	intron	32088769	32088880	.	+	.	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	CDS	32088881	32090619	1	+	2	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	exon	32088881	32090619	.	+	.	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
Phchi.S1	AUGUSTUS	stop_codon	32090620	32090622	.	+	0	transcript_id "Phchi.S1G511400.t1"; gene_id "Phchi.S1G511400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg822.t1 is derived from g10604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5719167	5721204	.	+	.	Phchi.S6G078100
Phchi.S6	AUGUSTUS	transcript	5719167	5721204	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	start_codon	5719167	5719169	.	+	0	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	CDS	5719167	5719550	0.44	+	0	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	exon	5719167	5719550	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	intron	5719551	5719666	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	CDS	5719667	5720500	0.66	+	0	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	exon	5719667	5720500	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	intron	5720501	5720641	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	CDS	5720642	5720727	1	+	0	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	exon	5720642	5720727	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	intron	5720728	5720820	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	CDS	5720821	5720973	1	+	1	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	exon	5720821	5720973	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	intron	5720974	5721059	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	CDS	5721060	5721204	1	+	1	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	exon	5721060	5721204	.	+	.	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
Phchi.S6	AUGUSTUS	stop_codon	5721205	5721207	.	+	0	transcript_id "Phchi.S6G078100.t1"; gene_id "Phchi.S6G078100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5774.t1 is derived from g2944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18893338	18894147	.	-	.	Phchi.S1G293300
Phchi.S1	AUGUSTUS	transcript	18893338	18894147	.	-	.	transcript_id "Phchi.S1G293300.t1"; gene_id "Phchi.S1G293300"
Phchi.S1	AUGUSTUS	stop_codon	18893335	18893337	.	-	0	transcript_id "Phchi.S1G293300.t1"; gene_id "Phchi.S1G293300"
Phchi.S1	AUGUSTUS	CDS	18893338	18894147	0.59	-	0	transcript_id "Phchi.S1G293300.t1"; gene_id "Phchi.S1G293300"
Phchi.S1	AUGUSTUS	exon	18893338	18894147	.	-	.	transcript_id "Phchi.S1G293300.t1"; gene_id "Phchi.S1G293300"
Phchi.S1	AUGUSTUS	start_codon	18894145	18894147	.	-	0	transcript_id "Phchi.S1G293300.t1"; gene_id "Phchi.S1G293300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5846.t1 is derived from g3016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19307077	19309244	.	-	.	Phchi.S1G300500
Phchi.S1	AUGUSTUS	transcript	19307077	19309244	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	stop_codon	19307074	19307076	.	-	0	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19307077	19307135	1	-	2	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19307077	19307135	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19307136	19307212	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19307213	19307290	1	-	2	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19307213	19307290	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19307291	19307418	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19307419	19307505	1	-	2	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19307419	19307505	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19307506	19307639	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19307640	19307980	0.99	-	1	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19307640	19307980	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19307981	19308105	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19308106	19308274	1	-	2	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19308106	19308274	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19308275	19308487	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19308488	19308685	1	-	2	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19308488	19308685	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19308686	19308783	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19308784	19308889	1	-	0	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19308784	19308889	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	intron	19308890	19308971	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	CDS	19308972	19309244	0.62	-	0	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	exon	19308972	19309244	.	-	.	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
Phchi.S1	AUGUSTUS	start_codon	19309242	19309244	.	-	0	transcript_id "Phchi.S1G300500.t1"; gene_id "Phchi.S1G300500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7150.t1 is derived from g4322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27200054	27200861	.	+	.	Phchi.S1G430900
Phchi.S1	AUGUSTUS	transcript	27200054	27200861	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	start_codon	27200054	27200056	.	+	0	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	CDS	27200054	27200165	0.39	+	0	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	exon	27200054	27200165	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	intron	27200166	27200312	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	CDS	27200313	27200392	1	+	2	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	exon	27200313	27200392	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	intron	27200393	27200516	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	CDS	27200517	27200609	1	+	0	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	exon	27200517	27200609	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	intron	27200610	27200699	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	CDS	27200700	27200861	1	+	0	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	exon	27200700	27200861	.	+	.	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
Phchi.S1	AUGUSTUS	stop_codon	27200862	27200864	.	+	0	transcript_id "Phchi.S1G430900.t1"; gene_id "Phchi.S1G430900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8698.t1 is derived from g5873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37511135	37513588	.	-	.	Phchi.S1G585700
Phchi.S1	AUGUSTUS	transcript	37511135	37513588	.	-	.	transcript_id "Phchi.S1G585700.t1"; gene_id "Phchi.S1G585700"
Phchi.S1	AUGUSTUS	stop_codon	37511132	37511134	.	-	0	transcript_id "Phchi.S1G585700.t1"; gene_id "Phchi.S1G585700"
Phchi.S1	AUGUSTUS	CDS	37511135	37513588	1	-	0	transcript_id "Phchi.S1G585700.t1"; gene_id "Phchi.S1G585700"
Phchi.S1	AUGUSTUS	exon	37511135	37513588	.	-	.	transcript_id "Phchi.S1G585700.t1"; gene_id "Phchi.S1G585700"
Phchi.S1	AUGUSTUS	start_codon	37513586	37513588	.	-	0	transcript_id "Phchi.S1G585700.t1"; gene_id "Phchi.S1G585700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10616.t1 is derived from g14666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1244257	1246361	.	+	.	Phchi.S4G019800
Phchi.S4	AUGUSTUS	transcript	1244257	1246361	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	start_codon	1244257	1244259	.	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1244257	1244270	0.99	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1244257	1244270	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1244271	1244464	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1244465	1244648	1	+	1	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1244465	1244648	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1244649	1244817	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1244818	1244910	0.4	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1244818	1244910	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1244911	1245055	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1245056	1245106	0.83	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1245056	1245106	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1245107	1245216	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1245217	1245313	1	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1245217	1245313	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1245314	1245415	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1245416	1245462	1	+	2	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1245416	1245462	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1245463	1245607	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1245608	1245827	0.96	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1245608	1245827	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1245828	1245930	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1245931	1246057	0.99	+	2	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1245931	1246057	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1246058	1246171	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1246172	1246214	1	+	1	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1246172	1246214	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	intron	1246215	1246295	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	CDS	1246296	1246361	1	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	exon	1246296	1246361	.	+	.	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
Phchi.S4	AUGUSTUS	stop_codon	1246362	1246364	.	+	0	transcript_id "Phchi.S4G019800.t1"; gene_id "Phchi.S4G019800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8069.t1 is derived from g5244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32798961	32799773	.	+	.	Phchi.S1G522800
Phchi.S1	AUGUSTUS	transcript	32798961	32799773	.	+	.	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	start_codon	32798961	32798963	.	+	0	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	CDS	32798961	32799590	0.62	+	0	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	exon	32798961	32799590	.	+	.	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	intron	32799591	32799695	.	+	.	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	CDS	32799696	32799773	0.54	+	0	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	exon	32799696	32799773	.	+	.	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
Phchi.S1	AUGUSTUS	stop_codon	32799774	32799776	.	+	0	transcript_id "Phchi.S1G522800.t1"; gene_id "Phchi.S1G522800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7318.t1 is derived from g4490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28476348	28478322	.	-	.	Phchi.S1G447700
Phchi.S1	AUGUSTUS	transcript	28476348	28478322	.	-	.	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	stop_codon	28476345	28476347	.	-	0	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	CDS	28476348	28476407	0.66	-	0	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	exon	28476348	28476407	.	-	.	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	intron	28476408	28476594	.	-	.	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	CDS	28476595	28476842	0.61	-	2	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	exon	28476595	28476842	.	-	.	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	intron	28476843	28477208	.	-	.	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	CDS	28477209	28478322	0.51	-	0	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	exon	28477209	28478322	.	-	.	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
Phchi.S1	AUGUSTUS	start_codon	28478320	28478322	.	-	0	transcript_id "Phchi.S1G447700.t1"; gene_id "Phchi.S1G447700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7792.t1 is derived from g4966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31201675	31202244	.	+	.	Phchi.S1G495100
Phchi.S1	AUGUSTUS	transcript	31201675	31202244	.	+	.	transcript_id "Phchi.S1G495100.t1"; gene_id "Phchi.S1G495100"
Phchi.S1	AUGUSTUS	start_codon	31201675	31201677	.	+	0	transcript_id "Phchi.S1G495100.t1"; gene_id "Phchi.S1G495100"
Phchi.S1	AUGUSTUS	CDS	31201675	31202244	0.98	+	0	transcript_id "Phchi.S1G495100.t1"; gene_id "Phchi.S1G495100"
Phchi.S1	AUGUSTUS	exon	31201675	31202244	.	+	.	transcript_id "Phchi.S1G495100.t1"; gene_id "Phchi.S1G495100"
Phchi.S1	AUGUSTUS	stop_codon	31202245	31202247	.	+	0	transcript_id "Phchi.S1G495100.t1"; gene_id "Phchi.S1G495100"
# This transcript jg7316.t2 is derived from g4488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7317.t1 is derived from g4489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28475326	28475979	.	-	.	Phchi.S1G447600
Phchi.S1	AUGUSTUS	transcript	28475326	28475979	.	-	.	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	stop_codon	28475323	28475325	.	-	0	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	CDS	28475326	28475375	0.87	-	2	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	exon	28475326	28475375	.	-	.	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	intron	28475376	28475541	.	-	.	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	CDS	28475542	28475614	0.81	-	0	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	exon	28475542	28475614	.	-	.	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	intron	28475615	28475721	.	-	.	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	CDS	28475722	28475979	0.42	-	0	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	exon	28475722	28475979	.	-	.	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
Phchi.S1	AUGUSTUS	start_codon	28475977	28475979	.	-	0	transcript_id "Phchi.S1G447600.t1"; gene_id "Phchi.S1G447600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12799.t1 is derived from g11264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2439279	2440443	.	+	.	Phchi.S3G011800
Phchi.S3	AUGUSTUS	transcript	2439279	2440443	.	+	.	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	start_codon	2439279	2439281	.	+	0	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	CDS	2439279	2439737	0.62	+	0	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	exon	2439279	2439737	.	+	.	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	intron	2439738	2440091	.	+	.	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	CDS	2440092	2440343	0.32	+	0	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	exon	2440092	2440343	.	+	.	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	intron	2440344	2440425	.	+	.	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	CDS	2440426	2440443	0.48	+	0	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	exon	2440426	2440443	.	+	.	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
Phchi.S3	AUGUSTUS	stop_codon	2440444	2440446	.	+	0	transcript_id "Phchi.S3G011800.t1"; gene_id "Phchi.S3G011800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7079.t1 is derived from g4251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26793837	26794799	.	-	.	Phchi.S1G423800
Phchi.S1	AUGUSTUS	transcript	26793837	26794799	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	stop_codon	26793834	26793836	.	-	0	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	CDS	26793837	26793888	1	-	1	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	exon	26793837	26793888	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	intron	26793889	26793962	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	CDS	26793963	26794099	1	-	0	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	exon	26793963	26794099	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	intron	26794100	26794194	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	CDS	26794195	26794412	1	-	2	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	exon	26794195	26794412	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	intron	26794413	26794744	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	CDS	26794745	26794799	0.88	-	0	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	exon	26794745	26794799	.	-	.	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
Phchi.S1	AUGUSTUS	start_codon	26794797	26794799	.	-	0	transcript_id "Phchi.S1G423800.t1"; gene_id "Phchi.S1G423800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5369.t1 is derived from g2539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16531668	16532036	.	+	.	Phchi.S1G252800
Phchi.S1	AUGUSTUS	transcript	16531668	16532036	.	+	.	transcript_id "Phchi.S1G252800.t1"; gene_id "Phchi.S1G252800"
Phchi.S1	AUGUSTUS	start_codon	16531668	16531670	.	+	0	transcript_id "Phchi.S1G252800.t1"; gene_id "Phchi.S1G252800"
Phchi.S1	AUGUSTUS	CDS	16531668	16532036	0.51	+	0	transcript_id "Phchi.S1G252800.t1"; gene_id "Phchi.S1G252800"
Phchi.S1	AUGUSTUS	exon	16531668	16532036	.	+	.	transcript_id "Phchi.S1G252800.t1"; gene_id "Phchi.S1G252800"
Phchi.S1	AUGUSTUS	stop_codon	16532037	16532039	.	+	0	transcript_id "Phchi.S1G252800.t1"; gene_id "Phchi.S1G252800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3839.t1 is derived from g1008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5955733	5957810	.	-	.	Phchi.S1G099800
Phchi.S1	AUGUSTUS	transcript	5955733	5957810	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	stop_codon	5955730	5955732	.	-	0	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	CDS	5955733	5955756	1	-	0	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	exon	5955733	5955756	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	intron	5955757	5955880	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	CDS	5955881	5956015	1	-	0	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	exon	5955881	5956015	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	intron	5956016	5956107	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	CDS	5956108	5956226	1	-	2	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	exon	5956108	5956226	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	intron	5956227	5956313	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	CDS	5956314	5956373	1	-	2	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	exon	5956314	5956373	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	intron	5956374	5956501	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	CDS	5956502	5956592	1	-	0	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	exon	5956502	5956592	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	intron	5956593	5956871	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	CDS	5956872	5957810	0.84	-	0	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	exon	5956872	5957810	.	-	.	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
Phchi.S1	AUGUSTUS	start_codon	5957808	5957810	.	-	0	transcript_id "Phchi.S1G099800.t1"; gene_id "Phchi.S1G099800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12449.t1 is derived from g8126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23141884	23144638	.	+	.	Phchi.S2G052900
Phchi.S2	AUGUSTUS	transcript	23141884	23144638	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	start_codon	23141884	23141886	.	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23141884	23141963	0.98	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23141884	23141963	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23141964	23142142	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23142143	23142226	0.97	+	1	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23142143	23142226	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23142227	23142457	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23142458	23142817	0.57	+	1	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23142458	23142817	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23142818	23142992	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23142993	23143170	0.65	+	1	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23142993	23143170	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23143171	23143587	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23143588	23143704	0.94	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23143588	23143704	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23143705	23143785	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23143786	23143924	1	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23143786	23143924	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23143925	23143999	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23144000	23144109	1	+	2	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23144000	23144109	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23144110	23144205	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23144206	23144275	1	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23144206	23144275	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23144276	23144358	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23144359	23144432	0.97	+	2	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23144359	23144432	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	intron	23144433	23144545	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	CDS	23144546	23144638	0.7	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	exon	23144546	23144638	.	+	.	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
Phchi.S2	AUGUSTUS	stop_codon	23144639	23144641	.	+	0	transcript_id "Phchi.S2G052900.t1"; gene_id "Phchi.S2G052900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4364.t1 is derived from g1533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10055765	10059703	.	-	.	Phchi.S1G152300
Phchi.S1	AUGUSTUS	transcript	10055765	10059703	.	-	.	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	stop_codon	10055762	10055764	.	-	0	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	CDS	10055765	10056243	0.35	-	2	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	exon	10055765	10056243	.	-	.	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	intron	10056244	10056330	.	-	.	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	CDS	10056331	10059703	0.25	-	0	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	exon	10056331	10059703	.	-	.	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
Phchi.S1	AUGUSTUS	start_codon	10059701	10059703	.	-	0	transcript_id "Phchi.S1G152300.t1"; gene_id "Phchi.S1G152300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3062.t1 is derived from g231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1400623	1401772	.	+	.	Phchi.S1G022100
Phchi.S1	AUGUSTUS	transcript	1400623	1401772	.	+	.	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	start_codon	1400623	1400625	.	+	0	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	CDS	1400623	1401165	1	+	0	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	exon	1400623	1401165	.	+	.	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	intron	1401166	1401520	.	+	.	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	CDS	1401521	1401772	0.98	+	0	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	exon	1401521	1401772	.	+	.	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
Phchi.S1	AUGUSTUS	stop_codon	1401773	1401775	.	+	0	transcript_id "Phchi.S1G022100.t1"; gene_id "Phchi.S1G022100"
# This transcript jg8199.t2 is derived from g5374.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8200.t1 is derived from g5375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34417057	34417780	.	+	.	Phchi.S1G535900
Phchi.S1	AUGUSTUS	transcript	34417057	34417780	.	+	.	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	start_codon	34417057	34417059	.	+	0	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	CDS	34417057	34417275	1	+	0	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	exon	34417057	34417275	.	+	.	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	intron	34417276	34417415	.	+	.	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	CDS	34417416	34417439	0.97	+	0	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	exon	34417416	34417439	.	+	.	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	intron	34417440	34417768	.	+	.	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	CDS	34417769	34417780	0.98	+	0	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	exon	34417769	34417780	.	+	.	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
Phchi.S1	AUGUSTUS	stop_codon	34417781	34417783	.	+	0	transcript_id "Phchi.S1G535900.t1"; gene_id "Phchi.S1G535900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5092.t1 is derived from g2262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14710548	14710855	.	+	.	Phchi.S1G225100
Phchi.S1	AUGUSTUS	transcript	14710548	14710855	.	+	.	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	start_codon	14710548	14710550	.	+	0	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	CDS	14710548	14710635	1	+	0	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	exon	14710548	14710635	.	+	.	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	intron	14710636	14710724	.	+	.	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	CDS	14710725	14710855	1	+	2	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	exon	14710725	14710855	.	+	.	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
Phchi.S1	AUGUSTUS	stop_codon	14710856	14710858	.	+	0	transcript_id "Phchi.S1G225100.t1"; gene_id "Phchi.S1G225100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8860.t1 is derived from g6035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38327314	38331062	.	+	.	Phchi.S1G601900
Phchi.S1	AUGUSTUS	transcript	38327314	38331062	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	start_codon	38327314	38327316	.	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38327314	38327383	0.84	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38327314	38327383	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38327384	38327982	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38327983	38328047	1	+	2	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38327983	38328047	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38328048	38328138	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38328139	38328228	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38328139	38328228	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38328229	38328319	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38328320	38328406	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38328320	38328406	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38328407	38328482	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38328483	38328542	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38328483	38328542	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38328543	38328693	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38328694	38328744	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38328694	38328744	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38328745	38328830	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38328831	38328926	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38328831	38328926	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38328927	38329008	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38329009	38329074	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38329009	38329074	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38329075	38329173	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38329174	38329391	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38329174	38329391	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38329392	38329480	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38329481	38329577	1	+	1	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38329481	38329577	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38329578	38329713	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38329714	38329800	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38329714	38329800	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38329801	38329892	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38329893	38330027	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38329893	38330027	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38330028	38330181	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38330182	38330286	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38330182	38330286	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38330287	38330364	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38330365	38330493	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38330365	38330493	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38330494	38330616	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38330617	38330720	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38330617	38330720	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38330721	38330800	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38330801	38330891	1	+	1	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38330801	38330891	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	intron	38330892	38330978	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	CDS	38330979	38331062	1	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	exon	38330979	38331062	.	+	.	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
Phchi.S1	AUGUSTUS	stop_codon	38331063	38331065	.	+	0	transcript_id "Phchi.S1G601900.t1"; gene_id "Phchi.S1G601900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg387.t1 is derived from g10169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2824561	2825026	.	-	.	Phchi.S6G034600
Phchi.S6	AUGUSTUS	transcript	2824561	2825026	.	-	.	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	stop_codon	2824558	2824560	.	-	0	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	CDS	2824561	2824707	0.59	-	0	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	exon	2824561	2824707	.	-	.	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	intron	2824708	2824783	.	-	.	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	CDS	2824784	2825026	0.62	-	0	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	exon	2824784	2825026	.	-	.	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
Phchi.S6	AUGUSTUS	start_codon	2825024	2825026	.	-	0	transcript_id "Phchi.S6G034600.t1"; gene_id "Phchi.S6G034600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7115.t1 is derived from g4287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27049611	27050277	.	-	.	Phchi.S1G427400
Phchi.S1	AUGUSTUS	transcript	27049611	27050277	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	stop_codon	27049608	27049610	.	-	0	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	CDS	27049611	27049775	1	-	0	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	exon	27049611	27049775	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	intron	27049776	27049862	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	CDS	27049863	27049914	0.94	-	1	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	exon	27049863	27049914	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	intron	27049915	27050007	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	CDS	27050008	27050108	0.52	-	0	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	exon	27050008	27050108	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	intron	27050109	27050202	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	CDS	27050203	27050277	0.35	-	0	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	exon	27050203	27050277	.	-	.	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
Phchi.S1	AUGUSTUS	start_codon	27050275	27050277	.	-	0	transcript_id "Phchi.S1G427400.t1"; gene_id "Phchi.S1G427400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2689.t1 is derived from g9609.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8224522	8225962	.	-	.	Phchi.S5G129800
Phchi.S5	AUGUSTUS	transcript	8224522	8225962	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	stop_codon	8224519	8224521	.	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8224522	8224632	0.72	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8224522	8224632	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8224633	8224963	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8224964	8225070	1	-	2	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8224964	8225070	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225071	8225285	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225286	8225310	0.79	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225286	8225310	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225311	8225409	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225410	8225426	0.79	-	2	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225410	8225426	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225427	8225512	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225513	8225606	1	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225513	8225606	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225607	8225745	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225746	8225814	1	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225746	8225814	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225815	8225890	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225891	8225962	0.95	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225891	8225962	.	-	.	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	start_codon	8225960	8225962	.	-	0	transcript_id "Phchi.S5G129800.t1"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	transcript	8224611	8225962	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	stop_codon	8224608	8224610	.	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8224611	8224628	0.59	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8224611	8224628	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8224629	8224963	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8224964	8225070	0.61	-	2	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8224964	8225070	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225071	8225285	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225286	8225310	0.71	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225286	8225310	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225311	8225409	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225410	8225426	0.71	-	2	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225410	8225426	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225427	8225512	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225513	8225606	1	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225513	8225606	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225607	8225745	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225746	8225814	1	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225746	8225814	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	intron	8225815	8225890	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	CDS	8225891	8225962	0.92	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	exon	8225891	8225962	.	-	.	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
Phchi.S5	AUGUSTUS	start_codon	8225960	8225962	.	-	0	transcript_id "Phchi.S5G129800.t2"; gene_id "Phchi.S5G129800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9303.t1 is derived from g6478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40859759	40862311	.	+	.	Phchi.S1G646200
Phchi.S1	AUGUSTUS	transcript	40859759	40862311	.	+	.	transcript_id "Phchi.S1G646200.t1"; gene_id "Phchi.S1G646200"
Phchi.S1	AUGUSTUS	start_codon	40859759	40859761	.	+	0	transcript_id "Phchi.S1G646200.t1"; gene_id "Phchi.S1G646200"
Phchi.S1	AUGUSTUS	CDS	40859759	40862311	0.76	+	0	transcript_id "Phchi.S1G646200.t1"; gene_id "Phchi.S1G646200"
Phchi.S1	AUGUSTUS	exon	40859759	40862311	.	+	.	transcript_id "Phchi.S1G646200.t1"; gene_id "Phchi.S1G646200"
Phchi.S1	AUGUSTUS	stop_codon	40862312	40862314	.	+	0	transcript_id "Phchi.S1G646200.t1"; gene_id "Phchi.S1G646200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7109.t1 is derived from g4281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27029918	27032823	.	-	.	Phchi.S1G426800
Phchi.S1	AUGUSTUS	transcript	27029918	27032823	.	-	.	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	stop_codon	27029915	27029917	.	-	0	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	CDS	27029918	27032387	0.79	-	1	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	exon	27029918	27032387	.	-	.	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	intron	27032388	27032542	.	-	.	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	CDS	27032543	27032823	0.72	-	0	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	exon	27032543	27032823	.	-	.	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
Phchi.S1	AUGUSTUS	start_codon	27032821	27032823	.	-	0	transcript_id "Phchi.S1G426800.t1"; gene_id "Phchi.S1G426800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1664.t1 is derived from g8583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2293955	2295229	.	+	.	Phchi.S5G027300
Phchi.S5	AUGUSTUS	transcript	2293955	2295229	.	+	.	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	start_codon	2293955	2293957	.	+	0	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	CDS	2293955	2294350	0.97	+	0	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	exon	2293955	2294350	.	+	.	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	intron	2294351	2294437	.	+	.	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	CDS	2294438	2295229	0.8	+	0	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	exon	2294438	2295229	.	+	.	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
Phchi.S5	AUGUSTUS	stop_codon	2295230	2295232	.	+	0	transcript_id "Phchi.S5G027300.t1"; gene_id "Phchi.S5G027300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4732.t1 is derived from g1902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12514737	12516680	.	-	.	Phchi.S1G189100
Phchi.S1	AUGUSTUS	transcript	12514737	12516680	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	stop_codon	12514734	12514736	.	-	0	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	CDS	12514737	12515405	0.98	-	0	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	exon	12514737	12515405	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	intron	12515406	12515497	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	CDS	12515498	12515846	1	-	1	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	exon	12515498	12515846	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	intron	12515847	12515940	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	CDS	12515941	12516092	1	-	0	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	exon	12515941	12516092	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	intron	12516093	12516173	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	CDS	12516174	12516680	1	-	0	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	exon	12516174	12516680	.	-	.	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
Phchi.S1	AUGUSTUS	start_codon	12516678	12516680	.	-	0	transcript_id "Phchi.S1G189100.t1"; gene_id "Phchi.S1G189100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11633.t1 is derived from g15684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7400742	7403251	.	-	.	Phchi.S4G121500
Phchi.S4	AUGUSTUS	transcript	7400742	7403251	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	stop_codon	7400739	7400741	.	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7400742	7400813	0.94	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7400742	7400813	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7400814	7400921	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7400922	7401023	0.97	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7400922	7401023	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7401024	7401123	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7401124	7401247	1	-	1	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7401124	7401247	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7401248	7401341	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7401342	7401427	1	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7401342	7401427	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7401428	7401522	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7401523	7401590	1	-	2	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7401523	7401590	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7401591	7401711	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7401712	7401730	1	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7401712	7401730	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7401731	7401868	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7401869	7401982	1	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7401869	7401982	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7401983	7402139	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7402140	7402208	0.63	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7402140	7402208	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7402209	7402375	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7402376	7402381	0.6	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7402376	7402381	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7402382	7402511	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7402512	7402590	0.62	-	1	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7402512	7402590	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7402591	7402673	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7402674	7402808	0.62	-	1	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7402674	7402808	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7402809	7402905	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7402906	7403013	0.62	-	1	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7402906	7403013	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7403014	7403105	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7403106	7403126	0.62	-	1	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7403106	7403126	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	intron	7403127	7403216	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	CDS	7403217	7403251	0.62	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	exon	7403217	7403251	.	-	.	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
Phchi.S4	AUGUSTUS	start_codon	7403249	7403251	.	-	0	transcript_id "Phchi.S4G121500.t1"; gene_id "Phchi.S4G121500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3106.t1 is derived from g275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1764388	1766197	.	-	.	Phchi.S1G026500
Phchi.S1	AUGUSTUS	transcript	1764388	1766197	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	stop_codon	1764385	1764387	.	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	CDS	1764388	1764508	0.51	-	1	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	exon	1764388	1764508	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	intron	1764509	1764700	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	CDS	1764701	1764972	0.73	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	exon	1764701	1764972	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	intron	1764973	1765078	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	CDS	1765079	1765327	0.91	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	exon	1765079	1765327	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	intron	1765328	1765499	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	CDS	1765500	1765640	0.53	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	exon	1765500	1765640	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	intron	1765641	1765844	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	CDS	1765845	1765955	0.96	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	exon	1765845	1765955	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	intron	1765956	1766044	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	CDS	1766045	1766197	0.94	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	exon	1766045	1766197	.	-	.	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
Phchi.S1	AUGUSTUS	start_codon	1766195	1766197	.	-	0	transcript_id "Phchi.S1G026500.t1"; gene_id "Phchi.S1G026500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1892.t1 is derived from g8812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3730336	3731763	.	+	.	Phchi.S5G050100
Phchi.S5	AUGUSTUS	transcript	3730336	3731763	.	+	.	transcript_id "Phchi.S5G050100.t1"; gene_id "Phchi.S5G050100"
Phchi.S5	AUGUSTUS	start_codon	3730336	3730338	.	+	0	transcript_id "Phchi.S5G050100.t1"; gene_id "Phchi.S5G050100"
Phchi.S5	AUGUSTUS	CDS	3730336	3731763	0.96	+	0	transcript_id "Phchi.S5G050100.t1"; gene_id "Phchi.S5G050100"
Phchi.S5	AUGUSTUS	exon	3730336	3731763	.	+	.	transcript_id "Phchi.S5G050100.t1"; gene_id "Phchi.S5G050100"
Phchi.S5	AUGUSTUS	stop_codon	3731764	3731766	.	+	0	transcript_id "Phchi.S5G050100.t1"; gene_id "Phchi.S5G050100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2475.t1 is derived from g9395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6835827	6837403	.	-	.	Phchi.S5G108400
Phchi.S5	AUGUSTUS	transcript	6835827	6837403	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	stop_codon	6835824	6835826	.	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6835827	6835891	1	-	2	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6835827	6835891	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6835892	6835980	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6835981	6836032	1	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6835981	6836032	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6836033	6836121	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6836122	6836357	1	-	2	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6836122	6836357	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6836358	6836442	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6836443	6836500	1	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6836443	6836500	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6836501	6836580	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6836581	6836649	1	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6836581	6836649	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6836650	6836731	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6836732	6836840	1	-	1	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6836732	6836840	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6836841	6836948	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6836949	6837016	1	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6836949	6837016	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6837017	6837103	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6837104	6837223	0.73	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6837104	6837223	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	intron	6837224	6837295	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	CDS	6837296	6837403	0.74	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	exon	6837296	6837403	.	-	.	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
Phchi.S5	AUGUSTUS	start_codon	6837401	6837403	.	-	0	transcript_id "Phchi.S5G108400.t1"; gene_id "Phchi.S5G108400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11749.t1 is derived from g15801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7988830	7994782	.	+	.	Phchi.S4G133100
Phchi.S4	AUGUSTUS	transcript	7988830	7994782	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	start_codon	7988830	7988832	.	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7988830	7988940	0.45	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7988830	7988940	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7988941	7989032	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989033	7989039	0.97	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989033	7989039	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989040	7989136	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989137	7989165	0.97	+	2	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989137	7989165	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989166	7989296	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989297	7989371	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989297	7989371	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989372	7989470	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989471	7989549	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989471	7989549	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989550	7989644	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989645	7989709	1	+	2	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989645	7989709	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989710	7989798	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989799	7989888	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989799	7989888	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989889	7990171	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990172	7990261	0.99	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990172	7990261	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990262	7990371	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990372	7990458	0.98	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990372	7990458	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990459	7990544	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990545	7990628	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990545	7990628	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990629	7990717	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990718	7990837	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990718	7990837	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990838	7990970	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990971	7991005	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990971	7991005	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7991006	7991097	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7991098	7991230	1	+	1	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7991098	7991230	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7991231	7991405	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7991406	7991816	0.97	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7991406	7991816	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7991817	7991924	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7991925	7992424	0.79	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7991925	7992424	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7992425	7992540	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7992541	7992604	0.99	+	1	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7992541	7992604	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7992605	7992689	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7992690	7992792	0.99	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7992690	7992792	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7992793	7992893	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7992894	7993081	0.97	+	2	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7992894	7993081	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7993082	7993168	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7993169	7993294	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7993169	7993294	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7993295	7993399	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7993400	7993470	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7993400	7993470	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7993471	7993635	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7993636	7993698	1	+	1	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7993636	7993698	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7993699	7993873	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7993874	7993946	1	+	1	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7993874	7993946	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7993947	7994093	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7994094	7994213	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7994094	7994213	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7994214	7994297	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7994298	7994375	1	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7994298	7994375	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7994376	7994497	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7994498	7994548	0.98	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7994498	7994548	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7994549	7994665	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7994666	7994782	0.96	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7994666	7994782	.	+	.	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	stop_codon	7994783	7994785	.	+	0	transcript_id "Phchi.S4G133100.t1"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	transcript	7988830	7991526	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	start_codon	7988830	7988832	.	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7988830	7988940	0.45	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7988830	7988940	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7988941	7989032	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989033	7989039	0.98	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989033	7989039	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989040	7989136	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989137	7989165	0.98	+	2	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989137	7989165	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989166	7989296	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989297	7989371	1	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989297	7989371	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989372	7989470	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989471	7989549	1	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989471	7989549	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989550	7989644	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989645	7989709	1	+	2	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989645	7989709	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989710	7989798	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7989799	7989888	1	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7989799	7989888	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7989889	7990171	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990172	7990261	0.99	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990172	7990261	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990262	7990371	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990372	7990458	0.96	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990372	7990458	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990459	7990544	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990545	7990628	1	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990545	7990628	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990629	7990717	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990718	7990837	1	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990718	7990837	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7990838	7990970	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7990971	7991005	1	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7990971	7991005	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7991006	7991097	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7991098	7991150	0.99	+	1	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7991098	7991150	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7991151	7991304	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7991305	7991347	0.99	+	2	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7991305	7991347	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	intron	7991348	7991447	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	CDS	7991448	7991526	0.95	+	1	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	exon	7991448	7991526	.	+	.	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
Phchi.S4	AUGUSTUS	stop_codon	7991527	7991529	.	+	0	transcript_id "Phchi.S4G133100.t2"; gene_id "Phchi.S4G133100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4942.t1 is derived from g2112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13669418	13671527	.	+	.	Phchi.S1G210100
Phchi.S1	AUGUSTUS	transcript	13669418	13671527	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	start_codon	13669418	13669420	.	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13669418	13669513	0.97	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13669418	13669513	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13669514	13669586	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13669587	13669802	1	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13669587	13669802	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13669803	13669894	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13669895	13670089	0.81	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13669895	13670089	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670090	13670272	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670273	13670383	1	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670273	13670383	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670384	13670476	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670477	13670605	0.88	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670477	13670605	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670606	13670720	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670721	13671077	1	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670721	13671077	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13671078	13671172	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13671173	13671250	1	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13671173	13671250	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13671251	13671509	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13671510	13671527	1	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13671510	13671527	.	+	.	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	stop_codon	13671528	13671530	.	+	0	transcript_id "Phchi.S1G210100.t1"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	transcript	13669418	13671527	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	start_codon	13669418	13669420	.	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13669418	13669513	0.98	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13669418	13669513	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13669514	13669586	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13669587	13669802	1	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13669587	13669802	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13669803	13669894	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13669895	13670089	0.82	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13669895	13670089	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670090	13670185	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670186	13670246	0.72	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670186	13670246	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670247	13670300	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670301	13670383	0.79	+	2	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670301	13670383	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670384	13670476	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670477	13670605	0.86	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670477	13670605	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13670606	13670720	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13670721	13671077	0.94	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13670721	13671077	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13671078	13671172	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13671173	13671250	1	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13671173	13671250	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	intron	13671251	13671509	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	CDS	13671510	13671527	1	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	exon	13671510	13671527	.	+	.	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
Phchi.S1	AUGUSTUS	stop_codon	13671528	13671530	.	+	0	transcript_id "Phchi.S1G210100.t2"; gene_id "Phchi.S1G210100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7126.t1 is derived from g4298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27084171	27086607	.	+	.	Phchi.S1G428500
Phchi.S1	AUGUSTUS	transcript	27084171	27086607	.	+	.	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	start_codon	27084171	27084173	.	+	0	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	CDS	27084171	27084394	0.2	+	0	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	exon	27084171	27084394	.	+	.	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	intron	27084395	27084549	.	+	.	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	CDS	27084550	27085163	0.68	+	1	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	exon	27084550	27085163	.	+	.	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	intron	27085164	27085234	.	+	.	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	CDS	27085235	27086607	0.82	+	2	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	exon	27085235	27086607	.	+	.	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
Phchi.S1	AUGUSTUS	stop_codon	27086608	27086610	.	+	0	transcript_id "Phchi.S1G428500.t1"; gene_id "Phchi.S1G428500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7654.t1 is derived from g4828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30427711	30431172	.	-	.	Phchi.S1G481300
Phchi.S1	AUGUSTUS	transcript	30427711	30431172	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	stop_codon	30427708	30427710	.	-	0	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	CDS	30427711	30428343	0.35	-	0	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	exon	30427711	30428343	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	intron	30428344	30428414	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	CDS	30428415	30428961	0.69	-	1	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	exon	30428415	30428961	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	intron	30428962	30429047	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	CDS	30429048	30429270	0.73	-	2	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	exon	30429048	30429270	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	intron	30429271	30429495	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	CDS	30429496	30429805	1	-	0	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	exon	30429496	30429805	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	intron	30429806	30429933	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	CDS	30429934	30431172	0.81	-	0	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	exon	30429934	30431172	.	-	.	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
Phchi.S1	AUGUSTUS	start_codon	30431170	30431172	.	-	0	transcript_id "Phchi.S1G481300.t1"; gene_id "Phchi.S1G481300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2178.t1 is derived from g9098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5243964	5246007	.	-	.	Phchi.S5G078700
Phchi.S5	AUGUSTUS	transcript	5243964	5246007	.	-	.	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	stop_codon	5243961	5243963	.	-	0	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	CDS	5243964	5245564	0.96	-	2	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	exon	5243964	5245564	.	-	.	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	intron	5245565	5245655	.	-	.	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	CDS	5245656	5245741	0.82	-	1	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	exon	5245656	5245741	.	-	.	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	intron	5245742	5245882	.	-	.	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	CDS	5245883	5246007	0.85	-	0	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	exon	5245883	5246007	.	-	.	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
Phchi.S5	AUGUSTUS	start_codon	5246005	5246007	.	-	0	transcript_id "Phchi.S5G078700.t1"; gene_id "Phchi.S5G078700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6510.t1 is derived from g3682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23374960	23377166	.	-	.	Phchi.S1G366900
Phchi.S1	AUGUSTUS	transcript	23374960	23377166	.	-	.	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	stop_codon	23374957	23374959	.	-	0	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	CDS	23374960	23375330	1	-	2	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	exon	23374960	23375330	.	-	.	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	intron	23375331	23375422	.	-	.	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	CDS	23375423	23377166	0.96	-	0	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	exon	23375423	23377166	.	-	.	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
Phchi.S1	AUGUSTUS	start_codon	23377164	23377166	.	-	0	transcript_id "Phchi.S1G366900.t1"; gene_id "Phchi.S1G366900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6331.t1 is derived from g3503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22310686	22311942	.	-	.	Phchi.S1G349000
Phchi.S1	AUGUSTUS	transcript	22310686	22311942	.	-	.	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	stop_codon	22310683	22310685	.	-	0	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	CDS	22310686	22311417	0.81	-	0	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	exon	22310686	22311417	.	-	.	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	intron	22311418	22311512	.	-	.	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	CDS	22311513	22311705	0.55	-	1	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	exon	22311513	22311705	.	-	.	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	intron	22311706	22311847	.	-	.	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	CDS	22311848	22311942	0.51	-	0	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	exon	22311848	22311942	.	-	.	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
Phchi.S1	AUGUSTUS	start_codon	22311940	22311942	.	-	0	transcript_id "Phchi.S1G349000.t1"; gene_id "Phchi.S1G349000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14203.t1 is derived from g12670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11485287	11485745	.	-	.	Phchi.S3G152200
Phchi.S3	AUGUSTUS	transcript	11485287	11485745	.	-	.	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	stop_codon	11485284	11485286	.	-	0	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	CDS	11485287	11485289	0.94	-	0	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	exon	11485287	11485289	.	-	.	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	intron	11485290	11485461	.	-	.	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	CDS	11485462	11485618	0.94	-	1	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	exon	11485462	11485618	.	-	.	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	intron	11485619	11485704	.	-	.	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	CDS	11485705	11485745	0.82	-	0	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	exon	11485705	11485745	.	-	.	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
Phchi.S3	AUGUSTUS	start_codon	11485743	11485745	.	-	0	transcript_id "Phchi.S3G152200.t1"; gene_id "Phchi.S3G152200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3087.t1 is derived from g256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1559956	1560924	.	+	.	Phchi.S1G024600
Phchi.S1	AUGUSTUS	transcript	1559956	1560924	.	+	.	transcript_id "Phchi.S1G024600.t1"; gene_id "Phchi.S1G024600"
Phchi.S1	AUGUSTUS	start_codon	1559956	1559958	.	+	0	transcript_id "Phchi.S1G024600.t1"; gene_id "Phchi.S1G024600"
Phchi.S1	AUGUSTUS	CDS	1559956	1560924	0.52	+	0	transcript_id "Phchi.S1G024600.t1"; gene_id "Phchi.S1G024600"
Phchi.S1	AUGUSTUS	exon	1559956	1560924	.	+	.	transcript_id "Phchi.S1G024600.t1"; gene_id "Phchi.S1G024600"
Phchi.S1	AUGUSTUS	stop_codon	1560925	1560927	.	+	0	transcript_id "Phchi.S1G024600.t1"; gene_id "Phchi.S1G024600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5464.t1 is derived from g2634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16967892	16969601	.	-	.	Phchi.S1G262300
Phchi.S1	AUGUSTUS	transcript	16967892	16969601	.	-	.	transcript_id "Phchi.S1G262300.t1"; gene_id "Phchi.S1G262300"
Phchi.S1	AUGUSTUS	stop_codon	16967889	16967891	.	-	0	transcript_id "Phchi.S1G262300.t1"; gene_id "Phchi.S1G262300"
Phchi.S1	AUGUSTUS	CDS	16967892	16969601	0.95	-	0	transcript_id "Phchi.S1G262300.t1"; gene_id "Phchi.S1G262300"
Phchi.S1	AUGUSTUS	exon	16967892	16969601	.	-	.	transcript_id "Phchi.S1G262300.t1"; gene_id "Phchi.S1G262300"
Phchi.S1	AUGUSTUS	start_codon	16969599	16969601	.	-	0	transcript_id "Phchi.S1G262300.t1"; gene_id "Phchi.S1G262300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12017.t1 is derived from g7692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	594328	597181	.	+	.	Phchi.S2G009700
Phchi.S2	AUGUSTUS	transcript	594328	597181	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	start_codon	594328	594330	.	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	594328	594838	0.99	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	594328	594838	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	594839	595000	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	595001	595067	1	+	2	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	595001	595067	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	595068	595140	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	595141	595273	1	+	1	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	595141	595273	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	595274	595366	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	595367	595449	1	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	595367	595449	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	595450	595531	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	595532	595646	1	+	1	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	595532	595646	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	595647	595779	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	595780	595837	1	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	595780	595837	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	595838	595924	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	595925	596043	1	+	2	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	595925	596043	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	596044	596147	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	596148	596267	1	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	596148	596267	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	596268	596374	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	596375	596476	1	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	596375	596476	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	596477	596552	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	596553	596625	1	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	596553	596625	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	596626	596712	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	596713	596780	1	+	2	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	596713	596780	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	596781	596875	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	596876	596936	1	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	596876	596936	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	intron	596937	597026	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	CDS	597027	597181	1	+	2	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	exon	597027	597181	.	+	.	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
Phchi.S2	AUGUSTUS	stop_codon	597182	597184	.	+	0	transcript_id "Phchi.S2G009700.t1"; gene_id "Phchi.S2G009700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3830.t1 is derived from g999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5919802	5920821	.	+	.	Phchi.S1G098900
Phchi.S1	AUGUSTUS	transcript	5919802	5920821	.	+	.	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	start_codon	5919802	5919804	.	+	0	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	CDS	5919802	5920334	1	+	0	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	exon	5919802	5920334	.	+	.	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	intron	5920335	5920418	.	+	.	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	CDS	5920419	5920821	1	+	1	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	exon	5920419	5920821	.	+	.	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
Phchi.S1	AUGUSTUS	stop_codon	5920822	5920824	.	+	0	transcript_id "Phchi.S1G098900.t1"; gene_id "Phchi.S1G098900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9597.t1 is derived from g6773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42869871	42871184	.	+	.	Phchi.S1G675600
Phchi.S1	AUGUSTUS	transcript	42869871	42871184	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	start_codon	42869871	42869873	.	+	0	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	CDS	42869871	42870079	1	+	0	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	exon	42869871	42870079	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	intron	42870080	42870241	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	CDS	42870242	42870339	1	+	1	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	exon	42870242	42870339	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	intron	42870340	42870514	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	CDS	42870515	42870898	1	+	2	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	exon	42870515	42870898	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	intron	42870899	42870987	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	CDS	42870988	42871024	1	+	2	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	exon	42870988	42871024	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	intron	42871025	42871108	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	CDS	42871109	42871184	0.75	+	1	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	exon	42871109	42871184	.	+	.	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
Phchi.S1	AUGUSTUS	stop_codon	42871185	42871187	.	+	0	transcript_id "Phchi.S1G675600.t1"; gene_id "Phchi.S1G675600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5678.t1 is derived from g2848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18266489	18268843	.	+	.	Phchi.S1G283700
Phchi.S1	AUGUSTUS	transcript	18266489	18268843	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	start_codon	18266489	18266491	.	+	0	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18266489	18266510	0.94	+	0	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18266489	18266510	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	intron	18266511	18266597	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18266598	18266679	1	+	2	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18266598	18266679	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	intron	18266680	18266773	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18266774	18266820	0.67	+	1	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18266774	18266820	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	intron	18266821	18266894	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18266895	18267155	0.88	+	2	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18266895	18267155	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	intron	18267156	18267323	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18267324	18268204	0.92	+	2	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18267324	18268204	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	intron	18268205	18268451	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18268452	18268577	0.6	+	0	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18268452	18268577	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	intron	18268578	18268696	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	CDS	18268697	18268843	0.91	+	0	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	exon	18268697	18268843	.	+	.	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
Phchi.S1	AUGUSTUS	stop_codon	18268844	18268846	.	+	0	transcript_id "Phchi.S1G283700.t1"; gene_id "Phchi.S1G283700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12823.t1 is derived from g11288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2576887	2577649	.	-	.	Phchi.S3G014200
Phchi.S3	AUGUSTUS	transcript	2576887	2577649	.	-	.	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	stop_codon	2576884	2576886	.	-	0	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	CDS	2576887	2577341	1	-	2	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	exon	2576887	2577341	.	-	.	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	intron	2577342	2577447	.	-	.	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	CDS	2577448	2577649	0.94	-	0	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	exon	2577448	2577649	.	-	.	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
Phchi.S3	AUGUSTUS	start_codon	2577647	2577649	.	-	0	transcript_id "Phchi.S3G014200.t1"; gene_id "Phchi.S3G014200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10558.t1 is derived from g14608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	978817	979473	.	+	.	Phchi.S4G014000
Phchi.S4	AUGUSTUS	transcript	978817	979473	.	+	.	transcript_id "Phchi.S4G014000.t1"; gene_id "Phchi.S4G014000"
Phchi.S4	AUGUSTUS	start_codon	978817	978819	.	+	0	transcript_id "Phchi.S4G014000.t1"; gene_id "Phchi.S4G014000"
Phchi.S4	AUGUSTUS	CDS	978817	979473	0.98	+	0	transcript_id "Phchi.S4G014000.t1"; gene_id "Phchi.S4G014000"
Phchi.S4	AUGUSTUS	exon	978817	979473	.	+	.	transcript_id "Phchi.S4G014000.t1"; gene_id "Phchi.S4G014000"
Phchi.S4	AUGUSTUS	stop_codon	979474	979476	.	+	0	transcript_id "Phchi.S4G014000.t1"; gene_id "Phchi.S4G014000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13343.t1 is derived from g11809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6184950	6186324	.	+	.	Phchi.S3G066200
Phchi.S3	AUGUSTUS	transcript	6184950	6186324	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	start_codon	6184950	6184952	.	+	0	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	CDS	6184950	6185525	1	+	0	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	exon	6184950	6185525	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	intron	6185526	6185719	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	CDS	6185720	6185841	0.67	+	0	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	exon	6185720	6185841	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	intron	6185842	6185954	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	CDS	6185955	6185980	0.65	+	1	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	exon	6185955	6185980	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	intron	6185981	6186103	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	CDS	6186104	6186324	0.67	+	2	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	exon	6186104	6186324	.	+	.	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
Phchi.S3	AUGUSTUS	stop_codon	6186325	6186327	.	+	0	transcript_id "Phchi.S3G066200.t1"; gene_id "Phchi.S3G066200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4695.t1 is derived from g1865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12332766	12333099	.	-	.	Phchi.S1G185400
Phchi.S1	AUGUSTUS	transcript	12332766	12333099	.	-	.	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	stop_codon	12332763	12332765	.	-	0	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	CDS	12332766	12332803	0.44	-	2	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	exon	12332766	12332803	.	-	.	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	intron	12332804	12332900	.	-	.	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	CDS	12332901	12333099	0.44	-	0	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	exon	12332901	12333099	.	-	.	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
Phchi.S1	AUGUSTUS	start_codon	12333097	12333099	.	-	0	transcript_id "Phchi.S1G185400.t1"; gene_id "Phchi.S1G185400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2436.t1 is derived from g9356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6629390	6630255	.	+	.	Phchi.S5G104500
Phchi.S5	AUGUSTUS	transcript	6629390	6630255	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	start_codon	6629390	6629392	.	+	0	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	CDS	6629390	6629505	0.51	+	0	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	exon	6629390	6629505	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	intron	6629506	6629648	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	CDS	6629649	6629671	0.66	+	1	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	exon	6629649	6629671	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	intron	6629672	6629868	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	CDS	6629869	6629947	0.77	+	2	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	exon	6629869	6629947	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	intron	6629948	6630152	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	CDS	6630153	6630255	0.75	+	1	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	exon	6630153	6630255	.	+	.	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
Phchi.S5	AUGUSTUS	stop_codon	6630256	6630258	.	+	0	transcript_id "Phchi.S5G104500.t1"; gene_id "Phchi.S5G104500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8420.t1 is derived from g5595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35872340	35874703	.	+	.	Phchi.S1G557900
Phchi.S1	AUGUSTUS	transcript	35872340	35874703	.	+	.	transcript_id "Phchi.S1G557900.t1"; gene_id "Phchi.S1G557900"
Phchi.S1	AUGUSTUS	start_codon	35872340	35872342	.	+	0	transcript_id "Phchi.S1G557900.t1"; gene_id "Phchi.S1G557900"
Phchi.S1	AUGUSTUS	CDS	35872340	35874703	0.71	+	0	transcript_id "Phchi.S1G557900.t1"; gene_id "Phchi.S1G557900"
Phchi.S1	AUGUSTUS	exon	35872340	35874703	.	+	.	transcript_id "Phchi.S1G557900.t1"; gene_id "Phchi.S1G557900"
Phchi.S1	AUGUSTUS	stop_codon	35874704	35874706	.	+	0	transcript_id "Phchi.S1G557900.t1"; gene_id "Phchi.S1G557900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10801.t1 is derived from g14851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2171044	2172918	.	+	.	Phchi.S4G038300
Phchi.S4	AUGUSTUS	transcript	2171044	2172918	.	+	.	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	start_codon	2171044	2171046	.	+	0	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	CDS	2171044	2171585	0.53	+	0	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	exon	2171044	2171585	.	+	.	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	intron	2171586	2171656	.	+	.	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	CDS	2171657	2172011	0.47	+	1	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	exon	2171657	2172011	.	+	.	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	intron	2172012	2172132	.	+	.	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	CDS	2172133	2172918	0.91	+	0	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	exon	2172133	2172918	.	+	.	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
Phchi.S4	AUGUSTUS	stop_codon	2172919	2172921	.	+	0	transcript_id "Phchi.S4G038300.t1"; gene_id "Phchi.S4G038300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7760.t1 is derived from g4934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31156817	31157209	.	+	.	Phchi.S1G491900
Phchi.S1	AUGUSTUS	transcript	31156817	31157209	.	+	.	transcript_id "Phchi.S1G491900.t1"; gene_id "Phchi.S1G491900"
Phchi.S1	AUGUSTUS	start_codon	31156817	31156819	.	+	0	transcript_id "Phchi.S1G491900.t1"; gene_id "Phchi.S1G491900"
Phchi.S1	AUGUSTUS	CDS	31156817	31157209	0.75	+	0	transcript_id "Phchi.S1G491900.t1"; gene_id "Phchi.S1G491900"
Phchi.S1	AUGUSTUS	exon	31156817	31157209	.	+	.	transcript_id "Phchi.S1G491900.t1"; gene_id "Phchi.S1G491900"
Phchi.S1	AUGUSTUS	stop_codon	31157210	31157212	.	+	0	transcript_id "Phchi.S1G491900.t1"; gene_id "Phchi.S1G491900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2896.t1 is derived from g65.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	378012	379476	.	-	.	Phchi.S1G005500
Phchi.S1	AUGUSTUS	transcript	378012	379476	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	stop_codon	378009	378011	.	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	CDS	378012	378140	1	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	exon	378012	378140	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	intron	378141	378266	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	CDS	378267	378387	1	-	1	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	exon	378267	378387	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	intron	378388	378481	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	CDS	378482	378576	1	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	exon	378482	378576	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	intron	378577	378663	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	CDS	378664	378837	1	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	exon	378664	378837	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	intron	378838	378913	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	CDS	378914	379003	1	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	exon	378914	379003	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	intron	379004	379170	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	CDS	379171	379476	0.84	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	exon	379171	379476	.	-	.	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
Phchi.S1	AUGUSTUS	start_codon	379474	379476	.	-	0	transcript_id "Phchi.S1G005500.t1"; gene_id "Phchi.S1G005500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8784.t1 is derived from g5959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37943084	37944399	.	-	.	Phchi.S1G594300
Phchi.S1	AUGUSTUS	transcript	37943084	37944399	.	-	.	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	stop_codon	37943081	37943083	.	-	0	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	CDS	37943084	37943348	0.8	-	1	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	exon	37943084	37943348	.	-	.	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	intron	37943349	37943425	.	-	.	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	CDS	37943426	37944399	0.57	-	0	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	exon	37943426	37944399	.	-	.	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
Phchi.S1	AUGUSTUS	start_codon	37944397	37944399	.	-	0	transcript_id "Phchi.S1G594300.t1"; gene_id "Phchi.S1G594300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3336.t1 is derived from g505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2976238	2979234	.	+	.	Phchi.S1G049500
Phchi.S1	AUGUSTUS	transcript	2976238	2979234	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	start_codon	2976238	2976240	.	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2976238	2976268	0.98	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2976238	2976268	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2976269	2976346	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2976347	2976517	0.82	+	2	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2976347	2976517	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2976518	2976633	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2976634	2976841	0.99	+	2	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2976634	2976841	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2976842	2976945	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2976946	2977109	0.99	+	1	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2976946	2977109	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2977110	2977230	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2977231	2977376	1	+	2	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2977231	2977376	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2977377	2977509	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2977510	2977572	1	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2977510	2977572	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2977573	2977737	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2977738	2977830	1	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2977738	2977830	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2977831	2977928	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2977929	2978090	1	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2977929	2978090	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2978091	2978195	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2978196	2978332	1	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2978196	2978332	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2978333	2978421	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2978422	2978615	1	+	1	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2978422	2978615	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2978616	2978708	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2978709	2978802	0.55	+	2	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2978709	2978802	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	intron	2978803	2979044	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	CDS	2979045	2979234	0.49	+	1	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	exon	2979045	2979234	.	+	.	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
Phchi.S1	AUGUSTUS	stop_codon	2979235	2979237	.	+	0	transcript_id "Phchi.S1G049500.t1"; gene_id "Phchi.S1G049500"
# This transcript jg15274.t2 is derived from g13742.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15275.t1 is derived from g13743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18107035	18108258	.	+	.	Phchi.S3G259400
Phchi.S3	AUGUSTUS	transcript	18107035	18108258	.	+	.	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	start_codon	18107035	18107037	.	+	0	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	CDS	18107035	18107452	0.53	+	0	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	exon	18107035	18107452	.	+	.	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	intron	18107453	18107686	.	+	.	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	CDS	18107687	18108258	0.26	+	2	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	exon	18107687	18108258	.	+	.	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
Phchi.S3	AUGUSTUS	stop_codon	18108259	18108261	.	+	0	transcript_id "Phchi.S3G259400.t1"; gene_id "Phchi.S3G259400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11349.t1 is derived from g15399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5688181	5690638	.	+	.	Phchi.S4G093100
Phchi.S4	AUGUSTUS	transcript	5688181	5690638	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	start_codon	5688181	5688183	.	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5688181	5688537	0.47	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5688181	5688537	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	intron	5688538	5688713	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5688714	5688959	0.69	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5688714	5688959	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	intron	5688960	5689059	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5689060	5689101	0.53	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5689060	5689101	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	intron	5689102	5689245	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5689246	5689413	0.8	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5689246	5689413	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	intron	5689414	5689589	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5689590	5689901	0.86	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5689590	5689901	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	intron	5689902	5690007	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5690008	5690457	0.98	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5690008	5690457	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	intron	5690458	5690566	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	CDS	5690567	5690638	1	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	exon	5690567	5690638	.	+	.	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
Phchi.S4	AUGUSTUS	stop_codon	5690639	5690641	.	+	0	transcript_id "Phchi.S4G093100.t1"; gene_id "Phchi.S4G093100"
# This transcript jg4500.t2 is derived from g1670.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4501.t1 is derived from g1671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10860046	10862341	.	+	.	Phchi.S1G166000
Phchi.S1	AUGUSTUS	transcript	10860046	10862341	.	+	.	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	start_codon	10860046	10860048	.	+	0	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	CDS	10860046	10861822	0.83	+	0	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	exon	10860046	10861822	.	+	.	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	intron	10861823	10861919	.	+	.	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	CDS	10861920	10862341	0.06	+	2	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	exon	10861920	10862341	.	+	.	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
Phchi.S1	AUGUSTUS	stop_codon	10862342	10862344	.	+	0	transcript_id "Phchi.S1G166000.t1"; gene_id "Phchi.S1G166000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14209.t1 is derived from g12676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11515438	11519012	.	+	.	Phchi.S3G152800
Phchi.S3	AUGUSTUS	transcript	11515438	11519012	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	start_codon	11515438	11515440	.	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11515438	11517270	0.99	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11515438	11517270	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	intron	11517271	11517447	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11517448	11517549	1	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11517448	11517549	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	intron	11517550	11517786	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11517787	11517798	0.76	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11517787	11517798	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	intron	11517799	11517911	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11517912	11517967	0.96	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11517912	11517967	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	intron	11517968	11518058	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11518059	11518179	1	+	1	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11518059	11518179	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	intron	11518180	11518289	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11518290	11518361	1	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11518290	11518361	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	intron	11518362	11518445	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	CDS	11518446	11519012	1	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	exon	11518446	11519012	.	+	.	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
Phchi.S3	AUGUSTUS	stop_codon	11519013	11519015	.	+	0	transcript_id "Phchi.S3G152800.t1"; gene_id "Phchi.S3G152800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13569.t1 is derived from g12036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7538273	7541182	.	+	.	Phchi.S3G088800
Phchi.S3	AUGUSTUS	transcript	7538273	7541182	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	start_codon	7538273	7538275	.	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7538273	7538354	1	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7538273	7538354	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7538355	7538504	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7538505	7538674	1	+	2	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7538505	7538674	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7538675	7538791	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7538792	7538863	1	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7538792	7538863	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7538864	7539067	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7539068	7539206	1	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7539068	7539206	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7539207	7539334	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7539335	7539443	1	+	2	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7539335	7539443	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7539444	7539617	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7539618	7539735	0.97	+	1	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7539618	7539735	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7539736	7539842	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7539843	7539990	1	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7539843	7539990	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7539991	7540115	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7540116	7540364	1	+	2	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7540116	7540364	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7540365	7540537	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7540538	7540663	1	+	2	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7540538	7540663	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7540664	7540743	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7540744	7540844	1	+	2	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7540744	7540844	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7540845	7540923	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7540924	7540998	1	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7540924	7540998	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	intron	7540999	7541125	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	CDS	7541126	7541182	1	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	exon	7541126	7541182	.	+	.	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
Phchi.S3	AUGUSTUS	stop_codon	7541183	7541185	.	+	0	transcript_id "Phchi.S3G088800.t1"; gene_id "Phchi.S3G088800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11539.t1 is derived from g15589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6964589	6966810	.	-	.	Phchi.S4G112100
Phchi.S4	AUGUSTUS	transcript	6964589	6966810	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	stop_codon	6964586	6964588	.	-	0	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	CDS	6964589	6964968	1	-	2	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	exon	6964589	6964968	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	intron	6964969	6965057	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	CDS	6965058	6966070	0.99	-	1	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	exon	6965058	6966070	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	intron	6966071	6966182	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	CDS	6966183	6966445	0.4	-	0	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	exon	6966183	6966445	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	intron	6966446	6966603	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	CDS	6966604	6966810	0.28	-	0	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	exon	6966604	6966810	.	-	.	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
Phchi.S4	AUGUSTUS	start_codon	6966808	6966810	.	-	0	transcript_id "Phchi.S4G112100.t1"; gene_id "Phchi.S4G112100"
# This transcript jg5539.t2 is derived from g2709.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5539.t3 is derived from g2709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5541.t1 is derived from g2711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17469109	17470265	.	-	.	Phchi.S1G270000
Phchi.S1	AUGUSTUS	transcript	17469109	17470265	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	stop_codon	17469106	17469108	.	-	0	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	CDS	17469109	17469112	1	-	1	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	exon	17469109	17469112	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	intron	17469113	17469200	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	CDS	17469201	17469325	1	-	0	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	exon	17469201	17469325	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	intron	17469326	17469569	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	CDS	17469570	17469635	1	-	0	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	exon	17469570	17469635	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	intron	17469636	17469737	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	CDS	17469738	17469910	1	-	2	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	exon	17469738	17469910	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	intron	17469911	17470050	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	CDS	17470051	17470106	1	-	1	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	exon	17470051	17470106	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	intron	17470107	17470203	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	CDS	17470204	17470265	1	-	0	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	exon	17470204	17470265	.	-	.	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
Phchi.S1	AUGUSTUS	start_codon	17470263	17470265	.	-	0	transcript_id "Phchi.S1G270000.t1"; gene_id "Phchi.S1G270000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2946.t1 is derived from g115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	711050	711884	.	+	.	Phchi.S1G010500
Phchi.S1	AUGUSTUS	transcript	711050	711884	.	+	.	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	start_codon	711050	711052	.	+	0	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	CDS	711050	711360	0.99	+	0	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	exon	711050	711360	.	+	.	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	intron	711361	711543	.	+	.	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	CDS	711544	711685	0.93	+	1	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	exon	711544	711685	.	+	.	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	intron	711686	711791	.	+	.	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	CDS	711792	711884	0.94	+	0	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	exon	711792	711884	.	+	.	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
Phchi.S1	AUGUSTUS	stop_codon	711885	711887	.	+	0	transcript_id "Phchi.S1G010500.t1"; gene_id "Phchi.S1G010500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg158.t1 is derived from g9940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	899876	901561	.	-	.	Phchi.S6G011700
Phchi.S6	AUGUSTUS	transcript	899876	901561	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	stop_codon	899873	899875	.	-	0	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	899876	899965	0.97	-	0	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	899876	899965	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	899966	900097	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	900098	900153	0.85	-	2	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	900098	900153	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	900154	900248	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	900249	900355	0.94	-	1	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	900249	900355	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	900356	900469	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	900470	900557	0.5	-	2	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	900470	900557	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	900558	900715	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	900716	900729	0.91	-	1	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	900716	900729	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	900730	900829	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	900830	900951	0.92	-	0	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	900830	900951	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	900952	901160	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	901161	901459	0.64	-	2	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	901161	901459	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	intron	901460	901551	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	CDS	901552	901561	0.97	-	0	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	exon	901552	901561	.	-	.	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
Phchi.S6	AUGUSTUS	start_codon	901559	901561	.	-	0	transcript_id "Phchi.S6G011700.t1"; gene_id "Phchi.S6G011700"
# This transcript jg6688.t2 is derived from g3860.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6689.t1 is derived from g3861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24521187	24522326	.	-	.	Phchi.S1G384800
Phchi.S1	AUGUSTUS	transcript	24521187	24522326	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	stop_codon	24521184	24521186	.	-	0	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	CDS	24521187	24521636	0.62	-	0	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	exon	24521187	24521636	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	intron	24521637	24521719	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	CDS	24521720	24521778	0.89	-	2	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	exon	24521720	24521778	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	intron	24521779	24521888	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	CDS	24521889	24521987	0.99	-	2	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	exon	24521889	24521987	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	intron	24521988	24522099	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	CDS	24522100	24522153	0.52	-	2	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	exon	24522100	24522153	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	intron	24522154	24522250	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	CDS	24522251	24522326	0.97	-	0	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	exon	24522251	24522326	.	-	.	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
Phchi.S1	AUGUSTUS	start_codon	24522324	24522326	.	-	0	transcript_id "Phchi.S1G384800.t1"; gene_id "Phchi.S1G384800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6928.t1 is derived from g4100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26029873	26031103	.	+	.	Phchi.S1G408700
Phchi.S1	AUGUSTUS	transcript	26029873	26031103	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	start_codon	26029873	26029875	.	+	0	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	CDS	26029873	26030050	0.99	+	0	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	exon	26029873	26030050	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	intron	26030051	26030144	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	CDS	26030145	26030237	1	+	2	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	exon	26030145	26030237	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	intron	26030238	26030353	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	CDS	26030354	26030478	1	+	2	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	exon	26030354	26030478	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	intron	26030479	26030971	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	CDS	26030972	26031103	1	+	0	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	exon	26030972	26031103	.	+	.	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
Phchi.S1	AUGUSTUS	stop_codon	26031104	26031106	.	+	0	transcript_id "Phchi.S1G408700.t1"; gene_id "Phchi.S1G408700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1729.t1 is derived from g8649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2746289	2748842	.	+	.	Phchi.S5G033800
Phchi.S5	AUGUSTUS	transcript	2746289	2748842	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	start_codon	2746289	2746291	.	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2746289	2746924	0.86	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2746289	2746924	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	intron	2746925	2747008	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2747009	2747134	1	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2747009	2747134	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	intron	2747135	2747233	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2747234	2747338	1	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2747234	2747338	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	intron	2747339	2747426	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2747427	2747820	0.97	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2747427	2747820	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	intron	2747821	2747921	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2747922	2748051	0.94	+	2	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2747922	2748051	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	intron	2748052	2748153	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2748154	2748448	0.92	+	1	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2748154	2748448	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	intron	2748449	2748560	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	CDS	2748561	2748842	0.39	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	exon	2748561	2748842	.	+	.	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
Phchi.S5	AUGUSTUS	stop_codon	2748843	2748845	.	+	0	transcript_id "Phchi.S5G033800.t1"; gene_id "Phchi.S5G033800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1947.t1 is derived from g8867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3955192	3955638	.	+	.	Phchi.S5G055600
Phchi.S5	AUGUSTUS	transcript	3955192	3955638	.	+	.	transcript_id "Phchi.S5G055600.t1"; gene_id "Phchi.S5G055600"
Phchi.S5	AUGUSTUS	start_codon	3955192	3955194	.	+	0	transcript_id "Phchi.S5G055600.t1"; gene_id "Phchi.S5G055600"
Phchi.S5	AUGUSTUS	CDS	3955192	3955638	0.39	+	0	transcript_id "Phchi.S5G055600.t1"; gene_id "Phchi.S5G055600"
Phchi.S5	AUGUSTUS	exon	3955192	3955638	.	+	.	transcript_id "Phchi.S5G055600.t1"; gene_id "Phchi.S5G055600"
Phchi.S5	AUGUSTUS	stop_codon	3955639	3955641	.	+	0	transcript_id "Phchi.S5G055600.t1"; gene_id "Phchi.S5G055600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5150.t1 is derived from g2320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15168118	15169049	.	-	.	Phchi.S1G230900
Phchi.S1	AUGUSTUS	transcript	15168118	15169049	.	-	.	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	stop_codon	15168115	15168117	.	-	0	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	CDS	15168118	15168296	0.72	-	2	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	exon	15168118	15168296	.	-	.	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	intron	15168297	15168391	.	-	.	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	CDS	15168392	15169049	0.72	-	0	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	exon	15168392	15169049	.	-	.	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
Phchi.S1	AUGUSTUS	start_codon	15169047	15169049	.	-	0	transcript_id "Phchi.S1G230900.t1"; gene_id "Phchi.S1G230900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3510.t1 is derived from g679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4143025	4143933	.	-	.	Phchi.S1G066900
Phchi.S1	AUGUSTUS	transcript	4143025	4143933	.	-	.	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	stop_codon	4143022	4143024	.	-	0	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	CDS	4143025	4143673	1	-	1	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	exon	4143025	4143673	.	-	.	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	intron	4143674	4143787	.	-	.	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	CDS	4143788	4143933	1	-	0	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	exon	4143788	4143933	.	-	.	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
Phchi.S1	AUGUSTUS	start_codon	4143931	4143933	.	-	0	transcript_id "Phchi.S1G066900.t1"; gene_id "Phchi.S1G066900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9577.t1 is derived from g6753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42741339	42742013	.	+	.	Phchi.S1G673600
Phchi.S1	AUGUSTUS	transcript	42741339	42742013	.	+	.	transcript_id "Phchi.S1G673600.t1"; gene_id "Phchi.S1G673600"
Phchi.S1	AUGUSTUS	start_codon	42741339	42741341	.	+	0	transcript_id "Phchi.S1G673600.t1"; gene_id "Phchi.S1G673600"
Phchi.S1	AUGUSTUS	CDS	42741339	42742013	0.93	+	0	transcript_id "Phchi.S1G673600.t1"; gene_id "Phchi.S1G673600"
Phchi.S1	AUGUSTUS	exon	42741339	42742013	.	+	.	transcript_id "Phchi.S1G673600.t1"; gene_id "Phchi.S1G673600"
Phchi.S1	AUGUSTUS	stop_codon	42742014	42742016	.	+	0	transcript_id "Phchi.S1G673600.t1"; gene_id "Phchi.S1G673600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15001.t1 is derived from g13469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16198225	16199154	.	+	.	Phchi.S3G232000
Phchi.S3	AUGUSTUS	transcript	16198225	16199154	.	+	.	transcript_id "Phchi.S3G232000.t1"; gene_id "Phchi.S3G232000"
Phchi.S3	AUGUSTUS	start_codon	16198225	16198227	.	+	0	transcript_id "Phchi.S3G232000.t1"; gene_id "Phchi.S3G232000"
Phchi.S3	AUGUSTUS	CDS	16198225	16199154	0.68	+	0	transcript_id "Phchi.S3G232000.t1"; gene_id "Phchi.S3G232000"
Phchi.S3	AUGUSTUS	exon	16198225	16199154	.	+	.	transcript_id "Phchi.S3G232000.t1"; gene_id "Phchi.S3G232000"
Phchi.S3	AUGUSTUS	stop_codon	16199155	16199157	.	+	0	transcript_id "Phchi.S3G232000.t1"; gene_id "Phchi.S3G232000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10360.t1 is derived from g7536.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47340228	47343840	.	+	.	Phchi.S1G751900
Phchi.S1	AUGUSTUS	transcript	47340228	47343840	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	start_codon	47340228	47340230	.	+	0	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47340228	47342121	0.28	+	0	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47340228	47342121	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	intron	47342122	47342442	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47342443	47342634	0.63	+	2	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47342443	47342634	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	intron	47342635	47342830	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47342831	47342883	1	+	2	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47342831	47342883	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	intron	47342884	47343063	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47343064	47343840	0.59	+	0	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47343064	47343840	.	+	.	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	stop_codon	47343841	47343843	.	+	0	transcript_id "Phchi.S1G751900.t1"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	transcript	47340228	47343840	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	start_codon	47340228	47340230	.	+	0	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47340228	47342121	0.32	+	0	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47340228	47342121	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	intron	47342122	47342442	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47342443	47342634	0.66	+	2	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47342443	47342634	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	intron	47342635	47342830	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47342831	47342883	1	+	2	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47342831	47342883	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	intron	47342884	47343204	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	CDS	47343205	47343840	0.45	+	0	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	exon	47343205	47343840	.	+	.	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
Phchi.S1	AUGUSTUS	stop_codon	47343841	47343843	.	+	0	transcript_id "Phchi.S1G751900.t2"; gene_id "Phchi.S1G751900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7250.t1 is derived from g4422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27860366	27861322	.	-	.	Phchi.S1G440900
Phchi.S1	AUGUSTUS	transcript	27860366	27861322	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	stop_codon	27860363	27860365	.	-	0	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	CDS	27860366	27860406	0.99	-	2	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	exon	27860366	27860406	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	intron	27860407	27860494	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	CDS	27860495	27860555	0.99	-	0	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	exon	27860495	27860555	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	intron	27860556	27860630	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	CDS	27860631	27860685	1	-	1	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	exon	27860631	27860685	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	intron	27860686	27860759	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	CDS	27860760	27860814	1	-	2	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	exon	27860760	27860814	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	intron	27860815	27860905	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	CDS	27860906	27860975	1	-	0	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	exon	27860906	27860975	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	intron	27860976	27861061	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	CDS	27861062	27861322	0.52	-	0	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	exon	27861062	27861322	.	-	.	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
Phchi.S1	AUGUSTUS	start_codon	27861320	27861322	.	-	0	transcript_id "Phchi.S1G440900.t1"; gene_id "Phchi.S1G440900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg53.t1 is derived from g9835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	138265	138674	.	+	.	Phchi.S6G001200
Phchi.S6	AUGUSTUS	transcript	138265	138674	.	+	.	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	start_codon	138265	138267	.	+	0	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	CDS	138265	138548	0.36	+	0	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	exon	138265	138548	.	+	.	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	intron	138549	138643	.	+	.	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	CDS	138644	138674	0.49	+	1	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	exon	138644	138674	.	+	.	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
Phchi.S6	AUGUSTUS	stop_codon	138675	138677	.	+	0	transcript_id "Phchi.S6G001200.t1"; gene_id "Phchi.S6G001200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11698.t1 is derived from g15749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7757104	7758013	.	-	.	Phchi.S4G128000
Phchi.S4	AUGUSTUS	transcript	7757104	7758013	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	stop_codon	7757101	7757103	.	-	0	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	CDS	7757104	7757151	1	-	0	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	exon	7757104	7757151	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	intron	7757152	7757234	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	CDS	7757235	7757309	1	-	0	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	exon	7757235	7757309	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	intron	7757310	7757451	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	CDS	7757452	7757513	0.99	-	2	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	exon	7757452	7757513	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	intron	7757514	7757670	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	CDS	7757671	7757767	0.85	-	0	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	exon	7757671	7757767	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	intron	7757768	7757944	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	CDS	7757945	7758013	0.65	-	0	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	exon	7757945	7758013	.	-	.	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
Phchi.S4	AUGUSTUS	start_codon	7758011	7758013	.	-	0	transcript_id "Phchi.S4G128000.t1"; gene_id "Phchi.S4G128000"
# This transcript jg12697.t2 is derived from g11162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12698.t1 is derived from g11163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	616427	617095	.	+	.	Phchi.S3G001700
Phchi.S3	AUGUSTUS	transcript	616427	617095	.	+	.	transcript_id "Phchi.S3G001700.t1"; gene_id "Phchi.S3G001700"
Phchi.S3	AUGUSTUS	start_codon	616427	616429	.	+	0	transcript_id "Phchi.S3G001700.t1"; gene_id "Phchi.S3G001700"
Phchi.S3	AUGUSTUS	CDS	616427	617095	0.98	+	0	transcript_id "Phchi.S3G001700.t1"; gene_id "Phchi.S3G001700"
Phchi.S3	AUGUSTUS	exon	616427	617095	.	+	.	transcript_id "Phchi.S3G001700.t1"; gene_id "Phchi.S3G001700"
Phchi.S3	AUGUSTUS	stop_codon	617096	617098	.	+	0	transcript_id "Phchi.S3G001700.t1"; gene_id "Phchi.S3G001700"
# This transcript jg3641.t2 is derived from g810.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3642.t1 is derived from g811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4908854	4910627	.	+	.	Phchi.S1G080100
Phchi.S1	AUGUSTUS	transcript	4909036	4910627	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	start_codon	4909036	4909038	.	+	0	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909036	4909050	0.99	+	0	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909036	4909050	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909051	4909148	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909149	4909174	1	+	0	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909149	4909174	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909175	4909265	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909266	4909366	1	+	1	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909266	4909366	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909367	4909463	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909464	4909561	1	+	2	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909464	4909561	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909562	4909651	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909652	4909828	0.97	+	0	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909652	4909828	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909829	4909899	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909900	4910270	0.99	+	0	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909900	4910270	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4910271	4910359	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4910360	4910627	0.43	+	1	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4910360	4910627	.	+	.	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	stop_codon	4910628	4910630	.	+	0	transcript_id "Phchi.S1G080100.t1"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	transcript	4908854	4910627	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	start_codon	4908854	4908856	.	+	0	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4908854	4908896	0.99	+	0	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4908854	4908896	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4908897	4909002	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909003	4909050	0.96	+	2	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909003	4909050	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909051	4909148	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909149	4909174	0.99	+	2	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909149	4909174	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909175	4909257	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909258	4909366	0.99	+	0	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909258	4909366	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909367	4909463	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909464	4909561	1	+	2	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909464	4909561	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909562	4909651	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909652	4909828	0.93	+	0	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909652	4909828	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4909829	4909899	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4909900	4910270	0.92	+	0	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4909900	4910270	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	intron	4910271	4910359	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	CDS	4910360	4910627	0.38	+	1	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	exon	4910360	4910627	.	+	.	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
Phchi.S1	AUGUSTUS	stop_codon	4910628	4910630	.	+	0	transcript_id "Phchi.S1G080100.t2"; gene_id "Phchi.S1G080100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9609.t1 is derived from g6785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42918870	42920716	.	+	.	Phchi.S1G676800
Phchi.S1	AUGUSTUS	transcript	42918870	42920716	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	start_codon	42918870	42918872	.	+	0	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42918870	42918913	0.78	+	0	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42918870	42918913	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	intron	42918914	42918993	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42918994	42919142	0.94	+	1	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42918994	42919142	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	intron	42919143	42919235	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42919236	42919469	0.97	+	2	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42919236	42919469	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	intron	42919470	42919570	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42919571	42919760	1	+	2	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42919571	42919760	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	intron	42919761	42919819	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42919820	42919945	1	+	1	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42919820	42919945	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	intron	42919946	42920140	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42920141	42920246	1	+	1	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42920141	42920246	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	intron	42920247	42920335	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	CDS	42920336	42920716	1	+	0	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	exon	42920336	42920716	.	+	.	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
Phchi.S1	AUGUSTUS	stop_codon	42920717	42920719	.	+	0	transcript_id "Phchi.S1G676800.t1"; gene_id "Phchi.S1G676800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5261.t1 is derived from g2431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15907639	15909121	.	+	.	Phchi.S1G242000
Phchi.S1	AUGUSTUS	transcript	15907639	15909121	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	start_codon	15907639	15907641	.	+	0	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	CDS	15907639	15907738	0.93	+	0	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	exon	15907639	15907738	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	intron	15907739	15907859	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	CDS	15907860	15908003	0.99	+	2	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	exon	15907860	15908003	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	intron	15908004	15908108	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	CDS	15908109	15908176	1	+	2	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	exon	15908109	15908176	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	intron	15908177	15908385	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	CDS	15908386	15908439	1	+	0	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	exon	15908386	15908439	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	intron	15908440	15908532	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	CDS	15908533	15908592	1	+	0	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	exon	15908533	15908592	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	intron	15908593	15908683	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	CDS	15908684	15909121	1	+	0	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	exon	15908684	15909121	.	+	.	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
Phchi.S1	AUGUSTUS	stop_codon	15909122	15909124	.	+	0	transcript_id "Phchi.S1G242000.t1"; gene_id "Phchi.S1G242000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3760.t1 is derived from g929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5570516	5570918	.	-	.	Phchi.S1G091900
Phchi.S1	AUGUSTUS	transcript	5570516	5570918	.	-	.	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	stop_codon	5570513	5570515	.	-	0	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	CDS	5570516	5570520	1	-	2	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	exon	5570516	5570520	.	-	.	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	intron	5570521	5570659	.	-	.	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	CDS	5570660	5570918	0.95	-	0	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	exon	5570660	5570918	.	-	.	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
Phchi.S1	AUGUSTUS	start_codon	5570916	5570918	.	-	0	transcript_id "Phchi.S1G091900.t1"; gene_id "Phchi.S1G091900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15691.t1 is derived from g14160.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20720115	20722408	.	-	.	Phchi.S3G301000
Phchi.S3	AUGUSTUS	transcript	20720115	20722408	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	stop_codon	20720112	20720114	.	-	0	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20720115	20720160	0.94	-	1	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20720115	20720160	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20720161	20720434	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20720435	20720504	0.99	-	2	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20720435	20720504	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20720505	20720595	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20720596	20720665	1	-	0	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20720596	20720665	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20720666	20721364	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721365	20721514	1	-	0	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721365	20721514	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721515	20721602	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721603	20721732	1	-	1	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721603	20721732	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721733	20721808	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721809	20721871	1	-	1	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721809	20721871	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721872	20722085	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20722086	20722105	1	-	0	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20722086	20722105	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20722106	20722405	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20722406	20722408	1	-	0	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20722406	20722408	.	-	.	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	start_codon	20722406	20722408	.	-	0	transcript_id "Phchi.S3G301000.t1"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	transcript	20720504	20722408	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	stop_codon	20720501	20720503	.	-	0	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20720504	20720504	1	-	1	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20720504	20720504	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20720505	20720595	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20720596	20720665	1	-	2	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20720596	20720665	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20720666	20720831	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20720832	20720960	0.56	-	2	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20720832	20720960	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20720961	20721126	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721127	20721214	0.68	-	0	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721127	20721214	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721215	20721364	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721365	20721514	0.99	-	0	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721365	20721514	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721515	20721602	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721603	20721732	1	-	1	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721603	20721732	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721733	20721808	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20721809	20721871	1	-	1	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20721809	20721871	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20721872	20722085	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20722086	20722105	1	-	0	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20722086	20722105	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	intron	20722106	20722405	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	CDS	20722406	20722408	1	-	0	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	exon	20722406	20722408	.	-	.	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
Phchi.S3	AUGUSTUS	start_codon	20722406	20722408	.	-	0	transcript_id "Phchi.S3G301000.t2"; gene_id "Phchi.S3G301000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9624.t1 is derived from g6800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42963148	42964606	.	-	.	Phchi.S1G678300
Phchi.S1	AUGUSTUS	transcript	42963148	42964606	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	stop_codon	42963145	42963147	.	-	0	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	CDS	42963148	42963172	0.95	-	1	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	exon	42963148	42963172	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	intron	42963173	42963255	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	CDS	42963256	42963312	0.67	-	1	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	exon	42963256	42963312	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	intron	42963313	42963508	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	CDS	42963509	42963762	0.67	-	0	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	exon	42963509	42963762	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	intron	42963763	42963855	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	CDS	42963856	42964080	1	-	0	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	exon	42963856	42964080	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	intron	42964081	42964156	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	CDS	42964157	42964606	1	-	0	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	exon	42964157	42964606	.	-	.	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
Phchi.S1	AUGUSTUS	start_codon	42964604	42964606	.	-	0	transcript_id "Phchi.S1G678300.t1"; gene_id "Phchi.S1G678300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6883.t1 is derived from g4055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25816012	25819718	.	+	.	Phchi.S1G404200
Phchi.S1	AUGUSTUS	transcript	25816012	25819718	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	start_codon	25816012	25816014	.	+	0	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	CDS	25816012	25816346	0.82	+	0	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	exon	25816012	25816346	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	intron	25816347	25816549	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	CDS	25816550	25817055	0.91	+	1	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	exon	25816550	25817055	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	intron	25817056	25817198	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	CDS	25817199	25817472	0.64	+	2	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	exon	25817199	25817472	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	intron	25817473	25817579	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	CDS	25817580	25818918	0.3	+	1	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	exon	25817580	25818918	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	intron	25818919	25819033	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	CDS	25819034	25819354	0.89	+	0	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	exon	25819034	25819354	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	intron	25819355	25819463	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	CDS	25819464	25819718	0.83	+	0	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	exon	25819464	25819718	.	+	.	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
Phchi.S1	AUGUSTUS	stop_codon	25819719	25819721	.	+	0	transcript_id "Phchi.S1G404200.t1"; gene_id "Phchi.S1G404200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg155.t1 is derived from g9937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	884623	886307	.	-	.	Phchi.S6G011400
Phchi.S6	AUGUSTUS	transcript	884623	886307	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	stop_codon	884620	884622	.	-	0	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	884623	884712	0.95	-	0	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	884623	884712	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	884713	884844	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	884845	884904	0.78	-	0	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	884845	884904	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	884905	885061	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	885062	885101	0.83	-	1	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	885062	885101	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	885102	885215	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	885216	885303	0.32	-	2	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	885216	885303	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	885304	885461	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	885462	885475	0.86	-	1	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	885462	885475	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	885476	885575	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	885576	885697	0.9	-	0	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	885576	885697	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	885698	885906	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	885907	886205	0.69	-	2	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	885907	886205	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	intron	886206	886297	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	CDS	886298	886307	0.98	-	0	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	exon	886298	886307	.	-	.	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
Phchi.S6	AUGUSTUS	start_codon	886305	886307	.	-	0	transcript_id "Phchi.S6G011400.t1"; gene_id "Phchi.S6G011400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4063.t1 is derived from g1232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7589451	7591778	.	-	.	Phchi.S1G122200
Phchi.S1	AUGUSTUS	transcript	7589451	7590287	.	-	.	transcript_id "Phchi.S1G122200.t1"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	stop_codon	7589448	7589450	.	-	0	transcript_id "Phchi.S1G122200.t1"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	CDS	7589451	7590287	0.59	-	0	transcript_id "Phchi.S1G122200.t1"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	exon	7589451	7590287	.	-	.	transcript_id "Phchi.S1G122200.t1"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	start_codon	7590285	7590287	.	-	0	transcript_id "Phchi.S1G122200.t1"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	transcript	7589451	7591778	.	-	.	transcript_id "Phchi.S1G122200.t2"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	stop_codon	7589448	7589450	.	-	0	transcript_id "Phchi.S1G122200.t2"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	CDS	7589451	7591778	0.55	-	0	transcript_id "Phchi.S1G122200.t2"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	exon	7589451	7591778	.	-	.	transcript_id "Phchi.S1G122200.t2"; gene_id "Phchi.S1G122200"
Phchi.S1	AUGUSTUS	start_codon	7591776	7591778	.	-	0	transcript_id "Phchi.S1G122200.t2"; gene_id "Phchi.S1G122200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8185.t1 is derived from g5360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34333972	34335485	.	-	.	Phchi.S1G534400
Phchi.S1	AUGUSTUS	transcript	34333972	34335485	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	stop_codon	34333969	34333971	.	-	0	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	CDS	34333972	34334736	1	-	0	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	exon	34333972	34334736	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	intron	34334737	34334820	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	CDS	34334821	34334919	0.53	-	0	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	exon	34334821	34334919	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	intron	34334920	34335002	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	CDS	34335003	34335095	0.49	-	0	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	exon	34335003	34335095	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	intron	34335096	34335182	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	CDS	34335183	34335485	0.77	-	0	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	exon	34335183	34335485	.	-	.	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
Phchi.S1	AUGUSTUS	start_codon	34335483	34335485	.	-	0	transcript_id "Phchi.S1G534400.t1"; gene_id "Phchi.S1G534400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8266.t1 is derived from g5441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35031285	35032104	.	+	.	Phchi.S1G542500
Phchi.S1	AUGUSTUS	transcript	35031285	35032104	.	+	.	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	start_codon	35031285	35031287	.	+	0	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	CDS	35031285	35031485	0.92	+	0	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	exon	35031285	35031485	.	+	.	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	intron	35031486	35031609	.	+	.	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	CDS	35031610	35032104	1	+	0	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	exon	35031610	35032104	.	+	.	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
Phchi.S1	AUGUSTUS	stop_codon	35032105	35032107	.	+	0	transcript_id "Phchi.S1G542500.t1"; gene_id "Phchi.S1G542500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15008.t1 is derived from g13476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16341792	16342513	.	-	.	Phchi.S3G232700
Phchi.S3	AUGUSTUS	transcript	16341792	16342513	.	-	.	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	stop_codon	16341789	16341791	.	-	0	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	CDS	16341792	16342136	0.67	-	0	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	exon	16341792	16342136	.	-	.	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	intron	16342137	16342243	.	-	.	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	CDS	16342244	16342405	0.17	-	0	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	exon	16342244	16342405	.	-	.	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	intron	16342406	16342504	.	-	.	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	CDS	16342505	16342513	0.78	-	0	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	exon	16342505	16342513	.	-	.	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
Phchi.S3	AUGUSTUS	start_codon	16342511	16342513	.	-	0	transcript_id "Phchi.S3G232700.t1"; gene_id "Phchi.S3G232700"
# This transcript jg5531.t2 is derived from g2701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5532.t1 is derived from g2702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17435061	17435868	.	-	.	Phchi.S1G269100
Phchi.S1	AUGUSTUS	transcript	17435061	17435868	.	-	.	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	stop_codon	17435058	17435060	.	-	0	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	CDS	17435061	17435149	1	-	2	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	exon	17435061	17435149	.	-	.	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	intron	17435150	17435280	.	-	.	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	CDS	17435281	17435383	1	-	0	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	exon	17435281	17435383	.	-	.	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	intron	17435384	17435487	.	-	.	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	CDS	17435488	17435868	0.74	-	0	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	exon	17435488	17435868	.	-	.	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
Phchi.S1	AUGUSTUS	start_codon	17435866	17435868	.	-	0	transcript_id "Phchi.S1G269100.t1"; gene_id "Phchi.S1G269100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12516.t1 is derived from g8193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32634991	32636507	.	-	.	Phchi.S2G059600
Phchi.S2	AUGUSTUS	transcript	32634991	32636507	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	stop_codon	32634988	32634990	.	-	0	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	CDS	32634991	32635084	1	-	1	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	exon	32634991	32635084	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	intron	32635085	32635210	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	CDS	32635211	32635331	1	-	2	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	exon	32635211	32635331	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	intron	32635332	32635449	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	CDS	32635450	32635543	1	-	0	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	exon	32635450	32635543	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	intron	32635544	32636098	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	CDS	32636099	32636257	1	-	0	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	exon	32636099	32636257	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	intron	32636258	32636447	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	CDS	32636448	32636507	0.99	-	0	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	exon	32636448	32636507	.	-	.	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
Phchi.S2	AUGUSTUS	start_codon	32636505	32636507	.	-	0	transcript_id "Phchi.S2G059600.t1"; gene_id "Phchi.S2G059600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2930.t1 is derived from g99.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	598158	602656	.	-	.	Phchi.S1G008900
Phchi.S1	AUGUSTUS	transcript	598158	602656	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	stop_codon	598155	598157	.	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	598158	598271	0.99	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	598158	598271	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	598272	598398	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	598399	598676	1	-	2	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	598399	598676	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	598677	598768	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	598769	598931	1	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	598769	598931	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	598932	599231	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	599232	599495	0.75	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	599232	599495	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	599496	599673	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	599674	599834	0.58	-	2	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	599674	599834	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	599835	600099	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	600100	601939	0.57	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	600100	601939	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	601940	602108	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	602109	602203	1	-	2	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	602109	602203	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	602204	602451	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	602452	602511	0.63	-	2	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	602452	602511	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	intron	602512	602589	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	CDS	602590	602656	0.63	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	exon	602590	602656	.	-	.	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
Phchi.S1	AUGUSTUS	start_codon	602654	602656	.	-	0	transcript_id "Phchi.S1G008900.t1"; gene_id "Phchi.S1G008900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg435.t1 is derived from g10217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3065465	3067100	.	-	.	Phchi.S6G039400
Phchi.S6	AUGUSTUS	transcript	3065465	3067100	.	-	.	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	stop_codon	3065462	3065464	.	-	0	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	CDS	3065465	3065601	0.9	-	2	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	exon	3065465	3065601	.	-	.	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	intron	3065602	3065768	.	-	.	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	CDS	3065769	3066660	0.93	-	0	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	exon	3065769	3066660	.	-	.	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	intron	3066661	3066743	.	-	.	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	CDS	3066744	3067100	1	-	0	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	exon	3066744	3067100	.	-	.	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
Phchi.S6	AUGUSTUS	start_codon	3067098	3067100	.	-	0	transcript_id "Phchi.S6G039400.t1"; gene_id "Phchi.S6G039400"
# This transcript jg11738.t2 is derived from g15790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11739.t1 is derived from g15791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7931399	7932831	.	-	.	Phchi.S4G132100
Phchi.S4	AUGUSTUS	transcript	7931399	7932831	.	-	.	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	stop_codon	7931396	7931398	.	-	0	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	CDS	7931399	7932325	0.93	-	0	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	exon	7931399	7932325	.	-	.	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	intron	7932326	7932499	.	-	.	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	CDS	7932500	7932614	0.91	-	1	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	exon	7932500	7932614	.	-	.	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	intron	7932615	7932697	.	-	.	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	CDS	7932698	7932831	0.98	-	0	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	exon	7932698	7932831	.	-	.	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
Phchi.S4	AUGUSTUS	start_codon	7932829	7932831	.	-	0	transcript_id "Phchi.S4G132100.t1"; gene_id "Phchi.S4G132100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5133.t1 is derived from g2303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15075367	15079645	.	-	.	Phchi.S1G229200
Phchi.S1	AUGUSTUS	transcript	15075367	15079645	.	-	.	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	stop_codon	15075364	15075366	.	-	0	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	CDS	15075367	15077240	0.47	-	2	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	exon	15075367	15077240	.	-	.	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	intron	15077241	15077334	.	-	.	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	CDS	15077335	15079256	0.43	-	1	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	exon	15077335	15079256	.	-	.	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	intron	15079257	15079403	.	-	.	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	CDS	15079404	15079645	0.92	-	0	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	exon	15079404	15079645	.	-	.	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
Phchi.S1	AUGUSTUS	start_codon	15079643	15079645	.	-	0	transcript_id "Phchi.S1G229200.t1"; gene_id "Phchi.S1G229200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10523.t1 is derived from g14573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	828902	830106	.	+	.	Phchi.S4G010500
Phchi.S4	AUGUSTUS	transcript	828902	830106	.	+	.	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	start_codon	828902	828904	.	+	0	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	CDS	828902	828998	0.86	+	0	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	exon	828902	828998	.	+	.	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	intron	828999	829103	.	+	.	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	CDS	829104	829261	0.83	+	2	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	exon	829104	829261	.	+	.	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	intron	829262	829386	.	+	.	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	CDS	829387	830106	1	+	0	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	exon	829387	830106	.	+	.	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
Phchi.S4	AUGUSTUS	stop_codon	830107	830109	.	+	0	transcript_id "Phchi.S4G010500.t1"; gene_id "Phchi.S4G010500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8293.t1 is derived from g5468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35128370	35129626	.	-	.	Phchi.S1G545200
Phchi.S1	AUGUSTUS	transcript	35128370	35129626	.	-	.	transcript_id "Phchi.S1G545200.t1"; gene_id "Phchi.S1G545200"
Phchi.S1	AUGUSTUS	stop_codon	35128367	35128369	.	-	0	transcript_id "Phchi.S1G545200.t1"; gene_id "Phchi.S1G545200"
Phchi.S1	AUGUSTUS	CDS	35128370	35129626	1	-	0	transcript_id "Phchi.S1G545200.t1"; gene_id "Phchi.S1G545200"
Phchi.S1	AUGUSTUS	exon	35128370	35129626	.	-	.	transcript_id "Phchi.S1G545200.t1"; gene_id "Phchi.S1G545200"
Phchi.S1	AUGUSTUS	start_codon	35129624	35129626	.	-	0	transcript_id "Phchi.S1G545200.t1"; gene_id "Phchi.S1G545200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg949.t1 is derived from g10731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6621555	6622100	.	-	.	Phchi.S6G090800
Phchi.S6	AUGUSTUS	transcript	6621555	6622100	.	-	.	transcript_id "Phchi.S6G090800.t1"; gene_id "Phchi.S6G090800"
Phchi.S6	AUGUSTUS	stop_codon	6621552	6621554	.	-	0	transcript_id "Phchi.S6G090800.t1"; gene_id "Phchi.S6G090800"
Phchi.S6	AUGUSTUS	CDS	6621555	6622100	0.5	-	0	transcript_id "Phchi.S6G090800.t1"; gene_id "Phchi.S6G090800"
Phchi.S6	AUGUSTUS	exon	6621555	6622100	.	-	.	transcript_id "Phchi.S6G090800.t1"; gene_id "Phchi.S6G090800"
Phchi.S6	AUGUSTUS	start_codon	6622098	6622100	.	-	0	transcript_id "Phchi.S6G090800.t1"; gene_id "Phchi.S6G090800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8383.t1 is derived from g5558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35607456	35608076	.	-	.	Phchi.S1G554200
Phchi.S1	AUGUSTUS	transcript	35607456	35608076	.	-	.	transcript_id "Phchi.S1G554200.t1"; gene_id "Phchi.S1G554200"
Phchi.S1	AUGUSTUS	stop_codon	35607453	35607455	.	-	0	transcript_id "Phchi.S1G554200.t1"; gene_id "Phchi.S1G554200"
Phchi.S1	AUGUSTUS	CDS	35607456	35608076	0.98	-	0	transcript_id "Phchi.S1G554200.t1"; gene_id "Phchi.S1G554200"
Phchi.S1	AUGUSTUS	exon	35607456	35608076	.	-	.	transcript_id "Phchi.S1G554200.t1"; gene_id "Phchi.S1G554200"
Phchi.S1	AUGUSTUS	start_codon	35608074	35608076	.	-	0	transcript_id "Phchi.S1G554200.t1"; gene_id "Phchi.S1G554200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2637.t1 is derived from g9557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7902951	7904201	.	+	.	Phchi.S5G124600
Phchi.S5	AUGUSTUS	transcript	7902951	7904201	.	+	.	transcript_id "Phchi.S5G124600.t1"; gene_id "Phchi.S5G124600"
Phchi.S5	AUGUSTUS	start_codon	7902951	7902953	.	+	0	transcript_id "Phchi.S5G124600.t1"; gene_id "Phchi.S5G124600"
Phchi.S5	AUGUSTUS	CDS	7902951	7904201	1	+	0	transcript_id "Phchi.S5G124600.t1"; gene_id "Phchi.S5G124600"
Phchi.S5	AUGUSTUS	exon	7902951	7904201	.	+	.	transcript_id "Phchi.S5G124600.t1"; gene_id "Phchi.S5G124600"
Phchi.S5	AUGUSTUS	stop_codon	7904202	7904204	.	+	0	transcript_id "Phchi.S5G124600.t1"; gene_id "Phchi.S5G124600"
# This transcript jg6707.t2 is derived from g3879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6708.t1 is derived from g3880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24643957	24646410	.	+	.	Phchi.S1G386700
Phchi.S1	AUGUSTUS	transcript	24643957	24646410	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	start_codon	24643957	24643959	.	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24643957	24645021	0.99	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24643957	24645021	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24645022	24645098	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24645099	24645180	1	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24645099	24645180	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24645181	24645284	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24645285	24645381	1	+	2	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24645285	24645381	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24645382	24645583	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24645584	24645647	1	+	1	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24645584	24645647	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24645648	24645787	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24645788	24645844	1	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24645788	24645844	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24645845	24645992	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24645993	24646030	1	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24645993	24646030	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24646031	24646117	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24646118	24646199	1	+	1	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24646118	24646199	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	intron	24646200	24646323	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	CDS	24646324	24646410	1	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	exon	24646324	24646410	.	+	.	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
Phchi.S1	AUGUSTUS	stop_codon	24646411	24646413	.	+	0	transcript_id "Phchi.S1G386700.t1"; gene_id "Phchi.S1G386700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13330.t1 is derived from g11796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6129723	6131322	.	-	.	Phchi.S3G064900
Phchi.S3	AUGUSTUS	transcript	6129723	6131322	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	stop_codon	6129720	6129722	.	-	0	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	CDS	6129723	6129958	0.86	-	2	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	exon	6129723	6129958	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	intron	6129959	6130041	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	CDS	6130042	6130327	1	-	0	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	exon	6130042	6130327	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	intron	6130328	6130421	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	CDS	6130422	6130609	1	-	2	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	exon	6130422	6130609	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	intron	6130610	6130716	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	CDS	6130717	6130923	0.99	-	2	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	exon	6130717	6130923	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	intron	6130924	6131036	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	CDS	6131037	6131322	0.9	-	0	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	exon	6131037	6131322	.	-	.	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
Phchi.S3	AUGUSTUS	start_codon	6131320	6131322	.	-	0	transcript_id "Phchi.S3G064900.t1"; gene_id "Phchi.S3G064900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4144.t1 is derived from g1313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8627964	8628539	.	-	.	Phchi.S1G130300
Phchi.S1	AUGUSTUS	transcript	8627964	8628539	.	-	.	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	stop_codon	8627961	8627963	.	-	0	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	CDS	8627964	8628131	1	-	0	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	exon	8627964	8628131	.	-	.	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	intron	8628132	8628201	.	-	.	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	CDS	8628202	8628292	1	-	1	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	exon	8628202	8628292	.	-	.	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	intron	8628293	8628390	.	-	.	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	CDS	8628391	8628539	1	-	0	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	exon	8628391	8628539	.	-	.	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
Phchi.S1	AUGUSTUS	start_codon	8628537	8628539	.	-	0	transcript_id "Phchi.S1G130300.t1"; gene_id "Phchi.S1G130300"
# This transcript jg12747.t2 is derived from g11212.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12748.t1 is derived from g11213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1794456	1796324	.	+	.	Phchi.S3G006700
Phchi.S3	AUGUSTUS	transcript	1794477	1796324	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	start_codon	1794477	1794479	.	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1794477	1794552	0.53	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1794477	1794552	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1794553	1794638	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1794639	1794721	1	+	2	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1794639	1794721	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1794722	1794823	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1794824	1794936	0.99	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1794824	1794936	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1794937	1795034	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795035	1795116	1	+	1	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795035	1795116	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795117	1795251	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795252	1795389	1	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795252	1795389	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795390	1795485	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795486	1795605	1	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795486	1795605	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795606	1795689	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795690	1795783	1	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795690	1795783	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795784	1795890	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795891	1795961	0.86	+	2	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795891	1795961	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795962	1796048	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1796049	1796324	0.63	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1796049	1796324	.	+	.	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	stop_codon	1796325	1796327	.	+	0	transcript_id "Phchi.S3G006700.t1"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	transcript	1794456	1796324	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	start_codon	1794456	1794458	.	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1794456	1794471	0.76	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1794456	1794471	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1794472	1794638	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1794639	1794721	1	+	2	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1794639	1794721	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1794722	1794823	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1794824	1794936	1	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1794824	1794936	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1794937	1795034	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795035	1795116	1	+	1	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795035	1795116	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795117	1795251	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795252	1795389	1	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795252	1795389	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795390	1795485	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795486	1795605	1	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795486	1795605	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795606	1795689	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795690	1795783	1	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795690	1795783	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795784	1795890	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1795891	1795961	0.79	+	2	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1795891	1795961	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	intron	1795962	1796048	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	CDS	1796049	1796324	0.58	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	exon	1796049	1796324	.	+	.	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
Phchi.S3	AUGUSTUS	stop_codon	1796325	1796327	.	+	0	transcript_id "Phchi.S3G006700.t2"; gene_id "Phchi.S3G006700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2422.t1 is derived from g9342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6574261	6577880	.	-	.	Phchi.S5G103100
Phchi.S5	AUGUSTUS	transcript	6574261	6577880	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	stop_codon	6574258	6574260	.	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6574261	6574322	0.91	-	2	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6574261	6574322	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6574323	6574430	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6574431	6574500	0.91	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6574431	6574500	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6574501	6574591	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6574592	6574745	1	-	1	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6574592	6574745	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6574746	6574834	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6574835	6574959	1	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6574835	6574959	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6574960	6575064	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6575065	6575136	0.99	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6575065	6575136	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6575137	6575242	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6575243	6575370	0.88	-	2	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6575243	6575370	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6575371	6575502	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6575503	6575698	1	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6575503	6575698	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6575699	6575800	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6575801	6575980	1	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6575801	6575980	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6575981	6576064	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6576065	6576205	0.99	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6576065	6576205	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6576206	6576316	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6576317	6576481	0.99	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6576317	6576481	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6576482	6576633	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6576634	6576780	1	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6576634	6576780	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6576781	6576921	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6576922	6577011	0.93	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6576922	6577011	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6577012	6577117	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6577118	6577324	0.89	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6577118	6577324	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6577325	6577448	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6577449	6577538	1	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6577449	6577538	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	intron	6577539	6577754	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	CDS	6577755	6577880	0.97	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	exon	6577755	6577880	.	-	.	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
Phchi.S5	AUGUSTUS	start_codon	6577878	6577880	.	-	0	transcript_id "Phchi.S5G103100.t1"; gene_id "Phchi.S5G103100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4752.t1 is derived from g1922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12628964	12630005	.	-	.	Phchi.S1G191100
Phchi.S1	AUGUSTUS	transcript	12628964	12630005	.	-	.	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	stop_codon	12628961	12628963	.	-	0	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	CDS	12628964	12629407	0.98	-	0	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	exon	12628964	12629407	.	-	.	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	intron	12629408	12629497	.	-	.	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	CDS	12629498	12629719	0.87	-	0	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	exon	12629498	12629719	.	-	.	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	intron	12629720	12629840	.	-	.	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	CDS	12629841	12630005	1	-	0	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	exon	12629841	12630005	.	-	.	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
Phchi.S1	AUGUSTUS	start_codon	12630003	12630005	.	-	0	transcript_id "Phchi.S1G191100.t1"; gene_id "Phchi.S1G191100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8173.t1 is derived from g5348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34277446	34280792	.	+	.	Phchi.S1G533200
Phchi.S1	AUGUSTUS	transcript	34277446	34280792	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	start_codon	34277446	34277448	.	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34277446	34277543	0.7	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34277446	34277543	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34277544	34277644	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34277645	34277765	1	+	1	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34277645	34277765	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34277766	34277868	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34277869	34278174	0.99	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34277869	34278174	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34278175	34278323	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34278324	34278434	1	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34278324	34278434	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34278435	34278572	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34278573	34278761	1	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34278573	34278761	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34278762	34278853	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34278854	34279116	1	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34278854	34279116	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34279117	34279294	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34279295	34279596	1	+	1	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34279295	34279596	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34279597	34279720	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34279721	34279899	0.99	+	2	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34279721	34279899	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34279900	34280037	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34280038	34280228	1	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34280038	34280228	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34280229	34280327	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34280328	34280467	1	+	1	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34280328	34280467	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34280468	34280556	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34280557	34280607	1	+	2	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34280557	34280607	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	intron	34280608	34280688	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	CDS	34280689	34280792	1	+	2	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	exon	34280689	34280792	.	+	.	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
Phchi.S1	AUGUSTUS	stop_codon	34280793	34280795	.	+	0	transcript_id "Phchi.S1G533200.t1"; gene_id "Phchi.S1G533200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg403.t1 is derived from g10185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2900141	2903849	.	-	.	Phchi.S6G036200
Phchi.S6	AUGUSTUS	transcript	2900141	2903849	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	stop_codon	2900138	2900140	.	-	0	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	CDS	2900141	2900171	0.97	-	1	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	exon	2900141	2900171	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	intron	2900172	2900383	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	CDS	2900384	2900437	0.89	-	1	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	exon	2900384	2900437	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	intron	2900438	2900761	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	CDS	2900762	2902363	0.39	-	1	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	exon	2900762	2902363	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	intron	2902364	2902437	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	CDS	2902438	2903849	0.84	-	0	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	exon	2902438	2903849	.	-	.	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
Phchi.S6	AUGUSTUS	start_codon	2903847	2903849	.	-	0	transcript_id "Phchi.S6G036200.t1"; gene_id "Phchi.S6G036200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13627.t1 is derived from g12094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7826048	7826811	.	-	.	Phchi.S3G094600
Phchi.S3	AUGUSTUS	transcript	7826048	7826811	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	stop_codon	7826045	7826047	.	-	0	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	CDS	7826048	7826123	1	-	1	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	exon	7826048	7826123	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	intron	7826124	7826216	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	CDS	7826217	7826272	1	-	0	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	exon	7826217	7826272	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	intron	7826273	7826414	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	CDS	7826415	7826497	1	-	2	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	exon	7826415	7826497	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	intron	7826498	7826639	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	CDS	7826640	7826811	0.75	-	0	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	exon	7826640	7826811	.	-	.	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
Phchi.S3	AUGUSTUS	start_codon	7826809	7826811	.	-	0	transcript_id "Phchi.S3G094600.t1"; gene_id "Phchi.S3G094600"
# This transcript jg12588.t2 is derived from g8265.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12588.t3 is derived from g8265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12589.t1 is derived from g8266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36273899	36274522	.	+	.	Phchi.S2G066900
Phchi.S2	AUGUSTUS	transcript	36273899	36274522	.	+	.	transcript_id "Phchi.S2G066900.t1"; gene_id "Phchi.S2G066900"
Phchi.S2	AUGUSTUS	start_codon	36273899	36273901	.	+	0	transcript_id "Phchi.S2G066900.t1"; gene_id "Phchi.S2G066900"
Phchi.S2	AUGUSTUS	CDS	36273899	36274522	0.96	+	0	transcript_id "Phchi.S2G066900.t1"; gene_id "Phchi.S2G066900"
Phchi.S2	AUGUSTUS	exon	36273899	36274522	.	+	.	transcript_id "Phchi.S2G066900.t1"; gene_id "Phchi.S2G066900"
Phchi.S2	AUGUSTUS	stop_codon	36274523	36274525	.	+	0	transcript_id "Phchi.S2G066900.t1"; gene_id "Phchi.S2G066900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7504.t1 is derived from g4678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29702711	29705012	.	-	.	Phchi.S1G466300
Phchi.S1	AUGUSTUS	transcript	29702711	29705012	.	-	.	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	stop_codon	29702708	29702710	.	-	0	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	CDS	29702711	29703616	0.81	-	0	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	exon	29702711	29703616	.	-	.	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	intron	29703617	29703806	.	-	.	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	CDS	29703807	29705012	0.68	-	0	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	exon	29703807	29705012	.	-	.	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
Phchi.S1	AUGUSTUS	start_codon	29705010	29705012	.	-	0	transcript_id "Phchi.S1G466300.t1"; gene_id "Phchi.S1G466300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5638.t1 is derived from g2808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17994289	17996558	.	-	.	Phchi.S1G279700
Phchi.S1	AUGUSTUS	transcript	17994289	17996558	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	stop_codon	17994286	17994288	.	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17994289	17994295	0.96	-	1	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17994289	17994295	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17994296	17994382	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17994383	17994420	0.93	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17994383	17994420	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17994421	17994484	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17994485	17994501	0.93	-	2	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17994485	17994501	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17994502	17994640	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17994641	17994752	1	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17994641	17994752	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17994753	17994840	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17994841	17994869	0.95	-	2	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17994841	17994869	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17994870	17994967	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17994968	17994982	0.94	-	2	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17994968	17994982	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17994983	17995079	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17995080	17995150	0.96	-	1	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17995080	17995150	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17995151	17995238	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17995239	17995405	1	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17995239	17995405	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17995406	17995515	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17995516	17995635	0.93	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17995516	17995635	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17995636	17995735	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17995736	17995834	0.91	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17995736	17995834	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17995835	17995985	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17995986	17996182	0.59	-	2	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17995986	17996182	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	intron	17996183	17996374	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	CDS	17996375	17996558	0.65	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	exon	17996375	17996558	.	-	.	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
Phchi.S1	AUGUSTUS	start_codon	17996556	17996558	.	-	0	transcript_id "Phchi.S1G279700.t1"; gene_id "Phchi.S1G279700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15430.t1 is derived from g13898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19052516	19054684	.	+	.	Phchi.S3G274900
Phchi.S3	AUGUSTUS	transcript	19052516	19054684	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	start_codon	19052516	19052518	.	+	0	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	CDS	19052516	19053790	0.76	+	0	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	exon	19052516	19053790	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	intron	19053791	19053881	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	CDS	19053882	19054083	0.44	+	0	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	exon	19053882	19054083	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	intron	19054084	19054215	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	CDS	19054216	19054248	0.42	+	2	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	exon	19054216	19054248	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	intron	19054249	19054489	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	CDS	19054490	19054581	0.42	+	2	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	exon	19054490	19054581	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	intron	19054582	19054654	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	CDS	19054655	19054684	1	+	0	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	exon	19054655	19054684	.	+	.	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
Phchi.S3	AUGUSTUS	stop_codon	19054685	19054687	.	+	0	transcript_id "Phchi.S3G274900.t1"; gene_id "Phchi.S3G274900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3026.t1 is derived from g195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1201452	1203995	.	-	.	Phchi.S1G018500
Phchi.S1	AUGUSTUS	transcript	1201452	1203995	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	stop_codon	1201449	1201451	.	-	0	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1201452	1202346	0.98	-	1	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1201452	1202346	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1202347	1202479	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1202480	1203042	0.97	-	0	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1202480	1203042	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203043	1203134	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203135	1203352	1	-	2	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203135	1203352	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203353	1203542	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203543	1203663	1	-	0	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203543	1203663	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203664	1203761	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203762	1203835	1	-	2	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203762	1203835	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203836	1203940	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203941	1203995	0.95	-	0	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203941	1203995	.	-	.	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	start_codon	1203993	1203995	.	-	0	transcript_id "Phchi.S1G018500.t1"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	transcript	1201452	1203995	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	stop_codon	1201449	1201451	.	-	0	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1201452	1202346	0.97	-	1	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1201452	1202346	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1202347	1202479	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1202480	1203042	0.95	-	0	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1202480	1203042	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203043	1203134	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203135	1203352	1	-	2	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203135	1203352	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203353	1203542	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203543	1203663	1	-	0	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203543	1203663	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203664	1203788	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203789	1203835	0.87	-	2	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203789	1203835	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	intron	1203836	1203940	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	CDS	1203941	1203995	0.89	-	0	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	exon	1203941	1203995	.	-	.	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
Phchi.S1	AUGUSTUS	start_codon	1203993	1203995	.	-	0	transcript_id "Phchi.S1G018500.t2"; gene_id "Phchi.S1G018500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1102.t1 is derived from g10885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7607574	7608125	.	-	.	Phchi.S6G106100
Phchi.S6	AUGUSTUS	transcript	7607574	7608125	.	-	.	transcript_id "Phchi.S6G106100.t1"; gene_id "Phchi.S6G106100"
Phchi.S6	AUGUSTUS	stop_codon	7607571	7607573	.	-	0	transcript_id "Phchi.S6G106100.t1"; gene_id "Phchi.S6G106100"
Phchi.S6	AUGUSTUS	CDS	7607574	7608125	0.59	-	0	transcript_id "Phchi.S6G106100.t1"; gene_id "Phchi.S6G106100"
Phchi.S6	AUGUSTUS	exon	7607574	7608125	.	-	.	transcript_id "Phchi.S6G106100.t1"; gene_id "Phchi.S6G106100"
Phchi.S6	AUGUSTUS	start_codon	7608123	7608125	.	-	0	transcript_id "Phchi.S6G106100.t1"; gene_id "Phchi.S6G106100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15503.t1 is derived from g13972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19569914	19571994	.	+	.	Phchi.S3G282200
Phchi.S3	AUGUSTUS	transcript	19569914	19571994	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	start_codon	19569914	19569916	.	+	0	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	CDS	19569914	19570280	0.98	+	0	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	exon	19569914	19570280	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	intron	19570281	19570430	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	CDS	19570431	19570993	0.97	+	2	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	exon	19570431	19570993	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	intron	19570994	19571494	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	CDS	19571495	19571638	0.32	+	0	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	exon	19571495	19571638	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	intron	19571639	19571770	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	CDS	19571771	19571880	0.97	+	0	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	exon	19571771	19571880	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	intron	19571881	19571972	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	CDS	19571973	19571994	1	+	1	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	exon	19571973	19571994	.	+	.	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
Phchi.S3	AUGUSTUS	stop_codon	19571995	19571997	.	+	0	transcript_id "Phchi.S3G282200.t1"; gene_id "Phchi.S3G282200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6315.t1 is derived from g3487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22226921	22227676	.	-	.	Phchi.S1G347400
Phchi.S1	AUGUSTUS	transcript	22226921	22227676	.	-	.	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	stop_codon	22226918	22226920	.	-	0	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	CDS	22226921	22226989	0.35	-	0	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	exon	22226921	22226989	.	-	.	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	intron	22226990	22227295	.	-	.	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	CDS	22227296	22227327	0.35	-	2	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	exon	22227296	22227327	.	-	.	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	intron	22227328	22227462	.	-	.	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	CDS	22227463	22227676	0.19	-	0	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	exon	22227463	22227676	.	-	.	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
Phchi.S1	AUGUSTUS	start_codon	22227674	22227676	.	-	0	transcript_id "Phchi.S1G347400.t1"; gene_id "Phchi.S1G347400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5161.t1 is derived from g2331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15212445	15213975	.	-	.	Phchi.S1G232000
Phchi.S1	AUGUSTUS	transcript	15212445	15213975	.	-	.	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	stop_codon	15212442	15212444	.	-	0	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	CDS	15212445	15213258	1	-	1	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	exon	15212445	15213258	.	-	.	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	intron	15213259	15213371	.	-	.	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	CDS	15213372	15213395	1	-	1	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	exon	15213372	15213395	.	-	.	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	intron	15213396	15213532	.	-	.	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	CDS	15213533	15213975	0.68	-	0	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	exon	15213533	15213975	.	-	.	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
Phchi.S1	AUGUSTUS	start_codon	15213973	15213975	.	-	0	transcript_id "Phchi.S1G232000.t1"; gene_id "Phchi.S1G232000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12973.t1 is derived from g11438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3397628	3397971	.	+	.	Phchi.S3G029200
Phchi.S3	AUGUSTUS	transcript	3397628	3397971	.	+	.	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	start_codon	3397628	3397630	.	+	0	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	CDS	3397628	3397873	0.64	+	0	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	exon	3397628	3397873	.	+	.	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	intron	3397874	3397959	.	+	.	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	CDS	3397960	3397971	0.99	+	0	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	exon	3397960	3397971	.	+	.	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
Phchi.S3	AUGUSTUS	stop_codon	3397972	3397974	.	+	0	transcript_id "Phchi.S3G029200.t1"; gene_id "Phchi.S3G029200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1624.t1 is derived from g8543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2075274	2077861	.	-	.	Phchi.S5G023300
Phchi.S5	AUGUSTUS	transcript	2075274	2077861	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	stop_codon	2075271	2075273	.	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2075274	2075465	0.99	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2075274	2075465	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2075466	2075565	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2075566	2075634	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2075566	2075634	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2075635	2075738	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2075739	2075840	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2075739	2075840	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2075841	2075929	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2075930	2076073	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2075930	2076073	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2076074	2076171	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2076172	2076288	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2076172	2076288	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2076289	2076409	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2076410	2076631	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2076410	2076631	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2076632	2076764	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2076765	2076947	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2076765	2076947	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2076948	2077110	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2077111	2077326	0.99	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2077111	2077326	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	intron	2077327	2077447	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	CDS	2077448	2077861	1	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	exon	2077448	2077861	.	-	.	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
Phchi.S5	AUGUSTUS	start_codon	2077859	2077861	.	-	0	transcript_id "Phchi.S5G023300.t1"; gene_id "Phchi.S5G023300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13621.t1 is derived from g12088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7779115	7782362	.	+	.	Phchi.S3G094000
Phchi.S3	AUGUSTUS	transcript	7779115	7782362	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	start_codon	7779115	7779117	.	+	0	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	CDS	7779115	7781260	1	+	0	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	exon	7779115	7781260	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	intron	7781261	7781395	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	CDS	7781396	7781496	1	+	2	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	exon	7781396	7781496	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	intron	7781497	7781672	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	CDS	7781673	7781801	1	+	0	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	exon	7781673	7781801	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	intron	7781802	7781914	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	CDS	7781915	7781985	1	+	0	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	exon	7781915	7781985	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	intron	7781986	7782133	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	CDS	7782134	7782362	1	+	1	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	exon	7782134	7782362	.	+	.	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
Phchi.S3	AUGUSTUS	stop_codon	7782363	7782365	.	+	0	transcript_id "Phchi.S3G094000.t1"; gene_id "Phchi.S3G094000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6113.t1 is derived from g3284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20993540	20997265	.	+	.	Phchi.S1G327200
Phchi.S1	AUGUSTUS	transcript	20993540	20997265	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	start_codon	20993540	20993542	.	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20993540	20993700	0.96	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20993540	20993700	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20993701	20993800	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20993801	20993900	1	+	1	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20993801	20993900	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20993901	20994020	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20994021	20994320	1	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20994021	20994320	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20994321	20994449	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20994450	20994890	1	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20994450	20994890	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20994891	20994964	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20994965	20995539	1	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20994965	20995539	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20995540	20995625	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20995626	20995771	1	+	1	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20995626	20995771	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20995772	20995853	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20995854	20996029	1	+	2	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20995854	20996029	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20996030	20996205	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20996206	20996358	1	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20996206	20996358	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20996359	20996447	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20996448	20996586	0.99	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20996448	20996586	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20996587	20996690	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20996691	20996747	0.71	+	2	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20996691	20996747	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20996748	20996883	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20996884	20997023	0.49	+	2	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20996884	20997023	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	intron	20997024	20997106	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	CDS	20997107	20997265	0.52	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	exon	20997107	20997265	.	+	.	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
Phchi.S1	AUGUSTUS	stop_codon	20997266	20997268	.	+	0	transcript_id "Phchi.S1G327200.t1"; gene_id "Phchi.S1G327200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9067.t1 is derived from g6242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39617233	39619230	.	+	.	Phchi.S1G622600
Phchi.S1	AUGUSTUS	transcript	39617233	39619230	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	start_codon	39617233	39617235	.	+	0	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	CDS	39617233	39617624	0.99	+	0	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	exon	39617233	39617624	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	intron	39617625	39617724	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	CDS	39617725	39617969	1	+	1	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	exon	39617725	39617969	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	intron	39617970	39618095	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	CDS	39618096	39618415	0.99	+	2	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	exon	39618096	39618415	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	intron	39618416	39618520	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	CDS	39618521	39618634	0.8	+	0	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	exon	39618521	39618634	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	intron	39618635	39618758	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	CDS	39618759	39618889	1	+	0	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	exon	39618759	39618889	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	intron	39618890	39618983	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	CDS	39618984	39619230	1	+	1	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	exon	39618984	39619230	.	+	.	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
Phchi.S1	AUGUSTUS	stop_codon	39619231	39619233	.	+	0	transcript_id "Phchi.S1G622600.t1"; gene_id "Phchi.S1G622600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10851.t1 is derived from g14901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2502534	2503221	.	-	.	Phchi.S4G043300
Phchi.S4	AUGUSTUS	transcript	2502534	2503221	.	-	.	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	stop_codon	2502531	2502533	.	-	0	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	CDS	2502534	2502551	0.59	-	0	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	exon	2502534	2502551	.	-	.	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	intron	2502552	2502669	.	-	.	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	CDS	2502670	2503221	0.3	-	0	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	exon	2502670	2503221	.	-	.	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
Phchi.S4	AUGUSTUS	start_codon	2503219	2503221	.	-	0	transcript_id "Phchi.S4G043300.t1"; gene_id "Phchi.S4G043300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3954.t1 is derived from g1123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6679491	6680321	.	-	.	Phchi.S1G111300
Phchi.S1	AUGUSTUS	transcript	6679491	6680321	.	-	.	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	stop_codon	6679488	6679490	.	-	0	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	CDS	6679491	6679536	1	-	1	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	exon	6679491	6679536	.	-	.	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	intron	6679537	6679668	.	-	.	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	CDS	6679669	6680321	0.86	-	0	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	exon	6679669	6680321	.	-	.	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
Phchi.S1	AUGUSTUS	start_codon	6680319	6680321	.	-	0	transcript_id "Phchi.S1G111300.t1"; gene_id "Phchi.S1G111300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6452.t1 is derived from g3624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23079650	23080857	.	+	.	Phchi.S1G361100
Phchi.S1	AUGUSTUS	transcript	23079650	23080857	.	+	.	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	start_codon	23079650	23079652	.	+	0	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	CDS	23079650	23079891	0.76	+	0	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	exon	23079650	23079891	.	+	.	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	intron	23079892	23080238	.	+	.	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	CDS	23080239	23080857	0.85	+	1	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	exon	23080239	23080857	.	+	.	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
Phchi.S1	AUGUSTUS	stop_codon	23080858	23080860	.	+	0	transcript_id "Phchi.S1G361100.t1"; gene_id "Phchi.S1G361100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12782.t1 is derived from g11247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2179361	2181684	.	+	.	Phchi.S3G010100
Phchi.S3	AUGUSTUS	transcript	2179361	2181684	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	start_codon	2179361	2179363	.	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2179361	2179849	0.91	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2179361	2179849	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2179850	2179937	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2179938	2180164	0.81	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2179938	2180164	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2180165	2180280	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2180281	2180638	0.98	+	1	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2180281	2180638	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2180639	2180764	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2180765	2180809	1	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2180765	2180809	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2180810	2180900	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2180901	2181047	1	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2180901	2181047	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2181048	2181143	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2181144	2181281	1	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2181144	2181281	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2181282	2181372	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2181373	2181406	1	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2181373	2181406	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	intron	2181407	2181514	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	CDS	2181515	2181684	0.98	+	2	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	exon	2181515	2181684	.	+	.	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
Phchi.S3	AUGUSTUS	stop_codon	2181685	2181687	.	+	0	transcript_id "Phchi.S3G010100.t1"; gene_id "Phchi.S3G010100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1141.t1 is derived from g10924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7950158	7950481	.	-	.	Phchi.S6G110000
Phchi.S6	AUGUSTUS	transcript	7950158	7950481	.	-	.	transcript_id "Phchi.S6G110000.t1"; gene_id "Phchi.S6G110000"
Phchi.S6	AUGUSTUS	stop_codon	7950155	7950157	.	-	0	transcript_id "Phchi.S6G110000.t1"; gene_id "Phchi.S6G110000"
Phchi.S6	AUGUSTUS	CDS	7950158	7950481	0.88	-	0	transcript_id "Phchi.S6G110000.t1"; gene_id "Phchi.S6G110000"
Phchi.S6	AUGUSTUS	exon	7950158	7950481	.	-	.	transcript_id "Phchi.S6G110000.t1"; gene_id "Phchi.S6G110000"
Phchi.S6	AUGUSTUS	start_codon	7950479	7950481	.	-	0	transcript_id "Phchi.S6G110000.t1"; gene_id "Phchi.S6G110000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6669.t1 is derived from g3841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24414980	24416716	.	+	.	Phchi.S1G382800
Phchi.S1	AUGUSTUS	transcript	24414980	24416716	.	+	.	transcript_id "Phchi.S1G382800.t1"; gene_id "Phchi.S1G382800"
Phchi.S1	AUGUSTUS	start_codon	24414980	24414982	.	+	0	transcript_id "Phchi.S1G382800.t1"; gene_id "Phchi.S1G382800"
Phchi.S1	AUGUSTUS	CDS	24414980	24416716	0.98	+	0	transcript_id "Phchi.S1G382800.t1"; gene_id "Phchi.S1G382800"
Phchi.S1	AUGUSTUS	exon	24414980	24416716	.	+	.	transcript_id "Phchi.S1G382800.t1"; gene_id "Phchi.S1G382800"
Phchi.S1	AUGUSTUS	stop_codon	24416717	24416719	.	+	0	transcript_id "Phchi.S1G382800.t1"; gene_id "Phchi.S1G382800"
# This transcript jg11476.t2 is derived from g15526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11477.t1 is derived from g15527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6559547	6561576	.	-	.	Phchi.S4G105900
Phchi.S4	AUGUSTUS	transcript	6559547	6561576	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	stop_codon	6559544	6559546	.	-	0	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	CDS	6559547	6560005	1	-	0	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	exon	6559547	6560005	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	intron	6560006	6560104	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	CDS	6560105	6560504	1	-	1	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	exon	6560105	6560504	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	intron	6560505	6560588	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	CDS	6560589	6560830	1	-	0	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	exon	6560589	6560830	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	intron	6560831	6560951	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	CDS	6560952	6561178	1	-	2	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	exon	6560952	6561178	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	intron	6561179	6561290	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	CDS	6561291	6561576	0.99	-	0	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	exon	6561291	6561576	.	-	.	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
Phchi.S4	AUGUSTUS	start_codon	6561574	6561576	.	-	0	transcript_id "Phchi.S4G105900.t1"; gene_id "Phchi.S4G105900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1923.t1 is derived from g8843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3858676	3871038	.	-	.	Phchi.S5G053200
Phchi.S5	AUGUSTUS	transcript	3858676	3871038	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	stop_codon	3858673	3858675	.	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3858676	3858732	1	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3858676	3858732	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3858733	3858822	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3858823	3858924	0.99	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3858823	3858924	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3858925	3859004	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3859005	3859097	0.38	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3859005	3859097	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3859098	3859223	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3859224	3859406	1	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3859224	3859406	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3859407	3859490	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3859491	3860426	0.98	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3859491	3860426	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3860427	3860577	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3860578	3860823	0.58	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3860578	3860823	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3860824	3860964	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3860965	3861104	0.34	-	2	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3860965	3861104	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3861105	3861634	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3861635	3861767	1	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3861635	3861767	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3861768	3861890	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3861891	3861977	0.61	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3861891	3861977	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3861978	3862065	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3862066	3862188	0.47	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3862066	3862188	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3862189	3862267	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3862268	3862738	0.26	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3862268	3862738	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3862739	3862902	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3862903	3865018	0.69	-	1	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3862903	3865018	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3865019	3865109	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3865110	3865381	1	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3865110	3865381	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3865382	3865478	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3865479	3865711	1	-	2	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3865479	3865711	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3865712	3865804	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3865805	3866089	0.96	-	2	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3865805	3866089	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3866090	3866194	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3866195	3867774	0.97	-	1	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3866195	3867774	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	intron	3867775	3867961	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	CDS	3867962	3871038	0.5	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	exon	3867962	3871038	.	-	.	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
Phchi.S5	AUGUSTUS	start_codon	3871036	3871038	.	-	0	transcript_id "Phchi.S5G053200.t1"; gene_id "Phchi.S5G053200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2827.t1 is derived from g9747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9065751	9068060	.	-	.	Phchi.S5G143600
Phchi.S5	AUGUSTUS	transcript	9065751	9068060	.	-	.	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	stop_codon	9065748	9065750	.	-	0	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	CDS	9065751	9067676	0.95	-	0	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	exon	9065751	9067676	.	-	.	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	intron	9067677	9067772	.	-	.	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	CDS	9067773	9067849	1	-	2	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	exon	9067773	9067849	.	-	.	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	intron	9067850	9067927	.	-	.	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	CDS	9067928	9068060	0.9	-	0	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	exon	9067928	9068060	.	-	.	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
Phchi.S5	AUGUSTUS	start_codon	9068058	9068060	.	-	0	transcript_id "Phchi.S5G143600.t1"; gene_id "Phchi.S5G143600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9296.t1 is derived from g6471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40825469	40826225	.	+	.	Phchi.S1G645500
Phchi.S1	AUGUSTUS	transcript	40825469	40826225	.	+	.	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	start_codon	40825469	40825471	.	+	0	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	CDS	40825469	40825693	0.9	+	0	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	exon	40825469	40825693	.	+	.	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	intron	40825694	40825829	.	+	.	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	CDS	40825830	40826225	0.98	+	0	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	exon	40825830	40826225	.	+	.	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
Phchi.S1	AUGUSTUS	stop_codon	40826226	40826228	.	+	0	transcript_id "Phchi.S1G645500.t1"; gene_id "Phchi.S1G645500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11548.t1 is derived from g15598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6990883	6992325	.	-	.	Phchi.S4G113000
Phchi.S4	AUGUSTUS	transcript	6990883	6992325	.	-	.	transcript_id "Phchi.S4G113000.t1"; gene_id "Phchi.S4G113000"
Phchi.S4	AUGUSTUS	stop_codon	6990880	6990882	.	-	0	transcript_id "Phchi.S4G113000.t1"; gene_id "Phchi.S4G113000"
Phchi.S4	AUGUSTUS	CDS	6990883	6992325	0.88	-	0	transcript_id "Phchi.S4G113000.t1"; gene_id "Phchi.S4G113000"
Phchi.S4	AUGUSTUS	exon	6990883	6992325	.	-	.	transcript_id "Phchi.S4G113000.t1"; gene_id "Phchi.S4G113000"
Phchi.S4	AUGUSTUS	start_codon	6992323	6992325	.	-	0	transcript_id "Phchi.S4G113000.t1"; gene_id "Phchi.S4G113000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg190.t1 is derived from g9972.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1075358	1078064	.	+	.	Phchi.S6G014900
Phchi.S6	AUGUSTUS	transcript	1075358	1078064	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	start_codon	1075358	1075360	.	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075358	1075410	0.98	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075358	1075410	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075411	1075625	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075626	1075803	1	+	1	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075626	1075803	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075804	1075892	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075893	1076147	1	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075893	1076147	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076148	1076232	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076233	1076407	1	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076233	1076407	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076408	1076495	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076496	1076560	1	+	2	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076496	1076560	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076561	1076635	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076636	1076799	1	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076636	1076799	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076800	1076904	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076905	1076999	1	+	1	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076905	1076999	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077000	1077087	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077088	1077146	1	+	2	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077088	1077146	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077147	1077243	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077244	1077296	1	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077244	1077296	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077297	1077372	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077373	1077388	1	+	1	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077373	1077388	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077389	1077488	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077489	1077576	0.99	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077489	1077576	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077577	1077678	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077679	1077764	1	+	2	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077679	1077764	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077765	1077863	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077864	1078064	1	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077864	1078064	.	+	.	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	stop_codon	1078065	1078067	.	+	0	transcript_id "Phchi.S6G014900.t1"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	transcript	1075358	1078064	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	start_codon	1075358	1075360	.	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075358	1075410	1	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075358	1075410	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075411	1075625	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075626	1075803	1	+	1	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075626	1075803	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075804	1075892	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075893	1076147	1	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075893	1076147	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076148	1076232	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076233	1076407	1	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076233	1076407	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076408	1076495	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076496	1076560	1	+	2	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076496	1076560	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076561	1076635	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076636	1076799	1	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076636	1076799	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076800	1076904	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076905	1076999	1	+	1	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076905	1076999	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077000	1077087	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077088	1077146	0.94	+	2	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077088	1077146	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077147	1077253	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077254	1077388	0.94	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077254	1077388	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077389	1077488	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077489	1077576	0.99	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077489	1077576	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077577	1077678	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077679	1077764	1	+	2	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077679	1077764	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077765	1077863	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077864	1078064	1	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077864	1078064	.	+	.	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	stop_codon	1078065	1078067	.	+	0	transcript_id "Phchi.S6G014900.t2"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	transcript	1075358	1078064	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	start_codon	1075358	1075360	.	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075358	1075410	1	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075358	1075410	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075411	1075625	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075626	1075796	0.48	+	1	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075626	1075796	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075797	1075892	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075893	1075901	0.29	+	1	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075893	1075901	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1075902	1075984	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1075985	1076147	0.29	+	1	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1075985	1076147	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076148	1076232	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076233	1076407	1	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076233	1076407	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076408	1076495	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076496	1076560	1	+	2	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076496	1076560	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076561	1076635	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076636	1076799	1	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076636	1076799	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1076800	1076904	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1076905	1076999	1	+	1	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1076905	1076999	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077000	1077087	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077088	1077146	1	+	2	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077088	1077146	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077147	1077243	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077244	1077296	0.91	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077244	1077296	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077297	1077372	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077373	1077388	0.91	+	1	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077373	1077388	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077389	1077488	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077489	1077576	1	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077489	1077576	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077577	1077678	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077679	1077764	1	+	2	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077679	1077764	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	intron	1077765	1077863	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	CDS	1077864	1078064	0.98	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	exon	1077864	1078064	.	+	.	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
Phchi.S6	AUGUSTUS	stop_codon	1078065	1078067	.	+	0	transcript_id "Phchi.S6G014900.t3"; gene_id "Phchi.S6G014900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9994.t1 is derived from g7170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44911643	44911978	.	-	.	Phchi.S1G715300
Phchi.S1	AUGUSTUS	transcript	44911643	44911978	.	-	.	transcript_id "Phchi.S1G715300.t1"; gene_id "Phchi.S1G715300"
Phchi.S1	AUGUSTUS	stop_codon	44911640	44911642	.	-	0	transcript_id "Phchi.S1G715300.t1"; gene_id "Phchi.S1G715300"
Phchi.S1	AUGUSTUS	CDS	44911643	44911978	0.47	-	0	transcript_id "Phchi.S1G715300.t1"; gene_id "Phchi.S1G715300"
Phchi.S1	AUGUSTUS	exon	44911643	44911978	.	-	.	transcript_id "Phchi.S1G715300.t1"; gene_id "Phchi.S1G715300"
Phchi.S1	AUGUSTUS	start_codon	44911976	44911978	.	-	0	transcript_id "Phchi.S1G715300.t1"; gene_id "Phchi.S1G715300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11792.t1 is derived from g15844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8181873	8182592	.	+	.	Phchi.S4G137400
Phchi.S4	AUGUSTUS	transcript	8181873	8182592	.	+	.	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	start_codon	8181873	8181875	.	+	0	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	CDS	8181873	8181931	0.44	+	0	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	exon	8181873	8181931	.	+	.	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	intron	8181932	8182018	.	+	.	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	CDS	8182019	8182592	0.46	+	1	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	exon	8182019	8182592	.	+	.	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
Phchi.S4	AUGUSTUS	stop_codon	8182593	8182595	.	+	0	transcript_id "Phchi.S4G137400.t1"; gene_id "Phchi.S4G137400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10062.t1 is derived from g7238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45590189	45592345	.	-	.	Phchi.S1G722100
Phchi.S1	AUGUSTUS	transcript	45590189	45592345	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	stop_codon	45590186	45590188	.	-	0	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45590189	45590286	0.24	-	2	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45590189	45590286	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	intron	45590287	45590390	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45590391	45590601	0.4	-	0	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45590391	45590601	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	intron	45590602	45590692	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45590693	45590751	0.62	-	2	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45590693	45590751	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	intron	45590752	45590822	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45590823	45590931	0.87	-	0	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45590823	45590931	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	intron	45590932	45591038	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45591039	45591227	1	-	0	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45591039	45591227	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	intron	45591228	45591330	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45591331	45592094	0.4	-	2	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45591331	45592094	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	intron	45592095	45592221	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	CDS	45592222	45592345	0.4	-	0	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	exon	45592222	45592345	.	-	.	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
Phchi.S1	AUGUSTUS	start_codon	45592343	45592345	.	-	0	transcript_id "Phchi.S1G722100.t1"; gene_id "Phchi.S1G722100"
# This transcript jg3142.t2 is derived from g311.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3143.t1 is derived from g312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1969892	1972397	.	-	.	Phchi.S1G030200
Phchi.S1	AUGUSTUS	transcript	1969892	1972397	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	stop_codon	1969889	1969891	.	-	0	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	CDS	1969892	1970737	0.89	-	0	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	exon	1969892	1970737	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	intron	1970738	1970994	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	CDS	1970995	1971085	0.51	-	1	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	exon	1970995	1971085	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	intron	1971086	1971198	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	CDS	1971199	1971828	0.36	-	1	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	exon	1971199	1971828	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	intron	1971829	1971971	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	CDS	1971972	1971999	0.49	-	2	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	exon	1971972	1971999	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	intron	1972000	1972387	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	CDS	1972388	1972397	0.59	-	0	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	exon	1972388	1972397	.	-	.	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
Phchi.S1	AUGUSTUS	start_codon	1972395	1972397	.	-	0	transcript_id "Phchi.S1G030200.t1"; gene_id "Phchi.S1G030200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5736.t1 is derived from g2906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18615273	18616312	.	-	.	Phchi.S1G289500
Phchi.S1	AUGUSTUS	transcript	18615273	18616312	.	-	.	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	stop_codon	18615270	18615272	.	-	0	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	CDS	18615273	18615605	1	-	0	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	exon	18615273	18615605	.	-	.	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	intron	18615606	18615697	.	-	.	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	CDS	18615698	18615835	1	-	0	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	exon	18615698	18615835	.	-	.	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	intron	18615836	18615988	.	-	.	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	CDS	18615989	18616312	0.72	-	0	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	exon	18615989	18616312	.	-	.	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
Phchi.S1	AUGUSTUS	start_codon	18616310	18616312	.	-	0	transcript_id "Phchi.S1G289500.t1"; gene_id "Phchi.S1G289500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4166.t1 is derived from g1335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8708085	8710903	.	-	.	Phchi.S1G132500
Phchi.S1	AUGUSTUS	transcript	8708085	8710903	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	stop_codon	8708082	8708084	.	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8708085	8708198	0.64	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8708085	8708198	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8708199	8708282	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8708283	8708366	1	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8708283	8708366	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8708367	8708552	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8708553	8708624	1	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8708553	8708624	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8708625	8708722	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8708723	8708774	1	-	1	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8708723	8708774	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8708775	8708921	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8708922	8708993	1	-	1	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8708922	8708993	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8708994	8709080	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8709081	8709156	1	-	2	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8709081	8709156	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8709157	8709256	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8709257	8709369	1	-	1	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8709257	8709369	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8709370	8709496	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8709497	8709644	1	-	2	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8709497	8709644	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8709645	8709792	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8709793	8709870	1	-	2	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8709793	8709870	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8709871	8709961	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8709962	8710091	1	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8709962	8710091	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8710092	8710188	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8710189	8710376	1	-	2	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8710189	8710376	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8710377	8710449	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8710450	8710510	1	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8710450	8710510	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8710511	8710604	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8710605	8710711	1	-	2	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8710605	8710711	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	intron	8710712	8710827	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	CDS	8710828	8710903	0.74	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	exon	8710828	8710903	.	-	.	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
Phchi.S1	AUGUSTUS	start_codon	8710901	8710903	.	-	0	transcript_id "Phchi.S1G132500.t1"; gene_id "Phchi.S1G132500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13009.t1 is derived from g11474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3620305	3621574	.	-	.	Phchi.S3G032800
Phchi.S3	AUGUSTUS	transcript	3620305	3621574	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	stop_codon	3620302	3620304	.	-	0	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620305	3620360	1	-	2	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620305	3620360	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3620361	3620444	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620445	3620601	1	-	0	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620445	3620601	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3620602	3620686	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620687	3620767	1	-	0	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620687	3620767	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3620768	3620911	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620912	3620999	1	-	1	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620912	3620999	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3621000	3621108	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3621109	3621193	1	-	2	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3621109	3621193	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3621194	3621323	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3621324	3621343	1	-	1	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3621324	3621343	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3621344	3621431	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3621432	3621574	1	-	0	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3621432	3621574	.	-	.	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	start_codon	3621572	3621574	.	-	0	transcript_id "Phchi.S3G032800.t1"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	transcript	3620305	3621574	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	stop_codon	3620302	3620304	.	-	0	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620305	3620345	1	-	2	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620305	3620345	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3620346	3620444	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620445	3620601	1	-	0	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620445	3620601	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3620602	3620686	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620687	3620767	1	-	0	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620687	3620767	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3620768	3620911	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3620912	3620999	1	-	1	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3620912	3620999	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3621000	3621108	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3621109	3621193	1	-	2	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3621109	3621193	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3621194	3621323	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3621324	3621343	1	-	1	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3621324	3621343	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	intron	3621344	3621431	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	CDS	3621432	3621574	0.98	-	0	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	exon	3621432	3621574	.	-	.	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
Phchi.S3	AUGUSTUS	start_codon	3621572	3621574	.	-	0	transcript_id "Phchi.S3G032800.t2"; gene_id "Phchi.S3G032800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10718.t1 is derived from g14768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1742979	1743806	.	-	.	Phchi.S4G030000
Phchi.S4	AUGUSTUS	transcript	1742979	1743806	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	stop_codon	1742976	1742978	.	-	0	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	CDS	1742979	1743009	1	-	1	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	exon	1742979	1743009	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	intron	1743010	1743094	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	CDS	1743095	1743281	1	-	2	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	exon	1743095	1743281	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	intron	1743282	1743367	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	CDS	1743368	1743506	0.99	-	0	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	exon	1743368	1743506	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	intron	1743507	1743608	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	CDS	1743609	1743681	0.84	-	1	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	exon	1743609	1743681	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	intron	1743682	1743783	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	CDS	1743784	1743806	0.63	-	0	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	exon	1743784	1743806	.	-	.	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
Phchi.S4	AUGUSTUS	start_codon	1743804	1743806	.	-	0	transcript_id "Phchi.S4G030000.t1"; gene_id "Phchi.S4G030000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14324.t1 is derived from g12791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12095232	12096152	.	-	.	Phchi.S3G164300
Phchi.S3	AUGUSTUS	transcript	12095232	12096152	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	stop_codon	12095229	12095231	.	-	0	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	CDS	12095232	12095375	0.81	-	0	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	exon	12095232	12095375	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	intron	12095376	12095458	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	CDS	12095459	12095513	0.67	-	1	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	exon	12095459	12095513	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	intron	12095514	12095590	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	CDS	12095591	12095778	1	-	0	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	exon	12095591	12095778	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	intron	12095779	12095918	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	CDS	12095919	12096152	0.52	-	0	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	exon	12095919	12096152	.	-	.	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
Phchi.S3	AUGUSTUS	start_codon	12096150	12096152	.	-	0	transcript_id "Phchi.S3G164300.t1"; gene_id "Phchi.S3G164300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9292.t1 is derived from g6467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40786610	40792015	.	-	.	Phchi.S1G645100
Phchi.S1	AUGUSTUS	transcript	40786610	40792015	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	stop_codon	40786607	40786609	.	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40786610	40786803	1	-	2	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40786610	40786803	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40786804	40786886	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40786887	40787021	1	-	2	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40786887	40787021	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787022	40787106	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40787107	40787248	1	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40787107	40787248	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787249	40787345	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40787346	40787408	1	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40787346	40787408	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787409	40787490	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40787491	40787499	0.55	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40787491	40787499	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787500	40787597	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40787598	40787633	0.8	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40787598	40787633	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787634	40787729	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40787730	40787785	0.98	-	2	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40787730	40787785	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787786	40787868	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40787869	40787889	0.98	-	2	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40787869	40787889	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40787890	40788048	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40788049	40788184	0.91	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40788049	40788184	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40788185	40788348	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40788349	40788436	1	-	1	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40788349	40788436	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40788437	40788600	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40788601	40788857	0.99	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40788601	40788857	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40788858	40788959	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40788960	40790123	0.98	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40788960	40790123	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40790124	40790209	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40790210	40790323	1	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40790210	40790323	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40790324	40790471	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40790472	40790812	0.78	-	2	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40790472	40790812	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40790813	40791585	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40791586	40791775	1	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40791586	40791775	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	intron	40791776	40791976	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	CDS	40791977	40792015	1	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	exon	40791977	40792015	.	-	.	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
Phchi.S1	AUGUSTUS	start_codon	40792013	40792015	.	-	0	transcript_id "Phchi.S1G645100.t1"; gene_id "Phchi.S1G645100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10815.t1 is derived from g14865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2246515	2248317	.	-	.	Phchi.S4G039700
Phchi.S4	AUGUSTUS	transcript	2246515	2248317	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	stop_codon	2246512	2246514	.	-	0	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2246515	2246555	0.55	-	2	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2246515	2246555	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	intron	2246556	2246680	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2246681	2246816	0.78	-	0	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2246681	2246816	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	intron	2246817	2246913	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2246914	2246976	1	-	0	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2246914	2246976	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	intron	2246977	2247052	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2247053	2247125	1	-	1	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2247053	2247125	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	intron	2247126	2247209	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2247210	2247288	0.78	-	2	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2247210	2247288	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	intron	2247289	2247621	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2247622	2247848	0.78	-	1	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2247622	2247848	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	intron	2247849	2247934	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	CDS	2247935	2248317	1	-	0	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	exon	2247935	2248317	.	-	.	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
Phchi.S4	AUGUSTUS	start_codon	2248315	2248317	.	-	0	transcript_id "Phchi.S4G039700.t1"; gene_id "Phchi.S4G039700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7369.t1 is derived from g4541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28802829	28803465	.	-	.	Phchi.S1G452800
Phchi.S1	AUGUSTUS	transcript	28802829	28803465	.	-	.	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	stop_codon	28802826	28802828	.	-	0	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	CDS	28802829	28802931	1	-	1	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	exon	28802829	28802931	.	-	.	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	intron	28802932	28803030	.	-	.	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	CDS	28803031	28803305	1	-	0	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	exon	28803031	28803305	.	-	.	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	intron	28803306	28803438	.	-	.	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	CDS	28803439	28803465	0.77	-	0	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	exon	28803439	28803465	.	-	.	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
Phchi.S1	AUGUSTUS	start_codon	28803463	28803465	.	-	0	transcript_id "Phchi.S1G452800.t1"; gene_id "Phchi.S1G452800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8686.t1 is derived from g5861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37447373	37449480	.	-	.	Phchi.S1G584500
Phchi.S1	AUGUSTUS	transcript	37447373	37449480	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	stop_codon	37447370	37447372	.	-	0	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37447373	37447479	1	-	2	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37447373	37447479	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37447480	37447583	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37447584	37447734	1	-	0	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37447584	37447734	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37447735	37447820	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37447821	37447883	1	-	0	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37447821	37447883	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37447884	37447993	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37447994	37448160	1	-	2	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37447994	37448160	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37448161	37448248	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37448249	37448290	1	-	2	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37448249	37448290	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37448291	37448417	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37448418	37448547	1	-	0	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37448418	37448547	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37448548	37448653	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37448654	37448726	1	-	1	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37448654	37448726	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37448727	37448821	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37448822	37449185	1	-	2	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37448822	37449185	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	intron	37449186	37449281	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	CDS	37449282	37449480	0.47	-	0	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	exon	37449282	37449480	.	-	.	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
Phchi.S1	AUGUSTUS	start_codon	37449478	37449480	.	-	0	transcript_id "Phchi.S1G584500.t1"; gene_id "Phchi.S1G584500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13349.t1 is derived from g11815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6237910	6244165	.	+	.	Phchi.S3G066800
Phchi.S3	AUGUSTUS	transcript	6237910	6244165	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	start_codon	6237910	6237912	.	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6237910	6237929	0.45	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6237910	6237929	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6237930	6238011	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6238012	6238209	0.85	+	1	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6238012	6238209	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6238210	6238365	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6238366	6238482	1	+	1	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6238366	6238482	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6238483	6238662	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6238663	6238730	1	+	1	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6238663	6238730	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6238731	6239446	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239447	6239524	1	+	2	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239447	6239524	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6239525	6239675	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239676	6239752	1	+	2	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239676	6239752	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6239753	6239944	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239945	6240004	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239945	6240004	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240005	6240133	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240134	6240194	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240134	6240194	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240195	6240282	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240283	6240395	1	+	2	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240283	6240395	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240396	6240487	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240488	6240603	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240488	6240603	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240604	6240681	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240682	6240780	1	+	1	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240682	6240780	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240781	6240867	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240868	6240943	1	+	1	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240868	6240943	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240944	6241141	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241142	6241230	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241142	6241230	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241231	6241387	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241388	6241451	1	+	1	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241388	6241451	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241452	6241541	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241542	6241688	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241542	6241688	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241689	6241777	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241778	6241859	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241778	6241859	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241860	6241937	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241938	6242005	1	+	2	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241938	6242005	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242006	6242089	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6242090	6242222	0.61	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6242090	6242222	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242223	6242329	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6242330	6242370	0.62	+	2	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6242330	6242370	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242371	6242656	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6242657	6242672	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6242657	6242672	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242673	6243047	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6243048	6243541	1	+	2	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6243048	6243541	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6243542	6243715	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6243716	6244165	1	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6243716	6244165	.	+	.	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	stop_codon	6244166	6244168	.	+	0	transcript_id "Phchi.S3G066800.t1"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	transcript	6238053	6244165	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	start_codon	6238053	6238055	.	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6238053	6238209	0.71	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6238053	6238209	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6238210	6238365	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6238366	6238482	1	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6238366	6238482	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6238483	6238662	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6238663	6238730	0.97	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6238663	6238730	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6238731	6239112	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239113	6239284	0.96	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239113	6239284	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6239285	6239485	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239486	6239524	0.58	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239486	6239524	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6239525	6239675	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239676	6239752	1	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239676	6239752	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6239753	6239944	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6239945	6240004	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6239945	6240004	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240005	6240133	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240134	6240194	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240134	6240194	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240195	6240282	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240283	6240395	1	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240283	6240395	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240396	6240487	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240488	6240603	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240488	6240603	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240604	6240681	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240682	6240780	1	+	1	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240682	6240780	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240781	6240867	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6240868	6240943	1	+	1	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6240868	6240943	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6240944	6241141	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241142	6241230	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241142	6241230	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241231	6241387	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241388	6241451	1	+	1	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241388	6241451	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241452	6241541	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241542	6241688	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241542	6241688	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241689	6241777	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241778	6241859	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241778	6241859	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6241860	6241937	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6241938	6242005	1	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6241938	6242005	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242006	6242089	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6242090	6242222	0.49	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6242090	6242222	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242223	6242329	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6242330	6242370	0.5	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6242330	6242370	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242371	6242656	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6242657	6242672	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6242657	6242672	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6242673	6243047	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6243048	6243541	1	+	2	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6243048	6243541	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	intron	6243542	6243715	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	CDS	6243716	6244165	1	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	exon	6243716	6244165	.	+	.	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
Phchi.S3	AUGUSTUS	stop_codon	6244166	6244168	.	+	0	transcript_id "Phchi.S3G066800.t2"; gene_id "Phchi.S3G066800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15546.t1 is derived from g14015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19823876	19825137	.	-	.	Phchi.S3G286500
Phchi.S3	AUGUSTUS	transcript	19823876	19825137	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	stop_codon	19823873	19823875	.	-	0	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	CDS	19823876	19823925	0.99	-	2	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	exon	19823876	19823925	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	intron	19823926	19824086	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	CDS	19824087	19824151	1	-	1	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	exon	19824087	19824151	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	intron	19824152	19824304	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	CDS	19824305	19824404	0.97	-	2	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	exon	19824305	19824404	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	intron	19824405	19824496	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	CDS	19824497	19824594	0.93	-	1	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	exon	19824497	19824594	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	intron	19824595	19824697	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	CDS	19824698	19824710	0.63	-	2	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	exon	19824698	19824710	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	intron	19824711	19824998	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	CDS	19824999	19825137	0.93	-	0	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	exon	19824999	19825137	.	-	.	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
Phchi.S3	AUGUSTUS	start_codon	19825135	19825137	.	-	0	transcript_id "Phchi.S3G286500.t1"; gene_id "Phchi.S3G286500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12731.t1 is derived from g11196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1423605	1427359	.	-	.	Phchi.S3G005000
Phchi.S3	AUGUSTUS	transcript	1423605	1427359	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	stop_codon	1423602	1423604	.	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1423605	1423775	0.98	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1423605	1423775	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1423776	1423867	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1423868	1424009	1	-	1	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1423868	1424009	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1424010	1424115	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1424116	1424181	0.91	-	1	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1424116	1424181	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1424182	1424286	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1424287	1424586	0.97	-	1	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1424287	1424586	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1424587	1424684	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1424685	1424770	1	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1424685	1424770	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1424771	1424856	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1424857	1425078	0.94	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1424857	1425078	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1425079	1425196	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1425197	1425328	1	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1425197	1425328	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1425329	1425421	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1425422	1425595	0.44	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1425422	1425595	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1425596	1425825	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1425826	1426881	0.25	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1425826	1426881	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	intron	1426882	1427005	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	CDS	1427006	1427359	0.67	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	exon	1427006	1427359	.	-	.	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
Phchi.S3	AUGUSTUS	start_codon	1427357	1427359	.	-	0	transcript_id "Phchi.S3G005000.t1"; gene_id "Phchi.S3G005000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7750.t1 is derived from g4924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30954253	30956049	.	+	.	Phchi.S1G490900
Phchi.S1	AUGUSTUS	transcript	30954253	30956049	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	start_codon	30954253	30954255	.	+	0	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	CDS	30954253	30954285	0.97	+	0	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	exon	30954253	30954285	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	intron	30954286	30954364	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	CDS	30954365	30954848	1	+	0	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	exon	30954365	30954848	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	intron	30954849	30954942	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	CDS	30954943	30955661	1	+	2	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	exon	30954943	30955661	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	intron	30955662	30955899	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	CDS	30955900	30956049	1	+	0	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	exon	30955900	30956049	.	+	.	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
Phchi.S1	AUGUSTUS	stop_codon	30956050	30956052	.	+	0	transcript_id "Phchi.S1G490900.t1"; gene_id "Phchi.S1G490900"
# This transcript jg11887.t2 is derived from g15939.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11888.t1 is derived from g15940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9034632	9036641	.	-	.	Phchi.S4G147000
Phchi.S4	AUGUSTUS	transcript	9034632	9036641	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	stop_codon	9034629	9034631	.	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9034632	9034688	1	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9034632	9034688	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9034689	9034840	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9034841	9034894	1	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9034841	9034894	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9034895	9034975	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9034976	9035076	1	-	2	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9034976	9035076	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9035077	9035200	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9035201	9035244	1	-	1	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9035201	9035244	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9035245	9035331	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9035332	9035374	0.86	-	2	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9035332	9035374	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9035375	9035469	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9035470	9035584	0.86	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9035470	9035584	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9035585	9035682	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9035683	9035739	1	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9035683	9035739	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9035740	9035845	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9035846	9035904	1	-	2	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9035846	9035904	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9035905	9036006	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9036007	9036063	0.97	-	2	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9036007	9036063	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9036064	9036203	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9036204	9036331	1	-	1	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9036204	9036331	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9036332	9036411	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9036412	9036544	1	-	2	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9036412	9036544	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	intron	9036545	9036634	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	CDS	9036635	9036641	1	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	exon	9036635	9036641	.	-	.	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
Phchi.S4	AUGUSTUS	start_codon	9036639	9036641	.	-	0	transcript_id "Phchi.S4G147000.t1"; gene_id "Phchi.S4G147000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6341.t1 is derived from g3513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22412868	22414687	.	-	.	Phchi.S1G350000
Phchi.S1	AUGUSTUS	transcript	22412868	22414687	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	stop_codon	22412865	22412867	.	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22412868	22412957	0.87	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22412868	22412957	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22412958	22413043	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22413044	22413130	1	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22413044	22413130	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22413131	22413215	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22413216	22413281	0.97	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22413216	22413281	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22413282	22413387	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22413388	22413477	0.97	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22413388	22413477	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22413478	22413556	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22413557	22413637	1	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22413557	22413637	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22413638	22413740	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22413741	22413818	0.96	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22413741	22413818	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22413819	22413908	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22413909	22413999	1	-	1	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22413909	22413999	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22414000	22414159	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22414160	22414307	1	-	2	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22414160	22414307	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	intron	22414308	22414572	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	CDS	22414573	22414687	0.77	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	exon	22414573	22414687	.	-	.	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
Phchi.S1	AUGUSTUS	start_codon	22414685	22414687	.	-	0	transcript_id "Phchi.S1G350000.t1"; gene_id "Phchi.S1G350000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8834.t1 is derived from g6009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38212367	38213467	.	-	.	Phchi.S1G599300
Phchi.S1	AUGUSTUS	transcript	38212367	38213467	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	stop_codon	38212364	38212366	.	-	0	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	CDS	38212367	38212486	1	-	0	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	exon	38212367	38212486	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	intron	38212487	38212574	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	CDS	38212575	38212767	1	-	1	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	exon	38212575	38212767	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	intron	38212768	38212830	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	CDS	38212831	38213078	1	-	0	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	exon	38212831	38213078	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	intron	38213079	38213161	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	CDS	38213162	38213357	1	-	1	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	exon	38213162	38213357	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	intron	38213358	38213441	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	CDS	38213442	38213467	1	-	0	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	exon	38213442	38213467	.	-	.	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
Phchi.S1	AUGUSTUS	start_codon	38213465	38213467	.	-	0	transcript_id "Phchi.S1G599300.t1"; gene_id "Phchi.S1G599300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2874.t1 is derived from g43.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	213670	214464	.	-	.	Phchi.S1G003300
Phchi.S1	AUGUSTUS	transcript	213670	214464	.	-	.	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	stop_codon	213667	213669	.	-	0	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	CDS	213670	214304	0.99	-	2	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	exon	213670	214304	.	-	.	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	intron	214305	214376	.	-	.	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	CDS	214377	214464	1	-	0	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	exon	214377	214464	.	-	.	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
Phchi.S1	AUGUSTUS	start_codon	214462	214464	.	-	0	transcript_id "Phchi.S1G003300.t1"; gene_id "Phchi.S1G003300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13653.t1 is derived from g12120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8021430	8023492	.	-	.	Phchi.S3G097200
Phchi.S3	AUGUSTUS	transcript	8021430	8023492	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	stop_codon	8021427	8021429	.	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8021430	8021540	1	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8021430	8021540	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8021541	8021625	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8021626	8021787	0.98	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8021626	8021787	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8021788	8021868	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8021869	8021964	0.95	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8021869	8021964	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8021965	8022044	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8022045	8022106	1	-	2	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8022045	8022106	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8022107	8022219	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8022220	8022295	0.96	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8022220	8022295	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8022296	8022386	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8022387	8022469	0.33	-	2	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8022387	8022469	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8022470	8022748	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8022749	8022891	0.63	-	1	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8022749	8022891	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8022892	8023032	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8023033	8023079	0.93	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8023033	8023079	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8023080	8023166	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8023167	8023238	0.85	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8023167	8023238	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	intron	8023239	8023312	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	CDS	8023313	8023492	0.85	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	exon	8023313	8023492	.	-	.	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
Phchi.S3	AUGUSTUS	start_codon	8023490	8023492	.	-	0	transcript_id "Phchi.S3G097200.t1"; gene_id "Phchi.S3G097200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13002.t1 is derived from g11467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3592513	3593689	.	+	.	Phchi.S3G032100
Phchi.S3	AUGUSTUS	transcript	3592513	3593689	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	start_codon	3592513	3592515	.	+	0	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	CDS	3592513	3592947	0.95	+	0	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	exon	3592513	3592947	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	intron	3592948	3593046	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	CDS	3593047	3593100	1	+	0	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	exon	3593047	3593100	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	intron	3593101	3593206	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	CDS	3593207	3593369	1	+	0	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	exon	3593207	3593369	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	intron	3593370	3593678	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	CDS	3593679	3593689	1	+	2	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	exon	3593679	3593689	.	+	.	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
Phchi.S3	AUGUSTUS	stop_codon	3593690	3593692	.	+	0	transcript_id "Phchi.S3G032100.t1"; gene_id "Phchi.S3G032100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1544.t1 is derived from g8463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1689972	1690553	.	-	.	Phchi.S5G015300
Phchi.S5	AUGUSTUS	transcript	1689972	1690553	.	-	.	transcript_id "Phchi.S5G015300.t1"; gene_id "Phchi.S5G015300"
Phchi.S5	AUGUSTUS	stop_codon	1689969	1689971	.	-	0	transcript_id "Phchi.S5G015300.t1"; gene_id "Phchi.S5G015300"
Phchi.S5	AUGUSTUS	CDS	1689972	1690553	1	-	0	transcript_id "Phchi.S5G015300.t1"; gene_id "Phchi.S5G015300"
Phchi.S5	AUGUSTUS	exon	1689972	1690553	.	-	.	transcript_id "Phchi.S5G015300.t1"; gene_id "Phchi.S5G015300"
Phchi.S5	AUGUSTUS	start_codon	1690551	1690553	.	-	0	transcript_id "Phchi.S5G015300.t1"; gene_id "Phchi.S5G015300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11181.t1 is derived from g15231.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4524443	4524936	.	+	.	Phchi.S4G076300
Phchi.S4	AUGUSTUS	transcript	4524443	4524765	.	+	.	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	start_codon	4524443	4524445	.	+	0	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	CDS	4524443	4524674	0.7	+	0	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	exon	4524443	4524674	.	+	.	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	intron	4524675	4524754	.	+	.	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	CDS	4524755	4524765	1	+	2	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	exon	4524755	4524765	.	+	.	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	stop_codon	4524766	4524768	.	+	0	transcript_id "Phchi.S4G076300.t1"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	transcript	4524443	4524936	.	+	.	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	start_codon	4524443	4524445	.	+	0	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	CDS	4524443	4524674	0.67	+	0	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	exon	4524443	4524674	.	+	.	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	intron	4524675	4524877	.	+	.	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	CDS	4524878	4524936	0.99	+	2	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	exon	4524878	4524936	.	+	.	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
Phchi.S4	AUGUSTUS	stop_codon	4524937	4524939	.	+	0	transcript_id "Phchi.S4G076300.t2"; gene_id "Phchi.S4G076300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15019.t1 is derived from g13487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16560972	16562043	.	+	.	Phchi.S3G233800
Phchi.S3	AUGUSTUS	transcript	16560972	16562043	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	start_codon	16560972	16560974	.	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	CDS	16560972	16561040	1	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	exon	16560972	16561040	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	intron	16561041	16561256	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	CDS	16561257	16561340	1	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	exon	16561257	16561340	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	intron	16561341	16561481	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	CDS	16561482	16561634	1	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	exon	16561482	16561634	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	intron	16561635	16561744	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	CDS	16561745	16561858	1	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	exon	16561745	16561858	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	intron	16561859	16561944	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	CDS	16561945	16562043	1	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	exon	16561945	16562043	.	+	.	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
Phchi.S3	AUGUSTUS	stop_codon	16562044	16562046	.	+	0	transcript_id "Phchi.S3G233800.t1"; gene_id "Phchi.S3G233800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8684.t1 is derived from g5859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37443004	37443908	.	+	.	Phchi.S1G584300
Phchi.S1	AUGUSTUS	transcript	37443004	37443908	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	start_codon	37443004	37443006	.	+	0	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	CDS	37443004	37443137	0.97	+	0	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	exon	37443004	37443137	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	intron	37443138	37443314	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	CDS	37443315	37443469	1	+	1	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	exon	37443315	37443469	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	intron	37443470	37443603	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	CDS	37443604	37443662	1	+	2	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	exon	37443604	37443662	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	intron	37443663	37443758	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	CDS	37443759	37443908	1	+	0	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	exon	37443759	37443908	.	+	.	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
Phchi.S1	AUGUSTUS	stop_codon	37443909	37443911	.	+	0	transcript_id "Phchi.S1G584300.t1"; gene_id "Phchi.S1G584300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1181.t1 is derived from g10964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8318550	8319916	.	+	.	Phchi.S6G114000
Phchi.S6	AUGUSTUS	transcript	8318550	8319916	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	start_codon	8318550	8318552	.	+	0	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	CDS	8318550	8318886	0.83	+	0	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	exon	8318550	8318886	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	intron	8318887	8319161	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	CDS	8319162	8319261	0.99	+	2	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	exon	8319162	8319261	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	intron	8319262	8319380	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	CDS	8319381	8319560	0.95	+	1	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	exon	8319381	8319560	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	intron	8319561	8319638	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	CDS	8319639	8319756	1	+	1	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	exon	8319639	8319756	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	intron	8319757	8319838	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	CDS	8319839	8319916	1	+	0	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	exon	8319839	8319916	.	+	.	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
Phchi.S6	AUGUSTUS	stop_codon	8319917	8319919	.	+	0	transcript_id "Phchi.S6G114000.t1"; gene_id "Phchi.S6G114000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13898.t1 is derived from g12365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9537912	9539176	.	-	.	Phchi.S3G121700
Phchi.S3	AUGUSTUS	transcript	9537912	9539176	.	-	.	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	stop_codon	9537909	9537911	.	-	0	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	CDS	9537912	9538933	0.61	-	2	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	exon	9537912	9538933	.	-	.	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	intron	9538934	9539103	.	-	.	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	CDS	9539104	9539176	0.71	-	0	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	exon	9539104	9539176	.	-	.	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
Phchi.S3	AUGUSTUS	start_codon	9539174	9539176	.	-	0	transcript_id "Phchi.S3G121700.t1"; gene_id "Phchi.S3G121700"
# This transcript jg5714.t2 is derived from g2884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5715.t1 is derived from g2885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18495996	18497298	.	-	.	Phchi.S1G287400
Phchi.S1	AUGUSTUS	transcript	18495996	18497298	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	stop_codon	18495993	18495995	.	-	0	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	CDS	18495996	18496094	1	-	0	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	exon	18495996	18496094	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	intron	18496095	18496179	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	CDS	18496180	18496362	1	-	0	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	exon	18496180	18496362	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	intron	18496363	18496442	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	CDS	18496443	18496560	1	-	1	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	exon	18496443	18496560	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	intron	18496561	18496682	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	CDS	18496683	18496915	1	-	0	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	exon	18496683	18496915	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	intron	18496916	18497241	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	CDS	18497242	18497298	0.97	-	0	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	exon	18497242	18497298	.	-	.	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
Phchi.S1	AUGUSTUS	start_codon	18497296	18497298	.	-	0	transcript_id "Phchi.S1G287400.t1"; gene_id "Phchi.S1G287400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4002.t1 is derived from g1171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6979893	6981569	.	+	.	Phchi.S1G116100
Phchi.S1	AUGUSTUS	transcript	6979893	6981569	.	+	.	transcript_id "Phchi.S1G116100.t1"; gene_id "Phchi.S1G116100"
Phchi.S1	AUGUSTUS	start_codon	6979893	6979895	.	+	0	transcript_id "Phchi.S1G116100.t1"; gene_id "Phchi.S1G116100"
Phchi.S1	AUGUSTUS	CDS	6979893	6981569	0.77	+	0	transcript_id "Phchi.S1G116100.t1"; gene_id "Phchi.S1G116100"
Phchi.S1	AUGUSTUS	exon	6979893	6981569	.	+	.	transcript_id "Phchi.S1G116100.t1"; gene_id "Phchi.S1G116100"
Phchi.S1	AUGUSTUS	stop_codon	6981570	6981572	.	+	0	transcript_id "Phchi.S1G116100.t1"; gene_id "Phchi.S1G116100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6924.t1 is derived from g4096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26013757	26016669	.	-	.	Phchi.S1G408300
Phchi.S1	AUGUSTUS	transcript	26013757	26016669	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	stop_codon	26013754	26013756	.	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26013757	26013948	0.97	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26013757	26013948	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26013949	26014037	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26014038	26014265	0.97	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26014038	26014265	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26014266	26014367	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26014368	26014573	0.99	-	2	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26014368	26014573	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26014574	26014657	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26014658	26014796	0.81	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26014658	26014796	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26014797	26014917	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26014918	26014977	0.8	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26014918	26014977	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26014978	26015076	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26015077	26015280	1	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26015077	26015280	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26015281	26015408	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26015409	26015529	1	-	1	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26015409	26015529	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26015530	26015674	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26015675	26015721	1	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26015675	26015721	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26015722	26015920	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26015921	26016219	0.95	-	2	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26015921	26016219	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26016220	26016347	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26016348	26016427	1	-	1	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26016348	26016427	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	intron	26016428	26016514	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	CDS	26016515	26016669	0.79	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	exon	26016515	26016669	.	-	.	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
Phchi.S1	AUGUSTUS	start_codon	26016667	26016669	.	-	0	transcript_id "Phchi.S1G408300.t1"; gene_id "Phchi.S1G408300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12835.t1 is derived from g11300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2610991	2614203	.	+	.	Phchi.S3G015400
Phchi.S3	AUGUSTUS	transcript	2610991	2614203	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	start_codon	2610991	2610993	.	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2610991	2611164	0.72	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2610991	2611164	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2611165	2611270	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2611271	2611326	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2611271	2611326	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2611327	2611425	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2611426	2611478	1	+	1	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2611426	2611478	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2611479	2611632	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2611633	2611759	0.82	+	2	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2611633	2611759	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2611760	2611864	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2611865	2611886	0.82	+	1	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2611865	2611886	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2611887	2611965	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2611966	2612058	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2611966	2612058	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2612059	2612198	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2612199	2612273	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2612199	2612273	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2612274	2612463	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2612464	2612568	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2612464	2612568	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2612569	2612708	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2612709	2612799	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2612709	2612799	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2612800	2612906	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2612907	2613112	0.66	+	2	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2612907	2613112	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2613113	2613254	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2613255	2613338	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2613255	2613338	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2613339	2613431	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2613432	2613497	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2613432	2613497	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2613498	2613617	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2613618	2613680	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2613618	2613680	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2613681	2613804	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2613805	2614045	1	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2613805	2614045	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	intron	2614046	2614135	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	CDS	2614136	2614203	0.99	+	2	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	exon	2614136	2614203	.	+	.	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
Phchi.S3	AUGUSTUS	stop_codon	2614204	2614206	.	+	0	transcript_id "Phchi.S3G015400.t1"; gene_id "Phchi.S3G015400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4924.t1 is derived from g2094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13594021	13594553	.	+	.	Phchi.S1G208300
Phchi.S1	AUGUSTUS	transcript	13594021	13594553	.	+	.	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	start_codon	13594021	13594023	.	+	0	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	CDS	13594021	13594090	0.83	+	0	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	exon	13594021	13594090	.	+	.	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	intron	13594091	13594187	.	+	.	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	CDS	13594188	13594403	0.83	+	2	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	exon	13594188	13594403	.	+	.	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	intron	13594404	13594500	.	+	.	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	CDS	13594501	13594553	1	+	2	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	exon	13594501	13594553	.	+	.	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
Phchi.S1	AUGUSTUS	stop_codon	13594554	13594556	.	+	0	transcript_id "Phchi.S1G208300.t1"; gene_id "Phchi.S1G208300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8969.t1 is derived from g6144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38884228	38886156	.	+	.	Phchi.S1G612800
Phchi.S1	AUGUSTUS	transcript	38884228	38886156	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	start_codon	38884228	38884230	.	+	0	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	CDS	38884228	38884377	0.86	+	0	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	exon	38884228	38884377	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	intron	38884378	38884470	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	CDS	38884471	38884571	0.99	+	0	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	exon	38884471	38884571	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	intron	38884572	38884685	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	CDS	38884686	38884753	1	+	1	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	exon	38884686	38884753	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	intron	38884754	38884882	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	CDS	38884883	38885276	1	+	2	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	exon	38884883	38885276	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	intron	38885277	38885429	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	CDS	38885430	38885757	1	+	1	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	exon	38885430	38885757	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	intron	38885758	38885847	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	CDS	38885848	38886156	1	+	0	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	exon	38885848	38886156	.	+	.	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
Phchi.S1	AUGUSTUS	stop_codon	38886157	38886159	.	+	0	transcript_id "Phchi.S1G612800.t1"; gene_id "Phchi.S1G612800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3427.t1 is derived from g596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3595742	3597109	.	-	.	Phchi.S1G058600
Phchi.S1	AUGUSTUS	transcript	3595742	3597109	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	stop_codon	3595739	3595741	.	-	0	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	CDS	3595742	3595866	0.98	-	2	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	exon	3595742	3595866	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	intron	3595867	3595975	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	CDS	3595976	3596400	0.99	-	1	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	exon	3595976	3596400	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	intron	3596401	3596478	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	CDS	3596479	3596672	1	-	0	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	exon	3596479	3596672	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	intron	3596673	3596839	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	CDS	3596840	3597109	1	-	0	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	exon	3596840	3597109	.	-	.	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
Phchi.S1	AUGUSTUS	start_codon	3597107	3597109	.	-	0	transcript_id "Phchi.S1G058600.t1"; gene_id "Phchi.S1G058600"
# This transcript jg6446.t2 is derived from g3618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6447.t1 is derived from g3619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23064638	23066028	.	+	.	Phchi.S1G360600
Phchi.S1	AUGUSTUS	transcript	23064638	23066028	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	start_codon	23064638	23064640	.	+	0	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	CDS	23064638	23064745	1	+	0	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	exon	23064638	23064745	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	intron	23064746	23064825	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	CDS	23064826	23065009	1	+	0	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	exon	23064826	23065009	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	intron	23065010	23065146	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	CDS	23065147	23065304	1	+	2	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	exon	23065147	23065304	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	intron	23065305	23065494	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	CDS	23065495	23065707	1	+	0	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	exon	23065495	23065707	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	intron	23065708	23065800	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	CDS	23065801	23066028	1	+	0	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	exon	23065801	23066028	.	+	.	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
Phchi.S1	AUGUSTUS	stop_codon	23066029	23066031	.	+	0	transcript_id "Phchi.S1G360600.t1"; gene_id "Phchi.S1G360600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9319.t1 is derived from g6494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40929804	40931673	.	+	.	Phchi.S1G647800
Phchi.S1	AUGUSTUS	transcript	40929804	40931673	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	start_codon	40929804	40929806	.	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40929804	40929869	0.65	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40929804	40929869	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40929870	40930145	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40930146	40930274	1	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40930146	40930274	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40930275	40930450	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40930451	40930504	1	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40930451	40930504	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40930505	40930690	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40930691	40930793	1	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40930691	40930793	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40930794	40930919	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40930920	40930978	1	+	2	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40930920	40930978	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40930979	40931065	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40931066	40931140	1	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40931066	40931140	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40931141	40931279	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40931280	40931337	1	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40931280	40931337	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40931338	40931432	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40931433	40931509	1	+	2	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40931433	40931509	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	intron	40931510	40931592	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	CDS	40931593	40931673	1	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	exon	40931593	40931673	.	+	.	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
Phchi.S1	AUGUSTUS	stop_codon	40931674	40931676	.	+	0	transcript_id "Phchi.S1G647800.t1"; gene_id "Phchi.S1G647800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14604.t1 is derived from g13072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13698824	13702363	.	-	.	Phchi.S3G192300
Phchi.S3	AUGUSTUS	transcript	13698824	13702363	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	stop_codon	13698821	13698823	.	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13698824	13699054	1	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13698824	13699054	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13699055	13699157	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13699158	13699335	0.8	-	1	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13699158	13699335	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13699336	13699422	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13699423	13699568	1	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13699423	13699568	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13699569	13699690	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13699691	13699861	1	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13699691	13699861	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13699862	13699969	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13699970	13700077	0.94	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13699970	13700077	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13700078	13700170	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13700171	13700274	1	-	2	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13700171	13700274	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13700275	13700379	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13700380	13700572	1	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13700380	13700572	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13700573	13700694	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13700695	13700807	0.9	-	2	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13700695	13700807	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13700808	13700922	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13700923	13701013	0.91	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13700923	13701013	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13701014	13701089	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13701090	13701232	0.96	-	2	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13701090	13701232	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13701233	13701316	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13701317	13701404	0.95	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13701317	13701404	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13701405	13701506	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13701507	13701636	0.89	-	1	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13701507	13701636	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13701637	13701799	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13701800	13701862	0.99	-	1	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13701800	13701862	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13701863	13702006	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13702007	13702185	0.86	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13702007	13702185	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	intron	13702186	13702276	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	CDS	13702277	13702363	0.8	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	exon	13702277	13702363	.	-	.	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
Phchi.S3	AUGUSTUS	start_codon	13702361	13702363	.	-	0	transcript_id "Phchi.S3G192300.t1"; gene_id "Phchi.S3G192300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9368.t1 is derived from g6544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41188707	41190182	.	-	.	Phchi.S1G652700
Phchi.S1	AUGUSTUS	transcript	41188707	41190182	.	-	.	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	stop_codon	41188704	41188706	.	-	0	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	CDS	41188707	41189774	0.56	-	0	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	exon	41188707	41189774	.	-	.	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	intron	41189775	41189891	.	-	.	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	CDS	41189892	41190182	0.99	-	0	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	exon	41189892	41190182	.	-	.	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
Phchi.S1	AUGUSTUS	start_codon	41190180	41190182	.	-	0	transcript_id "Phchi.S1G652700.t1"; gene_id "Phchi.S1G652700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10292.t1 is derived from g7468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46847160	46847498	.	+	.	Phchi.S1G745100
Phchi.S1	AUGUSTUS	transcript	46847160	46847498	.	+	.	transcript_id "Phchi.S1G745100.t1"; gene_id "Phchi.S1G745100"
Phchi.S1	AUGUSTUS	start_codon	46847160	46847162	.	+	0	transcript_id "Phchi.S1G745100.t1"; gene_id "Phchi.S1G745100"
Phchi.S1	AUGUSTUS	CDS	46847160	46847498	0.65	+	0	transcript_id "Phchi.S1G745100.t1"; gene_id "Phchi.S1G745100"
Phchi.S1	AUGUSTUS	exon	46847160	46847498	.	+	.	transcript_id "Phchi.S1G745100.t1"; gene_id "Phchi.S1G745100"
Phchi.S1	AUGUSTUS	stop_codon	46847499	46847501	.	+	0	transcript_id "Phchi.S1G745100.t1"; gene_id "Phchi.S1G745100"
# This transcript jg11520.t2 is derived from g15570.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11521.t1 is derived from g15571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6889177	6889824	.	-	.	Phchi.S4G110300
Phchi.S4	AUGUSTUS	transcript	6889177	6889824	.	-	.	transcript_id "Phchi.S4G110300.t1"; gene_id "Phchi.S4G110300"
Phchi.S4	AUGUSTUS	stop_codon	6889174	6889176	.	-	0	transcript_id "Phchi.S4G110300.t1"; gene_id "Phchi.S4G110300"
Phchi.S4	AUGUSTUS	CDS	6889177	6889824	0.84	-	0	transcript_id "Phchi.S4G110300.t1"; gene_id "Phchi.S4G110300"
Phchi.S4	AUGUSTUS	exon	6889177	6889824	.	-	.	transcript_id "Phchi.S4G110300.t1"; gene_id "Phchi.S4G110300"
Phchi.S4	AUGUSTUS	start_codon	6889822	6889824	.	-	0	transcript_id "Phchi.S4G110300.t1"; gene_id "Phchi.S4G110300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3723.t1 is derived from g892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5389155	5389397	.	+	.	Phchi.S1G088200
Phchi.S1	AUGUSTUS	transcript	5389155	5389397	.	+	.	transcript_id "Phchi.S1G088200.t1"; gene_id "Phchi.S1G088200"
Phchi.S1	AUGUSTUS	start_codon	5389155	5389157	.	+	0	transcript_id "Phchi.S1G088200.t1"; gene_id "Phchi.S1G088200"
Phchi.S1	AUGUSTUS	CDS	5389155	5389397	0.67	+	0	transcript_id "Phchi.S1G088200.t1"; gene_id "Phchi.S1G088200"
Phchi.S1	AUGUSTUS	exon	5389155	5389397	.	+	.	transcript_id "Phchi.S1G088200.t1"; gene_id "Phchi.S1G088200"
Phchi.S1	AUGUSTUS	stop_codon	5389398	5389400	.	+	0	transcript_id "Phchi.S1G088200.t1"; gene_id "Phchi.S1G088200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14938.t1 is derived from g13406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15632002	15632775	.	-	.	Phchi.S3G225700
Phchi.S3	AUGUSTUS	transcript	15632002	15632775	.	-	.	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	stop_codon	15631999	15632001	.	-	0	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	CDS	15632002	15632335	0.33	-	1	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	exon	15632002	15632335	.	-	.	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	intron	15632336	15632407	.	-	.	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	CDS	15632408	15632775	0.45	-	0	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	exon	15632408	15632775	.	-	.	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
Phchi.S3	AUGUSTUS	start_codon	15632773	15632775	.	-	0	transcript_id "Phchi.S3G225700.t1"; gene_id "Phchi.S3G225700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5977.t1 is derived from g3148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20193066	20195570	.	-	.	Phchi.S1G313600
Phchi.S1	AUGUSTUS	transcript	20193066	20195570	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	stop_codon	20193063	20193065	.	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	CDS	20193066	20193275	1	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	exon	20193066	20193275	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	intron	20193276	20193392	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	CDS	20193393	20193486	1	-	1	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	exon	20193393	20193486	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	intron	20193487	20193567	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	CDS	20193568	20193626	1	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	exon	20193568	20193626	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	intron	20193627	20193725	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	CDS	20193726	20193818	1	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	exon	20193726	20193818	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	intron	20193819	20193900	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	CDS	20193901	20194053	1	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	exon	20193901	20194053	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	intron	20194054	20194232	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	CDS	20194233	20195570	1	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	exon	20194233	20195570	.	-	.	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
Phchi.S1	AUGUSTUS	start_codon	20195568	20195570	.	-	0	transcript_id "Phchi.S1G313600.t1"; gene_id "Phchi.S1G313600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15312.t1 is derived from g13780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18347793	18348645	.	+	.	Phchi.S3G263100
Phchi.S3	AUGUSTUS	transcript	18347793	18348645	.	+	.	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	start_codon	18347793	18347795	.	+	0	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	CDS	18347793	18347942	1	+	0	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	exon	18347793	18347942	.	+	.	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	intron	18347943	18348034	.	+	.	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	CDS	18348035	18348083	1	+	0	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	exon	18348035	18348083	.	+	.	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	intron	18348084	18348166	.	+	.	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	CDS	18348167	18348645	1	+	2	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	exon	18348167	18348645	.	+	.	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
Phchi.S3	AUGUSTUS	stop_codon	18348646	18348648	.	+	0	transcript_id "Phchi.S3G263100.t1"; gene_id "Phchi.S3G263100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7636.t1 is derived from g4810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30346459	30349631	.	-	.	Phchi.S1G479500
Phchi.S1	AUGUSTUS	transcript	30346459	30349631	.	-	.	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	stop_codon	30346456	30346458	.	-	0	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	CDS	30346459	30348891	0.96	-	0	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	exon	30346459	30348891	.	-	.	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	intron	30348892	30349001	.	-	.	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	CDS	30349002	30349631	0.9	-	0	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	exon	30349002	30349631	.	-	.	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
Phchi.S1	AUGUSTUS	start_codon	30349629	30349631	.	-	0	transcript_id "Phchi.S1G479500.t1"; gene_id "Phchi.S1G479500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg843.t1 is derived from g10625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5852114	5853802	.	-	.	Phchi.S6G080200
Phchi.S6	AUGUSTUS	transcript	5852114	5853802	.	-	.	transcript_id "Phchi.S6G080200.t1"; gene_id "Phchi.S6G080200"
Phchi.S6	AUGUSTUS	stop_codon	5852111	5852113	.	-	0	transcript_id "Phchi.S6G080200.t1"; gene_id "Phchi.S6G080200"
Phchi.S6	AUGUSTUS	CDS	5852114	5853802	0.52	-	0	transcript_id "Phchi.S6G080200.t1"; gene_id "Phchi.S6G080200"
Phchi.S6	AUGUSTUS	exon	5852114	5853802	.	-	.	transcript_id "Phchi.S6G080200.t1"; gene_id "Phchi.S6G080200"
Phchi.S6	AUGUSTUS	start_codon	5853800	5853802	.	-	0	transcript_id "Phchi.S6G080200.t1"; gene_id "Phchi.S6G080200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9491.t1 is derived from g6667.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41999385	42000173	.	+	.	Phchi.S1G665000
Phchi.S1	AUGUSTUS	transcript	41999385	42000015	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	start_codon	41999385	41999387	.	+	0	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999385	41999445	0.49	+	0	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999385	41999445	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	intron	41999446	41999572	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999573	41999652	1	+	2	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999573	41999652	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	intron	41999653	41999733	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999734	41999820	1	+	0	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999734	41999820	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	intron	41999821	41999979	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999980	42000015	1	+	0	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999980	42000015	.	+	.	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	stop_codon	42000016	42000018	.	+	0	transcript_id "Phchi.S1G665000.t1"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	transcript	41999385	42000173	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	start_codon	41999385	41999387	.	+	0	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999385	41999445	0.42	+	0	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999385	41999445	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	intron	41999446	41999572	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999573	41999652	1	+	2	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999573	41999652	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	intron	41999653	41999733	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999734	41999815	1	+	0	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999734	41999815	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	intron	41999816	41999979	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	CDS	41999980	42000173	0.99	+	2	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	exon	41999980	42000173	.	+	.	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
Phchi.S1	AUGUSTUS	stop_codon	42000174	42000176	.	+	0	transcript_id "Phchi.S1G665000.t2"; gene_id "Phchi.S1G665000"
# This transcript jg2294.t2 is derived from g9214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2295.t1 is derived from g9215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5918586	5919467	.	-	.	Phchi.S5G090400
Phchi.S5	AUGUSTUS	transcript	5918586	5919467	.	-	.	transcript_id "Phchi.S5G090400.t1"; gene_id "Phchi.S5G090400"
Phchi.S5	AUGUSTUS	stop_codon	5918583	5918585	.	-	0	transcript_id "Phchi.S5G090400.t1"; gene_id "Phchi.S5G090400"
Phchi.S5	AUGUSTUS	CDS	5918586	5919467	0.44	-	0	transcript_id "Phchi.S5G090400.t1"; gene_id "Phchi.S5G090400"
Phchi.S5	AUGUSTUS	exon	5918586	5919467	.	-	.	transcript_id "Phchi.S5G090400.t1"; gene_id "Phchi.S5G090400"
Phchi.S5	AUGUSTUS	start_codon	5919465	5919467	.	-	0	transcript_id "Phchi.S5G090400.t1"; gene_id "Phchi.S5G090400"
# This transcript jg12600.t2 is derived from g8277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12601.t1 is derived from g8278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37410193	37412568	.	+	.	Phchi.S2G068100
Phchi.S2	AUGUSTUS	transcript	37410193	37412568	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	start_codon	37410193	37410195	.	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37410193	37410354	0.76	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37410193	37410354	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37410355	37410421	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37410422	37410509	1	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37410422	37410509	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37410510	37410631	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37410632	37410687	1	+	2	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37410632	37410687	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37410688	37410906	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37410907	37411052	1	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37410907	37411052	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37411053	37411228	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37411229	37411284	1	+	1	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37411229	37411284	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37411285	37411422	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37411423	37411499	1	+	2	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37411423	37411499	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37411500	37411682	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37411683	37411728	1	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37411683	37411728	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37411729	37411850	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37411851	37411960	1	+	2	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37411851	37411960	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37411961	37412135	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37412136	37412203	1	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37412136	37412203	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37412204	37412302	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37412303	37412390	1	+	1	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37412303	37412390	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	intron	37412391	37412475	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	CDS	37412476	37412568	1	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	exon	37412476	37412568	.	+	.	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
Phchi.S2	AUGUSTUS	stop_codon	37412569	37412571	.	+	0	transcript_id "Phchi.S2G068100.t1"; gene_id "Phchi.S2G068100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1217.t1 is derived from g11000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8444832	8447033	.	+	.	Phchi.S6G117600
Phchi.S6	AUGUSTUS	transcript	8444832	8447033	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	start_codon	8444832	8444834	.	+	0	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	CDS	8444832	8445973	0.87	+	0	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	exon	8444832	8445973	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	intron	8445974	8446083	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	CDS	8446084	8446118	0.71	+	1	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	exon	8446084	8446118	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	intron	8446119	8446206	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	CDS	8446207	8446382	0.68	+	2	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	exon	8446207	8446382	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	intron	8446383	8446528	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	CDS	8446529	8446589	1	+	0	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	exon	8446529	8446589	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	intron	8446590	8446771	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	CDS	8446772	8446869	1	+	2	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	exon	8446772	8446869	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	intron	8446870	8447018	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	CDS	8447019	8447033	1	+	0	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	exon	8447019	8447033	.	+	.	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
Phchi.S6	AUGUSTUS	stop_codon	8447034	8447036	.	+	0	transcript_id "Phchi.S6G117600.t1"; gene_id "Phchi.S6G117600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7041.t1 is derived from g4213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26551379	26551939	.	+	.	Phchi.S1G420000
Phchi.S1	AUGUSTUS	transcript	26551379	26551939	.	+	.	transcript_id "Phchi.S1G420000.t1"; gene_id "Phchi.S1G420000"
Phchi.S1	AUGUSTUS	start_codon	26551379	26551381	.	+	0	transcript_id "Phchi.S1G420000.t1"; gene_id "Phchi.S1G420000"
Phchi.S1	AUGUSTUS	CDS	26551379	26551939	0.44	+	0	transcript_id "Phchi.S1G420000.t1"; gene_id "Phchi.S1G420000"
Phchi.S1	AUGUSTUS	exon	26551379	26551939	.	+	.	transcript_id "Phchi.S1G420000.t1"; gene_id "Phchi.S1G420000"
Phchi.S1	AUGUSTUS	stop_codon	26551940	26551942	.	+	0	transcript_id "Phchi.S1G420000.t1"; gene_id "Phchi.S1G420000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg234.t1 is derived from g10016.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1595603	1597587	.	+	.	Phchi.S6G019300
Phchi.S6	AUGUSTUS	transcript	1595603	1597587	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	start_codon	1595603	1595605	.	+	0	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1595603	1595818	0.92	+	0	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1595603	1595818	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1595819	1595966	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1595967	1596100	0.86	+	0	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1595967	1596100	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596101	1596184	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596185	1596261	1	+	1	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596185	1596261	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596262	1596350	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596351	1596502	1	+	2	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596351	1596502	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596503	1596598	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596599	1596714	0.63	+	0	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596599	1596714	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596715	1596764	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596765	1597587	0.77	+	1	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596765	1597587	.	+	.	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	stop_codon	1597588	1597590	.	+	0	transcript_id "Phchi.S6G019300.t1"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	transcript	1595998	1597587	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	start_codon	1595998	1596000	.	+	0	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1595998	1596100	0.62	+	0	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1595998	1596100	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596101	1596184	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596185	1596261	1	+	2	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596185	1596261	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596262	1596340	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596341	1596502	1	+	0	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596341	1596502	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596503	1596598	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596599	1596714	0.62	+	0	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596599	1596714	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	intron	1596715	1596764	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	CDS	1596765	1597587	0.76	+	1	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	exon	1596765	1597587	.	+	.	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
Phchi.S6	AUGUSTUS	stop_codon	1597588	1597590	.	+	0	transcript_id "Phchi.S6G019300.t2"; gene_id "Phchi.S6G019300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1060.t1 is derived from g10843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7363924	7364694	.	-	.	Phchi.S6G101900
Phchi.S6	AUGUSTUS	transcript	7363924	7364694	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	stop_codon	7363921	7363923	.	-	0	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	CDS	7363924	7363994	0.65	-	2	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	exon	7363924	7363994	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	intron	7363995	7364146	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	CDS	7364147	7364318	0.47	-	0	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	exon	7364147	7364318	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	intron	7364319	7364486	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	CDS	7364487	7364547	0.54	-	1	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	exon	7364487	7364547	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	intron	7364548	7364626	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	CDS	7364627	7364694	0.55	-	0	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	exon	7364627	7364694	.	-	.	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
Phchi.S6	AUGUSTUS	start_codon	7364692	7364694	.	-	0	transcript_id "Phchi.S6G101900.t1"; gene_id "Phchi.S6G101900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15954.t1 is derived from g11137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	11461	12876	.	-	.	Phchi.C91G000100
Phchi.C91	AUGUSTUS	transcript	11461	12876	.	-	.	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	stop_codon	11458	11460	.	-	0	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	CDS	11461	11858	0.74	-	2	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	exon	11461	11858	.	-	.	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	intron	11859	11939	.	-	.	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	CDS	11940	12070	0.57	-	1	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	exon	11940	12070	.	-	.	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	intron	12071	12187	.	-	.	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	CDS	12188	12876	0.37	-	0	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	exon	12188	12876	.	-	.	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
Phchi.C91	AUGUSTUS	start_codon	12874	12876	.	-	0	transcript_id "Phchi.C91G000100.t1"; gene_id "Phchi.C91G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5755.t1 is derived from g2925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18753558	18755762	.	-	.	Phchi.S1G291400
Phchi.S1	AUGUSTUS	transcript	18753558	18755762	.	-	.	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	stop_codon	18753555	18753557	.	-	0	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	CDS	18753558	18754609	0.99	-	2	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	exon	18753558	18754609	.	-	.	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	intron	18754610	18754808	.	-	.	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	CDS	18754809	18755055	1	-	0	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	exon	18754809	18755055	.	-	.	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	intron	18755056	18755222	.	-	.	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	CDS	18755223	18755762	1	-	0	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	exon	18755223	18755762	.	-	.	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
Phchi.S1	AUGUSTUS	start_codon	18755760	18755762	.	-	0	transcript_id "Phchi.S1G291400.t1"; gene_id "Phchi.S1G291400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7722.t1 is derived from g4896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30796341	30800959	.	-	.	Phchi.S1G488100
Phchi.S1	AUGUSTUS	transcript	30796341	30800959	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	stop_codon	30796338	30796340	.	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796341	30796405	1	-	2	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796341	30796405	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796406	30796487	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796488	30796593	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796488	30796593	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796594	30796685	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796686	30796763	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796686	30796763	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796764	30796860	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796861	30796907	1	-	2	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796861	30796907	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796908	30796987	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796988	30797069	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796988	30797069	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797070	30797204	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797205	30797346	1	-	1	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797205	30797346	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797347	30797429	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797430	30797545	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797430	30797545	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797546	30797649	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797650	30797724	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797650	30797724	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797725	30797802	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797803	30797921	1	-	2	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797803	30797921	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797922	30798005	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798006	30798073	1	-	1	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798006	30798073	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798074	30798157	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798158	30798222	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798158	30798222	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798223	30798348	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798349	30798427	1	-	1	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798349	30798427	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798428	30798559	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798560	30798612	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798560	30798612	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798613	30798721	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798722	30798844	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798722	30798844	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798845	30798993	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798994	30799062	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798994	30799062	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799063	30799139	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799140	30799208	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799140	30799208	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799209	30799448	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799449	30799500	1	-	1	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799449	30799500	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799501	30799618	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799619	30799671	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799619	30799671	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799672	30799803	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799804	30799896	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799804	30799896	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799897	30800067	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800068	30800112	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800068	30800112	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30800113	30800245	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800246	30800320	1	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800246	30800320	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30800321	30800833	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800834	30800959	0.8	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800834	30800959	.	-	.	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	start_codon	30800957	30800959	.	-	0	transcript_id "Phchi.S1G488100.t1"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	transcript	30796341	30800959	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	stop_codon	30796338	30796340	.	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796341	30796405	1	-	2	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796341	30796405	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796406	30796487	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796488	30796593	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796488	30796593	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796594	30796685	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796686	30796763	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796686	30796763	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796764	30796860	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796861	30796907	1	-	2	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796861	30796907	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30796908	30796987	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30796988	30797069	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30796988	30797069	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797070	30797204	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797205	30797346	1	-	1	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797205	30797346	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797347	30797429	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797430	30797545	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797430	30797545	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797546	30797649	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797650	30797724	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797650	30797724	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797725	30797802	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30797803	30797921	1	-	2	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30797803	30797921	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30797922	30798005	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798006	30798073	1	-	1	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798006	30798073	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798074	30798157	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798158	30798222	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798158	30798222	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798223	30798348	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798349	30798427	1	-	1	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798349	30798427	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798428	30798559	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798560	30798612	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798560	30798612	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798613	30798721	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798722	30798844	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798722	30798844	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30798845	30798993	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30798994	30799062	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30798994	30799062	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799063	30799139	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799140	30799208	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799140	30799208	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799209	30799448	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799449	30799500	1	-	1	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799449	30799500	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799501	30799618	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799619	30799671	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799619	30799671	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799672	30799803	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30799804	30799896	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30799804	30799896	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30799897	30800067	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800068	30800112	1	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800068	30800112	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30800113	30800245	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800246	30800310	0.75	-	2	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800246	30800310	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30800311	30800495	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800496	30800541	0.83	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800496	30800541	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	intron	30800542	30800833	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	CDS	30800834	30800959	0.72	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	exon	30800834	30800959	.	-	.	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
Phchi.S1	AUGUSTUS	start_codon	30800957	30800959	.	-	0	transcript_id "Phchi.S1G488100.t2"; gene_id "Phchi.S1G488100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg419.t1 is derived from g10201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2964959	2965744	.	+	.	Phchi.S6G037800
Phchi.S6	AUGUSTUS	transcript	2964959	2965744	.	+	.	transcript_id "Phchi.S6G037800.t1"; gene_id "Phchi.S6G037800"
Phchi.S6	AUGUSTUS	start_codon	2964959	2964961	.	+	0	transcript_id "Phchi.S6G037800.t1"; gene_id "Phchi.S6G037800"
Phchi.S6	AUGUSTUS	CDS	2964959	2965744	0.41	+	0	transcript_id "Phchi.S6G037800.t1"; gene_id "Phchi.S6G037800"
Phchi.S6	AUGUSTUS	exon	2964959	2965744	.	+	.	transcript_id "Phchi.S6G037800.t1"; gene_id "Phchi.S6G037800"
Phchi.S6	AUGUSTUS	stop_codon	2965745	2965747	.	+	0	transcript_id "Phchi.S6G037800.t1"; gene_id "Phchi.S6G037800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12396.t1 is derived from g8073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17305120	17305329	.	+	.	Phchi.S2G047600
Phchi.S2	AUGUSTUS	transcript	17305120	17305329	.	+	.	transcript_id "Phchi.S2G047600.t1"; gene_id "Phchi.S2G047600"
Phchi.S2	AUGUSTUS	start_codon	17305120	17305122	.	+	0	transcript_id "Phchi.S2G047600.t1"; gene_id "Phchi.S2G047600"
Phchi.S2	AUGUSTUS	CDS	17305120	17305329	0.36	+	0	transcript_id "Phchi.S2G047600.t1"; gene_id "Phchi.S2G047600"
Phchi.S2	AUGUSTUS	exon	17305120	17305329	.	+	.	transcript_id "Phchi.S2G047600.t1"; gene_id "Phchi.S2G047600"
Phchi.S2	AUGUSTUS	stop_codon	17305330	17305332	.	+	0	transcript_id "Phchi.S2G047600.t1"; gene_id "Phchi.S2G047600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13311.t1 is derived from g11777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5752619	5754693	.	+	.	Phchi.S3G063000
Phchi.S3	AUGUSTUS	transcript	5752619	5754693	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	start_codon	5752619	5752621	.	+	0	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	CDS	5752619	5753007	1	+	0	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	exon	5752619	5753007	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	intron	5753008	5753117	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	CDS	5753118	5753406	1	+	1	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	exon	5753118	5753406	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	intron	5753407	5753520	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	CDS	5753521	5753814	1	+	0	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	exon	5753521	5753814	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	intron	5753815	5753954	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	CDS	5753955	5754322	1	+	0	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	exon	5753955	5754322	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	intron	5754323	5754440	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	CDS	5754441	5754693	1	+	1	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	exon	5754441	5754693	.	+	.	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
Phchi.S3	AUGUSTUS	stop_codon	5754694	5754696	.	+	0	transcript_id "Phchi.S3G063000.t1"; gene_id "Phchi.S3G063000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14686.t1 is derived from g13154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14166904	14167880	.	-	.	Phchi.S3G200500
Phchi.S3	AUGUSTUS	transcript	14166904	14167880	.	-	.	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	stop_codon	14166901	14166903	.	-	0	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	CDS	14166904	14167128	1	-	0	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	exon	14166904	14167128	.	-	.	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	intron	14167129	14167212	.	-	.	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	CDS	14167213	14167498	1	-	1	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	exon	14167213	14167498	.	-	.	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	intron	14167499	14167584	.	-	.	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	CDS	14167585	14167880	1	-	0	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	exon	14167585	14167880	.	-	.	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
Phchi.S3	AUGUSTUS	start_codon	14167878	14167880	.	-	0	transcript_id "Phchi.S3G200500.t1"; gene_id "Phchi.S3G200500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12209.t1 is derived from g7885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6744751	6745438	.	-	.	Phchi.S2G028900
Phchi.S2	AUGUSTUS	transcript	6744751	6745438	.	-	.	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	stop_codon	6744748	6744750	.	-	0	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	CDS	6744751	6745236	0.53	-	0	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	exon	6744751	6745236	.	-	.	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	intron	6745237	6745420	.	-	.	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	CDS	6745421	6745438	0.54	-	0	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	exon	6745421	6745438	.	-	.	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
Phchi.S2	AUGUSTUS	start_codon	6745436	6745438	.	-	0	transcript_id "Phchi.S2G028900.t1"; gene_id "Phchi.S2G028900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15453.t1 is derived from g13921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19238711	19240163	.	+	.	Phchi.S3G277200
Phchi.S3	AUGUSTUS	transcript	19238711	19240163	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	start_codon	19238711	19238713	.	+	0	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	CDS	19238711	19238891	0.67	+	0	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	exon	19238711	19238891	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	intron	19238892	19239361	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	CDS	19239362	19239423	1	+	2	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	exon	19239362	19239423	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	intron	19239424	19239561	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	CDS	19239562	19239637	0.97	+	0	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	exon	19239562	19239637	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	intron	19239638	19239750	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	CDS	19239751	19239867	0.7	+	2	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	exon	19239751	19239867	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	intron	19239868	19239957	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	CDS	19239958	19240163	0.63	+	2	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	exon	19239958	19240163	.	+	.	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
Phchi.S3	AUGUSTUS	stop_codon	19240164	19240166	.	+	0	transcript_id "Phchi.S3G277200.t1"; gene_id "Phchi.S3G277200"
# This transcript jg10407.t2 is derived from g7583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10408.t1 is derived from g7584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47680017	47681613	.	+	.	Phchi.S1G756700
Phchi.S1	AUGUSTUS	transcript	47680017	47681460	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	start_codon	47680017	47680019	.	+	0	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680017	47680023	1	+	0	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680017	47680023	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680024	47680118	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680119	47680185	1	+	2	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680119	47680185	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680186	47680434	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680435	47680443	1	+	1	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680435	47680443	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680444	47680723	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680724	47680741	0.98	+	1	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680724	47680741	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680742	47680986	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680987	47681073	1	+	1	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680987	47681073	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47681074	47681217	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47681218	47681300	1	+	1	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47681218	47681300	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47681301	47681440	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47681441	47681460	0.99	+	2	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47681441	47681460	.	+	.	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	stop_codon	47681461	47681463	.	+	0	transcript_id "Phchi.S1G756700.t1"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	transcript	47680017	47681613	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	start_codon	47680017	47680019	.	+	0	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680017	47680023	0.99	+	0	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680017	47680023	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680024	47680118	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680119	47680185	0.99	+	2	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680119	47680185	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680186	47680434	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680435	47680443	0.99	+	1	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680435	47680443	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680444	47680723	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680724	47680741	0.97	+	1	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680724	47680741	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680742	47680986	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680987	47681073	1	+	1	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680987	47681073	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47681074	47681217	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47681218	47681300	1	+	1	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47681218	47681300	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47681301	47681596	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47681597	47681613	1	+	2	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47681597	47681613	.	+	.	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	stop_codon	47681614	47681616	.	+	0	transcript_id "Phchi.S1G756700.t2"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	transcript	47680017	47681460	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	start_codon	47680017	47680019	.	+	0	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680017	47680023	0.7	+	0	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680017	47680023	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680024	47680118	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680119	47680127	0.7	+	2	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680119	47680127	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680128	47680230	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680231	47680260	0.68	+	2	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680231	47680260	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680261	47680434	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680435	47680481	0.45	+	2	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680435	47680481	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680482	47680691	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680692	47680741	0.63	+	0	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680692	47680741	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47680742	47680986	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47680987	47681073	1	+	1	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47680987	47681073	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47681074	47681217	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47681218	47681300	1	+	1	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47681218	47681300	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	intron	47681301	47681440	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	CDS	47681441	47681460	0.98	+	2	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	exon	47681441	47681460	.	+	.	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
Phchi.S1	AUGUSTUS	stop_codon	47681461	47681463	.	+	0	transcript_id "Phchi.S1G756700.t3"; gene_id "Phchi.S1G756700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2161.t1 is derived from g9081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5127993	5131766	.	+	.	Phchi.S5G077000
Phchi.S5	AUGUSTUS	transcript	5127993	5131746	.	+	.	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	start_codon	5127993	5127995	.	+	0	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5127993	5129694	0.73	+	0	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5127993	5129694	.	+	.	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	intron	5129695	5129925	.	+	.	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5129926	5131323	0.91	+	2	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5129926	5131323	.	+	.	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	intron	5131324	5131642	.	+	.	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5131643	5131746	0.99	+	2	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5131643	5131746	.	+	.	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	stop_codon	5131747	5131749	.	+	0	transcript_id "Phchi.S5G077000.t1"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	transcript	5127993	5131766	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	start_codon	5127993	5127995	.	+	0	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5127993	5129694	0.4	+	0	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5127993	5129694	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	intron	5129695	5129925	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5129926	5131323	0.33	+	2	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5129926	5131323	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	intron	5131324	5131394	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5131395	5131461	0.59	+	2	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5131395	5131461	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	intron	5131462	5131642	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	CDS	5131643	5131766	0.6	+	1	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	exon	5131643	5131766	.	+	.	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
Phchi.S5	AUGUSTUS	stop_codon	5131767	5131769	.	+	0	transcript_id "Phchi.S5G077000.t2"; gene_id "Phchi.S5G077000"
# This transcript jg2920.t2 is derived from g89.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2921.t1 is derived from g90.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	569486	570038	.	-	.	Phchi.S1G008000
Phchi.S1	AUGUSTUS	transcript	569486	570038	.	-	.	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	stop_codon	569483	569485	.	-	0	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	CDS	569486	569531	0.99	-	1	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	exon	569486	569531	.	-	.	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	intron	569532	569622	.	-	.	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	CDS	569623	570038	0.55	-	0	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	exon	569623	570038	.	-	.	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
Phchi.S1	AUGUSTUS	start_codon	570036	570038	.	-	0	transcript_id "Phchi.S1G008000.t1"; gene_id "Phchi.S1G008000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8250.t1 is derived from g5425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34687199	34687474	.	-	.	Phchi.S1G540900
Phchi.S1	AUGUSTUS	transcript	34687199	34687474	.	-	.	transcript_id "Phchi.S1G540900.t1"; gene_id "Phchi.S1G540900"
Phchi.S1	AUGUSTUS	stop_codon	34687196	34687198	.	-	0	transcript_id "Phchi.S1G540900.t1"; gene_id "Phchi.S1G540900"
Phchi.S1	AUGUSTUS	CDS	34687199	34687474	0.58	-	0	transcript_id "Phchi.S1G540900.t1"; gene_id "Phchi.S1G540900"
Phchi.S1	AUGUSTUS	exon	34687199	34687474	.	-	.	transcript_id "Phchi.S1G540900.t1"; gene_id "Phchi.S1G540900"
Phchi.S1	AUGUSTUS	start_codon	34687472	34687474	.	-	0	transcript_id "Phchi.S1G540900.t1"; gene_id "Phchi.S1G540900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5970.t1 is derived from g3141.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20158682	20161475	.	+	.	Phchi.S1G312900
Phchi.S1	AUGUSTUS	transcript	20158682	20161475	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	start_codon	20158682	20158684	.	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20158682	20158751	0.71	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20158682	20158751	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20158752	20158821	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20158822	20158938	0.96	+	2	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20158822	20158938	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20158939	20159051	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159052	20159141	0.99	+	2	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159052	20159141	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159142	20159300	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159301	20159338	1	+	2	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159301	20159338	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159339	20159506	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159507	20159550	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159507	20159550	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159551	20159686	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159687	20159843	1	+	1	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159687	20159843	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159844	20159996	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159997	20160083	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159997	20160083	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160084	20160223	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160224	20160307	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160224	20160307	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160308	20160425	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160426	20160527	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160426	20160527	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160528	20160743	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160744	20160791	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160744	20160791	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160792	20160955	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160956	20161084	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160956	20161084	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20161085	20161217	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20161218	20161310	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20161218	20161310	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20161311	20161388	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20161389	20161475	1	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20161389	20161475	.	+	.	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	stop_codon	20161476	20161478	.	+	0	transcript_id "Phchi.S1G312900.t1"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	transcript	20158682	20161008	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	start_codon	20158682	20158684	.	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20158682	20158751	0.54	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20158682	20158751	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20158752	20158821	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20158822	20158938	0.99	+	2	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20158822	20158938	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20158939	20159051	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159052	20159141	0.99	+	2	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159052	20159141	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159142	20159300	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159301	20159338	0.99	+	2	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159301	20159338	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159339	20159506	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159507	20159550	1	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159507	20159550	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159551	20159686	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159687	20159843	1	+	1	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159687	20159843	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159844	20159996	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159997	20160083	1	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159997	20160083	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160084	20160223	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160224	20160307	1	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160224	20160307	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160308	20160425	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160426	20160527	0.99	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160426	20160527	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160528	20160743	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160744	20160791	0.98	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160744	20160791	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160792	20160984	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160985	20161008	0.76	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160985	20161008	.	+	.	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	stop_codon	20161009	20161011	.	+	0	transcript_id "Phchi.S1G312900.t2"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	transcript	20158682	20161475	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	start_codon	20158682	20158684	.	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20158682	20158751	0.58	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20158682	20158751	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20158752	20158821	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20158822	20158938	0.98	+	2	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20158822	20158938	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20158939	20159051	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159052	20159184	0.7	+	2	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159052	20159184	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159185	20159300	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159301	20159397	0.86	+	1	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159301	20159397	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159398	20159506	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159507	20159550	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159507	20159550	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159551	20159686	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159687	20159843	1	+	1	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159687	20159843	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20159844	20159996	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20159997	20160083	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20159997	20160083	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160084	20160223	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160224	20160307	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160224	20160307	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160308	20160425	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160426	20160527	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160426	20160527	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160528	20160743	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160744	20160791	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160744	20160791	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20160792	20160955	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20160956	20161084	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20160956	20161084	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20161085	20161217	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20161218	20161310	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20161218	20161310	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	intron	20161311	20161388	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	CDS	20161389	20161475	1	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	exon	20161389	20161475	.	+	.	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
Phchi.S1	AUGUSTUS	stop_codon	20161476	20161478	.	+	0	transcript_id "Phchi.S1G312900.t3"; gene_id "Phchi.S1G312900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12575.t1 is derived from g8252.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35683289	35686258	.	-	.	Phchi.S2G065500
Phchi.S2	AUGUSTUS	transcript	35683289	35686258	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	stop_codon	35683286	35683288	.	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683289	35683399	1	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683289	35683399	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683400	35683498	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683499	35683662	1	-	2	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683499	35683662	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683663	35683739	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683740	35683833	1	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683740	35683833	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683834	35683920	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683921	35683977	1	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683921	35683977	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683978	35684064	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684065	35684107	1	-	1	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684065	35684107	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35684108	35684285	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684286	35684377	1	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684286	35684377	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35684378	35684620	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684621	35684786	1	-	1	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684621	35684786	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35684787	35684875	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684876	35685035	1	-	2	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684876	35685035	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35685036	35686110	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35686111	35686258	1	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35686111	35686258	.	-	.	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	start_codon	35686256	35686258	.	-	0	transcript_id "Phchi.S2G065500.t1"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	transcript	35683289	35685517	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	stop_codon	35683286	35683288	.	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683289	35683399	1	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683289	35683399	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683400	35683498	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683499	35683662	1	-	2	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683499	35683662	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683663	35683739	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683740	35683833	1	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683740	35683833	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683834	35683920	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35683921	35683977	1	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35683921	35683977	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35683978	35684064	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684065	35684107	1	-	1	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684065	35684107	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35684108	35684285	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684286	35684377	1	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684286	35684377	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35684378	35684620	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684621	35684786	1	-	1	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684621	35684786	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35684787	35684875	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35684876	35685035	0.95	-	2	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35684876	35685035	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	intron	35685036	35685471	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	CDS	35685472	35685517	0.92	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	exon	35685472	35685517	.	-	.	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
Phchi.S2	AUGUSTUS	start_codon	35685515	35685517	.	-	0	transcript_id "Phchi.S2G065500.t2"; gene_id "Phchi.S2G065500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7005.t1 is derived from g4177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26366565	26367530	.	-	.	Phchi.S1G416400
Phchi.S1	AUGUSTUS	transcript	26366565	26367530	.	-	.	transcript_id "Phchi.S1G416400.t1"; gene_id "Phchi.S1G416400"
Phchi.S1	AUGUSTUS	stop_codon	26366562	26366564	.	-	0	transcript_id "Phchi.S1G416400.t1"; gene_id "Phchi.S1G416400"
Phchi.S1	AUGUSTUS	CDS	26366565	26367530	0.95	-	0	transcript_id "Phchi.S1G416400.t1"; gene_id "Phchi.S1G416400"
Phchi.S1	AUGUSTUS	exon	26366565	26367530	.	-	.	transcript_id "Phchi.S1G416400.t1"; gene_id "Phchi.S1G416400"
Phchi.S1	AUGUSTUS	start_codon	26367528	26367530	.	-	0	transcript_id "Phchi.S1G416400.t1"; gene_id "Phchi.S1G416400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12019.t1 is derived from g7694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	610935	611699	.	+	.	Phchi.S2G009900
Phchi.S2	AUGUSTUS	transcript	610935	611699	.	+	.	transcript_id "Phchi.S2G009900.t1"; gene_id "Phchi.S2G009900"
Phchi.S2	AUGUSTUS	start_codon	610935	610937	.	+	0	transcript_id "Phchi.S2G009900.t1"; gene_id "Phchi.S2G009900"
Phchi.S2	AUGUSTUS	CDS	610935	611699	0.61	+	0	transcript_id "Phchi.S2G009900.t1"; gene_id "Phchi.S2G009900"
Phchi.S2	AUGUSTUS	exon	610935	611699	.	+	.	transcript_id "Phchi.S2G009900.t1"; gene_id "Phchi.S2G009900"
Phchi.S2	AUGUSTUS	stop_codon	611700	611702	.	+	0	transcript_id "Phchi.S2G009900.t1"; gene_id "Phchi.S2G009900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6527.t1 is derived from g3699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23494268	23495159	.	+	.	Phchi.S1G368600
Phchi.S1	AUGUSTUS	transcript	23494268	23495159	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	start_codon	23494268	23494270	.	+	0	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	CDS	23494268	23494304	0.99	+	0	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	exon	23494268	23494304	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	intron	23494305	23494561	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	CDS	23494562	23494642	1	+	2	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	exon	23494562	23494642	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	intron	23494643	23494735	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	CDS	23494736	23494765	1	+	2	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	exon	23494736	23494765	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	intron	23494766	23494876	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	CDS	23494877	23494991	1	+	2	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	exon	23494877	23494991	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	intron	23494992	23495077	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	CDS	23495078	23495159	1	+	1	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	exon	23495078	23495159	.	+	.	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
Phchi.S1	AUGUSTUS	stop_codon	23495160	23495162	.	+	0	transcript_id "Phchi.S1G368600.t1"; gene_id "Phchi.S1G368600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11261.t1 is derived from g15311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5062225	5064275	.	+	.	Phchi.S4G084300
Phchi.S4	AUGUSTUS	transcript	5062225	5064275	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	start_codon	5062225	5062227	.	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5062225	5062290	0.53	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5062225	5062290	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5062291	5062443	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5062444	5062569	1	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5062444	5062569	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5062570	5062687	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5062688	5062790	1	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5062688	5062790	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5062791	5062871	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5062872	5062919	1	+	2	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5062872	5062919	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5062920	5062991	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5062992	5063089	1	+	2	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5062992	5063089	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5063090	5063169	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5063170	5063284	1	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5063170	5063284	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5063285	5063427	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5063428	5063510	1	+	2	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5063428	5063510	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5063511	5063601	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5063602	5064112	0.99	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5063602	5064112	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	intron	5064113	5064231	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	CDS	5064232	5064275	1	+	2	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	exon	5064232	5064275	.	+	.	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
Phchi.S4	AUGUSTUS	stop_codon	5064276	5064278	.	+	0	transcript_id "Phchi.S4G084300.t1"; gene_id "Phchi.S4G084300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg776.t1 is derived from g10558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5458502	5458920	.	+	.	Phchi.S6G073500
Phchi.S6	AUGUSTUS	transcript	5458502	5458920	.	+	.	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	start_codon	5458502	5458504	.	+	0	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	CDS	5458502	5458723	0.45	+	0	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	exon	5458502	5458723	.	+	.	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	intron	5458724	5458872	.	+	.	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	CDS	5458873	5458920	0.88	+	0	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	exon	5458873	5458920	.	+	.	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
Phchi.S6	AUGUSTUS	stop_codon	5458921	5458923	.	+	0	transcript_id "Phchi.S6G073500.t1"; gene_id "Phchi.S6G073500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9402.t1 is derived from g6578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41349139	41351202	.	+	.	Phchi.S1G656100
Phchi.S1	AUGUSTUS	transcript	41350186	41351202	.	+	.	transcript_id "Phchi.S1G656100.t1"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	start_codon	41350186	41350188	.	+	0	transcript_id "Phchi.S1G656100.t1"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	CDS	41350186	41351202	0.57	+	0	transcript_id "Phchi.S1G656100.t1"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	exon	41350186	41351202	.	+	.	transcript_id "Phchi.S1G656100.t1"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	stop_codon	41351203	41351205	.	+	0	transcript_id "Phchi.S1G656100.t1"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	transcript	41349139	41351202	.	+	.	transcript_id "Phchi.S1G656100.t2"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	start_codon	41349139	41349141	.	+	0	transcript_id "Phchi.S1G656100.t2"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	CDS	41349139	41351202	0.54	+	0	transcript_id "Phchi.S1G656100.t2"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	exon	41349139	41351202	.	+	.	transcript_id "Phchi.S1G656100.t2"; gene_id "Phchi.S1G656100"
Phchi.S1	AUGUSTUS	stop_codon	41351203	41351205	.	+	0	transcript_id "Phchi.S1G656100.t2"; gene_id "Phchi.S1G656100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1882.t1 is derived from g8802.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3698400	3700290	.	+	.	Phchi.S5G049100
Phchi.S5	AUGUSTUS	transcript	3698400	3700290	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	start_codon	3698400	3698402	.	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698400	3698513	1	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698400	3698513	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698514	3698604	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698605	3698826	1	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698605	3698826	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698827	3698902	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698903	3698975	1	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698903	3698975	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698976	3699218	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699219	3699294	0.97	+	2	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699219	3699294	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699295	3699374	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699375	3699502	1	+	1	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699375	3699502	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699503	3699585	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699586	3699728	0.98	+	2	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699586	3699728	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699729	3699830	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699831	3699917	0.98	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699831	3699917	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699918	3700022	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3700023	3700197	0.98	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3700023	3700197	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3700198	3700279	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3700280	3700290	0.98	+	2	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3700280	3700290	.	+	.	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	stop_codon	3700291	3700293	.	+	0	transcript_id "Phchi.S5G049100.t1"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	transcript	3698400	3700290	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	start_codon	3698400	3698402	.	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698400	3698513	1	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698400	3698513	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698514	3698604	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698605	3698826	1	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698605	3698826	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698827	3698905	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698906	3698975	1	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698906	3698975	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698976	3699218	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699219	3699294	0.93	+	2	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699219	3699294	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699295	3699374	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699375	3699502	0.99	+	1	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699375	3699502	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699503	3699585	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699586	3699728	0.98	+	2	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699586	3699728	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699729	3699830	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699831	3699917	0.98	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699831	3699917	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3699918	3700022	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3700023	3700197	1	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3700023	3700197	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3700198	3700279	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3700280	3700290	1	+	2	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3700280	3700290	.	+	.	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	stop_codon	3700291	3700293	.	+	0	transcript_id "Phchi.S5G049100.t2"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	transcript	3698400	3699138	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	start_codon	3698400	3698402	.	+	0	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698400	3698513	1	+	0	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698400	3698513	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698514	3698604	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698605	3698826	1	+	0	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698605	3698826	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698827	3698902	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3698903	3698975	0.83	+	0	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3698903	3698975	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	intron	3698976	3699043	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	CDS	3699044	3699138	0.89	+	2	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	exon	3699044	3699138	.	+	.	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
Phchi.S5	AUGUSTUS	stop_codon	3699139	3699141	.	+	0	transcript_id "Phchi.S5G049100.t3"; gene_id "Phchi.S5G049100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5239.t1 is derived from g2409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15804638	15806085	.	+	.	Phchi.S1G239800
Phchi.S1	AUGUSTUS	transcript	15804638	15806085	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	start_codon	15804638	15804640	.	+	0	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	CDS	15804638	15804907	0.96	+	0	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	exon	15804638	15804907	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	intron	15804908	15804997	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	CDS	15804998	15805237	1	+	0	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	exon	15804998	15805237	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	intron	15805238	15805325	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	CDS	15805326	15805543	1	+	0	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	exon	15805326	15805543	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	intron	15805544	15805673	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	CDS	15805674	15806085	1	+	1	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	exon	15805674	15806085	.	+	.	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
Phchi.S1	AUGUSTUS	stop_codon	15806086	15806088	.	+	0	transcript_id "Phchi.S1G239800.t1"; gene_id "Phchi.S1G239800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9361.t1 is derived from g6537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41160377	41161442	.	-	.	Phchi.S1G652000
Phchi.S1	AUGUSTUS	transcript	41160377	41161442	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	stop_codon	41160374	41160376	.	-	0	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	CDS	41160377	41160454	0.97	-	0	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	exon	41160377	41160454	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	intron	41160455	41160529	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	CDS	41160530	41160634	1	-	0	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	exon	41160530	41160634	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	intron	41160635	41160826	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	CDS	41160827	41160899	1	-	1	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	exon	41160827	41160899	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	intron	41160900	41161011	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	CDS	41161012	41161100	1	-	0	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	exon	41161012	41161100	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	intron	41161101	41161193	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	CDS	41161194	41161442	1	-	0	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	exon	41161194	41161442	.	-	.	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
Phchi.S1	AUGUSTUS	start_codon	41161440	41161442	.	-	0	transcript_id "Phchi.S1G652000.t1"; gene_id "Phchi.S1G652000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg775.t1 is derived from g10557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5456165	5456743	.	-	.	Phchi.S6G073400
Phchi.S6	AUGUSTUS	transcript	5456165	5456743	.	-	.	transcript_id "Phchi.S6G073400.t1"; gene_id "Phchi.S6G073400"
Phchi.S6	AUGUSTUS	stop_codon	5456162	5456164	.	-	0	transcript_id "Phchi.S6G073400.t1"; gene_id "Phchi.S6G073400"
Phchi.S6	AUGUSTUS	CDS	5456165	5456743	0.99	-	0	transcript_id "Phchi.S6G073400.t1"; gene_id "Phchi.S6G073400"
Phchi.S6	AUGUSTUS	exon	5456165	5456743	.	-	.	transcript_id "Phchi.S6G073400.t1"; gene_id "Phchi.S6G073400"
Phchi.S6	AUGUSTUS	start_codon	5456741	5456743	.	-	0	transcript_id "Phchi.S6G073400.t1"; gene_id "Phchi.S6G073400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8000.t1 is derived from g5175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32370147	32370748	.	-	.	Phchi.S1G515900
Phchi.S1	AUGUSTUS	transcript	32370147	32370748	.	-	.	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	stop_codon	32370144	32370146	.	-	0	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	CDS	32370147	32370284	1	-	0	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	exon	32370147	32370284	.	-	.	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	intron	32370285	32370399	.	-	.	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	CDS	32370400	32370470	1	-	2	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	exon	32370400	32370470	.	-	.	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	intron	32370471	32370657	.	-	.	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	CDS	32370658	32370748	0.98	-	0	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	exon	32370658	32370748	.	-	.	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
Phchi.S1	AUGUSTUS	start_codon	32370746	32370748	.	-	0	transcript_id "Phchi.S1G515900.t1"; gene_id "Phchi.S1G515900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13978.t1 is derived from g12445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10017879	10018457	.	-	.	Phchi.S3G129700
Phchi.S3	AUGUSTUS	transcript	10017879	10018457	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	stop_codon	10017876	10017878	.	-	0	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	CDS	10017879	10018024	0.84	-	2	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	exon	10017879	10018024	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	intron	10018025	10018109	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	CDS	10018110	10018161	1	-	0	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	exon	10018110	10018161	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	intron	10018162	10018226	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	CDS	10018227	10018274	1	-	0	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	exon	10018227	10018274	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	intron	10018275	10018349	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	CDS	10018350	10018457	1	-	0	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	exon	10018350	10018457	.	-	.	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
Phchi.S3	AUGUSTUS	start_codon	10018455	10018457	.	-	0	transcript_id "Phchi.S3G129700.t1"; gene_id "Phchi.S3G129700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12105.t1 is derived from g7781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3404264	3404848	.	+	.	Phchi.S2G018500
Phchi.S2	AUGUSTUS	transcript	3404264	3404848	.	+	.	transcript_id "Phchi.S2G018500.t1"; gene_id "Phchi.S2G018500"
Phchi.S2	AUGUSTUS	start_codon	3404264	3404266	.	+	0	transcript_id "Phchi.S2G018500.t1"; gene_id "Phchi.S2G018500"
Phchi.S2	AUGUSTUS	CDS	3404264	3404848	0.94	+	0	transcript_id "Phchi.S2G018500.t1"; gene_id "Phchi.S2G018500"
Phchi.S2	AUGUSTUS	exon	3404264	3404848	.	+	.	transcript_id "Phchi.S2G018500.t1"; gene_id "Phchi.S2G018500"
Phchi.S2	AUGUSTUS	stop_codon	3404849	3404851	.	+	0	transcript_id "Phchi.S2G018500.t1"; gene_id "Phchi.S2G018500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg851.t1 is derived from g10633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5903957	5904638	.	-	.	Phchi.S6G081000
Phchi.S6	AUGUSTUS	transcript	5903957	5904638	.	-	.	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	stop_codon	5903954	5903956	.	-	0	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	CDS	5903957	5904226	0.68	-	0	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	exon	5903957	5904226	.	-	.	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	intron	5904227	5904359	.	-	.	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	CDS	5904360	5904638	0.38	-	0	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	exon	5904360	5904638	.	-	.	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
Phchi.S6	AUGUSTUS	start_codon	5904636	5904638	.	-	0	transcript_id "Phchi.S6G081000.t1"; gene_id "Phchi.S6G081000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3845.t1 is derived from g1014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6016569	6018296	.	+	.	Phchi.S1G100400
Phchi.S1	AUGUSTUS	transcript	6016569	6018296	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	start_codon	6016569	6016571	.	+	0	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	CDS	6016569	6016788	0.97	+	0	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	exon	6016569	6016788	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	intron	6016789	6016892	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	CDS	6016893	6016960	0.99	+	2	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	exon	6016893	6016960	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	intron	6016961	6017049	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	CDS	6017050	6017286	0.53	+	0	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	exon	6017050	6017286	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	intron	6017287	6017417	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	CDS	6017418	6017708	0.94	+	0	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	exon	6017418	6017708	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	intron	6017709	6017833	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	CDS	6017834	6018021	1	+	0	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	exon	6017834	6018021	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	intron	6018022	6018106	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	CDS	6018107	6018296	1	+	1	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	exon	6018107	6018296	.	+	.	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
Phchi.S1	AUGUSTUS	stop_codon	6018297	6018299	.	+	0	transcript_id "Phchi.S1G100400.t1"; gene_id "Phchi.S1G100400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7542.t1 is derived from g4716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29968440	29971795	.	+	.	Phchi.S1G470100
Phchi.S1	AUGUSTUS	transcript	29968440	29971795	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	start_codon	29968440	29968442	.	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29968440	29968496	0.26	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29968440	29968496	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29968497	29968580	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29968581	29968679	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29968581	29968679	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29968680	29968790	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29968791	29968865	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29968791	29968865	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29968866	29968957	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29968958	29969087	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29968958	29969087	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29969088	29969197	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29969198	29969289	1	+	2	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29969198	29969289	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29969290	29969386	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29969387	29969437	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29969387	29969437	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29969438	29969535	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29969536	29969615	0.99	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29969536	29969615	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29969616	29969754	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29969755	29969780	0.84	+	1	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29969755	29969780	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29969781	29969881	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29969882	29969982	0.9	+	2	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29969882	29969982	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29969983	29970101	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29970102	29970153	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29970102	29970153	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29970154	29970256	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29970257	29970302	1	+	2	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29970257	29970302	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29970303	29970421	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29970422	29970477	0.99	+	1	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29970422	29970477	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29970478	29970586	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29970587	29970638	1	+	2	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29970587	29970638	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29970639	29970738	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29970739	29970818	1	+	1	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29970739	29970818	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29970819	29970919	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29970920	29970990	1	+	2	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29970920	29970990	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29970991	29971087	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29971088	29971128	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29971088	29971128	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29971129	29971209	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29971210	29971309	0.89	+	1	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29971210	29971309	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29971310	29971421	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29971422	29971493	0.98	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29971422	29971493	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29971494	29971605	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29971606	29971683	0.98	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29971606	29971683	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	intron	29971684	29971762	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	CDS	29971763	29971795	1	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	exon	29971763	29971795	.	+	.	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
Phchi.S1	AUGUSTUS	stop_codon	29971796	29971798	.	+	0	transcript_id "Phchi.S1G470100.t1"; gene_id "Phchi.S1G470100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11835.t1 is derived from g15887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8490782	8492837	.	-	.	Phchi.S4G141700
Phchi.S4	AUGUSTUS	transcript	8490782	8492837	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	stop_codon	8490779	8490781	.	-	0	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	CDS	8490782	8490962	0.96	-	1	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	exon	8490782	8490962	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	intron	8490963	8491102	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	CDS	8491103	8491131	0.86	-	0	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	exon	8491103	8491131	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	intron	8491132	8491258	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	CDS	8491259	8491339	0.9	-	0	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	exon	8491259	8491339	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	intron	8491340	8491496	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	CDS	8491497	8491585	1	-	2	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	exon	8491497	8491585	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	intron	8491586	8491774	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	CDS	8491775	8492837	0.55	-	0	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	exon	8491775	8492837	.	-	.	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
Phchi.S4	AUGUSTUS	start_codon	8492835	8492837	.	-	0	transcript_id "Phchi.S4G141700.t1"; gene_id "Phchi.S4G141700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11675.t1 is derived from g15726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7606439	7607466	.	+	.	Phchi.S4G125700
Phchi.S4	AUGUSTUS	transcript	7606439	7607466	.	+	.	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	start_codon	7606439	7606441	.	+	0	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	CDS	7606439	7607057	0.52	+	0	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	exon	7606439	7607057	.	+	.	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	intron	7607058	7607142	.	+	.	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	CDS	7607143	7607157	0.54	+	2	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	exon	7607143	7607157	.	+	.	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	intron	7607158	7607290	.	+	.	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	CDS	7607291	7607466	0.92	+	2	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	exon	7607291	7607466	.	+	.	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
Phchi.S4	AUGUSTUS	stop_codon	7607467	7607469	.	+	0	transcript_id "Phchi.S4G125700.t1"; gene_id "Phchi.S4G125700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg638.t1 is derived from g10420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4548741	4549439	.	-	.	Phchi.S6G059700
Phchi.S6	AUGUSTUS	transcript	4548741	4549439	.	-	.	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	stop_codon	4548738	4548740	.	-	0	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	CDS	4548741	4548828	0.95	-	1	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	exon	4548741	4548828	.	-	.	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	intron	4548829	4549158	.	-	.	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	CDS	4549159	4549439	0.97	-	0	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	exon	4549159	4549439	.	-	.	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
Phchi.S6	AUGUSTUS	start_codon	4549437	4549439	.	-	0	transcript_id "Phchi.S6G059700.t1"; gene_id "Phchi.S6G059700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14775.t1 is derived from g13243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14649122	14650228	.	-	.	Phchi.S3G209400
Phchi.S3	AUGUSTUS	transcript	14649122	14650228	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	stop_codon	14649119	14649121	.	-	0	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	CDS	14649122	14649357	0.88	-	2	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	exon	14649122	14649357	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	intron	14649358	14649454	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	CDS	14649455	14649546	1	-	1	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	exon	14649455	14649546	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	intron	14649547	14649693	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	CDS	14649694	14649776	1	-	0	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	exon	14649694	14649776	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	intron	14649777	14649955	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	CDS	14649956	14650228	0.66	-	0	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	exon	14649956	14650228	.	-	.	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
Phchi.S3	AUGUSTUS	start_codon	14650226	14650228	.	-	0	transcript_id "Phchi.S3G209400.t1"; gene_id "Phchi.S3G209400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1612.t1 is derived from g8531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2023746	2026151	.	+	.	Phchi.S5G022100
Phchi.S5	AUGUSTUS	transcript	2023746	2026151	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	start_codon	2023746	2023748	.	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2023746	2023773	1	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2023746	2023773	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2023774	2023901	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2023902	2023987	1	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2023902	2023987	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2023988	2024110	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2024111	2024152	1	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2024111	2024152	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2024153	2024308	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2024309	2024354	1	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2024309	2024354	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2024355	2024499	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2024500	2024586	1	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2024500	2024586	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2024587	2024680	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2024681	2024736	1	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2024681	2024736	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2024737	2024959	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2024960	2025077	1	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2024960	2025077	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2025078	2025207	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2025208	2025266	1	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2025208	2025266	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2025267	2025366	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2025367	2025438	1	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2025367	2025438	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2025439	2025587	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2025588	2025651	1	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2025588	2025651	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2025652	2025743	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2025744	2025845	0.81	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2025744	2025845	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2025846	2025972	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2025973	2026044	0.7	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2025973	2026044	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	intron	2026045	2026137	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	CDS	2026138	2026151	0.7	+	2	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	exon	2026138	2026151	.	+	.	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
Phchi.S5	AUGUSTUS	stop_codon	2026152	2026154	.	+	0	transcript_id "Phchi.S5G022100.t1"; gene_id "Phchi.S5G022100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10713.t1 is derived from g14763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1714607	1716022	.	-	.	Phchi.S4G029500
Phchi.S4	AUGUSTUS	transcript	1714607	1716022	.	-	.	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	stop_codon	1714604	1714606	.	-	0	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	CDS	1714607	1715839	1	-	0	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	exon	1714607	1715839	.	-	.	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	intron	1715840	1715926	.	-	.	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	CDS	1715927	1716022	0.42	-	0	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	exon	1715927	1716022	.	-	.	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
Phchi.S4	AUGUSTUS	start_codon	1716020	1716022	.	-	0	transcript_id "Phchi.S4G029500.t1"; gene_id "Phchi.S4G029500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9275.t1 is derived from g6450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40727811	40728344	.	-	.	Phchi.S1G643400
Phchi.S1	AUGUSTUS	transcript	40727811	40728344	.	-	.	transcript_id "Phchi.S1G643400.t1"; gene_id "Phchi.S1G643400"
Phchi.S1	AUGUSTUS	stop_codon	40727808	40727810	.	-	0	transcript_id "Phchi.S1G643400.t1"; gene_id "Phchi.S1G643400"
Phchi.S1	AUGUSTUS	CDS	40727811	40728344	0.75	-	0	transcript_id "Phchi.S1G643400.t1"; gene_id "Phchi.S1G643400"
Phchi.S1	AUGUSTUS	exon	40727811	40728344	.	-	.	transcript_id "Phchi.S1G643400.t1"; gene_id "Phchi.S1G643400"
Phchi.S1	AUGUSTUS	start_codon	40728342	40728344	.	-	0	transcript_id "Phchi.S1G643400.t1"; gene_id "Phchi.S1G643400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15062.t1 is derived from g13530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16829933	16832048	.	+	.	Phchi.S3G238100
Phchi.S3	AUGUSTUS	transcript	16829933	16832048	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	start_codon	16829933	16829935	.	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16829933	16830052	1	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16829933	16830052	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16830053	16830166	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16830167	16830280	1	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16830167	16830280	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16830281	16830366	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16830367	16830531	1	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16830367	16830531	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16830532	16830614	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16830615	16830782	1	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16830615	16830782	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16830783	16830929	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16830930	16831090	1	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16830930	16831090	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16831091	16831209	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16831210	16831271	1	+	1	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16831210	16831271	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16831272	16831365	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16831366	16831822	1	+	2	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16831366	16831822	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	intron	16831823	16831918	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	CDS	16831919	16832048	1	+	1	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	exon	16831919	16832048	.	+	.	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
Phchi.S3	AUGUSTUS	stop_codon	16832049	16832051	.	+	0	transcript_id "Phchi.S3G238100.t1"; gene_id "Phchi.S3G238100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14725.t1 is derived from g13193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14377460	14378993	.	+	.	Phchi.S3G204400
Phchi.S3	AUGUSTUS	transcript	14377460	14378993	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	start_codon	14377460	14377462	.	+	0	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14377460	14378203	0.94	+	0	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14377460	14378203	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	intron	14378204	14378289	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378290	14378385	1	+	0	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378290	14378385	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	intron	14378386	14378543	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378544	14378753	1	+	0	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378544	14378753	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	intron	14378754	14378837	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378838	14378993	1	+	0	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378838	14378993	.	+	.	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	stop_codon	14378994	14378996	.	+	0	transcript_id "Phchi.S3G204400.t1"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	transcript	14377460	14378587	.	+	.	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	start_codon	14377460	14377462	.	+	0	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14377460	14378203	0.96	+	0	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14377460	14378203	.	+	.	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	intron	14378204	14378289	.	+	.	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378290	14378449	1	+	0	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378290	14378449	.	+	.	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	intron	14378450	14378543	.	+	.	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378544	14378587	0.78	+	2	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378544	14378587	.	+	.	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	stop_codon	14378588	14378590	.	+	0	transcript_id "Phchi.S3G204400.t2"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	transcript	14378655	14378993	.	+	.	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	start_codon	14378655	14378657	.	+	0	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378655	14378753	0.64	+	0	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378655	14378753	.	+	.	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	intron	14378754	14378837	.	+	.	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	CDS	14378838	14378993	1	+	0	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	exon	14378838	14378993	.	+	.	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
Phchi.S3	AUGUSTUS	stop_codon	14378994	14378996	.	+	0	transcript_id "Phchi.S3G204400.t3"; gene_id "Phchi.S3G204400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8959.t1 is derived from g6134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38846287	38847993	.	-	.	Phchi.S1G611800
Phchi.S1	AUGUSTUS	transcript	38846287	38847993	.	-	.	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	stop_codon	38846284	38846286	.	-	0	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	CDS	38846287	38847105	0.99	-	0	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	exon	38846287	38847105	.	-	.	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	intron	38847106	38847255	.	-	.	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	CDS	38847256	38847330	1	-	0	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	exon	38847256	38847330	.	-	.	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	intron	38847331	38847819	.	-	.	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	CDS	38847820	38847993	1	-	0	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	exon	38847820	38847993	.	-	.	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
Phchi.S1	AUGUSTUS	start_codon	38847991	38847993	.	-	0	transcript_id "Phchi.S1G611800.t1"; gene_id "Phchi.S1G611800"
# This transcript jg14585.t2 is derived from g13053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14586.t1 is derived from g13054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13590045	13593706	.	+	.	Phchi.S3G190500
Phchi.S3	AUGUSTUS	transcript	13590045	13593706	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	start_codon	13590045	13590047	.	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13590045	13590170	0.53	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13590045	13590170	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13590171	13590278	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13590279	13590419	0.45	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13590279	13590419	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13590420	13590526	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13590527	13590618	0.94	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13590527	13590618	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13590619	13590819	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13590820	13590916	1	+	1	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13590820	13590916	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13590917	13591015	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13591016	13591059	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13591016	13591059	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13591060	13591213	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13591214	13591302	1	+	1	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13591214	13591302	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13591303	13591533	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13591534	13591625	1	+	2	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13591534	13591625	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13591626	13591710	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13591711	13591863	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13591711	13591863	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13591864	13591958	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13591959	13592106	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13591959	13592106	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13592107	13592198	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13592199	13592275	1	+	2	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13592199	13592275	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13592276	13592370	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13592371	13592442	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13592371	13592442	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13592443	13592638	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13592639	13592686	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13592639	13592686	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13592687	13592866	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13592867	13592994	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13592867	13592994	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13592995	13593088	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13593089	13593245	1	+	1	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13593089	13593245	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13593246	13593355	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13593356	13593557	1	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13593356	13593557	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	intron	13593558	13593656	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	CDS	13593657	13593706	1	+	2	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	exon	13593657	13593706	.	+	.	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
Phchi.S3	AUGUSTUS	stop_codon	13593707	13593709	.	+	0	transcript_id "Phchi.S3G190500.t1"; gene_id "Phchi.S3G190500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6495.t1 is derived from g3667.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23294513	23296497	.	-	.	Phchi.S1G365400
Phchi.S1	AUGUSTUS	transcript	23294513	23296497	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	stop_codon	23294510	23294512	.	-	0	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	CDS	23294513	23294776	1	-	0	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	exon	23294513	23294776	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	intron	23294777	23294921	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	CDS	23294922	23295141	1	-	1	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	exon	23294922	23295141	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	intron	23295142	23295310	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	CDS	23295311	23295346	0.73	-	1	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	exon	23295311	23295346	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	intron	23295347	23295528	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	CDS	23295529	23295696	1	-	1	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	exon	23295529	23295696	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	intron	23295697	23296345	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	CDS	23296346	23296497	0.95	-	0	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	exon	23296346	23296497	.	-	.	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
Phchi.S1	AUGUSTUS	start_codon	23296495	23296497	.	-	0	transcript_id "Phchi.S1G365400.t1"; gene_id "Phchi.S1G365400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12007.t1 is derived from g7682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	507095	509314	.	-	.	Phchi.S2G008700
Phchi.S2	AUGUSTUS	transcript	507095	509314	.	-	.	transcript_id "Phchi.S2G008700.t1"; gene_id "Phchi.S2G008700"
Phchi.S2	AUGUSTUS	stop_codon	507092	507094	.	-	0	transcript_id "Phchi.S2G008700.t1"; gene_id "Phchi.S2G008700"
Phchi.S2	AUGUSTUS	CDS	507095	509314	0.99	-	0	transcript_id "Phchi.S2G008700.t1"; gene_id "Phchi.S2G008700"
Phchi.S2	AUGUSTUS	exon	507095	509314	.	-	.	transcript_id "Phchi.S2G008700.t1"; gene_id "Phchi.S2G008700"
Phchi.S2	AUGUSTUS	start_codon	509312	509314	.	-	0	transcript_id "Phchi.S2G008700.t1"; gene_id "Phchi.S2G008700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14732.t1 is derived from g13200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14411025	14411333	.	-	.	Phchi.S3G205100
Phchi.S3	AUGUSTUS	transcript	14411025	14411333	.	-	.	transcript_id "Phchi.S3G205100.t1"; gene_id "Phchi.S3G205100"
Phchi.S3	AUGUSTUS	stop_codon	14411022	14411024	.	-	0	transcript_id "Phchi.S3G205100.t1"; gene_id "Phchi.S3G205100"
Phchi.S3	AUGUSTUS	CDS	14411025	14411333	0.91	-	0	transcript_id "Phchi.S3G205100.t1"; gene_id "Phchi.S3G205100"
Phchi.S3	AUGUSTUS	exon	14411025	14411333	.	-	.	transcript_id "Phchi.S3G205100.t1"; gene_id "Phchi.S3G205100"
Phchi.S3	AUGUSTUS	start_codon	14411331	14411333	.	-	0	transcript_id "Phchi.S3G205100.t1"; gene_id "Phchi.S3G205100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10405.t1 is derived from g7581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47626176	47627855	.	+	.	Phchi.S1G756400
Phchi.S1	AUGUSTUS	transcript	47626176	47627855	.	+	.	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	start_codon	47626176	47626178	.	+	0	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	CDS	47626176	47626569	1	+	0	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	exon	47626176	47626569	.	+	.	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	intron	47626570	47626766	.	+	.	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	CDS	47626767	47627036	1	+	2	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	exon	47626767	47627036	.	+	.	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	intron	47627037	47627196	.	+	.	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	CDS	47627197	47627855	1	+	2	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	exon	47627197	47627855	.	+	.	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
Phchi.S1	AUGUSTUS	stop_codon	47627856	47627858	.	+	0	transcript_id "Phchi.S1G756400.t1"; gene_id "Phchi.S1G756400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4160.t1 is derived from g1329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8683460	8685829	.	+	.	Phchi.S1G131900
Phchi.S1	AUGUSTUS	transcript	8683460	8685829	.	+	.	transcript_id "Phchi.S1G131900.t1"; gene_id "Phchi.S1G131900"
Phchi.S1	AUGUSTUS	start_codon	8683460	8683462	.	+	0	transcript_id "Phchi.S1G131900.t1"; gene_id "Phchi.S1G131900"
Phchi.S1	AUGUSTUS	CDS	8683460	8685829	0.97	+	0	transcript_id "Phchi.S1G131900.t1"; gene_id "Phchi.S1G131900"
Phchi.S1	AUGUSTUS	exon	8683460	8685829	.	+	.	transcript_id "Phchi.S1G131900.t1"; gene_id "Phchi.S1G131900"
Phchi.S1	AUGUSTUS	stop_codon	8685830	8685832	.	+	0	transcript_id "Phchi.S1G131900.t1"; gene_id "Phchi.S1G131900"
# This transcript jg2530.t2 is derived from g9450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2530.t3 is derived from g9450.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2531.t1 is derived from g9451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7180699	7183160	.	+	.	Phchi.S5G114000
Phchi.S5	AUGUSTUS	transcript	7180699	7183160	.	+	.	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	start_codon	7180699	7180701	.	+	0	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	CDS	7180699	7180991	0.98	+	0	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	exon	7180699	7180991	.	+	.	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	intron	7180992	7181248	.	+	.	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	CDS	7181249	7183160	0.99	+	1	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	exon	7181249	7183160	.	+	.	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
Phchi.S5	AUGUSTUS	stop_codon	7183161	7183163	.	+	0	transcript_id "Phchi.S5G114000.t1"; gene_id "Phchi.S5G114000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4742.t1 is derived from g1912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12582395	12583579	.	+	.	Phchi.S1G190100
Phchi.S1	AUGUSTUS	transcript	12582395	12583579	.	+	.	transcript_id "Phchi.S1G190100.t1"; gene_id "Phchi.S1G190100"
Phchi.S1	AUGUSTUS	start_codon	12582395	12582397	.	+	0	transcript_id "Phchi.S1G190100.t1"; gene_id "Phchi.S1G190100"
Phchi.S1	AUGUSTUS	CDS	12582395	12583579	0.83	+	0	transcript_id "Phchi.S1G190100.t1"; gene_id "Phchi.S1G190100"
Phchi.S1	AUGUSTUS	exon	12582395	12583579	.	+	.	transcript_id "Phchi.S1G190100.t1"; gene_id "Phchi.S1G190100"
Phchi.S1	AUGUSTUS	stop_codon	12583580	12583582	.	+	0	transcript_id "Phchi.S1G190100.t1"; gene_id "Phchi.S1G190100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7441.t1 is derived from g4613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29128401	29128762	.	+	.	Phchi.S1G460000
Phchi.S1	AUGUSTUS	transcript	29128401	29128762	.	+	.	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	start_codon	29128401	29128403	.	+	0	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	CDS	29128401	29128582	1	+	0	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	exon	29128401	29128582	.	+	.	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	intron	29128583	29128671	.	+	.	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	CDS	29128672	29128762	0.76	+	1	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	exon	29128672	29128762	.	+	.	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
Phchi.S1	AUGUSTUS	stop_codon	29128763	29128765	.	+	0	transcript_id "Phchi.S1G460000.t1"; gene_id "Phchi.S1G460000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15402.t1 is derived from g13870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18824867	18827297	.	+	.	Phchi.S3G272100
Phchi.S3	AUGUSTUS	transcript	18824867	18827297	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	start_codon	18824867	18824869	.	+	0	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18824867	18824969	0.98	+	0	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18824867	18824969	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18824970	18825310	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18825311	18825395	1	+	2	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18825311	18825395	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18825396	18825491	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18825492	18825641	1	+	1	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18825492	18825641	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18825642	18825857	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18825858	18826011	1	+	1	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18825858	18826011	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18826012	18826133	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18826134	18826349	1	+	0	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18826134	18826349	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18826350	18826480	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18826481	18826617	1	+	0	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18826481	18826617	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18826618	18826696	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18826697	18826788	1	+	1	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18826697	18826788	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18826789	18826893	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18826894	18827073	1	+	2	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18826894	18827073	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	intron	18827074	18827217	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	CDS	18827218	18827297	1	+	2	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	exon	18827218	18827297	.	+	.	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
Phchi.S3	AUGUSTUS	stop_codon	18827298	18827300	.	+	0	transcript_id "Phchi.S3G272100.t1"; gene_id "Phchi.S3G272100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10726.t1 is derived from g14776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1775635	1776593	.	+	.	Phchi.S4G030800
Phchi.S4	AUGUSTUS	transcript	1775635	1776593	.	+	.	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	start_codon	1775635	1775637	.	+	0	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	CDS	1775635	1775904	0.36	+	0	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	exon	1775635	1775904	.	+	.	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	intron	1775905	1776025	.	+	.	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	CDS	1776026	1776275	0.97	+	0	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	exon	1776026	1776275	.	+	.	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	intron	1776276	1776369	.	+	.	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	CDS	1776370	1776593	1	+	2	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	exon	1776370	1776593	.	+	.	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
Phchi.S4	AUGUSTUS	stop_codon	1776594	1776596	.	+	0	transcript_id "Phchi.S4G030800.t1"; gene_id "Phchi.S4G030800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3949.t1 is derived from g1118.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6617525	6618425	.	+	.	Phchi.S1G110800
Phchi.S1	AUGUSTUS	transcript	6617604	6618191	.	+	.	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	start_codon	6617604	6617606	.	+	0	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6617604	6617705	1	+	0	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6617604	6617705	.	+	.	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	intron	6617706	6617888	.	+	.	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6617889	6618012	1	+	0	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6617889	6618012	.	+	.	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	intron	6618013	6618150	.	+	.	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6618151	6618191	1	+	2	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6618151	6618191	.	+	.	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	stop_codon	6618192	6618194	.	+	0	transcript_id "Phchi.S1G110800.t1"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	transcript	6617604	6618425	.	+	.	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	start_codon	6617604	6617606	.	+	0	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6617604	6617705	1	+	0	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6617604	6617705	.	+	.	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	intron	6617706	6617888	.	+	.	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6617889	6618012	0.99	+	0	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6617889	6618012	.	+	.	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	intron	6618013	6618399	.	+	.	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6618400	6618425	0.97	+	2	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6618400	6618425	.	+	.	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	stop_codon	6618426	6618428	.	+	0	transcript_id "Phchi.S1G110800.t2"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	transcript	6617525	6618191	.	+	.	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	start_codon	6617525	6617527	.	+	0	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6617525	6617698	0.82	+	0	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6617525	6617698	.	+	.	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	intron	6617699	6617888	.	+	.	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6617889	6618012	1	+	0	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6617889	6618012	.	+	.	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	intron	6618013	6618150	.	+	.	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	CDS	6618151	6618191	0.93	+	2	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	exon	6618151	6618191	.	+	.	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
Phchi.S1	AUGUSTUS	stop_codon	6618192	6618194	.	+	0	transcript_id "Phchi.S1G110800.t3"; gene_id "Phchi.S1G110800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12306.t1 is derived from g7982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9908327	9914171	.	+	.	Phchi.S2G038600
Phchi.S2	AUGUSTUS	transcript	9908327	9914171	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	start_codon	9908327	9908329	.	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9908327	9908661	0.42	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9908327	9908661	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9908662	9908793	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9908794	9909881	0.63	+	1	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9908794	9909881	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9909882	9909961	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9909962	9910052	0.79	+	2	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9909962	9910052	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9910053	9910148	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9910149	9912204	0.44	+	1	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9910149	9912204	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9912205	9912354	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9912355	9912691	0.32	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9912355	9912691	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9912692	9912792	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9912793	9912902	0.46	+	2	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9912793	9912902	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9912903	9912990	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9912991	9913249	0.91	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9912991	9913249	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9913250	9913405	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9913406	9913611	0.95	+	2	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9913406	9913611	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9913612	9913734	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9913735	9913929	1	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9913735	9913929	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	intron	9913930	9914006	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	CDS	9914007	9914171	0.98	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	exon	9914007	9914171	.	+	.	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
Phchi.S2	AUGUSTUS	stop_codon	9914172	9914174	.	+	0	transcript_id "Phchi.S2G038600.t1"; gene_id "Phchi.S2G038600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11546.t1 is derived from g15596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6985305	6987526	.	-	.	Phchi.S4G112800
Phchi.S4	AUGUSTUS	transcript	6985305	6987526	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	stop_codon	6985302	6985304	.	-	0	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	CDS	6985305	6985684	1	-	2	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	exon	6985305	6985684	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	intron	6985685	6985773	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	CDS	6985774	6986786	0.97	-	1	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	exon	6985774	6986786	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	intron	6986787	6986898	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	CDS	6986899	6987161	0.45	-	0	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	exon	6986899	6987161	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	intron	6987162	6987319	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	CDS	6987320	6987526	0.22	-	0	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	exon	6987320	6987526	.	-	.	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
Phchi.S4	AUGUSTUS	start_codon	6987524	6987526	.	-	0	transcript_id "Phchi.S4G112800.t1"; gene_id "Phchi.S4G112800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12022.t1 is derived from g7697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	615726	616513	.	-	.	Phchi.S2G010200
Phchi.S2	AUGUSTUS	transcript	615726	616513	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	stop_codon	615723	615725	.	-	0	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	CDS	615726	615913	0.62	-	2	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	exon	615726	615913	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	intron	615914	616037	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	CDS	616038	616110	0.96	-	0	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	exon	616038	616110	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	intron	616111	616211	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	CDS	616212	616322	0.86	-	0	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	exon	616212	616322	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	intron	616323	616498	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	CDS	616499	616513	0.86	-	0	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	exon	616499	616513	.	-	.	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
Phchi.S2	AUGUSTUS	start_codon	616511	616513	.	-	0	transcript_id "Phchi.S2G010200.t1"; gene_id "Phchi.S2G010200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg889.t1 is derived from g10671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6310171	6313021	.	-	.	Phchi.S6G084800
Phchi.S6	AUGUSTUS	transcript	6310171	6313021	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	stop_codon	6310168	6310170	.	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	CDS	6310171	6310443	0.97	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	exon	6310171	6310443	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	intron	6310444	6310573	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	CDS	6310574	6310900	0.6	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	exon	6310574	6310900	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	intron	6310901	6311017	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	CDS	6311018	6311740	1	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	exon	6311018	6311740	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	intron	6311741	6311822	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	CDS	6311823	6311975	0.81	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	exon	6311823	6311975	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	intron	6311976	6312053	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	CDS	6312054	6312722	0.28	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	exon	6312054	6312722	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	intron	6312723	6312865	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	CDS	6312866	6313021	0.62	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	exon	6312866	6313021	.	-	.	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
Phchi.S6	AUGUSTUS	start_codon	6313019	6313021	.	-	0	transcript_id "Phchi.S6G084800.t1"; gene_id "Phchi.S6G084800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11278.t1 is derived from g15328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5180572	5182217	.	-	.	Phchi.S4G086000
Phchi.S4	AUGUSTUS	transcript	5180572	5182217	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	stop_codon	5180569	5180571	.	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	CDS	5180572	5181249	1	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	exon	5180572	5181249	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	intron	5181250	5181350	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	CDS	5181351	5181596	0.95	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	exon	5181351	5181596	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	intron	5181597	5181665	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	CDS	5181666	5181818	0.97	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	exon	5181666	5181818	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	intron	5181819	5181903	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	CDS	5181904	5181951	0.35	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	exon	5181904	5181951	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	intron	5181952	5182127	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	CDS	5182128	5182217	0.21	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	exon	5182128	5182217	.	-	.	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
Phchi.S4	AUGUSTUS	start_codon	5182215	5182217	.	-	0	transcript_id "Phchi.S4G086000.t1"; gene_id "Phchi.S4G086000"
# This transcript jg10058.t2 is derived from g7234.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10058.t3 is derived from g7234.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10059.t1 is derived from g7235.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45571300	45572256	.	-	.	Phchi.S1G721800
Phchi.S1	AUGUSTUS	transcript	45571529	45572256	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	stop_codon	45571526	45571528	.	-	0	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45571529	45571530	0.97	-	2	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45571529	45571530	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	intron	45571531	45571692	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45571693	45571888	0.81	-	0	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45571693	45571888	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	intron	45571889	45572068	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45572069	45572087	0.76	-	1	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45572069	45572087	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	intron	45572088	45572251	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45572252	45572256	0.92	-	0	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45572252	45572256	.	-	.	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	start_codon	45572254	45572256	.	-	0	transcript_id "Phchi.S1G721800.t1"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	transcript	45571300	45572256	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	stop_codon	45571297	45571299	.	-	0	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45571300	45571607	0.69	-	2	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45571300	45571607	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	intron	45571608	45571692	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45571693	45571888	0.82	-	0	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45571693	45571888	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	intron	45571889	45572068	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45572069	45572087	0.73	-	1	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45572069	45572087	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	intron	45572088	45572251	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	CDS	45572252	45572256	0.9	-	0	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	exon	45572252	45572256	.	-	.	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
Phchi.S1	AUGUSTUS	start_codon	45572254	45572256	.	-	0	transcript_id "Phchi.S1G721800.t2"; gene_id "Phchi.S1G721800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7514.t1 is derived from g4688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29792751	29795979	.	+	.	Phchi.S1G467300
Phchi.S1	AUGUSTUS	transcript	29792751	29795979	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	start_codon	29792751	29792753	.	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29792751	29793881	0.42	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29792751	29793881	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29793882	29794027	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29794028	29794130	0.63	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29794028	29794130	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29794131	29794203	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29794204	29794544	0.95	+	2	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29794204	29794544	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29794545	29794711	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29794712	29794873	1	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29794712	29794873	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29794874	29794967	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29794968	29795084	1	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29794968	29795084	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29795085	29795216	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29795217	29795320	1	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29795217	29795320	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29795321	29795436	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29795437	29795574	1	+	1	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29795437	29795574	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29795575	29795649	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29795650	29795737	1	+	1	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29795650	29795737	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	intron	29795738	29795874	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	CDS	29795875	29795979	1	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	exon	29795875	29795979	.	+	.	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
Phchi.S1	AUGUSTUS	stop_codon	29795980	29795982	.	+	0	transcript_id "Phchi.S1G467300.t1"; gene_id "Phchi.S1G467300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13410.t1 is derived from g11876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6566655	6568287	.	-	.	Phchi.S3G072900
Phchi.S3	AUGUSTUS	transcript	6566655	6568287	.	-	.	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	stop_codon	6566652	6566654	.	-	0	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	CDS	6566655	6567997	0.47	-	2	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	exon	6566655	6567997	.	-	.	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	intron	6567998	6568235	.	-	.	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	CDS	6568236	6568287	1	-	0	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	exon	6568236	6568287	.	-	.	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
Phchi.S3	AUGUSTUS	start_codon	6568285	6568287	.	-	0	transcript_id "Phchi.S3G072900.t1"; gene_id "Phchi.S3G072900"
# This transcript jg10532.t2 is derived from g14582.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10533.t1 is derived from g14583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	856318	857334	.	-	.	Phchi.S4G011500
Phchi.S4	AUGUSTUS	transcript	856318	857334	.	-	.	transcript_id "Phchi.S4G011500.t1"; gene_id "Phchi.S4G011500"
Phchi.S4	AUGUSTUS	stop_codon	856315	856317	.	-	0	transcript_id "Phchi.S4G011500.t1"; gene_id "Phchi.S4G011500"
Phchi.S4	AUGUSTUS	CDS	856318	857334	1	-	0	transcript_id "Phchi.S4G011500.t1"; gene_id "Phchi.S4G011500"
Phchi.S4	AUGUSTUS	exon	856318	857334	.	-	.	transcript_id "Phchi.S4G011500.t1"; gene_id "Phchi.S4G011500"
Phchi.S4	AUGUSTUS	start_codon	857332	857334	.	-	0	transcript_id "Phchi.S4G011500.t1"; gene_id "Phchi.S4G011500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4543.t1 is derived from g1713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11033343	11033552	.	-	.	Phchi.S1G170200
Phchi.S1	AUGUSTUS	transcript	11033343	11033552	.	-	.	transcript_id "Phchi.S1G170200.t1"; gene_id "Phchi.S1G170200"
Phchi.S1	AUGUSTUS	stop_codon	11033340	11033342	.	-	0	transcript_id "Phchi.S1G170200.t1"; gene_id "Phchi.S1G170200"
Phchi.S1	AUGUSTUS	CDS	11033343	11033552	0.57	-	0	transcript_id "Phchi.S1G170200.t1"; gene_id "Phchi.S1G170200"
Phchi.S1	AUGUSTUS	exon	11033343	11033552	.	-	.	transcript_id "Phchi.S1G170200.t1"; gene_id "Phchi.S1G170200"
Phchi.S1	AUGUSTUS	start_codon	11033550	11033552	.	-	0	transcript_id "Phchi.S1G170200.t1"; gene_id "Phchi.S1G170200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6963.t1 is derived from g4135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26155511	26157404	.	-	.	Phchi.S1G412200
Phchi.S1	AUGUSTUS	transcript	26155511	26157404	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	stop_codon	26155508	26155510	.	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26155511	26155726	1	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26155511	26155726	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26155727	26155826	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26155827	26155895	1	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26155827	26155895	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26155896	26155984	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26155985	26156121	1	-	2	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26155985	26156121	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26156122	26156219	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26156220	26156308	1	-	1	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26156220	26156308	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26156309	26156400	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26156401	26156471	1	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26156401	26156471	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26156472	26156567	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26156568	26156636	1	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26156568	26156636	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26156637	26156725	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26156726	26156813	1	-	1	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26156726	26156813	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26156814	26156900	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26156901	26156973	1	-	2	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26156901	26156973	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26156974	26157051	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26157052	26157108	1	-	2	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26157052	26157108	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	intron	26157109	26157187	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	CDS	26157188	26157404	0.98	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	exon	26157188	26157404	.	-	.	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
Phchi.S1	AUGUSTUS	start_codon	26157402	26157404	.	-	0	transcript_id "Phchi.S1G412200.t1"; gene_id "Phchi.S1G412200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6679.t1 is derived from g3851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24460071	24465044	.	-	.	Phchi.S1G383800
Phchi.S1	AUGUSTUS	transcript	24460071	24465044	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	stop_codon	24460068	24460070	.	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24460071	24460309	1	-	2	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24460071	24460309	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24460310	24460584	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24460585	24460663	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24460585	24460663	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24460664	24460745	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24460746	24460991	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24460746	24460991	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24460992	24461078	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461079	24461231	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461079	24461231	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24461232	24461315	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461316	24461631	0.89	-	1	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461316	24461631	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24461632	24461767	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461768	24461853	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461768	24461853	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24461854	24461943	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461944	24462126	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461944	24462126	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462127	24462217	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462218	24462330	1	-	2	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462218	24462330	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462331	24462411	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462412	24462618	0.53	-	2	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462412	24462618	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462619	24462737	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462738	24462807	0.54	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462738	24462807	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462808	24462899	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462900	24462932	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462900	24462932	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462933	24463026	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463027	24463234	1	-	1	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463027	24463234	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24463235	24463333	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463334	24463421	1	-	2	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463334	24463421	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24463422	24463526	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463527	24463549	1	-	1	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463527	24463549	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24463550	24463682	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463683	24464680	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463683	24464680	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24464681	24464867	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24464868	24465044	1	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24464868	24465044	.	-	.	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	start_codon	24465042	24465044	.	-	0	transcript_id "Phchi.S1G383800.t1"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	transcript	24460238	24465044	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	stop_codon	24460235	24460237	.	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24460238	24460314	0.75	-	2	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24460238	24460314	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24460315	24460584	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24460585	24460663	0.75	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24460585	24460663	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24460664	24460745	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24460746	24460991	1	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24460746	24460991	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24460992	24461078	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461079	24461231	1	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461079	24461231	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24461232	24461315	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461316	24461631	0.87	-	1	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461316	24461631	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24461632	24461767	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461768	24461853	1	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461768	24461853	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24461854	24461943	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24461944	24462126	1	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24461944	24462126	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462127	24462217	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462218	24462330	1	-	2	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462218	24462330	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462331	24462411	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462412	24462618	0.61	-	2	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462412	24462618	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462619	24462737	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462738	24462807	0.63	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462738	24462807	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462808	24462899	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24462900	24462932	1	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24462900	24462932	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24462933	24463026	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463027	24463234	1	-	1	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463027	24463234	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24463235	24463333	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463334	24463421	1	-	2	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463334	24463421	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24463422	24463526	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463527	24463549	1	-	1	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463527	24463549	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24463550	24463682	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24463683	24464680	1	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24463683	24464680	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	intron	24464681	24464867	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	CDS	24464868	24465044	0.97	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	exon	24464868	24465044	.	-	.	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
Phchi.S1	AUGUSTUS	start_codon	24465042	24465044	.	-	0	transcript_id "Phchi.S1G383800.t2"; gene_id "Phchi.S1G383800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8389.t1 is derived from g5564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35670974	35672246	.	-	.	Phchi.S1G554800
Phchi.S1	AUGUSTUS	transcript	35670974	35672246	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	stop_codon	35670971	35670973	.	-	0	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35670974	35670999	1	-	2	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35670974	35670999	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	intron	35671000	35671080	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35671081	35671134	1	-	2	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35671081	35671134	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	intron	35671135	35671229	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35671230	35671305	1	-	0	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35671230	35671305	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	intron	35671306	35671396	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35671397	35671428	1	-	2	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35671397	35671428	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	intron	35671429	35671571	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35671572	35671667	1	-	2	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35671572	35671667	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	intron	35671668	35671794	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35671795	35671896	1	-	2	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35671795	35671896	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	intron	35671897	35672164	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	CDS	35672165	35672246	1	-	0	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	exon	35672165	35672246	.	-	.	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
Phchi.S1	AUGUSTUS	start_codon	35672244	35672246	.	-	0	transcript_id "Phchi.S1G554800.t1"; gene_id "Phchi.S1G554800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10251.t1 is derived from g7427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46602430	46602931	.	+	.	Phchi.S1G741000
Phchi.S1	AUGUSTUS	transcript	46602430	46602931	.	+	.	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	start_codon	46602430	46602432	.	+	0	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	CDS	46602430	46602471	0.87	+	0	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	exon	46602430	46602471	.	+	.	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	intron	46602472	46602552	.	+	.	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	CDS	46602553	46602770	0.88	+	0	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	exon	46602553	46602770	.	+	.	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	intron	46602771	46602921	.	+	.	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	CDS	46602922	46602931	1	+	1	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	exon	46602922	46602931	.	+	.	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
Phchi.S1	AUGUSTUS	stop_codon	46602932	46602934	.	+	0	transcript_id "Phchi.S1G741000.t1"; gene_id "Phchi.S1G741000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg599.t1 is derived from g10381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4345939	4347943	.	-	.	Phchi.S6G055800
Phchi.S6	AUGUSTUS	transcript	4345939	4347943	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	stop_codon	4345936	4345938	.	-	0	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4345939	4346027	0.78	-	2	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4345939	4346027	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	intron	4346028	4346157	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4346158	4346273	0.84	-	1	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4346158	4346273	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	intron	4346274	4346387	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4346388	4346521	0.84	-	0	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4346388	4346521	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	intron	4346522	4346610	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4346611	4346735	1	-	2	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4346611	4346735	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	intron	4346736	4346839	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4346840	4347033	0.99	-	1	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4346840	4347033	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	intron	4347034	4347214	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4347215	4347501	1	-	0	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4347215	4347501	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	intron	4347502	4347661	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	CDS	4347662	4347943	1	-	0	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	exon	4347662	4347943	.	-	.	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
Phchi.S6	AUGUSTUS	start_codon	4347941	4347943	.	-	0	transcript_id "Phchi.S6G055800.t1"; gene_id "Phchi.S6G055800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4516.t1 is derived from g1686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10912328	10913519	.	+	.	Phchi.S1G167500
Phchi.S1	AUGUSTUS	transcript	10912328	10913519	.	+	.	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	start_codon	10912328	10912330	.	+	0	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	CDS	10912328	10912642	0.51	+	0	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	exon	10912328	10912642	.	+	.	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	intron	10912643	10912802	.	+	.	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	CDS	10912803	10913519	0.45	+	0	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	exon	10912803	10913519	.	+	.	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
Phchi.S1	AUGUSTUS	stop_codon	10913520	10913522	.	+	0	transcript_id "Phchi.S1G167500.t1"; gene_id "Phchi.S1G167500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14781.t1 is derived from g13249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14672658	14673932	.	-	.	Phchi.S3G210000
Phchi.S3	AUGUSTUS	transcript	14672658	14673932	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	stop_codon	14672655	14672657	.	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	CDS	14672658	14672756	1	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	exon	14672658	14672756	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	intron	14672757	14672853	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	CDS	14672854	14672943	1	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	exon	14672854	14672943	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	intron	14672944	14673056	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	CDS	14673057	14673224	0.95	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	exon	14673057	14673224	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	intron	14673225	14673370	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	CDS	14673371	14673490	1	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	exon	14673371	14673490	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	intron	14673491	14673574	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	CDS	14673575	14673720	1	-	2	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	exon	14673575	14673720	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	intron	14673721	14673823	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	CDS	14673824	14673932	0.97	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	exon	14673824	14673932	.	-	.	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
Phchi.S3	AUGUSTUS	start_codon	14673930	14673932	.	-	0	transcript_id "Phchi.S3G210000.t1"; gene_id "Phchi.S3G210000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4635.t1 is derived from g1805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11490953	11493192	.	-	.	Phchi.S1G179400
Phchi.S1	AUGUSTUS	transcript	11490953	11493192	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	stop_codon	11490950	11490952	.	-	0	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	CDS	11490953	11491912	1	-	0	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	exon	11490953	11491912	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	intron	11491913	11492033	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	CDS	11492034	11492170	0.46	-	2	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	exon	11492034	11492170	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	intron	11492171	11492307	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	CDS	11492308	11492449	0.67	-	0	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	exon	11492308	11492449	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	intron	11492450	11492563	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	CDS	11492564	11492656	1	-	0	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	exon	11492564	11492656	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	intron	11492657	11492940	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	CDS	11492941	11493192	0.98	-	0	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	exon	11492941	11493192	.	-	.	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
Phchi.S1	AUGUSTUS	start_codon	11493190	11493192	.	-	0	transcript_id "Phchi.S1G179400.t1"; gene_id "Phchi.S1G179400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11525.t1 is derived from g15575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6900961	6902199	.	+	.	Phchi.S4G110700
Phchi.S4	AUGUSTUS	transcript	6901138	6902199	.	+	.	transcript_id "Phchi.S4G110700.t1"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	start_codon	6901138	6901140	.	+	0	transcript_id "Phchi.S4G110700.t1"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	CDS	6901138	6902199	0.67	+	0	transcript_id "Phchi.S4G110700.t1"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	exon	6901138	6902199	.	+	.	transcript_id "Phchi.S4G110700.t1"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	stop_codon	6902200	6902202	.	+	0	transcript_id "Phchi.S4G110700.t1"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	transcript	6900961	6902199	.	+	.	transcript_id "Phchi.S4G110700.t2"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	start_codon	6900961	6900963	.	+	0	transcript_id "Phchi.S4G110700.t2"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	CDS	6900961	6902199	0.58	+	0	transcript_id "Phchi.S4G110700.t2"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	exon	6900961	6902199	.	+	.	transcript_id "Phchi.S4G110700.t2"; gene_id "Phchi.S4G110700"
Phchi.S4	AUGUSTUS	stop_codon	6902200	6902202	.	+	0	transcript_id "Phchi.S4G110700.t2"; gene_id "Phchi.S4G110700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15041.t1 is derived from g13509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16711011	16713926	.	+	.	Phchi.S3G236000
Phchi.S3	AUGUSTUS	transcript	16711011	16713926	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	start_codon	16711011	16711013	.	+	0	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16711011	16711033	0.88	+	0	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16711011	16711033	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	intron	16711034	16711106	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16711107	16711317	0.88	+	1	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16711107	16711317	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	intron	16711318	16711406	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16711407	16711560	0.53	+	0	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16711407	16711560	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	intron	16711561	16711644	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16711645	16711861	0.54	+	2	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16711645	16711861	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	intron	16711862	16712020	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16712021	16712075	0.6	+	1	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16712021	16712075	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	intron	16712076	16712360	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16712361	16712644	0.21	+	0	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16712361	16712644	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	intron	16712645	16712935	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	CDS	16712936	16713926	0.97	+	1	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	exon	16712936	16713926	.	+	.	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
Phchi.S3	AUGUSTUS	stop_codon	16713927	16713929	.	+	0	transcript_id "Phchi.S3G236000.t1"; gene_id "Phchi.S3G236000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8690.t1 is derived from g5865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37456124	37456675	.	+	.	Phchi.S1G584900
Phchi.S1	AUGUSTUS	transcript	37456124	37456675	.	+	.	transcript_id "Phchi.S1G584900.t1"; gene_id "Phchi.S1G584900"
Phchi.S1	AUGUSTUS	start_codon	37456124	37456126	.	+	0	transcript_id "Phchi.S1G584900.t1"; gene_id "Phchi.S1G584900"
Phchi.S1	AUGUSTUS	CDS	37456124	37456675	0.35	+	0	transcript_id "Phchi.S1G584900.t1"; gene_id "Phchi.S1G584900"
Phchi.S1	AUGUSTUS	exon	37456124	37456675	.	+	.	transcript_id "Phchi.S1G584900.t1"; gene_id "Phchi.S1G584900"
Phchi.S1	AUGUSTUS	stop_codon	37456676	37456678	.	+	0	transcript_id "Phchi.S1G584900.t1"; gene_id "Phchi.S1G584900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7206.t1 is derived from g4378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27631316	27636281	.	+	.	Phchi.S1G436500
Phchi.S1	AUGUSTUS	transcript	27631316	27636281	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	start_codon	27631316	27631318	.	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27631316	27631438	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27631316	27631438	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27631439	27631811	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27631812	27631886	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27631812	27631886	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27631887	27632079	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27632080	27632193	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27632080	27632193	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27632194	27632319	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27632320	27632424	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27632320	27632424	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27632425	27632512	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27632513	27632719	0.99	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27632513	27632719	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27632720	27632973	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27632974	27633078	0.76	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27632974	27633078	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27633079	27633179	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27633180	27633287	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27633180	27633287	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27633288	27633427	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27633428	27633598	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27633428	27633598	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27633599	27633684	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27633685	27633882	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27633685	27633882	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27633883	27633971	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27633972	27634331	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27633972	27634331	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27634332	27634520	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27634521	27634751	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27634521	27634751	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27634752	27634838	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27634839	27635027	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27634839	27635027	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27635028	27635110	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27635111	27635191	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27635111	27635191	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27635192	27635317	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27635318	27635509	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27635318	27635509	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27635510	27635631	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27635632	27636003	1	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27635632	27636003	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	intron	27636004	27636086	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	CDS	27636087	27636281	0.7	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	exon	27636087	27636281	.	+	.	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
Phchi.S1	AUGUSTUS	stop_codon	27636282	27636284	.	+	0	transcript_id "Phchi.S1G436500.t1"; gene_id "Phchi.S1G436500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6670.t1 is derived from g3842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24417352	24418140	.	-	.	Phchi.S1G382900
Phchi.S1	AUGUSTUS	transcript	24417352	24418140	.	-	.	transcript_id "Phchi.S1G382900.t1"; gene_id "Phchi.S1G382900"
Phchi.S1	AUGUSTUS	stop_codon	24417349	24417351	.	-	0	transcript_id "Phchi.S1G382900.t1"; gene_id "Phchi.S1G382900"
Phchi.S1	AUGUSTUS	CDS	24417352	24418140	0.99	-	0	transcript_id "Phchi.S1G382900.t1"; gene_id "Phchi.S1G382900"
Phchi.S1	AUGUSTUS	exon	24417352	24418140	.	-	.	transcript_id "Phchi.S1G382900.t1"; gene_id "Phchi.S1G382900"
Phchi.S1	AUGUSTUS	start_codon	24418138	24418140	.	-	0	transcript_id "Phchi.S1G382900.t1"; gene_id "Phchi.S1G382900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15090.t1 is derived from g13558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16970373	16971477	.	+	.	Phchi.S3G240900
Phchi.S3	AUGUSTUS	transcript	16970373	16971477	.	+	.	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	start_codon	16970373	16970375	.	+	0	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	CDS	16970373	16970430	0.85	+	0	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	exon	16970373	16970430	.	+	.	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	intron	16970431	16970522	.	+	.	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	CDS	16970523	16970894	0.92	+	2	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	exon	16970523	16970894	.	+	.	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	intron	16970895	16971001	.	+	.	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	CDS	16971002	16971477	0.99	+	2	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	exon	16971002	16971477	.	+	.	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
Phchi.S3	AUGUSTUS	stop_codon	16971478	16971480	.	+	0	transcript_id "Phchi.S3G240900.t1"; gene_id "Phchi.S3G240900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg517.t1 is derived from g10299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3701873	3702478	.	+	.	Phchi.S6G047600
Phchi.S6	AUGUSTUS	transcript	3701873	3702478	.	+	.	transcript_id "Phchi.S6G047600.t1"; gene_id "Phchi.S6G047600"
Phchi.S6	AUGUSTUS	start_codon	3701873	3701875	.	+	0	transcript_id "Phchi.S6G047600.t1"; gene_id "Phchi.S6G047600"
Phchi.S6	AUGUSTUS	CDS	3701873	3702478	0.93	+	0	transcript_id "Phchi.S6G047600.t1"; gene_id "Phchi.S6G047600"
Phchi.S6	AUGUSTUS	exon	3701873	3702478	.	+	.	transcript_id "Phchi.S6G047600.t1"; gene_id "Phchi.S6G047600"
Phchi.S6	AUGUSTUS	stop_codon	3702479	3702481	.	+	0	transcript_id "Phchi.S6G047600.t1"; gene_id "Phchi.S6G047600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6320.t1 is derived from g3492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22249649	22250319	.	+	.	Phchi.S1G347900
Phchi.S1	AUGUSTUS	transcript	22249649	22250319	.	+	.	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	start_codon	22249649	22249651	.	+	0	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	CDS	22249649	22249801	1	+	0	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	exon	22249649	22249801	.	+	.	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	intron	22249802	22250058	.	+	.	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	CDS	22250059	22250115	1	+	0	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	exon	22250059	22250115	.	+	.	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	intron	22250116	22250316	.	+	.	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	CDS	22250317	22250319	1	+	0	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	exon	22250317	22250319	.	+	.	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
Phchi.S1	AUGUSTUS	stop_codon	22250320	22250322	.	+	0	transcript_id "Phchi.S1G347900.t1"; gene_id "Phchi.S1G347900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5506.t1 is derived from g2676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17159316	17161017	.	+	.	Phchi.S1G266500
Phchi.S1	AUGUSTUS	transcript	17159316	17161017	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	start_codon	17159316	17159318	.	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17159316	17159434	0.81	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17159316	17159434	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17159435	17159578	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17159579	17159633	0.94	+	1	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17159579	17159633	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17159634	17159790	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17159791	17159826	1	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17159791	17159826	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17159827	17159929	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17159930	17159974	1	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17159930	17159974	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17159975	17160097	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17160098	17160181	0.97	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17160098	17160181	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17160182	17160310	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17160311	17160376	1	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17160311	17160376	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17160377	17160492	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17160493	17160531	1	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17160493	17160531	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17160532	17160653	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17160654	17160753	1	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17160654	17160753	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	intron	17160754	17160838	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	CDS	17160839	17161017	1	+	2	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	exon	17160839	17161017	.	+	.	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
Phchi.S1	AUGUSTUS	stop_codon	17161018	17161020	.	+	0	transcript_id "Phchi.S1G266500.t1"; gene_id "Phchi.S1G266500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9775.t1 is derived from g6951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43620356	43620979	.	-	.	Phchi.S1G693400
Phchi.S1	AUGUSTUS	transcript	43620356	43620979	.	-	.	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	stop_codon	43620353	43620355	.	-	0	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	CDS	43620356	43620708	0.77	-	2	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	exon	43620356	43620708	.	-	.	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	intron	43620709	43620813	.	-	.	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	CDS	43620814	43620979	0.46	-	0	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	exon	43620814	43620979	.	-	.	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
Phchi.S1	AUGUSTUS	start_codon	43620977	43620979	.	-	0	transcript_id "Phchi.S1G693400.t1"; gene_id "Phchi.S1G693400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13158.t1 is derived from g11623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4439284	4441220	.	+	.	Phchi.S3G047700
Phchi.S3	AUGUSTUS	transcript	4439284	4441220	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	start_codon	4439284	4439286	.	+	0	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4439284	4439403	0.77	+	0	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4439284	4439403	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4439404	4439501	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4439502	4439656	1	+	0	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4439502	4439656	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4439657	4439743	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4439744	4439881	1	+	1	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4439744	4439881	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4439882	4439964	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4439965	4439989	1	+	1	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4439965	4439989	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4439990	4440072	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4440073	4440259	1	+	0	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4440073	4440259	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4440260	4440340	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4440341	4440521	1	+	2	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4440341	4440521	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4440522	4440634	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4440635	4440883	1	+	1	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4440635	4440883	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4440884	4440978	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4440979	4441039	1	+	1	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4440979	4441039	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	intron	4441040	4441172	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	CDS	4441173	4441220	0.99	+	0	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	exon	4441173	4441220	.	+	.	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
Phchi.S3	AUGUSTUS	stop_codon	4441221	4441223	.	+	0	transcript_id "Phchi.S3G047700.t1"; gene_id "Phchi.S3G047700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg704.t1 is derived from g10486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4979971	4980312	.	+	.	Phchi.S6G066300
Phchi.S6	AUGUSTUS	transcript	4979971	4980312	.	+	.	transcript_id "Phchi.S6G066300.t1"; gene_id "Phchi.S6G066300"
Phchi.S6	AUGUSTUS	start_codon	4979971	4979973	.	+	0	transcript_id "Phchi.S6G066300.t1"; gene_id "Phchi.S6G066300"
Phchi.S6	AUGUSTUS	CDS	4979971	4980312	0.75	+	0	transcript_id "Phchi.S6G066300.t1"; gene_id "Phchi.S6G066300"
Phchi.S6	AUGUSTUS	exon	4979971	4980312	.	+	.	transcript_id "Phchi.S6G066300.t1"; gene_id "Phchi.S6G066300"
Phchi.S6	AUGUSTUS	stop_codon	4980313	4980315	.	+	0	transcript_id "Phchi.S6G066300.t1"; gene_id "Phchi.S6G066300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg654.t1 is derived from g10436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4605670	4607163	.	-	.	Phchi.S6G061300
Phchi.S6	AUGUSTUS	transcript	4605670	4607163	.	-	.	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	stop_codon	4605667	4605669	.	-	0	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	CDS	4605670	4605702	0.03	-	0	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	exon	4605670	4605702	.	-	.	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	intron	4605703	4606146	.	-	.	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	CDS	4606147	4606162	0.33	-	1	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	exon	4606147	4606162	.	-	.	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	intron	4606163	4606996	.	-	.	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	CDS	4606997	4607163	0.8	-	0	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	exon	4606997	4607163	.	-	.	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
Phchi.S6	AUGUSTUS	start_codon	4607161	4607163	.	-	0	transcript_id "Phchi.S6G061300.t1"; gene_id "Phchi.S6G061300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2612.t1 is derived from g9532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7786093	7786710	.	+	.	Phchi.S5G122100
Phchi.S5	AUGUSTUS	transcript	7786093	7786710	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	start_codon	7786093	7786095	.	+	0	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	CDS	7786093	7786129	1	+	0	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	exon	7786093	7786129	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	intron	7786130	7786209	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	CDS	7786210	7786316	1	+	2	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	exon	7786210	7786316	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	intron	7786317	7786414	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	CDS	7786415	7786530	1	+	0	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	exon	7786415	7786530	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	intron	7786531	7786616	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	CDS	7786617	7786710	0.99	+	1	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	exon	7786617	7786710	.	+	.	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
Phchi.S5	AUGUSTUS	stop_codon	7786711	7786713	.	+	0	transcript_id "Phchi.S5G122100.t1"; gene_id "Phchi.S5G122100"
# This transcript jg3740.t2 is derived from g909.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3741.t1 is derived from g910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5463547	5464252	.	-	.	Phchi.S1G090000
Phchi.S1	AUGUSTUS	transcript	5463547	5464252	.	-	.	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	stop_codon	5463544	5463546	.	-	0	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	CDS	5463547	5463702	1	-	0	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	exon	5463547	5463702	.	-	.	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	intron	5463703	5463845	.	-	.	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	CDS	5463846	5463910	1	-	2	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	exon	5463846	5463910	.	-	.	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	intron	5463911	5464122	.	-	.	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	CDS	5464123	5464252	0.96	-	0	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	exon	5464123	5464252	.	-	.	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
Phchi.S1	AUGUSTUS	start_codon	5464250	5464252	.	-	0	transcript_id "Phchi.S1G090000.t1"; gene_id "Phchi.S1G090000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3332.t1 is derived from g501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2958044	2960288	.	-	.	Phchi.S1G049100
Phchi.S1	AUGUSTUS	transcript	2958044	2960288	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	stop_codon	2958041	2958043	.	-	0	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	CDS	2958044	2958170	0.88	-	1	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	exon	2958044	2958170	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	intron	2958171	2958255	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	CDS	2958256	2958430	1	-	2	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	exon	2958256	2958430	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	intron	2958431	2958597	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	CDS	2958598	2958725	1	-	1	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	exon	2958598	2958725	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	intron	2958726	2958833	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	CDS	2958834	2959145	0.98	-	1	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	exon	2958834	2959145	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	intron	2959146	2959233	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	CDS	2959234	2960288	1	-	0	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	exon	2959234	2960288	.	-	.	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
Phchi.S1	AUGUSTUS	start_codon	2960286	2960288	.	-	0	transcript_id "Phchi.S1G049100.t1"; gene_id "Phchi.S1G049100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6153.t1 is derived from g3324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21213318	21214076	.	-	.	Phchi.S1G331200
Phchi.S1	AUGUSTUS	transcript	21213318	21214076	.	-	.	transcript_id "Phchi.S1G331200.t1"; gene_id "Phchi.S1G331200"
Phchi.S1	AUGUSTUS	stop_codon	21213315	21213317	.	-	0	transcript_id "Phchi.S1G331200.t1"; gene_id "Phchi.S1G331200"
Phchi.S1	AUGUSTUS	CDS	21213318	21214076	0.78	-	0	transcript_id "Phchi.S1G331200.t1"; gene_id "Phchi.S1G331200"
Phchi.S1	AUGUSTUS	exon	21213318	21214076	.	-	.	transcript_id "Phchi.S1G331200.t1"; gene_id "Phchi.S1G331200"
Phchi.S1	AUGUSTUS	start_codon	21214074	21214076	.	-	0	transcript_id "Phchi.S1G331200.t1"; gene_id "Phchi.S1G331200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3981.t1 is derived from g1150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6854516	6857006	.	+	.	Phchi.S1G114000
Phchi.S1	AUGUSTUS	transcript	6854516	6857006	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	start_codon	6854516	6854518	.	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6854516	6854869	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6854516	6854869	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6854870	6855009	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6855010	6855084	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6855010	6855084	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6855085	6855177	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6855178	6855285	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6855178	6855285	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6855286	6855370	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6855371	6855531	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6855371	6855531	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6855532	6855646	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6855647	6855761	0.96	+	1	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6855647	6855761	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6855762	6855862	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6855863	6856017	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6855863	6856017	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6856018	6856222	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6856223	6856274	1	+	1	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6856223	6856274	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6856275	6856347	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6856348	6856416	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6856348	6856416	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6856417	6856588	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6856589	6856666	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6856589	6856666	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	intron	6856667	6856763	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	CDS	6856764	6857006	1	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	exon	6856764	6857006	.	+	.	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
Phchi.S1	AUGUSTUS	stop_codon	6857007	6857009	.	+	0	transcript_id "Phchi.S1G114000.t1"; gene_id "Phchi.S1G114000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4684.t1 is derived from g1854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12039916	12040695	.	+	.	Phchi.S1G184300
Phchi.S1	AUGUSTUS	transcript	12039916	12040695	.	+	.	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	start_codon	12039916	12039918	.	+	0	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	CDS	12039916	12040034	0.35	+	0	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	exon	12039916	12040034	.	+	.	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	intron	12040035	12040145	.	+	.	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	CDS	12040146	12040695	0.36	+	1	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	exon	12040146	12040695	.	+	.	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
Phchi.S1	AUGUSTUS	stop_codon	12040696	12040698	.	+	0	transcript_id "Phchi.S1G184300.t1"; gene_id "Phchi.S1G184300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15141.t1 is derived from g13609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17247117	17248981	.	+	.	Phchi.S3G246000
Phchi.S3	AUGUSTUS	transcript	17247117	17248981	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	start_codon	17247117	17247119	.	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17247117	17247174	0.48	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17247117	17247174	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	intron	17247175	17247365	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17247366	17247517	1	+	2	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17247366	17247517	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	intron	17247518	17247609	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17247610	17247684	1	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17247610	17247684	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	intron	17247685	17247808	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17247809	17248008	1	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17247809	17248008	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	intron	17248009	17248098	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17248099	17248267	1	+	1	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17248099	17248267	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	intron	17248268	17248359	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17248360	17248749	1	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17248360	17248749	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	intron	17248750	17248846	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	CDS	17248847	17248981	1	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	exon	17248847	17248981	.	+	.	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
Phchi.S3	AUGUSTUS	stop_codon	17248982	17248984	.	+	0	transcript_id "Phchi.S3G246000.t1"; gene_id "Phchi.S3G246000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13986.t1 is derived from g12453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10057927	10058940	.	-	.	Phchi.S3G130500
Phchi.S3	AUGUSTUS	transcript	10057927	10058940	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	stop_codon	10057924	10057926	.	-	0	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	CDS	10057927	10058046	0.95	-	0	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	exon	10057927	10058046	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	intron	10058047	10058146	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	CDS	10058147	10058299	0.95	-	0	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	exon	10058147	10058299	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	intron	10058300	10058514	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	CDS	10058515	10058649	1	-	0	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	exon	10058515	10058649	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	intron	10058650	10058853	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	CDS	10058854	10058940	0.66	-	0	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	exon	10058854	10058940	.	-	.	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
Phchi.S3	AUGUSTUS	start_codon	10058938	10058940	.	-	0	transcript_id "Phchi.S3G130500.t1"; gene_id "Phchi.S3G130500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3197.t1 is derived from g366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2202767	2203195	.	+	.	Phchi.S1G035600
Phchi.S1	AUGUSTUS	transcript	2202767	2203195	.	+	.	transcript_id "Phchi.S1G035600.t1"; gene_id "Phchi.S1G035600"
Phchi.S1	AUGUSTUS	start_codon	2202767	2202769	.	+	0	transcript_id "Phchi.S1G035600.t1"; gene_id "Phchi.S1G035600"
Phchi.S1	AUGUSTUS	CDS	2202767	2203195	0.9	+	0	transcript_id "Phchi.S1G035600.t1"; gene_id "Phchi.S1G035600"
Phchi.S1	AUGUSTUS	exon	2202767	2203195	.	+	.	transcript_id "Phchi.S1G035600.t1"; gene_id "Phchi.S1G035600"
Phchi.S1	AUGUSTUS	stop_codon	2203196	2203198	.	+	0	transcript_id "Phchi.S1G035600.t1"; gene_id "Phchi.S1G035600"
# This transcript jg975.t2 is derived from g10758.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg975.t3 is derived from g10758.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg975.t4 is derived from g10758.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg976.t1 is derived from g10759.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6756316	6757867	.	-	.	Phchi.S6G093500
Phchi.S6	AUGUSTUS	transcript	6756316	6757867	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	stop_codon	6756313	6756315	.	-	0	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6756316	6756876	1	-	0	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6756316	6756876	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6756877	6756954	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6756955	6757167	1	-	0	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6756955	6757167	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6757168	6757281	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6757282	6757331	1	-	2	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6757282	6757331	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6757332	6757556	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6757557	6757563	1	-	0	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6757557	6757563	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6757564	6757807	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6757808	6757867	0.78	-	0	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6757808	6757867	.	-	.	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	start_codon	6757865	6757867	.	-	0	transcript_id "Phchi.S6G093500.t1"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	transcript	6756316	6757867	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	stop_codon	6756313	6756315	.	-	0	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6756316	6756876	1	-	0	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6756316	6756876	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6756877	6756954	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6756955	6757167	1	-	0	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6756955	6757167	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6757168	6757281	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6757282	6757331	0.97	-	2	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6757282	6757331	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6757332	6757616	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6757617	6757623	0.97	-	0	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6757617	6757623	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	intron	6757624	6757807	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	CDS	6757808	6757867	0.72	-	0	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	exon	6757808	6757867	.	-	.	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
Phchi.S6	AUGUSTUS	start_codon	6757865	6757867	.	-	0	transcript_id "Phchi.S6G093500.t2"; gene_id "Phchi.S6G093500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4429.t1 is derived from g1598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10448211	10450299	.	-	.	Phchi.S1G158800
Phchi.S1	AUGUSTUS	transcript	10448211	10450299	.	-	.	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	stop_codon	10448208	10448210	.	-	0	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	CDS	10448211	10449545	0.95	-	0	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	exon	10448211	10449545	.	-	.	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	intron	10449546	10449652	.	-	.	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	CDS	10449653	10450076	0.99	-	1	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	exon	10449653	10450076	.	-	.	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	intron	10450077	10450153	.	-	.	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	CDS	10450154	10450299	0.99	-	0	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	exon	10450154	10450299	.	-	.	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
Phchi.S1	AUGUSTUS	start_codon	10450297	10450299	.	-	0	transcript_id "Phchi.S1G158800.t1"; gene_id "Phchi.S1G158800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2542.t1 is derived from g9462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7252065	7252967	.	+	.	Phchi.S5G115100
Phchi.S5	AUGUSTUS	transcript	7252065	7252967	.	+	.	transcript_id "Phchi.S5G115100.t1"; gene_id "Phchi.S5G115100"
Phchi.S5	AUGUSTUS	start_codon	7252065	7252067	.	+	0	transcript_id "Phchi.S5G115100.t1"; gene_id "Phchi.S5G115100"
Phchi.S5	AUGUSTUS	CDS	7252065	7252967	0.51	+	0	transcript_id "Phchi.S5G115100.t1"; gene_id "Phchi.S5G115100"
Phchi.S5	AUGUSTUS	exon	7252065	7252967	.	+	.	transcript_id "Phchi.S5G115100.t1"; gene_id "Phchi.S5G115100"
Phchi.S5	AUGUSTUS	stop_codon	7252968	7252970	.	+	0	transcript_id "Phchi.S5G115100.t1"; gene_id "Phchi.S5G115100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9645.t1 is derived from g6821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43040511	43045465	.	-	.	Phchi.S1G680400
Phchi.S1	AUGUSTUS	transcript	43040511	43045465	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	stop_codon	43040508	43040510	.	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43040511	43040664	1	-	1	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43040511	43040664	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43040665	43040746	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43040747	43040892	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43040747	43040892	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43040893	43040997	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43040998	43041097	1	-	1	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43040998	43041097	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43041098	43041222	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43041223	43041326	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43041223	43041326	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43041327	43041449	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43041450	43041950	0.97	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43041450	43041950	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43041951	43042041	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43042042	43042293	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43042042	43042293	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43042294	43042373	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43042374	43042782	0.98	-	1	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43042374	43042782	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43042783	43043002	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43043003	43043181	0.96	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43043003	43043181	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43043182	43043295	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43043296	43043466	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43043296	43043466	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43043467	43043566	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43043567	43043869	0.99	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43043567	43043869	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43043870	43043956	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43043957	43044014	1	-	1	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43043957	43044014	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044015	43044119	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43044120	43044199	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43044120	43044199	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044200	43044279	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43044280	43044363	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43044280	43044363	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044364	43044449	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43044450	43044527	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43044450	43044527	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044528	43044597	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43044598	43044681	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43044598	43044681	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044682	43044756	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43044757	43044822	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43044757	43044822	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044823	43044916	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43044917	43044989	1	-	1	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43044917	43044989	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43044990	43045076	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43045077	43045309	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43045077	43045309	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	intron	43045310	43045387	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	CDS	43045388	43045465	1	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	exon	43045388	43045465	.	-	.	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
Phchi.S1	AUGUSTUS	start_codon	43045463	43045465	.	-	0	transcript_id "Phchi.S1G680400.t1"; gene_id "Phchi.S1G680400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg522.t1 is derived from g10304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3742022	3743785	.	-	.	Phchi.S6G048100
Phchi.S6	AUGUSTUS	transcript	3742022	3743785	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	stop_codon	3742019	3742021	.	-	0	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3742022	3742135	0.95	-	0	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3742022	3742135	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3742136	3742256	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3742257	3742387	1	-	2	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3742257	3742387	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3742388	3742481	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3742482	3742564	0.94	-	1	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3742482	3742564	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3742565	3742784	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3742785	3742953	0.3	-	2	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3742785	3742953	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3742954	3743050	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3743051	3743150	1	-	0	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3743051	3743150	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3743151	3743272	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3743273	3743423	1	-	1	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3743273	3743423	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3743424	3743511	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3743512	3743594	1	-	0	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3743512	3743594	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	intron	3743595	3743671	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	CDS	3743672	3743785	1	-	0	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	exon	3743672	3743785	.	-	.	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
Phchi.S6	AUGUSTUS	start_codon	3743783	3743785	.	-	0	transcript_id "Phchi.S6G048100.t1"; gene_id "Phchi.S6G048100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12984.t1 is derived from g11449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3451264	3453394	.	+	.	Phchi.S3G030300
Phchi.S3	AUGUSTUS	transcript	3451264	3453394	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	start_codon	3451264	3451266	.	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451264	3451399	0.58	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451264	3451399	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3451400	3451510	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451511	3451714	0.88	+	2	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451511	3451714	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3451715	3451806	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451807	3451862	1	+	2	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451807	3451862	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3451863	3451956	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451957	3452008	1	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451957	3452008	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452009	3452085	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452086	3452165	1	+	2	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452086	3452165	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452166	3452260	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452261	3452347	1	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452261	3452347	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452348	3452435	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452436	3452489	1	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452436	3452489	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452490	3452556	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452557	3452796	1	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452557	3452796	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452797	3452876	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452877	3452970	1	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452877	3452970	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452971	3453059	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3453060	3453200	1	+	2	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3453060	3453200	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3453201	3453317	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3453318	3453394	1	+	2	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3453318	3453394	.	+	.	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	stop_codon	3453395	3453397	.	+	0	transcript_id "Phchi.S3G030300.t1"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	transcript	3451264	3453394	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	start_codon	3451264	3451266	.	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451264	3451399	0.5	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451264	3451399	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3451400	3451510	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451511	3451714	0.86	+	2	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451511	3451714	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3451715	3451806	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451807	3451862	1	+	2	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451807	3451862	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3451863	3451956	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3451957	3452008	1	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3451957	3452008	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452009	3452085	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452086	3452165	1	+	2	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452086	3452165	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452166	3452248	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452249	3452347	0.93	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452249	3452347	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452348	3452435	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452436	3452489	1	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452436	3452489	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452490	3452556	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452557	3452796	1	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452557	3452796	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452797	3452876	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3452877	3452970	1	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3452877	3452970	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3452971	3453059	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3453060	3453200	0.99	+	2	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3453060	3453200	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	intron	3453201	3453317	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	CDS	3453318	3453394	0.99	+	2	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	exon	3453318	3453394	.	+	.	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
Phchi.S3	AUGUSTUS	stop_codon	3453395	3453397	.	+	0	transcript_id "Phchi.S3G030300.t2"; gene_id "Phchi.S3G030300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7238.t1 is derived from g4410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27793433	27794054	.	-	.	Phchi.S1G439700
Phchi.S1	AUGUSTUS	transcript	27793433	27794054	.	-	.	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	stop_codon	27793430	27793432	.	-	0	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	CDS	27793433	27793612	1	-	0	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	exon	27793433	27793612	.	-	.	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	intron	27793613	27793727	.	-	.	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	CDS	27793728	27793769	1	-	0	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	exon	27793728	27793769	.	-	.	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	intron	27793770	27793931	.	-	.	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	CDS	27793932	27794054	1	-	0	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	exon	27793932	27794054	.	-	.	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
Phchi.S1	AUGUSTUS	start_codon	27794052	27794054	.	-	0	transcript_id "Phchi.S1G439700.t1"; gene_id "Phchi.S1G439700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9613.t1 is derived from g6789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42934332	42935124	.	+	.	Phchi.S1G677200
Phchi.S1	AUGUSTUS	transcript	42934332	42935124	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	start_codon	42934332	42934334	.	+	0	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	CDS	42934332	42934455	0.48	+	0	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	exon	42934332	42934455	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	intron	42934456	42934540	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	CDS	42934541	42934591	1	+	2	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	exon	42934541	42934591	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	intron	42934592	42934714	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	CDS	42934715	42934774	1	+	2	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	exon	42934715	42934774	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	intron	42934775	42934862	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	CDS	42934863	42934934	1	+	2	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	exon	42934863	42934934	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	intron	42934935	42935089	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	CDS	42935090	42935124	1	+	2	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	exon	42935090	42935124	.	+	.	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
Phchi.S1	AUGUSTUS	stop_codon	42935125	42935127	.	+	0	transcript_id "Phchi.S1G677200.t1"; gene_id "Phchi.S1G677200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13421.t1 is derived from g11888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6617435	6618844	.	+	.	Phchi.S3G074000
Phchi.S3	AUGUSTUS	transcript	6617435	6618844	.	+	.	transcript_id "Phchi.S3G074000.t1"; gene_id "Phchi.S3G074000"
Phchi.S3	AUGUSTUS	start_codon	6617435	6617437	.	+	0	transcript_id "Phchi.S3G074000.t1"; gene_id "Phchi.S3G074000"
Phchi.S3	AUGUSTUS	CDS	6617435	6618844	0.35	+	0	transcript_id "Phchi.S3G074000.t1"; gene_id "Phchi.S3G074000"
Phchi.S3	AUGUSTUS	exon	6617435	6618844	.	+	.	transcript_id "Phchi.S3G074000.t1"; gene_id "Phchi.S3G074000"
Phchi.S3	AUGUSTUS	stop_codon	6618845	6618847	.	+	0	transcript_id "Phchi.S3G074000.t1"; gene_id "Phchi.S3G074000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1312.t1 is derived from g11095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8948399	8950108	.	+	.	Phchi.S6G127100
Phchi.S6	AUGUSTUS	transcript	8948399	8950108	.	+	.	transcript_id "Phchi.S6G127100.t1"; gene_id "Phchi.S6G127100"
Phchi.S6	AUGUSTUS	start_codon	8948399	8948401	.	+	0	transcript_id "Phchi.S6G127100.t1"; gene_id "Phchi.S6G127100"
Phchi.S6	AUGUSTUS	CDS	8948399	8950108	0.52	+	0	transcript_id "Phchi.S6G127100.t1"; gene_id "Phchi.S6G127100"
Phchi.S6	AUGUSTUS	exon	8948399	8950108	.	+	.	transcript_id "Phchi.S6G127100.t1"; gene_id "Phchi.S6G127100"
Phchi.S6	AUGUSTUS	stop_codon	8950109	8950111	.	+	0	transcript_id "Phchi.S6G127100.t1"; gene_id "Phchi.S6G127100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3388.t1 is derived from g557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3307216	3308756	.	-	.	Phchi.S1G054700
Phchi.S1	AUGUSTUS	transcript	3307216	3308756	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	stop_codon	3307213	3307215	.	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	CDS	3307216	3307512	0.91	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	exon	3307216	3307512	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	intron	3307513	3307595	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	CDS	3307596	3307763	1	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	exon	3307596	3307763	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	intron	3307764	3307865	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	CDS	3307866	3307997	0.98	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	exon	3307866	3307997	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	intron	3307998	3308085	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	CDS	3308086	3308168	0.99	-	2	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	exon	3308086	3308168	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	intron	3308169	3308287	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	CDS	3308288	3308480	1	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	exon	3308288	3308480	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	intron	3308481	3308567	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	CDS	3308568	3308756	0.75	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	exon	3308568	3308756	.	-	.	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
Phchi.S1	AUGUSTUS	start_codon	3308754	3308756	.	-	0	transcript_id "Phchi.S1G054700.t1"; gene_id "Phchi.S1G054700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8361.t1 is derived from g5536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35509831	35511482	.	+	.	Phchi.S1G552000
Phchi.S1	AUGUSTUS	transcript	35509831	35511482	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	start_codon	35509831	35509833	.	+	0	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	CDS	35509831	35509858	0.98	+	0	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	exon	35509831	35509858	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	intron	35509859	35510425	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	CDS	35510426	35510755	1	+	2	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	exon	35510426	35510755	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	intron	35510756	35510935	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	CDS	35510936	35511123	1	+	2	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	exon	35510936	35511123	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	intron	35511124	35511212	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	CDS	35511213	35511482	0.99	+	0	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	exon	35511213	35511482	.	+	.	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
Phchi.S1	AUGUSTUS	stop_codon	35511483	35511485	.	+	0	transcript_id "Phchi.S1G552000.t1"; gene_id "Phchi.S1G552000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6416.t1 is derived from g3588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22897778	22898458	.	-	.	Phchi.S1G357500
Phchi.S1	AUGUSTUS	transcript	22897778	22898458	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	stop_codon	22897775	22897777	.	-	0	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	CDS	22897778	22897814	1	-	1	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	exon	22897778	22897814	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	intron	22897815	22897956	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	CDS	22897957	22898025	1	-	1	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	exon	22897957	22898025	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	intron	22898026	22898123	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	CDS	22898124	22898194	1	-	0	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	exon	22898124	22898194	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	intron	22898195	22898287	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	CDS	22898288	22898346	1	-	2	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	exon	22898288	22898346	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	intron	22898347	22898445	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	CDS	22898446	22898458	0.97	-	0	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	exon	22898446	22898458	.	-	.	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
Phchi.S1	AUGUSTUS	start_codon	22898456	22898458	.	-	0	transcript_id "Phchi.S1G357500.t1"; gene_id "Phchi.S1G357500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13612.t1 is derived from g12079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7688134	7689541	.	-	.	Phchi.S3G093100
Phchi.S3	AUGUSTUS	transcript	7688134	7689541	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	stop_codon	7688131	7688133	.	-	0	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	CDS	7688134	7688140	0.57	-	1	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	exon	7688134	7688140	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	intron	7688141	7688225	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	CDS	7688226	7688398	0.44	-	0	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	exon	7688226	7688398	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	intron	7688399	7688644	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	CDS	7688645	7689230	0.69	-	1	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	exon	7688645	7689230	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	intron	7689231	7689329	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	CDS	7689330	7689541	0.67	-	0	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	exon	7689330	7689541	.	-	.	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
Phchi.S3	AUGUSTUS	start_codon	7689539	7689541	.	-	0	transcript_id "Phchi.S3G093100.t1"; gene_id "Phchi.S3G093100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2669.t1 is derived from g9589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8124230	8127031	.	-	.	Phchi.S5G127800
Phchi.S5	AUGUSTUS	transcript	8124230	8127031	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	stop_codon	8124227	8124229	.	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8124230	8124397	0.94	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8124230	8124397	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8124398	8124498	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8124499	8124672	0.74	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8124499	8124672	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8124673	8124787	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8124788	8124850	1	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8124788	8124850	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8124851	8124939	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8124940	8125047	1	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8124940	8125047	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8125048	8125144	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8125145	8125260	1	-	2	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8125145	8125260	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8125261	8125389	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8125390	8125516	1	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8125390	8125516	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8125517	8125604	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8125605	8125774	1	-	2	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8125605	8125774	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8125775	8125877	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8125878	8125956	1	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8125878	8125956	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8125957	8126058	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8126059	8126170	0.98	-	1	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8126059	8126170	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8126171	8126291	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8126292	8126333	1	-	1	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8126292	8126333	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8126334	8126425	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8126426	8126556	1	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8126426	8126556	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	intron	8126557	8126713	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	CDS	8126714	8127031	1	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	exon	8126714	8127031	.	-	.	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
Phchi.S5	AUGUSTUS	start_codon	8127029	8127031	.	-	0	transcript_id "Phchi.S5G127800.t1"; gene_id "Phchi.S5G127800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12622.t1 is derived from g8299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37606183	37609719	.	+	.	Phchi.S2G070200
Phchi.S2	AUGUSTUS	transcript	37606183	37609719	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	start_codon	37606183	37606185	.	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37606183	37606482	0.89	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37606183	37606482	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37606483	37606625	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37606626	37606789	1	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37606626	37606789	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37606790	37606945	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37606946	37607074	0.94	+	1	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37606946	37607074	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37607075	37607188	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37607189	37607330	1	+	1	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37607189	37607330	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37607331	37607448	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37607449	37607510	1	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37607449	37607510	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37607511	37607598	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37607599	37607827	1	+	1	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37607599	37607827	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37607828	37607994	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37607995	37608810	0.98	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37607995	37608810	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37608811	37608900	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37608901	37609008	1	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37608901	37609008	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37609009	37609118	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37609119	37609368	0.99	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37609119	37609368	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	intron	37609369	37609462	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	CDS	37609463	37609719	0.73	+	2	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	exon	37609463	37609719	.	+	.	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
Phchi.S2	AUGUSTUS	stop_codon	37609720	37609722	.	+	0	transcript_id "Phchi.S2G070200.t1"; gene_id "Phchi.S2G070200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15875.t1 is derived from g14345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22002653	22004305	.	-	.	Phchi.S3G319400
Phchi.S3	AUGUSTUS	transcript	22002653	22004305	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	stop_codon	22002650	22002652	.	-	0	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	CDS	22002653	22003359	1	-	2	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	exon	22002653	22003359	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	intron	22003360	22003452	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	CDS	22003453	22003656	1	-	2	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	exon	22003453	22003656	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	intron	22003657	22003750	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	CDS	22003751	22003844	1	-	0	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	exon	22003751	22003844	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	intron	22003845	22004227	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	CDS	22004228	22004305	1	-	0	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	exon	22004228	22004305	.	-	.	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
Phchi.S3	AUGUSTUS	start_codon	22004303	22004305	.	-	0	transcript_id "Phchi.S3G319400.t1"; gene_id "Phchi.S3G319400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11072.t1 is derived from g15122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3970164	3971274	.	-	.	Phchi.S4G065400
Phchi.S4	AUGUSTUS	transcript	3970164	3971274	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	stop_codon	3970161	3970163	.	-	0	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	CDS	3970164	3970398	0.97	-	1	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	exon	3970164	3970398	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	intron	3970399	3970586	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	CDS	3970587	3970696	1	-	0	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	exon	3970587	3970696	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	intron	3970697	3970908	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	CDS	3970909	3971011	1	-	1	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	exon	3970909	3971011	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	intron	3971012	3971122	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	CDS	3971123	3971274	0.75	-	0	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	exon	3971123	3971274	.	-	.	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
Phchi.S4	AUGUSTUS	start_codon	3971272	3971274	.	-	0	transcript_id "Phchi.S4G065400.t1"; gene_id "Phchi.S4G065400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14021.t1 is derived from g12488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10341098	10344047	.	-	.	Phchi.S3G134000
Phchi.S3	AUGUSTUS	transcript	10341098	10344047	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	stop_codon	10341095	10341097	.	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10341098	10341181	0.93	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10341098	10341181	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10341182	10341276	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10341277	10341474	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10341277	10341474	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10341475	10341566	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10341567	10341653	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10341567	10341653	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10341654	10341740	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10341741	10341826	1	-	2	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10341741	10341826	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10341827	10341942	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10341943	10342038	1	-	2	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10341943	10342038	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10342039	10342181	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10342182	10342285	1	-	1	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10342182	10342285	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10342286	10342425	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10342426	10342502	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10342426	10342502	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10342503	10342599	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10342600	10342680	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10342600	10342680	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10342681	10342767	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10342768	10342884	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10342768	10342884	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10342885	10343010	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10343011	10343082	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10343011	10343082	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10343083	10343183	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10343184	10343358	1	-	1	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10343184	10343358	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10343359	10343449	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10343450	10343604	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10343450	10343604	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10343605	10343815	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10343816	10343908	1	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10343816	10343908	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	intron	10343909	10343984	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	CDS	10343985	10344047	0.96	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	exon	10343985	10344047	.	-	.	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
Phchi.S3	AUGUSTUS	start_codon	10344045	10344047	.	-	0	transcript_id "Phchi.S3G134000.t1"; gene_id "Phchi.S3G134000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4265.t1 is derived from g1434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9283465	9284168	.	-	.	Phchi.S1G142400
Phchi.S1	AUGUSTUS	transcript	9283465	9284168	.	-	.	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	stop_codon	9283462	9283464	.	-	0	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	CDS	9283465	9283847	0.91	-	2	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	exon	9283465	9283847	.	-	.	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	intron	9283848	9283933	.	-	.	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	CDS	9283934	9284168	0.5	-	0	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	exon	9283934	9284168	.	-	.	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
Phchi.S1	AUGUSTUS	start_codon	9284166	9284168	.	-	0	transcript_id "Phchi.S1G142400.t1"; gene_id "Phchi.S1G142400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg641.t1 is derived from g10423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4557107	4559419	.	-	.	Phchi.S6G060000
Phchi.S6	AUGUSTUS	transcript	4557107	4559419	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	stop_codon	4557104	4557106	.	-	0	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4557107	4557221	0.98	-	1	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4557107	4557221	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4557222	4557340	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4557341	4557425	1	-	2	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4557341	4557425	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4557426	4557522	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4557523	4557608	0.99	-	1	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4557523	4557608	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4557609	4557716	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4557717	4557796	0.99	-	0	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4557717	4557796	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4557797	4557911	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4557912	4557974	1	-	0	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4557912	4557974	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4557975	4558103	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4558104	4558198	1	-	2	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4558104	4558198	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4558199	4558288	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4558289	4558388	1	-	0	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4558289	4558388	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4558389	4558476	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4558477	4558535	0.98	-	2	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4558477	4558535	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4558536	4558638	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4558639	4558685	0.94	-	1	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4558639	4558685	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4558686	4558774	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4558775	4558909	0.98	-	1	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4558775	4558909	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4558910	4559018	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4559019	4559091	0.98	-	2	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4559019	4559091	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4559092	4559188	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4559189	4559305	0.92	-	2	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4559189	4559305	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	intron	4559306	4559382	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	CDS	4559383	4559419	0.9	-	0	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	exon	4559383	4559419	.	-	.	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
Phchi.S6	AUGUSTUS	start_codon	4559417	4559419	.	-	0	transcript_id "Phchi.S6G060000.t1"; gene_id "Phchi.S6G060000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12224.t1 is derived from g7900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6830030	6832643	.	+	.	Phchi.S2G030400
Phchi.S2	AUGUSTUS	transcript	6830030	6832643	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	start_codon	6830030	6830032	.	+	0	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6830030	6830268	0.87	+	0	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6830030	6830268	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	intron	6830269	6830347	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6830348	6830417	1	+	1	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6830348	6830417	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	intron	6830418	6830494	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6830495	6831595	1	+	0	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6830495	6831595	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	intron	6831596	6831740	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6831741	6832643	0.98	+	0	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6831741	6832643	.	+	.	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	stop_codon	6832644	6832646	.	+	0	transcript_id "Phchi.S2G030400.t1"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	transcript	6830030	6832643	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	start_codon	6830030	6830032	.	+	0	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6830030	6830268	0.75	+	0	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6830030	6830268	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	intron	6830269	6830347	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6830348	6830417	1	+	1	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6830348	6830417	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	intron	6830418	6830494	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6830495	6831595	1	+	0	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6830495	6831595	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	intron	6831596	6831680	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	CDS	6831681	6832643	0.97	+	0	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	exon	6831681	6832643	.	+	.	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
Phchi.S2	AUGUSTUS	stop_codon	6832644	6832646	.	+	0	transcript_id "Phchi.S2G030400.t2"; gene_id "Phchi.S2G030400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7332.t1 is derived from g4504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28550252	28551723	.	+	.	Phchi.S1G449100
Phchi.S1	AUGUSTUS	transcript	28550252	28551723	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	start_codon	28550252	28550254	.	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28550252	28550549	0.6	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28550252	28550549	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28550550	28550620	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28550621	28550751	1	+	2	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28550621	28550751	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28550752	28550831	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28550832	28550909	1	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28550832	28550909	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28550910	28550977	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28550978	28551022	1	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28550978	28551022	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28551023	28551094	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28551095	28551139	1	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28551095	28551139	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28551140	28551236	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28551237	28551288	1	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28551237	28551288	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28551289	28551365	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28551366	28551462	1	+	2	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28551366	28551462	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	intron	28551463	28551563	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	CDS	28551564	28551723	1	+	1	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	exon	28551564	28551723	.	+	.	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
Phchi.S1	AUGUSTUS	stop_codon	28551724	28551726	.	+	0	transcript_id "Phchi.S1G449100.t1"; gene_id "Phchi.S1G449100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6649.t1 is derived from g3821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24279321	24284202	.	+	.	Phchi.S1G380800
Phchi.S1	AUGUSTUS	transcript	24279321	24284202	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	start_codon	24279321	24279323	.	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24279321	24279950	1	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24279321	24279950	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24279951	24280098	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24280099	24280308	0.66	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24280099	24280308	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24280309	24280637	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24280638	24280721	0.65	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24280638	24280721	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24280722	24280837	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24280838	24280917	0.67	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24280838	24280917	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24280918	24281042	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24281043	24281093	0.99	+	1	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24281043	24281093	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24281094	24281439	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24281440	24281542	1	+	1	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24281440	24281542	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24281543	24281622	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24281623	24281705	0.95	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24281623	24281705	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24281706	24281842	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24281843	24281888	1	+	1	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24281843	24281888	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24281889	24282032	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24282033	24282120	1	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24282033	24282120	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24282121	24282202	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24282203	24283371	0.83	+	2	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24282203	24283371	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	intron	24283372	24283467	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	CDS	24283468	24284202	0.96	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	exon	24283468	24284202	.	+	.	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
Phchi.S1	AUGUSTUS	stop_codon	24284203	24284205	.	+	0	transcript_id "Phchi.S1G380800.t1"; gene_id "Phchi.S1G380800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3373.t1 is derived from g542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3232912	3233469	.	-	.	Phchi.S1G053200
Phchi.S1	AUGUSTUS	transcript	3232912	3233469	.	-	.	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	stop_codon	3232909	3232911	.	-	0	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	CDS	3232912	3233011	0.81	-	1	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	exon	3232912	3233011	.	-	.	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	intron	3233012	3233263	.	-	.	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	CDS	3233264	3233469	0.75	-	0	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	exon	3233264	3233469	.	-	.	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
Phchi.S1	AUGUSTUS	start_codon	3233467	3233469	.	-	0	transcript_id "Phchi.S1G053200.t1"; gene_id "Phchi.S1G053200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg621.t1 is derived from g10403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4447302	4448113	.	+	.	Phchi.S6G058000
Phchi.S6	AUGUSTUS	transcript	4447302	4448113	.	+	.	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	start_codon	4447302	4447304	.	+	0	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	CDS	4447302	4447572	0.99	+	0	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	exon	4447302	4447572	.	+	.	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	intron	4447573	4447656	.	+	.	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	CDS	4447657	4447870	1	+	2	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	exon	4447657	4447870	.	+	.	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	intron	4447871	4448091	.	+	.	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	CDS	4448092	4448113	1	+	1	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	exon	4448092	4448113	.	+	.	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
Phchi.S6	AUGUSTUS	stop_codon	4448114	4448116	.	+	0	transcript_id "Phchi.S6G058000.t1"; gene_id "Phchi.S6G058000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5753.t1 is derived from g2923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18737564	18739676	.	+	.	Phchi.S1G291200
Phchi.S1	AUGUSTUS	transcript	18737564	18739676	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	start_codon	18737564	18737566	.	+	0	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	CDS	18737564	18738124	0.99	+	0	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	exon	18737564	18738124	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	intron	18738125	18738246	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	CDS	18738247	18738487	1	+	0	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	exon	18738247	18738487	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	intron	18738488	18738619	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	CDS	18738620	18739050	0.49	+	2	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	exon	18738620	18739050	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	intron	18739051	18739136	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	CDS	18739137	18739676	1	+	0	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	exon	18739137	18739676	.	+	.	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
Phchi.S1	AUGUSTUS	stop_codon	18739677	18739679	.	+	0	transcript_id "Phchi.S1G291200.t1"; gene_id "Phchi.S1G291200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9732.t1 is derived from g6908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43441967	43442994	.	-	.	Phchi.S1G689100
Phchi.S1	AUGUSTUS	transcript	43441967	43442994	.	-	.	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	stop_codon	43441964	43441966	.	-	0	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	CDS	43441967	43442335	0.81	-	0	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	exon	43441967	43442335	.	-	.	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	intron	43442336	43442412	.	-	.	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	CDS	43442413	43442994	0.97	-	0	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	exon	43442413	43442994	.	-	.	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
Phchi.S1	AUGUSTUS	start_codon	43442992	43442994	.	-	0	transcript_id "Phchi.S1G689100.t1"; gene_id "Phchi.S1G689100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11722.t1 is derived from g15774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7840853	7843518	.	-	.	Phchi.S4G130400
Phchi.S4	AUGUSTUS	transcript	7840853	7843518	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	stop_codon	7840850	7840852	.	-	0	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7840853	7840960	0.99	-	0	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7840853	7840960	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7840961	7841045	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841046	7841152	1	-	2	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841046	7841152	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841153	7841229	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841230	7841353	1	-	0	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841230	7841353	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841354	7841437	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841438	7841603	0.54	-	1	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841438	7841603	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841604	7841717	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841718	7841792	0.45	-	1	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841718	7841792	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841793	7841902	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841903	7841964	0.98	-	0	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841903	7841964	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841965	7842092	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842093	7842220	0.93	-	2	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842093	7842220	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842221	7842309	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842310	7842354	0.93	-	2	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842310	7842354	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842355	7842510	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842511	7842542	0.93	-	1	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842511	7842542	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842543	7842757	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842758	7842868	0.96	-	1	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842758	7842868	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842869	7843117	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7843118	7843518	0.95	-	0	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7843118	7843518	.	-	.	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	start_codon	7843516	7843518	.	-	0	transcript_id "Phchi.S4G130400.t1"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	transcript	7840853	7843518	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	stop_codon	7840850	7840852	.	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7840853	7840960	0.98	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7840853	7840960	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7840961	7841045	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841046	7841152	1	-	2	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841046	7841152	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841153	7841229	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841230	7841353	1	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841230	7841353	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841354	7841437	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841438	7841603	0.52	-	1	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841438	7841603	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841604	7841717	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841718	7841792	0.43	-	1	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841718	7841792	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841793	7841902	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7841903	7841964	0.98	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7841903	7841964	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7841965	7842092	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842093	7842158	1	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842093	7842158	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842159	7842309	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842310	7842354	1	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842310	7842354	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842355	7842510	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842511	7842631	0.67	-	1	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842511	7842631	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842632	7842757	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7842758	7842868	0.68	-	1	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7842758	7842868	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	intron	7842869	7843117	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	CDS	7843118	7843518	0.98	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	exon	7843118	7843518	.	-	.	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
Phchi.S4	AUGUSTUS	start_codon	7843516	7843518	.	-	0	transcript_id "Phchi.S4G130400.t2"; gene_id "Phchi.S4G130400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6355.t1 is derived from g3527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22497575	22498024	.	+	.	Phchi.S1G351400
Phchi.S1	AUGUSTUS	transcript	22497575	22498024	.	+	.	transcript_id "Phchi.S1G351400.t1"; gene_id "Phchi.S1G351400"
Phchi.S1	AUGUSTUS	start_codon	22497575	22497577	.	+	0	transcript_id "Phchi.S1G351400.t1"; gene_id "Phchi.S1G351400"
Phchi.S1	AUGUSTUS	CDS	22497575	22498024	0.81	+	0	transcript_id "Phchi.S1G351400.t1"; gene_id "Phchi.S1G351400"
Phchi.S1	AUGUSTUS	exon	22497575	22498024	.	+	.	transcript_id "Phchi.S1G351400.t1"; gene_id "Phchi.S1G351400"
Phchi.S1	AUGUSTUS	stop_codon	22498025	22498027	.	+	0	transcript_id "Phchi.S1G351400.t1"; gene_id "Phchi.S1G351400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12583.t1 is derived from g8260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35971164	35972375	.	-	.	Phchi.S2G066300
Phchi.S2	AUGUSTUS	transcript	35971164	35972375	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	stop_codon	35971161	35971163	.	-	0	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	CDS	35971164	35971229	1	-	0	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	exon	35971164	35971229	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	intron	35971230	35971321	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	CDS	35971322	35971520	0.61	-	1	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	exon	35971322	35971520	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	intron	35971521	35971597	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	CDS	35971598	35971647	0.94	-	0	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	exon	35971598	35971647	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	intron	35971648	35971734	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	CDS	35971735	35971836	1	-	0	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	exon	35971735	35971836	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	intron	35971837	35972027	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	CDS	35972028	35972375	0.37	-	0	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	exon	35972028	35972375	.	-	.	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
Phchi.S2	AUGUSTUS	start_codon	35972373	35972375	.	-	0	transcript_id "Phchi.S2G066300.t1"; gene_id "Phchi.S2G066300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1584.t1 is derived from g8503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1887768	1889101	.	+	.	Phchi.S5G019300
Phchi.S5	AUGUSTUS	transcript	1887768	1889101	.	+	.	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	start_codon	1887768	1887770	.	+	0	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	CDS	1887768	1888057	0.42	+	0	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	exon	1887768	1888057	.	+	.	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	intron	1888058	1888168	.	+	.	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	CDS	1888169	1888700	0.98	+	1	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	exon	1888169	1888700	.	+	.	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	intron	1888701	1888798	.	+	.	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	CDS	1888799	1889101	1	+	0	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	exon	1888799	1889101	.	+	.	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
Phchi.S5	AUGUSTUS	stop_codon	1889102	1889104	.	+	0	transcript_id "Phchi.S5G019300.t1"; gene_id "Phchi.S5G019300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10450.t1 is derived from g14499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	390200	393376	.	+	.	Phchi.S4G003200
Phchi.S4	AUGUSTUS	transcript	390200	393376	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	start_codon	390200	390202	.	+	0	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	390200	390525	0.58	+	0	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	390200	390525	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	390526	390623	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	390624	390721	0.81	+	1	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	390624	390721	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	390722	390884	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	390885	390963	0.58	+	2	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	390885	390963	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	390964	391153	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	391154	391841	0.43	+	1	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	391154	391841	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	391842	392003	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	392004	392061	0.39	+	0	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	392004	392061	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	392062	392172	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	392173	392831	0.59	+	2	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	392173	392831	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	392832	392923	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	392924	392994	0.89	+	0	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	392924	392994	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	intron	392995	393072	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	CDS	393073	393376	0.88	+	1	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	exon	393073	393376	.	+	.	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
Phchi.S4	AUGUSTUS	stop_codon	393377	393379	.	+	0	transcript_id "Phchi.S4G003200.t1"; gene_id "Phchi.S4G003200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1982.t1 is derived from g8902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4219431	4220061	.	+	.	Phchi.S5G059100
Phchi.S5	AUGUSTUS	transcript	4219431	4220061	.	+	.	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	start_codon	4219431	4219433	.	+	0	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	CDS	4219431	4219440	1	+	0	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	exon	4219431	4219440	.	+	.	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	intron	4219441	4219786	.	+	.	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	CDS	4219787	4220061	0.81	+	2	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	exon	4219787	4220061	.	+	.	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
Phchi.S5	AUGUSTUS	stop_codon	4220062	4220064	.	+	0	transcript_id "Phchi.S5G059100.t1"; gene_id "Phchi.S5G059100"
# This transcript jg607.t2 is derived from g10389.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg608.t1 is derived from g10390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4389664	4390533	.	-	.	Phchi.S6G056700
Phchi.S6	AUGUSTUS	transcript	4389664	4390533	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	stop_codon	4389661	4389663	.	-	0	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	CDS	4389664	4389732	0.98	-	0	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	exon	4389664	4389732	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	intron	4389733	4389882	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	CDS	4389883	4389897	1	-	0	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	exon	4389883	4389897	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	intron	4389898	4389996	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	CDS	4389997	4390095	0.85	-	0	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	exon	4389997	4390095	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	intron	4390096	4390176	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	CDS	4390177	4390213	0.87	-	1	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	exon	4390177	4390213	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	intron	4390214	4390414	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	CDS	4390415	4390429	0.9	-	1	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	exon	4390415	4390429	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	intron	4390430	4390528	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	CDS	4390529	4390533	1	-	0	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	exon	4390529	4390533	.	-	.	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
Phchi.S6	AUGUSTUS	start_codon	4390531	4390533	.	-	0	transcript_id "Phchi.S6G056700.t1"; gene_id "Phchi.S6G056700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11861.t1 is derived from g15913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8807153	8808118	.	+	.	Phchi.S4G144300
Phchi.S4	AUGUSTUS	transcript	8807153	8808118	.	+	.	transcript_id "Phchi.S4G144300.t1"; gene_id "Phchi.S4G144300"
Phchi.S4	AUGUSTUS	start_codon	8807153	8807155	.	+	0	transcript_id "Phchi.S4G144300.t1"; gene_id "Phchi.S4G144300"
Phchi.S4	AUGUSTUS	CDS	8807153	8808118	0.86	+	0	transcript_id "Phchi.S4G144300.t1"; gene_id "Phchi.S4G144300"
Phchi.S4	AUGUSTUS	exon	8807153	8808118	.	+	.	transcript_id "Phchi.S4G144300.t1"; gene_id "Phchi.S4G144300"
Phchi.S4	AUGUSTUS	stop_codon	8808119	8808121	.	+	0	transcript_id "Phchi.S4G144300.t1"; gene_id "Phchi.S4G144300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg376.t1 is derived from g10158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2712832	2713808	.	+	.	Phchi.S6G033500
Phchi.S6	AUGUSTUS	transcript	2712832	2713808	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	start_codon	2712832	2712834	.	+	0	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	CDS	2712832	2712912	0.89	+	0	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	exon	2712832	2712912	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	intron	2712913	2713106	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	CDS	2713107	2713159	0.97	+	0	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	exon	2713107	2713159	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	intron	2713160	2713298	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	CDS	2713299	2713337	0.98	+	1	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	exon	2713299	2713337	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	intron	2713338	2713473	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	CDS	2713474	2713577	1	+	1	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	exon	2713474	2713577	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	intron	2713578	2713707	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	CDS	2713708	2713808	0.98	+	2	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	exon	2713708	2713808	.	+	.	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
Phchi.S6	AUGUSTUS	stop_codon	2713809	2713811	.	+	0	transcript_id "Phchi.S6G033500.t1"; gene_id "Phchi.S6G033500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15296.t1 is derived from g13764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18264044	18266291	.	+	.	Phchi.S3G261500
Phchi.S3	AUGUSTUS	transcript	18264044	18266291	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	start_codon	18264044	18264046	.	+	0	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18264044	18264068	0.62	+	0	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18264044	18264068	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18264069	18264165	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18264166	18264197	0.69	+	2	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18264166	18264197	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18264198	18264358	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18264359	18264393	0.85	+	0	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18264359	18264393	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18264394	18264541	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18264542	18264556	0.63	+	1	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18264542	18264556	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18264557	18264711	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18264712	18264864	0.62	+	1	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18264712	18264864	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18264865	18264970	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18264971	18265144	1	+	1	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18264971	18265144	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18265145	18265217	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18265218	18265427	1	+	1	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18265218	18265427	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18265428	18265549	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18265550	18265732	1	+	1	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18265550	18265732	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	intron	18265733	18265813	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	CDS	18265814	18266291	0.97	+	1	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	exon	18265814	18266291	.	+	.	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
Phchi.S3	AUGUSTUS	stop_codon	18266292	18266294	.	+	0	transcript_id "Phchi.S3G261500.t1"; gene_id "Phchi.S3G261500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15630.t1 is derived from g14099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20376756	20377661	.	-	.	Phchi.S3G294900
Phchi.S3	AUGUSTUS	transcript	20376756	20377661	.	-	.	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	stop_codon	20376753	20376755	.	-	0	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	CDS	20376756	20377488	0.77	-	1	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	exon	20376756	20377488	.	-	.	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	intron	20377489	20377653	.	-	.	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	CDS	20377654	20377661	0.99	-	0	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	exon	20377654	20377661	.	-	.	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
Phchi.S3	AUGUSTUS	start_codon	20377659	20377661	.	-	0	transcript_id "Phchi.S3G294900.t1"; gene_id "Phchi.S3G294900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8648.t1 is derived from g5823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37236530	37238724	.	+	.	Phchi.S1G580700
Phchi.S1	AUGUSTUS	transcript	37236530	37238724	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	start_codon	37236530	37236532	.	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37236530	37236913	0.68	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37236530	37236913	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37236914	37237004	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237005	37237178	0.94	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237005	37237178	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237179	37237301	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237302	37237459	0.99	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237302	37237459	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237460	37237553	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237554	37237621	1	+	1	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237554	37237621	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237622	37237789	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237790	37237904	1	+	2	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237790	37237904	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237905	37237976	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237977	37238115	1	+	1	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237977	37238115	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37238116	37238268	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37238269	37238379	1	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37238269	37238379	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37238380	37238456	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37238457	37238525	1	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37238457	37238525	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37238526	37238607	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37238608	37238724	1	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37238608	37238724	.	+	.	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	stop_codon	37238725	37238727	.	+	0	transcript_id "Phchi.S1G580700.t1"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	transcript	37236530	37238724	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	start_codon	37236530	37236532	.	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37236530	37236913	0.72	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37236530	37236913	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37236914	37237004	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237005	37237068	0.86	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237005	37237068	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237069	37237190	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237191	37237207	1	+	2	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237191	37237207	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237208	37237301	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237302	37237459	1	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237302	37237459	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237460	37237553	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237554	37237621	1	+	1	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237554	37237621	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237622	37237789	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237790	37237904	1	+	2	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237790	37237904	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37237905	37237976	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37237977	37238115	1	+	1	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37237977	37238115	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37238116	37238268	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37238269	37238379	1	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37238269	37238379	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37238380	37238456	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37238457	37238525	1	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37238457	37238525	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	intron	37238526	37238607	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	CDS	37238608	37238724	1	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	exon	37238608	37238724	.	+	.	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
Phchi.S1	AUGUSTUS	stop_codon	37238725	37238727	.	+	0	transcript_id "Phchi.S1G580700.t2"; gene_id "Phchi.S1G580700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13201.t1 is derived from g11666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4650823	4651986	.	-	.	Phchi.S3G052000
Phchi.S3	AUGUSTUS	transcript	4650823	4651986	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	stop_codon	4650820	4650822	.	-	0	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4650823	4651097	1	-	2	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4650823	4651097	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651098	4651189	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651190	4651301	1	-	0	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651190	4651301	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651302	4651404	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651405	4651609	0.59	-	1	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651405	4651609	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651610	4651741	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651742	4651986	0.98	-	0	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651742	4651986	.	-	.	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	start_codon	4651984	4651986	.	-	0	transcript_id "Phchi.S3G052000.t1"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	transcript	4650823	4651986	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	stop_codon	4650820	4650822	.	-	0	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4650823	4651097	0.99	-	2	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4650823	4651097	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651098	4651189	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651190	4651301	1	-	0	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651190	4651301	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651302	4651404	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651405	4651535	0.37	-	2	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651405	4651535	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651536	4651633	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651634	4651650	0.37	-	1	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651634	4651650	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	intron	4651651	4651741	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	CDS	4651742	4651986	0.97	-	0	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	exon	4651742	4651986	.	-	.	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
Phchi.S3	AUGUSTUS	start_codon	4651984	4651986	.	-	0	transcript_id "Phchi.S3G052000.t2"; gene_id "Phchi.S3G052000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2417.t1 is derived from g9337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6553400	6554908	.	-	.	Phchi.S5G102600
Phchi.S5	AUGUSTUS	transcript	6553400	6554908	.	-	.	transcript_id "Phchi.S5G102600.t1"; gene_id "Phchi.S5G102600"
Phchi.S5	AUGUSTUS	stop_codon	6553397	6553399	.	-	0	transcript_id "Phchi.S5G102600.t1"; gene_id "Phchi.S5G102600"
Phchi.S5	AUGUSTUS	CDS	6553400	6554908	1	-	0	transcript_id "Phchi.S5G102600.t1"; gene_id "Phchi.S5G102600"
Phchi.S5	AUGUSTUS	exon	6553400	6554908	.	-	.	transcript_id "Phchi.S5G102600.t1"; gene_id "Phchi.S5G102600"
Phchi.S5	AUGUSTUS	start_codon	6554906	6554908	.	-	0	transcript_id "Phchi.S5G102600.t1"; gene_id "Phchi.S5G102600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9148.t1 is derived from g6323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40097588	40098355	.	+	.	Phchi.S1G630700
Phchi.S1	AUGUSTUS	transcript	40097588	40098355	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	start_codon	40097588	40097590	.	+	0	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	CDS	40097588	40097746	1	+	0	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	exon	40097588	40097746	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	intron	40097747	40097860	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	CDS	40097861	40098028	0.58	+	0	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	exon	40097861	40098028	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	intron	40098029	40098123	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	CDS	40098124	40098195	0.54	+	0	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	exon	40098124	40098195	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	intron	40098196	40098343	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	CDS	40098344	40098355	0.66	+	0	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	exon	40098344	40098355	.	+	.	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
Phchi.S1	AUGUSTUS	stop_codon	40098356	40098358	.	+	0	transcript_id "Phchi.S1G630700.t1"; gene_id "Phchi.S1G630700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15853.t1 is derived from g14323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21825427	21828136	.	+	.	Phchi.S3G317200
Phchi.S3	AUGUSTUS	transcript	21825427	21828136	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	start_codon	21825427	21825429	.	+	0	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	CDS	21825427	21825723	0.91	+	0	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	exon	21825427	21825723	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	intron	21825724	21825893	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	CDS	21825894	21826169	0.69	+	0	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	exon	21825894	21826169	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	intron	21826170	21826292	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	CDS	21826293	21826430	0.78	+	0	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	exon	21826293	21826430	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	intron	21826431	21826585	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	CDS	21826586	21828136	0.98	+	0	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	exon	21826586	21828136	.	+	.	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
Phchi.S3	AUGUSTUS	stop_codon	21828137	21828139	.	+	0	transcript_id "Phchi.S3G317200.t1"; gene_id "Phchi.S3G317200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4462.t1 is derived from g1632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10618670	10619555	.	-	.	Phchi.S1G162100
Phchi.S1	AUGUSTUS	transcript	10618670	10619555	.	-	.	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	stop_codon	10618667	10618669	.	-	0	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	CDS	10618670	10618839	0.99	-	2	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	exon	10618670	10618839	.	-	.	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	intron	10618840	10618933	.	-	.	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	CDS	10618934	10619141	1	-	0	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	exon	10618934	10619141	.	-	.	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	intron	10619142	10619267	.	-	.	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	CDS	10619268	10619555	0.87	-	0	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	exon	10619268	10619555	.	-	.	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
Phchi.S1	AUGUSTUS	start_codon	10619553	10619555	.	-	0	transcript_id "Phchi.S1G162100.t1"; gene_id "Phchi.S1G162100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12342.t1 is derived from g8018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11885806	11888060	.	+	.	Phchi.S2G042200
Phchi.S2	AUGUSTUS	transcript	11885806	11888060	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	start_codon	11885806	11885808	.	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11885806	11885886	0.41	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11885806	11885886	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	intron	11885887	11886029	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11886030	11886061	0.96	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11886030	11886061	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	intron	11886062	11886291	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11886292	11886715	0.46	+	1	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11886292	11886715	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	intron	11886716	11886842	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11886843	11886889	0.46	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11886843	11886889	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	intron	11886890	11887080	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11887081	11887210	0.99	+	1	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11887081	11887210	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	intron	11887211	11887342	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11887343	11887939	0.97	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11887343	11887939	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	intron	11887940	11888024	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	CDS	11888025	11888060	1	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	exon	11888025	11888060	.	+	.	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
Phchi.S2	AUGUSTUS	stop_codon	11888061	11888063	.	+	0	transcript_id "Phchi.S2G042200.t1"; gene_id "Phchi.S2G042200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13680.t1 is derived from g12147.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8182800	8184930	.	+	.	Phchi.S3G099900
Phchi.S3	AUGUSTUS	transcript	8182800	8183886	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	start_codon	8182800	8182802	.	+	0	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8182800	8182802	0.99	+	0	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8182800	8182802	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8182803	8182931	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8182932	8182957	1	+	0	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8182932	8182957	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8182958	8183075	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183076	8183144	1	+	1	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183076	8183144	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8183145	8183229	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183230	8183413	1	+	1	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183230	8183413	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8183414	8183519	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183520	8183669	1	+	0	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183520	8183669	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8183670	8183826	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183827	8183886	0.8	+	0	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183827	8183886	.	+	.	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	stop_codon	8183887	8183889	.	+	0	transcript_id "Phchi.S3G099900.t1"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	transcript	8182800	8184930	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	start_codon	8182800	8182802	.	+	0	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8182800	8182802	0.99	+	0	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8182800	8182802	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8182803	8182931	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8182932	8182957	1	+	0	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8182932	8182957	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8182958	8183075	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183076	8183144	1	+	1	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183076	8183144	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8183145	8183229	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183230	8183413	0.99	+	1	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183230	8183413	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8183414	8183519	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8183520	8183669	0.82	+	0	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8183520	8183669	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8183670	8184606	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8184607	8184661	0.94	+	0	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8184607	8184661	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	intron	8184662	8184751	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	CDS	8184752	8184930	0.47	+	2	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	exon	8184752	8184930	.	+	.	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
Phchi.S3	AUGUSTUS	stop_codon	8184931	8184933	.	+	0	transcript_id "Phchi.S3G099900.t2"; gene_id "Phchi.S3G099900"
# This transcript jg12946.t2 is derived from g11411.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12946.t3 is derived from g11411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12947.t1 is derived from g11412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3275095	3276143	.	+	.	Phchi.S3G026600
Phchi.S3	AUGUSTUS	transcript	3275095	3276143	.	+	.	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	start_codon	3275095	3275097	.	+	0	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	CDS	3275095	3275813	0.63	+	0	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	exon	3275095	3275813	.	+	.	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	intron	3275814	3276070	.	+	.	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	CDS	3276071	3276143	0.94	+	1	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	exon	3276071	3276143	.	+	.	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
Phchi.S3	AUGUSTUS	stop_codon	3276144	3276146	.	+	0	transcript_id "Phchi.S3G026600.t1"; gene_id "Phchi.S3G026600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11084.t1 is derived from g15134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4004379	4005576	.	+	.	Phchi.S4G066600
Phchi.S4	AUGUSTUS	transcript	4004379	4005576	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	start_codon	4004379	4004381	.	+	0	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	CDS	4004379	4004543	1	+	0	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	exon	4004379	4004543	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	intron	4004544	4004631	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	CDS	4004632	4004767	1	+	0	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	exon	4004632	4004767	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	intron	4004768	4004988	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	CDS	4004989	4005113	1	+	2	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	exon	4004989	4005113	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	intron	4005114	4005193	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	CDS	4005194	4005340	0.76	+	0	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	exon	4005194	4005340	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	intron	4005341	4005444	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	CDS	4005445	4005576	1	+	0	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	exon	4005445	4005576	.	+	.	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
Phchi.S4	AUGUSTUS	stop_codon	4005577	4005579	.	+	0	transcript_id "Phchi.S4G066600.t1"; gene_id "Phchi.S4G066600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4472.t1 is derived from g1642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10678004	10678974	.	+	.	Phchi.S1G163100
Phchi.S1	AUGUSTUS	transcript	10678004	10678974	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	start_codon	10678004	10678006	.	+	0	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	CDS	10678004	10678102	1	+	0	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	exon	10678004	10678102	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	intron	10678103	10678191	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	CDS	10678192	10678230	0.73	+	0	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	exon	10678192	10678230	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	intron	10678231	10678310	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	CDS	10678311	10678351	0.66	+	0	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	exon	10678311	10678351	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	intron	10678352	10678608	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	CDS	10678609	10678622	0.82	+	1	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	exon	10678609	10678622	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	intron	10678623	10678739	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	CDS	10678740	10678773	0.94	+	2	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	exon	10678740	10678773	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	intron	10678774	10678916	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	CDS	10678917	10678974	0.98	+	1	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	exon	10678917	10678974	.	+	.	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
Phchi.S1	AUGUSTUS	stop_codon	10678975	10678977	.	+	0	transcript_id "Phchi.S1G163100.t1"; gene_id "Phchi.S1G163100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4576.t1 is derived from g1746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11176620	11180793	.	-	.	Phchi.S1G173500
Phchi.S1	AUGUSTUS	transcript	11176620	11180793	.	-	.	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	stop_codon	11176617	11176619	.	-	0	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	CDS	11176620	11180501	1	-	0	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	exon	11176620	11180501	.	-	.	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	intron	11180502	11180610	.	-	.	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	CDS	11180611	11180793	1	-	0	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	exon	11180611	11180793	.	-	.	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
Phchi.S1	AUGUSTUS	start_codon	11180791	11180793	.	-	0	transcript_id "Phchi.S1G173500.t1"; gene_id "Phchi.S1G173500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4249.t1 is derived from g1418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9168895	9169425	.	-	.	Phchi.S1G140800
Phchi.S1	AUGUSTUS	transcript	9168895	9169425	.	-	.	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	stop_codon	9168892	9168894	.	-	0	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	CDS	9168895	9168954	1	-	0	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	exon	9168895	9168954	.	-	.	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	intron	9168955	9169128	.	-	.	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	CDS	9169129	9169425	1	-	0	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	exon	9169129	9169425	.	-	.	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
Phchi.S1	AUGUSTUS	start_codon	9169423	9169425	.	-	0	transcript_id "Phchi.S1G140800.t1"; gene_id "Phchi.S1G140800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5543.t1 is derived from g2713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17472732	17473451	.	-	.	Phchi.S1G270200
Phchi.S1	AUGUSTUS	transcript	17472732	17473451	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	stop_codon	17472729	17472731	.	-	0	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	CDS	17472732	17472803	0.93	-	0	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	exon	17472732	17472803	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	intron	17472804	17472919	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	CDS	17472920	17473001	1	-	1	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	exon	17472920	17473001	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	intron	17473002	17473110	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	CDS	17473111	17473205	1	-	0	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	exon	17473111	17473205	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	intron	17473206	17473295	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	CDS	17473296	17473451	1	-	0	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	exon	17473296	17473451	.	-	.	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
Phchi.S1	AUGUSTUS	start_codon	17473449	17473451	.	-	0	transcript_id "Phchi.S1G270200.t1"; gene_id "Phchi.S1G270200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2526.t1 is derived from g9446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7140989	7142983	.	-	.	Phchi.S5G113500
Phchi.S5	AUGUSTUS	transcript	7140989	7142983	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	stop_codon	7140986	7140988	.	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7140989	7141105	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7140989	7141105	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7141106	7141199	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7141200	7141235	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7141200	7141235	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7141236	7141323	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7141324	7141398	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7141324	7141398	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7141399	7141487	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7141488	7141565	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7141488	7141565	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7141566	7141648	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7141649	7141727	1	-	1	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7141649	7141727	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7141728	7141854	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7141855	7142016	1	-	1	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7141855	7142016	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7142017	7142117	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7142118	7142182	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7142118	7142182	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7142183	7142325	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7142326	7142415	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7142326	7142415	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7142416	7142601	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7142602	7142717	1	-	2	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7142602	7142717	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	intron	7142718	7142856	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	CDS	7142857	7142983	1	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	exon	7142857	7142983	.	-	.	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
Phchi.S5	AUGUSTUS	start_codon	7142981	7142983	.	-	0	transcript_id "Phchi.S5G113500.t1"; gene_id "Phchi.S5G113500"
# This transcript jg8140.t2 is derived from g5315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8140.t3 is derived from g5315.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8141.t1 is derived from g5316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33974828	33976163	.	+	.	Phchi.S1G530000
Phchi.S1	AUGUSTUS	transcript	33974828	33976163	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	start_codon	33974828	33974830	.	+	0	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	CDS	33974828	33975408	1	+	0	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	exon	33974828	33975408	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	intron	33975409	33975541	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	CDS	33975542	33975782	1	+	1	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	exon	33975542	33975782	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	intron	33975783	33975866	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	CDS	33975867	33975984	1	+	0	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	exon	33975867	33975984	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	intron	33975985	33976080	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	CDS	33976081	33976163	0.93	+	2	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	exon	33976081	33976163	.	+	.	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
Phchi.S1	AUGUSTUS	stop_codon	33976164	33976166	.	+	0	transcript_id "Phchi.S1G530000.t1"; gene_id "Phchi.S1G530000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13012.t1 is derived from g11477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3630433	3630846	.	-	.	Phchi.S3G033100
Phchi.S3	AUGUSTUS	transcript	3630433	3630846	.	-	.	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	stop_codon	3630430	3630432	.	-	0	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	CDS	3630433	3630529	0.92	-	1	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	exon	3630433	3630529	.	-	.	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	intron	3630530	3630619	.	-	.	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	CDS	3630620	3630846	1	-	0	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	exon	3630620	3630846	.	-	.	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
Phchi.S3	AUGUSTUS	start_codon	3630844	3630846	.	-	0	transcript_id "Phchi.S3G033100.t1"; gene_id "Phchi.S3G033100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6741.t1 is derived from g3913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24806739	24807956	.	-	.	Phchi.S1G390000
Phchi.S1	AUGUSTUS	transcript	24806739	24807956	.	-	.	transcript_id "Phchi.S1G390000.t1"; gene_id "Phchi.S1G390000"
Phchi.S1	AUGUSTUS	stop_codon	24806736	24806738	.	-	0	transcript_id "Phchi.S1G390000.t1"; gene_id "Phchi.S1G390000"
Phchi.S1	AUGUSTUS	CDS	24806739	24807956	0.91	-	0	transcript_id "Phchi.S1G390000.t1"; gene_id "Phchi.S1G390000"
Phchi.S1	AUGUSTUS	exon	24806739	24807956	.	-	.	transcript_id "Phchi.S1G390000.t1"; gene_id "Phchi.S1G390000"
Phchi.S1	AUGUSTUS	start_codon	24807954	24807956	.	-	0	transcript_id "Phchi.S1G390000.t1"; gene_id "Phchi.S1G390000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14076.t1 is derived from g12543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10671028	10676753	.	+	.	Phchi.S3G139500
Phchi.S3	AUGUSTUS	transcript	10671028	10676753	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	start_codon	10671028	10671030	.	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10671028	10671154	0.98	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10671028	10671154	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10671155	10671736	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10671737	10671785	1	+	2	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10671737	10671785	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10671786	10671962	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10671963	10672167	1	+	1	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10671963	10672167	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10672168	10672264	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10672265	10672466	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10672265	10672466	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10672467	10672614	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10672615	10672645	0.9	+	2	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10672615	10672645	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10672646	10672736	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10672737	10673027	0.52	+	1	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10672737	10673027	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10673028	10673151	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10673152	10673347	1	+	1	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10673152	10673347	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10673348	10673464	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10673465	10673638	0.99	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10673465	10673638	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10673639	10673722	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10673723	10673783	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10673723	10673783	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10673784	10673897	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10673898	10673964	1	+	2	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10673898	10673964	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10673965	10674149	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10674150	10674398	1	+	1	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10674150	10674398	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10674399	10674536	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10674537	10674768	0.99	+	1	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10674537	10674768	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10674769	10674920	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10674921	10675036	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10674921	10675036	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10675037	10675118	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10675119	10675195	1	+	1	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10675119	10675195	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10675196	10675289	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10675290	10675450	1	+	2	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10675290	10675450	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10675451	10675530	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10675531	10675728	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10675531	10675728	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10675729	10675807	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10675808	10675913	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10675808	10675913	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10675914	10676040	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10676041	10676123	1	+	2	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10676041	10676123	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10676124	10676221	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10676222	10676359	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10676222	10676359	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10676360	10676453	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10676454	10676636	1	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10676454	10676636	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	intron	10676637	10676711	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	CDS	10676712	10676753	0.98	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	exon	10676712	10676753	.	+	.	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
Phchi.S3	AUGUSTUS	stop_codon	10676754	10676756	.	+	0	transcript_id "Phchi.S3G139500.t1"; gene_id "Phchi.S3G139500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1459.t1 is derived from g8378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1006594	1007871	.	-	.	Phchi.S5G006800
Phchi.S5	AUGUSTUS	transcript	1006594	1007871	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	stop_codon	1006591	1006593	.	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	CDS	1006594	1006809	1	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	exon	1006594	1006809	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	intron	1006810	1006895	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	CDS	1006896	1007006	1	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	exon	1006896	1007006	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	intron	1007007	1007145	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	CDS	1007146	1007274	1	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	exon	1007146	1007274	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	intron	1007275	1007374	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	CDS	1007375	1007510	1	-	1	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	exon	1007375	1007510	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	intron	1007511	1007628	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	CDS	1007629	1007741	1	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	exon	1007629	1007741	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	intron	1007742	1007826	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	CDS	1007827	1007871	0.58	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	exon	1007827	1007871	.	-	.	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
Phchi.S5	AUGUSTUS	start_codon	1007869	1007871	.	-	0	transcript_id "Phchi.S5G006800.t1"; gene_id "Phchi.S5G006800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3356.t1 is derived from g525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3098923	3100124	.	-	.	Phchi.S1G051500
Phchi.S1	AUGUSTUS	transcript	3098923	3100124	.	-	.	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	stop_codon	3098920	3098922	.	-	0	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	CDS	3098923	3098936	0.84	-	2	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	exon	3098923	3098936	.	-	.	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	intron	3098937	3099138	.	-	.	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	CDS	3099139	3099311	0.48	-	1	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	exon	3099139	3099311	.	-	.	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	intron	3099312	3099402	.	-	.	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	CDS	3099403	3100124	0.24	-	0	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	exon	3099403	3100124	.	-	.	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
Phchi.S1	AUGUSTUS	start_codon	3100122	3100124	.	-	0	transcript_id "Phchi.S1G051500.t1"; gene_id "Phchi.S1G051500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14673.t1 is derived from g13141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14121100	14125372	.	+	.	Phchi.S3G199200
Phchi.S3	AUGUSTUS	transcript	14121100	14125372	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	start_codon	14121100	14121102	.	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14121100	14121882	0.88	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14121100	14121882	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14121883	14122127	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14122128	14122360	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14122128	14122360	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14122361	14122485	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14122486	14122645	1	+	1	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14122486	14122645	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14122646	14122774	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14122775	14123047	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14122775	14123047	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14123048	14123213	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14123214	14123353	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14123214	14123353	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14123354	14123455	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14123456	14123786	1	+	1	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14123456	14123786	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14123787	14123867	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14123868	14124029	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14123868	14124029	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14124030	14124108	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14124109	14124183	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14124109	14124183	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14124184	14124276	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14124277	14124377	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14124277	14124377	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14124378	14124568	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14124569	14124638	1	+	1	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14124569	14124638	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14124639	14124731	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14124732	14124788	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14124732	14124788	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14124789	14124879	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14124880	14124941	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14124880	14124941	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14124942	14125038	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14125039	14125111	1	+	1	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14125039	14125111	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	intron	14125112	14125192	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	CDS	14125193	14125372	1	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	exon	14125193	14125372	.	+	.	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
Phchi.S3	AUGUSTUS	stop_codon	14125373	14125375	.	+	0	transcript_id "Phchi.S3G199200.t1"; gene_id "Phchi.S3G199200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8963.t1 is derived from g6138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38864682	38865759	.	+	.	Phchi.S1G612200
Phchi.S1	AUGUSTUS	transcript	38864682	38865759	.	+	.	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	start_codon	38864682	38864684	.	+	0	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	CDS	38864682	38865150	0.38	+	0	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	exon	38864682	38865150	.	+	.	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	intron	38865151	38865360	.	+	.	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	CDS	38865361	38865425	0.33	+	2	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	exon	38865361	38865425	.	+	.	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	intron	38865426	38865711	.	+	.	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	CDS	38865712	38865759	0.39	+	0	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	exon	38865712	38865759	.	+	.	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
Phchi.S1	AUGUSTUS	stop_codon	38865760	38865762	.	+	0	transcript_id "Phchi.S1G612200.t1"; gene_id "Phchi.S1G612200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11205.t1 is derived from g15255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4699028	4699527	.	-	.	Phchi.S4G078700
Phchi.S4	AUGUSTUS	transcript	4699028	4699527	.	-	.	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	stop_codon	4699025	4699027	.	-	0	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	CDS	4699028	4699260	0.8	-	2	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	exon	4699028	4699260	.	-	.	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	intron	4699261	4699394	.	-	.	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	CDS	4699395	4699527	0.49	-	0	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	exon	4699395	4699527	.	-	.	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
Phchi.S4	AUGUSTUS	start_codon	4699525	4699527	.	-	0	transcript_id "Phchi.S4G078700.t1"; gene_id "Phchi.S4G078700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11565.t1 is derived from g15616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7083288	7084262	.	+	.	Phchi.S4G114700
Phchi.S4	AUGUSTUS	transcript	7083288	7084262	.	+	.	transcript_id "Phchi.S4G114700.t1"; gene_id "Phchi.S4G114700"
Phchi.S4	AUGUSTUS	start_codon	7083288	7083290	.	+	0	transcript_id "Phchi.S4G114700.t1"; gene_id "Phchi.S4G114700"
Phchi.S4	AUGUSTUS	CDS	7083288	7084262	0.95	+	0	transcript_id "Phchi.S4G114700.t1"; gene_id "Phchi.S4G114700"
Phchi.S4	AUGUSTUS	exon	7083288	7084262	.	+	.	transcript_id "Phchi.S4G114700.t1"; gene_id "Phchi.S4G114700"
Phchi.S4	AUGUSTUS	stop_codon	7084263	7084265	.	+	0	transcript_id "Phchi.S4G114700.t1"; gene_id "Phchi.S4G114700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8815.t1 is derived from g5990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38117334	38118253	.	-	.	Phchi.S1G597400
Phchi.S1	AUGUSTUS	transcript	38117334	38118253	.	-	.	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	stop_codon	38117331	38117333	.	-	0	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	CDS	38117334	38117522	1	-	0	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	exon	38117334	38117522	.	-	.	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	intron	38117523	38117616	.	-	.	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	CDS	38117617	38118014	0.76	-	2	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	exon	38117617	38118014	.	-	.	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	intron	38118015	38118090	.	-	.	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	CDS	38118091	38118253	0.38	-	0	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	exon	38118091	38118253	.	-	.	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
Phchi.S1	AUGUSTUS	start_codon	38118251	38118253	.	-	0	transcript_id "Phchi.S1G597400.t1"; gene_id "Phchi.S1G597400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5686.t1 is derived from g2856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18315050	18317153	.	+	.	Phchi.S1G284500
Phchi.S1	AUGUSTUS	transcript	18315050	18317153	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	start_codon	18315050	18315052	.	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18315050	18315355	0.91	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18315050	18315355	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18315356	18315436	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18315437	18315644	1	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18315437	18315644	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18315645	18315730	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18315731	18315873	0.85	+	2	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18315731	18315873	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18315874	18315979	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18315980	18316013	0.92	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18315980	18316013	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18316014	18316146	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18316147	18316222	1	+	2	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18316147	18316222	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18316223	18316303	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18316304	18316481	1	+	1	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18316304	18316481	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18316482	18316611	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18316612	18316737	1	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18316612	18316737	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18316738	18316812	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18316813	18316909	1	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18316813	18316909	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	intron	18316910	18317004	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	CDS	18317005	18317153	1	+	2	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	exon	18317005	18317153	.	+	.	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
Phchi.S1	AUGUSTUS	stop_codon	18317154	18317156	.	+	0	transcript_id "Phchi.S1G284500.t1"; gene_id "Phchi.S1G284500"
# This transcript jg12575.t2 is derived from g8252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12576.t1 is derived from g8253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35800444	35806521	.	-	.	Phchi.S2G065600
Phchi.S2	AUGUSTUS	transcript	35800444	35806521	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	stop_codon	35800441	35800443	.	-	0	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	CDS	35800444	35802565	0.52	-	1	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	exon	35800444	35802565	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	intron	35802566	35802689	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	CDS	35802690	35805133	0.49	-	0	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	exon	35802690	35805133	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	intron	35805134	35805234	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	CDS	35805235	35805249	0.98	-	0	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	exon	35805235	35805249	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	intron	35805250	35805343	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	CDS	35805344	35805712	1	-	0	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	exon	35805344	35805712	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	intron	35805713	35806428	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	CDS	35806429	35806521	0.55	-	0	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	exon	35806429	35806521	.	-	.	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
Phchi.S2	AUGUSTUS	start_codon	35806519	35806521	.	-	0	transcript_id "Phchi.S2G065600.t1"; gene_id "Phchi.S2G065600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg572.t1 is derived from g10354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4152779	4155149	.	+	.	Phchi.S6G053100
Phchi.S6	AUGUSTUS	transcript	4152779	4155149	.	+	.	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	start_codon	4152779	4152781	.	+	0	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	CDS	4152779	4153316	0.7	+	0	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	exon	4152779	4153316	.	+	.	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	intron	4153317	4153416	.	+	.	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	CDS	4153417	4155149	0.9	+	2	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	exon	4153417	4155149	.	+	.	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
Phchi.S6	AUGUSTUS	stop_codon	4155150	4155152	.	+	0	transcript_id "Phchi.S6G053100.t1"; gene_id "Phchi.S6G053100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9072.t1 is derived from g6247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39718261	39721638	.	-	.	Phchi.S1G623100
Phchi.S1	AUGUSTUS	transcript	39718261	39721638	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	stop_codon	39718258	39718260	.	-	0	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	CDS	39718261	39718667	0.98	-	2	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	exon	39718261	39718667	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	intron	39718668	39718871	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	CDS	39718872	39720772	0.7	-	1	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	exon	39718872	39720772	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	intron	39720773	39720896	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	CDS	39720897	39721000	0.23	-	0	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	exon	39720897	39721000	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	intron	39721001	39721088	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	CDS	39721089	39721316	0.34	-	0	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	exon	39721089	39721316	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	intron	39721317	39721404	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	CDS	39721405	39721638	0.83	-	0	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	exon	39721405	39721638	.	-	.	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
Phchi.S1	AUGUSTUS	start_codon	39721636	39721638	.	-	0	transcript_id "Phchi.S1G623100.t1"; gene_id "Phchi.S1G623100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg859.t1 is derived from g10641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5969320	5969967	.	-	.	Phchi.S6G081800
Phchi.S6	AUGUSTUS	transcript	5969320	5969967	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	stop_codon	5969317	5969319	.	-	0	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	CDS	5969320	5969383	0.93	-	1	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	exon	5969320	5969383	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	intron	5969384	5969499	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	CDS	5969500	5969587	0.59	-	2	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	exon	5969500	5969587	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	intron	5969588	5969676	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	CDS	5969677	5969746	1	-	0	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	exon	5969677	5969746	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	intron	5969747	5969829	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	CDS	5969830	5969967	1	-	0	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	exon	5969830	5969967	.	-	.	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
Phchi.S6	AUGUSTUS	start_codon	5969965	5969967	.	-	0	transcript_id "Phchi.S6G081800.t1"; gene_id "Phchi.S6G081800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8887.t1 is derived from g6062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38492350	38494428	.	+	.	Phchi.S1G604600
Phchi.S1	AUGUSTUS	transcript	38492350	38494428	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	start_codon	38492350	38492352	.	+	0	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38492350	38492506	1	+	0	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38492350	38492506	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38492507	38492591	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38492592	38492836	1	+	2	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38492592	38492836	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38492837	38492961	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38492962	38493308	0.97	+	0	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38492962	38493308	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38493309	38493417	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38493418	38493548	0.93	+	1	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38493418	38493548	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38493549	38493678	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38493679	38493744	0.93	+	2	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38493679	38493744	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38493745	38493847	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38493848	38493954	0.94	+	2	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38493848	38493954	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38493955	38494099	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38494100	38494193	0.94	+	0	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38494100	38494193	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	intron	38494194	38494366	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	CDS	38494367	38494428	0.94	+	2	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	exon	38494367	38494428	.	+	.	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
Phchi.S1	AUGUSTUS	stop_codon	38494429	38494431	.	+	0	transcript_id "Phchi.S1G604600.t1"; gene_id "Phchi.S1G604600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6869.t1 is derived from g4041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25696600	25698553	.	+	.	Phchi.S1G402800
Phchi.S1	AUGUSTUS	transcript	25696600	25698553	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	start_codon	25696600	25696602	.	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25696600	25696622	1	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25696600	25696622	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25696623	25696693	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25696694	25696817	1	+	1	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25696694	25696817	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25696818	25696938	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25696939	25697069	0.92	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25696939	25697069	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25697070	25697154	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25697155	25697371	1	+	1	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25697155	25697371	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25697372	25697468	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25697469	25697653	1	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25697469	25697653	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25697654	25697731	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25697732	25697849	0.96	+	1	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25697732	25697849	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25697850	25698019	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25698020	25698055	0.96	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25698020	25698055	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25698056	25698144	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25698145	25698258	0.99	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25698145	25698258	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	intron	25698259	25698376	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	CDS	25698377	25698553	0.71	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	exon	25698377	25698553	.	+	.	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
Phchi.S1	AUGUSTUS	stop_codon	25698554	25698556	.	+	0	transcript_id "Phchi.S1G402800.t1"; gene_id "Phchi.S1G402800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10370.t1 is derived from g7546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47409895	47411060	.	-	.	Phchi.S1G752900
Phchi.S1	AUGUSTUS	transcript	47409895	47411060	.	-	.	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	stop_codon	47409892	47409894	.	-	0	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	CDS	47409895	47410036	0.51	-	1	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	exon	47409895	47410036	.	-	.	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	intron	47410037	47410158	.	-	.	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	CDS	47410159	47411060	0.55	-	0	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	exon	47410159	47411060	.	-	.	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
Phchi.S1	AUGUSTUS	start_codon	47411058	47411060	.	-	0	transcript_id "Phchi.S1G752900.t1"; gene_id "Phchi.S1G752900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2609.t1 is derived from g9529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7781220	7782988	.	-	.	Phchi.S5G121800
Phchi.S5	AUGUSTUS	transcript	7781220	7782988	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	stop_codon	7781217	7781219	.	-	0	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781220	7781225	1	-	0	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781220	7781225	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7781226	7781310	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781311	7781547	1	-	0	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781311	7781547	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7781548	7781803	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781804	7782045	1	-	2	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781804	7782045	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782046	7782283	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782284	7782315	1	-	1	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782284	7782315	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782316	7782514	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782515	7782520	0.83	-	1	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782515	7782520	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782521	7782614	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782615	7782637	0.73	-	0	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782615	7782637	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782638	7782844	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782845	7782988	1	-	0	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782845	7782988	.	-	.	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	start_codon	7782986	7782988	.	-	0	transcript_id "Phchi.S5G121800.t1"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	transcript	7781220	7782988	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	stop_codon	7781217	7781219	.	-	0	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781220	7781225	1	-	0	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781220	7781225	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7781226	7781310	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781311	7781383	1	-	1	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781311	7781383	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7781384	7781803	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781804	7781859	0.95	-	0	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781804	7781859	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7781860	7781971	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7781972	7782045	0.95	-	2	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7781972	7782045	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782046	7782283	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782284	7782315	0.99	-	1	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782284	7782315	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782316	7782514	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782515	7782520	0.86	-	1	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782515	7782520	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782521	7782614	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782615	7782637	0.67	-	0	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782615	7782637	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	intron	7782638	7782844	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	CDS	7782845	7782988	1	-	0	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	exon	7782845	7782988	.	-	.	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
Phchi.S5	AUGUSTUS	start_codon	7782986	7782988	.	-	0	transcript_id "Phchi.S5G121800.t2"; gene_id "Phchi.S5G121800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1122.t1 is derived from g10905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7815824	7816774	.	-	.	Phchi.S6G108100
Phchi.S6	AUGUSTUS	transcript	7815824	7816774	.	-	.	transcript_id "Phchi.S6G108100.t1"; gene_id "Phchi.S6G108100"
Phchi.S6	AUGUSTUS	stop_codon	7815821	7815823	.	-	0	transcript_id "Phchi.S6G108100.t1"; gene_id "Phchi.S6G108100"
Phchi.S6	AUGUSTUS	CDS	7815824	7816774	0.42	-	0	transcript_id "Phchi.S6G108100.t1"; gene_id "Phchi.S6G108100"
Phchi.S6	AUGUSTUS	exon	7815824	7816774	.	-	.	transcript_id "Phchi.S6G108100.t1"; gene_id "Phchi.S6G108100"
Phchi.S6	AUGUSTUS	start_codon	7816772	7816774	.	-	0	transcript_id "Phchi.S6G108100.t1"; gene_id "Phchi.S6G108100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8761.t1 is derived from g5936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37852894	37855195	.	-	.	Phchi.S1G592000
Phchi.S1	AUGUSTUS	transcript	37852894	37855195	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	stop_codon	37852891	37852893	.	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37852894	37853023	1	-	1	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37852894	37853023	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37853024	37853134	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37853135	37853220	1	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37853135	37853220	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37853221	37853322	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37853323	37853510	1	-	2	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37853323	37853510	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37853511	37853608	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37853609	37853816	1	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37853609	37853816	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37853817	37853908	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37853909	37854091	1	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37853909	37854091	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37854092	37854225	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37854226	37854366	1	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37854226	37854366	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37854367	37854457	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37854458	37854574	1	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37854458	37854574	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	intron	37854575	37854691	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	CDS	37854692	37855195	1	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	exon	37854692	37855195	.	-	.	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
Phchi.S1	AUGUSTUS	start_codon	37855193	37855195	.	-	0	transcript_id "Phchi.S1G592000.t1"; gene_id "Phchi.S1G592000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11812.t1 is derived from g15864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8343456	8344745	.	+	.	Phchi.S4G139400
Phchi.S4	AUGUSTUS	transcript	8343456	8344745	.	+	.	transcript_id "Phchi.S4G139400.t1"; gene_id "Phchi.S4G139400"
Phchi.S4	AUGUSTUS	start_codon	8343456	8343458	.	+	0	transcript_id "Phchi.S4G139400.t1"; gene_id "Phchi.S4G139400"
Phchi.S4	AUGUSTUS	CDS	8343456	8344745	0.82	+	0	transcript_id "Phchi.S4G139400.t1"; gene_id "Phchi.S4G139400"
Phchi.S4	AUGUSTUS	exon	8343456	8344745	.	+	.	transcript_id "Phchi.S4G139400.t1"; gene_id "Phchi.S4G139400"
Phchi.S4	AUGUSTUS	stop_codon	8344746	8344748	.	+	0	transcript_id "Phchi.S4G139400.t1"; gene_id "Phchi.S4G139400"
# This transcript jg3279.t2 is derived from g448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3280.t1 is derived from g449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2655561	2656765	.	-	.	Phchi.S1G043900
Phchi.S1	AUGUSTUS	transcript	2655561	2656765	.	-	.	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	stop_codon	2655558	2655560	.	-	0	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	CDS	2655561	2656017	0.79	-	1	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	exon	2655561	2656017	.	-	.	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	intron	2656018	2656130	.	-	.	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	CDS	2656131	2656765	0.86	-	0	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	exon	2656131	2656765	.	-	.	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
Phchi.S1	AUGUSTUS	start_codon	2656763	2656765	.	-	0	transcript_id "Phchi.S1G043900.t1"; gene_id "Phchi.S1G043900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12869.t1 is derived from g11334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2832415	2835832	.	+	.	Phchi.S3G018800
Phchi.S3	AUGUSTUS	transcript	2832415	2835832	.	+	.	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	start_codon	2832415	2832417	.	+	0	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	CDS	2832415	2832965	0.48	+	0	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	exon	2832415	2832965	.	+	.	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	intron	2832966	2833087	.	+	.	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	CDS	2833088	2834066	0.71	+	1	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	exon	2833088	2834066	.	+	.	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	intron	2834067	2834176	.	+	.	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	CDS	2834177	2835832	1	+	0	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	exon	2834177	2835832	.	+	.	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
Phchi.S3	AUGUSTUS	stop_codon	2835833	2835835	.	+	0	transcript_id "Phchi.S3G018800.t1"; gene_id "Phchi.S3G018800"
# This transcript jg4112.t2 is derived from g1281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4112.t3 is derived from g1281.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4113.t1 is derived from g1282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7942964	7943422	.	+	.	Phchi.S1G127200
Phchi.S1	AUGUSTUS	transcript	7942964	7943422	.	+	.	transcript_id "Phchi.S1G127200.t1"; gene_id "Phchi.S1G127200"
Phchi.S1	AUGUSTUS	start_codon	7942964	7942966	.	+	0	transcript_id "Phchi.S1G127200.t1"; gene_id "Phchi.S1G127200"
Phchi.S1	AUGUSTUS	CDS	7942964	7943422	1	+	0	transcript_id "Phchi.S1G127200.t1"; gene_id "Phchi.S1G127200"
Phchi.S1	AUGUSTUS	exon	7942964	7943422	.	+	.	transcript_id "Phchi.S1G127200.t1"; gene_id "Phchi.S1G127200"
Phchi.S1	AUGUSTUS	stop_codon	7943423	7943425	.	+	0	transcript_id "Phchi.S1G127200.t1"; gene_id "Phchi.S1G127200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13807.t1 is derived from g12274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9012175	9013158	.	+	.	Phchi.S3G112600
Phchi.S3	AUGUSTUS	transcript	9012175	9013158	.	+	.	transcript_id "Phchi.S3G112600.t1"; gene_id "Phchi.S3G112600"
Phchi.S3	AUGUSTUS	start_codon	9012175	9012177	.	+	0	transcript_id "Phchi.S3G112600.t1"; gene_id "Phchi.S3G112600"
Phchi.S3	AUGUSTUS	CDS	9012175	9013158	0.85	+	0	transcript_id "Phchi.S3G112600.t1"; gene_id "Phchi.S3G112600"
Phchi.S3	AUGUSTUS	exon	9012175	9013158	.	+	.	transcript_id "Phchi.S3G112600.t1"; gene_id "Phchi.S3G112600"
Phchi.S3	AUGUSTUS	stop_codon	9013159	9013161	.	+	0	transcript_id "Phchi.S3G112600.t1"; gene_id "Phchi.S3G112600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8645.t1 is derived from g5820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37221997	37222986	.	-	.	Phchi.S1G580400
Phchi.S1	AUGUSTUS	transcript	37221997	37222986	.	-	.	transcript_id "Phchi.S1G580400.t1"; gene_id "Phchi.S1G580400"
Phchi.S1	AUGUSTUS	stop_codon	37221994	37221996	.	-	0	transcript_id "Phchi.S1G580400.t1"; gene_id "Phchi.S1G580400"
Phchi.S1	AUGUSTUS	CDS	37221997	37222986	0.72	-	0	transcript_id "Phchi.S1G580400.t1"; gene_id "Phchi.S1G580400"
Phchi.S1	AUGUSTUS	exon	37221997	37222986	.	-	.	transcript_id "Phchi.S1G580400.t1"; gene_id "Phchi.S1G580400"
Phchi.S1	AUGUSTUS	start_codon	37222984	37222986	.	-	0	transcript_id "Phchi.S1G580400.t1"; gene_id "Phchi.S1G580400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5389.t1 is derived from g2559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16642288	16645242	.	+	.	Phchi.S1G254800
Phchi.S1	AUGUSTUS	transcript	16642288	16645242	.	+	.	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	start_codon	16642288	16642290	.	+	0	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	CDS	16642288	16642875	0.21	+	0	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	exon	16642288	16642875	.	+	.	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	intron	16642876	16643062	.	+	.	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	CDS	16643063	16643953	0.18	+	0	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	exon	16643063	16643953	.	+	.	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	intron	16643954	16644108	.	+	.	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	CDS	16644109	16645242	0.65	+	0	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	exon	16644109	16645242	.	+	.	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
Phchi.S1	AUGUSTUS	stop_codon	16645243	16645245	.	+	0	transcript_id "Phchi.S1G254800.t1"; gene_id "Phchi.S1G254800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1000.t1 is derived from g10783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6979671	6980074	.	+	.	Phchi.S6G095900
Phchi.S6	AUGUSTUS	transcript	6979671	6980074	.	+	.	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	start_codon	6979671	6979673	.	+	0	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	CDS	6979671	6979969	0.59	+	0	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	exon	6979671	6979969	.	+	.	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	intron	6979970	6980052	.	+	.	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	CDS	6980053	6980074	0.95	+	1	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	exon	6980053	6980074	.	+	.	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
Phchi.S6	AUGUSTUS	stop_codon	6980075	6980077	.	+	0	transcript_id "Phchi.S6G095900.t1"; gene_id "Phchi.S6G095900"
# This transcript jg4973.t2 is derived from g2143.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4974.t1 is derived from g2144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13832765	13833942	.	-	.	Phchi.S1G213300
Phchi.S1	AUGUSTUS	transcript	13832765	13833942	.	-	.	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	stop_codon	13832762	13832764	.	-	0	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	CDS	13832765	13833128	1	-	1	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	exon	13832765	13833128	.	-	.	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	intron	13833129	13833244	.	-	.	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	CDS	13833245	13833942	0.56	-	0	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	exon	13833245	13833942	.	-	.	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
Phchi.S1	AUGUSTUS	start_codon	13833940	13833942	.	-	0	transcript_id "Phchi.S1G213300.t1"; gene_id "Phchi.S1G213300"
# This transcript jg15106.t2 is derived from g13574.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15107.t1 is derived from g13575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17107638	17109941	.	-	.	Phchi.S3G242600
Phchi.S3	AUGUSTUS	transcript	17107638	17109941	.	-	.	transcript_id "Phchi.S3G242600.t1"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	stop_codon	17107635	17107637	.	-	0	transcript_id "Phchi.S3G242600.t1"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	CDS	17107638	17109941	0.99	-	0	transcript_id "Phchi.S3G242600.t1"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	exon	17107638	17109941	.	-	.	transcript_id "Phchi.S3G242600.t1"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	start_codon	17109939	17109941	.	-	0	transcript_id "Phchi.S3G242600.t1"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	transcript	17107638	17109881	.	-	.	transcript_id "Phchi.S3G242600.t2"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	stop_codon	17107635	17107637	.	-	0	transcript_id "Phchi.S3G242600.t2"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	CDS	17107638	17109881	0.58	-	0	transcript_id "Phchi.S3G242600.t2"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	exon	17107638	17109881	.	-	.	transcript_id "Phchi.S3G242600.t2"; gene_id "Phchi.S3G242600"
Phchi.S3	AUGUSTUS	start_codon	17109879	17109881	.	-	0	transcript_id "Phchi.S3G242600.t2"; gene_id "Phchi.S3G242600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10424.t1 is derived from g14473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	160219	160598	.	-	.	Phchi.S4G000600
Phchi.S4	AUGUSTUS	transcript	160219	160598	.	-	.	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	stop_codon	160216	160218	.	-	0	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	CDS	160219	160249	0.41	-	1	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	exon	160219	160249	.	-	.	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	intron	160250	160344	.	-	.	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	CDS	160345	160598	0.26	-	0	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	exon	160345	160598	.	-	.	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
Phchi.S4	AUGUSTUS	start_codon	160596	160598	.	-	0	transcript_id "Phchi.S4G000600.t1"; gene_id "Phchi.S4G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4691.t1 is derived from g1861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12168775	12169905	.	-	.	Phchi.S1G185000
Phchi.S1	AUGUSTUS	transcript	12168775	12169905	.	-	.	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	stop_codon	12168772	12168774	.	-	0	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	CDS	12168775	12169675	0.44	-	1	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	exon	12168775	12169675	.	-	.	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	intron	12169676	12169786	.	-	.	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	CDS	12169787	12169905	0.4	-	0	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	exon	12169787	12169905	.	-	.	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
Phchi.S1	AUGUSTUS	start_codon	12169903	12169905	.	-	0	transcript_id "Phchi.S1G185000.t1"; gene_id "Phchi.S1G185000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3604.t1 is derived from g773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4698389	4703758	.	+	.	Phchi.S1G076300
Phchi.S1	AUGUSTUS	transcript	4698389	4702071	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	start_codon	4698389	4698391	.	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4698389	4699274	0.49	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4698389	4699274	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4699275	4699370	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4699371	4699628	0.95	+	2	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4699371	4699628	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4699629	4699748	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4699749	4699930	0.84	+	2	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4699749	4699930	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4699931	4700018	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700019	4700348	1	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700019	4700348	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4700349	4700521	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700522	4700693	1	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700522	4700693	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4700694	4700819	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700820	4700902	1	+	2	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700820	4700902	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4700903	4700983	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700984	4701241	1	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700984	4701241	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4701242	4701419	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4701420	4701711	0.24	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4701420	4701711	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4701712	4701826	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4701827	4701900	0.71	+	2	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4701827	4701900	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4701901	4702065	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4702066	4702071	0.91	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4702066	4702071	.	+	.	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	stop_codon	4702072	4702074	.	+	0	transcript_id "Phchi.S1G076300.t1"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	transcript	4698389	4703758	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	start_codon	4698389	4698391	.	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4698389	4699274	0.54	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4698389	4699274	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4699275	4699370	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4699371	4699628	0.94	+	2	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4699371	4699628	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4699629	4699748	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4699749	4699930	0.86	+	2	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4699749	4699930	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4699931	4700018	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700019	4700348	1	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700019	4700348	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4700349	4700521	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700522	4700693	1	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700522	4700693	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4700694	4700819	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700820	4700902	1	+	2	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700820	4700902	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4700903	4700983	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4700984	4701241	1	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4700984	4701241	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4701242	4701419	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4701420	4701711	0.28	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4701420	4701711	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4701712	4701826	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4701827	4701900	0.68	+	2	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4701827	4701900	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4701901	4702349	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4702350	4702637	0.75	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4702350	4702637	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	intron	4702638	4702717	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	CDS	4702718	4703758	0.51	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	exon	4702718	4703758	.	+	.	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
Phchi.S1	AUGUSTUS	stop_codon	4703759	4703761	.	+	0	transcript_id "Phchi.S1G076300.t2"; gene_id "Phchi.S1G076300"
# This transcript jg3309.t2 is derived from g478.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3310.t1 is derived from g479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2778190	2779473	.	-	.	Phchi.S1G046900
Phchi.S1	AUGUSTUS	transcript	2778190	2779473	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	stop_codon	2778187	2778189	.	-	0	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	CDS	2778190	2778292	1	-	1	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	exon	2778190	2778292	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	intron	2778293	2778546	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	CDS	2778547	2778597	0.65	-	1	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	exon	2778547	2778597	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	intron	2778598	2778795	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	CDS	2778796	2778864	0.79	-	1	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	exon	2778796	2778864	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	intron	2778865	2778960	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	CDS	2778961	2778999	0.95	-	1	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	exon	2778961	2778999	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	intron	2779000	2779082	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	CDS	2779083	2779167	0.99	-	2	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	exon	2779083	2779167	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	intron	2779168	2779397	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	CDS	2779398	2779473	1	-	0	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	exon	2779398	2779473	.	-	.	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
Phchi.S1	AUGUSTUS	start_codon	2779471	2779473	.	-	0	transcript_id "Phchi.S1G046900.t1"; gene_id "Phchi.S1G046900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3386.t1 is derived from g555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3293097	3293390	.	-	.	Phchi.S1G054500
Phchi.S1	AUGUSTUS	transcript	3293097	3293390	.	-	.	transcript_id "Phchi.S1G054500.t1"; gene_id "Phchi.S1G054500"
Phchi.S1	AUGUSTUS	stop_codon	3293094	3293096	.	-	0	transcript_id "Phchi.S1G054500.t1"; gene_id "Phchi.S1G054500"
Phchi.S1	AUGUSTUS	CDS	3293097	3293390	0.78	-	0	transcript_id "Phchi.S1G054500.t1"; gene_id "Phchi.S1G054500"
Phchi.S1	AUGUSTUS	exon	3293097	3293390	.	-	.	transcript_id "Phchi.S1G054500.t1"; gene_id "Phchi.S1G054500"
Phchi.S1	AUGUSTUS	start_codon	3293388	3293390	.	-	0	transcript_id "Phchi.S1G054500.t1"; gene_id "Phchi.S1G054500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9244.t1 is derived from g6419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40569240	40571031	.	-	.	Phchi.S1G640300
Phchi.S1	AUGUSTUS	transcript	40569240	40571031	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	stop_codon	40569237	40569239	.	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40569240	40569311	1	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40569240	40569311	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	intron	40569312	40569395	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40569396	40569533	0.97	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40569396	40569533	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	intron	40569534	40569642	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40569643	40569790	0.95	-	1	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40569643	40569790	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	intron	40569791	40569893	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40569894	40570006	1	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40569894	40570006	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	intron	40570007	40570158	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40570159	40570406	1	-	2	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40570159	40570406	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	intron	40570407	40570488	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40570489	40570798	1	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40570489	40570798	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	intron	40570799	40570878	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	CDS	40570879	40571031	1	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	exon	40570879	40571031	.	-	.	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
Phchi.S1	AUGUSTUS	start_codon	40571029	40571031	.	-	0	transcript_id "Phchi.S1G640300.t1"; gene_id "Phchi.S1G640300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4387.t1 is derived from g1556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10180345	10183670	.	+	.	Phchi.S1G154600
Phchi.S1	AUGUSTUS	transcript	10180345	10183670	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	start_codon	10180345	10180347	.	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10180345	10180495	0.99	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10180345	10180495	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10180496	10180566	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10180567	10180666	1	+	2	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10180567	10180666	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10180667	10180753	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10180754	10180860	1	+	1	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10180754	10180860	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10180861	10181040	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10181041	10181183	1	+	2	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10181041	10181183	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10181184	10181348	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10181349	10181811	1	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10181349	10181811	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10181812	10181901	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10181902	10182071	1	+	2	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10181902	10182071	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10182072	10182186	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10182187	10182363	1	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10182187	10182363	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10182364	10182446	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10182447	10182503	1	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10182447	10182503	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10182504	10182586	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10182587	10182697	1	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10182587	10182697	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10182698	10182800	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10182801	10182902	1	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10182801	10182902	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10182903	10183009	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10183010	10183180	1	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10183010	10183180	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	intron	10183181	10183274	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	CDS	10183275	10183670	0.97	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	exon	10183275	10183670	.	+	.	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
Phchi.S1	AUGUSTUS	stop_codon	10183671	10183673	.	+	0	transcript_id "Phchi.S1G154600.t1"; gene_id "Phchi.S1G154600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5002.t1 is derived from g2172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13960498	13962328	.	+	.	Phchi.S1G216100
Phchi.S1	AUGUSTUS	transcript	13960498	13962328	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	start_codon	13960498	13960500	.	+	0	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	CDS	13960498	13960707	0.57	+	0	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	exon	13960498	13960707	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	intron	13960708	13960846	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	CDS	13960847	13961989	0.85	+	0	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	exon	13960847	13961989	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	intron	13961990	13962089	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	CDS	13962090	13962165	0.94	+	0	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	exon	13962090	13962165	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	intron	13962166	13962263	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	CDS	13962264	13962328	0.97	+	2	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	exon	13962264	13962328	.	+	.	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
Phchi.S1	AUGUSTUS	stop_codon	13962329	13962331	.	+	0	transcript_id "Phchi.S1G216100.t1"; gene_id "Phchi.S1G216100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5344.t1 is derived from g2514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16392279	16395096	.	+	.	Phchi.S1G250300
Phchi.S1	AUGUSTUS	transcript	16392279	16395096	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	start_codon	16392279	16392281	.	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16392279	16392744	0.96	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16392279	16392744	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16392745	16392838	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16392839	16392906	1	+	2	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16392839	16392906	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16392907	16392990	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16392991	16393088	0.91	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16392991	16393088	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393089	16393203	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16393204	16393251	0.99	+	1	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16393204	16393251	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393252	16393349	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16393350	16393422	1	+	1	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16393350	16393422	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393423	16393522	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16393523	16393567	1	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16393523	16393567	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393568	16393638	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16393639	16393707	1	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16393639	16393707	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393708	16393792	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16393793	16393825	1	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16393793	16393825	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393826	16393931	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16393932	16393972	1	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16393932	16393972	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16393973	16394089	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16394090	16394167	1	+	1	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16394090	16394167	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16394168	16394261	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16394262	16394366	1	+	1	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16394262	16394366	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16394367	16394452	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16394453	16394560	0.99	+	1	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16394453	16394560	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16394561	16394674	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16394675	16394729	0.99	+	1	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16394675	16394729	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16394730	16394815	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16394816	16394902	1	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16394816	16394902	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	intron	16394903	16394979	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	CDS	16394980	16395096	0.99	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	exon	16394980	16395096	.	+	.	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
Phchi.S1	AUGUSTUS	stop_codon	16395097	16395099	.	+	0	transcript_id "Phchi.S1G250300.t1"; gene_id "Phchi.S1G250300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5548.t1 is derived from g2718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17484514	17486547	.	+	.	Phchi.S1G270700
Phchi.S1	AUGUSTUS	transcript	17484514	17486547	.	+	.	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	start_codon	17484514	17484516	.	+	0	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	CDS	17484514	17485478	0.77	+	0	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	exon	17484514	17485478	.	+	.	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	intron	17485479	17485632	.	+	.	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	CDS	17485633	17486010	0.35	+	1	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	exon	17485633	17486010	.	+	.	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	intron	17486011	17486168	.	+	.	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	CDS	17486169	17486547	0.35	+	1	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	exon	17486169	17486547	.	+	.	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
Phchi.S1	AUGUSTUS	stop_codon	17486548	17486550	.	+	0	transcript_id "Phchi.S1G270700.t1"; gene_id "Phchi.S1G270700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5729.t1 is derived from g2899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18587040	18588782	.	+	.	Phchi.S1G288800
Phchi.S1	AUGUSTUS	transcript	18587040	18588782	.	+	.	transcript_id "Phchi.S1G288800.t1"; gene_id "Phchi.S1G288800"
Phchi.S1	AUGUSTUS	start_codon	18587040	18587042	.	+	0	transcript_id "Phchi.S1G288800.t1"; gene_id "Phchi.S1G288800"
Phchi.S1	AUGUSTUS	CDS	18587040	18588782	0.74	+	0	transcript_id "Phchi.S1G288800.t1"; gene_id "Phchi.S1G288800"
Phchi.S1	AUGUSTUS	exon	18587040	18588782	.	+	.	transcript_id "Phchi.S1G288800.t1"; gene_id "Phchi.S1G288800"
Phchi.S1	AUGUSTUS	stop_codon	18588783	18588785	.	+	0	transcript_id "Phchi.S1G288800.t1"; gene_id "Phchi.S1G288800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5221.t1 is derived from g2391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15554990	15556663	.	+	.	Phchi.S1G238000
Phchi.S1	AUGUSTUS	transcript	15554990	15556663	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	start_codon	15554990	15554992	.	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15554990	15555070	0.47	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15554990	15555070	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15555071	15555166	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15555167	15555202	0.47	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15555167	15555202	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15555203	15555347	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15555348	15555461	0.53	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15555348	15555461	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15555462	15555558	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15555559	15555698	0.98	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15555559	15555698	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15555699	15555799	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15555800	15555814	0.55	+	1	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15555800	15555814	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15555815	15555960	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15555961	15556081	0.6	+	1	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15555961	15556081	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15556082	15556161	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15556162	15556304	1	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15556162	15556304	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	intron	15556305	15556386	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	CDS	15556387	15556663	1	+	1	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	exon	15556387	15556663	.	+	.	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
Phchi.S1	AUGUSTUS	stop_codon	15556664	15556666	.	+	0	transcript_id "Phchi.S1G238000.t1"; gene_id "Phchi.S1G238000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9014.t1 is derived from g6189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39147242	39150020	.	-	.	Phchi.S1G617300
Phchi.S1	AUGUSTUS	transcript	39147242	39150020	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	stop_codon	39147239	39147241	.	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39147242	39148374	0.49	-	2	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39147242	39148374	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	intron	39148375	39148457	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39148458	39148530	0.52	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39148458	39148530	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	intron	39148531	39148692	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39148693	39148887	1	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39148693	39148887	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	intron	39148888	39149021	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39149022	39149108	1	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39149022	39149108	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	intron	39149109	39149265	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39149266	39149355	0.8	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39149266	39149355	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	intron	39149356	39149456	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39149457	39149543	0.8	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39149457	39149543	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	intron	39149544	39149972	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	CDS	39149973	39150020	0.75	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	exon	39149973	39150020	.	-	.	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
Phchi.S1	AUGUSTUS	start_codon	39150018	39150020	.	-	0	transcript_id "Phchi.S1G617300.t1"; gene_id "Phchi.S1G617300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15209.t1 is derived from g13677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17663575	17665318	.	-	.	Phchi.S3G252800
Phchi.S3	AUGUSTUS	transcript	17663575	17665318	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	stop_codon	17663572	17663574	.	-	0	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	CDS	17663575	17663821	1	-	1	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	exon	17663575	17663821	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	intron	17663822	17663903	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	CDS	17663904	17664121	1	-	0	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	exon	17663904	17664121	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	intron	17664122	17664206	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	CDS	17664207	17664698	0.99	-	0	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	exon	17664207	17664698	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	intron	17664699	17664820	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	CDS	17664821	17665318	0.96	-	0	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	exon	17664821	17665318	.	-	.	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
Phchi.S3	AUGUSTUS	start_codon	17665316	17665318	.	-	0	transcript_id "Phchi.S3G252800.t1"; gene_id "Phchi.S3G252800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2210.t1 is derived from g9130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5431633	5432942	.	+	.	Phchi.S5G081900
Phchi.S5	AUGUSTUS	transcript	5431633	5432942	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	start_codon	5431633	5431635	.	+	0	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	CDS	5431633	5431858	0.81	+	0	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	exon	5431633	5431858	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	intron	5431859	5431928	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	CDS	5431929	5432345	1	+	2	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	exon	5431929	5432345	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	intron	5432346	5432423	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	CDS	5432424	5432675	1	+	2	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	exon	5432424	5432675	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	intron	5432676	5432751	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	CDS	5432752	5432820	1	+	2	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	exon	5432752	5432820	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	intron	5432821	5432895	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	CDS	5432896	5432942	1	+	2	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	exon	5432896	5432942	.	+	.	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
Phchi.S5	AUGUSTUS	stop_codon	5432943	5432945	.	+	0	transcript_id "Phchi.S5G081900.t1"; gene_id "Phchi.S5G081900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8675.t1 is derived from g5850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37375851	37379527	.	+	.	Phchi.S1G583400
Phchi.S1	AUGUSTUS	transcript	37375851	37379527	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	start_codon	37375851	37375853	.	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37375851	37375882	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37375851	37375882	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37375883	37375980	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37375981	37376036	0.94	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37375981	37376036	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37376037	37376155	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37376156	37376170	1	+	2	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37376156	37376170	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37376171	37376327	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37376328	37376488	1	+	2	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37376328	37376488	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37376489	37376578	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37376579	37376709	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37376579	37376709	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37376710	37376804	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37376805	37377078	0.99	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37376805	37377078	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37377079	37377170	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37377171	37377245	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37377171	37377245	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37377246	37377370	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37377371	37377447	0.99	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37377371	37377447	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37377448	37377562	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37377563	37377665	1	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37377563	37377665	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37377666	37377757	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37377758	37377864	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37377758	37377864	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37377865	37378060	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37378061	37378130	1	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37378061	37378130	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37378131	37378269	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37378270	37378388	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37378270	37378388	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37378389	37378545	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37378546	37378647	1	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37378546	37378647	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37378648	37378745	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37378746	37378755	1	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37378746	37378755	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37378756	37378805	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37378806	37378823	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37378806	37378823	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37378824	37378917	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37378918	37379042	1	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37378918	37379042	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37379043	37379158	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37379159	37379332	0.98	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37379159	37379332	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	intron	37379333	37379424	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	CDS	37379425	37379527	0.46	+	1	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	exon	37379425	37379527	.	+	.	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
Phchi.S1	AUGUSTUS	stop_codon	37379528	37379530	.	+	0	transcript_id "Phchi.S1G583400.t1"; gene_id "Phchi.S1G583400"
# This transcript jg10592.t2 is derived from g14642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10593.t1 is derived from g14643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1097857	1100290	.	-	.	Phchi.S4G017500
Phchi.S4	AUGUSTUS	transcript	1097857	1100290	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	stop_codon	1097854	1097856	.	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1097857	1097961	0.81	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1097857	1097961	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1097962	1098078	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1098079	1098116	0.91	-	2	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1098079	1098116	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1098117	1098366	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1098367	1098557	0.99	-	1	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1098367	1098557	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1098558	1098666	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1098667	1098758	1	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1098667	1098758	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1098759	1098861	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1098862	1098889	1	-	1	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1098862	1098889	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1098890	1099027	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1099028	1099067	1	-	2	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1099028	1099067	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1099068	1099165	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1099166	1099227	1	-	1	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1099166	1099227	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1099228	1099366	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1099367	1099430	1	-	2	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1099367	1099430	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1099431	1099537	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1099538	1099576	0.99	-	2	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1099538	1099576	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1099577	1099738	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1099739	1099793	1	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1099739	1099793	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1099794	1099995	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1099996	1100019	0.67	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1099996	1100019	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1100020	1100118	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1100119	1100128	0.15	-	1	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1100119	1100128	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	intron	1100129	1100282	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	CDS	1100283	1100290	0.15	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	exon	1100283	1100290	.	-	.	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
Phchi.S4	AUGUSTUS	start_codon	1100288	1100290	.	-	0	transcript_id "Phchi.S4G017500.t1"; gene_id "Phchi.S4G017500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9043.t1 is derived from g6218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39272772	39274783	.	+	.	Phchi.S1G620200
Phchi.S1	AUGUSTUS	transcript	39272772	39274783	.	+	.	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	start_codon	39272772	39272774	.	+	0	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	CDS	39272772	39272900	0.55	+	0	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	exon	39272772	39272900	.	+	.	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	intron	39272901	39273013	.	+	.	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	CDS	39273014	39274783	0.85	+	0	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	exon	39273014	39274783	.	+	.	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
Phchi.S1	AUGUSTUS	stop_codon	39274784	39274786	.	+	0	transcript_id "Phchi.S1G620200.t1"; gene_id "Phchi.S1G620200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg771.t1 is derived from g10553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5444571	5445980	.	+	.	Phchi.S6G073000
Phchi.S6	AUGUSTUS	transcript	5444571	5445980	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	start_codon	5444571	5444573	.	+	0	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	CDS	5444571	5444803	0.45	+	0	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	exon	5444571	5444803	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	intron	5444804	5444882	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	CDS	5444883	5444900	0.83	+	1	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	exon	5444883	5444900	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	intron	5444901	5444994	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	CDS	5444995	5445194	0.83	+	1	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	exon	5444995	5445194	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	intron	5445195	5445390	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	CDS	5445391	5445458	0.8	+	2	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	exon	5445391	5445458	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	intron	5445459	5445550	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	CDS	5445551	5445784	0.91	+	0	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	exon	5445551	5445784	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	intron	5445785	5445860	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	CDS	5445861	5445980	1	+	0	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	exon	5445861	5445980	.	+	.	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
Phchi.S6	AUGUSTUS	stop_codon	5445981	5445983	.	+	0	transcript_id "Phchi.S6G073000.t1"; gene_id "Phchi.S6G073000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13866.t1 is derived from g12333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9306975	9309230	.	+	.	Phchi.S3G118500
Phchi.S3	AUGUSTUS	transcript	9306975	9309230	.	+	.	transcript_id "Phchi.S3G118500.t1"; gene_id "Phchi.S3G118500"
Phchi.S3	AUGUSTUS	start_codon	9306975	9306977	.	+	0	transcript_id "Phchi.S3G118500.t1"; gene_id "Phchi.S3G118500"
Phchi.S3	AUGUSTUS	CDS	9306975	9309230	0.99	+	0	transcript_id "Phchi.S3G118500.t1"; gene_id "Phchi.S3G118500"
Phchi.S3	AUGUSTUS	exon	9306975	9309230	.	+	.	transcript_id "Phchi.S3G118500.t1"; gene_id "Phchi.S3G118500"
Phchi.S3	AUGUSTUS	stop_codon	9309231	9309233	.	+	0	transcript_id "Phchi.S3G118500.t1"; gene_id "Phchi.S3G118500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11560.t1 is derived from g15611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7057373	7058627	.	+	.	Phchi.S4G114200
Phchi.S4	AUGUSTUS	transcript	7057373	7058627	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	start_codon	7057373	7057375	.	+	0	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	CDS	7057373	7057396	0.96	+	0	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	exon	7057373	7057396	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	intron	7057397	7057490	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	CDS	7057491	7057703	1	+	0	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	exon	7057491	7057703	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	intron	7057704	7057786	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	CDS	7057787	7058071	1	+	0	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	exon	7057787	7058071	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	intron	7058072	7058151	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	CDS	7058152	7058387	1	+	0	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	exon	7058152	7058387	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	intron	7058388	7058476	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	CDS	7058477	7058627	1	+	1	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	exon	7058477	7058627	.	+	.	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
Phchi.S4	AUGUSTUS	stop_codon	7058628	7058630	.	+	0	transcript_id "Phchi.S4G114200.t1"; gene_id "Phchi.S4G114200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7606.t1 is derived from g4780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30225122	30226711	.	+	.	Phchi.S1G476500
Phchi.S1	AUGUSTUS	transcript	30225122	30226711	.	+	.	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	start_codon	30225122	30225124	.	+	0	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	CDS	30225122	30226318	1	+	0	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	exon	30225122	30226318	.	+	.	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	intron	30226319	30226402	.	+	.	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	CDS	30226403	30226711	0.97	+	0	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	exon	30226403	30226711	.	+	.	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
Phchi.S1	AUGUSTUS	stop_codon	30226712	30226714	.	+	0	transcript_id "Phchi.S1G476500.t1"; gene_id "Phchi.S1G476500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5867.t1 is derived from g3037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19481236	19482558	.	+	.	Phchi.S1G302600
Phchi.S1	AUGUSTUS	transcript	19481236	19482558	.	+	.	transcript_id "Phchi.S1G302600.t1"; gene_id "Phchi.S1G302600"
Phchi.S1	AUGUSTUS	start_codon	19481236	19481238	.	+	0	transcript_id "Phchi.S1G302600.t1"; gene_id "Phchi.S1G302600"
Phchi.S1	AUGUSTUS	CDS	19481236	19482558	0.88	+	0	transcript_id "Phchi.S1G302600.t1"; gene_id "Phchi.S1G302600"
Phchi.S1	AUGUSTUS	exon	19481236	19482558	.	+	.	transcript_id "Phchi.S1G302600.t1"; gene_id "Phchi.S1G302600"
Phchi.S1	AUGUSTUS	stop_codon	19482559	19482561	.	+	0	transcript_id "Phchi.S1G302600.t1"; gene_id "Phchi.S1G302600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11670.t1 is derived from g15721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7594209	7596553	.	-	.	Phchi.S4G125200
Phchi.S4	AUGUSTUS	transcript	7594209	7596553	.	-	.	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	stop_codon	7594206	7594208	.	-	0	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	CDS	7594209	7595987	1	-	0	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	exon	7594209	7595987	.	-	.	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	intron	7595988	7596103	.	-	.	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	CDS	7596104	7596553	0.65	-	0	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	exon	7596104	7596553	.	-	.	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
Phchi.S4	AUGUSTUS	start_codon	7596551	7596553	.	-	0	transcript_id "Phchi.S4G125200.t1"; gene_id "Phchi.S4G125200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10456.t1 is derived from g14505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	416502	417857	.	-	.	Phchi.S4G003800
Phchi.S4	AUGUSTUS	transcript	416502	417857	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	stop_codon	416499	416501	.	-	0	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	CDS	416502	416837	0.7	-	0	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	exon	416502	416837	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	intron	416838	416964	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	CDS	416965	417061	0.69	-	1	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	exon	416965	417061	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	intron	417062	417169	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	CDS	417170	417342	0.75	-	0	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	exon	417170	417342	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	intron	417343	417429	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	CDS	417430	417633	1	-	0	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	exon	417430	417633	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	intron	417634	417713	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	CDS	417714	417857	0.46	-	0	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	exon	417714	417857	.	-	.	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
Phchi.S4	AUGUSTUS	start_codon	417855	417857	.	-	0	transcript_id "Phchi.S4G003800.t1"; gene_id "Phchi.S4G003800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5414.t1 is derived from g2584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16769290	16769678	.	-	.	Phchi.S1G257300
Phchi.S1	AUGUSTUS	transcript	16769290	16769678	.	-	.	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	stop_codon	16769287	16769289	.	-	0	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	CDS	16769290	16769296	0.99	-	1	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	exon	16769290	16769296	.	-	.	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	intron	16769297	16769475	.	-	.	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	CDS	16769476	16769678	0.6	-	0	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	exon	16769476	16769678	.	-	.	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
Phchi.S1	AUGUSTUS	start_codon	16769676	16769678	.	-	0	transcript_id "Phchi.S1G257300.t1"; gene_id "Phchi.S1G257300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg174.t1 is derived from g9956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1015538	1016621	.	+	.	Phchi.S6G013300
Phchi.S6	AUGUSTUS	transcript	1015538	1016621	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	start_codon	1015538	1015540	.	+	0	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	CDS	1015538	1015743	0.98	+	0	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	exon	1015538	1015743	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	intron	1015744	1015848	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	CDS	1015849	1015907	1	+	1	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	exon	1015849	1015907	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	intron	1015908	1016299	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	CDS	1016300	1016474	1	+	2	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	exon	1016300	1016474	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	intron	1016475	1016614	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	CDS	1016615	1016621	1	+	1	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	exon	1016615	1016621	.	+	.	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
Phchi.S6	AUGUSTUS	stop_codon	1016622	1016624	.	+	0	transcript_id "Phchi.S6G013300.t1"; gene_id "Phchi.S6G013300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8516.t1 is derived from g5691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36402146	36402491	.	+	.	Phchi.S1G567500
Phchi.S1	AUGUSTUS	transcript	36402146	36402491	.	+	.	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	start_codon	36402146	36402148	.	+	0	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	CDS	36402146	36402409	0.47	+	0	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	exon	36402146	36402409	.	+	.	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	intron	36402410	36402485	.	+	.	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	CDS	36402486	36402491	0.68	+	0	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	exon	36402486	36402491	.	+	.	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
Phchi.S1	AUGUSTUS	stop_codon	36402492	36402494	.	+	0	transcript_id "Phchi.S1G567500.t1"; gene_id "Phchi.S1G567500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5218.t1 is derived from g2388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15545515	15547505	.	+	.	Phchi.S1G237700
Phchi.S1	AUGUSTUS	transcript	15545515	15547505	.	+	.	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	start_codon	15545515	15545517	.	+	0	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	CDS	15545515	15547072	0.66	+	0	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	exon	15545515	15547072	.	+	.	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	intron	15547073	15547161	.	+	.	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	CDS	15547162	15547505	1	+	2	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	exon	15547162	15547505	.	+	.	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
Phchi.S1	AUGUSTUS	stop_codon	15547506	15547508	.	+	0	transcript_id "Phchi.S1G237700.t1"; gene_id "Phchi.S1G237700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10015.t1 is derived from g7191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45055954	45059830	.	+	.	Phchi.S1G717400
Phchi.S1	AUGUSTUS	transcript	45055954	45059830	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	start_codon	45055954	45055956	.	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45055954	45056009	0.56	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45055954	45056009	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	intron	45056010	45056137	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45056138	45056513	0.75	+	1	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45056138	45056513	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	intron	45056514	45056598	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45056599	45057000	1	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45056599	45057000	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	intron	45057001	45057095	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45057096	45057689	0.91	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45057096	45057689	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	intron	45057690	45057988	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45057989	45059181	0.68	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45057989	45059181	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	intron	45059182	45059291	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45059292	45059547	0.97	+	1	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45059292	45059547	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	intron	45059548	45059656	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	CDS	45059657	45059830	0.99	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	exon	45059657	45059830	.	+	.	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
Phchi.S1	AUGUSTUS	stop_codon	45059831	45059833	.	+	0	transcript_id "Phchi.S1G717400.t1"; gene_id "Phchi.S1G717400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14588.t1 is derived from g13056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13598187	13599827	.	-	.	Phchi.S3G190700
Phchi.S3	AUGUSTUS	transcript	13598187	13599827	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	stop_codon	13598184	13598186	.	-	0	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	CDS	13598187	13598216	0.26	-	0	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	exon	13598187	13598216	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	intron	13598217	13598320	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	CDS	13598321	13598613	0.24	-	2	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	exon	13598321	13598613	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	intron	13598614	13598904	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	CDS	13598905	13599238	0.28	-	0	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	exon	13598905	13599238	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	intron	13599239	13599361	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	CDS	13599362	13599523	0.88	-	0	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	exon	13599362	13599523	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	intron	13599524	13599650	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	CDS	13599651	13599827	0.59	-	0	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	exon	13599651	13599827	.	-	.	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
Phchi.S3	AUGUSTUS	start_codon	13599825	13599827	.	-	0	transcript_id "Phchi.S3G190700.t1"; gene_id "Phchi.S3G190700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10041.t1 is derived from g7217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45211589	45213127	.	-	.	Phchi.S1G720000
Phchi.S1	AUGUSTUS	transcript	45211589	45213127	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	stop_codon	45211586	45211588	.	-	0	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	CDS	45211589	45212045	1	-	1	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	exon	45211589	45212045	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	intron	45212046	45212129	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	CDS	45212130	45212292	1	-	2	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	exon	45212130	45212292	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	intron	45212293	45212414	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	CDS	45212415	45212484	1	-	0	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	exon	45212415	45212484	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	intron	45212485	45212612	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	CDS	45212613	45212741	1	-	0	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	exon	45212613	45212741	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	intron	45212742	45212863	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	CDS	45212864	45213127	1	-	0	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	exon	45212864	45213127	.	-	.	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
Phchi.S1	AUGUSTUS	start_codon	45213125	45213127	.	-	0	transcript_id "Phchi.S1G720000.t1"; gene_id "Phchi.S1G720000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10837.t1 is derived from g14887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2386365	2387612	.	+	.	Phchi.S4G041900
Phchi.S4	AUGUSTUS	transcript	2386365	2387612	.	+	.	transcript_id "Phchi.S4G041900.t1"; gene_id "Phchi.S4G041900"
Phchi.S4	AUGUSTUS	start_codon	2386365	2386367	.	+	0	transcript_id "Phchi.S4G041900.t1"; gene_id "Phchi.S4G041900"
Phchi.S4	AUGUSTUS	CDS	2386365	2387612	1	+	0	transcript_id "Phchi.S4G041900.t1"; gene_id "Phchi.S4G041900"
Phchi.S4	AUGUSTUS	exon	2386365	2387612	.	+	.	transcript_id "Phchi.S4G041900.t1"; gene_id "Phchi.S4G041900"
Phchi.S4	AUGUSTUS	stop_codon	2387613	2387615	.	+	0	transcript_id "Phchi.S4G041900.t1"; gene_id "Phchi.S4G041900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11369.t1 is derived from g15419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5920779	5921618	.	-	.	Phchi.S4G095100
Phchi.S4	AUGUSTUS	transcript	5920779	5921618	.	-	.	transcript_id "Phchi.S4G095100.t1"; gene_id "Phchi.S4G095100"
Phchi.S4	AUGUSTUS	stop_codon	5920776	5920778	.	-	0	transcript_id "Phchi.S4G095100.t1"; gene_id "Phchi.S4G095100"
Phchi.S4	AUGUSTUS	CDS	5920779	5921618	1	-	0	transcript_id "Phchi.S4G095100.t1"; gene_id "Phchi.S4G095100"
Phchi.S4	AUGUSTUS	exon	5920779	5921618	.	-	.	transcript_id "Phchi.S4G095100.t1"; gene_id "Phchi.S4G095100"
Phchi.S4	AUGUSTUS	start_codon	5921616	5921618	.	-	0	transcript_id "Phchi.S4G095100.t1"; gene_id "Phchi.S4G095100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5671.t1 is derived from g2841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18230024	18231222	.	+	.	Phchi.S1G283000
Phchi.S1	AUGUSTUS	transcript	18230024	18231222	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	start_codon	18230024	18230026	.	+	0	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	CDS	18230024	18230217	1	+	0	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	exon	18230024	18230217	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	intron	18230218	18230349	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	CDS	18230350	18230501	1	+	1	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	exon	18230350	18230501	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	intron	18230502	18230747	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	CDS	18230748	18230873	1	+	2	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	exon	18230748	18230873	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	intron	18230874	18231007	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	CDS	18231008	18231222	1	+	2	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	exon	18231008	18231222	.	+	.	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
Phchi.S1	AUGUSTUS	stop_codon	18231223	18231225	.	+	0	transcript_id "Phchi.S1G283000.t1"; gene_id "Phchi.S1G283000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7360.t1 is derived from g4532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28765757	28767367	.	-	.	Phchi.S1G451900
Phchi.S1	AUGUSTUS	transcript	28765757	28767367	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	stop_codon	28765754	28765756	.	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28765757	28765865	0.99	-	1	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28765757	28765865	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28765866	28765981	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28765982	28766052	1	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28765982	28766052	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28766053	28766146	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28766147	28766290	1	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28766147	28766290	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28766291	28766477	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28766478	28766534	0.99	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28766478	28766534	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28766535	28766641	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28766642	28766743	0.98	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28766642	28766743	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28766744	28766833	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28766834	28766931	1	-	2	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28766834	28766931	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28766932	28767033	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28767034	28767203	1	-	1	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28767034	28767203	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	intron	28767204	28767338	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	CDS	28767339	28767367	0.5	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	exon	28767339	28767367	.	-	.	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
Phchi.S1	AUGUSTUS	start_codon	28767365	28767367	.	-	0	transcript_id "Phchi.S1G451900.t1"; gene_id "Phchi.S1G451900"
# This transcript jg6716.t2 is derived from g3888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6717.t1 is derived from g3889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24693896	24694982	.	+	.	Phchi.S1G387600
Phchi.S1	AUGUSTUS	transcript	24693896	24694982	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	start_codon	24693896	24693898	.	+	0	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	CDS	24693896	24694159	0.91	+	0	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	exon	24693896	24694159	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	intron	24694160	24694301	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	CDS	24694302	24694362	1	+	0	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	exon	24694302	24694362	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	intron	24694363	24694486	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	CDS	24694487	24694549	1	+	2	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	exon	24694487	24694549	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	intron	24694550	24694666	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	CDS	24694667	24694725	1	+	2	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	exon	24694667	24694725	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	intron	24694726	24694820	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	CDS	24694821	24694982	0.71	+	0	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	exon	24694821	24694982	.	+	.	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
Phchi.S1	AUGUSTUS	stop_codon	24694983	24694985	.	+	0	transcript_id "Phchi.S1G387600.t1"; gene_id "Phchi.S1G387600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5211.t1 is derived from g2381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15494854	15496640	.	-	.	Phchi.S1G237000
Phchi.S1	AUGUSTUS	transcript	15494854	15496640	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	stop_codon	15494851	15494853	.	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15494854	15495084	1	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15494854	15495084	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15495085	15495174	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15495175	15495282	0.99	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15495175	15495282	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15495283	15495387	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15495388	15495489	0.99	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15495388	15495489	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15495490	15495566	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15495567	15495809	1	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15495567	15495809	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15495810	15495953	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15495954	15496155	1	-	1	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15495954	15496155	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15496156	15496237	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15496238	15496266	1	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15496238	15496266	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15496267	15496416	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15496417	15496473	0.99	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15496417	15496473	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	intron	15496474	15496571	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	CDS	15496572	15496640	0.34	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	exon	15496572	15496640	.	-	.	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
Phchi.S1	AUGUSTUS	start_codon	15496638	15496640	.	-	0	transcript_id "Phchi.S1G237000.t1"; gene_id "Phchi.S1G237000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12494.t1 is derived from g8171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30080219	30080704	.	+	.	Phchi.S2G057400
Phchi.S2	AUGUSTUS	transcript	30080219	30080704	.	+	.	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	start_codon	30080219	30080221	.	+	0	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	CDS	30080219	30080444	0.36	+	0	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	exon	30080219	30080444	.	+	.	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	intron	30080445	30080681	.	+	.	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	CDS	30080682	30080704	0.74	+	2	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	exon	30080682	30080704	.	+	.	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
Phchi.S2	AUGUSTUS	stop_codon	30080705	30080707	.	+	0	transcript_id "Phchi.S2G057400.t1"; gene_id "Phchi.S2G057400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8721.t1 is derived from g5896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37671877	37673154	.	-	.	Phchi.S1G588000
Phchi.S1	AUGUSTUS	transcript	37671877	37673154	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	stop_codon	37671874	37671876	.	-	0	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	CDS	37671877	37671942	1	-	0	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	exon	37671877	37671942	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	intron	37671943	37672014	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	CDS	37672015	37672077	1	-	0	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	exon	37672015	37672077	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	intron	37672078	37672209	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	CDS	37672210	37672320	1	-	0	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	exon	37672210	37672320	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	intron	37672321	37672404	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	CDS	37672405	37672597	1	-	1	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	exon	37672405	37672597	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	intron	37672598	37672676	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	CDS	37672677	37672815	1	-	2	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	exon	37672677	37672815	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	intron	37672816	37672901	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	CDS	37672902	37673154	0.56	-	0	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	exon	37672902	37673154	.	-	.	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
Phchi.S1	AUGUSTUS	start_codon	37673152	37673154	.	-	0	transcript_id "Phchi.S1G588000.t1"; gene_id "Phchi.S1G588000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4647.t1 is derived from g1817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11626675	11627958	.	-	.	Phchi.S1G180600
Phchi.S1	AUGUSTUS	transcript	11626675	11627958	.	-	.	transcript_id "Phchi.S1G180600.t1"; gene_id "Phchi.S1G180600"
Phchi.S1	AUGUSTUS	stop_codon	11626672	11626674	.	-	0	transcript_id "Phchi.S1G180600.t1"; gene_id "Phchi.S1G180600"
Phchi.S1	AUGUSTUS	CDS	11626675	11627958	0.54	-	0	transcript_id "Phchi.S1G180600.t1"; gene_id "Phchi.S1G180600"
Phchi.S1	AUGUSTUS	exon	11626675	11627958	.	-	.	transcript_id "Phchi.S1G180600.t1"; gene_id "Phchi.S1G180600"
Phchi.S1	AUGUSTUS	start_codon	11627956	11627958	.	-	0	transcript_id "Phchi.S1G180600.t1"; gene_id "Phchi.S1G180600"
# This transcript jg7889.t2 is derived from g5063.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7890.t1 is derived from g5064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31773398	31774956	.	+	.	Phchi.S1G504900
Phchi.S1	AUGUSTUS	transcript	31773398	31774956	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	start_codon	31773398	31773400	.	+	0	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	CDS	31773398	31773422	0.87	+	0	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	exon	31773398	31773422	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	intron	31773423	31773506	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	CDS	31773507	31773511	0.78	+	2	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	exon	31773507	31773511	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	intron	31773512	31773644	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	CDS	31773645	31773899	0.78	+	0	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	exon	31773645	31773899	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	intron	31773900	31773973	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	CDS	31773974	31774215	1	+	0	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	exon	31773974	31774215	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	intron	31774216	31774309	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	CDS	31774310	31774634	0.99	+	1	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	exon	31774310	31774634	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	intron	31774635	31774710	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	CDS	31774711	31774956	1	+	0	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	exon	31774711	31774956	.	+	.	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
Phchi.S1	AUGUSTUS	stop_codon	31774957	31774959	.	+	0	transcript_id "Phchi.S1G504900.t1"; gene_id "Phchi.S1G504900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13811.t1 is derived from g12278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9029266	9030510	.	-	.	Phchi.S3G113000
Phchi.S3	AUGUSTUS	transcript	9029266	9030510	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	stop_codon	9029263	9029265	.	-	0	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	CDS	9029266	9029418	1	-	0	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	exon	9029266	9029418	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	intron	9029419	9029567	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	CDS	9029568	9029693	1	-	0	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	exon	9029568	9029693	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	intron	9029694	9029773	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	CDS	9029774	9029827	1	-	0	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	exon	9029774	9029827	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	intron	9029828	9030162	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	CDS	9030163	9030510	0.96	-	0	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	exon	9030163	9030510	.	-	.	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
Phchi.S3	AUGUSTUS	start_codon	9030508	9030510	.	-	0	transcript_id "Phchi.S3G113000.t1"; gene_id "Phchi.S3G113000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4228.t1 is derived from g1397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9020170	9021110	.	+	.	Phchi.S1G138700
Phchi.S1	AUGUSTUS	transcript	9020170	9021110	.	+	.	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	start_codon	9020170	9020172	.	+	0	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	CDS	9020170	9020429	0.33	+	0	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	exon	9020170	9020429	.	+	.	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	intron	9020430	9020593	.	+	.	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	CDS	9020594	9021110	0.97	+	1	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	exon	9020594	9021110	.	+	.	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
Phchi.S1	AUGUSTUS	stop_codon	9021111	9021113	.	+	0	transcript_id "Phchi.S1G138700.t1"; gene_id "Phchi.S1G138700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4145.t1 is derived from g1314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8629786	8630676	.	+	.	Phchi.S1G130400
Phchi.S1	AUGUSTUS	transcript	8629786	8630676	.	+	.	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	start_codon	8629786	8629788	.	+	0	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	CDS	8629786	8630035	1	+	0	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	exon	8629786	8630035	.	+	.	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	intron	8630036	8630130	.	+	.	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	CDS	8630131	8630192	0.79	+	2	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	exon	8630131	8630192	.	+	.	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	intron	8630193	8630262	.	+	.	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	CDS	8630263	8630676	0.9	+	0	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	exon	8630263	8630676	.	+	.	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
Phchi.S1	AUGUSTUS	stop_codon	8630677	8630679	.	+	0	transcript_id "Phchi.S1G130400.t1"; gene_id "Phchi.S1G130400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13674.t1 is derived from g12141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8094117	8097989	.	+	.	Phchi.S3G099300
Phchi.S3	AUGUSTUS	transcript	8094117	8097989	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	start_codon	8094117	8094119	.	+	0	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8094117	8094709	1	+	0	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8094117	8094709	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8094710	8095082	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8095083	8095188	1	+	1	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8095083	8095188	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8095189	8095284	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8095285	8095481	0.99	+	0	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8095285	8095481	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8095482	8095716	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8095717	8095786	1	+	1	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8095717	8095786	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8095787	8095872	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8095873	8096101	0.95	+	0	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8095873	8096101	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8096102	8096199	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8096200	8096338	0.37	+	2	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8096200	8096338	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8096339	8096408	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8096409	8096515	0.51	+	1	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8096409	8096515	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8096516	8096653	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8096654	8096771	1	+	2	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8096654	8096771	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8096772	8096909	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8096910	8097041	1	+	1	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8096910	8097041	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8097042	8097269	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8097270	8097322	1	+	1	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8097270	8097322	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8097323	8097487	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8097488	8097533	1	+	2	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8097488	8097533	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8097534	8097652	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8097653	8097666	0.76	+	1	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8097653	8097666	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8097667	8097829	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8097830	8097882	0.75	+	2	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8097830	8097882	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	intron	8097883	8097956	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	CDS	8097957	8097989	1	+	0	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	exon	8097957	8097989	.	+	.	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
Phchi.S3	AUGUSTUS	stop_codon	8097990	8097992	.	+	0	transcript_id "Phchi.S3G099300.t1"; gene_id "Phchi.S3G099300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7240.t1 is derived from g4412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27796853	27799849	.	+	.	Phchi.S1G439900
Phchi.S1	AUGUSTUS	transcript	27796853	27799849	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	start_codon	27796853	27796855	.	+	0	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27796853	27797107	0.72	+	0	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27796853	27797107	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27797108	27797368	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27797369	27797777	0.85	+	0	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27797369	27797777	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27797778	27797879	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27797880	27798074	0.98	+	2	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27797880	27798074	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27798075	27798240	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27798241	27798707	0.59	+	2	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27798241	27798707	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27798708	27798837	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27798838	27799392	0.99	+	0	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27798838	27799392	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27799393	27799493	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27799494	27799705	1	+	0	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27799494	27799705	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27799706	27799788	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27799789	27799849	1	+	1	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27799789	27799849	.	+	.	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	stop_codon	27799850	27799852	.	+	0	transcript_id "Phchi.S1G439900.t1"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	transcript	27796853	27797420	.	+	.	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	start_codon	27796853	27796855	.	+	0	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27796853	27797112	0.79	+	0	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27796853	27797112	.	+	.	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	intron	27797113	27797368	.	+	.	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	CDS	27797369	27797420	0.42	+	1	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	exon	27797369	27797420	.	+	.	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
Phchi.S1	AUGUSTUS	stop_codon	27797421	27797423	.	+	0	transcript_id "Phchi.S1G439900.t2"; gene_id "Phchi.S1G439900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2076.t1 is derived from g8996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4721523	4722208	.	-	.	Phchi.S5G068500
Phchi.S5	AUGUSTUS	transcript	4721523	4722208	.	-	.	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	stop_codon	4721520	4721522	.	-	0	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	CDS	4721523	4721860	0.21	-	2	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	exon	4721523	4721860	.	-	.	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	intron	4721861	4721964	.	-	.	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	CDS	4721965	4722208	0.76	-	0	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	exon	4721965	4722208	.	-	.	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
Phchi.S5	AUGUSTUS	start_codon	4722206	4722208	.	-	0	transcript_id "Phchi.S5G068500.t1"; gene_id "Phchi.S5G068500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14595.t1 is derived from g13063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13627285	13628214	.	-	.	Phchi.S3G191400
Phchi.S3	AUGUSTUS	transcript	13627285	13628214	.	-	.	transcript_id "Phchi.S3G191400.t1"; gene_id "Phchi.S3G191400"
Phchi.S3	AUGUSTUS	stop_codon	13627282	13627284	.	-	0	transcript_id "Phchi.S3G191400.t1"; gene_id "Phchi.S3G191400"
Phchi.S3	AUGUSTUS	CDS	13627285	13628214	0.63	-	0	transcript_id "Phchi.S3G191400.t1"; gene_id "Phchi.S3G191400"
Phchi.S3	AUGUSTUS	exon	13627285	13628214	.	-	.	transcript_id "Phchi.S3G191400.t1"; gene_id "Phchi.S3G191400"
Phchi.S3	AUGUSTUS	start_codon	13628212	13628214	.	-	0	transcript_id "Phchi.S3G191400.t1"; gene_id "Phchi.S3G191400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg676.t1 is derived from g10458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4659428	4660483	.	-	.	Phchi.S6G063500
Phchi.S6	AUGUSTUS	transcript	4659428	4660483	.	-	.	transcript_id "Phchi.S6G063500.t1"; gene_id "Phchi.S6G063500"
Phchi.S6	AUGUSTUS	stop_codon	4659425	4659427	.	-	0	transcript_id "Phchi.S6G063500.t1"; gene_id "Phchi.S6G063500"
Phchi.S6	AUGUSTUS	CDS	4659428	4660483	0.8	-	0	transcript_id "Phchi.S6G063500.t1"; gene_id "Phchi.S6G063500"
Phchi.S6	AUGUSTUS	exon	4659428	4660483	.	-	.	transcript_id "Phchi.S6G063500.t1"; gene_id "Phchi.S6G063500"
Phchi.S6	AUGUSTUS	start_codon	4660481	4660483	.	-	0	transcript_id "Phchi.S6G063500.t1"; gene_id "Phchi.S6G063500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg794.t1 is derived from g10576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5610104	5610568	.	+	.	Phchi.S6G075300
Phchi.S6	AUGUSTUS	transcript	5610104	5610568	.	+	.	transcript_id "Phchi.S6G075300.t1"; gene_id "Phchi.S6G075300"
Phchi.S6	AUGUSTUS	start_codon	5610104	5610106	.	+	0	transcript_id "Phchi.S6G075300.t1"; gene_id "Phchi.S6G075300"
Phchi.S6	AUGUSTUS	CDS	5610104	5610568	0.28	+	0	transcript_id "Phchi.S6G075300.t1"; gene_id "Phchi.S6G075300"
Phchi.S6	AUGUSTUS	exon	5610104	5610568	.	+	.	transcript_id "Phchi.S6G075300.t1"; gene_id "Phchi.S6G075300"
Phchi.S6	AUGUSTUS	stop_codon	5610569	5610571	.	+	0	transcript_id "Phchi.S6G075300.t1"; gene_id "Phchi.S6G075300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1742.t1 is derived from g8662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2826528	2827031	.	+	.	Phchi.S5G035100
Phchi.S5	AUGUSTUS	transcript	2826528	2827031	.	+	.	transcript_id "Phchi.S5G035100.t1"; gene_id "Phchi.S5G035100"
Phchi.S5	AUGUSTUS	start_codon	2826528	2826530	.	+	0	transcript_id "Phchi.S5G035100.t1"; gene_id "Phchi.S5G035100"
Phchi.S5	AUGUSTUS	CDS	2826528	2827031	0.84	+	0	transcript_id "Phchi.S5G035100.t1"; gene_id "Phchi.S5G035100"
Phchi.S5	AUGUSTUS	exon	2826528	2827031	.	+	.	transcript_id "Phchi.S5G035100.t1"; gene_id "Phchi.S5G035100"
Phchi.S5	AUGUSTUS	stop_codon	2827032	2827034	.	+	0	transcript_id "Phchi.S5G035100.t1"; gene_id "Phchi.S5G035100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12842.t1 is derived from g11307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2654716	2657881	.	-	.	Phchi.S3G016100
Phchi.S3	AUGUSTUS	transcript	2654716	2657881	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	stop_codon	2654713	2654715	.	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2654716	2654904	1	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2654716	2654904	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2654905	2654980	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2654981	2655411	0.19	-	2	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2654981	2655411	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2655412	2655533	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2655534	2655579	0.46	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2655534	2655579	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2655580	2655722	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2655723	2655808	0.53	-	2	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2655723	2655808	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2655809	2655938	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2655939	2655998	0.68	-	2	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2655939	2655998	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2655999	2656108	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2656109	2656170	0.68	-	1	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2656109	2656170	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2656171	2656245	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2656246	2656333	1	-	2	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2656246	2656333	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2656334	2657133	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2657134	2657176	1	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2657134	2657176	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2657177	2657292	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2657293	2657319	0.9	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2657293	2657319	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2657320	2657421	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2657422	2657493	0.98	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2657422	2657493	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2657494	2657602	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2657603	2657715	0.96	-	2	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2657603	2657715	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	intron	2657716	2657799	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	CDS	2657800	2657881	1	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	exon	2657800	2657881	.	-	.	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
Phchi.S3	AUGUSTUS	start_codon	2657879	2657881	.	-	0	transcript_id "Phchi.S3G016100.t1"; gene_id "Phchi.S3G016100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7372.t1 is derived from g4544.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28813519	28816118	.	-	.	Phchi.S1G453100
Phchi.S1	AUGUSTUS	transcript	28813519	28816118	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	stop_codon	28813516	28813518	.	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28813519	28813581	0.99	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28813519	28813581	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28813582	28813663	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28813664	28813889	0.7	-	1	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28813664	28813889	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28813890	28813999	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28814000	28814266	0.77	-	1	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28814000	28814266	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28814267	28814393	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28814394	28814583	0.43	-	2	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28814394	28814583	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28814584	28814671	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28814672	28814744	0.95	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28814672	28814744	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28814745	28814884	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28814885	28815019	1	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28814885	28815019	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28815020	28815111	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28815112	28815147	0.99	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28815112	28815147	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28815148	28815237	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28815238	28815331	1	-	1	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28815238	28815331	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28815332	28815413	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28815414	28815609	0.71	-	2	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28815414	28815609	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28815610	28815684	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28815685	28815880	0.71	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28815685	28815880	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	intron	28815881	28815977	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	CDS	28815978	28816118	0.98	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	exon	28815978	28816118	.	-	.	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
Phchi.S1	AUGUSTUS	start_codon	28816116	28816118	.	-	0	transcript_id "Phchi.S1G453100.t1"; gene_id "Phchi.S1G453100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6775.t1 is derived from g3947.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25018679	25024363	.	-	.	Phchi.S1G393400
Phchi.S1	AUGUSTUS	transcript	25018679	25024363	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	stop_codon	25018676	25018678	.	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25018679	25018795	1	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25018679	25018795	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25018796	25018884	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25018885	25018947	1	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25018885	25018947	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25018948	25019027	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019028	25019066	1	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019028	25019066	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019067	25019169	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019170	25019247	0.96	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019170	25019247	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019248	25019350	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019351	25019452	0.94	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019351	25019452	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019453	25019615	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019616	25019684	1	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019616	25019684	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019685	25019834	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019835	25019894	1	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019835	25019894	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019895	25019994	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019995	25020052	1	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019995	25020052	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020053	25020178	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020179	25020360	1	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020179	25020360	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020361	25020479	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020480	25020597	0.98	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020480	25020597	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020598	25020710	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020711	25020743	0.98	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020711	25020743	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020744	25020828	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020829	25020866	0.69	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020829	25020866	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020867	25020983	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020984	25021038	0.33	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020984	25021038	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25021039	25021224	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25021225	25022460	0.2	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25021225	25022460	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25022461	25022682	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25022683	25023150	0.26	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25022683	25023150	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023151	25023425	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25023426	25023595	0.52	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25023426	25023595	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023596	25023676	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25023677	25023756	1	-	2	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25023677	25023756	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023757	25023855	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25023856	25023947	0.71	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25023856	25023947	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023948	25024034	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25024035	25024073	0.95	-	1	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25024035	25024073	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25024074	25024214	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25024215	25024363	0.95	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25024215	25024363	.	-	.	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	start_codon	25024361	25024363	.	-	0	transcript_id "Phchi.S1G393400.t1"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	transcript	25018679	25024363	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	stop_codon	25018676	25018678	.	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25018679	25018795	1	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25018679	25018795	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25018796	25018884	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25018885	25018947	1	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25018885	25018947	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25018948	25019027	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019028	25019066	1	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019028	25019066	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019067	25019169	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019170	25019247	0.92	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019170	25019247	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019248	25019350	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019351	25019452	0.95	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019351	25019452	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019453	25019615	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019616	25019684	1	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019616	25019684	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019685	25019834	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019835	25019894	1	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019835	25019894	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25019895	25019994	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25019995	25020052	1	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25019995	25020052	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020053	25020178	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020179	25020360	1	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020179	25020360	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020361	25020479	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020480	25020597	0.95	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020480	25020597	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020598	25020710	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020711	25020743	0.95	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020711	25020743	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020744	25020828	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020829	25020866	0.76	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020829	25020866	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25020867	25020983	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25020984	25021038	0.23	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25020984	25021038	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25021039	25021224	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25021225	25022460	0.28	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25021225	25022460	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25022461	25022682	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25022683	25023150	0.23	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25022683	25023150	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023151	25023425	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25023426	25023592	0.47	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25023426	25023592	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023593	25023676	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25023677	25023756	1	-	2	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25023677	25023756	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023757	25023855	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25023856	25023947	0.69	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25023856	25023947	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25023948	25024034	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25024035	25024073	0.95	-	1	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25024035	25024073	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	intron	25024074	25024214	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	CDS	25024215	25024363	0.95	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	exon	25024215	25024363	.	-	.	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
Phchi.S1	AUGUSTUS	start_codon	25024361	25024363	.	-	0	transcript_id "Phchi.S1G393400.t2"; gene_id "Phchi.S1G393400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1913.t1 is derived from g8833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3836532	3837128	.	-	.	Phchi.S5G052200
Phchi.S5	AUGUSTUS	transcript	3836532	3837128	.	-	.	transcript_id "Phchi.S5G052200.t1"; gene_id "Phchi.S5G052200"
Phchi.S5	AUGUSTUS	stop_codon	3836529	3836531	.	-	0	transcript_id "Phchi.S5G052200.t1"; gene_id "Phchi.S5G052200"
Phchi.S5	AUGUSTUS	CDS	3836532	3837128	0.48	-	0	transcript_id "Phchi.S5G052200.t1"; gene_id "Phchi.S5G052200"
Phchi.S5	AUGUSTUS	exon	3836532	3837128	.	-	.	transcript_id "Phchi.S5G052200.t1"; gene_id "Phchi.S5G052200"
Phchi.S5	AUGUSTUS	start_codon	3837126	3837128	.	-	0	transcript_id "Phchi.S5G052200.t1"; gene_id "Phchi.S5G052200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8229.t1 is derived from g5404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34561659	34562523	.	+	.	Phchi.S1G538800
Phchi.S1	AUGUSTUS	transcript	34561659	34562523	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	start_codon	34561659	34561661	.	+	0	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	CDS	34561659	34561736	1	+	0	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	exon	34561659	34561736	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	intron	34561737	34561933	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	CDS	34561934	34562039	1	+	0	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	exon	34561934	34562039	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	intron	34562040	34562179	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	CDS	34562180	34562359	1	+	2	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	exon	34562180	34562359	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	intron	34562360	34562503	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	CDS	34562504	34562523	1	+	2	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	exon	34562504	34562523	.	+	.	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
Phchi.S1	AUGUSTUS	stop_codon	34562524	34562526	.	+	0	transcript_id "Phchi.S1G538800.t1"; gene_id "Phchi.S1G538800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10552.t1 is derived from g14602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	961492	962848	.	+	.	Phchi.S4G013400
Phchi.S4	AUGUSTUS	transcript	961492	962848	.	+	.	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	start_codon	961492	961494	.	+	0	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	CDS	961492	961907	0.2	+	0	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	exon	961492	961907	.	+	.	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	intron	961908	962221	.	+	.	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	CDS	962222	962501	0.66	+	1	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	exon	962222	962501	.	+	.	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	intron	962502	962632	.	+	.	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	CDS	962633	962848	0.8	+	0	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	exon	962633	962848	.	+	.	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
Phchi.S4	AUGUSTUS	stop_codon	962849	962851	.	+	0	transcript_id "Phchi.S4G013400.t1"; gene_id "Phchi.S4G013400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8230.t1 is derived from g5405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34563129	34564174	.	-	.	Phchi.S1G538900
Phchi.S1	AUGUSTUS	transcript	34563129	34564174	.	-	.	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	stop_codon	34563126	34563128	.	-	0	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	CDS	34563129	34563468	0.91	-	1	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	exon	34563129	34563468	.	-	.	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	intron	34563469	34563545	.	-	.	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	CDS	34563546	34564174	0.43	-	0	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	exon	34563546	34564174	.	-	.	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
Phchi.S1	AUGUSTUS	start_codon	34564172	34564174	.	-	0	transcript_id "Phchi.S1G538900.t1"; gene_id "Phchi.S1G538900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7343.t1 is derived from g4515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28629112	28629738	.	-	.	Phchi.S1G450200
Phchi.S1	AUGUSTUS	transcript	28629112	28629738	.	-	.	transcript_id "Phchi.S1G450200.t1"; gene_id "Phchi.S1G450200"
Phchi.S1	AUGUSTUS	stop_codon	28629109	28629111	.	-	0	transcript_id "Phchi.S1G450200.t1"; gene_id "Phchi.S1G450200"
Phchi.S1	AUGUSTUS	CDS	28629112	28629738	0.31	-	0	transcript_id "Phchi.S1G450200.t1"; gene_id "Phchi.S1G450200"
Phchi.S1	AUGUSTUS	exon	28629112	28629738	.	-	.	transcript_id "Phchi.S1G450200.t1"; gene_id "Phchi.S1G450200"
Phchi.S1	AUGUSTUS	start_codon	28629736	28629738	.	-	0	transcript_id "Phchi.S1G450200.t1"; gene_id "Phchi.S1G450200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1615.t1 is derived from g8534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2032790	2035069	.	-	.	Phchi.S5G022400
Phchi.S5	AUGUSTUS	transcript	2032790	2035069	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	stop_codon	2032787	2032789	.	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2032790	2032978	0.58	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2032790	2032978	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2032979	2033099	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033100	2033366	0.95	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033100	2033366	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033367	2033441	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033442	2033514	0.95	-	1	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033442	2033514	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033515	2033595	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033596	2033657	1	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033596	2033657	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033658	2033758	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033759	2033854	1	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033759	2033854	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033855	2033946	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033947	2034007	1	-	1	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033947	2034007	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034008	2034144	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034145	2034150	0.89	-	1	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034145	2034150	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034151	2034247	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034248	2034396	0.75	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034248	2034396	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034397	2034480	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034481	2034554	1	-	2	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034481	2034554	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034555	2034687	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034688	2034793	1	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034688	2034793	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034794	2034868	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034869	2035069	0.93	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034869	2035069	.	-	.	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	start_codon	2035067	2035069	.	-	0	transcript_id "Phchi.S5G022400.t1"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	transcript	2032790	2035069	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	stop_codon	2032787	2032789	.	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2032790	2032978	0.5	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2032790	2032978	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2032979	2033099	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033100	2033366	0.98	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033100	2033366	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033367	2033441	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033442	2033514	0.98	-	1	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033442	2033514	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033515	2033595	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033596	2033657	1	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033596	2033657	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033658	2033758	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033759	2033854	1	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033759	2033854	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2033855	2033946	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2033947	2034007	1	-	1	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2033947	2034007	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034008	2034144	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034145	2034199	0.79	-	2	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034145	2034199	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034200	2034366	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034367	2034396	0.5	-	2	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034367	2034396	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034397	2034480	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034481	2034554	0.77	-	1	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034481	2034554	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034555	2034683	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034684	2034793	0.77	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034684	2034793	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	intron	2034794	2034868	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	CDS	2034869	2035069	0.94	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	exon	2034869	2035069	.	-	.	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
Phchi.S5	AUGUSTUS	start_codon	2035067	2035069	.	-	0	transcript_id "Phchi.S5G022400.t2"; gene_id "Phchi.S5G022400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2115.t1 is derived from g9035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4925260	4927295	.	+	.	Phchi.S5G072400
Phchi.S5	AUGUSTUS	transcript	4925260	4927295	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	start_codon	4925260	4925262	.	+	0	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	CDS	4925260	4926390	0.82	+	0	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	exon	4925260	4926390	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	intron	4926391	4926478	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	CDS	4926479	4926737	0.89	+	0	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	exon	4926479	4926737	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	intron	4926738	4926835	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	CDS	4926836	4927113	1	+	2	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	exon	4926836	4927113	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	intron	4927114	4927205	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	CDS	4927206	4927295	1	+	0	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	exon	4927206	4927295	.	+	.	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
Phchi.S5	AUGUSTUS	stop_codon	4927296	4927298	.	+	0	transcript_id "Phchi.S5G072400.t1"; gene_id "Phchi.S5G072400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg562.t1 is derived from g10344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4059299	4061595	.	+	.	Phchi.S6G052100
Phchi.S6	AUGUSTUS	transcript	4059299	4061595	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	start_codon	4059299	4059301	.	+	0	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4059299	4059544	1	+	0	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4059299	4059544	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	intron	4059545	4059639	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4059640	4059865	1	+	0	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4059640	4059865	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	intron	4059866	4059941	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4059942	4060834	0.97	+	2	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4059942	4060834	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	intron	4060835	4060914	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4060915	4061013	0.65	+	0	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4060915	4061013	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	intron	4061014	4061115	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4061116	4061213	0.29	+	0	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4061116	4061213	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	intron	4061214	4061363	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4061364	4061428	0.44	+	1	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4061364	4061428	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	intron	4061429	4061506	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	CDS	4061507	4061595	0.44	+	2	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	exon	4061507	4061595	.	+	.	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
Phchi.S6	AUGUSTUS	stop_codon	4061596	4061598	.	+	0	transcript_id "Phchi.S6G052100.t1"; gene_id "Phchi.S6G052100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1196.t1 is derived from g10979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8371375	8372881	.	-	.	Phchi.S6G115500
Phchi.S6	AUGUSTUS	transcript	8371375	8372881	.	-	.	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	stop_codon	8371372	8371374	.	-	0	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	CDS	8371375	8371953	0.55	-	0	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	exon	8371375	8371953	.	-	.	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	intron	8371954	8372089	.	-	.	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	CDS	8372090	8372881	0.94	-	0	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	exon	8372090	8372881	.	-	.	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
Phchi.S6	AUGUSTUS	start_codon	8372879	8372881	.	-	0	transcript_id "Phchi.S6G115500.t1"; gene_id "Phchi.S6G115500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12891.t1 is derived from g11356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3014482	3015990	.	-	.	Phchi.S3G021000
Phchi.S3	AUGUSTUS	transcript	3014482	3015990	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	stop_codon	3014479	3014481	.	-	0	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	CDS	3014482	3014944	0.62	-	1	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	exon	3014482	3014944	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	intron	3014945	3015209	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	CDS	3015210	3015572	0.99	-	1	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	exon	3015210	3015572	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	intron	3015573	3015689	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	CDS	3015690	3015835	0.99	-	0	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	exon	3015690	3015835	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	intron	3015836	3015963	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	CDS	3015964	3015990	0.97	-	0	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	exon	3015964	3015990	.	-	.	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
Phchi.S3	AUGUSTUS	start_codon	3015988	3015990	.	-	0	transcript_id "Phchi.S3G021000.t1"; gene_id "Phchi.S3G021000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9878.t1 is derived from g7054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44212890	44213668	.	+	.	Phchi.S1G703700
Phchi.S1	AUGUSTUS	transcript	44212890	44213668	.	+	.	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	start_codon	44212890	44212892	.	+	0	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	CDS	44212890	44213110	0.03	+	0	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	exon	44212890	44213110	.	+	.	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	intron	44213111	44213283	.	+	.	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	CDS	44213284	44213668	0.05	+	1	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	exon	44213284	44213668	.	+	.	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
Phchi.S1	AUGUSTUS	stop_codon	44213669	44213671	.	+	0	transcript_id "Phchi.S1G703700.t1"; gene_id "Phchi.S1G703700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11649.t1 is derived from g15700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7458864	7460268	.	+	.	Phchi.S4G123100
Phchi.S4	AUGUSTUS	transcript	7458864	7460268	.	+	.	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	start_codon	7458864	7458866	.	+	0	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	CDS	7458864	7459402	1	+	0	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	exon	7458864	7459402	.	+	.	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	intron	7459403	7459493	.	+	.	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	CDS	7459494	7459702	1	+	1	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	exon	7459494	7459702	.	+	.	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	intron	7459703	7459798	.	+	.	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	CDS	7459799	7460268	1	+	2	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	exon	7459799	7460268	.	+	.	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
Phchi.S4	AUGUSTUS	stop_codon	7460269	7460271	.	+	0	transcript_id "Phchi.S4G123100.t1"; gene_id "Phchi.S4G123100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13137.t1 is derived from g11602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4327064	4327576	.	-	.	Phchi.S3G045600
Phchi.S3	AUGUSTUS	transcript	4327064	4327576	.	-	.	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	stop_codon	4327061	4327063	.	-	0	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	CDS	4327064	4327075	1	-	0	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	exon	4327064	4327075	.	-	.	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	intron	4327076	4327173	.	-	.	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	CDS	4327174	4327363	1	-	1	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	exon	4327174	4327363	.	-	.	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	intron	4327364	4327460	.	-	.	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	CDS	4327461	4327576	0.99	-	0	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	exon	4327461	4327576	.	-	.	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
Phchi.S3	AUGUSTUS	start_codon	4327574	4327576	.	-	0	transcript_id "Phchi.S3G045600.t1"; gene_id "Phchi.S3G045600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4661.t1 is derived from g1831.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11676732	11680416	.	+	.	Phchi.S1G182000
Phchi.S1	AUGUSTUS	transcript	11676732	11680416	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	start_codon	11676732	11676734	.	+	0	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11676732	11676820	0.98	+	0	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11676732	11676820	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11676821	11676920	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11676921	11677073	1	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11676921	11677073	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677074	11677167	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677168	11677221	0.9	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677168	11677221	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677222	11677316	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677317	11677434	0.99	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677317	11677434	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677435	11677533	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677534	11677657	0.63	+	0	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677534	11677657	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677658	11677858	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677859	11678297	0.79	+	2	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677859	11678297	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678298	11678424	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678425	11678526	1	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678425	11678526	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678527	11678701	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678702	11678774	1	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678702	11678774	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678775	11678844	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678845	11678887	1	+	0	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678845	11678887	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678888	11679044	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679045	11679117	1	+	2	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679045	11679117	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679118	11679250	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679251	11679319	0.97	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679251	11679319	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679320	11679421	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679422	11679499	0.89	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679422	11679499	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679500	11679591	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679592	11679764	0.83	+	1	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679592	11679764	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679765	11679887	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679888	11679934	0.81	+	2	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679888	11679934	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679935	11680152	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11680153	11680416	0.31	+	0	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11680153	11680416	.	+	.	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	stop_codon	11680417	11680419	.	+	0	transcript_id "Phchi.S1G182000.t1"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	transcript	11676732	11680416	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	start_codon	11676732	11676734	.	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11676732	11676820	0.99	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11676732	11676820	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11676821	11676920	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11676921	11677073	1	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11676921	11677073	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677074	11677167	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677168	11677221	0.94	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677168	11677221	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677222	11677316	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677317	11677434	0.97	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677317	11677434	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677435	11677533	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677534	11677657	0.65	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677534	11677657	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677658	11677858	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677859	11678016	0.66	+	2	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677859	11678016	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678017	11678146	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678147	11678297	0.7	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678147	11678297	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678298	11678444	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678445	11678526	0.79	+	2	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678445	11678526	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678527	11678701	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678702	11678774	1	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678702	11678774	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678775	11678844	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678845	11678887	1	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678845	11678887	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678888	11679044	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679045	11679117	1	+	2	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679045	11679117	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679118	11679250	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679251	11679319	0.96	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679251	11679319	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679320	11679421	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679422	11679499	0.93	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679422	11679499	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679500	11679591	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679592	11679764	0.84	+	1	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679592	11679764	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679765	11679887	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679888	11679934	0.79	+	2	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679888	11679934	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679935	11680152	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11680153	11680416	0.34	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11680153	11680416	.	+	.	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	stop_codon	11680417	11680419	.	+	0	transcript_id "Phchi.S1G182000.t2"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	transcript	11676732	11680416	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	start_codon	11676732	11676734	.	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11676732	11676820	1	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11676732	11676820	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11676821	11676920	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11676921	11677041	0.37	+	1	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11676921	11677041	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677042	11677167	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677168	11677205	0.36	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677168	11677205	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677206	11677316	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677317	11677434	0.99	+	1	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677317	11677434	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677435	11677533	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677534	11677657	0.71	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677534	11677657	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11677658	11677858	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11677859	11678016	0.62	+	2	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11677859	11678016	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678017	11678146	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678147	11678297	0.69	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678147	11678297	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678298	11678444	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678445	11678526	0.77	+	2	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678445	11678526	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678527	11678701	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678702	11678774	1	+	1	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678702	11678774	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678775	11678844	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11678845	11678887	1	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11678845	11678887	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11678888	11679044	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679045	11679117	1	+	2	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679045	11679117	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679118	11679250	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679251	11679319	0.99	+	1	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679251	11679319	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679320	11679421	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679422	11679499	0.83	+	1	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679422	11679499	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679500	11679591	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679592	11679764	0.74	+	1	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679592	11679764	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679765	11679887	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11679888	11679934	0.74	+	2	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11679888	11679934	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	intron	11679935	11680152	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	CDS	11680153	11680416	0.31	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	exon	11680153	11680416	.	+	.	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
Phchi.S1	AUGUSTUS	stop_codon	11680417	11680419	.	+	0	transcript_id "Phchi.S1G182000.t3"; gene_id "Phchi.S1G182000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4261.t1 is derived from g1430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9213472	9215121	.	-	.	Phchi.S1G142000
Phchi.S1	AUGUSTUS	transcript	9213472	9215121	.	-	.	transcript_id "Phchi.S1G142000.t1"; gene_id "Phchi.S1G142000"
Phchi.S1	AUGUSTUS	stop_codon	9213469	9213471	.	-	0	transcript_id "Phchi.S1G142000.t1"; gene_id "Phchi.S1G142000"
Phchi.S1	AUGUSTUS	CDS	9213472	9215121	1	-	0	transcript_id "Phchi.S1G142000.t1"; gene_id "Phchi.S1G142000"
Phchi.S1	AUGUSTUS	exon	9213472	9215121	.	-	.	transcript_id "Phchi.S1G142000.t1"; gene_id "Phchi.S1G142000"
Phchi.S1	AUGUSTUS	start_codon	9215119	9215121	.	-	0	transcript_id "Phchi.S1G142000.t1"; gene_id "Phchi.S1G142000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15211.t1 is derived from g13679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17679739	17680824	.	+	.	Phchi.S3G253000
Phchi.S3	AUGUSTUS	transcript	17679739	17680824	.	+	.	transcript_id "Phchi.S3G253000.t1"; gene_id "Phchi.S3G253000"
Phchi.S3	AUGUSTUS	start_codon	17679739	17679741	.	+	0	transcript_id "Phchi.S3G253000.t1"; gene_id "Phchi.S3G253000"
Phchi.S3	AUGUSTUS	CDS	17679739	17680824	0.3	+	0	transcript_id "Phchi.S3G253000.t1"; gene_id "Phchi.S3G253000"
Phchi.S3	AUGUSTUS	exon	17679739	17680824	.	+	.	transcript_id "Phchi.S3G253000.t1"; gene_id "Phchi.S3G253000"
Phchi.S3	AUGUSTUS	stop_codon	17680825	17680827	.	+	0	transcript_id "Phchi.S3G253000.t1"; gene_id "Phchi.S3G253000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15497.t1 is derived from g13966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19515040	19516172	.	+	.	Phchi.S3G281600
Phchi.S3	AUGUSTUS	transcript	19515040	19516172	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	start_codon	19515040	19515042	.	+	0	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	CDS	19515040	19515221	0.99	+	0	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	exon	19515040	19515221	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	intron	19515222	19515387	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	CDS	19515388	19515662	0.99	+	1	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	exon	19515388	19515662	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	intron	19515663	19515801	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	CDS	19515802	19515857	1	+	2	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	exon	19515802	19515857	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	intron	19515858	19515980	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	CDS	19515981	19516172	1	+	0	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	exon	19515981	19516172	.	+	.	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
Phchi.S3	AUGUSTUS	stop_codon	19516173	19516175	.	+	0	transcript_id "Phchi.S3G281600.t1"; gene_id "Phchi.S3G281600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8928.t1 is derived from g6103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38710859	38713996	.	-	.	Phchi.S1G608700
Phchi.S1	AUGUSTUS	transcript	38710859	38713996	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	stop_codon	38710856	38710858	.	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38710859	38710939	0.98	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38710859	38710939	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38710940	38711022	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38711023	38711142	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38711023	38711142	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38711143	38711251	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38711252	38711281	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38711252	38711281	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38711282	38711411	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38711412	38711456	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38711412	38711456	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38711457	38711635	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38711636	38711680	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38711636	38711680	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38711681	38711785	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38711786	38712025	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38711786	38712025	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38712026	38712383	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38712384	38712458	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38712384	38712458	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38712459	38712775	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38712776	38712897	1	-	2	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38712776	38712897	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38712898	38713016	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38713017	38713155	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38713017	38713155	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38713156	38713251	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38713252	38713281	1	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38713252	38713281	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38713282	38713389	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38713390	38713558	0.52	-	1	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38713390	38713558	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38713559	38713628	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38713629	38713695	0.57	-	2	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38713629	38713695	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	intron	38713696	38713779	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38713780	38713996	0.98	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38713780	38713996	.	-	.	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	start_codon	38713994	38713996	.	-	0	transcript_id "Phchi.S1G608700.t1"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	transcript	38713784	38713996	.	-	.	transcript_id "Phchi.S1G608700.t2"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	stop_codon	38713693	38713695	.	-	0	transcript_id "Phchi.S1G608700.t2"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	CDS	38713784	38713996	0.98	-	0	transcript_id "Phchi.S1G608700.t2"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	exon	38713784	38713996	.	-	.	transcript_id "Phchi.S1G608700.t2"; gene_id "Phchi.S1G608700"
Phchi.S1	AUGUSTUS	start_codon	38713994	38713996	.	-	0	transcript_id "Phchi.S1G608700.t2"; gene_id "Phchi.S1G608700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11551.t1 is derived from g15602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7006194	7010082	.	-	.	Phchi.S4G113300
Phchi.S4	AUGUSTUS	transcript	7006194	7010082	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	stop_codon	7006191	7006193	.	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006194	7006454	1	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006194	7006454	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006455	7006551	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006552	7006629	1	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006552	7006629	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006630	7006716	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006717	7006769	0.92	-	2	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006717	7006769	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006770	7006867	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006868	7006910	0.69	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006868	7006910	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006911	7007003	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007004	7007216	0.26	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007004	7007216	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007217	7007317	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007318	7007423	0.93	-	1	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007318	7007423	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007424	7007544	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007545	7007633	1	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007545	7007633	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007634	7007722	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007723	7007795	1	-	1	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007723	7007795	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007796	7007888	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007889	7008028	1	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007889	7008028	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008029	7008134	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008135	7008256	0.99	-	2	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008135	7008256	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008257	7008371	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008372	7008459	1	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008372	7008459	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008460	7008601	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008602	7008817	1	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008602	7008817	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008818	7008914	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008915	7009115	0.78	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008915	7009115	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009116	7009326	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009327	7009370	0.62	-	2	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009327	7009370	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009371	7009464	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009465	7009594	0.94	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009465	7009594	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009595	7009721	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009722	7009841	0.89	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009722	7009841	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009842	7009920	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009921	7010082	0.54	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009921	7010082	.	-	.	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	start_codon	7010080	7010082	.	-	0	transcript_id "Phchi.S4G113300.t1"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	transcript	7006194	7010082	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	stop_codon	7006191	7006193	.	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006194	7006454	1	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006194	7006454	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006455	7006551	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006552	7006629	1	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006552	7006629	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006630	7006716	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006717	7006769	0.86	-	2	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006717	7006769	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006770	7006867	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7006868	7006910	0.77	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7006868	7006910	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7006911	7007003	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007004	7007216	0.41	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007004	7007216	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007217	7007317	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007318	7007423	0.9	-	1	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007318	7007423	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007424	7007544	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007545	7007633	1	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007545	7007633	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007634	7007722	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007723	7007795	1	-	1	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007723	7007795	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7007796	7007888	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7007889	7008028	1	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7007889	7008028	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008029	7008134	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008135	7008256	0.99	-	2	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008135	7008256	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008257	7008371	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008372	7008459	1	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008372	7008459	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008460	7008601	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008602	7008817	1	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008602	7008817	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7008818	7008914	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7008915	7009115	0.64	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7008915	7009115	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009116	7009326	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009327	7009370	0.48	-	2	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009327	7009370	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009371	7009470	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009471	7009594	0.84	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009471	7009594	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009595	7009721	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009722	7009841	0.89	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009722	7009841	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	intron	7009842	7009920	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	CDS	7009921	7010082	0.53	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	exon	7009921	7010082	.	-	.	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
Phchi.S4	AUGUSTUS	start_codon	7010080	7010082	.	-	0	transcript_id "Phchi.S4G113300.t2"; gene_id "Phchi.S4G113300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4269.t1 is derived from g1438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9326480	9328001	.	-	.	Phchi.S1G142800
Phchi.S1	AUGUSTUS	transcript	9326480	9328001	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	stop_codon	9326477	9326479	.	-	0	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	CDS	9326480	9327076	0.79	-	0	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	exon	9326480	9327076	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	intron	9327077	9327162	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	CDS	9327163	9327302	1	-	2	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	exon	9327163	9327302	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	intron	9327303	9327426	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	CDS	9327427	9327512	1	-	1	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	exon	9327427	9327512	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	intron	9327513	9327589	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	CDS	9327590	9327726	1	-	0	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	exon	9327590	9327726	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	intron	9327727	9327836	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	CDS	9327837	9328001	0.76	-	0	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	exon	9327837	9328001	.	-	.	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
Phchi.S1	AUGUSTUS	start_codon	9327999	9328001	.	-	0	transcript_id "Phchi.S1G142800.t1"; gene_id "Phchi.S1G142800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4699.t1 is derived from g1869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12347887	12348870	.	+	.	Phchi.S1G185800
Phchi.S1	AUGUSTUS	transcript	12347887	12348870	.	+	.	transcript_id "Phchi.S1G185800.t1"; gene_id "Phchi.S1G185800"
Phchi.S1	AUGUSTUS	start_codon	12347887	12347889	.	+	0	transcript_id "Phchi.S1G185800.t1"; gene_id "Phchi.S1G185800"
Phchi.S1	AUGUSTUS	CDS	12347887	12348870	0.99	+	0	transcript_id "Phchi.S1G185800.t1"; gene_id "Phchi.S1G185800"
Phchi.S1	AUGUSTUS	exon	12347887	12348870	.	+	.	transcript_id "Phchi.S1G185800.t1"; gene_id "Phchi.S1G185800"
Phchi.S1	AUGUSTUS	stop_codon	12348871	12348873	.	+	0	transcript_id "Phchi.S1G185800.t1"; gene_id "Phchi.S1G185800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9849.t1 is derived from g7025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44072687	44074730	.	-	.	Phchi.S1G700800
Phchi.S1	AUGUSTUS	transcript	44072687	44074730	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	stop_codon	44072684	44072686	.	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44072687	44072710	1	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44072687	44072710	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44072711	44072959	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44072960	44073061	1	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44072960	44073061	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44073062	44073161	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44073162	44073211	1	-	2	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44073162	44073211	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44073212	44073300	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44073301	44073418	1	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44073301	44073418	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44073419	44073489	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44073490	44073532	1	-	1	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44073490	44073532	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44073533	44073645	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44073646	44073770	1	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44073646	44073770	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44073771	44073894	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44073895	44073984	1	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44073895	44073984	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44073985	44074120	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44074121	44074253	1	-	1	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44074121	44074253	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	intron	44074254	44074578	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	CDS	44074579	44074730	1	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	exon	44074579	44074730	.	-	.	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
Phchi.S1	AUGUSTUS	start_codon	44074728	44074730	.	-	0	transcript_id "Phchi.S1G700800.t1"; gene_id "Phchi.S1G700800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8066.t1 is derived from g5241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32765775	32767348	.	+	.	Phchi.S1G522500
Phchi.S1	AUGUSTUS	transcript	32765775	32767348	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	start_codon	32765775	32765777	.	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32765775	32766056	0.72	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32765775	32766056	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32766057	32766185	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32766186	32766257	1	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32766186	32766257	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32766258	32766372	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32766373	32766423	1	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32766373	32766423	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32766424	32766557	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32766558	32766602	1	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32766558	32766602	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32766603	32766725	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32766726	32766818	1	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32766726	32766818	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32766819	32766960	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32766961	32767062	0.84	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32766961	32767062	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32767063	32767148	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32767149	32767224	0.8	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32767149	32767224	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	intron	32767225	32767346	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	CDS	32767347	32767348	0.84	+	2	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	exon	32767347	32767348	.	+	.	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
Phchi.S1	AUGUSTUS	stop_codon	32767349	32767351	.	+	0	transcript_id "Phchi.S1G522500.t1"; gene_id "Phchi.S1G522500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11311.t1 is derived from g15361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5318409	5319882	.	+	.	Phchi.S4G089300
Phchi.S4	AUGUSTUS	transcript	5318409	5319882	.	+	.	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	start_codon	5318409	5318411	.	+	0	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	CDS	5318409	5318454	0.91	+	0	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	exon	5318409	5318454	.	+	.	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	intron	5318455	5318528	.	+	.	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	CDS	5318529	5318611	0.41	+	2	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	exon	5318529	5318611	.	+	.	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	intron	5318612	5318820	.	+	.	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	CDS	5318821	5319882	0.31	+	0	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	exon	5318821	5319882	.	+	.	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
Phchi.S4	AUGUSTUS	stop_codon	5319883	5319885	.	+	0	transcript_id "Phchi.S4G089300.t1"; gene_id "Phchi.S4G089300"
# This transcript jg15693.t2 is derived from g14162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15694.t1 is derived from g14163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20729564	20730136	.	+	.	Phchi.S3G301300
Phchi.S3	AUGUSTUS	transcript	20729564	20730136	.	+	.	transcript_id "Phchi.S3G301300.t1"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	start_codon	20729564	20729566	.	+	0	transcript_id "Phchi.S3G301300.t1"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	CDS	20729564	20730136	1	+	0	transcript_id "Phchi.S3G301300.t1"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	exon	20729564	20730136	.	+	.	transcript_id "Phchi.S3G301300.t1"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	stop_codon	20730137	20730139	.	+	0	transcript_id "Phchi.S3G301300.t1"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	transcript	20729675	20730136	.	+	.	transcript_id "Phchi.S3G301300.t2"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	start_codon	20729675	20729677	.	+	0	transcript_id "Phchi.S3G301300.t2"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	CDS	20729675	20730136	0.91	+	0	transcript_id "Phchi.S3G301300.t2"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	exon	20729675	20730136	.	+	.	transcript_id "Phchi.S3G301300.t2"; gene_id "Phchi.S3G301300"
Phchi.S3	AUGUSTUS	stop_codon	20730137	20730139	.	+	0	transcript_id "Phchi.S3G301300.t2"; gene_id "Phchi.S3G301300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11886.t1 is derived from g15938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9005290	9007276	.	+	.	Phchi.S4G146800
Phchi.S4	AUGUSTUS	transcript	9005290	9007276	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	start_codon	9005290	9005292	.	+	0	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9005290	9005441	0.99	+	0	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9005290	9005441	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9005442	9005772	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9005773	9005782	1	+	1	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9005773	9005782	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9005783	9005868	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9005869	9005892	1	+	0	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9005869	9005892	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9005893	9006295	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9006296	9006380	1	+	0	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9006296	9006380	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9006381	9006530	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9006531	9006623	1	+	2	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9006531	9006623	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9006624	9006818	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9006819	9006907	1	+	2	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9006819	9006907	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9006908	9007070	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9007071	9007156	1	+	0	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9007071	9007156	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	intron	9007157	9007233	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	CDS	9007234	9007276	1	+	1	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	exon	9007234	9007276	.	+	.	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
Phchi.S4	AUGUSTUS	stop_codon	9007277	9007279	.	+	0	transcript_id "Phchi.S4G146800.t1"; gene_id "Phchi.S4G146800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9531.t1 is derived from g6707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42330010	42332462	.	-	.	Phchi.S1G669000
Phchi.S1	AUGUSTUS	transcript	42330010	42332462	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	stop_codon	42330007	42330009	.	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42330010	42330136	0.99	-	1	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42330010	42330136	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42330137	42330315	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42330316	42330413	1	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42330316	42330413	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42330414	42330549	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42330550	42330630	1	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42330550	42330630	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42330631	42330715	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42330716	42330835	1	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42330716	42330835	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42330836	42330935	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42330936	42331082	1	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42330936	42331082	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42331083	42331232	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42331233	42331334	1	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42331233	42331334	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42331335	42331486	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42331487	42331576	1	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42331487	42331576	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42331577	42331715	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42331716	42331787	0.76	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42331716	42331787	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	intron	42331788	42331928	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	CDS	42331929	42332462	0.61	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	exon	42331929	42332462	.	-	.	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
Phchi.S1	AUGUSTUS	start_codon	42332460	42332462	.	-	0	transcript_id "Phchi.S1G669000.t1"; gene_id "Phchi.S1G669000"
# This transcript jg7337.t2 is derived from g4509.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7338.t1 is derived from g4510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28585847	28592236	.	+	.	Phchi.S1G449700
Phchi.S1	AUGUSTUS	transcript	28585847	28592236	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	start_codon	28585847	28585849	.	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28585847	28586054	0.29	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28585847	28586054	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28586055	28586180	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28586181	28586293	0.38	+	2	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28586181	28586293	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28586294	28586547	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28586548	28587026	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28586548	28587026	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28587027	28587175	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28587176	28587839	0.99	+	1	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28587176	28587839	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28587840	28588051	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28588052	28588138	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28588052	28588138	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28588139	28588328	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28588329	28588375	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28588329	28588375	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28588376	28588614	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28588615	28588724	1	+	1	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28588615	28588724	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28588725	28588801	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28588802	28588902	1	+	2	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28588802	28588902	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28588903	28589029	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28589030	28589122	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28589030	28589122	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28589123	28589262	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28589263	28589346	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28589263	28589346	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28589347	28589430	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28589431	28589514	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28589431	28589514	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28589515	28589705	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28589706	28589774	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28589706	28589774	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28589775	28589891	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28589892	28589951	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28589892	28589951	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28589952	28590047	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28590048	28590119	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28590048	28590119	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28590120	28590319	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28590320	28590427	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28590320	28590427	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28590428	28590500	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28590501	28590568	0.79	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28590501	28590568	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28590569	28590666	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28590667	28590698	0.37	+	1	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28590667	28590698	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28590699	28590742	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28590743	28590749	0.37	+	2	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28590743	28590749	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28590750	28590838	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28590839	28590944	1	+	1	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28590839	28590944	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28590945	28591020	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28591021	28591101	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28591021	28591101	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28591102	28591227	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28591228	28591287	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28591228	28591287	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28591288	28591396	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28591397	28591492	1	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28591397	28591492	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28591493	28591589	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28591590	28591839	0.99	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28591590	28591839	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	intron	28591840	28591925	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	CDS	28591926	28592236	0.95	+	2	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	exon	28591926	28592236	.	+	.	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
Phchi.S1	AUGUSTUS	stop_codon	28592237	28592239	.	+	0	transcript_id "Phchi.S1G449700.t1"; gene_id "Phchi.S1G449700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2954.t1 is derived from g123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	752477	754524	.	+	.	Phchi.S1G011300
Phchi.S1	AUGUSTUS	transcript	752477	754524	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	start_codon	752477	752479	.	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	752477	752501	1	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	752477	752501	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	752502	752594	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	752595	752695	1	+	2	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	752595	752695	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	752696	752965	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	752966	753106	1	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	752966	753106	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	753107	753212	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	753213	753279	0.99	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	753213	753279	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	753280	753683	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	753684	753841	0.99	+	2	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	753684	753841	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	753842	753948	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	753949	754050	1	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	753949	754050	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	754051	754137	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	754138	754272	1	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	754138	754272	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	intron	754273	754350	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	CDS	754351	754524	1	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	exon	754351	754524	.	+	.	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
Phchi.S1	AUGUSTUS	stop_codon	754525	754527	.	+	0	transcript_id "Phchi.S1G011300.t1"; gene_id "Phchi.S1G011300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7489.t1 is derived from g4662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29622802	29624680	.	-	.	Phchi.S1G464800
Phchi.S1	AUGUSTUS	transcript	29622802	29624680	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	stop_codon	29622799	29622801	.	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29622802	29622824	0.38	-	2	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29622802	29622824	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29622825	29622950	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29622951	29622962	0.37	-	2	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29622951	29622962	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29622963	29623093	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29623094	29623255	0.49	-	2	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29623094	29623255	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29623256	29623342	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29623343	29623418	1	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29623343	29623418	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29623419	29623508	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29623509	29623586	0.57	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29623509	29623586	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29623587	29623688	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29623689	29623742	0.58	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29623689	29623742	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29623743	29623853	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29623854	29623919	1	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29623854	29623919	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29623920	29624024	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29624025	29624159	1	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29624025	29624159	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29624160	29624291	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29624292	29624441	1	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29624292	29624441	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	intron	29624442	29624587	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	CDS	29624588	29624680	0.71	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	exon	29624588	29624680	.	-	.	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
Phchi.S1	AUGUSTUS	start_codon	29624678	29624680	.	-	0	transcript_id "Phchi.S1G464800.t1"; gene_id "Phchi.S1G464800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8291.t1 is derived from g5466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35114495	35116198	.	+	.	Phchi.S1G545000
Phchi.S1	AUGUSTUS	transcript	35114495	35116198	.	+	.	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	start_codon	35114495	35114497	.	+	0	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	CDS	35114495	35115175	0.58	+	0	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	exon	35114495	35115175	.	+	.	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	intron	35115176	35115274	.	+	.	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	CDS	35115275	35116198	0.99	+	0	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	exon	35115275	35116198	.	+	.	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
Phchi.S1	AUGUSTUS	stop_codon	35116199	35116201	.	+	0	transcript_id "Phchi.S1G545000.t1"; gene_id "Phchi.S1G545000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3172.t1 is derived from g341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2096573	2098355	.	-	.	Phchi.S1G033100
Phchi.S1	AUGUSTUS	transcript	2096573	2098355	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	stop_codon	2096570	2096572	.	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2096573	2096848	0.98	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2096573	2096848	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	intron	2096849	2096937	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2096938	2097207	1	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2096938	2097207	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	intron	2097208	2097375	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2097376	2097466	1	-	1	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2097376	2097466	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	intron	2097467	2097556	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2097557	2097666	1	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2097557	2097666	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	intron	2097667	2097760	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2097761	2097911	0.4	-	1	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2097761	2097911	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	intron	2097912	2097985	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2097986	2098029	0.4	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2097986	2098029	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	intron	2098030	2098169	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	CDS	2098170	2098355	0.65	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	exon	2098170	2098355	.	-	.	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
Phchi.S1	AUGUSTUS	start_codon	2098353	2098355	.	-	0	transcript_id "Phchi.S1G033100.t1"; gene_id "Phchi.S1G033100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5719.t1 is derived from g2889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18507126	18508695	.	+	.	Phchi.S1G287800
Phchi.S1	AUGUSTUS	transcript	18507126	18508695	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	start_codon	18507126	18507128	.	+	0	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	CDS	18507126	18507221	0.41	+	0	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	exon	18507126	18507221	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	intron	18507222	18507321	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	CDS	18507322	18507412	0.75	+	0	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	exon	18507322	18507412	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	intron	18507413	18507557	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	CDS	18507558	18507682	0.94	+	2	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	exon	18507558	18507682	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	intron	18507683	18508401	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	CDS	18508402	18508695	0.93	+	0	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	exon	18508402	18508695	.	+	.	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
Phchi.S1	AUGUSTUS	stop_codon	18508696	18508698	.	+	0	transcript_id "Phchi.S1G287800.t1"; gene_id "Phchi.S1G287800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15599.t1 is derived from g14068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20198828	20199457	.	+	.	Phchi.S3G291800
Phchi.S3	AUGUSTUS	transcript	20198828	20199457	.	+	.	transcript_id "Phchi.S3G291800.t1"; gene_id "Phchi.S3G291800"
Phchi.S3	AUGUSTUS	start_codon	20198828	20198830	.	+	0	transcript_id "Phchi.S3G291800.t1"; gene_id "Phchi.S3G291800"
Phchi.S3	AUGUSTUS	CDS	20198828	20199457	0.76	+	0	transcript_id "Phchi.S3G291800.t1"; gene_id "Phchi.S3G291800"
Phchi.S3	AUGUSTUS	exon	20198828	20199457	.	+	.	transcript_id "Phchi.S3G291800.t1"; gene_id "Phchi.S3G291800"
Phchi.S3	AUGUSTUS	stop_codon	20199458	20199460	.	+	0	transcript_id "Phchi.S3G291800.t1"; gene_id "Phchi.S3G291800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9711.t1 is derived from g6887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43370421	43375320	.	+	.	Phchi.S1G687000
Phchi.S1	AUGUSTUS	transcript	43370421	43375320	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	start_codon	43370421	43370423	.	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43370421	43371527	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43370421	43371527	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43371528	43371626	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43371627	43371758	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43371627	43371758	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43371759	43371900	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43371901	43372128	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43371901	43372128	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43372129	43372284	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43372285	43372410	0.98	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43372285	43372410	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43372411	43372511	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43372512	43372574	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43372512	43372574	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43372575	43372653	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43372654	43372742	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43372654	43372742	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43372743	43372868	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43372869	43373100	1	+	1	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43372869	43373100	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43373101	43373198	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43373199	43373343	0.8	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43373199	43373343	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43373344	43373435	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43373436	43373607	0.82	+	2	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43373436	43373607	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43373608	43373697	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43373698	43373785	1	+	1	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43373698	43373785	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43373786	43373884	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43373885	43373951	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43373885	43373951	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43373952	43374067	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43374068	43374354	1	+	2	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43374068	43374354	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43374355	43374451	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43374452	43374517	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43374452	43374517	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43374518	43374594	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43374595	43374716	1	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43374595	43374716	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43374717	43374809	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43374810	43374966	0.79	+	1	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43374810	43374966	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	intron	43374967	43375071	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	CDS	43375072	43375320	0.41	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	exon	43375072	43375320	.	+	.	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
Phchi.S1	AUGUSTUS	stop_codon	43375321	43375323	.	+	0	transcript_id "Phchi.S1G687000.t1"; gene_id "Phchi.S1G687000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13654.t1 is derived from g12121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8029860	8030903	.	+	.	Phchi.S3G097300
Phchi.S3	AUGUSTUS	transcript	8029860	8030903	.	+	.	transcript_id "Phchi.S3G097300.t1"; gene_id "Phchi.S3G097300"
Phchi.S3	AUGUSTUS	start_codon	8029860	8029862	.	+	0	transcript_id "Phchi.S3G097300.t1"; gene_id "Phchi.S3G097300"
Phchi.S3	AUGUSTUS	CDS	8029860	8030903	1	+	0	transcript_id "Phchi.S3G097300.t1"; gene_id "Phchi.S3G097300"
Phchi.S3	AUGUSTUS	exon	8029860	8030903	.	+	.	transcript_id "Phchi.S3G097300.t1"; gene_id "Phchi.S3G097300"
Phchi.S3	AUGUSTUS	stop_codon	8030904	8030906	.	+	0	transcript_id "Phchi.S3G097300.t1"; gene_id "Phchi.S3G097300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13656.t1 is derived from g12123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8037195	8039379	.	+	.	Phchi.S3G097500
Phchi.S3	AUGUSTUS	transcript	8037195	8039379	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	start_codon	8037195	8037197	.	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8037195	8037246	1	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8037195	8037246	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8037247	8037466	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8037467	8037603	1	+	2	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8037467	8037603	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8037604	8037734	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8037735	8037781	1	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8037735	8037781	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8037782	8037876	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8037877	8038202	0.9	+	1	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8037877	8038202	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8038203	8038286	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8038287	8038369	1	+	2	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8038287	8038369	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8038370	8038475	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8038476	8038551	1	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8038476	8038551	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8038552	8038684	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8038685	8038746	1	+	2	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8038685	8038746	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8038747	8038825	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8038826	8038921	1	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8038826	8038921	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8038922	8039018	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8039019	8039180	1	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8039019	8039180	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	intron	8039181	8039271	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	CDS	8039272	8039379	0.99	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	exon	8039272	8039379	.	+	.	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
Phchi.S3	AUGUSTUS	stop_codon	8039380	8039382	.	+	0	transcript_id "Phchi.S3G097500.t1"; gene_id "Phchi.S3G097500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8264.t1 is derived from g5439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35006322	35007686	.	+	.	Phchi.S1G542300
Phchi.S1	AUGUSTUS	transcript	35006322	35007686	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	start_codon	35006322	35006324	.	+	0	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	CDS	35006322	35006719	0.74	+	0	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	exon	35006322	35006719	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	intron	35006720	35006799	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	CDS	35006800	35007063	0.48	+	1	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	exon	35006800	35007063	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	intron	35007064	35007228	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	CDS	35007229	35007299	0.83	+	1	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	exon	35007229	35007299	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	intron	35007300	35007411	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	CDS	35007412	35007686	0.91	+	2	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	exon	35007412	35007686	.	+	.	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
Phchi.S1	AUGUSTUS	stop_codon	35007687	35007689	.	+	0	transcript_id "Phchi.S1G542300.t1"; gene_id "Phchi.S1G542300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8719.t1 is derived from g5894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37667226	37669883	.	-	.	Phchi.S1G587800
Phchi.S1	AUGUSTUS	transcript	37667226	37669883	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	stop_codon	37667223	37667225	.	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37667226	37667336	0.97	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37667226	37667336	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37667337	37667441	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37667442	37667572	0.97	-	2	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37667442	37667572	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37667573	37667663	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37667664	37667795	0.67	-	2	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37667664	37667795	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37667796	37668023	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37668024	37668066	0.68	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37668024	37668066	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37668067	37668150	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37668151	37668306	1	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37668151	37668306	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37668307	37668421	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37668422	37668533	0.95	-	1	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37668422	37668533	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37668534	37668613	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37668614	37668723	1	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37668614	37668723	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37668724	37668813	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37668814	37669023	1	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37668814	37669023	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37669024	37669145	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37669146	37669382	0.99	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37669146	37669382	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	intron	37669383	37669463	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	CDS	37669464	37669883	0.83	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	exon	37669464	37669883	.	-	.	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
Phchi.S1	AUGUSTUS	start_codon	37669881	37669883	.	-	0	transcript_id "Phchi.S1G587800.t1"; gene_id "Phchi.S1G587800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14782.t1 is derived from g13250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14674494	14675021	.	+	.	Phchi.S3G210100
Phchi.S3	AUGUSTUS	transcript	14674494	14675021	.	+	.	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	start_codon	14674494	14674496	.	+	0	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	CDS	14674494	14674581	0.54	+	0	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	exon	14674494	14674581	.	+	.	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	intron	14674582	14674667	.	+	.	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	CDS	14674668	14674767	0.98	+	2	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	exon	14674668	14674767	.	+	.	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	intron	14674768	14674873	.	+	.	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	CDS	14674874	14675021	0.97	+	1	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	exon	14674874	14675021	.	+	.	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
Phchi.S3	AUGUSTUS	stop_codon	14675022	14675024	.	+	0	transcript_id "Phchi.S3G210100.t1"; gene_id "Phchi.S3G210100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5604.t1 is derived from g2774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17842183	17842836	.	-	.	Phchi.S1G276300
Phchi.S1	AUGUSTUS	transcript	17842183	17842836	.	-	.	transcript_id "Phchi.S1G276300.t1"; gene_id "Phchi.S1G276300"
Phchi.S1	AUGUSTUS	stop_codon	17842180	17842182	.	-	0	transcript_id "Phchi.S1G276300.t1"; gene_id "Phchi.S1G276300"
Phchi.S1	AUGUSTUS	CDS	17842183	17842836	0.9	-	0	transcript_id "Phchi.S1G276300.t1"; gene_id "Phchi.S1G276300"
Phchi.S1	AUGUSTUS	exon	17842183	17842836	.	-	.	transcript_id "Phchi.S1G276300.t1"; gene_id "Phchi.S1G276300"
Phchi.S1	AUGUSTUS	start_codon	17842834	17842836	.	-	0	transcript_id "Phchi.S1G276300.t1"; gene_id "Phchi.S1G276300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10476.t1 is derived from g14525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	568263	568690	.	+	.	Phchi.S4G005800
Phchi.S4	AUGUSTUS	transcript	568263	568690	.	+	.	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	start_codon	568263	568265	.	+	0	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	CDS	568263	568575	1	+	0	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	exon	568263	568575	.	+	.	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	intron	568576	568670	.	+	.	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	CDS	568671	568690	0.89	+	2	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	exon	568671	568690	.	+	.	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
Phchi.S4	AUGUSTUS	stop_codon	568691	568693	.	+	0	transcript_id "Phchi.S4G005800.t1"; gene_id "Phchi.S4G005800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15684.t1 is derived from g14153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20640274	20640693	.	-	.	Phchi.S3G300300
Phchi.S3	AUGUSTUS	transcript	20640274	20640693	.	-	.	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	stop_codon	20640271	20640273	.	-	0	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	CDS	20640274	20640372	0.97	-	0	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	exon	20640274	20640372	.	-	.	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	intron	20640373	20640462	.	-	.	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	CDS	20640463	20640693	0.99	-	0	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	exon	20640463	20640693	.	-	.	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
Phchi.S3	AUGUSTUS	start_codon	20640691	20640693	.	-	0	transcript_id "Phchi.S3G300300.t1"; gene_id "Phchi.S3G300300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14274.t1 is derived from g12741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11880249	11881201	.	-	.	Phchi.S3G159300
Phchi.S3	AUGUSTUS	transcript	11880249	11881201	.	-	.	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	stop_codon	11880246	11880248	.	-	0	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	CDS	11880249	11880557	0.81	-	0	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	exon	11880249	11880557	.	-	.	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	intron	11880558	11880637	.	-	.	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	CDS	11880638	11880778	0.95	-	0	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	exon	11880638	11880778	.	-	.	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	intron	11880779	11880883	.	-	.	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	CDS	11880884	11881201	0.59	-	0	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	exon	11880884	11881201	.	-	.	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
Phchi.S3	AUGUSTUS	start_codon	11881199	11881201	.	-	0	transcript_id "Phchi.S3G159300.t1"; gene_id "Phchi.S3G159300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6282.t1 is derived from g3454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22075570	22077348	.	+	.	Phchi.S1G344100
Phchi.S1	AUGUSTUS	transcript	22075570	22077348	.	+	.	transcript_id "Phchi.S1G344100.t1"; gene_id "Phchi.S1G344100"
Phchi.S1	AUGUSTUS	start_codon	22075570	22075572	.	+	0	transcript_id "Phchi.S1G344100.t1"; gene_id "Phchi.S1G344100"
Phchi.S1	AUGUSTUS	CDS	22075570	22077348	0.97	+	0	transcript_id "Phchi.S1G344100.t1"; gene_id "Phchi.S1G344100"
Phchi.S1	AUGUSTUS	exon	22075570	22077348	.	+	.	transcript_id "Phchi.S1G344100.t1"; gene_id "Phchi.S1G344100"
Phchi.S1	AUGUSTUS	stop_codon	22077349	22077351	.	+	0	transcript_id "Phchi.S1G344100.t1"; gene_id "Phchi.S1G344100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14050.t1 is derived from g12517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10486794	10487129	.	-	.	Phchi.S3G136900
Phchi.S3	AUGUSTUS	transcript	10486794	10487129	.	-	.	transcript_id "Phchi.S3G136900.t1"; gene_id "Phchi.S3G136900"
Phchi.S3	AUGUSTUS	stop_codon	10486791	10486793	.	-	0	transcript_id "Phchi.S3G136900.t1"; gene_id "Phchi.S3G136900"
Phchi.S3	AUGUSTUS	CDS	10486794	10487129	0.81	-	0	transcript_id "Phchi.S3G136900.t1"; gene_id "Phchi.S3G136900"
Phchi.S3	AUGUSTUS	exon	10486794	10487129	.	-	.	transcript_id "Phchi.S3G136900.t1"; gene_id "Phchi.S3G136900"
Phchi.S3	AUGUSTUS	start_codon	10487127	10487129	.	-	0	transcript_id "Phchi.S3G136900.t1"; gene_id "Phchi.S3G136900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1750.t1 is derived from g8670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2875806	2877548	.	+	.	Phchi.S5G035900
Phchi.S5	AUGUSTUS	transcript	2875806	2877548	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	start_codon	2875806	2875808	.	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2875806	2875987	1	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2875806	2875987	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2875988	2876179	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2876180	2876208	1	+	1	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2876180	2876208	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2876209	2876334	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2876335	2876408	1	+	2	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2876335	2876408	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2876409	2876507	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2876508	2876612	1	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2876508	2876612	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2876613	2876797	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2876798	2876831	0.98	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2876798	2876831	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2876832	2876916	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2876917	2877008	1	+	2	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2876917	2877008	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2877009	2877100	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2877101	2877262	1	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2877101	2877262	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	intron	2877263	2877425	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	CDS	2877426	2877548	0.99	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	exon	2877426	2877548	.	+	.	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
Phchi.S5	AUGUSTUS	stop_codon	2877549	2877551	.	+	0	transcript_id "Phchi.S5G035900.t1"; gene_id "Phchi.S5G035900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3033.t1 is derived from g202.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1255666	1256946	.	+	.	Phchi.S1G019200
Phchi.S1	AUGUSTUS	transcript	1255666	1256360	.	+	.	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	start_codon	1255666	1255668	.	+	0	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	CDS	1255666	1256209	0.92	+	0	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	exon	1255666	1256209	.	+	.	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	intron	1256210	1256295	.	+	.	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	CDS	1256296	1256360	0.7	+	2	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	exon	1256296	1256360	.	+	.	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	stop_codon	1256361	1256363	.	+	0	transcript_id "Phchi.S1G019200.t1"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	transcript	1255666	1256946	.	+	.	transcript_id "Phchi.S1G019200.t2"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	start_codon	1255666	1255668	.	+	0	transcript_id "Phchi.S1G019200.t2"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	CDS	1255666	1256946	1	+	0	transcript_id "Phchi.S1G019200.t2"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	exon	1255666	1256946	.	+	.	transcript_id "Phchi.S1G019200.t2"; gene_id "Phchi.S1G019200"
Phchi.S1	AUGUSTUS	stop_codon	1256947	1256949	.	+	0	transcript_id "Phchi.S1G019200.t2"; gene_id "Phchi.S1G019200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7373.t1 is derived from g4545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28817667	28819225	.	+	.	Phchi.S1G453200
Phchi.S1	AUGUSTUS	transcript	28817667	28819225	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	start_codon	28817667	28817669	.	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28817667	28817920	0.82	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28817667	28817920	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28817921	28818028	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818029	28818149	0.98	+	1	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818029	28818149	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818150	28818288	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818289	28818393	1	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818289	28818393	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818394	28818495	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818496	28818588	0.99	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818496	28818588	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818589	28818677	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818678	28818752	1	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818678	28818752	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818753	28818886	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818887	28818949	1	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818887	28818949	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818950	28819129	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28819130	28819225	1	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28819130	28819225	.	+	.	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	stop_codon	28819226	28819228	.	+	0	transcript_id "Phchi.S1G453200.t1"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	transcript	28817667	28819225	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	start_codon	28817667	28817669	.	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28817667	28817738	0.74	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28817667	28817738	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28817739	28817889	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28817890	28817944	0.88	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28817890	28817944	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28817945	28818028	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818029	28818149	0.91	+	2	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818029	28818149	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818150	28818288	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818289	28818334	0.91	+	1	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818289	28818334	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818335	28818495	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818496	28818588	1	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818496	28818588	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818589	28818677	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818678	28818752	1	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818678	28818752	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818753	28818886	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28818887	28818949	1	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28818887	28818949	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	intron	28818950	28819129	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	CDS	28819130	28819225	1	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	exon	28819130	28819225	.	+	.	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
Phchi.S1	AUGUSTUS	stop_codon	28819226	28819228	.	+	0	transcript_id "Phchi.S1G453200.t2"; gene_id "Phchi.S1G453200"
# This transcript jg12123.t2 is derived from g7799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12124.t1 is derived from g7800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3969390	3970715	.	+	.	Phchi.S2G020400
Phchi.S2	AUGUSTUS	transcript	3969390	3970715	.	+	.	transcript_id "Phchi.S2G020400.t1"; gene_id "Phchi.S2G020400"
Phchi.S2	AUGUSTUS	start_codon	3969390	3969392	.	+	0	transcript_id "Phchi.S2G020400.t1"; gene_id "Phchi.S2G020400"
Phchi.S2	AUGUSTUS	CDS	3969390	3970715	0.62	+	0	transcript_id "Phchi.S2G020400.t1"; gene_id "Phchi.S2G020400"
Phchi.S2	AUGUSTUS	exon	3969390	3970715	.	+	.	transcript_id "Phchi.S2G020400.t1"; gene_id "Phchi.S2G020400"
Phchi.S2	AUGUSTUS	stop_codon	3970716	3970718	.	+	0	transcript_id "Phchi.S2G020400.t1"; gene_id "Phchi.S2G020400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1805.t1 is derived from g8725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3132211	3132750	.	-	.	Phchi.S5G041400
Phchi.S5	AUGUSTUS	transcript	3132211	3132750	.	-	.	transcript_id "Phchi.S5G041400.t1"; gene_id "Phchi.S5G041400"
Phchi.S5	AUGUSTUS	stop_codon	3132208	3132210	.	-	0	transcript_id "Phchi.S5G041400.t1"; gene_id "Phchi.S5G041400"
Phchi.S5	AUGUSTUS	CDS	3132211	3132750	0.66	-	0	transcript_id "Phchi.S5G041400.t1"; gene_id "Phchi.S5G041400"
Phchi.S5	AUGUSTUS	exon	3132211	3132750	.	-	.	transcript_id "Phchi.S5G041400.t1"; gene_id "Phchi.S5G041400"
Phchi.S5	AUGUSTUS	start_codon	3132748	3132750	.	-	0	transcript_id "Phchi.S5G041400.t1"; gene_id "Phchi.S5G041400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11452.t1 is derived from g15502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6433667	6434335	.	-	.	Phchi.S4G103400
Phchi.S4	AUGUSTUS	transcript	6433667	6434335	.	-	.	transcript_id "Phchi.S4G103400.t1"; gene_id "Phchi.S4G103400"
Phchi.S4	AUGUSTUS	stop_codon	6433664	6433666	.	-	0	transcript_id "Phchi.S4G103400.t1"; gene_id "Phchi.S4G103400"
Phchi.S4	AUGUSTUS	CDS	6433667	6434335	0.12	-	0	transcript_id "Phchi.S4G103400.t1"; gene_id "Phchi.S4G103400"
Phchi.S4	AUGUSTUS	exon	6433667	6434335	.	-	.	transcript_id "Phchi.S4G103400.t1"; gene_id "Phchi.S4G103400"
Phchi.S4	AUGUSTUS	start_codon	6434333	6434335	.	-	0	transcript_id "Phchi.S4G103400.t1"; gene_id "Phchi.S4G103400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg818.t1 is derived from g10600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5709681	5710980	.	+	.	Phchi.S6G077700
Phchi.S6	AUGUSTUS	transcript	5709681	5710980	.	+	.	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	start_codon	5709681	5709683	.	+	0	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	CDS	5709681	5709996	0.86	+	0	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	exon	5709681	5709996	.	+	.	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	intron	5709997	5710369	.	+	.	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	CDS	5710370	5710980	1	+	2	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	exon	5710370	5710980	.	+	.	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
Phchi.S6	AUGUSTUS	stop_codon	5710981	5710983	.	+	0	transcript_id "Phchi.S6G077700.t1"; gene_id "Phchi.S6G077700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8624.t1 is derived from g5799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37094572	37094892	.	+	.	Phchi.S1G578300
Phchi.S1	AUGUSTUS	transcript	37094572	37094892	.	+	.	transcript_id "Phchi.S1G578300.t1"; gene_id "Phchi.S1G578300"
Phchi.S1	AUGUSTUS	start_codon	37094572	37094574	.	+	0	transcript_id "Phchi.S1G578300.t1"; gene_id "Phchi.S1G578300"
Phchi.S1	AUGUSTUS	CDS	37094572	37094892	0.8	+	0	transcript_id "Phchi.S1G578300.t1"; gene_id "Phchi.S1G578300"
Phchi.S1	AUGUSTUS	exon	37094572	37094892	.	+	.	transcript_id "Phchi.S1G578300.t1"; gene_id "Phchi.S1G578300"
Phchi.S1	AUGUSTUS	stop_codon	37094893	37094895	.	+	0	transcript_id "Phchi.S1G578300.t1"; gene_id "Phchi.S1G578300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9584.t1 is derived from g6760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42783818	42784949	.	+	.	Phchi.S1G674300
Phchi.S1	AUGUSTUS	transcript	42783818	42784949	.	+	.	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	start_codon	42783818	42783820	.	+	0	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	CDS	42783818	42783964	1	+	0	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	exon	42783818	42783964	.	+	.	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	intron	42783965	42784110	.	+	.	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	CDS	42784111	42784382	1	+	0	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	exon	42784111	42784382	.	+	.	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	intron	42784383	42784546	.	+	.	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	CDS	42784547	42784949	0.93	+	1	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	exon	42784547	42784949	.	+	.	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
Phchi.S1	AUGUSTUS	stop_codon	42784950	42784952	.	+	0	transcript_id "Phchi.S1G674300.t1"; gene_id "Phchi.S1G674300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11559.t1 is derived from g15610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7052342	7053062	.	-	.	Phchi.S4G114100
Phchi.S4	AUGUSTUS	transcript	7052342	7053062	.	-	.	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	stop_codon	7052339	7052341	.	-	0	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	CDS	7052342	7052638	0.63	-	0	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	exon	7052342	7052638	.	-	.	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	intron	7052639	7052771	.	-	.	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	CDS	7052772	7053062	0.61	-	0	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	exon	7052772	7053062	.	-	.	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
Phchi.S4	AUGUSTUS	start_codon	7053060	7053062	.	-	0	transcript_id "Phchi.S4G114100.t1"; gene_id "Phchi.S4G114100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7445.t1 is derived from g4617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29155876	29156333	.	+	.	Phchi.S1G460400
Phchi.S1	AUGUSTUS	transcript	29155876	29156333	.	+	.	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	start_codon	29155876	29155878	.	+	0	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	CDS	29155876	29156108	0.42	+	0	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	exon	29155876	29156108	.	+	.	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	intron	29156109	29156188	.	+	.	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	CDS	29156189	29156333	0.43	+	1	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	exon	29156189	29156333	.	+	.	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
Phchi.S1	AUGUSTUS	stop_codon	29156334	29156336	.	+	0	transcript_id "Phchi.S1G460400.t1"; gene_id "Phchi.S1G460400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12712.t1 is derived from g11177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	717318	718994	.	+	.	Phchi.S3G003100
Phchi.S3	AUGUSTUS	transcript	717318	718994	.	+	.	transcript_id "Phchi.S3G003100.t1"; gene_id "Phchi.S3G003100"
Phchi.S3	AUGUSTUS	start_codon	717318	717320	.	+	0	transcript_id "Phchi.S3G003100.t1"; gene_id "Phchi.S3G003100"
Phchi.S3	AUGUSTUS	CDS	717318	718994	0.84	+	0	transcript_id "Phchi.S3G003100.t1"; gene_id "Phchi.S3G003100"
Phchi.S3	AUGUSTUS	exon	717318	718994	.	+	.	transcript_id "Phchi.S3G003100.t1"; gene_id "Phchi.S3G003100"
Phchi.S3	AUGUSTUS	stop_codon	718995	718997	.	+	0	transcript_id "Phchi.S3G003100.t1"; gene_id "Phchi.S3G003100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4115.t1 is derived from g1284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8079941	8080712	.	-	.	Phchi.S1G127400
Phchi.S1	AUGUSTUS	transcript	8079941	8080712	.	-	.	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	stop_codon	8079938	8079940	.	-	0	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	CDS	8079941	8080023	0.87	-	2	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	exon	8079941	8080023	.	-	.	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	intron	8080024	8080132	.	-	.	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	CDS	8080133	8080712	0.81	-	0	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	exon	8080133	8080712	.	-	.	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
Phchi.S1	AUGUSTUS	start_codon	8080710	8080712	.	-	0	transcript_id "Phchi.S1G127400.t1"; gene_id "Phchi.S1G127400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2767.t1 is derived from g9687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8723243	8723922	.	+	.	Phchi.S5G137600
Phchi.S5	AUGUSTUS	transcript	8723243	8723922	.	+	.	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	start_codon	8723243	8723245	.	+	0	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	CDS	8723243	8723417	0.47	+	0	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	exon	8723243	8723417	.	+	.	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	intron	8723418	8723534	.	+	.	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	CDS	8723535	8723711	1	+	2	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	exon	8723535	8723711	.	+	.	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	intron	8723712	8723827	.	+	.	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	CDS	8723828	8723922	0.98	+	2	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	exon	8723828	8723922	.	+	.	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
Phchi.S5	AUGUSTUS	stop_codon	8723923	8723925	.	+	0	transcript_id "Phchi.S5G137600.t1"; gene_id "Phchi.S5G137600"
# This transcript jg7579.t2 is derived from g4753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7580.t1 is derived from g4754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30136037	30138070	.	-	.	Phchi.S1G473900
Phchi.S1	AUGUSTUS	transcript	30136037	30138070	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	stop_codon	30136034	30136036	.	-	0	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	CDS	30136037	30136119	0.7	-	2	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	exon	30136037	30136119	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	intron	30136120	30136414	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	CDS	30136415	30136457	0.7	-	0	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	exon	30136415	30136457	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	intron	30136458	30136804	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	CDS	30136805	30137008	0.7	-	0	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	exon	30136805	30137008	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	intron	30137009	30137142	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	CDS	30137143	30137664	1	-	0	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	exon	30137143	30137664	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	intron	30137665	30137830	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	CDS	30137831	30138070	1	-	0	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	exon	30137831	30138070	.	-	.	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
Phchi.S1	AUGUSTUS	start_codon	30138068	30138070	.	-	0	transcript_id "Phchi.S1G473900.t1"; gene_id "Phchi.S1G473900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8379.t1 is derived from g5554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35596391	35597095	.	-	.	Phchi.S1G553800
Phchi.S1	AUGUSTUS	transcript	35596391	35597095	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	stop_codon	35596388	35596390	.	-	0	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	CDS	35596391	35596488	1	-	2	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	exon	35596391	35596488	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	intron	35596489	35596572	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	CDS	35596573	35596748	1	-	1	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	exon	35596573	35596748	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	intron	35596749	35596874	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	CDS	35596875	35596933	1	-	0	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	exon	35596875	35596933	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	intron	35596934	35597023	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	CDS	35597024	35597095	0.71	-	0	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	exon	35597024	35597095	.	-	.	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
Phchi.S1	AUGUSTUS	start_codon	35597093	35597095	.	-	0	transcript_id "Phchi.S1G553800.t1"; gene_id "Phchi.S1G553800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15533.t1 is derived from g14002.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19743489	19746844	.	+	.	Phchi.S3G285200
Phchi.S3	AUGUSTUS	transcript	19743489	19746844	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	start_codon	19743489	19743491	.	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19743489	19743770	1	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19743489	19743770	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19743771	19743878	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19743879	19743921	1	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19743879	19743921	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19743922	19744041	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19744042	19744214	1	+	2	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19744042	19744214	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19744215	19744397	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19744398	19744605	1	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19744398	19744605	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19744606	19744707	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19744708	19744875	1	+	2	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19744708	19744875	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19744876	19745138	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745139	19745194	1	+	2	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745139	19745194	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745195	19745290	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745291	19745351	1	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745291	19745351	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745352	19745462	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745463	19745524	1	+	2	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745463	19745524	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745525	19745850	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745851	19745895	1	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745851	19745895	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745896	19746013	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19746014	19746082	1	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19746014	19746082	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19746083	19746274	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19746275	19746844	0.98	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19746275	19746844	.	+	.	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	stop_codon	19746845	19746847	.	+	0	transcript_id "Phchi.S3G285200.t1"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	transcript	19743489	19746844	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	start_codon	19743489	19743491	.	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19743489	19743770	1	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19743489	19743770	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19743771	19743878	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19743879	19743921	1	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19743879	19743921	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19743922	19744041	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19744042	19744214	1	+	2	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19744042	19744214	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19744215	19744397	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19744398	19744605	1	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19744398	19744605	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19744606	19744707	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19744708	19744875	1	+	2	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19744708	19744875	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19744876	19745141	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745142	19745194	1	+	2	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745142	19745194	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745195	19745290	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745291	19745351	1	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745291	19745351	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745352	19745462	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745463	19745524	1	+	2	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745463	19745524	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745525	19745850	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19745851	19745895	1	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19745851	19745895	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19745896	19746013	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19746014	19746082	1	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19746014	19746082	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	intron	19746083	19746274	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	CDS	19746275	19746844	0.88	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	exon	19746275	19746844	.	+	.	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
Phchi.S3	AUGUSTUS	stop_codon	19746845	19746847	.	+	0	transcript_id "Phchi.S3G285200.t2"; gene_id "Phchi.S3G285200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3588.t1 is derived from g757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4623312	4624031	.	-	.	Phchi.S1G074700
Phchi.S1	AUGUSTUS	transcript	4623312	4624031	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	stop_codon	4623309	4623311	.	-	0	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	CDS	4623312	4623411	0.73	-	1	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	exon	4623312	4623411	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	intron	4623412	4623503	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	CDS	4623504	4623575	1	-	1	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	exon	4623504	4623575	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	intron	4623576	4623695	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	CDS	4623696	4623803	1	-	1	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	exon	4623696	4623803	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	intron	4623804	4623897	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	CDS	4623898	4624031	1	-	0	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	exon	4623898	4624031	.	-	.	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
Phchi.S1	AUGUSTUS	start_codon	4624029	4624031	.	-	0	transcript_id "Phchi.S1G074700.t1"; gene_id "Phchi.S1G074700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5178.t1 is derived from g2348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15344043	15346241	.	-	.	Phchi.S1G233700
Phchi.S1	AUGUSTUS	transcript	15344043	15346241	.	-	.	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	stop_codon	15344040	15344042	.	-	0	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	CDS	15344043	15345345	0.96	-	1	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	exon	15344043	15345345	.	-	.	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	intron	15345346	15345633	.	-	.	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	CDS	15345634	15346241	0.74	-	0	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	exon	15345634	15346241	.	-	.	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
Phchi.S1	AUGUSTUS	start_codon	15346239	15346241	.	-	0	transcript_id "Phchi.S1G233700.t1"; gene_id "Phchi.S1G233700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8424.t1 is derived from g5599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35885022	35888234	.	-	.	Phchi.S1G558300
Phchi.S1	AUGUSTUS	transcript	35885022	35888234	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	stop_codon	35885019	35885021	.	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35885022	35885087	0.76	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35885022	35885087	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35885088	35885190	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35885191	35885247	0.76	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35885191	35885247	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35885248	35885321	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35885322	35885369	1	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35885322	35885369	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35885370	35885534	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35885535	35885591	1	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35885535	35885591	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35885592	35885682	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35885683	35885916	1	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35885683	35885916	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35885917	35886053	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35886054	35886194	1	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35886054	35886194	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35886195	35886325	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35886326	35886491	1	-	1	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35886326	35886491	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35886492	35886580	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35886581	35886630	1	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35886581	35886630	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35886631	35886717	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35886718	35886987	0.91	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35886718	35886987	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35886988	35887067	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35887068	35887136	1	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35887068	35887136	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35887137	35887421	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35887422	35887507	0.82	-	2	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35887422	35887507	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	intron	35887508	35887672	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	CDS	35887673	35888234	0.46	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	exon	35887673	35888234	.	-	.	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
Phchi.S1	AUGUSTUS	start_codon	35888232	35888234	.	-	0	transcript_id "Phchi.S1G558300.t1"; gene_id "Phchi.S1G558300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11466.t1 is derived from g15516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6500872	6503163	.	+	.	Phchi.S4G104800
Phchi.S4	AUGUSTUS	transcript	6500872	6503163	.	+	.	transcript_id "Phchi.S4G104800.t1"; gene_id "Phchi.S4G104800"
Phchi.S4	AUGUSTUS	start_codon	6500872	6500874	.	+	0	transcript_id "Phchi.S4G104800.t1"; gene_id "Phchi.S4G104800"
Phchi.S4	AUGUSTUS	CDS	6500872	6503163	0.94	+	0	transcript_id "Phchi.S4G104800.t1"; gene_id "Phchi.S4G104800"
Phchi.S4	AUGUSTUS	exon	6500872	6503163	.	+	.	transcript_id "Phchi.S4G104800.t1"; gene_id "Phchi.S4G104800"
Phchi.S4	AUGUSTUS	stop_codon	6503164	6503166	.	+	0	transcript_id "Phchi.S4G104800.t1"; gene_id "Phchi.S4G104800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11855.t1 is derived from g15907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8634317	8635457	.	-	.	Phchi.S4G143700
Phchi.S4	AUGUSTUS	transcript	8634317	8635457	.	-	.	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	stop_codon	8634314	8634316	.	-	0	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	CDS	8634317	8634665	1	-	1	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	exon	8634317	8634665	.	-	.	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	intron	8634666	8634810	.	-	.	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	CDS	8634811	8635457	0.96	-	0	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	exon	8634811	8635457	.	-	.	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
Phchi.S4	AUGUSTUS	start_codon	8635455	8635457	.	-	0	transcript_id "Phchi.S4G143700.t1"; gene_id "Phchi.S4G143700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9122.t1 is derived from g6297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39952214	39952882	.	-	.	Phchi.S1G628100
Phchi.S1	AUGUSTUS	transcript	39952214	39952882	.	-	.	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	stop_codon	39952211	39952213	.	-	0	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	CDS	39952214	39952361	1	-	1	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	exon	39952214	39952361	.	-	.	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	intron	39952362	39952475	.	-	.	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	CDS	39952476	39952882	0.87	-	0	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	exon	39952476	39952882	.	-	.	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
Phchi.S1	AUGUSTUS	start_codon	39952880	39952882	.	-	0	transcript_id "Phchi.S1G628100.t1"; gene_id "Phchi.S1G628100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15441.t1 is derived from g13909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19174069	19176367	.	-	.	Phchi.S3G276000
Phchi.S3	AUGUSTUS	transcript	19174069	19176367	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	stop_codon	19174066	19174068	.	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19174069	19174173	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19174069	19174173	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19174174	19174324	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19174325	19174405	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19174325	19174405	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19174406	19174499	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19174500	19174565	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19174500	19174565	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19174566	19174656	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19174657	19174734	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19174657	19174734	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19174735	19174820	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19174821	19174892	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19174821	19174892	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19174893	19175030	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19175031	19175120	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19175031	19175120	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19175121	19175217	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19175218	19175497	1	-	1	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19175218	19175497	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	intron	19175498	19176206	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	CDS	19176207	19176367	1	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	exon	19176207	19176367	.	-	.	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
Phchi.S3	AUGUSTUS	start_codon	19176365	19176367	.	-	0	transcript_id "Phchi.S3G276000.t1"; gene_id "Phchi.S3G276000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2479.t1 is derived from g9399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6855936	6857464	.	-	.	Phchi.S5G108800
Phchi.S5	AUGUSTUS	transcript	6855936	6857464	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	stop_codon	6855933	6855935	.	-	0	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	CDS	6855936	6855981	1	-	1	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	exon	6855936	6855981	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	intron	6855982	6856073	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	CDS	6856074	6857098	0.36	-	0	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	exon	6856074	6857098	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	intron	6857099	6857188	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	CDS	6857189	6857246	0.78	-	1	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	exon	6857189	6857246	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	intron	6857247	6857387	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	CDS	6857388	6857464	0.43	-	0	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	exon	6857388	6857464	.	-	.	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
Phchi.S5	AUGUSTUS	start_codon	6857462	6857464	.	-	0	transcript_id "Phchi.S5G108800.t1"; gene_id "Phchi.S5G108800"
# This transcript jg8830.t2 is derived from g6005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8831.t1 is derived from g6006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38171573	38172466	.	-	.	Phchi.S1G599000
Phchi.S1	AUGUSTUS	transcript	38171573	38172466	.	-	.	transcript_id "Phchi.S1G599000.t1"; gene_id "Phchi.S1G599000"
Phchi.S1	AUGUSTUS	stop_codon	38171570	38171572	.	-	0	transcript_id "Phchi.S1G599000.t1"; gene_id "Phchi.S1G599000"
Phchi.S1	AUGUSTUS	CDS	38171573	38172466	0.83	-	0	transcript_id "Phchi.S1G599000.t1"; gene_id "Phchi.S1G599000"
Phchi.S1	AUGUSTUS	exon	38171573	38172466	.	-	.	transcript_id "Phchi.S1G599000.t1"; gene_id "Phchi.S1G599000"
Phchi.S1	AUGUSTUS	start_codon	38172464	38172466	.	-	0	transcript_id "Phchi.S1G599000.t1"; gene_id "Phchi.S1G599000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14124.t1 is derived from g12591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10995879	11007787	.	+	.	Phchi.S3G144300
Phchi.S3	AUGUSTUS	transcript	10995879	11007787	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	start_codon	10995879	10995881	.	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10995879	10996110	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10995879	10996110	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996111	10996306	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10996307	10996404	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10996307	10996404	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996405	10996535	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10996536	10996696	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10996536	10996696	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996697	10996824	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10996825	10996954	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10996825	10996954	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996955	10997109	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997110	10997217	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997110	10997217	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997218	10997305	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997306	10997428	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997306	10997428	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997429	10997560	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997561	10997644	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997561	10997644	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997645	10997777	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997778	10997893	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997778	10997893	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997894	10998129	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998130	10998250	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998130	10998250	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10998251	10998500	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998501	10998620	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998501	10998620	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10998621	10998748	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998749	10998825	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998749	10998825	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10998826	10998932	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998933	10999014	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998933	10999014	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999015	10999146	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999147	10999281	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999147	10999281	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999282	10999377	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999378	10999480	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999378	10999480	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999481	10999636	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999637	10999760	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999637	10999760	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999761	10999922	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999923	11000109	0.99	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999923	11000109	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000110	11000216	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000217	11000269	0.98	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000217	11000269	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000270	11000355	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000356	11000416	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000356	11000416	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000417	11000534	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000535	11000616	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000535	11000616	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000617	11000695	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000696	11000745	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000696	11000745	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000746	11000964	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000965	11001051	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000965	11001051	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001052	11001215	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001216	11001307	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001216	11001307	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001308	11001443	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001444	11001468	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001444	11001468	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001469	11001635	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001636	11001733	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001636	11001733	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001734	11001815	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001816	11001897	0.97	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001816	11001897	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001898	11002002	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002003	11002163	0.96	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002003	11002163	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002164	11002321	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002322	11002451	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002322	11002451	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002452	11002537	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002538	11002635	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002538	11002635	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002636	11002723	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002724	11002814	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002724	11002814	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002815	11002901	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002902	11003062	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002902	11003062	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003063	11003147	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003148	11003257	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003148	11003257	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003258	11003349	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003350	11003529	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003350	11003529	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003530	11003620	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003621	11003689	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003621	11003689	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003690	11003847	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003848	11004013	0.93	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003848	11004013	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004014	11004117	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004118	11004232	0.93	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004118	11004232	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004233	11004307	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004308	11004427	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004308	11004427	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004428	11004510	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004511	11004626	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004511	11004626	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004627	11004716	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004717	11004800	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004717	11004800	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004801	11004877	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004878	11004907	0.94	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004878	11004907	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004908	11004972	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004973	11004989	0.94	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004973	11004989	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004990	11005109	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005110	11005162	0.98	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005110	11005162	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005163	11005257	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005258	11005434	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005258	11005434	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005435	11005594	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005595	11005642	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005595	11005642	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005643	11005768	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005769	11005814	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005769	11005814	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005815	11005909	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005910	11005921	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005910	11005921	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005922	11006010	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006011	11006123	1	+	2	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006011	11006123	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006124	11006282	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006283	11006371	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006283	11006371	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006372	11006517	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006518	11006673	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006518	11006673	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006674	11006754	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006755	11006857	1	+	1	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006755	11006857	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006858	11006961	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006962	11007081	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006962	11007081	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11007082	11007162	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11007163	11007213	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11007163	11007213	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11007214	11007294	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11007295	11007477	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11007295	11007477	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11007478	11007556	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11007557	11007787	1	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11007557	11007787	.	+	.	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	stop_codon	11007788	11007790	.	+	0	transcript_id "Phchi.S3G144300.t1"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	transcript	10995879	11007787	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	start_codon	10995879	10995881	.	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10995879	10996110	0.99	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10995879	10996110	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996111	10996306	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10996307	10996404	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10996307	10996404	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996405	10996535	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10996536	10996696	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10996536	10996696	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996697	10996824	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10996825	10996954	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10996825	10996954	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10996955	10997109	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997110	10997217	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997110	10997217	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997218	10997305	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997306	10997428	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997306	10997428	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997429	10997560	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997561	10997644	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997561	10997644	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997645	10997777	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10997778	10997893	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10997778	10997893	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10997894	10998129	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998130	10998250	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998130	10998250	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10998251	10998500	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998501	10998620	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998501	10998620	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10998621	10998748	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998749	10998825	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998749	10998825	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10998826	10998932	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10998933	10999014	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10998933	10999014	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999015	10999146	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999147	10999281	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999147	10999281	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999282	10999377	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999378	10999480	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999378	10999480	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999481	10999636	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999637	10999760	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999637	10999760	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	10999761	10999922	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	10999923	11000109	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	10999923	11000109	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000110	11000216	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000217	11000269	0.99	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000217	11000269	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000270	11000355	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000356	11000416	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000356	11000416	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000417	11000534	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000535	11000616	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000535	11000616	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000617	11000695	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000696	11000745	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000696	11000745	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11000746	11000964	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11000965	11001051	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11000965	11001051	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001052	11001215	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001216	11001307	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001216	11001307	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001308	11001443	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001444	11001468	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001444	11001468	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001469	11001638	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001639	11001733	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001639	11001733	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001734	11001815	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11001816	11001897	0.95	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11001816	11001897	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11001898	11002002	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002003	11002163	0.95	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002003	11002163	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002164	11002321	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002322	11002451	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002322	11002451	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002452	11002537	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002538	11002635	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002538	11002635	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002636	11002723	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002724	11002814	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002724	11002814	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11002815	11002901	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11002902	11003062	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11002902	11003062	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003063	11003147	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003148	11003257	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003148	11003257	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003258	11003349	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003350	11003529	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003350	11003529	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003530	11003620	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003621	11003689	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003621	11003689	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11003690	11003847	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11003848	11004013	0.96	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11003848	11004013	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004014	11004117	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004118	11004232	0.97	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004118	11004232	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004233	11004307	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004308	11004427	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004308	11004427	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004428	11004510	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004511	11004626	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004511	11004626	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004627	11004716	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004717	11004800	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004717	11004800	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004801	11004877	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004878	11004907	0.9	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004878	11004907	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004908	11004972	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11004973	11004989	0.9	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11004973	11004989	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11004990	11005109	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005110	11005162	0.96	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005110	11005162	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005163	11005257	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005258	11005434	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005258	11005434	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005435	11005594	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005595	11005642	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005595	11005642	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005643	11005768	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005769	11005814	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005769	11005814	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005815	11005909	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11005910	11005921	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11005910	11005921	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11005922	11006010	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006011	11006123	1	+	2	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006011	11006123	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006124	11006282	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006283	11006371	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006283	11006371	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006372	11006517	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006518	11006673	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006518	11006673	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006674	11006754	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006755	11006857	1	+	1	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006755	11006857	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11006858	11006961	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11006962	11007081	0.99	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11006962	11007081	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11007082	11007162	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11007163	11007213	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11007163	11007213	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11007214	11007294	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11007295	11007477	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11007295	11007477	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	intron	11007478	11007556	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	CDS	11007557	11007787	1	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	exon	11007557	11007787	.	+	.	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
Phchi.S3	AUGUSTUS	stop_codon	11007788	11007790	.	+	0	transcript_id "Phchi.S3G144300.t2"; gene_id "Phchi.S3G144300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1105.t1 is derived from g10888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7631251	7636639	.	+	.	Phchi.S6G106400
Phchi.S6	AUGUSTUS	transcript	7631251	7636639	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	start_codon	7631251	7631253	.	+	0	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7631251	7631279	0.77	+	0	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7631251	7631279	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7631280	7631373	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7631374	7631424	1	+	1	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7631374	7631424	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7631425	7631682	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7631683	7631790	0.99	+	1	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7631683	7631790	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7631791	7631875	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7631876	7631950	0.99	+	1	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7631876	7631950	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7631951	7632050	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7632051	7632171	1	+	1	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7632051	7632171	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7632172	7632417	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7632418	7632549	0.99	+	0	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7632418	7632549	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7632550	7632773	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7632774	7632872	1	+	0	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7632774	7632872	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7632873	7633035	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7633036	7633346	1	+	0	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7633036	7633346	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	intron	7633347	7633497	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	CDS	7633498	7636639	0.96	+	1	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	exon	7633498	7636639	.	+	.	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
Phchi.S6	AUGUSTUS	stop_codon	7636640	7636642	.	+	0	transcript_id "Phchi.S6G106400.t1"; gene_id "Phchi.S6G106400"
# This transcript jg14911.t2 is derived from g13379.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14912.t1 is derived from g13380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15476587	15478907	.	-	.	Phchi.S3G223100
Phchi.S3	AUGUSTUS	transcript	15476587	15478907	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	stop_codon	15476584	15476586	.	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15476587	15476596	1	-	1	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15476587	15476596	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15476597	15476683	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15476684	15476811	1	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15476684	15476811	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15476812	15476951	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15476952	15477059	1	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15476952	15477059	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15477060	15477174	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15477175	15477335	0.92	-	2	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15477175	15477335	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15477336	15477455	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15477456	15477611	0.98	-	2	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15477456	15477611	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15477612	15477995	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15477996	15478142	0.91	-	2	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15477996	15478142	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15478143	15478222	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15478223	15478319	0.56	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15478223	15478319	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15478320	15478394	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15478395	15478469	0.41	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15478395	15478469	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	intron	15478470	15478730	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	CDS	15478731	15478907	0.57	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	exon	15478731	15478907	.	-	.	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
Phchi.S3	AUGUSTUS	start_codon	15478905	15478907	.	-	0	transcript_id "Phchi.S3G223100.t1"; gene_id "Phchi.S3G223100"
# This transcript jg6065.t2 is derived from g3236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6066.t1 is derived from g3237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20707599	20713374	.	+	.	Phchi.S1G322500
Phchi.S1	AUGUSTUS	transcript	20707599	20713374	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	start_codon	20707599	20707601	.	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20707599	20707601	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20707599	20707601	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20707602	20707716	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20707717	20707737	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20707717	20707737	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20707738	20707831	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20707832	20707893	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20707832	20707893	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20707894	20708011	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20708012	20708066	1	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20708012	20708066	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20708067	20708214	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20708215	20708251	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20708215	20708251	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20708252	20708369	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20708370	20708695	1	+	2	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20708370	20708695	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20708696	20708768	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20708769	20708900	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20708769	20708900	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20708901	20709019	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20709020	20709168	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20709020	20709168	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20709169	20709309	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20709310	20709378	1	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20709310	20709378	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20709379	20709497	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20709498	20709648	1	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20709498	20709648	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20709649	20709737	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20709738	20709803	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20709738	20709803	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20709804	20709913	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20709914	20710102	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20709914	20710102	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20710103	20710188	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20710189	20710329	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20710189	20710329	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20710330	20710483	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20710484	20710558	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20710484	20710558	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20710559	20710689	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20710690	20710866	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20710690	20710866	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20710867	20711008	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20711009	20711100	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20711009	20711100	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20711101	20711179	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20711180	20711296	1	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20711180	20711296	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20711297	20711463	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20711464	20711578	1	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20711464	20711578	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20711579	20711665	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20711666	20711737	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20711666	20711737	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20711738	20711824	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20711825	20712021	0.96	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20711825	20712021	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20712022	20712125	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20712126	20712219	0.98	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20712126	20712219	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20712220	20712361	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20712362	20712471	1	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20712362	20712471	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20712472	20712591	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20712592	20712721	1	+	1	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20712592	20712721	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20712722	20712869	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20712870	20712996	0.88	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20712870	20712996	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20712997	20713223	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20713224	20713264	0.86	+	2	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20713224	20713264	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	intron	20713265	20713350	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	CDS	20713351	20713374	0.91	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	exon	20713351	20713374	.	+	.	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
Phchi.S1	AUGUSTUS	stop_codon	20713375	20713377	.	+	0	transcript_id "Phchi.S1G322500.t1"; gene_id "Phchi.S1G322500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg726.t1 is derived from g10508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5190025	5190405	.	+	.	Phchi.S6G068500
Phchi.S6	AUGUSTUS	transcript	5190025	5190405	.	+	.	transcript_id "Phchi.S6G068500.t1"; gene_id "Phchi.S6G068500"
Phchi.S6	AUGUSTUS	start_codon	5190025	5190027	.	+	0	transcript_id "Phchi.S6G068500.t1"; gene_id "Phchi.S6G068500"
Phchi.S6	AUGUSTUS	CDS	5190025	5190405	0.76	+	0	transcript_id "Phchi.S6G068500.t1"; gene_id "Phchi.S6G068500"
Phchi.S6	AUGUSTUS	exon	5190025	5190405	.	+	.	transcript_id "Phchi.S6G068500.t1"; gene_id "Phchi.S6G068500"
Phchi.S6	AUGUSTUS	stop_codon	5190406	5190408	.	+	0	transcript_id "Phchi.S6G068500.t1"; gene_id "Phchi.S6G068500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13766.t1 is derived from g12233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8808494	8812926	.	-	.	Phchi.S3G108500
Phchi.S3	AUGUSTUS	transcript	8808494	8812926	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	stop_codon	8808491	8808493	.	-	0	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8808494	8808970	0.71	-	0	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8808494	8808970	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8808971	8809087	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8809088	8809220	0.93	-	1	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8809088	8809220	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8809221	8809339	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8809340	8809535	1	-	2	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8809340	8809535	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8809536	8809642	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8809643	8809711	0.98	-	2	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8809643	8809711	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8809712	8809805	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8809806	8809932	1	-	0	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8809806	8809932	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8809933	8810026	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8810027	8810259	1	-	2	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8810027	8810259	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8810260	8810352	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8810353	8810552	0.99	-	1	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8810353	8810552	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8810553	8810672	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8810673	8810744	0.99	-	1	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8810673	8810744	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8810745	8810826	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8810827	8810898	0.99	-	1	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8810827	8810898	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8810899	8811023	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8811024	8811095	1	-	1	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8811024	8811095	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8811096	8811171	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8811172	8811304	1	-	2	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8811172	8811304	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8811305	8811412	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8811413	8811960	1	-	1	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8811413	8811960	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8811961	8812033	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8812034	8812263	0.9	-	0	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8812034	8812263	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8812264	8812391	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8812392	8812597	0.49	-	2	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8812392	8812597	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	intron	8812598	8812799	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	CDS	8812800	8812926	0.8	-	0	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	exon	8812800	8812926	.	-	.	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
Phchi.S3	AUGUSTUS	start_codon	8812924	8812926	.	-	0	transcript_id "Phchi.S3G108500.t1"; gene_id "Phchi.S3G108500"
# This transcript jg1721.t2 is derived from g8641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1722.t1 is derived from g8642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2704542	2705281	.	-	.	Phchi.S5G033100
Phchi.S5	AUGUSTUS	transcript	2704542	2705281	.	-	.	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	stop_codon	2704539	2704541	.	-	0	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	CDS	2704542	2705138	0.81	-	0	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	exon	2704542	2705138	.	-	.	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	intron	2705139	2705242	.	-	.	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	CDS	2705243	2705281	0.94	-	0	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	exon	2705243	2705281	.	-	.	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
Phchi.S5	AUGUSTUS	start_codon	2705279	2705281	.	-	0	transcript_id "Phchi.S5G033100.t1"; gene_id "Phchi.S5G033100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1294.t1 is derived from g11077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8872483	8874009	.	+	.	Phchi.S6G125300
Phchi.S6	AUGUSTUS	transcript	8872483	8874009	.	+	.	transcript_id "Phchi.S6G125300.t1"; gene_id "Phchi.S6G125300"
Phchi.S6	AUGUSTUS	start_codon	8872483	8872485	.	+	0	transcript_id "Phchi.S6G125300.t1"; gene_id "Phchi.S6G125300"
Phchi.S6	AUGUSTUS	CDS	8872483	8874009	0.91	+	0	transcript_id "Phchi.S6G125300.t1"; gene_id "Phchi.S6G125300"
Phchi.S6	AUGUSTUS	exon	8872483	8874009	.	+	.	transcript_id "Phchi.S6G125300.t1"; gene_id "Phchi.S6G125300"
Phchi.S6	AUGUSTUS	stop_codon	8874010	8874012	.	+	0	transcript_id "Phchi.S6G125300.t1"; gene_id "Phchi.S6G125300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13126.t1 is derived from g11591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4259241	4260729	.	-	.	Phchi.S3G044500
Phchi.S3	AUGUSTUS	transcript	4259241	4260729	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	stop_codon	4259238	4259240	.	-	0	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	CDS	4259241	4259350	1	-	2	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	exon	4259241	4259350	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	intron	4259351	4259427	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	CDS	4259428	4259605	1	-	0	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	exon	4259428	4259605	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	intron	4259606	4259686	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	CDS	4259687	4259890	1	-	0	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	exon	4259687	4259890	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	intron	4259891	4259980	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	CDS	4259981	4260386	1	-	1	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	exon	4259981	4260386	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	intron	4260387	4260463	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	CDS	4260464	4260729	0.99	-	0	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	exon	4260464	4260729	.	-	.	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
Phchi.S3	AUGUSTUS	start_codon	4260727	4260729	.	-	0	transcript_id "Phchi.S3G044500.t1"; gene_id "Phchi.S3G044500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13078.t1 is derived from g11543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4056555	4057727	.	+	.	Phchi.S3G039700
Phchi.S3	AUGUSTUS	transcript	4056555	4057727	.	+	.	transcript_id "Phchi.S3G039700.t1"; gene_id "Phchi.S3G039700"
Phchi.S3	AUGUSTUS	start_codon	4056555	4056557	.	+	0	transcript_id "Phchi.S3G039700.t1"; gene_id "Phchi.S3G039700"
Phchi.S3	AUGUSTUS	CDS	4056555	4057727	0.74	+	0	transcript_id "Phchi.S3G039700.t1"; gene_id "Phchi.S3G039700"
Phchi.S3	AUGUSTUS	exon	4056555	4057727	.	+	.	transcript_id "Phchi.S3G039700.t1"; gene_id "Phchi.S3G039700"
Phchi.S3	AUGUSTUS	stop_codon	4057728	4057730	.	+	0	transcript_id "Phchi.S3G039700.t1"; gene_id "Phchi.S3G039700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14268.t1 is derived from g12735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11863251	11864111	.	-	.	Phchi.S3G158700
Phchi.S3	AUGUSTUS	transcript	11863251	11864111	.	-	.	transcript_id "Phchi.S3G158700.t1"; gene_id "Phchi.S3G158700"
Phchi.S3	AUGUSTUS	stop_codon	11863248	11863250	.	-	0	transcript_id "Phchi.S3G158700.t1"; gene_id "Phchi.S3G158700"
Phchi.S3	AUGUSTUS	CDS	11863251	11864111	0.36	-	0	transcript_id "Phchi.S3G158700.t1"; gene_id "Phchi.S3G158700"
Phchi.S3	AUGUSTUS	exon	11863251	11864111	.	-	.	transcript_id "Phchi.S3G158700.t1"; gene_id "Phchi.S3G158700"
Phchi.S3	AUGUSTUS	start_codon	11864109	11864111	.	-	0	transcript_id "Phchi.S3G158700.t1"; gene_id "Phchi.S3G158700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5568.t1 is derived from g2738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17628412	17628675	.	-	.	Phchi.S1G272700
Phchi.S1	AUGUSTUS	transcript	17628412	17628675	.	-	.	transcript_id "Phchi.S1G272700.t1"; gene_id "Phchi.S1G272700"
Phchi.S1	AUGUSTUS	stop_codon	17628409	17628411	.	-	0	transcript_id "Phchi.S1G272700.t1"; gene_id "Phchi.S1G272700"
Phchi.S1	AUGUSTUS	CDS	17628412	17628675	0.98	-	0	transcript_id "Phchi.S1G272700.t1"; gene_id "Phchi.S1G272700"
Phchi.S1	AUGUSTUS	exon	17628412	17628675	.	-	.	transcript_id "Phchi.S1G272700.t1"; gene_id "Phchi.S1G272700"
Phchi.S1	AUGUSTUS	start_codon	17628673	17628675	.	-	0	transcript_id "Phchi.S1G272700.t1"; gene_id "Phchi.S1G272700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7011.t1 is derived from g4183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26392543	26393622	.	+	.	Phchi.S1G417000
Phchi.S1	AUGUSTUS	transcript	26392543	26393622	.	+	.	transcript_id "Phchi.S1G417000.t1"; gene_id "Phchi.S1G417000"
Phchi.S1	AUGUSTUS	start_codon	26392543	26392545	.	+	0	transcript_id "Phchi.S1G417000.t1"; gene_id "Phchi.S1G417000"
Phchi.S1	AUGUSTUS	CDS	26392543	26393622	1	+	0	transcript_id "Phchi.S1G417000.t1"; gene_id "Phchi.S1G417000"
Phchi.S1	AUGUSTUS	exon	26392543	26393622	.	+	.	transcript_id "Phchi.S1G417000.t1"; gene_id "Phchi.S1G417000"
Phchi.S1	AUGUSTUS	stop_codon	26393623	26393625	.	+	0	transcript_id "Phchi.S1G417000.t1"; gene_id "Phchi.S1G417000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5782.t1 is derived from g2952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18932479	18933945	.	-	.	Phchi.S1G294100
Phchi.S1	AUGUSTUS	transcript	18932479	18933945	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	stop_codon	18932476	18932478	.	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	CDS	18932479	18932796	1	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	exon	18932479	18932796	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	intron	18932797	18932906	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	CDS	18932907	18933038	0.99	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	exon	18932907	18933038	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	intron	18933039	18933150	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	CDS	18933151	18933294	0.73	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	exon	18933151	18933294	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	intron	18933295	18933439	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	CDS	18933440	18933691	1	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	exon	18933440	18933691	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	intron	18933692	18933858	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	CDS	18933859	18933945	1	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	exon	18933859	18933945	.	-	.	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
Phchi.S1	AUGUSTUS	start_codon	18933943	18933945	.	-	0	transcript_id "Phchi.S1G294100.t1"; gene_id "Phchi.S1G294100"
# This transcript jg9822.t2 is derived from g6998.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9823.t1 is derived from g6999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43963401	43965116	.	-	.	Phchi.S1G698200
Phchi.S1	AUGUSTUS	transcript	43963401	43965116	.	-	.	transcript_id "Phchi.S1G698200.t1"; gene_id "Phchi.S1G698200"
Phchi.S1	AUGUSTUS	stop_codon	43963398	43963400	.	-	0	transcript_id "Phchi.S1G698200.t1"; gene_id "Phchi.S1G698200"
Phchi.S1	AUGUSTUS	CDS	43963401	43965116	0.45	-	0	transcript_id "Phchi.S1G698200.t1"; gene_id "Phchi.S1G698200"
Phchi.S1	AUGUSTUS	exon	43963401	43965116	.	-	.	transcript_id "Phchi.S1G698200.t1"; gene_id "Phchi.S1G698200"
Phchi.S1	AUGUSTUS	start_codon	43965114	43965116	.	-	0	transcript_id "Phchi.S1G698200.t1"; gene_id "Phchi.S1G698200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9297.t1 is derived from g6472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40826408	40828472	.	-	.	Phchi.S1G645600
Phchi.S1	AUGUSTUS	transcript	40826408	40828472	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	stop_codon	40826405	40826407	.	-	0	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	CDS	40826408	40826794	0.62	-	0	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	exon	40826408	40826794	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	intron	40826795	40826905	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	CDS	40826906	40827228	0.66	-	2	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	exon	40826906	40827228	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	intron	40827229	40827320	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	CDS	40827321	40827552	1	-	0	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	exon	40827321	40827552	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	intron	40827553	40827648	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	CDS	40827649	40827936	1	-	0	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	exon	40827649	40827936	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	intron	40827937	40828049	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	CDS	40828050	40828282	1	-	2	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	exon	40828050	40828282	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	intron	40828283	40828384	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	CDS	40828385	40828472	0.48	-	0	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	exon	40828385	40828472	.	-	.	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
Phchi.S1	AUGUSTUS	start_codon	40828470	40828472	.	-	0	transcript_id "Phchi.S1G645600.t1"; gene_id "Phchi.S1G645600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7469.t1 is derived from g4642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29526804	29528174	.	-	.	Phchi.S1G462800
Phchi.S1	AUGUSTUS	transcript	29526804	29528174	.	-	.	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	stop_codon	29526801	29526803	.	-	0	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	CDS	29526804	29527329	1	-	1	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	exon	29526804	29527329	.	-	.	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	intron	29527330	29527404	.	-	.	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	CDS	29527405	29527506	1	-	1	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	exon	29527405	29527506	.	-	.	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	intron	29527507	29527602	.	-	.	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	CDS	29527603	29528174	1	-	0	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	exon	29527603	29528174	.	-	.	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
Phchi.S1	AUGUSTUS	start_codon	29528172	29528174	.	-	0	transcript_id "Phchi.S1G462800.t1"; gene_id "Phchi.S1G462800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7668.t1 is derived from g4842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30535567	30538368	.	+	.	Phchi.S1G482700
Phchi.S1	AUGUSTUS	transcript	30535567	30538368	.	+	.	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	start_codon	30535567	30535569	.	+	0	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	CDS	30535567	30536257	0.58	+	0	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	exon	30535567	30536257	.	+	.	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	intron	30536258	30536402	.	+	.	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	CDS	30536403	30536443	0.7	+	2	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	exon	30536403	30536443	.	+	.	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	intron	30536444	30536535	.	+	.	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	CDS	30536536	30538368	0.14	+	0	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	exon	30536536	30538368	.	+	.	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
Phchi.S1	AUGUSTUS	stop_codon	30538369	30538371	.	+	0	transcript_id "Phchi.S1G482700.t1"; gene_id "Phchi.S1G482700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1207.t1 is derived from g10990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8416242	8416647	.	+	.	Phchi.S6G116600
Phchi.S6	AUGUSTUS	transcript	8416242	8416647	.	+	.	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	start_codon	8416242	8416244	.	+	0	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	CDS	8416242	8416250	0.96	+	0	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	exon	8416242	8416250	.	+	.	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	intron	8416251	8416437	.	+	.	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	CDS	8416438	8416647	0.89	+	0	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	exon	8416438	8416647	.	+	.	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
Phchi.S6	AUGUSTUS	stop_codon	8416648	8416650	.	+	0	transcript_id "Phchi.S6G116600.t1"; gene_id "Phchi.S6G116600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6332.t1 is derived from g3504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22318575	22319452	.	-	.	Phchi.S1G349100
Phchi.S1	AUGUSTUS	transcript	22318575	22319452	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	stop_codon	22318572	22318574	.	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	CDS	22318575	22318672	0.86	-	2	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	exon	22318575	22318672	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	intron	22318673	22318759	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	CDS	22318760	22318796	0.84	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	exon	22318760	22318796	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	intron	22318797	22318867	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	CDS	22318868	22318912	0.84	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	exon	22318868	22318912	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	intron	22318913	22319225	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	CDS	22319226	22319279	0.58	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	exon	22319226	22319279	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	intron	22319280	22319329	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	CDS	22319330	22319338	0.64	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	exon	22319330	22319338	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	intron	22319339	22319428	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	CDS	22319429	22319452	0.89	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	exon	22319429	22319452	.	-	.	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
Phchi.S1	AUGUSTUS	start_codon	22319450	22319452	.	-	0	transcript_id "Phchi.S1G349100.t1"; gene_id "Phchi.S1G349100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14430.t1 is derived from g12898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12766123	12768195	.	+	.	Phchi.S3G174900
Phchi.S3	AUGUSTUS	transcript	12766123	12768195	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	start_codon	12766123	12766125	.	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12766123	12766222	0.92	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12766123	12766222	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	intron	12766223	12766300	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12766301	12766476	1	+	2	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12766301	12766476	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	intron	12766477	12766638	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12766639	12766698	0.99	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12766639	12766698	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	intron	12766699	12766806	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12766807	12767043	1	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12766807	12767043	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	intron	12767044	12767154	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12767155	12767340	1	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12767155	12767340	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	intron	12767341	12767422	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12767423	12767683	0.99	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12767423	12767683	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	intron	12767684	12767799	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	CDS	12767800	12768195	1	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	exon	12767800	12768195	.	+	.	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
Phchi.S3	AUGUSTUS	stop_codon	12768196	12768198	.	+	0	transcript_id "Phchi.S3G174900.t1"; gene_id "Phchi.S3G174900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6095.t1 is derived from g3266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20936435	20937047	.	-	.	Phchi.S1G325400
Phchi.S1	AUGUSTUS	transcript	20936435	20937047	.	-	.	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	stop_codon	20936432	20936434	.	-	0	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	CDS	20936435	20936634	0.76	-	2	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	exon	20936435	20936634	.	-	.	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	intron	20936635	20936731	.	-	.	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	CDS	20936732	20936830	0.77	-	2	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	exon	20936732	20936830	.	-	.	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	intron	20936831	20936989	.	-	.	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	CDS	20936990	20937047	0.43	-	0	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	exon	20936990	20937047	.	-	.	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
Phchi.S1	AUGUSTUS	start_codon	20937045	20937047	.	-	0	transcript_id "Phchi.S1G325400.t1"; gene_id "Phchi.S1G325400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg421.t1 is derived from g10203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2979407	2980987	.	-	.	Phchi.S6G038000
Phchi.S6	AUGUSTUS	transcript	2979407	2980987	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	stop_codon	2979404	2979406	.	-	0	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2979407	2979471	0.3	-	2	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2979407	2979471	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2979472	2979580	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2979581	2979651	0.29	-	1	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2979581	2979651	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2979652	2979847	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2979848	2979920	0.35	-	2	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2979848	2979920	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2979921	2980042	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2980043	2980066	0.73	-	2	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2980043	2980066	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2980067	2980211	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2980212	2980280	0.89	-	2	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2980212	2980280	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2980281	2980373	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2980374	2980393	0.87	-	1	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2980374	2980393	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2980394	2980549	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2980550	2980610	0.32	-	2	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2980550	2980610	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2980611	2980693	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2980694	2980772	0.32	-	0	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2980694	2980772	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	intron	2980773	2980984	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	CDS	2980985	2980987	0.85	-	0	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	exon	2980985	2980987	.	-	.	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
Phchi.S6	AUGUSTUS	start_codon	2980985	2980987	.	-	0	transcript_id "Phchi.S6G038000.t1"; gene_id "Phchi.S6G038000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg920.t1 is derived from g10702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6454103	6456687	.	+	.	Phchi.S6G087900
Phchi.S6	AUGUSTUS	transcript	6454103	6456687	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	start_codon	6454103	6454105	.	+	0	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6454103	6454273	0.88	+	0	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6454103	6454273	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6454274	6454554	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6454555	6454562	0.99	+	0	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6454555	6454562	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6454563	6454883	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6454884	6454930	0.99	+	1	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6454884	6454930	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6454931	6455068	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6455069	6455283	0.99	+	2	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6455069	6455283	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6455284	6455371	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6455372	6455438	0.85	+	0	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6455372	6455438	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6455439	6455555	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6455556	6455687	0.89	+	2	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6455556	6455687	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6455688	6455784	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6455785	6456044	0.63	+	2	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6455785	6456044	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6456045	6456126	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6456127	6456687	1	+	0	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6456127	6456687	.	+	.	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	stop_codon	6456688	6456690	.	+	0	transcript_id "Phchi.S6G087900.t1"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	transcript	6454103	6455087	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	start_codon	6454103	6454105	.	+	0	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6454103	6454273	0.67	+	0	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6454103	6454273	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6454274	6454554	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6454555	6454562	0.79	+	0	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6454555	6454562	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6454563	6454883	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6454884	6454988	0.78	+	1	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6454884	6454988	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	intron	6454989	6455068	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	CDS	6455069	6455087	0.78	+	1	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	exon	6455069	6455087	.	+	.	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
Phchi.S6	AUGUSTUS	stop_codon	6455088	6455090	.	+	0	transcript_id "Phchi.S6G087900.t2"; gene_id "Phchi.S6G087900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15798.t1 is derived from g14268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21425913	21426752	.	-	.	Phchi.S3G311700
Phchi.S3	AUGUSTUS	transcript	21425913	21426752	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	stop_codon	21425910	21425912	.	-	0	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	CDS	21425913	21426241	0.87	-	2	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	exon	21425913	21426241	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	intron	21426242	21426320	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	CDS	21426321	21426499	0.98	-	1	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	exon	21426321	21426499	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	intron	21426500	21426590	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	CDS	21426591	21426598	0.98	-	0	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	exon	21426591	21426598	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	intron	21426599	21426671	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	CDS	21426672	21426752	0.88	-	0	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	exon	21426672	21426752	.	-	.	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
Phchi.S3	AUGUSTUS	start_codon	21426750	21426752	.	-	0	transcript_id "Phchi.S3G311700.t1"; gene_id "Phchi.S3G311700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12229.t1 is derived from g7905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6850955	6851465	.	+	.	Phchi.S2G030900
Phchi.S2	AUGUSTUS	transcript	6850955	6851465	.	+	.	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	start_codon	6850955	6850957	.	+	0	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	CDS	6850955	6850998	0.68	+	0	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	exon	6850955	6850998	.	+	.	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	intron	6850999	6851105	.	+	.	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	CDS	6851106	6851182	0.68	+	1	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	exon	6851106	6851182	.	+	.	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	intron	6851183	6851361	.	+	.	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	CDS	6851362	6851465	0.68	+	2	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	exon	6851362	6851465	.	+	.	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
Phchi.S2	AUGUSTUS	stop_codon	6851466	6851468	.	+	0	transcript_id "Phchi.S2G030900.t1"; gene_id "Phchi.S2G030900"
# This transcript jg9238.t2 is derived from g6413.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9239.t1 is derived from g6414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40551851	40554140	.	+	.	Phchi.S1G639800
Phchi.S1	AUGUSTUS	transcript	40551851	40554140	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	start_codon	40551851	40551853	.	+	0	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40551851	40551964	0.87	+	0	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40551851	40551964	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40551965	40552058	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40552059	40552330	1	+	0	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40552059	40552330	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40552331	40552442	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40552443	40553123	0.81	+	1	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40552443	40553123	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40553124	40553205	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40553206	40553313	0.73	+	1	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40553206	40553313	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40553314	40553417	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40553418	40553583	0.92	+	1	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40553418	40553583	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40553584	40553664	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40553665	40553759	1	+	0	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40553665	40553759	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40553760	40553859	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40553860	40553941	1	+	1	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40553860	40553941	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	intron	40553942	40554068	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	CDS	40554069	40554140	0.93	+	0	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	exon	40554069	40554140	.	+	.	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
Phchi.S1	AUGUSTUS	stop_codon	40554141	40554143	.	+	0	transcript_id "Phchi.S1G639800.t1"; gene_id "Phchi.S1G639800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg629.t1 is derived from g10411.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4469655	4472717	.	-	.	Phchi.S6G058800
Phchi.S6	AUGUSTUS	transcript	4469655	4472717	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	stop_codon	4469652	4469654	.	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4469655	4469776	1	-	2	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4469655	4469776	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4469777	4469876	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4469877	4469917	1	-	1	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4469877	4469917	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4469918	4470001	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470002	4470090	1	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470002	4470090	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470091	4470173	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470174	4470214	0.86	-	2	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470174	4470214	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470215	4470308	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470309	4470603	0.79	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470309	4470603	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470604	4470714	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470715	4470801	0.94	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470715	4470801	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470802	4470884	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470885	4471118	1	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470885	4471118	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471119	4471190	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471191	4471442	0.99	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471191	4471442	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471443	4471521	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471522	4471611	0.9	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471522	4471611	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471612	4471724	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471725	4471778	0.97	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471725	4471778	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471779	4471880	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471881	4471983	1	-	1	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471881	4471983	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471984	4472080	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472081	4472183	1	-	2	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472081	4472183	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4472184	4472266	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472267	4472321	1	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472267	4472321	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4472322	4472451	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472452	4472492	1	-	2	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472452	4472492	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4472493	4472569	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472570	4472717	0.85	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472570	4472717	.	-	.	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	start_codon	4472715	4472717	.	-	0	transcript_id "Phchi.S6G058800.t1"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	transcript	4469655	4472717	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	stop_codon	4469652	4469654	.	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4469655	4469776	1	-	2	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4469655	4469776	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4469777	4469876	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4469877	4469917	1	-	1	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4469877	4469917	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4469918	4470001	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470002	4470090	1	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470002	4470090	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470091	4470173	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470174	4470218	1	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470174	4470218	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470219	4470308	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470309	4470416	1	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470309	4470416	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470417	4470521	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470522	4470584	0.31	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470522	4470584	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470585	4470714	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470715	4470801	0.84	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470715	4470801	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4470802	4470884	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4470885	4471118	1	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4470885	4471118	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471119	4471190	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471191	4471442	0.99	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471191	4471442	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471443	4471521	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471522	4471611	0.94	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471522	4471611	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471612	4471724	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471725	4471778	0.98	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471725	4471778	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471779	4471880	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4471881	4471983	0.98	-	1	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4471881	4471983	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4471984	4472080	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472081	4472183	1	-	2	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472081	4472183	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4472184	4472266	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472267	4472321	1	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472267	4472321	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4472322	4472451	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472452	4472492	1	-	2	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472452	4472492	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	intron	4472493	4472569	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	CDS	4472570	4472717	0.75	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	exon	4472570	4472717	.	-	.	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
Phchi.S6	AUGUSTUS	start_codon	4472715	4472717	.	-	0	transcript_id "Phchi.S6G058800.t2"; gene_id "Phchi.S6G058800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10234.t1 is derived from g7410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46507850	46508213	.	+	.	Phchi.S1G739300
Phchi.S1	AUGUSTUS	transcript	46507850	46508213	.	+	.	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	start_codon	46507850	46507852	.	+	0	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	CDS	46507850	46508050	1	+	0	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	exon	46507850	46508050	.	+	.	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	intron	46508051	46508198	.	+	.	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	CDS	46508199	46508213	1	+	0	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	exon	46508199	46508213	.	+	.	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
Phchi.S1	AUGUSTUS	stop_codon	46508214	46508216	.	+	0	transcript_id "Phchi.S1G739300.t1"; gene_id "Phchi.S1G739300"
# This transcript jg15616.t2 is derived from g14085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15617.t1 is derived from g14086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20307090	20308262	.	+	.	Phchi.S3G293600
Phchi.S3	AUGUSTUS	transcript	20307090	20308262	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	start_codon	20307090	20307092	.	+	0	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	CDS	20307090	20307294	1	+	0	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	exon	20307090	20307294	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	intron	20307295	20307447	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	CDS	20307448	20307522	0.94	+	2	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	exon	20307448	20307522	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	intron	20307523	20307630	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	CDS	20307631	20307681	0.94	+	2	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	exon	20307631	20307681	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	intron	20307682	20307780	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	CDS	20307781	20307860	1	+	2	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	exon	20307781	20307860	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	intron	20307861	20308031	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	CDS	20308032	20308076	1	+	0	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	exon	20308032	20308076	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	intron	20308077	20308163	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	CDS	20308164	20308262	1	+	0	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	exon	20308164	20308262	.	+	.	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
Phchi.S3	AUGUSTUS	stop_codon	20308263	20308265	.	+	0	transcript_id "Phchi.S3G293600.t1"; gene_id "Phchi.S3G293600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1041.t1 is derived from g10824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7263013	7263564	.	-	.	Phchi.S6G100000
Phchi.S6	AUGUSTUS	transcript	7263013	7263564	.	-	.	transcript_id "Phchi.S6G100000.t1"; gene_id "Phchi.S6G100000"
Phchi.S6	AUGUSTUS	stop_codon	7263010	7263012	.	-	0	transcript_id "Phchi.S6G100000.t1"; gene_id "Phchi.S6G100000"
Phchi.S6	AUGUSTUS	CDS	7263013	7263564	0.87	-	0	transcript_id "Phchi.S6G100000.t1"; gene_id "Phchi.S6G100000"
Phchi.S6	AUGUSTUS	exon	7263013	7263564	.	-	.	transcript_id "Phchi.S6G100000.t1"; gene_id "Phchi.S6G100000"
Phchi.S6	AUGUSTUS	start_codon	7263562	7263564	.	-	0	transcript_id "Phchi.S6G100000.t1"; gene_id "Phchi.S6G100000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11645.t1 is derived from g15696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7443527	7445682	.	-	.	Phchi.S4G122700
Phchi.S4	AUGUSTUS	transcript	7443527	7445682	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	stop_codon	7443524	7443526	.	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7443527	7443643	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7443527	7443643	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7443644	7443728	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7443729	7443932	0.99	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7443729	7443932	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7443933	7444006	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7444007	7444066	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7444007	7444066	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7444067	7444139	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7444140	7444240	1	-	2	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7444140	7444240	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7444241	7444342	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7444343	7444376	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7444343	7444376	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7444377	7444537	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7444538	7444642	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7444538	7444642	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7444643	7444734	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7444735	7444805	1	-	2	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7444735	7444805	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7444806	7444883	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7444884	7444986	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7444884	7444986	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7444987	7445114	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7445115	7445249	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7445115	7445249	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7445250	7445374	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7445375	7445437	1	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7445375	7445437	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	intron	7445438	7445556	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	CDS	7445557	7445682	0.98	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	exon	7445557	7445682	.	-	.	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
Phchi.S4	AUGUSTUS	start_codon	7445680	7445682	.	-	0	transcript_id "Phchi.S4G122700.t1"; gene_id "Phchi.S4G122700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5359.t1 is derived from g2529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16465937	16467735	.	+	.	Phchi.S1G251800
Phchi.S1	AUGUSTUS	transcript	16465937	16467735	.	+	.	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	start_codon	16465937	16465939	.	+	0	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	CDS	16465937	16466962	1	+	0	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	exon	16465937	16466962	.	+	.	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	intron	16466963	16467102	.	+	.	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	CDS	16467103	16467735	1	+	0	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	exon	16467103	16467735	.	+	.	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
Phchi.S1	AUGUSTUS	stop_codon	16467736	16467738	.	+	0	transcript_id "Phchi.S1G251800.t1"; gene_id "Phchi.S1G251800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14442.t1 is derived from g12910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12847720	12851056	.	-	.	Phchi.S3G176100
Phchi.S3	AUGUSTUS	transcript	12847720	12851056	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	stop_codon	12847717	12847719	.	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12847720	12847810	1	-	1	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12847720	12847810	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12847811	12847903	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12847904	12848027	1	-	2	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12847904	12848027	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12848028	12848126	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12848127	12848175	1	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12848127	12848175	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12848176	12848261	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12848262	12848327	1	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12848262	12848327	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12848328	12848422	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12848423	12848788	0.99	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12848423	12848788	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12848789	12848907	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12848908	12849066	0.99	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12848908	12849066	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12849067	12849201	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12849202	12849493	1	-	1	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12849202	12849493	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12849494	12849667	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12849668	12850014	0.97	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12849668	12850014	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12850015	12850142	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12850143	12850340	0.96	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12850143	12850340	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12850341	12850438	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12850439	12850722	1	-	2	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12850439	12850722	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	intron	12850723	12850812	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	CDS	12850813	12851056	0.93	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	exon	12850813	12851056	.	-	.	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
Phchi.S3	AUGUSTUS	start_codon	12851054	12851056	.	-	0	transcript_id "Phchi.S3G176100.t1"; gene_id "Phchi.S3G176100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2789.t1 is derived from g9709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8883359	8883955	.	-	.	Phchi.S5G139800
Phchi.S5	AUGUSTUS	transcript	8883359	8883955	.	-	.	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	stop_codon	8883356	8883358	.	-	0	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	CDS	8883359	8883565	0.86	-	0	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	exon	8883359	8883565	.	-	.	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	intron	8883566	8883652	.	-	.	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	CDS	8883653	8883955	0.48	-	0	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	exon	8883653	8883955	.	-	.	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
Phchi.S5	AUGUSTUS	start_codon	8883953	8883955	.	-	0	transcript_id "Phchi.S5G139800.t1"; gene_id "Phchi.S5G139800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9026.t1 is derived from g6201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39201989	39203579	.	-	.	Phchi.S1G618500
Phchi.S1	AUGUSTUS	transcript	39201989	39203579	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	stop_codon	39201986	39201988	.	-	0	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	CDS	39201989	39202862	0.34	-	1	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	exon	39201989	39202862	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	intron	39202863	39202951	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	CDS	39202952	39202965	0.55	-	0	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	exon	39202952	39202965	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	intron	39202966	39203050	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	CDS	39203051	39203140	1	-	0	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	exon	39203051	39203140	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	intron	39203141	39203237	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	CDS	39203238	39203579	0.87	-	0	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	exon	39203238	39203579	.	-	.	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
Phchi.S1	AUGUSTUS	start_codon	39203577	39203579	.	-	0	transcript_id "Phchi.S1G618500.t1"; gene_id "Phchi.S1G618500"
# This transcript jg1176.t2 is derived from g10959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1177.t1 is derived from g10960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8311678	8312034	.	+	.	Phchi.S6G113600
Phchi.S6	AUGUSTUS	transcript	8311678	8312034	.	+	.	transcript_id "Phchi.S6G113600.t1"; gene_id "Phchi.S6G113600"
Phchi.S6	AUGUSTUS	start_codon	8311678	8311680	.	+	0	transcript_id "Phchi.S6G113600.t1"; gene_id "Phchi.S6G113600"
Phchi.S6	AUGUSTUS	CDS	8311678	8312034	0.87	+	0	transcript_id "Phchi.S6G113600.t1"; gene_id "Phchi.S6G113600"
Phchi.S6	AUGUSTUS	exon	8311678	8312034	.	+	.	transcript_id "Phchi.S6G113600.t1"; gene_id "Phchi.S6G113600"
Phchi.S6	AUGUSTUS	stop_codon	8312035	8312037	.	+	0	transcript_id "Phchi.S6G113600.t1"; gene_id "Phchi.S6G113600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3700.t1 is derived from g869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5232531	5232968	.	+	.	Phchi.S1G085900
Phchi.S1	AUGUSTUS	transcript	5232531	5232968	.	+	.	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	start_codon	5232531	5232533	.	+	0	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	CDS	5232531	5232638	0.76	+	0	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	exon	5232531	5232638	.	+	.	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	intron	5232639	5232734	.	+	.	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	CDS	5232735	5232968	0.94	+	0	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	exon	5232735	5232968	.	+	.	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
Phchi.S1	AUGUSTUS	stop_codon	5232969	5232971	.	+	0	transcript_id "Phchi.S1G085900.t1"; gene_id "Phchi.S1G085900"
# This transcript jg3494.t2 is derived from g663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3495.t1 is derived from g664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4045304	4047172	.	-	.	Phchi.S1G065400
Phchi.S1	AUGUSTUS	transcript	4045304	4047172	.	-	.	transcript_id "Phchi.S1G065400.t1"; gene_id "Phchi.S1G065400"
Phchi.S1	AUGUSTUS	stop_codon	4045301	4045303	.	-	0	transcript_id "Phchi.S1G065400.t1"; gene_id "Phchi.S1G065400"
Phchi.S1	AUGUSTUS	CDS	4045304	4047172	0.77	-	0	transcript_id "Phchi.S1G065400.t1"; gene_id "Phchi.S1G065400"
Phchi.S1	AUGUSTUS	exon	4045304	4047172	.	-	.	transcript_id "Phchi.S1G065400.t1"; gene_id "Phchi.S1G065400"
Phchi.S1	AUGUSTUS	start_codon	4047170	4047172	.	-	0	transcript_id "Phchi.S1G065400.t1"; gene_id "Phchi.S1G065400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3031.t1 is derived from g200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1242264	1249160	.	-	.	Phchi.S1G019000
Phchi.S1	AUGUSTUS	transcript	1242264	1249160	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	stop_codon	1242261	1242263	.	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1242264	1246815	0.66	-	1	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1242264	1246815	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1246816	1246901	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1246902	1247051	1	-	1	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1246902	1247051	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1247052	1247123	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1247124	1247269	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1247124	1247269	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1247270	1247365	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1247366	1247461	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1247366	1247461	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1247462	1247562	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1247563	1247655	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1247563	1247655	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1247656	1247742	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1247743	1247796	0.82	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1247743	1247796	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1247797	1247885	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1247886	1247945	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1247886	1247945	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1247946	1248038	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1248039	1248164	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1248039	1248164	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1248165	1248250	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1248251	1248334	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1248251	1248334	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1248335	1248419	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1248420	1248560	1	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1248420	1248560	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	intron	1248561	1248692	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	CDS	1248693	1249160	0.54	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	exon	1248693	1249160	.	-	.	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
Phchi.S1	AUGUSTUS	start_codon	1249158	1249160	.	-	0	transcript_id "Phchi.S1G019000.t1"; gene_id "Phchi.S1G019000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6119.t1 is derived from g3290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21020440	21022007	.	+	.	Phchi.S1G327800
Phchi.S1	AUGUSTUS	transcript	21020440	21022007	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	start_codon	21020440	21020442	.	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21020440	21020572	0.98	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21020440	21020572	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21020573	21020738	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21020739	21020821	1	+	2	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21020739	21020821	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21020822	21020955	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21020956	21021015	0.85	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21020956	21021015	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21021016	21021119	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21021120	21021228	1	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21021120	21021228	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21021229	21021328	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21021329	21021381	1	+	2	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21021329	21021381	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21021382	21021548	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21021549	21021629	1	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21021549	21021629	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21021630	21021741	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21021742	21021854	1	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21021742	21021854	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	intron	21021855	21021952	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	CDS	21021953	21022007	1	+	1	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	exon	21021953	21022007	.	+	.	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
Phchi.S1	AUGUSTUS	stop_codon	21022008	21022010	.	+	0	transcript_id "Phchi.S1G327800.t1"; gene_id "Phchi.S1G327800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13169.t1 is derived from g11634.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4477961	4480497	.	+	.	Phchi.S3G048800
Phchi.S3	AUGUSTUS	transcript	4477961	4480497	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	start_codon	4477961	4477963	.	+	0	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4477961	4478066	0.98	+	0	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4477961	4478066	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4478067	4478148	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4478149	4478175	1	+	2	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4478149	4478175	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4478176	4478254	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4478255	4478723	0.81	+	2	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4478255	4478723	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4478724	4478818	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4478819	4479135	0.97	+	1	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4478819	4479135	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479136	4479323	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479324	4479495	1	+	2	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479324	4479495	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479496	4479591	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479592	4479648	1	+	1	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479592	4479648	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479649	4479750	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479751	4479886	0.82	+	1	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479751	4479886	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479887	4479968	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479969	4479977	0.52	+	0	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479969	4479977	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479978	4480045	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4480046	4480113	0.5	+	0	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4480046	4480113	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4480114	4480244	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4480245	4480497	0.53	+	1	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4480245	4480497	.	+	.	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	stop_codon	4480498	4480500	.	+	0	transcript_id "Phchi.S3G048800.t1"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	transcript	4477961	4480497	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	start_codon	4477961	4477963	.	+	0	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4477961	4478066	0.98	+	0	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4477961	4478066	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4478067	4478179	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4478180	4478723	0.95	+	2	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4478180	4478723	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4478724	4478818	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4478819	4479135	0.99	+	1	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4478819	4479135	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479136	4479323	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479324	4479495	1	+	2	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479324	4479495	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479496	4479591	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479592	4479648	0.99	+	1	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479592	4479648	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479649	4479750	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479751	4479886	0.79	+	1	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479751	4479886	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479887	4479968	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4479969	4479977	0.45	+	0	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4479969	4479977	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4479978	4480045	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4480046	4480113	0.45	+	0	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4480046	4480113	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	intron	4480114	4480244	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	CDS	4480245	4480497	0.47	+	1	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	exon	4480245	4480497	.	+	.	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
Phchi.S3	AUGUSTUS	stop_codon	4480498	4480500	.	+	0	transcript_id "Phchi.S3G048800.t2"; gene_id "Phchi.S3G048800"
# This transcript jg14729.t2 is derived from g13197.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14730.t1 is derived from g13198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14405364	14405811	.	-	.	Phchi.S3G204900
Phchi.S3	AUGUSTUS	transcript	14405364	14405811	.	-	.	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	stop_codon	14405361	14405363	.	-	0	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	CDS	14405364	14405443	0.74	-	2	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	exon	14405364	14405443	.	-	.	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	intron	14405444	14405615	.	-	.	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	CDS	14405616	14405811	0.87	-	0	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	exon	14405616	14405811	.	-	.	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
Phchi.S3	AUGUSTUS	start_codon	14405809	14405811	.	-	0	transcript_id "Phchi.S3G204900.t1"; gene_id "Phchi.S3G204900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2415.t1 is derived from g9335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6544320	6544863	.	+	.	Phchi.S5G102400
Phchi.S5	AUGUSTUS	transcript	6544320	6544863	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	start_codon	6544320	6544322	.	+	0	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	CDS	6544320	6544325	1	+	0	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	exon	6544320	6544325	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	intron	6544326	6544407	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	CDS	6544408	6544493	1	+	0	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	exon	6544408	6544493	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	intron	6544494	6544575	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	CDS	6544576	6544699	1	+	1	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	exon	6544576	6544699	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	intron	6544700	6544818	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	CDS	6544819	6544863	1	+	0	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	exon	6544819	6544863	.	+	.	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
Phchi.S5	AUGUSTUS	stop_codon	6544864	6544866	.	+	0	transcript_id "Phchi.S5G102400.t1"; gene_id "Phchi.S5G102400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6753.t1 is derived from g3925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24854383	24855485	.	-	.	Phchi.S1G391200
Phchi.S1	AUGUSTUS	transcript	24854383	24855485	.	-	.	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	stop_codon	24854380	24854382	.	-	0	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	CDS	24854383	24854797	0.66	-	1	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	exon	24854383	24854797	.	-	.	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	intron	24854798	24854901	.	-	.	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	CDS	24854902	24855485	0.7	-	0	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	exon	24854902	24855485	.	-	.	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
Phchi.S1	AUGUSTUS	start_codon	24855483	24855485	.	-	0	transcript_id "Phchi.S1G391200.t1"; gene_id "Phchi.S1G391200"
# This transcript jg8156.t2 is derived from g5331.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8157.t1 is derived from g5332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34159313	34162788	.	+	.	Phchi.S1G531600
Phchi.S1	AUGUSTUS	transcript	34159313	34162788	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	start_codon	34159313	34159315	.	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34159313	34159331	0.88	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34159313	34159331	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34159332	34159679	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34159680	34160638	0.98	+	2	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34159680	34160638	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34160639	34160957	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34160958	34161031	1	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34160958	34161031	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34161032	34161149	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34161150	34161204	1	+	1	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34161150	34161204	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34161205	34161364	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34161365	34161439	1	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34161365	34161439	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34161440	34161927	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34161928	34162001	1	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34161928	34162001	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34162002	34162217	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34162218	34162266	1	+	1	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34162218	34162266	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34162267	34162417	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34162418	34162502	1	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34162418	34162502	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34162503	34162592	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34162593	34162649	1	+	2	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34162593	34162649	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	intron	34162650	34162735	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	CDS	34162736	34162788	1	+	2	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	exon	34162736	34162788	.	+	.	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
Phchi.S1	AUGUSTUS	stop_codon	34162789	34162791	.	+	0	transcript_id "Phchi.S1G531600.t1"; gene_id "Phchi.S1G531600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4836.t1 is derived from g2006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13049532	13050734	.	+	.	Phchi.S1G199500
Phchi.S1	AUGUSTUS	transcript	13049532	13050734	.	+	.	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	start_codon	13049532	13049534	.	+	0	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	CDS	13049532	13050073	0.99	+	0	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	exon	13049532	13050073	.	+	.	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	intron	13050074	13050226	.	+	.	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	CDS	13050227	13050734	0.67	+	1	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	exon	13050227	13050734	.	+	.	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
Phchi.S1	AUGUSTUS	stop_codon	13050735	13050737	.	+	0	transcript_id "Phchi.S1G199500.t1"; gene_id "Phchi.S1G199500"
# This transcript jg8036.t2 is derived from g5211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8037.t1 is derived from g5212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32613822	32615620	.	-	.	Phchi.S1G519600
Phchi.S1	AUGUSTUS	transcript	32613822	32615620	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	stop_codon	32613819	32613821	.	-	0	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32613822	32613932	1	-	0	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32613822	32613932	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	intron	32613933	32614018	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32614019	32614066	0.43	-	0	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32614019	32614066	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	intron	32614067	32614191	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32614192	32614367	0.42	-	2	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32614192	32614367	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	intron	32614368	32614485	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32614486	32614755	0.99	-	2	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32614486	32614755	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	intron	32614756	32614888	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32614889	32615019	0.61	-	1	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32614889	32615019	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	intron	32615020	32615131	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32615132	32615356	0.49	-	1	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32615132	32615356	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	intron	32615357	32615603	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	CDS	32615604	32615620	0.93	-	0	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	exon	32615604	32615620	.	-	.	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
Phchi.S1	AUGUSTUS	start_codon	32615618	32615620	.	-	0	transcript_id "Phchi.S1G519600.t1"; gene_id "Phchi.S1G519600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2460.t1 is derived from g9380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6768924	6769510	.	+	.	Phchi.S5G106900
Phchi.S5	AUGUSTUS	transcript	6768924	6769510	.	+	.	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	start_codon	6768924	6768926	.	+	0	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	CDS	6768924	6769293	0.1	+	0	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	exon	6768924	6769293	.	+	.	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	intron	6769294	6769508	.	+	.	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	CDS	6769509	6769510	0.63	+	2	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	exon	6769509	6769510	.	+	.	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
Phchi.S5	AUGUSTUS	stop_codon	6769511	6769513	.	+	0	transcript_id "Phchi.S5G106900.t1"; gene_id "Phchi.S5G106900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13025.t1 is derived from g11490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3668967	3670716	.	-	.	Phchi.S3G034400
Phchi.S3	AUGUSTUS	transcript	3668967	3670716	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	stop_codon	3668964	3668966	.	-	0	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	CDS	3668967	3670132	0.34	-	2	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	exon	3668967	3670132	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	intron	3670133	3670211	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	CDS	3670212	3670246	0.43	-	1	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	exon	3670212	3670246	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	intron	3670247	3670333	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	CDS	3670334	3670396	0.38	-	1	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	exon	3670334	3670396	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	intron	3670397	3670494	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	CDS	3670495	3670612	0.45	-	2	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	exon	3670495	3670612	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	intron	3670613	3670691	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	CDS	3670692	3670716	0.37	-	0	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	exon	3670692	3670716	.	-	.	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
Phchi.S3	AUGUSTUS	start_codon	3670714	3670716	.	-	0	transcript_id "Phchi.S3G034400.t1"; gene_id "Phchi.S3G034400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15.t1 is derived from g1.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C103	AUGUSTUS	gene	45	5820	.	+	.	Phchi.C103G000100
Phchi.C103	AUGUSTUS	transcript	45	5820	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	45	302	0.83	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	45	302	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	303	539	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	540	931	0.96	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	540	931	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	932	1047	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	1048	1096	0.81	+	1	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	1048	1096	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	1097	1483	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	1484	1687	0.84	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	1484	1687	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	1688	1866	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	1867	1971	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	1867	1971	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	1972	2099	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	2100	2165	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	2100	2165	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	2166	2277	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	2278	2442	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	2278	2442	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	2443	2537	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	2538	2612	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	2538	2612	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	2613	2702	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	2703	2854	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	2703	2854	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	2855	2952	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	2953	3088	1	+	1	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	2953	3088	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	3089	3173	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	3174	3243	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	3174	3243	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	3244	3328	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	3329	3456	1	+	2	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	3329	3456	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	3457	3545	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	3546	3602	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	3546	3602	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	3603	3905	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	3906	4091	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	3906	4091	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	4092	4309	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	4310	4402	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	4310	4402	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	4403	4542	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	4543	4628	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	4543	4628	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	4629	4703	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	4704	4770	1	+	1	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	4704	4770	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	4771	4909	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	4910	4976	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	4910	4976	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	4977	5055	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	5056	5192	1	+	2	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	5056	5192	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	5193	5277	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	5278	5369	1	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	5278	5369	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	5370	5521	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	5522	5588	1	+	1	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	5522	5588	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	intron	5589	5673	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	CDS	5674	5820	0.97	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	exon	5674	5820	.	+	.	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
Phchi.C103	AUGUSTUS	stop_codon	5821	5823	.	+	0	transcript_id "Phchi.C103G000100.t1"; gene_id "Phchi.C103G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg7684.t1 is derived from g4858.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30613216	30615827	.	+	.	Phchi.S1G484300
Phchi.S1	AUGUSTUS	transcript	30613216	30615827	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	start_codon	30613216	30613218	.	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613216	30613278	1	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613216	30613278	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613279	30613363	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613364	30613481	1	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613364	30613481	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613482	30613608	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613609	30613679	1	+	2	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613609	30613679	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613680	30613748	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613749	30613805	1	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613749	30613805	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613806	30613906	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613907	30613998	1	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613907	30613998	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613999	30614144	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614145	30614192	0.99	+	1	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614145	30614192	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614193	30614295	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614296	30614419	0.99	+	1	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614296	30614419	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614420	30614517	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614518	30614564	0.82	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614518	30614564	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614565	30614693	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614694	30614775	0.87	+	1	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614694	30614775	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614776	30614876	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614877	30614953	0.92	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614877	30614953	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614954	30615053	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615054	30615173	1	+	1	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615054	30615173	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615174	30615253	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615254	30615328	1	+	1	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615254	30615328	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615329	30615412	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615413	30615555	1	+	1	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615413	30615555	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615556	30615747	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615748	30615827	0.99	+	2	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615748	30615827	.	+	.	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	stop_codon	30615828	30615830	.	+	0	transcript_id "Phchi.S1G484300.t1"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	transcript	30613216	30615827	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	start_codon	30613216	30613218	.	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613216	30613278	1	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613216	30613278	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613279	30613363	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613364	30613481	1	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613364	30613481	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613482	30613608	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613609	30613679	1	+	2	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613609	30613679	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613680	30613748	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613749	30613805	0.97	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613749	30613805	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613806	30613906	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613907	30613998	1	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613907	30613998	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613999	30614144	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614145	30614192	1	+	1	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614145	30614192	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614193	30614295	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614296	30614419	0.99	+	1	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614296	30614419	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614420	30614517	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614518	30614564	0.81	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614518	30614564	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614565	30614693	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614694	30614775	0.84	+	1	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614694	30614775	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614776	30614876	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614877	30614953	0.94	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614877	30614953	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614954	30615053	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615054	30615173	1	+	1	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615054	30615173	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615174	30615253	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615254	30615328	1	+	1	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615254	30615328	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615329	30615412	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615413	30615555	1	+	1	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615413	30615555	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615556	30615753	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615754	30615827	1	+	2	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615754	30615827	.	+	.	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	stop_codon	30615828	30615830	.	+	0	transcript_id "Phchi.S1G484300.t2"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	transcript	30613216	30615827	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	start_codon	30613216	30613218	.	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613216	30613278	1	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613216	30613278	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613279	30613363	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613364	30613481	1	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613364	30613481	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613482	30613608	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613609	30613679	1	+	2	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613609	30613679	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613680	30613748	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613749	30613805	0.97	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613749	30613805	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613806	30613906	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30613907	30613998	1	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30613907	30613998	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30613999	30614144	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614145	30614192	1	+	1	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614145	30614192	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614193	30614295	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614296	30614419	0.98	+	1	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614296	30614419	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614420	30614626	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614627	30614641	0.4	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614627	30614641	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614642	30614876	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30614877	30614953	0.86	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30614877	30614953	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30614954	30615053	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615054	30615173	1	+	1	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615054	30615173	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615174	30615253	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615254	30615328	1	+	1	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615254	30615328	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615329	30615412	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615413	30615555	1	+	1	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615413	30615555	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	intron	30615556	30615747	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	CDS	30615748	30615827	0.98	+	2	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	exon	30615748	30615827	.	+	.	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
Phchi.S1	AUGUSTUS	stop_codon	30615828	30615830	.	+	0	transcript_id "Phchi.S1G484300.t3"; gene_id "Phchi.S1G484300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13398.t1 is derived from g11864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6523690	6524772	.	-	.	Phchi.S3G071700
Phchi.S3	AUGUSTUS	transcript	6523690	6524772	.	-	.	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	stop_codon	6523687	6523689	.	-	0	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	CDS	6523690	6523961	0.95	-	2	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	exon	6523690	6523961	.	-	.	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	intron	6523962	6524116	.	-	.	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	CDS	6524117	6524346	0.87	-	1	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	exon	6524117	6524346	.	-	.	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	intron	6524347	6524626	.	-	.	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	CDS	6524627	6524772	1	-	0	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	exon	6524627	6524772	.	-	.	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
Phchi.S3	AUGUSTUS	start_codon	6524770	6524772	.	-	0	transcript_id "Phchi.S3G071700.t1"; gene_id "Phchi.S3G071700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10267.t1 is derived from g7443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46752042	46753221	.	-	.	Phchi.S1G742600
Phchi.S1	AUGUSTUS	transcript	46752042	46753221	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	stop_codon	46752039	46752041	.	-	0	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	CDS	46752042	46752321	0.51	-	1	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	exon	46752042	46752321	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	intron	46752322	46752456	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	CDS	46752457	46752720	0.59	-	1	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	exon	46752457	46752720	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	intron	46752721	46752855	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	CDS	46752856	46753097	0.8	-	0	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	exon	46752856	46753097	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	intron	46753098	46753170	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	CDS	46753171	46753221	0.87	-	0	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	exon	46753171	46753221	.	-	.	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
Phchi.S1	AUGUSTUS	start_codon	46753219	46753221	.	-	0	transcript_id "Phchi.S1G742600.t1"; gene_id "Phchi.S1G742600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3535.t1 is derived from g704.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4348526	4349274	.	-	.	Phchi.S1G069400
Phchi.S1	AUGUSTUS	transcript	4348526	4349274	.	-	.	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	stop_codon	4348523	4348525	.	-	0	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	CDS	4348526	4348539	1	-	2	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	exon	4348526	4348539	.	-	.	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	intron	4348540	4348927	.	-	.	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	CDS	4348928	4349102	1	-	0	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	exon	4348928	4349102	.	-	.	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	intron	4349103	4349190	.	-	.	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	CDS	4349191	4349274	0.95	-	0	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	exon	4349191	4349274	.	-	.	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	start_codon	4349272	4349274	.	-	0	transcript_id "Phchi.S1G069400.t1"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	transcript	4348526	4349274	.	-	.	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	stop_codon	4348523	4348525	.	-	0	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	CDS	4348526	4348554	0.75	-	2	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	exon	4348526	4348554	.	-	.	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	intron	4348555	4348927	.	-	.	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	CDS	4348928	4349102	0.9	-	0	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	exon	4348928	4349102	.	-	.	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	intron	4349103	4349190	.	-	.	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	CDS	4349191	4349274	0.82	-	0	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	exon	4349191	4349274	.	-	.	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
Phchi.S1	AUGUSTUS	start_codon	4349272	4349274	.	-	0	transcript_id "Phchi.S1G069400.t2"; gene_id "Phchi.S1G069400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14535.t1 is derived from g13003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13342136	13343041	.	-	.	Phchi.S3G185400
Phchi.S3	AUGUSTUS	transcript	13342136	13343041	.	-	.	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	stop_codon	13342133	13342135	.	-	0	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	CDS	13342136	13342378	0.99	-	0	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	exon	13342136	13342378	.	-	.	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	intron	13342379	13342660	.	-	.	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	CDS	13342661	13342723	1	-	0	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	exon	13342661	13342723	.	-	.	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	intron	13342724	13342882	.	-	.	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	CDS	13342883	13343041	0.8	-	0	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	exon	13342883	13343041	.	-	.	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
Phchi.S3	AUGUSTUS	start_codon	13343039	13343041	.	-	0	transcript_id "Phchi.S3G185400.t1"; gene_id "Phchi.S3G185400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11003.t1 is derived from g15053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3592510	3593693	.	-	.	Phchi.S4G058500
Phchi.S4	AUGUSTUS	transcript	3592510	3593693	.	-	.	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	stop_codon	3592507	3592509	.	-	0	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	CDS	3592510	3593312	0.49	-	2	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	exon	3592510	3593312	.	-	.	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	intron	3593313	3593386	.	-	.	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	CDS	3593387	3593693	0.21	-	0	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	exon	3593387	3593693	.	-	.	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
Phchi.S4	AUGUSTUS	start_codon	3593691	3593693	.	-	0	transcript_id "Phchi.S4G058500.t1"; gene_id "Phchi.S4G058500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11589.t1 is derived from g15640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7243198	7245314	.	+	.	Phchi.S4G117100
Phchi.S4	AUGUSTUS	transcript	7243198	7245314	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	start_codon	7243198	7243200	.	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	CDS	7243198	7243557	1	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	exon	7243198	7243557	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	intron	7243558	7243637	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	CDS	7243638	7243751	1	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	exon	7243638	7243751	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	intron	7243752	7243843	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	CDS	7243844	7243942	1	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	exon	7243844	7243942	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	intron	7243943	7244024	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	CDS	7244025	7244099	1	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	exon	7244025	7244099	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	intron	7244100	7245067	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	CDS	7245068	7245135	0.6	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	exon	7245068	7245135	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	intron	7245136	7245238	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	CDS	7245239	7245314	0.59	+	1	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	exon	7245239	7245314	.	+	.	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
Phchi.S4	AUGUSTUS	stop_codon	7245315	7245317	.	+	0	transcript_id "Phchi.S4G117100.t1"; gene_id "Phchi.S4G117100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8396.t1 is derived from g5571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35741089	35743218	.	+	.	Phchi.S1G555500
Phchi.S1	AUGUSTUS	transcript	35741089	35743218	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	start_codon	35741089	35741091	.	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741089	35741188	0.81	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741089	35741188	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35741189	35741471	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741472	35741638	0.56	+	2	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741472	35741638	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35741639	35741777	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741778	35742101	0.48	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741778	35742101	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742102	35742195	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742196	35742252	1	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742196	35742252	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742253	35742339	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742340	35742473	1	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742340	35742473	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742474	35742599	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742600	35742837	0.98	+	1	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742600	35742837	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742838	35742961	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742962	35743029	0.93	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742962	35743029	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35743030	35743208	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35743209	35743218	1	+	1	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35743209	35743218	.	+	.	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	stop_codon	35743219	35743221	.	+	0	transcript_id "Phchi.S1G555500.t1"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	transcript	35741089	35743218	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	start_codon	35741089	35741091	.	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741089	35741188	0.78	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741089	35741188	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35741189	35741447	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741448	35741638	0.51	+	2	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741448	35741638	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35741639	35741777	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741778	35742101	0.47	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741778	35742101	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742102	35742195	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742196	35742252	1	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742196	35742252	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742253	35742339	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742340	35742473	1	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742340	35742473	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742474	35742599	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742600	35742837	1	+	1	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742600	35742837	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742838	35742961	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742962	35743029	0.99	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742962	35743029	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35743030	35743208	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35743209	35743218	1	+	1	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35743209	35743218	.	+	.	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	stop_codon	35743219	35743221	.	+	0	transcript_id "Phchi.S1G555500.t2"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	transcript	35741089	35743218	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	start_codon	35741089	35741091	.	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741089	35741188	0.88	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741089	35741188	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35741189	35741447	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741448	35741638	0.21	+	2	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741448	35741638	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35741639	35741777	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35741778	35742101	0.52	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35741778	35742101	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742102	35742195	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742196	35742252	1	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742196	35742252	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742253	35742336	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742337	35742473	1	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742337	35742473	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742474	35742599	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742600	35742837	0.99	+	1	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742600	35742837	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35742838	35742961	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35742962	35743029	0.94	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35742962	35743029	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	intron	35743030	35743208	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	CDS	35743209	35743218	1	+	1	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	exon	35743209	35743218	.	+	.	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
Phchi.S1	AUGUSTUS	stop_codon	35743219	35743221	.	+	0	transcript_id "Phchi.S1G555500.t3"; gene_id "Phchi.S1G555500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14999.t1 is derived from g13467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16191006	16191604	.	-	.	Phchi.S3G231800
Phchi.S3	AUGUSTUS	transcript	16191006	16191604	.	-	.	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	stop_codon	16191003	16191005	.	-	0	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	CDS	16191006	16191101	1	-	0	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	exon	16191006	16191101	.	-	.	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	intron	16191102	16191333	.	-	.	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	CDS	16191334	16191489	1	-	0	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	exon	16191334	16191489	.	-	.	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	intron	16191490	16191571	.	-	.	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	CDS	16191572	16191604	1	-	0	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	exon	16191572	16191604	.	-	.	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	start_codon	16191602	16191604	.	-	0	transcript_id "Phchi.S3G231800.t1"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	transcript	16191006	16191604	.	-	.	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	stop_codon	16191003	16191005	.	-	0	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	CDS	16191006	16191101	1	-	0	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	exon	16191006	16191101	.	-	.	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	intron	16191102	16191333	.	-	.	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	CDS	16191334	16191489	1	-	0	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	exon	16191334	16191489	.	-	.	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	intron	16191490	16191577	.	-	.	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	CDS	16191578	16191604	0.99	-	0	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	exon	16191578	16191604	.	-	.	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
Phchi.S3	AUGUSTUS	start_codon	16191602	16191604	.	-	0	transcript_id "Phchi.S3G231800.t2"; gene_id "Phchi.S3G231800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3774.t1 is derived from g943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5637867	5642696	.	+	.	Phchi.S1G093300
Phchi.S1	AUGUSTUS	transcript	5637867	5642696	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	start_codon	5637867	5637869	.	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5637867	5637873	0.77	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5637867	5637873	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5637874	5637947	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5637948	5638027	1	+	2	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5637948	5638027	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5638028	5638108	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5638109	5638201	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5638109	5638201	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5638202	5638363	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5638364	5638465	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5638364	5638465	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5638466	5638553	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5638554	5638676	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5638554	5638676	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5638677	5638851	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5638852	5638913	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5638852	5638913	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5638914	5639004	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5639005	5639085	1	+	1	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5639005	5639085	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5639086	5639313	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5639314	5639368	1	+	1	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5639314	5639368	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5639369	5639465	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5639466	5639534	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5639466	5639534	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5639535	5639627	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5639628	5639807	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5639628	5639807	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5639808	5639879	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5639880	5639931	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5639880	5639931	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5639932	5640008	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5640009	5640057	1	+	2	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5640009	5640057	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5640058	5640136	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5640137	5640233	1	+	1	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5640137	5640233	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5640234	5640420	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5640421	5640642	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5640421	5640642	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5640643	5640735	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5640736	5640861	1	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5640736	5640861	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5640862	5640957	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5640958	5641032	0.75	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5640958	5641032	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5641033	5641155	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5641156	5641319	0.74	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5641156	5641319	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5641320	5641467	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5641468	5641567	1	+	1	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5641468	5641567	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5641568	5641805	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5641806	5641865	0.99	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5641806	5641865	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5641866	5641972	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5641973	5642059	0.96	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5641973	5642059	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5642060	5642166	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5642167	5642286	0.99	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5642167	5642286	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	intron	5642287	5642369	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	CDS	5642370	5642696	0.98	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	exon	5642370	5642696	.	+	.	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
Phchi.S1	AUGUSTUS	stop_codon	5642697	5642699	.	+	0	transcript_id "Phchi.S1G093300.t1"; gene_id "Phchi.S1G093300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13522.t1 is derived from g11989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7340719	7341425	.	-	.	Phchi.S3G084100
Phchi.S3	AUGUSTUS	transcript	7340719	7341425	.	-	.	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	stop_codon	7340716	7340718	.	-	0	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	CDS	7340719	7341122	1	-	2	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	exon	7340719	7341122	.	-	.	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	intron	7341123	7341418	.	-	.	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	CDS	7341419	7341425	0.77	-	0	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	exon	7341419	7341425	.	-	.	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
Phchi.S3	AUGUSTUS	start_codon	7341423	7341425	.	-	0	transcript_id "Phchi.S3G084100.t1"; gene_id "Phchi.S3G084100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15414.t1 is derived from g13882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18954585	18958756	.	-	.	Phchi.S3G273300
Phchi.S3	AUGUSTUS	transcript	18954585	18958756	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	stop_codon	18954582	18954584	.	-	0	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18954585	18955304	0.99	-	0	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18954585	18955304	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18955305	18955390	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18955391	18955536	0.99	-	2	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18955391	18955536	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18955537	18955679	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18955680	18955756	1	-	1	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18955680	18955756	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18955757	18955858	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18955859	18955909	1	-	1	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18955859	18955909	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18955910	18956009	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18956010	18956083	1	-	0	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18956010	18956083	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18956084	18956437	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18956438	18956526	1	-	2	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18956438	18956526	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18956527	18956749	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18956750	18956758	1	-	2	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18956750	18956758	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18956759	18957004	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18957005	18957087	1	-	1	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18957005	18957087	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18957088	18957272	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18957273	18957291	0.34	-	2	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18957273	18957291	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18957292	18957422	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18957423	18958060	0.31	-	1	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18957423	18958060	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18958061	18958137	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18958138	18958381	0.98	-	2	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18958138	18958381	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	intron	18958382	18958518	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	CDS	18958519	18958756	0.69	-	0	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	exon	18958519	18958756	.	-	.	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
Phchi.S3	AUGUSTUS	start_codon	18958754	18958756	.	-	0	transcript_id "Phchi.S3G273300.t1"; gene_id "Phchi.S3G273300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3622.t1 is derived from g791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4810739	4811786	.	-	.	Phchi.S1G078100
Phchi.S1	AUGUSTUS	transcript	4810739	4811786	.	-	.	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	stop_codon	4810736	4810738	.	-	0	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	CDS	4810739	4810831	0.25	-	0	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	exon	4810739	4810831	.	-	.	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	intron	4810832	4810931	.	-	.	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	CDS	4810932	4811786	0.09	-	0	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	exon	4810932	4811786	.	-	.	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
Phchi.S1	AUGUSTUS	start_codon	4811784	4811786	.	-	0	transcript_id "Phchi.S1G078100.t1"; gene_id "Phchi.S1G078100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9393.t1 is derived from g6569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41312925	41313920	.	-	.	Phchi.S1G655200
Phchi.S1	AUGUSTUS	transcript	41312925	41313920	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	stop_codon	41312922	41312924	.	-	0	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	CDS	41312925	41312972	1	-	0	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	exon	41312925	41312972	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	intron	41312973	41313113	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	CDS	41313114	41313368	0.75	-	0	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	exon	41313114	41313368	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	intron	41313369	41313469	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	CDS	41313470	41313515	0.83	-	1	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	exon	41313470	41313515	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	intron	41313516	41313723	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	CDS	41313724	41313920	0.54	-	0	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	exon	41313724	41313920	.	-	.	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
Phchi.S1	AUGUSTUS	start_codon	41313918	41313920	.	-	0	transcript_id "Phchi.S1G655200.t1"; gene_id "Phchi.S1G655200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10923.t1 is derived from g14973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2980098	2982197	.	-	.	Phchi.S4G050500
Phchi.S4	AUGUSTUS	transcript	2980098	2982197	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	stop_codon	2980095	2980097	.	-	0	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2980098	2980423	1	-	2	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2980098	2980423	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	intron	2980424	2980500	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2980501	2980670	1	-	1	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2980501	2980670	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	intron	2980671	2980753	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2980754	2980955	1	-	2	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2980754	2980955	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	intron	2980956	2981038	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2981039	2981254	0.99	-	2	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2981039	2981254	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	intron	2981255	2981356	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2981357	2981583	0.99	-	1	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2981357	2981583	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	intron	2981584	2981720	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2981721	2981937	0.96	-	2	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2981721	2981937	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	intron	2981938	2982046	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	CDS	2982047	2982197	0.56	-	0	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	exon	2982047	2982197	.	-	.	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
Phchi.S4	AUGUSTUS	start_codon	2982195	2982197	.	-	0	transcript_id "Phchi.S4G050500.t1"; gene_id "Phchi.S4G050500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11391.t1 is derived from g15441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6112617	6114607	.	-	.	Phchi.S4G097300
Phchi.S4	AUGUSTUS	transcript	6112617	6114607	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	stop_codon	6112614	6112616	.	-	0	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	CDS	6112617	6112645	0.98	-	2	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	exon	6112617	6112645	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	intron	6112646	6112763	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	CDS	6112764	6112978	0.67	-	1	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	exon	6112764	6112978	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	intron	6112979	6113089	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	CDS	6113090	6113881	0.98	-	1	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	exon	6113090	6113881	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	intron	6113882	6113998	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	CDS	6113999	6114368	1	-	2	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	exon	6113999	6114368	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	intron	6114369	6114510	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	CDS	6114511	6114607	1	-	0	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	exon	6114511	6114607	.	-	.	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
Phchi.S4	AUGUSTUS	start_codon	6114605	6114607	.	-	0	transcript_id "Phchi.S4G097300.t1"; gene_id "Phchi.S4G097300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13476.t1 is derived from g11943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7077638	7078765	.	-	.	Phchi.S3G079500
Phchi.S3	AUGUSTUS	transcript	7077638	7078765	.	-	.	transcript_id "Phchi.S3G079500.t1"; gene_id "Phchi.S3G079500"
Phchi.S3	AUGUSTUS	stop_codon	7077635	7077637	.	-	0	transcript_id "Phchi.S3G079500.t1"; gene_id "Phchi.S3G079500"
Phchi.S3	AUGUSTUS	CDS	7077638	7078765	0.96	-	0	transcript_id "Phchi.S3G079500.t1"; gene_id "Phchi.S3G079500"
Phchi.S3	AUGUSTUS	exon	7077638	7078765	.	-	.	transcript_id "Phchi.S3G079500.t1"; gene_id "Phchi.S3G079500"
Phchi.S3	AUGUSTUS	start_codon	7078763	7078765	.	-	0	transcript_id "Phchi.S3G079500.t1"; gene_id "Phchi.S3G079500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8837.t1 is derived from g6012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38217816	38219720	.	-	.	Phchi.S1G599600
Phchi.S1	AUGUSTUS	transcript	38217816	38219720	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	stop_codon	38217813	38217815	.	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38217816	38217995	1	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38217816	38217995	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38217996	38218140	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38218141	38218203	0.79	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38218141	38218203	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38218204	38218376	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38218377	38218439	0.83	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38218377	38218439	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38218440	38218541	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38218542	38218637	0.88	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38218542	38218637	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38218638	38218719	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38218720	38218814	1	-	2	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38218720	38218814	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38218815	38218895	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38218896	38218974	1	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38218896	38218974	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38218975	38219120	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38219121	38219212	1	-	2	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38219121	38219212	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	intron	38219213	38219569	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	CDS	38219570	38219720	0.99	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	exon	38219570	38219720	.	-	.	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
Phchi.S1	AUGUSTUS	start_codon	38219718	38219720	.	-	0	transcript_id "Phchi.S1G599600.t1"; gene_id "Phchi.S1G599600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8592.t1 is derived from g5767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36795226	36797078	.	+	.	Phchi.S1G575100
Phchi.S1	AUGUSTUS	transcript	36795226	36797078	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	start_codon	36795226	36795228	.	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	CDS	36795226	36795378	0.99	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	exon	36795226	36795378	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	intron	36795379	36795747	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	CDS	36795748	36796134	0.81	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	exon	36795748	36796134	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	intron	36796135	36796266	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	CDS	36796267	36796377	0.6	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	exon	36796267	36796377	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	intron	36796378	36796470	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	CDS	36796471	36796686	1	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	exon	36796471	36796686	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	intron	36796687	36796799	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	CDS	36796800	36797078	0.99	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	exon	36796800	36797078	.	+	.	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
Phchi.S1	AUGUSTUS	stop_codon	36797079	36797081	.	+	0	transcript_id "Phchi.S1G575100.t1"; gene_id "Phchi.S1G575100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6627.t1 is derived from g3799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24160860	24161660	.	-	.	Phchi.S1G378600
Phchi.S1	AUGUSTUS	transcript	24160860	24161660	.	-	.	transcript_id "Phchi.S1G378600.t1"; gene_id "Phchi.S1G378600"
Phchi.S1	AUGUSTUS	stop_codon	24160857	24160859	.	-	0	transcript_id "Phchi.S1G378600.t1"; gene_id "Phchi.S1G378600"
Phchi.S1	AUGUSTUS	CDS	24160860	24161660	0.86	-	0	transcript_id "Phchi.S1G378600.t1"; gene_id "Phchi.S1G378600"
Phchi.S1	AUGUSTUS	exon	24160860	24161660	.	-	.	transcript_id "Phchi.S1G378600.t1"; gene_id "Phchi.S1G378600"
Phchi.S1	AUGUSTUS	start_codon	24161658	24161660	.	-	0	transcript_id "Phchi.S1G378600.t1"; gene_id "Phchi.S1G378600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6027.t1 is derived from g3198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20500591	20502252	.	-	.	Phchi.S1G318600
Phchi.S1	AUGUSTUS	transcript	20500591	20502252	.	-	.	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	stop_codon	20500588	20500590	.	-	0	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	CDS	20500591	20501031	1	-	0	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	exon	20500591	20501031	.	-	.	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	intron	20501032	20501109	.	-	.	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	CDS	20501110	20502252	1	-	0	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	exon	20501110	20502252	.	-	.	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
Phchi.S1	AUGUSTUS	start_codon	20502250	20502252	.	-	0	transcript_id "Phchi.S1G318600.t1"; gene_id "Phchi.S1G318600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4898.t1 is derived from g2068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13300643	13319184	.	+	.	Phchi.S1G205700
Phchi.S1	AUGUSTUS	transcript	13300643	13319184	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	start_codon	13300643	13300645	.	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13300643	13300670	0.77	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13300643	13300670	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13300671	13300753	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13300754	13300854	1	+	2	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13300754	13300854	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13300855	13301100	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13301101	13301207	0.99	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13301101	13301207	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13301208	13301376	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13301377	13301529	0.92	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13301377	13301529	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13301530	13301819	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13301820	13301999	0.46	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13301820	13301999	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13302000	13302135	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13302136	13302229	0.88	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13302136	13302229	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13302230	13302312	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13302313	13302593	0.94	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13302313	13302593	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13302594	13302737	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13302738	13302848	0.99	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13302738	13302848	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13302849	13303142	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13303143	13303422	0.61	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13303143	13303422	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13303423	13303542	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13303543	13303794	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13303543	13303794	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13303795	13303928	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13303929	13304113	0.77	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13303929	13304113	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13304114	13304302	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13304303	13304397	1	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13304303	13304397	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13304398	13304556	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13304557	13304662	0.98	+	2	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13304557	13304662	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13304663	13304811	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13304812	13305064	0.54	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13304812	13305064	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13305065	13305251	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13305252	13305605	0.99	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13305252	13305605	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13305606	13305699	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13305700	13305963	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13305700	13305963	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13305964	13306058	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13306059	13306448	0.91	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13306059	13306448	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13306449	13306566	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13306567	13306794	0.91	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13306567	13306794	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13306795	13306872	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13306873	13306965	0.99	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13306873	13306965	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13306966	13307123	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13307124	13307285	0.71	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13307124	13307285	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13307286	13307414	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13307415	13307546	0.82	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13307415	13307546	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13307547	13307650	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13307651	13307908	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13307651	13307908	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13307909	13308021	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13308022	13308290	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13308022	13308290	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13308291	13308428	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13308429	13308615	1	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13308429	13308615	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13308616	13308767	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13308768	13309055	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13308768	13309055	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13309056	13309210	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13309211	13309354	0.99	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13309211	13309354	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13309355	13309440	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13309441	13309632	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13309441	13309632	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13309633	13309748	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13309749	13310174	0.66	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13309749	13310174	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13310175	13310292	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13310293	13311339	0.72	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13310293	13311339	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13311340	13311463	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13311464	13311625	0.91	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13311464	13311625	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13311626	13311732	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13311733	13311969	0.98	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13311733	13311969	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13311970	13312042	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13312043	13312210	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13312043	13312210	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13312211	13312372	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13312373	13312681	0.96	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13312373	13312681	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13312682	13312796	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13312797	13313147	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13312797	13313147	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13313148	13313314	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13313315	13313566	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13313315	13313566	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13313567	13313715	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13313716	13313880	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13313716	13313880	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13313881	13313969	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13313970	13314143	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13313970	13314143	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13314144	13314241	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13314242	13314433	0.44	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13314242	13314433	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13314434	13314660	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13314661	13314819	0.76	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13314661	13314819	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13314820	13314901	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13314902	13315198	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13314902	13315198	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13315199	13315279	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13315280	13315477	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13315280	13315477	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13315478	13315617	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13315618	13315743	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13315618	13315743	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13315744	13315849	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13315850	13316122	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13315850	13316122	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13316123	13316213	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13316214	13316318	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13316214	13316318	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13316319	13316407	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13316408	13316623	0.49	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13316408	13316623	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13316624	13316709	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13316710	13316717	0.49	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13316710	13316717	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13316718	13316782	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13316783	13316891	0.49	+	1	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13316783	13316891	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13316892	13316972	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13316973	13317125	0.99	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13316973	13317125	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13317126	13317213	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13317214	13317564	0.99	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13317214	13317564	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13317565	13317651	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13317652	13317756	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13317652	13317756	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13317757	13317833	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13317834	13318062	1	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13317834	13318062	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13318063	13318149	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13318150	13318421	1	+	2	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13318150	13318421	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13318422	13318517	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13318518	13318653	0.92	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13318518	13318653	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13318654	13318730	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13318731	13318985	0.59	+	2	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13318731	13318985	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	intron	13318986	13319065	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	CDS	13319066	13319184	1	+	2	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	exon	13319066	13319184	.	+	.	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
Phchi.S1	AUGUSTUS	stop_codon	13319185	13319187	.	+	0	transcript_id "Phchi.S1G205700.t1"; gene_id "Phchi.S1G205700"
# This transcript jg8984.t2 is derived from g6159.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8985.t1 is derived from g6160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38975181	38975798	.	+	.	Phchi.S1G614400
Phchi.S1	AUGUSTUS	transcript	38975181	38975798	.	+	.	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	start_codon	38975181	38975183	.	+	0	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	CDS	38975181	38975296	0.92	+	0	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	exon	38975181	38975296	.	+	.	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	intron	38975297	38975695	.	+	.	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	CDS	38975696	38975798	1	+	1	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	exon	38975696	38975798	.	+	.	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
Phchi.S1	AUGUSTUS	stop_codon	38975799	38975801	.	+	0	transcript_id "Phchi.S1G614400.t1"; gene_id "Phchi.S1G614400"
# This transcript jg3367.t2 is derived from g536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3368.t1 is derived from g537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3194388	3194609	.	+	.	Phchi.S1G052700
Phchi.S1	AUGUSTUS	transcript	3194388	3194609	.	+	.	transcript_id "Phchi.S1G052700.t1"; gene_id "Phchi.S1G052700"
Phchi.S1	AUGUSTUS	start_codon	3194388	3194390	.	+	0	transcript_id "Phchi.S1G052700.t1"; gene_id "Phchi.S1G052700"
Phchi.S1	AUGUSTUS	CDS	3194388	3194609	0.76	+	0	transcript_id "Phchi.S1G052700.t1"; gene_id "Phchi.S1G052700"
Phchi.S1	AUGUSTUS	exon	3194388	3194609	.	+	.	transcript_id "Phchi.S1G052700.t1"; gene_id "Phchi.S1G052700"
Phchi.S1	AUGUSTUS	stop_codon	3194610	3194612	.	+	0	transcript_id "Phchi.S1G052700.t1"; gene_id "Phchi.S1G052700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15862.t1 is derived from g14332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21925691	21930804	.	+	.	Phchi.S3G318100
Phchi.S3	AUGUSTUS	transcript	21925691	21930804	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	start_codon	21925691	21925693	.	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21925691	21926551	0.9	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21925691	21926551	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21926552	21926648	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21926649	21927188	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21926649	21927188	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21927189	21927285	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21927286	21927606	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21927286	21927606	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21927607	21927707	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21927708	21927794	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21927708	21927794	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21927795	21927875	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21927876	21928649	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21927876	21928649	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21928650	21928742	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21928743	21928907	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21928743	21928907	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21928908	21929022	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21929023	21929317	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21929023	21929317	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21929318	21929411	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21929412	21929626	1	+	2	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21929412	21929626	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21929627	21929712	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21929713	21930018	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21929713	21930018	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21930019	21930151	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21930152	21930215	1	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21930152	21930215	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21930216	21930331	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21930332	21930571	1	+	2	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21930332	21930571	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	intron	21930572	21930706	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	CDS	21930707	21930804	1	+	2	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	exon	21930707	21930804	.	+	.	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
Phchi.S3	AUGUSTUS	stop_codon	21930805	21930807	.	+	0	transcript_id "Phchi.S3G318100.t1"; gene_id "Phchi.S3G318100"
# This transcript jg7985.t2 is derived from g5160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7986.t1 is derived from g5161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32261749	32262863	.	+	.	Phchi.S1G514500
Phchi.S1	AUGUSTUS	transcript	32261749	32262863	.	+	.	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	start_codon	32261749	32261751	.	+	0	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	CDS	32261749	32262351	0.23	+	0	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	exon	32261749	32262351	.	+	.	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	intron	32262352	32262431	.	+	.	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	CDS	32262432	32262863	0.51	+	0	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	exon	32262432	32262863	.	+	.	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
Phchi.S1	AUGUSTUS	stop_codon	32262864	32262866	.	+	0	transcript_id "Phchi.S1G514500.t1"; gene_id "Phchi.S1G514500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg883.t1 is derived from g10665.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6261605	6268767	.	-	.	Phchi.S6G084200
Phchi.S6	AUGUSTUS	transcript	6261605	6268767	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	stop_codon	6261602	6261604	.	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6261605	6261814	1	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6261605	6261814	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6261815	6261903	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6261904	6262009	0.93	-	1	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6261904	6262009	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6262010	6262121	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6262122	6262369	0.98	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6262122	6262369	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6262370	6262475	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6262476	6264185	0.94	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6262476	6264185	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6264186	6264395	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6264396	6264689	0.29	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6264396	6264689	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6264690	6264808	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6264809	6265680	0.62	-	2	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6264809	6265680	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6265681	6265753	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6265754	6265931	1	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6265754	6265931	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6265932	6266095	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6266096	6266746	0.68	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6266096	6266746	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6266747	6266918	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6266919	6267095	1	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6266919	6267095	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267096	6267247	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267248	6267338	0.86	-	1	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267248	6267338	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267339	6267484	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267485	6267561	0.87	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267485	6267561	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267562	6267693	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267694	6267854	1	-	2	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267694	6267854	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267855	6267961	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267962	6268007	0.99	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267962	6268007	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6268008	6268190	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6268191	6268313	1	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6268191	6268313	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6268314	6268397	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6268398	6268472	1	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6268398	6268472	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6268473	6268569	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6268570	6268767	1	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6268570	6268767	.	-	.	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	start_codon	6268765	6268767	.	-	0	transcript_id "Phchi.S6G084200.t1"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	transcript	6261605	6268767	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	stop_codon	6261602	6261604	.	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6261605	6261814	1	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6261605	6261814	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6261815	6261903	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6261904	6262009	0.96	-	1	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6261904	6262009	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6262010	6262121	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6262122	6262369	1	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6262122	6262369	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6262370	6262475	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6262476	6264185	0.89	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6262476	6264185	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6264186	6264395	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6264396	6264689	0.29	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6264396	6264689	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6264690	6264808	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6264809	6265674	0.58	-	2	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6264809	6265674	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6265675	6265753	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6265754	6265931	1	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6265754	6265931	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6265932	6266095	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6266096	6266746	0.6	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6266096	6266746	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6266747	6266918	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6266919	6267095	0.99	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6266919	6267095	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267096	6267247	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267248	6267338	0.87	-	1	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267248	6267338	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267339	6267484	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267485	6267561	0.91	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267485	6267561	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267562	6267693	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267694	6267854	0.99	-	2	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267694	6267854	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6267855	6267961	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6267962	6268007	0.97	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6267962	6268007	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6268008	6268190	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6268191	6268313	1	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6268191	6268313	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6268314	6268397	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6268398	6268472	1	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6268398	6268472	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	intron	6268473	6268569	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	CDS	6268570	6268767	0.99	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	exon	6268570	6268767	.	-	.	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
Phchi.S6	AUGUSTUS	start_codon	6268765	6268767	.	-	0	transcript_id "Phchi.S6G084200.t2"; gene_id "Phchi.S6G084200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6575.t1 is derived from g3747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23819691	23823164	.	-	.	Phchi.S1G373400
Phchi.S1	AUGUSTUS	transcript	23819691	23823164	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	stop_codon	23819688	23819690	.	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23819691	23820362	0.82	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23819691	23820362	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23820363	23820471	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23820472	23820954	1	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23820472	23820954	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23820955	23821071	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23821072	23821284	0.96	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23821072	23821284	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23821285	23821401	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23821402	23821424	0.61	-	2	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23821402	23821424	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23821425	23821525	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23821526	23821690	0.63	-	2	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23821526	23821690	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23821691	23821819	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23821820	23821959	1	-	1	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23821820	23821959	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23821960	23822059	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23822060	23822288	0.97	-	2	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23822060	23822288	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23822289	23822397	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23822398	23822578	0.88	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23822398	23822578	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23822579	23822753	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23822754	23823002	0.44	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23822754	23823002	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	intron	23823003	23823146	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	CDS	23823147	23823164	0.35	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	exon	23823147	23823164	.	-	.	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
Phchi.S1	AUGUSTUS	start_codon	23823162	23823164	.	-	0	transcript_id "Phchi.S1G373400.t1"; gene_id "Phchi.S1G373400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8608.t1 is derived from g5783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36900354	36902860	.	-	.	Phchi.S1G576700
Phchi.S1	AUGUSTUS	transcript	36900354	36902860	.	-	.	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	stop_codon	36900351	36900353	.	-	0	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	CDS	36900354	36900512	0.81	-	0	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	exon	36900354	36900512	.	-	.	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	intron	36900513	36900598	.	-	.	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	CDS	36900599	36902860	0.57	-	0	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	exon	36900599	36902860	.	-	.	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
Phchi.S1	AUGUSTUS	start_codon	36902858	36902860	.	-	0	transcript_id "Phchi.S1G576700.t1"; gene_id "Phchi.S1G576700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12433.t1 is derived from g8110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19797313	19797699	.	+	.	Phchi.S2G051300
Phchi.S2	AUGUSTUS	transcript	19797313	19797699	.	+	.	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	start_codon	19797313	19797315	.	+	0	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	CDS	19797313	19797379	1	+	0	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	exon	19797313	19797379	.	+	.	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	intron	19797380	19797467	.	+	.	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	CDS	19797468	19797572	1	+	2	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	exon	19797468	19797572	.	+	.	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	intron	19797573	19797661	.	+	.	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	CDS	19797662	19797699	0.71	+	2	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	exon	19797662	19797699	.	+	.	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
Phchi.S2	AUGUSTUS	stop_codon	19797700	19797702	.	+	0	transcript_id "Phchi.S2G051300.t1"; gene_id "Phchi.S2G051300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14502.t1 is derived from g12970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13215063	13217699	.	+	.	Phchi.S3G182100
Phchi.S3	AUGUSTUS	transcript	13215063	13217699	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	start_codon	13215063	13215065	.	+	0	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13215063	13215268	0.48	+	0	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13215063	13215268	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13215269	13215356	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13215357	13215538	1	+	1	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13215357	13215538	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13215539	13215684	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13215685	13215821	1	+	2	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13215685	13215821	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13215822	13215898	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13215899	13216064	1	+	0	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13215899	13216064	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13216065	13216163	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13216164	13216280	0.58	+	2	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13216164	13216280	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13216281	13216397	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13216398	13216558	0.77	+	2	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13216398	13216558	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13216559	13216674	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13216675	13216850	0.76	+	0	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13216675	13216850	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13216851	13216956	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13216957	13216994	0.56	+	1	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13216957	13216994	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13216995	13217089	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13217090	13217142	0.58	+	2	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13217090	13217142	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13217143	13217240	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13217241	13217347	1	+	0	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13217241	13217347	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13217348	13217438	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13217439	13217473	1	+	1	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13217439	13217473	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	intron	13217474	13217664	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	CDS	13217665	13217699	1	+	2	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	exon	13217665	13217699	.	+	.	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
Phchi.S3	AUGUSTUS	stop_codon	13217700	13217702	.	+	0	transcript_id "Phchi.S3G182100.t1"; gene_id "Phchi.S3G182100"
# This transcript jg1227.t2 is derived from g11010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1228.t1 is derived from g11011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8508037	8510012	.	-	.	Phchi.S6G118700
Phchi.S6	AUGUSTUS	transcript	8508037	8510012	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	stop_codon	8508034	8508036	.	-	0	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	CDS	8508037	8508426	0.99	-	0	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	exon	8508037	8508426	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	intron	8508427	8508510	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	CDS	8508511	8508759	1	-	0	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	exon	8508511	8508759	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	intron	8508760	8508854	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	CDS	8508855	8509049	0.55	-	0	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	exon	8508855	8509049	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	intron	8509050	8509167	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	CDS	8509168	8509462	0.97	-	1	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	exon	8509168	8509462	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	intron	8509463	8509560	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	CDS	8509561	8510012	0.97	-	0	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	exon	8509561	8510012	.	-	.	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
Phchi.S6	AUGUSTUS	start_codon	8510010	8510012	.	-	0	transcript_id "Phchi.S6G118700.t1"; gene_id "Phchi.S6G118700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1280.t1 is derived from g11063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8797430	8798399	.	-	.	Phchi.S6G123900
Phchi.S6	AUGUSTUS	transcript	8797430	8798399	.	-	.	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	stop_codon	8797427	8797429	.	-	0	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	CDS	8797430	8797749	0.9	-	2	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	exon	8797430	8797749	.	-	.	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	intron	8797750	8797918	.	-	.	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	CDS	8797919	8797957	1	-	2	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	exon	8797919	8797957	.	-	.	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	intron	8797958	8798359	.	-	.	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	CDS	8798360	8798399	0.7	-	0	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	exon	8798360	8798399	.	-	.	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
Phchi.S6	AUGUSTUS	start_codon	8798397	8798399	.	-	0	transcript_id "Phchi.S6G123900.t1"; gene_id "Phchi.S6G123900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7205.t1 is derived from g4377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27628004	27628965	.	-	.	Phchi.S1G436400
Phchi.S1	AUGUSTUS	transcript	27628004	27628965	.	-	.	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	stop_codon	27628001	27628003	.	-	0	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	CDS	27628004	27628235	0.85	-	1	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	exon	27628004	27628235	.	-	.	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	intron	27628236	27628312	.	-	.	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	CDS	27628313	27628432	0.62	-	1	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	exon	27628313	27628432	.	-	.	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	intron	27628433	27628516	.	-	.	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	CDS	27628517	27628965	0.99	-	0	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	exon	27628517	27628965	.	-	.	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
Phchi.S1	AUGUSTUS	start_codon	27628963	27628965	.	-	0	transcript_id "Phchi.S1G436400.t1"; gene_id "Phchi.S1G436400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6714.t1 is derived from g3886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24672235	24673782	.	-	.	Phchi.S1G387300
Phchi.S1	AUGUSTUS	transcript	24672235	24673782	.	-	.	transcript_id "Phchi.S1G387300.t1"; gene_id "Phchi.S1G387300"
Phchi.S1	AUGUSTUS	stop_codon	24672232	24672234	.	-	0	transcript_id "Phchi.S1G387300.t1"; gene_id "Phchi.S1G387300"
Phchi.S1	AUGUSTUS	CDS	24672235	24673782	1	-	0	transcript_id "Phchi.S1G387300.t1"; gene_id "Phchi.S1G387300"
Phchi.S1	AUGUSTUS	exon	24672235	24673782	.	-	.	transcript_id "Phchi.S1G387300.t1"; gene_id "Phchi.S1G387300"
Phchi.S1	AUGUSTUS	start_codon	24673780	24673782	.	-	0	transcript_id "Phchi.S1G387300.t1"; gene_id "Phchi.S1G387300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1886.t1 is derived from g8806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3707157	3708287	.	+	.	Phchi.S5G049500
Phchi.S5	AUGUSTUS	transcript	3707157	3708287	.	+	.	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	start_codon	3707157	3707159	.	+	0	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	CDS	3707157	3707208	0.65	+	0	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	exon	3707157	3707208	.	+	.	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	intron	3707209	3707340	.	+	.	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	CDS	3707341	3708287	0.88	+	2	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	exon	3707341	3708287	.	+	.	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
Phchi.S5	AUGUSTUS	stop_codon	3708288	3708290	.	+	0	transcript_id "Phchi.S5G049500.t1"; gene_id "Phchi.S5G049500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8469.t1 is derived from g5644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36073839	36076411	.	+	.	Phchi.S1G562800
Phchi.S1	AUGUSTUS	transcript	36073839	36076411	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	start_codon	36073839	36073841	.	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36073839	36073901	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36073839	36073901	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36073902	36073981	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36073982	36074140	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36073982	36074140	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36074141	36074239	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36074240	36074410	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36074240	36074410	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36074411	36074500	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36074501	36074653	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36074501	36074653	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36074654	36074739	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36074740	36074808	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36074740	36074808	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36074809	36074905	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36074906	36075022	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36074906	36075022	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36075023	36075117	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36075118	36075192	1	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36075118	36075192	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36075193	36075284	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36075285	36075563	0.77	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36075285	36075563	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36075564	36075673	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36075674	36075723	0.98	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36075674	36075723	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36075724	36075801	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36075802	36075856	1	+	1	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36075802	36075856	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36075857	36075941	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36075942	36076121	0.27	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36075942	36076121	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	intron	36076122	36076273	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	CDS	36076274	36076411	0.43	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	exon	36076274	36076411	.	+	.	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
Phchi.S1	AUGUSTUS	stop_codon	36076412	36076414	.	+	0	transcript_id "Phchi.S1G562800.t1"; gene_id "Phchi.S1G562800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12910.t1 is derived from g11375.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3104310	3105045	.	-	.	Phchi.S3G022900
Phchi.S3	AUGUSTUS	transcript	3104492	3105045	.	-	.	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	stop_codon	3104489	3104491	.	-	0	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104492	3104523	1	-	2	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104492	3104523	.	-	.	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	intron	3104524	3104766	.	-	.	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104767	3104884	0.99	-	0	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104767	3104884	.	-	.	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	intron	3104885	3104964	.	-	.	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104965	3105045	0.62	-	0	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104965	3105045	.	-	.	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	start_codon	3105043	3105045	.	-	0	transcript_id "Phchi.S3G022900.t1"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	transcript	3104310	3105045	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	stop_codon	3104307	3104309	.	-	0	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104310	3104315	1	-	0	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104310	3104315	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	intron	3104316	3104388	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104389	3104435	0.67	-	2	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104389	3104435	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	intron	3104436	3104766	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104767	3104884	0.66	-	0	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104767	3104884	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	intron	3104885	3104964	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	CDS	3104965	3105045	0.45	-	0	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	exon	3104965	3105045	.	-	.	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
Phchi.S3	AUGUSTUS	start_codon	3105043	3105045	.	-	0	transcript_id "Phchi.S3G022900.t2"; gene_id "Phchi.S3G022900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6336.t1 is derived from g3508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22388996	22390244	.	+	.	Phchi.S1G349500
Phchi.S1	AUGUSTUS	transcript	22388996	22390244	.	+	.	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	start_codon	22388996	22388998	.	+	0	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	CDS	22388996	22389522	0.41	+	0	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	exon	22388996	22389522	.	+	.	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	intron	22389523	22389656	.	+	.	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	CDS	22389657	22390134	0.77	+	1	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	exon	22389657	22390134	.	+	.	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	intron	22390135	22390235	.	+	.	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	CDS	22390236	22390244	0.73	+	0	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	exon	22390236	22390244	.	+	.	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
Phchi.S1	AUGUSTUS	stop_codon	22390245	22390247	.	+	0	transcript_id "Phchi.S1G349500.t1"; gene_id "Phchi.S1G349500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10027.t1 is derived from g7203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45154886	45157180	.	-	.	Phchi.S1G718600
Phchi.S1	AUGUSTUS	transcript	45154886	45157180	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	stop_codon	45154883	45154885	.	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45154886	45155071	1	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45154886	45155071	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45155072	45155172	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45155173	45155376	1	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45155173	45155376	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45155377	45155479	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45155480	45155710	1	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45155480	45155710	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45155711	45155830	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45155831	45155879	0.99	-	1	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45155831	45155879	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45155880	45155988	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45155989	45156188	0.96	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45155989	45156188	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45156189	45156290	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45156291	45156533	1	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45156291	45156533	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45156534	45156668	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45156669	45156833	1	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45156669	45156833	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	intron	45156834	45156952	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	CDS	45156953	45157180	1	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	exon	45156953	45157180	.	-	.	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
Phchi.S1	AUGUSTUS	start_codon	45157178	45157180	.	-	0	transcript_id "Phchi.S1G718600.t1"; gene_id "Phchi.S1G718600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11308.t1 is derived from g15358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5311189	5312743	.	-	.	Phchi.S4G089000
Phchi.S4	AUGUSTUS	transcript	5311189	5312743	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	stop_codon	5311186	5311188	.	-	0	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	CDS	5311189	5311247	0.36	-	2	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	exon	5311189	5311247	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	intron	5311248	5311357	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	CDS	5311358	5311519	0.27	-	2	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	exon	5311358	5311519	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	intron	5311520	5311695	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	CDS	5311696	5311715	0.41	-	1	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	exon	5311696	5311715	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	intron	5311716	5311819	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	CDS	5311820	5311896	0.69	-	0	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	exon	5311820	5311896	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	intron	5311897	5311980	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	CDS	5311981	5312363	1	-	2	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	exon	5311981	5312363	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	intron	5312364	5312517	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	CDS	5312518	5312743	0.9	-	0	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	exon	5312518	5312743	.	-	.	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
Phchi.S4	AUGUSTUS	start_codon	5312741	5312743	.	-	0	transcript_id "Phchi.S4G089000.t1"; gene_id "Phchi.S4G089000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3987.t1 is derived from g1156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6880011	6882501	.	-	.	Phchi.S1G114600
Phchi.S1	AUGUSTUS	transcript	6880011	6882501	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	stop_codon	6880008	6880010	.	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6880011	6880247	0.8	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6880011	6880247	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	intron	6880248	6880375	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6880376	6880627	1	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6880376	6880627	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	intron	6880628	6880736	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6880737	6880985	1	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6880737	6880985	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	intron	6880986	6881100	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6881101	6881292	1	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6881101	6881292	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	intron	6881293	6881381	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6881382	6881489	1	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6881382	6881489	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	intron	6881490	6881616	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6881617	6881838	1	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6881617	6881838	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	intron	6881839	6881970	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	CDS	6881971	6882501	0.44	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	exon	6881971	6882501	.	-	.	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
Phchi.S1	AUGUSTUS	start_codon	6882499	6882501	.	-	0	transcript_id "Phchi.S1G114600.t1"; gene_id "Phchi.S1G114600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9375.t1 is derived from g6551.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41223400	41224044	.	-	.	Phchi.S1G653400
Phchi.S1	AUGUSTUS	transcript	41223624	41224044	.	-	.	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	stop_codon	41223621	41223623	.	-	0	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	CDS	41223624	41223686	0.36	-	0	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	exon	41223624	41223686	.	-	.	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	intron	41223687	41223765	.	-	.	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	CDS	41223766	41224044	0.98	-	0	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	exon	41223766	41224044	.	-	.	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	start_codon	41224042	41224044	.	-	0	transcript_id "Phchi.S1G653400.t1"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	transcript	41223400	41224044	.	-	.	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	stop_codon	41223397	41223399	.	-	0	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	CDS	41223400	41223651	0.79	-	0	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	exon	41223400	41223651	.	-	.	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	intron	41223652	41223765	.	-	.	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	CDS	41223766	41224044	0.82	-	0	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	exon	41223766	41224044	.	-	.	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
Phchi.S1	AUGUSTUS	start_codon	41224042	41224044	.	-	0	transcript_id "Phchi.S1G653400.t2"; gene_id "Phchi.S1G653400"
# This transcript jg1005.t2 is derived from g10788.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1006.t1 is derived from g10789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7065894	7066609	.	-	.	Phchi.S6G096500
Phchi.S6	AUGUSTUS	transcript	7065894	7066609	.	-	.	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	stop_codon	7065891	7065893	.	-	0	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	CDS	7065894	7066022	0.95	-	0	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	exon	7065894	7066022	.	-	.	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	intron	7066023	7066108	.	-	.	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	CDS	7066109	7066609	0.84	-	0	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	exon	7066109	7066609	.	-	.	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
Phchi.S6	AUGUSTUS	start_codon	7066607	7066609	.	-	0	transcript_id "Phchi.S6G096500.t1"; gene_id "Phchi.S6G096500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2772.t1 is derived from g9692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8754690	8755716	.	+	.	Phchi.S5G138100
Phchi.S5	AUGUSTUS	transcript	8754690	8755716	.	+	.	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	start_codon	8754690	8754692	.	+	0	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	CDS	8754690	8754711	1	+	0	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	exon	8754690	8754711	.	+	.	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	intron	8754712	8755270	.	+	.	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	CDS	8755271	8755716	1	+	2	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	exon	8755271	8755716	.	+	.	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
Phchi.S5	AUGUSTUS	stop_codon	8755717	8755719	.	+	0	transcript_id "Phchi.S5G138100.t1"; gene_id "Phchi.S5G138100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9616.t1 is derived from g6792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42942349	42943549	.	+	.	Phchi.S1G677500
Phchi.S1	AUGUSTUS	transcript	42942349	42943549	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	start_codon	42942349	42942351	.	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	CDS	42942349	42942673	0.95	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	exon	42942349	42942673	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	intron	42942674	42942759	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	CDS	42942760	42942806	1	+	2	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	exon	42942760	42942806	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	intron	42942807	42942914	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	CDS	42942915	42943040	1	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	exon	42942915	42943040	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	intron	42943041	42943150	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	CDS	42943151	42943207	1	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	exon	42943151	42943207	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	intron	42943208	42943290	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	CDS	42943291	42943362	1	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	exon	42943291	42943362	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	intron	42943363	42943462	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	CDS	42943463	42943549	1	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	exon	42943463	42943549	.	+	.	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
Phchi.S1	AUGUSTUS	stop_codon	42943550	42943552	.	+	0	transcript_id "Phchi.S1G677500.t1"; gene_id "Phchi.S1G677500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4773.t1 is derived from g1943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12770085	12770369	.	+	.	Phchi.S1G193200
Phchi.S1	AUGUSTUS	transcript	12770085	12770369	.	+	.	transcript_id "Phchi.S1G193200.t1"; gene_id "Phchi.S1G193200"
Phchi.S1	AUGUSTUS	start_codon	12770085	12770087	.	+	0	transcript_id "Phchi.S1G193200.t1"; gene_id "Phchi.S1G193200"
Phchi.S1	AUGUSTUS	CDS	12770085	12770369	0.84	+	0	transcript_id "Phchi.S1G193200.t1"; gene_id "Phchi.S1G193200"
Phchi.S1	AUGUSTUS	exon	12770085	12770369	.	+	.	transcript_id "Phchi.S1G193200.t1"; gene_id "Phchi.S1G193200"
Phchi.S1	AUGUSTUS	stop_codon	12770370	12770372	.	+	0	transcript_id "Phchi.S1G193200.t1"; gene_id "Phchi.S1G193200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg808.t1 is derived from g10590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5688974	5689531	.	+	.	Phchi.S6G076700
Phchi.S6	AUGUSTUS	transcript	5688974	5689531	.	+	.	transcript_id "Phchi.S6G076700.t1"; gene_id "Phchi.S6G076700"
Phchi.S6	AUGUSTUS	start_codon	5688974	5688976	.	+	0	transcript_id "Phchi.S6G076700.t1"; gene_id "Phchi.S6G076700"
Phchi.S6	AUGUSTUS	CDS	5688974	5689531	0.82	+	0	transcript_id "Phchi.S6G076700.t1"; gene_id "Phchi.S6G076700"
Phchi.S6	AUGUSTUS	exon	5688974	5689531	.	+	.	transcript_id "Phchi.S6G076700.t1"; gene_id "Phchi.S6G076700"
Phchi.S6	AUGUSTUS	stop_codon	5689532	5689534	.	+	0	transcript_id "Phchi.S6G076700.t1"; gene_id "Phchi.S6G076700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3876.t1 is derived from g1045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6165481	6169448	.	-	.	Phchi.S1G103500
Phchi.S1	AUGUSTUS	transcript	6165481	6169448	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	stop_codon	6165478	6165480	.	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6165481	6165523	1	-	1	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6165481	6165523	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6165524	6165605	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6165606	6165718	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6165606	6165718	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6165719	6165883	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6165884	6165962	1	-	1	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6165884	6165962	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6165963	6166033	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6166034	6166119	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6166034	6166119	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6166120	6166209	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6166210	6166305	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6166210	6166305	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6166306	6166385	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6166386	6166478	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6166386	6166478	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6166479	6166574	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6166575	6166658	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6166575	6166658	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6166659	6166756	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6166757	6166847	1	-	1	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6166757	6166847	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6166848	6166936	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6166937	6167052	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6166937	6167052	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6167053	6167227	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6167228	6167498	0.81	-	1	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6167228	6167498	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6167499	6167600	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6167601	6167665	0.99	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6167601	6167665	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6167666	6167763	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6167764	6167826	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6167764	6167826	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6167827	6167926	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6167927	6168018	1	-	2	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6167927	6168018	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6168019	6168106	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6168107	6168142	1	-	2	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6168107	6168142	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6168143	6168322	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6168323	6168407	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6168323	6168407	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6168408	6168488	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6168489	6168553	1	-	2	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6168489	6168553	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6168554	6168646	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6168647	6168716	1	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6168647	6168716	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6168717	6168836	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6168837	6168977	0.93	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6168837	6168977	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	intron	6168978	6169052	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	CDS	6169053	6169448	0.35	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	exon	6169053	6169448	.	-	.	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
Phchi.S1	AUGUSTUS	start_codon	6169446	6169448	.	-	0	transcript_id "Phchi.S1G103500.t1"; gene_id "Phchi.S1G103500"
# This transcript jg3949.t2 is derived from g1118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3949.t3 is derived from g1118.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3950.t1 is derived from g1119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6619978	6620373	.	-	.	Phchi.S1G110900
Phchi.S1	AUGUSTUS	transcript	6619978	6620373	.	-	.	transcript_id "Phchi.S1G110900.t1"; gene_id "Phchi.S1G110900"
Phchi.S1	AUGUSTUS	stop_codon	6619975	6619977	.	-	0	transcript_id "Phchi.S1G110900.t1"; gene_id "Phchi.S1G110900"
Phchi.S1	AUGUSTUS	CDS	6619978	6620373	0.6	-	0	transcript_id "Phchi.S1G110900.t1"; gene_id "Phchi.S1G110900"
Phchi.S1	AUGUSTUS	exon	6619978	6620373	.	-	.	transcript_id "Phchi.S1G110900.t1"; gene_id "Phchi.S1G110900"
Phchi.S1	AUGUSTUS	start_codon	6620371	6620373	.	-	0	transcript_id "Phchi.S1G110900.t1"; gene_id "Phchi.S1G110900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14536.t1 is derived from g13004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13353243	13353512	.	+	.	Phchi.S3G185500
Phchi.S3	AUGUSTUS	transcript	13353243	13353512	.	+	.	transcript_id "Phchi.S3G185500.t1"; gene_id "Phchi.S3G185500"
Phchi.S3	AUGUSTUS	start_codon	13353243	13353245	.	+	0	transcript_id "Phchi.S3G185500.t1"; gene_id "Phchi.S3G185500"
Phchi.S3	AUGUSTUS	CDS	13353243	13353512	0.4	+	0	transcript_id "Phchi.S3G185500.t1"; gene_id "Phchi.S3G185500"
Phchi.S3	AUGUSTUS	exon	13353243	13353512	.	+	.	transcript_id "Phchi.S3G185500.t1"; gene_id "Phchi.S3G185500"
Phchi.S3	AUGUSTUS	stop_codon	13353513	13353515	.	+	0	transcript_id "Phchi.S3G185500.t1"; gene_id "Phchi.S3G185500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6952.t1 is derived from g4124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26118440	26119012	.	+	.	Phchi.S1G411100
Phchi.S1	AUGUSTUS	transcript	26118440	26119012	.	+	.	transcript_id "Phchi.S1G411100.t1"; gene_id "Phchi.S1G411100"
Phchi.S1	AUGUSTUS	start_codon	26118440	26118442	.	+	0	transcript_id "Phchi.S1G411100.t1"; gene_id "Phchi.S1G411100"
Phchi.S1	AUGUSTUS	CDS	26118440	26119012	1	+	0	transcript_id "Phchi.S1G411100.t1"; gene_id "Phchi.S1G411100"
Phchi.S1	AUGUSTUS	exon	26118440	26119012	.	+	.	transcript_id "Phchi.S1G411100.t1"; gene_id "Phchi.S1G411100"
Phchi.S1	AUGUSTUS	stop_codon	26119013	26119015	.	+	0	transcript_id "Phchi.S1G411100.t1"; gene_id "Phchi.S1G411100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14879.t1 is derived from g13347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15252466	15253272	.	+	.	Phchi.S3G219800
Phchi.S3	AUGUSTUS	transcript	15252466	15253272	.	+	.	transcript_id "Phchi.S3G219800.t1"; gene_id "Phchi.S3G219800"
Phchi.S3	AUGUSTUS	start_codon	15252466	15252468	.	+	0	transcript_id "Phchi.S3G219800.t1"; gene_id "Phchi.S3G219800"
Phchi.S3	AUGUSTUS	CDS	15252466	15253272	0.56	+	0	transcript_id "Phchi.S3G219800.t1"; gene_id "Phchi.S3G219800"
Phchi.S3	AUGUSTUS	exon	15252466	15253272	.	+	.	transcript_id "Phchi.S3G219800.t1"; gene_id "Phchi.S3G219800"
Phchi.S3	AUGUSTUS	stop_codon	15253273	15253275	.	+	0	transcript_id "Phchi.S3G219800.t1"; gene_id "Phchi.S3G219800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15308.t1 is derived from g13776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18323769	18326412	.	+	.	Phchi.S3G262700
Phchi.S3	AUGUSTUS	transcript	18323769	18326412	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	start_codon	18323769	18323771	.	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18323769	18323913	1	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18323769	18323913	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18323914	18324267	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18324268	18324461	1	+	2	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18324268	18324461	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18324462	18324581	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18324582	18324710	1	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18324582	18324710	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18324711	18324822	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18324823	18324942	1	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18324823	18324942	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18324943	18325106	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18325107	18325243	1	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18325107	18325243	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18325244	18325349	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18325350	18325505	1	+	1	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18325350	18325505	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18325506	18325595	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18325596	18325974	1	+	1	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18325596	18325974	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18325975	18326091	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18326092	18326208	1	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18326092	18326208	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	intron	18326209	18326301	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	CDS	18326302	18326412	1	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	exon	18326302	18326412	.	+	.	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
Phchi.S3	AUGUSTUS	stop_codon	18326413	18326415	.	+	0	transcript_id "Phchi.S3G262700.t1"; gene_id "Phchi.S3G262700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11330.t1 is derived from g15380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5596201	5598285	.	-	.	Phchi.S4G091200
Phchi.S4	AUGUSTUS	transcript	5596201	5598285	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	stop_codon	5596198	5596200	.	-	0	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5596201	5596416	0.89	-	0	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5596201	5596416	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	intron	5596417	5596577	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5596578	5596690	0.69	-	2	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5596578	5596690	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	intron	5596691	5596766	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5596767	5597033	1	-	2	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5596767	5597033	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	intron	5597034	5597121	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5597122	5597407	1	-	0	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5597122	5597407	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	intron	5597408	5597506	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5597507	5597801	0.91	-	1	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5597507	5597801	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	intron	5597802	5597874	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5597875	5598103	0.58	-	2	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5597875	5598103	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	intron	5598104	5598218	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	CDS	5598219	5598285	0.75	-	0	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	exon	5598219	5598285	.	-	.	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
Phchi.S4	AUGUSTUS	start_codon	5598283	5598285	.	-	0	transcript_id "Phchi.S4G091200.t1"; gene_id "Phchi.S4G091200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14276.t1 is derived from g12743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11891693	11893097	.	-	.	Phchi.S3G159500
Phchi.S3	AUGUSTUS	transcript	11891693	11893097	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	stop_codon	11891690	11891692	.	-	0	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	CDS	11891693	11891854	0.17	-	0	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	exon	11891693	11891854	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	intron	11891855	11892089	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	CDS	11892090	11892197	0.97	-	0	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	exon	11892090	11892197	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	intron	11892198	11892291	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	CDS	11892292	11892426	0.84	-	0	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	exon	11892292	11892426	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	intron	11892427	11892508	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	CDS	11892509	11892684	0.9	-	2	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	exon	11892509	11892684	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	intron	11892685	11892769	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	CDS	11892770	11893097	1	-	0	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	exon	11892770	11893097	.	-	.	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
Phchi.S3	AUGUSTUS	start_codon	11893095	11893097	.	-	0	transcript_id "Phchi.S3G159500.t1"; gene_id "Phchi.S3G159500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5718.t1 is derived from g2888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18505609	18506471	.	+	.	Phchi.S1G287700
Phchi.S1	AUGUSTUS	transcript	18505609	18506471	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	start_codon	18505609	18505611	.	+	0	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	CDS	18505609	18505621	1	+	0	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	exon	18505609	18505621	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	intron	18505622	18505740	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	CDS	18505741	18506025	1	+	2	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	exon	18505741	18506025	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	intron	18506026	18506120	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	CDS	18506121	18506162	1	+	2	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	exon	18506121	18506162	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	intron	18506163	18506391	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	CDS	18506392	18506471	1	+	2	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	exon	18506392	18506471	.	+	.	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
Phchi.S1	AUGUSTUS	stop_codon	18506472	18506474	.	+	0	transcript_id "Phchi.S1G287700.t1"; gene_id "Phchi.S1G287700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13861.t1 is derived from g12328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9292858	9296140	.	-	.	Phchi.S3G118000
Phchi.S3	AUGUSTUS	transcript	9292858	9296140	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	stop_codon	9292855	9292857	.	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9292858	9292942	1	-	1	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9292858	9292942	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9292943	9293017	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9293018	9293112	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9293018	9293112	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9293113	9293201	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9293202	9293266	1	-	2	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9293202	9293266	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9293267	9293357	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9293358	9293415	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9293358	9293415	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9293416	9293518	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9293519	9293588	0.96	-	1	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9293519	9293588	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9293589	9293732	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9293733	9293812	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9293733	9293812	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9293813	9293902	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9293903	9293930	1	-	1	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9293903	9293930	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9293931	9294028	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9294029	9294090	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9294029	9294090	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9294091	9294188	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9294189	9294224	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9294189	9294224	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9294225	9294336	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9294337	9294434	1	-	2	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9294337	9294434	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9294435	9294543	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9294544	9294606	1	-	2	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9294544	9294606	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9294607	9294706	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9294707	9294758	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9294707	9294758	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9294759	9294868	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9294869	9294947	1	-	1	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9294869	9294947	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9294948	9295023	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9295024	9295065	0.88	-	1	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9295024	9295065	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9295066	9295177	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9295178	9295262	0.99	-	2	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9295178	9295262	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9295263	9295334	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9295335	9295446	1	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9295335	9295446	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9295447	9295528	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9295529	9295613	1	-	1	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9295529	9295613	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9295614	9295697	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9295698	9295764	1	-	2	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9295698	9295764	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	intron	9295765	9296061	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	CDS	9296062	9296140	0.74	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	exon	9296062	9296140	.	-	.	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
Phchi.S3	AUGUSTUS	start_codon	9296138	9296140	.	-	0	transcript_id "Phchi.S3G118000.t1"; gene_id "Phchi.S3G118000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13989.t1 is derived from g12456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10131194	10132486	.	+	.	Phchi.S3G130800
Phchi.S3	AUGUSTUS	transcript	10131194	10132486	.	+	.	transcript_id "Phchi.S3G130800.t1"; gene_id "Phchi.S3G130800"
Phchi.S3	AUGUSTUS	start_codon	10131194	10131196	.	+	0	transcript_id "Phchi.S3G130800.t1"; gene_id "Phchi.S3G130800"
Phchi.S3	AUGUSTUS	CDS	10131194	10132486	0.68	+	0	transcript_id "Phchi.S3G130800.t1"; gene_id "Phchi.S3G130800"
Phchi.S3	AUGUSTUS	exon	10131194	10132486	.	+	.	transcript_id "Phchi.S3G130800.t1"; gene_id "Phchi.S3G130800"
Phchi.S3	AUGUSTUS	stop_codon	10132487	10132489	.	+	0	transcript_id "Phchi.S3G130800.t1"; gene_id "Phchi.S3G130800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11948.t1 is derived from g7623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	158504	161950	.	+	.	Phchi.S2G002800
Phchi.S2	AUGUSTUS	transcript	158504	161950	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	start_codon	158504	158506	.	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	158504	158703	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	158504	158703	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	158704	158831	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	158832	158917	1	+	1	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	158832	158917	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	158918	159049	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159050	159138	1	+	2	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159050	159138	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159139	159224	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159225	159464	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159225	159464	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159465	159667	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159668	159789	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159668	159789	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159790	159909	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159910	159985	1	+	1	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159910	159985	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159986	160092	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	160093	160200	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	160093	160200	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	160201	160360	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	160361	160537	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	160361	160537	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	160538	160685	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	160686	160900	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	160686	160900	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	160901	161065	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161066	161198	1	+	1	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161066	161198	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	161199	161314	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161315	161538	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161315	161538	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	161539	161635	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161636	161789	1	+	1	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161636	161789	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	161790	161869	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161870	161950	1	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161870	161950	.	+	.	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	stop_codon	161951	161953	.	+	0	transcript_id "Phchi.S2G002800.t1"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	transcript	158504	161950	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	start_codon	158504	158506	.	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	158504	158703	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	158504	158703	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	158704	158831	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	158832	158917	1	+	1	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	158832	158917	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	158918	159049	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159050	159138	1	+	2	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159050	159138	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159139	159224	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159225	159319	0.76	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159225	159319	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159320	159519	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159520	159583	0.78	+	1	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159520	159583	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159584	159667	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159668	159789	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159668	159789	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159790	159909	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	159910	159985	1	+	1	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	159910	159985	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	159986	160092	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	160093	160200	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	160093	160200	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	160201	160360	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	160361	160537	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	160361	160537	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	160538	160685	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	160686	160900	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	160686	160900	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	160901	161065	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161066	161198	1	+	1	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161066	161198	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	161199	161314	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161315	161538	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161315	161538	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	161539	161635	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161636	161789	1	+	1	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161636	161789	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	intron	161790	161869	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	CDS	161870	161950	1	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	exon	161870	161950	.	+	.	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
Phchi.S2	AUGUSTUS	stop_codon	161951	161953	.	+	0	transcript_id "Phchi.S2G002800.t2"; gene_id "Phchi.S2G002800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7851.t1 is derived from g5025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31523289	31524311	.	+	.	Phchi.S1G501000
Phchi.S1	AUGUSTUS	transcript	31523289	31524311	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	start_codon	31523289	31523291	.	+	0	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	CDS	31523289	31523550	1	+	0	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	exon	31523289	31523550	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	intron	31523551	31523656	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	CDS	31523657	31523770	1	+	2	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	exon	31523657	31523770	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	intron	31523771	31523862	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	CDS	31523863	31524020	1	+	2	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	exon	31523863	31524020	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	intron	31524021	31524101	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	CDS	31524102	31524311	1	+	0	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	exon	31524102	31524311	.	+	.	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
Phchi.S1	AUGUSTUS	stop_codon	31524312	31524314	.	+	0	transcript_id "Phchi.S1G501000.t1"; gene_id "Phchi.S1G501000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13679.t1 is derived from g12146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8180038	8181604	.	+	.	Phchi.S3G099800
Phchi.S3	AUGUSTUS	transcript	8180038	8181604	.	+	.	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	start_codon	8180038	8180040	.	+	0	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	CDS	8180038	8180048	0.94	+	0	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	exon	8180038	8180048	.	+	.	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	intron	8180049	8180214	.	+	.	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	CDS	8180215	8181604	0.98	+	1	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	exon	8180215	8181604	.	+	.	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
Phchi.S3	AUGUSTUS	stop_codon	8181605	8181607	.	+	0	transcript_id "Phchi.S3G099800.t1"; gene_id "Phchi.S3G099800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5400.t1 is derived from g2570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16688799	16691138	.	-	.	Phchi.S1G255900
Phchi.S1	AUGUSTUS	transcript	16688799	16691138	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	stop_codon	16688796	16688798	.	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16688799	16688968	1	-	2	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16688799	16688968	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16688969	16689058	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16689059	16689157	1	-	2	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16689059	16689157	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16689158	16689249	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16689250	16689307	1	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16689250	16689307	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16689308	16689411	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16689412	16689463	1	-	1	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16689412	16689463	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16689464	16689551	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16689552	16689603	1	-	2	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16689552	16689603	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16689604	16689676	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16689677	16689788	1	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16689677	16689788	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16689789	16689875	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16689876	16689950	1	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16689876	16689950	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16689951	16690109	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16690110	16690157	1	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16690110	16690157	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16690158	16690266	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16690267	16690351	1	-	1	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16690267	16690351	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16690352	16690468	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16690469	16690524	1	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16690469	16690524	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16690525	16690645	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16690646	16690755	1	-	2	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16690646	16690755	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	intron	16690756	16690843	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	CDS	16690844	16691138	1	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	exon	16690844	16691138	.	-	.	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
Phchi.S1	AUGUSTUS	start_codon	16691136	16691138	.	-	0	transcript_id "Phchi.S1G255900.t1"; gene_id "Phchi.S1G255900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4627.t1 is derived from g1797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11459713	11462598	.	+	.	Phchi.S1G178600
Phchi.S1	AUGUSTUS	transcript	11459713	11462598	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	start_codon	11459713	11459715	.	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11459713	11460591	0.66	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11459713	11460591	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	intron	11460592	11460807	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11460808	11460951	1	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11460808	11460951	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	intron	11460952	11461086	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11461087	11461250	1	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11461087	11461250	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	intron	11461251	11461356	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11461357	11461485	1	+	1	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11461357	11461485	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	intron	11461486	11461570	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11461571	11461751	1	+	1	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11461571	11461751	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	intron	11461752	11462270	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11462271	11462315	1	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11462271	11462315	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	intron	11462316	11462454	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	CDS	11462455	11462598	0.97	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	exon	11462455	11462598	.	+	.	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
Phchi.S1	AUGUSTUS	stop_codon	11462599	11462601	.	+	0	transcript_id "Phchi.S1G178600.t1"; gene_id "Phchi.S1G178600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15705.t1 is derived from g14175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20795166	20796875	.	-	.	Phchi.S3G302400
Phchi.S3	AUGUSTUS	transcript	20795166	20796875	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	stop_codon	20795163	20795165	.	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20795166	20795291	0.94	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20795166	20795291	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	intron	20795292	20795401	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20795402	20795533	0.92	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20795402	20795533	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	intron	20795534	20795618	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20795619	20795732	1	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20795619	20795732	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	intron	20795733	20795813	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20795814	20796215	1	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20795814	20796215	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	intron	20796216	20796626	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20796627	20796875	0.91	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20796627	20796875	.	-	.	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	start_codon	20796873	20796875	.	-	0	transcript_id "Phchi.S3G302400.t1"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	transcript	20796212	20796875	.	-	.	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	stop_codon	20796209	20796211	.	-	0	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20796212	20796256	0.71	-	0	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20796212	20796256	.	-	.	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	intron	20796257	20796626	.	-	.	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	CDS	20796627	20796875	0.86	-	0	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	exon	20796627	20796875	.	-	.	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
Phchi.S3	AUGUSTUS	start_codon	20796873	20796875	.	-	0	transcript_id "Phchi.S3G302400.t2"; gene_id "Phchi.S3G302400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6272.t1 is derived from g3444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21950189	21951252	.	-	.	Phchi.S1G343100
Phchi.S1	AUGUSTUS	transcript	21950189	21951252	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	stop_codon	21950186	21950188	.	-	0	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	CDS	21950189	21950422	0.99	-	0	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	exon	21950189	21950422	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	intron	21950423	21950592	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	CDS	21950593	21950706	1	-	0	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	exon	21950593	21950706	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	intron	21950707	21950799	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	CDS	21950800	21950891	1	-	2	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	exon	21950800	21950891	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	intron	21950892	21951065	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	CDS	21951066	21951252	1	-	0	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	exon	21951066	21951252	.	-	.	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
Phchi.S1	AUGUSTUS	start_codon	21951250	21951252	.	-	0	transcript_id "Phchi.S1G343100.t1"; gene_id "Phchi.S1G343100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9535.t1 is derived from g6711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42367239	42369304	.	+	.	Phchi.S1G669400
Phchi.S1	AUGUSTUS	transcript	42367239	42369304	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	start_codon	42367239	42367241	.	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367239	42367319	0.86	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367239	42367319	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367320	42367487	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367488	42367615	1	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367488	42367615	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367616	42367698	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367699	42367789	1	+	1	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367699	42367789	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367790	42367876	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367877	42367997	1	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367877	42367997	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367998	42368092	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368093	42368285	0.94	+	2	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368093	42368285	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42368286	42368471	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368472	42368616	0.99	+	1	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368472	42368616	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42368617	42368705	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368706	42368796	1	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368706	42368796	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42368797	42368944	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368945	42369003	1	+	2	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368945	42369003	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42369004	42369106	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42369107	42369184	0.98	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42369107	42369184	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42369185	42369262	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42369263	42369304	0.99	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42369263	42369304	.	+	.	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	stop_codon	42369305	42369307	.	+	0	transcript_id "Phchi.S1G669400.t1"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	transcript	42367239	42369278	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	start_codon	42367239	42367241	.	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367239	42367319	0.89	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367239	42367319	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367320	42367487	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367488	42367615	1	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367488	42367615	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367616	42367698	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367699	42367789	1	+	1	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367699	42367789	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367790	42367876	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42367877	42367997	1	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42367877	42367997	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42367998	42368092	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368093	42368285	0.9	+	2	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368093	42368285	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42368286	42368471	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368472	42368616	0.99	+	1	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368472	42368616	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42368617	42368705	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368706	42368796	1	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368706	42368796	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42368797	42368944	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42368945	42369003	1	+	2	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42368945	42369003	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42369004	42369106	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42369107	42369184	1	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42369107	42369184	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	intron	42369185	42369275	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	CDS	42369276	42369278	1	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	exon	42369276	42369278	.	+	.	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
Phchi.S1	AUGUSTUS	stop_codon	42369279	42369281	.	+	0	transcript_id "Phchi.S1G669400.t2"; gene_id "Phchi.S1G669400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6508.t1 is derived from g3680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23367156	23368369	.	-	.	Phchi.S1G366700
Phchi.S1	AUGUSTUS	transcript	23367156	23368369	.	-	.	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	stop_codon	23367153	23367155	.	-	0	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	CDS	23367156	23367239	1	-	0	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	exon	23367156	23367239	.	-	.	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	intron	23367240	23367404	.	-	.	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	CDS	23367405	23367448	1	-	2	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	exon	23367405	23367448	.	-	.	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	intron	23367449	23368185	.	-	.	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	CDS	23368186	23368369	1	-	0	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	exon	23368186	23368369	.	-	.	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
Phchi.S1	AUGUSTUS	start_codon	23368367	23368369	.	-	0	transcript_id "Phchi.S1G366700.t1"; gene_id "Phchi.S1G366700"
# This transcript jg5480.t2 is derived from g2650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5481.t1 is derived from g2651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17054664	17057944	.	-	.	Phchi.S1G264000
Phchi.S1	AUGUSTUS	transcript	17054664	17057944	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	stop_codon	17054661	17054663	.	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17054664	17054666	1	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17054664	17054666	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	intron	17054667	17054759	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17054760	17054834	1	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17054760	17054834	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	intron	17054835	17054954	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17054955	17055260	0.74	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17054955	17055260	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	intron	17055261	17055357	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17055358	17055771	0.99	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17055358	17055771	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	intron	17055772	17055962	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17055963	17057592	0.86	-	1	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17055963	17057592	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	intron	17057593	17057651	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17057652	17057722	0.87	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17057652	17057722	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	intron	17057723	17057875	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	CDS	17057876	17057944	0.97	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	exon	17057876	17057944	.	-	.	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
Phchi.S1	AUGUSTUS	start_codon	17057942	17057944	.	-	0	transcript_id "Phchi.S1G264000.t1"; gene_id "Phchi.S1G264000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7909.t1 is derived from g5083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31842947	31847939	.	+	.	Phchi.S1G506800
Phchi.S1	AUGUSTUS	transcript	31842947	31847939	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	start_codon	31842947	31842949	.	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31842947	31843033	0.84	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31842947	31843033	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31843034	31843147	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31843148	31843435	0.8	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31843148	31843435	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31843436	31843525	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31843526	31843626	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31843526	31843626	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31843627	31843693	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31843694	31843850	1	+	1	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31843694	31843850	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31843851	31843968	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31843969	31844079	0.96	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31843969	31844079	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31844080	31844193	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31844194	31845252	0.58	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31844194	31845252	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31845253	31845442	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31845443	31845595	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31845443	31845595	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31845596	31845724	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31845725	31845824	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31845725	31845824	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31845825	31845971	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31845972	31846066	1	+	2	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31845972	31846066	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31846067	31846139	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31846140	31846322	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31846140	31846322	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31846323	31846415	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31846416	31846472	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31846416	31846472	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31846473	31846654	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31846655	31846726	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31846655	31846726	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31846727	31846858	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31846859	31846957	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31846859	31846957	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31846958	31847090	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31847091	31847222	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31847091	31847222	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31847223	31847343	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31847344	31847517	1	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31847344	31847517	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31847518	31847637	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31847638	31847731	0.57	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31847638	31847731	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31847732	31847816	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31847817	31847841	0.97	+	2	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31847817	31847841	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	intron	31847842	31847935	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	CDS	31847936	31847939	1	+	1	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	exon	31847936	31847939	.	+	.	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
Phchi.S1	AUGUSTUS	stop_codon	31847940	31847942	.	+	0	transcript_id "Phchi.S1G506800.t1"; gene_id "Phchi.S1G506800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14292.t1 is derived from g12759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11966743	11967126	.	-	.	Phchi.S3G161100
Phchi.S3	AUGUSTUS	transcript	11966743	11967126	.	-	.	transcript_id "Phchi.S3G161100.t1"; gene_id "Phchi.S3G161100"
Phchi.S3	AUGUSTUS	stop_codon	11966740	11966742	.	-	0	transcript_id "Phchi.S3G161100.t1"; gene_id "Phchi.S3G161100"
Phchi.S3	AUGUSTUS	CDS	11966743	11967126	0.45	-	0	transcript_id "Phchi.S3G161100.t1"; gene_id "Phchi.S3G161100"
Phchi.S3	AUGUSTUS	exon	11966743	11967126	.	-	.	transcript_id "Phchi.S3G161100.t1"; gene_id "Phchi.S3G161100"
Phchi.S3	AUGUSTUS	start_codon	11967124	11967126	.	-	0	transcript_id "Phchi.S3G161100.t1"; gene_id "Phchi.S3G161100"
# This transcript jg3042.t2 is derived from g211.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3043.t1 is derived from g212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1312014	1312764	.	-	.	Phchi.S1G020200
Phchi.S1	AUGUSTUS	transcript	1312014	1312764	.	-	.	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	stop_codon	1312011	1312013	.	-	0	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	CDS	1312014	1312033	1	-	2	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	exon	1312014	1312033	.	-	.	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	intron	1312034	1312183	.	-	.	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	CDS	1312184	1312416	0.73	-	1	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	exon	1312184	1312416	.	-	.	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	intron	1312417	1312519	.	-	.	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	CDS	1312520	1312764	0.58	-	0	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	exon	1312520	1312764	.	-	.	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
Phchi.S1	AUGUSTUS	start_codon	1312762	1312764	.	-	0	transcript_id "Phchi.S1G020200.t1"; gene_id "Phchi.S1G020200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3825.t1 is derived from g994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5898518	5899605	.	-	.	Phchi.S1G098400
Phchi.S1	AUGUSTUS	transcript	5898518	5899605	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	stop_codon	5898515	5898517	.	-	0	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5898518	5898751	1	-	0	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5898518	5898751	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5898752	5898845	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5898846	5898956	0.55	-	0	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5898846	5898956	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5898957	5899064	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5899065	5899216	0.6	-	2	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5899065	5899216	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5899217	5899314	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5899315	5899416	1	-	2	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5899315	5899416	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5899417	5899496	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5899497	5899605	1	-	0	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5899497	5899605	.	-	.	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	start_codon	5899603	5899605	.	-	0	transcript_id "Phchi.S1G098400.t1"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	transcript	5898518	5899605	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	stop_codon	5898515	5898517	.	-	0	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5898518	5898751	1	-	0	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5898518	5898751	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5898752	5898845	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5898846	5898956	0.44	-	0	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5898846	5898956	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5898957	5899064	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5899065	5899216	0.48	-	2	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5899065	5899216	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5899217	5899314	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5899315	5899413	0.99	-	2	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5899315	5899413	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	intron	5899414	5899496	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	CDS	5899497	5899605	1	-	0	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	exon	5899497	5899605	.	-	.	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
Phchi.S1	AUGUSTUS	start_codon	5899603	5899605	.	-	0	transcript_id "Phchi.S1G098400.t2"; gene_id "Phchi.S1G098400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13958.t1 is derived from g12425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9932054	9933007	.	+	.	Phchi.S3G127700
Phchi.S3	AUGUSTUS	transcript	9932054	9933007	.	+	.	transcript_id "Phchi.S3G127700.t1"; gene_id "Phchi.S3G127700"
Phchi.S3	AUGUSTUS	start_codon	9932054	9932056	.	+	0	transcript_id "Phchi.S3G127700.t1"; gene_id "Phchi.S3G127700"
Phchi.S3	AUGUSTUS	CDS	9932054	9933007	0.62	+	0	transcript_id "Phchi.S3G127700.t1"; gene_id "Phchi.S3G127700"
Phchi.S3	AUGUSTUS	exon	9932054	9933007	.	+	.	transcript_id "Phchi.S3G127700.t1"; gene_id "Phchi.S3G127700"
Phchi.S3	AUGUSTUS	stop_codon	9933008	9933010	.	+	0	transcript_id "Phchi.S3G127700.t1"; gene_id "Phchi.S3G127700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1966.t1 is derived from g8886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4067848	4068653	.	+	.	Phchi.S5G057500
Phchi.S5	AUGUSTUS	transcript	4067848	4068653	.	+	.	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	start_codon	4067848	4067850	.	+	0	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	CDS	4067848	4068310	0.41	+	0	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	exon	4067848	4068310	.	+	.	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	intron	4068311	4068414	.	+	.	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	CDS	4068415	4068653	1	+	2	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	exon	4068415	4068653	.	+	.	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
Phchi.S5	AUGUSTUS	stop_codon	4068654	4068656	.	+	0	transcript_id "Phchi.S5G057500.t1"; gene_id "Phchi.S5G057500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11314.t1 is derived from g15364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5328038	5329082	.	+	.	Phchi.S4G089600
Phchi.S4	AUGUSTUS	transcript	5328038	5329082	.	+	.	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	start_codon	5328038	5328040	.	+	0	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	CDS	5328038	5328276	0.84	+	0	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	exon	5328038	5328276	.	+	.	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	intron	5328277	5329015	.	+	.	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	CDS	5329016	5329082	0.77	+	1	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	exon	5329016	5329082	.	+	.	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
Phchi.S4	AUGUSTUS	stop_codon	5329083	5329085	.	+	0	transcript_id "Phchi.S4G089600.t1"; gene_id "Phchi.S4G089600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3911.t1 is derived from g1080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6410255	6411452	.	+	.	Phchi.S1G107000
Phchi.S1	AUGUSTUS	transcript	6410255	6411452	.	+	.	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	start_codon	6410255	6410257	.	+	0	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	CDS	6410255	6410804	0.89	+	0	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	exon	6410255	6410804	.	+	.	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	intron	6410805	6410898	.	+	.	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	CDS	6410899	6411452	0.99	+	2	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	exon	6410899	6411452	.	+	.	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
Phchi.S1	AUGUSTUS	stop_codon	6411453	6411455	.	+	0	transcript_id "Phchi.S1G107000.t1"; gene_id "Phchi.S1G107000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4824.t1 is derived from g1995.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13018070	13021824	.	+	.	Phchi.S1G198400
Phchi.S1	AUGUSTUS	transcript	13018339	13021824	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	start_codon	13018339	13018341	.	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018339	13018461	0.64	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018339	13018461	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018462	13018548	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018549	13018635	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018549	13018635	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018636	13018720	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018721	13018792	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018721	13018792	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018793	13018918	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018919	13019123	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018919	13019123	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019124	13019276	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13019277	13019404	1	+	2	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13019277	13019404	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019405	13019506	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13019507	13019633	0.98	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13019507	13019633	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019634	13019706	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13019707	13019876	1	+	2	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13019707	13019876	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019877	13020124	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020125	13020268	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020125	13020268	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13020269	13020349	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020350	13020463	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020350	13020463	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13020464	13020556	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020557	13020712	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020557	13020712	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13020713	13020830	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020831	13021114	0.96	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020831	13021114	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13021115	13021193	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13021194	13021317	1	+	1	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13021194	13021317	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13021318	13021409	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13021410	13021490	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13021410	13021490	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13021491	13021578	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13021579	13021824	1	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13021579	13021824	.	+	.	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	stop_codon	13021825	13021827	.	+	0	transcript_id "Phchi.S1G198400.t1"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	transcript	13018070	13021824	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	start_codon	13018070	13018072	.	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018070	13018198	0.69	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018070	13018198	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018199	13018326	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018327	13018461	0.68	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018327	13018461	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018462	13018548	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018549	13018635	1	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018549	13018635	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018636	13018720	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018721	13018792	0.99	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018721	13018792	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13018793	13018918	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13018919	13019123	0.99	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13018919	13019123	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019124	13019276	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13019277	13019404	0.99	+	2	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13019277	13019404	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019405	13019506	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13019507	13019633	0.97	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13019507	13019633	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019634	13019706	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13019707	13019876	1	+	2	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13019707	13019876	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13019877	13020124	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020125	13020268	1	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020125	13020268	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13020269	13020349	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020350	13020463	1	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020350	13020463	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13020464	13020556	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020557	13020712	1	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020557	13020712	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13020713	13020830	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13020831	13021114	0.99	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13020831	13021114	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13021115	13021193	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13021194	13021317	1	+	1	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13021194	13021317	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13021318	13021409	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13021410	13021490	1	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13021410	13021490	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	intron	13021491	13021578	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	CDS	13021579	13021824	1	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	exon	13021579	13021824	.	+	.	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
Phchi.S1	AUGUSTUS	stop_codon	13021825	13021827	.	+	0	transcript_id "Phchi.S1G198400.t2"; gene_id "Phchi.S1G198400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8707.t1 is derived from g5882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37559147	37560544	.	+	.	Phchi.S1G586600
Phchi.S1	AUGUSTUS	transcript	37559147	37560544	.	+	.	transcript_id "Phchi.S1G586600.t1"; gene_id "Phchi.S1G586600"
Phchi.S1	AUGUSTUS	start_codon	37559147	37559149	.	+	0	transcript_id "Phchi.S1G586600.t1"; gene_id "Phchi.S1G586600"
Phchi.S1	AUGUSTUS	CDS	37559147	37560544	0.62	+	0	transcript_id "Phchi.S1G586600.t1"; gene_id "Phchi.S1G586600"
Phchi.S1	AUGUSTUS	exon	37559147	37560544	.	+	.	transcript_id "Phchi.S1G586600.t1"; gene_id "Phchi.S1G586600"
Phchi.S1	AUGUSTUS	stop_codon	37560545	37560547	.	+	0	transcript_id "Phchi.S1G586600.t1"; gene_id "Phchi.S1G586600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6500.t1 is derived from g3672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23335402	23338322	.	+	.	Phchi.S1G365900
Phchi.S1	AUGUSTUS	transcript	23335402	23338322	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	start_codon	23335402	23335404	.	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23335402	23335474	1	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23335402	23335474	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23335475	23335599	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23335600	23335734	1	+	2	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23335600	23335734	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23335735	23335814	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23335815	23335909	1	+	2	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23335815	23335909	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23335910	23336045	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23336046	23336140	1	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23336046	23336140	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23336141	23336366	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23336367	23336502	1	+	1	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23336367	23336502	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23336503	23336650	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23336651	23336800	1	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23336651	23336800	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23336801	23336891	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23336892	23337482	0.98	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23336892	23337482	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23337483	23337619	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23337620	23337828	1	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23337620	23337828	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23337829	23337907	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23337908	23338040	1	+	1	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23337908	23338040	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	intron	23338041	23338187	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	CDS	23338188	23338322	1	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	exon	23338188	23338322	.	+	.	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
Phchi.S1	AUGUSTUS	stop_codon	23338323	23338325	.	+	0	transcript_id "Phchi.S1G365900.t1"; gene_id "Phchi.S1G365900"
# This transcript jg2967.t2 is derived from g136.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2968.t1 is derived from g137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	889390	890025	.	+	.	Phchi.S1G012700
Phchi.S1	AUGUSTUS	transcript	889390	890025	.	+	.	transcript_id "Phchi.S1G012700.t1"; gene_id "Phchi.S1G012700"
Phchi.S1	AUGUSTUS	start_codon	889390	889392	.	+	0	transcript_id "Phchi.S1G012700.t1"; gene_id "Phchi.S1G012700"
Phchi.S1	AUGUSTUS	CDS	889390	890025	0.8	+	0	transcript_id "Phchi.S1G012700.t1"; gene_id "Phchi.S1G012700"
Phchi.S1	AUGUSTUS	exon	889390	890025	.	+	.	transcript_id "Phchi.S1G012700.t1"; gene_id "Phchi.S1G012700"
Phchi.S1	AUGUSTUS	stop_codon	890026	890028	.	+	0	transcript_id "Phchi.S1G012700.t1"; gene_id "Phchi.S1G012700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3130.t1 is derived from g299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1876608	1879388	.	+	.	Phchi.S1G028900
Phchi.S1	AUGUSTUS	transcript	1876608	1879388	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	start_codon	1876608	1876610	.	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1876608	1877204	0.97	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1876608	1877204	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1877205	1877312	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1877313	1877358	0.99	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1877313	1877358	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1877359	1877463	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1877464	1877597	1	+	2	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1877464	1877597	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1877598	1877698	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1877699	1877842	1	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1877699	1877842	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1877843	1877968	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1877969	1878048	0.99	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1877969	1878048	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1878049	1878160	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1878161	1878199	1	+	1	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1878161	1878199	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1878200	1878294	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1878295	1878337	1	+	1	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1878295	1878337	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1878338	1878424	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1878425	1878529	1	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1878425	1878529	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1878530	1878742	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1878743	1878815	1	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1878743	1878815	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1878816	1878898	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1878899	1879001	1	+	2	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1878899	1879001	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1879002	1879114	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1879115	1879199	1	+	1	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1879115	1879199	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	intron	1879200	1879298	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	CDS	1879299	1879388	0.98	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	exon	1879299	1879388	.	+	.	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
Phchi.S1	AUGUSTUS	stop_codon	1879389	1879391	.	+	0	transcript_id "Phchi.S1G028900.t1"; gene_id "Phchi.S1G028900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg639.t1 is derived from g10421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4553023	4553604	.	-	.	Phchi.S6G059800
Phchi.S6	AUGUSTUS	transcript	4553023	4553604	.	-	.	transcript_id "Phchi.S6G059800.t1"; gene_id "Phchi.S6G059800"
Phchi.S6	AUGUSTUS	stop_codon	4553020	4553022	.	-	0	transcript_id "Phchi.S6G059800.t1"; gene_id "Phchi.S6G059800"
Phchi.S6	AUGUSTUS	CDS	4553023	4553604	0.99	-	0	transcript_id "Phchi.S6G059800.t1"; gene_id "Phchi.S6G059800"
Phchi.S6	AUGUSTUS	exon	4553023	4553604	.	-	.	transcript_id "Phchi.S6G059800.t1"; gene_id "Phchi.S6G059800"
Phchi.S6	AUGUSTUS	start_codon	4553602	4553604	.	-	0	transcript_id "Phchi.S6G059800.t1"; gene_id "Phchi.S6G059800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6070.t1 is derived from g3241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20731357	20736962	.	-	.	Phchi.S1G322900
Phchi.S1	AUGUSTUS	transcript	20731357	20736962	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	stop_codon	20731354	20731356	.	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20731357	20731503	0.81	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20731357	20731503	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20731504	20731594	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20731595	20731736	1	-	1	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20731595	20731736	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20731737	20731860	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20731861	20731922	1	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20731861	20731922	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20731923	20732104	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732105	20732111	0.66	-	1	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732105	20732111	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732112	20732203	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732204	20732283	1	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732204	20732283	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732284	20732441	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732442	20732605	1	-	2	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732442	20732605	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732606	20732794	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732795	20732963	1	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732795	20732963	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732964	20733096	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20733097	20733238	1	-	1	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20733097	20733238	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20733239	20733333	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20733334	20733847	0.89	-	2	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20733334	20733847	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20733848	20733943	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20733944	20734179	0.35	-	1	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20733944	20734179	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20734180	20734299	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20734300	20734462	0.22	-	2	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20734300	20734462	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20734463	20734542	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20734543	20734964	0.31	-	1	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20734543	20734964	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20734965	20735081	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735082	20735167	1	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735082	20735167	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735168	20735299	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735300	20735451	1	-	2	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735300	20735451	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735452	20735599	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735600	20735618	1	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735600	20735618	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735619	20735795	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735796	20736002	0.96	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735796	20736002	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20736003	20736095	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20736096	20736962	0.91	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20736096	20736962	.	-	.	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	start_codon	20736960	20736962	.	-	0	transcript_id "Phchi.S1G322900.t1"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	transcript	20731357	20736962	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	stop_codon	20731354	20731356	.	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20731357	20731503	0.74	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20731357	20731503	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20731504	20731594	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20731595	20731736	1	-	1	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20731595	20731736	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20731737	20731860	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20731861	20731922	1	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20731861	20731922	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20731923	20732104	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732105	20732111	0.59	-	1	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732105	20732111	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732112	20732203	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732204	20732283	1	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732204	20732283	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732284	20732441	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732442	20732605	1	-	2	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732442	20732605	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732606	20732794	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20732795	20732963	1	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20732795	20732963	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20732964	20733096	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20733097	20733238	1	-	1	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20733097	20733238	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20733239	20733333	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20733334	20733847	0.93	-	2	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20733334	20733847	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20733848	20733943	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20733944	20734179	0.27	-	1	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20733944	20734179	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20734180	20734299	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20734300	20734462	0.18	-	2	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20734300	20734462	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20734463	20734542	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20734543	20734964	0.22	-	1	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20734543	20734964	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20734965	20735081	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735082	20735167	1	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735082	20735167	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735168	20735299	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735300	20735451	1	-	2	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735300	20735451	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735452	20735599	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735600	20735618	1	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735600	20735618	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735619	20735795	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20735796	20735995	0.74	-	2	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20735796	20735995	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20735996	20736095	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20736096	20736145	0.72	-	1	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20736096	20736145	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	intron	20736146	20736258	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	CDS	20736259	20736962	0.38	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	exon	20736259	20736962	.	-	.	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
Phchi.S1	AUGUSTUS	start_codon	20736960	20736962	.	-	0	transcript_id "Phchi.S1G322900.t2"; gene_id "Phchi.S1G322900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4788.t1 is derived from g1958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12818326	12818865	.	-	.	Phchi.S1G194700
Phchi.S1	AUGUSTUS	transcript	12818326	12818865	.	-	.	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	stop_codon	12818323	12818325	.	-	0	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	CDS	12818326	12818411	0.9	-	2	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	exon	12818326	12818411	.	-	.	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	intron	12818412	12818577	.	-	.	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	CDS	12818578	12818615	0.92	-	1	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	exon	12818578	12818615	.	-	.	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	intron	12818616	12818791	.	-	.	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	CDS	12818792	12818865	0.5	-	0	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	exon	12818792	12818865	.	-	.	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
Phchi.S1	AUGUSTUS	start_codon	12818863	12818865	.	-	0	transcript_id "Phchi.S1G194700.t1"; gene_id "Phchi.S1G194700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1799.t1 is derived from g8719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3090760	3094404	.	-	.	Phchi.S5G040800
Phchi.S5	AUGUSTUS	transcript	3090760	3094404	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	stop_codon	3090757	3090759	.	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3090760	3091035	0.98	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3090760	3091035	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	intron	3091036	3091141	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3091142	3091489	0.73	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3091142	3091489	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	intron	3091490	3091568	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3091569	3092240	0.75	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3091569	3092240	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	intron	3092241	3092343	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3092344	3092615	0.98	-	2	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3092344	3092615	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	intron	3092616	3092703	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3092704	3093192	0.97	-	2	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3092704	3093192	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	intron	3093193	3093312	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3093313	3093535	0.86	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3093313	3093535	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	intron	3093536	3093699	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	CDS	3093700	3094404	0.56	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	exon	3093700	3094404	.	-	.	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
Phchi.S5	AUGUSTUS	start_codon	3094402	3094404	.	-	0	transcript_id "Phchi.S5G040800.t1"; gene_id "Phchi.S5G040800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10966.t1 is derived from g15016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3387035	3387549	.	+	.	Phchi.S4G054800
Phchi.S4	AUGUSTUS	transcript	3387035	3387549	.	+	.	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	start_codon	3387035	3387037	.	+	0	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	CDS	3387035	3387155	0.98	+	0	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	exon	3387035	3387155	.	+	.	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	intron	3387156	3387424	.	+	.	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	CDS	3387425	3387549	1	+	2	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	exon	3387425	3387549	.	+	.	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
Phchi.S4	AUGUSTUS	stop_codon	3387550	3387552	.	+	0	transcript_id "Phchi.S4G054800.t1"; gene_id "Phchi.S4G054800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11364.t1 is derived from g15414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5782311	5783774	.	+	.	Phchi.S4G094600
Phchi.S4	AUGUSTUS	transcript	5782311	5783774	.	+	.	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	start_codon	5782311	5782313	.	+	0	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	CDS	5782311	5782777	1	+	0	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	exon	5782311	5782777	.	+	.	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	intron	5782778	5782889	.	+	.	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	CDS	5782890	5783430	0.99	+	1	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	exon	5782890	5783430	.	+	.	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	intron	5783431	5783531	.	+	.	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	CDS	5783532	5783774	0.99	+	0	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	exon	5783532	5783774	.	+	.	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
Phchi.S4	AUGUSTUS	stop_codon	5783775	5783777	.	+	0	transcript_id "Phchi.S4G094600.t1"; gene_id "Phchi.S4G094600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg896.t1 is derived from g10678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6350605	6351027	.	+	.	Phchi.S6G085500
Phchi.S6	AUGUSTUS	transcript	6350605	6351027	.	+	.	transcript_id "Phchi.S6G085500.t1"; gene_id "Phchi.S6G085500"
Phchi.S6	AUGUSTUS	start_codon	6350605	6350607	.	+	0	transcript_id "Phchi.S6G085500.t1"; gene_id "Phchi.S6G085500"
Phchi.S6	AUGUSTUS	CDS	6350605	6351027	0.66	+	0	transcript_id "Phchi.S6G085500.t1"; gene_id "Phchi.S6G085500"
Phchi.S6	AUGUSTUS	exon	6350605	6351027	.	+	.	transcript_id "Phchi.S6G085500.t1"; gene_id "Phchi.S6G085500"
Phchi.S6	AUGUSTUS	stop_codon	6351028	6351030	.	+	0	transcript_id "Phchi.S6G085500.t1"; gene_id "Phchi.S6G085500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2964.t1 is derived from g133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	853986	859831	.	+	.	Phchi.S1G012300
Phchi.S1	AUGUSTUS	transcript	853986	859831	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	start_codon	853986	853988	.	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	853986	854007	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	853986	854007	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	854008	854140	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	854141	856161	0.25	+	2	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	854141	856161	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	856162	856268	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	856269	856589	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	856269	856589	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	856590	856687	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	856688	856774	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	856688	856774	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	856775	856897	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	856898	857596	0.8	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	856898	857596	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	857597	857702	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	857703	857867	0.95	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	857703	857867	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	857868	857959	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	857960	858254	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	857960	858254	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	858255	858397	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	858398	858612	1	+	2	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	858398	858612	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	858613	858711	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	858712	858960	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	858712	858960	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	858961	859044	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	859045	859101	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	859045	859101	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	859102	859190	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	859191	859254	1	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	859191	859254	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	859255	859349	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	859350	859589	1	+	2	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	859350	859589	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	intron	859590	859679	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	CDS	859680	859831	1	+	2	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	exon	859680	859831	.	+	.	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
Phchi.S1	AUGUSTUS	stop_codon	859832	859834	.	+	0	transcript_id "Phchi.S1G012300.t1"; gene_id "Phchi.S1G012300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12435.t1 is derived from g8112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19801340	19802885	.	-	.	Phchi.S2G051500
Phchi.S2	AUGUSTUS	transcript	19801340	19802885	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	stop_codon	19801337	19801339	.	-	0	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801340	19801381	0.95	-	0	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801340	19801381	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19801382	19801508	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801509	19801706	0.77	-	0	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801509	19801706	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19801707	19801798	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801799	19801873	1	-	0	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801799	19801873	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19801874	19801967	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801968	19802299	0.98	-	2	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801968	19802299	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19802300	19802419	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19802420	19802885	0.85	-	0	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19802420	19802885	.	-	.	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	start_codon	19802883	19802885	.	-	0	transcript_id "Phchi.S2G051500.t1"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	transcript	19801340	19802885	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	stop_codon	19801337	19801339	.	-	0	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801340	19801381	0.7	-	0	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801340	19801381	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19801382	19801601	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801602	19801706	0.7	-	0	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801602	19801706	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19801707	19801798	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801799	19801873	1	-	0	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801799	19801873	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19801874	19801967	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19801968	19802299	0.29	-	2	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19801968	19802299	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	intron	19802300	19802419	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	CDS	19802420	19802885	0.28	-	0	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	exon	19802420	19802885	.	-	.	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
Phchi.S2	AUGUSTUS	start_codon	19802883	19802885	.	-	0	transcript_id "Phchi.S2G051500.t2"; gene_id "Phchi.S2G051500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10933.t1 is derived from g14983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3165888	3166247	.	+	.	Phchi.S4G051500
Phchi.S4	AUGUSTUS	transcript	3165888	3166247	.	+	.	transcript_id "Phchi.S4G051500.t1"; gene_id "Phchi.S4G051500"
Phchi.S4	AUGUSTUS	start_codon	3165888	3165890	.	+	0	transcript_id "Phchi.S4G051500.t1"; gene_id "Phchi.S4G051500"
Phchi.S4	AUGUSTUS	CDS	3165888	3166247	0.71	+	0	transcript_id "Phchi.S4G051500.t1"; gene_id "Phchi.S4G051500"
Phchi.S4	AUGUSTUS	exon	3165888	3166247	.	+	.	transcript_id "Phchi.S4G051500.t1"; gene_id "Phchi.S4G051500"
Phchi.S4	AUGUSTUS	stop_codon	3166248	3166250	.	+	0	transcript_id "Phchi.S4G051500.t1"; gene_id "Phchi.S4G051500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14933.t1 is derived from g13401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15594417	15596794	.	+	.	Phchi.S3G225200
Phchi.S3	AUGUSTUS	transcript	15594417	15596794	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	start_codon	15594417	15594419	.	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15594417	15594478	1	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15594417	15594478	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15594479	15595252	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15595253	15595343	1	+	1	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15595253	15595343	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15595344	15595483	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15595484	15595552	1	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15595484	15595552	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15595553	15595696	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15595697	15595810	1	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15595697	15595810	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15595811	15595977	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15595978	15596058	1	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15595978	15596058	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15596059	15596160	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15596161	15596238	0.98	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15596161	15596238	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15596239	15596342	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15596343	15596405	0.99	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15596343	15596405	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15596406	15596516	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15596517	15596558	1	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15596517	15596558	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	intron	15596559	15596683	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	CDS	15596684	15596794	1	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	exon	15596684	15596794	.	+	.	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
Phchi.S3	AUGUSTUS	stop_codon	15596795	15596797	.	+	0	transcript_id "Phchi.S3G225200.t1"; gene_id "Phchi.S3G225200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11193.t1 is derived from g15243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4631648	4632156	.	+	.	Phchi.S4G077500
Phchi.S4	AUGUSTUS	transcript	4631648	4632156	.	+	.	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	start_codon	4631648	4631650	.	+	0	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	CDS	4631648	4631762	0.99	+	0	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	exon	4631648	4631762	.	+	.	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	intron	4631763	4631854	.	+	.	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	CDS	4631855	4632156	0.99	+	2	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	exon	4631855	4632156	.	+	.	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
Phchi.S4	AUGUSTUS	stop_codon	4632157	4632159	.	+	0	transcript_id "Phchi.S4G077500.t1"; gene_id "Phchi.S4G077500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11224.t1 is derived from g15274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4873458	4874204	.	+	.	Phchi.S4G080600
Phchi.S4	AUGUSTUS	transcript	4873458	4874204	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	start_codon	4873458	4873460	.	+	0	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	CDS	4873458	4873510	0.8	+	0	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	exon	4873458	4873510	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	intron	4873511	4873614	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	CDS	4873615	4873704	0.98	+	1	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	exon	4873615	4873704	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	intron	4873705	4873797	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	CDS	4873798	4873876	0.99	+	1	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	exon	4873798	4873876	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	intron	4873877	4873982	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	CDS	4873983	4874078	1	+	0	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	exon	4873983	4874078	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	intron	4874079	4874171	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	CDS	4874172	4874204	1	+	0	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	exon	4874172	4874204	.	+	.	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
Phchi.S4	AUGUSTUS	stop_codon	4874205	4874207	.	+	0	transcript_id "Phchi.S4G080600.t1"; gene_id "Phchi.S4G080600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14998.t1 is derived from g13466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16182035	16183062	.	-	.	Phchi.S3G231700
Phchi.S3	AUGUSTUS	transcript	16182035	16183062	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	stop_codon	16182032	16182034	.	-	0	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	CDS	16182035	16182119	0.62	-	1	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	exon	16182035	16182119	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	intron	16182120	16182281	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	CDS	16182282	16182293	0.95	-	1	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	exon	16182282	16182293	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	intron	16182294	16182507	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	CDS	16182508	16182548	0.96	-	0	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	exon	16182508	16182548	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	intron	16182549	16182660	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	CDS	16182661	16183062	0.79	-	0	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	exon	16182661	16183062	.	-	.	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
Phchi.S3	AUGUSTUS	start_codon	16183060	16183062	.	-	0	transcript_id "Phchi.S3G231700.t1"; gene_id "Phchi.S3G231700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6512.t1 is derived from g3684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23405623	23409366	.	+	.	Phchi.S1G367100
Phchi.S1	AUGUSTUS	transcript	23405623	23409366	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	start_codon	23405623	23405625	.	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23405623	23405742	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23405623	23405742	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23405743	23405878	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23405879	23405936	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23405879	23405936	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23405937	23406044	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23406045	23406328	1	+	2	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23406045	23406328	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23406329	23406455	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23406456	23406569	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23406456	23406569	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23406570	23406697	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23406698	23406758	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23406698	23406758	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23406759	23406856	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23406857	23406951	1	+	2	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23406857	23406951	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23406952	23407035	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23407036	23407110	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23407036	23407110	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23407111	23407207	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23407208	23407293	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23407208	23407293	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23407294	23407366	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23407367	23407416	1	+	1	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23407367	23407416	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23407417	23407507	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23407508	23407548	1	+	2	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23407508	23407548	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23407549	23407676	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23407677	23407847	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23407677	23407847	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23407848	23407963	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23407964	23407999	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23407964	23407999	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23408000	23408093	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23408094	23408161	1	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23408094	23408161	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23408162	23408247	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23408248	23408308	1	+	1	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23408248	23408308	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23408309	23408387	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23408388	23408766	0.99	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23408388	23408766	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	intron	23408767	23409325	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	CDS	23409326	23409366	0.99	+	2	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	exon	23409326	23409366	.	+	.	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
Phchi.S1	AUGUSTUS	stop_codon	23409367	23409369	.	+	0	transcript_id "Phchi.S1G367100.t1"; gene_id "Phchi.S1G367100"
# This transcript jg12180.t2 is derived from g7856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12181.t1 is derived from g7857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6114597	6114990	.	-	.	Phchi.S2G026100
Phchi.S2	AUGUSTUS	transcript	6114597	6114990	.	-	.	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	stop_codon	6114594	6114596	.	-	0	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	CDS	6114597	6114667	0.69	-	2	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	exon	6114597	6114667	.	-	.	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	intron	6114668	6114848	.	-	.	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	CDS	6114849	6114990	0.83	-	0	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	exon	6114849	6114990	.	-	.	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
Phchi.S2	AUGUSTUS	start_codon	6114988	6114990	.	-	0	transcript_id "Phchi.S2G026100.t1"; gene_id "Phchi.S2G026100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10590.t1 is derived from g14640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1089043	1092262	.	-	.	Phchi.S4G017200
Phchi.S4	AUGUSTUS	transcript	1089043	1092262	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	stop_codon	1089040	1089042	.	-	0	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	CDS	1089043	1089429	0.99	-	0	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	exon	1089043	1089429	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	intron	1089430	1089542	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	CDS	1089543	1089794	1	-	0	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	exon	1089543	1089794	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	intron	1089795	1089893	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	CDS	1089894	1090265	1	-	0	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	exon	1089894	1090265	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	intron	1090266	1090350	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	CDS	1090351	1090535	1	-	2	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	exon	1090351	1090535	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	intron	1090536	1090635	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	CDS	1090636	1092262	0.52	-	0	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	exon	1090636	1092262	.	-	.	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
Phchi.S4	AUGUSTUS	start_codon	1092260	1092262	.	-	0	transcript_id "Phchi.S4G017200.t1"; gene_id "Phchi.S4G017200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14878.t1 is derived from g13346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15247525	15252105	.	-	.	Phchi.S3G219700
Phchi.S3	AUGUSTUS	transcript	15247525	15252105	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	stop_codon	15247522	15247524	.	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15247525	15247660	1	-	1	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15247525	15247660	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15247661	15247772	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15247773	15247836	1	-	2	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15247773	15247836	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15247837	15247915	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15247916	15248025	1	-	1	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15247916	15248025	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15248026	15248104	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15248105	15248196	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15248105	15248196	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15248197	15248286	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15248287	15248439	0.92	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15248287	15248439	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15248440	15248547	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15248548	15248604	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15248548	15248604	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15248605	15248713	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15248714	15248905	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15248714	15248905	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15248906	15248988	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15248989	15249056	1	-	2	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15248989	15249056	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15249057	15249157	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15249158	15249280	1	-	2	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15249158	15249280	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15249281	15249399	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15249400	15249473	0.98	-	1	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15249400	15249473	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15249474	15249587	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15249588	15249695	0.98	-	1	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15249588	15249695	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15249696	15249784	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15249785	15249912	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15249785	15249912	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15249913	15249984	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15249985	15250092	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15249985	15250092	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15250093	15250188	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15250189	15250271	1	-	2	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15250189	15250271	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15250272	15250371	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15250372	15250465	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15250372	15250465	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15250466	15250560	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15250561	15250629	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15250561	15250629	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15250630	15250786	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15250787	15250873	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15250787	15250873	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15250874	15250949	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15250950	15251112	1	-	1	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15250950	15251112	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15251113	15251197	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15251198	15251307	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15251198	15251307	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15251308	15251501	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15251502	15251643	1	-	1	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15251502	15251643	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15251644	15251725	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15251726	15251799	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15251726	15251799	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	intron	15251800	15251874	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	CDS	15251875	15252105	1	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	exon	15251875	15252105	.	-	.	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
Phchi.S3	AUGUSTUS	start_codon	15252103	15252105	.	-	0	transcript_id "Phchi.S3G219700.t1"; gene_id "Phchi.S3G219700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6855.t1 is derived from g4027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25588954	25592031	.	-	.	Phchi.S1G401400
Phchi.S1	AUGUSTUS	transcript	25588954	25592031	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	stop_codon	25588951	25588953	.	-	0	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25588954	25588998	1	-	0	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25588954	25588998	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	intron	25588999	25589343	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25589344	25589404	1	-	1	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25589344	25589404	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	intron	25589405	25589504	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25589505	25590686	1	-	1	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25589505	25590686	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	intron	25590687	25590780	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25590781	25590858	1	-	1	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25590781	25590858	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	intron	25590859	25590941	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25590942	25590967	1	-	0	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25590942	25590967	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	intron	25590968	25591562	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25591563	25591694	0.82	-	0	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25591563	25591694	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	intron	25591695	25591971	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	CDS	25591972	25592031	0.44	-	0	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	exon	25591972	25592031	.	-	.	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
Phchi.S1	AUGUSTUS	start_codon	25592029	25592031	.	-	0	transcript_id "Phchi.S1G401400.t1"; gene_id "Phchi.S1G401400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6219.t1 is derived from g3391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21502238	21507388	.	+	.	Phchi.S1G337800
Phchi.S1	AUGUSTUS	transcript	21502238	21507388	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	start_codon	21502238	21502240	.	+	0	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	CDS	21502238	21505119	0.97	+	0	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	exon	21502238	21505119	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	intron	21505120	21505216	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	CDS	21505217	21505224	1	+	1	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	exon	21505217	21505224	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	intron	21505225	21505301	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	CDS	21505302	21506314	0.99	+	2	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	exon	21505302	21506314	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	intron	21506315	21506438	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	CDS	21506439	21506664	1	+	0	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	exon	21506439	21506664	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	intron	21506665	21506986	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	CDS	21506987	21507129	1	+	2	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	exon	21506987	21507129	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	intron	21507130	21507223	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	CDS	21507224	21507388	0.77	+	0	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	exon	21507224	21507388	.	+	.	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
Phchi.S1	AUGUSTUS	stop_codon	21507389	21507391	.	+	0	transcript_id "Phchi.S1G337800.t1"; gene_id "Phchi.S1G337800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5683.t1 is derived from g2853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18309919	18311645	.	-	.	Phchi.S1G284200
Phchi.S1	AUGUSTUS	transcript	18309919	18311645	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	stop_codon	18309916	18309918	.	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18309919	18310035	0.94	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18309919	18310035	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18310036	18310137	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18310138	18310303	0.94	-	1	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18310138	18310303	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18310304	18310397	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18310398	18310480	1	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18310398	18310480	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18310481	18310578	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18310579	18310812	0.97	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18310579	18310812	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18310813	18310923	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18310924	18310968	0.95	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18310924	18310968	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18310969	18311134	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18311135	18311174	1	-	1	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18311135	18311174	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18311175	18311364	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18311365	18311429	1	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18311365	18311429	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	intron	18311430	18311510	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	CDS	18311511	18311645	1	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	exon	18311511	18311645	.	-	.	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
Phchi.S1	AUGUSTUS	start_codon	18311643	18311645	.	-	0	transcript_id "Phchi.S1G284200.t1"; gene_id "Phchi.S1G284200"
# This transcript jg12595.t2 is derived from g8272.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12596.t1 is derived from g8273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37081057	37084636	.	-	.	Phchi.S2G067600
Phchi.S2	AUGUSTUS	transcript	37081275	37084636	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	stop_codon	37081272	37081274	.	-	0	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37081275	37081292	1	-	0	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37081275	37081292	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37081293	37081638	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37081639	37082445	0.99	-	0	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37081639	37082445	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37082446	37082597	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37082598	37083301	0.27	-	2	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37082598	37083301	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37083302	37083492	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37083493	37083717	1	-	2	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37083493	37083717	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37083718	37083979	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37083980	37084257	0.82	-	1	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37083980	37084257	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37084258	37084357	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37084358	37084382	0.82	-	2	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37084358	37084382	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37084383	37084554	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37084555	37084636	0.82	-	0	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37084555	37084636	.	-	.	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	start_codon	37084634	37084636	.	-	0	transcript_id "Phchi.S2G067600.t1"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	transcript	37081057	37084636	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	stop_codon	37081054	37081056	.	-	0	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37081057	37081107	1	-	0	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37081057	37081107	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37081108	37081638	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37081639	37082445	1	-	0	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37081639	37082445	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37082446	37082597	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37082598	37083301	0.34	-	2	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37082598	37083301	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37083302	37083492	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37083493	37083717	1	-	2	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37083493	37083717	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37083718	37083979	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37083980	37084257	0.76	-	1	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37083980	37084257	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37084258	37084357	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37084358	37084382	0.77	-	2	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37084358	37084382	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	intron	37084383	37084554	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	CDS	37084555	37084636	0.77	-	0	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	exon	37084555	37084636	.	-	.	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
Phchi.S2	AUGUSTUS	start_codon	37084634	37084636	.	-	0	transcript_id "Phchi.S2G067600.t2"; gene_id "Phchi.S2G067600"
# This transcript jg7340.t2 is derived from g4512.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7341.t1 is derived from g4513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28600951	28603447	.	-	.	Phchi.S1G450000
Phchi.S1	AUGUSTUS	transcript	28600951	28603447	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	stop_codon	28600948	28600950	.	-	0	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28600951	28601441	0.77	-	2	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28600951	28601441	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28601442	28601528	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28601529	28601736	1	-	0	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28601529	28601736	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28601737	28601836	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28601837	28602019	1	-	0	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28601837	28602019	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28602020	28602116	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28602117	28602221	1	-	0	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28602117	28602221	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28602222	28602300	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28602301	28602544	1	-	1	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28602301	28602544	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28602545	28602631	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28602632	28602862	1	-	1	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28602632	28602862	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28602863	28602935	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28602936	28603140	1	-	2	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28602936	28603140	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	intron	28603141	28603224	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	CDS	28603225	28603447	0.98	-	0	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	exon	28603225	28603447	.	-	.	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
Phchi.S1	AUGUSTUS	start_codon	28603445	28603447	.	-	0	transcript_id "Phchi.S1G450000.t1"; gene_id "Phchi.S1G450000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14391.t1 is derived from g12859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12570935	12572721	.	+	.	Phchi.S3G171000
Phchi.S3	AUGUSTUS	transcript	12570935	12572721	.	+	.	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	start_codon	12570935	12570937	.	+	0	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	CDS	12570935	12571515	0.46	+	0	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	exon	12570935	12571515	.	+	.	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	intron	12571516	12571607	.	+	.	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	CDS	12571608	12572721	0.99	+	1	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	exon	12571608	12572721	.	+	.	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
Phchi.S3	AUGUSTUS	stop_codon	12572722	12572724	.	+	0	transcript_id "Phchi.S3G171000.t1"; gene_id "Phchi.S3G171000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5819.t1 is derived from g2989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19099746	19106980	.	-	.	Phchi.S1G297800
Phchi.S1	AUGUSTUS	transcript	19099746	19106980	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	stop_codon	19099743	19099745	.	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19099746	19100456	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19099746	19100456	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19100457	19100542	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19100543	19100692	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19100543	19100692	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19100693	19100791	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19100792	19100950	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19100792	19100950	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19100951	19101040	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19101041	19101163	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19101041	19101163	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19101164	19101259	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19101260	19101375	0.99	-	2	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19101260	19101375	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19101376	19101501	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19101502	19101775	0.97	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19101502	19101775	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19101776	19101912	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19101913	19102137	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19101913	19102137	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19102138	19102285	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19102286	19102420	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19102286	19102420	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19102421	19102518	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19102519	19103160	1	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19102519	19103160	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19103161	19103266	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19103267	19103808	0.97	-	2	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19103267	19103808	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19103809	19103917	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19103918	19104152	0.98	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19103918	19104152	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19104153	19104259	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19104260	19104555	1	-	2	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19104260	19104555	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19104556	19104948	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19104949	19105080	1	-	2	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19104949	19105080	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19105081	19105274	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19105275	19105451	1	-	2	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19105275	19105451	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19105452	19105624	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19105625	19106250	0.92	-	1	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19105625	19106250	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	intron	19106251	19106369	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	CDS	19106370	19106980	0.83	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	exon	19106370	19106980	.	-	.	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
Phchi.S1	AUGUSTUS	start_codon	19106978	19106980	.	-	0	transcript_id "Phchi.S1G297800.t1"; gene_id "Phchi.S1G297800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6046.t1 is derived from g3217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20610032	20611703	.	-	.	Phchi.S1G320500
Phchi.S1	AUGUSTUS	transcript	20610032	20611703	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	stop_codon	20610029	20610031	.	-	0	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	CDS	20610032	20610278	0.94	-	1	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	exon	20610032	20610278	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	intron	20610279	20610373	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	CDS	20610374	20610594	0.61	-	0	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	exon	20610374	20610594	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	intron	20610595	20610703	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	CDS	20610704	20610871	0.12	-	0	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	exon	20610704	20610871	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	intron	20610872	20611016	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	CDS	20611017	20611160	0.32	-	0	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	exon	20611017	20611160	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	intron	20611161	20611397	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	CDS	20611398	20611703	0.56	-	0	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	exon	20611398	20611703	.	-	.	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
Phchi.S1	AUGUSTUS	start_codon	20611701	20611703	.	-	0	transcript_id "Phchi.S1G320500.t1"; gene_id "Phchi.S1G320500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6601.t1 is derived from g3773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23942832	23943597	.	+	.	Phchi.S1G376000
Phchi.S1	AUGUSTUS	transcript	23942832	23943597	.	+	.	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	start_codon	23942832	23942834	.	+	0	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	CDS	23942832	23942974	0.59	+	0	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	exon	23942832	23942974	.	+	.	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	intron	23942975	23943322	.	+	.	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	CDS	23943323	23943397	0.9	+	1	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	exon	23943323	23943397	.	+	.	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	intron	23943398	23943569	.	+	.	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	CDS	23943570	23943597	0.89	+	1	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	exon	23943570	23943597	.	+	.	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
Phchi.S1	AUGUSTUS	stop_codon	23943598	23943600	.	+	0	transcript_id "Phchi.S1G376000.t1"; gene_id "Phchi.S1G376000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15863.t1 is derived from g14333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21931037	21931361	.	-	.	Phchi.S3G318200
Phchi.S3	AUGUSTUS	transcript	21931037	21931361	.	-	.	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	stop_codon	21931034	21931036	.	-	0	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	CDS	21931037	21931165	1	-	0	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	exon	21931037	21931165	.	-	.	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	intron	21931166	21931238	.	-	.	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	CDS	21931239	21931361	1	-	0	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	exon	21931239	21931361	.	-	.	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
Phchi.S3	AUGUSTUS	start_codon	21931359	21931361	.	-	0	transcript_id "Phchi.S3G318200.t1"; gene_id "Phchi.S3G318200"
# This transcript jg14421.t2 is derived from g12889.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14422.t1 is derived from g12890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12747699	12748244	.	+	.	Phchi.S3G174100
Phchi.S3	AUGUSTUS	transcript	12747699	12748244	.	+	.	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	start_codon	12747699	12747701	.	+	0	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	CDS	12747699	12747965	0.56	+	0	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	exon	12747699	12747965	.	+	.	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	intron	12747966	12748184	.	+	.	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	CDS	12748185	12748244	0.54	+	0	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	exon	12748185	12748244	.	+	.	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
Phchi.S3	AUGUSTUS	stop_codon	12748245	12748247	.	+	0	transcript_id "Phchi.S3G174100.t1"; gene_id "Phchi.S3G174100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2271.t1 is derived from g9191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5792840	5793850	.	+	.	Phchi.S5G088000
Phchi.S5	AUGUSTUS	transcript	5792840	5793850	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	start_codon	5792840	5792842	.	+	0	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	CDS	5792840	5792997	1	+	0	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	exon	5792840	5792997	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	intron	5792998	5793164	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	CDS	5793165	5793288	1	+	1	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	exon	5793165	5793288	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	intron	5793289	5793383	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	CDS	5793384	5793501	1	+	0	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	exon	5793384	5793501	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	intron	5793502	5793596	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	CDS	5793597	5793850	1	+	2	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	exon	5793597	5793850	.	+	.	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
Phchi.S5	AUGUSTUS	stop_codon	5793851	5793853	.	+	0	transcript_id "Phchi.S5G088000.t1"; gene_id "Phchi.S5G088000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15640.t1 is derived from g14109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20433080	20433720	.	-	.	Phchi.S3G295900
Phchi.S3	AUGUSTUS	transcript	20433080	20433720	.	-	.	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	stop_codon	20433077	20433079	.	-	0	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	CDS	20433080	20433429	0.51	-	2	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	exon	20433080	20433429	.	-	.	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	intron	20433430	20433551	.	-	.	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	CDS	20433552	20433720	0.43	-	0	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	exon	20433552	20433720	.	-	.	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
Phchi.S3	AUGUSTUS	start_codon	20433718	20433720	.	-	0	transcript_id "Phchi.S3G295900.t1"; gene_id "Phchi.S3G295900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1579.t1 is derived from g8498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1856511	1857901	.	-	.	Phchi.S5G018800
Phchi.S5	AUGUSTUS	transcript	1856511	1857901	.	-	.	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	stop_codon	1856508	1856510	.	-	0	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	CDS	1856511	1856873	1	-	0	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	exon	1856511	1856873	.	-	.	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	intron	1856874	1856952	.	-	.	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	CDS	1856953	1857240	1	-	0	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	exon	1856953	1857240	.	-	.	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	intron	1857241	1857376	.	-	.	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	CDS	1857377	1857901	0.78	-	0	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	exon	1857377	1857901	.	-	.	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
Phchi.S5	AUGUSTUS	start_codon	1857899	1857901	.	-	0	transcript_id "Phchi.S5G018800.t1"; gene_id "Phchi.S5G018800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3230.t1 is derived from g399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2363260	2364958	.	-	.	Phchi.S1G038900
Phchi.S1	AUGUSTUS	transcript	2363260	2364958	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	stop_codon	2363257	2363259	.	-	0	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	CDS	2363260	2363447	0.94	-	2	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	exon	2363260	2363447	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	intron	2363448	2363568	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	CDS	2363569	2363854	0.95	-	0	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	exon	2363569	2363854	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	intron	2363855	2363940	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	CDS	2363941	2364212	0.53	-	2	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	exon	2363941	2364212	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	intron	2364213	2364332	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	CDS	2364333	2364533	0.84	-	2	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	exon	2364333	2364533	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	intron	2364534	2364720	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	CDS	2364721	2364958	0.54	-	0	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	exon	2364721	2364958	.	-	.	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
Phchi.S1	AUGUSTUS	start_codon	2364956	2364958	.	-	0	transcript_id "Phchi.S1G038900.t1"; gene_id "Phchi.S1G038900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2567.t1 is derived from g9487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7421762	7421962	.	+	.	Phchi.S5G117600
Phchi.S5	AUGUSTUS	transcript	7421762	7421962	.	+	.	transcript_id "Phchi.S5G117600.t1"; gene_id "Phchi.S5G117600"
Phchi.S5	AUGUSTUS	start_codon	7421762	7421764	.	+	0	transcript_id "Phchi.S5G117600.t1"; gene_id "Phchi.S5G117600"
Phchi.S5	AUGUSTUS	CDS	7421762	7421962	0.76	+	0	transcript_id "Phchi.S5G117600.t1"; gene_id "Phchi.S5G117600"
Phchi.S5	AUGUSTUS	exon	7421762	7421962	.	+	.	transcript_id "Phchi.S5G117600.t1"; gene_id "Phchi.S5G117600"
Phchi.S5	AUGUSTUS	stop_codon	7421963	7421965	.	+	0	transcript_id "Phchi.S5G117600.t1"; gene_id "Phchi.S5G117600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4759.t1 is derived from g1929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12682230	12683749	.	-	.	Phchi.S1G191800
Phchi.S1	AUGUSTUS	transcript	12682230	12683749	.	-	.	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	stop_codon	12682227	12682229	.	-	0	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	CDS	12682230	12682511	0.8	-	0	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	exon	12682230	12682511	.	-	.	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	intron	12682512	12682666	.	-	.	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	CDS	12682667	12683010	0.98	-	2	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	exon	12682667	12683010	.	-	.	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	intron	12683011	12683097	.	-	.	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	CDS	12683098	12683749	0.99	-	0	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	exon	12683098	12683749	.	-	.	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
Phchi.S1	AUGUSTUS	start_codon	12683747	12683749	.	-	0	transcript_id "Phchi.S1G191800.t1"; gene_id "Phchi.S1G191800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4109.t1 is derived from g1278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7872414	7874680	.	-	.	Phchi.S1G126800
Phchi.S1	AUGUSTUS	transcript	7872414	7874680	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	stop_codon	7872411	7872413	.	-	0	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7872414	7872441	0.95	-	1	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7872414	7872441	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7872442	7872529	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7872530	7872626	0.99	-	2	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7872530	7872626	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7872627	7873120	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873121	7873130	1	-	0	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873121	7873130	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873131	7873266	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873267	7873297	0.98	-	1	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873267	7873297	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873298	7873493	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873494	7873618	0.95	-	0	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873494	7873618	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873619	7873694	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873695	7873718	0.95	-	0	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873695	7873718	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873719	7874050	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7874051	7874680	0.91	-	0	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7874051	7874680	.	-	.	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	start_codon	7874678	7874680	.	-	0	transcript_id "Phchi.S1G126800.t1"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	transcript	7872414	7874680	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	stop_codon	7872411	7872413	.	-	0	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7872414	7872441	0.95	-	1	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7872414	7872441	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7872442	7872529	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7872530	7872626	0.99	-	2	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7872530	7872626	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7872627	7873120	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873121	7873130	1	-	0	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873121	7873130	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873131	7873222	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873223	7873233	0.54	-	2	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873223	7873233	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873234	7873312	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873313	7873396	0.38	-	2	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873313	7873396	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873397	7873600	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7873601	7873718	0.36	-	0	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7873601	7873718	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	intron	7873719	7874050	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	CDS	7874051	7874680	0.93	-	0	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	exon	7874051	7874680	.	-	.	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
Phchi.S1	AUGUSTUS	start_codon	7874678	7874680	.	-	0	transcript_id "Phchi.S1G126800.t2"; gene_id "Phchi.S1G126800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6161.t1 is derived from g3332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21252485	21253052	.	-	.	Phchi.S1G332000
Phchi.S1	AUGUSTUS	transcript	21252485	21253052	.	-	.	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	stop_codon	21252482	21252484	.	-	0	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	CDS	21252485	21252565	0.58	-	0	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	exon	21252485	21252565	.	-	.	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	intron	21252566	21252642	.	-	.	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	CDS	21252643	21252742	1	-	1	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	exon	21252643	21252742	.	-	.	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	intron	21252743	21252873	.	-	.	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	CDS	21252874	21253052	0.91	-	0	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	exon	21252874	21253052	.	-	.	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
Phchi.S1	AUGUSTUS	start_codon	21253050	21253052	.	-	0	transcript_id "Phchi.S1G332000.t1"; gene_id "Phchi.S1G332000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6256.t1 is derived from g3428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21899187	21899644	.	+	.	Phchi.S1G341500
Phchi.S1	AUGUSTUS	transcript	21899187	21899644	.	+	.	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	start_codon	21899187	21899189	.	+	0	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	CDS	21899187	21899358	1	+	0	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	exon	21899187	21899358	.	+	.	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	intron	21899359	21899459	.	+	.	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	CDS	21899460	21899644	1	+	2	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	exon	21899460	21899644	.	+	.	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
Phchi.S1	AUGUSTUS	stop_codon	21899645	21899647	.	+	0	transcript_id "Phchi.S1G341500.t1"; gene_id "Phchi.S1G341500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7567.t1 is derived from g4741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30078343	30078800	.	+	.	Phchi.S1G472600
Phchi.S1	AUGUSTUS	transcript	30078343	30078800	.	+	.	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	start_codon	30078343	30078345	.	+	0	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	CDS	30078343	30078428	0.48	+	0	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	exon	30078343	30078428	.	+	.	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	intron	30078429	30078584	.	+	.	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	CDS	30078585	30078697	0.99	+	1	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	exon	30078585	30078697	.	+	.	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	intron	30078698	30078783	.	+	.	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	CDS	30078784	30078800	0.99	+	2	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	exon	30078784	30078800	.	+	.	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
Phchi.S1	AUGUSTUS	stop_codon	30078801	30078803	.	+	0	transcript_id "Phchi.S1G472600.t1"; gene_id "Phchi.S1G472600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14217.t1 is derived from g12684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11553722	11557938	.	-	.	Phchi.S3G153600
Phchi.S3	AUGUSTUS	transcript	11553722	11557938	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	stop_codon	11553719	11553721	.	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11553722	11553820	0.96	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11553722	11553820	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11553821	11553911	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11553912	11554016	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11553912	11554016	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11554017	11554099	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11554100	11554198	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11554100	11554198	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11554199	11554283	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11554284	11554443	1	-	1	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11554284	11554443	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11554444	11554533	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11554534	11554611	1	-	1	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11554534	11554611	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11554612	11554723	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11554724	11554859	1	-	2	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11554724	11554859	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11554860	11554981	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11554982	11555125	0.44	-	2	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11554982	11555125	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11555126	11555240	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11555241	11555307	0.44	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11555241	11555307	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11555308	11555397	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11555398	11555457	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11555398	11555457	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11555458	11555563	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11555564	11555641	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11555564	11555641	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11555642	11555767	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11555768	11555842	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11555768	11555842	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11555843	11555961	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11555962	11556078	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11555962	11556078	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11556079	11556181	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11556182	11556412	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11556182	11556412	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11556413	11556528	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11556529	11556648	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11556529	11556648	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11556649	11556750	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11556751	11556827	1	-	2	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11556751	11556827	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11556828	11556964	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11556965	11557065	1	-	1	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11556965	11557065	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11557066	11557163	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11557164	11557270	1	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11557164	11557270	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11557271	11557392	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11557393	11557550	1	-	2	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11557393	11557550	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	intron	11557551	11557688	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	CDS	11557689	11557938	0.58	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	exon	11557689	11557938	.	-	.	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
Phchi.S3	AUGUSTUS	start_codon	11557936	11557938	.	-	0	transcript_id "Phchi.S3G153600.t1"; gene_id "Phchi.S3G153600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2662.t1 is derived from g9582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8106032	8106960	.	-	.	Phchi.S5G127100
Phchi.S5	AUGUSTUS	transcript	8106032	8106960	.	-	.	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	stop_codon	8106029	8106031	.	-	0	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	CDS	8106032	8106130	0.53	-	0	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	exon	8106032	8106130	.	-	.	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	intron	8106131	8106354	.	-	.	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	CDS	8106355	8106960	0.61	-	0	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	exon	8106355	8106960	.	-	.	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
Phchi.S5	AUGUSTUS	start_codon	8106958	8106960	.	-	0	transcript_id "Phchi.S5G127100.t1"; gene_id "Phchi.S5G127100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7366.t1 is derived from g4538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28790902	28794027	.	+	.	Phchi.S1G452500
Phchi.S1	AUGUSTUS	transcript	28790902	28794027	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	start_codon	28790902	28790904	.	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28790902	28791021	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28790902	28791021	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28791022	28791089	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28791090	28791155	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28791090	28791155	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28791156	28791270	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28791271	28791388	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28791271	28791388	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28791389	28791546	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28791547	28791628	1	+	2	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28791547	28791628	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28791629	28791835	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28791836	28791923	1	+	1	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28791836	28791923	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28791924	28792212	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28792213	28792371	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28792213	28792371	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28792372	28792447	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28792448	28792621	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28792448	28792621	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28792622	28792788	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28792789	28792920	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28792789	28792920	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28792921	28793027	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28793028	28793093	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28793028	28793093	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28793094	28793282	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28793283	28793347	1	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28793283	28793347	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28793348	28793440	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28793441	28793532	1	+	1	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28793441	28793532	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28793533	28793619	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28793620	28793776	1	+	2	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28793620	28793776	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	intron	28793777	28793903	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	CDS	28793904	28794027	1	+	1	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	exon	28793904	28794027	.	+	.	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
Phchi.S1	AUGUSTUS	stop_codon	28794028	28794030	.	+	0	transcript_id "Phchi.S1G452500.t1"; gene_id "Phchi.S1G452500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15610.t1 is derived from g14079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20283507	20284436	.	-	.	Phchi.S3G292900
Phchi.S3	AUGUSTUS	transcript	20283507	20284436	.	-	.	transcript_id "Phchi.S3G292900.t1"; gene_id "Phchi.S3G292900"
Phchi.S3	AUGUSTUS	stop_codon	20283504	20283506	.	-	0	transcript_id "Phchi.S3G292900.t1"; gene_id "Phchi.S3G292900"
Phchi.S3	AUGUSTUS	CDS	20283507	20284436	0.9	-	0	transcript_id "Phchi.S3G292900.t1"; gene_id "Phchi.S3G292900"
Phchi.S3	AUGUSTUS	exon	20283507	20284436	.	-	.	transcript_id "Phchi.S3G292900.t1"; gene_id "Phchi.S3G292900"
Phchi.S3	AUGUSTUS	start_codon	20284434	20284436	.	-	0	transcript_id "Phchi.S3G292900.t1"; gene_id "Phchi.S3G292900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13493.t1 is derived from g11960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7155244	7155944	.	-	.	Phchi.S3G081200
Phchi.S3	AUGUSTUS	transcript	7155244	7155944	.	-	.	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	stop_codon	7155241	7155243	.	-	0	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	CDS	7155244	7155551	0.93	-	2	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	exon	7155244	7155551	.	-	.	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	intron	7155552	7155679	.	-	.	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	CDS	7155680	7155944	1	-	0	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	exon	7155680	7155944	.	-	.	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
Phchi.S3	AUGUSTUS	start_codon	7155942	7155944	.	-	0	transcript_id "Phchi.S3G081200.t1"; gene_id "Phchi.S3G081200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3068.t1 is derived from g237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1419893	1420903	.	-	.	Phchi.S1G022700
Phchi.S1	AUGUSTUS	transcript	1419893	1420903	.	-	.	transcript_id "Phchi.S1G022700.t1"; gene_id "Phchi.S1G022700"
Phchi.S1	AUGUSTUS	stop_codon	1419890	1419892	.	-	0	transcript_id "Phchi.S1G022700.t1"; gene_id "Phchi.S1G022700"
Phchi.S1	AUGUSTUS	CDS	1419893	1420903	1	-	0	transcript_id "Phchi.S1G022700.t1"; gene_id "Phchi.S1G022700"
Phchi.S1	AUGUSTUS	exon	1419893	1420903	.	-	.	transcript_id "Phchi.S1G022700.t1"; gene_id "Phchi.S1G022700"
Phchi.S1	AUGUSTUS	start_codon	1420901	1420903	.	-	0	transcript_id "Phchi.S1G022700.t1"; gene_id "Phchi.S1G022700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4531.t1 is derived from g1701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10982648	10983746	.	+	.	Phchi.S1G169000
Phchi.S1	AUGUSTUS	transcript	10982648	10983746	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	start_codon	10982648	10982650	.	+	0	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	CDS	10982648	10982773	0.95	+	0	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	exon	10982648	10982773	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	intron	10982774	10982866	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	CDS	10982867	10983137	1	+	0	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	exon	10982867	10983137	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	intron	10983138	10983213	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	CDS	10983214	10983381	1	+	2	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	exon	10983214	10983381	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	intron	10983382	10983501	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	CDS	10983502	10983746	0.92	+	2	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	exon	10983502	10983746	.	+	.	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
Phchi.S1	AUGUSTUS	stop_codon	10983747	10983749	.	+	0	transcript_id "Phchi.S1G169000.t1"; gene_id "Phchi.S1G169000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7959.t1 is derived from g5134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32102102	32105580	.	+	.	Phchi.S1G511800
Phchi.S1	AUGUSTUS	transcript	32102102	32105580	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	start_codon	32102102	32102104	.	+	0	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32102102	32102302	1	+	0	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32102102	32102302	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	intron	32102303	32102743	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32102744	32102795	1	+	0	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32102744	32102795	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	intron	32102796	32102887	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32102888	32102933	0.97	+	2	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32102888	32102933	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	intron	32102934	32103038	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32103039	32103120	0.99	+	1	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32103039	32103120	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	intron	32103121	32103214	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32103215	32103759	0.69	+	0	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32103215	32103759	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	intron	32103760	32104543	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32104544	32104610	1	+	1	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32104544	32104610	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	intron	32104611	32104734	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	CDS	32104735	32105580	1	+	0	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	exon	32104735	32105580	.	+	.	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
Phchi.S1	AUGUSTUS	stop_codon	32105581	32105583	.	+	0	transcript_id "Phchi.S1G511800.t1"; gene_id "Phchi.S1G511800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8999.t1 is derived from g6174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39103394	39105370	.	+	.	Phchi.S1G615800
Phchi.S1	AUGUSTUS	transcript	39103394	39105370	.	+	.	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	start_codon	39103394	39103396	.	+	0	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	CDS	39103394	39104067	0.83	+	0	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	exon	39103394	39104067	.	+	.	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	intron	39104068	39104184	.	+	.	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	CDS	39104185	39105370	1	+	1	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	exon	39104185	39105370	.	+	.	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
Phchi.S1	AUGUSTUS	stop_codon	39105371	39105373	.	+	0	transcript_id "Phchi.S1G615800.t1"; gene_id "Phchi.S1G615800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15212.t1 is derived from g13680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17683797	17685538	.	-	.	Phchi.S3G253100
Phchi.S3	AUGUSTUS	transcript	17683797	17685538	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	stop_codon	17683794	17683796	.	-	0	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	CDS	17683797	17684043	0.98	-	1	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	exon	17683797	17684043	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	intron	17684044	17684147	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	CDS	17684148	17684341	0.83	-	0	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	exon	17684148	17684341	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	intron	17684342	17684426	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	CDS	17684427	17684918	1	-	0	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	exon	17684427	17684918	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	intron	17684919	17685040	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	CDS	17685041	17685538	0.93	-	0	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	exon	17685041	17685538	.	-	.	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
Phchi.S3	AUGUSTUS	start_codon	17685536	17685538	.	-	0	transcript_id "Phchi.S3G253100.t1"; gene_id "Phchi.S3G253100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10793.t1 is derived from g14843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2140366	2144442	.	-	.	Phchi.S4G037500
Phchi.S4	AUGUSTUS	transcript	2140366	2144442	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	stop_codon	2140363	2140365	.	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2140366	2140527	0.84	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2140366	2140527	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2140528	2140632	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2140633	2141267	0.39	-	2	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2140633	2141267	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2141268	2141435	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2141436	2141692	0.44	-	1	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2141436	2141692	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2141693	2141786	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2141787	2141854	0.35	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2141787	2141854	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2141855	2141948	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2141949	2141969	0.77	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2141949	2141969	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2141970	2142156	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2142157	2142306	0.77	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2142157	2142306	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2142307	2142819	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2142820	2143314	0.11	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2142820	2143314	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2143315	2143539	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2143540	2143990	0.54	-	1	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2143540	2143990	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2143991	2144095	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2144096	2144262	0.98	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2144096	2144262	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	intron	2144263	2144349	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	CDS	2144350	2144442	0.74	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	exon	2144350	2144442	.	-	.	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
Phchi.S4	AUGUSTUS	start_codon	2144440	2144442	.	-	0	transcript_id "Phchi.S4G037500.t1"; gene_id "Phchi.S4G037500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6160.t1 is derived from g3331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21249658	21252408	.	-	.	Phchi.S1G331900
Phchi.S1	AUGUSTUS	transcript	21249658	21252408	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	stop_codon	21249655	21249657	.	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21249658	21249881	1	-	2	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21249658	21249881	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21249882	21249979	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21249980	21250106	1	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21249980	21250106	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21250107	21250291	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21250292	21250444	1	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21250292	21250444	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21250445	21250526	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21250527	21250699	1	-	2	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21250527	21250699	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21250700	21250849	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21250850	21251010	1	-	1	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21250850	21251010	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21251011	21251090	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21251091	21251623	0.98	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21251091	21251623	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21251624	21251707	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21251708	21252178	1	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21251708	21252178	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	intron	21252179	21252276	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	CDS	21252277	21252408	0.38	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	exon	21252277	21252408	.	-	.	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
Phchi.S1	AUGUSTUS	start_codon	21252406	21252408	.	-	0	transcript_id "Phchi.S1G331900.t1"; gene_id "Phchi.S1G331900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5965.t1 is derived from g3136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20108047	20112307	.	+	.	Phchi.S1G312400
Phchi.S1	AUGUSTUS	transcript	20108047	20112307	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	start_codon	20108047	20108049	.	+	0	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	CDS	20108047	20108151	0.53	+	0	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	exon	20108047	20108151	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	intron	20108152	20108237	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	CDS	20108238	20108276	1	+	0	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	exon	20108238	20108276	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	intron	20108277	20108332	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	CDS	20108333	20108358	1	+	0	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	exon	20108333	20108358	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	intron	20108359	20108439	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	CDS	20108440	20112307	0.54	+	1	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	exon	20108440	20112307	.	+	.	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
Phchi.S1	AUGUSTUS	stop_codon	20112308	20112310	.	+	0	transcript_id "Phchi.S1G312400.t1"; gene_id "Phchi.S1G312400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4198.t1 is derived from g1367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8876302	8877804	.	-	.	Phchi.S1G135700
Phchi.S1	AUGUSTUS	transcript	8876302	8877804	.	-	.	transcript_id "Phchi.S1G135700.t1"; gene_id "Phchi.S1G135700"
Phchi.S1	AUGUSTUS	stop_codon	8876299	8876301	.	-	0	transcript_id "Phchi.S1G135700.t1"; gene_id "Phchi.S1G135700"
Phchi.S1	AUGUSTUS	CDS	8876302	8877804	0.9	-	0	transcript_id "Phchi.S1G135700.t1"; gene_id "Phchi.S1G135700"
Phchi.S1	AUGUSTUS	exon	8876302	8877804	.	-	.	transcript_id "Phchi.S1G135700.t1"; gene_id "Phchi.S1G135700"
Phchi.S1	AUGUSTUS	start_codon	8877802	8877804	.	-	0	transcript_id "Phchi.S1G135700.t1"; gene_id "Phchi.S1G135700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13452.t1 is derived from g11919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6859556	6860285	.	-	.	Phchi.S3G077100
Phchi.S3	AUGUSTUS	transcript	6859556	6860285	.	-	.	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	stop_codon	6859553	6859555	.	-	0	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	CDS	6859556	6859693	1	-	0	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	exon	6859556	6859693	.	-	.	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	intron	6859694	6859795	.	-	.	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	CDS	6859796	6859947	0.71	-	2	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	exon	6859796	6859947	.	-	.	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	intron	6859948	6860185	.	-	.	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	CDS	6860186	6860285	0.75	-	0	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	exon	6860186	6860285	.	-	.	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
Phchi.S3	AUGUSTUS	start_codon	6860283	6860285	.	-	0	transcript_id "Phchi.S3G077100.t1"; gene_id "Phchi.S3G077100"
# This transcript jg11796.t2 is derived from g15848.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11797.t1 is derived from g15849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8201351	8203745	.	+	.	Phchi.S4G137900
Phchi.S4	AUGUSTUS	transcript	8201351	8203745	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	start_codon	8201351	8201353	.	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8201351	8201689	0.7	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8201351	8201689	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8201690	8201801	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8201802	8201987	0.96	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8201802	8201987	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8201988	8202074	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8202075	8202187	1	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8202075	8202187	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8202188	8202269	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8202270	8202459	0.83	+	1	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8202270	8202459	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8202460	8202643	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8202644	8202741	1	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8202644	8202741	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8202742	8202885	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8202886	8203093	1	+	1	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8202886	8203093	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8203094	8203210	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8203211	8203465	1	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8203211	8203465	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	intron	8203466	8203550	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	CDS	8203551	8203745	0.91	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	exon	8203551	8203745	.	+	.	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
Phchi.S4	AUGUSTUS	stop_codon	8203746	8203748	.	+	0	transcript_id "Phchi.S4G137900.t1"; gene_id "Phchi.S4G137900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6393.t1 is derived from g3565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22714538	22715887	.	-	.	Phchi.S1G355200
Phchi.S1	AUGUSTUS	transcript	22714538	22715887	.	-	.	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	stop_codon	22714535	22714537	.	-	0	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	CDS	22714538	22714697	0.79	-	1	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	exon	22714538	22714697	.	-	.	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	intron	22714698	22714772	.	-	.	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	CDS	22714773	22715887	0.61	-	0	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	exon	22714773	22715887	.	-	.	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
Phchi.S1	AUGUSTUS	start_codon	22715885	22715887	.	-	0	transcript_id "Phchi.S1G355200.t1"; gene_id "Phchi.S1G355200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2379.t1 is derived from g9299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6422624	6425332	.	-	.	Phchi.S5G098800
Phchi.S5	AUGUSTUS	transcript	6422624	6425332	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	stop_codon	6422621	6422623	.	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6422624	6422699	1	-	1	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6422624	6422699	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6422700	6422794	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6422795	6422840	1	-	2	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6422795	6422840	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6422841	6422959	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6422960	6423157	1	-	2	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6422960	6423157	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6423158	6423247	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6423248	6423353	1	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6423248	6423353	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6423354	6423450	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6423451	6423522	1	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6423451	6423522	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6423523	6423615	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6423616	6423725	1	-	2	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6423616	6423725	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6423726	6423844	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6423845	6423995	1	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6423845	6423995	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6423996	6424148	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6424149	6424238	1	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6424149	6424238	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6424239	6424319	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6424320	6424448	0.97	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6424320	6424448	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6424449	6424553	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6424554	6424679	1	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6424554	6424679	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6424680	6424777	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6424778	6424915	1	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6424778	6424915	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	intron	6424916	6424987	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	CDS	6424988	6425332	0.98	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	exon	6424988	6425332	.	-	.	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
Phchi.S5	AUGUSTUS	start_codon	6425330	6425332	.	-	0	transcript_id "Phchi.S5G098800.t1"; gene_id "Phchi.S5G098800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9047.t1 is derived from g6222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39388934	39390422	.	+	.	Phchi.S1G620600
Phchi.S1	AUGUSTUS	transcript	39388934	39390422	.	+	.	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	start_codon	39388934	39388936	.	+	0	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	CDS	39388934	39389520	1	+	0	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	exon	39388934	39389520	.	+	.	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	intron	39389521	39389624	.	+	.	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	CDS	39389625	39389973	1	+	1	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	exon	39389625	39389973	.	+	.	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	intron	39389974	39390059	.	+	.	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	CDS	39390060	39390422	0.98	+	0	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	exon	39390060	39390422	.	+	.	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
Phchi.S1	AUGUSTUS	stop_codon	39390423	39390425	.	+	0	transcript_id "Phchi.S1G620600.t1"; gene_id "Phchi.S1G620600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15176.t1 is derived from g13644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17371246	17374154	.	+	.	Phchi.S3G249500
Phchi.S3	AUGUSTUS	transcript	17371246	17374154	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	start_codon	17371246	17371248	.	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17371246	17371350	0.83	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17371246	17371350	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17371351	17371621	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17371622	17371629	0.93	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17371622	17371629	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17371630	17371712	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17371713	17371723	0.93	+	1	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17371713	17371723	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17371724	17371815	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17371816	17371865	0.93	+	2	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17371816	17371865	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17371866	17371959	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17371960	17372080	0.93	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17371960	17372080	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17372081	17372297	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17372298	17372329	0.85	+	2	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17372298	17372329	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17372330	17372388	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17372389	17372418	0.93	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17372389	17372418	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17372419	17372549	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17372550	17372648	1	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17372550	17372648	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17372649	17372811	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17372812	17372892	0.99	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17372812	17372892	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17372893	17372998	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17372999	17373084	1	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17372999	17373084	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17373085	17373175	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17373176	17373401	1	+	1	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17373176	17373401	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17373402	17373482	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17373483	17373647	1	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17373483	17373647	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	intron	17373648	17373842	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	CDS	17373843	17374154	0.9	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	exon	17373843	17374154	.	+	.	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
Phchi.S3	AUGUSTUS	stop_codon	17374155	17374157	.	+	0	transcript_id "Phchi.S3G249500.t1"; gene_id "Phchi.S3G249500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11781.t1 is derived from g15833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8143414	8144982	.	-	.	Phchi.S4G136300
Phchi.S4	AUGUSTUS	transcript	8143414	8144982	.	-	.	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	stop_codon	8143411	8143413	.	-	0	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	CDS	8143414	8143592	1	-	2	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	exon	8143414	8143592	.	-	.	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	intron	8143593	8143692	.	-	.	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	CDS	8143693	8144516	0.87	-	1	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	exon	8143693	8144516	.	-	.	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	intron	8144517	8144587	.	-	.	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	CDS	8144588	8144982	0.6	-	0	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	exon	8144588	8144982	.	-	.	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
Phchi.S4	AUGUSTUS	start_codon	8144980	8144982	.	-	0	transcript_id "Phchi.S4G136300.t1"; gene_id "Phchi.S4G136300"
# This transcript jg5509.t2 is derived from g2679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5510.t1 is derived from g2680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17166683	17167101	.	+	.	Phchi.S1G266900
Phchi.S1	AUGUSTUS	transcript	17166683	17167101	.	+	.	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	start_codon	17166683	17166685	.	+	0	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	CDS	17166683	17166785	1	+	0	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	exon	17166683	17166785	.	+	.	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	intron	17166786	17166878	.	+	.	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	CDS	17166879	17167006	1	+	2	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	exon	17166879	17167006	.	+	.	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	intron	17167007	17167086	.	+	.	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	CDS	17167087	17167101	1	+	0	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	exon	17167087	17167101	.	+	.	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
Phchi.S1	AUGUSTUS	stop_codon	17167102	17167104	.	+	0	transcript_id "Phchi.S1G266900.t1"; gene_id "Phchi.S1G266900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2240.t1 is derived from g9160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5607138	5608316	.	+	.	Phchi.S5G084900
Phchi.S5	AUGUSTUS	transcript	5607138	5608316	.	+	.	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	start_codon	5607138	5607140	.	+	0	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	CDS	5607138	5607481	0.41	+	0	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	exon	5607138	5607481	.	+	.	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	intron	5607482	5608219	.	+	.	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	CDS	5608220	5608316	0.76	+	1	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	exon	5608220	5608316	.	+	.	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
Phchi.S5	AUGUSTUS	stop_codon	5608317	5608319	.	+	0	transcript_id "Phchi.S5G084900.t1"; gene_id "Phchi.S5G084900"
# This transcript jg14475.t2 is derived from g12943.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14475.t3 is derived from g12943.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14476.t1 is derived from g12944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13043226	13043554	.	+	.	Phchi.S3G179500
Phchi.S3	AUGUSTUS	transcript	13043226	13043554	.	+	.	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	start_codon	13043226	13043228	.	+	0	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	CDS	13043226	13043285	0.34	+	0	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	exon	13043226	13043285	.	+	.	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	intron	13043286	13043374	.	+	.	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	CDS	13043375	13043554	0.95	+	0	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	exon	13043375	13043554	.	+	.	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
Phchi.S3	AUGUSTUS	stop_codon	13043555	13043557	.	+	0	transcript_id "Phchi.S3G179500.t1"; gene_id "Phchi.S3G179500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1817.t1 is derived from g8737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3302588	3303974	.	+	.	Phchi.S5G042600
Phchi.S5	AUGUSTUS	transcript	3302588	3303974	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	start_codon	3302588	3302590	.	+	0	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	CDS	3302588	3302791	1	+	0	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	exon	3302588	3302791	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	intron	3302792	3302868	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	CDS	3302869	3303072	1	+	0	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	exon	3302869	3303072	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	intron	3303073	3303152	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	CDS	3303153	3303325	1	+	0	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	exon	3303153	3303325	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	intron	3303326	3303426	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	CDS	3303427	3303523	0.94	+	1	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	exon	3303427	3303523	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	intron	3303524	3303635	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	CDS	3303636	3303974	0.93	+	0	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	exon	3303636	3303974	.	+	.	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
Phchi.S5	AUGUSTUS	stop_codon	3303975	3303977	.	+	0	transcript_id "Phchi.S5G042600.t1"; gene_id "Phchi.S5G042600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7466.t1 is derived from g4639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29415247	29419377	.	-	.	Phchi.S1G462500
Phchi.S1	AUGUSTUS	transcript	29415247	29419377	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	stop_codon	29415244	29415246	.	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29415247	29415333	0.91	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29415247	29415333	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29415334	29415424	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29415425	29415539	0.92	-	1	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29415425	29415539	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29415540	29415640	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29415641	29415787	0.87	-	1	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29415641	29415787	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29415788	29415866	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29415867	29415997	1	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29415867	29415997	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29415998	29416110	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29416111	29416251	0.79	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29416111	29416251	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29416252	29416340	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29416341	29416541	0.77	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29416341	29416541	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29416542	29416642	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29416643	29416862	0.98	-	1	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29416643	29416862	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29416863	29417089	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29417090	29417256	0.98	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29417090	29417256	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29417257	29417481	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29417482	29417584	0.45	-	1	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29417482	29417584	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29417585	29417756	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29417757	29417935	0.95	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29417757	29417935	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29417936	29418050	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29418051	29418176	0.93	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29418051	29418176	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29418177	29418378	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29418379	29418634	0.93	-	1	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29418379	29418634	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29418635	29418761	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29418762	29418948	0.95	-	2	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29418762	29418948	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29418949	29419090	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29419091	29419166	1	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29419091	29419166	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	intron	29419167	29419368	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	CDS	29419369	29419377	0.93	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	exon	29419369	29419377	.	-	.	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
Phchi.S1	AUGUSTUS	start_codon	29419375	29419377	.	-	0	transcript_id "Phchi.S1G462500.t1"; gene_id "Phchi.S1G462500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13555.t1 is derived from g12022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7477628	7478875	.	+	.	Phchi.S3G087400
Phchi.S3	AUGUSTUS	transcript	7477628	7478875	.	+	.	transcript_id "Phchi.S3G087400.t1"; gene_id "Phchi.S3G087400"
Phchi.S3	AUGUSTUS	start_codon	7477628	7477630	.	+	0	transcript_id "Phchi.S3G087400.t1"; gene_id "Phchi.S3G087400"
Phchi.S3	AUGUSTUS	CDS	7477628	7478875	0.43	+	0	transcript_id "Phchi.S3G087400.t1"; gene_id "Phchi.S3G087400"
Phchi.S3	AUGUSTUS	exon	7477628	7478875	.	+	.	transcript_id "Phchi.S3G087400.t1"; gene_id "Phchi.S3G087400"
Phchi.S3	AUGUSTUS	stop_codon	7478876	7478878	.	+	0	transcript_id "Phchi.S3G087400.t1"; gene_id "Phchi.S3G087400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10677.t1 is derived from g14727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1555452	1556010	.	+	.	Phchi.S4G025900
Phchi.S4	AUGUSTUS	transcript	1555452	1556010	.	+	.	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	start_codon	1555452	1555454	.	+	0	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	CDS	1555452	1555633	0.52	+	0	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	exon	1555452	1555633	.	+	.	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	intron	1555634	1555718	.	+	.	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	CDS	1555719	1555768	0.52	+	1	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	exon	1555719	1555768	.	+	.	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	intron	1555769	1555903	.	+	.	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	CDS	1555904	1556010	0.9	+	2	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	exon	1555904	1556010	.	+	.	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
Phchi.S4	AUGUSTUS	stop_codon	1556011	1556013	.	+	0	transcript_id "Phchi.S4G025900.t1"; gene_id "Phchi.S4G025900"
# This transcript jg1792.t2 is derived from g8712.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1793.t1 is derived from g8713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3052441	3053425	.	-	.	Phchi.S5G040200
Phchi.S5	AUGUSTUS	transcript	3052441	3053425	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	stop_codon	3052438	3052440	.	-	0	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	CDS	3052441	3052477	0.34	-	1	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	exon	3052441	3052477	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	intron	3052478	3052578	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	CDS	3052579	3052658	0.31	-	0	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	exon	3052579	3052658	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	intron	3052659	3052742	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	CDS	3052743	3052874	1	-	0	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	exon	3052743	3052874	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	intron	3052875	3052991	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	CDS	3052992	3053187	0.22	-	1	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	exon	3052992	3053187	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	intron	3053188	3053387	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	CDS	3053388	3053425	0.28	-	0	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	exon	3053388	3053425	.	-	.	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
Phchi.S5	AUGUSTUS	start_codon	3053423	3053425	.	-	0	transcript_id "Phchi.S5G040200.t1"; gene_id "Phchi.S5G040200"
# This transcript jg14909.t1 is derived from g13377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15463501	15463938	.	-	.	Phchi.S3G222800
Phchi.S3	AUGUSTUS	transcript	15463501	15463938	.	-	.	transcript_id "Phchi.S3G222800.t1"; gene_id "Phchi.S3G222800"
Phchi.S3	AUGUSTUS	stop_codon	15463498	15463500	.	-	0	transcript_id "Phchi.S3G222800.t1"; gene_id "Phchi.S3G222800"
Phchi.S3	AUGUSTUS	CDS	15463501	15463938	0.73	-	0	transcript_id "Phchi.S3G222800.t1"; gene_id "Phchi.S3G222800"
Phchi.S3	AUGUSTUS	exon	15463501	15463938	.	-	.	transcript_id "Phchi.S3G222800.t1"; gene_id "Phchi.S3G222800"
Phchi.S3	AUGUSTUS	start_codon	15463936	15463938	.	-	0	transcript_id "Phchi.S3G222800.t1"; gene_id "Phchi.S3G222800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13467.t1 is derived from g11934.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7042308	7046028	.	+	.	Phchi.S3G078600
Phchi.S3	AUGUSTUS	transcript	7042308	7046028	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	start_codon	7042308	7042310	.	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7042308	7043315	0.98	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7042308	7043315	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7043316	7043434	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7043435	7043476	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7043435	7043476	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7043477	7043582	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7043583	7043813	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7043583	7043813	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7043814	7043989	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7043990	7044085	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7043990	7044085	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7044086	7044177	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7044178	7044396	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7044178	7044396	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7044397	7044536	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7044537	7044734	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7044537	7044734	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7044735	7045052	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045053	7045199	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045053	7045199	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7045200	7045347	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045348	7045497	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045348	7045497	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7045498	7045608	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045609	7045739	1	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045609	7045739	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7045740	7045841	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045842	7046028	1	+	1	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045842	7046028	.	+	.	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	stop_codon	7046029	7046031	.	+	0	transcript_id "Phchi.S3G078600.t1"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	transcript	7042308	7046028	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	start_codon	7042308	7042310	.	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7042308	7043315	0.97	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7042308	7043315	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7043316	7043434	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7043435	7043476	0.97	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7043435	7043476	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7043477	7043582	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7043583	7043813	1	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7043583	7043813	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7043814	7043989	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7043990	7044085	1	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7043990	7044085	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7044086	7044177	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7044178	7044396	1	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7044178	7044396	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7044397	7044533	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7044534	7044734	0.99	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7044534	7044734	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7044735	7045052	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045053	7045199	1	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045053	7045199	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7045200	7045347	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045348	7045497	1	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045348	7045497	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7045498	7045608	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045609	7045739	1	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045609	7045739	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	intron	7045740	7045841	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	CDS	7045842	7046028	0.99	+	1	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	exon	7045842	7046028	.	+	.	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
Phchi.S3	AUGUSTUS	stop_codon	7046029	7046031	.	+	0	transcript_id "Phchi.S3G078600.t2"; gene_id "Phchi.S3G078600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2031.t1 is derived from g8951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4532310	4533380	.	-	.	Phchi.S5G064000
Phchi.S5	AUGUSTUS	transcript	4532310	4533380	.	-	.	transcript_id "Phchi.S5G064000.t1"; gene_id "Phchi.S5G064000"
Phchi.S5	AUGUSTUS	stop_codon	4532307	4532309	.	-	0	transcript_id "Phchi.S5G064000.t1"; gene_id "Phchi.S5G064000"
Phchi.S5	AUGUSTUS	CDS	4532310	4533380	0.32	-	0	transcript_id "Phchi.S5G064000.t1"; gene_id "Phchi.S5G064000"
Phchi.S5	AUGUSTUS	exon	4532310	4533380	.	-	.	transcript_id "Phchi.S5G064000.t1"; gene_id "Phchi.S5G064000"
Phchi.S5	AUGUSTUS	start_codon	4533378	4533380	.	-	0	transcript_id "Phchi.S5G064000.t1"; gene_id "Phchi.S5G064000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5284.t1 is derived from g2454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16022103	16022901	.	-	.	Phchi.S1G244300
Phchi.S1	AUGUSTUS	transcript	16022103	16022901	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	stop_codon	16022100	16022102	.	-	0	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	CDS	16022103	16022281	0.59	-	2	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	exon	16022103	16022281	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	intron	16022282	16022363	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	CDS	16022364	16022449	0.59	-	1	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	exon	16022364	16022449	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	intron	16022450	16022554	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	CDS	16022555	16022599	0.99	-	1	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	exon	16022555	16022599	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	intron	16022600	16022672	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	CDS	16022673	16022700	0.84	-	2	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	exon	16022673	16022700	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	intron	16022701	16022795	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	CDS	16022796	16022901	0.42	-	0	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	exon	16022796	16022901	.	-	.	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
Phchi.S1	AUGUSTUS	start_codon	16022899	16022901	.	-	0	transcript_id "Phchi.S1G244300.t1"; gene_id "Phchi.S1G244300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2616.t1 is derived from g9536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7794314	7795692	.	+	.	Phchi.S5G122500
Phchi.S5	AUGUSTUS	transcript	7794314	7795692	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	start_codon	7794314	7794316	.	+	0	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	CDS	7794314	7794497	1	+	0	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	exon	7794314	7794497	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	intron	7794498	7794587	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	CDS	7794588	7794676	1	+	2	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	exon	7794588	7794676	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	intron	7794677	7794845	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	CDS	7794846	7794932	1	+	0	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	exon	7794846	7794932	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	intron	7794933	7795030	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	CDS	7795031	7795179	1	+	0	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	exon	7795031	7795179	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	intron	7795180	7795269	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	CDS	7795270	7795401	1	+	1	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	exon	7795270	7795401	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	intron	7795402	7795502	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	CDS	7795503	7795692	1	+	1	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	exon	7795503	7795692	.	+	.	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
Phchi.S5	AUGUSTUS	stop_codon	7795693	7795695	.	+	0	transcript_id "Phchi.S5G122500.t1"; gene_id "Phchi.S5G122500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9744.t1 is derived from g6920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43478225	43479208	.	-	.	Phchi.S1G690300
Phchi.S1	AUGUSTUS	transcript	43478225	43479208	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	stop_codon	43478222	43478224	.	-	0	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	CDS	43478225	43478267	0.56	-	1	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	exon	43478225	43478267	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	intron	43478268	43478362	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	CDS	43478363	43478521	0.76	-	1	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	exon	43478363	43478521	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	intron	43478522	43478606	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	CDS	43478607	43478869	1	-	0	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	exon	43478607	43478869	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	intron	43478870	43478947	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	CDS	43478948	43479208	1	-	0	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	exon	43478948	43479208	.	-	.	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
Phchi.S1	AUGUSTUS	start_codon	43479206	43479208	.	-	0	transcript_id "Phchi.S1G690300.t1"; gene_id "Phchi.S1G690300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8996.t1 is derived from g6171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39033002	39033727	.	+	.	Phchi.S1G615500
Phchi.S1	AUGUSTUS	transcript	39033002	39033727	.	+	.	transcript_id "Phchi.S1G615500.t1"; gene_id "Phchi.S1G615500"
Phchi.S1	AUGUSTUS	start_codon	39033002	39033004	.	+	0	transcript_id "Phchi.S1G615500.t1"; gene_id "Phchi.S1G615500"
Phchi.S1	AUGUSTUS	CDS	39033002	39033727	0.72	+	0	transcript_id "Phchi.S1G615500.t1"; gene_id "Phchi.S1G615500"
Phchi.S1	AUGUSTUS	exon	39033002	39033727	.	+	.	transcript_id "Phchi.S1G615500.t1"; gene_id "Phchi.S1G615500"
Phchi.S1	AUGUSTUS	stop_codon	39033728	39033730	.	+	0	transcript_id "Phchi.S1G615500.t1"; gene_id "Phchi.S1G615500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg784.t1 is derived from g10566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5477956	5478957	.	+	.	Phchi.S6G074300
Phchi.S6	AUGUSTUS	transcript	5477956	5478957	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	start_codon	5477956	5477958	.	+	0	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	CDS	5477956	5477971	0.88	+	0	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	exon	5477956	5477971	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	intron	5477972	5478101	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	CDS	5478102	5478241	1	+	2	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	exon	5478102	5478241	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	intron	5478242	5478418	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	CDS	5478419	5478544	1	+	0	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	exon	5478419	5478544	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	intron	5478545	5478819	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	CDS	5478820	5478957	0.99	+	0	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	exon	5478820	5478957	.	+	.	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
Phchi.S6	AUGUSTUS	stop_codon	5478958	5478960	.	+	0	transcript_id "Phchi.S6G074300.t1"; gene_id "Phchi.S6G074300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8015.t1 is derived from g5190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32483504	32484007	.	-	.	Phchi.S1G517400
Phchi.S1	AUGUSTUS	transcript	32483504	32484007	.	-	.	transcript_id "Phchi.S1G517400.t1"; gene_id "Phchi.S1G517400"
Phchi.S1	AUGUSTUS	stop_codon	32483501	32483503	.	-	0	transcript_id "Phchi.S1G517400.t1"; gene_id "Phchi.S1G517400"
Phchi.S1	AUGUSTUS	CDS	32483504	32484007	1	-	0	transcript_id "Phchi.S1G517400.t1"; gene_id "Phchi.S1G517400"
Phchi.S1	AUGUSTUS	exon	32483504	32484007	.	-	.	transcript_id "Phchi.S1G517400.t1"; gene_id "Phchi.S1G517400"
Phchi.S1	AUGUSTUS	start_codon	32484005	32484007	.	-	0	transcript_id "Phchi.S1G517400.t1"; gene_id "Phchi.S1G517400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4219.t1 is derived from g1388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8987688	8988679	.	-	.	Phchi.S1G137800
Phchi.S1	AUGUSTUS	transcript	8987688	8988679	.	-	.	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	stop_codon	8987685	8987687	.	-	0	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	CDS	8987688	8988262	0.38	-	2	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	exon	8987688	8988262	.	-	.	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	intron	8988263	8988543	.	-	.	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	CDS	8988544	8988679	0.65	-	0	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	exon	8988544	8988679	.	-	.	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
Phchi.S1	AUGUSTUS	start_codon	8988677	8988679	.	-	0	transcript_id "Phchi.S1G137800.t1"; gene_id "Phchi.S1G137800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6140.t1 is derived from g3311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21128343	21130699	.	-	.	Phchi.S1G329900
Phchi.S1	AUGUSTUS	transcript	21128343	21130699	.	-	.	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	stop_codon	21128340	21128342	.	-	0	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	CDS	21128343	21130276	0.76	-	2	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	exon	21128343	21130276	.	-	.	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	intron	21130277	21130410	.	-	.	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	CDS	21130411	21130699	0.36	-	0	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	exon	21130411	21130699	.	-	.	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
Phchi.S1	AUGUSTUS	start_codon	21130697	21130699	.	-	0	transcript_id "Phchi.S1G329900.t1"; gene_id "Phchi.S1G329900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3340.t1 is derived from g509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2994482	2995732	.	+	.	Phchi.S1G049900
Phchi.S1	AUGUSTUS	transcript	2994482	2995732	.	+	.	transcript_id "Phchi.S1G049900.t1"; gene_id "Phchi.S1G049900"
Phchi.S1	AUGUSTUS	start_codon	2994482	2994484	.	+	0	transcript_id "Phchi.S1G049900.t1"; gene_id "Phchi.S1G049900"
Phchi.S1	AUGUSTUS	CDS	2994482	2995732	0.76	+	0	transcript_id "Phchi.S1G049900.t1"; gene_id "Phchi.S1G049900"
Phchi.S1	AUGUSTUS	exon	2994482	2995732	.	+	.	transcript_id "Phchi.S1G049900.t1"; gene_id "Phchi.S1G049900"
Phchi.S1	AUGUSTUS	stop_codon	2995733	2995735	.	+	0	transcript_id "Phchi.S1G049900.t1"; gene_id "Phchi.S1G049900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1301.t1 is derived from g11084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8902089	8904902	.	+	.	Phchi.S6G126000
Phchi.S6	AUGUSTUS	transcript	8902089	8904902	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	start_codon	8902089	8902091	.	+	0	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	CDS	8902089	8903550	0.72	+	0	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	exon	8902089	8903550	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	intron	8903551	8903628	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	CDS	8903629	8903689	0.98	+	2	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	exon	8903629	8903689	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	intron	8903690	8903911	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	CDS	8903912	8903985	0.75	+	1	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	exon	8903912	8903985	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	intron	8903986	8904441	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	CDS	8904442	8904601	0.73	+	2	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	exon	8904442	8904601	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	intron	8904602	8904733	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	CDS	8904734	8904902	0.97	+	1	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	exon	8904734	8904902	.	+	.	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
Phchi.S6	AUGUSTUS	stop_codon	8904903	8904905	.	+	0	transcript_id "Phchi.S6G126000.t1"; gene_id "Phchi.S6G126000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8208.t1 is derived from g5383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34435824	34438051	.	+	.	Phchi.S1G536700
Phchi.S1	AUGUSTUS	transcript	34435824	34438051	.	+	.	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	start_codon	34435824	34435826	.	+	0	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	CDS	34435824	34436271	0.26	+	0	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	exon	34435824	34436271	.	+	.	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	intron	34436272	34436378	.	+	.	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	CDS	34436379	34438051	0.43	+	2	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	exon	34436379	34438051	.	+	.	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
Phchi.S1	AUGUSTUS	stop_codon	34438052	34438054	.	+	0	transcript_id "Phchi.S1G536700.t1"; gene_id "Phchi.S1G536700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15232.t1 is derived from g13700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17847908	17851464	.	-	.	Phchi.S3G255100
Phchi.S3	AUGUSTUS	transcript	17847908	17851464	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	stop_codon	17847905	17847907	.	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17847908	17848014	1	-	2	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17847908	17848014	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17848015	17848113	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17848114	17848189	1	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17848114	17848189	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17848190	17848422	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17848423	17848540	0.99	-	1	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17848423	17848540	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17848541	17848678	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17848679	17848915	1	-	1	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17848679	17848915	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17848916	17848996	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17848997	17849106	0.78	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17848997	17849106	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17849107	17849207	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17849208	17849429	0.99	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17849208	17849429	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17849430	17849512	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17849513	17849617	0.94	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17849513	17849617	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17849618	17849694	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17849695	17849824	0.91	-	1	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17849695	17849824	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17849825	17849947	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17849948	17850059	1	-	2	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17849948	17850059	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17850060	17850288	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17850289	17850453	0.98	-	2	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17850289	17850453	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17850454	17850561	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17850562	17850659	1	-	1	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17850562	17850659	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17850660	17850770	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17850771	17850871	0.99	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17850771	17850871	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17850872	17850979	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17850980	17851107	0.99	-	2	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17850980	17851107	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17851108	17851185	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17851186	17851218	0.99	-	2	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17851186	17851218	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	intron	17851219	17851451	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	CDS	17851452	17851464	0.45	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	exon	17851452	17851464	.	-	.	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
Phchi.S3	AUGUSTUS	start_codon	17851462	17851464	.	-	0	transcript_id "Phchi.S3G255100.t1"; gene_id "Phchi.S3G255100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3211.t1 is derived from g380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2263617	2264120	.	-	.	Phchi.S1G037000
Phchi.S1	AUGUSTUS	transcript	2263617	2264120	.	-	.	transcript_id "Phchi.S1G037000.t1"; gene_id "Phchi.S1G037000"
Phchi.S1	AUGUSTUS	stop_codon	2263614	2263616	.	-	0	transcript_id "Phchi.S1G037000.t1"; gene_id "Phchi.S1G037000"
Phchi.S1	AUGUSTUS	CDS	2263617	2264120	0.76	-	0	transcript_id "Phchi.S1G037000.t1"; gene_id "Phchi.S1G037000"
Phchi.S1	AUGUSTUS	exon	2263617	2264120	.	-	.	transcript_id "Phchi.S1G037000.t1"; gene_id "Phchi.S1G037000"
Phchi.S1	AUGUSTUS	start_codon	2264118	2264120	.	-	0	transcript_id "Phchi.S1G037000.t1"; gene_id "Phchi.S1G037000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8702.t1 is derived from g5877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37531041	37533726	.	-	.	Phchi.S1G586100
Phchi.S1	AUGUSTUS	transcript	37531041	37533726	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	stop_codon	37531038	37531040	.	-	0	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	CDS	37531041	37531061	1	-	0	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	exon	37531041	37531061	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	intron	37531062	37531191	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	CDS	37531192	37531284	1	-	0	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	exon	37531192	37531284	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	intron	37531285	37531374	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	CDS	37531375	37531461	0.73	-	0	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	exon	37531375	37531461	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	intron	37531462	37531572	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	CDS	37531573	37533726	0.53	-	0	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	exon	37531573	37533726	.	-	.	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
Phchi.S1	AUGUSTUS	start_codon	37533724	37533726	.	-	0	transcript_id "Phchi.S1G586100.t1"; gene_id "Phchi.S1G586100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4300.t1 is derived from g1469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9509855	9510166	.	-	.	Phchi.S1G145900
Phchi.S1	AUGUSTUS	transcript	9509855	9510166	.	-	.	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	stop_codon	9509852	9509854	.	-	0	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	CDS	9509855	9510009	1	-	2	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	exon	9509855	9510009	.	-	.	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	intron	9510010	9510093	.	-	.	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	CDS	9510094	9510166	0.74	-	0	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	exon	9510094	9510166	.	-	.	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
Phchi.S1	AUGUSTUS	start_codon	9510164	9510166	.	-	0	transcript_id "Phchi.S1G145900.t1"; gene_id "Phchi.S1G145900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10064.t1 is derived from g7240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45595133	45595608	.	-	.	Phchi.S1G722300
Phchi.S1	AUGUSTUS	transcript	45595133	45595608	.	-	.	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	stop_codon	45595130	45595132	.	-	0	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	CDS	45595133	45595145	1	-	1	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	exon	45595133	45595145	.	-	.	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	intron	45595146	45595303	.	-	.	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	CDS	45595304	45595419	0.77	-	0	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	exon	45595304	45595419	.	-	.	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	intron	45595420	45595530	.	-	.	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	CDS	45595531	45595608	0.72	-	0	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	exon	45595531	45595608	.	-	.	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
Phchi.S1	AUGUSTUS	start_codon	45595606	45595608	.	-	0	transcript_id "Phchi.S1G722300.t1"; gene_id "Phchi.S1G722300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10400.t1 is derived from g7576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47567777	47568579	.	+	.	Phchi.S1G755900
Phchi.S1	AUGUSTUS	transcript	47567777	47568579	.	+	.	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	start_codon	47567777	47567779	.	+	0	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	CDS	47567777	47568281	0.3	+	0	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	exon	47567777	47568281	.	+	.	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	intron	47568282	47568364	.	+	.	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	CDS	47568365	47568579	0.22	+	2	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	exon	47568365	47568579	.	+	.	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
Phchi.S1	AUGUSTUS	stop_codon	47568580	47568582	.	+	0	transcript_id "Phchi.S1G755900.t1"; gene_id "Phchi.S1G755900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5358.t1 is derived from g2528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16455259	16460088	.	+	.	Phchi.S1G251700
Phchi.S1	AUGUSTUS	transcript	16455259	16460088	.	+	.	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	start_codon	16455259	16455261	.	+	0	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	CDS	16455259	16455700	0.15	+	0	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	exon	16455259	16455700	.	+	.	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	intron	16455701	16455850	.	+	.	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	CDS	16455851	16456419	1	+	2	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	exon	16455851	16456419	.	+	.	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	intron	16456420	16460025	.	+	.	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	CDS	16460026	16460088	0.02	+	0	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	exon	16460026	16460088	.	+	.	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
Phchi.S1	AUGUSTUS	stop_codon	16460089	16460091	.	+	0	transcript_id "Phchi.S1G251700.t1"; gene_id "Phchi.S1G251700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12419.t1 is derived from g8096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19191101	19191733	.	+	.	Phchi.S2G049900
Phchi.S2	AUGUSTUS	transcript	19191101	19191733	.	+	.	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	start_codon	19191101	19191103	.	+	0	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	CDS	19191101	19191382	0.13	+	0	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	exon	19191101	19191382	.	+	.	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	intron	19191383	19191595	.	+	.	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	CDS	19191596	19191733	0.22	+	0	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	exon	19191596	19191733	.	+	.	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
Phchi.S2	AUGUSTUS	stop_codon	19191734	19191736	.	+	0	transcript_id "Phchi.S2G049900.t1"; gene_id "Phchi.S2G049900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9102.t1 is derived from g6277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39837221	39838877	.	+	.	Phchi.S1G626100
Phchi.S1	AUGUSTUS	transcript	39837221	39838877	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	start_codon	39837221	39837223	.	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39837221	39837316	1	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39837221	39837316	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39837317	39837414	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39837415	39837505	1	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39837415	39837505	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39837506	39837629	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39837630	39837796	1	+	2	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39837630	39837796	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39837797	39837884	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39837885	39837980	1	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39837885	39837980	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39837981	39838065	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39838066	39838140	1	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39838066	39838140	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39838141	39838225	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39838226	39838337	0.88	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39838226	39838337	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39838338	39838464	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39838465	39838633	0.86	+	2	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39838465	39838633	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	intron	39838634	39838756	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	CDS	39838757	39838877	0.68	+	1	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	exon	39838757	39838877	.	+	.	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
Phchi.S1	AUGUSTUS	stop_codon	39838878	39838880	.	+	0	transcript_id "Phchi.S1G626100.t1"; gene_id "Phchi.S1G626100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14108.t1 is derived from g12575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10885202	10886437	.	-	.	Phchi.S3G142700
Phchi.S3	AUGUSTUS	transcript	10885202	10886437	.	-	.	transcript_id "Phchi.S3G142700.t1"; gene_id "Phchi.S3G142700"
Phchi.S3	AUGUSTUS	stop_codon	10885199	10885201	.	-	0	transcript_id "Phchi.S3G142700.t1"; gene_id "Phchi.S3G142700"
Phchi.S3	AUGUSTUS	CDS	10885202	10886437	0.59	-	0	transcript_id "Phchi.S3G142700.t1"; gene_id "Phchi.S3G142700"
Phchi.S3	AUGUSTUS	exon	10885202	10886437	.	-	.	transcript_id "Phchi.S3G142700.t1"; gene_id "Phchi.S3G142700"
Phchi.S3	AUGUSTUS	start_codon	10886435	10886437	.	-	0	transcript_id "Phchi.S3G142700.t1"; gene_id "Phchi.S3G142700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11157.t1 is derived from g15207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4420994	4421950	.	+	.	Phchi.S4G073900
Phchi.S4	AUGUSTUS	transcript	4420994	4421950	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	start_codon	4420994	4420996	.	+	0	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	CDS	4420994	4421210	0.9	+	0	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	exon	4420994	4421210	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	intron	4421211	4421324	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	CDS	4421325	4421443	1	+	2	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	exon	4421325	4421443	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	intron	4421444	4421530	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	CDS	4421531	4421629	0.45	+	0	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	exon	4421531	4421629	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	intron	4421630	4421775	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	CDS	4421776	4421791	0.36	+	0	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	exon	4421776	4421791	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	intron	4421792	4421933	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	CDS	4421934	4421950	0.36	+	2	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	exon	4421934	4421950	.	+	.	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
Phchi.S4	AUGUSTUS	stop_codon	4421951	4421953	.	+	0	transcript_id "Phchi.S4G073900.t1"; gene_id "Phchi.S4G073900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4168.t1 is derived from g1337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8724335	8725749	.	-	.	Phchi.S1G132700
Phchi.S1	AUGUSTUS	transcript	8724335	8725749	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	stop_codon	8724332	8724334	.	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8724335	8724388	1	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8724335	8724388	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8724389	8724471	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8724472	8724567	1	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8724472	8724567	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8724568	8724664	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8724665	8724739	1	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8724665	8724739	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8724740	8724845	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8724846	8724948	0.95	-	1	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8724846	8724948	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8724949	8725026	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8725027	8725119	1	-	1	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8725027	8725119	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8725120	8725199	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8725200	8725309	1	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8725200	8725309	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8725310	8725398	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8725399	8725440	0.99	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8725399	8725440	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8725441	8725520	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8725521	8725541	0.66	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8725521	8725541	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	intron	8725542	8725626	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	CDS	8725627	8725749	0.95	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	exon	8725627	8725749	.	-	.	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
Phchi.S1	AUGUSTUS	start_codon	8725747	8725749	.	-	0	transcript_id "Phchi.S1G132700.t1"; gene_id "Phchi.S1G132700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2639.t1 is derived from g9559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7909850	7910416	.	+	.	Phchi.S5G124800
Phchi.S5	AUGUSTUS	transcript	7909850	7910416	.	+	.	transcript_id "Phchi.S5G124800.t1"; gene_id "Phchi.S5G124800"
Phchi.S5	AUGUSTUS	start_codon	7909850	7909852	.	+	0	transcript_id "Phchi.S5G124800.t1"; gene_id "Phchi.S5G124800"
Phchi.S5	AUGUSTUS	CDS	7909850	7910416	0.3	+	0	transcript_id "Phchi.S5G124800.t1"; gene_id "Phchi.S5G124800"
Phchi.S5	AUGUSTUS	exon	7909850	7910416	.	+	.	transcript_id "Phchi.S5G124800.t1"; gene_id "Phchi.S5G124800"
Phchi.S5	AUGUSTUS	stop_codon	7910417	7910419	.	+	0	transcript_id "Phchi.S5G124800.t1"; gene_id "Phchi.S5G124800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15083.t1 is derived from g13551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16944026	16946961	.	-	.	Phchi.S3G240200
Phchi.S3	AUGUSTUS	transcript	16944026	16946961	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	stop_codon	16944023	16944025	.	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16944026	16944181	0.62	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16944026	16944181	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16944182	16944260	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16944261	16944317	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16944261	16944317	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16944318	16944396	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16944397	16944532	1	-	1	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16944397	16944532	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16944533	16944617	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16944618	16944772	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16944618	16944772	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16944773	16944861	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16944862	16944962	1	-	2	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16944862	16944962	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16944963	16945105	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16945106	16945163	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16945106	16945163	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16945164	16945347	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16945348	16945399	1	-	1	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16945348	16945399	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16945400	16945505	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16945506	16945576	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16945506	16945576	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16945577	16945738	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16945739	16945831	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16945739	16945831	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16945832	16945910	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16945911	16945994	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16945911	16945994	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16945995	16946138	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16946139	16946211	1	-	1	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16946139	16946211	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16946212	16946335	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16946336	16946475	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16946336	16946475	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16946476	16946589	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16946590	16946673	1	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16946590	16946673	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	intron	16946674	16946868	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	CDS	16946869	16946961	0.52	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	exon	16946869	16946961	.	-	.	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
Phchi.S3	AUGUSTUS	start_codon	16946959	16946961	.	-	0	transcript_id "Phchi.S3G240200.t1"; gene_id "Phchi.S3G240200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3436.t1 is derived from g605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3639830	3640507	.	+	.	Phchi.S1G059500
Phchi.S1	AUGUSTUS	transcript	3639830	3640507	.	+	.	transcript_id "Phchi.S1G059500.t1"; gene_id "Phchi.S1G059500"
Phchi.S1	AUGUSTUS	start_codon	3639830	3639832	.	+	0	transcript_id "Phchi.S1G059500.t1"; gene_id "Phchi.S1G059500"
Phchi.S1	AUGUSTUS	CDS	3639830	3640507	0.98	+	0	transcript_id "Phchi.S1G059500.t1"; gene_id "Phchi.S1G059500"
Phchi.S1	AUGUSTUS	exon	3639830	3640507	.	+	.	transcript_id "Phchi.S1G059500.t1"; gene_id "Phchi.S1G059500"
Phchi.S1	AUGUSTUS	stop_codon	3640508	3640510	.	+	0	transcript_id "Phchi.S1G059500.t1"; gene_id "Phchi.S1G059500"
# This transcript jg13416.t2 is derived from g11882.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13417.t1 is derived from g11883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6602459	6604746	.	-	.	Phchi.S3G073600
Phchi.S3	AUGUSTUS	transcript	6602459	6604203	.	-	.	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	stop_codon	6602456	6602458	.	-	0	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	CDS	6602459	6603109	0.59	-	0	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	exon	6602459	6603109	.	-	.	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	intron	6603110	6603210	.	-	.	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	CDS	6603211	6604203	0.66	-	0	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	exon	6603211	6604203	.	-	.	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	start_codon	6604201	6604203	.	-	0	transcript_id "Phchi.S3G073600.t1"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	transcript	6602459	6604746	.	-	.	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	stop_codon	6602456	6602458	.	-	0	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	CDS	6602459	6603109	0.43	-	0	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	exon	6602459	6603109	.	-	.	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	intron	6603110	6603210	.	-	.	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	CDS	6603211	6604746	0.43	-	0	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	exon	6603211	6604746	.	-	.	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
Phchi.S3	AUGUSTUS	start_codon	6604744	6604746	.	-	0	transcript_id "Phchi.S3G073600.t2"; gene_id "Phchi.S3G073600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg91.t1 is derived from g9873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	464931	468209	.	-	.	Phchi.S6G005000
Phchi.S6	AUGUSTUS	transcript	464931	468209	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	stop_codon	464928	464930	.	-	0	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	CDS	464931	465612	0.71	-	1	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	exon	464931	465612	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	intron	465613	466209	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	CDS	466210	466718	0.51	-	0	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	exon	466210	466718	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	intron	466719	467060	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	CDS	467061	467505	0.43	-	1	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	exon	467061	467505	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	intron	467506	467679	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	CDS	467680	468209	0.46	-	0	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	exon	467680	468209	.	-	.	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
Phchi.S6	AUGUSTUS	start_codon	468207	468209	.	-	0	transcript_id "Phchi.S6G005000.t1"; gene_id "Phchi.S6G005000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2912.t1 is derived from g81.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	451790	459551	.	-	.	Phchi.S1G007100
Phchi.S1	AUGUSTUS	transcript	451790	459551	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	stop_codon	451787	451789	.	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	451790	451849	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	451790	451849	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	451850	451944	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	451945	452115	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	451945	452115	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	452116	452207	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	452208	452348	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	452208	452348	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	452349	452429	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	452430	452537	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	452430	452537	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	452538	452632	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	452633	452771	1	-	1	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	452633	452771	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	452772	452865	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	452866	452946	1	-	1	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	452866	452946	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	452947	453057	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	453058	453166	1	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	453058	453166	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	453167	453259	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	453260	453388	1	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	453260	453388	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	453389	453535	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	453536	453842	0.99	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	453536	453842	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	453843	453942	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	453943	454011	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	453943	454011	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	454012	454135	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	454136	454461	0.83	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	454136	454461	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	454462	454570	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	454571	454650	1	-	1	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	454571	454650	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	454651	454798	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	454799	454986	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	454799	454986	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	454987	455139	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	455140	455414	0.98	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	455140	455414	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	455415	455596	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	455597	455759	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	455597	455759	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	455760	455860	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	455861	456100	0.88	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	455861	456100	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	456101	456187	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	456188	456438	0.9	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	456188	456438	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	456439	456523	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	456524	456716	0.84	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	456524	456716	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	456717	456945	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	456946	457002	0.86	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	456946	457002	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	457003	457134	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	457135	457270	1	-	1	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	457135	457270	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	457271	457417	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	457418	457524	1	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	457418	457524	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	457525	457699	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	457700	457804	0.89	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	457700	457804	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	457805	457915	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	457916	457998	1	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	457916	457998	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	457999	458096	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	458097	458254	1	-	1	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	458097	458254	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	458255	458450	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	458451	458514	1	-	2	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	458451	458514	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	458515	458746	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	458747	459014	0.96	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	458747	459014	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	459015	459150	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	459151	459283	1	-	1	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	459151	459283	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	intron	459284	459384	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	CDS	459385	459551	0.66	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	exon	459385	459551	.	-	.	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
Phchi.S1	AUGUSTUS	start_codon	459549	459551	.	-	0	transcript_id "Phchi.S1G007100.t1"; gene_id "Phchi.S1G007100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12200.t1 is derived from g7876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6715108	6716192	.	+	.	Phchi.S2G028000
Phchi.S2	AUGUSTUS	transcript	6715108	6716192	.	+	.	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	start_codon	6715108	6715110	.	+	0	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	CDS	6715108	6715609	0.64	+	0	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	exon	6715108	6715609	.	+	.	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	intron	6715610	6715764	.	+	.	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	CDS	6715765	6716192	1	+	2	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	exon	6715765	6716192	.	+	.	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
Phchi.S2	AUGUSTUS	stop_codon	6716193	6716195	.	+	0	transcript_id "Phchi.S2G028000.t1"; gene_id "Phchi.S2G028000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11931.t1 is derived from g7606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	85255	88476	.	-	.	Phchi.S2G001100
Phchi.S2	AUGUSTUS	transcript	85255	88476	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	stop_codon	85252	85254	.	-	0	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	85255	85481	0.29	-	2	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	85255	85481	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	85482	85602	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	85603	85663	0.97	-	0	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	85603	85663	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	85664	85810	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	85811	85940	0.34	-	1	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	85811	85940	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	85941	86318	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	86319	86827	0.35	-	0	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	86319	86827	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	86828	86918	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	86919	86987	0.89	-	0	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	86919	86987	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	86988	87153	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	87154	87292	0.89	-	1	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	87154	87292	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	87293	87381	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	87382	87417	0.95	-	1	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	87382	87417	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	87418	87979	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	87980	88118	0.54	-	2	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	87980	88118	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	intron	88119	88367	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	CDS	88368	88476	0.39	-	0	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	exon	88368	88476	.	-	.	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
Phchi.S2	AUGUSTUS	start_codon	88474	88476	.	-	0	transcript_id "Phchi.S2G001100.t1"; gene_id "Phchi.S2G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13987.t1 is derived from g12454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10060837	10061546	.	+	.	Phchi.S3G130600
Phchi.S3	AUGUSTUS	transcript	10060837	10061546	.	+	.	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	start_codon	10060837	10060839	.	+	0	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	CDS	10060837	10061295	0.32	+	0	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	exon	10060837	10061295	.	+	.	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	intron	10061296	10061429	.	+	.	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	CDS	10061430	10061546	0.67	+	0	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	exon	10061430	10061546	.	+	.	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
Phchi.S3	AUGUSTUS	stop_codon	10061547	10061549	.	+	0	transcript_id "Phchi.S3G130600.t1"; gene_id "Phchi.S3G130600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10550.t1 is derived from g14600.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	947051	949836	.	+	.	Phchi.S4G013200
Phchi.S4	AUGUSTUS	transcript	947051	949836	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	start_codon	947051	947053	.	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947051	947251	1	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947051	947251	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947252	947329	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947330	947440	1	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947330	947440	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947441	947509	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947510	947616	1	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947510	947616	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947617	947754	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947755	947797	1	+	1	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947755	947797	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947798	947974	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947975	948073	1	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947975	948073	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948074	948155	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948156	948225	1	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948156	948225	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948226	948368	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948369	948463	1	+	2	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948369	948463	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948464	948544	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948545	948578	1	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948545	948578	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948579	948682	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948683	948767	1	+	2	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948683	948767	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948768	948886	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948887	948970	1	+	1	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948887	948970	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948971	949073	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949074	949121	1	+	1	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949074	949121	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	949122	949204	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949205	949237	1	+	1	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949205	949237	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	949238	949315	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949316	949424	1	+	1	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949316	949424	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	949425	949584	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949585	949836	0.95	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949585	949836	.	+	.	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	stop_codon	949837	949839	.	+	0	transcript_id "Phchi.S4G013200.t1"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	transcript	947051	949836	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	start_codon	947051	947053	.	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947051	947251	1	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947051	947251	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947252	947329	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947330	947440	1	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947330	947440	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947441	947509	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947510	947616	1	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947510	947616	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947617	947754	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947755	947797	1	+	1	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947755	947797	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	947798	947974	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	947975	948073	1	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	947975	948073	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948074	948155	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948156	948225	1	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948156	948225	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948226	948368	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948369	948463	1	+	2	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948369	948463	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948464	948544	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948545	948578	1	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948545	948578	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948579	948682	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948683	948767	1	+	2	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948683	948767	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948768	948886	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	948887	948970	1	+	1	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	948887	948970	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	948971	949073	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949074	949121	1	+	1	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949074	949121	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	949122	949204	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949205	949237	1	+	1	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949205	949237	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	949238	949315	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949316	949463	0.51	+	1	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949316	949463	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	intron	949464	949584	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	CDS	949585	949836	0.92	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	exon	949585	949836	.	+	.	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
Phchi.S4	AUGUSTUS	stop_codon	949837	949839	.	+	0	transcript_id "Phchi.S4G013200.t2"; gene_id "Phchi.S4G013200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2318.t1 is derived from g9238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6122943	6127466	.	-	.	Phchi.S5G092700
Phchi.S5	AUGUSTUS	transcript	6122943	6127466	.	-	.	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	stop_codon	6122940	6122942	.	-	0	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	CDS	6122943	6123526	0.29	-	2	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	exon	6122943	6123526	.	-	.	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	intron	6123527	6123952	.	-	.	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	CDS	6123953	6124018	0.39	-	2	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	exon	6123953	6124018	.	-	.	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	intron	6124019	6124099	.	-	.	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	CDS	6124100	6127466	0.63	-	0	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	exon	6124100	6127466	.	-	.	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
Phchi.S5	AUGUSTUS	start_codon	6127464	6127466	.	-	0	transcript_id "Phchi.S5G092700.t1"; gene_id "Phchi.S5G092700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2683.t1 is derived from g9603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8182767	8185726	.	-	.	Phchi.S5G129200
Phchi.S5	AUGUSTUS	transcript	8182767	8185726	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	stop_codon	8182764	8182766	.	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8182767	8182917	1	-	1	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8182767	8182917	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8182918	8183016	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183017	8183080	1	-	2	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183017	8183080	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183081	8183165	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183166	8183235	1	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183166	8183235	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183236	8183327	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183328	8183485	0.91	-	2	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183328	8183485	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183486	8183582	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183583	8183651	0.81	-	2	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183583	8183651	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183652	8183741	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183742	8183823	1	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183742	8183823	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183824	8183896	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183897	8184001	1	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183897	8184001	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184002	8184135	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184136	8184217	1	-	1	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184136	8184217	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184218	8184315	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184316	8184404	1	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184316	8184404	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184405	8184490	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184491	8184609	1	-	2	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184491	8184609	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184610	8184732	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184733	8184787	1	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184733	8184787	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184788	8184973	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184974	8185108	0.88	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184974	8185108	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8185109	8185213	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8185214	8185362	0.88	-	2	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8185214	8185362	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8185363	8185605	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8185606	8185726	0.86	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8185606	8185726	.	-	.	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	start_codon	8185724	8185726	.	-	0	transcript_id "Phchi.S5G129200.t1"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	transcript	8182767	8185726	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	stop_codon	8182764	8182766	.	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8182767	8182917	1	-	1	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8182767	8182917	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8182918	8183016	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183017	8183080	1	-	2	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183017	8183080	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183081	8183165	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183166	8183235	1	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183166	8183235	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183236	8183327	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183328	8183485	0.96	-	2	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183328	8183485	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183486	8183582	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183583	8183651	0.82	-	2	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183583	8183651	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183652	8183741	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183742	8183823	1	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183742	8183823	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8183824	8183896	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8183897	8184001	1	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8183897	8184001	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184002	8184135	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184136	8184217	1	-	1	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184136	8184217	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184218	8184315	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184316	8184404	1	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184316	8184404	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184405	8184490	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184491	8184609	0.96	-	2	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184491	8184609	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184610	8184787	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184788	8184798	0.91	-	1	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184788	8184798	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184799	8184973	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8184974	8184991	0.98	-	1	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8184974	8184991	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8184992	8185259	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8185260	8185362	0.49	-	2	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8185260	8185362	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	intron	8185363	8185605	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	CDS	8185606	8185726	0.83	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	exon	8185606	8185726	.	-	.	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
Phchi.S5	AUGUSTUS	start_codon	8185724	8185726	.	-	0	transcript_id "Phchi.S5G129200.t2"; gene_id "Phchi.S5G129200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2762.t1 is derived from g9682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8713178	8714464	.	+	.	Phchi.S5G137100
Phchi.S5	AUGUSTUS	transcript	8713178	8714464	.	+	.	transcript_id "Phchi.S5G137100.t1"; gene_id "Phchi.S5G137100"
Phchi.S5	AUGUSTUS	start_codon	8713178	8713180	.	+	0	transcript_id "Phchi.S5G137100.t1"; gene_id "Phchi.S5G137100"
Phchi.S5	AUGUSTUS	CDS	8713178	8714464	1	+	0	transcript_id "Phchi.S5G137100.t1"; gene_id "Phchi.S5G137100"
Phchi.S5	AUGUSTUS	exon	8713178	8714464	.	+	.	transcript_id "Phchi.S5G137100.t1"; gene_id "Phchi.S5G137100"
Phchi.S5	AUGUSTUS	stop_codon	8714465	8714467	.	+	0	transcript_id "Phchi.S5G137100.t1"; gene_id "Phchi.S5G137100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7172.t1 is derived from g4344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27392228	27393684	.	-	.	Phchi.S1G433100
Phchi.S1	AUGUSTUS	transcript	27392228	27393684	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	stop_codon	27392225	27392227	.	-	0	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	CDS	27392228	27392381	1	-	1	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	exon	27392228	27392381	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	intron	27392382	27392478	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	CDS	27392479	27392921	1	-	0	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	exon	27392479	27392921	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	intron	27392922	27393019	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	CDS	27393020	27393206	1	-	1	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	exon	27393020	27393206	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	intron	27393207	27393301	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	CDS	27393302	27393684	0.67	-	0	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	exon	27393302	27393684	.	-	.	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
Phchi.S1	AUGUSTUS	start_codon	27393682	27393684	.	-	0	transcript_id "Phchi.S1G433100.t1"; gene_id "Phchi.S1G433100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg14539.t1 is derived from g13007.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13395749	13398623	.	-	.	Phchi.S3G185800
Phchi.S3	AUGUSTUS	transcript	13395749	13396122	.	-	.	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	stop_codon	13395746	13395748	.	-	0	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13395749	13395759	1	-	2	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13395749	13395759	.	-	.	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13395760	13395917	.	-	.	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13395918	13396122	0.82	-	0	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13395918	13396122	.	-	.	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	start_codon	13396120	13396122	.	-	0	transcript_id "Phchi.S3G185800.t1"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	transcript	13395749	13398623	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	stop_codon	13395746	13395748	.	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13395749	13395759	1	-	2	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13395749	13395759	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13395760	13395917	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13395918	13396122	0.91	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13395918	13396122	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396123	13396223	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396224	13396310	0.91	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396224	13396310	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396311	13396445	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396446	13396617	0.95	-	1	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396446	13396617	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396618	13396725	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396726	13396855	0.93	-	2	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396726	13396855	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396856	13397279	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397280	13397364	0.98	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397280	13397364	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397365	13397444	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397445	13397488	0.61	-	2	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397445	13397488	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397489	13397591	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397592	13397665	0.46	-	1	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397592	13397665	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397666	13397776	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397777	13397931	0.78	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397777	13397931	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397932	13398024	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13398025	13398037	0.68	-	1	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13398025	13398037	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13398038	13398426	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13398427	13398623	0.57	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13398427	13398623	.	-	.	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	start_codon	13398621	13398623	.	-	0	transcript_id "Phchi.S3G185800.t2"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	transcript	13396262	13398623	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	stop_codon	13396259	13396261	.	-	0	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396262	13396310	0.87	-	1	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396262	13396310	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396311	13396445	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396446	13396588	0.87	-	0	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396446	13396588	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396589	13396725	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396726	13396855	0.99	-	1	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396726	13396855	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396856	13396999	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397000	13397048	1	-	2	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397000	13397048	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397049	13397279	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397280	13397364	1	-	0	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397280	13397364	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397365	13397444	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397445	13397488	0.58	-	2	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397445	13397488	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397489	13397591	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397592	13397665	0.44	-	1	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397592	13397665	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397666	13397776	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397777	13397931	0.68	-	0	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397777	13397931	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397932	13398024	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13398025	13398037	0.56	-	1	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13398025	13398037	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13398038	13398426	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13398427	13398623	0.55	-	0	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13398427	13398623	.	-	.	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	start_codon	13398621	13398623	.	-	0	transcript_id "Phchi.S3G185800.t3"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	transcript	13396262	13398623	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	stop_codon	13396259	13396261	.	-	0	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396262	13396310	0.83	-	1	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396262	13396310	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396311	13396445	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396446	13396588	0.84	-	0	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396446	13396588	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396589	13396725	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13396726	13396855	0.99	-	1	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13396726	13396855	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13396856	13396999	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397000	13397048	1	-	2	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397000	13397048	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397049	13397279	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397280	13397367	0.98	-	0	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397280	13397367	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397368	13397444	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397445	13397488	0.53	-	2	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397445	13397488	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397489	13397591	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397592	13397665	0.41	-	1	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397592	13397665	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397666	13397776	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13397777	13397931	0.7	-	0	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13397777	13397931	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13397932	13398024	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13398025	13398037	0.61	-	1	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13398025	13398037	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	intron	13398038	13398426	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	CDS	13398427	13398623	0.53	-	0	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	exon	13398427	13398623	.	-	.	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
Phchi.S3	AUGUSTUS	start_codon	13398621	13398623	.	-	0	transcript_id "Phchi.S3G185800.t4"; gene_id "Phchi.S3G185800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9657.t1 is derived from g6833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43106966	43107825	.	+	.	Phchi.S1G681600
Phchi.S1	AUGUSTUS	transcript	43106966	43107825	.	+	.	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	start_codon	43106966	43106968	.	+	0	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	CDS	43106966	43107278	0.73	+	0	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	exon	43106966	43107278	.	+	.	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	intron	43107279	43107364	.	+	.	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	CDS	43107365	43107428	0.91	+	2	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	exon	43107365	43107428	.	+	.	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	intron	43107429	43107809	.	+	.	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	CDS	43107810	43107825	0.91	+	1	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	exon	43107810	43107825	.	+	.	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
Phchi.S1	AUGUSTUS	stop_codon	43107826	43107828	.	+	0	transcript_id "Phchi.S1G681600.t1"; gene_id "Phchi.S1G681600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6576.t1 is derived from g3748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23828385	23829757	.	-	.	Phchi.S1G373500
Phchi.S1	AUGUSTUS	transcript	23828385	23829757	.	-	.	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	stop_codon	23828382	23828384	.	-	0	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	CDS	23828385	23828392	0.57	-	2	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	exon	23828385	23828392	.	-	.	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	intron	23828393	23828487	.	-	.	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	CDS	23828488	23829469	0.7	-	0	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	exon	23828488	23829469	.	-	.	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	intron	23829470	23829568	.	-	.	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	CDS	23829569	23829757	0.45	-	0	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	exon	23829569	23829757	.	-	.	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
Phchi.S1	AUGUSTUS	start_codon	23829755	23829757	.	-	0	transcript_id "Phchi.S1G373500.t1"; gene_id "Phchi.S1G373500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg79.t1 is derived from g9861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	408933	409702	.	-	.	Phchi.S6G003800
Phchi.S6	AUGUSTUS	transcript	408933	409702	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	stop_codon	408930	408932	.	-	0	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	CDS	408933	409126	1	-	2	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	exon	408933	409126	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	intron	409127	409216	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	CDS	409217	409263	1	-	1	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	exon	409217	409263	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	intron	409264	409354	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	CDS	409355	409445	1	-	2	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	exon	409355	409445	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	intron	409446	409531	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	CDS	409532	409613	1	-	0	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	exon	409532	409613	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	intron	409614	409699	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	CDS	409700	409702	0.98	-	0	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	exon	409700	409702	.	-	.	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
Phchi.S6	AUGUSTUS	start_codon	409700	409702	.	-	0	transcript_id "Phchi.S6G003800.t1"; gene_id "Phchi.S6G003800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2860.t1 is derived from g29.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	138326	140110	.	+	.	Phchi.S1G001900
Phchi.S1	AUGUSTUS	transcript	138326	140110	.	+	.	transcript_id "Phchi.S1G001900.t1"; gene_id "Phchi.S1G001900"
Phchi.S1	AUGUSTUS	start_codon	138326	138328	.	+	0	transcript_id "Phchi.S1G001900.t1"; gene_id "Phchi.S1G001900"
Phchi.S1	AUGUSTUS	CDS	138326	140110	1	+	0	transcript_id "Phchi.S1G001900.t1"; gene_id "Phchi.S1G001900"
Phchi.S1	AUGUSTUS	exon	138326	140110	.	+	.	transcript_id "Phchi.S1G001900.t1"; gene_id "Phchi.S1G001900"
Phchi.S1	AUGUSTUS	stop_codon	140111	140113	.	+	0	transcript_id "Phchi.S1G001900.t1"; gene_id "Phchi.S1G001900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14460.t1 is derived from g12928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12986623	12990065	.	+	.	Phchi.S3G177900
Phchi.S3	AUGUSTUS	transcript	12986623	12990065	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	start_codon	12986623	12986625	.	+	0	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12986623	12986635	0.33	+	0	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12986623	12986635	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12986636	12986709	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12986710	12986791	0.67	+	2	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12986710	12986791	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12986792	12986915	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12986916	12986953	0.93	+	1	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12986916	12986953	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12986954	12987050	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12987051	12987286	0.99	+	2	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12987051	12987286	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12987287	12987421	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12987422	12987662	0.95	+	0	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12987422	12987662	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12987663	12987838	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12987839	12987915	1	+	2	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12987839	12987915	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12987916	12988055	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12988056	12988098	1	+	0	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12988056	12988098	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12988099	12988205	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12988206	12988263	1	+	2	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12988206	12988263	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12988264	12988366	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12988367	12988436	1	+	1	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12988367	12988436	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12988437	12988528	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12988529	12989030	0.99	+	0	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12988529	12989030	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	intron	12989031	12989184	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	CDS	12989185	12990065	0.87	+	2	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	exon	12989185	12990065	.	+	.	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
Phchi.S3	AUGUSTUS	stop_codon	12990066	12990068	.	+	0	transcript_id "Phchi.S3G177900.t1"; gene_id "Phchi.S3G177900"
# This transcript jg6762.t2 is derived from g3934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6763.t1 is derived from g3935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24922609	24923814	.	+	.	Phchi.S1G392200
Phchi.S1	AUGUSTUS	transcript	24922609	24923814	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	start_codon	24922609	24922611	.	+	0	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	CDS	24922609	24922757	0.54	+	0	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	exon	24922609	24922757	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	intron	24922758	24922831	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	CDS	24922832	24922845	0.56	+	1	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	exon	24922832	24922845	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	intron	24922846	24922982	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	CDS	24922983	24923157	0.56	+	2	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	exon	24922983	24923157	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	intron	24923158	24923252	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	CDS	24923253	24923336	1	+	1	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	exon	24923253	24923336	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	intron	24923337	24923467	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	CDS	24923468	24923537	1	+	1	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	exon	24923468	24923537	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	intron	24923538	24923664	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	CDS	24923665	24923814	0.97	+	0	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	exon	24923665	24923814	.	+	.	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
Phchi.S1	AUGUSTUS	stop_codon	24923815	24923817	.	+	0	transcript_id "Phchi.S1G392200.t1"; gene_id "Phchi.S1G392200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8788.t1 is derived from g5963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37956041	37956721	.	+	.	Phchi.S1G594700
Phchi.S1	AUGUSTUS	transcript	37956041	37956721	.	+	.	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	start_codon	37956041	37956043	.	+	0	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	CDS	37956041	37956100	0.61	+	0	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	exon	37956041	37956100	.	+	.	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	intron	37956101	37956188	.	+	.	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	CDS	37956189	37956193	0.77	+	0	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	exon	37956189	37956193	.	+	.	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	intron	37956194	37956273	.	+	.	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	CDS	37956274	37956721	0.7	+	1	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	exon	37956274	37956721	.	+	.	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
Phchi.S1	AUGUSTUS	stop_codon	37956722	37956724	.	+	0	transcript_id "Phchi.S1G594700.t1"; gene_id "Phchi.S1G594700"
# This transcript jg4909.t2 is derived from g2079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4910.t1 is derived from g2080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13354025	13356625	.	+	.	Phchi.S1G206900
Phchi.S1	AUGUSTUS	transcript	13354025	13356625	.	+	.	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	start_codon	13354025	13354027	.	+	0	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	CDS	13354025	13354087	0.29	+	0	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	exon	13354025	13354087	.	+	.	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	intron	13354088	13354198	.	+	.	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	CDS	13354199	13356625	0.89	+	0	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	exon	13354199	13356625	.	+	.	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
Phchi.S1	AUGUSTUS	stop_codon	13356626	13356628	.	+	0	transcript_id "Phchi.S1G206900.t1"; gene_id "Phchi.S1G206900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13172.t1 is derived from g11637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4493352	4497705	.	+	.	Phchi.S3G049100
Phchi.S3	AUGUSTUS	transcript	4493352	4497705	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	start_codon	4493352	4493354	.	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4493352	4493862	0.99	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4493352	4493862	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4493863	4493951	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4493952	4494184	0.99	+	2	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4493952	4494184	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4494185	4494262	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4494263	4494337	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4494263	4494337	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4494338	4494428	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4494429	4494585	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4494429	4494585	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4494586	4494680	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4494681	4494735	0.96	+	2	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4494681	4494735	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4494736	4494812	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4494813	4494875	0.7	+	1	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4494813	4494875	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4494876	4494952	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4494953	4495040	1	+	1	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4494953	4495040	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4495041	4495108	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4495109	4495222	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4495109	4495222	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4495223	4495314	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4495315	4495395	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4495315	4495395	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4495396	4495472	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4495473	4495576	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4495473	4495576	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4495577	4495661	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4495662	4495810	1	+	1	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4495662	4495810	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4495811	4495900	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4495901	4496132	1	+	2	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4495901	4496132	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4496133	4496221	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4496222	4496599	1	+	1	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4496222	4496599	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4496600	4496692	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4496693	4496740	1	+	1	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4496693	4496740	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4496741	4496822	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4496823	4496874	1	+	1	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4496823	4496874	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4496875	4496957	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4496958	4497093	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4496958	4497093	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4497094	4497177	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4497178	4497344	1	+	2	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4497178	4497344	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	intron	4497345	4497423	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	CDS	4497424	4497705	1	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	exon	4497424	4497705	.	+	.	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
Phchi.S3	AUGUSTUS	stop_codon	4497706	4497708	.	+	0	transcript_id "Phchi.S3G049100.t1"; gene_id "Phchi.S3G049100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg485.t1 is derived from g10267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3392185	3393593	.	-	.	Phchi.S6G044400
Phchi.S6	AUGUSTUS	transcript	3392185	3393593	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	stop_codon	3392182	3392184	.	-	0	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392185	3392304	0.73	-	0	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392185	3392304	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3392305	3392387	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392388	3392411	1	-	0	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392388	3392411	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3392412	3392605	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392606	3392691	0.95	-	2	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392606	3392691	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3392692	3392864	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392865	3393034	1	-	1	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392865	3393034	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3393035	3393136	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3393137	3393181	1	-	1	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3393137	3393181	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3393182	3393269	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3393270	3393401	1	-	1	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3393270	3393401	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3393402	3393489	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3393490	3393593	1	-	0	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3393490	3393593	.	-	.	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	start_codon	3393591	3393593	.	-	0	transcript_id "Phchi.S6G044400.t1"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	transcript	3392185	3393593	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	stop_codon	3392182	3392184	.	-	0	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392185	3392304	0.8	-	0	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392185	3392304	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3392305	3392387	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392388	3392411	1	-	0	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392388	3392411	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3392412	3392605	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392606	3392640	0.94	-	2	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392606	3392640	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3392641	3392864	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3392865	3393034	1	-	1	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3392865	3393034	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3393035	3393136	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3393137	3393181	1	-	1	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3393137	3393181	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3393182	3393269	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3393270	3393401	1	-	1	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3393270	3393401	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	intron	3393402	3393489	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	CDS	3393490	3393593	0.98	-	0	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	exon	3393490	3393593	.	-	.	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
Phchi.S6	AUGUSTUS	start_codon	3393591	3393593	.	-	0	transcript_id "Phchi.S6G044400.t2"; gene_id "Phchi.S6G044400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5995.t1 is derived from g3166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20311325	20312550	.	+	.	Phchi.S1G315400
Phchi.S1	AUGUSTUS	transcript	20311325	20312550	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	start_codon	20311325	20311327	.	+	0	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	CDS	20311325	20311613	0.61	+	0	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	exon	20311325	20311613	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	intron	20311614	20311710	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	CDS	20311711	20312102	1	+	2	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	exon	20311711	20312102	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	intron	20312103	20312190	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	CDS	20312191	20312277	1	+	0	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	exon	20312191	20312277	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	intron	20312278	20312370	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	CDS	20312371	20312550	0.82	+	0	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	exon	20312371	20312550	.	+	.	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	stop_codon	20312551	20312553	.	+	0	transcript_id "Phchi.S1G315400.t1"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	transcript	20311325	20311735	.	+	.	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	start_codon	20311325	20311327	.	+	0	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	CDS	20311325	20311613	0.52	+	0	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	exon	20311325	20311613	.	+	.	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	intron	20311614	20311703	.	+	.	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	CDS	20311704	20311735	0.93	+	2	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	exon	20311704	20311735	.	+	.	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
Phchi.S1	AUGUSTUS	stop_codon	20311736	20311738	.	+	0	transcript_id "Phchi.S1G315400.t2"; gene_id "Phchi.S1G315400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14004.t1 is derived from g12471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10246657	10248065	.	+	.	Phchi.S3G132300
Phchi.S3	AUGUSTUS	transcript	10246657	10248065	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	start_codon	10246657	10246659	.	+	0	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	CDS	10246657	10247064	0.55	+	0	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	exon	10246657	10247064	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	intron	10247065	10247230	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	CDS	10247231	10247344	1	+	0	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	exon	10247231	10247344	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	intron	10247345	10247475	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	CDS	10247476	10247639	1	+	0	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	exon	10247476	10247639	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	intron	10247640	10247778	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	CDS	10247779	10247805	0.52	+	1	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	exon	10247779	10247805	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	intron	10247806	10247880	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	CDS	10247881	10247918	0.32	+	1	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	exon	10247881	10247918	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	intron	10247919	10248063	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	CDS	10248064	10248065	0.32	+	2	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	exon	10248064	10248065	.	+	.	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
Phchi.S3	AUGUSTUS	stop_codon	10248066	10248068	.	+	0	transcript_id "Phchi.S3G132300.t1"; gene_id "Phchi.S3G132300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11022.t1 is derived from g15072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3681502	3682140	.	+	.	Phchi.S4G060400
Phchi.S4	AUGUSTUS	transcript	3681502	3682140	.	+	.	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	start_codon	3681502	3681504	.	+	0	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	CDS	3681502	3681728	0.51	+	0	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	exon	3681502	3681728	.	+	.	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	intron	3681729	3681845	.	+	.	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	CDS	3681846	3682140	1	+	1	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	exon	3681846	3682140	.	+	.	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
Phchi.S4	AUGUSTUS	stop_codon	3682141	3682143	.	+	0	transcript_id "Phchi.S4G060400.t1"; gene_id "Phchi.S4G060400"
# This transcript jg12769.t2 is derived from g11234.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12770.t1 is derived from g11235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1962620	1967058	.	+	.	Phchi.S3G008900
Phchi.S3	AUGUSTUS	transcript	1962620	1967058	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	start_codon	1962620	1962622	.	+	0	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	CDS	1962620	1962703	1	+	0	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	exon	1962620	1962703	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	intron	1962704	1962788	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	CDS	1962789	1965432	0.77	+	0	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	exon	1962789	1965432	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	intron	1965433	1965689	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	CDS	1965690	1966018	0.45	+	2	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	exon	1965690	1966018	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	intron	1966019	1966109	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	CDS	1966110	1966321	1	+	0	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	exon	1966110	1966321	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	intron	1966322	1966396	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	CDS	1966397	1966765	0.81	+	1	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	exon	1966397	1966765	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	intron	1966766	1966937	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	CDS	1966938	1967058	0.65	+	1	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	exon	1966938	1967058	.	+	.	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
Phchi.S3	AUGUSTUS	stop_codon	1967059	1967061	.	+	0	transcript_id "Phchi.S3G008900.t1"; gene_id "Phchi.S3G008900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3990.t1 is derived from g1159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6887347	6888696	.	+	.	Phchi.S1G114900
Phchi.S1	AUGUSTUS	transcript	6887347	6888696	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	start_codon	6887347	6887349	.	+	0	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	CDS	6887347	6887536	1	+	0	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	exon	6887347	6887536	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	intron	6887537	6887666	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	CDS	6887667	6887808	1	+	2	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	exon	6887667	6887808	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	intron	6887809	6887895	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	CDS	6887896	6888016	1	+	1	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	exon	6887896	6888016	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	intron	6888017	6888226	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	CDS	6888227	6888289	1	+	0	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	exon	6888227	6888289	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	intron	6888290	6888552	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	CDS	6888553	6888696	0.58	+	0	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	exon	6888553	6888696	.	+	.	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
Phchi.S1	AUGUSTUS	stop_codon	6888697	6888699	.	+	0	transcript_id "Phchi.S1G114900.t1"; gene_id "Phchi.S1G114900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1432.t1 is derived from g8351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	815939	817490	.	-	.	Phchi.S5G004100
Phchi.S5	AUGUSTUS	transcript	815939	817490	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	stop_codon	815936	815938	.	-	0	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	CDS	815939	816494	1	-	1	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	exon	815939	816494	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	intron	816495	816661	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	CDS	816662	816807	1	-	0	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	exon	816662	816807	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	intron	816808	816987	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	CDS	816988	817055	1	-	2	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	exon	816988	817055	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	intron	817056	817354	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	CDS	817355	817490	0.96	-	0	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	exon	817355	817490	.	-	.	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
Phchi.S5	AUGUSTUS	start_codon	817488	817490	.	-	0	transcript_id "Phchi.S5G004100.t1"; gene_id "Phchi.S5G004100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1063.t1 is derived from g10846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7401175	7402067	.	-	.	Phchi.S6G102200
Phchi.S6	AUGUSTUS	transcript	7401175	7402067	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	stop_codon	7401172	7401174	.	-	0	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	CDS	7401175	7401194	0.88	-	2	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	exon	7401175	7401194	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	intron	7401195	7401306	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	CDS	7401307	7401357	0.88	-	2	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	exon	7401307	7401357	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	intron	7401358	7401625	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	CDS	7401626	7401695	0.49	-	0	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	exon	7401626	7401695	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	intron	7401696	7401824	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	CDS	7401825	7402067	0.59	-	0	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	exon	7401825	7402067	.	-	.	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
Phchi.S6	AUGUSTUS	start_codon	7402065	7402067	.	-	0	transcript_id "Phchi.S6G102200.t1"; gene_id "Phchi.S6G102200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5677.t1 is derived from g2847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18264058	18266051	.	-	.	Phchi.S1G283600
Phchi.S1	AUGUSTUS	transcript	18264058	18266051	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	stop_codon	18264055	18264057	.	-	0	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18264058	18264383	1	-	2	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18264058	18264383	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	intron	18264384	18264469	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18264470	18264713	1	-	0	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18264470	18264713	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	intron	18264714	18264835	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18264836	18265010	1	-	1	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18264836	18265010	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	intron	18265011	18265127	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18265128	18265239	1	-	2	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18265128	18265239	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	intron	18265240	18265326	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18265327	18265566	0.85	-	2	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18265327	18265566	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	intron	18265567	18265868	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18265869	18265945	0.76	-	1	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18265869	18265945	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	intron	18265946	18266028	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	CDS	18266029	18266051	0.85	-	0	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	exon	18266029	18266051	.	-	.	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
Phchi.S1	AUGUSTUS	start_codon	18266049	18266051	.	-	0	transcript_id "Phchi.S1G283600.t1"; gene_id "Phchi.S1G283600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10586.t1 is derived from g14636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1068584	1071176	.	+	.	Phchi.S4G016800
Phchi.S4	AUGUSTUS	transcript	1068584	1071176	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	start_codon	1068584	1068586	.	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1068584	1068640	0.75	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1068584	1068640	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1068641	1068715	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1068716	1068829	1	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1068716	1068829	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1068830	1068918	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1068919	1068990	1	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1068919	1068990	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1068991	1069125	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1069126	1069169	0.82	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1069126	1069169	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1069170	1069274	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1069275	1069416	0.5	+	1	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1069275	1069416	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1069417	1069507	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1069508	1069573	1	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1069508	1069573	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1069574	1069649	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1069650	1069729	1	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1069650	1069729	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1069730	1069809	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1069810	1069909	1	+	1	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1069810	1069909	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1069910	1070063	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1070064	1070230	1	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1070064	1070230	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1070231	1070319	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1070320	1070360	1	+	1	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1070320	1070360	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1070361	1070479	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1070480	1070508	1	+	2	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1070480	1070508	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1070509	1070594	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1070595	1070664	1	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1070595	1070664	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1070665	1070755	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1070756	1070845	1	+	2	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1070756	1070845	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	intron	1070846	1070931	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	CDS	1070932	1071176	0.94	+	2	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	exon	1070932	1071176	.	+	.	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
Phchi.S4	AUGUSTUS	stop_codon	1071177	1071179	.	+	0	transcript_id "Phchi.S4G016800.t1"; gene_id "Phchi.S4G016800"
# This transcript jg9430.t2 is derived from g6606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9431.t1 is derived from g6607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41433934	41434414	.	-	.	Phchi.S1G659000
Phchi.S1	AUGUSTUS	transcript	41433934	41434414	.	-	.	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	stop_codon	41433931	41433933	.	-	0	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	CDS	41433934	41434043	0.53	-	2	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	exon	41433934	41434043	.	-	.	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	intron	41434044	41434131	.	-	.	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	CDS	41434132	41434414	0.31	-	0	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	exon	41434132	41434414	.	-	.	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
Phchi.S1	AUGUSTUS	start_codon	41434412	41434414	.	-	0	transcript_id "Phchi.S1G659000.t1"; gene_id "Phchi.S1G659000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6893.t1 is derived from g4065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25863792	25867269	.	+	.	Phchi.S1G405200
Phchi.S1	AUGUSTUS	transcript	25863792	25867269	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	start_codon	25863792	25863794	.	+	0	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25863792	25864740	0.42	+	0	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25863792	25864740	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25864741	25864901	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25864902	25865156	0.61	+	2	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25864902	25865156	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25865157	25865238	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25865239	25865656	0.9	+	2	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25865239	25865656	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25865657	25865902	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25865903	25866047	0.89	+	1	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25865903	25866047	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25866048	25866351	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866352	25866467	1	+	0	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866352	25866467	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25866468	25866645	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866646	25866724	1	+	1	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866646	25866724	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25866725	25866844	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866845	25867078	1	+	0	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866845	25867078	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25867079	25867167	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25867168	25867269	0.59	+	0	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25867168	25867269	.	+	.	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	stop_codon	25867270	25867272	.	+	0	transcript_id "Phchi.S1G405200.t1"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	transcript	25863792	25867269	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	start_codon	25863792	25863794	.	+	0	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25863792	25864740	0.38	+	0	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25863792	25864740	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25864741	25864901	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25864902	25865156	0.56	+	2	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25864902	25865156	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25865157	25865238	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25865239	25865656	0.88	+	2	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25865239	25865656	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25865657	25865902	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25865903	25865994	0.59	+	1	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25865903	25865994	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25865995	25866070	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866071	25866087	0.99	+	2	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866071	25866087	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25866088	25866351	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866352	25866467	0.99	+	0	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866352	25866467	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25866468	25866645	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866646	25866724	1	+	1	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866646	25866724	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25866725	25866844	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25866845	25867078	1	+	0	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25866845	25867078	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	intron	25867079	25867167	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	CDS	25867168	25867269	0.63	+	0	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	exon	25867168	25867269	.	+	.	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
Phchi.S1	AUGUSTUS	stop_codon	25867270	25867272	.	+	0	transcript_id "Phchi.S1G405200.t2"; gene_id "Phchi.S1G405200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg816.t1 is derived from g10598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5705156	5705749	.	-	.	Phchi.S6G077500
Phchi.S6	AUGUSTUS	transcript	5705156	5705749	.	-	.	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	stop_codon	5705153	5705155	.	-	0	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	CDS	5705156	5705253	0.91	-	2	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	exon	5705156	5705253	.	-	.	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	intron	5705254	5705348	.	-	.	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	CDS	5705349	5705446	1	-	1	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	exon	5705349	5705446	.	-	.	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	intron	5705447	5705519	.	-	.	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	CDS	5705520	5705749	0.97	-	0	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	exon	5705520	5705749	.	-	.	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
Phchi.S6	AUGUSTUS	start_codon	5705747	5705749	.	-	0	transcript_id "Phchi.S6G077500.t1"; gene_id "Phchi.S6G077500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12955.t1 is derived from g11420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3296384	3297928	.	+	.	Phchi.S3G027400
Phchi.S3	AUGUSTUS	transcript	3296384	3297928	.	+	.	transcript_id "Phchi.S3G027400.t1"; gene_id "Phchi.S3G027400"
Phchi.S3	AUGUSTUS	start_codon	3296384	3296386	.	+	0	transcript_id "Phchi.S3G027400.t1"; gene_id "Phchi.S3G027400"
Phchi.S3	AUGUSTUS	CDS	3296384	3297928	1	+	0	transcript_id "Phchi.S3G027400.t1"; gene_id "Phchi.S3G027400"
Phchi.S3	AUGUSTUS	exon	3296384	3297928	.	+	.	transcript_id "Phchi.S3G027400.t1"; gene_id "Phchi.S3G027400"
Phchi.S3	AUGUSTUS	stop_codon	3297929	3297931	.	+	0	transcript_id "Phchi.S3G027400.t1"; gene_id "Phchi.S3G027400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10813.t1 is derived from g14863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2216622	2226754	.	+	.	Phchi.S4G039500
Phchi.S4	AUGUSTUS	transcript	2216622	2226754	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	start_codon	2216622	2216624	.	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2216622	2216746	0.32	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2216622	2216746	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2216747	2216850	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2216851	2217101	0.76	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2216851	2217101	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2217102	2217244	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2217245	2217427	1	+	2	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2217245	2217427	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2217428	2217563	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2217564	2217699	1	+	2	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2217564	2217699	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2217700	2217796	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2217797	2217927	0.99	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2217797	2217927	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2217928	2218047	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2218048	2218162	1	+	2	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2218048	2218162	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2218163	2218295	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2218296	2219388	0.99	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2218296	2219388	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2219389	2219504	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2219505	2219606	0.96	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2219505	2219606	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2219607	2219723	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2219724	2219782	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2219724	2219782	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2219783	2219917	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2219918	2220095	1	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2219918	2220095	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2220096	2220174	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2220175	2220448	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2220175	2220448	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2220449	2220534	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2220535	2220685	0.92	+	2	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2220535	2220685	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2220686	2220792	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2220793	2220904	0.92	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2220793	2220904	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2220905	2220995	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2220996	2221161	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2220996	2221161	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2221162	2221307	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2221308	2221378	1	+	2	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2221308	2221378	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2221379	2221485	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2221486	2221577	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2221486	2221577	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2221578	2221668	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2221669	2221831	1	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2221669	2221831	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2221832	2221923	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2221924	2221995	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2221924	2221995	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2221996	2222088	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2222089	2222463	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2222089	2222463	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2222464	2222539	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2222540	2222655	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2222540	2222655	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2222656	2222800	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2222801	2223098	0.99	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2222801	2223098	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2223099	2223197	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2223198	2223514	0.98	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2223198	2223514	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2223515	2223602	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2223603	2223948	1	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2223603	2223948	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2223949	2224030	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2224031	2224360	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2224031	2224360	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2224361	2224470	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2224471	2224575	0.97	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2224471	2224575	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2224576	2224693	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2224694	2224822	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2224694	2224822	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2224823	2224918	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2224919	2225299	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2224919	2225299	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2225300	2225420	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2225421	2225558	1	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2225421	2225558	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2225559	2225693	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2225694	2225930	0.98	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2225694	2225930	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2225931	2226010	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2226011	2226280	0.97	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2226011	2226280	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2226281	2226390	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2226391	2226425	0.99	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2226391	2226425	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2226426	2226517	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2226518	2226593	1	+	1	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2226518	2226593	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	intron	2226594	2226691	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	CDS	2226692	2226754	0.99	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	exon	2226692	2226754	.	+	.	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
Phchi.S4	AUGUSTUS	stop_codon	2226755	2226757	.	+	0	transcript_id "Phchi.S4G039500.t1"; gene_id "Phchi.S4G039500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7579.t1 is derived from g4753.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30135363	30135972	.	+	.	Phchi.S1G473800
Phchi.S1	AUGUSTUS	transcript	30135363	30135972	.	+	.	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	start_codon	30135363	30135365	.	+	0	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	CDS	30135363	30135512	0.89	+	0	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	exon	30135363	30135512	.	+	.	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	intron	30135513	30135652	.	+	.	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	CDS	30135653	30135699	1	+	0	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	exon	30135653	30135699	.	+	.	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	intron	30135700	30135788	.	+	.	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	CDS	30135789	30135972	0.69	+	1	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	exon	30135789	30135972	.	+	.	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	stop_codon	30135973	30135975	.	+	0	transcript_id "Phchi.S1G473800.t1"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	transcript	30135363	30135972	.	+	.	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	start_codon	30135363	30135365	.	+	0	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	CDS	30135363	30135512	0.66	+	0	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	exon	30135363	30135512	.	+	.	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	intron	30135513	30135598	.	+	.	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	CDS	30135599	30135699	0.76	+	0	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	exon	30135599	30135699	.	+	.	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	intron	30135700	30135788	.	+	.	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	CDS	30135789	30135972	0.71	+	1	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	exon	30135789	30135972	.	+	.	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
Phchi.S1	AUGUSTUS	stop_codon	30135973	30135975	.	+	0	transcript_id "Phchi.S1G473800.t2"; gene_id "Phchi.S1G473800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14425.t1 is derived from g12893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12754461	12756491	.	+	.	Phchi.S3G174400
Phchi.S3	AUGUSTUS	transcript	12754461	12756491	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	start_codon	12754461	12754463	.	+	0	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	CDS	12754461	12754508	0.32	+	0	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	exon	12754461	12754508	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	intron	12754509	12754685	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	CDS	12754686	12754823	1	+	0	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	exon	12754686	12754823	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	intron	12754824	12754992	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	CDS	12754993	12755073	0.94	+	0	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	exon	12754993	12755073	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	intron	12755074	12755198	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	CDS	12755199	12756491	0.97	+	0	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	exon	12755199	12756491	.	+	.	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
Phchi.S3	AUGUSTUS	stop_codon	12756492	12756494	.	+	0	transcript_id "Phchi.S3G174400.t1"; gene_id "Phchi.S3G174400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4976.t1 is derived from g2146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13839463	13839939	.	-	.	Phchi.S1G213500
Phchi.S1	AUGUSTUS	transcript	13839463	13839939	.	-	.	transcript_id "Phchi.S1G213500.t1"; gene_id "Phchi.S1G213500"
Phchi.S1	AUGUSTUS	stop_codon	13839460	13839462	.	-	0	transcript_id "Phchi.S1G213500.t1"; gene_id "Phchi.S1G213500"
Phchi.S1	AUGUSTUS	CDS	13839463	13839939	1	-	0	transcript_id "Phchi.S1G213500.t1"; gene_id "Phchi.S1G213500"
Phchi.S1	AUGUSTUS	exon	13839463	13839939	.	-	.	transcript_id "Phchi.S1G213500.t1"; gene_id "Phchi.S1G213500"
Phchi.S1	AUGUSTUS	start_codon	13839937	13839939	.	-	0	transcript_id "Phchi.S1G213500.t1"; gene_id "Phchi.S1G213500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7482.t1 is derived from g4655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29569547	29572045	.	+	.	Phchi.S1G464100
Phchi.S1	AUGUSTUS	transcript	29569547	29572045	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	start_codon	29569547	29569549	.	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29569547	29569877	0.91	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29569547	29569877	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29569878	29569981	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29569982	29570050	1	+	2	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29569982	29570050	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570051	29570259	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570260	29570318	1	+	2	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570260	29570318	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570319	29570496	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570497	29570583	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570497	29570583	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570584	29570715	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570716	29570783	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570716	29570783	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570784	29570866	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570867	29570937	0.96	+	1	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570867	29570937	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570938	29571055	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571056	29571110	1	+	2	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571056	29571110	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571111	29571201	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571202	29571259	1	+	1	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571202	29571259	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571260	29571358	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571359	29571409	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571359	29571409	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571410	29571496	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571497	29571547	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571497	29571547	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571548	29571670	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571671	29571712	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571671	29571712	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571713	29571803	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571804	29571914	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571804	29571914	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571915	29572000	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29572001	29572045	1	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29572001	29572045	.	+	.	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	stop_codon	29572046	29572048	.	+	0	transcript_id "Phchi.S1G464100.t1"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	transcript	29569991	29572045	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	start_codon	29569991	29569993	.	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29569991	29570050	0.85	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29569991	29570050	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570051	29570198	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570199	29570318	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570199	29570318	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570319	29570496	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570497	29570583	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570497	29570583	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570584	29570715	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570716	29570783	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570716	29570783	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570784	29570866	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29570867	29570937	0.95	+	1	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29570867	29570937	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29570938	29571055	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571056	29571110	1	+	2	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571056	29571110	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571111	29571201	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571202	29571259	1	+	1	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571202	29571259	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571260	29571358	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571359	29571409	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571359	29571409	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571410	29571496	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571497	29571547	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571497	29571547	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571548	29571670	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571671	29571712	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571671	29571712	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571713	29571803	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29571804	29571914	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29571804	29571914	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	intron	29571915	29572000	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	CDS	29572001	29572045	1	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	exon	29572001	29572045	.	+	.	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
Phchi.S1	AUGUSTUS	stop_codon	29572046	29572048	.	+	0	transcript_id "Phchi.S1G464100.t2"; gene_id "Phchi.S1G464100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6799.t1 is derived from g3971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25118530	25120425	.	+	.	Phchi.S1G395800
Phchi.S1	AUGUSTUS	transcript	25118530	25120425	.	+	.	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	start_codon	25118530	25118532	.	+	0	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	CDS	25118530	25118938	1	+	0	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	exon	25118530	25118938	.	+	.	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	intron	25118939	25119088	.	+	.	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	CDS	25119089	25120425	1	+	2	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	exon	25119089	25120425	.	+	.	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	stop_codon	25120426	25120428	.	+	0	transcript_id "Phchi.S1G395800.t1"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	transcript	25118530	25120255	.	+	.	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	start_codon	25118530	25118532	.	+	0	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	CDS	25118530	25118938	0.99	+	0	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	exon	25118530	25118938	.	+	.	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	intron	25118939	25119088	.	+	.	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	CDS	25119089	25120136	0.31	+	2	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	exon	25119089	25120136	.	+	.	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	intron	25120137	25120224	.	+	.	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	CDS	25120225	25120255	0.51	+	1	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	exon	25120225	25120255	.	+	.	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
Phchi.S1	AUGUSTUS	stop_codon	25120256	25120258	.	+	0	transcript_id "Phchi.S1G395800.t2"; gene_id "Phchi.S1G395800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg456.t1 is derived from g10238.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3187228	3196689	.	-	.	Phchi.S6G041500
Phchi.S6	AUGUSTUS	transcript	3187228	3196689	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	stop_codon	3187225	3187227	.	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3187228	3187377	0.98	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3187228	3187377	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3187378	3187456	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3187457	3187726	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3187457	3187726	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3187727	3187796	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3187797	3187988	0.99	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3187797	3187988	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3187989	3188090	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3188091	3188323	0.99	-	2	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3188091	3188323	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3188324	3188488	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3188489	3188637	1	-	1	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3188489	3188637	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3188638	3188730	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3188731	3189014	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3188731	3189014	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3189015	3189147	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3189148	3189446	0.64	-	2	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3189148	3189446	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3189447	3189577	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3189578	3189962	0.65	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3189578	3189962	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3189963	3190300	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3190301	3190438	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3190301	3190438	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3190439	3190556	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3190557	3190622	0.99	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3190557	3190622	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3190623	3190733	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3190734	3190991	0.99	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3190734	3190991	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3190992	3191073	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191074	3191196	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191074	3191196	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3191197	3191282	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191283	3191342	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191283	3191342	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3191343	3191434	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191435	3191623	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191435	3191623	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3191624	3191702	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191703	3192216	0.96	-	1	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191703	3192216	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3192217	3192447	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3192448	3192605	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3192448	3192605	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3192606	3192694	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3192695	3192778	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3192695	3192778	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3192779	3192921	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3192922	3193155	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3192922	3193155	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193156	3193292	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193293	3193355	0.99	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193293	3193355	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193356	3193563	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193564	3193647	0.95	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193564	3193647	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193648	3193738	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193739	3193843	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193739	3193843	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193844	3193946	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193947	3194006	1	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193947	3194006	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3194007	3194109	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3194110	3194308	0.99	-	1	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3194110	3194308	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3194309	3194605	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3194606	3196689	0.52	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3194606	3196689	.	-	.	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	start_codon	3196687	3196689	.	-	0	transcript_id "Phchi.S6G041500.t1"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	transcript	3187228	3196689	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	stop_codon	3187225	3187227	.	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3187228	3187377	0.99	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3187228	3187377	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3187378	3187456	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3187457	3187726	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3187457	3187726	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3187727	3187796	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3187797	3187988	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3187797	3187988	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3187989	3188090	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3188091	3188323	1	-	2	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3188091	3188323	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3188324	3188488	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3188489	3188637	1	-	1	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3188489	3188637	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3188638	3188730	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3188731	3189014	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3188731	3189014	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3189015	3189147	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3189148	3189446	0.55	-	2	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3189148	3189446	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3189447	3189577	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3189578	3189962	0.57	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3189578	3189962	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3189963	3190300	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3190301	3190438	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3190301	3190438	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3190439	3190556	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3190557	3190622	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3190557	3190622	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3190623	3190733	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3190734	3190991	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3190734	3190991	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3190992	3191073	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191074	3191196	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191074	3191196	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3191197	3191282	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191283	3191342	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191283	3191342	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3191343	3191434	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191435	3191623	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191435	3191623	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3191624	3191702	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3191703	3192216	0.97	-	1	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3191703	3192216	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3192217	3192447	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3192448	3192605	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3192448	3192605	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3192606	3192694	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3192695	3192778	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3192695	3192778	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3192779	3192921	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3192922	3193155	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3192922	3193155	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193156	3193292	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193293	3193355	1	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193293	3193355	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193356	3193484	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193485	3193625	0.73	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193485	3193625	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193626	3193738	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193739	3193843	0.91	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193739	3193843	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3193844	3193946	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3193947	3194006	0.99	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3193947	3194006	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3194007	3194109	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3194110	3194308	1	-	1	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3194110	3194308	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	intron	3194309	3194605	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	CDS	3194606	3196689	0.57	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	exon	3194606	3196689	.	-	.	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
Phchi.S6	AUGUSTUS	start_codon	3196687	3196689	.	-	0	transcript_id "Phchi.S6G041500.t2"; gene_id "Phchi.S6G041500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7021.t1 is derived from g4193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26434330	26436151	.	-	.	Phchi.S1G418000
Phchi.S1	AUGUSTUS	transcript	26434330	26436151	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	stop_codon	26434327	26434329	.	-	0	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	CDS	26434330	26434749	0.49	-	0	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	exon	26434330	26434749	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	intron	26434750	26434822	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	CDS	26434823	26434863	0.92	-	2	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	exon	26434823	26434863	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	intron	26434864	26435439	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	CDS	26435440	26435475	0.97	-	2	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	exon	26435440	26435475	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	intron	26435476	26435619	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	CDS	26435620	26435664	0.84	-	2	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	exon	26435620	26435664	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	intron	26435665	26435766	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	CDS	26435767	26435787	0.58	-	2	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	exon	26435767	26435787	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	intron	26435788	26435955	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	CDS	26435956	26436151	0.56	-	0	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	exon	26435956	26436151	.	-	.	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
Phchi.S1	AUGUSTUS	start_codon	26436149	26436151	.	-	0	transcript_id "Phchi.S1G418000.t1"; gene_id "Phchi.S1G418000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3671.t1 is derived from g840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5112639	5113079	.	+	.	Phchi.S1G083000
Phchi.S1	AUGUSTUS	transcript	5112639	5113079	.	+	.	transcript_id "Phchi.S1G083000.t1"; gene_id "Phchi.S1G083000"
Phchi.S1	AUGUSTUS	start_codon	5112639	5112641	.	+	0	transcript_id "Phchi.S1G083000.t1"; gene_id "Phchi.S1G083000"
Phchi.S1	AUGUSTUS	CDS	5112639	5113079	0.61	+	0	transcript_id "Phchi.S1G083000.t1"; gene_id "Phchi.S1G083000"
Phchi.S1	AUGUSTUS	exon	5112639	5113079	.	+	.	transcript_id "Phchi.S1G083000.t1"; gene_id "Phchi.S1G083000"
Phchi.S1	AUGUSTUS	stop_codon	5113080	5113082	.	+	0	transcript_id "Phchi.S1G083000.t1"; gene_id "Phchi.S1G083000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13405.t1 is derived from g11871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6551059	6551522	.	+	.	Phchi.S3G072400
Phchi.S3	AUGUSTUS	transcript	6551059	6551522	.	+	.	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	start_codon	6551059	6551061	.	+	0	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	CDS	6551059	6551206	0.28	+	0	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	exon	6551059	6551206	.	+	.	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	intron	6551207	6551274	.	+	.	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	CDS	6551275	6551522	0.39	+	2	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	exon	6551275	6551522	.	+	.	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
Phchi.S3	AUGUSTUS	stop_codon	6551523	6551525	.	+	0	transcript_id "Phchi.S3G072400.t1"; gene_id "Phchi.S3G072400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11023.t1 is derived from g15073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3690289	3690909	.	+	.	Phchi.S4G060500
Phchi.S4	AUGUSTUS	transcript	3690289	3690909	.	+	.	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	start_codon	3690289	3690291	.	+	0	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	CDS	3690289	3690512	0.85	+	0	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	exon	3690289	3690512	.	+	.	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	intron	3690513	3690593	.	+	.	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	CDS	3690594	3690909	0.83	+	1	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	exon	3690594	3690909	.	+	.	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
Phchi.S4	AUGUSTUS	stop_codon	3690910	3690912	.	+	0	transcript_id "Phchi.S4G060500.t1"; gene_id "Phchi.S4G060500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4580.t1 is derived from g1750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11196454	11198293	.	+	.	Phchi.S1G173900
Phchi.S1	AUGUSTUS	transcript	11196454	11198293	.	+	.	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	start_codon	11196454	11196456	.	+	0	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	CDS	11196454	11196586	0.97	+	0	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	exon	11196454	11196586	.	+	.	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	intron	11196587	11196674	.	+	.	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	CDS	11196675	11198293	0.92	+	2	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	exon	11196675	11198293	.	+	.	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
Phchi.S1	AUGUSTUS	stop_codon	11198294	11198296	.	+	0	transcript_id "Phchi.S1G173900.t1"; gene_id "Phchi.S1G173900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg590.t1 is derived from g10372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4322092	4322933	.	+	.	Phchi.S6G054900
Phchi.S6	AUGUSTUS	transcript	4322092	4322933	.	+	.	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	start_codon	4322092	4322094	.	+	0	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	CDS	4322092	4322337	1	+	0	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	exon	4322092	4322337	.	+	.	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	intron	4322338	4322432	.	+	.	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	CDS	4322433	4322576	1	+	0	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	exon	4322433	4322576	.	+	.	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	intron	4322577	4322666	.	+	.	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	CDS	4322667	4322933	1	+	0	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	exon	4322667	4322933	.	+	.	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
Phchi.S6	AUGUSTUS	stop_codon	4322934	4322936	.	+	0	transcript_id "Phchi.S6G054900.t1"; gene_id "Phchi.S6G054900"
# This transcript jg13801.t2 is derived from g12268.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13802.t1 is derived from g12269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8958948	8959657	.	+	.	Phchi.S3G112100
Phchi.S3	AUGUSTUS	transcript	8958948	8959657	.	+	.	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	start_codon	8958948	8958950	.	+	0	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	CDS	8958948	8959049	1	+	0	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	exon	8958948	8959049	.	+	.	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	intron	8959050	8959295	.	+	.	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	CDS	8959296	8959495	1	+	0	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	exon	8959296	8959495	.	+	.	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	intron	8959496	8959629	.	+	.	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	CDS	8959630	8959657	1	+	1	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	exon	8959630	8959657	.	+	.	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
Phchi.S3	AUGUSTUS	stop_codon	8959658	8959660	.	+	0	transcript_id "Phchi.S3G112100.t1"; gene_id "Phchi.S3G112100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6268.t1 is derived from g3440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21936114	21940905	.	-	.	Phchi.S1G342700
Phchi.S1	AUGUSTUS	transcript	21936114	21940905	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	stop_codon	21936111	21936113	.	-	0	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	CDS	21936114	21936179	1	-	0	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	exon	21936114	21936179	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	intron	21936180	21936586	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	CDS	21936587	21936713	1	-	1	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	exon	21936587	21936713	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	intron	21936714	21936886	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	CDS	21936887	21937051	0.95	-	1	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	exon	21936887	21937051	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	intron	21937052	21940315	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	CDS	21940316	21940905	0.94	-	0	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	exon	21940316	21940905	.	-	.	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
Phchi.S1	AUGUSTUS	start_codon	21940903	21940905	.	-	0	transcript_id "Phchi.S1G342700.t1"; gene_id "Phchi.S1G342700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4042.t1 is derived from g1211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7327619	7328218	.	-	.	Phchi.S1G120100
Phchi.S1	AUGUSTUS	transcript	7327619	7328218	.	-	.	transcript_id "Phchi.S1G120100.t1"; gene_id "Phchi.S1G120100"
Phchi.S1	AUGUSTUS	stop_codon	7327616	7327618	.	-	0	transcript_id "Phchi.S1G120100.t1"; gene_id "Phchi.S1G120100"
Phchi.S1	AUGUSTUS	CDS	7327619	7328218	1	-	0	transcript_id "Phchi.S1G120100.t1"; gene_id "Phchi.S1G120100"
Phchi.S1	AUGUSTUS	exon	7327619	7328218	.	-	.	transcript_id "Phchi.S1G120100.t1"; gene_id "Phchi.S1G120100"
Phchi.S1	AUGUSTUS	start_codon	7328216	7328218	.	-	0	transcript_id "Phchi.S1G120100.t1"; gene_id "Phchi.S1G120100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2532.t1 is derived from g9452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7183819	7184904	.	+	.	Phchi.S5G114100
Phchi.S5	AUGUSTUS	transcript	7183819	7184904	.	+	.	transcript_id "Phchi.S5G114100.t1"; gene_id "Phchi.S5G114100"
Phchi.S5	AUGUSTUS	start_codon	7183819	7183821	.	+	0	transcript_id "Phchi.S5G114100.t1"; gene_id "Phchi.S5G114100"
Phchi.S5	AUGUSTUS	CDS	7183819	7184904	1	+	0	transcript_id "Phchi.S5G114100.t1"; gene_id "Phchi.S5G114100"
Phchi.S5	AUGUSTUS	exon	7183819	7184904	.	+	.	transcript_id "Phchi.S5G114100.t1"; gene_id "Phchi.S5G114100"
Phchi.S5	AUGUSTUS	stop_codon	7184905	7184907	.	+	0	transcript_id "Phchi.S5G114100.t1"; gene_id "Phchi.S5G114100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13596.t1 is derived from g12063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7627988	7629445	.	-	.	Phchi.S3G091500
Phchi.S3	AUGUSTUS	transcript	7627988	7629445	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	stop_codon	7627985	7627987	.	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7627988	7628197	1	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7627988	7628197	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	intron	7628198	7628300	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7628301	7628402	1	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7628301	7628402	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	intron	7628403	7628479	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7628480	7628572	0.57	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7628480	7628572	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	intron	7628573	7628661	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7628662	7628673	0.57	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7628662	7628673	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	intron	7628674	7628758	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7628759	7628850	0.59	-	2	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7628759	7628850	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	intron	7628851	7628936	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7628937	7629085	0.59	-	1	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7628937	7629085	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	intron	7629086	7629335	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	CDS	7629336	7629445	0.45	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	exon	7629336	7629445	.	-	.	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
Phchi.S3	AUGUSTUS	start_codon	7629443	7629445	.	-	0	transcript_id "Phchi.S3G091500.t1"; gene_id "Phchi.S3G091500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9323.t1 is derived from g6498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40939816	40944226	.	-	.	Phchi.S1G648200
Phchi.S1	AUGUSTUS	transcript	40939816	40944226	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	stop_codon	40939813	40939815	.	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	CDS	40939816	40941168	0.67	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	exon	40939816	40941168	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	intron	40941169	40941314	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	CDS	40941315	40942099	0.98	-	2	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	exon	40941315	40942099	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	intron	40942100	40942190	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	CDS	40942191	40942392	0.67	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	exon	40942191	40942392	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	intron	40942393	40942518	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	CDS	40942519	40943664	0.53	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	exon	40942519	40943664	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	intron	40943665	40943732	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	CDS	40943733	40943783	0.99	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	exon	40943733	40943783	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	intron	40943784	40943920	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	CDS	40943921	40944226	0.74	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	exon	40943921	40944226	.	-	.	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
Phchi.S1	AUGUSTUS	start_codon	40944224	40944226	.	-	0	transcript_id "Phchi.S1G648200.t1"; gene_id "Phchi.S1G648200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14876.t1 is derived from g13344.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15239010	15244555	.	-	.	Phchi.S3G219500
Phchi.S3	AUGUSTUS	transcript	15239940	15244555	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	stop_codon	15239937	15239939	.	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15239940	15240054	0.76	-	1	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15239940	15240054	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240055	15240218	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240219	15240307	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240219	15240307	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240308	15240418	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240419	15240674	1	-	1	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240419	15240674	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240675	15240758	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240759	15240823	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240759	15240823	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240824	15240965	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240966	15241049	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240966	15241049	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241050	15241137	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241138	15241215	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241138	15241215	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241216	15241295	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241296	15241382	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241296	15241382	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241383	15241514	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241515	15241746	1	-	1	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241515	15241746	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241747	15241841	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241842	15241897	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241842	15241897	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241898	15242064	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15242065	15242121	1	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15242065	15242121	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15242122	15243564	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15243565	15243661	1	-	1	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15243565	15243661	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15243662	15243744	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15243745	15244284	0.61	-	1	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15243745	15244284	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15244285	15244445	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15244446	15244555	0.9	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15244446	15244555	.	-	.	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	start_codon	15244553	15244555	.	-	0	transcript_id "Phchi.S3G219500.t1"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	transcript	15239010	15244555	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	stop_codon	15239007	15239009	.	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15239010	15239048	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15239010	15239048	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15239049	15239146	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15239147	15239261	0.93	-	1	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15239147	15239261	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15239262	15240218	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240219	15240307	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240219	15240307	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240308	15240418	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240419	15240674	1	-	1	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240419	15240674	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240675	15240758	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240759	15240823	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240759	15240823	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15240824	15240965	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15240966	15241049	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15240966	15241049	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241050	15241137	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241138	15241215	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241138	15241215	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241216	15241295	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241296	15241382	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241296	15241382	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241383	15241514	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241515	15241746	1	-	1	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241515	15241746	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241747	15241841	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15241842	15241897	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15241842	15241897	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15241898	15242064	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15242065	15242121	1	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15242065	15242121	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15242122	15242539	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15242540	15242647	0.8	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15242540	15242647	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15242648	15243564	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15243565	15243661	1	-	1	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15243565	15243661	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15243662	15243744	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15243745	15244284	0.63	-	1	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15243745	15244284	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	intron	15244285	15244445	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	CDS	15244446	15244555	0.88	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	exon	15244446	15244555	.	-	.	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
Phchi.S3	AUGUSTUS	start_codon	15244553	15244555	.	-	0	transcript_id "Phchi.S3G219500.t2"; gene_id "Phchi.S3G219500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14437.t1 is derived from g12905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12815429	12816937	.	+	.	Phchi.S3G175600
Phchi.S3	AUGUSTUS	transcript	12815429	12816937	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	start_codon	12815429	12815431	.	+	0	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	CDS	12815429	12815682	0.8	+	0	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	exon	12815429	12815682	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	intron	12815683	12816363	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	CDS	12816364	12816416	0.96	+	1	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	exon	12816364	12816416	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	intron	12816417	12816492	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	CDS	12816493	12816568	1	+	2	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	exon	12816493	12816568	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	intron	12816569	12816870	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	CDS	12816871	12816937	1	+	1	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	exon	12816871	12816937	.	+	.	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
Phchi.S3	AUGUSTUS	stop_codon	12816938	12816940	.	+	0	transcript_id "Phchi.S3G175600.t1"; gene_id "Phchi.S3G175600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5564.t1 is derived from g2734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17605804	17606993	.	-	.	Phchi.S1G272300
Phchi.S1	AUGUSTUS	transcript	17605804	17606993	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	stop_codon	17605801	17605803	.	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17605804	17605987	1	-	1	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17605804	17605987	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	intron	17605988	17606084	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17606085	17606116	1	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17606085	17606116	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	intron	17606117	17606211	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17606212	17606217	0.99	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17606212	17606217	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	intron	17606218	17606306	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17606307	17606381	0.98	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17606307	17606381	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	intron	17606382	17606456	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17606457	17606561	1	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17606457	17606561	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	intron	17606562	17606643	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17606644	17606762	1	-	2	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17606644	17606762	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	intron	17606763	17606836	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	CDS	17606837	17606993	0.71	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	exon	17606837	17606993	.	-	.	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
Phchi.S1	AUGUSTUS	start_codon	17606991	17606993	.	-	0	transcript_id "Phchi.S1G272300.t1"; gene_id "Phchi.S1G272300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13517.t1 is derived from g11984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7271409	7272782	.	-	.	Phchi.S3G083600
Phchi.S3	AUGUSTUS	transcript	7271409	7272782	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	stop_codon	7271406	7271408	.	-	0	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	CDS	7271409	7271682	0.96	-	1	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	exon	7271409	7271682	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	intron	7271683	7271774	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	CDS	7271775	7271836	1	-	0	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	exon	7271775	7271836	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	intron	7271837	7271971	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	CDS	7271972	7272172	0.98	-	0	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	exon	7271972	7272172	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	intron	7272173	7272313	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	CDS	7272314	7272538	0.97	-	0	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	exon	7272314	7272538	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	intron	7272539	7272635	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	CDS	7272636	7272782	0.98	-	0	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	exon	7272636	7272782	.	-	.	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
Phchi.S3	AUGUSTUS	start_codon	7272780	7272782	.	-	0	transcript_id "Phchi.S3G083600.t1"; gene_id "Phchi.S3G083600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9410.t1 is derived from g6586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41367007	41367573	.	+	.	Phchi.S1G656900
Phchi.S1	AUGUSTUS	transcript	41367007	41367573	.	+	.	transcript_id "Phchi.S1G656900.t1"; gene_id "Phchi.S1G656900"
Phchi.S1	AUGUSTUS	start_codon	41367007	41367009	.	+	0	transcript_id "Phchi.S1G656900.t1"; gene_id "Phchi.S1G656900"
Phchi.S1	AUGUSTUS	CDS	41367007	41367573	0.58	+	0	transcript_id "Phchi.S1G656900.t1"; gene_id "Phchi.S1G656900"
Phchi.S1	AUGUSTUS	exon	41367007	41367573	.	+	.	transcript_id "Phchi.S1G656900.t1"; gene_id "Phchi.S1G656900"
Phchi.S1	AUGUSTUS	stop_codon	41367574	41367576	.	+	0	transcript_id "Phchi.S1G656900.t1"; gene_id "Phchi.S1G656900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11121.t1 is derived from g15171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4257128	4263124	.	+	.	Phchi.S4G070300
Phchi.S4	AUGUSTUS	transcript	4257128	4263124	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	start_codon	4257128	4257130	.	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4257128	4257283	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4257128	4257283	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4257284	4257742	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4257743	4257906	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4257743	4257906	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4257907	4258005	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4258006	4258120	1	+	1	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4258006	4258120	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4258121	4258219	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4258220	4258297	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4258220	4258297	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4258298	4258398	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4258399	4258467	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4258399	4258467	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4258468	4258561	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4258562	4258640	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4258562	4258640	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4258641	4258723	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4258724	4258800	1	+	2	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4258724	4258800	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4258801	4258945	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4258946	4259041	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4258946	4259041	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4259042	4259209	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4259210	4259354	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4259210	4259354	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4259355	4259627	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4259628	4259762	1	+	2	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4259628	4259762	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4259763	4259933	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4259934	4259998	1	+	2	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4259934	4259998	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4259999	4260134	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4260135	4260458	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4260135	4260458	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4260459	4260575	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4260576	4260701	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4260576	4260701	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4260702	4260859	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4260860	4260961	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4260860	4260961	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4260962	4261050	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4261051	4261197	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4261051	4261197	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4261198	4261393	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4261394	4261492	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4261394	4261492	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4261493	4261577	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4261578	4261666	1	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4261578	4261666	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4261667	4261771	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4261772	4261898	1	+	1	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4261772	4261898	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4261899	4262017	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4262018	4262111	0.78	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4262018	4262111	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4262112	4262212	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4262213	4262223	0.79	+	2	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4262213	4262223	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	intron	4262224	4262302	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	CDS	4262303	4263124	0.97	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	exon	4262303	4263124	.	+	.	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
Phchi.S4	AUGUSTUS	stop_codon	4263125	4263127	.	+	0	transcript_id "Phchi.S4G070300.t1"; gene_id "Phchi.S4G070300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6196.t1 is derived from g3367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21439049	21441765	.	-	.	Phchi.S1G335500
Phchi.S1	AUGUSTUS	transcript	21439049	21441765	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	stop_codon	21439046	21439048	.	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21439049	21439318	1	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21439049	21439318	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21439319	21439408	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21439409	21439588	1	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21439409	21439588	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21439589	21439695	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21439696	21439803	0.98	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21439696	21439803	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21439804	21439913	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21439914	21440135	0.7	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21439914	21440135	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21440136	21440397	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21440398	21440475	0.7	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21440398	21440475	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21440476	21440581	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21440582	21440662	0.99	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21440582	21440662	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21440663	21440806	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21440807	21440897	0.99	-	1	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21440807	21440897	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21440898	21440994	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21440995	21441058	0.99	-	2	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21440995	21441058	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21441059	21441190	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21441191	21441293	0.98	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21441191	21441293	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21441294	21441407	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21441408	21441522	0.84	-	1	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21441408	21441522	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	intron	21441523	21441631	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	CDS	21441632	21441765	0.84	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	exon	21441632	21441765	.	-	.	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
Phchi.S1	AUGUSTUS	start_codon	21441763	21441765	.	-	0	transcript_id "Phchi.S1G335500.t1"; gene_id "Phchi.S1G335500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13620.t1 is derived from g12087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7777069	7778612	.	+	.	Phchi.S3G093900
Phchi.S3	AUGUSTUS	transcript	7777069	7778612	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	start_codon	7777069	7777071	.	+	0	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	CDS	7777069	7777116	0.79	+	0	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	exon	7777069	7777116	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	intron	7777117	7777675	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	CDS	7777676	7777752	1	+	0	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	exon	7777676	7777752	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	intron	7777753	7777907	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	CDS	7777908	7777992	1	+	1	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	exon	7777908	7777992	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	intron	7777993	7778120	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	CDS	7778121	7778612	0.89	+	0	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	exon	7778121	7778612	.	+	.	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
Phchi.S3	AUGUSTUS	stop_codon	7778613	7778615	.	+	0	transcript_id "Phchi.S3G093900.t1"; gene_id "Phchi.S3G093900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14253.t1 is derived from g12720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11770460	11770934	.	-	.	Phchi.S3G157200
Phchi.S3	AUGUSTUS	transcript	11770460	11770934	.	-	.	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	stop_codon	11770457	11770459	.	-	0	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	CDS	11770460	11770711	0.98	-	0	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	exon	11770460	11770711	.	-	.	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	intron	11770712	11770811	.	-	.	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	CDS	11770812	11770934	0.66	-	0	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	exon	11770812	11770934	.	-	.	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
Phchi.S3	AUGUSTUS	start_codon	11770932	11770934	.	-	0	transcript_id "Phchi.S3G157200.t1"; gene_id "Phchi.S3G157200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15747.t1 is derived from g14217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21045064	21046663	.	-	.	Phchi.S3G306600
Phchi.S3	AUGUSTUS	transcript	21045064	21046663	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	stop_codon	21045061	21045063	.	-	0	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	CDS	21045064	21045653	0.99	-	2	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	exon	21045064	21045653	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	intron	21045654	21045753	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	CDS	21045754	21045868	1	-	0	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	exon	21045754	21045868	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	intron	21045869	21045964	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	CDS	21045965	21046139	1	-	1	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	exon	21045965	21046139	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	intron	21046140	21046277	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	CDS	21046278	21046663	1	-	0	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	exon	21046278	21046663	.	-	.	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
Phchi.S3	AUGUSTUS	start_codon	21046661	21046663	.	-	0	transcript_id "Phchi.S3G306600.t1"; gene_id "Phchi.S3G306600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg452.t1 is derived from g10234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3174066	3175387	.	-	.	Phchi.S6G041100
Phchi.S6	AUGUSTUS	transcript	3174066	3175387	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	stop_codon	3174063	3174065	.	-	0	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	CDS	3174066	3174136	0.52	-	2	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	exon	3174066	3174136	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	intron	3174137	3174288	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	CDS	3174289	3174604	0.31	-	0	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	exon	3174289	3174604	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	intron	3174605	3174687	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	CDS	3174688	3174924	0.98	-	0	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	exon	3174688	3174924	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	intron	3174925	3175000	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	CDS	3175001	3175387	1	-	0	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	exon	3175001	3175387	.	-	.	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
Phchi.S6	AUGUSTUS	start_codon	3175385	3175387	.	-	0	transcript_id "Phchi.S6G041100.t1"; gene_id "Phchi.S6G041100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6459.t1 is derived from g3631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23121579	23122402	.	-	.	Phchi.S1G361800
Phchi.S1	AUGUSTUS	transcript	23121579	23122402	.	-	.	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	stop_codon	23121576	23121578	.	-	0	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	CDS	23121579	23121916	0.79	-	2	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	exon	23121579	23121916	.	-	.	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	intron	23121917	23122008	.	-	.	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	CDS	23122009	23122402	0.99	-	0	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	exon	23122009	23122402	.	-	.	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
Phchi.S1	AUGUSTUS	start_codon	23122400	23122402	.	-	0	transcript_id "Phchi.S1G361800.t1"; gene_id "Phchi.S1G361800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1873.t1 is derived from g8793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3639701	3641654	.	-	.	Phchi.S5G048200
Phchi.S5	AUGUSTUS	transcript	3639701	3641654	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	stop_codon	3639698	3639700	.	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3639701	3639883	0.67	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3639701	3639883	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3639884	3639965	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3639966	3640035	0.44	-	1	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3639966	3640035	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3640036	3640290	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3640291	3640427	0.38	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3640291	3640427	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3640428	3640503	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3640504	3640599	0.63	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3640504	3640599	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3640600	3640697	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3640698	3640804	0.67	-	2	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3640698	3640804	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3640805	3640897	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3640898	3640940	0.7	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3640898	3640940	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3640941	3641298	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3641299	3641382	0.57	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3641299	3641382	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	intron	3641383	3641477	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	CDS	3641478	3641654	0.48	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	exon	3641478	3641654	.	-	.	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
Phchi.S5	AUGUSTUS	start_codon	3641652	3641654	.	-	0	transcript_id "Phchi.S5G048200.t1"; gene_id "Phchi.S5G048200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg890.t1 is derived from g10672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6314204	6315772	.	+	.	Phchi.S6G084900
Phchi.S6	AUGUSTUS	transcript	6314204	6315772	.	+	.	transcript_id "Phchi.S6G084900.t1"; gene_id "Phchi.S6G084900"
Phchi.S6	AUGUSTUS	start_codon	6314204	6314206	.	+	0	transcript_id "Phchi.S6G084900.t1"; gene_id "Phchi.S6G084900"
Phchi.S6	AUGUSTUS	CDS	6314204	6315772	0.91	+	0	transcript_id "Phchi.S6G084900.t1"; gene_id "Phchi.S6G084900"
Phchi.S6	AUGUSTUS	exon	6314204	6315772	.	+	.	transcript_id "Phchi.S6G084900.t1"; gene_id "Phchi.S6G084900"
Phchi.S6	AUGUSTUS	stop_codon	6315773	6315775	.	+	0	transcript_id "Phchi.S6G084900.t1"; gene_id "Phchi.S6G084900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13015.t1 is derived from g11480.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3636288	3639368	.	-	.	Phchi.S3G033400
Phchi.S3	AUGUSTUS	transcript	3636288	3639368	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	stop_codon	3636285	3636287	.	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636288	3636291	1	-	1	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636288	3636291	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636292	3636379	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636380	3636543	1	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636380	3636543	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636544	3636628	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636629	3636723	0.68	-	2	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636629	3636723	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636724	3636832	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636833	3636957	0.45	-	1	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636833	3636957	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636958	3637121	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637122	3637225	0.44	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637122	3637225	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3637226	3637339	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637340	3637454	0.39	-	1	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637340	3637454	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3637455	3637558	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637559	3637629	0.47	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637559	3637629	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3637630	3637730	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637731	3638166	0.57	-	1	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637731	3638166	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638167	3638234	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638235	3638298	0.48	-	2	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638235	3638298	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638299	3638436	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638437	3638534	1	-	1	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638437	3638534	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638535	3638683	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638684	3638817	1	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638684	3638817	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638818	3638912	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638913	3638999	1	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638913	3638999	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3639000	3639125	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3639126	3639368	0.78	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3639126	3639368	.	-	.	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	start_codon	3639366	3639368	.	-	0	transcript_id "Phchi.S3G033400.t1"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	transcript	3636288	3639368	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	stop_codon	3636285	3636287	.	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636288	3636291	0.99	-	1	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636288	3636291	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636292	3636379	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636380	3636543	0.99	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636380	3636543	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636544	3636628	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636629	3636723	0.78	-	2	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636629	3636723	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636724	3636832	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3636833	3636957	0.56	-	1	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3636833	3636957	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3636958	3637121	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637122	3637225	0.41	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637122	3637225	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3637226	3637339	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637340	3637454	0.44	-	1	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637340	3637454	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3637455	3637558	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637559	3637629	0.46	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637559	3637629	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3637630	3637730	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3637731	3638114	0.42	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3637731	3638114	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638115	3638225	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638226	3638311	0.39	-	2	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638226	3638311	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638312	3638436	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638437	3638534	0.59	-	1	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638437	3638534	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638535	3638683	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638684	3638817	1	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638684	3638817	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3638818	3638912	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3638913	3638999	1	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3638913	3638999	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	intron	3639000	3639125	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	CDS	3639126	3639368	0.77	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	exon	3639126	3639368	.	-	.	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
Phchi.S3	AUGUSTUS	start_codon	3639366	3639368	.	-	0	transcript_id "Phchi.S3G033400.t2"; gene_id "Phchi.S3G033400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4693.t1 is derived from g1863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12183262	12184041	.	-	.	Phchi.S1G185200
Phchi.S1	AUGUSTUS	transcript	12183262	12184041	.	-	.	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	stop_codon	12183259	12183261	.	-	0	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	CDS	12183262	12183811	0.56	-	1	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	exon	12183262	12183811	.	-	.	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	intron	12183812	12183922	.	-	.	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	CDS	12183923	12184041	0.57	-	0	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	exon	12183923	12184041	.	-	.	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
Phchi.S1	AUGUSTUS	start_codon	12184039	12184041	.	-	0	transcript_id "Phchi.S1G185200.t1"; gene_id "Phchi.S1G185200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14334.t1 is derived from g12801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12186359	12188723	.	+	.	Phchi.S3G165300
Phchi.S3	AUGUSTUS	transcript	12186359	12188723	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	start_codon	12186359	12186361	.	+	0	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12186359	12186776	1	+	0	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12186359	12186776	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12186777	12186876	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12186877	12186980	1	+	2	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12186877	12186980	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12186981	12187123	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12187124	12187323	1	+	0	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12187124	12187323	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12187324	12187417	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12187418	12187518	1	+	1	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12187418	12187518	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12187519	12187712	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12187713	12187923	1	+	2	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12187713	12187923	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12187924	12188039	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12188040	12188201	1	+	1	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12188040	12188201	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12188202	12188289	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12188290	12188371	1	+	1	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12188290	12188371	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12188372	12188453	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12188454	12188632	0.75	+	0	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12188454	12188632	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	intron	12188633	12188722	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	CDS	12188723	12188723	0.46	+	1	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	exon	12188723	12188723	.	+	.	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
Phchi.S3	AUGUSTUS	stop_codon	12188724	12188726	.	+	0	transcript_id "Phchi.S3G165300.t1"; gene_id "Phchi.S3G165300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg500.t1 is derived from g10282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3478893	3480509	.	-	.	Phchi.S6G045900
Phchi.S6	AUGUSTUS	transcript	3478893	3480448	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	stop_codon	3478890	3478892	.	-	0	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3478893	3478987	0.99	-	2	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3478893	3478987	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3478988	3479074	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479075	3479175	0.66	-	1	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479075	3479175	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479176	3479487	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479488	3479556	0.99	-	1	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479488	3479556	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479557	3479652	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479653	3479744	1	-	0	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479653	3479744	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479745	3479821	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479822	3479858	1	-	1	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479822	3479858	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479859	3480099	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3480100	3480201	1	-	1	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3480100	3480201	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3480202	3480285	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3480286	3480334	1	-	2	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3480286	3480334	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3480335	3480426	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3480427	3480448	0.97	-	0	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3480427	3480448	.	-	.	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	start_codon	3480446	3480448	.	-	0	transcript_id "Phchi.S6G045900.t1"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	transcript	3478893	3480509	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	stop_codon	3478890	3478892	.	-	0	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3478893	3478987	1	-	2	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3478893	3478987	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3478988	3479074	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479075	3479175	0.62	-	1	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479075	3479175	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479176	3479487	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479488	3479556	0.96	-	1	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479488	3479556	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479557	3479652	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479653	3479744	1	-	0	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479653	3479744	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479745	3479821	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3479822	3479858	0.99	-	1	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3479822	3479858	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3479859	3480099	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3480100	3480201	0.88	-	1	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3480100	3480201	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3480202	3480285	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3480286	3480321	0.7	-	1	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3480286	3480321	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	intron	3480322	3480426	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	CDS	3480427	3480509	0.7	-	0	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	exon	3480427	3480509	.	-	.	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
Phchi.S6	AUGUSTUS	start_codon	3480507	3480509	.	-	0	transcript_id "Phchi.S6G045900.t2"; gene_id "Phchi.S6G045900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12579.t1 is derived from g8256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35821225	35821662	.	-	.	Phchi.S2G065900
Phchi.S2	AUGUSTUS	transcript	35821225	35821662	.	-	.	transcript_id "Phchi.S2G065900.t1"; gene_id "Phchi.S2G065900"
Phchi.S2	AUGUSTUS	stop_codon	35821222	35821224	.	-	0	transcript_id "Phchi.S2G065900.t1"; gene_id "Phchi.S2G065900"
Phchi.S2	AUGUSTUS	CDS	35821225	35821662	0.8	-	0	transcript_id "Phchi.S2G065900.t1"; gene_id "Phchi.S2G065900"
Phchi.S2	AUGUSTUS	exon	35821225	35821662	.	-	.	transcript_id "Phchi.S2G065900.t1"; gene_id "Phchi.S2G065900"
Phchi.S2	AUGUSTUS	start_codon	35821660	35821662	.	-	0	transcript_id "Phchi.S2G065900.t1"; gene_id "Phchi.S2G065900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4880.t1 is derived from g2050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13195895	13199286	.	+	.	Phchi.S1G203900
Phchi.S1	AUGUSTUS	transcript	13195895	13199286	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	start_codon	13195895	13195897	.	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13195895	13195971	0.98	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13195895	13195971	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13195972	13196069	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13196070	13196229	1	+	1	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13196070	13196229	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13196230	13196338	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13196339	13196593	1	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13196339	13196593	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13196594	13196683	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13196684	13196712	0.96	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13196684	13196712	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13196713	13196780	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13196781	13196857	0.96	+	1	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13196781	13196857	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13196858	13196983	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13196984	13197045	1	+	2	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13196984	13197045	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13197046	13197190	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13197191	13197354	1	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13197191	13197354	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13197355	13197460	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13197461	13197561	1	+	1	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13197461	13197561	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13197562	13197653	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13197654	13197712	1	+	2	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13197654	13197712	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13197713	13197863	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13197864	13197998	1	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13197864	13197998	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13197999	13198080	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13198081	13198268	1	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13198081	13198268	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13198269	13198356	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13198357	13198504	1	+	1	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13198357	13198504	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13198505	13198622	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13198623	13198731	0.94	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13198623	13198731	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	intron	13198732	13198834	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	CDS	13198835	13199286	0.9	+	2	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	exon	13198835	13199286	.	+	.	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
Phchi.S1	AUGUSTUS	stop_codon	13199287	13199289	.	+	0	transcript_id "Phchi.S1G203900.t1"; gene_id "Phchi.S1G203900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14786.t1 is derived from g13254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14706695	14707729	.	+	.	Phchi.S3G210500
Phchi.S3	AUGUSTUS	transcript	14706695	14707729	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	start_codon	14706695	14706697	.	+	0	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14706695	14706697	0.54	+	0	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14706695	14706697	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14706698	14706780	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14706781	14706825	1	+	0	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14706781	14706825	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14706826	14706934	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14706935	14706998	0.99	+	0	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14706935	14706998	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14706999	14707327	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14707328	14707469	0.99	+	2	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14707328	14707469	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14707470	14707614	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14707615	14707729	1	+	1	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14707615	14707729	.	+	.	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	stop_codon	14707730	14707732	.	+	0	transcript_id "Phchi.S3G210500.t1"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	transcript	14706695	14707729	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	start_codon	14706695	14706697	.	+	0	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14706695	14706697	0.5	+	0	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14706695	14706697	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14706698	14706776	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14706777	14706825	0.97	+	0	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14706777	14706825	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14706826	14706890	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14706891	14706998	0.93	+	2	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14706891	14706998	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14706999	14707327	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14707328	14707469	1	+	2	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14707328	14707469	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	intron	14707470	14707614	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	CDS	14707615	14707729	1	+	1	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	exon	14707615	14707729	.	+	.	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
Phchi.S3	AUGUSTUS	stop_codon	14707730	14707732	.	+	0	transcript_id "Phchi.S3G210500.t2"; gene_id "Phchi.S3G210500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8533.t1 is derived from g5708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36522640	36524359	.	-	.	Phchi.S1G569200
Phchi.S1	AUGUSTUS	transcript	36522640	36524359	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	stop_codon	36522637	36522639	.	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36522640	36522816	0.69	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36522640	36522816	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	intron	36522817	36522996	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36522997	36523116	0.97	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36522997	36523116	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	intron	36523117	36523213	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36523214	36523333	1	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36523214	36523333	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	intron	36523334	36523444	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36523445	36523651	0.98	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36523445	36523651	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	intron	36523652	36523753	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36523754	36523933	0.91	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36523754	36523933	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	intron	36523934	36524070	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36524071	36524205	1	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36524071	36524205	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	intron	36524206	36524314	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	CDS	36524315	36524359	0.36	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	exon	36524315	36524359	.	-	.	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
Phchi.S1	AUGUSTUS	start_codon	36524357	36524359	.	-	0	transcript_id "Phchi.S1G569200.t1"; gene_id "Phchi.S1G569200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11563.t1 is derived from g15614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7073605	7075398	.	+	.	Phchi.S4G114500
Phchi.S4	AUGUSTUS	transcript	7073605	7075398	.	+	.	transcript_id "Phchi.S4G114500.t1"; gene_id "Phchi.S4G114500"
Phchi.S4	AUGUSTUS	start_codon	7073605	7073607	.	+	0	transcript_id "Phchi.S4G114500.t1"; gene_id "Phchi.S4G114500"
Phchi.S4	AUGUSTUS	CDS	7073605	7075398	1	+	0	transcript_id "Phchi.S4G114500.t1"; gene_id "Phchi.S4G114500"
Phchi.S4	AUGUSTUS	exon	7073605	7075398	.	+	.	transcript_id "Phchi.S4G114500.t1"; gene_id "Phchi.S4G114500"
Phchi.S4	AUGUSTUS	stop_codon	7075399	7075401	.	+	0	transcript_id "Phchi.S4G114500.t1"; gene_id "Phchi.S4G114500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1803.t1 is derived from g8723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3118367	3118924	.	-	.	Phchi.S5G041200
Phchi.S5	AUGUSTUS	transcript	3118367	3118924	.	-	.	transcript_id "Phchi.S5G041200.t1"; gene_id "Phchi.S5G041200"
Phchi.S5	AUGUSTUS	stop_codon	3118364	3118366	.	-	0	transcript_id "Phchi.S5G041200.t1"; gene_id "Phchi.S5G041200"
Phchi.S5	AUGUSTUS	CDS	3118367	3118924	0.4	-	0	transcript_id "Phchi.S5G041200.t1"; gene_id "Phchi.S5G041200"
Phchi.S5	AUGUSTUS	exon	3118367	3118924	.	-	.	transcript_id "Phchi.S5G041200.t1"; gene_id "Phchi.S5G041200"
Phchi.S5	AUGUSTUS	start_codon	3118922	3118924	.	-	0	transcript_id "Phchi.S5G041200.t1"; gene_id "Phchi.S5G041200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14928.t1 is derived from g13396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15555282	15564653	.	+	.	Phchi.S3G224700
Phchi.S3	AUGUSTUS	transcript	15555282	15564653	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	start_codon	15555282	15555284	.	+	0	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15555282	15555753	0.86	+	0	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15555282	15555753	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15555754	15556176	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15556177	15556308	0.66	+	2	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15556177	15556308	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15556309	15556407	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15556408	15557211	0.85	+	2	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15556408	15557211	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15557212	15557298	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15557299	15557471	0.96	+	2	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15557299	15557471	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15557472	15557570	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15557571	15557940	0.94	+	0	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15557571	15557940	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15557941	15558047	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15558048	15559150	1	+	2	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15558048	15559150	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15559151	15559236	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15559237	15559637	0.95	+	0	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15559237	15559637	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15559638	15559720	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15559721	15561572	0.93	+	1	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15559721	15561572	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15561573	15561657	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15561658	15562912	0.67	+	0	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15561658	15562912	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	intron	15562913	15562989	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15562990	15564653	0.67	+	2	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15562990	15564653	.	+	.	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	stop_codon	15564654	15564656	.	+	0	transcript_id "Phchi.S3G224700.t1"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	transcript	15563013	15564653	.	+	.	transcript_id "Phchi.S3G224700.t2"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	start_codon	15563013	15563015	.	+	0	transcript_id "Phchi.S3G224700.t2"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15563013	15564653	0.52	+	0	transcript_id "Phchi.S3G224700.t2"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15563013	15564653	.	+	.	transcript_id "Phchi.S3G224700.t2"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	stop_codon	15564654	15564656	.	+	0	transcript_id "Phchi.S3G224700.t2"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	transcript	15561649	15562974	.	+	.	transcript_id "Phchi.S3G224700.t3"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	start_codon	15561649	15561651	.	+	0	transcript_id "Phchi.S3G224700.t3"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	CDS	15561649	15562974	0.36	+	0	transcript_id "Phchi.S3G224700.t3"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	exon	15561649	15562974	.	+	.	transcript_id "Phchi.S3G224700.t3"; gene_id "Phchi.S3G224700"
Phchi.S3	AUGUSTUS	stop_codon	15562975	15562977	.	+	0	transcript_id "Phchi.S3G224700.t3"; gene_id "Phchi.S3G224700"
# This transcript jg1264.t2 is derived from g11047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1265.t1 is derived from g11048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8710554	8715644	.	+	.	Phchi.S6G122400
Phchi.S6	AUGUSTUS	transcript	8710554	8715644	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	start_codon	8710554	8710556	.	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8710554	8711358	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8710554	8711358	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8711359	8711506	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8711507	8711582	1	+	2	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8711507	8711582	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8711583	8711690	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8711691	8711810	0.94	+	1	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8711691	8711810	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8711811	8711952	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8711953	8712028	1	+	1	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8711953	8712028	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8712029	8712193	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8712194	8712262	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8712194	8712262	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8712263	8712367	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8712368	8712448	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8712368	8712448	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8712449	8712560	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8712561	8712632	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8712561	8712632	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8712633	8712751	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8712752	8712841	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8712752	8712841	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8712842	8712985	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8712986	8713144	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8712986	8713144	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8713145	8713281	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8713282	8713365	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8713282	8713365	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8713366	8713483	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8713484	8713627	0.98	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8713484	8713627	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8713628	8713738	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8713739	8713828	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8713739	8713828	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8713829	8713916	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8713917	8713999	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8713917	8713999	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8714000	8714091	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8714092	8714538	1	+	1	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8714092	8714538	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8714539	8714640	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8714641	8714881	1	+	1	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8714641	8714881	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	intron	8714882	8714981	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	CDS	8714982	8715644	1	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	exon	8714982	8715644	.	+	.	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
Phchi.S6	AUGUSTUS	stop_codon	8715645	8715647	.	+	0	transcript_id "Phchi.S6G122400.t1"; gene_id "Phchi.S6G122400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8727.t1 is derived from g5902.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37694733	37697153	.	+	.	Phchi.S1G588600
Phchi.S1	AUGUSTUS	transcript	37694733	37697153	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	start_codon	37694733	37694735	.	+	0	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37694733	37696167	1	+	0	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37694733	37696167	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696168	37696265	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696266	37696368	0.63	+	2	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696266	37696368	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696369	37696469	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696470	37696605	1	+	1	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696470	37696605	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696606	37696720	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696721	37696849	1	+	0	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696721	37696849	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696850	37696976	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696977	37697153	1	+	0	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696977	37697153	.	+	.	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	stop_codon	37697154	37697156	.	+	0	transcript_id "Phchi.S1G588600.t1"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	transcript	37694733	37697153	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	start_codon	37694733	37694735	.	+	0	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37694733	37696167	1	+	0	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37694733	37696167	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696168	37696265	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696266	37696368	0.58	+	2	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696266	37696368	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696369	37696469	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696470	37696605	1	+	1	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696470	37696605	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696606	37696699	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696700	37696849	0.99	+	0	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696700	37696849	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	intron	37696850	37696976	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	CDS	37696977	37697153	1	+	0	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	exon	37696977	37697153	.	+	.	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
Phchi.S1	AUGUSTUS	stop_codon	37697154	37697156	.	+	0	transcript_id "Phchi.S1G588600.t2"; gene_id "Phchi.S1G588600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4680.t1 is derived from g1850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11822528	11823830	.	+	.	Phchi.S1G183900
Phchi.S1	AUGUSTUS	transcript	11822528	11823830	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	start_codon	11822528	11822530	.	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11822528	11822578	1	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11822528	11822578	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	intron	11822579	11822704	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11822705	11822818	1	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11822705	11822818	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	intron	11822819	11823004	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11823005	11823118	0.8	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11823005	11823118	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	intron	11823119	11823202	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11823203	11823387	1	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11823203	11823387	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	intron	11823388	11823469	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11823470	11823560	1	+	1	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11823470	11823560	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	intron	11823561	11823651	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11823652	11823717	1	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11823652	11823717	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	intron	11823718	11823794	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	CDS	11823795	11823830	0.49	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	exon	11823795	11823830	.	+	.	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
Phchi.S1	AUGUSTUS	stop_codon	11823831	11823833	.	+	0	transcript_id "Phchi.S1G183900.t1"; gene_id "Phchi.S1G183900"
# This transcript jg10433.t2 is derived from g14482.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10434.t1 is derived from g14483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	319787	321807	.	-	.	Phchi.S4G001600
Phchi.S4	AUGUSTUS	transcript	319787	321807	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	stop_codon	319784	319786	.	-	0	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	CDS	319787	320228	0.26	-	1	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	exon	319787	320228	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	intron	320229	320342	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	CDS	320343	320612	0.4	-	1	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	exon	320343	320612	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	intron	320613	320754	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	CDS	320755	320883	0.83	-	1	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	exon	320755	320883	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	intron	320884	321043	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	CDS	321044	321235	0.64	-	1	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	exon	321044	321235	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	intron	321236	321528	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	CDS	321529	321596	0.61	-	0	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	exon	321529	321596	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	intron	321597	321735	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	CDS	321736	321807	0.61	-	0	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	exon	321736	321807	.	-	.	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
Phchi.S4	AUGUSTUS	start_codon	321805	321807	.	-	0	transcript_id "Phchi.S4G001600.t1"; gene_id "Phchi.S4G001600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15356.t1 is derived from g13824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18572355	18573455	.	-	.	Phchi.S3G267500
Phchi.S3	AUGUSTUS	transcript	18572355	18573455	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	stop_codon	18572352	18572354	.	-	0	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	CDS	18572355	18572542	0.99	-	2	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	exon	18572355	18572542	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	intron	18572543	18572637	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	CDS	18572638	18572758	1	-	0	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	exon	18572638	18572758	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	intron	18572759	18572877	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	CDS	18572878	18573118	1	-	1	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	exon	18572878	18573118	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	intron	18573119	18573252	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	CDS	18573253	18573455	0.99	-	0	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	exon	18573253	18573455	.	-	.	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
Phchi.S3	AUGUSTUS	start_codon	18573453	18573455	.	-	0	transcript_id "Phchi.S3G267500.t1"; gene_id "Phchi.S3G267500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10324.t1 is derived from g7500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47112399	47113238	.	-	.	Phchi.S1G748300
Phchi.S1	AUGUSTUS	transcript	47112399	47113238	.	-	.	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	stop_codon	47112396	47112398	.	-	0	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	CDS	47112399	47112645	1	-	1	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	exon	47112399	47112645	.	-	.	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	intron	47112646	47112739	.	-	.	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	CDS	47112740	47112937	1	-	1	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	exon	47112740	47112937	.	-	.	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	intron	47112938	47113056	.	-	.	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	CDS	47113057	47113238	0.75	-	0	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	exon	47113057	47113238	.	-	.	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
Phchi.S1	AUGUSTUS	start_codon	47113236	47113238	.	-	0	transcript_id "Phchi.S1G748300.t1"; gene_id "Phchi.S1G748300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6213.t1 is derived from g3385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21493070	21494163	.	+	.	Phchi.S1G337200
Phchi.S1	AUGUSTUS	transcript	21493070	21494163	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	start_codon	21493070	21493072	.	+	0	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	CDS	21493070	21493749	0.38	+	0	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	exon	21493070	21493749	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	intron	21493750	21493813	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	CDS	21493814	21493850	0.48	+	1	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	exon	21493814	21493850	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	intron	21493851	21493949	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	CDS	21493950	21494018	0.64	+	0	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	exon	21493950	21494018	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	intron	21494019	21494115	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	CDS	21494116	21494163	0.61	+	0	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	exon	21494116	21494163	.	+	.	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
Phchi.S1	AUGUSTUS	stop_codon	21494164	21494166	.	+	0	transcript_id "Phchi.S1G337200.t1"; gene_id "Phchi.S1G337200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11700.t1 is derived from g15751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7760922	7762718	.	+	.	Phchi.S4G128200
Phchi.S4	AUGUSTUS	transcript	7760922	7762718	.	+	.	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	start_codon	7760922	7760924	.	+	0	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	CDS	7760922	7762484	0.87	+	0	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	exon	7760922	7762484	.	+	.	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	intron	7762485	7762715	.	+	.	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	CDS	7762716	7762718	0.99	+	0	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	exon	7762716	7762718	.	+	.	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
Phchi.S4	AUGUSTUS	stop_codon	7762719	7762721	.	+	0	transcript_id "Phchi.S4G128200.t1"; gene_id "Phchi.S4G128200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1636.t1 is derived from g8555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2126714	2133035	.	-	.	Phchi.S5G024500
Phchi.S5	AUGUSTUS	transcript	2126714	2133035	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	stop_codon	2126711	2126713	.	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2126714	2126734	0.61	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2126714	2126734	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2126735	2126912	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2126913	2126993	1	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2126913	2126993	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2126994	2127086	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2127087	2127138	1	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2127087	2127138	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2127139	2127235	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2127236	2127320	0.66	-	2	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2127236	2127320	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2127321	2127422	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2127423	2127480	1	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2127423	2127480	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2127481	2127582	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2127583	2127760	1	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2127583	2127760	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2127761	2127886	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2127887	2127967	1	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2127887	2127967	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2127968	2128192	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2128193	2128364	1	-	2	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2128193	2128364	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2128365	2128466	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2128467	2128545	1	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2128467	2128545	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2128546	2128638	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2128639	2128738	1	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2128639	2128738	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2128739	2128918	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2128919	2129030	1	-	2	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2128919	2129030	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2129031	2129465	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2129466	2129613	1	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2129466	2129613	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2129614	2129711	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2129712	2129761	0.67	-	2	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2129712	2129761	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2129762	2129850	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2129851	2130071	0.62	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2129851	2130071	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2130072	2130182	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2130183	2130230	0.67	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2130183	2130230	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2130231	2130427	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2130428	2130526	0.84	-	1	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2130428	2130526	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2130527	2130671	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2130672	2132871	0.62	-	2	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2130672	2132871	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	intron	2132872	2132959	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	CDS	2132960	2133035	1	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	exon	2132960	2133035	.	-	.	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
Phchi.S5	AUGUSTUS	start_codon	2133033	2133035	.	-	0	transcript_id "Phchi.S5G024500.t1"; gene_id "Phchi.S5G024500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12621.t1 is derived from g8298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37602985	37605867	.	-	.	Phchi.S2G070100
Phchi.S2	AUGUSTUS	transcript	37602985	37605867	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	stop_codon	37602982	37602984	.	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37602985	37603064	0.5	-	2	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37602985	37603064	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37603065	37603208	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37603209	37603284	0.47	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37603209	37603284	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37603285	37603392	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37603393	37603667	0.76	-	2	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37603393	37603667	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37603668	37603793	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37603794	37603997	0.44	-	2	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37603794	37603997	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37603998	37604083	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37604084	37604146	0.58	-	2	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37604084	37604146	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37604147	37604308	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37604309	37604642	0.99	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37604309	37604642	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37604643	37604746	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37604747	37604889	1	-	2	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37604747	37604889	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37604890	37605061	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37605062	37605070	1	-	2	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37605062	37605070	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37605071	37605215	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37605216	37605279	1	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37605216	37605279	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37605280	37605389	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37605390	37605671	1	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37605390	37605671	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	intron	37605672	37605744	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	CDS	37605745	37605867	0.98	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	exon	37605745	37605867	.	-	.	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
Phchi.S2	AUGUSTUS	start_codon	37605865	37605867	.	-	0	transcript_id "Phchi.S2G070100.t1"; gene_id "Phchi.S2G070100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11251.t1 is derived from g15301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5007640	5009976	.	-	.	Phchi.S4G083300
Phchi.S4	AUGUSTUS	transcript	5007640	5009976	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	stop_codon	5007637	5007639	.	-	0	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	CDS	5007640	5007966	1	-	0	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	exon	5007640	5007966	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	intron	5007967	5008074	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	CDS	5008075	5008204	1	-	1	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	exon	5008075	5008204	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	intron	5008205	5008304	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	CDS	5008305	5008482	1	-	2	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	exon	5008305	5008482	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	intron	5008483	5008590	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	CDS	5008591	5008891	0.96	-	0	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	exon	5008591	5008891	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	intron	5008892	5009042	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	CDS	5009043	5009281	0.78	-	2	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	exon	5009043	5009281	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	intron	5009282	5009402	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	CDS	5009403	5009976	0.67	-	0	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	exon	5009403	5009976	.	-	.	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
Phchi.S4	AUGUSTUS	start_codon	5009974	5009976	.	-	0	transcript_id "Phchi.S4G083300.t1"; gene_id "Phchi.S4G083300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5685.t1 is derived from g2855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18313544	18314797	.	-	.	Phchi.S1G284400
Phchi.S1	AUGUSTUS	transcript	18313544	18314797	.	-	.	transcript_id "Phchi.S1G284400.t1"; gene_id "Phchi.S1G284400"
Phchi.S1	AUGUSTUS	stop_codon	18313541	18313543	.	-	0	transcript_id "Phchi.S1G284400.t1"; gene_id "Phchi.S1G284400"
Phchi.S1	AUGUSTUS	CDS	18313544	18314797	1	-	0	transcript_id "Phchi.S1G284400.t1"; gene_id "Phchi.S1G284400"
Phchi.S1	AUGUSTUS	exon	18313544	18314797	.	-	.	transcript_id "Phchi.S1G284400.t1"; gene_id "Phchi.S1G284400"
Phchi.S1	AUGUSTUS	start_codon	18314795	18314797	.	-	0	transcript_id "Phchi.S1G284400.t1"; gene_id "Phchi.S1G284400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8630.t1 is derived from g5805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37157660	37159606	.	-	.	Phchi.S1G578900
Phchi.S1	AUGUSTUS	transcript	37157660	37159606	.	-	.	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	stop_codon	37157657	37157659	.	-	0	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	CDS	37157660	37158915	1	-	2	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	exon	37157660	37158915	.	-	.	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	intron	37158916	37159023	.	-	.	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	CDS	37159024	37159606	0.99	-	0	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	exon	37159024	37159606	.	-	.	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
Phchi.S1	AUGUSTUS	start_codon	37159604	37159606	.	-	0	transcript_id "Phchi.S1G578900.t1"; gene_id "Phchi.S1G578900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7916.t1 is derived from g5090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31888397	31893016	.	+	.	Phchi.S1G507500
Phchi.S1	AUGUSTUS	transcript	31888397	31892692	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	start_codon	31888397	31888399	.	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31888397	31888970	0.44	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31888397	31888970	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31888971	31889165	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889166	31889185	0.87	+	2	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889166	31889185	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889186	31889255	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889256	31889335	1	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889256	31889335	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889336	31889415	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889416	31889487	1	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889416	31889487	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889488	31889608	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889609	31889648	1	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889609	31889648	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889649	31889752	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889753	31889854	1	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889753	31889854	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889855	31889997	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889998	31890119	1	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889998	31890119	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890120	31890403	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31890404	31890536	1	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31890404	31890536	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890537	31890723	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31890724	31890815	1	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31890724	31890815	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890816	31890904	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31890905	31890986	1	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31890905	31890986	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890987	31891259	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31891260	31891324	1	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31891260	31891324	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31891325	31891459	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31891460	31891732	1	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31891460	31891732	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31891733	31891864	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31891865	31891959	1	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31891865	31891959	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31891960	31892043	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31892044	31892108	1	+	2	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31892044	31892108	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31892109	31892198	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31892199	31892290	0.96	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31892199	31892290	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31892291	31892637	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31892638	31892692	0.91	+	1	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31892638	31892692	.	+	.	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	stop_codon	31892693	31892695	.	+	0	transcript_id "Phchi.S1G507500.t1"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	transcript	31888397	31893016	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	start_codon	31888397	31888399	.	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31888397	31888970	0.42	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31888397	31888970	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31888971	31889165	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889166	31889185	0.76	+	2	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889166	31889185	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889186	31889255	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889256	31889335	1	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889256	31889335	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889336	31889415	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889416	31889487	1	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889416	31889487	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889488	31889608	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889609	31889648	1	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889609	31889648	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889649	31889752	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889753	31889854	1	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889753	31889854	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31889855	31889997	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31889998	31890119	1	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31889998	31890119	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890120	31890403	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31890404	31890536	1	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31890404	31890536	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890537	31890723	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31890724	31890815	1	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31890724	31890815	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890816	31890904	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31890905	31890986	1	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31890905	31890986	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31890987	31891259	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31891260	31891324	1	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31891260	31891324	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31891325	31891459	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31891460	31891732	0.99	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31891460	31891732	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31891733	31891864	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31891865	31891959	1	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31891865	31891959	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31891960	31892043	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31892044	31892108	1	+	2	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31892044	31892108	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31892109	31892198	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31892199	31892290	0.82	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31892199	31892290	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	intron	31892291	31892976	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	CDS	31892977	31893016	0.82	+	1	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	exon	31892977	31893016	.	+	.	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
Phchi.S1	AUGUSTUS	stop_codon	31893017	31893019	.	+	0	transcript_id "Phchi.S1G507500.t2"; gene_id "Phchi.S1G507500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13459.t1 is derived from g11926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7009532	7010246	.	-	.	Phchi.S3G077800
Phchi.S3	AUGUSTUS	transcript	7009532	7010246	.	-	.	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	stop_codon	7009529	7009531	.	-	0	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	CDS	7009532	7009645	1	-	0	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	exon	7009532	7009645	.	-	.	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	intron	7009646	7009744	.	-	.	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	CDS	7009745	7009868	1	-	1	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	exon	7009745	7009868	.	-	.	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	intron	7009869	7010220	.	-	.	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	CDS	7010221	7010246	1	-	0	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	exon	7010221	7010246	.	-	.	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
Phchi.S3	AUGUSTUS	start_codon	7010244	7010246	.	-	0	transcript_id "Phchi.S3G077800.t1"; gene_id "Phchi.S3G077800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7189.t1 is derived from g4361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27467528	27470187	.	-	.	Phchi.S1G434800
Phchi.S1	AUGUSTUS	transcript	27467528	27470187	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	stop_codon	27467525	27467527	.	-	0	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27467528	27467696	0.99	-	1	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27467528	27467696	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27467697	27467784	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27467785	27467844	1	-	1	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27467785	27467844	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27467845	27467921	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27467922	27467933	0.92	-	1	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27467922	27467933	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27467934	27468340	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27468341	27468479	0.7	-	2	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27468341	27468479	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27468480	27468572	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27468573	27469378	0.35	-	1	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27468573	27469378	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27469379	27469720	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27469721	27470187	0.46	-	0	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27469721	27470187	.	-	.	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	start_codon	27470185	27470187	.	-	0	transcript_id "Phchi.S1G434800.t1"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	transcript	27467528	27470187	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	stop_codon	27467525	27467527	.	-	0	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27467528	27467696	0.97	-	1	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27467528	27467696	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27467697	27467784	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27467785	27467844	1	-	1	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27467785	27467844	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27467845	27467933	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27467934	27467941	0.59	-	0	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27467934	27467941	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27467942	27468243	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27468244	27468479	0.49	-	2	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27468244	27468479	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27468480	27468572	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27468573	27469378	0.32	-	1	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27468573	27469378	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	intron	27469379	27469720	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	CDS	27469721	27470187	0.46	-	0	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	exon	27469721	27470187	.	-	.	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
Phchi.S1	AUGUSTUS	start_codon	27470185	27470187	.	-	0	transcript_id "Phchi.S1G434800.t2"; gene_id "Phchi.S1G434800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9324.t1 is derived from g6499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40944725	40944994	.	+	.	Phchi.S1G648300
Phchi.S1	AUGUSTUS	transcript	40944725	40944994	.	+	.	transcript_id "Phchi.S1G648300.t1"; gene_id "Phchi.S1G648300"
Phchi.S1	AUGUSTUS	start_codon	40944725	40944727	.	+	0	transcript_id "Phchi.S1G648300.t1"; gene_id "Phchi.S1G648300"
Phchi.S1	AUGUSTUS	CDS	40944725	40944994	0.74	+	0	transcript_id "Phchi.S1G648300.t1"; gene_id "Phchi.S1G648300"
Phchi.S1	AUGUSTUS	exon	40944725	40944994	.	+	.	transcript_id "Phchi.S1G648300.t1"; gene_id "Phchi.S1G648300"
Phchi.S1	AUGUSTUS	stop_codon	40944995	40944997	.	+	0	transcript_id "Phchi.S1G648300.t1"; gene_id "Phchi.S1G648300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6437.t1 is derived from g3609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23031186	23033042	.	+	.	Phchi.S1G359600
Phchi.S1	AUGUSTUS	transcript	23031186	23033042	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	start_codon	23031186	23031188	.	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23031186	23031257	1	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23031186	23031257	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23031258	23031347	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23031348	23031436	1	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23031348	23031436	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23031437	23031661	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23031662	23031725	1	+	1	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23031662	23031725	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23031726	23031864	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23031865	23031942	1	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23031865	23031942	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23031943	23032076	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23032077	23032153	1	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23032077	23032153	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23032154	23032235	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23032236	23032302	1	+	1	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23032236	23032302	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23032303	23032395	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23032396	23032503	0.98	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23032396	23032503	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23032504	23032636	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23032637	23032669	1	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23032637	23032669	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23032670	23032851	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23032852	23032888	0.81	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23032852	23032888	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	intron	23032889	23033010	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	CDS	23033011	23033042	0.65	+	2	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	exon	23033011	23033042	.	+	.	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
Phchi.S1	AUGUSTUS	stop_codon	23033043	23033045	.	+	0	transcript_id "Phchi.S1G359600.t1"; gene_id "Phchi.S1G359600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15874.t1 is derived from g14344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21988040	21991835	.	+	.	Phchi.S3G319300
Phchi.S3	AUGUSTUS	transcript	21988040	21991835	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	start_codon	21988040	21988042	.	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21988040	21988595	0.84	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21988040	21988595	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21988596	21988722	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21988723	21988838	1	+	2	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21988723	21988838	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21988839	21988935	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21988936	21989061	1	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21988936	21989061	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21989062	21989145	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21989146	21989331	1	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21989146	21989331	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21989332	21989397	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21989398	21989613	1	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21989398	21989613	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21989614	21989699	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21989700	21989917	1	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21989700	21989917	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21989918	21990002	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21990003	21990078	1	+	1	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21990003	21990078	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21990079	21990216	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21990217	21990306	1	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21990217	21990306	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21990307	21990430	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21990431	21991607	0.92	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21990431	21991607	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	intron	21991608	21991821	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	CDS	21991822	21991835	0.92	+	2	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	exon	21991822	21991835	.	+	.	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
Phchi.S3	AUGUSTUS	stop_codon	21991836	21991838	.	+	0	transcript_id "Phchi.S3G319300.t1"; gene_id "Phchi.S3G319300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7377.t1 is derived from g4549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28827710	28831863	.	-	.	Phchi.S1G453600
Phchi.S1	AUGUSTUS	transcript	28827710	28831863	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	stop_codon	28827707	28827709	.	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28827710	28827967	1	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28827710	28827967	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28827968	28828060	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28828061	28828174	1	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28828061	28828174	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28828175	28828283	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28828284	28828478	1	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28828284	28828478	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28828479	28828585	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28828586	28828681	0.98	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28828586	28828681	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28828682	28828775	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28828776	28828997	1	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28828776	28828997	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28828998	28829093	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28829094	28829831	0.93	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28829094	28829831	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28829832	28829923	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28829924	28830755	0.98	-	1	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28829924	28830755	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28830756	28830884	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28830885	28831000	1	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28830885	28831000	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28831001	28831090	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28831091	28831209	1	-	2	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28831091	28831209	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28831210	28831354	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28831355	28831417	1	-	2	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28831355	28831417	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28831418	28831525	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28831526	28831653	1	-	1	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28831526	28831653	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	intron	28831654	28831738	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	CDS	28831739	28831863	0.76	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	exon	28831739	28831863	.	-	.	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
Phchi.S1	AUGUSTUS	start_codon	28831861	28831863	.	-	0	transcript_id "Phchi.S1G453600.t1"; gene_id "Phchi.S1G453600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8890.t1 is derived from g6065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38498329	38498716	.	-	.	Phchi.S1G604900
Phchi.S1	AUGUSTUS	transcript	38498329	38498716	.	-	.	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	stop_codon	38498326	38498328	.	-	0	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	CDS	38498329	38498337	0.71	-	0	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	exon	38498329	38498337	.	-	.	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	intron	38498338	38498464	.	-	.	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	CDS	38498465	38498716	0.12	-	0	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	exon	38498465	38498716	.	-	.	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
Phchi.S1	AUGUSTUS	start_codon	38498714	38498716	.	-	0	transcript_id "Phchi.S1G604900.t1"; gene_id "Phchi.S1G604900"
# This transcript jg5700.t2 is derived from g2870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5701.t1 is derived from g2871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18429273	18431099	.	+	.	Phchi.S1G286000
Phchi.S1	AUGUSTUS	transcript	18429273	18431099	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	start_codon	18429273	18429275	.	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18429273	18429459	0.99	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18429273	18429459	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18429460	18429610	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18429611	18429688	1	+	2	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18429611	18429688	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18429689	18429772	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18429773	18429879	1	+	2	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18429773	18429879	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18429880	18429986	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18429987	18430064	1	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18429987	18430064	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18430065	18430148	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18430149	18430250	1	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18430149	18430250	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18430251	18430337	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18430338	18430419	1	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18430338	18430419	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18430420	18430492	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18430493	18430548	0.44	+	2	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18430493	18430548	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18430549	18430705	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18430706	18430755	0.42	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18430706	18430755	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	intron	18430756	18430945	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	CDS	18430946	18431099	0.42	+	1	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	exon	18430946	18431099	.	+	.	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
Phchi.S1	AUGUSTUS	stop_codon	18431100	18431102	.	+	0	transcript_id "Phchi.S1G286000.t1"; gene_id "Phchi.S1G286000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13066.t1 is derived from g11531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3988717	3991560	.	-	.	Phchi.S3G038500
Phchi.S3	AUGUSTUS	transcript	3988717	3991560	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	stop_codon	3988714	3988716	.	-	0	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	CDS	3988717	3989107	1	-	1	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	exon	3988717	3989107	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	intron	3989108	3989190	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	CDS	3989191	3989309	1	-	0	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	exon	3989191	3989309	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	intron	3989310	3989404	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	CDS	3989405	3989710	1	-	0	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	exon	3989405	3989710	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	intron	3989711	3989797	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	CDS	3989798	3991072	1	-	0	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	exon	3989798	3991072	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	intron	3991073	3991276	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	CDS	3991277	3991377	0.8	-	2	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	exon	3991277	3991377	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	intron	3991378	3991550	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	CDS	3991551	3991560	0.18	-	0	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	exon	3991551	3991560	.	-	.	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
Phchi.S3	AUGUSTUS	start_codon	3991558	3991560	.	-	0	transcript_id "Phchi.S3G038500.t1"; gene_id "Phchi.S3G038500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12150.t1 is derived from g7826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4955895	4956479	.	-	.	Phchi.S2G023000
Phchi.S2	AUGUSTUS	transcript	4955895	4956479	.	-	.	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	stop_codon	4955892	4955894	.	-	0	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	CDS	4955895	4956056	0.99	-	0	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	exon	4955895	4956056	.	-	.	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	intron	4956057	4956146	.	-	.	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	CDS	4956147	4956479	0.88	-	0	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	exon	4956147	4956479	.	-	.	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
Phchi.S2	AUGUSTUS	start_codon	4956477	4956479	.	-	0	transcript_id "Phchi.S2G023000.t1"; gene_id "Phchi.S2G023000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12648.t1 is derived from g9.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C255	AUGUSTUS	gene	17055	17282	.	-	.	Phchi.C255G000100
Phchi.C255	AUGUSTUS	transcript	17055	17282	.	-	.	transcript_id "Phchi.C255G000100.t1"; gene_id "Phchi.C255G000100"
Phchi.C255	AUGUSTUS	stop_codon	17052	17054	.	-	0	transcript_id "Phchi.C255G000100.t1"; gene_id "Phchi.C255G000100"
Phchi.C255	AUGUSTUS	CDS	17055	17282	0.62	-	0	transcript_id "Phchi.C255G000100.t1"; gene_id "Phchi.C255G000100"
Phchi.C255	AUGUSTUS	exon	17055	17282	.	-	.	transcript_id "Phchi.C255G000100.t1"; gene_id "Phchi.C255G000100"
Phchi.C255	AUGUSTUS	start_codon	17280	17282	.	-	0	transcript_id "Phchi.C255G000100.t1"; gene_id "Phchi.C255G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7131.t1 is derived from g4303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27096794	27097099	.	-	.	Phchi.S1G429000
Phchi.S1	AUGUSTUS	transcript	27096794	27097099	.	-	.	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	stop_codon	27096791	27096793	.	-	0	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	CDS	27096794	27097001	0.93	-	1	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	exon	27096794	27097001	.	-	.	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	intron	27097002	27097094	.	-	.	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	CDS	27097095	27097099	0.97	-	0	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	exon	27097095	27097099	.	-	.	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
Phchi.S1	AUGUSTUS	start_codon	27097097	27097099	.	-	0	transcript_id "Phchi.S1G429000.t1"; gene_id "Phchi.S1G429000"
# This transcript jg13259.t2 is derived from g11724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13260.t1 is derived from g11725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4963064	4964551	.	-	.	Phchi.S3G057900
Phchi.S3	AUGUSTUS	transcript	4963064	4964551	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	stop_codon	4963061	4963063	.	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4963064	4963240	0.95	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4963064	4963240	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	intron	4963241	4963332	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4963333	4963476	1	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4963333	4963476	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	intron	4963477	4963570	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4963571	4963681	1	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4963571	4963681	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	intron	4963682	4963763	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4963764	4963919	1	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4963764	4963919	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	intron	4963920	4964017	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4964018	4964119	1	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4964018	4964119	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	intron	4964120	4964208	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4964209	4964280	1	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4964209	4964280	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	intron	4964281	4964362	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	CDS	4964363	4964551	0.55	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	exon	4964363	4964551	.	-	.	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
Phchi.S3	AUGUSTUS	start_codon	4964549	4964551	.	-	0	transcript_id "Phchi.S3G057900.t1"; gene_id "Phchi.S3G057900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8226.t1 is derived from g5401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34544957	34547080	.	+	.	Phchi.S1G538500
Phchi.S1	AUGUSTUS	transcript	34544957	34547080	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	start_codon	34544957	34544959	.	+	0	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	CDS	34544957	34545628	0.49	+	0	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	exon	34544957	34545628	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	intron	34545629	34545744	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	CDS	34545745	34545878	1	+	0	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	exon	34545745	34545878	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	intron	34545879	34545965	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	CDS	34545966	34546079	0.99	+	1	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	exon	34545966	34546079	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	intron	34546080	34546188	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	CDS	34546189	34546363	0.98	+	1	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	exon	34546189	34546363	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	intron	34546364	34546482	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	CDS	34546483	34546551	0.99	+	0	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	exon	34546483	34546551	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	intron	34546552	34546669	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	CDS	34546670	34547080	1	+	0	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	exon	34546670	34547080	.	+	.	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
Phchi.S1	AUGUSTUS	stop_codon	34547081	34547083	.	+	0	transcript_id "Phchi.S1G538500.t1"; gene_id "Phchi.S1G538500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4458.t1 is derived from g1628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10589405	10590539	.	-	.	Phchi.S1G161700
Phchi.S1	AUGUSTUS	transcript	10589405	10590539	.	-	.	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	stop_codon	10589402	10589404	.	-	0	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	CDS	10589405	10589488	0.74	-	0	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	exon	10589405	10589488	.	-	.	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	intron	10589489	10589760	.	-	.	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	CDS	10589761	10589825	0.63	-	2	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	exon	10589761	10589825	.	-	.	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	intron	10589826	10589947	.	-	.	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	CDS	10589948	10590539	0.74	-	0	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	exon	10589948	10590539	.	-	.	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
Phchi.S1	AUGUSTUS	start_codon	10590537	10590539	.	-	0	transcript_id "Phchi.S1G161700.t1"; gene_id "Phchi.S1G161700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15838.t1 is derived from g14308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21685046	21691310	.	+	.	Phchi.S3G315700
Phchi.S3	AUGUSTUS	transcript	21685046	21691310	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	start_codon	21685046	21685048	.	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21685046	21685072	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21685046	21685072	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21685073	21685361	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21685362	21685442	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21685362	21685442	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21685443	21686417	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21686418	21686469	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21686418	21686469	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21686470	21686672	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21686673	21686733	1	+	2	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21686673	21686733	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21686734	21686802	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21686803	21686971	1	+	1	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21686803	21686971	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21686972	21687097	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21687098	21687234	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21687098	21687234	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21687235	21687367	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21687368	21687439	1	+	1	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21687368	21687439	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21687440	21687547	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21687548	21687638	1	+	1	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21687548	21687638	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21687639	21687768	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21687769	21687844	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21687769	21687844	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21687845	21687967	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21687968	21688041	1	+	2	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21687968	21688041	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21688042	21688152	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21688153	21688260	0.97	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21688153	21688260	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21688261	21688374	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21688375	21688536	0.98	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21688375	21688536	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21688537	21688665	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21688666	21688770	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21688666	21688770	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21688771	21688947	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21688948	21689028	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21688948	21689028	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21689029	21689139	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21689140	21689365	1	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21689140	21689365	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21689366	21689446	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21689447	21690496	0.99	+	2	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21689447	21690496	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	intron	21690497	21691155	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	CDS	21691156	21691310	1	+	2	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	exon	21691156	21691310	.	+	.	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
Phchi.S3	AUGUSTUS	stop_codon	21691311	21691313	.	+	0	transcript_id "Phchi.S3G315700.t1"; gene_id "Phchi.S3G315700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2598.t1 is derived from g9518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7656530	7656847	.	+	.	Phchi.S5G120700
Phchi.S5	AUGUSTUS	transcript	7656530	7656847	.	+	.	transcript_id "Phchi.S5G120700.t1"; gene_id "Phchi.S5G120700"
Phchi.S5	AUGUSTUS	start_codon	7656530	7656532	.	+	0	transcript_id "Phchi.S5G120700.t1"; gene_id "Phchi.S5G120700"
Phchi.S5	AUGUSTUS	CDS	7656530	7656847	0.67	+	0	transcript_id "Phchi.S5G120700.t1"; gene_id "Phchi.S5G120700"
Phchi.S5	AUGUSTUS	exon	7656530	7656847	.	+	.	transcript_id "Phchi.S5G120700.t1"; gene_id "Phchi.S5G120700"
Phchi.S5	AUGUSTUS	stop_codon	7656848	7656850	.	+	0	transcript_id "Phchi.S5G120700.t1"; gene_id "Phchi.S5G120700"
# This transcript jg10665.t2 is derived from g14715.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10666.t1 is derived from g14716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1504823	1505665	.	+	.	Phchi.S4G024800
Phchi.S4	AUGUSTUS	transcript	1504823	1505665	.	+	.	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	start_codon	1504823	1504825	.	+	0	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	CDS	1504823	1505228	0.94	+	0	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	exon	1504823	1505228	.	+	.	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	intron	1505229	1505324	.	+	.	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	CDS	1505325	1505416	0.99	+	2	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	exon	1505325	1505416	.	+	.	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	intron	1505417	1505542	.	+	.	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	CDS	1505543	1505665	0.99	+	0	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	exon	1505543	1505665	.	+	.	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
Phchi.S4	AUGUSTUS	stop_codon	1505666	1505668	.	+	0	transcript_id "Phchi.S4G024800.t1"; gene_id "Phchi.S4G024800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7236.t1 is derived from g4408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27764085	27765407	.	+	.	Phchi.S1G439500
Phchi.S1	AUGUSTUS	transcript	27764085	27765407	.	+	.	transcript_id "Phchi.S1G439500.t1"; gene_id "Phchi.S1G439500"
Phchi.S1	AUGUSTUS	start_codon	27764085	27764087	.	+	0	transcript_id "Phchi.S1G439500.t1"; gene_id "Phchi.S1G439500"
Phchi.S1	AUGUSTUS	CDS	27764085	27765407	0.99	+	0	transcript_id "Phchi.S1G439500.t1"; gene_id "Phchi.S1G439500"
Phchi.S1	AUGUSTUS	exon	27764085	27765407	.	+	.	transcript_id "Phchi.S1G439500.t1"; gene_id "Phchi.S1G439500"
Phchi.S1	AUGUSTUS	stop_codon	27765408	27765410	.	+	0	transcript_id "Phchi.S1G439500.t1"; gene_id "Phchi.S1G439500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13422.t1 is derived from g11889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6624991	6625967	.	+	.	Phchi.S3G074100
Phchi.S3	AUGUSTUS	transcript	6624991	6625967	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	start_codon	6624991	6624993	.	+	0	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	CDS	6624991	6625037	1	+	0	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	exon	6624991	6625037	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	intron	6625038	6625187	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	CDS	6625188	6625221	1	+	1	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	exon	6625188	6625221	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	intron	6625222	6625303	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	CDS	6625304	6625470	1	+	0	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	exon	6625304	6625470	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	intron	6625471	6625593	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	CDS	6625594	6625645	1	+	1	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	exon	6625594	6625645	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	intron	6625646	6625734	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	CDS	6625735	6625802	1	+	0	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	exon	6625735	6625802	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	intron	6625803	6625903	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	CDS	6625904	6625967	1	+	1	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	exon	6625904	6625967	.	+	.	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
Phchi.S3	AUGUSTUS	stop_codon	6625968	6625970	.	+	0	transcript_id "Phchi.S3G074100.t1"; gene_id "Phchi.S3G074100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13377.t1 is derived from g11843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6422340	6425236	.	-	.	Phchi.S3G069600
Phchi.S3	AUGUSTUS	transcript	6422340	6425236	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	stop_codon	6422337	6422339	.	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6422340	6422490	0.95	-	1	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6422340	6422490	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6422491	6422619	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6422620	6422750	1	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6422620	6422750	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6422751	6422840	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6422841	6422912	1	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6422841	6422912	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6422913	6423006	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6423007	6423093	1	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6423007	6423093	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6423094	6423182	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6423183	6423251	1	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6423183	6423251	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6423252	6423387	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6423388	6423480	1	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6423388	6423480	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6423481	6423590	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6423591	6423679	0.81	-	2	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6423591	6423679	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6423680	6423881	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6423882	6423960	1	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6423882	6423960	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6423961	6424047	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6424048	6424177	1	-	1	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6424048	6424177	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6424178	6424321	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6424322	6424442	1	-	2	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6424322	6424442	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6424443	6424559	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6424560	6424667	1	-	2	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6424560	6424667	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6424668	6424746	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6424747	6424847	1	-	1	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6424747	6424847	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	intron	6424848	6425003	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	CDS	6425004	6425236	0.73	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	exon	6425004	6425236	.	-	.	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
Phchi.S3	AUGUSTUS	start_codon	6425234	6425236	.	-	0	transcript_id "Phchi.S3G069600.t1"; gene_id "Phchi.S3G069600"
# This transcript jg11798.t1 is derived from g15850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8203283	8203724	.	-	.	Phchi.S4G138000
Phchi.S4	AUGUSTUS	transcript	8203283	8203724	.	-	.	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	stop_codon	8203280	8203282	.	-	0	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	CDS	8203283	8203440	0.6	-	2	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	exon	8203283	8203440	.	-	.	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	intron	8203441	8203636	.	-	.	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	CDS	8203637	8203724	0.51	-	0	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	exon	8203637	8203724	.	-	.	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
Phchi.S4	AUGUSTUS	start_codon	8203722	8203724	.	-	0	transcript_id "Phchi.S4G138000.t1"; gene_id "Phchi.S4G138000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15972.t1 is derived from g14448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C266	AUGUSTUS	gene	19174	19849	.	+	.	Phchi.C266G000200
Phchi.C266	AUGUSTUS	transcript	19174	19849	.	+	.	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	start_codon	19174	19176	.	+	0	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	CDS	19174	19574	0.61	+	0	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	exon	19174	19574	.	+	.	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	intron	19575	19692	.	+	.	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	CDS	19693	19849	0.31	+	1	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	exon	19693	19849	.	+	.	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
Phchi.C266	AUGUSTUS	stop_codon	19850	19852	.	+	0	transcript_id "Phchi.C266G000200.t1"; gene_id "Phchi.C266G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1678.t1 is derived from g8597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2467707	2471306	.	-	.	Phchi.S5G028700
Phchi.S5	AUGUSTUS	transcript	2467707	2471306	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	stop_codon	2467704	2467706	.	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2467707	2467949	1	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2467707	2467949	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2467950	2468071	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2468072	2468173	1	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2468072	2468173	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2468174	2468330	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2468331	2468510	1	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2468331	2468510	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2468511	2468598	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2468599	2468676	1	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2468599	2468676	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2468677	2468858	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2468859	2468978	1	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2468859	2468978	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2468979	2469089	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2469090	2469182	0.79	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2469090	2469182	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2469183	2469283	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2469284	2469361	1	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2469284	2469361	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2469362	2469468	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2469469	2469567	0.71	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2469469	2469567	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2469568	2469686	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2469687	2470232	0.97	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2469687	2470232	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	intron	2470233	2470571	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	CDS	2470572	2471306	0.73	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	exon	2470572	2471306	.	-	.	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
Phchi.S5	AUGUSTUS	start_codon	2471304	2471306	.	-	0	transcript_id "Phchi.S5G028700.t1"; gene_id "Phchi.S5G028700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11139.t1 is derived from g15189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4363144	4364491	.	-	.	Phchi.S4G072100
Phchi.S4	AUGUSTUS	transcript	4363144	4364491	.	-	.	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	stop_codon	4363141	4363143	.	-	0	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	CDS	4363144	4363185	0.59	-	0	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	exon	4363144	4363185	.	-	.	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	intron	4363186	4363498	.	-	.	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	CDS	4363499	4364491	0.27	-	0	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	exon	4363499	4364491	.	-	.	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
Phchi.S4	AUGUSTUS	start_codon	4364489	4364491	.	-	0	transcript_id "Phchi.S4G072100.t1"; gene_id "Phchi.S4G072100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11038.t1 is derived from g15088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3764771	3767868	.	-	.	Phchi.S4G062000
Phchi.S4	AUGUSTUS	transcript	3764771	3767868	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	stop_codon	3764768	3764770	.	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3764771	3764818	0.53	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3764771	3764818	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3764819	3764883	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3764884	3764985	0.65	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3764884	3764985	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3764986	3765069	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765070	3765117	1	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765070	3765117	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765118	3765193	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765194	3765256	1	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765194	3765256	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765257	3765385	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765386	3765626	1	-	1	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765386	3765626	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765627	3765739	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765740	3765819	1	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765740	3765819	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765820	3765937	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765938	3766070	0.97	-	1	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765938	3766070	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766071	3766191	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3766192	3766397	0.99	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3766192	3766397	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766398	3766566	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3766567	3766632	1	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3766567	3766632	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766633	3766745	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3766746	3766863	0.73	-	1	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3766746	3766863	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766864	3767096	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767097	3767205	1	-	2	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767097	3767205	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3767206	3767366	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767367	3767460	1	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767367	3767460	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3767461	3767579	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767580	3767683	1	-	2	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767580	3767683	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3767684	3767774	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767775	3767868	0.85	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767775	3767868	.	-	.	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	start_codon	3767866	3767868	.	-	0	transcript_id "Phchi.S4G062000.t1"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	transcript	3764771	3767868	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	stop_codon	3764768	3764770	.	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3764771	3764818	0.46	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3764771	3764818	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3764819	3764883	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3764884	3764985	0.52	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3764884	3764985	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3764986	3765069	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765070	3765117	1	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765070	3765117	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765118	3765193	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765194	3765256	1	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765194	3765256	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765257	3765385	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765386	3765626	1	-	1	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765386	3765626	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765627	3765739	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765740	3765819	1	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765740	3765819	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3765820	3765937	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3765938	3766070	0.99	-	1	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3765938	3766070	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766071	3766191	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3766192	3766397	0.95	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3766192	3766397	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766398	3766566	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3766567	3766632	1	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3766567	3766632	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766633	3766745	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3766746	3766863	0.78	-	1	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3766746	3766863	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3766864	3767096	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767097	3767205	1	-	2	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767097	3767205	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3767206	3767366	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767367	3767460	1	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767367	3767460	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3767461	3767579	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767580	3767686	1	-	2	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767580	3767686	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	intron	3767687	3767774	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	CDS	3767775	3767868	0.87	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	exon	3767775	3767868	.	-	.	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
Phchi.S4	AUGUSTUS	start_codon	3767866	3767868	.	-	0	transcript_id "Phchi.S4G062000.t2"; gene_id "Phchi.S4G062000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg84.t1 is derived from g9866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	432587	433762	.	-	.	Phchi.S6G004300
Phchi.S6	AUGUSTUS	transcript	432587	433762	.	-	.	transcript_id "Phchi.S6G004300.t1"; gene_id "Phchi.S6G004300"
Phchi.S6	AUGUSTUS	stop_codon	432584	432586	.	-	0	transcript_id "Phchi.S6G004300.t1"; gene_id "Phchi.S6G004300"
Phchi.S6	AUGUSTUS	CDS	432587	433762	0.9	-	0	transcript_id "Phchi.S6G004300.t1"; gene_id "Phchi.S6G004300"
Phchi.S6	AUGUSTUS	exon	432587	433762	.	-	.	transcript_id "Phchi.S6G004300.t1"; gene_id "Phchi.S6G004300"
Phchi.S6	AUGUSTUS	start_codon	433760	433762	.	-	0	transcript_id "Phchi.S6G004300.t1"; gene_id "Phchi.S6G004300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6673.t1 is derived from g3845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24440208	24442370	.	+	.	Phchi.S1G383200
Phchi.S1	AUGUSTUS	transcript	24440208	24442370	.	+	.	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	start_codon	24440208	24440210	.	+	0	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	CDS	24440208	24441838	0.79	+	0	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	exon	24440208	24441838	.	+	.	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	intron	24441839	24441918	.	+	.	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	CDS	24441919	24441956	0.93	+	1	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	exon	24441919	24441956	.	+	.	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	intron	24441957	24442047	.	+	.	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	CDS	24442048	24442370	0.97	+	2	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	exon	24442048	24442370	.	+	.	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
Phchi.S1	AUGUSTUS	stop_codon	24442371	24442373	.	+	0	transcript_id "Phchi.S1G383200.t1"; gene_id "Phchi.S1G383200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10063.t1 is derived from g7239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45593112	45593852	.	+	.	Phchi.S1G722200
Phchi.S1	AUGUSTUS	transcript	45593112	45593852	.	+	.	transcript_id "Phchi.S1G722200.t1"; gene_id "Phchi.S1G722200"
Phchi.S1	AUGUSTUS	start_codon	45593112	45593114	.	+	0	transcript_id "Phchi.S1G722200.t1"; gene_id "Phchi.S1G722200"
Phchi.S1	AUGUSTUS	CDS	45593112	45593852	0.84	+	0	transcript_id "Phchi.S1G722200.t1"; gene_id "Phchi.S1G722200"
Phchi.S1	AUGUSTUS	exon	45593112	45593852	.	+	.	transcript_id "Phchi.S1G722200.t1"; gene_id "Phchi.S1G722200"
Phchi.S1	AUGUSTUS	stop_codon	45593853	45593855	.	+	0	transcript_id "Phchi.S1G722200.t1"; gene_id "Phchi.S1G722200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2224.t1 is derived from g9144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5516557	5517726	.	-	.	Phchi.S5G083300
Phchi.S5	AUGUSTUS	transcript	5516557	5517726	.	-	.	transcript_id "Phchi.S5G083300.t1"; gene_id "Phchi.S5G083300"
Phchi.S5	AUGUSTUS	stop_codon	5516554	5516556	.	-	0	transcript_id "Phchi.S5G083300.t1"; gene_id "Phchi.S5G083300"
Phchi.S5	AUGUSTUS	CDS	5516557	5517726	0.95	-	0	transcript_id "Phchi.S5G083300.t1"; gene_id "Phchi.S5G083300"
Phchi.S5	AUGUSTUS	exon	5516557	5517726	.	-	.	transcript_id "Phchi.S5G083300.t1"; gene_id "Phchi.S5G083300"
Phchi.S5	AUGUSTUS	start_codon	5517724	5517726	.	-	0	transcript_id "Phchi.S5G083300.t1"; gene_id "Phchi.S5G083300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15848.t1 is derived from g14318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21804112	21804592	.	-	.	Phchi.S3G316700
Phchi.S3	AUGUSTUS	transcript	21804112	21804592	.	-	.	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	stop_codon	21804109	21804111	.	-	0	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	CDS	21804112	21804173	0.95	-	2	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	exon	21804112	21804173	.	-	.	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	intron	21804174	21804285	.	-	.	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	CDS	21804286	21804495	0.8	-	2	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	exon	21804286	21804495	.	-	.	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	intron	21804496	21804570	.	-	.	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	CDS	21804571	21804592	0.8	-	0	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	exon	21804571	21804592	.	-	.	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
Phchi.S3	AUGUSTUS	start_codon	21804590	21804592	.	-	0	transcript_id "Phchi.S3G316700.t1"; gene_id "Phchi.S3G316700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7.t1 is derived from g3.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C31	AUGUSTUS	gene	71074	71912	.	-	.	Phchi.C31G000100
Phchi.C31	AUGUSTUS	transcript	71074	71912	.	-	.	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	stop_codon	71071	71073	.	-	0	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	CDS	71074	71163	0.61	-	0	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	exon	71074	71163	.	-	.	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	intron	71164	71257	.	-	.	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	CDS	71258	71362	0.54	-	0	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	exon	71258	71362	.	-	.	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	intron	71363	71492	.	-	.	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	CDS	71493	71912	0.49	-	0	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	exon	71493	71912	.	-	.	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
Phchi.C31	AUGUSTUS	start_codon	71910	71912	.	-	0	transcript_id "Phchi.C31G000100.t1"; gene_id "Phchi.C31G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5196.t1 is derived from g2368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15420453	15422024	.	-	.	Phchi.S1G235700
Phchi.S1	AUGUSTUS	transcript	15420453	15422024	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	stop_codon	15420450	15420452	.	-	0	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	CDS	15420453	15421242	0.33	-	1	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	exon	15420453	15421242	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	intron	15421243	15421451	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	CDS	15421452	15421525	0.35	-	0	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	exon	15421452	15421525	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	intron	15421526	15421870	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	CDS	15421871	15421906	0.39	-	0	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	exon	15421871	15421906	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	intron	15421907	15422000	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	CDS	15422001	15422024	0.9	-	0	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	exon	15422001	15422024	.	-	.	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
Phchi.S1	AUGUSTUS	start_codon	15422022	15422024	.	-	0	transcript_id "Phchi.S1G235700.t1"; gene_id "Phchi.S1G235700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9208.t1 is derived from g6383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40389367	40392294	.	-	.	Phchi.S1G636700
Phchi.S1	AUGUSTUS	transcript	40389367	40392294	.	-	.	transcript_id "Phchi.S1G636700.t1"; gene_id "Phchi.S1G636700"
Phchi.S1	AUGUSTUS	stop_codon	40389364	40389366	.	-	0	transcript_id "Phchi.S1G636700.t1"; gene_id "Phchi.S1G636700"
Phchi.S1	AUGUSTUS	CDS	40389367	40392294	0.31	-	0	transcript_id "Phchi.S1G636700.t1"; gene_id "Phchi.S1G636700"
Phchi.S1	AUGUSTUS	exon	40389367	40392294	.	-	.	transcript_id "Phchi.S1G636700.t1"; gene_id "Phchi.S1G636700"
Phchi.S1	AUGUSTUS	start_codon	40392292	40392294	.	-	0	transcript_id "Phchi.S1G636700.t1"; gene_id "Phchi.S1G636700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4934.t1 is derived from g2104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13642669	13644460	.	+	.	Phchi.S1G209300
Phchi.S1	AUGUSTUS	transcript	13642669	13644460	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	start_codon	13642669	13642671	.	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13642669	13642747	0.59	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13642669	13642747	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	intron	13642748	13642852	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13642853	13643109	0.7	+	2	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13642853	13643109	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	intron	13643110	13643224	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13643225	13643331	1	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13643225	13643331	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	intron	13643332	13643721	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13643722	13643833	1	+	1	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13643722	13643833	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	intron	13643834	13643955	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13643956	13644123	1	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13643956	13644123	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	intron	13644124	13644254	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13644255	13644305	1	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13644255	13644305	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	intron	13644306	13644400	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	CDS	13644401	13644460	0.99	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	exon	13644401	13644460	.	+	.	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
Phchi.S1	AUGUSTUS	stop_codon	13644461	13644463	.	+	0	transcript_id "Phchi.S1G209300.t1"; gene_id "Phchi.S1G209300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10575.t1 is derived from g14625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1037232	1037694	.	+	.	Phchi.S4G015700
Phchi.S4	AUGUSTUS	transcript	1037232	1037694	.	+	.	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	start_codon	1037232	1037234	.	+	0	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	CDS	1037232	1037385	0.95	+	0	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	exon	1037232	1037385	.	+	.	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	intron	1037386	1037487	.	+	.	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	CDS	1037488	1037603	0.99	+	2	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	exon	1037488	1037603	.	+	.	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	intron	1037604	1037688	.	+	.	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	CDS	1037689	1037694	1	+	0	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	exon	1037689	1037694	.	+	.	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
Phchi.S4	AUGUSTUS	stop_codon	1037695	1037697	.	+	0	transcript_id "Phchi.S4G015700.t1"; gene_id "Phchi.S4G015700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1685.t1 is derived from g8604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2493122	2499845	.	+	.	Phchi.S5G029400
Phchi.S5	AUGUSTUS	transcript	2493122	2499590	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	start_codon	2493122	2493124	.	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493122	2493156	0.65	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493122	2493156	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493157	2493360	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493361	2493394	0.88	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493361	2493394	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493395	2493623	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493624	2493630	0.88	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493624	2493630	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493631	2493707	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493708	2493739	0.88	+	2	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493708	2493739	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493740	2493832	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493833	2493866	0.88	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493833	2493866	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493867	2493933	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493934	2494103	0.88	+	2	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493934	2494103	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2494104	2494204	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2494205	2494548	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2494205	2494548	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2494549	2494663	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2494664	2494770	0.92	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2494664	2494770	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2494771	2494843	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2494844	2495020	0.53	+	2	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2494844	2495020	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495021	2495102	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495103	2495183	1	+	2	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495103	2495183	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495184	2495309	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495310	2495529	0.92	+	2	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495310	2495529	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495530	2495625	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495626	2495695	1	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495626	2495695	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495696	2495833	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495834	2495890	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495834	2495890	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495891	2495970	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495971	2496038	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495971	2496038	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496039	2496132	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496133	2496159	0.9	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496133	2496159	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496160	2496242	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496243	2496408	0.84	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496243	2496408	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496409	2496505	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496506	2496581	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496506	2496581	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496582	2496687	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496688	2496731	1	+	2	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496688	2496731	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496732	2496849	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496850	2496939	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496850	2496939	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496940	2497114	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497115	2497299	0.99	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497115	2497299	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497300	2497408	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497409	2497517	0.96	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497409	2497517	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497518	2497614	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497615	2497713	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497615	2497713	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497714	2497795	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497796	2497939	0.96	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497796	2497939	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497940	2498042	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498043	2498204	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498043	2498204	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2498205	2498337	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498338	2498559	0.94	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498338	2498559	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2498560	2498671	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498672	2498874	0.98	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498672	2498874	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2498875	2498955	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498956	2499127	1	+	1	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498956	2499127	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2499128	2499212	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2499213	2499395	1	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2499213	2499395	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2499396	2499491	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2499492	2499590	0.96	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2499492	2499590	.	+	.	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	stop_codon	2499591	2499593	.	+	0	transcript_id "Phchi.S5G029400.t1"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	transcript	2493122	2499845	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	start_codon	2493122	2493124	.	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493122	2493156	0.6	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493122	2493156	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493157	2493360	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493361	2493394	0.81	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493361	2493394	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493395	2493623	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493624	2493630	0.81	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493624	2493630	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493631	2493707	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493708	2493739	0.8	+	2	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493708	2493739	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493740	2493832	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493833	2493866	0.81	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493833	2493866	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2493867	2493933	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2493934	2494103	0.81	+	2	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2493934	2494103	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2494104	2494204	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2494205	2494548	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2494205	2494548	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2494549	2494663	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2494664	2494770	0.85	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2494664	2494770	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2494771	2494843	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2494844	2495020	0.3	+	2	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2494844	2495020	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495021	2495102	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495103	2495183	0.99	+	2	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495103	2495183	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495184	2495309	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495310	2495529	0.9	+	2	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495310	2495529	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495530	2495625	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495626	2495695	1	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495626	2495695	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495696	2495833	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495834	2495890	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495834	2495890	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2495891	2495970	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2495971	2496038	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2495971	2496038	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496039	2496132	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496133	2496159	0.88	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496133	2496159	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496160	2496242	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496243	2496408	0.87	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496243	2496408	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496409	2496505	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496506	2496581	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496506	2496581	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496582	2496687	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496688	2496731	1	+	2	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496688	2496731	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496732	2496849	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2496850	2496939	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2496850	2496939	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2496940	2497114	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497115	2497299	0.99	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497115	2497299	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497300	2497408	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497409	2497517	0.95	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497409	2497517	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497518	2497614	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497615	2497713	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497615	2497713	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497714	2497795	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2497796	2497939	0.98	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2497796	2497939	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2497940	2498042	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498043	2498204	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498043	2498204	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2498205	2498337	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498338	2498559	0.96	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498338	2498559	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2498560	2498671	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498672	2498874	0.97	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498672	2498874	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2498875	2498955	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2498956	2499127	1	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2498956	2499127	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2499128	2499212	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2499213	2499395	1	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2499213	2499395	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2499396	2499491	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2499492	2499529	0.87	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2499492	2499529	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2499530	2499633	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2499634	2499682	0.47	+	1	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2499634	2499682	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	intron	2499683	2499764	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	CDS	2499765	2499845	0.99	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	exon	2499765	2499845	.	+	.	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
Phchi.S5	AUGUSTUS	stop_codon	2499846	2499848	.	+	0	transcript_id "Phchi.S5G029400.t2"; gene_id "Phchi.S5G029400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8722.t1 is derived from g5897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37673545	37674701	.	-	.	Phchi.S1G588100
Phchi.S1	AUGUSTUS	transcript	37673545	37674701	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	stop_codon	37673542	37673544	.	-	0	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	CDS	37673545	37673669	0.88	-	2	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	exon	37673545	37673669	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	intron	37673670	37673818	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	CDS	37673819	37674068	1	-	0	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	exon	37673819	37674068	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	intron	37674069	37674222	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	CDS	37674223	37674291	1	-	0	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	exon	37674223	37674291	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	intron	37674292	37674455	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	CDS	37674456	37674701	0.84	-	0	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	exon	37674456	37674701	.	-	.	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
Phchi.S1	AUGUSTUS	start_codon	37674699	37674701	.	-	0	transcript_id "Phchi.S1G588100.t1"; gene_id "Phchi.S1G588100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3257.t1 is derived from g426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2538775	2540517	.	+	.	Phchi.S1G041600
Phchi.S1	AUGUSTUS	transcript	2538775	2540517	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	start_codon	2538775	2538777	.	+	0	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	CDS	2538775	2539066	1	+	0	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	exon	2538775	2539066	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	intron	2539067	2539244	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	CDS	2539245	2539312	1	+	2	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	exon	2539245	2539312	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	intron	2539313	2539446	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	CDS	2539447	2539636	1	+	0	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	exon	2539447	2539636	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	intron	2539637	2539746	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	CDS	2539747	2539821	0.99	+	2	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	exon	2539747	2539821	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	intron	2539822	2540008	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	CDS	2540009	2540166	0.99	+	2	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	exon	2540009	2540166	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	intron	2540167	2540313	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	CDS	2540314	2540517	0.99	+	0	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	exon	2540314	2540517	.	+	.	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
Phchi.S1	AUGUSTUS	stop_codon	2540518	2540520	.	+	0	transcript_id "Phchi.S1G041600.t1"; gene_id "Phchi.S1G041600"
# This transcript jg7492.t2 is derived from g4665.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7493.t1 is derived from g4666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29632904	29635397	.	+	.	Phchi.S1G465200
Phchi.S1	AUGUSTUS	transcript	29632904	29635397	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	start_codon	29632904	29632906	.	+	0	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29632904	29633585	0.97	+	0	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29632904	29633585	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29633586	29633682	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29633683	29633863	1	+	2	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29633683	29633863	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29633864	29633995	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29633996	29634235	0.98	+	1	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29633996	29634235	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29634236	29634334	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29634335	29634479	1	+	1	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29634335	29634479	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29634480	29634578	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29634579	29634713	1	+	0	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29634579	29634713	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29634714	29634788	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29634789	29634852	1	+	0	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29634789	29634852	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29634853	29634976	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29634977	29635054	1	+	2	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29634977	29635054	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29635055	29635142	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29635143	29635195	0.94	+	2	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29635143	29635195	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	intron	29635196	29635301	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	CDS	29635302	29635397	0.94	+	0	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	exon	29635302	29635397	.	+	.	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
Phchi.S1	AUGUSTUS	stop_codon	29635398	29635400	.	+	0	transcript_id "Phchi.S1G465200.t1"; gene_id "Phchi.S1G465200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12118.t1 is derived from g7794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3650968	3652770	.	+	.	Phchi.S2G019800
Phchi.S2	AUGUSTUS	transcript	3650968	3652770	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	start_codon	3650968	3650970	.	+	0	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	CDS	3650968	3651039	0.8	+	0	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	exon	3650968	3651039	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	intron	3651040	3651137	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	CDS	3651138	3651213	0.86	+	0	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	exon	3651138	3651213	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	intron	3651214	3651308	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	CDS	3651309	3651511	0.92	+	2	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	exon	3651309	3651511	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	intron	3651512	3651678	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	CDS	3651679	3652094	0.93	+	0	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	exon	3651679	3652094	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	intron	3652095	3652182	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	CDS	3652183	3652370	1	+	1	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	exon	3652183	3652370	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	intron	3652371	3652453	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	CDS	3652454	3652770	1	+	2	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	exon	3652454	3652770	.	+	.	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
Phchi.S2	AUGUSTUS	stop_codon	3652771	3652773	.	+	0	transcript_id "Phchi.S2G019800.t1"; gene_id "Phchi.S2G019800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1655.t1 is derived from g8574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2245804	2254238	.	+	.	Phchi.S5G026400
Phchi.S5	AUGUSTUS	transcript	2245804	2254238	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	start_codon	2245804	2245806	.	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2245804	2246235	0.38	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2245804	2246235	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2246236	2246331	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2246332	2246448	0.98	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2246332	2246448	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2246449	2246711	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2246712	2246957	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2246712	2246957	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2246958	2247114	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2247115	2247234	0.99	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2247115	2247234	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2247235	2247353	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2247354	2247629	0.74	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2247354	2247629	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2247630	2247722	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2247723	2248034	0.99	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2247723	2248034	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2248035	2248122	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2248123	2248341	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2248123	2248341	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2248342	2248447	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2248448	2248585	0.49	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2248448	2248585	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2248586	2248713	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2248714	2248959	0.73	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2248714	2248959	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2248960	2249109	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2249110	2249247	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2249110	2249247	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2249248	2249443	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2249444	2249566	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2249444	2249566	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2249567	2249683	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2249684	2249773	0.98	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2249684	2249773	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2249774	2249911	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2249912	2250253	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2249912	2250253	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2250254	2250361	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2250362	2250526	0.99	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2250362	2250526	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2250527	2250642	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2250643	2250763	0.47	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2250643	2250763	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2250764	2251013	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2251014	2251071	0.59	+	2	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2251014	2251071	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2251072	2251183	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2251184	2251262	1	+	1	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2251184	2251262	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2251263	2251366	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2251367	2251467	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2251367	2251467	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2251468	2251573	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2251574	2251633	0.99	+	1	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2251574	2251633	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2251634	2251763	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2251764	2251914	1	+	1	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2251764	2251914	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2251915	2252021	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2252022	2252180	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2252022	2252180	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2252181	2252279	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2252280	2252378	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2252280	2252378	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2252379	2252481	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2252482	2252744	0.99	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2252482	2252744	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2252745	2252875	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2252876	2253044	1	+	1	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2252876	2253044	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2253045	2253126	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2253127	2253273	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2253127	2253273	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2253274	2253424	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2253425	2253592	1	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2253425	2253592	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2253593	2253709	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2253710	2253841	0.96	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2253710	2253841	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2253842	2253943	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2253944	2254146	0.99	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2253944	2254146	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	intron	2254147	2254231	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	CDS	2254232	2254238	1	+	1	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	exon	2254232	2254238	.	+	.	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
Phchi.S5	AUGUSTUS	stop_codon	2254239	2254241	.	+	0	transcript_id "Phchi.S5G026400.t1"; gene_id "Phchi.S5G026400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9605.t1 is derived from g6781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42906808	42910339	.	-	.	Phchi.S1G676400
Phchi.S1	AUGUSTUS	transcript	42906808	42910339	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	stop_codon	42906805	42906807	.	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42906808	42906876	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42906808	42906876	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42906877	42906962	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42906963	42907079	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42906963	42907079	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42907080	42907169	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42907170	42907302	1	-	1	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42907170	42907302	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42907303	42907378	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42907379	42907455	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42907379	42907455	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42907456	42907548	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42907549	42907724	1	-	2	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42907549	42907724	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42907725	42907814	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42907815	42907896	0.99	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42907815	42907896	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42907897	42908005	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42908006	42908069	0.99	-	1	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42908006	42908069	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42908070	42908161	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42908162	42908257	1	-	1	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42908162	42908257	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42908258	42908358	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42908359	42908513	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42908359	42908513	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42908514	42908602	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42908603	42908702	0.99	-	1	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42908603	42908702	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42908703	42908819	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42908820	42908879	0.99	-	1	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42908820	42908879	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42908880	42908993	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42908994	42909094	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42908994	42909094	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42909095	42909196	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42909197	42909316	0.98	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42909197	42909316	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42909317	42909409	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42909410	42909472	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42909410	42909472	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42909473	42909611	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42909612	42909725	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42909612	42909725	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42909726	42909803	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42909804	42909859	1	-	2	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42909804	42909859	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42909860	42909950	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42909951	42910032	1	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42909951	42910032	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42910033	42910109	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42910110	42910197	1	-	1	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42910110	42910197	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	intron	42910198	42910328	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	CDS	42910329	42910339	0.71	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	exon	42910329	42910339	.	-	.	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
Phchi.S1	AUGUSTUS	start_codon	42910337	42910339	.	-	0	transcript_id "Phchi.S1G676400.t1"; gene_id "Phchi.S1G676400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3834.t1 is derived from g1003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5942389	5943539	.	-	.	Phchi.S1G099300
Phchi.S1	AUGUSTUS	transcript	5942389	5943539	.	-	.	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	stop_codon	5942386	5942388	.	-	0	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	CDS	5942389	5943069	0.63	-	0	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	exon	5942389	5943069	.	-	.	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	intron	5943070	5943183	.	-	.	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	CDS	5943184	5943404	0.6	-	2	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	exon	5943184	5943404	.	-	.	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	intron	5943405	5943514	.	-	.	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	CDS	5943515	5943539	0.73	-	0	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	exon	5943515	5943539	.	-	.	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
Phchi.S1	AUGUSTUS	start_codon	5943537	5943539	.	-	0	transcript_id "Phchi.S1G099300.t1"; gene_id "Phchi.S1G099300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3114.t1 is derived from g283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1779310	1783913	.	+	.	Phchi.S1G027300
Phchi.S1	AUGUSTUS	transcript	1779310	1783913	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	start_codon	1779310	1779312	.	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1779310	1779437	0.67	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1779310	1779437	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1779438	1779518	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1779519	1780244	0.97	+	1	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1779519	1780244	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1780245	1780396	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1780397	1780430	1	+	1	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1780397	1780430	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1780431	1780681	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1780682	1780704	1	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1780682	1780704	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1780705	1780785	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1780786	1780866	1	+	1	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1780786	1780866	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1780867	1780938	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1780939	1781086	0.96	+	1	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1780939	1781086	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1781087	1781195	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1781196	1781264	0.96	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1781196	1781264	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1781265	1781364	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1781365	1781472	1	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1781365	1781472	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1781473	1781686	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1781687	1781900	0.99	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1781687	1781900	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1781901	1781995	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1781996	1782051	0.98	+	2	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1781996	1782051	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1782052	1782164	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1782165	1782263	1	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1782165	1782263	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1782264	1782459	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1782460	1782546	1	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1782460	1782546	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1782547	1782687	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1782688	1782765	1	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1782688	1782765	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1782766	1782863	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1782864	1782949	1	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1782864	1782949	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1782950	1783068	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1783069	1783090	0.37	+	1	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1783069	1783090	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1783091	1783301	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1783302	1783307	0.4	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1783302	1783307	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1783308	1783390	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1783391	1783498	0.23	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1783391	1783498	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1783499	1783767	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1783768	1783802	0.26	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1783768	1783802	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	intron	1783803	1783873	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	CDS	1783874	1783913	1	+	1	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	exon	1783874	1783913	.	+	.	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
Phchi.S1	AUGUSTUS	stop_codon	1783914	1783916	.	+	0	transcript_id "Phchi.S1G027300.t1"; gene_id "Phchi.S1G027300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2936.t1 is derived from g105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	642721	644481	.	-	.	Phchi.S1G009500
Phchi.S1	AUGUSTUS	transcript	642721	644481	.	-	.	transcript_id "Phchi.S1G009500.t1"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	stop_codon	642718	642720	.	-	0	transcript_id "Phchi.S1G009500.t1"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	CDS	642721	644481	1	-	0	transcript_id "Phchi.S1G009500.t1"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	exon	642721	644481	.	-	.	transcript_id "Phchi.S1G009500.t1"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	start_codon	644479	644481	.	-	0	transcript_id "Phchi.S1G009500.t1"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	transcript	642721	643929	.	-	.	transcript_id "Phchi.S1G009500.t2"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	stop_codon	642718	642720	.	-	0	transcript_id "Phchi.S1G009500.t2"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	CDS	642721	643929	0.85	-	0	transcript_id "Phchi.S1G009500.t2"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	exon	642721	643929	.	-	.	transcript_id "Phchi.S1G009500.t2"; gene_id "Phchi.S1G009500"
Phchi.S1	AUGUSTUS	start_codon	643927	643929	.	-	0	transcript_id "Phchi.S1G009500.t2"; gene_id "Phchi.S1G009500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8586.t1 is derived from g5761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36745381	36746697	.	-	.	Phchi.S1G574500
Phchi.S1	AUGUSTUS	transcript	36745381	36746697	.	-	.	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	stop_codon	36745378	36745380	.	-	0	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	CDS	36745381	36746568	1	-	0	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	exon	36745381	36746568	.	-	.	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	intron	36746569	36746667	.	-	.	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	CDS	36746668	36746697	0.82	-	0	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	exon	36746668	36746697	.	-	.	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
Phchi.S1	AUGUSTUS	start_codon	36746695	36746697	.	-	0	transcript_id "Phchi.S1G574500.t1"; gene_id "Phchi.S1G574500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5928.t1 is derived from g3099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19896638	19897180	.	+	.	Phchi.S1G308700
Phchi.S1	AUGUSTUS	transcript	19896638	19897180	.	+	.	transcript_id "Phchi.S1G308700.t1"; gene_id "Phchi.S1G308700"
Phchi.S1	AUGUSTUS	start_codon	19896638	19896640	.	+	0	transcript_id "Phchi.S1G308700.t1"; gene_id "Phchi.S1G308700"
Phchi.S1	AUGUSTUS	CDS	19896638	19897180	0.46	+	0	transcript_id "Phchi.S1G308700.t1"; gene_id "Phchi.S1G308700"
Phchi.S1	AUGUSTUS	exon	19896638	19897180	.	+	.	transcript_id "Phchi.S1G308700.t1"; gene_id "Phchi.S1G308700"
Phchi.S1	AUGUSTUS	stop_codon	19897181	19897183	.	+	0	transcript_id "Phchi.S1G308700.t1"; gene_id "Phchi.S1G308700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9602.t1 is derived from g6778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42889315	42890542	.	+	.	Phchi.S1G676100
Phchi.S1	AUGUSTUS	transcript	42889315	42890542	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	start_codon	42889315	42889317	.	+	0	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42889315	42889317	1	+	0	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42889315	42889317	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	intron	42889318	42889404	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42889405	42889525	1	+	0	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42889405	42889525	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	intron	42889526	42889628	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42889629	42889665	1	+	2	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42889629	42889665	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	intron	42889666	42889811	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42889812	42889839	0.79	+	1	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42889812	42889839	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	intron	42889840	42889951	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42889952	42890104	1	+	0	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42889952	42890104	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	intron	42890105	42890254	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42890255	42890357	0.98	+	0	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42890255	42890357	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	intron	42890358	42890483	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	CDS	42890484	42890542	1	+	2	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	exon	42890484	42890542	.	+	.	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
Phchi.S1	AUGUSTUS	stop_codon	42890543	42890545	.	+	0	transcript_id "Phchi.S1G676100.t1"; gene_id "Phchi.S1G676100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12394.t1 is derived from g8071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17004121	17007917	.	+	.	Phchi.S2G047400
Phchi.S2	AUGUSTUS	transcript	17004121	17007917	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	start_codon	17004121	17004123	.	+	0	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	CDS	17004121	17005487	0.78	+	0	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	exon	17004121	17005487	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	intron	17005488	17005568	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	CDS	17005569	17005695	1	+	1	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	exon	17005569	17005695	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	intron	17005696	17005785	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	CDS	17005786	17007605	0.84	+	0	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	exon	17005786	17007605	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	intron	17007606	17007778	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	CDS	17007779	17007917	0.99	+	1	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	exon	17007779	17007917	.	+	.	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
Phchi.S2	AUGUSTUS	stop_codon	17007918	17007920	.	+	0	transcript_id "Phchi.S2G047400.t1"; gene_id "Phchi.S2G047400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9581.t1 is derived from g6757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42772642	42773256	.	-	.	Phchi.S1G674000
Phchi.S1	AUGUSTUS	transcript	42772642	42773256	.	-	.	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	stop_codon	42772639	42772641	.	-	0	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	CDS	42772642	42772980	0.95	-	0	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	exon	42772642	42772980	.	-	.	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	intron	42772981	42773073	.	-	.	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	CDS	42773074	42773256	0.92	-	0	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	exon	42773074	42773256	.	-	.	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
Phchi.S1	AUGUSTUS	start_codon	42773254	42773256	.	-	0	transcript_id "Phchi.S1G674000.t1"; gene_id "Phchi.S1G674000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1442.t1 is derived from g8361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	911129	913759	.	-	.	Phchi.S5G005100
Phchi.S5	AUGUSTUS	transcript	911129	913759	.	-	.	transcript_id "Phchi.S5G005100.t1"; gene_id "Phchi.S5G005100"
Phchi.S5	AUGUSTUS	stop_codon	911126	911128	.	-	0	transcript_id "Phchi.S5G005100.t1"; gene_id "Phchi.S5G005100"
Phchi.S5	AUGUSTUS	CDS	911129	913759	0.98	-	0	transcript_id "Phchi.S5G005100.t1"; gene_id "Phchi.S5G005100"
Phchi.S5	AUGUSTUS	exon	911129	913759	.	-	.	transcript_id "Phchi.S5G005100.t1"; gene_id "Phchi.S5G005100"
Phchi.S5	AUGUSTUS	start_codon	913757	913759	.	-	0	transcript_id "Phchi.S5G005100.t1"; gene_id "Phchi.S5G005100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3289.t1 is derived from g458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2697661	2698077	.	-	.	Phchi.S1G044800
Phchi.S1	AUGUSTUS	transcript	2697661	2698077	.	-	.	transcript_id "Phchi.S1G044800.t1"; gene_id "Phchi.S1G044800"
Phchi.S1	AUGUSTUS	stop_codon	2697658	2697660	.	-	0	transcript_id "Phchi.S1G044800.t1"; gene_id "Phchi.S1G044800"
Phchi.S1	AUGUSTUS	CDS	2697661	2698077	0.5	-	0	transcript_id "Phchi.S1G044800.t1"; gene_id "Phchi.S1G044800"
Phchi.S1	AUGUSTUS	exon	2697661	2698077	.	-	.	transcript_id "Phchi.S1G044800.t1"; gene_id "Phchi.S1G044800"
Phchi.S1	AUGUSTUS	start_codon	2698075	2698077	.	-	0	transcript_id "Phchi.S1G044800.t1"; gene_id "Phchi.S1G044800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10700.t1 is derived from g14750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1671010	1672257	.	+	.	Phchi.S4G028200
Phchi.S4	AUGUSTUS	transcript	1671010	1672257	.	+	.	transcript_id "Phchi.S4G028200.t1"; gene_id "Phchi.S4G028200"
Phchi.S4	AUGUSTUS	start_codon	1671010	1671012	.	+	0	transcript_id "Phchi.S4G028200.t1"; gene_id "Phchi.S4G028200"
Phchi.S4	AUGUSTUS	CDS	1671010	1672257	0.7	+	0	transcript_id "Phchi.S4G028200.t1"; gene_id "Phchi.S4G028200"
Phchi.S4	AUGUSTUS	exon	1671010	1672257	.	+	.	transcript_id "Phchi.S4G028200.t1"; gene_id "Phchi.S4G028200"
Phchi.S4	AUGUSTUS	stop_codon	1672258	1672260	.	+	0	transcript_id "Phchi.S4G028200.t1"; gene_id "Phchi.S4G028200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10711.t1 is derived from g14761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1710985	1712804	.	-	.	Phchi.S4G029300
Phchi.S4	AUGUSTUS	transcript	1710985	1712804	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	stop_codon	1710982	1710984	.	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	CDS	1710985	1711167	1	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	exon	1710985	1711167	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	intron	1711168	1711297	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	CDS	1711298	1711397	1	-	1	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	exon	1711298	1711397	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	intron	1711398	1711490	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	CDS	1711491	1711687	1	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	exon	1711491	1711687	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	intron	1711688	1711866	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	CDS	1711867	1711947	1	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	exon	1711867	1711947	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	intron	1711948	1712034	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	CDS	1712035	1712481	1	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	exon	1712035	1712481	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	intron	1712482	1712654	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	CDS	1712655	1712804	0.99	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	exon	1712655	1712804	.	-	.	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
Phchi.S4	AUGUSTUS	start_codon	1712802	1712804	.	-	0	transcript_id "Phchi.S4G029300.t1"; gene_id "Phchi.S4G029300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10621.t1 is derived from g14671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1274406	1274627	.	-	.	Phchi.S4G020300
Phchi.S4	AUGUSTUS	transcript	1274406	1274627	.	-	.	transcript_id "Phchi.S4G020300.t1"; gene_id "Phchi.S4G020300"
Phchi.S4	AUGUSTUS	stop_codon	1274403	1274405	.	-	0	transcript_id "Phchi.S4G020300.t1"; gene_id "Phchi.S4G020300"
Phchi.S4	AUGUSTUS	CDS	1274406	1274627	0.59	-	0	transcript_id "Phchi.S4G020300.t1"; gene_id "Phchi.S4G020300"
Phchi.S4	AUGUSTUS	exon	1274406	1274627	.	-	.	transcript_id "Phchi.S4G020300.t1"; gene_id "Phchi.S4G020300"
Phchi.S4	AUGUSTUS	start_codon	1274625	1274627	.	-	0	transcript_id "Phchi.S4G020300.t1"; gene_id "Phchi.S4G020300"
# This transcript jg15712.t2 is derived from g14182.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15713.t1 is derived from g14183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20812153	20814065	.	-	.	Phchi.S3G303200
Phchi.S3	AUGUSTUS	transcript	20812153	20814065	.	-	.	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	stop_codon	20812150	20812152	.	-	0	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	CDS	20812153	20812992	0.55	-	0	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	exon	20812153	20812992	.	-	.	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	intron	20812993	20813129	.	-	.	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	CDS	20813130	20814065	0.21	-	0	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	exon	20813130	20814065	.	-	.	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
Phchi.S3	AUGUSTUS	start_codon	20814063	20814065	.	-	0	transcript_id "Phchi.S3G303200.t1"; gene_id "Phchi.S3G303200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13883.t1 is derived from g12350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9452307	9453315	.	-	.	Phchi.S3G120200
Phchi.S3	AUGUSTUS	transcript	9452307	9453315	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	stop_codon	9452304	9452306	.	-	0	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	CDS	9452307	9452372	0.98	-	0	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	exon	9452307	9452372	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	intron	9452373	9452535	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	CDS	9452536	9452785	0.71	-	1	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	exon	9452536	9452785	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	intron	9452786	9452874	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	CDS	9452875	9452987	0.71	-	0	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	exon	9452875	9452987	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	intron	9452988	9453087	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	CDS	9453088	9453315	0.99	-	0	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	exon	9453088	9453315	.	-	.	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
Phchi.S3	AUGUSTUS	start_codon	9453313	9453315	.	-	0	transcript_id "Phchi.S3G120200.t1"; gene_id "Phchi.S3G120200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4895.t1 is derived from g2065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13288389	13289198	.	+	.	Phchi.S1G205400
Phchi.S1	AUGUSTUS	transcript	13288389	13289198	.	+	.	transcript_id "Phchi.S1G205400.t1"; gene_id "Phchi.S1G205400"
Phchi.S1	AUGUSTUS	start_codon	13288389	13288391	.	+	0	transcript_id "Phchi.S1G205400.t1"; gene_id "Phchi.S1G205400"
Phchi.S1	AUGUSTUS	CDS	13288389	13289198	0.75	+	0	transcript_id "Phchi.S1G205400.t1"; gene_id "Phchi.S1G205400"
Phchi.S1	AUGUSTUS	exon	13288389	13289198	.	+	.	transcript_id "Phchi.S1G205400.t1"; gene_id "Phchi.S1G205400"
Phchi.S1	AUGUSTUS	stop_codon	13289199	13289201	.	+	0	transcript_id "Phchi.S1G205400.t1"; gene_id "Phchi.S1G205400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9644.t1 is derived from g6820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43038512	43040215	.	+	.	Phchi.S1G680300
Phchi.S1	AUGUSTUS	transcript	43038512	43040215	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	start_codon	43038512	43038514	.	+	0	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	CDS	43038512	43038614	0.93	+	0	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	exon	43038512	43038614	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	intron	43038615	43038700	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	CDS	43038701	43038921	1	+	2	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	exon	43038701	43038921	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	intron	43038922	43039011	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	CDS	43039012	43039215	0.66	+	0	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	exon	43039012	43039215	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	intron	43039216	43039334	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	CDS	43039335	43039550	0.66	+	0	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	exon	43039335	43039550	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	intron	43039551	43039638	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	CDS	43039639	43039825	1	+	0	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	exon	43039639	43039825	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	intron	43039826	43039904	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	CDS	43039905	43040215	1	+	2	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	exon	43039905	43040215	.	+	.	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
Phchi.S1	AUGUSTUS	stop_codon	43040216	43040218	.	+	0	transcript_id "Phchi.S1G680300.t1"; gene_id "Phchi.S1G680300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11103.t1 is derived from g15153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4139526	4141385	.	-	.	Phchi.S4G068500
Phchi.S4	AUGUSTUS	transcript	4139526	4141385	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	stop_codon	4139523	4139525	.	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4139526	4139708	1	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4139526	4139708	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4139709	4139791	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4139792	4139878	1	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4139792	4139878	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4139879	4139965	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4139966	4140041	1	-	1	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4139966	4140041	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4140042	4140127	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4140128	4140378	1	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4140128	4140378	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4140379	4140449	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4140450	4140565	1	-	2	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4140450	4140565	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4140566	4140766	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4140767	4140974	0.64	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4140767	4140974	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4140975	4141059	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4141060	4141173	1	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4141060	4141173	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	intron	4141174	4141277	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	CDS	4141278	4141385	0.98	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	exon	4141278	4141385	.	-	.	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
Phchi.S4	AUGUSTUS	start_codon	4141383	4141385	.	-	0	transcript_id "Phchi.S4G068500.t1"; gene_id "Phchi.S4G068500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3035.t1 is derived from g204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1260927	1262300	.	-	.	Phchi.S1G019400
Phchi.S1	AUGUSTUS	transcript	1260927	1262300	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	stop_codon	1260924	1260926	.	-	0	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1260927	1261064	1	-	0	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1260927	1261064	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261065	1261159	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261160	1261231	1	-	0	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261160	1261231	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261232	1261326	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261327	1261435	1	-	1	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261327	1261435	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261436	1261523	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261524	1261551	0.99	-	2	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261524	1261551	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261552	1261642	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261643	1261653	0.81	-	1	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261643	1261653	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261654	1261815	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261816	1261872	1	-	1	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261816	1261872	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261873	1261988	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261989	1262038	1	-	0	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261989	1262038	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1262039	1262123	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1262124	1262300	1	-	0	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1262124	1262300	.	-	.	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	start_codon	1262298	1262300	.	-	0	transcript_id "Phchi.S1G019400.t1"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	transcript	1260927	1262300	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	stop_codon	1260924	1260926	.	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1260927	1261064	1	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1260927	1261064	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261065	1261159	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261160	1261231	1	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261160	1261231	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261232	1261326	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261327	1261435	1	-	1	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261327	1261435	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261436	1261523	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261524	1261621	0.98	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261524	1261621	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261622	1261815	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261816	1261864	0.83	-	1	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261816	1261864	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1261865	1261988	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1261989	1262038	0.85	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1261989	1262038	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	intron	1262039	1262123	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	CDS	1262124	1262300	0.99	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	exon	1262124	1262300	.	-	.	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
Phchi.S1	AUGUSTUS	start_codon	1262298	1262300	.	-	0	transcript_id "Phchi.S1G019400.t2"; gene_id "Phchi.S1G019400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10136.t1 is derived from g7312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45937508	45937950	.	-	.	Phchi.S1G729500
Phchi.S1	AUGUSTUS	transcript	45937508	45937950	.	-	.	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	stop_codon	45937505	45937507	.	-	0	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	CDS	45937508	45937842	0.49	-	2	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	exon	45937508	45937842	.	-	.	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	intron	45937843	45937937	.	-	.	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	CDS	45937938	45937950	0.93	-	0	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	exon	45937938	45937950	.	-	.	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
Phchi.S1	AUGUSTUS	start_codon	45937948	45937950	.	-	0	transcript_id "Phchi.S1G729500.t1"; gene_id "Phchi.S1G729500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9981.t1 is derived from g7157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44775711	44777176	.	-	.	Phchi.S1G714000
Phchi.S1	AUGUSTUS	transcript	44775711	44777176	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	stop_codon	44775708	44775710	.	-	0	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	CDS	44775711	44775819	0.97	-	1	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	exon	44775711	44775819	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	intron	44775820	44775973	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	CDS	44775974	44776011	0.97	-	0	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	exon	44775974	44776011	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	intron	44776012	44776079	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	CDS	44776080	44776116	1	-	1	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	exon	44776080	44776116	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	intron	44776117	44776206	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	CDS	44776207	44776248	0.65	-	1	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	exon	44776207	44776248	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	intron	44776249	44776483	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	CDS	44776484	44776837	0.71	-	1	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	exon	44776484	44776837	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	intron	44776838	44776988	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	CDS	44776989	44777176	0.43	-	0	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	exon	44776989	44777176	.	-	.	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
Phchi.S1	AUGUSTUS	start_codon	44777174	44777176	.	-	0	transcript_id "Phchi.S1G714000.t1"; gene_id "Phchi.S1G714000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4170.t1 is derived from g1339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8728620	8730506	.	+	.	Phchi.S1G132900
Phchi.S1	AUGUSTUS	transcript	8728620	8730506	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	start_codon	8728620	8728622	.	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8728620	8728778	0.62	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8728620	8728778	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8728779	8728962	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8728963	8729076	1	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8728963	8729076	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8729077	8729204	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8729205	8729367	1	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8729205	8729367	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8729368	8729454	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8729455	8729519	0.55	+	2	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8729455	8729519	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8729520	8729696	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8729697	8729797	0.99	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8729697	8729797	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8729798	8729887	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8729888	8730005	1	+	1	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8729888	8730005	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8730006	8730127	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8730128	8730265	0.87	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8730128	8730265	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	intron	8730266	8730377	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	CDS	8730378	8730506	0.75	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	exon	8730378	8730506	.	+	.	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
Phchi.S1	AUGUSTUS	stop_codon	8730507	8730509	.	+	0	transcript_id "Phchi.S1G132900.t1"; gene_id "Phchi.S1G132900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5759.t1 is derived from g2929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18834587	18836266	.	-	.	Phchi.S1G291800
Phchi.S1	AUGUSTUS	transcript	18834587	18836266	.	-	.	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	stop_codon	18834584	18834586	.	-	0	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	CDS	18834587	18835638	1	-	2	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	exon	18834587	18835638	.	-	.	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	intron	18835639	18835841	.	-	.	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	CDS	18835842	18836088	0.99	-	0	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	exon	18835842	18836088	.	-	.	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	intron	18836089	18836257	.	-	.	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	CDS	18836258	18836266	0.59	-	0	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	exon	18836258	18836266	.	-	.	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
Phchi.S1	AUGUSTUS	start_codon	18836264	18836266	.	-	0	transcript_id "Phchi.S1G291800.t1"; gene_id "Phchi.S1G291800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13182.t1 is derived from g11647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4565046	4567080	.	-	.	Phchi.S3G050100
Phchi.S3	AUGUSTUS	transcript	4565046	4567080	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	stop_codon	4565043	4565045	.	-	0	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4565046	4565112	1	-	1	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4565046	4565112	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4565113	4565189	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4565190	4565269	1	-	0	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4565190	4565269	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4565270	4565401	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4565402	4565447	1	-	1	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4565402	4565447	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4565448	4565542	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4565543	4565599	1	-	1	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4565543	4565599	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4565600	4565692	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4565693	4565751	1	-	0	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4565693	4565751	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4565752	4565830	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4565831	4565931	0.9	-	2	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4565831	4565931	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4565932	4566024	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4566025	4566146	0.9	-	1	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4566025	4566146	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4566147	4566362	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4566363	4566414	1	-	2	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4566363	4566414	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4566415	4566496	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4566497	4566592	1	-	2	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4566497	4566592	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4566593	4566669	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4566670	4566865	1	-	0	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4566670	4566865	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	intron	4566866	4566990	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	CDS	4566991	4567080	0.97	-	0	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	exon	4566991	4567080	.	-	.	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
Phchi.S3	AUGUSTUS	start_codon	4567078	4567080	.	-	0	transcript_id "Phchi.S3G050100.t1"; gene_id "Phchi.S3G050100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6006.t1 is derived from g3177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20356139	20359368	.	+	.	Phchi.S1G316500
Phchi.S1	AUGUSTUS	transcript	20356139	20359368	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	start_codon	20356139	20356141	.	+	0	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20356139	20356253	1	+	0	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20356139	20356253	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20356254	20356339	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20356340	20356442	1	+	2	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20356340	20356442	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20356443	20356534	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20356535	20356846	0.98	+	1	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20356535	20356846	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20356847	20356962	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20356963	20357143	0.95	+	1	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20356963	20357143	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20357144	20357232	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20357233	20357890	0.62	+	0	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20357233	20357890	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20357891	20357992	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20357993	20358117	1	+	2	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20357993	20358117	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20358118	20358245	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20358246	20358456	0.99	+	0	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20358246	20358456	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20358457	20358556	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20358557	20358785	0.98	+	2	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20358557	20358785	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20358786	20358902	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20358903	20359056	0.77	+	1	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20358903	20359056	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	intron	20359057	20359146	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	CDS	20359147	20359368	0.98	+	0	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	exon	20359147	20359368	.	+	.	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
Phchi.S1	AUGUSTUS	stop_codon	20359369	20359371	.	+	0	transcript_id "Phchi.S1G316500.t1"; gene_id "Phchi.S1G316500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13577.t1 is derived from g12044.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7558406	7561108	.	-	.	Phchi.S3G089600
Phchi.S3	AUGUSTUS	transcript	7558406	7561108	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	stop_codon	7558403	7558405	.	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7558406	7558511	0.94	-	1	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7558406	7558511	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7558512	7558728	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7558729	7558916	0.92	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7558729	7558916	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7558917	7558997	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7558998	7559111	0.55	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7558998	7559111	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7559112	7559265	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7559266	7559340	1	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7559266	7559340	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7559341	7559493	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7559494	7559637	1	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7559494	7559637	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7559638	7559729	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7559730	7559928	0.99	-	1	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7559730	7559928	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7559929	7560065	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7560066	7560292	1	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7560066	7560292	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7560293	7560422	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7560423	7560471	1	-	1	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7560423	7560471	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7560472	7560965	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7560966	7561108	0.71	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7560966	7561108	.	-	.	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	start_codon	7561106	7561108	.	-	0	transcript_id "Phchi.S3G089600.t1"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	transcript	7559636	7561108	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	stop_codon	7559633	7559635	.	-	0	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7559636	7559637	0.78	-	2	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7559636	7559637	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7559638	7559722	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7559723	7559928	0.76	-	1	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7559723	7559928	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7559929	7560065	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7560066	7560292	1	-	0	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7560066	7560292	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7560293	7560422	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7560423	7560471	1	-	1	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7560423	7560471	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	intron	7560472	7560965	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	CDS	7560966	7561108	0.69	-	0	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	exon	7560966	7561108	.	-	.	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
Phchi.S3	AUGUSTUS	start_codon	7561106	7561108	.	-	0	transcript_id "Phchi.S3G089600.t2"; gene_id "Phchi.S3G089600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3612.t1 is derived from g781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4745334	4745552	.	-	.	Phchi.S1G077100
Phchi.S1	AUGUSTUS	transcript	4745334	4745552	.	-	.	transcript_id "Phchi.S1G077100.t1"; gene_id "Phchi.S1G077100"
Phchi.S1	AUGUSTUS	stop_codon	4745331	4745333	.	-	0	transcript_id "Phchi.S1G077100.t1"; gene_id "Phchi.S1G077100"
Phchi.S1	AUGUSTUS	CDS	4745334	4745552	1	-	0	transcript_id "Phchi.S1G077100.t1"; gene_id "Phchi.S1G077100"
Phchi.S1	AUGUSTUS	exon	4745334	4745552	.	-	.	transcript_id "Phchi.S1G077100.t1"; gene_id "Phchi.S1G077100"
Phchi.S1	AUGUSTUS	start_codon	4745550	4745552	.	-	0	transcript_id "Phchi.S1G077100.t1"; gene_id "Phchi.S1G077100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5446.t1 is derived from g2616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16900119	16905060	.	-	.	Phchi.S1G260500
Phchi.S1	AUGUSTUS	transcript	16900119	16905060	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	stop_codon	16900116	16900118	.	-	0	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16900119	16901105	0.81	-	0	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16900119	16901105	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16901106	16901228	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16901229	16901832	0.96	-	1	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16901229	16901832	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16901833	16901933	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16901934	16902453	0.39	-	2	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16901934	16902453	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16902454	16902563	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16902564	16902783	0.32	-	0	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16902564	16902783	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16902784	16902911	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16902912	16903752	0.76	-	1	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16902912	16903752	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16903753	16903847	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16903848	16904048	0.96	-	1	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16903848	16904048	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16904049	16904228	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16904229	16904728	0.32	-	0	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16904229	16904728	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	intron	16904729	16904826	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	CDS	16904827	16905060	0.35	-	0	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	exon	16904827	16905060	.	-	.	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
Phchi.S1	AUGUSTUS	start_codon	16905058	16905060	.	-	0	transcript_id "Phchi.S1G260500.t1"; gene_id "Phchi.S1G260500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14305.t1 is derived from g12772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12025463	12028525	.	-	.	Phchi.S3G162400
Phchi.S3	AUGUSTUS	transcript	12025463	12028525	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	stop_codon	12025460	12025462	.	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12025463	12025751	0.74	-	1	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12025463	12025751	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12025752	12025834	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12025835	12025995	0.87	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12025835	12025995	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12025996	12026136	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12026137	12026292	0.87	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12026137	12026292	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12026293	12026403	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12026404	12026573	0.43	-	2	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12026404	12026573	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12026574	12026840	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12026841	12026961	0.43	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12026841	12026961	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12026962	12027091	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12027092	12027228	0.95	-	2	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12027092	12027228	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12027229	12027332	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12027333	12027379	0.96	-	1	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12027333	12027379	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12027380	12027540	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12027541	12027617	0.92	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12027541	12027617	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12027618	12027744	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12027745	12028074	1	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12027745	12028074	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12028075	12028169	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12028170	12028355	0.96	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12028170	12028355	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	intron	12028356	12028459	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	CDS	12028460	12028525	0.91	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	exon	12028460	12028525	.	-	.	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
Phchi.S3	AUGUSTUS	start_codon	12028523	12028525	.	-	0	transcript_id "Phchi.S3G162400.t1"; gene_id "Phchi.S3G162400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14522.t1 is derived from g12990.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13301710	13302790	.	-	.	Phchi.S3G184100
Phchi.S3	AUGUSTUS	transcript	13301834	13302790	.	-	.	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	stop_codon	13301831	13301833	.	-	0	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	CDS	13301834	13301841	0.96	-	2	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	exon	13301834	13301841	.	-	.	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	intron	13301842	13301987	.	-	.	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	CDS	13301988	13302419	0.91	-	2	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	exon	13301988	13302419	.	-	.	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	intron	13302420	13302519	.	-	.	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	CDS	13302520	13302790	1	-	0	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	exon	13302520	13302790	.	-	.	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	start_codon	13302788	13302790	.	-	0	transcript_id "Phchi.S3G184100.t1"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	transcript	13301710	13302790	.	-	.	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	stop_codon	13301707	13301709	.	-	0	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	CDS	13301710	13301822	0.42	-	2	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	exon	13301710	13301822	.	-	.	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	intron	13301823	13301987	.	-	.	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	CDS	13301988	13302419	0.95	-	2	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	exon	13301988	13302419	.	-	.	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	intron	13302420	13302519	.	-	.	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	CDS	13302520	13302790	0.98	-	0	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	exon	13302520	13302790	.	-	.	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
Phchi.S3	AUGUSTUS	start_codon	13302788	13302790	.	-	0	transcript_id "Phchi.S3G184100.t2"; gene_id "Phchi.S3G184100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1407.t1 is derived from g8326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	182674	183376	.	-	.	Phchi.S5G001600
Phchi.S5	AUGUSTUS	transcript	182674	183376	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	stop_codon	182671	182673	.	-	0	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	CDS	182674	182778	1	-	0	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	exon	182674	182778	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	intron	182779	182865	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	CDS	182866	182940	1	-	0	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	exon	182866	182940	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	intron	182941	183056	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	CDS	183057	183281	0.93	-	0	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	exon	183057	183281	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	intron	183282	183358	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	CDS	183359	183376	0.91	-	0	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	exon	183359	183376	.	-	.	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
Phchi.S5	AUGUSTUS	start_codon	183374	183376	.	-	0	transcript_id "Phchi.S5G001600.t1"; gene_id "Phchi.S5G001600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg854.t1 is derived from g10636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5949612	5949989	.	-	.	Phchi.S6G081300
Phchi.S6	AUGUSTUS	transcript	5949612	5949989	.	-	.	transcript_id "Phchi.S6G081300.t1"; gene_id "Phchi.S6G081300"
Phchi.S6	AUGUSTUS	stop_codon	5949609	5949611	.	-	0	transcript_id "Phchi.S6G081300.t1"; gene_id "Phchi.S6G081300"
Phchi.S6	AUGUSTUS	CDS	5949612	5949989	0.77	-	0	transcript_id "Phchi.S6G081300.t1"; gene_id "Phchi.S6G081300"
Phchi.S6	AUGUSTUS	exon	5949612	5949989	.	-	.	transcript_id "Phchi.S6G081300.t1"; gene_id "Phchi.S6G081300"
Phchi.S6	AUGUSTUS	start_codon	5949987	5949989	.	-	0	transcript_id "Phchi.S6G081300.t1"; gene_id "Phchi.S6G081300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3177.t1 is derived from g346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2113604	2115433	.	+	.	Phchi.S1G033600
Phchi.S1	AUGUSTUS	transcript	2113604	2115433	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	start_codon	2113604	2113606	.	+	0	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	CDS	2113604	2113679	0.79	+	0	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	exon	2113604	2113679	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	intron	2113680	2113787	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	CDS	2113788	2113964	0.87	+	2	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	exon	2113788	2113964	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	intron	2113965	2114102	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	CDS	2114103	2114261	1	+	2	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	exon	2114103	2114261	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	intron	2114262	2114338	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	CDS	2114339	2114566	1	+	2	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	exon	2114339	2114566	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	intron	2114567	2114735	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	CDS	2114736	2115433	0.93	+	2	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	exon	2114736	2115433	.	+	.	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
Phchi.S1	AUGUSTUS	stop_codon	2115434	2115436	.	+	0	transcript_id "Phchi.S1G033600.t1"; gene_id "Phchi.S1G033600"
# This transcript jg1690.t2 is derived from g8609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1691.t1 is derived from g8610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2524558	2524881	.	-	.	Phchi.S5G030000
Phchi.S5	AUGUSTUS	transcript	2524558	2524881	.	-	.	transcript_id "Phchi.S5G030000.t1"; gene_id "Phchi.S5G030000"
Phchi.S5	AUGUSTUS	stop_codon	2524555	2524557	.	-	0	transcript_id "Phchi.S5G030000.t1"; gene_id "Phchi.S5G030000"
Phchi.S5	AUGUSTUS	CDS	2524558	2524881	0.83	-	0	transcript_id "Phchi.S5G030000.t1"; gene_id "Phchi.S5G030000"
Phchi.S5	AUGUSTUS	exon	2524558	2524881	.	-	.	transcript_id "Phchi.S5G030000.t1"; gene_id "Phchi.S5G030000"
Phchi.S5	AUGUSTUS	start_codon	2524879	2524881	.	-	0	transcript_id "Phchi.S5G030000.t1"; gene_id "Phchi.S5G030000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11799.t1 is derived from g15851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8204336	8206663	.	-	.	Phchi.S4G138100
Phchi.S4	AUGUSTUS	transcript	8204336	8206663	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	stop_codon	8204333	8204335	.	-	0	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	CDS	8204336	8204767	0.97	-	0	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	exon	8204336	8204767	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	intron	8204768	8204917	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	CDS	8204918	8206318	1	-	0	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	exon	8204918	8206318	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	intron	8206319	8206450	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	CDS	8206451	8206572	0.92	-	2	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	exon	8206451	8206572	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	intron	8206573	8206653	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	CDS	8206654	8206663	0.92	-	0	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	exon	8206654	8206663	.	-	.	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
Phchi.S4	AUGUSTUS	start_codon	8206661	8206663	.	-	0	transcript_id "Phchi.S4G138100.t1"; gene_id "Phchi.S4G138100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6926.t1 is derived from g4098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26027071	26027812	.	-	.	Phchi.S1G408500
Phchi.S1	AUGUSTUS	transcript	26027071	26027812	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	stop_codon	26027068	26027070	.	-	0	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	CDS	26027071	26027136	1	-	0	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	exon	26027071	26027136	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	intron	26027137	26027214	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	CDS	26027215	26027262	1	-	0	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	exon	26027215	26027262	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	intron	26027263	26027458	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	CDS	26027459	26027616	1	-	2	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	exon	26027459	26027616	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	intron	26027617	26027718	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	CDS	26027719	26027812	1	-	0	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	exon	26027719	26027812	.	-	.	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
Phchi.S1	AUGUSTUS	start_codon	26027810	26027812	.	-	0	transcript_id "Phchi.S1G408500.t1"; gene_id "Phchi.S1G408500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4022.t1 is derived from g1191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7207312	7208815	.	-	.	Phchi.S1G118100
Phchi.S1	AUGUSTUS	transcript	7207312	7208815	.	-	.	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	stop_codon	7207309	7207311	.	-	0	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	CDS	7207312	7207536	0.98	-	0	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	exon	7207312	7207536	.	-	.	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	intron	7207537	7207733	.	-	.	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	CDS	7207734	7207835	0.94	-	0	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	exon	7207734	7207835	.	-	.	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	intron	7207836	7208374	.	-	.	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	CDS	7208375	7208815	0.41	-	0	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	exon	7208375	7208815	.	-	.	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
Phchi.S1	AUGUSTUS	start_codon	7208813	7208815	.	-	0	transcript_id "Phchi.S1G118100.t1"; gene_id "Phchi.S1G118100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6686.t1 is derived from g3858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24508135	24508560	.	-	.	Phchi.S1G384500
Phchi.S1	AUGUSTUS	transcript	24508135	24508560	.	-	.	transcript_id "Phchi.S1G384500.t1"; gene_id "Phchi.S1G384500"
Phchi.S1	AUGUSTUS	stop_codon	24508132	24508134	.	-	0	transcript_id "Phchi.S1G384500.t1"; gene_id "Phchi.S1G384500"
Phchi.S1	AUGUSTUS	CDS	24508135	24508560	0.44	-	0	transcript_id "Phchi.S1G384500.t1"; gene_id "Phchi.S1G384500"
Phchi.S1	AUGUSTUS	exon	24508135	24508560	.	-	.	transcript_id "Phchi.S1G384500.t1"; gene_id "Phchi.S1G384500"
Phchi.S1	AUGUSTUS	start_codon	24508558	24508560	.	-	0	transcript_id "Phchi.S1G384500.t1"; gene_id "Phchi.S1G384500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1896.t1 is derived from g8816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3768991	3769738	.	+	.	Phchi.S5G050500
Phchi.S5	AUGUSTUS	transcript	3768991	3769738	.	+	.	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	start_codon	3768991	3768993	.	+	0	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	CDS	3768991	3769323	0.19	+	0	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	exon	3768991	3769323	.	+	.	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	intron	3769324	3769545	.	+	.	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	CDS	3769546	3769620	0.36	+	0	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	exon	3769546	3769620	.	+	.	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	intron	3769621	3769699	.	+	.	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	CDS	3769700	3769738	0.48	+	0	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	exon	3769700	3769738	.	+	.	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
Phchi.S5	AUGUSTUS	stop_codon	3769739	3769741	.	+	0	transcript_id "Phchi.S5G050500.t1"; gene_id "Phchi.S5G050500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3762.t1 is derived from g931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5572638	5574144	.	-	.	Phchi.S1G092100
Phchi.S1	AUGUSTUS	transcript	5572638	5574144	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	stop_codon	5572635	5572637	.	-	0	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	CDS	5572638	5572838	1	-	0	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	exon	5572638	5572838	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	intron	5572839	5572931	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	CDS	5572932	5572954	0.97	-	2	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	exon	5572932	5572954	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	intron	5572955	5573098	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	CDS	5573099	5573138	0.99	-	0	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	exon	5573099	5573138	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	intron	5573139	5573229	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	CDS	5573230	5573421	1	-	0	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	exon	5573230	5573421	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	intron	5573422	5573511	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	CDS	5573512	5574144	0.96	-	0	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	exon	5573512	5574144	.	-	.	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
Phchi.S1	AUGUSTUS	start_codon	5574142	5574144	.	-	0	transcript_id "Phchi.S1G092100.t1"; gene_id "Phchi.S1G092100"
# This transcript jg5476.t2 is derived from g2646.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5476.t3 is derived from g2646.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5477.t1 is derived from g2647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17041545	17042638	.	+	.	Phchi.S1G263600
Phchi.S1	AUGUSTUS	transcript	17041545	17042638	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	start_codon	17041545	17041547	.	+	0	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	CDS	17041545	17041548	0.99	+	0	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	exon	17041545	17041548	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	intron	17041549	17041703	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	CDS	17041704	17041870	1	+	2	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	exon	17041704	17041870	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	intron	17041871	17042104	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	CDS	17042105	17042302	1	+	0	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	exon	17042105	17042302	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	intron	17042303	17042395	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	CDS	17042396	17042638	0.97	+	0	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	exon	17042396	17042638	.	+	.	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
Phchi.S1	AUGUSTUS	stop_codon	17042639	17042641	.	+	0	transcript_id "Phchi.S1G263600.t1"; gene_id "Phchi.S1G263600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5860.t1 is derived from g3030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19461414	19464062	.	-	.	Phchi.S1G301900
Phchi.S1	AUGUSTUS	transcript	19461414	19464062	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	stop_codon	19461411	19461413	.	-	0	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19461414	19461601	0.58	-	2	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19461414	19461601	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19461602	19461752	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19461753	19461821	1	-	2	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19461753	19461821	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19461822	19461906	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19461907	19462039	1	-	0	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19461907	19462039	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19462040	19462123	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19462124	19462347	1	-	2	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19462124	19462347	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19462348	19462438	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19462439	19462740	0.97	-	1	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19462439	19462740	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19462741	19462845	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19462846	19462914	1	-	1	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19462846	19462914	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19462915	19463153	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19463154	19463225	1	-	1	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19463154	19463225	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19463226	19463323	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19463324	19463395	1	-	1	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19463324	19463395	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19463396	19463467	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19463468	19463582	1	-	2	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19463468	19463582	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19463583	19463708	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19463709	19463947	1	-	1	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19463709	19463947	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	intron	19463948	19464039	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	CDS	19464040	19464062	1	-	0	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	exon	19464040	19464062	.	-	.	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
Phchi.S1	AUGUSTUS	start_codon	19464060	19464062	.	-	0	transcript_id "Phchi.S1G301900.t1"; gene_id "Phchi.S1G301900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11163.t1 is derived from g15213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4433077	4437119	.	+	.	Phchi.S4G074500
Phchi.S4	AUGUSTUS	transcript	4433077	4437119	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	start_codon	4433077	4433079	.	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4433077	4433119	0.92	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4433077	4433119	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4433120	4433237	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4433238	4433287	1	+	2	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4433238	4433287	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4433288	4433426	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4433427	4433459	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4433427	4433459	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4433460	4433606	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4433607	4434680	0.99	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4433607	4434680	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4434681	4434794	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4434795	4435349	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4434795	4435349	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4435350	4435529	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4435530	4435640	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4435530	4435640	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4435641	4435749	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4435750	4435839	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4435750	4435839	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4435840	4435949	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4435950	4436021	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4435950	4436021	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4436022	4436131	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4436132	4436242	0.97	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4436132	4436242	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4436243	4436321	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4436322	4436448	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4436322	4436448	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4436449	4436522	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4436523	4436716	1	+	2	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4436523	4436716	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	intron	4436717	4436789	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	CDS	4436790	4437119	1	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	exon	4436790	4437119	.	+	.	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
Phchi.S4	AUGUSTUS	stop_codon	4437120	4437122	.	+	0	transcript_id "Phchi.S4G074500.t1"; gene_id "Phchi.S4G074500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4343.t1 is derived from g1512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9861805	9864416	.	-	.	Phchi.S1G150200
Phchi.S1	AUGUSTUS	transcript	9861805	9864416	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	stop_codon	9861802	9861804	.	-	0	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	CDS	9861805	9861806	0.71	-	2	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	exon	9861805	9861806	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	intron	9861807	9861967	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	CDS	9861968	9862162	0.71	-	2	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	exon	9861968	9862162	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	intron	9862163	9862261	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	CDS	9862262	9862939	0.98	-	2	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	exon	9862262	9862939	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	intron	9862940	9863038	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	CDS	9863039	9864416	0.98	-	0	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	exon	9863039	9864416	.	-	.	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
Phchi.S1	AUGUSTUS	start_codon	9864414	9864416	.	-	0	transcript_id "Phchi.S1G150200.t1"; gene_id "Phchi.S1G150200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7905.t1 is derived from g5079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31826902	31827612	.	-	.	Phchi.S1G506400
Phchi.S1	AUGUSTUS	transcript	31826902	31827612	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	stop_codon	31826899	31826901	.	-	0	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	CDS	31826902	31826937	1	-	0	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	exon	31826902	31826937	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	intron	31826938	31827037	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	CDS	31827038	31827167	1	-	1	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	exon	31827038	31827167	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	intron	31827168	31827255	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	CDS	31827256	31827359	1	-	0	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	exon	31827256	31827359	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	intron	31827360	31827495	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	CDS	31827496	31827612	1	-	0	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	exon	31827496	31827612	.	-	.	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
Phchi.S1	AUGUSTUS	start_codon	31827610	31827612	.	-	0	transcript_id "Phchi.S1G506400.t1"; gene_id "Phchi.S1G506400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1622.t1 is derived from g8541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2064502	2065146	.	-	.	Phchi.S5G023100
Phchi.S5	AUGUSTUS	transcript	2064502	2065146	.	-	.	transcript_id "Phchi.S5G023100.t1"; gene_id "Phchi.S5G023100"
Phchi.S5	AUGUSTUS	stop_codon	2064499	2064501	.	-	0	transcript_id "Phchi.S5G023100.t1"; gene_id "Phchi.S5G023100"
Phchi.S5	AUGUSTUS	CDS	2064502	2065146	0.92	-	0	transcript_id "Phchi.S5G023100.t1"; gene_id "Phchi.S5G023100"
Phchi.S5	AUGUSTUS	exon	2064502	2065146	.	-	.	transcript_id "Phchi.S5G023100.t1"; gene_id "Phchi.S5G023100"
Phchi.S5	AUGUSTUS	start_codon	2065144	2065146	.	-	0	transcript_id "Phchi.S5G023100.t1"; gene_id "Phchi.S5G023100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8113.t1 is derived from g5288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33226097	33228271	.	-	.	Phchi.S1G527200
Phchi.S1	AUGUSTUS	transcript	33226097	33228271	.	-	.	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	stop_codon	33226094	33226096	.	-	0	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	CDS	33226097	33226141	1	-	0	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	exon	33226097	33226141	.	-	.	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	intron	33226142	33226235	.	-	.	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	CDS	33226236	33226325	1	-	0	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	exon	33226236	33226325	.	-	.	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	intron	33226326	33226474	.	-	.	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	CDS	33226475	33228271	0.76	-	0	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	exon	33226475	33228271	.	-	.	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
Phchi.S1	AUGUSTUS	start_codon	33228269	33228271	.	-	0	transcript_id "Phchi.S1G527200.t1"; gene_id "Phchi.S1G527200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15349.t1 is derived from g13817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18516108	18519453	.	+	.	Phchi.S3G266800
Phchi.S3	AUGUSTUS	transcript	18516108	18519453	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	start_codon	18516108	18516110	.	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18516108	18516141	0.47	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18516108	18516141	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18516142	18516229	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18516230	18516487	0.46	+	2	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18516230	18516487	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18516488	18516588	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18516589	18516640	1	+	2	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18516589	18516640	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18516641	18516791	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18516792	18516847	1	+	1	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18516792	18516847	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18516848	18516985	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18516986	18517144	1	+	2	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18516986	18517144	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18517145	18517248	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18517249	18517353	1	+	2	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18517249	18517353	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18517354	18517446	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18517447	18517553	1	+	2	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18517447	18517553	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18517554	18517623	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18517624	18517745	1	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18517624	18517745	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18517746	18517830	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18517831	18517939	1	+	1	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18517831	18517939	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18517940	18518015	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18518016	18518149	1	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18518016	18518149	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18518150	18518232	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18518233	18518623	1	+	1	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18518233	18518623	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18518624	18518698	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18518699	18518812	1	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18518699	18518812	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18518813	18518899	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18518900	18518985	1	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18518900	18518985	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18518986	18519073	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18519074	18519183	1	+	1	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18519074	18519183	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	intron	18519184	18519271	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	CDS	18519272	18519453	1	+	2	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	exon	18519272	18519453	.	+	.	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
Phchi.S3	AUGUSTUS	stop_codon	18519454	18519456	.	+	0	transcript_id "Phchi.S3G266800.t1"; gene_id "Phchi.S3G266800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15311.t1 is derived from g13779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18345956	18347267	.	+	.	Phchi.S3G263000
Phchi.S3	AUGUSTUS	transcript	18345956	18347267	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	start_codon	18345956	18345958	.	+	0	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	CDS	18345956	18346313	0.81	+	0	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	exon	18345956	18346313	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	intron	18346314	18346392	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	CDS	18346393	18346544	0.93	+	2	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	exon	18346393	18346544	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	intron	18346545	18346633	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	CDS	18346634	18346682	1	+	0	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	exon	18346634	18346682	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	intron	18346683	18346773	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	CDS	18346774	18347267	1	+	2	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	exon	18346774	18347267	.	+	.	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
Phchi.S3	AUGUSTUS	stop_codon	18347268	18347270	.	+	0	transcript_id "Phchi.S3G263000.t1"; gene_id "Phchi.S3G263000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4118.t1 is derived from g1287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8354590	8355138	.	+	.	Phchi.S1G127700
Phchi.S1	AUGUSTUS	transcript	8354590	8355138	.	+	.	transcript_id "Phchi.S1G127700.t1"; gene_id "Phchi.S1G127700"
Phchi.S1	AUGUSTUS	start_codon	8354590	8354592	.	+	0	transcript_id "Phchi.S1G127700.t1"; gene_id "Phchi.S1G127700"
Phchi.S1	AUGUSTUS	CDS	8354590	8355138	0.78	+	0	transcript_id "Phchi.S1G127700.t1"; gene_id "Phchi.S1G127700"
Phchi.S1	AUGUSTUS	exon	8354590	8355138	.	+	.	transcript_id "Phchi.S1G127700.t1"; gene_id "Phchi.S1G127700"
Phchi.S1	AUGUSTUS	stop_codon	8355139	8355141	.	+	0	transcript_id "Phchi.S1G127700.t1"; gene_id "Phchi.S1G127700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7837.t1 is derived from g5011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31461370	31468628	.	+	.	Phchi.S1G499600
Phchi.S1	AUGUSTUS	transcript	31461370	31468628	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	start_codon	31461370	31461372	.	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31461370	31461391	0.98	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31461370	31461391	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31461392	31461607	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31461608	31461694	0.98	+	2	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31461608	31461694	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31461695	31461835	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31461836	31462251	0.39	+	2	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31461836	31462251	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31462252	31462367	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31462368	31462813	0.39	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31462368	31462813	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31462814	31462970	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31462971	31463112	1	+	1	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31462971	31463112	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31463113	31463350	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31463351	31465742	0.93	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31463351	31465742	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31465743	31465825	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31465826	31466106	0.99	+	2	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31465826	31466106	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31466107	31466239	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31466240	31466333	1	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31466240	31466333	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31466334	31466474	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31466475	31466932	1	+	2	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31466475	31466932	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31466933	31467046	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31467047	31468219	1	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31467047	31468219	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31468220	31468395	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31468396	31468473	1	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31468396	31468473	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	intron	31468474	31468562	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	CDS	31468563	31468628	1	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	exon	31468563	31468628	.	+	.	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
Phchi.S1	AUGUSTUS	stop_codon	31468629	31468631	.	+	0	transcript_id "Phchi.S1G499600.t1"; gene_id "Phchi.S1G499600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8885.t1 is derived from g6060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38483558	38485057	.	-	.	Phchi.S1G604400
Phchi.S1	AUGUSTUS	transcript	38483558	38485057	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	stop_codon	38483555	38483557	.	-	0	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	CDS	38483558	38483595	0.97	-	2	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	exon	38483558	38483595	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	intron	38483596	38483670	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	CDS	38483671	38483797	0.73	-	0	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	exon	38483671	38483797	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	intron	38483798	38483909	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	CDS	38483910	38483971	0.71	-	2	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	exon	38483910	38483971	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	intron	38483972	38484067	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	CDS	38484068	38484447	1	-	1	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	exon	38484068	38484447	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	intron	38484448	38484527	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	CDS	38484528	38485057	1	-	0	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	exon	38484528	38485057	.	-	.	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
Phchi.S1	AUGUSTUS	start_codon	38485055	38485057	.	-	0	transcript_id "Phchi.S1G604400.t1"; gene_id "Phchi.S1G604400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3019.t1 is derived from g188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1168912	1172338	.	-	.	Phchi.S1G017800
Phchi.S1	AUGUSTUS	transcript	1168912	1172338	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	stop_codon	1168909	1168911	.	-	0	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1168912	1169014	0.49	-	1	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1168912	1169014	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1169015	1169100	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1169101	1169397	1	-	1	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1169101	1169397	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1169398	1169484	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1169485	1170362	0.97	-	0	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1169485	1170362	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1170363	1170499	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1170500	1170573	1	-	2	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1170500	1170573	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1170574	1170739	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1170740	1170774	1	-	1	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1170740	1170774	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1170775	1170871	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1170872	1171009	1	-	1	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1170872	1171009	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1171010	1171147	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1171148	1171200	0.98	-	0	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1171148	1171200	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1171201	1171342	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1171343	1171497	0.58	-	2	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1171343	1171497	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1171498	1171720	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1171721	1171791	0.85	-	1	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1171721	1171791	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	intron	1171792	1172030	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	CDS	1172031	1172338	0.7	-	0	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	exon	1172031	1172338	.	-	.	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
Phchi.S1	AUGUSTUS	start_codon	1172336	1172338	.	-	0	transcript_id "Phchi.S1G017800.t1"; gene_id "Phchi.S1G017800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12752.t1 is derived from g11217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1894028	1896042	.	-	.	Phchi.S3G007100
Phchi.S3	AUGUSTUS	transcript	1894028	1896042	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	stop_codon	1894025	1894027	.	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1894028	1894134	1	-	2	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1894028	1894134	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1894135	1894218	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1894219	1894289	1	-	1	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1894219	1894289	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1894290	1894514	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1894515	1894566	1	-	2	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1894515	1894566	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1894567	1894752	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1894753	1894849	1	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1894753	1894849	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1894850	1894935	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1894936	1895013	1	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1894936	1895013	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1895014	1895156	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1895157	1895273	1	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1895157	1895273	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1895274	1895365	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1895366	1895470	1	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1895366	1895470	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1895471	1895634	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1895635	1895709	1	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1895635	1895709	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1895710	1895798	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1895799	1895858	0.79	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1895799	1895858	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	intron	1895859	1895967	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	CDS	1895968	1896042	0.59	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	exon	1895968	1896042	.	-	.	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
Phchi.S3	AUGUSTUS	start_codon	1896040	1896042	.	-	0	transcript_id "Phchi.S3G007100.t1"; gene_id "Phchi.S3G007100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6048.t1 is derived from g3219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20618293	20620370	.	+	.	Phchi.S1G320700
Phchi.S1	AUGUSTUS	transcript	20618293	20620370	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	start_codon	20618293	20618295	.	+	0	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	CDS	20618293	20619022	0.57	+	0	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	exon	20618293	20619022	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	intron	20619023	20619137	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	CDS	20619138	20619325	0.93	+	2	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	exon	20619138	20619325	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	intron	20619326	20619388	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	CDS	20619389	20619689	0.87	+	0	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	exon	20619389	20619689	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	intron	20619690	20619763	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	CDS	20619764	20619822	0.81	+	2	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	exon	20619764	20619822	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	intron	20619823	20619909	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	CDS	20619910	20620112	0.68	+	0	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	exon	20619910	20620112	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	intron	20620113	20620186	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	CDS	20620187	20620370	1	+	1	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	exon	20620187	20620370	.	+	.	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
Phchi.S1	AUGUSTUS	stop_codon	20620371	20620373	.	+	0	transcript_id "Phchi.S1G320700.t1"; gene_id "Phchi.S1G320700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15404.t1 is derived from g13872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18829460	18830556	.	-	.	Phchi.S3G272300
Phchi.S3	AUGUSTUS	transcript	18829460	18830556	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	stop_codon	18829457	18829459	.	-	0	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	CDS	18829460	18829602	0.99	-	2	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	exon	18829460	18829602	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	intron	18829603	18829694	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	CDS	18829695	18830048	0.97	-	2	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	exon	18829695	18830048	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	intron	18830049	18830229	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	CDS	18830230	18830372	1	-	1	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	exon	18830230	18830372	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	intron	18830373	18830446	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	CDS	18830447	18830556	0.73	-	0	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	exon	18830447	18830556	.	-	.	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
Phchi.S3	AUGUSTUS	start_codon	18830554	18830556	.	-	0	transcript_id "Phchi.S3G272300.t1"; gene_id "Phchi.S3G272300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg359.t1 is derived from g10141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2627334	2628641	.	-	.	Phchi.S6G031800
Phchi.S6	AUGUSTUS	transcript	2627334	2628641	.	-	.	transcript_id "Phchi.S6G031800.t1"; gene_id "Phchi.S6G031800"
Phchi.S6	AUGUSTUS	stop_codon	2627331	2627333	.	-	0	transcript_id "Phchi.S6G031800.t1"; gene_id "Phchi.S6G031800"
Phchi.S6	AUGUSTUS	CDS	2627334	2628641	0.63	-	0	transcript_id "Phchi.S6G031800.t1"; gene_id "Phchi.S6G031800"
Phchi.S6	AUGUSTUS	exon	2627334	2628641	.	-	.	transcript_id "Phchi.S6G031800.t1"; gene_id "Phchi.S6G031800"
Phchi.S6	AUGUSTUS	start_codon	2628639	2628641	.	-	0	transcript_id "Phchi.S6G031800.t1"; gene_id "Phchi.S6G031800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5601.t1 is derived from g2771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17833065	17835218	.	+	.	Phchi.S1G276000
Phchi.S1	AUGUSTUS	transcript	17833065	17835218	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	start_codon	17833065	17833067	.	+	0	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17833065	17833189	0.86	+	0	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17833065	17833189	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17833190	17833386	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17833387	17833412	1	+	1	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17833387	17833412	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17833413	17833658	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17833659	17833748	1	+	2	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17833659	17833748	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17833749	17834141	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17834142	17834230	1	+	2	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17834142	17834230	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17834231	17834350	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17834351	17834440	0.7	+	0	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17834351	17834440	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17834441	17834543	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17834544	17834557	0.69	+	0	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17834544	17834557	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17834558	17834643	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17834644	17834720	0.79	+	1	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17834644	17834720	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17834721	17834811	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17834812	17834826	0.72	+	2	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17834812	17834826	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17834827	17834943	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17834944	17834996	1	+	2	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17834944	17834996	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	intron	17834997	17835158	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	CDS	17835159	17835218	1	+	0	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	exon	17835159	17835218	.	+	.	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
Phchi.S1	AUGUSTUS	stop_codon	17835219	17835221	.	+	0	transcript_id "Phchi.S1G276000.t1"; gene_id "Phchi.S1G276000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11457.t1 is derived from g15507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6462274	6463281	.	+	.	Phchi.S4G103900
Phchi.S4	AUGUSTUS	transcript	6462274	6463281	.	+	.	transcript_id "Phchi.S4G103900.t1"; gene_id "Phchi.S4G103900"
Phchi.S4	AUGUSTUS	start_codon	6462274	6462276	.	+	0	transcript_id "Phchi.S4G103900.t1"; gene_id "Phchi.S4G103900"
Phchi.S4	AUGUSTUS	CDS	6462274	6463281	0.38	+	0	transcript_id "Phchi.S4G103900.t1"; gene_id "Phchi.S4G103900"
Phchi.S4	AUGUSTUS	exon	6462274	6463281	.	+	.	transcript_id "Phchi.S4G103900.t1"; gene_id "Phchi.S4G103900"
Phchi.S4	AUGUSTUS	stop_codon	6463282	6463284	.	+	0	transcript_id "Phchi.S4G103900.t1"; gene_id "Phchi.S4G103900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg182.t1 is derived from g9964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1056395	1058349	.	+	.	Phchi.S6G014100
Phchi.S6	AUGUSTUS	transcript	1056395	1058349	.	+	.	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	start_codon	1056395	1056397	.	+	0	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	CDS	1056395	1056757	1	+	0	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	exon	1056395	1056757	.	+	.	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	intron	1056758	1056939	.	+	.	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	CDS	1056940	1058349	1	+	0	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	exon	1056940	1058349	.	+	.	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
Phchi.S6	AUGUSTUS	stop_codon	1058350	1058352	.	+	0	transcript_id "Phchi.S6G014100.t1"; gene_id "Phchi.S6G014100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6128.t1 is derived from g3299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21062643	21064653	.	-	.	Phchi.S1G328700
Phchi.S1	AUGUSTUS	transcript	21062643	21064653	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	stop_codon	21062640	21062642	.	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21062643	21062885	1	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21062643	21062885	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21062886	21062971	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21062972	21063130	1	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21062972	21063130	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21063131	21063216	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21063217	21063435	1	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21063217	21063435	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21063436	21063610	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21063611	21063720	1	-	2	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21063611	21063720	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21063721	21063792	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21063793	21063867	1	-	2	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21063793	21063867	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21063868	21063965	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21063966	21064149	1	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21063966	21064149	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21064150	21064265	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21064266	21064447	0.99	-	2	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21064266	21064447	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	intron	21064448	21064625	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	CDS	21064626	21064653	0.92	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	exon	21064626	21064653	.	-	.	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
Phchi.S1	AUGUSTUS	start_codon	21064651	21064653	.	-	0	transcript_id "Phchi.S1G328700.t1"; gene_id "Phchi.S1G328700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg367.t1 is derived from g10149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2675276	2675802	.	+	.	Phchi.S6G032600
Phchi.S6	AUGUSTUS	transcript	2675276	2675802	.	+	.	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	start_codon	2675276	2675278	.	+	0	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	CDS	2675276	2675427	0.45	+	0	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	exon	2675276	2675427	.	+	.	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	intron	2675428	2675565	.	+	.	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	CDS	2675566	2675628	0.39	+	1	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	exon	2675566	2675628	.	+	.	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	intron	2675629	2675768	.	+	.	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	CDS	2675769	2675802	0.97	+	1	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	exon	2675769	2675802	.	+	.	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
Phchi.S6	AUGUSTUS	stop_codon	2675803	2675805	.	+	0	transcript_id "Phchi.S6G032600.t1"; gene_id "Phchi.S6G032600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13573.t1 is derived from g12040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7548605	7551299	.	-	.	Phchi.S3G089200
Phchi.S3	AUGUSTUS	transcript	7548605	7550899	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	stop_codon	7548602	7548604	.	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7548605	7548814	1	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7548605	7548814	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7548815	7548905	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7548906	7548986	1	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7548906	7548986	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7548987	7549076	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549077	7549160	1	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549077	7549160	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549161	7549246	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549247	7549319	1	-	1	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549247	7549319	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549320	7549413	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549414	7549475	1	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549414	7549475	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549476	7549570	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549571	7549652	1	-	1	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549571	7549652	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549653	7549755	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549756	7549873	1	-	2	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549756	7549873	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549874	7549964	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549965	7550067	1	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549965	7550067	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550068	7550233	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550234	7550303	1	-	1	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550234	7550303	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550304	7550401	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550402	7550529	1	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550402	7550529	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550530	7550636	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550637	7550763	1	-	1	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550637	7550763	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550764	7550849	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550850	7550899	0.8	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550850	7550899	.	-	.	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	start_codon	7550897	7550899	.	-	0	transcript_id "Phchi.S3G089200.t1"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	transcript	7548605	7551299	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	stop_codon	7548602	7548604	.	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7548605	7548814	1	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7548605	7548814	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7548815	7548905	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7548906	7548986	1	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7548906	7548986	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7548987	7549076	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549077	7549160	1	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549077	7549160	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549161	7549246	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549247	7549319	1	-	1	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549247	7549319	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549320	7549413	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549414	7549475	1	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549414	7549475	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549476	7549570	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549571	7549652	1	-	1	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549571	7549652	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549653	7549755	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549756	7549873	1	-	2	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549756	7549873	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7549874	7549964	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7549965	7550067	1	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7549965	7550067	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550068	7550233	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550234	7550303	1	-	1	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550234	7550303	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550304	7550401	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550402	7550529	0.97	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550402	7550529	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550530	7550636	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550637	7550768	0.97	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550637	7550768	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7550769	7550849	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7550850	7551086	0.85	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7550850	7551086	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	intron	7551087	7551260	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	CDS	7551261	7551299	0.76	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	exon	7551261	7551299	.	-	.	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
Phchi.S3	AUGUSTUS	start_codon	7551297	7551299	.	-	0	transcript_id "Phchi.S3G089200.t2"; gene_id "Phchi.S3G089200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2811.t1 is derived from g9731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8977818	8979578	.	-	.	Phchi.S5G142000
Phchi.S5	AUGUSTUS	transcript	8977818	8979578	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	stop_codon	8977815	8977817	.	-	0	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	CDS	8977818	8977867	0.99	-	2	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	exon	8977818	8977867	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	intron	8977868	8977967	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	CDS	8977968	8978008	0.99	-	1	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	exon	8977968	8978008	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	intron	8978009	8978107	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	CDS	8978108	8978130	0.68	-	0	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	exon	8978108	8978130	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	intron	8978131	8978780	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	CDS	8978781	8979578	0.34	-	0	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	exon	8978781	8979578	.	-	.	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
Phchi.S5	AUGUSTUS	start_codon	8979576	8979578	.	-	0	transcript_id "Phchi.S5G142000.t1"; gene_id "Phchi.S5G142000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7771.t1 is derived from g4945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31171916	31172391	.	+	.	Phchi.S1G493000
Phchi.S1	AUGUSTUS	transcript	31171916	31172391	.	+	.	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	start_codon	31171916	31171918	.	+	0	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	CDS	31171916	31172131	0.87	+	0	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	exon	31171916	31172131	.	+	.	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	intron	31172132	31172211	.	+	.	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	CDS	31172212	31172391	0.78	+	0	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	exon	31172212	31172391	.	+	.	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
Phchi.S1	AUGUSTUS	stop_codon	31172392	31172394	.	+	0	transcript_id "Phchi.S1G493000.t1"; gene_id "Phchi.S1G493000"
# This transcript jg3651.t2 is derived from g820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3652.t1 is derived from g821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4978804	4979241	.	-	.	Phchi.S1G081100
Phchi.S1	AUGUSTUS	transcript	4978804	4979241	.	-	.	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	stop_codon	4978801	4978803	.	-	0	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	CDS	4978804	4979037	0.94	-	0	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	exon	4978804	4979037	.	-	.	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	intron	4979038	4979133	.	-	.	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	CDS	4979134	4979241	0.76	-	0	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	exon	4979134	4979241	.	-	.	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
Phchi.S1	AUGUSTUS	start_codon	4979239	4979241	.	-	0	transcript_id "Phchi.S1G081100.t1"; gene_id "Phchi.S1G081100"
# This transcript jg1349.t2 is derived from g11132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1349.t3 is derived from g11132.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1350.t1 is derived from g9804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C206	AUGUSTUS	gene	11934	13288	.	-	.	Phchi.C206G000100
Phchi.C206	AUGUSTUS	transcript	11934	13288	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	stop_codon	11931	11933	.	-	0	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	CDS	11934	12098	0.68	-	0	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	exon	11934	12098	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	intron	12099	12187	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	CDS	12188	12655	0.47	-	0	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	exon	12188	12655	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	intron	12656	12745	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	CDS	12746	12932	0.74	-	1	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	exon	12746	12932	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	intron	12933	13136	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	CDS	13137	13288	0.18	-	0	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	exon	13137	13288	.	-	.	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
Phchi.C206	AUGUSTUS	start_codon	13286	13288	.	-	0	transcript_id "Phchi.C206G000100.t1"; gene_id "Phchi.C206G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1162.t1 is derived from g10945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8106898	8109031	.	-	.	Phchi.S6G112100
Phchi.S6	AUGUSTUS	transcript	8106898	8109031	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	stop_codon	8106895	8106897	.	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8106898	8106911	0.66	-	2	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8106898	8106911	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8106912	8107028	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8107029	8107126	0.7	-	1	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8107029	8107126	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8107127	8107224	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8107225	8107286	0.71	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8107225	8107286	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8107287	8107368	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8107369	8107388	0.96	-	2	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8107369	8107388	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8107389	8107468	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8107469	8107475	0.99	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8107469	8107475	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8107476	8107562	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8107563	8107658	1	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8107563	8107658	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8107659	8107752	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8107753	8108193	0.99	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8107753	8108193	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8108194	8108317	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8108318	8108567	1	-	1	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8108318	8108567	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	intron	8108568	8108975	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	CDS	8108976	8109031	0.47	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	exon	8108976	8109031	.	-	.	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
Phchi.S6	AUGUSTUS	start_codon	8109029	8109031	.	-	0	transcript_id "Phchi.S6G112100.t1"; gene_id "Phchi.S6G112100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7191.t1 is derived from g4363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27480186	27483867	.	+	.	Phchi.S1G435000
Phchi.S1	AUGUSTUS	transcript	27480186	27483867	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	start_codon	27480186	27480188	.	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27480186	27480503	1	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27480186	27480503	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27480504	27480607	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27480608	27480791	1	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27480608	27480791	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27480792	27480886	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27480887	27481096	1	+	2	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27480887	27481096	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27481097	27481259	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27481260	27481349	1	+	2	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27481260	27481349	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27481350	27481543	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27481544	27481637	1	+	2	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27481544	27481637	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27481638	27481858	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27481859	27481922	1	+	1	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27481859	27481922	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27481923	27482022	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27482023	27482082	1	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27482023	27482082	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27482083	27482219	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27482220	27482386	1	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27482220	27482386	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27482387	27482598	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27482599	27482716	1	+	1	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27482599	27482716	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27482717	27482822	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27482823	27482958	1	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27482823	27482958	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27482959	27483049	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27483050	27483403	1	+	2	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27483050	27483403	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27483404	27483573	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27483574	27483665	1	+	2	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27483574	27483665	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27483666	27483738	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27483739	27483767	1	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27483739	27483767	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	intron	27483768	27483848	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	CDS	27483849	27483867	1	+	1	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	exon	27483849	27483867	.	+	.	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
Phchi.S1	AUGUSTUS	stop_codon	27483868	27483870	.	+	0	transcript_id "Phchi.S1G435000.t1"; gene_id "Phchi.S1G435000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3346.t1 is derived from g515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3050752	3053291	.	+	.	Phchi.S1G050500
Phchi.S1	AUGUSTUS	transcript	3050752	3053291	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	start_codon	3050752	3050754	.	+	0	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	CDS	3050752	3050877	1	+	0	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	exon	3050752	3050877	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	intron	3050878	3051000	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	CDS	3051001	3051142	1	+	0	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	exon	3051001	3051142	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	intron	3051143	3051234	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	CDS	3051235	3051515	1	+	2	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	exon	3051235	3051515	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	intron	3051516	3051734	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	CDS	3051735	3053291	1	+	0	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	exon	3051735	3053291	.	+	.	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
Phchi.S1	AUGUSTUS	stop_codon	3053292	3053294	.	+	0	transcript_id "Phchi.S1G050500.t1"; gene_id "Phchi.S1G050500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8581.t1 is derived from g5756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36734147	36734727	.	+	.	Phchi.S1G574000
Phchi.S1	AUGUSTUS	transcript	36734147	36734727	.	+	.	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	start_codon	36734147	36734149	.	+	0	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	CDS	36734147	36734219	0.96	+	0	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	exon	36734147	36734219	.	+	.	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	intron	36734220	36734419	.	+	.	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	CDS	36734420	36734515	1	+	2	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	exon	36734420	36734515	.	+	.	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	intron	36734516	36734647	.	+	.	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	CDS	36734648	36734727	1	+	2	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	exon	36734648	36734727	.	+	.	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	stop_codon	36734728	36734730	.	+	0	transcript_id "Phchi.S1G574000.t1"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	transcript	36734147	36734727	.	+	.	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	start_codon	36734147	36734149	.	+	0	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	CDS	36734147	36734330	0.67	+	0	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	exon	36734147	36734330	.	+	.	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	intron	36734331	36734419	.	+	.	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	CDS	36734420	36734515	1	+	2	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	exon	36734420	36734515	.	+	.	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	intron	36734516	36734647	.	+	.	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	CDS	36734648	36734727	1	+	2	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	exon	36734648	36734727	.	+	.	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
Phchi.S1	AUGUSTUS	stop_codon	36734728	36734730	.	+	0	transcript_id "Phchi.S1G574000.t2"; gene_id "Phchi.S1G574000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7713.t1 is derived from g4887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30763054	30765653	.	+	.	Phchi.S1G487200
Phchi.S1	AUGUSTUS	transcript	30763054	30765653	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	start_codon	30763054	30763056	.	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30763054	30763171	1	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30763054	30763171	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30763172	30763257	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30763258	30763643	1	+	2	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30763258	30763643	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30763644	30763723	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30763724	30763978	0.7	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30763724	30763978	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30763979	30764096	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30764097	30764260	0.8	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30764097	30764260	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30764261	30764341	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30764342	30764482	1	+	1	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30764342	30764482	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30764483	30764573	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30764574	30764688	1	+	1	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30764574	30764688	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30764689	30764794	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30764795	30765151	0.99	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30764795	30765151	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30765152	30765236	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30765237	30765461	1	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30765237	30765461	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	intron	30765462	30765542	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	CDS	30765543	30765653	1	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	exon	30765543	30765653	.	+	.	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
Phchi.S1	AUGUSTUS	stop_codon	30765654	30765656	.	+	0	transcript_id "Phchi.S1G487200.t1"; gene_id "Phchi.S1G487200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14386.t1 is derived from g12854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12556030	12558192	.	+	.	Phchi.S3G170500
Phchi.S3	AUGUSTUS	transcript	12556030	12558192	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	start_codon	12556030	12556032	.	+	0	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556030	12556207	0.91	+	0	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556030	12556207	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556208	12556307	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556308	12556558	1	+	2	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556308	12556558	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556559	12556644	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556645	12556771	1	+	0	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556645	12556771	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556772	12556869	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556870	12556938	1	+	2	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556870	12556938	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556939	12557023	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12557024	12557213	1	+	2	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12557024	12557213	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12557214	12557303	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12557304	12557430	1	+	1	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12557304	12557430	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12557431	12557551	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12557552	12557868	0.71	+	0	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12557552	12557868	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12557869	12557999	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12558000	12558192	0.68	+	1	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12558000	12558192	.	+	.	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	stop_codon	12558193	12558195	.	+	0	transcript_id "Phchi.S3G170500.t1"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	transcript	12556030	12558192	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	start_codon	12556030	12556032	.	+	0	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556030	12556207	0.87	+	0	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556030	12556207	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556208	12556304	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556305	12556558	1	+	2	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556305	12556558	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556559	12556644	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556645	12556771	1	+	0	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556645	12556771	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556772	12556869	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12556870	12556938	1	+	2	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12556870	12556938	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12556939	12557023	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12557024	12557213	1	+	2	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12557024	12557213	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12557214	12557303	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12557304	12557430	1	+	1	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12557304	12557430	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12557431	12557551	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12557552	12557868	0.7	+	0	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12557552	12557868	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	intron	12557869	12557999	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	CDS	12558000	12558192	0.69	+	1	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	exon	12558000	12558192	.	+	.	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
Phchi.S3	AUGUSTUS	stop_codon	12558193	12558195	.	+	0	transcript_id "Phchi.S3G170500.t2"; gene_id "Phchi.S3G170500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11971.t1 is derived from g7646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	249634	252249	.	+	.	Phchi.S2G005100
Phchi.S2	AUGUSTUS	transcript	249634	252249	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	start_codon	249634	249636	.	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	249634	249739	0.98	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	249634	249739	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	249740	249934	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	249935	250029	1	+	2	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	249935	250029	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250030	250191	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250192	250249	1	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250192	250249	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250250	250368	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250369	250563	0.99	+	2	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250369	250563	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250564	250696	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250697	250773	1	+	2	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250697	250773	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250774	250893	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250894	250976	1	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250894	250976	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250977	251063	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251064	251115	1	+	1	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251064	251115	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	251116	251290	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251291	251359	1	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251291	251359	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	251360	251722	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251723	251809	1	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251723	251809	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	251810	251946	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251947	252011	1	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251947	252011	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	252012	252116	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	252117	252249	1	+	1	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	252117	252249	.	+	.	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	stop_codon	252250	252252	.	+	0	transcript_id "Phchi.S2G005100.t1"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	transcript	249634	252249	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	start_codon	249634	249636	.	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	249634	249739	0.97	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	249634	249739	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	249740	249934	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	249935	250024	0.98	+	2	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	249935	250024	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250025	250191	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250192	250249	0.98	+	2	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250192	250249	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250250	250368	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250369	250442	0.84	+	1	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250369	250442	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250443	250515	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250516	250563	0.98	+	2	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250516	250563	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250564	250696	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250697	250773	1	+	2	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250697	250773	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250774	250893	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	250894	250976	1	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	250894	250976	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	250977	251063	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251064	251115	1	+	1	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251064	251115	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	251116	251290	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251291	251359	1	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251291	251359	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	251360	251722	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251723	251809	1	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251723	251809	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	251810	251946	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	251947	252011	1	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	251947	252011	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	intron	252012	252116	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	CDS	252117	252249	1	+	1	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	exon	252117	252249	.	+	.	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
Phchi.S2	AUGUSTUS	stop_codon	252250	252252	.	+	0	transcript_id "Phchi.S2G005100.t2"; gene_id "Phchi.S2G005100"
# This transcript jg6221.t2 is derived from g3393.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6222.t1 is derived from g3394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21756230	21759581	.	+	.	Phchi.S1G338100
Phchi.S1	AUGUSTUS	transcript	21756230	21759581	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	start_codon	21756230	21756232	.	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21756230	21756497	0.95	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21756230	21756497	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21756498	21756638	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21756639	21757438	1	+	2	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21756639	21757438	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21757439	21757520	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21757521	21757966	0.99	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21757521	21757966	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21757967	21758070	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21758071	21758173	0.9	+	1	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21758071	21758173	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21758174	21758282	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21758283	21758338	0.99	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21758283	21758338	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21758339	21758480	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21758481	21758544	1	+	1	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21758481	21758544	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21758545	21758635	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21758636	21758698	1	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21758636	21758698	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21758699	21758866	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21758867	21758925	1	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21758867	21758925	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21758926	21759049	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21759050	21759137	1	+	1	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21759050	21759137	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21759138	21759231	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21759232	21759294	1	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21759232	21759294	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21759295	21759377	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21759378	21759434	1	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21759378	21759434	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	intron	21759435	21759518	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	CDS	21759519	21759581	0.86	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	exon	21759519	21759581	.	+	.	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
Phchi.S1	AUGUSTUS	stop_codon	21759582	21759584	.	+	0	transcript_id "Phchi.S1G338100.t1"; gene_id "Phchi.S1G338100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6242.t1 is derived from g3414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21822275	21824751	.	-	.	Phchi.S1G340100
Phchi.S1	AUGUSTUS	transcript	21822275	21824751	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	stop_codon	21822272	21822274	.	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822275	21822445	1	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822275	21822445	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822446	21822535	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822536	21822591	1	-	2	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822536	21822591	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822592	21822673	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822674	21822748	1	-	2	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822674	21822748	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822749	21822848	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822849	21822948	1	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822849	21822948	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822949	21823057	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823058	21823153	1	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823058	21823153	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823154	21823276	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823277	21823346	0.98	-	1	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823277	21823346	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823347	21823448	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823449	21823539	1	-	2	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823449	21823539	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823540	21823659	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823660	21823729	1	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823660	21823729	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823730	21823822	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823823	21823908	0.99	-	2	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823823	21823908	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823909	21824011	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824012	21824176	0.99	-	2	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824012	21824176	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21824177	21824280	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824281	21824329	0.93	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824281	21824329	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21824330	21824427	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824428	21824751	0.85	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824428	21824751	.	-	.	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	start_codon	21824749	21824751	.	-	0	transcript_id "Phchi.S1G340100.t1"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	transcript	21822275	21824057	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	stop_codon	21822272	21822274	.	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822275	21822445	1	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822275	21822445	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822446	21822535	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822536	21822591	1	-	2	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822536	21822591	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822592	21822673	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822674	21822748	1	-	2	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822674	21822748	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822749	21822848	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21822849	21822948	1	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21822849	21822948	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21822949	21823057	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823058	21823153	1	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823058	21823153	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823154	21823276	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823277	21823346	0.96	-	1	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823277	21823346	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823347	21823448	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823449	21823539	1	-	2	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823449	21823539	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823540	21823659	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823660	21823729	1	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823660	21823729	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823730	21823822	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21823823	21823908	0.95	-	2	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21823823	21823908	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21823909	21824011	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824012	21824057	0.72	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824012	21824057	.	-	.	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	start_codon	21824055	21824057	.	-	0	transcript_id "Phchi.S1G340100.t2"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	transcript	21824187	21824751	.	-	.	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	stop_codon	21824184	21824186	.	-	0	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824187	21824188	0.97	-	2	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824187	21824188	.	-	.	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21824189	21824280	.	-	.	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824281	21824329	1	-	0	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824281	21824329	.	-	.	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	intron	21824330	21824427	.	-	.	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	CDS	21824428	21824751	0.86	-	0	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	exon	21824428	21824751	.	-	.	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
Phchi.S1	AUGUSTUS	start_codon	21824749	21824751	.	-	0	transcript_id "Phchi.S1G340100.t3"; gene_id "Phchi.S1G340100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg515.t1 is derived from g10297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3695830	3696872	.	-	.	Phchi.S6G047400
Phchi.S6	AUGUSTUS	transcript	3695830	3696872	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	stop_codon	3695827	3695829	.	-	0	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	CDS	3695830	3695884	0.94	-	1	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	exon	3695830	3695884	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	intron	3695885	3696051	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	CDS	3696052	3696077	0.94	-	0	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	exon	3696052	3696077	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	intron	3696078	3696311	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	CDS	3696312	3696506	0.76	-	0	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	exon	3696312	3696506	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	intron	3696507	3696608	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	CDS	3696609	3696698	0.99	-	0	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	exon	3696609	3696698	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	intron	3696699	3696791	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	CDS	3696792	3696872	1	-	0	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	exon	3696792	3696872	.	-	.	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
Phchi.S6	AUGUSTUS	start_codon	3696870	3696872	.	-	0	transcript_id "Phchi.S6G047400.t1"; gene_id "Phchi.S6G047400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1127.t1 is derived from g10910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7856009	7857920	.	-	.	Phchi.S6G108600
Phchi.S6	AUGUSTUS	transcript	7856009	7857920	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	stop_codon	7856006	7856008	.	-	0	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	CDS	7856009	7856286	0.99	-	2	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	exon	7856009	7856286	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	intron	7856287	7856406	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	CDS	7856407	7856845	1	-	0	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	exon	7856407	7856845	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	intron	7856846	7856944	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	CDS	7856945	7857219	1	-	2	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	exon	7856945	7857219	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	intron	7857220	7857403	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	CDS	7857404	7857920	1	-	0	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	exon	7857404	7857920	.	-	.	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
Phchi.S6	AUGUSTUS	start_codon	7857918	7857920	.	-	0	transcript_id "Phchi.S6G108600.t1"; gene_id "Phchi.S6G108600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1293.t1 is derived from g11076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8871346	8871747	.	+	.	Phchi.S6G125200
Phchi.S6	AUGUSTUS	transcript	8871346	8871747	.	+	.	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	start_codon	8871346	8871348	.	+	0	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	CDS	8871346	8871426	0.6	+	0	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	exon	8871346	8871426	.	+	.	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	intron	8871427	8871526	.	+	.	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	CDS	8871527	8871569	1	+	0	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	exon	8871527	8871569	.	+	.	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	intron	8871570	8871664	.	+	.	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	CDS	8871665	8871747	0.86	+	2	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	exon	8871665	8871747	.	+	.	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
Phchi.S6	AUGUSTUS	stop_codon	8871748	8871750	.	+	0	transcript_id "Phchi.S6G125200.t1"; gene_id "Phchi.S6G125200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8188.t1 is derived from g5363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34339967	34340569	.	+	.	Phchi.S1G534700
Phchi.S1	AUGUSTUS	transcript	34339967	34340569	.	+	.	transcript_id "Phchi.S1G534700.t1"; gene_id "Phchi.S1G534700"
Phchi.S1	AUGUSTUS	start_codon	34339967	34339969	.	+	0	transcript_id "Phchi.S1G534700.t1"; gene_id "Phchi.S1G534700"
Phchi.S1	AUGUSTUS	CDS	34339967	34340569	0.57	+	0	transcript_id "Phchi.S1G534700.t1"; gene_id "Phchi.S1G534700"
Phchi.S1	AUGUSTUS	exon	34339967	34340569	.	+	.	transcript_id "Phchi.S1G534700.t1"; gene_id "Phchi.S1G534700"
Phchi.S1	AUGUSTUS	stop_codon	34340570	34340572	.	+	0	transcript_id "Phchi.S1G534700.t1"; gene_id "Phchi.S1G534700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg258.t1 is derived from g10040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1746838	1748056	.	-	.	Phchi.S6G021700
Phchi.S6	AUGUSTUS	transcript	1746838	1748056	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	stop_codon	1746835	1746837	.	-	0	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	CDS	1746838	1747097	0.57	-	2	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	exon	1746838	1747097	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	intron	1747098	1747182	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	CDS	1747183	1747342	1	-	0	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	exon	1747183	1747342	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	intron	1747343	1747426	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	CDS	1747427	1747750	1	-	0	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	exon	1747427	1747750	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	intron	1747751	1747840	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	CDS	1747841	1748056	0.75	-	0	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	exon	1747841	1748056	.	-	.	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
Phchi.S6	AUGUSTUS	start_codon	1748054	1748056	.	-	0	transcript_id "Phchi.S6G021700.t1"; gene_id "Phchi.S6G021700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13487.t1 is derived from g11954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7130404	7131918	.	-	.	Phchi.S3G080600
Phchi.S3	AUGUSTUS	transcript	7130404	7131918	.	-	.	transcript_id "Phchi.S3G080600.t1"; gene_id "Phchi.S3G080600"
Phchi.S3	AUGUSTUS	stop_codon	7130401	7130403	.	-	0	transcript_id "Phchi.S3G080600.t1"; gene_id "Phchi.S3G080600"
Phchi.S3	AUGUSTUS	CDS	7130404	7131918	0.55	-	0	transcript_id "Phchi.S3G080600.t1"; gene_id "Phchi.S3G080600"
Phchi.S3	AUGUSTUS	exon	7130404	7131918	.	-	.	transcript_id "Phchi.S3G080600.t1"; gene_id "Phchi.S3G080600"
Phchi.S3	AUGUSTUS	start_codon	7131916	7131918	.	-	0	transcript_id "Phchi.S3G080600.t1"; gene_id "Phchi.S3G080600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11859.t1 is derived from g15911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8801161	8804209	.	-	.	Phchi.S4G144100
Phchi.S4	AUGUSTUS	transcript	8801161	8804209	.	-	.	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	stop_codon	8801158	8801160	.	-	0	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	CDS	8801161	8803580	1	-	2	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	exon	8801161	8803580	.	-	.	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	intron	8803581	8803764	.	-	.	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	CDS	8803765	8804209	0.61	-	0	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	exon	8803765	8804209	.	-	.	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
Phchi.S4	AUGUSTUS	start_codon	8804207	8804209	.	-	0	transcript_id "Phchi.S4G144100.t1"; gene_id "Phchi.S4G144100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12043.t1 is derived from g7718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	948437	950807	.	+	.	Phchi.S2G012300
Phchi.S2	AUGUSTUS	transcript	948437	950807	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	start_codon	948437	948439	.	+	0	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	948437	948691	0.98	+	0	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	948437	948691	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	948692	948833	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	948834	948899	0.73	+	0	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	948834	948899	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	948900	949024	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	949025	949029	0.7	+	0	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	949025	949029	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	949030	949103	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	949104	949225	0.66	+	1	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	949104	949225	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	949226	949315	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	949316	949383	0.75	+	2	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	949316	949383	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	949384	949524	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	949525	949645	1	+	0	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	949525	949645	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	949646	949782	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	949783	950554	1	+	2	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	949783	950554	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	intron	950555	950761	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	CDS	950762	950807	1	+	1	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	exon	950762	950807	.	+	.	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
Phchi.S2	AUGUSTUS	stop_codon	950808	950810	.	+	0	transcript_id "Phchi.S2G012300.t1"; gene_id "Phchi.S2G012300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3060.t1 is derived from g229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1388407	1388910	.	-	.	Phchi.S1G021900
Phchi.S1	AUGUSTUS	transcript	1388407	1388910	.	-	.	transcript_id "Phchi.S1G021900.t1"; gene_id "Phchi.S1G021900"
Phchi.S1	AUGUSTUS	stop_codon	1388404	1388406	.	-	0	transcript_id "Phchi.S1G021900.t1"; gene_id "Phchi.S1G021900"
Phchi.S1	AUGUSTUS	CDS	1388407	1388910	1	-	0	transcript_id "Phchi.S1G021900.t1"; gene_id "Phchi.S1G021900"
Phchi.S1	AUGUSTUS	exon	1388407	1388910	.	-	.	transcript_id "Phchi.S1G021900.t1"; gene_id "Phchi.S1G021900"
Phchi.S1	AUGUSTUS	start_codon	1388908	1388910	.	-	0	transcript_id "Phchi.S1G021900.t1"; gene_id "Phchi.S1G021900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11530.t1 is derived from g15580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6936226	6938299	.	+	.	Phchi.S4G111200
Phchi.S4	AUGUSTUS	transcript	6936226	6938299	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	start_codon	6936226	6936228	.	+	0	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6936226	6936343	1	+	0	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6936226	6936343	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6936344	6936485	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6936486	6936520	0.86	+	2	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6936486	6936520	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6936521	6936738	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6936739	6936811	0.86	+	0	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6936739	6936811	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6936812	6936897	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6936898	6936957	1	+	2	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6936898	6936957	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6936958	6937042	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6937043	6937121	0.44	+	2	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6937043	6937121	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6937122	6937233	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6937234	6937324	0.39	+	1	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6937234	6937324	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6937325	6937563	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6937564	6937577	0.63	+	0	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6937564	6937577	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6937578	6937691	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6937692	6937944	0.6	+	1	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6937692	6937944	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6937945	6938025	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6938026	6938081	1	+	0	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6938026	6938081	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	intron	6938082	6938181	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	CDS	6938182	6938299	0.98	+	1	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	exon	6938182	6938299	.	+	.	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
Phchi.S4	AUGUSTUS	stop_codon	6938300	6938302	.	+	0	transcript_id "Phchi.S4G111200.t1"; gene_id "Phchi.S4G111200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1051.t1 is derived from g10834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7287514	7288674	.	-	.	Phchi.S6G101000
Phchi.S6	AUGUSTUS	transcript	7287514	7288674	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	stop_codon	7287511	7287513	.	-	0	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	CDS	7287514	7287764	0.95	-	2	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	exon	7287514	7287764	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	intron	7287765	7287844	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	CDS	7287845	7288121	0.63	-	0	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	exon	7287845	7288121	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	intron	7288122	7288211	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	CDS	7288212	7288366	0.6	-	2	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	exon	7288212	7288366	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	intron	7288367	7288475	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	CDS	7288476	7288674	0.6	-	0	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	exon	7288476	7288674	.	-	.	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
Phchi.S6	AUGUSTUS	start_codon	7288672	7288674	.	-	0	transcript_id "Phchi.S6G101000.t1"; gene_id "Phchi.S6G101000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13442.t1 is derived from g11909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6722820	6724745	.	-	.	Phchi.S3G076100
Phchi.S3	AUGUSTUS	transcript	6722820	6724745	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	stop_codon	6722817	6722819	.	-	0	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	CDS	6722820	6723352	0.42	-	2	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	exon	6722820	6723352	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	intron	6723353	6723745	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	CDS	6723746	6723965	1	-	0	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	exon	6723746	6723965	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	intron	6723966	6724087	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	CDS	6724088	6724189	1	-	0	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	exon	6724088	6724189	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	intron	6724190	6724332	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	CDS	6724333	6724390	1	-	1	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	exon	6724333	6724390	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	intron	6724391	6724512	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	CDS	6724513	6724745	0.99	-	0	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	exon	6724513	6724745	.	-	.	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
Phchi.S3	AUGUSTUS	start_codon	6724743	6724745	.	-	0	transcript_id "Phchi.S3G076100.t1"; gene_id "Phchi.S3G076100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7281.t1 is derived from g4453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28128708	28129586	.	+	.	Phchi.S1G444000
Phchi.S1	AUGUSTUS	transcript	28128708	28129586	.	+	.	transcript_id "Phchi.S1G444000.t1"; gene_id "Phchi.S1G444000"
Phchi.S1	AUGUSTUS	start_codon	28128708	28128710	.	+	0	transcript_id "Phchi.S1G444000.t1"; gene_id "Phchi.S1G444000"
Phchi.S1	AUGUSTUS	CDS	28128708	28129586	1	+	0	transcript_id "Phchi.S1G444000.t1"; gene_id "Phchi.S1G444000"
Phchi.S1	AUGUSTUS	exon	28128708	28129586	.	+	.	transcript_id "Phchi.S1G444000.t1"; gene_id "Phchi.S1G444000"
Phchi.S1	AUGUSTUS	stop_codon	28129587	28129589	.	+	0	transcript_id "Phchi.S1G444000.t1"; gene_id "Phchi.S1G444000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7575.t1 is derived from g4749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30100461	30100943	.	-	.	Phchi.S1G473400
Phchi.S1	AUGUSTUS	transcript	30100461	30100793	.	-	.	transcript_id "Phchi.S1G473400.t1"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	stop_codon	30100458	30100460	.	-	0	transcript_id "Phchi.S1G473400.t1"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	CDS	30100461	30100793	0.72	-	0	transcript_id "Phchi.S1G473400.t1"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	exon	30100461	30100793	.	-	.	transcript_id "Phchi.S1G473400.t1"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	start_codon	30100791	30100793	.	-	0	transcript_id "Phchi.S1G473400.t1"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	transcript	30100461	30100943	.	-	.	transcript_id "Phchi.S1G473400.t2"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	stop_codon	30100458	30100460	.	-	0	transcript_id "Phchi.S1G473400.t2"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	CDS	30100461	30100943	0.61	-	0	transcript_id "Phchi.S1G473400.t2"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	exon	30100461	30100943	.	-	.	transcript_id "Phchi.S1G473400.t2"; gene_id "Phchi.S1G473400"
Phchi.S1	AUGUSTUS	start_codon	30100941	30100943	.	-	0	transcript_id "Phchi.S1G473400.t2"; gene_id "Phchi.S1G473400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2691.t1 is derived from g9611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8227919	8229028	.	+	.	Phchi.S5G130000
Phchi.S5	AUGUSTUS	transcript	8227919	8229028	.	+	.	transcript_id "Phchi.S5G130000.t1"; gene_id "Phchi.S5G130000"
Phchi.S5	AUGUSTUS	start_codon	8227919	8227921	.	+	0	transcript_id "Phchi.S5G130000.t1"; gene_id "Phchi.S5G130000"
Phchi.S5	AUGUSTUS	CDS	8227919	8229028	1	+	0	transcript_id "Phchi.S5G130000.t1"; gene_id "Phchi.S5G130000"
Phchi.S5	AUGUSTUS	exon	8227919	8229028	.	+	.	transcript_id "Phchi.S5G130000.t1"; gene_id "Phchi.S5G130000"
Phchi.S5	AUGUSTUS	stop_codon	8229029	8229031	.	+	0	transcript_id "Phchi.S5G130000.t1"; gene_id "Phchi.S5G130000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3417.t1 is derived from g586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3400374	3400655	.	-	.	Phchi.S1G057600
Phchi.S1	AUGUSTUS	transcript	3400374	3400655	.	-	.	transcript_id "Phchi.S1G057600.t1"; gene_id "Phchi.S1G057600"
Phchi.S1	AUGUSTUS	stop_codon	3400371	3400373	.	-	0	transcript_id "Phchi.S1G057600.t1"; gene_id "Phchi.S1G057600"
Phchi.S1	AUGUSTUS	CDS	3400374	3400655	0.91	-	0	transcript_id "Phchi.S1G057600.t1"; gene_id "Phchi.S1G057600"
Phchi.S1	AUGUSTUS	exon	3400374	3400655	.	-	.	transcript_id "Phchi.S1G057600.t1"; gene_id "Phchi.S1G057600"
Phchi.S1	AUGUSTUS	start_codon	3400653	3400655	.	-	0	transcript_id "Phchi.S1G057600.t1"; gene_id "Phchi.S1G057600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1455.t1 is derived from g8374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	992603	994441	.	-	.	Phchi.S5G006400
Phchi.S5	AUGUSTUS	transcript	992603	994441	.	-	.	transcript_id "Phchi.S5G006400.t1"; gene_id "Phchi.S5G006400"
Phchi.S5	AUGUSTUS	stop_codon	992600	992602	.	-	0	transcript_id "Phchi.S5G006400.t1"; gene_id "Phchi.S5G006400"
Phchi.S5	AUGUSTUS	CDS	992603	994441	1	-	0	transcript_id "Phchi.S5G006400.t1"; gene_id "Phchi.S5G006400"
Phchi.S5	AUGUSTUS	exon	992603	994441	.	-	.	transcript_id "Phchi.S5G006400.t1"; gene_id "Phchi.S5G006400"
Phchi.S5	AUGUSTUS	start_codon	994439	994441	.	-	0	transcript_id "Phchi.S5G006400.t1"; gene_id "Phchi.S5G006400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8041.t1 is derived from g5216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32637818	32641509	.	-	.	Phchi.S1G520000
Phchi.S1	AUGUSTUS	transcript	32637818	32641509	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	stop_codon	32637815	32637817	.	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32637818	32637964	1	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32637818	32637964	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32637965	32638042	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32638043	32638199	1	-	1	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32638043	32638199	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32638200	32638313	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32638314	32638429	0.77	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32638314	32638429	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32638430	32638539	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32638540	32638698	0.83	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32638540	32638698	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32638699	32638793	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32638794	32638982	0.99	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32638794	32638982	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32638983	32639129	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32639130	32639288	1	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32639130	32639288	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32639289	32639379	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32639380	32639524	1	-	1	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32639380	32639524	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32639525	32639606	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32639607	32639712	1	-	2	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32639607	32639712	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32639713	32639913	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32639914	32640103	0.91	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32639914	32640103	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32640104	32640220	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32640221	32640315	1	-	2	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32640221	32640315	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32640316	32640407	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32640408	32640462	1	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32640408	32640462	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32640463	32640611	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32640612	32640803	1	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32640612	32640803	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32640804	32640910	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32640911	32641125	0.73	-	2	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32640911	32641125	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	intron	32641126	32641346	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	CDS	32641347	32641509	1	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	exon	32641347	32641509	.	-	.	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
Phchi.S1	AUGUSTUS	start_codon	32641507	32641509	.	-	0	transcript_id "Phchi.S1G520000.t1"; gene_id "Phchi.S1G520000"
# This transcript jg3841.t2 is derived from g1010.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3842.t1 is derived from g1011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5987001	5988734	.	+	.	Phchi.S1G100100
Phchi.S1	AUGUSTUS	transcript	5987001	5988734	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	start_codon	5987001	5987003	.	+	0	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	CDS	5987001	5987226	0.99	+	0	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	exon	5987001	5987226	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	intron	5987227	5987330	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	CDS	5987331	5987398	1	+	2	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	exon	5987331	5987398	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	intron	5987399	5987487	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	CDS	5987488	5987724	0.57	+	0	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	exon	5987488	5987724	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	intron	5987725	5987855	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	CDS	5987856	5988146	0.99	+	0	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	exon	5987856	5988146	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	intron	5988147	5988271	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	CDS	5988272	5988459	1	+	0	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	exon	5988272	5988459	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	intron	5988460	5988544	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	CDS	5988545	5988734	1	+	1	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	exon	5988545	5988734	.	+	.	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
Phchi.S1	AUGUSTUS	stop_codon	5988735	5988737	.	+	0	transcript_id "Phchi.S1G100100.t1"; gene_id "Phchi.S1G100100"
# This transcript jg2492.t2 is derived from g9412.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2493.t1 is derived from g9413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6957424	6957846	.	-	.	Phchi.S5G110200
Phchi.S5	AUGUSTUS	transcript	6957424	6957846	.	-	.	transcript_id "Phchi.S5G110200.t1"; gene_id "Phchi.S5G110200"
Phchi.S5	AUGUSTUS	stop_codon	6957421	6957423	.	-	0	transcript_id "Phchi.S5G110200.t1"; gene_id "Phchi.S5G110200"
Phchi.S5	AUGUSTUS	CDS	6957424	6957846	0.49	-	0	transcript_id "Phchi.S5G110200.t1"; gene_id "Phchi.S5G110200"
Phchi.S5	AUGUSTUS	exon	6957424	6957846	.	-	.	transcript_id "Phchi.S5G110200.t1"; gene_id "Phchi.S5G110200"
Phchi.S5	AUGUSTUS	start_codon	6957844	6957846	.	-	0	transcript_id "Phchi.S5G110200.t1"; gene_id "Phchi.S5G110200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4396.t1 is derived from g1565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10230147	10233818	.	-	.	Phchi.S1G155500
Phchi.S1	AUGUSTUS	transcript	10230147	10233818	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	stop_codon	10230144	10230146	.	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10230147	10230263	0.96	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10230147	10230263	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10230264	10230368	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10230369	10230479	0.98	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10230369	10230479	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10230480	10230701	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10230702	10230761	1	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10230702	10230761	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10230762	10230851	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10230852	10230969	1	-	1	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10230852	10230969	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10230970	10231050	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10231051	10231151	1	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10231051	10231151	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10231152	10231245	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10231246	10231316	1	-	2	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10231246	10231316	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10231317	10231436	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10231437	10231549	1	-	1	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10231437	10231549	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10231550	10231648	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10231649	10231717	1	-	1	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10231649	10231717	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10231718	10231894	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10231895	10232014	1	-	1	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10231895	10232014	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10232015	10232120	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10232121	10232233	1	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10232121	10232233	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10232234	10232341	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10232342	10232413	1	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10232342	10232413	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10232414	10232505	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10232506	10232610	1	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10232506	10232610	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10232611	10232699	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10232700	10232813	0.89	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10232700	10232813	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10232814	10232925	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10232926	10233020	0.88	-	2	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10232926	10233020	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10233021	10233156	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10233157	10233293	1	-	1	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10233157	10233293	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10233294	10233434	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10233435	10233657	1	-	2	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10233435	10233657	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	intron	10233658	10233757	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	CDS	10233758	10233818	1	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	exon	10233758	10233818	.	-	.	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
Phchi.S1	AUGUSTUS	start_codon	10233816	10233818	.	-	0	transcript_id "Phchi.S1G155500.t1"; gene_id "Phchi.S1G155500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12885.t1 is derived from g11350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2939081	2939365	.	-	.	Phchi.S3G020400
Phchi.S3	AUGUSTUS	transcript	2939081	2939365	.	-	.	transcript_id "Phchi.S3G020400.t1"; gene_id "Phchi.S3G020400"
Phchi.S3	AUGUSTUS	stop_codon	2939078	2939080	.	-	0	transcript_id "Phchi.S3G020400.t1"; gene_id "Phchi.S3G020400"
Phchi.S3	AUGUSTUS	CDS	2939081	2939365	0.59	-	0	transcript_id "Phchi.S3G020400.t1"; gene_id "Phchi.S3G020400"
Phchi.S3	AUGUSTUS	exon	2939081	2939365	.	-	.	transcript_id "Phchi.S3G020400.t1"; gene_id "Phchi.S3G020400"
Phchi.S3	AUGUSTUS	start_codon	2939363	2939365	.	-	0	transcript_id "Phchi.S3G020400.t1"; gene_id "Phchi.S3G020400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8600.t1 is derived from g5775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36845718	36846607	.	-	.	Phchi.S1G575900
Phchi.S1	AUGUSTUS	transcript	36845718	36846607	.	-	.	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	stop_codon	36845715	36845717	.	-	0	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	CDS	36845718	36845963	1	-	0	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	exon	36845718	36845963	.	-	.	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	intron	36845964	36846054	.	-	.	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	CDS	36846055	36846369	1	-	0	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	exon	36846055	36846369	.	-	.	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	intron	36846370	36846463	.	-	.	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	CDS	36846464	36846607	0.68	-	0	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	exon	36846464	36846607	.	-	.	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
Phchi.S1	AUGUSTUS	start_codon	36846605	36846607	.	-	0	transcript_id "Phchi.S1G575900.t1"; gene_id "Phchi.S1G575900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12489.t1 is derived from g8166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	29074175	29074683	.	+	.	Phchi.S2G056900
Phchi.S2	AUGUSTUS	transcript	29074175	29074683	.	+	.	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	start_codon	29074175	29074177	.	+	0	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	CDS	29074175	29074430	0.71	+	0	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	exon	29074175	29074430	.	+	.	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	intron	29074431	29074615	.	+	.	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	CDS	29074616	29074683	0.47	+	2	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	exon	29074616	29074683	.	+	.	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
Phchi.S2	AUGUSTUS	stop_codon	29074684	29074686	.	+	0	transcript_id "Phchi.S2G056900.t1"; gene_id "Phchi.S2G056900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2885.t1 is derived from g54.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	280650	282461	.	-	.	Phchi.S1G004400
Phchi.S1	AUGUSTUS	transcript	280650	282461	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	stop_codon	280647	280649	.	-	0	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	CDS	280650	281026	0.4	-	2	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	exon	280650	281026	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	intron	281027	281132	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	CDS	281133	281566	0.33	-	1	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	exon	281133	281566	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	intron	281567	281640	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	CDS	281641	281917	0.42	-	2	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	exon	281641	281917	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	intron	281918	282067	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	CDS	282068	282461	0.38	-	0	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	exon	282068	282461	.	-	.	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
Phchi.S1	AUGUSTUS	start_codon	282459	282461	.	-	0	transcript_id "Phchi.S1G004400.t1"; gene_id "Phchi.S1G004400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg5457.t1 is derived from g2627.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16942829	16944657	.	-	.	Phchi.S1G261600
Phchi.S1	AUGUSTUS	transcript	16943387	16944657	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	stop_codon	16943384	16943386	.	-	0	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943387	16943387	1	-	1	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943387	16943387	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943388	16943479	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943480	16943571	1	-	0	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943480	16943571	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943572	16943673	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943674	16943789	0.94	-	2	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943674	16943789	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943790	16943915	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943916	16944035	0.96	-	2	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943916	16944035	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16944036	16944467	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16944468	16944657	1	-	0	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16944468	16944657	.	-	.	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	start_codon	16944655	16944657	.	-	0	transcript_id "Phchi.S1G261600.t1"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	transcript	16942829	16944657	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	stop_codon	16942826	16942828	.	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16942829	16942906	0.92	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16942829	16942906	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16942907	16942985	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16942986	16943054	1	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16942986	16943054	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943055	16943145	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943146	16943214	1	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943146	16943214	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943215	16943293	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943294	16943315	1	-	1	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943294	16943315	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943316	16943479	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943480	16943571	0.99	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943480	16943571	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943572	16943673	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943674	16943789	0.92	-	2	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943674	16943789	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943790	16943915	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943916	16944035	0.96	-	2	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943916	16944035	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16944036	16944467	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16944468	16944657	0.99	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16944468	16944657	.	-	.	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	start_codon	16944655	16944657	.	-	0	transcript_id "Phchi.S1G261600.t2"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	transcript	16942829	16943350	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	stop_codon	16942826	16942828	.	-	0	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16942829	16942906	0.93	-	0	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16942829	16942906	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16942907	16942985	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16942986	16943054	1	-	0	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16942986	16943054	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943055	16943145	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943146	16943214	1	-	0	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943146	16943214	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943215	16943293	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943294	16943350	0.77	-	0	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943294	16943350	.	-	.	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	start_codon	16943348	16943350	.	-	0	transcript_id "Phchi.S1G261600.t3"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	transcript	16943387	16944657	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	stop_codon	16943384	16943386	.	-	0	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943387	16943387	1	-	1	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943387	16943387	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943388	16943479	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943480	16943571	0.98	-	0	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943480	16943571	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943572	16943673	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16943674	16943789	0.85	-	2	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16943674	16943789	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16943790	16944022	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16944023	16944035	0.24	-	0	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16944023	16944035	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	intron	16944036	16944471	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	CDS	16944472	16944657	0.39	-	0	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	exon	16944472	16944657	.	-	.	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
Phchi.S1	AUGUSTUS	start_codon	16944655	16944657	.	-	0	transcript_id "Phchi.S1G261600.t4"; gene_id "Phchi.S1G261600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5690.t1 is derived from g2860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18328001	18330715	.	-	.	Phchi.S1G284900
Phchi.S1	AUGUSTUS	transcript	18328001	18330715	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	stop_codon	18327998	18328000	.	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18328001	18328135	1	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18328001	18328135	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18328136	18328209	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18328210	18328280	1	-	2	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18328210	18328280	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18328281	18328352	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18328353	18328431	1	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18328353	18328431	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18328432	18328511	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18328512	18328553	1	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18328512	18328553	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18328554	18328648	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18328649	18328702	0.96	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18328649	18328702	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18328703	18328961	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18328962	18329042	0.96	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18328962	18329042	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18329043	18329123	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18329124	18329210	1	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18329124	18329210	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18329211	18329375	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18329376	18329409	0.87	-	1	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18329376	18329409	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18329410	18329526	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18329527	18329744	0.92	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18329527	18329744	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18329745	18329841	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18329842	18329964	1	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18329842	18329964	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18329965	18330101	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18330102	18330148	0.9	-	2	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18330102	18330148	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18330149	18330341	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18330342	18330453	0.91	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18330342	18330453	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	intron	18330454	18330550	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	CDS	18330551	18330715	0.39	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	exon	18330551	18330715	.	-	.	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
Phchi.S1	AUGUSTUS	start_codon	18330713	18330715	.	-	0	transcript_id "Phchi.S1G284900.t1"; gene_id "Phchi.S1G284900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11769.t1 is derived from g15821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8098308	8099042	.	-	.	Phchi.S4G135100
Phchi.S4	AUGUSTUS	transcript	8098308	8099042	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	stop_codon	8098305	8098307	.	-	0	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	CDS	8098308	8098329	0.8	-	1	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	exon	8098308	8098329	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	intron	8098330	8098420	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	CDS	8098421	8098533	0.8	-	0	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	exon	8098421	8098533	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	intron	8098534	8098788	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	CDS	8098789	8098823	0.79	-	2	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	exon	8098789	8098823	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	intron	8098824	8098931	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	CDS	8098932	8098952	0.62	-	2	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	exon	8098932	8098952	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	intron	8098953	8099035	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	CDS	8099036	8099042	0.62	-	0	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	exon	8099036	8099042	.	-	.	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
Phchi.S4	AUGUSTUS	start_codon	8099040	8099042	.	-	0	transcript_id "Phchi.S4G135100.t1"; gene_id "Phchi.S4G135100"
# This transcript jg9337.t2 is derived from g6512.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9338.t1 is derived from g6513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40999307	40999639	.	+	.	Phchi.S1G649700
Phchi.S1	AUGUSTUS	transcript	40999307	40999639	.	+	.	transcript_id "Phchi.S1G649700.t1"; gene_id "Phchi.S1G649700"
Phchi.S1	AUGUSTUS	start_codon	40999307	40999309	.	+	0	transcript_id "Phchi.S1G649700.t1"; gene_id "Phchi.S1G649700"
Phchi.S1	AUGUSTUS	CDS	40999307	40999639	0.64	+	0	transcript_id "Phchi.S1G649700.t1"; gene_id "Phchi.S1G649700"
Phchi.S1	AUGUSTUS	exon	40999307	40999639	.	+	.	transcript_id "Phchi.S1G649700.t1"; gene_id "Phchi.S1G649700"
Phchi.S1	AUGUSTUS	stop_codon	40999640	40999642	.	+	0	transcript_id "Phchi.S1G649700.t1"; gene_id "Phchi.S1G649700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12953.t1 is derived from g11418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3289366	3293664	.	+	.	Phchi.S3G027200
Phchi.S3	AUGUSTUS	transcript	3289366	3293664	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	start_codon	3289366	3289368	.	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3289366	3289455	0.82	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3289366	3289455	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3289456	3289544	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3289545	3289668	1	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3289545	3289668	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3289669	3289750	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3289751	3289888	1	+	2	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3289751	3289888	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3289889	3289990	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3289991	3290199	1	+	2	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3289991	3290199	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3290200	3290309	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3290310	3290488	0.98	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3290310	3290488	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3290489	3290577	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3290578	3290656	0.98	+	1	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3290578	3290656	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3290657	3290779	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3290780	3290914	0.89	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3290780	3290914	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3290915	3291017	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3291018	3291167	0.89	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3291018	3291167	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3291168	3291263	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3291264	3291924	0.64	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3291264	3291924	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3291925	3292049	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3292050	3292303	0.73	+	2	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3292050	3292303	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3292304	3292399	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3292400	3292672	1	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3292400	3292672	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3292673	3292772	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3292773	3292982	1	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3292773	3292982	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3292983	3293076	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3293077	3293231	1	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3293077	3293231	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	intron	3293232	3293336	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	CDS	3293337	3293664	0.95	+	1	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	exon	3293337	3293664	.	+	.	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
Phchi.S3	AUGUSTUS	stop_codon	3293665	3293667	.	+	0	transcript_id "Phchi.S3G027200.t1"; gene_id "Phchi.S3G027200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8604.t1 is derived from g5779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36858809	36859675	.	+	.	Phchi.S1G576300
Phchi.S1	AUGUSTUS	transcript	36858809	36859675	.	+	.	transcript_id "Phchi.S1G576300.t1"; gene_id "Phchi.S1G576300"
Phchi.S1	AUGUSTUS	start_codon	36858809	36858811	.	+	0	transcript_id "Phchi.S1G576300.t1"; gene_id "Phchi.S1G576300"
Phchi.S1	AUGUSTUS	CDS	36858809	36859675	0.92	+	0	transcript_id "Phchi.S1G576300.t1"; gene_id "Phchi.S1G576300"
Phchi.S1	AUGUSTUS	exon	36858809	36859675	.	+	.	transcript_id "Phchi.S1G576300.t1"; gene_id "Phchi.S1G576300"
Phchi.S1	AUGUSTUS	stop_codon	36859676	36859678	.	+	0	transcript_id "Phchi.S1G576300.t1"; gene_id "Phchi.S1G576300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15612.t1 is derived from g14081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20288303	20289637	.	-	.	Phchi.S3G293100
Phchi.S3	AUGUSTUS	transcript	20288303	20289637	.	-	.	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	stop_codon	20288300	20288302	.	-	0	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	CDS	20288303	20289157	1	-	0	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	exon	20288303	20289157	.	-	.	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	intron	20289158	20289238	.	-	.	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	CDS	20289239	20289637	0.98	-	0	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	exon	20289239	20289637	.	-	.	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
Phchi.S3	AUGUSTUS	start_codon	20289635	20289637	.	-	0	transcript_id "Phchi.S3G293100.t1"; gene_id "Phchi.S3G293100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3146.t1 is derived from g315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1980884	1981276	.	+	.	Phchi.S1G030500
Phchi.S1	AUGUSTUS	transcript	1980884	1981276	.	+	.	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	start_codon	1980884	1980886	.	+	0	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	CDS	1980884	1980976	0.51	+	0	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	exon	1980884	1980976	.	+	.	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	intron	1980977	1981168	.	+	.	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	CDS	1981169	1981276	0.68	+	0	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	exon	1981169	1981276	.	+	.	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
Phchi.S1	AUGUSTUS	stop_codon	1981277	1981279	.	+	0	transcript_id "Phchi.S1G030500.t1"; gene_id "Phchi.S1G030500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15939.t1 is derived from g6.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C143	AUGUSTUS	gene	9272	10175	.	-	.	Phchi.C143G000100
Phchi.C143	AUGUSTUS	transcript	9272	10175	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	stop_codon	9198	9200	.	-	0	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	CDS	9272	9371	0.64	-	1	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	exon	9272	9371	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	intron	9372	9445	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	CDS	9446	9767	0.59	-	2	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	exon	9446	9767	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	intron	9768	9854	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	CDS	9855	9903	1	-	0	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	exon	9855	9903	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	intron	9904	10028	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	CDS	10029	10175	1	-	0	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	exon	10029	10175	.	-	.	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
Phchi.C143	AUGUSTUS	start_codon	10173	10175	.	-	0	transcript_id "Phchi.C143G000100.t1"; gene_id "Phchi.C143G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2748.t1 is derived from g9668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8602310	8604731	.	+	.	Phchi.S5G135700
Phchi.S5	AUGUSTUS	transcript	8602310	8604731	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	start_codon	8602310	8602312	.	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8602310	8602494	0.84	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8602310	8602494	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8602495	8602716	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8602717	8602957	1	+	1	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8602717	8602957	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8602958	8603047	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8603048	8603197	1	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8603048	8603197	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8603198	8603316	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8603317	8603374	1	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8603317	8603374	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8603375	8603462	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8603463	8603555	1	+	2	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8603463	8603555	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8603556	8603642	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8603643	8603741	1	+	2	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8603643	8603741	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8603742	8603884	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8603885	8603976	1	+	2	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8603885	8603976	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8603977	8604221	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8604222	8604281	0.97	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8604222	8604281	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	intron	8604282	8604389	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	CDS	8604390	8604731	0.98	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	exon	8604390	8604731	.	+	.	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
Phchi.S5	AUGUSTUS	stop_codon	8604732	8604734	.	+	0	transcript_id "Phchi.S5G135700.t1"; gene_id "Phchi.S5G135700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2121.t1 is derived from g9041.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4940743	4946302	.	+	.	Phchi.S5G073000
Phchi.S5	AUGUSTUS	transcript	4940743	4946302	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	start_codon	4940743	4940745	.	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4940743	4941333	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4940743	4941333	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4941334	4941586	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4941587	4941649	0.81	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4941587	4941649	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4941650	4941824	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4941825	4941884	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4941825	4941884	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4941885	4941988	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4941989	4942068	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4941989	4942068	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4942069	4942229	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4942230	4942279	1	+	1	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4942230	4942279	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4942280	4942367	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4942368	4942570	0.99	+	2	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4942368	4942570	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4942571	4942659	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4942660	4942769	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4942660	4942769	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4942770	4942883	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4942884	4942962	1	+	1	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4942884	4942962	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4942963	4943083	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4943084	4943125	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4943084	4943125	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4943126	4943224	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4943225	4943344	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4943225	4943344	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4943345	4943435	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4943436	4943498	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4943436	4943498	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4943499	4943577	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4943578	4944035	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4943578	4944035	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4944036	4944139	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4944140	4944218	1	+	1	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4944140	4944218	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4944219	4944314	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4944315	4944374	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4944315	4944374	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4944375	4944468	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4944469	4944573	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4944469	4944573	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4944574	4944666	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4944667	4944749	0.99	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4944667	4944749	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4944750	4944853	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4944854	4945004	1	+	1	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4944854	4945004	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4945005	4945123	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4945124	4945204	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4945124	4945204	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4945205	4945304	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4945305	4945368	1	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4945305	4945368	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4945369	4945460	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4945461	4945546	0.85	+	2	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4945461	4945546	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4945547	4945694	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4945695	4945730	0.84	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4945695	4945730	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4945731	4945820	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4945821	4945896	0.96	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4945821	4945896	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	intron	4945897	4946186	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	CDS	4946187	4946302	0.84	+	2	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	exon	4946187	4946302	.	+	.	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
Phchi.S5	AUGUSTUS	stop_codon	4946303	4946305	.	+	0	transcript_id "Phchi.S5G073000.t1"; gene_id "Phchi.S5G073000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9985.t1 is derived from g7161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44787592	44792055	.	-	.	Phchi.S1G714400
Phchi.S1	AUGUSTUS	transcript	44787592	44792055	.	-	.	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	stop_codon	44787589	44787591	.	-	0	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	CDS	44787592	44788731	1	-	0	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	exon	44787592	44788731	.	-	.	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	intron	44788732	44788850	.	-	.	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	CDS	44788851	44790346	1	-	2	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	exon	44788851	44790346	.	-	.	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	intron	44790347	44790458	.	-	.	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	CDS	44790459	44792055	0.73	-	0	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	exon	44790459	44792055	.	-	.	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
Phchi.S1	AUGUSTUS	start_codon	44792053	44792055	.	-	0	transcript_id "Phchi.S1G714400.t1"; gene_id "Phchi.S1G714400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12205.t1 is derived from g7881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6728559	6731215	.	+	.	Phchi.S2G028500
Phchi.S2	AUGUSTUS	transcript	6728559	6731215	.	+	.	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	start_codon	6728559	6728561	.	+	0	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	CDS	6728559	6728825	0.55	+	0	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	exon	6728559	6728825	.	+	.	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	intron	6728826	6728945	.	+	.	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	CDS	6728946	6729432	0.74	+	0	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	exon	6728946	6729432	.	+	.	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	intron	6729433	6729524	.	+	.	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	CDS	6729525	6731215	0.93	+	2	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	exon	6729525	6731215	.	+	.	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
Phchi.S2	AUGUSTUS	stop_codon	6731216	6731218	.	+	0	transcript_id "Phchi.S2G028500.t1"; gene_id "Phchi.S2G028500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13759.t1 is derived from g12226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8738720	8742936	.	-	.	Phchi.S3G107800
Phchi.S3	AUGUSTUS	transcript	8738720	8742936	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	stop_codon	8738717	8738719	.	-	0	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8738720	8738799	0.98	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8738720	8738799	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8738800	8738899	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8738900	8739167	0.97	-	0	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8738900	8739167	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8739168	8739252	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8739253	8739379	1	-	1	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8739253	8739379	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8739380	8739470	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8739471	8739633	1	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8739471	8739633	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8739634	8739713	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8739714	8739746	1	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8739714	8739746	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8739747	8739834	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8739835	8739903	1	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8739835	8739903	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8739904	8739991	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8739992	8740118	1	-	0	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8739992	8740118	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8740119	8740214	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8740215	8740447	1	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8740215	8740447	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8740448	8740539	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8740540	8740694	1	-	1	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8740540	8740694	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8740695	8740775	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8740776	8740847	1	-	1	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8740776	8740847	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8740848	8740927	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8740928	8740999	0.99	-	1	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8740928	8740999	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8741000	8741274	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8741275	8741410	0.89	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8741275	8741410	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8741411	8741524	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8741525	8742072	1	-	1	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8741525	8742072	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8742073	8742152	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8742153	8742385	1	-	0	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8742153	8742385	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8742386	8742464	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8742465	8742471	0.82	-	1	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8742465	8742471	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8742472	8742563	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8742564	8742717	0.8	-	2	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8742564	8742717	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	intron	8742718	8742797	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	CDS	8742798	8742936	0.84	-	0	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	exon	8742798	8742936	.	-	.	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
Phchi.S3	AUGUSTUS	start_codon	8742934	8742936	.	-	0	transcript_id "Phchi.S3G107800.t1"; gene_id "Phchi.S3G107800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8781.t1 is derived from g5956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37923420	37924301	.	+	.	Phchi.S1G594000
Phchi.S1	AUGUSTUS	transcript	37923420	37924301	.	+	.	transcript_id "Phchi.S1G594000.t1"; gene_id "Phchi.S1G594000"
Phchi.S1	AUGUSTUS	start_codon	37923420	37923422	.	+	0	transcript_id "Phchi.S1G594000.t1"; gene_id "Phchi.S1G594000"
Phchi.S1	AUGUSTUS	CDS	37923420	37924301	1	+	0	transcript_id "Phchi.S1G594000.t1"; gene_id "Phchi.S1G594000"
Phchi.S1	AUGUSTUS	exon	37923420	37924301	.	+	.	transcript_id "Phchi.S1G594000.t1"; gene_id "Phchi.S1G594000"
Phchi.S1	AUGUSTUS	stop_codon	37924302	37924304	.	+	0	transcript_id "Phchi.S1G594000.t1"; gene_id "Phchi.S1G594000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12738.t1 is derived from g11203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1458929	1461877	.	+	.	Phchi.S3G005700
Phchi.S3	AUGUSTUS	transcript	1458929	1461877	.	+	.	transcript_id "Phchi.S3G005700.t1"; gene_id "Phchi.S3G005700"
Phchi.S3	AUGUSTUS	start_codon	1458929	1458931	.	+	0	transcript_id "Phchi.S3G005700.t1"; gene_id "Phchi.S3G005700"
Phchi.S3	AUGUSTUS	CDS	1458929	1461877	0.62	+	0	transcript_id "Phchi.S3G005700.t1"; gene_id "Phchi.S3G005700"
Phchi.S3	AUGUSTUS	exon	1458929	1461877	.	+	.	transcript_id "Phchi.S3G005700.t1"; gene_id "Phchi.S3G005700"
Phchi.S3	AUGUSTUS	stop_codon	1461878	1461880	.	+	0	transcript_id "Phchi.S3G005700.t1"; gene_id "Phchi.S3G005700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12918.t1 is derived from g11383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3163584	3166276	.	+	.	Phchi.S3G023700
Phchi.S3	AUGUSTUS	transcript	3163584	3166276	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	start_codon	3163584	3163586	.	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3163584	3163898	1	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3163584	3163898	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3163899	3163982	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3163983	3164132	0.98	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3163983	3164132	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3164133	3164244	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3164245	3164297	1	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3164245	3164297	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3164298	3164384	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3164385	3164493	1	+	1	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3164385	3164493	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3164494	3164594	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3164595	3164729	1	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3164595	3164729	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3164730	3164824	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3164825	3164869	1	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3164825	3164869	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3164870	3165230	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3165231	3165418	1	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3165231	3165418	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3165419	3165556	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3165557	3165698	0.97	+	1	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3165557	3165698	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3165699	3165800	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3165801	3165847	0.98	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3165801	3165847	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3165848	3165938	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3165939	3166026	1	+	1	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3165939	3166026	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	intron	3166027	3166123	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	CDS	3166124	3166276	1	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	exon	3166124	3166276	.	+	.	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
Phchi.S3	AUGUSTUS	stop_codon	3166277	3166279	.	+	0	transcript_id "Phchi.S3G023700.t1"; gene_id "Phchi.S3G023700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7381.t1 is derived from g4553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28849412	28854463	.	-	.	Phchi.S1G454000
Phchi.S1	AUGUSTUS	transcript	28849412	28854463	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	stop_codon	28849409	28849411	.	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28849412	28849455	1	-	2	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28849412	28849455	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28849456	28850071	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850072	28850195	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850072	28850195	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850196	28850285	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850286	28850346	1	-	1	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850286	28850346	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850347	28850455	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850456	28850578	1	-	1	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850456	28850578	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850579	28850686	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850687	28850769	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850687	28850769	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850770	28850915	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850916	28850993	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850916	28850993	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850994	28851148	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28851149	28851280	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28851149	28851280	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28851281	28851422	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28851423	28851466	1	-	2	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28851423	28851466	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28851467	28851931	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28851932	28852056	1	-	1	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28851932	28852056	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28852057	28852310	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28852311	28852741	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28852311	28852741	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28852742	28852896	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28852897	28853047	1	-	1	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28852897	28853047	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853048	28853164	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28853165	28853301	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28853165	28853301	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853302	28853485	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28853486	28853653	0.77	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28853486	28853653	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853654	28853778	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28853779	28853939	1	-	2	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28853779	28853939	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853940	28854324	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28854325	28854463	1	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28854325	28854463	.	-	.	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	start_codon	28854461	28854463	.	-	0	transcript_id "Phchi.S1G454000.t1"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	transcript	28849412	28854463	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	stop_codon	28849409	28849411	.	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28849412	28849455	1	-	2	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28849412	28849455	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28849456	28850071	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850072	28850195	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850072	28850195	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850196	28850285	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850286	28850346	1	-	1	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850286	28850346	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850347	28850455	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850456	28850578	1	-	1	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850456	28850578	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850579	28850686	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850687	28850769	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850687	28850769	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850770	28850915	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28850916	28850993	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28850916	28850993	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28850994	28851148	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28851149	28851280	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28851149	28851280	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28851281	28851422	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28851423	28851466	1	-	2	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28851423	28851466	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28851467	28851931	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28851932	28852056	1	-	1	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28851932	28852056	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28852057	28852310	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28852311	28852741	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28852311	28852741	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28852742	28852896	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28852897	28853047	1	-	1	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28852897	28853047	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853048	28853164	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28853165	28853301	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28853165	28853301	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853302	28853485	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28853486	28853656	0.58	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28853486	28853656	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853657	28853778	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28853779	28853939	1	-	2	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28853779	28853939	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	intron	28853940	28854324	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	CDS	28854325	28854463	1	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	exon	28854325	28854463	.	-	.	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
Phchi.S1	AUGUSTUS	start_codon	28854461	28854463	.	-	0	transcript_id "Phchi.S1G454000.t2"; gene_id "Phchi.S1G454000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg593.t1 is derived from g10375.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4327773	4328887	.	+	.	Phchi.S6G055200
Phchi.S6	AUGUSTUS	transcript	4327773	4328887	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	start_codon	4327773	4327775	.	+	0	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4327773	4327862	1	+	0	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4327773	4327862	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4327863	4328035	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328036	4328201	1	+	0	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328036	4328201	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4328202	4328289	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328290	4328373	1	+	2	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328290	4328373	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4328374	4328474	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328475	4328675	1	+	2	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328475	4328675	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4328676	4328798	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328799	4328887	1	+	2	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328799	4328887	.	+	.	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	stop_codon	4328888	4328890	.	+	0	transcript_id "Phchi.S6G055200.t1"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	transcript	4327773	4328887	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	start_codon	4327773	4327775	.	+	0	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4327773	4327862	1	+	0	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4327773	4327862	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4327863	4328032	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328033	4328201	0.95	+	0	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328033	4328201	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4328202	4328289	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328290	4328373	1	+	2	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328290	4328373	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4328374	4328474	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328475	4328675	1	+	2	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328475	4328675	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	intron	4328676	4328798	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	CDS	4328799	4328887	1	+	2	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	exon	4328799	4328887	.	+	.	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
Phchi.S6	AUGUSTUS	stop_codon	4328888	4328890	.	+	0	transcript_id "Phchi.S6G055200.t2"; gene_id "Phchi.S6G055200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6028.t1 is derived from g3199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20504674	20508568	.	+	.	Phchi.S1G318700
Phchi.S1	AUGUSTUS	transcript	20504674	20508568	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	start_codon	20504674	20504676	.	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20504674	20505053	0.65	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20504674	20505053	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20505054	20505229	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20505230	20505446	1	+	1	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20505230	20505446	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20505447	20505524	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20505525	20505617	1	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20505525	20505617	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20505618	20505756	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20505757	20505864	1	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20505757	20505864	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20505865	20506005	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20506006	20506179	0.49	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20506006	20506179	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20506180	20506285	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20506286	20506374	1	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20506286	20506374	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20506375	20506529	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20506530	20506651	1	+	1	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20506530	20506651	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20506652	20506884	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20506885	20507078	1	+	2	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20506885	20507078	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20507079	20507166	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20507167	20507460	1	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20507167	20507460	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20507461	20507542	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20507543	20507690	1	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20507543	20507690	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	intron	20507691	20507789	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	CDS	20507790	20508568	1	+	2	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	exon	20507790	20508568	.	+	.	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
Phchi.S1	AUGUSTUS	stop_codon	20508569	20508571	.	+	0	transcript_id "Phchi.S1G318700.t1"; gene_id "Phchi.S1G318700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10756.t1 is derived from g14806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1958613	1961806	.	+	.	Phchi.S4G033800
Phchi.S4	AUGUSTUS	transcript	1958613	1961806	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	start_codon	1958613	1958615	.	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1958613	1958618	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1958613	1958618	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1958619	1958760	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1958761	1958856	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1958761	1958856	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1958857	1959000	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1959001	1959114	0.97	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1959001	1959114	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1959115	1959219	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1959220	1959390	0.61	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1959220	1959390	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1959391	1959489	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1959490	1959549	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1959490	1959549	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1959550	1959671	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1959672	1959821	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1959672	1959821	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1959822	1959894	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1959895	1960017	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1959895	1960017	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1960018	1960135	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1960136	1960234	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1960136	1960234	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1960235	1960312	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1960313	1960450	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1960313	1960450	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1960451	1960565	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1960566	1960666	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1960566	1960666	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1960667	1960742	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1960743	1960941	1	+	1	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1960743	1960941	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1960942	1961026	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1961027	1961134	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1961027	1961134	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1961135	1961217	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1961218	1961309	1	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1961218	1961309	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1961310	1961456	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1961457	1961641	1	+	1	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1961457	1961641	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	intron	1961642	1961741	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	CDS	1961742	1961806	1	+	2	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	exon	1961742	1961806	.	+	.	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
Phchi.S4	AUGUSTUS	stop_codon	1961807	1961809	.	+	0	transcript_id "Phchi.S4G033800.t1"; gene_id "Phchi.S4G033800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15578.t1 is derived from g14047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20108123	20110162	.	+	.	Phchi.S3G289700
Phchi.S3	AUGUSTUS	transcript	20108123	20110162	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	start_codon	20108123	20108125	.	+	0	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	CDS	20108123	20108704	0.57	+	0	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	exon	20108123	20108704	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	intron	20108705	20108798	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	CDS	20108799	20108875	0.91	+	0	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	exon	20108799	20108875	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	intron	20108876	20108964	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	CDS	20108965	20109190	0.97	+	1	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	exon	20108965	20109190	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	intron	20109191	20109267	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	CDS	20109268	20109637	0.96	+	0	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	exon	20109268	20109637	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	intron	20109638	20109723	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	CDS	20109724	20109953	1	+	2	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	exon	20109724	20109953	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	intron	20109954	20110036	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	CDS	20110037	20110162	1	+	0	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	exon	20110037	20110162	.	+	.	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
Phchi.S3	AUGUSTUS	stop_codon	20110163	20110165	.	+	0	transcript_id "Phchi.S3G289700.t1"; gene_id "Phchi.S3G289700"
# This transcript jg9086.t2 is derived from g6261.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9086.t3 is derived from g6261.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9087.t1 is derived from g6262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39794492	39796439	.	+	.	Phchi.S1G624600
Phchi.S1	AUGUSTUS	transcript	39794492	39796439	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	start_codon	39794492	39794494	.	+	0	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	CDS	39794492	39794754	1	+	0	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	exon	39794492	39794754	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	intron	39794755	39795245	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	CDS	39795246	39795390	1	+	1	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	exon	39795246	39795390	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	intron	39795391	39795462	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	CDS	39795463	39795577	1	+	0	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	exon	39795463	39795577	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	intron	39795578	39795758	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	CDS	39795759	39795822	1	+	2	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	exon	39795759	39795822	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	intron	39795823	39795907	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	CDS	39795908	39796073	1	+	1	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	exon	39795908	39796073	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	intron	39796074	39796199	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	CDS	39796200	39796439	1	+	0	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	exon	39796200	39796439	.	+	.	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
Phchi.S1	AUGUSTUS	stop_codon	39796440	39796442	.	+	0	transcript_id "Phchi.S1G624600.t1"; gene_id "Phchi.S1G624600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11656.t1 is derived from g15707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7533519	7534733	.	-	.	Phchi.S4G123800
Phchi.S4	AUGUSTUS	transcript	7533519	7534733	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	stop_codon	7533516	7533518	.	-	0	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	CDS	7533519	7533611	0.98	-	0	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	exon	7533519	7533611	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	intron	7533612	7533693	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	CDS	7533694	7533742	1	-	1	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	exon	7533694	7533742	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	intron	7533743	7533905	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	CDS	7533906	7533947	1	-	1	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	exon	7533906	7533947	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	intron	7533948	7534093	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	CDS	7534094	7534407	1	-	0	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	exon	7534094	7534407	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	intron	7534408	7534537	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	CDS	7534538	7534637	0.75	-	1	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	exon	7534538	7534637	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	intron	7534638	7534719	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	CDS	7534720	7534733	0.99	-	0	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	exon	7534720	7534733	.	-	.	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
Phchi.S4	AUGUSTUS	start_codon	7534731	7534733	.	-	0	transcript_id "Phchi.S4G123800.t1"; gene_id "Phchi.S4G123800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10077.t1 is derived from g7253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45636756	45637372	.	+	.	Phchi.S1G723600
Phchi.S1	AUGUSTUS	transcript	45636756	45637372	.	+	.	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	start_codon	45636756	45636758	.	+	0	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	CDS	45636756	45636866	1	+	0	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	exon	45636756	45636866	.	+	.	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	intron	45636867	45637036	.	+	.	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	CDS	45637037	45637237	1	+	0	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	exon	45637037	45637237	.	+	.	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	intron	45637238	45637321	.	+	.	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	CDS	45637322	45637372	0.98	+	0	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	exon	45637322	45637372	.	+	.	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
Phchi.S1	AUGUSTUS	stop_codon	45637373	45637375	.	+	0	transcript_id "Phchi.S1G723600.t1"; gene_id "Phchi.S1G723600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1915.t1 is derived from g8835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3839988	3840448	.	-	.	Phchi.S5G052400
Phchi.S5	AUGUSTUS	transcript	3839988	3840448	.	-	.	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	stop_codon	3839985	3839987	.	-	0	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	CDS	3839988	3840060	0.6	-	1	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	exon	3839988	3840060	.	-	.	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	intron	3840061	3840145	.	-	.	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	CDS	3840146	3840276	1	-	0	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	exon	3840146	3840276	.	-	.	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	intron	3840277	3840442	.	-	.	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	CDS	3840443	3840448	1	-	0	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	exon	3840443	3840448	.	-	.	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
Phchi.S5	AUGUSTUS	start_codon	3840446	3840448	.	-	0	transcript_id "Phchi.S5G052400.t1"; gene_id "Phchi.S5G052400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13872.t1 is derived from g12339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9401782	9403823	.	+	.	Phchi.S3G119100
Phchi.S3	AUGUSTUS	transcript	9401782	9403823	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	start_codon	9401782	9401784	.	+	0	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9401782	9402048	0.48	+	0	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9401782	9402048	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	intron	9402049	9402127	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9402128	9402217	1	+	0	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9402128	9402217	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	intron	9402218	9402303	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9402304	9402448	1	+	0	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9402304	9402448	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	intron	9402449	9402580	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9402581	9402726	1	+	2	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9402581	9402726	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	intron	9402727	9402828	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9402829	9402983	0.95	+	0	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9402829	9402983	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	intron	9402984	9403090	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9403091	9403326	0.98	+	1	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9403091	9403326	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	intron	9403327	9403413	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	CDS	9403414	9403823	1	+	2	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	exon	9403414	9403823	.	+	.	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
Phchi.S3	AUGUSTUS	stop_codon	9403824	9403826	.	+	0	transcript_id "Phchi.S3G119100.t1"; gene_id "Phchi.S3G119100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13273.t1 is derived from g11738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5083755	5085561	.	-	.	Phchi.S3G059200
Phchi.S3	AUGUSTUS	transcript	5083755	5085561	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	stop_codon	5083752	5083754	.	-	0	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5083755	5083988	0.58	-	0	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5083755	5083988	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	intron	5083989	5084060	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5084061	5084318	1	-	0	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5084061	5084318	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	intron	5084319	5084439	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5084440	5084525	1	-	2	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5084440	5084525	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	intron	5084526	5084680	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5084681	5084865	1	-	1	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5084681	5084865	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	intron	5084866	5084960	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5084961	5085182	1	-	1	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5084961	5085182	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	intron	5085183	5085266	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5085267	5085330	1	-	2	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5085267	5085330	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	intron	5085331	5085446	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	CDS	5085447	5085561	0.98	-	0	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	exon	5085447	5085561	.	-	.	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
Phchi.S3	AUGUSTUS	start_codon	5085559	5085561	.	-	0	transcript_id "Phchi.S3G059200.t1"; gene_id "Phchi.S3G059200"
# This transcript jg12224.t2 is derived from g7900.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12225.t1 is derived from g7901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6833143	6835640	.	-	.	Phchi.S2G030500
Phchi.S2	AUGUSTUS	transcript	6833143	6835640	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	stop_codon	6833140	6833142	.	-	0	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6833143	6833202	0.99	-	0	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6833143	6833202	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6833203	6833281	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6833282	6833417	1	-	1	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6833282	6833417	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6833418	6833526	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6833527	6833644	0.99	-	2	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6833527	6833644	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6833645	6833761	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6833762	6833863	1	-	2	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6833762	6833863	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6833864	6834051	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6834052	6834119	1	-	1	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6834052	6834119	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6834120	6834590	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6834591	6834808	1	-	0	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6834591	6834808	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6834809	6834901	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6834902	6835306	1	-	0	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6834902	6835306	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	intron	6835307	6835559	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	CDS	6835560	6835640	1	-	0	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	exon	6835560	6835640	.	-	.	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
Phchi.S2	AUGUSTUS	start_codon	6835638	6835640	.	-	0	transcript_id "Phchi.S2G030500.t1"; gene_id "Phchi.S2G030500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1941.t1 is derived from g8861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3929854	3932030	.	-	.	Phchi.S5G055000
Phchi.S5	AUGUSTUS	transcript	3929854	3932030	.	-	.	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	stop_codon	3929851	3929853	.	-	0	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	CDS	3929854	3929893	1	-	1	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	exon	3929854	3929893	.	-	.	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	intron	3929894	3930061	.	-	.	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	CDS	3930062	3930115	1	-	1	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	exon	3930062	3930115	.	-	.	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	intron	3930116	3930267	.	-	.	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	CDS	3930268	3932030	0.71	-	0	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	exon	3930268	3932030	.	-	.	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
Phchi.S5	AUGUSTUS	start_codon	3932028	3932030	.	-	0	transcript_id "Phchi.S5G055000.t1"; gene_id "Phchi.S5G055000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8366.t1 is derived from g5541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35526455	35528170	.	-	.	Phchi.S1G552500
Phchi.S1	AUGUSTUS	transcript	35526455	35528170	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	stop_codon	35526452	35526454	.	-	0	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	CDS	35526455	35526503	0.98	-	1	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	exon	35526455	35526503	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	intron	35526504	35526589	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	CDS	35526590	35526956	0.96	-	2	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	exon	35526590	35526956	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	intron	35526957	35527056	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	CDS	35527057	35527153	0.96	-	0	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	exon	35527057	35527153	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	intron	35527154	35527270	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	CDS	35527271	35528170	0.38	-	0	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	exon	35527271	35528170	.	-	.	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
Phchi.S1	AUGUSTUS	start_codon	35528168	35528170	.	-	0	transcript_id "Phchi.S1G552500.t1"; gene_id "Phchi.S1G552500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6177.t1 is derived from g3348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21327276	21327907	.	+	.	Phchi.S1G333600
Phchi.S1	AUGUSTUS	transcript	21327276	21327907	.	+	.	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	start_codon	21327276	21327278	.	+	0	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	CDS	21327276	21327763	0.73	+	0	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	exon	21327276	21327763	.	+	.	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	intron	21327764	21327906	.	+	.	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	CDS	21327907	21327907	0.67	+	1	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	exon	21327907	21327907	.	+	.	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
Phchi.S1	AUGUSTUS	stop_codon	21327908	21327910	.	+	0	transcript_id "Phchi.S1G333600.t1"; gene_id "Phchi.S1G333600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3812.t1 is derived from g981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5842534	5842986	.	-	.	Phchi.S1G097100
Phchi.S1	AUGUSTUS	transcript	5842534	5842986	.	-	.	transcript_id "Phchi.S1G097100.t1"; gene_id "Phchi.S1G097100"
Phchi.S1	AUGUSTUS	stop_codon	5842531	5842533	.	-	0	transcript_id "Phchi.S1G097100.t1"; gene_id "Phchi.S1G097100"
Phchi.S1	AUGUSTUS	CDS	5842534	5842986	0.64	-	0	transcript_id "Phchi.S1G097100.t1"; gene_id "Phchi.S1G097100"
Phchi.S1	AUGUSTUS	exon	5842534	5842986	.	-	.	transcript_id "Phchi.S1G097100.t1"; gene_id "Phchi.S1G097100"
Phchi.S1	AUGUSTUS	start_codon	5842984	5842986	.	-	0	transcript_id "Phchi.S1G097100.t1"; gene_id "Phchi.S1G097100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7497.t1 is derived from g4671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29669797	29670321	.	+	.	Phchi.S1G465600
Phchi.S1	AUGUSTUS	transcript	29669797	29670321	.	+	.	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	start_codon	29669797	29669799	.	+	0	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	CDS	29669797	29670031	0.93	+	0	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	exon	29669797	29670031	.	+	.	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	intron	29670032	29670133	.	+	.	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	CDS	29670134	29670321	0.5	+	2	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	exon	29670134	29670321	.	+	.	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
Phchi.S1	AUGUSTUS	stop_codon	29670322	29670324	.	+	0	transcript_id "Phchi.S1G465600.t1"; gene_id "Phchi.S1G465600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7351.t1 is derived from g4523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28703306	28711137	.	+	.	Phchi.S1G451000
Phchi.S1	AUGUSTUS	transcript	28703306	28711137	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	start_codon	28703306	28703308	.	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28703306	28705039	0.99	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28703306	28705039	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28705040	28705222	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28705223	28705435	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28705223	28705435	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28705436	28705543	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28705544	28705635	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28705544	28705635	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28705636	28705749	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28705750	28705869	1	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28705750	28705869	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28705870	28706022	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28706023	28706110	1	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28706023	28706110	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28706111	28706241	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28706242	28706331	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28706242	28706331	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28706332	28706730	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28706731	28706853	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28706731	28706853	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28706854	28706935	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28706936	28707160	0.9	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28706936	28707160	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28707161	28707236	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28707237	28707332	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28707237	28707332	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28707333	28707452	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28707453	28707545	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28707453	28707545	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28707546	28707724	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28707725	28707798	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28707725	28707798	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28707799	28707885	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28707886	28708084	1	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28707886	28708084	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28708085	28708158	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28708159	28708247	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28708159	28708247	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28708248	28708333	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28708334	28708773	0.99	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28708334	28708773	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28708774	28708905	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28708906	28709167	1	+	2	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28708906	28709167	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28709168	28709255	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28709256	28709336	1	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28709256	28709336	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28709337	28709414	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28709415	28710146	1	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28709415	28710146	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28710147	28710240	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28710241	28710430	1	+	1	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28710241	28710430	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28710431	28710626	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28710627	28710689	1	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28710627	28710689	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28710690	28710783	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28710784	28710828	0.82	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28710784	28710828	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28710829	28710921	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28710922	28710991	0.81	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28710922	28710991	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	intron	28710992	28711081	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	CDS	28711082	28711137	0.82	+	2	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	exon	28711082	28711137	.	+	.	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
Phchi.S1	AUGUSTUS	stop_codon	28711138	28711140	.	+	0	transcript_id "Phchi.S1G451000.t1"; gene_id "Phchi.S1G451000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10867.t1 is derived from g14917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2664847	2665626	.	-	.	Phchi.S4G044900
Phchi.S4	AUGUSTUS	transcript	2664847	2665626	.	-	.	transcript_id "Phchi.S4G044900.t1"; gene_id "Phchi.S4G044900"
Phchi.S4	AUGUSTUS	stop_codon	2664844	2664846	.	-	0	transcript_id "Phchi.S4G044900.t1"; gene_id "Phchi.S4G044900"
Phchi.S4	AUGUSTUS	CDS	2664847	2665626	0.58	-	0	transcript_id "Phchi.S4G044900.t1"; gene_id "Phchi.S4G044900"
Phchi.S4	AUGUSTUS	exon	2664847	2665626	.	-	.	transcript_id "Phchi.S4G044900.t1"; gene_id "Phchi.S4G044900"
Phchi.S4	AUGUSTUS	start_codon	2665624	2665626	.	-	0	transcript_id "Phchi.S4G044900.t1"; gene_id "Phchi.S4G044900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg173.t1 is derived from g9955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1014692	1015398	.	+	.	Phchi.S6G013200
Phchi.S6	AUGUSTUS	transcript	1014692	1015398	.	+	.	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	start_codon	1014692	1014694	.	+	0	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	CDS	1014692	1014778	1	+	0	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	exon	1014692	1014778	.	+	.	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	intron	1014779	1014872	.	+	.	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	CDS	1014873	1014964	0.96	+	0	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	exon	1014873	1014964	.	+	.	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	intron	1014965	1015232	.	+	.	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	CDS	1015233	1015398	0.94	+	1	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	exon	1015233	1015398	.	+	.	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
Phchi.S6	AUGUSTUS	stop_codon	1015399	1015401	.	+	0	transcript_id "Phchi.S6G013200.t1"; gene_id "Phchi.S6G013200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15741.t1 is derived from g14211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21019301	21022548	.	-	.	Phchi.S3G306000
Phchi.S3	AUGUSTUS	transcript	21019301	21022548	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	stop_codon	21019298	21019300	.	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21019301	21019341	0.99	-	2	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21019301	21019341	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21019342	21019426	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21019427	21019698	0.99	-	1	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21019427	21019698	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21019699	21019793	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21019794	21020107	0.99	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21019794	21020107	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21020108	21020184	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21020185	21020316	0.96	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21020185	21020316	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21020317	21020508	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21020509	21020604	1	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21020509	21020604	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21020605	21020699	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21020700	21020873	1	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21020700	21020873	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21020874	21020963	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21020964	21021130	1	-	2	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21020964	21021130	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21021131	21021205	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21021206	21021371	1	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21021206	21021371	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21021372	21021518	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21021519	21021657	0.97	-	1	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21021519	21021657	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21021658	21021800	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21021801	21021993	0.75	-	2	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21021801	21021993	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21021994	21022145	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21022146	21022228	1	-	1	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21022146	21022228	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	intron	21022229	21022444	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	CDS	21022445	21022548	0.85	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	exon	21022445	21022548	.	-	.	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
Phchi.S3	AUGUSTUS	start_codon	21022546	21022548	.	-	0	transcript_id "Phchi.S3G306000.t1"; gene_id "Phchi.S3G306000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg228.t1 is derived from g10010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1549830	1554679	.	+	.	Phchi.S6G018700
Phchi.S6	AUGUSTUS	transcript	1549830	1554679	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	start_codon	1549830	1549832	.	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1549830	1549866	0.94	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1549830	1549866	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1549867	1550611	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1550612	1550685	1	+	2	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1550612	1550685	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1550686	1550802	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1550803	1550866	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1550803	1550866	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1550867	1550988	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1550989	1551101	1	+	2	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1550989	1551101	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1551102	1551231	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1551232	1551279	0.83	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1551232	1551279	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1551280	1551385	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1551386	1551457	0.83	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1551386	1551457	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1551458	1551600	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1551601	1551690	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1551601	1551690	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1551691	1551794	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1551795	1551968	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1551795	1551968	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1551969	1552281	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1552282	1552365	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1552282	1552365	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1552366	1552503	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1552504	1552559	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1552504	1552559	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1552560	1552731	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1552732	1552862	1	+	1	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1552732	1552862	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1552863	1552958	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1552959	1553051	1	+	2	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1552959	1553051	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1553052	1553206	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1553207	1553268	1	+	2	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1553207	1553268	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1553269	1553389	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1553390	1553533	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1553390	1553533	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1553534	1553633	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1553634	1553677	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1553634	1553677	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1553678	1553769	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1553770	1553853	1	+	1	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1553770	1553853	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1553854	1553989	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1553990	1554063	1	+	1	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1553990	1554063	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1554064	1554175	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1554176	1554288	1	+	2	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1554176	1554288	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1554289	1554384	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1554385	1554480	1	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1554385	1554480	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	intron	1554481	1554562	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	CDS	1554563	1554679	0.96	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	exon	1554563	1554679	.	+	.	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
Phchi.S6	AUGUSTUS	stop_codon	1554680	1554682	.	+	0	transcript_id "Phchi.S6G018700.t1"; gene_id "Phchi.S6G018700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7942.t1 is derived from g5116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32029301	32030708	.	+	.	Phchi.S1G510100
Phchi.S1	AUGUSTUS	transcript	32029301	32030708	.	+	.	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	start_codon	32029301	32029303	.	+	0	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	CDS	32029301	32030180	0.4	+	0	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	exon	32029301	32030180	.	+	.	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	intron	32030181	32030296	.	+	.	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	CDS	32030297	32030401	1	+	2	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	exon	32030297	32030401	.	+	.	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	intron	32030402	32030484	.	+	.	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	CDS	32030485	32030708	0.93	+	2	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	exon	32030485	32030708	.	+	.	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
Phchi.S1	AUGUSTUS	stop_codon	32030709	32030711	.	+	0	transcript_id "Phchi.S1G510100.t1"; gene_id "Phchi.S1G510100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1362.t1 is derived from g15998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C81	AUGUSTUS	gene	22937	23489	.	-	.	Phchi.C81G000400
Phchi.C81	AUGUSTUS	transcript	22937	23489	.	-	.	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	stop_codon	22934	22936	.	-	0	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	CDS	22937	22995	0.84	-	2	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	exon	22937	22995	.	-	.	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	intron	22996	23101	.	-	.	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	CDS	23102	23489	0.45	-	0	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	exon	23102	23489	.	-	.	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
Phchi.C81	AUGUSTUS	start_codon	23487	23489	.	-	0	transcript_id "Phchi.C81G000400.t1"; gene_id "Phchi.C81G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12287.t1 is derived from g7963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8838363	8840553	.	-	.	Phchi.S2G036700
Phchi.S2	AUGUSTUS	transcript	8838363	8840553	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	stop_codon	8838360	8838362	.	-	0	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8838363	8838364	0.43	-	2	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8838363	8838364	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	intron	8838365	8838718	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8838719	8838879	0.43	-	1	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8838719	8838879	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	intron	8838880	8838959	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8838960	8839148	0.75	-	1	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8838960	8839148	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	intron	8839149	8839257	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8839258	8839377	0.81	-	1	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8839258	8839377	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	intron	8839378	8839505	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8839506	8839705	1	-	0	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8839506	8839705	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	intron	8839706	8839814	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8839815	8839915	1	-	2	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8839815	8839915	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	intron	8839916	8840006	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	CDS	8840007	8840553	0.75	-	0	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	exon	8840007	8840553	.	-	.	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
Phchi.S2	AUGUSTUS	start_codon	8840551	8840553	.	-	0	transcript_id "Phchi.S2G036700.t1"; gene_id "Phchi.S2G036700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13682.t1 is derived from g12149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8187006	8189004	.	+	.	Phchi.S3G100100
Phchi.S3	AUGUSTUS	transcript	8187006	8189004	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	start_codon	8187006	8187008	.	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187006	8187084	0.47	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187006	8187084	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187085	8187166	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187167	8187354	1	+	2	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187167	8187354	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187355	8187438	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187439	8187525	1	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187439	8187525	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187526	8187659	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187660	8187785	1	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187660	8187785	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187786	8187876	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187877	8187999	1	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187877	8187999	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188000	8188088	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188089	8188224	0.88	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188089	8188224	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188225	8188300	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188301	8188317	0.89	+	2	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188301	8188317	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188318	8188407	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188408	8188465	0.99	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188408	8188465	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188466	8188558	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188559	8188716	0.98	+	2	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188559	8188716	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188717	8188944	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188945	8189004	1	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188945	8189004	.	+	.	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	stop_codon	8189005	8189007	.	+	0	transcript_id "Phchi.S3G100100.t1"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	transcript	8187006	8189004	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	start_codon	8187006	8187008	.	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187006	8187084	0.56	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187006	8187084	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187085	8187166	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187167	8187354	1	+	2	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187167	8187354	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187355	8187438	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187439	8187525	1	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187439	8187525	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187526	8187659	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187660	8187785	1	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187660	8187785	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8187786	8187876	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8187877	8187999	1	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8187877	8187999	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188000	8188088	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188089	8188151	0.62	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188089	8188151	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188152	8188300	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188301	8188317	1	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188301	8188317	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188318	8188390	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188391	8188465	1	+	1	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188391	8188465	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188466	8188558	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188559	8188590	0.99	+	1	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188559	8188590	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188591	8188693	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188694	8188716	0.97	+	2	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188694	8188716	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	intron	8188717	8188944	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	CDS	8188945	8189004	0.99	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	exon	8188945	8189004	.	+	.	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
Phchi.S3	AUGUSTUS	stop_codon	8189005	8189007	.	+	0	transcript_id "Phchi.S3G100100.t2"; gene_id "Phchi.S3G100100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9622.t1 is derived from g6798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42955444	42961792	.	-	.	Phchi.S1G678100
Phchi.S1	AUGUSTUS	transcript	42955444	42961792	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	stop_codon	42955441	42955443	.	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42955444	42955480	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42955444	42955480	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42955481	42955562	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42955563	42955691	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42955563	42955691	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42955692	42955771	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42955772	42955905	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42955772	42955905	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42955906	42956004	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42956005	42956067	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42956005	42956067	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42956068	42956229	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42956230	42956380	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42956230	42956380	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42956381	42956466	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42956467	42956519	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42956467	42956519	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42956520	42956610	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42956611	42956736	0.99	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42956611	42956736	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42956737	42956840	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42956841	42957165	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42956841	42957165	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42957166	42957259	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42957260	42957429	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42957260	42957429	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42957430	42957579	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42957580	42957781	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42957580	42957781	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42957782	42957890	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42957891	42958099	0.98	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42957891	42958099	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42958100	42958268	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42958269	42958478	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42958269	42958478	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42958479	42958604	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42958605	42958734	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42958605	42958734	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42958735	42958858	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42958859	42958973	1	-	2	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42958859	42958973	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42958974	42959058	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42959059	42959186	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42959059	42959186	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42959187	42959384	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42959385	42959477	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42959385	42959477	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42959478	42959569	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42959570	42959781	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42959570	42959781	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42959782	42959978	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42959979	42960086	0.91	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42959979	42960086	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42960087	42960189	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42960190	42960294	0.82	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42960190	42960294	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42960295	42960382	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42960383	42960553	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42960383	42960553	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42960554	42960658	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42960659	42960837	1	-	2	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42960659	42960837	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42960838	42960934	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42960935	42961163	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42960935	42961163	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42961164	42961243	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42961244	42961358	1	-	1	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42961244	42961358	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42961359	42961466	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42961467	42961642	1	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42961467	42961642	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	intron	42961643	42961735	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	CDS	42961736	42961792	0.75	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	exon	42961736	42961792	.	-	.	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
Phchi.S1	AUGUSTUS	start_codon	42961790	42961792	.	-	0	transcript_id "Phchi.S1G678100.t1"; gene_id "Phchi.S1G678100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1676.t1 is derived from g8595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2437963	2440068	.	+	.	Phchi.S5G028500
Phchi.S5	AUGUSTUS	transcript	2437963	2440068	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	start_codon	2437963	2437965	.	+	0	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	CDS	2437963	2438378	0.97	+	0	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	exon	2437963	2438378	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	intron	2438379	2438588	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	CDS	2438589	2438886	1	+	1	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	exon	2438589	2438886	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	intron	2438887	2439018	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	CDS	2439019	2439296	1	+	0	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	exon	2439019	2439296	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	intron	2439297	2439403	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	CDS	2439404	2439753	0.99	+	1	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	exon	2439404	2439753	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	intron	2439754	2439877	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	CDS	2439878	2440068	0.97	+	2	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	exon	2439878	2440068	.	+	.	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
Phchi.S5	AUGUSTUS	stop_codon	2440069	2440071	.	+	0	transcript_id "Phchi.S5G028500.t1"; gene_id "Phchi.S5G028500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3376.t1 is derived from g545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3240054	3241131	.	+	.	Phchi.S1G053500
Phchi.S1	AUGUSTUS	transcript	3240054	3241131	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	start_codon	3240054	3240056	.	+	0	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	CDS	3240054	3240304	0.24	+	0	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	exon	3240054	3240304	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	intron	3240305	3240449	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	CDS	3240450	3240475	0.7	+	1	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	exon	3240450	3240475	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	intron	3240476	3240658	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	CDS	3240659	3240746	0.99	+	2	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	exon	3240659	3240746	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	intron	3240747	3240840	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	CDS	3240841	3240942	0.99	+	1	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	exon	3240841	3240942	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	intron	3240943	3241130	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	CDS	3241131	3241131	0.99	+	1	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	exon	3241131	3241131	.	+	.	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
Phchi.S1	AUGUSTUS	stop_codon	3241132	3241134	.	+	0	transcript_id "Phchi.S1G053500.t1"; gene_id "Phchi.S1G053500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4365.t1 is derived from g1534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10067539	10067847	.	-	.	Phchi.S1G152400
Phchi.S1	AUGUSTUS	transcript	10067539	10067847	.	-	.	transcript_id "Phchi.S1G152400.t1"; gene_id "Phchi.S1G152400"
Phchi.S1	AUGUSTUS	stop_codon	10067536	10067538	.	-	0	transcript_id "Phchi.S1G152400.t1"; gene_id "Phchi.S1G152400"
Phchi.S1	AUGUSTUS	CDS	10067539	10067847	0.52	-	0	transcript_id "Phchi.S1G152400.t1"; gene_id "Phchi.S1G152400"
Phchi.S1	AUGUSTUS	exon	10067539	10067847	.	-	.	transcript_id "Phchi.S1G152400.t1"; gene_id "Phchi.S1G152400"
Phchi.S1	AUGUSTUS	start_codon	10067845	10067847	.	-	0	transcript_id "Phchi.S1G152400.t1"; gene_id "Phchi.S1G152400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10624.t1 is derived from g14674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1284929	1285504	.	-	.	Phchi.S4G020600
Phchi.S4	AUGUSTUS	transcript	1284929	1285504	.	-	.	transcript_id "Phchi.S4G020600.t1"; gene_id "Phchi.S4G020600"
Phchi.S4	AUGUSTUS	stop_codon	1284926	1284928	.	-	0	transcript_id "Phchi.S4G020600.t1"; gene_id "Phchi.S4G020600"
Phchi.S4	AUGUSTUS	CDS	1284929	1285504	0.59	-	0	transcript_id "Phchi.S4G020600.t1"; gene_id "Phchi.S4G020600"
Phchi.S4	AUGUSTUS	exon	1284929	1285504	.	-	.	transcript_id "Phchi.S4G020600.t1"; gene_id "Phchi.S4G020600"
Phchi.S4	AUGUSTUS	start_codon	1285502	1285504	.	-	0	transcript_id "Phchi.S4G020600.t1"; gene_id "Phchi.S4G020600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4289.t1 is derived from g1458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9438630	9438962	.	+	.	Phchi.S1G144800
Phchi.S1	AUGUSTUS	transcript	9438630	9438962	.	+	.	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	start_codon	9438630	9438632	.	+	0	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	CDS	9438630	9438738	0.97	+	0	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	exon	9438630	9438738	.	+	.	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	intron	9438739	9438837	.	+	.	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	CDS	9438838	9438962	0.88	+	2	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	exon	9438838	9438962	.	+	.	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
Phchi.S1	AUGUSTUS	stop_codon	9438963	9438965	.	+	0	transcript_id "Phchi.S1G144800.t1"; gene_id "Phchi.S1G144800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10118.t1 is derived from g7294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45815930	45820385	.	+	.	Phchi.S1G727700
Phchi.S1	AUGUSTUS	transcript	45815930	45820385	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	start_codon	45815930	45815932	.	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45815930	45815957	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45815930	45815957	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45815958	45816216	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45816217	45816282	0.93	+	2	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45816217	45816282	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45816283	45816386	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45816387	45816439	0.93	+	2	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45816387	45816439	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45816440	45816532	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45816533	45817240	0.91	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45816533	45817240	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45817241	45817343	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45817344	45817406	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45817344	45817406	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45817407	45817504	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45817505	45817582	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45817505	45817582	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45817583	45817689	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45817690	45817893	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45817690	45817893	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45817894	45818098	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45818099	45818155	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45818099	45818155	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45818156	45818247	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45818248	45818322	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45818248	45818322	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45818323	45818441	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45818442	45818513	0.94	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45818442	45818513	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45818514	45818611	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45818612	45818674	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45818612	45818674	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45818675	45818758	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45818759	45818857	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45818759	45818857	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45818858	45818965	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45818966	45819067	0.69	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45818966	45819067	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45819068	45819164	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45819165	45819233	0.79	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45819165	45819233	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45819234	45819319	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45819320	45819367	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45819320	45819367	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45819368	45819451	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45819452	45819547	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45819452	45819547	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45819548	45819659	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45819660	45819742	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45819660	45819742	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45819743	45819869	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45819870	45819912	1	+	1	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45819870	45819912	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45819913	45820008	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45820009	45820101	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45820009	45820101	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45820102	45820190	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45820191	45820235	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45820191	45820235	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	intron	45820236	45820316	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	CDS	45820317	45820385	1	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	exon	45820317	45820385	.	+	.	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
Phchi.S1	AUGUSTUS	stop_codon	45820386	45820388	.	+	0	transcript_id "Phchi.S1G727700.t1"; gene_id "Phchi.S1G727700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2102.t1 is derived from g9022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4878373	4881360	.	+	.	Phchi.S5G071100
Phchi.S5	AUGUSTUS	transcript	4878373	4881360	.	+	.	transcript_id "Phchi.S5G071100.t1"; gene_id "Phchi.S5G071100"
Phchi.S5	AUGUSTUS	start_codon	4878373	4878375	.	+	0	transcript_id "Phchi.S5G071100.t1"; gene_id "Phchi.S5G071100"
Phchi.S5	AUGUSTUS	CDS	4878373	4881360	0.84	+	0	transcript_id "Phchi.S5G071100.t1"; gene_id "Phchi.S5G071100"
Phchi.S5	AUGUSTUS	exon	4878373	4881360	.	+	.	transcript_id "Phchi.S5G071100.t1"; gene_id "Phchi.S5G071100"
Phchi.S5	AUGUSTUS	stop_codon	4881361	4881363	.	+	0	transcript_id "Phchi.S5G071100.t1"; gene_id "Phchi.S5G071100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15357.t1 is derived from g13825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18574003	18575518	.	-	.	Phchi.S3G267600
Phchi.S3	AUGUSTUS	transcript	18574003	18575518	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	stop_codon	18574000	18574002	.	-	0	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	CDS	18574003	18574726	0.94	-	1	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	exon	18574003	18574726	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	intron	18574727	18574835	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	CDS	18574836	18574875	0.97	-	2	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	exon	18574836	18574875	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	intron	18574876	18575095	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	CDS	18575096	18575122	0.73	-	2	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	exon	18575096	18575122	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	intron	18575123	18575252	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	CDS	18575253	18575304	0.99	-	0	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	exon	18575253	18575304	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	intron	18575305	18575398	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	CDS	18575399	18575518	0.99	-	0	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	exon	18575399	18575518	.	-	.	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
Phchi.S3	AUGUSTUS	start_codon	18575516	18575518	.	-	0	transcript_id "Phchi.S3G267600.t1"; gene_id "Phchi.S3G267600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5237.t1 is derived from g2407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15789101	15790762	.	+	.	Phchi.S1G239600
Phchi.S1	AUGUSTUS	transcript	15789101	15790762	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	start_codon	15789101	15789103	.	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15789101	15789187	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15789101	15789187	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15789188	15789328	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15789329	15789418	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15789329	15789418	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15789419	15789515	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15789516	15789617	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15789516	15789617	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15789618	15789739	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15789740	15789841	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15789740	15789841	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15789842	15789933	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15789934	15790029	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15789934	15790029	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15790030	15790127	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15790128	15790361	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15790128	15790361	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15790362	15790439	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15790440	15790538	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15790440	15790538	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	intron	15790539	15790636	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	CDS	15790637	15790762	1	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	exon	15790637	15790762	.	+	.	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
Phchi.S1	AUGUSTUS	stop_codon	15790763	15790765	.	+	0	transcript_id "Phchi.S1G239600.t1"; gene_id "Phchi.S1G239600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11484.t1 is derived from g15534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6593354	6598310	.	+	.	Phchi.S4G106600
Phchi.S4	AUGUSTUS	transcript	6593354	6598310	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	start_codon	6593354	6593356	.	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6593354	6593510	0.91	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6593354	6593510	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6593511	6593609	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6593610	6594178	0.98	+	2	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6593610	6594178	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6594179	6594315	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6594316	6594387	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6594316	6594387	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6594388	6594504	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6594505	6594579	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6594505	6594579	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6594580	6594663	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6594664	6594778	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6594664	6594778	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6594779	6594970	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6594971	6595032	1	+	2	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6594971	6595032	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6595033	6595109	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6595110	6595157	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6595110	6595157	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6595158	6595281	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6595282	6595566	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6595282	6595566	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6595567	6595668	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6595669	6595728	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6595669	6595728	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6595729	6595892	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6595893	6595976	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6595893	6595976	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6595977	6596142	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6596143	6596208	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6596143	6596208	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6596209	6596302	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6596303	6596401	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6596303	6596401	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6596402	6596487	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6596488	6596706	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6596488	6596706	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6596707	6596791	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6596792	6596903	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6596792	6596903	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6596904	6596993	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6596994	6597226	1	+	2	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6596994	6597226	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6597227	6597340	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6597341	6597400	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6597341	6597400	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6597401	6597524	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6597525	6597638	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6597525	6597638	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6597639	6597823	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6597824	6597898	1	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6597824	6597898	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6597899	6597993	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6597994	6598025	0.81	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6597994	6598025	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	intron	6598026	6598162	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	CDS	6598163	6598310	0.38	+	1	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	exon	6598163	6598310	.	+	.	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
Phchi.S4	AUGUSTUS	stop_codon	6598311	6598313	.	+	0	transcript_id "Phchi.S4G106600.t1"; gene_id "Phchi.S4G106600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4876.t1 is derived from g2046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13187016	13188142	.	+	.	Phchi.S1G203500
Phchi.S1	AUGUSTUS	transcript	13187016	13188142	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	start_codon	13187016	13187018	.	+	0	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	CDS	13187016	13187146	0.63	+	0	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	exon	13187016	13187146	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	intron	13187147	13187395	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	CDS	13187396	13187439	0.53	+	1	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	exon	13187396	13187439	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	intron	13187440	13187519	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	CDS	13187520	13187677	0.71	+	2	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	exon	13187520	13187677	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	intron	13187678	13187766	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	CDS	13187767	13187842	1	+	0	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	exon	13187767	13187842	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	intron	13187843	13187939	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	CDS	13187940	13188142	1	+	2	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	exon	13187940	13188142	.	+	.	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
Phchi.S1	AUGUSTUS	stop_codon	13188143	13188145	.	+	0	transcript_id "Phchi.S1G203500.t1"; gene_id "Phchi.S1G203500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9388.t1 is derived from g6564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41292076	41293629	.	+	.	Phchi.S1G654700
Phchi.S1	AUGUSTUS	transcript	41292076	41293629	.	+	.	transcript_id "Phchi.S1G654700.t1"; gene_id "Phchi.S1G654700"
Phchi.S1	AUGUSTUS	start_codon	41292076	41292078	.	+	0	transcript_id "Phchi.S1G654700.t1"; gene_id "Phchi.S1G654700"
Phchi.S1	AUGUSTUS	CDS	41292076	41293629	1	+	0	transcript_id "Phchi.S1G654700.t1"; gene_id "Phchi.S1G654700"
Phchi.S1	AUGUSTUS	exon	41292076	41293629	.	+	.	transcript_id "Phchi.S1G654700.t1"; gene_id "Phchi.S1G654700"
Phchi.S1	AUGUSTUS	stop_codon	41293630	41293632	.	+	0	transcript_id "Phchi.S1G654700.t1"; gene_id "Phchi.S1G654700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2600.t1 is derived from g9520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7676213	7676530	.	+	.	Phchi.S5G120900
Phchi.S5	AUGUSTUS	transcript	7676213	7676530	.	+	.	transcript_id "Phchi.S5G120900.t1"; gene_id "Phchi.S5G120900"
Phchi.S5	AUGUSTUS	start_codon	7676213	7676215	.	+	0	transcript_id "Phchi.S5G120900.t1"; gene_id "Phchi.S5G120900"
Phchi.S5	AUGUSTUS	CDS	7676213	7676530	0.82	+	0	transcript_id "Phchi.S5G120900.t1"; gene_id "Phchi.S5G120900"
Phchi.S5	AUGUSTUS	exon	7676213	7676530	.	+	.	transcript_id "Phchi.S5G120900.t1"; gene_id "Phchi.S5G120900"
Phchi.S5	AUGUSTUS	stop_codon	7676531	7676533	.	+	0	transcript_id "Phchi.S5G120900.t1"; gene_id "Phchi.S5G120900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5964.t1 is derived from g3135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20106636	20107513	.	-	.	Phchi.S1G312300
Phchi.S1	AUGUSTUS	transcript	20106636	20107513	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	stop_codon	20106633	20106635	.	-	0	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	CDS	20106636	20106699	0.36	-	1	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	exon	20106636	20106699	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	intron	20106700	20106839	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	CDS	20106840	20106926	0.41	-	1	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	exon	20106840	20106926	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	intron	20106927	20107177	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	CDS	20107178	20107237	0.59	-	1	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	exon	20107178	20107237	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	intron	20107238	20107424	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	CDS	20107425	20107513	0.59	-	0	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	exon	20107425	20107513	.	-	.	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
Phchi.S1	AUGUSTUS	start_codon	20107511	20107513	.	-	0	transcript_id "Phchi.S1G312300.t1"; gene_id "Phchi.S1G312300"
# This transcript jg11765.t2 is derived from g15817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11765.t3 is derived from g15817.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11766.t1 is derived from g15818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8077271	8080298	.	+	.	Phchi.S4G134800
Phchi.S4	AUGUSTUS	transcript	8077271	8080298	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	start_codon	8077271	8077273	.	+	0	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	CDS	8077271	8077499	0.99	+	0	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	exon	8077271	8077499	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	intron	8077500	8078042	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	CDS	8078043	8078303	0.93	+	2	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	exon	8078043	8078303	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	intron	8078304	8078392	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	CDS	8078393	8078537	0.51	+	2	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	exon	8078393	8078537	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	intron	8078538	8078692	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	CDS	8078693	8079369	0.98	+	1	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	exon	8078693	8079369	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	intron	8079370	8080221	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	CDS	8080222	8080298	1	+	2	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	exon	8080222	8080298	.	+	.	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
Phchi.S4	AUGUSTUS	stop_codon	8080299	8080301	.	+	0	transcript_id "Phchi.S4G134800.t1"; gene_id "Phchi.S4G134800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15561.t1 is derived from g14030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19921064	19923025	.	+	.	Phchi.S3G288000
Phchi.S3	AUGUSTUS	transcript	19921064	19923025	.	+	.	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	start_codon	19921064	19921066	.	+	0	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	CDS	19921064	19921140	0.51	+	0	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	exon	19921064	19921140	.	+	.	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	intron	19921141	19921255	.	+	.	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	CDS	19921256	19921270	0.99	+	1	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	exon	19921256	19921270	.	+	.	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	intron	19921271	19921470	.	+	.	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	CDS	19921471	19923025	1	+	1	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	exon	19921471	19923025	.	+	.	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
Phchi.S3	AUGUSTUS	stop_codon	19923026	19923028	.	+	0	transcript_id "Phchi.S3G288000.t1"; gene_id "Phchi.S3G288000"
# This transcript jg12190.t2 is derived from g7866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12191.t1 is derived from g7867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6377442	6380402	.	+	.	Phchi.S2G027100
Phchi.S2	AUGUSTUS	transcript	6377442	6380402	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	start_codon	6377442	6377444	.	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6377442	6377600	0.87	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6377442	6377600	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6377601	6377821	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6377822	6377884	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6377822	6377884	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6377885	6378058	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378059	6378130	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378059	6378130	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378131	6378249	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378250	6378357	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378250	6378357	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378358	6378485	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378486	6378566	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378486	6378566	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378567	6378653	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378654	6378707	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378654	6378707	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378708	6378903	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378904	6379029	0.98	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378904	6379029	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379030	6379130	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379131	6379220	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379131	6379220	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379221	6379381	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379382	6379504	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379382	6379504	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379505	6379619	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379620	6379739	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379620	6379739	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379740	6379830	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379831	6379947	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379831	6379947	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379948	6380029	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6380030	6380086	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6380030	6380086	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6380087	6380164	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6380165	6380239	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6380165	6380239	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6380240	6380324	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6380325	6380402	1	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6380325	6380402	.	+	.	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	stop_codon	6380403	6380405	.	+	0	transcript_id "Phchi.S2G027100.t1"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	transcript	6377442	6380402	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	start_codon	6377442	6377444	.	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6377442	6377600	0.8	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6377442	6377600	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6377601	6377821	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6377822	6377884	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6377822	6377884	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6377885	6378058	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378059	6378130	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378059	6378130	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378131	6378249	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378250	6378357	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378250	6378357	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378358	6378485	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378486	6378566	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378486	6378566	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378567	6378653	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378654	6378707	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378654	6378707	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6378708	6378903	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6378904	6379029	0.99	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6378904	6379029	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379030	6379143	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379144	6379220	0.96	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379144	6379220	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379221	6379371	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379372	6379504	1	+	1	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379372	6379504	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379505	6379619	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379620	6379739	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379620	6379739	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379740	6379830	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6379831	6379947	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6379831	6379947	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6379948	6380029	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6380030	6380086	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6380030	6380086	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6380087	6380164	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6380165	6380239	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6380165	6380239	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	intron	6380240	6380324	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	CDS	6380325	6380402	1	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	exon	6380325	6380402	.	+	.	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
Phchi.S2	AUGUSTUS	stop_codon	6380403	6380405	.	+	0	transcript_id "Phchi.S2G027100.t2"; gene_id "Phchi.S2G027100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8805.t1 is derived from g5980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38070957	38072402	.	+	.	Phchi.S1G596400
Phchi.S1	AUGUSTUS	transcript	38070957	38072402	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	start_codon	38070957	38070959	.	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38070957	38070959	1	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38070957	38070959	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38070960	38071053	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38071054	38071137	1	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38071054	38071137	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38071138	38071433	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38071434	38071480	0.99	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38071434	38071480	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38071481	38071603	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38071604	38071677	1	+	1	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38071604	38071677	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38071678	38071776	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38071777	38071835	1	+	2	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38071777	38071835	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38071836	38071930	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38071931	38071990	1	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38071931	38071990	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38071991	38072073	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38072074	38072154	1	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38072074	38072154	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	intron	38072155	38072321	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	CDS	38072322	38072402	1	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	exon	38072322	38072402	.	+	.	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
Phchi.S1	AUGUSTUS	stop_codon	38072403	38072405	.	+	0	transcript_id "Phchi.S1G596400.t1"; gene_id "Phchi.S1G596400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13091.t1 is derived from g11556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4107011	4110125	.	+	.	Phchi.S3G041000
Phchi.S3	AUGUSTUS	transcript	4107011	4110125	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	start_codon	4107011	4107013	.	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4107011	4107122	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4107011	4107122	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4107123	4107221	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4107222	4107265	1	+	2	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4107222	4107265	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4107266	4107358	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4107359	4107433	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4107359	4107433	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4107434	4107516	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4107517	4107644	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4107517	4107644	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4107645	4107812	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4107813	4107935	1	+	1	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4107813	4107935	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4107936	4108077	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4108078	4108231	1	+	1	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4108078	4108231	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4108232	4108327	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4108328	4108431	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4108328	4108431	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4108432	4108532	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4108533	4108611	1	+	1	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4108533	4108611	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4108612	4108709	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4108710	4108806	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4108710	4108806	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4108807	4108902	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4108903	4108924	0.99	+	2	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4108903	4108924	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4108925	4109015	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4109016	4109040	1	+	1	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4109016	4109040	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4109041	4109125	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4109126	4109347	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4109126	4109347	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4109348	4109482	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4109483	4109674	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4109483	4109674	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4109675	4109756	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4109757	4109897	1	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4109757	4109897	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	intron	4109898	4109972	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	CDS	4109973	4110125	0.98	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	exon	4109973	4110125	.	+	.	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
Phchi.S3	AUGUSTUS	stop_codon	4110126	4110128	.	+	0	transcript_id "Phchi.S3G041000.t1"; gene_id "Phchi.S3G041000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5684.t1 is derived from g2854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18311806	18313517	.	+	.	Phchi.S1G284300
Phchi.S1	AUGUSTUS	transcript	18311806	18313517	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	start_codon	18311806	18311808	.	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18311806	18312014	1	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18311806	18312014	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18312015	18312098	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18312099	18312201	1	+	1	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18312099	18312201	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18312202	18312292	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18312293	18312400	1	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18312293	18312400	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18312401	18312525	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18312526	18312635	1	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18312526	18312635	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18312636	18312720	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18312721	18312828	1	+	1	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18312721	18312828	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18312829	18312921	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18312922	18312967	1	+	1	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18312922	18312967	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18312968	18313066	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18313067	18313198	0.78	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18313067	18313198	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	intron	18313199	18313355	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	CDS	18313356	18313517	0.64	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	exon	18313356	18313517	.	+	.	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
Phchi.S1	AUGUSTUS	stop_codon	18313518	18313520	.	+	0	transcript_id "Phchi.S1G284300.t1"; gene_id "Phchi.S1G284300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg852.t1 is derived from g10634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5908947	5909348	.	-	.	Phchi.S6G081100
Phchi.S6	AUGUSTUS	transcript	5908947	5909348	.	-	.	transcript_id "Phchi.S6G081100.t1"; gene_id "Phchi.S6G081100"
Phchi.S6	AUGUSTUS	stop_codon	5908944	5908946	.	-	0	transcript_id "Phchi.S6G081100.t1"; gene_id "Phchi.S6G081100"
Phchi.S6	AUGUSTUS	CDS	5908947	5909348	0.94	-	0	transcript_id "Phchi.S6G081100.t1"; gene_id "Phchi.S6G081100"
Phchi.S6	AUGUSTUS	exon	5908947	5909348	.	-	.	transcript_id "Phchi.S6G081100.t1"; gene_id "Phchi.S6G081100"
Phchi.S6	AUGUSTUS	start_codon	5909346	5909348	.	-	0	transcript_id "Phchi.S6G081100.t1"; gene_id "Phchi.S6G081100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4084.t1 is derived from g1253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7712139	7713310	.	+	.	Phchi.S1G124300
Phchi.S1	AUGUSTUS	transcript	7712139	7713310	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	start_codon	7712139	7712141	.	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	CDS	7712139	7712162	0.69	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	exon	7712139	7712162	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	intron	7712163	7712275	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	CDS	7712276	7712554	0.84	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	exon	7712276	7712554	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	intron	7712555	7712678	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	CDS	7712679	7712810	0.99	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	exon	7712679	7712810	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	intron	7712811	7712937	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	CDS	7712938	7713084	1	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	exon	7712938	7713084	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	intron	7713085	7713181	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	CDS	7713182	7713310	1	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	exon	7713182	7713310	.	+	.	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
Phchi.S1	AUGUSTUS	stop_codon	7713311	7713313	.	+	0	transcript_id "Phchi.S1G124300.t1"; gene_id "Phchi.S1G124300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7545.t1 is derived from g4719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29978883	29981480	.	+	.	Phchi.S1G470400
Phchi.S1	AUGUSTUS	transcript	29978883	29981480	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	start_codon	29978883	29978885	.	+	0	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	CDS	29978883	29980146	0.92	+	0	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	exon	29978883	29980146	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	intron	29980147	29980235	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	CDS	29980236	29980303	0.7	+	2	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	exon	29980236	29980303	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	intron	29980304	29980404	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	CDS	29980405	29980560	0.97	+	0	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	exon	29980405	29980560	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	intron	29980561	29980652	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	CDS	29980653	29981480	1	+	0	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	exon	29980653	29981480	.	+	.	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
Phchi.S1	AUGUSTUS	stop_codon	29981481	29981483	.	+	0	transcript_id "Phchi.S1G470400.t1"; gene_id "Phchi.S1G470400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3127.t1 is derived from g296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1865829	1867952	.	+	.	Phchi.S1G028600
Phchi.S1	AUGUSTUS	transcript	1865829	1867952	.	+	.	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	start_codon	1865829	1865831	.	+	0	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	CDS	1865829	1866414	1	+	0	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	exon	1865829	1866414	.	+	.	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	intron	1866415	1867018	.	+	.	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	CDS	1867019	1867176	1	+	2	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	exon	1867019	1867176	.	+	.	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	intron	1867177	1867736	.	+	.	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	CDS	1867737	1867952	0.3	+	0	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	exon	1867737	1867952	.	+	.	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
Phchi.S1	AUGUSTUS	stop_codon	1867953	1867955	.	+	0	transcript_id "Phchi.S1G028600.t1"; gene_id "Phchi.S1G028600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9356.t1 is derived from g6532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41141934	41142383	.	-	.	Phchi.S1G651500
Phchi.S1	AUGUSTUS	transcript	41141934	41142383	.	-	.	transcript_id "Phchi.S1G651500.t1"; gene_id "Phchi.S1G651500"
Phchi.S1	AUGUSTUS	stop_codon	41141931	41141933	.	-	0	transcript_id "Phchi.S1G651500.t1"; gene_id "Phchi.S1G651500"
Phchi.S1	AUGUSTUS	CDS	41141934	41142383	0.81	-	0	transcript_id "Phchi.S1G651500.t1"; gene_id "Phchi.S1G651500"
Phchi.S1	AUGUSTUS	exon	41141934	41142383	.	-	.	transcript_id "Phchi.S1G651500.t1"; gene_id "Phchi.S1G651500"
Phchi.S1	AUGUSTUS	start_codon	41142381	41142383	.	-	0	transcript_id "Phchi.S1G651500.t1"; gene_id "Phchi.S1G651500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9495.t1 is derived from g6671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42022548	42023473	.	-	.	Phchi.S1G665400
Phchi.S1	AUGUSTUS	transcript	42022548	42023473	.	-	.	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	stop_codon	42022545	42022547	.	-	0	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	CDS	42022548	42023150	0.53	-	0	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	exon	42022548	42023150	.	-	.	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	intron	42023151	42023305	.	-	.	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	CDS	42023306	42023473	0.84	-	0	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	exon	42023306	42023473	.	-	.	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
Phchi.S1	AUGUSTUS	start_codon	42023471	42023473	.	-	0	transcript_id "Phchi.S1G665400.t1"; gene_id "Phchi.S1G665400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13790.t1 is derived from g12257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8901138	8901583	.	-	.	Phchi.S3G110900
Phchi.S3	AUGUSTUS	transcript	8901138	8901583	.	-	.	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	stop_codon	8901135	8901137	.	-	0	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	CDS	8901138	8901194	1	-	0	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	exon	8901138	8901194	.	-	.	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	intron	8901195	8901281	.	-	.	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	CDS	8901282	8901404	0.71	-	0	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	exon	8901282	8901404	.	-	.	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	intron	8901405	8901514	.	-	.	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	CDS	8901515	8901583	0.87	-	0	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	exon	8901515	8901583	.	-	.	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
Phchi.S3	AUGUSTUS	start_codon	8901581	8901583	.	-	0	transcript_id "Phchi.S3G110900.t1"; gene_id "Phchi.S3G110900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7644.t1 is derived from g4818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30380387	30380974	.	+	.	Phchi.S1G480300
Phchi.S1	AUGUSTUS	transcript	30380387	30380974	.	+	.	transcript_id "Phchi.S1G480300.t1"; gene_id "Phchi.S1G480300"
Phchi.S1	AUGUSTUS	start_codon	30380387	30380389	.	+	0	transcript_id "Phchi.S1G480300.t1"; gene_id "Phchi.S1G480300"
Phchi.S1	AUGUSTUS	CDS	30380387	30380974	1	+	0	transcript_id "Phchi.S1G480300.t1"; gene_id "Phchi.S1G480300"
Phchi.S1	AUGUSTUS	exon	30380387	30380974	.	+	.	transcript_id "Phchi.S1G480300.t1"; gene_id "Phchi.S1G480300"
Phchi.S1	AUGUSTUS	stop_codon	30380975	30380977	.	+	0	transcript_id "Phchi.S1G480300.t1"; gene_id "Phchi.S1G480300"
# This transcript jg9886.t2 is derived from g7062.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9886.t3 is derived from g7062.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9887.t1 is derived from g7063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44268971	44270743	.	+	.	Phchi.S1G704600
Phchi.S1	AUGUSTUS	transcript	44268971	44270743	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	start_codon	44268971	44268973	.	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44268971	44269048	0.98	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44268971	44269048	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	intron	44269049	44269252	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44269253	44269336	1	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44269253	44269336	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	intron	44269337	44269462	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44269463	44269567	1	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44269463	44269567	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	intron	44269568	44269725	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44269726	44269875	1	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44269726	44269875	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	intron	44269876	44269969	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44269970	44270215	0.97	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44269970	44270215	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	intron	44270216	44270370	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44270371	44270502	1	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44270371	44270502	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	intron	44270503	44270599	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	CDS	44270600	44270743	1	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	exon	44270600	44270743	.	+	.	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
Phchi.S1	AUGUSTUS	stop_codon	44270744	44270746	.	+	0	transcript_id "Phchi.S1G704600.t1"; gene_id "Phchi.S1G704600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3832.t1 is derived from g1001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5933172	5934012	.	-	.	Phchi.S1G099100
Phchi.S1	AUGUSTUS	transcript	5933172	5934012	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	stop_codon	5933169	5933171	.	-	0	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	CDS	5933172	5933276	1	-	0	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	exon	5933172	5933276	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	intron	5933277	5933372	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	CDS	5933373	5933453	1	-	0	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	exon	5933373	5933453	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	intron	5933454	5933540	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	CDS	5933541	5933612	1	-	0	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	exon	5933541	5933612	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	intron	5933613	5933715	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	CDS	5933716	5934012	0.64	-	0	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	exon	5933716	5934012	.	-	.	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
Phchi.S1	AUGUSTUS	start_codon	5934010	5934012	.	-	0	transcript_id "Phchi.S1G099100.t1"; gene_id "Phchi.S1G099100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2370.t1 is derived from g9290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6382033	6384232	.	+	.	Phchi.S5G097900
Phchi.S5	AUGUSTUS	transcript	6382033	6384232	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	start_codon	6382033	6382035	.	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6382033	6382213	0.98	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6382033	6382213	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6382214	6382307	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6382308	6382669	1	+	2	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6382308	6382669	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6382670	6382792	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6382793	6383224	1	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6382793	6383224	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6383225	6383308	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6383309	6383482	1	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6383309	6383482	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6383483	6383567	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6383568	6383681	1	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6383568	6383681	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6383682	6383769	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6383770	6383871	1	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6383770	6383871	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6383872	6383987	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6383988	6384054	1	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6383988	6384054	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	intron	6384055	6384167	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	CDS	6384168	6384232	1	+	2	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	exon	6384168	6384232	.	+	.	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
Phchi.S5	AUGUSTUS	stop_codon	6384233	6384235	.	+	0	transcript_id "Phchi.S5G097900.t1"; gene_id "Phchi.S5G097900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10201.t1 is derived from g7377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46350331	46350642	.	+	.	Phchi.S1G736000
Phchi.S1	AUGUSTUS	transcript	46350331	46350642	.	+	.	transcript_id "Phchi.S1G736000.t1"; gene_id "Phchi.S1G736000"
Phchi.S1	AUGUSTUS	start_codon	46350331	46350333	.	+	0	transcript_id "Phchi.S1G736000.t1"; gene_id "Phchi.S1G736000"
Phchi.S1	AUGUSTUS	CDS	46350331	46350642	0.72	+	0	transcript_id "Phchi.S1G736000.t1"; gene_id "Phchi.S1G736000"
Phchi.S1	AUGUSTUS	exon	46350331	46350642	.	+	.	transcript_id "Phchi.S1G736000.t1"; gene_id "Phchi.S1G736000"
Phchi.S1	AUGUSTUS	stop_codon	46350643	46350645	.	+	0	transcript_id "Phchi.S1G736000.t1"; gene_id "Phchi.S1G736000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6697.t1 is derived from g3869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24575698	24581055	.	-	.	Phchi.S1G385600
Phchi.S1	AUGUSTUS	transcript	24575698	24581055	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	stop_codon	24575695	24575697	.	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24575698	24575784	0.44	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24575698	24575784	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24575785	24575870	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24575871	24576392	0.72	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24575871	24576392	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24576393	24576494	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24576495	24576550	0.97	-	2	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24576495	24576550	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24576551	24576700	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24576701	24576830	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24576701	24576830	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24576831	24576914	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24576915	24577036	1	-	2	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24576915	24577036	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24577037	24577141	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24577142	24577265	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24577142	24577265	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24577266	24577385	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24577386	24577470	1	-	1	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24577386	24577470	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24577471	24577602	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24577603	24577685	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24577603	24577685	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24577686	24577817	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24577818	24577985	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24577818	24577985	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24577986	24578074	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24578075	24578208	0.75	-	2	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24578075	24578208	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24578209	24578291	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24578292	24578808	0.23	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24578292	24578808	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24578809	24578972	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24578973	24579028	1	-	2	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24578973	24579028	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24579029	24579116	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24579117	24579368	0.74	-	2	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24579117	24579368	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24579369	24579563	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24579564	24579687	0.98	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24579564	24579687	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24579688	24579809	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24579810	24579894	0.97	-	1	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24579810	24579894	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24579895	24579973	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24579974	24580074	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24579974	24580074	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24580075	24580190	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24580191	24580358	0.98	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24580191	24580358	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24580359	24580472	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24580473	24580625	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24580473	24580625	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	intron	24580626	24580932	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	CDS	24580933	24581055	1	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	exon	24580933	24581055	.	-	.	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
Phchi.S1	AUGUSTUS	start_codon	24581053	24581055	.	-	0	transcript_id "Phchi.S1G385600.t1"; gene_id "Phchi.S1G385600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5220.t1 is derived from g2390.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15552402	15553941	.	-	.	Phchi.S1G237900
Phchi.S1	AUGUSTUS	transcript	15552402	15553941	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	stop_codon	15552399	15552401	.	-	0	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	CDS	15552402	15552676	1	-	2	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	exon	15552402	15552676	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	intron	15552677	15552799	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	CDS	15552800	15552878	1	-	0	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	exon	15552800	15552878	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	intron	15552879	15553060	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	CDS	15553061	15553300	1	-	0	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	exon	15553061	15553300	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	intron	15553301	15553391	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	CDS	15553392	15553406	0.68	-	0	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	exon	15553392	15553406	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	intron	15553407	15553503	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	CDS	15553504	15553941	0.91	-	0	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	exon	15553504	15553941	.	-	.	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
Phchi.S1	AUGUSTUS	start_codon	15553939	15553941	.	-	0	transcript_id "Phchi.S1G237900.t1"; gene_id "Phchi.S1G237900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6450.t1 is derived from g3622.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23072051	23075308	.	+	.	Phchi.S1G360900
Phchi.S1	AUGUSTUS	transcript	23072051	23075308	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	start_codon	23072051	23072053	.	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23072051	23072111	1	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23072051	23072111	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23072112	23072264	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23072265	23072410	1	+	2	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23072265	23072410	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23072411	23072574	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23072575	23072932	0.85	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23072575	23072932	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23072933	23073111	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073112	23073209	1	+	2	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073112	23073209	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073210	23073308	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073309	23073355	1	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073309	23073355	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073356	23073456	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073457	23073607	1	+	1	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073457	23073607	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073608	23073687	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073688	23073751	0.89	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073688	23073751	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073752	23073858	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073859	23074017	0.89	+	2	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073859	23074017	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074018	23074106	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074107	23074228	1	+	2	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074107	23074228	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074229	23074316	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074317	23074391	1	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074317	23074391	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074392	23074614	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074615	23074668	1	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074615	23074668	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074669	23074752	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074753	23074826	1	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074753	23074826	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074827	23074920	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074921	23074995	1	+	1	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074921	23074995	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074996	23075091	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23075092	23075308	1	+	1	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23075092	23075308	.	+	.	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	stop_codon	23075309	23075311	.	+	0	transcript_id "Phchi.S1G360900.t1"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	transcript	23072051	23075308	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	start_codon	23072051	23072053	.	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23072051	23072111	1	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23072051	23072111	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23072112	23072264	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23072265	23072425	1	+	2	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23072265	23072425	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23072426	23072574	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23072575	23072932	0.79	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23072575	23072932	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23072933	23073111	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073112	23073209	1	+	2	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073112	23073209	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073210	23073308	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073309	23073355	1	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073309	23073355	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073356	23073456	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073457	23073607	1	+	1	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073457	23073607	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073608	23073687	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073688	23073751	0.89	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073688	23073751	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23073752	23073858	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23073859	23074017	0.9	+	2	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23073859	23074017	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074018	23074106	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074107	23074228	1	+	2	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074107	23074228	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074229	23074316	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074317	23074391	1	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074317	23074391	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074392	23074614	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074615	23074668	1	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074615	23074668	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074669	23074752	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074753	23074826	1	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074753	23074826	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074827	23074920	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23074921	23074995	1	+	1	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23074921	23074995	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	intron	23074996	23075091	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	CDS	23075092	23075308	0.97	+	1	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	exon	23075092	23075308	.	+	.	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
Phchi.S1	AUGUSTUS	stop_codon	23075309	23075311	.	+	0	transcript_id "Phchi.S1G360900.t2"; gene_id "Phchi.S1G360900"
# This transcript jg13349.t2 is derived from g11815.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13350.t1 is derived from g11816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6279547	6282835	.	-	.	Phchi.S3G066900
Phchi.S3	AUGUSTUS	transcript	6279547	6282835	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	stop_codon	6279544	6279546	.	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6279547	6279906	0.69	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6279547	6279906	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	intron	6279907	6280009	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6280010	6280081	0.89	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6280010	6280081	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	intron	6280082	6280226	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6280227	6280295	1	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6280227	6280295	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	intron	6280296	6280415	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6280416	6280481	1	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6280416	6280481	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	intron	6280482	6280609	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6280610	6280825	1	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6280610	6280825	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	intron	6280826	6280943	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6280944	6281167	0.7	-	2	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6280944	6281167	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	intron	6281168	6281286	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	CDS	6281287	6282835	0.66	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	exon	6281287	6282835	.	-	.	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
Phchi.S3	AUGUSTUS	start_codon	6282833	6282835	.	-	0	transcript_id "Phchi.S3G066900.t1"; gene_id "Phchi.S3G066900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4165.t1 is derived from g1334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8707027	8707972	.	-	.	Phchi.S1G132400
Phchi.S1	AUGUSTUS	transcript	8707027	8707972	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	stop_codon	8707024	8707026	.	-	0	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	CDS	8707027	8707098	1	-	0	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	exon	8707027	8707098	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	intron	8707099	8707193	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	CDS	8707194	8707289	1	-	0	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	exon	8707194	8707289	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	intron	8707290	8707399	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	CDS	8707400	8707461	0.99	-	2	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	exon	8707400	8707461	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	intron	8707462	8707542	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	CDS	8707543	8707595	1	-	1	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	exon	8707543	8707595	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	intron	8707596	8707699	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	CDS	8707700	8707768	0.99	-	1	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	exon	8707700	8707768	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	intron	8707769	8707892	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	CDS	8707893	8707972	0.64	-	0	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	exon	8707893	8707972	.	-	.	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
Phchi.S1	AUGUSTUS	start_codon	8707970	8707972	.	-	0	transcript_id "Phchi.S1G132400.t1"; gene_id "Phchi.S1G132400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1829.t1 is derived from g8749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3374403	3375249	.	+	.	Phchi.S5G043800
Phchi.S5	AUGUSTUS	transcript	3374403	3375249	.	+	.	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	start_codon	3374403	3374405	.	+	0	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	CDS	3374403	3374606	1	+	0	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	exon	3374403	3374606	.	+	.	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	intron	3374607	3374683	.	+	.	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	CDS	3374684	3374887	1	+	0	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	exon	3374684	3374887	.	+	.	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	intron	3374888	3374967	.	+	.	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	CDS	3374968	3375249	0.79	+	0	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	exon	3374968	3375249	.	+	.	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
Phchi.S5	AUGUSTUS	stop_codon	3375250	3375252	.	+	0	transcript_id "Phchi.S5G043800.t1"; gene_id "Phchi.S5G043800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12684.t1 is derived from g11149.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	64846	66630	.	+	.	Phchi.S3G000300
Phchi.S3	AUGUSTUS	transcript	64846	65306	.	+	.	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	start_codon	64846	64848	.	+	0	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	CDS	64846	65120	0.84	+	0	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	exon	64846	65120	.	+	.	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	intron	65121	65221	.	+	.	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	CDS	65222	65306	0.85	+	1	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	exon	65222	65306	.	+	.	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	stop_codon	65307	65309	.	+	0	transcript_id "Phchi.S3G000300.t1"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	transcript	64846	66197	.	+	.	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	start_codon	64846	64848	.	+	0	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	CDS	64846	66112	0.51	+	0	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	exon	64846	66112	.	+	.	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	intron	66113	66183	.	+	.	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	CDS	66184	66197	0.77	+	2	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	exon	66184	66197	.	+	.	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	stop_codon	66198	66200	.	+	0	transcript_id "Phchi.S3G000300.t2"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	transcript	64846	66630	.	+	.	transcript_id "Phchi.S3G000300.t3"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	start_codon	64846	64848	.	+	0	transcript_id "Phchi.S3G000300.t3"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	CDS	64846	66630	0.98	+	0	transcript_id "Phchi.S3G000300.t3"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	exon	64846	66630	.	+	.	transcript_id "Phchi.S3G000300.t3"; gene_id "Phchi.S3G000300"
Phchi.S3	AUGUSTUS	stop_codon	66631	66633	.	+	0	transcript_id "Phchi.S3G000300.t3"; gene_id "Phchi.S3G000300"
# This transcript jg3557.t2 is derived from g726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3558.t1 is derived from g727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4483547	4486190	.	+	.	Phchi.S1G071700
Phchi.S1	AUGUSTUS	transcript	4483547	4486190	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	start_codon	4483547	4483549	.	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4483547	4483764	0.85	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4483547	4483764	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4483765	4484276	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4484277	4484595	1	+	1	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4484277	4484595	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4484596	4484719	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4484720	4484869	1	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4484720	4484869	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4484870	4484965	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4484966	4485223	0.99	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4484966	4485223	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4485224	4485335	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4485336	4485425	0.91	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4485336	4485425	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4485426	4485527	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4485528	4485606	0.9	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4485528	4485606	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4485607	4485709	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4485710	4485935	0.99	+	2	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4485710	4485935	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	intron	4485936	4486033	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	CDS	4486034	4486190	1	+	1	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	exon	4486034	4486190	.	+	.	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
Phchi.S1	AUGUSTUS	stop_codon	4486191	4486193	.	+	0	transcript_id "Phchi.S1G071700.t1"; gene_id "Phchi.S1G071700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9763.t1 is derived from g6939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43584760	43585965	.	+	.	Phchi.S1G692200
Phchi.S1	AUGUSTUS	transcript	43584760	43585965	.	+	.	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	start_codon	43584760	43584762	.	+	0	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	CDS	43584760	43585228	1	+	0	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	exon	43584760	43585228	.	+	.	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	intron	43585229	43585327	.	+	.	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	CDS	43585328	43585487	1	+	2	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	exon	43585328	43585487	.	+	.	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	intron	43585488	43585598	.	+	.	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	CDS	43585599	43585965	1	+	1	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	exon	43585599	43585965	.	+	.	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
Phchi.S1	AUGUSTUS	stop_codon	43585966	43585968	.	+	0	transcript_id "Phchi.S1G692200.t1"; gene_id "Phchi.S1G692200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14841.t1 is derived from g13309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14956889	14959792	.	+	.	Phchi.S3G216000
Phchi.S3	AUGUSTUS	transcript	14956889	14959792	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	start_codon	14956889	14956891	.	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14956889	14957098	0.91	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14956889	14957098	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14957099	14957164	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14957165	14957242	0.91	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14957165	14957242	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14957243	14957729	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14957730	14957898	1	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14957730	14957898	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14957899	14958035	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14958036	14958100	1	+	2	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14958036	14958100	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14958101	14958240	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14958241	14958595	1	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14958241	14958595	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14958596	14958695	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14958696	14958861	1	+	2	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14958696	14958861	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14958862	14958957	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14958958	14959067	1	+	1	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14958958	14959067	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14959068	14959159	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14959160	14959215	1	+	2	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14959160	14959215	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14959216	14959305	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14959306	14959362	0.99	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14959306	14959362	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14959363	14959466	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14959467	14959610	0.67	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14959467	14959610	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	intron	14959611	14959708	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	CDS	14959709	14959792	0.55	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	exon	14959709	14959792	.	+	.	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
Phchi.S3	AUGUSTUS	stop_codon	14959793	14959795	.	+	0	transcript_id "Phchi.S3G216000.t1"; gene_id "Phchi.S3G216000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3793.t1 is derived from g962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5766987	5767596	.	-	.	Phchi.S1G095200
Phchi.S1	AUGUSTUS	transcript	5766987	5767596	.	-	.	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	stop_codon	5766984	5766986	.	-	0	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	CDS	5766987	5767032	1	-	1	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	exon	5766987	5767032	.	-	.	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	intron	5767033	5767184	.	-	.	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	CDS	5767185	5767382	0.37	-	1	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	exon	5767185	5767382	.	-	.	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	intron	5767383	5767483	.	-	.	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	CDS	5767484	5767596	0.37	-	0	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	exon	5767484	5767596	.	-	.	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
Phchi.S1	AUGUSTUS	start_codon	5767594	5767596	.	-	0	transcript_id "Phchi.S1G095200.t1"; gene_id "Phchi.S1G095200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10101.t1 is derived from g7277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45749240	45750045	.	+	.	Phchi.S1G726000
Phchi.S1	AUGUSTUS	transcript	45749240	45750045	.	+	.	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	start_codon	45749240	45749242	.	+	0	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	CDS	45749240	45749893	0.58	+	0	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	exon	45749240	45749893	.	+	.	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	intron	45749894	45749997	.	+	.	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	CDS	45749998	45750045	0.34	+	0	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	exon	45749998	45750045	.	+	.	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
Phchi.S1	AUGUSTUS	stop_codon	45750046	45750048	.	+	0	transcript_id "Phchi.S1G726000.t1"; gene_id "Phchi.S1G726000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7301.t1 is derived from g4473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28385557	28387658	.	-	.	Phchi.S1G446000
Phchi.S1	AUGUSTUS	transcript	28385557	28387658	.	-	.	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	stop_codon	28385554	28385556	.	-	0	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	CDS	28385557	28385857	1	-	1	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	exon	28385557	28385857	.	-	.	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	intron	28385858	28385952	.	-	.	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	CDS	28385953	28387127	0.99	-	0	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	exon	28385953	28387127	.	-	.	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	intron	28387128	28387250	.	-	.	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	CDS	28387251	28387658	0.99	-	0	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	exon	28387251	28387658	.	-	.	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
Phchi.S1	AUGUSTUS	start_codon	28387656	28387658	.	-	0	transcript_id "Phchi.S1G446000.t1"; gene_id "Phchi.S1G446000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8464.t1 is derived from g5639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36058732	36060283	.	-	.	Phchi.S1G562300
Phchi.S1	AUGUSTUS	transcript	36058732	36060283	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	stop_codon	36058729	36058731	.	-	0	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36058732	36058877	0.98	-	2	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36058732	36058877	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36058878	36058971	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36058972	36059029	1	-	0	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36058972	36059029	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36059030	36059122	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36059123	36059245	1	-	0	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36059123	36059245	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36059246	36059330	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36059331	36059465	1	-	0	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36059331	36059465	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36059466	36059547	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36059548	36059644	1	-	1	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36059548	36059644	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36059645	36059744	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36059745	36059826	1	-	2	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36059745	36059826	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36059827	36059910	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36059911	36060003	1	-	2	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36059911	36060003	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	intron	36060004	36060090	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	CDS	36060091	36060283	1	-	0	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	exon	36060091	36060283	.	-	.	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
Phchi.S1	AUGUSTUS	start_codon	36060281	36060283	.	-	0	transcript_id "Phchi.S1G562300.t1"; gene_id "Phchi.S1G562300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3309.t1 is derived from g478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2774971	2777685	.	-	.	Phchi.S1G046800
Phchi.S1	AUGUSTUS	transcript	2774971	2776640	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	stop_codon	2774968	2774970	.	-	0	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2774971	2775267	0.99	-	0	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2774971	2775267	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2775268	2775381	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2775382	2775705	0.99	-	0	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2775382	2775705	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2775706	2775884	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2775885	2776108	0.97	-	2	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2775885	2776108	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2776109	2776220	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2776221	2776418	0.98	-	2	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2776221	2776418	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2776419	2776501	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2776502	2776640	1	-	0	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2776502	2776640	.	-	.	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	start_codon	2776638	2776640	.	-	0	transcript_id "Phchi.S1G046800.t1"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	transcript	2774971	2777685	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	stop_codon	2774968	2774970	.	-	0	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2774971	2775267	0.95	-	0	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2774971	2775267	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2775268	2775381	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2775382	2775705	0.97	-	0	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2775382	2775705	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2775706	2775884	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2775885	2776108	0.98	-	2	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2775885	2776108	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2776109	2776220	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2776221	2776418	1	-	2	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2776221	2776418	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2776419	2776501	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2776502	2776775	1	-	0	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2776502	2776775	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2776776	2776896	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2776897	2777287	0.99	-	1	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2776897	2777287	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	intron	2777288	2777380	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	CDS	2777381	2777685	0.94	-	0	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	exon	2777381	2777685	.	-	.	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
Phchi.S1	AUGUSTUS	start_codon	2777683	2777685	.	-	0	transcript_id "Phchi.S1G046800.t2"; gene_id "Phchi.S1G046800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15607.t1 is derived from g14076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20255128	20256231	.	-	.	Phchi.S3G292600
Phchi.S3	AUGUSTUS	transcript	20255128	20256231	.	-	.	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	stop_codon	20255125	20255127	.	-	0	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	CDS	20255128	20255286	0.98	-	0	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	exon	20255128	20255286	.	-	.	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	intron	20255287	20255475	.	-	.	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	CDS	20255476	20256231	0.91	-	0	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	exon	20255476	20256231	.	-	.	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
Phchi.S3	AUGUSTUS	start_codon	20256229	20256231	.	-	0	transcript_id "Phchi.S3G292600.t1"; gene_id "Phchi.S3G292600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15728.t1 is derived from g14198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20910215	20911959	.	-	.	Phchi.S3G304700
Phchi.S3	AUGUSTUS	transcript	20910215	20911959	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	stop_codon	20910212	20910214	.	-	0	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910215	20910316	1	-	0	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910215	20910316	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910317	20910401	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910402	20910544	1	-	2	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910402	20910544	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910545	20910633	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910634	20910736	1	-	0	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910634	20910736	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910737	20910853	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910854	20910990	0.5	-	2	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910854	20910990	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910991	20911182	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911183	20911286	0.61	-	1	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911183	20911286	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911287	20911429	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911430	20911539	1	-	0	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911430	20911539	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911540	20911612	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911613	20911728	1	-	2	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911613	20911728	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911729	20911838	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911839	20911959	0.99	-	0	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911839	20911959	.	-	.	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	start_codon	20911957	20911959	.	-	0	transcript_id "Phchi.S3G304700.t1"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	transcript	20910215	20911959	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	stop_codon	20910212	20910214	.	-	0	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910215	20910316	1	-	0	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910215	20910316	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910317	20910401	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910402	20910544	1	-	2	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910402	20910544	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910545	20910633	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910634	20910736	1	-	0	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910634	20910736	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20910737	20910853	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20910854	20911103	0.5	-	1	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20910854	20911103	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911104	20911222	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911223	20911286	0.49	-	2	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911223	20911286	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911287	20911425	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911426	20911454	0.71	-	1	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911426	20911454	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911455	20911531	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911532	20911539	0.71	-	0	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911532	20911539	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911540	20911612	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911613	20911728	1	-	2	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911613	20911728	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	intron	20911729	20911838	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	CDS	20911839	20911959	1	-	0	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	exon	20911839	20911959	.	-	.	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
Phchi.S3	AUGUSTUS	start_codon	20911957	20911959	.	-	0	transcript_id "Phchi.S3G304700.t2"; gene_id "Phchi.S3G304700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2285.t1 is derived from g9205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5870824	5871444	.	-	.	Phchi.S5G089400
Phchi.S5	AUGUSTUS	transcript	5870824	5871444	.	-	.	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	stop_codon	5870821	5870823	.	-	0	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	CDS	5870824	5870892	0.99	-	0	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	exon	5870824	5870892	.	-	.	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	intron	5870893	5871075	.	-	.	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	CDS	5871076	5871444	0.85	-	0	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	exon	5871076	5871444	.	-	.	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
Phchi.S5	AUGUSTUS	start_codon	5871442	5871444	.	-	0	transcript_id "Phchi.S5G089400.t1"; gene_id "Phchi.S5G089400"
# This transcript jg12067.t2 is derived from g7742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12068.t1 is derived from g7743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1824822	1828888	.	-	.	Phchi.S2G014800
Phchi.S2	AUGUSTUS	transcript	1824822	1828888	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	stop_codon	1824819	1824821	.	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1824822	1824872	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1824822	1824872	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1824873	1824964	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1824965	1825036	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1824965	1825036	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1825037	1825154	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1825155	1825268	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1825155	1825268	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1825269	1825426	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1825427	1825540	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1825427	1825540	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1825541	1825677	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1825678	1825778	1	-	2	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1825678	1825778	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1825779	1825858	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1825859	1825937	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1825859	1825937	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1825938	1826021	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1826022	1826096	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1826022	1826096	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1826097	1826224	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1826225	1826287	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1826225	1826287	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1826288	1826403	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1826404	1826484	0.79	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1826404	1826484	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1826485	1826589	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1826590	1826715	0.99	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1826590	1826715	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1826716	1826815	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1826816	1826940	1	-	2	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1826816	1826940	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1826941	1827093	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1827094	1827211	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1827094	1827211	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1827212	1827327	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1827328	1827462	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1827328	1827462	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1827463	1827548	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1827549	1827695	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1827549	1827695	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1827696	1827863	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1827864	1828018	0.27	-	2	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1827864	1828018	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1828019	1828091	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1828092	1828246	0.36	-	1	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1828092	1828246	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1828247	1828353	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1828354	1828424	0.35	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1828354	1828424	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1828425	1828508	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1828509	1828742	0.36	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1828509	1828742	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	intron	1828743	1828837	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	CDS	1828838	1828888	1	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	exon	1828838	1828888	.	-	.	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
Phchi.S2	AUGUSTUS	start_codon	1828886	1828888	.	-	0	transcript_id "Phchi.S2G014800.t1"; gene_id "Phchi.S2G014800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2339.t1 is derived from g9259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6229754	6230562	.	-	.	Phchi.S5G094800
Phchi.S5	AUGUSTUS	transcript	6229754	6230562	.	-	.	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	stop_codon	6229751	6229753	.	-	0	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	CDS	6229754	6230050	1	-	0	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	exon	6229754	6230050	.	-	.	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	intron	6230051	6230439	.	-	.	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	CDS	6230440	6230562	1	-	0	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	exon	6230440	6230562	.	-	.	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
Phchi.S5	AUGUSTUS	start_codon	6230560	6230562	.	-	0	transcript_id "Phchi.S5G094800.t1"; gene_id "Phchi.S5G094800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11049.t1 is derived from g15099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3825345	3826236	.	+	.	Phchi.S4G063100
Phchi.S4	AUGUSTUS	transcript	3825345	3826236	.	+	.	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	start_codon	3825345	3825347	.	+	0	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	CDS	3825345	3825505	1	+	0	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	exon	3825345	3825505	.	+	.	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	intron	3825506	3825587	.	+	.	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	CDS	3825588	3826236	1	+	1	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	exon	3825588	3826236	.	+	.	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
Phchi.S4	AUGUSTUS	stop_codon	3826237	3826239	.	+	0	transcript_id "Phchi.S4G063100.t1"; gene_id "Phchi.S4G063100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2803.t1 is derived from g9723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8957299	8957905	.	+	.	Phchi.S5G141200
Phchi.S5	AUGUSTUS	transcript	8957299	8957905	.	+	.	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	start_codon	8957299	8957301	.	+	0	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	CDS	8957299	8957447	0.44	+	0	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	exon	8957299	8957447	.	+	.	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	intron	8957448	8957537	.	+	.	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	CDS	8957538	8957628	1	+	1	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	exon	8957538	8957628	.	+	.	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	intron	8957629	8957737	.	+	.	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	CDS	8957738	8957905	0.99	+	0	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	exon	8957738	8957905	.	+	.	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
Phchi.S5	AUGUSTUS	stop_codon	8957906	8957908	.	+	0	transcript_id "Phchi.S5G141200.t1"; gene_id "Phchi.S5G141200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13803.t1 is derived from g12270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8962193	8963296	.	+	.	Phchi.S3G112200
Phchi.S3	AUGUSTUS	transcript	8962193	8963296	.	+	.	transcript_id "Phchi.S3G112200.t1"; gene_id "Phchi.S3G112200"
Phchi.S3	AUGUSTUS	start_codon	8962193	8962195	.	+	0	transcript_id "Phchi.S3G112200.t1"; gene_id "Phchi.S3G112200"
Phchi.S3	AUGUSTUS	CDS	8962193	8963296	1	+	0	transcript_id "Phchi.S3G112200.t1"; gene_id "Phchi.S3G112200"
Phchi.S3	AUGUSTUS	exon	8962193	8963296	.	+	.	transcript_id "Phchi.S3G112200.t1"; gene_id "Phchi.S3G112200"
Phchi.S3	AUGUSTUS	stop_codon	8963297	8963299	.	+	0	transcript_id "Phchi.S3G112200.t1"; gene_id "Phchi.S3G112200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15929.t1 is derived from g14399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22259310	22261288	.	+	.	Phchi.S3G324800
Phchi.S3	AUGUSTUS	transcript	22259310	22261288	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	start_codon	22259310	22259312	.	+	0	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	CDS	22259310	22259991	0.65	+	0	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	exon	22259310	22259991	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	intron	22259992	22260107	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	CDS	22260108	22260598	0.68	+	2	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	exon	22260108	22260598	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	intron	22260599	22260703	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	CDS	22260704	22261155	0.93	+	0	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	exon	22260704	22261155	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	intron	22261156	22261236	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	CDS	22261237	22261288	0.98	+	1	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	exon	22261237	22261288	.	+	.	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
Phchi.S3	AUGUSTUS	stop_codon	22261289	22261291	.	+	0	transcript_id "Phchi.S3G324800.t1"; gene_id "Phchi.S3G324800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1821.t1 is derived from g8741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3315738	3317022	.	+	.	Phchi.S5G043000
Phchi.S5	AUGUSTUS	transcript	3315738	3317022	.	+	.	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	start_codon	3315738	3315740	.	+	0	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	CDS	3315738	3316459	0.79	+	0	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	exon	3315738	3316459	.	+	.	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	intron	3316460	3316580	.	+	.	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	CDS	3316581	3317022	0.8	+	1	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	exon	3316581	3317022	.	+	.	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
Phchi.S5	AUGUSTUS	stop_codon	3317023	3317025	.	+	0	transcript_id "Phchi.S5G043000.t1"; gene_id "Phchi.S5G043000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12279.t1 is derived from g7955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8081307	8083727	.	-	.	Phchi.S2G035900
Phchi.S2	AUGUSTUS	transcript	8081307	8083727	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	stop_codon	8081304	8081306	.	-	0	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	CDS	8081307	8081505	0.48	-	1	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	exon	8081307	8081505	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	intron	8081506	8081769	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	CDS	8081770	8081785	0.99	-	2	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	exon	8081770	8081785	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	intron	8081786	8081908	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	CDS	8081909	8081922	0.99	-	1	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	exon	8081909	8081922	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	intron	8081923	8082001	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	CDS	8082002	8082148	0.65	-	1	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	exon	8082002	8082148	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	intron	8082149	8082341	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	CDS	8082342	8082401	0.82	-	1	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	exon	8082342	8082401	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	intron	8082402	8082489	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	CDS	8082490	8083727	0.52	-	0	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	exon	8082490	8083727	.	-	.	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
Phchi.S2	AUGUSTUS	start_codon	8083725	8083727	.	-	0	transcript_id "Phchi.S2G035900.t1"; gene_id "Phchi.S2G035900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14061.t1 is derived from g12528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10584902	10586121	.	-	.	Phchi.S3G138000
Phchi.S3	AUGUSTUS	transcript	10584902	10586121	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	stop_codon	10584899	10584901	.	-	0	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	CDS	10584902	10585168	0.62	-	0	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	exon	10584902	10585168	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	intron	10585169	10585269	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	CDS	10585270	10585513	1	-	1	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	exon	10585270	10585513	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	intron	10585514	10585618	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	CDS	10585619	10585720	1	-	1	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	exon	10585619	10585720	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	intron	10585721	10585804	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	CDS	10585805	10586121	0.8	-	0	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	exon	10585805	10586121	.	-	.	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
Phchi.S3	AUGUSTUS	start_codon	10586119	10586121	.	-	0	transcript_id "Phchi.S3G138000.t1"; gene_id "Phchi.S3G138000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11447.t1 is derived from g15497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6399790	6401099	.	-	.	Phchi.S4G102900
Phchi.S4	AUGUSTUS	transcript	6399790	6401099	.	-	.	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	stop_codon	6399787	6399789	.	-	0	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	CDS	6399790	6400649	0.87	-	2	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	exon	6399790	6400649	.	-	.	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	intron	6400650	6400729	.	-	.	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	CDS	6400730	6401099	0.48	-	0	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	exon	6400730	6401099	.	-	.	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
Phchi.S4	AUGUSTUS	start_codon	6401097	6401099	.	-	0	transcript_id "Phchi.S4G102900.t1"; gene_id "Phchi.S4G102900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1596.t1 is derived from g8515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1942125	1943187	.	-	.	Phchi.S5G020500
Phchi.S5	AUGUSTUS	transcript	1942125	1943187	.	-	.	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	stop_codon	1942122	1942124	.	-	0	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	CDS	1942125	1942206	0.86	-	1	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	exon	1942125	1942206	.	-	.	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	intron	1942207	1942336	.	-	.	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	CDS	1942337	1942427	0.91	-	2	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	exon	1942337	1942427	.	-	.	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	intron	1942428	1942679	.	-	.	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	CDS	1942680	1943187	0.9	-	0	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	exon	1942680	1943187	.	-	.	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
Phchi.S5	AUGUSTUS	start_codon	1943185	1943187	.	-	0	transcript_id "Phchi.S5G020500.t1"; gene_id "Phchi.S5G020500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6662.t1 is derived from g3834.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24362379	24364307	.	+	.	Phchi.S1G382100
Phchi.S1	AUGUSTUS	transcript	24362379	24364307	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	start_codon	24362379	24362381	.	+	0	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	CDS	24362379	24362757	0.41	+	0	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	exon	24362379	24362757	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	intron	24362758	24362868	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	CDS	24362869	24363464	0.76	+	2	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	exon	24362869	24363464	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	intron	24363465	24363553	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	CDS	24363554	24363802	0.98	+	0	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	exon	24363554	24363802	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	intron	24363803	24363929	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	CDS	24363930	24364307	0.95	+	0	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	exon	24363930	24364307	.	+	.	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
Phchi.S1	AUGUSTUS	stop_codon	24364308	24364310	.	+	0	transcript_id "Phchi.S1G382100.t1"; gene_id "Phchi.S1G382100"
# This transcript jg6765.t2 is derived from g3937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6766.t1 is derived from g3938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24964010	24968261	.	-	.	Phchi.S1G392500
Phchi.S1	AUGUSTUS	transcript	24964010	24968261	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	stop_codon	24964007	24964009	.	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24964010	24964030	1	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24964010	24964030	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24964031	24964225	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24964226	24964272	1	-	2	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24964226	24964272	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24964273	24964514	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24964515	24964533	0.98	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24964515	24964533	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24964534	24964625	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24964626	24964665	0.59	-	1	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24964626	24964665	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24964666	24965109	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24965110	24965174	0.99	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24965110	24965174	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24965175	24965352	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24965353	24965421	0.81	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24965353	24965421	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24965422	24965569	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24965570	24965633	1	-	1	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24965570	24965633	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24965634	24965719	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24965720	24965802	1	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24965720	24965802	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24965803	24965916	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24965917	24965982	1	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24965917	24965982	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24965983	24966113	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24966114	24966204	1	-	1	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24966114	24966204	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24966205	24966511	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24966512	24966669	1	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24966512	24966669	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24966670	24966859	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24966860	24967054	1	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24966860	24967054	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24967055	24967242	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24967243	24967372	1	-	1	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24967243	24967372	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24967373	24967722	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24967723	24968051	0.44	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24967723	24968051	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	intron	24968052	24968249	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	CDS	24968250	24968261	0.43	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	exon	24968250	24968261	.	-	.	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
Phchi.S1	AUGUSTUS	start_codon	24968259	24968261	.	-	0	transcript_id "Phchi.S1G392500.t1"; gene_id "Phchi.S1G392500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9358.t1 is derived from g6534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41153401	41154897	.	+	.	Phchi.S1G651700
Phchi.S1	AUGUSTUS	transcript	41153401	41154897	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	start_codon	41153401	41153403	.	+	0	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	CDS	41153401	41153639	0.83	+	0	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	exon	41153401	41153639	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	intron	41153640	41153749	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	CDS	41153750	41154476	0.98	+	1	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	exon	41153750	41154476	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	intron	41154477	41154564	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	CDS	41154565	41154774	1	+	0	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	exon	41154565	41154774	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	intron	41154775	41154864	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	CDS	41154865	41154897	1	+	0	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	exon	41154865	41154897	.	+	.	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
Phchi.S1	AUGUSTUS	stop_codon	41154898	41154900	.	+	0	transcript_id "Phchi.S1G651700.t1"; gene_id "Phchi.S1G651700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4477.t1 is derived from g1647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10701316	10702498	.	-	.	Phchi.S1G163600
Phchi.S1	AUGUSTUS	transcript	10701316	10702498	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	stop_codon	10701313	10701315	.	-	0	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	CDS	10701316	10701490	0.99	-	1	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	exon	10701316	10701490	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	intron	10701491	10701574	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	CDS	10701575	10701784	1	-	1	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	exon	10701575	10701784	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	intron	10701785	10701878	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	CDS	10701879	10702326	0.99	-	2	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	exon	10701879	10702326	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	intron	10702327	10702398	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	CDS	10702399	10702498	1	-	0	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	exon	10702399	10702498	.	-	.	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
Phchi.S1	AUGUSTUS	start_codon	10702496	10702498	.	-	0	transcript_id "Phchi.S1G163600.t1"; gene_id "Phchi.S1G163600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11083.t1 is derived from g15133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4002809	4003867	.	-	.	Phchi.S4G066500
Phchi.S4	AUGUSTUS	transcript	4002809	4003867	.	-	.	transcript_id "Phchi.S4G066500.t1"; gene_id "Phchi.S4G066500"
Phchi.S4	AUGUSTUS	stop_codon	4002806	4002808	.	-	0	transcript_id "Phchi.S4G066500.t1"; gene_id "Phchi.S4G066500"
Phchi.S4	AUGUSTUS	CDS	4002809	4003867	0.93	-	0	transcript_id "Phchi.S4G066500.t1"; gene_id "Phchi.S4G066500"
Phchi.S4	AUGUSTUS	exon	4002809	4003867	.	-	.	transcript_id "Phchi.S4G066500.t1"; gene_id "Phchi.S4G066500"
Phchi.S4	AUGUSTUS	start_codon	4003865	4003867	.	-	0	transcript_id "Phchi.S4G066500.t1"; gene_id "Phchi.S4G066500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg319.t1 is derived from g10101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2244096	2245098	.	-	.	Phchi.S6G027800
Phchi.S6	AUGUSTUS	transcript	2244096	2245098	.	-	.	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	stop_codon	2244093	2244095	.	-	0	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	CDS	2244096	2244260	1	-	0	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	exon	2244096	2244260	.	-	.	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	intron	2244261	2244432	.	-	.	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	CDS	2244433	2245098	0.54	-	0	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	exon	2244433	2245098	.	-	.	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
Phchi.S6	AUGUSTUS	start_codon	2245096	2245098	.	-	0	transcript_id "Phchi.S6G027800.t1"; gene_id "Phchi.S6G027800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13088.t1 is derived from g11553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4101376	4102336	.	+	.	Phchi.S3G040700
Phchi.S3	AUGUSTUS	transcript	4101376	4102336	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	start_codon	4101376	4101378	.	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	CDS	4101376	4101450	0.9	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	exon	4101376	4101450	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	intron	4101451	4101687	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	CDS	4101688	4101729	1	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	exon	4101688	4101729	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	intron	4101730	4101858	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	CDS	4101859	4102029	1	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	exon	4101859	4102029	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	intron	4102030	4102132	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	CDS	4102133	4102219	1	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	exon	4102133	4102219	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	intron	4102220	4102300	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	CDS	4102301	4102336	1	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	exon	4102301	4102336	.	+	.	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
Phchi.S3	AUGUSTUS	stop_codon	4102337	4102339	.	+	0	transcript_id "Phchi.S3G040700.t1"; gene_id "Phchi.S3G040700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10928.t1 is derived from g14978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3016782	3018578	.	+	.	Phchi.S4G051000
Phchi.S4	AUGUSTUS	transcript	3016782	3018578	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	start_codon	3016782	3016784	.	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3016782	3017005	0.98	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3016782	3017005	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3017006	3017092	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3017093	3017364	0.26	+	1	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3017093	3017364	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3017365	3017456	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3017457	3017608	0.2	+	2	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3017457	3017608	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3017609	3017709	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3017710	3017868	0.52	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3017710	3017868	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3017869	3017989	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3017990	3018043	1	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3017990	3018043	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3018044	3018158	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3018159	3018251	0.99	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3018159	3018251	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3018252	3018336	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3018337	3018393	1	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3018337	3018393	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	intron	3018394	3018476	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	CDS	3018477	3018578	1	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	exon	3018477	3018578	.	+	.	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
Phchi.S4	AUGUSTUS	stop_codon	3018579	3018581	.	+	0	transcript_id "Phchi.S4G051000.t1"; gene_id "Phchi.S4G051000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7484.t1 is derived from g4657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29581050	29582320	.	-	.	Phchi.S1G464300
Phchi.S1	AUGUSTUS	transcript	29581050	29582320	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	stop_codon	29581047	29581049	.	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29581050	29581154	1	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29581050	29581154	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	intron	29581155	29581232	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29581233	29581376	1	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29581233	29581376	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	intron	29581377	29581455	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29581456	29581536	0.97	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29581456	29581536	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	intron	29581537	29581643	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29581644	29581682	0.9	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29581644	29581682	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	intron	29581683	29581837	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29581838	29581903	0.81	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29581838	29581903	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	intron	29581904	29582075	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29582076	29582147	0.78	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29582076	29582147	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	intron	29582148	29582299	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	CDS	29582300	29582320	0.83	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	exon	29582300	29582320	.	-	.	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
Phchi.S1	AUGUSTUS	start_codon	29582318	29582320	.	-	0	transcript_id "Phchi.S1G464300.t1"; gene_id "Phchi.S1G464300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1556.t1 is derived from g8475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1755518	1757579	.	+	.	Phchi.S5G016500
Phchi.S5	AUGUSTUS	transcript	1755518	1757579	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	start_codon	1755518	1755520	.	+	0	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	CDS	1755518	1755704	0.96	+	0	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	exon	1755518	1755704	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	intron	1755705	1755794	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	CDS	1755795	1756012	1	+	2	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	exon	1755795	1756012	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	intron	1756013	1756106	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	CDS	1756107	1756675	1	+	0	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	exon	1756107	1756675	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	intron	1756676	1756757	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	CDS	1756758	1757091	0.47	+	1	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	exon	1756758	1757091	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	intron	1757092	1757258	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	CDS	1757259	1757579	0.83	+	0	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	exon	1757259	1757579	.	+	.	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
Phchi.S5	AUGUSTUS	stop_codon	1757580	1757582	.	+	0	transcript_id "Phchi.S5G016500.t1"; gene_id "Phchi.S5G016500"
# This transcript jg4947.t2 is derived from g2117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4947.t3 is derived from g2117.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4948.t1 is derived from g2118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13686329	13690186	.	+	.	Phchi.S1G210700
Phchi.S1	AUGUSTUS	transcript	13686329	13690186	.	+	.	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	start_codon	13686329	13686331	.	+	0	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686329	13686592	1	+	0	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686329	13686592	.	+	.	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	intron	13686593	13686664	.	+	.	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686665	13686777	1	+	0	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686665	13686777	.	+	.	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	intron	13686778	13686858	.	+	.	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686859	13690186	0.98	+	1	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686859	13690186	.	+	.	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	stop_codon	13690187	13690189	.	+	0	transcript_id "Phchi.S1G210700.t1"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	transcript	13686329	13690186	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	start_codon	13686329	13686331	.	+	0	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686329	13686488	0.31	+	0	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686329	13686488	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	intron	13686489	13686582	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686583	13686592	0.31	+	2	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686583	13686592	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	intron	13686593	13686675	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686676	13686777	0.6	+	1	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686676	13686777	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	intron	13686778	13686858	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	CDS	13686859	13690186	0.99	+	1	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	exon	13686859	13690186	.	+	.	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
Phchi.S1	AUGUSTUS	stop_codon	13690187	13690189	.	+	0	transcript_id "Phchi.S1G210700.t2"; gene_id "Phchi.S1G210700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7225.t1 is derived from g4397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27708282	27710236	.	+	.	Phchi.S1G438400
Phchi.S1	AUGUSTUS	transcript	27708282	27710236	.	+	.	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	start_codon	27708282	27708284	.	+	0	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	CDS	27708282	27708970	0.35	+	0	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	exon	27708282	27708970	.	+	.	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	intron	27708971	27709167	.	+	.	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	CDS	27709168	27710236	0.53	+	1	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	exon	27709168	27710236	.	+	.	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
Phchi.S1	AUGUSTUS	stop_codon	27710237	27710239	.	+	0	transcript_id "Phchi.S1G438400.t1"; gene_id "Phchi.S1G438400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14733.t1 is derived from g13201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14439559	14439765	.	-	.	Phchi.S3G205200
Phchi.S3	AUGUSTUS	transcript	14439559	14439765	.	-	.	transcript_id "Phchi.S3G205200.t1"; gene_id "Phchi.S3G205200"
Phchi.S3	AUGUSTUS	stop_codon	14439556	14439558	.	-	0	transcript_id "Phchi.S3G205200.t1"; gene_id "Phchi.S3G205200"
Phchi.S3	AUGUSTUS	CDS	14439559	14439765	0.69	-	0	transcript_id "Phchi.S3G205200.t1"; gene_id "Phchi.S3G205200"
Phchi.S3	AUGUSTUS	exon	14439559	14439765	.	-	.	transcript_id "Phchi.S3G205200.t1"; gene_id "Phchi.S3G205200"
Phchi.S3	AUGUSTUS	start_codon	14439763	14439765	.	-	0	transcript_id "Phchi.S3G205200.t1"; gene_id "Phchi.S3G205200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1981.t1 is derived from g8901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4216859	4217562	.	+	.	Phchi.S5G059000
Phchi.S5	AUGUSTUS	transcript	4216859	4217562	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	start_codon	4216859	4216861	.	+	0	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	CDS	4216859	4216899	0.65	+	0	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	exon	4216859	4216899	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	intron	4216900	4217049	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	CDS	4217050	4217102	0.51	+	1	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	exon	4217050	4217102	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	intron	4217103	4217199	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	CDS	4217200	4217297	0.91	+	2	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	exon	4217200	4217297	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	intron	4217298	4217490	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	CDS	4217491	4217562	1	+	0	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	exon	4217491	4217562	.	+	.	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
Phchi.S5	AUGUSTUS	stop_codon	4217563	4217565	.	+	0	transcript_id "Phchi.S5G059000.t1"; gene_id "Phchi.S5G059000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11479.t1 is derived from g15529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6573069	6573817	.	-	.	Phchi.S4G106100
Phchi.S4	AUGUSTUS	transcript	6573069	6573817	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	stop_codon	6573066	6573068	.	-	0	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	CDS	6573069	6573095	0.37	-	0	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	exon	6573069	6573095	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	intron	6573096	6573191	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	CDS	6573192	6573303	0.32	-	1	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	exon	6573192	6573303	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	intron	6573304	6573388	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	CDS	6573389	6573451	0.9	-	1	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	exon	6573389	6573451	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	intron	6573452	6573737	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	CDS	6573738	6573817	0.97	-	0	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	exon	6573738	6573817	.	-	.	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
Phchi.S4	AUGUSTUS	start_codon	6573815	6573817	.	-	0	transcript_id "Phchi.S4G106100.t1"; gene_id "Phchi.S4G106100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3726.t1 is derived from g895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5417330	5417782	.	+	.	Phchi.S1G088500
Phchi.S1	AUGUSTUS	transcript	5417330	5417782	.	+	.	transcript_id "Phchi.S1G088500.t1"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	start_codon	5417330	5417332	.	+	0	transcript_id "Phchi.S1G088500.t1"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	CDS	5417330	5417782	0.32	+	0	transcript_id "Phchi.S1G088500.t1"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	exon	5417330	5417782	.	+	.	transcript_id "Phchi.S1G088500.t1"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	stop_codon	5417783	5417785	.	+	0	transcript_id "Phchi.S1G088500.t1"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	transcript	5417390	5417782	.	+	.	transcript_id "Phchi.S1G088500.t2"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	start_codon	5417390	5417392	.	+	0	transcript_id "Phchi.S1G088500.t2"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	CDS	5417390	5417782	0.3	+	0	transcript_id "Phchi.S1G088500.t2"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	exon	5417390	5417782	.	+	.	transcript_id "Phchi.S1G088500.t2"; gene_id "Phchi.S1G088500"
Phchi.S1	AUGUSTUS	stop_codon	5417783	5417785	.	+	0	transcript_id "Phchi.S1G088500.t2"; gene_id "Phchi.S1G088500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5717.t1 is derived from g2887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18504214	18505411	.	+	.	Phchi.S1G287600
Phchi.S1	AUGUSTUS	transcript	18504214	18505411	.	+	.	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	start_codon	18504214	18504216	.	+	0	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	CDS	18504214	18504716	0.55	+	0	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	exon	18504214	18504716	.	+	.	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	intron	18504717	18504930	.	+	.	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	CDS	18504931	18505411	1	+	1	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	exon	18504931	18505411	.	+	.	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
Phchi.S1	AUGUSTUS	stop_codon	18505412	18505414	.	+	0	transcript_id "Phchi.S1G287600.t1"; gene_id "Phchi.S1G287600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11492.t1 is derived from g15542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6635408	6638678	.	+	.	Phchi.S4G107400
Phchi.S4	AUGUSTUS	transcript	6635408	6638678	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	start_codon	6635408	6635410	.	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6635408	6636070	0.98	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6635408	6636070	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6636071	6636187	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6636188	6636254	0.97	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6636188	6636254	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6636255	6636370	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6636371	6636429	0.99	+	2	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6636371	6636429	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6636430	6636533	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6636534	6636642	0.58	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6636534	6636642	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6636643	6636717	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6636718	6636789	0.99	+	2	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6636718	6636789	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6636790	6636871	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6636872	6636959	0.9	+	2	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6636872	6636959	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6636960	6637080	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6637081	6637336	0.78	+	1	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6637081	6637336	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6637337	6637455	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6637456	6637571	0.99	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6637456	6637571	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6637572	6637658	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6637659	6637870	1	+	1	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6637659	6637870	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6637871	6637962	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6637963	6637994	1	+	2	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6637963	6637994	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6637995	6638089	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6638090	6638195	1	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6638090	6638195	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6638196	6638295	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6638296	6638398	1	+	2	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6638296	6638398	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	intron	6638399	6638500	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	CDS	6638501	6638678	0.82	+	1	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	exon	6638501	6638678	.	+	.	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
Phchi.S4	AUGUSTUS	stop_codon	6638679	6638681	.	+	0	transcript_id "Phchi.S4G107400.t1"; gene_id "Phchi.S4G107400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9197.t1 is derived from g6372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40304182	40310761	.	+	.	Phchi.S1G635600
Phchi.S1	AUGUSTUS	transcript	40304182	40310761	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	start_codon	40304182	40304184	.	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40304182	40304435	0.95	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40304182	40304435	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40304436	40304575	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40304576	40304678	0.57	+	1	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40304576	40304678	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40304679	40304869	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40304870	40304934	0.48	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40304870	40304934	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40304935	40305085	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40305086	40305463	0.66	+	1	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40305086	40305463	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40305464	40305589	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40305590	40305677	0.99	+	1	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40305590	40305677	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40305678	40305761	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40305762	40305889	1	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40305762	40305889	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40305890	40306017	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40306018	40306073	0.91	+	1	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40306018	40306073	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40306074	40306404	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40306405	40306530	0.77	+	2	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40306405	40306530	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40306531	40306686	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40306687	40306751	0.83	+	2	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40306687	40306751	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40306752	40306835	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40306836	40306886	0.65	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40306836	40306886	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40306887	40306960	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40306961	40308012	0.71	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40306961	40308012	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40308013	40308104	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40308105	40308439	0.97	+	1	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40308105	40308439	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40308440	40308541	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40308542	40308942	0.3	+	2	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40308542	40308942	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40308943	40309048	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40309049	40309159	1	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40309049	40309159	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40309160	40309266	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40309267	40309479	1	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40309267	40309479	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40309480	40309642	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40309643	40310341	1	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40309643	40310341	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	intron	40310342	40310467	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	CDS	40310468	40310761	0.99	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	exon	40310468	40310761	.	+	.	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
Phchi.S1	AUGUSTUS	stop_codon	40310762	40310764	.	+	0	transcript_id "Phchi.S1G635600.t1"; gene_id "Phchi.S1G635600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6052.t1 is derived from g3223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20644797	20646559	.	-	.	Phchi.S1G321100
Phchi.S1	AUGUSTUS	transcript	20644797	20646559	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	stop_codon	20644794	20644796	.	-	0	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	CDS	20644797	20645046	1	-	1	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	exon	20644797	20645046	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	intron	20645047	20645147	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	CDS	20645148	20645365	1	-	0	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	exon	20645148	20645365	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	intron	20645366	20645449	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	CDS	20645450	20645941	1	-	0	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	exon	20645450	20645941	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	intron	20645942	20646058	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	CDS	20646059	20646559	0.99	-	0	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	exon	20646059	20646559	.	-	.	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
Phchi.S1	AUGUSTUS	start_codon	20646557	20646559	.	-	0	transcript_id "Phchi.S1G321100.t1"; gene_id "Phchi.S1G321100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6214.t1 is derived from g3386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21494556	21495701	.	-	.	Phchi.S1G337300
Phchi.S1	AUGUSTUS	transcript	21494556	21495701	.	-	.	transcript_id "Phchi.S1G337300.t1"; gene_id "Phchi.S1G337300"
Phchi.S1	AUGUSTUS	stop_codon	21494553	21494555	.	-	0	transcript_id "Phchi.S1G337300.t1"; gene_id "Phchi.S1G337300"
Phchi.S1	AUGUSTUS	CDS	21494556	21495701	0.97	-	0	transcript_id "Phchi.S1G337300.t1"; gene_id "Phchi.S1G337300"
Phchi.S1	AUGUSTUS	exon	21494556	21495701	.	-	.	transcript_id "Phchi.S1G337300.t1"; gene_id "Phchi.S1G337300"
Phchi.S1	AUGUSTUS	start_codon	21495699	21495701	.	-	0	transcript_id "Phchi.S1G337300.t1"; gene_id "Phchi.S1G337300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11272.t1 is derived from g15322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5130271	5131875	.	-	.	Phchi.S4G085400
Phchi.S4	AUGUSTUS	transcript	5130271	5131875	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	stop_codon	5130268	5130270	.	-	0	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	CDS	5130271	5130423	1	-	0	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	exon	5130271	5130423	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	intron	5130424	5130514	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	CDS	5130515	5130659	1	-	1	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	exon	5130515	5130659	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	intron	5130660	5130747	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	CDS	5130748	5130886	0.86	-	2	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	exon	5130748	5130886	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	intron	5130887	5131211	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	CDS	5131212	5131294	1	-	1	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	exon	5131212	5131294	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	intron	5131295	5131375	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	CDS	5131376	5131462	1	-	1	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	exon	5131376	5131462	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	intron	5131463	5131549	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	CDS	5131550	5131875	1	-	0	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	exon	5131550	5131875	.	-	.	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
Phchi.S4	AUGUSTUS	start_codon	5131873	5131875	.	-	0	transcript_id "Phchi.S4G085400.t1"; gene_id "Phchi.S4G085400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12175.t1 is derived from g7851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6080528	6081567	.	+	.	Phchi.S2G025500
Phchi.S2	AUGUSTUS	transcript	6080528	6081567	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	start_codon	6080528	6080530	.	+	0	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	CDS	6080528	6080688	0.48	+	0	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	exon	6080528	6080688	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	intron	6080689	6080957	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	CDS	6080958	6081074	0.65	+	1	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	exon	6080958	6081074	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	intron	6081075	6081257	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	CDS	6081258	6081314	0.85	+	1	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	exon	6081258	6081314	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	intron	6081315	6081470	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	CDS	6081471	6081567	0.82	+	1	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	exon	6081471	6081567	.	+	.	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
Phchi.S2	AUGUSTUS	stop_codon	6081568	6081570	.	+	0	transcript_id "Phchi.S2G025500.t1"; gene_id "Phchi.S2G025500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg932.t1 is derived from g10714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6490391	6491393	.	-	.	Phchi.S6G089100
Phchi.S6	AUGUSTUS	transcript	6490391	6491393	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	stop_codon	6490388	6490390	.	-	0	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	CDS	6490391	6490507	0.99	-	0	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	exon	6490391	6490507	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	intron	6490508	6490593	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	CDS	6490594	6490767	1	-	0	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	exon	6490594	6490767	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	intron	6490768	6490851	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	CDS	6490852	6491046	1	-	0	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	exon	6490852	6491046	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	intron	6491047	6491141	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	CDS	6491142	6491220	1	-	1	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	exon	6491142	6491220	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	intron	6491221	6491304	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	CDS	6491305	6491393	0.91	-	0	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	exon	6491305	6491393	.	-	.	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
Phchi.S6	AUGUSTUS	start_codon	6491391	6491393	.	-	0	transcript_id "Phchi.S6G089100.t1"; gene_id "Phchi.S6G089100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3865.t1 is derived from g1034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6090649	6092074	.	-	.	Phchi.S1G102400
Phchi.S1	AUGUSTUS	transcript	6090649	6092074	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	stop_codon	6090646	6090648	.	-	0	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	CDS	6090649	6090838	1	-	1	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	exon	6090649	6090838	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	intron	6090839	6090923	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	CDS	6090924	6091111	1	-	0	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	exon	6090924	6091111	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	intron	6091112	6091236	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	CDS	6091237	6091527	0.97	-	0	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	exon	6091237	6091527	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	intron	6091528	6091658	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	CDS	6091659	6091895	0.91	-	0	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	exon	6091659	6091895	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	intron	6091896	6091984	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	CDS	6091985	6092074	0.52	-	0	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	exon	6091985	6092074	.	-	.	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
Phchi.S1	AUGUSTUS	start_codon	6092072	6092074	.	-	0	transcript_id "Phchi.S1G102400.t1"; gene_id "Phchi.S1G102400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3001.t1 is derived from g170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1081123	1083255	.	+	.	Phchi.S1G016000
Phchi.S1	AUGUSTUS	transcript	1081123	1083255	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	start_codon	1081123	1081125	.	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1081123	1081318	0.9	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1081123	1081318	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1081319	1081458	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1081459	1081586	1	+	2	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1081459	1081586	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1081587	1081731	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1081732	1081803	1	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1081732	1081803	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1081804	1082030	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1082031	1082173	1	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1082031	1082173	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1082174	1082272	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1082273	1082387	1	+	1	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1082273	1082387	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1082388	1082478	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1082479	1082559	1	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1082479	1082559	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1082560	1082639	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1082640	1082771	1	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1082640	1082771	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1082772	1082852	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1082853	1082940	1	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1082853	1082940	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1082941	1083035	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1083036	1083121	0.61	+	2	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1083036	1083121	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	intron	1083122	1083204	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	CDS	1083205	1083255	0.68	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	exon	1083205	1083255	.	+	.	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
Phchi.S1	AUGUSTUS	stop_codon	1083256	1083258	.	+	0	transcript_id "Phchi.S1G016000.t1"; gene_id "Phchi.S1G016000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10125.t1 is derived from g7301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45846338	45848369	.	+	.	Phchi.S1G728400
Phchi.S1	AUGUSTUS	transcript	45846338	45848369	.	+	.	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	start_codon	45846338	45846340	.	+	0	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	CDS	45846338	45848191	0.17	+	0	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	exon	45846338	45848191	.	+	.	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	intron	45848192	45848303	.	+	.	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	CDS	45848304	45848369	0.83	+	0	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	exon	45848304	45848369	.	+	.	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
Phchi.S1	AUGUSTUS	stop_codon	45848370	45848372	.	+	0	transcript_id "Phchi.S1G728400.t1"; gene_id "Phchi.S1G728400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14126.t1 is derived from g12593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11013261	11016240	.	-	.	Phchi.S3G144500
Phchi.S3	AUGUSTUS	transcript	11013261	11016240	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	stop_codon	11013258	11013260	.	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013261	11013290	0.93	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013261	11013290	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11013291	11013426	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013427	11013452	0.78	-	2	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013427	11013452	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11013453	11013679	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013680	11013881	0.74	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013680	11013881	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11013882	11013988	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013989	11014126	0.72	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013989	11014126	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014127	11014280	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11014281	11014384	1	-	2	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11014281	11014384	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014385	11014473	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11014474	11014677	0.88	-	2	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11014474	11014677	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014678	11014827	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11014828	11014924	1	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11014828	11014924	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014925	11015046	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015047	11015111	1	-	2	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015047	11015111	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015112	11015208	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015209	11015302	1	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015209	11015302	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015303	11015395	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015396	11015550	1	-	2	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015396	11015550	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015551	11015639	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015640	11015717	1	-	2	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015640	11015717	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015718	11015978	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015979	11016240	0.97	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015979	11016240	.	-	.	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	start_codon	11016238	11016240	.	-	0	transcript_id "Phchi.S3G144500.t1"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	transcript	11013261	11016240	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	stop_codon	11013258	11013260	.	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013261	11013290	0.96	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013261	11013290	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11013291	11013426	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013427	11013452	0.77	-	2	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013427	11013452	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11013453	11013679	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013680	11013881	0.69	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013680	11013881	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11013882	11013988	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11013989	11014126	0.69	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11013989	11014126	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014127	11014280	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11014281	11014381	0.99	-	2	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11014281	11014381	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014382	11014473	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11014474	11014677	0.9	-	2	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11014474	11014677	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014678	11014827	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11014828	11014924	1	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11014828	11014924	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11014925	11015046	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015047	11015111	1	-	2	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015047	11015111	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015112	11015208	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015209	11015302	1	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015209	11015302	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015303	11015395	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015396	11015550	1	-	2	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015396	11015550	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015551	11015639	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015640	11015717	1	-	2	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015640	11015717	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	intron	11015718	11015978	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	CDS	11015979	11016240	0.97	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	exon	11015979	11016240	.	-	.	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
Phchi.S3	AUGUSTUS	start_codon	11016238	11016240	.	-	0	transcript_id "Phchi.S3G144500.t2"; gene_id "Phchi.S3G144500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10777.t1 is derived from g14827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2064577	2064909	.	+	.	Phchi.S4G035900
Phchi.S4	AUGUSTUS	transcript	2064577	2064909	.	+	.	transcript_id "Phchi.S4G035900.t1"; gene_id "Phchi.S4G035900"
Phchi.S4	AUGUSTUS	start_codon	2064577	2064579	.	+	0	transcript_id "Phchi.S4G035900.t1"; gene_id "Phchi.S4G035900"
Phchi.S4	AUGUSTUS	CDS	2064577	2064909	0.84	+	0	transcript_id "Phchi.S4G035900.t1"; gene_id "Phchi.S4G035900"
Phchi.S4	AUGUSTUS	exon	2064577	2064909	.	+	.	transcript_id "Phchi.S4G035900.t1"; gene_id "Phchi.S4G035900"
Phchi.S4	AUGUSTUS	stop_codon	2064910	2064912	.	+	0	transcript_id "Phchi.S4G035900.t1"; gene_id "Phchi.S4G035900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3571.t1 is derived from g740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4557784	4560018	.	-	.	Phchi.S1G073000
Phchi.S1	AUGUSTUS	transcript	4557784	4560018	.	-	.	transcript_id "Phchi.S1G073000.t1"; gene_id "Phchi.S1G073000"
Phchi.S1	AUGUSTUS	stop_codon	4557781	4557783	.	-	0	transcript_id "Phchi.S1G073000.t1"; gene_id "Phchi.S1G073000"
Phchi.S1	AUGUSTUS	CDS	4557784	4560018	0.93	-	0	transcript_id "Phchi.S1G073000.t1"; gene_id "Phchi.S1G073000"
Phchi.S1	AUGUSTUS	exon	4557784	4560018	.	-	.	transcript_id "Phchi.S1G073000.t1"; gene_id "Phchi.S1G073000"
Phchi.S1	AUGUSTUS	start_codon	4560016	4560018	.	-	0	transcript_id "Phchi.S1G073000.t1"; gene_id "Phchi.S1G073000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10955.t1 is derived from g15005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3272189	3273616	.	+	.	Phchi.S4G053700
Phchi.S4	AUGUSTUS	transcript	3272189	3273616	.	+	.	transcript_id "Phchi.S4G053700.t1"; gene_id "Phchi.S4G053700"
Phchi.S4	AUGUSTUS	start_codon	3272189	3272191	.	+	0	transcript_id "Phchi.S4G053700.t1"; gene_id "Phchi.S4G053700"
Phchi.S4	AUGUSTUS	CDS	3272189	3273616	0.99	+	0	transcript_id "Phchi.S4G053700.t1"; gene_id "Phchi.S4G053700"
Phchi.S4	AUGUSTUS	exon	3272189	3273616	.	+	.	transcript_id "Phchi.S4G053700.t1"; gene_id "Phchi.S4G053700"
Phchi.S4	AUGUSTUS	stop_codon	3273617	3273619	.	+	0	transcript_id "Phchi.S4G053700.t1"; gene_id "Phchi.S4G053700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8080.t1 is derived from g5255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32863997	32866563	.	-	.	Phchi.S1G523900
Phchi.S1	AUGUSTUS	transcript	32863997	32866563	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	stop_codon	32863994	32863996	.	-	0	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	CDS	32863997	32864458	1	-	0	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	exon	32863997	32864458	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	intron	32864459	32864579	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	CDS	32864580	32864781	0.41	-	1	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	exon	32864580	32864781	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	intron	32864782	32865084	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	CDS	32865085	32865332	0.6	-	0	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	exon	32865085	32865332	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	intron	32865333	32865456	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	CDS	32865457	32865784	0.93	-	1	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	exon	32865457	32865784	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	intron	32865785	32865892	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	CDS	32865893	32866140	0.99	-	0	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	exon	32865893	32866140	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	intron	32866141	32866221	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	CDS	32866222	32866563	0.6	-	0	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	exon	32866222	32866563	.	-	.	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
Phchi.S1	AUGUSTUS	start_codon	32866561	32866563	.	-	0	transcript_id "Phchi.S1G523900.t1"; gene_id "Phchi.S1G523900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1736.t1 is derived from g8656.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2778884	2780997	.	+	.	Phchi.S5G034500
Phchi.S5	AUGUSTUS	transcript	2778884	2780997	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	start_codon	2778884	2778886	.	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2778884	2779115	1	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2778884	2779115	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779116	2779193	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779194	2779381	1	+	2	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779194	2779381	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779382	2779566	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779567	2779656	1	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779567	2779656	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779657	2779785	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779786	2779888	1	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779786	2779888	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779889	2779981	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779982	2780130	1	+	2	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779982	2780130	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780131	2780214	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780215	2780306	1	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780215	2780306	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780307	2780402	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780403	2780565	1	+	1	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780403	2780565	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780566	2780655	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780656	2780754	1	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780656	2780754	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780755	2780835	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780836	2780997	1	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780836	2780997	.	+	.	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	stop_codon	2780998	2781000	.	+	0	transcript_id "Phchi.S5G034500.t1"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	transcript	2778884	2780997	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	start_codon	2778884	2778886	.	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2778884	2779115	0.99	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2778884	2779115	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779116	2779193	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779194	2779381	1	+	2	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779194	2779381	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779382	2779551	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779552	2779656	0.76	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779552	2779656	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779657	2779785	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779786	2779888	1	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779786	2779888	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2779889	2779981	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2779982	2780130	1	+	2	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2779982	2780130	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780131	2780214	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780215	2780306	1	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780215	2780306	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780307	2780402	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780403	2780565	1	+	1	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780403	2780565	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780566	2780655	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780656	2780754	1	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780656	2780754	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	intron	2780755	2780835	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	CDS	2780836	2780997	1	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	exon	2780836	2780997	.	+	.	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
Phchi.S5	AUGUSTUS	stop_codon	2780998	2781000	.	+	0	transcript_id "Phchi.S5G034500.t2"; gene_id "Phchi.S5G034500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15111.t1 is derived from g13579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17119888	17122424	.	-	.	Phchi.S3G243000
Phchi.S3	AUGUSTUS	transcript	17119888	17122424	.	-	.	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	stop_codon	17119885	17119887	.	-	0	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	CDS	17119888	17121790	0.58	-	1	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	exon	17119888	17121790	.	-	.	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	intron	17121791	17121906	.	-	.	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	CDS	17121907	17122424	0.54	-	0	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	exon	17121907	17122424	.	-	.	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
Phchi.S3	AUGUSTUS	start_codon	17122422	17122424	.	-	0	transcript_id "Phchi.S3G243000.t1"; gene_id "Phchi.S3G243000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11426.t1 is derived from g15476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6281519	6283567	.	+	.	Phchi.S4G100800
Phchi.S4	AUGUSTUS	transcript	6281519	6283567	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	start_codon	6281519	6281521	.	+	0	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	CDS	6281519	6281935	0.51	+	0	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	exon	6281519	6281935	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	intron	6281936	6282276	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	CDS	6282277	6282477	1	+	0	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	exon	6282277	6282477	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	intron	6282478	6282558	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	CDS	6282559	6282681	1	+	0	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	exon	6282559	6282681	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	intron	6282682	6282774	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	CDS	6282775	6282998	1	+	0	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	exon	6282775	6282998	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	intron	6282999	6283077	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	CDS	6283078	6283567	0.61	+	1	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	exon	6283078	6283567	.	+	.	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
Phchi.S4	AUGUSTUS	stop_codon	6283568	6283570	.	+	0	transcript_id "Phchi.S4G100800.t1"; gene_id "Phchi.S4G100800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15248.t1 is derived from g13716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17894973	17896725	.	+	.	Phchi.S3G256700
Phchi.S3	AUGUSTUS	transcript	17894973	17896725	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	start_codon	17894973	17894975	.	+	0	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	CDS	17894973	17895521	0.37	+	0	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	exon	17894973	17895521	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	intron	17895522	17895623	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	CDS	17895624	17895761	1	+	0	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	exon	17895624	17895761	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	intron	17895762	17895845	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	CDS	17895846	17895989	1	+	0	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	exon	17895846	17895989	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	intron	17895990	17896106	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	CDS	17896107	17896300	1	+	0	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	exon	17896107	17896300	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	intron	17896301	17896403	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	CDS	17896404	17896725	1	+	1	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	exon	17896404	17896725	.	+	.	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
Phchi.S3	AUGUSTUS	stop_codon	17896726	17896728	.	+	0	transcript_id "Phchi.S3G256700.t1"; gene_id "Phchi.S3G256700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4690.t1 is derived from g1860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12162641	12163836	.	-	.	Phchi.S1G184900
Phchi.S1	AUGUSTUS	transcript	12162641	12163836	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	stop_codon	12162638	12162640	.	-	0	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	CDS	12162641	12162720	1	-	2	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	exon	12162641	12162720	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	intron	12162721	12162875	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	CDS	12162876	12163086	0.61	-	0	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	exon	12162876	12163086	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	intron	12163087	12163419	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	CDS	12163420	12163520	0.57	-	2	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	exon	12163420	12163520	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	intron	12163521	12163592	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	CDS	12163593	12163836	0.37	-	0	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	exon	12163593	12163836	.	-	.	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
Phchi.S1	AUGUSTUS	start_codon	12163834	12163836	.	-	0	transcript_id "Phchi.S1G184900.t1"; gene_id "Phchi.S1G184900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg504.t1 is derived from g10286.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3498005	3499064	.	-	.	Phchi.S6G046300
Phchi.S6	AUGUSTUS	transcript	3498005	3499003	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	stop_codon	3498002	3498004	.	-	0	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498005	3498110	0.7	-	1	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498005	3498110	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498111	3498207	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498208	3498299	1	-	0	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498208	3498299	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498300	3498376	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498377	3498413	1	-	1	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498377	3498413	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498414	3498654	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498655	3498756	1	-	1	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498655	3498756	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498757	3498840	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498841	3498889	1	-	2	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498841	3498889	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498890	3498981	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498982	3499003	1	-	0	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498982	3499003	.	-	.	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	start_codon	3499001	3499003	.	-	0	transcript_id "Phchi.S6G046300.t1"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	transcript	3498005	3499064	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	stop_codon	3498002	3498004	.	-	0	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498005	3498110	0.73	-	1	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498005	3498110	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498111	3498207	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498208	3498299	1	-	0	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498208	3498299	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498300	3498376	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498377	3498413	0.99	-	1	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498377	3498413	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498414	3498654	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498655	3498756	0.72	-	1	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498655	3498756	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498757	3498840	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498841	3498876	0.59	-	1	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498841	3498876	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	intron	3498877	3498981	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	CDS	3498982	3499064	0.59	-	0	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	exon	3498982	3499064	.	-	.	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
Phchi.S6	AUGUSTUS	start_codon	3499062	3499064	.	-	0	transcript_id "Phchi.S6G046300.t2"; gene_id "Phchi.S6G046300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14533.t1 is derived from g13001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13332124	13332682	.	-	.	Phchi.S3G185200
Phchi.S3	AUGUSTUS	transcript	13332124	13332682	.	-	.	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	stop_codon	13332121	13332123	.	-	0	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	CDS	13332124	13332195	1	-	0	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	exon	13332124	13332195	.	-	.	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	intron	13332196	13332271	.	-	.	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	CDS	13332272	13332682	1	-	0	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	exon	13332272	13332682	.	-	.	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
Phchi.S3	AUGUSTUS	start_codon	13332680	13332682	.	-	0	transcript_id "Phchi.S3G185200.t1"; gene_id "Phchi.S3G185200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9162.t1 is derived from g6337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40152795	40155014	.	-	.	Phchi.S1G632100
Phchi.S1	AUGUSTUS	transcript	40152795	40155014	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	stop_codon	40152792	40152794	.	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40152795	40153091	0.99	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40152795	40153091	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	intron	40153092	40153176	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40153177	40153428	1	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40153177	40153428	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	intron	40153429	40153528	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40153529	40153960	1	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40153529	40153960	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	intron	40153961	40154042	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40154043	40154129	1	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40154043	40154129	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	intron	40154130	40154285	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40154286	40154507	1	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40154286	40154507	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	intron	40154508	40154645	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40154646	40154694	0.65	-	1	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40154646	40154694	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	intron	40154695	40154781	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	CDS	40154782	40155014	0.58	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	exon	40154782	40155014	.	-	.	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
Phchi.S1	AUGUSTUS	start_codon	40155012	40155014	.	-	0	transcript_id "Phchi.S1G632100.t1"; gene_id "Phchi.S1G632100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2933.t1 is derived from g102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	609103	610351	.	-	.	Phchi.S1G009200
Phchi.S1	AUGUSTUS	transcript	609103	610351	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	stop_codon	609100	609102	.	-	0	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	CDS	609103	609491	0.84	-	2	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	exon	609103	609491	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	intron	609492	609569	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	CDS	609570	609735	1	-	0	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	exon	609570	609735	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	intron	609736	609806	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	CDS	609807	609998	1	-	0	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	exon	609807	609998	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	intron	609999	610129	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	CDS	610130	610351	0.98	-	0	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	exon	610130	610351	.	-	.	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
Phchi.S1	AUGUSTUS	start_codon	610349	610351	.	-	0	transcript_id "Phchi.S1G009200.t1"; gene_id "Phchi.S1G009200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2539.t1 is derived from g9459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7221114	7221659	.	-	.	Phchi.S5G114800
Phchi.S5	AUGUSTUS	transcript	7221114	7221659	.	-	.	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	stop_codon	7221111	7221113	.	-	0	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	CDS	7221114	7221333	0.99	-	1	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	exon	7221114	7221333	.	-	.	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	intron	7221334	7221405	.	-	.	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	CDS	7221406	7221659	0.62	-	0	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	exon	7221406	7221659	.	-	.	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
Phchi.S5	AUGUSTUS	start_codon	7221657	7221659	.	-	0	transcript_id "Phchi.S5G114800.t1"; gene_id "Phchi.S5G114800"
# This transcript jg10639.t2 is derived from g14689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10640.t1 is derived from g14690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1373988	1376594	.	-	.	Phchi.S4G022200
Phchi.S4	AUGUSTUS	transcript	1373988	1376594	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	stop_codon	1373985	1373987	.	-	0	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1373988	1374055	0.79	-	2	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1373988	1374055	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374056	1374140	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1374141	1374211	1	-	1	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1374141	1374211	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374212	1374299	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1374300	1374370	1	-	0	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1374300	1374370	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374371	1374463	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1374464	1374562	1	-	0	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1374464	1374562	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374563	1374699	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1374700	1374715	1	-	1	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1374700	1374715	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374716	1374795	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1374796	1374835	0.63	-	2	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1374796	1374835	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374836	1374924	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1374925	1374982	1	-	0	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1374925	1374982	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1374983	1375241	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1375242	1375323	1	-	1	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1375242	1375323	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	intron	1375324	1375584	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	CDS	1375585	1376594	0.98	-	0	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	exon	1375585	1376594	.	-	.	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
Phchi.S4	AUGUSTUS	start_codon	1376592	1376594	.	-	0	transcript_id "Phchi.S4G022200.t1"; gene_id "Phchi.S4G022200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3915.t1 is derived from g1084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6416369	6418193	.	-	.	Phchi.S1G107400
Phchi.S1	AUGUSTUS	transcript	6416369	6418193	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	stop_codon	6416366	6416368	.	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6416369	6416500	0.81	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6416369	6416500	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	intron	6416501	6416625	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6416626	6416706	1	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6416626	6416706	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	intron	6416707	6416837	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6416838	6416954	1	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6416838	6416954	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	intron	6416955	6417174	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6417175	6417276	1	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6417175	6417276	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	intron	6417277	6417406	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6417407	6417542	0.92	-	1	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6417407	6417542	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	intron	6417543	6417733	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6417734	6417895	1	-	1	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6417734	6417895	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	intron	6417896	6417975	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	CDS	6417976	6418193	0.91	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	exon	6417976	6418193	.	-	.	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
Phchi.S1	AUGUSTUS	start_codon	6418191	6418193	.	-	0	transcript_id "Phchi.S1G107400.t1"; gene_id "Phchi.S1G107400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1042.t1 is derived from g10825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7264646	7265332	.	-	.	Phchi.S6G100100
Phchi.S6	AUGUSTUS	transcript	7264646	7265332	.	-	.	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	stop_codon	7264643	7264645	.	-	0	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	CDS	7264646	7264764	0.98	-	2	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	exon	7264646	7264764	.	-	.	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	intron	7264765	7264914	.	-	.	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	CDS	7264915	7265034	1	-	2	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	exon	7264915	7265034	.	-	.	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	intron	7265035	7265223	.	-	.	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	CDS	7265224	7265332	0.89	-	0	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	exon	7265224	7265332	.	-	.	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
Phchi.S6	AUGUSTUS	start_codon	7265330	7265332	.	-	0	transcript_id "Phchi.S6G100100.t1"; gene_id "Phchi.S6G100100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15774.t1 is derived from g14244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21287084	21287518	.	-	.	Phchi.S3G309300
Phchi.S3	AUGUSTUS	transcript	21287084	21287518	.	-	.	transcript_id "Phchi.S3G309300.t1"; gene_id "Phchi.S3G309300"
Phchi.S3	AUGUSTUS	stop_codon	21287081	21287083	.	-	0	transcript_id "Phchi.S3G309300.t1"; gene_id "Phchi.S3G309300"
Phchi.S3	AUGUSTUS	CDS	21287084	21287518	0.68	-	0	transcript_id "Phchi.S3G309300.t1"; gene_id "Phchi.S3G309300"
Phchi.S3	AUGUSTUS	exon	21287084	21287518	.	-	.	transcript_id "Phchi.S3G309300.t1"; gene_id "Phchi.S3G309300"
Phchi.S3	AUGUSTUS	start_codon	21287516	21287518	.	-	0	transcript_id "Phchi.S3G309300.t1"; gene_id "Phchi.S3G309300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6631.t1 is derived from g3803.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24172280	24174589	.	+	.	Phchi.S1G379000
Phchi.S1	AUGUSTUS	transcript	24172280	24174589	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	start_codon	24172280	24172282	.	+	0	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	CDS	24172280	24172375	0.25	+	0	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	exon	24172280	24172375	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	intron	24172376	24172497	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	CDS	24172498	24172659	0.66	+	0	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	exon	24172498	24172659	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	intron	24172660	24172747	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	CDS	24172748	24172816	0.83	+	0	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	exon	24172748	24172816	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	intron	24172817	24173029	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	CDS	24173030	24174589	0.85	+	0	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	exon	24173030	24174589	.	+	.	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	stop_codon	24174590	24174592	.	+	0	transcript_id "Phchi.S1G379000.t1"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	transcript	24173636	24174589	.	+	.	transcript_id "Phchi.S1G379000.t2"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	start_codon	24173636	24173638	.	+	0	transcript_id "Phchi.S1G379000.t2"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	CDS	24173636	24174589	1	+	0	transcript_id "Phchi.S1G379000.t2"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	exon	24173636	24174589	.	+	.	transcript_id "Phchi.S1G379000.t2"; gene_id "Phchi.S1G379000"
Phchi.S1	AUGUSTUS	stop_codon	24174590	24174592	.	+	0	transcript_id "Phchi.S1G379000.t2"; gene_id "Phchi.S1G379000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15789.t1 is derived from g14259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21352365	21353636	.	+	.	Phchi.S3G310800
Phchi.S3	AUGUSTUS	transcript	21352365	21353636	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	start_codon	21352365	21352367	.	+	0	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	CDS	21352365	21352511	0.63	+	0	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	exon	21352365	21352511	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	intron	21352512	21352648	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	CDS	21352649	21352780	1	+	0	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	exon	21352649	21352780	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	intron	21352781	21352866	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	CDS	21352867	21352904	1	+	0	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	exon	21352867	21352904	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	intron	21352905	21353002	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	CDS	21353003	21353069	1	+	1	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	exon	21353003	21353069	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	intron	21353070	21353156	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	CDS	21353157	21353636	0.99	+	0	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	exon	21353157	21353636	.	+	.	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
Phchi.S3	AUGUSTUS	stop_codon	21353637	21353639	.	+	0	transcript_id "Phchi.S3G310800.t1"; gene_id "Phchi.S3G310800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13997.t1 is derived from g12464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10160899	10172243	.	-	.	Phchi.S3G131600
Phchi.S3	AUGUSTUS	transcript	10160899	10172243	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	stop_codon	10160896	10160898	.	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10160899	10162077	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10160899	10162077	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10162078	10162164	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10162165	10162407	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10162165	10162407	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10162408	10162508	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10162509	10162793	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10162509	10162793	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10162794	10162882	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10162883	10163221	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10162883	10163221	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10163222	10163308	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10163309	10163636	0.95	-	1	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10163309	10163636	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10163637	10163715	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10163716	10163954	0.75	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10163716	10163954	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10163955	10164074	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10164075	10164254	0.75	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10164075	10164254	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10164255	10164333	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10164334	10164606	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10164334	10164606	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10164607	10164687	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10164688	10164797	0.66	-	2	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10164688	10164797	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10164798	10165048	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10165049	10165079	0.73	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10165049	10165079	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10165080	10165243	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10165244	10165378	0.65	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10165244	10165378	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10165379	10165483	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10165484	10165756	0.96	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10165484	10165756	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10165757	10165857	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10165858	10165992	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10165858	10165992	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10165993	10166128	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10166129	10166374	0.86	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10166129	10166374	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10166375	10166485	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10166486	10166698	0.87	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10166486	10166698	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10166699	10166803	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10166804	10167088	0.93	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10166804	10167088	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10167089	10167176	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10167177	10167290	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10167177	10167290	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10167291	10167367	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10167368	10167665	1	-	1	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10167368	10167665	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10167666	10167815	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10167816	10168216	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10167816	10168216	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10168217	10168444	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10168445	10168658	0.93	-	1	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10168445	10168658	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10168659	10168746	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10168747	10168766	0.93	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10168747	10168766	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10168767	10168843	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10168844	10168912	0.79	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10168844	10168912	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10168913	10168987	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10168988	10169094	1	-	2	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10168988	10169094	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10169095	10169192	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10169193	10169769	0.79	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10169193	10169769	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10169770	10169931	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10169932	10170069	0.75	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10169932	10170069	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10170070	10170203	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10170204	10170518	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10170204	10170518	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10170519	10170603	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10170604	10170910	1	-	1	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10170604	10170910	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10170911	10171085	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10171086	10171387	1	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10171086	10171387	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10171388	10171514	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10171515	10171687	1	-	2	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10171515	10171687	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10171688	10171825	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10171826	10172004	1	-	1	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10171826	10172004	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	intron	10172005	10172121	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	CDS	10172122	10172243	0.44	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	exon	10172122	10172243	.	-	.	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
Phchi.S3	AUGUSTUS	start_codon	10172241	10172243	.	-	0	transcript_id "Phchi.S3G131600.t1"; gene_id "Phchi.S3G131600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6009.t1 is derived from g3180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20413255	20415915	.	-	.	Phchi.S1G316800
Phchi.S1	AUGUSTUS	transcript	20413255	20415915	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	stop_codon	20413252	20413254	.	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20413255	20413338	1	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20413255	20413338	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20413339	20413444	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20413445	20413526	1	-	1	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20413445	20413526	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20413527	20413643	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20413644	20413690	1	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20413644	20413690	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20413691	20413807	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20413808	20413881	0.9	-	2	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20413808	20413881	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20413882	20413963	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20413964	20414175	0.9	-	1	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20413964	20414175	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20414176	20414342	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20414343	20414414	1	-	1	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20414343	20414414	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20414415	20414584	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20414585	20414832	0.99	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20414585	20414832	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20414833	20414938	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20414939	20415010	1	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20414939	20415010	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20415011	20415101	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20415102	20415182	1	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20415102	20415182	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20415183	20415328	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20415329	20415399	0.71	-	2	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20415329	20415399	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20415400	20415482	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20415483	20415601	0.84	-	1	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20415483	20415601	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	intron	20415602	20415718	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	CDS	20415719	20415915	0.49	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	exon	20415719	20415915	.	-	.	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
Phchi.S1	AUGUSTUS	start_codon	20415913	20415915	.	-	0	transcript_id "Phchi.S1G316800.t1"; gene_id "Phchi.S1G316800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5766.t1 is derived from g2936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18866593	18867534	.	-	.	Phchi.S1G292500
Phchi.S1	AUGUSTUS	transcript	18866593	18867534	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	stop_codon	18866590	18866592	.	-	0	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	CDS	18866593	18866679	0.91	-	0	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	exon	18866593	18866679	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	intron	18866680	18866820	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	CDS	18866821	18866864	0.91	-	2	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	exon	18866821	18866864	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	intron	18866865	18867012	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	CDS	18867013	18867088	0.88	-	0	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	exon	18867013	18867088	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	intron	18867089	18867198	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	CDS	18867199	18867534	0.52	-	0	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	exon	18867199	18867534	.	-	.	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
Phchi.S1	AUGUSTUS	start_codon	18867532	18867534	.	-	0	transcript_id "Phchi.S1G292500.t1"; gene_id "Phchi.S1G292500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11891.t1 is derived from g15943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9048301	9056077	.	+	.	Phchi.S4G147300
Phchi.S4	AUGUSTUS	transcript	9048301	9056077	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	start_codon	9048301	9048303	.	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9048301	9048327	0.86	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9048301	9048327	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9048328	9048503	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9048504	9048617	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9048504	9048617	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9048618	9048709	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9048710	9048787	0.99	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9048710	9048787	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9048788	9048897	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9048898	9049014	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9048898	9049014	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9049015	9049182	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9049183	9049271	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9049183	9049271	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9049272	9049368	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9049369	9049513	1	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9049369	9049513	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9049514	9049603	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9049604	9049699	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9049604	9049699	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9049700	9049872	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9049873	9049964	0.96	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9049873	9049964	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9049965	9050079	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9050080	9050181	0.98	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9050080	9050181	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9050182	9050293	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9050294	9050440	1	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9050294	9050440	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9050441	9050540	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9050541	9050691	1	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9050541	9050691	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9050692	9050781	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9050782	9050844	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9050782	9050844	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9050845	9050918	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9050919	9051155	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9050919	9051155	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9051156	9051260	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9051261	9051359	0.99	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9051261	9051359	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9051360	9051473	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9051474	9051587	0.99	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9051474	9051587	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9051588	9051735	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9051736	9052683	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9051736	9052683	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9052684	9052860	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9052861	9053314	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9052861	9053314	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9053315	9054147	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9054148	9054283	0.47	+	2	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9054148	9054283	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9054284	9054853	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9054854	9054892	0.52	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9054854	9054892	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9054893	9055079	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9055080	9055122	1	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9055080	9055122	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9055123	9055260	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9055261	9055379	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9055261	9055379	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9055380	9055491	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9055492	9055594	1	+	1	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9055492	9055594	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9055595	9055753	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9055754	9055819	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9055754	9055819	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	intron	9055820	9055966	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	CDS	9055967	9056077	1	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	exon	9055967	9056077	.	+	.	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
Phchi.S4	AUGUSTUS	stop_codon	9056078	9056080	.	+	0	transcript_id "Phchi.S4G147300.t1"; gene_id "Phchi.S4G147300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12737.t1 is derived from g11202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1458406	1458875	.	-	.	Phchi.S3G005600
Phchi.S3	AUGUSTUS	transcript	1458406	1458875	.	-	.	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	stop_codon	1458403	1458405	.	-	0	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	CDS	1458406	1458716	0.83	-	2	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	exon	1458406	1458716	.	-	.	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	intron	1458717	1458805	.	-	.	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	CDS	1458806	1458875	0.73	-	0	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	exon	1458806	1458875	.	-	.	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
Phchi.S3	AUGUSTUS	start_codon	1458873	1458875	.	-	0	transcript_id "Phchi.S3G005600.t1"; gene_id "Phchi.S3G005600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1121.t1 is derived from g10904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7803767	7805239	.	-	.	Phchi.S6G108000
Phchi.S6	AUGUSTUS	transcript	7803767	7805239	.	-	.	transcript_id "Phchi.S6G108000.t1"; gene_id "Phchi.S6G108000"
Phchi.S6	AUGUSTUS	stop_codon	7803764	7803766	.	-	0	transcript_id "Phchi.S6G108000.t1"; gene_id "Phchi.S6G108000"
Phchi.S6	AUGUSTUS	CDS	7803767	7805239	0.35	-	0	transcript_id "Phchi.S6G108000.t1"; gene_id "Phchi.S6G108000"
Phchi.S6	AUGUSTUS	exon	7803767	7805239	.	-	.	transcript_id "Phchi.S6G108000.t1"; gene_id "Phchi.S6G108000"
Phchi.S6	AUGUSTUS	start_codon	7805237	7805239	.	-	0	transcript_id "Phchi.S6G108000.t1"; gene_id "Phchi.S6G108000"
# This transcript jg1656.t2 is derived from g8575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1657.t1 is derived from g8576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2260639	2267817	.	+	.	Phchi.S5G026600
Phchi.S5	AUGUSTUS	transcript	2260639	2267817	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	start_codon	2260639	2260641	.	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2260639	2260889	0.2	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2260639	2260889	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2260890	2261006	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2261007	2261219	1	+	1	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2261007	2261219	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2261220	2261306	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2261307	2261375	0.98	+	1	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2261307	2261375	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2261376	2261496	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2261497	2261527	0.98	+	1	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2261497	2261527	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2261528	2261611	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2261612	2261917	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2261612	2261917	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2261918	2262062	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2262063	2262167	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2262063	2262167	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2262168	2262275	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2262276	2262391	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2262276	2262391	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2262392	2262482	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2262483	2262588	1	+	1	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2262483	2262588	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2262589	2262665	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2262666	2262863	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2262666	2262863	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2262864	2262937	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2262938	2263111	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2262938	2263111	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2263112	2263193	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2263194	2263259	0.99	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2263194	2263259	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2263260	2263360	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2263361	2263495	0.94	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2263361	2263495	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2263496	2263625	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2263626	2263850	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2263626	2263850	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2263851	2263945	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2263946	2264080	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2263946	2264080	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2264081	2264186	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2264187	2264268	0.52	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2264187	2264268	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2264269	2264422	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2264423	2264607	0.8	+	2	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2264423	2264607	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2264608	2264724	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2264725	2264913	0.65	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2264725	2264913	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2264914	2265017	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2265018	2265158	0.6	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2265018	2265158	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2265159	2265260	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2265261	2265399	0.59	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2265261	2265399	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2265400	2265482	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2265483	2265604	0.99	+	2	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2265483	2265604	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2265605	2265690	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2265691	2265891	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2265691	2265891	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2265892	2266030	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2266031	2266222	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2266031	2266222	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2266223	2266305	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2266306	2266749	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2266306	2266749	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2266750	2266837	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2266838	2267070	1	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2266838	2267070	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2267071	2267148	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2267149	2267467	1	+	1	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2267149	2267467	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	intron	2267468	2267583	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	CDS	2267584	2267817	0.88	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	exon	2267584	2267817	.	+	.	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
Phchi.S5	AUGUSTUS	stop_codon	2267818	2267820	.	+	0	transcript_id "Phchi.S5G026600.t1"; gene_id "Phchi.S5G026600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10495.t1 is derived from g14544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	689808	692803	.	+	.	Phchi.S4G007700
Phchi.S4	AUGUSTUS	transcript	689808	692803	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	start_codon	689808	689810	.	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	689808	689877	0.76	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	689808	689877	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	689878	689958	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	689959	690150	0.97	+	2	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	689959	690150	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	690151	690224	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	690225	690266	1	+	2	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	690225	690266	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	690267	690347	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	690348	690421	1	+	2	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	690348	690421	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	690422	690494	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	690495	690707	0.55	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	690495	690707	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	690708	690993	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	690994	691431	0.48	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	690994	691431	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	691432	691770	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	691771	692279	0.51	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	691771	692279	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	692280	692408	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	692409	692670	0.55	+	1	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	692409	692670	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	intron	692671	692770	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	CDS	692771	692803	0.73	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	exon	692771	692803	.	+	.	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
Phchi.S4	AUGUSTUS	stop_codon	692804	692806	.	+	0	transcript_id "Phchi.S4G007700.t1"; gene_id "Phchi.S4G007700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14351.t1 is derived from g12818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12334043	12334833	.	-	.	Phchi.S3G167000
Phchi.S3	AUGUSTUS	transcript	12334043	12334833	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	stop_codon	12334040	12334042	.	-	0	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	CDS	12334043	12334135	0.99	-	0	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	exon	12334043	12334135	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	intron	12334136	12334247	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	CDS	12334248	12334396	0.99	-	2	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	exon	12334248	12334396	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	intron	12334397	12334474	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	CDS	12334475	12334580	1	-	0	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	exon	12334475	12334580	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	intron	12334581	12334668	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	CDS	12334669	12334833	0.93	-	0	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	exon	12334669	12334833	.	-	.	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
Phchi.S3	AUGUSTUS	start_codon	12334831	12334833	.	-	0	transcript_id "Phchi.S3G167000.t1"; gene_id "Phchi.S3G167000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3610.t1 is derived from g779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4735032	4737923	.	-	.	Phchi.S1G076900
Phchi.S1	AUGUSTUS	transcript	4735032	4737923	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	stop_codon	4735029	4735031	.	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4735032	4735085	1	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4735032	4735085	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4735086	4735184	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4735185	4735280	1	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4735185	4735280	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4735281	4735367	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4735368	4735451	1	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4735368	4735451	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4735452	4735567	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4735568	4735636	1	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4735568	4735636	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4735637	4735767	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4735768	4735869	1	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4735768	4735869	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4735870	4735957	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4735958	4736023	0.99	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4735958	4736023	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4736024	4736135	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4736136	4736186	0.98	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4736136	4736186	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4736187	4736389	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4736390	4736485	1	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4736390	4736485	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4736486	4736630	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4736631	4736730	1	-	1	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4736631	4736730	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4736731	4737036	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4737037	4737118	1	-	2	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4737037	4737118	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4737119	4737311	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4737312	4737555	0.78	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4737312	4737555	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	intron	4737556	4737794	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	CDS	4737795	4737923	0.81	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	exon	4737795	4737923	.	-	.	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
Phchi.S1	AUGUSTUS	start_codon	4737921	4737923	.	-	0	transcript_id "Phchi.S1G076900.t1"; gene_id "Phchi.S1G076900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9762.t1 is derived from g6938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43558610	43558907	.	-	.	Phchi.S1G692100
Phchi.S1	AUGUSTUS	transcript	43558610	43558907	.	-	.	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	stop_codon	43558607	43558609	.	-	0	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	CDS	43558610	43558705	1	-	0	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	exon	43558610	43558705	.	-	.	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	intron	43558706	43558796	.	-	.	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	CDS	43558797	43558907	1	-	0	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	exon	43558797	43558907	.	-	.	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
Phchi.S1	AUGUSTUS	start_codon	43558905	43558907	.	-	0	transcript_id "Phchi.S1G692100.t1"; gene_id "Phchi.S1G692100"
# This transcript jg3880.t2 is derived from g1049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3881.t1 is derived from g1050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6196205	6196702	.	-	.	Phchi.S1G104000
Phchi.S1	AUGUSTUS	transcript	6196205	6196702	.	-	.	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	stop_codon	6196202	6196204	.	-	0	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	CDS	6196205	6196249	0.82	-	0	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	exon	6196205	6196249	.	-	.	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	intron	6196250	6196329	.	-	.	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	CDS	6196330	6196408	0.79	-	1	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	exon	6196330	6196408	.	-	.	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	intron	6196409	6196595	.	-	.	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	CDS	6196596	6196702	0.7	-	0	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	exon	6196596	6196702	.	-	.	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
Phchi.S1	AUGUSTUS	start_codon	6196700	6196702	.	-	0	transcript_id "Phchi.S1G104000.t1"; gene_id "Phchi.S1G104000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg176.t1 is derived from g9958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1023914	1024478	.	+	.	Phchi.S6G013500
Phchi.S6	AUGUSTUS	transcript	1023914	1024478	.	+	.	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	start_codon	1023914	1023916	.	+	0	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	CDS	1023914	1024300	0.85	+	0	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	exon	1023914	1024300	.	+	.	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	intron	1024301	1024442	.	+	.	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	CDS	1024443	1024478	1	+	0	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	exon	1024443	1024478	.	+	.	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
Phchi.S6	AUGUSTUS	stop_codon	1024479	1024481	.	+	0	transcript_id "Phchi.S6G013500.t1"; gene_id "Phchi.S6G013500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12670.t1 is derived from g14404.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	1526	3758	.	-	.	Phchi.C62G000100
Phchi.C62	AUGUSTUS	transcript	1526	3758	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	stop_codon	1523	1525	.	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	1526	1642	0.64	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	1526	1642	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	1643	1736	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	1737	1838	1	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	1737	1838	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	1839	1928	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	1929	1955	0.98	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	1929	1955	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	1956	2013	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2014	2022	1	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2014	2022	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	2023	2216	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2217	2426	1	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2217	2426	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	2427	2582	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2583	2689	0.69	-	2	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2583	2689	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	2690	2957	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2958	3625	0.46	-	1	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2958	3625	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	3626	3729	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	3730	3758	0.52	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	3730	3758	.	-	.	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	start_codon	3756	3758	.	-	0	transcript_id "Phchi.C62G000100.t1"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	transcript	1526	3758	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	stop_codon	1523	1525	.	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	1526	1642	0.56	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	1526	1642	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	1643	1736	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	1737	1838	1	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	1737	1838	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	1839	1928	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	1929	1955	0.97	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	1929	1955	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	1956	2013	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2014	2022	1	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2014	2022	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	2023	2216	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2217	2468	0.9	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2217	2468	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	2469	2582	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2583	2689	0.57	-	2	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2583	2689	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	2690	2957	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	2958	3625	0.44	-	1	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	2958	3625	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	intron	3626	3729	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	CDS	3730	3758	0.63	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	exon	3730	3758	.	-	.	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
Phchi.C62	AUGUSTUS	start_codon	3756	3758	.	-	0	transcript_id "Phchi.C62G000100.t2"; gene_id "Phchi.C62G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3729.t1 is derived from g898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5424267	5427535	.	+	.	Phchi.S1G088800
Phchi.S1	AUGUSTUS	transcript	5424267	5427535	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	start_codon	5424267	5424269	.	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5424267	5424404	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5424267	5424404	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5424405	5424779	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5424780	5424834	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5424780	5424834	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5424835	5424926	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5424927	5425078	1	+	2	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5424927	5425078	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5425079	5425153	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5425154	5425193	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5425154	5425193	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5425194	5425374	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5425375	5425473	1	+	2	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5425375	5425473	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5425474	5425561	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5425562	5425668	1	+	2	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5425562	5425668	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5425669	5425747	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5425748	5425822	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5425748	5425822	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5425823	5425970	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5425971	5426216	0.64	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5425971	5426216	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5426217	5426338	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5426339	5426416	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5426339	5426416	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5426417	5426512	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5426513	5426530	0.92	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5426513	5426530	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5426531	5426607	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5426608	5426655	0.83	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5426608	5426655	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5426656	5426780	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5426781	5426848	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5426781	5426848	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5426849	5427002	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5427003	5427117	1	+	1	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5427003	5427117	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5427118	5427213	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5427214	5427370	1	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5427214	5427370	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	intron	5427371	5427443	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	CDS	5427444	5427535	1	+	2	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	exon	5427444	5427535	.	+	.	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
Phchi.S1	AUGUSTUS	stop_codon	5427536	5427538	.	+	0	transcript_id "Phchi.S1G088800.t1"; gene_id "Phchi.S1G088800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14264.t1 is derived from g12731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11817830	11818798	.	+	.	Phchi.S3G158300
Phchi.S3	AUGUSTUS	transcript	11817830	11818798	.	+	.	transcript_id "Phchi.S3G158300.t1"; gene_id "Phchi.S3G158300"
Phchi.S3	AUGUSTUS	start_codon	11817830	11817832	.	+	0	transcript_id "Phchi.S3G158300.t1"; gene_id "Phchi.S3G158300"
Phchi.S3	AUGUSTUS	CDS	11817830	11818798	1	+	0	transcript_id "Phchi.S3G158300.t1"; gene_id "Phchi.S3G158300"
Phchi.S3	AUGUSTUS	exon	11817830	11818798	.	+	.	transcript_id "Phchi.S3G158300.t1"; gene_id "Phchi.S3G158300"
Phchi.S3	AUGUSTUS	stop_codon	11818799	11818801	.	+	0	transcript_id "Phchi.S3G158300.t1"; gene_id "Phchi.S3G158300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13673.t1 is derived from g12140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8090950	8093888	.	-	.	Phchi.S3G099200
Phchi.S3	AUGUSTUS	transcript	8090950	8093888	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	stop_codon	8090947	8090949	.	-	0	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8090950	8091063	0.82	-	0	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8090950	8091063	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8091064	8091257	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8091258	8091320	0.77	-	0	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8091258	8091320	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8091321	8091510	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8091511	8091553	0.71	-	1	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8091511	8091553	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8091554	8091649	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8091650	8091768	0.94	-	0	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8091650	8091768	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8091769	8091870	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8091871	8092030	0.94	-	1	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8091871	8092030	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8092031	8092134	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8092135	8093508	0.96	-	1	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8092135	8093508	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8093509	8093640	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8093641	8093761	0.99	-	2	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8093641	8093761	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	intron	8093762	8093845	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	CDS	8093846	8093888	1	-	0	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	exon	8093846	8093888	.	-	.	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
Phchi.S3	AUGUSTUS	start_codon	8093886	8093888	.	-	0	transcript_id "Phchi.S3G099200.t1"; gene_id "Phchi.S3G099200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3753.t1 is derived from g922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5502972	5503964	.	+	.	Phchi.S1G091200
Phchi.S1	AUGUSTUS	transcript	5502972	5503964	.	+	.	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	start_codon	5502972	5502974	.	+	0	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	CDS	5502972	5503292	0.19	+	0	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	exon	5502972	5503292	.	+	.	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	intron	5503293	5503397	.	+	.	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	CDS	5503398	5503611	0.77	+	0	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	exon	5503398	5503611	.	+	.	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	intron	5503612	5503743	.	+	.	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	CDS	5503744	5503964	0.47	+	2	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	exon	5503744	5503964	.	+	.	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
Phchi.S1	AUGUSTUS	stop_codon	5503965	5503967	.	+	0	transcript_id "Phchi.S1G091200.t1"; gene_id "Phchi.S1G091200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15013.t1 is derived from g13481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16527568	16530724	.	+	.	Phchi.S3G233200
Phchi.S3	AUGUSTUS	transcript	16527568	16530724	.	+	.	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	start_codon	16527568	16527570	.	+	0	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	CDS	16527568	16527973	0.27	+	0	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	exon	16527568	16527973	.	+	.	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	intron	16527974	16528086	.	+	.	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	CDS	16528087	16529265	0.17	+	2	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	exon	16528087	16529265	.	+	.	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	intron	16529266	16529438	.	+	.	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	CDS	16529439	16530724	0.34	+	2	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	exon	16529439	16530724	.	+	.	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
Phchi.S3	AUGUSTUS	stop_codon	16530725	16530727	.	+	0	transcript_id "Phchi.S3G233200.t1"; gene_id "Phchi.S3G233200"
# This transcript jg1334.t2 is derived from g11117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1335.t1 is derived from g11118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9087745	9088984	.	-	.	Phchi.S6G129400
Phchi.S6	AUGUSTUS	transcript	9087745	9088984	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	stop_codon	9087742	9087744	.	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	CDS	9087745	9087900	0.98	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	exon	9087745	9087900	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	intron	9087901	9087995	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	CDS	9087996	9088130	0.82	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	exon	9087996	9088130	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	intron	9088131	9088242	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	CDS	9088243	9088407	1	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	exon	9088243	9088407	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	intron	9088408	9088523	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	CDS	9088524	9088679	1	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	exon	9088524	9088679	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	intron	9088680	9088832	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	CDS	9088833	9088858	0.91	-	2	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	exon	9088833	9088858	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	intron	9088859	9088950	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	CDS	9088951	9088984	0.91	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	exon	9088951	9088984	.	-	.	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
Phchi.S6	AUGUSTUS	start_codon	9088982	9088984	.	-	0	transcript_id "Phchi.S6G129400.t1"; gene_id "Phchi.S6G129400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5342.t1 is derived from g2512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16373861	16375771	.	+	.	Phchi.S1G250100
Phchi.S1	AUGUSTUS	transcript	16373861	16375771	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	start_codon	16373861	16373863	.	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16373861	16374052	0.55	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16373861	16374052	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16374053	16374142	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16374143	16374360	1	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16374143	16374360	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16374361	16374449	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16374450	16374564	1	+	1	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16374450	16374564	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16374565	16374674	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16374675	16374764	1	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16374675	16374764	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16374765	16374864	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16374865	16375047	0.97	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16374865	16375047	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16375048	16375149	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16375150	16375266	1	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16375150	16375266	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16375267	16375350	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16375351	16375461	1	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16375351	16375461	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16375462	16375559	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16375560	16375645	1	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16375560	16375645	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	intron	16375646	16375719	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	CDS	16375720	16375771	1	+	1	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	exon	16375720	16375771	.	+	.	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
Phchi.S1	AUGUSTUS	stop_codon	16375772	16375774	.	+	0	transcript_id "Phchi.S1G250100.t1"; gene_id "Phchi.S1G250100"
# This transcript jg1764.t2 is derived from g8684.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1765.t1 is derived from g8685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2929807	2930412	.	-	.	Phchi.S5G037400
Phchi.S5	AUGUSTUS	transcript	2929807	2930412	.	-	.	transcript_id "Phchi.S5G037400.t1"; gene_id "Phchi.S5G037400"
Phchi.S5	AUGUSTUS	stop_codon	2929804	2929806	.	-	0	transcript_id "Phchi.S5G037400.t1"; gene_id "Phchi.S5G037400"
Phchi.S5	AUGUSTUS	CDS	2929807	2930412	0.37	-	0	transcript_id "Phchi.S5G037400.t1"; gene_id "Phchi.S5G037400"
Phchi.S5	AUGUSTUS	exon	2929807	2930412	.	-	.	transcript_id "Phchi.S5G037400.t1"; gene_id "Phchi.S5G037400"
Phchi.S5	AUGUSTUS	start_codon	2930410	2930412	.	-	0	transcript_id "Phchi.S5G037400.t1"; gene_id "Phchi.S5G037400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8227.t1 is derived from g5402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34548381	34550049	.	+	.	Phchi.S1G538600
Phchi.S1	AUGUSTUS	transcript	34548381	34550049	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	start_codon	34548381	34548383	.	+	0	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	CDS	34548381	34548929	0.77	+	0	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	exon	34548381	34548929	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	intron	34548930	34549032	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	CDS	34549033	34549166	0.99	+	0	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	exon	34549033	34549166	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	intron	34549167	34549270	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	CDS	34549271	34549390	1	+	1	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	exon	34549271	34549390	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	intron	34549391	34549500	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	CDS	34549501	34549669	0.96	+	1	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	exon	34549501	34549669	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	intron	34549670	34549777	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	CDS	34549778	34549846	1	+	0	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	exon	34549778	34549846	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	intron	34549847	34549950	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	CDS	34549951	34550049	1	+	0	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	exon	34549951	34550049	.	+	.	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
Phchi.S1	AUGUSTUS	stop_codon	34550050	34550052	.	+	0	transcript_id "Phchi.S1G538600.t1"; gene_id "Phchi.S1G538600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8053.t1 is derived from g5228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32722027	32722568	.	+	.	Phchi.S1G521200
Phchi.S1	AUGUSTUS	transcript	32722027	32722568	.	+	.	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	start_codon	32722027	32722029	.	+	0	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	CDS	32722027	32722106	0.81	+	0	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	exon	32722027	32722106	.	+	.	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	intron	32722107	32722187	.	+	.	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	CDS	32722188	32722294	0.85	+	1	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	exon	32722188	32722294	.	+	.	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	intron	32722295	32722398	.	+	.	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	CDS	32722399	32722568	0.99	+	2	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	exon	32722399	32722568	.	+	.	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
Phchi.S1	AUGUSTUS	stop_codon	32722569	32722571	.	+	0	transcript_id "Phchi.S1G521200.t1"; gene_id "Phchi.S1G521200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1801.t1 is derived from g8721.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3112482	3114130	.	-	.	Phchi.S5G041000
Phchi.S5	AUGUSTUS	transcript	3112482	3114130	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	stop_codon	3112479	3112481	.	-	0	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3112482	3112639	0.98	-	2	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3112482	3112639	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3112640	3112730	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3112731	3112877	1	-	2	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3112731	3112877	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3112878	3113071	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113072	3113191	0.51	-	2	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113072	3113191	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113192	3113308	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113309	3113351	0.35	-	0	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113309	3113351	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113352	3113434	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113435	3113482	0.98	-	0	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113435	3113482	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113483	3113823	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113824	3113859	0.98	-	0	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113824	3113859	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113860	3113938	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113939	3114030	0.98	-	2	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113939	3114030	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3114031	3114114	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3114115	3114130	0.88	-	0	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3114115	3114130	.	-	.	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	start_codon	3114128	3114130	.	-	0	transcript_id "Phchi.S5G041000.t1"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	transcript	3112482	3114130	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	stop_codon	3112479	3112481	.	-	0	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3112482	3112639	0.99	-	2	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3112482	3112639	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3112640	3112730	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3112731	3112823	1	-	2	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3112731	3112823	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3112824	3113071	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113072	3113191	0.46	-	2	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113072	3113191	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113192	3113308	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113309	3113351	0.36	-	0	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113309	3113351	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113352	3113434	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113435	3113482	0.97	-	0	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113435	3113482	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113483	3113823	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113824	3113859	0.94	-	0	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113824	3113859	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3113860	3113938	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3113939	3114030	0.98	-	2	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3113939	3114030	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	intron	3114031	3114114	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	CDS	3114115	3114130	0.9	-	0	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	exon	3114115	3114130	.	-	.	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
Phchi.S5	AUGUSTUS	start_codon	3114128	3114130	.	-	0	transcript_id "Phchi.S5G041000.t2"; gene_id "Phchi.S5G041000"
# This transcript jg12161.t2 is derived from g7837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12162.t1 is derived from g7838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5078109	5078519	.	+	.	Phchi.S2G024200
Phchi.S2	AUGUSTUS	transcript	5078109	5078519	.	+	.	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	start_codon	5078109	5078111	.	+	0	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	CDS	5078109	5078121	0.88	+	0	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	exon	5078109	5078121	.	+	.	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	intron	5078122	5078210	.	+	.	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	CDS	5078211	5078328	0.91	+	2	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	exon	5078211	5078328	.	+	.	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	intron	5078329	5078398	.	+	.	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	CDS	5078399	5078519	0.95	+	1	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	exon	5078399	5078519	.	+	.	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
Phchi.S2	AUGUSTUS	stop_codon	5078520	5078522	.	+	0	transcript_id "Phchi.S2G024200.t1"; gene_id "Phchi.S2G024200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3097.t1 is derived from g266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1742412	1743340	.	+	.	Phchi.S1G025600
Phchi.S1	AUGUSTUS	transcript	1742412	1743340	.	+	.	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	start_codon	1742412	1742414	.	+	0	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	CDS	1742412	1742761	0.44	+	0	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	exon	1742412	1742761	.	+	.	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	intron	1742762	1742877	.	+	.	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	CDS	1742878	1743340	0.48	+	1	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	exon	1742878	1743340	.	+	.	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
Phchi.S1	AUGUSTUS	stop_codon	1743341	1743343	.	+	0	transcript_id "Phchi.S1G025600.t1"; gene_id "Phchi.S1G025600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3704.t1 is derived from g873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5240823	5247379	.	-	.	Phchi.S1G086300
Phchi.S1	AUGUSTUS	transcript	5240823	5247379	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	stop_codon	5240820	5240822	.	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5240823	5240860	1	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5240823	5240860	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5240861	5240955	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5240956	5240974	1	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5240956	5240974	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5240975	5241245	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5241246	5241296	0.38	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5241246	5241296	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5241297	5241391	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5241392	5241455	1	-	1	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5241392	5241455	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5241456	5241609	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5241610	5241626	1	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5241610	5241626	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5241627	5241722	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5241723	5241748	1	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5241723	5241748	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5241749	5241821	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5241822	5241877	0.84	-	1	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5241822	5241877	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5241878	5241977	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5241978	5242023	0.5	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5241978	5242023	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5242024	5242479	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5242480	5243172	0.48	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5242480	5243172	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5243173	5243333	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5243334	5244543	0.84	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5243334	5244543	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5244544	5244658	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5244659	5245089	0.87	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5244659	5245089	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5245090	5245172	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5245173	5245308	0.99	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5245173	5245308	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5245309	5245477	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5245478	5245536	0.97	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5245478	5245536	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5245537	5245785	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5245786	5245921	0.55	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5245786	5245921	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5245922	5246003	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5246004	5246280	1	-	1	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5246004	5246280	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5246281	5246450	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5246451	5246527	0.85	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5246451	5246527	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5246528	5246687	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5246688	5247113	0.35	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5246688	5247113	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5247114	5247218	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5247219	5247286	0.48	-	2	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5247219	5247286	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	intron	5247287	5247363	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	CDS	5247364	5247379	0.91	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	exon	5247364	5247379	.	-	.	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
Phchi.S1	AUGUSTUS	start_codon	5247377	5247379	.	-	0	transcript_id "Phchi.S1G086300.t1"; gene_id "Phchi.S1G086300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12552.t1 is derived from g8229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34592372	34592677	.	+	.	Phchi.S2G063200
Phchi.S2	AUGUSTUS	transcript	34592372	34592677	.	+	.	transcript_id "Phchi.S2G063200.t1"; gene_id "Phchi.S2G063200"
Phchi.S2	AUGUSTUS	start_codon	34592372	34592374	.	+	0	transcript_id "Phchi.S2G063200.t1"; gene_id "Phchi.S2G063200"
Phchi.S2	AUGUSTUS	CDS	34592372	34592677	0.33	+	0	transcript_id "Phchi.S2G063200.t1"; gene_id "Phchi.S2G063200"
Phchi.S2	AUGUSTUS	exon	34592372	34592677	.	+	.	transcript_id "Phchi.S2G063200.t1"; gene_id "Phchi.S2G063200"
Phchi.S2	AUGUSTUS	stop_codon	34592678	34592680	.	+	0	transcript_id "Phchi.S2G063200.t1"; gene_id "Phchi.S2G063200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1059.t1 is derived from g10842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7362930	7363237	.	+	.	Phchi.S6G101800
Phchi.S6	AUGUSTUS	transcript	7362930	7363237	.	+	.	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	start_codon	7362930	7362932	.	+	0	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	CDS	7362930	7363113	0.57	+	0	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	exon	7362930	7363113	.	+	.	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	intron	7363114	7363193	.	+	.	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	CDS	7363194	7363237	0.57	+	2	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	exon	7363194	7363237	.	+	.	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
Phchi.S6	AUGUSTUS	stop_codon	7363238	7363240	.	+	0	transcript_id "Phchi.S6G101800.t1"; gene_id "Phchi.S6G101800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5854.t1 is derived from g3024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19348911	19353901	.	-	.	Phchi.S1G301300
Phchi.S1	AUGUSTUS	transcript	19348911	19353901	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	stop_codon	19348908	19348910	.	-	0	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19348911	19349061	0.74	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19348911	19349061	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19349062	19349230	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19349231	19349260	0.99	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19349231	19349260	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19349261	19349353	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19349354	19349670	0.88	-	0	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19349354	19349670	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19349671	19349767	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19349768	19349897	0.98	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19349768	19349897	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19349898	19349999	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19350000	19350186	0.96	-	2	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19350000	19350186	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19350187	19350351	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19350352	19350420	1	-	2	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19350352	19350420	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19350421	19350505	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19350506	19350638	1	-	0	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19350506	19350638	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19350639	19350722	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19350723	19350946	1	-	2	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19350723	19350946	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19350947	19351037	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19351038	19351288	1	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19351038	19351288	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19351289	19351386	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19351387	19351455	1	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19351387	19351455	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19351456	19351693	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19351694	19351765	1	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19351694	19351765	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19351766	19351863	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19351864	19351935	1	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19351864	19351935	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19351936	19352007	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19352008	19352122	0.99	-	2	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19352008	19352122	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19352123	19352248	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19352249	19352487	0.99	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19352249	19352487	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19352488	19352579	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19352580	19352942	1	-	1	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19352580	19352942	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19352943	19353083	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19353084	19353657	0.94	-	2	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19353084	19353657	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	intron	19353658	19353807	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	CDS	19353808	19353901	0.89	-	0	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	exon	19353808	19353901	.	-	.	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
Phchi.S1	AUGUSTUS	start_codon	19353899	19353901	.	-	0	transcript_id "Phchi.S1G301300.t1"; gene_id "Phchi.S1G301300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6559.t1 is derived from g3731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23722892	23724962	.	-	.	Phchi.S1G371800
Phchi.S1	AUGUSTUS	transcript	23722892	23724962	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	stop_codon	23722889	23722891	.	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23722892	23723170	1	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23722892	23723170	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23723171	23723273	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23723274	23723379	1	-	1	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23723274	23723379	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23723380	23723456	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23723457	23723650	1	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23723457	23723650	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23723651	23723734	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23723735	23723956	1	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23723735	23723956	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23723957	23724039	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23724040	23724278	1	-	2	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23724040	23724278	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23724279	23724395	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23724396	23724600	1	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23724396	23724600	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23724601	23724688	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23724689	23724760	1	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23724689	23724760	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	intron	23724761	23724950	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	CDS	23724951	23724962	0.88	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	exon	23724951	23724962	.	-	.	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
Phchi.S1	AUGUSTUS	start_codon	23724960	23724962	.	-	0	transcript_id "Phchi.S1G371800.t1"; gene_id "Phchi.S1G371800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4657.t1 is derived from g1827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11660913	11662124	.	-	.	Phchi.S1G181600
Phchi.S1	AUGUSTUS	transcript	11660913	11662124	.	-	.	transcript_id "Phchi.S1G181600.t1"; gene_id "Phchi.S1G181600"
Phchi.S1	AUGUSTUS	stop_codon	11660910	11660912	.	-	0	transcript_id "Phchi.S1G181600.t1"; gene_id "Phchi.S1G181600"
Phchi.S1	AUGUSTUS	CDS	11660913	11662124	0.93	-	0	transcript_id "Phchi.S1G181600.t1"; gene_id "Phchi.S1G181600"
Phchi.S1	AUGUSTUS	exon	11660913	11662124	.	-	.	transcript_id "Phchi.S1G181600.t1"; gene_id "Phchi.S1G181600"
Phchi.S1	AUGUSTUS	start_codon	11662122	11662124	.	-	0	transcript_id "Phchi.S1G181600.t1"; gene_id "Phchi.S1G181600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13448.t1 is derived from g11915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6773980	6775951	.	-	.	Phchi.S3G076700
Phchi.S3	AUGUSTUS	transcript	6773980	6775951	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	stop_codon	6773977	6773979	.	-	0	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	CDS	6773980	6774552	1	-	0	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	exon	6773980	6774552	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	intron	6774553	6774640	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	CDS	6774641	6774690	1	-	2	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	exon	6774641	6774690	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	intron	6774691	6774787	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	CDS	6774788	6774856	1	-	2	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	exon	6774788	6774856	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	intron	6774857	6775017	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	CDS	6775018	6775143	1	-	2	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	exon	6775018	6775143	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	intron	6775144	6775266	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	CDS	6775267	6775329	0.74	-	2	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	exon	6775267	6775329	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	intron	6775330	6775605	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	CDS	6775606	6775951	0.98	-	0	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	exon	6775606	6775951	.	-	.	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
Phchi.S3	AUGUSTUS	start_codon	6775949	6775951	.	-	0	transcript_id "Phchi.S3G076700.t1"; gene_id "Phchi.S3G076700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11166.t1 is derived from g15216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4441517	4443930	.	+	.	Phchi.S4G074800
Phchi.S4	AUGUSTUS	transcript	4441517	4443930	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	start_codon	4441517	4441519	.	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4441517	4441706	0.99	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4441517	4441706	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	intron	4441707	4441788	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4441789	4441859	1	+	2	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4441789	4441859	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	intron	4441860	4441932	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4441933	4442268	0.71	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4441933	4442268	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	intron	4442269	4442381	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4442382	4442489	0.98	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4442382	4442489	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	intron	4442490	4442594	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4442595	4442789	1	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4442595	4442789	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	intron	4442790	4442892	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4442893	4443297	0.59	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4442893	4443297	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	intron	4443298	4443393	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	CDS	4443394	4443930	0.97	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	exon	4443394	4443930	.	+	.	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
Phchi.S4	AUGUSTUS	stop_codon	4443931	4443933	.	+	0	transcript_id "Phchi.S4G074800.t1"; gene_id "Phchi.S4G074800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1187.t1 is derived from g10970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8343770	8344297	.	-	.	Phchi.S6G114600
Phchi.S6	AUGUSTUS	transcript	8343770	8344297	.	-	.	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	stop_codon	8343767	8343769	.	-	0	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	CDS	8343770	8343977	0.73	-	1	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	exon	8343770	8343977	.	-	.	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	intron	8343978	8344118	.	-	.	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	CDS	8344119	8344297	0.97	-	0	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	exon	8344119	8344297	.	-	.	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
Phchi.S6	AUGUSTUS	start_codon	8344295	8344297	.	-	0	transcript_id "Phchi.S6G114600.t1"; gene_id "Phchi.S6G114600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11892.t1 is derived from g15944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9056780	9058506	.	-	.	Phchi.S4G147400
Phchi.S4	AUGUSTUS	transcript	9056780	9058506	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	stop_codon	9056777	9056779	.	-	0	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	CDS	9056780	9057325	0.27	-	0	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	exon	9056780	9057325	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	intron	9057326	9057393	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	CDS	9057394	9057525	0.31	-	0	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	exon	9057394	9057525	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	intron	9057526	9057811	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	CDS	9057812	9058123	1	-	0	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	exon	9057812	9058123	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	intron	9058124	9058206	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	CDS	9058207	9058506	0.97	-	0	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	exon	9058207	9058506	.	-	.	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
Phchi.S4	AUGUSTUS	start_codon	9058504	9058506	.	-	0	transcript_id "Phchi.S4G147400.t1"; gene_id "Phchi.S4G147400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8344.t1 is derived from g5519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35408099	35409202	.	-	.	Phchi.S1G550300
Phchi.S1	AUGUSTUS	transcript	35408099	35409202	.	-	.	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	stop_codon	35408096	35408098	.	-	0	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	CDS	35408099	35409037	0.89	-	0	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	exon	35408099	35409037	.	-	.	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	intron	35409038	35409127	.	-	.	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	CDS	35409128	35409202	1	-	0	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	exon	35409128	35409202	.	-	.	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
Phchi.S1	AUGUSTUS	start_codon	35409200	35409202	.	-	0	transcript_id "Phchi.S1G550300.t1"; gene_id "Phchi.S1G550300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6479.t1 is derived from g3651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23194826	23198260	.	-	.	Phchi.S1G363800
Phchi.S1	AUGUSTUS	transcript	23194826	23198260	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	stop_codon	23194823	23194825	.	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23194826	23194929	1	-	2	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23194826	23194929	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23194930	23195010	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23195011	23195089	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23195011	23195089	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23195090	23195170	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23195171	23195299	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23195171	23195299	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23195300	23195418	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23195419	23195538	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23195419	23195538	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23195539	23195689	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23195690	23195803	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23195690	23195803	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23195804	23195891	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23195892	23195968	1	-	2	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23195892	23195968	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23195969	23196111	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23196112	23196200	1	-	1	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23196112	23196200	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23196201	23196362	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23196363	23196417	1	-	2	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23196363	23196417	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23196418	23196618	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23196619	23196721	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23196619	23196721	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23196722	23196878	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23196879	23196953	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23196879	23196953	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23196954	23197106	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23197107	23197182	0.76	-	1	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23197107	23197182	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23197183	23197356	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23197357	23197440	0.71	-	1	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23197357	23197440	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23197441	23197577	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23197578	23197679	1	-	1	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23197578	23197679	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23197680	23197802	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23197803	23197940	1	-	1	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23197803	23197940	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	intron	23197941	23198189	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	CDS	23198190	23198260	1	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	exon	23198190	23198260	.	-	.	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
Phchi.S1	AUGUSTUS	start_codon	23198258	23198260	.	-	0	transcript_id "Phchi.S1G363800.t1"; gene_id "Phchi.S1G363800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6327.t1 is derived from g3499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22295438	22295833	.	+	.	Phchi.S1G348600
Phchi.S1	AUGUSTUS	transcript	22295438	22295833	.	+	.	transcript_id "Phchi.S1G348600.t1"; gene_id "Phchi.S1G348600"
Phchi.S1	AUGUSTUS	start_codon	22295438	22295440	.	+	0	transcript_id "Phchi.S1G348600.t1"; gene_id "Phchi.S1G348600"
Phchi.S1	AUGUSTUS	CDS	22295438	22295833	0.4	+	0	transcript_id "Phchi.S1G348600.t1"; gene_id "Phchi.S1G348600"
Phchi.S1	AUGUSTUS	exon	22295438	22295833	.	+	.	transcript_id "Phchi.S1G348600.t1"; gene_id "Phchi.S1G348600"
Phchi.S1	AUGUSTUS	stop_codon	22295834	22295836	.	+	0	transcript_id "Phchi.S1G348600.t1"; gene_id "Phchi.S1G348600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13506.t1 is derived from g11973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7223889	7225961	.	-	.	Phchi.S3G082500
Phchi.S3	AUGUSTUS	transcript	7223889	7225961	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	stop_codon	7223886	7223888	.	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7223889	7224068	1	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7223889	7224068	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7224069	7224146	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7224147	7224355	1	-	2	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7224147	7224355	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7224356	7224437	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7224438	7224631	0.99	-	1	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7224438	7224631	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7224632	7224722	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7224723	7224787	1	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7224723	7224787	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7224788	7224870	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7224871	7225321	0.99	-	1	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7224871	7225321	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7225322	7225422	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7225423	7225655	0.98	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7225423	7225655	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7225656	7225731	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7225732	7225791	0.99	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7225732	7225791	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	intron	7225792	7225901	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	CDS	7225902	7225961	0.59	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	exon	7225902	7225961	.	-	.	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
Phchi.S3	AUGUSTUS	start_codon	7225959	7225961	.	-	0	transcript_id "Phchi.S3G082500.t1"; gene_id "Phchi.S3G082500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15936.t1 is derived from g9787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C18	AUGUSTUS	gene	104148	105213	.	-	.	Phchi.C18G000300
Phchi.C18	AUGUSTUS	transcript	104148	105213	.	-	.	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	stop_codon	104145	104147	.	-	0	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	CDS	104148	104250	0.76	-	1	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	exon	104148	104250	.	-	.	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	intron	104251	104703	.	-	.	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	CDS	104704	104743	0.77	-	2	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	exon	104704	104743	.	-	.	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	intron	104744	104819	.	-	.	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	CDS	104820	105213	0.64	-	0	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	exon	104820	105213	.	-	.	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
Phchi.C18	AUGUSTUS	start_codon	105211	105213	.	-	0	transcript_id "Phchi.C18G000300.t1"; gene_id "Phchi.C18G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15394.t1 is derived from g13862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18814945	18816085	.	-	.	Phchi.S3G271300
Phchi.S3	AUGUSTUS	transcript	18814945	18816085	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	stop_codon	18814942	18814944	.	-	0	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	CDS	18814945	18814972	1	-	1	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	exon	18814945	18814972	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	intron	18814973	18815061	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	CDS	18815062	18815231	1	-	0	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	exon	18815062	18815231	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	intron	18815232	18815364	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	CDS	18815365	18815424	1	-	0	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	exon	18815365	18815424	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	intron	18815425	18815514	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	CDS	18815515	18815667	1	-	0	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	exon	18815515	18815667	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	intron	18815668	18815833	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	CDS	18815834	18816085	0.99	-	0	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	exon	18815834	18816085	.	-	.	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
Phchi.S3	AUGUSTUS	start_codon	18816083	18816085	.	-	0	transcript_id "Phchi.S3G271300.t1"; gene_id "Phchi.S3G271300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6408.t1 is derived from g3580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22813185	22815008	.	+	.	Phchi.S1G356700
Phchi.S1	AUGUSTUS	transcript	22813185	22815008	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	start_codon	22813185	22813187	.	+	0	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	CDS	22813185	22814209	0.43	+	0	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	exon	22813185	22814209	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	intron	22814210	22814384	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	CDS	22814385	22814493	1	+	1	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	exon	22814385	22814493	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	intron	22814494	22814580	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	CDS	22814581	22814716	1	+	0	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	exon	22814581	22814716	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	intron	22814717	22814877	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	CDS	22814878	22815008	1	+	2	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	exon	22814878	22815008	.	+	.	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
Phchi.S1	AUGUSTUS	stop_codon	22815009	22815011	.	+	0	transcript_id "Phchi.S1G356700.t1"; gene_id "Phchi.S1G356700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14196.t1 is derived from g12663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11427845	11429497	.	+	.	Phchi.S3G151500
Phchi.S3	AUGUSTUS	transcript	11427845	11429497	.	+	.	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	start_codon	11427845	11427847	.	+	0	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	CDS	11427845	11427980	1	+	0	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	exon	11427845	11427980	.	+	.	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	intron	11427981	11428070	.	+	.	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	CDS	11428071	11429497	1	+	2	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	exon	11428071	11429497	.	+	.	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
Phchi.S3	AUGUSTUS	stop_codon	11429498	11429500	.	+	0	transcript_id "Phchi.S3G151500.t1"; gene_id "Phchi.S3G151500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11386.t1 is derived from g15436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6047730	6049263	.	+	.	Phchi.S4G096800
Phchi.S4	AUGUSTUS	transcript	6047730	6049263	.	+	.	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	start_codon	6047730	6047732	.	+	0	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	CDS	6047730	6047826	1	+	0	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	exon	6047730	6047826	.	+	.	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	intron	6047827	6047971	.	+	.	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	CDS	6047972	6048341	1	+	2	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	exon	6047972	6048341	.	+	.	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	intron	6048342	6048458	.	+	.	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	CDS	6048459	6049263	0.98	+	1	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	exon	6048459	6049263	.	+	.	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
Phchi.S4	AUGUSTUS	stop_codon	6049264	6049266	.	+	0	transcript_id "Phchi.S4G096800.t1"; gene_id "Phchi.S4G096800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11015.t1 is derived from g15065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3642777	3643700	.	-	.	Phchi.S4G059700
Phchi.S4	AUGUSTUS	transcript	3642777	3643554	.	-	.	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	stop_codon	3642774	3642776	.	-	0	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3642777	3642788	0.96	-	0	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3642777	3642788	.	-	.	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	intron	3642789	3642953	.	-	.	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3642954	3643041	0.96	-	1	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3642954	3643041	.	-	.	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	intron	3643042	3643333	.	-	.	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3643334	3643554	0.96	-	0	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3643334	3643554	.	-	.	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	start_codon	3643552	3643554	.	-	0	transcript_id "Phchi.S4G059700.t1"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	transcript	3642777	3643700	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	stop_codon	3642774	3642776	.	-	0	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3642777	3642788	0.74	-	0	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3642777	3642788	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	intron	3642789	3642953	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3642954	3643076	0.62	-	0	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3642954	3643076	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	intron	3643077	3643333	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3643334	3643406	0.21	-	1	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3643334	3643406	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	intron	3643407	3643623	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	CDS	3643624	3643700	0.17	-	0	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	exon	3643624	3643700	.	-	.	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
Phchi.S4	AUGUSTUS	start_codon	3643698	3643700	.	-	0	transcript_id "Phchi.S4G059700.t2"; gene_id "Phchi.S4G059700"
# This transcript jg3085.t2 is derived from g254.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3086.t1 is derived from g255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1558781	1559833	.	+	.	Phchi.S1G024500
Phchi.S1	AUGUSTUS	transcript	1558781	1559833	.	+	.	transcript_id "Phchi.S1G024500.t1"; gene_id "Phchi.S1G024500"
Phchi.S1	AUGUSTUS	start_codon	1558781	1558783	.	+	0	transcript_id "Phchi.S1G024500.t1"; gene_id "Phchi.S1G024500"
Phchi.S1	AUGUSTUS	CDS	1558781	1559833	0.5	+	0	transcript_id "Phchi.S1G024500.t1"; gene_id "Phchi.S1G024500"
Phchi.S1	AUGUSTUS	exon	1558781	1559833	.	+	.	transcript_id "Phchi.S1G024500.t1"; gene_id "Phchi.S1G024500"
Phchi.S1	AUGUSTUS	stop_codon	1559834	1559836	.	+	0	transcript_id "Phchi.S1G024500.t1"; gene_id "Phchi.S1G024500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12190.t1 is derived from g7866.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6375569	6376611	.	-	.	Phchi.S2G027000
Phchi.S2	AUGUSTUS	transcript	6375569	6376611	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	stop_codon	6375566	6375568	.	-	0	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6375569	6375595	1	-	0	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6375569	6375595	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6375596	6375726	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6375727	6375854	1	-	2	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6375727	6375854	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6375855	6375950	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6375951	6376130	1	-	2	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6375951	6376130	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6376131	6376224	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6376225	6376334	1	-	1	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6376225	6376334	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6376335	6376470	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6376471	6376506	1	-	1	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6376471	6376506	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6376507	6376594	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6376595	6376611	0.62	-	0	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6376595	6376611	.	-	.	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	start_codon	6376609	6376611	.	-	0	transcript_id "Phchi.S2G027000.t1"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	transcript	6375569	6376611	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	stop_codon	6375566	6375568	.	-	0	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6375569	6375595	0.81	-	0	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6375569	6375595	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6375596	6375705	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6375706	6375854	0.75	-	2	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6375706	6375854	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6375855	6375950	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6375951	6376130	1	-	2	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6375951	6376130	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6376131	6376224	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6376225	6376334	1	-	1	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6376225	6376334	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6376335	6376470	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6376471	6376506	1	-	1	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6376471	6376506	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	intron	6376507	6376594	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	CDS	6376595	6376611	0.54	-	0	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	exon	6376595	6376611	.	-	.	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
Phchi.S2	AUGUSTUS	start_codon	6376609	6376611	.	-	0	transcript_id "Phchi.S2G027000.t2"; gene_id "Phchi.S2G027000"
# This transcript jg13467.t2 is derived from g11934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13468.t1 is derived from g11935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7046486	7048306	.	-	.	Phchi.S3G078700
Phchi.S3	AUGUSTUS	transcript	7046486	7048306	.	-	.	transcript_id "Phchi.S3G078700.t1"; gene_id "Phchi.S3G078700"
Phchi.S3	AUGUSTUS	stop_codon	7046483	7046485	.	-	0	transcript_id "Phchi.S3G078700.t1"; gene_id "Phchi.S3G078700"
Phchi.S3	AUGUSTUS	CDS	7046486	7048306	0.61	-	0	transcript_id "Phchi.S3G078700.t1"; gene_id "Phchi.S3G078700"
Phchi.S3	AUGUSTUS	exon	7046486	7048306	.	-	.	transcript_id "Phchi.S3G078700.t1"; gene_id "Phchi.S3G078700"
Phchi.S3	AUGUSTUS	start_codon	7048304	7048306	.	-	0	transcript_id "Phchi.S3G078700.t1"; gene_id "Phchi.S3G078700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15598.t1 is derived from g14067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20196341	20196541	.	+	.	Phchi.S3G291700
Phchi.S3	AUGUSTUS	transcript	20196341	20196541	.	+	.	transcript_id "Phchi.S3G291700.t1"; gene_id "Phchi.S3G291700"
Phchi.S3	AUGUSTUS	start_codon	20196341	20196343	.	+	0	transcript_id "Phchi.S3G291700.t1"; gene_id "Phchi.S3G291700"
Phchi.S3	AUGUSTUS	CDS	20196341	20196541	0.54	+	0	transcript_id "Phchi.S3G291700.t1"; gene_id "Phchi.S3G291700"
Phchi.S3	AUGUSTUS	exon	20196341	20196541	.	+	.	transcript_id "Phchi.S3G291700.t1"; gene_id "Phchi.S3G291700"
Phchi.S3	AUGUSTUS	stop_codon	20196542	20196544	.	+	0	transcript_id "Phchi.S3G291700.t1"; gene_id "Phchi.S3G291700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8241.t1 is derived from g5416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34638417	34639580	.	-	.	Phchi.S1G540000
Phchi.S1	AUGUSTUS	transcript	34638417	34639580	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	stop_codon	34638414	34638416	.	-	0	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34638417	34638529	1	-	2	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34638417	34638529	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	intron	34638530	34638605	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34638606	34638660	1	-	0	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34638606	34638660	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	intron	34638661	34638814	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34638815	34638897	1	-	2	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34638815	34638897	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	intron	34638898	34639026	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34639027	34639120	1	-	0	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34639027	34639120	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	intron	34639121	34639206	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34639207	34639280	1	-	2	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34639207	34639280	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	intron	34639281	34639377	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34639378	34639414	1	-	0	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34639378	34639414	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	intron	34639415	34639508	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	CDS	34639509	34639580	1	-	0	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	exon	34639509	34639580	.	-	.	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
Phchi.S1	AUGUSTUS	start_codon	34639578	34639580	.	-	0	transcript_id "Phchi.S1G540000.t1"; gene_id "Phchi.S1G540000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg226.t1 is derived from g10008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1539349	1539819	.	+	.	Phchi.S6G018500
Phchi.S6	AUGUSTUS	transcript	1539349	1539819	.	+	.	transcript_id "Phchi.S6G018500.t1"; gene_id "Phchi.S6G018500"
Phchi.S6	AUGUSTUS	start_codon	1539349	1539351	.	+	0	transcript_id "Phchi.S6G018500.t1"; gene_id "Phchi.S6G018500"
Phchi.S6	AUGUSTUS	CDS	1539349	1539819	0.83	+	0	transcript_id "Phchi.S6G018500.t1"; gene_id "Phchi.S6G018500"
Phchi.S6	AUGUSTUS	exon	1539349	1539819	.	+	.	transcript_id "Phchi.S6G018500.t1"; gene_id "Phchi.S6G018500"
Phchi.S6	AUGUSTUS	stop_codon	1539820	1539822	.	+	0	transcript_id "Phchi.S6G018500.t1"; gene_id "Phchi.S6G018500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg487.t1 is derived from g10269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3408725	3409337	.	+	.	Phchi.S6G044600
Phchi.S6	AUGUSTUS	transcript	3408725	3409337	.	+	.	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	start_codon	3408725	3408727	.	+	0	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	CDS	3408725	3408971	0.99	+	0	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	exon	3408725	3408971	.	+	.	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	intron	3408972	3409077	.	+	.	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	CDS	3409078	3409140	1	+	2	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	exon	3409078	3409140	.	+	.	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	intron	3409141	3409224	.	+	.	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	CDS	3409225	3409337	0.91	+	2	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	exon	3409225	3409337	.	+	.	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
Phchi.S6	AUGUSTUS	stop_codon	3409338	3409340	.	+	0	transcript_id "Phchi.S6G044600.t1"; gene_id "Phchi.S6G044600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15511.t1 is derived from g13980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19615334	19617060	.	-	.	Phchi.S3G283000
Phchi.S3	AUGUSTUS	transcript	19615800	19617060	.	-	.	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	stop_codon	19615797	19615799	.	-	0	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	CDS	19615800	19615847	0.85	-	0	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	exon	19615800	19615847	.	-	.	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	intron	19615848	19616016	.	-	.	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	CDS	19616017	19617060	0.91	-	0	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	exon	19616017	19617060	.	-	.	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	start_codon	19617058	19617060	.	-	0	transcript_id "Phchi.S3G283000.t1"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	transcript	19615334	19617060	.	-	.	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	stop_codon	19615331	19615333	.	-	0	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	CDS	19615334	19615672	0.82	-	0	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	exon	19615334	19615672	.	-	.	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	intron	19615673	19615794	.	-	.	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	CDS	19615795	19617060	0.81	-	0	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	exon	19615795	19617060	.	-	.	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	start_codon	19617058	19617060	.	-	0	transcript_id "Phchi.S3G283000.t2"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	transcript	19615887	19617060	.	-	.	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	stop_codon	19615884	19615886	.	-	0	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	CDS	19615887	19615902	0.75	-	1	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	exon	19615887	19615902	.	-	.	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	intron	19615903	19615999	.	-	.	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	CDS	19616000	19617060	0.98	-	0	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	exon	19616000	19617060	.	-	.	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
Phchi.S3	AUGUSTUS	start_codon	19617058	19617060	.	-	0	transcript_id "Phchi.S3G283000.t3"; gene_id "Phchi.S3G283000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5176.t1 is derived from g2346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15338888	15341234	.	+	.	Phchi.S1G233500
Phchi.S1	AUGUSTUS	transcript	15338888	15341234	.	+	.	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	start_codon	15338888	15338890	.	+	0	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	CDS	15338888	15340129	0.53	+	0	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	exon	15338888	15340129	.	+	.	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	intron	15340130	15340225	.	+	.	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	CDS	15340226	15340646	1	+	0	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	exon	15340226	15340646	.	+	.	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	intron	15340647	15340743	.	+	.	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	CDS	15340744	15341234	1	+	2	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	exon	15340744	15341234	.	+	.	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
Phchi.S1	AUGUSTUS	stop_codon	15341235	15341237	.	+	0	transcript_id "Phchi.S1G233500.t1"; gene_id "Phchi.S1G233500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7028.t1 is derived from g4200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26487083	26489468	.	+	.	Phchi.S1G418700
Phchi.S1	AUGUSTUS	transcript	26487083	26489468	.	+	.	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	start_codon	26487083	26487085	.	+	0	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	CDS	26487083	26488570	0.86	+	0	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	exon	26487083	26488570	.	+	.	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	intron	26488571	26488670	.	+	.	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	CDS	26488671	26489468	0.65	+	0	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	exon	26488671	26489468	.	+	.	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
Phchi.S1	AUGUSTUS	stop_codon	26489469	26489471	.	+	0	transcript_id "Phchi.S1G418700.t1"; gene_id "Phchi.S1G418700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8598.t1 is derived from g5773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36842077	36842938	.	-	.	Phchi.S1G575700
Phchi.S1	AUGUSTUS	transcript	36842077	36842938	.	-	.	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	stop_codon	36842074	36842076	.	-	0	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	CDS	36842077	36842279	0.78	-	2	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	exon	36842077	36842279	.	-	.	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	intron	36842280	36842391	.	-	.	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	CDS	36842392	36842613	0.42	-	2	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	exon	36842392	36842613	.	-	.	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	intron	36842614	36842832	.	-	.	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	CDS	36842833	36842938	0.6	-	0	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	exon	36842833	36842938	.	-	.	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
Phchi.S1	AUGUSTUS	start_codon	36842936	36842938	.	-	0	transcript_id "Phchi.S1G575700.t1"; gene_id "Phchi.S1G575700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1621.t1 is derived from g8540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2057425	2057801	.	+	.	Phchi.S5G023000
Phchi.S5	AUGUSTUS	transcript	2057425	2057801	.	+	.	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	start_codon	2057425	2057427	.	+	0	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	CDS	2057425	2057447	0.91	+	0	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	exon	2057425	2057447	.	+	.	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	intron	2057448	2057581	.	+	.	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	CDS	2057582	2057801	0.85	+	1	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	exon	2057582	2057801	.	+	.	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
Phchi.S5	AUGUSTUS	stop_codon	2057802	2057804	.	+	0	transcript_id "Phchi.S5G023000.t1"; gene_id "Phchi.S5G023000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg112.t1 is derived from g9894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	599869	600225	.	+	.	Phchi.S6G007100
Phchi.S6	AUGUSTUS	transcript	599869	600225	.	+	.	transcript_id "Phchi.S6G007100.t1"; gene_id "Phchi.S6G007100"
Phchi.S6	AUGUSTUS	start_codon	599869	599871	.	+	0	transcript_id "Phchi.S6G007100.t1"; gene_id "Phchi.S6G007100"
Phchi.S6	AUGUSTUS	CDS	599869	600225	0.98	+	0	transcript_id "Phchi.S6G007100.t1"; gene_id "Phchi.S6G007100"
Phchi.S6	AUGUSTUS	exon	599869	600225	.	+	.	transcript_id "Phchi.S6G007100.t1"; gene_id "Phchi.S6G007100"
Phchi.S6	AUGUSTUS	stop_codon	600226	600228	.	+	0	transcript_id "Phchi.S6G007100.t1"; gene_id "Phchi.S6G007100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11595.t1 is derived from g15646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7266148	7270105	.	-	.	Phchi.S4G117700
Phchi.S4	AUGUSTUS	transcript	7266148	7270105	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	stop_codon	7266145	7266147	.	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7266148	7266255	0.99	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7266148	7266255	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7266256	7266346	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7266347	7266415	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7266347	7266415	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7266416	7266509	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7266510	7266596	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7266510	7266596	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7266597	7266696	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7266697	7266846	0.99	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7266697	7266846	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7266847	7266933	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7266934	7267074	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7266934	7267074	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7267075	7267153	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7267154	7267315	0.89	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7267154	7267315	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7267316	7267435	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7267436	7267681	0.89	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7267436	7267681	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7267682	7267815	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7267816	7267858	1	-	1	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7267816	7267858	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7267859	7267955	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7267956	7268016	1	-	2	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7267956	7268016	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7268017	7268114	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7268115	7268220	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7268115	7268220	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7268221	7268317	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7268318	7268434	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7268318	7268434	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7268435	7268536	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7268537	7268617	0.74	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7268537	7268617	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7268618	7268731	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7268732	7268774	1	-	1	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7268732	7268774	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7268775	7268854	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7268855	7268966	0.85	-	2	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7268855	7268966	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7268967	7269045	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7269046	7269115	0.85	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7269046	7269115	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7269116	7269261	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7269262	7269308	1	-	2	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7269262	7269308	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7269309	7269396	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7269397	7269529	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7269397	7269529	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7269530	7269601	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7269602	7269670	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7269602	7269670	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7269671	7269800	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7269801	7269887	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7269801	7269887	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	intron	7269888	7269973	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	CDS	7269974	7270105	1	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	exon	7269974	7270105	.	-	.	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
Phchi.S4	AUGUSTUS	start_codon	7270103	7270105	.	-	0	transcript_id "Phchi.S4G117700.t1"; gene_id "Phchi.S4G117700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1409.t1 is derived from g8328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	268003	268431	.	+	.	Phchi.S5G001800
Phchi.S5	AUGUSTUS	transcript	268003	268431	.	+	.	transcript_id "Phchi.S5G001800.t1"; gene_id "Phchi.S5G001800"
Phchi.S5	AUGUSTUS	start_codon	268003	268005	.	+	0	transcript_id "Phchi.S5G001800.t1"; gene_id "Phchi.S5G001800"
Phchi.S5	AUGUSTUS	CDS	268003	268431	0.55	+	0	transcript_id "Phchi.S5G001800.t1"; gene_id "Phchi.S5G001800"
Phchi.S5	AUGUSTUS	exon	268003	268431	.	+	.	transcript_id "Phchi.S5G001800.t1"; gene_id "Phchi.S5G001800"
Phchi.S5	AUGUSTUS	stop_codon	268432	268434	.	+	0	transcript_id "Phchi.S5G001800.t1"; gene_id "Phchi.S5G001800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7388.t1 is derived from g4560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28889368	28890871	.	-	.	Phchi.S1G454700
Phchi.S1	AUGUSTUS	transcript	28889368	28890871	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	stop_codon	28889365	28889367	.	-	0	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	CDS	28889368	28889595	1	-	0	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	exon	28889368	28889595	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	intron	28889596	28889669	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	CDS	28889670	28889808	1	-	1	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	exon	28889670	28889808	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	intron	28889809	28889898	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	CDS	28889899	28890002	1	-	0	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	exon	28889899	28890002	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	intron	28890003	28890091	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	CDS	28890092	28890871	0.98	-	0	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	exon	28890092	28890871	.	-	.	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
Phchi.S1	AUGUSTUS	start_codon	28890869	28890871	.	-	0	transcript_id "Phchi.S1G454700.t1"; gene_id "Phchi.S1G454700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3349.t1 is derived from g518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3058571	3063723	.	+	.	Phchi.S1G050800
Phchi.S1	AUGUSTUS	transcript	3058571	3063723	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	start_codon	3058571	3058573	.	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3058571	3058840	0.74	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3058571	3058840	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3058841	3059000	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3059001	3059223	0.92	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3059001	3059223	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3059224	3059581	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3059582	3060615	0.99	+	2	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3059582	3060615	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3060616	3060781	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3060782	3060898	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3060782	3060898	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3060899	3061098	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3061099	3061296	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3061099	3061296	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3061297	3061448	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3061449	3061703	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3061449	3061703	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3061704	3061844	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3061845	3061913	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3061845	3061913	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3061914	3062035	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3062036	3062183	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3062036	3062183	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3062184	3062475	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3062476	3062624	1	+	2	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3062476	3062624	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3062625	3062730	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3062731	3062901	0.99	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3062731	3062901	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3062902	3063141	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3063142	3063339	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3063142	3063339	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	intron	3063340	3063429	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	CDS	3063430	3063723	1	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	exon	3063430	3063723	.	+	.	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
Phchi.S1	AUGUSTUS	stop_codon	3063724	3063726	.	+	0	transcript_id "Phchi.S1G050800.t1"; gene_id "Phchi.S1G050800"
# This transcript jg11038.t2 is derived from g15088.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11039.t1 is derived from g15089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3775563	3776416	.	+	.	Phchi.S4G062100
Phchi.S4	AUGUSTUS	transcript	3775563	3776416	.	+	.	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	start_codon	3775563	3775565	.	+	0	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	CDS	3775563	3776054	0.68	+	0	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	exon	3775563	3776054	.	+	.	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	intron	3776055	3776170	.	+	.	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	CDS	3776171	3776416	0.49	+	0	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	exon	3776171	3776416	.	+	.	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
Phchi.S4	AUGUSTUS	stop_codon	3776417	3776419	.	+	0	transcript_id "Phchi.S4G062100.t1"; gene_id "Phchi.S4G062100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7883.t1 is derived from g5057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31749521	31750440	.	+	.	Phchi.S1G504200
Phchi.S1	AUGUSTUS	transcript	31749521	31750440	.	+	.	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	start_codon	31749521	31749523	.	+	0	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	CDS	31749521	31750018	1	+	0	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	exon	31749521	31750018	.	+	.	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	intron	31750019	31750122	.	+	.	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	CDS	31750123	31750440	1	+	0	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	exon	31750123	31750440	.	+	.	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
Phchi.S1	AUGUSTUS	stop_codon	31750441	31750443	.	+	0	transcript_id "Phchi.S1G504200.t1"; gene_id "Phchi.S1G504200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8040.t1 is derived from g5215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32632723	32636333	.	-	.	Phchi.S1G519900
Phchi.S1	AUGUSTUS	transcript	32632723	32636333	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	stop_codon	32632720	32632722	.	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32632723	32632784	0.92	-	2	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32632723	32632784	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32632785	32632976	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32632977	32633006	0.75	-	2	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32632977	32633006	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32633007	32633477	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32633478	32633745	0.79	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32633478	32633745	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32633746	32633829	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32633830	32633889	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32633830	32633889	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32633890	32634002	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32634003	32634112	1	-	2	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32634003	32634112	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32634113	32634271	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32634272	32634356	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32634272	32634356	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32634357	32634441	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32634442	32634522	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32634442	32634522	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32634523	32634607	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32634608	32634703	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32634608	32634703	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32634704	32634863	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32634864	32634928	1	-	2	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32634864	32634928	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32634929	32635026	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32635027	32635102	0.77	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32635027	32635102	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32635103	32635244	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32635245	32635283	0.6	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32635245	32635283	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32635284	32635393	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32635394	32635459	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32635394	32635459	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32635460	32635627	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32635628	32635687	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32635628	32635687	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32635688	32635824	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32635825	32635914	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32635825	32635914	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32635915	32636000	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32636001	32636063	1	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32636001	32636063	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	intron	32636064	32636186	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	CDS	32636187	32636333	0.76	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	exon	32636187	32636333	.	-	.	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
Phchi.S1	AUGUSTUS	start_codon	32636331	32636333	.	-	0	transcript_id "Phchi.S1G519900.t1"; gene_id "Phchi.S1G519900"
# This transcript jg10470.t2 is derived from g14519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10471.t1 is derived from g14520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	549304	550019	.	-	.	Phchi.S4G005300
Phchi.S4	AUGUSTUS	transcript	549304	550019	.	-	.	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	stop_codon	549301	549303	.	-	0	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	CDS	549304	549370	0.46	-	1	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	exon	549304	549370	.	-	.	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	intron	549371	549487	.	-	.	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	CDS	549488	549671	0.41	-	2	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	exon	549488	549671	.	-	.	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	intron	549672	549928	.	-	.	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	CDS	549929	550019	0.47	-	0	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	exon	549929	550019	.	-	.	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
Phchi.S4	AUGUSTUS	start_codon	550017	550019	.	-	0	transcript_id "Phchi.S4G005300.t1"; gene_id "Phchi.S4G005300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14147.t1 is derived from g12614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11161887	11162640	.	-	.	Phchi.S3G146600
Phchi.S3	AUGUSTUS	transcript	11161887	11162640	.	-	.	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	stop_codon	11161884	11161886	.	-	0	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	CDS	11161887	11161913	0.82	-	0	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	exon	11161887	11161913	.	-	.	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	intron	11161914	11162103	.	-	.	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	CDS	11162104	11162640	0.79	-	0	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	exon	11162104	11162640	.	-	.	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
Phchi.S3	AUGUSTUS	start_codon	11162638	11162640	.	-	0	transcript_id "Phchi.S3G146600.t1"; gene_id "Phchi.S3G146600"
# This transcript jg1015.t1 is derived from g10799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7122683	7122880	.	-	.	Phchi.S6G097400
Phchi.S6	AUGUSTUS	transcript	7122683	7122880	.	-	.	transcript_id "Phchi.S6G097400.t1"; gene_id "Phchi.S6G097400"
Phchi.S6	AUGUSTUS	stop_codon	7122680	7122682	.	-	0	transcript_id "Phchi.S6G097400.t1"; gene_id "Phchi.S6G097400"
Phchi.S6	AUGUSTUS	CDS	7122683	7122880	0.92	-	0	transcript_id "Phchi.S6G097400.t1"; gene_id "Phchi.S6G097400"
Phchi.S6	AUGUSTUS	exon	7122683	7122880	.	-	.	transcript_id "Phchi.S6G097400.t1"; gene_id "Phchi.S6G097400"
Phchi.S6	AUGUSTUS	start_codon	7122878	7122880	.	-	0	transcript_id "Phchi.S6G097400.t1"; gene_id "Phchi.S6G097400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2716.t1 is derived from g9636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8312792	8314503	.	+	.	Phchi.S5G132500
Phchi.S5	AUGUSTUS	transcript	8312792	8314503	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	start_codon	8312792	8312794	.	+	0	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	CDS	8312792	8312969	0.19	+	0	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	exon	8312792	8312969	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	intron	8312970	8313085	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	CDS	8313086	8313270	1	+	2	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	exon	8313086	8313270	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	intron	8313271	8313343	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	CDS	8313344	8313829	0.97	+	0	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	exon	8313344	8313829	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	intron	8313830	8313918	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	CDS	8313919	8314136	0.99	+	0	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	exon	8313919	8314136	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	intron	8314137	8314265	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	CDS	8314266	8314503	1	+	1	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	exon	8314266	8314503	.	+	.	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
Phchi.S5	AUGUSTUS	stop_codon	8314504	8314506	.	+	0	transcript_id "Phchi.S5G132500.t1"; gene_id "Phchi.S5G132500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11987.t1 is derived from g7662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	387396	388694	.	+	.	Phchi.S2G006700
Phchi.S2	AUGUSTUS	transcript	387396	388694	.	+	.	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	start_codon	387396	387398	.	+	0	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	CDS	387396	387647	0.52	+	0	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	exon	387396	387647	.	+	.	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	intron	387648	387740	.	+	.	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	CDS	387741	388694	0.91	+	0	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	exon	387741	388694	.	+	.	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
Phchi.S2	AUGUSTUS	stop_codon	388695	388697	.	+	0	transcript_id "Phchi.S2G006700.t1"; gene_id "Phchi.S2G006700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15923.t1 is derived from g14393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22243842	22244522	.	-	.	Phchi.S3G324200
Phchi.S3	AUGUSTUS	transcript	22243842	22244522	.	-	.	transcript_id "Phchi.S3G324200.t1"; gene_id "Phchi.S3G324200"
Phchi.S3	AUGUSTUS	stop_codon	22243839	22243841	.	-	0	transcript_id "Phchi.S3G324200.t1"; gene_id "Phchi.S3G324200"
Phchi.S3	AUGUSTUS	CDS	22243842	22244522	0.91	-	0	transcript_id "Phchi.S3G324200.t1"; gene_id "Phchi.S3G324200"
Phchi.S3	AUGUSTUS	exon	22243842	22244522	.	-	.	transcript_id "Phchi.S3G324200.t1"; gene_id "Phchi.S3G324200"
Phchi.S3	AUGUSTUS	start_codon	22244520	22244522	.	-	0	transcript_id "Phchi.S3G324200.t1"; gene_id "Phchi.S3G324200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11415.t1 is derived from g15465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6247074	6252069	.	-	.	Phchi.S4G099700
Phchi.S4	AUGUSTUS	transcript	6247074	6252069	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	stop_codon	6247071	6247073	.	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6247074	6247291	1	-	2	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6247074	6247291	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6247292	6247650	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6247651	6247771	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6247651	6247771	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6247772	6247858	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6247859	6248015	1	-	1	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6247859	6248015	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248016	6248092	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6248093	6248229	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6248093	6248229	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248230	6248538	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6248539	6248679	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6248539	6248679	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248680	6248758	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6248759	6248968	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6248759	6248968	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248969	6249098	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249099	6249318	1	-	1	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249099	6249318	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6249319	6249409	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249410	6249579	0.95	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249410	6249579	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6249580	6249671	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249672	6249792	0.88	-	1	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249672	6249792	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6249793	6250105	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6250106	6250161	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6250106	6250161	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6250162	6250283	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6250284	6250409	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6250284	6250409	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6250410	6250575	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6250576	6250903	0.99	-	1	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6250576	6250903	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6250904	6251125	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6251126	6251309	1	-	2	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6251126	6251309	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6251310	6251517	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6251518	6251616	0.94	-	2	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6251518	6251616	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6251617	6251864	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6251865	6251914	0.92	-	1	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6251865	6251914	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6251915	6252001	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6252002	6252069	1	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6252002	6252069	.	-	.	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	start_codon	6252067	6252069	.	-	0	transcript_id "Phchi.S4G099700.t1"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	transcript	6247074	6252069	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	stop_codon	6247071	6247073	.	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6247074	6247291	1	-	2	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6247074	6247291	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6247292	6247650	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6247651	6247771	1	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6247651	6247771	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6247772	6247858	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6247859	6248015	1	-	1	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6247859	6248015	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248016	6248092	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6248093	6248229	1	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6248093	6248229	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248230	6248538	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6248539	6248679	1	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6248539	6248679	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248680	6248758	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6248759	6248968	1	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6248759	6248968	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6248969	6249098	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249099	6249318	1	-	1	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249099	6249318	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6249319	6249409	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249410	6249579	0.45	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249410	6249579	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6249580	6249671	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249672	6249792	0.4	-	1	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249672	6249792	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6249793	6249984	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6249985	6250118	0.46	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6249985	6250118	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6250119	6250283	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6250284	6250409	0.98	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6250284	6250409	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6250410	6250575	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6250576	6250903	0.98	-	1	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6250576	6250903	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6250904	6251125	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6251126	6251309	1	-	2	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6251126	6251309	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6251310	6251517	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6251518	6251616	0.96	-	2	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6251518	6251616	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6251617	6251864	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6251865	6251914	0.93	-	1	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6251865	6251914	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	intron	6251915	6252001	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	CDS	6252002	6252069	1	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	exon	6252002	6252069	.	-	.	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
Phchi.S4	AUGUSTUS	start_codon	6252067	6252069	.	-	0	transcript_id "Phchi.S4G099700.t2"; gene_id "Phchi.S4G099700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12560.t1 is derived from g8237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34760238	34765232	.	-	.	Phchi.S2G064000
Phchi.S2	AUGUSTUS	transcript	34760238	34765232	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	stop_codon	34760235	34760237	.	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34760238	34760786	0.94	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34760238	34760786	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34760787	34760880	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34760881	34760979	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34760881	34760979	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34760980	34761066	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34761067	34761480	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34761067	34761480	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34761481	34761662	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34761663	34762094	0.96	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34761663	34762094	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762095	34762187	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34762188	34762406	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34762188	34762406	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762407	34762675	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34762676	34762966	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34762676	34762966	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762967	34763091	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763092	34763271	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763092	34763271	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763272	34763405	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763406	34763547	1	-	1	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763406	34763547	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763548	34763912	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763913	34763968	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763913	34763968	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763969	34764052	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764053	34764163	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764053	34764163	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34764164	34764299	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764300	34764554	1	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764300	34764554	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34764555	34764875	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764876	34765232	0.64	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764876	34765232	.	-	.	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	start_codon	34765230	34765232	.	-	0	transcript_id "Phchi.S2G064000.t1"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	transcript	34760238	34765232	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	stop_codon	34760235	34760237	.	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34760238	34760786	0.97	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34760238	34760786	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34760787	34760880	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34760881	34760979	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34760881	34760979	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34760980	34761066	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34761067	34761480	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34761067	34761480	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34761481	34761662	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34761663	34762094	0.91	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34761663	34762094	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762095	34762187	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34762188	34762406	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34762188	34762406	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762407	34762675	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34762676	34762966	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34762676	34762966	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762967	34763091	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763092	34763271	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763092	34763271	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763272	34763405	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763406	34763547	1	-	1	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763406	34763547	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763548	34763912	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763913	34763968	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763913	34763968	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763969	34764061	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764062	34764163	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764062	34764163	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34764164	34764299	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764300	34764560	1	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764300	34764560	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34764561	34764875	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764876	34765232	0.66	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764876	34765232	.	-	.	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	start_codon	34765230	34765232	.	-	0	transcript_id "Phchi.S2G064000.t2"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	transcript	34760238	34765232	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	stop_codon	34760235	34760237	.	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34760238	34760786	0.94	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34760238	34760786	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34760787	34760880	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34760881	34760979	1	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34760881	34760979	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34760980	34761066	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34761067	34761480	0.99	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34761067	34761480	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34761481	34761662	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34761663	34762094	0.9	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34761663	34762094	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762095	34762187	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34762188	34762406	1	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34762188	34762406	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762407	34762675	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34762676	34762966	1	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34762676	34762966	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34762967	34763091	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763092	34763271	1	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763092	34763271	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763272	34763405	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763406	34763547	1	-	1	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763406	34763547	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763548	34763912	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34763913	34763968	1	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34763913	34763968	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34763969	34764061	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764062	34764163	0.99	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764062	34764163	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34764164	34764299	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764300	34764554	1	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764300	34764554	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	intron	34764555	34764875	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	CDS	34764876	34765232	0.73	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	exon	34764876	34765232	.	-	.	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
Phchi.S2	AUGUSTUS	start_codon	34765230	34765232	.	-	0	transcript_id "Phchi.S2G064000.t3"; gene_id "Phchi.S2G064000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11872.t1 is derived from g15924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8938657	8940094	.	-	.	Phchi.S4G145400
Phchi.S4	AUGUSTUS	transcript	8938657	8940094	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	stop_codon	8938654	8938656	.	-	0	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	CDS	8938657	8938801	1	-	1	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	exon	8938657	8938801	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	intron	8938802	8938911	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	CDS	8938912	8939101	0.87	-	2	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	exon	8938912	8939101	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	intron	8939102	8939198	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	CDS	8939199	8939361	1	-	0	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	exon	8939199	8939361	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	intron	8939362	8939443	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	CDS	8939444	8939635	1	-	0	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	exon	8939444	8939635	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	intron	8939636	8939729	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	CDS	8939730	8939902	1	-	2	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	exon	8939730	8939902	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	intron	8939903	8939973	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	CDS	8939974	8940094	1	-	0	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	exon	8939974	8940094	.	-	.	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
Phchi.S4	AUGUSTUS	start_codon	8940092	8940094	.	-	0	transcript_id "Phchi.S4G145400.t1"; gene_id "Phchi.S4G145400"
# This transcript jg1515.t2 is derived from g8434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1515.t3 is derived from g8434.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1516.t1 is derived from g8435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1503208	1504594	.	-	.	Phchi.S5G012500
Phchi.S5	AUGUSTUS	transcript	1503208	1504594	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	stop_codon	1503205	1503207	.	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1503208	1503278	1	-	2	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1503208	1503278	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	intron	1503279	1503354	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1503355	1503412	1	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1503355	1503412	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	intron	1503413	1503490	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1503491	1503527	1	-	1	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1503491	1503527	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	intron	1503528	1503650	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1503651	1503841	1	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1503651	1503841	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	intron	1503842	1503932	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1503933	1504043	1	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1503933	1504043	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	intron	1504044	1504160	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1504161	1504214	1	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1504161	1504214	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	intron	1504215	1504465	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	CDS	1504466	1504594	0.75	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	exon	1504466	1504594	.	-	.	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
Phchi.S5	AUGUSTUS	start_codon	1504592	1504594	.	-	0	transcript_id "Phchi.S5G012500.t1"; gene_id "Phchi.S5G012500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12672.t1 is derived from g14406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	7196	8768	.	-	.	Phchi.C62G000300
Phchi.C62	AUGUSTUS	transcript	7196	8768	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	stop_codon	7193	7195	.	-	0	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	CDS	7196	7407	1	-	2	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	exon	7196	7407	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	intron	7408	7494	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	CDS	7495	7759	1	-	0	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	exon	7495	7759	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	intron	7760	7829	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	CDS	7830	8066	0.7	-	0	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	exon	7830	8066	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	intron	8067	8196	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	CDS	8197	8225	0.82	-	2	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	exon	8197	8225	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	intron	8226	8399	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	CDS	8400	8526	1	-	0	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	exon	8400	8526	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	intron	8527	8609	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	CDS	8610	8768	1	-	0	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	exon	8610	8768	.	-	.	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
Phchi.C62	AUGUSTUS	start_codon	8766	8768	.	-	0	transcript_id "Phchi.C62G000300.t1"; gene_id "Phchi.C62G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6613.t1 is derived from g3785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24006534	24008512	.	+	.	Phchi.S1G377200
Phchi.S1	AUGUSTUS	transcript	24006534	24008512	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	start_codon	24006534	24006536	.	+	0	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24006534	24006766	0.91	+	0	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24006534	24006766	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24006767	24006858	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24006859	24006998	1	+	1	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24006859	24006998	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24006999	24007116	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24007117	24007152	0.96	+	2	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24007117	24007152	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24007153	24007268	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24007269	24007364	1	+	2	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24007269	24007364	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24007365	24007484	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24007485	24007564	1	+	2	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24007485	24007564	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24007565	24007649	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24007650	24007736	1	+	0	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24007650	24007736	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24007737	24007847	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24007848	24007880	1	+	0	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24007848	24007880	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24007881	24007970	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24007971	24008127	1	+	0	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24007971	24008127	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24008128	24008229	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24008230	24008287	1	+	2	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24008230	24008287	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	intron	24008288	24008373	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	CDS	24008374	24008512	1	+	1	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	exon	24008374	24008512	.	+	.	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
Phchi.S1	AUGUSTUS	stop_codon	24008513	24008515	.	+	0	transcript_id "Phchi.S1G377200.t1"; gene_id "Phchi.S1G377200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1658.t1 is derived from g8577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2268406	2270426	.	-	.	Phchi.S5G026700
Phchi.S5	AUGUSTUS	transcript	2268406	2270426	.	-	.	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	stop_codon	2268403	2268405	.	-	0	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	CDS	2268406	2269014	0.51	-	0	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	exon	2268406	2269014	.	-	.	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	intron	2269015	2269205	.	-	.	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	CDS	2269206	2270426	0.59	-	0	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	exon	2269206	2270426	.	-	.	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
Phchi.S5	AUGUSTUS	start_codon	2270424	2270426	.	-	0	transcript_id "Phchi.S5G026700.t1"; gene_id "Phchi.S5G026700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14057.t1 is derived from g12524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10534950	10538788	.	-	.	Phchi.S3G137600
Phchi.S3	AUGUSTUS	transcript	10534950	10538788	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	stop_codon	10534947	10534949	.	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10534950	10535005	0.85	-	2	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10534950	10535005	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10535006	10535124	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10535125	10535827	0.72	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10535125	10535827	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10535828	10535970	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10535971	10536078	0.99	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10535971	10536078	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10536079	10536167	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10536168	10536265	0.89	-	2	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10536168	10536265	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10536266	10536348	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10536349	10536499	0.85	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10536349	10536499	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10536500	10536589	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10536590	10536732	0.45	-	2	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10536590	10536732	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10536733	10536834	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10536835	10537271	0.23	-	1	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10536835	10537271	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10537272	10537370	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10537371	10537546	1	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10537371	10537546	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10537547	10537654	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10537655	10537720	0.93	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10537655	10537720	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10537721	10537801	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10537802	10538106	0.82	-	2	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10537802	10538106	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10538107	10538197	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10538198	10538444	0.63	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10538198	10538444	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	intron	10538445	10538602	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	CDS	10538603	10538788	0.63	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	exon	10538603	10538788	.	-	.	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
Phchi.S3	AUGUSTUS	start_codon	10538786	10538788	.	-	0	transcript_id "Phchi.S3G137600.t1"; gene_id "Phchi.S3G137600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9532.t1 is derived from g6708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42333295	42334435	.	-	.	Phchi.S1G669100
Phchi.S1	AUGUSTUS	transcript	42333295	42334435	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	stop_codon	42333292	42333294	.	-	0	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	CDS	42333295	42333328	1	-	1	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	exon	42333295	42333328	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	intron	42333329	42333456	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	CDS	42333457	42333520	1	-	2	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	exon	42333457	42333520	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	intron	42333521	42333608	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	CDS	42333609	42333682	1	-	1	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	exon	42333609	42333682	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	intron	42333683	42333779	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	CDS	42333780	42333895	1	-	0	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	exon	42333780	42333895	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	intron	42333896	42333978	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	CDS	42333979	42334244	0.92	-	2	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	exon	42333979	42334244	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	intron	42334245	42334344	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	CDS	42334345	42334435	0.7	-	0	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	exon	42334345	42334435	.	-	.	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
Phchi.S1	AUGUSTUS	start_codon	42334433	42334435	.	-	0	transcript_id "Phchi.S1G669100.t1"; gene_id "Phchi.S1G669100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2258.t1 is derived from g9178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5713107	5715512	.	+	.	Phchi.S5G086700
Phchi.S5	AUGUSTUS	transcript	5713107	5715512	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	start_codon	5713107	5713109	.	+	0	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	CDS	5713107	5713160	0.99	+	0	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	exon	5713107	5713160	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	intron	5713161	5713259	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	CDS	5713260	5713382	1	+	0	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	exon	5713260	5713382	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	intron	5713383	5713463	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	CDS	5713464	5713798	0.96	+	0	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	exon	5713464	5713798	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	intron	5713799	5713927	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	CDS	5713928	5714854	1	+	1	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	exon	5713928	5714854	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	intron	5714855	5715367	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	CDS	5715368	5715512	0.97	+	1	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	exon	5715368	5715512	.	+	.	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
Phchi.S5	AUGUSTUS	stop_codon	5715513	5715515	.	+	0	transcript_id "Phchi.S5G086700.t1"; gene_id "Phchi.S5G086700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6684.t1 is derived from g3856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24502230	24505195	.	-	.	Phchi.S1G384300
Phchi.S1	AUGUSTUS	transcript	24502230	24505195	.	-	.	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	stop_codon	24502227	24502229	.	-	0	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	CDS	24502230	24502966	0.94	-	2	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	exon	24502230	24502966	.	-	.	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	intron	24502967	24503241	.	-	.	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	CDS	24503242	24505195	0.71	-	0	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	exon	24503242	24505195	.	-	.	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
Phchi.S1	AUGUSTUS	start_codon	24505193	24505195	.	-	0	transcript_id "Phchi.S1G384300.t1"; gene_id "Phchi.S1G384300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12184.t1 is derived from g7860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6119691	6122155	.	-	.	Phchi.S2G026400
Phchi.S2	AUGUSTUS	transcript	6119691	6122155	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	stop_codon	6119688	6119690	.	-	0	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	CDS	6119691	6119742	0.99	-	1	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	exon	6119691	6119742	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	intron	6119743	6119829	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	CDS	6119830	6120281	0.87	-	0	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	exon	6119830	6120281	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	intron	6120282	6120398	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	CDS	6120399	6120898	0.97	-	2	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	exon	6120399	6120898	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	intron	6120899	6121253	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	CDS	6121254	6121919	0.87	-	2	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	exon	6121254	6121919	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	intron	6121920	6122079	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	CDS	6122080	6122155	0.75	-	0	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	exon	6122080	6122155	.	-	.	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
Phchi.S2	AUGUSTUS	start_codon	6122153	6122155	.	-	0	transcript_id "Phchi.S2G026400.t1"; gene_id "Phchi.S2G026400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1795.t1 is derived from g8715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3064423	3065378	.	+	.	Phchi.S5G040400
Phchi.S5	AUGUSTUS	transcript	3064423	3065378	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	start_codon	3064423	3064425	.	+	0	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	CDS	3064423	3064577	0.43	+	0	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	exon	3064423	3064577	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	intron	3064578	3064681	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	CDS	3064682	3064801	0.69	+	1	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	exon	3064682	3064801	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	intron	3064802	3064899	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	CDS	3064900	3064946	0.72	+	1	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	exon	3064900	3064946	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	intron	3064947	3065085	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	CDS	3065086	3065378	0.7	+	2	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	exon	3065086	3065378	.	+	.	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
Phchi.S5	AUGUSTUS	stop_codon	3065379	3065381	.	+	0	transcript_id "Phchi.S5G040400.t1"; gene_id "Phchi.S5G040400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12178.t1 is derived from g7854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6103663	6105014	.	+	.	Phchi.S2G025800
Phchi.S2	AUGUSTUS	transcript	6103663	6105014	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	start_codon	6103663	6103665	.	+	0	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	CDS	6103663	6103799	0.36	+	0	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	exon	6103663	6103799	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	intron	6103800	6103896	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	CDS	6103897	6104132	1	+	1	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	exon	6103897	6104132	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	intron	6104133	6104226	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	CDS	6104227	6104767	1	+	2	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	exon	6104227	6104767	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	intron	6104768	6104863	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	CDS	6104864	6105014	0.98	+	1	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	exon	6104864	6105014	.	+	.	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
Phchi.S2	AUGUSTUS	stop_codon	6105015	6105017	.	+	0	transcript_id "Phchi.S2G025800.t1"; gene_id "Phchi.S2G025800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8538.t1 is derived from g5713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36539234	36541671	.	+	.	Phchi.S1G569700
Phchi.S1	AUGUSTUS	transcript	36539234	36541671	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	start_codon	36539234	36539236	.	+	0	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36539234	36539313	0.41	+	0	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36539234	36539313	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36539314	36539392	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36539393	36539397	0.98	+	1	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36539393	36539397	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36539398	36539483	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36539484	36539606	1	+	2	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36539484	36539606	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36539607	36539735	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36539736	36539836	1	+	2	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36539736	36539836	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36539837	36540006	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36540007	36540079	1	+	0	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36540007	36540079	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36540080	36540201	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36540202	36540288	1	+	2	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36540202	36540288	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36540289	36540392	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36540393	36540470	1	+	2	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36540393	36540470	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36540471	36540701	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36540702	36540771	1	+	2	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36540702	36540771	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36540772	36540860	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36540861	36541176	0.9	+	1	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36540861	36541176	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36541177	36541264	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36541265	36541387	1	+	0	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36541265	36541387	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	intron	36541388	36541479	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	CDS	36541480	36541671	1	+	0	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	exon	36541480	36541671	.	+	.	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
Phchi.S1	AUGUSTUS	stop_codon	36541672	36541674	.	+	0	transcript_id "Phchi.S1G569700.t1"; gene_id "Phchi.S1G569700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5898.t1 is derived from g3068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19645077	19647836	.	-	.	Phchi.S1G305700
Phchi.S1	AUGUSTUS	transcript	19645077	19647836	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	stop_codon	19645074	19645076	.	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645077	19645220	0.81	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645077	19645220	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645221	19645337	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645338	19645439	0.99	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645338	19645439	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645440	19645607	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645608	19645673	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645608	19645673	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645674	19645858	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645859	19645924	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645859	19645924	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645925	19646022	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646023	19646082	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646023	19646082	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646083	19646178	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646179	19646250	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646179	19646250	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646251	19646328	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646329	19646439	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646329	19646439	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646440	19646538	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646539	19646616	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646539	19646616	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646617	19646709	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646710	19646936	1	-	2	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646710	19646936	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646937	19647021	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19647022	19647103	1	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19647022	19647103	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19647104	19647389	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19647390	19647836	0.99	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19647390	19647836	.	-	.	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	start_codon	19647834	19647836	.	-	0	transcript_id "Phchi.S1G305700.t1"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	transcript	19645077	19647836	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	stop_codon	19645074	19645076	.	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645077	19645220	0.76	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645077	19645220	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645221	19645337	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645338	19645439	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645338	19645439	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645440	19645607	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645608	19645623	0.78	-	1	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645608	19645623	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645624	19645704	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645705	19645742	0.78	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645705	19645742	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645743	19645858	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19645859	19645924	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19645859	19645924	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19645925	19646022	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646023	19646082	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646023	19646082	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646083	19646178	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646179	19646250	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646179	19646250	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646251	19646328	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646329	19646439	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646329	19646439	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646440	19646538	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646539	19646616	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646539	19646616	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646617	19646709	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19646710	19646936	0.98	-	2	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19646710	19646936	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19646937	19647021	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19647022	19647103	1	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19647022	19647103	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	intron	19647104	19647389	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	CDS	19647390	19647836	0.99	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	exon	19647390	19647836	.	-	.	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
Phchi.S1	AUGUSTUS	start_codon	19647834	19647836	.	-	0	transcript_id "Phchi.S1G305700.t2"; gene_id "Phchi.S1G305700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2800.t1 is derived from g9720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8941432	8943557	.	-	.	Phchi.S5G140900
Phchi.S5	AUGUSTUS	transcript	8941432	8943557	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	stop_codon	8941429	8941431	.	-	0	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	CDS	8941432	8941460	0.87	-	2	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	exon	8941432	8941460	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	intron	8941461	8941585	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	CDS	8941586	8941702	0.85	-	2	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	exon	8941586	8941702	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	intron	8941703	8941921	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	CDS	8941922	8942516	0.6	-	0	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	exon	8941922	8942516	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	intron	8942517	8942888	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	CDS	8942889	8943557	0.51	-	0	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	exon	8942889	8943557	.	-	.	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
Phchi.S5	AUGUSTUS	start_codon	8943555	8943557	.	-	0	transcript_id "Phchi.S5G140900.t1"; gene_id "Phchi.S5G140900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3851.t1 is derived from g1020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6033609	6035033	.	+	.	Phchi.S1G101000
Phchi.S1	AUGUSTUS	transcript	6033609	6035033	.	+	.	transcript_id "Phchi.S1G101000.t1"; gene_id "Phchi.S1G101000"
Phchi.S1	AUGUSTUS	start_codon	6033609	6033611	.	+	0	transcript_id "Phchi.S1G101000.t1"; gene_id "Phchi.S1G101000"
Phchi.S1	AUGUSTUS	CDS	6033609	6035033	0.61	+	0	transcript_id "Phchi.S1G101000.t1"; gene_id "Phchi.S1G101000"
Phchi.S1	AUGUSTUS	exon	6033609	6035033	.	+	.	transcript_id "Phchi.S1G101000.t1"; gene_id "Phchi.S1G101000"
Phchi.S1	AUGUSTUS	stop_codon	6035034	6035036	.	+	0	transcript_id "Phchi.S1G101000.t1"; gene_id "Phchi.S1G101000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5586.t1 is derived from g2756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17753418	17754173	.	-	.	Phchi.S1G274500
Phchi.S1	AUGUSTUS	transcript	17753418	17754173	.	-	.	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	stop_codon	17753415	17753417	.	-	0	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	CDS	17753418	17753737	0.98	-	2	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	exon	17753418	17753737	.	-	.	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	intron	17753738	17753824	.	-	.	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	CDS	17753825	17754173	0.49	-	0	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	exon	17753825	17754173	.	-	.	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
Phchi.S1	AUGUSTUS	start_codon	17754171	17754173	.	-	0	transcript_id "Phchi.S1G274500.t1"; gene_id "Phchi.S1G274500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13963.t1 is derived from g12430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9943385	9945118	.	+	.	Phchi.S3G128200
Phchi.S3	AUGUSTUS	transcript	9943385	9945118	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	start_codon	9943385	9943387	.	+	0	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	CDS	9943385	9943456	0.64	+	0	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	exon	9943385	9943456	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	intron	9943457	9943685	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	CDS	9943686	9943949	0.69	+	0	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	exon	9943686	9943949	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	intron	9943950	9944022	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	CDS	9944023	9944060	0.39	+	0	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	exon	9944023	9944060	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	intron	9944061	9944214	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	CDS	9944215	9944322	0.65	+	1	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	exon	9944215	9944322	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	intron	9944323	9944417	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	CDS	9944418	9944745	1	+	1	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	exon	9944418	9944745	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	intron	9944746	9944833	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	CDS	9944834	9945118	1	+	0	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	exon	9944834	9945118	.	+	.	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
Phchi.S3	AUGUSTUS	stop_codon	9945119	9945121	.	+	0	transcript_id "Phchi.S3G128200.t1"; gene_id "Phchi.S3G128200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14704.t1 is derived from g13172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14260835	14262770	.	+	.	Phchi.S3G202300
Phchi.S3	AUGUSTUS	transcript	14260835	14262770	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	start_codon	14260835	14260837	.	+	0	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14260835	14260863	0.97	+	0	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14260835	14260863	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14260864	14261500	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14261501	14261619	1	+	1	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14261501	14261619	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14261620	14261952	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14261953	14262132	1	+	2	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14261953	14262132	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14262133	14262337	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14262338	14262575	1	+	2	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14262338	14262575	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14262576	14262718	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14262719	14262770	1	+	1	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14262719	14262770	.	+	.	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	stop_codon	14262771	14262773	.	+	0	transcript_id "Phchi.S3G202300.t1"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	transcript	14260835	14262729	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	start_codon	14260835	14260837	.	+	0	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14260835	14260863	0.97	+	0	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14260835	14260863	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14260864	14261500	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14261501	14261619	1	+	1	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14261501	14261619	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14261620	14261952	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14261953	14262132	0.6	+	2	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14261953	14262132	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14262133	14262203	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14262204	14262239	0.48	+	2	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14262204	14262239	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14262240	14262337	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14262338	14262493	1	+	2	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14262338	14262493	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	intron	14262494	14262718	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	CDS	14262719	14262729	0.99	+	2	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	exon	14262719	14262729	.	+	.	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
Phchi.S3	AUGUSTUS	stop_codon	14262730	14262732	.	+	0	transcript_id "Phchi.S3G202300.t2"; gene_id "Phchi.S3G202300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13407.t1 is derived from g11873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6553722	6554759	.	+	.	Phchi.S3G072600
Phchi.S3	AUGUSTUS	transcript	6553722	6554759	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	start_codon	6553722	6553724	.	+	0	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	CDS	6553722	6553909	0.99	+	0	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	exon	6553722	6553909	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	intron	6553910	6553994	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	CDS	6553995	6554155	1	+	1	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	exon	6553995	6554155	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	intron	6554156	6554224	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	CDS	6554225	6554371	1	+	2	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	exon	6554225	6554371	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	intron	6554372	6554512	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	CDS	6554513	6554589	1	+	2	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	exon	6554513	6554589	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	intron	6554590	6554675	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	CDS	6554676	6554759	0.99	+	0	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	exon	6554676	6554759	.	+	.	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
Phchi.S3	AUGUSTUS	stop_codon	6554760	6554762	.	+	0	transcript_id "Phchi.S3G072600.t1"; gene_id "Phchi.S3G072600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12122.t1 is derived from g7798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3858835	3860015	.	+	.	Phchi.S2G020200
Phchi.S2	AUGUSTUS	transcript	3858835	3860015	.	+	.	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	start_codon	3858835	3858837	.	+	0	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	CDS	3858835	3859068	0.53	+	0	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	exon	3858835	3859068	.	+	.	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	intron	3859069	3859176	.	+	.	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	CDS	3859177	3859275	0.51	+	0	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	exon	3859177	3859275	.	+	.	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	intron	3859276	3859355	.	+	.	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	CDS	3859356	3860015	0.3	+	0	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	exon	3859356	3860015	.	+	.	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
Phchi.S2	AUGUSTUS	stop_codon	3860016	3860018	.	+	0	transcript_id "Phchi.S2G020200.t1"; gene_id "Phchi.S2G020200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14682.t1 is derived from g13150.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14147144	14151179	.	-	.	Phchi.S3G200100
Phchi.S3	AUGUSTUS	transcript	14147144	14151179	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	stop_codon	14147141	14147143	.	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14147144	14147237	1	-	1	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14147144	14147237	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14147238	14147442	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14147443	14147552	1	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14147443	14147552	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14147553	14148376	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14148377	14148547	1	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14148377	14148547	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14148548	14148676	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14148677	14148773	1	-	1	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14148677	14148773	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14148774	14148853	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14148854	14148984	1	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14148854	14148984	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14148985	14149090	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14149091	14149194	0.93	-	2	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14149091	14149194	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14149195	14149663	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14149664	14149735	0.88	-	2	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14149664	14149735	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14149736	14150241	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14150242	14150695	0.92	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14150242	14150695	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14150696	14150981	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14150982	14151179	0.45	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14150982	14151179	.	-	.	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	start_codon	14151177	14151179	.	-	0	transcript_id "Phchi.S3G200100.t1"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	transcript	14147144	14151179	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	stop_codon	14147141	14147143	.	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14147144	14147237	1	-	1	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14147144	14147237	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14147238	14147442	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14147443	14147552	1	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14147443	14147552	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14147553	14148376	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14148377	14148541	0.7	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14148377	14148541	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14148542	14148676	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14148677	14148773	1	-	1	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14148677	14148773	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14148774	14148853	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14148854	14148984	1	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14148854	14148984	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14148985	14149090	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14149091	14149194	1	-	2	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14149091	14149194	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14149195	14150241	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14150242	14150695	1	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14150242	14150695	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	intron	14150696	14150981	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	CDS	14150982	14151179	0.44	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	exon	14150982	14151179	.	-	.	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
Phchi.S3	AUGUSTUS	start_codon	14151177	14151179	.	-	0	transcript_id "Phchi.S3G200100.t2"; gene_id "Phchi.S3G200100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg34.t1 is derived from g9788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C48	AUGUSTUS	gene	45829	46509	.	-	.	Phchi.C48G000100
Phchi.C48	AUGUSTUS	transcript	45829	46509	.	-	.	transcript_id "Phchi.C48G000100.t1"; gene_id "Phchi.C48G000100"
Phchi.C48	AUGUSTUS	stop_codon	45826	45828	.	-	0	transcript_id "Phchi.C48G000100.t1"; gene_id "Phchi.C48G000100"
Phchi.C48	AUGUSTUS	CDS	45829	46509	0.56	-	0	transcript_id "Phchi.C48G000100.t1"; gene_id "Phchi.C48G000100"
Phchi.C48	AUGUSTUS	exon	45829	46509	.	-	.	transcript_id "Phchi.C48G000100.t1"; gene_id "Phchi.C48G000100"
Phchi.C48	AUGUSTUS	start_codon	46507	46509	.	-	0	transcript_id "Phchi.C48G000100.t1"; gene_id "Phchi.C48G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15300.t1 is derived from g13768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18288424	18288912	.	-	.	Phchi.S3G261900
Phchi.S3	AUGUSTUS	transcript	18288424	18288912	.	-	.	transcript_id "Phchi.S3G261900.t1"; gene_id "Phchi.S3G261900"
Phchi.S3	AUGUSTUS	stop_codon	18288421	18288423	.	-	0	transcript_id "Phchi.S3G261900.t1"; gene_id "Phchi.S3G261900"
Phchi.S3	AUGUSTUS	CDS	18288424	18288912	0.9	-	0	transcript_id "Phchi.S3G261900.t1"; gene_id "Phchi.S3G261900"
Phchi.S3	AUGUSTUS	exon	18288424	18288912	.	-	.	transcript_id "Phchi.S3G261900.t1"; gene_id "Phchi.S3G261900"
Phchi.S3	AUGUSTUS	start_codon	18288910	18288912	.	-	0	transcript_id "Phchi.S3G261900.t1"; gene_id "Phchi.S3G261900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1665.t1 is derived from g8584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2295688	2296203	.	+	.	Phchi.S5G027400
Phchi.S5	AUGUSTUS	transcript	2295688	2296203	.	+	.	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	start_codon	2295688	2295690	.	+	0	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	CDS	2295688	2295786	0.84	+	0	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	exon	2295688	2295786	.	+	.	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	intron	2295787	2295874	.	+	.	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	CDS	2295875	2295972	1	+	0	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	exon	2295875	2295972	.	+	.	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	intron	2295973	2296043	.	+	.	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	CDS	2296044	2296203	0.82	+	1	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	exon	2296044	2296203	.	+	.	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
Phchi.S5	AUGUSTUS	stop_codon	2296204	2296206	.	+	0	transcript_id "Phchi.S5G027400.t1"; gene_id "Phchi.S5G027400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8758.t1 is derived from g5933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37839033	37839486	.	-	.	Phchi.S1G591700
Phchi.S1	AUGUSTUS	transcript	37839033	37839486	.	-	.	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	stop_codon	37839030	37839032	.	-	0	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	CDS	37839033	37839067	0.85	-	2	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	exon	37839033	37839067	.	-	.	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	intron	37839068	37839152	.	-	.	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	CDS	37839153	37839213	0.81	-	0	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	exon	37839153	37839213	.	-	.	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	intron	37839214	37839321	.	-	.	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	CDS	37839322	37839486	0.34	-	0	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	exon	37839322	37839486	.	-	.	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
Phchi.S1	AUGUSTUS	start_codon	37839484	37839486	.	-	0	transcript_id "Phchi.S1G591700.t1"; gene_id "Phchi.S1G591700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg70.t1 is derived from g9852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	349998	351608	.	+	.	Phchi.S6G002900
Phchi.S6	AUGUSTUS	transcript	349998	351608	.	+	.	transcript_id "Phchi.S6G002900.t1"; gene_id "Phchi.S6G002900"
Phchi.S6	AUGUSTUS	start_codon	349998	350000	.	+	0	transcript_id "Phchi.S6G002900.t1"; gene_id "Phchi.S6G002900"
Phchi.S6	AUGUSTUS	CDS	349998	351608	0.94	+	0	transcript_id "Phchi.S6G002900.t1"; gene_id "Phchi.S6G002900"
Phchi.S6	AUGUSTUS	exon	349998	351608	.	+	.	transcript_id "Phchi.S6G002900.t1"; gene_id "Phchi.S6G002900"
Phchi.S6	AUGUSTUS	stop_codon	351609	351611	.	+	0	transcript_id "Phchi.S6G002900.t1"; gene_id "Phchi.S6G002900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8296.t1 is derived from g5471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35138904	35139298	.	+	.	Phchi.S1G545500
Phchi.S1	AUGUSTUS	transcript	35138904	35139298	.	+	.	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	start_codon	35138904	35138906	.	+	0	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	CDS	35138904	35138948	0.89	+	0	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	exon	35138904	35138948	.	+	.	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	intron	35138949	35139112	.	+	.	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	CDS	35139113	35139298	0.91	+	0	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	exon	35139113	35139298	.	+	.	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
Phchi.S1	AUGUSTUS	stop_codon	35139299	35139301	.	+	0	transcript_id "Phchi.S1G545500.t1"; gene_id "Phchi.S1G545500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8177.t1 is derived from g5352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34293857	34294822	.	+	.	Phchi.S1G533600
Phchi.S1	AUGUSTUS	transcript	34293857	34294822	.	+	.	transcript_id "Phchi.S1G533600.t1"; gene_id "Phchi.S1G533600"
Phchi.S1	AUGUSTUS	start_codon	34293857	34293859	.	+	0	transcript_id "Phchi.S1G533600.t1"; gene_id "Phchi.S1G533600"
Phchi.S1	AUGUSTUS	CDS	34293857	34294822	0.96	+	0	transcript_id "Phchi.S1G533600.t1"; gene_id "Phchi.S1G533600"
Phchi.S1	AUGUSTUS	exon	34293857	34294822	.	+	.	transcript_id "Phchi.S1G533600.t1"; gene_id "Phchi.S1G533600"
Phchi.S1	AUGUSTUS	stop_codon	34294823	34294825	.	+	0	transcript_id "Phchi.S1G533600.t1"; gene_id "Phchi.S1G533600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8254.t1 is derived from g5429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34718511	34723525	.	-	.	Phchi.S1G541300
Phchi.S1	AUGUSTUS	transcript	34718511	34723525	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	stop_codon	34718508	34718510	.	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34718511	34718771	0.48	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34718511	34718771	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34718772	34718857	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34718858	34718956	1	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34718858	34718956	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34718957	34719046	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34719047	34719115	1	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34719047	34719115	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34719116	34719199	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34719200	34719274	1	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34719200	34719274	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34719275	34719368	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34719369	34719437	1	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34719369	34719437	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34719438	34719527	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34719528	34719618	1	-	1	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34719528	34719618	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34719619	34719759	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34719760	34719797	0.62	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34719760	34719797	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34719798	34719900	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34719901	34720128	0.83	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34719901	34720128	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34720129	34720239	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34720240	34720344	0.81	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34720240	34720344	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34720345	34720586	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34720587	34720964	0.84	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34720587	34720964	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34720965	34721089	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34721090	34721159	0.67	-	1	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34721090	34721159	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34721160	34721293	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34721294	34721460	0.99	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34721294	34721460	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34721461	34721579	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34721580	34721686	0.67	-	2	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34721580	34721686	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34721687	34721797	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34721798	34721899	0.71	-	2	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34721798	34721899	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34721900	34721998	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34721999	34722084	1	-	1	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34721999	34722084	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34722085	34722211	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34722212	34722305	0.49	-	2	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34722212	34722305	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34722306	34722398	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34722399	34722492	0.27	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34722399	34722492	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34722493	34722573	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34722574	34722748	1	-	1	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34722574	34722748	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	intron	34722749	34722935	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	CDS	34722936	34723525	0.57	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	exon	34722936	34723525	.	-	.	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
Phchi.S1	AUGUSTUS	start_codon	34723523	34723525	.	-	0	transcript_id "Phchi.S1G541300.t1"; gene_id "Phchi.S1G541300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg252.t1 is derived from g10034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1717911	1720711	.	+	.	Phchi.S6G021100
Phchi.S6	AUGUSTUS	transcript	1717911	1720711	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	start_codon	1717911	1717913	.	+	0	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1717911	1718006	1	+	0	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1717911	1718006	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1718007	1718135	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1718136	1718439	1	+	0	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1718136	1718439	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1718440	1718578	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1718579	1718751	1	+	2	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1718579	1718751	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1718752	1718830	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1718831	1718928	1	+	0	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1718831	1718928	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1718929	1719008	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1719009	1719146	1	+	1	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1719009	1719146	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1719147	1719240	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1719241	1719430	1	+	1	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1719241	1719430	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1719431	1719514	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1719515	1719638	1	+	0	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1719515	1719638	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	intron	1719639	1719722	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	CDS	1719723	1720711	0.98	+	2	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	exon	1719723	1720711	.	+	.	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
Phchi.S6	AUGUSTUS	stop_codon	1720712	1720714	.	+	0	transcript_id "Phchi.S6G021100.t1"; gene_id "Phchi.S6G021100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4195.t1 is derived from g1364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8868039	8868943	.	+	.	Phchi.S1G135400
Phchi.S1	AUGUSTUS	transcript	8868039	8868943	.	+	.	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	start_codon	8868039	8868041	.	+	0	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	CDS	8868039	8868369	0.99	+	0	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	exon	8868039	8868369	.	+	.	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	intron	8868370	8868494	.	+	.	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	CDS	8868495	8868943	0.98	+	2	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	exon	8868495	8868943	.	+	.	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
Phchi.S1	AUGUSTUS	stop_codon	8868944	8868946	.	+	0	transcript_id "Phchi.S1G135400.t1"; gene_id "Phchi.S1G135400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1862.t1 is derived from g8782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3580649	3582783	.	-	.	Phchi.S5G047100
Phchi.S5	AUGUSTUS	transcript	3580649	3582783	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	stop_codon	3580646	3580648	.	-	0	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	CDS	3580649	3580742	0.99	-	1	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	exon	3580649	3580742	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	intron	3580743	3580860	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	CDS	3580861	3581180	0.97	-	0	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	exon	3580861	3581180	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	intron	3581181	3581274	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	CDS	3581275	3581406	1	-	0	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	exon	3581275	3581406	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	intron	3581407	3581559	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	CDS	3581560	3581868	1	-	0	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	exon	3581560	3581868	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	intron	3581869	3581955	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	CDS	3581956	3582783	1	-	0	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	exon	3581956	3582783	.	-	.	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
Phchi.S5	AUGUSTUS	start_codon	3582781	3582783	.	-	0	transcript_id "Phchi.S5G047100.t1"; gene_id "Phchi.S5G047100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15673.t1 is derived from g14142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20602889	20605846	.	+	.	Phchi.S3G299200
Phchi.S3	AUGUSTUS	transcript	20602889	20605846	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	start_codon	20602889	20602891	.	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20602889	20603054	0.92	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20602889	20603054	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20603055	20603208	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20603209	20603297	1	+	2	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20603209	20603297	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20603298	20603442	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20603443	20603549	1	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20603443	20603549	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20603550	20603772	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20603773	20603808	1	+	1	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20603773	20603808	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20603809	20603912	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20603913	20603998	1	+	1	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20603913	20603998	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20603999	20604146	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20604147	20604211	1	+	2	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20604147	20604211	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20604212	20604317	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20604318	20604425	0.94	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20604318	20604425	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20604426	20604534	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20604535	20604669	0.86	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20604535	20604669	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20604670	20604747	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20604748	20604891	1	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20604748	20604891	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20604892	20605028	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20605029	20605137	1	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20605029	20605137	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20605138	20605303	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20605304	20605364	1	+	2	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20605304	20605364	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20605365	20605442	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20605443	20605518	0.93	+	1	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20605443	20605518	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20605519	20605619	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20605620	20605655	1	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20605620	20605655	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	intron	20605656	20605756	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	CDS	20605757	20605846	1	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	exon	20605757	20605846	.	+	.	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
Phchi.S3	AUGUSTUS	stop_codon	20605847	20605849	.	+	0	transcript_id "Phchi.S3G299200.t1"; gene_id "Phchi.S3G299200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3225.t1 is derived from g394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2352995	2353368	.	-	.	Phchi.S1G038400
Phchi.S1	AUGUSTUS	transcript	2352995	2353368	.	-	.	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	stop_codon	2352901	2352903	.	-	0	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	CDS	2352995	2353059	0.7	-	2	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	exon	2352995	2353059	.	-	.	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	intron	2353060	2353139	.	-	.	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	CDS	2353140	2353281	0.63	-	0	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	exon	2353140	2353281	.	-	.	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	intron	2353282	2353365	.	-	.	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	CDS	2353366	2353368	0.56	-	0	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	exon	2353366	2353368	.	-	.	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
Phchi.S1	AUGUSTUS	start_codon	2353366	2353368	.	-	0	transcript_id "Phchi.S1G038400.t1"; gene_id "Phchi.S1G038400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12855.t1 is derived from g11320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2747149	2749347	.	+	.	Phchi.S3G017400
Phchi.S3	AUGUSTUS	transcript	2747149	2749347	.	+	.	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	start_codon	2747149	2747151	.	+	0	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	CDS	2747149	2748355	0.38	+	0	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	exon	2747149	2748355	.	+	.	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	intron	2748356	2748516	.	+	.	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	CDS	2748517	2749214	0.41	+	2	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	exon	2748517	2749214	.	+	.	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	intron	2749215	2749320	.	+	.	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	CDS	2749321	2749347	1	+	0	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	exon	2749321	2749347	.	+	.	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
Phchi.S3	AUGUSTUS	stop_codon	2749348	2749350	.	+	0	transcript_id "Phchi.S3G017400.t1"; gene_id "Phchi.S3G017400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15270.t1 is derived from g13738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18039915	18041055	.	+	.	Phchi.S3G258900
Phchi.S3	AUGUSTUS	transcript	18039915	18041055	.	+	.	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	start_codon	18039915	18039917	.	+	0	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	CDS	18039915	18040272	0.49	+	0	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	exon	18039915	18040272	.	+	.	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	intron	18040273	18040365	.	+	.	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	CDS	18040366	18040643	1	+	2	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	exon	18040366	18040643	.	+	.	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	intron	18040644	18040743	.	+	.	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	CDS	18040744	18041055	1	+	0	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	exon	18040744	18041055	.	+	.	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
Phchi.S3	AUGUSTUS	stop_codon	18041056	18041058	.	+	0	transcript_id "Phchi.S3G258900.t1"; gene_id "Phchi.S3G258900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12683.t1 is derived from g11148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	50859	53563	.	+	.	Phchi.S3G000200
Phchi.S3	AUGUSTUS	transcript	50859	53563	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	start_codon	50859	50861	.	+	0	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	CDS	50859	50882	0.69	+	0	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	exon	50859	50882	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	intron	50883	50960	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	CDS	50961	50992	0.71	+	0	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	exon	50961	50992	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	intron	50993	51301	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	CDS	51302	51342	0.8	+	1	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	exon	51302	51342	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	intron	51343	51617	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	CDS	51618	53563	0.7	+	2	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	exon	51618	53563	.	+	.	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
Phchi.S3	AUGUSTUS	stop_codon	53564	53566	.	+	0	transcript_id "Phchi.S3G000200.t1"; gene_id "Phchi.S3G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7799.t1 is derived from g4973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31212371	31218464	.	+	.	Phchi.S1G495800
Phchi.S1	AUGUSTUS	transcript	31212371	31218464	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	start_codon	31212371	31212373	.	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31212371	31212469	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31212371	31212469	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31212470	31212556	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31212557	31212663	0.99	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31212557	31212663	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31212664	31212785	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31212786	31212914	1	+	1	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31212786	31212914	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31212915	31213029	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31213030	31213213	0.92	+	1	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31213030	31213213	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31213214	31213336	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31213337	31213625	0.91	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31213337	31213625	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31213626	31213717	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31213718	31213863	0.99	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31213718	31213863	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31213864	31213961	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31213962	31214051	0.85	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31213962	31214051	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31214052	31214179	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31214180	31214248	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31214180	31214248	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31214249	31214330	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31214331	31214450	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31214331	31214450	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31214451	31214560	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31214561	31214794	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31214561	31214794	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31214795	31214878	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31214879	31215025	0.98	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31214879	31215025	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31215026	31215134	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31215135	31215249	0.99	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31215135	31215249	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31215250	31215371	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31215372	31215556	1	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31215372	31215556	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31215557	31215649	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31215650	31215769	0.96	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31215650	31215769	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31215770	31215917	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31215918	31215981	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31215918	31215981	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31215982	31216064	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31216065	31216216	1	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31216065	31216216	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31216217	31216297	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31216298	31216391	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31216298	31216391	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31216392	31216474	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31216475	31216533	1	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31216475	31216533	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31216534	31216633	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31216634	31216741	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31216634	31216741	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31216742	31216888	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31216889	31217003	1	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31216889	31217003	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31217004	31217094	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31217095	31217216	1	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31217095	31217216	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31217217	31217300	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31217301	31217484	0.97	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31217301	31217484	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31217485	31217588	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31217589	31217717	0.97	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31217589	31217717	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31217718	31217858	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31217859	31217887	1	+	2	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31217859	31217887	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31217888	31217979	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31217980	31218140	0.99	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31217980	31218140	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	intron	31218141	31218256	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	CDS	31218257	31218464	0.99	+	1	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	exon	31218257	31218464	.	+	.	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
Phchi.S1	AUGUSTUS	stop_codon	31218465	31218467	.	+	0	transcript_id "Phchi.S1G495800.t1"; gene_id "Phchi.S1G495800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2067.t1 is derived from g8987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4676561	4682690	.	-	.	Phchi.S5G067600
Phchi.S5	AUGUSTUS	transcript	4676561	4682690	.	-	.	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	stop_codon	4676558	4676560	.	-	0	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	CDS	4676561	4682022	0.98	-	2	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	exon	4676561	4682022	.	-	.	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	intron	4682023	4682140	.	-	.	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	CDS	4682141	4682351	0.96	-	0	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	exon	4682141	4682351	.	-	.	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	intron	4682352	4682459	.	-	.	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	CDS	4682460	4682690	0.87	-	0	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	exon	4682460	4682690	.	-	.	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
Phchi.S5	AUGUSTUS	start_codon	4682688	4682690	.	-	0	transcript_id "Phchi.S5G067600.t1"; gene_id "Phchi.S5G067600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7753.t1 is derived from g4927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31096928	31097356	.	+	.	Phchi.S1G491200
Phchi.S1	AUGUSTUS	transcript	31096928	31097356	.	+	.	transcript_id "Phchi.S1G491200.t1"; gene_id "Phchi.S1G491200"
Phchi.S1	AUGUSTUS	start_codon	31096928	31096930	.	+	0	transcript_id "Phchi.S1G491200.t1"; gene_id "Phchi.S1G491200"
Phchi.S1	AUGUSTUS	CDS	31096928	31097356	0.37	+	0	transcript_id "Phchi.S1G491200.t1"; gene_id "Phchi.S1G491200"
Phchi.S1	AUGUSTUS	exon	31096928	31097356	.	+	.	transcript_id "Phchi.S1G491200.t1"; gene_id "Phchi.S1G491200"
Phchi.S1	AUGUSTUS	stop_codon	31097357	31097359	.	+	0	transcript_id "Phchi.S1G491200.t1"; gene_id "Phchi.S1G491200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5952.t1 is derived from g3123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20054945	20056294	.	+	.	Phchi.S1G311100
Phchi.S1	AUGUSTUS	transcript	20054945	20056294	.	+	.	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	start_codon	20054945	20054947	.	+	0	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	CDS	20054945	20055641	1	+	0	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	exon	20054945	20055641	.	+	.	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	intron	20055642	20055731	.	+	.	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	CDS	20055732	20056294	0.91	+	2	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	exon	20055732	20056294	.	+	.	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
Phchi.S1	AUGUSTUS	stop_codon	20056295	20056297	.	+	0	transcript_id "Phchi.S1G311100.t1"; gene_id "Phchi.S1G311100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11877.t1 is derived from g15929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8951759	8953593	.	-	.	Phchi.S4G145900
Phchi.S4	AUGUSTUS	transcript	8951759	8953593	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	stop_codon	8951756	8951758	.	-	0	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	CDS	8951759	8952051	1	-	2	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	exon	8951759	8952051	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	intron	8952052	8952167	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	CDS	8952168	8952280	0.52	-	1	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	exon	8952168	8952280	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	intron	8952281	8952489	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	CDS	8952490	8952603	0.84	-	1	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	exon	8952490	8952603	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	intron	8952604	8952738	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	CDS	8952739	8952821	1	-	0	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	exon	8952739	8952821	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	intron	8952822	8952970	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	CDS	8952971	8953142	0.96	-	1	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	exon	8952971	8953142	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	intron	8953143	8953270	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	CDS	8953271	8953593	0.89	-	0	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	exon	8953271	8953593	.	-	.	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
Phchi.S4	AUGUSTUS	start_codon	8953591	8953593	.	-	0	transcript_id "Phchi.S4G145900.t1"; gene_id "Phchi.S4G145900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5325.t1 is derived from g2495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16300056	16301104	.	+	.	Phchi.S1G248400
Phchi.S1	AUGUSTUS	transcript	16300056	16301104	.	+	.	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	start_codon	16300056	16300058	.	+	0	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	CDS	16300056	16300695	0.98	+	0	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	exon	16300056	16300695	.	+	.	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	intron	16300696	16301042	.	+	.	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	CDS	16301043	16301104	0.62	+	2	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	exon	16301043	16301104	.	+	.	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
Phchi.S1	AUGUSTUS	stop_codon	16301105	16301107	.	+	0	transcript_id "Phchi.S1G248400.t1"; gene_id "Phchi.S1G248400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15082.t1 is derived from g13550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16942308	16943906	.	+	.	Phchi.S3G240100
Phchi.S3	AUGUSTUS	transcript	16942308	16943906	.	+	.	transcript_id "Phchi.S3G240100.t1"; gene_id "Phchi.S3G240100"
Phchi.S3	AUGUSTUS	start_codon	16942308	16942310	.	+	0	transcript_id "Phchi.S3G240100.t1"; gene_id "Phchi.S3G240100"
Phchi.S3	AUGUSTUS	CDS	16942308	16943906	0.98	+	0	transcript_id "Phchi.S3G240100.t1"; gene_id "Phchi.S3G240100"
Phchi.S3	AUGUSTUS	exon	16942308	16943906	.	+	.	transcript_id "Phchi.S3G240100.t1"; gene_id "Phchi.S3G240100"
Phchi.S3	AUGUSTUS	stop_codon	16943907	16943909	.	+	0	transcript_id "Phchi.S3G240100.t1"; gene_id "Phchi.S3G240100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5071.t1 is derived from g2241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14539647	14542407	.	+	.	Phchi.S1G223000
Phchi.S1	AUGUSTUS	transcript	14539647	14542407	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	start_codon	14539647	14539649	.	+	0	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14539647	14539816	0.53	+	0	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14539647	14539816	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14539817	14539996	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14539997	14540045	0.93	+	1	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14539997	14540045	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14540046	14540138	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14540139	14540187	0.89	+	0	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14540139	14540187	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14540188	14540312	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14540313	14540387	0.96	+	2	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14540313	14540387	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14540388	14540474	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14540475	14540631	0.99	+	2	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14540475	14540631	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14540632	14540723	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14540724	14541217	1	+	1	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14540724	14541217	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14541218	14541319	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14541320	14541622	0.99	+	2	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14541320	14541622	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	intron	14541623	14541814	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	CDS	14541815	14542407	0.72	+	2	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	exon	14541815	14542407	.	+	.	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
Phchi.S1	AUGUSTUS	stop_codon	14542408	14542410	.	+	0	transcript_id "Phchi.S1G223000.t1"; gene_id "Phchi.S1G223000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6306.t1 is derived from g3478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22191567	22194316	.	+	.	Phchi.S1G346500
Phchi.S1	AUGUSTUS	transcript	22191567	22194316	.	+	.	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	start_codon	22191567	22191569	.	+	0	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	CDS	22191567	22192196	0.89	+	0	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	exon	22191567	22192196	.	+	.	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	intron	22192197	22192315	.	+	.	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	CDS	22192316	22194316	1	+	0	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	exon	22192316	22194316	.	+	.	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
Phchi.S1	AUGUSTUS	stop_codon	22194317	22194319	.	+	0	transcript_id "Phchi.S1G346500.t1"; gene_id "Phchi.S1G346500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6727.t1 is derived from g3899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24754366	24754911	.	-	.	Phchi.S1G388600
Phchi.S1	AUGUSTUS	transcript	24754366	24754911	.	-	.	transcript_id "Phchi.S1G388600.t1"; gene_id "Phchi.S1G388600"
Phchi.S1	AUGUSTUS	stop_codon	24754363	24754365	.	-	0	transcript_id "Phchi.S1G388600.t1"; gene_id "Phchi.S1G388600"
Phchi.S1	AUGUSTUS	CDS	24754366	24754911	0.58	-	0	transcript_id "Phchi.S1G388600.t1"; gene_id "Phchi.S1G388600"
Phchi.S1	AUGUSTUS	exon	24754366	24754911	.	-	.	transcript_id "Phchi.S1G388600.t1"; gene_id "Phchi.S1G388600"
Phchi.S1	AUGUSTUS	start_codon	24754909	24754911	.	-	0	transcript_id "Phchi.S1G388600.t1"; gene_id "Phchi.S1G388600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1987.t1 is derived from g8907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4289167	4291625	.	+	.	Phchi.S5G059600
Phchi.S5	AUGUSTUS	transcript	4289167	4291625	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	start_codon	4289167	4289169	.	+	0	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	CDS	4289167	4289299	0.99	+	0	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	exon	4289167	4289299	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	intron	4289300	4289392	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	CDS	4289393	4289454	1	+	2	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	exon	4289393	4289454	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	intron	4289455	4289541	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	CDS	4289542	4289696	0.95	+	0	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	exon	4289542	4289696	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	intron	4289697	4290007	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	CDS	4290008	4291625	0.73	+	1	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	exon	4290008	4291625	.	+	.	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
Phchi.S5	AUGUSTUS	stop_codon	4291626	4291628	.	+	0	transcript_id "Phchi.S5G059600.t1"; gene_id "Phchi.S5G059600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6738.t1 is derived from g3910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24799814	24801221	.	-	.	Phchi.S1G389700
Phchi.S1	AUGUSTUS	transcript	24799814	24801221	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	stop_codon	24799811	24799813	.	-	0	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	CDS	24799814	24800028	1	-	2	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	exon	24799814	24800028	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	intron	24800029	24800113	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	CDS	24800114	24800240	1	-	0	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	exon	24800114	24800240	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	intron	24800241	24800373	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	CDS	24800374	24800607	1	-	0	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	exon	24800374	24800607	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	intron	24800608	24800936	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	CDS	24800937	24801221	0.54	-	0	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	exon	24800937	24801221	.	-	.	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
Phchi.S1	AUGUSTUS	start_codon	24801219	24801221	.	-	0	transcript_id "Phchi.S1G389700.t1"; gene_id "Phchi.S1G389700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2671.t1 is derived from g9591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8135730	8136043	.	-	.	Phchi.S5G128000
Phchi.S5	AUGUSTUS	transcript	8135730	8136043	.	-	.	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	stop_codon	8135727	8135729	.	-	0	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	CDS	8135730	8135888	1	-	0	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	exon	8135730	8135888	.	-	.	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	intron	8135889	8135983	.	-	.	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	CDS	8135984	8136043	1	-	0	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	exon	8135984	8136043	.	-	.	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
Phchi.S5	AUGUSTUS	start_codon	8136041	8136043	.	-	0	transcript_id "Phchi.S5G128000.t1"; gene_id "Phchi.S5G128000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4311.t1 is derived from g1480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9572057	9572766	.	-	.	Phchi.S1G147000
Phchi.S1	AUGUSTUS	transcript	9572057	9572766	.	-	.	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	stop_codon	9572054	9572056	.	-	0	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	CDS	9572057	9572089	0.99	-	0	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	exon	9572057	9572089	.	-	.	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	intron	9572090	9572187	.	-	.	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	CDS	9572188	9572766	0.76	-	0	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	exon	9572188	9572766	.	-	.	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
Phchi.S1	AUGUSTUS	start_codon	9572764	9572766	.	-	0	transcript_id "Phchi.S1G147000.t1"; gene_id "Phchi.S1G147000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7881.t1 is derived from g5055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31742864	31743385	.	-	.	Phchi.S1G504000
Phchi.S1	AUGUSTUS	transcript	31742864	31743385	.	-	.	transcript_id "Phchi.S1G504000.t1"; gene_id "Phchi.S1G504000"
Phchi.S1	AUGUSTUS	stop_codon	31742861	31742863	.	-	0	transcript_id "Phchi.S1G504000.t1"; gene_id "Phchi.S1G504000"
Phchi.S1	AUGUSTUS	CDS	31742864	31743385	0.74	-	0	transcript_id "Phchi.S1G504000.t1"; gene_id "Phchi.S1G504000"
Phchi.S1	AUGUSTUS	exon	31742864	31743385	.	-	.	transcript_id "Phchi.S1G504000.t1"; gene_id "Phchi.S1G504000"
Phchi.S1	AUGUSTUS	start_codon	31743383	31743385	.	-	0	transcript_id "Phchi.S1G504000.t1"; gene_id "Phchi.S1G504000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10172.t1 is derived from g7348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46096910	46101332	.	-	.	Phchi.S1G733100
Phchi.S1	AUGUSTUS	transcript	46096910	46101332	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	stop_codon	46096907	46096909	.	-	0	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	CDS	46096910	46098043	0.85	-	0	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	exon	46096910	46098043	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	intron	46098044	46098160	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	CDS	46098161	46098894	0.69	-	2	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	exon	46098161	46098894	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	intron	46098895	46098992	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	CDS	46098993	46099619	0.47	-	2	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	exon	46098993	46099619	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	intron	46099620	46099774	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	CDS	46099775	46101332	0.52	-	0	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	exon	46099775	46101332	.	-	.	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
Phchi.S1	AUGUSTUS	start_codon	46101330	46101332	.	-	0	transcript_id "Phchi.S1G733100.t1"; gene_id "Phchi.S1G733100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10266.t1 is derived from g7442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46748447	46749781	.	-	.	Phchi.S1G742500
Phchi.S1	AUGUSTUS	transcript	46748447	46749781	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	stop_codon	46748444	46748446	.	-	0	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	CDS	46748447	46748616	0.54	-	2	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	exon	46748447	46748616	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	intron	46748617	46748851	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	CDS	46748852	46748896	1	-	2	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	exon	46748852	46748896	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	intron	46748897	46748977	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	CDS	46748978	46749421	0.87	-	2	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	exon	46748978	46749421	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	intron	46749422	46749543	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	CDS	46749544	46749781	0.46	-	0	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	exon	46749544	46749781	.	-	.	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
Phchi.S1	AUGUSTUS	start_codon	46749779	46749781	.	-	0	transcript_id "Phchi.S1G742500.t1"; gene_id "Phchi.S1G742500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1047.t1 is derived from g10830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7278332	7278919	.	-	.	Phchi.S6G100600
Phchi.S6	AUGUSTUS	transcript	7278332	7278919	.	-	.	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	stop_codon	7278329	7278331	.	-	0	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	CDS	7278332	7278523	1	-	0	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	exon	7278332	7278523	.	-	.	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	intron	7278524	7278649	.	-	.	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	CDS	7278650	7278919	0.95	-	0	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	exon	7278650	7278919	.	-	.	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
Phchi.S6	AUGUSTUS	start_codon	7278917	7278919	.	-	0	transcript_id "Phchi.S6G100600.t1"; gene_id "Phchi.S6G100600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12365.t1 is derived from g8041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12818877	12822445	.	-	.	Phchi.S2G044500
Phchi.S2	AUGUSTUS	transcript	12818877	12822445	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	stop_codon	12818874	12818876	.	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12818877	12818916	0.76	-	1	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12818877	12818916	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12818917	12819089	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12819090	12819097	0.76	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12819090	12819097	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12819098	12819340	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12819341	12819454	0.98	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12819341	12819454	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12819455	12819586	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12819587	12819793	1	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12819587	12819793	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12819794	12819996	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12819997	12820074	1	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12819997	12820074	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12820075	12820388	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12820389	12820892	1	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12820389	12820892	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12820893	12821021	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12821022	12821120	0.96	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12821022	12821120	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12821121	12821221	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12821222	12821366	0.92	-	1	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12821222	12821366	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12821367	12821571	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12821572	12821648	1	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12821572	12821648	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12821649	12821740	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12821741	12821841	1	-	2	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12821741	12821841	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12821842	12822065	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12822066	12822117	0.99	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12822066	12822117	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12822118	12822188	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12822189	12822222	1	-	1	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12822189	12822222	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	intron	12822223	12822320	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	CDS	12822321	12822445	1	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	exon	12822321	12822445	.	-	.	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
Phchi.S2	AUGUSTUS	start_codon	12822443	12822445	.	-	0	transcript_id "Phchi.S2G044500.t1"; gene_id "Phchi.S2G044500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13973.t1 is derived from g12440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10003275	10005653	.	+	.	Phchi.S3G129200
Phchi.S3	AUGUSTUS	transcript	10003275	10005653	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	start_codon	10003275	10003277	.	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10003275	10003906	0.63	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10003275	10003906	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10003907	10004122	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10004123	10004245	0.98	+	1	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10004123	10004245	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10004246	10004353	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10004354	10004525	0.98	+	1	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10004354	10004525	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10004526	10004622	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10004623	10004660	1	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10004623	10004660	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10004661	10004768	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10004769	10004967	1	+	1	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10004769	10004967	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10004968	10005111	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10005112	10005264	1	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10005112	10005264	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10005265	10005353	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10005354	10005488	1	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10005354	10005488	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	intron	10005489	10005587	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	CDS	10005588	10005653	1	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	exon	10005588	10005653	.	+	.	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
Phchi.S3	AUGUSTUS	stop_codon	10005654	10005656	.	+	0	transcript_id "Phchi.S3G129200.t1"; gene_id "Phchi.S3G129200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9695.t1 is derived from g6871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43313117	43313873	.	+	.	Phchi.S1G685400
Phchi.S1	AUGUSTUS	transcript	43313117	43313873	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	start_codon	43313117	43313119	.	+	0	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	CDS	43313117	43313227	0.96	+	0	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	exon	43313117	43313227	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	intron	43313228	43313316	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	CDS	43313317	43313538	1	+	0	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	exon	43313317	43313538	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	intron	43313539	43313630	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	CDS	43313631	43313741	1	+	0	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	exon	43313631	43313741	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	intron	43313742	43313828	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	CDS	43313829	43313873	0.99	+	0	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	exon	43313829	43313873	.	+	.	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
Phchi.S1	AUGUSTUS	stop_codon	43313874	43313876	.	+	0	transcript_id "Phchi.S1G685400.t1"; gene_id "Phchi.S1G685400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13703.t1 is derived from g12170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8280656	8287645	.	+	.	Phchi.S3G102200
Phchi.S3	AUGUSTUS	transcript	8280656	8287645	.	+	.	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	start_codon	8280656	8280658	.	+	0	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	CDS	8280656	8280739	0.03	+	0	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	exon	8280656	8280739	.	+	.	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	intron	8280740	8285765	.	+	.	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	CDS	8285766	8286012	1	+	0	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	exon	8285766	8286012	.	+	.	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	intron	8286013	8287568	.	+	.	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	CDS	8287569	8287645	0.74	+	2	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	exon	8287569	8287645	.	+	.	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
Phchi.S3	AUGUSTUS	stop_codon	8287646	8287648	.	+	0	transcript_id "Phchi.S3G102200.t1"; gene_id "Phchi.S3G102200"
# This transcript jg9967.t2 is derived from g7143.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg9968.t1 is derived from g7144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44699152	44701965	.	-	.	Phchi.S1G712700
Phchi.S1	AUGUSTUS	transcript	44699152	44701088	.	-	.	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	stop_codon	44699149	44699151	.	-	0	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44699152	44700341	0.97	-	2	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44699152	44700341	.	-	.	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	intron	44700342	44700460	.	-	.	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44700461	44701088	0.59	-	0	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44700461	44701088	.	-	.	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	start_codon	44701086	44701088	.	-	0	transcript_id "Phchi.S1G712700.t1"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	transcript	44699152	44701965	.	-	.	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	stop_codon	44699149	44699151	.	-	0	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44699152	44700341	0.98	-	2	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44699152	44700341	.	-	.	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	intron	44700342	44700460	.	-	.	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44700461	44701391	0.87	-	0	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44700461	44701391	.	-	.	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	intron	44701392	44701539	.	-	.	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44701540	44701965	0.37	-	0	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44701540	44701965	.	-	.	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	start_codon	44701963	44701965	.	-	0	transcript_id "Phchi.S1G712700.t2"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	transcript	44700429	44701965	.	-	.	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	stop_codon	44700426	44700428	.	-	0	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44700429	44701391	0.86	-	0	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44700429	44701391	.	-	.	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	intron	44701392	44701539	.	-	.	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44701540	44701965	0.38	-	0	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44701540	44701965	.	-	.	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	start_codon	44701963	44701965	.	-	0	transcript_id "Phchi.S1G712700.t3"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	transcript	44699152	44699664	.	-	.	transcript_id "Phchi.S1G712700.t4"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	stop_codon	44699149	44699151	.	-	0	transcript_id "Phchi.S1G712700.t4"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	CDS	44699152	44699664	0.71	-	0	transcript_id "Phchi.S1G712700.t4"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	exon	44699152	44699664	.	-	.	transcript_id "Phchi.S1G712700.t4"; gene_id "Phchi.S1G712700"
Phchi.S1	AUGUSTUS	start_codon	44699662	44699664	.	-	0	transcript_id "Phchi.S1G712700.t4"; gene_id "Phchi.S1G712700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3444.t1 is derived from g613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3754287	3755900	.	-	.	Phchi.S1G060300
Phchi.S1	AUGUSTUS	transcript	3755077	3755900	.	-	.	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	stop_codon	3755074	3755076	.	-	0	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	CDS	3755077	3755703	0.81	-	0	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	exon	3755077	3755703	.	-	.	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	intron	3755704	3755804	.	-	.	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	CDS	3755805	3755900	0.53	-	0	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	exon	3755805	3755900	.	-	.	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	start_codon	3755898	3755900	.	-	0	transcript_id "Phchi.S1G060300.t1"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	transcript	3754287	3755574	.	-	.	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	stop_codon	3754284	3754286	.	-	0	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	CDS	3754287	3754978	0.57	-	2	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	exon	3754287	3754978	.	-	.	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	intron	3754979	3755090	.	-	.	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	CDS	3755091	3755574	0.28	-	0	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	exon	3755091	3755574	.	-	.	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
Phchi.S1	AUGUSTUS	start_codon	3755572	3755574	.	-	0	transcript_id "Phchi.S1G060300.t2"; gene_id "Phchi.S1G060300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10873.t1 is derived from g14923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2693678	2695231	.	-	.	Phchi.S4G045500
Phchi.S4	AUGUSTUS	transcript	2693678	2695231	.	-	.	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	stop_codon	2693675	2693677	.	-	0	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	CDS	2693678	2694049	0.51	-	0	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	exon	2693678	2694049	.	-	.	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	intron	2694050	2694123	.	-	.	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	CDS	2694124	2694152	0.54	-	2	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	exon	2694124	2694152	.	-	.	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	intron	2694153	2694270	.	-	.	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	CDS	2694271	2695231	0.32	-	0	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	exon	2694271	2695231	.	-	.	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
Phchi.S4	AUGUSTUS	start_codon	2695229	2695231	.	-	0	transcript_id "Phchi.S4G045500.t1"; gene_id "Phchi.S4G045500"
# This transcript jg2650.t2 is derived from g9570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2650.t3 is derived from g9570.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2651.t1 is derived from g9571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8006936	8009320	.	-	.	Phchi.S5G126000
Phchi.S5	AUGUSTUS	transcript	8006936	8009320	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	stop_codon	8006933	8006935	.	-	0	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8006936	8006981	0.87	-	1	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8006936	8006981	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8006982	8007238	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007239	8007306	0.87	-	0	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007239	8007306	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007307	8007389	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007390	8007478	0.65	-	2	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007390	8007478	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007479	8007618	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007619	8007702	0.34	-	2	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007619	8007702	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007703	8007777	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007778	8007802	0.56	-	0	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007778	8007802	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007803	8008060	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8008061	8008149	0.99	-	2	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8008061	8008149	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8008150	8008305	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8008306	8009320	0.66	-	0	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8008306	8009320	.	-	.	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	start_codon	8009318	8009320	.	-	0	transcript_id "Phchi.S5G126000.t1"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	transcript	8006953	8009320	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	stop_codon	8006950	8006952	.	-	0	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8006953	8006981	1	-	2	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8006953	8006981	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8006982	8007191	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007192	8007306	0.82	-	0	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007192	8007306	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007307	8007389	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007390	8007478	0.69	-	2	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007390	8007478	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007479	8007618	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007619	8007702	0.35	-	2	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007619	8007702	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007703	8007777	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007778	8007802	0.47	-	0	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007778	8007802	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007803	8008060	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8008061	8008149	0.99	-	2	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8008061	8008149	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8008150	8008305	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8008306	8009320	0.62	-	0	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8008306	8009320	.	-	.	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	start_codon	8009318	8009320	.	-	0	transcript_id "Phchi.S5G126000.t2"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	transcript	8006953	8009320	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	stop_codon	8006950	8006952	.	-	0	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8006953	8006981	1	-	2	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8006953	8006981	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8006982	8007071	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007072	8007306	0.64	-	0	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007072	8007306	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007307	8007389	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007390	8007478	0.5	-	2	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007390	8007478	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007479	8007618	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007619	8007702	0.51	-	2	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007619	8007702	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007703	8007777	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8007778	8007802	0.59	-	0	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8007778	8007802	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8007803	8008060	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8008061	8008149	1	-	2	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8008061	8008149	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	intron	8008150	8008305	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	CDS	8008306	8009320	0.66	-	0	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	exon	8008306	8009320	.	-	.	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
Phchi.S5	AUGUSTUS	start_codon	8009318	8009320	.	-	0	transcript_id "Phchi.S5G126000.t3"; gene_id "Phchi.S5G126000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10703.t1 is derived from g14753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1676320	1677616	.	+	.	Phchi.S4G028500
Phchi.S4	AUGUSTUS	transcript	1676320	1677616	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	start_codon	1676320	1676322	.	+	0	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	CDS	1676320	1676476	1	+	0	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	exon	1676320	1676476	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	intron	1676477	1676614	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	CDS	1676615	1676679	1	+	2	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	exon	1676615	1676679	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	intron	1676680	1676903	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	CDS	1676904	1676976	1	+	0	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	exon	1676904	1676976	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	intron	1676977	1677075	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	CDS	1677076	1677129	1	+	2	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	exon	1677076	1677129	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	intron	1677130	1677222	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	CDS	1677223	1677466	0.42	+	2	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	exon	1677223	1677466	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	intron	1677467	1677567	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	CDS	1677568	1677616	0.27	+	1	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	exon	1677568	1677616	.	+	.	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
Phchi.S4	AUGUSTUS	stop_codon	1677617	1677619	.	+	0	transcript_id "Phchi.S4G028500.t1"; gene_id "Phchi.S4G028500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg959.t1 is derived from g10741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6656610	6659276	.	+	.	Phchi.S6G091800
Phchi.S6	AUGUSTUS	transcript	6656610	6659276	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	start_codon	6656610	6656612	.	+	0	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6656610	6656748	0.7	+	0	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6656610	6656748	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6656749	6656843	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6656844	6656926	1	+	2	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6656844	6656926	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6656927	6657011	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6657012	6657124	1	+	0	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6657012	6657124	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6657125	6657275	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6657276	6657303	0.85	+	1	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6657276	6657303	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6657304	6657438	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6657439	6657836	0.8	+	0	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6657439	6657836	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6657837	6658466	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6658467	6658793	0.12	+	1	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6658467	6658793	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6658794	6658969	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6658970	6659276	0.53	+	1	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6658970	6659276	.	+	.	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	stop_codon	6659277	6659279	.	+	0	transcript_id "Phchi.S6G091800.t1"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	transcript	6656610	6659276	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	start_codon	6656610	6656612	.	+	0	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6656610	6656748	0.59	+	0	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6656610	6656748	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6656749	6656843	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6656844	6656926	1	+	2	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6656844	6656926	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6656927	6657011	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6657012	6657102	0.86	+	0	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6657012	6657102	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6657103	6657275	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6657276	6657295	0.72	+	2	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6657276	6657295	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6657296	6657438	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6657439	6657836	0.83	+	0	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6657439	6657836	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6657837	6658466	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6658467	6658793	0.18	+	1	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6658467	6658793	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	intron	6658794	6658969	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	CDS	6658970	6659276	0.56	+	1	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	exon	6658970	6659276	.	+	.	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
Phchi.S6	AUGUSTUS	stop_codon	6659277	6659279	.	+	0	transcript_id "Phchi.S6G091800.t2"; gene_id "Phchi.S6G091800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12049.t1 is derived from g7724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1011744	1016087	.	-	.	Phchi.S2G012900
Phchi.S2	AUGUSTUS	transcript	1011744	1016087	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	stop_codon	1011741	1011743	.	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1011744	1011783	0.95	-	1	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1011744	1011783	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1011784	1011874	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1011875	1012083	0.95	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1011875	1012083	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1012084	1012219	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1012220	1012304	1	-	1	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1012220	1012304	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1012305	1012430	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1012431	1012573	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1012431	1012573	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1012574	1012655	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1012656	1012838	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1012656	1012838	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1012839	1012934	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1012935	1013179	1	-	2	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1012935	1013179	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1013180	1013466	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1013467	1013590	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1013467	1013590	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1013591	1013686	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1013687	1013785	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1013687	1013785	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1013786	1013973	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1013974	1014090	0.83	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1013974	1014090	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1014091	1014205	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1014206	1014283	0.77	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1014206	1014283	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1014284	1014633	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1014634	1014819	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1014634	1014819	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1014820	1015029	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1015030	1015161	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1015030	1015161	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1015162	1015442	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1015443	1015583	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1015443	1015583	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1015584	1015681	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1015682	1015816	1	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1015682	1015816	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	intron	1015817	1015952	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	CDS	1015953	1016087	0.99	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	exon	1015953	1016087	.	-	.	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
Phchi.S2	AUGUSTUS	start_codon	1016085	1016087	.	-	0	transcript_id "Phchi.S2G012900.t1"; gene_id "Phchi.S2G012900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8268.t1 is derived from g5443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35044364	35046295	.	-	.	Phchi.S1G542700
Phchi.S1	AUGUSTUS	transcript	35044364	35046295	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	stop_codon	35044361	35044363	.	-	0	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35044364	35044429	1	-	0	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35044364	35044429	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35044430	35044519	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35044520	35044643	1	-	1	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35044520	35044643	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35044644	35044754	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35044755	35044982	0.99	-	1	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35044755	35044982	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35044983	35045067	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045068	35045290	0.89	-	2	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045068	35045290	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045291	35045407	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045408	35045567	1	-	0	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045408	35045567	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045568	35045704	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045705	35045787	1	-	2	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045705	35045787	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045788	35045879	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045880	35045931	1	-	0	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045880	35045931	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045932	35046020	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35046021	35046111	1	-	1	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35046021	35046111	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35046112	35046236	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35046237	35046295	1	-	0	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35046237	35046295	.	-	.	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	start_codon	35046293	35046295	.	-	0	transcript_id "Phchi.S1G542700.t1"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	transcript	35044364	35046295	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	stop_codon	35044361	35044363	.	-	0	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35044364	35044429	1	-	0	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35044364	35044429	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35044430	35044519	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35044520	35044643	1	-	1	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35044520	35044643	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35044644	35044754	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35044755	35044982	1	-	1	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35044755	35044982	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35044983	35045067	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045068	35045290	0.95	-	2	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045068	35045290	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045291	35045407	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045408	35045473	0.55	-	2	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045408	35045473	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045474	35045596	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045597	35045618	0.99	-	0	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045597	35045618	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045619	35045704	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045705	35045787	1	-	2	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045705	35045787	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045788	35045879	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35045880	35045931	1	-	0	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35045880	35045931	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35045932	35046020	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35046021	35046111	1	-	1	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35046021	35046111	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	intron	35046112	35046236	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	CDS	35046237	35046295	1	-	0	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	exon	35046237	35046295	.	-	.	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
Phchi.S1	AUGUSTUS	start_codon	35046293	35046295	.	-	0	transcript_id "Phchi.S1G542700.t2"; gene_id "Phchi.S1G542700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1231.t1 is derived from g11014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8517093	8524229	.	-	.	Phchi.S6G119000
Phchi.S6	AUGUSTUS	transcript	8517093	8524229	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	stop_codon	8517090	8517092	.	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8517093	8517188	0.69	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8517093	8517188	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8517189	8517281	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8517282	8517289	0.69	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8517282	8517289	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8517290	8517345	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8517346	8517364	0.69	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8517346	8517364	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8517365	8517446	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8517447	8517506	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8517447	8517506	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8517507	8517590	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8517591	8517764	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8517591	8517764	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8517765	8517877	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8517878	8517970	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8517878	8517970	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8517971	8518157	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8518158	8518301	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8518158	8518301	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8518302	8518451	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8518452	8518580	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8518452	8518580	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8518581	8518721	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8518722	8518944	1	-	1	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8518722	8518944	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8518945	8519073	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8519074	8519220	1	-	1	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8519074	8519220	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8519221	8519298	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8519299	8519540	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8519299	8519540	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8519541	8519621	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8519622	8519810	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8519622	8519810	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8519811	8519894	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8519895	8520068	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8519895	8520068	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8520069	8520224	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8520225	8520326	0.99	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8520225	8520326	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8520327	8520430	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8520431	8520573	0.73	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8520431	8520573	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8520574	8520671	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8520672	8520686	0.73	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8520672	8520686	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8520687	8520837	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8520838	8521025	1	-	1	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8520838	8521025	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8521026	8521183	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8521184	8521387	1	-	1	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8521184	8521387	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8521388	8521558	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8521559	8521679	1	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8521559	8521679	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8521680	8521835	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8521836	8521931	1	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8521836	8521931	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8521932	8522080	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8522081	8522101	1	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8522081	8522101	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8522102	8522290	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8522291	8522385	0.99	-	1	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8522291	8522385	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8522386	8522492	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8522493	8522593	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8522493	8522593	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8522594	8522678	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8522679	8522744	0.99	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8522679	8522744	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8522745	8522855	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8522856	8522962	0.73	-	2	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8522856	8522962	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8522963	8523236	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8523237	8523465	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8523237	8523465	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8523466	8523653	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8523654	8523746	1	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8523654	8523746	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8523747	8523830	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8523831	8523890	0.98	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8523831	8523890	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	intron	8523891	8524001	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	CDS	8524002	8524229	0.95	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	exon	8524002	8524229	.	-	.	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
Phchi.S6	AUGUSTUS	start_codon	8524227	8524229	.	-	0	transcript_id "Phchi.S6G119000.t1"; gene_id "Phchi.S6G119000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6079.t1 is derived from g3250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20823541	20823960	.	-	.	Phchi.S1G323800
Phchi.S1	AUGUSTUS	transcript	20823541	20823960	.	-	.	transcript_id "Phchi.S1G323800.t1"; gene_id "Phchi.S1G323800"
Phchi.S1	AUGUSTUS	stop_codon	20823538	20823540	.	-	0	transcript_id "Phchi.S1G323800.t1"; gene_id "Phchi.S1G323800"
Phchi.S1	AUGUSTUS	CDS	20823541	20823960	0.5	-	0	transcript_id "Phchi.S1G323800.t1"; gene_id "Phchi.S1G323800"
Phchi.S1	AUGUSTUS	exon	20823541	20823960	.	-	.	transcript_id "Phchi.S1G323800.t1"; gene_id "Phchi.S1G323800"
Phchi.S1	AUGUSTUS	start_codon	20823958	20823960	.	-	0	transcript_id "Phchi.S1G323800.t1"; gene_id "Phchi.S1G323800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1120.t1 is derived from g10903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7792094	7794023	.	+	.	Phchi.S6G107900
Phchi.S6	AUGUSTUS	transcript	7792094	7794023	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	start_codon	7792094	7792096	.	+	0	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	CDS	7792094	7792260	0.99	+	0	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	exon	7792094	7792260	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	intron	7792261	7792423	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	CDS	7792424	7792619	1	+	1	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	exon	7792424	7792619	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	intron	7792620	7792788	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	CDS	7792789	7792855	0.85	+	0	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	exon	7792789	7792855	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	intron	7792856	7792971	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	CDS	7792972	7793340	0.4	+	2	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	exon	7792972	7793340	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	intron	7793341	7793417	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	CDS	7793418	7793465	0.6	+	2	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	exon	7793418	7793465	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	intron	7793466	7793631	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	CDS	7793632	7794023	0.67	+	2	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	exon	7793632	7794023	.	+	.	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
Phchi.S6	AUGUSTUS	stop_codon	7794024	7794026	.	+	0	transcript_id "Phchi.S6G107900.t1"; gene_id "Phchi.S6G107900"
# This transcript jg262.t2 is derived from g10044.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg263.t1 is derived from g10045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1775334	1776351	.	+	.	Phchi.S6G022200
Phchi.S6	AUGUSTUS	transcript	1775334	1776351	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	start_codon	1775334	1775336	.	+	0	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	CDS	1775334	1775437	0.6	+	0	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	exon	1775334	1775437	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	intron	1775438	1775769	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	CDS	1775770	1775869	0.51	+	1	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	exon	1775770	1775869	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	intron	1775870	1776043	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	CDS	1776044	1776101	0.38	+	0	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	exon	1776044	1776101	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	intron	1776102	1776346	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	CDS	1776347	1776351	0.54	+	2	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	exon	1776347	1776351	.	+	.	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
Phchi.S6	AUGUSTUS	stop_codon	1776352	1776354	.	+	0	transcript_id "Phchi.S6G022200.t1"; gene_id "Phchi.S6G022200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14113.t1 is derived from g12580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10901576	10902512	.	-	.	Phchi.S3G143200
Phchi.S3	AUGUSTUS	transcript	10901576	10902512	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	stop_codon	10901573	10901575	.	-	0	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10901576	10901742	0.94	-	2	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10901576	10901742	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10901743	10901842	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10901843	10901926	0.92	-	2	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10901843	10901926	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10901927	10902067	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10902068	10902149	0.89	-	0	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10902068	10902149	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10902150	10902256	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10902257	10902323	1	-	1	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10902257	10902323	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10902324	10902462	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10902463	10902512	0.86	-	0	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10902463	10902512	.	-	.	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	start_codon	10902510	10902512	.	-	0	transcript_id "Phchi.S3G143200.t1"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	transcript	10901576	10902480	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	stop_codon	10901573	10901575	.	-	0	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10901576	10901742	0.95	-	2	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10901576	10901742	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10901743	10901842	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10901843	10901926	0.89	-	2	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10901843	10901926	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10901927	10902067	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10902068	10902149	0.86	-	0	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10902068	10902149	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10902150	10902256	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10902257	10902323	0.97	-	1	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10902257	10902323	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	intron	10902324	10902457	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	CDS	10902458	10902480	0.57	-	0	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	exon	10902458	10902480	.	-	.	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
Phchi.S3	AUGUSTUS	start_codon	10902478	10902480	.	-	0	transcript_id "Phchi.S3G143200.t2"; gene_id "Phchi.S3G143200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13042.t1 is derived from g11507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3847434	3849045	.	-	.	Phchi.S3G036100
Phchi.S3	AUGUSTUS	transcript	3847434	3849045	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	stop_codon	3847431	3847433	.	-	0	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3847434	3847494	1	-	1	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3847434	3847494	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3847495	3847616	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3847617	3847703	1	-	1	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3847617	3847703	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3847704	3847781	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3847782	3847926	1	-	2	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3847782	3847926	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3847927	3848012	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3848013	3848160	1	-	0	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3848013	3848160	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3848161	3848252	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3848253	3848371	1	-	2	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3848253	3848371	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3848372	3848464	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3848465	3848533	1	-	2	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3848465	3848533	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3848534	3848616	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3848617	3848683	1	-	0	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3848617	3848683	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3848684	3848755	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3848756	3848877	0.99	-	2	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3848756	3848877	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	intron	3848878	3848984	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	CDS	3848985	3849045	0.99	-	0	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	exon	3848985	3849045	.	-	.	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
Phchi.S3	AUGUSTUS	start_codon	3849043	3849045	.	-	0	transcript_id "Phchi.S3G036100.t1"; gene_id "Phchi.S3G036100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11708.t1 is derived from g15759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7782355	7785547	.	-	.	Phchi.S4G129000
Phchi.S4	AUGUSTUS	transcript	7782355	7784596	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	stop_codon	7782352	7782354	.	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7782355	7782471	0.93	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7782355	7782471	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7782472	7782566	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7782567	7782833	1	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7782567	7782833	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7782834	7782920	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7782921	7783115	1	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7782921	7783115	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783116	7783217	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7783218	7783360	1	-	2	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7783218	7783360	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783361	7783433	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7783434	7783578	0.99	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7783434	7783578	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783579	7783681	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7783682	7783966	0.99	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7783682	7783966	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783967	7784086	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784087	7784182	0.98	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784087	7784182	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784183	7784281	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784282	7784422	1	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784282	7784422	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784423	7784536	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784537	7784596	1	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784537	7784596	.	-	.	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	start_codon	7784594	7784596	.	-	0	transcript_id "Phchi.S4G129000.t1"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	transcript	7782355	7785547	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	stop_codon	7782352	7782354	.	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7782355	7782471	0.93	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7782355	7782471	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7782472	7782566	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7782567	7782833	1	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7782567	7782833	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7782834	7782920	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7782921	7783115	0.99	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7782921	7783115	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783116	7783217	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7783218	7783360	1	-	2	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7783218	7783360	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783361	7783433	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7783434	7783578	1	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7783434	7783578	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783579	7783681	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7783682	7783966	1	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7783682	7783966	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7783967	7784086	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784087	7784182	0.94	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784087	7784182	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784183	7784281	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784282	7784422	1	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784282	7784422	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784423	7784536	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784537	7784599	0.97	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784537	7784599	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784600	7784720	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784721	7784792	1	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784721	7784792	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784793	7784894	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7784895	7784993	0.77	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7784895	7784993	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	intron	7784994	7785307	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	CDS	7785308	7785547	1	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	exon	7785308	7785547	.	-	.	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
Phchi.S4	AUGUSTUS	start_codon	7785545	7785547	.	-	0	transcript_id "Phchi.S4G129000.t2"; gene_id "Phchi.S4G129000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11593.t1 is derived from g15644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7261652	7264252	.	-	.	Phchi.S4G117500
Phchi.S4	AUGUSTUS	transcript	7261652	7264252	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	stop_codon	7261649	7261651	.	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7261652	7261669	1	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7261652	7261669	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7261670	7261751	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7261752	7261850	1	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7261752	7261850	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7261851	7261948	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7261949	7262028	0.52	-	2	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7261949	7262028	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7262029	7262149	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7262150	7262219	0.51	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7262150	7262219	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7262220	7262322	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7262323	7262397	0.99	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7262323	7262397	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7262398	7262534	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7262535	7262730	1	-	1	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7262535	7262730	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7262731	7262874	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7262875	7263023	1	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7262875	7263023	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7263024	7263124	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7263125	7263139	0.65	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7263125	7263139	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7263140	7263357	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7263358	7263460	1	-	1	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7263358	7263460	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7263461	7263587	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7263588	7263716	0.97	-	1	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7263588	7263716	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7263717	7263817	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7263818	7263904	0.99	-	1	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7263818	7263904	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	intron	7263905	7264007	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	CDS	7264008	7264252	0.62	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	exon	7264008	7264252	.	-	.	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
Phchi.S4	AUGUSTUS	start_codon	7264250	7264252	.	-	0	transcript_id "Phchi.S4G117500.t1"; gene_id "Phchi.S4G117500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5224.t1 is derived from g2394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15611397	15612069	.	-	.	Phchi.S1G238300
Phchi.S1	AUGUSTUS	transcript	15611397	15612069	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	stop_codon	15611394	15611396	.	-	0	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	CDS	15611397	15611500	0.68	-	2	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	exon	15611397	15611500	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	intron	15611501	15611624	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	CDS	15611625	15611656	0.7	-	1	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	exon	15611625	15611656	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	intron	15611657	15611770	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	CDS	15611771	15611859	0.71	-	0	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	exon	15611771	15611859	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	intron	15611860	15612015	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	CDS	15612016	15612069	0.7	-	0	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	exon	15612016	15612069	.	-	.	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
Phchi.S1	AUGUSTUS	start_codon	15612067	15612069	.	-	0	transcript_id "Phchi.S1G238300.t1"; gene_id "Phchi.S1G238300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8909.t1 is derived from g6084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38588143	38589330	.	+	.	Phchi.S1G606800
Phchi.S1	AUGUSTUS	transcript	38588143	38589330	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	start_codon	38588143	38588145	.	+	0	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	CDS	38588143	38588649	0.33	+	0	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	exon	38588143	38588649	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	intron	38588650	38588799	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	CDS	38588800	38588918	1	+	0	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	exon	38588800	38588918	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	intron	38588919	38589004	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	CDS	38589005	38589086	1	+	1	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	exon	38589005	38589086	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	intron	38589087	38589180	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	CDS	38589181	38589330	1	+	0	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	exon	38589181	38589330	.	+	.	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
Phchi.S1	AUGUSTUS	stop_codon	38589331	38589333	.	+	0	transcript_id "Phchi.S1G606800.t1"; gene_id "Phchi.S1G606800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3797.t1 is derived from g966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5792817	5793470	.	+	.	Phchi.S1G095600
Phchi.S1	AUGUSTUS	transcript	5792817	5793470	.	+	.	transcript_id "Phchi.S1G095600.t1"; gene_id "Phchi.S1G095600"
Phchi.S1	AUGUSTUS	start_codon	5792817	5792819	.	+	0	transcript_id "Phchi.S1G095600.t1"; gene_id "Phchi.S1G095600"
Phchi.S1	AUGUSTUS	CDS	5792817	5793470	0.93	+	0	transcript_id "Phchi.S1G095600.t1"; gene_id "Phchi.S1G095600"
Phchi.S1	AUGUSTUS	exon	5792817	5793470	.	+	.	transcript_id "Phchi.S1G095600.t1"; gene_id "Phchi.S1G095600"
Phchi.S1	AUGUSTUS	stop_codon	5793471	5793473	.	+	0	transcript_id "Phchi.S1G095600.t1"; gene_id "Phchi.S1G095600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4236.t1 is derived from g1405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9044791	9046355	.	-	.	Phchi.S1G139500
Phchi.S1	AUGUSTUS	transcript	9044791	9046355	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	stop_codon	9044788	9044790	.	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9044791	9044880	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9044791	9044880	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	intron	9044881	9044979	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9044980	9045036	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9044980	9045036	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	intron	9045037	9045126	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9045127	9045252	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9045127	9045252	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	intron	9045253	9045350	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9045351	9045485	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9045351	9045485	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	intron	9045486	9045576	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9045577	9045648	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9045577	9045648	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	intron	9045649	9045736	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9045737	9045799	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9045737	9045799	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	intron	9045800	9045887	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	CDS	9045888	9046355	1	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	exon	9045888	9046355	.	-	.	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
Phchi.S1	AUGUSTUS	start_codon	9046353	9046355	.	-	0	transcript_id "Phchi.S1G139500.t1"; gene_id "Phchi.S1G139500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8160.t1 is derived from g5335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34226812	34228131	.	-	.	Phchi.S1G531900
Phchi.S1	AUGUSTUS	transcript	34226812	34228131	.	-	.	transcript_id "Phchi.S1G531900.t1"; gene_id "Phchi.S1G531900"
Phchi.S1	AUGUSTUS	stop_codon	34226809	34226811	.	-	0	transcript_id "Phchi.S1G531900.t1"; gene_id "Phchi.S1G531900"
Phchi.S1	AUGUSTUS	CDS	34226812	34228131	1	-	0	transcript_id "Phchi.S1G531900.t1"; gene_id "Phchi.S1G531900"
Phchi.S1	AUGUSTUS	exon	34226812	34228131	.	-	.	transcript_id "Phchi.S1G531900.t1"; gene_id "Phchi.S1G531900"
Phchi.S1	AUGUSTUS	start_codon	34228129	34228131	.	-	0	transcript_id "Phchi.S1G531900.t1"; gene_id "Phchi.S1G531900"
# This transcript jg705.t2 is derived from g10487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg705.t3 is derived from g10487.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg706.t1 is derived from g10488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4984681	4987732	.	+	.	Phchi.S6G066500
Phchi.S6	AUGUSTUS	transcript	4984681	4987732	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	start_codon	4984681	4984683	.	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4984681	4985023	0.94	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4984681	4985023	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4985024	4985278	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4985279	4985542	0.69	+	2	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4985279	4985542	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4985543	4985883	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4985884	4985932	0.4	+	2	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4985884	4985932	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4985933	4986086	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4986087	4986133	0.83	+	1	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4986087	4986133	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4986134	4986215	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4986216	4986403	0.57	+	2	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4986216	4986403	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4986404	4986517	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4986518	4987072	0.59	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4986518	4987072	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4987073	4987176	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4987177	4987344	0.99	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4987177	4987344	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4987345	4987428	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4987429	4987557	1	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4987429	4987557	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4987558	4987663	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4987664	4987732	0.84	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4987664	4987732	.	+	.	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	stop_codon	4987733	4987735	.	+	0	transcript_id "Phchi.S6G066500.t1"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	transcript	4984681	4987732	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	start_codon	4984681	4984683	.	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4984681	4985023	0.94	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4984681	4985023	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4985024	4985263	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4985264	4985542	0.65	+	2	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4985264	4985542	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4985543	4985883	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4985884	4985932	0.34	+	2	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4985884	4985932	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4985933	4986086	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4986087	4986133	0.77	+	1	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4986087	4986133	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4986134	4986215	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4986216	4986403	0.56	+	2	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4986216	4986403	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4986404	4986517	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4986518	4987072	0.56	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4986518	4987072	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4987073	4987176	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4987177	4987344	1	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4987177	4987344	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4987345	4987428	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4987429	4987557	1	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4987429	4987557	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	intron	4987558	4987663	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	CDS	4987664	4987732	0.7	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	exon	4987664	4987732	.	+	.	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
Phchi.S6	AUGUSTUS	stop_codon	4987733	4987735	.	+	0	transcript_id "Phchi.S6G066500.t2"; gene_id "Phchi.S6G066500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8911.t1 is derived from g6086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38595889	38596462	.	-	.	Phchi.S1G607000
Phchi.S1	AUGUSTUS	transcript	38595889	38596462	.	-	.	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	stop_codon	38595886	38595888	.	-	0	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	CDS	38595889	38596072	1	-	1	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	exon	38595889	38596072	.	-	.	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	intron	38596073	38596154	.	-	.	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	CDS	38596155	38596270	1	-	0	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	exon	38596155	38596270	.	-	.	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	intron	38596271	38596363	.	-	.	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	CDS	38596364	38596462	0.98	-	0	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	exon	38596364	38596462	.	-	.	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
Phchi.S1	AUGUSTUS	start_codon	38596460	38596462	.	-	0	transcript_id "Phchi.S1G607000.t1"; gene_id "Phchi.S1G607000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13735.t1 is derived from g12202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8646105	8647099	.	+	.	Phchi.S3G105400
Phchi.S3	AUGUSTUS	transcript	8646105	8647099	.	+	.	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	start_codon	8646105	8646107	.	+	0	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	CDS	8646105	8646190	0.62	+	0	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	exon	8646105	8646190	.	+	.	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	intron	8646191	8646276	.	+	.	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	CDS	8646277	8646515	0.5	+	1	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	exon	8646277	8646515	.	+	.	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	intron	8646516	8646776	.	+	.	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	CDS	8646777	8647099	0.45	+	2	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	exon	8646777	8647099	.	+	.	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	stop_codon	8647100	8647102	.	+	0	transcript_id "Phchi.S3G105400.t1"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	transcript	8646615	8647099	.	+	.	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	start_codon	8646615	8646617	.	+	0	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	CDS	8646615	8646698	0.32	+	0	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	exon	8646615	8646698	.	+	.	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	intron	8646699	8646832	.	+	.	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	CDS	8646833	8647099	0.32	+	0	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	exon	8646833	8647099	.	+	.	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
Phchi.S3	AUGUSTUS	stop_codon	8647100	8647102	.	+	0	transcript_id "Phchi.S3G105400.t2"; gene_id "Phchi.S3G105400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5410.t1 is derived from g2580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16735163	16737669	.	+	.	Phchi.S1G256900
Phchi.S1	AUGUSTUS	transcript	16735163	16737669	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	start_codon	16735163	16735165	.	+	0	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	CDS	16735163	16735744	0.5	+	0	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	exon	16735163	16735744	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	intron	16735745	16735887	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	CDS	16735888	16736211	0.86	+	0	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	exon	16735888	16736211	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	intron	16736212	16736327	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	CDS	16736328	16737098	1	+	0	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	exon	16736328	16737098	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	intron	16737099	16737189	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	CDS	16737190	16737221	1	+	0	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	exon	16737190	16737221	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	intron	16737222	16737317	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	CDS	16737318	16737669	0.91	+	1	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	exon	16737318	16737669	.	+	.	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
Phchi.S1	AUGUSTUS	stop_codon	16737670	16737672	.	+	0	transcript_id "Phchi.S1G256900.t1"; gene_id "Phchi.S1G256900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13734.t1 is derived from g12201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8643959	8644653	.	-	.	Phchi.S3G105300
Phchi.S3	AUGUSTUS	transcript	8643959	8644653	.	-	.	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	stop_codon	8643956	8643958	.	-	0	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	CDS	8643959	8644374	0.36	-	2	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	exon	8643959	8644374	.	-	.	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	intron	8644375	8644460	.	-	.	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	CDS	8644461	8644653	0.6	-	0	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	exon	8644461	8644653	.	-	.	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
Phchi.S3	AUGUSTUS	start_codon	8644651	8644653	.	-	0	transcript_id "Phchi.S3G105300.t1"; gene_id "Phchi.S3G105300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5515.t1 is derived from g2685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17185190	17186954	.	-	.	Phchi.S1G267400
Phchi.S1	AUGUSTUS	transcript	17185190	17186954	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	stop_codon	17185187	17185189	.	-	0	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	CDS	17185190	17185450	0.99	-	0	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	exon	17185190	17185450	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	intron	17185451	17185540	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	CDS	17185541	17185639	1	-	0	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	exon	17185541	17185639	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	intron	17185640	17185736	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	CDS	17185737	17186064	1	-	1	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	exon	17185737	17186064	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	intron	17186065	17186182	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	CDS	17186183	17186247	1	-	0	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	exon	17186183	17186247	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	intron	17186248	17186447	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	CDS	17186448	17186954	0.7	-	0	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	exon	17186448	17186954	.	-	.	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
Phchi.S1	AUGUSTUS	start_codon	17186952	17186954	.	-	0	transcript_id "Phchi.S1G267400.t1"; gene_id "Phchi.S1G267400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg766.t1 is derived from g10548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5407676	5408697	.	+	.	Phchi.S6G072500
Phchi.S6	AUGUSTUS	transcript	5407676	5408697	.	+	.	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	start_codon	5407676	5407678	.	+	0	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	CDS	5407676	5407887	0.82	+	0	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	exon	5407676	5407887	.	+	.	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	intron	5407888	5408002	.	+	.	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	CDS	5408003	5408214	0.84	+	1	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	exon	5408003	5408214	.	+	.	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	intron	5408215	5408329	.	+	.	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	CDS	5408330	5408697	1	+	2	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	exon	5408330	5408697	.	+	.	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
Phchi.S6	AUGUSTUS	stop_codon	5408698	5408700	.	+	0	transcript_id "Phchi.S6G072500.t1"; gene_id "Phchi.S6G072500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12355.t1 is derived from g8031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12689172	12690141	.	+	.	Phchi.S2G043500
Phchi.S2	AUGUSTUS	transcript	12689172	12690141	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	start_codon	12689172	12689174	.	+	0	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	CDS	12689172	12689199	0.97	+	0	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	exon	12689172	12689199	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	intron	12689200	12689395	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	CDS	12689396	12689490	1	+	2	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	exon	12689396	12689490	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	intron	12689491	12689671	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	CDS	12689672	12689737	0.93	+	0	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	exon	12689672	12689737	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	intron	12689738	12689842	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	CDS	12689843	12689923	0.98	+	0	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	exon	12689843	12689923	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	intron	12689924	12690090	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	CDS	12690091	12690141	0.85	+	0	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	exon	12690091	12690141	.	+	.	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
Phchi.S2	AUGUSTUS	stop_codon	12690142	12690144	.	+	0	transcript_id "Phchi.S2G043500.t1"; gene_id "Phchi.S2G043500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8552.t1 is derived from g5727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36587645	36589123	.	+	.	Phchi.S1G571100
Phchi.S1	AUGUSTUS	transcript	36587645	36589123	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	start_codon	36587645	36587647	.	+	0	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	CDS	36587645	36587805	0.86	+	0	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	exon	36587645	36587805	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	intron	36587806	36588354	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	CDS	36588355	36588511	1	+	1	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	exon	36588355	36588511	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	intron	36588512	36588690	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	CDS	36588691	36588741	1	+	0	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	exon	36588691	36588741	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	intron	36588742	36588859	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	CDS	36588860	36588952	1	+	0	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	exon	36588860	36588952	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	intron	36588953	36589039	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	CDS	36589040	36589123	1	+	0	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	exon	36589040	36589123	.	+	.	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
Phchi.S1	AUGUSTUS	stop_codon	36589124	36589126	.	+	0	transcript_id "Phchi.S1G571100.t1"; gene_id "Phchi.S1G571100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9147.t1 is derived from g6322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40095427	40096469	.	+	.	Phchi.S1G630600
Phchi.S1	AUGUSTUS	transcript	40095427	40096469	.	+	.	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	start_codon	40095427	40095429	.	+	0	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	CDS	40095427	40095963	0.71	+	0	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	exon	40095427	40095963	.	+	.	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	intron	40095964	40096055	.	+	.	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	CDS	40096056	40096469	0.81	+	0	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	exon	40096056	40096469	.	+	.	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
Phchi.S1	AUGUSTUS	stop_codon	40096470	40096472	.	+	0	transcript_id "Phchi.S1G630600.t1"; gene_id "Phchi.S1G630600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg68.t1 is derived from g9850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	334364	335203	.	+	.	Phchi.S6G002700
Phchi.S6	AUGUSTUS	transcript	334364	335203	.	+	.	transcript_id "Phchi.S6G002700.t1"; gene_id "Phchi.S6G002700"
Phchi.S6	AUGUSTUS	start_codon	334364	334366	.	+	0	transcript_id "Phchi.S6G002700.t1"; gene_id "Phchi.S6G002700"
Phchi.S6	AUGUSTUS	CDS	334364	335203	0.96	+	0	transcript_id "Phchi.S6G002700.t1"; gene_id "Phchi.S6G002700"
Phchi.S6	AUGUSTUS	exon	334364	335203	.	+	.	transcript_id "Phchi.S6G002700.t1"; gene_id "Phchi.S6G002700"
Phchi.S6	AUGUSTUS	stop_codon	335204	335206	.	+	0	transcript_id "Phchi.S6G002700.t1"; gene_id "Phchi.S6G002700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6343.t1 is derived from g3515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22417555	22419303	.	-	.	Phchi.S1G350200
Phchi.S1	AUGUSTUS	transcript	22417555	22419303	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	stop_codon	22417552	22417554	.	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22417555	22417770	0.99	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22417555	22417770	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22417771	22417904	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22417905	22418007	1	-	1	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22417905	22418007	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22418008	22418085	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22418086	22418165	1	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22418086	22418165	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22418166	22418252	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22418253	22418335	1	-	2	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22418253	22418335	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22418336	22418498	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22418499	22418547	0.99	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22418499	22418547	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22418548	22418649	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22418650	22418715	0.99	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22418650	22418715	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22418716	22418829	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22418830	22418879	1	-	2	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22418830	22418879	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22418880	22418989	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22418990	22419114	1	-	1	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22418990	22419114	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	intron	22419115	22419289	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	CDS	22419290	22419303	1	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	exon	22419290	22419303	.	-	.	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
Phchi.S1	AUGUSTUS	start_codon	22419301	22419303	.	-	0	transcript_id "Phchi.S1G350200.t1"; gene_id "Phchi.S1G350200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12760.t1 is derived from g11225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1936534	1938123	.	-	.	Phchi.S3G007900
Phchi.S3	AUGUSTUS	transcript	1936534	1938123	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	stop_codon	1936531	1936533	.	-	0	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	CDS	1936534	1936786	0.99	-	1	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	exon	1936534	1936786	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	intron	1936787	1936876	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	CDS	1936877	1937229	0.98	-	0	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	exon	1936877	1937229	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	intron	1937230	1937342	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	CDS	1937343	1937432	0.98	-	0	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	exon	1937343	1937432	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	intron	1937433	1937526	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	CDS	1937527	1937807	1	-	2	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	exon	1937527	1937807	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	intron	1937808	1937906	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	CDS	1937907	1938123	1	-	0	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	exon	1937907	1938123	.	-	.	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
Phchi.S3	AUGUSTUS	start_codon	1938121	1938123	.	-	0	transcript_id "Phchi.S3G007900.t1"; gene_id "Phchi.S3G007900"
# This transcript jg2746.t2 is derived from g9666.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2747.t1 is derived from g9667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8595042	8601678	.	-	.	Phchi.S5G135600
Phchi.S5	AUGUSTUS	transcript	8595042	8601678	.	-	.	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	stop_codon	8595039	8595041	.	-	0	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	CDS	8595042	8595057	0.04	-	1	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	exon	8595042	8595057	.	-	.	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	intron	8595058	8599277	.	-	.	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	CDS	8599278	8599375	1	-	0	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	exon	8599278	8599375	.	-	.	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	intron	8599376	8601546	.	-	.	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	CDS	8601547	8601678	0.63	-	0	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	exon	8601547	8601678	.	-	.	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
Phchi.S5	AUGUSTUS	start_codon	8601676	8601678	.	-	0	transcript_id "Phchi.S5G135600.t1"; gene_id "Phchi.S5G135600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15225.t1 is derived from g13693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17824695	17825247	.	+	.	Phchi.S3G254400
Phchi.S3	AUGUSTUS	transcript	17824695	17825247	.	+	.	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	start_codon	17824695	17824697	.	+	0	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	CDS	17824695	17824875	0.63	+	0	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	exon	17824695	17824875	.	+	.	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	intron	17824876	17824978	.	+	.	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	CDS	17824979	17825027	0.68	+	2	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	exon	17824979	17825027	.	+	.	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	intron	17825028	17825195	.	+	.	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	CDS	17825196	17825247	0.84	+	1	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	exon	17825196	17825247	.	+	.	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
Phchi.S3	AUGUSTUS	stop_codon	17825248	17825250	.	+	0	transcript_id "Phchi.S3G254400.t1"; gene_id "Phchi.S3G254400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8740.t1 is derived from g5915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37754818	37759315	.	-	.	Phchi.S1G589900
Phchi.S1	AUGUSTUS	transcript	37754818	37759315	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	stop_codon	37754815	37754817	.	-	0	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37754818	37754838	0.9	-	0	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37754818	37754838	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37754839	37754980	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37754981	37755015	0.97	-	2	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37754981	37755015	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37755016	37755109	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37755110	37755200	0.97	-	0	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37755110	37755200	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37755201	37755308	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37755309	37756968	0.84	-	1	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37755309	37756968	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37756969	37757037	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37757038	37757205	0.75	-	1	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37757038	37757205	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37757206	37757346	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37757347	37757428	0.48	-	2	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37757347	37757428	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37757429	37757732	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37757733	37758441	0.96	-	0	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37757733	37758441	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37758442	37758544	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37758545	37759040	0.97	-	1	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37758545	37759040	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	intron	37759041	37759115	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	CDS	37759116	37759315	0.82	-	0	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	exon	37759116	37759315	.	-	.	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
Phchi.S1	AUGUSTUS	start_codon	37759313	37759315	.	-	0	transcript_id "Phchi.S1G589900.t1"; gene_id "Phchi.S1G589900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8297.t1 is derived from g5472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35139818	35143333	.	+	.	Phchi.S1G545600
Phchi.S1	AUGUSTUS	transcript	35139818	35143333	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	start_codon	35139818	35139820	.	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35139818	35139967	0.63	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35139818	35139967	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35139968	35140190	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35140191	35140309	1	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35140191	35140309	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35140310	35140549	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35140550	35140647	1	+	1	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35140550	35140647	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35140648	35140778	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35140779	35140838	1	+	2	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35140779	35140838	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35140839	35140954	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35140955	35141001	0.8	+	2	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35140955	35141001	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35141002	35141120	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35141121	35141176	0.6	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35141121	35141176	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35141177	35141271	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35141272	35141314	0.58	+	1	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35141272	35141314	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35141315	35141419	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35141420	35141466	0.98	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35141420	35141466	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35141467	35141581	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35141582	35141648	1	+	1	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35141582	35141648	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35141649	35141778	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35141779	35141879	1	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35141779	35141879	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35141880	35142021	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35142022	35142123	1	+	1	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35142022	35142123	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35142124	35142385	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35142386	35142524	1	+	1	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35142386	35142524	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35142525	35142650	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35142651	35142713	0.99	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35142651	35142713	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35142714	35142824	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35142825	35142908	0.98	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35142825	35142908	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	intron	35142909	35142994	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	CDS	35142995	35143333	0.55	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	exon	35142995	35143333	.	+	.	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
Phchi.S1	AUGUSTUS	stop_codon	35143334	35143336	.	+	0	transcript_id "Phchi.S1G545600.t1"; gene_id "Phchi.S1G545600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2626.t1 is derived from g9546.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7832555	7833549	.	-	.	Phchi.S5G123500
Phchi.S5	AUGUSTUS	transcript	7832571	7833549	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	stop_codon	7832568	7832570	.	-	0	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7832571	7832603	0.97	-	0	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7832571	7832603	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7832604	7832918	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7832919	7832961	0.91	-	1	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7832919	7832961	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7832962	7833093	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7833094	7833181	0.97	-	2	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7833094	7833181	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7833182	7833350	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7833351	7833422	0.99	-	2	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7833351	7833422	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7833423	7833521	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7833522	7833549	0.73	-	0	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7833522	7833549	.	-	.	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	start_codon	7833547	7833549	.	-	0	transcript_id "Phchi.S5G123500.t1"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	transcript	7832555	7833549	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	stop_codon	7832552	7832554	.	-	0	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7832555	7832603	0.9	-	1	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7832555	7832603	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7832604	7833093	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7833094	7833181	0.91	-	2	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7833094	7833181	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7833182	7833350	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7833351	7833422	0.92	-	2	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7833351	7833422	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	intron	7833423	7833521	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	CDS	7833522	7833549	0.64	-	0	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	exon	7833522	7833549	.	-	.	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
Phchi.S5	AUGUSTUS	start_codon	7833547	7833549	.	-	0	transcript_id "Phchi.S5G123500.t2"; gene_id "Phchi.S5G123500"
# This transcript jg6836.t2 is derived from g4008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6837.t1 is derived from g4009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25488708	25489190	.	-	.	Phchi.S1G399600
Phchi.S1	AUGUSTUS	transcript	25488708	25489190	.	-	.	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	stop_codon	25488705	25488707	.	-	0	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	CDS	25488708	25488969	1	-	1	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	exon	25488708	25488969	.	-	.	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	intron	25488970	25489101	.	-	.	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	CDS	25489102	25489190	0.44	-	0	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	exon	25489102	25489190	.	-	.	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
Phchi.S1	AUGUSTUS	start_codon	25489188	25489190	.	-	0	transcript_id "Phchi.S1G399600.t1"; gene_id "Phchi.S1G399600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9365.t1 is derived from g6541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41169734	41170426	.	-	.	Phchi.S1G652400
Phchi.S1	AUGUSTUS	transcript	41169734	41170426	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	stop_codon	41169731	41169733	.	-	0	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	CDS	41169734	41169843	0.78	-	2	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	exon	41169734	41169843	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	intron	41169844	41170006	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	CDS	41170007	41170059	1	-	1	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	exon	41170007	41170059	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	intron	41170060	41170179	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	CDS	41170180	41170270	0.99	-	2	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	exon	41170180	41170270	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	intron	41170271	41170350	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	CDS	41170351	41170426	0.92	-	0	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	exon	41170351	41170426	.	-	.	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
Phchi.S1	AUGUSTUS	start_codon	41170424	41170426	.	-	0	transcript_id "Phchi.S1G652400.t1"; gene_id "Phchi.S1G652400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5746.t1 is derived from g2916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18693332	18695163	.	-	.	Phchi.S1G290500
Phchi.S1	AUGUSTUS	transcript	18693332	18695163	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	stop_codon	18693329	18693331	.	-	0	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	CDS	18693332	18694210	1	-	0	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	exon	18693332	18694210	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	intron	18694211	18694321	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	CDS	18694322	18694459	1	-	0	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	exon	18694322	18694459	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	intron	18694460	18694567	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	CDS	18694568	18694898	1	-	1	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	exon	18694568	18694898	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	intron	18694899	18695095	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	CDS	18695096	18695163	0.49	-	0	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	exon	18695096	18695163	.	-	.	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
Phchi.S1	AUGUSTUS	start_codon	18695161	18695163	.	-	0	transcript_id "Phchi.S1G290500.t1"; gene_id "Phchi.S1G290500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8998.t1 is derived from g6173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39073620	39074111	.	-	.	Phchi.S1G615700
Phchi.S1	AUGUSTUS	transcript	39073620	39074111	.	-	.	transcript_id "Phchi.S1G615700.t1"; gene_id "Phchi.S1G615700"
Phchi.S1	AUGUSTUS	stop_codon	39073617	39073619	.	-	0	transcript_id "Phchi.S1G615700.t1"; gene_id "Phchi.S1G615700"
Phchi.S1	AUGUSTUS	CDS	39073620	39074111	0.73	-	0	transcript_id "Phchi.S1G615700.t1"; gene_id "Phchi.S1G615700"
Phchi.S1	AUGUSTUS	exon	39073620	39074111	.	-	.	transcript_id "Phchi.S1G615700.t1"; gene_id "Phchi.S1G615700"
Phchi.S1	AUGUSTUS	start_codon	39074109	39074111	.	-	0	transcript_id "Phchi.S1G615700.t1"; gene_id "Phchi.S1G615700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2537.t1 is derived from g9457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7213612	7215240	.	-	.	Phchi.S5G114600
Phchi.S5	AUGUSTUS	transcript	7213612	7215240	.	-	.	transcript_id "Phchi.S5G114600.t1"; gene_id "Phchi.S5G114600"
Phchi.S5	AUGUSTUS	stop_codon	7213609	7213611	.	-	0	transcript_id "Phchi.S5G114600.t1"; gene_id "Phchi.S5G114600"
Phchi.S5	AUGUSTUS	CDS	7213612	7215240	1	-	0	transcript_id "Phchi.S5G114600.t1"; gene_id "Phchi.S5G114600"
Phchi.S5	AUGUSTUS	exon	7213612	7215240	.	-	.	transcript_id "Phchi.S5G114600.t1"; gene_id "Phchi.S5G114600"
Phchi.S5	AUGUSTUS	start_codon	7215238	7215240	.	-	0	transcript_id "Phchi.S5G114600.t1"; gene_id "Phchi.S5G114600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10110.t1 is derived from g7286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45778737	45780291	.	+	.	Phchi.S1G726900
Phchi.S1	AUGUSTUS	transcript	45778737	45780291	.	+	.	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	start_codon	45778737	45778739	.	+	0	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	CDS	45778737	45779635	0.86	+	0	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	exon	45778737	45779635	.	+	.	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	intron	45779636	45780101	.	+	.	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	CDS	45780102	45780291	0.51	+	1	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	exon	45780102	45780291	.	+	.	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
Phchi.S1	AUGUSTUS	stop_codon	45780292	45780294	.	+	0	transcript_id "Phchi.S1G726900.t1"; gene_id "Phchi.S1G726900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1463.t1 is derived from g8382.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1021360	1022300	.	-	.	Phchi.S5G007200
Phchi.S5	AUGUSTUS	transcript	1021360	1022300	.	-	.	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	stop_codon	1021357	1021359	.	-	0	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	CDS	1021360	1021990	0.85	-	1	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	exon	1021360	1021990	.	-	.	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	intron	1021991	1022118	.	-	.	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	CDS	1022119	1022300	0.83	-	0	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	exon	1022119	1022300	.	-	.	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	start_codon	1022298	1022300	.	-	0	transcript_id "Phchi.S5G007200.t1"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	transcript	1021360	1021860	.	-	.	transcript_id "Phchi.S5G007200.t2"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	stop_codon	1021357	1021359	.	-	0	transcript_id "Phchi.S5G007200.t2"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	CDS	1021360	1021860	0.99	-	0	transcript_id "Phchi.S5G007200.t2"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	exon	1021360	1021860	.	-	.	transcript_id "Phchi.S5G007200.t2"; gene_id "Phchi.S5G007200"
Phchi.S5	AUGUSTUS	start_codon	1021858	1021860	.	-	0	transcript_id "Phchi.S5G007200.t2"; gene_id "Phchi.S5G007200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7770.t1 is derived from g4944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31170270	31171771	.	+	.	Phchi.S1G492900
Phchi.S1	AUGUSTUS	transcript	31170270	31171771	.	+	.	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	start_codon	31170270	31170272	.	+	0	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	CDS	31170270	31171212	0.67	+	0	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	exon	31170270	31171212	.	+	.	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	intron	31171213	31171520	.	+	.	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	CDS	31171521	31171771	0.71	+	2	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	exon	31171521	31171771	.	+	.	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
Phchi.S1	AUGUSTUS	stop_codon	31171772	31171774	.	+	0	transcript_id "Phchi.S1G492900.t1"; gene_id "Phchi.S1G492900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14762.t1 is derived from g13230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14582389	14584573	.	-	.	Phchi.S3G208100
Phchi.S3	AUGUSTUS	transcript	14582389	14584573	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	stop_codon	14582386	14582388	.	-	0	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14582389	14582397	0.99	-	0	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14582389	14582397	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14582398	14582491	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14582492	14582780	0.97	-	1	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14582492	14582780	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14582781	14582899	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14582900	14582984	1	-	2	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14582900	14582984	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14582985	14583067	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14583068	14583216	1	-	1	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14583068	14583216	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14583217	14583366	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14583367	14583456	1	-	1	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14583367	14583456	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14583457	14583628	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14583629	14583732	1	-	0	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14583629	14583732	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14583733	14583806	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14583807	14583905	1	-	0	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14583807	14583905	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14583906	14584005	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14584006	14584060	1	-	1	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14584006	14584060	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14584061	14584152	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14584153	14584386	1	-	1	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14584153	14584386	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14584387	14584481	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14584482	14584573	1	-	0	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14584482	14584573	.	-	.	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	start_codon	14584571	14584573	.	-	0	transcript_id "Phchi.S3G208100.t1"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	transcript	14583672	14584573	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	stop_codon	14583669	14583671	.	-	0	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14583672	14583719	0.64	-	0	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14583672	14583719	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14583720	14583806	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14583807	14583905	1	-	0	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14583807	14583905	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14583906	14584005	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14584006	14584060	1	-	1	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14584006	14584060	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14584061	14584152	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14584153	14584386	1	-	1	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14584153	14584386	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	intron	14584387	14584481	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	CDS	14584482	14584573	0.98	-	0	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	exon	14584482	14584573	.	-	.	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
Phchi.S3	AUGUSTUS	start_codon	14584571	14584573	.	-	0	transcript_id "Phchi.S3G208100.t2"; gene_id "Phchi.S3G208100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1413.t1 is derived from g8332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	502588	505857	.	-	.	Phchi.S5G002200
Phchi.S5	AUGUSTUS	transcript	502588	505857	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	stop_codon	502585	502587	.	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	502588	502788	1	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	502588	502788	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	502789	502881	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	502882	502941	1	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	502882	502941	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	502942	503044	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	503045	503455	1	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	503045	503455	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	503456	503542	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	503543	503873	1	-	1	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	503543	503873	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	503874	503964	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	503965	504051	1	-	1	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	503965	504051	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	504052	504221	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	504222	504604	1	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	504222	504604	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	504605	504723	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	504724	505062	0.27	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	504724	505062	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	505063	505172	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	505173	505255	0.27	-	2	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	505173	505255	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	intron	505256	505625	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	CDS	505626	505857	1	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	exon	505626	505857	.	-	.	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
Phchi.S5	AUGUSTUS	start_codon	505855	505857	.	-	0	transcript_id "Phchi.S5G002200.t1"; gene_id "Phchi.S5G002200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2068.t1 is derived from g8988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4701911	4706575	.	-	.	Phchi.S5G067700
Phchi.S5	AUGUSTUS	transcript	4703803	4706575	.	-	.	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	stop_codon	4703800	4703802	.	-	0	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	CDS	4703803	4705445	0.99	-	2	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	exon	4703803	4705445	.	-	.	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	intron	4705446	4705617	.	-	.	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	CDS	4705618	4706575	1	-	0	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	exon	4705618	4706575	.	-	.	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	start_codon	4706573	4706575	.	-	0	transcript_id "Phchi.S5G067700.t1"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	transcript	4701911	4706575	.	-	.	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	stop_codon	4701908	4701910	.	-	0	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	CDS	4701911	4703837	0.88	-	1	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	exon	4701911	4703837	.	-	.	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	intron	4703838	4703926	.	-	.	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	CDS	4703927	4705445	0.87	-	2	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	exon	4703927	4705445	.	-	.	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	intron	4705446	4705617	.	-	.	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	CDS	4705618	4706575	0.99	-	0	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	exon	4705618	4706575	.	-	.	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
Phchi.S5	AUGUSTUS	start_codon	4706573	4706575	.	-	0	transcript_id "Phchi.S5G067700.t2"; gene_id "Phchi.S5G067700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7557.t1 is derived from g4731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30024975	30026260	.	-	.	Phchi.S1G471600
Phchi.S1	AUGUSTUS	transcript	30024975	30026260	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	stop_codon	30024972	30024974	.	-	0	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	CDS	30024975	30025312	0.64	-	2	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	exon	30024975	30025312	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	intron	30025313	30025408	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	CDS	30025409	30025683	0.95	-	1	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	exon	30025409	30025683	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	intron	30025684	30025779	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	CDS	30025780	30025906	0.96	-	2	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	exon	30025780	30025906	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	intron	30025907	30025995	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	CDS	30025996	30026260	0.7	-	0	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	exon	30025996	30026260	.	-	.	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
Phchi.S1	AUGUSTUS	start_codon	30026258	30026260	.	-	0	transcript_id "Phchi.S1G471600.t1"; gene_id "Phchi.S1G471600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7160.t1 is derived from g4332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27340161	27340652	.	+	.	Phchi.S1G431900
Phchi.S1	AUGUSTUS	transcript	27340161	27340652	.	+	.	transcript_id "Phchi.S1G431900.t1"; gene_id "Phchi.S1G431900"
Phchi.S1	AUGUSTUS	start_codon	27340161	27340163	.	+	0	transcript_id "Phchi.S1G431900.t1"; gene_id "Phchi.S1G431900"
Phchi.S1	AUGUSTUS	CDS	27340161	27340652	0.54	+	0	transcript_id "Phchi.S1G431900.t1"; gene_id "Phchi.S1G431900"
Phchi.S1	AUGUSTUS	exon	27340161	27340652	.	+	.	transcript_id "Phchi.S1G431900.t1"; gene_id "Phchi.S1G431900"
Phchi.S1	AUGUSTUS	stop_codon	27340653	27340655	.	+	0	transcript_id "Phchi.S1G431900.t1"; gene_id "Phchi.S1G431900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1806.t1 is derived from g8726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3133334	3133834	.	-	.	Phchi.S5G041500
Phchi.S5	AUGUSTUS	transcript	3133334	3133834	.	-	.	transcript_id "Phchi.S5G041500.t1"; gene_id "Phchi.S5G041500"
Phchi.S5	AUGUSTUS	stop_codon	3133331	3133333	.	-	0	transcript_id "Phchi.S5G041500.t1"; gene_id "Phchi.S5G041500"
Phchi.S5	AUGUSTUS	CDS	3133334	3133834	0.72	-	0	transcript_id "Phchi.S5G041500.t1"; gene_id "Phchi.S5G041500"
Phchi.S5	AUGUSTUS	exon	3133334	3133834	.	-	.	transcript_id "Phchi.S5G041500.t1"; gene_id "Phchi.S5G041500"
Phchi.S5	AUGUSTUS	start_codon	3133832	3133834	.	-	0	transcript_id "Phchi.S5G041500.t1"; gene_id "Phchi.S5G041500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1522.t1 is derived from g8441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1535085	1536071	.	+	.	Phchi.S5G013100
Phchi.S5	AUGUSTUS	transcript	1535085	1536071	.	+	.	transcript_id "Phchi.S5G013100.t1"; gene_id "Phchi.S5G013100"
Phchi.S5	AUGUSTUS	start_codon	1535085	1535087	.	+	0	transcript_id "Phchi.S5G013100.t1"; gene_id "Phchi.S5G013100"
Phchi.S5	AUGUSTUS	CDS	1535085	1536071	0.99	+	0	transcript_id "Phchi.S5G013100.t1"; gene_id "Phchi.S5G013100"
Phchi.S5	AUGUSTUS	exon	1535085	1536071	.	+	.	transcript_id "Phchi.S5G013100.t1"; gene_id "Phchi.S5G013100"
Phchi.S5	AUGUSTUS	stop_codon	1536072	1536074	.	+	0	transcript_id "Phchi.S5G013100.t1"; gene_id "Phchi.S5G013100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15549.t1 is derived from g14018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19873605	19874907	.	+	.	Phchi.S3G286800
Phchi.S3	AUGUSTUS	transcript	19873605	19874907	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	start_codon	19873605	19873607	.	+	0	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	CDS	19873605	19873889	1	+	0	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	exon	19873605	19873889	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	intron	19873890	19873992	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	CDS	19873993	19874199	1	+	0	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	exon	19873993	19874199	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	intron	19874200	19874283	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	CDS	19874284	19874364	1	+	0	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	exon	19874284	19874364	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	intron	19874365	19874448	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	CDS	19874449	19874907	0.95	+	0	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	exon	19874449	19874907	.	+	.	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
Phchi.S3	AUGUSTUS	stop_codon	19874908	19874910	.	+	0	transcript_id "Phchi.S3G286800.t1"; gene_id "Phchi.S3G286800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg64.t1 is derived from g9846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	322080	323675	.	+	.	Phchi.S6G002300
Phchi.S6	AUGUSTUS	transcript	322080	323675	.	+	.	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	start_codon	322080	322082	.	+	0	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	CDS	322080	322480	0.71	+	0	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	exon	322080	322480	.	+	.	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	intron	322481	322684	.	+	.	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	CDS	322685	323675	0.22	+	1	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	exon	322685	323675	.	+	.	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
Phchi.S6	AUGUSTUS	stop_codon	323676	323678	.	+	0	transcript_id "Phchi.S6G002300.t1"; gene_id "Phchi.S6G002300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1385.t1 is derived from g16018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	6414	7676	.	-	.	Phchi.C243G000300
Phchi.C243	AUGUSTUS	transcript	6414	7676	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	stop_codon	6411	6413	.	-	0	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	CDS	6414	6521	0.98	-	0	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	exon	6414	6521	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	intron	6522	6667	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	CDS	6668	6808	1	-	0	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	exon	6668	6808	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	intron	6809	6908	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	CDS	6909	7207	0.43	-	2	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	exon	6909	7207	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	intron	7208	7327	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	CDS	7328	7676	0.39	-	0	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	exon	7328	7676	.	-	.	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
Phchi.C243	AUGUSTUS	start_codon	7674	7676	.	-	0	transcript_id "Phchi.C243G000300.t1"; gene_id "Phchi.C243G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2287.t1 is derived from g9207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5873875	5874747	.	-	.	Phchi.S5G089600
Phchi.S5	AUGUSTUS	transcript	5873875	5874747	.	-	.	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	stop_codon	5873872	5873874	.	-	0	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	CDS	5873875	5873895	0.6	-	0	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	exon	5873875	5873895	.	-	.	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	intron	5873896	5874474	.	-	.	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	CDS	5874475	5874747	0.4	-	0	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	exon	5874475	5874747	.	-	.	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
Phchi.S5	AUGUSTUS	start_codon	5874745	5874747	.	-	0	transcript_id "Phchi.S5G089600.t1"; gene_id "Phchi.S5G089600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12174.t1 is derived from g7850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6039499	6039876	.	+	.	Phchi.S2G025400
Phchi.S2	AUGUSTUS	transcript	6039499	6039876	.	+	.	transcript_id "Phchi.S2G025400.t1"; gene_id "Phchi.S2G025400"
Phchi.S2	AUGUSTUS	start_codon	6039499	6039501	.	+	0	transcript_id "Phchi.S2G025400.t1"; gene_id "Phchi.S2G025400"
Phchi.S2	AUGUSTUS	CDS	6039499	6039876	0.85	+	0	transcript_id "Phchi.S2G025400.t1"; gene_id "Phchi.S2G025400"
Phchi.S2	AUGUSTUS	exon	6039499	6039876	.	+	.	transcript_id "Phchi.S2G025400.t1"; gene_id "Phchi.S2G025400"
Phchi.S2	AUGUSTUS	stop_codon	6039877	6039879	.	+	0	transcript_id "Phchi.S2G025400.t1"; gene_id "Phchi.S2G025400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15030.t1 is derived from g13498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16606729	16608982	.	-	.	Phchi.S3G234900
Phchi.S3	AUGUSTUS	transcript	16606729	16608982	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	stop_codon	16606726	16606728	.	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16606729	16607079	0.98	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16606729	16607079	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16607080	16607185	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16607186	16607287	0.98	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16607186	16607287	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16607288	16607408	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16607409	16608017	0.94	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16607409	16608017	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16608018	16608113	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16608114	16608184	1	-	2	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16608114	16608184	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16608185	16608300	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16608301	16608415	1	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16608301	16608415	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16608416	16608539	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16608540	16608585	1	-	1	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16608540	16608585	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16608586	16608675	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16608676	16608751	1	-	2	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16608676	16608751	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	intron	16608752	16608957	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	CDS	16608958	16608982	1	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	exon	16608958	16608982	.	-	.	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
Phchi.S3	AUGUSTUS	start_codon	16608980	16608982	.	-	0	transcript_id "Phchi.S3G234900.t1"; gene_id "Phchi.S3G234900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5878.t1 is derived from g3048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19552719	19553807	.	+	.	Phchi.S1G303700
Phchi.S1	AUGUSTUS	transcript	19552719	19553807	.	+	.	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	start_codon	19552719	19552721	.	+	0	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	CDS	19552719	19552797	0.77	+	0	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	exon	19552719	19552797	.	+	.	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	intron	19552798	19552920	.	+	.	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	CDS	19552921	19553807	1	+	2	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	exon	19552921	19553807	.	+	.	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
Phchi.S1	AUGUSTUS	stop_codon	19553808	19553810	.	+	0	transcript_id "Phchi.S1G303700.t1"; gene_id "Phchi.S1G303700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3680.t1 is derived from g849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5150866	5151579	.	+	.	Phchi.S1G083900
Phchi.S1	AUGUSTUS	transcript	5150866	5151579	.	+	.	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	start_codon	5150866	5150868	.	+	0	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	CDS	5150866	5151316	0.4	+	0	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	exon	5150866	5151316	.	+	.	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	intron	5151317	5151448	.	+	.	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	CDS	5151449	5151579	0.5	+	2	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	exon	5151449	5151579	.	+	.	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
Phchi.S1	AUGUSTUS	stop_codon	5151580	5151582	.	+	0	transcript_id "Phchi.S1G083900.t1"; gene_id "Phchi.S1G083900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12857.t1 is derived from g11322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2753916	2754482	.	+	.	Phchi.S3G017600
Phchi.S3	AUGUSTUS	transcript	2753916	2754482	.	+	.	transcript_id "Phchi.S3G017600.t1"; gene_id "Phchi.S3G017600"
Phchi.S3	AUGUSTUS	start_codon	2753916	2753918	.	+	0	transcript_id "Phchi.S3G017600.t1"; gene_id "Phchi.S3G017600"
Phchi.S3	AUGUSTUS	CDS	2753916	2754482	1	+	0	transcript_id "Phchi.S3G017600.t1"; gene_id "Phchi.S3G017600"
Phchi.S3	AUGUSTUS	exon	2753916	2754482	.	+	.	transcript_id "Phchi.S3G017600.t1"; gene_id "Phchi.S3G017600"
Phchi.S3	AUGUSTUS	stop_codon	2754483	2754485	.	+	0	transcript_id "Phchi.S3G017600.t1"; gene_id "Phchi.S3G017600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2402.t1 is derived from g9322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6490749	6491987	.	-	.	Phchi.S5G101100
Phchi.S5	AUGUSTUS	transcript	6490749	6491987	.	-	.	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	stop_codon	6490746	6490748	.	-	0	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	CDS	6490749	6491256	0.77	-	1	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	exon	6490749	6491256	.	-	.	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	intron	6491257	6491447	.	-	.	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	CDS	6491448	6491602	0.27	-	0	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	exon	6491448	6491602	.	-	.	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	intron	6491603	6491729	.	-	.	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	CDS	6491730	6491987	0.33	-	0	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	exon	6491730	6491987	.	-	.	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
Phchi.S5	AUGUSTUS	start_codon	6491985	6491987	.	-	0	transcript_id "Phchi.S5G101100.t1"; gene_id "Phchi.S5G101100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1859.t1 is derived from g8779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3576908	3577800	.	+	.	Phchi.S5G046800
Phchi.S5	AUGUSTUS	transcript	3576908	3577800	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	start_codon	3576908	3576910	.	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	CDS	3576908	3576967	0.89	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	exon	3576908	3576967	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	intron	3576968	3577091	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	CDS	3577092	3577142	1	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	exon	3577092	3577142	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	intron	3577143	3577216	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	CDS	3577217	3577312	1	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	exon	3577217	3577312	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	intron	3577313	3577458	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	CDS	3577459	3577584	1	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	exon	3577459	3577584	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	intron	3577585	3577677	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	CDS	3577678	3577721	1	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	exon	3577678	3577721	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	intron	3577722	3577796	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	CDS	3577797	3577800	1	+	1	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	exon	3577797	3577800	.	+	.	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
Phchi.S5	AUGUSTUS	stop_codon	3577801	3577803	.	+	0	transcript_id "Phchi.S5G046800.t1"; gene_id "Phchi.S5G046800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8116.t1 is derived from g5291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33433903	33434734	.	-	.	Phchi.S1G527500
Phchi.S1	AUGUSTUS	transcript	33433903	33434734	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	stop_codon	33433900	33433902	.	-	0	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	CDS	33433903	33434034	0.86	-	0	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	exon	33433903	33434034	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	intron	33434035	33434140	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	CDS	33434141	33434233	0.86	-	0	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	exon	33434141	33434233	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	intron	33434234	33434371	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	CDS	33434372	33434402	1	-	1	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	exon	33434372	33434402	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	intron	33434403	33434538	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	CDS	33434539	33434638	1	-	2	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	exon	33434539	33434638	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	intron	33434639	33434724	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	CDS	33434725	33434734	0.62	-	0	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	exon	33434725	33434734	.	-	.	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
Phchi.S1	AUGUSTUS	start_codon	33434732	33434734	.	-	0	transcript_id "Phchi.S1G527500.t1"; gene_id "Phchi.S1G527500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8125.t1 is derived from g5300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33521653	33525603	.	+	.	Phchi.S1G528400
Phchi.S1	AUGUSTUS	transcript	33521653	33524332	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	start_codon	33521653	33521655	.	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33521653	33521901	1	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33521653	33521901	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33521902	33522197	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522198	33522315	1	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522198	33522315	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33522316	33522559	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522560	33522618	1	+	2	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522560	33522618	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33522619	33522764	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522765	33522829	1	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522765	33522829	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33522830	33522990	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522991	33523084	1	+	1	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522991	33523084	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523085	33523219	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523220	33523300	1	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523220	33523300	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523301	33523505	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523506	33523611	1	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523506	33523611	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523612	33523698	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523699	33523753	1	+	2	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523699	33523753	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523754	33523848	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523849	33524091	0.87	+	1	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523849	33524091	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33524092	33524179	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33524180	33524237	0.87	+	1	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33524180	33524237	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33524238	33524326	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33524327	33524332	0.87	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33524327	33524332	.	+	.	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	stop_codon	33524333	33524335	.	+	0	transcript_id "Phchi.S1G528400.t1"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	transcript	33521653	33525603	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	start_codon	33521653	33521655	.	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33521653	33521901	0.99	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33521653	33521901	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33521902	33522197	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522198	33522315	1	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522198	33522315	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33522316	33522559	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522560	33522618	1	+	2	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522560	33522618	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33522619	33522764	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522765	33522829	1	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522765	33522829	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33522830	33522990	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33522991	33523084	1	+	1	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33522991	33523084	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523085	33523219	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523220	33523300	1	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523220	33523300	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523301	33523505	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523506	33523611	1	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523506	33523611	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523612	33523698	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523699	33523753	1	+	2	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523699	33523753	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33523754	33523848	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33523849	33524084	1	+	1	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33523849	33524084	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33524085	33524162	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33524163	33524237	1	+	2	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33524163	33524237	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33524238	33524326	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33524327	33524676	0.88	+	2	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33524327	33524676	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33524677	33524840	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33524841	33525054	0.39	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33524841	33525054	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33525055	33525202	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33525203	33525273	1	+	2	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33525203	33525273	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	intron	33525274	33525390	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	CDS	33525391	33525603	0.97	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	exon	33525391	33525603	.	+	.	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
Phchi.S1	AUGUSTUS	stop_codon	33525604	33525606	.	+	0	transcript_id "Phchi.S1G528400.t2"; gene_id "Phchi.S1G528400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12416.t1 is derived from g8093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18883482	18887002	.	+	.	Phchi.S2G049600
Phchi.S2	AUGUSTUS	transcript	18883482	18887002	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	start_codon	18883482	18883484	.	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18883482	18883675	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18883482	18883675	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18883676	18883909	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18883910	18883992	1	+	1	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18883910	18883992	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18883993	18884161	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18884162	18884214	1	+	2	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18884162	18884214	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18884215	18884329	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18884330	18884404	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18884330	18884404	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18884405	18884488	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18884489	18884581	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18884489	18884581	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18884582	18884728	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18884729	18884756	0.87	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18884729	18884756	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18884757	18884887	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18884888	18884967	0.88	+	2	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18884888	18884967	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18884968	18885094	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18885095	18885167	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18885095	18885167	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18885168	18885285	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18885286	18885383	0.62	+	2	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18885286	18885383	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18885384	18885571	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18885572	18885657	0.72	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18885572	18885657	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18885658	18885766	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18885767	18885842	0.72	+	1	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18885767	18885842	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18885843	18885917	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18885918	18885985	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18885918	18885985	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18885986	18886150	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18886151	18886217	1	+	1	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18886151	18886217	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18886218	18886321	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18886322	18886417	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18886322	18886417	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18886418	18886537	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18886538	18886640	1	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18886538	18886640	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18886641	18886728	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18886729	18886824	1	+	2	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18886729	18886824	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	intron	18886825	18886934	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	CDS	18886935	18887002	1	+	2	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	exon	18886935	18887002	.	+	.	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
Phchi.S2	AUGUSTUS	stop_codon	18887003	18887005	.	+	0	transcript_id "Phchi.S2G049600.t1"; gene_id "Phchi.S2G049600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6201.t1 is derived from g3372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21451250	21453684	.	-	.	Phchi.S1G336000
Phchi.S1	AUGUSTUS	transcript	21451250	21453684	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	stop_codon	21451247	21451249	.	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	CDS	21451250	21452053	0.59	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	exon	21451250	21452053	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	intron	21452054	21452169	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	CDS	21452170	21452355	0.99	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	exon	21452170	21452355	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	intron	21452356	21452449	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	CDS	21452450	21452500	0.97	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	exon	21452450	21452500	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	intron	21452501	21452658	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	CDS	21452659	21452907	0.52	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	exon	21452659	21452907	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	intron	21452908	21453312	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	CDS	21453313	21453428	1	-	2	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	exon	21453313	21453428	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	intron	21453429	21453602	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	CDS	21453603	21453684	1	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	exon	21453603	21453684	.	-	.	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
Phchi.S1	AUGUSTUS	start_codon	21453682	21453684	.	-	0	transcript_id "Phchi.S1G336000.t1"; gene_id "Phchi.S1G336000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10308.t1 is derived from g7484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47065345	47068841	.	-	.	Phchi.S1G746700
Phchi.S1	AUGUSTUS	transcript	47065345	47068841	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	stop_codon	47065342	47065344	.	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47065345	47065401	0.94	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47065345	47065401	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47065402	47065648	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47065649	47065717	0.94	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47065649	47065717	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47065718	47065788	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47065789	47065842	1	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47065789	47065842	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47065843	47065985	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47065986	47066112	1	-	1	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47065986	47066112	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47066113	47066357	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47066358	47066434	1	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47066358	47066434	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47066435	47066631	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47066632	47066913	0.99	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47066632	47066913	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47066914	47067030	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47067031	47067137	1	-	2	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47067031	47067137	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47067138	47067227	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47067228	47067279	1	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47067228	47067279	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47067280	47067411	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47067412	47067597	0.76	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47067412	47067597	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47067598	47067761	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47067762	47067926	0.78	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47067762	47067926	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	intron	47067927	47068097	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	CDS	47068098	47068841	1	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	exon	47068098	47068841	.	-	.	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
Phchi.S1	AUGUSTUS	start_codon	47068839	47068841	.	-	0	transcript_id "Phchi.S1G746700.t1"; gene_id "Phchi.S1G746700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8555.t1 is derived from g5730.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36607014	36608346	.	+	.	Phchi.S1G571400
Phchi.S1	AUGUSTUS	transcript	36607014	36608346	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	start_codon	36607014	36607016	.	+	0	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607014	36607193	0.81	+	0	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607014	36607193	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	intron	36607194	36607293	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607294	36607596	1	+	0	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607294	36607596	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	intron	36607597	36607730	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607731	36607826	0.64	+	0	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607731	36607826	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	intron	36607827	36607929	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607930	36608346	0.54	+	0	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607930	36608346	.	+	.	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	stop_codon	36608347	36608349	.	+	0	transcript_id "Phchi.S1G571400.t1"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	transcript	36607014	36608346	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	start_codon	36607014	36607016	.	+	0	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607014	36607193	0.7	+	0	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607014	36607193	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	intron	36607194	36607305	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607306	36607596	0.97	+	0	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607306	36607596	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	intron	36607597	36607730	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607731	36607826	0.6	+	0	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607731	36607826	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	intron	36607827	36607929	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	CDS	36607930	36608346	0.42	+	0	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	exon	36607930	36608346	.	+	.	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
Phchi.S1	AUGUSTUS	stop_codon	36608347	36608349	.	+	0	transcript_id "Phchi.S1G571400.t2"; gene_id "Phchi.S1G571400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8547.t1 is derived from g5722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36574695	36575455	.	+	.	Phchi.S1G570600
Phchi.S1	AUGUSTUS	transcript	36574695	36575455	.	+	.	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	start_codon	36574695	36574697	.	+	0	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	CDS	36574695	36574757	1	+	0	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	exon	36574695	36574757	.	+	.	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	intron	36574758	36575023	.	+	.	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	CDS	36575024	36575455	1	+	0	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	exon	36575024	36575455	.	+	.	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
Phchi.S1	AUGUSTUS	stop_codon	36575456	36575458	.	+	0	transcript_id "Phchi.S1G570600.t1"; gene_id "Phchi.S1G570600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13384.t1 is derived from g11850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6478291	6479865	.	-	.	Phchi.S3G070300
Phchi.S3	AUGUSTUS	transcript	6478291	6479865	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	stop_codon	6478288	6478290	.	-	0	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	CDS	6478291	6478447	0.92	-	1	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	exon	6478291	6478447	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	intron	6478448	6478694	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	CDS	6478695	6478820	1	-	1	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	exon	6478695	6478820	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	intron	6478821	6478907	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	CDS	6478908	6479002	1	-	0	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	exon	6478908	6479002	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	intron	6479003	6479105	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	CDS	6479106	6479191	1	-	2	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	exon	6479106	6479191	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	intron	6479192	6479287	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	CDS	6479288	6479437	1	-	2	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	exon	6479288	6479437	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	intron	6479438	6479564	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	CDS	6479565	6479865	0.95	-	0	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	exon	6479565	6479865	.	-	.	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
Phchi.S3	AUGUSTUS	start_codon	6479863	6479865	.	-	0	transcript_id "Phchi.S3G070300.t1"; gene_id "Phchi.S3G070300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14917.t1 is derived from g13385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15487289	15489534	.	+	.	Phchi.S3G223600
Phchi.S3	AUGUSTUS	transcript	15487289	15489534	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	start_codon	15487289	15487291	.	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	CDS	15487289	15487450	1	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	exon	15487289	15487450	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	intron	15487451	15487764	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	CDS	15487765	15488023	1	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	exon	15487765	15488023	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	intron	15488024	15488155	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	CDS	15488156	15488304	1	+	2	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	exon	15488156	15488304	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	intron	15488305	15488398	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	CDS	15488399	15488677	0.99	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	exon	15488399	15488677	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	intron	15488678	15488775	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	CDS	15488776	15489021	1	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	exon	15488776	15489021	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	intron	15489022	15489369	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	CDS	15489370	15489534	1	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	exon	15489370	15489534	.	+	.	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
Phchi.S3	AUGUSTUS	stop_codon	15489535	15489537	.	+	0	transcript_id "Phchi.S3G223600.t1"; gene_id "Phchi.S3G223600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11895.t1 is derived from g15947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9069683	9072296	.	-	.	Phchi.S4G147700
Phchi.S4	AUGUSTUS	transcript	9069683	9072296	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	stop_codon	9069680	9069682	.	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9069683	9069901	0.99	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9069683	9069901	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9069902	9069995	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9069996	9070136	1	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9069996	9070136	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9070137	9070228	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9070229	9070306	0.96	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9070229	9070306	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9070307	9070409	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9070410	9070589	0.86	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9070410	9070589	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9070590	9070687	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9070688	9070843	0.99	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9070688	9070843	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9070844	9070950	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9070951	9071082	0.67	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9070951	9071082	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9071083	9071184	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9071185	9071254	0.98	-	1	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9071185	9071254	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9071255	9071391	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9071392	9071618	1	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9071392	9071618	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9071619	9071729	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9071730	9071808	1	-	1	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9071730	9071808	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9071809	9071947	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9071948	9072083	1	-	2	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9071948	9072083	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	intron	9072084	9072223	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	CDS	9072224	9072296	1	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	exon	9072224	9072296	.	-	.	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
Phchi.S4	AUGUSTUS	start_codon	9072294	9072296	.	-	0	transcript_id "Phchi.S4G147700.t1"; gene_id "Phchi.S4G147700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9061.t1 is derived from g6236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39537558	39540078	.	+	.	Phchi.S1G622000
Phchi.S1	AUGUSTUS	transcript	39537558	39540078	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	start_codon	39537558	39537560	.	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39537558	39537641	0.99	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39537558	39537641	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39537642	39537765	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39537766	39537812	1	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39537766	39537812	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39537813	39537891	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39537892	39537962	1	+	1	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39537892	39537962	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39537963	39538054	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39538055	39538168	1	+	2	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39538055	39538168	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39538169	39538254	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39538255	39538430	1	+	2	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39538255	39538430	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39538431	39538540	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39538541	39538629	1	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39538541	39538629	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39538630	39538802	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39538803	39538920	1	+	1	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39538803	39538920	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39538921	39539017	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39539018	39539091	1	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39539018	39539091	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39539092	39539175	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39539176	39539223	0.99	+	1	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39539176	39539223	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39539224	39539344	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39539345	39539405	0.37	+	1	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39539345	39539405	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39539406	39539595	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39539596	39539805	1	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39539596	39539805	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	intron	39539806	39539889	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	CDS	39539890	39540078	0.61	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	exon	39539890	39540078	.	+	.	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
Phchi.S1	AUGUSTUS	stop_codon	39540079	39540081	.	+	0	transcript_id "Phchi.S1G622000.t1"; gene_id "Phchi.S1G622000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10490.t1 is derived from g14539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	675042	678675	.	-	.	Phchi.S4G007200
Phchi.S4	AUGUSTUS	transcript	675042	678675	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	stop_codon	675039	675041	.	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	675042	675095	0.97	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	675042	675095	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	675096	675190	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	675191	675230	0.85	-	1	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	675191	675230	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	675231	675441	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	675442	675520	0.99	-	2	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	675442	675520	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	675521	675627	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	675628	675676	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	675628	675676	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	675677	675783	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	675784	675840	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	675784	675840	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	675841	675928	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	675929	676000	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	675929	676000	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	676001	676099	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	676100	676191	1	-	2	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	676100	676191	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	676192	676290	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	676291	676363	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	676291	676363	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	676364	676454	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	676455	676529	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	676455	676529	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	676530	676619	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	676620	676684	1	-	2	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	676620	676684	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	676685	676776	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	676777	676867	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	676777	676867	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	676868	677000	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	677001	677042	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	677001	677042	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	677043	677130	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	677131	677220	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	677131	677220	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	677221	677309	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	677310	677348	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	677310	677348	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	677349	677438	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	677439	677522	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	677439	677522	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	677523	677622	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	677623	677708	1	-	2	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	677623	677708	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	677709	677813	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	677814	677927	0.99	-	2	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	677814	677927	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	677928	678075	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	678076	678187	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	678076	678187	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	intron	678188	678546	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	CDS	678547	678675	1	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	exon	678547	678675	.	-	.	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
Phchi.S4	AUGUSTUS	start_codon	678673	678675	.	-	0	transcript_id "Phchi.S4G007200.t1"; gene_id "Phchi.S4G007200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14720.t1 is derived from g13188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14356945	14358513	.	+	.	Phchi.S3G203900
Phchi.S3	AUGUSTUS	transcript	14356945	14358513	.	+	.	transcript_id "Phchi.S3G203900.t1"; gene_id "Phchi.S3G203900"
Phchi.S3	AUGUSTUS	start_codon	14356945	14356947	.	+	0	transcript_id "Phchi.S3G203900.t1"; gene_id "Phchi.S3G203900"
Phchi.S3	AUGUSTUS	CDS	14356945	14358513	0.75	+	0	transcript_id "Phchi.S3G203900.t1"; gene_id "Phchi.S3G203900"
Phchi.S3	AUGUSTUS	exon	14356945	14358513	.	+	.	transcript_id "Phchi.S3G203900.t1"; gene_id "Phchi.S3G203900"
Phchi.S3	AUGUSTUS	stop_codon	14358514	14358516	.	+	0	transcript_id "Phchi.S3G203900.t1"; gene_id "Phchi.S3G203900"
# This transcript jg15677.t2 is derived from g14146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15678.t1 is derived from g14147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20626052	20627414	.	+	.	Phchi.S3G299700
Phchi.S3	AUGUSTUS	transcript	20626052	20627414	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	start_codon	20626052	20626054	.	+	0	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	CDS	20626052	20626192	1	+	0	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	exon	20626052	20626192	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	intron	20626193	20626308	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	CDS	20626309	20626490	1	+	0	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	exon	20626309	20626490	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	intron	20626491	20626583	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	CDS	20626584	20626827	1	+	1	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	exon	20626584	20626827	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	intron	20626828	20626917	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	CDS	20626918	20627094	1	+	0	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	exon	20626918	20627094	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	intron	20627095	20627195	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	CDS	20627196	20627414	1	+	0	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	exon	20627196	20627414	.	+	.	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
Phchi.S3	AUGUSTUS	stop_codon	20627415	20627417	.	+	0	transcript_id "Phchi.S3G299700.t1"; gene_id "Phchi.S3G299700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6261.t1 is derived from g3433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21920657	21922093	.	+	.	Phchi.S1G342000
Phchi.S1	AUGUSTUS	transcript	21920657	21922093	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	start_codon	21920657	21920659	.	+	0	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21920657	21920840	0.99	+	0	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21920657	21920840	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	intron	21920841	21920934	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21920935	21921011	1	+	2	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21920935	21921011	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	intron	21921012	21921098	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21921099	21921373	1	+	0	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21921099	21921373	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	intron	21921374	21921464	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21921465	21921533	0.88	+	1	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21921465	21921533	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	intron	21921534	21921650	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21921651	21921715	0.89	+	1	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21921651	21921715	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	intron	21921716	21921795	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21921796	21921897	1	+	2	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21921796	21921897	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	intron	21921898	21921986	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	CDS	21921987	21922093	0.99	+	2	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	exon	21921987	21922093	.	+	.	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
Phchi.S1	AUGUSTUS	stop_codon	21922094	21922096	.	+	0	transcript_id "Phchi.S1G342000.t1"; gene_id "Phchi.S1G342000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15171.t1 is derived from g13639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17356851	17357446	.	+	.	Phchi.S3G249000
Phchi.S3	AUGUSTUS	transcript	17356851	17357446	.	+	.	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	start_codon	17356851	17356853	.	+	0	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	CDS	17356851	17357180	0.98	+	0	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	exon	17356851	17357180	.	+	.	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	intron	17357181	17357275	.	+	.	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	CDS	17357276	17357446	0.87	+	0	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	exon	17357276	17357446	.	+	.	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
Phchi.S3	AUGUSTUS	stop_codon	17357447	17357449	.	+	0	transcript_id "Phchi.S3G249000.t1"; gene_id "Phchi.S3G249000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7744.t1 is derived from g4918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30925612	30929571	.	-	.	Phchi.S1G490300
Phchi.S1	AUGUSTUS	transcript	30925612	30929571	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	stop_codon	30925609	30925611	.	-	0	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	CDS	30925612	30925839	0.98	-	0	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	exon	30925612	30925839	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	intron	30925840	30925962	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	CDS	30925963	30927023	0.99	-	2	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	exon	30925963	30927023	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	intron	30927024	30927160	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	CDS	30927161	30927315	1	-	1	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	exon	30927161	30927315	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	intron	30927316	30927403	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	CDS	30927404	30927836	1	-	2	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	exon	30927404	30927836	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	intron	30927837	30927935	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	CDS	30927936	30928270	1	-	1	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	exon	30927936	30928270	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	intron	30928271	30928393	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	CDS	30928394	30929571	0.53	-	0	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	exon	30928394	30929571	.	-	.	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
Phchi.S1	AUGUSTUS	start_codon	30929569	30929571	.	-	0	transcript_id "Phchi.S1G490300.t1"; gene_id "Phchi.S1G490300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2787.t1 is derived from g9707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8865494	8865925	.	-	.	Phchi.S5G139600
Phchi.S5	AUGUSTUS	transcript	8865494	8865925	.	-	.	transcript_id "Phchi.S5G139600.t1"; gene_id "Phchi.S5G139600"
Phchi.S5	AUGUSTUS	stop_codon	8865491	8865493	.	-	0	transcript_id "Phchi.S5G139600.t1"; gene_id "Phchi.S5G139600"
Phchi.S5	AUGUSTUS	CDS	8865494	8865925	0.49	-	0	transcript_id "Phchi.S5G139600.t1"; gene_id "Phchi.S5G139600"
Phchi.S5	AUGUSTUS	exon	8865494	8865925	.	-	.	transcript_id "Phchi.S5G139600.t1"; gene_id "Phchi.S5G139600"
Phchi.S5	AUGUSTUS	start_codon	8865923	8865925	.	-	0	transcript_id "Phchi.S5G139600.t1"; gene_id "Phchi.S5G139600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12517.t1 is derived from g8194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32636557	32640958	.	+	.	Phchi.S2G059700
Phchi.S2	AUGUSTUS	transcript	32636557	32640958	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	start_codon	32636557	32636559	.	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32636557	32637185	0.99	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32636557	32637185	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32637186	32637315	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32637316	32637766	1	+	1	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32637316	32637766	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32637767	32637909	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32637910	32638506	0.99	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32637910	32638506	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32638507	32638760	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32638761	32639125	1	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32638761	32639125	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32639126	32639229	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32639230	32639533	0.99	+	1	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32639230	32639533	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32639534	32639637	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32639638	32639760	1	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32639638	32639760	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32639761	32639915	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32639916	32640110	0.49	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32639916	32640110	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32640111	32640334	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32640335	32640373	0.8	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32640335	32640373	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	intron	32640374	32640505	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	CDS	32640506	32640958	0.96	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	exon	32640506	32640958	.	+	.	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
Phchi.S2	AUGUSTUS	stop_codon	32640959	32640961	.	+	0	transcript_id "Phchi.S2G059700.t1"; gene_id "Phchi.S2G059700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6468.t1 is derived from g3640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23146002	23146748	.	-	.	Phchi.S1G362700
Phchi.S1	AUGUSTUS	transcript	23146002	23146748	.	-	.	transcript_id "Phchi.S1G362700.t1"; gene_id "Phchi.S1G362700"
Phchi.S1	AUGUSTUS	stop_codon	23145999	23146001	.	-	0	transcript_id "Phchi.S1G362700.t1"; gene_id "Phchi.S1G362700"
Phchi.S1	AUGUSTUS	CDS	23146002	23146748	0.61	-	0	transcript_id "Phchi.S1G362700.t1"; gene_id "Phchi.S1G362700"
Phchi.S1	AUGUSTUS	exon	23146002	23146748	.	-	.	transcript_id "Phchi.S1G362700.t1"; gene_id "Phchi.S1G362700"
Phchi.S1	AUGUSTUS	start_codon	23146746	23146748	.	-	0	transcript_id "Phchi.S1G362700.t1"; gene_id "Phchi.S1G362700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4502.t1 is derived from g1672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10863126	10864591	.	+	.	Phchi.S1G166100
Phchi.S1	AUGUSTUS	transcript	10863126	10864591	.	+	.	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	start_codon	10863126	10863128	.	+	0	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	CDS	10863126	10863296	0.16	+	0	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	exon	10863126	10863296	.	+	.	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	intron	10863297	10863457	.	+	.	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	CDS	10863458	10864591	0.94	+	0	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	exon	10863458	10864591	.	+	.	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
Phchi.S1	AUGUSTUS	stop_codon	10864592	10864594	.	+	0	transcript_id "Phchi.S1G166100.t1"; gene_id "Phchi.S1G166100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15730.t1 is derived from g14200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20917717	20920966	.	+	.	Phchi.S3G304900
Phchi.S3	AUGUSTUS	transcript	20917717	20920966	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	start_codon	20917717	20917719	.	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20917717	20917842	1	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20917717	20917842	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20917843	20918314	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20918315	20918430	1	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20918315	20918430	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20918431	20918563	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20918564	20918625	1	+	1	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20918564	20918625	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20918626	20918797	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20918798	20918836	1	+	2	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20918798	20918836	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20918837	20918932	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20918933	20919033	1	+	2	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20918933	20919033	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20919034	20919182	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20919183	20919292	1	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20919183	20919292	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20919293	20919446	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20919447	20919546	1	+	1	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20919447	20919546	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20919547	20919684	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20919685	20919885	0.95	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20919685	20919885	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20919886	20919987	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20919988	20920048	0.95	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20919988	20920048	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20920049	20920160	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20920161	20920258	1	+	2	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20920161	20920258	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20920259	20920349	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20920350	20920492	1	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20920350	20920492	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20920493	20920581	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20920582	20920665	1	+	1	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20920582	20920665	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20920666	20920738	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20920739	20920828	1	+	1	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20920739	20920828	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	intron	20920829	20920905	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	CDS	20920906	20920966	1	+	1	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	exon	20920906	20920966	.	+	.	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
Phchi.S3	AUGUSTUS	stop_codon	20920967	20920969	.	+	0	transcript_id "Phchi.S3G304900.t1"; gene_id "Phchi.S3G304900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7242.t1 is derived from g4414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27803604	27804668	.	-	.	Phchi.S1G440100
Phchi.S1	AUGUSTUS	transcript	27803604	27804668	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	stop_codon	27803601	27803603	.	-	0	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	CDS	27803604	27803801	0.96	-	0	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	exon	27803604	27803801	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	intron	27803802	27803908	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	CDS	27803909	27804166	0.93	-	0	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	exon	27803909	27804166	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	intron	27804167	27804240	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	CDS	27804241	27804378	0.97	-	0	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	exon	27804241	27804378	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	intron	27804379	27804461	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	CDS	27804462	27804668	0.61	-	0	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	exon	27804462	27804668	.	-	.	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
Phchi.S1	AUGUSTUS	start_codon	27804666	27804668	.	-	0	transcript_id "Phchi.S1G440100.t1"; gene_id "Phchi.S1G440100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12400.t1 is derived from g8077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17574028	17583058	.	+	.	Phchi.S2G048000
Phchi.S2	AUGUSTUS	transcript	17574028	17583058	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	start_codon	17574028	17574030	.	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17574028	17574360	0.77	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17574028	17574360	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17574361	17575099	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575100	17575255	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575100	17575255	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17575256	17575390	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575391	17575453	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575391	17575453	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17575454	17575605	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575606	17575674	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575606	17575674	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17575675	17575961	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575962	17576133	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575962	17576133	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576134	17576224	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17576225	17576386	1	+	2	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17576225	17576386	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576387	17576598	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17576599	17576696	1	+	2	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17576599	17576696	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576697	17576807	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17576808	17576882	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17576808	17576882	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576883	17577017	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577018	17577086	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577018	17577086	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577087	17577212	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577213	17577298	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577213	17577298	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577299	17577401	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577402	17577519	1	+	1	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577402	17577519	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577520	17577714	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577715	17577813	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577715	17577813	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577814	17578042	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17578043	17578394	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17578043	17578394	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17578395	17578511	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17578512	17579573	0.87	+	2	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17578512	17579573	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17579574	17579653	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17579654	17579905	0.92	+	2	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17579654	17579905	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17579906	17580031	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580032	17580124	1	+	2	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580032	17580124	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17580125	17580211	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580212	17580330	1	+	2	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580212	17580330	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17580331	17580512	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580513	17580602	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580513	17580602	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17580603	17580938	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580939	17581043	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580939	17581043	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581044	17581134	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17581135	17581221	0.76	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17581135	17581221	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581222	17581558	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17581559	17581627	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17581559	17581627	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581628	17581733	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17581734	17581802	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17581734	17581802	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581803	17582618	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17582619	17582720	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17582619	17582720	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17582721	17582812	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17582813	17582935	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17582813	17582935	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17582936	17583025	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17583026	17583058	1	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17583026	17583058	.	+	.	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	stop_codon	17583059	17583061	.	+	0	transcript_id "Phchi.S2G048000.t1"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	transcript	17574028	17583058	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	start_codon	17574028	17574030	.	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17574028	17574360	0.78	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17574028	17574360	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17574361	17575099	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575100	17575255	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575100	17575255	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17575256	17575390	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575391	17575453	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575391	17575453	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17575454	17575605	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575606	17575674	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575606	17575674	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17575675	17575961	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17575962	17576133	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17575962	17576133	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576134	17576224	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17576225	17576386	1	+	2	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17576225	17576386	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576387	17576598	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17576599	17576696	1	+	2	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17576599	17576696	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576697	17576807	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17576808	17576882	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17576808	17576882	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17576883	17577017	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577018	17577086	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577018	17577086	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577087	17577212	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577213	17577298	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577213	17577298	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577299	17577401	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577402	17577519	1	+	1	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577402	17577519	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577520	17577714	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17577715	17577813	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17577715	17577813	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17577814	17578042	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17578043	17578394	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17578043	17578394	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17578395	17578511	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17578512	17579573	0.86	+	2	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17578512	17579573	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17579574	17579653	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17579654	17579905	0.9	+	2	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17579654	17579905	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17579906	17580031	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580032	17580124	1	+	2	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580032	17580124	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17580125	17580211	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580212	17580330	1	+	2	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580212	17580330	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17580331	17580512	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580513	17580602	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580513	17580602	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17580603	17580935	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17580936	17581043	0.98	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17580936	17581043	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581044	17581134	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17581135	17581221	0.73	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17581135	17581221	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581222	17581558	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17581559	17581627	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17581559	17581627	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581628	17581733	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17581734	17581802	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17581734	17581802	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17581803	17582618	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17582619	17582720	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17582619	17582720	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17582721	17582812	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17582813	17582935	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17582813	17582935	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	intron	17582936	17583025	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	CDS	17583026	17583058	1	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	exon	17583026	17583058	.	+	.	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
Phchi.S2	AUGUSTUS	stop_codon	17583059	17583061	.	+	0	transcript_id "Phchi.S2G048000.t2"; gene_id "Phchi.S2G048000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3365.t1 is derived from g534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3169765	3170595	.	+	.	Phchi.S1G052400
Phchi.S1	AUGUSTUS	transcript	3169765	3170595	.	+	.	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	start_codon	3169765	3169767	.	+	0	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	CDS	3169765	3169815	0.98	+	0	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	exon	3169765	3169815	.	+	.	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	intron	3169816	3169902	.	+	.	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	CDS	3169903	3170044	1	+	0	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	exon	3169903	3170044	.	+	.	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	intron	3170045	3170137	.	+	.	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	CDS	3170138	3170595	0.97	+	2	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	exon	3170138	3170595	.	+	.	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
Phchi.S1	AUGUSTUS	stop_codon	3170596	3170598	.	+	0	transcript_id "Phchi.S1G052400.t1"; gene_id "Phchi.S1G052400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4835.t1 is derived from g2005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13048967	13049236	.	-	.	Phchi.S1G199400
Phchi.S1	AUGUSTUS	transcript	13048967	13049236	.	-	.	transcript_id "Phchi.S1G199400.t1"; gene_id "Phchi.S1G199400"
Phchi.S1	AUGUSTUS	stop_codon	13048964	13048966	.	-	0	transcript_id "Phchi.S1G199400.t1"; gene_id "Phchi.S1G199400"
Phchi.S1	AUGUSTUS	CDS	13048967	13049236	0.27	-	0	transcript_id "Phchi.S1G199400.t1"; gene_id "Phchi.S1G199400"
Phchi.S1	AUGUSTUS	exon	13048967	13049236	.	-	.	transcript_id "Phchi.S1G199400.t1"; gene_id "Phchi.S1G199400"
Phchi.S1	AUGUSTUS	start_codon	13049234	13049236	.	-	0	transcript_id "Phchi.S1G199400.t1"; gene_id "Phchi.S1G199400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6856.t1 is derived from g4028.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25594635	25602695	.	-	.	Phchi.S1G401500
Phchi.S1	AUGUSTUS	transcript	25594635	25602695	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	stop_codon	25594632	25594634	.	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25594635	25594667	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25594635	25594667	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25594668	25594755	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25594756	25594851	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25594756	25594851	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25594852	25595011	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25595012	25595029	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25595012	25595029	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25595030	25595120	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25595121	25595220	1	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25595121	25595220	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25595221	25595352	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25595353	25595475	1	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25595353	25595475	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25595476	25595614	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25595615	25595820	0.68	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25595615	25595820	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25595821	25595898	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25595899	25596162	0.6	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25595899	25596162	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25596163	25596250	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25596251	25596328	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25596251	25596328	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25596329	25596431	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25596432	25596722	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25596432	25596722	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25596723	25596954	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25596955	25597307	0.68	-	2	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25596955	25597307	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25597308	25597396	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25597397	25597607	0.64	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25597397	25597607	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25597608	25597714	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25597715	25597756	0.89	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25597715	25597756	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25597757	25597882	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25597883	25597987	0.74	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25597883	25597987	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25597988	25598161	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25598162	25598188	0.74	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25598162	25598188	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25598189	25598417	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25598418	25598501	0.96	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25598418	25598501	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25598502	25598590	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25598591	25598672	1	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25598591	25598672	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25598673	25598769	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25598770	25598849	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25598770	25598849	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25598850	25598942	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25598943	25599048	1	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25598943	25599048	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25599049	25599168	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25599169	25599236	0.99	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25599169	25599236	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25599237	25599314	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25599315	25599428	0.85	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25599315	25599428	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25599429	25599526	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25599527	25599602	1	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25599527	25599602	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25599603	25599746	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25599747	25599851	1	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25599747	25599851	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25599852	25599939	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25599940	25600028	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25599940	25600028	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25600029	25600214	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25600215	25600343	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25600215	25600343	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25600344	25600530	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25600531	25600634	0.82	-	2	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25600531	25600634	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25600635	25600762	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25600763	25600820	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25600763	25600820	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25600821	25600939	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25600940	25601029	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25600940	25601029	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25601030	25601210	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25601211	25601261	1	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25601211	25601261	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25601262	25601451	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25601452	25601536	0.59	-	1	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25601452	25601536	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25601537	25601807	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25601808	25601925	1	-	2	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25601808	25601925	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25601926	25602015	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25602016	25602219	0.85	-	2	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25602016	25602219	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	intron	25602220	25602610	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	CDS	25602611	25602695	0.44	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	exon	25602611	25602695	.	-	.	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
Phchi.S1	AUGUSTUS	start_codon	25602693	25602695	.	-	0	transcript_id "Phchi.S1G401500.t1"; gene_id "Phchi.S1G401500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5502.t1 is derived from g2672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17149965	17153237	.	+	.	Phchi.S1G266100
Phchi.S1	AUGUSTUS	transcript	17149965	17153237	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	start_codon	17149965	17149967	.	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17149965	17150233	0.97	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17149965	17150233	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17150234	17150346	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17150347	17150728	1	+	1	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17150347	17150728	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17150729	17150812	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17150813	17151100	1	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17150813	17151100	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17151101	17151214	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17151215	17151385	1	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17151215	17151385	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17151386	17151476	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17151477	17151740	1	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17151477	17151740	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17151741	17151867	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17151868	17152041	0.99	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17151868	17152041	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17152042	17152142	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17152143	17152291	1	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17152143	17152291	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17152292	17152385	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17152386	17152568	1	+	1	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17152386	17152568	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	intron	17152569	17152735	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	CDS	17152736	17153237	1	+	1	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	exon	17152736	17153237	.	+	.	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
Phchi.S1	AUGUSTUS	stop_codon	17153238	17153240	.	+	0	transcript_id "Phchi.S1G266100.t1"; gene_id "Phchi.S1G266100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9929.t1 is derived from g7105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44523759	44524909	.	-	.	Phchi.S1G708800
Phchi.S1	AUGUSTUS	transcript	44523759	44524909	.	-	.	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	stop_codon	44523756	44523758	.	-	0	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	CDS	44523759	44523763	0.55	-	2	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	exon	44523759	44523763	.	-	.	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	intron	44523764	44524017	.	-	.	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	CDS	44524018	44524243	0.64	-	0	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	exon	44524018	44524243	.	-	.	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	intron	44524244	44524444	.	-	.	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	CDS	44524445	44524909	0.1	-	0	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	exon	44524445	44524909	.	-	.	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
Phchi.S1	AUGUSTUS	start_codon	44524907	44524909	.	-	0	transcript_id "Phchi.S1G708800.t1"; gene_id "Phchi.S1G708800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12341.t1 is derived from g8017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11871949	11874409	.	+	.	Phchi.S2G042100
Phchi.S2	AUGUSTUS	transcript	11871949	11874409	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	start_codon	11871949	11871951	.	+	0	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11871949	11872317	0.78	+	0	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11871949	11872317	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	intron	11872318	11872420	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11872421	11872746	0.99	+	0	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11872421	11872746	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	intron	11872747	11872833	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11872834	11873410	0.98	+	1	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11872834	11873410	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	intron	11873411	11873503	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11873504	11873621	0.86	+	0	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11873504	11873621	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	intron	11873622	11873741	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11873742	11873808	0.63	+	2	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11873742	11873808	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	intron	11873809	11873925	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11873926	11874193	0.42	+	1	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11873926	11874193	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	intron	11874194	11874349	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	CDS	11874350	11874409	0.27	+	0	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	exon	11874350	11874409	.	+	.	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
Phchi.S2	AUGUSTUS	stop_codon	11874410	11874412	.	+	0	transcript_id "Phchi.S2G042100.t1"; gene_id "Phchi.S2G042100"
# This transcript jg2623.t2 is derived from g9543.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2624.t1 is derived from g9544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7810107	7819778	.	+	.	Phchi.S5G123300
Phchi.S5	AUGUSTUS	transcript	7810107	7819778	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	start_codon	7810107	7810109	.	+	0	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7810107	7810161	0.99	+	0	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7810107	7810161	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7810162	7810358	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7810359	7810703	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7810359	7810703	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7810704	7810961	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7810962	7811315	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7810962	7811315	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7811316	7811486	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7811487	7811816	0.98	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7811487	7811816	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7811817	7811913	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7811914	7812276	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7811914	7812276	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7812277	7812464	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7812465	7812830	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7812465	7812830	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7812831	7812994	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7812995	7813366	0.9	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7812995	7813366	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7813367	7813444	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7813445	7813834	0.88	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7813445	7813834	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7813835	7813936	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7813937	7814305	0.64	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7813937	7814305	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7814306	7814383	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7814384	7814725	0.96	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7814384	7814725	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7814726	7814812	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7814813	7815133	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7814813	7815133	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7815134	7815211	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7815212	7815559	0.92	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7815212	7815559	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7815560	7815648	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7815649	7815996	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7815649	7815996	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7815997	7816092	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7816093	7816428	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7816093	7816428	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7816429	7816500	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7816501	7816866	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7816501	7816866	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7816867	7817025	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817026	7817331	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817026	7817331	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7817332	7817411	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817412	7817479	1	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817412	7817479	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7817480	7817617	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817618	7817838	0.96	+	0	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817618	7817838	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7817839	7817956	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817957	7818127	0.84	+	1	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817957	7818127	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7818128	7818201	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7818202	7818422	1	+	1	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7818202	7818422	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7818423	7818515	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7818516	7818718	0.59	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7818516	7818718	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7818719	7818889	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7818890	7819064	1	+	0	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7818890	7819064	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7819065	7819162	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7819163	7819365	0.74	+	2	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7819163	7819365	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7819366	7819450	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7819451	7819560	0.68	+	0	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7819451	7819560	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7819561	7819675	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7819676	7819778	0.68	+	1	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7819676	7819778	.	+	.	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	stop_codon	7819779	7819781	.	+	0	transcript_id "Phchi.S5G123300.t1"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	transcript	7810107	7819778	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	start_codon	7810107	7810109	.	+	0	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7810107	7810161	0.97	+	0	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7810107	7810161	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7810162	7810358	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7810359	7810703	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7810359	7810703	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7810704	7810961	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7810962	7811315	0.99	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7810962	7811315	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7811316	7811486	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7811487	7811816	0.98	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7811487	7811816	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7811817	7811913	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7811914	7812276	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7811914	7812276	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7812277	7812464	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7812465	7812830	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7812465	7812830	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7812831	7812994	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7812995	7813366	0.88	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7812995	7813366	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7813367	7813444	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7813445	7813834	0.88	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7813445	7813834	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7813835	7813936	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7813937	7814305	0.68	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7813937	7814305	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7814306	7814400	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7814401	7814418	0.99	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7814401	7814418	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7814419	7814551	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7814552	7814725	0.98	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7814552	7814725	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7814726	7814812	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7814813	7815133	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7814813	7815133	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7815134	7815211	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7815212	7815559	0.9	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7815212	7815559	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7815560	7815648	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7815649	7815996	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7815649	7815996	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7815997	7816092	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7816093	7816428	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7816093	7816428	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7816429	7816500	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7816501	7816866	0.99	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7816501	7816866	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7816867	7817025	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817026	7817331	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817026	7817331	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7817332	7817411	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817412	7817479	1	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817412	7817479	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7817480	7817617	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817618	7817838	0.98	+	0	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817618	7817838	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7817839	7817956	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7817957	7818127	0.85	+	1	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7817957	7818127	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7818128	7818201	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7818202	7818422	1	+	1	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7818202	7818422	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7818423	7818515	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7818516	7818718	0.62	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7818516	7818718	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7818719	7818889	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7818890	7819064	0.98	+	0	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7818890	7819064	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7819065	7819162	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7819163	7819365	0.64	+	2	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7819163	7819365	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7819366	7819450	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7819451	7819560	0.57	+	0	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7819451	7819560	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	intron	7819561	7819675	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	CDS	7819676	7819778	0.58	+	1	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	exon	7819676	7819778	.	+	.	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
Phchi.S5	AUGUSTUS	stop_codon	7819779	7819781	.	+	0	transcript_id "Phchi.S5G123300.t2"; gene_id "Phchi.S5G123300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6953.t1 is derived from g4125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26120556	26124805	.	-	.	Phchi.S1G411200
Phchi.S1	AUGUSTUS	transcript	26120556	26124805	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	stop_codon	26120553	26120555	.	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26120556	26121696	0.88	-	1	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26120556	26121696	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26121697	26121835	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26121836	26121955	0.92	-	1	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26121836	26121955	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26121956	26122051	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26122052	26122239	1	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26122052	26122239	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26122240	26122338	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26122339	26122425	1	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26122339	26122425	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26122426	26122543	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26122544	26122698	1	-	2	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26122544	26122698	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26122699	26122794	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26122795	26122864	1	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26122795	26122864	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26122865	26122976	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26122977	26123152	1	-	2	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26122977	26123152	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26123153	26123241	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26123242	26123409	1	-	2	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26123242	26123409	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26123410	26123481	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26123482	26123561	1	-	1	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26123482	26123561	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26123562	26123658	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26123659	26123912	0.71	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26123659	26123912	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26123913	26124321	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26124322	26124354	0.53	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26124322	26124354	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26124355	26124434	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26124435	26124496	0.49	-	2	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26124435	26124496	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	intron	26124497	26124591	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	CDS	26124592	26124805	0.39	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	exon	26124592	26124805	.	-	.	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
Phchi.S1	AUGUSTUS	start_codon	26124803	26124805	.	-	0	transcript_id "Phchi.S1G411200.t1"; gene_id "Phchi.S1G411200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1580.t1 is derived from g8499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1865389	1865754	.	-	.	Phchi.S5G018900
Phchi.S5	AUGUSTUS	transcript	1865389	1865754	.	-	.	transcript_id "Phchi.S5G018900.t1"; gene_id "Phchi.S5G018900"
Phchi.S5	AUGUSTUS	stop_codon	1865386	1865388	.	-	0	transcript_id "Phchi.S5G018900.t1"; gene_id "Phchi.S5G018900"
Phchi.S5	AUGUSTUS	CDS	1865389	1865754	0.89	-	0	transcript_id "Phchi.S5G018900.t1"; gene_id "Phchi.S5G018900"
Phchi.S5	AUGUSTUS	exon	1865389	1865754	.	-	.	transcript_id "Phchi.S5G018900.t1"; gene_id "Phchi.S5G018900"
Phchi.S5	AUGUSTUS	start_codon	1865752	1865754	.	-	0	transcript_id "Phchi.S5G018900.t1"; gene_id "Phchi.S5G018900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12659.t1 is derived from g14458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	35887	37081	.	-	.	Phchi.C12G000900
Phchi.C12	AUGUSTUS	transcript	35887	37081	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	stop_codon	35884	35886	.	-	0	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	CDS	35887	36018	0.82	-	0	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	exon	35887	36018	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	intron	36019	36106	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	CDS	36107	36250	0.89	-	0	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	exon	36107	36250	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	intron	36251	36336	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	CDS	36337	36510	0.87	-	0	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	exon	36337	36510	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	intron	36511	36796	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	CDS	36797	37081	0.54	-	0	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	exon	36797	37081	.	-	.	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
Phchi.C12	AUGUSTUS	start_codon	37079	37081	.	-	0	transcript_id "Phchi.C12G000900.t1"; gene_id "Phchi.C12G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2581.t1 is derived from g9501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7481580	7483566	.	-	.	Phchi.S5G119000
Phchi.S5	AUGUSTUS	transcript	7481580	7483566	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	stop_codon	7481577	7481579	.	-	0	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	CDS	7481580	7481784	1	-	1	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	exon	7481580	7481784	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	intron	7481785	7481888	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	CDS	7481889	7482055	1	-	0	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	exon	7481889	7482055	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	intron	7482056	7482132	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	CDS	7482133	7483240	1	-	1	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	exon	7482133	7483240	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	intron	7483241	7483369	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	CDS	7483370	7483566	0.69	-	0	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	exon	7483370	7483566	.	-	.	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
Phchi.S5	AUGUSTUS	start_codon	7483564	7483566	.	-	0	transcript_id "Phchi.S5G119000.t1"; gene_id "Phchi.S5G119000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10045.t1 is derived from g7221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45232104	45233509	.	-	.	Phchi.S1G720400
Phchi.S1	AUGUSTUS	transcript	45232104	45233509	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	stop_codon	45232101	45232103	.	-	0	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232104	45232194	0.97	-	1	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232104	45232194	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232195	45232303	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232304	45232422	0.99	-	0	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232304	45232422	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232423	45232598	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232599	45232705	1	-	2	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232599	45232705	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232706	45232798	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232799	45232877	0.99	-	0	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232799	45232877	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232878	45233002	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45233003	45233092	0.99	-	0	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45233003	45233092	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45233093	45233248	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45233249	45233509	0.76	-	0	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45233249	45233509	.	-	.	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	start_codon	45233507	45233509	.	-	0	transcript_id "Phchi.S1G720400.t1"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	transcript	45232104	45233509	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	stop_codon	45232101	45232103	.	-	0	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232104	45232194	0.97	-	1	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232104	45232194	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232195	45232303	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232304	45232422	0.97	-	0	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232304	45232422	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232423	45232598	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232599	45232705	1	-	2	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232599	45232705	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232706	45232798	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45232799	45232913	0.98	-	0	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45232799	45232913	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45232914	45233002	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45233003	45233092	0.99	-	0	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45233003	45233092	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	intron	45233093	45233248	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	CDS	45233249	45233509	0.73	-	0	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	exon	45233249	45233509	.	-	.	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
Phchi.S1	AUGUSTUS	start_codon	45233507	45233509	.	-	0	transcript_id "Phchi.S1G720400.t2"; gene_id "Phchi.S1G720400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2105.t1 is derived from g9025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4892708	4893957	.	-	.	Phchi.S5G071400
Phchi.S5	AUGUSTUS	transcript	4892708	4893957	.	-	.	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	stop_codon	4892705	4892707	.	-	0	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	CDS	4892708	4893767	1	-	1	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	exon	4892708	4893767	.	-	.	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	intron	4893768	4893862	.	-	.	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	CDS	4893863	4893957	1	-	0	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	exon	4893863	4893957	.	-	.	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
Phchi.S5	AUGUSTUS	start_codon	4893955	4893957	.	-	0	transcript_id "Phchi.S5G071400.t1"; gene_id "Phchi.S5G071400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8039.t1 is derived from g5214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32625406	32632006	.	+	.	Phchi.S1G519800
Phchi.S1	AUGUSTUS	transcript	32625406	32632006	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	start_codon	32625406	32625408	.	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32625406	32625579	0.99	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32625406	32625579	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32625580	32625819	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32625820	32625976	0.9	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32625820	32625976	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32625977	32626083	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32626084	32626106	0.76	+	2	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32626084	32626106	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32626107	32626458	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32626459	32626548	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32626459	32626548	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32626549	32626682	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32626683	32626760	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32626683	32626760	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32626761	32626916	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32626917	32626997	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32626917	32626997	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32626998	32627120	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32627121	32627171	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32627121	32627171	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32627172	32627313	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32627314	32627399	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32627314	32627399	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32627400	32627580	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32627581	32627647	1	+	1	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32627581	32627647	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32627648	32627793	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32627794	32627850	0.97	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32627794	32627850	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32627851	32627963	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32627964	32627993	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32627964	32627993	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32627994	32628123	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32628124	32628186	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32628124	32628186	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32628187	32628289	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32628290	32628406	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32628290	32628406	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32628407	32628533	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32628534	32628647	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32628534	32628647	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32628648	32628794	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32628795	32628893	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32628795	32628893	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32628894	32629023	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32629024	32629149	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32629024	32629149	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32629150	32629235	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32629236	32629310	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32629236	32629310	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32629311	32629424	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32629425	32629496	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32629425	32629496	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32629497	32629710	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32629711	32629821	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32629711	32629821	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32629822	32629994	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32629995	32630078	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32629995	32630078	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32630079	32630278	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32630279	32630386	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32630279	32630386	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32630387	32630514	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32630515	32630616	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32630515	32630616	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32630617	32630707	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32630708	32630770	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32630708	32630770	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32630771	32630874	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32630875	32630946	0.45	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32630875	32630946	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32630947	32631066	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32631067	32631141	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32631067	32631141	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32631142	32631242	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32631243	32631367	0.99	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32631243	32631367	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32631368	32631457	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32631458	32631509	1	+	1	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32631458	32631509	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32631510	32631594	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32631595	32631663	0.91	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32631595	32631663	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32631664	32631773	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32631774	32631833	0.91	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32631774	32631833	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	intron	32631834	32631922	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	CDS	32631923	32632006	1	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	exon	32631923	32632006	.	+	.	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
Phchi.S1	AUGUSTUS	stop_codon	32632007	32632009	.	+	0	transcript_id "Phchi.S1G519800.t1"; gene_id "Phchi.S1G519800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg764.t1 is derived from g10546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5392209	5393092	.	+	.	Phchi.S6G072300
Phchi.S6	AUGUSTUS	transcript	5392209	5393092	.	+	.	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	start_codon	5392209	5392211	.	+	0	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	CDS	5392209	5392535	0.76	+	0	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	exon	5392209	5392535	.	+	.	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	intron	5392536	5392632	.	+	.	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	CDS	5392633	5392764	0.38	+	0	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	exon	5392633	5392764	.	+	.	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	intron	5392765	5392924	.	+	.	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	CDS	5392925	5393092	0.77	+	0	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	exon	5392925	5393092	.	+	.	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
Phchi.S6	AUGUSTUS	stop_codon	5393093	5393095	.	+	0	transcript_id "Phchi.S6G072300.t1"; gene_id "Phchi.S6G072300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8883.t1 is derived from g6058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38479713	38480288	.	+	.	Phchi.S1G604200
Phchi.S1	AUGUSTUS	transcript	38479713	38480288	.	+	.	transcript_id "Phchi.S1G604200.t1"; gene_id "Phchi.S1G604200"
Phchi.S1	AUGUSTUS	start_codon	38479713	38479715	.	+	0	transcript_id "Phchi.S1G604200.t1"; gene_id "Phchi.S1G604200"
Phchi.S1	AUGUSTUS	CDS	38479713	38480288	0.86	+	0	transcript_id "Phchi.S1G604200.t1"; gene_id "Phchi.S1G604200"
Phchi.S1	AUGUSTUS	exon	38479713	38480288	.	+	.	transcript_id "Phchi.S1G604200.t1"; gene_id "Phchi.S1G604200"
Phchi.S1	AUGUSTUS	stop_codon	38480289	38480291	.	+	0	transcript_id "Phchi.S1G604200.t1"; gene_id "Phchi.S1G604200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8879.t1 is derived from g6054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38446796	38447371	.	+	.	Phchi.S1G603800
Phchi.S1	AUGUSTUS	transcript	38446796	38447371	.	+	.	transcript_id "Phchi.S1G603800.t1"; gene_id "Phchi.S1G603800"
Phchi.S1	AUGUSTUS	start_codon	38446796	38446798	.	+	0	transcript_id "Phchi.S1G603800.t1"; gene_id "Phchi.S1G603800"
Phchi.S1	AUGUSTUS	CDS	38446796	38447371	0.81	+	0	transcript_id "Phchi.S1G603800.t1"; gene_id "Phchi.S1G603800"
Phchi.S1	AUGUSTUS	exon	38446796	38447371	.	+	.	transcript_id "Phchi.S1G603800.t1"; gene_id "Phchi.S1G603800"
Phchi.S1	AUGUSTUS	stop_codon	38447372	38447374	.	+	0	transcript_id "Phchi.S1G603800.t1"; gene_id "Phchi.S1G603800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5958.t1 is derived from g3129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20082040	20085866	.	+	.	Phchi.S1G311700
Phchi.S1	AUGUSTUS	transcript	20082040	20085866	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	start_codon	20082040	20082042	.	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20082040	20082405	0.64	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20082040	20082405	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20082406	20082498	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20082499	20082800	0.95	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20082499	20082800	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20082801	20082937	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20082938	20082968	1	+	1	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20082938	20082968	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20082969	20083085	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20083086	20083196	1	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20083086	20083196	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20083197	20083400	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20083401	20083528	1	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20083401	20083528	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20083529	20083614	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20083615	20083647	1	+	1	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20083615	20083647	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20083648	20083904	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20083905	20084000	1	+	1	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20083905	20084000	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20084001	20084116	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20084117	20084213	1	+	1	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20084117	20084213	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20084214	20084295	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20084296	20084423	1	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20084296	20084423	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20084424	20084535	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20084536	20084670	0.67	+	1	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20084536	20084670	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20084671	20084788	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20084789	20084918	1	+	1	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20084789	20084918	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20084919	20085114	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20085115	20085231	1	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20085115	20085231	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20085232	20085353	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20085354	20085572	1	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20085354	20085572	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	intron	20085573	20085689	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	CDS	20085690	20085866	0.54	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	exon	20085690	20085866	.	+	.	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
Phchi.S1	AUGUSTUS	stop_codon	20085867	20085869	.	+	0	transcript_id "Phchi.S1G311700.t1"; gene_id "Phchi.S1G311700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3202.t1 is derived from g371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2226304	2227772	.	+	.	Phchi.S1G036100
Phchi.S1	AUGUSTUS	transcript	2226304	2227772	.	+	.	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	start_codon	2226304	2226306	.	+	0	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	CDS	2226304	2226680	0.54	+	0	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	exon	2226304	2226680	.	+	.	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	intron	2226681	2226762	.	+	.	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	CDS	2226763	2227294	1	+	1	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	exon	2226763	2227294	.	+	.	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	intron	2227295	2227442	.	+	.	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	CDS	2227443	2227772	1	+	0	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	exon	2227443	2227772	.	+	.	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
Phchi.S1	AUGUSTUS	stop_codon	2227773	2227775	.	+	0	transcript_id "Phchi.S1G036100.t1"; gene_id "Phchi.S1G036100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14003.t1 is derived from g12470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10244663	10246573	.	+	.	Phchi.S3G132200
Phchi.S3	AUGUSTUS	transcript	10244663	10246573	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	start_codon	10244663	10244665	.	+	0	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	CDS	10244663	10245049	0.78	+	0	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	exon	10244663	10245049	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	intron	10245050	10245201	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	CDS	10245202	10245366	1	+	0	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	exon	10245202	10245366	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	intron	10245367	10245464	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	CDS	10245465	10245476	0.88	+	0	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	exon	10245465	10245476	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	intron	10245477	10245586	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	CDS	10245587	10246573	0.51	+	0	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	exon	10245587	10246573	.	+	.	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
Phchi.S3	AUGUSTUS	stop_codon	10246574	10246576	.	+	0	transcript_id "Phchi.S3G132200.t1"; gene_id "Phchi.S3G132200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14944.t1 is derived from g13412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15652412	15653744	.	-	.	Phchi.S3G226300
Phchi.S3	AUGUSTUS	transcript	15652412	15653744	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	stop_codon	15652409	15652411	.	-	0	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	CDS	15652412	15652572	1	-	2	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	exon	15652412	15652572	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	intron	15652573	15652652	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	CDS	15652653	15652875	1	-	0	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	exon	15652653	15652875	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	intron	15652876	15653053	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	CDS	15653054	15653223	1	-	2	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	exon	15653054	15653223	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	intron	15653224	15653307	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	CDS	15653308	15653467	1	-	0	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	exon	15653308	15653467	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	intron	15653468	15653555	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	CDS	15653556	15653744	1	-	0	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	exon	15653556	15653744	.	-	.	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
Phchi.S3	AUGUSTUS	start_codon	15653742	15653744	.	-	0	transcript_id "Phchi.S3G226300.t1"; gene_id "Phchi.S3G226300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6170.t1 is derived from g3341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21282451	21285553	.	-	.	Phchi.S1G332900
Phchi.S1	AUGUSTUS	transcript	21282451	21285553	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	stop_codon	21282448	21282450	.	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21282451	21282624	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21282451	21282624	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21282625	21282694	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21282695	21282823	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21282695	21282823	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21282824	21282942	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21282943	21283035	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21282943	21283035	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21283036	21283140	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21283141	21283209	0.99	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21283141	21283209	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21283210	21283334	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21283335	21283403	0.91	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21283335	21283403	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21283404	21283548	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21283549	21283644	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21283549	21283644	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21283645	21283726	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21283727	21283801	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21283727	21283801	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21283802	21283934	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21283935	21284018	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21283935	21284018	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21284019	21284094	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21284095	21284172	1	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21284095	21284172	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21284173	21284280	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21284281	21284362	1	-	1	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21284281	21284362	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21284363	21284443	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21284444	21284557	1	-	1	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21284444	21284557	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21284558	21284701	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21284702	21285233	0.7	-	2	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21284702	21285233	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21285234	21285370	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21285371	21285450	0.67	-	1	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21285371	21285450	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	intron	21285451	21285524	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	CDS	21285525	21285553	0.62	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	exon	21285525	21285553	.	-	.	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
Phchi.S1	AUGUSTUS	start_codon	21285551	21285553	.	-	0	transcript_id "Phchi.S1G332900.t1"; gene_id "Phchi.S1G332900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8550.t1 is derived from g5725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36580317	36581821	.	-	.	Phchi.S1G570900
Phchi.S1	AUGUSTUS	transcript	36580317	36581821	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	stop_codon	36580314	36580316	.	-	0	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	CDS	36580317	36580489	1	-	2	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	exon	36580317	36580489	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	intron	36580490	36580578	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	CDS	36580579	36580633	1	-	0	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	exon	36580579	36580633	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	intron	36580634	36580718	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	CDS	36580719	36580874	1	-	0	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	exon	36580719	36580874	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	intron	36580875	36580969	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	CDS	36580970	36581202	1	-	2	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	exon	36580970	36581202	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	intron	36581203	36581288	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	CDS	36581289	36581547	1	-	0	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	exon	36581289	36581547	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	intron	36581548	36581626	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	CDS	36581627	36581821	0.98	-	0	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	exon	36581627	36581821	.	-	.	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
Phchi.S1	AUGUSTUS	start_codon	36581819	36581821	.	-	0	transcript_id "Phchi.S1G570900.t1"; gene_id "Phchi.S1G570900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12525.t1 is derived from g8202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32978657	32984784	.	+	.	Phchi.S2G060500
Phchi.S2	AUGUSTUS	transcript	32978657	32984784	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	start_codon	32978657	32978659	.	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32978657	32979340	0.5	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32978657	32979340	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32979341	32979511	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32979512	32980037	0.69	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32979512	32980037	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32980038	32980130	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32980131	32980232	1	+	2	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32980131	32980232	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32980233	32980364	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32980365	32980525	1	+	2	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32980365	32980525	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32980526	32980612	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32980613	32980681	1	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32980613	32980681	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32980682	32980845	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32980846	32980966	0.8	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32980846	32980966	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32980967	32981058	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32981059	32981109	0.81	+	2	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32981059	32981109	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32981110	32981319	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32981320	32981431	0.99	+	2	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32981320	32981431	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32981432	32981581	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32981582	32981626	1	+	1	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32981582	32981626	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32981627	32981771	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32981772	32981859	1	+	1	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32981772	32981859	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32981860	32982005	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32982006	32982065	1	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32982006	32982065	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32982066	32982142	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32982143	32982195	1	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32982143	32982195	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32982196	32982288	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32982289	32982470	1	+	1	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32982289	32982470	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32982471	32982568	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32982569	32982791	1	+	2	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32982569	32982791	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32982792	32983107	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32983108	32983165	1	+	1	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32983108	32983165	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32983166	32983323	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32983324	32983380	1	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32983324	32983380	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32983381	32983469	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32983470	32983538	0.99	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32983470	32983538	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32983539	32983625	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32983626	32983694	0.99	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32983626	32983694	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32983695	32983842	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32983843	32983899	0.84	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32983843	32983899	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32983900	32984013	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32984014	32984069	0.93	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32984014	32984069	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32984070	32984295	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32984296	32984389	1	+	1	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32984296	32984389	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32984390	32984464	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32984465	32984605	1	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32984465	32984605	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	intron	32984606	32984685	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	CDS	32984686	32984784	1	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	exon	32984686	32984784	.	+	.	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
Phchi.S2	AUGUSTUS	stop_codon	32984785	32984787	.	+	0	transcript_id "Phchi.S2G060500.t1"; gene_id "Phchi.S2G060500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13276.t1 is derived from g11741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5108699	5108929	.	-	.	Phchi.S3G059500
Phchi.S3	AUGUSTUS	transcript	5108699	5108929	.	-	.	transcript_id "Phchi.S3G059500.t1"; gene_id "Phchi.S3G059500"
Phchi.S3	AUGUSTUS	stop_codon	5108696	5108698	.	-	0	transcript_id "Phchi.S3G059500.t1"; gene_id "Phchi.S3G059500"
Phchi.S3	AUGUSTUS	CDS	5108699	5108929	0.72	-	0	transcript_id "Phchi.S3G059500.t1"; gene_id "Phchi.S3G059500"
Phchi.S3	AUGUSTUS	exon	5108699	5108929	.	-	.	transcript_id "Phchi.S3G059500.t1"; gene_id "Phchi.S3G059500"
Phchi.S3	AUGUSTUS	start_codon	5108927	5108929	.	-	0	transcript_id "Phchi.S3G059500.t1"; gene_id "Phchi.S3G059500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8709.t1 is derived from g5884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37581975	37586733	.	+	.	Phchi.S1G586800
Phchi.S1	AUGUSTUS	transcript	37581975	37586733	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	start_codon	37581975	37581977	.	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37581975	37582167	0.64	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37581975	37582167	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37582168	37582302	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37582303	37582635	0.99	+	2	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37582303	37582635	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37582636	37582812	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37582813	37582910	0.99	+	2	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37582813	37582910	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37582911	37583008	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37583009	37583144	0.99	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37583009	37583144	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37583145	37583309	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37583310	37583462	0.98	+	2	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37583310	37583462	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37583463	37583561	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37583562	37584724	0.95	+	2	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37583562	37584724	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37584725	37584827	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37584828	37586414	0.99	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37584828	37586414	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37586415	37586523	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37586524	37586607	1	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37586524	37586607	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	intron	37586608	37586682	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	CDS	37586683	37586733	1	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	exon	37586683	37586733	.	+	.	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
Phchi.S1	AUGUSTUS	stop_codon	37586734	37586736	.	+	0	transcript_id "Phchi.S1G586800.t1"; gene_id "Phchi.S1G586800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12170.t1 is derived from g7846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5842487	5843134	.	+	.	Phchi.S2G025000
Phchi.S2	AUGUSTUS	transcript	5842487	5843134	.	+	.	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	start_codon	5842487	5842489	.	+	0	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	CDS	5842487	5842853	0.92	+	0	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	exon	5842487	5842853	.	+	.	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	intron	5842854	5843075	.	+	.	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	CDS	5843076	5843134	0.79	+	2	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	exon	5843076	5843134	.	+	.	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
Phchi.S2	AUGUSTUS	stop_codon	5843135	5843137	.	+	0	transcript_id "Phchi.S2G025000.t1"; gene_id "Phchi.S2G025000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2158.t1 is derived from g9078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5099807	5100998	.	+	.	Phchi.S5G076700
Phchi.S5	AUGUSTUS	transcript	5099807	5100998	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	start_codon	5099807	5099809	.	+	0	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5099807	5099888	1	+	0	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5099807	5099888	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5099889	5100142	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5100143	5100321	0.99	+	2	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5100143	5100321	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5100322	5100402	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5100403	5100573	0.98	+	0	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5100403	5100573	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5100574	5100680	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5100681	5100998	0.99	+	0	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5100681	5100998	.	+	.	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	stop_codon	5100999	5101001	.	+	0	transcript_id "Phchi.S5G076700.t1"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	transcript	5099817	5100998	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	start_codon	5099817	5099819	.	+	0	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5099817	5099849	0.72	+	0	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5099817	5099849	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5099850	5099947	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5099948	5100059	0.8	+	0	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5099948	5100059	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5100060	5100142	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5100143	5100321	0.97	+	2	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5100143	5100321	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5100322	5100402	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5100403	5100573	0.99	+	0	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5100403	5100573	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	intron	5100574	5100680	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	CDS	5100681	5100998	0.99	+	0	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	exon	5100681	5100998	.	+	.	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
Phchi.S5	AUGUSTUS	stop_codon	5100999	5101001	.	+	0	transcript_id "Phchi.S5G076700.t2"; gene_id "Phchi.S5G076700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15998.t1 is derived from g15976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C244	AUGUSTUS	gene	5636	6127	.	-	.	Phchi.C244G000200
Phchi.C244	AUGUSTUS	transcript	5636	6127	.	-	.	transcript_id "Phchi.C244G000200.t1"; gene_id "Phchi.C244G000200"
Phchi.C244	AUGUSTUS	stop_codon	5633	5635	.	-	0	transcript_id "Phchi.C244G000200.t1"; gene_id "Phchi.C244G000200"
Phchi.C244	AUGUSTUS	CDS	5636	6127	0.55	-	0	transcript_id "Phchi.C244G000200.t1"; gene_id "Phchi.C244G000200"
Phchi.C244	AUGUSTUS	exon	5636	6127	.	-	.	transcript_id "Phchi.C244G000200.t1"; gene_id "Phchi.C244G000200"
Phchi.C244	AUGUSTUS	start_codon	6125	6127	.	-	0	transcript_id "Phchi.C244G000200.t1"; gene_id "Phchi.C244G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg964.t1 is derived from g10746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6693425	6694374	.	-	.	Phchi.S6G092300
Phchi.S6	AUGUSTUS	transcript	6693425	6694374	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	stop_codon	6693422	6693424	.	-	0	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	CDS	6693425	6693743	1	-	1	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	exon	6693425	6693743	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	intron	6693744	6693930	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	CDS	6693931	6694001	1	-	0	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	exon	6693931	6694001	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	intron	6694002	6694084	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	CDS	6694085	6694216	1	-	0	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	exon	6694085	6694216	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	intron	6694217	6694320	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	CDS	6694321	6694374	0.98	-	0	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	exon	6694321	6694374	.	-	.	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
Phchi.S6	AUGUSTUS	start_codon	6694372	6694374	.	-	0	transcript_id "Phchi.S6G092300.t1"; gene_id "Phchi.S6G092300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9245.t1 is derived from g6420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40571416	40575454	.	+	.	Phchi.S1G640400
Phchi.S1	AUGUSTUS	transcript	40571416	40575454	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	start_codon	40571416	40571418	.	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40571416	40571478	0.86	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40571416	40571478	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40571479	40571585	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40571586	40571675	1	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40571586	40571675	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40571676	40571808	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40571809	40571913	1	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40571809	40571913	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40571914	40571999	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40572000	40572101	1	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40572000	40572101	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40572102	40572231	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40572232	40572316	1	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40572232	40572316	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40572317	40572558	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40572559	40572625	1	+	2	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40572559	40572625	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40572626	40572709	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40572710	40572754	1	+	1	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40572710	40572754	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40572755	40572850	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40572851	40573632	0.96	+	1	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40572851	40573632	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	intron	40573633	40573781	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	CDS	40573782	40575454	0.89	+	2	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	exon	40573782	40575454	.	+	.	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
Phchi.S1	AUGUSTUS	stop_codon	40575455	40575457	.	+	0	transcript_id "Phchi.S1G640400.t1"; gene_id "Phchi.S1G640400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11238.t1 is derived from g15288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4949905	4950882	.	-	.	Phchi.S4G082000
Phchi.S4	AUGUSTUS	transcript	4949905	4950882	.	-	.	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	stop_codon	4949902	4949904	.	-	0	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	CDS	4949905	4949951	0.57	-	2	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	exon	4949905	4949951	.	-	.	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	intron	4949952	4950131	.	-	.	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	CDS	4950132	4950353	0.54	-	2	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	exon	4950132	4950353	.	-	.	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	intron	4950354	4950524	.	-	.	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	CDS	4950525	4950882	0.93	-	0	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	exon	4950525	4950882	.	-	.	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
Phchi.S4	AUGUSTUS	start_codon	4950880	4950882	.	-	0	transcript_id "Phchi.S4G082000.t1"; gene_id "Phchi.S4G082000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11910.t1 is derived from g15962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9271474	9272548	.	-	.	Phchi.S4G149200
Phchi.S4	AUGUSTUS	transcript	9271474	9272548	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	stop_codon	9271471	9271473	.	-	0	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	CDS	9271474	9271499	0.86	-	2	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	exon	9271474	9271499	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	intron	9271500	9271573	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	CDS	9271574	9271610	0.93	-	0	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	exon	9271574	9271610	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	intron	9271611	9271742	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	CDS	9271743	9271810	1	-	2	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	exon	9271743	9271810	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	intron	9271811	9271951	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	CDS	9271952	9271975	1	-	2	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	exon	9271952	9271975	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	intron	9271976	9272174	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	CDS	9272175	9272351	0.95	-	2	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	exon	9272175	9272351	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	intron	9272352	9272433	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	CDS	9272434	9272548	0.97	-	0	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	exon	9272434	9272548	.	-	.	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
Phchi.S4	AUGUSTUS	start_codon	9272546	9272548	.	-	0	transcript_id "Phchi.S4G149200.t1"; gene_id "Phchi.S4G149200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6411.t1 is derived from g3583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22843595	22844493	.	+	.	Phchi.S1G357000
Phchi.S1	AUGUSTUS	transcript	22843595	22844493	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	start_codon	22843595	22843597	.	+	0	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	CDS	22843595	22843652	1	+	0	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	exon	22843595	22843652	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	intron	22843653	22843726	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	CDS	22843727	22843945	1	+	2	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	exon	22843727	22843945	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	intron	22843946	22844028	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	CDS	22844029	22844126	0.96	+	2	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	exon	22844029	22844126	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	intron	22844127	22844267	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	CDS	22844268	22844310	0.53	+	0	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	exon	22844268	22844310	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	intron	22844311	22844392	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	CDS	22844393	22844493	0.89	+	2	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	exon	22844393	22844493	.	+	.	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
Phchi.S1	AUGUSTUS	stop_codon	22844494	22844496	.	+	0	transcript_id "Phchi.S1G357000.t1"; gene_id "Phchi.S1G357000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1763.t1 is derived from g8683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2926670	2927533	.	+	.	Phchi.S5G037200
Phchi.S5	AUGUSTUS	transcript	2926670	2927533	.	+	.	transcript_id "Phchi.S5G037200.t1"; gene_id "Phchi.S5G037200"
Phchi.S5	AUGUSTUS	start_codon	2926670	2926672	.	+	0	transcript_id "Phchi.S5G037200.t1"; gene_id "Phchi.S5G037200"
Phchi.S5	AUGUSTUS	CDS	2926670	2927533	1	+	0	transcript_id "Phchi.S5G037200.t1"; gene_id "Phchi.S5G037200"
Phchi.S5	AUGUSTUS	exon	2926670	2927533	.	+	.	transcript_id "Phchi.S5G037200.t1"; gene_id "Phchi.S5G037200"
Phchi.S5	AUGUSTUS	stop_codon	2927534	2927536	.	+	0	transcript_id "Phchi.S5G037200.t1"; gene_id "Phchi.S5G037200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5688.t1 is derived from g2858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18320721	18321671	.	-	.	Phchi.S1G284700
Phchi.S1	AUGUSTUS	transcript	18320721	18321671	.	-	.	transcript_id "Phchi.S1G284700.t1"; gene_id "Phchi.S1G284700"
Phchi.S1	AUGUSTUS	stop_codon	18320718	18320720	.	-	0	transcript_id "Phchi.S1G284700.t1"; gene_id "Phchi.S1G284700"
Phchi.S1	AUGUSTUS	CDS	18320721	18321671	0.98	-	0	transcript_id "Phchi.S1G284700.t1"; gene_id "Phchi.S1G284700"
Phchi.S1	AUGUSTUS	exon	18320721	18321671	.	-	.	transcript_id "Phchi.S1G284700.t1"; gene_id "Phchi.S1G284700"
Phchi.S1	AUGUSTUS	start_codon	18321669	18321671	.	-	0	transcript_id "Phchi.S1G284700.t1"; gene_id "Phchi.S1G284700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7621.t1 is derived from g4795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30301350	30302534	.	-	.	Phchi.S1G478000
Phchi.S1	AUGUSTUS	transcript	30301350	30302534	.	-	.	transcript_id "Phchi.S1G478000.t1"; gene_id "Phchi.S1G478000"
Phchi.S1	AUGUSTUS	stop_codon	30301347	30301349	.	-	0	transcript_id "Phchi.S1G478000.t1"; gene_id "Phchi.S1G478000"
Phchi.S1	AUGUSTUS	CDS	30301350	30302534	0.36	-	0	transcript_id "Phchi.S1G478000.t1"; gene_id "Phchi.S1G478000"
Phchi.S1	AUGUSTUS	exon	30301350	30302534	.	-	.	transcript_id "Phchi.S1G478000.t1"; gene_id "Phchi.S1G478000"
Phchi.S1	AUGUSTUS	start_codon	30302532	30302534	.	-	0	transcript_id "Phchi.S1G478000.t1"; gene_id "Phchi.S1G478000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4507.t1 is derived from g1677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10880057	10881335	.	+	.	Phchi.S1G166600
Phchi.S1	AUGUSTUS	transcript	10880057	10881335	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	start_codon	10880057	10880059	.	+	0	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	CDS	10880057	10880105	0.79	+	0	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	exon	10880057	10880105	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	intron	10880106	10880207	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	CDS	10880208	10880362	0.73	+	2	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	exon	10880208	10880362	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	intron	10880363	10880524	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	CDS	10880525	10880632	0.88	+	0	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	exon	10880525	10880632	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	intron	10880633	10880728	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	CDS	10880729	10880896	0.82	+	0	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	exon	10880729	10880896	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	intron	10880897	10881039	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	CDS	10881040	10881196	0.75	+	0	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	exon	10881040	10881196	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	intron	10881197	10881276	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	CDS	10881277	10881335	0.38	+	2	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	exon	10881277	10881335	.	+	.	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
Phchi.S1	AUGUSTUS	stop_codon	10881336	10881338	.	+	0	transcript_id "Phchi.S1G166600.t1"; gene_id "Phchi.S1G166600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10448.t1 is derived from g14497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	372163	373794	.	-	.	Phchi.S4G003000
Phchi.S4	AUGUSTUS	transcript	372163	373794	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	stop_codon	372160	372162	.	-	0	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	CDS	372163	372332	0.74	-	2	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	exon	372163	372332	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	intron	372333	372435	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	CDS	372436	372706	0.99	-	0	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	exon	372436	372706	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	intron	372707	372821	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	CDS	372822	373170	1	-	1	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	exon	372822	373170	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	intron	373171	373366	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	CDS	373367	373794	1	-	0	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	exon	373367	373794	.	-	.	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
Phchi.S4	AUGUSTUS	start_codon	373792	373794	.	-	0	transcript_id "Phchi.S4G003000.t1"; gene_id "Phchi.S4G003000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8387.t1 is derived from g5562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35664872	35667639	.	-	.	Phchi.S1G554600
Phchi.S1	AUGUSTUS	transcript	35664872	35667639	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	stop_codon	35664869	35664871	.	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35664872	35664929	1	-	1	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35664872	35664929	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35664930	35665043	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665044	35665139	1	-	1	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665044	35665139	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665140	35665228	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665229	35665291	1	-	1	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665229	35665291	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665292	35665386	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665387	35665475	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665387	35665475	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665476	35665598	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665599	35665637	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665599	35665637	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665638	35665755	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665756	35665839	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665756	35665839	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665840	35665953	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665954	35666001	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665954	35666001	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666002	35666120	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666121	35666192	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666121	35666192	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666193	35666320	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666321	35666415	1	-	2	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666321	35666415	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666416	35666558	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666559	35666647	1	-	1	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666559	35666647	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666648	35666723	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666724	35667535	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666724	35667535	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35667536	35667615	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35667616	35667639	1	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35667616	35667639	.	-	.	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	start_codon	35667637	35667639	.	-	0	transcript_id "Phchi.S1G554600.t1"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	transcript	35664872	35667639	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	stop_codon	35664869	35664871	.	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35664872	35664929	1	-	1	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35664872	35664929	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35664930	35665043	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665044	35665139	1	-	1	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665044	35665139	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665140	35665228	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665229	35665291	1	-	1	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665229	35665291	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665292	35665386	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665387	35665475	1	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665387	35665475	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665476	35665598	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665599	35665637	1	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665599	35665637	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665638	35665755	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665756	35665839	1	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665756	35665839	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35665840	35665953	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35665954	35666001	1	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35665954	35666001	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666002	35666120	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666121	35666192	1	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666121	35666192	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666193	35666320	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666321	35666415	1	-	2	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666321	35666415	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666416	35666558	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666559	35666647	1	-	1	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666559	35666647	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35666648	35666723	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35666724	35667454	0.54	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35666724	35667454	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	intron	35667455	35667615	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	CDS	35667616	35667639	0.54	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	exon	35667616	35667639	.	-	.	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
Phchi.S1	AUGUSTUS	start_codon	35667637	35667639	.	-	0	transcript_id "Phchi.S1G554600.t2"; gene_id "Phchi.S1G554600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7496.t1 is derived from g4670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29660864	29661381	.	-	.	Phchi.S1G465500
Phchi.S1	AUGUSTUS	transcript	29660864	29661381	.	-	.	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	stop_codon	29660861	29660863	.	-	0	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	CDS	29660864	29661005	0.58	-	1	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	exon	29660864	29661005	.	-	.	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	intron	29661006	29661142	.	-	.	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	CDS	29661143	29661381	0.59	-	0	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	exon	29661143	29661381	.	-	.	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
Phchi.S1	AUGUSTUS	start_codon	29661379	29661381	.	-	0	transcript_id "Phchi.S1G465500.t1"; gene_id "Phchi.S1G465500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6861.t1 is derived from g4033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25622258	25622977	.	+	.	Phchi.S1G402000
Phchi.S1	AUGUSTUS	transcript	25622258	25622977	.	+	.	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	start_codon	25622258	25622260	.	+	0	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	CDS	25622258	25622330	0.99	+	0	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	exon	25622258	25622330	.	+	.	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	intron	25622331	25622426	.	+	.	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	CDS	25622427	25622977	1	+	2	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	exon	25622427	25622977	.	+	.	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
Phchi.S1	AUGUSTUS	stop_codon	25622978	25622980	.	+	0	transcript_id "Phchi.S1G402000.t1"; gene_id "Phchi.S1G402000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg10020.t1 is derived from g7196.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45091054	45096254	.	-	.	Phchi.S1G717900
Phchi.S1	AUGUSTUS	transcript	45091054	45096254	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	stop_codon	45091051	45091053	.	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091054	45091475	0.99	-	2	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091054	45091475	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091476	45091561	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091562	45091633	1	-	2	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091562	45091633	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091634	45091960	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091961	45092067	1	-	1	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091961	45092067	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092068	45092163	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092164	45092289	1	-	1	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092164	45092289	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092290	45092378	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092379	45092446	0.99	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092379	45092446	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092447	45092544	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092545	45092560	0.99	-	1	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092545	45092560	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092561	45092774	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092775	45092796	0.95	-	2	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092775	45092796	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092797	45092888	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092889	45092988	0.99	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092889	45092988	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092989	45093072	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093073	45093157	1	-	1	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093073	45093157	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093158	45093293	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093294	45093391	0.99	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093294	45093391	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093392	45093792	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093793	45093923	0.9	-	2	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093793	45093923	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093924	45094007	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094008	45094066	0.48	-	1	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094008	45094066	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094067	45094139	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094140	45094219	0.48	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094140	45094219	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094220	45094392	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094393	45094468	1	-	1	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094393	45094468	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094469	45094652	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094653	45094824	1	-	2	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094653	45094824	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094825	45094906	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094907	45095047	0.98	-	2	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094907	45095047	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095048	45095159	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095160	45095430	1	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095160	45095430	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095431	45095562	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095563	45095763	1	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095563	45095763	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095764	45095936	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095937	45096254	1	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095937	45096254	.	-	.	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	start_codon	45096252	45096254	.	-	0	transcript_id "Phchi.S1G717900.t1"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	transcript	45091054	45096254	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	stop_codon	45091051	45091053	.	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091054	45091475	1	-	2	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091054	45091475	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091476	45091561	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091562	45091633	1	-	2	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091562	45091633	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091634	45091960	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091961	45092067	1	-	1	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091961	45092067	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092068	45092163	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092164	45092289	1	-	1	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092164	45092289	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092290	45092378	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092379	45092441	0.92	-	1	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092379	45092441	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092442	45092544	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092545	45092659	0.91	-	2	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092545	45092659	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092660	45092774	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092775	45092796	0.98	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092775	45092796	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092797	45092888	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092889	45092939	0.99	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092889	45092939	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092940	45093072	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093073	45093157	1	-	1	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093073	45093157	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093158	45093293	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093294	45093391	0.99	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093294	45093391	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093392	45093792	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093793	45093923	0.85	-	2	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093793	45093923	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093924	45094007	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094008	45094066	0.53	-	1	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094008	45094066	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094067	45094139	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094140	45094219	0.53	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094140	45094219	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094220	45094392	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094393	45094468	1	-	1	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094393	45094468	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094469	45094652	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094653	45094824	1	-	2	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094653	45094824	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094825	45094906	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094907	45095047	0.99	-	2	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094907	45095047	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095048	45095159	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095160	45095430	1	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095160	45095430	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095431	45095562	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095563	45095763	1	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095563	45095763	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095764	45095936	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095937	45096254	0.99	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095937	45096254	.	-	.	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	start_codon	45096252	45096254	.	-	0	transcript_id "Phchi.S1G717900.t2"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	transcript	45091054	45096254	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	stop_codon	45091051	45091053	.	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091054	45091475	1	-	2	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091054	45091475	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091476	45091561	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091562	45091633	1	-	2	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091562	45091633	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091634	45091960	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091961	45092067	1	-	1	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091961	45092067	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092068	45092163	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092164	45092289	0.98	-	1	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092164	45092289	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092290	45092378	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092379	45092446	0.97	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092379	45092446	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092447	45092544	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092545	45092560	0.97	-	1	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092545	45092560	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092561	45092755	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092756	45092796	0.83	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092756	45092796	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092797	45092888	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092889	45092939	0.88	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092889	45092939	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092940	45093072	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093073	45093157	1	-	1	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093073	45093157	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093158	45093293	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093294	45093391	0.97	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093294	45093391	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093392	45093792	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093793	45093923	0.87	-	2	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093793	45093923	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093924	45094007	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094008	45094066	0.53	-	1	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094008	45094066	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094067	45094139	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094140	45094219	0.53	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094140	45094219	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094220	45094392	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094393	45094468	1	-	1	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094393	45094468	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094469	45094652	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094653	45094824	1	-	2	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094653	45094824	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094825	45094906	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094907	45095047	0.99	-	2	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094907	45095047	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095048	45095159	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095160	45095430	1	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095160	45095430	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095431	45095562	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095563	45095763	1	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095563	45095763	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095764	45095936	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095937	45096254	1	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095937	45096254	.	-	.	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	start_codon	45096252	45096254	.	-	0	transcript_id "Phchi.S1G717900.t3"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	transcript	45091054	45096254	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	stop_codon	45091051	45091053	.	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091054	45091475	1	-	2	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091054	45091475	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091476	45091561	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091562	45091633	1	-	2	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091562	45091633	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45091634	45091960	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45091961	45092067	1	-	1	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45091961	45092067	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092068	45092163	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092164	45092289	1	-	1	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092164	45092289	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092290	45092378	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092379	45092446	0.97	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092379	45092446	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092447	45092544	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092545	45092560	0.97	-	1	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092545	45092560	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092561	45092755	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092756	45092796	0.79	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092756	45092796	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092797	45092888	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45092889	45092939	0.82	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45092889	45092939	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45092940	45093072	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093073	45093157	0.99	-	1	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093073	45093157	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093158	45093293	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093294	45093391	0.98	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093294	45093391	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093392	45093792	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45093793	45093923	0.85	-	2	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45093793	45093923	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45093924	45094007	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094008	45094066	0.47	-	1	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094008	45094066	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094067	45094139	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094140	45094219	0.47	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094140	45094219	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094220	45094368	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094369	45094468	1	-	1	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094369	45094468	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094469	45094652	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094653	45094824	1	-	2	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094653	45094824	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45094825	45094906	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45094907	45095047	1	-	2	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45094907	45095047	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095048	45095159	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095160	45095430	1	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095160	45095430	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095431	45095562	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095563	45095763	1	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095563	45095763	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	intron	45095764	45095936	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	CDS	45095937	45096254	1	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	exon	45095937	45096254	.	-	.	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
Phchi.S1	AUGUSTUS	start_codon	45096252	45096254	.	-	0	transcript_id "Phchi.S1G717900.t4"; gene_id "Phchi.S1G717900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10740.t1 is derived from g14790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1869304	1870468	.	+	.	Phchi.S4G032200
Phchi.S4	AUGUSTUS	transcript	1869304	1870468	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	start_codon	1869304	1869306	.	+	0	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	CDS	1869304	1869326	0.8	+	0	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	exon	1869304	1869326	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	intron	1869327	1869587	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	CDS	1869588	1869660	1	+	1	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	exon	1869588	1869660	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	intron	1869661	1869786	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	CDS	1869787	1869925	1	+	0	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	exon	1869787	1869925	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	intron	1869926	1870164	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	CDS	1870165	1870351	1	+	2	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	exon	1870165	1870351	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	intron	1870352	1870437	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	CDS	1870438	1870468	1	+	1	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	exon	1870438	1870468	.	+	.	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
Phchi.S4	AUGUSTUS	stop_codon	1870469	1870471	.	+	0	transcript_id "Phchi.S4G032200.t1"; gene_id "Phchi.S4G032200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6058.t1 is derived from g3230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20678154	20681852	.	+	.	Phchi.S1G321800
Phchi.S1	AUGUSTUS	transcript	20678154	20681852	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	start_codon	20678154	20678156	.	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20678154	20678326	0.61	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20678154	20678326	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20678327	20678496	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20678497	20678599	0.6	+	1	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20678497	20678599	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20678600	20678706	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20678707	20679018	0.57	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20678707	20679018	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20679019	20679112	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20679113	20679559	1	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20679113	20679559	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20679560	20679638	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20679639	20680210	0.99	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20679639	20680210	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20680211	20680292	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20680293	20680447	1	+	1	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20680293	20680447	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20680448	20680541	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20680542	20680711	1	+	2	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20680542	20680711	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20680712	20680853	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20680854	20681006	1	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20680854	20681006	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20681007	20681158	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20681159	20681291	1	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20681159	20681291	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20681292	20681363	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20681364	20681501	0.88	+	2	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20681364	20681501	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	intron	20681502	20681748	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	CDS	20681749	20681852	0.98	+	2	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	exon	20681749	20681852	.	+	.	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
Phchi.S1	AUGUSTUS	stop_codon	20681853	20681855	.	+	0	transcript_id "Phchi.S1G321800.t1"; gene_id "Phchi.S1G321800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg335.t1 is derived from g10117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2455731	2456191	.	-	.	Phchi.S6G029400
Phchi.S6	AUGUSTUS	transcript	2455731	2456191	.	-	.	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	stop_codon	2455728	2455730	.	-	0	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	CDS	2455731	2455731	1	-	1	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	exon	2455731	2455731	.	-	.	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	intron	2455732	2455873	.	-	.	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	CDS	2455874	2456077	1	-	1	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	exon	2455874	2456077	.	-	.	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	intron	2456078	2456153	.	-	.	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	CDS	2456154	2456191	1	-	0	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	exon	2456154	2456191	.	-	.	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
Phchi.S6	AUGUSTUS	start_codon	2456189	2456191	.	-	0	transcript_id "Phchi.S6G029400.t1"; gene_id "Phchi.S6G029400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5645.t1 is derived from g2815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18043102	18043579	.	+	.	Phchi.S1G280400
Phchi.S1	AUGUSTUS	transcript	18043102	18043579	.	+	.	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	start_codon	18043102	18043104	.	+	0	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	CDS	18043102	18043180	0.46	+	0	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	exon	18043102	18043180	.	+	.	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	intron	18043181	18043268	.	+	.	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	CDS	18043269	18043277	0.75	+	2	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	exon	18043269	18043277	.	+	.	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	intron	18043278	18043415	.	+	.	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	CDS	18043416	18043579	0.44	+	2	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	exon	18043416	18043579	.	+	.	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
Phchi.S1	AUGUSTUS	stop_codon	18043580	18043582	.	+	0	transcript_id "Phchi.S1G280400.t1"; gene_id "Phchi.S1G280400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3579.t1 is derived from g748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4599248	4600315	.	+	.	Phchi.S1G073800
Phchi.S1	AUGUSTUS	transcript	4599248	4600315	.	+	.	transcript_id "Phchi.S1G073800.t1"; gene_id "Phchi.S1G073800"
Phchi.S1	AUGUSTUS	start_codon	4599248	4599250	.	+	0	transcript_id "Phchi.S1G073800.t1"; gene_id "Phchi.S1G073800"
Phchi.S1	AUGUSTUS	CDS	4599248	4600315	0.56	+	0	transcript_id "Phchi.S1G073800.t1"; gene_id "Phchi.S1G073800"
Phchi.S1	AUGUSTUS	exon	4599248	4600315	.	+	.	transcript_id "Phchi.S1G073800.t1"; gene_id "Phchi.S1G073800"
Phchi.S1	AUGUSTUS	stop_codon	4600316	4600318	.	+	0	transcript_id "Phchi.S1G073800.t1"; gene_id "Phchi.S1G073800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13218.t1 is derived from g11683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4736393	4737592	.	-	.	Phchi.S3G053700
Phchi.S3	AUGUSTUS	transcript	4736393	4737592	.	-	.	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	stop_codon	4736390	4736392	.	-	0	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	CDS	4736393	4737315	0.98	-	2	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	exon	4736393	4737315	.	-	.	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	intron	4737316	4737405	.	-	.	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	CDS	4737406	4737592	0.99	-	0	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	exon	4737406	4737592	.	-	.	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
Phchi.S3	AUGUSTUS	start_codon	4737590	4737592	.	-	0	transcript_id "Phchi.S3G053700.t1"; gene_id "Phchi.S3G053700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1673.t1 is derived from g8592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2410350	2411327	.	-	.	Phchi.S5G028200
Phchi.S5	AUGUSTUS	transcript	2410350	2411327	.	-	.	transcript_id "Phchi.S5G028200.t1"; gene_id "Phchi.S5G028200"
Phchi.S5	AUGUSTUS	stop_codon	2410347	2410349	.	-	0	transcript_id "Phchi.S5G028200.t1"; gene_id "Phchi.S5G028200"
Phchi.S5	AUGUSTUS	CDS	2410350	2411327	1	-	0	transcript_id "Phchi.S5G028200.t1"; gene_id "Phchi.S5G028200"
Phchi.S5	AUGUSTUS	exon	2410350	2411327	.	-	.	transcript_id "Phchi.S5G028200.t1"; gene_id "Phchi.S5G028200"
Phchi.S5	AUGUSTUS	start_codon	2411325	2411327	.	-	0	transcript_id "Phchi.S5G028200.t1"; gene_id "Phchi.S5G028200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9950.t1 is derived from g7126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44627858	44633840	.	-	.	Phchi.S1G710900
Phchi.S1	AUGUSTUS	transcript	44627858	44633840	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	stop_codon	44627855	44627857	.	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44627858	44628227	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44627858	44628227	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44628228	44628322	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44628323	44628424	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44628323	44628424	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44628425	44628499	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44628500	44628601	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44628500	44628601	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44628602	44628676	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44628677	44628778	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44628677	44628778	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44628779	44628859	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44628860	44628961	0.99	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44628860	44628961	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44628962	44629062	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44629063	44629122	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44629063	44629122	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44629123	44629207	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44629208	44629321	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44629208	44629321	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44629322	44629403	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44629404	44629505	1	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44629404	44629505	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44629506	44629620	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44629621	44629911	0.66	-	1	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44629621	44629911	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44629912	44630064	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44630065	44630531	0.68	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44630065	44630531	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44630532	44630655	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44630656	44631423	0.95	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44630656	44631423	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44631424	44631527	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44631528	44631805	0.71	-	2	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44631528	44631805	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44631806	44631975	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44631976	44632179	0.93	-	2	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44631976	44632179	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44632180	44632310	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44632311	44632494	0.96	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44632311	44632494	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44632495	44632590	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44632591	44632749	0.75	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44632591	44632749	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44632750	44632947	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44632948	44633355	0.96	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44632948	44633355	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	intron	44633356	44633513	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	CDS	44633514	44633840	0.99	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	exon	44633514	44633840	.	-	.	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
Phchi.S1	AUGUSTUS	start_codon	44633838	44633840	.	-	0	transcript_id "Phchi.S1G710900.t1"; gene_id "Phchi.S1G710900"
# This transcript jg9269.t2 is derived from g6444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9270.t1 is derived from g6445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40686194	40687792	.	+	.	Phchi.S1G642900
Phchi.S1	AUGUSTUS	transcript	40686194	40687792	.	+	.	transcript_id "Phchi.S1G642900.t1"; gene_id "Phchi.S1G642900"
Phchi.S1	AUGUSTUS	start_codon	40686194	40686196	.	+	0	transcript_id "Phchi.S1G642900.t1"; gene_id "Phchi.S1G642900"
Phchi.S1	AUGUSTUS	CDS	40686194	40687792	0.93	+	0	transcript_id "Phchi.S1G642900.t1"; gene_id "Phchi.S1G642900"
Phchi.S1	AUGUSTUS	exon	40686194	40687792	.	+	.	transcript_id "Phchi.S1G642900.t1"; gene_id "Phchi.S1G642900"
Phchi.S1	AUGUSTUS	stop_codon	40687793	40687795	.	+	0	transcript_id "Phchi.S1G642900.t1"; gene_id "Phchi.S1G642900"
# This transcript jg15910.t2 is derived from g14380.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15911.t1 is derived from g14381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22164596	22171029	.	-	.	Phchi.S3G323000
Phchi.S3	AUGUSTUS	transcript	22164596	22171029	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	stop_codon	22164593	22164595	.	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22164596	22164653	1	-	1	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22164596	22164653	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22164654	22165568	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22165569	22165699	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22165569	22165699	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22165700	22165829	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22165830	22166102	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22165830	22166102	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166103	22166202	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166203	22166286	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166203	22166286	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166287	22166421	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166422	22166491	1	-	1	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166422	22166491	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166492	22166609	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166610	22166767	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166610	22166767	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166768	22166849	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166850	22166957	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166850	22166957	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166958	22167051	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167052	22167135	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167052	22167135	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167136	22167262	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167263	22167323	1	-	1	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167263	22167323	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167324	22167465	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167466	22167518	0.72	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167466	22167518	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167519	22167620	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167621	22167938	0.68	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167621	22167938	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167939	22168048	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22168049	22168255	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22168049	22168255	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22168256	22168353	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22168354	22168597	1	-	1	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22168354	22168597	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22168598	22168741	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22168742	22168829	1	-	2	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22168742	22168829	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22168830	22169103	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169104	22169173	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169104	22169173	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169174	22169269	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169270	22169403	1	-	2	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169270	22169403	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169404	22169565	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169566	22169685	1	-	2	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169566	22169685	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169686	22169800	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169801	22169945	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169801	22169945	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169946	22170052	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170053	22170122	0.99	-	1	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170053	22170122	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170123	22170211	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170212	22170282	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170212	22170282	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170283	22170451	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170452	22170528	1	-	2	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170452	22170528	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170529	22170615	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170616	22170652	1	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170616	22170652	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170653	22170948	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170949	22171029	0.97	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170949	22171029	.	-	.	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	start_codon	22171027	22171029	.	-	0	transcript_id "Phchi.S3G323000.t1"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	transcript	22164596	22171029	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	stop_codon	22164593	22164595	.	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22164596	22164653	1	-	1	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22164596	22164653	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22164654	22165568	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22165569	22165699	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22165569	22165699	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22165700	22165829	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22165830	22166102	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22165830	22166102	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166103	22166202	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166203	22166289	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166203	22166289	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166290	22166421	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166422	22166491	1	-	1	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166422	22166491	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166492	22166609	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166610	22166767	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166610	22166767	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166768	22166849	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22166850	22166957	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22166850	22166957	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22166958	22167051	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167052	22167135	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167052	22167135	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167136	22167262	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167263	22167323	1	-	1	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167263	22167323	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167324	22167465	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167466	22167518	0.69	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167466	22167518	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167519	22167620	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22167621	22167938	0.61	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22167621	22167938	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22167939	22168048	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22168049	22168255	0.98	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22168049	22168255	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22168256	22168353	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22168354	22168597	1	-	1	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22168354	22168597	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22168598	22168741	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22168742	22168829	1	-	2	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22168742	22168829	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22168830	22169103	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169104	22169173	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169104	22169173	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169174	22169269	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169270	22169403	1	-	2	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169270	22169403	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169404	22169565	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169566	22169685	1	-	2	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169566	22169685	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169686	22169800	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22169801	22169945	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22169801	22169945	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22169946	22170052	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170053	22170122	0.99	-	1	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170053	22170122	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170123	22170211	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170212	22170282	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170212	22170282	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170283	22170451	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170452	22170528	1	-	2	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170452	22170528	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170529	22170615	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170616	22170652	1	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170616	22170652	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	intron	22170653	22170948	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	CDS	22170949	22171029	0.98	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	exon	22170949	22171029	.	-	.	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
Phchi.S3	AUGUSTUS	start_codon	22171027	22171029	.	-	0	transcript_id "Phchi.S3G323000.t2"; gene_id "Phchi.S3G323000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7263.t1 is derived from g4435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27913122	27915237	.	+	.	Phchi.S1G442200
Phchi.S1	AUGUSTUS	transcript	27913122	27915237	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	start_codon	27913122	27913124	.	+	0	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	CDS	27913122	27913448	0.69	+	0	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	exon	27913122	27913448	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	intron	27913449	27913546	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	CDS	27913547	27913768	0.95	+	0	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	exon	27913547	27913768	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	intron	27913769	27913921	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	CDS	27913922	27913968	0.98	+	0	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	exon	27913922	27913968	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	intron	27913969	27914150	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	CDS	27914151	27914579	0.99	+	1	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	exon	27914151	27914579	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	intron	27914580	27914667	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	CDS	27914668	27915000	0.49	+	1	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	exon	27914668	27915000	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	intron	27915001	27915092	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	CDS	27915093	27915237	0.49	+	1	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	exon	27915093	27915237	.	+	.	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
Phchi.S1	AUGUSTUS	stop_codon	27915238	27915240	.	+	0	transcript_id "Phchi.S1G442200.t1"; gene_id "Phchi.S1G442200"
# This transcript jg10832.t1 is derived from g14881.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2330038	2331846	.	-	.	Phchi.S4G041300
Phchi.S4	AUGUSTUS	transcript	2330038	2331846	.	-	.	transcript_id "Phchi.S4G041300.t1"; gene_id "Phchi.S4G041300"
Phchi.S4	AUGUSTUS	stop_codon	2330035	2330037	.	-	0	transcript_id "Phchi.S4G041300.t1"; gene_id "Phchi.S4G041300"
Phchi.S4	AUGUSTUS	CDS	2330038	2331846	0.41	-	0	transcript_id "Phchi.S4G041300.t1"; gene_id "Phchi.S4G041300"
Phchi.S4	AUGUSTUS	exon	2330038	2331846	.	-	.	transcript_id "Phchi.S4G041300.t1"; gene_id "Phchi.S4G041300"
Phchi.S4	AUGUSTUS	start_codon	2331844	2331846	.	-	0	transcript_id "Phchi.S4G041300.t1"; gene_id "Phchi.S4G041300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14891.t1 is derived from g13359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15299876	15301658	.	+	.	Phchi.S3G221000
Phchi.S3	AUGUSTUS	transcript	15299876	15301658	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	start_codon	15299876	15299878	.	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15299876	15300017	0.86	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15299876	15300017	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15300018	15300124	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15300125	15300174	1	+	2	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15300125	15300174	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15300175	15300357	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15300358	15300430	1	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15300358	15300430	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15300431	15300592	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15300593	15300672	1	+	2	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15300593	15300672	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15300673	15300783	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15300784	15300935	1	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15300784	15300935	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15300936	15301044	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15301045	15301204	1	+	1	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15301045	15301204	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15301205	15301288	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15301289	15301336	1	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15301289	15301336	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15301337	15301410	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15301411	15301491	1	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15301411	15301491	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	intron	15301492	15301577	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	CDS	15301578	15301658	1	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	exon	15301578	15301658	.	+	.	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
Phchi.S3	AUGUSTUS	stop_codon	15301659	15301661	.	+	0	transcript_id "Phchi.S3G221000.t1"; gene_id "Phchi.S3G221000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10349.t1 is derived from g7525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47298710	47303397	.	-	.	Phchi.S1G750800
Phchi.S1	AUGUSTUS	transcript	47298710	47303397	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	stop_codon	47298707	47298709	.	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47298710	47299088	1	-	1	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47298710	47299088	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47299089	47299195	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47299196	47299782	1	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47299196	47299782	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47299783	47299859	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47299860	47299982	0.62	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47299860	47299982	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47299983	47300066	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47300067	47300279	1	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47300067	47300279	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47300280	47300363	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47300364	47301368	1	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47300364	47301368	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47301369	47301461	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47301462	47302002	1	-	1	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47301462	47302002	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47302003	47302115	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47302116	47302573	0.96	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47302116	47302573	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47302574	47302661	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47302662	47303021	0.53	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47302662	47303021	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	intron	47303022	47303178	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	CDS	47303179	47303397	0.94	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	exon	47303179	47303397	.	-	.	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
Phchi.S1	AUGUSTUS	start_codon	47303395	47303397	.	-	0	transcript_id "Phchi.S1G750800.t1"; gene_id "Phchi.S1G750800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11286.t1 is derived from g15336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5197990	5198350	.	-	.	Phchi.S4G086800
Phchi.S4	AUGUSTUS	transcript	5197990	5198350	.	-	.	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	stop_codon	5197987	5197989	.	-	0	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	CDS	5197990	5198104	0.8	-	1	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	exon	5197990	5198104	.	-	.	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	intron	5198105	5198255	.	-	.	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	CDS	5198256	5198350	0.7	-	0	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	exon	5198256	5198350	.	-	.	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
Phchi.S4	AUGUSTUS	start_codon	5198348	5198350	.	-	0	transcript_id "Phchi.S4G086800.t1"; gene_id "Phchi.S4G086800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6329.t1 is derived from g3501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22303401	22303843	.	+	.	Phchi.S1G348800
Phchi.S1	AUGUSTUS	transcript	22303401	22303843	.	+	.	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	start_codon	22303401	22303403	.	+	0	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	CDS	22303401	22303494	1	+	0	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	exon	22303401	22303494	.	+	.	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	intron	22303495	22303580	.	+	.	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	CDS	22303581	22303843	0.34	+	2	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	exon	22303581	22303843	.	+	.	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
Phchi.S1	AUGUSTUS	stop_codon	22303844	22303846	.	+	0	transcript_id "Phchi.S1G348800.t1"; gene_id "Phchi.S1G348800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2533.t1 is derived from g9453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7185614	7188891	.	-	.	Phchi.S5G114200
Phchi.S5	AUGUSTUS	transcript	7185614	7188891	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	stop_codon	7185611	7185613	.	-	0	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7185614	7185825	0.99	-	2	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7185614	7185825	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7185826	7186141	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7186142	7186385	1	-	0	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7186142	7186385	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7186386	7186473	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7186474	7186540	0.76	-	1	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7186474	7186540	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7186541	7186702	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7186703	7186779	0.76	-	0	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7186703	7186779	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7186780	7186906	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7186907	7187036	1	-	1	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7186907	7187036	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7187037	7187399	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7187400	7187473	1	-	0	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7187400	7187473	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7187474	7188236	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7188237	7188381	0.92	-	1	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7188237	7188381	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7188382	7188528	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7188529	7188597	0.92	-	1	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7188529	7188597	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	intron	7188598	7188859	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	CDS	7188860	7188891	0.51	-	0	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	exon	7188860	7188891	.	-	.	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
Phchi.S5	AUGUSTUS	start_codon	7188889	7188891	.	-	0	transcript_id "Phchi.S5G114200.t1"; gene_id "Phchi.S5G114200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7447.t1 is derived from g4619.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29192253	29195063	.	-	.	Phchi.S1G460600
Phchi.S1	AUGUSTUS	transcript	29192253	29195063	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	stop_codon	29192250	29192252	.	-	0	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29192253	29192279	0.99	-	0	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29192253	29192279	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29192280	29192371	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29192372	29192456	0.69	-	1	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29192372	29192456	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29192457	29192989	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29192990	29193399	0.25	-	0	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29192990	29193399	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29193400	29193487	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29193488	29193667	0.49	-	0	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29193488	29193667	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29193668	29193893	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29193894	29194044	1	-	1	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29193894	29194044	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29194045	29194366	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29194367	29194477	0.46	-	1	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29194367	29194477	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29194478	29194622	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29194623	29194728	0.46	-	2	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29194623	29194728	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29194729	29194888	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29194889	29195063	0.97	-	0	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29194889	29195063	.	-	.	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	start_codon	29195061	29195063	.	-	0	transcript_id "Phchi.S1G460600.t1"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	transcript	29192253	29195063	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	stop_codon	29192250	29192252	.	-	0	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29192253	29192279	0.94	-	0	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29192253	29192279	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29192280	29192371	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29192372	29192456	0.61	-	1	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29192372	29192456	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29192457	29192989	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29192990	29193399	0.24	-	0	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29192990	29193399	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29193400	29193487	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29193488	29193667	0.44	-	0	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29193488	29193667	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29193668	29193749	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29193750	29194044	1	-	1	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29193750	29194044	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29194045	29194366	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29194367	29194477	0.55	-	1	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29194367	29194477	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29194478	29194622	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29194623	29194728	0.55	-	2	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29194623	29194728	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	intron	29194729	29194888	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	CDS	29194889	29195063	0.98	-	0	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	exon	29194889	29195063	.	-	.	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
Phchi.S1	AUGUSTUS	start_codon	29195061	29195063	.	-	0	transcript_id "Phchi.S1G460600.t2"; gene_id "Phchi.S1G460600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7289.t1 is derived from g4461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28334159	28334940	.	-	.	Phchi.S1G444800
Phchi.S1	AUGUSTUS	transcript	28334159	28334940	.	-	.	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	stop_codon	28334156	28334158	.	-	0	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	CDS	28334159	28334288	0.96	-	1	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	exon	28334159	28334288	.	-	.	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	intron	28334289	28334374	.	-	.	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	CDS	28334375	28334510	1	-	2	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	exon	28334375	28334510	.	-	.	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	intron	28334511	28334807	.	-	.	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	CDS	28334808	28334940	1	-	0	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	exon	28334808	28334940	.	-	.	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
Phchi.S1	AUGUSTUS	start_codon	28334938	28334940	.	-	0	transcript_id "Phchi.S1G444800.t1"; gene_id "Phchi.S1G444800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4070.t1 is derived from g1239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7623029	7627592	.	-	.	Phchi.S1G122900
Phchi.S1	AUGUSTUS	transcript	7623029	7627592	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	stop_codon	7623026	7623028	.	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7623029	7623157	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7623029	7623157	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7623158	7623276	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7623277	7623420	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7623277	7623420	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7623421	7623498	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7623499	7623575	1	-	2	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7623499	7623575	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7623576	7623703	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7623704	7623809	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7623704	7623809	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7623810	7623890	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7623891	7624054	1	-	2	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7623891	7624054	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7624055	7624146	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7624147	7624258	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7624147	7624258	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7624259	7624336	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7624337	7624474	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7624337	7624474	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7624475	7624682	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7624683	7624761	1	-	1	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7624683	7624761	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7624762	7624868	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7624869	7624978	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7624869	7624978	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7624979	7625061	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7625062	7625187	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7625062	7625187	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7625188	7625318	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7625319	7625393	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7625319	7625393	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7625394	7625499	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7625500	7625609	0.78	-	2	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7625500	7625609	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7625610	7625696	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7625697	7626010	0.77	-	1	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7625697	7626010	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7626011	7626089	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7626090	7626477	1	-	2	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7626090	7626477	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7626478	7626555	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7626556	7626811	1	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7626556	7626811	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7626812	7627069	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7627070	7627320	1	-	2	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7627070	7627320	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	intron	7627321	7627420	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	CDS	7627421	7627592	0.57	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	exon	7627421	7627592	.	-	.	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
Phchi.S1	AUGUSTUS	start_codon	7627590	7627592	.	-	0	transcript_id "Phchi.S1G122900.t1"; gene_id "Phchi.S1G122900"
# This transcript jg13818.t2 is derived from g12285.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13819.t1 is derived from g12286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9060479	9061712	.	-	.	Phchi.S3G113800
Phchi.S3	AUGUSTUS	transcript	9060479	9061712	.	-	.	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	stop_codon	9060476	9060478	.	-	0	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	CDS	9060479	9061282	0.9	-	0	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	exon	9060479	9061282	.	-	.	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	intron	9061283	9061439	.	-	.	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	CDS	9061440	9061539	0.99	-	1	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	exon	9061440	9061539	.	-	.	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	intron	9061540	9061638	.	-	.	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	CDS	9061639	9061712	0.81	-	0	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	exon	9061639	9061712	.	-	.	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
Phchi.S3	AUGUSTUS	start_codon	9061710	9061712	.	-	0	transcript_id "Phchi.S3G113800.t1"; gene_id "Phchi.S3G113800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1754.t1 is derived from g8674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2889957	2890596	.	+	.	Phchi.S5G036300
Phchi.S5	AUGUSTUS	transcript	2889957	2890596	.	+	.	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	start_codon	2889957	2889959	.	+	0	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	CDS	2889957	2890171	0.97	+	0	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	exon	2889957	2890171	.	+	.	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	intron	2890172	2890264	.	+	.	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	CDS	2890265	2890336	1	+	1	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	exon	2890265	2890336	.	+	.	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	intron	2890337	2890454	.	+	.	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	CDS	2890455	2890596	1	+	1	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	exon	2890455	2890596	.	+	.	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
Phchi.S5	AUGUSTUS	stop_codon	2890597	2890599	.	+	0	transcript_id "Phchi.S5G036300.t1"; gene_id "Phchi.S5G036300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg661.t1 is derived from g10443.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4624574	4625531	.	-	.	Phchi.S6G062000
Phchi.S6	AUGUSTUS	transcript	4624574	4625531	.	-	.	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	stop_codon	4624571	4624573	.	-	0	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	CDS	4624574	4624708	0.87	-	0	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	exon	4624574	4624708	.	-	.	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	intron	4624709	4624919	.	-	.	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	CDS	4624920	4625362	1	-	2	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	exon	4624920	4625362	.	-	.	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	intron	4625363	4625446	.	-	.	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	CDS	4625447	4625531	0.65	-	0	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	exon	4625447	4625531	.	-	.	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	start_codon	4625529	4625531	.	-	0	transcript_id "Phchi.S6G062000.t1"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	transcript	4624574	4625531	.	-	.	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	stop_codon	4624571	4624573	.	-	0	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	CDS	4624574	4624708	0.8	-	0	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	exon	4624574	4624708	.	-	.	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	intron	4624709	4624919	.	-	.	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	CDS	4624920	4625362	1	-	2	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	exon	4624920	4625362	.	-	.	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	intron	4625363	4625443	.	-	.	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	CDS	4625444	4625531	0.72	-	0	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	exon	4625444	4625531	.	-	.	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
Phchi.S6	AUGUSTUS	start_codon	4625529	4625531	.	-	0	transcript_id "Phchi.S6G062000.t2"; gene_id "Phchi.S6G062000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg786.t1 is derived from g10568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5504270	5505037	.	-	.	Phchi.S6G074500
Phchi.S6	AUGUSTUS	transcript	5504270	5505037	.	-	.	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	stop_codon	5504267	5504269	.	-	0	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	CDS	5504270	5504624	0.73	-	1	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	exon	5504270	5504624	.	-	.	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	intron	5504625	5504730	.	-	.	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	CDS	5504731	5504827	0.93	-	2	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	exon	5504731	5504827	.	-	.	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	intron	5504828	5504913	.	-	.	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	CDS	5504914	5505037	0.78	-	0	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	exon	5504914	5505037	.	-	.	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
Phchi.S6	AUGUSTUS	start_codon	5505035	5505037	.	-	0	transcript_id "Phchi.S6G074500.t1"; gene_id "Phchi.S6G074500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12662.t1 is derived from g14461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	86527	88113	.	-	.	Phchi.C12G001200
Phchi.C12	AUGUSTUS	transcript	86527	88113	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	stop_codon	86524	86526	.	-	0	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	CDS	86527	87123	0.4	-	0	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	exon	86527	87123	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	intron	87124	87245	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	CDS	87246	87360	0.19	-	1	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	exon	87246	87360	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	intron	87361	87485	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	CDS	87486	87910	0.15	-	0	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	exon	87486	87910	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	intron	87911	87993	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	CDS	87994	88113	0.25	-	0	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	exon	87994	88113	.	-	.	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
Phchi.C12	AUGUSTUS	start_codon	88111	88113	.	-	0	transcript_id "Phchi.C12G001200.t1"; gene_id "Phchi.C12G001200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9473.t1 is derived from g6649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41714468	41720963	.	-	.	Phchi.S1G663200
Phchi.S1	AUGUSTUS	transcript	41714468	41720963	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	stop_codon	41714465	41714467	.	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41714468	41715592	0.99	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41714468	41715592	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41715593	41715699	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41715700	41716142	0.49	-	2	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41715700	41716142	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41716143	41716228	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41716229	41716424	1	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41716229	41716424	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41716425	41716567	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41716568	41716747	1	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41716568	41716747	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41716748	41716846	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41716847	41716928	1	-	1	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41716847	41716928	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41716929	41717123	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41717124	41717291	1	-	1	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41717124	41717291	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41717292	41717375	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41717376	41718013	0.96	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41717376	41718013	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41718014	41718130	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41718131	41718297	1	-	2	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41718131	41718297	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41718298	41718430	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41718431	41718761	0.99	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41718431	41718761	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41718762	41718881	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41718882	41719332	0.84	-	1	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41718882	41719332	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41719333	41719433	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41719434	41720257	0.85	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41719434	41720257	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	intron	41720258	41720330	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	CDS	41720331	41720963	0.47	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	exon	41720331	41720963	.	-	.	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
Phchi.S1	AUGUSTUS	start_codon	41720961	41720963	.	-	0	transcript_id "Phchi.S1G663200.t1"; gene_id "Phchi.S1G663200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg336.t1 is derived from g10118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2468311	2468771	.	-	.	Phchi.S6G029500
Phchi.S6	AUGUSTUS	transcript	2468311	2468771	.	-	.	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	stop_codon	2468308	2468310	.	-	0	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	CDS	2468311	2468311	1	-	1	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	exon	2468311	2468311	.	-	.	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	intron	2468312	2468453	.	-	.	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	CDS	2468454	2468657	1	-	1	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	exon	2468454	2468657	.	-	.	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	intron	2468658	2468733	.	-	.	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	CDS	2468734	2468771	0.97	-	0	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	exon	2468734	2468771	.	-	.	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
Phchi.S6	AUGUSTUS	start_codon	2468769	2468771	.	-	0	transcript_id "Phchi.S6G029500.t1"; gene_id "Phchi.S6G029500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15859.t1 is derived from g14329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21894907	21895362	.	+	.	Phchi.S3G317800
Phchi.S3	AUGUSTUS	transcript	21894907	21895362	.	+	.	transcript_id "Phchi.S3G317800.t1"; gene_id "Phchi.S3G317800"
Phchi.S3	AUGUSTUS	start_codon	21894907	21894909	.	+	0	transcript_id "Phchi.S3G317800.t1"; gene_id "Phchi.S3G317800"
Phchi.S3	AUGUSTUS	CDS	21894907	21895362	0.61	+	0	transcript_id "Phchi.S3G317800.t1"; gene_id "Phchi.S3G317800"
Phchi.S3	AUGUSTUS	exon	21894907	21895362	.	+	.	transcript_id "Phchi.S3G317800.t1"; gene_id "Phchi.S3G317800"
Phchi.S3	AUGUSTUS	stop_codon	21895363	21895365	.	+	0	transcript_id "Phchi.S3G317800.t1"; gene_id "Phchi.S3G317800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13188.t1 is derived from g11653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4595398	4596286	.	-	.	Phchi.S3G050700
Phchi.S3	AUGUSTUS	transcript	4595398	4596286	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	stop_codon	4595395	4595397	.	-	0	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	CDS	4595398	4595454	1	-	0	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	exon	4595398	4595454	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	intron	4595455	4595530	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	CDS	4595531	4595589	1	-	2	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	exon	4595531	4595589	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	intron	4595590	4595681	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	CDS	4595682	4595831	1	-	2	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	exon	4595682	4595831	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	intron	4595832	4595910	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	CDS	4595911	4596114	1	-	2	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	exon	4595911	4596114	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	intron	4596115	4596204	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	CDS	4596205	4596286	1	-	0	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	exon	4596205	4596286	.	-	.	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
Phchi.S3	AUGUSTUS	start_codon	4596284	4596286	.	-	0	transcript_id "Phchi.S3G050700.t1"; gene_id "Phchi.S3G050700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11856.t1 is derived from g15908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8635931	8638783	.	+	.	Phchi.S4G143800
Phchi.S4	AUGUSTUS	transcript	8635931	8638783	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	start_codon	8635931	8635933	.	+	0	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8635931	8636072	0.75	+	0	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8635931	8636072	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8636073	8636231	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8636232	8636391	1	+	2	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8636232	8636391	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8636392	8636485	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8636486	8636499	0.99	+	1	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8636486	8636499	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8636500	8636634	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8636635	8636653	0.98	+	2	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8636635	8636653	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8636654	8636829	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8636830	8638186	0.57	+	1	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8636830	8638186	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8638187	8638317	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8638318	8638420	0.82	+	0	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8638318	8638420	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8638421	8638542	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8638543	8638624	0.84	+	2	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8638543	8638624	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	intron	8638625	8638764	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	CDS	8638765	8638783	0.93	+	1	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	exon	8638765	8638783	.	+	.	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
Phchi.S4	AUGUSTUS	stop_codon	8638784	8638786	.	+	0	transcript_id "Phchi.S4G143800.t1"; gene_id "Phchi.S4G143800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13228.t1 is derived from g11693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4787387	4789813	.	+	.	Phchi.S3G054700
Phchi.S3	AUGUSTUS	transcript	4787387	4789813	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	start_codon	4787387	4787389	.	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4787387	4787401	0.61	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4787387	4787401	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4787402	4787470	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4787471	4787669	0.88	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4787471	4787669	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4787670	4787758	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4787759	4788045	1	+	2	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4787759	4788045	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4788046	4788138	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4788139	4788379	1	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4788139	4788379	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4788380	4788472	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4788473	4788927	0.98	+	2	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4788473	4788927	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4788928	4789036	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4789037	4789141	1	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4789037	4789141	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4789142	4789241	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4789242	4789576	1	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4789242	4789576	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	intron	4789577	4789656	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	CDS	4789657	4789813	0.97	+	1	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	exon	4789657	4789813	.	+	.	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
Phchi.S3	AUGUSTUS	stop_codon	4789814	4789816	.	+	0	transcript_id "Phchi.S3G054700.t1"; gene_id "Phchi.S3G054700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13171.t1 is derived from g11636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4485259	4487259	.	+	.	Phchi.S3G049000
Phchi.S3	AUGUSTUS	transcript	4485259	4487259	.	+	.	transcript_id "Phchi.S3G049000.t1"; gene_id "Phchi.S3G049000"
Phchi.S3	AUGUSTUS	start_codon	4485259	4485261	.	+	0	transcript_id "Phchi.S3G049000.t1"; gene_id "Phchi.S3G049000"
Phchi.S3	AUGUSTUS	CDS	4485259	4487259	0.69	+	0	transcript_id "Phchi.S3G049000.t1"; gene_id "Phchi.S3G049000"
Phchi.S3	AUGUSTUS	exon	4485259	4487259	.	+	.	transcript_id "Phchi.S3G049000.t1"; gene_id "Phchi.S3G049000"
Phchi.S3	AUGUSTUS	stop_codon	4487260	4487262	.	+	0	transcript_id "Phchi.S3G049000.t1"; gene_id "Phchi.S3G049000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12594.t1 is derived from g8271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36927896	36931326	.	+	.	Phchi.S2G067400
Phchi.S2	AUGUSTUS	transcript	36927896	36931326	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	start_codon	36927896	36927898	.	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36927896	36927959	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36927896	36927959	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36927960	36928122	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36928123	36928415	1	+	2	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36928123	36928415	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36928416	36928498	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36928499	36928570	0.96	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36928499	36928570	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36928571	36928707	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36928708	36928755	0.99	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36928708	36928755	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36928756	36928837	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36928838	36928908	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36928838	36928908	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36928909	36929086	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36929087	36929205	1	+	1	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36929087	36929205	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36929206	36929363	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36929364	36929480	0.58	+	2	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36929364	36929480	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36929481	36929628	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36929629	36929672	0.9	+	2	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36929629	36929672	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36929673	36929844	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36929845	36929925	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36929845	36929925	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36929926	36930142	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36930143	36930243	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36930143	36930243	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36930244	36930326	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36930327	36930435	1	+	1	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36930327	36930435	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36930436	36930609	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36930610	36930715	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36930610	36930715	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36930716	36930870	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36930871	36930956	1	+	2	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36930871	36930956	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36930957	36931037	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36931038	36931163	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36931038	36931163	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	intron	36931164	36931239	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	CDS	36931240	36931326	1	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	exon	36931240	36931326	.	+	.	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
Phchi.S2	AUGUSTUS	stop_codon	36931327	36931329	.	+	0	transcript_id "Phchi.S2G067400.t1"; gene_id "Phchi.S2G067400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13253.t1 is derived from g11718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4932855	4935541	.	-	.	Phchi.S3G057200
Phchi.S3	AUGUSTUS	transcript	4932855	4935541	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	stop_codon	4932852	4932854	.	-	0	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4932855	4932920	0.66	-	0	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4932855	4932920	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4932921	4933151	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4933152	4933253	0.64	-	0	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4933152	4933253	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4933254	4933462	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4933463	4933744	1	-	0	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4933463	4933744	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4933745	4933829	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4933830	4934020	1	-	2	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4933830	4934020	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4934021	4934143	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4934144	4934361	1	-	1	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4934144	4934361	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4934362	4934538	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4934539	4934863	1	-	2	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4934539	4934863	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4934864	4934951	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4934952	4935143	1	-	2	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4934952	4935143	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	intron	4935144	4935237	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	CDS	4935238	4935541	0.93	-	0	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	exon	4935238	4935541	.	-	.	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
Phchi.S3	AUGUSTUS	start_codon	4935539	4935541	.	-	0	transcript_id "Phchi.S3G057200.t1"; gene_id "Phchi.S3G057200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1989.t1 is derived from g8909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4332756	4334586	.	+	.	Phchi.S5G059800
Phchi.S5	AUGUSTUS	transcript	4332756	4334586	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	start_codon	4332756	4332758	.	+	0	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	CDS	4332756	4332805	0.42	+	0	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	exon	4332756	4332805	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	intron	4332806	4332972	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	CDS	4332973	4333053	0.98	+	1	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	exon	4332973	4333053	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	intron	4333054	4333392	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	CDS	4333393	4333538	1	+	1	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	exon	4333393	4333538	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	intron	4333539	4333696	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	CDS	4333697	4333865	1	+	2	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	exon	4333697	4333865	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	intron	4333866	4334079	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	CDS	4334080	4334266	1	+	1	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	exon	4334080	4334266	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	intron	4334267	4334358	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	CDS	4334359	4334586	1	+	0	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	exon	4334359	4334586	.	+	.	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
Phchi.S5	AUGUSTUS	stop_codon	4334587	4334589	.	+	0	transcript_id "Phchi.S5G059800.t1"; gene_id "Phchi.S5G059800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2151.t1 is derived from g9071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5079907	5084543	.	-	.	Phchi.S5G076000
Phchi.S5	AUGUSTUS	transcript	5079907	5084543	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	stop_codon	5079904	5079906	.	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5079907	5079995	0.99	-	2	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5079907	5079995	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5079996	5080080	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5080081	5080138	1	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5080081	5080138	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5080139	5080318	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5080319	5080921	0.67	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5080319	5080921	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5080922	5081101	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5081102	5081805	0.88	-	2	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5081102	5081805	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5081806	5081987	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5081988	5082066	0.83	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5081988	5082066	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082067	5082150	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5082151	5082172	0.88	-	1	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5082151	5082172	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082173	5082372	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5082373	5082636	1	-	1	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5082373	5082636	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082637	5082738	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5082739	5082923	1	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5082739	5082923	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082924	5083009	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083010	5083126	1	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083010	5083126	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5083127	5083232	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083233	5083385	1	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083233	5083385	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5083386	5083539	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083540	5083668	1	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083540	5083668	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5083669	5083796	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083797	5084543	0.94	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083797	5084543	.	-	.	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	start_codon	5084541	5084543	.	-	0	transcript_id "Phchi.S5G076000.t1"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	transcript	5079907	5084543	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	stop_codon	5079904	5079906	.	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5079907	5079995	1	-	2	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5079907	5079995	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5079996	5080080	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5080081	5080150	1	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5080081	5080150	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5080151	5080318	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5080319	5080921	0.67	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5080319	5080921	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5080922	5081101	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5081102	5081805	0.9	-	2	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5081102	5081805	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5081806	5081987	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5081988	5082066	0.75	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5081988	5082066	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082067	5082150	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5082151	5082172	0.81	-	1	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5082151	5082172	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082173	5082372	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5082373	5082636	1	-	1	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5082373	5082636	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082637	5082738	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5082739	5082923	0.98	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5082739	5082923	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5082924	5083009	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083010	5083126	1	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083010	5083126	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5083127	5083232	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083233	5083385	1	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083233	5083385	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5083386	5083539	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083540	5083668	1	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083540	5083668	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	intron	5083669	5083796	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	CDS	5083797	5084543	0.98	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	exon	5083797	5084543	.	-	.	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
Phchi.S5	AUGUSTUS	start_codon	5084541	5084543	.	-	0	transcript_id "Phchi.S5G076000.t2"; gene_id "Phchi.S5G076000"
# This transcript jg9946.t2 is derived from g7122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9947.t1 is derived from g7123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44619231	44621004	.	-	.	Phchi.S1G710600
Phchi.S1	AUGUSTUS	transcript	44619231	44621004	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	stop_codon	44619228	44619230	.	-	0	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	CDS	44619231	44619546	1	-	1	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	exon	44619231	44619546	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	intron	44619547	44619642	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	CDS	44619643	44619893	1	-	0	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	exon	44619643	44619893	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	intron	44619894	44619965	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	CDS	44619966	44620277	0.95	-	0	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	exon	44619966	44620277	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	intron	44620278	44620354	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	CDS	44620355	44620631	1	-	1	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	exon	44620355	44620631	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	intron	44620632	44620735	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	CDS	44620736	44621004	1	-	0	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	exon	44620736	44621004	.	-	.	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
Phchi.S1	AUGUSTUS	start_codon	44621002	44621004	.	-	0	transcript_id "Phchi.S1G710600.t1"; gene_id "Phchi.S1G710600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6605.t1 is derived from g3777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23961300	23961827	.	-	.	Phchi.S1G376400
Phchi.S1	AUGUSTUS	transcript	23961300	23961827	.	-	.	transcript_id "Phchi.S1G376400.t1"; gene_id "Phchi.S1G376400"
Phchi.S1	AUGUSTUS	stop_codon	23961297	23961299	.	-	0	transcript_id "Phchi.S1G376400.t1"; gene_id "Phchi.S1G376400"
Phchi.S1	AUGUSTUS	CDS	23961300	23961827	0.48	-	0	transcript_id "Phchi.S1G376400.t1"; gene_id "Phchi.S1G376400"
Phchi.S1	AUGUSTUS	exon	23961300	23961827	.	-	.	transcript_id "Phchi.S1G376400.t1"; gene_id "Phchi.S1G376400"
Phchi.S1	AUGUSTUS	start_codon	23961825	23961827	.	-	0	transcript_id "Phchi.S1G376400.t1"; gene_id "Phchi.S1G376400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5459.t1 is derived from g2629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16950871	16952361	.	-	.	Phchi.S1G261800
Phchi.S1	AUGUSTUS	transcript	16951085	16952361	.	-	.	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	stop_codon	16951082	16951084	.	-	0	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	CDS	16951085	16951145	0.69	-	1	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	exon	16951085	16951145	.	-	.	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	intron	16951146	16951228	.	-	.	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	CDS	16951229	16952361	0.42	-	0	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	exon	16951229	16952361	.	-	.	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	start_codon	16952359	16952361	.	-	0	transcript_id "Phchi.S1G261800.t1"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	transcript	16950871	16952361	.	-	.	transcript_id "Phchi.S1G261800.t2"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	stop_codon	16950868	16950870	.	-	0	transcript_id "Phchi.S1G261800.t2"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	CDS	16950871	16952361	0.55	-	0	transcript_id "Phchi.S1G261800.t2"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	exon	16950871	16952361	.	-	.	transcript_id "Phchi.S1G261800.t2"; gene_id "Phchi.S1G261800"
Phchi.S1	AUGUSTUS	start_codon	16952359	16952361	.	-	0	transcript_id "Phchi.S1G261800.t2"; gene_id "Phchi.S1G261800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8912.t1 is derived from g6087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38596705	38599239	.	-	.	Phchi.S1G607100
Phchi.S1	AUGUSTUS	transcript	38596705	38599239	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	stop_codon	38596702	38596704	.	-	0	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38596705	38598550	0.97	-	1	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38596705	38598550	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598551	38598642	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38598643	38598812	1	-	0	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38598643	38598812	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598813	38598894	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38598895	38598974	1	-	2	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38598895	38598974	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598975	38599058	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38599059	38599239	0.99	-	0	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38599059	38599239	.	-	.	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	start_codon	38599237	38599239	.	-	0	transcript_id "Phchi.S1G607100.t1"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	transcript	38596705	38599239	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	stop_codon	38596702	38596704	.	-	0	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38596705	38598543	0.6	-	0	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38596705	38598543	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598544	38598642	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38598643	38598691	0.52	-	1	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38598643	38598691	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598692	38598744	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38598745	38598812	0.53	-	0	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38598745	38598812	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598813	38598894	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38598895	38598974	1	-	2	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38598895	38598974	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	intron	38598975	38599058	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	CDS	38599059	38599239	1	-	0	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	exon	38599059	38599239	.	-	.	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
Phchi.S1	AUGUSTUS	start_codon	38599237	38599239	.	-	0	transcript_id "Phchi.S1G607100.t2"; gene_id "Phchi.S1G607100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12676.t1 is derived from g14410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	18111	18414	.	+	.	Phchi.C62G000700
Phchi.C62	AUGUSTUS	transcript	18111	18414	.	+	.	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	start_codon	18111	18113	.	+	0	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	CDS	18111	18123	0.49	+	0	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	exon	18111	18123	.	+	.	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	intron	18124	18205	.	+	.	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	CDS	18206	18414	0.58	+	2	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	exon	18206	18414	.	+	.	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
Phchi.C62	AUGUSTUS	stop_codon	18415	18417	.	+	0	transcript_id "Phchi.C62G000700.t1"; gene_id "Phchi.C62G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11935.t1 is derived from g7610.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	95603	98988	.	+	.	Phchi.S2G001500
Phchi.S2	AUGUSTUS	transcript	95603	98988	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	start_codon	95603	95605	.	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	95603	96019	0.55	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	95603	96019	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96020	96102	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96103	96225	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96103	96225	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96226	96315	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96316	96483	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96316	96483	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96484	96576	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96577	96660	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96577	96660	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96661	96782	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96783	96833	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96783	96833	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96834	96916	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96917	96976	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96917	96976	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96977	97050	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97051	97133	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97051	97133	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97134	97224	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97225	97351	0.89	+	1	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97225	97351	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97352	97452	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97453	97512	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97453	97512	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97513	97746	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97747	97839	0.51	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97747	97839	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97840	97922	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97923	97976	0.42	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97923	97976	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97977	98086	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98087	98173	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98087	98173	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98174	98256	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98257	98404	0.83	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98257	98404	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98405	98506	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98507	98634	0.79	+	2	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98507	98634	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98635	98763	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98764	98811	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98764	98811	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98812	98898	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98899	98988	1	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98899	98988	.	+	.	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	stop_codon	98989	98991	.	+	0	transcript_id "Phchi.S2G001500.t1"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	transcript	95603	98988	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	start_codon	95603	95605	.	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	95603	96019	0.56	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	95603	96019	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96020	96102	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96103	96225	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96103	96225	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96226	96315	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96316	96483	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96316	96483	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96484	96576	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96577	96660	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96577	96660	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96661	96782	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96783	96833	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96783	96833	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96834	96916	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	96917	96976	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	96917	96976	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	96977	97050	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97051	97133	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97051	97133	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97134	97224	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97225	97351	0.9	+	1	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97225	97351	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97352	97452	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97453	97534	0.86	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97453	97534	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97535	97746	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97747	97763	0.68	+	2	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97747	97763	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97764	97889	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	97890	97976	0.45	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	97890	97976	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	97977	98086	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98087	98173	0.83	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98087	98173	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98174	98256	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98257	98404	0.76	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98257	98404	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98405	98506	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98507	98634	0.7	+	2	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98507	98634	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98635	98763	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98764	98811	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98764	98811	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	intron	98812	98898	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	CDS	98899	98988	1	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	exon	98899	98988	.	+	.	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
Phchi.S2	AUGUSTUS	stop_codon	98989	98991	.	+	0	transcript_id "Phchi.S2G001500.t2"; gene_id "Phchi.S2G001500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14338.t1 is derived from g12805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12297397	12299462	.	-	.	Phchi.S3G165700
Phchi.S3	AUGUSTUS	transcript	12297397	12299462	.	-	.	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	stop_codon	12297394	12297396	.	-	0	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	CDS	12297397	12298715	1	-	2	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	exon	12297397	12298715	.	-	.	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	intron	12298716	12298816	.	-	.	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	CDS	12298817	12299041	0.95	-	2	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	exon	12298817	12299041	.	-	.	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	intron	12299042	12299152	.	-	.	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	CDS	12299153	12299462	0.47	-	0	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	exon	12299153	12299462	.	-	.	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
Phchi.S3	AUGUSTUS	start_codon	12299460	12299462	.	-	0	transcript_id "Phchi.S3G165700.t1"; gene_id "Phchi.S3G165700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9630.t1 is derived from g6806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42990212	42990557	.	-	.	Phchi.S1G678900
Phchi.S1	AUGUSTUS	transcript	42990212	42990557	.	-	.	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	stop_codon	42990209	42990211	.	-	0	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	CDS	42990212	42990278	0.98	-	1	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	exon	42990212	42990278	.	-	.	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	intron	42990279	42990420	.	-	.	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	CDS	42990421	42990557	0.98	-	0	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	exon	42990421	42990557	.	-	.	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
Phchi.S1	AUGUSTUS	start_codon	42990555	42990557	.	-	0	transcript_id "Phchi.S1G678900.t1"; gene_id "Phchi.S1G678900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7342.t1 is derived from g4514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28627815	28628375	.	+	.	Phchi.S1G450100
Phchi.S1	AUGUSTUS	transcript	28627815	28628375	.	+	.	transcript_id "Phchi.S1G450100.t1"; gene_id "Phchi.S1G450100"
Phchi.S1	AUGUSTUS	start_codon	28627815	28627817	.	+	0	transcript_id "Phchi.S1G450100.t1"; gene_id "Phchi.S1G450100"
Phchi.S1	AUGUSTUS	CDS	28627815	28628375	0.83	+	0	transcript_id "Phchi.S1G450100.t1"; gene_id "Phchi.S1G450100"
Phchi.S1	AUGUSTUS	exon	28627815	28628375	.	+	.	transcript_id "Phchi.S1G450100.t1"; gene_id "Phchi.S1G450100"
Phchi.S1	AUGUSTUS	stop_codon	28628376	28628378	.	+	0	transcript_id "Phchi.S1G450100.t1"; gene_id "Phchi.S1G450100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10710.t1 is derived from g14760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1707996	1710473	.	-	.	Phchi.S4G029200
Phchi.S4	AUGUSTUS	transcript	1707996	1710473	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	stop_codon	1707993	1707995	.	-	0	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1707996	1708184	1	-	0	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1707996	1708184	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1708185	1708268	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1708269	1708386	1	-	1	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1708269	1708386	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1708387	1708527	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1708528	1708724	0.77	-	0	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1708528	1708724	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1708725	1708811	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1708812	1709108	1	-	0	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1708812	1709108	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1709109	1709259	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1709260	1709345	1	-	2	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1709260	1709345	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1709346	1709476	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1709477	1709569	0.99	-	2	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1709477	1709569	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1709570	1709656	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1709657	1709752	1	-	2	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1709657	1709752	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1709753	1709947	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1709948	1710055	1	-	2	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1709948	1710055	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	intron	1710056	1710184	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	CDS	1710185	1710473	0.89	-	0	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	exon	1710185	1710473	.	-	.	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
Phchi.S4	AUGUSTUS	start_codon	1710471	1710473	.	-	0	transcript_id "Phchi.S4G029200.t1"; gene_id "Phchi.S4G029200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11584.t1 is derived from g15635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7200513	7201766	.	+	.	Phchi.S4G116600
Phchi.S4	AUGUSTUS	transcript	7200513	7201766	.	+	.	transcript_id "Phchi.S4G116600.t1"; gene_id "Phchi.S4G116600"
Phchi.S4	AUGUSTUS	start_codon	7200513	7200515	.	+	0	transcript_id "Phchi.S4G116600.t1"; gene_id "Phchi.S4G116600"
Phchi.S4	AUGUSTUS	CDS	7200513	7201766	0.76	+	0	transcript_id "Phchi.S4G116600.t1"; gene_id "Phchi.S4G116600"
Phchi.S4	AUGUSTUS	exon	7200513	7201766	.	+	.	transcript_id "Phchi.S4G116600.t1"; gene_id "Phchi.S4G116600"
Phchi.S4	AUGUSTUS	stop_codon	7201767	7201769	.	+	0	transcript_id "Phchi.S4G116600.t1"; gene_id "Phchi.S4G116600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5569.t1 is derived from g2739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17628970	17630468	.	+	.	Phchi.S1G272800
Phchi.S1	AUGUSTUS	transcript	17628970	17630468	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	start_codon	17628970	17628972	.	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	CDS	17628970	17629317	0.64	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	exon	17628970	17629317	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	intron	17629318	17629405	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	CDS	17629406	17629505	1	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	exon	17629406	17629505	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	intron	17629506	17629586	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	CDS	17629587	17629747	1	+	2	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	exon	17629587	17629747	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	intron	17629748	17629824	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	CDS	17629825	17630022	1	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	exon	17629825	17630022	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	intron	17630023	17630125	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	CDS	17630126	17630230	0.55	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	exon	17630126	17630230	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	intron	17630231	17630324	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	CDS	17630325	17630468	0.49	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	exon	17630325	17630468	.	+	.	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
Phchi.S1	AUGUSTUS	stop_codon	17630469	17630471	.	+	0	transcript_id "Phchi.S1G272800.t1"; gene_id "Phchi.S1G272800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg160.t1 is derived from g9942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	910059	911744	.	-	.	Phchi.S6G011900
Phchi.S6	AUGUSTUS	transcript	910059	911744	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	stop_codon	910056	910058	.	-	0	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	910059	910148	0.97	-	0	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	910059	910148	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	910149	910280	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	910281	910336	0.9	-	2	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	910281	910336	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	910337	910431	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	910432	910538	0.98	-	1	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	910432	910538	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	910539	910652	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	910653	910740	0.45	-	2	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	910653	910740	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	910741	910898	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	910899	910912	0.9	-	1	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	910899	910912	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	910913	911012	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	911013	911134	0.93	-	0	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	911013	911134	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	911135	911343	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	911344	911642	0.66	-	2	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	911344	911642	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	intron	911643	911734	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	CDS	911735	911744	0.97	-	0	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	exon	911735	911744	.	-	.	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
Phchi.S6	AUGUSTUS	start_codon	911742	911744	.	-	0	transcript_id "Phchi.S6G011900.t1"; gene_id "Phchi.S6G011900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5592.t1 is derived from g2762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17790820	17800642	.	-	.	Phchi.S1G275100
Phchi.S1	AUGUSTUS	transcript	17790820	17800642	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	stop_codon	17790817	17790819	.	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17790820	17790828	0.69	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17790820	17790828	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17790829	17790925	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17790926	17791070	0.45	-	1	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17790926	17791070	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17791071	17791174	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17791175	17791198	0.32	-	1	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17791175	17791198	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17791199	17791286	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17791287	17791378	0.61	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17791287	17791378	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17791379	17791477	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17791478	17794036	0.8	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17791478	17794036	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17794037	17794125	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17794126	17794233	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17794126	17794233	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17794234	17794393	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17794394	17794489	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17794394	17794489	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17794490	17794715	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17794716	17795530	0.71	-	2	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17794716	17795530	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17795531	17795634	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17795635	17795770	0.81	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17795635	17795770	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17795771	17795980	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17795981	17796097	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17795981	17796097	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17796098	17796251	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17796252	17796440	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17796252	17796440	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17796441	17796613	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17796614	17796941	1	-	1	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17796614	17796941	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17796942	17797069	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17797070	17797225	0.6	-	1	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17797070	17797225	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17797226	17797363	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17797364	17797570	1	-	1	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17797364	17797570	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17797571	17797700	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17797701	17798110	0.87	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17797701	17798110	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17798111	17798221	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17798222	17798452	0.99	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17798222	17798452	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17798453	17798569	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17798570	17798704	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17798570	17798704	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17798705	17798791	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17798792	17798923	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17798792	17798923	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17798924	17799022	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17799023	17799205	0.99	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17799023	17799205	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17799206	17799312	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17799313	17799639	0.99	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17799313	17799639	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17799640	17799811	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17799812	17799973	1	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17799812	17799973	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17799974	17800115	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17800116	17800266	1	-	1	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17800116	17800266	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	intron	17800267	17800490	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	CDS	17800491	17800642	0.81	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	exon	17800491	17800642	.	-	.	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
Phchi.S1	AUGUSTUS	start_codon	17800640	17800642	.	-	0	transcript_id "Phchi.S1G275100.t1"; gene_id "Phchi.S1G275100"
# This transcript jg15705.t2 is derived from g14175.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15706.t1 is derived from g14176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20797154	20797519	.	+	.	Phchi.S3G302500
Phchi.S3	AUGUSTUS	transcript	20797154	20797519	.	+	.	transcript_id "Phchi.S3G302500.t1"; gene_id "Phchi.S3G302500"
Phchi.S3	AUGUSTUS	start_codon	20797154	20797156	.	+	0	transcript_id "Phchi.S3G302500.t1"; gene_id "Phchi.S3G302500"
Phchi.S3	AUGUSTUS	CDS	20797154	20797519	0.94	+	0	transcript_id "Phchi.S3G302500.t1"; gene_id "Phchi.S3G302500"
Phchi.S3	AUGUSTUS	exon	20797154	20797519	.	+	.	transcript_id "Phchi.S3G302500.t1"; gene_id "Phchi.S3G302500"
Phchi.S3	AUGUSTUS	stop_codon	20797520	20797522	.	+	0	transcript_id "Phchi.S3G302500.t1"; gene_id "Phchi.S3G302500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2438.t1 is derived from g9358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6638285	6640838	.	+	.	Phchi.S5G104700
Phchi.S5	AUGUSTUS	transcript	6638285	6640838	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	start_codon	6638285	6638287	.	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6638285	6638508	0.98	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6638285	6638508	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6638509	6638579	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6638580	6638643	1	+	1	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6638580	6638643	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6638644	6638723	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6638724	6638834	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6638724	6638834	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6638835	6638914	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6638915	6638974	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6638915	6638974	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6638975	6639068	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6639069	6639176	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6639069	6639176	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6639177	6639260	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6639261	6639333	0.98	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6639261	6639333	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6639334	6639458	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6639459	6639508	0.99	+	2	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6639459	6639508	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6639509	6639626	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6639627	6639707	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6639627	6639707	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6639708	6639793	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6639794	6639829	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6639794	6639829	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6639830	6639921	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6639922	6640005	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6639922	6640005	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6640006	6640088	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6640089	6640225	1	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6640089	6640225	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6640226	6640293	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6640294	6640382	1	+	1	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6640294	6640382	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6640383	6640469	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6640470	6640615	1	+	2	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6640470	6640615	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	intron	6640616	6640706	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	CDS	6640707	6640838	0.99	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	exon	6640707	6640838	.	+	.	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
Phchi.S5	AUGUSTUS	stop_codon	6640839	6640841	.	+	0	transcript_id "Phchi.S5G104700.t1"; gene_id "Phchi.S5G104700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10080.t1 is derived from g7256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45645324	45648140	.	+	.	Phchi.S1G723900
Phchi.S1	AUGUSTUS	transcript	45645324	45646136	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	start_codon	45645324	45645326	.	+	0	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645324	45645446	1	+	0	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645324	45645446	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45645447	45645528	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645529	45645624	1	+	0	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645529	45645624	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45645625	45645712	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645713	45645799	1	+	0	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645713	45645799	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45645800	45645980	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645981	45646027	0.92	+	0	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645981	45646027	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646028	45646126	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646127	45646136	0.92	+	1	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646127	45646136	.	+	.	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	stop_codon	45646137	45646139	.	+	0	transcript_id "Phchi.S1G723900.t1"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	transcript	45645324	45648140	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	start_codon	45645324	45645326	.	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645324	45645446	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645324	45645446	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45645447	45645528	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645529	45645624	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645529	45645624	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45645625	45645712	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45645713	45645799	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45645713	45645799	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45645800	45646149	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646150	45646206	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646150	45646206	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646207	45646289	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646290	45646370	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646290	45646370	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646371	45646451	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646452	45646596	0.93	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646452	45646596	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646597	45646706	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646707	45646935	0.95	+	2	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646707	45646935	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646936	45647022	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647023	45647062	0.55	+	1	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647023	45647062	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647063	45647136	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647137	45647169	0.98	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647137	45647169	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647170	45647262	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647263	45647346	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647263	45647346	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647347	45647443	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647444	45647553	1	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647444	45647553	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647554	45647650	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647651	45647855	0.94	+	1	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647651	45647855	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647856	45647960	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647961	45648140	0.94	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647961	45648140	.	+	.	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	stop_codon	45648141	45648143	.	+	0	transcript_id "Phchi.S1G723900.t2"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	transcript	45646183	45648140	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	start_codon	45646183	45646185	.	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646183	45646206	0.88	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646183	45646206	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646207	45646289	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646290	45646370	1	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646290	45646370	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646371	45646451	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646452	45646596	0.99	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646452	45646596	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646597	45646706	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45646707	45646935	0.95	+	2	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45646707	45646935	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45646936	45647022	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647023	45647062	0.51	+	1	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647023	45647062	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647063	45647136	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647137	45647169	1	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647137	45647169	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647170	45647262	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647263	45647346	1	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647263	45647346	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647347	45647443	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647444	45647553	1	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647444	45647553	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647554	45647650	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647651	45647855	0.96	+	1	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647651	45647855	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	intron	45647856	45647960	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	CDS	45647961	45648140	0.96	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	exon	45647961	45648140	.	+	.	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
Phchi.S1	AUGUSTUS	stop_codon	45648141	45648143	.	+	0	transcript_id "Phchi.S1G723900.t3"; gene_id "Phchi.S1G723900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg199.t1 is derived from g9981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1120321	1122463	.	+	.	Phchi.S6G015800
Phchi.S6	AUGUSTUS	transcript	1120321	1122463	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	start_codon	1120321	1120323	.	+	0	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120321	1120392	0.64	+	0	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120321	1120392	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120393	1120469	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120470	1120590	1	+	0	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120470	1120590	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120591	1120678	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120679	1120782	1	+	2	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120679	1120782	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120783	1120934	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120935	1122252	0.98	+	0	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120935	1122252	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1122253	1122434	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1122435	1122463	0.97	+	2	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1122435	1122463	.	+	.	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	stop_codon	1122464	1122466	.	+	0	transcript_id "Phchi.S6G015800.t1"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	transcript	1120321	1122463	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	start_codon	1120321	1120323	.	+	0	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120321	1120392	0.55	+	0	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120321	1120392	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120393	1120469	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120470	1120586	0.92	+	0	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120470	1120586	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120587	1120678	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120679	1120686	0.92	+	0	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120679	1120686	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120687	1120772	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120773	1120782	0.92	+	1	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120773	1120782	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1120783	1120934	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1120935	1122252	0.94	+	0	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1120935	1122252	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	intron	1122253	1122434	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	CDS	1122435	1122463	0.98	+	2	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	exon	1122435	1122463	.	+	.	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
Phchi.S6	AUGUSTUS	stop_codon	1122464	1122466	.	+	0	transcript_id "Phchi.S6G015800.t2"; gene_id "Phchi.S6G015800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10706.t1 is derived from g14756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1680600	1683185	.	-	.	Phchi.S4G028800
Phchi.S4	AUGUSTUS	transcript	1680600	1683185	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	stop_codon	1680597	1680599	.	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1680600	1680602	1	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1680600	1680602	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1680603	1680746	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1680747	1680834	0.99	-	1	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1680747	1680834	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1680835	1681001	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681002	1681043	0.97	-	1	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681002	1681043	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1681044	1681121	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681122	1681206	1	-	2	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681122	1681206	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1681207	1681304	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681305	1681374	1	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681305	1681374	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1681375	1681490	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681491	1681558	0.99	-	2	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681491	1681558	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1681559	1681633	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681634	1681709	1	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681634	1681709	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1681710	1681780	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681781	1681862	1	-	1	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681781	1681862	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1681863	1681990	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1681991	1682078	0.99	-	2	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1681991	1682078	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1682079	1682204	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1682205	1682382	0.99	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1682205	1682382	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1682383	1682462	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1682463	1682553	1	-	1	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1682463	1682553	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1682554	1682645	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1682646	1682692	1	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1682646	1682692	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1682693	1682776	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1682777	1682804	1	-	1	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1682777	1682804	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1682805	1682887	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1682888	1682945	1	-	2	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1682888	1682945	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	intron	1682946	1683052	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	CDS	1683053	1683185	0.99	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	exon	1683053	1683185	.	-	.	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
Phchi.S4	AUGUSTUS	start_codon	1683183	1683185	.	-	0	transcript_id "Phchi.S4G028800.t1"; gene_id "Phchi.S4G028800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12156.t1 is derived from g7832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5040139	5041993	.	-	.	Phchi.S2G023600
Phchi.S2	AUGUSTUS	transcript	5040139	5041993	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	stop_codon	5040136	5040138	.	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	CDS	5040139	5040216	0.76	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	exon	5040139	5040216	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	intron	5040217	5040309	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	CDS	5040310	5040513	0.73	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	exon	5040310	5040513	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	intron	5040514	5040638	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	CDS	5040639	5041103	0.43	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	exon	5040639	5041103	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	intron	5041104	5041186	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	CDS	5041187	5041361	0.64	-	1	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	exon	5041187	5041361	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	intron	5041362	5041518	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	CDS	5041519	5041820	0.29	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	exon	5041519	5041820	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	intron	5041821	5041909	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	CDS	5041910	5041993	0.2	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	exon	5041910	5041993	.	-	.	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
Phchi.S2	AUGUSTUS	start_codon	5041991	5041993	.	-	0	transcript_id "Phchi.S2G023600.t1"; gene_id "Phchi.S2G023600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8563.t1 is derived from g5738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36628162	36632267	.	+	.	Phchi.S1G572200
Phchi.S1	AUGUSTUS	transcript	36628162	36629211	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	start_codon	36628162	36628164	.	+	0	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36628162	36628643	0.99	+	0	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36628162	36628643	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36628644	36628743	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36628744	36628840	1	+	1	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36628744	36628840	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36628841	36628927	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36628928	36629030	1	+	0	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36628928	36629030	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629031	36629185	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629186	36629211	1	+	2	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629186	36629211	.	+	.	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	stop_codon	36629212	36629214	.	+	0	transcript_id "Phchi.S1G572200.t1"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	transcript	36629237	36632267	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	start_codon	36629237	36629239	.	+	0	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629237	36629404	0.89	+	0	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629237	36629404	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629405	36629490	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629491	36629597	0.99	+	0	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629491	36629597	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629598	36629662	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629663	36629745	0.79	+	1	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629663	36629745	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629746	36629909	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629910	36630393	0.7	+	2	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629910	36630393	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36630394	36630540	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36630541	36630649	1	+	1	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36630541	36630649	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36630650	36630796	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36630797	36631617	0.9	+	0	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36630797	36631617	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36631618	36631730	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36631731	36631795	0.98	+	1	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36631731	36631795	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36631796	36631911	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36631912	36631996	0.85	+	2	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36631912	36631996	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36631997	36632083	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36632084	36632267	0.91	+	1	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36632084	36632267	.	+	.	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	stop_codon	36632268	36632270	.	+	0	transcript_id "Phchi.S1G572200.t2"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	transcript	36628162	36632267	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	start_codon	36628162	36628164	.	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36628162	36628643	0.98	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36628162	36628643	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36628644	36628743	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36628744	36628840	1	+	1	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36628744	36628840	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36628841	36628927	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36628928	36629041	1	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36628928	36629041	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629042	36629185	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629186	36629404	1	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629186	36629404	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629405	36629490	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629491	36629597	0.99	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629491	36629597	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629598	36629662	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629663	36629745	0.72	+	1	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629663	36629745	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36629746	36629909	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36629910	36630393	0.61	+	2	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36629910	36630393	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36630394	36630540	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36630541	36630649	1	+	1	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36630541	36630649	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36630650	36630796	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36630797	36631617	0.88	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36630797	36631617	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36631618	36631730	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36631731	36631795	0.87	+	1	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36631731	36631795	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36631796	36631911	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36631912	36631996	0.77	+	2	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36631912	36631996	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	intron	36631997	36632083	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	CDS	36632084	36632267	0.86	+	1	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	exon	36632084	36632267	.	+	.	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
Phchi.S1	AUGUSTUS	stop_codon	36632268	36632270	.	+	0	transcript_id "Phchi.S1G572200.t3"; gene_id "Phchi.S1G572200"
# This transcript jg8108.t2 is derived from g5283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8109.t1 is derived from g5284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33163248	33166274	.	-	.	Phchi.S1G526800
Phchi.S1	AUGUSTUS	transcript	33163248	33166274	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	stop_codon	33163245	33163247	.	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33163248	33163325	0.99	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33163248	33163325	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	intron	33163326	33163413	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33163414	33163560	0.98	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33163414	33163560	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	intron	33163561	33163650	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33163651	33163961	0.67	-	2	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33163651	33163961	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	intron	33163962	33164035	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33164036	33165743	0.52	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33164036	33165743	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	intron	33165744	33165852	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33165853	33165961	1	-	1	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33165853	33165961	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	intron	33165962	33166047	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33166048	33166109	1	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33166048	33166109	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	intron	33166110	33166190	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	CDS	33166191	33166274	0.81	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	exon	33166191	33166274	.	-	.	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
Phchi.S1	AUGUSTUS	start_codon	33166272	33166274	.	-	0	transcript_id "Phchi.S1G526800.t1"; gene_id "Phchi.S1G526800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7462.t1 is derived from g4635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29396187	29396586	.	-	.	Phchi.S1G462100
Phchi.S1	AUGUSTUS	transcript	29396187	29396586	.	-	.	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	stop_codon	29396184	29396186	.	-	0	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	CDS	29396187	29396190	0.77	-	1	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	exon	29396187	29396190	.	-	.	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	intron	29396191	29396332	.	-	.	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	CDS	29396333	29396586	0.37	-	0	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	exon	29396333	29396586	.	-	.	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
Phchi.S1	AUGUSTUS	start_codon	29396584	29396586	.	-	0	transcript_id "Phchi.S1G462100.t1"; gene_id "Phchi.S1G462100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15945.t1 is derived from g14438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	3834	4516	.	-	.	Phchi.C116G000100
Phchi.C116	AUGUSTUS	transcript	3834	4516	.	-	.	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	stop_codon	3831	3833	.	-	0	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	CDS	3834	4172	0.29	-	0	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	exon	3834	4172	.	-	.	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	intron	4173	4468	.	-	.	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	CDS	4469	4516	0.02	-	0	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	exon	4469	4516	.	-	.	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
Phchi.C116	AUGUSTUS	start_codon	4514	4516	.	-	0	transcript_id "Phchi.C116G000100.t1"; gene_id "Phchi.C116G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11955.t1 is derived from g7630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	184259	186041	.	-	.	Phchi.S2G003500
Phchi.S2	AUGUSTUS	transcript	184259	186041	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	stop_codon	184256	184258	.	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	184259	184321	0.89	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	184259	184321	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	intron	184322	184492	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	184493	184579	1	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	184493	184579	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	intron	184580	184671	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	184672	184764	1	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	184672	184764	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	intron	184765	184902	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	184903	184975	1	-	1	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	184903	184975	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	intron	184976	185112	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	185113	185207	1	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	185113	185207	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	intron	185208	185454	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	185455	185542	0.99	-	1	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	185455	185542	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	intron	185543	185667	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	CDS	185668	186041	0.58	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	exon	185668	186041	.	-	.	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
Phchi.S2	AUGUSTUS	start_codon	186039	186041	.	-	0	transcript_id "Phchi.S2G003500.t1"; gene_id "Phchi.S2G003500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11130.t1 is derived from g15180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4307312	4312584	.	-	.	Phchi.S4G071200
Phchi.S4	AUGUSTUS	transcript	4307312	4312584	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	stop_codon	4307309	4307311	.	-	0	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4307312	4307610	1	-	2	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4307312	4307610	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4307611	4307690	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4307691	4307878	1	-	1	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4307691	4307878	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4307879	4307967	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4307968	4308170	1	-	0	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4307968	4308170	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4308171	4308344	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4308345	4308618	0.96	-	1	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4308345	4308618	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4308619	4308723	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4308724	4308825	0.69	-	1	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4308724	4308825	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4308826	4308912	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4308913	4309012	0.7	-	2	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4308913	4309012	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4309013	4309094	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4309095	4309221	0.23	-	0	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4309095	4309221	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4309222	4309320	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4309321	4309419	0.23	-	0	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4309321	4309419	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	intron	4309420	4309674	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	CDS	4309675	4312584	0.6	-	0	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	exon	4309675	4312584	.	-	.	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
Phchi.S4	AUGUSTUS	start_codon	4312582	4312584	.	-	0	transcript_id "Phchi.S4G071200.t1"; gene_id "Phchi.S4G071200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12778.t1 is derived from g11243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2108198	2108754	.	-	.	Phchi.S3G009700
Phchi.S3	AUGUSTUS	transcript	2108198	2108754	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	stop_codon	2108195	2108197	.	-	0	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	CDS	2108198	2108207	0.85	-	1	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	exon	2108198	2108207	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	intron	2108208	2108339	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	CDS	2108340	2108397	0.83	-	2	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	exon	2108340	2108397	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	intron	2108398	2108511	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	CDS	2108512	2108548	0.84	-	0	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	exon	2108512	2108548	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	intron	2108549	2108631	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	CDS	2108632	2108754	0.55	-	0	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	exon	2108632	2108754	.	-	.	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
Phchi.S3	AUGUSTUS	start_codon	2108752	2108754	.	-	0	transcript_id "Phchi.S3G009700.t1"; gene_id "Phchi.S3G009700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11623.t1 is derived from g15674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7361803	7364445	.	+	.	Phchi.S4G120500
Phchi.S4	AUGUSTUS	transcript	7361803	7364445	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	start_codon	7361803	7361805	.	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7361803	7361819	0.9	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7361803	7361819	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7361820	7361894	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7361895	7361934	0.65	+	1	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7361895	7361934	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7361935	7362085	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7362086	7362142	0.66	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7362086	7362142	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7362143	7362418	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7362419	7362469	1	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7362419	7362469	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7362470	7362564	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7362565	7362685	1	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7362565	7362685	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7362686	7362780	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7362781	7362865	1	+	2	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7362781	7362865	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7362866	7362949	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7362950	7363031	1	+	1	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7362950	7363031	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7363032	7363118	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7363119	7363254	1	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7363119	7363254	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7363255	7363412	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7363413	7363585	1	+	2	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7363413	7363585	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7363586	7363685	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7363686	7363846	1	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7363686	7363846	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7363847	7363939	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7363940	7364057	1	+	1	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7363940	7364057	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7364058	7364146	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7364147	7364248	1	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7364147	7364248	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	intron	7364249	7364337	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	CDS	7364338	7364445	1	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	exon	7364338	7364445	.	+	.	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
Phchi.S4	AUGUSTUS	stop_codon	7364446	7364448	.	+	0	transcript_id "Phchi.S4G120500.t1"; gene_id "Phchi.S4G120500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8797.t1 is derived from g5972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38042919	38045069	.	-	.	Phchi.S1G595600
Phchi.S1	AUGUSTUS	transcript	38042919	38045069	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	stop_codon	38042916	38042918	.	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38042919	38043228	1	-	1	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38042919	38043228	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38043229	38043329	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38043330	38043511	0.98	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38043330	38043511	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38043512	38043638	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38043639	38043890	1	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38043639	38043890	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38043891	38044014	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38044015	38044071	1	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38044015	38044071	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38044072	38044171	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38044172	38044243	1	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38044172	38044243	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38044244	38044320	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38044321	38044422	1	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38044321	38044422	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38044423	38044516	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38044517	38044591	1	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38044517	38044591	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38044592	38044717	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38044718	38044944	0.95	-	2	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38044718	38044944	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	intron	38044945	38045026	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	CDS	38045027	38045069	1	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	exon	38045027	38045069	.	-	.	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
Phchi.S1	AUGUSTUS	start_codon	38045067	38045069	.	-	0	transcript_id "Phchi.S1G595600.t1"; gene_id "Phchi.S1G595600"
# This transcript jg5776.t2 is derived from g2946.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5777.t1 is derived from g2947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18902311	18903480	.	+	.	Phchi.S1G293600
Phchi.S1	AUGUSTUS	transcript	18902311	18903480	.	+	.	transcript_id "Phchi.S1G293600.t1"; gene_id "Phchi.S1G293600"
Phchi.S1	AUGUSTUS	start_codon	18902311	18902313	.	+	0	transcript_id "Phchi.S1G293600.t1"; gene_id "Phchi.S1G293600"
Phchi.S1	AUGUSTUS	CDS	18902311	18903480	1	+	0	transcript_id "Phchi.S1G293600.t1"; gene_id "Phchi.S1G293600"
Phchi.S1	AUGUSTUS	exon	18902311	18903480	.	+	.	transcript_id "Phchi.S1G293600.t1"; gene_id "Phchi.S1G293600"
Phchi.S1	AUGUSTUS	stop_codon	18903481	18903483	.	+	0	transcript_id "Phchi.S1G293600.t1"; gene_id "Phchi.S1G293600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10562.t1 is derived from g14612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	993016	993351	.	+	.	Phchi.S4G014400
Phchi.S4	AUGUSTUS	transcript	993016	993351	.	+	.	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	start_codon	993016	993018	.	+	0	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	CDS	993016	993195	0.76	+	0	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	exon	993016	993195	.	+	.	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	intron	993196	993267	.	+	.	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	CDS	993268	993351	0.3	+	0	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	exon	993268	993351	.	+	.	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
Phchi.S4	AUGUSTUS	stop_codon	993352	993354	.	+	0	transcript_id "Phchi.S4G014400.t1"; gene_id "Phchi.S4G014400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9218.t1 is derived from g6393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40460542	40462101	.	-	.	Phchi.S1G637700
Phchi.S1	AUGUSTUS	transcript	40460542	40462101	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	stop_codon	40460539	40460541	.	-	0	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	CDS	40460542	40460882	0.98	-	2	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	exon	40460542	40460882	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	intron	40460883	40460990	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	CDS	40460991	40461360	1	-	0	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	exon	40460991	40461360	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	intron	40461361	40461458	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	CDS	40461459	40461727	0.92	-	2	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	exon	40461459	40461727	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	intron	40461728	40461863	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	CDS	40461864	40462101	0.91	-	0	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	exon	40461864	40462101	.	-	.	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
Phchi.S1	AUGUSTUS	start_codon	40462099	40462101	.	-	0	transcript_id "Phchi.S1G637700.t1"; gene_id "Phchi.S1G637700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5739.t1 is derived from g2909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18671174	18673667	.	-	.	Phchi.S1G289800
Phchi.S1	AUGUSTUS	transcript	18671174	18673667	.	-	.	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	stop_codon	18671171	18671173	.	-	0	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	CDS	18671174	18671985	0.79	-	2	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	exon	18671174	18671985	.	-	.	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	intron	18671986	18672109	.	-	.	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	CDS	18672110	18673667	0.47	-	0	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	exon	18672110	18673667	.	-	.	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
Phchi.S1	AUGUSTUS	start_codon	18673665	18673667	.	-	0	transcript_id "Phchi.S1G289800.t1"; gene_id "Phchi.S1G289800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1771.t1 is derived from g8691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2944140	2945860	.	+	.	Phchi.S5G038000
Phchi.S5	AUGUSTUS	transcript	2944140	2945860	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	start_codon	2944140	2944142	.	+	0	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	CDS	2944140	2944516	0.14	+	0	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	exon	2944140	2944516	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	intron	2944517	2944594	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	CDS	2944595	2944641	0.6	+	1	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	exon	2944595	2944641	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	intron	2944642	2945361	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	CDS	2945362	2945429	0.75	+	2	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	exon	2945362	2945429	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	intron	2945430	2945743	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	CDS	2945744	2945860	0.75	+	0	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	exon	2945744	2945860	.	+	.	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
Phchi.S5	AUGUSTUS	stop_codon	2945861	2945863	.	+	0	transcript_id "Phchi.S5G038000.t1"; gene_id "Phchi.S5G038000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5109.t1 is derived from g2279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14776724	14777088	.	-	.	Phchi.S1G226800
Phchi.S1	AUGUSTUS	transcript	14776724	14777088	.	-	.	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	stop_codon	14776721	14776723	.	-	0	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	CDS	14776724	14776733	1	-	1	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	exon	14776724	14776733	.	-	.	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	intron	14776734	14776822	.	-	.	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	CDS	14776823	14777088	0.89	-	0	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	exon	14776823	14777088	.	-	.	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
Phchi.S1	AUGUSTUS	start_codon	14777086	14777088	.	-	0	transcript_id "Phchi.S1G226800.t1"; gene_id "Phchi.S1G226800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15228.t1 is derived from g13696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17834105	17837147	.	+	.	Phchi.S3G254700
Phchi.S3	AUGUSTUS	transcript	17834105	17837147	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	start_codon	17834105	17834107	.	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17834105	17834429	0.47	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17834105	17834429	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17834430	17834888	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17834889	17834986	1	+	2	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17834889	17834986	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17834987	17835077	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17835078	17835164	1	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17835078	17835164	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17835165	17835253	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17835254	17835351	1	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17835254	17835351	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17835352	17835511	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17835512	17835569	1	+	1	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17835512	17835569	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17835570	17835706	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17835707	17835808	1	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17835707	17835808	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17835809	17835893	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17835894	17835955	1	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17835894	17835955	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17835956	17836188	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17836189	17836299	1	+	1	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17836189	17836299	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17836300	17836392	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17836393	17836474	1	+	1	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17836393	17836474	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17836475	17836586	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17836587	17836709	1	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17836587	17836709	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17836710	17836800	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17836801	17836917	1	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17836801	17836917	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	intron	17836918	17837009	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	CDS	17837010	17837147	0.82	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	exon	17837010	17837147	.	+	.	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
Phchi.S3	AUGUSTUS	stop_codon	17837148	17837150	.	+	0	transcript_id "Phchi.S3G254700.t1"; gene_id "Phchi.S3G254700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg531.t1 is derived from g10313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3833543	3834000	.	-	.	Phchi.S6G049000
Phchi.S6	AUGUSTUS	transcript	3833543	3834000	.	-	.	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	stop_codon	3833540	3833542	.	-	0	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	CDS	3833543	3833798	0.96	-	1	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	exon	3833543	3833798	.	-	.	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	intron	3833799	3833932	.	-	.	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	CDS	3833933	3834000	0.85	-	0	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	exon	3833933	3834000	.	-	.	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
Phchi.S6	AUGUSTUS	start_codon	3833998	3834000	.	-	0	transcript_id "Phchi.S6G049000.t1"; gene_id "Phchi.S6G049000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7409.t1 is derived from g4581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29015272	29017647	.	-	.	Phchi.S1G456800
Phchi.S1	AUGUSTUS	transcript	29015272	29017647	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	stop_codon	29015269	29015271	.	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015272	29015403	0.99	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015272	29015403	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015404	29015507	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015508	29015696	0.99	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015508	29015696	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015697	29015863	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015864	29015916	1	-	2	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015864	29015916	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015917	29016115	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016116	29016139	0.98	-	2	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016116	29016139	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016140	29016224	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016225	29016244	0.69	-	1	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016225	29016244	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016245	29016658	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016659	29016717	0.69	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016659	29016717	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016718	29016793	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016794	29016853	1	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016794	29016853	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016854	29017002	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29017003	29017055	0.79	-	2	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29017003	29017055	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29017056	29017172	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29017173	29017647	0.68	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29017173	29017647	.	-	.	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	start_codon	29017645	29017647	.	-	0	transcript_id "Phchi.S1G456800.t1"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	transcript	29015272	29017647	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	stop_codon	29015269	29015271	.	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015272	29015403	0.77	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015272	29015403	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015404	29015507	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015508	29015566	0.41	-	2	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015508	29015566	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015567	29015642	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015643	29015696	0.86	-	2	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015643	29015696	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015697	29015863	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29015864	29015916	1	-	1	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29015864	29015916	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29015917	29016115	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016116	29016139	1	-	1	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016116	29016139	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016140	29016224	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016225	29016244	1	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016225	29016244	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016245	29016639	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016640	29016717	1	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016640	29016717	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016718	29016793	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29016794	29016853	1	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29016794	29016853	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29016854	29017002	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29017003	29017055	0.74	-	2	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29017003	29017055	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	intron	29017056	29017172	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	CDS	29017173	29017647	0.74	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	exon	29017173	29017647	.	-	.	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
Phchi.S1	AUGUSTUS	start_codon	29017645	29017647	.	-	0	transcript_id "Phchi.S1G456800.t2"; gene_id "Phchi.S1G456800"
# This transcript jg4012.t2 is derived from g1181.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4013.t1 is derived from g1182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7152829	7153506	.	+	.	Phchi.S1G117200
Phchi.S1	AUGUSTUS	transcript	7152829	7153506	.	+	.	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	start_codon	7152829	7152831	.	+	0	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	CDS	7152829	7153007	1	+	0	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	exon	7152829	7153007	.	+	.	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	intron	7153008	7153137	.	+	.	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	CDS	7153138	7153246	1	+	1	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	exon	7153138	7153246	.	+	.	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	intron	7153247	7153425	.	+	.	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	CDS	7153426	7153506	0.99	+	0	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	exon	7153426	7153506	.	+	.	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
Phchi.S1	AUGUSTUS	stop_codon	7153507	7153509	.	+	0	transcript_id "Phchi.S1G117200.t1"; gene_id "Phchi.S1G117200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9916.t1 is derived from g7092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44429864	44432370	.	-	.	Phchi.S1G707500
Phchi.S1	AUGUSTUS	transcript	44429864	44432370	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	stop_codon	44429861	44429863	.	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44429864	44429870	0.53	-	1	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44429864	44429870	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44429871	44429971	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44429972	44430057	0.48	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44429972	44430057	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44430058	44430136	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44430137	44430244	1	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44430137	44430244	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44430245	44430335	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44430336	44430509	1	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44430336	44430509	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44430510	44430606	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44430607	44430735	1	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44430607	44430735	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44430736	44430820	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44430821	44430948	0.69	-	2	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44430821	44430948	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44430949	44431040	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44431041	44431110	0.71	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44431041	44431110	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44431111	44431202	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44431203	44431432	1	-	2	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44431203	44431432	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	intron	44431433	44431517	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	CDS	44431518	44432370	0.95	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	exon	44431518	44432370	.	-	.	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
Phchi.S1	AUGUSTUS	start_codon	44432368	44432370	.	-	0	transcript_id "Phchi.S1G707500.t1"; gene_id "Phchi.S1G707500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4485.t1 is derived from g1655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10764591	10767224	.	+	.	Phchi.S1G164400
Phchi.S1	AUGUSTUS	transcript	10764591	10767224	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	start_codon	10764591	10764593	.	+	0	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	CDS	10764591	10765151	0.91	+	0	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	exon	10764591	10765151	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	intron	10765152	10765304	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	CDS	10765305	10765346	0.26	+	0	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	exon	10765305	10765346	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	intron	10765347	10765471	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	CDS	10765472	10765795	0.08	+	0	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	exon	10765472	10765795	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	intron	10765796	10765964	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	CDS	10765965	10766026	0.3	+	0	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	exon	10765965	10766026	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	intron	10766027	10766157	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	CDS	10766158	10766772	0.52	+	1	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	exon	10766158	10766772	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	intron	10766773	10766878	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	CDS	10766879	10767224	0.87	+	1	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	exon	10766879	10767224	.	+	.	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
Phchi.S1	AUGUSTUS	stop_codon	10767225	10767227	.	+	0	transcript_id "Phchi.S1G164400.t1"; gene_id "Phchi.S1G164400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8658.t1 is derived from g5833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37306918	37308809	.	-	.	Phchi.S1G581700
Phchi.S1	AUGUSTUS	transcript	37306918	37308809	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	stop_codon	37306915	37306917	.	-	0	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	CDS	37306918	37307173	1	-	1	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	exon	37306918	37307173	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	intron	37307174	37307275	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	CDS	37307276	37307643	0.96	-	0	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	exon	37307276	37307643	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	intron	37307644	37307813	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	CDS	37307814	37308107	1	-	0	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	exon	37307814	37308107	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	intron	37308108	37308242	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	CDS	37308243	37308501	1	-	1	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	exon	37308243	37308501	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	intron	37308502	37308624	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	CDS	37308625	37308809	0.47	-	0	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	exon	37308625	37308809	.	-	.	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
Phchi.S1	AUGUSTUS	start_codon	37308807	37308809	.	-	0	transcript_id "Phchi.S1G581700.t1"; gene_id "Phchi.S1G581700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1836.t1 is derived from g8756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3486681	3487136	.	-	.	Phchi.S5G044500
Phchi.S5	AUGUSTUS	transcript	3486681	3487136	.	-	.	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	stop_codon	3486678	3486680	.	-	0	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	CDS	3486681	3486756	0.82	-	1	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	exon	3486681	3486756	.	-	.	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	intron	3486757	3486904	.	-	.	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	CDS	3486905	3487010	0.49	-	2	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	exon	3486905	3487010	.	-	.	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	intron	3487011	3487087	.	-	.	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	CDS	3487088	3487136	0.73	-	0	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	exon	3487088	3487136	.	-	.	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
Phchi.S5	AUGUSTUS	start_codon	3487134	3487136	.	-	0	transcript_id "Phchi.S5G044500.t1"; gene_id "Phchi.S5G044500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4717.t1 is derived from g1887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12452361	12453632	.	-	.	Phchi.S1G187600
Phchi.S1	AUGUSTUS	transcript	12452361	12453632	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	stop_codon	12452358	12452360	.	-	0	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	CDS	12452361	12452426	0.99	-	0	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	exon	12452361	12452426	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	intron	12452427	12452514	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	CDS	12452515	12452538	0.53	-	0	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	exon	12452515	12452538	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	intron	12452539	12452916	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	CDS	12452917	12453128	0.97	-	2	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	exon	12452917	12453128	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	intron	12453129	12453266	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	CDS	12453267	12453436	1	-	1	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	exon	12453267	12453436	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	intron	12453437	12453615	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	CDS	12453616	12453632	1	-	0	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	exon	12453616	12453632	.	-	.	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
Phchi.S1	AUGUSTUS	start_codon	12453630	12453632	.	-	0	transcript_id "Phchi.S1G187600.t1"; gene_id "Phchi.S1G187600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2194.t1 is derived from g9114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5329786	5330541	.	+	.	Phchi.S5G080300
Phchi.S5	AUGUSTUS	transcript	5329786	5330541	.	+	.	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	start_codon	5329786	5329788	.	+	0	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	CDS	5329786	5329835	1	+	0	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	exon	5329786	5329835	.	+	.	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	intron	5329836	5329978	.	+	.	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	CDS	5329979	5330082	1	+	1	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	exon	5329979	5330082	.	+	.	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	intron	5330083	5330170	.	+	.	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	CDS	5330171	5330541	0.95	+	2	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	exon	5330171	5330541	.	+	.	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
Phchi.S5	AUGUSTUS	stop_codon	5330542	5330544	.	+	0	transcript_id "Phchi.S5G080300.t1"; gene_id "Phchi.S5G080300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11192.t1 is derived from g15242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4581946	4583421	.	+	.	Phchi.S4G077400
Phchi.S4	AUGUSTUS	transcript	4581946	4583421	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	start_codon	4581946	4581948	.	+	0	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	CDS	4581946	4582033	0.98	+	0	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	exon	4581946	4582033	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	intron	4582034	4582136	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	CDS	4582137	4582322	1	+	2	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	exon	4582137	4582322	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	intron	4582323	4582401	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	CDS	4582402	4582673	1	+	2	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	exon	4582402	4582673	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	intron	4582674	4582768	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	CDS	4582769	4583069	0.97	+	0	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	exon	4582769	4583069	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	intron	4583070	4583197	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	CDS	4583198	4583421	0.9	+	2	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	exon	4583198	4583421	.	+	.	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
Phchi.S4	AUGUSTUS	stop_codon	4583422	4583424	.	+	0	transcript_id "Phchi.S4G077400.t1"; gene_id "Phchi.S4G077400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10581.t1 is derived from g14631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1049574	1050641	.	-	.	Phchi.S4G016300
Phchi.S4	AUGUSTUS	transcript	1049574	1050641	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	stop_codon	1049571	1049573	.	-	0	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	CDS	1049574	1049870	1	-	0	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	exon	1049574	1049870	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	intron	1049871	1050053	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	CDS	1050054	1050114	1	-	1	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	exon	1050054	1050114	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	intron	1050115	1050188	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	CDS	1050189	1050302	1	-	1	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	exon	1050189	1050302	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	intron	1050303	1050390	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	CDS	1050391	1050446	1	-	0	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	exon	1050391	1050446	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	intron	1050447	1050536	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	CDS	1050537	1050641	1	-	0	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	exon	1050537	1050641	.	-	.	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
Phchi.S4	AUGUSTUS	start_codon	1050639	1050641	.	-	0	transcript_id "Phchi.S4G016300.t1"; gene_id "Phchi.S4G016300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11899.t1 is derived from g15951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9152213	9152783	.	-	.	Phchi.S4G148100
Phchi.S4	AUGUSTUS	transcript	9152213	9152783	.	-	.	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	stop_codon	9152210	9152212	.	-	0	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	CDS	9152213	9152350	1	-	0	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	exon	9152213	9152350	.	-	.	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	intron	9152351	9152447	.	-	.	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	CDS	9152448	9152626	1	-	2	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	exon	9152448	9152626	.	-	.	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	intron	9152627	9152701	.	-	.	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	CDS	9152702	9152783	0.98	-	0	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	exon	9152702	9152783	.	-	.	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
Phchi.S4	AUGUSTUS	start_codon	9152781	9152783	.	-	0	transcript_id "Phchi.S4G148100.t1"; gene_id "Phchi.S4G148100"
# This transcript jg3167.t2 is derived from g336.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3168.t1 is derived from g337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2060306	2060728	.	+	.	Phchi.S1G032700
Phchi.S1	AUGUSTUS	transcript	2060306	2060728	.	+	.	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	start_codon	2060306	2060308	.	+	0	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	CDS	2060306	2060489	0.56	+	0	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	exon	2060306	2060489	.	+	.	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	intron	2060490	2060663	.	+	.	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	CDS	2060664	2060728	0.58	+	2	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	exon	2060664	2060728	.	+	.	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
Phchi.S1	AUGUSTUS	stop_codon	2060729	2060731	.	+	0	transcript_id "Phchi.S1G032700.t1"; gene_id "Phchi.S1G032700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6560.t1 is derived from g3732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23728102	23728536	.	-	.	Phchi.S1G371900
Phchi.S1	AUGUSTUS	transcript	23728102	23728536	.	-	.	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	stop_codon	23728099	23728101	.	-	0	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	CDS	23728102	23728189	0.93	-	1	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	exon	23728102	23728189	.	-	.	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	intron	23728190	23728315	.	-	.	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	CDS	23728316	23728536	0.95	-	0	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	exon	23728316	23728536	.	-	.	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
Phchi.S1	AUGUSTUS	start_codon	23728534	23728536	.	-	0	transcript_id "Phchi.S1G371900.t1"; gene_id "Phchi.S1G371900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15618.t1 is derived from g14087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20308512	20309809	.	+	.	Phchi.S3G293700
Phchi.S3	AUGUSTUS	transcript	20308512	20309809	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	start_codon	20308512	20308514	.	+	0	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	CDS	20308512	20308990	0.45	+	0	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	exon	20308512	20308990	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	intron	20308991	20309093	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	CDS	20309094	20309168	1	+	1	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	exon	20309094	20309168	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	intron	20309169	20309296	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	CDS	20309297	20309360	1	+	1	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	exon	20309297	20309360	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	intron	20309361	20309449	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	CDS	20309450	20309651	0.98	+	0	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	exon	20309450	20309651	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	intron	20309652	20309756	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	CDS	20309757	20309809	0.48	+	2	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	exon	20309757	20309809	.	+	.	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
Phchi.S3	AUGUSTUS	stop_codon	20309810	20309812	.	+	0	transcript_id "Phchi.S3G293700.t1"; gene_id "Phchi.S3G293700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg106.t1 is derived from g9888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	568306	569033	.	+	.	Phchi.S6G006500
Phchi.S6	AUGUSTUS	transcript	568306	569033	.	+	.	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	start_codon	568306	568308	.	+	0	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	CDS	568306	568620	0.94	+	0	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	exon	568306	568620	.	+	.	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	intron	568621	568715	.	+	.	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	CDS	568716	569033	0.39	+	0	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	exon	568716	569033	.	+	.	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
Phchi.S6	AUGUSTUS	stop_codon	569034	569036	.	+	0	transcript_id "Phchi.S6G006500.t1"; gene_id "Phchi.S6G006500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13758.t1 is derived from g12225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8736031	8737662	.	+	.	Phchi.S3G107700
Phchi.S3	AUGUSTUS	transcript	8736031	8737662	.	+	.	transcript_id "Phchi.S3G107700.t1"; gene_id "Phchi.S3G107700"
Phchi.S3	AUGUSTUS	start_codon	8736031	8736033	.	+	0	transcript_id "Phchi.S3G107700.t1"; gene_id "Phchi.S3G107700"
Phchi.S3	AUGUSTUS	CDS	8736031	8737662	1	+	0	transcript_id "Phchi.S3G107700.t1"; gene_id "Phchi.S3G107700"
Phchi.S3	AUGUSTUS	exon	8736031	8737662	.	+	.	transcript_id "Phchi.S3G107700.t1"; gene_id "Phchi.S3G107700"
Phchi.S3	AUGUSTUS	stop_codon	8737663	8737665	.	+	0	transcript_id "Phchi.S3G107700.t1"; gene_id "Phchi.S3G107700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5654.t1 is derived from g2824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18153482	18154939	.	+	.	Phchi.S1G281300
Phchi.S1	AUGUSTUS	transcript	18153482	18154939	.	+	.	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	start_codon	18153482	18153484	.	+	0	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	CDS	18153482	18154432	0.6	+	0	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	exon	18153482	18154432	.	+	.	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	intron	18154433	18154721	.	+	.	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	CDS	18154722	18154844	0.67	+	0	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	exon	18154722	18154844	.	+	.	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	intron	18154845	18154927	.	+	.	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	CDS	18154928	18154939	1	+	0	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	exon	18154928	18154939	.	+	.	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
Phchi.S1	AUGUSTUS	stop_codon	18154940	18154942	.	+	0	transcript_id "Phchi.S1G281300.t1"; gene_id "Phchi.S1G281300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3004.t1 is derived from g173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1089250	1091343	.	-	.	Phchi.S1G016300
Phchi.S1	AUGUSTUS	transcript	1089250	1091343	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	stop_codon	1089247	1089249	.	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1089250	1089385	0.98	-	1	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1089250	1089385	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1089386	1089479	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1089480	1089544	1	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1089480	1089544	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1089545	1089628	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1089629	1089703	1	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1089629	1089703	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1089704	1089794	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1089795	1089898	0.53	-	2	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1089795	1089898	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1089899	1090001	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1090002	1090398	0.63	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1090002	1090398	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1090399	1090481	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1090482	1090574	0.98	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1090482	1090574	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1090575	1090708	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1090709	1090827	0.73	-	2	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1090709	1090827	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1090828	1090923	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1090924	1091017	1	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1090924	1091017	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1091018	1091087	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1091088	1091198	1	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1091088	1091198	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	intron	1091199	1091280	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	CDS	1091281	1091343	1	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	exon	1091281	1091343	.	-	.	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
Phchi.S1	AUGUSTUS	start_codon	1091341	1091343	.	-	0	transcript_id "Phchi.S1G016300.t1"; gene_id "Phchi.S1G016300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12650.t1 is derived from g9811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C8	AUGUSTUS	gene	82050	83040	.	-	.	Phchi.C8G000100
Phchi.C8	AUGUSTUS	transcript	82050	83040	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	stop_codon	82047	82049	.	-	0	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	CDS	82050	82080	0.7	-	1	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	exon	82050	82080	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	intron	82081	82155	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	CDS	82156	82198	0.71	-	2	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	exon	82156	82198	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	intron	82199	82337	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	CDS	82338	82461	1	-	0	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	exon	82338	82461	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	intron	82462	82537	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	CDS	82538	82600	0.78	-	0	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	exon	82538	82600	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	intron	82601	82687	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	CDS	82688	82742	0.32	-	1	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	exon	82688	82742	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	intron	82743	82855	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	CDS	82856	83040	0.38	-	0	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	exon	82856	83040	.	-	.	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
Phchi.C8	AUGUSTUS	start_codon	83038	83040	.	-	0	transcript_id "Phchi.C8G000100.t1"; gene_id "Phchi.C8G000100"
# This transcript jg14624.t2 is derived from g13092.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14625.t1 is derived from g13093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13825111	13826127	.	-	.	Phchi.S3G194400
Phchi.S3	AUGUSTUS	transcript	13825111	13826127	.	-	.	transcript_id "Phchi.S3G194400.t1"; gene_id "Phchi.S3G194400"
Phchi.S3	AUGUSTUS	stop_codon	13825108	13825110	.	-	0	transcript_id "Phchi.S3G194400.t1"; gene_id "Phchi.S3G194400"
Phchi.S3	AUGUSTUS	CDS	13825111	13826127	0.59	-	0	transcript_id "Phchi.S3G194400.t1"; gene_id "Phchi.S3G194400"
Phchi.S3	AUGUSTUS	exon	13825111	13826127	.	-	.	transcript_id "Phchi.S3G194400.t1"; gene_id "Phchi.S3G194400"
Phchi.S3	AUGUSTUS	start_codon	13826125	13826127	.	-	0	transcript_id "Phchi.S3G194400.t1"; gene_id "Phchi.S3G194400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10461.t1 is derived from g14510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	447000	448370	.	-	.	Phchi.S4G004300
Phchi.S4	AUGUSTUS	transcript	447000	448370	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	stop_codon	446997	446999	.	-	0	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	CDS	447000	447326	0.98	-	0	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	exon	447000	447326	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	intron	447327	447420	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	CDS	447421	447517	1	-	1	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	exon	447421	447517	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	intron	447518	447605	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	CDS	447606	447778	1	-	0	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	exon	447606	447778	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	intron	447779	447867	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	CDS	447868	448071	1	-	0	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	exon	447868	448071	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	intron	448072	448157	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	CDS	448158	448370	1	-	0	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	exon	448158	448370	.	-	.	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
Phchi.S4	AUGUSTUS	start_codon	448368	448370	.	-	0	transcript_id "Phchi.S4G004300.t1"; gene_id "Phchi.S4G004300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4830.t1 is derived from g2000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13034061	13035807	.	+	.	Phchi.S1G198900
Phchi.S1	AUGUSTUS	transcript	13034061	13035807	.	+	.	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	start_codon	13034061	13034063	.	+	0	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	CDS	13034061	13034667	0.82	+	0	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	exon	13034061	13034667	.	+	.	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	intron	13034668	13034777	.	+	.	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	CDS	13034778	13035570	0.6	+	2	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	exon	13034778	13035570	.	+	.	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	intron	13035571	13035758	.	+	.	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	CDS	13035759	13035807	0.62	+	1	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	exon	13035759	13035807	.	+	.	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
Phchi.S1	AUGUSTUS	stop_codon	13035808	13035810	.	+	0	transcript_id "Phchi.S1G198900.t1"; gene_id "Phchi.S1G198900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13074.t1 is derived from g11539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4034574	4036412	.	-	.	Phchi.S3G039300
Phchi.S3	AUGUSTUS	transcript	4034574	4036412	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	stop_codon	4034571	4034573	.	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4034574	4034683	0.99	-	2	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4034574	4034683	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4034684	4034786	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4034787	4034860	0.99	-	1	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4034787	4034860	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4034861	4034949	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4034950	4035025	0.99	-	2	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4034950	4035025	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4035026	4035137	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4035138	4035197	0.53	-	2	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4035138	4035197	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4035198	4035294	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4035295	4035385	0.54	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4035295	4035385	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4035386	4035468	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4035469	4035498	1	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4035469	4035498	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4035499	4035615	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4035616	4035696	1	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4035616	4035696	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4035697	4035810	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4035811	4035882	1	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4035811	4035882	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4035883	4035996	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4035997	4036136	0.99	-	2	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4035997	4036136	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	intron	4036137	4036225	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	CDS	4036226	4036412	0.85	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	exon	4036226	4036412	.	-	.	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
Phchi.S3	AUGUSTUS	start_codon	4036410	4036412	.	-	0	transcript_id "Phchi.S3G039300.t1"; gene_id "Phchi.S3G039300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15927.t1 is derived from g14397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22255430	22257140	.	-	.	Phchi.S3G324600
Phchi.S3	AUGUSTUS	transcript	22255430	22257140	.	-	.	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	stop_codon	22255427	22255429	.	-	0	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	CDS	22255430	22255925	0.52	-	1	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	exon	22255430	22255925	.	-	.	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	intron	22255926	22256044	.	-	.	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	CDS	22256045	22256250	0.39	-	0	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	exon	22256045	22256250	.	-	.	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	intron	22256251	22256360	.	-	.	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	CDS	22256361	22257140	0.7	-	0	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	exon	22256361	22257140	.	-	.	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
Phchi.S3	AUGUSTUS	start_codon	22257138	22257140	.	-	0	transcript_id "Phchi.S3G324600.t1"; gene_id "Phchi.S3G324600"
# This transcript jg4602.t2 is derived from g1772.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4603.t1 is derived from g1773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11311656	11312304	.	+	.	Phchi.S1G176200
Phchi.S1	AUGUSTUS	transcript	11311656	11312304	.	+	.	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	start_codon	11311656	11311658	.	+	0	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	CDS	11311656	11311795	0.51	+	0	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	exon	11311656	11311795	.	+	.	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	intron	11311796	11311937	.	+	.	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	CDS	11311938	11312304	0.64	+	1	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	exon	11311938	11312304	.	+	.	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
Phchi.S1	AUGUSTUS	stop_codon	11312305	11312307	.	+	0	transcript_id "Phchi.S1G176200.t1"; gene_id "Phchi.S1G176200"
# This transcript jg12771.t2 is derived from g11236.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12772.t1 is derived from g11237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1972631	1973182	.	+	.	Phchi.S3G009100
Phchi.S3	AUGUSTUS	transcript	1972631	1973182	.	+	.	transcript_id "Phchi.S3G009100.t1"; gene_id "Phchi.S3G009100"
Phchi.S3	AUGUSTUS	start_codon	1972631	1972633	.	+	0	transcript_id "Phchi.S3G009100.t1"; gene_id "Phchi.S3G009100"
Phchi.S3	AUGUSTUS	CDS	1972631	1973182	0.83	+	0	transcript_id "Phchi.S3G009100.t1"; gene_id "Phchi.S3G009100"
Phchi.S3	AUGUSTUS	exon	1972631	1973182	.	+	.	transcript_id "Phchi.S3G009100.t1"; gene_id "Phchi.S3G009100"
Phchi.S3	AUGUSTUS	stop_codon	1973183	1973185	.	+	0	transcript_id "Phchi.S3G009100.t1"; gene_id "Phchi.S3G009100"
# This transcript jg12686.t2 is derived from g11151.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12686.t3 is derived from g11151.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12687.t1 is derived from g11152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	227975	228372	.	-	.	Phchi.S3G000600
Phchi.S3	AUGUSTUS	transcript	227975	228372	.	-	.	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	stop_codon	227972	227974	.	-	0	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	CDS	227975	228150	0.87	-	2	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	exon	227975	228150	.	-	.	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	intron	228151	228305	.	-	.	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	CDS	228306	228372	0.88	-	0	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	exon	228306	228372	.	-	.	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
Phchi.S3	AUGUSTUS	start_codon	228370	228372	.	-	0	transcript_id "Phchi.S3G000600.t1"; gene_id "Phchi.S3G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6729.t1 is derived from g3901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24758415	24760584	.	+	.	Phchi.S1G388800
Phchi.S1	AUGUSTUS	transcript	24758415	24760584	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	start_codon	24758415	24758417	.	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24758415	24758603	1	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24758415	24758603	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24758604	24758705	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24758706	24758891	1	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24758706	24758891	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24758892	24758998	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24758999	24759111	0.99	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24758999	24759111	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24759112	24759208	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24759209	24759392	0.76	+	1	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24759209	24759392	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24759393	24759507	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24759508	24759605	0.99	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24759508	24759605	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24759606	24759707	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24759708	24759915	0.88	+	1	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24759708	24759915	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24759916	24760015	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24760016	24760270	1	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24760016	24760270	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	intron	24760271	24760407	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	CDS	24760408	24760584	1	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	exon	24760408	24760584	.	+	.	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
Phchi.S1	AUGUSTUS	stop_codon	24760585	24760587	.	+	0	transcript_id "Phchi.S1G388800.t1"; gene_id "Phchi.S1G388800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6987.t1 is derived from g4159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26291548	26293233	.	+	.	Phchi.S1G414600
Phchi.S1	AUGUSTUS	transcript	26291548	26293233	.	+	.	transcript_id "Phchi.S1G414600.t1"; gene_id "Phchi.S1G414600"
Phchi.S1	AUGUSTUS	start_codon	26291548	26291550	.	+	0	transcript_id "Phchi.S1G414600.t1"; gene_id "Phchi.S1G414600"
Phchi.S1	AUGUSTUS	CDS	26291548	26293233	1	+	0	transcript_id "Phchi.S1G414600.t1"; gene_id "Phchi.S1G414600"
Phchi.S1	AUGUSTUS	exon	26291548	26293233	.	+	.	transcript_id "Phchi.S1G414600.t1"; gene_id "Phchi.S1G414600"
Phchi.S1	AUGUSTUS	stop_codon	26293234	26293236	.	+	0	transcript_id "Phchi.S1G414600.t1"; gene_id "Phchi.S1G414600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13382.t1 is derived from g11848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6468536	6470828	.	-	.	Phchi.S3G070100
Phchi.S3	AUGUSTUS	transcript	6468536	6470828	.	-	.	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	stop_codon	6468533	6468535	.	-	0	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	CDS	6468536	6470010	0.41	-	2	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	exon	6468536	6470010	.	-	.	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	intron	6470011	6470176	.	-	.	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	CDS	6470177	6470828	0.42	-	0	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	exon	6470177	6470828	.	-	.	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
Phchi.S3	AUGUSTUS	start_codon	6470826	6470828	.	-	0	transcript_id "Phchi.S3G070100.t1"; gene_id "Phchi.S3G070100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3690.t1 is derived from g859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5189124	5189561	.	-	.	Phchi.S1G084900
Phchi.S1	AUGUSTUS	transcript	5189124	5189561	.	-	.	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	stop_codon	5189121	5189123	.	-	0	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	CDS	5189124	5189343	0.87	-	1	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	exon	5189124	5189343	.	-	.	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	intron	5189344	5189436	.	-	.	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	CDS	5189437	5189561	0.82	-	0	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	exon	5189437	5189561	.	-	.	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
Phchi.S1	AUGUSTUS	start_codon	5189559	5189561	.	-	0	transcript_id "Phchi.S1G084900.t1"; gene_id "Phchi.S1G084900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3193.t1 is derived from g362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2157114	2157599	.	-	.	Phchi.S1G035200
Phchi.S1	AUGUSTUS	transcript	2157114	2157599	.	-	.	transcript_id "Phchi.S1G035200.t1"; gene_id "Phchi.S1G035200"
Phchi.S1	AUGUSTUS	stop_codon	2157111	2157113	.	-	0	transcript_id "Phchi.S1G035200.t1"; gene_id "Phchi.S1G035200"
Phchi.S1	AUGUSTUS	CDS	2157114	2157599	0.89	-	0	transcript_id "Phchi.S1G035200.t1"; gene_id "Phchi.S1G035200"
Phchi.S1	AUGUSTUS	exon	2157114	2157599	.	-	.	transcript_id "Phchi.S1G035200.t1"; gene_id "Phchi.S1G035200"
Phchi.S1	AUGUSTUS	start_codon	2157597	2157599	.	-	0	transcript_id "Phchi.S1G035200.t1"; gene_id "Phchi.S1G035200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8907.t1 is derived from g6082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38586068	38587297	.	-	.	Phchi.S1G606600
Phchi.S1	AUGUSTUS	transcript	38586068	38587297	.	-	.	transcript_id "Phchi.S1G606600.t1"; gene_id "Phchi.S1G606600"
Phchi.S1	AUGUSTUS	stop_codon	38586065	38586067	.	-	0	transcript_id "Phchi.S1G606600.t1"; gene_id "Phchi.S1G606600"
Phchi.S1	AUGUSTUS	CDS	38586068	38587297	1	-	0	transcript_id "Phchi.S1G606600.t1"; gene_id "Phchi.S1G606600"
Phchi.S1	AUGUSTUS	exon	38586068	38587297	.	-	.	transcript_id "Phchi.S1G606600.t1"; gene_id "Phchi.S1G606600"
Phchi.S1	AUGUSTUS	start_codon	38587295	38587297	.	-	0	transcript_id "Phchi.S1G606600.t1"; gene_id "Phchi.S1G606600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2458.t1 is derived from g9378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6764088	6764800	.	-	.	Phchi.S5G106700
Phchi.S5	AUGUSTUS	transcript	6764088	6764800	.	-	.	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	stop_codon	6764085	6764087	.	-	0	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	CDS	6764088	6764222	0.92	-	0	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	exon	6764088	6764222	.	-	.	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	intron	6764223	6764308	.	-	.	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	CDS	6764309	6764800	0.93	-	0	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	exon	6764309	6764800	.	-	.	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
Phchi.S5	AUGUSTUS	start_codon	6764798	6764800	.	-	0	transcript_id "Phchi.S5G106700.t1"; gene_id "Phchi.S5G106700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6425.t1 is derived from g3597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22952375	22954310	.	-	.	Phchi.S1G358400
Phchi.S1	AUGUSTUS	transcript	22952375	22954310	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	stop_codon	22952372	22952374	.	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952375	22952411	1	-	1	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952375	22952411	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952412	22952553	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952554	22952622	1	-	1	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952554	22952622	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952623	22952720	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952721	22952791	1	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952721	22952791	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952792	22952884	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952885	22952943	1	-	2	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952885	22952943	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952944	22953042	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953043	22953129	0.95	-	2	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953043	22953129	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953130	22953187	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953188	22953260	0.95	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953188	22953260	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953261	22953359	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953360	22953441	0.92	-	1	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953360	22953441	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953442	22953569	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953570	22953628	0.92	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953570	22953628	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953629	22953743	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953744	22953854	1	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953744	22953854	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953855	22953950	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953951	22954057	0.78	-	2	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953951	22954057	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22954058	22954147	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22954148	22954310	0.59	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22954148	22954310	.	-	.	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	start_codon	22954308	22954310	.	-	0	transcript_id "Phchi.S1G358400.t1"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	transcript	22952406	22954310	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	stop_codon	22952403	22952405	.	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952406	22952411	0.92	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952406	22952411	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952412	22952555	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952556	22952622	0.92	-	1	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952556	22952622	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952623	22952720	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952721	22952791	1	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952721	22952791	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952792	22952884	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22952885	22952943	1	-	2	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22952885	22952943	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22952944	22953042	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953043	22953129	0.99	-	2	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953043	22953129	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953130	22953187	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953188	22953260	0.99	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953188	22953260	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953261	22953359	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953360	22953441	0.84	-	1	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953360	22953441	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953442	22953569	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953570	22953628	0.84	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953570	22953628	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953629	22953743	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953744	22953854	1	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953744	22953854	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22953855	22953950	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22953951	22954057	0.82	-	2	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22953951	22954057	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	intron	22954058	22954147	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	CDS	22954148	22954310	0.55	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	exon	22954148	22954310	.	-	.	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
Phchi.S1	AUGUSTUS	start_codon	22954308	22954310	.	-	0	transcript_id "Phchi.S1G358400.t2"; gene_id "Phchi.S1G358400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7030.t1 is derived from g4202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26491398	26492850	.	-	.	Phchi.S1G418900
Phchi.S1	AUGUSTUS	transcript	26491398	26492850	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	stop_codon	26491395	26491397	.	-	0	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26491398	26491473	0.99	-	1	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26491398	26491473	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	intron	26491474	26491628	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26491629	26491808	1	-	1	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26491629	26491808	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	intron	26491809	26491907	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26491908	26492064	1	-	2	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26491908	26492064	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	intron	26492065	26492148	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26492149	26492154	1	-	2	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26492149	26492154	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	intron	26492155	26492228	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26492229	26492289	0.87	-	0	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26492229	26492289	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	intron	26492290	26492373	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26492374	26492516	1	-	2	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26492374	26492516	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	intron	26492517	26492600	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	CDS	26492601	26492850	1	-	0	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	exon	26492601	26492850	.	-	.	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
Phchi.S1	AUGUSTUS	start_codon	26492848	26492850	.	-	0	transcript_id "Phchi.S1G418900.t1"; gene_id "Phchi.S1G418900"
# This transcript jg2683.t2 is derived from g9603.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2684.t1 is derived from g9604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8186187	8187841	.	+	.	Phchi.S5G129300
Phchi.S5	AUGUSTUS	transcript	8186187	8187841	.	+	.	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	start_codon	8186187	8186189	.	+	0	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	CDS	8186187	8186584	0.37	+	0	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	exon	8186187	8186584	.	+	.	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	intron	8186585	8186964	.	+	.	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	CDS	8186965	8187204	0.45	+	1	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	exon	8186965	8187204	.	+	.	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	intron	8187205	8187552	.	+	.	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	CDS	8187553	8187841	0.76	+	1	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	exon	8187553	8187841	.	+	.	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
Phchi.S5	AUGUSTUS	stop_codon	8187842	8187844	.	+	0	transcript_id "Phchi.S5G129300.t1"; gene_id "Phchi.S5G129300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9987.t1 is derived from g7163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44802694	44805793	.	+	.	Phchi.S1G714600
Phchi.S1	AUGUSTUS	transcript	44802694	44805793	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	start_codon	44802694	44802696	.	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44802694	44802819	0.6	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44802694	44802819	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44802820	44802954	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44802955	44803161	0.76	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44802955	44803161	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44803162	44803246	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44803247	44803957	0.53	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44803247	44803957	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44803958	44804174	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44804175	44804264	0.59	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44804175	44804264	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44804265	44804596	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44804597	44804689	0.58	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44804597	44804689	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44804690	44804775	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44804776	44804919	0.61	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44804776	44804919	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44804920	44805007	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44805008	44805136	1	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44805008	44805136	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44805137	44805230	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44805231	44805297	0.58	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44805231	44805297	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44805298	44805418	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44805419	44805516	0.57	+	2	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44805419	44805516	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	intron	44805517	44805631	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	CDS	44805632	44805793	0.99	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	exon	44805632	44805793	.	+	.	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
Phchi.S1	AUGUSTUS	stop_codon	44805794	44805796	.	+	0	transcript_id "Phchi.S1G714600.t1"; gene_id "Phchi.S1G714600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11787.t1 is derived from g15839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8153091	8155575	.	-	.	Phchi.S4G136900
Phchi.S4	AUGUSTUS	transcript	8153091	8155575	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	stop_codon	8153088	8153090	.	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	CDS	8153091	8153807	0.47	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	exon	8153091	8153807	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	intron	8153808	8153890	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	CDS	8153891	8153948	0.54	-	1	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	exon	8153891	8153948	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	intron	8153949	8154092	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	CDS	8154093	8154256	1	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	exon	8154093	8154256	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	intron	8154257	8154362	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	CDS	8154363	8154557	1	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	exon	8154363	8154557	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	intron	8154558	8154767	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	CDS	8154768	8155190	0.99	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	exon	8154768	8155190	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	intron	8155191	8155308	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	CDS	8155309	8155575	0.48	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	exon	8155309	8155575	.	-	.	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
Phchi.S4	AUGUSTUS	start_codon	8155573	8155575	.	-	0	transcript_id "Phchi.S4G136900.t1"; gene_id "Phchi.S4G136900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg161.t1 is derived from g9943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	915187	916872	.	-	.	Phchi.S6G012000
Phchi.S6	AUGUSTUS	transcript	915187	916872	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	stop_codon	915184	915186	.	-	0	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	915187	915276	1	-	0	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	915187	915276	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	915277	915408	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	915409	915464	0.86	-	2	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	915409	915464	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	915465	915559	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	915560	915666	0.99	-	1	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	915560	915666	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	915667	915780	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	915781	915868	0.43	-	2	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	915781	915868	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	915869	916026	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	916027	916040	0.94	-	1	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	916027	916040	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	916041	916140	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	916141	916262	0.97	-	0	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	916141	916262	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	916263	916471	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	916472	916770	0.68	-	2	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	916472	916770	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	intron	916771	916862	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	CDS	916863	916872	0.97	-	0	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	exon	916863	916872	.	-	.	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
Phchi.S6	AUGUSTUS	start_codon	916870	916872	.	-	0	transcript_id "Phchi.S6G012000.t1"; gene_id "Phchi.S6G012000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg15915.t1 is derived from g14385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22193520	22195942	.	+	.	Phchi.S3G323400
Phchi.S3	AUGUSTUS	transcript	22193520	22195820	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	start_codon	22193520	22193522	.	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193520	22193527	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193520	22193527	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193528	22193624	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193625	22193727	1	+	1	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193625	22193727	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193728	22193818	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193819	22193995	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193819	22193995	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193996	22194068	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194069	22194169	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194069	22194169	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194170	22194255	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194256	22194310	1	+	1	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194256	22194310	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194311	22194397	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194398	22194484	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194398	22194484	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194485	22194568	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194569	22194620	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194569	22194620	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194621	22194753	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194754	22194839	1	+	2	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194754	22194839	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194840	22194930	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194931	22194984	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194931	22194984	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194985	22195124	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195125	22195208	1	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195125	22195208	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195209	22195377	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195378	22195409	0.97	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195378	22195409	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195410	22195516	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195517	22195528	0.97	+	1	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195517	22195528	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195529	22195694	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195695	22195730	0.97	+	1	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195695	22195730	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195731	22195819	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195820	22195820	0.97	+	1	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195820	22195820	.	+	.	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	stop_codon	22195821	22195823	.	+	0	transcript_id "Phchi.S3G323400.t1"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	transcript	22193520	22195942	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	start_codon	22193520	22193522	.	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193520	22193527	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193520	22193527	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193528	22193624	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193625	22193727	1	+	1	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193625	22193727	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193728	22193818	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193819	22193995	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193819	22193995	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193996	22194068	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194069	22194169	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194069	22194169	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194170	22194255	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194256	22194310	1	+	1	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194256	22194310	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194311	22194397	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194398	22194484	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194398	22194484	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194485	22194568	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194569	22194620	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194569	22194620	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194621	22194753	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194754	22194839	0.99	+	2	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194754	22194839	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194840	22194930	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194931	22194984	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194931	22194984	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194985	22195124	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195125	22195208	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195125	22195208	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195209	22195337	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195338	22195409	0.91	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195338	22195409	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195410	22195516	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195517	22195597	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195517	22195597	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195598	22195694	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195695	22195730	1	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195695	22195730	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195731	22195819	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195820	22195942	0.98	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195820	22195942	.	+	.	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	stop_codon	22195943	22195945	.	+	0	transcript_id "Phchi.S3G323400.t2"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	transcript	22193520	22195942	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	start_codon	22193520	22193522	.	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193520	22193527	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193520	22193527	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193528	22193624	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193625	22193727	1	+	1	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193625	22193727	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193728	22193818	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193819	22193995	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193819	22193995	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193996	22194068	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194069	22194169	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194069	22194169	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194170	22194255	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194256	22194310	1	+	1	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194256	22194310	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194311	22194397	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194398	22194484	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194398	22194484	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194485	22194568	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194569	22194620	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194569	22194620	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194621	22194753	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194754	22194839	1	+	2	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194754	22194839	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194840	22194930	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194931	22194984	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194931	22194984	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194985	22195124	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195125	22195208	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195125	22195208	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195209	22195377	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195378	22195409	0.91	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195378	22195409	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195410	22195536	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195537	22195597	0.91	+	1	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195537	22195597	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195598	22195694	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195695	22195730	1	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195695	22195730	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195731	22195819	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195820	22195942	0.98	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195820	22195942	.	+	.	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	stop_codon	22195943	22195945	.	+	0	transcript_id "Phchi.S3G323400.t3"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	transcript	22193520	22195942	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	start_codon	22193520	22193522	.	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193520	22193527	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193520	22193527	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193528	22193624	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193625	22193727	1	+	1	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193625	22193727	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193728	22193818	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22193819	22193995	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22193819	22193995	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22193996	22194068	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194069	22194169	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194069	22194169	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194170	22194255	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194256	22194310	1	+	1	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194256	22194310	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194311	22194397	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194398	22194484	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194398	22194484	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194485	22194568	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194569	22194620	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194569	22194620	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194621	22194762	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194763	22194839	0.99	+	2	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194763	22194839	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194840	22194930	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22194931	22194984	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22194931	22194984	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22194985	22195124	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195125	22195208	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195125	22195208	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195209	22195377	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195378	22195409	0.85	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195378	22195409	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195410	22195536	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195537	22195597	0.85	+	1	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195537	22195597	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195598	22195694	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195695	22195730	1	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195695	22195730	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	intron	22195731	22195819	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	CDS	22195820	22195942	0.97	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	exon	22195820	22195942	.	+	.	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
Phchi.S3	AUGUSTUS	stop_codon	22195943	22195945	.	+	0	transcript_id "Phchi.S3G323400.t4"; gene_id "Phchi.S3G323400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8014.t1 is derived from g5189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32481562	32483227	.	-	.	Phchi.S1G517300
Phchi.S1	AUGUSTUS	transcript	32481562	32483227	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	stop_codon	32481559	32481561	.	-	0	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32481562	32481656	1	-	2	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32481562	32481656	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	intron	32481657	32481733	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32481734	32481971	0.99	-	0	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32481734	32481971	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	intron	32481972	32482076	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32482077	32482267	0.93	-	2	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32482077	32482267	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	intron	32482268	32482352	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32482353	32482412	0.99	-	2	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32482353	32482412	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	intron	32482413	32482502	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32482503	32482533	0.99	-	0	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32482503	32482533	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	intron	32482534	32482675	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32482676	32482882	1	-	0	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32482676	32482882	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	intron	32482883	32483032	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	CDS	32483033	32483227	0.99	-	0	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	exon	32483033	32483227	.	-	.	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
Phchi.S1	AUGUSTUS	start_codon	32483225	32483227	.	-	0	transcript_id "Phchi.S1G517300.t1"; gene_id "Phchi.S1G517300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5896.t1 is derived from g3066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19640986	19642725	.	-	.	Phchi.S1G305500
Phchi.S1	AUGUSTUS	transcript	19640986	19642725	.	-	.	transcript_id "Phchi.S1G305500.t1"; gene_id "Phchi.S1G305500"
Phchi.S1	AUGUSTUS	stop_codon	19640983	19640985	.	-	0	transcript_id "Phchi.S1G305500.t1"; gene_id "Phchi.S1G305500"
Phchi.S1	AUGUSTUS	CDS	19640986	19642725	0.95	-	0	transcript_id "Phchi.S1G305500.t1"; gene_id "Phchi.S1G305500"
Phchi.S1	AUGUSTUS	exon	19640986	19642725	.	-	.	transcript_id "Phchi.S1G305500.t1"; gene_id "Phchi.S1G305500"
Phchi.S1	AUGUSTUS	start_codon	19642723	19642725	.	-	0	transcript_id "Phchi.S1G305500.t1"; gene_id "Phchi.S1G305500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5466.t1 is derived from g2636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16980928	16981730	.	-	.	Phchi.S1G262500
Phchi.S1	AUGUSTUS	transcript	16980928	16981730	.	-	.	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	stop_codon	16980925	16980927	.	-	0	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	CDS	16980928	16981297	0.12	-	1	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	exon	16980928	16981297	.	-	.	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	intron	16981298	16981398	.	-	.	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	CDS	16981399	16981730	0.44	-	0	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	exon	16981399	16981730	.	-	.	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
Phchi.S1	AUGUSTUS	start_codon	16981728	16981730	.	-	0	transcript_id "Phchi.S1G262500.t1"; gene_id "Phchi.S1G262500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3069.t1 is derived from g238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1431716	1432578	.	+	.	Phchi.S1G022800
Phchi.S1	AUGUSTUS	transcript	1431716	1432578	.	+	.	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	start_codon	1431716	1431718	.	+	0	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	CDS	1431716	1432030	1	+	0	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	exon	1431716	1432030	.	+	.	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	intron	1432031	1432110	.	+	.	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	CDS	1432111	1432347	1	+	0	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	exon	1432111	1432347	.	+	.	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	intron	1432348	1432440	.	+	.	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	CDS	1432441	1432578	1	+	0	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	exon	1432441	1432578	.	+	.	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
Phchi.S1	AUGUSTUS	stop_codon	1432579	1432581	.	+	0	transcript_id "Phchi.S1G022800.t1"; gene_id "Phchi.S1G022800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11542.t1 is derived from g15592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6970162	6972050	.	-	.	Phchi.S4G112400
Phchi.S4	AUGUSTUS	transcript	6970162	6972050	.	-	.	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	stop_codon	6970159	6970161	.	-	0	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	CDS	6970162	6971508	0.62	-	0	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	exon	6970162	6971508	.	-	.	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	intron	6971509	6971756	.	-	.	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	CDS	6971757	6972050	0.58	-	0	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	exon	6971757	6972050	.	-	.	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
Phchi.S4	AUGUSTUS	start_codon	6972048	6972050	.	-	0	transcript_id "Phchi.S4G112400.t1"; gene_id "Phchi.S4G112400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12055.t1 is derived from g7730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1059501	1061977	.	-	.	Phchi.S2G013500
Phchi.S2	AUGUSTUS	transcript	1059501	1061977	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	stop_codon	1059498	1059500	.	-	0	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1059501	1059638	1	-	0	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1059501	1059638	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1059639	1059712	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1059713	1059815	1	-	1	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1059713	1059815	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1059816	1059893	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1059894	1059960	1	-	2	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1059894	1059960	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1059961	1060103	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1060104	1060193	1	-	2	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1060104	1060193	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1060194	1060282	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1060283	1060378	0.4	-	2	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1060283	1060378	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1060379	1060705	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1060706	1061168	0.41	-	0	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1060706	1061168	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1061169	1061274	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1061275	1061484	0.97	-	0	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1061275	1061484	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	intron	1061485	1061593	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	CDS	1061594	1061977	1	-	0	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	exon	1061594	1061977	.	-	.	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
Phchi.S2	AUGUSTUS	start_codon	1061975	1061977	.	-	0	transcript_id "Phchi.S2G013500.t1"; gene_id "Phchi.S2G013500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1474.t1 is derived from g8393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1106522	1107934	.	+	.	Phchi.S5G008300
Phchi.S5	AUGUSTUS	transcript	1106522	1107934	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	start_codon	1106522	1106524	.	+	0	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	CDS	1106522	1107414	0.47	+	0	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	exon	1106522	1107414	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	intron	1107415	1107509	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	CDS	1107510	1107561	0.94	+	1	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	exon	1107510	1107561	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	intron	1107562	1107653	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	CDS	1107654	1107774	0.27	+	0	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	exon	1107654	1107774	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	intron	1107775	1107881	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	CDS	1107882	1107934	0.28	+	2	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	exon	1107882	1107934	.	+	.	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
Phchi.S5	AUGUSTUS	stop_codon	1107935	1107937	.	+	0	transcript_id "Phchi.S5G008300.t1"; gene_id "Phchi.S5G008300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7475.t1 is derived from g4648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29544867	29545546	.	+	.	Phchi.S1G463400
Phchi.S1	AUGUSTUS	transcript	29544867	29545546	.	+	.	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	start_codon	29544867	29544869	.	+	0	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	CDS	29544867	29545050	1	+	0	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	exon	29544867	29545050	.	+	.	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	intron	29545051	29545148	.	+	.	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	CDS	29545149	29545546	1	+	2	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	exon	29545149	29545546	.	+	.	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
Phchi.S1	AUGUSTUS	stop_codon	29545547	29545549	.	+	0	transcript_id "Phchi.S1G463400.t1"; gene_id "Phchi.S1G463400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4915.t1 is derived from g2085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13462225	13463691	.	+	.	Phchi.S1G207400
Phchi.S1	AUGUSTUS	transcript	13462225	13463691	.	+	.	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	start_codon	13462225	13462227	.	+	0	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	CDS	13462225	13462573	1	+	0	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	exon	13462225	13462573	.	+	.	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	intron	13462574	13462720	.	+	.	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	CDS	13462721	13463090	1	+	2	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	exon	13462721	13463090	.	+	.	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	intron	13463091	13463213	.	+	.	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	CDS	13463214	13463691	0.99	+	1	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	exon	13463214	13463691	.	+	.	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
Phchi.S1	AUGUSTUS	stop_codon	13463692	13463694	.	+	0	transcript_id "Phchi.S1G207400.t1"; gene_id "Phchi.S1G207400"
# This transcript jg4030.t2 is derived from g1199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4031.t1 is derived from g1200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7264518	7264901	.	+	.	Phchi.S1G119000
Phchi.S1	AUGUSTUS	transcript	7264518	7264901	.	+	.	transcript_id "Phchi.S1G119000.t1"; gene_id "Phchi.S1G119000"
Phchi.S1	AUGUSTUS	start_codon	7264518	7264520	.	+	0	transcript_id "Phchi.S1G119000.t1"; gene_id "Phchi.S1G119000"
Phchi.S1	AUGUSTUS	CDS	7264518	7264901	0.41	+	0	transcript_id "Phchi.S1G119000.t1"; gene_id "Phchi.S1G119000"
Phchi.S1	AUGUSTUS	exon	7264518	7264901	.	+	.	transcript_id "Phchi.S1G119000.t1"; gene_id "Phchi.S1G119000"
Phchi.S1	AUGUSTUS	stop_codon	7264902	7264904	.	+	0	transcript_id "Phchi.S1G119000.t1"; gene_id "Phchi.S1G119000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12301.t1 is derived from g7977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9632709	9634135	.	+	.	Phchi.S2G038100
Phchi.S2	AUGUSTUS	transcript	9632709	9634135	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	start_codon	9632709	9632711	.	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9632709	9632938	0.67	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9632709	9632938	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9632939	9633153	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633154	9633202	1	+	1	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633154	9633202	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633203	9633294	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633295	9633350	1	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633295	9633350	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633351	9633481	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633482	9633530	1	+	1	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633482	9633530	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633531	9633636	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633637	9633723	1	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633637	9633723	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633724	9633812	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633813	9633932	1	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633813	9633932	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633933	9634036	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9634037	9634135	0.36	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9634037	9634135	.	+	.	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	stop_codon	9634136	9634138	.	+	0	transcript_id "Phchi.S2G038100.t1"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	transcript	9632709	9634074	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	start_codon	9632709	9632711	.	+	0	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9632709	9632938	0.64	+	0	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9632709	9632938	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9632939	9633153	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633154	9633202	1	+	1	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633154	9633202	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633203	9633294	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633295	9633350	1	+	0	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633295	9633350	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633351	9633481	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633482	9633530	0.99	+	1	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633482	9633530	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633531	9633636	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633637	9633723	0.99	+	0	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633637	9633723	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	intron	9633724	9633816	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	CDS	9633817	9634074	0.34	+	0	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	exon	9633817	9634074	.	+	.	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
Phchi.S2	AUGUSTUS	stop_codon	9634075	9634077	.	+	0	transcript_id "Phchi.S2G038100.t2"; gene_id "Phchi.S2G038100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3288.t1 is derived from g457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2696044	2696700	.	-	.	Phchi.S1G044700
Phchi.S1	AUGUSTUS	transcript	2696044	2696700	.	-	.	transcript_id "Phchi.S1G044700.t1"; gene_id "Phchi.S1G044700"
Phchi.S1	AUGUSTUS	stop_codon	2696041	2696043	.	-	0	transcript_id "Phchi.S1G044700.t1"; gene_id "Phchi.S1G044700"
Phchi.S1	AUGUSTUS	CDS	2696044	2696700	0.76	-	0	transcript_id "Phchi.S1G044700.t1"; gene_id "Phchi.S1G044700"
Phchi.S1	AUGUSTUS	exon	2696044	2696700	.	-	.	transcript_id "Phchi.S1G044700.t1"; gene_id "Phchi.S1G044700"
Phchi.S1	AUGUSTUS	start_codon	2696698	2696700	.	-	0	transcript_id "Phchi.S1G044700.t1"; gene_id "Phchi.S1G044700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2506.t1 is derived from g9426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7047127	7049803	.	-	.	Phchi.S5G111500
Phchi.S5	AUGUSTUS	transcript	7047127	7049803	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	stop_codon	7047124	7047126	.	-	0	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	CDS	7047127	7047228	0.98	-	0	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	exon	7047127	7047228	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	intron	7047229	7047379	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	CDS	7047380	7047684	0.99	-	2	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	exon	7047380	7047684	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	intron	7047685	7047769	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	CDS	7047770	7047941	1	-	0	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	exon	7047770	7047941	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	intron	7047942	7048081	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	CDS	7048082	7049262	1	-	2	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	exon	7048082	7049262	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	intron	7049263	7049403	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	CDS	7049404	7049803	0.97	-	0	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	exon	7049404	7049803	.	-	.	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
Phchi.S5	AUGUSTUS	start_codon	7049801	7049803	.	-	0	transcript_id "Phchi.S5G111500.t1"; gene_id "Phchi.S5G111500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13840.t1 is derived from g12307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9150452	9154035	.	-	.	Phchi.S3G115900
Phchi.S3	AUGUSTUS	transcript	9150452	9154035	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	stop_codon	9150449	9150451	.	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9150452	9150684	0.63	-	2	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9150452	9150684	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9150685	9150851	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9150852	9151029	0.91	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9150852	9151029	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9151030	9151150	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9151151	9151270	1	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9151151	9151270	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9151271	9151346	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9151347	9151449	1	-	1	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9151347	9151449	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9151450	9151575	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9151576	9151659	1	-	1	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9151576	9151659	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9151660	9151779	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9151780	9151886	1	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9151780	9151886	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9151887	9152010	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9152011	9152079	1	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9152011	9152079	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9152080	9152188	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9152189	9152332	0.99	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9152189	9152332	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9152333	9152431	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9152432	9152578	1	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9152432	9152578	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9152579	9152675	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9152676	9152786	0.99	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9152676	9152786	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9152787	9152902	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9152903	9153202	0.97	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9152903	9153202	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9153203	9153310	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9153311	9153382	0.97	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9153311	9153382	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9153383	9153481	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9153482	9153553	1	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9153482	9153553	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9153554	9153668	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9153669	9153752	0.99	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9153669	9153752	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	intron	9153753	9153843	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	CDS	9153844	9154035	0.75	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	exon	9153844	9154035	.	-	.	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
Phchi.S3	AUGUSTUS	start_codon	9154033	9154035	.	-	0	transcript_id "Phchi.S3G115900.t1"; gene_id "Phchi.S3G115900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg134.t1 is derived from g9916.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	753068	757530	.	-	.	Phchi.S6G009300
Phchi.S6	AUGUSTUS	transcript	753068	757530	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	stop_codon	753065	753067	.	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753068	753235	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753068	753235	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753236	753325	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753326	753461	0.88	-	1	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753326	753461	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753462	753572	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753573	753637	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753573	753637	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753638	753725	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753726	753818	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753726	753818	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753819	753904	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753905	753970	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753905	753970	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753971	754067	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754068	754148	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754068	754148	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754149	754259	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754260	754315	0.99	-	2	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754260	754315	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754316	754408	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754409	754497	1	-	1	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754409	754497	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754498	754628	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754629	754714	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754629	754714	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754715	754847	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754848	754964	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754848	754964	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754965	755078	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755079	755224	1	-	2	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755079	755224	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755225	755339	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755340	755400	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755340	755400	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755401	755493	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755494	755577	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755494	755577	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755578	755660	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755661	755768	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755661	755768	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755769	756090	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756091	756169	0.74	-	1	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756091	756169	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756170	756285	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756286	756329	0.74	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756286	756329	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756330	756428	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756429	756490	1	-	2	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756429	756490	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756491	756582	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756583	756745	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756583	756745	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756746	756841	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756842	757100	1	-	1	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756842	757100	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	757101	757324	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	757325	757530	1	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	757325	757530	.	-	.	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	start_codon	757528	757530	.	-	0	transcript_id "Phchi.S6G009300.t1"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	transcript	753068	757530	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	stop_codon	753065	753067	.	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753068	753235	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753068	753235	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753236	753325	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753326	753461	0.8	-	1	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753326	753461	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753462	753572	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753573	753637	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753573	753637	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753638	753725	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753726	753818	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753726	753818	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753819	753904	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	753905	753970	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	753905	753970	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	753971	754067	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754068	754148	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754068	754148	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754149	754259	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754260	754315	1	-	2	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754260	754315	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754316	754408	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754409	754497	1	-	1	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754409	754497	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754498	754628	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754629	754714	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754629	754714	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754715	754847	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	754848	754964	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	754848	754964	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	754965	755078	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755079	755224	1	-	2	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755079	755224	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755225	755339	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755340	755400	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755340	755400	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755401	755493	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755494	755577	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755494	755577	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755578	755660	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	755661	755768	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	755661	755768	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	755769	756090	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756091	756169	0.75	-	1	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756091	756169	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756170	756285	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756286	756329	0.74	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756286	756329	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756330	756428	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756429	756490	1	-	2	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756429	756490	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756491	756582	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756583	756745	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756583	756745	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	756746	756841	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	756842	757166	1	-	1	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	756842	757166	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	intron	757167	757324	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	CDS	757325	757530	1	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	exon	757325	757530	.	-	.	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
Phchi.S6	AUGUSTUS	start_codon	757528	757530	.	-	0	transcript_id "Phchi.S6G009300.t2"; gene_id "Phchi.S6G009300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8696.t1 is derived from g5871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37504388	37507030	.	+	.	Phchi.S1G585500
Phchi.S1	AUGUSTUS	transcript	37504388	37507030	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	start_codon	37504388	37504390	.	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37504388	37504830	0.67	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37504388	37504830	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37504831	37504928	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37504929	37504998	1	+	1	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37504929	37504998	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37504999	37505071	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37505072	37505244	1	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37505072	37505244	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37505245	37505407	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37505408	37505582	1	+	1	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37505408	37505582	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37505583	37505670	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37505671	37505837	1	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37505671	37505837	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37505838	37505927	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37505928	37506147	1	+	1	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37505928	37506147	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37506148	37506237	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37506238	37506342	1	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37506238	37506342	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37506343	37506600	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37506601	37506753	0.99	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37506601	37506753	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	intron	37506754	37506871	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	CDS	37506872	37507030	1	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	exon	37506872	37507030	.	+	.	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
Phchi.S1	AUGUSTUS	stop_codon	37507031	37507033	.	+	0	transcript_id "Phchi.S1G585500.t1"; gene_id "Phchi.S1G585500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6012.t1 is derived from g3183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20424338	20429010	.	+	.	Phchi.S1G317100
Phchi.S1	AUGUSTUS	transcript	20424338	20429010	.	+	.	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	start_codon	20424338	20424340	.	+	0	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	CDS	20424338	20425348	0.97	+	0	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	exon	20424338	20425348	.	+	.	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	intron	20425349	20425449	.	+	.	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	CDS	20425450	20429010	0.99	+	0	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	exon	20425450	20429010	.	+	.	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	stop_codon	20429011	20429013	.	+	0	transcript_id "Phchi.S1G317100.t1"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	transcript	20427703	20429010	.	+	.	transcript_id "Phchi.S1G317100.t2"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	start_codon	20427703	20427705	.	+	0	transcript_id "Phchi.S1G317100.t2"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	CDS	20427703	20429010	0.75	+	0	transcript_id "Phchi.S1G317100.t2"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	exon	20427703	20429010	.	+	.	transcript_id "Phchi.S1G317100.t2"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	stop_codon	20429011	20429013	.	+	0	transcript_id "Phchi.S1G317100.t2"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	transcript	20428531	20429010	.	+	.	transcript_id "Phchi.S1G317100.t3"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	start_codon	20428531	20428533	.	+	0	transcript_id "Phchi.S1G317100.t3"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	CDS	20428531	20429010	0.26	+	0	transcript_id "Phchi.S1G317100.t3"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	exon	20428531	20429010	.	+	.	transcript_id "Phchi.S1G317100.t3"; gene_id "Phchi.S1G317100"
Phchi.S1	AUGUSTUS	stop_codon	20429011	20429013	.	+	0	transcript_id "Phchi.S1G317100.t3"; gene_id "Phchi.S1G317100"
# This transcript jg10099.t2 is derived from g7275.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10099.t3 is derived from g7275.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10099.t4 is derived from g7275.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10099.t5 is derived from g7275.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10100.t1 is derived from g7276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45744823	45746453	.	+	.	Phchi.S1G725900
Phchi.S1	AUGUSTUS	transcript	45744823	45746453	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	start_codon	45744823	45744825	.	+	0	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45744823	45745145	0.65	+	0	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45744823	45745145	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	intron	45745146	45745289	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45745290	45745394	0.73	+	1	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45745290	45745394	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	intron	45745395	45745534	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45745535	45745613	0.99	+	1	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45745535	45745613	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	intron	45745614	45745718	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45745719	45745738	0.99	+	0	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45745719	45745738	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	intron	45745739	45745834	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45745835	45745954	0.97	+	1	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45745835	45745954	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	intron	45745955	45746136	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45746137	45746167	0.98	+	1	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45746137	45746167	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	intron	45746168	45746255	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	CDS	45746256	45746453	1	+	0	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	exon	45746256	45746453	.	+	.	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
Phchi.S1	AUGUSTUS	stop_codon	45746454	45746456	.	+	0	transcript_id "Phchi.S1G725900.t1"; gene_id "Phchi.S1G725900"
# This transcript jg15794.t2 is derived from g14264.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15795.t1 is derived from g14265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21371153	21373583	.	+	.	Phchi.S3G311400
Phchi.S3	AUGUSTUS	transcript	21371153	21373583	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	start_codon	21371153	21371155	.	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371153	21371306	1	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371153	21371306	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21371307	21371414	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371415	21371527	0.57	+	2	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371415	21371527	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21371528	21371773	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371774	21371908	0.99	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371774	21371908	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21371909	21371995	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371996	21372067	1	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371996	21372067	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372068	21372149	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372150	21372357	0.98	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372150	21372357	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372358	21372495	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372496	21372547	0.98	+	2	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372496	21372547	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372548	21372710	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372711	21372945	1	+	1	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372711	21372945	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372946	21373065	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21373066	21373152	1	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21373066	21373152	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21373153	21373241	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21373242	21373400	1	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21373242	21373400	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21373401	21373484	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21373485	21373583	1	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21373485	21373583	.	+	.	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	stop_codon	21373584	21373586	.	+	0	transcript_id "Phchi.S3G311400.t1"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	transcript	21371153	21373583	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	start_codon	21371153	21371155	.	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371153	21371306	1	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371153	21371306	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21371307	21371414	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371415	21371527	0.48	+	2	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371415	21371527	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21371528	21371773	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371774	21371908	0.99	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371774	21371908	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21371909	21371995	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21371996	21372067	1	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21371996	21372067	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372068	21372149	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372150	21372357	0.54	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372150	21372357	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372358	21372495	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372496	21372547	0.35	+	2	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372496	21372547	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372548	21372696	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372697	21372766	0.27	+	1	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372697	21372766	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372767	21372858	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21372859	21372945	0.32	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21372859	21372945	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21372946	21373065	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21373066	21373152	1	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21373066	21373152	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21373153	21373241	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21373242	21373400	1	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21373242	21373400	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	intron	21373401	21373484	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	CDS	21373485	21373583	1	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	exon	21373485	21373583	.	+	.	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
Phchi.S3	AUGUSTUS	stop_codon	21373584	21373586	.	+	0	transcript_id "Phchi.S3G311400.t2"; gene_id "Phchi.S3G311400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5282.t1 is derived from g2452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16016284	16016625	.	+	.	Phchi.S1G244100
Phchi.S1	AUGUSTUS	transcript	16016284	16016625	.	+	.	transcript_id "Phchi.S1G244100.t1"; gene_id "Phchi.S1G244100"
Phchi.S1	AUGUSTUS	start_codon	16016284	16016286	.	+	0	transcript_id "Phchi.S1G244100.t1"; gene_id "Phchi.S1G244100"
Phchi.S1	AUGUSTUS	CDS	16016284	16016625	0.9	+	0	transcript_id "Phchi.S1G244100.t1"; gene_id "Phchi.S1G244100"
Phchi.S1	AUGUSTUS	exon	16016284	16016625	.	+	.	transcript_id "Phchi.S1G244100.t1"; gene_id "Phchi.S1G244100"
Phchi.S1	AUGUSTUS	stop_codon	16016626	16016628	.	+	0	transcript_id "Phchi.S1G244100.t1"; gene_id "Phchi.S1G244100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8967.t1 is derived from g6142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38880623	38881138	.	+	.	Phchi.S1G612600
Phchi.S1	AUGUSTUS	transcript	38880623	38881138	.	+	.	transcript_id "Phchi.S1G612600.t1"; gene_id "Phchi.S1G612600"
Phchi.S1	AUGUSTUS	start_codon	38880623	38880625	.	+	0	transcript_id "Phchi.S1G612600.t1"; gene_id "Phchi.S1G612600"
Phchi.S1	AUGUSTUS	CDS	38880623	38881138	0.57	+	0	transcript_id "Phchi.S1G612600.t1"; gene_id "Phchi.S1G612600"
Phchi.S1	AUGUSTUS	exon	38880623	38881138	.	+	.	transcript_id "Phchi.S1G612600.t1"; gene_id "Phchi.S1G612600"
Phchi.S1	AUGUSTUS	stop_codon	38881139	38881141	.	+	0	transcript_id "Phchi.S1G612600.t1"; gene_id "Phchi.S1G612600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5201.t1 is derived from g2371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15439206	15441031	.	+	.	Phchi.S1G236000
Phchi.S1	AUGUSTUS	transcript	15439206	15441031	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	start_codon	15439206	15439208	.	+	0	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15439206	15439315	0.5	+	0	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15439206	15439315	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	intron	15439316	15439399	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15439400	15439497	1	+	1	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15439400	15439497	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	intron	15439498	15439573	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15439574	15439644	1	+	2	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15439574	15439644	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	intron	15439645	15439784	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15439785	15439873	1	+	0	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15439785	15439873	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	intron	15439874	15439965	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15439966	15440190	1	+	1	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15439966	15440190	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	intron	15440191	15440271	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15440272	15440492	0.95	+	1	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15440272	15440492	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	intron	15440493	15440570	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	CDS	15440571	15441031	0.9	+	2	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	exon	15440571	15441031	.	+	.	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
Phchi.S1	AUGUSTUS	stop_codon	15441032	15441034	.	+	0	transcript_id "Phchi.S1G236000.t1"; gene_id "Phchi.S1G236000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8349.t1 is derived from g5524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35440127	35442310	.	-	.	Phchi.S1G550800
Phchi.S1	AUGUSTUS	transcript	35440127	35442310	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	stop_codon	35440124	35440126	.	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35440127	35440666	1	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35440127	35440666	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	intron	35440667	35440779	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35440780	35440919	1	-	2	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35440780	35440919	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	intron	35440920	35441040	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35441041	35441344	0.62	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35441041	35441344	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	intron	35441345	35441451	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35441452	35441562	0.53	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35441452	35441562	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	intron	35441563	35441668	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35441669	35441767	1	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35441669	35441767	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	intron	35441768	35441886	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35441887	35441997	1	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35441887	35441997	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	intron	35441998	35442154	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	CDS	35442155	35442310	1	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	exon	35442155	35442310	.	-	.	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
Phchi.S1	AUGUSTUS	start_codon	35442308	35442310	.	-	0	transcript_id "Phchi.S1G550800.t1"; gene_id "Phchi.S1G550800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3810.t1 is derived from g979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5828260	5830549	.	+	.	Phchi.S1G096900
Phchi.S1	AUGUSTUS	transcript	5828260	5830549	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	start_codon	5828260	5828262	.	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5828260	5828332	0.97	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5828260	5828332	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5828333	5828402	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5828403	5828518	0.99	+	2	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5828403	5828518	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5828519	5828663	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5828664	5828801	1	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5828664	5828801	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5828802	5828900	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5828901	5829083	1	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5828901	5829083	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5829084	5829172	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5829173	5829330	0.96	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5829173	5829330	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5829331	5829435	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5829436	5829535	1	+	1	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5829436	5829535	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5829536	5829673	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5829674	5829785	1	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5829674	5829785	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5829786	5829884	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5829885	5830024	1	+	2	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5829885	5830024	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5830025	5830116	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5830117	5830302	1	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5830117	5830302	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	intron	5830303	5830384	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	CDS	5830385	5830549	1	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	exon	5830385	5830549	.	+	.	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
Phchi.S1	AUGUSTUS	stop_codon	5830550	5830552	.	+	0	transcript_id "Phchi.S1G096900.t1"; gene_id "Phchi.S1G096900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15766.t1 is derived from g14236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21252210	21254317	.	+	.	Phchi.S3G308500
Phchi.S3	AUGUSTUS	transcript	21252210	21254317	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	start_codon	21252210	21252212	.	+	0	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21252210	21252388	0.99	+	0	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21252210	21252388	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21252389	21252547	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21252548	21252622	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21252548	21252622	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21252623	21252722	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21252723	21252797	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21252723	21252797	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21252798	21252938	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21252939	21253139	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21252939	21253139	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21253140	21253268	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21253269	21253299	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21253269	21253299	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21253300	21253414	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21253415	21253524	1	+	0	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21253415	21253524	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21253525	21253655	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21253656	21253742	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21253656	21253742	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21253743	21253819	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21253820	21253906	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21253820	21253906	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21253907	21253999	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21254000	21254065	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21254000	21254065	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	intron	21254066	21254145	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	CDS	21254146	21254317	1	+	1	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	exon	21254146	21254317	.	+	.	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
Phchi.S3	AUGUSTUS	stop_codon	21254318	21254320	.	+	0	transcript_id "Phchi.S3G308500.t1"; gene_id "Phchi.S3G308500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11857.t1 is derived from g15909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8639817	8641909	.	+	.	Phchi.S4G143900
Phchi.S4	AUGUSTUS	transcript	8639817	8641909	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	start_codon	8639817	8639819	.	+	0	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8639817	8640022	0.81	+	0	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8639817	8640022	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	intron	8640023	8640336	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8640337	8640622	0.97	+	1	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8640337	8640622	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	intron	8640623	8640725	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8640726	8641079	0.98	+	0	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8640726	8641079	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	intron	8641080	8641180	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8641181	8641434	0.73	+	0	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8641181	8641434	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	intron	8641435	8641545	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8641546	8641909	0.69	+	1	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8641546	8641909	.	+	.	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	stop_codon	8641910	8641912	.	+	0	transcript_id "Phchi.S4G143900.t1"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	transcript	8639817	8640308	.	+	.	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	start_codon	8639817	8639819	.	+	0	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8639817	8640022	0.78	+	0	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8639817	8640022	.	+	.	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	intron	8640023	8640232	.	+	.	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	CDS	8640233	8640308	0.56	+	1	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	exon	8640233	8640308	.	+	.	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
Phchi.S4	AUGUSTUS	stop_codon	8640309	8640311	.	+	0	transcript_id "Phchi.S4G143900.t2"; gene_id "Phchi.S4G143900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15427.t1 is derived from g13895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19041575	19042843	.	-	.	Phchi.S3G274600
Phchi.S3	AUGUSTUS	transcript	19041575	19042473	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	stop_codon	19041572	19041574	.	-	0	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19041575	19041620	1	-	1	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19041575	19041620	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19041621	19041717	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19041718	19041809	1	-	0	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19041718	19041809	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19041810	19041892	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19041893	19041964	1	-	0	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19041893	19041964	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19041965	19042044	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19042045	19042147	1	-	1	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19042045	19042147	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19042148	19042342	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19042343	19042473	0.84	-	0	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19042343	19042473	.	-	.	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	start_codon	19042471	19042473	.	-	0	transcript_id "Phchi.S3G274600.t1"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	transcript	19041575	19042843	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	stop_codon	19041572	19041574	.	-	0	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19041575	19041620	1	-	1	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19041575	19041620	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19041621	19041717	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19041718	19041809	1	-	0	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19041718	19041809	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19041810	19041892	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19041893	19041964	1	-	0	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19041893	19041964	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19041965	19042044	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19042045	19042147	1	-	1	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19042045	19042147	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19042148	19042434	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19042435	19042440	0.92	-	1	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19042435	19042440	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	intron	19042441	19042694	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	CDS	19042695	19042843	0.65	-	0	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	exon	19042695	19042843	.	-	.	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
Phchi.S3	AUGUSTUS	start_codon	19042841	19042843	.	-	0	transcript_id "Phchi.S3G274600.t2"; gene_id "Phchi.S3G274600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10802.t1 is derived from g14852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2173140	2176379	.	-	.	Phchi.S4G038400
Phchi.S4	AUGUSTUS	transcript	2173140	2176379	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	stop_codon	2173137	2173139	.	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2173140	2173247	1	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2173140	2173247	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2173248	2173334	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2173335	2173462	1	-	2	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2173335	2173462	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2173463	2173539	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2173540	2173663	0.8	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2173540	2173663	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2173664	2173765	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2173766	2173973	0.77	-	1	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2173766	2173973	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2173974	2174077	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2174078	2174258	0.93	-	2	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2174078	2174258	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2174259	2174419	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2174420	2174592	1	-	1	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2174420	2174592	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2174593	2174706	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2174707	2174740	1	-	2	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2174707	2174740	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2174741	2174826	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2174827	2174924	1	-	1	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2174827	2174924	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2174925	2175052	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2175053	2175507	1	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2175053	2175507	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2175508	2175600	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2175601	2175852	0.99	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2175601	2175852	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2175853	2175950	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2175951	2176002	1	-	1	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2175951	2176002	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	intron	2176003	2176113	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	CDS	2176114	2176379	0.79	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	exon	2176114	2176379	.	-	.	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
Phchi.S4	AUGUSTUS	start_codon	2176377	2176379	.	-	0	transcript_id "Phchi.S4G038400.t1"; gene_id "Phchi.S4G038400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10646.t1 is derived from g14696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1398527	1401230	.	+	.	Phchi.S4G022800
Phchi.S4	AUGUSTUS	transcript	1398527	1401230	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	start_codon	1398527	1398529	.	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1398527	1398807	1	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1398527	1398807	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1398808	1398915	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1398916	1399149	1	+	1	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1398916	1399149	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1399150	1399269	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1399270	1399435	1	+	1	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1399270	1399435	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1399436	1399588	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1399589	1399735	1	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1399589	1399735	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1399736	1399822	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1399823	1399895	1	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1399823	1399895	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1399896	1400017	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1400018	1400103	0.99	+	2	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1400018	1400103	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1400104	1400224	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1400225	1400391	1	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1400225	1400391	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1400392	1400486	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1400487	1400576	1	+	1	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1400487	1400576	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1400577	1400663	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1400664	1400746	1	+	1	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1400664	1400746	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1400747	1400861	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1400862	1401007	0.98	+	2	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1400862	1401007	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	intron	1401008	1401119	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	CDS	1401120	1401230	0.96	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	exon	1401120	1401230	.	+	.	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
Phchi.S4	AUGUSTUS	stop_codon	1401231	1401233	.	+	0	transcript_id "Phchi.S4G022800.t1"; gene_id "Phchi.S4G022800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1318.t1 is derived from g11101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9005769	9007273	.	+	.	Phchi.S6G127700
Phchi.S6	AUGUSTUS	transcript	9005769	9007273	.	+	.	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	start_codon	9005769	9005771	.	+	0	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	CDS	9005769	9005834	0.5	+	0	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	exon	9005769	9005834	.	+	.	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	intron	9005835	9005964	.	+	.	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	CDS	9005965	9006068	0.5	+	0	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	exon	9005965	9006068	.	+	.	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	intron	9006069	9006465	.	+	.	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	CDS	9006466	9007273	0.78	+	1	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	exon	9006466	9007273	.	+	.	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
Phchi.S6	AUGUSTUS	stop_codon	9007274	9007276	.	+	0	transcript_id "Phchi.S6G127700.t1"; gene_id "Phchi.S6G127700"
# This transcript jg8035.t2 is derived from g5210.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8036.t1 is derived from g5211.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32608419	32610788	.	-	.	Phchi.S1G519500
Phchi.S1	AUGUSTUS	transcript	32608419	32610788	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	stop_codon	32608416	32608418	.	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32608419	32608485	1	-	1	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32608419	32608485	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32608486	32608573	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32608574	32608830	1	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32608574	32608830	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32608831	32608929	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32608930	32609157	1	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32608930	32609157	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609158	32609281	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609282	32609301	0.95	-	2	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609282	32609301	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609302	32609459	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609460	32609533	1	-	1	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609460	32609533	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609534	32609790	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609791	32609872	1	-	2	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609791	32609872	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609873	32609941	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609942	32609973	1	-	1	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609942	32609973	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609974	32610110	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610111	32610194	1	-	1	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610111	32610194	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32610195	32610289	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610290	32610351	1	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610290	32610351	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32610352	32610495	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610496	32610609	1	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610496	32610609	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32610610	32610695	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610696	32610788	0.65	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610696	32610788	.	-	.	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	start_codon	32610786	32610788	.	-	0	transcript_id "Phchi.S1G519500.t1"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	transcript	32608419	32610788	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	stop_codon	32608416	32608418	.	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32608419	32608485	1	-	1	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32608419	32608485	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32608486	32608573	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32608574	32608830	1	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32608574	32608830	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32608831	32608929	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32608930	32609157	1	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32608930	32609157	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609158	32609281	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609282	32609358	0.79	-	2	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609282	32609358	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609359	32609459	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609460	32609533	0.92	-	1	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609460	32609533	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609534	32609790	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609791	32609872	1	-	2	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609791	32609872	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609873	32609941	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32609942	32609973	1	-	1	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32609942	32609973	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32609974	32610110	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610111	32610194	1	-	1	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610111	32610194	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32610195	32610289	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610290	32610351	1	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610290	32610351	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32610352	32610495	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610496	32610609	1	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610496	32610609	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	intron	32610610	32610695	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	CDS	32610696	32610788	0.57	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	exon	32610696	32610788	.	-	.	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
Phchi.S1	AUGUSTUS	start_codon	32610786	32610788	.	-	0	transcript_id "Phchi.S1G519500.t2"; gene_id "Phchi.S1G519500"
# This transcript jg15826.t2 is derived from g14296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15827.t1 is derived from g14297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21640320	21641015	.	+	.	Phchi.S3G314600
Phchi.S3	AUGUSTUS	transcript	21640320	21641015	.	+	.	transcript_id "Phchi.S3G314600.t1"; gene_id "Phchi.S3G314600"
Phchi.S3	AUGUSTUS	start_codon	21640320	21640322	.	+	0	transcript_id "Phchi.S3G314600.t1"; gene_id "Phchi.S3G314600"
Phchi.S3	AUGUSTUS	CDS	21640320	21641015	0.22	+	0	transcript_id "Phchi.S3G314600.t1"; gene_id "Phchi.S3G314600"
Phchi.S3	AUGUSTUS	exon	21640320	21641015	.	+	.	transcript_id "Phchi.S3G314600.t1"; gene_id "Phchi.S3G314600"
Phchi.S3	AUGUSTUS	stop_codon	21641016	21641018	.	+	0	transcript_id "Phchi.S3G314600.t1"; gene_id "Phchi.S3G314600"
# This transcript jg11995.t2 is derived from g7670.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11996.t1 is derived from g7671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	447163	448032	.	+	.	Phchi.S2G007600
Phchi.S2	AUGUSTUS	transcript	447163	448032	.	+	.	transcript_id "Phchi.S2G007600.t1"; gene_id "Phchi.S2G007600"
Phchi.S2	AUGUSTUS	start_codon	447163	447165	.	+	0	transcript_id "Phchi.S2G007600.t1"; gene_id "Phchi.S2G007600"
Phchi.S2	AUGUSTUS	CDS	447163	448032	0.84	+	0	transcript_id "Phchi.S2G007600.t1"; gene_id "Phchi.S2G007600"
Phchi.S2	AUGUSTUS	exon	447163	448032	.	+	.	transcript_id "Phchi.S2G007600.t1"; gene_id "Phchi.S2G007600"
Phchi.S2	AUGUSTUS	stop_codon	448033	448035	.	+	0	transcript_id "Phchi.S2G007600.t1"; gene_id "Phchi.S2G007600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12851.t1 is derived from g11316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2706043	2706664	.	+	.	Phchi.S3G017000
Phchi.S3	AUGUSTUS	transcript	2706043	2706664	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	start_codon	2706043	2706045	.	+	0	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	CDS	2706043	2706059	0.58	+	0	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	exon	2706043	2706059	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	intron	2706060	2706197	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	CDS	2706198	2706273	1	+	1	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	exon	2706198	2706273	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	intron	2706274	2706373	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	CDS	2706374	2706536	1	+	0	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	exon	2706374	2706536	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	intron	2706537	2706635	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	CDS	2706636	2706664	0.35	+	2	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	exon	2706636	2706664	.	+	.	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
Phchi.S3	AUGUSTUS	stop_codon	2706665	2706667	.	+	0	transcript_id "Phchi.S3G017000.t1"; gene_id "Phchi.S3G017000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7392.t1 is derived from g4564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28898041	28898463	.	+	.	Phchi.S1G455100
Phchi.S1	AUGUSTUS	transcript	28898041	28898463	.	+	.	transcript_id "Phchi.S1G455100.t1"; gene_id "Phchi.S1G455100"
Phchi.S1	AUGUSTUS	start_codon	28898041	28898043	.	+	0	transcript_id "Phchi.S1G455100.t1"; gene_id "Phchi.S1G455100"
Phchi.S1	AUGUSTUS	CDS	28898041	28898463	0.94	+	0	transcript_id "Phchi.S1G455100.t1"; gene_id "Phchi.S1G455100"
Phchi.S1	AUGUSTUS	exon	28898041	28898463	.	+	.	transcript_id "Phchi.S1G455100.t1"; gene_id "Phchi.S1G455100"
Phchi.S1	AUGUSTUS	stop_codon	28898464	28898466	.	+	0	transcript_id "Phchi.S1G455100.t1"; gene_id "Phchi.S1G455100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3424.t1 is derived from g593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3575494	3577018	.	+	.	Phchi.S1G058300
Phchi.S1	AUGUSTUS	transcript	3575494	3577018	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	start_codon	3575494	3575496	.	+	0	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	CDS	3575494	3576078	0.9	+	0	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	exon	3575494	3576078	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	intron	3576079	3576194	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	CDS	3576195	3576336	1	+	0	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	exon	3576195	3576336	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	intron	3576337	3576492	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	CDS	3576493	3576782	0.67	+	2	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	exon	3576493	3576782	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	intron	3576783	3576913	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	CDS	3576914	3577018	0.95	+	0	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	exon	3576914	3577018	.	+	.	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
Phchi.S1	AUGUSTUS	stop_codon	3577019	3577021	.	+	0	transcript_id "Phchi.S1G058300.t1"; gene_id "Phchi.S1G058300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1423.t1 is derived from g8342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	782891	784559	.	-	.	Phchi.S5G003200
Phchi.S5	AUGUSTUS	transcript	782891	784559	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	stop_codon	782888	782890	.	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	782891	783016	1	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	782891	783016	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	783017	783088	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	783089	783186	1	-	2	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	783089	783186	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	783187	783286	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	783287	783341	1	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	783287	783341	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	783342	783424	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	783425	783526	1	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	783425	783526	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	783527	783645	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	783646	783768	1	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	783646	783768	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	783769	783894	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	783895	783953	1	-	2	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	783895	783953	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	783954	784041	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	784042	784180	1	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	784042	784180	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	intron	784181	784259	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	CDS	784260	784559	1	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	exon	784260	784559	.	-	.	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
Phchi.S5	AUGUSTUS	start_codon	784557	784559	.	-	0	transcript_id "Phchi.S5G003200.t1"; gene_id "Phchi.S5G003200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11460.t1 is derived from g15510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6480278	6480928	.	-	.	Phchi.S4G104200
Phchi.S4	AUGUSTUS	transcript	6480278	6480928	.	-	.	transcript_id "Phchi.S4G104200.t1"; gene_id "Phchi.S4G104200"
Phchi.S4	AUGUSTUS	stop_codon	6480275	6480277	.	-	0	transcript_id "Phchi.S4G104200.t1"; gene_id "Phchi.S4G104200"
Phchi.S4	AUGUSTUS	CDS	6480278	6480928	0.98	-	0	transcript_id "Phchi.S4G104200.t1"; gene_id "Phchi.S4G104200"
Phchi.S4	AUGUSTUS	exon	6480278	6480928	.	-	.	transcript_id "Phchi.S4G104200.t1"; gene_id "Phchi.S4G104200"
Phchi.S4	AUGUSTUS	start_codon	6480926	6480928	.	-	0	transcript_id "Phchi.S4G104200.t1"; gene_id "Phchi.S4G104200"
# This transcript jg14404.t2 is derived from g12872.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14405.t1 is derived from g12873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12679652	12680212	.	+	.	Phchi.S3G172400
Phchi.S3	AUGUSTUS	transcript	12679652	12680212	.	+	.	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	start_codon	12679652	12679654	.	+	0	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	CDS	12679652	12679751	0.76	+	0	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	exon	12679652	12679751	.	+	.	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	intron	12679752	12679847	.	+	.	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	CDS	12679848	12680212	1	+	2	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	exon	12679848	12680212	.	+	.	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
Phchi.S3	AUGUSTUS	stop_codon	12680213	12680215	.	+	0	transcript_id "Phchi.S3G172400.t1"; gene_id "Phchi.S3G172400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4148.t1 is derived from g1317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8647327	8647952	.	+	.	Phchi.S1G130700
Phchi.S1	AUGUSTUS	transcript	8647327	8647952	.	+	.	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	start_codon	8647327	8647329	.	+	0	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	CDS	8647327	8647475	0.99	+	0	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	exon	8647327	8647475	.	+	.	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	intron	8647476	8647577	.	+	.	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	CDS	8647578	8647668	1	+	1	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	exon	8647578	8647668	.	+	.	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	intron	8647669	8647784	.	+	.	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	CDS	8647785	8647952	1	+	0	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	exon	8647785	8647952	.	+	.	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
Phchi.S1	AUGUSTUS	stop_codon	8647953	8647955	.	+	0	transcript_id "Phchi.S1G130700.t1"; gene_id "Phchi.S1G130700"
# This transcript jg12369.t1 is derived from g8044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13084272	13085178	.	+	.	Phchi.S2G044800
Phchi.S2	AUGUSTUS	transcript	13084272	13085178	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	start_codon	13084272	13084274	.	+	0	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	CDS	13084272	13084311	0.79	+	0	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	exon	13084272	13084311	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	intron	13084312	13084393	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	CDS	13084394	13084537	0.92	+	2	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	exon	13084394	13084537	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	intron	13084538	13084636	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	CDS	13084637	13084698	1	+	2	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	exon	13084637	13084698	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	intron	13084699	13084856	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	CDS	13084857	13084937	0.78	+	0	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	exon	13084857	13084937	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	intron	13084938	13085025	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	CDS	13085026	13085178	0.77	+	0	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	exon	13085026	13085178	.	+	.	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
Phchi.S2	AUGUSTUS	stop_codon	13085179	13085181	.	+	0	transcript_id "Phchi.S2G044800.t1"; gene_id "Phchi.S2G044800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1827.t1 is derived from g8747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3368155	3369441	.	-	.	Phchi.S5G043600
Phchi.S5	AUGUSTUS	transcript	3368155	3369441	.	-	.	transcript_id "Phchi.S5G043600.t1"; gene_id "Phchi.S5G043600"
Phchi.S5	AUGUSTUS	stop_codon	3368152	3368154	.	-	0	transcript_id "Phchi.S5G043600.t1"; gene_id "Phchi.S5G043600"
Phchi.S5	AUGUSTUS	CDS	3368155	3369441	0.99	-	0	transcript_id "Phchi.S5G043600.t1"; gene_id "Phchi.S5G043600"
Phchi.S5	AUGUSTUS	exon	3368155	3369441	.	-	.	transcript_id "Phchi.S5G043600.t1"; gene_id "Phchi.S5G043600"
Phchi.S5	AUGUSTUS	start_codon	3369439	3369441	.	-	0	transcript_id "Phchi.S5G043600.t1"; gene_id "Phchi.S5G043600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3938.t1 is derived from g1107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6569534	6569866	.	+	.	Phchi.S1G109700
Phchi.S1	AUGUSTUS	transcript	6569534	6569866	.	+	.	transcript_id "Phchi.S1G109700.t1"; gene_id "Phchi.S1G109700"
Phchi.S1	AUGUSTUS	start_codon	6569534	6569536	.	+	0	transcript_id "Phchi.S1G109700.t1"; gene_id "Phchi.S1G109700"
Phchi.S1	AUGUSTUS	CDS	6569534	6569866	0.74	+	0	transcript_id "Phchi.S1G109700.t1"; gene_id "Phchi.S1G109700"
Phchi.S1	AUGUSTUS	exon	6569534	6569866	.	+	.	transcript_id "Phchi.S1G109700.t1"; gene_id "Phchi.S1G109700"
Phchi.S1	AUGUSTUS	stop_codon	6569867	6569869	.	+	0	transcript_id "Phchi.S1G109700.t1"; gene_id "Phchi.S1G109700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2035.t1 is derived from g8955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4544917	4547849	.	+	.	Phchi.S5G064400
Phchi.S5	AUGUSTUS	transcript	4544917	4547849	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	start_codon	4544917	4544919	.	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4544917	4545711	0.71	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4544917	4545711	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4545712	4545805	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4545806	4545892	1	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4545806	4545892	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4545893	4545988	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4545989	4546096	1	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4545989	4546096	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4546097	4546226	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4546227	4546496	1	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4546227	4546496	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4546497	4546594	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4546595	4546678	1	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4546595	4546678	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4546679	4546774	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4546775	4546991	1	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4546775	4546991	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4546992	4547081	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4547082	4547167	0.99	+	2	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4547082	4547167	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4547168	4547268	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4547269	4547586	1	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4547269	4547586	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	intron	4547587	4547672	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	CDS	4547673	4547849	0.99	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	exon	4547673	4547849	.	+	.	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
Phchi.S5	AUGUSTUS	stop_codon	4547850	4547852	.	+	0	transcript_id "Phchi.S5G064400.t1"; gene_id "Phchi.S5G064400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4470.t1 is derived from g1640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10672794	10675048	.	+	.	Phchi.S1G162900
Phchi.S1	AUGUSTUS	transcript	10672794	10675048	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	start_codon	10672794	10672796	.	+	0	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	CDS	10672794	10673089	0.99	+	0	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	exon	10672794	10673089	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	intron	10673090	10673220	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	CDS	10673221	10673322	0.94	+	1	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	exon	10673221	10673322	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	intron	10673323	10673532	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	CDS	10673533	10674060	0.44	+	1	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	exon	10673533	10674060	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	intron	10674061	10674206	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	CDS	10674207	10674385	0.67	+	1	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	exon	10674207	10674385	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	intron	10674386	10674461	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	CDS	10674462	10675048	0.97	+	2	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	exon	10674462	10675048	.	+	.	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
Phchi.S1	AUGUSTUS	stop_codon	10675049	10675051	.	+	0	transcript_id "Phchi.S1G162900.t1"; gene_id "Phchi.S1G162900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15475.t1 is derived from g13943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19367585	19369579	.	-	.	Phchi.S3G279400
Phchi.S3	AUGUSTUS	transcript	19367585	19369579	.	-	.	transcript_id "Phchi.S3G279400.t1"; gene_id "Phchi.S3G279400"
Phchi.S3	AUGUSTUS	stop_codon	19367582	19367584	.	-	0	transcript_id "Phchi.S3G279400.t1"; gene_id "Phchi.S3G279400"
Phchi.S3	AUGUSTUS	CDS	19367585	19369579	1	-	0	transcript_id "Phchi.S3G279400.t1"; gene_id "Phchi.S3G279400"
Phchi.S3	AUGUSTUS	exon	19367585	19369579	.	-	.	transcript_id "Phchi.S3G279400.t1"; gene_id "Phchi.S3G279400"
Phchi.S3	AUGUSTUS	start_codon	19369577	19369579	.	-	0	transcript_id "Phchi.S3G279400.t1"; gene_id "Phchi.S3G279400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3123.t1 is derived from g292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1850329	1851984	.	-	.	Phchi.S1G028200
Phchi.S1	AUGUSTUS	transcript	1850329	1851984	.	-	.	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	stop_codon	1850326	1850328	.	-	0	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	CDS	1850329	1851563	1	-	2	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	exon	1850329	1851563	.	-	.	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	intron	1851564	1851656	.	-	.	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	CDS	1851657	1851984	0.68	-	0	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	exon	1851657	1851984	.	-	.	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
Phchi.S1	AUGUSTUS	start_codon	1851982	1851984	.	-	0	transcript_id "Phchi.S1G028200.t1"; gene_id "Phchi.S1G028200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4082.t1 is derived from g1251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7694930	7695367	.	+	.	Phchi.S1G124100
Phchi.S1	AUGUSTUS	transcript	7694930	7695367	.	+	.	transcript_id "Phchi.S1G124100.t1"; gene_id "Phchi.S1G124100"
Phchi.S1	AUGUSTUS	start_codon	7694930	7694932	.	+	0	transcript_id "Phchi.S1G124100.t1"; gene_id "Phchi.S1G124100"
Phchi.S1	AUGUSTUS	CDS	7694930	7695367	0.54	+	0	transcript_id "Phchi.S1G124100.t1"; gene_id "Phchi.S1G124100"
Phchi.S1	AUGUSTUS	exon	7694930	7695367	.	+	.	transcript_id "Phchi.S1G124100.t1"; gene_id "Phchi.S1G124100"
Phchi.S1	AUGUSTUS	stop_codon	7695368	7695370	.	+	0	transcript_id "Phchi.S1G124100.t1"; gene_id "Phchi.S1G124100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2099.t1 is derived from g9019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4860792	4868888	.	-	.	Phchi.S5G070800
Phchi.S5	AUGUSTUS	transcript	4860792	4868888	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	stop_codon	4860789	4860791	.	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4860792	4860971	0.91	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4860792	4860971	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4860972	4861149	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4861150	4861188	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4861150	4861188	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4861189	4861319	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4861320	4861820	0.9	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4861320	4861820	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4861821	4862028	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4862029	4862145	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4862029	4862145	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4862146	4862263	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4862264	4862346	1	-	2	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4862264	4862346	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4862347	4862459	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4862460	4862672	0.96	-	2	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4862460	4862672	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4862673	4862762	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4862763	4863261	0.95	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4862763	4863261	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4863262	4863373	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4863374	4864289	0.21	-	1	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4863374	4864289	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4864290	4864383	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4864384	4864826	0.4	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4864384	4864826	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4864827	4864954	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4864955	4865110	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4864955	4865110	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4865111	4865282	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4865283	4865591	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4865283	4865591	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4865592	4865739	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4865740	4866522	0.55	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4865740	4866522	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4866523	4866636	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4866637	4866978	0.81	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4866637	4866978	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4866979	4867076	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4867077	4867274	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4867077	4867274	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4867275	4867448	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4867449	4867511	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4867449	4867511	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4867512	4867651	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4867652	4867723	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4867652	4867723	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4867724	4867831	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4867832	4868228	0.98	-	1	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4867832	4868228	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4868229	4868402	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4868403	4868736	1	-	2	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4868403	4868736	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	intron	4868737	4868833	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	CDS	4868834	4868888	1	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	exon	4868834	4868888	.	-	.	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
Phchi.S5	AUGUSTUS	start_codon	4868886	4868888	.	-	0	transcript_id "Phchi.S5G070800.t1"; gene_id "Phchi.S5G070800"
# This transcript jg9794.t2 is derived from g6970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9795.t1 is derived from g6971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43723686	43727064	.	-	.	Phchi.S1G695400
Phchi.S1	AUGUSTUS	transcript	43723686	43727064	.	-	.	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	stop_codon	43723683	43723685	.	-	0	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	CDS	43723686	43724383	0.65	-	2	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	exon	43723686	43724383	.	-	.	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	intron	43724384	43724679	.	-	.	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	CDS	43724680	43725336	0.01	-	2	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	exon	43724680	43725336	.	-	.	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	intron	43725337	43726916	.	-	.	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	CDS	43726917	43727064	0.01	-	0	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	exon	43726917	43727064	.	-	.	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
Phchi.S1	AUGUSTUS	start_codon	43727062	43727064	.	-	0	transcript_id "Phchi.S1G695400.t1"; gene_id "Phchi.S1G695400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg675.t1 is derived from g10457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4658141	4658447	.	+	.	Phchi.S6G063400
Phchi.S6	AUGUSTUS	transcript	4658141	4658447	.	+	.	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	start_codon	4658141	4658143	.	+	0	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	CDS	4658141	4658233	1	+	0	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	exon	4658141	4658233	.	+	.	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	intron	4658234	4658327	.	+	.	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	CDS	4658328	4658447	1	+	0	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	exon	4658328	4658447	.	+	.	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
Phchi.S6	AUGUSTUS	stop_codon	4658448	4658450	.	+	0	transcript_id "Phchi.S6G063400.t1"; gene_id "Phchi.S6G063400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1644.t1 is derived from g8563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2172962	2173871	.	-	.	Phchi.S5G025300
Phchi.S5	AUGUSTUS	transcript	2172962	2173871	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	stop_codon	2172959	2172961	.	-	0	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	CDS	2172962	2173141	0.78	-	0	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	exon	2172962	2173141	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	intron	2173142	2173256	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	CDS	2173257	2173487	1	-	0	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	exon	2173257	2173487	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	intron	2173488	2173612	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	CDS	2173613	2173651	1	-	0	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	exon	2173613	2173651	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	intron	2173652	2173763	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	CDS	2173764	2173871	0.84	-	0	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	exon	2173764	2173871	.	-	.	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
Phchi.S5	AUGUSTUS	start_codon	2173869	2173871	.	-	0	transcript_id "Phchi.S5G025300.t1"; gene_id "Phchi.S5G025300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6810.t1 is derived from g3982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25155195	25157473	.	+	.	Phchi.S1G396900
Phchi.S1	AUGUSTUS	transcript	25155195	25157473	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	start_codon	25155195	25155197	.	+	0	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	CDS	25155195	25155243	0.98	+	0	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	exon	25155195	25155243	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	intron	25155244	25155522	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	CDS	25155523	25155668	0.83	+	2	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	exon	25155523	25155668	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	intron	25155669	25155817	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	CDS	25155818	25156532	0.94	+	0	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	exon	25155818	25156532	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	intron	25156533	25156699	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	CDS	25156700	25156789	0.33	+	2	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	exon	25156700	25156789	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	intron	25156790	25156938	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	CDS	25156939	25157069	0.76	+	2	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	exon	25156939	25157069	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	intron	25157070	25157155	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	CDS	25157156	25157473	0.92	+	0	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	exon	25157156	25157473	.	+	.	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
Phchi.S1	AUGUSTUS	stop_codon	25157474	25157476	.	+	0	transcript_id "Phchi.S1G396900.t1"; gene_id "Phchi.S1G396900"
# This transcript jg12629.t2 is derived from g8306.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12630.t1 is derived from g8307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37657032	37659316	.	-	.	Phchi.S2G071000
Phchi.S2	AUGUSTUS	transcript	37657032	37659316	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	stop_codon	37657029	37657031	.	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37657032	37657043	0.66	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37657032	37657043	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37657044	37657764	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37657765	37657872	0.97	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37657765	37657872	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37657873	37657939	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37657940	37658187	0.99	-	2	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37657940	37658187	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37658188	37658301	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37658302	37658467	0.95	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37658302	37658467	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37658468	37658618	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37658619	37658702	1	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37658619	37658702	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37658703	37658809	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37658810	37658926	1	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37658810	37658926	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37658927	37659000	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37659001	37659096	1	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37659001	37659096	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	intron	37659097	37659172	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	CDS	37659173	37659316	0.56	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	exon	37659173	37659316	.	-	.	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
Phchi.S2	AUGUSTUS	start_codon	37659314	37659316	.	-	0	transcript_id "Phchi.S2G071000.t1"; gene_id "Phchi.S2G071000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4280.t1 is derived from g1449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9383389	9383985	.	-	.	Phchi.S1G143900
Phchi.S1	AUGUSTUS	transcript	9383389	9383985	.	-	.	transcript_id "Phchi.S1G143900.t1"; gene_id "Phchi.S1G143900"
Phchi.S1	AUGUSTUS	stop_codon	9383386	9383388	.	-	0	transcript_id "Phchi.S1G143900.t1"; gene_id "Phchi.S1G143900"
Phchi.S1	AUGUSTUS	CDS	9383389	9383985	0.56	-	0	transcript_id "Phchi.S1G143900.t1"; gene_id "Phchi.S1G143900"
Phchi.S1	AUGUSTUS	exon	9383389	9383985	.	-	.	transcript_id "Phchi.S1G143900.t1"; gene_id "Phchi.S1G143900"
Phchi.S1	AUGUSTUS	start_codon	9383983	9383985	.	-	0	transcript_id "Phchi.S1G143900.t1"; gene_id "Phchi.S1G143900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12430.t1 is derived from g8107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19595516	19596679	.	-	.	Phchi.S2G051000
Phchi.S2	AUGUSTUS	transcript	19595516	19596679	.	-	.	transcript_id "Phchi.S2G051000.t1"; gene_id "Phchi.S2G051000"
Phchi.S2	AUGUSTUS	stop_codon	19595513	19595515	.	-	0	transcript_id "Phchi.S2G051000.t1"; gene_id "Phchi.S2G051000"
Phchi.S2	AUGUSTUS	CDS	19595516	19596679	0.56	-	0	transcript_id "Phchi.S2G051000.t1"; gene_id "Phchi.S2G051000"
Phchi.S2	AUGUSTUS	exon	19595516	19596679	.	-	.	transcript_id "Phchi.S2G051000.t1"; gene_id "Phchi.S2G051000"
Phchi.S2	AUGUSTUS	start_codon	19596677	19596679	.	-	0	transcript_id "Phchi.S2G051000.t1"; gene_id "Phchi.S2G051000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10055.t1 is derived from g7231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45530047	45530686	.	-	.	Phchi.S1G721400
Phchi.S1	AUGUSTUS	transcript	45530047	45530686	.	-	.	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	stop_codon	45530044	45530046	.	-	0	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	CDS	45530047	45530197	0.51	-	1	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	exon	45530047	45530197	.	-	.	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	intron	45530198	45530321	.	-	.	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	CDS	45530322	45530686	0.61	-	0	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	exon	45530322	45530686	.	-	.	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
Phchi.S1	AUGUSTUS	start_codon	45530684	45530686	.	-	0	transcript_id "Phchi.S1G721400.t1"; gene_id "Phchi.S1G721400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11207.t1 is derived from g15257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4762584	4763615	.	-	.	Phchi.S4G078900
Phchi.S4	AUGUSTUS	transcript	4762584	4763615	.	-	.	transcript_id "Phchi.S4G078900.t1"; gene_id "Phchi.S4G078900"
Phchi.S4	AUGUSTUS	stop_codon	4762581	4762583	.	-	0	transcript_id "Phchi.S4G078900.t1"; gene_id "Phchi.S4G078900"
Phchi.S4	AUGUSTUS	CDS	4762584	4763615	0.69	-	0	transcript_id "Phchi.S4G078900.t1"; gene_id "Phchi.S4G078900"
Phchi.S4	AUGUSTUS	exon	4762584	4763615	.	-	.	transcript_id "Phchi.S4G078900.t1"; gene_id "Phchi.S4G078900"
Phchi.S4	AUGUSTUS	start_codon	4763613	4763615	.	-	0	transcript_id "Phchi.S4G078900.t1"; gene_id "Phchi.S4G078900"
# This transcript jg13548.t2 is derived from g12015.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13549.t1 is derived from g12016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7455485	7459254	.	+	.	Phchi.S3G086800
Phchi.S3	AUGUSTUS	transcript	7455485	7459254	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	start_codon	7455485	7455487	.	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7455485	7455769	0.53	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7455485	7455769	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7455770	7455857	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7455858	7456158	0.79	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7455858	7456158	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7456159	7456249	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7456250	7456731	1	+	2	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7456250	7456731	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7456732	7456818	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7456819	7457040	1	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7456819	7457040	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7457041	7457184	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7457185	7457535	1	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7457185	7457535	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7457536	7457643	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7457644	7458012	0.72	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7457644	7458012	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7458013	7458126	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7458127	7458906	0.98	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7458127	7458906	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7458907	7458977	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7458978	7459109	1	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7458978	7459109	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	intron	7459110	7459191	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	CDS	7459192	7459254	1	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	exon	7459192	7459254	.	+	.	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
Phchi.S3	AUGUSTUS	stop_codon	7459255	7459257	.	+	0	transcript_id "Phchi.S3G086800.t1"; gene_id "Phchi.S3G086800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14652.t1 is derived from g13120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13952798	13954696	.	+	.	Phchi.S3G197100
Phchi.S3	AUGUSTUS	transcript	13952798	13954696	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	start_codon	13952798	13952800	.	+	0	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	CDS	13952798	13952914	0.68	+	0	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	exon	13952798	13952914	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	intron	13952915	13953057	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	CDS	13953058	13953096	0.75	+	0	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	exon	13953058	13953096	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	intron	13953097	13953180	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	CDS	13953181	13953444	1	+	0	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	exon	13953181	13953444	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	intron	13953445	13953548	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	CDS	13953549	13953805	1	+	0	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	exon	13953549	13953805	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	intron	13953806	13953894	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	CDS	13953895	13954696	1	+	1	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	exon	13953895	13954696	.	+	.	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
Phchi.S3	AUGUSTUS	stop_codon	13954697	13954699	.	+	0	transcript_id "Phchi.S3G197100.t1"; gene_id "Phchi.S3G197100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6897.t1 is derived from g4069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25874694	25876137	.	-	.	Phchi.S1G405600
Phchi.S1	AUGUSTUS	transcript	25874694	25876137	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	stop_codon	25874691	25874693	.	-	0	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	CDS	25874694	25874954	0.9	-	0	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	exon	25874694	25874954	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	intron	25874955	25875048	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	CDS	25875049	25875142	0.98	-	1	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	exon	25875049	25875142	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	intron	25875143	25875246	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	CDS	25875247	25875322	0.53	-	2	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	exon	25875247	25875322	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	intron	25875323	25875425	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	CDS	25875426	25876137	0.71	-	0	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	exon	25875426	25876137	.	-	.	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
Phchi.S1	AUGUSTUS	start_codon	25876135	25876137	.	-	0	transcript_id "Phchi.S1G405600.t1"; gene_id "Phchi.S1G405600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5618.t1 is derived from g2788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17914612	17915268	.	+	.	Phchi.S1G277700
Phchi.S1	AUGUSTUS	transcript	17914612	17915268	.	+	.	transcript_id "Phchi.S1G277700.t1"; gene_id "Phchi.S1G277700"
Phchi.S1	AUGUSTUS	start_codon	17914612	17914614	.	+	0	transcript_id "Phchi.S1G277700.t1"; gene_id "Phchi.S1G277700"
Phchi.S1	AUGUSTUS	CDS	17914612	17915268	0.98	+	0	transcript_id "Phchi.S1G277700.t1"; gene_id "Phchi.S1G277700"
Phchi.S1	AUGUSTUS	exon	17914612	17915268	.	+	.	transcript_id "Phchi.S1G277700.t1"; gene_id "Phchi.S1G277700"
Phchi.S1	AUGUSTUS	stop_codon	17915269	17915271	.	+	0	transcript_id "Phchi.S1G277700.t1"; gene_id "Phchi.S1G277700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15603.t1 is derived from g14072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20239053	20240054	.	-	.	Phchi.S3G292200
Phchi.S3	AUGUSTUS	transcript	20239053	20240054	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	stop_codon	20239050	20239052	.	-	0	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	CDS	20239053	20239129	1	-	2	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	exon	20239053	20239129	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	intron	20239130	20239232	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	CDS	20239233	20239287	0.97	-	0	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	exon	20239233	20239287	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	intron	20239288	20239376	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	CDS	20239377	20239667	1	-	0	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	exon	20239377	20239667	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	intron	20239668	20239760	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	CDS	20239761	20240054	0.65	-	0	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	exon	20239761	20240054	.	-	.	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
Phchi.S3	AUGUSTUS	start_codon	20240052	20240054	.	-	0	transcript_id "Phchi.S3G292200.t1"; gene_id "Phchi.S3G292200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1921.t1 is derived from g8841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3854763	3857081	.	+	.	Phchi.S5G053000
Phchi.S5	AUGUSTUS	transcript	3854763	3857081	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	start_codon	3854763	3854765	.	+	0	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	CDS	3854763	3854912	0.57	+	0	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	exon	3854763	3854912	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	intron	3854913	3855095	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	CDS	3855096	3855628	1	+	0	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	exon	3855096	3855628	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	intron	3855629	3855724	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	CDS	3855725	3855889	1	+	1	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	exon	3855725	3855889	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	intron	3855890	3855973	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	CDS	3855974	3856669	0.91	+	1	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	exon	3855974	3856669	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	intron	3856670	3856795	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	CDS	3856796	3857081	1	+	1	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	exon	3856796	3857081	.	+	.	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
Phchi.S5	AUGUSTUS	stop_codon	3857082	3857084	.	+	0	transcript_id "Phchi.S5G053000.t1"; gene_id "Phchi.S5G053000"
# This transcript jg241.t2 is derived from g10023.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg241.t3 is derived from g10023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg241.t4 is derived from g10023.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg242.t1 is derived from g10024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1677917	1678725	.	-	.	Phchi.S6G020100
Phchi.S6	AUGUSTUS	transcript	1677917	1678725	.	-	.	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	stop_codon	1677914	1677916	.	-	0	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	CDS	1677917	1678220	0.47	-	1	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	exon	1677917	1678220	.	-	.	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	intron	1678221	1678316	.	-	.	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	CDS	1678317	1678362	0.44	-	2	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	exon	1678317	1678362	.	-	.	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	intron	1678363	1678436	.	-	.	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	CDS	1678437	1678725	0.38	-	0	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	exon	1678437	1678725	.	-	.	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
Phchi.S6	AUGUSTUS	start_codon	1678723	1678725	.	-	0	transcript_id "Phchi.S6G020100.t1"; gene_id "Phchi.S6G020100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14473.t1 is derived from g12941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13030739	13033698	.	-	.	Phchi.S3G179200
Phchi.S3	AUGUSTUS	transcript	13030739	13033698	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	stop_codon	13030736	13030738	.	-	0	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	CDS	13030739	13030832	0.49	-	1	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	exon	13030739	13030832	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	intron	13030833	13030908	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	CDS	13030909	13032219	0.76	-	1	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	exon	13030909	13032219	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	intron	13032220	13032291	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	CDS	13032292	13032438	0.64	-	1	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	exon	13032292	13032438	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	intron	13032439	13032542	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	CDS	13032543	13033351	0.42	-	0	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	exon	13032543	13033351	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	intron	13033352	13033443	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	CDS	13033444	13033698	0.99	-	0	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	exon	13033444	13033698	.	-	.	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
Phchi.S3	AUGUSTUS	start_codon	13033696	13033698	.	-	0	transcript_id "Phchi.S3G179200.t1"; gene_id "Phchi.S3G179200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8753.t1 is derived from g5928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37800886	37805112	.	-	.	Phchi.S1G591200
Phchi.S1	AUGUSTUS	transcript	37800886	37805112	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	stop_codon	37800883	37800885	.	-	0	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37800886	37800980	0.83	-	2	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37800886	37800980	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37800981	37801083	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37801084	37801255	0.87	-	0	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37801084	37801255	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37801256	37801589	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37801590	37801623	1	-	1	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37801590	37801623	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37801624	37801717	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37801718	37801740	0.87	-	0	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37801718	37801740	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37801741	37801892	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37801893	37801910	0.87	-	0	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37801893	37801910	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37801911	37802069	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37802070	37803004	0.38	-	2	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37802070	37803004	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37803005	37803090	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37803091	37803474	0.24	-	2	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37803091	37803474	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	intron	37803475	37803569	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	CDS	37803570	37805112	0.3	-	0	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	exon	37803570	37805112	.	-	.	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
Phchi.S1	AUGUSTUS	start_codon	37805110	37805112	.	-	0	transcript_id "Phchi.S1G591200.t1"; gene_id "Phchi.S1G591200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13909.t1 is derived from g12376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9628735	9629119	.	+	.	Phchi.S3G122800
Phchi.S3	AUGUSTUS	transcript	9628735	9629119	.	+	.	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	start_codon	9628735	9628737	.	+	0	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	CDS	9628735	9628847	0.63	+	0	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	exon	9628735	9628847	.	+	.	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	intron	9628848	9628971	.	+	.	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	CDS	9628972	9629119	0.64	+	1	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	exon	9628972	9629119	.	+	.	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
Phchi.S3	AUGUSTUS	stop_codon	9629120	9629122	.	+	0	transcript_id "Phchi.S3G122800.t1"; gene_id "Phchi.S3G122800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11547.t1 is derived from g15597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6987979	6989937	.	+	.	Phchi.S4G112900
Phchi.S4	AUGUSTUS	transcript	6987979	6989937	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	start_codon	6987979	6987981	.	+	0	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6987979	6988096	1	+	0	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6987979	6988096	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6988097	6988238	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6988239	6988273	0.91	+	2	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6988239	6988273	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6988274	6988491	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6988492	6988564	0.9	+	0	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6988492	6988564	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6988565	6988650	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6988651	6988710	1	+	2	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6988651	6988710	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6988711	6988852	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6988853	6988874	0.49	+	2	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6988853	6988874	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6988875	6988986	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6988987	6989077	0.46	+	1	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6988987	6989077	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6989078	6989316	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6989317	6989330	0.66	+	0	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6989317	6989330	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6989331	6989444	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6989445	6989596	0.32	+	1	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6989445	6989596	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6989597	6989778	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6989779	6989834	0.24	+	2	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6989779	6989834	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	intron	6989835	6989934	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	CDS	6989935	6989937	0.62	+	0	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	exon	6989935	6989937	.	+	.	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
Phchi.S4	AUGUSTUS	stop_codon	6989938	6989940	.	+	0	transcript_id "Phchi.S4G112900.t1"; gene_id "Phchi.S4G112900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13714.t1 is derived from g12181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8334088	8340741	.	+	.	Phchi.S3G103300
Phchi.S3	AUGUSTUS	transcript	8334088	8340741	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	start_codon	8334088	8334090	.	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8334088	8334092	0.65	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8334088	8334092	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8334093	8334304	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8334305	8334383	0.76	+	1	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8334305	8334383	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8334384	8334547	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8334548	8337304	0.76	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8334548	8337304	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8337305	8337601	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8337602	8337973	0.83	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8337602	8337973	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8337974	8338125	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8338126	8339099	0.78	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8338126	8339099	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8339100	8339221	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8339222	8339624	0.52	+	1	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8339222	8339624	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8339625	8339747	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8339748	8340556	0.96	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8339748	8340556	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	intron	8340557	8340698	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	CDS	8340699	8340741	0.97	+	1	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	exon	8340699	8340741	.	+	.	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
Phchi.S3	AUGUSTUS	stop_codon	8340742	8340744	.	+	0	transcript_id "Phchi.S3G103300.t1"; gene_id "Phchi.S3G103300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6074.t1 is derived from g3245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20742488	20742832	.	+	.	Phchi.S1G323300
Phchi.S1	AUGUSTUS	transcript	20742488	20742832	.	+	.	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	start_codon	20742488	20742490	.	+	0	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	CDS	20742488	20742681	0.7	+	0	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	exon	20742488	20742681	.	+	.	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	intron	20742682	20742780	.	+	.	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	CDS	20742781	20742832	0.92	+	1	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	exon	20742781	20742832	.	+	.	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
Phchi.S1	AUGUSTUS	stop_codon	20742833	20742835	.	+	0	transcript_id "Phchi.S1G323300.t1"; gene_id "Phchi.S1G323300"
# This transcript jg8681.t2 is derived from g5856.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8682.t1 is derived from g5857.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37428563	37431419	.	-	.	Phchi.S1G584100
Phchi.S1	AUGUSTUS	transcript	37428563	37431419	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	stop_codon	37428560	37428562	.	-	0	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37428563	37428704	0.51	-	1	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37428563	37428704	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37428705	37428951	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37428952	37429054	0.54	-	2	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37428952	37429054	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37429055	37429152	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37429153	37429230	0.76	-	2	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37429153	37429230	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37429231	37429378	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37429379	37429918	0.99	-	2	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37429379	37429918	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37429919	37430113	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37430114	37430574	1	-	1	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37430114	37430574	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37430575	37430698	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37430699	37430858	1	-	2	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37430699	37430858	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37430859	37430963	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37430964	37431088	1	-	1	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37430964	37431088	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37431089	37431199	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37431200	37431255	1	-	0	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37431200	37431255	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37431256	37431338	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37431339	37431419	0.99	-	0	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37431339	37431419	.	-	.	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	start_codon	37431417	37431419	.	-	0	transcript_id "Phchi.S1G584100.t1"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	transcript	37428563	37431419	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	stop_codon	37428560	37428562	.	-	0	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37428563	37428704	0.47	-	1	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37428563	37428704	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37428705	37428951	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37428952	37429054	0.5	-	2	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37428952	37429054	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37429055	37429152	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37429153	37429230	0.75	-	2	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37429153	37429230	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37429231	37429378	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37429379	37429909	0.98	-	2	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37429379	37429909	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37429910	37430113	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37430114	37430574	1	-	1	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37430114	37430574	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37430575	37430698	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37430699	37430858	1	-	2	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37430699	37430858	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37430859	37430963	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37430964	37431088	1	-	1	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37430964	37431088	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37431089	37431199	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37431200	37431255	1	-	0	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37431200	37431255	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	intron	37431256	37431338	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	CDS	37431339	37431419	0.98	-	0	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	exon	37431339	37431419	.	-	.	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
Phchi.S1	AUGUSTUS	start_codon	37431417	37431419	.	-	0	transcript_id "Phchi.S1G584100.t2"; gene_id "Phchi.S1G584100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6699.t1 is derived from g3871.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24584719	24595258	.	+	.	Phchi.S1G385800
Phchi.S1	AUGUSTUS	transcript	24584719	24595258	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	start_codon	24584719	24584721	.	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24584719	24585192	0.64	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24584719	24585192	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24585193	24585276	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24585277	24586202	0.55	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24585277	24586202	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24586203	24586300	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24586301	24586358	1	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24586301	24586358	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24586359	24586467	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24586468	24586590	0.97	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24586468	24586590	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24586591	24586681	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24586682	24586739	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24586682	24586739	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24586740	24586829	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24586830	24586966	1	+	2	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24586830	24586966	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24586967	24587049	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24587050	24587208	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24587050	24587208	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24587209	24587359	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24587360	24587446	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24587360	24587446	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24587447	24587530	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24587531	24587734	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24587531	24587734	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24587735	24587887	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24587888	24588040	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24587888	24588040	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24588041	24588120	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24588121	24588312	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24588121	24588312	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24588313	24588398	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24588399	24588467	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24588399	24588467	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24588468	24588602	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24588603	24588698	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24588603	24588698	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24588699	24589449	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24589450	24589557	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24589450	24589557	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24589558	24589736	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24589737	24589853	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24589737	24589853	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24589854	24589950	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24589951	24590158	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24589951	24590158	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24590159	24590273	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24590274	24590341	1	+	2	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24590274	24590341	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24590342	24590545	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24590546	24590604	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24590546	24590604	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24590605	24590742	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24590743	24590874	1	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24590743	24590874	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24590875	24590962	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24590963	24591125	1	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24590963	24591125	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24591126	24591216	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24591217	24591540	0.99	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24591217	24591540	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24591541	24591702	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24591703	24591888	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24591703	24591888	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24591889	24591972	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24591973	24592046	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24591973	24592046	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24592047	24592221	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24592222	24592300	1	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24592222	24592300	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24592301	24592399	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24592400	24592552	0.99	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24592400	24592552	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24592553	24592655	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24592656	24592795	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24592656	24592795	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24592796	24592886	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24592887	24593010	1	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24592887	24593010	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24593011	24593147	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24593148	24593221	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24593148	24593221	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24593222	24593388	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24593389	24593533	1	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24593389	24593533	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24593534	24593648	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24593649	24593795	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24593649	24593795	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24593796	24593903	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24593904	24593999	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24593904	24593999	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24594000	24594087	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24594088	24594183	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24594088	24594183	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24594184	24594291	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24594292	24594551	1	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24594292	24594551	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24594552	24594658	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24594659	24594848	0.69	+	1	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24594659	24594848	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24594849	24594945	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24594946	24595029	0.68	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24594946	24595029	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	intron	24595030	24595195	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	CDS	24595196	24595258	0.73	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	exon	24595196	24595258	.	+	.	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
Phchi.S1	AUGUSTUS	stop_codon	24595259	24595261	.	+	0	transcript_id "Phchi.S1G385800.t1"; gene_id "Phchi.S1G385800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12563.t1 is derived from g8240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35293934	35294348	.	+	.	Phchi.S2G064300
Phchi.S2	AUGUSTUS	transcript	35293934	35294348	.	+	.	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	start_codon	35293934	35293936	.	+	0	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	CDS	35293934	35294053	0.92	+	0	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	exon	35293934	35294053	.	+	.	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	intron	35294054	35294146	.	+	.	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	CDS	35294147	35294218	0.99	+	0	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	exon	35294147	35294218	.	+	.	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	intron	35294219	35294309	.	+	.	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	CDS	35294310	35294348	0.87	+	0	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	exon	35294310	35294348	.	+	.	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
Phchi.S2	AUGUSTUS	stop_codon	35294349	35294351	.	+	0	transcript_id "Phchi.S2G064300.t1"; gene_id "Phchi.S2G064300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16002.t1 is derived from g16024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C289	AUGUSTUS	gene	12892	14128	.	+	.	Phchi.C289G000100
Phchi.C289	AUGUSTUS	transcript	12892	14128	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	start_codon	12892	12894	.	+	0	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	CDS	12892	13232	0.8	+	0	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	exon	12892	13232	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	intron	13233	13374	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	CDS	13375	13627	0.76	+	1	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	exon	13375	13627	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	intron	13628	13727	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	CDS	13728	13868	0.98	+	0	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	exon	13728	13868	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	intron	13869	14014	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	CDS	14015	14128	0.96	+	0	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	exon	14015	14128	.	+	.	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
Phchi.C289	AUGUSTUS	stop_codon	14129	14131	.	+	0	transcript_id "Phchi.C289G000100.t1"; gene_id "Phchi.C289G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6911.t1 is derived from g4083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25967432	25969629	.	+	.	Phchi.S1G407000
Phchi.S1	AUGUSTUS	transcript	25967432	25969629	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	start_codon	25967432	25967434	.	+	0	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25967432	25967688	0.93	+	0	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25967432	25967688	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25967689	25967779	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25967780	25967985	1	+	1	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25967780	25967985	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25967986	25968125	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25968126	25968456	1	+	2	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25968126	25968456	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25968457	25968558	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25968559	25968769	1	+	1	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25968559	25968769	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25968770	25968929	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25968930	25969037	1	+	0	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25968930	25969037	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25969038	25969123	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25969124	25969279	1	+	0	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25969124	25969279	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25969280	25969364	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25969365	25969443	1	+	0	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25969365	25969443	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	intron	25969444	25969543	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	CDS	25969544	25969629	1	+	2	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	exon	25969544	25969629	.	+	.	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
Phchi.S1	AUGUSTUS	stop_codon	25969630	25969632	.	+	0	transcript_id "Phchi.S1G407000.t1"; gene_id "Phchi.S1G407000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5973.t1 is derived from g3144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20175698	20180244	.	-	.	Phchi.S1G313200
Phchi.S1	AUGUSTUS	transcript	20175698	20180244	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	stop_codon	20175695	20175697	.	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20175698	20175740	1	-	1	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20175698	20175740	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20175741	20176834	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20176835	20176958	1	-	2	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20176835	20176958	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20176959	20177325	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20177326	20177429	1	-	1	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20177326	20177429	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20177430	20177520	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20177521	20177681	1	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20177521	20177681	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20177682	20177831	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20177832	20177961	1	-	1	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20177832	20177961	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20177962	20178082	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20178083	20178258	1	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20178083	20178258	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20178259	20178407	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20178408	20178603	1	-	1	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20178408	20178603	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20178604	20178681	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20178682	20178695	1	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20178682	20178695	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20178696	20178766	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20178767	20178832	0.96	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20178767	20178832	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20178833	20179093	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20179094	20179195	1	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20179094	20179195	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20179196	20179341	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20179342	20179410	1	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20179342	20179410	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	intron	20179411	20179605	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	CDS	20179606	20180244	0.71	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	exon	20179606	20180244	.	-	.	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
Phchi.S1	AUGUSTUS	start_codon	20180242	20180244	.	-	0	transcript_id "Phchi.S1G313200.t1"; gene_id "Phchi.S1G313200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8660.t1 is derived from g5835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37312693	37315135	.	-	.	Phchi.S1G581900
Phchi.S1	AUGUSTUS	transcript	37312693	37315135	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	stop_codon	37312690	37312692	.	-	0	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	CDS	37312693	37312827	0.93	-	0	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	exon	37312693	37312827	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	intron	37312828	37312930	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	CDS	37312931	37312985	0.97	-	1	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	exon	37312931	37312985	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	intron	37312986	37313108	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	CDS	37313109	37313205	1	-	2	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	exon	37313109	37313205	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	intron	37313206	37313336	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	CDS	37313337	37314058	0.42	-	1	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	exon	37313337	37314058	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	intron	37314059	37314165	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	CDS	37314166	37314724	0.4	-	2	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	exon	37314166	37314724	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	intron	37314725	37314840	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	CDS	37314841	37315135	0.77	-	0	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	exon	37314841	37315135	.	-	.	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
Phchi.S1	AUGUSTUS	start_codon	37315133	37315135	.	-	0	transcript_id "Phchi.S1G581900.t1"; gene_id "Phchi.S1G581900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6155.t1 is derived from g3326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21223545	21225264	.	-	.	Phchi.S1G331400
Phchi.S1	AUGUSTUS	transcript	21223545	21225264	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	stop_codon	21223542	21223544	.	-	0	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	CDS	21223545	21223693	0.99	-	2	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	exon	21223545	21223693	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	intron	21223694	21223834	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	CDS	21223835	21223864	0.96	-	2	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	exon	21223835	21223864	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	intron	21223865	21223968	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	CDS	21223969	21224239	0.97	-	0	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	exon	21223969	21224239	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	intron	21224240	21224328	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	CDS	21224329	21225264	0.36	-	0	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	exon	21224329	21225264	.	-	.	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
Phchi.S1	AUGUSTUS	start_codon	21225262	21225264	.	-	0	transcript_id "Phchi.S1G331400.t1"; gene_id "Phchi.S1G331400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4492.t1 is derived from g1662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10789648	10792321	.	-	.	Phchi.S1G165100
Phchi.S1	AUGUSTUS	transcript	10789648	10792321	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	stop_codon	10789645	10789647	.	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10789648	10789704	1	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10789648	10789704	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10789705	10789791	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10789792	10789859	1	-	2	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10789792	10789859	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10789860	10789947	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10789948	10790049	1	-	2	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10789948	10790049	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10790050	10790134	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10790135	10790262	1	-	1	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10790135	10790262	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10790263	10790347	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10790348	10790439	0.98	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10790348	10790439	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10790440	10790549	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10790550	10790621	1	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10790550	10790621	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10790622	10790718	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10790719	10790787	1	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10790719	10790787	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10790788	10790883	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10790884	10790967	1	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10790884	10790967	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10790968	10791140	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10791141	10791253	1	-	2	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10791141	10791253	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10791254	10791412	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10791413	10791526	1	-	2	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10791413	10791526	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10791527	10791622	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10791623	10791749	0.82	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10791623	10791749	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10791750	10791851	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10791852	10791958	0.82	-	2	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10791852	10791958	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10791959	10792047	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10792048	10792177	1	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10792048	10792177	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	intron	10792178	10792255	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	CDS	10792256	10792321	0.85	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	exon	10792256	10792321	.	-	.	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
Phchi.S1	AUGUSTUS	start_codon	10792319	10792321	.	-	0	transcript_id "Phchi.S1G165100.t1"; gene_id "Phchi.S1G165100"
# This transcript jg2008.t2 is derived from g8928.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2008.t3 is derived from g8928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2009.t1 is derived from g8929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4442639	4444862	.	+	.	Phchi.S5G061800
Phchi.S5	AUGUSTUS	transcript	4442639	4444862	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	start_codon	4442639	4442641	.	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4442639	4442671	0.64	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4442639	4442671	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4442672	4442746	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4442747	4442847	0.96	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4442747	4442847	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4442848	4442933	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4442934	4443049	0.96	+	1	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4442934	4443049	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4443050	4443147	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4443148	4443155	0.88	+	2	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4443148	4443155	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4443156	4443390	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4443391	4443468	0.96	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4443391	4443468	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4443469	4443612	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4443613	4443702	1	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4443613	4443702	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4443703	4443952	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4443953	4444012	1	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4443953	4444012	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4444013	4444153	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4444154	4444237	0.69	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4444154	4444237	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4444238	4444321	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4444322	4444391	0.51	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4444322	4444391	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4444392	4444516	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4444517	4444590	1	+	2	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4444517	4444590	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	intron	4444591	4444745	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	CDS	4444746	4444862	0.97	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	exon	4444746	4444862	.	+	.	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
Phchi.S5	AUGUSTUS	stop_codon	4444863	4444865	.	+	0	transcript_id "Phchi.S5G061800.t1"; gene_id "Phchi.S5G061800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg97.t1 is derived from g9879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	500183	502264	.	+	.	Phchi.S6G005600
Phchi.S6	AUGUSTUS	transcript	500183	502264	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	start_codon	500183	500185	.	+	0	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	500183	500308	0.47	+	0	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	500183	500308	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	500309	500409	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	500410	500564	0.77	+	0	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	500410	500564	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	500565	500735	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	500736	500861	0.99	+	1	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	500736	500861	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	500862	500979	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	500980	501275	0.99	+	1	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	500980	501275	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	501276	501409	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	501410	501590	1	+	2	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	501410	501590	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	501591	501714	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	501715	501963	1	+	1	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	501715	501963	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	501964	502048	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	502049	502109	0.99	+	1	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	502049	502109	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	intron	502110	502216	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	CDS	502217	502264	0.81	+	0	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	exon	502217	502264	.	+	.	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
Phchi.S6	AUGUSTUS	stop_codon	502265	502267	.	+	0	transcript_id "Phchi.S6G005600.t1"; gene_id "Phchi.S6G005600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5332.t1 is derived from g2502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16333484	16336381	.	+	.	Phchi.S1G249100
Phchi.S1	AUGUSTUS	transcript	16333484	16336381	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	start_codon	16333484	16333486	.	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16333484	16333547	0.81	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16333484	16333547	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16333548	16333757	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16333758	16333881	0.89	+	2	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16333758	16333881	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16333882	16334366	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16334367	16334411	0.98	+	1	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16334367	16334411	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16334412	16334519	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16334520	16334658	0.98	+	1	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16334520	16334658	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16334659	16334836	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16334837	16334986	1	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16334837	16334986	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16334987	16335162	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16335163	16335414	1	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16335163	16335414	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16335415	16335497	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16335498	16336037	0.9	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16335498	16336037	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	intron	16336038	16336147	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	CDS	16336148	16336381	0.99	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	exon	16336148	16336381	.	+	.	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
Phchi.S1	AUGUSTUS	stop_codon	16336382	16336384	.	+	0	transcript_id "Phchi.S1G249100.t1"; gene_id "Phchi.S1G249100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1356.t1 is derived from g14423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C23	AUGUSTUS	gene	64633	65214	.	+	.	Phchi.C23G000500
Phchi.C23	AUGUSTUS	transcript	64633	65214	.	+	.	transcript_id "Phchi.C23G000500.t1"; gene_id "Phchi.C23G000500"
Phchi.C23	AUGUSTUS	start_codon	64633	64635	.	+	0	transcript_id "Phchi.C23G000500.t1"; gene_id "Phchi.C23G000500"
Phchi.C23	AUGUSTUS	CDS	64633	65214	0.45	+	0	transcript_id "Phchi.C23G000500.t1"; gene_id "Phchi.C23G000500"
Phchi.C23	AUGUSTUS	exon	64633	65214	.	+	.	transcript_id "Phchi.C23G000500.t1"; gene_id "Phchi.C23G000500"
Phchi.C23	AUGUSTUS	stop_codon	65215	65217	.	+	0	transcript_id "Phchi.C23G000500.t1"; gene_id "Phchi.C23G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3284.t1 is derived from g453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2686823	2691212	.	+	.	Phchi.S1G044300
Phchi.S1	AUGUSTUS	transcript	2686823	2691212	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	start_codon	2686823	2686825	.	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2686823	2686957	0.98	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2686823	2686957	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2686958	2687067	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2687068	2687115	0.99	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2687068	2687115	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2687116	2687197	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2687198	2687323	1	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2687198	2687323	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2687324	2687453	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2687454	2687810	1	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2687454	2687810	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2687811	2687942	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2687943	2688042	1	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2687943	2688042	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2688043	2688152	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2688153	2688198	0.92	+	2	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2688153	2688198	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2688199	2688341	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2688342	2688435	1	+	1	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2688342	2688435	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2688436	2688583	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2688584	2688655	1	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2688584	2688655	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2688656	2688750	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2688751	2688809	1	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2688751	2688809	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2688810	2688885	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2688886	2688954	1	+	1	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2688886	2688954	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2688955	2689060	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2689061	2689112	1	+	1	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2689061	2689112	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2689113	2689239	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2689240	2689298	0.99	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2689240	2689298	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2689299	2689479	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2689480	2689512	0.9	+	1	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2689480	2689512	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2689513	2689773	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2689774	2689894	1	+	1	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2689774	2689894	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2689895	2689972	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2689973	2690020	1	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2689973	2690020	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2690021	2690175	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2690176	2691069	0.56	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2690176	2691069	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	intron	2691070	2691158	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	CDS	2691159	2691212	0.42	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	exon	2691159	2691212	.	+	.	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
Phchi.S1	AUGUSTUS	stop_codon	2691213	2691215	.	+	0	transcript_id "Phchi.S1G044300.t1"; gene_id "Phchi.S1G044300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1392.t1 is derived from g8311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9797	11816	.	+	.	Phchi.S5G000100
Phchi.S5	AUGUSTUS	transcript	9797	11816	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	start_codon	9797	9799	.	+	0	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	CDS	9797	10822	0.99	+	0	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	exon	9797	10822	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	intron	10823	10885	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	CDS	10886	10990	0.99	+	0	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	exon	10886	10990	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	intron	10991	11079	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	CDS	11080	11207	1	+	0	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	exon	11080	11207	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	intron	11208	11287	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	CDS	11288	11435	1	+	1	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	exon	11288	11435	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	intron	11436	11552	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	CDS	11553	11816	0.97	+	0	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	exon	11553	11816	.	+	.	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
Phchi.S5	AUGUSTUS	stop_codon	11817	11819	.	+	0	transcript_id "Phchi.S5G000100.t1"; gene_id "Phchi.S5G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7604.t1 is derived from g4778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30220690	30221673	.	+	.	Phchi.S1G476300
Phchi.S1	AUGUSTUS	transcript	30220690	30221673	.	+	.	transcript_id "Phchi.S1G476300.t1"; gene_id "Phchi.S1G476300"
Phchi.S1	AUGUSTUS	start_codon	30220690	30220692	.	+	0	transcript_id "Phchi.S1G476300.t1"; gene_id "Phchi.S1G476300"
Phchi.S1	AUGUSTUS	CDS	30220690	30221673	0.99	+	0	transcript_id "Phchi.S1G476300.t1"; gene_id "Phchi.S1G476300"
Phchi.S1	AUGUSTUS	exon	30220690	30221673	.	+	.	transcript_id "Phchi.S1G476300.t1"; gene_id "Phchi.S1G476300"
Phchi.S1	AUGUSTUS	stop_codon	30221674	30221676	.	+	0	transcript_id "Phchi.S1G476300.t1"; gene_id "Phchi.S1G476300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11540.t1 is derived from g15590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6967263	6968338	.	+	.	Phchi.S4G112200
Phchi.S4	AUGUSTUS	transcript	6967263	6968338	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	start_codon	6967263	6967265	.	+	0	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	CDS	6967263	6967380	1	+	0	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	exon	6967263	6967380	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	intron	6967381	6967522	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	CDS	6967523	6967557	0.89	+	2	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	exon	6967523	6967557	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	intron	6967558	6967775	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	CDS	6967776	6967848	0.89	+	0	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	exon	6967776	6967848	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	intron	6967849	6967934	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	CDS	6967935	6967994	1	+	2	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	exon	6967935	6967994	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	intron	6967995	6968136	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	CDS	6968137	6968148	0.64	+	2	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	exon	6968137	6968148	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	intron	6968149	6968291	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	CDS	6968292	6968338	0.62	+	2	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	exon	6968292	6968338	.	+	.	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
Phchi.S4	AUGUSTUS	stop_codon	6968339	6968341	.	+	0	transcript_id "Phchi.S4G112200.t1"; gene_id "Phchi.S4G112200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12012.t1 is derived from g7687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	518262	518883	.	+	.	Phchi.S2G009200
Phchi.S2	AUGUSTUS	transcript	518262	518883	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	start_codon	518262	518264	.	+	0	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	CDS	518262	518347	1	+	0	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	exon	518262	518347	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	intron	518348	518435	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	CDS	518436	518535	1	+	1	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	exon	518436	518535	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	intron	518536	518612	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	CDS	518613	518735	1	+	0	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	exon	518613	518735	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	intron	518736	518817	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	CDS	518818	518883	1	+	0	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	exon	518818	518883	.	+	.	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
Phchi.S2	AUGUSTUS	stop_codon	518884	518886	.	+	0	transcript_id "Phchi.S2G009200.t1"; gene_id "Phchi.S2G009200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3157.t1 is derived from g326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2015371	2016427	.	+	.	Phchi.S1G031600
Phchi.S1	AUGUSTUS	transcript	2015371	2016427	.	+	.	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	start_codon	2015371	2015373	.	+	0	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	CDS	2015371	2015638	0.9	+	0	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	exon	2015371	2015638	.	+	.	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	intron	2015639	2015792	.	+	.	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	CDS	2015793	2016427	1	+	2	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	exon	2015793	2016427	.	+	.	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
Phchi.S1	AUGUSTUS	stop_codon	2016428	2016430	.	+	0	transcript_id "Phchi.S1G031600.t1"; gene_id "Phchi.S1G031600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg523.t1 is derived from g10305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3757366	3759521	.	-	.	Phchi.S6G048200
Phchi.S6	AUGUSTUS	transcript	3757366	3759521	.	-	.	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	stop_codon	3757363	3757365	.	-	0	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	CDS	3757366	3758861	0.88	-	2	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	exon	3757366	3758861	.	-	.	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	intron	3758862	3758962	.	-	.	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	CDS	3758963	3759521	0.83	-	0	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	exon	3758963	3759521	.	-	.	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
Phchi.S6	AUGUSTUS	start_codon	3759519	3759521	.	-	0	transcript_id "Phchi.S6G048200.t1"; gene_id "Phchi.S6G048200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5159.t1 is derived from g2329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15195987	15198476	.	+	.	Phchi.S1G231800
Phchi.S1	AUGUSTUS	transcript	15195987	15198476	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	start_codon	15195987	15195989	.	+	0	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15195987	15197164	0.37	+	0	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15195987	15197164	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15197165	15197346	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15197347	15197381	0.91	+	1	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15197347	15197381	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15197382	15197478	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15197479	15197615	0.92	+	2	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15197479	15197615	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15197616	15197696	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15197697	15197759	1	+	0	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15197697	15197759	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15197760	15197838	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15197839	15197912	1	+	0	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15197839	15197912	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15197913	15198012	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15198013	15198064	0.92	+	1	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15198013	15198064	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15198065	15198193	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15198194	15198233	0.59	+	0	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15198194	15198233	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15198234	15198315	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15198316	15198388	0.63	+	2	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15198316	15198388	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	intron	15198389	15198475	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	CDS	15198476	15198476	0.63	+	1	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	exon	15198476	15198476	.	+	.	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
Phchi.S1	AUGUSTUS	stop_codon	15198477	15198479	.	+	0	transcript_id "Phchi.S1G231800.t1"; gene_id "Phchi.S1G231800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6496.t1 is derived from g3668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23320896	23322331	.	+	.	Phchi.S1G365500
Phchi.S1	AUGUSTUS	transcript	23320896	23322331	.	+	.	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	start_codon	23320896	23320898	.	+	0	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	CDS	23320896	23320969	0.72	+	0	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	exon	23320896	23320969	.	+	.	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	intron	23320970	23321061	.	+	.	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	CDS	23321062	23322331	0.72	+	1	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	exon	23321062	23322331	.	+	.	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
Phchi.S1	AUGUSTUS	stop_codon	23322332	23322334	.	+	0	transcript_id "Phchi.S1G365500.t1"; gene_id "Phchi.S1G365500"
# This transcript jg2633.t2 is derived from g9553.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2634.t1 is derived from g9554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7888118	7892286	.	-	.	Phchi.S5G124300
Phchi.S5	AUGUSTUS	transcript	7888118	7892286	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	stop_codon	7888115	7888117	.	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7888118	7888693	0.99	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7888118	7888693	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7888694	7888809	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7888810	7889282	0.58	-	2	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7888810	7889282	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7889283	7889398	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7889399	7889683	0.99	-	2	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7889399	7889683	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7889684	7889757	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7889758	7889989	1	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7889758	7889989	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7889990	7890079	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7890080	7890571	0.9	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7890080	7890571	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7890572	7890675	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7890676	7890816	0.88	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7890676	7890816	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7890817	7890925	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7890926	7891947	0.88	-	2	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7890926	7891947	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	intron	7891948	7892078	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	CDS	7892079	7892286	0.74	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	exon	7892079	7892286	.	-	.	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
Phchi.S5	AUGUSTUS	start_codon	7892284	7892286	.	-	0	transcript_id "Phchi.S5G124300.t1"; gene_id "Phchi.S5G124300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8605.t1 is derived from g5780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36865513	36872230	.	+	.	Phchi.S1G576400
Phchi.S1	AUGUSTUS	transcript	36865513	36872230	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	start_codon	36865513	36865515	.	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36865513	36865731	1	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36865513	36865731	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	intron	36865732	36866139	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36866140	36867264	0.98	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36866140	36867264	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	intron	36867265	36867367	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36867368	36867465	1	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36867368	36867465	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	intron	36867466	36867557	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36867558	36867732	0.99	+	1	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36867558	36867732	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	intron	36867733	36867840	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36867841	36870045	0.95	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36867841	36870045	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	intron	36870046	36870160	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36870161	36871227	0.98	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36870161	36871227	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	intron	36871228	36871374	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	CDS	36871375	36872230	0.85	+	1	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	exon	36871375	36872230	.	+	.	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
Phchi.S1	AUGUSTUS	stop_codon	36872231	36872233	.	+	0	transcript_id "Phchi.S1G576400.t1"; gene_id "Phchi.S1G576400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14167.t1 is derived from g12634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11244840	11248177	.	+	.	Phchi.S3G148600
Phchi.S3	AUGUSTUS	transcript	11244840	11248177	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	start_codon	11244840	11244842	.	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11244840	11245025	0.62	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11244840	11245025	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11245026	11245143	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11245144	11245239	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11245144	11245239	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11245240	11245393	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11245394	11245514	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11245394	11245514	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11245515	11245597	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11245598	11245704	1	+	2	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11245598	11245704	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11245705	11245787	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11245788	11246005	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11245788	11246005	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11246006	11246112	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11246113	11246290	1	+	1	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11246113	11246290	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11246291	11246414	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11246415	11246534	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11246415	11246534	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11246535	11246817	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11246818	11246904	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11246818	11246904	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11246905	11247045	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11247046	11247174	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11247046	11247174	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	intron	11247175	11247268	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	CDS	11247269	11248177	1	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	exon	11247269	11248177	.	+	.	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
Phchi.S3	AUGUSTUS	stop_codon	11248178	11248180	.	+	0	transcript_id "Phchi.S3G148600.t1"; gene_id "Phchi.S3G148600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4882.t1 is derived from g2052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13203326	13204458	.	+	.	Phchi.S1G204100
Phchi.S1	AUGUSTUS	transcript	13203326	13204458	.	+	.	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	start_codon	13203326	13203328	.	+	0	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	CDS	13203326	13203895	0.67	+	0	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	exon	13203326	13203895	.	+	.	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	intron	13203896	13203981	.	+	.	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	CDS	13203982	13204458	1	+	0	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	exon	13203982	13204458	.	+	.	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
Phchi.S1	AUGUSTUS	stop_codon	13204459	13204461	.	+	0	transcript_id "Phchi.S1G204100.t1"; gene_id "Phchi.S1G204100"
# This transcript jg504.t2 is derived from g10286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg505.t1 is derived from g10287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3504405	3504861	.	+	.	Phchi.S6G046400
Phchi.S6	AUGUSTUS	transcript	3504405	3504861	.	+	.	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	start_codon	3504405	3504407	.	+	0	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	CDS	3504405	3504551	0.97	+	0	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	exon	3504405	3504551	.	+	.	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	intron	3504552	3504690	.	+	.	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	CDS	3504691	3504861	1	+	0	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	exon	3504691	3504861	.	+	.	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
Phchi.S6	AUGUSTUS	stop_codon	3504862	3504864	.	+	0	transcript_id "Phchi.S6G046400.t1"; gene_id "Phchi.S6G046400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6394.t1 is derived from g3566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22717302	22723983	.	-	.	Phchi.S1G355300
Phchi.S1	AUGUSTUS	transcript	22717302	22723983	.	-	.	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	stop_codon	22717299	22717301	.	-	0	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	CDS	22717302	22722978	0.54	-	1	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	exon	22717302	22722978	.	-	.	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	intron	22722979	22723054	.	-	.	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	CDS	22723055	22723983	0.43	-	0	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	exon	22723055	22723983	.	-	.	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
Phchi.S1	AUGUSTUS	start_codon	22723981	22723983	.	-	0	transcript_id "Phchi.S1G355300.t1"; gene_id "Phchi.S1G355300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10230.t1 is derived from g7406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46492008	46495727	.	-	.	Phchi.S1G738900
Phchi.S1	AUGUSTUS	transcript	46492008	46495727	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	stop_codon	46492005	46492007	.	-	0	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	CDS	46492008	46492041	0.34	-	1	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	exon	46492008	46492041	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	intron	46492042	46492133	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	CDS	46492134	46492937	0.17	-	1	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	exon	46492134	46492937	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	intron	46492938	46493141	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	CDS	46493142	46494606	0.23	-	2	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	exon	46493142	46494606	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	intron	46494607	46494712	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	CDS	46494713	46494890	0.58	-	0	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	exon	46494713	46494890	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	intron	46494891	46495193	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	CDS	46495194	46495294	0.83	-	2	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	exon	46495194	46495294	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	intron	46495295	46495486	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	CDS	46495487	46495727	0.84	-	0	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	exon	46495487	46495727	.	-	.	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
Phchi.S1	AUGUSTUS	start_codon	46495725	46495727	.	-	0	transcript_id "Phchi.S1G738900.t1"; gene_id "Phchi.S1G738900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg107.t1 is derived from g9889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	569607	571825	.	+	.	Phchi.S6G006600
Phchi.S6	AUGUSTUS	transcript	569607	571825	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	start_codon	569607	569609	.	+	0	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	569607	569702	0.18	+	0	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	569607	569702	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	intron	569703	569817	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	569818	570091	1	+	0	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	569818	570091	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	intron	570092	570177	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	570178	570355	1	+	2	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	570178	570355	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	intron	570356	570450	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	570451	570748	1	+	1	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	570451	570748	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	intron	570749	570880	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	570881	571201	1	+	0	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	570881	571201	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	intron	571202	571282	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	571283	571448	1	+	0	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	571283	571448	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	intron	571449	571535	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	CDS	571536	571825	0.89	+	2	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	exon	571536	571825	.	+	.	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
Phchi.S6	AUGUSTUS	stop_codon	571826	571828	.	+	0	transcript_id "Phchi.S6G006600.t1"; gene_id "Phchi.S6G006600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9406.t1 is derived from g6582.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41354496	41355412	.	-	.	Phchi.S1G656500
Phchi.S1	AUGUSTUS	transcript	41354496	41355412	.	-	.	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	stop_codon	41354493	41354495	.	-	0	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41354496	41354813	0.56	-	0	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41354496	41354813	.	-	.	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	intron	41354814	41354948	.	-	.	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41354949	41355028	1	-	2	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41354949	41355028	.	-	.	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	intron	41355029	41355363	.	-	.	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41355364	41355412	1	-	0	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41355364	41355412	.	-	.	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	start_codon	41355410	41355412	.	-	0	transcript_id "Phchi.S1G656500.t1"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	transcript	41354496	41355412	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	stop_codon	41354493	41354495	.	-	0	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41354496	41354608	0.57	-	2	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41354496	41354608	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	intron	41354609	41354724	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41354725	41354773	0.74	-	0	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41354725	41354773	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	intron	41354774	41354948	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41354949	41355028	1	-	2	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41354949	41355028	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	intron	41355029	41355363	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	CDS	41355364	41355412	1	-	0	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	exon	41355364	41355412	.	-	.	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
Phchi.S1	AUGUSTUS	start_codon	41355410	41355412	.	-	0	transcript_id "Phchi.S1G656500.t2"; gene_id "Phchi.S1G656500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6383.t1 is derived from g3555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22656887	22659013	.	+	.	Phchi.S1G354200
Phchi.S1	AUGUSTUS	transcript	22656887	22659013	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	start_codon	22656887	22656889	.	+	0	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	CDS	22656887	22657144	0.7	+	0	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	exon	22656887	22657144	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	intron	22657145	22657437	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	CDS	22657438	22657445	0.81	+	0	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	exon	22657438	22657445	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	intron	22657446	22657531	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	CDS	22657532	22657634	0.81	+	1	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	exon	22657532	22657634	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	intron	22657635	22657727	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	CDS	22657728	22658045	1	+	0	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	exon	22657728	22658045	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	intron	22658046	22658129	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	CDS	22658130	22658175	0.98	+	0	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	exon	22658130	22658175	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	intron	22658176	22658291	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	CDS	22658292	22659013	0.61	+	2	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	exon	22658292	22659013	.	+	.	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
Phchi.S1	AUGUSTUS	stop_codon	22659014	22659016	.	+	0	transcript_id "Phchi.S1G354200.t1"; gene_id "Phchi.S1G354200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14608.t1 is derived from g13076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13735455	13738844	.	-	.	Phchi.S3G192700
Phchi.S3	AUGUSTUS	transcript	13735455	13738844	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	stop_codon	13735452	13735454	.	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13735455	13735505	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13735455	13735505	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13735506	13735597	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13735598	13735652	1	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13735598	13735652	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13735653	13735750	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13735751	13735876	1	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13735751	13735876	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13735877	13735975	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13735976	13736042	1	-	2	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13735976	13736042	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13736043	13736133	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13736134	13736205	1	-	2	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13736134	13736205	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13736206	13736325	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13736326	13736422	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13736326	13736422	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13736423	13736494	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13736495	13736591	1	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13736495	13736591	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13736592	13736675	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13736676	13736759	0.92	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13736676	13736759	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13736760	13737052	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13737053	13737091	1	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13737053	13737091	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13737092	13737239	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13737240	13737277	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13737240	13737277	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13737278	13737521	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13737522	13737612	1	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13737522	13737612	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13737613	13737706	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13737707	13737799	1	-	1	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13737707	13737799	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13737800	13737936	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13737937	13737998	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13737937	13737998	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13737999	13738086	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13738087	13738143	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13738087	13738143	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13738144	13738281	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13738282	13738371	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13738282	13738371	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13738372	13738489	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13738490	13738612	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13738490	13738612	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	intron	13738613	13738685	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	CDS	13738686	13738844	1	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	exon	13738686	13738844	.	-	.	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
Phchi.S3	AUGUSTUS	start_codon	13738842	13738844	.	-	0	transcript_id "Phchi.S3G192700.t1"; gene_id "Phchi.S3G192700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11992.t1 is derived from g7667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	426071	427473	.	-	.	Phchi.S2G007200
Phchi.S2	AUGUSTUS	transcript	426071	427473	.	-	.	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	stop_codon	426068	426070	.	-	0	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	CDS	426071	427070	0.81	-	1	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	exon	426071	427070	.	-	.	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	intron	427071	427153	.	-	.	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	CDS	427154	427473	0.48	-	0	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	exon	427154	427473	.	-	.	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
Phchi.S2	AUGUSTUS	start_codon	427471	427473	.	-	0	transcript_id "Phchi.S2G007200.t1"; gene_id "Phchi.S2G007200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3236.t1 is derived from g405.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2393195	2395137	.	-	.	Phchi.S1G039500
Phchi.S1	AUGUSTUS	transcript	2393195	2395137	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	stop_codon	2393192	2393194	.	-	0	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2393195	2393339	1	-	1	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2393195	2393339	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2393340	2393442	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2393443	2393777	1	-	0	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2393443	2393777	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2393778	2393865	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2393866	2394199	1	-	1	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2393866	2394199	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2394200	2394391	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2394392	2394429	1	-	0	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2394392	2394429	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2394430	2394520	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2394521	2394573	1	-	2	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2394521	2394573	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2394574	2394650	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2394651	2395137	0.93	-	0	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2394651	2395137	.	-	.	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	start_codon	2395135	2395137	.	-	0	transcript_id "Phchi.S1G039500.t1"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	transcript	2393195	2395137	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	stop_codon	2393192	2393194	.	-	0	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2393195	2393339	0.99	-	1	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2393195	2393339	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2393340	2393442	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2393443	2393777	1	-	0	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2393443	2393777	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2393778	2393865	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2393866	2394205	1	-	1	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2393866	2394205	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2394206	2394391	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2394392	2394429	1	-	0	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2394392	2394429	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2394430	2394520	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2394521	2394573	1	-	2	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2394521	2394573	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	intron	2394574	2394650	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	CDS	2394651	2395137	0.93	-	0	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	exon	2394651	2395137	.	-	.	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
Phchi.S1	AUGUSTUS	start_codon	2395135	2395137	.	-	0	transcript_id "Phchi.S1G039500.t2"; gene_id "Phchi.S1G039500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5162.t1 is derived from g2332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15225439	15228908	.	+	.	Phchi.S1G232100
Phchi.S1	AUGUSTUS	transcript	15225439	15228908	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	start_codon	15225439	15225441	.	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15225439	15225542	0.56	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15225439	15225542	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15225543	15225844	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15225845	15225874	0.57	+	1	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15225845	15225874	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15225875	15226008	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15226009	15226189	1	+	1	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15226009	15226189	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15226190	15226264	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15226265	15226393	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15226265	15226393	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15226394	15226477	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15226478	15226537	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15226478	15226537	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15226538	15226617	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15226618	15226731	0.99	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15226618	15226731	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15226732	15226836	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15226837	15226924	0.97	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15226837	15226924	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15226925	15227042	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15227043	15227185	0.92	+	2	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15227043	15227185	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15227186	15227308	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15227309	15227410	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15227309	15227410	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15227411	15227544	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15227545	15227616	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15227545	15227616	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15227617	15227708	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15227709	15227808	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15227709	15227808	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15227809	15227904	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15227905	15227987	1	+	2	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15227905	15227987	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15227988	15228068	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15228069	15228146	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15228069	15228146	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15228147	15228243	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15228244	15228342	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15228244	15228342	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15228343	15228444	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15228445	15228495	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15228445	15228495	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15228496	15228589	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15228590	15228646	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15228590	15228646	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15228647	15228731	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15228732	15228773	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15228732	15228773	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	intron	15228774	15228851	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	CDS	15228852	15228908	1	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	exon	15228852	15228908	.	+	.	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
Phchi.S1	AUGUSTUS	stop_codon	15228909	15228911	.	+	0	transcript_id "Phchi.S1G232100.t1"; gene_id "Phchi.S1G232100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7197.t1 is derived from g4369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27601714	27603571	.	+	.	Phchi.S1G435600
Phchi.S1	AUGUSTUS	transcript	27601714	27603571	.	+	.	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	start_codon	27601714	27601716	.	+	0	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	CDS	27601714	27603105	0.92	+	0	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	exon	27601714	27603105	.	+	.	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	intron	27603106	27603187	.	+	.	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	CDS	27603188	27603571	0.99	+	0	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	exon	27603188	27603571	.	+	.	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
Phchi.S1	AUGUSTUS	stop_codon	27603572	27603574	.	+	0	transcript_id "Phchi.S1G435600.t1"; gene_id "Phchi.S1G435600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg833.t1 is derived from g10615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5789256	5791263	.	+	.	Phchi.S6G079200
Phchi.S6	AUGUSTUS	transcript	5789256	5791263	.	+	.	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	start_codon	5789256	5789258	.	+	0	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	CDS	5789256	5790665	0.91	+	0	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	exon	5789256	5790665	.	+	.	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	intron	5790666	5790825	.	+	.	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	CDS	5790826	5791263	0.92	+	0	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	exon	5790826	5791263	.	+	.	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
Phchi.S6	AUGUSTUS	stop_codon	5791264	5791266	.	+	0	transcript_id "Phchi.S6G079200.t1"; gene_id "Phchi.S6G079200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12223.t1 is derived from g7899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6827793	6829449	.	+	.	Phchi.S2G030300
Phchi.S2	AUGUSTUS	transcript	6827793	6829449	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	start_codon	6827793	6827795	.	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6827793	6828143	1	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6827793	6828143	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6828144	6828241	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6828242	6828287	1	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6828242	6828287	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6828288	6828366	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6828367	6828453	1	+	2	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6828367	6828453	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6828454	6828545	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6828546	6828670	1	+	2	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6828546	6828670	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6828671	6828770	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6828771	6828910	0.57	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6828771	6828910	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6828911	6829017	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6829018	6829069	0.99	+	1	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6829018	6829069	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6829070	6829163	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6829164	6829274	1	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6829164	6829274	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	intron	6829275	6829359	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	CDS	6829360	6829449	1	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	exon	6829360	6829449	.	+	.	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
Phchi.S2	AUGUSTUS	stop_codon	6829450	6829452	.	+	0	transcript_id "Phchi.S2G030300.t1"; gene_id "Phchi.S2G030300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg484.t1 is derived from g10266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3380586	3381039	.	+	.	Phchi.S6G044300
Phchi.S6	AUGUSTUS	transcript	3380586	3381039	.	+	.	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	start_codon	3380586	3380588	.	+	0	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	CDS	3380586	3380627	0.96	+	0	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	exon	3380586	3380627	.	+	.	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	intron	3380628	3380802	.	+	.	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	CDS	3380803	3381039	0.88	+	0	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	exon	3380803	3381039	.	+	.	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
Phchi.S6	AUGUSTUS	stop_codon	3381040	3381042	.	+	0	transcript_id "Phchi.S6G044300.t1"; gene_id "Phchi.S6G044300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8003.t1 is derived from g5178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32392263	32395766	.	+	.	Phchi.S1G516200
Phchi.S1	AUGUSTUS	transcript	32392263	32395766	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	start_codon	32392263	32392265	.	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32392263	32392487	0.71	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32392263	32392487	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32392488	32392591	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32392592	32392668	1	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32392592	32392668	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32392669	32393074	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32393075	32393324	1	+	1	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32393075	32393324	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32393325	32393418	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32393419	32393976	1	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32393419	32393976	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32393977	32394049	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32394050	32394223	1	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32394050	32394223	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32394224	32394389	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32394390	32394716	1	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32394390	32394716	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32394717	32394803	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32394804	32395004	0.99	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32394804	32395004	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	intron	32395005	32395094	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	CDS	32395095	32395766	1	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	exon	32395095	32395766	.	+	.	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
Phchi.S1	AUGUSTUS	stop_codon	32395767	32395769	.	+	0	transcript_id "Phchi.S1G516200.t1"; gene_id "Phchi.S1G516200"
# This transcript jg11367.t2 is derived from g15417.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11368.t1 is derived from g15418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5871247	5871582	.	-	.	Phchi.S4G095000
Phchi.S4	AUGUSTUS	transcript	5871247	5871582	.	-	.	transcript_id "Phchi.S4G095000.t1"; gene_id "Phchi.S4G095000"
Phchi.S4	AUGUSTUS	stop_codon	5871244	5871246	.	-	0	transcript_id "Phchi.S4G095000.t1"; gene_id "Phchi.S4G095000"
Phchi.S4	AUGUSTUS	CDS	5871247	5871582	1	-	0	transcript_id "Phchi.S4G095000.t1"; gene_id "Phchi.S4G095000"
Phchi.S4	AUGUSTUS	exon	5871247	5871582	.	-	.	transcript_id "Phchi.S4G095000.t1"; gene_id "Phchi.S4G095000"
Phchi.S4	AUGUSTUS	start_codon	5871580	5871582	.	-	0	transcript_id "Phchi.S4G095000.t1"; gene_id "Phchi.S4G095000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13299.t1 is derived from g11765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5528456	5528827	.	+	.	Phchi.S3G061800
Phchi.S3	AUGUSTUS	transcript	5528456	5528827	.	+	.	transcript_id "Phchi.S3G061800.t1"; gene_id "Phchi.S3G061800"
Phchi.S3	AUGUSTUS	start_codon	5528456	5528458	.	+	0	transcript_id "Phchi.S3G061800.t1"; gene_id "Phchi.S3G061800"
Phchi.S3	AUGUSTUS	CDS	5528456	5528827	0.5	+	0	transcript_id "Phchi.S3G061800.t1"; gene_id "Phchi.S3G061800"
Phchi.S3	AUGUSTUS	exon	5528456	5528827	.	+	.	transcript_id "Phchi.S3G061800.t1"; gene_id "Phchi.S3G061800"
Phchi.S3	AUGUSTUS	stop_codon	5528828	5528830	.	+	0	transcript_id "Phchi.S3G061800.t1"; gene_id "Phchi.S3G061800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12445.t1 is derived from g8122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20867900	20869102	.	-	.	Phchi.S2G052500
Phchi.S2	AUGUSTUS	transcript	20867900	20869102	.	-	.	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	stop_codon	20867897	20867899	.	-	0	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	CDS	20867900	20868863	0.98	-	1	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	exon	20867900	20868863	.	-	.	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	intron	20868864	20868944	.	-	.	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	CDS	20868945	20869102	0.9	-	0	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	exon	20868945	20869102	.	-	.	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
Phchi.S2	AUGUSTUS	start_codon	20869100	20869102	.	-	0	transcript_id "Phchi.S2G052500.t1"; gene_id "Phchi.S2G052500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13063.t1 is derived from g11528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3968747	3970849	.	+	.	Phchi.S3G038200
Phchi.S3	AUGUSTUS	transcript	3968747	3970849	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	start_codon	3968747	3968749	.	+	0	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3968747	3968844	0.99	+	0	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3968747	3968844	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	intron	3968845	3968948	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3968949	3969153	1	+	1	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3968949	3969153	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	intron	3969154	3969246	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3969247	3969447	1	+	0	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3969247	3969447	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	intron	3969448	3969533	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3969534	3969748	1	+	0	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3969534	3969748	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	intron	3969749	3969853	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3969854	3970107	1	+	1	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3969854	3970107	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	intron	3970108	3970188	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3970189	3970241	1	+	2	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3970189	3970241	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	intron	3970242	3970321	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	CDS	3970322	3970849	0.99	+	0	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	exon	3970322	3970849	.	+	.	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
Phchi.S3	AUGUSTUS	stop_codon	3970850	3970852	.	+	0	transcript_id "Phchi.S3G038200.t1"; gene_id "Phchi.S3G038200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3464.t1 is derived from g633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3889309	3889764	.	+	.	Phchi.S1G062300
Phchi.S1	AUGUSTUS	transcript	3889309	3889764	.	+	.	transcript_id "Phchi.S1G062300.t1"; gene_id "Phchi.S1G062300"
Phchi.S1	AUGUSTUS	start_codon	3889309	3889311	.	+	0	transcript_id "Phchi.S1G062300.t1"; gene_id "Phchi.S1G062300"
Phchi.S1	AUGUSTUS	CDS	3889309	3889764	0.99	+	0	transcript_id "Phchi.S1G062300.t1"; gene_id "Phchi.S1G062300"
Phchi.S1	AUGUSTUS	exon	3889309	3889764	.	+	.	transcript_id "Phchi.S1G062300.t1"; gene_id "Phchi.S1G062300"
Phchi.S1	AUGUSTUS	stop_codon	3889765	3889767	.	+	0	transcript_id "Phchi.S1G062300.t1"; gene_id "Phchi.S1G062300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg237.t1 is derived from g10019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1607482	1608405	.	-	.	Phchi.S6G019600
Phchi.S6	AUGUSTUS	transcript	1607482	1608405	.	-	.	transcript_id "Phchi.S6G019600.t1"; gene_id "Phchi.S6G019600"
Phchi.S6	AUGUSTUS	stop_codon	1607479	1607481	.	-	0	transcript_id "Phchi.S6G019600.t1"; gene_id "Phchi.S6G019600"
Phchi.S6	AUGUSTUS	CDS	1607482	1608405	1	-	0	transcript_id "Phchi.S6G019600.t1"; gene_id "Phchi.S6G019600"
Phchi.S6	AUGUSTUS	exon	1607482	1608405	.	-	.	transcript_id "Phchi.S6G019600.t1"; gene_id "Phchi.S6G019600"
Phchi.S6	AUGUSTUS	start_codon	1608403	1608405	.	-	0	transcript_id "Phchi.S6G019600.t1"; gene_id "Phchi.S6G019600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14306.t1 is derived from g12773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12029040	12032750	.	+	.	Phchi.S3G162500
Phchi.S3	AUGUSTUS	transcript	12029040	12032750	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	start_codon	12029040	12029042	.	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12029040	12029199	0.87	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12029040	12029199	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12029200	12029308	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12029309	12029553	0.88	+	2	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12029309	12029553	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12029554	12029628	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12029629	12031095	1	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12029629	12031095	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12031096	12031229	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12031230	12031367	1	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12031230	12031367	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12031368	12031567	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12031568	12031669	1	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12031568	12031669	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12031670	12031766	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12031767	12032318	0.96	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12031767	12032318	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12032319	12032474	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12032475	12032603	1	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12032475	12032603	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	intron	12032604	12032681	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	CDS	12032682	12032750	1	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	exon	12032682	12032750	.	+	.	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
Phchi.S3	AUGUSTUS	stop_codon	12032751	12032753	.	+	0	transcript_id "Phchi.S3G162500.t1"; gene_id "Phchi.S3G162500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4793.t1 is derived from g1963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12828202	12830378	.	-	.	Phchi.S1G195200
Phchi.S1	AUGUSTUS	transcript	12828202	12830378	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	stop_codon	12828199	12828201	.	-	0	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	CDS	12828202	12828268	1	-	1	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	exon	12828202	12828268	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	intron	12828269	12828365	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	CDS	12828366	12828580	1	-	0	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	exon	12828366	12828580	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	intron	12828581	12828661	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	CDS	12828662	12829029	1	-	2	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	exon	12828662	12829029	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	intron	12829030	12829126	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	CDS	12829127	12829411	1	-	2	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	exon	12829127	12829411	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	intron	12829412	12829540	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	CDS	12829541	12829677	1	-	1	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	exon	12829541	12829677	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	intron	12829678	12829806	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	CDS	12829807	12830378	0.97	-	0	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	exon	12829807	12830378	.	-	.	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
Phchi.S1	AUGUSTUS	start_codon	12830376	12830378	.	-	0	transcript_id "Phchi.S1G195200.t1"; gene_id "Phchi.S1G195200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10842.t1 is derived from g14892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2428308	2429555	.	+	.	Phchi.S4G042400
Phchi.S4	AUGUSTUS	transcript	2428308	2429555	.	+	.	transcript_id "Phchi.S4G042400.t1"; gene_id "Phchi.S4G042400"
Phchi.S4	AUGUSTUS	start_codon	2428308	2428310	.	+	0	transcript_id "Phchi.S4G042400.t1"; gene_id "Phchi.S4G042400"
Phchi.S4	AUGUSTUS	CDS	2428308	2429555	0.98	+	0	transcript_id "Phchi.S4G042400.t1"; gene_id "Phchi.S4G042400"
Phchi.S4	AUGUSTUS	exon	2428308	2429555	.	+	.	transcript_id "Phchi.S4G042400.t1"; gene_id "Phchi.S4G042400"
Phchi.S4	AUGUSTUS	stop_codon	2429556	2429558	.	+	0	transcript_id "Phchi.S4G042400.t1"; gene_id "Phchi.S4G042400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg940.t1 is derived from g10722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6542527	6544453	.	+	.	Phchi.S6G089900
Phchi.S6	AUGUSTUS	transcript	6542527	6544453	.	+	.	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	start_codon	6542527	6542529	.	+	0	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	CDS	6542527	6543634	0.9	+	0	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	exon	6542527	6543634	.	+	.	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	intron	6543635	6543859	.	+	.	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	CDS	6543860	6544014	1	+	2	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	exon	6543860	6544014	.	+	.	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	intron	6544015	6544105	.	+	.	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	CDS	6544106	6544453	1	+	0	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	exon	6544106	6544453	.	+	.	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
Phchi.S6	AUGUSTUS	stop_codon	6544454	6544456	.	+	0	transcript_id "Phchi.S6G089900.t1"; gene_id "Phchi.S6G089900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11333.t1 is derived from g15383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5608604	5610649	.	-	.	Phchi.S4G091500
Phchi.S4	AUGUSTUS	transcript	5608604	5610649	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	stop_codon	5608601	5608603	.	-	0	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5608604	5608900	0.97	-	0	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5608604	5608900	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	intron	5608901	5608995	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5608996	5609108	0.96	-	2	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5608996	5609108	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	intron	5609109	5609186	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5609187	5609453	0.97	-	2	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5609187	5609453	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	intron	5609454	5609555	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5609556	5609841	0.97	-	0	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5609556	5609841	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	intron	5609842	5609921	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5609922	5610205	1	-	2	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5609922	5610205	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	intron	5610206	5610280	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5610281	5610466	0.89	-	2	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5610281	5610466	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	intron	5610467	5610582	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	CDS	5610583	5610649	0.92	-	0	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	exon	5610583	5610649	.	-	.	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
Phchi.S4	AUGUSTUS	start_codon	5610647	5610649	.	-	0	transcript_id "Phchi.S4G091500.t1"; gene_id "Phchi.S4G091500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9452.t1 is derived from g6628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41535831	41536490	.	+	.	Phchi.S1G661100
Phchi.S1	AUGUSTUS	transcript	41535831	41536490	.	+	.	transcript_id "Phchi.S1G661100.t1"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	start_codon	41535831	41535833	.	+	0	transcript_id "Phchi.S1G661100.t1"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	CDS	41535831	41536490	1	+	0	transcript_id "Phchi.S1G661100.t1"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	exon	41535831	41536490	.	+	.	transcript_id "Phchi.S1G661100.t1"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	stop_codon	41536491	41536493	.	+	0	transcript_id "Phchi.S1G661100.t1"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	transcript	41536173	41536490	.	+	.	transcript_id "Phchi.S1G661100.t2"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	start_codon	41536173	41536175	.	+	0	transcript_id "Phchi.S1G661100.t2"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	CDS	41536173	41536490	0.38	+	0	transcript_id "Phchi.S1G661100.t2"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	exon	41536173	41536490	.	+	.	transcript_id "Phchi.S1G661100.t2"; gene_id "Phchi.S1G661100"
Phchi.S1	AUGUSTUS	stop_codon	41536491	41536493	.	+	0	transcript_id "Phchi.S1G661100.t2"; gene_id "Phchi.S1G661100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14369.t1 is derived from g12836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12391498	12400397	.	+	.	Phchi.S3G168800
Phchi.S3	AUGUSTUS	transcript	12391498	12400397	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	start_codon	12391498	12391500	.	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12391498	12393104	0.96	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12391498	12393104	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12393105	12393370	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12393371	12393509	0.93	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12393371	12393509	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12393510	12393616	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12393617	12393793	0.98	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12393617	12393793	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12393794	12393885	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12393886	12394107	0.75	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12393886	12394107	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12394108	12394209	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12394210	12394395	0.67	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12394210	12394395	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12394396	12394493	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12394494	12394647	0.91	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12394494	12394647	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12394648	12394773	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12394774	12394858	1	+	2	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12394774	12394858	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12394859	12394951	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12394952	12395151	0.79	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12394952	12395151	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12395152	12395303	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12395304	12395401	0.83	+	2	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12395304	12395401	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12395402	12395576	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12395577	12396025	0.31	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12395577	12396025	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12396026	12396101	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12396102	12396150	0.99	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12396102	12396150	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12396151	12396248	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12396249	12396335	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12396249	12396335	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12396336	12396437	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12396438	12396557	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12396438	12396557	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12396558	12396640	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12396641	12396874	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12396641	12396874	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12396875	12397005	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12397006	12397122	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12397006	12397122	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12397123	12397267	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12397268	12397701	0.78	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12397268	12397701	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12397702	12397785	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12397786	12397878	1	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12397786	12397878	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12397879	12398021	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12398022	12398103	1	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12398022	12398103	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12398104	12398201	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12398202	12398255	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12398202	12398255	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12398256	12398354	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12398355	12398429	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12398355	12398429	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12398430	12398519	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12398520	12398616	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12398520	12398616	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12398617	12398689	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12398690	12398858	1	+	2	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12398690	12398858	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12398859	12398955	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12398956	12399113	0.99	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12398956	12399113	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12399114	12399212	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12399213	12399436	0.82	+	2	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12399213	12399436	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12399437	12399573	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12399574	12399683	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12399574	12399683	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12399684	12399760	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12399761	12399839	1	+	1	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12399761	12399839	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12399840	12399924	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12399925	12400099	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12399925	12400099	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12400100	12400180	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12400181	12400287	1	+	2	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12400181	12400287	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	intron	12400288	12400373	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	CDS	12400374	12400397	1	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	exon	12400374	12400397	.	+	.	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
Phchi.S3	AUGUSTUS	stop_codon	12400398	12400400	.	+	0	transcript_id "Phchi.S3G168800.t1"; gene_id "Phchi.S3G168800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15667.t1 is derived from g14136.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20580884	20581876	.	-	.	Phchi.S3G298600
Phchi.S3	AUGUSTUS	transcript	20580884	20581876	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	stop_codon	20580881	20580883	.	-	0	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20580884	20581021	0.83	-	0	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20580884	20581021	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	intron	20581022	20581121	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20581122	20581385	1	-	0	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20581122	20581385	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	intron	20581386	20581522	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20581523	20581675	1	-	0	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20581523	20581675	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	intron	20581676	20581858	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20581859	20581876	1	-	0	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20581859	20581876	.	-	.	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	start_codon	20581874	20581876	.	-	0	transcript_id "Phchi.S3G298600.t1"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	transcript	20580884	20581876	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	stop_codon	20580881	20580883	.	-	0	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20580884	20581021	0.8	-	0	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20580884	20581021	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	intron	20581022	20581121	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20581122	20581382	1	-	0	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20581122	20581382	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	intron	20581383	20581522	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20581523	20581675	1	-	0	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20581523	20581675	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	intron	20581676	20581858	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	CDS	20581859	20581876	1	-	0	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	exon	20581859	20581876	.	-	.	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
Phchi.S3	AUGUSTUS	start_codon	20581874	20581876	.	-	0	transcript_id "Phchi.S3G298600.t2"; gene_id "Phchi.S3G298600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9272.t1 is derived from g6447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40694679	40695646	.	-	.	Phchi.S1G643100
Phchi.S1	AUGUSTUS	transcript	40694679	40695646	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	stop_codon	40694676	40694678	.	-	0	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	CDS	40694679	40694777	0.96	-	0	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	exon	40694679	40694777	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	intron	40694778	40694932	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	CDS	40694933	40694955	0.5	-	2	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	exon	40694933	40694955	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	intron	40694956	40695232	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	CDS	40695233	40695278	0.71	-	0	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	exon	40695233	40695278	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	intron	40695279	40695369	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	CDS	40695370	40695443	0.55	-	2	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	exon	40695370	40695443	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	intron	40695444	40695525	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	CDS	40695526	40695646	0.47	-	0	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	exon	40695526	40695646	.	-	.	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
Phchi.S1	AUGUSTUS	start_codon	40695644	40695646	.	-	0	transcript_id "Phchi.S1G643100.t1"; gene_id "Phchi.S1G643100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11464.t1 is derived from g15514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6493104	6495408	.	+	.	Phchi.S4G104600
Phchi.S4	AUGUSTUS	transcript	6493104	6495408	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	start_codon	6493104	6493106	.	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6493104	6493118	1	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6493104	6493118	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6493119	6493201	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6493202	6493298	1	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6493202	6493298	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6493299	6493384	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6493385	6493722	1	+	2	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6493385	6493722	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6493723	6493817	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6493818	6494000	0.99	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6493818	6494000	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6494001	6494089	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6494090	6494359	0.99	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6494090	6494359	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6494360	6494439	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6494440	6494703	0.86	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6494440	6494703	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6494704	6494804	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6494805	6494894	0.86	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6494805	6494894	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6494895	6494994	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6494995	6495062	1	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6494995	6495062	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	intron	6495063	6495164	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	CDS	6495165	6495408	0.99	+	1	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	exon	6495165	6495408	.	+	.	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
Phchi.S4	AUGUSTUS	stop_codon	6495409	6495411	.	+	0	transcript_id "Phchi.S4G104600.t1"; gene_id "Phchi.S4G104600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10416.t1 is derived from g7592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47755445	47757286	.	-	.	Phchi.S1G757500
Phchi.S1	AUGUSTUS	transcript	47755445	47757286	.	-	.	transcript_id "Phchi.S1G757500.t1"; gene_id "Phchi.S1G757500"
Phchi.S1	AUGUSTUS	stop_codon	47755442	47755444	.	-	0	transcript_id "Phchi.S1G757500.t1"; gene_id "Phchi.S1G757500"
Phchi.S1	AUGUSTUS	CDS	47755445	47757286	0.34	-	0	transcript_id "Phchi.S1G757500.t1"; gene_id "Phchi.S1G757500"
Phchi.S1	AUGUSTUS	exon	47755445	47757286	.	-	.	transcript_id "Phchi.S1G757500.t1"; gene_id "Phchi.S1G757500"
Phchi.S1	AUGUSTUS	start_codon	47757284	47757286	.	-	0	transcript_id "Phchi.S1G757500.t1"; gene_id "Phchi.S1G757500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8522.t1 is derived from g5697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36420151	36421038	.	-	.	Phchi.S1G568100
Phchi.S1	AUGUSTUS	transcript	36420151	36421038	.	-	.	transcript_id "Phchi.S1G568100.t1"; gene_id "Phchi.S1G568100"
Phchi.S1	AUGUSTUS	stop_codon	36420148	36420150	.	-	0	transcript_id "Phchi.S1G568100.t1"; gene_id "Phchi.S1G568100"
Phchi.S1	AUGUSTUS	CDS	36420151	36421038	0.97	-	0	transcript_id "Phchi.S1G568100.t1"; gene_id "Phchi.S1G568100"
Phchi.S1	AUGUSTUS	exon	36420151	36421038	.	-	.	transcript_id "Phchi.S1G568100.t1"; gene_id "Phchi.S1G568100"
Phchi.S1	AUGUSTUS	start_codon	36421036	36421038	.	-	0	transcript_id "Phchi.S1G568100.t1"; gene_id "Phchi.S1G568100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5812.t1 is derived from g2982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19071434	19072432	.	+	.	Phchi.S1G297100
Phchi.S1	AUGUSTUS	transcript	19071434	19072432	.	+	.	transcript_id "Phchi.S1G297100.t1"; gene_id "Phchi.S1G297100"
Phchi.S1	AUGUSTUS	start_codon	19071434	19071436	.	+	0	transcript_id "Phchi.S1G297100.t1"; gene_id "Phchi.S1G297100"
Phchi.S1	AUGUSTUS	CDS	19071434	19072432	0.69	+	0	transcript_id "Phchi.S1G297100.t1"; gene_id "Phchi.S1G297100"
Phchi.S1	AUGUSTUS	exon	19071434	19072432	.	+	.	transcript_id "Phchi.S1G297100.t1"; gene_id "Phchi.S1G297100"
Phchi.S1	AUGUSTUS	stop_codon	19072433	19072435	.	+	0	transcript_id "Phchi.S1G297100.t1"; gene_id "Phchi.S1G297100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13742.t1 is derived from g12209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8667596	8669231	.	+	.	Phchi.S3G106100
Phchi.S3	AUGUSTUS	transcript	8667596	8669231	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	start_codon	8667596	8667598	.	+	0	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	CDS	8667596	8667872	0.44	+	0	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	exon	8667596	8667872	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	intron	8667873	8668032	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	CDS	8668033	8668202	0.39	+	2	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	exon	8668033	8668202	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	intron	8668203	8668306	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	CDS	8668307	8668555	0.96	+	0	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	exon	8668307	8668555	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	intron	8668556	8668643	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	CDS	8668644	8668908	0.99	+	0	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	exon	8668644	8668908	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	intron	8668909	8669007	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	CDS	8669008	8669231	0.98	+	2	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	exon	8669008	8669231	.	+	.	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
Phchi.S3	AUGUSTUS	stop_codon	8669232	8669234	.	+	0	transcript_id "Phchi.S3G106100.t1"; gene_id "Phchi.S3G106100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1542.t1 is derived from g8461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1683991	1685917	.	+	.	Phchi.S5G015100
Phchi.S5	AUGUSTUS	transcript	1683991	1685917	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	start_codon	1683991	1683993	.	+	0	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	CDS	1683991	1684599	1	+	0	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	exon	1683991	1684599	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	intron	1684600	1684825	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	CDS	1684826	1684901	0.76	+	0	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	exon	1684826	1684901	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	intron	1684902	1685057	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	CDS	1685058	1685311	0.79	+	2	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	exon	1685058	1685311	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	intron	1685312	1685404	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	CDS	1685405	1685917	0.81	+	0	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	exon	1685405	1685917	.	+	.	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
Phchi.S5	AUGUSTUS	stop_codon	1685918	1685920	.	+	0	transcript_id "Phchi.S5G015100.t1"; gene_id "Phchi.S5G015100"
# This transcript jg3444.t2 is derived from g613.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3445.t1 is derived from g614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3757260	3758738	.	-	.	Phchi.S1G060400
Phchi.S1	AUGUSTUS	transcript	3757260	3758738	.	-	.	transcript_id "Phchi.S1G060400.t1"; gene_id "Phchi.S1G060400"
Phchi.S1	AUGUSTUS	stop_codon	3757257	3757259	.	-	0	transcript_id "Phchi.S1G060400.t1"; gene_id "Phchi.S1G060400"
Phchi.S1	AUGUSTUS	CDS	3757260	3758738	0.87	-	0	transcript_id "Phchi.S1G060400.t1"; gene_id "Phchi.S1G060400"
Phchi.S1	AUGUSTUS	exon	3757260	3758738	.	-	.	transcript_id "Phchi.S1G060400.t1"; gene_id "Phchi.S1G060400"
Phchi.S1	AUGUSTUS	start_codon	3758736	3758738	.	-	0	transcript_id "Phchi.S1G060400.t1"; gene_id "Phchi.S1G060400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7702.t1 is derived from g4876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30707249	30708468	.	+	.	Phchi.S1G486100
Phchi.S1	AUGUSTUS	transcript	30707249	30708468	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	start_codon	30707249	30707251	.	+	0	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	CDS	30707249	30707335	0.48	+	0	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	exon	30707249	30707335	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	intron	30707336	30707406	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	CDS	30707407	30707568	1	+	0	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	exon	30707407	30707568	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	intron	30707569	30707663	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	CDS	30707664	30707780	1	+	0	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	exon	30707664	30707780	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	intron	30707781	30707886	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	CDS	30707887	30708468	1	+	0	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	exon	30707887	30708468	.	+	.	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
Phchi.S1	AUGUSTUS	stop_codon	30708469	30708471	.	+	0	transcript_id "Phchi.S1G486100.t1"; gene_id "Phchi.S1G486100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3071.t1 is derived from g240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1435247	1435789	.	-	.	Phchi.S1G023000
Phchi.S1	AUGUSTUS	transcript	1435247	1435789	.	-	.	transcript_id "Phchi.S1G023000.t1"; gene_id "Phchi.S1G023000"
Phchi.S1	AUGUSTUS	stop_codon	1435244	1435246	.	-	0	transcript_id "Phchi.S1G023000.t1"; gene_id "Phchi.S1G023000"
Phchi.S1	AUGUSTUS	CDS	1435247	1435789	0.78	-	0	transcript_id "Phchi.S1G023000.t1"; gene_id "Phchi.S1G023000"
Phchi.S1	AUGUSTUS	exon	1435247	1435789	.	-	.	transcript_id "Phchi.S1G023000.t1"; gene_id "Phchi.S1G023000"
Phchi.S1	AUGUSTUS	start_codon	1435787	1435789	.	-	0	transcript_id "Phchi.S1G023000.t1"; gene_id "Phchi.S1G023000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4399.t1 is derived from g1568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10236558	10237133	.	+	.	Phchi.S1G155800
Phchi.S1	AUGUSTUS	transcript	10236558	10237133	.	+	.	transcript_id "Phchi.S1G155800.t1"; gene_id "Phchi.S1G155800"
Phchi.S1	AUGUSTUS	start_codon	10236558	10236560	.	+	0	transcript_id "Phchi.S1G155800.t1"; gene_id "Phchi.S1G155800"
Phchi.S1	AUGUSTUS	CDS	10236558	10237133	0.87	+	0	transcript_id "Phchi.S1G155800.t1"; gene_id "Phchi.S1G155800"
Phchi.S1	AUGUSTUS	exon	10236558	10237133	.	+	.	transcript_id "Phchi.S1G155800.t1"; gene_id "Phchi.S1G155800"
Phchi.S1	AUGUSTUS	stop_codon	10237134	10237136	.	+	0	transcript_id "Phchi.S1G155800.t1"; gene_id "Phchi.S1G155800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3531.t1 is derived from g700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4240708	4242634	.	-	.	Phchi.S1G069000
Phchi.S1	AUGUSTUS	transcript	4240708	4242634	.	-	.	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	stop_codon	4240705	4240707	.	-	0	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	CDS	4240708	4242215	0.91	-	2	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	exon	4240708	4242215	.	-	.	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	intron	4242216	4242411	.	-	.	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	CDS	4242412	4242634	0.86	-	0	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	exon	4242412	4242634	.	-	.	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	start_codon	4242632	4242634	.	-	0	transcript_id "Phchi.S1G069000.t1"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	transcript	4242238	4242634	.	-	.	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	stop_codon	4242235	4242237	.	-	0	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	CDS	4242238	4242251	0.41	-	2	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	exon	4242238	4242251	.	-	.	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	intron	4242252	4242411	.	-	.	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	CDS	4242412	4242634	0.4	-	0	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	exon	4242412	4242634	.	-	.	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
Phchi.S1	AUGUSTUS	start_codon	4242632	4242634	.	-	0	transcript_id "Phchi.S1G069000.t2"; gene_id "Phchi.S1G069000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1494.t1 is derived from g8413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1194674	1196564	.	-	.	Phchi.S5G010300
Phchi.S5	AUGUSTUS	transcript	1194674	1196564	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	stop_codon	1194671	1194673	.	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1194674	1194740	0.99	-	1	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1194674	1194740	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1194741	1194858	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1194859	1194961	0.99	-	2	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1194859	1194961	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1194962	1195039	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1195040	1195196	0.98	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1195040	1195196	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1195197	1195309	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1195310	1195408	1	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1195310	1195408	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1195409	1195535	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1195536	1195640	1	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1195536	1195640	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1195641	1195768	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1195769	1195882	1	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1195769	1195882	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1195883	1196028	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1196029	1196216	1	-	2	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1196029	1196216	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	intron	1196217	1196296	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	CDS	1196297	1196564	1	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	exon	1196297	1196564	.	-	.	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
Phchi.S5	AUGUSTUS	start_codon	1196562	1196564	.	-	0	transcript_id "Phchi.S5G010300.t1"; gene_id "Phchi.S5G010300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7788.t1 is derived from g4962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31193663	31195376	.	+	.	Phchi.S1G494700
Phchi.S1	AUGUSTUS	transcript	31193663	31195376	.	+	.	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	start_codon	31193663	31193665	.	+	0	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	CDS	31193663	31193875	0.23	+	0	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	exon	31193663	31193875	.	+	.	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	intron	31193876	31194323	.	+	.	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	CDS	31194324	31194594	0.05	+	0	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	exon	31194324	31194594	.	+	.	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	intron	31194595	31195065	.	+	.	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	CDS	31195066	31195376	0.04	+	2	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	exon	31195066	31195376	.	+	.	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
Phchi.S1	AUGUSTUS	stop_codon	31195377	31195379	.	+	0	transcript_id "Phchi.S1G494700.t1"; gene_id "Phchi.S1G494700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1768.t1 is derived from g8688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2933574	2934588	.	+	.	Phchi.S5G037700
Phchi.S5	AUGUSTUS	transcript	2933574	2934588	.	+	.	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	start_codon	2933574	2933576	.	+	0	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	CDS	2933574	2933853	0.94	+	0	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	exon	2933574	2933853	.	+	.	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	intron	2933854	2933977	.	+	.	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	CDS	2933978	2934291	1	+	2	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	exon	2933978	2934291	.	+	.	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	intron	2934292	2934402	.	+	.	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	CDS	2934403	2934588	1	+	0	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	exon	2934403	2934588	.	+	.	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
Phchi.S5	AUGUSTUS	stop_codon	2934589	2934591	.	+	0	transcript_id "Phchi.S5G037700.t1"; gene_id "Phchi.S5G037700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11981.t1 is derived from g7656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	327362	330329	.	-	.	Phchi.S2G006100
Phchi.S2	AUGUSTUS	transcript	327362	330329	.	-	.	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	stop_codon	327359	327361	.	-	0	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	CDS	327362	327546	0.01	-	2	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	exon	327362	327546	.	-	.	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	intron	327547	329260	.	-	.	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	CDS	329261	329381	0.21	-	0	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	exon	329261	329381	.	-	.	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	intron	329382	330251	.	-	.	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	CDS	330252	330329	0.03	-	0	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	exon	330252	330329	.	-	.	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
Phchi.S2	AUGUSTUS	start_codon	330327	330329	.	-	0	transcript_id "Phchi.S2G006100.t1"; gene_id "Phchi.S2G006100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6330.t1 is derived from g3502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22307368	22309927	.	-	.	Phchi.S1G348900
Phchi.S1	AUGUSTUS	transcript	22307368	22309927	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	stop_codon	22307365	22307367	.	-	0	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	CDS	22307368	22308048	0.97	-	0	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	exon	22307368	22308048	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	intron	22308049	22308127	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	CDS	22308128	22308316	1	-	0	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	exon	22308128	22308316	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	intron	22308317	22308433	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	CDS	22308434	22308582	0.88	-	2	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	exon	22308434	22308582	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	intron	22308583	22308699	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	CDS	22308700	22309927	0.88	-	0	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	exon	22308700	22309927	.	-	.	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
Phchi.S1	AUGUSTUS	start_codon	22309925	22309927	.	-	0	transcript_id "Phchi.S1G348900.t1"; gene_id "Phchi.S1G348900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8487.t1 is derived from g5662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36188424	36191056	.	-	.	Phchi.S1G564600
Phchi.S1	AUGUSTUS	transcript	36188424	36191056	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	stop_codon	36188421	36188423	.	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36188424	36188446	0.34	-	2	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36188424	36188446	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36188447	36188665	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36188666	36188729	0.34	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36188666	36188729	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36188730	36188868	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36188869	36189009	0.67	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36188869	36189009	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36189010	36189181	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36189182	36189249	0.48	-	2	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36189182	36189249	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36189250	36189376	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36189377	36189445	1	-	2	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36189377	36189445	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36189446	36189529	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36189530	36189594	1	-	1	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36189530	36189594	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36189595	36189751	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36189752	36189789	1	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36189752	36189789	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36189790	36189954	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36189955	36190062	1	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36189955	36190062	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36190063	36190202	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36190203	36190379	1	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36190203	36190379	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	intron	36190380	36190474	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	CDS	36190475	36191056	1	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	exon	36190475	36191056	.	-	.	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
Phchi.S1	AUGUSTUS	start_codon	36191054	36191056	.	-	0	transcript_id "Phchi.S1G564600.t1"; gene_id "Phchi.S1G564600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12126.t1 is derived from g7802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4008883	4010292	.	-	.	Phchi.S2G020600
Phchi.S2	AUGUSTUS	transcript	4008883	4010292	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	stop_codon	4008880	4008882	.	-	0	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	CDS	4008883	4009201	1	-	1	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	exon	4008883	4009201	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	intron	4009202	4009291	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	CDS	4009292	4009422	1	-	0	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	exon	4009292	4009422	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	intron	4009423	4009501	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	CDS	4009502	4009609	1	-	0	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	exon	4009502	4009609	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	intron	4009610	4009722	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	CDS	4009723	4009894	1	-	1	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	exon	4009723	4009894	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	intron	4009895	4010149	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	CDS	4010150	4010292	1	-	0	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	exon	4010150	4010292	.	-	.	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
Phchi.S2	AUGUSTUS	start_codon	4010290	4010292	.	-	0	transcript_id "Phchi.S2G020600.t1"; gene_id "Phchi.S2G020600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7177.t1 is derived from g4349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27421112	27422677	.	-	.	Phchi.S1G433600
Phchi.S1	AUGUSTUS	transcript	27421112	27422677	.	-	.	transcript_id "Phchi.S1G433600.t1"; gene_id "Phchi.S1G433600"
Phchi.S1	AUGUSTUS	stop_codon	27421109	27421111	.	-	0	transcript_id "Phchi.S1G433600.t1"; gene_id "Phchi.S1G433600"
Phchi.S1	AUGUSTUS	CDS	27421112	27422677	1	-	0	transcript_id "Phchi.S1G433600.t1"; gene_id "Phchi.S1G433600"
Phchi.S1	AUGUSTUS	exon	27421112	27422677	.	-	.	transcript_id "Phchi.S1G433600.t1"; gene_id "Phchi.S1G433600"
Phchi.S1	AUGUSTUS	start_codon	27422675	27422677	.	-	0	transcript_id "Phchi.S1G433600.t1"; gene_id "Phchi.S1G433600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9633.t1 is derived from g6809.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42999882	43001768	.	-	.	Phchi.S1G679200
Phchi.S1	AUGUSTUS	transcript	43000101	43001768	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	stop_codon	43000098	43000100	.	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000101	43000153	0.94	-	2	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000101	43000153	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000154	43000241	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000242	43000342	0.87	-	1	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000242	43000342	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000343	43000490	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000491	43000522	1	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000491	43000522	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000523	43000606	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000607	43000726	1	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000607	43000726	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000727	43000822	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000823	43000960	1	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000823	43000960	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000961	43001099	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001100	43001181	1	-	1	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001100	43001181	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43001182	43001285	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001286	43001398	1	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001286	43001398	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43001399	43001501	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001502	43001584	1	-	2	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001502	43001584	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43001585	43001674	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001675	43001768	0.75	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001675	43001768	.	-	.	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	start_codon	43001766	43001768	.	-	0	transcript_id "Phchi.S1G679200.t1"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	transcript	42999882	43001768	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	stop_codon	42999879	42999881	.	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	42999882	42999902	0.59	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	42999882	42999902	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	42999903	43000006	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000007	43000153	0.61	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000007	43000153	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000154	43000241	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000242	43000312	0.58	-	2	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000242	43000312	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000313	43000526	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000527	43000539	0.79	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000527	43000539	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000540	43000606	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000607	43000726	0.99	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000607	43000726	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000727	43000822	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43000823	43000960	1	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43000823	43000960	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43000961	43001099	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001100	43001181	1	-	1	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001100	43001181	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43001182	43001285	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001286	43001398	0.97	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001286	43001398	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43001399	43001501	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001502	43001584	0.98	-	2	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001502	43001584	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	intron	43001585	43001674	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	CDS	43001675	43001768	0.67	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	exon	43001675	43001768	.	-	.	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
Phchi.S1	AUGUSTUS	start_codon	43001766	43001768	.	-	0	transcript_id "Phchi.S1G679200.t2"; gene_id "Phchi.S1G679200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4040.t1 is derived from g1209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7308430	7309405	.	+	.	Phchi.S1G119900
Phchi.S1	AUGUSTUS	transcript	7308430	7309405	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	start_codon	7308430	7308432	.	+	0	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	CDS	7308430	7308557	0.47	+	0	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	exon	7308430	7308557	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	intron	7308558	7308652	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	CDS	7308653	7308714	0.89	+	1	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	exon	7308653	7308714	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	intron	7308715	7308822	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	CDS	7308823	7308992	0.84	+	2	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	exon	7308823	7308992	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	intron	7308993	7309144	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	CDS	7309145	7309243	0.71	+	0	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	exon	7309145	7309243	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	intron	7309244	7309345	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	CDS	7309346	7309405	0.71	+	0	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	exon	7309346	7309405	.	+	.	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
Phchi.S1	AUGUSTUS	stop_codon	7309406	7309408	.	+	0	transcript_id "Phchi.S1G119900.t1"; gene_id "Phchi.S1G119900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14222.t1 is derived from g12689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11635331	11636770	.	-	.	Phchi.S3G154100
Phchi.S3	AUGUSTUS	transcript	11635331	11636770	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	stop_codon	11635328	11635330	.	-	0	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11635331	11635468	1	-	0	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11635331	11635468	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	intron	11635469	11635562	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11635563	11635622	1	-	0	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11635563	11635622	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	intron	11635623	11635712	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11635713	11635833	1	-	1	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11635713	11635833	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	intron	11635834	11635925	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11635926	11636002	1	-	0	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11635926	11636002	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	intron	11636003	11636214	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11636215	11636300	1	-	2	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11636215	11636300	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	intron	11636301	11636387	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11636388	11636494	1	-	1	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11636388	11636494	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	intron	11636495	11636588	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	CDS	11636589	11636770	0.9	-	0	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	exon	11636589	11636770	.	-	.	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
Phchi.S3	AUGUSTUS	start_codon	11636768	11636770	.	-	0	transcript_id "Phchi.S3G154100.t1"; gene_id "Phchi.S3G154100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14166.t1 is derived from g12633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11235674	11238572	.	+	.	Phchi.S3G148500
Phchi.S3	AUGUSTUS	transcript	11235674	11238572	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	start_codon	11235674	11235676	.	+	0	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	CDS	11235674	11235892	0.39	+	0	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	exon	11235674	11235892	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	intron	11235893	11236002	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	CDS	11236003	11236501	0.28	+	0	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	exon	11236003	11236501	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	intron	11236502	11236938	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	CDS	11236939	11237327	0.32	+	2	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	exon	11236939	11237327	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	intron	11237328	11237528	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	CDS	11237529	11238572	0.29	+	0	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	exon	11237529	11238572	.	+	.	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
Phchi.S3	AUGUSTUS	stop_codon	11238573	11238575	.	+	0	transcript_id "Phchi.S3G148500.t1"; gene_id "Phchi.S3G148500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11280.t1 is derived from g15330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5186911	5188149	.	+	.	Phchi.S4G086200
Phchi.S4	AUGUSTUS	transcript	5186911	5188149	.	+	.	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	start_codon	5186911	5186913	.	+	0	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	CDS	5186911	5187942	0.97	+	0	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	exon	5186911	5187942	.	+	.	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	intron	5187943	5188077	.	+	.	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	CDS	5188078	5188149	1	+	0	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	exon	5188078	5188149	.	+	.	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
Phchi.S4	AUGUSTUS	stop_codon	5188150	5188152	.	+	0	transcript_id "Phchi.S4G086200.t1"; gene_id "Phchi.S4G086200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7630.t1 is derived from g4804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30323913	30324716	.	+	.	Phchi.S1G478900
Phchi.S1	AUGUSTUS	transcript	30323913	30324716	.	+	.	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	start_codon	30323913	30323915	.	+	0	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	CDS	30323913	30324152	0.87	+	0	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	exon	30323913	30324152	.	+	.	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	intron	30324153	30324229	.	+	.	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	CDS	30324230	30324427	0.51	+	0	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	exon	30324230	30324427	.	+	.	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	intron	30324428	30324617	.	+	.	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	CDS	30324618	30324716	0.63	+	0	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	exon	30324618	30324716	.	+	.	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
Phchi.S1	AUGUSTUS	stop_codon	30324717	30324719	.	+	0	transcript_id "Phchi.S1G478900.t1"; gene_id "Phchi.S1G478900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6440.t1 is derived from g3612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23035425	23037339	.	-	.	Phchi.S1G359900
Phchi.S1	AUGUSTUS	transcript	23035425	23037339	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	stop_codon	23035422	23035424	.	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23035425	23035678	0.83	-	2	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23035425	23035678	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	intron	23035679	23036016	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23036017	23036146	0.83	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23036017	23036146	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	intron	23036147	23036267	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23036268	23036369	1	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23036268	23036369	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	intron	23036370	23036449	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23036450	23036581	1	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23036450	23036581	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	intron	23036582	23036706	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23036707	23036841	1	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23036707	23036841	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	intron	23036842	23036938	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23036939	23037055	1	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23036939	23037055	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	intron	23037056	23037207	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	CDS	23037208	23037339	1	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	exon	23037208	23037339	.	-	.	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
Phchi.S1	AUGUSTUS	start_codon	23037337	23037339	.	-	0	transcript_id "Phchi.S1G359900.t1"; gene_id "Phchi.S1G359900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9137.t1 is derived from g6312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40036950	40037460	.	-	.	Phchi.S1G629600
Phchi.S1	AUGUSTUS	transcript	40036950	40037460	.	-	.	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	stop_codon	40036947	40036949	.	-	0	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	CDS	40036950	40036998	0.32	-	1	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	exon	40036950	40036998	.	-	.	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	intron	40036999	40037130	.	-	.	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	CDS	40037131	40037184	0.3	-	1	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	exon	40037131	40037184	.	-	.	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	intron	40037185	40037353	.	-	.	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	CDS	40037354	40037460	0.58	-	0	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	exon	40037354	40037460	.	-	.	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
Phchi.S1	AUGUSTUS	start_codon	40037458	40037460	.	-	0	transcript_id "Phchi.S1G629600.t1"; gene_id "Phchi.S1G629600"
# This transcript jg8446.t2 is derived from g5621.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8446.t3 is derived from g5621.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8447.t1 is derived from g5622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35979342	35980446	.	+	.	Phchi.S1G560600
Phchi.S1	AUGUSTUS	transcript	35979342	35980446	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	start_codon	35979342	35979344	.	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35979342	35979452	0.75	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35979342	35979452	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	intron	35979453	35979535	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35979536	35979619	1	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35979536	35979619	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	intron	35979620	35979707	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35979708	35979754	1	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35979708	35979754	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	intron	35979755	35979825	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35979826	35979863	1	+	1	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35979826	35979863	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	intron	35979864	35979937	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35979938	35979993	1	+	2	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35979938	35979993	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	intron	35979994	35980111	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35980112	35980183	1	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35980112	35980183	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	intron	35980184	35980293	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	CDS	35980294	35980446	1	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	exon	35980294	35980446	.	+	.	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
Phchi.S1	AUGUSTUS	stop_codon	35980447	35980449	.	+	0	transcript_id "Phchi.S1G560600.t1"; gene_id "Phchi.S1G560600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10133.t1 is derived from g7309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45912444	45915437	.	-	.	Phchi.S1G729200
Phchi.S1	AUGUSTUS	transcript	45912444	45915437	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	stop_codon	45912441	45912443	.	-	0	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	CDS	45912444	45912762	0.67	-	1	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	exon	45912444	45912762	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	intron	45912763	45912895	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	CDS	45912896	45913227	0.71	-	0	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	exon	45912896	45913227	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	intron	45913228	45913359	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	CDS	45913360	45914732	1	-	2	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	exon	45913360	45914732	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	intron	45914733	45914827	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	CDS	45914828	45915437	0.98	-	0	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	exon	45914828	45915437	.	-	.	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
Phchi.S1	AUGUSTUS	start_codon	45915435	45915437	.	-	0	transcript_id "Phchi.S1G729200.t1"; gene_id "Phchi.S1G729200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4981.t1 is derived from g2151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13864045	13865694	.	+	.	Phchi.S1G214000
Phchi.S1	AUGUSTUS	transcript	13864045	13865694	.	+	.	transcript_id "Phchi.S1G214000.t1"; gene_id "Phchi.S1G214000"
Phchi.S1	AUGUSTUS	start_codon	13864045	13864047	.	+	0	transcript_id "Phchi.S1G214000.t1"; gene_id "Phchi.S1G214000"
Phchi.S1	AUGUSTUS	CDS	13864045	13865694	0.53	+	0	transcript_id "Phchi.S1G214000.t1"; gene_id "Phchi.S1G214000"
Phchi.S1	AUGUSTUS	exon	13864045	13865694	.	+	.	transcript_id "Phchi.S1G214000.t1"; gene_id "Phchi.S1G214000"
Phchi.S1	AUGUSTUS	stop_codon	13865695	13865697	.	+	0	transcript_id "Phchi.S1G214000.t1"; gene_id "Phchi.S1G214000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2491.t1 is derived from g9411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6933826	6934212	.	+	.	Phchi.S5G110000
Phchi.S5	AUGUSTUS	transcript	6933826	6934212	.	+	.	transcript_id "Phchi.S5G110000.t1"; gene_id "Phchi.S5G110000"
Phchi.S5	AUGUSTUS	start_codon	6933826	6933828	.	+	0	transcript_id "Phchi.S5G110000.t1"; gene_id "Phchi.S5G110000"
Phchi.S5	AUGUSTUS	CDS	6933826	6934212	0.96	+	0	transcript_id "Phchi.S5G110000.t1"; gene_id "Phchi.S5G110000"
Phchi.S5	AUGUSTUS	exon	6933826	6934212	.	+	.	transcript_id "Phchi.S5G110000.t1"; gene_id "Phchi.S5G110000"
Phchi.S5	AUGUSTUS	stop_codon	6934213	6934215	.	+	0	transcript_id "Phchi.S5G110000.t1"; gene_id "Phchi.S5G110000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4447.t1 is derived from g1616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10553846	10554649	.	-	.	Phchi.S1G160600
Phchi.S1	AUGUSTUS	transcript	10553846	10554649	.	-	.	transcript_id "Phchi.S1G160600.t1"; gene_id "Phchi.S1G160600"
Phchi.S1	AUGUSTUS	stop_codon	10553843	10553845	.	-	0	transcript_id "Phchi.S1G160600.t1"; gene_id "Phchi.S1G160600"
Phchi.S1	AUGUSTUS	CDS	10553846	10554649	0.78	-	0	transcript_id "Phchi.S1G160600.t1"; gene_id "Phchi.S1G160600"
Phchi.S1	AUGUSTUS	exon	10553846	10554649	.	-	.	transcript_id "Phchi.S1G160600.t1"; gene_id "Phchi.S1G160600"
Phchi.S1	AUGUSTUS	start_codon	10554647	10554649	.	-	0	transcript_id "Phchi.S1G160600.t1"; gene_id "Phchi.S1G160600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13771.t1 is derived from g12238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8837771	8838790	.	-	.	Phchi.S3G109000
Phchi.S3	AUGUSTUS	transcript	8837771	8838790	.	-	.	transcript_id "Phchi.S3G109000.t1"; gene_id "Phchi.S3G109000"
Phchi.S3	AUGUSTUS	stop_codon	8837768	8837770	.	-	0	transcript_id "Phchi.S3G109000.t1"; gene_id "Phchi.S3G109000"
Phchi.S3	AUGUSTUS	CDS	8837771	8838790	0.76	-	0	transcript_id "Phchi.S3G109000.t1"; gene_id "Phchi.S3G109000"
Phchi.S3	AUGUSTUS	exon	8837771	8838790	.	-	.	transcript_id "Phchi.S3G109000.t1"; gene_id "Phchi.S3G109000"
Phchi.S3	AUGUSTUS	start_codon	8838788	8838790	.	-	0	transcript_id "Phchi.S3G109000.t1"; gene_id "Phchi.S3G109000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4798.t1 is derived from g1968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12836604	12839232	.	-	.	Phchi.S1G195700
Phchi.S1	AUGUSTUS	transcript	12836604	12839232	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	stop_codon	12836601	12836603	.	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12836604	12836893	1	-	2	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12836604	12836893	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12836894	12836975	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12836976	12837024	1	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12836976	12837024	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12837025	12837106	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12837107	12837189	1	-	2	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12837107	12837189	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12837190	12837318	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12837319	12837457	1	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12837319	12837457	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12837458	12837535	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12837536	12837633	1	-	2	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12837536	12837633	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12837634	12837720	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12837721	12837800	1	-	1	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12837721	12837800	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12837801	12837937	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12837938	12838008	1	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12837938	12838008	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12838009	12838135	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12838136	12838217	1	-	1	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12838136	12838217	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12838218	12838349	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12838350	12838429	1	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12838350	12838429	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12838430	12838538	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12838539	12838590	1	-	1	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12838539	12838590	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	intron	12838591	12839029	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	CDS	12839030	12839232	0.76	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	exon	12839030	12839232	.	-	.	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
Phchi.S1	AUGUSTUS	start_codon	12839230	12839232	.	-	0	transcript_id "Phchi.S1G195700.t1"; gene_id "Phchi.S1G195700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7427.t1 is derived from g4599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29087469	29088720	.	+	.	Phchi.S1G458600
Phchi.S1	AUGUSTUS	transcript	29087469	29088720	.	+	.	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	start_codon	29087469	29087471	.	+	0	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	CDS	29087469	29087562	0.99	+	0	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	exon	29087469	29087562	.	+	.	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	intron	29087563	29087929	.	+	.	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	CDS	29087930	29088018	0.98	+	2	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	exon	29087930	29088018	.	+	.	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	intron	29088019	29088636	.	+	.	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	CDS	29088637	29088720	0.51	+	0	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	exon	29088637	29088720	.	+	.	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
Phchi.S1	AUGUSTUS	stop_codon	29088721	29088723	.	+	0	transcript_id "Phchi.S1G458600.t1"; gene_id "Phchi.S1G458600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13938.t1 is derived from g12405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9810322	9810564	.	+	.	Phchi.S3G125700
Phchi.S3	AUGUSTUS	transcript	9810322	9810564	.	+	.	transcript_id "Phchi.S3G125700.t1"; gene_id "Phchi.S3G125700"
Phchi.S3	AUGUSTUS	start_codon	9810322	9810324	.	+	0	transcript_id "Phchi.S3G125700.t1"; gene_id "Phchi.S3G125700"
Phchi.S3	AUGUSTUS	CDS	9810322	9810564	0.74	+	0	transcript_id "Phchi.S3G125700.t1"; gene_id "Phchi.S3G125700"
Phchi.S3	AUGUSTUS	exon	9810322	9810564	.	+	.	transcript_id "Phchi.S3G125700.t1"; gene_id "Phchi.S3G125700"
Phchi.S3	AUGUSTUS	stop_codon	9810565	9810567	.	+	0	transcript_id "Phchi.S3G125700.t1"; gene_id "Phchi.S3G125700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15852.t1 is derived from g14322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21824141	21825076	.	+	.	Phchi.S3G317100
Phchi.S3	AUGUSTUS	transcript	21824141	21825076	.	+	.	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	start_codon	21824141	21824143	.	+	0	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	CDS	21824141	21824375	0.47	+	0	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	exon	21824141	21824375	.	+	.	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	intron	21824376	21825074	.	+	.	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	CDS	21825075	21825076	0.88	+	2	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	exon	21825075	21825076	.	+	.	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
Phchi.S3	AUGUSTUS	stop_codon	21825077	21825079	.	+	0	transcript_id "Phchi.S3G317100.t1"; gene_id "Phchi.S3G317100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7412.t1 is derived from g4584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29029823	29031643	.	-	.	Phchi.S1G457100
Phchi.S1	AUGUSTUS	transcript	29029823	29031643	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	stop_codon	29029820	29029822	.	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29029823	29029975	1	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29029823	29029975	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29029976	29030063	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29030064	29030202	1	-	1	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29030064	29030202	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29030203	29030273	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29030274	29030395	1	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29030274	29030395	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29030396	29030479	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29030480	29030701	1	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29030480	29030701	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29030702	29030787	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29030788	29030849	1	-	2	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29030788	29030849	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29030850	29030933	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29030934	29031060	0.98	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29030934	29031060	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29031061	29031175	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29031176	29031454	0.97	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29031176	29031454	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	intron	29031455	29031577	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	CDS	29031578	29031643	0.97	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	exon	29031578	29031643	.	-	.	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
Phchi.S1	AUGUSTUS	start_codon	29031641	29031643	.	-	0	transcript_id "Phchi.S1G457100.t1"; gene_id "Phchi.S1G457100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12562.t1 is derived from g8239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35291363	35293764	.	+	.	Phchi.S2G064200
Phchi.S2	AUGUSTUS	transcript	35291363	35293764	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	start_codon	35291363	35291365	.	+	0	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35291363	35291839	0.97	+	0	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35291363	35291839	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35291840	35291977	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35291978	35292192	1	+	0	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35291978	35292192	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35292193	35292316	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35292317	35292469	1	+	1	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35292317	35292469	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35292470	35292788	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35292789	35292919	1	+	1	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35292789	35292919	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35292920	35293037	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35293038	35293144	1	+	2	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35293038	35293144	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35293145	35293240	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35293241	35293347	1	+	0	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35293241	35293347	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35293348	35293498	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35293499	35293636	0.93	+	1	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35293499	35293636	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	intron	35293637	35293724	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	CDS	35293725	35293764	0.93	+	1	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	exon	35293725	35293764	.	+	.	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
Phchi.S2	AUGUSTUS	stop_codon	35293765	35293767	.	+	0	transcript_id "Phchi.S2G064200.t1"; gene_id "Phchi.S2G064200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15651.t1 is derived from g14120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20491363	20492056	.	-	.	Phchi.S3G297000
Phchi.S3	AUGUSTUS	transcript	20491363	20492056	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	stop_codon	20491360	20491362	.	-	0	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	CDS	20491363	20491467	1	-	0	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	exon	20491363	20491467	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	intron	20491468	20491561	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	CDS	20491562	20491768	1	-	0	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	exon	20491562	20491768	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	intron	20491769	20491857	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	CDS	20491858	20491956	1	-	0	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	exon	20491858	20491956	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	intron	20491957	20492035	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	CDS	20492036	20492056	0.92	-	0	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	exon	20492036	20492056	.	-	.	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
Phchi.S3	AUGUSTUS	start_codon	20492054	20492056	.	-	0	transcript_id "Phchi.S3G297000.t1"; gene_id "Phchi.S3G297000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9714.t1 is derived from g6890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43384230	43385860	.	-	.	Phchi.S1G687300
Phchi.S1	AUGUSTUS	transcript	43384230	43385860	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	stop_codon	43384227	43384229	.	-	0	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	CDS	43384230	43384231	0.39	-	2	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	exon	43384230	43384231	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	intron	43384232	43384365	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	CDS	43384366	43384560	0.75	-	2	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	exon	43384366	43384560	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	intron	43384561	43384716	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	CDS	43384717	43385183	0.68	-	1	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	exon	43384717	43385183	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	intron	43385184	43385311	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	CDS	43385312	43385476	0.5	-	1	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	exon	43385312	43385476	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	intron	43385477	43385594	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	CDS	43385595	43385860	0.39	-	0	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	exon	43385595	43385860	.	-	.	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
Phchi.S1	AUGUSTUS	start_codon	43385858	43385860	.	-	0	transcript_id "Phchi.S1G687300.t1"; gene_id "Phchi.S1G687300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6093.t1 is derived from g3264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20927814	20929854	.	+	.	Phchi.S1G325200
Phchi.S1	AUGUSTUS	transcript	20927814	20929854	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	start_codon	20927814	20927816	.	+	0	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	CDS	20927814	20928254	0.99	+	0	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	exon	20927814	20928254	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	intron	20928255	20928339	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	CDS	20928340	20928470	1	+	0	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	exon	20928340	20928470	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	intron	20928471	20928583	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	CDS	20928584	20928890	1	+	1	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	exon	20928584	20928890	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	intron	20928891	20928969	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	CDS	20928970	20929286	0.53	+	0	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	exon	20928970	20929286	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	intron	20929287	20929396	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	CDS	20929397	20929525	0.77	+	1	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	exon	20929397	20929525	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	intron	20929526	20929826	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	CDS	20929827	20929854	0.72	+	1	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	exon	20929827	20929854	.	+	.	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
Phchi.S1	AUGUSTUS	stop_codon	20929855	20929857	.	+	0	transcript_id "Phchi.S1G325200.t1"; gene_id "Phchi.S1G325200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8336.t1 is derived from g5511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35378392	35379739	.	-	.	Phchi.S1G549500
Phchi.S1	AUGUSTUS	transcript	35378392	35379739	.	-	.	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	stop_codon	35378389	35378391	.	-	0	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	CDS	35378392	35378722	0.96	-	1	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	exon	35378392	35378722	.	-	.	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	intron	35378723	35378889	.	-	.	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	CDS	35378890	35379218	0.94	-	0	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	exon	35378890	35379218	.	-	.	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	intron	35379219	35379307	.	-	.	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	CDS	35379308	35379739	0.64	-	0	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	exon	35379308	35379739	.	-	.	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
Phchi.S1	AUGUSTUS	start_codon	35379737	35379739	.	-	0	transcript_id "Phchi.S1G549500.t1"; gene_id "Phchi.S1G549500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12565.t1 is derived from g8242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35383954	35384546	.	-	.	Phchi.S2G064500
Phchi.S2	AUGUSTUS	transcript	35383954	35384546	.	-	.	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	stop_codon	35383951	35383953	.	-	0	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	CDS	35383954	35383999	1	-	1	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	exon	35383954	35383999	.	-	.	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	intron	35384000	35384346	.	-	.	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	CDS	35384347	35384546	0.57	-	0	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	exon	35384347	35384546	.	-	.	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
Phchi.S2	AUGUSTUS	start_codon	35384544	35384546	.	-	0	transcript_id "Phchi.S2G064500.t1"; gene_id "Phchi.S2G064500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1070.t1 is derived from g10853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7428210	7431620	.	+	.	Phchi.S6G102900
Phchi.S6	AUGUSTUS	transcript	7428210	7431620	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	start_codon	7428210	7428212	.	+	0	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	CDS	7428210	7428938	0.35	+	0	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	exon	7428210	7428938	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	intron	7428939	7429098	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	CDS	7429099	7429146	0.58	+	0	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	exon	7429099	7429146	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	intron	7429147	7429562	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	CDS	7429563	7430898	0.44	+	0	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	exon	7429563	7430898	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	intron	7430899	7430984	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	CDS	7430985	7431045	0.66	+	2	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	exon	7430985	7431045	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	intron	7431046	7431144	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	CDS	7431145	7431230	0.59	+	1	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	exon	7431145	7431230	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	intron	7431231	7431417	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	CDS	7431418	7431620	0.87	+	2	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	exon	7431418	7431620	.	+	.	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
Phchi.S6	AUGUSTUS	stop_codon	7431621	7431623	.	+	0	transcript_id "Phchi.S6G102900.t1"; gene_id "Phchi.S6G102900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6594.t1 is derived from g3766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23908816	23911014	.	-	.	Phchi.S1G375300
Phchi.S1	AUGUSTUS	transcript	23908816	23911014	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	stop_codon	23908813	23908815	.	-	0	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	CDS	23908816	23908818	1	-	0	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	exon	23908816	23908818	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	intron	23908819	23908914	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	CDS	23908915	23908985	1	-	2	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	exon	23908915	23908985	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	intron	23908986	23909123	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	CDS	23909124	23909507	0.46	-	2	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	exon	23909124	23909507	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	intron	23909508	23909774	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	CDS	23909775	23911014	0.3	-	0	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	exon	23909775	23911014	.	-	.	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
Phchi.S1	AUGUSTUS	start_codon	23911012	23911014	.	-	0	transcript_id "Phchi.S1G375300.t1"; gene_id "Phchi.S1G375300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13732.t1 is derived from g12199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8597370	8597927	.	-	.	Phchi.S3G105100
Phchi.S3	AUGUSTUS	transcript	8597370	8597927	.	-	.	transcript_id "Phchi.S3G105100.t1"; gene_id "Phchi.S3G105100"
Phchi.S3	AUGUSTUS	stop_codon	8597367	8597369	.	-	0	transcript_id "Phchi.S3G105100.t1"; gene_id "Phchi.S3G105100"
Phchi.S3	AUGUSTUS	CDS	8597370	8597927	0.72	-	0	transcript_id "Phchi.S3G105100.t1"; gene_id "Phchi.S3G105100"
Phchi.S3	AUGUSTUS	exon	8597370	8597927	.	-	.	transcript_id "Phchi.S3G105100.t1"; gene_id "Phchi.S3G105100"
Phchi.S3	AUGUSTUS	start_codon	8597925	8597927	.	-	0	transcript_id "Phchi.S3G105100.t1"; gene_id "Phchi.S3G105100"
# This transcript jg13735.t2 is derived from g12202.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13736.t1 is derived from g12203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8648554	8649102	.	-	.	Phchi.S3G105500
Phchi.S3	AUGUSTUS	transcript	8648554	8649102	.	-	.	transcript_id "Phchi.S3G105500.t1"; gene_id "Phchi.S3G105500"
Phchi.S3	AUGUSTUS	stop_codon	8648551	8648553	.	-	0	transcript_id "Phchi.S3G105500.t1"; gene_id "Phchi.S3G105500"
Phchi.S3	AUGUSTUS	CDS	8648554	8649102	0.8	-	0	transcript_id "Phchi.S3G105500.t1"; gene_id "Phchi.S3G105500"
Phchi.S3	AUGUSTUS	exon	8648554	8649102	.	-	.	transcript_id "Phchi.S3G105500.t1"; gene_id "Phchi.S3G105500"
Phchi.S3	AUGUSTUS	start_codon	8649100	8649102	.	-	0	transcript_id "Phchi.S3G105500.t1"; gene_id "Phchi.S3G105500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5809.t1 is derived from g2979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19052286	19052780	.	+	.	Phchi.S1G296800
Phchi.S1	AUGUSTUS	transcript	19052286	19052780	.	+	.	transcript_id "Phchi.S1G296800.t1"; gene_id "Phchi.S1G296800"
Phchi.S1	AUGUSTUS	start_codon	19052286	19052288	.	+	0	transcript_id "Phchi.S1G296800.t1"; gene_id "Phchi.S1G296800"
Phchi.S1	AUGUSTUS	CDS	19052286	19052780	0.77	+	0	transcript_id "Phchi.S1G296800.t1"; gene_id "Phchi.S1G296800"
Phchi.S1	AUGUSTUS	exon	19052286	19052780	.	+	.	transcript_id "Phchi.S1G296800.t1"; gene_id "Phchi.S1G296800"
Phchi.S1	AUGUSTUS	stop_codon	19052781	19052783	.	+	0	transcript_id "Phchi.S1G296800.t1"; gene_id "Phchi.S1G296800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6077.t1 is derived from g3248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20820650	20821105	.	-	.	Phchi.S1G323600
Phchi.S1	AUGUSTUS	transcript	20820650	20821105	.	-	.	transcript_id "Phchi.S1G323600.t1"; gene_id "Phchi.S1G323600"
Phchi.S1	AUGUSTUS	stop_codon	20820647	20820649	.	-	0	transcript_id "Phchi.S1G323600.t1"; gene_id "Phchi.S1G323600"
Phchi.S1	AUGUSTUS	CDS	20820650	20821105	0.59	-	0	transcript_id "Phchi.S1G323600.t1"; gene_id "Phchi.S1G323600"
Phchi.S1	AUGUSTUS	exon	20820650	20821105	.	-	.	transcript_id "Phchi.S1G323600.t1"; gene_id "Phchi.S1G323600"
Phchi.S1	AUGUSTUS	start_codon	20821103	20821105	.	-	0	transcript_id "Phchi.S1G323600.t1"; gene_id "Phchi.S1G323600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11141.t1 is derived from g15191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4366603	4370759	.	+	.	Phchi.S4G072300
Phchi.S4	AUGUSTUS	transcript	4366603	4370759	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	start_codon	4366603	4366605	.	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4366603	4366757	0.64	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4366603	4366757	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4366758	4366869	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4366870	4366981	0.92	+	1	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4366870	4366981	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4366982	4367182	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4367183	4367365	0.95	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4367183	4367365	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4367366	4367467	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4367468	4367515	0.99	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4367468	4367515	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4367516	4367637	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4367638	4367832	0.97	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4367638	4367832	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4367833	4367965	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4367966	4368043	0.99	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4367966	4368043	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4368044	4368149	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4368150	4368239	0.97	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4368150	4368239	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4368240	4368363	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4368364	4368444	0.93	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4368364	4368444	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4368445	4368551	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4368552	4368620	1	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4368552	4368620	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4368621	4368713	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4368714	4368806	1	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4368714	4368806	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4368807	4368920	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4368921	4369085	0.96	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4368921	4369085	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4369086	4369196	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4369197	4369252	0.77	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4369197	4369252	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4369253	4369368	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4369369	4369489	0.99	+	1	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4369369	4369489	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4369490	4369576	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4369577	4369744	1	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4369577	4369744	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4369745	4369826	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4369827	4369892	0.4	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4369827	4369892	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4369893	4370029	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4370030	4370299	0.42	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4370030	4370299	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4370300	4370375	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4370376	4370546	1	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4370376	4370546	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	intron	4370547	4370645	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	CDS	4370646	4370759	1	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	exon	4370646	4370759	.	+	.	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
Phchi.S4	AUGUSTUS	stop_codon	4370760	4370762	.	+	0	transcript_id "Phchi.S4G072300.t1"; gene_id "Phchi.S4G072300"
# This transcript jg15903.t2 is derived from g14373.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15903.t3 is derived from g14373.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15904.t1 is derived from g14374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22082548	22086517	.	-	.	Phchi.S3G322300
Phchi.S3	AUGUSTUS	transcript	22082548	22086517	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	stop_codon	22082545	22082547	.	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22082548	22082979	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22082548	22082979	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22082980	22083069	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22083070	22083117	0.91	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22083070	22083117	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22083118	22083203	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22083204	22083287	0.76	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22083204	22083287	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22083288	22083365	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22083366	22083518	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22083366	22083518	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22083519	22083592	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22083593	22083778	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22083593	22083778	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22083779	22083863	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22083864	22083997	1	-	2	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22083864	22083997	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22083998	22084144	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22084145	22084622	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22084145	22084622	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22084623	22084748	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22084749	22084827	1	-	1	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22084749	22084827	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22084828	22084932	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22084933	22085253	0.85	-	1	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22084933	22085253	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22085254	22085375	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22085376	22085416	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22085376	22085416	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22085417	22085515	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22085516	22085696	1	-	1	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22085516	22085696	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22085697	22085813	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22085814	22085956	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22085814	22085956	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22085957	22086054	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22086055	22086132	1	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22086055	22086132	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	intron	22086133	22086475	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	CDS	22086476	22086517	0.43	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	exon	22086476	22086517	.	-	.	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
Phchi.S3	AUGUSTUS	start_codon	22086515	22086517	.	-	0	transcript_id "Phchi.S3G322300.t1"; gene_id "Phchi.S3G322300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5756.t1 is derived from g2926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18756065	18757837	.	+	.	Phchi.S1G291500
Phchi.S1	AUGUSTUS	transcript	18756065	18757837	.	+	.	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	start_codon	18756065	18756067	.	+	0	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	CDS	18756065	18757549	0.97	+	0	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	exon	18756065	18757549	.	+	.	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	intron	18757550	18757672	.	+	.	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	CDS	18757673	18757837	1	+	0	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	exon	18757673	18757837	.	+	.	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
Phchi.S1	AUGUSTUS	stop_codon	18757838	18757840	.	+	0	transcript_id "Phchi.S1G291500.t1"; gene_id "Phchi.S1G291500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11065.t1 is derived from g15115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3948187	3951126	.	-	.	Phchi.S4G064700
Phchi.S4	AUGUSTUS	transcript	3948187	3951126	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	stop_codon	3948184	3948186	.	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3948187	3948216	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3948187	3948216	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3948217	3948292	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3948293	3948385	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3948293	3948385	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3948386	3948478	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3948479	3948643	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3948479	3948643	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3948644	3948729	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3948730	3948879	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3948730	3948879	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3948880	3949000	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3949001	3949048	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3949001	3949048	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3949049	3949139	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3949140	3949352	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3949140	3949352	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3949353	3949539	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3949540	3949665	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3949540	3949665	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3949666	3949766	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3949767	3949838	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3949767	3949838	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3949839	3949936	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3949937	3950416	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3949937	3950416	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3950417	3950548	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3950549	3950608	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3950549	3950608	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	intron	3950609	3950718	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	CDS	3950719	3951126	1	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	exon	3950719	3951126	.	-	.	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
Phchi.S4	AUGUSTUS	start_codon	3951124	3951126	.	-	0	transcript_id "Phchi.S4G064700.t1"; gene_id "Phchi.S4G064700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1126.t1 is derived from g10909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7854727	7855317	.	+	.	Phchi.S6G108500
Phchi.S6	AUGUSTUS	transcript	7854727	7855317	.	+	.	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	start_codon	7854727	7854729	.	+	0	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	CDS	7854727	7854874	0.98	+	0	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	exon	7854727	7854874	.	+	.	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	intron	7854875	7854956	.	+	.	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	CDS	7854957	7855161	0.59	+	2	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	exon	7854957	7855161	.	+	.	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	intron	7855162	7855247	.	+	.	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	CDS	7855248	7855317	0.58	+	1	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	exon	7855248	7855317	.	+	.	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
Phchi.S6	AUGUSTUS	stop_codon	7855318	7855320	.	+	0	transcript_id "Phchi.S6G108500.t1"; gene_id "Phchi.S6G108500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12004.t1 is derived from g7679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	499961	501036	.	-	.	Phchi.S2G008400
Phchi.S2	AUGUSTUS	transcript	499961	501036	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	stop_codon	499958	499960	.	-	0	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	CDS	499961	500076	0.98	-	2	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	exon	499961	500076	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	intron	500077	500259	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	CDS	500260	500286	0.94	-	2	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	exon	500260	500286	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	intron	500287	500611	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	CDS	500612	500715	0.8	-	1	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	exon	500612	500715	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	intron	500716	500842	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	CDS	500843	501036	0.99	-	0	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	exon	500843	501036	.	-	.	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
Phchi.S2	AUGUSTUS	start_codon	501034	501036	.	-	0	transcript_id "Phchi.S2G008400.t1"; gene_id "Phchi.S2G008400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2861.t1 is derived from g30.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	140182	142251	.	+	.	Phchi.S1G002000
Phchi.S1	AUGUSTUS	transcript	140182	142251	.	+	.	transcript_id "Phchi.S1G002000.t1"; gene_id "Phchi.S1G002000"
Phchi.S1	AUGUSTUS	start_codon	140182	140184	.	+	0	transcript_id "Phchi.S1G002000.t1"; gene_id "Phchi.S1G002000"
Phchi.S1	AUGUSTUS	CDS	140182	142251	1	+	0	transcript_id "Phchi.S1G002000.t1"; gene_id "Phchi.S1G002000"
Phchi.S1	AUGUSTUS	exon	140182	142251	.	+	.	transcript_id "Phchi.S1G002000.t1"; gene_id "Phchi.S1G002000"
Phchi.S1	AUGUSTUS	stop_codon	142252	142254	.	+	0	transcript_id "Phchi.S1G002000.t1"; gene_id "Phchi.S1G002000"
# This transcript jg7155.t2 is derived from g4327.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7156.t1 is derived from g4328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27322853	27326928	.	-	.	Phchi.S1G431500
Phchi.S1	AUGUSTUS	transcript	27322853	27326928	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	stop_codon	27322850	27322852	.	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27322853	27322916	1	-	1	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27322853	27322916	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27322917	27322995	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27322996	27323117	1	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27322996	27323117	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27323118	27323207	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27323208	27323303	1	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27323208	27323303	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27323304	27323399	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27323400	27323516	1	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27323400	27323516	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27323517	27323634	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27323635	27323706	1	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27323635	27323706	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27323707	27323805	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27323806	27323969	0.97	-	2	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27323806	27323969	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27323970	27324071	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27324072	27324172	1	-	1	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27324072	27324172	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27324173	27324320	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27324321	27324417	1	-	2	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27324321	27324417	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27324418	27324500	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27324501	27324636	1	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27324501	27324636	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27324637	27324712	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27324713	27324849	1	-	2	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27324713	27324849	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27324850	27325101	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27325102	27325311	1	-	2	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27325102	27325311	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27325312	27325631	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27325632	27325753	0.72	-	1	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27325632	27325753	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27325754	27325911	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27325912	27326016	0.67	-	1	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27325912	27326016	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27326017	27326239	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27326240	27326582	1	-	2	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27326240	27326582	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	intron	27326583	27326876	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	CDS	27326877	27326928	0.57	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	exon	27326877	27326928	.	-	.	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
Phchi.S1	AUGUSTUS	start_codon	27326926	27326928	.	-	0	transcript_id "Phchi.S1G431500.t1"; gene_id "Phchi.S1G431500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8910.t1 is derived from g6085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38591982	38595712	.	+	.	Phchi.S1G606900
Phchi.S1	AUGUSTUS	transcript	38591982	38595712	.	+	.	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	start_codon	38591982	38591984	.	+	0	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	CDS	38591982	38595261	0.78	+	0	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	exon	38591982	38595261	.	+	.	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	intron	38595262	38595353	.	+	.	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	CDS	38595354	38595712	1	+	2	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	exon	38595354	38595712	.	+	.	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
Phchi.S1	AUGUSTUS	stop_codon	38595713	38595715	.	+	0	transcript_id "Phchi.S1G606900.t1"; gene_id "Phchi.S1G606900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5470.t1 is derived from g2640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16996266	16998464	.	+	.	Phchi.S1G262900
Phchi.S1	AUGUSTUS	transcript	16996266	16998464	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	start_codon	16996266	16996268	.	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16996266	16996478	0.16	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16996266	16996478	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16996479	16996581	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16996582	16996710	0.63	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16996582	16996710	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16996711	16996798	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16996799	16996939	1	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16996799	16996939	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16996940	16997115	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16997116	16997289	0.99	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16997116	16997289	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16997290	16997407	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16997408	16997623	1	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16997408	16997623	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16997624	16997745	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16997746	16997777	1	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16997746	16997777	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16997778	16997945	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16997946	16998222	0.99	+	1	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16997946	16998222	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	intron	16998223	16998314	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	CDS	16998315	16998464	0.99	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	exon	16998315	16998464	.	+	.	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
Phchi.S1	AUGUSTUS	stop_codon	16998465	16998467	.	+	0	transcript_id "Phchi.S1G262900.t1"; gene_id "Phchi.S1G262900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15198.t1 is derived from g13666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17524635	17527387	.	-	.	Phchi.S3G251700
Phchi.S3	AUGUSTUS	transcript	17524635	17527387	.	-	.	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	stop_codon	17524632	17524634	.	-	0	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	CDS	17524635	17527239	0.37	-	1	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	exon	17524635	17527239	.	-	.	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	intron	17527240	17527325	.	-	.	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	CDS	17527326	17527387	0.66	-	0	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	exon	17527326	17527387	.	-	.	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
Phchi.S3	AUGUSTUS	start_codon	17527385	17527387	.	-	0	transcript_id "Phchi.S3G251700.t1"; gene_id "Phchi.S3G251700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9621.t1 is derived from g6797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42952537	42953202	.	-	.	Phchi.S1G678000
Phchi.S1	AUGUSTUS	transcript	42952537	42953202	.	-	.	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	stop_codon	42952534	42952536	.	-	0	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	CDS	42952537	42952698	0.93	-	0	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	exon	42952537	42952698	.	-	.	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	intron	42952699	42952778	.	-	.	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	CDS	42952779	42952840	1	-	2	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	exon	42952779	42952840	.	-	.	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	intron	42952841	42953018	.	-	.	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	CDS	42953019	42953202	0.56	-	0	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	exon	42953019	42953202	.	-	.	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
Phchi.S1	AUGUSTUS	start_codon	42953200	42953202	.	-	0	transcript_id "Phchi.S1G678000.t1"; gene_id "Phchi.S1G678000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13941.t1 is derived from g12408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9828076	9828874	.	+	.	Phchi.S3G126000
Phchi.S3	AUGUSTUS	transcript	9828076	9828874	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	start_codon	9828076	9828078	.	+	0	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	CDS	9828076	9828111	0.72	+	0	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	exon	9828076	9828111	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	intron	9828112	9828304	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	CDS	9828305	9828403	1	+	0	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	exon	9828305	9828403	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	intron	9828404	9828508	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	CDS	9828509	9828584	0.98	+	0	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	exon	9828509	9828584	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	intron	9828585	9828704	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	CDS	9828705	9828874	0.99	+	2	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	exon	9828705	9828874	.	+	.	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
Phchi.S3	AUGUSTUS	stop_codon	9828875	9828877	.	+	0	transcript_id "Phchi.S3G126000.t1"; gene_id "Phchi.S3G126000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg430.t1 is derived from g10212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3044986	3046080	.	-	.	Phchi.S6G038900
Phchi.S6	AUGUSTUS	transcript	3044986	3046080	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	stop_codon	3044983	3044985	.	-	0	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	CDS	3044986	3045409	0.59	-	1	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	exon	3044986	3045409	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	intron	3045410	3045629	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	CDS	3045630	3045649	0.35	-	0	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	exon	3045630	3045649	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	intron	3045650	3045791	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	CDS	3045792	3045800	0.35	-	0	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	exon	3045792	3045800	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	intron	3045801	3046062	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	CDS	3046063	3046080	0.69	-	0	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	exon	3046063	3046080	.	-	.	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
Phchi.S6	AUGUSTUS	start_codon	3046078	3046080	.	-	0	transcript_id "Phchi.S6G038900.t1"; gene_id "Phchi.S6G038900"
# This transcript jg10362.t2 is derived from g7538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10363.t1 is derived from g7539.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47389544	47390623	.	+	.	Phchi.S1G752200
Phchi.S1	AUGUSTUS	transcript	47389544	47390310	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	start_codon	47389544	47389546	.	+	0	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47389544	47389723	0.99	+	0	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47389544	47389723	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47389724	47389806	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47389807	47389908	0.99	+	0	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47389807	47389908	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47389909	47390078	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47390079	47390177	0.94	+	0	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47390079	47390177	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47390178	47390265	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47390266	47390310	0.99	+	0	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47390266	47390310	.	+	.	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	stop_codon	47390311	47390313	.	+	0	transcript_id "Phchi.S1G752200.t1"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	transcript	47389544	47390623	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	start_codon	47389544	47389546	.	+	0	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47389544	47389723	0.76	+	0	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47389544	47389723	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47389724	47389806	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47389807	47389908	0.72	+	0	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47389807	47389908	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47389909	47390078	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47390079	47390177	0.71	+	0	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47390079	47390177	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47390178	47390336	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47390337	47390469	0.5	+	0	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47390337	47390469	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	intron	47390470	47390594	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	CDS	47390595	47390623	0.42	+	2	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	exon	47390595	47390623	.	+	.	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
Phchi.S1	AUGUSTUS	stop_codon	47390624	47390626	.	+	0	transcript_id "Phchi.S1G752200.t2"; gene_id "Phchi.S1G752200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg493.t1 is derived from g10275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3428483	3432326	.	+	.	Phchi.S6G045200
Phchi.S6	AUGUSTUS	transcript	3428483	3432326	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	start_codon	3428483	3428485	.	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3428483	3428515	0.46	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3428483	3428515	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3428516	3428644	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3428645	3428782	0.99	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3428645	3428782	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3428783	3428882	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3428883	3428994	0.9	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3428883	3428994	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3428995	3429092	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3429093	3429154	0.67	+	2	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3429093	3429154	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3429155	3429323	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3429324	3429560	1	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3429324	3429560	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3429561	3429648	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3429649	3431341	0.94	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3429649	3431341	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3431342	3431451	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3431452	3431537	0.83	+	2	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3431452	3431537	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	intron	3431538	3431636	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	CDS	3431637	3432326	1	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	exon	3431637	3432326	.	+	.	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
Phchi.S6	AUGUSTUS	stop_codon	3432327	3432329	.	+	0	transcript_id "Phchi.S6G045200.t1"; gene_id "Phchi.S6G045200"
# This transcript jg7271.t2 is derived from g4443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7271.t3 is derived from g4443.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7272.t1 is derived from g4444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28077121	28078191	.	-	.	Phchi.S1G443100
Phchi.S1	AUGUSTUS	transcript	28077121	28078191	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	stop_codon	28077118	28077120	.	-	0	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	CDS	28077121	28077380	0.75	-	2	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	exon	28077121	28077380	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	intron	28077381	28077492	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	CDS	28077493	28077619	0.93	-	0	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	exon	28077493	28077619	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	intron	28077620	28077713	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	CDS	28077714	28077815	0.99	-	0	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	exon	28077714	28077815	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	intron	28077816	28077930	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	CDS	28077931	28078191	0.86	-	0	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	exon	28077931	28078191	.	-	.	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
Phchi.S1	AUGUSTUS	start_codon	28078189	28078191	.	-	0	transcript_id "Phchi.S1G443100.t1"; gene_id "Phchi.S1G443100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5146.t1 is derived from g2316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15140550	15141959	.	+	.	Phchi.S1G230500
Phchi.S1	AUGUSTUS	transcript	15140550	15141959	.	+	.	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	start_codon	15140550	15140552	.	+	0	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	CDS	15140550	15141683	0.43	+	0	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	exon	15140550	15141683	.	+	.	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	intron	15141684	15141791	.	+	.	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	CDS	15141792	15141959	1	+	0	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	exon	15141792	15141959	.	+	.	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
Phchi.S1	AUGUSTUS	stop_codon	15141960	15141962	.	+	0	transcript_id "Phchi.S1G230500.t1"; gene_id "Phchi.S1G230500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11591.t1 is derived from g15642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7247057	7251312	.	-	.	Phchi.S4G117300
Phchi.S4	AUGUSTUS	transcript	7247057	7251312	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	stop_codon	7247054	7247056	.	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7247057	7247137	0.67	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7247057	7247137	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7247138	7247223	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7247224	7247311	1	-	1	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7247224	7247311	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7247312	7247390	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7247391	7247470	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7247391	7247470	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7247471	7247560	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7247561	7247656	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7247561	7247656	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7247657	7247757	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7247758	7247862	0.97	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7247758	7247862	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7247863	7248027	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7248028	7248126	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7248028	7248126	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7248127	7248240	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7248241	7248390	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7248241	7248390	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7248391	7248484	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7248485	7248577	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7248485	7248577	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7248578	7248653	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7248654	7248728	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7248654	7248728	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7248729	7248849	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7248850	7248921	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7248850	7248921	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7248922	7249101	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7249102	7249155	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7249102	7249155	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7249156	7249298	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7249299	7249390	1	-	2	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7249299	7249390	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7249391	7249475	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7249476	7249604	1	-	2	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7249476	7249604	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7249605	7249797	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7249798	7249903	1	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7249798	7249903	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7249904	7250045	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7250046	7250137	1	-	2	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7250046	7250137	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7250138	7250299	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7250300	7250449	0.95	-	2	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7250300	7250449	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7250450	7251029	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7251030	7251091	0.71	-	1	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7251030	7251091	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	intron	7251092	7251295	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	CDS	7251296	7251312	0.36	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	exon	7251296	7251312	.	-	.	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
Phchi.S4	AUGUSTUS	start_codon	7251310	7251312	.	-	0	transcript_id "Phchi.S4G117300.t1"; gene_id "Phchi.S4G117300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13722.t1 is derived from g12189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8507578	8512354	.	-	.	Phchi.S3G104100
Phchi.S3	AUGUSTUS	transcript	8507578	8512354	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	stop_codon	8507575	8507577	.	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8507578	8507769	0.99	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8507578	8507769	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8507770	8507959	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8507960	8508130	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8507960	8508130	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8508131	8508215	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8508216	8508284	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8508216	8508284	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8508285	8508375	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8508376	8508549	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8508376	8508549	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8508550	8508691	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8508692	8508823	0.76	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8508692	8508823	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8508824	8508931	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8508932	8509153	0.77	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8508932	8509153	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8509154	8509237	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8509238	8509375	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8509238	8509375	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8509376	8509485	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8509486	8509536	0.97	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8509486	8509536	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8509537	8509646	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8509647	8509802	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8509647	8509802	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8509803	8509902	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8509903	8510074	1	-	1	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8509903	8510074	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8510075	8510161	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8510162	8510412	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8510162	8510412	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8510413	8510505	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8510506	8510739	0.99	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8510506	8510739	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8510740	8510836	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8510837	8510944	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8510837	8510944	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8510945	8511033	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8511034	8511135	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8511034	8511135	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8511136	8511234	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8511235	8511435	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8511235	8511435	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8511436	8511523	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8511524	8511637	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8511524	8511637	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8511638	8511736	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8511737	8511787	1	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8511737	8511787	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8511788	8511869	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8511870	8511967	1	-	2	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8511870	8511967	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	intron	8511968	8512302	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	CDS	8512303	8512354	0.86	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	exon	8512303	8512354	.	-	.	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
Phchi.S3	AUGUSTUS	start_codon	8512352	8512354	.	-	0	transcript_id "Phchi.S3G104100.t1"; gene_id "Phchi.S3G104100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7053.t1 is derived from g4225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26632969	26633982	.	-	.	Phchi.S1G421200
Phchi.S1	AUGUSTUS	transcript	26632969	26633982	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	stop_codon	26632966	26632968	.	-	0	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	CDS	26632969	26633243	0.31	-	2	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	exon	26632969	26633243	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	intron	26633244	26633329	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	CDS	26633330	26633386	0.8	-	2	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	exon	26633330	26633386	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	intron	26633387	26633499	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	CDS	26633500	26633581	0.7	-	0	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	exon	26633500	26633581	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	intron	26633582	26633728	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	CDS	26633729	26633789	0.96	-	1	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	exon	26633729	26633789	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	intron	26633790	26633914	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	CDS	26633915	26633982	0.96	-	0	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	exon	26633915	26633982	.	-	.	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
Phchi.S1	AUGUSTUS	start_codon	26633980	26633982	.	-	0	transcript_id "Phchi.S1G421200.t1"; gene_id "Phchi.S1G421200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8331.t1 is derived from g5506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35341246	35342924	.	-	.	Phchi.S1G549000
Phchi.S1	AUGUSTUS	transcript	35341246	35342924	.	-	.	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	stop_codon	35341243	35341245	.	-	0	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35341246	35341508	0.93	-	2	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35341246	35341508	.	-	.	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	intron	35341509	35341647	.	-	.	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35341648	35341995	0.99	-	2	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35341648	35341995	.	-	.	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	intron	35341996	35342176	.	-	.	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35342177	35342924	0.58	-	0	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35342177	35342924	.	-	.	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	start_codon	35342922	35342924	.	-	0	transcript_id "Phchi.S1G549000.t1"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	transcript	35341246	35342924	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	stop_codon	35341243	35341245	.	-	0	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35341246	35341508	0.88	-	2	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35341246	35341508	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	intron	35341509	35341647	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35341648	35341894	0.61	-	0	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35341648	35341894	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	intron	35341895	35341991	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35341992	35342014	0.7	-	2	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35341992	35342014	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	intron	35342015	35342176	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	CDS	35342177	35342924	0.49	-	0	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	exon	35342177	35342924	.	-	.	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
Phchi.S1	AUGUSTUS	start_codon	35342922	35342924	.	-	0	transcript_id "Phchi.S1G549000.t2"; gene_id "Phchi.S1G549000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9747.t1 is derived from g6923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43485959	43487655	.	+	.	Phchi.S1G690600
Phchi.S1	AUGUSTUS	transcript	43485959	43487655	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	start_codon	43485959	43485961	.	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43485959	43486021	1	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43485959	43486021	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43486022	43486139	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43486140	43486241	1	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43486140	43486241	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43486242	43486323	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43486324	43486561	1	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43486324	43486561	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43486562	43486658	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43486659	43486744	1	+	2	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43486659	43486744	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43486745	43486834	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43486835	43486939	1	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43486835	43486939	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43486940	43487014	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43487015	43487105	0.87	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43487015	43487105	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43487106	43487240	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43487241	43487264	0.82	+	2	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43487241	43487264	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43487265	43487438	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43487439	43487496	0.42	+	2	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43487439	43487496	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	intron	43487497	43487585	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	CDS	43487586	43487655	0.79	+	1	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	exon	43487586	43487655	.	+	.	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
Phchi.S1	AUGUSTUS	stop_codon	43487656	43487658	.	+	0	transcript_id "Phchi.S1G690600.t1"; gene_id "Phchi.S1G690600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11377.t1 is derived from g15427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5965774	5966157	.	-	.	Phchi.S4G095900
Phchi.S4	AUGUSTUS	transcript	5965774	5966157	.	-	.	transcript_id "Phchi.S4G095900.t1"; gene_id "Phchi.S4G095900"
Phchi.S4	AUGUSTUS	stop_codon	5965771	5965773	.	-	0	transcript_id "Phchi.S4G095900.t1"; gene_id "Phchi.S4G095900"
Phchi.S4	AUGUSTUS	CDS	5965774	5966157	0.93	-	0	transcript_id "Phchi.S4G095900.t1"; gene_id "Phchi.S4G095900"
Phchi.S4	AUGUSTUS	exon	5965774	5966157	.	-	.	transcript_id "Phchi.S4G095900.t1"; gene_id "Phchi.S4G095900"
Phchi.S4	AUGUSTUS	start_codon	5966155	5966157	.	-	0	transcript_id "Phchi.S4G095900.t1"; gene_id "Phchi.S4G095900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14064.t1 is derived from g12531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10620273	10621304	.	+	.	Phchi.S3G138300
Phchi.S3	AUGUSTUS	transcript	10620273	10621304	.	+	.	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	start_codon	10620273	10620275	.	+	0	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	CDS	10620273	10620555	0.66	+	0	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	exon	10620273	10620555	.	+	.	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	intron	10620556	10620723	.	+	.	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	CDS	10620724	10621304	1	+	2	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	exon	10620724	10621304	.	+	.	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
Phchi.S3	AUGUSTUS	stop_codon	10621305	10621307	.	+	0	transcript_id "Phchi.S3G138300.t1"; gene_id "Phchi.S3G138300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5708.t1 is derived from g2878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18471663	18473697	.	+	.	Phchi.S1G286700
Phchi.S1	AUGUSTUS	transcript	18471663	18473697	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	start_codon	18471663	18471665	.	+	0	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	CDS	18471663	18471779	1	+	0	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	exon	18471663	18471779	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	intron	18471780	18471910	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	CDS	18471911	18472399	0.99	+	0	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	exon	18471911	18472399	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	intron	18472400	18472493	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	CDS	18472494	18472715	1	+	0	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	exon	18472494	18472715	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	intron	18472716	18472856	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	CDS	18472857	18472926	1	+	0	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	exon	18472857	18472926	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	intron	18472927	18473097	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	CDS	18473098	18473208	1	+	2	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	exon	18473098	18473208	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	intron	18473209	18473296	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	CDS	18473297	18473697	0.9	+	2	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	exon	18473297	18473697	.	+	.	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
Phchi.S1	AUGUSTUS	stop_codon	18473698	18473700	.	+	0	transcript_id "Phchi.S1G286700.t1"; gene_id "Phchi.S1G286700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3804.t1 is derived from g973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5814962	5816373	.	+	.	Phchi.S1G096300
Phchi.S1	AUGUSTUS	transcript	5814962	5816373	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	start_codon	5814962	5814964	.	+	0	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	CDS	5814962	5815270	1	+	0	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	exon	5814962	5815270	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	intron	5815271	5815370	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	CDS	5815371	5815514	1	+	0	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	exon	5815371	5815514	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	intron	5815515	5815662	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	CDS	5815663	5815911	1	+	0	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	exon	5815663	5815911	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	intron	5815912	5816045	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	CDS	5816046	5816154	1	+	0	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	exon	5816046	5816154	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	intron	5816155	5816269	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	CDS	5816270	5816373	1	+	2	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	exon	5816270	5816373	.	+	.	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
Phchi.S1	AUGUSTUS	stop_codon	5816374	5816376	.	+	0	transcript_id "Phchi.S1G096300.t1"; gene_id "Phchi.S1G096300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2585.t1 is derived from g9505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7492861	7494551	.	+	.	Phchi.S5G119400
Phchi.S5	AUGUSTUS	transcript	7492861	7494551	.	+	.	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	start_codon	7492861	7492863	.	+	0	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	CDS	7492861	7493977	0.42	+	0	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	exon	7492861	7493977	.	+	.	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	intron	7493978	7494054	.	+	.	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	CDS	7494055	7494551	1	+	2	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	exon	7494055	7494551	.	+	.	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
Phchi.S5	AUGUSTUS	stop_codon	7494552	7494554	.	+	0	transcript_id "Phchi.S5G119400.t1"; gene_id "Phchi.S5G119400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg246.t1 is derived from g10028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1698992	1700124	.	+	.	Phchi.S6G020500
Phchi.S6	AUGUSTUS	transcript	1698992	1700124	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	start_codon	1698992	1698994	.	+	0	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	CDS	1698992	1699208	0.44	+	0	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	exon	1698992	1699208	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	intron	1699209	1699369	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	CDS	1699370	1699403	0.4	+	2	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	exon	1699370	1699403	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	intron	1699404	1699535	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	CDS	1699536	1699677	0.33	+	1	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	exon	1699536	1699677	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	intron	1699678	1699962	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	CDS	1699963	1700124	0.35	+	0	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	exon	1699963	1700124	.	+	.	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
Phchi.S6	AUGUSTUS	stop_codon	1700125	1700127	.	+	0	transcript_id "Phchi.S6G020500.t1"; gene_id "Phchi.S6G020500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10727.t1 is derived from g14777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1778830	1780692	.	-	.	Phchi.S4G030900
Phchi.S4	AUGUSTUS	transcript	1778830	1780692	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	stop_codon	1778827	1778829	.	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1778830	1778925	0.78	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1778830	1778925	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1778926	1779353	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1779354	1779443	0.54	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1779354	1779443	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1779444	1779550	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1779551	1779587	0.85	-	1	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1779551	1779587	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1779588	1779748	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1779749	1779886	0.98	-	1	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1779749	1779886	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1779887	1779971	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1779972	1780081	0.8	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1779972	1780081	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1780082	1780161	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1780162	1780217	1	-	2	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1780162	1780217	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1780218	1780302	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1780303	1780423	1	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1780303	1780423	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	intron	1780424	1780533	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	CDS	1780534	1780692	1	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	exon	1780534	1780692	.	-	.	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
Phchi.S4	AUGUSTUS	start_codon	1780690	1780692	.	-	0	transcript_id "Phchi.S4G030900.t1"; gene_id "Phchi.S4G030900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5451.t1 is derived from g2621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16918269	16919166	.	-	.	Phchi.S1G261000
Phchi.S1	AUGUSTUS	transcript	16918269	16919166	.	-	.	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	stop_codon	16918266	16918268	.	-	0	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	CDS	16918269	16919014	0.99	-	2	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	exon	16918269	16919014	.	-	.	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	intron	16919015	16919093	.	-	.	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	CDS	16919094	16919166	0.99	-	0	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	exon	16919094	16919166	.	-	.	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
Phchi.S1	AUGUSTUS	start_codon	16919164	16919166	.	-	0	transcript_id "Phchi.S1G261000.t1"; gene_id "Phchi.S1G261000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10863.t1 is derived from g14913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2650235	2650912	.	-	.	Phchi.S4G044500
Phchi.S4	AUGUSTUS	transcript	2650235	2650912	.	-	.	transcript_id "Phchi.S4G044500.t1"; gene_id "Phchi.S4G044500"
Phchi.S4	AUGUSTUS	stop_codon	2650232	2650234	.	-	0	transcript_id "Phchi.S4G044500.t1"; gene_id "Phchi.S4G044500"
Phchi.S4	AUGUSTUS	CDS	2650235	2650912	0.49	-	0	transcript_id "Phchi.S4G044500.t1"; gene_id "Phchi.S4G044500"
Phchi.S4	AUGUSTUS	exon	2650235	2650912	.	-	.	transcript_id "Phchi.S4G044500.t1"; gene_id "Phchi.S4G044500"
Phchi.S4	AUGUSTUS	start_codon	2650910	2650912	.	-	0	transcript_id "Phchi.S4G044500.t1"; gene_id "Phchi.S4G044500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5513.t1 is derived from g2683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17179430	17179888	.	+	.	Phchi.S1G267200
Phchi.S1	AUGUSTUS	transcript	17179430	17179888	.	+	.	transcript_id "Phchi.S1G267200.t1"; gene_id "Phchi.S1G267200"
Phchi.S1	AUGUSTUS	start_codon	17179430	17179432	.	+	0	transcript_id "Phchi.S1G267200.t1"; gene_id "Phchi.S1G267200"
Phchi.S1	AUGUSTUS	CDS	17179430	17179888	1	+	0	transcript_id "Phchi.S1G267200.t1"; gene_id "Phchi.S1G267200"
Phchi.S1	AUGUSTUS	exon	17179430	17179888	.	+	.	transcript_id "Phchi.S1G267200.t1"; gene_id "Phchi.S1G267200"
Phchi.S1	AUGUSTUS	stop_codon	17179889	17179891	.	+	0	transcript_id "Phchi.S1G267200.t1"; gene_id "Phchi.S1G267200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8741.t1 is derived from g5916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37760425	37761452	.	-	.	Phchi.S1G590000
Phchi.S1	AUGUSTUS	transcript	37760425	37761452	.	-	.	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	stop_codon	37760422	37760424	.	-	0	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	CDS	37760425	37760968	0.99	-	1	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	exon	37760425	37760968	.	-	.	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	intron	37760969	37761120	.	-	.	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	CDS	37761121	37761452	0.93	-	0	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	exon	37761121	37761452	.	-	.	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
Phchi.S1	AUGUSTUS	start_codon	37761450	37761452	.	-	0	transcript_id "Phchi.S1G590000.t1"; gene_id "Phchi.S1G590000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15988.t1 is derived from g14425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C148	AUGUSTUS	gene	12682	14583	.	-	.	Phchi.C148G000100
Phchi.C148	AUGUSTUS	transcript	12682	14583	.	-	.	transcript_id "Phchi.C148G000100.t1"; gene_id "Phchi.C148G000100"
Phchi.C148	AUGUSTUS	stop_codon	12679	12681	.	-	0	transcript_id "Phchi.C148G000100.t1"; gene_id "Phchi.C148G000100"
Phchi.C148	AUGUSTUS	CDS	12682	14583	0.69	-	0	transcript_id "Phchi.C148G000100.t1"; gene_id "Phchi.C148G000100"
Phchi.C148	AUGUSTUS	exon	12682	14583	.	-	.	transcript_id "Phchi.C148G000100.t1"; gene_id "Phchi.C148G000100"
Phchi.C148	AUGUSTUS	start_codon	14581	14583	.	-	0	transcript_id "Phchi.C148G000100.t1"; gene_id "Phchi.C148G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11471.t1 is derived from g15521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6515454	6515660	.	-	.	Phchi.S4G105300
Phchi.S4	AUGUSTUS	transcript	6515454	6515660	.	-	.	transcript_id "Phchi.S4G105300.t1"; gene_id "Phchi.S4G105300"
Phchi.S4	AUGUSTUS	stop_codon	6515451	6515453	.	-	0	transcript_id "Phchi.S4G105300.t1"; gene_id "Phchi.S4G105300"
Phchi.S4	AUGUSTUS	CDS	6515454	6515660	0.95	-	0	transcript_id "Phchi.S4G105300.t1"; gene_id "Phchi.S4G105300"
Phchi.S4	AUGUSTUS	exon	6515454	6515660	.	-	.	transcript_id "Phchi.S4G105300.t1"; gene_id "Phchi.S4G105300"
Phchi.S4	AUGUSTUS	start_codon	6515658	6515660	.	-	0	transcript_id "Phchi.S4G105300.t1"; gene_id "Phchi.S4G105300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2131.t1 is derived from g9051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4988715	4994174	.	-	.	Phchi.S5G074000
Phchi.S5	AUGUSTUS	transcript	4988715	4994174	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	stop_codon	4988712	4988714	.	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4988715	4988822	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4988715	4988822	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4988823	4988917	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4988918	4989001	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4988918	4989001	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989002	4989096	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4989097	4989177	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4989097	4989177	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989178	4989302	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4989303	4989324	0.43	-	1	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4989303	4989324	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989325	4989422	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4989423	4989479	0.43	-	1	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4989423	4989479	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989480	4989559	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4989560	4989703	0.91	-	1	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4989560	4989703	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989704	4989792	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4989793	4989839	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4989793	4989839	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989840	4989939	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4989940	4989996	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4989940	4989996	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4989997	4990149	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4990150	4990248	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4990150	4990248	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4990249	4990428	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4990429	4990551	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4990429	4990551	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4990552	4990657	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4990658	4990780	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4990658	4990780	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4990781	4990866	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4990867	4990980	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4990867	4990980	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4990981	4991065	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4991066	4991254	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4991066	4991254	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4991255	4991348	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4991349	4991515	1	-	2	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4991349	4991515	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4991516	4991633	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4991634	4991718	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4991634	4991718	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4991719	4991798	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4991799	4991996	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4991799	4991996	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4991997	4992109	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4992110	4992199	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4992110	4992199	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4992200	4992294	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4992295	4992480	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4992295	4992480	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4992481	4992573	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4992574	4992848	0.54	-	2	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4992574	4992848	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4992849	4993168	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4993169	4993228	0.74	-	2	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4993169	4993228	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4993229	4993383	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4993384	4993473	0.94	-	2	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4993384	4993473	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4993474	4993628	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4993629	4993695	1	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4993629	4993695	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	intron	4993696	4994087	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	CDS	4994088	4994174	0.92	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	exon	4994088	4994174	.	-	.	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
Phchi.S5	AUGUSTUS	start_codon	4994172	4994174	.	-	0	transcript_id "Phchi.S5G074000.t1"; gene_id "Phchi.S5G074000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1879.t1 is derived from g8799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3680662	3681147	.	-	.	Phchi.S5G048800
Phchi.S5	AUGUSTUS	transcript	3680662	3681147	.	-	.	transcript_id "Phchi.S5G048800.t1"; gene_id "Phchi.S5G048800"
Phchi.S5	AUGUSTUS	stop_codon	3680659	3680661	.	-	0	transcript_id "Phchi.S5G048800.t1"; gene_id "Phchi.S5G048800"
Phchi.S5	AUGUSTUS	CDS	3680662	3681147	0.96	-	0	transcript_id "Phchi.S5G048800.t1"; gene_id "Phchi.S5G048800"
Phchi.S5	AUGUSTUS	exon	3680662	3681147	.	-	.	transcript_id "Phchi.S5G048800.t1"; gene_id "Phchi.S5G048800"
Phchi.S5	AUGUSTUS	start_codon	3681145	3681147	.	-	0	transcript_id "Phchi.S5G048800.t1"; gene_id "Phchi.S5G048800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1564.t1 is derived from g8483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1776908	1777540	.	-	.	Phchi.S5G017300
Phchi.S5	AUGUSTUS	transcript	1776908	1777540	.	-	.	transcript_id "Phchi.S5G017300.t1"; gene_id "Phchi.S5G017300"
Phchi.S5	AUGUSTUS	stop_codon	1776905	1776907	.	-	0	transcript_id "Phchi.S5G017300.t1"; gene_id "Phchi.S5G017300"
Phchi.S5	AUGUSTUS	CDS	1776908	1777540	1	-	0	transcript_id "Phchi.S5G017300.t1"; gene_id "Phchi.S5G017300"
Phchi.S5	AUGUSTUS	exon	1776908	1777540	.	-	.	transcript_id "Phchi.S5G017300.t1"; gene_id "Phchi.S5G017300"
Phchi.S5	AUGUSTUS	start_codon	1777538	1777540	.	-	0	transcript_id "Phchi.S5G017300.t1"; gene_id "Phchi.S5G017300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13128.t1 is derived from g11593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4263430	4264662	.	-	.	Phchi.S3G044700
Phchi.S3	AUGUSTUS	transcript	4263430	4264662	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	stop_codon	4263427	4263429	.	-	0	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	CDS	4263430	4263468	0.84	-	0	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	exon	4263430	4263468	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	intron	4263469	4263588	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	CDS	4263589	4263640	0.92	-	1	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	exon	4263589	4263640	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	intron	4263641	4263718	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	CDS	4263719	4263730	0.97	-	1	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	exon	4263719	4263730	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	intron	4263731	4263929	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	CDS	4263930	4263939	0.94	-	2	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	exon	4263930	4263939	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	intron	4263940	4264036	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	CDS	4264037	4264136	0.93	-	0	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	exon	4264037	4264136	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	intron	4264137	4264296	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	CDS	4264297	4264662	0.46	-	0	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	exon	4264297	4264662	.	-	.	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
Phchi.S3	AUGUSTUS	start_codon	4264660	4264662	.	-	0	transcript_id "Phchi.S3G044700.t1"; gene_id "Phchi.S3G044700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2886.t1 is derived from g55.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	285436	285773	.	-	.	Phchi.S1G004500
Phchi.S1	AUGUSTUS	transcript	285436	285773	.	-	.	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	stop_codon	285433	285435	.	-	0	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	CDS	285436	285514	0.72	-	1	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	exon	285436	285514	.	-	.	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	intron	285515	285627	.	-	.	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	CDS	285628	285773	0.72	-	0	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	exon	285628	285773	.	-	.	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
Phchi.S1	AUGUSTUS	start_codon	285771	285773	.	-	0	transcript_id "Phchi.S1G004500.t1"; gene_id "Phchi.S1G004500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5792.t1 is derived from g2962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18971282	18975535	.	+	.	Phchi.S1G295100
Phchi.S1	AUGUSTUS	transcript	18971282	18975535	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	start_codon	18971282	18971284	.	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18971282	18971459	0.98	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18971282	18971459	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18971460	18971565	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18971566	18971624	1	+	2	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18971566	18971624	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18971625	18971724	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18971725	18971806	1	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18971725	18971806	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18971807	18971979	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18971980	18972092	1	+	2	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18971980	18972092	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18972093	18972188	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18972189	18972257	1	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18972189	18972257	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18972258	18972391	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18972392	18973039	0.92	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18972392	18973039	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18973040	18973235	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18973236	18973629	0.89	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18973236	18973629	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18973630	18973860	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18973861	18973912	0.89	+	2	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18973861	18973912	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18973913	18973992	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18973993	18974057	1	+	1	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18973993	18974057	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18974058	18974129	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18974130	18974209	1	+	2	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18974130	18974209	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18974210	18974282	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18974283	18974387	1	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18974283	18974387	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18974388	18974507	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18974508	18974647	1	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18974508	18974647	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18974648	18974812	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18974813	18974956	1	+	1	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18974813	18974956	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18974957	18975040	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18975041	18975193	1	+	1	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18975041	18975193	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	intron	18975194	18975327	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	CDS	18975328	18975535	1	+	1	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	exon	18975328	18975535	.	+	.	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
Phchi.S1	AUGUSTUS	stop_codon	18975536	18975538	.	+	0	transcript_id "Phchi.S1G295100.t1"; gene_id "Phchi.S1G295100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11030.t1 is derived from g15080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3727006	3729001	.	-	.	Phchi.S4G061200
Phchi.S4	AUGUSTUS	transcript	3727006	3729001	.	-	.	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	stop_codon	3727003	3727005	.	-	0	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	CDS	3727006	3727136	0.73	-	2	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	exon	3727006	3727136	.	-	.	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	intron	3727137	3727259	.	-	.	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	CDS	3727260	3728172	0.7	-	0	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	exon	3727260	3728172	.	-	.	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	intron	3728173	3728407	.	-	.	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	CDS	3728408	3729001	0.97	-	0	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	exon	3728408	3729001	.	-	.	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
Phchi.S4	AUGUSTUS	start_codon	3728999	3729001	.	-	0	transcript_id "Phchi.S4G061200.t1"; gene_id "Phchi.S4G061200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4385.t1 is derived from g1554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10174383	10174838	.	-	.	Phchi.S1G154400
Phchi.S1	AUGUSTUS	transcript	10174383	10174838	.	-	.	transcript_id "Phchi.S1G154400.t1"; gene_id "Phchi.S1G154400"
Phchi.S1	AUGUSTUS	stop_codon	10174380	10174382	.	-	0	transcript_id "Phchi.S1G154400.t1"; gene_id "Phchi.S1G154400"
Phchi.S1	AUGUSTUS	CDS	10174383	10174838	0.75	-	0	transcript_id "Phchi.S1G154400.t1"; gene_id "Phchi.S1G154400"
Phchi.S1	AUGUSTUS	exon	10174383	10174838	.	-	.	transcript_id "Phchi.S1G154400.t1"; gene_id "Phchi.S1G154400"
Phchi.S1	AUGUSTUS	start_codon	10174836	10174838	.	-	0	transcript_id "Phchi.S1G154400.t1"; gene_id "Phchi.S1G154400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13484.t1 is derived from g11951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7121652	7122943	.	-	.	Phchi.S3G080300
Phchi.S3	AUGUSTUS	transcript	7121652	7122943	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	stop_codon	7121649	7121651	.	-	0	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	CDS	7121652	7121796	0.41	-	1	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	exon	7121652	7121796	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	intron	7121797	7121898	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	CDS	7121899	7122018	0.81	-	1	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	exon	7121899	7122018	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	intron	7122019	7122126	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	CDS	7122127	7122332	1	-	0	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	exon	7122127	7122332	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	intron	7122333	7122464	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	CDS	7122465	7122535	1	-	2	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	exon	7122465	7122535	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	intron	7122536	7122629	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	CDS	7122630	7122678	1	-	0	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	exon	7122630	7122678	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	intron	7122679	7122940	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	CDS	7122941	7122943	1	-	0	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	exon	7122941	7122943	.	-	.	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
Phchi.S3	AUGUSTUS	start_codon	7122941	7122943	.	-	0	transcript_id "Phchi.S3G080300.t1"; gene_id "Phchi.S3G080300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4254.t1 is derived from g1423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9178016	9179111	.	-	.	Phchi.S1G141300
Phchi.S1	AUGUSTUS	transcript	9178016	9179111	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	stop_codon	9178013	9178015	.	-	0	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	CDS	9178016	9178111	0.27	-	0	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	exon	9178016	9178111	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	intron	9178112	9178313	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	CDS	9178314	9178378	1	-	2	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	exon	9178314	9178378	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	intron	9178379	9178631	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	CDS	9178632	9178654	1	-	1	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	exon	9178632	9178654	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	intron	9178655	9178724	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	CDS	9178725	9178738	1	-	0	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	exon	9178725	9178738	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	intron	9178739	9178860	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	CDS	9178861	9178945	1	-	1	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	exon	9178861	9178945	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	intron	9178946	9179031	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	CDS	9179032	9179111	0.89	-	0	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	exon	9179032	9179111	.	-	.	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
Phchi.S1	AUGUSTUS	start_codon	9179109	9179111	.	-	0	transcript_id "Phchi.S1G141300.t1"; gene_id "Phchi.S1G141300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12499.t1 is derived from g8176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30846717	30847953	.	-	.	Phchi.S2G057900
Phchi.S2	AUGUSTUS	transcript	30846717	30847953	.	-	.	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	stop_codon	30846714	30846716	.	-	0	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	CDS	30846717	30847227	0.75	-	1	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	exon	30846717	30847227	.	-	.	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	intron	30847228	30847304	.	-	.	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	CDS	30847305	30847473	0.51	-	2	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	exon	30847305	30847473	.	-	.	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	intron	30847474	30847727	.	-	.	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	CDS	30847728	30847953	0.21	-	0	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	exon	30847728	30847953	.	-	.	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
Phchi.S2	AUGUSTUS	start_codon	30847951	30847953	.	-	0	transcript_id "Phchi.S2G057900.t1"; gene_id "Phchi.S2G057900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10198.t1 is derived from g7375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46342430	46346241	.	-	.	Phchi.S1G735800
Phchi.S1	AUGUSTUS	transcript	46342430	46346241	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	stop_codon	46342427	46342429	.	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46342430	46343797	0.9	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46342430	46343797	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46343798	46343889	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46343890	46343950	1	-	1	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46343890	46343950	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46343951	46344040	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46344041	46344360	0.98	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46344041	46344360	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46344361	46344437	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46344438	46344533	0.6	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46344438	46344533	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46344534	46344661	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46344662	46344793	0.91	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46344662	46344793	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46344794	46344883	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46344884	46345004	1	-	1	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46344884	46345004	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345005	46345089	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46345090	46345226	0.93	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46345090	46345226	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345227	46345359	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46345360	46345370	0.58	-	2	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46345360	46345370	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345371	46345462	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46345463	46345529	1	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46345463	46345529	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345530	46345606	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46345607	46345623	1	-	2	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46345607	46345623	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345624	46345675	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46345676	46345682	1	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46345676	46345682	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345683	46345854	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46345855	46345966	1	-	1	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46345855	46345966	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	intron	46345967	46346041	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	CDS	46346042	46346241	0.99	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	exon	46346042	46346241	.	-	.	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
Phchi.S1	AUGUSTUS	start_codon	46346239	46346241	.	-	0	transcript_id "Phchi.S1G735800.t1"; gene_id "Phchi.S1G735800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13199.t1 is derived from g11664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4648018	4648518	.	+	.	Phchi.S3G051800
Phchi.S3	AUGUSTUS	transcript	4648018	4648518	.	+	.	transcript_id "Phchi.S3G051800.t1"; gene_id "Phchi.S3G051800"
Phchi.S3	AUGUSTUS	start_codon	4648018	4648020	.	+	0	transcript_id "Phchi.S3G051800.t1"; gene_id "Phchi.S3G051800"
Phchi.S3	AUGUSTUS	CDS	4648018	4648518	0.99	+	0	transcript_id "Phchi.S3G051800.t1"; gene_id "Phchi.S3G051800"
Phchi.S3	AUGUSTUS	exon	4648018	4648518	.	+	.	transcript_id "Phchi.S3G051800.t1"; gene_id "Phchi.S3G051800"
Phchi.S3	AUGUSTUS	stop_codon	4648519	4648521	.	+	0	transcript_id "Phchi.S3G051800.t1"; gene_id "Phchi.S3G051800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9189.t1 is derived from g6364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40269966	40271649	.	-	.	Phchi.S1G634800
Phchi.S1	AUGUSTUS	transcript	40269966	40271649	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	stop_codon	40269963	40269965	.	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40269966	40270024	1	-	2	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40269966	40270024	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40270025	40270120	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40270121	40270300	1	-	2	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40270121	40270300	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40270301	40270373	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40270374	40270464	1	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40270374	40270464	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40270465	40270593	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40270594	40270642	1	-	1	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40270594	40270642	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40270643	40270792	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40270793	40270957	0.99	-	1	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40270793	40270957	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40270958	40271061	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40271062	40271108	0.91	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40271062	40271108	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40271109	40271224	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40271225	40271347	0.88	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40271225	40271347	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40271348	40271443	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40271444	40271509	0.99	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40271444	40271509	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	intron	40271510	40271634	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	CDS	40271635	40271649	0.83	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	exon	40271635	40271649	.	-	.	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
Phchi.S1	AUGUSTUS	start_codon	40271647	40271649	.	-	0	transcript_id "Phchi.S1G634800.t1"; gene_id "Phchi.S1G634800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14449.t1 is derived from g12917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12894109	12894806	.	+	.	Phchi.S3G176800
Phchi.S3	AUGUSTUS	transcript	12894109	12894806	.	+	.	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	start_codon	12894109	12894111	.	+	0	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	CDS	12894109	12894347	0.34	+	0	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	exon	12894109	12894347	.	+	.	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	intron	12894348	12894463	.	+	.	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	CDS	12894464	12894806	0.18	+	1	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	exon	12894464	12894806	.	+	.	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
Phchi.S3	AUGUSTUS	stop_codon	12894807	12894809	.	+	0	transcript_id "Phchi.S3G176800.t1"; gene_id "Phchi.S3G176800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4434.t1 is derived from g1603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10488102	10490127	.	+	.	Phchi.S1G159300
Phchi.S1	AUGUSTUS	transcript	10488102	10490127	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	start_codon	10488102	10488104	.	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10488102	10488162	1	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10488102	10488162	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10488163	10488251	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10488252	10488336	0.83	+	2	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10488252	10488336	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10488337	10488442	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10488443	10488518	1	+	1	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10488443	10488518	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10488519	10488593	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10488594	10488754	1	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10488594	10488754	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10488755	10488876	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10488877	10489042	1	+	1	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10488877	10489042	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10489043	10489260	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10489261	10489377	1	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10489261	10489377	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10489378	10489585	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10489586	10489681	1	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10489586	10489681	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	intron	10489682	10489851	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	CDS	10489852	10490127	0.99	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	exon	10489852	10490127	.	+	.	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
Phchi.S1	AUGUSTUS	stop_codon	10490128	10490130	.	+	0	transcript_id "Phchi.S1G159300.t1"; gene_id "Phchi.S1G159300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7740.t1 is derived from g4914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30916396	30918613	.	-	.	Phchi.S1G489900
Phchi.S1	AUGUSTUS	transcript	30916396	30918613	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	stop_codon	30916393	30916395	.	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30916396	30916473	1	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30916396	30916473	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	intron	30916474	30916554	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30916555	30916620	1	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30916555	30916620	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	intron	30916621	30916705	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30916706	30916899	0.84	-	2	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30916706	30916899	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	intron	30916900	30917003	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30917004	30917262	1	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30917004	30917262	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	intron	30917263	30917450	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30917451	30917675	0.99	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30917451	30917675	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	intron	30917676	30917768	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30917769	30918129	1	-	1	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30917769	30918129	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	intron	30918130	30918224	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	CDS	30918225	30918613	0.97	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	exon	30918225	30918613	.	-	.	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
Phchi.S1	AUGUSTUS	start_codon	30918611	30918613	.	-	0	transcript_id "Phchi.S1G489900.t1"; gene_id "Phchi.S1G489900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11571.t1 is derived from g15622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7108259	7110406	.	-	.	Phchi.S4G115300
Phchi.S4	AUGUSTUS	transcript	7108259	7110406	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	stop_codon	7108256	7108258	.	-	0	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	CDS	7108259	7108769	0.98	-	1	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	exon	7108259	7108769	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	intron	7108770	7108982	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	CDS	7108983	7109224	1	-	0	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	exon	7108983	7109224	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	intron	7109225	7109409	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	CDS	7109410	7109798	0.99	-	2	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	exon	7109410	7109798	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	intron	7109799	7110288	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	CDS	7110289	7110406	0.92	-	0	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	exon	7110289	7110406	.	-	.	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
Phchi.S4	AUGUSTUS	start_codon	7110404	7110406	.	-	0	transcript_id "Phchi.S4G115300.t1"; gene_id "Phchi.S4G115300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14178.t1 is derived from g12645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11305498	11307561	.	+	.	Phchi.S3G149700
Phchi.S3	AUGUSTUS	transcript	11305498	11307561	.	+	.	transcript_id "Phchi.S3G149700.t1"; gene_id "Phchi.S3G149700"
Phchi.S3	AUGUSTUS	start_codon	11305498	11305500	.	+	0	transcript_id "Phchi.S3G149700.t1"; gene_id "Phchi.S3G149700"
Phchi.S3	AUGUSTUS	CDS	11305498	11307561	1	+	0	transcript_id "Phchi.S3G149700.t1"; gene_id "Phchi.S3G149700"
Phchi.S3	AUGUSTUS	exon	11305498	11307561	.	+	.	transcript_id "Phchi.S3G149700.t1"; gene_id "Phchi.S3G149700"
Phchi.S3	AUGUSTUS	stop_codon	11307562	11307564	.	+	0	transcript_id "Phchi.S3G149700.t1"; gene_id "Phchi.S3G149700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11498.t1 is derived from g15548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6668308	6669047	.	+	.	Phchi.S4G108000
Phchi.S4	AUGUSTUS	transcript	6668308	6669047	.	+	.	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	start_codon	6668308	6668310	.	+	0	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	CDS	6668308	6668635	0.9	+	0	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	exon	6668308	6668635	.	+	.	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	intron	6668636	6668739	.	+	.	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	CDS	6668740	6669047	0.84	+	2	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	exon	6668740	6669047	.	+	.	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
Phchi.S4	AUGUSTUS	stop_codon	6669048	6669050	.	+	0	transcript_id "Phchi.S4G108000.t1"; gene_id "Phchi.S4G108000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1268.t1 is derived from g11051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8744961	8747572	.	-	.	Phchi.S6G122700
Phchi.S6	AUGUSTUS	transcript	8744961	8747572	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	stop_codon	8744958	8744960	.	-	0	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8744961	8745337	0.91	-	2	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8744961	8745337	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	intron	8745338	8745413	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8745414	8745687	0.85	-	0	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8745414	8745687	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	intron	8745688	8745774	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8745775	8746369	0.95	-	1	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8745775	8746369	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	intron	8746370	8746432	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8746433	8746476	0.81	-	0	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8746433	8746476	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	intron	8746477	8746633	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8746634	8746734	0.68	-	2	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8746634	8746734	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	intron	8746735	8746900	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8746901	8747097	0.98	-	1	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8746901	8747097	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	intron	8747098	8747372	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	CDS	8747373	8747572	0.91	-	0	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	exon	8747373	8747572	.	-	.	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
Phchi.S6	AUGUSTUS	start_codon	8747570	8747572	.	-	0	transcript_id "Phchi.S6G122700.t1"; gene_id "Phchi.S6G122700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15005.t1 is derived from g13473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16330754	16331878	.	+	.	Phchi.S3G232400
Phchi.S3	AUGUSTUS	transcript	16330754	16331878	.	+	.	transcript_id "Phchi.S3G232400.t1"; gene_id "Phchi.S3G232400"
Phchi.S3	AUGUSTUS	start_codon	16330754	16330756	.	+	0	transcript_id "Phchi.S3G232400.t1"; gene_id "Phchi.S3G232400"
Phchi.S3	AUGUSTUS	CDS	16330754	16331878	1	+	0	transcript_id "Phchi.S3G232400.t1"; gene_id "Phchi.S3G232400"
Phchi.S3	AUGUSTUS	exon	16330754	16331878	.	+	.	transcript_id "Phchi.S3G232400.t1"; gene_id "Phchi.S3G232400"
Phchi.S3	AUGUSTUS	stop_codon	16331879	16331881	.	+	0	transcript_id "Phchi.S3G232400.t1"; gene_id "Phchi.S3G232400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2443.t1 is derived from g9363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6652220	6654522	.	-	.	Phchi.S5G105200
Phchi.S5	AUGUSTUS	transcript	6652220	6654522	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	stop_codon	6652217	6652219	.	-	0	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	CDS	6652220	6652401	0.67	-	2	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	exon	6652220	6652401	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	intron	6652402	6652534	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	CDS	6652535	6652638	0.61	-	1	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	exon	6652535	6652638	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	intron	6652639	6652769	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	CDS	6652770	6652826	1	-	1	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	exon	6652770	6652826	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	intron	6652827	6653338	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	CDS	6653339	6654522	0.76	-	0	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	exon	6653339	6654522	.	-	.	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
Phchi.S5	AUGUSTUS	start_codon	6654520	6654522	.	-	0	transcript_id "Phchi.S5G105200.t1"; gene_id "Phchi.S5G105200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6819.t1 is derived from g3991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25199116	25200535	.	+	.	Phchi.S1G397800
Phchi.S1	AUGUSTUS	transcript	25199116	25200535	.	+	.	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	start_codon	25199116	25199118	.	+	0	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	CDS	25199116	25199397	0.19	+	0	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	exon	25199116	25199397	.	+	.	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	intron	25199398	25199494	.	+	.	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	CDS	25199495	25200535	0.3	+	0	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	exon	25199495	25200535	.	+	.	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
Phchi.S1	AUGUSTUS	stop_codon	25200536	25200538	.	+	0	transcript_id "Phchi.S1G397800.t1"; gene_id "Phchi.S1G397800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5074.t1 is derived from g2244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14558115	14558900	.	-	.	Phchi.S1G223300
Phchi.S1	AUGUSTUS	transcript	14558115	14558900	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	stop_codon	14558112	14558114	.	-	0	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	CDS	14558115	14558203	0.97	-	2	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	exon	14558115	14558203	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	intron	14558204	14558302	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	CDS	14558303	14558504	1	-	0	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	exon	14558303	14558504	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	intron	14558505	14558584	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	CDS	14558585	14558731	1	-	0	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	exon	14558585	14558731	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	intron	14558732	14558879	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	CDS	14558880	14558900	1	-	0	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	exon	14558880	14558900	.	-	.	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
Phchi.S1	AUGUSTUS	start_codon	14558898	14558900	.	-	0	transcript_id "Phchi.S1G223300.t1"; gene_id "Phchi.S1G223300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10635.t1 is derived from g14685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1358170	1359231	.	+	.	Phchi.S4G021700
Phchi.S4	AUGUSTUS	transcript	1358170	1359231	.	+	.	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	start_codon	1358170	1358172	.	+	0	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	CDS	1358170	1358448	0.88	+	0	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	exon	1358170	1358448	.	+	.	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	intron	1358449	1358537	.	+	.	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	CDS	1358538	1358987	0.83	+	0	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	exon	1358538	1358987	.	+	.	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	intron	1358988	1359219	.	+	.	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	CDS	1359220	1359231	0.83	+	0	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	exon	1359220	1359231	.	+	.	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
Phchi.S4	AUGUSTUS	stop_codon	1359232	1359234	.	+	0	transcript_id "Phchi.S4G021700.t1"; gene_id "Phchi.S4G021700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13451.t1 is derived from g11918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6833267	6833874	.	-	.	Phchi.S3G077000
Phchi.S3	AUGUSTUS	transcript	6833267	6833874	.	-	.	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	stop_codon	6833264	6833266	.	-	0	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	CDS	6833267	6833428	0.98	-	0	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	exon	6833267	6833428	.	-	.	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	intron	6833429	6833517	.	-	.	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	CDS	6833518	6833546	0.54	-	2	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	exon	6833518	6833546	.	-	.	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	intron	6833547	6833705	.	-	.	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	CDS	6833706	6833874	0.24	-	0	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	exon	6833706	6833874	.	-	.	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
Phchi.S3	AUGUSTUS	start_codon	6833872	6833874	.	-	0	transcript_id "Phchi.S3G077000.t1"; gene_id "Phchi.S3G077000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8287.t1 is derived from g5462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35102945	35105335	.	-	.	Phchi.S1G544600
Phchi.S1	AUGUSTUS	transcript	35102945	35105335	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	stop_codon	35102942	35102944	.	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35102945	35102998	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35102945	35102998	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35102999	35103095	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35103096	35103187	1	-	2	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35103096	35103187	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35103188	35103270	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35103271	35103343	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35103271	35103343	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35103344	35103423	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35103424	35103492	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35103424	35103492	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35103493	35103592	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35103593	35103655	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35103593	35103655	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35103656	35103755	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35103756	35103812	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35103756	35103812	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35103813	35104019	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35104020	35104112	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35104020	35104112	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35104113	35104234	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35104235	35104300	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35104235	35104300	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35104301	35104402	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35104403	35104454	1	-	1	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35104403	35104454	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35104455	35104592	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35104593	35104640	1	-	1	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35104593	35104640	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35104641	35104765	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35104766	35104845	1	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35104766	35104845	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35104846	35104978	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35104979	35105136	1	-	2	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35104979	35105136	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	intron	35105137	35105265	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	CDS	35105266	35105335	0.8	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	exon	35105266	35105335	.	-	.	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
Phchi.S1	AUGUSTUS	start_codon	35105333	35105335	.	-	0	transcript_id "Phchi.S1G544600.t1"; gene_id "Phchi.S1G544600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8216.t1 is derived from g5391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34458044	34459351	.	-	.	Phchi.S1G537500
Phchi.S1	AUGUSTUS	transcript	34458044	34459351	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	stop_codon	34458041	34458043	.	-	0	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	CDS	34458044	34458163	0.98	-	0	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	exon	34458044	34458163	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	intron	34458164	34458263	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	CDS	34458264	34458277	0.76	-	2	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	exon	34458264	34458277	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	intron	34458278	34458431	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	CDS	34458432	34459058	0.53	-	2	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	exon	34458432	34459058	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	intron	34459059	34459281	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	CDS	34459282	34459351	0.74	-	0	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	exon	34459282	34459351	.	-	.	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
Phchi.S1	AUGUSTUS	start_codon	34459349	34459351	.	-	0	transcript_id "Phchi.S1G537500.t1"; gene_id "Phchi.S1G537500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9321.t1 is derived from g6496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40933798	40935701	.	+	.	Phchi.S1G648000
Phchi.S1	AUGUSTUS	transcript	40933798	40935701	.	+	.	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	start_codon	40933798	40933800	.	+	0	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	CDS	40933798	40934766	0.5	+	0	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	exon	40933798	40934766	.	+	.	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	intron	40934767	40934852	.	+	.	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	CDS	40934853	40935136	1	+	0	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	exon	40934853	40935136	.	+	.	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	intron	40935137	40935211	.	+	.	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	CDS	40935212	40935701	0.87	+	1	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	exon	40935212	40935701	.	+	.	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
Phchi.S1	AUGUSTUS	stop_codon	40935702	40935704	.	+	0	transcript_id "Phchi.S1G648000.t1"; gene_id "Phchi.S1G648000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11348.t1 is derived from g15398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5673680	5679033	.	+	.	Phchi.S4G093000
Phchi.S4	AUGUSTUS	transcript	5673680	5679033	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	start_codon	5673680	5673682	.	+	0	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5673680	5673694	0.79	+	0	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5673680	5673694	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5673695	5673961	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5673962	5673981	0.69	+	0	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5673962	5673981	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5673982	5674143	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5674144	5674273	0.63	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5674144	5674273	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5674274	5674491	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5674492	5674819	0.85	+	0	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5674492	5674819	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5674820	5674896	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5674897	5675029	1	+	2	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5674897	5675029	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5675030	5675122	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5675123	5675197	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5675123	5675197	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5675198	5675322	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5675323	5675394	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5675323	5675394	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5675395	5675479	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5675480	5675551	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5675480	5675551	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5675552	5675652	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5675653	5675724	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5675653	5675724	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5675725	5675802	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5675803	5675874	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5675803	5675874	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5675875	5675957	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5675958	5676050	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5675958	5676050	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5676051	5676158	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5676159	5676230	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5676159	5676230	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5676231	5676346	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5676347	5676418	0.99	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5676347	5676418	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5676419	5676510	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5676511	5676570	0.99	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5676511	5676570	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5676571	5676678	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5676679	5676869	1	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5676679	5676869	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5676870	5676954	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5676955	5677182	0.97	+	2	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5676955	5677182	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5677183	5677295	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5677296	5677364	0.96	+	2	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5677296	5677364	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5677365	5677447	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5677448	5677507	1	+	2	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5677448	5677507	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5677508	5677592	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5677593	5677655	1	+	2	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5677593	5677655	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5677656	5677756	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5677757	5677817	1	+	2	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5677757	5677817	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5677818	5677941	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5677942	5678203	0.99	+	1	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5677942	5678203	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	intron	5678204	5678322	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	CDS	5678323	5679033	1	+	0	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	exon	5678323	5679033	.	+	.	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
Phchi.S4	AUGUSTUS	stop_codon	5679034	5679036	.	+	0	transcript_id "Phchi.S4G093000.t1"; gene_id "Phchi.S4G093000"
# This transcript jg13435.t2 is derived from g11902.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13436.t1 is derived from g11903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6687671	6689802	.	-	.	Phchi.S3G075500
Phchi.S3	AUGUSTUS	transcript	6687671	6689265	.	-	.	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	stop_codon	6687668	6687670	.	-	0	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6687671	6688024	0.94	-	0	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6687671	6688024	.	-	.	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	intron	6688025	6688261	.	-	.	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6688262	6688737	0.78	-	2	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6688262	6688737	.	-	.	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	intron	6688738	6688886	.	-	.	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6688887	6689265	0.37	-	0	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6688887	6689265	.	-	.	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	start_codon	6689263	6689265	.	-	0	transcript_id "Phchi.S3G075500.t1"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	transcript	6687671	6689802	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	stop_codon	6687668	6687670	.	-	0	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6687671	6688024	0.93	-	0	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6687671	6688024	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	intron	6688025	6688261	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6688262	6688737	0.66	-	2	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6688262	6688737	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	intron	6688738	6688886	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6688887	6689150	0.36	-	2	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6688887	6689150	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	intron	6689151	6689277	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6689278	6689424	0.76	-	2	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6689278	6689424	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	intron	6689425	6689552	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	CDS	6689553	6689802	0.91	-	0	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	exon	6689553	6689802	.	-	.	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
Phchi.S3	AUGUSTUS	start_codon	6689800	6689802	.	-	0	transcript_id "Phchi.S3G075500.t2"; gene_id "Phchi.S3G075500"
# This transcript jg8283.t1 is derived from g5458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35082065	35082675	.	+	.	Phchi.S1G544200
Phchi.S1	AUGUSTUS	transcript	35082065	35082675	.	+	.	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	start_codon	35082065	35082067	.	+	0	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	CDS	35082065	35082364	0.57	+	0	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	exon	35082065	35082364	.	+	.	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	intron	35082365	35082441	.	+	.	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	CDS	35082442	35082675	0.8	+	0	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	exon	35082442	35082675	.	+	.	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
Phchi.S1	AUGUSTUS	stop_codon	35082676	35082678	.	+	0	transcript_id "Phchi.S1G544200.t1"; gene_id "Phchi.S1G544200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1668.t1 is derived from g8587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2323993	2325561	.	-	.	Phchi.S5G027700
Phchi.S5	AUGUSTUS	transcript	2323993	2325561	.	-	.	transcript_id "Phchi.S5G027700.t1"; gene_id "Phchi.S5G027700"
Phchi.S5	AUGUSTUS	stop_codon	2323990	2323992	.	-	0	transcript_id "Phchi.S5G027700.t1"; gene_id "Phchi.S5G027700"
Phchi.S5	AUGUSTUS	CDS	2323993	2325561	0.94	-	0	transcript_id "Phchi.S5G027700.t1"; gene_id "Phchi.S5G027700"
Phchi.S5	AUGUSTUS	exon	2323993	2325561	.	-	.	transcript_id "Phchi.S5G027700.t1"; gene_id "Phchi.S5G027700"
Phchi.S5	AUGUSTUS	start_codon	2325559	2325561	.	-	0	transcript_id "Phchi.S5G027700.t1"; gene_id "Phchi.S5G027700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5175.t1 is derived from g2345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15336736	15338333	.	+	.	Phchi.S1G233400
Phchi.S1	AUGUSTUS	transcript	15336736	15338333	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	start_codon	15336736	15336738	.	+	0	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15336736	15336858	0.28	+	0	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15336736	15336858	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	intron	15336859	15337049	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15337050	15337071	1	+	0	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15337050	15337071	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	intron	15337072	15337147	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15337148	15337200	1	+	2	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15337148	15337200	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	intron	15337201	15337290	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15337291	15337494	0.62	+	0	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15337291	15337494	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	intron	15337495	15337640	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15337641	15337711	0.88	+	0	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15337641	15337711	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	intron	15337712	15337805	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15337806	15337897	0.96	+	1	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15337806	15337897	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	intron	15337898	15338073	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	CDS	15338074	15338333	0.69	+	2	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	exon	15338074	15338333	.	+	.	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
Phchi.S1	AUGUSTUS	stop_codon	15338334	15338336	.	+	0	transcript_id "Phchi.S1G233400.t1"; gene_id "Phchi.S1G233400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13779.t1 is derived from g12246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8869946	8870637	.	+	.	Phchi.S3G109800
Phchi.S3	AUGUSTUS	transcript	8869946	8870637	.	+	.	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	start_codon	8869946	8869948	.	+	0	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	CDS	8869946	8869963	0.37	+	0	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	exon	8869946	8869963	.	+	.	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	intron	8869964	8870106	.	+	.	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	CDS	8870107	8870396	0.82	+	0	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	exon	8870107	8870396	.	+	.	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	intron	8870397	8870531	.	+	.	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	CDS	8870532	8870637	0.81	+	1	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	exon	8870532	8870637	.	+	.	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
Phchi.S3	AUGUSTUS	stop_codon	8870638	8870640	.	+	0	transcript_id "Phchi.S3G109800.t1"; gene_id "Phchi.S3G109800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6909.t1 is derived from g4081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25936579	25942892	.	+	.	Phchi.S1G406800
Phchi.S1	AUGUSTUS	transcript	25936579	25942892	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	start_codon	25936579	25936581	.	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25936579	25936704	0.95	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25936579	25936704	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25936705	25937025	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25937026	25937076	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25937026	25937076	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25937077	25937508	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25937509	25937563	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25937509	25937563	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25937564	25937616	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25937617	25937625	1	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25937617	25937625	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25937626	25937935	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25937936	25938034	1	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25937936	25938034	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25938035	25938255	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25938256	25938320	1	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25938256	25938320	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25938321	25938470	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25938471	25938588	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25938471	25938588	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25938589	25938674	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25938675	25939017	0.99	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25938675	25939017	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25939018	25939151	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25939152	25939299	0.98	+	1	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25939152	25939299	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25939300	25939409	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25939410	25939511	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25939410	25939511	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25939512	25939952	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25939953	25940072	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25939953	25940072	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25940073	25940162	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25940163	25940186	0.87	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25940163	25940186	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25940187	25940350	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25940351	25940478	0.94	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25940351	25940478	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25940479	25940638	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25940639	25940723	1	+	1	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25940639	25940723	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25940724	25940864	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25940865	25940988	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25940865	25940988	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25940989	25941132	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25941133	25941212	1	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25941133	25941212	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25941213	25941302	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25941303	25941359	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25941303	25941359	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25941360	25941466	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25941467	25941629	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25941467	25941629	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25941630	25941718	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25941719	25941770	0.89	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25941719	25941770	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25941771	25941859	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25941860	25941902	0.87	+	1	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25941860	25941902	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25941903	25942022	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25942023	25942136	0.99	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25942023	25942136	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25942137	25942220	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25942221	25942288	1	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25942221	25942288	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25942289	25942392	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25942393	25942562	1	+	1	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25942393	25942562	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	intron	25942563	25942656	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	CDS	25942657	25942892	0.99	+	2	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	exon	25942657	25942892	.	+	.	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
Phchi.S1	AUGUSTUS	stop_codon	25942893	25942895	.	+	0	transcript_id "Phchi.S1G406800.t1"; gene_id "Phchi.S1G406800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg645.t1 is derived from g10427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4567089	4568321	.	+	.	Phchi.S6G060400
Phchi.S6	AUGUSTUS	transcript	4567089	4568321	.	+	.	transcript_id "Phchi.S6G060400.t1"; gene_id "Phchi.S6G060400"
Phchi.S6	AUGUSTUS	start_codon	4567089	4567091	.	+	0	transcript_id "Phchi.S6G060400.t1"; gene_id "Phchi.S6G060400"
Phchi.S6	AUGUSTUS	CDS	4567089	4568321	0.94	+	0	transcript_id "Phchi.S6G060400.t1"; gene_id "Phchi.S6G060400"
Phchi.S6	AUGUSTUS	exon	4567089	4568321	.	+	.	transcript_id "Phchi.S6G060400.t1"; gene_id "Phchi.S6G060400"
Phchi.S6	AUGUSTUS	stop_codon	4568322	4568324	.	+	0	transcript_id "Phchi.S6G060400.t1"; gene_id "Phchi.S6G060400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15044.t1 is derived from g13512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16731780	16734028	.	-	.	Phchi.S3G236300
Phchi.S3	AUGUSTUS	transcript	16731780	16734028	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	stop_codon	16731777	16731779	.	-	0	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	CDS	16731780	16731783	0.18	-	1	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	exon	16731780	16731783	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	intron	16731784	16731922	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	CDS	16731923	16733673	0.35	-	0	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	exon	16731923	16733673	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	intron	16733674	16733760	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	CDS	16733761	16733854	0.69	-	1	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	exon	16733761	16733854	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	intron	16733855	16733930	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	CDS	16733931	16734028	0.61	-	0	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	exon	16733931	16734028	.	-	.	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
Phchi.S3	AUGUSTUS	start_codon	16734026	16734028	.	-	0	transcript_id "Phchi.S3G236300.t1"; gene_id "Phchi.S3G236300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10543.t1 is derived from g14593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	883033	886650	.	+	.	Phchi.S4G012500
Phchi.S4	AUGUSTUS	transcript	883033	886650	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	start_codon	883033	883035	.	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	883033	883270	0.65	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	883033	883270	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	883271	883367	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	883368	883429	1	+	2	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	883368	883429	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	883430	883523	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	883524	883733	1	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	883524	883733	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	883734	883842	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	883843	883930	1	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	883843	883930	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	883931	884053	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	884054	884216	1	+	2	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	884054	884216	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	884217	884313	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	884314	884512	0.9	+	1	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	884314	884512	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	884513	884775	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	884776	884973	1	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	884776	884973	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	884974	885162	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	885163	885294	1	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	885163	885294	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	885295	885451	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	885452	885572	1	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	885452	885572	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	885573	885711	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	885712	885822	1	+	2	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	885712	885822	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	885823	885905	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	885906	885975	1	+	2	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	885906	885975	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	885976	886165	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	886166	886349	1	+	1	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	886166	886349	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	intron	886350	886437	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	CDS	886438	886650	0.98	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	exon	886438	886650	.	+	.	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
Phchi.S4	AUGUSTUS	stop_codon	886651	886653	.	+	0	transcript_id "Phchi.S4G012500.t1"; gene_id "Phchi.S4G012500"
# This transcript jg1500.t2 is derived from g8419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1501.t1 is derived from g8420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1222840	1228020	.	-	.	Phchi.S5G011000
Phchi.S5	AUGUSTUS	transcript	1222840	1228020	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	stop_codon	1222837	1222839	.	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1222840	1222941	1	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1222840	1222941	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1222942	1223027	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1223028	1223387	0.67	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1223028	1223387	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1223388	1223506	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1223507	1224362	0.68	-	1	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1223507	1224362	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1224363	1224451	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1224452	1224597	1	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1224452	1224597	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1224598	1224695	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1224696	1226504	0.52	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1224696	1226504	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1226505	1226662	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1226663	1226781	0.56	-	2	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1226663	1226781	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1226782	1226901	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1226902	1227028	0.89	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1226902	1227028	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1227029	1227158	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1227159	1227257	0.96	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1227159	1227257	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1227258	1227332	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1227333	1227395	1	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1227333	1227395	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1227396	1227477	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1227478	1227635	0.88	-	2	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1227478	1227635	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1227636	1227754	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1227755	1227867	0.96	-	1	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1227755	1227867	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	intron	1227868	1227964	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	CDS	1227965	1228020	0.65	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	exon	1227965	1228020	.	-	.	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
Phchi.S5	AUGUSTUS	start_codon	1228018	1228020	.	-	0	transcript_id "Phchi.S5G011000.t1"; gene_id "Phchi.S5G011000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9335.t1 is derived from g6510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40990426	40992642	.	-	.	Phchi.S1G649400
Phchi.S1	AUGUSTUS	transcript	40990426	40992642	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	stop_codon	40990423	40990425	.	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40990426	40990446	1	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40990426	40990446	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40990447	40990528	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40990529	40990623	1	-	2	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40990529	40990623	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40990624	40990923	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40990924	40990969	1	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40990924	40990969	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40990970	40991122	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991123	40991179	1	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991123	40991179	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991180	40991274	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991275	40991410	1	-	1	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991275	40991410	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991411	40991586	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991587	40991655	1	-	1	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991587	40991655	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991656	40991803	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991804	40991874	0.95	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991804	40991874	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991875	40991980	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991981	40992081	1	-	2	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991981	40992081	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40992082	40992179	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40992180	40992324	1	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40992180	40992324	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40992325	40992411	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40992412	40992642	0.61	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40992412	40992642	.	-	.	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	start_codon	40992640	40992642	.	-	0	transcript_id "Phchi.S1G649400.t1"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	transcript	40990426	40992642	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	stop_codon	40990423	40990425	.	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40990426	40990446	1	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40990426	40990446	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40990447	40990528	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40990529	40990623	1	-	2	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40990529	40990623	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40990624	40990923	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40990924	40990969	1	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40990924	40990969	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40990970	40991122	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991123	40991179	1	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991123	40991179	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991180	40991274	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991275	40991410	1	-	1	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991275	40991410	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991411	40991586	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991587	40991655	1	-	1	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991587	40991655	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991656	40991803	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991804	40991874	0.99	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991804	40991874	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40991875	40991980	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40991981	40992078	0.55	-	2	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40991981	40992078	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40992079	40992179	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40992180	40992324	0.9	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40992180	40992324	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	intron	40992325	40992411	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	CDS	40992412	40992642	0.6	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	exon	40992412	40992642	.	-	.	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
Phchi.S1	AUGUSTUS	start_codon	40992640	40992642	.	-	0	transcript_id "Phchi.S1G649400.t2"; gene_id "Phchi.S1G649400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15477.t1 is derived from g13945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19371880	19373078	.	+	.	Phchi.S3G279600
Phchi.S3	AUGUSTUS	transcript	19371880	19373078	.	+	.	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	start_codon	19371880	19371882	.	+	0	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	CDS	19371880	19372101	0.8	+	0	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	exon	19371880	19372101	.	+	.	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	intron	19372102	19372245	.	+	.	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	CDS	19372246	19372380	1	+	0	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	exon	19372246	19372380	.	+	.	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	intron	19372381	19372529	.	+	.	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	CDS	19372530	19373078	1	+	0	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	exon	19372530	19373078	.	+	.	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
Phchi.S3	AUGUSTUS	stop_codon	19373079	19373081	.	+	0	transcript_id "Phchi.S3G279600.t1"; gene_id "Phchi.S3G279600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2476.t1 is derived from g9396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6837716	6839786	.	+	.	Phchi.S5G108500
Phchi.S5	AUGUSTUS	transcript	6837716	6839786	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	start_codon	6837716	6837718	.	+	0	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6837716	6837775	1	+	0	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6837716	6837775	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6837776	6838004	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6838005	6838129	1	+	0	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6838005	6838129	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6838130	6838215	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6838216	6838276	1	+	1	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6838216	6838276	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6838277	6838420	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6838421	6838587	1	+	0	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6838421	6838587	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6838588	6838728	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6838729	6838843	1	+	1	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6838729	6838843	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6838844	6839079	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6839080	6839282	1	+	0	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6839080	6839282	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6839283	6839400	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6839401	6839541	0.99	+	1	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6839401	6839541	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	intron	6839542	6839653	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	CDS	6839654	6839786	1	+	1	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	exon	6839654	6839786	.	+	.	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
Phchi.S5	AUGUSTUS	stop_codon	6839787	6839789	.	+	0	transcript_id "Phchi.S5G108500.t1"; gene_id "Phchi.S5G108500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5874.t1 is derived from g3044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19523496	19524640	.	+	.	Phchi.S1G303300
Phchi.S1	AUGUSTUS	transcript	19523530	19524640	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	start_codon	19523530	19523532	.	+	0	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19523530	19523552	0.94	+	0	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19523530	19523552	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19523553	19523641	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19523642	19523792	1	+	1	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19523642	19523792	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19523793	19523947	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19523948	19524004	1	+	0	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19523948	19524004	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524005	19524196	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524197	19524256	1	+	0	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524197	19524256	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524257	19524416	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524417	19524423	1	+	0	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524417	19524423	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524424	19524499	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524500	19524529	1	+	2	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524500	19524529	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524530	19524614	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524615	19524640	1	+	2	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524615	19524640	.	+	.	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	stop_codon	19524641	19524643	.	+	0	transcript_id "Phchi.S1G303300.t1"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	transcript	19523496	19524640	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	start_codon	19523496	19523498	.	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19523496	19523552	0.32	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19523496	19523552	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19523553	19523627	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19523628	19523792	0.98	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19523628	19523792	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19523793	19523947	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19523948	19524004	1	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19523948	19524004	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524005	19524196	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524197	19524256	1	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524197	19524256	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524257	19524416	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524417	19524423	1	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524417	19524423	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524424	19524499	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524500	19524529	1	+	2	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524500	19524529	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	intron	19524530	19524614	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	CDS	19524615	19524640	1	+	2	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	exon	19524615	19524640	.	+	.	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
Phchi.S1	AUGUSTUS	stop_codon	19524641	19524643	.	+	0	transcript_id "Phchi.S1G303300.t2"; gene_id "Phchi.S1G303300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8877.t1 is derived from g6052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38418865	38419236	.	-	.	Phchi.S1G603600
Phchi.S1	AUGUSTUS	transcript	38418865	38419236	.	-	.	transcript_id "Phchi.S1G603600.t1"; gene_id "Phchi.S1G603600"
Phchi.S1	AUGUSTUS	stop_codon	38418862	38418864	.	-	0	transcript_id "Phchi.S1G603600.t1"; gene_id "Phchi.S1G603600"
Phchi.S1	AUGUSTUS	CDS	38418865	38419236	0.77	-	0	transcript_id "Phchi.S1G603600.t1"; gene_id "Phchi.S1G603600"
Phchi.S1	AUGUSTUS	exon	38418865	38419236	.	-	.	transcript_id "Phchi.S1G603600.t1"; gene_id "Phchi.S1G603600"
Phchi.S1	AUGUSTUS	start_codon	38419234	38419236	.	-	0	transcript_id "Phchi.S1G603600.t1"; gene_id "Phchi.S1G603600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4535.t1 is derived from g1705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10997927	11002303	.	+	.	Phchi.S1G169400
Phchi.S1	AUGUSTUS	transcript	10997927	11002303	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	start_codon	10997927	10997929	.	+	0	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	10997927	10998072	0.8	+	0	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	10997927	10998072	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	10998073	10998226	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	10998227	10998324	0.66	+	1	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	10998227	10998324	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	10998325	10998441	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	10998442	10998491	0.67	+	2	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	10998442	10998491	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	10998492	10998593	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	10998594	10998652	0.98	+	0	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	10998594	10998652	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	10998653	10998741	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	10998742	10999784	0.95	+	1	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	10998742	10999784	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	10999785	10999944	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	10999945	11000080	1	+	2	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	10999945	11000080	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	11000081	11000173	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	11000174	11000310	1	+	1	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	11000174	11000310	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	11000311	11000403	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	11000404	11001458	1	+	2	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	11000404	11001458	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	11001459	11001547	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	11001548	11001581	1	+	0	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	11001548	11001581	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	11001582	11001747	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	11001748	11001868	1	+	2	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	11001748	11001868	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	11001869	11001958	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	11001959	11002115	1	+	1	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	11001959	11002115	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	intron	11002116	11002207	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	CDS	11002208	11002303	1	+	0	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	exon	11002208	11002303	.	+	.	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
Phchi.S1	AUGUSTUS	stop_codon	11002304	11002306	.	+	0	transcript_id "Phchi.S1G169400.t1"; gene_id "Phchi.S1G169400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14309.t1 is derived from g12776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12039742	12041638	.	+	.	Phchi.S3G162800
Phchi.S3	AUGUSTUS	transcript	12039742	12041638	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	start_codon	12039742	12039744	.	+	0	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	CDS	12039742	12039788	0.82	+	0	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	exon	12039742	12039788	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	intron	12039789	12039926	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	CDS	12039927	12039946	0.62	+	1	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	exon	12039927	12039946	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	intron	12039947	12040068	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	CDS	12040069	12040339	0.72	+	2	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	exon	12040069	12040339	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	intron	12040340	12040470	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	CDS	12040471	12040777	0.98	+	1	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	exon	12040471	12040777	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	intron	12040778	12040876	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	CDS	12040877	12041638	0.99	+	0	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	exon	12040877	12041638	.	+	.	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
Phchi.S3	AUGUSTUS	stop_codon	12041639	12041641	.	+	0	transcript_id "Phchi.S3G162800.t1"; gene_id "Phchi.S3G162800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12267.t1 is derived from g7943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7324635	7327918	.	+	.	Phchi.S2G034700
Phchi.S2	AUGUSTUS	transcript	7324635	7327918	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	start_codon	7324635	7324637	.	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7324635	7324769	0.46	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7324635	7324769	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7324770	7324878	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7324879	7325001	0.98	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7324879	7325001	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7325002	7325305	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7325306	7325443	1	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7325306	7325443	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7325444	7325637	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7325638	7325723	1	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7325638	7325723	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7325724	7325869	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7325870	7325969	1	+	1	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7325870	7325969	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7325970	7326169	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7326170	7326245	1	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7326170	7326245	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7326246	7326528	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7326529	7326611	1	+	2	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7326529	7326611	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7326612	7326880	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7326881	7326951	1	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7326881	7326951	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7326952	7327129	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7327130	7327204	1	+	1	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7327130	7327204	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7327205	7327368	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7327369	7327456	1	+	1	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7327369	7327456	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7327457	7327541	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7327542	7327658	1	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7327542	7327658	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	intron	7327659	7327753	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	CDS	7327754	7327918	0.71	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	exon	7327754	7327918	.	+	.	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
Phchi.S2	AUGUSTUS	stop_codon	7327919	7327921	.	+	0	transcript_id "Phchi.S2G034700.t1"; gene_id "Phchi.S2G034700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9962.t1 is derived from g7138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44682234	44682877	.	-	.	Phchi.S1G712100
Phchi.S1	AUGUSTUS	transcript	44682234	44682877	.	-	.	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	stop_codon	44682231	44682233	.	-	0	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	CDS	44682234	44682436	0.99	-	2	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	exon	44682234	44682436	.	-	.	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	intron	44682437	44682594	.	-	.	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	CDS	44682595	44682877	0.97	-	0	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	exon	44682595	44682877	.	-	.	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
Phchi.S1	AUGUSTUS	start_codon	44682875	44682877	.	-	0	transcript_id "Phchi.S1G712100.t1"; gene_id "Phchi.S1G712100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3502.t1 is derived from g671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4113391	4113939	.	+	.	Phchi.S1G066100
Phchi.S1	AUGUSTUS	transcript	4113391	4113939	.	+	.	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	start_codon	4113391	4113393	.	+	0	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	CDS	4113391	4113682	0.69	+	0	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	exon	4113391	4113682	.	+	.	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	intron	4113683	4113790	.	+	.	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	CDS	4113791	4113939	0.83	+	2	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	exon	4113791	4113939	.	+	.	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
Phchi.S1	AUGUSTUS	stop_codon	4113940	4113942	.	+	0	transcript_id "Phchi.S1G066100.t1"; gene_id "Phchi.S1G066100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg957.t1 is derived from g10739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6652219	6652817	.	-	.	Phchi.S6G091600
Phchi.S6	AUGUSTUS	transcript	6652219	6652817	.	-	.	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	stop_codon	6652216	6652218	.	-	0	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	CDS	6652219	6652633	0.35	-	1	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	exon	6652219	6652633	.	-	.	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	intron	6652634	6652704	.	-	.	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	CDS	6652705	6652817	0.46	-	0	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	exon	6652705	6652817	.	-	.	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
Phchi.S6	AUGUSTUS	start_codon	6652815	6652817	.	-	0	transcript_id "Phchi.S6G091600.t1"; gene_id "Phchi.S6G091600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13397.t1 is derived from g11863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6521556	6523111	.	+	.	Phchi.S3G071600
Phchi.S3	AUGUSTUS	transcript	6521556	6523111	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	start_codon	6521556	6521558	.	+	0	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6521556	6521565	1	+	0	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6521556	6521565	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	intron	6521566	6521729	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6521730	6521826	1	+	2	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6521730	6521826	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	intron	6521827	6521909	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6521910	6521995	1	+	1	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6521910	6521995	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	intron	6521996	6522098	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6522099	6522143	1	+	2	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6522099	6522143	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	intron	6522144	6522254	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6522255	6522385	1	+	2	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6522255	6522385	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	intron	6522386	6522638	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6522639	6522677	0.8	+	0	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6522639	6522677	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	intron	6522678	6522856	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	CDS	6522857	6523111	0.92	+	0	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	exon	6522857	6523111	.	+	.	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
Phchi.S3	AUGUSTUS	stop_codon	6523112	6523114	.	+	0	transcript_id "Phchi.S3G071600.t1"; gene_id "Phchi.S3G071600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12099.t1 is derived from g7774.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2773381	2777025	.	-	.	Phchi.S2G017900
Phchi.S2	AUGUSTUS	transcript	2773381	2777025	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	stop_codon	2773378	2773380	.	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2773381	2773485	0.97	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2773381	2773485	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2773486	2773589	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2773590	2773646	0.97	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2773590	2773646	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2773647	2773804	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2773805	2773948	1	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2773805	2773948	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2773949	2774243	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2774244	2774408	1	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2774244	2774408	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2774409	2774489	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2774490	2774699	1	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2774490	2774699	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2774700	2775733	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2775734	2775986	1	-	1	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2775734	2775986	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2775987	2776256	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2776257	2776381	1	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2776257	2776381	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2776382	2776527	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2776528	2776623	1	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2776528	2776623	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2776624	2776782	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2776783	2777025	1	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2776783	2777025	.	-	.	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	start_codon	2777023	2777025	.	-	0	transcript_id "Phchi.S2G017900.t1"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	transcript	2773381	2777025	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	stop_codon	2773378	2773380	.	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2773381	2773485	0.94	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2773381	2773485	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2773486	2773589	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2773590	2773646	0.94	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2773590	2773646	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2773647	2773804	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2773805	2773948	1	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2773805	2773948	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2773949	2774243	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2774244	2774408	1	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2774244	2774408	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2774409	2774489	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2774490	2774699	1	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2774490	2774699	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2774700	2775733	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2775734	2775983	1	-	1	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2775734	2775983	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2775984	2776256	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2776257	2776381	1	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2776257	2776381	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2776382	2776527	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2776528	2776623	1	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2776528	2776623	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	intron	2776624	2776782	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	CDS	2776783	2777025	0.99	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	exon	2776783	2777025	.	-	.	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
Phchi.S2	AUGUSTUS	start_codon	2777023	2777025	.	-	0	transcript_id "Phchi.S2G017900.t2"; gene_id "Phchi.S2G017900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11998.t1 is derived from g7673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	450974	451480	.	+	.	Phchi.S2G007800
Phchi.S2	AUGUSTUS	transcript	450974	451480	.	+	.	transcript_id "Phchi.S2G007800.t1"; gene_id "Phchi.S2G007800"
Phchi.S2	AUGUSTUS	start_codon	450974	450976	.	+	0	transcript_id "Phchi.S2G007800.t1"; gene_id "Phchi.S2G007800"
Phchi.S2	AUGUSTUS	CDS	450974	451480	0.49	+	0	transcript_id "Phchi.S2G007800.t1"; gene_id "Phchi.S2G007800"
Phchi.S2	AUGUSTUS	exon	450974	451480	.	+	.	transcript_id "Phchi.S2G007800.t1"; gene_id "Phchi.S2G007800"
Phchi.S2	AUGUSTUS	stop_codon	451481	451483	.	+	0	transcript_id "Phchi.S2G007800.t1"; gene_id "Phchi.S2G007800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2207.t1 is derived from g9127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5419480	5425006	.	-	.	Phchi.S5G081600
Phchi.S5	AUGUSTUS	transcript	5419480	5425006	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	stop_codon	5419477	5419479	.	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5419480	5419573	0.99	-	1	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5419480	5419573	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5419574	5419703	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5419704	5419888	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5419704	5419888	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5419889	5419970	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5419971	5420153	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5419971	5420153	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5420154	5420232	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5420233	5420406	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5420233	5420406	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5420407	5420502	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5420503	5420663	0.98	-	2	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5420503	5420663	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5420664	5420770	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5420771	5420852	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5420771	5420852	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5420853	5420986	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5420987	5421019	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5420987	5421019	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5421020	5421148	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5421149	5421387	1	-	2	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5421149	5421387	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5421388	5421468	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5421469	5421633	1	-	2	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5421469	5421633	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5421634	5421806	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5421807	5421830	0.85	-	2	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5421807	5421830	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5421831	5421907	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5421908	5421950	0.85	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5421908	5421950	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5421951	5422035	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5422036	5422140	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5422036	5422140	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5422141	5422268	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5422269	5422391	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5422269	5422391	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5422392	5422487	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5422488	5422607	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5422488	5422607	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5422608	5422770	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5422771	5422890	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5422771	5422890	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5422891	5422995	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5422996	5423202	0.99	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5422996	5423202	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5423203	5423325	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5423326	5423505	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5423326	5423505	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5423506	5423618	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5423619	5423753	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5423619	5423753	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5423754	5423858	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5423859	5423996	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5423859	5423996	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5423997	5424097	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5424098	5424196	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5424098	5424196	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5424197	5424666	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5424667	5424786	1	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5424667	5424786	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	intron	5424787	5424919	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	CDS	5424920	5425006	0.84	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	exon	5424920	5425006	.	-	.	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
Phchi.S5	AUGUSTUS	start_codon	5425004	5425006	.	-	0	transcript_id "Phchi.S5G081600.t1"; gene_id "Phchi.S5G081600"
# This transcript jg12729.t2 is derived from g11194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12730.t1 is derived from g11195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1422519	1423229	.	+	.	Phchi.S3G004900
Phchi.S3	AUGUSTUS	transcript	1422519	1423229	.	+	.	transcript_id "Phchi.S3G004900.t1"; gene_id "Phchi.S3G004900"
Phchi.S3	AUGUSTUS	start_codon	1422519	1422521	.	+	0	transcript_id "Phchi.S3G004900.t1"; gene_id "Phchi.S3G004900"
Phchi.S3	AUGUSTUS	CDS	1422519	1423229	0.53	+	0	transcript_id "Phchi.S3G004900.t1"; gene_id "Phchi.S3G004900"
Phchi.S3	AUGUSTUS	exon	1422519	1423229	.	+	.	transcript_id "Phchi.S3G004900.t1"; gene_id "Phchi.S3G004900"
Phchi.S3	AUGUSTUS	stop_codon	1423230	1423232	.	+	0	transcript_id "Phchi.S3G004900.t1"; gene_id "Phchi.S3G004900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3521.t1 is derived from g690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4188249	4188988	.	-	.	Phchi.S1G068000
Phchi.S1	AUGUSTUS	transcript	4188249	4188988	.	-	.	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	stop_codon	4188246	4188248	.	-	0	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	CDS	4188249	4188740	0.78	-	0	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	exon	4188249	4188740	.	-	.	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	intron	4188741	4188844	.	-	.	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	CDS	4188845	4188988	0.8	-	0	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	exon	4188845	4188988	.	-	.	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
Phchi.S1	AUGUSTUS	start_codon	4188986	4188988	.	-	0	transcript_id "Phchi.S1G068000.t1"; gene_id "Phchi.S1G068000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4568.t1 is derived from g1738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11156982	11157653	.	+	.	Phchi.S1G172700
Phchi.S1	AUGUSTUS	transcript	11156982	11157653	.	+	.	transcript_id "Phchi.S1G172700.t1"; gene_id "Phchi.S1G172700"
Phchi.S1	AUGUSTUS	start_codon	11156982	11156984	.	+	0	transcript_id "Phchi.S1G172700.t1"; gene_id "Phchi.S1G172700"
Phchi.S1	AUGUSTUS	CDS	11156982	11157653	0.56	+	0	transcript_id "Phchi.S1G172700.t1"; gene_id "Phchi.S1G172700"
Phchi.S1	AUGUSTUS	exon	11156982	11157653	.	+	.	transcript_id "Phchi.S1G172700.t1"; gene_id "Phchi.S1G172700"
Phchi.S1	AUGUSTUS	stop_codon	11157654	11157656	.	+	0	transcript_id "Phchi.S1G172700.t1"; gene_id "Phchi.S1G172700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2264.t1 is derived from g9184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5730633	5732918	.	+	.	Phchi.S5G087300
Phchi.S5	AUGUSTUS	transcript	5730633	5732918	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	start_codon	5730633	5730635	.	+	0	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	CDS	5730633	5730930	1	+	0	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	exon	5730633	5730930	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	intron	5730931	5731055	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	CDS	5731056	5731570	0.54	+	2	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	exon	5731056	5731570	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	intron	5731571	5731779	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	CDS	5731780	5732216	0.46	+	0	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	exon	5731780	5732216	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	intron	5732217	5732300	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	CDS	5732301	5732469	0.95	+	1	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	exon	5732301	5732469	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	intron	5732470	5732572	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	CDS	5732573	5732692	0.99	+	0	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	exon	5732573	5732692	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	intron	5732693	5732777	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	CDS	5732778	5732918	0.96	+	0	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	exon	5732778	5732918	.	+	.	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
Phchi.S5	AUGUSTUS	stop_codon	5732919	5732921	.	+	0	transcript_id "Phchi.S5G087300.t1"; gene_id "Phchi.S5G087300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1346.t1 is derived from g11129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9123265	9125178	.	-	.	Phchi.S6G130500
Phchi.S6	AUGUSTUS	transcript	9123265	9125178	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	stop_codon	9123262	9123264	.	-	0	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9123265	9123578	1	-	2	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9123265	9123578	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	intron	9123579	9123670	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9123671	9123869	1	-	0	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9123671	9123869	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	intron	9123870	9123985	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9123986	9124128	1	-	2	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9123986	9124128	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	intron	9124129	9124252	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9124253	9124386	1	-	1	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9124253	9124386	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	intron	9124387	9124499	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9124500	9124644	1	-	2	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9124500	9124644	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	intron	9124645	9124737	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9124738	9124906	1	-	0	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9124738	9124906	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	intron	9124907	9125025	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	CDS	9125026	9125178	0.82	-	0	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	exon	9125026	9125178	.	-	.	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
Phchi.S6	AUGUSTUS	start_codon	9125176	9125178	.	-	0	transcript_id "Phchi.S6G130500.t1"; gene_id "Phchi.S6G130500"
# This transcript jg11971.t2 is derived from g7646.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11972.t1 is derived from g7647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	252453	253297	.	-	.	Phchi.S2G005200
Phchi.S2	AUGUSTUS	transcript	252453	253297	.	-	.	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	stop_codon	252450	252452	.	-	0	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	CDS	252453	253040	1	-	0	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	exon	252453	253040	.	-	.	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	intron	253041	253207	.	-	.	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	CDS	253208	253297	1	-	0	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	exon	253208	253297	.	-	.	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
Phchi.S2	AUGUSTUS	start_codon	253295	253297	.	-	0	transcript_id "Phchi.S2G005200.t1"; gene_id "Phchi.S2G005200"
# This transcript jg4063.t2 is derived from g1232.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4064.t1 is derived from g1233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7601737	7605715	.	+	.	Phchi.S1G122300
Phchi.S1	AUGUSTUS	transcript	7601737	7605715	.	+	.	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	start_codon	7601737	7601739	.	+	0	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	CDS	7601737	7602841	0.98	+	0	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	exon	7601737	7602841	.	+	.	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	intron	7602842	7602933	.	+	.	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	CDS	7602934	7603388	0.63	+	2	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	exon	7602934	7603388	.	+	.	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	intron	7603389	7603480	.	+	.	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	CDS	7603481	7605715	0.41	+	0	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	exon	7603481	7605715	.	+	.	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
Phchi.S1	AUGUSTUS	stop_codon	7605716	7605718	.	+	0	transcript_id "Phchi.S1G122300.t1"; gene_id "Phchi.S1G122300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg236.t1 is derived from g10018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1599827	1602566	.	+	.	Phchi.S6G019500
Phchi.S6	AUGUSTUS	transcript	1599827	1602566	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	start_codon	1599827	1599829	.	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1599827	1599886	0.93	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1599827	1599886	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1599887	1599962	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1599963	1600100	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1599963	1600100	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1600101	1600201	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1600202	1600564	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1600202	1600564	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1600565	1600680	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1600681	1600762	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1600681	1600762	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1600763	1600850	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1600851	1600981	1	+	2	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1600851	1600981	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1600982	1601073	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1601074	1601136	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1601074	1601136	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1601137	1601285	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1601286	1601465	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1601286	1601465	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1601466	1601545	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1601546	1601599	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1601546	1601599	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1601600	1601690	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1601691	1601779	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1601691	1601779	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1601780	1601857	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1601858	1601948	1	+	1	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1601858	1601948	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1601949	1602014	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1602015	1602095	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1602015	1602095	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1602096	1602169	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1602170	1602237	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1602170	1602237	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1602238	1602328	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1602329	1602413	1	+	1	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1602329	1602413	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	intron	1602414	1602494	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	CDS	1602495	1602566	1	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	exon	1602495	1602566	.	+	.	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
Phchi.S6	AUGUSTUS	stop_codon	1602567	1602569	.	+	0	transcript_id "Phchi.S6G019500.t1"; gene_id "Phchi.S6G019500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13121.t1 is derived from g11586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4224564	4226309	.	-	.	Phchi.S3G044000
Phchi.S3	AUGUSTUS	transcript	4224564	4226309	.	-	.	transcript_id "Phchi.S3G044000.t1"; gene_id "Phchi.S3G044000"
Phchi.S3	AUGUSTUS	stop_codon	4224561	4224563	.	-	0	transcript_id "Phchi.S3G044000.t1"; gene_id "Phchi.S3G044000"
Phchi.S3	AUGUSTUS	CDS	4224564	4226309	0.7	-	0	transcript_id "Phchi.S3G044000.t1"; gene_id "Phchi.S3G044000"
Phchi.S3	AUGUSTUS	exon	4224564	4226309	.	-	.	transcript_id "Phchi.S3G044000.t1"; gene_id "Phchi.S3G044000"
Phchi.S3	AUGUSTUS	start_codon	4226307	4226309	.	-	0	transcript_id "Phchi.S3G044000.t1"; gene_id "Phchi.S3G044000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6590.t1 is derived from g3762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23903259	23903807	.	+	.	Phchi.S1G374900
Phchi.S1	AUGUSTUS	transcript	23903259	23903807	.	+	.	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	start_codon	23903259	23903261	.	+	0	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	CDS	23903259	23903413	0.82	+	0	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	exon	23903259	23903413	.	+	.	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	intron	23903414	23903518	.	+	.	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	CDS	23903519	23903807	0.9	+	1	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	exon	23903519	23903807	.	+	.	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
Phchi.S1	AUGUSTUS	stop_codon	23903808	23903810	.	+	0	transcript_id "Phchi.S1G374900.t1"; gene_id "Phchi.S1G374900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14813.t1 is derived from g13281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14820423	14823239	.	-	.	Phchi.S3G213200
Phchi.S3	AUGUSTUS	transcript	14820423	14823239	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	stop_codon	14820420	14820422	.	-	0	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14820423	14820550	0.98	-	2	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14820423	14820550	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	intron	14820551	14820747	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14820748	14820831	0.97	-	2	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14820748	14820831	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	intron	14820832	14820932	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14820933	14821034	0.51	-	2	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14820933	14821034	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	intron	14821035	14821157	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14821158	14821762	0.47	-	1	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14821158	14821762	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	intron	14821763	14821902	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14821903	14822675	0.82	-	0	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14821903	14822675	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	intron	14822676	14822784	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14822785	14822870	1	-	2	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14822785	14822870	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	intron	14822871	14823127	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	CDS	14823128	14823239	1	-	0	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	exon	14823128	14823239	.	-	.	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
Phchi.S3	AUGUSTUS	start_codon	14823237	14823239	.	-	0	transcript_id "Phchi.S3G213200.t1"; gene_id "Phchi.S3G213200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2089.t1 is derived from g9009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4813706	4818384	.	+	.	Phchi.S5G069800
Phchi.S5	AUGUSTUS	transcript	4813706	4818384	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	start_codon	4813706	4813708	.	+	0	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4813706	4813767	0.28	+	0	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4813706	4813767	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4813768	4814196	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4814197	4814242	0.36	+	1	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4814197	4814242	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4814243	4814404	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4814405	4816656	0.24	+	0	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4814405	4816656	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4816657	4816730	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4816731	4816775	0.69	+	1	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4816731	4816775	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4816776	4816945	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4816946	4817108	0.99	+	1	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4816946	4817108	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4817109	4817303	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4817304	4817467	1	+	0	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4817304	4817467	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4817468	4817897	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4817898	4818156	1	+	1	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4817898	4818156	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	intron	4818157	4818279	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	CDS	4818280	4818384	0.86	+	0	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	exon	4818280	4818384	.	+	.	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
Phchi.S5	AUGUSTUS	stop_codon	4818385	4818387	.	+	0	transcript_id "Phchi.S5G069800.t1"; gene_id "Phchi.S5G069800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14263.t1 is derived from g12730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11812869	11815727	.	+	.	Phchi.S3G158200
Phchi.S3	AUGUSTUS	transcript	11812869	11815727	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	start_codon	11812869	11812871	.	+	0	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11812869	11812883	0.96	+	0	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11812869	11812883	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	intron	11812884	11813102	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11813103	11813119	0.95	+	0	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11813103	11813119	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	intron	11813120	11813633	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11813634	11813838	0.92	+	1	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11813634	11813838	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	intron	11813839	11814183	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11814184	11814319	0.47	+	0	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11814184	11814319	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	intron	11814320	11814391	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11814392	11814714	0.54	+	2	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11814392	11814714	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	intron	11814715	11814825	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11814826	11815019	0.99	+	0	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11814826	11815019	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	intron	11815020	11815120	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	CDS	11815121	11815727	1	+	1	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	exon	11815121	11815727	.	+	.	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
Phchi.S3	AUGUSTUS	stop_codon	11815728	11815730	.	+	0	transcript_id "Phchi.S3G158200.t1"; gene_id "Phchi.S3G158200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13897.t1 is derived from g12364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9530852	9531936	.	-	.	Phchi.S3G121600
Phchi.S3	AUGUSTUS	transcript	9530852	9531936	.	-	.	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	stop_codon	9530849	9530851	.	-	0	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	CDS	9530852	9531263	1	-	1	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	exon	9530852	9531263	.	-	.	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	intron	9531264	9531344	.	-	.	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	CDS	9531345	9531538	1	-	0	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	exon	9531345	9531538	.	-	.	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	intron	9531539	9531699	.	-	.	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	CDS	9531700	9531936	0.69	-	0	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	exon	9531700	9531936	.	-	.	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
Phchi.S3	AUGUSTUS	start_codon	9531934	9531936	.	-	0	transcript_id "Phchi.S3G121600.t1"; gene_id "Phchi.S3G121600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11046.t1 is derived from g15096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3804165	3804895	.	+	.	Phchi.S4G062800
Phchi.S4	AUGUSTUS	transcript	3804165	3804895	.	+	.	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	start_codon	3804165	3804167	.	+	0	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	CDS	3804165	3804180	1	+	0	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	exon	3804165	3804180	.	+	.	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	intron	3804181	3804351	.	+	.	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	CDS	3804352	3804706	0.99	+	2	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	exon	3804352	3804706	.	+	.	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	intron	3804707	3804813	.	+	.	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	CDS	3804814	3804895	1	+	1	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	exon	3804814	3804895	.	+	.	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
Phchi.S4	AUGUSTUS	stop_codon	3804896	3804898	.	+	0	transcript_id "Phchi.S4G062800.t1"; gene_id "Phchi.S4G062800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12926.t1 is derived from g11391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3182648	3183024	.	+	.	Phchi.S3G024500
Phchi.S3	AUGUSTUS	transcript	3182648	3183024	.	+	.	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	start_codon	3182648	3182650	.	+	0	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	CDS	3182648	3182718	0.62	+	0	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	exon	3182648	3182718	.	+	.	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	intron	3182719	3182807	.	+	.	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	CDS	3182808	3183024	0.97	+	1	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	exon	3182808	3183024	.	+	.	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
Phchi.S3	AUGUSTUS	stop_codon	3183025	3183027	.	+	0	transcript_id "Phchi.S3G024500.t1"; gene_id "Phchi.S3G024500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6082.t1 is derived from g3253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20864640	20865746	.	+	.	Phchi.S1G324100
Phchi.S1	AUGUSTUS	transcript	20864640	20865746	.	+	.	transcript_id "Phchi.S1G324100.t1"; gene_id "Phchi.S1G324100"
Phchi.S1	AUGUSTUS	start_codon	20864640	20864642	.	+	0	transcript_id "Phchi.S1G324100.t1"; gene_id "Phchi.S1G324100"
Phchi.S1	AUGUSTUS	CDS	20864640	20865746	0.88	+	0	transcript_id "Phchi.S1G324100.t1"; gene_id "Phchi.S1G324100"
Phchi.S1	AUGUSTUS	exon	20864640	20865746	.	+	.	transcript_id "Phchi.S1G324100.t1"; gene_id "Phchi.S1G324100"
Phchi.S1	AUGUSTUS	stop_codon	20865747	20865749	.	+	0	transcript_id "Phchi.S1G324100.t1"; gene_id "Phchi.S1G324100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13650.t1 is derived from g12117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8010115	8012681	.	-	.	Phchi.S3G096900
Phchi.S3	AUGUSTUS	transcript	8010115	8012681	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	stop_codon	8010112	8010114	.	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8010115	8010213	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8010115	8010213	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8010214	8010290	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8010291	8010372	1	-	1	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8010291	8010372	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8010373	8010483	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8010484	8010638	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8010484	8010638	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8010639	8010755	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8010756	8010816	1	-	1	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8010756	8010816	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8010817	8010901	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8010902	8011017	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8010902	8011017	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8011018	8011113	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8011114	8011182	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8011114	8011182	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8011183	8011273	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8011274	8011372	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8011274	8011372	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8011373	8011475	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8011476	8011529	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8011476	8011529	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8011530	8011620	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8011621	8011683	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8011621	8011683	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8011684	8011818	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8011819	8011870	1	-	1	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8011819	8011870	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8011871	8011988	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8011989	8012096	1	-	1	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8011989	8012096	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8012097	8012218	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8012219	8012355	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8012219	8012355	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	intron	8012356	8012489	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	CDS	8012490	8012681	1	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	exon	8012490	8012681	.	-	.	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
Phchi.S3	AUGUSTUS	start_codon	8012679	8012681	.	-	0	transcript_id "Phchi.S3G096900.t1"; gene_id "Phchi.S3G096900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4173.t1 is derived from g1342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8739873	8741667	.	+	.	Phchi.S1G133200
Phchi.S1	AUGUSTUS	transcript	8739873	8741099	.	+	.	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	start_codon	8739873	8739875	.	+	0	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	CDS	8739873	8739902	0.79	+	0	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	exon	8739873	8739902	.	+	.	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	intron	8739903	8739993	.	+	.	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	CDS	8739994	8741014	0.97	+	0	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	exon	8739994	8741014	.	+	.	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	intron	8741015	8741094	.	+	.	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	CDS	8741095	8741099	0.7	+	2	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	exon	8741095	8741099	.	+	.	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	stop_codon	8741100	8741102	.	+	0	transcript_id "Phchi.S1G133200.t1"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	transcript	8739873	8741667	.	+	.	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	start_codon	8739873	8739875	.	+	0	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	CDS	8739873	8739902	0.58	+	0	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	exon	8739873	8739902	.	+	.	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	intron	8739903	8739993	.	+	.	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	CDS	8739994	8741667	0.73	+	0	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	exon	8739994	8741667	.	+	.	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
Phchi.S1	AUGUSTUS	stop_codon	8741668	8741670	.	+	0	transcript_id "Phchi.S1G133200.t2"; gene_id "Phchi.S1G133200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9379.t1 is derived from g6555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41242886	41246779	.	+	.	Phchi.S1G653800
Phchi.S1	AUGUSTUS	transcript	41242886	41246779	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	start_codon	41242886	41242888	.	+	0	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	CDS	41242886	41242975	0.67	+	0	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	exon	41242886	41242975	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	intron	41242976	41243100	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	CDS	41243101	41243418	0.73	+	0	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	exon	41243101	41243418	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	intron	41243419	41243587	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	CDS	41243588	41245590	1	+	0	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	exon	41243588	41245590	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	intron	41245591	41245679	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	CDS	41245680	41245830	0.98	+	1	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	exon	41245680	41245830	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	intron	41245831	41245948	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	CDS	41245949	41246779	0.98	+	0	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	exon	41245949	41246779	.	+	.	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
Phchi.S1	AUGUSTUS	stop_codon	41246780	41246782	.	+	0	transcript_id "Phchi.S1G653800.t1"; gene_id "Phchi.S1G653800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14298.t1 is derived from g12765.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11989271	11991459	.	-	.	Phchi.S3G161700
Phchi.S3	AUGUSTUS	transcript	11989271	11991459	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	stop_codon	11989268	11989270	.	-	0	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11989271	11989549	0.87	-	0	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11989271	11989549	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11989550	11989661	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11989662	11989828	0.97	-	2	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11989662	11989828	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11989829	11989965	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11989966	11990105	1	-	1	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11989966	11990105	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990106	11990244	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990245	11990443	1	-	2	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990245	11990443	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990444	11990619	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990620	11990725	0.99	-	0	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990620	11990725	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990726	11990852	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990853	11991046	0.68	-	2	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990853	11991046	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11991047	11991148	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11991149	11991265	0.7	-	2	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11991149	11991265	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11991266	11991404	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11991405	11991459	0.98	-	0	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11991405	11991459	.	-	.	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	start_codon	11991457	11991459	.	-	0	transcript_id "Phchi.S3G161700.t1"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	transcript	11989271	11991459	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	stop_codon	11989268	11989270	.	-	0	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11989271	11989549	0.84	-	0	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11989271	11989549	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11989550	11989661	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11989662	11989828	0.96	-	2	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11989662	11989828	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11989829	11989965	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11989966	11990105	1	-	1	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11989966	11990105	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990106	11990244	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990245	11990443	1	-	2	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990245	11990443	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990444	11990619	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990620	11990743	0.56	-	0	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990620	11990743	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990744	11990852	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990853	11991046	0.63	-	2	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990853	11991046	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11991047	11991148	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11991149	11991265	0.63	-	2	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11991149	11991265	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11991266	11991404	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11991405	11991459	0.99	-	0	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11991405	11991459	.	-	.	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	start_codon	11991457	11991459	.	-	0	transcript_id "Phchi.S3G161700.t2"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	transcript	11990468	11991459	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	stop_codon	11990465	11990467	.	-	0	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990468	11990481	0.89	-	2	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990468	11990481	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990482	11990619	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990620	11990725	1	-	0	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990620	11990725	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11990726	11990852	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11990853	11991046	0.56	-	2	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11990853	11991046	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11991047	11991148	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11991149	11991265	0.59	-	2	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11991149	11991265	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	intron	11991266	11991404	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	CDS	11991405	11991459	1	-	0	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	exon	11991405	11991459	.	-	.	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
Phchi.S3	AUGUSTUS	start_codon	11991457	11991459	.	-	0	transcript_id "Phchi.S3G161700.t3"; gene_id "Phchi.S3G161700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12469.t1 is derived from g8146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	25815218	25815793	.	+	.	Phchi.S2G054900
Phchi.S2	AUGUSTUS	transcript	25815218	25815793	.	+	.	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	start_codon	25815218	25815220	.	+	0	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	CDS	25815218	25815341	0.54	+	0	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	exon	25815218	25815341	.	+	.	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	intron	25815342	25815491	.	+	.	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	CDS	25815492	25815793	0.81	+	2	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	exon	25815492	25815793	.	+	.	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
Phchi.S2	AUGUSTUS	stop_codon	25815794	25815796	.	+	0	transcript_id "Phchi.S2G054900.t1"; gene_id "Phchi.S2G054900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6418.t1 is derived from g3590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22900122	22901020	.	+	.	Phchi.S1G357700
Phchi.S1	AUGUSTUS	transcript	22900122	22901020	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	start_codon	22900122	22900124	.	+	0	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	CDS	22900122	22900179	1	+	0	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	exon	22900122	22900179	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	intron	22900180	22900253	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	CDS	22900254	22900472	1	+	2	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	exon	22900254	22900472	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	intron	22900473	22900555	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	CDS	22900556	22900653	1	+	2	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	exon	22900556	22900653	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	intron	22900654	22900794	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	CDS	22900795	22900837	1	+	0	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	exon	22900795	22900837	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	intron	22900838	22900919	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	CDS	22900920	22901020	0.67	+	2	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	exon	22900920	22901020	.	+	.	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
Phchi.S1	AUGUSTUS	stop_codon	22901021	22901023	.	+	0	transcript_id "Phchi.S1G357700.t1"; gene_id "Phchi.S1G357700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14702.t1 is derived from g13170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14257403	14258805	.	+	.	Phchi.S3G202100
Phchi.S3	AUGUSTUS	transcript	14257403	14258805	.	+	.	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	start_codon	14257403	14257405	.	+	0	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	CDS	14257403	14257695	0.37	+	0	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	exon	14257403	14257695	.	+	.	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	intron	14257696	14257820	.	+	.	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	CDS	14257821	14258805	0.32	+	1	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	exon	14257821	14258805	.	+	.	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
Phchi.S3	AUGUSTUS	stop_codon	14258806	14258808	.	+	0	transcript_id "Phchi.S3G202100.t1"; gene_id "Phchi.S3G202100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6918.t1 is derived from g4090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25985514	25987472	.	-	.	Phchi.S1G407700
Phchi.S1	AUGUSTUS	transcript	25985514	25987472	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	stop_codon	25985511	25985513	.	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25985514	25985600	1	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25985514	25985600	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25985601	25985679	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25985680	25985772	1	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25985680	25985772	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25985773	25985851	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25985852	25985925	1	-	2	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25985852	25985925	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25985926	25986025	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25986026	25986083	1	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25986026	25986083	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25986084	25986269	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25986270	25986401	1	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25986270	25986401	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25986402	25986502	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25986503	25986712	0.97	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25986503	25986712	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25986713	25986897	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25986898	25986970	0.99	-	1	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25986898	25986970	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25986971	25987074	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25987075	25987100	0.87	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25987075	25987100	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25987101	25987206	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25987207	25987307	0.99	-	2	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25987207	25987307	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	intron	25987308	25987444	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	CDS	25987445	25987472	0.92	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	exon	25987445	25987472	.	-	.	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
Phchi.S1	AUGUSTUS	start_codon	25987470	25987472	.	-	0	transcript_id "Phchi.S1G407700.t1"; gene_id "Phchi.S1G407700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg171.t1 is derived from g9953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1011267	1012043	.	+	.	Phchi.S6G013000
Phchi.S6	AUGUSTUS	transcript	1011267	1012043	.	+	.	transcript_id "Phchi.S6G013000.t1"; gene_id "Phchi.S6G013000"
Phchi.S6	AUGUSTUS	start_codon	1011267	1011269	.	+	0	transcript_id "Phchi.S6G013000.t1"; gene_id "Phchi.S6G013000"
Phchi.S6	AUGUSTUS	CDS	1011267	1012043	0.85	+	0	transcript_id "Phchi.S6G013000.t1"; gene_id "Phchi.S6G013000"
Phchi.S6	AUGUSTUS	exon	1011267	1012043	.	+	.	transcript_id "Phchi.S6G013000.t1"; gene_id "Phchi.S6G013000"
Phchi.S6	AUGUSTUS	stop_codon	1012044	1012046	.	+	0	transcript_id "Phchi.S6G013000.t1"; gene_id "Phchi.S6G013000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1773.t1 is derived from g8693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2963090	2964301	.	+	.	Phchi.S5G038200
Phchi.S5	AUGUSTUS	transcript	2963090	2964301	.	+	.	transcript_id "Phchi.S5G038200.t1"; gene_id "Phchi.S5G038200"
Phchi.S5	AUGUSTUS	start_codon	2963090	2963092	.	+	0	transcript_id "Phchi.S5G038200.t1"; gene_id "Phchi.S5G038200"
Phchi.S5	AUGUSTUS	CDS	2963090	2964301	0.72	+	0	transcript_id "Phchi.S5G038200.t1"; gene_id "Phchi.S5G038200"
Phchi.S5	AUGUSTUS	exon	2963090	2964301	.	+	.	transcript_id "Phchi.S5G038200.t1"; gene_id "Phchi.S5G038200"
Phchi.S5	AUGUSTUS	stop_codon	2964302	2964304	.	+	0	transcript_id "Phchi.S5G038200.t1"; gene_id "Phchi.S5G038200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1114.t1 is derived from g10897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7734740	7735767	.	+	.	Phchi.S6G107300
Phchi.S6	AUGUSTUS	transcript	7734740	7735767	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	start_codon	7734740	7734742	.	+	0	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	CDS	7734740	7734944	0.94	+	0	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	exon	7734740	7734944	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	intron	7734945	7735096	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	CDS	7735097	7735129	0.78	+	2	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	exon	7735097	7735129	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	intron	7735130	7735213	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	CDS	7735214	7735285	0.95	+	2	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	exon	7735214	7735285	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	intron	7735286	7735390	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	CDS	7735391	7735603	0.76	+	2	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	exon	7735391	7735603	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	intron	7735604	7735705	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	CDS	7735706	7735767	0.52	+	2	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	exon	7735706	7735767	.	+	.	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
Phchi.S6	AUGUSTUS	stop_codon	7735768	7735770	.	+	0	transcript_id "Phchi.S6G107300.t1"; gene_id "Phchi.S6G107300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15150.t1 is derived from g13618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17271586	17272101	.	-	.	Phchi.S3G246900
Phchi.S3	AUGUSTUS	transcript	17271586	17272101	.	-	.	transcript_id "Phchi.S3G246900.t1"; gene_id "Phchi.S3G246900"
Phchi.S3	AUGUSTUS	stop_codon	17271583	17271585	.	-	0	transcript_id "Phchi.S3G246900.t1"; gene_id "Phchi.S3G246900"
Phchi.S3	AUGUSTUS	CDS	17271586	17272101	0.66	-	0	transcript_id "Phchi.S3G246900.t1"; gene_id "Phchi.S3G246900"
Phchi.S3	AUGUSTUS	exon	17271586	17272101	.	-	.	transcript_id "Phchi.S3G246900.t1"; gene_id "Phchi.S3G246900"
Phchi.S3	AUGUSTUS	start_codon	17272099	17272101	.	-	0	transcript_id "Phchi.S3G246900.t1"; gene_id "Phchi.S3G246900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15241.t1 is derived from g13709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17876772	17879050	.	+	.	Phchi.S3G256000
Phchi.S3	AUGUSTUS	transcript	17876772	17879050	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	start_codon	17876772	17876774	.	+	0	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17876772	17877050	1	+	0	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17876772	17877050	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17877051	17877147	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17877148	17877277	1	+	0	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17877148	17877277	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17877278	17877343	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17877344	17877445	0.38	+	2	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17877344	17877445	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17877446	17877561	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17877562	17877658	0.82	+	2	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17877562	17877658	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17877659	17877876	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17877877	17877965	1	+	1	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17877877	17877965	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17877966	17878084	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17878085	17878237	1	+	2	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17878085	17878237	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17878238	17878323	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17878324	17878460	1	+	2	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17878324	17878460	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17878461	17878546	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17878547	17878716	1	+	0	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17878547	17878716	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	intron	17878717	17878806	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	CDS	17878807	17879050	1	+	1	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	exon	17878807	17879050	.	+	.	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
Phchi.S3	AUGUSTUS	stop_codon	17879051	17879053	.	+	0	transcript_id "Phchi.S3G256000.t1"; gene_id "Phchi.S3G256000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8251.t1 is derived from g5426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34711240	34714803	.	-	.	Phchi.S1G541000
Phchi.S1	AUGUSTUS	transcript	34711240	34714803	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	stop_codon	34711237	34711239	.	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34711240	34711305	1	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34711240	34711305	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34711306	34711410	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34711411	34711533	1	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34711411	34711533	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34711534	34711690	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34711691	34711751	0.9	-	1	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34711691	34711751	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34711752	34711932	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34711933	34712021	0.9	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34711933	34712021	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34712022	34712187	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34712188	34712274	1	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34712188	34712274	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34712275	34712403	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34712404	34714098	0.82	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34712404	34714098	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34714099	34714264	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34714265	34714350	0.33	-	2	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34714265	34714350	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	intron	34714351	34714589	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	CDS	34714590	34714803	0.34	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	exon	34714590	34714803	.	-	.	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
Phchi.S1	AUGUSTUS	start_codon	34714801	34714803	.	-	0	transcript_id "Phchi.S1G541000.t1"; gene_id "Phchi.S1G541000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2.t1 is derived from g9764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C178	AUGUSTUS	gene	7292	13635	.	-	.	Phchi.C178G000100
Phchi.C178	AUGUSTUS	transcript	7292	13635	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	stop_codon	7289	7291	.	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	7292	7499	1	-	1	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	7292	7499	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	7500	7584	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	7585	7757	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	7585	7757	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	7758	7837	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	7838	8029	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	7838	8029	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	8030	8129	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	8130	8225	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	8130	8225	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	8226	8314	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	8315	8443	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	8315	8443	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	8444	8520	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	8521	8700	0.98	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	8521	8700	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	8701	8788	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	8789	8899	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	8789	8899	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	8900	8980	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	8981	9130	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	8981	9130	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	9131	9322	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	9323	9436	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	9323	9436	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	9437	9632	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	9633	9800	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	9633	9800	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	9801	9950	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	9951	10185	0.98	-	1	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	9951	10185	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	10186	10316	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	10317	10444	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	10317	10444	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	10445	10539	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	10540	10635	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	10540	10635	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	10636	10720	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	10721	10822	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	10721	10822	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	10823	11064	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	11065	11138	1	-	2	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	11065	11138	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	11139	11232	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	11233	11302	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	11233	11302	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	11303	11404	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	11405	11514	0.84	-	2	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	11405	11514	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	11515	11590	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	11591	11729	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	11591	11729	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	11730	11811	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	11812	11924	1	-	2	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	11812	11924	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	11925	12083	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	12084	12210	1	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	12084	12210	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	12211	12348	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	12349	12526	1	-	1	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	12349	12526	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	12527	12700	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	12701	12859	1	-	1	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	12701	12859	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	12860	12945	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	12946	13059	1	-	1	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	12946	13059	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	13060	13196	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	13197	13376	1	-	1	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	13197	13376	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	intron	13377	13555	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	CDS	13556	13635	0.92	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	exon	13556	13635	.	-	.	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
Phchi.C178	AUGUSTUS	start_codon	13633	13635	.	-	0	transcript_id "Phchi.C178G000100.t1"; gene_id "Phchi.C178G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8304.t1 is derived from g5479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35192564	35194293	.	+	.	Phchi.S1G546300
Phchi.S1	AUGUSTUS	transcript	35192564	35194293	.	+	.	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	start_codon	35192564	35192566	.	+	0	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	CDS	35192564	35194035	0.51	+	0	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	exon	35192564	35194035	.	+	.	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	intron	35194036	35194124	.	+	.	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	CDS	35194125	35194293	1	+	1	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	exon	35194125	35194293	.	+	.	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
Phchi.S1	AUGUSTUS	stop_codon	35194294	35194296	.	+	0	transcript_id "Phchi.S1G546300.t1"; gene_id "Phchi.S1G546300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3846.t1 is derived from g1015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6018845	6020038	.	+	.	Phchi.S1G100500
Phchi.S1	AUGUSTUS	transcript	6018845	6020038	.	+	.	transcript_id "Phchi.S1G100500.t1"; gene_id "Phchi.S1G100500"
Phchi.S1	AUGUSTUS	start_codon	6018845	6018847	.	+	0	transcript_id "Phchi.S1G100500.t1"; gene_id "Phchi.S1G100500"
Phchi.S1	AUGUSTUS	CDS	6018845	6020038	0.88	+	0	transcript_id "Phchi.S1G100500.t1"; gene_id "Phchi.S1G100500"
Phchi.S1	AUGUSTUS	exon	6018845	6020038	.	+	.	transcript_id "Phchi.S1G100500.t1"; gene_id "Phchi.S1G100500"
Phchi.S1	AUGUSTUS	stop_codon	6020039	6020041	.	+	0	transcript_id "Phchi.S1G100500.t1"; gene_id "Phchi.S1G100500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9626.t1 is derived from g6802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42966599	42968509	.	+	.	Phchi.S1G678500
Phchi.S1	AUGUSTUS	transcript	42966599	42968509	.	+	.	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	start_codon	42966599	42966601	.	+	0	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	CDS	42966599	42967621	0.35	+	0	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	exon	42966599	42967621	.	+	.	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	intron	42967622	42967771	.	+	.	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	CDS	42967772	42967839	0.98	+	0	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	exon	42967772	42967839	.	+	.	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	intron	42967840	42968109	.	+	.	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	CDS	42968110	42968509	0.9	+	1	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	exon	42968110	42968509	.	+	.	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	stop_codon	42968510	42968512	.	+	0	transcript_id "Phchi.S1G678500.t1"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	transcript	42966599	42968148	.	+	.	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	start_codon	42966599	42966601	.	+	0	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	CDS	42966599	42967519	0.34	+	0	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	exon	42966599	42967519	.	+	.	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	intron	42967520	42967631	.	+	.	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	CDS	42967632	42967839	0.61	+	0	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	exon	42967632	42967839	.	+	.	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	intron	42967840	42968104	.	+	.	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	CDS	42968105	42968148	0.64	+	2	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	exon	42968105	42968148	.	+	.	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
Phchi.S1	AUGUSTUS	stop_codon	42968149	42968151	.	+	0	transcript_id "Phchi.S1G678500.t2"; gene_id "Phchi.S1G678500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1273.t1 is derived from g11056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8770816	8772651	.	-	.	Phchi.S6G123200
Phchi.S6	AUGUSTUS	transcript	8770816	8772651	.	-	.	transcript_id "Phchi.S6G123200.t1"; gene_id "Phchi.S6G123200"
Phchi.S6	AUGUSTUS	stop_codon	8770813	8770815	.	-	0	transcript_id "Phchi.S6G123200.t1"; gene_id "Phchi.S6G123200"
Phchi.S6	AUGUSTUS	CDS	8770816	8772651	0.93	-	0	transcript_id "Phchi.S6G123200.t1"; gene_id "Phchi.S6G123200"
Phchi.S6	AUGUSTUS	exon	8770816	8772651	.	-	.	transcript_id "Phchi.S6G123200.t1"; gene_id "Phchi.S6G123200"
Phchi.S6	AUGUSTUS	start_codon	8772649	8772651	.	-	0	transcript_id "Phchi.S6G123200.t1"; gene_id "Phchi.S6G123200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15031.t1 is derived from g13499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16612484	16616694	.	-	.	Phchi.S3G235000
Phchi.S3	AUGUSTUS	transcript	16612484	16616694	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	stop_codon	16612481	16612483	.	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16612484	16612742	1	-	1	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16612484	16612742	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16612743	16612985	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16612986	16613170	1	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16612986	16613170	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16613171	16613401	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16613402	16613572	1	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16613402	16613572	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16613573	16613761	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16613762	16613998	1	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16613762	16613998	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16613999	16614093	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16614094	16614156	1	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16614094	16614156	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16614157	16614285	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16614286	16614351	1	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16614286	16614351	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16614352	16614649	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16614650	16614819	0.75	-	2	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16614650	16614819	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	intron	16614820	16614899	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	CDS	16614900	16616694	0.47	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	exon	16614900	16616694	.	-	.	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
Phchi.S3	AUGUSTUS	start_codon	16616692	16616694	.	-	0	transcript_id "Phchi.S3G235000.t1"; gene_id "Phchi.S3G235000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15588.t1 is derived from g14057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20148833	20150820	.	+	.	Phchi.S3G290700
Phchi.S3	AUGUSTUS	transcript	20148833	20150820	.	+	.	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	start_codon	20148833	20148835	.	+	0	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	CDS	20148833	20149509	1	+	0	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	exon	20148833	20149509	.	+	.	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	intron	20149510	20149625	.	+	.	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	CDS	20149626	20149707	1	+	1	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	exon	20149626	20149707	.	+	.	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	intron	20149708	20149782	.	+	.	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	CDS	20149783	20150820	0.83	+	0	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	exon	20149783	20150820	.	+	.	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
Phchi.S3	AUGUSTUS	stop_codon	20150821	20150823	.	+	0	transcript_id "Phchi.S3G290700.t1"; gene_id "Phchi.S3G290700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6053.t1 is derived from g3224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20651301	20651853	.	-	.	Phchi.S1G321200
Phchi.S1	AUGUSTUS	transcript	20651301	20651853	.	-	.	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	stop_codon	20651298	20651300	.	-	0	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	CDS	20651301	20651359	0.9	-	2	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	exon	20651301	20651359	.	-	.	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	intron	20651360	20651465	.	-	.	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	CDS	20651466	20651853	0.51	-	0	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	exon	20651466	20651853	.	-	.	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
Phchi.S1	AUGUSTUS	start_codon	20651851	20651853	.	-	0	transcript_id "Phchi.S1G321200.t1"; gene_id "Phchi.S1G321200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15886.t1 is derived from g14356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22028729	22031748	.	+	.	Phchi.S3G320500
Phchi.S3	AUGUSTUS	transcript	22028729	22031748	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	start_codon	22028729	22028731	.	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22028729	22028806	0.81	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22028729	22028806	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22028807	22028903	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22028904	22028940	0.75	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22028904	22028940	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22028941	22029053	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22029054	22029243	0.78	+	2	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22029054	22029243	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22029244	22029341	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22029342	22029420	0.95	+	1	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22029342	22029420	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22029421	22029506	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22029507	22029551	0.95	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22029507	22029551	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22029552	22029635	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22029636	22029785	0.99	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22029636	22029785	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22029786	22029885	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22029886	22030009	1	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22029886	22030009	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22030010	22030098	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22030099	22030199	0.93	+	2	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22030099	22030199	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22030200	22030285	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22030286	22030383	1	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22030286	22030383	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22030384	22030485	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22030486	22030578	0.97	+	1	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22030486	22030578	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22030579	22030687	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22030688	22030890	0.97	+	1	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22030688	22030890	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	intron	22030891	22031005	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	CDS	22031006	22031748	0.9	+	2	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	exon	22031006	22031748	.	+	.	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
Phchi.S3	AUGUSTUS	stop_codon	22031749	22031751	.	+	0	transcript_id "Phchi.S3G320500.t1"; gene_id "Phchi.S3G320500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2083.t1 is derived from g9003.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4771077	4773405	.	+	.	Phchi.S5G069200
Phchi.S5	AUGUSTUS	transcript	4771145	4771931	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	start_codon	4771145	4771147	.	+	0	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771145	4771273	0.97	+	0	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771145	4771273	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771274	4771415	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771416	4771524	1	+	0	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771416	4771524	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771525	4771602	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771603	4771687	1	+	2	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771603	4771687	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771688	4771852	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771853	4771931	1	+	1	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771853	4771931	.	+	.	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	stop_codon	4771932	4771934	.	+	0	transcript_id "Phchi.S5G069200.t1"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	transcript	4771077	4771931	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	start_codon	4771077	4771079	.	+	0	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771077	4771157	0.99	+	0	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771077	4771157	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771158	4771292	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771293	4771524	0.88	+	0	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771293	4771524	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771525	4771602	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771603	4771687	1	+	2	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771603	4771687	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771688	4771852	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771853	4771931	1	+	1	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771853	4771931	.	+	.	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	stop_codon	4771932	4771934	.	+	0	transcript_id "Phchi.S5G069200.t2"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	transcript	4771077	4773405	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	start_codon	4771077	4771079	.	+	0	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771077	4771157	0.95	+	0	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771077	4771157	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771158	4771292	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771293	4771524	0.79	+	0	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771293	4771524	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771525	4771602	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771603	4771687	1	+	2	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771603	4771687	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4771688	4771856	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4771857	4772452	0.69	+	1	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4771857	4772452	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	intron	4772453	4773049	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	CDS	4773050	4773405	0.78	+	2	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	exon	4773050	4773405	.	+	.	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
Phchi.S5	AUGUSTUS	stop_codon	4773406	4773408	.	+	0	transcript_id "Phchi.S5G069200.t3"; gene_id "Phchi.S5G069200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg899.t1 is derived from g10681.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6354946	6355725	.	+	.	Phchi.S6G085800
Phchi.S6	AUGUSTUS	transcript	6355050	6355725	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	start_codon	6355050	6355052	.	+	0	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355050	6355055	1	+	0	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355050	6355055	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	intron	6355056	6355141	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355142	6355265	1	+	0	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355142	6355265	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	intron	6355266	6355383	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355384	6355590	1	+	2	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355384	6355590	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	intron	6355591	6355681	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355682	6355725	1	+	2	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355682	6355725	.	+	.	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	stop_codon	6355726	6355728	.	+	0	transcript_id "Phchi.S6G085800.t1"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	transcript	6354946	6355725	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	start_codon	6354946	6354948	.	+	0	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6354946	6354948	0.96	+	0	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6354946	6354948	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	intron	6354949	6355141	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355142	6355265	1	+	0	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355142	6355265	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	intron	6355266	6355383	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355384	6355590	1	+	2	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355384	6355590	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	intron	6355591	6355681	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	CDS	6355682	6355725	1	+	2	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	exon	6355682	6355725	.	+	.	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
Phchi.S6	AUGUSTUS	stop_codon	6355726	6355728	.	+	0	transcript_id "Phchi.S6G085800.t2"; gene_id "Phchi.S6G085800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5596.t1 is derived from g2766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17814166	17816160	.	-	.	Phchi.S1G275500
Phchi.S1	AUGUSTUS	transcript	17814166	17816160	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	stop_codon	17814163	17814165	.	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17814166	17814346	1	-	1	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17814166	17814346	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17814347	17814444	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17814445	17814566	1	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17814445	17814566	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17814567	17814645	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17814646	17814866	1	-	2	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17814646	17814866	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17814867	17814947	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17814948	17815086	1	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17814948	17815086	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17815087	17815166	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17815167	17815390	1	-	2	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17815167	17815390	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17815391	17815467	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17815468	17815579	1	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17815468	17815579	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17815580	17815681	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17815682	17815882	1	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17815682	17815882	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	intron	17815883	17815980	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	CDS	17815981	17816160	1	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	exon	17815981	17816160	.	-	.	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
Phchi.S1	AUGUSTUS	start_codon	17816158	17816160	.	-	0	transcript_id "Phchi.S1G275500.t1"; gene_id "Phchi.S1G275500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14811.t1 is derived from g13279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14814644	14816964	.	-	.	Phchi.S3G213000
Phchi.S3	AUGUSTUS	transcript	14814644	14816964	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	stop_codon	14814641	14814643	.	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14814644	14814905	1	-	1	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14814644	14814905	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14814906	14814990	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14814991	14815079	1	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14814991	14815079	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14815080	14815173	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14815174	14815362	1	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14815174	14815362	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14815363	14815443	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14815444	14815623	1	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14815444	14815623	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14815624	14815759	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14815760	14815971	1	-	2	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14815760	14815971	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14815972	14816080	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14816081	14816201	1	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14816081	14816201	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14816202	14816299	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14816300	14816497	0.99	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14816300	14816497	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14816498	14816612	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14816613	14816755	1	-	2	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14816613	14816755	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	intron	14816756	14816879	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	CDS	14816880	14816964	0.87	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	exon	14816880	14816964	.	-	.	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
Phchi.S3	AUGUSTUS	start_codon	14816962	14816964	.	-	0	transcript_id "Phchi.S3G213000.t1"; gene_id "Phchi.S3G213000"
# This transcript jg12402.t2 is derived from g8079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12403.t1 is derived from g8080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18137487	18138996	.	+	.	Phchi.S2G048300
Phchi.S2	AUGUSTUS	transcript	18137487	18138996	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	start_codon	18137487	18137489	.	+	0	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	CDS	18137487	18137999	1	+	0	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	exon	18137487	18137999	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	intron	18138000	18138399	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	CDS	18138400	18138522	1	+	0	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	exon	18138400	18138522	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	intron	18138523	18138678	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	CDS	18138679	18138795	1	+	0	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	exon	18138679	18138795	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	intron	18138796	18138978	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	CDS	18138979	18138996	1	+	0	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	exon	18138979	18138996	.	+	.	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
Phchi.S2	AUGUSTUS	stop_codon	18138997	18138999	.	+	0	transcript_id "Phchi.S2G048300.t1"; gene_id "Phchi.S2G048300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5512.t1 is derived from g2682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17177167	17178450	.	+	.	Phchi.S1G267100
Phchi.S1	AUGUSTUS	transcript	17177167	17178450	.	+	.	transcript_id "Phchi.S1G267100.t1"; gene_id "Phchi.S1G267100"
Phchi.S1	AUGUSTUS	start_codon	17177167	17177169	.	+	0	transcript_id "Phchi.S1G267100.t1"; gene_id "Phchi.S1G267100"
Phchi.S1	AUGUSTUS	CDS	17177167	17178450	0.58	+	0	transcript_id "Phchi.S1G267100.t1"; gene_id "Phchi.S1G267100"
Phchi.S1	AUGUSTUS	exon	17177167	17178450	.	+	.	transcript_id "Phchi.S1G267100.t1"; gene_id "Phchi.S1G267100"
Phchi.S1	AUGUSTUS	stop_codon	17178451	17178453	.	+	0	transcript_id "Phchi.S1G267100.t1"; gene_id "Phchi.S1G267100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14711.t1 is derived from g13179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14325911	14327536	.	-	.	Phchi.S3G203000
Phchi.S3	AUGUSTUS	transcript	14325911	14327536	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	stop_codon	14325908	14325910	.	-	0	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	CDS	14325911	14326054	0.74	-	0	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	exon	14325911	14326054	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	intron	14326055	14326410	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	CDS	14326411	14326515	1	-	0	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	exon	14326411	14326515	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	intron	14326516	14326602	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	CDS	14326603	14326788	0.95	-	0	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	exon	14326603	14326788	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	intron	14326789	14326872	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	CDS	14326873	14327104	0.77	-	1	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	exon	14326873	14327104	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	intron	14327105	14327207	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	CDS	14327208	14327536	0.93	-	0	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	exon	14327208	14327536	.	-	.	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
Phchi.S3	AUGUSTUS	start_codon	14327534	14327536	.	-	0	transcript_id "Phchi.S3G203000.t1"; gene_id "Phchi.S3G203000"
# This transcript jg5197.t1 is derived from g2366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15418929	15420333	.	-	.	Phchi.S1G235500
Phchi.S1	AUGUSTUS	transcript	15418929	15420333	.	-	.	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	stop_codon	15418926	15418928	.	-	0	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	CDS	15418929	15419277	0.38	-	1	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	exon	15418929	15419277	.	-	.	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	intron	15419278	15419665	.	-	.	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	CDS	15419666	15420333	0.45	-	0	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	exon	15419666	15420333	.	-	.	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
Phchi.S1	AUGUSTUS	start_codon	15420331	15420333	.	-	0	transcript_id "Phchi.S1G235500.t1"; gene_id "Phchi.S1G235500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1353.t1 is derived from g14420.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C23	AUGUSTUS	gene	54492	56040	.	+	.	Phchi.C23G000200
Phchi.C23	AUGUSTUS	transcript	54492	56040	.	+	.	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	start_codon	54492	54494	.	+	0	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	CDS	54492	54688	0.39	+	0	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	exon	54492	54688	.	+	.	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	intron	54689	54796	.	+	.	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	CDS	54797	55257	0.31	+	1	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	exon	54797	55257	.	+	.	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	intron	55258	55402	.	+	.	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	CDS	55403	56040	0.63	+	2	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	exon	55403	56040	.	+	.	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	stop_codon	56041	56043	.	+	0	transcript_id "Phchi.C23G000200.t1"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	transcript	54492	54874	.	+	.	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	start_codon	54492	54494	.	+	0	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	CDS	54492	54688	0.62	+	0	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	exon	54492	54688	.	+	.	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	intron	54689	54789	.	+	.	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	CDS	54790	54874	0.55	+	1	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	exon	54790	54874	.	+	.	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
Phchi.C23	AUGUSTUS	stop_codon	54875	54877	.	+	0	transcript_id "Phchi.C23G000200.t2"; gene_id "Phchi.C23G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13365.t1 is derived from g11831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6360939	6361255	.	+	.	Phchi.S3G068400
Phchi.S3	AUGUSTUS	transcript	6360939	6361255	.	+	.	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	start_codon	6360939	6360941	.	+	0	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	CDS	6360939	6361133	0.81	+	0	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	exon	6360939	6361133	.	+	.	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	intron	6361134	6361228	.	+	.	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	CDS	6361229	6361255	0.91	+	0	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	exon	6361229	6361255	.	+	.	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
Phchi.S3	AUGUSTUS	stop_codon	6361256	6361258	.	+	0	transcript_id "Phchi.S3G068400.t1"; gene_id "Phchi.S3G068400"
# This transcript jg10427.t2 is derived from g14476.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10428.t1 is derived from g14477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	212636	213904	.	-	.	Phchi.S4G001000
Phchi.S4	AUGUSTUS	transcript	212636	213904	.	-	.	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	stop_codon	212633	212635	.	-	0	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	CDS	212636	213175	0.14	-	0	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	exon	212636	213175	.	-	.	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	intron	213176	213266	.	-	.	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	CDS	213267	213406	0.19	-	2	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	exon	213267	213406	.	-	.	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	intron	213407	213501	.	-	.	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	CDS	213502	213904	0.86	-	0	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	exon	213502	213904	.	-	.	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
Phchi.S4	AUGUSTUS	start_codon	213902	213904	.	-	0	transcript_id "Phchi.S4G001000.t1"; gene_id "Phchi.S4G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg245.t1 is derived from g10027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1693420	1695624	.	+	.	Phchi.S6G020400
Phchi.S6	AUGUSTUS	transcript	1693420	1695624	.	+	.	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	start_codon	1693420	1693422	.	+	0	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	CDS	1693420	1693797	1	+	0	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	exon	1693420	1693797	.	+	.	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	intron	1693798	1694029	.	+	.	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	CDS	1694030	1694177	0.81	+	0	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	exon	1694030	1694177	.	+	.	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	intron	1694178	1694260	.	+	.	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	CDS	1694261	1695624	0.56	+	2	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	exon	1694261	1695624	.	+	.	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
Phchi.S6	AUGUSTUS	stop_codon	1695625	1695627	.	+	0	transcript_id "Phchi.S6G020400.t1"; gene_id "Phchi.S6G020400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15966.t1 is derived from g16005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	8999	11297	.	-	.	Phchi.C133G000500
Phchi.C133	AUGUSTUS	transcript	8999	11297	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	stop_codon	8996	8998	.	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	8999	9101	0.99	-	1	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	8999	9101	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	9102	9255	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	9256	9377	1	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	9256	9377	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	9378	9501	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	9502	9608	0.91	-	2	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	9502	9608	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	9609	9694	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	9695	9773	0.76	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	9695	9773	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	9774	9889	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	9890	9976	1	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	9890	9976	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	9977	10060	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	10061	10324	0.99	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	10061	10324	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	10325	10431	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	10432	10581	0.99	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	10432	10581	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	10582	10676	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	10677	11004	0.63	-	1	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	10677	11004	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	intron	11005	11088	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	CDS	11089	11297	0.49	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	exon	11089	11297	.	-	.	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
Phchi.C133	AUGUSTUS	start_codon	11295	11297	.	-	0	transcript_id "Phchi.C133G000500.t1"; gene_id "Phchi.C133G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg524.t1 is derived from g10306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3760373	3766878	.	+	.	Phchi.S6G048300
Phchi.S6	AUGUSTUS	transcript	3760373	3766878	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	start_codon	3760373	3760375	.	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3760373	3760375	0.24	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3760373	3760375	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3760376	3760629	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3760630	3760723	0.53	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3760630	3760723	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3760724	3760804	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3760805	3760862	0.52	+	2	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3760805	3760862	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3760863	3760919	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3760920	3760933	0.46	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3760920	3760933	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3760934	3761015	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3761016	3761107	0.46	+	2	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3761016	3761107	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3761108	3761448	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3761449	3761527	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3761449	3761527	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3761528	3761660	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3761661	3761743	0.87	+	2	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3761661	3761743	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3761744	3761848	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3761849	3761998	0.87	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3761849	3761998	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3761999	3762090	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3762091	3762206	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3762091	3762206	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3762207	3762317	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3762318	3762423	0.69	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3762318	3762423	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3762424	3762548	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3762549	3762620	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3762549	3762620	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3762621	3762757	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3762758	3762873	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3762758	3762873	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3762874	3762966	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3762967	3763102	1	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3762967	3763102	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3763103	3763307	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3763308	3763385	0.78	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3763308	3763385	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3763386	3763494	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3763495	3763548	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3763495	3763548	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3763549	3763641	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3763642	3763712	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3763642	3763712	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3763713	3763809	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3763810	3763864	1	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3763810	3763864	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3763865	3763942	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3763943	3764038	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3763943	3764038	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3764039	3764122	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3764123	3764251	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3764123	3764251	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3764252	3764445	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3764446	3764528	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3764446	3764528	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3764529	3764626	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3764627	3764857	1	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3764627	3764857	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3764858	3764952	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3764953	3765088	1	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3764953	3765088	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3765089	3765166	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3765167	3765289	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3765167	3765289	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3765290	3765427	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3765428	3765559	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3765428	3765559	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3765560	3765651	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3765652	3765708	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3765652	3765708	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3765709	3765842	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3765843	3765940	1	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3765843	3765940	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3765941	3766082	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3766083	3766141	1	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3766083	3766141	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3766142	3766236	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3766237	3766348	1	+	2	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3766237	3766348	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3766349	3766504	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3766505	3766599	0.88	+	1	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3766505	3766599	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	intron	3766600	3766702	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	CDS	3766703	3766878	0.85	+	2	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	exon	3766703	3766878	.	+	.	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
Phchi.S6	AUGUSTUS	stop_codon	3766879	3766881	.	+	0	transcript_id "Phchi.S6G048300.t1"; gene_id "Phchi.S6G048300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9685.t1 is derived from g6861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43280787	43282591	.	+	.	Phchi.S1G684400
Phchi.S1	AUGUSTUS	transcript	43280787	43282591	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	start_codon	43280787	43280789	.	+	0	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	CDS	43280787	43280819	0.76	+	0	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	exon	43280787	43280819	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	intron	43280820	43280914	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	CDS	43280915	43281508	0.57	+	0	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	exon	43280915	43281508	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	intron	43281509	43281663	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	CDS	43281664	43282043	0.17	+	0	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	exon	43281664	43282043	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	intron	43282044	43282221	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	CDS	43282222	43282591	0.45	+	1	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	exon	43282222	43282591	.	+	.	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
Phchi.S1	AUGUSTUS	stop_codon	43282592	43282594	.	+	0	transcript_id "Phchi.S1G684400.t1"; gene_id "Phchi.S1G684400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11762.t1 is derived from g15814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8041614	8042723	.	-	.	Phchi.S4G134400
Phchi.S4	AUGUSTUS	transcript	8041614	8042441	.	-	.	transcript_id "Phchi.S4G134400.t1"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	stop_codon	8041611	8041613	.	-	0	transcript_id "Phchi.S4G134400.t1"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	CDS	8041614	8042441	1	-	0	transcript_id "Phchi.S4G134400.t1"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	exon	8041614	8042441	.	-	.	transcript_id "Phchi.S4G134400.t1"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	start_codon	8042439	8042441	.	-	0	transcript_id "Phchi.S4G134400.t1"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	transcript	8041614	8042723	.	-	.	transcript_id "Phchi.S4G134400.t2"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	stop_codon	8041611	8041613	.	-	0	transcript_id "Phchi.S4G134400.t2"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	CDS	8041614	8042723	1	-	0	transcript_id "Phchi.S4G134400.t2"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	exon	8041614	8042723	.	-	.	transcript_id "Phchi.S4G134400.t2"; gene_id "Phchi.S4G134400"
Phchi.S4	AUGUSTUS	start_codon	8042721	8042723	.	-	0	transcript_id "Phchi.S4G134400.t2"; gene_id "Phchi.S4G134400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4980.t1 is derived from g2150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13859367	13862494	.	+	.	Phchi.S1G213900
Phchi.S1	AUGUSTUS	transcript	13859367	13862494	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	start_codon	13859367	13859369	.	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13859367	13859593	0.94	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13859367	13859593	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13859594	13859784	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13859785	13859866	0.85	+	1	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13859785	13859866	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13859867	13859939	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13859940	13860080	0.91	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13859940	13860080	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13860081	13860180	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13860181	13860387	1	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13860181	13860387	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13860388	13860542	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13860543	13860793	1	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13860543	13860793	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13860794	13860881	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13860882	13861101	1	+	1	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13860882	13861101	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13861102	13861277	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13861278	13861382	0.83	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13861278	13861382	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13861383	13861493	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13861494	13861766	0.86	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13861494	13861766	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13861767	13862002	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13862003	13862124	1	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13862003	13862124	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13862125	13862202	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13862203	13862322	1	+	1	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13862203	13862322	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	intron	13862323	13862409	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	CDS	13862410	13862494	1	+	1	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	exon	13862410	13862494	.	+	.	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
Phchi.S1	AUGUSTUS	stop_codon	13862495	13862497	.	+	0	transcript_id "Phchi.S1G213900.t1"; gene_id "Phchi.S1G213900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6515.t1 is derived from g3687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23418314	23420771	.	-	.	Phchi.S1G367400
Phchi.S1	AUGUSTUS	transcript	23418314	23420771	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	stop_codon	23418311	23418313	.	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23418314	23418688	0.87	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23418314	23418688	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23418689	23418772	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23418773	23418833	0.91	-	1	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23418773	23418833	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23418834	23418920	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23418921	23418988	0.97	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23418921	23418988	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23418989	23419072	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23419073	23419108	0.93	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23419073	23419108	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23419109	23419223	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23419224	23419451	0.67	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23419224	23419451	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23419452	23419570	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23419571	23419611	0.42	-	2	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23419571	23419611	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23419612	23419736	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23419737	23419786	0.42	-	1	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23419737	23419786	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23419787	23419875	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23419876	23419961	0.75	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23419876	23419961	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23419962	23420103	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23420104	23420163	0.44	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23420104	23420163	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23420164	23420270	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23420271	23420371	0.78	-	2	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23420271	23420371	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23420372	23420498	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23420499	23420559	0.77	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23420499	23420559	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	intron	23420560	23420648	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	CDS	23420649	23420771	0.77	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	exon	23420649	23420771	.	-	.	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
Phchi.S1	AUGUSTUS	start_codon	23420769	23420771	.	-	0	transcript_id "Phchi.S1G367400.t1"; gene_id "Phchi.S1G367400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3512.t1 is derived from g681.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4149226	4150741	.	+	.	Phchi.S1G067100
Phchi.S1	AUGUSTUS	transcript	4149226	4150741	.	+	.	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	start_codon	4149226	4149228	.	+	0	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	CDS	4149226	4149972	0.88	+	0	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	exon	4149226	4149972	.	+	.	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	intron	4149973	4150063	.	+	.	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	CDS	4150064	4150741	0.9	+	0	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	exon	4150064	4150741	.	+	.	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	stop_codon	4150742	4150744	.	+	0	transcript_id "Phchi.S1G067100.t1"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	transcript	4149226	4150002	.	+	.	transcript_id "Phchi.S1G067100.t2"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	start_codon	4149226	4149228	.	+	0	transcript_id "Phchi.S1G067100.t2"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	CDS	4149226	4150002	1	+	0	transcript_id "Phchi.S1G067100.t2"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	exon	4149226	4150002	.	+	.	transcript_id "Phchi.S1G067100.t2"; gene_id "Phchi.S1G067100"
Phchi.S1	AUGUSTUS	stop_codon	4150003	4150005	.	+	0	transcript_id "Phchi.S1G067100.t2"; gene_id "Phchi.S1G067100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2204.t1 is derived from g9124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5410046	5411771	.	-	.	Phchi.S5G081300
Phchi.S5	AUGUSTUS	transcript	5410046	5411771	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	stop_codon	5410043	5410045	.	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5410046	5410249	1	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5410046	5410249	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	intron	5410250	5410321	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5410322	5410417	1	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5410322	5410417	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	intron	5410418	5410503	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5410504	5410530	1	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5410504	5410530	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	intron	5410531	5410642	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5410643	5410789	1	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5410643	5410789	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	intron	5410790	5410912	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5410913	5410999	1	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5410913	5410999	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	intron	5411000	5411091	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5411092	5411310	0.98	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5411092	5411310	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	intron	5411311	5411423	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	CDS	5411424	5411771	0.55	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	exon	5411424	5411771	.	-	.	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
Phchi.S5	AUGUSTUS	start_codon	5411769	5411771	.	-	0	transcript_id "Phchi.S5G081300.t1"; gene_id "Phchi.S5G081300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4505.t1 is derived from g1675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10869922	10872098	.	+	.	Phchi.S1G166400
Phchi.S1	AUGUSTUS	transcript	10869922	10872098	.	+	.	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	start_codon	10869922	10869924	.	+	0	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	CDS	10869922	10871668	0.98	+	0	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	exon	10869922	10871668	.	+	.	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	intron	10871669	10871757	.	+	.	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	CDS	10871758	10872098	0.78	+	2	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	exon	10871758	10872098	.	+	.	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
Phchi.S1	AUGUSTUS	stop_codon	10872099	10872101	.	+	0	transcript_id "Phchi.S1G166400.t1"; gene_id "Phchi.S1G166400"
# This transcript jg3089.t2 is derived from g258.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3089.t3 is derived from g258.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3090.t1 is derived from g259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1699693	1700161	.	-	.	Phchi.S1G024900
Phchi.S1	AUGUSTUS	transcript	1699693	1700161	.	-	.	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	stop_codon	1699690	1699692	.	-	0	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	CDS	1699693	1699870	0.7	-	1	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	exon	1699693	1699870	.	-	.	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	intron	1699871	1699991	.	-	.	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	CDS	1699992	1700161	0.83	-	0	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	exon	1699992	1700161	.	-	.	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
Phchi.S1	AUGUSTUS	start_codon	1700159	1700161	.	-	0	transcript_id "Phchi.S1G024900.t1"; gene_id "Phchi.S1G024900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8120.t1 is derived from g5295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33449199	33449633	.	-	.	Phchi.S1G527900
Phchi.S1	AUGUSTUS	transcript	33449199	33449633	.	-	.	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	stop_codon	33449196	33449198	.	-	0	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	CDS	33449199	33449288	1	-	0	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	exon	33449199	33449288	.	-	.	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	intron	33449289	33449375	.	-	.	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	CDS	33449376	33449633	0.6	-	0	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	exon	33449376	33449633	.	-	.	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
Phchi.S1	AUGUSTUS	start_codon	33449631	33449633	.	-	0	transcript_id "Phchi.S1G527900.t1"; gene_id "Phchi.S1G527900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13018.t1 is derived from g11483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3649298	3649912	.	+	.	Phchi.S3G033700
Phchi.S3	AUGUSTUS	transcript	3649298	3649912	.	+	.	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	start_codon	3649298	3649300	.	+	0	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	CDS	3649298	3649351	0.58	+	0	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	exon	3649298	3649351	.	+	.	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	intron	3649352	3649582	.	+	.	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	CDS	3649583	3649912	0.9	+	0	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	exon	3649583	3649912	.	+	.	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
Phchi.S3	AUGUSTUS	stop_codon	3649913	3649915	.	+	0	transcript_id "Phchi.S3G033700.t1"; gene_id "Phchi.S3G033700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12997.t1 is derived from g11462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3564532	3565481	.	-	.	Phchi.S3G031600
Phchi.S3	AUGUSTUS	transcript	3564532	3565481	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	stop_codon	3564529	3564531	.	-	0	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	CDS	3564532	3564696	1	-	0	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	exon	3564532	3564696	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	intron	3564697	3564786	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	CDS	3564787	3564855	1	-	0	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	exon	3564787	3564855	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	intron	3564856	3564943	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	CDS	3564944	3565025	1	-	1	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	exon	3564944	3565025	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	intron	3565026	3565118	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	CDS	3565119	3565285	1	-	0	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	exon	3565119	3565285	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	intron	3565286	3565370	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	CDS	3565371	3565481	0.33	-	0	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	exon	3565371	3565481	.	-	.	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
Phchi.S3	AUGUSTUS	start_codon	3565479	3565481	.	-	0	transcript_id "Phchi.S3G031600.t1"; gene_id "Phchi.S3G031600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12497.t1 is derived from g8174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30522403	30522894	.	-	.	Phchi.S2G057700
Phchi.S2	AUGUSTUS	transcript	30522403	30522894	.	-	.	transcript_id "Phchi.S2G057700.t1"; gene_id "Phchi.S2G057700"
Phchi.S2	AUGUSTUS	stop_codon	30522400	30522402	.	-	0	transcript_id "Phchi.S2G057700.t1"; gene_id "Phchi.S2G057700"
Phchi.S2	AUGUSTUS	CDS	30522403	30522894	0.76	-	0	transcript_id "Phchi.S2G057700.t1"; gene_id "Phchi.S2G057700"
Phchi.S2	AUGUSTUS	exon	30522403	30522894	.	-	.	transcript_id "Phchi.S2G057700.t1"; gene_id "Phchi.S2G057700"
Phchi.S2	AUGUSTUS	start_codon	30522892	30522894	.	-	0	transcript_id "Phchi.S2G057700.t1"; gene_id "Phchi.S2G057700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10570.t1 is derived from g14620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1014558	1015220	.	-	.	Phchi.S4G015200
Phchi.S4	AUGUSTUS	transcript	1014558	1015220	.	-	.	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	stop_codon	1014555	1014557	.	-	0	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	CDS	1014558	1014645	1	-	1	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	exon	1014558	1014645	.	-	.	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	intron	1014646	1014730	.	-	.	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	CDS	1014731	1014765	0.6	-	0	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	exon	1014731	1014765	.	-	.	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	intron	1014766	1014884	.	-	.	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	CDS	1014885	1015220	0.59	-	0	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	exon	1014885	1015220	.	-	.	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
Phchi.S4	AUGUSTUS	start_codon	1015218	1015220	.	-	0	transcript_id "Phchi.S4G015200.t1"; gene_id "Phchi.S4G015200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13129.t1 is derived from g11594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4265039	4266197	.	-	.	Phchi.S3G044800
Phchi.S3	AUGUSTUS	transcript	4265039	4266197	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	stop_codon	4265036	4265038	.	-	0	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	CDS	4265039	4265264	0.55	-	1	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	exon	4265039	4265264	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	intron	4265265	4265373	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	CDS	4265374	4265459	0.99	-	0	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	exon	4265374	4265459	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	intron	4265460	4265540	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	CDS	4265541	4265603	1	-	0	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	exon	4265541	4265603	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	intron	4265604	4265687	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	CDS	4265688	4266197	1	-	0	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	exon	4265688	4266197	.	-	.	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
Phchi.S3	AUGUSTUS	start_codon	4266195	4266197	.	-	0	transcript_id "Phchi.S3G044800.t1"; gene_id "Phchi.S3G044800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12431.t1 is derived from g8108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19597357	19601400	.	+	.	Phchi.S2G051100
Phchi.S2	AUGUSTUS	transcript	19597357	19601400	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	start_codon	19597357	19597359	.	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19597357	19597543	0.75	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19597357	19597543	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19597544	19597619	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19597620	19597993	0.99	+	2	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19597620	19597993	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19597994	19598174	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19598175	19598267	1	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19598175	19598267	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19598268	19598368	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19598369	19598623	0.97	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19598369	19598623	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19598624	19598761	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19598762	19598834	1	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19598762	19598834	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19598835	19598919	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19598920	19599052	1	+	2	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19598920	19599052	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19599053	19599226	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19599227	19599380	1	+	1	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19599227	19599380	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19599381	19599537	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19599538	19599612	1	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19599538	19599612	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19599613	19599741	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19599742	19599855	0.99	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19599742	19599855	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19599856	19599965	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19599966	19600130	0.85	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19599966	19600130	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19600131	19600247	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19600248	19600382	0.86	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19600248	19600382	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19600383	19600474	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19600475	19600570	1	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19600475	19600570	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19600571	19600697	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19600698	19600898	1	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19600698	19600898	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19600899	19600977	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19600978	19601021	1	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19600978	19601021	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	intron	19601022	19601144	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	CDS	19601145	19601400	0.99	+	1	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	exon	19601145	19601400	.	+	.	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
Phchi.S2	AUGUSTUS	stop_codon	19601401	19601403	.	+	0	transcript_id "Phchi.S2G051100.t1"; gene_id "Phchi.S2G051100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8193.t1 is derived from g5368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34359765	34364079	.	-	.	Phchi.S1G535200
Phchi.S1	AUGUSTUS	transcript	34359765	34364079	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	stop_codon	34359762	34359764	.	-	0	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34359765	34359913	0.46	-	2	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34359765	34359913	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34359914	34360044	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34360045	34360158	0.38	-	2	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34360045	34360158	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34360159	34360232	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34360233	34360353	0.7	-	0	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34360233	34360353	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34360354	34360437	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34360438	34360589	1	-	2	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34360438	34360589	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34360590	34360724	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34360725	34361015	1	-	2	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34360725	34361015	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34361016	34361187	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34361188	34363245	1	-	2	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34361188	34363245	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34363246	34363657	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34363658	34363664	1	-	0	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34363658	34363664	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	intron	34363665	34364010	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	CDS	34364011	34364079	0.81	-	0	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	exon	34364011	34364079	.	-	.	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
Phchi.S1	AUGUSTUS	start_codon	34364077	34364079	.	-	0	transcript_id "Phchi.S1G535200.t1"; gene_id "Phchi.S1G535200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15363.t1 is derived from g13831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18592751	18596081	.	+	.	Phchi.S3G268200
Phchi.S3	AUGUSTUS	transcript	18592751	18596081	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	start_codon	18592751	18592753	.	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18592751	18592893	0.6	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18592751	18592893	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18592894	18593097	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18593098	18593121	0.99	+	1	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18593098	18593121	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18593122	18593261	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18593262	18593367	1	+	1	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18593262	18593367	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18593368	18593453	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18593454	18593487	1	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18593454	18593487	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18593488	18593596	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18593597	18593652	1	+	2	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18593597	18593652	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18593653	18593744	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18593745	18593879	1	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18593745	18593879	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18593880	18593970	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18593971	18594119	1	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18593971	18594119	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18594120	18594206	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18594207	18594296	1	+	1	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18594207	18594296	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18594297	18594464	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18594465	18594531	0.99	+	1	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18594465	18594531	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18594532	18594638	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18594639	18594739	1	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18594639	18594739	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18594740	18594843	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18594844	18594977	1	+	1	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18594844	18594977	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18594978	18595087	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18595088	18595198	1	+	2	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18595088	18595198	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18595199	18595293	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18595294	18595355	1	+	2	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18595294	18595355	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18595356	18595485	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18595486	18595538	1	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18595486	18595538	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18595539	18595666	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18595667	18595742	1	+	1	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18595667	18595742	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18595743	18595821	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18595822	18595891	0.69	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18595822	18595891	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	intron	18595892	18595977	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	CDS	18595978	18596081	0.69	+	2	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	exon	18595978	18596081	.	+	.	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
Phchi.S3	AUGUSTUS	stop_codon	18596082	18596084	.	+	0	transcript_id "Phchi.S3G268200.t1"; gene_id "Phchi.S3G268200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2062.t1 is derived from g8982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4664289	4664817	.	+	.	Phchi.S5G067100
Phchi.S5	AUGUSTUS	transcript	4664289	4664817	.	+	.	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	start_codon	4664289	4664291	.	+	0	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	CDS	4664289	4664486	0.65	+	0	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	exon	4664289	4664486	.	+	.	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	intron	4664487	4664640	.	+	.	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	CDS	4664641	4664817	0.91	+	0	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	exon	4664641	4664817	.	+	.	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	stop_codon	4664818	4664820	.	+	0	transcript_id "Phchi.S5G067100.t1"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	transcript	4664289	4664528	.	+	.	transcript_id "Phchi.S5G067100.t2"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	start_codon	4664289	4664291	.	+	0	transcript_id "Phchi.S5G067100.t2"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	CDS	4664289	4664528	0.53	+	0	transcript_id "Phchi.S5G067100.t2"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	exon	4664289	4664528	.	+	.	transcript_id "Phchi.S5G067100.t2"; gene_id "Phchi.S5G067100"
Phchi.S5	AUGUSTUS	stop_codon	4664529	4664531	.	+	0	transcript_id "Phchi.S5G067100.t2"; gene_id "Phchi.S5G067100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6294.t1 is derived from g3466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22131790	22132278	.	-	.	Phchi.S1G345300
Phchi.S1	AUGUSTUS	transcript	22131790	22132278	.	-	.	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	stop_codon	22131787	22131789	.	-	0	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	CDS	22131790	22131859	0.44	-	1	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	exon	22131790	22131859	.	-	.	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	intron	22131860	22131982	.	-	.	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	CDS	22131983	22132278	0.42	-	0	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	exon	22131983	22132278	.	-	.	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
Phchi.S1	AUGUSTUS	start_codon	22132276	22132278	.	-	0	transcript_id "Phchi.S1G345300.t1"; gene_id "Phchi.S1G345300"
# This transcript jg9237.t2 is derived from g6412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9238.t1 is derived from g6413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40547915	40550891	.	-	.	Phchi.S1G639700
Phchi.S1	AUGUSTUS	transcript	40547915	40550891	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	stop_codon	40547912	40547914	.	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40547915	40548028	1	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40547915	40548028	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548029	40548122	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548123	40548220	1	-	2	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548123	40548220	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548221	40548299	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548300	40548341	1	-	2	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548300	40548341	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548342	40548484	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548485	40548572	1	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548485	40548572	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548573	40548702	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548703	40548752	1	-	2	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548703	40548752	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548753	40548877	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548878	40549001	1	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548878	40549001	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549002	40549086	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549087	40549167	1	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549087	40549167	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549168	40549248	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549249	40549364	1	-	2	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549249	40549364	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549365	40549439	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549440	40549535	1	-	2	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549440	40549535	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549536	40549629	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549630	40549882	1	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549630	40549882	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549883	40549988	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549989	40550014	1	-	2	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549989	40550014	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40550015	40550303	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40550304	40550395	1	-	1	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40550304	40550395	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40550396	40550547	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40550548	40550891	0.99	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40550548	40550891	.	-	.	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	start_codon	40550889	40550891	.	-	0	transcript_id "Phchi.S1G639700.t1"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	transcript	40547915	40550891	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	stop_codon	40547912	40547914	.	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40547915	40548028	1	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40547915	40548028	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548029	40548122	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548123	40548220	1	-	2	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548123	40548220	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548221	40548299	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548300	40548344	0.95	-	2	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548300	40548344	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548345	40548484	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548485	40548572	1	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548485	40548572	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548573	40548702	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548703	40548752	1	-	2	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548703	40548752	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40548753	40548877	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40548878	40549001	1	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40548878	40549001	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549002	40549086	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549087	40549167	1	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549087	40549167	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549168	40549248	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549249	40549364	1	-	2	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549249	40549364	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549365	40549439	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549440	40549535	1	-	2	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549440	40549535	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549536	40549629	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549630	40549882	0.98	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549630	40549882	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40549883	40549988	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40549989	40550014	1	-	2	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40549989	40550014	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40550015	40550303	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40550304	40550395	1	-	1	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40550304	40550395	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	intron	40550396	40550547	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	CDS	40550548	40550891	1	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	exon	40550548	40550891	.	-	.	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
Phchi.S1	AUGUSTUS	start_codon	40550889	40550891	.	-	0	transcript_id "Phchi.S1G639700.t2"; gene_id "Phchi.S1G639700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9753.t1 is derived from g6929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43515055	43515684	.	-	.	Phchi.S1G691200
Phchi.S1	AUGUSTUS	transcript	43515055	43515684	.	-	.	transcript_id "Phchi.S1G691200.t1"; gene_id "Phchi.S1G691200"
Phchi.S1	AUGUSTUS	stop_codon	43515052	43515054	.	-	0	transcript_id "Phchi.S1G691200.t1"; gene_id "Phchi.S1G691200"
Phchi.S1	AUGUSTUS	CDS	43515055	43515684	0.87	-	0	transcript_id "Phchi.S1G691200.t1"; gene_id "Phchi.S1G691200"
Phchi.S1	AUGUSTUS	exon	43515055	43515684	.	-	.	transcript_id "Phchi.S1G691200.t1"; gene_id "Phchi.S1G691200"
Phchi.S1	AUGUSTUS	start_codon	43515682	43515684	.	-	0	transcript_id "Phchi.S1G691200.t1"; gene_id "Phchi.S1G691200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12311.t1 is derived from g7987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10146326	10149562	.	-	.	Phchi.S2G039100
Phchi.S2	AUGUSTUS	transcript	10146326	10149562	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	stop_codon	10146323	10146325	.	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10146326	10146337	1	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10146326	10146337	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10146338	10146492	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10146493	10146657	1	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10146493	10146657	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10146658	10146871	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10146872	10146947	1	-	1	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10146872	10146947	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10146948	10147188	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10147189	10147311	1	-	1	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10147189	10147311	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10147312	10147404	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10147405	10147569	0.96	-	1	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10147405	10147569	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10147570	10147673	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10147674	10147764	1	-	2	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10147674	10147764	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10147765	10147840	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10147841	10147925	1	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10147841	10147925	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10147926	10148084	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10148085	10148243	0.97	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10148085	10148243	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10148244	10148363	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10148364	10148420	1	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10148364	10148420	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10148421	10148514	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10148515	10148619	1	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10148515	10148619	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10148620	10148823	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10148824	10148942	1	-	2	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10148824	10148942	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	intron	10148943	10149555	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	CDS	10149556	10149562	0.8	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	exon	10149556	10149562	.	-	.	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
Phchi.S2	AUGUSTUS	start_codon	10149560	10149562	.	-	0	transcript_id "Phchi.S2G039100.t1"; gene_id "Phchi.S2G039100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12703.t1 is derived from g11168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	633319	637740	.	+	.	Phchi.S3G002200
Phchi.S3	AUGUSTUS	transcript	633319	637740	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	start_codon	633319	633321	.	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	633319	633367	0.41	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	633319	633367	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	633368	633466	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	633467	633542	0.59	+	2	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	633467	633542	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	633543	633620	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	633621	633633	0.87	+	1	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	633621	633633	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	633634	633714	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	633715	633849	0.99	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	633715	633849	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	633850	633942	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	633943	634020	1	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	633943	634020	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	634021	634154	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	634155	634313	0.99	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	634155	634313	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	634314	634444	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	634445	634511	1	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	634445	634511	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	634512	634651	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	634652	634716	1	+	2	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	634652	634716	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	634717	634806	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	634807	634946	1	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	634807	634946	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	634947	635082	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	635083	635209	1	+	1	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	635083	635209	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	635210	635300	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	635301	635415	1	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	635301	635415	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	635416	635534	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	635535	635623	1	+	2	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	635535	635623	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	635624	635743	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	635744	635827	1	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	635744	635827	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	635828	635914	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	635915	636322	0.92	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	635915	636322	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	636323	636395	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	636396	637391	0.92	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	636396	637391	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	637392	637503	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	637504	637563	0.99	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	637504	637563	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	intron	637564	637641	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	CDS	637642	637740	0.99	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	exon	637642	637740	.	+	.	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
Phchi.S3	AUGUSTUS	stop_codon	637741	637743	.	+	0	transcript_id "Phchi.S3G002200.t1"; gene_id "Phchi.S3G002200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12808.t1 is derived from g11273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2472220	2472867	.	-	.	Phchi.S3G012700
Phchi.S3	AUGUSTUS	transcript	2472220	2472867	.	-	.	transcript_id "Phchi.S3G012700.t1"; gene_id "Phchi.S3G012700"
Phchi.S3	AUGUSTUS	stop_codon	2472217	2472219	.	-	0	transcript_id "Phchi.S3G012700.t1"; gene_id "Phchi.S3G012700"
Phchi.S3	AUGUSTUS	CDS	2472220	2472867	0.91	-	0	transcript_id "Phchi.S3G012700.t1"; gene_id "Phchi.S3G012700"
Phchi.S3	AUGUSTUS	exon	2472220	2472867	.	-	.	transcript_id "Phchi.S3G012700.t1"; gene_id "Phchi.S3G012700"
Phchi.S3	AUGUSTUS	start_codon	2472865	2472867	.	-	0	transcript_id "Phchi.S3G012700.t1"; gene_id "Phchi.S3G012700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13456.t1 is derived from g11923.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6975147	6975807	.	-	.	Phchi.S3G077500
Phchi.S3	AUGUSTUS	transcript	6975147	6975807	.	-	.	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	stop_codon	6975144	6975146	.	-	0	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	CDS	6975147	6975308	1	-	0	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	exon	6975147	6975308	.	-	.	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	intron	6975309	6975397	.	-	.	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	CDS	6975398	6975586	1	-	0	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	exon	6975398	6975586	.	-	.	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	intron	6975587	6975657	.	-	.	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	CDS	6975658	6975807	0.3	-	0	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	exon	6975658	6975807	.	-	.	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
Phchi.S3	AUGUSTUS	start_codon	6975805	6975807	.	-	0	transcript_id "Phchi.S3G077500.t1"; gene_id "Phchi.S3G077500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4540.t1 is derived from g1710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11016129	11020644	.	-	.	Phchi.S1G169900
Phchi.S1	AUGUSTUS	transcript	11016129	11020644	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	stop_codon	11016126	11016128	.	-	0	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	CDS	11016129	11017262	0.58	-	0	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	exon	11016129	11017262	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	intron	11017263	11017423	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	CDS	11017424	11017429	0.64	-	0	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	exon	11017424	11017429	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	intron	11017430	11017845	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	CDS	11017846	11018266	0.45	-	1	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	exon	11017846	11018266	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	intron	11018267	11018346	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	CDS	11018347	11018806	0.62	-	2	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	exon	11018347	11018806	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	intron	11018807	11018903	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	CDS	11018904	11020644	0.79	-	0	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	exon	11018904	11020644	.	-	.	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
Phchi.S1	AUGUSTUS	start_codon	11020642	11020644	.	-	0	transcript_id "Phchi.S1G169900.t1"; gene_id "Phchi.S1G169900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11586.t1 is derived from g15637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7232927	7233796	.	-	.	Phchi.S4G116800
Phchi.S4	AUGUSTUS	transcript	7232927	7233796	.	-	.	transcript_id "Phchi.S4G116800.t1"; gene_id "Phchi.S4G116800"
Phchi.S4	AUGUSTUS	stop_codon	7232924	7232926	.	-	0	transcript_id "Phchi.S4G116800.t1"; gene_id "Phchi.S4G116800"
Phchi.S4	AUGUSTUS	CDS	7232927	7233796	0.61	-	0	transcript_id "Phchi.S4G116800.t1"; gene_id "Phchi.S4G116800"
Phchi.S4	AUGUSTUS	exon	7232927	7233796	.	-	.	transcript_id "Phchi.S4G116800.t1"; gene_id "Phchi.S4G116800"
Phchi.S4	AUGUSTUS	start_codon	7233794	7233796	.	-	0	transcript_id "Phchi.S4G116800.t1"; gene_id "Phchi.S4G116800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6362.t1 is derived from g3534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22563707	22564343	.	-	.	Phchi.S1G352100
Phchi.S1	AUGUSTUS	transcript	22563707	22564343	.	-	.	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	stop_codon	22563704	22563706	.	-	0	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	CDS	22563707	22563832	1	-	0	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	exon	22563707	22563832	.	-	.	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	intron	22563833	22563972	.	-	.	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	CDS	22563973	22564095	1	-	0	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	exon	22563973	22564095	.	-	.	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	intron	22564096	22564187	.	-	.	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	CDS	22564188	22564343	1	-	0	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	exon	22564188	22564343	.	-	.	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
Phchi.S1	AUGUSTUS	start_codon	22564341	22564343	.	-	0	transcript_id "Phchi.S1G352100.t1"; gene_id "Phchi.S1G352100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3401.t1 is derived from g570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3357429	3358314	.	+	.	Phchi.S1G056000
Phchi.S1	AUGUSTUS	transcript	3357429	3358314	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	start_codon	3357429	3357431	.	+	0	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	CDS	3357429	3357566	1	+	0	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	exon	3357429	3357566	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	intron	3357567	3357649	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	CDS	3357650	3357719	1	+	0	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	exon	3357650	3357719	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	intron	3357720	3357807	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	CDS	3357808	3357974	1	+	2	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	exon	3357808	3357974	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	intron	3357975	3358056	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	CDS	3358057	3358130	1	+	0	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	exon	3358057	3358130	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	intron	3358131	3358226	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	CDS	3358227	3358314	1	+	1	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	exon	3358227	3358314	.	+	.	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
Phchi.S1	AUGUSTUS	stop_codon	3358315	3358317	.	+	0	transcript_id "Phchi.S1G056000.t1"; gene_id "Phchi.S1G056000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5346.t1 is derived from g2516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16398375	16401750	.	+	.	Phchi.S1G250500
Phchi.S1	AUGUSTUS	transcript	16398375	16401750	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	start_codon	16398375	16398377	.	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16398375	16398394	0.93	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16398375	16398394	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16398395	16398515	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16398516	16398726	0.93	+	1	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16398516	16398726	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16398727	16398866	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16398867	16399019	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16398867	16399019	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16399020	16399271	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16399272	16399320	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16399272	16399320	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16399321	16399469	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16399470	16399553	1	+	2	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16399470	16399553	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16399554	16399655	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16399656	16399759	0.94	+	2	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16399656	16399759	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16399760	16399869	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16399870	16399956	0.87	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16399870	16399956	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16399957	16400100	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16400101	16400154	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16400101	16400154	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16400155	16400306	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16400307	16400402	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16400307	16400402	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16400403	16400505	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16400506	16400633	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16400506	16400633	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16400634	16400758	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16400759	16400885	1	+	1	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16400759	16400885	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16400886	16400972	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16400973	16401032	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16400973	16401032	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16401033	16401125	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16401126	16401233	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16401126	16401233	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16401234	16401320	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16401321	16401421	1	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16401321	16401421	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16401422	16401495	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16401496	16401547	0.98	+	1	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16401496	16401547	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	intron	16401548	16401654	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	CDS	16401655	16401750	0.5	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	exon	16401655	16401750	.	+	.	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
Phchi.S1	AUGUSTUS	stop_codon	16401751	16401753	.	+	0	transcript_id "Phchi.S1G250500.t1"; gene_id "Phchi.S1G250500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15178.t1 is derived from g13646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17380830	17381966	.	+	.	Phchi.S3G249700
Phchi.S3	AUGUSTUS	transcript	17380830	17381966	.	+	.	transcript_id "Phchi.S3G249700.t1"; gene_id "Phchi.S3G249700"
Phchi.S3	AUGUSTUS	start_codon	17380830	17380832	.	+	0	transcript_id "Phchi.S3G249700.t1"; gene_id "Phchi.S3G249700"
Phchi.S3	AUGUSTUS	CDS	17380830	17381966	0.87	+	0	transcript_id "Phchi.S3G249700.t1"; gene_id "Phchi.S3G249700"
Phchi.S3	AUGUSTUS	exon	17380830	17381966	.	+	.	transcript_id "Phchi.S3G249700.t1"; gene_id "Phchi.S3G249700"
Phchi.S3	AUGUSTUS	stop_codon	17381967	17381969	.	+	0	transcript_id "Phchi.S3G249700.t1"; gene_id "Phchi.S3G249700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7933.t1 is derived from g5107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31993868	31994345	.	-	.	Phchi.S1G509200
Phchi.S1	AUGUSTUS	transcript	31993868	31994345	.	-	.	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	stop_codon	31993865	31993867	.	-	0	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	CDS	31993868	31994005	1	-	0	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	exon	31993868	31994005	.	-	.	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	intron	31994006	31994099	.	-	.	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	CDS	31994100	31994345	0.79	-	0	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	exon	31994100	31994345	.	-	.	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
Phchi.S1	AUGUSTUS	start_codon	31994343	31994345	.	-	0	transcript_id "Phchi.S1G509200.t1"; gene_id "Phchi.S1G509200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8793.t1 is derived from g5968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37990347	37991021	.	+	.	Phchi.S1G595200
Phchi.S1	AUGUSTUS	transcript	37990347	37991021	.	+	.	transcript_id "Phchi.S1G595200.t1"; gene_id "Phchi.S1G595200"
Phchi.S1	AUGUSTUS	start_codon	37990347	37990349	.	+	0	transcript_id "Phchi.S1G595200.t1"; gene_id "Phchi.S1G595200"
Phchi.S1	AUGUSTUS	CDS	37990347	37991021	0.93	+	0	transcript_id "Phchi.S1G595200.t1"; gene_id "Phchi.S1G595200"
Phchi.S1	AUGUSTUS	exon	37990347	37991021	.	+	.	transcript_id "Phchi.S1G595200.t1"; gene_id "Phchi.S1G595200"
Phchi.S1	AUGUSTUS	stop_codon	37991022	37991024	.	+	0	transcript_id "Phchi.S1G595200.t1"; gene_id "Phchi.S1G595200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11276.t1 is derived from g15326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5171212	5174980	.	+	.	Phchi.S4G085800
Phchi.S4	AUGUSTUS	transcript	5171212	5174980	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	start_codon	5171212	5171214	.	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5171212	5171352	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5171212	5171352	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5171353	5171435	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5171436	5171522	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5171436	5171522	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5171523	5171605	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5171606	5171703	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5171606	5171703	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5171704	5171801	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5171802	5171862	1	+	1	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5171802	5171862	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5171863	5172082	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5172083	5172163	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5172083	5172163	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5172164	5172320	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5172321	5172413	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5172321	5172413	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5172414	5172513	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5172514	5172603	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5172514	5172603	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5172604	5172779	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5172780	5172907	1	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5172780	5172907	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5172908	5173020	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5173021	5173132	1	+	1	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5173021	5173132	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5173133	5173319	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5173320	5173375	0.53	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5173320	5173375	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5173376	5173819	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5173820	5174027	0.39	+	1	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5173820	5174027	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5174028	5174219	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5174220	5174279	0.36	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5174220	5174279	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5174280	5174373	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5174374	5174891	0.59	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5174374	5174891	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	intron	5174892	5174973	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	CDS	5174974	5174980	1	+	1	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	exon	5174974	5174980	.	+	.	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
Phchi.S4	AUGUSTUS	stop_codon	5174981	5174983	.	+	0	transcript_id "Phchi.S4G085800.t1"; gene_id "Phchi.S4G085800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13298.t1 is derived from g11764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5414539	5417654	.	+	.	Phchi.S3G061700
Phchi.S3	AUGUSTUS	transcript	5414539	5417654	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	start_codon	5414539	5414541	.	+	0	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5414539	5415518	0.65	+	0	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5414539	5415518	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5415519	5415603	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5415604	5415707	0.91	+	1	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5415604	5415707	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5415708	5415799	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5415800	5416004	1	+	2	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5415800	5416004	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5416005	5416091	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5416092	5416148	0.99	+	1	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5416092	5416148	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5416149	5416277	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5416278	5416376	1	+	1	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5416278	5416376	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5416377	5416464	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5416465	5416692	1	+	1	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5416465	5416692	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5416693	5416782	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5416783	5416921	1	+	1	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5416783	5416921	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5416922	5417011	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5417012	5417257	1	+	0	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5417012	5417257	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	intron	5417258	5417372	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	CDS	5417373	5417654	1	+	0	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	exon	5417373	5417654	.	+	.	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
Phchi.S3	AUGUSTUS	stop_codon	5417655	5417657	.	+	0	transcript_id "Phchi.S3G061700.t1"; gene_id "Phchi.S3G061700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1972.t1 is derived from g8892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4087725	4088921	.	-	.	Phchi.S5G058100
Phchi.S5	AUGUSTUS	transcript	4087725	4088921	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	stop_codon	4087722	4087724	.	-	0	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	CDS	4087725	4087746	0.89	-	1	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	exon	4087725	4087746	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	intron	4087747	4088047	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	CDS	4088048	4088059	0.89	-	1	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	exon	4088048	4088059	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	intron	4088060	4088181	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	CDS	4088182	4088275	0.91	-	2	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	exon	4088182	4088275	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	intron	4088276	4088381	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	CDS	4088382	4088415	0.91	-	0	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	exon	4088382	4088415	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	intron	4088416	4088542	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	CDS	4088543	4088691	1	-	2	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	exon	4088543	4088691	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	intron	4088692	4088839	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	CDS	4088840	4088921	0.68	-	0	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	exon	4088840	4088921	.	-	.	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
Phchi.S5	AUGUSTUS	start_codon	4088919	4088921	.	-	0	transcript_id "Phchi.S5G058100.t1"; gene_id "Phchi.S5G058100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13284.t1 is derived from g11750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5181757	5182887	.	-	.	Phchi.S3G060300
Phchi.S3	AUGUSTUS	transcript	5181757	5182887	.	-	.	transcript_id "Phchi.S3G060300.t1"; gene_id "Phchi.S3G060300"
Phchi.S3	AUGUSTUS	stop_codon	5181754	5181756	.	-	0	transcript_id "Phchi.S3G060300.t1"; gene_id "Phchi.S3G060300"
Phchi.S3	AUGUSTUS	CDS	5181757	5182887	0.74	-	0	transcript_id "Phchi.S3G060300.t1"; gene_id "Phchi.S3G060300"
Phchi.S3	AUGUSTUS	exon	5181757	5182887	.	-	.	transcript_id "Phchi.S3G060300.t1"; gene_id "Phchi.S3G060300"
Phchi.S3	AUGUSTUS	start_codon	5182885	5182887	.	-	0	transcript_id "Phchi.S3G060300.t1"; gene_id "Phchi.S3G060300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11271.t1 is derived from g15321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5107920	5116904	.	+	.	Phchi.S4G085300
Phchi.S4	AUGUSTUS	transcript	5107920	5116904	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	start_codon	5107920	5107922	.	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5107920	5107970	0.72	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5107920	5107970	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5107971	5108063	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5108064	5108300	1	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5108064	5108300	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5108301	5108375	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5108376	5114928	0.99	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5108376	5114928	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5114929	5115015	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5115016	5115719	0.99	+	2	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5115016	5115719	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5115720	5115811	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5115812	5115953	1	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5115812	5115953	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5115954	5116094	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5116095	5116176	0.55	+	2	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5116095	5116176	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5116177	5116286	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5116287	5116323	0.54	+	1	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5116287	5116323	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5116324	5116602	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5116603	5116619	0.99	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5116603	5116619	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5116620	5116704	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5116705	5116760	0.99	+	1	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5116705	5116760	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	intron	5116761	5116857	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	CDS	5116858	5116904	0.99	+	2	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	exon	5116858	5116904	.	+	.	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
Phchi.S4	AUGUSTUS	stop_codon	5116905	5116907	.	+	0	transcript_id "Phchi.S4G085300.t1"; gene_id "Phchi.S4G085300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1938.t1 is derived from g8858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3920166	3920775	.	+	.	Phchi.S5G054700
Phchi.S5	AUGUSTUS	transcript	3920166	3920775	.	+	.	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	start_codon	3920166	3920168	.	+	0	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	CDS	3920166	3920350	0.63	+	0	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	exon	3920166	3920350	.	+	.	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	intron	3920351	3920440	.	+	.	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	CDS	3920441	3920524	1	+	1	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	exon	3920441	3920524	.	+	.	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	intron	3920525	3920729	.	+	.	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	CDS	3920730	3920775	0.9	+	1	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	exon	3920730	3920775	.	+	.	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
Phchi.S5	AUGUSTUS	stop_codon	3920776	3920778	.	+	0	transcript_id "Phchi.S5G054700.t1"; gene_id "Phchi.S5G054700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5775.t1 is derived from g2945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18894398	18895252	.	-	.	Phchi.S1G293400
Phchi.S1	AUGUSTUS	transcript	18894398	18895252	.	-	.	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	stop_codon	18894395	18894397	.	-	0	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	CDS	18894398	18894964	0.51	-	0	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	exon	18894398	18894964	.	-	.	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	intron	18894965	18895041	.	-	.	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	CDS	18895042	18895125	1	-	0	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	exon	18895042	18895125	.	-	.	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	intron	18895126	18895198	.	-	.	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	CDS	18895199	18895252	0.94	-	0	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	exon	18895199	18895252	.	-	.	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
Phchi.S1	AUGUSTUS	start_codon	18895250	18895252	.	-	0	transcript_id "Phchi.S1G293400.t1"; gene_id "Phchi.S1G293400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13471.t1 is derived from g11938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7065499	7066517	.	-	.	Phchi.S3G079000
Phchi.S3	AUGUSTUS	transcript	7065499	7066517	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	stop_codon	7065496	7065498	.	-	0	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	CDS	7065499	7065672	1	-	0	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	exon	7065499	7065672	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	intron	7065673	7065772	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	CDS	7065773	7065909	0.97	-	2	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	exon	7065773	7065909	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	intron	7065910	7065987	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	CDS	7065988	7066124	0.93	-	1	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	exon	7065988	7066124	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	intron	7066125	7066236	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	CDS	7066237	7066517	1	-	0	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	exon	7066237	7066517	.	-	.	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
Phchi.S3	AUGUSTUS	start_codon	7066515	7066517	.	-	0	transcript_id "Phchi.S3G079000.t1"; gene_id "Phchi.S3G079000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15517.t1 is derived from g13986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19659680	19663243	.	+	.	Phchi.S3G283600
Phchi.S3	AUGUSTUS	transcript	19659680	19663243	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	start_codon	19659680	19659682	.	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19659680	19660024	0.7	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19659680	19660024	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19660025	19660470	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19660471	19660557	1	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19660471	19660557	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19660558	19660724	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19660725	19660859	1	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19660725	19660859	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19660860	19660963	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19660964	19661019	1	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19660964	19661019	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19661020	19661144	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19661145	19661258	1	+	1	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19661145	19661258	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19661259	19661547	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19661548	19661657	1	+	1	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19661548	19661657	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19661658	19661741	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19661742	19661790	1	+	2	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19661742	19661790	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19661791	19661861	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19661862	19661868	1	+	1	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19661862	19661868	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19661869	19661943	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19661944	19662011	1	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19661944	19662011	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19662012	19662110	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19662111	19662177	1	+	1	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19662111	19662177	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19662178	19662263	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19662264	19662527	1	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19662264	19662527	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19662528	19662693	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19662694	19662746	0.71	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19662694	19662746	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19662747	19662819	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19662820	19662886	0.71	+	1	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19662820	19662886	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19662887	19662970	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19662971	19663067	0.71	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19662971	19663067	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	intron	19663068	19663154	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	CDS	19663155	19663243	0.71	+	2	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	exon	19663155	19663243	.	+	.	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
Phchi.S3	AUGUSTUS	stop_codon	19663244	19663246	.	+	0	transcript_id "Phchi.S3G283600.t1"; gene_id "Phchi.S3G283600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3006.t1 is derived from g175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1108843	1110403	.	+	.	Phchi.S1G016500
Phchi.S1	AUGUSTUS	transcript	1108843	1110403	.	+	.	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	start_codon	1108843	1108845	.	+	0	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	CDS	1108843	1109432	0.98	+	0	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	exon	1108843	1109432	.	+	.	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	intron	1109433	1109553	.	+	.	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	CDS	1109554	1110403	0.98	+	1	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	exon	1109554	1110403	.	+	.	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
Phchi.S1	AUGUSTUS	stop_codon	1110404	1110406	.	+	0	transcript_id "Phchi.S1G016500.t1"; gene_id "Phchi.S1G016500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3685.t1 is derived from g854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5166461	5166694	.	-	.	Phchi.S1G084400
Phchi.S1	AUGUSTUS	transcript	5166461	5166694	.	-	.	transcript_id "Phchi.S1G084400.t1"; gene_id "Phchi.S1G084400"
Phchi.S1	AUGUSTUS	stop_codon	5166458	5166460	.	-	0	transcript_id "Phchi.S1G084400.t1"; gene_id "Phchi.S1G084400"
Phchi.S1	AUGUSTUS	CDS	5166461	5166694	0.76	-	0	transcript_id "Phchi.S1G084400.t1"; gene_id "Phchi.S1G084400"
Phchi.S1	AUGUSTUS	exon	5166461	5166694	.	-	.	transcript_id "Phchi.S1G084400.t1"; gene_id "Phchi.S1G084400"
Phchi.S1	AUGUSTUS	start_codon	5166692	5166694	.	-	0	transcript_id "Phchi.S1G084400.t1"; gene_id "Phchi.S1G084400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11585.t1 is derived from g15636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7201855	7205570	.	-	.	Phchi.S4G116700
Phchi.S4	AUGUSTUS	transcript	7201855	7205570	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	stop_codon	7201852	7201854	.	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7201855	7201962	1	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7201855	7201962	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7201963	7202247	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7202248	7202346	0.83	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7202248	7202346	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7202347	7202517	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7202518	7202805	0.76	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7202518	7202805	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7202806	7202892	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7202893	7203051	0.98	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7202893	7203051	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7203052	7203152	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7203153	7203218	0.44	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7203153	7203218	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7203219	7203301	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7203302	7203365	0.72	-	1	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7203302	7203365	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7203366	7203458	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7203459	7203674	0.49	-	1	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7203459	7203674	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7203675	7203981	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7203982	7204079	0.57	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7203982	7204079	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7204080	7204250	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7204251	7204561	0.61	-	2	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7204251	7204561	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7204562	7204700	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7204701	7204803	0.67	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7204701	7204803	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7204804	7204962	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7204963	7205039	0.99	-	2	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7204963	7205039	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7205040	7205164	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7205165	7205333	1	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7205165	7205333	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	intron	7205334	7205489	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	CDS	7205490	7205570	0.37	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	exon	7205490	7205570	.	-	.	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
Phchi.S4	AUGUSTUS	start_codon	7205568	7205570	.	-	0	transcript_id "Phchi.S4G116700.t1"; gene_id "Phchi.S4G116700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg886.t1 is derived from g10668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6282276	6284083	.	-	.	Phchi.S6G084500
Phchi.S6	AUGUSTUS	transcript	6282276	6284083	.	-	.	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	stop_codon	6282273	6282275	.	-	0	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	CDS	6282276	6282785	0.71	-	0	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	exon	6282276	6282785	.	-	.	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	intron	6282786	6282931	.	-	.	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	CDS	6282932	6284083	0.73	-	0	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	exon	6282932	6284083	.	-	.	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
Phchi.S6	AUGUSTUS	start_codon	6284081	6284083	.	-	0	transcript_id "Phchi.S6G084500.t1"; gene_id "Phchi.S6G084500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5574.t1 is derived from g2744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17673135	17676018	.	+	.	Phchi.S1G273300
Phchi.S1	AUGUSTUS	transcript	17673135	17676018	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	start_codon	17673135	17673137	.	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673135	17673269	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673135	17673269	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673270	17673363	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673364	17673432	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673364	17673432	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673433	17673550	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673551	17673622	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673551	17673622	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673623	17673718	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673719	17673796	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673719	17673796	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673797	17673895	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673896	17673961	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673896	17673961	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673962	17674038	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674039	17674111	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674039	17674111	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674112	17674341	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674342	17674448	1	+	2	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674342	17674448	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674449	17674545	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674546	17674605	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674546	17674605	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674606	17674700	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674701	17674751	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674701	17674751	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674752	17674928	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674929	17674976	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674929	17674976	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674977	17675139	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675140	17675274	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675140	17675274	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675275	17675430	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675431	17675535	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675431	17675535	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675536	17675653	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675654	17675746	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675654	17675746	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675747	17675940	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675941	17676018	1	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675941	17676018	.	+	.	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	stop_codon	17676019	17676021	.	+	0	transcript_id "Phchi.S1G273300.t1"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	transcript	17673135	17676018	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	start_codon	17673135	17673137	.	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673135	17673269	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673135	17673269	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673270	17673363	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673364	17673432	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673364	17673432	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673433	17673550	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673551	17673622	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673551	17673622	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673623	17673718	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673719	17673796	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673719	17673796	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673797	17673895	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17673896	17673961	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17673896	17673961	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17673962	17674038	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674039	17674111	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674039	17674111	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674112	17674341	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674342	17674448	1	+	2	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674342	17674448	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674449	17674545	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674546	17674605	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674546	17674605	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674606	17674700	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674701	17674751	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674701	17674751	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674752	17674928	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17674929	17674976	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17674929	17674976	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17674977	17675139	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675140	17675232	0.94	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675140	17675232	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675233	17675318	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675319	17675330	0.94	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675319	17675330	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675331	17675430	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675431	17675535	0.99	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675431	17675535	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675536	17675653	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675654	17675746	0.99	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675654	17675746	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	intron	17675747	17675940	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	CDS	17675941	17676018	1	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	exon	17675941	17676018	.	+	.	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
Phchi.S1	AUGUSTUS	stop_codon	17676019	17676021	.	+	0	transcript_id "Phchi.S1G273300.t2"; gene_id "Phchi.S1G273300"
# This transcript jg1685.t2 is derived from g8604.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1686.t1 is derived from g8605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2500335	2501914	.	-	.	Phchi.S5G029500
Phchi.S5	AUGUSTUS	transcript	2500335	2501914	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	stop_codon	2500332	2500334	.	-	0	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	CDS	2500335	2500531	0.91	-	2	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	exon	2500335	2500531	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	intron	2500532	2500613	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	CDS	2500614	2500841	1	-	2	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	exon	2500614	2500841	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	intron	2500842	2500931	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	CDS	2500932	2501217	1	-	0	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	exon	2500932	2501217	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	intron	2501218	2501345	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	CDS	2501346	2501478	1	-	1	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	exon	2501346	2501478	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	intron	2501479	2501578	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	CDS	2501579	2501685	1	-	0	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	exon	2501579	2501685	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	intron	2501686	2501791	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	CDS	2501792	2501914	1	-	0	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	exon	2501792	2501914	.	-	.	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
Phchi.S5	AUGUSTUS	start_codon	2501912	2501914	.	-	0	transcript_id "Phchi.S5G029500.t1"; gene_id "Phchi.S5G029500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14039.t1 is derived from g12506.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10412596	10417820	.	+	.	Phchi.S3G135800
Phchi.S3	AUGUSTUS	transcript	10412596	10417820	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	start_codon	10412596	10412598	.	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10412596	10412889	0.45	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10412596	10412889	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10412890	10412977	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10412978	10413052	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10412978	10413052	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413053	10413136	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413137	10413252	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413137	10413252	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413253	10413333	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413334	10413448	1	+	1	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413334	10413448	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413449	10413577	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413578	10413706	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413578	10413706	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413707	10413848	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413849	10413896	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413849	10413896	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413897	10413996	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413997	10414199	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413997	10414199	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10414200	10414285	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10414286	10414482	1	+	1	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10414286	10414482	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10414483	10414577	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10414578	10414870	0.71	+	2	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10414578	10414870	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10414871	10414977	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10414978	10415127	0.99	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10414978	10415127	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10415128	10415231	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10415232	10415684	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10415232	10415684	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10415685	10415827	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10415828	10415977	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10415828	10415977	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10415978	10416103	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416104	10416179	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416104	10416179	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10416180	10416350	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416351	10416478	1	+	2	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416351	10416478	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10416479	10416572	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416573	10416764	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416573	10416764	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10416765	10416876	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416877	10417014	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416877	10417014	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10417015	10417096	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10417097	10417234	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10417097	10417234	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10417235	10417316	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10417317	10417541	1	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10417317	10417541	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10417542	10417673	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10417674	10417820	0.98	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10417674	10417820	.	+	.	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	stop_codon	10417821	10417823	.	+	0	transcript_id "Phchi.S3G135800.t1"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	transcript	10412596	10417820	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	start_codon	10412596	10412598	.	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10412596	10412889	0.39	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10412596	10412889	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10412890	10412977	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10412978	10413052	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10412978	10413052	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413053	10413136	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413137	10413252	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413137	10413252	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413253	10413333	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413334	10413448	1	+	1	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413334	10413448	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413449	10413577	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413578	10413706	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413578	10413706	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413707	10413848	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413849	10413896	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413849	10413896	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10413897	10413996	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10413997	10414199	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10413997	10414199	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10414200	10414285	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10414286	10414482	1	+	1	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10414286	10414482	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10414483	10414577	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10414578	10414870	0.71	+	2	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10414578	10414870	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10414871	10414977	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10414978	10415127	0.99	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10414978	10415127	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10415128	10415231	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10415232	10415684	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10415232	10415684	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10415685	10415827	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10415828	10415977	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10415828	10415977	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10415978	10416103	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416104	10416173	0.99	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416104	10416173	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10416174	10416350	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416351	10416478	0.99	+	2	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416351	10416478	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10416479	10416572	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416573	10416764	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416573	10416764	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10416765	10416876	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10416877	10417014	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10416877	10417014	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10417015	10417096	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10417097	10417234	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10417097	10417234	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10417235	10417316	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10417317	10417541	1	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10417317	10417541	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	intron	10417542	10417673	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	CDS	10417674	10417820	0.99	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	exon	10417674	10417820	.	+	.	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
Phchi.S3	AUGUSTUS	stop_codon	10417821	10417823	.	+	0	transcript_id "Phchi.S3G135800.t2"; gene_id "Phchi.S3G135800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11335.t1 is derived from g15385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5614758	5616957	.	-	.	Phchi.S4G091700
Phchi.S4	AUGUSTUS	transcript	5614758	5616957	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	stop_codon	5614755	5614757	.	-	0	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5614758	5615254	0.5	-	2	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5614758	5615254	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	intron	5615255	5615340	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5615341	5615607	1	-	2	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5615341	5615607	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	intron	5615608	5615705	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5615706	5615823	0.95	-	0	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5615706	5615823	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	intron	5615824	5615909	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5615910	5615990	0.93	-	0	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5615910	5615990	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	intron	5615991	5616168	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5616169	5616464	1	-	2	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5616169	5616464	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	intron	5616465	5616544	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5616545	5616730	1	-	2	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5616545	5616730	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	intron	5616731	5616881	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	CDS	5616882	5616957	0.58	-	0	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	exon	5616882	5616957	.	-	.	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
Phchi.S4	AUGUSTUS	start_codon	5616955	5616957	.	-	0	transcript_id "Phchi.S4G091700.t1"; gene_id "Phchi.S4G091700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14102.t1 is derived from g12569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10843743	10847404	.	+	.	Phchi.S3G142100
Phchi.S3	AUGUSTUS	transcript	10843743	10847404	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	start_codon	10843743	10843745	.	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10843743	10843946	0.47	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10843743	10843946	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10843947	10844014	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10844015	10844239	0.72	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10844015	10844239	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10844240	10844348	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10844349	10844483	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10844349	10844483	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10844484	10844586	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10844587	10844727	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10844587	10844727	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10844728	10844813	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10844814	10844925	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10844814	10844925	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10844926	10845021	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10845022	10845092	1	+	2	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10845022	10845092	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10845093	10845184	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10845185	10845339	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10845185	10845339	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10845340	10845444	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10845445	10845559	1	+	1	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10845445	10845559	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10845560	10845642	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10845643	10845744	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10845643	10845744	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10845745	10845944	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10845945	10846005	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10845945	10846005	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10846006	10846097	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10846098	10846269	1	+	2	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10846098	10846269	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10846270	10846390	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10846391	10846487	1	+	1	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10846391	10846487	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10846488	10846573	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10846574	10846668	1	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10846574	10846668	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10846669	10846788	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10846789	10846925	1	+	1	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10846789	10846925	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10846926	10847004	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10847005	10847098	1	+	2	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10847005	10847098	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	intron	10847099	10847178	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	CDS	10847179	10847404	0.95	+	1	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	exon	10847179	10847404	.	+	.	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
Phchi.S3	AUGUSTUS	stop_codon	10847405	10847407	.	+	0	transcript_id "Phchi.S3G142100.t1"; gene_id "Phchi.S3G142100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7948.t1 is derived from g5122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32058600	32060834	.	-	.	Phchi.S1G510700
Phchi.S1	AUGUSTUS	transcript	32058600	32060834	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	stop_codon	32058597	32058599	.	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32058600	32058686	0.93	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32058600	32058686	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32058687	32058776	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32058777	32058860	1	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32058777	32058860	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32058861	32059020	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32059021	32059077	1	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32059021	32059077	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32059078	32059173	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32059174	32059302	1	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32059174	32059302	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32059303	32059404	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32059405	32059491	0.72	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32059405	32059491	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32059492	32059607	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32059608	32059655	1	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32059608	32059655	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32059656	32059770	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32059771	32059927	0.96	-	1	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32059771	32059927	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32059928	32060001	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32060002	32060143	1	-	2	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32060002	32060143	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32060144	32060235	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32060236	32060387	1	-	1	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32060236	32060387	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	intron	32060388	32060571	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	CDS	32060572	32060834	0.88	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	exon	32060572	32060834	.	-	.	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
Phchi.S1	AUGUSTUS	start_codon	32060832	32060834	.	-	0	transcript_id "Phchi.S1G510700.t1"; gene_id "Phchi.S1G510700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12052.t1 is derived from g7727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1035486	1036702	.	+	.	Phchi.S2G013200
Phchi.S2	AUGUSTUS	transcript	1035486	1036702	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	start_codon	1035486	1035488	.	+	0	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	CDS	1035486	1035582	0.38	+	0	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	exon	1035486	1035582	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	intron	1035583	1035655	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	CDS	1035656	1035817	0.67	+	2	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	exon	1035656	1035817	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	intron	1035818	1035984	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	CDS	1035985	1036102	0.84	+	2	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	exon	1035985	1036102	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	intron	1036103	1036353	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	CDS	1036354	1036702	0.8	+	1	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	exon	1036354	1036702	.	+	.	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
Phchi.S2	AUGUSTUS	stop_codon	1036703	1036705	.	+	0	transcript_id "Phchi.S2G013200.t1"; gene_id "Phchi.S2G013200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2682.t1 is derived from g9602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8180959	8182667	.	+	.	Phchi.S5G129100
Phchi.S5	AUGUSTUS	transcript	8180959	8182667	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	start_codon	8180959	8180961	.	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8180959	8181056	0.99	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8180959	8181056	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8181057	8181281	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8181282	8181376	1	+	1	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8181282	8181376	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8181377	8181455	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8181456	8181565	1	+	2	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8181456	8181565	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8181566	8181669	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8181670	8181779	1	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8181670	8181779	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8181780	8181861	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8181862	8181922	1	+	1	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8181862	8181922	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8181923	8182018	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8182019	8182057	0.73	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8182019	8182057	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8182058	8182129	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8182130	8182190	0.53	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8182130	8182190	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8182191	8182276	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8182277	8182315	0.8	+	2	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8182277	8182315	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8182316	8182420	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8182421	8182461	0.8	+	2	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8182421	8182461	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	intron	8182462	8182532	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	CDS	8182533	8182667	0.8	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	exon	8182533	8182667	.	+	.	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
Phchi.S5	AUGUSTUS	stop_codon	8182668	8182670	.	+	0	transcript_id "Phchi.S5G129100.t1"; gene_id "Phchi.S5G129100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7967.t1 is derived from g5142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32155161	32156732	.	+	.	Phchi.S1G512600
Phchi.S1	AUGUSTUS	transcript	32155161	32156732	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	start_codon	32155161	32155163	.	+	0	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	CDS	32155161	32155172	0.51	+	0	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	exon	32155161	32155172	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	intron	32155173	32155314	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	CDS	32155315	32155519	0.88	+	0	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	exon	32155315	32155519	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	intron	32155520	32155716	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	CDS	32155717	32155925	0.9	+	2	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	exon	32155717	32155925	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	intron	32155926	32156213	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	CDS	32156214	32156732	0.82	+	0	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	exon	32156214	32156732	.	+	.	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
Phchi.S1	AUGUSTUS	stop_codon	32156733	32156735	.	+	0	transcript_id "Phchi.S1G512600.t1"; gene_id "Phchi.S1G512600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg82.t1 is derived from g9864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	422048	424578	.	-	.	Phchi.S6G004100
Phchi.S6	AUGUSTUS	transcript	422048	424578	.	-	.	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	stop_codon	422045	422047	.	-	0	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	CDS	422048	423015	0.96	-	2	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	exon	422048	423015	.	-	.	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	intron	423016	423092	.	-	.	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	CDS	423093	424578	0.48	-	0	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	exon	423093	424578	.	-	.	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
Phchi.S6	AUGUSTUS	start_codon	424576	424578	.	-	0	transcript_id "Phchi.S6G004100.t1"; gene_id "Phchi.S6G004100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4277.t1 is derived from g1446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9351254	9352282	.	+	.	Phchi.S1G143600
Phchi.S1	AUGUSTUS	transcript	9351254	9352282	.	+	.	transcript_id "Phchi.S1G143600.t1"; gene_id "Phchi.S1G143600"
Phchi.S1	AUGUSTUS	start_codon	9351254	9351256	.	+	0	transcript_id "Phchi.S1G143600.t1"; gene_id "Phchi.S1G143600"
Phchi.S1	AUGUSTUS	CDS	9351254	9352282	0.53	+	0	transcript_id "Phchi.S1G143600.t1"; gene_id "Phchi.S1G143600"
Phchi.S1	AUGUSTUS	exon	9351254	9352282	.	+	.	transcript_id "Phchi.S1G143600.t1"; gene_id "Phchi.S1G143600"
Phchi.S1	AUGUSTUS	stop_codon	9352283	9352285	.	+	0	transcript_id "Phchi.S1G143600.t1"; gene_id "Phchi.S1G143600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8655.t1 is derived from g5830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37287207	37287657	.	-	.	Phchi.S1G581400
Phchi.S1	AUGUSTUS	transcript	37287207	37287657	.	-	.	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	stop_codon	37287204	37287206	.	-	0	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	CDS	37287207	37287348	0.53	-	1	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	exon	37287207	37287348	.	-	.	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	intron	37287349	37287472	.	-	.	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	CDS	37287473	37287657	0.29	-	0	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	exon	37287473	37287657	.	-	.	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
Phchi.S1	AUGUSTUS	start_codon	37287655	37287657	.	-	0	transcript_id "Phchi.S1G581400.t1"; gene_id "Phchi.S1G581400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14760.t1 is derived from g13228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14577632	14579541	.	+	.	Phchi.S3G207900
Phchi.S3	AUGUSTUS	transcript	14577632	14579541	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	start_codon	14577632	14577634	.	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14577632	14577801	0.75	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14577632	14577801	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14577802	14577890	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14577891	14577996	1	+	1	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14577891	14577996	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14577997	14578072	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14578073	14578318	1	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14578073	14578318	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14578319	14578422	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14578423	14578533	1	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14578423	14578533	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14578534	14578620	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14578621	14578779	1	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14578621	14578779	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14578780	14578860	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14578861	14579007	1	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14578861	14579007	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14579008	14579108	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14579109	14579267	1	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14579109	14579267	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	intron	14579268	14579424	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	CDS	14579425	14579541	0.99	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	exon	14579425	14579541	.	+	.	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
Phchi.S3	AUGUSTUS	stop_codon	14579542	14579544	.	+	0	transcript_id "Phchi.S3G207900.t1"; gene_id "Phchi.S3G207900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10023.t1 is derived from g7199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45134333	45135655	.	-	.	Phchi.S1G718200
Phchi.S1	AUGUSTUS	transcript	45134333	45135655	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	stop_codon	45134330	45134332	.	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	CDS	45134333	45134365	0.9	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	exon	45134333	45134365	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	intron	45134366	45134532	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	CDS	45134533	45134547	0.93	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	exon	45134533	45134547	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	intron	45134548	45134638	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	CDS	45134639	45134725	0.92	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	exon	45134639	45134725	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	intron	45134726	45134896	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	CDS	45134897	45134911	0.83	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	exon	45134897	45134911	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	intron	45134912	45135054	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	CDS	45135055	45135076	0.99	-	1	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	exon	45135055	45135076	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	intron	45135077	45135272	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	CDS	45135273	45135655	0.79	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	exon	45135273	45135655	.	-	.	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
Phchi.S1	AUGUSTUS	start_codon	45135653	45135655	.	-	0	transcript_id "Phchi.S1G718200.t1"; gene_id "Phchi.S1G718200"
# This transcript jg9787.t2 is derived from g6963.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9788.t1 is derived from g6964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43694206	43695387	.	+	.	Phchi.S1G694700
Phchi.S1	AUGUSTUS	transcript	43694206	43695387	.	+	.	transcript_id "Phchi.S1G694700.t1"; gene_id "Phchi.S1G694700"
Phchi.S1	AUGUSTUS	start_codon	43694206	43694208	.	+	0	transcript_id "Phchi.S1G694700.t1"; gene_id "Phchi.S1G694700"
Phchi.S1	AUGUSTUS	CDS	43694206	43695387	0.78	+	0	transcript_id "Phchi.S1G694700.t1"; gene_id "Phchi.S1G694700"
Phchi.S1	AUGUSTUS	exon	43694206	43695387	.	+	.	transcript_id "Phchi.S1G694700.t1"; gene_id "Phchi.S1G694700"
Phchi.S1	AUGUSTUS	stop_codon	43695388	43695390	.	+	0	transcript_id "Phchi.S1G694700.t1"; gene_id "Phchi.S1G694700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8446.t1 is derived from g5621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35960962	35963873	.	-	.	Phchi.S1G560500
Phchi.S1	AUGUSTUS	transcript	35960962	35963873	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	stop_codon	35960959	35960961	.	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35960962	35960993	0.99	-	2	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35960962	35960993	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35960994	35961253	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961254	35961319	0.59	-	2	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961254	35961319	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961320	35961441	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961442	35961881	0.51	-	1	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961442	35961881	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961882	35961973	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961974	35962044	1	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961974	35962044	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962045	35962180	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962181	35962238	1	-	1	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962181	35962238	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962239	35962381	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962382	35962521	1	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962382	35962521	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962522	35962614	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962615	35962732	1	-	1	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962615	35962732	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962733	35962826	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962827	35962947	1	-	2	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962827	35962947	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962948	35963015	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963016	35963088	1	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963016	35963088	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963089	35963170	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963171	35963313	1	-	2	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963171	35963313	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963314	35963410	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963411	35963501	1	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963411	35963501	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963502	35963587	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963588	35963669	1	-	1	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963588	35963669	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963670	35963763	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963764	35963873	1	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963764	35963873	.	-	.	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	start_codon	35963871	35963873	.	-	0	transcript_id "Phchi.S1G560500.t1"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	transcript	35960962	35963873	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	stop_codon	35960959	35960961	.	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35960962	35960993	1	-	2	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35960962	35960993	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35960994	35961253	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961254	35961319	0.61	-	2	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961254	35961319	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961320	35961441	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961442	35961881	0.55	-	1	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961442	35961881	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961882	35961973	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961974	35962044	1	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961974	35962044	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962045	35962381	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962382	35962396	0.82	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962382	35962396	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962397	35962473	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962474	35962521	0.82	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962474	35962521	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962522	35962614	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962615	35962732	1	-	1	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962615	35962732	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962733	35962826	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962827	35962947	1	-	2	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962827	35962947	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962948	35963015	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963016	35963088	1	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963016	35963088	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963089	35963170	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963171	35963313	1	-	2	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963171	35963313	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963314	35963410	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963411	35963501	1	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963411	35963501	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963502	35963587	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963588	35963669	1	-	1	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963588	35963669	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963670	35963763	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963764	35963873	1	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963764	35963873	.	-	.	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	start_codon	35963871	35963873	.	-	0	transcript_id "Phchi.S1G560500.t2"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	transcript	35961168	35963873	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	stop_codon	35961165	35961167	.	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961168	35961169	0.95	-	2	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961168	35961169	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961170	35961253	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961254	35961319	0.46	-	2	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961254	35961319	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961320	35961441	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961442	35961881	0.42	-	1	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961442	35961881	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35961882	35961973	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35961974	35962044	1	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35961974	35962044	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962045	35962381	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962382	35962396	0.83	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962382	35962396	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962397	35962473	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962474	35962521	0.83	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962474	35962521	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962522	35962614	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962615	35962732	1	-	1	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962615	35962732	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962733	35962826	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35962827	35962947	1	-	2	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35962827	35962947	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35962948	35963015	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963016	35963088	1	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963016	35963088	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963089	35963170	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963171	35963313	1	-	2	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963171	35963313	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963314	35963410	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963411	35963501	1	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963411	35963501	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963502	35963587	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963588	35963669	1	-	1	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963588	35963669	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	intron	35963670	35963763	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	CDS	35963764	35963873	1	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	exon	35963764	35963873	.	-	.	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
Phchi.S1	AUGUSTUS	start_codon	35963871	35963873	.	-	0	transcript_id "Phchi.S1G560500.t3"; gene_id "Phchi.S1G560500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg230.t1 is derived from g10012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1570096	1571406	.	-	.	Phchi.S6G018900
Phchi.S6	AUGUSTUS	transcript	1570096	1571406	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	stop_codon	1570093	1570095	.	-	0	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1570096	1570394	1	-	2	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1570096	1570394	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	intron	1570395	1570554	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1570555	1570669	0.91	-	0	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1570555	1570669	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	intron	1570670	1570764	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1570765	1570781	0.98	-	2	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1570765	1570781	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	intron	1570782	1570866	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1570867	1571002	0.98	-	0	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1570867	1571002	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	intron	1571003	1571097	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1571098	1571151	1	-	0	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1571098	1571151	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	intron	1571152	1571251	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1571252	1571294	1	-	1	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1571252	1571294	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	intron	1571295	1571389	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	CDS	1571390	1571406	1	-	0	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	exon	1571390	1571406	.	-	.	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
Phchi.S6	AUGUSTUS	start_codon	1571404	1571406	.	-	0	transcript_id "Phchi.S6G018900.t1"; gene_id "Phchi.S6G018900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3318.t1 is derived from g487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2872793	2873773	.	-	.	Phchi.S1G047700
Phchi.S1	AUGUSTUS	transcript	2872793	2873773	.	-	.	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	stop_codon	2872790	2872792	.	-	0	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	CDS	2872793	2873265	1	-	2	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	exon	2872793	2873265	.	-	.	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	intron	2873266	2873368	.	-	.	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	CDS	2873369	2873417	1	-	0	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	exon	2873369	2873417	.	-	.	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	intron	2873418	2873626	.	-	.	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	CDS	2873627	2873773	1	-	0	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	exon	2873627	2873773	.	-	.	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
Phchi.S1	AUGUSTUS	start_codon	2873771	2873773	.	-	0	transcript_id "Phchi.S1G047700.t1"; gene_id "Phchi.S1G047700"
# This transcript jg629.t2 is derived from g10411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg630.t1 is derived from g10412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4473773	4474164	.	+	.	Phchi.S6G058900
Phchi.S6	AUGUSTUS	transcript	4473773	4474164	.	+	.	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	start_codon	4473773	4473775	.	+	0	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	CDS	4473773	4473920	1	+	0	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	exon	4473773	4473920	.	+	.	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	intron	4473921	4474045	.	+	.	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	CDS	4474046	4474164	1	+	2	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	exon	4474046	4474164	.	+	.	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
Phchi.S6	AUGUSTUS	stop_codon	4474165	4474167	.	+	0	transcript_id "Phchi.S6G058900.t1"; gene_id "Phchi.S6G058900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1278.t1 is derived from g11061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8792979	8793810	.	-	.	Phchi.S6G123700
Phchi.S6	AUGUSTUS	transcript	8792979	8793810	.	-	.	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	stop_codon	8792976	8792978	.	-	0	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	CDS	8792979	8793059	1	-	0	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	exon	8792979	8793059	.	-	.	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	intron	8793060	8793130	.	-	.	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	CDS	8793131	8793247	1	-	0	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	exon	8793131	8793247	.	-	.	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	intron	8793248	8793423	.	-	.	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	CDS	8793424	8793810	0.94	-	0	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	exon	8793424	8793810	.	-	.	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
Phchi.S6	AUGUSTUS	start_codon	8793808	8793810	.	-	0	transcript_id "Phchi.S6G123700.t1"; gene_id "Phchi.S6G123700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7688.t1 is derived from g4862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30626978	30630977	.	+	.	Phchi.S1G484700
Phchi.S1	AUGUSTUS	transcript	30626978	30630977	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	start_codon	30626978	30626980	.	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30626978	30627337	1	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30626978	30627337	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30627338	30627414	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30627415	30627633	0.92	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30627415	30627633	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30627634	30627751	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30627752	30628145	0.93	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30627752	30628145	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30628146	30628229	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30628230	30628315	1	+	2	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30628230	30628315	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30628316	30628394	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30628395	30628542	1	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30628395	30628542	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30628543	30628633	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30628634	30629058	0.86	+	2	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30628634	30629058	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30629059	30629182	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30629183	30629679	0.95	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30629183	30629679	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30629680	30629755	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30629756	30629816	1	+	1	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30629756	30629816	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30629817	30629913	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30629914	30630153	1	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30629914	30630153	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30630154	30630235	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30630236	30630372	1	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30630236	30630372	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30630373	30630457	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30630458	30630597	1	+	1	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30630458	30630597	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30630598	30630674	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30630675	30630773	1	+	2	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30630675	30630773	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	intron	30630774	30630864	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	CDS	30630865	30630977	0.99	+	2	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	exon	30630865	30630977	.	+	.	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
Phchi.S1	AUGUSTUS	stop_codon	30630978	30630980	.	+	0	transcript_id "Phchi.S1G484700.t1"; gene_id "Phchi.S1G484700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14330.t1 is derived from g12797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12119913	12123647	.	-	.	Phchi.S3G164900
Phchi.S3	AUGUSTUS	transcript	12119913	12123647	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	stop_codon	12119910	12119912	.	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12119913	12119972	0.6	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12119913	12119972	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12119973	12120287	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12120288	12120306	0.32	-	1	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12120288	12120306	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12120307	12120397	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12120398	12120519	0.32	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12120398	12120519	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12120520	12120611	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12120612	12120845	1	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12120612	12120845	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12120846	12120937	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12120938	12121216	1	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12120938	12121216	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12121217	12121358	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12121359	12121638	1	-	1	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12121359	12121638	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12121639	12121791	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12121792	12122093	1	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12121792	12122093	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12122094	12122257	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12122258	12122452	1	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12122258	12122452	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12122453	12122545	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12122546	12122755	1	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12122546	12122755	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12122756	12122870	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12122871	12122934	1	-	1	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12122871	12122934	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12122935	12123021	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12123022	12123174	1	-	1	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12123022	12123174	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	intron	12123175	12123360	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	CDS	12123361	12123647	0.45	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	exon	12123361	12123647	.	-	.	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
Phchi.S3	AUGUSTUS	start_codon	12123645	12123647	.	-	0	transcript_id "Phchi.S3G164900.t1"; gene_id "Phchi.S3G164900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5251.t1 is derived from g2421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15860078	15861103	.	-	.	Phchi.S1G241000
Phchi.S1	AUGUSTUS	transcript	15860078	15861103	.	-	.	transcript_id "Phchi.S1G241000.t1"; gene_id "Phchi.S1G241000"
Phchi.S1	AUGUSTUS	stop_codon	15860075	15860077	.	-	0	transcript_id "Phchi.S1G241000.t1"; gene_id "Phchi.S1G241000"
Phchi.S1	AUGUSTUS	CDS	15860078	15861103	0.42	-	0	transcript_id "Phchi.S1G241000.t1"; gene_id "Phchi.S1G241000"
Phchi.S1	AUGUSTUS	exon	15860078	15861103	.	-	.	transcript_id "Phchi.S1G241000.t1"; gene_id "Phchi.S1G241000"
Phchi.S1	AUGUSTUS	start_codon	15861101	15861103	.	-	0	transcript_id "Phchi.S1G241000.t1"; gene_id "Phchi.S1G241000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12490.t1 is derived from g8167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	29207921	29208705	.	+	.	Phchi.S2G057000
Phchi.S2	AUGUSTUS	transcript	29207921	29208705	.	+	.	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	start_codon	29207921	29207923	.	+	0	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	CDS	29207921	29208455	0.99	+	0	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	exon	29207921	29208455	.	+	.	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	intron	29208456	29208601	.	+	.	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	CDS	29208602	29208705	0.72	+	2	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	exon	29208602	29208705	.	+	.	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
Phchi.S2	AUGUSTUS	stop_codon	29208706	29208708	.	+	0	transcript_id "Phchi.S2G057000.t1"; gene_id "Phchi.S2G057000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6589.t1 is derived from g3761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23896164	23897435	.	+	.	Phchi.S1G374800
Phchi.S1	AUGUSTUS	transcript	23896164	23897435	.	+	.	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	start_codon	23896164	23896166	.	+	0	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	CDS	23896164	23896488	0.78	+	0	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	exon	23896164	23896488	.	+	.	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	intron	23896489	23896644	.	+	.	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	CDS	23896645	23896809	0.99	+	2	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	exon	23896645	23896809	.	+	.	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	intron	23896810	23896911	.	+	.	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	CDS	23896912	23897435	0.53	+	2	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	exon	23896912	23897435	.	+	.	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
Phchi.S1	AUGUSTUS	stop_codon	23897436	23897438	.	+	0	transcript_id "Phchi.S1G374800.t1"; gene_id "Phchi.S1G374800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6469.t1 is derived from g3641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23147192	23148922	.	-	.	Phchi.S1G362800
Phchi.S1	AUGUSTUS	transcript	23147192	23148922	.	-	.	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	stop_codon	23147189	23147191	.	-	0	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	CDS	23147192	23148402	0.51	-	2	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	exon	23147192	23148402	.	-	.	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	intron	23148403	23148500	.	-	.	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	CDS	23148501	23148731	0.65	-	2	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	exon	23148501	23148731	.	-	.	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	intron	23148732	23148840	.	-	.	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	CDS	23148841	23148922	0.46	-	0	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	exon	23148841	23148922	.	-	.	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
Phchi.S1	AUGUSTUS	start_codon	23148920	23148922	.	-	0	transcript_id "Phchi.S1G362800.t1"; gene_id "Phchi.S1G362800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12130.t1 is derived from g7806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4043185	4044606	.	+	.	Phchi.S2G021000
Phchi.S2	AUGUSTUS	transcript	4043185	4044606	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	start_codon	4043185	4043187	.	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4043185	4043276	1	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4043185	4043276	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4043277	4043440	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4043441	4043484	1	+	1	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4043441	4043484	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4043485	4043578	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4043579	4043675	1	+	2	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4043579	4043675	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4043676	4043812	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4043813	4043876	1	+	1	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4043813	4043876	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4043877	4043958	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4043959	4044078	1	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4043959	4044078	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4044079	4044152	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4044153	4044261	1	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4044153	4044261	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4044262	4044349	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4044350	4044369	0.67	+	2	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4044350	4044369	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4044370	4044463	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4044464	4044487	0.57	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4044464	4044487	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	intron	4044488	4044576	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	CDS	4044577	4044606	0.9	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	exon	4044577	4044606	.	+	.	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
Phchi.S2	AUGUSTUS	stop_codon	4044607	4044609	.	+	0	transcript_id "Phchi.S2G021000.t1"; gene_id "Phchi.S2G021000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1807.t1 is derived from g8727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3135202	3136605	.	+	.	Phchi.S5G041600
Phchi.S5	AUGUSTUS	transcript	3135202	3136605	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	start_codon	3135202	3135204	.	+	0	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	CDS	3135202	3135414	1	+	0	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	exon	3135202	3135414	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	intron	3135415	3135518	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	CDS	3135519	3135722	1	+	0	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	exon	3135519	3135722	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	intron	3135723	3135802	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	CDS	3135803	3135975	1	+	0	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	exon	3135803	3135975	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	intron	3135976	3136076	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	CDS	3136077	3136173	0.96	+	1	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	exon	3136077	3136173	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	intron	3136174	3136266	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	CDS	3136267	3136342	1	+	0	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	exon	3136267	3136342	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	intron	3136343	3136420	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	CDS	3136421	3136605	0.87	+	2	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	exon	3136421	3136605	.	+	.	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
Phchi.S5	AUGUSTUS	stop_codon	3136606	3136608	.	+	0	transcript_id "Phchi.S5G041600.t1"; gene_id "Phchi.S5G041600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12987.t1 is derived from g11452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3481733	3485135	.	+	.	Phchi.S3G030600
Phchi.S3	AUGUSTUS	transcript	3481733	3485135	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	start_codon	3481733	3481735	.	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3481733	3481820	0.54	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3481733	3481820	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3481821	3481894	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3481895	3482067	0.41	+	2	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3481895	3482067	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482068	3482150	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482151	3482180	0.58	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482151	3482180	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482181	3482265	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482266	3482631	0.57	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482266	3482631	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482632	3482716	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482717	3482911	1	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482717	3482911	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482912	3482992	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482993	3483198	0.51	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482993	3483198	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483199	3483278	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3483279	3483434	0.79	+	1	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3483279	3483434	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483435	3483538	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3483539	3483845	0.86	+	1	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3483539	3483845	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483846	3483955	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3483956	3483986	1	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3483956	3483986	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483987	3484184	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3484185	3484318	1	+	2	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3484185	3484318	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3484319	3485015	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3485016	3485135	0.72	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3485016	3485135	.	+	.	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	stop_codon	3485136	3485138	.	+	0	transcript_id "Phchi.S3G030600.t1"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	transcript	3481733	3485135	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	start_codon	3481733	3481735	.	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3481733	3481820	0.46	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3481733	3481820	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3481821	3481894	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3481895	3482067	0.32	+	2	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3481895	3482067	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482068	3482150	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482151	3482180	0.56	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482151	3482180	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482181	3482265	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482266	3482631	0.55	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482266	3482631	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482632	3482716	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482717	3482911	1	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482717	3482911	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3482912	3482992	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3482993	3483198	0.56	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3482993	3483198	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483199	3483278	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3483279	3483434	0.75	+	1	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3483279	3483434	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483435	3483538	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3483539	3483845	0.82	+	1	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3483539	3483845	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483846	3483935	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3483936	3483958	0.64	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3483936	3483958	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3483959	3484047	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3484048	3484318	0.49	+	1	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3484048	3484318	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	intron	3484319	3485015	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	CDS	3485016	3485135	0.73	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	exon	3485016	3485135	.	+	.	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
Phchi.S3	AUGUSTUS	stop_codon	3485136	3485138	.	+	0	transcript_id "Phchi.S3G030600.t2"; gene_id "Phchi.S3G030600"
# This transcript jg10898.t2 is derived from g14948.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10899.t1 is derived from g14949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2813336	2814328	.	+	.	Phchi.S4G048100
Phchi.S4	AUGUSTUS	transcript	2813336	2814328	.	+	.	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	start_codon	2813336	2813338	.	+	0	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	CDS	2813336	2813414	0.36	+	0	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	exon	2813336	2813414	.	+	.	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	intron	2813415	2813632	.	+	.	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	CDS	2813633	2813679	0.36	+	2	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	exon	2813633	2813679	.	+	.	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	intron	2813680	2813830	.	+	.	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	CDS	2813831	2814328	0.53	+	0	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	exon	2813831	2814328	.	+	.	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
Phchi.S4	AUGUSTUS	stop_codon	2814329	2814331	.	+	0	transcript_id "Phchi.S4G048100.t1"; gene_id "Phchi.S4G048100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5615.t1 is derived from g2785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17909003	17910048	.	-	.	Phchi.S1G277400
Phchi.S1	AUGUSTUS	transcript	17909003	17910048	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	stop_codon	17909000	17909002	.	-	0	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	CDS	17909003	17909026	1	-	0	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	exon	17909003	17909026	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	intron	17909027	17909116	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	CDS	17909117	17909183	1	-	1	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	exon	17909117	17909183	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	intron	17909184	17909488	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	CDS	17909489	17909591	1	-	2	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	exon	17909489	17909591	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	intron	17909592	17909698	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	CDS	17909699	17909785	1	-	2	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	exon	17909699	17909785	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	intron	17909786	17909945	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	CDS	17909946	17910048	1	-	0	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	exon	17909946	17910048	.	-	.	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
Phchi.S1	AUGUSTUS	start_codon	17910046	17910048	.	-	0	transcript_id "Phchi.S1G277400.t1"; gene_id "Phchi.S1G277400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6885.t1 is derived from g4057.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25821125	25822383	.	+	.	Phchi.S1G404400
Phchi.S1	AUGUSTUS	transcript	25821125	25822383	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	start_codon	25821125	25821127	.	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821125	25821166	0.96	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821125	25821166	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25821167	25821261	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821262	25821510	1	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821262	25821510	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25821511	25821645	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821646	25821828	1	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821646	25821828	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25821829	25821943	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821944	25822090	1	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821944	25822090	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25822091	25822188	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25822189	25822383	1	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25822189	25822383	.	+	.	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	stop_codon	25822384	25822386	.	+	0	transcript_id "Phchi.S1G404400.t1"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	transcript	25821217	25822383	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	start_codon	25821217	25821219	.	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821217	25821237	0.45	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821217	25821237	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25821238	25821321	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821322	25821510	0.45	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821322	25821510	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25821511	25821645	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821646	25821828	1	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821646	25821828	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25821829	25821943	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25821944	25822090	1	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25821944	25822090	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	intron	25822091	25822188	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	CDS	25822189	25822383	1	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	exon	25822189	25822383	.	+	.	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
Phchi.S1	AUGUSTUS	stop_codon	25822384	25822386	.	+	0	transcript_id "Phchi.S1G404400.t2"; gene_id "Phchi.S1G404400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2812.t1 is derived from g9732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8983052	8987286	.	-	.	Phchi.S5G142100
Phchi.S5	AUGUSTUS	transcript	8983052	8987286	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	stop_codon	8983049	8983051	.	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8983052	8983201	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8983052	8983201	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8983202	8983299	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8983300	8983438	1	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8983300	8983438	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8983439	8983536	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8983537	8983781	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8983537	8983781	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8983782	8984003	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8984004	8984325	1	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8984004	8984325	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8984326	8984415	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8984416	8984640	1	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8984416	8984640	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8984641	8984738	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8984739	8984905	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8984739	8984905	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8984906	8984989	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8984990	8985106	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8984990	8985106	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8985107	8985218	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8985219	8985395	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8985219	8985395	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8985396	8985519	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8985520	8985615	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8985520	8985615	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8985616	8985715	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8985716	8985932	1	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8985716	8985932	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8985933	8986016	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8986017	8986135	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8986017	8986135	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8986136	8986213	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8986214	8986409	1	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8986214	8986409	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8986410	8986551	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8986552	8986718	1	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8986552	8986718	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8986719	8986800	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8986801	8986930	1	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8986801	8986930	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8986931	8987015	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8987016	8987069	0.45	-	1	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8987016	8987069	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	intron	8987070	8987194	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	CDS	8987195	8987286	0.43	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	exon	8987195	8987286	.	-	.	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
Phchi.S5	AUGUSTUS	start_codon	8987284	8987286	.	-	0	transcript_id "Phchi.S5G142100.t1"; gene_id "Phchi.S5G142100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9652.t1 is derived from g6828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43063756	43065984	.	+	.	Phchi.S1G681100
Phchi.S1	AUGUSTUS	transcript	43063756	43065984	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	start_codon	43063756	43063758	.	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43063756	43063802	0.93	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43063756	43063802	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43063803	43063994	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43063995	43064236	0.72	+	1	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43063995	43064236	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43064237	43064400	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43064401	43064468	0.93	+	2	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43064401	43064468	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43064469	43064685	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43064686	43064743	1	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43064686	43064743	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43064744	43064856	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43064857	43064987	1	+	2	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43064857	43064987	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43064988	43065083	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43065084	43065146	1	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43065084	43065146	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43065147	43065224	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43065225	43065378	1	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43065225	43065378	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43065379	43065469	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43065470	43065574	1	+	2	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43065470	43065574	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43065575	43065649	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43065650	43065735	1	+	2	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43065650	43065735	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	intron	43065736	43065834	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	CDS	43065835	43065984	0.9	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	exon	43065835	43065984	.	+	.	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
Phchi.S1	AUGUSTUS	stop_codon	43065985	43065987	.	+	0	transcript_id "Phchi.S1G681100.t1"; gene_id "Phchi.S1G681100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1820.t1 is derived from g8740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3312596	3315113	.	-	.	Phchi.S5G042900
Phchi.S5	AUGUSTUS	transcript	3312596	3315113	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	stop_codon	3312593	3312595	.	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3312596	3312695	1	-	1	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3312596	3312695	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3312696	3312824	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3312825	3312943	1	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3312825	3312943	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3312944	3313056	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3313057	3313163	1	-	2	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3313057	3313163	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3313164	3313300	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3313301	3313379	1	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3313301	3313379	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3313380	3313588	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3313589	3313678	1	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3313589	3313678	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3313679	3313803	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3313804	3314064	1	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3313804	3314064	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3314065	3314206	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3314207	3314362	1	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3314207	3314362	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3314363	3314486	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3314487	3314799	1	-	1	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3314487	3314799	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	intron	3314800	3314898	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	CDS	3314899	3315113	1	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	exon	3314899	3315113	.	-	.	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
Phchi.S5	AUGUSTUS	start_codon	3315111	3315113	.	-	0	transcript_id "Phchi.S5G042900.t1"; gene_id "Phchi.S5G042900"
# This transcript jg12803.t2 is derived from g11268.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12804.t1 is derived from g11269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2455761	2458480	.	-	.	Phchi.S3G012300
Phchi.S3	AUGUSTUS	transcript	2455761	2458480	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	stop_codon	2455758	2455760	.	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2455761	2455847	1	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2455761	2455847	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	intron	2455848	2455933	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2455934	2456119	1	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2455934	2456119	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	intron	2456120	2456244	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2456245	2456352	1	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2456245	2456352	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	intron	2456353	2456470	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2456471	2456616	1	-	2	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2456471	2456616	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	intron	2456617	2456709	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2456710	2457390	0.99	-	2	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2456710	2457390	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	intron	2457391	2457679	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2457680	2458148	0.53	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2457680	2458148	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	intron	2458149	2458402	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	CDS	2458403	2458480	0.33	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	exon	2458403	2458480	.	-	.	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
Phchi.S3	AUGUSTUS	start_codon	2458478	2458480	.	-	0	transcript_id "Phchi.S3G012300.t1"; gene_id "Phchi.S3G012300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8772.t1 is derived from g5947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37893668	37894105	.	+	.	Phchi.S1G593100
Phchi.S1	AUGUSTUS	transcript	37893668	37894105	.	+	.	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	start_codon	37893668	37893670	.	+	0	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	CDS	37893668	37893704	1	+	0	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	exon	37893668	37893704	.	+	.	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	intron	37893705	37893787	.	+	.	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	CDS	37893788	37893873	1	+	2	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	exon	37893788	37893873	.	+	.	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	intron	37893874	37894009	.	+	.	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	CDS	37894010	37894105	0.72	+	0	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	exon	37894010	37894105	.	+	.	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
Phchi.S1	AUGUSTUS	stop_codon	37894106	37894108	.	+	0	transcript_id "Phchi.S1G593100.t1"; gene_id "Phchi.S1G593100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15914.t1 is derived from g14384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22192419	22193475	.	+	.	Phchi.S3G323300
Phchi.S3	AUGUSTUS	transcript	22192419	22193475	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	start_codon	22192419	22192421	.	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22192419	22192514	0.75	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22192419	22192514	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	intron	22192515	22192611	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22192612	22192710	1	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22192612	22192710	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	intron	22192711	22192868	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22192869	22192940	1	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22192869	22192940	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	intron	22192941	22193066	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22193067	22193156	1	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22193067	22193156	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	intron	22193157	22193241	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22193242	22193256	0.87	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22193242	22193256	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	intron	22193257	22193346	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22193347	22193378	0.99	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22193347	22193378	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	intron	22193379	22193468	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	CDS	22193469	22193475	1	+	1	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	exon	22193469	22193475	.	+	.	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
Phchi.S3	AUGUSTUS	stop_codon	22193476	22193478	.	+	0	transcript_id "Phchi.S3G323300.t1"; gene_id "Phchi.S3G323300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14657.t1 is derived from g13125.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13992566	13994512	.	+	.	Phchi.S3G197600
Phchi.S3	AUGUSTUS	transcript	13992566	13994304	.	+	.	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	start_codon	13992566	13992568	.	+	0	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	CDS	13992566	13994171	0.76	+	0	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	exon	13992566	13994171	.	+	.	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	intron	13994172	13994257	.	+	.	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	CDS	13994258	13994304	0.76	+	2	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	exon	13994258	13994304	.	+	.	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	stop_codon	13994305	13994307	.	+	0	transcript_id "Phchi.S3G197600.t1"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	transcript	13992566	13994512	.	+	.	transcript_id "Phchi.S3G197600.t2"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	start_codon	13992566	13992568	.	+	0	transcript_id "Phchi.S3G197600.t2"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	CDS	13992566	13994512	1	+	0	transcript_id "Phchi.S3G197600.t2"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	exon	13992566	13994512	.	+	.	transcript_id "Phchi.S3G197600.t2"; gene_id "Phchi.S3G197600"
Phchi.S3	AUGUSTUS	stop_codon	13994513	13994515	.	+	0	transcript_id "Phchi.S3G197600.t2"; gene_id "Phchi.S3G197600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4542.t1 is derived from g1712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11024356	11025440	.	-	.	Phchi.S1G170100
Phchi.S1	AUGUSTUS	transcript	11024356	11025440	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	stop_codon	11024353	11024355	.	-	0	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	CDS	11024356	11024414	0.69	-	2	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	exon	11024356	11024414	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	intron	11024415	11024494	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	CDS	11024495	11024651	0.78	-	0	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	exon	11024495	11024651	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	intron	11024652	11024746	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	CDS	11024747	11024962	0.99	-	0	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	exon	11024747	11024962	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	intron	11024963	11025058	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	CDS	11025059	11025221	0.53	-	1	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	exon	11025059	11025221	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	intron	11025222	11025327	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	CDS	11025328	11025440	0.53	-	0	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	exon	11025328	11025440	.	-	.	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
Phchi.S1	AUGUSTUS	start_codon	11025438	11025440	.	-	0	transcript_id "Phchi.S1G170100.t1"; gene_id "Phchi.S1G170100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3682.t1 is derived from g851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5161160	5161597	.	+	.	Phchi.S1G084100
Phchi.S1	AUGUSTUS	transcript	5161160	5161597	.	+	.	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	start_codon	5161160	5161162	.	+	0	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	CDS	5161160	5161284	0.85	+	0	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	exon	5161160	5161284	.	+	.	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	intron	5161285	5161377	.	+	.	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	CDS	5161378	5161597	0.88	+	1	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	exon	5161378	5161597	.	+	.	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
Phchi.S1	AUGUSTUS	stop_codon	5161598	5161600	.	+	0	transcript_id "Phchi.S1G084100.t1"; gene_id "Phchi.S1G084100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3778.t1 is derived from g947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5652863	5654329	.	-	.	Phchi.S1G093700
Phchi.S1	AUGUSTUS	transcript	5652863	5654329	.	-	.	transcript_id "Phchi.S1G093700.t1"; gene_id "Phchi.S1G093700"
Phchi.S1	AUGUSTUS	stop_codon	5652860	5652862	.	-	0	transcript_id "Phchi.S1G093700.t1"; gene_id "Phchi.S1G093700"
Phchi.S1	AUGUSTUS	CDS	5652863	5654329	0.47	-	0	transcript_id "Phchi.S1G093700.t1"; gene_id "Phchi.S1G093700"
Phchi.S1	AUGUSTUS	exon	5652863	5654329	.	-	.	transcript_id "Phchi.S1G093700.t1"; gene_id "Phchi.S1G093700"
Phchi.S1	AUGUSTUS	start_codon	5654327	5654329	.	-	0	transcript_id "Phchi.S1G093700.t1"; gene_id "Phchi.S1G093700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg790.t1 is derived from g10572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5596319	5599539	.	+	.	Phchi.S6G074900
Phchi.S6	AUGUSTUS	transcript	5596319	5599539	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	start_codon	5596319	5596321	.	+	0	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	CDS	5596319	5596765	0.99	+	0	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	exon	5596319	5596765	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	intron	5596766	5596923	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	CDS	5596924	5597277	0.94	+	0	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	exon	5596924	5597277	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	intron	5597278	5597398	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	CDS	5597399	5597568	0.93	+	0	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	exon	5597399	5597568	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	intron	5597569	5597769	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	CDS	5597770	5598218	1	+	1	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	exon	5597770	5598218	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	intron	5598219	5598418	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	CDS	5598419	5598841	1	+	2	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	exon	5598419	5598841	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	intron	5598842	5598934	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	CDS	5598935	5599539	0.99	+	2	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	exon	5598935	5599539	.	+	.	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
Phchi.S6	AUGUSTUS	stop_codon	5599540	5599542	.	+	0	transcript_id "Phchi.S6G074900.t1"; gene_id "Phchi.S6G074900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7297.t1 is derived from g4469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28376306	28378143	.	+	.	Phchi.S1G445600
Phchi.S1	AUGUSTUS	transcript	28376306	28378143	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	start_codon	28376306	28376308	.	+	0	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28376306	28376339	1	+	0	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28376306	28376339	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	intron	28376340	28376542	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28376543	28376656	1	+	2	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28376543	28376656	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	intron	28376657	28377003	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28377004	28377117	1	+	2	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28377004	28377117	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	intron	28377118	28377256	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28377257	28377369	1	+	2	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28377257	28377369	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	intron	28377370	28377526	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28377527	28377595	1	+	0	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28377527	28377595	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	intron	28377596	28377932	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28377933	28377998	1	+	0	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28377933	28377998	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	intron	28377999	28378104	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	CDS	28378105	28378143	0.99	+	0	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	exon	28378105	28378143	.	+	.	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
Phchi.S1	AUGUSTUS	stop_codon	28378144	28378146	.	+	0	transcript_id "Phchi.S1G445600.t1"; gene_id "Phchi.S1G445600"
# This transcript jg15572.t2 is derived from g14041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15573.t1 is derived from g14042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20077867	20078424	.	-	.	Phchi.S3G289200
Phchi.S3	AUGUSTUS	transcript	20077867	20078424	.	-	.	transcript_id "Phchi.S3G289200.t1"; gene_id "Phchi.S3G289200"
Phchi.S3	AUGUSTUS	stop_codon	20077864	20077866	.	-	0	transcript_id "Phchi.S3G289200.t1"; gene_id "Phchi.S3G289200"
Phchi.S3	AUGUSTUS	CDS	20077867	20078424	0.92	-	0	transcript_id "Phchi.S3G289200.t1"; gene_id "Phchi.S3G289200"
Phchi.S3	AUGUSTUS	exon	20077867	20078424	.	-	.	transcript_id "Phchi.S3G289200.t1"; gene_id "Phchi.S3G289200"
Phchi.S3	AUGUSTUS	start_codon	20078422	20078424	.	-	0	transcript_id "Phchi.S3G289200.t1"; gene_id "Phchi.S3G289200"
# This transcript jg7012.t2 is derived from g4184.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7013.t1 is derived from g4185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26400824	26405282	.	-	.	Phchi.S1G417200
Phchi.S1	AUGUSTUS	transcript	26400824	26405282	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	stop_codon	26400821	26400823	.	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26400824	26400846	0.28	-	2	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26400824	26400846	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26400847	26400929	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26400930	26401008	0.33	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26400930	26401008	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26401009	26401114	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26401115	26401348	0.89	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26401115	26401348	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26401349	26401446	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26401447	26401992	0.93	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26401447	26401992	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26401993	26402480	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26402481	26403683	1	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26402481	26403683	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26403684	26403766	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26403767	26403888	1	-	2	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26403767	26403888	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26403889	26403997	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26403998	26404561	1	-	2	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26403998	26404561	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26404562	26404649	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26404650	26404822	0.31	-	1	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26404650	26404822	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	intron	26404823	26404905	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	CDS	26404906	26405282	0.3	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	exon	26404906	26405282	.	-	.	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
Phchi.S1	AUGUSTUS	start_codon	26405280	26405282	.	-	0	transcript_id "Phchi.S1G417200.t1"; gene_id "Phchi.S1G417200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1263.t1 is derived from g11046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8706276	8709512	.	+	.	Phchi.S6G122200
Phchi.S6	AUGUSTUS	transcript	8706276	8709512	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	start_codon	8706276	8706278	.	+	0	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8706276	8706444	0.67	+	0	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8706276	8706444	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8706445	8706524	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8706525	8706597	1	+	2	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8706525	8706597	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8706598	8706689	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8706690	8706808	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8706690	8706808	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8706809	8706887	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8706888	8706988	0.67	+	2	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8706888	8706988	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8706989	8707267	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8707268	8707361	0.62	+	0	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8707268	8707361	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8707362	8707447	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8707448	8707580	1	+	2	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8707448	8707580	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8707581	8707664	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8707665	8707847	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8707665	8707847	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8707848	8707939	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8707940	8708011	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8707940	8708011	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708012	8708085	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8708086	8708157	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8708086	8708157	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708158	8708258	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8708259	8708330	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8708259	8708330	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708331	8708412	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8708413	8708484	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8708413	8708484	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708485	8708569	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8708570	8708641	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8708570	8708641	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708642	8708747	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8708748	8708819	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8708748	8708819	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708820	8708910	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8708911	8708982	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8708911	8708982	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8708983	8709058	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8709059	8709124	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8709059	8709124	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8709125	8709207	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8709208	8709270	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8709208	8709270	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	intron	8709271	8709361	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	CDS	8709362	8709512	1	+	1	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	exon	8709362	8709512	.	+	.	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
Phchi.S6	AUGUSTUS	stop_codon	8709513	8709515	.	+	0	transcript_id "Phchi.S6G122200.t1"; gene_id "Phchi.S6G122200"
# This transcript jg10877.t2 is derived from g14927.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10878.t1 is derived from g14928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2727351	2728243	.	-	.	Phchi.S4G046000
Phchi.S4	AUGUSTUS	transcript	2727351	2728243	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	stop_codon	2727348	2727350	.	-	0	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	CDS	2727351	2727436	1	-	2	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	exon	2727351	2727436	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	intron	2727437	2727593	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	CDS	2727594	2727723	1	-	0	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	exon	2727594	2727723	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	intron	2727724	2727839	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	CDS	2727840	2727968	1	-	0	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	exon	2727840	2727968	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	intron	2727969	2728039	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	CDS	2728040	2728162	1	-	0	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	exon	2728040	2728162	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	intron	2728163	2728240	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	CDS	2728241	2728243	1	-	0	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	exon	2728241	2728243	.	-	.	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
Phchi.S4	AUGUSTUS	start_codon	2728241	2728243	.	-	0	transcript_id "Phchi.S4G046000.t1"; gene_id "Phchi.S4G046000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6647.t1 is derived from g3819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24269379	24271266	.	-	.	Phchi.S1G380600
Phchi.S1	AUGUSTUS	transcript	24269379	24271266	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	stop_codon	24269376	24269378	.	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24269379	24269426	0.89	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24269379	24269426	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	intron	24269427	24269524	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24269525	24269649	1	-	2	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24269525	24269649	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	intron	24269650	24269856	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24269857	24269920	1	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24269857	24269920	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	intron	24269921	24270006	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24270007	24270147	0.91	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24270007	24270147	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	intron	24270148	24270273	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24270274	24270405	0.74	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24270274	24270405	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	intron	24270406	24270587	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24270588	24270707	0.72	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24270588	24270707	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	intron	24270708	24270792	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	CDS	24270793	24271266	1	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	exon	24270793	24271266	.	-	.	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
Phchi.S1	AUGUSTUS	start_codon	24271264	24271266	.	-	0	transcript_id "Phchi.S1G380600.t1"; gene_id "Phchi.S1G380600"
# This transcript jg14999.t2 is derived from g13467.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15000.t1 is derived from g13468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16192776	16193320	.	+	.	Phchi.S3G231900
Phchi.S3	AUGUSTUS	transcript	16192776	16193320	.	+	.	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	start_codon	16192776	16192778	.	+	0	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	CDS	16192776	16192880	0.96	+	0	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	exon	16192776	16192880	.	+	.	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	intron	16192881	16193020	.	+	.	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	CDS	16193021	16193176	1	+	0	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	exon	16193021	16193176	.	+	.	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	intron	16193177	16193248	.	+	.	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	CDS	16193249	16193320	1	+	0	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	exon	16193249	16193320	.	+	.	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
Phchi.S3	AUGUSTUS	stop_codon	16193321	16193323	.	+	0	transcript_id "Phchi.S3G231900.t1"; gene_id "Phchi.S3G231900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5632.t1 is derived from g2802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17973397	17976735	.	+	.	Phchi.S1G279100
Phchi.S1	AUGUSTUS	transcript	17973397	17976735	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	start_codon	17973397	17973399	.	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17973397	17973492	0.21	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17973397	17973492	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17973493	17973761	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17973762	17973992	1	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17973762	17973992	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17973993	17974206	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17974207	17974263	1	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17974207	17974263	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17974264	17974435	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17974436	17974564	1	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17974436	17974564	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17974565	17974644	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17974645	17974722	1	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17974645	17974722	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17974723	17974813	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17974814	17974884	1	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17974814	17974884	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17974885	17975022	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17975023	17975075	1	+	1	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17975023	17975075	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17975076	17975196	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17975197	17975419	1	+	2	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17975197	17975419	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17975420	17975501	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17975502	17975904	0.88	+	1	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17975502	17975904	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17975905	17976028	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17976029	17976172	1	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17976029	17976172	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17976173	17976258	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17976259	17976339	0.98	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17976259	17976339	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17976340	17976428	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17976429	17976444	0.98	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17976429	17976444	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	intron	17976445	17976523	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	CDS	17976524	17976735	0.98	+	2	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	exon	17976524	17976735	.	+	.	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
Phchi.S1	AUGUSTUS	stop_codon	17976736	17976738	.	+	0	transcript_id "Phchi.S1G279100.t1"; gene_id "Phchi.S1G279100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15097.t1 is derived from g13565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16997186	16997843	.	-	.	Phchi.S3G241600
Phchi.S3	AUGUSTUS	transcript	16997186	16997843	.	-	.	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	stop_codon	16997183	16997185	.	-	0	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	CDS	16997186	16997433	1	-	2	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	exon	16997186	16997433	.	-	.	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	intron	16997434	16997509	.	-	.	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	CDS	16997510	16997699	0.72	-	0	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	exon	16997510	16997699	.	-	.	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	intron	16997700	16997813	.	-	.	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	CDS	16997814	16997843	0.27	-	0	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	exon	16997814	16997843	.	-	.	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
Phchi.S3	AUGUSTUS	start_codon	16997841	16997843	.	-	0	transcript_id "Phchi.S3G241600.t1"; gene_id "Phchi.S3G241600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13922.t1 is derived from g12389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9665233	9669977	.	-	.	Phchi.S3G124100
Phchi.S3	AUGUSTUS	transcript	9665233	9669977	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	stop_codon	9665230	9665232	.	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9665233	9665623	1	-	1	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9665233	9665623	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9665624	9665711	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9665712	9665895	1	-	2	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9665712	9665895	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9665896	9665998	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9665999	9666401	0.98	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9665999	9666401	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9666402	9666529	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9666530	9666751	1	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9666530	9666751	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9666752	9666869	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9666870	9667058	1	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9666870	9667058	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9667059	9667170	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9667171	9667650	1	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9667171	9667650	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9667651	9667745	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9667746	9668595	0.98	-	1	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9667746	9668595	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9668596	9668702	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9668703	9668818	1	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9668703	9668818	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9668819	9668904	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9668905	9669358	1	-	1	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9668905	9669358	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9669359	9669455	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9669456	9669577	1	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9669456	9669577	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	intron	9669578	9669689	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	CDS	9669690	9669977	1	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	exon	9669690	9669977	.	-	.	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
Phchi.S3	AUGUSTUS	start_codon	9669975	9669977	.	-	0	transcript_id "Phchi.S3G124100.t1"; gene_id "Phchi.S3G124100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2519.t1 is derived from g9439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7111615	7113238	.	-	.	Phchi.S5G112800
Phchi.S5	AUGUSTUS	transcript	7111615	7113238	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	stop_codon	7111612	7111614	.	-	0	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	CDS	7111615	7111866	0.91	-	0	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	exon	7111615	7111866	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	intron	7111867	7111980	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	CDS	7111981	7112107	1	-	1	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	exon	7111981	7112107	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	intron	7112108	7112466	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	CDS	7112467	7112689	1	-	2	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	exon	7112467	7112689	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	intron	7112690	7112816	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	CDS	7112817	7112849	1	-	2	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	exon	7112817	7112849	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	intron	7112850	7113138	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	CDS	7113139	7113238	0.67	-	0	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	exon	7113139	7113238	.	-	.	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
Phchi.S5	AUGUSTUS	start_codon	7113236	7113238	.	-	0	transcript_id "Phchi.S5G112800.t1"; gene_id "Phchi.S5G112800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10605.t1 is derived from g14655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1162330	1164032	.	+	.	Phchi.S4G018700
Phchi.S4	AUGUSTUS	transcript	1162330	1164032	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	start_codon	1162330	1162332	.	+	0	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	CDS	1162330	1162973	0.8	+	0	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	exon	1162330	1162973	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	intron	1162974	1163058	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	CDS	1163059	1163383	1	+	1	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	exon	1163059	1163383	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	intron	1163384	1163469	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	CDS	1163470	1163616	1	+	0	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	exon	1163470	1163616	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	intron	1163617	1163708	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	CDS	1163709	1164032	0.99	+	0	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	exon	1163709	1164032	.	+	.	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
Phchi.S4	AUGUSTUS	stop_codon	1164033	1164035	.	+	0	transcript_id "Phchi.S4G018700.t1"; gene_id "Phchi.S4G018700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11693.t1 is derived from g15744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7704618	7709172	.	-	.	Phchi.S4G127500
Phchi.S4	AUGUSTUS	transcript	7704618	7709172	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	stop_codon	7704615	7704617	.	-	0	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7704618	7704674	1	-	0	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7704618	7704674	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	intron	7704675	7704760	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7704761	7704939	0.83	-	2	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7704761	7704939	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	intron	7704940	7705034	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7705035	7705106	0.81	-	2	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7705035	7705106	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	intron	7705107	7705471	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7705472	7705540	0.55	-	2	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7705472	7705540	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	intron	7705541	7705746	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7705747	7705760	0.83	-	1	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7705747	7705760	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	intron	7705761	7705849	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7705850	7706033	0.78	-	2	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7705850	7706033	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	intron	7706034	7706114	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	CDS	7706115	7709172	0.64	-	0	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	exon	7706115	7709172	.	-	.	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
Phchi.S4	AUGUSTUS	start_codon	7709170	7709172	.	-	0	transcript_id "Phchi.S4G127500.t1"; gene_id "Phchi.S4G127500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1110.t1 is derived from g10893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7668196	7668892	.	-	.	Phchi.S6G106900
Phchi.S6	AUGUSTUS	transcript	7668196	7668892	.	-	.	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	stop_codon	7668193	7668195	.	-	0	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	CDS	7668196	7668304	1	-	1	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	exon	7668196	7668304	.	-	.	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	intron	7668305	7668485	.	-	.	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	CDS	7668486	7668892	0.58	-	0	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	exon	7668486	7668892	.	-	.	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
Phchi.S6	AUGUSTUS	start_codon	7668890	7668892	.	-	0	transcript_id "Phchi.S6G106900.t1"; gene_id "Phchi.S6G106900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15049.t1 is derived from g13517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16744581	16746394	.	-	.	Phchi.S3G236800
Phchi.S3	AUGUSTUS	transcript	16744581	16746394	.	-	.	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	stop_codon	16744578	16744580	.	-	0	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	CDS	16744581	16744834	0.59	-	2	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	exon	16744581	16744834	.	-	.	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	intron	16744835	16745007	.	-	.	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	CDS	16745008	16746394	0.56	-	0	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	exon	16745008	16746394	.	-	.	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
Phchi.S3	AUGUSTUS	start_codon	16746392	16746394	.	-	0	transcript_id "Phchi.S3G236800.t1"; gene_id "Phchi.S3G236800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5424.t1 is derived from g2594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16809117	16809830	.	-	.	Phchi.S1G258300
Phchi.S1	AUGUSTUS	transcript	16809117	16809830	.	-	.	transcript_id "Phchi.S1G258300.t1"; gene_id "Phchi.S1G258300"
Phchi.S1	AUGUSTUS	stop_codon	16809114	16809116	.	-	0	transcript_id "Phchi.S1G258300.t1"; gene_id "Phchi.S1G258300"
Phchi.S1	AUGUSTUS	CDS	16809117	16809830	0.97	-	0	transcript_id "Phchi.S1G258300.t1"; gene_id "Phchi.S1G258300"
Phchi.S1	AUGUSTUS	exon	16809117	16809830	.	-	.	transcript_id "Phchi.S1G258300.t1"; gene_id "Phchi.S1G258300"
Phchi.S1	AUGUSTUS	start_codon	16809828	16809830	.	-	0	transcript_id "Phchi.S1G258300.t1"; gene_id "Phchi.S1G258300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3355.t1 is derived from g524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3098193	3098701	.	-	.	Phchi.S1G051400
Phchi.S1	AUGUSTUS	transcript	3098193	3098701	.	-	.	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	stop_codon	3098190	3098192	.	-	0	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	CDS	3098193	3098299	0.98	-	2	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	exon	3098193	3098299	.	-	.	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	intron	3098300	3098466	.	-	.	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	CDS	3098467	3098701	0.79	-	0	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	exon	3098467	3098701	.	-	.	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
Phchi.S1	AUGUSTUS	start_codon	3098699	3098701	.	-	0	transcript_id "Phchi.S1G051400.t1"; gene_id "Phchi.S1G051400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13669.t1 is derived from g12136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8079387	8081102	.	-	.	Phchi.S3G098800
Phchi.S3	AUGUSTUS	transcript	8079387	8081102	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	stop_codon	8079384	8079386	.	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	CDS	8079387	8079578	0.87	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	exon	8079387	8079578	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	intron	8079579	8079739	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	CDS	8079740	8079805	1	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	exon	8079740	8079805	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	intron	8079806	8079934	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	CDS	8079935	8079994	1	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	exon	8079935	8079994	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	intron	8079995	8080115	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	CDS	8080116	8080231	1	-	2	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	exon	8080116	8080231	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	intron	8080232	8080369	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	CDS	8080370	8080460	1	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	exon	8080370	8080460	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	intron	8080461	8081045	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	CDS	8081046	8081102	1	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	exon	8081046	8081102	.	-	.	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
Phchi.S3	AUGUSTUS	start_codon	8081100	8081102	.	-	0	transcript_id "Phchi.S3G098800.t1"; gene_id "Phchi.S3G098800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6075.t1 is derived from g3246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20746800	20747948	.	-	.	Phchi.S1G323400
Phchi.S1	AUGUSTUS	transcript	20746800	20747948	.	-	.	transcript_id "Phchi.S1G323400.t1"; gene_id "Phchi.S1G323400"
Phchi.S1	AUGUSTUS	stop_codon	20746797	20746799	.	-	0	transcript_id "Phchi.S1G323400.t1"; gene_id "Phchi.S1G323400"
Phchi.S1	AUGUSTUS	CDS	20746800	20747948	1	-	0	transcript_id "Phchi.S1G323400.t1"; gene_id "Phchi.S1G323400"
Phchi.S1	AUGUSTUS	exon	20746800	20747948	.	-	.	transcript_id "Phchi.S1G323400.t1"; gene_id "Phchi.S1G323400"
Phchi.S1	AUGUSTUS	start_codon	20747946	20747948	.	-	0	transcript_id "Phchi.S1G323400.t1"; gene_id "Phchi.S1G323400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15700.t1 is derived from g14169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20762263	20763991	.	-	.	Phchi.S3G301900
Phchi.S3	AUGUSTUS	transcript	20762263	20763991	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	stop_codon	20762260	20762262	.	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	CDS	20762263	20762418	0.59	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	exon	20762263	20762418	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	intron	20762419	20762614	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	CDS	20762615	20762782	0.94	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	exon	20762615	20762782	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	intron	20762783	20762897	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	CDS	20762898	20763143	0.99	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	exon	20762898	20763143	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	intron	20763144	20763254	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	CDS	20763255	20763548	0.99	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	exon	20763255	20763548	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	intron	20763549	20763653	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	CDS	20763654	20763831	0.99	-	1	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	exon	20763654	20763831	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	intron	20763832	20763977	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	CDS	20763978	20763991	0.48	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	exon	20763978	20763991	.	-	.	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
Phchi.S3	AUGUSTUS	start_codon	20763989	20763991	.	-	0	transcript_id "Phchi.S3G301900.t1"; gene_id "Phchi.S3G301900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3214.t1 is derived from g383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2275416	2276471	.	-	.	Phchi.S1G037300
Phchi.S1	AUGUSTUS	transcript	2275416	2276471	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	stop_codon	2275413	2275415	.	-	0	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	CDS	2275416	2275607	1	-	0	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	exon	2275416	2275607	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	intron	2275608	2275711	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	CDS	2275712	2275899	1	-	2	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	exon	2275712	2275899	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	intron	2275900	2276054	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	CDS	2276055	2276086	1	-	1	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	exon	2276055	2276086	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	intron	2276087	2276217	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	CDS	2276218	2276471	0.97	-	0	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	exon	2276218	2276471	.	-	.	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
Phchi.S1	AUGUSTUS	start_codon	2276469	2276471	.	-	0	transcript_id "Phchi.S1G037300.t1"; gene_id "Phchi.S1G037300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg930.t1 is derived from g10712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6487691	6489592	.	-	.	Phchi.S6G088900
Phchi.S6	AUGUSTUS	transcript	6487691	6489592	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	stop_codon	6487688	6487690	.	-	0	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6487691	6488174	1	-	1	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6487691	6488174	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6488175	6488250	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6488251	6488425	1	-	2	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6488251	6488425	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6488426	6488513	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6488514	6488582	1	-	2	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6488514	6488582	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6488583	6488678	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6488679	6489102	1	-	0	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6488679	6489102	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6489103	6489219	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6489220	6489468	0.8	-	0	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6489220	6489468	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6489469	6489574	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6489575	6489592	0.72	-	0	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6489575	6489592	.	-	.	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	start_codon	6489590	6489592	.	-	0	transcript_id "Phchi.S6G088900.t1"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	transcript	6487691	6489592	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	stop_codon	6487688	6487690	.	-	0	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6487691	6488174	1	-	1	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6487691	6488174	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6488175	6488250	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6488251	6488437	0.98	-	2	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6488251	6488437	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6488438	6488513	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6488514	6488582	1	-	2	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6488514	6488582	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6488583	6488678	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6488679	6489102	0.99	-	0	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6488679	6489102	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6489103	6489219	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6489220	6489468	0.8	-	0	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6489220	6489468	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	intron	6489469	6489574	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	CDS	6489575	6489592	0.69	-	0	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	exon	6489575	6489592	.	-	.	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
Phchi.S6	AUGUSTUS	start_codon	6489590	6489592	.	-	0	transcript_id "Phchi.S6G088900.t2"; gene_id "Phchi.S6G088900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4756.t1 is derived from g1926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12667025	12668534	.	-	.	Phchi.S1G191500
Phchi.S1	AUGUSTUS	transcript	12667025	12667797	.	-	.	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	stop_codon	12667022	12667024	.	-	0	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12667025	12667157	0.92	-	1	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12667025	12667157	.	-	.	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	intron	12667158	12667250	.	-	.	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12667251	12667590	0.93	-	2	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12667251	12667590	.	-	.	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	intron	12667591	12667670	.	-	.	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12667671	12667797	0.67	-	0	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12667671	12667797	.	-	.	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	start_codon	12667795	12667797	.	-	0	transcript_id "Phchi.S1G191500.t1"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	transcript	12667025	12668534	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	stop_codon	12667022	12667024	.	-	0	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12667025	12667157	0.89	-	1	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12667025	12667157	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	intron	12667158	12667250	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12667251	12667590	0.92	-	2	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12667251	12667590	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	intron	12667591	12667670	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12667671	12667797	0.99	-	0	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12667671	12667797	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	intron	12667798	12668114	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	CDS	12668115	12668534	0.46	-	0	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	exon	12668115	12668534	.	-	.	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
Phchi.S1	AUGUSTUS	start_codon	12668532	12668534	.	-	0	transcript_id "Phchi.S1G191500.t2"; gene_id "Phchi.S1G191500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6024.t1 is derived from g3195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20489798	20490469	.	+	.	Phchi.S1G318300
Phchi.S1	AUGUSTUS	transcript	20489798	20490469	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	start_codon	20489798	20489800	.	+	0	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	CDS	20489798	20489825	0.62	+	0	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	exon	20489798	20489825	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	intron	20489826	20489971	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	CDS	20489972	20490012	0.46	+	2	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	exon	20489972	20490012	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	intron	20490013	20490110	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	CDS	20490111	20490205	0.57	+	0	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	exon	20490111	20490205	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	intron	20490206	20490384	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	CDS	20490385	20490469	0.62	+	1	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	exon	20490385	20490469	.	+	.	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
Phchi.S1	AUGUSTUS	stop_codon	20490470	20490472	.	+	0	transcript_id "Phchi.S1G318300.t1"; gene_id "Phchi.S1G318300"
# This transcript jg4401.t2 is derived from g1570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4402.t1 is derived from g1571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10246943	10250421	.	-	.	Phchi.S1G156100
Phchi.S1	AUGUSTUS	transcript	10246943	10250421	.	-	.	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	stop_codon	10246940	10246942	.	-	0	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	CDS	10246943	10249275	0.96	-	2	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	exon	10246943	10249275	.	-	.	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	intron	10249276	10249530	.	-	.	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	CDS	10249531	10250045	0.7	-	1	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	exon	10249531	10250045	.	-	.	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	intron	10250046	10250143	.	-	.	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	CDS	10250144	10250421	0.34	-	0	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	exon	10250144	10250421	.	-	.	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
Phchi.S1	AUGUSTUS	start_codon	10250419	10250421	.	-	0	transcript_id "Phchi.S1G156100.t1"; gene_id "Phchi.S1G156100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13490.t1 is derived from g11957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7147189	7148547	.	-	.	Phchi.S3G080900
Phchi.S3	AUGUSTUS	transcript	7147189	7148547	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	stop_codon	7147186	7147188	.	-	0	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	CDS	7147189	7147379	1	-	2	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	exon	7147189	7147379	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	intron	7147380	7147560	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	CDS	7147561	7147651	1	-	0	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	exon	7147561	7147651	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	intron	7147652	7147837	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	CDS	7147838	7147952	1	-	1	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	exon	7147838	7147952	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	intron	7147953	7148150	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	CDS	7148151	7148270	1	-	1	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	exon	7148151	7148270	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	intron	7148271	7148443	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	CDS	7148444	7148547	0.62	-	0	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	exon	7148444	7148547	.	-	.	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
Phchi.S3	AUGUSTUS	start_codon	7148545	7148547	.	-	0	transcript_id "Phchi.S3G080900.t1"; gene_id "Phchi.S3G080900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2209.t1 is derived from g9129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5429486	5430848	.	+	.	Phchi.S5G081800
Phchi.S5	AUGUSTUS	transcript	5429486	5430848	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	start_codon	5429486	5429488	.	+	0	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	CDS	5429486	5429566	0.99	+	0	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	exon	5429486	5429566	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	intron	5429567	5429656	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	CDS	5429657	5429885	1	+	0	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	exon	5429657	5429885	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	intron	5429886	5430007	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	CDS	5430008	5430393	0.97	+	2	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	exon	5430008	5430393	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	intron	5430394	5430485	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	CDS	5430486	5430848	1	+	0	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	exon	5430486	5430848	.	+	.	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
Phchi.S5	AUGUSTUS	stop_codon	5430849	5430851	.	+	0	transcript_id "Phchi.S5G081800.t1"; gene_id "Phchi.S5G081800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7251.t1 is derived from g4423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27865806	27866610	.	+	.	Phchi.S1G441000
Phchi.S1	AUGUSTUS	transcript	27865806	27866610	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	start_codon	27865806	27865808	.	+	0	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	CDS	27865806	27865967	0.81	+	0	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	exon	27865806	27865967	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	intron	27865968	27866065	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	CDS	27866066	27866147	0.99	+	0	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	exon	27866066	27866147	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	intron	27866148	27866251	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	CDS	27866252	27866359	0.99	+	2	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	exon	27866252	27866359	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	intron	27866360	27866551	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	CDS	27866552	27866610	0.97	+	2	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	exon	27866552	27866610	.	+	.	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
Phchi.S1	AUGUSTUS	stop_codon	27866611	27866613	.	+	0	transcript_id "Phchi.S1G441000.t1"; gene_id "Phchi.S1G441000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11499.t1 is derived from g15549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6669411	6670228	.	+	.	Phchi.S4G108100
Phchi.S4	AUGUSTUS	transcript	6669411	6670228	.	+	.	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	start_codon	6669411	6669413	.	+	0	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	CDS	6669411	6669753	0.54	+	0	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	exon	6669411	6669753	.	+	.	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	intron	6669754	6669845	.	+	.	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	CDS	6669846	6670228	0.97	+	2	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	exon	6669846	6670228	.	+	.	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
Phchi.S4	AUGUSTUS	stop_codon	6670229	6670231	.	+	0	transcript_id "Phchi.S4G108100.t1"; gene_id "Phchi.S4G108100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7252.t1 is derived from g4424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27866798	27868201	.	+	.	Phchi.S1G441100
Phchi.S1	AUGUSTUS	transcript	27866798	27868201	.	+	.	transcript_id "Phchi.S1G441100.t1"; gene_id "Phchi.S1G441100"
Phchi.S1	AUGUSTUS	start_codon	27866798	27866800	.	+	0	transcript_id "Phchi.S1G441100.t1"; gene_id "Phchi.S1G441100"
Phchi.S1	AUGUSTUS	CDS	27866798	27868201	0.99	+	0	transcript_id "Phchi.S1G441100.t1"; gene_id "Phchi.S1G441100"
Phchi.S1	AUGUSTUS	exon	27866798	27868201	.	+	.	transcript_id "Phchi.S1G441100.t1"; gene_id "Phchi.S1G441100"
Phchi.S1	AUGUSTUS	stop_codon	27868202	27868204	.	+	0	transcript_id "Phchi.S1G441100.t1"; gene_id "Phchi.S1G441100"
# This transcript jg7565.t2 is derived from g4739.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7566.t1 is derived from g4740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30075537	30077590	.	-	.	Phchi.S1G472500
Phchi.S1	AUGUSTUS	transcript	30075537	30077590	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	stop_codon	30075534	30075536	.	-	0	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	CDS	30075537	30075540	0.79	-	1	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	exon	30075537	30075540	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	intron	30075541	30075679	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	CDS	30075680	30076793	0.78	-	2	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	exon	30075680	30076793	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	intron	30076794	30076976	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	CDS	30076977	30077121	0.44	-	0	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	exon	30076977	30077121	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	intron	30077122	30077201	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	CDS	30077202	30077438	0.44	-	0	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	exon	30077202	30077438	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	intron	30077439	30077581	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	CDS	30077582	30077590	1	-	0	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	exon	30077582	30077590	.	-	.	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
Phchi.S1	AUGUSTUS	start_codon	30077588	30077590	.	-	0	transcript_id "Phchi.S1G472500.t1"; gene_id "Phchi.S1G472500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14859.t1 is derived from g13327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15086992	15090095	.	+	.	Phchi.S3G217800
Phchi.S3	AUGUSTUS	transcript	15086992	15090095	.	+	.	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	start_codon	15086992	15086994	.	+	0	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	CDS	15086992	15088541	0.99	+	0	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	exon	15086992	15088541	.	+	.	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	intron	15088542	15088621	.	+	.	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	CDS	15088622	15090095	0.99	+	1	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	exon	15088622	15090095	.	+	.	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
Phchi.S3	AUGUSTUS	stop_codon	15090096	15090098	.	+	0	transcript_id "Phchi.S3G217800.t1"; gene_id "Phchi.S3G217800"
# This transcript jg13005.t2 is derived from g11470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13006.t1 is derived from g11471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3606335	3608194	.	+	.	Phchi.S3G032500
Phchi.S3	AUGUSTUS	transcript	3606335	3608194	.	+	.	transcript_id "Phchi.S3G032500.t1"; gene_id "Phchi.S3G032500"
Phchi.S3	AUGUSTUS	start_codon	3606335	3606337	.	+	0	transcript_id "Phchi.S3G032500.t1"; gene_id "Phchi.S3G032500"
Phchi.S3	AUGUSTUS	CDS	3606335	3608194	0.96	+	0	transcript_id "Phchi.S3G032500.t1"; gene_id "Phchi.S3G032500"
Phchi.S3	AUGUSTUS	exon	3606335	3608194	.	+	.	transcript_id "Phchi.S3G032500.t1"; gene_id "Phchi.S3G032500"
Phchi.S3	AUGUSTUS	stop_codon	3608195	3608197	.	+	0	transcript_id "Phchi.S3G032500.t1"; gene_id "Phchi.S3G032500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12598.t1 is derived from g8275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37331997	37334189	.	+	.	Phchi.S2G067800
Phchi.S2	AUGUSTUS	transcript	37331997	37334189	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	start_codon	37331997	37331999	.	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37331997	37332025	0.7	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37331997	37332025	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37332026	37332189	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37332190	37332368	0.29	+	1	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37332190	37332368	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37332369	37332603	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37332604	37332668	0.53	+	2	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37332604	37332668	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37332669	37333025	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37333026	37333113	1	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37333026	37333113	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37333114	37333241	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37333242	37333351	1	+	2	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37333242	37333351	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37333352	37333471	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37333472	37333535	1	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37333472	37333535	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37333536	37333660	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37333661	37333725	1	+	2	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37333661	37333725	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37333726	37333845	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37333846	37333911	1	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37333846	37333911	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	intron	37333912	37334093	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	CDS	37334094	37334189	0.96	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	exon	37334094	37334189	.	+	.	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
Phchi.S2	AUGUSTUS	stop_codon	37334190	37334192	.	+	0	transcript_id "Phchi.S2G067800.t1"; gene_id "Phchi.S2G067800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15386.t1 is derived from g13854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18754486	18757570	.	+	.	Phchi.S3G270500
Phchi.S3	AUGUSTUS	transcript	18754486	18757570	.	+	.	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	start_codon	18754486	18754488	.	+	0	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	CDS	18754486	18755275	0.64	+	0	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	exon	18754486	18755275	.	+	.	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	intron	18755276	18755357	.	+	.	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	CDS	18755358	18757570	0.44	+	2	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	exon	18755358	18757570	.	+	.	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
Phchi.S3	AUGUSTUS	stop_codon	18757571	18757573	.	+	0	transcript_id "Phchi.S3G270500.t1"; gene_id "Phchi.S3G270500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9832.t1 is derived from g7008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43999776	44000082	.	+	.	Phchi.S1G699100
Phchi.S1	AUGUSTUS	transcript	43999776	44000082	.	+	.	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	start_codon	43999776	43999778	.	+	0	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	CDS	43999776	43999896	0.55	+	0	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	exon	43999776	43999896	.	+	.	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	intron	43999897	43999993	.	+	.	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	CDS	43999994	44000082	0.85	+	2	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	exon	43999994	44000082	.	+	.	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
Phchi.S1	AUGUSTUS	stop_codon	44000083	44000085	.	+	0	transcript_id "Phchi.S1G699100.t1"; gene_id "Phchi.S1G699100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2477.t1 is derived from g9397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6841065	6842978	.	+	.	Phchi.S5G108600
Phchi.S5	AUGUSTUS	transcript	6841065	6842978	.	+	.	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	start_codon	6841065	6841067	.	+	0	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	CDS	6841065	6841193	0.68	+	0	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	exon	6841065	6841193	.	+	.	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	intron	6841194	6841273	.	+	.	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	CDS	6841274	6841320	1	+	0	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	exon	6841274	6841320	.	+	.	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	intron	6841321	6841420	.	+	.	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	CDS	6841421	6842978	0.99	+	1	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	exon	6841421	6842978	.	+	.	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
Phchi.S5	AUGUSTUS	stop_codon	6842979	6842981	.	+	0	transcript_id "Phchi.S5G108600.t1"; gene_id "Phchi.S5G108600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8428.t1 is derived from g5603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35893086	35893879	.	+	.	Phchi.S1G558700
Phchi.S1	AUGUSTUS	transcript	35893086	35893879	.	+	.	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	start_codon	35893086	35893088	.	+	0	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	CDS	35893086	35893579	0.32	+	0	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	exon	35893086	35893579	.	+	.	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	intron	35893580	35893689	.	+	.	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	CDS	35893690	35893879	0.33	+	1	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	exon	35893690	35893879	.	+	.	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
Phchi.S1	AUGUSTUS	stop_codon	35893880	35893882	.	+	0	transcript_id "Phchi.S1G558700.t1"; gene_id "Phchi.S1G558700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14415.t1 is derived from g12883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12716844	12718000	.	-	.	Phchi.S3G173400
Phchi.S3	AUGUSTUS	transcript	12716844	12718000	.	-	.	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	stop_codon	12716841	12716843	.	-	0	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	CDS	12716844	12716985	1	-	1	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	exon	12716844	12716985	.	-	.	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	intron	12716986	12717080	.	-	.	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	CDS	12717081	12718000	1	-	0	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	exon	12717081	12718000	.	-	.	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
Phchi.S3	AUGUSTUS	start_codon	12717998	12718000	.	-	0	transcript_id "Phchi.S3G173400.t1"; gene_id "Phchi.S3G173400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4409.t1 is derived from g1578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10266819	10267681	.	-	.	Phchi.S1G156800
Phchi.S1	AUGUSTUS	transcript	10266819	10267681	.	-	.	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	stop_codon	10266816	10266818	.	-	0	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	CDS	10266819	10267001	0.99	-	0	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	exon	10266819	10267001	.	-	.	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	intron	10267002	10267068	.	-	.	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	CDS	10267069	10267407	1	-	0	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	exon	10267069	10267407	.	-	.	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	intron	10267408	10267498	.	-	.	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	CDS	10267499	10267681	1	-	0	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	exon	10267499	10267681	.	-	.	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
Phchi.S1	AUGUSTUS	start_codon	10267679	10267681	.	-	0	transcript_id "Phchi.S1G156800.t1"; gene_id "Phchi.S1G156800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12860.t1 is derived from g11325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2779493	2780065	.	+	.	Phchi.S3G017900
Phchi.S3	AUGUSTUS	transcript	2779493	2780065	.	+	.	transcript_id "Phchi.S3G017900.t1"; gene_id "Phchi.S3G017900"
Phchi.S3	AUGUSTUS	start_codon	2779493	2779495	.	+	0	transcript_id "Phchi.S3G017900.t1"; gene_id "Phchi.S3G017900"
Phchi.S3	AUGUSTUS	CDS	2779493	2780065	1	+	0	transcript_id "Phchi.S3G017900.t1"; gene_id "Phchi.S3G017900"
Phchi.S3	AUGUSTUS	exon	2779493	2780065	.	+	.	transcript_id "Phchi.S3G017900.t1"; gene_id "Phchi.S3G017900"
Phchi.S3	AUGUSTUS	stop_codon	2780066	2780068	.	+	0	transcript_id "Phchi.S3G017900.t1"; gene_id "Phchi.S3G017900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13443.t1 is derived from g11910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6735632	6737495	.	+	.	Phchi.S3G076200
Phchi.S3	AUGUSTUS	transcript	6735632	6737495	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	start_codon	6735632	6735634	.	+	0	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6735632	6735665	0.62	+	0	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6735632	6735665	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	intron	6735666	6735746	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6735747	6735914	0.63	+	2	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6735747	6735914	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	intron	6735915	6735996	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6735997	6736338	0.87	+	2	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6735997	6736338	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	intron	6736339	6736441	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6736442	6736498	0.92	+	2	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6736442	6736498	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	intron	6736499	6736598	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6736599	6736796	0.58	+	2	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6736599	6736796	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	intron	6736797	6736906	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6736907	6737040	0.58	+	2	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6736907	6737040	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	intron	6737041	6737144	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	CDS	6737145	6737495	0.57	+	0	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	exon	6737145	6737495	.	+	.	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
Phchi.S3	AUGUSTUS	stop_codon	6737496	6737498	.	+	0	transcript_id "Phchi.S3G076200.t1"; gene_id "Phchi.S3G076200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10277.t1 is derived from g7453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46792167	46793671	.	+	.	Phchi.S1G743600
Phchi.S1	AUGUSTUS	transcript	46792167	46793671	.	+	.	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	start_codon	46792167	46792169	.	+	0	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	CDS	46792167	46792861	0.57	+	0	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	exon	46792167	46792861	.	+	.	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	intron	46792862	46793082	.	+	.	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	CDS	46793083	46793389	0.99	+	1	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	exon	46793083	46793389	.	+	.	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	intron	46793390	46793518	.	+	.	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	CDS	46793519	46793671	0.88	+	0	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	exon	46793519	46793671	.	+	.	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
Phchi.S1	AUGUSTUS	stop_codon	46793672	46793674	.	+	0	transcript_id "Phchi.S1G743600.t1"; gene_id "Phchi.S1G743600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12915.t1 is derived from g11380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3120245	3120499	.	-	.	Phchi.S3G023400
Phchi.S3	AUGUSTUS	transcript	3120245	3120499	.	-	.	transcript_id "Phchi.S3G023400.t1"; gene_id "Phchi.S3G023400"
Phchi.S3	AUGUSTUS	stop_codon	3120242	3120244	.	-	0	transcript_id "Phchi.S3G023400.t1"; gene_id "Phchi.S3G023400"
Phchi.S3	AUGUSTUS	CDS	3120245	3120499	0.37	-	0	transcript_id "Phchi.S3G023400.t1"; gene_id "Phchi.S3G023400"
Phchi.S3	AUGUSTUS	exon	3120245	3120499	.	-	.	transcript_id "Phchi.S3G023400.t1"; gene_id "Phchi.S3G023400"
Phchi.S3	AUGUSTUS	start_codon	3120497	3120499	.	-	0	transcript_id "Phchi.S3G023400.t1"; gene_id "Phchi.S3G023400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1165.t1 is derived from g10948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8118708	8120052	.	-	.	Phchi.S6G112400
Phchi.S6	AUGUSTUS	transcript	8118708	8120052	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	stop_codon	8118705	8118707	.	-	0	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	CDS	8118708	8118748	0.98	-	2	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	exon	8118708	8118748	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	intron	8118749	8118860	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	CDS	8118861	8118972	1	-	0	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	exon	8118861	8118972	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	intron	8118973	8119065	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	CDS	8119066	8119232	1	-	2	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	exon	8119066	8119232	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	intron	8119233	8119309	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	CDS	8119310	8119708	1	-	2	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	exon	8119310	8119708	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	intron	8119709	8119808	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	CDS	8119809	8120052	0.8	-	0	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	exon	8119809	8120052	.	-	.	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
Phchi.S6	AUGUSTUS	start_codon	8120050	8120052	.	-	0	transcript_id "Phchi.S6G112400.t1"; gene_id "Phchi.S6G112400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5401.t1 is derived from g2571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16691916	16692727	.	-	.	Phchi.S1G256000
Phchi.S1	AUGUSTUS	transcript	16691916	16692727	.	-	.	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	stop_codon	16691913	16691915	.	-	0	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	CDS	16691916	16692069	0.64	-	1	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	exon	16691916	16692069	.	-	.	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	intron	16692070	16692323	.	-	.	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	CDS	16692324	16692449	0.57	-	1	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	exon	16692324	16692449	.	-	.	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	intron	16692450	16692566	.	-	.	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	CDS	16692567	16692727	0.97	-	0	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	exon	16692567	16692727	.	-	.	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
Phchi.S1	AUGUSTUS	start_codon	16692725	16692727	.	-	0	transcript_id "Phchi.S1G256000.t1"; gene_id "Phchi.S1G256000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6401.t1 is derived from g3573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22774776	22775456	.	-	.	Phchi.S1G356000
Phchi.S1	AUGUSTUS	transcript	22774776	22775456	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	stop_codon	22774773	22774775	.	-	0	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	CDS	22774776	22774812	1	-	1	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	exon	22774776	22774812	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	intron	22774813	22774954	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	CDS	22774955	22775023	1	-	1	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	exon	22774955	22775023	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	intron	22775024	22775121	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	CDS	22775122	22775192	1	-	0	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	exon	22775122	22775192	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	intron	22775193	22775285	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	CDS	22775286	22775344	1	-	2	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	exon	22775286	22775344	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	intron	22775345	22775443	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	CDS	22775444	22775456	0.9	-	0	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	exon	22775444	22775456	.	-	.	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
Phchi.S1	AUGUSTUS	start_codon	22775454	22775456	.	-	0	transcript_id "Phchi.S1G356000.t1"; gene_id "Phchi.S1G356000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7350.t1 is derived from g4522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28653234	28655237	.	-	.	Phchi.S1G450900
Phchi.S1	AUGUSTUS	transcript	28653234	28655237	.	-	.	transcript_id "Phchi.S1G450900.t1"; gene_id "Phchi.S1G450900"
Phchi.S1	AUGUSTUS	stop_codon	28653231	28653233	.	-	0	transcript_id "Phchi.S1G450900.t1"; gene_id "Phchi.S1G450900"
Phchi.S1	AUGUSTUS	CDS	28653234	28655237	0.97	-	0	transcript_id "Phchi.S1G450900.t1"; gene_id "Phchi.S1G450900"
Phchi.S1	AUGUSTUS	exon	28653234	28655237	.	-	.	transcript_id "Phchi.S1G450900.t1"; gene_id "Phchi.S1G450900"
Phchi.S1	AUGUSTUS	start_codon	28655235	28655237	.	-	0	transcript_id "Phchi.S1G450900.t1"; gene_id "Phchi.S1G450900"
# This transcript jg4779.t2 is derived from g1949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4780.t1 is derived from g1950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12784953	12790319	.	-	.	Phchi.S1G193900
Phchi.S1	AUGUSTUS	transcript	12788571	12790319	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	stop_codon	12788568	12788570	.	-	0	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788571	12788631	0.99	-	1	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788571	12788631	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12788632	12788770	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788771	12788862	1	-	0	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788771	12788862	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12788863	12788950	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788951	12789178	1	-	0	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788951	12789178	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12789179	12789304	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12789305	12789520	1	-	0	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12789305	12789520	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12789521	12789599	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12789600	12789700	1	-	2	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12789600	12789700	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12789701	12789778	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12789779	12790319	0.93	-	0	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12789779	12790319	.	-	.	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	start_codon	12790317	12790319	.	-	0	transcript_id "Phchi.S1G193900.t1"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	transcript	12784953	12790319	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	stop_codon	12784950	12784952	.	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12784953	12785747	0.95	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12784953	12785747	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12785748	12785908	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12785909	12786204	0.67	-	2	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12785909	12786204	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12786205	12786287	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12786288	12787011	0.45	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12786288	12787011	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12787012	12787094	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12787095	12787209	1	-	1	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12787095	12787209	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12787210	12787287	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12787288	12788132	1	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12787288	12788132	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12788133	12788269	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788270	12788362	1	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788270	12788362	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12788363	12788499	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788500	12788593	1	-	1	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788500	12788593	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12788594	12788770	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788771	12788862	1	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788771	12788862	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12788863	12788950	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12788951	12789178	1	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12788951	12789178	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12789179	12789304	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12789305	12789520	1	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12789305	12789520	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12789521	12789599	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12789600	12789700	1	-	2	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12789600	12789700	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	intron	12789701	12789778	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	CDS	12789779	12790319	0.93	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	exon	12789779	12790319	.	-	.	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
Phchi.S1	AUGUSTUS	start_codon	12790317	12790319	.	-	0	transcript_id "Phchi.S1G193900.t2"; gene_id "Phchi.S1G193900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1524.t1 is derived from g8443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1581596	1583262	.	+	.	Phchi.S5G013300
Phchi.S5	AUGUSTUS	transcript	1581596	1583262	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	start_codon	1581596	1581598	.	+	0	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	CDS	1581596	1581680	1	+	0	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	exon	1581596	1581680	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	intron	1581681	1581774	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	CDS	1581775	1581834	0.99	+	2	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	exon	1581775	1581834	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	intron	1581835	1581916	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	CDS	1581917	1582762	0.82	+	2	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	exon	1581917	1582762	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	intron	1582763	1582885	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	CDS	1582886	1583137	0.63	+	2	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	exon	1582886	1583137	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	intron	1583138	1583236	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	CDS	1583237	1583262	0.99	+	2	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	exon	1583237	1583262	.	+	.	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
Phchi.S5	AUGUSTUS	stop_codon	1583263	1583265	.	+	0	transcript_id "Phchi.S5G013300.t1"; gene_id "Phchi.S5G013300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11901.t1 is derived from g15953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9181822	9182364	.	-	.	Phchi.S4G148300
Phchi.S4	AUGUSTUS	transcript	9181822	9182364	.	-	.	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	stop_codon	9181819	9181821	.	-	0	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	CDS	9181822	9181867	0.99	-	1	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	exon	9181822	9181867	.	-	.	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	intron	9181868	9182017	.	-	.	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	CDS	9182018	9182364	0.76	-	0	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	exon	9182018	9182364	.	-	.	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
Phchi.S4	AUGUSTUS	start_codon	9182362	9182364	.	-	0	transcript_id "Phchi.S4G148300.t1"; gene_id "Phchi.S4G148300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3631.t1 is derived from g800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4856121	4858105	.	-	.	Phchi.S1G079000
Phchi.S1	AUGUSTUS	transcript	4856121	4858105	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	stop_codon	4856118	4856120	.	-	0	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	CDS	4856121	4856352	0.96	-	1	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	exon	4856121	4856352	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	intron	4856353	4856500	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	CDS	4856501	4856862	1	-	0	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	exon	4856501	4856862	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	intron	4856863	4856969	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	CDS	4856970	4857290	1	-	0	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	exon	4856970	4857290	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	intron	4857291	4857394	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	CDS	4857395	4857647	1	-	1	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	exon	4857395	4857647	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	intron	4857648	4857737	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	CDS	4857738	4858105	0.57	-	0	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	exon	4857738	4858105	.	-	.	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
Phchi.S1	AUGUSTUS	start_codon	4858103	4858105	.	-	0	transcript_id "Phchi.S1G079000.t1"; gene_id "Phchi.S1G079000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6541.t1 is derived from g3713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23557275	23560457	.	-	.	Phchi.S1G370000
Phchi.S1	AUGUSTUS	transcript	23557275	23560457	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	stop_codon	23557272	23557274	.	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23557275	23557352	0.56	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23557275	23557352	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23557353	23557491	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23557492	23557545	1	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23557492	23557545	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23557546	23557650	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23557651	23557722	1	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23557651	23557722	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23557723	23557795	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23557796	23557883	1	-	1	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23557796	23557883	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23557884	23558007	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23558008	23558075	0.98	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23558008	23558075	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23558076	23558160	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23558161	23558286	0.52	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23558161	23558286	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23558287	23558401	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23558402	23558821	1	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23558402	23558821	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23558822	23558904	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23558905	23558989	1	-	1	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23558905	23558989	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23558990	23559093	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23559094	23559173	1	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23559094	23559173	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23559174	23559255	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23559256	23559333	1	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23559256	23559333	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23559334	23559458	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23559459	23559619	1	-	2	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23559459	23559619	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	intron	23559620	23559850	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	CDS	23559851	23560457	0.57	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	exon	23559851	23560457	.	-	.	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
Phchi.S1	AUGUSTUS	start_codon	23560455	23560457	.	-	0	transcript_id "Phchi.S1G370000.t1"; gene_id "Phchi.S1G370000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg350.t1 is derived from g10132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2537061	2538342	.	+	.	Phchi.S6G030900
Phchi.S6	AUGUSTUS	transcript	2537061	2538342	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	start_codon	2537061	2537063	.	+	0	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	CDS	2537061	2537162	0.63	+	0	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	exon	2537061	2537162	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	intron	2537163	2537307	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	CDS	2537308	2537553	0.99	+	0	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	exon	2537308	2537553	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	intron	2537554	2537653	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	CDS	2537654	2537749	1	+	0	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	exon	2537654	2537749	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	intron	2537750	2537885	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	CDS	2537886	2538034	1	+	0	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	exon	2537886	2538034	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	intron	2538035	2538119	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	CDS	2538120	2538342	1	+	1	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	exon	2538120	2538342	.	+	.	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
Phchi.S6	AUGUSTUS	stop_codon	2538343	2538345	.	+	0	transcript_id "Phchi.S6G030900.t1"; gene_id "Phchi.S6G030900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14048.t1 is derived from g12515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10481219	10482513	.	+	.	Phchi.S3G136700
Phchi.S3	AUGUSTUS	transcript	10481219	10482513	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	start_codon	10481219	10481221	.	+	0	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10481219	10481304	1	+	0	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10481219	10481304	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	intron	10481305	10481458	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10481459	10481509	1	+	1	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10481459	10481509	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	intron	10481510	10481623	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10481624	10481704	1	+	1	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10481624	10481704	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	intron	10481705	10481824	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10481825	10481891	1	+	1	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10481825	10481891	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	intron	10481892	10482004	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10482005	10482121	1	+	0	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10482005	10482121	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	intron	10482122	10482196	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10482197	10482357	1	+	0	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10482197	10482357	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	intron	10482358	10482443	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	CDS	10482444	10482513	1	+	1	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	exon	10482444	10482513	.	+	.	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
Phchi.S3	AUGUSTUS	stop_codon	10482514	10482516	.	+	0	transcript_id "Phchi.S3G136700.t1"; gene_id "Phchi.S3G136700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14315.t1 is derived from g12782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12066185	12067855	.	+	.	Phchi.S3G163400
Phchi.S3	AUGUSTUS	transcript	12066185	12067855	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	start_codon	12066185	12066187	.	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12066185	12066256	0.69	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12066185	12066256	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12066257	12066362	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12066363	12066593	0.96	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12066363	12066593	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12066594	12066699	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12066700	12066867	1	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12066700	12066867	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12066868	12066962	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12066963	12067092	1	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12066963	12067092	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12067093	12067188	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12067189	12067327	1	+	2	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12067189	12067327	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12067328	12067412	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12067413	12067533	1	+	1	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12067413	12067533	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12067534	12067632	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12067633	12067712	1	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12067633	12067712	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	intron	12067713	12067842	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	CDS	12067843	12067855	1	+	1	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	exon	12067843	12067855	.	+	.	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
Phchi.S3	AUGUSTUS	stop_codon	12067856	12067858	.	+	0	transcript_id "Phchi.S3G163400.t1"; gene_id "Phchi.S3G163400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3468.t1 is derived from g637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3907594	3909298	.	+	.	Phchi.S1G062700
Phchi.S1	AUGUSTUS	transcript	3907594	3909298	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	start_codon	3907594	3907596	.	+	0	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	CDS	3907594	3907846	0.41	+	0	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	exon	3907594	3907846	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	intron	3907847	3908063	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	CDS	3908064	3908092	0.5	+	2	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	exon	3908064	3908092	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	intron	3908093	3908263	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	CDS	3908264	3908636	0.65	+	0	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	exon	3908264	3908636	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	intron	3908637	3908732	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	CDS	3908733	3909298	0.96	+	2	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	exon	3908733	3909298	.	+	.	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
Phchi.S1	AUGUSTUS	stop_codon	3909299	3909301	.	+	0	transcript_id "Phchi.S1G062700.t1"; gene_id "Phchi.S1G062700"
# This transcript jg12895.t2 is derived from g11360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12896.t1 is derived from g11361.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3035530	3037407	.	-	.	Phchi.S3G021500
Phchi.S3	AUGUSTUS	transcript	3035530	3037407	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	stop_codon	3035527	3035529	.	-	0	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3035530	3035828	0.89	-	2	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3035530	3035828	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3035829	3036029	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3036030	3036644	0.64	-	2	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3036030	3036644	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3036645	3036923	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3036924	3036964	0.97	-	1	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3036924	3036964	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3036965	3037273	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3037274	3037305	0.81	-	0	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3037274	3037305	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3037306	3037383	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3037384	3037407	0.81	-	0	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3037384	3037407	.	-	.	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	start_codon	3037405	3037407	.	-	0	transcript_id "Phchi.S3G021500.t1"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	transcript	3035810	3037407	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	stop_codon	3035807	3035809	.	-	0	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3035810	3035828	0.8	-	1	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3035810	3035828	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3035829	3035905	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3035906	3036644	0.52	-	2	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3035906	3036644	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3036645	3036923	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3036924	3036964	1	-	1	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3036924	3036964	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3036965	3037273	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3037274	3037305	0.79	-	0	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3037274	3037305	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	intron	3037306	3037383	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	CDS	3037384	3037407	0.78	-	0	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	exon	3037384	3037407	.	-	.	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
Phchi.S3	AUGUSTUS	start_codon	3037405	3037407	.	-	0	transcript_id "Phchi.S3G021500.t2"; gene_id "Phchi.S3G021500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11004.t1 is derived from g15054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3597494	3602140	.	-	.	Phchi.S4G058600
Phchi.S4	AUGUSTUS	transcript	3597494	3602140	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	stop_codon	3597491	3597493	.	-	0	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	CDS	3597494	3597552	1	-	2	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	exon	3597494	3597552	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	intron	3597553	3597725	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	CDS	3597726	3599730	0.54	-	0	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	exon	3597726	3599730	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	intron	3599731	3599834	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	CDS	3599835	3601443	0.56	-	1	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	exon	3599835	3601443	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	intron	3601444	3601542	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	CDS	3601543	3601576	0.99	-	2	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	exon	3601543	3601576	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	intron	3601577	3601906	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	CDS	3601907	3601969	0.97	-	2	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	exon	3601907	3601969	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	intron	3601970	3602052	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	CDS	3602053	3602140	0.79	-	0	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	exon	3602053	3602140	.	-	.	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
Phchi.S4	AUGUSTUS	start_codon	3602138	3602140	.	-	0	transcript_id "Phchi.S4G058600.t1"; gene_id "Phchi.S4G058600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8917.t1 is derived from g6092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38664009	38665747	.	+	.	Phchi.S1G607600
Phchi.S1	AUGUSTUS	transcript	38664009	38665747	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	start_codon	38664009	38664011	.	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	CDS	38664009	38664131	0.97	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	exon	38664009	38664131	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	intron	38664132	38664245	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	CDS	38664246	38664362	0.66	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	exon	38664246	38664362	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	intron	38664363	38664470	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	CDS	38664471	38664569	0.99	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	exon	38664471	38664569	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	intron	38664570	38664651	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	CDS	38664652	38664840	1	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	exon	38664652	38664840	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	intron	38664841	38665044	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	CDS	38665045	38665226	1	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	exon	38665045	38665226	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	intron	38665227	38665341	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	CDS	38665342	38665747	0.85	+	1	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	exon	38665342	38665747	.	+	.	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
Phchi.S1	AUGUSTUS	stop_codon	38665748	38665750	.	+	0	transcript_id "Phchi.S1G607600.t1"; gene_id "Phchi.S1G607600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8735.t1 is derived from g5910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37718575	37720850	.	-	.	Phchi.S1G589400
Phchi.S1	AUGUSTUS	transcript	37718575	37720850	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	stop_codon	37718572	37718574	.	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37718575	37718681	0.86	-	2	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37718575	37718681	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37718682	37718772	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37718773	37718876	1	-	1	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37718773	37718876	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37718877	37718967	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37718968	37719067	1	-	2	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37718968	37719067	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37719068	37719151	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37719152	37719249	0.96	-	1	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37719152	37719249	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37719250	37719361	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37719362	37719414	0.96	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37719362	37719414	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37719415	37719507	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37719508	37719567	1	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37719508	37719567	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37719568	37719647	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37719648	37719719	1	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37719648	37719719	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37719720	37719946	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37719947	37720012	1	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37719947	37720012	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37720013	37720100	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37720101	37720193	1	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37720101	37720193	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37720194	37720280	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37720281	37720348	1	-	2	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37720281	37720348	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37720349	37720426	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37720427	37720501	0.99	-	2	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37720427	37720501	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	intron	37720502	37720609	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	CDS	37720610	37720850	1	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	exon	37720610	37720850	.	-	.	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
Phchi.S1	AUGUSTUS	start_codon	37720848	37720850	.	-	0	transcript_id "Phchi.S1G589400.t1"; gene_id "Phchi.S1G589400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11983.t1 is derived from g7658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	342565	344023	.	-	.	Phchi.S2G006300
Phchi.S2	AUGUSTUS	transcript	342565	344023	.	-	.	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	stop_codon	342562	342564	.	-	0	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	CDS	342565	342839	0.12	-	2	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	exon	342565	342839	.	-	.	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	intron	342840	342954	.	-	.	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	CDS	342955	343075	0.18	-	0	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	exon	342955	343075	.	-	.	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	intron	343076	343945	.	-	.	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	CDS	343946	344023	0.04	-	0	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	exon	343946	344023	.	-	.	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
Phchi.S2	AUGUSTUS	start_codon	344021	344023	.	-	0	transcript_id "Phchi.S2G006300.t1"; gene_id "Phchi.S2G006300"
# This transcript jg4720.t2 is derived from g1890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4721.t1 is derived from g1891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12471843	12476339	.	-	.	Phchi.S1G188000
Phchi.S1	AUGUSTUS	transcript	12471843	12476339	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	stop_codon	12471840	12471842	.	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12471843	12472459	0.75	-	2	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12471843	12472459	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12472460	12472566	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12472567	12472768	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12472567	12472768	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12472769	12472857	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12472858	12472938	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12472858	12472938	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12472939	12473020	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12473021	12473233	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12473021	12473233	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12473234	12473311	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12473312	12473521	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12473312	12473521	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12473522	12473609	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12473610	12473834	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12473610	12473834	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12473835	12473931	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12473932	12474093	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12473932	12474093	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12474094	12474199	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12474200	12474427	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12474200	12474427	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12474428	12474564	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12474565	12474594	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12474565	12474594	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12474595	12474708	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12474709	12475077	0.98	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12474709	12475077	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12475078	12475176	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12475177	12475392	0.99	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12475177	12475392	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12475393	12475676	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12475677	12476158	1	-	2	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12475677	12476158	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	intron	12476159	12476293	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	CDS	12476294	12476339	1	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	exon	12476294	12476339	.	-	.	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
Phchi.S1	AUGUSTUS	start_codon	12476337	12476339	.	-	0	transcript_id "Phchi.S1G188000.t1"; gene_id "Phchi.S1G188000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13146.t1 is derived from g11611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4388803	4391067	.	-	.	Phchi.S3G046500
Phchi.S3	AUGUSTUS	transcript	4388803	4391067	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	stop_codon	4388800	4388802	.	-	0	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4388803	4388833	0.63	-	1	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4388803	4388833	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4388834	4388929	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4388930	4389034	0.87	-	1	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4388930	4389034	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4389035	4389109	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4389110	4389368	0.93	-	2	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4389110	4389368	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4389369	4389454	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4389455	4389592	0.99	-	2	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4389455	4389592	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4389593	4389676	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4389677	4389814	1	-	2	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4389677	4389814	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4389815	4389890	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4389891	4390023	1	-	0	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4389891	4390023	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4390024	4390102	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4390103	4390308	1	-	2	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4390103	4390308	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4390309	4390462	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4390463	4390590	1	-	1	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4390463	4390590	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4390591	4390689	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4390690	4390796	0.79	-	0	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4390690	4390796	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	intron	4390797	4390926	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	CDS	4390927	4391067	0.92	-	0	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	exon	4390927	4391067	.	-	.	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
Phchi.S3	AUGUSTUS	start_codon	4391065	4391067	.	-	0	transcript_id "Phchi.S3G046500.t1"; gene_id "Phchi.S3G046500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9506.t1 is derived from g6682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42105362	42110312	.	+	.	Phchi.S1G666500
Phchi.S1	AUGUSTUS	transcript	42105362	42110312	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	start_codon	42105362	42105364	.	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42105362	42105764	0.68	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42105362	42105764	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42105765	42105861	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42105862	42105966	1	+	2	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42105862	42105966	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42105967	42106053	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42106054	42106214	1	+	2	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42106054	42106214	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42106215	42106292	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42106293	42106385	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42106293	42106385	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42106386	42106473	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42106474	42106659	0.96	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42106474	42106659	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42106660	42106764	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42106765	42107071	0.95	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42106765	42107071	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42107072	42107181	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42107182	42107324	1	+	2	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42107182	42107324	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42107325	42107417	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42107418	42107474	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42107418	42107474	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42107475	42107561	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42107562	42107641	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42107562	42107641	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42107642	42107745	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42107746	42107821	1	+	1	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42107746	42107821	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42107822	42107944	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42107945	42108130	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42107945	42108130	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42108131	42108226	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42108227	42108294	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42108227	42108294	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42108295	42108428	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42108429	42108547	0.96	+	1	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42108429	42108547	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42108548	42108654	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42108655	42108776	0.99	+	2	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42108655	42108776	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42108777	42108893	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42108894	42108992	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42108894	42108992	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42108993	42109090	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42109091	42109570	0.99	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42109091	42109570	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42109571	42109688	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42109689	42109787	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42109689	42109787	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42109788	42109888	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42109889	42110131	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42109889	42110131	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	intron	42110132	42110228	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	CDS	42110229	42110312	1	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	exon	42110229	42110312	.	+	.	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
Phchi.S1	AUGUSTUS	stop_codon	42110313	42110315	.	+	0	transcript_id "Phchi.S1G666500.t1"; gene_id "Phchi.S1G666500"
# This transcript jg8682.t2 is derived from g5857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8683.t1 is derived from g5858.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37438136	37440878	.	-	.	Phchi.S1G584200
Phchi.S1	AUGUSTUS	transcript	37438136	37440878	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	stop_codon	37438133	37438135	.	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37438136	37438200	1	-	2	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37438136	37438200	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37438201	37438287	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37438288	37438450	1	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37438288	37438450	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37438451	37438525	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37438526	37438674	1	-	2	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37438526	37438674	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37438675	37438778	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37438779	37438916	1	-	2	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37438779	37438916	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37438917	37439046	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37439047	37439158	1	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37439047	37439158	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37439159	37439250	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37439251	37439314	1	-	1	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37439251	37439314	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37439315	37439449	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37439450	37439796	1	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37439450	37439796	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37439797	37439890	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37439891	37439896	1	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37439891	37439896	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37439897	37440149	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37440150	37440362	0.98	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37440150	37440362	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37440363	37440485	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37440486	37440591	1	-	1	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37440486	37440591	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	intron	37440592	37440678	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	CDS	37440679	37440878	0.86	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	exon	37440679	37440878	.	-	.	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
Phchi.S1	AUGUSTUS	start_codon	37440876	37440878	.	-	0	transcript_id "Phchi.S1G584200.t1"; gene_id "Phchi.S1G584200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11942.t1 is derived from g7617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	137962	141404	.	+	.	Phchi.S2G002200
Phchi.S2	AUGUSTUS	transcript	137962	141404	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	start_codon	137962	137964	.	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	137962	138048	1	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	137962	138048	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	138049	138148	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	138149	138328	1	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	138149	138328	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	138329	138432	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	138433	138464	1	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	138433	138464	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	138465	138544	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	138545	138589	1	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	138545	138589	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	138590	138785	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	138786	138854	1	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	138786	138854	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	138855	138949	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	138950	139184	0.97	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	138950	139184	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	139185	139354	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	139355	139521	1	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	139355	139521	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	139522	139687	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	139688	139772	1	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	139688	139772	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	139773	139927	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	139928	140050	0.91	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	139928	140050	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	140051	140166	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	140167	140276	0.98	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	140167	140276	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	140277	140385	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	140386	140517	1	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	140386	140517	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	140518	140638	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	140639	140741	1	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	140639	140741	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	140742	140851	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	140852	140970	0.82	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	140852	140970	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	intron	140971	141082	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	CDS	141083	141404	1	+	1	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	exon	141083	141404	.	+	.	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
Phchi.S2	AUGUSTUS	stop_codon	141405	141407	.	+	0	transcript_id "Phchi.S2G002200.t1"; gene_id "Phchi.S2G002200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8541.t1 is derived from g5716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36547107	36549529	.	+	.	Phchi.S1G570000
Phchi.S1	AUGUSTUS	transcript	36547107	36549529	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	start_codon	36547107	36547109	.	+	0	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	CDS	36547107	36547159	0.92	+	0	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	exon	36547107	36547159	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	intron	36547160	36547248	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	CDS	36547249	36547327	0.76	+	1	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	exon	36547249	36547327	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	intron	36547328	36547502	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	CDS	36547503	36547595	0.44	+	0	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	exon	36547503	36547595	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	intron	36547596	36547727	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	CDS	36547728	36548523	0.55	+	0	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	exon	36547728	36548523	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	intron	36548524	36548841	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	CDS	36548842	36549398	0.77	+	2	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	exon	36548842	36549398	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	intron	36549399	36549502	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	CDS	36549503	36549529	0.82	+	0	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	exon	36549503	36549529	.	+	.	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
Phchi.S1	AUGUSTUS	stop_codon	36549530	36549532	.	+	0	transcript_id "Phchi.S1G570000.t1"; gene_id "Phchi.S1G570000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10331.t1 is derived from g7507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47208490	47211358	.	+	.	Phchi.S1G749000
Phchi.S1	AUGUSTUS	transcript	47208490	47211358	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	start_codon	47208490	47208492	.	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47208490	47208806	0.35	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47208490	47208806	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47208807	47208902	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47208903	47208978	0.59	+	1	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47208903	47208978	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47208979	47209084	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47209085	47209207	0.98	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47209085	47209207	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47209208	47209320	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47209321	47209413	1	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47209321	47209413	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47209414	47209540	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47209541	47209673	1	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47209541	47209673	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47209674	47209765	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47209766	47209847	1	+	2	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47209766	47209847	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47209848	47209958	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47209959	47210091	1	+	1	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47209959	47210091	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47210092	47210211	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47210212	47210543	0.69	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47210212	47210543	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47210544	47210645	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47210646	47210955	0.74	+	1	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47210646	47210955	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	intron	47210956	47211049	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	CDS	47211050	47211358	0.92	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	exon	47211050	47211358	.	+	.	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
Phchi.S1	AUGUSTUS	stop_codon	47211359	47211361	.	+	0	transcript_id "Phchi.S1G749000.t1"; gene_id "Phchi.S1G749000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4425.t1 is derived from g1594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10436880	10437979	.	-	.	Phchi.S1G158400
Phchi.S1	AUGUSTUS	transcript	10436880	10437979	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	stop_codon	10436877	10436879	.	-	0	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	CDS	10436880	10437165	0.91	-	1	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	exon	10436880	10437165	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	intron	10437166	10437278	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	CDS	10437279	10437577	0.93	-	0	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	exon	10437279	10437577	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	intron	10437578	10437650	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	CDS	10437651	10437759	0.95	-	1	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	exon	10437651	10437759	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	intron	10437760	10437890	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	CDS	10437891	10437979	0.88	-	0	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	exon	10437891	10437979	.	-	.	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
Phchi.S1	AUGUSTUS	start_codon	10437977	10437979	.	-	0	transcript_id "Phchi.S1G158400.t1"; gene_id "Phchi.S1G158400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9552.t1 is derived from g6728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42422699	42423897	.	-	.	Phchi.S1G671100
Phchi.S1	AUGUSTUS	transcript	42422699	42423897	.	-	.	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	stop_codon	42422696	42422698	.	-	0	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	CDS	42422699	42423127	0.29	-	0	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	exon	42422699	42423127	.	-	.	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	intron	42423128	42423266	.	-	.	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	CDS	42423267	42423438	0.34	-	1	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	exon	42423267	42423438	.	-	.	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	intron	42423439	42423814	.	-	.	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	CDS	42423815	42423897	0.73	-	0	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	exon	42423815	42423897	.	-	.	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
Phchi.S1	AUGUSTUS	start_codon	42423895	42423897	.	-	0	transcript_id "Phchi.S1G671100.t1"; gene_id "Phchi.S1G671100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3115.t1 is derived from g284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1802440	1803351	.	+	.	Phchi.S1G027400
Phchi.S1	AUGUSTUS	transcript	1802440	1803351	.	+	.	transcript_id "Phchi.S1G027400.t1"; gene_id "Phchi.S1G027400"
Phchi.S1	AUGUSTUS	start_codon	1802440	1802442	.	+	0	transcript_id "Phchi.S1G027400.t1"; gene_id "Phchi.S1G027400"
Phchi.S1	AUGUSTUS	CDS	1802440	1803351	0.49	+	0	transcript_id "Phchi.S1G027400.t1"; gene_id "Phchi.S1G027400"
Phchi.S1	AUGUSTUS	exon	1802440	1803351	.	+	.	transcript_id "Phchi.S1G027400.t1"; gene_id "Phchi.S1G027400"
Phchi.S1	AUGUSTUS	stop_codon	1803352	1803354	.	+	0	transcript_id "Phchi.S1G027400.t1"; gene_id "Phchi.S1G027400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13258.t1 is derived from g11723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4950980	4952684	.	+	.	Phchi.S3G057700
Phchi.S3	AUGUSTUS	transcript	4950980	4952684	.	+	.	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	start_codon	4950980	4950982	.	+	0	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	CDS	4950980	4951190	1	+	0	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	exon	4950980	4951190	.	+	.	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	intron	4951191	4951284	.	+	.	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	CDS	4951285	4952684	0.55	+	2	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	exon	4951285	4952684	.	+	.	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
Phchi.S3	AUGUSTUS	stop_codon	4952685	4952687	.	+	0	transcript_id "Phchi.S3G057700.t1"; gene_id "Phchi.S3G057700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5895.t1 is derived from g3065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19637483	19640267	.	-	.	Phchi.S1G305400
Phchi.S1	AUGUSTUS	transcript	19637483	19640267	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	stop_codon	19637480	19637482	.	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19637483	19637773	1	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19637483	19637773	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	intron	19637774	19637868	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19637869	19638210	1	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19637869	19638210	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	intron	19638211	19638348	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19638349	19638681	1	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19638349	19638681	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	intron	19638682	19638792	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19638793	19639286	1	-	2	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19638793	19639286	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	intron	19639287	19639558	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19639559	19639632	1	-	1	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19639559	19639632	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	intron	19639633	19639792	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19639793	19639848	1	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19639793	19639848	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	intron	19639849	19640135	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	CDS	19640136	19640267	1	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	exon	19640136	19640267	.	-	.	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
Phchi.S1	AUGUSTUS	start_codon	19640265	19640267	.	-	0	transcript_id "Phchi.S1G305400.t1"; gene_id "Phchi.S1G305400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13198.t1 is derived from g11663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4645179	4646173	.	-	.	Phchi.S3G051700
Phchi.S3	AUGUSTUS	transcript	4645179	4646173	.	-	.	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	stop_codon	4645176	4645178	.	-	0	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	CDS	4645179	4645242	0.99	-	1	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	exon	4645179	4645242	.	-	.	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	intron	4645243	4645336	.	-	.	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	CDS	4645337	4645715	1	-	2	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	exon	4645337	4645715	.	-	.	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	intron	4645716	4645866	.	-	.	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	CDS	4645867	4646173	0.5	-	0	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	exon	4645867	4646173	.	-	.	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
Phchi.S3	AUGUSTUS	start_codon	4646171	4646173	.	-	0	transcript_id "Phchi.S3G051700.t1"; gene_id "Phchi.S3G051700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9340.t1 is derived from g6515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41016311	41017024	.	+	.	Phchi.S1G649900
Phchi.S1	AUGUSTUS	transcript	41016311	41017024	.	+	.	transcript_id "Phchi.S1G649900.t1"; gene_id "Phchi.S1G649900"
Phchi.S1	AUGUSTUS	start_codon	41016311	41016313	.	+	0	transcript_id "Phchi.S1G649900.t1"; gene_id "Phchi.S1G649900"
Phchi.S1	AUGUSTUS	CDS	41016311	41017024	1	+	0	transcript_id "Phchi.S1G649900.t1"; gene_id "Phchi.S1G649900"
Phchi.S1	AUGUSTUS	exon	41016311	41017024	.	+	.	transcript_id "Phchi.S1G649900.t1"; gene_id "Phchi.S1G649900"
Phchi.S1	AUGUSTUS	stop_codon	41017025	41017027	.	+	0	transcript_id "Phchi.S1G649900.t1"; gene_id "Phchi.S1G649900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14842.t1 is derived from g13310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14960301	14960534	.	+	.	Phchi.S3G216100
Phchi.S3	AUGUSTUS	transcript	14960301	14960534	.	+	.	transcript_id "Phchi.S3G216100.t1"; gene_id "Phchi.S3G216100"
Phchi.S3	AUGUSTUS	start_codon	14960301	14960303	.	+	0	transcript_id "Phchi.S3G216100.t1"; gene_id "Phchi.S3G216100"
Phchi.S3	AUGUSTUS	CDS	14960301	14960534	0.52	+	0	transcript_id "Phchi.S3G216100.t1"; gene_id "Phchi.S3G216100"
Phchi.S3	AUGUSTUS	exon	14960301	14960534	.	+	.	transcript_id "Phchi.S3G216100.t1"; gene_id "Phchi.S3G216100"
Phchi.S3	AUGUSTUS	stop_codon	14960535	14960537	.	+	0	transcript_id "Phchi.S3G216100.t1"; gene_id "Phchi.S3G216100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3158.t1 is derived from g327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2017180	2017551	.	+	.	Phchi.S1G031700
Phchi.S1	AUGUSTUS	transcript	2017180	2017551	.	+	.	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	start_codon	2017180	2017182	.	+	0	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	CDS	2017180	2017351	0.83	+	0	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	exon	2017180	2017351	.	+	.	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	intron	2017352	2017438	.	+	.	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	CDS	2017439	2017551	1	+	2	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	exon	2017439	2017551	.	+	.	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
Phchi.S1	AUGUSTUS	stop_codon	2017552	2017554	.	+	0	transcript_id "Phchi.S1G031700.t1"; gene_id "Phchi.S1G031700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg576.t1 is derived from g10358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4251245	4251847	.	+	.	Phchi.S6G053500
Phchi.S6	AUGUSTUS	transcript	4251245	4251847	.	+	.	transcript_id "Phchi.S6G053500.t1"; gene_id "Phchi.S6G053500"
Phchi.S6	AUGUSTUS	start_codon	4251245	4251247	.	+	0	transcript_id "Phchi.S6G053500.t1"; gene_id "Phchi.S6G053500"
Phchi.S6	AUGUSTUS	CDS	4251245	4251847	0.69	+	0	transcript_id "Phchi.S6G053500.t1"; gene_id "Phchi.S6G053500"
Phchi.S6	AUGUSTUS	exon	4251245	4251847	.	+	.	transcript_id "Phchi.S6G053500.t1"; gene_id "Phchi.S6G053500"
Phchi.S6	AUGUSTUS	stop_codon	4251848	4251850	.	+	0	transcript_id "Phchi.S6G053500.t1"; gene_id "Phchi.S6G053500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13257.t1 is derived from g11722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4948773	4950731	.	-	.	Phchi.S3G057600
Phchi.S3	AUGUSTUS	transcript	4948773	4950731	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	stop_codon	4948770	4948772	.	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4948773	4948901	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4948773	4948901	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4948902	4948987	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4948988	4949047	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4948988	4949047	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4949048	4949155	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4949156	4949233	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4949156	4949233	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4949234	4949351	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4949352	4949429	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4949352	4949429	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4949430	4949515	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4949516	4949592	1	-	2	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4949516	4949592	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4949593	4949747	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4949748	4949856	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4949748	4949856	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4949857	4949960	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4949961	4950026	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4949961	4950026	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4950027	4950168	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4950169	4950315	1	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4950169	4950315	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	intron	4950316	4950446	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	CDS	4950447	4950731	0.58	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	exon	4950447	4950731	.	-	.	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
Phchi.S3	AUGUSTUS	start_codon	4950729	4950731	.	-	0	transcript_id "Phchi.S3G057600.t1"; gene_id "Phchi.S3G057600"
# This transcript jg3934.t2 is derived from g1103.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg3934.t3 is derived from g1103.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3935.t1 is derived from g1104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6563295	6564216	.	-	.	Phchi.S1G109400
Phchi.S1	AUGUSTUS	transcript	6563295	6564216	.	-	.	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	stop_codon	6563292	6563294	.	-	0	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	CDS	6563295	6563489	0.95	-	0	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	exon	6563295	6563489	.	-	.	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	intron	6563490	6563569	.	-	.	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	CDS	6563570	6563833	0.99	-	0	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	exon	6563570	6563833	.	-	.	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	intron	6563834	6563943	.	-	.	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	CDS	6563944	6564216	0.83	-	0	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	exon	6563944	6564216	.	-	.	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
Phchi.S1	AUGUSTUS	start_codon	6564214	6564216	.	-	0	transcript_id "Phchi.S1G109400.t1"; gene_id "Phchi.S1G109400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15919.t1 is derived from g14389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22219529	22220700	.	+	.	Phchi.S3G323800
Phchi.S3	AUGUSTUS	transcript	22219529	22220700	.	+	.	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	start_codon	22219529	22219531	.	+	0	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	CDS	22219529	22219810	0.98	+	0	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	exon	22219529	22219810	.	+	.	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	intron	22219811	22219952	.	+	.	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	CDS	22219953	22220079	1	+	0	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	exon	22219953	22220079	.	+	.	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	intron	22220080	22220230	.	+	.	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	CDS	22220231	22220700	0.98	+	2	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	exon	22220231	22220700	.	+	.	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
Phchi.S3	AUGUSTUS	stop_codon	22220701	22220703	.	+	0	transcript_id "Phchi.S3G323800.t1"; gene_id "Phchi.S3G323800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12998.t1 is derived from g11463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3567279	3569153	.	+	.	Phchi.S3G031700
Phchi.S3	AUGUSTUS	transcript	3567279	3569153	.	+	.	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	start_codon	3567279	3567281	.	+	0	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	CDS	3567279	3568272	0.76	+	0	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	exon	3567279	3568272	.	+	.	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	intron	3568273	3568536	.	+	.	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	CDS	3568537	3569153	0.33	+	2	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	exon	3568537	3569153	.	+	.	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
Phchi.S3	AUGUSTUS	stop_codon	3569154	3569156	.	+	0	transcript_id "Phchi.S3G031700.t1"; gene_id "Phchi.S3G031700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11933.t1 is derived from g7608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	90755	94015	.	-	.	Phchi.S2G001300
Phchi.S2	AUGUSTUS	transcript	90755	94015	.	-	.	transcript_id "Phchi.S2G001300.t1"; gene_id "Phchi.S2G001300"
Phchi.S2	AUGUSTUS	stop_codon	90752	90754	.	-	0	transcript_id "Phchi.S2G001300.t1"; gene_id "Phchi.S2G001300"
Phchi.S2	AUGUSTUS	CDS	90755	94015	0.97	-	0	transcript_id "Phchi.S2G001300.t1"; gene_id "Phchi.S2G001300"
Phchi.S2	AUGUSTUS	exon	90755	94015	.	-	.	transcript_id "Phchi.S2G001300.t1"; gene_id "Phchi.S2G001300"
Phchi.S2	AUGUSTUS	start_codon	94013	94015	.	-	0	transcript_id "Phchi.S2G001300.t1"; gene_id "Phchi.S2G001300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8148.t1 is derived from g5323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34073176	34074123	.	+	.	Phchi.S1G530700
Phchi.S1	AUGUSTUS	transcript	34073176	34074123	.	+	.	transcript_id "Phchi.S1G530700.t1"; gene_id "Phchi.S1G530700"
Phchi.S1	AUGUSTUS	start_codon	34073176	34073178	.	+	0	transcript_id "Phchi.S1G530700.t1"; gene_id "Phchi.S1G530700"
Phchi.S1	AUGUSTUS	CDS	34073176	34074123	0.95	+	0	transcript_id "Phchi.S1G530700.t1"; gene_id "Phchi.S1G530700"
Phchi.S1	AUGUSTUS	exon	34073176	34074123	.	+	.	transcript_id "Phchi.S1G530700.t1"; gene_id "Phchi.S1G530700"
Phchi.S1	AUGUSTUS	stop_codon	34074124	34074126	.	+	0	transcript_id "Phchi.S1G530700.t1"; gene_id "Phchi.S1G530700"
# This transcript jg5494.t2 is derived from g2664.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5495.t1 is derived from g2665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17121313	17122665	.	-	.	Phchi.S1G265400
Phchi.S1	AUGUSTUS	transcript	17121313	17122665	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	stop_codon	17121310	17121312	.	-	0	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	CDS	17121313	17121358	1	-	1	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	exon	17121313	17121358	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	intron	17121359	17121435	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	CDS	17121436	17121652	1	-	2	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	exon	17121436	17121652	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	intron	17121653	17121729	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	CDS	17121730	17121818	1	-	1	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	exon	17121730	17121818	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	intron	17121819	17121931	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	CDS	17121932	17122665	0.89	-	0	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	exon	17121932	17122665	.	-	.	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
Phchi.S1	AUGUSTUS	start_codon	17122663	17122665	.	-	0	transcript_id "Phchi.S1G265400.t1"; gene_id "Phchi.S1G265400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7062.t1 is derived from g4234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26686513	26688940	.	+	.	Phchi.S1G422100
Phchi.S1	AUGUSTUS	transcript	26686513	26688940	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	start_codon	26686513	26686515	.	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26686513	26686834	0.79	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26686513	26686834	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26686835	26686958	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26686959	26687043	1	+	2	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26686959	26687043	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26687044	26687133	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26687134	26687199	1	+	1	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26687134	26687199	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26687200	26687321	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26687322	26687397	1	+	1	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26687322	26687397	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26687398	26687491	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26687492	26687547	1	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26687492	26687547	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26687548	26687738	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26687739	26687823	1	+	1	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26687739	26687823	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26687824	26687938	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26687939	26687999	1	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26687939	26687999	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26688000	26688068	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26688069	26688121	1	+	2	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26688069	26688121	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26688122	26688231	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26688232	26688302	1	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26688232	26688302	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26688303	26688397	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26688398	26688470	0.99	+	1	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26688398	26688470	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26688471	26688582	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26688583	26688687	1	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26688583	26688687	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	intron	26688688	26688781	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	CDS	26688782	26688940	0.83	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	exon	26688782	26688940	.	+	.	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
Phchi.S1	AUGUSTUS	stop_codon	26688941	26688943	.	+	0	transcript_id "Phchi.S1G422100.t1"; gene_id "Phchi.S1G422100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15179.t1 is derived from g13647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17426813	17429651	.	-	.	Phchi.S3G249800
Phchi.S3	AUGUSTUS	transcript	17426813	17429651	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	stop_codon	17426810	17426812	.	-	0	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17426813	17426954	1	-	1	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17426813	17426954	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	intron	17426955	17427081	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17427082	17427182	1	-	0	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17427082	17427182	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	intron	17427183	17427487	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17427488	17427547	1	-	0	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17427488	17427547	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	intron	17427548	17427632	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17427633	17427729	1	-	1	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17427633	17427729	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	intron	17427730	17427835	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17427836	17427971	1	-	2	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17427836	17427971	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	intron	17427972	17428108	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17428109	17428402	1	-	2	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17428109	17428402	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	intron	17428403	17428540	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	CDS	17428541	17429651	1	-	0	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	exon	17428541	17429651	.	-	.	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
Phchi.S3	AUGUSTUS	start_codon	17429649	17429651	.	-	0	transcript_id "Phchi.S3G249800.t1"; gene_id "Phchi.S3G249800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg481.t1 is derived from g10263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3359187	3360023	.	+	.	Phchi.S6G044000
Phchi.S6	AUGUSTUS	transcript	3359187	3360023	.	+	.	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	start_codon	3359187	3359189	.	+	0	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	CDS	3359187	3359892	0.55	+	0	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	exon	3359187	3359892	.	+	.	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	intron	3359893	3359997	.	+	.	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	CDS	3359998	3360023	0.63	+	2	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	exon	3359998	3360023	.	+	.	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
Phchi.S6	AUGUSTUS	stop_codon	3360024	3360026	.	+	0	transcript_id "Phchi.S6G044000.t1"; gene_id "Phchi.S6G044000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5724.t1 is derived from g2894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18562556	18564202	.	+	.	Phchi.S1G288300
Phchi.S1	AUGUSTUS	transcript	18562556	18564202	.	+	.	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	start_codon	18562556	18562558	.	+	0	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	CDS	18562556	18562739	0.97	+	0	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	exon	18562556	18562739	.	+	.	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	intron	18562740	18562964	.	+	.	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	CDS	18562965	18564202	0.99	+	2	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	exon	18562965	18564202	.	+	.	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
Phchi.S1	AUGUSTUS	stop_codon	18564203	18564205	.	+	0	transcript_id "Phchi.S1G288300.t1"; gene_id "Phchi.S1G288300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2014.t1 is derived from g8934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4463006	4463797	.	+	.	Phchi.S5G062300
Phchi.S5	AUGUSTUS	transcript	4463006	4463797	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	start_codon	4463006	4463008	.	+	0	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	CDS	4463006	4463258	0.72	+	0	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	exon	4463006	4463258	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	intron	4463259	4463346	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	CDS	4463347	4463452	1	+	2	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	exon	4463347	4463452	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	intron	4463453	4463534	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	CDS	4463535	4463634	1	+	1	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	exon	4463535	4463634	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	intron	4463635	4463707	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	CDS	4463708	4463797	1	+	0	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	exon	4463708	4463797	.	+	.	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
Phchi.S5	AUGUSTUS	stop_codon	4463798	4463800	.	+	0	transcript_id "Phchi.S5G062300.t1"; gene_id "Phchi.S5G062300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11334.t1 is derived from g15384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5611957	5614072	.	-	.	Phchi.S4G091600
Phchi.S4	AUGUSTUS	transcript	5611957	5614072	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	stop_codon	5611954	5611956	.	-	0	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	CDS	5611957	5612453	1	-	2	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	exon	5611957	5612453	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	intron	5612454	5612547	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	CDS	5612548	5612814	1	-	2	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	exon	5612548	5612814	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	intron	5612815	5612925	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	CDS	5612926	5613211	1	-	0	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	exon	5612926	5613211	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	intron	5613212	5613295	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	CDS	5613296	5613591	1	-	2	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	exon	5613296	5613591	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	intron	5613592	5613687	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	CDS	5613688	5613873	0.99	-	2	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	exon	5613688	5613873	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	intron	5613874	5614008	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	CDS	5614009	5614072	0.42	-	0	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	exon	5614009	5614072	.	-	.	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
Phchi.S4	AUGUSTUS	start_codon	5614070	5614072	.	-	0	transcript_id "Phchi.S4G091600.t1"; gene_id "Phchi.S4G091600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7523.t1 is derived from g4697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29866556	29868497	.	+	.	Phchi.S1G468200
Phchi.S1	AUGUSTUS	transcript	29866556	29868497	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	start_codon	29866556	29866558	.	+	0	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	CDS	29866556	29867194	0.99	+	0	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	exon	29866556	29867194	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	intron	29867195	29867320	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	CDS	29867321	29868107	0.84	+	0	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	exon	29867321	29868107	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	intron	29868108	29868236	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	CDS	29868237	29868361	0.81	+	2	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	exon	29868237	29868361	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	intron	29868362	29868461	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	CDS	29868462	29868497	0.36	+	0	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	exon	29868462	29868497	.	+	.	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
Phchi.S1	AUGUSTUS	stop_codon	29868498	29868500	.	+	0	transcript_id "Phchi.S1G468200.t1"; gene_id "Phchi.S1G468200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4083.t1 is derived from g1252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7701310	7703450	.	-	.	Phchi.S1G124200
Phchi.S1	AUGUSTUS	transcript	7701310	7703450	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	stop_codon	7701307	7701309	.	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7701310	7701807	0.77	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7701310	7701807	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7701808	7701970	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7701971	7702045	1	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7701971	7702045	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7702046	7702137	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7702138	7702269	1	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7702138	7702269	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7702270	7702367	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7702368	7702439	1	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7702368	7702439	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7702440	7702525	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7702526	7702571	1	-	1	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7702526	7702571	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7702572	7702664	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7702665	7702810	1	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7702665	7702810	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7702811	7702895	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7702896	7703002	0.96	-	2	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7702896	7703002	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7703003	7703142	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7703143	7703208	0.95	-	2	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7703143	7703208	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	intron	7703209	7703347	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	CDS	7703348	7703450	0.83	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	exon	7703348	7703450	.	-	.	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
Phchi.S1	AUGUSTUS	start_codon	7703448	7703450	.	-	0	transcript_id "Phchi.S1G124200.t1"; gene_id "Phchi.S1G124200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4140.t1 is derived from g1309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8473139	8474221	.	-	.	Phchi.S1G129900
Phchi.S1	AUGUSTUS	transcript	8473139	8474221	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	stop_codon	8473136	8473138	.	-	0	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	CDS	8473139	8473233	0.69	-	2	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	exon	8473139	8473233	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	intron	8473234	8473337	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	CDS	8473338	8473464	1	-	0	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	exon	8473338	8473464	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	intron	8473465	8473571	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	CDS	8473572	8473631	0.99	-	0	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	exon	8473572	8473631	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	intron	8473632	8473758	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	CDS	8473759	8473962	0.99	-	0	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	exon	8473759	8473962	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	intron	8473963	8474122	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	CDS	8474123	8474221	0.99	-	0	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	exon	8474123	8474221	.	-	.	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
Phchi.S1	AUGUSTUS	start_codon	8474219	8474221	.	-	0	transcript_id "Phchi.S1G129900.t1"; gene_id "Phchi.S1G129900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6709.t1 is derived from g3881.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24648220	24650668	.	+	.	Phchi.S1G386800
Phchi.S1	AUGUSTUS	transcript	24648220	24650668	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	start_codon	24648220	24648222	.	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24648220	24648327	1	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24648220	24648327	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24648328	24648906	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24648907	24649008	1	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24648907	24649008	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649009	24649125	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649126	24649238	0.99	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649126	24649238	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649239	24649346	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649347	24649416	0.93	+	1	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649347	24649416	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649417	24649500	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649501	24649578	1	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649501	24649578	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649579	24649795	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649796	24649909	1	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649796	24649909	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649910	24650028	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650029	24650123	0.99	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650029	24650123	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24650124	24650232	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650233	24650312	1	+	1	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650233	24650312	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24650313	24650398	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650399	24650458	1	+	2	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650399	24650458	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24650459	24650543	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650544	24650668	1	+	2	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650544	24650668	.	+	.	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	stop_codon	24650669	24650671	.	+	0	transcript_id "Phchi.S1G386800.t1"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	transcript	24648220	24650668	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	start_codon	24648220	24648222	.	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24648220	24648327	0.59	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24648220	24648327	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24648328	24648418	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24648419	24648439	0.47	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24648419	24648439	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24648440	24648903	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24648904	24649008	0.45	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24648904	24649008	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649009	24649125	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649126	24649238	1	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649126	24649238	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649239	24649346	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649347	24649416	0.93	+	1	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649347	24649416	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649417	24649500	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649501	24649578	1	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649501	24649578	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649579	24649795	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24649796	24649909	1	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24649796	24649909	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24649910	24650028	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650029	24650123	0.98	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650029	24650123	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24650124	24650232	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650233	24650312	1	+	1	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650233	24650312	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24650313	24650398	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650399	24650458	1	+	2	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650399	24650458	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	intron	24650459	24650543	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	CDS	24650544	24650668	1	+	2	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	exon	24650544	24650668	.	+	.	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
Phchi.S1	AUGUSTUS	stop_codon	24650669	24650671	.	+	0	transcript_id "Phchi.S1G386800.t2"; gene_id "Phchi.S1G386800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12448.t1 is derived from g8125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	22682560	22682937	.	+	.	Phchi.S2G052800
Phchi.S2	AUGUSTUS	transcript	22682560	22682937	.	+	.	transcript_id "Phchi.S2G052800.t1"; gene_id "Phchi.S2G052800"
Phchi.S2	AUGUSTUS	start_codon	22682560	22682562	.	+	0	transcript_id "Phchi.S2G052800.t1"; gene_id "Phchi.S2G052800"
Phchi.S2	AUGUSTUS	CDS	22682560	22682937	0.69	+	0	transcript_id "Phchi.S2G052800.t1"; gene_id "Phchi.S2G052800"
Phchi.S2	AUGUSTUS	exon	22682560	22682937	.	+	.	transcript_id "Phchi.S2G052800.t1"; gene_id "Phchi.S2G052800"
Phchi.S2	AUGUSTUS	stop_codon	22682938	22682940	.	+	0	transcript_id "Phchi.S2G052800.t1"; gene_id "Phchi.S2G052800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9858.t1 is derived from g7034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44107869	44108240	.	-	.	Phchi.S1G701700
Phchi.S1	AUGUSTUS	transcript	44107869	44108240	.	-	.	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	stop_codon	44107866	44107868	.	-	0	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	CDS	44107869	44107892	0.89	-	0	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	exon	44107869	44107892	.	-	.	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	intron	44107893	44107994	.	-	.	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	CDS	44107995	44108240	0.78	-	0	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	exon	44107995	44108240	.	-	.	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
Phchi.S1	AUGUSTUS	start_codon	44108238	44108240	.	-	0	transcript_id "Phchi.S1G701700.t1"; gene_id "Phchi.S1G701700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10404.t1 is derived from g7580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47623327	47625122	.	+	.	Phchi.S1G756300
Phchi.S1	AUGUSTUS	transcript	47623327	47625122	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	start_codon	47623327	47623329	.	+	0	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	CDS	47623327	47623591	0.3	+	0	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	exon	47623327	47623591	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	intron	47623592	47623664	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	CDS	47623665	47624087	0.68	+	2	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	exon	47623665	47624087	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	intron	47624088	47624239	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	CDS	47624240	47624323	0.75	+	2	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	exon	47624240	47624323	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	intron	47624324	47624421	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	CDS	47624422	47625122	0.55	+	2	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	exon	47624422	47625122	.	+	.	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
Phchi.S1	AUGUSTUS	stop_codon	47625123	47625125	.	+	0	transcript_id "Phchi.S1G756300.t1"; gene_id "Phchi.S1G756300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15930.t1 is derived from g16031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C71	AUGUSTUS	gene	19229	19903	.	-	.	Phchi.C71G000100
Phchi.C71	AUGUSTUS	transcript	19229	19903	.	-	.	transcript_id "Phchi.C71G000100.t1"; gene_id "Phchi.C71G000100"
Phchi.C71	AUGUSTUS	stop_codon	19226	19228	.	-	0	transcript_id "Phchi.C71G000100.t1"; gene_id "Phchi.C71G000100"
Phchi.C71	AUGUSTUS	CDS	19229	19903	0.81	-	0	transcript_id "Phchi.C71G000100.t1"; gene_id "Phchi.C71G000100"
Phchi.C71	AUGUSTUS	exon	19229	19903	.	-	.	transcript_id "Phchi.C71G000100.t1"; gene_id "Phchi.C71G000100"
Phchi.C71	AUGUSTUS	start_codon	19901	19903	.	-	0	transcript_id "Phchi.C71G000100.t1"; gene_id "Phchi.C71G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11240.t1 is derived from g15290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4958149	4964183	.	-	.	Phchi.S4G082200
Phchi.S4	AUGUSTUS	transcript	4958149	4964183	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	stop_codon	4958146	4958148	.	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958149	4958217	0.94	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958149	4958217	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958218	4958304	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958305	4958382	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958305	4958382	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958383	4958489	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958490	4958663	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958490	4958663	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958664	4958760	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958761	4958817	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958761	4958817	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958818	4958932	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958933	4958984	1	-	1	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958933	4958984	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958985	4959129	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959130	4959218	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959130	4959218	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959219	4959370	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959371	4959456	1	-	2	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959371	4959456	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959457	4959563	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959564	4959768	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959564	4959768	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959769	4959855	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959856	4959948	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959856	4959948	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959949	4960072	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4960073	4960213	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4960073	4960213	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4960214	4960336	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4960337	4960429	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4960337	4960429	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4960430	4960565	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4960566	4960806	1	-	1	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4960566	4960806	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4960807	4961235	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4961236	4961408	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4961236	4961408	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4961409	4961536	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4961537	4961913	0.96	-	2	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4961537	4961913	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4961914	4961989	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4961990	4962064	0.92	-	2	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4961990	4962064	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4962065	4962272	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4962273	4962831	0.75	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4962273	4962831	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4962832	4962971	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4962972	4963023	1	-	1	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4962972	4963023	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4963024	4963109	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4963110	4963156	0.97	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4963110	4963156	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4963157	4963286	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4963287	4964183	1	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4963287	4964183	.	-	.	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	start_codon	4964181	4964183	.	-	0	transcript_id "Phchi.S4G082200.t1"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	transcript	4958149	4964183	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	stop_codon	4958146	4958148	.	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958149	4958217	0.96	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958149	4958217	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958218	4958304	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958305	4958382	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958305	4958382	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958383	4958489	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958490	4958663	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958490	4958663	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958664	4958760	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958761	4958817	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958761	4958817	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958818	4958932	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4958933	4958984	1	-	1	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4958933	4958984	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4958985	4959129	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959130	4959218	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959130	4959218	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959219	4959370	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959371	4959456	1	-	2	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959371	4959456	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959457	4959563	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959564	4959768	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959564	4959768	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959769	4959855	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4959856	4959948	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4959856	4959948	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4959949	4960072	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4960073	4960213	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4960073	4960213	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4960214	4960336	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4960337	4960429	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4960337	4960429	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4960430	4960565	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4960566	4960806	1	-	1	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4960566	4960806	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4960807	4961235	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4961236	4961408	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4961236	4961408	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4961409	4961536	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4961537	4961819	0.68	-	1	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4961537	4961819	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4961820	4961989	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4961990	4962064	0.89	-	1	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4961990	4962064	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4962065	4962149	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4962150	4962388	0.54	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4962150	4962388	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4962389	4962526	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4962527	4962601	0.53	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4962527	4962601	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4962602	4962684	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4962685	4962831	0.54	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4962685	4962831	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4962832	4962971	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4962972	4963023	1	-	1	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4962972	4963023	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4963024	4963109	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4963110	4963156	0.99	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4963110	4963156	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	intron	4963157	4963286	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	CDS	4963287	4964183	1	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	exon	4963287	4964183	.	-	.	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
Phchi.S4	AUGUSTUS	start_codon	4964181	4964183	.	-	0	transcript_id "Phchi.S4G082200.t2"; gene_id "Phchi.S4G082200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2030.t1 is derived from g8950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4527516	4531493	.	+	.	Phchi.S5G063900
Phchi.S5	AUGUSTUS	transcript	4527516	4531493	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	start_codon	4527516	4527518	.	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4527516	4527746	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4527516	4527746	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4527747	4527945	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4527946	4528118	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4527946	4528118	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4528119	4528243	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4528244	4528316	0.99	+	1	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4528244	4528316	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4528317	4528433	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4528434	4528568	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4528434	4528568	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4528569	4528680	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4528681	4528891	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4528681	4528891	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4528892	4528975	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4528976	4529124	1	+	2	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4528976	4529124	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4529125	4529220	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4529221	4529319	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4529221	4529319	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4529320	4529395	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4529396	4529453	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4529396	4529453	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4529454	4529543	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4529544	4529709	1	+	2	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4529544	4529709	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4529710	4529815	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4529816	4529910	1	+	1	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4529816	4529910	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4529911	4530082	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4530083	4530191	1	+	2	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4530083	4530191	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4530192	4530285	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4530286	4530451	1	+	1	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4530286	4530451	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4530452	4530601	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4530602	4530763	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4530602	4530763	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4530764	4530874	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4530875	4531055	0.94	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4530875	4531055	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4531056	4531283	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4531284	4531315	0.91	+	2	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4531284	4531315	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	intron	4531316	4531451	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	CDS	4531452	4531493	1	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	exon	4531452	4531493	.	+	.	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
Phchi.S5	AUGUSTUS	stop_codon	4531494	4531496	.	+	0	transcript_id "Phchi.S5G063900.t1"; gene_id "Phchi.S5G063900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9049.t1 is derived from g6224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39395263	39396212	.	-	.	Phchi.S1G620800
Phchi.S1	AUGUSTUS	transcript	39395263	39396212	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	stop_codon	39395260	39395262	.	-	0	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	CDS	39395263	39395456	1	-	2	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	exon	39395263	39395456	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	intron	39395457	39395562	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	CDS	39395563	39395793	1	-	2	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	exon	39395563	39395793	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	intron	39395794	39395880	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	CDS	39395881	39395994	0.73	-	2	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	exon	39395881	39395994	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	intron	39395995	39396121	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	CDS	39396122	39396212	0.72	-	0	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	exon	39396122	39396212	.	-	.	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
Phchi.S1	AUGUSTUS	start_codon	39396210	39396212	.	-	0	transcript_id "Phchi.S1G620800.t1"; gene_id "Phchi.S1G620800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4272.t1 is derived from g1441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9337564	9338181	.	+	.	Phchi.S1G143100
Phchi.S1	AUGUSTUS	transcript	9337564	9338181	.	+	.	transcript_id "Phchi.S1G143100.t1"; gene_id "Phchi.S1G143100"
Phchi.S1	AUGUSTUS	start_codon	9337564	9337566	.	+	0	transcript_id "Phchi.S1G143100.t1"; gene_id "Phchi.S1G143100"
Phchi.S1	AUGUSTUS	CDS	9337564	9338181	0.61	+	0	transcript_id "Phchi.S1G143100.t1"; gene_id "Phchi.S1G143100"
Phchi.S1	AUGUSTUS	exon	9337564	9338181	.	+	.	transcript_id "Phchi.S1G143100.t1"; gene_id "Phchi.S1G143100"
Phchi.S1	AUGUSTUS	stop_codon	9338182	9338184	.	+	0	transcript_id "Phchi.S1G143100.t1"; gene_id "Phchi.S1G143100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6548.t1 is derived from g3720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23581158	23581526	.	-	.	Phchi.S1G370700
Phchi.S1	AUGUSTUS	transcript	23581158	23581526	.	-	.	transcript_id "Phchi.S1G370700.t1"; gene_id "Phchi.S1G370700"
Phchi.S1	AUGUSTUS	stop_codon	23581155	23581157	.	-	0	transcript_id "Phchi.S1G370700.t1"; gene_id "Phchi.S1G370700"
Phchi.S1	AUGUSTUS	CDS	23581158	23581526	0.43	-	0	transcript_id "Phchi.S1G370700.t1"; gene_id "Phchi.S1G370700"
Phchi.S1	AUGUSTUS	exon	23581158	23581526	.	-	.	transcript_id "Phchi.S1G370700.t1"; gene_id "Phchi.S1G370700"
Phchi.S1	AUGUSTUS	start_codon	23581524	23581526	.	-	0	transcript_id "Phchi.S1G370700.t1"; gene_id "Phchi.S1G370700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg665.t1 is derived from g10447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4641250	4641768	.	+	.	Phchi.S6G062400
Phchi.S6	AUGUSTUS	transcript	4641250	4641768	.	+	.	transcript_id "Phchi.S6G062400.t1"; gene_id "Phchi.S6G062400"
Phchi.S6	AUGUSTUS	start_codon	4641250	4641252	.	+	0	transcript_id "Phchi.S6G062400.t1"; gene_id "Phchi.S6G062400"
Phchi.S6	AUGUSTUS	CDS	4641250	4641768	0.65	+	0	transcript_id "Phchi.S6G062400.t1"; gene_id "Phchi.S6G062400"
Phchi.S6	AUGUSTUS	exon	4641250	4641768	.	+	.	transcript_id "Phchi.S6G062400.t1"; gene_id "Phchi.S6G062400"
Phchi.S6	AUGUSTUS	stop_codon	4641769	4641771	.	+	0	transcript_id "Phchi.S6G062400.t1"; gene_id "Phchi.S6G062400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12921.t1 is derived from g11386.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3169360	3171755	.	-	.	Phchi.S3G024000
Phchi.S3	AUGUSTUS	transcript	3169360	3171755	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	stop_codon	3169357	3169359	.	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169360	3169464	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169360	3169464	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3169465	3169536	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169537	3169665	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169537	3169665	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3169666	3169741	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169742	3169831	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169742	3169831	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3169832	3169924	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169925	3170004	1	-	2	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169925	3170004	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170005	3170147	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170148	3170228	1	-	2	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170148	3170228	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170229	3170328	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170329	3170389	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170329	3170389	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170390	3170481	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170482	3170601	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170482	3170601	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170602	3170695	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170696	3170702	1	-	1	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170696	3170702	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170703	3170787	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170788	3170825	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170788	3170825	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170826	3170938	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170939	3170989	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170939	3170989	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170990	3171077	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171078	3171164	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171078	3171164	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3171165	3171261	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171262	3171369	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171262	3171369	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3171370	3171450	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171451	3171612	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171451	3171612	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3171613	3171704	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171705	3171755	1	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171705	3171755	.	-	.	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	start_codon	3171753	3171755	.	-	0	transcript_id "Phchi.S3G024000.t1"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	transcript	3169360	3171755	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	stop_codon	3169357	3169359	.	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169360	3169464	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169360	3169464	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3169465	3169536	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169537	3169665	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169537	3169665	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3169666	3169741	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169742	3169831	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169742	3169831	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3169832	3169924	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3169925	3170004	1	-	2	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3169925	3170004	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170005	3170147	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170148	3170228	1	-	2	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170148	3170228	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170229	3170328	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170329	3170389	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170329	3170389	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170390	3170481	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170482	3170601	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170482	3170601	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170602	3170753	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170754	3170825	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170754	3170825	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170826	3170938	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3170939	3170989	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3170939	3170989	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3170990	3171077	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171078	3171164	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171078	3171164	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3171165	3171261	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171262	3171369	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171262	3171369	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3171370	3171450	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171451	3171612	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171451	3171612	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	intron	3171613	3171704	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	CDS	3171705	3171755	1	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	exon	3171705	3171755	.	-	.	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
Phchi.S3	AUGUSTUS	start_codon	3171753	3171755	.	-	0	transcript_id "Phchi.S3G024000.t2"; gene_id "Phchi.S3G024000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3705.t1 is derived from g874.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5248131	5251414	.	-	.	Phchi.S1G086400
Phchi.S1	AUGUSTUS	transcript	5248131	5251414	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	stop_codon	5248128	5248130	.	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5248131	5248503	0.86	-	1	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5248131	5248503	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5248504	5248591	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5248592	5248638	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5248592	5248638	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5248639	5248741	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5248742	5248823	0.99	-	1	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5248742	5248823	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5248824	5249061	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249062	5249120	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249062	5249120	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249121	5249373	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249374	5249436	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249374	5249436	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249437	5249581	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249582	5249587	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249582	5249587	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249588	5249682	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249683	5249744	1	-	2	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249683	5249744	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249745	5249859	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249860	5250019	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249860	5250019	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250020	5250092	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250093	5250172	1	-	2	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250093	5250172	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250173	5250293	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250294	5250357	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250294	5250357	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250358	5250451	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250452	5250620	1	-	1	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250452	5250620	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250621	5250732	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250733	5250785	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250733	5250785	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250786	5251267	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5251268	5251414	1	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5251268	5251414	.	-	.	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	start_codon	5251412	5251414	.	-	0	transcript_id "Phchi.S1G086400.t1"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	transcript	5248131	5251414	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	stop_codon	5248128	5248130	.	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5248131	5248503	0.79	-	1	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5248131	5248503	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5248504	5248591	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5248592	5248638	1	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5248592	5248638	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5248639	5248741	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5248742	5248823	0.99	-	1	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5248742	5248823	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5248824	5249061	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249062	5249120	1	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249062	5249120	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249121	5249373	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249374	5249436	1	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249374	5249436	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249437	5249682	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249683	5249744	1	-	2	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249683	5249744	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5249745	5249859	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5249860	5250019	1	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5249860	5250019	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250020	5250092	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250093	5250172	1	-	2	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250093	5250172	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250173	5250293	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250294	5250357	1	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250294	5250357	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250358	5250451	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250452	5250620	1	-	1	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250452	5250620	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250621	5250732	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250733	5250785	0.97	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250733	5250785	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5250786	5250997	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5250998	5251038	0.94	-	2	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5250998	5251038	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5251039	5251115	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5251116	5251230	0.68	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5251116	5251230	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	intron	5251231	5251321	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	CDS	5251322	5251414	0.63	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	exon	5251322	5251414	.	-	.	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
Phchi.S1	AUGUSTUS	start_codon	5251412	5251414	.	-	0	transcript_id "Phchi.S1G086400.t2"; gene_id "Phchi.S1G086400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8757.t1 is derived from g5932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37835964	37838873	.	+	.	Phchi.S1G591600
Phchi.S1	AUGUSTUS	transcript	37835964	37838873	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	start_codon	37835964	37835966	.	+	0	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	CDS	37835964	37836176	0.08	+	0	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	exon	37835964	37836176	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	intron	37836177	37836264	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	CDS	37836265	37836316	1	+	0	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	exon	37836265	37836316	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	intron	37836317	37836668	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	CDS	37836669	37836795	1	+	2	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	exon	37836669	37836795	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	intron	37836796	37838749	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	CDS	37838750	37838873	0.02	+	1	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	exon	37838750	37838873	.	+	.	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
Phchi.S1	AUGUSTUS	stop_codon	37838874	37838876	.	+	0	transcript_id "Phchi.S1G591600.t1"; gene_id "Phchi.S1G591600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7832.t1 is derived from g5006.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31424675	31428064	.	+	.	Phchi.S1G499100
Phchi.S1	AUGUSTUS	transcript	31424675	31427414	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	start_codon	31424675	31424677	.	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31424675	31424836	0.99	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31424675	31424836	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31424837	31425060	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425061	31425119	1	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425061	31425119	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425120	31425236	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425237	31425369	1	+	1	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425237	31425369	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425370	31425495	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425496	31425572	1	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425496	31425572	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425573	31425661	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425662	31425770	1	+	1	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425662	31425770	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425771	31425900	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425901	31426097	1	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425901	31426097	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426098	31426284	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426285	31426517	1	+	1	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426285	31426517	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426518	31426603	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426604	31426699	1	+	2	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426604	31426699	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426700	31426781	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426782	31426903	1	+	2	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426782	31426903	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426904	31426984	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426985	31427086	0.62	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426985	31427086	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31427087	31427187	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31427188	31427285	0.99	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31427188	31427285	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31427286	31427383	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31427384	31427414	0.97	+	1	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31427384	31427414	.	+	.	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	stop_codon	31427415	31427417	.	+	0	transcript_id "Phchi.S1G499100.t1"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	transcript	31424675	31428064	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	start_codon	31424675	31424677	.	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31424675	31424836	0.92	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31424675	31424836	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31424837	31425060	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425061	31425119	1	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425061	31425119	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425120	31425236	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425237	31425369	1	+	1	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425237	31425369	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425370	31425495	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425496	31425572	1	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425496	31425572	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425573	31425661	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425662	31425770	1	+	1	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425662	31425770	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31425771	31425900	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31425901	31426097	1	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31425901	31426097	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426098	31426284	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426285	31426517	0.97	+	1	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426285	31426517	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426518	31426603	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426604	31426699	1	+	2	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426604	31426699	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426700	31426781	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426782	31426903	1	+	2	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426782	31426903	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31426904	31426984	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31426985	31427086	0.6	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31426985	31427086	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31427087	31427187	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31427188	31427285	0.96	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31427188	31427285	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31427286	31427387	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31427388	31427475	0.49	+	1	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31427388	31427475	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31427476	31427584	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31427585	31427769	0.54	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31427585	31427769	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	intron	31427770	31427877	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	CDS	31427878	31428064	0.55	+	1	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	exon	31427878	31428064	.	+	.	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
Phchi.S1	AUGUSTUS	stop_codon	31428065	31428067	.	+	0	transcript_id "Phchi.S1G499100.t2"; gene_id "Phchi.S1G499100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6501.t1 is derived from g3673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23338847	23342251	.	-	.	Phchi.S1G366000
Phchi.S1	AUGUSTUS	transcript	23338847	23342251	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	stop_codon	23338844	23338846	.	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23338847	23339263	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23338847	23339263	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23339264	23339343	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23339344	23339404	1	-	1	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23339344	23339404	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23339405	23339533	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23339534	23339601	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23339534	23339601	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23339602	23339707	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23339708	23339743	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23339708	23339743	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23339744	23339834	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23339835	23340035	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23339835	23340035	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23340036	23340182	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23340183	23340223	1	-	2	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23340183	23340223	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23340224	23340352	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23340353	23340402	1	-	1	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23340353	23340402	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23340403	23340492	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23340493	23340578	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23340493	23340578	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23340579	23340651	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23340652	23340726	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23340652	23340726	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23340727	23340842	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23340843	23340952	1	-	2	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23340843	23340952	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23340953	23341081	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23341082	23341142	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23341082	23341142	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23341143	23341239	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23341240	23341356	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23341240	23341356	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23341357	23341439	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23341440	23341651	1	-	2	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23341440	23341651	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23341652	23341740	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23341741	23341798	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23341741	23341798	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23341799	23341888	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23341889	23341995	1	-	2	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23341889	23341995	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	intron	23341996	23342241	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	CDS	23342242	23342251	1	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	exon	23342242	23342251	.	-	.	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
Phchi.S1	AUGUSTUS	start_codon	23342249	23342251	.	-	0	transcript_id "Phchi.S1G366000.t1"; gene_id "Phchi.S1G366000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1074.t1 is derived from g10857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7445519	7446667	.	+	.	Phchi.S6G103300
Phchi.S6	AUGUSTUS	transcript	7445519	7446667	.	+	.	transcript_id "Phchi.S6G103300.t1"; gene_id "Phchi.S6G103300"
Phchi.S6	AUGUSTUS	start_codon	7445519	7445521	.	+	0	transcript_id "Phchi.S6G103300.t1"; gene_id "Phchi.S6G103300"
Phchi.S6	AUGUSTUS	CDS	7445519	7446667	0.99	+	0	transcript_id "Phchi.S6G103300.t1"; gene_id "Phchi.S6G103300"
Phchi.S6	AUGUSTUS	exon	7445519	7446667	.	+	.	transcript_id "Phchi.S6G103300.t1"; gene_id "Phchi.S6G103300"
Phchi.S6	AUGUSTUS	stop_codon	7446668	7446670	.	+	0	transcript_id "Phchi.S6G103300.t1"; gene_id "Phchi.S6G103300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12642.t1 is derived from g16010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	4995	6332	.	-	.	Phchi.C136G000300
Phchi.C136	AUGUSTUS	transcript	4995	6332	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	stop_codon	4992	4994	.	-	0	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	CDS	4995	5075	0.93	-	0	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	exon	4995	5075	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	intron	5076	5359	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	CDS	5360	5509	0.96	-	0	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	exon	5360	5509	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	intron	5510	5635	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	CDS	5636	5963	1	-	1	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	exon	5636	5963	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	intron	5964	6054	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	CDS	6055	6332	0.5	-	0	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	exon	6055	6332	.	-	.	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	start_codon	6330	6332	.	-	0	transcript_id "Phchi.C136G000300.t1"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	transcript	5618	6332	.	-	.	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	stop_codon	5615	5617	.	-	0	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	CDS	5618	5963	1	-	1	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	exon	5618	5963	.	-	.	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	intron	5964	6054	.	-	.	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	CDS	6055	6332	0.53	-	0	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	exon	6055	6332	.	-	.	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
Phchi.C136	AUGUSTUS	start_codon	6330	6332	.	-	0	transcript_id "Phchi.C136G000300.t2"; gene_id "Phchi.C136G000300"
# This transcript jg5970.t2 is derived from g3141.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5970.t3 is derived from g3141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5971.t1 is derived from g3142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20162167	20163180	.	-	.	Phchi.S1G313000
Phchi.S1	AUGUSTUS	transcript	20162167	20163180	.	-	.	transcript_id "Phchi.S1G313000.t1"; gene_id "Phchi.S1G313000"
Phchi.S1	AUGUSTUS	stop_codon	20162164	20162166	.	-	0	transcript_id "Phchi.S1G313000.t1"; gene_id "Phchi.S1G313000"
Phchi.S1	AUGUSTUS	CDS	20162167	20163180	1	-	0	transcript_id "Phchi.S1G313000.t1"; gene_id "Phchi.S1G313000"
Phchi.S1	AUGUSTUS	exon	20162167	20163180	.	-	.	transcript_id "Phchi.S1G313000.t1"; gene_id "Phchi.S1G313000"
Phchi.S1	AUGUSTUS	start_codon	20163178	20163180	.	-	0	transcript_id "Phchi.S1G313000.t1"; gene_id "Phchi.S1G313000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6874.t1 is derived from g4046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25754784	25756203	.	+	.	Phchi.S1G403300
Phchi.S1	AUGUSTUS	transcript	25754784	25756203	.	+	.	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	start_codon	25754784	25754786	.	+	0	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	CDS	25754784	25755293	1	+	0	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	exon	25754784	25755293	.	+	.	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	intron	25755294	25755385	.	+	.	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	CDS	25755386	25755788	0.68	+	0	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	exon	25755386	25755788	.	+	.	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	intron	25755789	25755916	.	+	.	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	CDS	25755917	25756203	0.92	+	2	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	exon	25755917	25756203	.	+	.	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
Phchi.S1	AUGUSTUS	stop_codon	25756204	25756206	.	+	0	transcript_id "Phchi.S1G403300.t1"; gene_id "Phchi.S1G403300"
# This transcript jg1388.t2 is derived from g16021.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1388.t3 is derived from g16021.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1388.t4 is derived from g16021.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1389.t1 is derived from g16022.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	21026	22856	.	-	.	Phchi.C243G000700
Phchi.C243	AUGUSTUS	transcript	21387	22856	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	stop_codon	21384	21386	.	-	0	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	21387	21447	0.51	-	1	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	21387	21447	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	21448	21630	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	21631	21750	1	-	1	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	21631	21750	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	21751	21953	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	21954	21982	0.98	-	0	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	21954	21982	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	21983	22235	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	22236	22295	0.99	-	0	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	22236	22295	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	22296	22508	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	22509	22612	0.87	-	2	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	22509	22612	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	22613	22783	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	22784	22856	0.83	-	0	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	22784	22856	.	-	.	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	start_codon	22854	22856	.	-	0	transcript_id "Phchi.C243G000700.t1"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	transcript	21026	22856	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	stop_codon	21023	21025	.	-	0	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	21026	21086	0.41	-	1	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	21026	21086	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	21087	21630	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	21631	21750	0.49	-	1	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	21631	21750	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	21751	21953	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	21954	21982	0.85	-	0	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	21954	21982	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	21983	22235	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	22236	22295	0.86	-	0	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	22236	22295	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	22296	22508	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	22509	22612	0.88	-	2	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	22509	22612	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	intron	22613	22783	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	CDS	22784	22856	0.79	-	0	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	exon	22784	22856	.	-	.	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
Phchi.C243	AUGUSTUS	start_codon	22854	22856	.	-	0	transcript_id "Phchi.C243G000700.t2"; gene_id "Phchi.C243G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6519.t1 is derived from g3691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23459509	23462350	.	+	.	Phchi.S1G367800
Phchi.S1	AUGUSTUS	transcript	23459509	23462350	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	start_codon	23459509	23459511	.	+	0	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	CDS	23459509	23459653	0.56	+	0	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	exon	23459509	23459653	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	intron	23459654	23459751	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	CDS	23459752	23461334	0.5	+	2	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	exon	23459752	23461334	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	intron	23461335	23461474	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	CDS	23461475	23461588	0.63	+	0	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	exon	23461475	23461588	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	intron	23461589	23461684	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	CDS	23461685	23461975	0.97	+	0	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	exon	23461685	23461975	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	intron	23461976	23462092	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	CDS	23462093	23462350	0.86	+	0	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	exon	23462093	23462350	.	+	.	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
Phchi.S1	AUGUSTUS	stop_codon	23462351	23462353	.	+	0	transcript_id "Phchi.S1G367800.t1"; gene_id "Phchi.S1G367800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15975.t1 is derived from g9818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C54	AUGUSTUS	gene	40788	41963	.	+	.	Phchi.C54G000200
Phchi.C54	AUGUSTUS	transcript	40788	41963	.	+	.	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	start_codon	40788	40790	.	+	0	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	CDS	40788	41404	0.23	+	0	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	exon	40788	41404	.	+	.	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	intron	41405	41743	.	+	.	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	CDS	41744	41963	0.59	+	1	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	exon	41744	41963	.	+	.	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
Phchi.C54	AUGUSTUS	stop_codon	41964	41966	.	+	0	transcript_id "Phchi.C54G000200.t1"; gene_id "Phchi.C54G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14969.t1 is derived from g13437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15791401	15791891	.	+	.	Phchi.S3G228800
Phchi.S3	AUGUSTUS	transcript	15791401	15791891	.	+	.	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	start_codon	15791401	15791403	.	+	0	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	CDS	15791401	15791517	1	+	0	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	exon	15791401	15791517	.	+	.	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	intron	15791518	15791618	.	+	.	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	CDS	15791619	15791758	1	+	0	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	exon	15791619	15791758	.	+	.	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	intron	15791759	15791845	.	+	.	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	CDS	15791846	15791891	1	+	1	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	exon	15791846	15791891	.	+	.	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
Phchi.S3	AUGUSTUS	stop_codon	15791892	15791894	.	+	0	transcript_id "Phchi.S3G228800.t1"; gene_id "Phchi.S3G228800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5594.t1 is derived from g2764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17803691	17804751	.	-	.	Phchi.S1G275300
Phchi.S1	AUGUSTUS	transcript	17803691	17804751	.	-	.	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	stop_codon	17803688	17803690	.	-	0	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	CDS	17803691	17804506	0.95	-	0	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	exon	17803691	17804506	.	-	.	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	intron	17804507	17804649	.	-	.	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	CDS	17804650	17804751	0.65	-	0	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	exon	17804650	17804751	.	-	.	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
Phchi.S1	AUGUSTUS	start_codon	17804749	17804751	.	-	0	transcript_id "Phchi.S1G275300.t1"; gene_id "Phchi.S1G275300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8544.t1 is derived from g5719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36565828	36568820	.	+	.	Phchi.S1G570300
Phchi.S1	AUGUSTUS	transcript	36565828	36568820	.	+	.	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	start_codon	36565828	36565830	.	+	0	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	CDS	36565828	36567258	1	+	0	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	exon	36565828	36567258	.	+	.	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	intron	36567259	36567366	.	+	.	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	CDS	36567367	36567510	1	+	0	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	exon	36567367	36567510	.	+	.	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	intron	36567511	36567653	.	+	.	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	CDS	36567654	36568820	0.74	+	0	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	exon	36567654	36568820	.	+	.	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
Phchi.S1	AUGUSTUS	stop_codon	36568821	36568823	.	+	0	transcript_id "Phchi.S1G570300.t1"; gene_id "Phchi.S1G570300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4890.t1 is derived from g2060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13262300	13264035	.	-	.	Phchi.S1G204900
Phchi.S1	AUGUSTUS	transcript	13262300	13264035	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	stop_codon	13262297	13262299	.	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13262300	13262359	1	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13262300	13262359	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	intron	13262360	13262454	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13262455	13262505	0.98	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13262455	13262505	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	intron	13262506	13262634	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13262635	13262802	0.97	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13262635	13262802	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	intron	13262803	13262923	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13262924	13263035	0.93	-	1	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13262924	13263035	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	intron	13263036	13263416	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13263417	13263523	1	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13263417	13263523	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	intron	13263524	13263612	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13263613	13263869	0.46	-	2	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13263613	13263869	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	intron	13263870	13263956	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	CDS	13263957	13264035	0.42	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	exon	13263957	13264035	.	-	.	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
Phchi.S1	AUGUSTUS	start_codon	13264033	13264035	.	-	0	transcript_id "Phchi.S1G204900.t1"; gene_id "Phchi.S1G204900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5278.t1 is derived from g2448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16008012	16008742	.	-	.	Phchi.S1G243700
Phchi.S1	AUGUSTUS	transcript	16008012	16008742	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	stop_codon	16008009	16008011	.	-	0	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	CDS	16008012	16008122	0.93	-	0	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	exon	16008012	16008122	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	intron	16008123	16008208	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	CDS	16008209	16008290	0.99	-	1	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	exon	16008209	16008290	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	intron	16008291	16008395	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	CDS	16008396	16008440	1	-	1	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	exon	16008396	16008440	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	intron	16008441	16008513	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	CDS	16008514	16008541	0.8	-	2	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	exon	16008514	16008541	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	intron	16008542	16008636	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	CDS	16008637	16008742	0.39	-	0	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	exon	16008637	16008742	.	-	.	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
Phchi.S1	AUGUSTUS	start_codon	16008740	16008742	.	-	0	transcript_id "Phchi.S1G243700.t1"; gene_id "Phchi.S1G243700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10268.t1 is derived from g7444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46755174	46756309	.	-	.	Phchi.S1G742700
Phchi.S1	AUGUSTUS	transcript	46755174	46756309	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	stop_codon	46755171	46755173	.	-	0	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	CDS	46755174	46755207	1	-	1	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	exon	46755174	46755207	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	intron	46755208	46755299	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	CDS	46755300	46755414	0.93	-	2	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	exon	46755300	46755414	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	intron	46755415	46755644	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	CDS	46755645	46755709	0.92	-	1	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	exon	46755645	46755709	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	intron	46755710	46755857	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	CDS	46755858	46756309	0.73	-	0	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	exon	46755858	46756309	.	-	.	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
Phchi.S1	AUGUSTUS	start_codon	46756307	46756309	.	-	0	transcript_id "Phchi.S1G742700.t1"; gene_id "Phchi.S1G742700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8289.t1 is derived from g5464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35106530	35109894	.	-	.	Phchi.S1G544800
Phchi.S1	AUGUSTUS	transcript	35106530	35109894	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	stop_codon	35106527	35106529	.	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35106530	35107086	0.99	-	2	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35106530	35107086	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35107087	35107202	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35107203	35107281	1	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35107203	35107281	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35107282	35107463	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35107464	35107832	0.99	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35107464	35107832	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35107833	35107962	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35107963	35108025	0.99	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35107963	35108025	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35108026	35108132	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35108133	35108270	1	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35108133	35108270	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35108271	35108350	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35108351	35108518	0.99	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35108351	35108518	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35108519	35108628	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35108629	35108697	0.9	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35108629	35108697	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35108698	35108946	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35108947	35109054	0.71	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35108947	35109054	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35109055	35109147	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35109148	35109248	1	-	2	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35109148	35109248	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35109249	35109331	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35109332	35109455	1	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35109332	35109455	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	intron	35109456	35109561	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	CDS	35109562	35109894	0.82	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	exon	35109562	35109894	.	-	.	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
Phchi.S1	AUGUSTUS	start_codon	35109892	35109894	.	-	0	transcript_id "Phchi.S1G544800.t1"; gene_id "Phchi.S1G544800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13138.t1 is derived from g11603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4328099	4336350	.	+	.	Phchi.S3G045700
Phchi.S3	AUGUSTUS	transcript	4328099	4336350	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	start_codon	4328099	4328101	.	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4328099	4328156	0.41	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4328099	4328156	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4328157	4328248	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4328249	4328559	0.53	+	2	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4328249	4328559	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4328560	4328656	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4328657	4329010	0.94	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4328657	4329010	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4329011	4329253	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4329254	4329386	0.88	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4329254	4329386	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4329387	4329491	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4329492	4329667	0.83	+	2	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4329492	4329667	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4329668	4329780	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4329781	4329854	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4329781	4329854	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4329855	4329948	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4329949	4329984	1	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4329949	4329984	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4329985	4330077	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4330078	4330156	1	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4330078	4330156	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4330157	4330254	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4330255	4330421	0.61	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4330255	4330421	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4330422	4330557	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4330558	4330658	0.16	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4330558	4330658	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4330659	4330792	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4330793	4330995	0.77	+	2	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4330793	4330995	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4330996	4331075	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4331076	4331177	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4331076	4331177	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4331178	4331271	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4331272	4331382	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4331272	4331382	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4331383	4331471	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4331472	4331537	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4331472	4331537	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4331538	4331628	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4331629	4331727	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4331629	4331727	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4331728	4331857	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4331858	4332172	0.95	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4331858	4332172	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4332173	4332248	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4332249	4332560	0.99	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4332249	4332560	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4332561	4332836	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4332837	4332847	0.53	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4332837	4332847	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4332848	4332944	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4332945	4333047	1	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4332945	4333047	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4333048	4333139	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4333140	4333285	0.73	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4333140	4333285	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4333286	4333405	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4333406	4333485	1	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4333406	4333485	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4333486	4333579	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4333580	4333725	1	+	2	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4333580	4333725	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4333726	4333813	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4333814	4333993	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4333814	4333993	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4333994	4334066	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4334067	4334443	0.53	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4334067	4334443	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4334444	4334684	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4334685	4335188	0.5	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4334685	4335188	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4335189	4335277	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4335278	4335301	1	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4335278	4335301	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4335302	4335405	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4335406	4335656	1	+	1	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4335406	4335656	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4335657	4335746	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4335747	4336042	1	+	2	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4335747	4336042	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	intron	4336043	4336131	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	CDS	4336132	4336350	1	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	exon	4336132	4336350	.	+	.	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
Phchi.S3	AUGUSTUS	stop_codon	4336351	4336353	.	+	0	transcript_id "Phchi.S3G045700.t1"; gene_id "Phchi.S3G045700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14528.t1 is derived from g12996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13321434	13323715	.	-	.	Phchi.S3G184700
Phchi.S3	AUGUSTUS	transcript	13321434	13323715	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	stop_codon	13321431	13321433	.	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13321434	13321535	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13321434	13321535	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13321536	13321660	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13321661	13321696	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13321661	13321696	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13321697	13321798	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13321799	13321912	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13321799	13321912	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13321913	13322015	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13322016	13322231	0.99	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13322016	13322231	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13322232	13322320	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13322321	13322446	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13322321	13322446	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13322447	13322533	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13322534	13322608	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13322534	13322608	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13322609	13322702	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13322703	13322707	1	-	2	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13322703	13322707	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13322708	13322851	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13322852	13323011	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13322852	13323011	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13323012	13323124	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13323125	13323205	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13323125	13323205	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13323206	13323309	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13323310	13323378	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13323310	13323378	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	intron	13323379	13323649	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	CDS	13323650	13323715	1	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	exon	13323650	13323715	.	-	.	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
Phchi.S3	AUGUSTUS	start_codon	13323713	13323715	.	-	0	transcript_id "Phchi.S3G184700.t1"; gene_id "Phchi.S3G184700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg603.t1 is derived from g10385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4369950	4370625	.	-	.	Phchi.S6G056200
Phchi.S6	AUGUSTUS	transcript	4369950	4370625	.	-	.	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	stop_codon	4369947	4369949	.	-	0	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	CDS	4369950	4370108	0.99	-	0	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	exon	4369950	4370108	.	-	.	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	intron	4370109	4370196	.	-	.	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	CDS	4370197	4370319	0.74	-	0	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	exon	4370197	4370319	.	-	.	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	intron	4370320	4370562	.	-	.	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	CDS	4370563	4370625	0.13	-	0	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	exon	4370563	4370625	.	-	.	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
Phchi.S6	AUGUSTUS	start_codon	4370623	4370625	.	-	0	transcript_id "Phchi.S6G056200.t1"; gene_id "Phchi.S6G056200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8473.t1 is derived from g5648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36111092	36114482	.	-	.	Phchi.S1G563200
Phchi.S1	AUGUSTUS	transcript	36111092	36114482	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	stop_codon	36111089	36111091	.	-	0	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	CDS	36111092	36111163	0.97	-	0	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	exon	36111092	36111163	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	intron	36111164	36111311	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	CDS	36111312	36112664	1	-	0	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	exon	36111312	36112664	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	intron	36112665	36112778	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	CDS	36112779	36112855	0.99	-	2	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	exon	36112779	36112855	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	intron	36112856	36112967	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	CDS	36112968	36113369	0.99	-	2	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	exon	36112968	36113369	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	intron	36113370	36113489	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	CDS	36113490	36113642	1	-	2	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	exon	36113490	36113642	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	intron	36113643	36114196	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	CDS	36114197	36114482	0.8	-	0	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	exon	36114197	36114482	.	-	.	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
Phchi.S1	AUGUSTUS	start_codon	36114480	36114482	.	-	0	transcript_id "Phchi.S1G563200.t1"; gene_id "Phchi.S1G563200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2129.t1 is derived from g9049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4982324	4983231	.	+	.	Phchi.S5G073800
Phchi.S5	AUGUSTUS	transcript	4982324	4983231	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	start_codon	4982324	4982326	.	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	CDS	4982324	4982400	1	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	exon	4982324	4982400	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	intron	4982401	4982471	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	CDS	4982472	4982538	1	+	1	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	exon	4982472	4982538	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	intron	4982539	4982630	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	CDS	4982631	4982753	1	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	exon	4982631	4982753	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	intron	4982754	4982826	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	CDS	4982827	4982910	1	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	exon	4982827	4982910	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	intron	4982911	4982980	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	CDS	4982981	4983067	1	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	exon	4982981	4983067	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	intron	4983068	4983147	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	CDS	4983148	4983231	1	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	exon	4983148	4983231	.	+	.	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
Phchi.S5	AUGUSTUS	stop_codon	4983232	4983234	.	+	0	transcript_id "Phchi.S5G073800.t1"; gene_id "Phchi.S5G073800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9933.t1 is derived from g7109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44533818	44534768	.	+	.	Phchi.S1G709200
Phchi.S1	AUGUSTUS	transcript	44533818	44534768	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	start_codon	44533818	44533820	.	+	0	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	CDS	44533818	44533895	0.57	+	0	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	exon	44533818	44533895	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	intron	44533896	44533994	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	CDS	44533995	44534059	1	+	0	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	exon	44533995	44534059	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	intron	44534060	44534241	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	CDS	44534242	44534304	1	+	1	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	exon	44534242	44534304	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	intron	44534305	44534384	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	CDS	44534385	44534445	1	+	1	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	exon	44534385	44534445	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	intron	44534446	44534552	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	CDS	44534553	44534603	1	+	0	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	exon	44534553	44534603	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	intron	44534604	44534684	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	CDS	44534685	44534768	0.61	+	0	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	exon	44534685	44534768	.	+	.	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
Phchi.S1	AUGUSTUS	stop_codon	44534769	44534771	.	+	0	transcript_id "Phchi.S1G709200.t1"; gene_id "Phchi.S1G709200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5837.t1 is derived from g3007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19198417	19201379	.	+	.	Phchi.S1G299600
Phchi.S1	AUGUSTUS	transcript	19198417	19201379	.	+	.	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	start_codon	19198417	19198419	.	+	0	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	CDS	19198417	19201283	0.74	+	0	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	exon	19198417	19201283	.	+	.	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	intron	19201284	19201375	.	+	.	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	CDS	19201376	19201379	1	+	1	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	exon	19201376	19201379	.	+	.	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
Phchi.S1	AUGUSTUS	stop_codon	19201380	19201382	.	+	0	transcript_id "Phchi.S1G299600.t1"; gene_id "Phchi.S1G299600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10113.t1 is derived from g7289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45786561	45787684	.	+	.	Phchi.S1G727200
Phchi.S1	AUGUSTUS	transcript	45786561	45787684	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	start_codon	45786561	45786563	.	+	0	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	CDS	45786561	45786944	1	+	0	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	exon	45786561	45786944	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	intron	45786945	45787026	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	CDS	45787027	45787160	1	+	0	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	exon	45787027	45787160	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	intron	45787161	45787249	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	CDS	45787250	45787402	1	+	1	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	exon	45787250	45787402	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	intron	45787403	45787497	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	CDS	45787498	45787684	0.96	+	1	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	exon	45787498	45787684	.	+	.	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
Phchi.S1	AUGUSTUS	stop_codon	45787685	45787687	.	+	0	transcript_id "Phchi.S1G727200.t1"; gene_id "Phchi.S1G727200"
# This transcript jg5351.t2 is derived from g2521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5352.t1 is derived from g2522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16442256	16442677	.	+	.	Phchi.S1G251100
Phchi.S1	AUGUSTUS	transcript	16442256	16442677	.	+	.	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	start_codon	16442256	16442258	.	+	0	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	CDS	16442256	16442382	0.85	+	0	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	exon	16442256	16442382	.	+	.	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	intron	16442383	16442573	.	+	.	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	CDS	16442574	16442677	0.77	+	2	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	exon	16442574	16442677	.	+	.	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
Phchi.S1	AUGUSTUS	stop_codon	16442678	16442680	.	+	0	transcript_id "Phchi.S1G251100.t1"; gene_id "Phchi.S1G251100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg90.t1 is derived from g9872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	462874	463406	.	+	.	Phchi.S6G004900
Phchi.S6	AUGUSTUS	transcript	462874	463406	.	+	.	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	start_codon	462874	462876	.	+	0	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	CDS	462874	462953	0.74	+	0	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	exon	462874	462953	.	+	.	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	intron	462954	463036	.	+	.	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	CDS	463037	463162	0.74	+	1	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	exon	463037	463162	.	+	.	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	intron	463163	463327	.	+	.	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	CDS	463328	463406	1	+	1	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	exon	463328	463406	.	+	.	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
Phchi.S6	AUGUSTUS	stop_codon	463407	463409	.	+	0	transcript_id "Phchi.S6G004900.t1"; gene_id "Phchi.S6G004900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2398.t1 is derived from g9318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6477994	6479232	.	+	.	Phchi.S5G100700
Phchi.S5	AUGUSTUS	transcript	6477994	6479232	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	start_codon	6477994	6477996	.	+	0	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	CDS	6477994	6478564	0.98	+	0	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	exon	6477994	6478564	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	intron	6478565	6478646	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	CDS	6478647	6478723	1	+	2	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	exon	6478647	6478723	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	intron	6478724	6478859	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	CDS	6478860	6478938	1	+	0	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	exon	6478860	6478938	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	intron	6478939	6479089	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	CDS	6479090	6479232	1	+	2	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	exon	6479090	6479232	.	+	.	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
Phchi.S5	AUGUSTUS	stop_codon	6479233	6479235	.	+	0	transcript_id "Phchi.S5G100700.t1"; gene_id "Phchi.S5G100700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11975.t1 is derived from g7650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	258381	260750	.	-	.	Phchi.S2G005500
Phchi.S2	AUGUSTUS	transcript	258381	260750	.	-	.	transcript_id "Phchi.S2G005500.t1"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	stop_codon	258378	258380	.	-	0	transcript_id "Phchi.S2G005500.t1"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	CDS	258381	260750	1	-	0	transcript_id "Phchi.S2G005500.t1"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	exon	258381	260750	.	-	.	transcript_id "Phchi.S2G005500.t1"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	start_codon	260748	260750	.	-	0	transcript_id "Phchi.S2G005500.t1"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	transcript	258381	260117	.	-	.	transcript_id "Phchi.S2G005500.t2"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	stop_codon	258378	258380	.	-	0	transcript_id "Phchi.S2G005500.t2"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	CDS	258381	260117	0.52	-	0	transcript_id "Phchi.S2G005500.t2"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	exon	258381	260117	.	-	.	transcript_id "Phchi.S2G005500.t2"; gene_id "Phchi.S2G005500"
Phchi.S2	AUGUSTUS	start_codon	260115	260117	.	-	0	transcript_id "Phchi.S2G005500.t2"; gene_id "Phchi.S2G005500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8828.t1 is derived from g6003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38155475	38157546	.	-	.	Phchi.S1G598700
Phchi.S1	AUGUSTUS	transcript	38155475	38157546	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	stop_codon	38155472	38155474	.	-	0	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	CDS	38155475	38155663	1	-	0	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	exon	38155475	38155663	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	intron	38155664	38155813	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	CDS	38155814	38156131	1	-	0	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	exon	38155814	38156131	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	intron	38156132	38156290	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	CDS	38156291	38156421	0.46	-	2	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	exon	38156291	38156421	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	intron	38156422	38156513	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	CDS	38156514	38157546	0.36	-	0	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	exon	38156514	38157546	.	-	.	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
Phchi.S1	AUGUSTUS	start_codon	38157544	38157546	.	-	0	transcript_id "Phchi.S1G598700.t1"; gene_id "Phchi.S1G598700"
# This transcript jg13361.t2 is derived from g11827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13362.t1 is derived from g11828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6354587	6355278	.	+	.	Phchi.S3G068100
Phchi.S3	AUGUSTUS	transcript	6354587	6355278	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	start_codon	6354587	6354589	.	+	0	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	CDS	6354587	6354679	0.5	+	0	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	exon	6354587	6354679	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	intron	6354680	6354776	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	CDS	6354777	6354867	0.9	+	0	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	exon	6354777	6354867	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	intron	6354868	6354972	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	CDS	6354973	6355101	0.9	+	2	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	exon	6354973	6355101	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	intron	6355102	6355192	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	CDS	6355193	6355278	1	+	2	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	exon	6355193	6355278	.	+	.	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
Phchi.S3	AUGUSTUS	stop_codon	6355279	6355281	.	+	0	transcript_id "Phchi.S3G068100.t1"; gene_id "Phchi.S3G068100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3669.t1 is derived from g838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5109705	5110142	.	+	.	Phchi.S1G082800
Phchi.S1	AUGUSTUS	transcript	5109705	5110142	.	+	.	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	start_codon	5109705	5109707	.	+	0	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	CDS	5109705	5109829	0.79	+	0	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	exon	5109705	5109829	.	+	.	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	intron	5109830	5109922	.	+	.	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	CDS	5109923	5110142	0.82	+	1	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	exon	5109923	5110142	.	+	.	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
Phchi.S1	AUGUSTUS	stop_codon	5110143	5110145	.	+	0	transcript_id "Phchi.S1G082800.t1"; gene_id "Phchi.S1G082800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3761.t1 is derived from g930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5571368	5571964	.	+	.	Phchi.S1G092000
Phchi.S1	AUGUSTUS	transcript	5571368	5571964	.	+	.	transcript_id "Phchi.S1G092000.t1"; gene_id "Phchi.S1G092000"
Phchi.S1	AUGUSTUS	start_codon	5571368	5571370	.	+	0	transcript_id "Phchi.S1G092000.t1"; gene_id "Phchi.S1G092000"
Phchi.S1	AUGUSTUS	CDS	5571368	5571964	0.97	+	0	transcript_id "Phchi.S1G092000.t1"; gene_id "Phchi.S1G092000"
Phchi.S1	AUGUSTUS	exon	5571368	5571964	.	+	.	transcript_id "Phchi.S1G092000.t1"; gene_id "Phchi.S1G092000"
Phchi.S1	AUGUSTUS	stop_codon	5572052	5572054	.	+	0	transcript_id "Phchi.S1G092000.t1"; gene_id "Phchi.S1G092000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10444.t1 is derived from g14493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	363318	365379	.	+	.	Phchi.S4G002600
Phchi.S4	AUGUSTUS	transcript	363318	365379	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	start_codon	363318	363320	.	+	0	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	363318	363324	1	+	0	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	363318	363324	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	intron	363325	363499	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	363500	363640	1	+	2	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	363500	363640	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	intron	363641	363729	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	363730	363809	1	+	2	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	363730	363809	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	intron	363810	363886	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	363887	364045	1	+	0	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	363887	364045	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	intron	364046	364218	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	364219	364243	0.6	+	0	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	364219	364243	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	intron	364244	364382	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	364383	365146	0.46	+	2	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	364383	365146	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	intron	365147	365370	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	CDS	365371	365379	0.79	+	0	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	exon	365371	365379	.	+	.	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
Phchi.S4	AUGUSTUS	stop_codon	365380	365382	.	+	0	transcript_id "Phchi.S4G002600.t1"; gene_id "Phchi.S4G002600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3998.t1 is derived from g1167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6909420	6913119	.	+	.	Phchi.S1G115700
Phchi.S1	AUGUSTUS	transcript	6909420	6913119	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	start_codon	6909420	6909422	.	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6909420	6911336	1	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6909420	6911336	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6911337	6911460	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6911461	6911613	1	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6911461	6911613	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6911614	6911748	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6911749	6911820	1	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6911749	6911820	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6911821	6911915	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6911916	6912039	0.99	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6911916	6912039	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6912040	6912121	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6912122	6912188	1	+	2	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6912122	6912188	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6912189	6912265	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6912266	6912325	0.98	+	1	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6912266	6912325	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6912326	6912444	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6912445	6912517	0.55	+	1	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6912445	6912517	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6912518	6912830	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6912831	6912918	0.37	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6912831	6912918	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	intron	6912919	6913111	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	CDS	6913112	6913119	0.91	+	2	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	exon	6913112	6913119	.	+	.	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
Phchi.S1	AUGUSTUS	stop_codon	6913120	6913122	.	+	0	transcript_id "Phchi.S1G115700.t1"; gene_id "Phchi.S1G115700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg469.t1 is derived from g10251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3300826	3301379	.	-	.	Phchi.S6G042800
Phchi.S6	AUGUSTUS	transcript	3300826	3301379	.	-	.	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	stop_codon	3300823	3300825	.	-	0	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	CDS	3300826	3300845	0.67	-	2	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	exon	3300826	3300845	.	-	.	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	intron	3300846	3300930	.	-	.	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	CDS	3300931	3300981	0.63	-	2	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	exon	3300931	3300981	.	-	.	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	intron	3300982	3301087	.	-	.	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	CDS	3301088	3301379	0.67	-	0	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	exon	3301088	3301379	.	-	.	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
Phchi.S6	AUGUSTUS	start_codon	3301377	3301379	.	-	0	transcript_id "Phchi.S6G042800.t1"; gene_id "Phchi.S6G042800"
# This transcript jg7327.t2 is derived from g4499.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7328.t1 is derived from g4500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28529543	28531723	.	+	.	Phchi.S1G448700
Phchi.S1	AUGUSTUS	transcript	28529543	28531723	.	+	.	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	start_codon	28529543	28529545	.	+	0	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	CDS	28529543	28529625	0.01	+	0	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	exon	28529543	28529625	.	+	.	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	intron	28529626	28530146	.	+	.	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	CDS	28530147	28530210	0.01	+	1	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	exon	28530147	28530210	.	+	.	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	intron	28530211	28531630	.	+	.	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	CDS	28531631	28531723	0.41	+	0	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	exon	28531631	28531723	.	+	.	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
Phchi.S1	AUGUSTUS	stop_codon	28531724	28531726	.	+	0	transcript_id "Phchi.S1G448700.t1"; gene_id "Phchi.S1G448700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15367.t1 is derived from g13835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18659286	18663914	.	+	.	Phchi.S3G268600
Phchi.S3	AUGUSTUS	transcript	18659286	18663914	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	start_codon	18659286	18659288	.	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18659286	18659323	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18659286	18659323	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18659324	18659479	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18659480	18659537	1	+	1	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18659480	18659537	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18659538	18659775	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18659776	18659870	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18659776	18659870	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18659871	18659967	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18659968	18660276	1	+	1	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18659968	18660276	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18660277	18660362	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18660363	18660549	1	+	1	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18660363	18660549	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18660550	18660642	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18660643	18660711	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18660643	18660711	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18660712	18660805	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18660806	18660907	0.96	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18660806	18660907	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18660908	18661022	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18661023	18661112	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18661023	18661112	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18661113	18661329	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18661330	18661449	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18661330	18661449	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18661450	18661578	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18661579	18661674	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18661579	18661674	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18661675	18661763	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18661764	18661820	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18661764	18661820	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18661821	18661955	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18661956	18662099	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18661956	18662099	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18662100	18662271	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18662272	18662359	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18662272	18662359	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18662360	18662499	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18662500	18662585	1	+	2	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18662500	18662585	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18662586	18662715	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18662716	18662841	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18662716	18662841	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18662842	18662952	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18662953	18663054	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18662953	18663054	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18663055	18663168	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18663169	18663276	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18663169	18663276	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18663277	18663476	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18663477	18663608	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18663477	18663608	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	intron	18663609	18663854	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	CDS	18663855	18663914	1	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	exon	18663855	18663914	.	+	.	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
Phchi.S3	AUGUSTUS	stop_codon	18663915	18663917	.	+	0	transcript_id "Phchi.S3G268600.t1"; gene_id "Phchi.S3G268600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4217.t1 is derived from g1386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8965054	8967043	.	+	.	Phchi.S1G137600
Phchi.S1	AUGUSTUS	transcript	8965054	8967043	.	+	.	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	start_codon	8965054	8965056	.	+	0	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	CDS	8965054	8965530	0.86	+	0	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	exon	8965054	8965530	.	+	.	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	intron	8965531	8965630	.	+	.	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	CDS	8965631	8967043	0.96	+	0	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	exon	8965631	8967043	.	+	.	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
Phchi.S1	AUGUSTUS	stop_codon	8967044	8967046	.	+	0	transcript_id "Phchi.S1G137600.t1"; gene_id "Phchi.S1G137600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12573.t1 is derived from g8250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35615723	35616376	.	-	.	Phchi.S2G065300
Phchi.S2	AUGUSTUS	transcript	35615723	35616376	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	stop_codon	35615720	35615722	.	-	0	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	CDS	35615723	35615784	0.3	-	2	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	exon	35615723	35615784	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	intron	35615785	35615863	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	CDS	35615864	35615925	0.53	-	1	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	exon	35615864	35615925	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	intron	35615926	35616030	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	CDS	35616031	35616065	0.53	-	0	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	exon	35616031	35616065	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	intron	35616066	35616121	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	CDS	35616122	35616147	0.65	-	2	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	exon	35616122	35616147	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	intron	35616148	35616327	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	CDS	35616328	35616376	0.99	-	0	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	exon	35616328	35616376	.	-	.	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
Phchi.S2	AUGUSTUS	start_codon	35616374	35616376	.	-	0	transcript_id "Phchi.S2G065300.t1"; gene_id "Phchi.S2G065300"
# This transcript jg15969.t2 is derived from g14402.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15970.t1 is derived from g14403.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C26	AUGUSTUS	gene	86411	87088	.	+	.	Phchi.C26G000200
Phchi.C26	AUGUSTUS	transcript	86411	87088	.	+	.	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	start_codon	86411	86413	.	+	0	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	CDS	86411	86589	0.95	+	0	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	exon	86411	86589	.	+	.	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	intron	86590	86719	.	+	.	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	CDS	86720	86828	1	+	1	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	exon	86720	86828	.	+	.	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	intron	86829	87007	.	+	.	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	CDS	87008	87088	0.97	+	0	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	exon	87008	87088	.	+	.	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	stop_codon	87089	87091	.	+	0	transcript_id "Phchi.C26G000200.t1"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	transcript	86411	87088	.	+	.	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	start_codon	86411	86413	.	+	0	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	CDS	86411	86502	0.9	+	0	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	exon	86411	86502	.	+	.	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	intron	86503	86719	.	+	.	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	CDS	86720	86828	1	+	1	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	exon	86720	86828	.	+	.	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	intron	86829	87007	.	+	.	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	CDS	87008	87088	0.99	+	0	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	exon	87008	87088	.	+	.	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
Phchi.C26	AUGUSTUS	stop_codon	87089	87091	.	+	0	transcript_id "Phchi.C26G000200.t2"; gene_id "Phchi.C26G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9279.t1 is derived from g6454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40740102	40741791	.	-	.	Phchi.S1G643800
Phchi.S1	AUGUSTUS	transcript	40740102	40741791	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	stop_codon	40740099	40740101	.	-	0	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	CDS	40740102	40740800	0.85	-	0	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	exon	40740102	40740800	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	intron	40740801	40740889	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	CDS	40740890	40740985	1	-	0	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	exon	40740890	40740985	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	intron	40740986	40741241	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	CDS	40741242	40741489	0.7	-	2	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	exon	40741242	40741489	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	intron	40741490	40741598	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	CDS	40741599	40741791	0.45	-	0	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	exon	40741599	40741791	.	-	.	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
Phchi.S1	AUGUSTUS	start_codon	40741789	40741791	.	-	0	transcript_id "Phchi.S1G643800.t1"; gene_id "Phchi.S1G643800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10069.t1 is derived from g7245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45621458	45622873	.	-	.	Phchi.S1G722800
Phchi.S1	AUGUSTUS	transcript	45621458	45622873	.	-	.	transcript_id "Phchi.S1G722800.t1"; gene_id "Phchi.S1G722800"
Phchi.S1	AUGUSTUS	stop_codon	45621455	45621457	.	-	0	transcript_id "Phchi.S1G722800.t1"; gene_id "Phchi.S1G722800"
Phchi.S1	AUGUSTUS	CDS	45621458	45622873	0.7	-	0	transcript_id "Phchi.S1G722800.t1"; gene_id "Phchi.S1G722800"
Phchi.S1	AUGUSTUS	exon	45621458	45622873	.	-	.	transcript_id "Phchi.S1G722800.t1"; gene_id "Phchi.S1G722800"
Phchi.S1	AUGUSTUS	start_codon	45622871	45622873	.	-	0	transcript_id "Phchi.S1G722800.t1"; gene_id "Phchi.S1G722800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8330.t1 is derived from g5505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35338588	35340694	.	-	.	Phchi.S1G548900
Phchi.S1	AUGUSTUS	transcript	35338588	35340694	.	-	.	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	stop_codon	35338585	35338587	.	-	0	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	CDS	35338588	35339415	0.82	-	0	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	exon	35338588	35339415	.	-	.	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	intron	35339416	35339612	.	-	.	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	CDS	35339613	35339804	0.99	-	0	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	exon	35339613	35339804	.	-	.	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	intron	35339805	35339905	.	-	.	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	CDS	35339906	35340694	0.29	-	0	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	exon	35339906	35340694	.	-	.	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
Phchi.S1	AUGUSTUS	start_codon	35340692	35340694	.	-	0	transcript_id "Phchi.S1G548900.t1"; gene_id "Phchi.S1G548900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2579.t1 is derived from g9499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7468516	7469159	.	+	.	Phchi.S5G118800
Phchi.S5	AUGUSTUS	transcript	7468516	7469159	.	+	.	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	start_codon	7468516	7468518	.	+	0	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	CDS	7468516	7468636	0.41	+	0	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	exon	7468516	7468636	.	+	.	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	intron	7468637	7468803	.	+	.	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	CDS	7468804	7469159	0.62	+	2	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	exon	7468804	7469159	.	+	.	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
Phchi.S5	AUGUSTUS	stop_codon	7469160	7469162	.	+	0	transcript_id "Phchi.S5G118800.t1"; gene_id "Phchi.S5G118800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4532.t1 is derived from g1702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10986218	10987786	.	+	.	Phchi.S1G169100
Phchi.S1	AUGUSTUS	transcript	10986218	10987786	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	start_codon	10986218	10986220	.	+	0	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10986218	10986407	0.9	+	0	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10986218	10986407	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	intron	10986408	10986547	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10986548	10986660	1	+	2	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10986548	10986660	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	intron	10986661	10986752	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10986753	10987008	1	+	0	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10986753	10987008	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	intron	10987009	10987162	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10987163	10987199	1	+	2	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10987163	10987199	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	intron	10987200	10987285	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10987286	10987391	0.97	+	1	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10987286	10987391	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	intron	10987392	10987499	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10987500	10987610	0.97	+	0	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10987500	10987610	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	intron	10987611	10987678	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	CDS	10987679	10987786	0.93	+	0	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	exon	10987679	10987786	.	+	.	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
Phchi.S1	AUGUSTUS	stop_codon	10987787	10987789	.	+	0	transcript_id "Phchi.S1G169100.t1"; gene_id "Phchi.S1G169100"
# This transcript jg14019.t2 is derived from g12486.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14020.t1 is derived from g12487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10333868	10338130	.	-	.	Phchi.S3G133900
Phchi.S3	AUGUSTUS	transcript	10333868	10338130	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	stop_codon	10333865	10333867	.	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10333868	10334065	0.27	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10333868	10334065	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10334066	10334170	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10334171	10334959	0.69	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10334171	10334959	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10334960	10335064	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10335065	10335490	1	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10335065	10335490	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10335491	10335567	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10335568	10335711	1	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10335568	10335711	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10335712	10335801	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10335802	10335956	0.89	-	2	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10335802	10335956	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10335957	10336053	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10336054	10336096	0.76	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10336054	10336096	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10336097	10336281	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10336282	10336499	0.7	-	2	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10336282	10336499	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10336500	10336655	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10336656	10336852	0.87	-	1	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10336656	10336852	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10336853	10336953	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10336954	10337075	0.93	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10336954	10337075	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10337076	10337199	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10337200	10337321	1	-	2	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10337200	10337321	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10337322	10337584	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10337585	10337894	0.76	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10337585	10337894	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	intron	10337895	10337983	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	CDS	10337984	10338130	0.52	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	exon	10337984	10338130	.	-	.	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
Phchi.S3	AUGUSTUS	start_codon	10338128	10338130	.	-	0	transcript_id "Phchi.S3G133900.t1"; gene_id "Phchi.S3G133900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3742.t1 is derived from g911.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5464590	5467341	.	+	.	Phchi.S1G090100
Phchi.S1	AUGUSTUS	transcript	5464590	5467341	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	start_codon	5464590	5464592	.	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5464590	5464647	0.95	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5464590	5464647	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5464648	5464825	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5464826	5465091	0.89	+	2	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5464826	5465091	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5465092	5465169	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5465170	5465334	1	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5465170	5465334	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5465335	5465496	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5465497	5465502	0.95	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5465497	5465502	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5465503	5465656	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5465657	5465772	0.95	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5465657	5465772	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5465773	5465861	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5465862	5465903	1	+	1	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5465862	5465903	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5465904	5465991	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5465992	5466047	1	+	1	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5465992	5466047	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5466048	5466141	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5466142	5466218	1	+	2	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5466142	5466218	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5466219	5466351	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5466352	5466471	1	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5466352	5466471	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5466472	5466549	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5466550	5466626	1	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5466550	5466626	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5466627	5466715	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5466716	5466779	1	+	1	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5466716	5466779	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5466780	5466924	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5466925	5466975	1	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5466925	5466975	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5466976	5467068	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5467069	5467117	1	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5467069	5467117	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	intron	5467118	5467210	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	CDS	5467211	5467341	0.87	+	2	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	exon	5467211	5467341	.	+	.	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
Phchi.S1	AUGUSTUS	stop_codon	5467342	5467344	.	+	0	transcript_id "Phchi.S1G090100.t1"; gene_id "Phchi.S1G090100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9551.t1 is derived from g6727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42421154	42422083	.	+	.	Phchi.S1G671000
Phchi.S1	AUGUSTUS	transcript	42421154	42422083	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	start_codon	42421154	42421156	.	+	0	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	CDS	42421154	42421237	1	+	0	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	exon	42421154	42421237	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	intron	42421238	42421321	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	CDS	42421322	42421443	1	+	0	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	exon	42421322	42421443	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	intron	42421444	42421521	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	CDS	42421522	42421647	1	+	1	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	exon	42421522	42421647	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	intron	42421648	42421721	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	CDS	42421722	42421782	1	+	1	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	exon	42421722	42421782	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	intron	42421783	42421912	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	CDS	42421913	42422083	1	+	0	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	exon	42421913	42422083	.	+	.	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
Phchi.S1	AUGUSTUS	stop_codon	42422084	42422086	.	+	0	transcript_id "Phchi.S1G671000.t1"; gene_id "Phchi.S1G671000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12606.t1 is derived from g8283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37552737	37553263	.	-	.	Phchi.S2G068600
Phchi.S2	AUGUSTUS	transcript	37552737	37553263	.	-	.	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	stop_codon	37552734	37552736	.	-	0	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	CDS	37552737	37552850	1	-	0	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	exon	37552737	37552850	.	-	.	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	intron	37552851	37552964	.	-	.	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	CDS	37552965	37553105	1	-	0	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	exon	37552965	37553105	.	-	.	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	intron	37553106	37553242	.	-	.	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	CDS	37553243	37553263	0.79	-	0	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	exon	37553243	37553263	.	-	.	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
Phchi.S2	AUGUSTUS	start_codon	37553261	37553263	.	-	0	transcript_id "Phchi.S2G068600.t1"; gene_id "Phchi.S2G068600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6998.t1 is derived from g4170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26323622	26324724	.	-	.	Phchi.S1G415700
Phchi.S1	AUGUSTUS	transcript	26323622	26324724	.	-	.	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	stop_codon	26323619	26323621	.	-	0	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	CDS	26323622	26324072	0.44	-	1	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	exon	26323622	26324072	.	-	.	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	intron	26324073	26324182	.	-	.	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	CDS	26324183	26324724	0.38	-	0	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	exon	26324183	26324724	.	-	.	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
Phchi.S1	AUGUSTUS	start_codon	26324722	26324724	.	-	0	transcript_id "Phchi.S1G415700.t1"; gene_id "Phchi.S1G415700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2096.t1 is derived from g9016.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4849071	4850871	.	-	.	Phchi.S5G070500
Phchi.S5	AUGUSTUS	transcript	4849071	4850871	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	stop_codon	4849068	4849070	.	-	0	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849071	4849074	1	-	1	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849071	4849074	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849075	4849354	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849355	4849439	1	-	2	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849355	4849439	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849440	4849520	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849521	4849576	1	-	1	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849521	4849576	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849577	4849847	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849848	4849879	0.66	-	0	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849848	4849879	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849880	4850226	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850227	4850310	0.65	-	0	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850227	4850310	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4850311	4850514	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850515	4850692	0.96	-	1	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850515	4850692	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4850693	4850851	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850852	4850871	0.51	-	0	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850852	4850871	.	-	.	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	start_codon	4850869	4850871	.	-	0	transcript_id "Phchi.S5G070500.t1"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	transcript	4849071	4850871	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	stop_codon	4849068	4849070	.	-	0	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849071	4849074	0.99	-	1	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849071	4849074	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849075	4849354	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849355	4849439	0.98	-	2	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849355	4849439	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849440	4849520	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849521	4849576	0.98	-	1	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849521	4849576	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849577	4849729	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849730	4849760	0.82	-	2	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849730	4849760	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849761	4850198	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850199	4850310	0.87	-	0	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850199	4850310	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4850311	4850514	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850515	4850692	0.74	-	1	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850515	4850692	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4850693	4850851	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850852	4850871	0.5	-	0	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850852	4850871	.	-	.	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	start_codon	4850869	4850871	.	-	0	transcript_id "Phchi.S5G070500.t2"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	transcript	4849071	4850871	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	stop_codon	4849068	4849070	.	-	0	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849071	4849074	0.86	-	1	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849071	4849074	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849075	4849354	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849355	4849467	0.8	-	0	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849355	4849467	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849468	4849754	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4849755	4849879	0.75	-	2	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4849755	4849879	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4849880	4850198	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850199	4850310	0.85	-	0	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850199	4850310	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4850311	4850514	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850515	4850692	0.82	-	1	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850515	4850692	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	intron	4850693	4850851	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	CDS	4850852	4850871	0.47	-	0	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	exon	4850852	4850871	.	-	.	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
Phchi.S5	AUGUSTUS	start_codon	4850869	4850871	.	-	0	transcript_id "Phchi.S5G070500.t3"; gene_id "Phchi.S5G070500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9382.t1 is derived from g6558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41257295	41258710	.	-	.	Phchi.S1G654100
Phchi.S1	AUGUSTUS	transcript	41257295	41258710	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	stop_codon	41257292	41257294	.	-	0	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	CDS	41257295	41257347	1	-	2	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	exon	41257295	41257347	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	intron	41257348	41257435	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	CDS	41257436	41257503	1	-	1	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	exon	41257436	41257503	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	intron	41257504	41257861	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	CDS	41257862	41258414	0.64	-	2	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	exon	41257862	41258414	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	intron	41258415	41258514	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	CDS	41258515	41258710	0.51	-	0	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	exon	41258515	41258710	.	-	.	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
Phchi.S1	AUGUSTUS	start_codon	41258708	41258710	.	-	0	transcript_id "Phchi.S1G654100.t1"; gene_id "Phchi.S1G654100"
# This transcript jg14522.t2 is derived from g12990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14523.t1 is derived from g12991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13305389	13307442	.	-	.	Phchi.S3G184200
Phchi.S3	AUGUSTUS	transcript	13305389	13307442	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	stop_codon	13305386	13305388	.	-	0	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13305389	13305538	0.8	-	0	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13305389	13305538	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	intron	13305539	13305649	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13305650	13305697	1	-	0	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13305650	13305697	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	intron	13305698	13305806	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13305807	13305918	1	-	1	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13305807	13305918	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	intron	13305919	13306004	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13306005	13306023	1	-	2	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13306005	13306023	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	intron	13306024	13306529	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13306530	13306592	1	-	2	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13306530	13306592	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	intron	13306593	13306712	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13306713	13306751	1	-	2	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13306713	13306751	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	intron	13306752	13307339	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	CDS	13307340	13307442	0.98	-	0	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	exon	13307340	13307442	.	-	.	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
Phchi.S3	AUGUSTUS	start_codon	13307440	13307442	.	-	0	transcript_id "Phchi.S3G184200.t1"; gene_id "Phchi.S3G184200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5555.t1 is derived from g2725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17577805	17579297	.	-	.	Phchi.S1G271400
Phchi.S1	AUGUSTUS	transcript	17577805	17579297	.	-	.	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	stop_codon	17577802	17577804	.	-	0	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	CDS	17577805	17578183	0.51	-	1	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	exon	17577805	17578183	.	-	.	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	intron	17578184	17578338	.	-	.	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	CDS	17578339	17579297	0.91	-	0	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	exon	17578339	17579297	.	-	.	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
Phchi.S1	AUGUSTUS	start_codon	17579295	17579297	.	-	0	transcript_id "Phchi.S1G271400.t1"; gene_id "Phchi.S1G271400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3040.t1 is derived from g209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1303119	1304035	.	-	.	Phchi.S1G019900
Phchi.S1	AUGUSTUS	transcript	1303119	1304035	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	stop_codon	1303116	1303118	.	-	0	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	CDS	1303119	1303144	0.45	-	2	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	exon	1303119	1303144	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	intron	1303145	1303233	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	CDS	1303234	1303272	0.31	-	2	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	exon	1303234	1303272	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	intron	1303273	1303376	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	CDS	1303377	1303522	0.3	-	1	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	exon	1303377	1303522	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	intron	1303523	1303668	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	CDS	1303669	1303729	0.55	-	2	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	exon	1303669	1303729	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	intron	1303730	1303808	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	CDS	1303809	1303859	0.53	-	2	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	exon	1303809	1303859	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	intron	1303860	1303950	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	CDS	1303951	1304035	0.45	-	0	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	exon	1303951	1304035	.	-	.	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
Phchi.S1	AUGUSTUS	start_codon	1304033	1304035	.	-	0	transcript_id "Phchi.S1G019900.t1"; gene_id "Phchi.S1G019900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6715.t1 is derived from g3887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24689114	24691107	.	-	.	Phchi.S1G387400
Phchi.S1	AUGUSTUS	transcript	24689114	24691107	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	stop_codon	24689111	24689113	.	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24689114	24689234	1	-	1	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24689114	24689234	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24689235	24689321	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24689322	24689378	1	-	1	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24689322	24689378	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24689379	24689483	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24689484	24689584	1	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24689484	24689584	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24689585	24689664	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24689665	24689733	1	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24689665	24689733	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24689734	24689834	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24689835	24689878	1	-	2	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24689835	24689878	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24689879	24689986	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24689987	24690041	1	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24689987	24690041	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24690042	24690131	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24690132	24690216	1	-	1	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24690132	24690216	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24690217	24690343	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24690344	24690447	1	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24690344	24690447	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24690448	24690551	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24690552	24690632	0.99	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24690552	24690632	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24690633	24690746	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24690747	24690797	1	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24690747	24690797	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24690798	24690933	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24690934	24690989	0.97	-	2	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24690934	24690989	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	intron	24690990	24691091	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	CDS	24691092	24691107	0.78	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	exon	24691092	24691107	.	-	.	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
Phchi.S1	AUGUSTUS	start_codon	24691105	24691107	.	-	0	transcript_id "Phchi.S1G387400.t1"; gene_id "Phchi.S1G387400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11550.t1 is derived from g15601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7001260	7005543	.	-	.	Phchi.S4G113200
Phchi.S4	AUGUSTUS	transcript	7001260	7005543	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	stop_codon	7001257	7001259	.	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7001260	7001301	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7001260	7001301	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7001302	7001378	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7001379	7001555	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7001379	7001555	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7001556	7001653	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7001654	7001730	1	-	2	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7001654	7001730	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7001731	7001801	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7001802	7001924	1	-	2	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7001802	7001924	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7001925	7002008	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7002009	7002087	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7002009	7002087	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7002088	7002178	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7002179	7002262	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7002179	7002262	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7002263	7002469	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7002470	7002538	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7002470	7002538	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7002539	7002706	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7002707	7002788	1	-	1	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7002707	7002788	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7002789	7002910	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7002911	7002985	1	-	1	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7002911	7002985	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7002986	7003119	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7003120	7003205	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7003120	7003205	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7003206	7003330	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7003331	7003405	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7003331	7003405	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7003406	7003561	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7003562	7003605	1	-	2	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7003562	7003605	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7003606	7003750	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7003751	7003811	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7003751	7003811	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7003812	7003898	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7003899	7003979	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7003899	7003979	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7003980	7004074	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7004075	7004125	0.79	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7004075	7004125	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7004126	7004216	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7004217	7004295	0.97	-	1	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7004217	7004295	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7004296	7004442	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7004443	7004476	1	-	2	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7004443	7004476	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7004477	7004587	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7004588	7004650	0.98	-	2	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7004588	7004650	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7004651	7004820	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7004821	7004878	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7004821	7004878	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7004879	7004997	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7004998	7005102	1	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7004998	7005102	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7005103	7005210	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7005211	7005263	0.35	-	2	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7005211	7005263	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	intron	7005264	7005368	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	CDS	7005369	7005543	0.42	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	exon	7005369	7005543	.	-	.	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
Phchi.S4	AUGUSTUS	start_codon	7005541	7005543	.	-	0	transcript_id "Phchi.S4G113200.t1"; gene_id "Phchi.S4G113200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13733.t1 is derived from g12200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8642069	8642562	.	-	.	Phchi.S3G105200
Phchi.S3	AUGUSTUS	transcript	8642069	8642562	.	-	.	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	stop_codon	8642066	8642068	.	-	0	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	CDS	8642069	8642335	0.98	-	0	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	exon	8642069	8642335	.	-	.	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	intron	8642336	8642418	.	-	.	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	CDS	8642419	8642562	0.86	-	0	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	exon	8642419	8642562	.	-	.	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
Phchi.S3	AUGUSTUS	start_codon	8642560	8642562	.	-	0	transcript_id "Phchi.S3G105200.t1"; gene_id "Phchi.S3G105200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10563.t1 is derived from g14613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	994412	995392	.	+	.	Phchi.S4G014500
Phchi.S4	AUGUSTUS	transcript	994412	995392	.	+	.	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	start_codon	994412	994414	.	+	0	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	CDS	994412	994640	0.46	+	0	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	exon	994412	994640	.	+	.	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	intron	994641	994733	.	+	.	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	CDS	994734	995392	0.93	+	2	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	exon	994734	995392	.	+	.	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
Phchi.S4	AUGUSTUS	stop_codon	995393	995395	.	+	0	transcript_id "Phchi.S4G014500.t1"; gene_id "Phchi.S4G014500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4906.t1 is derived from g2076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13341593	13342772	.	+	.	Phchi.S1G206500
Phchi.S1	AUGUSTUS	transcript	13341593	13342772	.	+	.	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	start_codon	13341593	13341595	.	+	0	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	CDS	13341593	13341824	0.55	+	0	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	exon	13341593	13341824	.	+	.	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	intron	13341825	13341907	.	+	.	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	CDS	13341908	13342273	0.39	+	2	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	exon	13341908	13342273	.	+	.	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	intron	13342274	13342365	.	+	.	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	CDS	13342366	13342772	0.63	+	2	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	exon	13342366	13342772	.	+	.	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
Phchi.S1	AUGUSTUS	stop_codon	13342773	13342775	.	+	0	transcript_id "Phchi.S1G206500.t1"; gene_id "Phchi.S1G206500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8303.t1 is derived from g5478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35190104	35191285	.	-	.	Phchi.S1G546200
Phchi.S1	AUGUSTUS	transcript	35190104	35191285	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	stop_codon	35190101	35190103	.	-	0	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	CDS	35190104	35190255	0.78	-	2	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	exon	35190104	35190255	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	intron	35190256	35190410	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	CDS	35190411	35190592	0.43	-	1	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	exon	35190411	35190592	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	intron	35190593	35190705	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	CDS	35190706	35190829	0.88	-	2	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	exon	35190706	35190829	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	intron	35190830	35191056	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	CDS	35191057	35191116	0.54	-	2	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	exon	35191057	35191116	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	intron	35191117	35191263	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	CDS	35191264	35191285	0.48	-	0	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	exon	35191264	35191285	.	-	.	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
Phchi.S1	AUGUSTUS	start_codon	35191283	35191285	.	-	0	transcript_id "Phchi.S1G546200.t1"; gene_id "Phchi.S1G546200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg736.t1 is derived from g10518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5246176	5246640	.	-	.	Phchi.S6G069500
Phchi.S6	AUGUSTUS	transcript	5246176	5246640	.	-	.	transcript_id "Phchi.S6G069500.t1"; gene_id "Phchi.S6G069500"
Phchi.S6	AUGUSTUS	stop_codon	5246173	5246175	.	-	0	transcript_id "Phchi.S6G069500.t1"; gene_id "Phchi.S6G069500"
Phchi.S6	AUGUSTUS	CDS	5246176	5246640	0.75	-	0	transcript_id "Phchi.S6G069500.t1"; gene_id "Phchi.S6G069500"
Phchi.S6	AUGUSTUS	exon	5246176	5246640	.	-	.	transcript_id "Phchi.S6G069500.t1"; gene_id "Phchi.S6G069500"
Phchi.S6	AUGUSTUS	start_codon	5246638	5246640	.	-	0	transcript_id "Phchi.S6G069500.t1"; gene_id "Phchi.S6G069500"
# This transcript jg6984.t2 is derived from g4156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6984.t3 is derived from g4156.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6985.t1 is derived from g4157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26273810	26277077	.	+	.	Phchi.S1G414400
Phchi.S1	AUGUSTUS	transcript	26273810	26277077	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	start_codon	26273810	26273812	.	+	0	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	CDS	26273810	26275039	1	+	0	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	exon	26273810	26275039	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	intron	26275040	26275156	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	CDS	26275157	26275457	0.99	+	0	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	exon	26275157	26275457	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	intron	26275458	26275572	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	CDS	26275573	26276434	0.89	+	2	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	exon	26275573	26276434	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	intron	26276435	26276550	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	CDS	26276551	26276600	0.98	+	1	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	exon	26276551	26276600	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	intron	26276601	26276700	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	CDS	26276701	26277077	0.99	+	2	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	exon	26276701	26277077	.	+	.	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
Phchi.S1	AUGUSTUS	stop_codon	26277078	26277080	.	+	0	transcript_id "Phchi.S1G414400.t1"; gene_id "Phchi.S1G414400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4062.t1 is derived from g1231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7587783	7588608	.	+	.	Phchi.S1G122100
Phchi.S1	AUGUSTUS	transcript	7587783	7588608	.	+	.	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	start_codon	7587783	7587785	.	+	0	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	CDS	7587783	7587930	0.47	+	0	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	exon	7587783	7587930	.	+	.	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	intron	7587931	7588025	.	+	.	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	CDS	7588026	7588213	1	+	2	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	exon	7588026	7588213	.	+	.	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	intron	7588214	7588356	.	+	.	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	CDS	7588357	7588608	1	+	0	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	exon	7588357	7588608	.	+	.	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
Phchi.S1	AUGUSTUS	stop_codon	7588609	7588611	.	+	0	transcript_id "Phchi.S1G122100.t1"; gene_id "Phchi.S1G122100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9059.t1 is derived from g6234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39528894	39530036	.	+	.	Phchi.S1G621800
Phchi.S1	AUGUSTUS	transcript	39528894	39530036	.	+	.	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	start_codon	39528894	39528896	.	+	0	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	CDS	39528894	39529403	0.2	+	0	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	exon	39528894	39529403	.	+	.	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	intron	39529404	39529487	.	+	.	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	CDS	39529488	39529667	0.88	+	0	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	exon	39529488	39529667	.	+	.	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	intron	39529668	39529799	.	+	.	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	CDS	39529800	39530036	0.44	+	0	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	exon	39529800	39530036	.	+	.	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
Phchi.S1	AUGUSTUS	stop_codon	39530037	39530039	.	+	0	transcript_id "Phchi.S1G621800.t1"; gene_id "Phchi.S1G621800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7431.t1 is derived from g4603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29094533	29095088	.	-	.	Phchi.S1G459000
Phchi.S1	AUGUSTUS	transcript	29094533	29095088	.	-	.	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	stop_codon	29094530	29094532	.	-	0	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	CDS	29094533	29094718	0.99	-	0	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	exon	29094533	29094718	.	-	.	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	intron	29094719	29094824	.	-	.	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	CDS	29094825	29094941	0.99	-	0	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	exon	29094825	29094941	.	-	.	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	intron	29094942	29095016	.	-	.	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	CDS	29095017	29095088	0.77	-	0	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	exon	29095017	29095088	.	-	.	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
Phchi.S1	AUGUSTUS	start_codon	29095086	29095088	.	-	0	transcript_id "Phchi.S1G459000.t1"; gene_id "Phchi.S1G459000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3371.t1 is derived from g540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3211532	3214516	.	+	.	Phchi.S1G053000
Phchi.S1	AUGUSTUS	transcript	3211532	3214516	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	start_codon	3211532	3211534	.	+	0	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	CDS	3211532	3213416	0.81	+	0	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	exon	3211532	3213416	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	intron	3213417	3213507	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	CDS	3213508	3213666	0.7	+	2	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	exon	3213508	3213666	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	intron	3213667	3213794	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	CDS	3213795	3214017	0.67	+	2	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	exon	3213795	3214017	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	intron	3214018	3214170	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	CDS	3214171	3214516	0.94	+	1	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	exon	3214171	3214516	.	+	.	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
Phchi.S1	AUGUSTUS	stop_codon	3214517	3214519	.	+	0	transcript_id "Phchi.S1G053000.t1"; gene_id "Phchi.S1G053000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13005.t1 is derived from g11470.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3602867	3603847	.	-	.	Phchi.S3G032400
Phchi.S3	AUGUSTUS	transcript	3603387	3603847	.	-	.	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	stop_codon	3603384	3603386	.	-	0	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	CDS	3603387	3603467	1	-	0	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	exon	3603387	3603467	.	-	.	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	intron	3603468	3603580	.	-	.	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	CDS	3603581	3603847	0.84	-	0	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	exon	3603581	3603847	.	-	.	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	start_codon	3603845	3603847	.	-	0	transcript_id "Phchi.S3G032400.t1"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	transcript	3602867	3603847	.	-	.	transcript_id "Phchi.S3G032400.t2"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	stop_codon	3602864	3602866	.	-	0	transcript_id "Phchi.S3G032400.t2"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	CDS	3602867	3603847	0.98	-	0	transcript_id "Phchi.S3G032400.t2"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	exon	3602867	3603847	.	-	.	transcript_id "Phchi.S3G032400.t2"; gene_id "Phchi.S3G032400"
Phchi.S3	AUGUSTUS	start_codon	3603845	3603847	.	-	0	transcript_id "Phchi.S3G032400.t2"; gene_id "Phchi.S3G032400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15550.t1 is derived from g14019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19875153	19876705	.	-	.	Phchi.S3G286900
Phchi.S3	AUGUSTUS	transcript	19875153	19876084	.	-	.	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	stop_codon	19875150	19875152	.	-	0	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	CDS	19875153	19875884	0.65	-	0	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	exon	19875153	19875884	.	-	.	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	intron	19875885	19876012	.	-	.	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	CDS	19876013	19876084	0.54	-	0	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	exon	19876013	19876084	.	-	.	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	start_codon	19876082	19876084	.	-	0	transcript_id "Phchi.S3G286900.t1"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	transcript	19875153	19876705	.	-	.	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	stop_codon	19875150	19875152	.	-	0	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	CDS	19875153	19876075	0.57	-	2	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	exon	19875153	19876075	.	-	.	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	intron	19876076	19876263	.	-	.	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	CDS	19876264	19876705	0.4	-	0	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	exon	19876264	19876705	.	-	.	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
Phchi.S3	AUGUSTUS	start_codon	19876703	19876705	.	-	0	transcript_id "Phchi.S3G286900.t2"; gene_id "Phchi.S3G286900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8514.t1 is derived from g5689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36398715	36400289	.	+	.	Phchi.S1G567300
Phchi.S1	AUGUSTUS	transcript	36398715	36400289	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	start_codon	36398715	36398717	.	+	0	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	CDS	36398715	36398844	0.68	+	0	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	exon	36398715	36398844	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	intron	36398845	36398922	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	CDS	36398923	36399103	1	+	2	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	exon	36398923	36399103	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	intron	36399104	36399189	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	CDS	36399190	36399368	1	+	1	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	exon	36399190	36399368	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	intron	36399369	36399484	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	CDS	36399485	36399676	0.97	+	2	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	exon	36399485	36399676	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	intron	36399677	36399780	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	CDS	36399781	36400289	0.81	+	2	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	exon	36399781	36400289	.	+	.	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
Phchi.S1	AUGUSTUS	stop_codon	36400290	36400292	.	+	0	transcript_id "Phchi.S1G567300.t1"; gene_id "Phchi.S1G567300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14512.t1 is derived from g12980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13240905	13243727	.	+	.	Phchi.S3G183100
Phchi.S3	AUGUSTUS	transcript	13240905	13243727	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	start_codon	13240905	13240907	.	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13240905	13241091	0.57	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13240905	13241091	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13241092	13241196	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13241197	13241396	0.57	+	2	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13241197	13241396	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13241397	13241485	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13241486	13241689	0.66	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13241486	13241689	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13241690	13241830	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13241831	13241922	0.92	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13241831	13241922	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13241923	13242058	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13242059	13242282	1	+	1	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13242059	13242282	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13242283	13242415	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13242416	13242717	1	+	2	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13242416	13242717	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13242718	13242805	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13242806	13242941	1	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13242806	13242941	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13242942	13243037	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13243038	13243212	1	+	2	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13243038	13243212	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13243213	13243296	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13243297	13243456	1	+	1	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13243297	13243456	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	intron	13243457	13243589	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	CDS	13243590	13243727	0.36	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	exon	13243590	13243727	.	+	.	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
Phchi.S3	AUGUSTUS	stop_codon	13243728	13243730	.	+	0	transcript_id "Phchi.S3G183100.t1"; gene_id "Phchi.S3G183100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14880.t1 is derived from g13348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15254045	15255861	.	-	.	Phchi.S3G219900
Phchi.S3	AUGUSTUS	transcript	15254045	15254784	.	-	.	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	stop_codon	15254042	15254044	.	-	0	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	CDS	15254045	15254578	0.97	-	0	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	exon	15254045	15254578	.	-	.	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	intron	15254579	15254658	.	-	.	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	CDS	15254659	15254784	0.71	-	0	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	exon	15254659	15254784	.	-	.	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	start_codon	15254782	15254784	.	-	0	transcript_id "Phchi.S3G219900.t1"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	transcript	15254045	15255861	.	-	.	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	stop_codon	15254042	15254044	.	-	0	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	CDS	15254045	15254578	1	-	0	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	exon	15254045	15254578	.	-	.	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	intron	15254579	15254658	.	-	.	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	CDS	15254659	15255861	0.51	-	0	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	exon	15254659	15255861	.	-	.	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
Phchi.S3	AUGUSTUS	start_codon	15255859	15255861	.	-	0	transcript_id "Phchi.S3G219900.t2"; gene_id "Phchi.S3G219900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9327.t1 is derived from g6502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40953767	40954114	.	-	.	Phchi.S1G648600
Phchi.S1	AUGUSTUS	transcript	40953767	40954114	.	-	.	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	stop_codon	40953764	40953766	.	-	0	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	CDS	40953767	40953887	1	-	1	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	exon	40953767	40953887	.	-	.	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	intron	40953888	40954028	.	-	.	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	CDS	40954029	40954114	0.93	-	0	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	exon	40954029	40954114	.	-	.	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
Phchi.S1	AUGUSTUS	start_codon	40954112	40954114	.	-	0	transcript_id "Phchi.S1G648600.t1"; gene_id "Phchi.S1G648600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11608.t1 is derived from g15659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7310587	7312637	.	+	.	Phchi.S4G119000
Phchi.S4	AUGUSTUS	transcript	7310587	7312637	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	start_codon	7310587	7310589	.	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7310587	7311342	0.79	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7310587	7311342	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	intron	7311343	7311427	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7311428	7311568	1	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7311428	7311568	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	intron	7311569	7311738	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7311739	7311852	1	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7311739	7311852	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	intron	7311853	7311961	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7311962	7312135	1	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7311962	7312135	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	intron	7312136	7312226	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7312227	7312342	0.96	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7312227	7312342	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	intron	7312343	7312444	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7312445	7312550	1	+	1	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7312445	7312550	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	intron	7312551	7312634	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	CDS	7312635	7312637	1	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	exon	7312635	7312637	.	+	.	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
Phchi.S4	AUGUSTUS	stop_codon	7312638	7312640	.	+	0	transcript_id "Phchi.S4G119000.t1"; gene_id "Phchi.S4G119000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4847.t1 is derived from g2017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13083323	13084349	.	+	.	Phchi.S1G200600
Phchi.S1	AUGUSTUS	transcript	13083323	13084349	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	start_codon	13083323	13083325	.	+	0	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	CDS	13083323	13083413	0.65	+	0	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	exon	13083323	13083413	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	intron	13083414	13083677	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	CDS	13083678	13083713	0.24	+	2	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	exon	13083678	13083713	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	intron	13083714	13084125	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	CDS	13084126	13084222	0.79	+	2	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	exon	13084126	13084222	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	intron	13084223	13084321	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	CDS	13084322	13084349	0.98	+	1	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	exon	13084322	13084349	.	+	.	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
Phchi.S1	AUGUSTUS	stop_codon	13084350	13084352	.	+	0	transcript_id "Phchi.S1G200600.t1"; gene_id "Phchi.S1G200600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2849.t1 is derived from g18.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16323	17856	.	-	.	Phchi.S1G000800
Phchi.S1	AUGUSTUS	transcript	16323	17856	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	stop_codon	16320	16322	.	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	16323	16517	1	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	16323	16517	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	16518	16615	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	16616	16702	1	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	16616	16702	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	16703	16774	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	16775	16869	1	-	2	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	16775	16869	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	16870	16954	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	16955	17075	1	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	16955	17075	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	17076	17154	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	17155	17288	1	-	2	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	17155	17288	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	17289	17371	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	17372	17456	1	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	17372	17456	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	17457	17549	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	17550	17695	1	-	2	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	17550	17695	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	intron	17696	17783	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	CDS	17784	17856	0.98	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	exon	17784	17856	.	-	.	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
Phchi.S1	AUGUSTUS	start_codon	17854	17856	.	-	0	transcript_id "Phchi.S1G000800.t1"; gene_id "Phchi.S1G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6444.t1 is derived from g3616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23048159	23049987	.	+	.	Phchi.S1G360300
Phchi.S1	AUGUSTUS	transcript	23048159	23049987	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	start_codon	23048159	23048161	.	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23048159	23048389	0.46	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23048159	23048389	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23048390	23048647	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23048648	23048820	0.97	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23048648	23048820	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23048821	23048906	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23048907	23048982	1	+	1	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23048907	23048982	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23048983	23049069	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049070	23049109	1	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049070	23049109	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049110	23049201	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049202	23049260	1	+	2	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049202	23049260	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049261	23049341	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049342	23049379	1	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049342	23049379	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049380	23049480	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049481	23049544	1	+	1	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049481	23049544	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049545	23049670	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049671	23049724	1	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049671	23049724	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049725	23049801	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049802	23049987	0.37	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049802	23049987	.	+	.	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	stop_codon	23049988	23049990	.	+	0	transcript_id "Phchi.S1G360300.t1"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	transcript	23048159	23049987	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	start_codon	23048159	23048161	.	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23048159	23048389	0.47	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23048159	23048389	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23048390	23048551	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23048552	23048820	0.6	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23048552	23048820	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23048821	23048906	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23048907	23048982	1	+	1	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23048907	23048982	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23048983	23049069	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049070	23049109	1	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049070	23049109	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049110	23049201	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049202	23049260	1	+	2	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049202	23049260	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049261	23049341	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049342	23049379	1	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049342	23049379	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049380	23049480	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049481	23049544	1	+	1	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049481	23049544	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049545	23049670	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049671	23049724	1	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049671	23049724	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	intron	23049725	23049801	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	CDS	23049802	23049987	0.39	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	exon	23049802	23049987	.	+	.	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
Phchi.S1	AUGUSTUS	stop_codon	23049988	23049990	.	+	0	transcript_id "Phchi.S1G360300.t2"; gene_id "Phchi.S1G360300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11150.t1 is derived from g15200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4390318	4392382	.	-	.	Phchi.S4G073200
Phchi.S4	AUGUSTUS	transcript	4390318	4392382	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	stop_codon	4390315	4390317	.	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4390318	4390458	0.98	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4390318	4390458	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4390459	4390550	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4390551	4390630	1	-	2	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4390551	4390630	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4390631	4390705	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4390706	4390955	1	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4390706	4390955	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4390956	4391040	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4391041	4391224	1	-	1	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4391041	4391224	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4391225	4391313	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4391314	4391411	1	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4391314	4391411	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4391412	4391531	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4391532	4391645	1	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4391532	4391645	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4391646	4391734	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4391735	4391989	1	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4391735	4391989	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	intron	4391990	4392058	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	CDS	4392059	4392382	0.98	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	exon	4392059	4392382	.	-	.	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
Phchi.S4	AUGUSTUS	start_codon	4392380	4392382	.	-	0	transcript_id "Phchi.S4G073200.t1"; gene_id "Phchi.S4G073200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10280.t1 is derived from g7456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46798807	46799385	.	-	.	Phchi.S1G743900
Phchi.S1	AUGUSTUS	transcript	46798807	46799385	.	-	.	transcript_id "Phchi.S1G743900.t1"; gene_id "Phchi.S1G743900"
Phchi.S1	AUGUSTUS	stop_codon	46798804	46798806	.	-	0	transcript_id "Phchi.S1G743900.t1"; gene_id "Phchi.S1G743900"
Phchi.S1	AUGUSTUS	CDS	46798807	46799385	1	-	0	transcript_id "Phchi.S1G743900.t1"; gene_id "Phchi.S1G743900"
Phchi.S1	AUGUSTUS	exon	46798807	46799385	.	-	.	transcript_id "Phchi.S1G743900.t1"; gene_id "Phchi.S1G743900"
Phchi.S1	AUGUSTUS	start_codon	46799383	46799385	.	-	0	transcript_id "Phchi.S1G743900.t1"; gene_id "Phchi.S1G743900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10766.t1 is derived from g14816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2009027	2010370	.	+	.	Phchi.S4G034800
Phchi.S4	AUGUSTUS	transcript	2009027	2010370	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	start_codon	2009027	2009029	.	+	0	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	CDS	2009027	2009071	0.44	+	0	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	exon	2009027	2009071	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	intron	2009072	2009160	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	CDS	2009161	2009220	0.45	+	0	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	exon	2009161	2009220	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	intron	2009221	2009420	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	CDS	2009421	2009783	0.97	+	0	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	exon	2009421	2009783	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	intron	2009784	2009878	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	CDS	2009879	2010370	0.99	+	0	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	exon	2009879	2010370	.	+	.	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
Phchi.S4	AUGUSTUS	stop_codon	2010371	2010373	.	+	0	transcript_id "Phchi.S4G034800.t1"; gene_id "Phchi.S4G034800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8854.t1 is derived from g6029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38292134	38292614	.	-	.	Phchi.S1G601300
Phchi.S1	AUGUSTUS	transcript	38292134	38292614	.	-	.	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	stop_codon	38292131	38292133	.	-	0	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	CDS	38292134	38292283	1	-	0	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	exon	38292134	38292283	.	-	.	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	intron	38292284	38292370	.	-	.	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	CDS	38292371	38292472	1	-	0	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	exon	38292371	38292472	.	-	.	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	intron	38292473	38292551	.	-	.	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	CDS	38292552	38292614	0.76	-	0	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	exon	38292552	38292614	.	-	.	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
Phchi.S1	AUGUSTUS	start_codon	38292612	38292614	.	-	0	transcript_id "Phchi.S1G601300.t1"; gene_id "Phchi.S1G601300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13658.t1 is derived from g12125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8041885	8044725	.	+	.	Phchi.S3G097700
Phchi.S3	AUGUSTUS	transcript	8041885	8044725	.	+	.	transcript_id "Phchi.S3G097700.t1"; gene_id "Phchi.S3G097700"
Phchi.S3	AUGUSTUS	start_codon	8041885	8041887	.	+	0	transcript_id "Phchi.S3G097700.t1"; gene_id "Phchi.S3G097700"
Phchi.S3	AUGUSTUS	CDS	8041885	8044725	0.51	+	0	transcript_id "Phchi.S3G097700.t1"; gene_id "Phchi.S3G097700"
Phchi.S3	AUGUSTUS	exon	8041885	8044725	.	+	.	transcript_id "Phchi.S3G097700.t1"; gene_id "Phchi.S3G097700"
Phchi.S3	AUGUSTUS	stop_codon	8044726	8044728	.	+	0	transcript_id "Phchi.S3G097700.t1"; gene_id "Phchi.S3G097700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg417.t1 is derived from g10199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2961560	2962992	.	-	.	Phchi.S6G037600
Phchi.S6	AUGUSTUS	transcript	2961560	2962992	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	stop_codon	2961557	2961559	.	-	0	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	CDS	2961560	2961614	0.6	-	1	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	exon	2961560	2961614	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	intron	2961615	2961788	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	CDS	2961789	2961984	0.45	-	2	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	exon	2961789	2961984	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	intron	2961985	2962299	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	CDS	2962300	2962533	0.72	-	2	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	exon	2962300	2962533	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	intron	2962534	2962655	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	CDS	2962656	2962992	0.44	-	0	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	exon	2962656	2962992	.	-	.	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
Phchi.S6	AUGUSTUS	start_codon	2962990	2962992	.	-	0	transcript_id "Phchi.S6G037600.t1"; gene_id "Phchi.S6G037600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5668.t1 is derived from g2838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18204862	18207794	.	+	.	Phchi.S1G282700
Phchi.S1	AUGUSTUS	transcript	18204862	18207794	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	start_codon	18204862	18204864	.	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18204862	18204901	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18204862	18204901	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18204902	18204993	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18204994	18205091	1	+	2	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18204994	18205091	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18205092	18205165	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18205166	18205204	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18205166	18205204	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18205205	18205326	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18205327	18205383	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18205327	18205383	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18205384	18205488	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18205489	18205557	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18205489	18205557	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18205558	18205815	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18205816	18205884	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18205816	18205884	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18205885	18205978	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18205979	18206024	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18205979	18206024	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18206025	18206153	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18206154	18206202	1	+	2	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18206154	18206202	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18206203	18206292	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18206293	18206386	1	+	1	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18206293	18206386	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18206387	18206508	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18206509	18206561	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18206509	18206561	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18206562	18206660	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18206661	18206745	1	+	1	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18206661	18206745	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18206746	18206836	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18206837	18206939	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18206837	18206939	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18206940	18207033	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18207034	18207126	1	+	2	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18207034	18207126	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18207127	18207215	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18207216	18207282	1	+	2	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18207216	18207282	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18207283	18207368	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18207369	18207435	1	+	1	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18207369	18207435	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18207436	18207526	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18207527	18207580	1	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18207527	18207580	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	intron	18207581	18207662	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	CDS	18207663	18207794	0.99	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	exon	18207663	18207794	.	+	.	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
Phchi.S1	AUGUSTUS	stop_codon	18207795	18207797	.	+	0	transcript_id "Phchi.S1G282700.t1"; gene_id "Phchi.S1G282700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14134.t1 is derived from g12601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11078671	11080560	.	-	.	Phchi.S3G145300
Phchi.S3	AUGUSTUS	transcript	11078671	11080063	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	stop_codon	11078668	11078670	.	-	0	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11078671	11078745	1	-	0	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11078671	11078745	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11078746	11079088	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079089	11079197	1	-	1	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079089	11079197	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079198	11079300	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079301	11079383	1	-	0	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079301	11079383	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079384	11079547	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079548	11079682	1	-	0	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079548	11079682	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079683	11079769	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079770	11080063	0.47	-	0	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079770	11080063	.	-	.	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	start_codon	11080061	11080063	.	-	0	transcript_id "Phchi.S3G145300.t1"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	transcript	11080147	11080560	.	-	.	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	stop_codon	11080144	11080146	.	-	0	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11080147	11080156	0.65	-	1	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11080147	11080156	.	-	.	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11080157	11080232	.	-	.	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11080233	11080331	1	-	1	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11080233	11080331	.	-	.	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11080332	11080426	.	-	.	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11080427	11080560	0.88	-	0	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11080427	11080560	.	-	.	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	start_codon	11080558	11080560	.	-	0	transcript_id "Phchi.S3G145300.t2"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	transcript	11078671	11080560	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	stop_codon	11078668	11078670	.	-	0	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11078671	11078745	1	-	0	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11078671	11078745	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11078746	11079088	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079089	11079197	0.99	-	1	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079089	11079197	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079198	11079300	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079301	11079383	0.99	-	0	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079301	11079383	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079384	11079547	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079548	11079682	1	-	0	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079548	11079682	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079683	11079769	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079770	11079849	0.74	-	2	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079770	11079849	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11079850	11079954	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11079955	11080151	0.53	-	1	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11079955	11080151	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11080152	11080232	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11080233	11080331	1	-	1	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11080233	11080331	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	intron	11080332	11080426	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	CDS	11080427	11080560	0.8	-	0	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	exon	11080427	11080560	.	-	.	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
Phchi.S3	AUGUSTUS	start_codon	11080558	11080560	.	-	0	transcript_id "Phchi.S3G145300.t3"; gene_id "Phchi.S3G145300"
# This transcript jg11032.t2 is derived from g15082.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11033.t1 is derived from g15083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3735594	3736949	.	-	.	Phchi.S4G061500
Phchi.S4	AUGUSTUS	transcript	3735594	3736949	.	-	.	transcript_id "Phchi.S4G061500.t1"; gene_id "Phchi.S4G061500"
Phchi.S4	AUGUSTUS	stop_codon	3735591	3735593	.	-	0	transcript_id "Phchi.S4G061500.t1"; gene_id "Phchi.S4G061500"
Phchi.S4	AUGUSTUS	CDS	3735594	3736949	0.51	-	0	transcript_id "Phchi.S4G061500.t1"; gene_id "Phchi.S4G061500"
Phchi.S4	AUGUSTUS	exon	3735594	3736949	.	-	.	transcript_id "Phchi.S4G061500.t1"; gene_id "Phchi.S4G061500"
Phchi.S4	AUGUSTUS	start_codon	3736947	3736949	.	-	0	transcript_id "Phchi.S4G061500.t1"; gene_id "Phchi.S4G061500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3725.t1 is derived from g894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5407853	5412617	.	-	.	Phchi.S1G088400
Phchi.S1	AUGUSTUS	transcript	5407853	5412617	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	stop_codon	5407850	5407852	.	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5407853	5407963	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5407853	5407963	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5407964	5408037	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5408038	5408268	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5408038	5408268	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5408269	5408358	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5408359	5408421	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5408359	5408421	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5408422	5408515	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5408516	5408654	1	-	1	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5408516	5408654	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5408655	5408740	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5408741	5408925	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5408741	5408925	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5408926	5409010	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5409011	5409094	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5409011	5409094	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5409095	5409199	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5409200	5409322	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5409200	5409322	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5409323	5409425	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5409426	5409605	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5409426	5409605	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5409606	5409770	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5409771	5409938	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5409771	5409938	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5409939	5410038	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5410039	5410132	1	-	1	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5410039	5410132	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5410133	5410250	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5410251	5410347	0.99	-	2	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5410251	5410347	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5410348	5410465	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5410466	5410541	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5410466	5410541	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5410542	5410647	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5410648	5410800	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5410648	5410800	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5410801	5410897	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5410898	5411068	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5410898	5411068	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5411069	5411141	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5411142	5411203	1	-	2	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5411142	5411203	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5411204	5411308	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5411309	5411370	0.99	-	1	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5411309	5411370	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5411371	5411473	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5411474	5411519	0.98	-	2	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5411474	5411519	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5411520	5411604	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5411605	5411707	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5411605	5411707	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5411708	5411797	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5411798	5411836	1	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5411798	5411836	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5411837	5411922	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5411923	5412014	1	-	2	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5411923	5412014	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5412015	5412111	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5412112	5412233	1	-	1	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5412112	5412233	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	intron	5412234	5412330	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	CDS	5412331	5412617	0.77	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	exon	5412331	5412617	.	-	.	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
Phchi.S1	AUGUSTUS	start_codon	5412615	5412617	.	-	0	transcript_id "Phchi.S1G088400.t1"; gene_id "Phchi.S1G088400"
# This transcript jg10126.t2 is derived from g7302.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10127.t1 is derived from g7303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45854770	45857474	.	+	.	Phchi.S1G728600
Phchi.S1	AUGUSTUS	transcript	45854770	45857474	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	start_codon	45854770	45854772	.	+	0	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	CDS	45854770	45855004	0.55	+	0	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	exon	45854770	45855004	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	intron	45855005	45855088	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	CDS	45855089	45855198	1	+	2	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	exon	45855089	45855198	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	intron	45855199	45855288	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	CDS	45855289	45855476	1	+	0	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	exon	45855289	45855476	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	intron	45855477	45855556	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	CDS	45855557	45857474	0.97	+	1	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	exon	45855557	45857474	.	+	.	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
Phchi.S1	AUGUSTUS	stop_codon	45857475	45857477	.	+	0	transcript_id "Phchi.S1G728600.t1"; gene_id "Phchi.S1G728600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6879.t1 is derived from g4051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25774944	25775762	.	-	.	Phchi.S1G403800
Phchi.S1	AUGUSTUS	transcript	25774944	25775762	.	-	.	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	stop_codon	25774941	25774943	.	-	0	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	CDS	25774944	25775600	0.94	-	0	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	exon	25774944	25775600	.	-	.	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	intron	25775601	25775708	.	-	.	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	CDS	25775709	25775762	0.92	-	0	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	exon	25775709	25775762	.	-	.	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
Phchi.S1	AUGUSTUS	start_codon	25775760	25775762	.	-	0	transcript_id "Phchi.S1G403800.t1"; gene_id "Phchi.S1G403800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15473.t1 is derived from g13941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19365644	19366165	.	-	.	Phchi.S3G279200
Phchi.S3	AUGUSTUS	transcript	19365644	19366165	.	-	.	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	stop_codon	19365641	19365643	.	-	0	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	CDS	19365644	19365759	0.73	-	2	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	exon	19365644	19365759	.	-	.	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	intron	19365760	19365845	.	-	.	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	CDS	19365846	19365924	0.99	-	0	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	exon	19365846	19365924	.	-	.	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	intron	19365925	19365991	.	-	.	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	CDS	19365992	19366165	0.51	-	0	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	exon	19365992	19366165	.	-	.	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
Phchi.S3	AUGUSTUS	start_codon	19366163	19366165	.	-	0	transcript_id "Phchi.S3G279200.t1"; gene_id "Phchi.S3G279200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2768.t1 is derived from g9688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8729739	8730593	.	-	.	Phchi.S5G137700
Phchi.S5	AUGUSTUS	transcript	8729739	8730593	.	-	.	transcript_id "Phchi.S5G137700.t1"; gene_id "Phchi.S5G137700"
Phchi.S5	AUGUSTUS	stop_codon	8729736	8729738	.	-	0	transcript_id "Phchi.S5G137700.t1"; gene_id "Phchi.S5G137700"
Phchi.S5	AUGUSTUS	CDS	8729739	8730593	0.99	-	0	transcript_id "Phchi.S5G137700.t1"; gene_id "Phchi.S5G137700"
Phchi.S5	AUGUSTUS	exon	8729739	8730593	.	-	.	transcript_id "Phchi.S5G137700.t1"; gene_id "Phchi.S5G137700"
Phchi.S5	AUGUSTUS	start_codon	8730591	8730593	.	-	0	transcript_id "Phchi.S5G137700.t1"; gene_id "Phchi.S5G137700"
# This transcript jg11928.t2 is derived from g7603.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11929.t1 is derived from g7604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	71766	75193	.	-	.	Phchi.S2G000900
Phchi.S2	AUGUSTUS	transcript	71766	75193	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	stop_codon	71763	71765	.	-	0	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	CDS	71766	72412	0.54	-	2	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	exon	71766	72412	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	intron	72413	72615	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	CDS	72616	73029	0.56	-	2	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	exon	72616	73029	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	intron	73030	73140	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	CDS	73141	73675	0.63	-	0	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	exon	73141	73675	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	intron	73676	73888	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	CDS	73889	74714	0.82	-	1	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	exon	73889	74714	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	intron	74715	74804	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	CDS	74805	74992	1	-	0	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	exon	74805	74992	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	intron	74993	75079	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	CDS	75080	75193	1	-	0	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	exon	75080	75193	.	-	.	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
Phchi.S2	AUGUSTUS	start_codon	75191	75193	.	-	0	transcript_id "Phchi.S2G000900.t1"; gene_id "Phchi.S2G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12340.t1 is derived from g8016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11651469	11652793	.	+	.	Phchi.S2G042000
Phchi.S2	AUGUSTUS	transcript	11651469	11652793	.	+	.	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	start_codon	11651469	11651471	.	+	0	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	CDS	11651469	11651788	0.21	+	0	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	exon	11651469	11651788	.	+	.	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	intron	11651789	11652129	.	+	.	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	CDS	11652130	11652793	0.75	+	1	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	exon	11652130	11652793	.	+	.	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
Phchi.S2	AUGUSTUS	stop_codon	11652794	11652796	.	+	0	transcript_id "Phchi.S2G042000.t1"; gene_id "Phchi.S2G042000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15222.t1 is derived from g13690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17812061	17813083	.	-	.	Phchi.S3G254100
Phchi.S3	AUGUSTUS	transcript	17812061	17813083	.	-	.	transcript_id "Phchi.S3G254100.t1"; gene_id "Phchi.S3G254100"
Phchi.S3	AUGUSTUS	stop_codon	17812058	17812060	.	-	0	transcript_id "Phchi.S3G254100.t1"; gene_id "Phchi.S3G254100"
Phchi.S3	AUGUSTUS	CDS	17812061	17813083	0.52	-	0	transcript_id "Phchi.S3G254100.t1"; gene_id "Phchi.S3G254100"
Phchi.S3	AUGUSTUS	exon	17812061	17813083	.	-	.	transcript_id "Phchi.S3G254100.t1"; gene_id "Phchi.S3G254100"
Phchi.S3	AUGUSTUS	start_codon	17813081	17813083	.	-	0	transcript_id "Phchi.S3G254100.t1"; gene_id "Phchi.S3G254100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11429.t1 is derived from g15479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6295240	6295554	.	-	.	Phchi.S4G101100
Phchi.S4	AUGUSTUS	transcript	6295240	6295554	.	-	.	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	stop_codon	6295237	6295239	.	-	0	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	CDS	6295240	6295424	0.86	-	2	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	exon	6295240	6295424	.	-	.	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	intron	6295425	6295502	.	-	.	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	CDS	6295503	6295554	0.45	-	0	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	exon	6295503	6295554	.	-	.	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
Phchi.S4	AUGUSTUS	start_codon	6295552	6295554	.	-	0	transcript_id "Phchi.S4G101100.t1"; gene_id "Phchi.S4G101100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6228.t1 is derived from g3400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21774853	21776172	.	-	.	Phchi.S1G338700
Phchi.S1	AUGUSTUS	transcript	21774853	21776172	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	stop_codon	21774850	21774852	.	-	0	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21774853	21774929	1	-	2	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21774853	21774929	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	intron	21774930	21775005	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21775006	21775063	1	-	0	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21775006	21775063	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	intron	21775064	21775150	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21775151	21775187	1	-	1	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21775151	21775187	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	intron	21775188	21775326	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21775327	21775523	1	-	0	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21775327	21775523	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	intron	21775524	21775619	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21775620	21775668	0.91	-	1	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21775620	21775668	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	intron	21775669	21775910	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21775911	21775939	0.78	-	0	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21775911	21775939	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	intron	21775940	21776037	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	CDS	21776038	21776172	0.99	-	0	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	exon	21776038	21776172	.	-	.	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
Phchi.S1	AUGUSTUS	start_codon	21776170	21776172	.	-	0	transcript_id "Phchi.S1G338700.t1"; gene_id "Phchi.S1G338700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12001.t1 is derived from g7676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	456361	462760	.	-	.	Phchi.S2G008100
Phchi.S2	AUGUSTUS	transcript	456361	462760	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	stop_codon	456358	456360	.	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	456361	456453	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	456361	456453	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	456454	456564	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	456565	456666	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	456565	456666	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	456667	456796	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	456797	456892	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	456797	456892	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	456893	457022	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	457023	457166	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	457023	457166	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	457167	457362	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	457363	457410	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	457363	457410	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	457411	457495	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	457496	457597	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	457496	457597	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	457598	457692	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	457693	457868	1	-	2	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	457693	457868	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	457869	458005	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	458006	458075	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	458006	458075	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	458076	458753	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	458754	459062	0.59	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	458754	459062	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	459063	459162	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	459163	459260	0.45	-	2	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	459163	459260	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	459261	459348	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	459349	459420	1	-	2	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	459349	459420	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	459421	459498	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	459499	459563	1	-	1	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	459499	459563	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	459564	459723	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	459724	459819	0.96	-	1	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	459724	459819	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	459820	459930	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	459931	460031	0.96	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	459931	460031	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	460032	460260	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	460261	460295	1	-	2	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	460261	460295	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	460296	460390	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	460391	460519	1	-	2	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	460391	460519	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	460520	460786	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	460787	460863	1	-	1	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	460787	460863	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	460864	460952	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	460953	461008	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	460953	461008	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	461009	461107	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	461108	461173	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	461108	461173	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	461174	461340	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	461341	461394	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	461341	461394	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	461395	461560	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	461561	461635	1	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	461561	461635	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	461636	461793	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	461794	462010	0.39	-	1	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	461794	462010	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	462011	462092	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	462093	462136	0.44	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	462093	462136	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	462137	462275	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	462276	462458	0.94	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	462276	462458	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	intron	462459	462736	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	CDS	462737	462760	0.83	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	exon	462737	462760	.	-	.	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
Phchi.S2	AUGUSTUS	start_codon	462758	462760	.	-	0	transcript_id "Phchi.S2G008100.t1"; gene_id "Phchi.S2G008100"
# This transcript jg10870.t2 is derived from g14919.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10871.t1 is derived from g14921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2681390	2681858	.	-	.	Phchi.S4G045300
Phchi.S4	AUGUSTUS	transcript	2681390	2681858	.	-	.	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	stop_codon	2681387	2681389	.	-	0	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	CDS	2681390	2681443	0.56	-	0	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	exon	2681390	2681443	.	-	.	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	intron	2681444	2681600	.	-	.	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	CDS	2681601	2681858	0.62	-	0	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	exon	2681601	2681858	.	-	.	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
Phchi.S4	AUGUSTUS	start_codon	2681856	2681858	.	-	0	transcript_id "Phchi.S4G045300.t1"; gene_id "Phchi.S4G045300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11920.t1 is derived from g15972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9318055	9318399	.	+	.	Phchi.S4G150200
Phchi.S4	AUGUSTUS	transcript	9318055	9318399	.	+	.	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	start_codon	9318055	9318057	.	+	0	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	CDS	9318055	9318105	0.86	+	0	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	exon	9318055	9318105	.	+	.	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	intron	9318106	9318249	.	+	.	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	CDS	9318250	9318399	0.99	+	0	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	exon	9318250	9318399	.	+	.	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
Phchi.S4	AUGUSTUS	stop_codon	9318400	9318402	.	+	0	transcript_id "Phchi.S4G150200.t1"; gene_id "Phchi.S4G150200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5981.t1 is derived from g3152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20227071	20227577	.	+	.	Phchi.S1G314000
Phchi.S1	AUGUSTUS	transcript	20227071	20227577	.	+	.	transcript_id "Phchi.S1G314000.t1"; gene_id "Phchi.S1G314000"
Phchi.S1	AUGUSTUS	start_codon	20227071	20227073	.	+	0	transcript_id "Phchi.S1G314000.t1"; gene_id "Phchi.S1G314000"
Phchi.S1	AUGUSTUS	CDS	20227071	20227577	0.84	+	0	transcript_id "Phchi.S1G314000.t1"; gene_id "Phchi.S1G314000"
Phchi.S1	AUGUSTUS	exon	20227071	20227577	.	+	.	transcript_id "Phchi.S1G314000.t1"; gene_id "Phchi.S1G314000"
Phchi.S1	AUGUSTUS	stop_codon	20227578	20227580	.	+	0	transcript_id "Phchi.S1G314000.t1"; gene_id "Phchi.S1G314000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5498.t1 is derived from g2668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17130932	17132868	.	+	.	Phchi.S1G265700
Phchi.S1	AUGUSTUS	transcript	17130932	17132868	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	start_codon	17130932	17130934	.	+	0	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	CDS	17130932	17131291	0.56	+	0	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	exon	17130932	17131291	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	intron	17131292	17131404	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	CDS	17131405	17131537	1	+	0	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	exon	17131405	17131537	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	intron	17131538	17131677	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	CDS	17131678	17132489	0.88	+	2	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	exon	17131678	17132489	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	intron	17132490	17132592	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	CDS	17132593	17132868	0.99	+	0	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	exon	17132593	17132868	.	+	.	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
Phchi.S1	AUGUSTUS	stop_codon	17132869	17132871	.	+	0	transcript_id "Phchi.S1G265700.t1"; gene_id "Phchi.S1G265700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4953.t1 is derived from g2123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13709307	13718382	.	+	.	Phchi.S1G211200
Phchi.S1	AUGUSTUS	transcript	13709307	13718382	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	start_codon	13709307	13709309	.	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13709307	13709620	0.55	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13709307	13709620	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13709621	13709748	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13709749	13709872	1	+	1	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13709749	13709872	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13709873	13709986	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13709987	13710079	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13709987	13710079	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13710080	13710185	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13710186	13710576	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13710186	13710576	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13710577	13710720	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13710721	13711213	1	+	2	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13710721	13711213	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13711214	13711336	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13711337	13712127	0.98	+	1	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13711337	13712127	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13712128	13712265	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13712266	13712777	0.9	+	2	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13712266	13712777	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13712778	13712864	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13712865	13712936	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13712865	13712936	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13712937	13713060	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13713061	13713365	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13713061	13713365	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13713366	13713457	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13713458	13713912	0.98	+	1	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13713458	13713912	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13713913	13714015	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13714016	13715674	0.98	+	2	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13714016	13715674	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13715675	13715798	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13715799	13715905	1	+	2	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13715799	13715905	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13715906	13716013	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13716014	13716268	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13716014	13716268	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13716269	13716353	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13716354	13716827	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13716354	13716827	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13716828	13716943	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13716944	13717105	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13716944	13717105	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13717106	13717184	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13717185	13717382	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13717185	13717382	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13717383	13717491	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13717492	13717770	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13717492	13717770	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13717771	13717859	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13717860	13718102	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13717860	13718102	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	intron	13718103	13718193	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	CDS	13718194	13718382	1	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	exon	13718194	13718382	.	+	.	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
Phchi.S1	AUGUSTUS	stop_codon	13718383	13718385	.	+	0	transcript_id "Phchi.S1G211200.t1"; gene_id "Phchi.S1G211200"
# This transcript jg13990.t2 is derived from g12457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13991.t1 is derived from g12458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10137514	10138806	.	+	.	Phchi.S3G131000
Phchi.S3	AUGUSTUS	transcript	10137514	10138806	.	+	.	transcript_id "Phchi.S3G131000.t1"; gene_id "Phchi.S3G131000"
Phchi.S3	AUGUSTUS	start_codon	10137514	10137516	.	+	0	transcript_id "Phchi.S3G131000.t1"; gene_id "Phchi.S3G131000"
Phchi.S3	AUGUSTUS	CDS	10137514	10138806	0.67	+	0	transcript_id "Phchi.S3G131000.t1"; gene_id "Phchi.S3G131000"
Phchi.S3	AUGUSTUS	exon	10137514	10138806	.	+	.	transcript_id "Phchi.S3G131000.t1"; gene_id "Phchi.S3G131000"
Phchi.S3	AUGUSTUS	stop_codon	10138807	10138809	.	+	0	transcript_id "Phchi.S3G131000.t1"; gene_id "Phchi.S3G131000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13267.t1 is derived from g11732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4986567	4988905	.	+	.	Phchi.S3G058600
Phchi.S3	AUGUSTUS	transcript	4986567	4988905	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	start_codon	4986567	4986569	.	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4986567	4987174	0.62	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4986567	4987174	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4987175	4987309	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4987310	4987400	1	+	1	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4987310	4987400	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4987401	4987530	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4987531	4987578	1	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4987531	4987578	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4987579	4987696	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4987697	4987755	1	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4987697	4987755	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4987756	4987888	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4987889	4987964	1	+	1	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4987889	4987964	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4987965	4988115	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4988116	4988247	1	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4988116	4988247	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4988248	4988358	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4988359	4988466	1	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4988359	4988466	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4988467	4988550	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4988551	4988605	1	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4988551	4988605	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	intron	4988606	4988693	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	CDS	4988694	4988905	1	+	2	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	exon	4988694	4988905	.	+	.	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
Phchi.S3	AUGUSTUS	stop_codon	4988906	4988908	.	+	0	transcript_id "Phchi.S3G058600.t1"; gene_id "Phchi.S3G058600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6945.t1 is derived from g4117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26089519	26091075	.	+	.	Phchi.S1G410400
Phchi.S1	AUGUSTUS	transcript	26089519	26091075	.	+	.	transcript_id "Phchi.S1G410400.t1"; gene_id "Phchi.S1G410400"
Phchi.S1	AUGUSTUS	start_codon	26089519	26089521	.	+	0	transcript_id "Phchi.S1G410400.t1"; gene_id "Phchi.S1G410400"
Phchi.S1	AUGUSTUS	CDS	26089519	26091075	0.66	+	0	transcript_id "Phchi.S1G410400.t1"; gene_id "Phchi.S1G410400"
Phchi.S1	AUGUSTUS	exon	26089519	26091075	.	+	.	transcript_id "Phchi.S1G410400.t1"; gene_id "Phchi.S1G410400"
Phchi.S1	AUGUSTUS	stop_codon	26091076	26091078	.	+	0	transcript_id "Phchi.S1G410400.t1"; gene_id "Phchi.S1G410400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15033.t1 is derived from g13501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16637824	16640375	.	-	.	Phchi.S3G235200
Phchi.S3	AUGUSTUS	transcript	16637824	16640375	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	stop_codon	16637821	16637823	.	-	0	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16637824	16638461	0.95	-	2	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16637824	16638461	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	intron	16638462	16638547	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16638548	16639342	0.91	-	2	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16638548	16639342	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	intron	16639343	16639448	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16639449	16639581	0.99	-	0	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16639449	16639581	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	intron	16639582	16639726	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16639727	16639787	1	-	1	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16639727	16639787	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	intron	16639788	16639938	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16639939	16639992	0.92	-	1	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16639939	16639992	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	intron	16639993	16640090	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16640091	16640193	0.85	-	2	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16640091	16640193	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	intron	16640194	16640281	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	CDS	16640282	16640375	0.76	-	0	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	exon	16640282	16640375	.	-	.	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
Phchi.S3	AUGUSTUS	start_codon	16640373	16640375	.	-	0	transcript_id "Phchi.S3G235200.t1"; gene_id "Phchi.S3G235200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7519.t1 is derived from g4693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29812541	29813961	.	+	.	Phchi.S1G467800
Phchi.S1	AUGUSTUS	transcript	29812541	29813961	.	+	.	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	start_codon	29812541	29812543	.	+	0	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	CDS	29812541	29812951	0.89	+	0	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	exon	29812541	29812951	.	+	.	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	intron	29812952	29813037	.	+	.	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	CDS	29813038	29813961	1	+	0	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	exon	29813038	29813961	.	+	.	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
Phchi.S1	AUGUSTUS	stop_codon	29813962	29813964	.	+	0	transcript_id "Phchi.S1G467800.t1"; gene_id "Phchi.S1G467800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11564.t1 is derived from g15615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7078931	7080284	.	-	.	Phchi.S4G114600
Phchi.S4	AUGUSTUS	transcript	7078931	7080284	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	stop_codon	7078928	7078930	.	-	0	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	CDS	7078931	7078937	1	-	1	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	exon	7078931	7078937	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	intron	7078938	7079014	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	CDS	7079015	7079130	1	-	0	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	exon	7079015	7079130	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	intron	7079131	7079322	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	CDS	7079323	7079468	0.87	-	2	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	exon	7079323	7079468	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	intron	7079469	7079596	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	CDS	7079597	7079777	0.55	-	0	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	exon	7079597	7079777	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	intron	7079778	7080025	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	CDS	7080026	7080106	0.47	-	0	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	exon	7080026	7080106	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	intron	7080107	7080206	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	CDS	7080207	7080284	0.35	-	0	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	exon	7080207	7080284	.	-	.	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
Phchi.S4	AUGUSTUS	start_codon	7080282	7080284	.	-	0	transcript_id "Phchi.S4G114600.t1"; gene_id "Phchi.S4G114600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15976.t1 is derived from g9819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C54	AUGUSTUS	gene	43166	44192	.	+	.	Phchi.C54G000300
Phchi.C54	AUGUSTUS	transcript	43166	44192	.	+	.	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	start_codon	43166	43168	.	+	0	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	CDS	43166	43573	0.39	+	0	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	exon	43166	43573	.	+	.	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	intron	43574	43643	.	+	.	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	CDS	43644	44192	0.42	+	0	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	exon	43644	44192	.	+	.	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
Phchi.C54	AUGUSTUS	stop_codon	44193	44195	.	+	0	transcript_id "Phchi.C54G000300.t1"; gene_id "Phchi.C54G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14423.t1 is derived from g12891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12749251	12749914	.	-	.	Phchi.S3G174200
Phchi.S3	AUGUSTUS	transcript	12749251	12749914	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	stop_codon	12749248	12749250	.	-	0	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	CDS	12749251	12749482	0.64	-	1	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	exon	12749251	12749482	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	intron	12749483	12749565	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	CDS	12749566	12749607	0.63	-	1	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	exon	12749566	12749607	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	intron	12749608	12749728	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	CDS	12749729	12749748	0.8	-	0	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	exon	12749729	12749748	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	intron	12749749	12749842	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	CDS	12749843	12749914	0.8	-	0	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	exon	12749843	12749914	.	-	.	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
Phchi.S3	AUGUSTUS	start_codon	12749912	12749914	.	-	0	transcript_id "Phchi.S3G174200.t1"; gene_id "Phchi.S3G174200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9500.t1 is derived from g6676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42071961	42074020	.	-	.	Phchi.S1G665900
Phchi.S1	AUGUSTUS	transcript	42071961	42074020	.	-	.	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	stop_codon	42071958	42071960	.	-	0	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	CDS	42071961	42072784	1	-	2	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	exon	42071961	42072784	.	-	.	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	intron	42072785	42072966	.	-	.	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	CDS	42072967	42074020	1	-	0	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	exon	42072967	42074020	.	-	.	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
Phchi.S1	AUGUSTUS	start_codon	42074018	42074020	.	-	0	transcript_id "Phchi.S1G665900.t1"; gene_id "Phchi.S1G665900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10514.t1 is derived from g14564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	788482	790977	.	+	.	Phchi.S4G009600
Phchi.S4	AUGUSTUS	transcript	788482	790977	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	start_codon	788482	788484	.	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	788482	788814	0.94	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	788482	788814	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	788815	788973	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	788974	789482	0.58	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	788974	789482	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	789483	789638	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	789639	789725	1	+	1	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	789639	789725	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	789726	789832	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	789833	789889	1	+	1	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	789833	789889	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	789890	790019	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	790020	790258	1	+	1	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	790020	790258	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	790259	790373	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	790374	790492	1	+	2	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	790374	790492	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	790493	790622	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	790623	790709	1	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	790623	790709	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	790710	790791	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	790792	790842	1	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	790792	790842	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	intron	790843	790920	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	CDS	790921	790977	1	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	exon	790921	790977	.	+	.	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
Phchi.S4	AUGUSTUS	stop_codon	790978	790980	.	+	0	transcript_id "Phchi.S4G009600.t1"; gene_id "Phchi.S4G009600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2556.t1 is derived from g9476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7335954	7337234	.	-	.	Phchi.S5G116500
Phchi.S5	AUGUSTUS	transcript	7335954	7337234	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	stop_codon	7335951	7335953	.	-	0	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	CDS	7335954	7336114	0.46	-	2	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	exon	7335954	7336114	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	intron	7336115	7336226	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	CDS	7336227	7336239	0.58	-	0	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	exon	7336227	7336239	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	intron	7336240	7336382	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	CDS	7336383	7336469	1	-	0	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	exon	7336383	7336469	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	intron	7336470	7336560	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	CDS	7336561	7336598	1	-	2	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	exon	7336561	7336598	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	intron	7336599	7337014	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	CDS	7337015	7337234	0.41	-	0	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	exon	7337015	7337234	.	-	.	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
Phchi.S5	AUGUSTUS	start_codon	7337232	7337234	.	-	0	transcript_id "Phchi.S5G116500.t1"; gene_id "Phchi.S5G116500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13073.t1 is derived from g11538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4033501	4033872	.	-	.	Phchi.S3G039200
Phchi.S3	AUGUSTUS	transcript	4033501	4033872	.	-	.	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	stop_codon	4033498	4033500	.	-	0	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	CDS	4033501	4033665	1	-	0	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	exon	4033501	4033665	.	-	.	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	intron	4033666	4033746	.	-	.	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	CDS	4033747	4033872	0.74	-	0	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	exon	4033747	4033872	.	-	.	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
Phchi.S3	AUGUSTUS	start_codon	4033870	4033872	.	-	0	transcript_id "Phchi.S3G039200.t1"; gene_id "Phchi.S3G039200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg763.t1 is derived from g10545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5388003	5389024	.	+	.	Phchi.S6G072200
Phchi.S6	AUGUSTUS	transcript	5388003	5389024	.	+	.	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	start_codon	5388003	5388005	.	+	0	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	CDS	5388003	5388214	0.77	+	0	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	exon	5388003	5388214	.	+	.	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	intron	5388215	5388329	.	+	.	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	CDS	5388330	5388541	0.78	+	1	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	exon	5388330	5388541	.	+	.	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	intron	5388542	5388656	.	+	.	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	CDS	5388657	5389024	0.99	+	2	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	exon	5388657	5389024	.	+	.	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
Phchi.S6	AUGUSTUS	stop_codon	5389025	5389027	.	+	0	transcript_id "Phchi.S6G072200.t1"; gene_id "Phchi.S6G072200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14008.t1 is derived from g12475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10288220	10289771	.	+	.	Phchi.S3G132700
Phchi.S3	AUGUSTUS	transcript	10288220	10289771	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	start_codon	10288220	10288222	.	+	0	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	CDS	10288220	10288341	0.91	+	0	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	exon	10288220	10288341	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	intron	10288342	10288438	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	CDS	10288439	10288582	0.62	+	1	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	exon	10288439	10288582	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	intron	10288583	10288687	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	CDS	10288688	10288818	1	+	1	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	exon	10288688	10288818	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	intron	10288819	10288908	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	CDS	10288909	10289067	1	+	2	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	exon	10288909	10289067	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	intron	10289068	10289148	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	CDS	10289149	10289771	1	+	2	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	exon	10289149	10289771	.	+	.	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
Phchi.S3	AUGUSTUS	stop_codon	10289772	10289774	.	+	0	transcript_id "Phchi.S3G132700.t1"; gene_id "Phchi.S3G132700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg600.t1 is derived from g10382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4348721	4350998	.	+	.	Phchi.S6G055900
Phchi.S6	AUGUSTUS	transcript	4348721	4350998	.	+	.	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	start_codon	4348721	4348723	.	+	0	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	CDS	4348721	4350166	0.54	+	0	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	exon	4348721	4350166	.	+	.	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	intron	4350167	4350469	.	+	.	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	CDS	4350470	4350855	0.28	+	0	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	exon	4350470	4350855	.	+	.	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	intron	4350856	4350961	.	+	.	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	CDS	4350962	4350998	0.9	+	1	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	exon	4350962	4350998	.	+	.	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
Phchi.S6	AUGUSTUS	stop_codon	4350999	4351001	.	+	0	transcript_id "Phchi.S6G055900.t1"; gene_id "Phchi.S6G055900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14638.t1 is derived from g13106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13882916	13883834	.	+	.	Phchi.S3G195700
Phchi.S3	AUGUSTUS	transcript	13882916	13883834	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	start_codon	13882916	13882918	.	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	CDS	13882916	13882918	1	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	exon	13882916	13882918	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	intron	13882919	13883071	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	CDS	13883072	13883146	1	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	exon	13883072	13883146	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	intron	13883147	13883231	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	CDS	13883232	13883393	1	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	exon	13883232	13883393	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	intron	13883394	13883471	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	CDS	13883472	13883630	1	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	exon	13883472	13883630	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	intron	13883631	13883753	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	CDS	13883754	13883834	1	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	exon	13883754	13883834	.	+	.	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
Phchi.S3	AUGUSTUS	stop_codon	13883835	13883837	.	+	0	transcript_id "Phchi.S3G195700.t1"; gene_id "Phchi.S3G195700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11487.t1 is derived from g15537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6616225	6617324	.	+	.	Phchi.S4G106900
Phchi.S4	AUGUSTUS	transcript	6616225	6617324	.	+	.	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	start_codon	6616225	6616227	.	+	0	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	CDS	6616225	6616971	0.74	+	0	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	exon	6616225	6616971	.	+	.	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	intron	6616972	6617151	.	+	.	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	CDS	6617152	6617222	0.36	+	0	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	exon	6617152	6617222	.	+	.	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	intron	6617223	6617299	.	+	.	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	CDS	6617300	6617324	0.51	+	1	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	exon	6617300	6617324	.	+	.	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
Phchi.S4	AUGUSTUS	stop_codon	6617325	6617327	.	+	0	transcript_id "Phchi.S4G106900.t1"; gene_id "Phchi.S4G106900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg385.t1 is derived from g10167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2799106	2800447	.	+	.	Phchi.S6G034400
Phchi.S6	AUGUSTUS	transcript	2799106	2800447	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	start_codon	2799106	2799108	.	+	0	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	CDS	2799106	2799227	1	+	0	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	exon	2799106	2799227	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	intron	2799228	2799420	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	CDS	2799421	2799474	1	+	1	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	exon	2799421	2799474	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	intron	2799475	2799598	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	CDS	2799599	2799650	1	+	1	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	exon	2799599	2799650	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	intron	2799651	2799757	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	CDS	2799758	2800447	0.41	+	0	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	exon	2799758	2800447	.	+	.	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
Phchi.S6	AUGUSTUS	stop_codon	2800448	2800450	.	+	0	transcript_id "Phchi.S6G034400.t1"; gene_id "Phchi.S6G034400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15878.t1 is derived from g14348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22010462	22011242	.	-	.	Phchi.S3G319700
Phchi.S3	AUGUSTUS	transcript	22010462	22011242	.	-	.	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	stop_codon	22010459	22010461	.	-	0	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	CDS	22010462	22010565	0.44	-	2	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	exon	22010462	22010565	.	-	.	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	intron	22010566	22010679	.	-	.	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	CDS	22010680	22010760	0.74	-	2	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	exon	22010680	22010760	.	-	.	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	intron	22010761	22010956	.	-	.	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	CDS	22010957	22011242	0.57	-	0	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	exon	22010957	22011242	.	-	.	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
Phchi.S3	AUGUSTUS	start_codon	22011240	22011242	.	-	0	transcript_id "Phchi.S3G319700.t1"; gene_id "Phchi.S3G319700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11528.t1 is derived from g15578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6923927	6924835	.	+	.	Phchi.S4G111000
Phchi.S4	AUGUSTUS	transcript	6923927	6924835	.	+	.	transcript_id "Phchi.S4G111000.t1"; gene_id "Phchi.S4G111000"
Phchi.S4	AUGUSTUS	start_codon	6923927	6923929	.	+	0	transcript_id "Phchi.S4G111000.t1"; gene_id "Phchi.S4G111000"
Phchi.S4	AUGUSTUS	CDS	6923927	6924835	0.9	+	0	transcript_id "Phchi.S4G111000.t1"; gene_id "Phchi.S4G111000"
Phchi.S4	AUGUSTUS	exon	6923927	6924835	.	+	.	transcript_id "Phchi.S4G111000.t1"; gene_id "Phchi.S4G111000"
Phchi.S4	AUGUSTUS	stop_codon	6924836	6924838	.	+	0	transcript_id "Phchi.S4G111000.t1"; gene_id "Phchi.S4G111000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2517.t1 is derived from g9437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7106801	7107838	.	+	.	Phchi.S5G112600
Phchi.S5	AUGUSTUS	transcript	7106801	7107838	.	+	.	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	start_codon	7106801	7106803	.	+	0	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	CDS	7106801	7107175	0.9	+	0	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	exon	7106801	7107175	.	+	.	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	intron	7107176	7107337	.	+	.	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	CDS	7107338	7107838	0.99	+	0	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	exon	7107338	7107838	.	+	.	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
Phchi.S5	AUGUSTUS	stop_codon	7107839	7107841	.	+	0	transcript_id "Phchi.S5G112600.t1"; gene_id "Phchi.S5G112600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11741.t1 is derived from g15793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7948658	7953234	.	+	.	Phchi.S4G132300
Phchi.S4	AUGUSTUS	transcript	7948658	7953234	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	start_codon	7948658	7948660	.	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7948658	7949617	1	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7948658	7949617	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7949618	7949711	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7949712	7950360	1	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7949712	7950360	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7950361	7950501	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7950502	7950632	1	+	2	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7950502	7950632	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7950633	7950797	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7950798	7951148	1	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7950798	7951148	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7951149	7951263	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7951264	7951420	1	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7951264	7951420	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7951421	7951519	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7951520	7951812	1	+	2	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7951520	7951812	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7951813	7951911	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7951912	7951971	1	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7951912	7951971	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7951972	7952144	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7952145	7952400	0.99	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7952145	7952400	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7952401	7952502	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7952503	7952633	1	+	2	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7952503	7952633	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7952634	7952772	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7952773	7952974	0.54	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7952773	7952974	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	intron	7952975	7953067	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	CDS	7953068	7953234	0.54	+	2	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	exon	7953068	7953234	.	+	.	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
Phchi.S4	AUGUSTUS	stop_codon	7953235	7953237	.	+	0	transcript_id "Phchi.S4G132300.t1"; gene_id "Phchi.S4G132300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10995.t1 is derived from g15045.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3569314	3570278	.	-	.	Phchi.S4G057700
Phchi.S4	AUGUSTUS	transcript	3569314	3570278	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	stop_codon	3569311	3569313	.	-	0	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3569314	3569621	1	-	2	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3569314	3569621	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	intron	3569622	3569705	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3569706	3569811	1	-	0	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3569706	3569811	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	intron	3569812	3569903	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3569904	3570009	1	-	1	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3569904	3570009	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	intron	3570010	3570168	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3570169	3570278	1	-	0	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3570169	3570278	.	-	.	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	start_codon	3570276	3570278	.	-	0	transcript_id "Phchi.S4G057700.t1"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	transcript	3569314	3570278	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	stop_codon	3569311	3569313	.	-	0	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3569314	3569624	0.99	-	2	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3569314	3569624	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	intron	3569625	3569705	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3569706	3569811	1	-	0	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3569706	3569811	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	intron	3569812	3569903	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3569904	3570009	1	-	1	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3569904	3570009	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	intron	3570010	3570168	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	CDS	3570169	3570278	1	-	0	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	exon	3570169	3570278	.	-	.	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
Phchi.S4	AUGUSTUS	start_codon	3570276	3570278	.	-	0	transcript_id "Phchi.S4G057700.t2"; gene_id "Phchi.S4G057700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9022.t1 is derived from g6197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39184440	39186112	.	-	.	Phchi.S1G618100
Phchi.S1	AUGUSTUS	transcript	39184440	39186112	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	stop_codon	39184437	39184439	.	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39184440	39184511	1	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39184440	39184511	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39184512	39184602	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39184603	39184716	1	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39184603	39184716	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39184717	39184838	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39184839	39184868	1	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39184839	39184868	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39184869	39184960	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39184961	39185066	0.97	-	1	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39184961	39185066	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39185067	39185171	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39185172	39185238	0.95	-	2	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39185172	39185238	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39185239	39185325	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39185326	39185405	0.85	-	1	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39185326	39185405	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39185406	39185491	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39185492	39185601	1	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39185492	39185601	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39185602	39185756	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39185757	39185881	1	-	2	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39185757	39185881	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	intron	39185882	39186015	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	CDS	39186016	39186112	1	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	exon	39186016	39186112	.	-	.	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
Phchi.S1	AUGUSTUS	start_codon	39186110	39186112	.	-	0	transcript_id "Phchi.S1G618100.t1"; gene_id "Phchi.S1G618100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8674.t1 is derived from g5849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37372277	37374243	.	-	.	Phchi.S1G583300
Phchi.S1	AUGUSTUS	transcript	37372277	37374243	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	stop_codon	37372274	37372276	.	-	0	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	CDS	37372277	37372529	1	-	1	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	exon	37372277	37372529	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	intron	37372530	37372620	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	CDS	37372621	37372988	1	-	0	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	exon	37372621	37372988	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	intron	37372989	37373086	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	CDS	37373087	37373401	1	-	0	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	exon	37373087	37373401	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	intron	37373402	37373496	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	CDS	37373497	37373731	1	-	1	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	exon	37373497	37373731	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	intron	37373732	37373803	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	CDS	37373804	37374243	0.83	-	0	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	exon	37373804	37374243	.	-	.	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
Phchi.S1	AUGUSTUS	start_codon	37374241	37374243	.	-	0	transcript_id "Phchi.S1G583300.t1"; gene_id "Phchi.S1G583300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15263.t1 is derived from g13731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18015713	18017535	.	+	.	Phchi.S3G258200
Phchi.S3	AUGUSTUS	transcript	18015713	18017535	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	start_codon	18015713	18015715	.	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18015713	18016084	0.87	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18015713	18016084	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016085	18016178	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18016179	18016379	1	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18016179	18016379	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016380	18016480	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18016481	18016678	0.96	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18016481	18016678	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016679	18016764	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18016765	18016852	0.95	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18016765	18016852	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016853	18017133	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18017134	18017186	1	+	2	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18017134	18017186	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18017187	18017278	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18017279	18017348	1	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18017279	18017348	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18017349	18017506	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18017507	18017535	1	+	2	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18017507	18017535	.	+	.	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	stop_codon	18017536	18017538	.	+	0	transcript_id "Phchi.S3G258200.t1"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	transcript	18015713	18017535	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	start_codon	18015713	18015715	.	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18015713	18016084	0.76	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18015713	18016084	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016085	18016178	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18016179	18016379	1	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18016179	18016379	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016380	18016480	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18016481	18016678	0.9	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18016481	18016678	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016679	18016764	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18016765	18016852	0.84	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18016765	18016852	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18016853	18017013	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18017014	18017186	0.93	+	2	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18017014	18017186	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18017187	18017278	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18017279	18017348	0.93	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18017279	18017348	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	intron	18017349	18017506	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	CDS	18017507	18017535	0.93	+	2	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	exon	18017507	18017535	.	+	.	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
Phchi.S3	AUGUSTUS	stop_codon	18017536	18017538	.	+	0	transcript_id "Phchi.S3G258200.t2"; gene_id "Phchi.S3G258200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7050.t1 is derived from g4222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26621314	26622222	.	-	.	Phchi.S1G420900
Phchi.S1	AUGUSTUS	transcript	26621314	26622222	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	stop_codon	26621311	26621313	.	-	0	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	CDS	26621314	26621580	0.62	-	0	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	exon	26621314	26621580	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	intron	26621581	26621744	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	CDS	26621745	26621825	0.76	-	0	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	exon	26621745	26621825	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	intron	26621826	26621914	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	CDS	26621915	26622010	0.81	-	0	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	exon	26621915	26622010	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	intron	26622011	26622144	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	CDS	26622145	26622222	0.81	-	0	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	exon	26622145	26622222	.	-	.	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
Phchi.S1	AUGUSTUS	start_codon	26622220	26622222	.	-	0	transcript_id "Phchi.S1G420900.t1"; gene_id "Phchi.S1G420900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13908.t1 is derived from g12375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9626668	9627684	.	+	.	Phchi.S3G122700
Phchi.S3	AUGUSTUS	transcript	9626668	9627684	.	+	.	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	start_codon	9626668	9626670	.	+	0	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	CDS	9626668	9627304	0.93	+	0	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	exon	9626668	9627304	.	+	.	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	intron	9627305	9627397	.	+	.	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	CDS	9627398	9627684	1	+	2	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	exon	9627398	9627684	.	+	.	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
Phchi.S3	AUGUSTUS	stop_codon	9627685	9627687	.	+	0	transcript_id "Phchi.S3G122700.t1"; gene_id "Phchi.S3G122700"
# This transcript jg4604.t2 is derived from g1774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4604.t3 is derived from g1774.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4605.t1 is derived from g1775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11320351	11321641	.	-	.	Phchi.S1G176400
Phchi.S1	AUGUSTUS	transcript	11320351	11321641	.	-	.	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	stop_codon	11320348	11320350	.	-	0	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	CDS	11320351	11321033	0.39	-	2	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	exon	11320351	11321033	.	-	.	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	intron	11321034	11321127	.	-	.	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	CDS	11321128	11321641	0.78	-	0	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	exon	11321128	11321641	.	-	.	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
Phchi.S1	AUGUSTUS	start_codon	11321639	11321641	.	-	0	transcript_id "Phchi.S1G176400.t1"; gene_id "Phchi.S1G176400"
# This transcript jg2546.t2 is derived from g9466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2547.t1 is derived from g9467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7269964	7270758	.	-	.	Phchi.S5G115600
Phchi.S5	AUGUSTUS	transcript	7269964	7270758	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	stop_codon	7269961	7269963	.	-	0	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	CDS	7269964	7270093	0.5	-	1	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	exon	7269964	7270093	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	intron	7270094	7270199	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	CDS	7270200	7270332	0.56	-	2	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	exon	7270200	7270332	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	intron	7270333	7270547	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	CDS	7270548	7270639	0.94	-	1	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	exon	7270548	7270639	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	intron	7270640	7270732	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	CDS	7270733	7270758	0.45	-	0	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	exon	7270733	7270758	.	-	.	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
Phchi.S5	AUGUSTUS	start_codon	7270756	7270758	.	-	0	transcript_id "Phchi.S5G115600.t1"; gene_id "Phchi.S5G115600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10164.t1 is derived from g7340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46054482	46056155	.	-	.	Phchi.S1G732300
Phchi.S1	AUGUSTUS	transcript	46054482	46056155	.	-	.	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	stop_codon	46054479	46054481	.	-	0	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	CDS	46054482	46055363	0.62	-	0	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	exon	46054482	46055363	.	-	.	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	intron	46055364	46055522	.	-	.	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	CDS	46055523	46056155	0.45	-	0	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	exon	46055523	46056155	.	-	.	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
Phchi.S1	AUGUSTUS	start_codon	46056153	46056155	.	-	0	transcript_id "Phchi.S1G732300.t1"; gene_id "Phchi.S1G732300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8795.t1 is derived from g5970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38004386	38005060	.	+	.	Phchi.S1G595400
Phchi.S1	AUGUSTUS	transcript	38004386	38005060	.	+	.	transcript_id "Phchi.S1G595400.t1"; gene_id "Phchi.S1G595400"
Phchi.S1	AUGUSTUS	start_codon	38004386	38004388	.	+	0	transcript_id "Phchi.S1G595400.t1"; gene_id "Phchi.S1G595400"
Phchi.S1	AUGUSTUS	CDS	38004386	38005060	0.9	+	0	transcript_id "Phchi.S1G595400.t1"; gene_id "Phchi.S1G595400"
Phchi.S1	AUGUSTUS	exon	38004386	38005060	.	+	.	transcript_id "Phchi.S1G595400.t1"; gene_id "Phchi.S1G595400"
Phchi.S1	AUGUSTUS	stop_codon	38005061	38005063	.	+	0	transcript_id "Phchi.S1G595400.t1"; gene_id "Phchi.S1G595400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7538.t1 is derived from g4712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29952823	29956142	.	+	.	Phchi.S1G469700
Phchi.S1	AUGUSTUS	transcript	29952823	29956142	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	start_codon	29952823	29952825	.	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29952823	29952922	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29952823	29952922	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29952923	29953351	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29953352	29953449	1	+	2	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29953352	29953449	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29953450	29953568	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29953569	29953745	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29953569	29953745	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29953746	29954031	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29954032	29954132	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29954032	29954132	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29954133	29954272	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29954273	29954348	1	+	1	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29954273	29954348	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29954349	29954424	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29954425	29954484	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29954425	29954484	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29954485	29954570	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29954571	29954755	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29954571	29954755	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29954756	29954843	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29954844	29954940	1	+	1	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29954844	29954940	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29954941	29955030	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29955031	29955117	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29955031	29955117	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29955118	29955220	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29955221	29955279	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29955221	29955279	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29955280	29955365	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29955366	29955457	1	+	1	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29955366	29955457	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29955458	29955541	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29955542	29955619	1	+	2	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29955542	29955619	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29955620	29955701	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29955702	29955862	1	+	2	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29955702	29955862	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	intron	29955863	29955935	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	CDS	29955936	29956142	1	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	exon	29955936	29956142	.	+	.	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
Phchi.S1	AUGUSTUS	stop_codon	29956143	29956145	.	+	0	transcript_id "Phchi.S1G469700.t1"; gene_id "Phchi.S1G469700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14710.t1 is derived from g13178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14325238	14325886	.	-	.	Phchi.S3G202900
Phchi.S3	AUGUSTUS	transcript	14325238	14325886	.	-	.	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	stop_codon	14325235	14325237	.	-	0	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	CDS	14325238	14325261	0.81	-	0	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	exon	14325238	14325261	.	-	.	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	intron	14325262	14325478	.	-	.	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	CDS	14325479	14325638	0.82	-	1	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	exon	14325479	14325638	.	-	.	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	intron	14325639	14325806	.	-	.	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	CDS	14325807	14325886	0.73	-	0	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	exon	14325807	14325886	.	-	.	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
Phchi.S3	AUGUSTUS	start_codon	14325884	14325886	.	-	0	transcript_id "Phchi.S3G202900.t1"; gene_id "Phchi.S3G202900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10374.t1 is derived from g7550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47431125	47432036	.	-	.	Phchi.S1G753300
Phchi.S1	AUGUSTUS	transcript	47431125	47432036	.	-	.	transcript_id "Phchi.S1G753300.t1"; gene_id "Phchi.S1G753300"
Phchi.S1	AUGUSTUS	stop_codon	47431122	47431124	.	-	0	transcript_id "Phchi.S1G753300.t1"; gene_id "Phchi.S1G753300"
Phchi.S1	AUGUSTUS	CDS	47431125	47432036	0.65	-	0	transcript_id "Phchi.S1G753300.t1"; gene_id "Phchi.S1G753300"
Phchi.S1	AUGUSTUS	exon	47431125	47432036	.	-	.	transcript_id "Phchi.S1G753300.t1"; gene_id "Phchi.S1G753300"
Phchi.S1	AUGUSTUS	start_codon	47432034	47432036	.	-	0	transcript_id "Phchi.S1G753300.t1"; gene_id "Phchi.S1G753300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10473.t1 is derived from g14522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	552354	555456	.	+	.	Phchi.S4G005500
Phchi.S4	AUGUSTUS	transcript	552354	555456	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	start_codon	552354	552356	.	+	0	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	CDS	552354	552474	0.99	+	0	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	exon	552354	552474	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	intron	552475	552552	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	CDS	552553	552608	1	+	2	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	exon	552553	552608	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	intron	552609	552727	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	CDS	552728	552918	0.53	+	0	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	exon	552728	552918	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	intron	552919	553031	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	CDS	553032	554885	0.71	+	1	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	exon	553032	554885	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	intron	554886	555215	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	CDS	555216	555456	0.44	+	1	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	exon	555216	555456	.	+	.	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
Phchi.S4	AUGUSTUS	stop_codon	555457	555459	.	+	0	transcript_id "Phchi.S4G005500.t1"; gene_id "Phchi.S4G005500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5027.t1 is derived from g2197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14139302	14142035	.	+	.	Phchi.S1G218600
Phchi.S1	AUGUSTUS	transcript	14139302	14142035	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	start_codon	14139302	14139304	.	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14139302	14139576	1	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14139302	14139576	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14139577	14139716	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14139717	14140038	1	+	1	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14139717	14140038	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14140039	14140156	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14140157	14140306	1	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14140157	14140306	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14140307	14140428	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14140429	14140683	1	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14140429	14140683	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14140684	14140827	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14140828	14140914	1	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14140828	14140914	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14140915	14141020	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14141021	14141099	1	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14141021	14141099	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14141100	14141341	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14141342	14141448	1	+	2	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14141342	14141448	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14141449	14141588	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14141589	14141707	1	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14141589	14141707	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	intron	14141708	14141938	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	CDS	14141939	14142035	1	+	1	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	exon	14141939	14142035	.	+	.	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
Phchi.S1	AUGUSTUS	stop_codon	14142036	14142038	.	+	0	transcript_id "Phchi.S1G218600.t1"; gene_id "Phchi.S1G218600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10286.t1 is derived from g7462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46819607	46820574	.	-	.	Phchi.S1G744500
Phchi.S1	AUGUSTUS	transcript	46819607	46820574	.	-	.	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	stop_codon	46819604	46819606	.	-	0	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	CDS	46819607	46819949	0.96	-	1	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	exon	46819607	46819949	.	-	.	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	intron	46819950	46820065	.	-	.	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	CDS	46820066	46820291	0.65	-	2	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	exon	46820066	46820291	.	-	.	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	intron	46820292	46820414	.	-	.	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	CDS	46820415	46820574	0.87	-	0	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	exon	46820415	46820574	.	-	.	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
Phchi.S1	AUGUSTUS	start_codon	46820572	46820574	.	-	0	transcript_id "Phchi.S1G744500.t1"; gene_id "Phchi.S1G744500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12647.t1 is derived from g16014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	28579	30332	.	+	.	Phchi.C136G000700
Phchi.C136	AUGUSTUS	transcript	28579	30332	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	start_codon	28579	28581	.	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	28579	28668	0.6	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	28579	28668	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	28669	28774	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	28775	28897	0.83	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	28775	28897	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	28898	29071	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	29072	29263	1	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	29072	29263	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	29264	29357	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	29358	29441	1	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	29358	29441	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	29442	29538	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	29539	29625	1	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	29539	29625	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	29626	29708	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	29709	29762	1	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	29709	29762	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	29763	29888	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	29889	29971	1	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	29889	29971	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	29972	30065	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	30066	30176	1	+	1	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	30066	30176	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	intron	30177	30256	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	CDS	30257	30332	0.99	+	1	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	exon	30257	30332	.	+	.	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
Phchi.C136	AUGUSTUS	stop_codon	30333	30335	.	+	0	transcript_id "Phchi.C136G000700.t1"; gene_id "Phchi.C136G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg550.t1 is derived from g10332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4016012	4017151	.	+	.	Phchi.S6G050900
Phchi.S6	AUGUSTUS	transcript	4016012	4017151	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	start_codon	4016012	4016014	.	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	CDS	4016012	4016230	0.59	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	exon	4016012	4016230	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	intron	4016231	4016310	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	CDS	4016311	4016411	1	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	exon	4016311	4016411	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	intron	4016412	4016613	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	CDS	4016614	4016653	1	+	1	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	exon	4016614	4016653	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	intron	4016654	4016737	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	CDS	4016738	4016809	1	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	exon	4016738	4016809	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	intron	4016810	4016946	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	CDS	4016947	4017003	1	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	exon	4016947	4017003	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	intron	4017004	4017094	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	CDS	4017095	4017151	1	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	exon	4017095	4017151	.	+	.	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
Phchi.S6	AUGUSTUS	stop_codon	4017152	4017154	.	+	0	transcript_id "Phchi.S6G050900.t1"; gene_id "Phchi.S6G050900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13453.t1 is derived from g11920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6860630	6864989	.	-	.	Phchi.S3G077200
Phchi.S3	AUGUSTUS	transcript	6860630	6864989	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	stop_codon	6860627	6860629	.	-	0	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6860630	6861226	1	-	0	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6860630	6861226	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6861227	6861324	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6861325	6861374	1	-	2	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6861325	6861374	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6861375	6861468	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6861469	6861537	1	-	2	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6861469	6861537	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6861538	6861663	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6861664	6861790	1	-	0	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6861664	6861790	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6861791	6861912	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6861913	6862145	0.91	-	2	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6861913	6862145	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6862146	6862247	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6862248	6862543	1	-	1	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6862248	6862543	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6862544	6862649	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6862650	6862718	1	-	1	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6862650	6862718	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6862719	6862812	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6862813	6862884	1	-	1	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6862813	6862884	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6862885	6862966	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6862967	6863035	1	-	1	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6862967	6863035	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6863036	6863148	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6863149	6863263	1	-	2	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6863149	6863263	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6863264	6863373	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6863374	6863618	0.99	-	1	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6863374	6863618	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6863619	6863706	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6863707	6863979	1	-	1	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6863707	6863979	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6863980	6864084	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6864085	6864356	1	-	0	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6864085	6864356	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6864357	6864442	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6864443	6864726	1	-	2	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6864443	6864726	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	intron	6864727	6864820	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	CDS	6864821	6864989	0.64	-	0	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	exon	6864821	6864989	.	-	.	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
Phchi.S3	AUGUSTUS	start_codon	6864987	6864989	.	-	0	transcript_id "Phchi.S3G077200.t1"; gene_id "Phchi.S3G077200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg471.t1 is derived from g10253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3312410	3313531	.	+	.	Phchi.S6G043000
Phchi.S6	AUGUSTUS	transcript	3312410	3313531	.	+	.	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	start_codon	3312410	3312412	.	+	0	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	CDS	3312410	3312944	1	+	0	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	exon	3312410	3312944	.	+	.	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	intron	3312945	3313154	.	+	.	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	CDS	3313155	3313531	0.96	+	2	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	exon	3313155	3313531	.	+	.	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
Phchi.S6	AUGUSTUS	stop_codon	3313532	3313534	.	+	0	transcript_id "Phchi.S6G043000.t1"; gene_id "Phchi.S6G043000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8430.t1 is derived from g5605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35896114	35904261	.	-	.	Phchi.S1G558900
Phchi.S1	AUGUSTUS	transcript	35896114	35904261	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	stop_codon	35896111	35896113	.	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35896114	35897784	0.33	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35896114	35897784	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35897785	35897893	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35897894	35897978	0.92	-	1	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35897894	35897978	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35897979	35898079	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35898080	35898192	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35898080	35898192	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35898193	35898328	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35898329	35898460	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35898329	35898460	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35898461	35898902	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35898903	35899086	1	-	1	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35898903	35899086	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35899087	35899166	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35899167	35899300	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35899167	35899300	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35899301	35899392	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35899393	35899497	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35899393	35899497	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35899498	35899590	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35899591	35899692	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35899591	35899692	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35899693	35899786	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35899787	35899879	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35899787	35899879	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35899880	35899977	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35899978	35900274	0.98	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35899978	35900274	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35900275	35900346	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35900347	35900448	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35900347	35900448	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35900449	35900546	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35900547	35900609	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35900547	35900609	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35900610	35900743	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35900744	35901212	0.5	-	1	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35900744	35901212	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35901213	35901312	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35901313	35901470	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35901313	35901470	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35901471	35901568	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35901569	35902090	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35901569	35902090	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35902091	35902170	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35902171	35902212	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35902171	35902212	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35902213	35902303	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35902304	35902435	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35902304	35902435	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35902436	35902772	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35902773	35902828	1	-	2	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35902773	35902828	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35902829	35902995	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35902996	35903134	0.74	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35902996	35903134	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35903135	35903220	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35903221	35903414	0.74	-	2	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35903221	35903414	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35903415	35903498	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35903499	35903571	0.99	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35903499	35903571	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35903572	35903677	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35903678	35903770	0.99	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35903678	35903770	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35903771	35903872	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35903873	35903937	0.99	-	2	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35903873	35903937	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	intron	35903938	35904194	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	CDS	35904195	35904261	1	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	exon	35904195	35904261	.	-	.	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
Phchi.S1	AUGUSTUS	start_codon	35904259	35904261	.	-	0	transcript_id "Phchi.S1G558900.t1"; gene_id "Phchi.S1G558900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15210.t1 is derived from g13678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17665683	17667790	.	+	.	Phchi.S3G252900
Phchi.S3	AUGUSTUS	transcript	17665683	17667790	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	start_codon	17665683	17665685	.	+	0	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	CDS	17665683	17666373	0.87	+	0	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	exon	17665683	17666373	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	intron	17666374	17666478	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	CDS	17666479	17666672	0.97	+	2	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	exon	17666479	17666672	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	intron	17666673	17666762	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	CDS	17666763	17667185	1	+	0	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	exon	17666763	17667185	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	intron	17667186	17667302	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	CDS	17667303	17667520	0.98	+	0	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	exon	17667303	17667520	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	intron	17667521	17667612	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	CDS	17667613	17667790	1	+	1	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	exon	17667613	17667790	.	+	.	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
Phchi.S3	AUGUSTUS	stop_codon	17667791	17667793	.	+	0	transcript_id "Phchi.S3G252900.t1"; gene_id "Phchi.S3G252900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7450.t1 is derived from g4622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29270377	29274936	.	-	.	Phchi.S1G460900
Phchi.S1	AUGUSTUS	transcript	29270377	29274936	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	stop_codon	29270374	29270376	.	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29270377	29270404	0.99	-	1	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29270377	29270404	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29270405	29270480	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29270481	29270634	0.8	-	2	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29270481	29270634	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29270635	29270741	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29270742	29270860	0.45	-	1	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29270742	29270860	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29270861	29270972	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29270973	29271133	1	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29270973	29271133	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29271134	29271250	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29271251	29271403	1	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29271251	29271403	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29271404	29271524	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29271525	29271663	0.86	-	1	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29271525	29271663	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29271664	29271773	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29271774	29271874	0.94	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29271774	29271874	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29271875	29271987	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29271988	29272659	1	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29271988	29272659	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29272660	29272769	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29272770	29272855	1	-	2	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29272770	29272855	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29272856	29273034	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29273035	29273673	0.98	-	2	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29273035	29273673	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29273674	29273763	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29273764	29274018	1	-	2	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29273764	29274018	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29274019	29274167	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29274168	29274292	1	-	1	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29274168	29274292	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29274293	29274385	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29274386	29274540	0.99	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29274386	29274540	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	intron	29274541	29274672	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	CDS	29274673	29274936	0.47	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	exon	29274673	29274936	.	-	.	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
Phchi.S1	AUGUSTUS	start_codon	29274934	29274936	.	-	0	transcript_id "Phchi.S1G460900.t1"; gene_id "Phchi.S1G460900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15143.t1 is derived from g13611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17251881	17254048	.	-	.	Phchi.S3G246200
Phchi.S3	AUGUSTUS	transcript	17251881	17254048	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	stop_codon	17251878	17251880	.	-	0	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	CDS	17251881	17251966	1	-	2	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	exon	17251881	17251966	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	intron	17251967	17252053	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	CDS	17252054	17252564	1	-	0	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	exon	17252054	17252564	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	intron	17252565	17252660	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	CDS	17252661	17252750	0.99	-	0	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	exon	17252661	17252750	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	intron	17252751	17252854	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	CDS	17252855	17252898	0.99	-	2	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	exon	17252855	17252898	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	intron	17252899	17252994	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	CDS	17252995	17254048	0.94	-	0	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	exon	17252995	17254048	.	-	.	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
Phchi.S3	AUGUSTUS	start_codon	17254046	17254048	.	-	0	transcript_id "Phchi.S3G246200.t1"; gene_id "Phchi.S3G246200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8720.t1 is derived from g5895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37670218	37671804	.	+	.	Phchi.S1G587900
Phchi.S1	AUGUSTUS	transcript	37670218	37671804	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	start_codon	37670218	37670220	.	+	0	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37670218	37670320	1	+	0	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37670218	37670320	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37670321	37670420	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37670421	37670599	1	+	2	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37670421	37670599	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37670600	37670780	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37670781	37670851	1	+	0	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37670781	37670851	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37670852	37670954	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37670955	37670992	1	+	1	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37670955	37670992	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37670993	37671074	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37671075	37671185	1	+	2	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37671075	37671185	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37671186	37671285	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37671286	37671376	1	+	2	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37671286	37671376	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37671377	37671462	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37671463	37671598	1	+	1	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37671463	37671598	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	intron	37671599	37671687	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	CDS	37671688	37671804	1	+	0	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	exon	37671688	37671804	.	+	.	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
Phchi.S1	AUGUSTUS	stop_codon	37671805	37671807	.	+	0	transcript_id "Phchi.S1G587900.t1"; gene_id "Phchi.S1G587900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13741.t1 is derived from g12208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8665267	8666989	.	+	.	Phchi.S3G106000
Phchi.S3	AUGUSTUS	transcript	8665267	8666989	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	start_codon	8665267	8665269	.	+	0	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	CDS	8665267	8665564	0.84	+	0	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	exon	8665267	8665564	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	intron	8665565	8665720	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	CDS	8665721	8665851	0.99	+	2	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	exon	8665721	8665851	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	intron	8665852	8665944	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	CDS	8665945	8666187	0.85	+	0	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	exon	8665945	8666187	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	intron	8666188	8666327	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	CDS	8666328	8666601	1	+	0	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	exon	8666328	8666601	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	intron	8666602	8666801	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	CDS	8666802	8666989	0.96	+	2	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	exon	8666802	8666989	.	+	.	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
Phchi.S3	AUGUSTUS	stop_codon	8666990	8666992	.	+	0	transcript_id "Phchi.S3G106000.t1"; gene_id "Phchi.S3G106000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5674.t1 is derived from g2844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18243878	18245440	.	+	.	Phchi.S1G283300
Phchi.S1	AUGUSTUS	transcript	18243878	18245440	.	+	.	transcript_id "Phchi.S1G283300.t1"; gene_id "Phchi.S1G283300"
Phchi.S1	AUGUSTUS	start_codon	18243878	18243880	.	+	0	transcript_id "Phchi.S1G283300.t1"; gene_id "Phchi.S1G283300"
Phchi.S1	AUGUSTUS	CDS	18243878	18245440	0.75	+	0	transcript_id "Phchi.S1G283300.t1"; gene_id "Phchi.S1G283300"
Phchi.S1	AUGUSTUS	exon	18243878	18245440	.	+	.	transcript_id "Phchi.S1G283300.t1"; gene_id "Phchi.S1G283300"
Phchi.S1	AUGUSTUS	stop_codon	18245441	18245443	.	+	0	transcript_id "Phchi.S1G283300.t1"; gene_id "Phchi.S1G283300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13818.t1 is derived from g12285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9055558	9059400	.	-	.	Phchi.S3G113700
Phchi.S3	AUGUSTUS	transcript	9055558	9059400	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	stop_codon	9055555	9055557	.	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9055558	9056151	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9055558	9056151	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9056152	9056234	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9056235	9056492	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9056235	9056492	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9056493	9056561	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9056562	9056828	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9056562	9056828	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9056829	9056952	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9056953	9057045	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9056953	9057045	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057046	9057145	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057146	9057217	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057146	9057217	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057218	9057365	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057366	9057444	0.7	-	1	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057366	9057444	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057445	9057546	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057547	9057650	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057547	9057650	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057651	9057800	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057801	9057854	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057801	9057854	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057855	9058036	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058037	9058114	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058037	9058114	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058115	9058265	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058266	9058343	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058266	9058343	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058344	9058551	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058552	9058695	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058552	9058695	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058696	9058828	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058829	9058906	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058829	9058906	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058907	9059067	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9059068	9059154	1	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9059068	9059154	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9059155	9059262	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9059263	9059400	0.59	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9059263	9059400	.	-	.	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	start_codon	9059398	9059400	.	-	0	transcript_id "Phchi.S3G113700.t1"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	transcript	9055558	9059400	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	stop_codon	9055555	9055557	.	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9055558	9056151	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9055558	9056151	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9056152	9056234	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9056235	9056489	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9056235	9056489	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9056490	9056561	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9056562	9056828	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9056562	9056828	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9056829	9056952	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9056953	9057045	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9056953	9057045	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057046	9057145	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057146	9057217	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057146	9057217	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057218	9057365	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057366	9057444	0.67	-	1	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057366	9057444	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057445	9057546	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057547	9057650	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057547	9057650	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057651	9057800	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9057801	9057854	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9057801	9057854	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9057855	9058036	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058037	9058114	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058037	9058114	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058115	9058265	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058266	9058343	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058266	9058343	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058344	9058551	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058552	9058695	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058552	9058695	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058696	9058828	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9058829	9058906	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9058829	9058906	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9058907	9059067	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9059068	9059154	1	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9059068	9059154	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	intron	9059155	9059262	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	CDS	9059263	9059400	0.56	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	exon	9059263	9059400	.	-	.	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
Phchi.S3	AUGUSTUS	start_codon	9059398	9059400	.	-	0	transcript_id "Phchi.S3G113700.t2"; gene_id "Phchi.S3G113700"
# This transcript jg3183.t2 is derived from g352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3184.t1 is derived from g353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2133959	2135170	.	-	.	Phchi.S1G034300
Phchi.S1	AUGUSTUS	transcript	2133959	2135170	.	-	.	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	stop_codon	2133956	2133958	.	-	0	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	CDS	2133959	2134741	0.67	-	0	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	exon	2133959	2134741	.	-	.	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	intron	2134742	2134831	.	-	.	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	CDS	2134832	2135170	0.99	-	0	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	exon	2134832	2135170	.	-	.	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
Phchi.S1	AUGUSTUS	start_codon	2135168	2135170	.	-	0	transcript_id "Phchi.S1G034300.t1"; gene_id "Phchi.S1G034300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2027.t1 is derived from g8947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4505905	4509598	.	-	.	Phchi.S5G063600
Phchi.S5	AUGUSTUS	transcript	4505905	4509598	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	stop_codon	4505902	4505904	.	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4505905	4505938	1	-	1	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4505905	4505938	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4505939	4506017	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4506018	4506148	1	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4506018	4506148	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4506149	4506289	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4506290	4506394	1	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4506290	4506394	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4506395	4506489	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4506490	4506622	1	-	1	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4506490	4506622	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4506623	4506763	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4506764	4506968	1	-	2	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4506764	4506968	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4506969	4507068	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4507069	4507174	1	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4507069	4507174	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4507175	4507344	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4507345	4508460	0.92	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4507345	4508460	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4508461	4508613	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4508614	4508719	1	-	1	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4508614	4508719	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4508720	4508845	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4508846	4509018	1	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4508846	4509018	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4509019	4509113	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4509114	4509396	0.51	-	1	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4509114	4509396	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4509397	4509512	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4509513	4509598	0.53	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4509513	4509598	.	-	.	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	start_codon	4509596	4509598	.	-	0	transcript_id "Phchi.S5G063600.t1"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	transcript	4508363	4509598	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	stop_codon	4508360	4508362	.	-	0	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4508363	4508407	0.82	-	0	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4508363	4508407	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4508408	4508613	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4508614	4508719	1	-	1	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4508614	4508719	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4508720	4508845	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4508846	4509018	1	-	0	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4508846	4509018	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4509019	4509113	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4509114	4509396	0.38	-	1	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4509114	4509396	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	intron	4509397	4509512	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	CDS	4509513	4509598	0.41	-	0	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	exon	4509513	4509598	.	-	.	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
Phchi.S5	AUGUSTUS	start_codon	4509596	4509598	.	-	0	transcript_id "Phchi.S5G063600.t2"; gene_id "Phchi.S5G063600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15463.t1 is derived from g13931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19300874	19301594	.	+	.	Phchi.S3G278200
Phchi.S3	AUGUSTUS	transcript	19300874	19301594	.	+	.	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	start_codon	19300874	19300876	.	+	0	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	CDS	19300874	19300897	0.4	+	0	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	exon	19300874	19300897	.	+	.	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	intron	19300898	19300974	.	+	.	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	CDS	19300975	19301180	0.99	+	0	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	exon	19300975	19301180	.	+	.	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	intron	19301181	19301302	.	+	.	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	CDS	19301303	19301594	0.95	+	1	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	exon	19301303	19301594	.	+	.	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
Phchi.S3	AUGUSTUS	stop_codon	19301595	19301597	.	+	0	transcript_id "Phchi.S3G278200.t1"; gene_id "Phchi.S3G278200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6107.t1 is derived from g3278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20972071	20972956	.	-	.	Phchi.S1G326600
Phchi.S1	AUGUSTUS	transcript	20972071	20972956	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	stop_codon	20972068	20972070	.	-	0	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	CDS	20972071	20972142	1	-	0	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	exon	20972071	20972142	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	intron	20972143	20972230	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	CDS	20972231	20972285	1	-	1	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	exon	20972231	20972285	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	intron	20972286	20972366	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	CDS	20972367	20972474	1	-	1	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	exon	20972367	20972474	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	intron	20972475	20972556	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	CDS	20972557	20972658	1	-	1	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	exon	20972557	20972658	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	intron	20972659	20972750	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	CDS	20972751	20972780	1	-	1	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	exon	20972751	20972780	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	intron	20972781	20972867	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	CDS	20972868	20972956	1	-	0	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	exon	20972868	20972956	.	-	.	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
Phchi.S1	AUGUSTUS	start_codon	20972954	20972956	.	-	0	transcript_id "Phchi.S1G326600.t1"; gene_id "Phchi.S1G326600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5008.t1 is derived from g2178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14008454	14009576	.	-	.	Phchi.S1G216700
Phchi.S1	AUGUSTUS	transcript	14008454	14009576	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	stop_codon	14008451	14008453	.	-	0	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	CDS	14008454	14008618	0.9	-	0	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	exon	14008454	14008618	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	intron	14008619	14008702	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	CDS	14008703	14008860	1	-	2	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	exon	14008703	14008860	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	intron	14008861	14008935	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	CDS	14008936	14009034	1	-	2	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	exon	14008936	14009034	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	intron	14009035	14009120	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	CDS	14009121	14009372	1	-	2	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	exon	14009121	14009372	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	intron	14009373	14009470	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	CDS	14009471	14009576	1	-	0	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	exon	14009471	14009576	.	-	.	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
Phchi.S1	AUGUSTUS	start_codon	14009574	14009576	.	-	0	transcript_id "Phchi.S1G216700.t1"; gene_id "Phchi.S1G216700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5113.t1 is derived from g2283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14791656	14793357	.	+	.	Phchi.S1G227200
Phchi.S1	AUGUSTUS	transcript	14791656	14793357	.	+	.	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	start_codon	14791656	14791658	.	+	0	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	CDS	14791656	14791907	1	+	0	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	exon	14791656	14791907	.	+	.	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	intron	14791908	14792047	.	+	.	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	CDS	14792048	14792455	1	+	0	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	exon	14792048	14792455	.	+	.	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	intron	14792456	14792544	.	+	.	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	CDS	14792545	14793357	1	+	0	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	exon	14792545	14793357	.	+	.	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
Phchi.S1	AUGUSTUS	stop_codon	14793358	14793360	.	+	0	transcript_id "Phchi.S1G227200.t1"; gene_id "Phchi.S1G227200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8889.t1 is derived from g6064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38497069	38498150	.	-	.	Phchi.S1G604800
Phchi.S1	AUGUSTUS	transcript	38497069	38498150	.	-	.	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	stop_codon	38497066	38497068	.	-	0	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	CDS	38497069	38497473	0.99	-	0	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	exon	38497069	38497473	.	-	.	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	intron	38497474	38497562	.	-	.	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	CDS	38497563	38497687	1	-	2	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	exon	38497563	38497687	.	-	.	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	intron	38497688	38497780	.	-	.	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	CDS	38497781	38498150	0.84	-	0	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	exon	38497781	38498150	.	-	.	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
Phchi.S1	AUGUSTUS	start_codon	38498148	38498150	.	-	0	transcript_id "Phchi.S1G604800.t1"; gene_id "Phchi.S1G604800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4263.t1 is derived from g1432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9235529	9236808	.	+	.	Phchi.S1G142200
Phchi.S1	AUGUSTUS	transcript	9235529	9236808	.	+	.	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	start_codon	9235529	9235531	.	+	0	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	CDS	9235529	9236225	0.95	+	0	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	exon	9235529	9236225	.	+	.	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	intron	9236226	9236338	.	+	.	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	CDS	9236339	9236403	1	+	2	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	exon	9236339	9236403	.	+	.	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	intron	9236404	9236508	.	+	.	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	CDS	9236509	9236808	0.98	+	0	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	exon	9236509	9236808	.	+	.	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
Phchi.S1	AUGUSTUS	stop_codon	9236809	9236811	.	+	0	transcript_id "Phchi.S1G142200.t1"; gene_id "Phchi.S1G142200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg674.t1 is derived from g10456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4656835	4657967	.	-	.	Phchi.S6G063300
Phchi.S6	AUGUSTUS	transcript	4656835	4657967	.	-	.	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	stop_codon	4656832	4656834	.	-	0	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	CDS	4656835	4657043	0.98	-	2	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	exon	4656835	4657043	.	-	.	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	intron	4657044	4657126	.	-	.	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	CDS	4657127	4657967	0.95	-	0	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	exon	4657127	4657967	.	-	.	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
Phchi.S6	AUGUSTUS	start_codon	4657965	4657967	.	-	0	transcript_id "Phchi.S6G063300.t1"; gene_id "Phchi.S6G063300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8449.t1 is derived from g5624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35988057	35988856	.	-	.	Phchi.S1G560800
Phchi.S1	AUGUSTUS	transcript	35988057	35988856	.	-	.	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	stop_codon	35988054	35988056	.	-	0	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	CDS	35988057	35988215	1	-	0	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	exon	35988057	35988215	.	-	.	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	intron	35988216	35988329	.	-	.	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	CDS	35988330	35988473	1	-	0	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	exon	35988330	35988473	.	-	.	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	intron	35988474	35988670	.	-	.	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	CDS	35988671	35988856	0.96	-	0	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	exon	35988671	35988856	.	-	.	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
Phchi.S1	AUGUSTUS	start_codon	35988854	35988856	.	-	0	transcript_id "Phchi.S1G560800.t1"; gene_id "Phchi.S1G560800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4225.t1 is derived from g1394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9005462	9006799	.	+	.	Phchi.S1G138400
Phchi.S1	AUGUSTUS	transcript	9005462	9006799	.	+	.	transcript_id "Phchi.S1G138400.t1"; gene_id "Phchi.S1G138400"
Phchi.S1	AUGUSTUS	start_codon	9005462	9005464	.	+	0	transcript_id "Phchi.S1G138400.t1"; gene_id "Phchi.S1G138400"
Phchi.S1	AUGUSTUS	CDS	9005462	9006799	1	+	0	transcript_id "Phchi.S1G138400.t1"; gene_id "Phchi.S1G138400"
Phchi.S1	AUGUSTUS	exon	9005462	9006799	.	+	.	transcript_id "Phchi.S1G138400.t1"; gene_id "Phchi.S1G138400"
Phchi.S1	AUGUSTUS	stop_codon	9006800	9006802	.	+	0	transcript_id "Phchi.S1G138400.t1"; gene_id "Phchi.S1G138400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6796.t1 is derived from g3968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25113934	25114745	.	+	.	Phchi.S1G395500
Phchi.S1	AUGUSTUS	transcript	25113934	25114745	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	start_codon	25113934	25113936	.	+	0	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	CDS	25113934	25113952	1	+	0	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	exon	25113934	25113952	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	intron	25113953	25114235	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	CDS	25114236	25114366	0.98	+	2	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	exon	25114236	25114366	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	intron	25114367	25114469	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	CDS	25114470	25114551	0.99	+	0	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	exon	25114470	25114551	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	intron	25114552	25114695	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	CDS	25114696	25114745	1	+	2	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	exon	25114696	25114745	.	+	.	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
Phchi.S1	AUGUSTUS	stop_codon	25114746	25114748	.	+	0	transcript_id "Phchi.S1G395500.t1"; gene_id "Phchi.S1G395500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5876.t1 is derived from g3046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19527321	19528352	.	+	.	Phchi.S1G303500
Phchi.S1	AUGUSTUS	transcript	19527321	19528352	.	+	.	transcript_id "Phchi.S1G303500.t1"; gene_id "Phchi.S1G303500"
Phchi.S1	AUGUSTUS	start_codon	19527321	19527323	.	+	0	transcript_id "Phchi.S1G303500.t1"; gene_id "Phchi.S1G303500"
Phchi.S1	AUGUSTUS	CDS	19527321	19528352	0.65	+	0	transcript_id "Phchi.S1G303500.t1"; gene_id "Phchi.S1G303500"
Phchi.S1	AUGUSTUS	exon	19527321	19528352	.	+	.	transcript_id "Phchi.S1G303500.t1"; gene_id "Phchi.S1G303500"
Phchi.S1	AUGUSTUS	stop_codon	19528353	19528355	.	+	0	transcript_id "Phchi.S1G303500.t1"; gene_id "Phchi.S1G303500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13718.t1 is derived from g12185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8497468	8498397	.	+	.	Phchi.S3G103700
Phchi.S3	AUGUSTUS	transcript	8497468	8498397	.	+	.	transcript_id "Phchi.S3G103700.t1"; gene_id "Phchi.S3G103700"
Phchi.S3	AUGUSTUS	start_codon	8497468	8497470	.	+	0	transcript_id "Phchi.S3G103700.t1"; gene_id "Phchi.S3G103700"
Phchi.S3	AUGUSTUS	CDS	8497468	8498397	0.91	+	0	transcript_id "Phchi.S3G103700.t1"; gene_id "Phchi.S3G103700"
Phchi.S3	AUGUSTUS	exon	8497468	8498397	.	+	.	transcript_id "Phchi.S3G103700.t1"; gene_id "Phchi.S3G103700"
Phchi.S3	AUGUSTUS	stop_codon	8498398	8498400	.	+	0	transcript_id "Phchi.S3G103700.t1"; gene_id "Phchi.S3G103700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2623.t1 is derived from g9543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7807933	7809123	.	-	.	Phchi.S5G123200
Phchi.S5	AUGUSTUS	transcript	7807933	7809123	.	-	.	transcript_id "Phchi.S5G123200.t1"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	stop_codon	7807930	7807932	.	-	0	transcript_id "Phchi.S5G123200.t1"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	CDS	7807933	7809123	0.49	-	0	transcript_id "Phchi.S5G123200.t1"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	exon	7807933	7809123	.	-	.	transcript_id "Phchi.S5G123200.t1"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	start_codon	7809121	7809123	.	-	0	transcript_id "Phchi.S5G123200.t1"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	transcript	7807933	7808463	.	-	.	transcript_id "Phchi.S5G123200.t2"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	stop_codon	7807930	7807932	.	-	0	transcript_id "Phchi.S5G123200.t2"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	CDS	7807933	7808463	0.44	-	0	transcript_id "Phchi.S5G123200.t2"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	exon	7807933	7808463	.	-	.	transcript_id "Phchi.S5G123200.t2"; gene_id "Phchi.S5G123200"
Phchi.S5	AUGUSTUS	start_codon	7808461	7808463	.	-	0	transcript_id "Phchi.S5G123200.t2"; gene_id "Phchi.S5G123200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7637.t1 is derived from g4811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30350067	30350465	.	-	.	Phchi.S1G479600
Phchi.S1	AUGUSTUS	transcript	30350067	30350465	.	-	.	transcript_id "Phchi.S1G479600.t1"; gene_id "Phchi.S1G479600"
Phchi.S1	AUGUSTUS	stop_codon	30350064	30350066	.	-	0	transcript_id "Phchi.S1G479600.t1"; gene_id "Phchi.S1G479600"
Phchi.S1	AUGUSTUS	CDS	30350067	30350465	0.76	-	0	transcript_id "Phchi.S1G479600.t1"; gene_id "Phchi.S1G479600"
Phchi.S1	AUGUSTUS	exon	30350067	30350465	.	-	.	transcript_id "Phchi.S1G479600.t1"; gene_id "Phchi.S1G479600"
Phchi.S1	AUGUSTUS	start_codon	30350463	30350465	.	-	0	transcript_id "Phchi.S1G479600.t1"; gene_id "Phchi.S1G479600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10692.t1 is derived from g14742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1601187	1604798	.	-	.	Phchi.S4G027400
Phchi.S4	AUGUSTUS	transcript	1601187	1604798	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	stop_codon	1601184	1601186	.	-	0	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1601187	1601329	0.96	-	2	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1601187	1601329	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1601330	1601517	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1601518	1601589	1	-	2	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1601518	1601589	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1601590	1601671	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1601672	1601741	1	-	0	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1601672	1601741	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1601742	1601914	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1601915	1602002	1	-	1	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1601915	1602002	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1602003	1602101	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1602102	1602178	1	-	0	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1602102	1602178	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1602179	1602386	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1602387	1602555	1	-	1	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1602387	1602555	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1602556	1602698	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1602699	1602929	1	-	1	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1602699	1602929	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1602930	1603072	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1603073	1603317	0.99	-	0	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1603073	1603317	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1603318	1603468	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1603469	1603601	1	-	1	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1603469	1603601	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	intron	1603602	1604469	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	CDS	1604470	1604798	0.9	-	0	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	exon	1604470	1604798	.	-	.	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
Phchi.S4	AUGUSTUS	start_codon	1604796	1604798	.	-	0	transcript_id "Phchi.S4G027400.t1"; gene_id "Phchi.S4G027400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3478.t1 is derived from g647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3984579	3984974	.	-	.	Phchi.S1G063700
Phchi.S1	AUGUSTUS	transcript	3984579	3984974	.	-	.	transcript_id "Phchi.S1G063700.t1"; gene_id "Phchi.S1G063700"
Phchi.S1	AUGUSTUS	stop_codon	3984576	3984578	.	-	0	transcript_id "Phchi.S1G063700.t1"; gene_id "Phchi.S1G063700"
Phchi.S1	AUGUSTUS	CDS	3984579	3984974	0.8	-	0	transcript_id "Phchi.S1G063700.t1"; gene_id "Phchi.S1G063700"
Phchi.S1	AUGUSTUS	exon	3984579	3984974	.	-	.	transcript_id "Phchi.S1G063700.t1"; gene_id "Phchi.S1G063700"
Phchi.S1	AUGUSTUS	start_codon	3984972	3984974	.	-	0	transcript_id "Phchi.S1G063700.t1"; gene_id "Phchi.S1G063700"
# This transcript jg1639.t2 is derived from g8558.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1640.t1 is derived from g8559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2151749	2153102	.	-	.	Phchi.S5G024900
Phchi.S5	AUGUSTUS	transcript	2151749	2153102	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	stop_codon	2151746	2151748	.	-	0	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	CDS	2151749	2151934	0.96	-	0	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	exon	2151749	2151934	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	intron	2151935	2152011	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	CDS	2152012	2152364	0.85	-	2	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	exon	2152012	2152364	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	intron	2152365	2152455	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	CDS	2152456	2152687	1	-	0	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	exon	2152456	2152687	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	intron	2152688	2152830	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	CDS	2152831	2152880	1	-	2	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	exon	2152831	2152880	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	intron	2152881	2152960	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	CDS	2152961	2153102	0.99	-	0	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	exon	2152961	2153102	.	-	.	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
Phchi.S5	AUGUSTUS	start_codon	2153100	2153102	.	-	0	transcript_id "Phchi.S5G024900.t1"; gene_id "Phchi.S5G024900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15066.t1 is derived from g13534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16845380	16852329	.	-	.	Phchi.S3G238500
Phchi.S3	AUGUSTUS	transcript	16845380	16852329	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	stop_codon	16845377	16845379	.	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16845380	16845667	0.72	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16845380	16845667	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16845668	16845769	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16845770	16846024	0.89	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16845770	16846024	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16846025	16846143	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16846144	16846315	1	-	1	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16846144	16846315	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16846316	16846397	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16846398	16846625	1	-	1	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16846398	16846625	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16846626	16846747	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16846748	16846881	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16846748	16846881	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16846882	16846978	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16846979	16847062	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16846979	16847062	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16847063	16847155	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16847156	16847446	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16847156	16847446	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16847447	16847542	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16847543	16847875	0.89	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16847543	16847875	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16847876	16848010	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16848011	16848165	1	-	2	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16848011	16848165	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16848166	16848301	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16848302	16848421	1	-	2	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16848302	16848421	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16848422	16848529	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16848530	16848692	0.98	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16848530	16848692	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16848693	16848774	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16848775	16848875	1	-	2	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16848775	16848875	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16848876	16848958	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16848959	16849119	1	-	1	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16848959	16849119	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16849120	16849210	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16849211	16849527	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16849211	16849527	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16849528	16849664	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16849665	16849946	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16849665	16849946	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16849947	16850031	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16850032	16850333	1	-	2	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16850032	16850333	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16850334	16850418	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16850419	16850509	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16850419	16850509	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16850510	16850617	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16850618	16850671	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16850618	16850671	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16850672	16850764	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16850765	16850841	1	-	2	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16850765	16850841	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16850842	16850978	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16850979	16851138	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16850979	16851138	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16851139	16851265	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16851266	16851350	1	-	1	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16851266	16851350	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16851351	16851440	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16851441	16851529	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16851441	16851529	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16851530	16851618	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16851619	16851739	1	-	1	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16851619	16851739	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	intron	16851740	16851916	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	CDS	16851917	16852329	1	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	exon	16851917	16852329	.	-	.	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
Phchi.S3	AUGUSTUS	start_codon	16852327	16852329	.	-	0	transcript_id "Phchi.S3G238500.t1"; gene_id "Phchi.S3G238500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14246.t1 is derived from g12713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11737572	11738877	.	+	.	Phchi.S3G156500
Phchi.S3	AUGUSTUS	transcript	11737572	11738877	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	start_codon	11737572	11737574	.	+	0	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	CDS	11737572	11737650	1	+	0	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	exon	11737572	11737650	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	intron	11737651	11737725	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	CDS	11737726	11737937	1	+	2	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	exon	11737726	11737937	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	intron	11737938	11738033	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	CDS	11738034	11738204	1	+	0	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	exon	11738034	11738204	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	intron	11738205	11738287	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	CDS	11738288	11738535	1	+	0	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	exon	11738288	11738535	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	intron	11738536	11738630	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	CDS	11738631	11738877	1	+	1	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	exon	11738631	11738877	.	+	.	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
Phchi.S3	AUGUSTUS	stop_codon	11738878	11738880	.	+	0	transcript_id "Phchi.S3G156500.t1"; gene_id "Phchi.S3G156500"
# This transcript jg15293.t2 is derived from g13761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15294.t1 is derived from g13762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18237487	18244569	.	-	.	Phchi.S3G261300
Phchi.S3	AUGUSTUS	transcript	18237487	18244569	.	-	.	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	stop_codon	18237484	18237486	.	-	0	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	CDS	18237487	18239045	0.81	-	2	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	exon	18237487	18239045	.	-	.	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	intron	18239046	18239219	.	-	.	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	CDS	18239220	18240255	0.61	-	0	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	exon	18239220	18240255	.	-	.	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	intron	18240256	18240375	.	-	.	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	CDS	18240376	18244569	0.98	-	0	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	exon	18240376	18244569	.	-	.	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
Phchi.S3	AUGUSTUS	start_codon	18244567	18244569	.	-	0	transcript_id "Phchi.S3G261300.t1"; gene_id "Phchi.S3G261300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10649.t1 is derived from g14699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1426151	1426697	.	+	.	Phchi.S4G023100
Phchi.S4	AUGUSTUS	transcript	1426151	1426697	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	start_codon	1426151	1426153	.	+	0	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	CDS	1426151	1426165	0.9	+	0	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	exon	1426151	1426165	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	intron	1426166	1426237	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	CDS	1426238	1426334	0.81	+	0	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	exon	1426238	1426334	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	intron	1426335	1426410	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	CDS	1426411	1426499	0.75	+	2	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	exon	1426411	1426499	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	intron	1426500	1426601	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	CDS	1426602	1426697	0.82	+	0	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	exon	1426602	1426697	.	+	.	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
Phchi.S4	AUGUSTUS	stop_codon	1426698	1426700	.	+	0	transcript_id "Phchi.S4G023100.t1"; gene_id "Phchi.S4G023100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14948.t1 is derived from g13416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15662123	15662838	.	+	.	Phchi.S3G226700
Phchi.S3	AUGUSTUS	transcript	15662123	15662838	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	start_codon	15662123	15662125	.	+	0	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	CDS	15662123	15662236	0.94	+	0	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	exon	15662123	15662236	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	intron	15662237	15662354	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	CDS	15662355	15662406	1	+	0	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	exon	15662355	15662406	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	intron	15662407	15662517	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	CDS	15662518	15662549	0.91	+	2	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	exon	15662518	15662549	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	intron	15662550	15662653	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	CDS	15662654	15662687	0.91	+	0	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	exon	15662654	15662687	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	intron	15662688	15662770	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	CDS	15662771	15662838	0.85	+	2	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	exon	15662771	15662838	.	+	.	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
Phchi.S3	AUGUSTUS	stop_codon	15662839	15662841	.	+	0	transcript_id "Phchi.S3G226700.t1"; gene_id "Phchi.S3G226700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10317.t1 is derived from g7493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47090812	47092373	.	-	.	Phchi.S1G747600
Phchi.S1	AUGUSTUS	transcript	47090812	47092373	.	-	.	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	stop_codon	47090809	47090811	.	-	0	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	CDS	47090812	47091795	0.91	-	0	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	exon	47090812	47091795	.	-	.	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	intron	47091796	47091920	.	-	.	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	CDS	47091921	47092373	0.91	-	0	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	exon	47091921	47092373	.	-	.	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	start_codon	47092371	47092373	.	-	0	transcript_id "Phchi.S1G747600.t1"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	transcript	47090812	47091468	.	-	.	transcript_id "Phchi.S1G747600.t2"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	stop_codon	47090809	47090811	.	-	0	transcript_id "Phchi.S1G747600.t2"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	CDS	47090812	47091468	0.33	-	0	transcript_id "Phchi.S1G747600.t2"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	exon	47090812	47091468	.	-	.	transcript_id "Phchi.S1G747600.t2"; gene_id "Phchi.S1G747600"
Phchi.S1	AUGUSTUS	start_codon	47091466	47091468	.	-	0	transcript_id "Phchi.S1G747600.t2"; gene_id "Phchi.S1G747600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14308.t1 is derived from g12775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12035570	12036909	.	-	.	Phchi.S3G162700
Phchi.S3	AUGUSTUS	transcript	12035570	12036909	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	stop_codon	12035567	12035569	.	-	0	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	CDS	12035570	12035623	0.83	-	0	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	exon	12035570	12035623	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	intron	12035624	12035776	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	CDS	12035777	12035863	1	-	0	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	exon	12035777	12035863	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	intron	12035864	12035985	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	CDS	12035986	12036077	1	-	2	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	exon	12035986	12036077	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	intron	12036078	12036201	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	CDS	12036202	12036314	1	-	1	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	exon	12036202	12036314	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	intron	12036315	12036517	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	CDS	12036518	12036909	1	-	0	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	exon	12036518	12036909	.	-	.	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
Phchi.S3	AUGUSTUS	start_codon	12036907	12036909	.	-	0	transcript_id "Phchi.S3G162700.t1"; gene_id "Phchi.S3G162700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7408.t1 is derived from g4580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29002947	29003396	.	-	.	Phchi.S1G456700
Phchi.S1	AUGUSTUS	transcript	29002947	29003396	.	-	.	transcript_id "Phchi.S1G456700.t1"; gene_id "Phchi.S1G456700"
Phchi.S1	AUGUSTUS	stop_codon	29002944	29002946	.	-	0	transcript_id "Phchi.S1G456700.t1"; gene_id "Phchi.S1G456700"
Phchi.S1	AUGUSTUS	CDS	29002947	29003396	0.92	-	0	transcript_id "Phchi.S1G456700.t1"; gene_id "Phchi.S1G456700"
Phchi.S1	AUGUSTUS	exon	29002947	29003396	.	-	.	transcript_id "Phchi.S1G456700.t1"; gene_id "Phchi.S1G456700"
Phchi.S1	AUGUSTUS	start_codon	29003394	29003396	.	-	0	transcript_id "Phchi.S1G456700.t1"; gene_id "Phchi.S1G456700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4527.t1 is derived from g1697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10973602	10974342	.	-	.	Phchi.S1G168600
Phchi.S1	AUGUSTUS	transcript	10973602	10974342	.	-	.	transcript_id "Phchi.S1G168600.t1"; gene_id "Phchi.S1G168600"
Phchi.S1	AUGUSTUS	stop_codon	10973599	10973601	.	-	0	transcript_id "Phchi.S1G168600.t1"; gene_id "Phchi.S1G168600"
Phchi.S1	AUGUSTUS	CDS	10973602	10974342	1	-	0	transcript_id "Phchi.S1G168600.t1"; gene_id "Phchi.S1G168600"
Phchi.S1	AUGUSTUS	exon	10973602	10974342	.	-	.	transcript_id "Phchi.S1G168600.t1"; gene_id "Phchi.S1G168600"
Phchi.S1	AUGUSTUS	start_codon	10974340	10974342	.	-	0	transcript_id "Phchi.S1G168600.t1"; gene_id "Phchi.S1G168600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5338.t1 is derived from g2508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16365836	16367621	.	+	.	Phchi.S1G249700
Phchi.S1	AUGUSTUS	transcript	16365836	16367621	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	start_codon	16365836	16365838	.	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16365836	16365851	0.53	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16365836	16365851	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16365852	16365929	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16365930	16366057	1	+	2	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16365930	16366057	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366058	16366144	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366145	16366210	1	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366145	16366210	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366211	16366308	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366309	16366506	0.98	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366309	16366506	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366507	16366609	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366610	16366728	1	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366610	16366728	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366729	16366855	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366856	16366961	1	+	1	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366856	16366961	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366962	16367090	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16367091	16367238	0.72	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16367091	16367238	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16367239	16367334	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16367335	16367621	0.35	+	2	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16367335	16367621	.	+	.	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	stop_codon	16367622	16367624	.	+	0	transcript_id "Phchi.S1G249700.t1"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	transcript	16365836	16367621	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	start_codon	16365836	16365838	.	+	0	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16365836	16365851	0.64	+	0	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16365836	16365851	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16365852	16365929	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16365930	16366057	0.99	+	2	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16365930	16366057	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366058	16366144	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366145	16366210	1	+	0	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366145	16366210	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366211	16366308	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366309	16366546	0.68	+	0	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366309	16366546	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366547	16366728	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366729	16366774	0.68	+	2	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366729	16366774	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366775	16366855	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16366856	16366961	0.99	+	1	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16366856	16366961	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16366962	16367090	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16367091	16367238	0.7	+	0	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16367091	16367238	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	intron	16367239	16367334	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	CDS	16367335	16367621	0.28	+	2	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	exon	16367335	16367621	.	+	.	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
Phchi.S1	AUGUSTUS	stop_codon	16367622	16367624	.	+	0	transcript_id "Phchi.S1G249700.t2"; gene_id "Phchi.S1G249700"
# This transcript jg7086.t2 is derived from g4258.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7087.t1 is derived from g4259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26849834	26852295	.	+	.	Phchi.S1G424600
Phchi.S1	AUGUSTUS	transcript	26849834	26852295	.	+	.	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	start_codon	26849834	26849836	.	+	0	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	CDS	26849834	26849911	0.39	+	0	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	exon	26849834	26849911	.	+	.	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	intron	26849912	26850054	.	+	.	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	CDS	26850055	26850367	0.54	+	0	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	exon	26850055	26850367	.	+	.	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	intron	26850368	26851135	.	+	.	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	CDS	26851136	26852295	0.58	+	2	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	exon	26851136	26852295	.	+	.	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
Phchi.S1	AUGUSTUS	stop_codon	26852296	26852298	.	+	0	transcript_id "Phchi.S1G424600.t1"; gene_id "Phchi.S1G424600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12714.t1 is derived from g11179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	747167	748415	.	+	.	Phchi.S3G003300
Phchi.S3	AUGUSTUS	transcript	747167	748415	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	start_codon	747167	747169	.	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	747167	747272	0.75	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	747167	747272	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	intron	747273	747359	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	747360	747448	0.88	+	2	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	747360	747448	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	intron	747449	747528	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	747529	747606	1	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	747529	747606	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	intron	747607	747688	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	747689	747736	0.8	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	747689	747736	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	intron	747737	747900	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	747901	748020	0.66	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	747901	748020	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	intron	748021	748170	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	748171	748226	0.94	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	748171	748226	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	intron	748227	748372	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	CDS	748373	748415	0.87	+	1	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	exon	748373	748415	.	+	.	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
Phchi.S3	AUGUSTUS	stop_codon	748416	748418	.	+	0	transcript_id "Phchi.S3G003300.t1"; gene_id "Phchi.S3G003300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4262.t1 is derived from g1431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9221822	9223449	.	-	.	Phchi.S1G142100
Phchi.S1	AUGUSTUS	transcript	9221822	9223449	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	stop_codon	9221819	9221821	.	-	0	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	CDS	9221822	9222013	1	-	0	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	exon	9221822	9222013	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	intron	9222014	9222087	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	CDS	9222088	9222160	0.59	-	1	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	exon	9222088	9222160	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	intron	9222161	9222300	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	CDS	9222301	9222382	0.94	-	2	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	exon	9222301	9222382	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	intron	9222383	9222478	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	CDS	9222479	9222738	0.99	-	1	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	exon	9222479	9222738	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	intron	9222739	9222840	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	CDS	9222841	9222864	1	-	1	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	exon	9222841	9222864	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	intron	9222865	9222985	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	CDS	9222986	9223449	0.58	-	0	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	exon	9222986	9223449	.	-	.	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
Phchi.S1	AUGUSTUS	start_codon	9223447	9223449	.	-	0	transcript_id "Phchi.S1G142100.t1"; gene_id "Phchi.S1G142100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13184.t1 is derived from g11649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4576897	4578931	.	-	.	Phchi.S3G050300
Phchi.S3	AUGUSTUS	transcript	4576897	4578931	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	stop_codon	4576894	4576896	.	-	0	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4576897	4576963	1	-	1	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4576897	4576963	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4576964	4577040	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4577041	4577120	1	-	0	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4577041	4577120	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4577121	4577252	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4577253	4577298	1	-	1	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4577253	4577298	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4577299	4577393	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4577394	4577450	1	-	1	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4577394	4577450	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4577451	4577543	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4577544	4577602	1	-	0	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4577544	4577602	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4577603	4577681	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4577682	4577782	1	-	2	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4577682	4577782	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4577783	4577875	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4577876	4577997	1	-	1	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4577876	4577997	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4577998	4578213	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4578214	4578265	1	-	2	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4578214	4578265	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4578266	4578347	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4578348	4578443	1	-	2	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4578348	4578443	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4578444	4578520	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4578521	4578716	1	-	0	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4578521	4578716	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	intron	4578717	4578841	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	CDS	4578842	4578931	0.99	-	0	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	exon	4578842	4578931	.	-	.	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
Phchi.S3	AUGUSTUS	start_codon	4578929	4578931	.	-	0	transcript_id "Phchi.S3G050300.t1"; gene_id "Phchi.S3G050300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4285.t1 is derived from g1454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9409507	9410673	.	-	.	Phchi.S1G144400
Phchi.S1	AUGUSTUS	transcript	9409507	9410673	.	-	.	transcript_id "Phchi.S1G144400.t1"; gene_id "Phchi.S1G144400"
Phchi.S1	AUGUSTUS	stop_codon	9409504	9409506	.	-	0	transcript_id "Phchi.S1G144400.t1"; gene_id "Phchi.S1G144400"
Phchi.S1	AUGUSTUS	CDS	9409507	9410673	0.89	-	0	transcript_id "Phchi.S1G144400.t1"; gene_id "Phchi.S1G144400"
Phchi.S1	AUGUSTUS	exon	9409507	9410673	.	-	.	transcript_id "Phchi.S1G144400.t1"; gene_id "Phchi.S1G144400"
Phchi.S1	AUGUSTUS	start_codon	9410671	9410673	.	-	0	transcript_id "Phchi.S1G144400.t1"; gene_id "Phchi.S1G144400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10656.t1 is derived from g14706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1448666	1448920	.	-	.	Phchi.S4G023800
Phchi.S4	AUGUSTUS	transcript	1448666	1448920	.	-	.	transcript_id "Phchi.S4G023800.t1"; gene_id "Phchi.S4G023800"
Phchi.S4	AUGUSTUS	stop_codon	1448663	1448665	.	-	0	transcript_id "Phchi.S4G023800.t1"; gene_id "Phchi.S4G023800"
Phchi.S4	AUGUSTUS	CDS	1448666	1448920	0.69	-	0	transcript_id "Phchi.S4G023800.t1"; gene_id "Phchi.S4G023800"
Phchi.S4	AUGUSTUS	exon	1448666	1448920	.	-	.	transcript_id "Phchi.S4G023800.t1"; gene_id "Phchi.S4G023800"
Phchi.S4	AUGUSTUS	start_codon	1448918	1448920	.	-	0	transcript_id "Phchi.S4G023800.t1"; gene_id "Phchi.S4G023800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7528.t1 is derived from g4702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29892572	29895173	.	+	.	Phchi.S1G468700
Phchi.S1	AUGUSTUS	transcript	29892572	29895173	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	start_codon	29892572	29892574	.	+	0	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	CDS	29892572	29893299	0.4	+	0	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	exon	29892572	29893299	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	intron	29893300	29893403	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	CDS	29893404	29893512	0.39	+	1	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	exon	29893404	29893512	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	intron	29893513	29893601	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	CDS	29893602	29894181	0.82	+	0	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	exon	29893602	29894181	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	intron	29894182	29894310	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	CDS	29894311	29894915	0.97	+	2	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	exon	29894311	29894915	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	intron	29894916	29895155	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	CDS	29895156	29895173	0.98	+	0	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	exon	29895156	29895173	.	+	.	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
Phchi.S1	AUGUSTUS	stop_codon	29895174	29895176	.	+	0	transcript_id "Phchi.S1G468700.t1"; gene_id "Phchi.S1G468700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4240.t1 is derived from g1409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9109494	9110107	.	-	.	Phchi.S1G139900
Phchi.S1	AUGUSTUS	transcript	9109494	9110107	.	-	.	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	stop_codon	9109491	9109493	.	-	0	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	CDS	9109494	9109586	1	-	0	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	exon	9109494	9109586	.	-	.	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	intron	9109587	9110068	.	-	.	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	CDS	9110069	9110107	0.01	-	0	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	exon	9110069	9110107	.	-	.	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
Phchi.S1	AUGUSTUS	start_codon	9110105	9110107	.	-	0	transcript_id "Phchi.S1G139900.t1"; gene_id "Phchi.S1G139900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15887.t1 is derived from g14357.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22032338	22033834	.	-	.	Phchi.S3G320600
Phchi.S3	AUGUSTUS	transcript	22032338	22033834	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	stop_codon	22032335	22032337	.	-	0	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22032338	22032414	0.6	-	2	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22032338	22032414	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22032415	22032496	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22032497	22032632	1	-	0	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22032497	22032632	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22032633	22032757	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22032758	22032783	1	-	2	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22032758	22032783	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22032784	22032880	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22032881	22032925	1	-	2	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22032881	22032925	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22032926	22033063	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22033064	22033179	1	-	1	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22033064	22033179	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22033180	22033364	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22033365	22033464	0.6	-	2	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22033365	22033464	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22033465	22033524	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22033525	22033563	0.83	-	2	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22033525	22033563	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	intron	22033564	22033653	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	CDS	22033654	22033834	0.69	-	0	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	exon	22033654	22033834	.	-	.	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
Phchi.S3	AUGUSTUS	start_codon	22033832	22033834	.	-	0	transcript_id "Phchi.S3G320600.t1"; gene_id "Phchi.S3G320600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12426.t1 is derived from g8103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19579728	19580876	.	-	.	Phchi.S2G050600
Phchi.S2	AUGUSTUS	transcript	19579728	19580876	.	-	.	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	stop_codon	19579725	19579727	.	-	0	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	CDS	19579728	19579830	0.99	-	1	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	exon	19579728	19579830	.	-	.	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	intron	19579831	19579930	.	-	.	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	CDS	19579931	19580677	1	-	1	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	exon	19579931	19580677	.	-	.	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	intron	19580678	19580766	.	-	.	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	CDS	19580767	19580876	0.86	-	0	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	exon	19580767	19580876	.	-	.	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
Phchi.S2	AUGUSTUS	start_codon	19580874	19580876	.	-	0	transcript_id "Phchi.S2G050600.t1"; gene_id "Phchi.S2G050600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9355.t1 is derived from g6531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41102694	41103581	.	-	.	Phchi.S1G651400
Phchi.S1	AUGUSTUS	transcript	41102694	41103581	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	stop_codon	41102691	41102693	.	-	0	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	CDS	41102694	41102745	0.37	-	1	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	exon	41102694	41102745	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	intron	41102746	41102825	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	CDS	41102826	41102908	1	-	0	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	exon	41102826	41102908	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	intron	41102909	41103011	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	CDS	41103012	41103184	0.93	-	2	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	exon	41103012	41103184	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	intron	41103185	41103282	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	CDS	41103283	41103358	0.94	-	0	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	exon	41103283	41103358	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	intron	41103359	41103437	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	CDS	41103438	41103581	0.8	-	0	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	exon	41103438	41103581	.	-	.	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
Phchi.S1	AUGUSTUS	start_codon	41103579	41103581	.	-	0	transcript_id "Phchi.S1G651400.t1"; gene_id "Phchi.S1G651400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3099.t1 is derived from g268.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1752547	1753236	.	-	.	Phchi.S1G025800
Phchi.S1	AUGUSTUS	transcript	1752547	1753236	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	stop_codon	1752544	1752546	.	-	0	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1752547	1752592	0.51	-	1	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1752547	1752592	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	intron	1752593	1752767	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1752768	1752788	0.55	-	1	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1752768	1752788	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	intron	1752789	1752881	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1752882	1752935	0.67	-	1	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1752882	1752935	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	intron	1752936	1753054	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1753055	1753236	0.63	-	0	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1753055	1753236	.	-	.	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	start_codon	1753234	1753236	.	-	0	transcript_id "Phchi.S1G025800.t1"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	transcript	1752579	1753236	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	stop_codon	1752576	1752578	.	-	0	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1752579	1752592	0.74	-	2	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1752579	1752592	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	intron	1752593	1752763	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1752764	1752780	0.31	-	1	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1752764	1752780	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	intron	1752781	1752881	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1752882	1752935	0.3	-	1	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1752882	1752935	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	intron	1752936	1753054	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	CDS	1753055	1753236	0.36	-	0	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	exon	1753055	1753236	.	-	.	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
Phchi.S1	AUGUSTUS	start_codon	1753234	1753236	.	-	0	transcript_id "Phchi.S1G025800.t2"; gene_id "Phchi.S1G025800"
# This transcript jg9130.t2 is derived from g6305.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9130.t3 is derived from g6305.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9131.t1 is derived from g6306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40014493	40017183	.	+	.	Phchi.S1G629000
Phchi.S1	AUGUSTUS	transcript	40014493	40017183	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	start_codon	40014493	40014495	.	+	0	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40014493	40014566	1	+	0	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40014493	40014566	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40014567	40014659	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40014660	40014743	1	+	1	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40014660	40014743	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40014744	40014835	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40014836	40014899	1	+	1	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40014836	40014899	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40014900	40015041	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40015042	40015088	1	+	0	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40015042	40015088	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40015089	40015187	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40015188	40015242	1	+	1	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40015188	40015242	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40015243	40015338	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40015339	40015393	0.89	+	0	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40015339	40015393	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40015394	40015472	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40015473	40015604	0.99	+	2	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40015473	40015604	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40015605	40015735	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40015736	40015852	0.78	+	2	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40015736	40015852	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	intron	40015853	40016350	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	CDS	40016351	40017183	0.88	+	2	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	exon	40016351	40017183	.	+	.	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
Phchi.S1	AUGUSTUS	stop_codon	40017184	40017186	.	+	0	transcript_id "Phchi.S1G629000.t1"; gene_id "Phchi.S1G629000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1816.t1 is derived from g8736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3287161	3287726	.	+	.	Phchi.S5G042500
Phchi.S5	AUGUSTUS	transcript	3287161	3287726	.	+	.	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	start_codon	3287161	3287163	.	+	0	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	CDS	3287161	3287265	1	+	0	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	exon	3287161	3287265	.	+	.	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	intron	3287266	3287378	.	+	.	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	CDS	3287379	3287497	1	+	0	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	exon	3287379	3287497	.	+	.	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	intron	3287498	3287626	.	+	.	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	CDS	3287627	3287726	1	+	1	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	exon	3287627	3287726	.	+	.	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
Phchi.S5	AUGUSTUS	stop_codon	3287727	3287729	.	+	0	transcript_id "Phchi.S5G042500.t1"; gene_id "Phchi.S5G042500"
# This transcript jg13009.t2 is derived from g11474.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13010.t1 is derived from g11475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3621829	3622558	.	+	.	Phchi.S3G032900
Phchi.S3	AUGUSTUS	transcript	3621829	3622558	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	start_codon	3621829	3621831	.	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	CDS	3621829	3621831	0.84	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	exon	3621829	3621831	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	intron	3621832	3621918	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	CDS	3621919	3621949	0.84	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	exon	3621919	3621949	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	intron	3621950	3622048	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	CDS	3622049	3622107	1	+	2	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	exon	3622049	3622107	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	intron	3622108	3622206	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	CDS	3622207	3622275	1	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	exon	3622207	3622275	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	intron	3622276	3622353	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	CDS	3622354	3622416	1	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	exon	3622354	3622416	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	intron	3622417	3622501	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	CDS	3622502	3622558	1	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	exon	3622502	3622558	.	+	.	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
Phchi.S3	AUGUSTUS	stop_codon	3622559	3622561	.	+	0	transcript_id "Phchi.S3G032900.t1"; gene_id "Phchi.S3G032900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12432.t1 is derived from g8109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19602805	19605451	.	-	.	Phchi.S2G051200
Phchi.S2	AUGUSTUS	transcript	19602805	19605451	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	stop_codon	19602802	19602804	.	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19602805	19603028	0.94	-	2	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19602805	19603028	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19603029	19603176	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19603177	19603243	1	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19603177	19603243	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19603244	19603434	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19603435	19603497	1	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19603435	19603497	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19603498	19603673	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19603674	19604075	1	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19603674	19604075	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19604076	19604157	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19604158	19604361	1	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19604158	19604361	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19604362	19604641	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19604642	19604882	1	-	1	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19604642	19604882	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19604883	19604979	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19604980	19605089	1	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19604980	19605089	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	intron	19605090	19605175	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	CDS	19605176	19605451	0.6	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	exon	19605176	19605451	.	-	.	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
Phchi.S2	AUGUSTUS	start_codon	19605449	19605451	.	-	0	transcript_id "Phchi.S2G051200.t1"; gene_id "Phchi.S2G051200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10375.t1 is derived from g7551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47436200	47437102	.	+	.	Phchi.S1G753400
Phchi.S1	AUGUSTUS	transcript	47436200	47437102	.	+	.	transcript_id "Phchi.S1G753400.t1"; gene_id "Phchi.S1G753400"
Phchi.S1	AUGUSTUS	start_codon	47436200	47436202	.	+	0	transcript_id "Phchi.S1G753400.t1"; gene_id "Phchi.S1G753400"
Phchi.S1	AUGUSTUS	CDS	47436200	47437102	0.86	+	0	transcript_id "Phchi.S1G753400.t1"; gene_id "Phchi.S1G753400"
Phchi.S1	AUGUSTUS	exon	47436200	47437102	.	+	.	transcript_id "Phchi.S1G753400.t1"; gene_id "Phchi.S1G753400"
Phchi.S1	AUGUSTUS	stop_codon	47437103	47437105	.	+	0	transcript_id "Phchi.S1G753400.t1"; gene_id "Phchi.S1G753400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13289.t1 is derived from g11755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5192715	5193120	.	+	.	Phchi.S3G060800
Phchi.S3	AUGUSTUS	transcript	5192715	5193120	.	+	.	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	start_codon	5192715	5192717	.	+	0	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	CDS	5192715	5192894	0.61	+	0	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	exon	5192715	5192894	.	+	.	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	intron	5192895	5192985	.	+	.	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	CDS	5192986	5193120	0.69	+	0	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	exon	5192986	5193120	.	+	.	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
Phchi.S3	AUGUSTUS	stop_codon	5193121	5193123	.	+	0	transcript_id "Phchi.S3G060800.t1"; gene_id "Phchi.S3G060800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7964.t1 is derived from g5139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32122416	32122622	.	+	.	Phchi.S1G512300
Phchi.S1	AUGUSTUS	transcript	32122416	32122622	.	+	.	transcript_id "Phchi.S1G512300.t1"; gene_id "Phchi.S1G512300"
Phchi.S1	AUGUSTUS	start_codon	32122416	32122418	.	+	0	transcript_id "Phchi.S1G512300.t1"; gene_id "Phchi.S1G512300"
Phchi.S1	AUGUSTUS	CDS	32122416	32122622	0.64	+	0	transcript_id "Phchi.S1G512300.t1"; gene_id "Phchi.S1G512300"
Phchi.S1	AUGUSTUS	exon	32122416	32122622	.	+	.	transcript_id "Phchi.S1G512300.t1"; gene_id "Phchi.S1G512300"
Phchi.S1	AUGUSTUS	stop_codon	32122623	32122625	.	+	0	transcript_id "Phchi.S1G512300.t1"; gene_id "Phchi.S1G512300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3875.t1 is derived from g1044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6162922	6165430	.	-	.	Phchi.S1G103400
Phchi.S1	AUGUSTUS	transcript	6162922	6165430	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	stop_codon	6162919	6162921	.	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6162922	6163083	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6162922	6163083	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6163084	6163172	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6163173	6163247	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6163173	6163247	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6163248	6163345	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6163346	6163469	1	-	1	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6163346	6163469	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6163470	6163558	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6163559	6163612	0.63	-	1	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6163559	6163612	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6163613	6163671	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6163672	6163744	1	-	2	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6163672	6163744	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6163745	6163828	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6163829	6163928	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6163829	6163928	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6163929	6164027	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6164028	6164082	0.99	-	1	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6164028	6164082	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6164083	6164195	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6164196	6164275	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6164196	6164275	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6164276	6164365	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6164366	6164446	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6164366	6164446	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6164447	6164533	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6164534	6164645	1	-	1	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6164534	6164645	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6164646	6164760	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6164761	6164804	0.59	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6164761	6164804	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6164805	6164895	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6164896	6165188	0.94	-	2	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6164896	6165188	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6165189	6165268	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6165269	6165332	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6165269	6165332	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	intron	6165333	6165427	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	CDS	6165428	6165430	1	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	exon	6165428	6165430	.	-	.	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
Phchi.S1	AUGUSTUS	start_codon	6165428	6165430	.	-	0	transcript_id "Phchi.S1G103400.t1"; gene_id "Phchi.S1G103400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1019.t1 is derived from g10802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7139409	7144816	.	+	.	Phchi.S6G097800
Phchi.S6	AUGUSTUS	transcript	7139409	7144816	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	start_codon	7139409	7139411	.	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7139409	7139510	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7139409	7139510	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7139511	7139596	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7139597	7139701	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7139597	7139701	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7139702	7139858	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7139859	7139975	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7139859	7139975	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7139976	7140061	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7140062	7140121	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7140062	7140121	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7140122	7140254	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7140255	7140322	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7140255	7140322	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7140323	7140547	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7140548	7140590	1	+	1	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7140548	7140590	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7140591	7140716	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7140717	7140782	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7140717	7140782	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7140783	7140911	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7140912	7140950	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7140912	7140950	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7140951	7141033	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7141034	7141116	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7141034	7141116	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7141117	7141201	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7141202	7141316	1	+	1	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7141202	7141316	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7141317	7141402	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7141403	7141481	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7141403	7141481	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7141482	7141677	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7141678	7141832	1	+	2	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7141678	7141832	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7141833	7141941	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7141942	7142049	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7141942	7142049	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7142050	7142137	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7142138	7142245	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7142138	7142245	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7142246	7142330	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7142331	7142471	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7142331	7142471	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7142472	7142564	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7142565	7142669	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7142565	7142669	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7142670	7142771	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7142772	7142993	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7142772	7142993	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7142994	7143123	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7143124	7143240	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7143124	7143240	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7143241	7143350	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7143351	7143566	0.99	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7143351	7143566	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7143567	7143671	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7143672	7143731	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7143672	7143731	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7143732	7143848	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7143849	7143962	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7143849	7143962	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7143963	7144043	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7144044	7144129	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7144044	7144129	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7144130	7144252	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7144253	7144361	1	+	1	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7144253	7144361	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7144362	7144459	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7144460	7144638	1	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7144460	7144638	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	intron	7144639	7144734	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	CDS	7144735	7144816	0.97	+	1	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	exon	7144735	7144816	.	+	.	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
Phchi.S6	AUGUSTUS	stop_codon	7144817	7144819	.	+	0	transcript_id "Phchi.S6G097800.t1"; gene_id "Phchi.S6G097800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1652.t1 is derived from g8571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2237203	2240089	.	+	.	Phchi.S5G026100
Phchi.S5	AUGUSTUS	transcript	2237203	2240089	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	start_codon	2237203	2237205	.	+	0	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237203	2237361	1	+	0	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237203	2237361	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2237362	2237447	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237448	2237724	0.72	+	0	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237448	2237724	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2237725	2237837	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237838	2238030	1	+	2	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237838	2238030	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2238031	2238233	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2238234	2238437	1	+	1	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2238234	2238437	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2238438	2238563	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2238564	2238854	0.99	+	1	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2238564	2238854	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2238855	2238984	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2238985	2240089	0.91	+	1	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2238985	2240089	.	+	.	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	stop_codon	2240090	2240092	.	+	0	transcript_id "Phchi.S5G026100.t1"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	transcript	2237203	2240089	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	start_codon	2237203	2237205	.	+	0	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237203	2237361	1	+	0	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237203	2237361	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2237362	2237447	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237448	2237724	0.62	+	0	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237448	2237724	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2237725	2237837	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237838	2237887	0.82	+	2	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237838	2237887	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2237888	2237984	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2237985	2238030	0.88	+	0	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2237985	2238030	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2238031	2238202	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2238203	2238437	1	+	2	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2238203	2238437	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2238438	2238563	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2238564	2238854	1	+	1	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2238564	2238854	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	intron	2238855	2238984	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	CDS	2238985	2240089	0.92	+	1	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	exon	2238985	2240089	.	+	.	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
Phchi.S5	AUGUSTUS	stop_codon	2240090	2240092	.	+	0	transcript_id "Phchi.S5G026100.t2"; gene_id "Phchi.S5G026100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2875.t1 is derived from g44.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	223759	225179	.	+	.	Phchi.S1G003400
Phchi.S1	AUGUSTUS	transcript	223759	225179	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	start_codon	223759	223761	.	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	223759	223827	1	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	223759	223827	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	223828	223909	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	223910	224060	0.96	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	223910	224060	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224061	224181	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224182	224267	0.75	+	2	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224182	224267	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224268	224368	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224369	224440	0.9	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224369	224440	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224441	224562	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224563	224674	1	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224563	224674	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224675	224836	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224837	224994	1	+	2	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224837	224994	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224995	225128	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	225129	225179	0.98	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	225129	225179	.	+	.	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	stop_codon	225180	225182	.	+	0	transcript_id "Phchi.S1G003400.t1"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	transcript	223759	225114	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	start_codon	223759	223761	.	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	223759	223827	0.99	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	223759	223827	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	223828	223909	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	223910	224060	0.97	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	223910	224060	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224061	224181	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224182	224267	0.75	+	2	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224182	224267	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224268	224368	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224369	224440	0.91	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224369	224440	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224441	224562	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224563	224674	1	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224563	224674	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224675	224836	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	224837	224994	0.83	+	2	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	224837	224994	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	intron	224995	225108	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	CDS	225109	225114	0.73	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	exon	225109	225114	.	+	.	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
Phchi.S1	AUGUSTUS	stop_codon	225115	225117	.	+	0	transcript_id "Phchi.S1G003400.t2"; gene_id "Phchi.S1G003400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3364.t1 is derived from g533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3153796	3154002	.	+	.	Phchi.S1G052300
Phchi.S1	AUGUSTUS	transcript	3153796	3154002	.	+	.	transcript_id "Phchi.S1G052300.t1"; gene_id "Phchi.S1G052300"
Phchi.S1	AUGUSTUS	start_codon	3153796	3153798	.	+	0	transcript_id "Phchi.S1G052300.t1"; gene_id "Phchi.S1G052300"
Phchi.S1	AUGUSTUS	CDS	3153796	3154002	0.55	+	0	transcript_id "Phchi.S1G052300.t1"; gene_id "Phchi.S1G052300"
Phchi.S1	AUGUSTUS	exon	3153796	3154002	.	+	.	transcript_id "Phchi.S1G052300.t1"; gene_id "Phchi.S1G052300"
Phchi.S1	AUGUSTUS	stop_codon	3154003	3154005	.	+	0	transcript_id "Phchi.S1G052300.t1"; gene_id "Phchi.S1G052300"
# This transcript jg1232.t2 is derived from g11015.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1233.t1 is derived from g11016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8528645	8530264	.	-	.	Phchi.S6G119200
Phchi.S6	AUGUSTUS	transcript	8528645	8530264	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	stop_codon	8528642	8528644	.	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	CDS	8528645	8528671	1	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	exon	8528645	8528671	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	intron	8528672	8528768	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	CDS	8528769	8528858	1	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	exon	8528769	8528858	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	intron	8528859	8528934	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	CDS	8528935	8529030	1	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	exon	8528935	8529030	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	intron	8529031	8529124	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	CDS	8529125	8529196	1	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	exon	8529125	8529196	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	intron	8529197	8529275	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	CDS	8529276	8529333	1	-	1	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	exon	8529276	8529333	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	intron	8529334	8530130	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	CDS	8530131	8530264	0.9	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	exon	8530131	8530264	.	-	.	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
Phchi.S6	AUGUSTUS	start_codon	8530262	8530264	.	-	0	transcript_id "Phchi.S6G119200.t1"; gene_id "Phchi.S6G119200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12637.t1 is derived from g9789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C183	AUGUSTUS	gene	2939	3819	.	+	.	Phchi.C183G000100
Phchi.C183	AUGUSTUS	transcript	2939	3819	.	+	.	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	start_codon	2939	2941	.	+	0	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	CDS	2939	3303	0.26	+	0	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	exon	2939	3303	.	+	.	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	intron	3304	3674	.	+	.	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	CDS	3675	3819	0.53	+	1	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	exon	3675	3819	.	+	.	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
Phchi.C183	AUGUSTUS	stop_codon	3820	3822	.	+	0	transcript_id "Phchi.C183G000100.t1"; gene_id "Phchi.C183G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13675.t1 is derived from g12142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8098300	8100885	.	-	.	Phchi.S3G099400
Phchi.S3	AUGUSTUS	transcript	8098300	8100885	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	stop_codon	8098297	8098299	.	-	0	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	CDS	8098300	8098374	0.98	-	0	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	exon	8098300	8098374	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	intron	8098375	8098460	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	CDS	8098461	8098494	0.89	-	1	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	exon	8098461	8098494	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	intron	8098495	8098757	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	CDS	8098758	8099145	0.31	-	2	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	exon	8098758	8099145	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	intron	8099146	8099282	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	CDS	8099283	8099400	0.41	-	0	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	exon	8099283	8099400	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	intron	8099401	8099539	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	CDS	8099540	8100253	0.72	-	0	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	exon	8099540	8100253	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	intron	8100254	8100333	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	CDS	8100334	8100885	1	-	0	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	exon	8100334	8100885	.	-	.	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
Phchi.S3	AUGUSTUS	start_codon	8100883	8100885	.	-	0	transcript_id "Phchi.S3G099400.t1"; gene_id "Phchi.S3G099400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14966.t1 is derived from g13434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15782918	15785641	.	-	.	Phchi.S3G228500
Phchi.S3	AUGUSTUS	transcript	15782918	15785641	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	stop_codon	15782915	15782917	.	-	0	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15782918	15783231	0.95	-	2	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15782918	15783231	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15783232	15783315	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15783316	15783387	1	-	2	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15783316	15783387	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15783388	15783487	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15783488	15783548	1	-	0	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15783488	15783548	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15783549	15783647	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15783648	15783753	1	-	1	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15783648	15783753	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15783754	15783845	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15783846	15783922	1	-	0	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15783846	15783922	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15783923	15784007	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15784008	15784143	1	-	1	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15784008	15784143	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15784144	15784266	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15784267	15784494	1	-	1	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15784267	15784494	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15784495	15784584	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15784585	15784823	1	-	0	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15784585	15784823	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15784824	15785027	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15785028	15785172	1	-	1	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15785028	15785172	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	intron	15785173	15785318	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	CDS	15785319	15785641	0.7	-	0	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	exon	15785319	15785641	.	-	.	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
Phchi.S3	AUGUSTUS	start_codon	15785639	15785641	.	-	0	transcript_id "Phchi.S3G228500.t1"; gene_id "Phchi.S3G228500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10859.t1 is derived from g14909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2589829	2591322	.	+	.	Phchi.S4G044100
Phchi.S4	AUGUSTUS	transcript	2589829	2591322	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	start_codon	2589829	2589831	.	+	0	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2589829	2589978	0.76	+	0	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2589829	2589978	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	intron	2589979	2590056	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2590057	2590109	1	+	0	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2590057	2590109	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	intron	2590110	2590214	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2590215	2590324	1	+	1	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2590215	2590324	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	intron	2590325	2590524	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2590525	2590692	1	+	2	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2590525	2590692	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	intron	2590693	2590833	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2590834	2590931	1	+	2	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2590834	2590931	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	intron	2590932	2591011	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2591012	2591138	1	+	0	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2591012	2591138	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	intron	2591139	2591224	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	CDS	2591225	2591322	1	+	2	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	exon	2591225	2591322	.	+	.	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
Phchi.S4	AUGUSTUS	stop_codon	2591323	2591325	.	+	0	transcript_id "Phchi.S4G044100.t1"; gene_id "Phchi.S4G044100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1472.t1 is derived from g8391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1097622	1098341	.	+	.	Phchi.S5G008100
Phchi.S5	AUGUSTUS	transcript	1097622	1098341	.	+	.	transcript_id "Phchi.S5G008100.t1"; gene_id "Phchi.S5G008100"
Phchi.S5	AUGUSTUS	start_codon	1097622	1097624	.	+	0	transcript_id "Phchi.S5G008100.t1"; gene_id "Phchi.S5G008100"
Phchi.S5	AUGUSTUS	CDS	1097622	1098341	1	+	0	transcript_id "Phchi.S5G008100.t1"; gene_id "Phchi.S5G008100"
Phchi.S5	AUGUSTUS	exon	1097622	1098341	.	+	.	transcript_id "Phchi.S5G008100.t1"; gene_id "Phchi.S5G008100"
Phchi.S5	AUGUSTUS	stop_codon	1098342	1098344	.	+	0	transcript_id "Phchi.S5G008100.t1"; gene_id "Phchi.S5G008100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9060.t1 is derived from g6235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39530872	39532311	.	-	.	Phchi.S1G621900
Phchi.S1	AUGUSTUS	transcript	39530872	39532311	.	-	.	transcript_id "Phchi.S1G621900.t1"; gene_id "Phchi.S1G621900"
Phchi.S1	AUGUSTUS	stop_codon	39530869	39530871	.	-	0	transcript_id "Phchi.S1G621900.t1"; gene_id "Phchi.S1G621900"
Phchi.S1	AUGUSTUS	CDS	39530872	39532311	0.51	-	0	transcript_id "Phchi.S1G621900.t1"; gene_id "Phchi.S1G621900"
Phchi.S1	AUGUSTUS	exon	39530872	39532311	.	-	.	transcript_id "Phchi.S1G621900.t1"; gene_id "Phchi.S1G621900"
Phchi.S1	AUGUSTUS	start_codon	39532309	39532311	.	-	0	transcript_id "Phchi.S1G621900.t1"; gene_id "Phchi.S1G621900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14051.t1 is derived from g12518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10490205	10491556	.	+	.	Phchi.S3G137000
Phchi.S3	AUGUSTUS	transcript	10490205	10491556	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	start_codon	10490205	10490207	.	+	0	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	CDS	10490205	10490293	0.43	+	0	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	exon	10490205	10490293	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	intron	10490294	10490889	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	CDS	10490890	10490982	0.63	+	1	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	exon	10490890	10490982	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	intron	10490983	10491291	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	CDS	10491292	10491370	0.95	+	1	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	exon	10491292	10491370	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	intron	10491371	10491547	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	CDS	10491548	10491556	0.97	+	0	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	exon	10491548	10491556	.	+	.	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
Phchi.S3	AUGUSTUS	stop_codon	10491557	10491559	.	+	0	transcript_id "Phchi.S3G137000.t1"; gene_id "Phchi.S3G137000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8357.t1 is derived from g5532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35479288	35479777	.	-	.	Phchi.S1G551600
Phchi.S1	AUGUSTUS	transcript	35479288	35479777	.	-	.	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	stop_codon	35479285	35479287	.	-	0	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	CDS	35479288	35479479	0.84	-	0	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	exon	35479288	35479479	.	-	.	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	intron	35479480	35479624	.	-	.	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	CDS	35479625	35479777	0.67	-	0	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	exon	35479625	35479777	.	-	.	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
Phchi.S1	AUGUSTUS	start_codon	35479775	35479777	.	-	0	transcript_id "Phchi.S1G551600.t1"; gene_id "Phchi.S1G551600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14059.t1 is derived from g12526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10580633	10582225	.	+	.	Phchi.S3G137800
Phchi.S3	AUGUSTUS	transcript	10580633	10582225	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	start_codon	10580633	10580635	.	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10580633	10580683	0.98	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10580633	10580683	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	intron	10580684	10580920	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10580921	10581064	1	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10580921	10581064	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	intron	10581065	10581366	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10581367	10581440	1	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10581367	10581440	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	intron	10581441	10581526	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10581527	10581581	1	+	1	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10581527	10581581	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	intron	10581582	10581739	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10581740	10581802	0.89	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10581740	10581802	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	intron	10581803	10581910	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10581911	10582038	0.81	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10581911	10582038	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	intron	10582039	10582149	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	CDS	10582150	10582225	0.79	+	1	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	exon	10582150	10582225	.	+	.	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
Phchi.S3	AUGUSTUS	stop_codon	10582226	10582228	.	+	0	transcript_id "Phchi.S3G137800.t1"; gene_id "Phchi.S3G137800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1251.t1 is derived from g11034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8649620	8650861	.	+	.	Phchi.S6G121000
Phchi.S6	AUGUSTUS	transcript	8649620	8650861	.	+	.	transcript_id "Phchi.S6G121000.t1"; gene_id "Phchi.S6G121000"
Phchi.S6	AUGUSTUS	start_codon	8649620	8649622	.	+	0	transcript_id "Phchi.S6G121000.t1"; gene_id "Phchi.S6G121000"
Phchi.S6	AUGUSTUS	CDS	8649620	8650861	0.62	+	0	transcript_id "Phchi.S6G121000.t1"; gene_id "Phchi.S6G121000"
Phchi.S6	AUGUSTUS	exon	8649620	8650861	.	+	.	transcript_id "Phchi.S6G121000.t1"; gene_id "Phchi.S6G121000"
Phchi.S6	AUGUSTUS	stop_codon	8650862	8650864	.	+	0	transcript_id "Phchi.S6G121000.t1"; gene_id "Phchi.S6G121000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1137.t1 is derived from g10920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7885635	7887383	.	+	.	Phchi.S6G109600
Phchi.S6	AUGUSTUS	transcript	7885635	7887383	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	start_codon	7885635	7885637	.	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7885635	7885877	0.47	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7885635	7885877	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	intron	7885878	7885986	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7885987	7886097	1	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7885987	7886097	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	intron	7886098	7886219	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7886220	7886228	0.57	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7886220	7886228	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	intron	7886229	7886341	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7886342	7886717	0.3	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7886342	7886717	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	intron	7886718	7886830	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7886831	7886949	0.8	+	2	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7886831	7886949	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	intron	7886950	7887085	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7887086	7887136	0.81	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7887086	7887136	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	intron	7887137	7887215	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	CDS	7887216	7887383	0.84	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	exon	7887216	7887383	.	+	.	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
Phchi.S6	AUGUSTUS	stop_codon	7887384	7887386	.	+	0	transcript_id "Phchi.S6G109600.t1"; gene_id "Phchi.S6G109600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7161.t1 is derived from g4334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27341338	27342669	.	-	.	Phchi.S1G432100
Phchi.S1	AUGUSTUS	transcript	27341338	27342669	.	-	.	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	stop_codon	27341335	27341337	.	-	0	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	CDS	27341338	27342398	0.95	-	2	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	exon	27341338	27342398	.	-	.	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	intron	27342399	27342566	.	-	.	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	CDS	27342567	27342669	1	-	0	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	exon	27342567	27342669	.	-	.	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
Phchi.S1	AUGUSTUS	start_codon	27342667	27342669	.	-	0	transcript_id "Phchi.S1G432100.t1"; gene_id "Phchi.S1G432100"
# This transcript jg11148.t2 is derived from g15198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11149.t1 is derived from g15199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4388537	4389774	.	+	.	Phchi.S4G073100
Phchi.S4	AUGUSTUS	transcript	4388537	4389774	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	start_codon	4388537	4388539	.	+	0	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	CDS	4388537	4388913	0.28	+	0	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	exon	4388537	4388913	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	intron	4388914	4389021	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	CDS	4389022	4389141	1	+	1	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	exon	4389022	4389141	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	intron	4389142	4389226	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	CDS	4389227	4389359	1	+	1	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	exon	4389227	4389359	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	intron	4389360	4389465	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	CDS	4389466	4389774	0.81	+	0	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	exon	4389466	4389774	.	+	.	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
Phchi.S4	AUGUSTUS	stop_codon	4389775	4389777	.	+	0	transcript_id "Phchi.S4G073100.t1"; gene_id "Phchi.S4G073100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3840.t1 is derived from g1009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5958016	5959089	.	-	.	Phchi.S1G099900
Phchi.S1	AUGUSTUS	transcript	5958016	5959089	.	-	.	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	stop_codon	5958013	5958015	.	-	0	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	CDS	5958016	5958101	0.95	-	2	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	exon	5958016	5958101	.	-	.	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	intron	5958102	5958221	.	-	.	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	CDS	5958222	5958330	0.99	-	0	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	exon	5958222	5958330	.	-	.	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	intron	5958331	5958417	.	-	.	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	CDS	5958418	5959089	0.56	-	0	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	exon	5958418	5959089	.	-	.	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
Phchi.S1	AUGUSTUS	start_codon	5959087	5959089	.	-	0	transcript_id "Phchi.S1G099900.t1"; gene_id "Phchi.S1G099900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9649.t1 is derived from g6825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43052961	43054734	.	+	.	Phchi.S1G680800
Phchi.S1	AUGUSTUS	transcript	43052961	43054734	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	start_codon	43052961	43052963	.	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43052961	43053186	0.8	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43052961	43053186	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	intron	43053187	43053308	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43053309	43053448	0.55	+	2	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43053309	43053448	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	intron	43053449	43053572	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43053573	43053881	0.43	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43053573	43053881	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	intron	43053882	43053986	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43053987	43054034	0.5	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43053987	43054034	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	intron	43054035	43054373	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43054374	43054448	0.84	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43054374	43054448	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	intron	43054449	43054621	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43054622	43054653	1	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43054622	43054653	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	intron	43054654	43054733	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	CDS	43054734	43054734	1	+	1	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	exon	43054734	43054734	.	+	.	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
Phchi.S1	AUGUSTUS	stop_codon	43054735	43054737	.	+	0	transcript_id "Phchi.S1G680800.t1"; gene_id "Phchi.S1G680800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8098.t1 is derived from g5273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32944097	32945280	.	-	.	Phchi.S1G525700
Phchi.S1	AUGUSTUS	transcript	32944097	32945280	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	stop_codon	32944094	32944096	.	-	0	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	CDS	32944097	32944246	1	-	0	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	exon	32944097	32944246	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	intron	32944247	32944390	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	CDS	32944391	32944627	1	-	0	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	exon	32944391	32944627	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	intron	32944628	32944779	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	CDS	32944780	32944957	1	-	1	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	exon	32944780	32944957	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	intron	32944958	32945152	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	CDS	32945153	32945280	0.71	-	0	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	exon	32945153	32945280	.	-	.	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
Phchi.S1	AUGUSTUS	start_codon	32945278	32945280	.	-	0	transcript_id "Phchi.S1G525700.t1"; gene_id "Phchi.S1G525700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10414.t1 is derived from g7590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47739361	47742160	.	-	.	Phchi.S1G757300
Phchi.S1	AUGUSTUS	transcript	47739361	47742160	.	-	.	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	stop_codon	47739358	47739360	.	-	0	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	CDS	47739361	47741348	0.25	-	2	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	exon	47739361	47741348	.	-	.	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	intron	47741349	47741588	.	-	.	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	CDS	47741589	47741598	0.34	-	0	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	exon	47741589	47741598	.	-	.	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	intron	47741599	47741980	.	-	.	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	CDS	47741981	47742160	0.62	-	0	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	exon	47741981	47742160	.	-	.	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
Phchi.S1	AUGUSTUS	start_codon	47742158	47742160	.	-	0	transcript_id "Phchi.S1G757300.t1"; gene_id "Phchi.S1G757300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11703.t1 is derived from g15754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7766187	7767535	.	-	.	Phchi.S4G128500
Phchi.S4	AUGUSTUS	transcript	7766187	7767535	.	-	.	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	stop_codon	7766184	7766186	.	-	0	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	CDS	7766187	7766272	0.89	-	2	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	exon	7766187	7766272	.	-	.	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	intron	7766273	7766607	.	-	.	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	CDS	7766608	7767535	1	-	0	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	exon	7766608	7767535	.	-	.	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
Phchi.S4	AUGUSTUS	start_codon	7767533	7767535	.	-	0	transcript_id "Phchi.S4G128500.t1"; gene_id "Phchi.S4G128500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6494.t1 is derived from g3666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23285640	23288667	.	+	.	Phchi.S1G365300
Phchi.S1	AUGUSTUS	transcript	23285640	23288667	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	start_codon	23285640	23285642	.	+	0	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23285640	23285814	1	+	0	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23285640	23285814	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	intron	23285815	23285905	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23285906	23285985	1	+	2	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23285906	23285985	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	intron	23285986	23286079	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23286080	23286242	1	+	0	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23286080	23286242	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	intron	23286243	23286328	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23286329	23286423	1	+	2	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23286329	23286423	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	intron	23286424	23286506	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23286507	23287888	0.66	+	0	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23286507	23287888	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	intron	23287889	23288010	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23288011	23288298	0.32	+	1	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23288011	23288298	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	intron	23288299	23288618	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	CDS	23288619	23288667	0.55	+	1	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	exon	23288619	23288667	.	+	.	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
Phchi.S1	AUGUSTUS	stop_codon	23288668	23288670	.	+	0	transcript_id "Phchi.S1G365300.t1"; gene_id "Phchi.S1G365300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11215.t1 is derived from g15265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4810035	4810781	.	+	.	Phchi.S4G079700
Phchi.S4	AUGUSTUS	transcript	4810035	4810781	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	start_codon	4810035	4810037	.	+	0	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	CDS	4810035	4810087	0.7	+	0	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	exon	4810035	4810087	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	intron	4810088	4810191	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	CDS	4810192	4810281	1	+	1	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	exon	4810192	4810281	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	intron	4810282	4810374	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	CDS	4810375	4810453	1	+	1	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	exon	4810375	4810453	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	intron	4810454	4810559	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	CDS	4810560	4810655	1	+	0	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	exon	4810560	4810655	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	intron	4810656	4810748	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	CDS	4810749	4810781	1	+	0	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	exon	4810749	4810781	.	+	.	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
Phchi.S4	AUGUSTUS	stop_codon	4810782	4810784	.	+	0	transcript_id "Phchi.S4G079700.t1"; gene_id "Phchi.S4G079700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2086.t1 is derived from g9006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4780698	4781288	.	-	.	Phchi.S5G069500
Phchi.S5	AUGUSTUS	transcript	4780698	4781288	.	-	.	transcript_id "Phchi.S5G069500.t1"; gene_id "Phchi.S5G069500"
Phchi.S5	AUGUSTUS	stop_codon	4780695	4780697	.	-	0	transcript_id "Phchi.S5G069500.t1"; gene_id "Phchi.S5G069500"
Phchi.S5	AUGUSTUS	CDS	4780698	4781288	0.72	-	0	transcript_id "Phchi.S5G069500.t1"; gene_id "Phchi.S5G069500"
Phchi.S5	AUGUSTUS	exon	4780698	4781288	.	-	.	transcript_id "Phchi.S5G069500.t1"; gene_id "Phchi.S5G069500"
Phchi.S5	AUGUSTUS	start_codon	4781286	4781288	.	-	0	transcript_id "Phchi.S5G069500.t1"; gene_id "Phchi.S5G069500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14111.t1 is derived from g12578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10895682	10899076	.	-	.	Phchi.S3G143000
Phchi.S3	AUGUSTUS	transcript	10895682	10899076	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	stop_codon	10895679	10895681	.	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10895682	10895975	0.95	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10895682	10895975	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10895976	10896061	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10896062	10896215	1	-	1	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10896062	10896215	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10896216	10896342	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10896343	10896419	1	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10896343	10896419	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10896420	10896555	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10896556	10896748	1	-	1	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10896556	10896748	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10896749	10896949	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10896950	10897135	1	-	1	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10896950	10897135	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10897136	10897272	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10897273	10897679	1	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10897273	10897679	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10897680	10897758	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10897759	10898028	0.57	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10897759	10898028	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10898029	10898189	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10898190	10898516	0.74	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10898190	10898516	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10898517	10898601	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10898602	10898648	0.66	-	2	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10898602	10898648	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10898649	10898781	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10898782	10898816	0.98	-	1	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10898782	10898816	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	intron	10898817	10899005	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	CDS	10899006	10899076	0.36	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	exon	10899006	10899076	.	-	.	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
Phchi.S3	AUGUSTUS	start_codon	10899074	10899076	.	-	0	transcript_id "Phchi.S3G143000.t1"; gene_id "Phchi.S3G143000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8775.t1 is derived from g5950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37899377	37901474	.	-	.	Phchi.S1G593400
Phchi.S1	AUGUSTUS	transcript	37899377	37901474	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	stop_codon	37899374	37899376	.	-	0	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	CDS	37899377	37899383	0.47	-	1	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	exon	37899377	37899383	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	intron	37899384	37899475	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	CDS	37899476	37900074	0.41	-	0	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	exon	37899476	37900074	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	intron	37900075	37900263	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	CDS	37900264	37900439	0.77	-	2	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	exon	37900264	37900439	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	intron	37900440	37900670	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	CDS	37900671	37900874	0.99	-	2	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	exon	37900671	37900874	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	intron	37900875	37900954	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	CDS	37900955	37901195	0.87	-	0	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	exon	37900955	37901195	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	intron	37901196	37901294	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	CDS	37901295	37901474	0.63	-	0	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	exon	37901295	37901474	.	-	.	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
Phchi.S1	AUGUSTUS	start_codon	37901472	37901474	.	-	0	transcript_id "Phchi.S1G593400.t1"; gene_id "Phchi.S1G593400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1010.t1 is derived from g10793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7094078	7094685	.	-	.	Phchi.S6G096900
Phchi.S6	AUGUSTUS	transcript	7094078	7094685	.	-	.	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	stop_codon	7094075	7094077	.	-	0	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	CDS	7094078	7094455	0.64	-	0	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	exon	7094078	7094455	.	-	.	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	intron	7094456	7094538	.	-	.	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	CDS	7094539	7094685	0.39	-	0	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	exon	7094539	7094685	.	-	.	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
Phchi.S6	AUGUSTUS	start_codon	7094683	7094685	.	-	0	transcript_id "Phchi.S6G096900.t1"; gene_id "Phchi.S6G096900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg546.t1 is derived from g10328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4000337	4001214	.	+	.	Phchi.S6G050500
Phchi.S6	AUGUSTUS	transcript	4000337	4001214	.	+	.	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	start_codon	4000337	4000339	.	+	0	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	CDS	4000337	4000582	0.37	+	0	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	exon	4000337	4000582	.	+	.	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	intron	4000583	4000752	.	+	.	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	CDS	4000753	4001017	0.16	+	0	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	exon	4000753	4001017	.	+	.	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	intron	4001018	4001110	.	+	.	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	CDS	4001111	4001214	0.36	+	2	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	exon	4001111	4001214	.	+	.	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
Phchi.S6	AUGUSTUS	stop_codon	4001215	4001217	.	+	0	transcript_id "Phchi.S6G050500.t1"; gene_id "Phchi.S6G050500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8616.t1 is derived from g5791.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36934207	36935027	.	-	.	Phchi.S1G577500
Phchi.S1	AUGUSTUS	transcript	36934207	36935027	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	stop_codon	36934204	36934206	.	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934207	36934329	0.83	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934207	36934329	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934330	36934472	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934473	36934547	0.47	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934473	36934547	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934548	36934632	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934633	36934710	0.87	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934633	36934710	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934711	36934868	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934869	36934880	0.82	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934869	36934880	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934881	36934970	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934971	36935027	0.78	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934971	36935027	.	-	.	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	start_codon	36935025	36935027	.	-	0	transcript_id "Phchi.S1G577500.t1"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	transcript	36934207	36934977	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	stop_codon	36934204	36934206	.	-	0	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934207	36934329	0.75	-	0	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934207	36934329	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934330	36934472	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934473	36934547	0.41	-	0	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934473	36934547	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934548	36934632	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934633	36934655	0.46	-	2	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934633	36934655	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934656	36934746	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934747	36934776	0.81	-	2	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934747	36934776	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934777	36934868	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934869	36934977	0.73	-	0	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934869	36934977	.	-	.	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	start_codon	36934975	36934977	.	-	0	transcript_id "Phchi.S1G577500.t2"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	transcript	36934207	36935027	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	stop_codon	36934204	36934206	.	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934207	36934329	0.7	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934207	36934329	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934330	36934472	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934473	36934538	0.8	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934473	36934538	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934539	36934632	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934633	36934710	0.45	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934633	36934710	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934711	36934868	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934869	36934880	0.45	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934869	36934880	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	intron	36934881	36934970	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	CDS	36934971	36935027	0.42	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	exon	36934971	36935027	.	-	.	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
Phchi.S1	AUGUSTUS	start_codon	36935025	36935027	.	-	0	transcript_id "Phchi.S1G577500.t3"; gene_id "Phchi.S1G577500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9872.t1 is derived from g7048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44183075	44188576	.	-	.	Phchi.S1G703100
Phchi.S1	AUGUSTUS	transcript	44184087	44188576	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	stop_codon	44184084	44184086	.	-	0	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184087	44184098	0.93	-	0	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184087	44184098	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44184099	44184358	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184359	44184550	0.94	-	0	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184359	44184550	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44184551	44184657	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184658	44185413	0.78	-	0	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184658	44185413	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44185414	44185527	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44185528	44186699	1	-	2	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44185528	44186699	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44186700	44186782	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44186783	44186908	1	-	2	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44186783	44186908	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44186909	44186997	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44186998	44188576	0.97	-	0	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44186998	44188576	.	-	.	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	start_codon	44188574	44188576	.	-	0	transcript_id "Phchi.S1G703100.t1"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	transcript	44183075	44188576	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	stop_codon	44183072	44183074	.	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44183075	44183107	0.73	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44183075	44183107	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44183108	44183362	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44183363	44183467	0.73	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44183363	44183467	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44183468	44183618	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44183619	44183703	0.72	-	1	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44183619	44183703	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44183704	44183820	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44183821	44183868	0.69	-	1	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44183821	44183868	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44183869	44184044	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184045	44184098	0.83	-	1	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184045	44184098	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44184099	44184186	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184187	44184291	0.96	-	1	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184187	44184291	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44184292	44184368	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184369	44184550	0.88	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184369	44184550	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44184551	44184657	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44184658	44185413	0.7	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44184658	44185413	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44185414	44185527	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44185528	44186699	1	-	2	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44185528	44186699	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44186700	44186782	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44186783	44186908	1	-	2	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44186783	44186908	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	intron	44186909	44186997	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	CDS	44186998	44188576	0.98	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	exon	44186998	44188576	.	-	.	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
Phchi.S1	AUGUSTUS	start_codon	44188574	44188576	.	-	0	transcript_id "Phchi.S1G703100.t2"; gene_id "Phchi.S1G703100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4080.t1 is derived from g1249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7681854	7683431	.	+	.	Phchi.S1G123900
Phchi.S1	AUGUSTUS	transcript	7681854	7683431	.	+	.	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	start_codon	7681854	7681856	.	+	0	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	CDS	7681854	7682548	0.91	+	0	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	exon	7681854	7682548	.	+	.	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	intron	7682549	7682653	.	+	.	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	CDS	7682654	7683431	0.63	+	1	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	exon	7682654	7683431	.	+	.	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
Phchi.S1	AUGUSTUS	stop_codon	7683432	7683434	.	+	0	transcript_id "Phchi.S1G123900.t1"; gene_id "Phchi.S1G123900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7110.t1 is derived from g4282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27033297	27034836	.	-	.	Phchi.S1G426900
Phchi.S1	AUGUSTUS	transcript	27033297	27034836	.	-	.	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	stop_codon	27033294	27033296	.	-	0	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	CDS	27033297	27034325	1	-	0	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	exon	27033297	27034325	.	-	.	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	intron	27034326	27034401	.	-	.	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	CDS	27034402	27034836	1	-	0	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	exon	27034402	27034836	.	-	.	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
Phchi.S1	AUGUSTUS	start_codon	27034834	27034836	.	-	0	transcript_id "Phchi.S1G426900.t1"; gene_id "Phchi.S1G426900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3010.t1 is derived from g179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1116660	1117500	.	-	.	Phchi.S1G016900
Phchi.S1	AUGUSTUS	transcript	1116660	1117500	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	stop_codon	1116657	1116659	.	-	0	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	CDS	1116660	1116762	0.96	-	1	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	exon	1116660	1116762	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	intron	1116763	1116848	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	CDS	1116849	1117037	1	-	1	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	exon	1116849	1117037	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	intron	1117038	1117157	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	CDS	1117158	1117318	1	-	0	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	exon	1117158	1117318	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	intron	1117319	1117497	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	CDS	1117498	1117500	1	-	0	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	exon	1117498	1117500	.	-	.	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
Phchi.S1	AUGUSTUS	start_codon	1117498	1117500	.	-	0	transcript_id "Phchi.S1G016900.t1"; gene_id "Phchi.S1G016900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12063.t1 is derived from g7738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1435391	1436333	.	+	.	Phchi.S2G014300
Phchi.S2	AUGUSTUS	transcript	1435391	1436333	.	+	.	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	start_codon	1435391	1435393	.	+	0	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	CDS	1435391	1435705	0.32	+	0	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	exon	1435391	1435705	.	+	.	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	intron	1435706	1435869	.	+	.	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	CDS	1435870	1435999	0.35	+	0	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	exon	1435870	1435999	.	+	.	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	intron	1436000	1436115	.	+	.	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	CDS	1436116	1436333	0.51	+	2	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	exon	1436116	1436333	.	+	.	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
Phchi.S2	AUGUSTUS	stop_codon	1436334	1436336	.	+	0	transcript_id "Phchi.S2G014300.t1"; gene_id "Phchi.S2G014300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11556.t1 is derived from g15607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7021804	7022262	.	-	.	Phchi.S4G113800
Phchi.S4	AUGUSTUS	transcript	7021804	7022262	.	-	.	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	stop_codon	7021801	7021803	.	-	0	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	CDS	7021804	7021874	0.5	-	2	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	exon	7021804	7021874	.	-	.	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	intron	7021875	7022028	.	-	.	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	CDS	7022029	7022033	0.49	-	1	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	exon	7022029	7022033	.	-	.	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	intron	7022034	7022131	.	-	.	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	CDS	7022132	7022262	0.49	-	0	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	exon	7022132	7022262	.	-	.	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
Phchi.S4	AUGUSTUS	start_codon	7022260	7022262	.	-	0	transcript_id "Phchi.S4G113800.t1"; gene_id "Phchi.S4G113800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1270.t1 is derived from g11053.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8751930	8754490	.	+	.	Phchi.S6G122900
Phchi.S6	AUGUSTUS	transcript	8751930	8754490	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	start_codon	8751930	8751932	.	+	0	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8751930	8752065	0.56	+	0	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8751930	8752065	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	intron	8752066	8752158	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8752159	8752561	1	+	2	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8752159	8752561	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	intron	8752562	8752648	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8752649	8752776	1	+	1	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8752649	8752776	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	intron	8752777	8752862	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8752863	8752883	1	+	2	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8752863	8752883	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	intron	8752884	8753044	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8753045	8753172	1	+	2	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8753045	8753172	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	intron	8753173	8753292	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8753293	8754033	0.99	+	0	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8753293	8754033	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	intron	8754034	8754232	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	CDS	8754233	8754490	1	+	0	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	exon	8754233	8754490	.	+	.	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
Phchi.S6	AUGUSTUS	stop_codon	8754491	8754493	.	+	0	transcript_id "Phchi.S6G122900.t1"; gene_id "Phchi.S6G122900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14665.t1 is derived from g13133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14026454	14028876	.	-	.	Phchi.S3G198400
Phchi.S3	AUGUSTUS	transcript	14026454	14028876	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	stop_codon	14026451	14026453	.	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14026454	14026516	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14026454	14026516	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14026517	14026647	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14026648	14026703	1	-	2	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14026648	14026703	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14026704	14026796	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14026797	14026848	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14026797	14026848	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14026849	14026966	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14026967	14027056	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14026967	14027056	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14027057	14027146	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14027147	14027338	0.97	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14027147	14027338	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14027339	14027439	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14027440	14027506	0.98	-	1	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14027440	14027506	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14027507	14027615	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14027616	14027656	0.97	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14027616	14027656	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14027657	14027796	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14027797	14027868	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14027797	14027868	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14027869	14028016	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14028017	14028088	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14028017	14028088	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14028089	14028226	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14028227	14028310	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14028227	14028310	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14028311	14028618	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14028619	14028675	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14028619	14028675	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	intron	14028676	14028783	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	CDS	14028784	14028876	1	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	exon	14028784	14028876	.	-	.	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
Phchi.S3	AUGUSTUS	start_codon	14028874	14028876	.	-	0	transcript_id "Phchi.S3G198400.t1"; gene_id "Phchi.S3G198400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5955.t1 is derived from g3126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20062780	20063616	.	+	.	Phchi.S1G311400
Phchi.S1	AUGUSTUS	transcript	20062780	20063616	.	+	.	transcript_id "Phchi.S1G311400.t1"; gene_id "Phchi.S1G311400"
Phchi.S1	AUGUSTUS	start_codon	20062780	20062782	.	+	0	transcript_id "Phchi.S1G311400.t1"; gene_id "Phchi.S1G311400"
Phchi.S1	AUGUSTUS	CDS	20062780	20063616	0.98	+	0	transcript_id "Phchi.S1G311400.t1"; gene_id "Phchi.S1G311400"
Phchi.S1	AUGUSTUS	exon	20062780	20063616	.	+	.	transcript_id "Phchi.S1G311400.t1"; gene_id "Phchi.S1G311400"
Phchi.S1	AUGUSTUS	stop_codon	20063617	20063619	.	+	0	transcript_id "Phchi.S1G311400.t1"; gene_id "Phchi.S1G311400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1454.t1 is derived from g8373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	965960	971022	.	-	.	Phchi.S5G006300
Phchi.S5	AUGUSTUS	transcript	965960	971022	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	stop_codon	965957	965959	.	-	0	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	CDS	965960	966216	0.92	-	2	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	exon	965960	966216	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	intron	966217	966404	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	CDS	966405	967236	0.95	-	0	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	exon	966405	967236	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	intron	967237	967345	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	CDS	967346	967728	0.67	-	2	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	exon	967346	967728	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	intron	967729	967809	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	CDS	967810	968094	1	-	2	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	exon	967810	968094	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	intron	968095	968196	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	CDS	968197	969909	0.35	-	2	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	exon	968197	969909	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	intron	969910	970022	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	CDS	970023	971022	0.2	-	0	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	exon	970023	971022	.	-	.	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
Phchi.S5	AUGUSTUS	start_codon	971020	971022	.	-	0	transcript_id "Phchi.S5G006300.t1"; gene_id "Phchi.S5G006300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15665.t1 is derived from g14134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20573106	20576202	.	+	.	Phchi.S3G298400
Phchi.S3	AUGUSTUS	transcript	20573106	20576202	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	start_codon	20573106	20573108	.	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20573106	20573447	0.96	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20573106	20573447	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20573448	20573744	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20573745	20573921	0.99	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20573745	20573921	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20573922	20574027	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20574028	20574156	0.91	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20574028	20574156	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20574157	20574259	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20574260	20574436	1	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20574260	20574436	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20574437	20574649	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20574650	20574756	1	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20574650	20574756	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20574757	20574870	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20574871	20574991	1	+	1	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20574871	20574991	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20574992	20575114	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20575115	20575176	1	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20575115	20575176	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20575177	20575281	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20575282	20575584	1	+	1	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20575282	20575584	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20575585	20575705	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20575706	20576000	1	+	1	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20575706	20576000	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	intron	20576001	20576085	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	CDS	20576086	20576202	1	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	exon	20576086	20576202	.	+	.	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
Phchi.S3	AUGUSTUS	stop_codon	20576203	20576205	.	+	0	transcript_id "Phchi.S3G298400.t1"; gene_id "Phchi.S3G298400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14414.t1 is derived from g12882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12715039	12716492	.	-	.	Phchi.S3G173300
Phchi.S3	AUGUSTUS	transcript	12715039	12716492	.	-	.	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	stop_codon	12715036	12715038	.	-	0	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	CDS	12715039	12715485	0.62	-	0	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	exon	12715039	12715485	.	-	.	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	intron	12715486	12715561	.	-	.	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	CDS	12715562	12716180	0.44	-	1	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	exon	12715562	12716180	.	-	.	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	intron	12716181	12716235	.	-	.	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	CDS	12716236	12716492	0.63	-	0	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	exon	12716236	12716492	.	-	.	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
Phchi.S3	AUGUSTUS	start_codon	12716490	12716492	.	-	0	transcript_id "Phchi.S3G173300.t1"; gene_id "Phchi.S3G173300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2906.t1 is derived from g75.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	416603	417089	.	+	.	Phchi.S1G006500
Phchi.S1	AUGUSTUS	transcript	416603	417089	.	+	.	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	start_codon	416603	416605	.	+	0	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	CDS	416603	416720	0.57	+	0	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	exon	416603	416720	.	+	.	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	intron	416721	416798	.	+	.	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	CDS	416799	416862	0.64	+	2	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	exon	416799	416862	.	+	.	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	intron	416863	416968	.	+	.	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	CDS	416969	417089	0.68	+	1	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	exon	416969	417089	.	+	.	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
Phchi.S1	AUGUSTUS	stop_codon	417090	417092	.	+	0	transcript_id "Phchi.S1G006500.t1"; gene_id "Phchi.S1G006500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10529.t1 is derived from g14579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	842008	843551	.	+	.	Phchi.S4G011100
Phchi.S4	AUGUSTUS	transcript	842008	843551	.	+	.	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	start_codon	842008	842010	.	+	0	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	CDS	842008	842765	0.9	+	0	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	exon	842008	842765	.	+	.	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	intron	842766	842953	.	+	.	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	CDS	842954	843551	0.78	+	1	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	exon	842954	843551	.	+	.	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
Phchi.S4	AUGUSTUS	stop_codon	843552	843554	.	+	0	transcript_id "Phchi.S4G011100.t1"; gene_id "Phchi.S4G011100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7581.t1 is derived from g4755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30138923	30139826	.	-	.	Phchi.S1G474000
Phchi.S1	AUGUSTUS	transcript	30138923	30139826	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	stop_codon	30138920	30138922	.	-	0	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	CDS	30138923	30139069	0.93	-	0	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	exon	30138923	30139069	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	intron	30139070	30139229	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	CDS	30139230	30139391	1	-	0	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	exon	30139230	30139391	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	intron	30139392	30139504	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	CDS	30139505	30139593	1	-	2	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	exon	30139505	30139593	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	intron	30139594	30139687	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	CDS	30139688	30139826	0.51	-	0	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	exon	30139688	30139826	.	-	.	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
Phchi.S1	AUGUSTUS	start_codon	30139824	30139826	.	-	0	transcript_id "Phchi.S1G474000.t1"; gene_id "Phchi.S1G474000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2672.t1 is derived from g9592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8138887	8140755	.	-	.	Phchi.S5G128100
Phchi.S5	AUGUSTUS	transcript	8138887	8140755	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	stop_codon	8138884	8138886	.	-	0	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	CDS	8138887	8139334	1	-	1	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	exon	8138887	8139334	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	intron	8139335	8139410	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	CDS	8139411	8139694	1	-	0	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	exon	8139411	8139694	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	intron	8139695	8139792	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	CDS	8139793	8140072	0.84	-	1	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	exon	8139793	8140072	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	intron	8140073	8140166	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	CDS	8140167	8140204	1	-	0	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	exon	8140167	8140204	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	intron	8140205	8140380	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	CDS	8140381	8140755	0.96	-	0	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	exon	8140381	8140755	.	-	.	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
Phchi.S5	AUGUSTUS	start_codon	8140753	8140755	.	-	0	transcript_id "Phchi.S5G128100.t1"; gene_id "Phchi.S5G128100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15027.t1 is derived from g13495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16595015	16597234	.	+	.	Phchi.S3G234600
Phchi.S3	AUGUSTUS	transcript	16595015	16597234	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	start_codon	16595015	16595017	.	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595015	16595164	0.94	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595015	16595164	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16595165	16595250	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595251	16595282	0.94	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595251	16595282	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16595283	16595336	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595337	16595361	0.99	+	1	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595337	16595361	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16595362	16595448	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595449	16595484	0.99	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595449	16595484	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16595485	16595584	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595585	16595644	0.99	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595585	16595644	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16595645	16595767	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595768	16595825	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595768	16595825	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16595826	16595902	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16595903	16596000	1	+	2	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16595903	16596000	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16596001	16596077	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16596078	16596167	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16596078	16596167	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16596168	16596340	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16596341	16596409	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16596341	16596409	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16596410	16596484	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16596485	16596571	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16596485	16596571	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16596572	16596679	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16596680	16596775	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16596680	16596775	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16596776	16596879	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16596880	16596957	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16596880	16596957	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16596958	16597036	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16597037	16597123	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16597037	16597123	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	intron	16597124	16597201	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	CDS	16597202	16597234	1	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	exon	16597202	16597234	.	+	.	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
Phchi.S3	AUGUSTUS	stop_codon	16597235	16597237	.	+	0	transcript_id "Phchi.S3G234600.t1"; gene_id "Phchi.S3G234600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11902.t1 is derived from g15954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9204298	9204594	.	+	.	Phchi.S4G148400
Phchi.S4	AUGUSTUS	transcript	9204298	9204594	.	+	.	transcript_id "Phchi.S4G148400.t1"; gene_id "Phchi.S4G148400"
Phchi.S4	AUGUSTUS	start_codon	9204298	9204300	.	+	0	transcript_id "Phchi.S4G148400.t1"; gene_id "Phchi.S4G148400"
Phchi.S4	AUGUSTUS	CDS	9204298	9204594	0.63	+	0	transcript_id "Phchi.S4G148400.t1"; gene_id "Phchi.S4G148400"
Phchi.S4	AUGUSTUS	exon	9204298	9204594	.	+	.	transcript_id "Phchi.S4G148400.t1"; gene_id "Phchi.S4G148400"
Phchi.S4	AUGUSTUS	stop_codon	9204595	9204597	.	+	0	transcript_id "Phchi.S4G148400.t1"; gene_id "Phchi.S4G148400"
# This transcript jg15387.t2 is derived from g13855.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15388.t1 is derived from g13856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18766734	18769466	.	-	.	Phchi.S3G270700
Phchi.S3	AUGUSTUS	transcript	18766734	18769466	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	stop_codon	18766731	18766733	.	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18766734	18766998	1	-	1	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18766734	18766998	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	intron	18766999	18767119	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18767120	18767346	1	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18767120	18767346	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	intron	18767347	18767513	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18767514	18767678	1	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18767514	18767678	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	intron	18767679	18767773	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18767774	18768011	1	-	1	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18767774	18768011	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	intron	18768012	18768145	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18768146	18768834	1	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18768146	18768834	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	intron	18768835	18768928	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18768929	18769222	1	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18768929	18769222	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	intron	18769223	18769376	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	CDS	18769377	18769466	0.55	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	exon	18769377	18769466	.	-	.	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
Phchi.S3	AUGUSTUS	start_codon	18769464	18769466	.	-	0	transcript_id "Phchi.S3G270700.t1"; gene_id "Phchi.S3G270700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4867.t1 is derived from g2037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13161177	13163308	.	+	.	Phchi.S1G202600
Phchi.S1	AUGUSTUS	transcript	13161177	13163308	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	start_codon	13161177	13161179	.	+	0	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13161177	13161222	0.64	+	0	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13161177	13161222	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13161223	13161374	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13161375	13161493	0.74	+	2	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13161375	13161493	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13161494	13161583	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13161584	13161705	0.98	+	0	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13161584	13161705	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13161706	13161826	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13161827	13161915	1	+	1	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13161827	13161915	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13161916	13162369	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13162370	13162389	0.92	+	2	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13162370	13162389	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13162390	13162477	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13162478	13162589	0.92	+	0	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13162478	13162589	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13162590	13163010	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13163011	13163154	0.99	+	2	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13163011	13163154	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	intron	13163155	13163237	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	CDS	13163238	13163308	0.95	+	2	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	exon	13163238	13163308	.	+	.	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
Phchi.S1	AUGUSTUS	stop_codon	13163309	13163311	.	+	0	transcript_id "Phchi.S1G202600.t1"; gene_id "Phchi.S1G202600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg394.t1 is derived from g10176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2868438	2869735	.	-	.	Phchi.S6G035300
Phchi.S6	AUGUSTUS	transcript	2868438	2869735	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	stop_codon	2868435	2868437	.	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2868438	2868613	1	-	2	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2868438	2868613	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	intron	2868614	2868686	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2868687	2868775	1	-	1	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2868687	2868775	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	intron	2868776	2868857	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2868858	2868997	1	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2868858	2868997	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	intron	2868998	2869081	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2869082	2869192	1	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2869082	2869192	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	intron	2869193	2869297	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2869298	2869408	1	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2869298	2869408	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	intron	2869409	2869481	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2869482	2869553	1	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2869482	2869553	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	intron	2869554	2869675	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	CDS	2869676	2869735	1	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	exon	2869676	2869735	.	-	.	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
Phchi.S6	AUGUSTUS	start_codon	2869733	2869735	.	-	0	transcript_id "Phchi.S6G035300.t1"; gene_id "Phchi.S6G035300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12198.t1 is derived from g7874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6698102	6699990	.	+	.	Phchi.S2G027800
Phchi.S2	AUGUSTUS	transcript	6698102	6699990	.	+	.	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	start_codon	6698102	6698104	.	+	0	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	CDS	6698102	6698288	0.83	+	0	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	exon	6698102	6698288	.	+	.	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	intron	6698289	6698497	.	+	.	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	CDS	6698498	6699990	0.99	+	2	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	exon	6698498	6699990	.	+	.	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
Phchi.S2	AUGUSTUS	stop_codon	6699991	6699993	.	+	0	transcript_id "Phchi.S2G027800.t1"; gene_id "Phchi.S2G027800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1797.t1 is derived from g8717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3068696	3070764	.	-	.	Phchi.S5G040600
Phchi.S5	AUGUSTUS	transcript	3068696	3070764	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	stop_codon	3068693	3068695	.	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3068696	3068887	0.91	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3068696	3068887	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	intron	3068888	3068966	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3068967	3069039	0.99	-	1	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3068967	3069039	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	intron	3069040	3069107	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3069108	3069262	0.44	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3069108	3069262	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	intron	3069263	3069395	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3069396	3069470	1	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3069396	3069470	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	intron	3069471	3069637	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3069638	3069799	1	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3069638	3069799	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	intron	3069800	3070015	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3070016	3070336	1	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3070016	3070336	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	intron	3070337	3070509	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	CDS	3070510	3070764	1	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	exon	3070510	3070764	.	-	.	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
Phchi.S5	AUGUSTUS	start_codon	3070762	3070764	.	-	0	transcript_id "Phchi.S5G040600.t1"; gene_id "Phchi.S5G040600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1339.t1 is derived from g11122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9099565	9101253	.	+	.	Phchi.S6G129800
Phchi.S6	AUGUSTUS	transcript	9099565	9101253	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	start_codon	9099565	9099567	.	+	0	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	CDS	9099565	9099636	1	+	0	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	exon	9099565	9099636	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	intron	9099637	9099905	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	CDS	9099906	9100075	1	+	0	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	exon	9099906	9100075	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	intron	9100076	9100282	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	CDS	9100283	9100472	0.63	+	1	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	exon	9100283	9100472	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	intron	9100473	9100584	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	CDS	9100585	9100691	1	+	0	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	exon	9100585	9100691	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	intron	9100692	9101180	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	CDS	9101181	9101253	0.95	+	1	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	exon	9101181	9101253	.	+	.	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
Phchi.S6	AUGUSTUS	stop_codon	9101254	9101256	.	+	0	transcript_id "Phchi.S6G129800.t1"; gene_id "Phchi.S6G129800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8401.t1 is derived from g5576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35759683	35761103	.	+	.	Phchi.S1G556000
Phchi.S1	AUGUSTUS	transcript	35759683	35761103	.	+	.	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	start_codon	35759683	35759685	.	+	0	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	CDS	35759683	35759847	0.45	+	0	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	exon	35759683	35759847	.	+	.	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	intron	35759848	35759921	.	+	.	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	CDS	35759922	35761103	0.89	+	0	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	exon	35759922	35761103	.	+	.	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
Phchi.S1	AUGUSTUS	stop_codon	35761104	35761106	.	+	0	transcript_id "Phchi.S1G556000.t1"; gene_id "Phchi.S1G556000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg965.t1 is derived from g10747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6705881	6706174	.	+	.	Phchi.S6G092400
Phchi.S6	AUGUSTUS	transcript	6705881	6706174	.	+	.	transcript_id "Phchi.S6G092400.t1"; gene_id "Phchi.S6G092400"
Phchi.S6	AUGUSTUS	start_codon	6705881	6705883	.	+	0	transcript_id "Phchi.S6G092400.t1"; gene_id "Phchi.S6G092400"
Phchi.S6	AUGUSTUS	CDS	6705881	6706174	0.69	+	0	transcript_id "Phchi.S6G092400.t1"; gene_id "Phchi.S6G092400"
Phchi.S6	AUGUSTUS	exon	6705881	6706174	.	+	.	transcript_id "Phchi.S6G092400.t1"; gene_id "Phchi.S6G092400"
Phchi.S6	AUGUSTUS	stop_codon	6706175	6706177	.	+	0	transcript_id "Phchi.S6G092400.t1"; gene_id "Phchi.S6G092400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15285.t1 is derived from g13753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18164126	18166404	.	+	.	Phchi.S3G260400
Phchi.S3	AUGUSTUS	transcript	18164126	18166404	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	start_codon	18164126	18164128	.	+	0	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18164126	18164247	0.43	+	0	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18164126	18164247	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	intron	18164248	18164451	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18164452	18164457	0.36	+	1	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18164452	18164457	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	intron	18164458	18164560	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18164561	18165237	0.4	+	1	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18164561	18165237	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	intron	18165238	18165322	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18165323	18165544	1	+	2	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18165323	18165544	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	intron	18165545	18165621	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18165622	18165869	1	+	2	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18165622	18165869	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	intron	18165870	18165997	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18165998	18166137	1	+	0	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18165998	18166137	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	intron	18166138	18166232	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	CDS	18166233	18166404	1	+	1	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	exon	18166233	18166404	.	+	.	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
Phchi.S3	AUGUSTUS	stop_codon	18166405	18166407	.	+	0	transcript_id "Phchi.S3G260400.t1"; gene_id "Phchi.S3G260400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13123.t1 is derived from g11588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4238250	4240402	.	-	.	Phchi.S3G044200
Phchi.S3	AUGUSTUS	transcript	4238250	4240402	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	stop_codon	4238247	4238249	.	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4238250	4238510	1	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4238250	4238510	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4238511	4238593	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4238594	4238668	1	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4238594	4238668	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4238669	4238805	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4238806	4238922	1	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4238806	4238922	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4238923	4239021	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4239022	4239085	1	-	1	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4239022	4239085	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4239086	4239179	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4239180	4239271	1	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4239180	4239271	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4239272	4239396	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4239397	4239622	0.99	-	1	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4239397	4239622	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4239623	4239722	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4239723	4239776	1	-	1	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4239723	4239776	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4239777	4239871	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4239872	4239975	0.94	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4239872	4239975	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4239976	4240117	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4240118	4240208	0.55	-	1	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4240118	4240208	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	intron	4240209	4240307	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	CDS	4240308	4240402	1	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	exon	4240308	4240402	.	-	.	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
Phchi.S3	AUGUSTUS	start_codon	4240400	4240402	.	-	0	transcript_id "Phchi.S3G044200.t1"; gene_id "Phchi.S3G044200"
# This transcript jg10976.t2 is derived from g15026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10977.t1 is derived from g15027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3468963	3469557	.	+	.	Phchi.S4G055900
Phchi.S4	AUGUSTUS	transcript	3468963	3469557	.	+	.	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	start_codon	3468963	3468965	.	+	0	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	CDS	3468963	3469041	0.84	+	0	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	exon	3468963	3469041	.	+	.	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	intron	3469042	3469202	.	+	.	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	CDS	3469203	3469265	1	+	2	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	exon	3469203	3469265	.	+	.	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	intron	3469266	3469351	.	+	.	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	CDS	3469352	3469557	1	+	2	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	exon	3469352	3469557	.	+	.	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
Phchi.S4	AUGUSTUS	stop_codon	3469558	3469560	.	+	0	transcript_id "Phchi.S4G055900.t1"; gene_id "Phchi.S4G055900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10722.t1 is derived from g14772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1760731	1763205	.	+	.	Phchi.S4G030400
Phchi.S4	AUGUSTUS	transcript	1760731	1763205	.	+	.	transcript_id "Phchi.S4G030400.t1"; gene_id "Phchi.S4G030400"
Phchi.S4	AUGUSTUS	start_codon	1760731	1760733	.	+	0	transcript_id "Phchi.S4G030400.t1"; gene_id "Phchi.S4G030400"
Phchi.S4	AUGUSTUS	CDS	1760731	1763205	0.34	+	0	transcript_id "Phchi.S4G030400.t1"; gene_id "Phchi.S4G030400"
Phchi.S4	AUGUSTUS	exon	1760731	1763205	.	+	.	transcript_id "Phchi.S4G030400.t1"; gene_id "Phchi.S4G030400"
Phchi.S4	AUGUSTUS	stop_codon	1763206	1763208	.	+	0	transcript_id "Phchi.S4G030400.t1"; gene_id "Phchi.S4G030400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9124.t1 is derived from g6299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39956591	39958630	.	+	.	Phchi.S1G628300
Phchi.S1	AUGUSTUS	transcript	39956591	39958630	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	start_codon	39956591	39956593	.	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39956591	39956776	0.46	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39956591	39956776	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	intron	39956777	39956867	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39956868	39957176	1	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39956868	39957176	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	intron	39957177	39957304	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39957305	39957504	1	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39957305	39957504	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	intron	39957505	39957659	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39957660	39957895	1	+	1	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39957660	39957895	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	intron	39957896	39957996	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39957997	39958139	1	+	2	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39957997	39958139	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	intron	39958140	39958220	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39958221	39958292	1	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39958221	39958292	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	intron	39958293	39958411	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	CDS	39958412	39958630	0.9	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	exon	39958412	39958630	.	+	.	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
Phchi.S1	AUGUSTUS	stop_codon	39958631	39958633	.	+	0	transcript_id "Phchi.S1G628300.t1"; gene_id "Phchi.S1G628300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8004.t1 is derived from g5179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32413397	32414880	.	+	.	Phchi.S1G516300
Phchi.S1	AUGUSTUS	transcript	32413397	32414880	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	start_codon	32413397	32413399	.	+	0	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32413397	32413419	0.58	+	0	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32413397	32413419	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32413420	32413622	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32413623	32413732	0.95	+	1	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32413623	32413732	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32413733	32413861	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32413862	32413959	0.96	+	2	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32413862	32413959	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32413960	32414147	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32414148	32414244	1	+	0	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32414148	32414244	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32414245	32414328	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32414329	32414414	1	+	2	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32414329	32414414	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32414415	32414503	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32414504	32414536	0.86	+	0	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32414504	32414536	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32414537	32414616	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32414617	32414683	0.83	+	0	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32414617	32414683	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	intron	32414684	32414824	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	CDS	32414825	32414880	0.84	+	2	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	exon	32414825	32414880	.	+	.	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
Phchi.S1	AUGUSTUS	stop_codon	32414881	32414883	.	+	0	transcript_id "Phchi.S1G516300.t1"; gene_id "Phchi.S1G516300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1920.t1 is derived from g8840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3849557	3853181	.	-	.	Phchi.S5G052900
Phchi.S5	AUGUSTUS	transcript	3849557	3853181	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	stop_codon	3849554	3849556	.	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3849557	3849700	0.95	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3849557	3849700	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3849701	3849794	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3849795	3849899	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3849795	3849899	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3849900	3850091	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3850092	3850111	0.92	-	2	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3850092	3850111	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3850112	3850247	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3850248	3850344	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3850248	3850344	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3850345	3850424	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3850425	3850515	1	-	1	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3850425	3850515	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3850516	3850604	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3850605	3850705	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3850605	3850705	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3850706	3850814	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3850815	3850913	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3850815	3850913	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3850914	3851032	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3851033	3851170	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3851033	3851170	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3851171	3851257	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3851258	3851935	0.7	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3851258	3851935	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3851936	3852064	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3852065	3852244	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3852065	3852244	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3852245	3852335	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3852336	3852471	1	-	1	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3852336	3852471	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3852472	3852595	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3852596	3852627	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3852596	3852627	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3852628	3852709	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3852710	3852766	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3852710	3852766	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	intron	3852767	3853013	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	CDS	3853014	3853181	1	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	exon	3853014	3853181	.	-	.	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
Phchi.S5	AUGUSTUS	start_codon	3853179	3853181	.	-	0	transcript_id "Phchi.S5G052900.t1"; gene_id "Phchi.S5G052900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9333.t1 is derived from g6508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40967576	40968979	.	+	.	Phchi.S1G649200
Phchi.S1	AUGUSTUS	transcript	40967576	40968979	.	+	.	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	start_codon	40967576	40967578	.	+	0	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	CDS	40967576	40968484	0.46	+	0	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	exon	40967576	40968484	.	+	.	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	intron	40968485	40968691	.	+	.	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	CDS	40968692	40968979	0.81	+	0	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	exon	40968692	40968979	.	+	.	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
Phchi.S1	AUGUSTUS	stop_codon	40968980	40968982	.	+	0	transcript_id "Phchi.S1G649200.t1"; gene_id "Phchi.S1G649200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5705.t1 is derived from g2875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18448258	18451370	.	+	.	Phchi.S1G286400
Phchi.S1	AUGUSTUS	transcript	18448258	18451370	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	start_codon	18448258	18448260	.	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18448258	18448294	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18448258	18448294	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18448295	18448392	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18448393	18448485	1	+	2	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18448393	18448485	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18448486	18448598	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18448599	18448666	0.99	+	2	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18448599	18448666	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18448667	18448765	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18448766	18448838	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18448766	18448838	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18448839	18448981	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18448982	18449037	1	+	2	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18448982	18449037	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18449038	18449129	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18449130	18449255	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18449130	18449255	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18449256	18449430	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18449431	18449505	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18449431	18449505	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18449506	18449604	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18449605	18449692	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18449605	18449692	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18449693	18449916	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18449917	18449934	0.49	+	2	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18449917	18449934	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18449935	18450022	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18450023	18450081	1	+	2	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18450023	18450081	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18450082	18450210	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18450211	18450266	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18450211	18450266	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18450267	18450357	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18450358	18450456	1	+	1	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18450358	18450456	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18450457	18450561	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18450562	18450618	0.99	+	1	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18450562	18450618	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18450619	18450704	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18450705	18450809	1	+	1	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18450705	18450809	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18450810	18450903	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18450904	18450952	1	+	1	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18450904	18450952	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18450953	18451151	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18451152	18451220	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18451152	18451220	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	intron	18451221	18451301	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	CDS	18451302	18451370	1	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	exon	18451302	18451370	.	+	.	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
Phchi.S1	AUGUSTUS	stop_codon	18451371	18451373	.	+	0	transcript_id "Phchi.S1G286400.t1"; gene_id "Phchi.S1G286400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7457.t1 is derived from g4629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29378618	29379993	.	+	.	Phchi.S1G461600
Phchi.S1	AUGUSTUS	transcript	29378618	29379993	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	start_codon	29378618	29378620	.	+	0	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	CDS	29378618	29378733	0.38	+	0	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	exon	29378618	29378733	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	intron	29378734	29378966	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	CDS	29378967	29379022	0.41	+	1	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	exon	29378967	29379022	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	intron	29379023	29379335	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	CDS	29379336	29379443	0.44	+	2	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	exon	29379336	29379443	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	intron	29379444	29379606	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	CDS	29379607	29379615	0.68	+	2	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	exon	29379607	29379615	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	intron	29379616	29379777	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	CDS	29379778	29379899	0.66	+	2	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	exon	29379778	29379899	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	intron	29379900	29379990	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	CDS	29379991	29379993	0.73	+	0	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	exon	29379991	29379993	.	+	.	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
Phchi.S1	AUGUSTUS	stop_codon	29379994	29379996	.	+	0	transcript_id "Phchi.S1G461600.t1"; gene_id "Phchi.S1G461600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13795.t1 is derived from g12262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8927271	8929272	.	-	.	Phchi.S3G111400
Phchi.S3	AUGUSTUS	transcript	8927271	8929272	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	stop_codon	8927268	8927270	.	-	0	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8927271	8927271	1	-	1	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8927271	8927271	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8927272	8927403	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8927404	8927568	1	-	1	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8927404	8927568	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8927569	8927661	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8927662	8927813	1	-	0	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8927662	8927813	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8927814	8927928	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8927929	8928087	1	-	0	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8927929	8928087	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8928088	8928206	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8928207	8928486	1	-	1	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8928207	8928486	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8928487	8928638	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8928639	8928755	1	-	1	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8928639	8928755	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8928756	8928848	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8928849	8928908	1	-	1	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8928849	8928908	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	intron	8928909	8929090	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	CDS	8929091	8929272	0.64	-	0	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	exon	8929091	8929272	.	-	.	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
Phchi.S3	AUGUSTUS	start_codon	8929270	8929272	.	-	0	transcript_id "Phchi.S3G111400.t1"; gene_id "Phchi.S3G111400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12471.t1 is derived from g8148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	25981158	25981942	.	+	.	Phchi.S2G055100
Phchi.S2	AUGUSTUS	transcript	25981158	25981942	.	+	.	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	start_codon	25981158	25981160	.	+	0	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	CDS	25981158	25981356	0.22	+	0	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	exon	25981158	25981356	.	+	.	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	intron	25981357	25981475	.	+	.	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	CDS	25981476	25981530	0.16	+	2	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	exon	25981476	25981530	.	+	.	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	intron	25981531	25981674	.	+	.	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	CDS	25981675	25981942	0.8	+	1	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	exon	25981675	25981942	.	+	.	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
Phchi.S2	AUGUSTUS	stop_codon	25981943	25981945	.	+	0	transcript_id "Phchi.S2G055100.t1"; gene_id "Phchi.S2G055100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8622.t1 is derived from g5797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37053275	37055077	.	+	.	Phchi.S1G578100
Phchi.S1	AUGUSTUS	transcript	37053275	37055077	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	start_codon	37053275	37053277	.	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37053275	37053354	0.85	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37053275	37053354	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37053355	37053433	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37053434	37053455	0.95	+	1	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37053434	37053455	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37053456	37053608	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37053609	37053686	0.95	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37053609	37053686	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37053687	37053780	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37053781	37053846	0.96	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37053781	37053846	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37053847	37053989	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37053990	37054055	1	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37053990	37054055	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37054056	37054128	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37054129	37054393	0.99	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37054129	37054393	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37054394	37054550	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37054551	37054810	0.76	+	2	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37054551	37054810	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	intron	37054811	37054936	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	CDS	37054937	37055077	0.75	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	exon	37054937	37055077	.	+	.	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
Phchi.S1	AUGUSTUS	stop_codon	37055078	37055080	.	+	0	transcript_id "Phchi.S1G578100.t1"; gene_id "Phchi.S1G578100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11825.t1 is derived from g15877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8413751	8429734	.	-	.	Phchi.S4G140700
Phchi.S4	AUGUSTUS	transcript	8413751	8429734	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	stop_codon	8413748	8413750	.	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8413751	8413780	0.93	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8413751	8413780	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8413781	8413909	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8413910	8413974	0.93	-	2	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8413910	8413974	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8413975	8414071	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8414072	8414737	0.56	-	2	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8414072	8414737	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8414738	8414886	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8414887	8415082	0.56	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8414887	8415082	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8415083	8415292	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8415293	8415676	0.94	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8415293	8415676	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8415677	8415883	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8415884	8416009	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8415884	8416009	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416010	8416138	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416139	8416345	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416139	8416345	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416346	8416432	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416433	8416526	1	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416433	8416526	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416527	8416663	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416664	8416710	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416664	8416710	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416711	8416791	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416792	8417244	0.99	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416792	8417244	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8417245	8417347	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8417348	8417680	0.96	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8417348	8417680	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8417681	8417810	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8417811	8418275	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8417811	8418275	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8418276	8418398	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8418399	8418620	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8418399	8418620	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8418621	8418763	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8418764	8418965	1	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8418764	8418965	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8418966	8419107	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8419108	8419599	0.57	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8419108	8419599	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8419600	8419693	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8419694	8419836	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8419694	8419836	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8419837	8419956	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8419957	8420133	0.95	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8419957	8420133	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8420134	8420281	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8420282	8420509	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8420282	8420509	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8420510	8420596	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8420597	8420884	0.92	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8420597	8420884	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8420885	8421016	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8421017	8421263	1	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8421017	8421263	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8421264	8421395	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8421396	8421584	1	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8421396	8421584	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8421585	8421741	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8421742	8422084	0.99	-	2	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8421742	8422084	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8422085	8422215	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8422216	8422717	0.92	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8422216	8422717	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8422718	8422828	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8422829	8423147	0.92	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8422829	8423147	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8423148	8423395	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8423396	8423556	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8423396	8423556	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8423557	8423719	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8423720	8423917	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8423720	8423917	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8423918	8424013	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8424014	8424358	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8424014	8424358	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8424359	8424695	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8424696	8424737	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8424696	8424737	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8424738	8424911	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8424912	8425067	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8424912	8425067	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8425068	8425161	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8425162	8425311	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8425162	8425311	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8425312	8425463	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8425464	8425625	0.98	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8425464	8425625	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8425626	8425748	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8425749	8426216	0.88	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8425749	8426216	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8426217	8426401	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8426402	8426747	1	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8426402	8426747	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8426748	8427006	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427007	8427198	0.75	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427007	8427198	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8427199	8427310	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427311	8427421	0.83	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427311	8427421	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8427422	8427607	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427608	8427730	0.95	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427608	8427730	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8427731	8427830	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427831	8428032	0.99	-	2	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427831	8428032	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8428033	8428145	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8428146	8428535	0.52	-	2	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8428146	8428535	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8428536	8428632	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8428633	8428794	1	-	2	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8428633	8428794	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8428795	8429105	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8429106	8429334	1	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8429106	8429334	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8429335	8429427	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8429428	8429491	0.66	-	1	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8429428	8429491	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8429492	8429597	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8429598	8429734	0.45	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8429598	8429734	.	-	.	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	start_codon	8429732	8429734	.	-	0	transcript_id "Phchi.S4G140700.t1"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	transcript	8413751	8429734	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	stop_codon	8413748	8413750	.	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8413751	8413780	0.89	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8413751	8413780	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8413781	8413909	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8413910	8413974	0.89	-	2	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8413910	8413974	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8413975	8414071	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8414072	8414737	0.64	-	2	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8414072	8414737	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8414738	8414886	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8414887	8415079	0.65	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8414887	8415079	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8415080	8415292	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8415293	8415676	0.91	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8415293	8415676	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8415677	8415883	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8415884	8416009	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8415884	8416009	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416010	8416138	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416139	8416345	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416139	8416345	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416346	8416432	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416433	8416526	1	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416433	8416526	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416527	8416663	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416664	8416710	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416664	8416710	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8416711	8416791	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8416792	8417244	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8416792	8417244	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8417245	8417347	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8417348	8417680	0.96	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8417348	8417680	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8417681	8417810	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8417811	8418275	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8417811	8418275	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8418276	8418398	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8418399	8418620	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8418399	8418620	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8418621	8418763	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8418764	8418965	1	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8418764	8418965	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8418966	8419107	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8419108	8419599	0.55	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8419108	8419599	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8419600	8419693	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8419694	8419836	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8419694	8419836	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8419837	8419956	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8419957	8420133	0.97	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8419957	8420133	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8420134	8420281	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8420282	8420509	0.99	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8420282	8420509	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8420510	8420596	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8420597	8420884	0.9	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8420597	8420884	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8420885	8421016	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8421017	8421263	1	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8421017	8421263	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8421264	8421395	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8421396	8421584	1	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8421396	8421584	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8421585	8421741	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8421742	8422084	1	-	2	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8421742	8422084	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8422085	8422215	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8422216	8422717	0.91	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8422216	8422717	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8422718	8422828	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8422829	8423147	0.89	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8422829	8423147	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8423148	8423395	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8423396	8423556	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8423396	8423556	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8423557	8423719	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8423720	8423917	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8423720	8423917	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8423918	8424013	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8424014	8424358	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8424014	8424358	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8424359	8424695	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8424696	8424737	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8424696	8424737	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8424738	8424911	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8424912	8425067	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8424912	8425067	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8425068	8425161	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8425162	8425311	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8425162	8425311	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8425312	8425463	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8425464	8425625	0.93	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8425464	8425625	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8425626	8425748	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8425749	8426216	0.96	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8425749	8426216	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8426217	8426401	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8426402	8426747	1	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8426402	8426747	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8426748	8427006	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427007	8427198	0.71	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427007	8427198	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8427199	8427310	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427311	8427421	0.78	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427311	8427421	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8427422	8427607	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427608	8427730	0.97	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427608	8427730	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8427731	8427830	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8427831	8428032	0.98	-	2	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8427831	8428032	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8428033	8428145	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8428146	8428535	0.46	-	2	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8428146	8428535	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8428536	8428632	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8428633	8428794	1	-	2	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8428633	8428794	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8428795	8429105	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8429106	8429334	1	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8429106	8429334	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8429335	8429427	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8429428	8429491	0.68	-	1	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8429428	8429491	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	intron	8429492	8429597	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	CDS	8429598	8429734	0.49	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	exon	8429598	8429734	.	-	.	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
Phchi.S4	AUGUSTUS	start_codon	8429732	8429734	.	-	0	transcript_id "Phchi.S4G140700.t2"; gene_id "Phchi.S4G140700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6558.t1 is derived from g3730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23712621	23714650	.	+	.	Phchi.S1G371700
Phchi.S1	AUGUSTUS	transcript	23712621	23714650	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	start_codon	23712621	23712623	.	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23712621	23712904	0.29	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23712621	23712904	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23712905	23713202	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23713203	23713270	0.9	+	1	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23713203	23713270	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23713271	23713499	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23713500	23713579	1	+	2	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23713500	23713579	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23713580	23713721	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23713722	23713745	0.99	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23713722	23713745	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23713746	23713838	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23713839	23713859	1	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23713839	23713859	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23713860	23713949	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23713950	23714051	0.93	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23713950	23714051	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23714052	23714160	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23714161	23714174	1	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23714161	23714174	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23714175	23714262	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23714263	23714320	1	+	1	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23714263	23714320	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23714321	23714447	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23714448	23714513	1	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23714448	23714513	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	intron	23714514	23714608	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	CDS	23714609	23714650	0.99	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	exon	23714609	23714650	.	+	.	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
Phchi.S1	AUGUSTUS	stop_codon	23714651	23714653	.	+	0	transcript_id "Phchi.S1G371700.t1"; gene_id "Phchi.S1G371700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14632.t1 is derived from g13100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13842552	13845104	.	+	.	Phchi.S3G195100
Phchi.S3	AUGUSTUS	transcript	13842552	13845104	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	start_codon	13842552	13842554	.	+	0	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	CDS	13842552	13842980	0.4	+	0	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	exon	13842552	13842980	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	intron	13842981	13843194	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	CDS	13843195	13843460	0.84	+	0	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	exon	13843195	13843460	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	intron	13843461	13843535	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	CDS	13843536	13844164	0.94	+	1	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	exon	13843536	13844164	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	intron	13844165	13844269	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	CDS	13844270	13844632	0.74	+	2	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	exon	13844270	13844632	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	intron	13844633	13844748	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	CDS	13844749	13845104	0.77	+	2	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	exon	13844749	13845104	.	+	.	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
Phchi.S3	AUGUSTUS	stop_codon	13845105	13845107	.	+	0	transcript_id "Phchi.S3G195100.t1"; gene_id "Phchi.S3G195100"
# This transcript jg6665.t2 is derived from g3837.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6666.t1 is derived from g3838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24400609	24403633	.	+	.	Phchi.S1G382500
Phchi.S1	AUGUSTUS	transcript	24400609	24403633	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	start_codon	24400609	24400611	.	+	0	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	CDS	24400609	24400849	0.59	+	0	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	exon	24400609	24400849	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	intron	24400850	24400927	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	CDS	24400928	24400959	0.53	+	2	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	exon	24400928	24400959	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	intron	24400960	24401065	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	CDS	24401066	24401134	0.71	+	0	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	exon	24401066	24401134	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	intron	24401135	24401215	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	CDS	24401216	24403006	0.84	+	0	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	exon	24401216	24403006	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	intron	24403007	24403348	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	CDS	24403349	24403633	0.69	+	0	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	exon	24403349	24403633	.	+	.	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
Phchi.S1	AUGUSTUS	stop_codon	24403634	24403636	.	+	0	transcript_id "Phchi.S1G382500.t1"; gene_id "Phchi.S1G382500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2125.t1 is derived from g9045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4973030	4976697	.	-	.	Phchi.S5G073400
Phchi.S5	AUGUSTUS	transcript	4973030	4976697	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	stop_codon	4973027	4973029	.	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4973030	4973062	0.59	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4973030	4973062	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4973063	4973240	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4973241	4973375	0.67	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4973241	4973375	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4973376	4973452	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4973453	4973560	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4973453	4973560	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4973561	4973641	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4973642	4973716	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4973642	4973716	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4973717	4973804	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4973805	4973975	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4973805	4973975	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4973976	4974064	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4974065	4974165	0.99	-	2	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4974065	4974165	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4974166	4974269	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4974270	4974347	0.98	-	2	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4974270	4974347	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4974348	4974446	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4974447	4974603	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4974447	4974603	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4974604	4974750	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4974751	4975020	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4974751	4975020	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4975021	4975150	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4975151	4975270	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4975151	4975270	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4975271	4975416	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4975417	4975515	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4975417	4975515	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4975516	4975697	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4975698	4975910	0.99	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4975698	4975910	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4975911	4976004	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4976005	4976077	0.71	-	1	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4976005	4976077	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4976078	4976160	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4976161	4976171	0.98	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4976161	4976171	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	intron	4976172	4976265	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	CDS	4976266	4976697	1	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	exon	4976266	4976697	.	-	.	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
Phchi.S5	AUGUSTUS	start_codon	4976695	4976697	.	-	0	transcript_id "Phchi.S5G073400.t1"; gene_id "Phchi.S5G073400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6896.t1 is derived from g4068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25872137	25873827	.	+	.	Phchi.S1G405500
Phchi.S1	AUGUSTUS	transcript	25872137	25873827	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	start_codon	25872137	25872139	.	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25872137	25872163	0.97	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25872137	25872163	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25872164	25872283	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25872284	25872353	1	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25872284	25872353	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25872354	25872445	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25872446	25872474	1	+	2	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25872446	25872474	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25872475	25872582	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25872583	25872736	1	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25872583	25872736	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25872737	25872840	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25872841	25872913	1	+	2	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25872841	25872913	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25872914	25873053	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25873054	25873120	1	+	1	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25873054	25873120	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25873121	25873271	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25873272	25873331	1	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25873272	25873331	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25873332	25873421	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25873422	25873482	1	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25873422	25873482	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25873483	25873569	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25873570	25873611	1	+	2	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25873570	25873611	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	intron	25873612	25873702	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	CDS	25873703	25873827	1	+	2	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	exon	25873703	25873827	.	+	.	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
Phchi.S1	AUGUSTUS	stop_codon	25873828	25873830	.	+	0	transcript_id "Phchi.S1G405500.t1"; gene_id "Phchi.S1G405500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7039.t1 is derived from g4211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26536371	26539085	.	+	.	Phchi.S1G419800
Phchi.S1	AUGUSTUS	transcript	26536371	26539085	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	start_codon	26536371	26536373	.	+	0	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26536371	26536566	0.97	+	0	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26536371	26536566	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	intron	26536567	26536664	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26536665	26536702	0.33	+	2	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26536665	26536702	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	intron	26536703	26536956	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26536957	26537083	0.54	+	0	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26536957	26537083	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	intron	26537084	26537187	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26537188	26537406	0.93	+	2	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26537188	26537406	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	intron	26537407	26537494	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26537495	26537557	1	+	2	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26537495	26537557	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	intron	26537558	26537686	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26537687	26538690	1	+	2	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26537687	26538690	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	intron	26538691	26538830	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	CDS	26538831	26539085	0.94	+	0	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	exon	26538831	26539085	.	+	.	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
Phchi.S1	AUGUSTUS	stop_codon	26539086	26539088	.	+	0	transcript_id "Phchi.S1G419800.t1"; gene_id "Phchi.S1G419800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7961.t1 is derived from g5136.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32112451	32114653	.	+	.	Phchi.S1G512000
Phchi.S1	AUGUSTUS	transcript	32112451	32114653	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	start_codon	32112451	32112453	.	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32112451	32112660	1	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32112451	32112660	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32112661	32112739	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32112740	32112829	1	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32112740	32112829	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32112830	32112976	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32112977	32113203	1	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32112977	32113203	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32113204	32113334	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32113335	32113398	1	+	1	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32113335	32113398	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32113399	32113497	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32113498	32114190	1	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32113498	32114190	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32114191	32114355	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32114356	32114504	1	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32114356	32114504	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32114505	32114637	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32114638	32114653	1	+	1	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32114638	32114653	.	+	.	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	stop_codon	32114654	32114656	.	+	0	transcript_id "Phchi.S1G512000.t1"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	transcript	32112451	32114639	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	start_codon	32112451	32112453	.	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32112451	32112660	1	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32112451	32112660	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32112661	32112739	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32112740	32112829	1	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32112740	32112829	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32112830	32112976	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32112977	32113203	1	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32112977	32113203	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32113204	32113334	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32113335	32113398	1	+	1	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32113335	32113398	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32113399	32113497	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32113498	32114190	0.99	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32113498	32114190	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32114191	32114355	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32114356	32114452	0.85	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32114356	32114452	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	intron	32114453	32114637	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	CDS	32114638	32114639	0.82	+	2	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	exon	32114638	32114639	.	+	.	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
Phchi.S1	AUGUSTUS	stop_codon	32114640	32114642	.	+	0	transcript_id "Phchi.S1G512000.t2"; gene_id "Phchi.S1G512000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6951.t1 is derived from g4123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26116415	26117990	.	-	.	Phchi.S1G411000
Phchi.S1	AUGUSTUS	transcript	26116415	26117990	.	-	.	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	stop_codon	26116412	26116414	.	-	0	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	CDS	26116415	26117201	0.98	-	1	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	exon	26116415	26117201	.	-	.	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	intron	26117202	26117560	.	-	.	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	CDS	26117561	26117700	0.93	-	0	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	exon	26117561	26117700	.	-	.	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	intron	26117701	26117828	.	-	.	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	CDS	26117829	26117990	0.95	-	0	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	exon	26117829	26117990	.	-	.	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
Phchi.S1	AUGUSTUS	start_codon	26117988	26117990	.	-	0	transcript_id "Phchi.S1G411000.t1"; gene_id "Phchi.S1G411000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4997.t1 is derived from g2167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13936734	13941165	.	-	.	Phchi.S1G215600
Phchi.S1	AUGUSTUS	transcript	13936734	13941165	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	stop_codon	13936731	13936733	.	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13936734	13936811	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13936734	13936811	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13936812	13936891	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13936892	13937002	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13936892	13937002	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13937003	13937080	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13937081	13937154	1	-	2	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13937081	13937154	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13937155	13937251	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13937252	13937321	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13937252	13937321	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13937322	13937396	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13937397	13937444	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13937397	13937444	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13937445	13937529	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13937530	13937606	0.98	-	2	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13937530	13937606	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13937607	13937721	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13937722	13937911	0.92	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13937722	13937911	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13937912	13938021	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13938022	13938114	0.87	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13938022	13938114	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13938115	13938223	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13938224	13938337	0.98	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13938224	13938337	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13938338	13938460	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13938461	13938655	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13938461	13938655	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13938656	13938808	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13938809	13938889	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13938809	13938889	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13938890	13938980	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13938981	13939060	1	-	2	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13938981	13939060	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13939061	13939203	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13939204	13939351	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13939204	13939351	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13939352	13939440	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13939441	13939525	1	-	1	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13939441	13939525	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13939526	13939622	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13939623	13939709	1	-	1	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13939623	13939709	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13939710	13939846	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13939847	13939951	1	-	1	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13939847	13939951	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13939952	13940080	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13940081	13940235	0.91	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13940081	13940235	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13940236	13940405	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13940406	13940504	1	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13940406	13940504	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13940505	13940582	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13940583	13940661	0.98	-	1	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13940583	13940661	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13940662	13940769	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13940770	13940841	0.98	-	1	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13940770	13940841	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	intron	13940842	13940941	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	CDS	13940942	13941165	0.57	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	exon	13940942	13941165	.	-	.	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
Phchi.S1	AUGUSTUS	start_codon	13941163	13941165	.	-	0	transcript_id "Phchi.S1G215600.t1"; gene_id "Phchi.S1G215600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13930.t1 is derived from g12397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9768519	9771071	.	-	.	Phchi.S3G124900
Phchi.S3	AUGUSTUS	transcript	9768519	9771071	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	stop_codon	9768516	9768518	.	-	0	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	CDS	9768519	9768812	1	-	0	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	exon	9768519	9768812	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	intron	9768813	9768906	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	CDS	9768907	9768963	1	-	0	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	exon	9768907	9768963	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	intron	9768964	9769050	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	CDS	9769051	9769154	1	-	2	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	exon	9769051	9769154	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	intron	9769155	9769227	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	CDS	9769228	9769301	1	-	1	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	exon	9769228	9769301	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	intron	9769302	9769404	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	CDS	9769405	9769487	0.44	-	0	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	exon	9769405	9769487	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	intron	9769488	9769874	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	CDS	9769875	9771071	0.53	-	0	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	exon	9769875	9771071	.	-	.	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
Phchi.S3	AUGUSTUS	start_codon	9771069	9771071	.	-	0	transcript_id "Phchi.S3G124900.t1"; gene_id "Phchi.S3G124900"
# This transcript jg9201.t2 is derived from g6376.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9202.t1 is derived from g6377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40351396	40353820	.	+	.	Phchi.S1G636100
Phchi.S1	AUGUSTUS	transcript	40351396	40353820	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	start_codon	40351396	40351398	.	+	0	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40351396	40351792	1	+	0	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40351396	40351792	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	intron	40351793	40351886	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40351887	40351945	1	+	2	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40351887	40351945	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	intron	40351946	40352146	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40352147	40352562	1	+	0	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40352147	40352562	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	intron	40352563	40352686	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40352687	40352786	1	+	1	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40352687	40352786	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	intron	40352787	40352909	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40352910	40353264	0.61	+	0	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40352910	40353264	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	intron	40353265	40353369	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40353370	40353427	0.69	+	2	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40353370	40353427	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	intron	40353428	40353528	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	CDS	40353529	40353820	1	+	1	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	exon	40353529	40353820	.	+	.	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
Phchi.S1	AUGUSTUS	stop_codon	40353821	40353823	.	+	0	transcript_id "Phchi.S1G636100.t1"; gene_id "Phchi.S1G636100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13880.t1 is derived from g12347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9436473	9437072	.	-	.	Phchi.S3G119900
Phchi.S3	AUGUSTUS	transcript	9436473	9437072	.	-	.	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	stop_codon	9436470	9436472	.	-	0	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	CDS	9436473	9436520	1	-	0	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	exon	9436473	9436520	.	-	.	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	intron	9436521	9436676	.	-	.	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	CDS	9436677	9436725	0.99	-	1	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	exon	9436677	9436725	.	-	.	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	intron	9436726	9436935	.	-	.	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	CDS	9436936	9437072	0.45	-	0	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	exon	9436936	9437072	.	-	.	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
Phchi.S3	AUGUSTUS	start_codon	9437070	9437072	.	-	0	transcript_id "Phchi.S3G119900.t1"; gene_id "Phchi.S3G119900"
# This transcript jg14600.t2 is derived from g13068.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14600.t3 is derived from g13068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14601.t1 is derived from g13069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13681834	13689298	.	+	.	Phchi.S3G192000
Phchi.S3	AUGUSTUS	transcript	13681834	13689298	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	start_codon	13681834	13681836	.	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13681834	13681881	0.57	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13681834	13681881	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13681882	13682186	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13682187	13682293	1	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13682187	13682293	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13682294	13682484	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13682485	13685560	1	+	1	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13682485	13685560	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13685561	13685684	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13685685	13685756	0.75	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13685685	13685756	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13685757	13685881	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13685882	13688222	0.76	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13685882	13688222	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13688223	13688351	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13688352	13688806	1	+	2	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13688352	13688806	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13688807	13688896	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13688897	13689013	1	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13688897	13689013	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	intron	13689014	13689157	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	CDS	13689158	13689298	1	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	exon	13689158	13689298	.	+	.	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
Phchi.S3	AUGUSTUS	stop_codon	13689299	13689301	.	+	0	transcript_id "Phchi.S3G192000.t1"; gene_id "Phchi.S3G192000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3688.t1 is derived from g857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5186491	5186928	.	-	.	Phchi.S1G084700
Phchi.S1	AUGUSTUS	transcript	5186491	5186928	.	-	.	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	stop_codon	5186488	5186490	.	-	0	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	CDS	5186491	5186724	0.96	-	0	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	exon	5186491	5186724	.	-	.	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	intron	5186725	5186820	.	-	.	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	CDS	5186821	5186928	0.69	-	0	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	exon	5186821	5186928	.	-	.	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
Phchi.S1	AUGUSTUS	start_codon	5186926	5186928	.	-	0	transcript_id "Phchi.S1G084700.t1"; gene_id "Phchi.S1G084700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10780.t1 is derived from g14830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2079132	2081002	.	+	.	Phchi.S4G036200
Phchi.S4	AUGUSTUS	transcript	2079132	2081002	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	start_codon	2079132	2079134	.	+	0	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	CDS	2079132	2079418	0.96	+	0	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	exon	2079132	2079418	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	intron	2079419	2079541	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	CDS	2079542	2079836	1	+	1	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	exon	2079542	2079836	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	intron	2079837	2079915	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	CDS	2079916	2080227	1	+	0	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	exon	2079916	2080227	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	intron	2080228	2080327	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	CDS	2080328	2080581	1	+	0	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	exon	2080328	2080581	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	intron	2080582	2080671	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	CDS	2080672	2081002	0.86	+	1	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	exon	2080672	2081002	.	+	.	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
Phchi.S4	AUGUSTUS	stop_codon	2081003	2081005	.	+	0	transcript_id "Phchi.S4G036200.t1"; gene_id "Phchi.S4G036200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12242.t1 is derived from g7918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6943982	6946566	.	-	.	Phchi.S2G032200
Phchi.S2	AUGUSTUS	transcript	6943982	6946566	.	-	.	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	stop_codon	6943979	6943981	.	-	0	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	CDS	6943982	6945961	0.46	-	0	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	exon	6943982	6945961	.	-	.	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	intron	6945962	6946089	.	-	.	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	CDS	6946090	6946566	0.71	-	0	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	exon	6946090	6946566	.	-	.	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
Phchi.S2	AUGUSTUS	start_codon	6946564	6946566	.	-	0	transcript_id "Phchi.S2G032200.t1"; gene_id "Phchi.S2G032200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7266.t1 is derived from g4438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27923473	27927920	.	-	.	Phchi.S1G442500
Phchi.S1	AUGUSTUS	transcript	27923473	27927920	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	stop_codon	27923470	27923472	.	-	0	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27923473	27924059	0.98	-	2	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27923473	27924059	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	intron	27924060	27924142	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27924143	27924492	0.99	-	1	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27924143	27924492	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	intron	27924493	27924578	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27924579	27924823	1	-	0	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27924579	27924823	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	intron	27924824	27925646	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27925647	27926018	0.99	-	0	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27925647	27926018	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	intron	27926019	27926131	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27926132	27926571	0.76	-	2	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27926132	27926571	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	intron	27926572	27926672	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27926673	27927101	0.79	-	2	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27926673	27927101	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	intron	27927102	27927226	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	CDS	27927227	27927920	0.63	-	0	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	exon	27927227	27927920	.	-	.	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
Phchi.S1	AUGUSTUS	start_codon	27927918	27927920	.	-	0	transcript_id "Phchi.S1G442500.t1"; gene_id "Phchi.S1G442500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10415.t1 is derived from g7591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47744478	47745475	.	+	.	Phchi.S1G757400
Phchi.S1	AUGUSTUS	transcript	47744478	47745475	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	start_codon	47744478	47744480	.	+	0	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	CDS	47744478	47744542	0.71	+	0	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	exon	47744478	47744542	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	intron	47744543	47744634	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	CDS	47744635	47744655	0.97	+	1	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	exon	47744635	47744655	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	intron	47744656	47744821	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	CDS	47744822	47744841	0.96	+	1	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	exon	47744822	47744841	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	intron	47744842	47745078	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	CDS	47745079	47745087	1	+	2	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	exon	47745079	47745087	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	intron	47745088	47745173	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	CDS	47745174	47745475	0.97	+	2	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	exon	47745174	47745475	.	+	.	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
Phchi.S1	AUGUSTUS	stop_codon	47745476	47745478	.	+	0	transcript_id "Phchi.S1G757400.t1"; gene_id "Phchi.S1G757400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5191.t1 is derived from g2361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15405763	15407112	.	-	.	Phchi.S1G235000
Phchi.S1	AUGUSTUS	transcript	15405763	15407112	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	stop_codon	15405760	15405762	.	-	0	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	CDS	15405763	15405842	0.96	-	2	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	exon	15405763	15405842	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	intron	15405843	15406053	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	CDS	15406054	15406130	0.96	-	1	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	exon	15406054	15406130	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	intron	15406131	15406318	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	CDS	15406319	15406370	0.69	-	2	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	exon	15406319	15406370	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	intron	15406371	15406514	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	CDS	15406515	15406601	0.64	-	2	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	exon	15406515	15406601	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	intron	15406602	15406748	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	CDS	15406749	15406779	0.59	-	0	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	exon	15406749	15406779	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	intron	15406780	15406920	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	CDS	15406921	15407112	0.26	-	0	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	exon	15406921	15407112	.	-	.	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
Phchi.S1	AUGUSTUS	start_codon	15407110	15407112	.	-	0	transcript_id "Phchi.S1G235000.t1"; gene_id "Phchi.S1G235000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1786.t1 is derived from g8706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2997191	2998333	.	-	.	Phchi.S5G039500
Phchi.S5	AUGUSTUS	transcript	2997191	2998333	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	stop_codon	2997188	2997190	.	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2997191	2997300	1	-	2	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2997191	2997300	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	intron	2997301	2997373	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2997374	2997491	1	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2997374	2997491	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	intron	2997492	2997573	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2997574	2997624	1	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2997574	2997624	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	intron	2997625	2997699	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2997700	2997762	1	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2997700	2997762	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	intron	2997763	2997844	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2997845	2997897	1	-	2	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2997845	2997897	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	intron	2997898	2997983	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2997984	2998149	1	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2997984	2998149	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	intron	2998150	2998222	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	CDS	2998223	2998333	0.79	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	exon	2998223	2998333	.	-	.	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
Phchi.S5	AUGUSTUS	start_codon	2998331	2998333	.	-	0	transcript_id "Phchi.S5G039500.t1"; gene_id "Phchi.S5G039500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6168.t1 is derived from g3339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21277124	21279587	.	-	.	Phchi.S1G332700
Phchi.S1	AUGUSTUS	transcript	21277124	21279587	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	stop_codon	21277121	21277123	.	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21277124	21277263	1	-	2	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21277124	21277263	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21277264	21277347	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21277348	21277408	1	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21277348	21277408	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21277409	21277536	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21277537	21277659	1	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21277537	21277659	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21277660	21277834	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21277835	21277901	1	-	1	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21277835	21277901	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21277902	21277986	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21277987	21278057	1	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21277987	21278057	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21278058	21278149	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21278150	21278247	1	-	2	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21278150	21278247	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21278248	21278340	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21278341	21278417	1	-	1	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21278341	21278417	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21278418	21278508	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21278509	21278576	1	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21278509	21278576	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21278577	21278668	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21278669	21278770	1	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21278669	21278770	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21278771	21278864	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21278865	21278896	1	-	2	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21278865	21278896	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21278897	21278980	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21278981	21279027	1	-	1	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21278981	21279027	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21279028	21279167	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21279168	21279221	1	-	1	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21279168	21279221	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	intron	21279222	21279498	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	CDS	21279499	21279587	0.99	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	exon	21279499	21279587	.	-	.	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
Phchi.S1	AUGUSTUS	start_codon	21279585	21279587	.	-	0	transcript_id "Phchi.S1G332700.t1"; gene_id "Phchi.S1G332700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9267.t1 is derived from g6442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40669874	40671931	.	-	.	Phchi.S1G642600
Phchi.S1	AUGUSTUS	transcript	40669874	40671931	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	stop_codon	40669871	40669873	.	-	0	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40669874	40670248	0.72	-	0	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40669874	40670248	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40670249	40670357	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40670358	40670573	0.93	-	0	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40670358	40670573	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40670574	40670664	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40670665	40670795	1	-	2	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40670665	40670795	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40670796	40670886	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40670887	40671073	1	-	0	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40670887	40671073	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40671074	40671239	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40671240	40671277	0.99	-	2	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40671240	40671277	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40671278	40671356	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40671357	40671487	1	-	1	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40671357	40671487	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40671488	40671580	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40671581	40671592	0.97	-	1	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40671581	40671592	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	intron	40671593	40671698	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	CDS	40671699	40671931	0.96	-	0	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	exon	40671699	40671931	.	-	.	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
Phchi.S1	AUGUSTUS	start_codon	40671929	40671931	.	-	0	transcript_id "Phchi.S1G642600.t1"; gene_id "Phchi.S1G642600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10423.t1 is derived from g14472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	151133	152738	.	-	.	Phchi.S4G000500
Phchi.S4	AUGUSTUS	transcript	151133	152738	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	stop_codon	151130	151132	.	-	0	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	CDS	151133	151415	0.61	-	1	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	exon	151133	151415	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	intron	151416	151516	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	CDS	151517	151822	0.75	-	1	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	exon	151517	151822	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	intron	151823	152192	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	CDS	152193	152225	0.51	-	1	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	exon	152193	152225	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	intron	152226	152607	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	CDS	152608	152639	0.75	-	0	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	exon	152608	152639	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	intron	152640	152717	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	CDS	152718	152738	0.75	-	0	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	exon	152718	152738	.	-	.	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
Phchi.S4	AUGUSTUS	start_codon	152736	152738	.	-	0	transcript_id "Phchi.S4G000500.t1"; gene_id "Phchi.S4G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10796.t1 is derived from g14846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2152148	2152456	.	-	.	Phchi.S4G037800
Phchi.S4	AUGUSTUS	transcript	2152148	2152456	.	-	.	transcript_id "Phchi.S4G037800.t1"; gene_id "Phchi.S4G037800"
Phchi.S4	AUGUSTUS	stop_codon	2152145	2152147	.	-	0	transcript_id "Phchi.S4G037800.t1"; gene_id "Phchi.S4G037800"
Phchi.S4	AUGUSTUS	CDS	2152148	2152456	0.96	-	0	transcript_id "Phchi.S4G037800.t1"; gene_id "Phchi.S4G037800"
Phchi.S4	AUGUSTUS	exon	2152148	2152456	.	-	.	transcript_id "Phchi.S4G037800.t1"; gene_id "Phchi.S4G037800"
Phchi.S4	AUGUSTUS	start_codon	2152454	2152456	.	-	0	transcript_id "Phchi.S4G037800.t1"; gene_id "Phchi.S4G037800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7862.t1 is derived from g5036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31573769	31575486	.	+	.	Phchi.S1G502100
Phchi.S1	AUGUSTUS	transcript	31573769	31575486	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	start_codon	31573769	31573771	.	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31573769	31573957	0.68	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31573769	31573957	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	intron	31573958	31574068	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31574069	31574239	0.75	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31574069	31574239	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	intron	31574240	31574356	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31574357	31574521	0.94	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31574357	31574521	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	intron	31574522	31574630	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31574631	31574795	1	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31574631	31574795	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	intron	31574796	31574886	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31574887	31575021	1	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31574887	31575021	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	intron	31575022	31575107	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31575108	31575205	1	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31575108	31575205	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	intron	31575206	31575299	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	CDS	31575300	31575486	1	+	1	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	exon	31575300	31575486	.	+	.	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
Phchi.S1	AUGUSTUS	stop_codon	31575487	31575489	.	+	0	transcript_id "Phchi.S1G502100.t1"; gene_id "Phchi.S1G502100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg952.t1 is derived from g10734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6629419	6634850	.	+	.	Phchi.S6G091100
Phchi.S6	AUGUSTUS	transcript	6629419	6634850	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	start_codon	6629419	6629421	.	+	0	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6629419	6629603	0.99	+	0	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6629419	6629603	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	intron	6629604	6629712	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6629713	6629833	1	+	1	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6629713	6629833	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	intron	6629834	6629904	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6629905	6630515	0.99	+	0	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6629905	6630515	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	intron	6630516	6630652	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6630653	6630848	0.51	+	1	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6630653	6630848	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	intron	6630849	6630949	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6630950	6631060	0.32	+	0	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6630950	6631060	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	intron	6631061	6631458	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6631459	6633472	0.64	+	0	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6631459	6633472	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	intron	6633473	6633603	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	CDS	6633604	6634850	0.74	+	2	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	exon	6633604	6634850	.	+	.	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
Phchi.S6	AUGUSTUS	stop_codon	6634851	6634853	.	+	0	transcript_id "Phchi.S6G091100.t1"; gene_id "Phchi.S6G091100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6612.t1 is derived from g3784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24002396	24005943	.	+	.	Phchi.S1G377100
Phchi.S1	AUGUSTUS	transcript	24002396	24005943	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	start_codon	24002396	24002398	.	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24002396	24002673	0.93	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24002396	24002673	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24002674	24003080	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24003081	24003231	1	+	1	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24003081	24003231	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24003232	24003327	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24003328	24003435	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24003328	24003435	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24003436	24003610	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24003611	24003703	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24003611	24003703	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24003704	24003842	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24003843	24003926	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24003843	24003926	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24003927	24004051	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24004052	24004120	0.97	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24004052	24004120	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24004121	24004229	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24004230	24004300	0.95	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24004230	24004300	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24004301	24004415	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24004416	24004484	1	+	1	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24004416	24004484	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24004485	24004635	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24004636	24004729	1	+	1	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24004636	24004729	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24004730	24004855	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24004856	24004945	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24004856	24004945	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24004946	24005097	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24005098	24005178	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24005098	24005178	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24005179	24005275	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24005276	24005368	0.99	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24005276	24005368	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24005369	24005473	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24005474	24005554	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24005474	24005554	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24005555	24005639	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24005640	24005709	1	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24005640	24005709	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	intron	24005710	24005857	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	CDS	24005858	24005943	1	+	2	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	exon	24005858	24005943	.	+	.	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
Phchi.S1	AUGUSTUS	stop_codon	24005944	24005946	.	+	0	transcript_id "Phchi.S1G377100.t1"; gene_id "Phchi.S1G377100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12978.t1 is derived from g11443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3415869	3419587	.	-	.	Phchi.S3G029700
Phchi.S3	AUGUSTUS	transcript	3415869	3419587	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	stop_codon	3415866	3415868	.	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3415869	3415892	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3415869	3415892	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3415893	3415975	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3415976	3416059	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3415976	3416059	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3416060	3416154	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3416155	3416311	1	-	1	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3416155	3416311	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3416312	3416399	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3416400	3416452	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3416400	3416452	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3416453	3416549	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3416550	3416715	1	-	1	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3416550	3416715	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3416716	3416806	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3416807	3416880	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3416807	3416880	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3416881	3416955	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3416956	3417033	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3416956	3417033	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3417034	3417162	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3417163	3417261	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3417163	3417261	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3417262	3417391	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3417392	3417583	0.97	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3417392	3417583	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3417584	3417683	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3417684	3417728	0.69	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3417684	3417728	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3417729	3417817	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3417818	3417862	0.61	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3417818	3417862	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3417863	3417958	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3417959	3418058	1	-	1	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3417959	3418058	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3418059	3418151	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3418152	3418213	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3418152	3418213	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3418214	3418300	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3418301	3418387	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3418301	3418387	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3418388	3418477	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3418478	3418537	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3418478	3418537	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3418538	3418625	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3418626	3418777	1	-	2	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3418626	3418777	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3418778	3418921	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3418922	3418985	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3418922	3418985	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3418986	3419085	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3419086	3419178	1	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3419086	3419178	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3419179	3419261	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3419262	3419367	0.95	-	1	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3419262	3419367	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	intron	3419368	3419489	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	CDS	3419490	3419587	0.99	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	exon	3419490	3419587	.	-	.	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
Phchi.S3	AUGUSTUS	start_codon	3419585	3419587	.	-	0	transcript_id "Phchi.S3G029700.t1"; gene_id "Phchi.S3G029700"
# This transcript jg13160.t2 is derived from g11625.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13161.t1 is derived from g11626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4449241	4450342	.	-	.	Phchi.S3G048000
Phchi.S3	AUGUSTUS	transcript	4449241	4450342	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	stop_codon	4449238	4449240	.	-	0	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	CDS	4449241	4449360	1	-	0	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	exon	4449241	4449360	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	intron	4449361	4449516	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	CDS	4449517	4449902	0.71	-	2	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	exon	4449517	4449902	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	intron	4449903	4450093	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	CDS	4450094	4450158	0.6	-	1	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	exon	4450094	4450158	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	intron	4450159	4450328	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	CDS	4450329	4450342	1	-	0	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	exon	4450329	4450342	.	-	.	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
Phchi.S3	AUGUSTUS	start_codon	4450340	4450342	.	-	0	transcript_id "Phchi.S3G048000.t1"; gene_id "Phchi.S3G048000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14433.t1 is derived from g12901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12774833	12776138	.	-	.	Phchi.S3G175200
Phchi.S3	AUGUSTUS	transcript	12774833	12776138	.	-	.	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	stop_codon	12774830	12774832	.	-	0	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	CDS	12774833	12775863	0.68	-	2	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	exon	12774833	12775863	.	-	.	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	intron	12775864	12776002	.	-	.	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	CDS	12776003	12776138	0.52	-	0	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	exon	12776003	12776138	.	-	.	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
Phchi.S3	AUGUSTUS	start_codon	12776136	12776138	.	-	0	transcript_id "Phchi.S3G175200.t1"; gene_id "Phchi.S3G175200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15305.t1 is derived from g13773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18306748	18316243	.	-	.	Phchi.S3G262400
Phchi.S3	AUGUSTUS	transcript	18306748	18316243	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	stop_codon	18306745	18306747	.	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18306748	18307178	0.63	-	2	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18306748	18307178	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18307179	18307258	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18307259	18307346	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18307259	18307346	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18307347	18307435	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18307436	18307681	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18307436	18307681	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18307682	18307778	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18307779	18308337	1	-	1	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18307779	18308337	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18308338	18308441	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18308442	18308664	0.96	-	2	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18308442	18308664	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18308665	18308741	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18308742	18308962	1	-	1	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18308742	18308962	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18308963	18309054	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18309055	18309110	0.82	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18309055	18309110	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18309111	18309220	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18309221	18309415	0.99	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18309221	18309415	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18309416	18309493	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18309494	18309581	1	-	1	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18309494	18309581	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18309582	18309664	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18309665	18309881	1	-	2	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18309665	18309881	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18309882	18309980	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18309981	18310925	0.72	-	2	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18309981	18310925	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18310926	18311020	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18311021	18311041	0.72	-	2	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18311021	18311041	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18311042	18311116	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18311117	18311240	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18311117	18311240	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18311241	18311320	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18311321	18311578	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18311321	18311578	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18311579	18311650	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18311651	18311740	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18311651	18311740	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18311741	18311834	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18311835	18312203	0.95	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18311835	18312203	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18312204	18312307	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18312308	18312490	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18312308	18312490	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18312491	18312582	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18312583	18312708	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18312583	18312708	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18312709	18312843	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18312844	18313056	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18312844	18313056	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18313057	18313145	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18313146	18313253	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18313146	18313253	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18313254	18313327	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18313328	18313609	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18313328	18313609	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18313610	18313707	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18313708	18313830	1	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18313708	18313830	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18313831	18313984	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18313985	18314099	1	-	1	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18313985	18314099	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18314100	18314203	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18314204	18314637	0.97	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18314204	18314637	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18314638	18314734	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18314735	18314866	0.75	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18314735	18314866	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18314867	18314952	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18314953	18314998	0.42	-	1	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18314953	18314998	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18314999	18315086	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18315087	18315097	0.38	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18315087	18315097	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18315098	18315173	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18315174	18315351	0.88	-	1	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18315174	18315351	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	intron	18315352	18315467	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	CDS	18315468	18316243	0.54	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	exon	18315468	18316243	.	-	.	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
Phchi.S3	AUGUSTUS	start_codon	18316241	18316243	.	-	0	transcript_id "Phchi.S3G262400.t1"; gene_id "Phchi.S3G262400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6376.t1 is derived from g3548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22641284	22642428	.	-	.	Phchi.S1G353500
Phchi.S1	AUGUSTUS	transcript	22641284	22642428	.	-	.	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	stop_codon	22641281	22641283	.	-	0	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	CDS	22641284	22641664	0.67	-	0	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	exon	22641284	22641664	.	-	.	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	intron	22641665	22641801	.	-	.	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	CDS	22641802	22642428	0.62	-	0	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	exon	22641802	22642428	.	-	.	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
Phchi.S1	AUGUSTUS	start_codon	22642426	22642428	.	-	0	transcript_id "Phchi.S1G353500.t1"; gene_id "Phchi.S1G353500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12616.t1 is derived from g8293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37581577	37583400	.	-	.	Phchi.S2G069600
Phchi.S2	AUGUSTUS	transcript	37581577	37583400	.	-	.	transcript_id "Phchi.S2G069600.t1"; gene_id "Phchi.S2G069600"
Phchi.S2	AUGUSTUS	stop_codon	37581574	37581576	.	-	0	transcript_id "Phchi.S2G069600.t1"; gene_id "Phchi.S2G069600"
Phchi.S2	AUGUSTUS	CDS	37581577	37583400	0.99	-	0	transcript_id "Phchi.S2G069600.t1"; gene_id "Phchi.S2G069600"
Phchi.S2	AUGUSTUS	exon	37581577	37583400	.	-	.	transcript_id "Phchi.S2G069600.t1"; gene_id "Phchi.S2G069600"
Phchi.S2	AUGUSTUS	start_codon	37583398	37583400	.	-	0	transcript_id "Phchi.S2G069600.t1"; gene_id "Phchi.S2G069600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3334.t1 is derived from g503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2973145	2973405	.	-	.	Phchi.S1G049300
Phchi.S1	AUGUSTUS	transcript	2973145	2973405	.	-	.	transcript_id "Phchi.S1G049300.t1"; gene_id "Phchi.S1G049300"
Phchi.S1	AUGUSTUS	stop_codon	2973142	2973144	.	-	0	transcript_id "Phchi.S1G049300.t1"; gene_id "Phchi.S1G049300"
Phchi.S1	AUGUSTUS	CDS	2973145	2973405	0.84	-	0	transcript_id "Phchi.S1G049300.t1"; gene_id "Phchi.S1G049300"
Phchi.S1	AUGUSTUS	exon	2973145	2973405	.	-	.	transcript_id "Phchi.S1G049300.t1"; gene_id "Phchi.S1G049300"
Phchi.S1	AUGUSTUS	start_codon	2973403	2973405	.	-	0	transcript_id "Phchi.S1G049300.t1"; gene_id "Phchi.S1G049300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7785.t1 is derived from g4959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31190536	31191644	.	+	.	Phchi.S1G494400
Phchi.S1	AUGUSTUS	transcript	31190536	31191644	.	+	.	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	start_codon	31190536	31190538	.	+	0	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	CDS	31190536	31190940	0.49	+	0	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	exon	31190536	31190940	.	+	.	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	intron	31190941	31191236	.	+	.	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	CDS	31191237	31191644	0.97	+	0	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	exon	31191237	31191644	.	+	.	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
Phchi.S1	AUGUSTUS	stop_codon	31191645	31191647	.	+	0	transcript_id "Phchi.S1G494400.t1"; gene_id "Phchi.S1G494400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11024.t1 is derived from g15074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3691853	3692803	.	-	.	Phchi.S4G060600
Phchi.S4	AUGUSTUS	transcript	3691853	3692803	.	-	.	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	stop_codon	3691850	3691852	.	-	0	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	CDS	3691853	3692156	1	-	1	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	exon	3691853	3692156	.	-	.	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	intron	3692157	3692257	.	-	.	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	CDS	3692258	3692573	1	-	2	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	exon	3692258	3692573	.	-	.	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	intron	3692574	3692673	.	-	.	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	CDS	3692674	3692803	0.76	-	0	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	exon	3692674	3692803	.	-	.	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
Phchi.S4	AUGUSTUS	start_codon	3692801	3692803	.	-	0	transcript_id "Phchi.S4G060600.t1"; gene_id "Phchi.S4G060600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2676.t1 is derived from g9596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8151123	8152232	.	-	.	Phchi.S5G128500
Phchi.S5	AUGUSTUS	transcript	8151123	8152232	.	-	.	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	stop_codon	8151120	8151122	.	-	0	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	CDS	8151123	8151398	0.48	-	0	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	exon	8151123	8151398	.	-	.	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	intron	8151399	8151505	.	-	.	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	CDS	8151506	8151874	1	-	0	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	exon	8151506	8151874	.	-	.	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	intron	8151875	8152013	.	-	.	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	CDS	8152014	8152232	0.96	-	0	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	exon	8152014	8152232	.	-	.	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
Phchi.S5	AUGUSTUS	start_codon	8152230	8152232	.	-	0	transcript_id "Phchi.S5G128500.t1"; gene_id "Phchi.S5G128500"
# This transcript jg13682.t2 is derived from g12149.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13683.t1 is derived from g12150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8189150	8192077	.	-	.	Phchi.S3G100200
Phchi.S3	AUGUSTUS	transcript	8189150	8192077	.	-	.	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	stop_codon	8189147	8189149	.	-	0	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	CDS	8189150	8191863	0.97	-	2	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	exon	8189150	8191863	.	-	.	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	intron	8191864	8192010	.	-	.	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	CDS	8192011	8192077	0.51	-	0	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	exon	8192011	8192077	.	-	.	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
Phchi.S3	AUGUSTUS	start_codon	8192075	8192077	.	-	0	transcript_id "Phchi.S3G100200.t1"; gene_id "Phchi.S3G100200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14014.t1 is derived from g12481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10312531	10316400	.	+	.	Phchi.S3G133300
Phchi.S3	AUGUSTUS	transcript	10312531	10316400	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	start_codon	10312531	10312533	.	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10312531	10313955	0.96	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10312531	10313955	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10313956	10314045	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10314046	10314091	1	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10314046	10314091	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10314092	10314187	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10314188	10314337	1	+	2	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10314188	10314337	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10314338	10314420	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10314421	10314512	1	+	2	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10314421	10314512	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10314513	10314720	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10314721	10314789	0.81	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10314721	10314789	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10314790	10314958	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10314959	10314977	0.76	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10314959	10314977	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10314978	10315061	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10315062	10315142	0.98	+	2	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10315062	10315142	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10315143	10315218	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10315219	10315607	0.97	+	2	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10315219	10315607	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10315608	10315744	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10315745	10315811	1	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10315745	10315811	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10315812	10315896	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10315897	10316027	1	+	2	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10315897	10316027	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10316028	10316113	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10316114	10316204	0.86	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10316114	10316204	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	intron	10316205	10316302	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	CDS	10316303	10316400	0.83	+	2	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	exon	10316303	10316400	.	+	.	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
Phchi.S3	AUGUSTUS	stop_codon	10316401	10316403	.	+	0	transcript_id "Phchi.S3G133300.t1"; gene_id "Phchi.S3G133300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12609.t1 is derived from g8286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37563607	37564158	.	-	.	Phchi.S2G068900
Phchi.S2	AUGUSTUS	transcript	37563607	37564158	.	-	.	transcript_id "Phchi.S2G068900.t1"; gene_id "Phchi.S2G068900"
Phchi.S2	AUGUSTUS	stop_codon	37563604	37563606	.	-	0	transcript_id "Phchi.S2G068900.t1"; gene_id "Phchi.S2G068900"
Phchi.S2	AUGUSTUS	CDS	37563607	37564158	0.62	-	0	transcript_id "Phchi.S2G068900.t1"; gene_id "Phchi.S2G068900"
Phchi.S2	AUGUSTUS	exon	37563607	37564158	.	-	.	transcript_id "Phchi.S2G068900.t1"; gene_id "Phchi.S2G068900"
Phchi.S2	AUGUSTUS	start_codon	37564156	37564158	.	-	0	transcript_id "Phchi.S2G068900.t1"; gene_id "Phchi.S2G068900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14419.t1 is derived from g12887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12724184	12724957	.	-	.	Phchi.S3G173800
Phchi.S3	AUGUSTUS	transcript	12724184	12724957	.	-	.	transcript_id "Phchi.S3G173800.t1"; gene_id "Phchi.S3G173800"
Phchi.S3	AUGUSTUS	stop_codon	12724181	12724183	.	-	0	transcript_id "Phchi.S3G173800.t1"; gene_id "Phchi.S3G173800"
Phchi.S3	AUGUSTUS	CDS	12724184	12724957	0.7	-	0	transcript_id "Phchi.S3G173800.t1"; gene_id "Phchi.S3G173800"
Phchi.S3	AUGUSTUS	exon	12724184	12724957	.	-	.	transcript_id "Phchi.S3G173800.t1"; gene_id "Phchi.S3G173800"
Phchi.S3	AUGUSTUS	start_codon	12724955	12724957	.	-	0	transcript_id "Phchi.S3G173800.t1"; gene_id "Phchi.S3G173800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg5054.t1 is derived from g2224.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14415353	14417477	.	-	.	Phchi.S1G221300
Phchi.S1	AUGUSTUS	transcript	14415353	14417477	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	stop_codon	14415350	14415352	.	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415353	14415418	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415353	14415418	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415419	14415556	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415557	14415709	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415557	14415709	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415710	14415787	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415788	14415943	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415788	14415943	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415944	14416047	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416048	14416125	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416048	14416125	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416126	14416217	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416218	14416298	0.43	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416218	14416298	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416299	14416428	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416429	14416496	0.59	-	2	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416429	14416496	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416497	14416570	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416571	14416627	1	-	2	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416571	14416627	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416628	14416702	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416703	14416772	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416703	14416772	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416773	14416854	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416855	14416924	1	-	1	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416855	14416924	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416925	14416995	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416996	14417099	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416996	14417099	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417100	14417184	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417185	14417240	1	-	2	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417185	14417240	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417241	14417317	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417318	14417369	1	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417318	14417369	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417370	14417438	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417439	14417477	0.92	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417439	14417477	.	-	.	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	start_codon	14417475	14417477	.	-	0	transcript_id "Phchi.S1G221300.t1"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	transcript	14415353	14417477	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	stop_codon	14415350	14415352	.	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415353	14415418	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415353	14415418	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415419	14415556	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415557	14415709	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415557	14415709	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415710	14415787	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415788	14415943	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415788	14415943	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415944	14416047	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416048	14416125	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416048	14416125	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416126	14416217	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416218	14416298	0.35	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416218	14416298	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416299	14416428	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416429	14416484	0.48	-	2	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416429	14416484	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416485	14416570	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416571	14416627	1	-	2	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416571	14416627	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416628	14416702	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416703	14416772	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416703	14416772	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416773	14416854	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416855	14416924	1	-	1	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416855	14416924	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416925	14416995	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416996	14417099	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416996	14417099	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417100	14417184	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417185	14417240	1	-	2	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417185	14417240	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417241	14417317	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417318	14417369	1	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417318	14417369	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417370	14417438	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417439	14417477	0.88	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417439	14417477	.	-	.	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	start_codon	14417475	14417477	.	-	0	transcript_id "Phchi.S1G221300.t2"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	transcript	14415353	14417477	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	stop_codon	14415350	14415352	.	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415353	14415418	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415353	14415418	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415419	14415556	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415557	14415709	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415557	14415709	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415710	14415787	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415788	14415943	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415788	14415943	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415944	14416047	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416048	14416125	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416048	14416125	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416126	14416217	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416218	14416271	0.5	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416218	14416271	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416272	14416378	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416379	14416506	0.26	-	2	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416379	14416506	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416507	14416570	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416571	14416627	1	-	2	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416571	14416627	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416628	14416702	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416703	14416772	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416703	14416772	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416773	14416854	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416855	14416924	1	-	1	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416855	14416924	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416925	14416995	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416996	14417099	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416996	14417099	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417100	14417184	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417185	14417240	1	-	2	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417185	14417240	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417241	14417317	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417318	14417369	1	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417318	14417369	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417370	14417438	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417439	14417477	0.9	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417439	14417477	.	-	.	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	start_codon	14417475	14417477	.	-	0	transcript_id "Phchi.S1G221300.t3"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	transcript	14415353	14417477	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	stop_codon	14415350	14415352	.	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415353	14415400	0.56	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415353	14415400	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415401	14415556	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415557	14415709	0.6	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415557	14415709	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415710	14415787	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14415788	14415943	1	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14415788	14415943	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14415944	14416047	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416048	14416125	1	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416048	14416125	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416126	14416217	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416218	14416298	0.45	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416218	14416298	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416299	14416428	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416429	14416496	0.54	-	2	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416429	14416496	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416497	14416570	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416571	14416627	1	-	2	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416571	14416627	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416628	14416702	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416703	14416772	1	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416703	14416772	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416773	14416854	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416855	14416924	1	-	1	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416855	14416924	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14416925	14416995	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14416996	14417099	1	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14416996	14417099	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417100	14417184	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417185	14417240	1	-	2	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417185	14417240	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417241	14417317	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417318	14417369	1	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417318	14417369	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	intron	14417370	14417438	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	CDS	14417439	14417477	0.85	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	exon	14417439	14417477	.	-	.	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
Phchi.S1	AUGUSTUS	start_codon	14417475	14417477	.	-	0	transcript_id "Phchi.S1G221300.t4"; gene_id "Phchi.S1G221300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1022.t1 is derived from g10805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7163670	7165455	.	-	.	Phchi.S6G098100
Phchi.S6	AUGUSTUS	transcript	7163670	7165455	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	stop_codon	7163667	7163669	.	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7163670	7163723	1	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7163670	7163723	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7163724	7163811	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7163812	7163881	1	-	1	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7163812	7163881	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7163882	7164011	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7164012	7164145	1	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7164012	7164145	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7164146	7164314	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7164315	7164359	0.99	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7164315	7164359	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7164360	7164461	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7164462	7164503	0.95	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7164462	7164503	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7164504	7164658	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7164659	7164720	1	-	2	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7164659	7164720	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7164721	7164822	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7164823	7164941	0.99	-	1	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7164823	7164941	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7164942	7165086	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7165087	7165238	1	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7165087	7165238	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	intron	7165239	7165317	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	CDS	7165318	7165455	1	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	exon	7165318	7165455	.	-	.	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
Phchi.S6	AUGUSTUS	start_codon	7165453	7165455	.	-	0	transcript_id "Phchi.S6G098100.t1"; gene_id "Phchi.S6G098100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14225.t1 is derived from g12692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11642975	11644756	.	+	.	Phchi.S3G154400
Phchi.S3	AUGUSTUS	transcript	11642975	11644756	.	+	.	transcript_id "Phchi.S3G154400.t1"; gene_id "Phchi.S3G154400"
Phchi.S3	AUGUSTUS	start_codon	11642975	11642977	.	+	0	transcript_id "Phchi.S3G154400.t1"; gene_id "Phchi.S3G154400"
Phchi.S3	AUGUSTUS	CDS	11642975	11644756	0.56	+	0	transcript_id "Phchi.S3G154400.t1"; gene_id "Phchi.S3G154400"
Phchi.S3	AUGUSTUS	exon	11642975	11644756	.	+	.	transcript_id "Phchi.S3G154400.t1"; gene_id "Phchi.S3G154400"
Phchi.S3	AUGUSTUS	stop_codon	11644757	11644759	.	+	0	transcript_id "Phchi.S3G154400.t1"; gene_id "Phchi.S3G154400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12726.t1 is derived from g11191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1414746	1416382	.	-	.	Phchi.S3G004500
Phchi.S3	AUGUSTUS	transcript	1414746	1416382	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	stop_codon	1414743	1414745	.	-	0	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1414746	1414827	0.95	-	1	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1414746	1414827	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	intron	1414828	1414908	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1414909	1415017	1	-	2	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1414909	1415017	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	intron	1415018	1415099	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1415100	1415127	1	-	0	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1415100	1415127	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	intron	1415128	1415227	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1415228	1415400	1	-	2	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1415228	1415400	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	intron	1415401	1415555	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1415556	1415673	1	-	0	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1415556	1415673	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	intron	1415674	1415777	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1415778	1415846	0.85	-	0	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1415778	1415846	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	intron	1415847	1416115	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	CDS	1416116	1416382	1	-	0	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	exon	1416116	1416382	.	-	.	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
Phchi.S3	AUGUSTUS	start_codon	1416380	1416382	.	-	0	transcript_id "Phchi.S3G004500.t1"; gene_id "Phchi.S3G004500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13136.t1 is derived from g11601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4321124	4323997	.	+	.	Phchi.S3G045500
Phchi.S3	AUGUSTUS	transcript	4321124	4323997	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	start_codon	4321124	4321126	.	+	0	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	CDS	4321124	4321470	0.34	+	0	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	exon	4321124	4321470	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	intron	4321471	4321848	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	CDS	4321849	4323479	0.3	+	1	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	exon	4321849	4323479	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	intron	4323480	4323561	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	CDS	4323562	4323764	0.47	+	2	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	exon	4323562	4323764	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	intron	4323765	4323961	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	CDS	4323962	4323997	0.68	+	0	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	exon	4323962	4323997	.	+	.	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
Phchi.S3	AUGUSTUS	stop_codon	4323998	4324000	.	+	0	transcript_id "Phchi.S3G045500.t1"; gene_id "Phchi.S3G045500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5454.t1 is derived from g2624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16922696	16928264	.	-	.	Phchi.S1G261300
Phchi.S1	AUGUSTUS	transcript	16922696	16928264	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	stop_codon	16922693	16922695	.	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16922696	16922816	0.81	-	1	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16922696	16922816	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16922817	16922903	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16922904	16923145	0.81	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16922904	16923145	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16923146	16923244	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16923245	16923407	1	-	1	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16923245	16923407	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16923408	16923479	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16923480	16923556	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16923480	16923556	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16923557	16923648	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16923649	16923761	1	-	2	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16923649	16923761	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16923762	16923884	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16923885	16923978	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16923885	16923978	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16923979	16924083	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16924084	16924158	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16924084	16924158	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16924159	16924295	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16924296	16924458	1	-	1	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16924296	16924458	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16924459	16924601	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16924602	16924708	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16924602	16924708	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16924709	16924816	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16924817	16924999	0.97	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16924817	16924999	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16925000	16925191	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16925192	16925317	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16925192	16925317	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16925318	16925426	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16925427	16925531	0.93	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16925427	16925531	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16925532	16925687	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16925688	16925831	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16925688	16925831	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16925832	16925936	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16925937	16925989	1	-	2	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16925937	16925989	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16925990	16926088	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16926089	16926254	1	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16926089	16926254	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16926255	16926352	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16926353	16926528	1	-	2	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16926353	16926528	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16926529	16926834	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16926835	16927641	1	-	2	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16926835	16927641	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	intron	16927642	16927771	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	CDS	16927772	16928264	0.64	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	exon	16927772	16928264	.	-	.	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
Phchi.S1	AUGUSTUS	start_codon	16928262	16928264	.	-	0	transcript_id "Phchi.S1G261300.t1"; gene_id "Phchi.S1G261300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12273.t1 is derived from g7949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7570307	7570912	.	-	.	Phchi.S2G035300
Phchi.S2	AUGUSTUS	transcript	7570307	7570912	.	-	.	transcript_id "Phchi.S2G035300.t1"; gene_id "Phchi.S2G035300"
Phchi.S2	AUGUSTUS	stop_codon	7570304	7570306	.	-	0	transcript_id "Phchi.S2G035300.t1"; gene_id "Phchi.S2G035300"
Phchi.S2	AUGUSTUS	CDS	7570307	7570912	0.38	-	0	transcript_id "Phchi.S2G035300.t1"; gene_id "Phchi.S2G035300"
Phchi.S2	AUGUSTUS	exon	7570307	7570912	.	-	.	transcript_id "Phchi.S2G035300.t1"; gene_id "Phchi.S2G035300"
Phchi.S2	AUGUSTUS	start_codon	7570910	7570912	.	-	0	transcript_id "Phchi.S2G035300.t1"; gene_id "Phchi.S2G035300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8253.t1 is derived from g5428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34717147	34717998	.	-	.	Phchi.S1G541200
Phchi.S1	AUGUSTUS	transcript	34717147	34717998	.	-	.	transcript_id "Phchi.S1G541200.t1"; gene_id "Phchi.S1G541200"
Phchi.S1	AUGUSTUS	stop_codon	34717144	34717146	.	-	0	transcript_id "Phchi.S1G541200.t1"; gene_id "Phchi.S1G541200"
Phchi.S1	AUGUSTUS	CDS	34717147	34717998	0.38	-	0	transcript_id "Phchi.S1G541200.t1"; gene_id "Phchi.S1G541200"
Phchi.S1	AUGUSTUS	exon	34717147	34717998	.	-	.	transcript_id "Phchi.S1G541200.t1"; gene_id "Phchi.S1G541200"
Phchi.S1	AUGUSTUS	start_codon	34717996	34717998	.	-	0	transcript_id "Phchi.S1G541200.t1"; gene_id "Phchi.S1G541200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg444.t1 is derived from g10226.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3110193	3113710	.	+	.	Phchi.S6G040300
Phchi.S6	AUGUSTUS	transcript	3110193	3113710	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	start_codon	3110193	3110195	.	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3110193	3110340	0.5	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3110193	3110340	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3110341	3110507	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3110508	3111095	1	+	2	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3110508	3111095	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3111096	3111184	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3111185	3111253	0.98	+	2	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3111185	3111253	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3111254	3111337	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3111338	3111690	0.98	+	2	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3111338	3111690	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3111691	3111804	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3111805	3112050	0.95	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3111805	3112050	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3112051	3112147	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3112148	3112381	0.97	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3112148	3112381	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3112382	3112536	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3112537	3112710	0.98	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3112537	3112710	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3112711	3112875	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3112876	3113365	0.82	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3112876	3113365	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3113366	3113453	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3113454	3113710	0.98	+	2	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3113454	3113710	.	+	.	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	stop_codon	3113711	3113713	.	+	0	transcript_id "Phchi.S6G040300.t1"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	transcript	3110193	3111394	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	start_codon	3110193	3110195	.	+	0	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3110193	3110340	0.49	+	0	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3110193	3110340	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3110341	3110507	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3110508	3111095	1	+	2	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3110508	3111095	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3111096	3111184	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3111185	3111258	1	+	2	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3111185	3111258	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	intron	3111259	3111337	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	CDS	3111338	3111394	0.89	+	0	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	exon	3111338	3111394	.	+	.	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
Phchi.S6	AUGUSTUS	stop_codon	3111395	3111397	.	+	0	transcript_id "Phchi.S6G040300.t2"; gene_id "Phchi.S6G040300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4755.t1 is derived from g1925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12665040	12666430	.	+	.	Phchi.S1G191400
Phchi.S1	AUGUSTUS	transcript	12665040	12666430	.	+	.	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	start_codon	12665040	12665042	.	+	0	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	CDS	12665040	12665638	0.66	+	0	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	exon	12665040	12665638	.	+	.	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	intron	12665639	12665739	.	+	.	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	CDS	12665740	12666430	1	+	1	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	exon	12665740	12666430	.	+	.	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
Phchi.S1	AUGUSTUS	stop_codon	12666431	12666433	.	+	0	transcript_id "Phchi.S1G191400.t1"; gene_id "Phchi.S1G191400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6633.t1 is derived from g3805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24178980	24179718	.	-	.	Phchi.S1G379200
Phchi.S1	AUGUSTUS	transcript	24178980	24179689	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	stop_codon	24178977	24178979	.	-	0	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24178980	24179007	1	-	1	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24178980	24179007	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	intron	24179008	24179095	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24179096	24179210	1	-	2	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24179096	24179210	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	intron	24179211	24179328	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24179329	24179493	0.91	-	2	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24179329	24179493	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	intron	24179494	24179580	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24179581	24179689	0.45	-	0	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24179581	24179689	.	-	.	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	start_codon	24179687	24179689	.	-	0	transcript_id "Phchi.S1G379200.t1"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	transcript	24178980	24179718	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	stop_codon	24178977	24178979	.	-	0	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24178980	24179007	1	-	1	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24178980	24179007	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	intron	24179008	24179095	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24179096	24179210	0.95	-	2	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24179096	24179210	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	intron	24179211	24179328	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24179329	24179485	0.67	-	0	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24179329	24179485	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	intron	24179486	24179580	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	CDS	24179581	24179718	0.34	-	0	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	exon	24179581	24179718	.	-	.	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
Phchi.S1	AUGUSTUS	start_codon	24179716	24179718	.	-	0	transcript_id "Phchi.S1G379200.t2"; gene_id "Phchi.S1G379200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13320.t1 is derived from g11786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6093762	6094515	.	+	.	Phchi.S3G063900
Phchi.S3	AUGUSTUS	transcript	6093762	6094515	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	start_codon	6093762	6093764	.	+	0	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	CDS	6093762	6093948	0.55	+	0	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	exon	6093762	6093948	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	intron	6093949	6094098	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	CDS	6094099	6094135	0.72	+	2	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	exon	6094099	6094135	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	intron	6094136	6094294	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	CDS	6094295	6094350	0.51	+	1	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	exon	6094295	6094350	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	intron	6094351	6094486	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	CDS	6094487	6094515	0.73	+	2	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	exon	6094487	6094515	.	+	.	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
Phchi.S3	AUGUSTUS	stop_codon	6094516	6094518	.	+	0	transcript_id "Phchi.S3G063900.t1"; gene_id "Phchi.S3G063900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg241.t1 is derived from g10023.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1665893	1668051	.	-	.	Phchi.S6G020000
Phchi.S6	AUGUSTUS	transcript	1665893	1668051	.	-	.	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	stop_codon	1665890	1665892	.	-	0	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	CDS	1665893	1667790	0.91	-	2	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	exon	1665893	1667790	.	-	.	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	intron	1667791	1667909	.	-	.	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	CDS	1667910	1668051	0.59	-	0	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	exon	1667910	1668051	.	-	.	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	start_codon	1668049	1668051	.	-	0	transcript_id "Phchi.S6G020000.t1"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	transcript	1665893	1667170	.	-	.	transcript_id "Phchi.S6G020000.t2"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	stop_codon	1665890	1665892	.	-	0	transcript_id "Phchi.S6G020000.t2"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	CDS	1665893	1667170	1	-	0	transcript_id "Phchi.S6G020000.t2"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	exon	1665893	1667170	.	-	.	transcript_id "Phchi.S6G020000.t2"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	start_codon	1667168	1667170	.	-	0	transcript_id "Phchi.S6G020000.t2"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	transcript	1665893	1667668	.	-	.	transcript_id "Phchi.S6G020000.t3"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	stop_codon	1665890	1665892	.	-	0	transcript_id "Phchi.S6G020000.t3"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	CDS	1665893	1667668	1	-	0	transcript_id "Phchi.S6G020000.t3"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	exon	1665893	1667668	.	-	.	transcript_id "Phchi.S6G020000.t3"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	start_codon	1667666	1667668	.	-	0	transcript_id "Phchi.S6G020000.t3"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	transcript	1665893	1667584	.	-	.	transcript_id "Phchi.S6G020000.t4"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	stop_codon	1665890	1665892	.	-	0	transcript_id "Phchi.S6G020000.t4"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	CDS	1665893	1667584	0.93	-	0	transcript_id "Phchi.S6G020000.t4"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	exon	1665893	1667584	.	-	.	transcript_id "Phchi.S6G020000.t4"; gene_id "Phchi.S6G020000"
Phchi.S6	AUGUSTUS	start_codon	1667582	1667584	.	-	0	transcript_id "Phchi.S6G020000.t4"; gene_id "Phchi.S6G020000"
# This transcript jg4662.t2 is derived from g1832.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4663.t1 is derived from g1833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11688595	11688891	.	-	.	Phchi.S1G182200
Phchi.S1	AUGUSTUS	transcript	11688595	11688891	.	-	.	transcript_id "Phchi.S1G182200.t1"; gene_id "Phchi.S1G182200"
Phchi.S1	AUGUSTUS	stop_codon	11688592	11688594	.	-	0	transcript_id "Phchi.S1G182200.t1"; gene_id "Phchi.S1G182200"
Phchi.S1	AUGUSTUS	CDS	11688595	11688891	0.41	-	0	transcript_id "Phchi.S1G182200.t1"; gene_id "Phchi.S1G182200"
Phchi.S1	AUGUSTUS	exon	11688595	11688891	.	-	.	transcript_id "Phchi.S1G182200.t1"; gene_id "Phchi.S1G182200"
Phchi.S1	AUGUSTUS	start_codon	11688889	11688891	.	-	0	transcript_id "Phchi.S1G182200.t1"; gene_id "Phchi.S1G182200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1163.t1 is derived from g10946.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8109470	8112102	.	+	.	Phchi.S6G112200
Phchi.S6	AUGUSTUS	transcript	8109561	8112102	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	start_codon	8109561	8109563	.	+	0	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109561	8109587	0.84	+	0	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109561	8109587	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8109588	8109672	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109673	8109698	0.85	+	0	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109673	8109698	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8109699	8109905	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109906	8111184	0.47	+	1	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109906	8111184	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111185	8111290	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111291	8111295	0.48	+	0	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111291	8111295	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111296	8111384	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111385	8111797	0.4	+	1	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111385	8111797	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111798	8111881	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111882	8112102	0.94	+	2	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111882	8112102	.	+	.	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	stop_codon	8112103	8112105	.	+	0	transcript_id "Phchi.S6G112200.t1"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	transcript	8109481	8112102	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	start_codon	8109481	8109483	.	+	0	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109481	8109587	0.97	+	0	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109481	8109587	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8109588	8109905	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109906	8111184	0.44	+	1	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109906	8111184	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111185	8111290	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111291	8111295	0.4	+	0	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111291	8111295	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111296	8111384	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111385	8111797	0.37	+	1	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111385	8111797	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111798	8111881	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111882	8112102	0.94	+	2	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111882	8112102	.	+	.	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	stop_codon	8112103	8112105	.	+	0	transcript_id "Phchi.S6G112200.t2"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	transcript	8109470	8112102	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	start_codon	8109470	8109472	.	+	0	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109470	8109587	1	+	0	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109470	8109587	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8109588	8109913	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8109914	8111184	0.35	+	2	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8109914	8111184	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111185	8111290	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111291	8111295	0.33	+	0	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111291	8111295	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111296	8111384	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111385	8111797	0.3	+	1	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111385	8111797	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	intron	8111798	8111881	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	CDS	8111882	8112102	0.99	+	2	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	exon	8111882	8112102	.	+	.	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
Phchi.S6	AUGUSTUS	stop_codon	8112103	8112105	.	+	0	transcript_id "Phchi.S6G112200.t3"; gene_id "Phchi.S6G112200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg606.t1 is derived from g10388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4379678	4380961	.	-	.	Phchi.S6G056500
Phchi.S6	AUGUSTUS	transcript	4379678	4380961	.	-	.	transcript_id "Phchi.S6G056500.t1"; gene_id "Phchi.S6G056500"
Phchi.S6	AUGUSTUS	stop_codon	4379675	4379677	.	-	0	transcript_id "Phchi.S6G056500.t1"; gene_id "Phchi.S6G056500"
Phchi.S6	AUGUSTUS	CDS	4379678	4380961	0.97	-	0	transcript_id "Phchi.S6G056500.t1"; gene_id "Phchi.S6G056500"
Phchi.S6	AUGUSTUS	exon	4379678	4380961	.	-	.	transcript_id "Phchi.S6G056500.t1"; gene_id "Phchi.S6G056500"
Phchi.S6	AUGUSTUS	start_codon	4380959	4380961	.	-	0	transcript_id "Phchi.S6G056500.t1"; gene_id "Phchi.S6G056500"
# This transcript jg12624.t2 is derived from g8301.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12625.t1 is derived from g8302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37645999	37647444	.	+	.	Phchi.S2G070500
Phchi.S2	AUGUSTUS	transcript	37645999	37647444	.	+	.	transcript_id "Phchi.S2G070500.t1"; gene_id "Phchi.S2G070500"
Phchi.S2	AUGUSTUS	start_codon	37645999	37646001	.	+	0	transcript_id "Phchi.S2G070500.t1"; gene_id "Phchi.S2G070500"
Phchi.S2	AUGUSTUS	CDS	37645999	37647444	0.6	+	0	transcript_id "Phchi.S2G070500.t1"; gene_id "Phchi.S2G070500"
Phchi.S2	AUGUSTUS	exon	37645999	37647444	.	+	.	transcript_id "Phchi.S2G070500.t1"; gene_id "Phchi.S2G070500"
Phchi.S2	AUGUSTUS	stop_codon	37647445	37647447	.	+	0	transcript_id "Phchi.S2G070500.t1"; gene_id "Phchi.S2G070500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13697.t1 is derived from g12164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8251270	8251754	.	-	.	Phchi.S3G101600
Phchi.S3	AUGUSTUS	transcript	8251270	8251754	.	-	.	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	stop_codon	8251267	8251269	.	-	0	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	CDS	8251270	8251401	1	-	0	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	exon	8251270	8251401	.	-	.	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	intron	8251402	8251484	.	-	.	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	CDS	8251485	8251597	1	-	2	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	exon	8251485	8251597	.	-	.	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	intron	8251598	8251675	.	-	.	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	CDS	8251676	8251754	0.89	-	0	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	exon	8251676	8251754	.	-	.	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
Phchi.S3	AUGUSTUS	start_codon	8251752	8251754	.	-	0	transcript_id "Phchi.S3G101600.t1"; gene_id "Phchi.S3G101600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11712.t1 is derived from g15763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7794423	7796647	.	+	.	Phchi.S4G129400
Phchi.S4	AUGUSTUS	transcript	7794423	7796647	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	start_codon	7794423	7794425	.	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7794423	7794746	1	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7794423	7794746	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7794747	7794927	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7794928	7795240	0.6	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7794928	7795240	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7795241	7795330	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7795331	7795482	0.68	+	2	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7795331	7795482	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7795483	7795584	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7795585	7795873	1	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7795585	7795873	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7795874	7795989	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7795990	7796097	1	+	2	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7795990	7796097	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7796098	7796190	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7796191	7796267	0.31	+	2	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7796191	7796267	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7796268	7796351	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7796352	7796453	0.29	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7796352	7796453	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	intron	7796454	7796644	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	CDS	7796645	7796647	0.29	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	exon	7796645	7796647	.	+	.	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
Phchi.S4	AUGUSTUS	stop_codon	7796648	7796650	.	+	0	transcript_id "Phchi.S4G129400.t1"; gene_id "Phchi.S4G129400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8218.t1 is derived from g5393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34465955	34466197	.	+	.	Phchi.S1G537700
Phchi.S1	AUGUSTUS	transcript	34465955	34466197	.	+	.	transcript_id "Phchi.S1G537700.t1"; gene_id "Phchi.S1G537700"
Phchi.S1	AUGUSTUS	start_codon	34465955	34465957	.	+	0	transcript_id "Phchi.S1G537700.t1"; gene_id "Phchi.S1G537700"
Phchi.S1	AUGUSTUS	CDS	34465955	34466197	0.55	+	0	transcript_id "Phchi.S1G537700.t1"; gene_id "Phchi.S1G537700"
Phchi.S1	AUGUSTUS	exon	34465955	34466197	.	+	.	transcript_id "Phchi.S1G537700.t1"; gene_id "Phchi.S1G537700"
Phchi.S1	AUGUSTUS	stop_codon	34466198	34466200	.	+	0	transcript_id "Phchi.S1G537700.t1"; gene_id "Phchi.S1G537700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6890.t1 is derived from g4062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25856024	25857091	.	+	.	Phchi.S1G404900
Phchi.S1	AUGUSTUS	transcript	25856024	25857091	.	+	.	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	start_codon	25856024	25856026	.	+	0	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	CDS	25856024	25856065	0.99	+	0	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	exon	25856024	25856065	.	+	.	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	intron	25856066	25856254	.	+	.	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	CDS	25856255	25857091	0.98	+	0	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	exon	25856255	25857091	.	+	.	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
Phchi.S1	AUGUSTUS	stop_codon	25857092	25857094	.	+	0	transcript_id "Phchi.S1G404900.t1"; gene_id "Phchi.S1G404900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4517.t1 is derived from g1687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10914284	10917097	.	-	.	Phchi.S1G167600
Phchi.S1	AUGUSTUS	transcript	10914284	10917097	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	stop_codon	10914281	10914283	.	-	0	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10914284	10914405	0.53	-	2	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10914284	10914405	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10914406	10914491	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10914492	10914673	0.55	-	1	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10914492	10914673	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10914674	10914754	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10914755	10914832	0.99	-	1	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10914755	10914832	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10914833	10914947	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10914948	10915202	0.63	-	1	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10914948	10915202	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10915203	10915355	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10915356	10915427	1	-	1	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10915356	10915427	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10915428	10915519	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10915520	10916596	0.48	-	1	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10915520	10916596	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10916597	10916689	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10916690	10916918	1	-	2	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10916690	10916918	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	intron	10916919	10917018	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	CDS	10917019	10917097	0.98	-	0	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	exon	10917019	10917097	.	-	.	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
Phchi.S1	AUGUSTUS	start_codon	10917095	10917097	.	-	0	transcript_id "Phchi.S1G167600.t1"; gene_id "Phchi.S1G167600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2565.t1 is derived from g9485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7417228	7417764	.	-	.	Phchi.S5G117400
Phchi.S5	AUGUSTUS	transcript	7417228	7417764	.	-	.	transcript_id "Phchi.S5G117400.t1"; gene_id "Phchi.S5G117400"
Phchi.S5	AUGUSTUS	stop_codon	7417225	7417227	.	-	0	transcript_id "Phchi.S5G117400.t1"; gene_id "Phchi.S5G117400"
Phchi.S5	AUGUSTUS	CDS	7417228	7417764	0.93	-	0	transcript_id "Phchi.S5G117400.t1"; gene_id "Phchi.S5G117400"
Phchi.S5	AUGUSTUS	exon	7417228	7417764	.	-	.	transcript_id "Phchi.S5G117400.t1"; gene_id "Phchi.S5G117400"
Phchi.S5	AUGUSTUS	start_codon	7417762	7417764	.	-	0	transcript_id "Phchi.S5G117400.t1"; gene_id "Phchi.S5G117400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11489.t1 is derived from g15539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6624064	6627488	.	+	.	Phchi.S4G107100
Phchi.S4	AUGUSTUS	transcript	6624064	6627488	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	start_codon	6624064	6624066	.	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6624064	6624261	0.81	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6624064	6624261	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6624262	6624391	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6624392	6624527	1	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6624392	6624527	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6624528	6624672	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6624673	6624817	1	+	2	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6624673	6624817	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6624818	6624959	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6624960	6625129	1	+	1	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6624960	6625129	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6625130	6625228	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6625229	6625305	1	+	2	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6625229	6625305	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6625306	6625402	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6625403	6625616	0.72	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6625403	6625616	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6625617	6625786	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6625787	6625958	0.99	+	2	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6625787	6625958	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6625959	6626119	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6626120	6626171	0.99	+	1	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6626120	6626171	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6626172	6626247	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6626248	6626345	1	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6626248	6626345	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6626346	6626431	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6626432	6626483	1	+	1	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6626432	6626483	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6626484	6626609	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6626610	6626681	1	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6626610	6626681	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6626682	6626772	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6626773	6626944	1	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6626773	6626944	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6626945	6627048	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6627049	6627153	1	+	2	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6627049	6627153	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6627154	6627239	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6627240	6627324	1	+	2	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6627240	6627324	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	intron	6627325	6627406	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	CDS	6627407	6627488	1	+	1	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	exon	6627407	6627488	.	+	.	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
Phchi.S4	AUGUSTUS	stop_codon	6627489	6627491	.	+	0	transcript_id "Phchi.S4G107100.t1"; gene_id "Phchi.S4G107100"
# This transcript jg2657.t2 is derived from g9577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2658.t1 is derived from g9578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8068543	8069217	.	+	.	Phchi.S5G126700
Phchi.S5	AUGUSTUS	transcript	8068543	8069217	.	+	.	transcript_id "Phchi.S5G126700.t1"; gene_id "Phchi.S5G126700"
Phchi.S5	AUGUSTUS	start_codon	8068543	8068545	.	+	0	transcript_id "Phchi.S5G126700.t1"; gene_id "Phchi.S5G126700"
Phchi.S5	AUGUSTUS	CDS	8068543	8069217	0.83	+	0	transcript_id "Phchi.S5G126700.t1"; gene_id "Phchi.S5G126700"
Phchi.S5	AUGUSTUS	exon	8068543	8069217	.	+	.	transcript_id "Phchi.S5G126700.t1"; gene_id "Phchi.S5G126700"
Phchi.S5	AUGUSTUS	stop_codon	8069218	8069220	.	+	0	transcript_id "Phchi.S5G126700.t1"; gene_id "Phchi.S5G126700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8673.t1 is derived from g5848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37369291	37370873	.	-	.	Phchi.S1G583200
Phchi.S1	AUGUSTUS	transcript	37369291	37370873	.	-	.	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	stop_codon	37369288	37369290	.	-	0	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	CDS	37369291	37370576	0.87	-	2	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	exon	37369291	37370576	.	-	.	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	intron	37370577	37370845	.	-	.	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	CDS	37370846	37370873	1	-	0	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	exon	37370846	37370873	.	-	.	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
Phchi.S1	AUGUSTUS	start_codon	37370871	37370873	.	-	0	transcript_id "Phchi.S1G583200.t1"; gene_id "Phchi.S1G583200"
# This transcript jg9015.t2 is derived from g6190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9016.t1 is derived from g6191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39155871	39157094	.	+	.	Phchi.S1G617500
Phchi.S1	AUGUSTUS	transcript	39155871	39157094	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	start_codon	39155871	39155873	.	+	0	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	CDS	39155871	39155943	1	+	0	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	exon	39155871	39155943	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	intron	39155944	39156083	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	CDS	39156084	39156215	0.99	+	2	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	exon	39156084	39156215	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	intron	39156216	39156363	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	CDS	39156364	39156433	0.66	+	2	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	exon	39156364	39156433	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	intron	39156434	39156633	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	CDS	39156634	39156985	0.26	+	1	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	exon	39156634	39156985	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	intron	39156986	39157088	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	CDS	39157089	39157094	0.62	+	0	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	exon	39157089	39157094	.	+	.	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
Phchi.S1	AUGUSTUS	stop_codon	39157095	39157097	.	+	0	transcript_id "Phchi.S1G617500.t1"; gene_id "Phchi.S1G617500"
# This transcript jg7025.t2 is derived from g4197.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7026.t1 is derived from g4198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26479279	26480184	.	+	.	Phchi.S1G418500
Phchi.S1	AUGUSTUS	transcript	26479279	26480184	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	start_codon	26479279	26479281	.	+	0	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26479279	26479285	0.97	+	0	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26479279	26479285	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	intron	26479286	26479381	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26479382	26479632	0.84	+	2	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26479382	26479632	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	intron	26479633	26479726	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26479727	26479826	0.87	+	0	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26479727	26479826	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	intron	26479827	26480092	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26480093	26480184	0.95	+	2	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26480093	26480184	.	+	.	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	stop_codon	26480185	26480187	.	+	0	transcript_id "Phchi.S1G418500.t1"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	transcript	26479279	26480076	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	start_codon	26479279	26479281	.	+	0	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26479279	26479285	0.97	+	0	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26479279	26479285	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	intron	26479286	26479381	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26479382	26479632	0.83	+	2	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26479382	26479632	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	intron	26479633	26479726	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26479727	26479826	0.86	+	0	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26479727	26479826	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	intron	26479827	26480065	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	CDS	26480066	26480076	0.94	+	2	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	exon	26480066	26480076	.	+	.	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
Phchi.S1	AUGUSTUS	stop_codon	26480077	26480079	.	+	0	transcript_id "Phchi.S1G418500.t2"; gene_id "Phchi.S1G418500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6004.t1 is derived from g3175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20350973	20352032	.	-	.	Phchi.S1G316300
Phchi.S1	AUGUSTUS	transcript	20350973	20352032	.	-	.	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	stop_codon	20350970	20350972	.	-	0	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	CDS	20350973	20350991	0.69	-	1	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	exon	20350973	20350991	.	-	.	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	intron	20350992	20351097	.	-	.	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	CDS	20351098	20352032	0.76	-	0	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	exon	20351098	20352032	.	-	.	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
Phchi.S1	AUGUSTUS	start_codon	20352030	20352032	.	-	0	transcript_id "Phchi.S1G316300.t1"; gene_id "Phchi.S1G316300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12961.t1 is derived from g11426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3337432	3338718	.	-	.	Phchi.S3G028000
Phchi.S3	AUGUSTUS	transcript	3337432	3338718	.	-	.	transcript_id "Phchi.S3G028000.t1"; gene_id "Phchi.S3G028000"
Phchi.S3	AUGUSTUS	stop_codon	3337429	3337431	.	-	0	transcript_id "Phchi.S3G028000.t1"; gene_id "Phchi.S3G028000"
Phchi.S3	AUGUSTUS	CDS	3337432	3338718	0.94	-	0	transcript_id "Phchi.S3G028000.t1"; gene_id "Phchi.S3G028000"
Phchi.S3	AUGUSTUS	exon	3337432	3338718	.	-	.	transcript_id "Phchi.S3G028000.t1"; gene_id "Phchi.S3G028000"
Phchi.S3	AUGUSTUS	start_codon	3338716	3338718	.	-	0	transcript_id "Phchi.S3G028000.t1"; gene_id "Phchi.S3G028000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6370.t1 is derived from g3542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22597885	22601282	.	+	.	Phchi.S1G352900
Phchi.S1	AUGUSTUS	transcript	22597885	22601282	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	start_codon	22597885	22597887	.	+	0	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22597885	22597972	1	+	0	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22597885	22597972	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22597973	22598322	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22598323	22599207	1	+	2	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22598323	22599207	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22599208	22599438	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22599439	22599542	1	+	2	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22599439	22599542	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22599543	22599627	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22599628	22599809	1	+	0	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22599628	22599809	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22599810	22599924	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22599925	22600033	1	+	1	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22599925	22600033	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22600034	22600126	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22600127	22600328	0.86	+	0	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22600127	22600328	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22600329	22600470	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22600471	22600593	0.86	+	2	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22600471	22600593	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22600594	22600680	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22600681	22601021	1	+	2	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22600681	22601021	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	intron	22601022	22601120	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	CDS	22601121	22601282	1	+	0	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	exon	22601121	22601282	.	+	.	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
Phchi.S1	AUGUSTUS	stop_codon	22601283	22601285	.	+	0	transcript_id "Phchi.S1G352900.t1"; gene_id "Phchi.S1G352900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg598.t1 is derived from g10380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4343758	4344510	.	-	.	Phchi.S6G055700
Phchi.S6	AUGUSTUS	transcript	4343758	4344510	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	stop_codon	4343755	4343757	.	-	0	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	CDS	4343758	4343847	1	-	0	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	exon	4343758	4343847	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	intron	4343848	4343947	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	CDS	4343948	4344040	1	-	0	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	exon	4343948	4344040	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	intron	4344041	4344136	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	CDS	4344137	4344196	1	-	0	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	exon	4344137	4344196	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	intron	4344197	4344321	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	CDS	4344322	4344510	0.69	-	0	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	exon	4344322	4344510	.	-	.	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
Phchi.S6	AUGUSTUS	start_codon	4344508	4344510	.	-	0	transcript_id "Phchi.S6G055700.t1"; gene_id "Phchi.S6G055700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15437.t1 is derived from g13905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19093564	19094361	.	-	.	Phchi.S3G275600
Phchi.S3	AUGUSTUS	transcript	19093564	19094361	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	stop_codon	19093561	19093563	.	-	0	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	CDS	19093564	19093576	0.99	-	1	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	exon	19093564	19093576	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	intron	19093577	19093662	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	CDS	19093663	19093721	0.99	-	0	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	exon	19093663	19093721	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	intron	19093722	19093798	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	CDS	19093799	19093843	1	-	0	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	exon	19093799	19093843	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	intron	19093844	19093959	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	CDS	19093960	19094060	1	-	2	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	exon	19093960	19094060	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	intron	19094061	19094216	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	CDS	19094217	19094361	1	-	0	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	exon	19094217	19094361	.	-	.	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
Phchi.S3	AUGUSTUS	start_codon	19094359	19094361	.	-	0	transcript_id "Phchi.S3G275600.t1"; gene_id "Phchi.S3G275600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9284.t1 is derived from g6459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40757799	40759208	.	+	.	Phchi.S1G644300
Phchi.S1	AUGUSTUS	transcript	40757799	40759208	.	+	.	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	start_codon	40757799	40757801	.	+	0	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	CDS	40757799	40757894	0.52	+	0	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	exon	40757799	40757894	.	+	.	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	intron	40757895	40758044	.	+	.	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	CDS	40758045	40759208	0.81	+	0	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	exon	40758045	40759208	.	+	.	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
Phchi.S1	AUGUSTUS	stop_codon	40759209	40759211	.	+	0	transcript_id "Phchi.S1G644300.t1"; gene_id "Phchi.S1G644300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8519.t1 is derived from g5694.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36413002	36414989	.	+	.	Phchi.S1G567800
Phchi.S1	AUGUSTUS	transcript	36413002	36414989	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	start_codon	36413002	36413004	.	+	0	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413002	36413182	0.88	+	0	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413002	36413182	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413183	36413285	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413286	36413406	0.99	+	2	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413286	36413406	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413407	36413511	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413512	36413619	1	+	1	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413512	36413619	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413620	36413710	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413711	36413834	0.83	+	1	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413711	36413834	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413835	36413924	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413925	36414009	0.97	+	0	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413925	36414009	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414010	36414089	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414090	36414171	1	+	2	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414090	36414171	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414172	36414300	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414301	36414360	1	+	1	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414301	36414360	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414361	36414475	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414476	36414524	1	+	1	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414476	36414524	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414525	36414607	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414608	36414742	1	+	0	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414608	36414742	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414743	36414860	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414861	36414989	1	+	0	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414861	36414989	.	+	.	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	stop_codon	36414990	36414992	.	+	0	transcript_id "Phchi.S1G567800.t1"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	transcript	36413002	36414989	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	start_codon	36413002	36413004	.	+	0	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413002	36413182	0.86	+	0	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413002	36413182	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413183	36413285	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413286	36413406	0.99	+	2	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413286	36413406	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413407	36413511	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413512	36413619	1	+	1	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413512	36413619	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413620	36413710	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413711	36413841	0.55	+	1	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413711	36413841	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36413842	36413948	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36413949	36414005	0.63	+	2	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36413949	36414005	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414006	36414086	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414087	36414171	1	+	2	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414087	36414171	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414172	36414300	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414301	36414360	1	+	1	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414301	36414360	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414361	36414475	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414476	36414524	1	+	1	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414476	36414524	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414525	36414607	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414608	36414742	1	+	0	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414608	36414742	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	intron	36414743	36414860	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	CDS	36414861	36414989	1	+	0	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	exon	36414861	36414989	.	+	.	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
Phchi.S1	AUGUSTUS	stop_codon	36414990	36414992	.	+	0	transcript_id "Phchi.S1G567800.t2"; gene_id "Phchi.S1G567800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13401.t1 is derived from g11867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6534096	6536967	.	+	.	Phchi.S3G072000
Phchi.S3	AUGUSTUS	transcript	6534096	6536967	.	+	.	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	start_codon	6534096	6534098	.	+	0	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	CDS	6534096	6535689	0.74	+	0	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	exon	6534096	6535689	.	+	.	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	intron	6535690	6535810	.	+	.	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	CDS	6535811	6536967	0.98	+	2	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	exon	6535811	6536967	.	+	.	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
Phchi.S3	AUGUSTUS	stop_codon	6536968	6536970	.	+	0	transcript_id "Phchi.S3G072000.t1"; gene_id "Phchi.S3G072000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1610.t1 is derived from g8529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2018528	2019405	.	+	.	Phchi.S5G021900
Phchi.S5	AUGUSTUS	transcript	2018528	2019405	.	+	.	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	start_codon	2018528	2018530	.	+	0	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	CDS	2018528	2018758	0.82	+	0	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	exon	2018528	2018758	.	+	.	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	intron	2018759	2018985	.	+	.	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	CDS	2018986	2019405	0.93	+	0	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	exon	2018986	2019405	.	+	.	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
Phchi.S5	AUGUSTUS	stop_codon	2019406	2019408	.	+	0	transcript_id "Phchi.S5G021900.t1"; gene_id "Phchi.S5G021900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1588.t1 is derived from g8507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1900386	1902636	.	+	.	Phchi.S5G019700
Phchi.S5	AUGUSTUS	transcript	1900386	1902636	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	start_codon	1900386	1900388	.	+	0	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1900386	1900424	0.93	+	0	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1900386	1900424	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1900425	1900605	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1900606	1900660	0.92	+	0	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1900606	1900660	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1900661	1900747	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1900748	1900755	0.95	+	2	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1900748	1900755	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1900756	1900838	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1900839	1901107	0.96	+	0	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1900839	1901107	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1901108	1901252	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1901253	1901397	1	+	1	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1901253	1901397	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1901398	1901476	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1901477	1901576	1	+	0	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1901477	1901576	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1901577	1901696	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1901697	1901925	1	+	2	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1901697	1901925	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1901926	1902316	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1902317	1902375	0.36	+	1	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1902317	1902375	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	intron	1902376	1902523	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	CDS	1902524	1902636	0.32	+	2	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	exon	1902524	1902636	.	+	.	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
Phchi.S5	AUGUSTUS	stop_codon	1902637	1902639	.	+	0	transcript_id "Phchi.S5G019700.t1"; gene_id "Phchi.S5G019700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10134.t1 is derived from g7310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45915792	45916136	.	-	.	Phchi.S1G729300
Phchi.S1	AUGUSTUS	transcript	45915792	45916136	.	-	.	transcript_id "Phchi.S1G729300.t1"; gene_id "Phchi.S1G729300"
Phchi.S1	AUGUSTUS	stop_codon	45915789	45915791	.	-	0	transcript_id "Phchi.S1G729300.t1"; gene_id "Phchi.S1G729300"
Phchi.S1	AUGUSTUS	CDS	45915792	45916136	0.41	-	0	transcript_id "Phchi.S1G729300.t1"; gene_id "Phchi.S1G729300"
Phchi.S1	AUGUSTUS	exon	45915792	45916136	.	-	.	transcript_id "Phchi.S1G729300.t1"; gene_id "Phchi.S1G729300"
Phchi.S1	AUGUSTUS	start_codon	45916134	45916136	.	-	0	transcript_id "Phchi.S1G729300.t1"; gene_id "Phchi.S1G729300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2448.t1 is derived from g9368.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6666161	6668250	.	+	.	Phchi.S5G105700
Phchi.S5	AUGUSTUS	transcript	6666161	6666927	.	+	.	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	start_codon	6666161	6666163	.	+	0	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6666161	6666523	0.71	+	0	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6666161	6666523	.	+	.	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6666524	6666607	.	+	.	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6666608	6666824	1	+	0	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6666608	6666824	.	+	.	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6666825	6666919	.	+	.	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6666920	6666927	1	+	2	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6666920	6666927	.	+	.	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	stop_codon	6666928	6666930	.	+	0	transcript_id "Phchi.S5G105700.t1"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	transcript	6666161	6668250	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	start_codon	6666161	6666163	.	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6666161	6666523	0.68	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6666161	6666523	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6666524	6666607	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6666608	6666820	1	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6666608	6666820	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6666821	6666919	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6666920	6667021	0.74	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6666920	6667021	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6667022	6667135	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6667136	6667273	0.74	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6667136	6667273	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6667274	6667384	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6667385	6667689	0.97	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6667385	6667689	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6667690	6667809	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6667810	6667963	1	+	1	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6667810	6667963	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	intron	6667964	6668103	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	CDS	6668104	6668250	1	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	exon	6668104	6668250	.	+	.	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
Phchi.S5	AUGUSTUS	stop_codon	6668251	6668253	.	+	0	transcript_id "Phchi.S5G105700.t2"; gene_id "Phchi.S5G105700"
# This transcript jg4926.t2 is derived from g2096.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4927.t1 is derived from g2097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13605454	13606172	.	+	.	Phchi.S1G208600
Phchi.S1	AUGUSTUS	transcript	13605454	13606172	.	+	.	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	start_codon	13605454	13605456	.	+	0	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	CDS	13605454	13605529	0.94	+	0	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	exon	13605454	13605529	.	+	.	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	intron	13605530	13605801	.	+	.	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	CDS	13605802	13606172	1	+	2	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	exon	13605802	13606172	.	+	.	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
Phchi.S1	AUGUSTUS	stop_codon	13606173	13606175	.	+	0	transcript_id "Phchi.S1G208600.t1"; gene_id "Phchi.S1G208600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2163.t1 is derived from g9083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5133929	5135702	.	+	.	Phchi.S5G077200
Phchi.S5	AUGUSTUS	transcript	5133929	5135702	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	start_codon	5133929	5133931	.	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5133929	5133973	0.36	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5133929	5133973	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5133974	5134078	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5134079	5134174	0.96	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5134079	5134174	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5134175	5134255	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5134256	5134322	1	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5134256	5134322	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5134323	5134410	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5134411	5134553	1	+	2	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5134411	5134553	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5134554	5134641	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5134642	5134674	0.42	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5134642	5134674	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5134675	5134763	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5134764	5134888	0.31	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5134764	5134888	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5134889	5134970	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5134971	5135079	1	+	1	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5134971	5135079	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5135080	5135166	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5135167	5135367	1	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5135167	5135367	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	intron	5135368	5135459	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	CDS	5135460	5135702	0.99	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	exon	5135460	5135702	.	+	.	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
Phchi.S5	AUGUSTUS	stop_codon	5135703	5135705	.	+	0	transcript_id "Phchi.S5G077200.t1"; gene_id "Phchi.S5G077200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9560.t1 is derived from g6736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42666246	42667940	.	-	.	Phchi.S1G671900
Phchi.S1	AUGUSTUS	transcript	42666246	42667940	.	-	.	transcript_id "Phchi.S1G671900.t1"; gene_id "Phchi.S1G671900"
Phchi.S1	AUGUSTUS	stop_codon	42666243	42666245	.	-	0	transcript_id "Phchi.S1G671900.t1"; gene_id "Phchi.S1G671900"
Phchi.S1	AUGUSTUS	CDS	42666246	42667940	0.99	-	0	transcript_id "Phchi.S1G671900.t1"; gene_id "Phchi.S1G671900"
Phchi.S1	AUGUSTUS	exon	42666246	42667940	.	-	.	transcript_id "Phchi.S1G671900.t1"; gene_id "Phchi.S1G671900"
Phchi.S1	AUGUSTUS	start_codon	42667938	42667940	.	-	0	transcript_id "Phchi.S1G671900.t1"; gene_id "Phchi.S1G671900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5905.t1 is derived from g3075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19682685	19684388	.	-	.	Phchi.S1G306400
Phchi.S1	AUGUSTUS	transcript	19682685	19684388	.	-	.	transcript_id "Phchi.S1G306400.t1"; gene_id "Phchi.S1G306400"
Phchi.S1	AUGUSTUS	stop_codon	19682682	19682684	.	-	0	transcript_id "Phchi.S1G306400.t1"; gene_id "Phchi.S1G306400"
Phchi.S1	AUGUSTUS	CDS	19682685	19684388	0.36	-	0	transcript_id "Phchi.S1G306400.t1"; gene_id "Phchi.S1G306400"
Phchi.S1	AUGUSTUS	exon	19682685	19684388	.	-	.	transcript_id "Phchi.S1G306400.t1"; gene_id "Phchi.S1G306400"
Phchi.S1	AUGUSTUS	start_codon	19684386	19684388	.	-	0	transcript_id "Phchi.S1G306400.t1"; gene_id "Phchi.S1G306400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12802.t1 is derived from g11267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2450634	2452596	.	+	.	Phchi.S3G012100
Phchi.S3	AUGUSTUS	transcript	2450634	2452596	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	start_codon	2450634	2450636	.	+	0	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2450634	2450849	1	+	0	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2450634	2450849	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	intron	2450850	2451054	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2451055	2451128	1	+	0	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2451055	2451128	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	intron	2451129	2451315	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2451316	2451415	1	+	1	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2451316	2451415	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	intron	2451416	2451589	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2451590	2451715	1	+	0	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2451590	2451715	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	intron	2451716	2451804	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2451805	2451856	1	+	0	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2451805	2451856	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	intron	2451857	2451950	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2451951	2452391	1	+	2	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2451951	2452391	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	intron	2452392	2452483	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	CDS	2452484	2452596	1	+	2	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	exon	2452484	2452596	.	+	.	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
Phchi.S3	AUGUSTUS	stop_codon	2452597	2452599	.	+	0	transcript_id "Phchi.S3G012100.t1"; gene_id "Phchi.S3G012100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11394.t1 is derived from g15444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6130904	6131332	.	+	.	Phchi.S4G097600
Phchi.S4	AUGUSTUS	transcript	6130904	6131332	.	+	.	transcript_id "Phchi.S4G097600.t1"; gene_id "Phchi.S4G097600"
Phchi.S4	AUGUSTUS	start_codon	6130904	6130906	.	+	0	transcript_id "Phchi.S4G097600.t1"; gene_id "Phchi.S4G097600"
Phchi.S4	AUGUSTUS	CDS	6130904	6131332	0.91	+	0	transcript_id "Phchi.S4G097600.t1"; gene_id "Phchi.S4G097600"
Phchi.S4	AUGUSTUS	exon	6130904	6131332	.	+	.	transcript_id "Phchi.S4G097600.t1"; gene_id "Phchi.S4G097600"
Phchi.S4	AUGUSTUS	stop_codon	6131333	6131335	.	+	0	transcript_id "Phchi.S4G097600.t1"; gene_id "Phchi.S4G097600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4946.t1 is derived from g2116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13681739	13682575	.	+	.	Phchi.S1G210500
Phchi.S1	AUGUSTUS	transcript	13681739	13682575	.	+	.	transcript_id "Phchi.S1G210500.t1"; gene_id "Phchi.S1G210500"
Phchi.S1	AUGUSTUS	start_codon	13681739	13681741	.	+	0	transcript_id "Phchi.S1G210500.t1"; gene_id "Phchi.S1G210500"
Phchi.S1	AUGUSTUS	CDS	13681739	13682575	0.7	+	0	transcript_id "Phchi.S1G210500.t1"; gene_id "Phchi.S1G210500"
Phchi.S1	AUGUSTUS	exon	13681739	13682575	.	+	.	transcript_id "Phchi.S1G210500.t1"; gene_id "Phchi.S1G210500"
Phchi.S1	AUGUSTUS	stop_codon	13682576	13682578	.	+	0	transcript_id "Phchi.S1G210500.t1"; gene_id "Phchi.S1G210500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1229.t1 is derived from g11012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8514489	8515648	.	+	.	Phchi.S6G118800
Phchi.S6	AUGUSTUS	transcript	8514489	8515648	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	start_codon	8514489	8514491	.	+	0	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	CDS	8514489	8514738	1	+	0	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	exon	8514489	8514738	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	intron	8514739	8514893	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	CDS	8514894	8515152	0.98	+	2	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	exon	8514894	8515152	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	intron	8515153	8515232	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	CDS	8515233	8515242	0.98	+	1	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	exon	8515233	8515242	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	intron	8515243	8515333	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	CDS	8515334	8515463	0.98	+	0	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	exon	8515334	8515463	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	intron	8515464	8515556	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	CDS	8515557	8515648	0.97	+	2	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	exon	8515557	8515648	.	+	.	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
Phchi.S6	AUGUSTUS	stop_codon	8515649	8515651	.	+	0	transcript_id "Phchi.S6G118800.t1"; gene_id "Phchi.S6G118800"
# This transcript jg3058.t2 is derived from g227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3059.t1 is derived from g228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1384073	1388135	.	+	.	Phchi.S1G021800
Phchi.S1	AUGUSTUS	transcript	1384073	1388135	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	start_codon	1384073	1384075	.	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1384073	1384945	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1384073	1384945	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1384946	1385096	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1385097	1385159	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1385097	1385159	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1385160	1385247	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1385248	1385336	0.97	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1385248	1385336	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1385337	1385442	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1385443	1385503	1	+	1	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1385443	1385503	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1385504	1385695	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1385696	1385777	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1385696	1385777	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1385778	1385909	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1385910	1386046	1	+	2	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1385910	1386046	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1386047	1386177	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1386178	1386336	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1386178	1386336	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1386337	1386422	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1386423	1386502	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1386423	1386502	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1386503	1386734	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1386735	1386874	1	+	1	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1386735	1386874	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1386875	1386992	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1386993	1387024	1	+	2	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1386993	1387024	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1387025	1387117	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1387118	1387192	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1387118	1387192	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1387193	1387310	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1387311	1387383	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1387311	1387383	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1387384	1387466	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1387467	1387555	1	+	2	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1387467	1387555	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1387556	1387660	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1387661	1387705	0.57	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1387661	1387705	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1387706	1387794	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1387795	1387947	1	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1387795	1387947	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	intron	1387948	1388021	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	CDS	1388022	1388135	0.99	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	exon	1388022	1388135	.	+	.	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
Phchi.S1	AUGUSTUS	stop_codon	1388136	1388138	.	+	0	transcript_id "Phchi.S1G021800.t1"; gene_id "Phchi.S1G021800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6792.t1 is derived from g3964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25099586	25101137	.	+	.	Phchi.S1G395100
Phchi.S1	AUGUSTUS	transcript	25099586	25101137	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	start_codon	25099586	25099588	.	+	0	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	CDS	25099586	25099927	0.66	+	0	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	exon	25099586	25099927	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	intron	25099928	25100110	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	CDS	25100111	25100393	0.59	+	0	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	exon	25100111	25100393	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	intron	25100394	25100483	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	CDS	25100484	25100579	0.59	+	2	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	exon	25100484	25100579	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	intron	25100580	25100730	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	CDS	25100731	25101137	0.76	+	2	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	exon	25100731	25101137	.	+	.	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
Phchi.S1	AUGUSTUS	stop_codon	25101138	25101140	.	+	0	transcript_id "Phchi.S1G395100.t1"; gene_id "Phchi.S1G395100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15524.t1 is derived from g13993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19721453	19724105	.	+	.	Phchi.S3G284300
Phchi.S3	AUGUSTUS	transcript	19721453	19724105	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	start_codon	19721453	19721455	.	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19721453	19721818	0.53	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19721453	19721818	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19721819	19722151	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19722152	19722396	0.99	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19722152	19722396	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19722397	19722487	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19722488	19722641	1	+	1	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19722488	19722641	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19722642	19722838	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19722839	19723053	1	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19722839	19723053	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19723054	19723182	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19723183	19723300	1	+	1	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19723183	19723300	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19723301	19723429	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19723430	19723637	1	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19723430	19723637	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19723638	19723733	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19723734	19723795	1	+	2	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19723734	19723795	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	intron	19723796	19723889	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	CDS	19723890	19724105	0.28	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	exon	19723890	19724105	.	+	.	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
Phchi.S3	AUGUSTUS	stop_codon	19724106	19724108	.	+	0	transcript_id "Phchi.S3G284300.t1"; gene_id "Phchi.S3G284300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12044.t1 is derived from g7719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	951125	952026	.	-	.	Phchi.S2G012400
Phchi.S2	AUGUSTUS	transcript	951125	952026	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	stop_codon	951122	951124	.	-	0	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	CDS	951125	951343	0.99	-	0	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	exon	951125	951343	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	intron	951344	951417	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	CDS	951418	951491	1	-	2	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	exon	951418	951491	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	intron	951492	951578	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	CDS	951579	951678	0.91	-	0	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	exon	951579	951678	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	intron	951679	951770	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	CDS	951771	951809	0.98	-	0	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	exon	951771	951809	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	intron	951810	951885	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	CDS	951886	952026	0.99	-	0	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	exon	951886	952026	.	-	.	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
Phchi.S2	AUGUSTUS	start_codon	952024	952026	.	-	0	transcript_id "Phchi.S2G012400.t1"; gene_id "Phchi.S2G012400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7227.t1 is derived from g4399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27719367	27722131	.	+	.	Phchi.S1G438600
Phchi.S1	AUGUSTUS	transcript	27719367	27720948	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	start_codon	27719367	27719369	.	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719367	27719453	1	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719367	27719453	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27719454	27719595	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719596	27719634	1	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719596	27719634	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27719635	27719708	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719709	27719801	1	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719709	27719801	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27719802	27719890	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719891	27720007	1	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719891	27720007	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720008	27720107	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720108	27720114	0.98	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720108	27720114	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720115	27720195	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720196	27720206	0.98	+	2	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720196	27720206	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720207	27720522	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720523	27720636	1	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720523	27720636	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720637	27720761	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720762	27720815	1	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720762	27720815	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720816	27720915	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720916	27720948	0.95	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720916	27720948	.	+	.	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	stop_codon	27720949	27720951	.	+	0	transcript_id "Phchi.S1G438600.t1"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	transcript	27719367	27722131	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	start_codon	27719367	27719369	.	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719367	27719453	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719367	27719453	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27719454	27719595	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719596	27719634	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719596	27719634	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27719635	27719708	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719709	27719801	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719709	27719801	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27719802	27719890	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27719891	27720007	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27719891	27720007	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720008	27720107	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720108	27720114	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720108	27720114	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720115	27720195	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720196	27720206	1	+	2	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720196	27720206	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720207	27720522	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720523	27720636	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720523	27720636	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720637	27720761	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720762	27720815	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720762	27720815	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27720816	27720958	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27720959	27721006	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27720959	27721006	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27721007	27721130	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27721131	27721293	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27721131	27721293	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27721294	27721464	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27721465	27721471	0.7	+	2	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27721465	27721471	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27721472	27721735	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27721736	27721805	1	+	1	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27721736	27721805	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	intron	27721806	27721885	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	CDS	27721886	27722131	1	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	exon	27721886	27722131	.	+	.	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
Phchi.S1	AUGUSTUS	stop_codon	27722132	27722134	.	+	0	transcript_id "Phchi.S1G438600.t2"; gene_id "Phchi.S1G438600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3872.t1 is derived from g1041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6152840	6155460	.	-	.	Phchi.S1G103100
Phchi.S1	AUGUSTUS	transcript	6152840	6155460	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	stop_codon	6152837	6152839	.	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6152840	6152980	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6152840	6152980	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6152981	6153065	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6153066	6153216	1	-	1	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6153066	6153216	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6153217	6153310	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6153311	6153453	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6153311	6153453	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6153454	6153553	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6153554	6153616	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6153554	6153616	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6153617	6153713	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6153714	6153827	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6153714	6153827	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6153828	6153914	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6153915	6154068	1	-	1	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6153915	6154068	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6154069	6154168	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6154169	6154371	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6154169	6154371	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6154372	6154470	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6154471	6154539	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6154471	6154539	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6154540	6154640	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6154641	6154729	1	-	2	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6154641	6154729	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6154730	6154862	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6154863	6155064	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6154863	6155064	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6155065	6155143	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6155144	6155182	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6155144	6155182	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	intron	6155183	6155265	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	CDS	6155266	6155460	1	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	exon	6155266	6155460	.	-	.	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
Phchi.S1	AUGUSTUS	start_codon	6155458	6155460	.	-	0	transcript_id "Phchi.S1G103100.t1"; gene_id "Phchi.S1G103100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg845.t1 is derived from g10627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5859053	5861673	.	-	.	Phchi.S6G080400
Phchi.S6	AUGUSTUS	transcript	5859053	5861673	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	stop_codon	5859050	5859052	.	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5859053	5859292	1	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5859053	5859292	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5859293	5859437	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5859438	5859512	1	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5859438	5859512	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5859513	5859597	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5859598	5859696	0.81	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5859598	5859696	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5859697	5859895	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5859896	5860000	1	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5859896	5860000	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5860001	5860256	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5860257	5860398	1	-	1	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5860257	5860398	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5860399	5860520	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5860521	5860682	1	-	1	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5860521	5860682	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5860683	5860807	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5860808	5860980	1	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5860808	5860980	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	intron	5860981	5861205	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	CDS	5861206	5861673	1	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	exon	5861206	5861673	.	-	.	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
Phchi.S6	AUGUSTUS	start_codon	5861671	5861673	.	-	0	transcript_id "Phchi.S6G080400.t1"; gene_id "Phchi.S6G080400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg113.t1 is derived from g9895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	601090	601721	.	-	.	Phchi.S6G007200
Phchi.S6	AUGUSTUS	transcript	601090	601721	.	-	.	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	stop_codon	601087	601089	.	-	0	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	CDS	601090	601345	0.35	-	1	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	exon	601090	601345	.	-	.	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	intron	601346	601446	.	-	.	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	CDS	601447	601721	0.4	-	0	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	exon	601447	601721	.	-	.	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
Phchi.S6	AUGUSTUS	start_codon	601719	601721	.	-	0	transcript_id "Phchi.S6G007200.t1"; gene_id "Phchi.S6G007200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10227.t1 is derived from g7403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46475443	46479500	.	-	.	Phchi.S1G738600
Phchi.S1	AUGUSTUS	transcript	46475443	46479500	.	-	.	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	stop_codon	46475440	46475442	.	-	0	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	CDS	46475443	46476651	0.95	-	0	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	exon	46475443	46476651	.	-	.	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	intron	46476652	46476790	.	-	.	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	CDS	46476791	46478822	0.45	-	1	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	exon	46476791	46478822	.	-	.	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	intron	46478823	46478919	.	-	.	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	CDS	46478920	46479500	0.4	-	0	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	exon	46478920	46479500	.	-	.	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
Phchi.S1	AUGUSTUS	start_codon	46479498	46479500	.	-	0	transcript_id "Phchi.S1G738600.t1"; gene_id "Phchi.S1G738600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4244.t1 is derived from g1413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9147087	9147980	.	+	.	Phchi.S1G140300
Phchi.S1	AUGUSTUS	transcript	9147087	9147980	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	start_codon	9147087	9147089	.	+	0	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	CDS	9147087	9147144	0.54	+	0	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	exon	9147087	9147144	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	intron	9147145	9147231	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	CDS	9147232	9147357	0.71	+	2	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	exon	9147232	9147357	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	intron	9147358	9147453	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	CDS	9147454	9147497	0.97	+	2	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	exon	9147454	9147497	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	intron	9147498	9147587	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	CDS	9147588	9147650	1	+	0	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	exon	9147588	9147650	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	intron	9147651	9147743	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	CDS	9147744	9147980	0.25	+	0	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	exon	9147744	9147980	.	+	.	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
Phchi.S1	AUGUSTUS	stop_codon	9147981	9147983	.	+	0	transcript_id "Phchi.S1G140300.t1"; gene_id "Phchi.S1G140300"
# This transcript jg3714.t2 is derived from g883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3715.t1 is derived from g884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5345457	5348016	.	-	.	Phchi.S1G087400
Phchi.S1	AUGUSTUS	transcript	5345457	5348016	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	stop_codon	5345454	5345456	.	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5345457	5345531	0.96	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5345457	5345531	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5345532	5345603	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5345604	5345675	1	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5345604	5345675	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5345676	5345755	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5345756	5345892	1	-	2	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5345756	5345892	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5345893	5346011	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5346012	5346087	1	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5346012	5346087	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5346088	5346222	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5346223	5346249	1	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5346223	5346249	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5346250	5346401	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5346402	5346448	1	-	2	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5346402	5346448	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5346449	5346632	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5346633	5346744	1	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5346633	5346744	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5346745	5346848	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5346849	5346899	0.99	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5346849	5346899	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5346900	5347057	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5347058	5347699	1	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5347058	5347699	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	intron	5347700	5347965	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	CDS	5347966	5348016	0.6	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	exon	5347966	5348016	.	-	.	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
Phchi.S1	AUGUSTUS	start_codon	5348014	5348016	.	-	0	transcript_id "Phchi.S1G087400.t1"; gene_id "Phchi.S1G087400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7676.t1 is derived from g4850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30577106	30578197	.	+	.	Phchi.S1G483500
Phchi.S1	AUGUSTUS	transcript	30577106	30578197	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	start_codon	30577106	30577108	.	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30577106	30577182	1	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30577106	30577182	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	intron	30577183	30577275	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30577276	30577407	1	+	1	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30577276	30577407	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	intron	30577408	30577492	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30577493	30577550	1	+	1	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30577493	30577550	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	intron	30577551	30577682	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30577683	30577727	1	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30577683	30577727	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	intron	30577728	30577812	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30577813	30577893	1	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30577813	30577893	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	intron	30577894	30577967	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30577968	30578051	1	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30577968	30578051	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	intron	30578052	30578173	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	CDS	30578174	30578197	1	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	exon	30578174	30578197	.	+	.	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
Phchi.S1	AUGUSTUS	stop_codon	30578198	30578200	.	+	0	transcript_id "Phchi.S1G483500.t1"; gene_id "Phchi.S1G483500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8647.t1 is derived from g5822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37230138	37232844	.	+	.	Phchi.S1G580600
Phchi.S1	AUGUSTUS	transcript	37230138	37232844	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	start_codon	37230138	37230140	.	+	0	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	CDS	37230138	37230153	0.91	+	0	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	exon	37230138	37230153	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	intron	37230154	37230286	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	CDS	37230287	37230438	1	+	2	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	exon	37230287	37230438	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	intron	37230439	37230724	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	CDS	37230725	37230791	1	+	0	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	exon	37230725	37230791	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	intron	37230792	37230999	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	CDS	37231000	37231207	0.89	+	2	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	exon	37231000	37231207	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	intron	37231208	37231340	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	CDS	37231341	37232844	0.89	+	1	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	exon	37231341	37232844	.	+	.	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
Phchi.S1	AUGUSTUS	stop_codon	37232845	37232847	.	+	0	transcript_id "Phchi.S1G580600.t1"; gene_id "Phchi.S1G580600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1004.t1 is derived from g10787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7052746	7053366	.	-	.	Phchi.S6G096300
Phchi.S6	AUGUSTUS	transcript	7052746	7053366	.	-	.	transcript_id "Phchi.S6G096300.t1"; gene_id "Phchi.S6G096300"
Phchi.S6	AUGUSTUS	stop_codon	7052743	7052745	.	-	0	transcript_id "Phchi.S6G096300.t1"; gene_id "Phchi.S6G096300"
Phchi.S6	AUGUSTUS	CDS	7052746	7053366	1	-	0	transcript_id "Phchi.S6G096300.t1"; gene_id "Phchi.S6G096300"
Phchi.S6	AUGUSTUS	exon	7052746	7053366	.	-	.	transcript_id "Phchi.S6G096300.t1"; gene_id "Phchi.S6G096300"
Phchi.S6	AUGUSTUS	start_codon	7053364	7053366	.	-	0	transcript_id "Phchi.S6G096300.t1"; gene_id "Phchi.S6G096300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7473.t1 is derived from g4646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29540019	29540516	.	-	.	Phchi.S1G463200
Phchi.S1	AUGUSTUS	transcript	29540019	29540516	.	-	.	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	stop_codon	29540016	29540018	.	-	0	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	CDS	29540019	29540129	0.75	-	0	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	exon	29540019	29540129	.	-	.	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	intron	29540130	29540225	.	-	.	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	CDS	29540226	29540516	0.77	-	0	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	exon	29540226	29540516	.	-	.	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
Phchi.S1	AUGUSTUS	start_codon	29540514	29540516	.	-	0	transcript_id "Phchi.S1G463200.t1"; gene_id "Phchi.S1G463200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7395.t1 is derived from g4567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28930642	28932215	.	-	.	Phchi.S1G455400
Phchi.S1	AUGUSTUS	transcript	28930642	28932215	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	stop_codon	28930639	28930641	.	-	0	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	CDS	28930642	28930917	1	-	0	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	exon	28930642	28930917	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	intron	28930918	28931030	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	CDS	28931031	28931163	1	-	1	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	exon	28931031	28931163	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	intron	28931164	28931260	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	CDS	28931261	28931364	1	-	0	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	exon	28931261	28931364	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	intron	28931365	28931453	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	CDS	28931454	28932215	0.79	-	0	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	exon	28931454	28932215	.	-	.	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
Phchi.S1	AUGUSTUS	start_codon	28932213	28932215	.	-	0	transcript_id "Phchi.S1G455400.t1"; gene_id "Phchi.S1G455400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10886.t1 is derived from g14936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2761829	2763066	.	-	.	Phchi.S4G046800
Phchi.S4	AUGUSTUS	transcript	2761829	2763066	.	-	.	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	stop_codon	2761826	2761828	.	-	0	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	CDS	2761829	2762217	0.99	-	2	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	exon	2761829	2762217	.	-	.	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	intron	2762218	2762346	.	-	.	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	CDS	2762347	2762478	1	-	2	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	exon	2762347	2762478	.	-	.	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	intron	2762479	2762585	.	-	.	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	CDS	2762586	2763066	0.99	-	0	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	exon	2762586	2763066	.	-	.	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
Phchi.S4	AUGUSTUS	start_codon	2763064	2763066	.	-	0	transcript_id "Phchi.S4G046800.t1"; gene_id "Phchi.S4G046800"
# This transcript jg7116.t2 is derived from g4288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7116.t3 is derived from g4288.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7117.t1 is derived from g4289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27059625	27060105	.	-	.	Phchi.S1G427600
Phchi.S1	AUGUSTUS	transcript	27059625	27060105	.	-	.	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	stop_codon	27059622	27059624	.	-	0	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	CDS	27059625	27059819	0.8	-	0	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	exon	27059625	27059819	.	-	.	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	intron	27059820	27059943	.	-	.	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	CDS	27059944	27060105	1	-	0	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	exon	27059944	27060105	.	-	.	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
Phchi.S1	AUGUSTUS	start_codon	27060103	27060105	.	-	0	transcript_id "Phchi.S1G427600.t1"; gene_id "Phchi.S1G427600"
# This transcript jg11744.t2 is derived from g15796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 6 different transcripts
# This transcript jg11745.t1 is derived from g15797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7979044	7983069	.	+	.	Phchi.S4G132700
Phchi.S4	AUGUSTUS	transcript	7979044	7981214	.	+	.	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	start_codon	7979044	7979046	.	+	0	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7979044	7981035	0.95	+	0	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7979044	7981035	.	+	.	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	intron	7981036	7981157	.	+	.	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7981158	7981214	0.93	+	0	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7981158	7981214	.	+	.	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	stop_codon	7981215	7981217	.	+	0	transcript_id "Phchi.S4G132700.t1"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	transcript	7979044	7982476	.	+	.	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	start_codon	7979044	7979046	.	+	0	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7979044	7982394	0.81	+	0	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7979044	7982394	.	+	.	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	intron	7982395	7982467	.	+	.	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7982468	7982476	0.8	+	0	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7982468	7982476	.	+	.	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	stop_codon	7982477	7982479	.	+	0	transcript_id "Phchi.S4G132700.t2"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	transcript	7979044	7981997	.	+	.	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	start_codon	7979044	7979046	.	+	0	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7979044	7981910	0.61	+	0	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7979044	7981910	.	+	.	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	intron	7981911	7981990	.	+	.	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7981991	7981997	0.64	+	1	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7981991	7981997	.	+	.	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	stop_codon	7981998	7982000	.	+	0	transcript_id "Phchi.S4G132700.t3"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	transcript	7979044	7982081	.	+	.	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	start_codon	7979044	7979046	.	+	0	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7979044	7981920	0.96	+	0	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7979044	7981920	.	+	.	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	intron	7981921	7982024	.	+	.	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7982025	7982081	0.39	+	0	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7982025	7982081	.	+	.	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	stop_codon	7982082	7982084	.	+	0	transcript_id "Phchi.S4G132700.t4"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	transcript	7979044	7983069	.	+	.	transcript_id "Phchi.S4G132700.t5"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	start_codon	7979044	7979046	.	+	0	transcript_id "Phchi.S4G132700.t5"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7979044	7983069	0.83	+	0	transcript_id "Phchi.S4G132700.t5"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7979044	7983069	.	+	.	transcript_id "Phchi.S4G132700.t5"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	stop_codon	7983070	7983072	.	+	0	transcript_id "Phchi.S4G132700.t5"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	transcript	7980079	7983069	.	+	.	transcript_id "Phchi.S4G132700.t6"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	start_codon	7980079	7980081	.	+	0	transcript_id "Phchi.S4G132700.t6"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	CDS	7980079	7983069	0.66	+	0	transcript_id "Phchi.S4G132700.t6"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	exon	7980079	7983069	.	+	.	transcript_id "Phchi.S4G132700.t6"; gene_id "Phchi.S4G132700"
Phchi.S4	AUGUSTUS	stop_codon	7983070	7983072	.	+	0	transcript_id "Phchi.S4G132700.t6"; gene_id "Phchi.S4G132700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15135.t1 is derived from g13603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17208922	17209904	.	+	.	Phchi.S3G245400
Phchi.S3	AUGUSTUS	transcript	17208922	17209904	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	start_codon	17208922	17208924	.	+	0	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	CDS	17208922	17209128	0.87	+	0	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	exon	17208922	17209128	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	intron	17209129	17209306	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	CDS	17209307	17209483	0.92	+	0	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	exon	17209307	17209483	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	intron	17209484	17209577	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	CDS	17209578	17209691	1	+	0	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	exon	17209578	17209691	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	intron	17209692	17209784	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	CDS	17209785	17209904	1	+	0	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	exon	17209785	17209904	.	+	.	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
Phchi.S3	AUGUSTUS	stop_codon	17209905	17209907	.	+	0	transcript_id "Phchi.S3G245400.t1"; gene_id "Phchi.S3G245400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5195.t1 is derived from g2365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15414966	15418304	.	-	.	Phchi.S1G235400
Phchi.S1	AUGUSTUS	transcript	15414966	15418304	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	stop_codon	15414963	15414965	.	-	0	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15414966	15415008	1	-	1	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15414966	15415008	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15415009	15415200	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15415201	15415613	1	-	0	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15415201	15415613	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15415614	15415719	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15415720	15415904	0.98	-	2	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15415720	15415904	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15415905	15415993	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15415994	15416188	1	-	2	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15415994	15416188	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15416189	15416330	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15416331	15417156	1	-	0	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15416331	15417156	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15417157	15417389	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15417390	15417418	0.86	-	2	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15417390	15417418	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15417419	15417543	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15417544	15417698	0.66	-	1	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15417544	15417698	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15417699	15418066	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15418067	15418106	0.93	-	2	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15418067	15418106	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	intron	15418107	15418177	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	CDS	15418178	15418304	0.98	-	0	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	exon	15418178	15418304	.	-	.	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
Phchi.S1	AUGUSTUS	start_codon	15418302	15418304	.	-	0	transcript_id "Phchi.S1G235400.t1"; gene_id "Phchi.S1G235400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1488.t1 is derived from g8407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1152425	1156521	.	-	.	Phchi.S5G009700
Phchi.S5	AUGUSTUS	transcript	1152425	1156521	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	stop_codon	1152422	1152424	.	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1152425	1152499	0.36	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1152425	1152499	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1152500	1152624	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1152625	1152769	1	-	1	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1152625	1152769	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1152770	1152952	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1152953	1152994	1	-	1	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1152953	1152994	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1152995	1153138	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1153139	1153191	1	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1153139	1153191	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1153192	1153445	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1153446	1153895	0.96	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1153446	1153895	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1153896	1153989	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1153990	1154169	1	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1153990	1154169	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1154170	1154303	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1154304	1154383	1	-	2	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1154304	1154383	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1154384	1154596	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1154597	1154695	1	-	2	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1154597	1154695	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1154696	1155079	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1155080	1155232	0.93	-	2	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1155080	1155232	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	intron	1155233	1155812	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	CDS	1155813	1156521	0.83	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	exon	1155813	1156521	.	-	.	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
Phchi.S5	AUGUSTUS	start_codon	1156519	1156521	.	-	0	transcript_id "Phchi.S5G009700.t1"; gene_id "Phchi.S5G009700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10124.t1 is derived from g7300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45844918	45845931	.	+	.	Phchi.S1G728300
Phchi.S1	AUGUSTUS	transcript	45844918	45845931	.	+	.	transcript_id "Phchi.S1G728300.t1"; gene_id "Phchi.S1G728300"
Phchi.S1	AUGUSTUS	start_codon	45844918	45844920	.	+	0	transcript_id "Phchi.S1G728300.t1"; gene_id "Phchi.S1G728300"
Phchi.S1	AUGUSTUS	CDS	45844918	45845931	0.83	+	0	transcript_id "Phchi.S1G728300.t1"; gene_id "Phchi.S1G728300"
Phchi.S1	AUGUSTUS	exon	45844918	45845931	.	+	.	transcript_id "Phchi.S1G728300.t1"; gene_id "Phchi.S1G728300"
Phchi.S1	AUGUSTUS	stop_codon	45845932	45845934	.	+	0	transcript_id "Phchi.S1G728300.t1"; gene_id "Phchi.S1G728300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4028.t1 is derived from g1197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7228222	7229361	.	+	.	Phchi.S1G118700
Phchi.S1	AUGUSTUS	transcript	7228222	7229361	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	start_codon	7228222	7228224	.	+	0	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	CDS	7228222	7228304	1	+	0	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	exon	7228222	7228304	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	intron	7228305	7228387	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	CDS	7228388	7228574	1	+	1	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	exon	7228388	7228574	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	intron	7228575	7228667	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	CDS	7228668	7228874	1	+	0	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	exon	7228668	7228874	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	intron	7228875	7228948	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	CDS	7228949	7229143	1	+	0	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	exon	7228949	7229143	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	intron	7229144	7229226	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	CDS	7229227	7229361	1	+	0	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	exon	7229227	7229361	.	+	.	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
Phchi.S1	AUGUSTUS	stop_codon	7229362	7229364	.	+	0	transcript_id "Phchi.S1G118700.t1"; gene_id "Phchi.S1G118700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10200.t1 is derived from g7376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46349502	46350304	.	+	.	Phchi.S1G735900
Phchi.S1	AUGUSTUS	transcript	46349502	46350304	.	+	.	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	start_codon	46349502	46349504	.	+	0	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	CDS	46349502	46349584	0.89	+	0	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	exon	46349502	46349584	.	+	.	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	intron	46349585	46349780	.	+	.	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	CDS	46349781	46349832	0.91	+	1	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	exon	46349781	46349832	.	+	.	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	intron	46349833	46350175	.	+	.	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	CDS	46350176	46350304	0.78	+	0	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	exon	46350176	46350304	.	+	.	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
Phchi.S1	AUGUSTUS	stop_codon	46350305	46350307	.	+	0	transcript_id "Phchi.S1G735900.t1"; gene_id "Phchi.S1G735900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10257.t1 is derived from g7433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46717264	46717721	.	-	.	Phchi.S1G741600
Phchi.S1	AUGUSTUS	transcript	46717264	46717721	.	-	.	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	stop_codon	46717261	46717263	.	-	0	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	CDS	46717264	46717347	0.85	-	0	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	exon	46717264	46717347	.	-	.	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	intron	46717348	46717418	.	-	.	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	CDS	46717419	46717721	0.92	-	0	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	exon	46717419	46717721	.	-	.	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
Phchi.S1	AUGUSTUS	start_codon	46717719	46717721	.	-	0	transcript_id "Phchi.S1G741600.t1"; gene_id "Phchi.S1G741600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8071.t1 is derived from g5246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32801035	32802177	.	-	.	Phchi.S1G523000
Phchi.S1	AUGUSTUS	transcript	32801035	32802177	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	stop_codon	32801032	32801034	.	-	0	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	CDS	32801035	32801132	0.98	-	2	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	exon	32801035	32801132	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	intron	32801133	32801478	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	CDS	32801479	32801616	0.62	-	2	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	exon	32801479	32801616	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	intron	32801617	32801945	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	CDS	32801946	32801962	0.35	-	1	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	exon	32801946	32801962	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	intron	32801963	32802076	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	CDS	32802077	32802177	0.33	-	0	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	exon	32802077	32802177	.	-	.	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
Phchi.S1	AUGUSTUS	start_codon	32802175	32802177	.	-	0	transcript_id "Phchi.S1G523000.t1"; gene_id "Phchi.S1G523000"
# This transcript jg276.t2 is derived from g10058.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg277.t1 is derived from g10059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1997485	1999708	.	+	.	Phchi.S6G023600
Phchi.S6	AUGUSTUS	transcript	1997485	1999708	.	+	.	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	start_codon	1997485	1997487	.	+	0	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	CDS	1997485	1997602	0.02	+	0	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	exon	1997485	1997602	.	+	.	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	intron	1997603	1997702	.	+	.	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	CDS	1997703	1999708	0.98	+	2	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	exon	1997703	1999708	.	+	.	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
Phchi.S6	AUGUSTUS	stop_codon	1999709	1999711	.	+	0	transcript_id "Phchi.S6G023600.t1"; gene_id "Phchi.S6G023600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1776.t1 is derived from g8696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2967360	2968598	.	-	.	Phchi.S5G038500
Phchi.S5	AUGUSTUS	transcript	2967360	2968598	.	-	.	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	stop_codon	2967357	2967359	.	-	0	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	CDS	2967360	2967701	0.97	-	0	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	exon	2967360	2967701	.	-	.	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	intron	2967702	2968340	.	-	.	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	CDS	2968341	2968598	0.7	-	0	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	exon	2968341	2968598	.	-	.	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
Phchi.S5	AUGUSTUS	start_codon	2968596	2968598	.	-	0	transcript_id "Phchi.S5G038500.t1"; gene_id "Phchi.S5G038500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1368.t1 is derived from g9813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C217	AUGUSTUS	gene	18058	19297	.	+	.	Phchi.C217G000200
Phchi.C217	AUGUSTUS	transcript	18058	19297	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	start_codon	18058	18060	.	+	0	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	CDS	18058	18190	0.98	+	0	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	exon	18058	18190	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	intron	18191	18296	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	CDS	18297	18532	0.98	+	2	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	exon	18297	18532	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	intron	18533	18613	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	CDS	18614	18780	0.91	+	0	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	exon	18614	18780	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	intron	18781	18867	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	CDS	18868	19297	0.96	+	1	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	exon	18868	19297	.	+	.	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
Phchi.C217	AUGUSTUS	stop_codon	19298	19300	.	+	0	transcript_id "Phchi.C217G000200.t1"; gene_id "Phchi.C217G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10104.t1 is derived from g7280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45755758	45758517	.	-	.	Phchi.S1G726300
Phchi.S1	AUGUSTUS	transcript	45755758	45758517	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	stop_codon	45755755	45755757	.	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45755758	45755846	0.99	-	2	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45755758	45755846	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45755847	45755938	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45755939	45756057	1	-	1	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45755939	45756057	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45756058	45756155	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45756156	45756265	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45756156	45756265	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45756266	45756463	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45756464	45756565	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45756464	45756565	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45756566	45756668	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45756669	45756818	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45756669	45756818	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45756819	45756896	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45756897	45757052	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45756897	45757052	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45757053	45757214	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45757215	45757391	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45757215	45757391	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45757392	45757491	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45757492	45757581	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45757492	45757581	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45757582	45757673	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45757674	45757793	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45757674	45757793	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45757794	45757899	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45757900	45757995	1	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45757900	45757995	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45757996	45758092	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45758093	45758229	0.99	-	2	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45758093	45758229	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	intron	45758230	45758336	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	CDS	45758337	45758517	0.95	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	exon	45758337	45758517	.	-	.	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
Phchi.S1	AUGUSTUS	start_codon	45758515	45758517	.	-	0	transcript_id "Phchi.S1G726300.t1"; gene_id "Phchi.S1G726300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9797.t1 is derived from g6973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43735804	43736123	.	-	.	Phchi.S1G695600
Phchi.S1	AUGUSTUS	transcript	43735804	43736123	.	-	.	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	stop_codon	43735801	43735803	.	-	0	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	CDS	43735804	43735847	0.53	-	2	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	exon	43735804	43735847	.	-	.	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	intron	43735848	43735942	.	-	.	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	CDS	43735943	43736123	0.53	-	0	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	exon	43735943	43736123	.	-	.	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
Phchi.S1	AUGUSTUS	start_codon	43736121	43736123	.	-	0	transcript_id "Phchi.S1G695600.t1"; gene_id "Phchi.S1G695600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10712.t1 is derived from g14762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1713006	1714064	.	+	.	Phchi.S4G029400
Phchi.S4	AUGUSTUS	transcript	1713006	1714064	.	+	.	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	start_codon	1713006	1713008	.	+	0	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	CDS	1713006	1713894	0.9	+	0	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	exon	1713006	1713894	.	+	.	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	intron	1713895	1713996	.	+	.	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	CDS	1713997	1714064	0.75	+	2	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	exon	1713997	1714064	.	+	.	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
Phchi.S4	AUGUSTUS	stop_codon	1714065	1714067	.	+	0	transcript_id "Phchi.S4G029400.t1"; gene_id "Phchi.S4G029400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10513.t1 is derived from g14563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	775904	777192	.	-	.	Phchi.S4G009500
Phchi.S4	AUGUSTUS	transcript	775904	777192	.	-	.	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	stop_codon	775901	775903	.	-	0	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	CDS	775904	776266	1	-	0	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	exon	775904	776266	.	-	.	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	intron	776267	776359	.	-	.	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	CDS	776360	776711	1	-	1	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	exon	776360	776711	.	-	.	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	intron	776712	776800	.	-	.	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	CDS	776801	777192	0.76	-	0	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	exon	776801	777192	.	-	.	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
Phchi.S4	AUGUSTUS	start_codon	777190	777192	.	-	0	transcript_id "Phchi.S4G009500.t1"; gene_id "Phchi.S4G009500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9903.t1 is derived from g7079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44373702	44378874	.	-	.	Phchi.S1G706200
Phchi.S1	AUGUSTUS	transcript	44373702	44378874	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	stop_codon	44373699	44373701	.	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44373702	44374020	1	-	1	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44373702	44374020	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44374021	44374106	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44374107	44374225	1	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44374107	44374225	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44374226	44374314	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44374315	44374359	1	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44374315	44374359	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44374360	44374447	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44374448	44374677	0.45	-	2	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44374448	44374677	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44374678	44374769	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44374770	44374851	1	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44374770	44374851	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44374852	44374970	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44374971	44375030	1	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44374971	44375030	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44375031	44375107	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44375108	44375216	1	-	1	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44375108	44375216	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44375217	44375299	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44375300	44375343	1	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44375300	44375343	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44375344	44375433	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44375434	44375520	1	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44375434	44375520	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44375521	44375599	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44375600	44375675	1	-	1	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44375600	44375675	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44375676	44375809	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44375810	44376438	0.66	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44375810	44376438	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44376439	44376560	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44376561	44377334	0.96	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44376561	44377334	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44377335	44377448	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44377449	44377652	0.96	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44377449	44377652	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44377653	44377730	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44377731	44377927	0.94	-	2	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44377731	44377927	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44377928	44378039	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44378040	44378552	0.81	-	2	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44378040	44378552	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	intron	44378553	44378663	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	CDS	44378664	44378874	0.7	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	exon	44378664	44378874	.	-	.	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
Phchi.S1	AUGUSTUS	start_codon	44378872	44378874	.	-	0	transcript_id "Phchi.S1G706200.t1"; gene_id "Phchi.S1G706200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1679.t1 is derived from g8598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2474781	2476462	.	+	.	Phchi.S5G028800
Phchi.S5	AUGUSTUS	transcript	2474781	2476462	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	start_codon	2474781	2474783	.	+	0	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	CDS	2474781	2475714	0.41	+	0	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	exon	2474781	2475714	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	intron	2475715	2475875	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	CDS	2475876	2475895	1	+	2	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	exon	2475876	2475895	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	intron	2475896	2476118	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	CDS	2476119	2476297	0.45	+	0	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	exon	2476119	2476297	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	intron	2476298	2476410	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	CDS	2476411	2476462	0.45	+	1	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	exon	2476411	2476462	.	+	.	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
Phchi.S5	AUGUSTUS	stop_codon	2476463	2476465	.	+	0	transcript_id "Phchi.S5G028800.t1"; gene_id "Phchi.S5G028800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg346.t1 is derived from g10128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2526403	2527427	.	+	.	Phchi.S6G030500
Phchi.S6	AUGUSTUS	transcript	2526403	2527427	.	+	.	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	start_codon	2526403	2526405	.	+	0	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	CDS	2526403	2526954	0.28	+	0	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	exon	2526403	2526954	.	+	.	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	intron	2526955	2527088	.	+	.	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	CDS	2527089	2527427	0.42	+	0	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	exon	2527089	2527427	.	+	.	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
Phchi.S6	AUGUSTUS	stop_codon	2527428	2527430	.	+	0	transcript_id "Phchi.S6G030500.t1"; gene_id "Phchi.S6G030500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7537.t1 is derived from g4711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29946430	29947979	.	-	.	Phchi.S1G469600
Phchi.S1	AUGUSTUS	transcript	29946430	29947979	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	stop_codon	29946427	29946429	.	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29946430	29946459	0.46	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29946430	29946459	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29946460	29946562	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29946563	29946619	0.55	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29946563	29946619	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29946620	29946700	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29946701	29946745	0.86	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29946701	29946745	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29946746	29946864	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29946865	29946981	0.86	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29946865	29946981	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29946982	29947060	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29947061	29947317	0.99	-	2	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29947061	29947317	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29947318	29947424	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29947425	29947521	1	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29947425	29947521	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29947522	29947610	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29947611	29947843	0.99	-	2	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29947611	29947843	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	intron	29947844	29947927	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	CDS	29947928	29947979	0.82	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	exon	29947928	29947979	.	-	.	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
Phchi.S1	AUGUSTUS	start_codon	29947977	29947979	.	-	0	transcript_id "Phchi.S1G469600.t1"; gene_id "Phchi.S1G469600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8118.t1 is derived from g5293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33440634	33445059	.	+	.	Phchi.S1G527700
Phchi.S1	AUGUSTUS	transcript	33440634	33445059	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	start_codon	33440634	33440636	.	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33440634	33441240	0.96	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33440634	33441240	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33441241	33441477	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33441478	33441575	1	+	2	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33441478	33441575	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33441576	33441693	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33441694	33441867	1	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33441694	33441867	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33441868	33441957	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33441958	33442058	1	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33441958	33442058	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33442059	33442370	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33442371	33442506	1	+	1	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33442371	33442506	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33442507	33442682	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33442683	33442733	1	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33442683	33442733	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33442734	33442950	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33442951	33443232	0.99	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33442951	33443232	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33443233	33443969	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33443970	33444204	1	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33443970	33444204	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33444205	33444458	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33444459	33444598	1	+	2	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33444459	33444598	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33444599	33444691	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33444692	33444739	0.9	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33444692	33444739	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	intron	33444740	33444840	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	CDS	33444841	33445059	0.86	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	exon	33444841	33445059	.	+	.	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
Phchi.S1	AUGUSTUS	stop_codon	33445060	33445062	.	+	0	transcript_id "Phchi.S1G527700.t1"; gene_id "Phchi.S1G527700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13319.t1 is derived from g11785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6089325	6091448	.	-	.	Phchi.S3G063800
Phchi.S3	AUGUSTUS	transcript	6089325	6091448	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	stop_codon	6089322	6089324	.	-	0	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	CDS	6089325	6089583	0.92	-	1	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	exon	6089325	6089583	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	intron	6089584	6089693	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	CDS	6089694	6090061	1	-	0	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	exon	6089694	6090061	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	intron	6090062	6090208	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	CDS	6090209	6090502	1	-	0	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	exon	6090209	6090502	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	intron	6090503	6090678	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	CDS	6090679	6090967	1	-	1	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	exon	6090679	6090967	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	intron	6090968	6091059	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	CDS	6091060	6091448	0.96	-	0	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	exon	6091060	6091448	.	-	.	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
Phchi.S3	AUGUSTUS	start_codon	6091446	6091448	.	-	0	transcript_id "Phchi.S3G063800.t1"; gene_id "Phchi.S3G063800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7001.t1 is derived from g4173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26346055	26349242	.	+	.	Phchi.S1G416000
Phchi.S1	AUGUSTUS	transcript	26346055	26349242	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	start_codon	26346055	26346057	.	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26346055	26346438	0.38	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26346055	26346438	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26346439	26346579	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26346580	26346626	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26346580	26346626	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26346627	26346753	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26346754	26346793	1	+	1	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26346754	26346793	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26346794	26346948	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26346949	26346969	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26346949	26346969	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26346970	26347061	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26347062	26347199	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26347062	26347199	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26347200	26347384	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26347385	26347468	0.95	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26347385	26347468	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26347469	26347647	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26347648	26347701	0.98	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26347648	26347701	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26347702	26347777	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26347778	26347846	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26347778	26347846	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26347847	26347932	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26347933	26348062	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26347933	26348062	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26348063	26348174	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26348175	26348215	1	+	2	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26348175	26348215	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26348216	26348301	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26348302	26348529	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26348302	26348529	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26348530	26348635	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26348636	26348684	1	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26348636	26348684	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26348685	26348780	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26348781	26348935	1	+	2	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26348781	26348935	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	intron	26348936	26349065	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	CDS	26349066	26349242	0.95	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	exon	26349066	26349242	.	+	.	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
Phchi.S1	AUGUSTUS	stop_codon	26349243	26349245	.	+	0	transcript_id "Phchi.S1G416000.t1"; gene_id "Phchi.S1G416000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1438.t1 is derived from g8357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	848642	849346	.	-	.	Phchi.S5G004700
Phchi.S5	AUGUSTUS	transcript	848642	849346	.	-	.	transcript_id "Phchi.S5G004700.t1"; gene_id "Phchi.S5G004700"
Phchi.S5	AUGUSTUS	stop_codon	848639	848641	.	-	0	transcript_id "Phchi.S5G004700.t1"; gene_id "Phchi.S5G004700"
Phchi.S5	AUGUSTUS	CDS	848642	849346	0.45	-	0	transcript_id "Phchi.S5G004700.t1"; gene_id "Phchi.S5G004700"
Phchi.S5	AUGUSTUS	exon	848642	849346	.	-	.	transcript_id "Phchi.S5G004700.t1"; gene_id "Phchi.S5G004700"
Phchi.S5	AUGUSTUS	start_codon	849344	849346	.	-	0	transcript_id "Phchi.S5G004700.t1"; gene_id "Phchi.S5G004700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9705.t1 is derived from g6881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43346683	43348386	.	+	.	Phchi.S1G686400
Phchi.S1	AUGUSTUS	transcript	43346683	43348386	.	+	.	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	start_codon	43346683	43346685	.	+	0	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	CDS	43346683	43347761	0.68	+	0	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	exon	43346683	43347761	.	+	.	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	intron	43347762	43347882	.	+	.	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	CDS	43347883	43347915	0.87	+	1	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	exon	43347883	43347915	.	+	.	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	intron	43347916	43348301	.	+	.	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	CDS	43348302	43348386	0.86	+	1	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	exon	43348302	43348386	.	+	.	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
Phchi.S1	AUGUSTUS	stop_codon	43348387	43348389	.	+	0	transcript_id "Phchi.S1G686400.t1"; gene_id "Phchi.S1G686400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1692.t1 is derived from g8611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2525918	2528052	.	+	.	Phchi.S5G030100
Phchi.S5	AUGUSTUS	transcript	2525918	2528052	.	+	.	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	start_codon	2525918	2525920	.	+	0	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	CDS	2525918	2526272	0.97	+	0	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	exon	2525918	2526272	.	+	.	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	intron	2526273	2526418	.	+	.	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	CDS	2526419	2528052	0.95	+	2	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	exon	2526419	2528052	.	+	.	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
Phchi.S5	AUGUSTUS	stop_codon	2528053	2528055	.	+	0	transcript_id "Phchi.S5G030100.t1"; gene_id "Phchi.S5G030100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1900.t1 is derived from g8820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3781104	3781987	.	+	.	Phchi.S5G050900
Phchi.S5	AUGUSTUS	transcript	3781104	3781987	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	start_codon	3781104	3781106	.	+	0	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	CDS	3781104	3781181	0.96	+	0	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	exon	3781104	3781181	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	intron	3781182	3781276	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	CDS	3781277	3781390	0.82	+	0	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	exon	3781277	3781390	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	intron	3781391	3781502	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	CDS	3781503	3781637	0.99	+	0	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	exon	3781503	3781637	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	intron	3781638	3781717	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	CDS	3781718	3781987	0.91	+	0	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	exon	3781718	3781987	.	+	.	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
Phchi.S5	AUGUSTUS	stop_codon	3781988	3781990	.	+	0	transcript_id "Phchi.S5G050900.t1"; gene_id "Phchi.S5G050900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7590.t1 is derived from g4764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30178564	30181729	.	+	.	Phchi.S1G474900
Phchi.S1	AUGUSTUS	transcript	30178564	30181729	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	start_codon	30178564	30178566	.	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30178564	30178785	0.89	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30178564	30178785	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30178786	30178889	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30178890	30179003	1	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30178890	30179003	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30179004	30179217	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30179218	30179278	0.75	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30179218	30179278	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30179279	30179510	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30179511	30179641	0.99	+	2	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30179511	30179641	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30179642	30179793	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30179794	30179946	1	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30179794	30179946	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30179947	30180033	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30180034	30180171	1	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30180034	30180171	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30180172	30180325	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30180326	30180430	0.83	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30180326	30180430	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30180431	30180707	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30180708	30180722	0.97	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30180708	30180722	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30180723	30180902	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30180903	30180965	1	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30180903	30180965	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30180966	30181167	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30181168	30181370	0.89	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30181168	30181370	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30181371	30181597	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30181598	30181635	0.87	+	1	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30181598	30181635	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	intron	30181636	30181727	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	CDS	30181728	30181729	0.87	+	2	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	exon	30181728	30181729	.	+	.	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
Phchi.S1	AUGUSTUS	stop_codon	30181730	30181732	.	+	0	transcript_id "Phchi.S1G474900.t1"; gene_id "Phchi.S1G474900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12753.t1 is derived from g11218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1896165	1897591	.	-	.	Phchi.S3G007200
Phchi.S3	AUGUSTUS	transcript	1896165	1897591	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	stop_codon	1896162	1896164	.	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1896165	1896282	0.63	-	1	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1896165	1896282	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1896283	1896376	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1896377	1896500	1	-	2	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1896377	1896500	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1896501	1896640	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1896641	1896791	1	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1896641	1896791	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1896792	1896865	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1896866	1896952	1	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1896866	1896952	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1896953	1897035	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1897036	1897098	1	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1897036	1897098	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1897099	1897235	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1897236	1897307	1	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1897236	1897307	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1897308	1897397	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1897398	1897483	1	-	2	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1897398	1897483	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	intron	1897484	1897578	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	CDS	1897579	1897591	0.72	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	exon	1897579	1897591	.	-	.	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
Phchi.S3	AUGUSTUS	start_codon	1897589	1897591	.	-	0	transcript_id "Phchi.S3G007200.t1"; gene_id "Phchi.S3G007200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9589.t1 is derived from g6765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42806948	42809338	.	-	.	Phchi.S1G674800
Phchi.S1	AUGUSTUS	transcript	42806948	42809338	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	stop_codon	42806945	42806947	.	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42806948	42807105	1	-	2	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42806948	42807105	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42807106	42807191	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42807192	42807297	1	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42807192	42807297	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42807298	42807382	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42807383	42807622	1	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42807383	42807622	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42807623	42807704	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42807705	42807872	0.59	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42807705	42807872	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42807873	42808007	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42808008	42808197	1	-	1	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42808008	42808197	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42808198	42808294	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42808295	42808410	1	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42808295	42808410	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42808411	42808555	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42808556	42808681	1	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42808556	42808681	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42808682	42808861	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42808862	42808982	1	-	1	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42808862	42808982	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42808983	42809107	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42809108	42809233	1	-	1	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42809108	42809233	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	intron	42809234	42809318	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	CDS	42809319	42809338	1	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	exon	42809319	42809338	.	-	.	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
Phchi.S1	AUGUSTUS	start_codon	42809336	42809338	.	-	0	transcript_id "Phchi.S1G674800.t1"; gene_id "Phchi.S1G674800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1819.t1 is derived from g8739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3309929	3310775	.	-	.	Phchi.S5G042800
Phchi.S5	AUGUSTUS	transcript	3309929	3310775	.	-	.	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	stop_codon	3309926	3309928	.	-	0	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	CDS	3309929	3310210	0.88	-	0	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	exon	3309929	3310210	.	-	.	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	intron	3310211	3310290	.	-	.	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	CDS	3310291	3310494	1	-	0	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	exon	3310291	3310494	.	-	.	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	intron	3310495	3310571	.	-	.	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	CDS	3310572	3310775	0.99	-	0	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	exon	3310572	3310775	.	-	.	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
Phchi.S5	AUGUSTUS	start_codon	3310773	3310775	.	-	0	transcript_id "Phchi.S5G042800.t1"; gene_id "Phchi.S5G042800"
# This transcript jg5582.t2 is derived from g2752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5583.t1 is derived from g2753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17739693	17740317	.	+	.	Phchi.S1G274200
Phchi.S1	AUGUSTUS	transcript	17739693	17740317	.	+	.	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	start_codon	17739693	17739695	.	+	0	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	CDS	17739693	17739732	1	+	0	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	exon	17739693	17739732	.	+	.	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	intron	17739733	17739870	.	+	.	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	CDS	17739871	17740034	1	+	2	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	exon	17739871	17740034	.	+	.	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	intron	17740035	17740203	.	+	.	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	CDS	17740204	17740317	0.77	+	0	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	exon	17740204	17740317	.	+	.	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
Phchi.S1	AUGUSTUS	stop_codon	17740318	17740320	.	+	0	transcript_id "Phchi.S1G274200.t1"; gene_id "Phchi.S1G274200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1200.t1 is derived from g10983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8385664	8386853	.	+	.	Phchi.S6G115900
Phchi.S6	AUGUSTUS	transcript	8385664	8386853	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	start_codon	8385664	8385666	.	+	0	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	CDS	8385664	8385932	1	+	0	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	exon	8385664	8385932	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	intron	8385933	8386052	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	CDS	8386053	8386165	1	+	1	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	exon	8386053	8386165	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	intron	8386166	8386247	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	CDS	8386248	8386366	1	+	2	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	exon	8386248	8386366	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	intron	8386367	8386462	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	CDS	8386463	8386511	1	+	0	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	exon	8386463	8386511	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	intron	8386512	8386590	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	CDS	8386591	8386853	1	+	2	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	exon	8386591	8386853	.	+	.	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
Phchi.S6	AUGUSTUS	stop_codon	8386854	8386856	.	+	0	transcript_id "Phchi.S6G115900.t1"; gene_id "Phchi.S6G115900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10013.t1 is derived from g7189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45051298	45052238	.	-	.	Phchi.S1G717200
Phchi.S1	AUGUSTUS	transcript	45051298	45052238	.	-	.	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	stop_codon	45051295	45051297	.	-	0	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	CDS	45051298	45051887	0.94	-	2	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	exon	45051298	45051887	.	-	.	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	intron	45051888	45051970	.	-	.	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	CDS	45051971	45052238	0.63	-	0	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	exon	45051971	45052238	.	-	.	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
Phchi.S1	AUGUSTUS	start_codon	45052236	45052238	.	-	0	transcript_id "Phchi.S1G717200.t1"; gene_id "Phchi.S1G717200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3491.t1 is derived from g660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4037015	4037696	.	-	.	Phchi.S1G065000
Phchi.S1	AUGUSTUS	transcript	4037015	4037696	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	stop_codon	4037012	4037014	.	-	0	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	CDS	4037015	4037033	1	-	1	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	exon	4037015	4037033	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	intron	4037034	4037188	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	CDS	4037189	4037278	0.52	-	1	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	exon	4037189	4037278	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	intron	4037279	4037387	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	CDS	4037388	4037579	0.89	-	1	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	exon	4037388	4037579	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	intron	4037580	4037673	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	CDS	4037674	4037696	0.87	-	0	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	exon	4037674	4037696	.	-	.	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
Phchi.S1	AUGUSTUS	start_codon	4037694	4037696	.	-	0	transcript_id "Phchi.S1G065000.t1"; gene_id "Phchi.S1G065000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2352.t1 is derived from g9272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6317241	6319087	.	+	.	Phchi.S5G096100
Phchi.S5	AUGUSTUS	transcript	6317241	6319087	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	start_codon	6317241	6317243	.	+	0	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	CDS	6317241	6317282	1	+	0	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	exon	6317241	6317282	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	intron	6317283	6317915	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	CDS	6317916	6317955	1	+	0	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	exon	6317916	6317955	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	intron	6317956	6318045	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	CDS	6318046	6318123	1	+	2	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	exon	6318046	6318123	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	intron	6318124	6318209	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	CDS	6318210	6318408	1	+	2	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	exon	6318210	6318408	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	intron	6318409	6318498	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	CDS	6318499	6318775	1	+	1	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	exon	6318499	6318775	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	intron	6318776	6318868	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	CDS	6318869	6319087	1	+	0	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	exon	6318869	6319087	.	+	.	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
Phchi.S5	AUGUSTUS	stop_codon	6319088	6319090	.	+	0	transcript_id "Phchi.S5G096100.t1"; gene_id "Phchi.S5G096100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9954.t1 is derived from g7130.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44641441	44644794	.	+	.	Phchi.S1G711300
Phchi.S1	AUGUSTUS	transcript	44641441	44644794	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	start_codon	44641441	44641443	.	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44641441	44641466	0.88	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44641441	44641466	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44641467	44641554	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44641555	44641590	0.83	+	1	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44641555	44641590	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44641591	44641667	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44641668	44641817	0.66	+	1	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44641668	44641817	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44641818	44642107	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642108	44642250	0.97	+	1	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642108	44642250	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44642251	44642379	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642380	44642447	0.99	+	2	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642380	44642447	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44642448	44642758	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642759	44642869	0.99	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642759	44642869	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44642870	44642989	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642990	44643173	1	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642990	44643173	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643174	44643264	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44643265	44643371	0.97	+	2	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44643265	44643371	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643372	44643581	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44643582	44643633	1	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44643582	44643633	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643634	44643878	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44643879	44643929	1	+	2	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44643879	44643929	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643930	44644270	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44644271	44644358	0.99	+	2	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44644271	44644358	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44644359	44644450	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44644451	44644544	1	+	1	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44644451	44644544	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44644545	44644641	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44644642	44644794	1	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44644642	44644794	.	+	.	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	stop_codon	44644795	44644797	.	+	0	transcript_id "Phchi.S1G711300.t1"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	transcript	44641441	44644794	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	start_codon	44641441	44641443	.	+	0	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44641441	44641466	0.84	+	0	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44641441	44641466	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44641467	44641554	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44641555	44641590	0.81	+	1	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44641555	44641590	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44641591	44641667	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44641668	44641817	0.64	+	1	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44641668	44641817	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44641818	44642107	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642108	44642250	1	+	1	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642108	44642250	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44642251	44642379	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642380	44642447	1	+	2	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642380	44642447	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44642448	44642758	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642759	44642869	0.99	+	0	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642759	44642869	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44642870	44642989	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44642990	44643173	1	+	0	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44642990	44643173	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643174	44643264	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44643265	44643537	1	+	2	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44643265	44643537	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643538	44643878	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44643879	44643929	1	+	2	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44643879	44643929	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44643930	44644270	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44644271	44644358	0.99	+	2	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44644271	44644358	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44644359	44644450	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44644451	44644544	1	+	1	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44644451	44644544	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	intron	44644545	44644641	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	CDS	44644642	44644794	1	+	0	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	exon	44644642	44644794	.	+	.	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
Phchi.S1	AUGUSTUS	stop_codon	44644795	44644797	.	+	0	transcript_id "Phchi.S1G711300.t2"; gene_id "Phchi.S1G711300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14360.t1 is derived from g12827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12360558	12362278	.	+	.	Phchi.S3G167900
Phchi.S3	AUGUSTUS	transcript	12360558	12362278	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	start_codon	12360558	12360560	.	+	0	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	CDS	12360558	12361107	0.74	+	0	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	exon	12360558	12361107	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	intron	12361108	12361210	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	CDS	12361211	12361288	1	+	2	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	exon	12361211	12361288	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	intron	12361289	12361370	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	CDS	12361371	12361477	1	+	2	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	exon	12361371	12361477	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	intron	12361478	12361622	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	CDS	12361623	12361800	1	+	0	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	exon	12361623	12361800	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	intron	12361801	12361916	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	CDS	12361917	12362070	1	+	2	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	exon	12361917	12362070	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	intron	12362071	12362166	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	CDS	12362167	12362278	0.97	+	1	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	exon	12362167	12362278	.	+	.	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
Phchi.S3	AUGUSTUS	stop_codon	12362279	12362281	.	+	0	transcript_id "Phchi.S3G167900.t1"; gene_id "Phchi.S3G167900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14146.t1 is derived from g12613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11160451	11161341	.	+	.	Phchi.S3G146500
Phchi.S3	AUGUSTUS	transcript	11160451	11161341	.	+	.	transcript_id "Phchi.S3G146500.t1"; gene_id "Phchi.S3G146500"
Phchi.S3	AUGUSTUS	start_codon	11160451	11160453	.	+	0	transcript_id "Phchi.S3G146500.t1"; gene_id "Phchi.S3G146500"
Phchi.S3	AUGUSTUS	CDS	11160451	11161341	1	+	0	transcript_id "Phchi.S3G146500.t1"; gene_id "Phchi.S3G146500"
Phchi.S3	AUGUSTUS	exon	11160451	11161341	.	+	.	transcript_id "Phchi.S3G146500.t1"; gene_id "Phchi.S3G146500"
Phchi.S3	AUGUSTUS	stop_codon	11161342	11161344	.	+	0	transcript_id "Phchi.S3G146500.t1"; gene_id "Phchi.S3G146500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14284.t1 is derived from g12751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11913592	11916560	.	+	.	Phchi.S3G160300
Phchi.S3	AUGUSTUS	transcript	11913592	11916560	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	start_codon	11913592	11913594	.	+	0	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11913592	11913627	0.66	+	0	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11913592	11913627	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11913628	11913749	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11913750	11913843	1	+	0	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11913750	11913843	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11913844	11913967	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11913968	11914237	1	+	2	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11913968	11914237	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11914238	11914335	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11914336	11914377	0.79	+	2	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11914336	11914377	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11914378	11914550	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11914551	11914589	0.74	+	2	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11914551	11914589	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11914590	11914827	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11914828	11914952	1	+	2	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11914828	11914952	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11914953	11915054	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11915055	11915531	1	+	0	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11915055	11915531	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	intron	11915532	11915645	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	CDS	11915646	11916560	1	+	0	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	exon	11915646	11916560	.	+	.	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
Phchi.S3	AUGUSTUS	stop_codon	11916561	11916563	.	+	0	transcript_id "Phchi.S3G160300.t1"; gene_id "Phchi.S3G160300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4665.t1 is derived from g1835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11705134	11705343	.	-	.	Phchi.S1G182400
Phchi.S1	AUGUSTUS	transcript	11705134	11705343	.	-	.	transcript_id "Phchi.S1G182400.t1"; gene_id "Phchi.S1G182400"
Phchi.S1	AUGUSTUS	stop_codon	11705131	11705133	.	-	0	transcript_id "Phchi.S1G182400.t1"; gene_id "Phchi.S1G182400"
Phchi.S1	AUGUSTUS	CDS	11705134	11705343	0.68	-	0	transcript_id "Phchi.S1G182400.t1"; gene_id "Phchi.S1G182400"
Phchi.S1	AUGUSTUS	exon	11705134	11705343	.	-	.	transcript_id "Phchi.S1G182400.t1"; gene_id "Phchi.S1G182400"
Phchi.S1	AUGUSTUS	start_codon	11705341	11705343	.	-	0	transcript_id "Phchi.S1G182400.t1"; gene_id "Phchi.S1G182400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4410.t1 is derived from g1579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10268429	10269193	.	-	.	Phchi.S1G156900
Phchi.S1	AUGUSTUS	transcript	10268429	10269193	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	stop_codon	10268426	10268428	.	-	0	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10268429	10268548	0.99	-	0	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10268429	10268548	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	intron	10268549	10268645	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10268646	10268717	0.83	-	0	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10268646	10268717	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	intron	10268718	10268833	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10268834	10268884	0.93	-	0	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10268834	10268884	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	intron	10268885	10269151	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10269152	10269193	1	-	0	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10269152	10269193	.	-	.	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	start_codon	10269191	10269193	.	-	0	transcript_id "Phchi.S1G156900.t1"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	transcript	10268429	10269193	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	stop_codon	10268426	10268428	.	-	0	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10268429	10268548	0.9	-	0	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10268429	10268548	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	intron	10268549	10268632	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10268633	10268675	0.87	-	1	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10268633	10268675	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	intron	10268676	10268819	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10268820	10268884	0.87	-	0	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10268820	10268884	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	intron	10268885	10269151	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	CDS	10269152	10269193	1	-	0	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	exon	10269152	10269193	.	-	.	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
Phchi.S1	AUGUSTUS	start_codon	10269191	10269193	.	-	0	transcript_id "Phchi.S1G156900.t2"; gene_id "Phchi.S1G156900"
# This transcript jg9316.t2 is derived from g6491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9317.t1 is derived from g6492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40918599	40923001	.	+	.	Phchi.S1G647600
Phchi.S1	AUGUSTUS	transcript	40918599	40923001	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	start_codon	40918599	40918601	.	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40918599	40919009	0.99	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40918599	40919009	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40919010	40919090	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40919091	40919228	1	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40919091	40919228	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40919229	40919306	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40919307	40919429	0.99	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40919307	40919429	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40919430	40919534	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40919535	40919723	0.99	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40919535	40919723	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40919724	40919900	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40919901	40919959	0.95	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40919901	40919959	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40919960	40920097	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40920098	40920125	0.92	+	1	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40920098	40920125	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40920126	40920208	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40920209	40920358	0.93	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40920209	40920358	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40920359	40920462	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40920463	40920551	0.98	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40920463	40920551	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40920552	40920718	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40920719	40920811	1	+	1	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40920719	40920811	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40920812	40920918	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40920919	40921012	1	+	1	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40920919	40921012	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40921013	40921203	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40921204	40921257	0.99	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40921204	40921257	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40921258	40921358	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40921359	40921490	0.43	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40921359	40921490	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40921491	40921613	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40921614	40921781	1	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40921614	40921781	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40921782	40921859	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40921860	40921939	1	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40921860	40921939	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40921940	40922027	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40922028	40922100	1	+	1	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40922028	40922100	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40922101	40922209	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40922210	40922424	1	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40922210	40922424	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40922425	40922523	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40922524	40922608	0.88	+	1	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40922524	40922608	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40922609	40922727	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40922728	40922866	1	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40922728	40922866	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	intron	40922867	40922945	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	CDS	40922946	40923001	1	+	2	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	exon	40922946	40923001	.	+	.	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
Phchi.S1	AUGUSTUS	stop_codon	40923002	40923004	.	+	0	transcript_id "Phchi.S1G647600.t1"; gene_id "Phchi.S1G647600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7802.t1 is derived from g4976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31254776	31256183	.	+	.	Phchi.S1G496100
Phchi.S1	AUGUSTUS	transcript	31254776	31256183	.	+	.	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	start_codon	31254776	31254778	.	+	0	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	CDS	31254776	31255230	1	+	0	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	exon	31254776	31255230	.	+	.	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	intron	31255231	31255570	.	+	.	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	CDS	31255571	31256183	1	+	1	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	exon	31255571	31256183	.	+	.	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
Phchi.S1	AUGUSTUS	stop_codon	31256184	31256186	.	+	0	transcript_id "Phchi.S1G496100.t1"; gene_id "Phchi.S1G496100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13716.t1 is derived from g12183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8487033	8487386	.	+	.	Phchi.S3G103500
Phchi.S3	AUGUSTUS	transcript	8487033	8487386	.	+	.	transcript_id "Phchi.S3G103500.t1"; gene_id "Phchi.S3G103500"
Phchi.S3	AUGUSTUS	start_codon	8487033	8487035	.	+	0	transcript_id "Phchi.S3G103500.t1"; gene_id "Phchi.S3G103500"
Phchi.S3	AUGUSTUS	CDS	8487033	8487386	0.83	+	0	transcript_id "Phchi.S3G103500.t1"; gene_id "Phchi.S3G103500"
Phchi.S3	AUGUSTUS	exon	8487033	8487386	.	+	.	transcript_id "Phchi.S3G103500.t1"; gene_id "Phchi.S3G103500"
Phchi.S3	AUGUSTUS	stop_codon	8487387	8487389	.	+	0	transcript_id "Phchi.S3G103500.t1"; gene_id "Phchi.S3G103500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12460.t1 is derived from g8137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24370750	24371295	.	-	.	Phchi.S2G054000
Phchi.S2	AUGUSTUS	transcript	24370750	24371295	.	-	.	transcript_id "Phchi.S2G054000.t1"; gene_id "Phchi.S2G054000"
Phchi.S2	AUGUSTUS	stop_codon	24370747	24370749	.	-	0	transcript_id "Phchi.S2G054000.t1"; gene_id "Phchi.S2G054000"
Phchi.S2	AUGUSTUS	CDS	24370750	24371295	0.54	-	0	transcript_id "Phchi.S2G054000.t1"; gene_id "Phchi.S2G054000"
Phchi.S2	AUGUSTUS	exon	24370750	24371295	.	-	.	transcript_id "Phchi.S2G054000.t1"; gene_id "Phchi.S2G054000"
Phchi.S2	AUGUSTUS	start_codon	24371293	24371295	.	-	0	transcript_id "Phchi.S2G054000.t1"; gene_id "Phchi.S2G054000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13221.t1 is derived from g11686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4744119	4744796	.	-	.	Phchi.S3G054000
Phchi.S3	AUGUSTUS	transcript	4744119	4744796	.	-	.	transcript_id "Phchi.S3G054000.t1"; gene_id "Phchi.S3G054000"
Phchi.S3	AUGUSTUS	stop_codon	4744116	4744118	.	-	0	transcript_id "Phchi.S3G054000.t1"; gene_id "Phchi.S3G054000"
Phchi.S3	AUGUSTUS	CDS	4744119	4744796	0.89	-	0	transcript_id "Phchi.S3G054000.t1"; gene_id "Phchi.S3G054000"
Phchi.S3	AUGUSTUS	exon	4744119	4744796	.	-	.	transcript_id "Phchi.S3G054000.t1"; gene_id "Phchi.S3G054000"
Phchi.S3	AUGUSTUS	start_codon	4744794	4744796	.	-	0	transcript_id "Phchi.S3G054000.t1"; gene_id "Phchi.S3G054000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9558.t1 is derived from g6734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42657154	42660143	.	-	.	Phchi.S1G671700
Phchi.S1	AUGUSTUS	transcript	42657154	42660143	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	stop_codon	42657151	42657153	.	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42657154	42657288	0.98	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42657154	42657288	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42657289	42657378	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42657379	42657492	1	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42657379	42657492	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42657493	42657577	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42657578	42657679	1	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42657578	42657679	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42657680	42657794	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42657795	42657912	0.67	-	1	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42657795	42657912	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42657913	42657991	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42657992	42658176	1	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42657992	42658176	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42658177	42658264	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42658265	42658481	1	-	1	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42658265	42658481	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42658482	42658566	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42658567	42658697	0.86	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42658567	42658697	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42658698	42658819	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42658820	42658943	1	-	1	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42658820	42658943	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42658944	42659025	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42659026	42659128	1	-	2	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42659026	42659128	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42659129	42659377	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42659378	42659437	0.95	-	2	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42659378	42659437	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42659438	42659565	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42659566	42659665	0.94	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42659566	42659665	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42659666	42659743	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42659744	42659984	1	-	1	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42659744	42659984	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	intron	42659985	42660072	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	CDS	42660073	42660143	1	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	exon	42660073	42660143	.	-	.	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
Phchi.S1	AUGUSTUS	start_codon	42660141	42660143	.	-	0	transcript_id "Phchi.S1G671700.t1"; gene_id "Phchi.S1G671700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12283.t1 is derived from g7959.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8749933	8751200	.	+	.	Phchi.S2G036300
Phchi.S2	AUGUSTUS	transcript	8749933	8751200	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	start_codon	8749933	8749935	.	+	0	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	CDS	8749933	8749943	0.81	+	0	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	exon	8749933	8749943	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	intron	8749944	8750165	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	CDS	8750166	8750297	0.98	+	1	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	exon	8750166	8750297	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	intron	8750298	8750404	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	CDS	8750405	8750498	0.97	+	1	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	exon	8750405	8750498	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	intron	8750499	8750651	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	CDS	8750652	8750681	0.97	+	0	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	exon	8750652	8750681	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	intron	8750682	8750927	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	CDS	8750928	8751044	1	+	0	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	exon	8750928	8751044	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	intron	8751045	8751164	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	CDS	8751165	8751200	0.92	+	0	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	exon	8751165	8751200	.	+	.	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
Phchi.S2	AUGUSTUS	stop_codon	8751201	8751203	.	+	0	transcript_id "Phchi.S2G036300.t1"; gene_id "Phchi.S2G036300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14837.t1 is derived from g13305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14934352	14942147	.	-	.	Phchi.S3G215600
Phchi.S3	AUGUSTUS	transcript	14934352	14942147	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	stop_codon	14934349	14934351	.	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14934352	14934474	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14934352	14934474	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14934475	14934554	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14934555	14934659	0.97	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14934555	14934659	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14934660	14934767	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14934768	14934908	0.95	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14934768	14934908	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14934909	14935030	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14935031	14935168	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14935031	14935168	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14935169	14935295	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14935296	14935403	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14935296	14935403	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14935404	14935613	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14935614	14935724	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14935614	14935724	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14935725	14935821	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14935822	14935888	1	-	1	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14935822	14935888	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14935889	14936010	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14936011	14936193	1	-	1	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14936011	14936193	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14936194	14936292	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14936293	14936373	1	-	1	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14936293	14936373	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14936374	14936612	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14936613	14936698	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14936613	14936698	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14936699	14936824	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14936825	14936914	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14936825	14936914	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14936915	14937015	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14937016	14937096	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14937016	14937096	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14937097	14937184	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14937185	14937283	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14937185	14937283	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14937284	14937383	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14937384	14937449	0.99	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14937384	14937449	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14937450	14937555	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14937556	14937664	0.69	-	1	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14937556	14937664	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14937665	14937772	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14937773	14937870	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14937773	14937870	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14937871	14938041	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14938042	14938152	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14938042	14938152	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14938153	14938235	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14938236	14938295	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14938236	14938295	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14938296	14938439	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14938440	14938640	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14938440	14938640	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14938641	14938731	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14938732	14938824	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14938732	14938824	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14938825	14938941	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14938942	14939049	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14938942	14939049	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14939050	14939258	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14939259	14939303	0.99	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14939259	14939303	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14939304	14939407	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14939408	14939470	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14939408	14939470	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14939471	14939599	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14939600	14939677	0.95	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14939600	14939677	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14939678	14939782	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14939783	14939851	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14939783	14939851	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14939852	14939987	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14939988	14940126	1	-	1	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14939988	14940126	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14940127	14940244	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14940245	14940327	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14940245	14940327	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14940328	14940400	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14940401	14940508	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14940401	14940508	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14940509	14940588	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14940589	14940660	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14940589	14940660	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14940661	14940759	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14940760	14940852	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14940760	14940852	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14940853	14940995	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14940996	14941112	1	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14940996	14941112	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	intron	14941113	14942051	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	CDS	14942052	14942147	0.88	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	exon	14942052	14942147	.	-	.	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
Phchi.S3	AUGUSTUS	start_codon	14942145	14942147	.	-	0	transcript_id "Phchi.S3G215600.t1"; gene_id "Phchi.S3G215600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13769.t1 is derived from g12236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8829989	8832077	.	+	.	Phchi.S3G108800
Phchi.S3	AUGUSTUS	transcript	8829989	8832077	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	start_codon	8829989	8829991	.	+	0	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8829989	8830048	0.38	+	0	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8829989	8830048	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8830049	8830341	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8830342	8830393	0.43	+	0	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8830342	8830393	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8830394	8830469	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8830470	8830649	1	+	2	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8830470	8830649	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8830650	8830812	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8830813	8831012	1	+	2	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8830813	8831012	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8831013	8831100	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8831101	8831194	1	+	0	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8831101	8831194	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8831195	8831310	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8831311	8831348	1	+	2	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8831311	8831348	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8831349	8831424	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8831425	8831560	1	+	0	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8831425	8831560	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	intron	8831561	8831643	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	CDS	8831644	8832077	0.97	+	2	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	exon	8831644	8832077	.	+	.	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
Phchi.S3	AUGUSTUS	stop_codon	8832078	8832080	.	+	0	transcript_id "Phchi.S3G108800.t1"; gene_id "Phchi.S3G108800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15151.t1 is derived from g13619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17277079	17280029	.	+	.	Phchi.S3G247000
Phchi.S3	AUGUSTUS	transcript	17277079	17280029	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	start_codon	17277079	17277081	.	+	0	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	CDS	17277079	17277343	0.52	+	0	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	exon	17277079	17277343	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	intron	17277344	17277585	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	CDS	17277586	17277788	1	+	2	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	exon	17277586	17277788	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	intron	17277789	17277874	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	CDS	17277875	17279207	0.99	+	0	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	exon	17277875	17279207	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	intron	17279208	17279302	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	CDS	17279303	17279673	1	+	2	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	exon	17279303	17279673	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	intron	17279674	17279752	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	CDS	17279753	17279821	0.51	+	0	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	exon	17279753	17279821	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	intron	17279822	17279900	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	CDS	17279901	17280029	1	+	0	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	exon	17279901	17280029	.	+	.	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
Phchi.S3	AUGUSTUS	stop_codon	17280030	17280032	.	+	0	transcript_id "Phchi.S3G247000.t1"; gene_id "Phchi.S3G247000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg393.t1 is derived from g10175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2862765	2863840	.	+	.	Phchi.S6G035200
Phchi.S6	AUGUSTUS	transcript	2862765	2863840	.	+	.	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	start_codon	2862765	2862767	.	+	0	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	CDS	2862765	2863229	0.98	+	0	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	exon	2862765	2863229	.	+	.	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	intron	2863230	2863324	.	+	.	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	CDS	2863325	2863840	0.97	+	0	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	exon	2863325	2863840	.	+	.	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
Phchi.S6	AUGUSTUS	stop_codon	2863841	2863843	.	+	0	transcript_id "Phchi.S6G035200.t1"; gene_id "Phchi.S6G035200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6382.t1 is derived from g3554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22656065	22656328	.	-	.	Phchi.S1G354100
Phchi.S1	AUGUSTUS	transcript	22656065	22656328	.	-	.	transcript_id "Phchi.S1G354100.t1"; gene_id "Phchi.S1G354100"
Phchi.S1	AUGUSTUS	stop_codon	22656062	22656064	.	-	0	transcript_id "Phchi.S1G354100.t1"; gene_id "Phchi.S1G354100"
Phchi.S1	AUGUSTUS	CDS	22656065	22656328	0.63	-	0	transcript_id "Phchi.S1G354100.t1"; gene_id "Phchi.S1G354100"
Phchi.S1	AUGUSTUS	exon	22656065	22656328	.	-	.	transcript_id "Phchi.S1G354100.t1"; gene_id "Phchi.S1G354100"
Phchi.S1	AUGUSTUS	start_codon	22656326	22656328	.	-	0	transcript_id "Phchi.S1G354100.t1"; gene_id "Phchi.S1G354100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2838.t1 is derived from g9758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9124820	9126718	.	+	.	Phchi.S5G144700
Phchi.S5	AUGUSTUS	transcript	9124820	9126718	.	+	.	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	start_codon	9124820	9124822	.	+	0	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	CDS	9124820	9125365	0.92	+	0	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	exon	9124820	9125365	.	+	.	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	intron	9125366	9125525	.	+	.	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	CDS	9125526	9125573	0.82	+	0	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	exon	9125526	9125573	.	+	.	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	intron	9125574	9125665	.	+	.	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	CDS	9125666	9126718	0.63	+	0	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	exon	9125666	9126718	.	+	.	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
Phchi.S5	AUGUSTUS	stop_codon	9126719	9126721	.	+	0	transcript_id "Phchi.S5G144700.t1"; gene_id "Phchi.S5G144700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7007.t1 is derived from g4179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26368811	26369974	.	-	.	Phchi.S1G416600
Phchi.S1	AUGUSTUS	transcript	26368811	26369974	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	stop_codon	26368808	26368810	.	-	0	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	CDS	26368811	26368812	1	-	2	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	exon	26368811	26368812	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	intron	26368813	26368944	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	CDS	26368945	26369182	0.93	-	0	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	exon	26368945	26369182	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	intron	26369183	26369356	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	CDS	26369357	26369361	0.93	-	2	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	exon	26369357	26369361	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	intron	26369362	26369663	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	CDS	26369664	26369747	0.34	-	2	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	exon	26369664	26369747	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	intron	26369748	26369832	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	CDS	26369833	26369974	0.66	-	0	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	exon	26369833	26369974	.	-	.	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
Phchi.S1	AUGUSTUS	start_codon	26369972	26369974	.	-	0	transcript_id "Phchi.S1G416600.t1"; gene_id "Phchi.S1G416600"
# This transcript jg14382.t2 is derived from g12850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14383.t1 is derived from g12851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12471941	12473199	.	-	.	Phchi.S3G170200
Phchi.S3	AUGUSTUS	transcript	12471941	12473199	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	stop_codon	12471938	12471940	.	-	0	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	CDS	12471941	12472404	0.95	-	2	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	exon	12471941	12472404	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	intron	12472405	12472522	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	CDS	12472523	12472590	0.89	-	1	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	exon	12472523	12472590	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	intron	12472591	12472716	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	CDS	12472717	12472812	1	-	1	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	exon	12472717	12472812	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	intron	12472813	12473029	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	CDS	12473030	12473199	0.64	-	0	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	exon	12473030	12473199	.	-	.	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
Phchi.S3	AUGUSTUS	start_codon	12473197	12473199	.	-	0	transcript_id "Phchi.S3G170200.t1"; gene_id "Phchi.S3G170200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg40.t1 is derived from g9800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C67	AUGUSTUS	gene	46922	48326	.	+	.	Phchi.C67G000600
Phchi.C67	AUGUSTUS	transcript	46922	48326	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	start_codon	46922	46924	.	+	0	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	46922	46924	0.94	+	0	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	46922	46924	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	intron	46925	47136	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	47137	47195	0.69	+	0	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	47137	47195	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	intron	47196	47297	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	47298	47358	0.51	+	1	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	47298	47358	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	intron	47359	47482	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	47483	47534	0.45	+	0	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	47483	47534	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	intron	47535	47624	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	47625	47693	0.9	+	2	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	47625	47693	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	intron	47694	47985	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	47986	48054	0.96	+	2	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	47986	48054	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	intron	48055	48234	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	CDS	48235	48326	0.89	+	2	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	exon	48235	48326	.	+	.	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
Phchi.C67	AUGUSTUS	stop_codon	48327	48329	.	+	0	transcript_id "Phchi.C67G000600.t1"; gene_id "Phchi.C67G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1232.t1 is derived from g11015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8524520	8528323	.	+	.	Phchi.S6G119100
Phchi.S6	AUGUSTUS	transcript	8524520	8528323	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	start_codon	8524520	8524522	.	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8524520	8524522	0.97	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8524520	8524522	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8524523	8524670	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8524671	8524814	0.76	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8524671	8524814	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8524815	8524919	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8524920	8525123	0.3	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8524920	8525123	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525124	8525257	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525258	8525318	0.99	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525258	8525318	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525319	8525516	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525517	8525593	1	+	2	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525517	8525593	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525594	8525746	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525747	8525845	1	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525747	8525845	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525846	8525920	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525921	8526001	1	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525921	8526001	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526002	8526135	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526136	8526287	0.57	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526136	8526287	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526288	8526412	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526413	8526473	0.37	+	1	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526413	8526473	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526474	8526577	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526578	8526727	1	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526578	8526727	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526728	8526809	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526810	8526913	1	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526810	8526913	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526914	8526997	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526998	8527051	1	+	1	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526998	8527051	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527052	8527233	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527234	8527324	1	+	1	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527234	8527324	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527325	8527421	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527422	8527505	1	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527422	8527505	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527506	8527604	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527605	8527782	1	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527605	8527782	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527783	8527865	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527866	8527941	0.29	+	2	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527866	8527941	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527942	8528066	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8528067	8528143	0.67	+	1	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8528067	8528143	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8528144	8528300	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8528301	8528323	0.9	+	2	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8528301	8528323	.	+	.	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	stop_codon	8528324	8528326	.	+	0	transcript_id "Phchi.S6G119100.t1"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	transcript	8524520	8528323	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	start_codon	8524520	8524522	.	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8524520	8524522	0.97	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8524520	8524522	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8524523	8524670	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8524671	8524814	0.66	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8524671	8524814	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8524815	8524919	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8524920	8525123	0.28	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8524920	8525123	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525124	8525359	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525360	8525426	0.74	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525360	8525426	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525427	8525516	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525517	8525593	0.88	+	2	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525517	8525593	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525594	8525746	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525747	8525845	1	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525747	8525845	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8525846	8525920	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8525921	8526001	1	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8525921	8526001	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526002	8526135	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526136	8526287	0.62	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526136	8526287	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526288	8526412	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526413	8526473	0.43	+	1	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526413	8526473	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526474	8526577	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526578	8526727	1	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526578	8526727	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526728	8526809	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526810	8526913	1	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526810	8526913	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8526914	8526997	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8526998	8527051	1	+	1	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8526998	8527051	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527052	8527233	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527234	8527324	1	+	1	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527234	8527324	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527325	8527421	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527422	8527505	1	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527422	8527505	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527506	8527604	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527605	8527782	1	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527605	8527782	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527783	8527865	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8527866	8527941	0.32	+	2	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8527866	8527941	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8527942	8528066	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8528067	8528143	0.75	+	1	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8528067	8528143	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	intron	8528144	8528300	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	CDS	8528301	8528323	0.91	+	2	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	exon	8528301	8528323	.	+	.	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
Phchi.S6	AUGUSTUS	stop_codon	8528324	8528326	.	+	0	transcript_id "Phchi.S6G119100.t2"; gene_id "Phchi.S6G119100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1023.t1 is derived from g10806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7166076	7169092	.	+	.	Phchi.S6G098200
Phchi.S6	AUGUSTUS	transcript	7166076	7169092	.	+	.	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	start_codon	7166076	7166078	.	+	0	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	CDS	7166076	7166218	0.86	+	0	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	exon	7166076	7166218	.	+	.	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	intron	7166219	7166307	.	+	.	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	CDS	7166308	7169092	0.99	+	1	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	exon	7166308	7169092	.	+	.	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
Phchi.S6	AUGUSTUS	stop_codon	7169093	7169095	.	+	0	transcript_id "Phchi.S6G098200.t1"; gene_id "Phchi.S6G098200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8626.t1 is derived from g5801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37138336	37142009	.	-	.	Phchi.S1G578500
Phchi.S1	AUGUSTUS	transcript	37138336	37142009	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	stop_codon	37138333	37138335	.	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37138336	37138852	0.41	-	1	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37138336	37138852	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37138853	37138931	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37138932	37138940	0.42	-	1	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37138932	37138940	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37138941	37139135	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37139136	37139196	0.96	-	2	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37139136	37139196	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37139197	37139285	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37139286	37139367	0.98	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37139286	37139367	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37139368	37139471	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37139472	37139606	0.61	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37139472	37139606	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37139607	37139676	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37139677	37139823	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37139677	37139823	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37139824	37139904	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37139905	37140007	1	-	1	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37139905	37140007	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37140008	37140169	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37140170	37140339	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37140170	37140339	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37140340	37140411	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37140412	37140492	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37140412	37140492	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37140493	37140625	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37140626	37140694	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37140626	37140694	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37140695	37140849	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37140850	37140903	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37140850	37140903	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37140904	37140987	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37140988	37141045	1	-	1	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37140988	37141045	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37141046	37141222	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37141223	37141306	1	-	1	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37141223	37141306	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37141307	37141391	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37141392	37141555	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37141392	37141555	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	intron	37141556	37141646	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	CDS	37141647	37142009	1	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	exon	37141647	37142009	.	-	.	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
Phchi.S1	AUGUSTUS	start_codon	37142007	37142009	.	-	0	transcript_id "Phchi.S1G578500.t1"; gene_id "Phchi.S1G578500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg570.t1 is derived from g10352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4147566	4148234	.	+	.	Phchi.S6G052900
Phchi.S6	AUGUSTUS	transcript	4147566	4148234	.	+	.	transcript_id "Phchi.S6G052900.t1"; gene_id "Phchi.S6G052900"
Phchi.S6	AUGUSTUS	start_codon	4147566	4147568	.	+	0	transcript_id "Phchi.S6G052900.t1"; gene_id "Phchi.S6G052900"
Phchi.S6	AUGUSTUS	CDS	4147566	4148234	0.34	+	0	transcript_id "Phchi.S6G052900.t1"; gene_id "Phchi.S6G052900"
Phchi.S6	AUGUSTUS	exon	4147566	4148234	.	+	.	transcript_id "Phchi.S6G052900.t1"; gene_id "Phchi.S6G052900"
Phchi.S6	AUGUSTUS	stop_codon	4148235	4148237	.	+	0	transcript_id "Phchi.S6G052900.t1"; gene_id "Phchi.S6G052900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14810.t1 is derived from g13278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14812548	14813885	.	-	.	Phchi.S3G212900
Phchi.S3	AUGUSTUS	transcript	14812548	14813885	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	stop_codon	14812545	14812547	.	-	0	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	CDS	14812548	14812692	0.93	-	1	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	exon	14812548	14812692	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	intron	14812693	14812795	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	CDS	14812796	14813357	0.93	-	2	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	exon	14812796	14813357	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	intron	14813358	14813460	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	CDS	14813461	14813681	0.97	-	1	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	exon	14813461	14813681	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	intron	14813682	14813781	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	CDS	14813782	14813885	0.99	-	0	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	exon	14813782	14813885	.	-	.	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
Phchi.S3	AUGUSTUS	start_codon	14813883	14813885	.	-	0	transcript_id "Phchi.S3G212900.t1"; gene_id "Phchi.S3G212900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8110.t1 is derived from g5285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33167104	33168531	.	-	.	Phchi.S1G526900
Phchi.S1	AUGUSTUS	transcript	33167104	33168531	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	stop_codon	33167101	33167103	.	-	0	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33167104	33167164	0.65	-	1	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33167104	33167164	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	intron	33167165	33167258	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33167259	33167341	1	-	0	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33167259	33167341	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	intron	33167342	33167660	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33167661	33167749	0.84	-	2	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33167661	33167749	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	intron	33167750	33167834	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33167835	33167960	1	-	2	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33167835	33167960	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	intron	33167961	33168120	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33168121	33168185	0.76	-	1	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33168121	33168185	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	intron	33168186	33168290	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33168291	33168347	0.25	-	1	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33168291	33168347	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	intron	33168348	33168430	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	CDS	33168431	33168531	0.22	-	0	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	exon	33168431	33168531	.	-	.	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
Phchi.S1	AUGUSTUS	start_codon	33168529	33168531	.	-	0	transcript_id "Phchi.S1G526900.t1"; gene_id "Phchi.S1G526900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11441.t1 is derived from g15491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6388167	6388528	.	-	.	Phchi.S4G102300
Phchi.S4	AUGUSTUS	transcript	6388167	6388528	.	-	.	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	stop_codon	6388164	6388166	.	-	0	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	CDS	6388167	6388280	0.51	-	0	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	exon	6388167	6388280	.	-	.	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	intron	6388281	6388423	.	-	.	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	CDS	6388424	6388528	0.46	-	0	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	exon	6388424	6388528	.	-	.	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
Phchi.S4	AUGUSTUS	start_codon	6388526	6388528	.	-	0	transcript_id "Phchi.S4G102300.t1"; gene_id "Phchi.S4G102300"
# This transcript jg12710.t2 is derived from g11175.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12711.t1 is derived from g11176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	716098	716790	.	+	.	Phchi.S3G003000
Phchi.S3	AUGUSTUS	transcript	716098	716790	.	+	.	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	start_codon	716098	716100	.	+	0	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	CDS	716098	716230	0.46	+	0	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	exon	716098	716230	.	+	.	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	intron	716231	716301	.	+	.	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	CDS	716302	716384	0.29	+	2	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	exon	716302	716384	.	+	.	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	intron	716385	716766	.	+	.	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	CDS	716767	716790	0.71	+	0	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	exon	716767	716790	.	+	.	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
Phchi.S3	AUGUSTUS	stop_codon	716791	716793	.	+	0	transcript_id "Phchi.S3G003000.t1"; gene_id "Phchi.S3G003000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4959.t1 is derived from g2129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13766004	13766696	.	+	.	Phchi.S1G211800
Phchi.S1	AUGUSTUS	transcript	13766004	13766696	.	+	.	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	start_codon	13766004	13766006	.	+	0	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	CDS	13766004	13766246	0.6	+	0	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	exon	13766004	13766246	.	+	.	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	intron	13766247	13766360	.	+	.	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	CDS	13766361	13766696	0.98	+	0	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	exon	13766361	13766696	.	+	.	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
Phchi.S1	AUGUSTUS	stop_codon	13766697	13766699	.	+	0	transcript_id "Phchi.S1G211800.t1"; gene_id "Phchi.S1G211800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10457.t1 is derived from g14506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	435959	436614	.	-	.	Phchi.S4G003900
Phchi.S4	AUGUSTUS	transcript	435959	436614	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	stop_codon	435956	435958	.	-	0	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	CDS	435959	436064	1	-	1	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	exon	435959	436064	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	intron	436065	436198	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	CDS	436199	436254	1	-	0	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	exon	436199	436254	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	intron	436255	436329	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	CDS	436330	436402	1	-	1	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	exon	436330	436402	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	intron	436403	436513	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	CDS	436514	436614	0.99	-	0	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	exon	436514	436614	.	-	.	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
Phchi.S4	AUGUSTUS	start_codon	436612	436614	.	-	0	transcript_id "Phchi.S4G003900.t1"; gene_id "Phchi.S4G003900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11434.t1 is derived from g15484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6360722	6363364	.	-	.	Phchi.S4G101600
Phchi.S4	AUGUSTUS	transcript	6360722	6363364	.	-	.	transcript_id "Phchi.S4G101600.t1"; gene_id "Phchi.S4G101600"
Phchi.S4	AUGUSTUS	stop_codon	6360719	6360721	.	-	0	transcript_id "Phchi.S4G101600.t1"; gene_id "Phchi.S4G101600"
Phchi.S4	AUGUSTUS	CDS	6360722	6363364	1	-	0	transcript_id "Phchi.S4G101600.t1"; gene_id "Phchi.S4G101600"
Phchi.S4	AUGUSTUS	exon	6360722	6363364	.	-	.	transcript_id "Phchi.S4G101600.t1"; gene_id "Phchi.S4G101600"
Phchi.S4	AUGUSTUS	start_codon	6363362	6363364	.	-	0	transcript_id "Phchi.S4G101600.t1"; gene_id "Phchi.S4G101600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11189.t1 is derived from g15239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4550357	4551797	.	-	.	Phchi.S4G077100
Phchi.S4	AUGUSTUS	transcript	4550357	4551797	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	stop_codon	4550354	4550356	.	-	0	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	CDS	4550357	4550489	0.93	-	1	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	exon	4550357	4550489	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	intron	4550490	4550598	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	CDS	4550599	4550722	0.9	-	2	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	exon	4550599	4550722	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	intron	4550723	4550815	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	CDS	4550816	4550900	0.88	-	0	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	exon	4550816	4550900	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	intron	4550901	4550995	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	CDS	4550996	4551190	0.68	-	0	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	exon	4550996	4551190	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	intron	4551191	4551295	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	CDS	4551296	4551559	0.79	-	0	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	exon	4551296	4551559	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	intron	4551560	4551644	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	CDS	4551645	4551797	0.96	-	0	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	exon	4551645	4551797	.	-	.	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
Phchi.S4	AUGUSTUS	start_codon	4551795	4551797	.	-	0	transcript_id "Phchi.S4G077100.t1"; gene_id "Phchi.S4G077100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9364.t1 is derived from g6540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41167313	41168475	.	+	.	Phchi.S1G652300
Phchi.S1	AUGUSTUS	transcript	41167313	41168475	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	start_codon	41167313	41167315	.	+	0	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	CDS	41167313	41167346	0.8	+	0	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	exon	41167313	41167346	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	intron	41167347	41167445	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	CDS	41167446	41167800	0.95	+	2	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	exon	41167446	41167800	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	intron	41167801	41167902	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	CDS	41167903	41168073	1	+	1	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	exon	41167903	41168073	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	intron	41168074	41168303	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	CDS	41168304	41168475	1	+	1	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	exon	41168304	41168475	.	+	.	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
Phchi.S1	AUGUSTUS	stop_codon	41168476	41168478	.	+	0	transcript_id "Phchi.S1G652300.t1"; gene_id "Phchi.S1G652300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6600.t1 is derived from g3772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23933207	23935054	.	-	.	Phchi.S1G375900
Phchi.S1	AUGUSTUS	transcript	23933207	23935054	.	-	.	transcript_id "Phchi.S1G375900.t1"; gene_id "Phchi.S1G375900"
Phchi.S1	AUGUSTUS	stop_codon	23933204	23933206	.	-	0	transcript_id "Phchi.S1G375900.t1"; gene_id "Phchi.S1G375900"
Phchi.S1	AUGUSTUS	CDS	23933207	23935054	0.99	-	0	transcript_id "Phchi.S1G375900.t1"; gene_id "Phchi.S1G375900"
Phchi.S1	AUGUSTUS	exon	23933207	23935054	.	-	.	transcript_id "Phchi.S1G375900.t1"; gene_id "Phchi.S1G375900"
Phchi.S1	AUGUSTUS	start_codon	23935052	23935054	.	-	0	transcript_id "Phchi.S1G375900.t1"; gene_id "Phchi.S1G375900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10225.t1 is derived from g7401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46473552	46473830	.	+	.	Phchi.S1G738400
Phchi.S1	AUGUSTUS	transcript	46473552	46473830	.	+	.	transcript_id "Phchi.S1G738400.t1"; gene_id "Phchi.S1G738400"
Phchi.S1	AUGUSTUS	start_codon	46473552	46473554	.	+	0	transcript_id "Phchi.S1G738400.t1"; gene_id "Phchi.S1G738400"
Phchi.S1	AUGUSTUS	CDS	46473552	46473830	0.72	+	0	transcript_id "Phchi.S1G738400.t1"; gene_id "Phchi.S1G738400"
Phchi.S1	AUGUSTUS	exon	46473552	46473830	.	+	.	transcript_id "Phchi.S1G738400.t1"; gene_id "Phchi.S1G738400"
Phchi.S1	AUGUSTUS	stop_codon	46473831	46473833	.	+	0	transcript_id "Phchi.S1G738400.t1"; gene_id "Phchi.S1G738400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14925.t1 is derived from g13393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15544249	15544812	.	-	.	Phchi.S3G224400
Phchi.S3	AUGUSTUS	transcript	15544249	15544812	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	stop_codon	15544246	15544248	.	-	0	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	CDS	15544249	15544293	0.39	-	0	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	exon	15544249	15544293	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	intron	15544294	15544396	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	CDS	15544397	15544520	0.72	-	1	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	exon	15544397	15544520	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	intron	15544521	15544629	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	CDS	15544630	15544715	0.85	-	0	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	exon	15544630	15544715	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	intron	15544716	15544806	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	CDS	15544807	15544812	1	-	0	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	exon	15544807	15544812	.	-	.	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
Phchi.S3	AUGUSTUS	start_codon	15544810	15544812	.	-	0	transcript_id "Phchi.S3G224400.t1"; gene_id "Phchi.S3G224400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8580.t1 is derived from g5755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36730655	36732986	.	-	.	Phchi.S1G573900
Phchi.S1	AUGUSTUS	transcript	36730655	36732986	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	stop_codon	36730652	36730654	.	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36730655	36730811	0.98	-	1	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36730655	36730811	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36730812	36730903	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36730904	36731089	1	-	1	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36730904	36731089	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36731090	36731178	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36731179	36731378	1	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36731179	36731378	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36731379	36731473	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36731474	36731587	1	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36731474	36731587	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36731588	36731667	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36731668	36731804	1	-	2	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36731668	36731804	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36731805	36731900	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36731901	36732011	1	-	2	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36731901	36732011	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36732012	36732086	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36732087	36732339	1	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36732087	36732339	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36732340	36732422	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36732423	36732521	1	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36732423	36732521	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	intron	36732522	36732659	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	CDS	36732660	36732986	0.96	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	exon	36732660	36732986	.	-	.	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
Phchi.S1	AUGUSTUS	start_codon	36732984	36732986	.	-	0	transcript_id "Phchi.S1G573900.t1"; gene_id "Phchi.S1G573900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7593.t1 is derived from g4767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30186361	30188091	.	+	.	Phchi.S1G475200
Phchi.S1	AUGUSTUS	transcript	30186361	30188091	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	start_codon	30186361	30186363	.	+	0	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	CDS	30186361	30186552	0.81	+	0	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	exon	30186361	30186552	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	intron	30186553	30186708	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	CDS	30186709	30186856	1	+	0	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	exon	30186709	30186856	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	intron	30186857	30186956	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	CDS	30186957	30187372	1	+	2	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	exon	30186957	30187372	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	intron	30187373	30187458	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	CDS	30187459	30188091	1	+	0	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	exon	30187459	30188091	.	+	.	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
Phchi.S1	AUGUSTUS	stop_codon	30188092	30188094	.	+	0	transcript_id "Phchi.S1G475200.t1"; gene_id "Phchi.S1G475200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9727.t1 is derived from g6903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43415175	43415486	.	+	.	Phchi.S1G688600
Phchi.S1	AUGUSTUS	transcript	43415175	43415486	.	+	.	transcript_id "Phchi.S1G688600.t1"; gene_id "Phchi.S1G688600"
Phchi.S1	AUGUSTUS	start_codon	43415175	43415177	.	+	0	transcript_id "Phchi.S1G688600.t1"; gene_id "Phchi.S1G688600"
Phchi.S1	AUGUSTUS	CDS	43415175	43415486	0.77	+	0	transcript_id "Phchi.S1G688600.t1"; gene_id "Phchi.S1G688600"
Phchi.S1	AUGUSTUS	exon	43415175	43415486	.	+	.	transcript_id "Phchi.S1G688600.t1"; gene_id "Phchi.S1G688600"
Phchi.S1	AUGUSTUS	stop_codon	43415487	43415489	.	+	0	transcript_id "Phchi.S1G688600.t1"; gene_id "Phchi.S1G688600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3836.t1 is derived from g1005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5946553	5946955	.	-	.	Phchi.S1G099500
Phchi.S1	AUGUSTUS	transcript	5946553	5946955	.	-	.	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	stop_codon	5946550	5946552	.	-	0	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	CDS	5946553	5946693	0.4	-	0	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	exon	5946553	5946693	.	-	.	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	intron	5946694	5946871	.	-	.	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	CDS	5946872	5946955	0.75	-	0	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	exon	5946872	5946955	.	-	.	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
Phchi.S1	AUGUSTUS	start_codon	5946953	5946955	.	-	0	transcript_id "Phchi.S1G099500.t1"; gene_id "Phchi.S1G099500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7700.t1 is derived from g4874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30702941	30703624	.	+	.	Phchi.S1G485900
Phchi.S1	AUGUSTUS	transcript	30702941	30703624	.	+	.	transcript_id "Phchi.S1G485900.t1"; gene_id "Phchi.S1G485900"
Phchi.S1	AUGUSTUS	start_codon	30702941	30702943	.	+	0	transcript_id "Phchi.S1G485900.t1"; gene_id "Phchi.S1G485900"
Phchi.S1	AUGUSTUS	CDS	30702941	30703624	0.85	+	0	transcript_id "Phchi.S1G485900.t1"; gene_id "Phchi.S1G485900"
Phchi.S1	AUGUSTUS	exon	30702941	30703624	.	+	.	transcript_id "Phchi.S1G485900.t1"; gene_id "Phchi.S1G485900"
Phchi.S1	AUGUSTUS	stop_codon	30703625	30703627	.	+	0	transcript_id "Phchi.S1G485900.t1"; gene_id "Phchi.S1G485900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10394.t1 is derived from g7570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47521160	47525643	.	-	.	Phchi.S1G755300
Phchi.S1	AUGUSTUS	transcript	47521160	47525643	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	stop_codon	47521157	47521159	.	-	0	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	CDS	47521160	47522949	0.85	-	2	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	exon	47521160	47522949	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	intron	47522950	47523183	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	CDS	47523184	47523570	0.77	-	2	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	exon	47523184	47523570	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	intron	47523571	47524120	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	CDS	47524121	47525156	0.62	-	0	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	exon	47524121	47525156	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	intron	47525157	47525292	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	CDS	47525293	47525643	0.47	-	0	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	exon	47525293	47525643	.	-	.	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	start_codon	47525641	47525643	.	-	0	transcript_id "Phchi.S1G755300.t1"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	transcript	47521160	47522488	.	-	.	transcript_id "Phchi.S1G755300.t2"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	stop_codon	47521157	47521159	.	-	0	transcript_id "Phchi.S1G755300.t2"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	CDS	47521160	47522488	0.69	-	0	transcript_id "Phchi.S1G755300.t2"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	exon	47521160	47522488	.	-	.	transcript_id "Phchi.S1G755300.t2"; gene_id "Phchi.S1G755300"
Phchi.S1	AUGUSTUS	start_codon	47522486	47522488	.	-	0	transcript_id "Phchi.S1G755300.t2"; gene_id "Phchi.S1G755300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8062.t1 is derived from g5237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32747348	32750303	.	+	.	Phchi.S1G522100
Phchi.S1	AUGUSTUS	transcript	32747348	32750303	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	start_codon	32747348	32747350	.	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32747348	32747587	0.5	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32747348	32747587	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32747588	32747747	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32747748	32747916	1	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32747748	32747916	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32747917	32748010	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32748011	32748075	1	+	2	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32748011	32748075	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32748076	32748173	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32748174	32748446	0.92	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32748174	32748446	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32748447	32748542	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32748543	32748704	0.92	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32748543	32748704	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32748705	32748863	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32748864	32748904	1	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32748864	32748904	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32748905	32749019	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32749020	32749729	0.8	+	1	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32749020	32749729	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	intron	32749730	32749863	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	CDS	32749864	32750303	0.66	+	2	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	exon	32749864	32750303	.	+	.	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
Phchi.S1	AUGUSTUS	stop_codon	32750304	32750306	.	+	0	transcript_id "Phchi.S1G522100.t1"; gene_id "Phchi.S1G522100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4929.t1 is derived from g2099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13613797	13617642	.	+	.	Phchi.S1G208800
Phchi.S1	AUGUSTUS	transcript	13613797	13617642	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	start_codon	13613797	13613799	.	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13613797	13614410	1	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13613797	13614410	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13614411	13614598	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13614599	13614698	0.84	+	1	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13614599	13614698	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13614699	13614815	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13614816	13615182	0.85	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13614816	13615182	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13615183	13615461	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13615462	13615574	1	+	2	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13615462	13615574	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13615575	13615709	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13615710	13615838	1	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13615710	13615838	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13615839	13616046	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13616047	13616140	1	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13616047	13616140	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13616141	13616326	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13616327	13616457	1	+	2	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13616327	13616457	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13616458	13616593	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13616594	13616853	1	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13616594	13616853	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13616854	13616948	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13616949	13617093	1	+	1	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13616949	13617093	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13617094	13617215	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13617216	13617316	1	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13617216	13617316	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13617317	13617394	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13617395	13617473	1	+	1	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13617395	13617473	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	intron	13617474	13617555	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	CDS	13617556	13617642	1	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	exon	13617556	13617642	.	+	.	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
Phchi.S1	AUGUSTUS	stop_codon	13617643	13617645	.	+	0	transcript_id "Phchi.S1G208800.t1"; gene_id "Phchi.S1G208800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12541.t1 is derived from g8218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34039071	34048947	.	+	.	Phchi.S2G062100
Phchi.S2	AUGUSTUS	transcript	34039071	34048947	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	start_codon	34039071	34039073	.	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34039071	34039421	0.56	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34039071	34039421	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34039422	34039511	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34039512	34039631	0.99	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34039512	34039631	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34039632	34039715	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34039716	34039734	0.99	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34039716	34039734	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34039735	34039793	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34039794	34039831	0.97	+	2	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34039794	34039831	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34039832	34039923	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34039924	34040076	1	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34039924	34040076	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34040077	34040161	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34040162	34040262	0.99	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34040162	34040262	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34040263	34040364	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34040365	34040429	1	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34040365	34040429	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34040430	34040576	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34040577	34040685	1	+	2	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34040577	34040685	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34040686	34041157	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34041158	34041261	1	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34041158	34041261	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34041262	34041399	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34041400	34041428	0.39	+	2	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34041400	34041428	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34041429	34041487	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34041488	34041578	0.42	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34041488	34041578	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34041579	34041795	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34041796	34042139	1	+	2	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34041796	34042139	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34042140	34042270	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34042271	34042341	1	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34042271	34042341	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34042342	34042534	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34042535	34043004	1	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34042535	34043004	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34043005	34043159	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34043160	34044031	0.42	+	2	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34043160	34044031	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34044032	34044178	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34044179	34044295	0.44	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34044179	34044295	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34044296	34044439	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34044440	34044601	1	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34044440	34044601	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34044602	34044720	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34044721	34044967	0.65	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34044721	34044967	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34044968	34045116	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34045117	34045144	0.41	+	2	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34045117	34045144	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34045145	34045223	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34045224	34046316	0.4	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34045224	34046316	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34046317	34046443	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34046444	34046635	1	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34046444	34046635	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34046636	34046909	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34046910	34047178	1	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34046910	34047178	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34047179	34047266	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34047267	34047572	0.97	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34047267	34047572	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34047573	34047678	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34047679	34047783	0.43	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34047679	34047783	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34047784	34047877	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34047878	34047944	0.74	+	1	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34047878	34047944	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34047945	34048159	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34048160	34048417	1	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34048160	34048417	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	intron	34048418	34048506	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	CDS	34048507	34048947	0.99	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	exon	34048507	34048947	.	+	.	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
Phchi.S2	AUGUSTUS	stop_codon	34048948	34048950	.	+	0	transcript_id "Phchi.S2G062100.t1"; gene_id "Phchi.S2G062100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg538.t1 is derived from g10320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3937661	3938349	.	-	.	Phchi.S6G049700
Phchi.S6	AUGUSTUS	transcript	3937661	3938349	.	-	.	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	stop_codon	3937658	3937660	.	-	0	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	CDS	3937661	3937724	1	-	1	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	exon	3937661	3937724	.	-	.	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	intron	3937725	3937868	.	-	.	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	CDS	3937869	3938083	0.72	-	0	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	exon	3937869	3938083	.	-	.	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	intron	3938084	3938271	.	-	.	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	CDS	3938272	3938349	0.45	-	0	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	exon	3938272	3938349	.	-	.	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
Phchi.S6	AUGUSTUS	start_codon	3938347	3938349	.	-	0	transcript_id "Phchi.S6G049700.t1"; gene_id "Phchi.S6G049700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3191.t1 is derived from g360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2154917	2155595	.	+	.	Phchi.S1G035000
Phchi.S1	AUGUSTUS	transcript	2154917	2155595	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	start_codon	2154917	2154919	.	+	0	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	CDS	2154917	2154919	1	+	0	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	exon	2154917	2154919	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	intron	2154920	2155046	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	CDS	2155047	2155238	1	+	0	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	exon	2155047	2155238	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	intron	2155239	2155394	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	CDS	2155395	2155437	1	+	0	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	exon	2155395	2155437	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	intron	2155438	2155524	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	CDS	2155525	2155595	1	+	2	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	exon	2155525	2155595	.	+	.	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
Phchi.S1	AUGUSTUS	stop_codon	2155596	2155598	.	+	0	transcript_id "Phchi.S1G035000.t1"; gene_id "Phchi.S1G035000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11035.t1 is derived from g15085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3739965	3740474	.	+	.	Phchi.S4G061700
Phchi.S4	AUGUSTUS	transcript	3739965	3740474	.	+	.	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	start_codon	3739965	3739967	.	+	0	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	CDS	3739965	3740183	0.67	+	0	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	exon	3739965	3740183	.	+	.	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	intron	3740184	3740303	.	+	.	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	CDS	3740304	3740474	0.81	+	0	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	exon	3740304	3740474	.	+	.	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
Phchi.S4	AUGUSTUS	stop_codon	3740475	3740477	.	+	0	transcript_id "Phchi.S4G061700.t1"; gene_id "Phchi.S4G061700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg214.t1 is derived from g9996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1334692	1335267	.	+	.	Phchi.S6G017300
Phchi.S6	AUGUSTUS	transcript	1334692	1335267	.	+	.	transcript_id "Phchi.S6G017300.t1"; gene_id "Phchi.S6G017300"
Phchi.S6	AUGUSTUS	start_codon	1334692	1334694	.	+	0	transcript_id "Phchi.S6G017300.t1"; gene_id "Phchi.S6G017300"
Phchi.S6	AUGUSTUS	CDS	1334692	1335267	0.59	+	0	transcript_id "Phchi.S6G017300.t1"; gene_id "Phchi.S6G017300"
Phchi.S6	AUGUSTUS	exon	1334692	1335267	.	+	.	transcript_id "Phchi.S6G017300.t1"; gene_id "Phchi.S6G017300"
Phchi.S6	AUGUSTUS	stop_codon	1335268	1335270	.	+	0	transcript_id "Phchi.S6G017300.t1"; gene_id "Phchi.S6G017300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1306.t1 is derived from g11089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8926326	8930024	.	-	.	Phchi.S6G126500
Phchi.S6	AUGUSTUS	transcript	8926326	8930024	.	-	.	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	stop_codon	8926323	8926325	.	-	0	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	CDS	8926326	8927873	0.98	-	0	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	exon	8926326	8927873	.	-	.	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	intron	8927874	8928023	.	-	.	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	CDS	8928024	8928716	1	-	0	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	exon	8928024	8928716	.	-	.	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	intron	8928717	8928932	.	-	.	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	CDS	8928933	8930024	0.99	-	0	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	exon	8928933	8930024	.	-	.	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
Phchi.S6	AUGUSTUS	start_codon	8930022	8930024	.	-	0	transcript_id "Phchi.S6G126500.t1"; gene_id "Phchi.S6G126500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2166.t1 is derived from g9086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5144689	5146358	.	-	.	Phchi.S5G077500
Phchi.S5	AUGUSTUS	transcript	5144689	5145856	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	stop_codon	5144686	5144688	.	-	0	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5144689	5144763	1	-	0	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5144689	5144763	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5144764	5144832	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5144833	5145223	1	-	1	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5144833	5145223	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145224	5145349	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145350	5145513	1	-	0	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145350	5145513	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145514	5145616	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145617	5145856	0.56	-	0	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145617	5145856	.	-	.	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	start_codon	5145854	5145856	.	-	0	transcript_id "Phchi.S5G077500.t1"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	transcript	5144689	5145856	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	stop_codon	5144686	5144688	.	-	0	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5144689	5144763	0.99	-	0	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5144689	5144763	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5144764	5144832	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5144833	5145223	0.99	-	1	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5144833	5145223	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145224	5145349	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145350	5145443	0.63	-	2	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145350	5145443	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145444	5145616	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145617	5145624	0.63	-	1	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145617	5145624	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145625	5145701	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145702	5145856	0.22	-	0	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145702	5145856	.	-	.	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	start_codon	5145854	5145856	.	-	0	transcript_id "Phchi.S5G077500.t2"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	transcript	5144689	5146358	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	stop_codon	5144686	5144688	.	-	0	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5144689	5144763	1	-	0	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5144689	5144763	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5144764	5144832	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5144833	5145223	0.98	-	1	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5144833	5145223	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145224	5145349	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145350	5145443	0.68	-	2	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145350	5145443	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145444	5145616	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145617	5145624	0.68	-	1	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145617	5145624	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5145625	5145940	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5145941	5146014	0.3	-	0	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5145941	5146014	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	intron	5146015	5146247	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	CDS	5146248	5146358	0.28	-	0	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	exon	5146248	5146358	.	-	.	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
Phchi.S5	AUGUSTUS	start_codon	5146356	5146358	.	-	0	transcript_id "Phchi.S5G077500.t3"; gene_id "Phchi.S5G077500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1328.t1 is derived from g11111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9048728	9051407	.	+	.	Phchi.S6G128700
Phchi.S6	AUGUSTUS	transcript	9048728	9051407	.	+	.	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	start_codon	9048728	9048730	.	+	0	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	CDS	9048728	9049153	0.99	+	0	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	exon	9048728	9049153	.	+	.	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	intron	9049154	9049265	.	+	.	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	CDS	9049266	9051231	0.99	+	0	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	exon	9049266	9051231	.	+	.	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	intron	9051232	9051402	.	+	.	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	CDS	9051403	9051407	0.83	+	2	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	exon	9051403	9051407	.	+	.	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
Phchi.S6	AUGUSTUS	stop_codon	9051408	9051410	.	+	0	transcript_id "Phchi.S6G128700.t1"; gene_id "Phchi.S6G128700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6711.t1 is derived from g3883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24661967	24665824	.	+	.	Phchi.S1G387000
Phchi.S1	AUGUSTUS	transcript	24661967	24665824	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	start_codon	24661967	24661969	.	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24661967	24662176	0.99	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24661967	24662176	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24662177	24662376	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24662377	24662727	0.9	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24662377	24662727	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24662728	24662816	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24662817	24663014	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24662817	24663014	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24663015	24663176	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24663177	24663503	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24663177	24663503	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24663504	24663611	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24663612	24663665	0.96	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24663612	24663665	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24663666	24663773	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24663774	24663839	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24663774	24663839	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24663840	24664016	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24664017	24664120	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24664017	24664120	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24664121	24664210	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24664211	24664298	1	+	1	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24664211	24664298	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24664299	24664383	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24664384	24664556	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24664384	24664556	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24664557	24664648	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24664649	24664688	1	+	1	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24664649	24664688	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24664689	24664779	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24664780	24664904	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24664780	24664904	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24664905	24665028	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24665029	24665101	1	+	1	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24665029	24665101	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24665102	24665199	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24665200	24665289	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24665200	24665289	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24665290	24665375	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24665376	24665565	1	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24665376	24665565	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	intron	24665566	24665642	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	CDS	24665643	24665824	0.99	+	2	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	exon	24665643	24665824	.	+	.	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
Phchi.S1	AUGUSTUS	stop_codon	24665825	24665827	.	+	0	transcript_id "Phchi.S1G387000.t1"; gene_id "Phchi.S1G387000"
# This transcript jg15410.t2 is derived from g13878.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15410.t3 is derived from g13878.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15411.t1 is derived from g13879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18885576	18886133	.	+	.	Phchi.S3G273000
Phchi.S3	AUGUSTUS	transcript	18885576	18886133	.	+	.	transcript_id "Phchi.S3G273000.t1"; gene_id "Phchi.S3G273000"
Phchi.S3	AUGUSTUS	start_codon	18885576	18885578	.	+	0	transcript_id "Phchi.S3G273000.t1"; gene_id "Phchi.S3G273000"
Phchi.S3	AUGUSTUS	CDS	18885576	18886133	0.84	+	0	transcript_id "Phchi.S3G273000.t1"; gene_id "Phchi.S3G273000"
Phchi.S3	AUGUSTUS	exon	18885576	18886133	.	+	.	transcript_id "Phchi.S3G273000.t1"; gene_id "Phchi.S3G273000"
Phchi.S3	AUGUSTUS	stop_codon	18886134	18886136	.	+	0	transcript_id "Phchi.S3G273000.t1"; gene_id "Phchi.S3G273000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4497.t1 is derived from g1667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10819010	10820302	.	-	.	Phchi.S1G165600
Phchi.S1	AUGUSTUS	transcript	10819010	10820302	.	-	.	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	stop_codon	10819007	10819009	.	-	0	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	CDS	10819010	10819727	0.72	-	1	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	exon	10819010	10819727	.	-	.	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	intron	10819728	10820171	.	-	.	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	CDS	10820172	10820302	1	-	0	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	exon	10820172	10820302	.	-	.	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
Phchi.S1	AUGUSTUS	start_codon	10820300	10820302	.	-	0	transcript_id "Phchi.S1G165600.t1"; gene_id "Phchi.S1G165600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5232.t1 is derived from g2402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15756039	15756839	.	-	.	Phchi.S1G239100
Phchi.S1	AUGUSTUS	transcript	15756039	15756839	.	-	.	transcript_id "Phchi.S1G239100.t1"; gene_id "Phchi.S1G239100"
Phchi.S1	AUGUSTUS	stop_codon	15756036	15756038	.	-	0	transcript_id "Phchi.S1G239100.t1"; gene_id "Phchi.S1G239100"
Phchi.S1	AUGUSTUS	CDS	15756039	15756839	0.6	-	0	transcript_id "Phchi.S1G239100.t1"; gene_id "Phchi.S1G239100"
Phchi.S1	AUGUSTUS	exon	15756039	15756839	.	-	.	transcript_id "Phchi.S1G239100.t1"; gene_id "Phchi.S1G239100"
Phchi.S1	AUGUSTUS	start_codon	15756837	15756839	.	-	0	transcript_id "Phchi.S1G239100.t1"; gene_id "Phchi.S1G239100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14524.t1 is derived from g12992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13308047	13309261	.	+	.	Phchi.S3G184300
Phchi.S3	AUGUSTUS	transcript	13308047	13309261	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	start_codon	13308047	13308049	.	+	0	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	CDS	13308047	13308194	0.88	+	0	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	exon	13308047	13308194	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	intron	13308195	13308284	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	CDS	13308285	13308350	1	+	2	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	exon	13308285	13308350	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	intron	13308351	13308450	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	CDS	13308451	13308597	1	+	2	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	exon	13308451	13308597	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	intron	13308598	13308695	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	CDS	13308696	13308809	1	+	2	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	exon	13308696	13308809	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	intron	13308810	13308942	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	CDS	13308943	13309038	1	+	2	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	exon	13308943	13309038	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	intron	13309039	13309133	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	CDS	13309134	13309261	0.98	+	2	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	exon	13309134	13309261	.	+	.	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
Phchi.S3	AUGUSTUS	stop_codon	13309262	13309264	.	+	0	transcript_id "Phchi.S3G184300.t1"; gene_id "Phchi.S3G184300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8407.t1 is derived from g5582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35811118	35814713	.	+	.	Phchi.S1G556600
Phchi.S1	AUGUSTUS	transcript	35811118	35814713	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	start_codon	35811118	35811120	.	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35811118	35811204	0.74	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35811118	35811204	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35811205	35811335	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35811336	35811467	1	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35811336	35811467	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35811468	35811710	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35811711	35811836	1	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35811711	35811836	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35811837	35811946	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35811947	35812033	1	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35811947	35812033	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35812034	35812183	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35812184	35812513	0.95	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35812184	35812513	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35812514	35812619	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35812620	35812783	0.98	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35812620	35812783	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35812784	35812878	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35812879	35812981	1	+	1	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35812879	35812981	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35812982	35813102	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35813103	35813336	0.45	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35813103	35813336	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35813337	35813533	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35813534	35813670	0.7	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35813534	35813670	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35813671	35813775	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35813776	35813840	0.39	+	1	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35813776	35813840	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35813841	35813924	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35813925	35813978	0.44	+	2	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35813925	35813978	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35813979	35814312	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35814313	35814438	0.42	+	2	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35814313	35814438	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35814439	35814523	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35814524	35814570	1	+	2	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35814524	35814570	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	intron	35814571	35814647	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	CDS	35814648	35814713	1	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	exon	35814648	35814713	.	+	.	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
Phchi.S1	AUGUSTUS	stop_codon	35814714	35814716	.	+	0	transcript_id "Phchi.S1G556600.t1"; gene_id "Phchi.S1G556600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8035.t1 is derived from g5210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32576594	32579437	.	-	.	Phchi.S1G519400
Phchi.S1	AUGUSTUS	transcript	32576594	32579437	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	stop_codon	32576591	32576593	.	-	0	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32576594	32576611	0.99	-	0	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32576594	32576611	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32576612	32577059	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577060	32577256	0.99	-	2	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577060	32577256	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577257	32577363	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577364	32577491	1	-	1	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577364	32577491	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577492	32577650	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577651	32577696	1	-	2	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577651	32577696	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577697	32577770	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577771	32577867	1	-	0	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577771	32577867	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577868	32578010	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578011	32578093	1	-	2	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578011	32578093	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578094	32578213	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578214	32578292	1	-	0	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578214	32578292	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578293	32578457	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578458	32578509	1	-	1	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578458	32578509	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578510	32578865	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578866	32578953	1	-	2	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578866	32578953	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578954	32579352	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32579353	32579437	1	-	0	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32579353	32579437	.	-	.	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	start_codon	32579435	32579437	.	-	0	transcript_id "Phchi.S1G519400.t1"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	transcript	32576594	32579437	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	stop_codon	32576591	32576593	.	-	0	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32576594	32576611	1	-	0	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32576594	32576611	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32576612	32577005	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577006	32577256	0.97	-	2	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577006	32577256	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577257	32577363	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577364	32577491	1	-	1	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577364	32577491	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577492	32577650	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577651	32577696	1	-	2	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577651	32577696	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577697	32577770	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32577771	32577867	1	-	0	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32577771	32577867	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32577868	32578010	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578011	32578093	1	-	2	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578011	32578093	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578094	32578213	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578214	32578292	1	-	0	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578214	32578292	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578293	32578457	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578458	32578509	1	-	1	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578458	32578509	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578510	32578865	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32578866	32578953	1	-	2	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32578866	32578953	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	intron	32578954	32579352	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	CDS	32579353	32579437	1	-	0	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	exon	32579353	32579437	.	-	.	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
Phchi.S1	AUGUSTUS	start_codon	32579435	32579437	.	-	0	transcript_id "Phchi.S1G519400.t2"; gene_id "Phchi.S1G519400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12334.t1 is derived from g8010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11003855	11007349	.	+	.	Phchi.S2G041400
Phchi.S2	AUGUSTUS	transcript	11003855	11007349	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	start_codon	11003855	11003857	.	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11003855	11004003	0.97	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11003855	11004003	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11004004	11004363	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11004364	11004526	1	+	1	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11004364	11004526	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11004527	11004632	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11004633	11004765	1	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11004633	11004765	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11004766	11004871	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11004872	11005042	1	+	2	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11004872	11005042	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11005043	11005131	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11005132	11005210	0.96	+	2	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11005132	11005210	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11005211	11005317	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11005318	11005428	0.65	+	1	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11005318	11005428	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11005429	11005559	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11005560	11005626	1	+	1	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11005560	11005626	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11005627	11005830	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11005831	11005936	1	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11005831	11005936	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11005937	11006098	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11006099	11006157	1	+	2	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11006099	11006157	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11006158	11006251	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11006252	11006382	1	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11006252	11006382	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11006383	11006516	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11006517	11006653	1	+	1	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11006517	11006653	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11006654	11006748	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11006749	11006834	1	+	2	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11006749	11006834	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11006835	11006957	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11006958	11007047	1	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11006958	11007047	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	intron	11007048	11007127	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	CDS	11007128	11007349	1	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	exon	11007128	11007349	.	+	.	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
Phchi.S2	AUGUSTUS	stop_codon	11007350	11007352	.	+	0	transcript_id "Phchi.S2G041400.t1"; gene_id "Phchi.S2G041400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15292.t1 is derived from g13760.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18229085	18233597	.	+	.	Phchi.S3G261100
Phchi.S3	AUGUSTUS	transcript	18229085	18233597	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	start_codon	18229085	18229087	.	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18229085	18230615	0.95	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18229085	18230615	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18230616	18230702	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18230703	18230962	1	+	2	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18230703	18230962	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18230963	18231067	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231068	18231283	1	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231068	18231283	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18231284	18231380	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231381	18231599	1	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231381	18231599	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18231600	18231778	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231779	18231823	0.68	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231779	18231823	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18231824	18231912	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231913	18231943	0.68	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231913	18231943	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18231944	18232301	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18232302	18232541	0.69	+	2	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18232302	18232541	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18232542	18232631	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18232632	18232753	1	+	2	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18232632	18232753	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18232754	18232838	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18232839	18232934	1	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18232839	18232934	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18232935	18233017	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18233018	18233116	1	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18233018	18233116	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18233117	18233237	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18233238	18233426	1	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18233238	18233426	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18233427	18233549	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18233550	18233597	1	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18233550	18233597	.	+	.	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	stop_codon	18233598	18233600	.	+	0	transcript_id "Phchi.S3G261100.t1"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	transcript	18229085	18231754	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	start_codon	18229085	18229087	.	+	0	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18229085	18230615	0.98	+	0	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18229085	18230615	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18230616	18230702	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18230703	18230962	1	+	2	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18230703	18230962	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18230963	18231067	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231068	18231283	1	+	0	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231068	18231283	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18231284	18231380	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231381	18231599	0.36	+	0	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231381	18231599	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	intron	18231600	18231739	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	CDS	18231740	18231754	0.35	+	0	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	exon	18231740	18231754	.	+	.	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
Phchi.S3	AUGUSTUS	stop_codon	18231755	18231757	.	+	0	transcript_id "Phchi.S3G261100.t2"; gene_id "Phchi.S3G261100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9191.t1 is derived from g6366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40275396	40277290	.	+	.	Phchi.S1G635000
Phchi.S1	AUGUSTUS	transcript	40275396	40277290	.	+	.	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	start_codon	40275396	40275398	.	+	0	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	CDS	40275396	40275914	0.95	+	0	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	exon	40275396	40275914	.	+	.	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	intron	40275915	40276047	.	+	.	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	CDS	40276048	40276267	1	+	0	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	exon	40276048	40276267	.	+	.	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	intron	40276268	40276415	.	+	.	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	CDS	40276416	40277290	1	+	2	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	exon	40276416	40277290	.	+	.	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
Phchi.S1	AUGUSTUS	stop_codon	40277291	40277293	.	+	0	transcript_id "Phchi.S1G635000.t1"; gene_id "Phchi.S1G635000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2856.t1 is derived from g25.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	70044	70352	.	+	.	Phchi.S1G001500
Phchi.S1	AUGUSTUS	transcript	70044	70352	.	+	.	transcript_id "Phchi.S1G001500.t1"; gene_id "Phchi.S1G001500"
Phchi.S1	AUGUSTUS	start_codon	70044	70046	.	+	0	transcript_id "Phchi.S1G001500.t1"; gene_id "Phchi.S1G001500"
Phchi.S1	AUGUSTUS	CDS	70044	70352	0.58	+	0	transcript_id "Phchi.S1G001500.t1"; gene_id "Phchi.S1G001500"
Phchi.S1	AUGUSTUS	exon	70044	70352	.	+	.	transcript_id "Phchi.S1G001500.t1"; gene_id "Phchi.S1G001500"
Phchi.S1	AUGUSTUS	stop_codon	70353	70355	.	+	0	transcript_id "Phchi.S1G001500.t1"; gene_id "Phchi.S1G001500"
# This transcript jg7979.t2 is derived from g5154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7980.t1 is derived from g5155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32208795	32211935	.	+	.	Phchi.S1G513900
Phchi.S1	AUGUSTUS	transcript	32208795	32211935	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	start_codon	32208795	32208797	.	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32208795	32208797	0.28	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32208795	32208797	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32208798	32208992	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32208993	32209146	0.37	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32208993	32209146	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32209147	32209511	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32209512	32209658	1	+	2	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32209512	32209658	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32209659	32209776	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32209777	32209919	1	+	2	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32209777	32209919	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32209920	32210037	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32210038	32210191	1	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32210038	32210191	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32210192	32210293	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32210294	32210523	1	+	2	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32210294	32210523	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32210524	32210622	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32210623	32210712	1	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32210623	32210712	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32210713	32210786	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32210787	32210960	1	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32210787	32210960	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32210961	32211068	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32211069	32211206	1	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32211069	32211206	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32211207	32211290	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32211291	32211428	1	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32211291	32211428	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32211429	32211510	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32211511	32211572	1	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32211511	32211572	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	intron	32211573	32211664	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	CDS	32211665	32211935	1	+	1	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	exon	32211665	32211935	.	+	.	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
Phchi.S1	AUGUSTUS	stop_codon	32211936	32211938	.	+	0	transcript_id "Phchi.S1G513900.t1"; gene_id "Phchi.S1G513900"
# This transcript jg15219.t2 is derived from g13687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15220.t1 is derived from g13688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17806350	17807821	.	-	.	Phchi.S3G253900
Phchi.S3	AUGUSTUS	transcript	17806350	17807821	.	-	.	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	stop_codon	17806347	17806349	.	-	0	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	CDS	17806350	17807298	1	-	1	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	exon	17806350	17807298	.	-	.	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	intron	17807299	17807402	.	-	.	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	CDS	17807403	17807821	0.99	-	0	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	exon	17807403	17807821	.	-	.	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
Phchi.S3	AUGUSTUS	start_codon	17807819	17807821	.	-	0	transcript_id "Phchi.S3G253900.t1"; gene_id "Phchi.S3G253900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5035.t1 is derived from g2205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14191243	14192113	.	-	.	Phchi.S1G219400
Phchi.S1	AUGUSTUS	transcript	14191243	14192113	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	stop_codon	14191240	14191242	.	-	0	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	CDS	14191243	14191290	1	-	0	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	exon	14191243	14191290	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	intron	14191291	14191446	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	CDS	14191447	14191538	0.98	-	2	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	exon	14191447	14191538	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	intron	14191539	14191663	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	CDS	14191664	14191805	0.98	-	0	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	exon	14191664	14191805	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	intron	14191806	14192086	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	CDS	14192087	14192113	1	-	0	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	exon	14192087	14192113	.	-	.	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
Phchi.S1	AUGUSTUS	start_codon	14192111	14192113	.	-	0	transcript_id "Phchi.S1G219400.t1"; gene_id "Phchi.S1G219400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8156.t1 is derived from g5331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34155905	34158416	.	-	.	Phchi.S1G531500
Phchi.S1	AUGUSTUS	transcript	34155905	34158416	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	stop_codon	34155902	34155904	.	-	0	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34155905	34155909	0.79	-	2	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34155905	34155909	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34155910	34156454	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34156455	34156491	1	-	0	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34156455	34156491	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34156492	34156661	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34156662	34156727	1	-	0	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34156662	34156727	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34156728	34156815	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34156816	34156894	1	-	1	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34156816	34156894	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34156895	34157006	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34157007	34157105	1	-	1	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34157007	34157105	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34157106	34157653	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34157654	34158029	1	-	2	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34157654	34158029	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34158030	34158286	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34158287	34158416	0.48	-	0	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34158287	34158416	.	-	.	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	start_codon	34158414	34158416	.	-	0	transcript_id "Phchi.S1G531500.t1"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	transcript	34155905	34158416	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	stop_codon	34155902	34155904	.	-	0	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34155905	34155909	0.71	-	2	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34155905	34155909	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34155910	34156454	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34156455	34156491	1	-	0	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34156455	34156491	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34156492	34156661	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34156662	34156727	1	-	0	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34156662	34156727	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34156728	34156815	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34156816	34156894	1	-	1	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34156816	34156894	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34156895	34157006	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34157007	34157105	1	-	1	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34157007	34157105	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34157106	34157653	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34157654	34158029	1	-	2	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34157654	34158029	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	intron	34158030	34158166	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	CDS	34158167	34158416	0.62	-	0	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	exon	34158167	34158416	.	-	.	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
Phchi.S1	AUGUSTUS	start_codon	34158414	34158416	.	-	0	transcript_id "Phchi.S1G531500.t2"; gene_id "Phchi.S1G531500"
# This transcript jg14962.t2 is derived from g13430.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14963.t1 is derived from g13431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15776662	15778191	.	-	.	Phchi.S3G228200
Phchi.S3	AUGUSTUS	transcript	15776662	15778191	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	stop_codon	15776659	15776661	.	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15776662	15776745	0.99	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15776662	15776745	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15776746	15776854	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15776855	15776911	0.99	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15776855	15776911	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15776912	15777004	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15777005	15777073	1	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15777005	15777073	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15777074	15777235	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15777236	15777340	1	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15777236	15777340	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15777341	15777493	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15777494	15777562	1	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15777494	15777562	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15777563	15777641	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15777642	15777737	1	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15777642	15777737	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15777738	15777815	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15777816	15777867	0.81	-	1	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15777816	15777867	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15777868	15777974	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15777975	15778063	0.87	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15777975	15778063	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	intron	15778064	15778152	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	CDS	15778153	15778191	0.67	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	exon	15778153	15778191	.	-	.	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
Phchi.S3	AUGUSTUS	start_codon	15778189	15778191	.	-	0	transcript_id "Phchi.S3G228200.t1"; gene_id "Phchi.S3G228200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2429.t1 is derived from g9349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6599241	6600158	.	+	.	Phchi.S5G103800
Phchi.S5	AUGUSTUS	transcript	6599241	6600158	.	+	.	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	start_codon	6599241	6599243	.	+	0	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	CDS	6599241	6599551	0.97	+	0	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	exon	6599241	6599551	.	+	.	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	intron	6599552	6599706	.	+	.	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	CDS	6599707	6599842	0.9	+	1	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	exon	6599707	6599842	.	+	.	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	intron	6599843	6599951	.	+	.	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	CDS	6599952	6600158	0.98	+	0	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	exon	6599952	6600158	.	+	.	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
Phchi.S5	AUGUSTUS	stop_codon	6600159	6600161	.	+	0	transcript_id "Phchi.S5G103800.t1"; gene_id "Phchi.S5G103800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg644.t1 is derived from g10426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4566384	4567034	.	+	.	Phchi.S6G060300
Phchi.S6	AUGUSTUS	transcript	4566384	4567034	.	+	.	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	start_codon	4566384	4566386	.	+	0	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	CDS	4566384	4566684	0.83	+	0	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	exon	4566384	4566684	.	+	.	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	intron	4566685	4566773	.	+	.	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	CDS	4566774	4566811	0.83	+	2	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	exon	4566774	4566811	.	+	.	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	intron	4566812	4566914	.	+	.	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	CDS	4566915	4567034	0.92	+	0	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	exon	4566915	4567034	.	+	.	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
Phchi.S6	AUGUSTUS	stop_codon	4567035	4567037	.	+	0	transcript_id "Phchi.S6G060300.t1"; gene_id "Phchi.S6G060300"
# This transcript jg2062.t2 is derived from g8982.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2063.t1 is derived from g8983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4665202	4666367	.	-	.	Phchi.S5G067200
Phchi.S5	AUGUSTUS	transcript	4665202	4666367	.	-	.	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	stop_codon	4665199	4665201	.	-	0	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	CDS	4665202	4666004	0.22	-	2	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	exon	4665202	4666004	.	-	.	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	intron	4666005	4666090	.	-	.	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	CDS	4666091	4666367	0.26	-	0	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	exon	4666091	4666367	.	-	.	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
Phchi.S5	AUGUSTUS	start_codon	4666365	4666367	.	-	0	transcript_id "Phchi.S5G067200.t1"; gene_id "Phchi.S5G067200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12628.t1 is derived from g8305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37650694	37652926	.	+	.	Phchi.S2G070800
Phchi.S2	AUGUSTUS	transcript	37650694	37652926	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	start_codon	37650694	37650696	.	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37650694	37650754	0.98	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37650694	37650754	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37650755	37650959	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37650960	37651005	1	+	2	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37650960	37651005	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37651006	37651097	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37651098	37651109	0.99	+	1	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37651098	37651109	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37651110	37651212	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37651213	37651297	0.95	+	1	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37651213	37651297	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37651298	37651383	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37651384	37651497	1	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37651384	37651497	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37651498	37651595	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37651596	37651753	1	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37651596	37651753	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37651754	37651845	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37651846	37651948	1	+	1	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37651846	37651948	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37651949	37652044	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37652045	37652140	1	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37652045	37652140	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37652141	37652260	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37652261	37652326	1	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37652261	37652326	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37652327	37652424	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37652425	37652544	0.96	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37652425	37652544	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37652545	37652752	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37652753	37652767	0.87	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37652753	37652767	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	intron	37652768	37652860	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	CDS	37652861	37652926	0.87	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	exon	37652861	37652926	.	+	.	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
Phchi.S2	AUGUSTUS	stop_codon	37652927	37652929	.	+	0	transcript_id "Phchi.S2G070800.t1"; gene_id "Phchi.S2G070800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2215.t1 is derived from g9135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5453843	5455181	.	-	.	Phchi.S5G082400
Phchi.S5	AUGUSTUS	transcript	5453843	5455181	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	stop_codon	5453840	5453842	.	-	0	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5453843	5453848	0.91	-	0	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5453843	5453848	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5453849	5453935	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5453936	5453949	0.68	-	2	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5453936	5453949	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5453950	5454191	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5454192	5454230	0.77	-	2	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5454192	5454230	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5454231	5454329	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5454330	5454334	0.8	-	1	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5454330	5454334	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5454335	5454442	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5454443	5454467	0.39	-	2	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5454443	5454467	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5454468	5454562	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5454563	5454601	0.48	-	2	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5454563	5454601	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5454602	5454686	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5454687	5454710	0.3	-	2	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5454687	5454710	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5454711	5455034	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5455035	5455073	0.33	-	2	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5455035	5455073	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	intron	5455074	5455162	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	CDS	5455163	5455181	0.33	-	0	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	exon	5455163	5455181	.	-	.	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
Phchi.S5	AUGUSTUS	start_codon	5455179	5455181	.	-	0	transcript_id "Phchi.S5G082400.t1"; gene_id "Phchi.S5G082400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10568.t1 is derived from g14618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1007444	1008986	.	+	.	Phchi.S4G015000
Phchi.S4	AUGUSTUS	transcript	1007444	1008986	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	start_codon	1007444	1007446	.	+	0	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	CDS	1007444	1007749	1	+	0	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	exon	1007444	1007749	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	intron	1007750	1007892	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	CDS	1007893	1008152	1	+	0	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	exon	1007893	1008152	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	intron	1008153	1008245	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	CDS	1008246	1008567	0.85	+	1	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	exon	1008246	1008567	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	intron	1008568	1008722	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	CDS	1008723	1008986	1	+	0	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	exon	1008723	1008986	.	+	.	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
Phchi.S4	AUGUSTUS	stop_codon	1008987	1008989	.	+	0	transcript_id "Phchi.S4G015000.t1"; gene_id "Phchi.S4G015000"
# This transcript jg10768.t2 is derived from g14818.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10769.t1 is derived from g14819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2015942	2017069	.	+	.	Phchi.S4G035100
Phchi.S4	AUGUSTUS	transcript	2015942	2017069	.	+	.	transcript_id "Phchi.S4G035100.t1"; gene_id "Phchi.S4G035100"
Phchi.S4	AUGUSTUS	start_codon	2015942	2015944	.	+	0	transcript_id "Phchi.S4G035100.t1"; gene_id "Phchi.S4G035100"
Phchi.S4	AUGUSTUS	CDS	2015942	2017069	0.68	+	0	transcript_id "Phchi.S4G035100.t1"; gene_id "Phchi.S4G035100"
Phchi.S4	AUGUSTUS	exon	2015942	2017069	.	+	.	transcript_id "Phchi.S4G035100.t1"; gene_id "Phchi.S4G035100"
Phchi.S4	AUGUSTUS	stop_codon	2017070	2017072	.	+	0	transcript_id "Phchi.S4G035100.t1"; gene_id "Phchi.S4G035100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14123.t1 is derived from g12590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10985754	10986278	.	-	.	Phchi.S3G144200
Phchi.S3	AUGUSTUS	transcript	10985754	10986278	.	-	.	transcript_id "Phchi.S3G144200.t1"; gene_id "Phchi.S3G144200"
Phchi.S3	AUGUSTUS	stop_codon	10985751	10985753	.	-	0	transcript_id "Phchi.S3G144200.t1"; gene_id "Phchi.S3G144200"
Phchi.S3	AUGUSTUS	CDS	10985754	10986278	0.52	-	0	transcript_id "Phchi.S3G144200.t1"; gene_id "Phchi.S3G144200"
Phchi.S3	AUGUSTUS	exon	10985754	10986278	.	-	.	transcript_id "Phchi.S3G144200.t1"; gene_id "Phchi.S3G144200"
Phchi.S3	AUGUSTUS	start_codon	10986276	10986278	.	-	0	transcript_id "Phchi.S3G144200.t1"; gene_id "Phchi.S3G144200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9833.t1 is derived from g7009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44000383	44002691	.	-	.	Phchi.S1G699200
Phchi.S1	AUGUSTUS	transcript	44000383	44002691	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	stop_codon	44000380	44000382	.	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44000383	44000383	1	-	1	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44000383	44000383	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44000384	44000518	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44000519	44000634	1	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44000519	44000634	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44000635	44000739	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44000740	44000808	0.99	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44000740	44000808	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44000809	44000914	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44000915	44001112	0.99	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44000915	44001112	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44001113	44001190	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44001191	44001394	1	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44001191	44001394	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44001395	44001479	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44001480	44001620	1	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44001480	44001620	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44001621	44001710	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44001711	44001920	1	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44001711	44001920	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	intron	44001921	44002007	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	CDS	44002008	44002691	0.34	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	exon	44002008	44002691	.	-	.	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
Phchi.S1	AUGUSTUS	start_codon	44002689	44002691	.	-	0	transcript_id "Phchi.S1G699200.t1"; gene_id "Phchi.S1G699200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1317.t1 is derived from g11100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8990601	8992700	.	-	.	Phchi.S6G127600
Phchi.S6	AUGUSTUS	transcript	8990601	8992700	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	stop_codon	8990598	8990600	.	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8990601	8990686	1	-	2	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8990601	8990686	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8990687	8990765	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8990766	8990851	1	-	1	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8990766	8990851	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8990852	8990950	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8990951	8991050	1	-	2	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8990951	8991050	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8991051	8991140	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8991141	8991240	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8991141	8991240	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8991241	8991322	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8991323	8991415	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8991323	8991415	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8991416	8991491	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8991492	8991692	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8991492	8991692	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8991693	8991779	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8991780	8991836	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8991780	8991836	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8991837	8991922	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8991923	8992027	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8991923	8992027	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8992028	8992109	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8992110	8992178	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8992110	8992178	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8992179	8992270	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8992271	8992372	1	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8992271	8992372	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	intron	8992373	8992469	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	CDS	8992470	8992700	0.85	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	exon	8992470	8992700	.	-	.	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
Phchi.S6	AUGUSTUS	start_codon	8992698	8992700	.	-	0	transcript_id "Phchi.S6G127600.t1"; gene_id "Phchi.S6G127600"
# This transcript jg3411.t2 is derived from g580.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3412.t1 is derived from g581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3382661	3384260	.	-	.	Phchi.S1G057100
Phchi.S1	AUGUSTUS	transcript	3382661	3384260	.	-	.	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	stop_codon	3382658	3382660	.	-	0	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	CDS	3382661	3383648	1	-	1	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	exon	3382661	3383648	.	-	.	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	intron	3383649	3384186	.	-	.	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	CDS	3384187	3384260	0.77	-	0	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	exon	3384187	3384260	.	-	.	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
Phchi.S1	AUGUSTUS	start_codon	3384258	3384260	.	-	0	transcript_id "Phchi.S1G057100.t1"; gene_id "Phchi.S1G057100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4347.t1 is derived from g1516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9901486	9905307	.	-	.	Phchi.S1G150600
Phchi.S1	AUGUSTUS	transcript	9901486	9905307	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	stop_codon	9901483	9901485	.	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9901486	9901517	0.74	-	2	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9901486	9901517	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9901518	9901611	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9901612	9901651	0.74	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9901612	9901651	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9901652	9901743	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9901744	9901798	0.74	-	1	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9901744	9901798	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9901799	9901895	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9901896	9902009	0.51	-	1	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9901896	9902009	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9902010	9902102	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9902103	9902227	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9902103	9902227	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9902228	9902379	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9902380	9902469	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9902380	9902469	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9902470	9902553	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9902554	9902616	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9902554	9902616	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9902617	9902709	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9902710	9902801	1	-	2	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9902710	9902801	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9902802	9902976	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9902977	9903058	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9902977	9903058	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9903059	9903169	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9903170	9903343	0.99	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9903170	9903343	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9903344	9903454	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9903455	9903536	1	-	1	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9903455	9903536	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9903537	9903689	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9903690	9903814	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9903690	9903814	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9903815	9903934	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9903935	9904012	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9903935	9904012	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9904013	9904213	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9904214	9904572	0.99	-	2	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9904214	9904572	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	intron	9904573	9904700	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	CDS	9904701	9905307	1	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	exon	9904701	9905307	.	-	.	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
Phchi.S1	AUGUSTUS	start_codon	9905305	9905307	.	-	0	transcript_id "Phchi.S1G150600.t1"; gene_id "Phchi.S1G150600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15654.t1 is derived from g14123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20498375	20499041	.	+	.	Phchi.S3G297300
Phchi.S3	AUGUSTUS	transcript	20498375	20499041	.	+	.	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	start_codon	20498375	20498377	.	+	0	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	CDS	20498375	20498493	1	+	0	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	exon	20498375	20498493	.	+	.	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	intron	20498494	20498677	.	+	.	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	CDS	20498678	20499041	0.76	+	1	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	exon	20498678	20499041	.	+	.	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
Phchi.S3	AUGUSTUS	stop_codon	20499042	20499044	.	+	0	transcript_id "Phchi.S3G297300.t1"; gene_id "Phchi.S3G297300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10459.t1 is derived from g14508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	443469	444124	.	+	.	Phchi.S4G004100
Phchi.S4	AUGUSTUS	transcript	443469	444124	.	+	.	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	start_codon	443469	443471	.	+	0	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	CDS	443469	443486	0.94	+	0	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	exon	443469	443486	.	+	.	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	intron	443487	443556	.	+	.	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	CDS	443557	443943	0.78	+	0	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	exon	443557	443943	.	+	.	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	intron	443944	444055	.	+	.	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	CDS	444056	444124	0.43	+	0	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	exon	444056	444124	.	+	.	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
Phchi.S4	AUGUSTUS	stop_codon	444125	444127	.	+	0	transcript_id "Phchi.S4G004100.t1"; gene_id "Phchi.S4G004100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12450.t1 is derived from g8127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23246374	23246830	.	-	.	Phchi.S2G053000
Phchi.S2	AUGUSTUS	transcript	23246374	23246830	.	-	.	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	stop_codon	23246371	23246373	.	-	0	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	CDS	23246374	23246381	0.71	-	2	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	exon	23246374	23246381	.	-	.	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	intron	23246382	23246580	.	-	.	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	CDS	23246581	23246830	0.73	-	0	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	exon	23246581	23246830	.	-	.	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
Phchi.S2	AUGUSTUS	start_codon	23246828	23246830	.	-	0	transcript_id "Phchi.S2G053000.t1"; gene_id "Phchi.S2G053000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13431.t1 is derived from g11898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6671808	6674744	.	-	.	Phchi.S3G075000
Phchi.S3	AUGUSTUS	transcript	6671808	6674744	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	stop_codon	6671805	6671807	.	-	0	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	CDS	6671808	6672222	0.7	-	1	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	exon	6671808	6672222	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	intron	6672223	6672571	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	CDS	6672572	6673085	0.33	-	2	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	exon	6672572	6673085	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	intron	6673086	6673177	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	CDS	6673178	6674095	1	-	2	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	exon	6673178	6674095	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	intron	6674096	6674182	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	CDS	6674183	6674744	0.95	-	0	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	exon	6674183	6674744	.	-	.	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
Phchi.S3	AUGUSTUS	start_codon	6674742	6674744	.	-	0	transcript_id "Phchi.S3G075000.t1"; gene_id "Phchi.S3G075000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7921.t1 is derived from g5095.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31917673	31918342	.	+	.	Phchi.S1G508000
Phchi.S1	AUGUSTUS	transcript	31917673	31918342	.	+	.	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	start_codon	31917673	31917675	.	+	0	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	CDS	31917673	31917700	1	+	0	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	exon	31917673	31917700	.	+	.	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	intron	31917701	31917777	.	+	.	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	CDS	31917778	31917973	1	+	2	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	exon	31917778	31917973	.	+	.	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	intron	31917974	31918068	.	+	.	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	CDS	31918069	31918342	1	+	1	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	exon	31918069	31918342	.	+	.	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	stop_codon	31918343	31918345	.	+	0	transcript_id "Phchi.S1G508000.t1"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	transcript	31917673	31918342	.	+	.	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	start_codon	31917673	31917675	.	+	0	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	CDS	31917673	31917700	1	+	0	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	exon	31917673	31917700	.	+	.	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	intron	31917701	31917774	.	+	.	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	CDS	31917775	31917973	0.99	+	2	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	exon	31917775	31917973	.	+	.	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	intron	31917974	31918068	.	+	.	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	CDS	31918069	31918342	1	+	1	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	exon	31918069	31918342	.	+	.	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
Phchi.S1	AUGUSTUS	stop_codon	31918343	31918345	.	+	0	transcript_id "Phchi.S1G508000.t2"; gene_id "Phchi.S1G508000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2854.t1 is derived from g23.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35589	36863	.	+	.	Phchi.S1G001300
Phchi.S1	AUGUSTUS	transcript	35589	36863	.	+	.	transcript_id "Phchi.S1G001300.t1"; gene_id "Phchi.S1G001300"
Phchi.S1	AUGUSTUS	start_codon	35589	35591	.	+	0	transcript_id "Phchi.S1G001300.t1"; gene_id "Phchi.S1G001300"
Phchi.S1	AUGUSTUS	CDS	35589	36863	0.69	+	0	transcript_id "Phchi.S1G001300.t1"; gene_id "Phchi.S1G001300"
Phchi.S1	AUGUSTUS	exon	35589	36863	.	+	.	transcript_id "Phchi.S1G001300.t1"; gene_id "Phchi.S1G001300"
Phchi.S1	AUGUSTUS	stop_codon	36864	36866	.	+	0	transcript_id "Phchi.S1G001300.t1"; gene_id "Phchi.S1G001300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15194.t1 is derived from g13662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17502494	17503127	.	-	.	Phchi.S3G251300
Phchi.S3	AUGUSTUS	transcript	17502494	17503127	.	-	.	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	stop_codon	17502491	17502493	.	-	0	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	CDS	17502494	17502496	0.98	-	0	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	exon	17502494	17502496	.	-	.	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	intron	17502497	17502833	.	-	.	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	CDS	17502834	17502955	0.98	-	2	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	exon	17502834	17502955	.	-	.	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	intron	17502956	17503054	.	-	.	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	CDS	17503055	17503127	0.98	-	0	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	exon	17503055	17503127	.	-	.	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
Phchi.S3	AUGUSTUS	start_codon	17503125	17503127	.	-	0	transcript_id "Phchi.S3G251300.t1"; gene_id "Phchi.S3G251300"
# This transcript jg13190.t2 is derived from g11655.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13191.t1 is derived from g11656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4615240	4616192	.	-	.	Phchi.S3G051000
Phchi.S3	AUGUSTUS	transcript	4615240	4616192	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	stop_codon	4615237	4615239	.	-	0	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	CDS	4615240	4615302	1	-	0	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	exon	4615240	4615302	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	intron	4615303	4615390	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	CDS	4615391	4615492	1	-	0	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	exon	4615391	4615492	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	intron	4615493	4615645	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	CDS	4615646	4615780	0.97	-	0	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	exon	4615646	4615780	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	intron	4615781	4615897	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	CDS	4615898	4616007	0.97	-	2	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	exon	4615898	4616007	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	intron	4616008	4616158	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	CDS	4616159	4616192	0.52	-	0	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	exon	4616159	4616192	.	-	.	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
Phchi.S3	AUGUSTUS	start_codon	4616190	4616192	.	-	0	transcript_id "Phchi.S3G051000.t1"; gene_id "Phchi.S3G051000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11850.t1 is derived from g15902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8618856	8619593	.	-	.	Phchi.S4G143200
Phchi.S4	AUGUSTUS	transcript	8618856	8619593	.	-	.	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	stop_codon	8618853	8618855	.	-	0	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	CDS	8618856	8618900	0.92	-	0	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	exon	8618856	8618900	.	-	.	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	intron	8618901	8619141	.	-	.	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	CDS	8619142	8619332	0.92	-	2	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	exon	8619142	8619332	.	-	.	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	intron	8619333	8619502	.	-	.	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	CDS	8619503	8619593	0.91	-	0	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	exon	8619503	8619593	.	-	.	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
Phchi.S4	AUGUSTUS	start_codon	8619591	8619593	.	-	0	transcript_id "Phchi.S4G143200.t1"; gene_id "Phchi.S4G143200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12872.t1 is derived from g11337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2847312	2847692	.	+	.	Phchi.S3G019100
Phchi.S3	AUGUSTUS	transcript	2847312	2847692	.	+	.	transcript_id "Phchi.S3G019100.t1"; gene_id "Phchi.S3G019100"
Phchi.S3	AUGUSTUS	start_codon	2847312	2847314	.	+	0	transcript_id "Phchi.S3G019100.t1"; gene_id "Phchi.S3G019100"
Phchi.S3	AUGUSTUS	CDS	2847312	2847692	0.98	+	0	transcript_id "Phchi.S3G019100.t1"; gene_id "Phchi.S3G019100"
Phchi.S3	AUGUSTUS	exon	2847312	2847692	.	+	.	transcript_id "Phchi.S3G019100.t1"; gene_id "Phchi.S3G019100"
Phchi.S3	AUGUSTUS	stop_codon	2847693	2847695	.	+	0	transcript_id "Phchi.S3G019100.t1"; gene_id "Phchi.S3G019100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4391.t1 is derived from g1560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10197886	10198166	.	+	.	Phchi.S1G155000
Phchi.S1	AUGUSTUS	transcript	10197886	10198166	.	+	.	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	start_codon	10197886	10197888	.	+	0	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	CDS	10197886	10197959	0.96	+	0	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	exon	10197886	10197959	.	+	.	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	intron	10197960	10198042	.	+	.	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	CDS	10198043	10198166	0.95	+	1	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	exon	10198043	10198166	.	+	.	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
Phchi.S1	AUGUSTUS	stop_codon	10198167	10198169	.	+	0	transcript_id "Phchi.S1G155000.t1"; gene_id "Phchi.S1G155000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10311.t1 is derived from g7487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47078198	47080161	.	-	.	Phchi.S1G747000
Phchi.S1	AUGUSTUS	transcript	47078198	47080161	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	stop_codon	47078195	47078197	.	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47078198	47078275	1	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47078198	47078275	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47078276	47078348	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47078349	47078429	1	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47078349	47078429	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47078430	47078525	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47078526	47078573	1	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47078526	47078573	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47078574	47078663	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47078664	47078823	1	-	1	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47078664	47078823	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47078824	47078940	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47078941	47079092	1	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47078941	47079092	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47079093	47079239	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47079240	47079319	1	-	2	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47079240	47079319	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47079320	47079418	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47079419	47079487	1	-	2	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47079419	47079487	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47079488	47079575	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47079576	47079629	1	-	2	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47079576	47079629	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	intron	47079630	47079980	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	CDS	47079981	47080161	0.73	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	exon	47079981	47080161	.	-	.	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
Phchi.S1	AUGUSTUS	start_codon	47080159	47080161	.	-	0	transcript_id "Phchi.S1G747000.t1"; gene_id "Phchi.S1G747000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7896.t1 is derived from g5070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31793260	31795936	.	+	.	Phchi.S1G505500
Phchi.S1	AUGUSTUS	transcript	31793260	31795936	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	start_codon	31793260	31793262	.	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31793260	31793445	1	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31793260	31793445	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31793446	31793588	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31793589	31793671	1	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31793589	31793671	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31793672	31793809	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31793810	31794133	0.99	+	1	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31793810	31794133	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31794134	31794331	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31794332	31794590	1	+	1	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31794332	31794590	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31794591	31794736	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31794737	31794817	1	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31794737	31794817	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31794818	31794946	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31794947	31795054	1	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31794947	31795054	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31795055	31795158	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31795159	31795188	1	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31795159	31795188	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31795189	31795315	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31795316	31795453	0.86	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31795316	31795453	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31795454	31795560	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31795561	31795598	0.98	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31795561	31795598	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31795599	31795681	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31795682	31795781	1	+	1	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31795682	31795781	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	intron	31795782	31795864	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	CDS	31795865	31795936	1	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	exon	31795865	31795936	.	+	.	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
Phchi.S1	AUGUSTUS	stop_codon	31795937	31795939	.	+	0	transcript_id "Phchi.S1G505500.t1"; gene_id "Phchi.S1G505500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2281.t1 is derived from g9201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5859587	5860175	.	+	.	Phchi.S5G089000
Phchi.S5	AUGUSTUS	transcript	5859587	5860175	.	+	.	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	start_codon	5859587	5859589	.	+	0	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	CDS	5859587	5859846	0.84	+	0	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	exon	5859587	5859846	.	+	.	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	intron	5859847	5859991	.	+	.	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	CDS	5859992	5860175	1	+	1	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	exon	5859992	5860175	.	+	.	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
Phchi.S5	AUGUSTUS	stop_codon	5860176	5860178	.	+	0	transcript_id "Phchi.S5G089000.t1"; gene_id "Phchi.S5G089000"
# This transcript jg1838.t2 is derived from g8758.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1838.t3 is derived from g8758.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1839.t1 is derived from g8759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3519311	3520729	.	-	.	Phchi.S5G044800
Phchi.S5	AUGUSTUS	transcript	3519311	3520729	.	-	.	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	stop_codon	3519308	3519310	.	-	0	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	CDS	3519311	3519804	0.71	-	2	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	exon	3519311	3519804	.	-	.	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	intron	3519805	3520016	.	-	.	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	CDS	3520017	3520098	0.99	-	0	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	exon	3520017	3520098	.	-	.	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	intron	3520099	3520186	.	-	.	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	CDS	3520187	3520729	0.96	-	0	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	exon	3520187	3520729	.	-	.	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
Phchi.S5	AUGUSTUS	start_codon	3520727	3520729	.	-	0	transcript_id "Phchi.S5G044800.t1"; gene_id "Phchi.S5G044800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14624.t1 is derived from g13092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13821766	13824382	.	+	.	Phchi.S3G194300
Phchi.S3	AUGUSTUS	transcript	13821766	13824382	.	+	.	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	start_codon	13821766	13821768	.	+	0	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	CDS	13821766	13823527	0.75	+	0	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	exon	13821766	13823527	.	+	.	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	intron	13823528	13823640	.	+	.	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	CDS	13823641	13823823	0.62	+	2	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	exon	13823641	13823823	.	+	.	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	intron	13823824	13824017	.	+	.	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	CDS	13824018	13824382	0.89	+	2	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	exon	13824018	13824382	.	+	.	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	stop_codon	13824383	13824385	.	+	0	transcript_id "Phchi.S3G194300.t1"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	transcript	13821766	13823500	.	+	.	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	start_codon	13821766	13821768	.	+	0	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	CDS	13821766	13823388	0.33	+	0	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	exon	13821766	13823388	.	+	.	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	intron	13823389	13823485	.	+	.	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	CDS	13823486	13823500	0.4	+	0	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	exon	13823486	13823500	.	+	.	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
Phchi.S3	AUGUSTUS	stop_codon	13823501	13823503	.	+	0	transcript_id "Phchi.S3G194300.t2"; gene_id "Phchi.S3G194300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14322.t1 is derived from g12789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12089494	12091553	.	-	.	Phchi.S3G164100
Phchi.S3	AUGUSTUS	transcript	12089494	12091553	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	stop_codon	12089491	12089493	.	-	0	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12089494	12089712	1	-	0	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12089494	12089712	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12089713	12089802	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12089803	12090025	1	-	1	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12089803	12090025	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12090026	12090139	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12090140	12090204	1	-	0	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12090140	12090204	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12090205	12090444	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12090445	12090563	1	-	2	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12090445	12090563	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12090564	12090696	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12090697	12090799	1	-	0	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12090697	12090799	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12090800	12090957	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12090958	12091094	1	-	2	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12090958	12091094	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12091095	12091178	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12091179	12091327	1	-	1	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12091179	12091327	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	intron	12091328	12091467	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	CDS	12091468	12091553	0.51	-	0	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	exon	12091468	12091553	.	-	.	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
Phchi.S3	AUGUSTUS	start_codon	12091551	12091553	.	-	0	transcript_id "Phchi.S3G164100.t1"; gene_id "Phchi.S3G164100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8768.t1 is derived from g5943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37869061	37869866	.	-	.	Phchi.S1G592700
Phchi.S1	AUGUSTUS	transcript	37869061	37869866	.	-	.	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	stop_codon	37869058	37869060	.	-	0	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	CDS	37869061	37869463	0.99	-	1	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	exon	37869061	37869463	.	-	.	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	intron	37869464	37869538	.	-	.	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	CDS	37869539	37869591	0.99	-	0	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	exon	37869539	37869591	.	-	.	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	intron	37869592	37869686	.	-	.	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	CDS	37869687	37869866	0.85	-	0	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	exon	37869687	37869866	.	-	.	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
Phchi.S1	AUGUSTUS	start_codon	37869864	37869866	.	-	0	transcript_id "Phchi.S1G592700.t1"; gene_id "Phchi.S1G592700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10297.t1 is derived from g7473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46987252	46988976	.	+	.	Phchi.S1G745600
Phchi.S1	AUGUSTUS	transcript	46987252	46988976	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	start_codon	46987252	46987254	.	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46987252	46987356	0.7	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46987252	46987356	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46987357	46987495	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46987496	46987544	1	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46987496	46987544	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46987545	46987631	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46987632	46987720	1	+	2	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46987632	46987720	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46987721	46987799	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46987800	46987856	1	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46987800	46987856	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46987857	46987941	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46987942	46988004	1	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46987942	46988004	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46988005	46988096	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46988097	46988162	1	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46988097	46988162	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46988163	46988261	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46988262	46988348	1	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46988262	46988348	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46988349	46988529	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46988530	46988623	1	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46988530	46988623	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	intron	46988624	46988755	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	CDS	46988756	46988976	0.53	+	2	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	exon	46988756	46988976	.	+	.	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
Phchi.S1	AUGUSTUS	stop_codon	46988977	46988979	.	+	0	transcript_id "Phchi.S1G745600.t1"; gene_id "Phchi.S1G745600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9337.t1 is derived from g6512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40996198	40997985	.	-	.	Phchi.S1G649600
Phchi.S1	AUGUSTUS	transcript	40996198	40997985	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	stop_codon	40996195	40996197	.	-	0	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996198	40996316	0.94	-	2	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996198	40996316	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40996317	40996421	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996422	40996481	1	-	2	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996422	40996481	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40996482	40996614	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996615	40996803	0.99	-	2	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996615	40996803	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40996804	40996944	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996945	40997047	1	-	0	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996945	40997047	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40997048	40997192	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40997193	40997311	1	-	2	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40997193	40997311	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40997312	40997407	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40997408	40997495	1	-	0	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40997408	40997495	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40997496	40997757	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40997758	40997985	1	-	0	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40997758	40997985	.	-	.	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	start_codon	40997983	40997985	.	-	0	transcript_id "Phchi.S1G649600.t1"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	transcript	40996198	40997985	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	stop_codon	40996195	40996197	.	-	0	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996198	40996316	0.88	-	2	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996198	40996316	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40996317	40996421	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996422	40996481	0.98	-	2	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996422	40996481	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40996482	40996614	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996615	40996791	0.99	-	2	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996615	40996791	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40996792	40996944	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40996945	40997047	1	-	0	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40996945	40997047	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40997048	40997192	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40997193	40997311	1	-	2	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40997193	40997311	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40997312	40997407	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40997408	40997495	1	-	0	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40997408	40997495	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	intron	40997496	40997757	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	CDS	40997758	40997985	0.99	-	0	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	exon	40997758	40997985	.	-	.	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
Phchi.S1	AUGUSTUS	start_codon	40997983	40997985	.	-	0	transcript_id "Phchi.S1G649600.t2"; gene_id "Phchi.S1G649600"
# This transcript jg15286.t2 is derived from g13754.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15287.t1 is derived from g13755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18214329	18216465	.	-	.	Phchi.S3G260600
Phchi.S3	AUGUSTUS	transcript	18214329	18216465	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	stop_codon	18214326	18214328	.	-	0	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18214329	18214647	0.96	-	1	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18214329	18214647	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	intron	18214648	18214735	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18214736	18215103	0.97	-	0	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18214736	18215103	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	intron	18215104	18215383	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18215384	18215543	0.98	-	1	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18215384	18215543	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	intron	18215544	18215653	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18215654	18215698	0.99	-	1	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18215654	18215698	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	intron	18215699	18215812	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18215813	18215922	0.81	-	0	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18215813	18215922	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	intron	18215923	18216060	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18216061	18216255	0.13	-	0	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18216061	18216255	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	intron	18216256	18216429	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	CDS	18216430	18216465	0.34	-	0	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	exon	18216430	18216465	.	-	.	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
Phchi.S3	AUGUSTUS	start_codon	18216463	18216465	.	-	0	transcript_id "Phchi.S3G260600.t1"; gene_id "Phchi.S3G260600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10274.t1 is derived from g7450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46787310	46787801	.	-	.	Phchi.S1G743300
Phchi.S1	AUGUSTUS	transcript	46787310	46787801	.	-	.	transcript_id "Phchi.S1G743300.t1"; gene_id "Phchi.S1G743300"
Phchi.S1	AUGUSTUS	stop_codon	46787307	46787309	.	-	0	transcript_id "Phchi.S1G743300.t1"; gene_id "Phchi.S1G743300"
Phchi.S1	AUGUSTUS	CDS	46787310	46787801	0.46	-	0	transcript_id "Phchi.S1G743300.t1"; gene_id "Phchi.S1G743300"
Phchi.S1	AUGUSTUS	exon	46787310	46787801	.	-	.	transcript_id "Phchi.S1G743300.t1"; gene_id "Phchi.S1G743300"
Phchi.S1	AUGUSTUS	start_codon	46787799	46787801	.	-	0	transcript_id "Phchi.S1G743300.t1"; gene_id "Phchi.S1G743300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12674.t1 is derived from g14408.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	14603	16636	.	-	.	Phchi.C62G000500
Phchi.C62	AUGUSTUS	transcript	14603	16636	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	stop_codon	14600	14602	.	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	14603	14848	0.74	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	14603	14848	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	14849	14932	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	14933	15049	1	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	14933	15049	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15050	15143	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15144	15245	1	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15144	15245	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15246	15335	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15336	15362	0.96	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15336	15362	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15363	15420	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15421	15429	1	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15421	15429	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15430	15623	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15624	15875	0.97	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15624	15875	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15876	15989	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15990	16223	0.55	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15990	16223	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	16224	16327	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	16328	16636	0.49	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	16328	16636	.	-	.	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	start_codon	16634	16636	.	-	0	transcript_id "Phchi.C62G000500.t1"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	transcript	14603	16636	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	stop_codon	14600	14602	.	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	14603	14848	0.77	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	14603	14848	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	14849	14932	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	14933	15049	1	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	14933	15049	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15050	15143	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15144	15245	1	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15144	15245	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15246	15335	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15336	15362	0.97	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15336	15362	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15363	15420	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15421	15429	1	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15421	15429	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15430	15623	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15624	15833	1	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15624	15833	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	15834	15989	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	15990	16223	0.49	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	15990	16223	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	intron	16224	16327	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	CDS	16328	16636	0.46	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	exon	16328	16636	.	-	.	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
Phchi.C62	AUGUSTUS	start_codon	16634	16636	.	-	0	transcript_id "Phchi.C62G000500.t2"; gene_id "Phchi.C62G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13256.t1 is derived from g11721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4945829	4947345	.	-	.	Phchi.S3G057500
Phchi.S3	AUGUSTUS	transcript	4945829	4947345	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	stop_codon	4945826	4945828	.	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4945829	4945917	0.75	-	2	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4945829	4945917	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	intron	4945918	4946026	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4946027	4946114	0.96	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4946027	4946114	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	intron	4946115	4946253	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4946254	4946307	1	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4946254	4946307	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	intron	4946308	4946392	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4946393	4946503	1	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4946393	4946503	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	intron	4946504	4946626	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4946627	4946782	1	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4946627	4946782	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	intron	4946783	4946881	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4946882	4947019	1	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4946882	4947019	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	intron	4947020	4947117	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	CDS	4947118	4947345	0.94	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	exon	4947118	4947345	.	-	.	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
Phchi.S3	AUGUSTUS	start_codon	4947343	4947345	.	-	0	transcript_id "Phchi.S3G057500.t1"; gene_id "Phchi.S3G057500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15913.t1 is derived from g14383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22191357	22192001	.	+	.	Phchi.S3G323200
Phchi.S3	AUGUSTUS	transcript	22191357	22192001	.	+	.	transcript_id "Phchi.S3G323200.t1"; gene_id "Phchi.S3G323200"
Phchi.S3	AUGUSTUS	start_codon	22191357	22191359	.	+	0	transcript_id "Phchi.S3G323200.t1"; gene_id "Phchi.S3G323200"
Phchi.S3	AUGUSTUS	CDS	22191357	22192001	0.37	+	0	transcript_id "Phchi.S3G323200.t1"; gene_id "Phchi.S3G323200"
Phchi.S3	AUGUSTUS	exon	22191357	22192001	.	+	.	transcript_id "Phchi.S3G323200.t1"; gene_id "Phchi.S3G323200"
Phchi.S3	AUGUSTUS	stop_codon	22192002	22192004	.	+	0	transcript_id "Phchi.S3G323200.t1"; gene_id "Phchi.S3G323200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8543.t1 is derived from g5718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36561774	36564608	.	+	.	Phchi.S1G570200
Phchi.S1	AUGUSTUS	transcript	36561774	36564608	.	+	.	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	start_codon	36561774	36561776	.	+	0	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	CDS	36561774	36561932	1	+	0	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	exon	36561774	36561932	.	+	.	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	intron	36561933	36562088	.	+	.	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	CDS	36562089	36563105	1	+	0	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	exon	36562089	36563105	.	+	.	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	intron	36563106	36563258	.	+	.	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	CDS	36563259	36564608	1	+	0	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	exon	36563259	36564608	.	+	.	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
Phchi.S1	AUGUSTUS	stop_codon	36564609	36564611	.	+	0	transcript_id "Phchi.S1G570200.t1"; gene_id "Phchi.S1G570200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg439.t1 is derived from g10221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3089169	3089978	.	+	.	Phchi.S6G039800
Phchi.S6	AUGUSTUS	transcript	3089169	3089978	.	+	.	transcript_id "Phchi.S6G039800.t1"; gene_id "Phchi.S6G039800"
Phchi.S6	AUGUSTUS	start_codon	3089169	3089171	.	+	0	transcript_id "Phchi.S6G039800.t1"; gene_id "Phchi.S6G039800"
Phchi.S6	AUGUSTUS	CDS	3089169	3089978	0.55	+	0	transcript_id "Phchi.S6G039800.t1"; gene_id "Phchi.S6G039800"
Phchi.S6	AUGUSTUS	exon	3089169	3089978	.	+	.	transcript_id "Phchi.S6G039800.t1"; gene_id "Phchi.S6G039800"
Phchi.S6	AUGUSTUS	stop_codon	3089979	3089981	.	+	0	transcript_id "Phchi.S6G039800.t1"; gene_id "Phchi.S6G039800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5073.t1 is derived from g2243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14543871	14545916	.	-	.	Phchi.S1G223200
Phchi.S1	AUGUSTUS	transcript	14543871	14545916	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	stop_codon	14543868	14543870	.	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14543871	14543942	0.99	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14543871	14543942	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14543943	14544054	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14544055	14544217	0.99	-	1	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14544055	14544217	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14544218	14544316	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14544317	14544509	1	-	2	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14544317	14544509	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14544510	14544616	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14544617	14544688	1	-	2	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14544617	14544688	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14544689	14544835	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14544836	14544908	1	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14544836	14544908	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14544909	14545058	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14545059	14545163	1	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14545059	14545163	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14545164	14545279	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14545280	14545402	1	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14545280	14545402	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14545403	14545537	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14545538	14545614	1	-	2	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14545538	14545614	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	intron	14545615	14545705	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	CDS	14545706	14545916	0.99	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	exon	14545706	14545916	.	-	.	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
Phchi.S1	AUGUSTUS	start_codon	14545914	14545916	.	-	0	transcript_id "Phchi.S1G223200.t1"; gene_id "Phchi.S1G223200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3885.t1 is derived from g1054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6204830	6205519	.	+	.	Phchi.S1G104400
Phchi.S1	AUGUSTUS	transcript	6204830	6205519	.	+	.	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	start_codon	6204830	6204832	.	+	0	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	CDS	6204830	6205079	0.82	+	0	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	exon	6204830	6205079	.	+	.	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	intron	6205080	6205382	.	+	.	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	CDS	6205383	6205519	1	+	2	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	exon	6205383	6205519	.	+	.	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
Phchi.S1	AUGUSTUS	stop_codon	6205520	6205522	.	+	0	transcript_id "Phchi.S1G104400.t1"; gene_id "Phchi.S1G104400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13921.t1 is derived from g12388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9662200	9662734	.	-	.	Phchi.S3G124000
Phchi.S3	AUGUSTUS	transcript	9662200	9662734	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	stop_codon	9662197	9662199	.	-	0	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	CDS	9662200	9662276	0.61	-	2	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	exon	9662200	9662276	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	intron	9662277	9662350	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	CDS	9662351	9662405	1	-	0	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	exon	9662351	9662405	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	intron	9662406	9662549	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	CDS	9662550	9662633	1	-	0	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	exon	9662550	9662633	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	intron	9662634	9662710	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	CDS	9662711	9662734	0.97	-	0	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	exon	9662711	9662734	.	-	.	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
Phchi.S3	AUGUSTUS	start_codon	9662732	9662734	.	-	0	transcript_id "Phchi.S3G124000.t1"; gene_id "Phchi.S3G124000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12038.t1 is derived from g7713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	845380	848353	.	-	.	Phchi.S2G011800
Phchi.S2	AUGUSTUS	transcript	845380	848353	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	stop_codon	845377	845379	.	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	845380	845502	0.9	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	845380	845502	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	845503	845655	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	845656	845707	0.44	-	1	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	845656	845707	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	845708	845863	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	845864	846117	0.68	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	845864	846117	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	846118	846232	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	846233	846661	0.89	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	846233	846661	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	846662	846809	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	846810	846869	1	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	846810	846869	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	846870	847077	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	847078	847331	0.74	-	2	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	847078	847331	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	847332	847456	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	847457	847610	0.82	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	847457	847610	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	intron	847611	847717	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	CDS	847718	848353	0.6	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	exon	847718	848353	.	-	.	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
Phchi.S2	AUGUSTUS	start_codon	848351	848353	.	-	0	transcript_id "Phchi.S2G011800.t1"; gene_id "Phchi.S2G011800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3553.t1 is derived from g722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4456196	4457502	.	-	.	Phchi.S1G071200
Phchi.S1	AUGUSTUS	transcript	4456196	4457502	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	stop_codon	4456193	4456195	.	-	0	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	CDS	4456196	4456593	1	-	2	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	exon	4456196	4456593	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	intron	4456594	4456729	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	CDS	4456730	4456889	1	-	0	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	exon	4456730	4456889	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	intron	4456890	4456978	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	CDS	4456979	4457164	1	-	0	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	exon	4456979	4457164	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	intron	4457165	4457274	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	CDS	4457275	4457502	0.66	-	0	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	exon	4457275	4457502	.	-	.	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
Phchi.S1	AUGUSTUS	start_codon	4457500	4457502	.	-	0	transcript_id "Phchi.S1G071200.t1"; gene_id "Phchi.S1G071200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4994.t1 is derived from g2164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13932103	13933915	.	-	.	Phchi.S1G215300
Phchi.S1	AUGUSTUS	transcript	13932103	13933915	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	stop_codon	13932100	13932102	.	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13932103	13932576	0.81	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13932103	13932576	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	intron	13932577	13932673	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13932674	13932748	1	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13932674	13932748	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	intron	13932749	13932837	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13932838	13932912	1	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13932838	13932912	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	intron	13932913	13933080	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13933081	13933146	1	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13933081	13933146	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	intron	13933147	13933327	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13933328	13933404	0.98	-	2	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13933328	13933404	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	intron	13933405	13933481	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13933482	13933684	0.53	-	1	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13933482	13933684	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	intron	13933685	13933763	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	CDS	13933764	13933915	1	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	exon	13933764	13933915	.	-	.	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
Phchi.S1	AUGUSTUS	start_codon	13933913	13933915	.	-	0	transcript_id "Phchi.S1G215300.t1"; gene_id "Phchi.S1G215300"
# This transcript jg14017.t2 is derived from g12484.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14018.t1 is derived from g12485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10329687	10331672	.	-	.	Phchi.S3G133700
Phchi.S3	AUGUSTUS	transcript	10329687	10331672	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	stop_codon	10329684	10329686	.	-	0	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10329687	10329752	1	-	0	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10329687	10329752	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	intron	10329753	10329831	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10329832	10330317	0.83	-	0	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10329832	10330317	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	intron	10330318	10330425	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10330426	10330564	0.64	-	1	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10330426	10330564	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	intron	10330565	10330638	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10330639	10330728	0.42	-	1	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10330639	10330728	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	intron	10330729	10330997	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10330998	10331200	1	-	0	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10330998	10331200	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	intron	10331201	10331342	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10331343	10331416	1	-	2	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10331343	10331416	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	intron	10331417	10331629	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	CDS	10331630	10331672	0.7	-	0	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	exon	10331630	10331672	.	-	.	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
Phchi.S3	AUGUSTUS	start_codon	10331670	10331672	.	-	0	transcript_id "Phchi.S3G133700.t1"; gene_id "Phchi.S3G133700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5070.t1 is derived from g2240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14537079	14538953	.	-	.	Phchi.S1G222900
Phchi.S1	AUGUSTUS	transcript	14537079	14538953	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	stop_codon	14537076	14537078	.	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	CDS	14537079	14537303	1	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	exon	14537079	14537303	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	intron	14537304	14537407	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	CDS	14537408	14537686	0.99	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	exon	14537408	14537686	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	intron	14537687	14537791	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	CDS	14537792	14538022	1	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	exon	14537792	14538022	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	intron	14538023	14538130	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	CDS	14538131	14538316	1	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	exon	14538131	14538316	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	intron	14538317	14538393	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	CDS	14538394	14538743	1	-	2	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	exon	14538394	14538743	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	intron	14538744	14538826	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	CDS	14538827	14538953	0.86	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	exon	14538827	14538953	.	-	.	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
Phchi.S1	AUGUSTUS	start_codon	14538951	14538953	.	-	0	transcript_id "Phchi.S1G222900.t1"; gene_id "Phchi.S1G222900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg888.t1 is derived from g10670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6297308	6299723	.	+	.	Phchi.S6G084700
Phchi.S6	AUGUSTUS	transcript	6297308	6299723	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	start_codon	6297308	6297310	.	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6297308	6297579	0.8	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6297308	6297579	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6297580	6297785	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6297786	6298110	1	+	1	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6297786	6298110	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6298111	6298202	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6298203	6298352	0.96	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6298203	6298352	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6298353	6298462	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6298463	6298717	1	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6298463	6298717	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6298718	6298867	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6298868	6298960	1	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6298868	6298960	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6298961	6299039	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6299040	6299118	1	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6299040	6299118	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6299119	6299236	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6299237	6299343	1	+	2	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6299237	6299343	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	intron	6299344	6299510	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	CDS	6299511	6299723	0.99	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	exon	6299511	6299723	.	+	.	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
Phchi.S6	AUGUSTUS	stop_codon	6299724	6299726	.	+	0	transcript_id "Phchi.S6G084700.t1"; gene_id "Phchi.S6G084700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg1103.t1 is derived from g10886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7619326	7623147	.	+	.	Phchi.S6G106200
Phchi.S6	AUGUSTUS	transcript	7619326	7621599	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	start_codon	7619326	7619328	.	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619326	7619410	0.85	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619326	7619410	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619411	7619510	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619511	7619626	1	+	2	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619511	7619626	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619627	7619710	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619711	7619816	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619711	7619816	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619817	7619914	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619915	7620037	1	+	2	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619915	7620037	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620038	7620148	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620149	7620222	1	+	2	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620149	7620222	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620223	7620311	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620312	7620356	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620312	7620356	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620357	7620504	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620505	7620555	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620505	7620555	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620556	7620651	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620652	7620720	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620652	7620720	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620721	7620863	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620864	7620922	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620864	7620922	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620923	7621061	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621062	7621131	0.98	+	1	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621062	7621131	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621132	7621233	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621234	7621314	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621234	7621314	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621315	7621393	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621394	7621493	1	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621394	7621493	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621494	7621576	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621577	7621599	1	+	2	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621577	7621599	.	+	.	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	stop_codon	7621600	7621602	.	+	0	transcript_id "Phchi.S6G106200.t1"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	transcript	7621630	7623147	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	start_codon	7621630	7621632	.	+	0	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621630	7621698	0.68	+	0	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621630	7621698	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621699	7621783	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621784	7621846	1	+	0	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621784	7621846	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621847	7621981	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621982	7622059	1	+	0	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621982	7622059	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7622060	7622685	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7622686	7622831	1	+	0	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7622686	7622831	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7622832	7622908	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7622909	7622979	1	+	1	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7622909	7622979	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7622980	7623067	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7623068	7623147	0.94	+	2	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7623068	7623147	.	+	.	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	stop_codon	7623148	7623150	.	+	0	transcript_id "Phchi.S6G106200.t2"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	transcript	7619326	7621599	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	start_codon	7619326	7619328	.	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619326	7619410	0.8	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619326	7619410	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619411	7619510	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619511	7619626	1	+	2	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619511	7619626	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619627	7619705	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619706	7619816	1	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619706	7619816	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619817	7619914	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619915	7619990	0.67	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619915	7619990	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619991	7620148	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620149	7620222	1	+	2	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620149	7620222	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620223	7620311	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620312	7620356	1	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620312	7620356	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620357	7620504	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620505	7620555	1	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620505	7620555	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620556	7620651	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620652	7620720	1	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620652	7620720	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620721	7620863	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620864	7620922	1	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620864	7620922	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620923	7621061	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621062	7621131	0.98	+	1	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621062	7621131	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621132	7621233	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621234	7621314	1	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621234	7621314	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621315	7621393	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621394	7621493	0.98	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621394	7621493	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621494	7621576	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621577	7621599	0.98	+	2	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621577	7621599	.	+	.	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	stop_codon	7621600	7621602	.	+	0	transcript_id "Phchi.S6G106200.t3"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	transcript	7619326	7623147	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	start_codon	7619326	7619328	.	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619326	7619410	0.74	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619326	7619410	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619411	7619510	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619511	7619626	1	+	2	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619511	7619626	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619627	7619705	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619706	7619816	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619706	7619816	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619817	7619914	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7619915	7619990	0.61	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7619915	7619990	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7619991	7620148	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620149	7620222	1	+	2	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620149	7620222	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620223	7620311	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620312	7620356	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620312	7620356	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620357	7620504	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620505	7620555	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620505	7620555	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620556	7620651	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620652	7620720	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620652	7620720	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620721	7620863	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7620864	7620922	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7620864	7620922	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7620923	7621061	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621062	7621131	0.97	+	1	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621062	7621131	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621132	7621233	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621234	7621314	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621234	7621314	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621315	7621393	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621394	7621441	0.79	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621394	7621441	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621442	7621543	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621544	7621576	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621544	7621576	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621577	7621783	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621784	7621846	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621784	7621846	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7621847	7621981	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7621982	7622059	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7621982	7622059	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7622060	7622685	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7622686	7622831	1	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7622686	7622831	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7622832	7622908	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7622909	7622979	1	+	1	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7622909	7622979	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	intron	7622980	7623067	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	CDS	7623068	7623147	0.89	+	2	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	exon	7623068	7623147	.	+	.	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
Phchi.S6	AUGUSTUS	stop_codon	7623148	7623150	.	+	0	transcript_id "Phchi.S6G106200.t4"; gene_id "Phchi.S6G106200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3476.t1 is derived from g645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3979141	3980502	.	+	.	Phchi.S1G063500
Phchi.S1	AUGUSTUS	transcript	3979141	3980502	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	start_codon	3979141	3979143	.	+	0	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	CDS	3979141	3979284	0.64	+	0	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	exon	3979141	3979284	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	intron	3979285	3979436	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	CDS	3979437	3979553	0.63	+	0	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	exon	3979437	3979553	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	intron	3979554	3979687	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	CDS	3979688	3980279	0.43	+	0	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	exon	3979688	3980279	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	intron	3980280	3980383	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	CDS	3980384	3980502	0.36	+	2	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	exon	3980384	3980502	.	+	.	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
Phchi.S1	AUGUSTUS	stop_codon	3980503	3980505	.	+	0	transcript_id "Phchi.S1G063500.t1"; gene_id "Phchi.S1G063500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1682.t1 is derived from g8601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2485456	2486667	.	+	.	Phchi.S5G029100
Phchi.S5	AUGUSTUS	transcript	2485456	2486667	.	+	.	transcript_id "Phchi.S5G029100.t1"; gene_id "Phchi.S5G029100"
Phchi.S5	AUGUSTUS	start_codon	2485456	2485458	.	+	0	transcript_id "Phchi.S5G029100.t1"; gene_id "Phchi.S5G029100"
Phchi.S5	AUGUSTUS	CDS	2485456	2486667	0.87	+	0	transcript_id "Phchi.S5G029100.t1"; gene_id "Phchi.S5G029100"
Phchi.S5	AUGUSTUS	exon	2485456	2486667	.	+	.	transcript_id "Phchi.S5G029100.t1"; gene_id "Phchi.S5G029100"
Phchi.S5	AUGUSTUS	stop_codon	2486668	2486670	.	+	0	transcript_id "Phchi.S5G029100.t1"; gene_id "Phchi.S5G029100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10254.t1 is derived from g7430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46696367	46698198	.	-	.	Phchi.S1G741300
Phchi.S1	AUGUSTUS	transcript	46696367	46698198	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	stop_codon	46696364	46696366	.	-	0	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	CDS	46696367	46696456	1	-	0	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	exon	46696367	46696456	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	intron	46696457	46696553	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	CDS	46696554	46696724	1	-	0	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	exon	46696554	46696724	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	intron	46696725	46696804	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	CDS	46696805	46697062	1	-	0	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	exon	46696805	46697062	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	intron	46697063	46697154	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	CDS	46697155	46698198	1	-	0	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	exon	46697155	46698198	.	-	.	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
Phchi.S1	AUGUSTUS	start_codon	46698196	46698198	.	-	0	transcript_id "Phchi.S1G741300.t1"; gene_id "Phchi.S1G741300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4190.t1 is derived from g1359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8842364	8843458	.	-	.	Phchi.S1G134900
Phchi.S1	AUGUSTUS	transcript	8842364	8843458	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	stop_codon	8842361	8842363	.	-	0	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	CDS	8842364	8842383	0.61	-	2	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	exon	8842364	8842383	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	intron	8842384	8842525	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	CDS	8842526	8842647	0.48	-	1	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	exon	8842526	8842647	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	intron	8842648	8842802	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	CDS	8842803	8842838	0.48	-	1	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	exon	8842803	8842838	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	intron	8842839	8842974	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	CDS	8842975	8843190	0.69	-	1	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	exon	8842975	8843190	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	intron	8843191	8843390	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	CDS	8843391	8843458	0.75	-	0	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	exon	8843391	8843458	.	-	.	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
Phchi.S1	AUGUSTUS	start_codon	8843456	8843458	.	-	0	transcript_id "Phchi.S1G134900.t1"; gene_id "Phchi.S1G134900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12798.t1 is derived from g11263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2437330	2437779	.	+	.	Phchi.S3G011700
Phchi.S3	AUGUSTUS	transcript	2437330	2437779	.	+	.	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	start_codon	2437330	2437332	.	+	0	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	CDS	2437330	2437579	0.65	+	0	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	exon	2437330	2437579	.	+	.	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	intron	2437580	2437774	.	+	.	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	CDS	2437775	2437779	1	+	2	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	exon	2437775	2437779	.	+	.	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
Phchi.S3	AUGUSTUS	stop_codon	2437780	2437782	.	+	0	transcript_id "Phchi.S3G011700.t1"; gene_id "Phchi.S3G011700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5699.t1 is derived from g2869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18390723	18397516	.	-	.	Phchi.S1G285800
Phchi.S1	AUGUSTUS	transcript	18390723	18397516	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	stop_codon	18390720	18390722	.	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18390723	18391133	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18390723	18391133	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18391134	18391230	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18391231	18391404	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18391231	18391404	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18391405	18391498	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18391499	18392047	0.8	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18391499	18392047	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18392048	18392148	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18392149	18392298	0.95	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18392149	18392298	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18392299	18392390	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18392391	18392588	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18392391	18392588	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18392589	18392662	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18392663	18392874	1	-	2	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18392663	18392874	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18392875	18392969	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18392970	18393040	0.87	-	1	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18392970	18393040	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18393041	18393108	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18393109	18393233	0.83	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18393109	18393233	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18393234	18393447	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18393448	18393731	0.7	-	2	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18393448	18393731	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18393732	18393882	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18393883	18394057	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18393883	18394057	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18394058	18394173	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18394174	18394428	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18394174	18394428	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18394429	18394525	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18394526	18394660	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18394526	18394660	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18394661	18394796	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18394797	18395093	0.99	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18394797	18395093	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18395094	18395194	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18395195	18395393	0.8	-	1	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18395195	18395393	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18395394	18395478	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18395479	18396121	0.95	-	2	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18395479	18396121	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18396122	18396220	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18396221	18396332	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18396221	18396332	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18396333	18396416	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18396417	18396494	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18396417	18396494	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18396495	18396589	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18396590	18397115	0.73	-	1	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18396590	18397115	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18397116	18397221	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18397222	18397311	0.91	-	1	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18397222	18397311	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	intron	18397312	18397511	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	CDS	18397512	18397516	1	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	exon	18397512	18397516	.	-	.	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
Phchi.S1	AUGUSTUS	start_codon	18397514	18397516	.	-	0	transcript_id "Phchi.S1G285800.t1"; gene_id "Phchi.S1G285800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2340.t1 is derived from g9260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6244870	6246822	.	-	.	Phchi.S5G094900
Phchi.S5	AUGUSTUS	transcript	6244870	6246822	.	-	.	transcript_id "Phchi.S5G094900.t1"; gene_id "Phchi.S5G094900"
Phchi.S5	AUGUSTUS	stop_codon	6244867	6244869	.	-	0	transcript_id "Phchi.S5G094900.t1"; gene_id "Phchi.S5G094900"
Phchi.S5	AUGUSTUS	CDS	6244870	6246822	1	-	0	transcript_id "Phchi.S5G094900.t1"; gene_id "Phchi.S5G094900"
Phchi.S5	AUGUSTUS	exon	6244870	6246822	.	-	.	transcript_id "Phchi.S5G094900.t1"; gene_id "Phchi.S5G094900"
Phchi.S5	AUGUSTUS	start_codon	6246820	6246822	.	-	0	transcript_id "Phchi.S5G094900.t1"; gene_id "Phchi.S5G094900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7670.t1 is derived from g4844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30562677	30563398	.	-	.	Phchi.S1G482900
Phchi.S1	AUGUSTUS	transcript	30562677	30563398	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	stop_codon	30562674	30562676	.	-	0	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30562677	30562744	1	-	2	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30562677	30562744	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	intron	30562745	30562872	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30562873	30562968	1	-	2	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30562873	30562968	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	intron	30562969	30563114	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30563115	30563235	1	-	0	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30563115	30563235	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	intron	30563236	30563317	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30563318	30563398	0.67	-	0	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30563318	30563398	.	-	.	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	start_codon	30563396	30563398	.	-	0	transcript_id "Phchi.S1G482900.t1"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	transcript	30562677	30563398	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	stop_codon	30562674	30562676	.	-	0	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30562677	30562744	1	-	2	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30562677	30562744	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	intron	30562745	30562872	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30562873	30562965	1	-	2	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30562873	30562965	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	intron	30562966	30563114	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30563115	30563235	1	-	0	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30563115	30563235	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	intron	30563236	30563317	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	CDS	30563318	30563398	0.61	-	0	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	exon	30563318	30563398	.	-	.	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
Phchi.S1	AUGUSTUS	start_codon	30563396	30563398	.	-	0	transcript_id "Phchi.S1G482900.t2"; gene_id "Phchi.S1G482900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6247.t1 is derived from g3419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21860764	21864177	.	+	.	Phchi.S1G340600
Phchi.S1	AUGUSTUS	transcript	21860764	21864177	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	start_codon	21860764	21860766	.	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21860764	21861060	0.55	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21860764	21861060	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21861061	21861188	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21861189	21861209	0.57	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21861189	21861209	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21861210	21861305	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21861306	21861520	1	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21861306	21861520	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21861521	21861716	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21861717	21862153	0.54	+	1	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21861717	21862153	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21862154	21862341	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21862342	21862423	0.51	+	2	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21862342	21862423	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21862424	21862558	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21862559	21862655	1	+	1	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21862559	21862655	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21862656	21862809	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21862810	21862901	1	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21862810	21862901	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21862902	21863028	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21863029	21863149	1	+	1	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21863029	21863149	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21863150	21863279	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21863280	21863365	1	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21863280	21863365	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21863366	21863473	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21863474	21863525	0.6	+	1	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21863474	21863525	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	intron	21863526	21863637	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	CDS	21863638	21864177	0.84	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	exon	21863638	21864177	.	+	.	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
Phchi.S1	AUGUSTUS	stop_codon	21864178	21864180	.	+	0	transcript_id "Phchi.S1G340600.t1"; gene_id "Phchi.S1G340600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10565.t1 is derived from g14615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	997493	1000428	.	+	.	Phchi.S4G014700
Phchi.S4	AUGUSTUS	transcript	997493	1000428	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	start_codon	997493	997495	.	+	0	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	997493	997676	0.48	+	0	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	997493	997676	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	intron	997677	997777	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	997778	997812	0.36	+	2	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	997778	997812	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	intron	997813	997886	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	997887	998049	0.45	+	0	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	997887	998049	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	intron	998050	998133	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	998134	998201	1	+	2	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	998134	998201	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	intron	998202	998288	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	998289	998548	0.63	+	0	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	998289	998548	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	intron	998549	998646	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	998647	1000333	0.36	+	1	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	998647	1000333	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	intron	1000334	1000422	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	CDS	1000423	1000428	0.64	+	0	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	exon	1000423	1000428	.	+	.	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
Phchi.S4	AUGUSTUS	stop_codon	1000429	1000431	.	+	0	transcript_id "Phchi.S4G014700.t1"; gene_id "Phchi.S4G014700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2843.t1 is derived from g12.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3060	4400	.	+	.	Phchi.S1G000200
Phchi.S1	AUGUSTUS	transcript	3060	4400	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	start_codon	3060	3062	.	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	CDS	3060	3221	0.7	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	exon	3060	3221	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	intron	3222	3426	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	CDS	3427	3633	0.76	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	exon	3427	3633	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	intron	3634	3743	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	CDS	3744	3854	0.75	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	exon	3744	3854	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	intron	3855	3969	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	CDS	3970	4146	0.97	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	exon	3970	4146	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	intron	4147	4232	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	CDS	4233	4400	0.58	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	exon	4233	4400	.	+	.	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
Phchi.S1	AUGUSTUS	stop_codon	4401	4403	.	+	0	transcript_id "Phchi.S1G000200.t1"; gene_id "Phchi.S1G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1085.t1 is derived from g10868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7518130	7519153	.	+	.	Phchi.S6G104400
Phchi.S6	AUGUSTUS	transcript	7518130	7519153	.	+	.	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	start_codon	7518130	7518132	.	+	0	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	CDS	7518130	7518369	0.75	+	0	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	exon	7518130	7518369	.	+	.	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	intron	7518370	7518656	.	+	.	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	CDS	7518657	7518830	0.24	+	0	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	exon	7518657	7518830	.	+	.	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	intron	7518831	7519027	.	+	.	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	CDS	7519028	7519153	0.65	+	0	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	exon	7519028	7519153	.	+	.	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
Phchi.S6	AUGUSTUS	stop_codon	7519154	7519156	.	+	0	transcript_id "Phchi.S6G104400.t1"; gene_id "Phchi.S6G104400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12677.t1 is derived from g14411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	18591	19433	.	-	.	Phchi.C62G000800
Phchi.C62	AUGUSTUS	transcript	18591	19433	.	-	.	transcript_id "Phchi.C62G000800.t1"; gene_id "Phchi.C62G000800"
Phchi.C62	AUGUSTUS	stop_codon	18588	18590	.	-	0	transcript_id "Phchi.C62G000800.t1"; gene_id "Phchi.C62G000800"
Phchi.C62	AUGUSTUS	CDS	18591	19433	0.56	-	0	transcript_id "Phchi.C62G000800.t1"; gene_id "Phchi.C62G000800"
Phchi.C62	AUGUSTUS	exon	18591	19433	.	-	.	transcript_id "Phchi.C62G000800.t1"; gene_id "Phchi.C62G000800"
Phchi.C62	AUGUSTUS	start_codon	19431	19433	.	-	0	transcript_id "Phchi.C62G000800.t1"; gene_id "Phchi.C62G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9596.t1 is derived from g6772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42869049	42869566	.	-	.	Phchi.S1G675500
Phchi.S1	AUGUSTUS	transcript	42869049	42869566	.	-	.	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	stop_codon	42869046	42869048	.	-	0	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	CDS	42869049	42869160	1	-	1	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	exon	42869049	42869160	.	-	.	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	intron	42869161	42869254	.	-	.	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	CDS	42869255	42869412	1	-	0	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	exon	42869255	42869412	.	-	.	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	intron	42869413	42869485	.	-	.	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	CDS	42869486	42869566	1	-	0	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	exon	42869486	42869566	.	-	.	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
Phchi.S1	AUGUSTUS	start_codon	42869564	42869566	.	-	0	transcript_id "Phchi.S1G675500.t1"; gene_id "Phchi.S1G675500"
# This transcript jg3923.t2 is derived from g1092.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3924.t1 is derived from g1093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6444435	6446245	.	+	.	Phchi.S1G108300
Phchi.S1	AUGUSTUS	transcript	6444435	6446245	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	start_codon	6444435	6444437	.	+	0	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6444435	6444465	0.65	+	0	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6444435	6444465	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6444466	6444554	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6444555	6444666	0.93	+	2	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6444555	6444666	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6444667	6444766	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6444767	6444815	0.93	+	1	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6444767	6444815	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6444816	6444928	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6444929	6445020	1	+	0	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6444929	6445020	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6445021	6445177	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6445178	6445329	1	+	1	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6445178	6445329	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6445330	6445469	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6445470	6445516	1	+	2	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6445470	6445516	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6445517	6445599	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6445600	6445800	1	+	0	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6445600	6445800	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6445801	6445878	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6445879	6445975	1	+	0	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6445879	6445975	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	intron	6445976	6446066	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	CDS	6446067	6446245	0.99	+	2	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	exon	6446067	6446245	.	+	.	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
Phchi.S1	AUGUSTUS	stop_codon	6446246	6446248	.	+	0	transcript_id "Phchi.S1G108300.t1"; gene_id "Phchi.S1G108300"
# This transcript jg2501.t2 is derived from g9421.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2502.t1 is derived from g9422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6999899	7000234	.	-	.	Phchi.S5G111100
Phchi.S5	AUGUSTUS	transcript	6999899	7000234	.	-	.	transcript_id "Phchi.S5G111100.t1"; gene_id "Phchi.S5G111100"
Phchi.S5	AUGUSTUS	stop_codon	6999896	6999898	.	-	0	transcript_id "Phchi.S5G111100.t1"; gene_id "Phchi.S5G111100"
Phchi.S5	AUGUSTUS	CDS	6999899	7000234	1	-	0	transcript_id "Phchi.S5G111100.t1"; gene_id "Phchi.S5G111100"
Phchi.S5	AUGUSTUS	exon	6999899	7000234	.	-	.	transcript_id "Phchi.S5G111100.t1"; gene_id "Phchi.S5G111100"
Phchi.S5	AUGUSTUS	start_codon	7000232	7000234	.	-	0	transcript_id "Phchi.S5G111100.t1"; gene_id "Phchi.S5G111100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6516.t1 is derived from g3688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23423082	23426231	.	-	.	Phchi.S1G367500
Phchi.S1	AUGUSTUS	transcript	23423082	23426231	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	stop_codon	23423079	23423081	.	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23423082	23423336	0.96	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23423082	23423336	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23423337	23423415	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23423416	23423476	1	-	1	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23423416	23423476	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23423477	23423645	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23423646	23423713	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23423646	23423713	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23423714	23423835	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23423836	23423871	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23423836	23423871	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23423872	23423979	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23423980	23424177	0.97	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23423980	23424177	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23424178	23424290	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23424291	23424331	1	-	2	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23424291	23424331	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23424332	23424421	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23424422	23424471	1	-	1	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23424422	23424471	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23424472	23424557	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23424558	23424643	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23424558	23424643	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23424644	23424762	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23424763	23424837	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23424763	23424837	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23424838	23424924	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23424925	23425013	1	-	2	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23424925	23425013	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23425014	23425108	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23425109	23425169	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23425109	23425169	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23425170	23425259	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23425260	23425270	0.8	-	2	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23425260	23425270	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23425271	23425348	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23425349	23425376	0.8	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23425349	23425376	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23425377	23425457	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23425458	23425714	1	-	2	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23425458	23425714	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23425715	23425807	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23425808	23425865	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23425808	23425865	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	intron	23425866	23426114	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	CDS	23426115	23426231	1	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	exon	23426115	23426231	.	-	.	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
Phchi.S1	AUGUSTUS	start_codon	23426229	23426231	.	-	0	transcript_id "Phchi.S1G367500.t1"; gene_id "Phchi.S1G367500"
# This transcript jg10319.t2 is derived from g7495.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10320.t1 is derived from g7496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47095870	47096192	.	+	.	Phchi.S1G747900
Phchi.S1	AUGUSTUS	transcript	47095870	47096192	.	+	.	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	start_codon	47095870	47095872	.	+	0	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	CDS	47095870	47096012	0.44	+	0	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	exon	47095870	47096012	.	+	.	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	intron	47096013	47096104	.	+	.	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	CDS	47096105	47096192	0.62	+	1	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	exon	47096105	47096192	.	+	.	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
Phchi.S1	AUGUSTUS	stop_codon	47096193	47096195	.	+	0	transcript_id "Phchi.S1G747900.t1"; gene_id "Phchi.S1G747900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3098.t1 is derived from g267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1746523	1749381	.	-	.	Phchi.S1G025700
Phchi.S1	AUGUSTUS	transcript	1746523	1749381	.	-	.	transcript_id "Phchi.S1G025700.t1"; gene_id "Phchi.S1G025700"
Phchi.S1	AUGUSTUS	stop_codon	1746520	1746522	.	-	0	transcript_id "Phchi.S1G025700.t1"; gene_id "Phchi.S1G025700"
Phchi.S1	AUGUSTUS	CDS	1746523	1749381	1	-	0	transcript_id "Phchi.S1G025700.t1"; gene_id "Phchi.S1G025700"
Phchi.S1	AUGUSTUS	exon	1746523	1749381	.	-	.	transcript_id "Phchi.S1G025700.t1"; gene_id "Phchi.S1G025700"
Phchi.S1	AUGUSTUS	start_codon	1749379	1749381	.	-	0	transcript_id "Phchi.S1G025700.t1"; gene_id "Phchi.S1G025700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10079.t1 is derived from g7255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45643210	45644832	.	+	.	Phchi.S1G723800
Phchi.S1	AUGUSTUS	transcript	45643210	45644832	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	start_codon	45643210	45643212	.	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	CDS	45643210	45643266	0.38	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	exon	45643210	45643266	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	intron	45643267	45643795	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	CDS	45643796	45643924	0.41	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	exon	45643796	45643924	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	intron	45643925	45644125	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	CDS	45644126	45644299	0.97	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	exon	45644126	45644299	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	intron	45644300	45644398	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	CDS	45644399	45644512	1	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	exon	45644399	45644512	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	intron	45644513	45644721	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	CDS	45644722	45644832	1	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	exon	45644722	45644832	.	+	.	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
Phchi.S1	AUGUSTUS	stop_codon	45644833	45644835	.	+	0	transcript_id "Phchi.S1G723800.t1"; gene_id "Phchi.S1G723800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg231.t1 is derived from g10013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1572674	1573439	.	-	.	Phchi.S6G019000
Phchi.S6	AUGUSTUS	transcript	1572674	1573439	.	-	.	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	stop_codon	1572671	1572673	.	-	0	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	CDS	1572674	1572966	0.99	-	2	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	exon	1572674	1572966	.	-	.	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	intron	1572967	1573068	.	-	.	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	CDS	1573069	1573270	0.99	-	0	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	exon	1573069	1573270	.	-	.	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	intron	1573271	1573430	.	-	.	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	CDS	1573431	1573439	0.91	-	0	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	exon	1573431	1573439	.	-	.	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
Phchi.S6	AUGUSTUS	start_codon	1573437	1573439	.	-	0	transcript_id "Phchi.S6G019000.t1"; gene_id "Phchi.S6G019000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13881.t1 is derived from g12348.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9437433	9443692	.	-	.	Phchi.S3G120000
Phchi.S3	AUGUSTUS	transcript	9437433	9443692	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	stop_codon	9437430	9437432	.	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9437433	9437500	0.55	-	2	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9437433	9437500	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9437501	9437804	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9437805	9437884	0.71	-	1	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9437805	9437884	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9437885	9438090	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438091	9438366	0.95	-	1	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438091	9438366	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9438367	9438456	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438457	9438644	1	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438457	9438644	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9438645	9438740	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438741	9438853	1	-	2	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438741	9438853	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9438854	9438921	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438922	9439031	1	-	1	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438922	9439031	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9439032	9439194	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9439195	9439400	0.69	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9439195	9439400	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9439401	9439521	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9439522	9439717	0.99	-	1	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9439522	9439717	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9439718	9439815	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9439816	9440837	1	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9439816	9440837	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9440838	9440943	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9440944	9442621	0.99	-	1	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9440944	9442621	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9442622	9442833	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9442834	9442910	1	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9442834	9442910	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9442911	9443302	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9443303	9443447	0.99	-	1	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9443303	9443447	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9443448	9443540	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9443541	9443692	1	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9443541	9443692	.	-	.	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	start_codon	9443690	9443692	.	-	0	transcript_id "Phchi.S3G120000.t1"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	transcript	9437433	9443692	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	stop_codon	9437430	9437432	.	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9437433	9437500	0.45	-	2	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9437433	9437500	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9437501	9437813	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9437814	9437884	0.49	-	1	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9437814	9437884	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9437885	9438090	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438091	9438366	0.93	-	1	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438091	9438366	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9438367	9438456	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438457	9438644	1	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438457	9438644	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9438645	9438740	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438741	9438853	1	-	2	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438741	9438853	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9438854	9438921	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9438922	9439031	1	-	1	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9438922	9439031	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9439032	9439194	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9439195	9439400	0.74	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9439195	9439400	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9439401	9439521	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9439522	9439717	0.99	-	1	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9439522	9439717	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9439718	9439815	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9439816	9440837	1	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9439816	9440837	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9440838	9440943	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9440944	9442621	0.98	-	1	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9440944	9442621	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9442622	9442833	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9442834	9442910	0.99	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9442834	9442910	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9442911	9443302	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9443303	9443447	0.98	-	1	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9443303	9443447	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	intron	9443448	9443540	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	CDS	9443541	9443692	1	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	exon	9443541	9443692	.	-	.	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
Phchi.S3	AUGUSTUS	start_codon	9443690	9443692	.	-	0	transcript_id "Phchi.S3G120000.t2"; gene_id "Phchi.S3G120000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10834.t1 is derived from g14884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2335642	2336889	.	+	.	Phchi.S4G041600
Phchi.S4	AUGUSTUS	transcript	2335642	2336889	.	+	.	transcript_id "Phchi.S4G041600.t1"; gene_id "Phchi.S4G041600"
Phchi.S4	AUGUSTUS	start_codon	2335642	2335644	.	+	0	transcript_id "Phchi.S4G041600.t1"; gene_id "Phchi.S4G041600"
Phchi.S4	AUGUSTUS	CDS	2335642	2336889	1	+	0	transcript_id "Phchi.S4G041600.t1"; gene_id "Phchi.S4G041600"
Phchi.S4	AUGUSTUS	exon	2335642	2336889	.	+	.	transcript_id "Phchi.S4G041600.t1"; gene_id "Phchi.S4G041600"
Phchi.S4	AUGUSTUS	stop_codon	2336890	2336892	.	+	0	transcript_id "Phchi.S4G041600.t1"; gene_id "Phchi.S4G041600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg1388.t1 is derived from g16021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	13705	16963	.	-	.	Phchi.C243G000600
Phchi.C243	AUGUSTUS	transcript	13705	16963	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	stop_codon	13702	13704	.	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	13705	13930	1	-	1	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	13705	13930	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	13931	14015	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14016	14117	1	-	1	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14016	14117	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14118	14204	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14205	14359	1	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14205	14359	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14360	14448	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14449	14538	1	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14449	14538	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14539	14683	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14684	14782	1	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14684	14782	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14783	14875	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14876	14942	1	-	1	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14876	14942	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14943	15042	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15043	15136	1	-	2	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15043	15136	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15137	15284	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15285	15420	1	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15285	15420	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15421	15500	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15501	15559	1	-	2	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15501	15559	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15560	15704	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15705	15779	0.98	-	2	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15705	15779	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15780	15909	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15910	16117	0.9	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15910	16117	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16118	16173	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16174	16187	0.97	-	2	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16174	16187	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16188	16279	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16280	16347	0.97	-	1	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16280	16347	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16348	16913	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16914	16963	0.83	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16914	16963	.	-	.	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	start_codon	16961	16963	.	-	0	transcript_id "Phchi.C243G000600.t1"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	transcript	13705	16963	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	stop_codon	13702	13704	.	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	13705	13930	1	-	1	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	13705	13930	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	13931	14015	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14016	14117	1	-	1	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14016	14117	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14118	14204	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14205	14359	1	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14205	14359	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14360	14448	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14449	14538	1	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14449	14538	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14539	14683	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14684	14782	1	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14684	14782	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14783	14875	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14876	14942	1	-	1	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14876	14942	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14943	15042	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15043	15136	1	-	2	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15043	15136	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15137	15284	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15285	15420	1	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15285	15420	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15421	15500	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15501	15559	1	-	2	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15501	15559	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15560	15704	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15705	15779	0.99	-	2	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15705	15779	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15780	15909	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15910	16117	0.84	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15910	16117	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16118	16173	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16174	16181	1	-	2	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16174	16181	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16182	16279	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16280	16347	1	-	1	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16280	16347	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16348	16913	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16914	16963	0.83	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16914	16963	.	-	.	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	start_codon	16961	16963	.	-	0	transcript_id "Phchi.C243G000600.t2"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	transcript	13705	16963	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	stop_codon	13702	13704	.	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	13705	13930	1	-	1	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	13705	13930	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	13931	14015	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14016	14117	1	-	1	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14016	14117	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14118	14204	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14205	14359	1	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14205	14359	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14360	14448	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14449	14538	1	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14449	14538	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14539	14683	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14684	14782	1	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14684	14782	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14783	14875	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14876	14942	1	-	1	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14876	14942	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14943	15042	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15043	15136	1	-	2	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15043	15136	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15137	15284	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15285	15420	1	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15285	15420	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15421	15500	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15501	15559	1	-	2	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15501	15559	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15560	15704	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15705	15779	0.95	-	2	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15705	15779	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15780	15915	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15916	16117	0.65	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15916	16117	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16118	16173	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16174	16187	0.99	-	2	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16174	16187	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16188	16279	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16280	16347	1	-	1	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16280	16347	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16348	16913	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16914	16963	0.89	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16914	16963	.	-	.	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	start_codon	16961	16963	.	-	0	transcript_id "Phchi.C243G000600.t3"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	transcript	13705	16963	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	stop_codon	13702	13704	.	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	13705	13930	1	-	1	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	13705	13930	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	13931	14015	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14016	14117	1	-	1	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14016	14117	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14118	14204	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14205	14359	1	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14205	14359	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14360	14448	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14449	14538	1	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14449	14538	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14539	14683	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14684	14782	1	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14684	14782	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14783	14875	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	14876	14942	1	-	1	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	14876	14942	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	14943	15042	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15043	15145	0.57	-	2	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15043	15145	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15146	15284	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15285	15420	0.99	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15285	15420	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15421	15500	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15501	15559	1	-	2	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15501	15559	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15560	15704	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15705	15779	0.93	-	2	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15705	15779	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	15780	15909	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	15910	16117	0.76	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	15910	16117	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16118	16173	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16174	16187	1	-	2	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16174	16187	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16188	16279	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16280	16347	1	-	1	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16280	16347	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	intron	16348	16913	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	CDS	16914	16963	0.86	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	exon	16914	16963	.	-	.	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
Phchi.C243	AUGUSTUS	start_codon	16961	16963	.	-	0	transcript_id "Phchi.C243G000600.t4"; gene_id "Phchi.C243G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11602.t1 is derived from g15653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7288594	7289376	.	+	.	Phchi.S4G118400
Phchi.S4	AUGUSTUS	transcript	7288594	7289376	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	start_codon	7288594	7288596	.	+	0	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	CDS	7288594	7288642	0.99	+	0	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	exon	7288594	7288642	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	intron	7288643	7288735	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	CDS	7288736	7288809	1	+	2	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	exon	7288736	7288809	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	intron	7288810	7288890	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	CDS	7288891	7289018	1	+	0	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	exon	7288891	7289018	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	intron	7289019	7289092	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	CDS	7289093	7289161	1	+	1	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	exon	7289093	7289161	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	intron	7289162	7289342	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	CDS	7289343	7289376	1	+	1	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	exon	7289343	7289376	.	+	.	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
Phchi.S4	AUGUSTUS	stop_codon	7289377	7289379	.	+	0	transcript_id "Phchi.S4G118400.t1"; gene_id "Phchi.S4G118400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10340.t1 is derived from g7516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47251547	47252553	.	-	.	Phchi.S1G749900
Phchi.S1	AUGUSTUS	transcript	47251547	47252553	.	-	.	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	stop_codon	47251544	47251546	.	-	0	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	CDS	47251547	47251559	0.7	-	1	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	exon	47251547	47251559	.	-	.	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	intron	47251560	47251651	.	-	.	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	CDS	47251652	47252553	0.75	-	0	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	exon	47251652	47252553	.	-	.	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
Phchi.S1	AUGUSTUS	start_codon	47252551	47252553	.	-	0	transcript_id "Phchi.S1G749900.t1"; gene_id "Phchi.S1G749900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9726.t1 is derived from g6902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43411047	43413098	.	+	.	Phchi.S1G688500
Phchi.S1	AUGUSTUS	transcript	43411047	43413098	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	start_codon	43411047	43411049	.	+	0	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	CDS	43411047	43411054	0.34	+	0	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	exon	43411047	43411054	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	intron	43411055	43411210	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	CDS	43411211	43411424	0.32	+	1	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	exon	43411211	43411424	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	intron	43411425	43411541	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	CDS	43411542	43411634	0.66	+	0	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	exon	43411542	43411634	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	intron	43411635	43411756	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	CDS	43411757	43411885	0.81	+	0	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	exon	43411757	43411885	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	intron	43411886	43411966	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	CDS	43411967	43412061	1	+	0	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	exon	43411967	43412061	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	intron	43412062	43412164	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	CDS	43412165	43413098	0.97	+	1	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	exon	43412165	43413098	.	+	.	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
Phchi.S1	AUGUSTUS	stop_codon	43413099	43413101	.	+	0	transcript_id "Phchi.S1G688500.t1"; gene_id "Phchi.S1G688500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11625.t1 is derived from g15676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7376570	7376875	.	+	.	Phchi.S4G120700
Phchi.S4	AUGUSTUS	transcript	7376570	7376875	.	+	.	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	start_codon	7376570	7376572	.	+	0	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	CDS	7376570	7376680	0.92	+	0	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	exon	7376570	7376680	.	+	.	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	intron	7376681	7376779	.	+	.	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	CDS	7376780	7376875	0.92	+	0	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	exon	7376780	7376875	.	+	.	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
Phchi.S4	AUGUSTUS	stop_codon	7376876	7376878	.	+	0	transcript_id "Phchi.S4G120700.t1"; gene_id "Phchi.S4G120700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg454.t1 is derived from g10236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3182759	3184118	.	-	.	Phchi.S6G041300
Phchi.S6	AUGUSTUS	transcript	3182759	3184118	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	stop_codon	3182756	3182758	.	-	0	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	CDS	3182759	3182892	0.98	-	2	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	exon	3182759	3182892	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	intron	3182893	3182972	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	CDS	3182973	3183204	1	-	0	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	exon	3182973	3183204	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	intron	3183205	3183306	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	CDS	3183307	3183504	1	-	0	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	exon	3183307	3183504	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	intron	3183505	3183638	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	CDS	3183639	3183901	1	-	2	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	exon	3183639	3183901	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	intron	3183902	3184000	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	CDS	3184001	3184118	0.97	-	0	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	exon	3184001	3184118	.	-	.	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
Phchi.S6	AUGUSTUS	start_codon	3184116	3184118	.	-	0	transcript_id "Phchi.S6G041300.t1"; gene_id "Phchi.S6G041300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6620.t1 is derived from g3792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24031273	24034301	.	+	.	Phchi.S1G377900
Phchi.S1	AUGUSTUS	transcript	24031273	24034301	.	+	.	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	start_codon	24031273	24031275	.	+	0	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	CDS	24031273	24032211	0.73	+	0	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	exon	24031273	24032211	.	+	.	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	intron	24032212	24032276	.	+	.	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	CDS	24032277	24034301	0.69	+	0	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	exon	24032277	24034301	.	+	.	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
Phchi.S1	AUGUSTUS	stop_codon	24034302	24034304	.	+	0	transcript_id "Phchi.S1G377900.t1"; gene_id "Phchi.S1G377900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4057.t1 is derived from g1226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7569979	7571608	.	+	.	Phchi.S1G121600
Phchi.S1	AUGUSTUS	transcript	7569979	7571608	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	start_codon	7569979	7569981	.	+	0	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7569979	7570505	0.99	+	0	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7569979	7570505	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	intron	7570506	7570585	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7570586	7570628	1	+	1	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7570586	7570628	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	intron	7570629	7570766	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7570767	7570823	1	+	0	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7570767	7570823	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	intron	7570824	7570920	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7570921	7571035	1	+	0	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7570921	7571035	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	intron	7571036	7571126	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7571127	7571244	1	+	2	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7571127	7571244	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	intron	7571245	7571320	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7571321	7571420	1	+	1	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7571321	7571420	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	intron	7571421	7571503	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	CDS	7571504	7571608	0.58	+	0	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	exon	7571504	7571608	.	+	.	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
Phchi.S1	AUGUSTUS	stop_codon	7571609	7571611	.	+	0	transcript_id "Phchi.S1G121600.t1"; gene_id "Phchi.S1G121600"
# This transcript jg15925.t2 is derived from g14395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15926.t1 is derived from g14396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22252862	22255152	.	-	.	Phchi.S3G324500
Phchi.S3	AUGUSTUS	transcript	22252862	22255152	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	stop_codon	22252859	22252861	.	-	0	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	CDS	22252862	22253416	0.69	-	0	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	exon	22252862	22253416	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	intron	22253417	22253494	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	CDS	22253495	22254633	0.73	-	2	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	exon	22253495	22254633	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	intron	22254634	22254716	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	CDS	22254717	22254879	0.61	-	0	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	exon	22254717	22254879	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	intron	22254880	22255032	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	CDS	22255033	22255152	0.63	-	0	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	exon	22255033	22255152	.	-	.	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
Phchi.S3	AUGUSTUS	start_codon	22255150	22255152	.	-	0	transcript_id "Phchi.S3G324500.t1"; gene_id "Phchi.S3G324500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10239.t1 is derived from g7415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46516085	46516843	.	+	.	Phchi.S1G739800
Phchi.S1	AUGUSTUS	transcript	46516085	46516843	.	+	.	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	start_codon	46516085	46516087	.	+	0	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	CDS	46516085	46516439	0.62	+	0	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	exon	46516085	46516439	.	+	.	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	intron	46516440	46516516	.	+	.	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	CDS	46516517	46516523	0.62	+	2	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	exon	46516517	46516523	.	+	.	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	intron	46516524	46516761	.	+	.	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	CDS	46516762	46516843	1	+	1	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	exon	46516762	46516843	.	+	.	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
Phchi.S1	AUGUSTUS	stop_codon	46516844	46516846	.	+	0	transcript_id "Phchi.S1G739800.t1"; gene_id "Phchi.S1G739800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4123.t1 is derived from g1292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8367870	8369779	.	+	.	Phchi.S1G128200
Phchi.S1	AUGUSTUS	transcript	8367870	8369779	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	start_codon	8367870	8367872	.	+	0	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	CDS	8367870	8368229	0.49	+	0	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	exon	8367870	8368229	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	intron	8368230	8368347	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	CDS	8368348	8368686	0.99	+	0	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	exon	8368348	8368686	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	intron	8368687	8368774	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	CDS	8368775	8369182	0.99	+	0	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	exon	8368775	8369182	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	intron	8369183	8369281	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	CDS	8369282	8369779	1	+	0	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	exon	8369282	8369779	.	+	.	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
Phchi.S1	AUGUSTUS	stop_codon	8369780	8369782	.	+	0	transcript_id "Phchi.S1G128200.t1"; gene_id "Phchi.S1G128200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11486.t1 is derived from g15536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6611323	6612315	.	-	.	Phchi.S4G106800
Phchi.S4	AUGUSTUS	transcript	6611323	6612315	.	-	.	transcript_id "Phchi.S4G106800.t1"; gene_id "Phchi.S4G106800"
Phchi.S4	AUGUSTUS	stop_codon	6611320	6611322	.	-	0	transcript_id "Phchi.S4G106800.t1"; gene_id "Phchi.S4G106800"
Phchi.S4	AUGUSTUS	CDS	6611323	6612315	0.72	-	0	transcript_id "Phchi.S4G106800.t1"; gene_id "Phchi.S4G106800"
Phchi.S4	AUGUSTUS	exon	6611323	6612315	.	-	.	transcript_id "Phchi.S4G106800.t1"; gene_id "Phchi.S4G106800"
Phchi.S4	AUGUSTUS	start_codon	6612313	6612315	.	-	0	transcript_id "Phchi.S4G106800.t1"; gene_id "Phchi.S4G106800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4803.t1 is derived from g1973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12900039	12901352	.	-	.	Phchi.S1G196200
Phchi.S1	AUGUSTUS	transcript	12900039	12901352	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	stop_codon	12900036	12900038	.	-	0	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	CDS	12900039	12900174	0.45	-	1	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	exon	12900039	12900174	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	intron	12900175	12900280	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	CDS	12900281	12900813	0.19	-	0	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	exon	12900281	12900813	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	intron	12900814	12900974	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	CDS	12900975	12901128	0.36	-	1	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	exon	12900975	12901128	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	intron	12901129	12901212	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	CDS	12901213	12901352	1	-	0	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	exon	12901213	12901352	.	-	.	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
Phchi.S1	AUGUSTUS	start_codon	12901350	12901352	.	-	0	transcript_id "Phchi.S1G196200.t1"; gene_id "Phchi.S1G196200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6547.t1 is derived from g3719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23574887	23576823	.	+	.	Phchi.S1G370600
Phchi.S1	AUGUSTUS	transcript	23574887	23576823	.	+	.	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	start_codon	23574887	23574889	.	+	0	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	CDS	23574887	23575183	0.02	+	0	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	exon	23574887	23575183	.	+	.	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	intron	23575184	23575255	.	+	.	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	CDS	23575256	23575347	1	+	0	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	exon	23575256	23575347	.	+	.	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	intron	23575348	23576744	.	+	.	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	CDS	23576745	23576823	0.07	+	1	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	exon	23576745	23576823	.	+	.	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
Phchi.S1	AUGUSTUS	stop_codon	23576824	23576826	.	+	0	transcript_id "Phchi.S1G370600.t1"; gene_id "Phchi.S1G370600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg924.t1 is derived from g10706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6470761	6473583	.	+	.	Phchi.S6G088300
Phchi.S6	AUGUSTUS	transcript	6470761	6473583	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	start_codon	6470761	6470763	.	+	0	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6470761	6470854	0.99	+	0	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6470761	6470854	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6470855	6471096	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6471097	6471106	0.98	+	2	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6471097	6471106	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6471107	6471182	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6471183	6471205	0.99	+	1	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6471183	6471205	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6471206	6471304	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6471305	6471337	1	+	2	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6471305	6471337	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6471338	6471533	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6471534	6471796	0.77	+	2	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6471534	6471796	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6471797	6471894	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6471895	6472611	0.98	+	0	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6471895	6472611	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6472612	6472707	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6472708	6472846	0.82	+	0	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6472708	6472846	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	intron	6472847	6473071	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	CDS	6473072	6473583	0.99	+	2	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	exon	6473072	6473583	.	+	.	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
Phchi.S6	AUGUSTUS	stop_codon	6473584	6473586	.	+	0	transcript_id "Phchi.S6G088300.t1"; gene_id "Phchi.S6G088300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15632.t1 is derived from g14101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20379662	20385541	.	-	.	Phchi.S3G295100
Phchi.S3	AUGUSTUS	transcript	20379662	20385541	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	stop_codon	20379659	20379661	.	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20379662	20379935	0.94	-	1	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20379662	20379935	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20379936	20380019	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20380020	20380292	1	-	1	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20380020	20380292	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20380293	20380394	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20380395	20380606	0.98	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20380395	20380606	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20380607	20380816	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20380817	20381092	0.99	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20380817	20381092	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20381093	20381187	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20381188	20382552	0.99	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20381188	20382552	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20382553	20382653	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20382654	20382819	0.98	-	1	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20382654	20382819	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20382820	20382915	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20382916	20383048	1	-	2	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20382916	20383048	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20383049	20383205	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20383206	20383560	0.39	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20383206	20383560	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20383561	20383736	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20383737	20383909	0.5	-	2	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20383737	20383909	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20383910	20384112	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20384113	20384539	0.38	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20384113	20384539	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20384540	20384626	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20384627	20384746	1	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20384627	20384746	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20384747	20384844	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20384845	20384922	1	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20384845	20384922	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20384923	20385055	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20385056	20385541	1	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20385056	20385541	.	-	.	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	start_codon	20385539	20385541	.	-	0	transcript_id "Phchi.S3G295100.t1"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	transcript	20382742	20385541	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	stop_codon	20382739	20382741	.	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20382742	20382841	0.95	-	1	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20382742	20382841	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20382842	20382915	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20382916	20383048	0.99	-	2	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20382916	20383048	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20383049	20383205	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20383206	20383560	0.4	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20383206	20383560	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20383561	20383736	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20383737	20383909	0.45	-	2	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20383737	20383909	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20383910	20384112	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20384113	20384539	0.37	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20384113	20384539	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20384540	20384626	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20384627	20384746	1	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20384627	20384746	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20384747	20384844	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20384845	20384922	1	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20384845	20384922	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	intron	20384923	20385055	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	CDS	20385056	20385541	1	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	exon	20385056	20385541	.	-	.	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
Phchi.S3	AUGUSTUS	start_codon	20385539	20385541	.	-	0	transcript_id "Phchi.S3G295100.t2"; gene_id "Phchi.S3G295100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15652.t1 is derived from g14121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20492092	20495007	.	-	.	Phchi.S3G297100
Phchi.S3	AUGUSTUS	transcript	20492092	20495007	.	-	.	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	stop_codon	20492089	20492091	.	-	0	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	CDS	20492092	20492160	1	-	0	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	exon	20492092	20492160	.	-	.	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	intron	20492161	20492779	.	-	.	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	CDS	20492780	20493000	1	-	2	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	exon	20492780	20493000	.	-	.	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	intron	20493001	20494931	.	-	.	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	CDS	20494932	20495007	0.29	-	0	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	exon	20494932	20495007	.	-	.	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
Phchi.S3	AUGUSTUS	start_codon	20495005	20495007	.	-	0	transcript_id "Phchi.S3G297100.t1"; gene_id "Phchi.S3G297100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6480.t1 is derived from g3652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23198852	23202225	.	+	.	Phchi.S1G363900
Phchi.S1	AUGUSTUS	transcript	23198852	23202225	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	start_codon	23198852	23198854	.	+	0	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23198852	23199577	0.3	+	0	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23198852	23199577	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23199578	23199675	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23199676	23201722	0.99	+	0	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23199676	23201722	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23201723	23201882	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23201883	23201918	0.44	+	2	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23201883	23201918	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23201919	23202033	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23202034	23202067	0.5	+	2	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23202034	23202067	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23202068	23202218	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23202219	23202225	1	+	1	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23202219	23202225	.	+	.	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	stop_codon	23202226	23202228	.	+	0	transcript_id "Phchi.S1G363900.t1"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	transcript	23198852	23202225	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	start_codon	23198852	23198854	.	+	0	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23198852	23199577	0.3	+	0	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23198852	23199577	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23199578	23199672	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23199673	23201722	0.98	+	0	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23199673	23201722	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23201723	23201882	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23201883	23201918	0.38	+	2	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23201883	23201918	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23201919	23202033	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23202034	23202067	0.41	+	2	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23202034	23202067	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23202068	23202218	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23202219	23202225	1	+	1	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23202219	23202225	.	+	.	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	stop_codon	23202226	23202228	.	+	0	transcript_id "Phchi.S1G363900.t2"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	transcript	23198852	23202225	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	start_codon	23198852	23198854	.	+	0	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23198852	23199577	0.25	+	0	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23198852	23199577	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23199578	23199672	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23199673	23201797	0.58	+	0	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23199673	23201797	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23201798	23201882	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23201883	23201918	0.37	+	2	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23201883	23201918	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23201919	23202033	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23202034	23202067	0.42	+	2	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23202034	23202067	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	intron	23202068	23202218	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	CDS	23202219	23202225	0.99	+	1	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	exon	23202219	23202225	.	+	.	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
Phchi.S1	AUGUSTUS	stop_codon	23202226	23202228	.	+	0	transcript_id "Phchi.S1G363900.t3"; gene_id "Phchi.S1G363900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15126.t1 is derived from g13594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17185956	17188321	.	-	.	Phchi.S3G244500
Phchi.S3	AUGUSTUS	transcript	17185956	17188321	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	stop_codon	17185953	17185955	.	-	0	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	CDS	17185956	17186172	1	-	1	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	exon	17185956	17186172	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	intron	17186173	17186270	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	CDS	17186271	17186488	0.7	-	0	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	exon	17186271	17186488	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	intron	17186489	17186639	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	CDS	17186640	17187214	0.88	-	2	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	exon	17186640	17187214	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	intron	17187215	17187561	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	CDS	17187562	17188321	0.39	-	0	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	exon	17187562	17188321	.	-	.	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
Phchi.S3	AUGUSTUS	start_codon	17188319	17188321	.	-	0	transcript_id "Phchi.S3G244500.t1"; gene_id "Phchi.S3G244500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5627.t1 is derived from g2797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17951178	17952391	.	+	.	Phchi.S1G278600
Phchi.S1	AUGUSTUS	transcript	17951178	17952391	.	+	.	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	start_codon	17951178	17951180	.	+	0	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	CDS	17951178	17951555	0.81	+	0	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	exon	17951178	17951555	.	+	.	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	intron	17951556	17952358	.	+	.	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	CDS	17952359	17952391	1	+	0	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	exon	17952359	17952391	.	+	.	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
Phchi.S1	AUGUSTUS	stop_codon	17952392	17952394	.	+	0	transcript_id "Phchi.S1G278600.t1"; gene_id "Phchi.S1G278600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10758.t1 is derived from g14808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1982808	1985098	.	-	.	Phchi.S4G034000
Phchi.S4	AUGUSTUS	transcript	1982808	1985098	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	stop_codon	1982805	1982807	.	-	0	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1982808	1982984	1	-	0	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1982808	1982984	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	intron	1982985	1983092	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1983093	1983302	0.99	-	0	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1983093	1983302	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	intron	1983303	1983388	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1983389	1983518	1	-	1	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1983389	1983518	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	intron	1983519	1983608	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1983609	1983779	1	-	1	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1983609	1983779	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	intron	1983780	1983866	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1983867	1983989	1	-	1	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1983867	1983989	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	intron	1983990	1984090	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1984091	1984195	1	-	1	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1984091	1984195	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	intron	1984196	1984292	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	CDS	1984293	1985098	0.72	-	0	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	exon	1984293	1985098	.	-	.	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
Phchi.S4	AUGUSTUS	start_codon	1985096	1985098	.	-	0	transcript_id "Phchi.S4G034000.t1"; gene_id "Phchi.S4G034000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1075.t1 is derived from g10858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7451130	7452295	.	-	.	Phchi.S6G103400
Phchi.S6	AUGUSTUS	transcript	7451130	7452295	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	stop_codon	7451127	7451129	.	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7451130	7451216	1	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7451130	7451216	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	intron	7451217	7451329	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7451330	7451419	1	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7451330	7451419	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	intron	7451420	7451562	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7451563	7451667	1	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7451563	7451667	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	intron	7451668	7451788	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7451789	7451863	0.72	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7451789	7451863	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	intron	7451864	7451982	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7451983	7452010	0.69	-	1	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7451983	7452010	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	intron	7452011	7452115	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7452116	7452168	1	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7452116	7452168	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	intron	7452169	7452283	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	CDS	7452284	7452295	0.98	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	exon	7452284	7452295	.	-	.	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
Phchi.S6	AUGUSTUS	start_codon	7452293	7452295	.	-	0	transcript_id "Phchi.S6G103400.t1"; gene_id "Phchi.S6G103400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4931.t1 is derived from g2101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13619742	13622254	.	-	.	Phchi.S1G209000
Phchi.S1	AUGUSTUS	transcript	13619742	13622254	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	stop_codon	13619739	13619741	.	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13619742	13619799	1	-	1	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13619742	13619799	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13619800	13619970	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13619971	13619993	1	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13619971	13619993	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13619994	13620188	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13620189	13620301	1	-	2	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13620189	13620301	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13620302	13620376	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13620377	13620434	1	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13620377	13620434	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13620435	13620690	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13620691	13620696	1	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13620691	13620696	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13620697	13620778	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13620779	13620784	1	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13620779	13620784	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13620785	13621033	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13621034	13621098	1	-	2	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13621034	13621098	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13621099	13621266	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13621267	13622254	1	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13621267	13622254	.	-	.	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	start_codon	13622252	13622254	.	-	0	transcript_id "Phchi.S1G209000.t1"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	transcript	13621077	13622254	.	-	.	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	stop_codon	13621074	13621076	.	-	0	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13621077	13621129	0.9	-	2	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13621077	13621129	.	-	.	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	intron	13621130	13621266	.	-	.	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	CDS	13621267	13622254	0.99	-	0	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	exon	13621267	13622254	.	-	.	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
Phchi.S1	AUGUSTUS	start_codon	13622252	13622254	.	-	0	transcript_id "Phchi.S1G209000.t2"; gene_id "Phchi.S1G209000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14023.t1 is derived from g12490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10348043	10348513	.	+	.	Phchi.S3G134200
Phchi.S3	AUGUSTUS	transcript	10348043	10348513	.	+	.	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	start_codon	10348043	10348045	.	+	0	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	CDS	10348043	10348288	0.36	+	0	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	exon	10348043	10348288	.	+	.	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	intron	10348289	10348447	.	+	.	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	CDS	10348448	10348513	0.74	+	0	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	exon	10348448	10348513	.	+	.	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
Phchi.S3	AUGUSTUS	stop_codon	10348514	10348516	.	+	0	transcript_id "Phchi.S3G134200.t1"; gene_id "Phchi.S3G134200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7679.t1 is derived from g4853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30589269	30590120	.	-	.	Phchi.S1G483800
Phchi.S1	AUGUSTUS	transcript	30589269	30590120	.	-	.	transcript_id "Phchi.S1G483800.t1"; gene_id "Phchi.S1G483800"
Phchi.S1	AUGUSTUS	stop_codon	30589266	30589268	.	-	0	transcript_id "Phchi.S1G483800.t1"; gene_id "Phchi.S1G483800"
Phchi.S1	AUGUSTUS	CDS	30589269	30590120	0.94	-	0	transcript_id "Phchi.S1G483800.t1"; gene_id "Phchi.S1G483800"
Phchi.S1	AUGUSTUS	exon	30589269	30590120	.	-	.	transcript_id "Phchi.S1G483800.t1"; gene_id "Phchi.S1G483800"
Phchi.S1	AUGUSTUS	start_codon	30590118	30590120	.	-	0	transcript_id "Phchi.S1G483800.t1"; gene_id "Phchi.S1G483800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14839.t1 is derived from g13307.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14951854	14954008	.	-	.	Phchi.S3G215800
Phchi.S3	AUGUSTUS	transcript	14951854	14954008	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	stop_codon	14951851	14951853	.	-	0	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14951854	14952499	0.73	-	1	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14951854	14952499	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14952500	14952573	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14952574	14952767	0.92	-	0	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14952574	14952767	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14952768	14952928	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14952929	14953116	1	-	2	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14952929	14953116	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14953117	14953257	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14953258	14953367	1	-	1	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14953258	14953367	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14953368	14953835	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14953836	14954008	1	-	0	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14953836	14954008	.	-	.	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	start_codon	14954006	14954008	.	-	0	transcript_id "Phchi.S3G215800.t1"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	transcript	14951854	14953514	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	stop_codon	14951851	14951853	.	-	0	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14951854	14952499	0.77	-	1	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14951854	14952499	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14952500	14952573	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14952574	14952767	0.93	-	0	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14952574	14952767	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14952768	14952928	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14952929	14953116	1	-	2	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14952929	14953116	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14953117	14953257	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14953258	14953367	0.85	-	1	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14953258	14953367	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	intron	14953368	14953509	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	CDS	14953510	14953514	0.82	-	0	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	exon	14953510	14953514	.	-	.	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
Phchi.S3	AUGUSTUS	start_codon	14953512	14953514	.	-	0	transcript_id "Phchi.S3G215800.t2"; gene_id "Phchi.S3G215800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg805.t1 is derived from g10587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5683308	5684113	.	+	.	Phchi.S6G076400
Phchi.S6	AUGUSTUS	transcript	5683308	5684113	.	+	.	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	start_codon	5683308	5683310	.	+	0	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	CDS	5683308	5683397	1	+	0	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	exon	5683308	5683397	.	+	.	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	intron	5683398	5683834	.	+	.	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	CDS	5683835	5684113	0.99	+	0	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	exon	5683835	5684113	.	+	.	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
Phchi.S6	AUGUSTUS	stop_codon	5684114	5684116	.	+	0	transcript_id "Phchi.S6G076400.t1"; gene_id "Phchi.S6G076400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6337.t1 is derived from g3509.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22392040	22393776	.	-	.	Phchi.S1G349600
Phchi.S1	AUGUSTUS	transcript	22392755	22393776	.	-	.	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	stop_codon	22392752	22392754	.	-	0	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	CDS	22392755	22392769	0.81	-	0	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	exon	22392755	22392769	.	-	.	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	intron	22392770	22392903	.	-	.	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	CDS	22392904	22393776	0.83	-	0	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	exon	22392904	22393776	.	-	.	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	start_codon	22393774	22393776	.	-	0	transcript_id "Phchi.S1G349600.t1"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	transcript	22392040	22393776	.	-	.	transcript_id "Phchi.S1G349600.t2"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	stop_codon	22392037	22392039	.	-	0	transcript_id "Phchi.S1G349600.t2"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	CDS	22392040	22393776	0.9	-	0	transcript_id "Phchi.S1G349600.t2"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	exon	22392040	22393776	.	-	.	transcript_id "Phchi.S1G349600.t2"; gene_id "Phchi.S1G349600"
Phchi.S1	AUGUSTUS	start_codon	22393774	22393776	.	-	0	transcript_id "Phchi.S1G349600.t2"; gene_id "Phchi.S1G349600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8652.t1 is derived from g5827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37245841	37247248	.	-	.	Phchi.S1G581100
Phchi.S1	AUGUSTUS	transcript	37245841	37247248	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	stop_codon	37245838	37245840	.	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	CDS	37245841	37246008	1	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	exon	37245841	37246008	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	intron	37246009	37246147	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	CDS	37246148	37246261	1	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	exon	37246148	37246261	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	intron	37246262	37246396	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	CDS	37246397	37246501	1	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	exon	37246397	37246501	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	intron	37246502	37246584	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	CDS	37246585	37246794	1	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	exon	37246585	37246794	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	intron	37246795	37246900	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	CDS	37246901	37246948	0.67	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	exon	37246901	37246948	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	intron	37246949	37247113	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	CDS	37247114	37247248	0.65	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	exon	37247114	37247248	.	-	.	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
Phchi.S1	AUGUSTUS	start_codon	37247246	37247248	.	-	0	transcript_id "Phchi.S1G581100.t1"; gene_id "Phchi.S1G581100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10971.t1 is derived from g15021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3416761	3417469	.	-	.	Phchi.S4G055300
Phchi.S4	AUGUSTUS	transcript	3416761	3417469	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	stop_codon	3416758	3416760	.	-	0	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	CDS	3416761	3416778	1	-	0	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	exon	3416761	3416778	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	intron	3416779	3416938	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	CDS	3416939	3417117	0.93	-	2	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	exon	3416939	3417117	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	intron	3417118	3417230	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	CDS	3417231	3417342	0.5	-	0	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	exon	3417231	3417342	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	intron	3417343	3417466	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	CDS	3417467	3417469	0.37	-	0	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	exon	3417467	3417469	.	-	.	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
Phchi.S4	AUGUSTUS	start_codon	3417467	3417469	.	-	0	transcript_id "Phchi.S4G055300.t1"; gene_id "Phchi.S4G055300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4130.t1 is derived from g1299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8399819	8401824	.	+	.	Phchi.S1G128900
Phchi.S1	AUGUSTUS	transcript	8399819	8401824	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	start_codon	8399819	8399821	.	+	0	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8399819	8400006	1	+	0	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8399819	8400006	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	intron	8400007	8400253	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8400254	8400379	1	+	1	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8400254	8400379	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	intron	8400380	8400472	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8400473	8400630	1	+	1	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8400473	8400630	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	intron	8400631	8400854	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8400855	8400942	1	+	2	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8400855	8400942	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	intron	8400943	8401122	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8401123	8401307	0.81	+	1	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8401123	8401307	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	intron	8401308	8401399	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8401400	8401554	1	+	2	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8401400	8401554	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	intron	8401555	8401677	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	CDS	8401678	8401824	0.4	+	0	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	exon	8401678	8401824	.	+	.	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
Phchi.S1	AUGUSTUS	stop_codon	8401825	8401827	.	+	0	transcript_id "Phchi.S1G128900.t1"; gene_id "Phchi.S1G128900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11070.t1 is derived from g15120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3961829	3962377	.	+	.	Phchi.S4G065200
Phchi.S4	AUGUSTUS	transcript	3961829	3962377	.	+	.	transcript_id "Phchi.S4G065200.t1"; gene_id "Phchi.S4G065200"
Phchi.S4	AUGUSTUS	start_codon	3961829	3961831	.	+	0	transcript_id "Phchi.S4G065200.t1"; gene_id "Phchi.S4G065200"
Phchi.S4	AUGUSTUS	CDS	3961829	3962377	1	+	0	transcript_id "Phchi.S4G065200.t1"; gene_id "Phchi.S4G065200"
Phchi.S4	AUGUSTUS	exon	3961829	3962377	.	+	.	transcript_id "Phchi.S4G065200.t1"; gene_id "Phchi.S4G065200"
Phchi.S4	AUGUSTUS	stop_codon	3962378	3962380	.	+	0	transcript_id "Phchi.S4G065200.t1"; gene_id "Phchi.S4G065200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3615.t1 is derived from g784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4753108	4753737	.	+	.	Phchi.S1G077400
Phchi.S1	AUGUSTUS	transcript	4753108	4753737	.	+	.	transcript_id "Phchi.S1G077400.t1"; gene_id "Phchi.S1G077400"
Phchi.S1	AUGUSTUS	start_codon	4753108	4753110	.	+	0	transcript_id "Phchi.S1G077400.t1"; gene_id "Phchi.S1G077400"
Phchi.S1	AUGUSTUS	CDS	4753108	4753737	0.82	+	0	transcript_id "Phchi.S1G077400.t1"; gene_id "Phchi.S1G077400"
Phchi.S1	AUGUSTUS	exon	4753108	4753737	.	+	.	transcript_id "Phchi.S1G077400.t1"; gene_id "Phchi.S1G077400"
Phchi.S1	AUGUSTUS	stop_codon	4753738	4753740	.	+	0	transcript_id "Phchi.S1G077400.t1"; gene_id "Phchi.S1G077400"
# This transcript jg860.t2 is derived from g10642.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg861.t1 is derived from g10643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5977596	5978483	.	-	.	Phchi.S6G082000
Phchi.S6	AUGUSTUS	transcript	5977622	5978483	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	stop_codon	5977619	5977621	.	-	0	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5977622	5977682	1	-	1	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5977622	5977682	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5977683	5977778	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5977779	5977852	1	-	0	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5977779	5977852	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5977853	5977936	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5977937	5978103	1	-	2	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5977937	5978103	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5978104	5978192	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5978193	5978262	1	-	0	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5978193	5978262	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5978263	5978345	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5978346	5978483	1	-	0	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5978346	5978483	.	-	.	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	start_codon	5978481	5978483	.	-	0	transcript_id "Phchi.S6G082000.t1"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	transcript	5977596	5978483	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	stop_codon	5977593	5977595	.	-	0	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5977596	5977682	0.84	-	0	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5977596	5977682	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5977683	5977936	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5977937	5978103	0.86	-	2	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5977937	5978103	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5978104	5978192	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5978193	5978262	1	-	0	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5978193	5978262	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	intron	5978263	5978345	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	CDS	5978346	5978483	0.99	-	0	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	exon	5978346	5978483	.	-	.	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
Phchi.S6	AUGUSTUS	start_codon	5978481	5978483	.	-	0	transcript_id "Phchi.S6G082000.t2"; gene_id "Phchi.S6G082000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1091.t1 is derived from g10874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7530725	7533746	.	-	.	Phchi.S6G105000
Phchi.S6	AUGUSTUS	transcript	7530725	7533746	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	stop_codon	7530722	7530724	.	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7530725	7530832	0.72	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7530725	7530832	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7530833	7530913	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7530914	7531011	1	-	2	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7530914	7531011	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7531012	7531103	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7531104	7531155	1	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7531104	7531155	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7531156	7531231	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7531232	7531343	1	-	1	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7531232	7531343	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7531344	7531435	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7531436	7531524	1	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7531436	7531524	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7531525	7531637	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7531638	7531703	0.99	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7531638	7531703	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7531704	7531849	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7531850	7532039	1	-	1	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7531850	7532039	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7532040	7532138	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7532139	7532356	1	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7532139	7532356	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7532357	7532446	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7532447	7532527	1	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7532447	7532527	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7532528	7532664	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7532665	7532735	1	-	2	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7532665	7532735	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7532736	7532822	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7532823	7532924	0.37	-	2	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7532823	7532924	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7532925	7533025	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7533026	7533253	0.66	-	2	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7533026	7533253	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7533254	7533336	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7533337	7533440	1	-	1	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7533337	7533440	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	intron	7533441	7533540	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	CDS	7533541	7533746	0.6	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	exon	7533541	7533746	.	-	.	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
Phchi.S6	AUGUSTUS	start_codon	7533744	7533746	.	-	0	transcript_id "Phchi.S6G105000.t1"; gene_id "Phchi.S6G105000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15474.t1 is derived from g13942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19366609	19367028	.	-	.	Phchi.S3G279300
Phchi.S3	AUGUSTUS	transcript	19366609	19367028	.	-	.	transcript_id "Phchi.S3G279300.t1"; gene_id "Phchi.S3G279300"
Phchi.S3	AUGUSTUS	stop_codon	19366606	19366608	.	-	0	transcript_id "Phchi.S3G279300.t1"; gene_id "Phchi.S3G279300"
Phchi.S3	AUGUSTUS	CDS	19366609	19367028	0.99	-	0	transcript_id "Phchi.S3G279300.t1"; gene_id "Phchi.S3G279300"
Phchi.S3	AUGUSTUS	exon	19366609	19367028	.	-	.	transcript_id "Phchi.S3G279300.t1"; gene_id "Phchi.S3G279300"
Phchi.S3	AUGUSTUS	start_codon	19367026	19367028	.	-	0	transcript_id "Phchi.S3G279300.t1"; gene_id "Phchi.S3G279300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10129.t1 is derived from g7305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45866939	45867268	.	+	.	Phchi.S1G728800
Phchi.S1	AUGUSTUS	transcript	45866939	45867268	.	+	.	transcript_id "Phchi.S1G728800.t1"; gene_id "Phchi.S1G728800"
Phchi.S1	AUGUSTUS	start_codon	45866939	45866941	.	+	0	transcript_id "Phchi.S1G728800.t1"; gene_id "Phchi.S1G728800"
Phchi.S1	AUGUSTUS	CDS	45866939	45867268	0.52	+	0	transcript_id "Phchi.S1G728800.t1"; gene_id "Phchi.S1G728800"
Phchi.S1	AUGUSTUS	exon	45866939	45867268	.	+	.	transcript_id "Phchi.S1G728800.t1"; gene_id "Phchi.S1G728800"
Phchi.S1	AUGUSTUS	stop_codon	45867269	45867271	.	+	0	transcript_id "Phchi.S1G728800.t1"; gene_id "Phchi.S1G728800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14862.t1 is derived from g13330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15093523	15094930	.	+	.	Phchi.S3G218100
Phchi.S3	AUGUSTUS	transcript	15093523	15094930	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	start_codon	15093523	15093525	.	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15093523	15093789	0.61	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15093523	15093789	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15093790	15093913	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15093914	15093970	1	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15093914	15093970	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15093971	15094097	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094098	15094133	1	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094098	15094133	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094134	15094233	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094234	15094298	1	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094234	15094298	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094299	15094406	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094407	15094470	1	+	1	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094407	15094470	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094471	15094598	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094599	15094716	1	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094599	15094716	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094717	15094892	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094893	15094930	1	+	2	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094893	15094930	.	+	.	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	stop_codon	15094931	15094933	.	+	0	transcript_id "Phchi.S3G218100.t1"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	transcript	15093523	15094930	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	start_codon	15093523	15093525	.	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15093523	15093789	0.53	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15093523	15093789	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15093790	15093913	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15093914	15093970	1	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15093914	15093970	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15093971	15094097	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094098	15094133	1	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094098	15094133	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094134	15094226	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094227	15094249	0.82	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094227	15094249	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094250	15094406	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094407	15094470	0.82	+	1	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094407	15094470	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094471	15094598	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094599	15094716	1	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094599	15094716	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	intron	15094717	15094892	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	CDS	15094893	15094930	0.98	+	2	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	exon	15094893	15094930	.	+	.	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
Phchi.S3	AUGUSTUS	stop_codon	15094931	15094933	.	+	0	transcript_id "Phchi.S3G218100.t2"; gene_id "Phchi.S3G218100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12031.t1 is derived from g7706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	704782	708308	.	+	.	Phchi.S2G011100
Phchi.S2	AUGUSTUS	transcript	704782	708308	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	start_codon	704782	704784	.	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	704782	704898	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	704782	704898	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	704899	704990	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	704991	705068	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	704991	705068	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	705069	705191	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	705192	705314	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	705192	705314	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	705315	705422	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	705423	705489	0.86	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	705423	705489	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	705490	705599	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	705600	705661	0.86	+	2	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	705600	705661	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	705662	705784	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	705785	705924	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	705785	705924	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	705925	706017	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	706018	706144	1	+	1	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	706018	706144	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	706145	706249	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	706250	706358	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	706250	706358	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	706359	706441	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	706442	706530	1	+	2	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	706442	706530	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	706531	706615	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	706616	706699	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	706616	706699	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	706700	706776	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	706777	707148	0.86	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	706777	707148	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	707149	707227	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	707228	707977	0.81	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	707228	707977	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	707978	708120	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	708121	708180	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	708121	708180	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	intron	708181	708260	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	CDS	708261	708308	1	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	exon	708261	708308	.	+	.	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
Phchi.S2	AUGUSTUS	stop_codon	708309	708311	.	+	0	transcript_id "Phchi.S2G011100.t1"; gene_id "Phchi.S2G011100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg16000.t1 is derived from g15978.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C244	AUGUSTUS	gene	11865	12947	.	-	.	Phchi.C244G000400
Phchi.C244	AUGUSTUS	transcript	11865	12947	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	stop_codon	11862	11864	.	-	0	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	11865	12001	0.98	-	2	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	11865	12001	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	intron	12002	12329	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	12330	12462	1	-	0	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	12330	12462	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	intron	12463	12642	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	12643	12729	0.9	-	0	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	12643	12729	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	intron	12730	12842	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	12843	12947	0.6	-	0	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	12843	12947	.	-	.	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	start_codon	12945	12947	.	-	0	transcript_id "Phchi.C244G000400.t1"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	transcript	11865	12838	.	-	.	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	stop_codon	11862	11864	.	-	0	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	11865	12001	0.3	-	2	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	11865	12001	.	-	.	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	intron	12002	12309	.	-	.	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	12310	12462	0.27	-	2	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	12310	12462	.	-	.	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	intron	12463	12768	.	-	.	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	CDS	12769	12838	0.17	-	0	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	exon	12769	12838	.	-	.	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
Phchi.C244	AUGUSTUS	start_codon	12836	12838	.	-	0	transcript_id "Phchi.C244G000400.t2"; gene_id "Phchi.C244G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7911.t1 is derived from g5085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31869364	31882489	.	+	.	Phchi.S1G507000
Phchi.S1	AUGUSTUS	transcript	31869364	31882489	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	start_codon	31869364	31869366	.	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31869364	31869523	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31869364	31869523	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31869524	31870119	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31870120	31870225	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31870120	31870225	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31870226	31870414	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31870415	31870538	1	+	1	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31870415	31870538	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31870539	31870771	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31870772	31870851	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31870772	31870851	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31870852	31871042	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31871043	31871220	1	+	1	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31871043	31871220	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31871221	31871313	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31871314	31871378	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31871314	31871378	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31871379	31871460	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31871461	31871546	1	+	1	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31871461	31871546	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31871547	31871643	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31871644	31871729	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31871644	31871729	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31871730	31871835	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31871836	31871949	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31871836	31871949	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31871950	31872140	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31872141	31872260	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31872141	31872260	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31872261	31872363	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31872364	31872466	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31872364	31872466	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31872467	31872661	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31872662	31872798	0.98	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31872662	31872798	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31872799	31872904	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31872905	31872970	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31872905	31872970	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31872971	31873053	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31873054	31873171	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31873054	31873171	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31873172	31873264	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31873265	31873311	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31873265	31873311	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31873312	31873398	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31873399	31873482	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31873399	31873482	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31873483	31873635	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31873636	31873731	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31873636	31873731	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31873732	31873953	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31873954	31874059	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31873954	31874059	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31874060	31874234	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31874235	31874347	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31874235	31874347	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31874348	31874459	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31874460	31874544	0.99	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31874460	31874544	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31874545	31874648	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31874649	31874749	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31874649	31874749	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31874750	31874849	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31874850	31874957	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31874850	31874957	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31874958	31875141	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31875142	31875247	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31875142	31875247	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31875248	31875346	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31875347	31875426	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31875347	31875426	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31875427	31875501	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31875502	31875651	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31875502	31875651	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31875652	31875789	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31875790	31875865	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31875790	31875865	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31875866	31875959	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31875960	31876084	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31875960	31876084	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31876085	31876160	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31876161	31876271	0.99	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31876161	31876271	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31876272	31876379	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31876380	31876529	0.98	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31876380	31876529	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31876530	31876619	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31876620	31876694	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31876620	31876694	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31876695	31876812	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31876813	31876891	0.99	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31876813	31876891	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31876892	31876999	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31877000	31877130	0.93	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31877000	31877130	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31877131	31877485	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31877486	31877587	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31877486	31877587	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31877588	31877679	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31877680	31877754	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31877680	31877754	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31877755	31877827	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31877828	31877923	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31877828	31877923	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31877924	31877992	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31877993	31878094	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31877993	31878094	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31878095	31878193	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31878194	31878295	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31878194	31878295	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31878296	31878383	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31878384	31878566	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31878384	31878566	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31878567	31878683	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31878684	31878795	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31878684	31878795	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31878796	31879031	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31879032	31879108	1	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31879032	31879108	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31879109	31879181	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31879182	31879261	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31879182	31879261	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31879262	31879430	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31879431	31879496	1	+	1	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31879431	31879496	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31879497	31879581	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31879582	31879729	1	+	1	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31879582	31879729	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31879730	31879827	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31879828	31879950	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31879828	31879950	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31879951	31880045	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31880046	31880123	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31880046	31880123	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31880124	31880244	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31880245	31880394	0.68	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31880245	31880394	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31880395	31880489	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31880490	31880648	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31880490	31880648	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31880649	31880736	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31880737	31880834	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31880737	31880834	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31880835	31880986	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31880987	31881143	1	+	1	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31880987	31881143	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31881144	31881243	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31881244	31881363	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31881244	31881363	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31881364	31881525	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31881526	31881621	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31881526	31881621	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31881622	31881704	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31881705	31881776	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31881705	31881776	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31881777	31881857	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31881858	31882119	1	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31881858	31882119	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	intron	31882120	31882205	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	CDS	31882206	31882489	0.97	+	2	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	exon	31882206	31882489	.	+	.	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
Phchi.S1	AUGUSTUS	stop_codon	31882490	31882492	.	+	0	transcript_id "Phchi.S1G507000.t1"; gene_id "Phchi.S1G507000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5294.t1 is derived from g2464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16048649	16049623	.	-	.	Phchi.S1G245300
Phchi.S1	AUGUSTUS	transcript	16048649	16049623	.	-	.	transcript_id "Phchi.S1G245300.t1"; gene_id "Phchi.S1G245300"
Phchi.S1	AUGUSTUS	stop_codon	16048646	16048648	.	-	0	transcript_id "Phchi.S1G245300.t1"; gene_id "Phchi.S1G245300"
Phchi.S1	AUGUSTUS	CDS	16048649	16049623	0.96	-	0	transcript_id "Phchi.S1G245300.t1"; gene_id "Phchi.S1G245300"
Phchi.S1	AUGUSTUS	exon	16048649	16049623	.	-	.	transcript_id "Phchi.S1G245300.t1"; gene_id "Phchi.S1G245300"
Phchi.S1	AUGUSTUS	start_codon	16049621	16049623	.	-	0	transcript_id "Phchi.S1G245300.t1"; gene_id "Phchi.S1G245300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9225.t1 is derived from g6400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40480913	40483030	.	-	.	Phchi.S1G638400
Phchi.S1	AUGUSTUS	transcript	40480913	40483030	.	-	.	transcript_id "Phchi.S1G638400.t1"; gene_id "Phchi.S1G638400"
Phchi.S1	AUGUSTUS	stop_codon	40480910	40480912	.	-	0	transcript_id "Phchi.S1G638400.t1"; gene_id "Phchi.S1G638400"
Phchi.S1	AUGUSTUS	CDS	40480913	40483030	0.98	-	0	transcript_id "Phchi.S1G638400.t1"; gene_id "Phchi.S1G638400"
Phchi.S1	AUGUSTUS	exon	40480913	40483030	.	-	.	transcript_id "Phchi.S1G638400.t1"; gene_id "Phchi.S1G638400"
Phchi.S1	AUGUSTUS	start_codon	40483028	40483030	.	-	0	transcript_id "Phchi.S1G638400.t1"; gene_id "Phchi.S1G638400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14789.t1 is derived from g13257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14719393	14719965	.	-	.	Phchi.S3G210800
Phchi.S3	AUGUSTUS	transcript	14719393	14719965	.	-	.	transcript_id "Phchi.S3G210800.t1"; gene_id "Phchi.S3G210800"
Phchi.S3	AUGUSTUS	stop_codon	14719390	14719392	.	-	0	transcript_id "Phchi.S3G210800.t1"; gene_id "Phchi.S3G210800"
Phchi.S3	AUGUSTUS	CDS	14719393	14719965	0.9	-	0	transcript_id "Phchi.S3G210800.t1"; gene_id "Phchi.S3G210800"
Phchi.S3	AUGUSTUS	exon	14719393	14719965	.	-	.	transcript_id "Phchi.S3G210800.t1"; gene_id "Phchi.S3G210800"
Phchi.S3	AUGUSTUS	start_codon	14719963	14719965	.	-	0	transcript_id "Phchi.S3G210800.t1"; gene_id "Phchi.S3G210800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9233.t1 is derived from g6408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40523353	40526765	.	-	.	Phchi.S1G639200
Phchi.S1	AUGUSTUS	transcript	40523353	40526765	.	-	.	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	stop_codon	40523350	40523352	.	-	0	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	CDS	40523353	40525247	0.21	-	2	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	exon	40523353	40525247	.	-	.	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	intron	40525248	40525411	.	-	.	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	CDS	40525412	40526765	0.48	-	0	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	exon	40525412	40526765	.	-	.	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
Phchi.S1	AUGUSTUS	start_codon	40526763	40526765	.	-	0	transcript_id "Phchi.S1G639200.t1"; gene_id "Phchi.S1G639200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4463.t1 is derived from g1633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10626709	10627733	.	+	.	Phchi.S1G162200
Phchi.S1	AUGUSTUS	transcript	10626709	10627733	.	+	.	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	start_codon	10626709	10626711	.	+	0	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	CDS	10626709	10627017	0.8	+	0	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	exon	10626709	10627017	.	+	.	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	intron	10627018	10627253	.	+	.	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	CDS	10627254	10627461	1	+	0	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	exon	10627254	10627461	.	+	.	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	intron	10627462	10627578	.	+	.	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	CDS	10627579	10627733	1	+	2	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	exon	10627579	10627733	.	+	.	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
Phchi.S1	AUGUSTUS	stop_codon	10627734	10627736	.	+	0	transcript_id "Phchi.S1G162200.t1"; gene_id "Phchi.S1G162200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9880.t1 is derived from g7056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44235058	44239381	.	+	.	Phchi.S1G703900
Phchi.S1	AUGUSTUS	transcript	44235058	44239381	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	start_codon	44235058	44235060	.	+	0	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	CDS	44235058	44236648	0.82	+	0	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	exon	44235058	44236648	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	intron	44236649	44236753	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	CDS	44236754	44238123	0.32	+	2	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	exon	44236754	44238123	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	intron	44238124	44238236	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	CDS	44238237	44238449	0.98	+	0	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	exon	44238237	44238449	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	intron	44238450	44238569	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	CDS	44238570	44238665	0.35	+	0	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	exon	44238570	44238665	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	intron	44238666	44238787	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	CDS	44238788	44239381	0.41	+	0	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	exon	44238788	44239381	.	+	.	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
Phchi.S1	AUGUSTUS	stop_codon	44239382	44239384	.	+	0	transcript_id "Phchi.S1G703900.t1"; gene_id "Phchi.S1G703900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg383.t1 is derived from g10165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2760778	2763058	.	-	.	Phchi.S6G034200
Phchi.S6	AUGUSTUS	transcript	2760778	2763058	.	-	.	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	stop_codon	2760775	2760777	.	-	0	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	CDS	2760778	2761716	0.99	-	0	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	exon	2760778	2761716	.	-	.	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	intron	2761717	2761918	.	-	.	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	CDS	2761919	2763058	0.97	-	0	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	exon	2761919	2763058	.	-	.	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
Phchi.S6	AUGUSTUS	start_codon	2763056	2763058	.	-	0	transcript_id "Phchi.S6G034200.t1"; gene_id "Phchi.S6G034200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5367.t1 is derived from g2537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16526540	16528875	.	+	.	Phchi.S1G252600
Phchi.S1	AUGUSTUS	transcript	16526540	16528875	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	start_codon	16526540	16526542	.	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	CDS	16526540	16526614	0.92	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	exon	16526540	16526614	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	intron	16526615	16526780	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	CDS	16526781	16526850	1	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	exon	16526781	16526850	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	intron	16526851	16526995	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	CDS	16526996	16528134	1	+	2	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	exon	16526996	16528134	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	intron	16528135	16528219	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	CDS	16528220	16528291	1	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	exon	16528220	16528291	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	intron	16528292	16528464	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	CDS	16528465	16528584	1	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	exon	16528465	16528584	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	intron	16528585	16528719	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	CDS	16528720	16528875	1	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	exon	16528720	16528875	.	+	.	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
Phchi.S1	AUGUSTUS	stop_codon	16528876	16528878	.	+	0	transcript_id "Phchi.S1G252600.t1"; gene_id "Phchi.S1G252600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11396.t1 is derived from g15446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6135858	6136736	.	+	.	Phchi.S4G097800
Phchi.S4	AUGUSTUS	transcript	6135858	6136736	.	+	.	transcript_id "Phchi.S4G097800.t1"; gene_id "Phchi.S4G097800"
Phchi.S4	AUGUSTUS	start_codon	6135858	6135860	.	+	0	transcript_id "Phchi.S4G097800.t1"; gene_id "Phchi.S4G097800"
Phchi.S4	AUGUSTUS	CDS	6135858	6136736	0.85	+	0	transcript_id "Phchi.S4G097800.t1"; gene_id "Phchi.S4G097800"
Phchi.S4	AUGUSTUS	exon	6135858	6136736	.	+	.	transcript_id "Phchi.S4G097800.t1"; gene_id "Phchi.S4G097800"
Phchi.S4	AUGUSTUS	stop_codon	6136737	6136739	.	+	0	transcript_id "Phchi.S4G097800.t1"; gene_id "Phchi.S4G097800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg332.t1 is derived from g10114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2311706	2312377	.	+	.	Phchi.S6G029100
Phchi.S6	AUGUSTUS	transcript	2311706	2312377	.	+	.	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	start_codon	2311706	2311708	.	+	0	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	CDS	2311706	2311766	0.46	+	0	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	exon	2311706	2311766	.	+	.	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	intron	2311767	2311904	.	+	.	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	CDS	2311905	2312377	0.36	+	2	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	exon	2311905	2312377	.	+	.	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
Phchi.S6	AUGUSTUS	stop_codon	2312378	2312380	.	+	0	transcript_id "Phchi.S6G029100.t1"; gene_id "Phchi.S6G029100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1320.t1 is derived from g11103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9009922	9011447	.	+	.	Phchi.S6G127900
Phchi.S6	AUGUSTUS	transcript	9009922	9011447	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	start_codon	9009922	9009924	.	+	0	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	CDS	9009922	9010068	1	+	0	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	exon	9009922	9010068	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	intron	9010069	9010399	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	CDS	9010400	9010470	1	+	0	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	exon	9010400	9010470	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	intron	9010471	9010626	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	CDS	9010627	9010715	1	+	1	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	exon	9010627	9010715	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	intron	9010716	9010813	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	CDS	9010814	9010925	1	+	2	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	exon	9010814	9010925	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	intron	9010926	9011122	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	CDS	9011123	9011213	1	+	1	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	exon	9011123	9011213	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	intron	9011214	9011300	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	CDS	9011301	9011447	0.6	+	0	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	exon	9011301	9011447	.	+	.	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
Phchi.S6	AUGUSTUS	stop_codon	9011448	9011450	.	+	0	transcript_id "Phchi.S6G127900.t1"; gene_id "Phchi.S6G127900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12446.t1 is derived from g8123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	21331078	21335023	.	+	.	Phchi.S2G052600
Phchi.S2	AUGUSTUS	transcript	21331078	21335023	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	start_codon	21331078	21331080	.	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21331078	21331143	1	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21331078	21331143	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21331144	21331278	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21331279	21331285	0.93	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21331279	21331285	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21331286	21331371	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21331372	21331394	0.85	+	2	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21331372	21331394	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21331395	21331631	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21331632	21331694	1	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21331632	21331694	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21331695	21331929	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21331930	21332078	1	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21331930	21332078	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21332079	21332659	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21332660	21333300	0.43	+	1	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21332660	21333300	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21333301	21333621	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21333622	21333821	0.88	+	2	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21333622	21333821	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21333822	21333937	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21333938	21334039	1	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21333938	21334039	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21334040	21334122	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21334123	21334188	1	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21334123	21334188	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21334189	21334268	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21334269	21334334	1	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21334269	21334334	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21334335	21334565	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21334566	21334697	0.78	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21334566	21334697	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21334698	21334790	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21334791	21334858	0.69	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21334791	21334858	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	intron	21334859	21335013	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	CDS	21335014	21335023	0.98	+	1	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	exon	21335014	21335023	.	+	.	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
Phchi.S2	AUGUSTUS	stop_codon	21335024	21335026	.	+	0	transcript_id "Phchi.S2G052600.t1"; gene_id "Phchi.S2G052600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1340.t1 is derived from g11123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9101679	9103983	.	-	.	Phchi.S6G129900
Phchi.S6	AUGUSTUS	transcript	9101679	9103983	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	stop_codon	9101676	9101678	.	-	0	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9101679	9101927	1	-	0	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9101679	9101927	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9101928	9102016	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9102017	9102161	1	-	1	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9102017	9102161	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9102162	9102245	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9102246	9102643	1	-	0	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9102246	9102643	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9102644	9102749	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9102750	9102876	1	-	1	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9102750	9102876	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9102877	9102998	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9102999	9103217	1	-	1	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9102999	9103217	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9103218	9103326	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9103327	9103388	1	-	0	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9103327	9103388	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9103389	9103476	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9103477	9103733	1	-	2	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9103477	9103733	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	intron	9103734	9103826	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	CDS	9103827	9103983	1	-	0	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	exon	9103827	9103983	.	-	.	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
Phchi.S6	AUGUSTUS	start_codon	9103981	9103983	.	-	0	transcript_id "Phchi.S6G129900.t1"; gene_id "Phchi.S6G129900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9042.t1 is derived from g6217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39262297	39262938	.	+	.	Phchi.S1G620100
Phchi.S1	AUGUSTUS	transcript	39262297	39262938	.	+	.	transcript_id "Phchi.S1G620100.t1"; gene_id "Phchi.S1G620100"
Phchi.S1	AUGUSTUS	start_codon	39262297	39262299	.	+	0	transcript_id "Phchi.S1G620100.t1"; gene_id "Phchi.S1G620100"
Phchi.S1	AUGUSTUS	CDS	39262297	39262938	0.12	+	0	transcript_id "Phchi.S1G620100.t1"; gene_id "Phchi.S1G620100"
Phchi.S1	AUGUSTUS	exon	39262297	39262938	.	+	.	transcript_id "Phchi.S1G620100.t1"; gene_id "Phchi.S1G620100"
Phchi.S1	AUGUSTUS	stop_codon	39262939	39262941	.	+	0	transcript_id "Phchi.S1G620100.t1"; gene_id "Phchi.S1G620100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15973.t1 is derived from g14463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C196	AUGUSTUS	gene	26730	27331	.	+	.	Phchi.C196G000100
Phchi.C196	AUGUSTUS	transcript	26730	27331	.	+	.	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	start_codon	26730	26732	.	+	0	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	CDS	26730	26764	0.84	+	0	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	exon	26730	26764	.	+	.	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	intron	26765	26895	.	+	.	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	CDS	26896	27331	0.87	+	1	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	exon	26896	27331	.	+	.	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
Phchi.C196	AUGUSTUS	stop_codon	27332	27334	.	+	0	transcript_id "Phchi.C196G000100.t1"; gene_id "Phchi.C196G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15334.t1 is derived from g13802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18441497	18443049	.	-	.	Phchi.S3G265300
Phchi.S3	AUGUSTUS	transcript	18441497	18443049	.	-	.	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	stop_codon	18441494	18441496	.	-	0	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	CDS	18441497	18441501	0.73	-	2	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	exon	18441497	18441501	.	-	.	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	intron	18441502	18441617	.	-	.	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	CDS	18441618	18443049	0.55	-	0	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	exon	18441618	18443049	.	-	.	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
Phchi.S3	AUGUSTUS	start_codon	18443047	18443049	.	-	0	transcript_id "Phchi.S3G265300.t1"; gene_id "Phchi.S3G265300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12600.t1 is derived from g8277.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37404178	37410092	.	-	.	Phchi.S2G068000
Phchi.S2	AUGUSTUS	transcript	37404178	37410092	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	stop_codon	37404175	37404177	.	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37404178	37404315	0.92	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37404178	37404315	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37404316	37404449	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37404450	37404656	0.93	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37404450	37404656	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37404657	37404830	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37404831	37404971	1	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37404831	37404971	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37404972	37405125	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37405126	37405203	0.94	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37405126	37405203	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37405204	37405313	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37405314	37405579	0.92	-	2	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37405314	37405579	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37405580	37405721	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37405722	37405796	1	-	2	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37405722	37405796	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37405797	37406192	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37406193	37406271	1	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37406193	37406271	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37406272	37406531	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37406532	37406714	1	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37406532	37406714	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37406715	37406970	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37406971	37407270	1	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37406971	37407270	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37407271	37407481	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37407482	37407669	0.66	-	2	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37407482	37407669	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37407670	37407878	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37407879	37408001	0.6	-	2	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37407879	37408001	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37408002	37408265	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37408266	37408353	0.95	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37408266	37408353	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37408354	37408452	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37408453	37408587	0.93	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37408453	37408587	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37408588	37408766	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37408767	37409070	0.97	-	1	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37408767	37409070	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37409071	37409265	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37409266	37410092	0.99	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37409266	37410092	.	-	.	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	start_codon	37410090	37410092	.	-	0	transcript_id "Phchi.S2G068000.t1"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	transcript	37404178	37410092	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	stop_codon	37404175	37404177	.	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37404178	37404315	0.97	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37404178	37404315	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37404316	37404449	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37404450	37404656	0.97	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37404450	37404656	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37404657	37404830	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37404831	37404971	1	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37404831	37404971	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37404972	37405125	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37405126	37405203	0.88	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37405126	37405203	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37405204	37405313	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37405314	37405579	0.87	-	2	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37405314	37405579	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37405580	37405721	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37405722	37405796	1	-	2	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37405722	37405796	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37405797	37406192	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37406193	37406271	1	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37406193	37406271	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37406272	37406531	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37406532	37406714	1	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37406532	37406714	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37406715	37406970	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37406971	37407270	1	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37406971	37407270	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37407271	37407481	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37407482	37407669	0.57	-	2	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37407482	37407669	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37407670	37407878	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37407879	37408001	0.56	-	2	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37407879	37408001	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37408002	37408265	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37408266	37408353	0.79	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37408266	37408353	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37408354	37408452	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37408453	37408491	0.79	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37408453	37408491	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37408492	37408766	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37408767	37409070	0.99	-	1	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37408767	37409070	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	intron	37409071	37409265	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	CDS	37409266	37410092	0.99	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	exon	37409266	37410092	.	-	.	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
Phchi.S2	AUGUSTUS	start_codon	37410090	37410092	.	-	0	transcript_id "Phchi.S2G068000.t2"; gene_id "Phchi.S2G068000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14609.t1 is derived from g13077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13739021	13740024	.	+	.	Phchi.S3G192800
Phchi.S3	AUGUSTUS	transcript	13739021	13740024	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	start_codon	13739021	13739023	.	+	0	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	CDS	13739021	13739136	1	+	0	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	exon	13739021	13739136	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	intron	13739137	13739350	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	CDS	13739351	13739496	1	+	1	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	exon	13739351	13739496	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	intron	13739497	13739596	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	CDS	13739597	13739760	1	+	2	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	exon	13739597	13739760	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	intron	13739761	13739886	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	CDS	13739887	13740024	1	+	0	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	exon	13739887	13740024	.	+	.	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
Phchi.S3	AUGUSTUS	stop_codon	13740025	13740027	.	+	0	transcript_id "Phchi.S3G192800.t1"; gene_id "Phchi.S3G192800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2934.t1 is derived from g103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	636738	639963	.	+	.	Phchi.S1G009300
Phchi.S1	AUGUSTUS	transcript	636738	639963	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	start_codon	636738	636740	.	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	636738	636938	0.71	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	636738	636938	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	636939	637031	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637032	637097	0.95	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637032	637097	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637098	637211	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637212	637321	0.95	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637212	637321	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637322	637415	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637416	637476	1	+	1	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637416	637476	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637477	637567	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637568	637651	1	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637568	637651	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637652	637754	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637755	637811	1	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637755	637811	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637812	637903	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637904	637961	1	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637904	637961	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637962	638044	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638045	638091	1	+	2	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638045	638091	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638092	638190	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638191	638253	0.97	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638191	638253	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638254	638379	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638380	638559	1	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638380	638559	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638560	638779	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638780	639097	1	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638780	639097	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639098	639198	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639199	639277	0.97	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639199	639277	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639278	639363	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639364	639537	1	+	2	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639364	639537	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639538	639617	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639618	639823	1	+	2	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639618	639823	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639824	639906	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639907	639963	1	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639907	639963	.	+	.	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	stop_codon	639964	639966	.	+	0	transcript_id "Phchi.S1G009300.t1"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	transcript	636738	639963	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	start_codon	636738	636740	.	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	636738	636938	0.76	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	636738	636938	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	636939	637031	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637032	637097	0.97	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637032	637097	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637098	637211	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637212	637321	0.97	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637212	637321	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637322	637415	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637416	637476	1	+	1	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637416	637476	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637477	637567	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637568	637651	1	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637568	637651	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637652	637754	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637755	637811	1	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637755	637811	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637812	637903	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	637904	637961	1	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	637904	637961	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	637962	638044	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638045	638091	1	+	2	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638045	638091	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638092	638190	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638191	638253	0.9	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638191	638253	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638254	638379	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638380	638559	0.96	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638380	638559	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638560	638657	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638658	638681	1	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638658	638681	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	638682	638779	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	638780	639097	1	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	638780	639097	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639098	639198	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639199	639277	0.97	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639199	639277	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639278	639363	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639364	639534	1	+	2	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639364	639534	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639535	639617	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639618	639823	1	+	2	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639618	639823	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	intron	639824	639906	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	CDS	639907	639963	1	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	exon	639907	639963	.	+	.	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
Phchi.S1	AUGUSTUS	stop_codon	639964	639966	.	+	0	transcript_id "Phchi.S1G009300.t2"; gene_id "Phchi.S1G009300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3480.t1 is derived from g649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3997345	3998589	.	+	.	Phchi.S1G063900
Phchi.S1	AUGUSTUS	transcript	3997345	3998589	.	+	.	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	start_codon	3997345	3997347	.	+	0	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	CDS	3997345	3997469	0.34	+	0	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	exon	3997345	3997469	.	+	.	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	intron	3997470	3997582	.	+	.	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	CDS	3997583	3997972	0.14	+	1	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	exon	3997583	3997972	.	+	.	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	intron	3997973	3998039	.	+	.	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	CDS	3998040	3998589	0.45	+	1	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	exon	3998040	3998589	.	+	.	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
Phchi.S1	AUGUSTUS	stop_codon	3998590	3998592	.	+	0	transcript_id "Phchi.S1G063900.t1"; gene_id "Phchi.S1G063900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11558.t1 is derived from g15609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7043262	7046471	.	+	.	Phchi.S4G114000
Phchi.S4	AUGUSTUS	transcript	7043262	7046471	.	+	.	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	start_codon	7043262	7043264	.	+	0	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	CDS	7043262	7044412	0.62	+	0	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	exon	7043262	7044412	.	+	.	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	intron	7044413	7044492	.	+	.	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	CDS	7044493	7045967	0.68	+	1	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	exon	7044493	7045967	.	+	.	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	intron	7045968	7046058	.	+	.	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	CDS	7046059	7046471	0.93	+	2	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	exon	7046059	7046471	.	+	.	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
Phchi.S4	AUGUSTUS	stop_codon	7046472	7046474	.	+	0	transcript_id "Phchi.S4G114000.t1"; gene_id "Phchi.S4G114000"
# This transcript jg4572.t2 is derived from g1742.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4573.t1 is derived from g1743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11168000	11170272	.	-	.	Phchi.S1G173200
Phchi.S1	AUGUSTUS	transcript	11168000	11170272	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	stop_codon	11167997	11167999	.	-	0	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11168000	11168341	1	-	0	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11168000	11168341	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11168342	11168428	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11168429	11168558	0.98	-	1	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11168429	11168558	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11168559	11168673	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11168674	11168963	1	-	0	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11168674	11168963	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11168964	11169068	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11169069	11169250	0.96	-	2	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11169069	11169250	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11169251	11169358	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11169359	11169578	0.77	-	0	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11169359	11169578	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11169579	11169702	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11169703	11169721	0.82	-	1	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11169703	11169721	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11169722	11169839	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11169840	11170100	0.96	-	1	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11169840	11170100	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	intron	11170101	11170183	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	CDS	11170184	11170272	0.98	-	0	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	exon	11170184	11170272	.	-	.	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
Phchi.S1	AUGUSTUS	start_codon	11170270	11170272	.	-	0	transcript_id "Phchi.S1G173200.t1"; gene_id "Phchi.S1G173200"
# This transcript jg15068.t2 is derived from g13536.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15069.t1 is derived from g13537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16872418	16884708	.	-	.	Phchi.S3G238800
Phchi.S3	AUGUSTUS	transcript	16872418	16884708	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	stop_codon	16872415	16872417	.	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16872418	16872437	0.77	-	2	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16872418	16872437	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16872438	16872513	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16872514	16873750	0.63	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16872514	16873750	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16873751	16873839	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16873840	16873986	1	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16873840	16873986	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16873987	16874069	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16874070	16874373	1	-	1	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16874070	16874373	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16874374	16874470	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16874471	16874779	1	-	1	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16874471	16874779	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16874780	16874860	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16874861	16876616	0.81	-	2	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16874861	16876616	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16876617	16876776	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16876777	16877858	0.95	-	1	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16876777	16877858	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16877859	16878003	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16878004	16878716	0.92	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16878004	16878716	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16878717	16878808	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16878809	16879671	0.84	-	2	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16878809	16879671	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16879672	16879749	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16879750	16880861	0.96	-	1	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16879750	16880861	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16880862	16880984	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16880985	16881087	1	-	2	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16880985	16881087	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16881088	16881184	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16881185	16881944	1	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16881185	16881944	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16881945	16882084	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16882085	16883253	0.92	-	2	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16882085	16883253	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16883254	16883379	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16883380	16883494	0.91	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16883380	16883494	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16883495	16883727	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16883728	16883793	1	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16883728	16883793	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16883794	16883905	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16883906	16884097	0.99	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16883906	16884097	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16884098	16884297	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16884298	16884453	1	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16884298	16884453	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	intron	16884454	16884543	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	CDS	16884544	16884708	1	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	exon	16884544	16884708	.	-	.	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
Phchi.S3	AUGUSTUS	start_codon	16884706	16884708	.	-	0	transcript_id "Phchi.S3G238800.t1"; gene_id "Phchi.S3G238800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10348.t1 is derived from g7524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47292721	47294154	.	-	.	Phchi.S1G750700
Phchi.S1	AUGUSTUS	transcript	47292721	47294154	.	-	.	transcript_id "Phchi.S1G750700.t1"; gene_id "Phchi.S1G750700"
Phchi.S1	AUGUSTUS	stop_codon	47292718	47292720	.	-	0	transcript_id "Phchi.S1G750700.t1"; gene_id "Phchi.S1G750700"
Phchi.S1	AUGUSTUS	CDS	47292721	47294154	1	-	0	transcript_id "Phchi.S1G750700.t1"; gene_id "Phchi.S1G750700"
Phchi.S1	AUGUSTUS	exon	47292721	47294154	.	-	.	transcript_id "Phchi.S1G750700.t1"; gene_id "Phchi.S1G750700"
Phchi.S1	AUGUSTUS	start_codon	47294152	47294154	.	-	0	transcript_id "Phchi.S1G750700.t1"; gene_id "Phchi.S1G750700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12717.t1 is derived from g11182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1085027	1087599	.	+	.	Phchi.S3G003600
Phchi.S3	AUGUSTUS	transcript	1085027	1087599	.	+	.	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	start_codon	1085027	1085029	.	+	0	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	CDS	1085027	1085043	0.7	+	0	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	exon	1085027	1085043	.	+	.	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	intron	1085044	1085352	.	+	.	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	CDS	1085353	1085393	0.87	+	1	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	exon	1085353	1085393	.	+	.	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	intron	1085394	1085668	.	+	.	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	CDS	1085669	1087599	0.77	+	2	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	exon	1085669	1087599	.	+	.	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
Phchi.S3	AUGUSTUS	stop_codon	1087600	1087602	.	+	0	transcript_id "Phchi.S3G003600.t1"; gene_id "Phchi.S3G003600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7895.t1 is derived from g5069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31788336	31789333	.	+	.	Phchi.S1G505400
Phchi.S1	AUGUSTUS	transcript	31788336	31789333	.	+	.	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	start_codon	31788336	31788338	.	+	0	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	CDS	31788336	31788774	0.3	+	0	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	exon	31788336	31788774	.	+	.	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	intron	31788775	31788854	.	+	.	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	CDS	31788855	31789333	0.68	+	2	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	exon	31788855	31789333	.	+	.	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
Phchi.S1	AUGUSTUS	stop_codon	31789334	31789336	.	+	0	transcript_id "Phchi.S1G505400.t1"; gene_id "Phchi.S1G505400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14221.t1 is derived from g12688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11632906	11634151	.	+	.	Phchi.S3G154000
Phchi.S3	AUGUSTUS	transcript	11632906	11634151	.	+	.	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	start_codon	11632906	11632908	.	+	0	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	CDS	11632906	11633343	1	+	0	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	exon	11632906	11633343	.	+	.	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	intron	11633344	11633423	.	+	.	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	CDS	11633424	11633589	1	+	0	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	exon	11633424	11633589	.	+	.	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	intron	11633590	11633735	.	+	.	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	CDS	11633736	11634151	1	+	2	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	exon	11633736	11634151	.	+	.	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
Phchi.S3	AUGUSTUS	stop_codon	11634152	11634154	.	+	0	transcript_id "Phchi.S3G154000.t1"; gene_id "Phchi.S3G154000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5362.t1 is derived from g2532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16474476	16475713	.	+	.	Phchi.S1G252100
Phchi.S1	AUGUSTUS	transcript	16474476	16475713	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	start_codon	16474476	16474478	.	+	0	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16474476	16474505	0.93	+	0	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16474476	16474505	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16474506	16474638	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16474639	16475122	0.93	+	0	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16474639	16475122	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475123	16475205	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475206	16475246	0.56	+	2	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475206	16475246	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475247	16475314	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475315	16475347	0.77	+	0	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475315	16475347	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475348	16475432	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475433	16475487	0.85	+	0	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475433	16475487	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475488	16475624	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475625	16475713	0.77	+	2	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475625	16475713	.	+	.	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	stop_codon	16475714	16475716	.	+	0	transcript_id "Phchi.S1G252100.t1"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	transcript	16474498	16475713	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	start_codon	16474498	16474500	.	+	0	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16474498	16474500	0.97	+	0	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16474498	16474500	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16474501	16474638	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16474639	16475122	1	+	0	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16474639	16475122	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475123	16475205	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475206	16475246	0.47	+	2	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475206	16475246	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475247	16475314	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475315	16475347	0.71	+	0	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475315	16475347	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475348	16475432	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475433	16475487	0.75	+	0	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475433	16475487	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	intron	16475488	16475624	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	CDS	16475625	16475713	0.71	+	2	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	exon	16475625	16475713	.	+	.	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
Phchi.S1	AUGUSTUS	stop_codon	16475714	16475716	.	+	0	transcript_id "Phchi.S1G252100.t2"; gene_id "Phchi.S1G252100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13926.t1 is derived from g12393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9721860	9723344	.	-	.	Phchi.S3G124500
Phchi.S3	AUGUSTUS	transcript	9721860	9723344	.	-	.	transcript_id "Phchi.S3G124500.t1"; gene_id "Phchi.S3G124500"
Phchi.S3	AUGUSTUS	stop_codon	9721857	9721859	.	-	0	transcript_id "Phchi.S3G124500.t1"; gene_id "Phchi.S3G124500"
Phchi.S3	AUGUSTUS	CDS	9721860	9723344	0.88	-	0	transcript_id "Phchi.S3G124500.t1"; gene_id "Phchi.S3G124500"
Phchi.S3	AUGUSTUS	exon	9721860	9723344	.	-	.	transcript_id "Phchi.S3G124500.t1"; gene_id "Phchi.S3G124500"
Phchi.S3	AUGUSTUS	start_codon	9723342	9723344	.	-	0	transcript_id "Phchi.S3G124500.t1"; gene_id "Phchi.S3G124500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11302.t1 is derived from g15352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5298920	5301249	.	+	.	Phchi.S4G088400
Phchi.S4	AUGUSTUS	transcript	5298992	5301249	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	start_codon	5298992	5298994	.	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5298992	5299204	0.72	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5298992	5299204	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5299205	5299735	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5299736	5299800	1	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5299736	5299800	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5299801	5300055	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300056	5300154	1	+	1	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300056	5300154	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300155	5300353	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300354	5300401	1	+	1	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300354	5300401	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300402	5300487	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300488	5300557	1	+	1	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300488	5300557	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300558	5300737	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300738	5300809	1	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300738	5300809	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300810	5300890	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300891	5301016	1	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300891	5301016	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5301017	5301108	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5301109	5301249	0.94	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5301109	5301249	.	+	.	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	stop_codon	5301250	5301252	.	+	0	transcript_id "Phchi.S4G088400.t1"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	transcript	5298920	5301249	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	start_codon	5298920	5298922	.	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5298920	5298943	0.68	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5298920	5298943	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5298944	5299040	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5299041	5299204	0.68	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5299041	5299204	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5299205	5299392	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5299393	5299420	0.47	+	1	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5299393	5299420	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5299421	5299735	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5299736	5299800	0.75	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5299736	5299800	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5299801	5300055	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300056	5300154	1	+	1	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300056	5300154	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300155	5300353	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300354	5300401	1	+	1	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300354	5300401	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300402	5300487	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300488	5300557	1	+	1	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300488	5300557	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300558	5300737	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300738	5300809	1	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300738	5300809	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5300810	5300890	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5300891	5301016	1	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5300891	5301016	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	intron	5301017	5301108	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	CDS	5301109	5301249	0.98	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	exon	5301109	5301249	.	+	.	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
Phchi.S4	AUGUSTUS	stop_codon	5301250	5301252	.	+	0	transcript_id "Phchi.S4G088400.t2"; gene_id "Phchi.S4G088400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8651.t1 is derived from g5826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37243585	37245323	.	-	.	Phchi.S1G581000
Phchi.S1	AUGUSTUS	transcript	37243585	37245323	.	-	.	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	stop_codon	37243582	37243584	.	-	0	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	CDS	37243585	37245151	0.58	-	1	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	exon	37243585	37245151	.	-	.	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	intron	37245152	37245267	.	-	.	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	CDS	37245268	37245323	0.69	-	0	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	exon	37245268	37245323	.	-	.	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
Phchi.S1	AUGUSTUS	start_codon	37245321	37245323	.	-	0	transcript_id "Phchi.S1G581000.t1"; gene_id "Phchi.S1G581000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11836.t1 is derived from g15888.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8493442	8496919	.	+	.	Phchi.S4G141800
Phchi.S4	AUGUSTUS	transcript	8493442	8496919	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	start_codon	8493442	8493444	.	+	0	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8493442	8493649	1	+	0	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8493442	8493649	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8493650	8493801	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8493802	8493951	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8493802	8493951	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8493952	8494038	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8494039	8494206	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8494039	8494206	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8494207	8494401	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8494402	8494554	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8494402	8494554	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8494555	8494727	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8494728	8494880	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8494728	8494880	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8494881	8495171	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8495172	8495333	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8495172	8495333	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8495334	8495536	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8495537	8495722	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8495537	8495722	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8495723	8495893	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8495894	8496071	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8495894	8496071	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8496072	8496333	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8496334	8496523	1	+	1	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8496334	8496523	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8496524	8496693	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8496694	8496790	1	+	0	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8496694	8496790	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8496791	8496866	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8496867	8496919	1	+	2	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8496867	8496919	.	+	.	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	stop_codon	8496920	8496922	.	+	0	transcript_id "Phchi.S4G141800.t1"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	transcript	8493442	8496919	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	start_codon	8493442	8493444	.	+	0	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8493442	8493649	1	+	0	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8493442	8493649	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8493650	8493801	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8493802	8493951	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8493802	8493951	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8493952	8494038	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8494039	8494206	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8494039	8494206	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8494207	8494401	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8494402	8494554	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8494402	8494554	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8494555	8494727	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8494728	8494880	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8494728	8494880	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8494881	8495171	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8495172	8495333	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8495172	8495333	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8495334	8495536	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8495537	8495647	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8495537	8495647	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8495648	8495893	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8495894	8496071	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8495894	8496071	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8496072	8496333	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8496334	8496523	1	+	1	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8496334	8496523	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8496524	8496693	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8496694	8496790	1	+	0	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8496694	8496790	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	intron	8496791	8496866	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	CDS	8496867	8496919	1	+	2	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	exon	8496867	8496919	.	+	.	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
Phchi.S4	AUGUSTUS	stop_codon	8496920	8496922	.	+	0	transcript_id "Phchi.S4G141800.t2"; gene_id "Phchi.S4G141800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg307.t1 is derived from g10089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2205457	2205916	.	+	.	Phchi.S6G026600
Phchi.S6	AUGUSTUS	transcript	2205457	2205916	.	+	.	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	start_codon	2205457	2205459	.	+	0	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	CDS	2205457	2205751	0.36	+	0	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	exon	2205457	2205751	.	+	.	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	intron	2205752	2205902	.	+	.	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	CDS	2205903	2205916	0.89	+	2	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	exon	2205903	2205916	.	+	.	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
Phchi.S6	AUGUSTUS	stop_codon	2205917	2205919	.	+	0	transcript_id "Phchi.S6G026600.t1"; gene_id "Phchi.S6G026600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7209.t1 is derived from g4381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27642027	27644138	.	+	.	Phchi.S1G436800
Phchi.S1	AUGUSTUS	transcript	27642027	27644138	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	start_codon	27642027	27642029	.	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27642027	27642035	1	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27642027	27642035	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27642036	27642600	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27642601	27642785	1	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27642601	27642785	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27642786	27642879	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27642880	27643000	1	+	1	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27642880	27643000	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27643001	27643197	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27643198	27643371	1	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27643198	27643371	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27643372	27643445	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27643446	27643609	1	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27643446	27643609	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27643610	27643725	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27643726	27643813	1	+	1	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27643726	27643813	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27643814	27643915	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27643916	27643969	1	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27643916	27643969	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	intron	27643970	27644051	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	CDS	27644052	27644138	1	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	exon	27644052	27644138	.	+	.	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
Phchi.S1	AUGUSTUS	stop_codon	27644139	27644141	.	+	0	transcript_id "Phchi.S1G436800.t1"; gene_id "Phchi.S1G436800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1738.t1 is derived from g8658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2782551	2785550	.	-	.	Phchi.S5G034700
Phchi.S5	AUGUSTUS	transcript	2782551	2785550	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	stop_codon	2782548	2782550	.	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2782551	2782667	0.99	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2782551	2782667	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2782668	2782758	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2782759	2782926	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2782759	2782926	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2782927	2783026	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783027	2783107	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783027	2783107	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783108	2783211	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783212	2783358	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783212	2783358	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783359	2783466	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783467	2783577	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783467	2783577	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783578	2783747	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783748	2783867	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783748	2783867	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783868	2783946	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783947	2784093	0.97	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783947	2784093	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784094	2784208	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784209	2784265	0.8	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784209	2784265	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784266	2784351	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784352	2784471	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784352	2784471	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784472	2784558	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784559	2784653	1	-	2	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784559	2784653	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784654	2784828	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784829	2784979	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784829	2784979	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784980	2785182	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2785183	2785326	0.98	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2785183	2785326	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2785327	2785445	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2785446	2785550	1	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2785446	2785550	.	-	.	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	start_codon	2785548	2785550	.	-	0	transcript_id "Phchi.S5G034700.t1"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	transcript	2782551	2785550	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	stop_codon	2782548	2782550	.	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2782551	2782667	0.98	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2782551	2782667	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2782668	2782758	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2782759	2782926	1	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2782759	2782926	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2782927	2783026	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783027	2783107	1	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783027	2783107	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783108	2783211	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783212	2783358	1	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783212	2783358	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783359	2783466	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783467	2783577	1	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783467	2783577	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783578	2783747	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783748	2783867	1	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783748	2783867	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2783868	2783946	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2783947	2784093	0.96	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2783947	2784093	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784094	2784208	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784209	2784265	0.72	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784209	2784265	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784266	2784351	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784352	2784471	1	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784352	2784471	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784472	2784558	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784559	2784653	1	-	2	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784559	2784653	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784654	2784828	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784829	2784878	0.78	-	1	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784829	2784878	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784879	2784970	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2784971	2784975	0.8	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2784971	2784975	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2784976	2785182	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2785183	2785326	0.8	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2785183	2785326	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	intron	2785327	2785445	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	CDS	2785446	2785550	0.76	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	exon	2785446	2785550	.	-	.	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
Phchi.S5	AUGUSTUS	start_codon	2785548	2785550	.	-	0	transcript_id "Phchi.S5G034700.t2"; gene_id "Phchi.S5G034700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg839.t1 is derived from g10621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5835685	5836936	.	-	.	Phchi.S6G079800
Phchi.S6	AUGUSTUS	transcript	5835685	5836936	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	stop_codon	5835682	5835684	.	-	0	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	CDS	5835685	5835686	0.89	-	2	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	exon	5835685	5835686	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	intron	5835687	5835808	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	CDS	5835809	5836379	0.4	-	0	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	exon	5835809	5836379	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	intron	5836380	5836631	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	CDS	5836632	5836651	0.58	-	2	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	exon	5836632	5836651	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	intron	5836652	5836836	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	CDS	5836837	5836936	0.66	-	0	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	exon	5836837	5836936	.	-	.	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
Phchi.S6	AUGUSTUS	start_codon	5836934	5836936	.	-	0	transcript_id "Phchi.S6G079800.t1"; gene_id "Phchi.S6G079800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12682.t1 is derived from g11147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	29698	30147	.	+	.	Phchi.S3G000100
Phchi.S3	AUGUSTUS	transcript	29698	30147	.	+	.	transcript_id "Phchi.S3G000100.t1"; gene_id "Phchi.S3G000100"
Phchi.S3	AUGUSTUS	start_codon	29698	29700	.	+	0	transcript_id "Phchi.S3G000100.t1"; gene_id "Phchi.S3G000100"
Phchi.S3	AUGUSTUS	CDS	29698	30147	0.73	+	0	transcript_id "Phchi.S3G000100.t1"; gene_id "Phchi.S3G000100"
Phchi.S3	AUGUSTUS	exon	29698	30147	.	+	.	transcript_id "Phchi.S3G000100.t1"; gene_id "Phchi.S3G000100"
Phchi.S3	AUGUSTUS	stop_codon	30148	30150	.	+	0	transcript_id "Phchi.S3G000100.t1"; gene_id "Phchi.S3G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13039.t1 is derived from g11504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3832037	3837108	.	-	.	Phchi.S3G035800
Phchi.S3	AUGUSTUS	transcript	3832037	3837108	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	stop_codon	3832034	3832036	.	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3832037	3832134	0.97	-	2	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3832037	3832134	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3832135	3832633	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3832634	3832709	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3832634	3832709	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3832710	3832788	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3832789	3832953	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3832789	3832953	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3832954	3833034	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3833035	3833364	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3833035	3833364	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3833365	3833462	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3833463	3833520	1	-	1	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3833463	3833520	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3833521	3833604	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3833605	3833699	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3833605	3833699	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3833700	3833776	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3833777	3833839	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3833777	3833839	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3833840	3833931	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3833932	3833992	1	-	1	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3833932	3833992	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3833993	3834081	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3834082	3834141	1	-	1	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3834082	3834141	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3834142	3834221	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3834222	3834238	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3834222	3834238	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3834239	3834363	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3834364	3834446	1	-	2	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3834364	3834446	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3834447	3834563	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3834564	3834612	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3834564	3834612	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3834613	3834752	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3834753	3834816	1	-	1	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3834753	3834816	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3834817	3834964	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3834965	3835057	1	-	1	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3834965	3835057	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3835058	3835154	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3835155	3835288	1	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3835155	3835288	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3835289	3835369	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3835370	3835591	0.94	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3835370	3835591	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3835592	3835701	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3835702	3835824	0.68	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3835702	3835824	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3835825	3835930	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3835931	3836095	0.94	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3835931	3836095	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	intron	3836096	3836205	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	CDS	3836206	3837108	0.99	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	exon	3836206	3837108	.	-	.	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
Phchi.S3	AUGUSTUS	start_codon	3837106	3837108	.	-	0	transcript_id "Phchi.S3G035800.t1"; gene_id "Phchi.S3G035800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10354.t1 is derived from g7530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47325369	47326481	.	-	.	Phchi.S1G751300
Phchi.S1	AUGUSTUS	transcript	47325369	47326481	.	-	.	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	stop_codon	47325366	47325368	.	-	0	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	CDS	47325369	47325511	1	-	2	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	exon	47325369	47325511	.	-	.	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	intron	47325512	47325634	.	-	.	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	CDS	47325635	47325726	1	-	1	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	exon	47325635	47325726	.	-	.	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	intron	47325727	47325852	.	-	.	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	CDS	47325853	47326481	1	-	0	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	exon	47325853	47326481	.	-	.	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
Phchi.S1	AUGUSTUS	start_codon	47326479	47326481	.	-	0	transcript_id "Phchi.S1G751300.t1"; gene_id "Phchi.S1G751300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5216.t1 is derived from g2386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15516045	15518437	.	+	.	Phchi.S1G237500
Phchi.S1	AUGUSTUS	transcript	15516045	15518437	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	start_codon	15516045	15516047	.	+	0	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516045	15516246	0.93	+	0	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516045	15516246	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15516247	15516410	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516411	15516555	1	+	2	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516411	15516555	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15516556	15516692	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516693	15516739	0.87	+	1	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516693	15516739	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15516740	15516965	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516966	15517052	0.89	+	2	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516966	15517052	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517053	15517143	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517144	15517218	0.98	+	2	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517144	15517218	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517219	15517310	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517311	15517399	1	+	2	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517311	15517399	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517400	15517531	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517532	15517714	1	+	0	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517532	15517714	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517715	15517838	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517839	15517923	0.84	+	0	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517839	15517923	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517924	15518210	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15518211	15518321	0.82	+	2	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15518211	15518321	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15518322	15518414	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15518415	15518437	0.99	+	2	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15518415	15518437	.	+	.	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	stop_codon	15518438	15518440	.	+	0	transcript_id "Phchi.S1G237500.t1"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	transcript	15516045	15518437	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	start_codon	15516045	15516047	.	+	0	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516045	15516246	0.97	+	0	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516045	15516246	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15516247	15516410	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516411	15516555	1	+	2	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516411	15516555	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15516556	15516692	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516693	15516739	0.8	+	1	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516693	15516739	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15516740	15516965	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15516966	15517052	0.9	+	2	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15516966	15517052	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517053	15517143	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517144	15517218	0.99	+	2	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517144	15517218	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517219	15517310	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517311	15517399	1	+	2	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517311	15517399	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517400	15517478	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517479	15517519	0.85	+	0	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517479	15517519	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517520	15517599	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517600	15517714	0.92	+	1	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517600	15517714	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517715	15517838	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15517839	15517923	0.87	+	0	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15517839	15517923	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15517924	15518210	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15518211	15518321	0.84	+	2	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15518211	15518321	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	intron	15518322	15518414	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	CDS	15518415	15518437	0.97	+	2	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	exon	15518415	15518437	.	+	.	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
Phchi.S1	AUGUSTUS	stop_codon	15518438	15518440	.	+	0	transcript_id "Phchi.S1G237500.t2"; gene_id "Phchi.S1G237500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13097.t1 is derived from g11562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4131658	4133253	.	-	.	Phchi.S3G041600
Phchi.S3	AUGUSTUS	transcript	4131658	4133253	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	stop_codon	4131655	4131657	.	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4131658	4131894	1	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4131658	4131894	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4131895	4131981	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4131982	4132083	1	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4131982	4132083	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4132084	4132172	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4132173	4132186	1	-	2	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4132173	4132186	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4132187	4132319	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4132320	4132428	1	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4132320	4132428	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4132429	4132524	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4132525	4132604	1	-	2	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4132525	4132604	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4132605	4132693	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4132694	4132785	0.99	-	1	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4132694	4132785	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4132786	4132889	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4132890	4132993	1	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4132890	4132993	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	intron	4132994	4133166	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	CDS	4133167	4133253	0.75	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	exon	4133167	4133253	.	-	.	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
Phchi.S3	AUGUSTUS	start_codon	4133251	4133253	.	-	0	transcript_id "Phchi.S3G041600.t1"; gene_id "Phchi.S3G041600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2619.t1 is derived from g9539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7800716	7802437	.	+	.	Phchi.S5G122800
Phchi.S5	AUGUSTUS	transcript	7800716	7802437	.	+	.	transcript_id "Phchi.S5G122800.t1"; gene_id "Phchi.S5G122800"
Phchi.S5	AUGUSTUS	start_codon	7800716	7800718	.	+	0	transcript_id "Phchi.S5G122800.t1"; gene_id "Phchi.S5G122800"
Phchi.S5	AUGUSTUS	CDS	7800716	7802437	0.85	+	0	transcript_id "Phchi.S5G122800.t1"; gene_id "Phchi.S5G122800"
Phchi.S5	AUGUSTUS	exon	7800716	7802437	.	+	.	transcript_id "Phchi.S5G122800.t1"; gene_id "Phchi.S5G122800"
Phchi.S5	AUGUSTUS	stop_codon	7802438	7802440	.	+	0	transcript_id "Phchi.S5G122800.t1"; gene_id "Phchi.S5G122800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5330.t1 is derived from g2500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16320673	16322630	.	-	.	Phchi.S1G248900
Phchi.S1	AUGUSTUS	transcript	16320673	16322630	.	-	.	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	stop_codon	16320670	16320672	.	-	0	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	CDS	16320673	16321072	0.68	-	1	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	exon	16320673	16321072	.	-	.	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	intron	16321073	16321273	.	-	.	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	CDS	16321274	16321312	0.94	-	1	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	exon	16321274	16321312	.	-	.	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	intron	16321313	16321497	.	-	.	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	CDS	16321498	16322630	0.99	-	0	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	exon	16321498	16322630	.	-	.	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
Phchi.S1	AUGUSTUS	start_codon	16322628	16322630	.	-	0	transcript_id "Phchi.S1G248900.t1"; gene_id "Phchi.S1G248900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7180.t1 is derived from g4352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27426700	27428771	.	-	.	Phchi.S1G433900
Phchi.S1	AUGUSTUS	transcript	27426700	27428771	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	stop_codon	27426697	27426699	.	-	0	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	CDS	27426700	27427342	0.99	-	1	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	exon	27426700	27427342	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	intron	27427343	27427479	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	CDS	27427480	27427561	0.97	-	2	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	exon	27427480	27427561	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	intron	27427562	27427656	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	CDS	27427657	27427779	0.65	-	2	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	exon	27427657	27427779	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	intron	27427780	27427864	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	CDS	27427865	27428479	0.92	-	2	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	exon	27427865	27428479	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	intron	27428480	27428608	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	CDS	27428609	27428771	0.85	-	0	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	exon	27428609	27428771	.	-	.	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
Phchi.S1	AUGUSTUS	start_codon	27428769	27428771	.	-	0	transcript_id "Phchi.S1G433900.t1"; gene_id "Phchi.S1G433900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13386.t1 is derived from g11852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6489161	6491775	.	+	.	Phchi.S3G070500
Phchi.S3	AUGUSTUS	transcript	6489161	6491775	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	start_codon	6489161	6489163	.	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6489161	6489235	0.69	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6489161	6489235	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6489236	6489393	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6489394	6489414	1	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6489394	6489414	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6489415	6489638	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6489639	6489867	1	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6489639	6489867	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6489868	6489963	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6489964	6490040	1	+	2	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6489964	6490040	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6490041	6490269	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6490270	6490324	1	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6490270	6490324	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6490325	6490419	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6490420	6490486	1	+	2	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6490420	6490486	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6490487	6490659	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6490660	6490729	1	+	1	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6490660	6490729	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	intron	6490730	6490815	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	CDS	6490816	6491775	0.95	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	exon	6490816	6491775	.	+	.	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
Phchi.S3	AUGUSTUS	stop_codon	6491776	6491778	.	+	0	transcript_id "Phchi.S3G070500.t1"; gene_id "Phchi.S3G070500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2120.t1 is derived from g9040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4938571	4940214	.	-	.	Phchi.S5G072900
Phchi.S5	AUGUSTUS	transcript	4938571	4940214	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	stop_codon	4938568	4938570	.	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4938571	4938792	0.99	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4938571	4938792	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	intron	4938793	4938880	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4938881	4938952	1	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4938881	4938952	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	intron	4938953	4939027	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4939028	4939147	1	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4939028	4939147	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	intron	4939148	4939245	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4939246	4939434	0.98	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4939246	4939434	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	intron	4939435	4939539	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4939540	4939638	0.98	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4939540	4939638	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	intron	4939639	4939730	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4939731	4939877	1	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4939731	4939877	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	intron	4939878	4939989	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	CDS	4939990	4940214	1	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	exon	4939990	4940214	.	-	.	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
Phchi.S5	AUGUSTUS	start_codon	4940212	4940214	.	-	0	transcript_id "Phchi.S5G072900.t1"; gene_id "Phchi.S5G072900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3179.t1 is derived from g348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2118217	2119345	.	+	.	Phchi.S1G033800
Phchi.S1	AUGUSTUS	transcript	2118217	2119345	.	+	.	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	start_codon	2118217	2118219	.	+	0	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	CDS	2118217	2119151	0.85	+	0	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	exon	2118217	2119151	.	+	.	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	intron	2119152	2119332	.	+	.	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	CDS	2119333	2119345	0.99	+	1	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	exon	2119333	2119345	.	+	.	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
Phchi.S1	AUGUSTUS	stop_codon	2119346	2119348	.	+	0	transcript_id "Phchi.S1G033800.t1"; gene_id "Phchi.S1G033800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9331.t1 is derived from g6506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40964823	40966845	.	-	.	Phchi.S1G649000
Phchi.S1	AUGUSTUS	transcript	40964823	40966845	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	stop_codon	40964820	40964822	.	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40964823	40964942	0.8	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40964823	40964942	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40964943	40965028	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40965029	40965187	1	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40965029	40965187	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40965188	40965294	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40965295	40965381	1	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40965295	40965381	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40965382	40965515	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40965516	40965590	1	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40965516	40965590	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40965591	40965687	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40965688	40965766	1	-	1	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40965688	40965766	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40965767	40965917	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40965918	40966150	1	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40965918	40966150	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40966151	40966252	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40966253	40966351	0.99	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40966253	40966351	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40966352	40966449	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40966450	40966550	1	-	2	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40966450	40966550	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	intron	40966551	40966634	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	CDS	40966635	40966845	0.86	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	exon	40966635	40966845	.	-	.	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
Phchi.S1	AUGUSTUS	start_codon	40966843	40966845	.	-	0	transcript_id "Phchi.S1G649000.t1"; gene_id "Phchi.S1G649000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11076.t1 is derived from g15126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3979814	3981081	.	+	.	Phchi.S4G065800
Phchi.S4	AUGUSTUS	transcript	3979814	3981081	.	+	.	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	start_codon	3979814	3979816	.	+	0	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	CDS	3979814	3980116	0.44	+	0	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	exon	3979814	3980116	.	+	.	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	intron	3980117	3980402	.	+	.	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	CDS	3980403	3980518	1	+	0	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	exon	3980403	3980518	.	+	.	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	intron	3980519	3980609	.	+	.	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	CDS	3980610	3981081	0.93	+	1	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	exon	3980610	3981081	.	+	.	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
Phchi.S4	AUGUSTUS	stop_codon	3981082	3981084	.	+	0	transcript_id "Phchi.S4G065800.t1"; gene_id "Phchi.S4G065800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6033.t1 is derived from g3204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20521592	20522745	.	-	.	Phchi.S1G319200
Phchi.S1	AUGUSTUS	transcript	20521592	20522745	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	stop_codon	20521589	20521591	.	-	0	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	CDS	20521592	20521785	0.66	-	2	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	exon	20521592	20521785	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	intron	20521786	20521871	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	CDS	20521872	20521940	1	-	2	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	exon	20521872	20521940	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	intron	20521941	20522106	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	CDS	20522107	20522233	1	-	0	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	exon	20522107	20522233	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	intron	20522234	20522413	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	CDS	20522414	20522436	1	-	2	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	exon	20522414	20522436	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	intron	20522437	20522528	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	CDS	20522529	20522654	0.79	-	2	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	exon	20522529	20522654	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	intron	20522655	20522735	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	CDS	20522736	20522745	0.94	-	0	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	exon	20522736	20522745	.	-	.	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
Phchi.S1	AUGUSTUS	start_codon	20522743	20522745	.	-	0	transcript_id "Phchi.S1G319200.t1"; gene_id "Phchi.S1G319200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14477.t1 is derived from g12945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13045184	13046618	.	+	.	Phchi.S3G179600
Phchi.S3	AUGUSTUS	transcript	13045184	13046618	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	start_codon	13045184	13045186	.	+	0	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	CDS	13045184	13045698	0.97	+	0	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	exon	13045184	13045698	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	intron	13045699	13045812	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	CDS	13045813	13046202	0.95	+	1	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	exon	13045813	13046202	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	intron	13046203	13046285	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	CDS	13046286	13046444	1	+	1	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	exon	13046286	13046444	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	intron	13046445	13046530	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	CDS	13046531	13046618	1	+	1	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	exon	13046531	13046618	.	+	.	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
Phchi.S3	AUGUSTUS	stop_codon	13046619	13046621	.	+	0	transcript_id "Phchi.S3G179600.t1"; gene_id "Phchi.S3G179600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10657.t1 is derived from g14707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1454221	1455590	.	-	.	Phchi.S4G023900
Phchi.S4	AUGUSTUS	transcript	1454221	1455590	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	stop_codon	1454218	1454220	.	-	0	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	CDS	1454221	1454331	1	-	0	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	exon	1454221	1454331	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	intron	1454332	1454432	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	CDS	1454433	1454540	1	-	0	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	exon	1454433	1454540	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	intron	1454541	1454624	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	CDS	1454625	1454698	1	-	2	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	exon	1454625	1454698	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	intron	1454699	1454785	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	CDS	1454786	1454863	1	-	2	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	exon	1454786	1454863	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	intron	1454864	1454946	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	CDS	1454947	1455340	0.99	-	0	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	exon	1454947	1455340	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	intron	1455341	1455530	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	CDS	1455531	1455590	0.41	-	0	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	exon	1455531	1455590	.	-	.	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
Phchi.S4	AUGUSTUS	start_codon	1455588	1455590	.	-	0	transcript_id "Phchi.S4G023900.t1"; gene_id "Phchi.S4G023900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7641.t1 is derived from g4815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30376069	30376443	.	+	.	Phchi.S1G480000
Phchi.S1	AUGUSTUS	transcript	30376069	30376443	.	+	.	transcript_id "Phchi.S1G480000.t1"; gene_id "Phchi.S1G480000"
Phchi.S1	AUGUSTUS	start_codon	30376069	30376071	.	+	0	transcript_id "Phchi.S1G480000.t1"; gene_id "Phchi.S1G480000"
Phchi.S1	AUGUSTUS	CDS	30376069	30376443	0.64	+	0	transcript_id "Phchi.S1G480000.t1"; gene_id "Phchi.S1G480000"
Phchi.S1	AUGUSTUS	exon	30376069	30376443	.	+	.	transcript_id "Phchi.S1G480000.t1"; gene_id "Phchi.S1G480000"
Phchi.S1	AUGUSTUS	stop_codon	30376444	30376446	.	+	0	transcript_id "Phchi.S1G480000.t1"; gene_id "Phchi.S1G480000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15756.t1 is derived from g14226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21081979	21086538	.	+	.	Phchi.S3G307500
Phchi.S3	AUGUSTUS	transcript	21081979	21086538	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	start_codon	21081979	21081981	.	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21081979	21082324	0.97	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21081979	21082324	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21082325	21082433	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21082434	21082498	1	+	2	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21082434	21082498	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21082499	21082647	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21082648	21082866	1	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21082648	21082866	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21082867	21083135	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21083136	21083285	0.99	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21083136	21083285	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21083286	21083400	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21083401	21083658	0.32	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21083401	21083658	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21083659	21083741	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21083742	21083804	0.32	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21083742	21083804	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21083805	21083911	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21083912	21084171	1	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21083912	21084171	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21084172	21084256	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21084257	21084475	1	+	1	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21084257	21084475	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21084476	21084583	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21084584	21084791	0.99	+	1	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21084584	21084791	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21084792	21084919	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21084920	21085073	1	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21084920	21085073	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21085074	21085232	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21085233	21085835	1	+	2	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21085233	21085835	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	intron	21085836	21085939	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	CDS	21085940	21086538	1	+	2	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	exon	21085940	21086538	.	+	.	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
Phchi.S3	AUGUSTUS	stop_codon	21086539	21086541	.	+	0	transcript_id "Phchi.S3G307500.t1"; gene_id "Phchi.S3G307500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5139.t1 is derived from g2309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15121016	15123391	.	-	.	Phchi.S1G229800
Phchi.S1	AUGUSTUS	transcript	15121016	15123391	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	stop_codon	15121013	15121015	.	-	0	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15121016	15121055	1	-	1	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15121016	15121055	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	intron	15121056	15121158	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15121159	15121387	0.68	-	2	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15121159	15121387	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	intron	15121388	15121606	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15121607	15122089	0.61	-	2	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15121607	15122089	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	intron	15122090	15122323	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15122324	15122654	0.82	-	0	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15122324	15122654	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	intron	15122655	15122780	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15122781	15122971	0.72	-	2	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15122781	15122971	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	intron	15122972	15123069	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15123070	15123138	0.87	-	2	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15123070	15123138	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	intron	15123139	15123279	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	CDS	15123280	15123391	0.72	-	0	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	exon	15123280	15123391	.	-	.	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
Phchi.S1	AUGUSTUS	start_codon	15123389	15123391	.	-	0	transcript_id "Phchi.S1G229800.t1"; gene_id "Phchi.S1G229800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14185.t1 is derived from g12652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11361793	11364962	.	+	.	Phchi.S3G150400
Phchi.S3	AUGUSTUS	transcript	11361793	11364962	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	start_codon	11361793	11361795	.	+	0	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	CDS	11361793	11362001	0.77	+	0	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	exon	11361793	11362001	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	intron	11362002	11362123	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	CDS	11362124	11363495	0.84	+	1	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	exon	11362124	11363495	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	intron	11363496	11363647	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	CDS	11363648	11363949	1	+	0	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	exon	11363648	11363949	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	intron	11363950	11364052	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	CDS	11364053	11364269	1	+	1	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	exon	11364053	11364269	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	intron	11364270	11364409	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	CDS	11364410	11364606	1	+	0	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	exon	11364410	11364606	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	intron	11364607	11364700	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	CDS	11364701	11364962	0.93	+	1	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	exon	11364701	11364962	.	+	.	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
Phchi.S3	AUGUSTUS	stop_codon	11364963	11364965	.	+	0	transcript_id "Phchi.S3G150400.t1"; gene_id "Phchi.S3G150400"
# This transcript jg831.t2 is derived from g10613.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg831.t3 is derived from g10613.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg832.t1 is derived from g10614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5777513	5778128	.	-	.	Phchi.S6G079100
Phchi.S6	AUGUSTUS	transcript	5777513	5778128	.	-	.	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	stop_codon	5777510	5777512	.	-	0	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	CDS	5777513	5777634	0.03	-	2	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	exon	5777513	5777634	.	-	.	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	intron	5777635	5778004	.	-	.	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	CDS	5778005	5778128	0.01	-	0	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	exon	5778005	5778128	.	-	.	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
Phchi.S6	AUGUSTUS	start_codon	5778126	5778128	.	-	0	transcript_id "Phchi.S6G079100.t1"; gene_id "Phchi.S6G079100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4908.t1 is derived from g2078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13347287	13347894	.	-	.	Phchi.S1G206700
Phchi.S1	AUGUSTUS	transcript	13347287	13347894	.	-	.	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	stop_codon	13347284	13347286	.	-	0	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	CDS	13347287	13347469	0.42	-	0	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	exon	13347287	13347469	.	-	.	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	intron	13347470	13347651	.	-	.	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	CDS	13347652	13347894	0.32	-	0	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	exon	13347652	13347894	.	-	.	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
Phchi.S1	AUGUSTUS	start_codon	13347892	13347894	.	-	0	transcript_id "Phchi.S1G206700.t1"; gene_id "Phchi.S1G206700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9819.t1 is derived from g6995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43944168	43944787	.	+	.	Phchi.S1G697800
Phchi.S1	AUGUSTUS	transcript	43944168	43944787	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	start_codon	43944168	43944170	.	+	0	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	CDS	43944168	43944293	1	+	0	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	exon	43944168	43944293	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	intron	43944294	43944380	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	CDS	43944381	43944443	1	+	0	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	exon	43944381	43944443	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	intron	43944444	43944531	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	CDS	43944532	43944596	1	+	0	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	exon	43944532	43944596	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	intron	43944597	43944678	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	CDS	43944679	43944787	1	+	1	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	exon	43944679	43944787	.	+	.	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
Phchi.S1	AUGUSTUS	stop_codon	43944788	43944790	.	+	0	transcript_id "Phchi.S1G697800.t1"; gene_id "Phchi.S1G697800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15123.t1 is derived from g13591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17170101	17172133	.	-	.	Phchi.S3G244200
Phchi.S3	AUGUSTUS	transcript	17170101	17172133	.	-	.	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	stop_codon	17170098	17170100	.	-	0	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	CDS	17170101	17171012	0.51	-	0	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	exon	17170101	17171012	.	-	.	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	intron	17171013	17171113	.	-	.	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	CDS	17171114	17172133	0.62	-	0	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	exon	17171114	17172133	.	-	.	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
Phchi.S3	AUGUSTUS	start_codon	17172131	17172133	.	-	0	transcript_id "Phchi.S3G244200.t1"; gene_id "Phchi.S3G244200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15530.t1 is derived from g13999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19738495	19739758	.	-	.	Phchi.S3G284900
Phchi.S3	AUGUSTUS	transcript	19738495	19739758	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	stop_codon	19738492	19738494	.	-	0	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	CDS	19738495	19738886	0.99	-	2	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	exon	19738495	19738886	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	intron	19738887	19738971	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	CDS	19738972	19739137	1	-	0	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	exon	19738972	19739137	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	intron	19739138	19739232	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	CDS	19739233	19739427	0.99	-	0	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	exon	19739233	19739427	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	intron	19739428	19739536	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	CDS	19739537	19739758	0.9	-	0	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	exon	19739537	19739758	.	-	.	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
Phchi.S3	AUGUSTUS	start_codon	19739756	19739758	.	-	0	transcript_id "Phchi.S3G284900.t1"; gene_id "Phchi.S3G284900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4015.t1 is derived from g1184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7186314	7187300	.	-	.	Phchi.S1G117400
Phchi.S1	AUGUSTUS	transcript	7186314	7187300	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	stop_codon	7186311	7186313	.	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	CDS	7186314	7186469	0.64	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	exon	7186314	7186469	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	intron	7186470	7186568	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	CDS	7186569	7186751	1	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	exon	7186569	7186751	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	intron	7186752	7186873	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	CDS	7186874	7187002	1	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	exon	7186874	7187002	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	intron	7187003	7187121	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	CDS	7187122	7187211	1	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	exon	7187122	7187211	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	intron	7187212	7187297	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	CDS	7187298	7187300	0.99	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	exon	7187298	7187300	.	-	.	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
Phchi.S1	AUGUSTUS	start_codon	7187298	7187300	.	-	0	transcript_id "Phchi.S1G117400.t1"; gene_id "Phchi.S1G117400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1290.t1 is derived from g11073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8860087	8862280	.	+	.	Phchi.S6G124900
Phchi.S6	AUGUSTUS	transcript	8860087	8862280	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	start_codon	8860087	8860089	.	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8860087	8860457	1	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8860087	8860457	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8860458	8860891	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8860892	8860931	1	+	1	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8860892	8860931	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8860932	8861044	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8861045	8861104	1	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8861045	8861104	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8861105	8861236	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8861237	8861289	1	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8861237	8861289	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8861290	8861382	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8861383	8861438	1	+	1	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8861383	8861438	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8861439	8861527	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8861528	8861561	1	+	2	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8861528	8861561	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8861562	8861665	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8861666	8861738	1	+	1	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8861666	8861738	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8861739	8861818	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8861819	8861911	1	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8861819	8861911	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	intron	8861912	8862010	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	CDS	8862011	8862280	1	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	exon	8862011	8862280	.	+	.	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
Phchi.S6	AUGUSTUS	stop_codon	8862281	8862283	.	+	0	transcript_id "Phchi.S6G124900.t1"; gene_id "Phchi.S6G124900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2910.t1 is derived from g79.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	448969	450780	.	+	.	Phchi.S1G006900
Phchi.S1	AUGUSTUS	transcript	448969	450780	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	start_codon	448969	448971	.	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	448969	449561	0.33	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	448969	449561	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	intron	449562	449753	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	449754	449793	1	+	1	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	449754	449793	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	intron	449794	449910	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	449911	449975	1	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	449911	449975	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	intron	449976	450116	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	450117	450201	1	+	1	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	450117	450201	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	intron	450202	450421	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	450422	450490	1	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	450422	450490	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	intron	450491	450577	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	450578	450640	1	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	450578	450640	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	intron	450641	450723	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	CDS	450724	450780	1	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	exon	450724	450780	.	+	.	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
Phchi.S1	AUGUSTUS	stop_codon	450781	450783	.	+	0	transcript_id "Phchi.S1G006900.t1"; gene_id "Phchi.S1G006900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1461.t1 is derived from g8380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1014559	1015787	.	+	.	Phchi.S5G007000
Phchi.S5	AUGUSTUS	transcript	1014559	1015787	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	start_codon	1014559	1014561	.	+	0	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	CDS	1014559	1015022	0.6	+	0	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	exon	1014559	1015022	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	intron	1015023	1015198	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	CDS	1015199	1015315	0.16	+	1	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	exon	1015199	1015315	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	intron	1015316	1015478	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	CDS	1015479	1015575	0.45	+	1	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	exon	1015479	1015575	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	intron	1015576	1015736	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	CDS	1015737	1015787	0.51	+	0	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	exon	1015737	1015787	.	+	.	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
Phchi.S5	AUGUSTUS	stop_codon	1015788	1015790	.	+	0	transcript_id "Phchi.S5G007000.t1"; gene_id "Phchi.S5G007000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12811.t1 is derived from g11276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2475730	2476925	.	-	.	Phchi.S3G013000
Phchi.S3	AUGUSTUS	transcript	2475730	2476925	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	stop_codon	2475727	2475729	.	-	0	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2475730	2475810	1	-	0	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2475730	2475810	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	intron	2475811	2475890	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2475891	2475971	1	-	0	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2475891	2475971	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	intron	2475972	2476054	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2476055	2476125	1	-	2	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2476055	2476125	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	intron	2476126	2476216	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2476217	2476392	1	-	1	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2476217	2476392	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	intron	2476393	2476522	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2476523	2476596	1	-	0	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2476523	2476596	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	intron	2476597	2476673	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2476674	2476773	1	-	1	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2476674	2476773	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	intron	2476774	2476863	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	CDS	2476864	2476925	1	-	0	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	exon	2476864	2476925	.	-	.	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
Phchi.S3	AUGUSTUS	start_codon	2476923	2476925	.	-	0	transcript_id "Phchi.S3G013000.t1"; gene_id "Phchi.S3G013000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3422.t1 is derived from g591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3534176	3535999	.	-	.	Phchi.S1G058100
Phchi.S1	AUGUSTUS	transcript	3534176	3535999	.	-	.	transcript_id "Phchi.S1G058100.t1"; gene_id "Phchi.S1G058100"
Phchi.S1	AUGUSTUS	stop_codon	3534173	3534175	.	-	0	transcript_id "Phchi.S1G058100.t1"; gene_id "Phchi.S1G058100"
Phchi.S1	AUGUSTUS	CDS	3534176	3535999	0.83	-	0	transcript_id "Phchi.S1G058100.t1"; gene_id "Phchi.S1G058100"
Phchi.S1	AUGUSTUS	exon	3534176	3535999	.	-	.	transcript_id "Phchi.S1G058100.t1"; gene_id "Phchi.S1G058100"
Phchi.S1	AUGUSTUS	start_codon	3535997	3535999	.	-	0	transcript_id "Phchi.S1G058100.t1"; gene_id "Phchi.S1G058100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10347.t1 is derived from g7523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47289747	47292251	.	+	.	Phchi.S1G750600
Phchi.S1	AUGUSTUS	transcript	47289747	47292251	.	+	.	transcript_id "Phchi.S1G750600.t1"; gene_id "Phchi.S1G750600"
Phchi.S1	AUGUSTUS	start_codon	47289747	47289749	.	+	0	transcript_id "Phchi.S1G750600.t1"; gene_id "Phchi.S1G750600"
Phchi.S1	AUGUSTUS	CDS	47289747	47292251	0.99	+	0	transcript_id "Phchi.S1G750600.t1"; gene_id "Phchi.S1G750600"
Phchi.S1	AUGUSTUS	exon	47289747	47292251	.	+	.	transcript_id "Phchi.S1G750600.t1"; gene_id "Phchi.S1G750600"
Phchi.S1	AUGUSTUS	stop_codon	47292252	47292254	.	+	0	transcript_id "Phchi.S1G750600.t1"; gene_id "Phchi.S1G750600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3952.t1 is derived from g1121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6640414	6641948	.	+	.	Phchi.S1G111100
Phchi.S1	AUGUSTUS	transcript	6640414	6641948	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	start_codon	6640414	6640416	.	+	0	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6640414	6640614	0.54	+	0	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6640414	6640614	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6640615	6640777	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6640778	6640901	0.77	+	0	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6640778	6640901	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6640902	6640974	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6640975	6641039	0.91	+	2	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6640975	6641039	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6641040	6641288	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6641289	6641450	0.91	+	0	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6641289	6641450	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6641451	6641657	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6641658	6641948	0.99	+	0	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6641658	6641948	.	+	.	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	stop_codon	6641949	6641951	.	+	0	transcript_id "Phchi.S1G111100.t1"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	transcript	6640414	6641948	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	start_codon	6640414	6640416	.	+	0	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6640414	6640587	0.36	+	0	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6640414	6640587	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6640588	6640777	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6640778	6640901	0.48	+	0	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6640778	6640901	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6640902	6640974	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6640975	6641039	0.83	+	2	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6640975	6641039	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6641040	6641288	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6641289	6641450	0.9	+	0	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6641289	6641450	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	intron	6641451	6641657	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	CDS	6641658	6641948	0.97	+	0	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	exon	6641658	6641948	.	+	.	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
Phchi.S1	AUGUSTUS	stop_codon	6641949	6641951	.	+	0	transcript_id "Phchi.S1G111100.t2"; gene_id "Phchi.S1G111100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg767.t1 is derived from g10549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5411888	5412771	.	+	.	Phchi.S6G072600
Phchi.S6	AUGUSTUS	transcript	5411888	5412771	.	+	.	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	start_codon	5411888	5411890	.	+	0	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	CDS	5411888	5412214	0.74	+	0	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	exon	5411888	5412214	.	+	.	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	intron	5412215	5412311	.	+	.	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	CDS	5412312	5412443	0.4	+	0	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	exon	5412312	5412443	.	+	.	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	intron	5412444	5412603	.	+	.	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	CDS	5412604	5412771	0.79	+	0	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	exon	5412604	5412771	.	+	.	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
Phchi.S6	AUGUSTUS	stop_codon	5412772	5412774	.	+	0	transcript_id "Phchi.S6G072600.t1"; gene_id "Phchi.S6G072600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9567.t1 is derived from g6743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42707983	42708936	.	+	.	Phchi.S1G672600
Phchi.S1	AUGUSTUS	transcript	42707983	42708936	.	+	.	transcript_id "Phchi.S1G672600.t1"; gene_id "Phchi.S1G672600"
Phchi.S1	AUGUSTUS	start_codon	42707983	42707985	.	+	0	transcript_id "Phchi.S1G672600.t1"; gene_id "Phchi.S1G672600"
Phchi.S1	AUGUSTUS	CDS	42707983	42708936	0.51	+	0	transcript_id "Phchi.S1G672600.t1"; gene_id "Phchi.S1G672600"
Phchi.S1	AUGUSTUS	exon	42707983	42708936	.	+	.	transcript_id "Phchi.S1G672600.t1"; gene_id "Phchi.S1G672600"
Phchi.S1	AUGUSTUS	stop_codon	42708937	42708939	.	+	0	transcript_id "Phchi.S1G672600.t1"; gene_id "Phchi.S1G672600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6657.t1 is derived from g3829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24330293	24333429	.	+	.	Phchi.S1G381600
Phchi.S1	AUGUSTUS	transcript	24330293	24333429	.	+	.	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	start_codon	24330293	24330295	.	+	0	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	CDS	24330293	24331955	0.62	+	0	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	exon	24330293	24331955	.	+	.	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	intron	24331956	24332008	.	+	.	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	CDS	24332009	24333429	0.5	+	2	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	exon	24332009	24333429	.	+	.	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
Phchi.S1	AUGUSTUS	stop_codon	24333430	24333432	.	+	0	transcript_id "Phchi.S1G381600.t1"; gene_id "Phchi.S1G381600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1720.t1 is derived from g8640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2690584	2693616	.	-	.	Phchi.S5G032900
Phchi.S5	AUGUSTUS	transcript	2690584	2693616	.	-	.	transcript_id "Phchi.S5G032900.t1"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	stop_codon	2690581	2690583	.	-	0	transcript_id "Phchi.S5G032900.t1"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	CDS	2690584	2693616	0.95	-	0	transcript_id "Phchi.S5G032900.t1"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	exon	2690584	2693616	.	-	.	transcript_id "Phchi.S5G032900.t1"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	start_codon	2693614	2693616	.	-	0	transcript_id "Phchi.S5G032900.t1"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	transcript	2690584	2691423	.	-	.	transcript_id "Phchi.S5G032900.t2"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	stop_codon	2690581	2690583	.	-	0	transcript_id "Phchi.S5G032900.t2"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	CDS	2690584	2691423	0.47	-	0	transcript_id "Phchi.S5G032900.t2"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	exon	2690584	2691423	.	-	.	transcript_id "Phchi.S5G032900.t2"; gene_id "Phchi.S5G032900"
Phchi.S5	AUGUSTUS	start_codon	2691421	2691423	.	-	0	transcript_id "Phchi.S5G032900.t2"; gene_id "Phchi.S5G032900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6397.t1 is derived from g3569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22762397	22763020	.	-	.	Phchi.S1G355600
Phchi.S1	AUGUSTUS	transcript	22762397	22763020	.	-	.	transcript_id "Phchi.S1G355600.t1"; gene_id "Phchi.S1G355600"
Phchi.S1	AUGUSTUS	stop_codon	22762394	22762396	.	-	0	transcript_id "Phchi.S1G355600.t1"; gene_id "Phchi.S1G355600"
Phchi.S1	AUGUSTUS	CDS	22762397	22763020	0.82	-	0	transcript_id "Phchi.S1G355600.t1"; gene_id "Phchi.S1G355600"
Phchi.S1	AUGUSTUS	exon	22762397	22763020	.	-	.	transcript_id "Phchi.S1G355600.t1"; gene_id "Phchi.S1G355600"
Phchi.S1	AUGUSTUS	start_codon	22763018	22763020	.	-	0	transcript_id "Phchi.S1G355600.t1"; gene_id "Phchi.S1G355600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg353.t1 is derived from g10135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2579937	2581482	.	-	.	Phchi.S6G031200
Phchi.S6	AUGUSTUS	transcript	2579937	2581482	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	stop_codon	2579934	2579936	.	-	0	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	CDS	2579937	2580231	0.83	-	1	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	exon	2579937	2580231	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	intron	2580232	2580321	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	CDS	2580322	2580515	1	-	0	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	exon	2580322	2580515	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	intron	2580516	2580606	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	CDS	2580607	2580774	1	-	0	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	exon	2580607	2580774	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	intron	2580775	2580864	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	CDS	2580865	2581482	0.69	-	0	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	exon	2580865	2581482	.	-	.	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
Phchi.S6	AUGUSTUS	start_codon	2581480	2581482	.	-	0	transcript_id "Phchi.S6G031200.t1"; gene_id "Phchi.S6G031200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3045.t1 is derived from g214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1333675	1334010	.	+	.	Phchi.S1G020400
Phchi.S1	AUGUSTUS	transcript	1333675	1334010	.	+	.	transcript_id "Phchi.S1G020400.t1"; gene_id "Phchi.S1G020400"
Phchi.S1	AUGUSTUS	start_codon	1333675	1333677	.	+	0	transcript_id "Phchi.S1G020400.t1"; gene_id "Phchi.S1G020400"
Phchi.S1	AUGUSTUS	CDS	1333675	1334010	0.84	+	0	transcript_id "Phchi.S1G020400.t1"; gene_id "Phchi.S1G020400"
Phchi.S1	AUGUSTUS	exon	1333675	1334010	.	+	.	transcript_id "Phchi.S1G020400.t1"; gene_id "Phchi.S1G020400"
Phchi.S1	AUGUSTUS	stop_codon	1334011	1334013	.	+	0	transcript_id "Phchi.S1G020400.t1"; gene_id "Phchi.S1G020400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2312.t1 is derived from g9232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6017035	6017655	.	-	.	Phchi.S5G092100
Phchi.S5	AUGUSTUS	transcript	6017035	6017655	.	-	.	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	stop_codon	6017032	6017034	.	-	0	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	CDS	6017035	6017270	0.77	-	2	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	exon	6017035	6017270	.	-	.	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	intron	6017271	6017368	.	-	.	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	CDS	6017369	6017494	0.76	-	2	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	exon	6017369	6017494	.	-	.	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	intron	6017495	6017591	.	-	.	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	CDS	6017592	6017655	0.56	-	0	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	exon	6017592	6017655	.	-	.	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
Phchi.S5	AUGUSTUS	start_codon	6017653	6017655	.	-	0	transcript_id "Phchi.S5G092100.t1"; gene_id "Phchi.S5G092100"
# This transcript jg15107.t2 is derived from g13575.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15108.t1 is derived from g13576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17111802	17113008	.	+	.	Phchi.S3G242700
Phchi.S3	AUGUSTUS	transcript	17111802	17113008	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	start_codon	17111802	17111804	.	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17111802	17111921	0.77	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17111802	17111921	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	intron	17111922	17112061	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17112062	17112202	1	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17112062	17112202	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	intron	17112203	17112296	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17112297	17112342	0.99	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17112297	17112342	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	intron	17112343	17112434	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17112435	17112445	1	+	2	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17112435	17112445	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	intron	17112446	17112534	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17112535	17112584	1	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17112535	17112584	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	intron	17112585	17112747	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17112748	17112877	1	+	1	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17112748	17112877	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	intron	17112878	17112969	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	CDS	17112970	17113008	1	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	exon	17112970	17113008	.	+	.	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
Phchi.S3	AUGUSTUS	stop_codon	17113009	17113011	.	+	0	transcript_id "Phchi.S3G242700.t1"; gene_id "Phchi.S3G242700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3005.t1 is derived from g174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1092754	1095132	.	+	.	Phchi.S1G016400
Phchi.S1	AUGUSTUS	transcript	1092754	1095132	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	start_codon	1092754	1092756	.	+	0	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	CDS	1092754	1093770	0.69	+	0	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	exon	1092754	1093770	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	intron	1093771	1093912	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	CDS	1093913	1094046	0.62	+	0	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	exon	1093913	1094046	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	intron	1094047	1094133	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	CDS	1094134	1094247	0.99	+	1	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	exon	1094134	1094247	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	intron	1094248	1094339	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	CDS	1094340	1094505	0.96	+	1	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	exon	1094340	1094505	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	intron	1094506	1094599	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	CDS	1094600	1094668	0.96	+	0	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	exon	1094600	1094668	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	intron	1094669	1094742	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	CDS	1094743	1095132	1	+	0	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	exon	1094743	1095132	.	+	.	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
Phchi.S1	AUGUSTUS	stop_codon	1095133	1095135	.	+	0	transcript_id "Phchi.S1G016400.t1"; gene_id "Phchi.S1G016400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5129.t1 is derived from g2299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15052109	15053962	.	-	.	Phchi.S1G228800
Phchi.S1	AUGUSTUS	transcript	15052109	15053962	.	-	.	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	stop_codon	15052106	15052108	.	-	0	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	CDS	15052109	15053241	1	-	2	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	exon	15052109	15053241	.	-	.	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	intron	15053242	15053393	.	-	.	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	CDS	15053394	15053564	1	-	2	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	exon	15053394	15053564	.	-	.	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	intron	15053565	15053691	.	-	.	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	CDS	15053692	15053962	0.99	-	0	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	exon	15053692	15053962	.	-	.	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
Phchi.S1	AUGUSTUS	start_codon	15053960	15053962	.	-	0	transcript_id "Phchi.S1G228800.t1"; gene_id "Phchi.S1G228800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15051.t1 is derived from g13519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16753511	16755271	.	-	.	Phchi.S3G237000
Phchi.S3	AUGUSTUS	transcript	16753511	16755271	.	-	.	transcript_id "Phchi.S3G237000.t1"; gene_id "Phchi.S3G237000"
Phchi.S3	AUGUSTUS	stop_codon	16753508	16753510	.	-	0	transcript_id "Phchi.S3G237000.t1"; gene_id "Phchi.S3G237000"
Phchi.S3	AUGUSTUS	CDS	16753511	16755271	1	-	0	transcript_id "Phchi.S3G237000.t1"; gene_id "Phchi.S3G237000"
Phchi.S3	AUGUSTUS	exon	16753511	16755271	.	-	.	transcript_id "Phchi.S3G237000.t1"; gene_id "Phchi.S3G237000"
Phchi.S3	AUGUSTUS	start_codon	16755269	16755271	.	-	0	transcript_id "Phchi.S3G237000.t1"; gene_id "Phchi.S3G237000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14868.t1 is derived from g13336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15129919	15131111	.	-	.	Phchi.S3G218700
Phchi.S3	AUGUSTUS	transcript	15129919	15131111	.	-	.	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	stop_codon	15129916	15129918	.	-	0	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	CDS	15129919	15130479	1	-	0	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	exon	15129919	15130479	.	-	.	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	intron	15130480	15130576	.	-	.	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	CDS	15130577	15130768	1	-	0	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	exon	15130577	15130768	.	-	.	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	intron	15130769	15130877	.	-	.	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	CDS	15130878	15131111	0.92	-	0	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	exon	15130878	15131111	.	-	.	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
Phchi.S3	AUGUSTUS	start_codon	15131109	15131111	.	-	0	transcript_id "Phchi.S3G218700.t1"; gene_id "Phchi.S3G218700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10975.t1 is derived from g15025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3462322	3464879	.	+	.	Phchi.S4G055700
Phchi.S4	AUGUSTUS	transcript	3462322	3464879	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	start_codon	3462322	3462324	.	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3462322	3462584	1	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3462322	3462584	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	intron	3462585	3462739	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3462740	3463577	1	+	1	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3462740	3463577	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	intron	3463578	3463680	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3463681	3463911	1	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3463681	3463911	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	intron	3463912	3464043	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3464044	3464056	0.94	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3464044	3464056	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	intron	3464057	3464139	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3464140	3464183	0.86	+	2	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3464140	3464183	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	intron	3464184	3464297	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3464298	3464498	0.98	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3464298	3464498	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	intron	3464499	3464588	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	CDS	3464589	3464879	1	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	exon	3464589	3464879	.	+	.	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
Phchi.S4	AUGUSTUS	stop_codon	3464880	3464882	.	+	0	transcript_id "Phchi.S4G055700.t1"; gene_id "Phchi.S4G055700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14346.t1 is derived from g12813.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12318316	12320081	.	+	.	Phchi.S3G166500
Phchi.S3	AUGUSTUS	transcript	12318316	12319442	.	+	.	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	start_codon	12318316	12318318	.	+	0	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12318316	12318665	0.67	+	0	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12318316	12318665	.	+	.	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	intron	12318666	12319056	.	+	.	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12319057	12319237	1	+	1	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12319057	12319237	.	+	.	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	intron	12319238	12319388	.	+	.	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12319389	12319442	1	+	0	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12319389	12319442	.	+	.	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	stop_codon	12319443	12319445	.	+	0	transcript_id "Phchi.S3G166500.t1"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	transcript	12318316	12320081	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	start_codon	12318316	12318318	.	+	0	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12318316	12318665	0.7	+	0	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12318316	12318665	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	intron	12318666	12319056	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12319057	12319237	1	+	1	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12319057	12319237	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	intron	12319238	12319388	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12319389	12319424	0.88	+	0	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12319389	12319424	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	intron	12319425	12320000	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	CDS	12320001	12320081	0.88	+	0	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	exon	12320001	12320081	.	+	.	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
Phchi.S3	AUGUSTUS	stop_codon	12320082	12320084	.	+	0	transcript_id "Phchi.S3G166500.t2"; gene_id "Phchi.S3G166500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3666.t1 is derived from g835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5070497	5070934	.	-	.	Phchi.S1G082500
Phchi.S1	AUGUSTUS	transcript	5070497	5070934	.	-	.	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	stop_codon	5070494	5070496	.	-	0	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	CDS	5070497	5070716	0.77	-	1	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	exon	5070497	5070716	.	-	.	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	intron	5070717	5070809	.	-	.	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	CDS	5070810	5070934	0.77	-	0	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	exon	5070810	5070934	.	-	.	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
Phchi.S1	AUGUSTUS	start_codon	5070932	5070934	.	-	0	transcript_id "Phchi.S1G082500.t1"; gene_id "Phchi.S1G082500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4646.t1 is derived from g1816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11623249	11624334	.	-	.	Phchi.S1G180500
Phchi.S1	AUGUSTUS	transcript	11623249	11624334	.	-	.	transcript_id "Phchi.S1G180500.t1"; gene_id "Phchi.S1G180500"
Phchi.S1	AUGUSTUS	stop_codon	11623246	11623248	.	-	0	transcript_id "Phchi.S1G180500.t1"; gene_id "Phchi.S1G180500"
Phchi.S1	AUGUSTUS	CDS	11623249	11624334	0.57	-	0	transcript_id "Phchi.S1G180500.t1"; gene_id "Phchi.S1G180500"
Phchi.S1	AUGUSTUS	exon	11623249	11624334	.	-	.	transcript_id "Phchi.S1G180500.t1"; gene_id "Phchi.S1G180500"
Phchi.S1	AUGUSTUS	start_codon	11624332	11624334	.	-	0	transcript_id "Phchi.S1G180500.t1"; gene_id "Phchi.S1G180500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15767.t1 is derived from g14237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21255341	21260400	.	+	.	Phchi.S3G308600
Phchi.S3	AUGUSTUS	transcript	21255341	21260400	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	start_codon	21255341	21255343	.	+	0	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21255341	21255446	1	+	0	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21255341	21255446	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21255447	21255585	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21255586	21255706	1	+	2	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21255586	21255706	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21255707	21255806	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21255807	21255884	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21255807	21255884	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21255885	21255966	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21255967	21256041	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21255967	21256041	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21256042	21256156	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21256157	21256228	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21256157	21256228	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21256229	21256323	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21256324	21256491	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21256324	21256491	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21256492	21256608	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21256609	21256683	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21256609	21256683	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21256684	21256791	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21256792	21256863	0.99	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21256792	21256863	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21256864	21256964	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21256965	21257036	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21256965	21257036	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21257037	21257194	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21257195	21257263	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21257195	21257263	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21257264	21257358	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21257359	21257433	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21257359	21257433	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21257434	21257548	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21257549	21257620	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21257549	21257620	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21257621	21257802	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21257803	21257939	1	+	1	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21257803	21257939	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21257940	21258021	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21258022	21258119	0.53	+	2	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21258022	21258119	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21258120	21258205	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21258206	21258488	0.87	+	0	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21258206	21258488	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21258489	21258612	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21258613	21258765	1	+	2	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21258613	21258765	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21258766	21258847	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21258848	21259210	0.77	+	2	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21258848	21259210	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21259211	21259311	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21259312	21259550	0.93	+	2	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21259312	21259550	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21259551	21259620	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21259621	21259968	0.88	+	0	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21259621	21259968	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21259969	21260235	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21260236	21260293	0.98	+	0	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21260236	21260293	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	intron	21260294	21260371	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	CDS	21260372	21260400	1	+	2	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	exon	21260372	21260400	.	+	.	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
Phchi.S3	AUGUSTUS	stop_codon	21260401	21260403	.	+	0	transcript_id "Phchi.S3G308600.t1"; gene_id "Phchi.S3G308600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6118.t1 is derived from g3289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21018519	21019822	.	-	.	Phchi.S1G327700
Phchi.S1	AUGUSTUS	transcript	21018519	21019822	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	stop_codon	21018516	21018518	.	-	0	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21018519	21018635	0.99	-	0	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21018519	21018635	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	intron	21018636	21018728	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21018729	21018794	1	-	0	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21018729	21018794	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	intron	21018795	21018867	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21018868	21018952	1	-	1	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21018868	21018952	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	intron	21018953	21019078	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21019079	21019172	1	-	2	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21019079	21019172	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	intron	21019173	21019275	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21019276	21019333	1	-	0	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21019276	21019333	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	intron	21019334	21019460	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21019461	21019501	1	-	2	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21019461	21019501	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	intron	21019502	21019674	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	CDS	21019675	21019822	1	-	0	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	exon	21019675	21019822	.	-	.	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
Phchi.S1	AUGUSTUS	start_codon	21019820	21019822	.	-	0	transcript_id "Phchi.S1G327700.t1"; gene_id "Phchi.S1G327700"
# This transcript jg12689.t2 is derived from g11154.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12689.t3 is derived from g11154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12690.t1 is derived from g11155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	554427	556400	.	-	.	Phchi.S3G000900
Phchi.S3	AUGUSTUS	transcript	554427	556400	.	-	.	transcript_id "Phchi.S3G000900.t1"; gene_id "Phchi.S3G000900"
Phchi.S3	AUGUSTUS	stop_codon	554424	554426	.	-	0	transcript_id "Phchi.S3G000900.t1"; gene_id "Phchi.S3G000900"
Phchi.S3	AUGUSTUS	CDS	554427	556400	1	-	0	transcript_id "Phchi.S3G000900.t1"; gene_id "Phchi.S3G000900"
Phchi.S3	AUGUSTUS	exon	554427	556400	.	-	.	transcript_id "Phchi.S3G000900.t1"; gene_id "Phchi.S3G000900"
Phchi.S3	AUGUSTUS	start_codon	556398	556400	.	-	0	transcript_id "Phchi.S3G000900.t1"; gene_id "Phchi.S3G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9861.t1 is derived from g7037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44125620	44127914	.	+	.	Phchi.S1G702000
Phchi.S1	AUGUSTUS	transcript	44125620	44127914	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	start_codon	44125620	44125622	.	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44125620	44125994	0.95	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44125620	44125994	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44125995	44126152	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44126153	44126218	1	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44126153	44126218	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44126219	44126308	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44126309	44126504	1	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44126309	44126504	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44126505	44126592	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44126593	44126789	1	+	2	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44126593	44126789	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44126790	44126883	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44126884	44126934	1	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44126884	44126934	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44126935	44127076	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44127077	44127168	1	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44127077	44127168	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44127169	44127311	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44127312	44127435	1	+	1	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44127312	44127435	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44127436	44127554	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44127555	44127659	0.98	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44127555	44127659	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	intron	44127660	44127767	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	CDS	44127768	44127914	0.98	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	exon	44127768	44127914	.	+	.	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
Phchi.S1	AUGUSTUS	stop_codon	44127915	44127917	.	+	0	transcript_id "Phchi.S1G702000.t1"; gene_id "Phchi.S1G702000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3858.t1 is derived from g1027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6058674	6059931	.	-	.	Phchi.S1G101700
Phchi.S1	AUGUSTUS	transcript	6058674	6059931	.	-	.	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	stop_codon	6058671	6058673	.	-	0	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	CDS	6058674	6059276	1	-	0	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	exon	6058674	6059276	.	-	.	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	intron	6059277	6059371	.	-	.	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	CDS	6059372	6059566	1	-	0	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	exon	6059372	6059566	.	-	.	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	intron	6059567	6059685	.	-	.	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	CDS	6059686	6059931	0.87	-	0	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	exon	6059686	6059931	.	-	.	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
Phchi.S1	AUGUSTUS	start_codon	6059929	6059931	.	-	0	transcript_id "Phchi.S1G101700.t1"; gene_id "Phchi.S1G101700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6608.t1 is derived from g3780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23995435	23996511	.	+	.	Phchi.S1G376700
Phchi.S1	AUGUSTUS	transcript	23995435	23996511	.	+	.	transcript_id "Phchi.S1G376700.t1"; gene_id "Phchi.S1G376700"
Phchi.S1	AUGUSTUS	start_codon	23995435	23995437	.	+	0	transcript_id "Phchi.S1G376700.t1"; gene_id "Phchi.S1G376700"
Phchi.S1	AUGUSTUS	CDS	23995435	23996511	0.54	+	0	transcript_id "Phchi.S1G376700.t1"; gene_id "Phchi.S1G376700"
Phchi.S1	AUGUSTUS	exon	23995435	23996511	.	+	.	transcript_id "Phchi.S1G376700.t1"; gene_id "Phchi.S1G376700"
Phchi.S1	AUGUSTUS	stop_codon	23996512	23996514	.	+	0	transcript_id "Phchi.S1G376700.t1"; gene_id "Phchi.S1G376700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12358.t1 is derived from g8034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12698685	12699217	.	-	.	Phchi.S2G043800
Phchi.S2	AUGUSTUS	transcript	12698685	12699217	.	-	.	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	stop_codon	12698682	12698684	.	-	0	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	CDS	12698685	12698720	1	-	0	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	exon	12698685	12698720	.	-	.	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	intron	12698721	12698805	.	-	.	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	CDS	12698806	12698948	0.44	-	2	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	exon	12698806	12698948	.	-	.	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	intron	12698949	12699060	.	-	.	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	CDS	12699061	12699217	0.24	-	0	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	exon	12699061	12699217	.	-	.	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
Phchi.S2	AUGUSTUS	start_codon	12699215	12699217	.	-	0	transcript_id "Phchi.S2G043800.t1"; gene_id "Phchi.S2G043800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4375.t1 is derived from g1544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10123643	10124254	.	+	.	Phchi.S1G153400
Phchi.S1	AUGUSTUS	transcript	10123643	10124254	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	start_codon	10123643	10123645	.	+	0	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	CDS	10123643	10123732	0.3	+	0	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	exon	10123643	10123732	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	intron	10123733	10123834	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	CDS	10123835	10123924	1	+	0	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	exon	10123835	10123924	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	intron	10123925	10124004	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	CDS	10124005	10124082	0.87	+	0	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	exon	10124005	10124082	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	intron	10124083	10124164	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	CDS	10124165	10124254	0.35	+	0	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	exon	10124165	10124254	.	+	.	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
Phchi.S1	AUGUSTUS	stop_codon	10124255	10124257	.	+	0	transcript_id "Phchi.S1G153400.t1"; gene_id "Phchi.S1G153400"
# This transcript jg14704.t2 is derived from g13172.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14705.t1 is derived from g13173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14263285	14263763	.	-	.	Phchi.S3G202400
Phchi.S3	AUGUSTUS	transcript	14263285	14263763	.	-	.	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	stop_codon	14263282	14263284	.	-	0	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	CDS	14263285	14263412	0.87	-	2	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	exon	14263285	14263412	.	-	.	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	intron	14263413	14263510	.	-	.	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	CDS	14263511	14263763	0.84	-	0	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	exon	14263511	14263763	.	-	.	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
Phchi.S3	AUGUSTUS	start_codon	14263761	14263763	.	-	0	transcript_id "Phchi.S3G202400.t1"; gene_id "Phchi.S3G202400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6569.t1 is derived from g3741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23753872	23755497	.	+	.	Phchi.S1G372800
Phchi.S1	AUGUSTUS	transcript	23753872	23755497	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	start_codon	23753872	23753874	.	+	0	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	CDS	23753872	23753969	1	+	0	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	exon	23753872	23753969	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	intron	23753970	23754121	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	CDS	23754122	23754130	1	+	1	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	exon	23754122	23754130	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	intron	23754131	23754187	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	CDS	23754188	23754202	0.68	+	1	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	exon	23754188	23754202	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	intron	23754203	23754710	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	CDS	23754711	23755497	1	+	1	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	exon	23754711	23755497	.	+	.	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
Phchi.S1	AUGUSTUS	stop_codon	23755498	23755500	.	+	0	transcript_id "Phchi.S1G372800.t1"; gene_id "Phchi.S1G372800"
# This transcript jg7927.t2 is derived from g5101.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7928.t1 is derived from g5102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31937565	31938122	.	+	.	Phchi.S1G508700
Phchi.S1	AUGUSTUS	transcript	31937565	31938122	.	+	.	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	start_codon	31937565	31937567	.	+	0	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	CDS	31937565	31937730	0.91	+	0	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	exon	31937565	31937730	.	+	.	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	intron	31937731	31937892	.	+	.	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	CDS	31937893	31938122	1	+	2	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	exon	31937893	31938122	.	+	.	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
Phchi.S1	AUGUSTUS	stop_codon	31938123	31938125	.	+	0	transcript_id "Phchi.S1G508700.t1"; gene_id "Phchi.S1G508700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4726.t1 is derived from g1896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12495069	12495700	.	-	.	Phchi.S1G188500
Phchi.S1	AUGUSTUS	transcript	12495069	12495700	.	-	.	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	stop_codon	12495066	12495068	.	-	0	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	CDS	12495069	12495167	1	-	0	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	exon	12495069	12495167	.	-	.	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	intron	12495168	12495288	.	-	.	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	CDS	12495289	12495366	0.84	-	0	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	exon	12495289	12495366	.	-	.	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	intron	12495367	12495514	.	-	.	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	CDS	12495515	12495700	0.5	-	0	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	exon	12495515	12495700	.	-	.	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
Phchi.S1	AUGUSTUS	start_codon	12495698	12495700	.	-	0	transcript_id "Phchi.S1G188500.t1"; gene_id "Phchi.S1G188500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13408.t1 is derived from g11874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6555757	6556386	.	+	.	Phchi.S3G072700
Phchi.S3	AUGUSTUS	transcript	6555757	6556386	.	+	.	transcript_id "Phchi.S3G072700.t1"; gene_id "Phchi.S3G072700"
Phchi.S3	AUGUSTUS	start_codon	6555757	6555759	.	+	0	transcript_id "Phchi.S3G072700.t1"; gene_id "Phchi.S3G072700"
Phchi.S3	AUGUSTUS	CDS	6555757	6556386	0.71	+	0	transcript_id "Phchi.S3G072700.t1"; gene_id "Phchi.S3G072700"
Phchi.S3	AUGUSTUS	exon	6555757	6556386	.	+	.	transcript_id "Phchi.S3G072700.t1"; gene_id "Phchi.S3G072700"
Phchi.S3	AUGUSTUS	stop_codon	6556387	6556389	.	+	0	transcript_id "Phchi.S3G072700.t1"; gene_id "Phchi.S3G072700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5893.t1 is derived from g3063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19633329	19634372	.	+	.	Phchi.S1G305200
Phchi.S1	AUGUSTUS	transcript	19633329	19634372	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	start_codon	19633329	19633331	.	+	0	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	CDS	19633329	19633422	0.56	+	0	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	exon	19633329	19633422	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	intron	19633423	19633524	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	CDS	19633525	19633722	0.98	+	2	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	exon	19633525	19633722	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	intron	19633723	19633864	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	CDS	19633865	19633990	1	+	2	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	exon	19633865	19633990	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	intron	19633991	19634077	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	CDS	19634078	19634203	0.9	+	2	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	exon	19634078	19634203	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	intron	19634204	19634307	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	CDS	19634308	19634372	0.9	+	2	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	exon	19634308	19634372	.	+	.	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
Phchi.S1	AUGUSTUS	stop_codon	19634373	19634375	.	+	0	transcript_id "Phchi.S1G305200.t1"; gene_id "Phchi.S1G305200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5703.t1 is derived from g2873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18440851	18442195	.	-	.	Phchi.S1G286200
Phchi.S1	AUGUSTUS	transcript	18440851	18442195	.	-	.	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	stop_codon	18440848	18440850	.	-	0	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	CDS	18440851	18441415	0.97	-	1	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	exon	18440851	18441415	.	-	.	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	intron	18441416	18441529	.	-	.	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	CDS	18441530	18441717	0.99	-	0	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	exon	18441530	18441717	.	-	.	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	intron	18441718	18441826	.	-	.	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	CDS	18441827	18442195	0.99	-	0	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	exon	18441827	18442195	.	-	.	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
Phchi.S1	AUGUSTUS	start_codon	18442193	18442195	.	-	0	transcript_id "Phchi.S1G286200.t1"; gene_id "Phchi.S1G286200"
# This transcript jg7355.t2 is derived from g4527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7356.t1 is derived from g4528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28749201	28752366	.	+	.	Phchi.S1G451500
Phchi.S1	AUGUSTUS	transcript	28749201	28752366	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	start_codon	28749201	28749203	.	+	0	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	CDS	28749201	28749330	0.87	+	0	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	exon	28749201	28749330	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	intron	28749331	28749418	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	CDS	28749419	28749498	1	+	2	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	exon	28749419	28749498	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	intron	28749499	28749586	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	CDS	28749587	28749734	1	+	0	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	exon	28749587	28749734	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	intron	28749735	28749813	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	CDS	28749814	28749902	1	+	2	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	exon	28749814	28749902	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	intron	28749903	28749980	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	CDS	28749981	28752111	0.33	+	0	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	exon	28749981	28752111	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	intron	28752112	28752331	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	CDS	28752332	28752366	0.25	+	2	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	exon	28752332	28752366	.	+	.	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
Phchi.S1	AUGUSTUS	stop_codon	28752367	28752369	.	+	0	transcript_id "Phchi.S1G451500.t1"; gene_id "Phchi.S1G451500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3964.t1 is derived from g1133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6770269	6771724	.	+	.	Phchi.S1G112300
Phchi.S1	AUGUSTUS	transcript	6770269	6771724	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	start_codon	6770269	6770271	.	+	0	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	CDS	6770269	6770370	1	+	0	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	exon	6770269	6770370	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	intron	6770371	6770553	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	CDS	6770554	6770677	0.96	+	0	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	exon	6770554	6770677	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	intron	6770678	6770750	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	CDS	6770751	6770815	0.84	+	2	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	exon	6770751	6770815	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	intron	6770816	6771064	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	CDS	6771065	6771226	0.82	+	0	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	exon	6771065	6771226	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	intron	6771227	6771433	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	CDS	6771434	6771724	0.94	+	0	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	exon	6771434	6771724	.	+	.	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
Phchi.S1	AUGUSTUS	stop_codon	6771725	6771727	.	+	0	transcript_id "Phchi.S1G112300.t1"; gene_id "Phchi.S1G112300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8306.t1 is derived from g5481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35197539	35199044	.	+	.	Phchi.S1G546500
Phchi.S1	AUGUSTUS	transcript	35197539	35199044	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	start_codon	35197539	35197541	.	+	0	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	CDS	35197539	35197541	0.97	+	0	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	exon	35197539	35197541	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	intron	35197542	35197895	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	CDS	35197896	35198040	1	+	0	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	exon	35197896	35198040	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	intron	35198041	35198132	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	CDS	35198133	35198210	1	+	2	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	exon	35198133	35198210	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	intron	35198211	35198321	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	CDS	35198322	35198434	1	+	2	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	exon	35198322	35198434	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	intron	35198435	35198551	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	CDS	35198552	35198655	1	+	0	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	exon	35198552	35198655	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	intron	35198656	35198743	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	CDS	35198744	35199044	0.97	+	1	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	exon	35198744	35199044	.	+	.	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
Phchi.S1	AUGUSTUS	stop_codon	35199045	35199047	.	+	0	transcript_id "Phchi.S1G546500.t1"; gene_id "Phchi.S1G546500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13054.t1 is derived from g11519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3922386	3924140	.	-	.	Phchi.S3G037300
Phchi.S3	AUGUSTUS	transcript	3922386	3924140	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	stop_codon	3922383	3922385	.	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3922386	3922461	1	-	1	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3922386	3922461	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3922462	3922542	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3922543	3922653	1	-	1	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3922543	3922653	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3922654	3922747	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3922748	3922830	1	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3922748	3922830	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3922831	3922956	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3922957	3923010	1	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3922957	3923010	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3923011	3923093	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3923094	3923180	1	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3923094	3923180	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3923181	3923277	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3923278	3923361	1	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3923278	3923361	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3923362	3923455	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3923456	3923647	1	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3923456	3923647	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3923648	3923821	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3923822	3923944	0.81	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3923822	3923944	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	intron	3923945	3924050	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	CDS	3924051	3924140	0.51	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	exon	3924051	3924140	.	-	.	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
Phchi.S3	AUGUSTUS	start_codon	3924138	3924140	.	-	0	transcript_id "Phchi.S3G037300.t1"; gene_id "Phchi.S3G037300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15144.t1 is derived from g13612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17255633	17256463	.	-	.	Phchi.S3G246300
Phchi.S3	AUGUSTUS	transcript	17255633	17256463	.	-	.	transcript_id "Phchi.S3G246300.t1"; gene_id "Phchi.S3G246300"
Phchi.S3	AUGUSTUS	stop_codon	17255630	17255632	.	-	0	transcript_id "Phchi.S3G246300.t1"; gene_id "Phchi.S3G246300"
Phchi.S3	AUGUSTUS	CDS	17255633	17256463	0.94	-	0	transcript_id "Phchi.S3G246300.t1"; gene_id "Phchi.S3G246300"
Phchi.S3	AUGUSTUS	exon	17255633	17256463	.	-	.	transcript_id "Phchi.S3G246300.t1"; gene_id "Phchi.S3G246300"
Phchi.S3	AUGUSTUS	start_codon	17256461	17256463	.	-	0	transcript_id "Phchi.S3G246300.t1"; gene_id "Phchi.S3G246300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg290.t1 is derived from g10072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2090672	2091667	.	-	.	Phchi.S6G024900
Phchi.S6	AUGUSTUS	transcript	2090672	2091667	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	stop_codon	2090669	2090671	.	-	0	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	CDS	2090672	2090988	0.67	-	2	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	exon	2090672	2090988	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	intron	2090989	2091082	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	CDS	2091083	2091178	0.66	-	2	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	exon	2091083	2091178	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	intron	2091179	2091347	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	CDS	2091348	2091465	0.65	-	0	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	exon	2091348	2091465	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	intron	2091466	2091631	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	CDS	2091632	2091667	0.58	-	0	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	exon	2091632	2091667	.	-	.	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
Phchi.S6	AUGUSTUS	start_codon	2091665	2091667	.	-	0	transcript_id "Phchi.S6G024900.t1"; gene_id "Phchi.S6G024900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15984.t1 is derived from g9773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C16	AUGUSTUS	gene	35630	36061	.	-	.	Phchi.C16G000200
Phchi.C16	AUGUSTUS	transcript	35630	36061	.	-	.	transcript_id "Phchi.C16G000200.t1"; gene_id "Phchi.C16G000200"
Phchi.C16	AUGUSTUS	stop_codon	35627	35629	.	-	0	transcript_id "Phchi.C16G000200.t1"; gene_id "Phchi.C16G000200"
Phchi.C16	AUGUSTUS	CDS	35630	36061	1	-	0	transcript_id "Phchi.C16G000200.t1"; gene_id "Phchi.C16G000200"
Phchi.C16	AUGUSTUS	exon	35630	36061	.	-	.	transcript_id "Phchi.C16G000200.t1"; gene_id "Phchi.C16G000200"
Phchi.C16	AUGUSTUS	start_codon	36059	36061	.	-	0	transcript_id "Phchi.C16G000200.t1"; gene_id "Phchi.C16G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15238.t1 is derived from g13706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17873082	17873761	.	+	.	Phchi.S3G255700
Phchi.S3	AUGUSTUS	transcript	17873082	17873761	.	+	.	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	start_codon	17873082	17873084	.	+	0	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	CDS	17873082	17873321	1	+	0	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	exon	17873082	17873321	.	+	.	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	intron	17873322	17873752	.	+	.	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	CDS	17873753	17873761	1	+	0	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	exon	17873753	17873761	.	+	.	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
Phchi.S3	AUGUSTUS	stop_codon	17873762	17873764	.	+	0	transcript_id "Phchi.S3G255700.t1"; gene_id "Phchi.S3G255700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg320.t1 is derived from g10102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2260562	2261844	.	+	.	Phchi.S6G027900
Phchi.S6	AUGUSTUS	transcript	2260562	2261844	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	start_codon	2260562	2260564	.	+	0	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	CDS	2260562	2260671	0.33	+	0	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	exon	2260562	2260671	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	intron	2260672	2260773	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	CDS	2260774	2260791	0.91	+	1	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	exon	2260774	2260791	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	intron	2260792	2260945	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	CDS	2260946	2261075	1	+	1	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	exon	2260946	2261075	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	intron	2261076	2261160	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	CDS	2261161	2261278	0.99	+	0	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	exon	2261161	2261278	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	intron	2261279	2261388	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	CDS	2261389	2261605	0.99	+	2	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	exon	2261389	2261605	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	intron	2261606	2261699	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	CDS	2261700	2261844	1	+	1	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	exon	2261700	2261844	.	+	.	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
Phchi.S6	AUGUSTUS	stop_codon	2261845	2261847	.	+	0	transcript_id "Phchi.S6G027900.t1"; gene_id "Phchi.S6G027900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13429.t1 is derived from g11896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6650167	6651299	.	-	.	Phchi.S3G074800
Phchi.S3	AUGUSTUS	transcript	6650167	6651299	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	stop_codon	6650164	6650166	.	-	0	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6650167	6650346	0.97	-	0	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6650167	6650346	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	intron	6650347	6650472	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6650473	6650635	1	-	1	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6650473	6650635	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	intron	6650636	6650820	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6650821	6650994	1	-	1	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6650821	6650994	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	intron	6650995	6651120	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6651121	6651299	0.98	-	0	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6651121	6651299	.	-	.	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	start_codon	6651297	6651299	.	-	0	transcript_id "Phchi.S3G074800.t1"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	transcript	6650167	6651299	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	stop_codon	6650164	6650166	.	-	0	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6650167	6650346	0.99	-	0	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6650167	6650346	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	intron	6650347	6650472	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6650473	6650635	1	-	1	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6650473	6650635	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	intron	6650636	6650820	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6650821	6650994	0.99	-	1	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6650821	6650994	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	intron	6650995	6651078	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	CDS	6651079	6651299	0.97	-	0	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	exon	6651079	6651299	.	-	.	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
Phchi.S3	AUGUSTUS	start_codon	6651297	6651299	.	-	0	transcript_id "Phchi.S3G074800.t2"; gene_id "Phchi.S3G074800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6083.t1 is derived from g3254.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20866052	20870007	.	-	.	Phchi.S1G324200
Phchi.S1	AUGUSTUS	transcript	20866052	20870007	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	stop_codon	20866049	20866051	.	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20866052	20866241	1	-	1	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20866052	20866241	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20866242	20866331	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20866332	20866519	1	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20866332	20866519	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20866520	20866617	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20866618	20866908	1	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20866618	20866908	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20866909	20867073	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20867074	20867310	1	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20867074	20867310	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20867311	20867405	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20867406	20867473	1	-	2	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20867406	20867473	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20867474	20867585	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20867586	20867722	1	-	1	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20867586	20867722	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20867723	20867891	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20867892	20867898	1	-	2	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20867892	20867898	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20867899	20868317	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20868318	20868351	0.71	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20868318	20868351	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20868352	20868491	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20868492	20868569	0.91	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20868492	20868569	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20868570	20868671	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20868672	20868743	1	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20868672	20868743	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20868744	20868860	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20868861	20868983	0.99	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20868861	20868983	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20868984	20869048	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20869049	20869054	0.92	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20869049	20869054	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20869055	20869157	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20869158	20869250	0.99	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20869158	20869250	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20869251	20869372	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20869373	20869453	1	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20869373	20869453	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20869454	20869543	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20869544	20869620	1	-	2	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20869544	20869620	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	intron	20869621	20869703	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	CDS	20869704	20870007	0.93	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	exon	20869704	20870007	.	-	.	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
Phchi.S1	AUGUSTUS	start_codon	20870005	20870007	.	-	0	transcript_id "Phchi.S1G324200.t1"; gene_id "Phchi.S1G324200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2925.t1 is derived from g94.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	582534	584382	.	+	.	Phchi.S1G008400
Phchi.S1	AUGUSTUS	transcript	582534	584382	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	start_codon	582534	582536	.	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	582534	582623	0.85	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	582534	582623	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	582624	582727	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	582728	582790	0.79	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	582728	582790	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	582791	582897	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	582898	583122	0.97	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	582898	583122	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	583123	583217	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	583218	583295	1	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	583218	583295	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	583296	583383	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	583384	583455	1	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	583384	583455	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	583456	583550	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	583551	583847	0.98	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	583551	583847	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	583848	584089	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	584090	584153	1	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	584090	584153	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	intron	584154	584233	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	CDS	584234	584382	1	+	2	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	exon	584234	584382	.	+	.	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
Phchi.S1	AUGUSTUS	stop_codon	584383	584385	.	+	0	transcript_id "Phchi.S1G008400.t1"; gene_id "Phchi.S1G008400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8861.t1 is derived from g6036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38333059	38333577	.	+	.	Phchi.S1G602000
Phchi.S1	AUGUSTUS	transcript	38333059	38333577	.	+	.	transcript_id "Phchi.S1G602000.t1"; gene_id "Phchi.S1G602000"
Phchi.S1	AUGUSTUS	start_codon	38333059	38333061	.	+	0	transcript_id "Phchi.S1G602000.t1"; gene_id "Phchi.S1G602000"
Phchi.S1	AUGUSTUS	CDS	38333059	38333577	0.93	+	0	transcript_id "Phchi.S1G602000.t1"; gene_id "Phchi.S1G602000"
Phchi.S1	AUGUSTUS	exon	38333059	38333577	.	+	.	transcript_id "Phchi.S1G602000.t1"; gene_id "Phchi.S1G602000"
Phchi.S1	AUGUSTUS	stop_codon	38333578	38333580	.	+	0	transcript_id "Phchi.S1G602000.t1"; gene_id "Phchi.S1G602000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6344.t1 is derived from g3516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22419784	22420906	.	-	.	Phchi.S1G350300
Phchi.S1	AUGUSTUS	transcript	22419784	22420906	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	stop_codon	22419781	22419783	.	-	0	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22419784	22419787	0.74	-	1	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22419784	22419787	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	intron	22419788	22419935	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22419936	22419952	0.74	-	0	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22419936	22419952	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	intron	22419953	22420022	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22420023	22420098	0.7	-	1	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22420023	22420098	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	intron	22420099	22420183	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22420184	22420188	0.82	-	0	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22420184	22420188	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	intron	22420189	22420286	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22420287	22420435	0.81	-	2	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22420287	22420435	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	intron	22420436	22420597	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22420598	22420624	0.88	-	2	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22420598	22420624	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	intron	22420625	22420707	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	CDS	22420708	22420906	0.41	-	0	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	exon	22420708	22420906	.	-	.	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
Phchi.S1	AUGUSTUS	start_codon	22420904	22420906	.	-	0	transcript_id "Phchi.S1G350300.t1"; gene_id "Phchi.S1G350300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2025.t1 is derived from g8945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4497701	4499374	.	-	.	Phchi.S5G063400
Phchi.S5	AUGUSTUS	transcript	4497701	4499374	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	stop_codon	4497534	4497536	.	-	0	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4497701	4497771	0.97	-	2	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4497701	4497771	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4497772	4497866	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4497867	4497903	0.48	-	0	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4497867	4497903	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4497904	4498063	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4498064	4498129	0.84	-	0	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4498064	4498129	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4498130	4498299	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4498300	4498387	1	-	1	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4498300	4498387	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4498388	4498550	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4498551	4498613	1	-	1	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4498551	4498613	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4498614	4498786	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4498787	4498860	1	-	0	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4498787	4498860	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4498861	4498936	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4498937	4498986	1	-	2	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4498937	4498986	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4498987	4499187	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4499188	4499258	1	-	1	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4499188	4499258	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	intron	4499259	4499342	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	CDS	4499343	4499374	1	-	0	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	exon	4499343	4499374	.	-	.	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
Phchi.S5	AUGUSTUS	start_codon	4499372	4499374	.	-	0	transcript_id "Phchi.S5G063400.t1"; gene_id "Phchi.S5G063400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8770.t1 is derived from g5945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37889192	37890508	.	-	.	Phchi.S1G592900
Phchi.S1	AUGUSTUS	transcript	37889192	37890508	.	-	.	transcript_id "Phchi.S1G592900.t1"; gene_id "Phchi.S1G592900"
Phchi.S1	AUGUSTUS	stop_codon	37889189	37889191	.	-	0	transcript_id "Phchi.S1G592900.t1"; gene_id "Phchi.S1G592900"
Phchi.S1	AUGUSTUS	CDS	37889192	37890508	1	-	0	transcript_id "Phchi.S1G592900.t1"; gene_id "Phchi.S1G592900"
Phchi.S1	AUGUSTUS	exon	37889192	37890508	.	-	.	transcript_id "Phchi.S1G592900.t1"; gene_id "Phchi.S1G592900"
Phchi.S1	AUGUSTUS	start_codon	37890506	37890508	.	-	0	transcript_id "Phchi.S1G592900.t1"; gene_id "Phchi.S1G592900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1508.t1 is derived from g8427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1287726	1290634	.	-	.	Phchi.S5G011700
Phchi.S5	AUGUSTUS	transcript	1287726	1290634	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	stop_codon	1287723	1287725	.	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1287726	1287836	0.67	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1287726	1287836	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1287837	1287961	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1287962	1288051	1	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1287962	1288051	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1288052	1288138	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1288139	1288197	0.74	-	2	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1288139	1288197	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1288198	1288274	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1288275	1288443	0.74	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1288275	1288443	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1288444	1288609	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1288610	1288728	1	-	2	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1288610	1288728	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1288729	1288822	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1288823	1288868	1	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1288823	1288868	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1288869	1289009	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1289010	1289030	1	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1289010	1289030	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1289031	1289160	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1289161	1289242	0.99	-	1	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1289161	1289242	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1289243	1289347	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1289348	1289427	1	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1289348	1289427	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1289428	1289545	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1289546	1289632	1	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1289546	1289632	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1289633	1289731	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1289732	1289917	1	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1289732	1289917	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	intron	1289918	1290001	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	CDS	1290002	1290634	0.78	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	exon	1290002	1290634	.	-	.	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
Phchi.S5	AUGUSTUS	start_codon	1290632	1290634	.	-	0	transcript_id "Phchi.S5G011700.t1"; gene_id "Phchi.S5G011700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8625.t1 is derived from g5800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37117643	37118146	.	+	.	Phchi.S1G578400
Phchi.S1	AUGUSTUS	transcript	37117643	37118146	.	+	.	transcript_id "Phchi.S1G578400.t1"; gene_id "Phchi.S1G578400"
Phchi.S1	AUGUSTUS	start_codon	37117643	37117645	.	+	0	transcript_id "Phchi.S1G578400.t1"; gene_id "Phchi.S1G578400"
Phchi.S1	AUGUSTUS	CDS	37117643	37118146	0.91	+	0	transcript_id "Phchi.S1G578400.t1"; gene_id "Phchi.S1G578400"
Phchi.S1	AUGUSTUS	exon	37117643	37118146	.	+	.	transcript_id "Phchi.S1G578400.t1"; gene_id "Phchi.S1G578400"
Phchi.S1	AUGUSTUS	stop_codon	37118147	37118149	.	+	0	transcript_id "Phchi.S1G578400.t1"; gene_id "Phchi.S1G578400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12618.t1 is derived from g8295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37593439	37595239	.	+	.	Phchi.S2G069800
Phchi.S2	AUGUSTUS	transcript	37593439	37595239	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	start_codon	37593439	37593441	.	+	0	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	CDS	37593439	37593535	0.4	+	0	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	exon	37593439	37593535	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	intron	37593536	37593779	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	CDS	37593780	37593848	0.76	+	2	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	exon	37593780	37593848	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	intron	37593849	37593945	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	CDS	37593946	37594267	0.74	+	2	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	exon	37593946	37594267	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	intron	37594268	37594497	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	CDS	37594498	37594528	0.99	+	1	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	exon	37594498	37594528	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	intron	37594529	37594623	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	CDS	37594624	37594875	0.97	+	0	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	exon	37594624	37594875	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	intron	37594876	37594966	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	CDS	37594967	37595239	1	+	0	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	exon	37594967	37595239	.	+	.	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
Phchi.S2	AUGUSTUS	stop_codon	37595240	37595242	.	+	0	transcript_id "Phchi.S2G069800.t1"; gene_id "Phchi.S2G069800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8233.t1 is derived from g5408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34568513	34570364	.	+	.	Phchi.S1G539200
Phchi.S1	AUGUSTUS	transcript	34568513	34570364	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	start_codon	34568513	34568515	.	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34568513	34568672	0.85	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34568513	34568672	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34568673	34568750	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34568751	34569013	0.6	+	2	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34568751	34569013	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34569014	34569103	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34569104	34569339	1	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34569104	34569339	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34569340	34569465	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34569466	34569698	1	+	1	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34569466	34569698	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34569699	34569800	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34569801	34569865	1	+	2	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34569801	34569865	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34569866	34569948	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34569949	34570044	1	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34569949	34570044	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34570045	34570133	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34570134	34570196	1	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34570134	34570196	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	intron	34570197	34570292	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	CDS	34570293	34570364	1	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	exon	34570293	34570364	.	+	.	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
Phchi.S1	AUGUSTUS	stop_codon	34570365	34570367	.	+	0	transcript_id "Phchi.S1G539200.t1"; gene_id "Phchi.S1G539200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15321.t1 is derived from g13789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18381702	18384259	.	+	.	Phchi.S3G264000
Phchi.S3	AUGUSTUS	transcript	18381702	18384259	.	+	.	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	start_codon	18381702	18381704	.	+	0	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	CDS	18381702	18381873	0.88	+	0	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	exon	18381702	18381873	.	+	.	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	intron	18381874	18382004	.	+	.	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	CDS	18382005	18382161	0.89	+	2	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	exon	18382005	18382161	.	+	.	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	intron	18382162	18382293	.	+	.	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	CDS	18382294	18384259	1	+	1	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	exon	18382294	18384259	.	+	.	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
Phchi.S3	AUGUSTUS	stop_codon	18384260	18384262	.	+	0	transcript_id "Phchi.S3G264000.t1"; gene_id "Phchi.S3G264000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5345.t1 is derived from g2515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16395842	16397392	.	-	.	Phchi.S1G250400
Phchi.S1	AUGUSTUS	transcript	16395842	16397392	.	-	.	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	stop_codon	16395839	16395841	.	-	0	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	CDS	16395842	16397046	0.89	-	2	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	exon	16395842	16397046	.	-	.	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	intron	16397047	16397205	.	-	.	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	CDS	16397206	16397392	0.61	-	0	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	exon	16397206	16397392	.	-	.	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
Phchi.S1	AUGUSTUS	start_codon	16397390	16397392	.	-	0	transcript_id "Phchi.S1G250400.t1"; gene_id "Phchi.S1G250400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg652.t1 is derived from g10434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4586321	4594683	.	+	.	Phchi.S6G061100
Phchi.S6	AUGUSTUS	transcript	4586321	4594683	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	start_codon	4586321	4586323	.	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4586321	4586427	0.99	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4586321	4586427	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4586428	4586524	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4586525	4586629	1	+	1	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4586525	4586629	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4586630	4586816	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4586817	4586865	1	+	1	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4586817	4586865	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4586866	4586956	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4586957	4587034	1	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4586957	4587034	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4587035	4587132	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4587133	4587208	0.86	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4587133	4587208	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4587209	4587509	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4587510	4587532	0.53	+	2	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4587510	4587532	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4587533	4587737	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4587738	4587819	0.9	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4587738	4587819	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4587820	4587945	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4587946	4588136	0.75	+	2	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4587946	4588136	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4588137	4588287	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4588288	4588407	0.85	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4588288	4588407	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4588408	4588492	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4588493	4588539	1	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4588493	4588539	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4588540	4588685	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4588686	4588752	1	+	1	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4588686	4588752	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4588753	4588886	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4588887	4588977	1	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4588887	4588977	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4588978	4589295	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4589296	4589422	0.99	+	2	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4589296	4589422	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4589423	4589552	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4589553	4589654	0.6	+	1	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4589553	4589654	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4589655	4589765	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4589766	4589907	0.58	+	1	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4589766	4589907	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4589908	4589981	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4589982	4590759	0.76	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4589982	4590759	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4590760	4590886	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4590887	4591158	0.86	+	2	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4590887	4591158	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4591159	4591250	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4591251	4591460	1	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4591251	4591460	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4591461	4591541	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4591542	4591916	1	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4591542	4591916	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4591917	4592003	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4592004	4592365	0.97	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4592004	4592365	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4592366	4592454	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4592455	4592626	0.99	+	1	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4592455	4592626	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	intron	4592627	4592721	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	CDS	4592722	4594683	0.97	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	exon	4592722	4594683	.	+	.	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
Phchi.S6	AUGUSTUS	stop_codon	4594684	4594686	.	+	0	transcript_id "Phchi.S6G061100.t1"; gene_id "Phchi.S6G061100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7371.t1 is derived from g4543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28811887	28813362	.	+	.	Phchi.S1G453000
Phchi.S1	AUGUSTUS	transcript	28811887	28813362	.	+	.	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	start_codon	28811887	28811889	.	+	0	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	CDS	28811887	28812402	0.69	+	0	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	exon	28811887	28812402	.	+	.	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	intron	28812403	28812512	.	+	.	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	CDS	28812513	28812599	0.91	+	0	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	exon	28812513	28812599	.	+	.	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	intron	28812600	28812702	.	+	.	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	CDS	28812703	28813362	0.8	+	0	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	exon	28812703	28813362	.	+	.	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
Phchi.S1	AUGUSTUS	stop_codon	28813363	28813365	.	+	0	transcript_id "Phchi.S1G453000.t1"; gene_id "Phchi.S1G453000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7072.t1 is derived from g4244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26745781	26748455	.	+	.	Phchi.S1G423100
Phchi.S1	AUGUSTUS	transcript	26745781	26748455	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	start_codon	26745781	26745783	.	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26745781	26746005	0.57	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26745781	26746005	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26746006	26746125	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26746126	26746172	1	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26746126	26746172	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26746173	26746297	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26746298	26746337	1	+	1	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26746298	26746337	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26746338	26746448	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26746449	26746514	1	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26746449	26746514	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26746515	26746611	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26746612	26746759	0.67	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26746612	26746759	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26746760	26746928	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26746929	26747086	0.8	+	2	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26746929	26747086	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26747087	26747193	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26747194	26747247	1	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26747194	26747247	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26747248	26747324	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26747325	26747393	1	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26747325	26747393	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26747394	26747494	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26747495	26747624	1	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26747495	26747624	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26747625	26747740	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26747741	26747781	0.69	+	2	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26747741	26747781	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26747782	26747871	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26747872	26748174	0.69	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26747872	26748174	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	intron	26748175	26748323	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	CDS	26748324	26748455	0.17	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	exon	26748324	26748455	.	+	.	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
Phchi.S1	AUGUSTUS	stop_codon	26748456	26748458	.	+	0	transcript_id "Phchi.S1G423100.t1"; gene_id "Phchi.S1G423100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13600.t1 is derived from g12067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7644886	7647345	.	-	.	Phchi.S3G091900
Phchi.S3	AUGUSTUS	transcript	7644886	7647345	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	stop_codon	7644883	7644885	.	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7644886	7645011	0.99	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7644886	7645011	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7645012	7645109	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7645110	7645371	0.93	-	1	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7645110	7645371	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7645372	7645487	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7645488	7645801	0.91	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7645488	7645801	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7645802	7645886	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7645887	7646018	1	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7645887	7646018	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7646019	7646111	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7646112	7646207	1	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7646112	7646207	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7646208	7646326	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7646327	7646500	1	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7646327	7646500	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7646501	7646652	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7646653	7646676	0.94	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7646653	7646676	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7646677	7646727	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7646728	7646845	0.94	-	1	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7646728	7646845	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7646846	7647078	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7647079	7647159	1	-	1	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7647079	7647159	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	intron	7647160	7647241	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	CDS	7647242	7647345	1	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	exon	7647242	7647345	.	-	.	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
Phchi.S3	AUGUSTUS	start_codon	7647343	7647345	.	-	0	transcript_id "Phchi.S3G091900.t1"; gene_id "Phchi.S3G091900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9692.t1 is derived from g6868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43304084	43305316	.	-	.	Phchi.S1G685100
Phchi.S1	AUGUSTUS	transcript	43304084	43305316	.	-	.	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	stop_codon	43304081	43304083	.	-	0	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	CDS	43304084	43304773	1	-	0	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	exon	43304084	43304773	.	-	.	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	intron	43304774	43304866	.	-	.	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	CDS	43304867	43305316	0.74	-	0	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	exon	43304867	43305316	.	-	.	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
Phchi.S1	AUGUSTUS	start_codon	43305314	43305316	.	-	0	transcript_id "Phchi.S1G685100.t1"; gene_id "Phchi.S1G685100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4968.t1 is derived from g2138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13805876	13809117	.	-	.	Phchi.S1G212700
Phchi.S1	AUGUSTUS	transcript	13805876	13809117	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	stop_codon	13805873	13805875	.	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13805876	13805923	0.9	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13805876	13805923	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13805924	13805998	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13805999	13806157	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13805999	13806157	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13806158	13806252	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13806253	13806333	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13806253	13806333	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13806334	13806414	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13806415	13806516	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13806415	13806516	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13806517	13806605	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13806606	13806676	1	-	2	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13806606	13806676	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13806677	13806794	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13806795	13806918	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13806795	13806918	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13806919	13807002	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13807003	13807061	1	-	2	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13807003	13807061	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13807062	13807196	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13807197	13807266	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13807197	13807266	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13807267	13807351	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13807352	13807463	1	-	1	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13807352	13807463	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13807464	13807583	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13807584	13807778	1	-	1	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13807584	13807778	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13807779	13807904	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13807905	13808059	0.83	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13807905	13808059	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13808060	13808170	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13808171	13808218	0.96	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13808171	13808218	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13808219	13808303	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13808304	13808375	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13808304	13808375	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	intron	13808376	13808535	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	CDS	13808536	13809117	1	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	exon	13808536	13809117	.	-	.	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
Phchi.S1	AUGUSTUS	start_codon	13809115	13809117	.	-	0	transcript_id "Phchi.S1G212700.t1"; gene_id "Phchi.S1G212700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15113.t1 is derived from g13581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17137859	17139020	.	+	.	Phchi.S3G243200
Phchi.S3	AUGUSTUS	transcript	17137859	17139020	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	start_codon	17137859	17137861	.	+	0	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	CDS	17137859	17138373	0.99	+	0	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	exon	17137859	17138373	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	intron	17138374	17138577	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	CDS	17138578	17138674	1	+	1	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	exon	17138578	17138674	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	intron	17138675	17138795	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	CDS	17138796	17138855	1	+	0	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	exon	17138796	17138855	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	intron	17138856	17138939	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	CDS	17138940	17139020	0.99	+	0	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	exon	17138940	17139020	.	+	.	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
Phchi.S3	AUGUSTUS	stop_codon	17139021	17139023	.	+	0	transcript_id "Phchi.S3G243200.t1"; gene_id "Phchi.S3G243200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14549.t1 is derived from g13017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13433644	13434054	.	+	.	Phchi.S3G186800
Phchi.S3	AUGUSTUS	transcript	13433644	13434054	.	+	.	transcript_id "Phchi.S3G186800.t1"; gene_id "Phchi.S3G186800"
Phchi.S3	AUGUSTUS	start_codon	13433644	13433646	.	+	0	transcript_id "Phchi.S3G186800.t1"; gene_id "Phchi.S3G186800"
Phchi.S3	AUGUSTUS	CDS	13433644	13434054	0.67	+	0	transcript_id "Phchi.S3G186800.t1"; gene_id "Phchi.S3G186800"
Phchi.S3	AUGUSTUS	exon	13433644	13434054	.	+	.	transcript_id "Phchi.S3G186800.t1"; gene_id "Phchi.S3G186800"
Phchi.S3	AUGUSTUS	stop_codon	13434055	13434057	.	+	0	transcript_id "Phchi.S3G186800.t1"; gene_id "Phchi.S3G186800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9698.t1 is derived from g6874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43326140	43327071	.	-	.	Phchi.S1G685700
Phchi.S1	AUGUSTUS	transcript	43326140	43327071	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	stop_codon	43326137	43326139	.	-	0	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	CDS	43326140	43326254	0.54	-	1	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	exon	43326140	43326254	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	intron	43326255	43326392	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	CDS	43326393	43326411	0.54	-	2	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	exon	43326393	43326411	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	intron	43326412	43326492	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	CDS	43326493	43326584	0.5	-	1	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	exon	43326493	43326584	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	intron	43326585	43326982	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	CDS	43326983	43327071	0.41	-	0	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	exon	43326983	43327071	.	-	.	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
Phchi.S1	AUGUSTUS	start_codon	43327069	43327071	.	-	0	transcript_id "Phchi.S1G685700.t1"; gene_id "Phchi.S1G685700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14094.t1 is derived from g12561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10824148	10825449	.	-	.	Phchi.S3G141300
Phchi.S3	AUGUSTUS	transcript	10824148	10825449	.	-	.	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	stop_codon	10824145	10824147	.	-	0	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	CDS	10824148	10824322	0.92	-	1	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	exon	10824148	10824322	.	-	.	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	intron	10824323	10824748	.	-	.	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	CDS	10824749	10825449	0.85	-	0	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	exon	10824749	10825449	.	-	.	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
Phchi.S3	AUGUSTUS	start_codon	10825447	10825449	.	-	0	transcript_id "Phchi.S3G141300.t1"; gene_id "Phchi.S3G141300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11889.t1 is derived from g15941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9038783	9040173	.	-	.	Phchi.S4G147100
Phchi.S4	AUGUSTUS	transcript	9038783	9040173	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	stop_codon	9038780	9038782	.	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	CDS	9038783	9038941	1	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	exon	9038783	9038941	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	intron	9038942	9039024	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	CDS	9039025	9039129	1	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	exon	9039025	9039129	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	intron	9039130	9039239	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	CDS	9039240	9039365	0.65	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	exon	9039240	9039365	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	intron	9039366	9039484	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	CDS	9039485	9039566	0.24	-	1	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	exon	9039485	9039566	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	intron	9039567	9039674	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	CDS	9039675	9039793	0.51	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	exon	9039675	9039793	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	intron	9039794	9040020	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	CDS	9040021	9040173	0.5	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	exon	9040021	9040173	.	-	.	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
Phchi.S4	AUGUSTUS	start_codon	9040171	9040173	.	-	0	transcript_id "Phchi.S4G147100.t1"; gene_id "Phchi.S4G147100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10569.t1 is derived from g14619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1009310	1012826	.	-	.	Phchi.S4G015100
Phchi.S4	AUGUSTUS	transcript	1009310	1012826	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	stop_codon	1009307	1009309	.	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1009310	1009363	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1009310	1009363	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1009364	1009454	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1009455	1009598	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1009455	1009598	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1009599	1009690	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1009691	1009989	1	-	2	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1009691	1009989	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1009990	1010091	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1010092	1010212	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1010092	1010212	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1010213	1010407	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1010408	1010503	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1010408	1010503	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1010504	1010575	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1010576	1010696	1	-	1	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1010576	1010696	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1010697	1010798	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1010799	1010953	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1010799	1010953	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1010954	1011028	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1011029	1011118	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1011029	1011118	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1011119	1011214	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1011215	1011310	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1011215	1011310	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1011311	1011496	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1011497	1011595	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1011497	1011595	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1011596	1011680	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1011681	1011815	0.96	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1011681	1011815	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1011816	1011944	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1011945	1012076	0.99	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1011945	1012076	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1012077	1012228	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1012229	1012288	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1012229	1012288	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1012289	1012443	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1012444	1012503	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1012444	1012503	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	intron	1012504	1012784	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	CDS	1012785	1012826	1	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	exon	1012785	1012826	.	-	.	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
Phchi.S4	AUGUSTUS	start_codon	1012824	1012826	.	-	0	transcript_id "Phchi.S4G015100.t1"; gene_id "Phchi.S4G015100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2236.t1 is derived from g9156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5587360	5590387	.	-	.	Phchi.S5G084500
Phchi.S5	AUGUSTUS	transcript	5587360	5590387	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	stop_codon	5587357	5587359	.	-	0	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5587360	5587835	0.99	-	2	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5587360	5587835	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5587836	5587918	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5587919	5588003	1	-	0	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5587919	5588003	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5588004	5588105	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5588106	5588198	0.96	-	0	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5588106	5588198	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5588199	5588276	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5588277	5588344	1	-	2	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5588277	5588344	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5588345	5588425	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5588426	5588478	1	-	1	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5588426	5588478	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5588479	5588557	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5588558	5588819	0.8	-	2	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5588558	5588819	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5588820	5588911	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5588912	5589217	0.96	-	2	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5588912	5589217	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5589218	5589323	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5589324	5589863	0.62	-	2	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5589324	5589863	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	intron	5589864	5589942	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	CDS	5589943	5590387	0.49	-	0	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	exon	5589943	5590387	.	-	.	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
Phchi.S5	AUGUSTUS	start_codon	5590385	5590387	.	-	0	transcript_id "Phchi.S5G084500.t1"; gene_id "Phchi.S5G084500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1492.t1 is derived from g8411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1180476	1184040	.	+	.	Phchi.S5G010100
Phchi.S5	AUGUSTUS	transcript	1180476	1184040	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	start_codon	1180476	1180478	.	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1180476	1180586	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1180476	1180586	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1180587	1180821	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1180822	1180986	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1180822	1180986	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1180987	1181123	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1181124	1181251	0.84	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1181124	1181251	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1181252	1181339	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1181340	1181366	0.64	+	1	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1181340	1181366	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1181367	1181437	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1181438	1181442	0.83	+	1	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1181438	1181442	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1181443	1181529	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1181530	1181774	1	+	2	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1181530	1181774	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1181775	1181877	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1181878	1182057	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1181878	1182057	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1182058	1182191	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1182192	1182270	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1182192	1182270	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1182271	1182417	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1182418	1182499	1	+	2	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1182418	1182499	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1182500	1182584	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1182585	1182647	1	+	1	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1182585	1182647	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1182648	1182729	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1182730	1182868	1	+	1	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1182730	1182868	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1182869	1182962	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1182963	1183140	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1182963	1183140	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1183141	1183221	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1183222	1183356	1	+	2	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1183222	1183356	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1183357	1183451	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1183452	1183510	1	+	2	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1183452	1183510	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1183511	1183587	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1183588	1183725	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1183588	1183725	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	intron	1183726	1183875	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	CDS	1183876	1184040	1	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	exon	1183876	1184040	.	+	.	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
Phchi.S5	AUGUSTUS	stop_codon	1184041	1184043	.	+	0	transcript_id "Phchi.S5G010100.t1"; gene_id "Phchi.S5G010100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2914.t1 is derived from g83.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	464057	464824	.	-	.	Phchi.S1G007300
Phchi.S1	AUGUSTUS	transcript	464057	464824	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	stop_codon	464054	464056	.	-	0	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	CDS	464057	464227	1	-	0	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	exon	464057	464227	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	intron	464228	464317	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	CDS	464318	464420	0.88	-	1	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	exon	464318	464420	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	intron	464421	464528	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	CDS	464529	464648	0.91	-	1	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	exon	464529	464648	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	intron	464649	464729	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	CDS	464730	464824	0.89	-	0	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	exon	464730	464824	.	-	.	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
Phchi.S1	AUGUSTUS	start_codon	464822	464824	.	-	0	transcript_id "Phchi.S1G007300.t1"; gene_id "Phchi.S1G007300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5825.t1 is derived from g2995.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19135350	19139441	.	-	.	Phchi.S1G298400
Phchi.S1	AUGUSTUS	transcript	19135350	19139441	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	stop_codon	19135347	19135349	.	-	0	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19135350	19135476	0.92	-	1	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19135350	19135476	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19135477	19135569	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19135570	19135663	1	-	2	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19135570	19135663	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19135664	19135902	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19135903	19136184	0.94	-	2	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19135903	19136184	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19136185	19136293	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19136294	19137185	0.76	-	0	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19136294	19137185	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137186	19137309	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137310	19137434	0.96	-	2	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137310	19137434	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137435	19137530	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137531	19137548	0.8	-	2	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137531	19137548	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137549	19137646	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137647	19137854	0.68	-	0	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137647	19137854	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137855	19137936	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137937	19138106	1	-	2	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137937	19138106	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19138107	19138346	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19138347	19138457	1	-	2	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19138347	19138457	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19138458	19138561	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19138562	19138676	1	-	0	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19138562	19138676	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19138677	19139171	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19139172	19139441	1	-	0	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19139172	19139441	.	-	.	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	start_codon	19139439	19139441	.	-	0	transcript_id "Phchi.S1G298400.t1"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	transcript	19135350	19139441	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	stop_codon	19135347	19135349	.	-	0	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19135350	19135476	0.98	-	1	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19135350	19135476	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19135477	19135569	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19135570	19135663	1	-	2	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19135570	19135663	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19135664	19135902	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19135903	19136184	0.71	-	2	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19135903	19136184	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19136185	19136293	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19136294	19137185	0.5	-	0	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19136294	19137185	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137186	19137309	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137310	19137431	0.97	-	2	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137310	19137431	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137432	19137526	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137527	19137854	0.89	-	0	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137527	19137854	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19137855	19137936	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19137937	19138106	1	-	2	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19137937	19138106	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19138107	19138346	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19138347	19138457	1	-	2	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19138347	19138457	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19138458	19138561	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19138562	19138676	1	-	0	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19138562	19138676	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	intron	19138677	19139171	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	CDS	19139172	19139441	1	-	0	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	exon	19139172	19139441	.	-	.	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
Phchi.S1	AUGUSTUS	start_codon	19139439	19139441	.	-	0	transcript_id "Phchi.S1G298400.t2"; gene_id "Phchi.S1G298400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15078.t1 is derived from g13546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16936683	16938121	.	+	.	Phchi.S3G239700
Phchi.S3	AUGUSTUS	transcript	16936683	16938121	.	+	.	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	start_codon	16936683	16936685	.	+	0	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	CDS	16936683	16936794	0.45	+	0	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	exon	16936683	16936794	.	+	.	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	intron	16936795	16936868	.	+	.	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	CDS	16936869	16938121	0.99	+	2	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	exon	16936869	16938121	.	+	.	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
Phchi.S3	AUGUSTUS	stop_codon	16938122	16938124	.	+	0	transcript_id "Phchi.S3G239700.t1"; gene_id "Phchi.S3G239700"
# This transcript jg9568.t2 is derived from g6744.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9569.t1 is derived from g6745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42717529	42719044	.	-	.	Phchi.S1G672800
Phchi.S1	AUGUSTUS	transcript	42717529	42719044	.	-	.	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	stop_codon	42717526	42717528	.	-	0	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	CDS	42717529	42717543	0.45	-	0	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	exon	42717529	42717543	.	-	.	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	intron	42717544	42717734	.	-	.	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	CDS	42717735	42717773	0.42	-	0	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	exon	42717735	42717773	.	-	.	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	intron	42717774	42717850	.	-	.	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	CDS	42717851	42719044	0.46	-	0	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	exon	42717851	42719044	.	-	.	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
Phchi.S1	AUGUSTUS	start_codon	42719042	42719044	.	-	0	transcript_id "Phchi.S1G672800.t1"; gene_id "Phchi.S1G672800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3819.t1 is derived from g988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5886373	5887681	.	-	.	Phchi.S1G097800
Phchi.S1	AUGUSTUS	transcript	5886373	5887681	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	stop_codon	5886370	5886372	.	-	0	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	CDS	5886373	5886660	1	-	0	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	exon	5886373	5886660	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	intron	5886661	5886749	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	CDS	5886750	5886891	1	-	1	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	exon	5886750	5886891	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	intron	5886892	5886981	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	CDS	5886982	5887050	1	-	1	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	exon	5886982	5887050	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	intron	5887051	5887168	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	CDS	5887169	5887367	1	-	2	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	exon	5887169	5887367	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	intron	5887368	5887443	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	CDS	5887444	5887681	1	-	0	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	exon	5887444	5887681	.	-	.	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
Phchi.S1	AUGUSTUS	start_codon	5887679	5887681	.	-	0	transcript_id "Phchi.S1G097800.t1"; gene_id "Phchi.S1G097800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10578.t1 is derived from g14628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1043404	1046560	.	-	.	Phchi.S4G016000
Phchi.S4	AUGUSTUS	transcript	1043404	1046560	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	stop_codon	1043401	1043403	.	-	0	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	CDS	1043404	1043405	0.66	-	2	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	exon	1043404	1043405	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	intron	1043406	1043535	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	CDS	1043536	1046017	0.33	-	0	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	exon	1043536	1046017	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	intron	1046018	1046101	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	CDS	1046102	1046196	0.87	-	2	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	exon	1046102	1046196	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	intron	1046197	1046309	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	CDS	1046310	1046359	0.83	-	1	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	exon	1046310	1046359	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	intron	1046360	1046489	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	CDS	1046490	1046560	0.86	-	0	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	exon	1046490	1046560	.	-	.	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
Phchi.S4	AUGUSTUS	start_codon	1046558	1046560	.	-	0	transcript_id "Phchi.S4G016000.t1"; gene_id "Phchi.S4G016000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6174.t1 is derived from g3345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21297808	21300259	.	+	.	Phchi.S1G333300
Phchi.S1	AUGUSTUS	transcript	21297808	21300259	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	start_codon	21297808	21297810	.	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21297808	21297995	1	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21297808	21297995	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21297996	21298134	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21298135	21298203	1	+	1	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21298135	21298203	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21298204	21298301	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21298302	21298437	0.98	+	1	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21298302	21298437	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21298438	21298548	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21298549	21298796	1	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21298549	21298796	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21298797	21298890	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21298891	21299117	1	+	1	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21298891	21299117	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21299118	21299222	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21299223	21299338	1	+	2	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21299223	21299338	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21299339	21299436	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21299437	21299613	0.89	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21299437	21299613	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21299614	21299722	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21299723	21299911	0.99	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21299723	21299911	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21299912	21299992	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21299993	21300055	1	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21299993	21300055	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	intron	21300056	21300142	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	CDS	21300143	21300259	1	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	exon	21300143	21300259	.	+	.	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
Phchi.S1	AUGUSTUS	stop_codon	21300260	21300262	.	+	0	transcript_id "Phchi.S1G333300.t1"; gene_id "Phchi.S1G333300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11375.t1 is derived from g15425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5946257	5948259	.	+	.	Phchi.S4G095700
Phchi.S4	AUGUSTUS	transcript	5946257	5948259	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	start_codon	5946257	5946259	.	+	0	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	CDS	5946257	5946353	1	+	0	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	exon	5946257	5946353	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	intron	5946354	5946501	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	CDS	5946502	5946871	1	+	2	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	exon	5946502	5946871	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	intron	5946872	5946988	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	CDS	5946989	5947781	0.86	+	1	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	exon	5946989	5947781	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	intron	5947782	5947860	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	CDS	5947861	5948106	0.66	+	0	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	exon	5947861	5948106	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	intron	5948107	5948220	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	CDS	5948221	5948259	0.86	+	0	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	exon	5948221	5948259	.	+	.	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
Phchi.S4	AUGUSTUS	stop_codon	5948260	5948262	.	+	0	transcript_id "Phchi.S4G095700.t1"; gene_id "Phchi.S4G095700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11776.t1 is derived from g15828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8118493	8119260	.	+	.	Phchi.S4G135800
Phchi.S4	AUGUSTUS	transcript	8118493	8119260	.	+	.	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	start_codon	8118493	8118495	.	+	0	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	CDS	8118493	8118731	1	+	0	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	exon	8118493	8118731	.	+	.	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	intron	8118732	8118877	.	+	.	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	CDS	8118878	8119043	0.87	+	1	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	exon	8118878	8119043	.	+	.	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	intron	8119044	8119149	.	+	.	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	CDS	8119150	8119260	0.99	+	0	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	exon	8119150	8119260	.	+	.	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
Phchi.S4	AUGUSTUS	stop_codon	8119261	8119263	.	+	0	transcript_id "Phchi.S4G135800.t1"; gene_id "Phchi.S4G135800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12260.t1 is derived from g7936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7060378	7060824	.	+	.	Phchi.S2G034000
Phchi.S2	AUGUSTUS	transcript	7060378	7060824	.	+	.	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	start_codon	7060378	7060380	.	+	0	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	CDS	7060378	7060717	0.42	+	0	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	exon	7060378	7060717	.	+	.	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	intron	7060718	7060801	.	+	.	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	CDS	7060802	7060824	0.47	+	2	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	exon	7060802	7060824	.	+	.	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
Phchi.S2	AUGUSTUS	stop_codon	7060825	7060827	.	+	0	transcript_id "Phchi.S2G034000.t1"; gene_id "Phchi.S2G034000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2174.t1 is derived from g9094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5217910	5219428	.	+	.	Phchi.S5G078300
Phchi.S5	AUGUSTUS	transcript	5217910	5219428	.	+	.	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	start_codon	5217910	5217912	.	+	0	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	CDS	5217910	5218780	0.59	+	0	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	exon	5217910	5218780	.	+	.	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	intron	5218781	5218876	.	+	.	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	CDS	5218877	5219080	1	+	2	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	exon	5218877	5219080	.	+	.	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	intron	5219081	5219165	.	+	.	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	CDS	5219166	5219428	0.47	+	2	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	exon	5219166	5219428	.	+	.	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
Phchi.S5	AUGUSTUS	stop_codon	5219429	5219431	.	+	0	transcript_id "Phchi.S5G078300.t1"; gene_id "Phchi.S5G078300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1730.t1 is derived from g8650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2749119	2753184	.	+	.	Phchi.S5G033900
Phchi.S5	AUGUSTUS	transcript	2749119	2753184	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	start_codon	2749119	2749121	.	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2749119	2749296	0.68	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2749119	2749296	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2749297	2749386	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2749387	2749913	1	+	2	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2749387	2749913	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2749914	2750004	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2750005	2750075	1	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2750005	2750075	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2750076	2750166	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2750167	2750287	1	+	1	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2750167	2750287	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2750288	2750429	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2750430	2750740	1	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2750430	2750740	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2750741	2750876	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2750877	2751183	0.98	+	1	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2750877	2751183	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2751184	2751314	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2751315	2751851	1	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2751315	2751851	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2751852	2751926	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2751927	2752013	1	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2751927	2752013	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2752014	2752104	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2752105	2752295	1	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2752105	2752295	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2752296	2752444	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2752445	2752640	1	+	1	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2752445	2752640	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2752641	2752739	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2752740	2752804	1	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2752740	2752804	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2752805	2752881	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2752882	2752983	1	+	1	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2752882	2752983	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	intron	2752984	2753081	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	CDS	2753082	2753184	1	+	1	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	exon	2753082	2753184	.	+	.	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
Phchi.S5	AUGUSTUS	stop_codon	2753185	2753187	.	+	0	transcript_id "Phchi.S5G033900.t1"; gene_id "Phchi.S5G033900"
# This transcript jg8325.t2 is derived from g5500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8325.t3 is derived from g5500.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8326.t1 is derived from g5501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35330430	35331424	.	+	.	Phchi.S1G548500
Phchi.S1	AUGUSTUS	transcript	35330430	35331424	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	start_codon	35330430	35330432	.	+	0	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	CDS	35330430	35330522	0.61	+	0	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	exon	35330430	35330522	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	intron	35330523	35330621	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	CDS	35330622	35330952	0.69	+	0	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	exon	35330622	35330952	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	intron	35330953	35331060	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	CDS	35331061	35331191	0.71	+	2	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	exon	35331061	35331191	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	intron	35331192	35331277	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	CDS	35331278	35331424	0.99	+	0	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	exon	35331278	35331424	.	+	.	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
Phchi.S1	AUGUSTUS	stop_codon	35331425	35331427	.	+	0	transcript_id "Phchi.S1G548500.t1"; gene_id "Phchi.S1G548500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2940.t1 is derived from g109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	672882	681203	.	+	.	Phchi.S1G009900
Phchi.S1	AUGUSTUS	transcript	672882	681203	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	start_codon	672882	672884	.	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	672882	672966	0.84	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	672882	672966	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	672967	673049	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673050	673232	1	+	2	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673050	673232	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	673233	673326	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673327	673522	0.75	+	2	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673327	673522	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	673523	673690	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673691	673738	0.61	+	1	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673691	673738	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	673739	673868	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673869	674229	0.57	+	1	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673869	674229	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	674230	674342	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	674343	674414	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	674343	674414	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	674415	674618	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	674619	675158	0.98	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	674619	675158	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675159	675262	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675263	675319	0.99	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675263	675319	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675320	675439	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675440	675501	0.95	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675440	675501	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675502	675620	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675621	675753	0.89	+	1	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675621	675753	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675754	675880	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675881	675991	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675881	675991	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675992	676068	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676069	676165	0.99	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676069	676165	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676166	676280	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676281	676363	0.99	+	2	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676281	676363	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676364	676475	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676476	676538	0.96	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676476	676538	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676539	676648	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676649	676780	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676649	676780	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676781	676878	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676879	676934	0.98	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676879	676934	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676935	677059	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677060	677117	0.99	+	1	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677060	677117	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677118	677232	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677233	677343	0.95	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677233	677343	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677344	677426	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677427	677483	0.99	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677427	677483	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677484	677584	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677585	677722	0.95	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677585	677722	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677723	677835	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677836	678054	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677836	678054	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678055	678193	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678194	678233	0.36	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678194	678233	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678234	678411	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678412	678493	0.58	+	2	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678412	678493	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678494	678605	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678606	678678	1	+	1	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678606	678678	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678679	678767	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678768	678872	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678768	678872	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678873	678954	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678955	679122	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678955	679122	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679123	679258	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679259	679334	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679259	679334	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679335	679402	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679403	679554	1	+	2	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679403	679554	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679555	679649	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679650	679727	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679650	679727	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679728	679825	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679826	679918	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679826	679918	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679919	680002	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680003	680143	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680003	680143	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680144	680225	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680226	680265	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680226	680265	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680266	680369	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680370	680443	0.93	+	2	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680370	680443	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680444	680547	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680548	680712	0.7	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680548	680712	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680713	680798	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680799	680921	0.98	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680799	680921	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680922	681006	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	681007	681078	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	681007	681078	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	681079	681158	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	681159	681203	1	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	681159	681203	.	+	.	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	stop_codon	681204	681206	.	+	0	transcript_id "Phchi.S1G009900.t1"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	transcript	672882	681203	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	start_codon	672882	672884	.	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	672882	672966	0.8	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	672882	672966	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	672967	673049	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673050	673232	1	+	2	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673050	673232	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	673233	673326	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673327	673522	0.72	+	2	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673327	673522	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	673523	673690	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673691	673738	0.62	+	1	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673691	673738	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	673739	673868	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	673869	674229	0.57	+	1	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	673869	674229	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	674230	674342	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	674343	674414	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	674343	674414	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	674415	674618	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	674619	675158	0.99	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	674619	675158	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675159	675262	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675263	675319	0.99	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675263	675319	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675320	675439	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675440	675501	0.94	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675440	675501	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675502	675620	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675621	675753	0.97	+	1	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675621	675753	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675754	675880	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	675881	675991	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	675881	675991	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	675992	676068	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676069	676165	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676069	676165	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676166	676280	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676281	676363	1	+	2	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676281	676363	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676364	676475	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676476	676538	0.93	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676476	676538	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676539	676648	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676649	676780	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676649	676780	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676781	676878	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	676879	676934	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	676879	676934	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	676935	677059	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677060	677117	1	+	1	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677060	677117	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677118	677232	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677233	677343	0.95	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677233	677343	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677344	677426	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677427	677483	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677427	677483	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677484	677584	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677585	677722	0.99	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677585	677722	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	677723	677835	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	677836	678054	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	677836	678054	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678055	678193	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678194	678233	0.25	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678194	678233	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678234	678411	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678412	678493	0.56	+	2	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678412	678493	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678494	678605	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678606	678678	1	+	1	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678606	678678	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678679	678767	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678768	678872	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678768	678872	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	678873	678954	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	678955	679116	0.77	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	678955	679116	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679117	679258	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679259	679334	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679259	679334	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679335	679402	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679403	679554	1	+	2	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679403	679554	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679555	679649	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679650	679727	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679650	679727	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679728	679825	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	679826	679918	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	679826	679918	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	679919	680002	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680003	680143	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680003	680143	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680144	680225	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680226	680265	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680226	680265	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680266	680369	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680370	680443	0.91	+	2	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680370	680443	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680444	680547	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680548	680712	0.58	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680548	680712	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680713	680798	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	680799	680921	0.99	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	680799	680921	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	680922	681006	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	681007	681078	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	681007	681078	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	intron	681079	681158	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	CDS	681159	681203	1	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	exon	681159	681203	.	+	.	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
Phchi.S1	AUGUSTUS	stop_codon	681204	681206	.	+	0	transcript_id "Phchi.S1G009900.t2"; gene_id "Phchi.S1G009900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9123.t1 is derived from g6298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39954236	39956408	.	-	.	Phchi.S1G628200
Phchi.S1	AUGUSTUS	transcript	39954236	39956408	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	stop_codon	39954233	39954235	.	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39954236	39954487	0.96	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39954236	39954487	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39954488	39954567	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39954568	39954693	1	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39954568	39954693	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39954694	39954770	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39954771	39954827	1	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39954771	39954827	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39954828	39954917	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39954918	39954968	0.71	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39954918	39954968	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39954969	39955106	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39955107	39955142	0.53	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39955107	39955142	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39955143	39955247	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39955248	39955344	1	-	1	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39955248	39955344	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39955345	39955442	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39955443	39955537	1	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39955443	39955537	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39955538	39955617	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39955618	39955703	1	-	2	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39955618	39955703	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39955704	39955843	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39955844	39955974	1	-	1	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39955844	39955974	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39955975	39956066	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39956067	39956145	1	-	2	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39956067	39956145	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	intron	39956146	39956269	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	CDS	39956270	39956408	0.82	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	exon	39956270	39956408	.	-	.	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
Phchi.S1	AUGUSTUS	start_codon	39956406	39956408	.	-	0	transcript_id "Phchi.S1G628200.t1"; gene_id "Phchi.S1G628200"
# This transcript jg15691.t2 is derived from g14160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15692.t1 is derived from g14161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20722816	20724295	.	+	.	Phchi.S3G301100
Phchi.S3	AUGUSTUS	transcript	20722816	20724295	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	start_codon	20722816	20722818	.	+	0	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	CDS	20722816	20722861	0.58	+	0	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	exon	20722816	20722861	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	intron	20722862	20723107	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	CDS	20723108	20723172	0.84	+	2	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	exon	20723108	20723172	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	intron	20723173	20723278	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	CDS	20723279	20723426	1	+	0	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	exon	20723279	20723426	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	intron	20723427	20723521	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	CDS	20723522	20723598	0.44	+	2	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	exon	20723522	20723598	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	intron	20723599	20723817	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	CDS	20723818	20724083	0.46	+	0	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	exon	20723818	20724083	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	intron	20724084	20724282	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	CDS	20724283	20724295	0.65	+	1	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	exon	20724283	20724295	.	+	.	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
Phchi.S3	AUGUSTUS	stop_codon	20724296	20724298	.	+	0	transcript_id "Phchi.S3G301100.t1"; gene_id "Phchi.S3G301100"
# This transcript jg8012.t2 is derived from g5187.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8013.t1 is derived from g5188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32477030	32477266	.	+	.	Phchi.S1G517200
Phchi.S1	AUGUSTUS	transcript	32477030	32477266	.	+	.	transcript_id "Phchi.S1G517200.t1"; gene_id "Phchi.S1G517200"
Phchi.S1	AUGUSTUS	start_codon	32477030	32477032	.	+	0	transcript_id "Phchi.S1G517200.t1"; gene_id "Phchi.S1G517200"
Phchi.S1	AUGUSTUS	CDS	32477030	32477266	0.65	+	0	transcript_id "Phchi.S1G517200.t1"; gene_id "Phchi.S1G517200"
Phchi.S1	AUGUSTUS	exon	32477030	32477266	.	+	.	transcript_id "Phchi.S1G517200.t1"; gene_id "Phchi.S1G517200"
Phchi.S1	AUGUSTUS	stop_codon	32477267	32477269	.	+	0	transcript_id "Phchi.S1G517200.t1"; gene_id "Phchi.S1G517200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13532.t1 is derived from g11999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7393864	7394841	.	+	.	Phchi.S3G085100
Phchi.S3	AUGUSTUS	transcript	7393864	7394841	.	+	.	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	start_codon	7393864	7393866	.	+	0	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	CDS	7393864	7394155	0.96	+	0	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	exon	7393864	7394155	.	+	.	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	intron	7394156	7394486	.	+	.	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	CDS	7394487	7394599	0.63	+	2	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	exon	7394487	7394599	.	+	.	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	intron	7394600	7394772	.	+	.	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	CDS	7394773	7394841	0.8	+	0	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	exon	7394773	7394841	.	+	.	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
Phchi.S3	AUGUSTUS	stop_codon	7394842	7394844	.	+	0	transcript_id "Phchi.S3G085100.t1"; gene_id "Phchi.S3G085100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13538.t1 is derived from g12005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7411044	7411866	.	-	.	Phchi.S3G085700
Phchi.S3	AUGUSTUS	transcript	7411044	7411866	.	-	.	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	stop_codon	7411041	7411043	.	-	0	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	CDS	7411044	7411451	1	-	0	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	exon	7411044	7411451	.	-	.	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	intron	7411452	7411553	.	-	.	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	CDS	7411554	7411643	1	-	0	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	exon	7411554	7411643	.	-	.	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	intron	7411644	7411788	.	-	.	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	CDS	7411789	7411866	0.47	-	0	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	exon	7411789	7411866	.	-	.	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
Phchi.S3	AUGUSTUS	start_codon	7411864	7411866	.	-	0	transcript_id "Phchi.S3G085700.t1"; gene_id "Phchi.S3G085700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14164.t1 is derived from g12631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11231229	11232736	.	-	.	Phchi.S3G148300
Phchi.S3	AUGUSTUS	transcript	11231229	11232736	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	stop_codon	11231226	11231228	.	-	0	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	CDS	11231229	11231274	0.5	-	1	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	exon	11231229	11231274	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	intron	11231275	11231416	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	CDS	11231417	11231590	0.28	-	1	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	exon	11231417	11231590	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	intron	11231591	11231889	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	CDS	11231890	11232140	0.37	-	0	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	exon	11231890	11232140	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	intron	11232141	11232226	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	CDS	11232227	11232736	0.82	-	0	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	exon	11232227	11232736	.	-	.	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
Phchi.S3	AUGUSTUS	start_codon	11232734	11232736	.	-	0	transcript_id "Phchi.S3G148300.t1"; gene_id "Phchi.S3G148300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7396.t1 is derived from g4568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28937078	28938922	.	+	.	Phchi.S1G455500
Phchi.S1	AUGUSTUS	transcript	28937078	28938922	.	+	.	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	start_codon	28937078	28937080	.	+	0	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	CDS	28937078	28937284	0.96	+	0	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	exon	28937078	28937284	.	+	.	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	intron	28937285	28937369	.	+	.	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	CDS	28937370	28938718	0.61	+	0	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	exon	28937370	28938718	.	+	.	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	intron	28938719	28938915	.	+	.	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	CDS	28938916	28938922	0.68	+	1	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	exon	28938916	28938922	.	+	.	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
Phchi.S1	AUGUSTUS	stop_codon	28938923	28938925	.	+	0	transcript_id "Phchi.S1G455500.t1"; gene_id "Phchi.S1G455500"
# This transcript jg14772.t2 is derived from g13240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14773.t1 is derived from g13241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14644816	14646058	.	+	.	Phchi.S3G209200
Phchi.S3	AUGUSTUS	transcript	14644816	14646058	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	start_codon	14644816	14644818	.	+	0	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	CDS	14644816	14644965	1	+	0	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	exon	14644816	14644965	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	intron	14644966	14645047	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	CDS	14645048	14645217	1	+	0	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	exon	14645048	14645217	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	intron	14645218	14645298	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	CDS	14645299	14645376	1	+	1	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	exon	14645299	14645376	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	intron	14645377	14645461	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	CDS	14645462	14645612	1	+	1	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	exon	14645462	14645612	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	intron	14645613	14645695	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	CDS	14645696	14646058	0.81	+	0	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	exon	14645696	14646058	.	+	.	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
Phchi.S3	AUGUSTUS	stop_codon	14646059	14646061	.	+	0	transcript_id "Phchi.S3G209200.t1"; gene_id "Phchi.S3G209200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13317.t1 is derived from g11783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6087538	6088092	.	-	.	Phchi.S3G063600
Phchi.S3	AUGUSTUS	transcript	6087538	6088092	.	-	.	transcript_id "Phchi.S3G063600.t1"; gene_id "Phchi.S3G063600"
Phchi.S3	AUGUSTUS	stop_codon	6087535	6087537	.	-	0	transcript_id "Phchi.S3G063600.t1"; gene_id "Phchi.S3G063600"
Phchi.S3	AUGUSTUS	CDS	6087538	6088092	0.69	-	0	transcript_id "Phchi.S3G063600.t1"; gene_id "Phchi.S3G063600"
Phchi.S3	AUGUSTUS	exon	6087538	6088092	.	-	.	transcript_id "Phchi.S3G063600.t1"; gene_id "Phchi.S3G063600"
Phchi.S3	AUGUSTUS	start_codon	6088090	6088092	.	-	0	transcript_id "Phchi.S3G063600.t1"; gene_id "Phchi.S3G063600"
# This transcript jg4735.t2 is derived from g1905.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4736.t1 is derived from g1906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12542591	12543565	.	-	.	Phchi.S1G189500
Phchi.S1	AUGUSTUS	transcript	12542591	12543565	.	-	.	transcript_id "Phchi.S1G189500.t1"; gene_id "Phchi.S1G189500"
Phchi.S1	AUGUSTUS	stop_codon	12542588	12542590	.	-	0	transcript_id "Phchi.S1G189500.t1"; gene_id "Phchi.S1G189500"
Phchi.S1	AUGUSTUS	CDS	12542591	12543565	0.44	-	0	transcript_id "Phchi.S1G189500.t1"; gene_id "Phchi.S1G189500"
Phchi.S1	AUGUSTUS	exon	12542591	12543565	.	-	.	transcript_id "Phchi.S1G189500.t1"; gene_id "Phchi.S1G189500"
Phchi.S1	AUGUSTUS	start_codon	12543563	12543565	.	-	0	transcript_id "Phchi.S1G189500.t1"; gene_id "Phchi.S1G189500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg938.t1 is derived from g10720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6535451	6537326	.	+	.	Phchi.S6G089700
Phchi.S6	AUGUSTUS	transcript	6535451	6537326	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	start_codon	6535451	6535453	.	+	0	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	CDS	6535451	6535989	0.66	+	0	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	exon	6535451	6535989	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	intron	6535990	6536098	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	CDS	6536099	6536219	1	+	1	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	exon	6536099	6536219	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	intron	6536220	6536375	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	CDS	6536376	6536498	1	+	0	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	exon	6536376	6536498	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	intron	6536499	6536609	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	CDS	6536610	6536840	0.99	+	0	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	exon	6536610	6536840	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	intron	6536841	6536987	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	CDS	6536988	6537326	0.64	+	0	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	exon	6536988	6537326	.	+	.	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
Phchi.S6	AUGUSTUS	stop_codon	6537327	6537329	.	+	0	transcript_id "Phchi.S6G089700.t1"; gene_id "Phchi.S6G089700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14794.t1 is derived from g13262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14744887	14745693	.	+	.	Phchi.S3G211300
Phchi.S3	AUGUSTUS	transcript	14744887	14745693	.	+	.	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	start_codon	14744887	14744889	.	+	0	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	CDS	14744887	14745022	0.9	+	0	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	exon	14744887	14745022	.	+	.	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	intron	14745023	14745321	.	+	.	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	CDS	14745322	14745364	0.72	+	2	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	exon	14745322	14745364	.	+	.	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	intron	14745365	14745641	.	+	.	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	CDS	14745642	14745693	0.45	+	1	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	exon	14745642	14745693	.	+	.	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
Phchi.S3	AUGUSTUS	stop_codon	14745694	14745696	.	+	0	transcript_id "Phchi.S3G211300.t1"; gene_id "Phchi.S3G211300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10704.t1 is derived from g14754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1677779	1678925	.	+	.	Phchi.S4G028600
Phchi.S4	AUGUSTUS	transcript	1677779	1678925	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	start_codon	1677779	1677781	.	+	0	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	CDS	1677779	1677874	0.2	+	0	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	exon	1677779	1677874	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	intron	1677875	1677999	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	CDS	1678000	1678015	0.44	+	0	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	exon	1678000	1678015	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	intron	1678016	1678112	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	CDS	1678113	1678216	1	+	2	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	exon	1678113	1678216	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	intron	1678217	1678442	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	CDS	1678443	1678520	1	+	0	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	exon	1678443	1678520	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	intron	1678521	1678600	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	CDS	1678601	1678788	0.98	+	0	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	exon	1678601	1678788	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	intron	1678789	1678873	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	CDS	1678874	1678925	0.74	+	1	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	exon	1678874	1678925	.	+	.	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
Phchi.S4	AUGUSTUS	stop_codon	1678926	1678928	.	+	0	transcript_id "Phchi.S4G028600.t1"; gene_id "Phchi.S4G028600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5375.t1 is derived from g2545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16560155	16564378	.	-	.	Phchi.S1G253400
Phchi.S1	AUGUSTUS	transcript	16560155	16564378	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	stop_codon	16560152	16560154	.	-	0	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16560155	16560191	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16560155	16560191	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16560192	16560274	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16560275	16560418	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16560275	16560418	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16560419	16560501	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16560502	16560648	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16560502	16560648	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16560649	16560738	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16560739	16560784	1	-	2	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16560739	16560784	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16560785	16560886	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16560887	16560952	1	-	2	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16560887	16560952	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16560953	16561071	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16561072	16561198	1	-	0	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16561072	16561198	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16561199	16561279	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16561280	16561503	1	-	2	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16561280	16561503	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16561504	16561637	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16561638	16561836	0.94	-	0	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16561638	16561836	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16561837	16561922	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16561923	16562049	0.9	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16561923	16562049	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16562050	16562127	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16562128	16562190	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16562128	16562190	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16562191	16562261	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16562262	16562330	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16562262	16562330	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16562331	16562425	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16562426	16562500	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16562426	16562500	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16562501	16562620	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16562621	16562756	1	-	2	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16562621	16562756	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16562757	16562856	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16562857	16563086	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16562857	16563086	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16563087	16563184	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16563185	16563442	1	-	1	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16563185	16563442	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16563443	16563527	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16563528	16563793	1	-	0	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16563528	16563793	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16563794	16563886	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16563887	16564197	0.88	-	2	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16563887	16564197	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	intron	16564198	16564323	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	CDS	16564324	16564378	0.69	-	0	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	exon	16564324	16564378	.	-	.	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
Phchi.S1	AUGUSTUS	start_codon	16564376	16564378	.	-	0	transcript_id "Phchi.S1G253400.t1"; gene_id "Phchi.S1G253400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4567.t1 is derived from g1737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11148566	11150345	.	+	.	Phchi.S1G172600
Phchi.S1	AUGUSTUS	transcript	11148566	11150345	.	+	.	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	start_codon	11148566	11148568	.	+	0	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	CDS	11148566	11149999	1	+	0	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	exon	11148566	11149999	.	+	.	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	intron	11150000	11150303	.	+	.	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	CDS	11150304	11150345	1	+	0	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	exon	11150304	11150345	.	+	.	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
Phchi.S1	AUGUSTUS	stop_codon	11150346	11150348	.	+	0	transcript_id "Phchi.S1G172600.t1"; gene_id "Phchi.S1G172600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4854.t1 is derived from g2024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13113676	13116890	.	+	.	Phchi.S1G201300
Phchi.S1	AUGUSTUS	transcript	13113676	13116890	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	start_codon	13113676	13113678	.	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13113676	13113909	0.99	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13113676	13113909	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13113910	13114078	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13114079	13114228	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13114079	13114228	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13114229	13114315	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13114316	13114762	0.99	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13114316	13114762	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13114763	13114871	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13114872	13115027	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13114872	13115027	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13115028	13115109	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13115110	13115343	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13115110	13115343	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13115344	13115421	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13115422	13115510	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13115422	13115510	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13115511	13115640	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13115641	13115731	1	+	1	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13115641	13115731	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13115732	13115811	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13115812	13115892	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13115812	13115892	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13115893	13116011	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13116012	13116079	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13116012	13116079	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13116080	13116179	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13116180	13116258	1	+	1	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13116180	13116258	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13116259	13116346	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13116347	13116374	1	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13116347	13116374	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13116375	13116447	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13116448	13116456	1	+	2	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13116448	13116456	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13116457	13116541	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13116542	13116605	0.75	+	2	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13116542	13116605	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	intron	13116606	13116880	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	CDS	13116881	13116890	0.42	+	1	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	exon	13116881	13116890	.	+	.	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
Phchi.S1	AUGUSTUS	stop_codon	13116891	13116893	.	+	0	transcript_id "Phchi.S1G201300.t1"; gene_id "Phchi.S1G201300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12505.t1 is derived from g8182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31070704	31070940	.	-	.	Phchi.S2G058500
Phchi.S2	AUGUSTUS	transcript	31070704	31070940	.	-	.	transcript_id "Phchi.S2G058500.t1"; gene_id "Phchi.S2G058500"
Phchi.S2	AUGUSTUS	stop_codon	31070701	31070703	.	-	0	transcript_id "Phchi.S2G058500.t1"; gene_id "Phchi.S2G058500"
Phchi.S2	AUGUSTUS	CDS	31070704	31070940	0.72	-	0	transcript_id "Phchi.S2G058500.t1"; gene_id "Phchi.S2G058500"
Phchi.S2	AUGUSTUS	exon	31070704	31070940	.	-	.	transcript_id "Phchi.S2G058500.t1"; gene_id "Phchi.S2G058500"
Phchi.S2	AUGUSTUS	start_codon	31070938	31070940	.	-	0	transcript_id "Phchi.S2G058500.t1"; gene_id "Phchi.S2G058500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11736.t1 is derived from g15788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7912980	7915139	.	-	.	Phchi.S4G131800
Phchi.S4	AUGUSTUS	transcript	7912980	7915139	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	stop_codon	7912977	7912979	.	-	0	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7912980	7913041	1	-	2	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7912980	7913041	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7913042	7913125	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7913126	7913234	1	-	0	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7913126	7913234	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7913235	7913411	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7913412	7913627	1	-	0	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7913412	7913627	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7913628	7913713	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7913714	7913979	1	-	2	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7913714	7913979	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7913980	7914090	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7914091	7914361	1	-	0	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7914091	7914361	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7914362	7914461	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7914462	7914630	1	-	1	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7914462	7914630	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7914631	7914764	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7914765	7914909	1	-	2	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7914765	7914909	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	intron	7914910	7914988	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	CDS	7914989	7915139	1	-	0	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	exon	7914989	7915139	.	-	.	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
Phchi.S4	AUGUSTUS	start_codon	7915137	7915139	.	-	0	transcript_id "Phchi.S4G131800.t1"; gene_id "Phchi.S4G131800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14543.t1 is derived from g13011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13405486	13409057	.	+	.	Phchi.S3G186200
Phchi.S3	AUGUSTUS	transcript	13405486	13409057	.	+	.	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	start_codon	13405486	13405488	.	+	0	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	CDS	13405486	13405878	0.72	+	0	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	exon	13405486	13405878	.	+	.	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	intron	13405879	13405964	.	+	.	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	CDS	13405965	13409057	0.56	+	0	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	exon	13405965	13409057	.	+	.	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	stop_codon	13409058	13409060	.	+	0	transcript_id "Phchi.S3G186200.t1"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	transcript	13405486	13407037	.	+	.	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	start_codon	13405486	13405488	.	+	0	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	CDS	13405486	13405878	0.57	+	0	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	exon	13405486	13405878	.	+	.	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	intron	13405879	13405964	.	+	.	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	CDS	13405965	13406955	0.31	+	0	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	exon	13405965	13406955	.	+	.	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	intron	13406956	13407029	.	+	.	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	CDS	13407030	13407037	0.59	+	2	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	exon	13407030	13407037	.	+	.	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
Phchi.S3	AUGUSTUS	stop_codon	13407038	13407040	.	+	0	transcript_id "Phchi.S3G186200.t2"; gene_id "Phchi.S3G186200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3585.t1 is derived from g754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4613989	4616112	.	+	.	Phchi.S1G074400
Phchi.S1	AUGUSTUS	transcript	4613989	4616112	.	+	.	transcript_id "Phchi.S1G074400.t1"; gene_id "Phchi.S1G074400"
Phchi.S1	AUGUSTUS	start_codon	4613989	4613991	.	+	0	transcript_id "Phchi.S1G074400.t1"; gene_id "Phchi.S1G074400"
Phchi.S1	AUGUSTUS	CDS	4613989	4616112	1	+	0	transcript_id "Phchi.S1G074400.t1"; gene_id "Phchi.S1G074400"
Phchi.S1	AUGUSTUS	exon	4613989	4616112	.	+	.	transcript_id "Phchi.S1G074400.t1"; gene_id "Phchi.S1G074400"
Phchi.S1	AUGUSTUS	stop_codon	4616113	4616115	.	+	0	transcript_id "Phchi.S1G074400.t1"; gene_id "Phchi.S1G074400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9993.t1 is derived from g7169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44899012	44902753	.	+	.	Phchi.S1G715200
Phchi.S1	AUGUSTUS	transcript	44899012	44902753	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	start_codon	44899012	44899014	.	+	0	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44899012	44900166	0.98	+	0	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44899012	44900166	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44900167	44900280	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44900281	44900761	0.98	+	0	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44900281	44900761	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44900762	44900861	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44900862	44900962	0.7	+	2	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44900862	44900962	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44900963	44901124	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44901125	44901414	0.71	+	0	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44901125	44901414	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44901415	44901628	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44901629	44901811	0.4	+	1	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44901629	44901811	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44901812	44901976	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44901977	44902065	0.69	+	1	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44901977	44902065	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44902066	44902211	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44902212	44902316	1	+	2	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44902212	44902316	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	intron	44902317	44902571	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	CDS	44902572	44902753	1	+	2	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	exon	44902572	44902753	.	+	.	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
Phchi.S1	AUGUSTUS	stop_codon	44902754	44902756	.	+	0	transcript_id "Phchi.S1G715200.t1"; gene_id "Phchi.S1G715200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1887.t1 is derived from g8807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3708912	3710512	.	-	.	Phchi.S5G049600
Phchi.S5	AUGUSTUS	transcript	3708912	3710512	.	-	.	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	stop_codon	3708909	3708911	.	-	0	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	CDS	3708912	3709675	0.48	-	2	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	exon	3708912	3709675	.	-	.	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	intron	3709676	3709755	.	-	.	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	CDS	3709756	3709882	0.4	-	0	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	exon	3709756	3709882	.	-	.	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	intron	3709883	3709963	.	-	.	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	CDS	3709964	3710512	1	-	0	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	exon	3709964	3710512	.	-	.	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
Phchi.S5	AUGUSTUS	start_codon	3710510	3710512	.	-	0	transcript_id "Phchi.S5G049600.t1"; gene_id "Phchi.S5G049600"
# This transcript jg2763.t2 is derived from g9683.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2764.t1 is derived from g9684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8716994	8719067	.	+	.	Phchi.S5G137300
Phchi.S5	AUGUSTUS	transcript	8716994	8719067	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	start_codon	8716994	8716996	.	+	0	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	CDS	8716994	8717189	0.69	+	0	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	exon	8716994	8717189	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	intron	8717190	8717377	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	CDS	8717378	8717565	0.92	+	2	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	exon	8717378	8717565	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	intron	8717566	8717660	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	CDS	8717661	8717909	1	+	0	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	exon	8717661	8717909	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	intron	8717910	8717990	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	CDS	8717991	8718455	1	+	0	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	exon	8717991	8718455	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	intron	8718456	8718545	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	CDS	8718546	8719067	0.99	+	0	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	exon	8718546	8719067	.	+	.	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
Phchi.S5	AUGUSTUS	stop_codon	8719068	8719070	.	+	0	transcript_id "Phchi.S5G137300.t1"; gene_id "Phchi.S5G137300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6061.t1 is derived from g3232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20689806	20691288	.	+	.	Phchi.S1G322000
Phchi.S1	AUGUSTUS	transcript	20689806	20691288	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	start_codon	20689806	20689808	.	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	CDS	20689806	20690134	1	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	exon	20689806	20690134	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	intron	20690135	20690263	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	CDS	20690264	20690297	1	+	1	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	exon	20690264	20690297	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	intron	20690298	20690465	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	CDS	20690466	20690720	1	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	exon	20690466	20690720	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	intron	20690721	20690821	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	CDS	20690822	20690908	1	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	exon	20690822	20690908	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	intron	20690909	20691022	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	CDS	20691023	20691088	0.91	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	exon	20691023	20691088	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	intron	20691089	20691195	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	CDS	20691196	20691288	0.29	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	exon	20691196	20691288	.	+	.	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
Phchi.S1	AUGUSTUS	stop_codon	20691289	20691291	.	+	0	transcript_id "Phchi.S1G322000.t1"; gene_id "Phchi.S1G322000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9806.t1 is derived from g6982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43828170	43832759	.	-	.	Phchi.S1G696500
Phchi.S1	AUGUSTUS	transcript	43828170	43832759	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	stop_codon	43828167	43828169	.	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43828170	43828436	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43828170	43828436	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43828437	43828511	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43828512	43828688	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43828512	43828688	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43828689	43828778	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43828779	43828859	0.96	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43828779	43828859	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43828860	43828965	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43828966	43829262	0.92	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43828966	43829262	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43829263	43829349	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43829350	43829493	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43829350	43829493	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43829494	43829581	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43829582	43829671	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43829582	43829671	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43829672	43829770	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43829771	43829847	1	-	2	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43829771	43829847	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43829848	43829971	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43829972	43830089	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43829972	43830089	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43830090	43830231	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43830232	43830489	0.85	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43830232	43830489	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43830490	43830620	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43830621	43830779	0.93	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43830621	43830779	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43830780	43830884	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43830885	43831082	0.98	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43830885	43831082	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43831083	43831171	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43831172	43831267	0.55	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43831172	43831267	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43831268	43831375	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43831376	43831561	0.53	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43831376	43831561	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43831562	43831693	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43831694	43831863	0.96	-	2	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43831694	43831863	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43831864	43831966	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43831967	43832198	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43831967	43832198	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	intron	43832199	43832366	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	CDS	43832367	43832759	1	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	exon	43832367	43832759	.	-	.	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
Phchi.S1	AUGUSTUS	start_codon	43832757	43832759	.	-	0	transcript_id "Phchi.S1G696500.t1"; gene_id "Phchi.S1G696500"
# This transcript jg9276.t2 is derived from g6451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9277.t1 is derived from g6452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40734288	40736912	.	+	.	Phchi.S1G643600
Phchi.S1	AUGUSTUS	transcript	40734288	40736912	.	+	.	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	start_codon	40734288	40734290	.	+	0	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	CDS	40734288	40734597	0.96	+	0	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	exon	40734288	40734597	.	+	.	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	intron	40734598	40734695	.	+	.	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	CDS	40734696	40735507	0.57	+	2	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	exon	40734696	40735507	.	+	.	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	intron	40735508	40735811	.	+	.	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	CDS	40735812	40736912	0.46	+	0	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	exon	40735812	40736912	.	+	.	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
Phchi.S1	AUGUSTUS	stop_codon	40736913	40736915	.	+	0	transcript_id "Phchi.S1G643600.t1"; gene_id "Phchi.S1G643600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1414.t1 is derived from g8333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	561074	564416	.	+	.	Phchi.S5G002300
Phchi.S5	AUGUSTUS	transcript	561074	564416	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	start_codon	561074	561076	.	+	0	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	561074	561466	0.5	+	0	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	561074	561466	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	561467	561609	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	561610	561700	0.62	+	0	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	561610	561700	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	561701	561781	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	561782	561903	1	+	2	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	561782	561903	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	561904	562002	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	562003	563993	0.75	+	0	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	562003	563993	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	563994	564103	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	564104	564184	0.93	+	1	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	564104	564184	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	564185	564367	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	564368	564416	0.94	+	1	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	564368	564416	.	+	.	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	stop_codon	564417	564419	.	+	0	transcript_id "Phchi.S5G002300.t1"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	transcript	561074	564416	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	start_codon	561074	561076	.	+	0	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	561074	561466	0.43	+	0	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	561074	561466	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	561467	561609	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	561610	561700	0.47	+	0	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	561610	561700	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	561701	561772	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	561773	561903	0.97	+	2	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	561773	561903	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	561904	562002	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	562003	563993	0.6	+	0	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	562003	563993	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	563994	564103	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	564104	564184	0.87	+	1	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	564104	564184	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	intron	564185	564367	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	CDS	564368	564416	0.87	+	1	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	exon	564368	564416	.	+	.	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
Phchi.S5	AUGUSTUS	stop_codon	564417	564419	.	+	0	transcript_id "Phchi.S5G002300.t2"; gene_id "Phchi.S5G002300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg667.t1 is derived from g10449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4645585	4646447	.	-	.	Phchi.S6G062600
Phchi.S6	AUGUSTUS	transcript	4645585	4646447	.	-	.	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	stop_codon	4645582	4645584	.	-	0	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	CDS	4645585	4645627	0.94	-	1	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	exon	4645585	4645627	.	-	.	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	intron	4645628	4645761	.	-	.	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	CDS	4645762	4646447	0.74	-	0	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	exon	4645762	4646447	.	-	.	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
Phchi.S6	AUGUSTUS	start_codon	4646445	4646447	.	-	0	transcript_id "Phchi.S6G062600.t1"; gene_id "Phchi.S6G062600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2681.t1 is derived from g9601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8173859	8180532	.	-	.	Phchi.S5G129000
Phchi.S5	AUGUSTUS	transcript	8173859	8180532	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	stop_codon	8173856	8173858	.	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8173859	8173984	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8173859	8173984	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8173985	8174068	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8174069	8174173	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8174069	8174173	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8174174	8174260	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8174261	8174357	1	-	1	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8174261	8174357	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8174358	8174451	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8174452	8174557	1	-	2	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8174452	8174557	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8174558	8174669	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8174670	8174742	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8174670	8174742	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8174743	8174839	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8174840	8174983	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8174840	8174983	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8174984	8175098	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8175099	8175891	0.43	-	1	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8175099	8175891	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8175892	8176097	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8176098	8176252	0.75	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8176098	8176252	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8176253	8176584	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8176585	8176629	0.67	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8176585	8176629	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8176630	8176722	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8176723	8176788	0.48	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8176723	8176788	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8176789	8176898	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8176899	8177077	0.66	-	2	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8176899	8177077	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8177078	8177216	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8177217	8177316	0.91	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8177217	8177316	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8177317	8177463	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8177464	8177596	0.92	-	1	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8177464	8177596	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8177597	8177741	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8177742	8177791	0.81	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8177742	8177791	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8177792	8177854	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8177855	8177971	0.82	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8177855	8177971	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8177972	8178068	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8178069	8178167	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8178069	8178167	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8178168	8178277	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8178278	8178367	0.97	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8178278	8178367	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8178368	8178547	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8178548	8178680	0.92	-	1	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8178548	8178680	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8178681	8178793	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8178794	8178879	0.99	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8178794	8178879	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8178880	8178976	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8178977	8179252	0.37	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8178977	8179252	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8179253	8179330	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8179331	8179462	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8179331	8179462	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8179463	8179571	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8179572	8179643	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8179572	8179643	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8179644	8179777	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8179778	8179858	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8179778	8179858	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8179859	8179997	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8179998	8180198	1	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8179998	8180198	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	intron	8180199	8180499	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	CDS	8180500	8180532	0.73	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	exon	8180500	8180532	.	-	.	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
Phchi.S5	AUGUSTUS	start_codon	8180530	8180532	.	-	0	transcript_id "Phchi.S5G129000.t1"; gene_id "Phchi.S5G129000"
# This transcript jg6136.t2 is derived from g3307.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6137.t1 is derived from g3308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21107181	21111594	.	+	.	Phchi.S1G329600
Phchi.S1	AUGUSTUS	transcript	21107181	21111594	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	start_codon	21107181	21107183	.	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21107181	21107447	0.97	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21107181	21107447	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21107448	21107782	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21107783	21107839	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21107783	21107839	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21107840	21107985	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21107986	21108080	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21107986	21108080	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21108081	21108387	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21108388	21108544	1	+	1	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21108388	21108544	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21108545	21108633	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21108634	21108759	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21108634	21108759	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21108760	21108859	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21108860	21109007	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21108860	21109007	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21109008	21109120	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21109121	21109181	1	+	2	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21109121	21109181	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21109182	21109290	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21109291	21109537	1	+	1	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21109291	21109537	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21109538	21109686	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21109687	21109809	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21109687	21109809	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21109810	21109940	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21109941	21110099	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21109941	21110099	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21110100	21110189	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21110190	21110421	0.9	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21110190	21110421	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21110422	21110536	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21110537	21111019	0.99	+	2	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21110537	21111019	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21111020	21111175	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21111176	21111204	1	+	2	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21111176	21111204	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21111205	21111309	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21111310	21111347	1	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21111310	21111347	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	intron	21111348	21111503	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	CDS	21111504	21111594	0.97	+	1	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	exon	21111504	21111594	.	+	.	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
Phchi.S1	AUGUSTUS	stop_codon	21111595	21111597	.	+	0	transcript_id "Phchi.S1G329600.t1"; gene_id "Phchi.S1G329600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7383.t1 is derived from g4555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28857622	28859672	.	-	.	Phchi.S1G454200
Phchi.S1	AUGUSTUS	transcript	28857622	28859672	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	stop_codon	28857619	28857621	.	-	0	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	CDS	28857622	28857807	0.99	-	0	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	exon	28857622	28857807	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	intron	28857808	28857893	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	CDS	28857894	28858029	1	-	1	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	exon	28857894	28858029	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	intron	28858030	28858133	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	CDS	28858134	28858237	1	-	0	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	exon	28858134	28858237	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	intron	28858238	28858329	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	CDS	28858330	28858936	0.63	-	1	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	exon	28858330	28858936	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	intron	28858937	28859135	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	CDS	28859136	28859300	0.63	-	1	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	exon	28859136	28859300	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	intron	28859301	28859505	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	CDS	28859506	28859672	0.99	-	0	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	exon	28859506	28859672	.	-	.	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
Phchi.S1	AUGUSTUS	start_codon	28859670	28859672	.	-	0	transcript_id "Phchi.S1G454200.t1"; gene_id "Phchi.S1G454200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14509.t1 is derived from g12977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13230507	13231841	.	-	.	Phchi.S3G182800
Phchi.S3	AUGUSTUS	transcript	13230507	13231841	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	stop_codon	13230504	13230506	.	-	0	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13230507	13230824	0.99	-	0	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13230507	13230824	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	intron	13230825	13230903	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13230904	13231190	0.49	-	2	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13230904	13231190	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	intron	13231191	13231288	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13231289	13231600	0.53	-	2	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13231289	13231600	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	intron	13231601	13231765	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13231766	13231841	0.89	-	0	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13231766	13231841	.	-	.	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	start_codon	13231839	13231841	.	-	0	transcript_id "Phchi.S3G182800.t1"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	transcript	13230507	13231777	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	stop_codon	13230504	13230506	.	-	0	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13230507	13230824	1	-	0	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13230507	13230824	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	intron	13230825	13230903	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13230904	13231190	0.51	-	2	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13230904	13231190	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	intron	13231191	13231288	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13231289	13231600	0.55	-	2	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13231289	13231600	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	intron	13231601	13231758	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	CDS	13231759	13231777	0.43	-	0	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	exon	13231759	13231777	.	-	.	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
Phchi.S3	AUGUSTUS	start_codon	13231775	13231777	.	-	0	transcript_id "Phchi.S3G182800.t2"; gene_id "Phchi.S3G182800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9182.t1 is derived from g6357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40241762	40244113	.	+	.	Phchi.S1G634100
Phchi.S1	AUGUSTUS	transcript	40241762	40244113	.	+	.	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	start_codon	40241762	40241764	.	+	0	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	CDS	40241762	40243585	0.3	+	0	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	exon	40241762	40243585	.	+	.	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	intron	40243586	40243954	.	+	.	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	CDS	40243955	40244113	0.32	+	0	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	exon	40243955	40244113	.	+	.	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
Phchi.S1	AUGUSTUS	stop_codon	40244114	40244116	.	+	0	transcript_id "Phchi.S1G634100.t1"; gene_id "Phchi.S1G634100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13233.t1 is derived from g11698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4847263	4849262	.	+	.	Phchi.S3G055200
Phchi.S3	AUGUSTUS	transcript	4847263	4849262	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	start_codon	4847263	4847265	.	+	0	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4847263	4847450	0.96	+	0	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4847263	4847450	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4847451	4847651	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4847652	4847711	0.97	+	1	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4847652	4847711	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4847712	4847852	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4847853	4847969	0.97	+	1	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4847853	4847969	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4847970	4848064	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4848065	4848356	0.94	+	1	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4848065	4848356	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4848357	4848459	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4848460	4848591	0.86	+	0	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4848460	4848591	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4848592	4848722	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4848723	4848874	0.95	+	0	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4848723	4848874	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4848875	4848970	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4848971	4849124	0.89	+	1	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4848971	4849124	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	intron	4849125	4849211	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	CDS	4849212	4849262	0.89	+	0	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	exon	4849212	4849262	.	+	.	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
Phchi.S3	AUGUSTUS	stop_codon	4849263	4849265	.	+	0	transcript_id "Phchi.S3G055200.t1"; gene_id "Phchi.S3G055200"
# This transcript jg12214.t2 is derived from g7890.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12215.t1 is derived from g7891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6799408	6802604	.	-	.	Phchi.S2G029500
Phchi.S2	AUGUSTUS	transcript	6799408	6802604	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	stop_codon	6799405	6799407	.	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6799408	6799633	0.99	-	1	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6799408	6799633	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6799634	6799731	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6799732	6799847	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6799732	6799847	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6799848	6799948	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6799949	6800080	0.97	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6799949	6800080	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6800081	6800209	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6800210	6800284	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6800210	6800284	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6800285	6800404	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6800405	6800503	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6800405	6800503	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6800504	6800593	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6800594	6800689	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6800594	6800689	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6800690	6800855	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6800856	6800963	0.99	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6800856	6800963	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6800964	6801418	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6801419	6801437	0.99	-	1	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6801419	6801437	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6801438	6801534	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6801535	6801613	0.99	-	2	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6801535	6801613	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6801614	6801824	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6801825	6801948	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6801825	6801948	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6801949	6802025	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6802026	6802043	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6802026	6802043	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6802044	6802101	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6802102	6802131	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6802102	6802131	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6802132	6802222	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6802223	6802295	1	-	1	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6802223	6802295	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6802296	6802368	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6802369	6802469	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6802369	6802469	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	intron	6802470	6802550	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	CDS	6802551	6802604	1	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	exon	6802551	6802604	.	-	.	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
Phchi.S2	AUGUSTUS	start_codon	6802602	6802604	.	-	0	transcript_id "Phchi.S2G029500.t1"; gene_id "Phchi.S2G029500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8595.t1 is derived from g5770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36801350	36804159	.	-	.	Phchi.S1G575400
Phchi.S1	AUGUSTUS	transcript	36801350	36804159	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	stop_codon	36801347	36801349	.	-	0	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36801350	36802021	0.82	-	0	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36801350	36802021	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36802022	36802146	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36802147	36802245	0.91	-	0	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36802147	36802245	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36802246	36802366	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36802367	36802490	0.72	-	1	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36802367	36802490	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36802491	36802613	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36802614	36802862	0.92	-	1	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36802614	36802862	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36802863	36802968	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36802969	36803318	1	-	0	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36802969	36803318	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36803319	36803409	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36803410	36803752	0.85	-	1	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36803410	36803752	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36803753	36803839	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36803840	36803951	0.87	-	2	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36803840	36803951	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36803952	36804035	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36804036	36804159	0.76	-	0	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36804036	36804159	.	-	.	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	start_codon	36804157	36804159	.	-	0	transcript_id "Phchi.S1G575400.t1"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	transcript	36801350	36802207	.	-	.	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	stop_codon	36801347	36801349	.	-	0	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36801350	36801906	0.43	-	2	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36801350	36801906	.	-	.	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	intron	36801907	36802071	.	-	.	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	CDS	36802072	36802207	0.26	-	0	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	exon	36802072	36802207	.	-	.	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
Phchi.S1	AUGUSTUS	start_codon	36802205	36802207	.	-	0	transcript_id "Phchi.S1G575400.t2"; gene_id "Phchi.S1G575400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5317.t1 is derived from g2487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16262976	16263858	.	+	.	Phchi.S1G247600
Phchi.S1	AUGUSTUS	transcript	16262976	16263858	.	+	.	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	start_codon	16262976	16262978	.	+	0	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	CDS	16262976	16263226	0.97	+	0	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	exon	16262976	16263226	.	+	.	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	intron	16263227	16263518	.	+	.	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	CDS	16263519	16263858	1	+	1	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	exon	16263519	16263858	.	+	.	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
Phchi.S1	AUGUSTUS	stop_codon	16263859	16263861	.	+	0	transcript_id "Phchi.S1G247600.t1"; gene_id "Phchi.S1G247600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2641.t1 is derived from g9561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7912371	7919745	.	-	.	Phchi.S5G125000
Phchi.S5	AUGUSTUS	transcript	7912371	7919745	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	stop_codon	7912368	7912370	.	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7912371	7912588	1	-	2	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7912371	7912588	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7912589	7912681	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7912682	7912831	1	-	2	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7912682	7912831	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7912832	7912936	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7912937	7913100	0.99	-	1	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7912937	7913100	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7913101	7913189	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7913190	7914527	0.98	-	1	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7913190	7914527	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7914528	7914630	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7914631	7915491	0.89	-	1	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7914631	7915491	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7915492	7915730	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7915731	7916698	0.89	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7915731	7916698	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7916699	7916790	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7916791	7916919	0.35	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7916791	7916919	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7916920	7917033	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7917034	7917378	0.73	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7917034	7917378	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7917379	7917528	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7917529	7918395	1	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7917529	7918395	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7918396	7918497	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7918498	7918600	1	-	1	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7918498	7918600	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7918601	7918767	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7918768	7918864	1	-	2	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7918768	7918864	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	intron	7918865	7918958	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	CDS	7918959	7919745	0.45	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	exon	7918959	7919745	.	-	.	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
Phchi.S5	AUGUSTUS	start_codon	7919743	7919745	.	-	0	transcript_id "Phchi.S5G125000.t1"; gene_id "Phchi.S5G125000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12530.t1 is derived from g8207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33339596	33340540	.	-	.	Phchi.S2G061000
Phchi.S2	AUGUSTUS	transcript	33339596	33340540	.	-	.	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	stop_codon	33339593	33339595	.	-	0	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	CDS	33339596	33340025	0.71	-	1	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	exon	33339596	33340025	.	-	.	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	intron	33340026	33340196	.	-	.	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	CDS	33340197	33340540	0.65	-	0	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	exon	33340197	33340540	.	-	.	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
Phchi.S2	AUGUSTUS	start_codon	33340538	33340540	.	-	0	transcript_id "Phchi.S2G061000.t1"; gene_id "Phchi.S2G061000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3048.t1 is derived from g217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1356006	1357598	.	+	.	Phchi.S1G020700
Phchi.S1	AUGUSTUS	transcript	1356006	1357598	.	+	.	transcript_id "Phchi.S1G020700.t1"; gene_id "Phchi.S1G020700"
Phchi.S1	AUGUSTUS	start_codon	1356006	1356008	.	+	0	transcript_id "Phchi.S1G020700.t1"; gene_id "Phchi.S1G020700"
Phchi.S1	AUGUSTUS	CDS	1356006	1357598	0.74	+	0	transcript_id "Phchi.S1G020700.t1"; gene_id "Phchi.S1G020700"
Phchi.S1	AUGUSTUS	exon	1356006	1357598	.	+	.	transcript_id "Phchi.S1G020700.t1"; gene_id "Phchi.S1G020700"
Phchi.S1	AUGUSTUS	stop_codon	1357599	1357601	.	+	0	transcript_id "Phchi.S1G020700.t1"; gene_id "Phchi.S1G020700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg743.t1 is derived from g10525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5285232	5287942	.	-	.	Phchi.S6G070200
Phchi.S6	AUGUSTUS	transcript	5285232	5287942	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	stop_codon	5285229	5285231	.	-	0	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	CDS	5285232	5286629	0.91	-	0	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	exon	5285232	5286629	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	intron	5286630	5286763	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	CDS	5286764	5287383	1	-	2	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	exon	5286764	5287383	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	intron	5287384	5287501	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	CDS	5287502	5287785	1	-	1	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	exon	5287502	5287785	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	intron	5287786	5287859	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	CDS	5287860	5287942	0.88	-	0	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	exon	5287860	5287942	.	-	.	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
Phchi.S6	AUGUSTUS	start_codon	5287940	5287942	.	-	0	transcript_id "Phchi.S6G070200.t1"; gene_id "Phchi.S6G070200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1697.t1 is derived from g8616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2568809	2570439	.	-	.	Phchi.S5G030600
Phchi.S5	AUGUSTUS	transcript	2568809	2570439	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	stop_codon	2568806	2568808	.	-	0	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	CDS	2568809	2569198	1	-	0	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	exon	2568809	2569198	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	intron	2569199	2569297	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	CDS	2569298	2569503	1	-	2	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	exon	2569298	2569503	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	intron	2569504	2569624	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	CDS	2569625	2569731	0.91	-	1	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	exon	2569625	2569731	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	intron	2569732	2569827	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	CDS	2569828	2570019	0.91	-	1	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	exon	2569828	2570019	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	intron	2570020	2570122	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	CDS	2570123	2570439	0.99	-	0	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	exon	2570123	2570439	.	-	.	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
Phchi.S5	AUGUSTUS	start_codon	2570437	2570439	.	-	0	transcript_id "Phchi.S5G030600.t1"; gene_id "Phchi.S5G030600"
# This transcript jg4247.t2 is derived from g1416.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4248.t1 is derived from g1417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9161374	9163395	.	-	.	Phchi.S1G140700
Phchi.S1	AUGUSTUS	transcript	9161374	9163395	.	-	.	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	stop_codon	9161371	9161373	.	-	0	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	CDS	9161374	9161819	1	-	2	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	exon	9161374	9161819	.	-	.	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	intron	9161820	9161935	.	-	.	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	CDS	9161936	9162485	0.96	-	0	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	exon	9161936	9162485	.	-	.	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	intron	9162486	9162624	.	-	.	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	CDS	9162625	9163395	0.81	-	0	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	exon	9162625	9163395	.	-	.	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
Phchi.S1	AUGUSTUS	start_codon	9163393	9163395	.	-	0	transcript_id "Phchi.S1G140700.t1"; gene_id "Phchi.S1G140700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2457.t1 is derived from g9377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6746991	6748712	.	-	.	Phchi.S5G106600
Phchi.S5	AUGUSTUS	transcript	6746991	6748712	.	-	.	transcript_id "Phchi.S5G106600.t1"; gene_id "Phchi.S5G106600"
Phchi.S5	AUGUSTUS	stop_codon	6746988	6746990	.	-	0	transcript_id "Phchi.S5G106600.t1"; gene_id "Phchi.S5G106600"
Phchi.S5	AUGUSTUS	CDS	6746991	6748712	0.97	-	0	transcript_id "Phchi.S5G106600.t1"; gene_id "Phchi.S5G106600"
Phchi.S5	AUGUSTUS	exon	6746991	6748712	.	-	.	transcript_id "Phchi.S5G106600.t1"; gene_id "Phchi.S5G106600"
Phchi.S5	AUGUSTUS	start_codon	6748710	6748712	.	-	0	transcript_id "Phchi.S5G106600.t1"; gene_id "Phchi.S5G106600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2704.t1 is derived from g9624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8259376	8264473	.	+	.	Phchi.S5G131300
Phchi.S5	AUGUSTUS	transcript	8259376	8264473	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	start_codon	8259376	8259378	.	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8259376	8259407	1	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8259376	8259407	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8259408	8259933	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8259934	8260303	1	+	1	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8259934	8260303	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8260304	8260519	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8260520	8260760	0.89	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8260520	8260760	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8260761	8260864	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8260865	8260914	0.9	+	2	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8260865	8260914	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8260915	8261033	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261034	8261126	0.94	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261034	8261126	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261127	8261226	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261227	8261315	1	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261227	8261315	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261316	8261567	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261568	8261646	1	+	1	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261568	8261646	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261647	8261740	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261741	8261823	1	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261741	8261823	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261824	8261943	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261944	8262022	1	+	1	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261944	8262022	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8262023	8262178	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8262179	8262962	1	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8262179	8262962	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8262963	8263144	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8263145	8263516	0.8	+	2	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8263145	8263516	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8263517	8263626	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8263627	8263885	0.75	+	2	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8263627	8263885	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8263886	8264009	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8264010	8264074	0.82	+	1	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8264010	8264074	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8264075	8264222	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8264223	8264251	0.91	+	2	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8264223	8264251	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8264252	8264341	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8264342	8264473	0.9	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8264342	8264473	.	+	.	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	stop_codon	8264474	8264476	.	+	0	transcript_id "Phchi.S5G131300.t1"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	transcript	8259376	8264473	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	start_codon	8259376	8259378	.	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8259376	8259407	1	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8259376	8259407	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8259408	8259933	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8259934	8260303	1	+	1	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8259934	8260303	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8260304	8260519	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8260520	8260760	0.91	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8260520	8260760	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8260761	8260864	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8260865	8260914	0.92	+	2	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8260865	8260914	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8260915	8261033	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261034	8261126	0.99	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261034	8261126	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261127	8261226	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261227	8261315	1	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261227	8261315	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261316	8261567	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261568	8261646	1	+	1	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261568	8261646	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261647	8261740	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261741	8261823	1	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261741	8261823	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8261824	8261943	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8261944	8262022	1	+	1	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8261944	8262022	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8262023	8262178	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8262179	8262962	1	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8262179	8262962	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8262963	8263144	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8263145	8263516	0.76	+	2	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8263145	8263516	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8263517	8263626	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8263627	8263885	0.77	+	2	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8263627	8263885	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8263886	8264009	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8264010	8264074	0.51	+	1	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8264010	8264074	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8264075	8264222	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8264223	8264251	0.59	+	2	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8264223	8264251	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	intron	8264252	8264338	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	CDS	8264339	8264473	0.57	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	exon	8264339	8264473	.	+	.	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
Phchi.S5	AUGUSTUS	stop_codon	8264474	8264476	.	+	0	transcript_id "Phchi.S5G131300.t2"; gene_id "Phchi.S5G131300"
# This transcript jg2940.t2 is derived from g109.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2941.t1 is derived from g110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	692433	694167	.	+	.	Phchi.S1G010000
Phchi.S1	AUGUSTUS	transcript	692433	694167	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	start_codon	692433	692435	.	+	0	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	CDS	692433	692496	0.86	+	0	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	exon	692433	692496	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	intron	692497	692617	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	CDS	692618	693034	0.81	+	2	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	exon	692618	693034	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	intron	693035	693096	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	CDS	693097	693245	0.84	+	2	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	exon	693097	693245	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	intron	693246	693330	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	CDS	693331	694167	1	+	0	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	exon	693331	694167	.	+	.	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
Phchi.S1	AUGUSTUS	stop_codon	694168	694170	.	+	0	transcript_id "Phchi.S1G010000.t1"; gene_id "Phchi.S1G010000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2837.t1 is derived from g9757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9122408	9122772	.	+	.	Phchi.S5G144600
Phchi.S5	AUGUSTUS	transcript	9122408	9122772	.	+	.	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	start_codon	9122408	9122410	.	+	0	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	CDS	9122408	9122537	1	+	0	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	exon	9122408	9122537	.	+	.	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	intron	9122538	9122626	.	+	.	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	CDS	9122627	9122772	0.83	+	2	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	exon	9122627	9122772	.	+	.	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
Phchi.S5	AUGUSTUS	stop_codon	9122773	9122775	.	+	0	transcript_id "Phchi.S5G144600.t1"; gene_id "Phchi.S5G144600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14277.t1 is derived from g12744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11893425	11894181	.	+	.	Phchi.S3G159600
Phchi.S3	AUGUSTUS	transcript	11893425	11894181	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	start_codon	11893425	11893427	.	+	0	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	CDS	11893425	11893438	0.97	+	0	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	exon	11893425	11893438	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	intron	11893439	11893670	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	CDS	11893671	11893747	1	+	1	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	exon	11893671	11893747	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	intron	11893748	11893841	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	CDS	11893842	11894033	0.98	+	2	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	exon	11893842	11894033	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	intron	11894034	11894122	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	CDS	11894123	11894181	0.85	+	2	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	exon	11894123	11894181	.	+	.	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
Phchi.S3	AUGUSTUS	stop_codon	11894182	11894184	.	+	0	transcript_id "Phchi.S3G159600.t1"; gene_id "Phchi.S3G159600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8577.t1 is derived from g5752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36711822	36712776	.	+	.	Phchi.S1G573600
Phchi.S1	AUGUSTUS	transcript	36711822	36712776	.	+	.	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	start_codon	36711822	36711824	.	+	0	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	CDS	36711822	36712255	0.58	+	0	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	exon	36711822	36712255	.	+	.	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	intron	36712256	36712400	.	+	.	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	CDS	36712401	36712776	0.92	+	1	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	exon	36712401	36712776	.	+	.	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
Phchi.S1	AUGUSTUS	stop_codon	36712777	36712779	.	+	0	transcript_id "Phchi.S1G573600.t1"; gene_id "Phchi.S1G573600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4055.t1 is derived from g1224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7555802	7557073	.	-	.	Phchi.S1G121400
Phchi.S1	AUGUSTUS	transcript	7555802	7557073	.	-	.	transcript_id "Phchi.S1G121400.t1"; gene_id "Phchi.S1G121400"
Phchi.S1	AUGUSTUS	stop_codon	7555799	7555801	.	-	0	transcript_id "Phchi.S1G121400.t1"; gene_id "Phchi.S1G121400"
Phchi.S1	AUGUSTUS	CDS	7555802	7557073	0.99	-	0	transcript_id "Phchi.S1G121400.t1"; gene_id "Phchi.S1G121400"
Phchi.S1	AUGUSTUS	exon	7555802	7557073	.	-	.	transcript_id "Phchi.S1G121400.t1"; gene_id "Phchi.S1G121400"
Phchi.S1	AUGUSTUS	start_codon	7557071	7557073	.	-	0	transcript_id "Phchi.S1G121400.t1"; gene_id "Phchi.S1G121400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg802.t1 is derived from g10584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5678548	5678986	.	-	.	Phchi.S6G076100
Phchi.S6	AUGUSTUS	transcript	5678548	5678986	.	-	.	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	stop_codon	5678545	5678547	.	-	0	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	CDS	5678548	5678644	0.98	-	1	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	exon	5678548	5678644	.	-	.	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	intron	5678645	5678855	.	-	.	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	CDS	5678856	5678986	0.99	-	0	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	exon	5678856	5678986	.	-	.	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
Phchi.S6	AUGUSTUS	start_codon	5678984	5678986	.	-	0	transcript_id "Phchi.S6G076100.t1"; gene_id "Phchi.S6G076100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg325.t1 is derived from g10107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2273477	2274205	.	-	.	Phchi.S6G028400
Phchi.S6	AUGUSTUS	transcript	2273477	2274205	.	-	.	transcript_id "Phchi.S6G028400.t1"; gene_id "Phchi.S6G028400"
Phchi.S6	AUGUSTUS	stop_codon	2273474	2273476	.	-	0	transcript_id "Phchi.S6G028400.t1"; gene_id "Phchi.S6G028400"
Phchi.S6	AUGUSTUS	CDS	2273477	2274205	0.78	-	0	transcript_id "Phchi.S6G028400.t1"; gene_id "Phchi.S6G028400"
Phchi.S6	AUGUSTUS	exon	2273477	2274205	.	-	.	transcript_id "Phchi.S6G028400.t1"; gene_id "Phchi.S6G028400"
Phchi.S6	AUGUSTUS	start_codon	2274203	2274205	.	-	0	transcript_id "Phchi.S6G028400.t1"; gene_id "Phchi.S6G028400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8367.t1 is derived from g5542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35531878	35534444	.	+	.	Phchi.S1G552600
Phchi.S1	AUGUSTUS	transcript	35531878	35534444	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	start_codon	35531878	35531880	.	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35531878	35531986	0.98	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35531878	35531986	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35531987	35532202	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35532203	35532865	0.98	+	2	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35532203	35532865	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35532866	35533015	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35533016	35533071	0.99	+	2	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35533016	35533071	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35533072	35533186	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35533187	35533261	1	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35533187	35533261	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35533262	35533347	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35533348	35533488	1	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35533348	35533488	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35533489	35533615	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35533616	35533852	1	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35533616	35533852	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35533853	35533953	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35533954	35534067	1	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35533954	35534067	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35534068	35534160	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35534161	35534289	1	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35534161	35534289	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	intron	35534290	35534378	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	CDS	35534379	35534444	1	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	exon	35534379	35534444	.	+	.	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
Phchi.S1	AUGUSTUS	stop_codon	35534445	35534447	.	+	0	transcript_id "Phchi.S1G552600.t1"; gene_id "Phchi.S1G552600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6207.t1 is derived from g3378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21471636	21472767	.	-	.	Phchi.S1G336600
Phchi.S1	AUGUSTUS	transcript	21471636	21472767	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	stop_codon	21471633	21471635	.	-	0	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	CDS	21471636	21471764	0.76	-	0	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	exon	21471636	21471764	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	intron	21471765	21471961	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	CDS	21471962	21472035	0.72	-	2	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	exon	21471962	21472035	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	intron	21472036	21472148	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	CDS	21472149	21472218	0.48	-	0	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	exon	21472149	21472218	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	intron	21472219	21472311	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	CDS	21472312	21472364	0.97	-	2	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	exon	21472312	21472364	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	intron	21472365	21472455	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	CDS	21472456	21472535	0.94	-	1	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	exon	21472456	21472535	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	intron	21472536	21472651	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	CDS	21472652	21472767	0.66	-	0	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	exon	21472652	21472767	.	-	.	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
Phchi.S1	AUGUSTUS	start_codon	21472765	21472767	.	-	0	transcript_id "Phchi.S1G336600.t1"; gene_id "Phchi.S1G336600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1420.t1 is derived from g8339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	774237	775368	.	+	.	Phchi.S5G002900
Phchi.S5	AUGUSTUS	transcript	774237	775368	.	+	.	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	start_codon	774237	774239	.	+	0	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	CDS	774237	774803	0.7	+	0	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	exon	774237	774803	.	+	.	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	intron	774804	774909	.	+	.	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	CDS	774910	775368	1	+	0	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	exon	774910	775368	.	+	.	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
Phchi.S5	AUGUSTUS	stop_codon	775369	775371	.	+	0	transcript_id "Phchi.S5G002900.t1"; gene_id "Phchi.S5G002900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9904.t1 is derived from g7080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44379446	44382342	.	+	.	Phchi.S1G706300
Phchi.S1	AUGUSTUS	transcript	44379446	44382342	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	start_codon	44379446	44379448	.	+	0	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	CDS	44379446	44380044	0.53	+	0	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	exon	44379446	44380044	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	intron	44380045	44380149	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	CDS	44380150	44380408	0.98	+	1	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	exon	44380150	44380408	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	intron	44380409	44380502	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	CDS	44380503	44380521	0.97	+	0	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	exon	44380503	44380521	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	intron	44380522	44380604	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	CDS	44380605	44380640	0.96	+	2	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	exon	44380605	44380640	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	intron	44380641	44380739	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	CDS	44380740	44380972	1	+	2	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	exon	44380740	44380972	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	intron	44380973	44381064	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	CDS	44381065	44382342	1	+	0	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	exon	44381065	44382342	.	+	.	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
Phchi.S1	AUGUSTUS	stop_codon	44382343	44382345	.	+	0	transcript_id "Phchi.S1G706300.t1"; gene_id "Phchi.S1G706300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14028.t1 is derived from g12495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10368712	10369021	.	+	.	Phchi.S3G134700
Phchi.S3	AUGUSTUS	transcript	10368712	10369021	.	+	.	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	start_codon	10368712	10368714	.	+	0	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	CDS	10368712	10368825	0.97	+	0	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	exon	10368712	10368825	.	+	.	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	intron	10368826	10368913	.	+	.	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	CDS	10368914	10369021	1	+	0	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	exon	10368914	10369021	.	+	.	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
Phchi.S3	AUGUSTUS	stop_codon	10369022	10369024	.	+	0	transcript_id "Phchi.S3G134700.t1"; gene_id "Phchi.S3G134700"
# This transcript jg2554.t2 is derived from g9474.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2555.t1 is derived from g9475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7328801	7329427	.	-	.	Phchi.S5G116400
Phchi.S5	AUGUSTUS	transcript	7328801	7329427	.	-	.	transcript_id "Phchi.S5G116400.t1"; gene_id "Phchi.S5G116400"
Phchi.S5	AUGUSTUS	stop_codon	7328798	7328800	.	-	0	transcript_id "Phchi.S5G116400.t1"; gene_id "Phchi.S5G116400"
Phchi.S5	AUGUSTUS	CDS	7328801	7329427	0.85	-	0	transcript_id "Phchi.S5G116400.t1"; gene_id "Phchi.S5G116400"
Phchi.S5	AUGUSTUS	exon	7328801	7329427	.	-	.	transcript_id "Phchi.S5G116400.t1"; gene_id "Phchi.S5G116400"
Phchi.S5	AUGUSTUS	start_codon	7329425	7329427	.	-	0	transcript_id "Phchi.S5G116400.t1"; gene_id "Phchi.S5G116400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15290.t1 is derived from g13758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18224378	18224755	.	-	.	Phchi.S3G260900
Phchi.S3	AUGUSTUS	transcript	18224378	18224755	.	-	.	transcript_id "Phchi.S3G260900.t1"; gene_id "Phchi.S3G260900"
Phchi.S3	AUGUSTUS	stop_codon	18224375	18224377	.	-	0	transcript_id "Phchi.S3G260900.t1"; gene_id "Phchi.S3G260900"
Phchi.S3	AUGUSTUS	CDS	18224378	18224755	0.64	-	0	transcript_id "Phchi.S3G260900.t1"; gene_id "Phchi.S3G260900"
Phchi.S3	AUGUSTUS	exon	18224378	18224755	.	-	.	transcript_id "Phchi.S3G260900.t1"; gene_id "Phchi.S3G260900"
Phchi.S3	AUGUSTUS	start_codon	18224753	18224755	.	-	0	transcript_id "Phchi.S3G260900.t1"; gene_id "Phchi.S3G260900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12735.t1 is derived from g11200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1448566	1450396	.	+	.	Phchi.S3G005400
Phchi.S3	AUGUSTUS	transcript	1448566	1450396	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	start_codon	1448566	1448568	.	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1448566	1448937	0.87	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1448566	1448937	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1448938	1449012	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1449013	1449132	0.99	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1449013	1449132	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1449133	1449234	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1449235	1449329	0.98	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1449235	1449329	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1449330	1449435	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1449436	1449520	1	+	1	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1449436	1449520	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1449521	1449608	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1449609	1449800	0.99	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1449609	1449800	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1449801	1449901	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1449902	1450006	1	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1449902	1450006	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1450007	1450092	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1450093	1450143	1	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1450093	1450143	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	intron	1450144	1450222	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	CDS	1450223	1450396	1	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	exon	1450223	1450396	.	+	.	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
Phchi.S3	AUGUSTUS	stop_codon	1450397	1450399	.	+	0	transcript_id "Phchi.S3G005400.t1"; gene_id "Phchi.S3G005400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9782.t1 is derived from g6958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43654105	43656618	.	-	.	Phchi.S1G694100
Phchi.S1	AUGUSTUS	transcript	43654105	43656618	.	-	.	transcript_id "Phchi.S1G694100.t1"; gene_id "Phchi.S1G694100"
Phchi.S1	AUGUSTUS	stop_codon	43654102	43654104	.	-	0	transcript_id "Phchi.S1G694100.t1"; gene_id "Phchi.S1G694100"
Phchi.S1	AUGUSTUS	CDS	43654105	43656618	0.97	-	0	transcript_id "Phchi.S1G694100.t1"; gene_id "Phchi.S1G694100"
Phchi.S1	AUGUSTUS	exon	43654105	43656618	.	-	.	transcript_id "Phchi.S1G694100.t1"; gene_id "Phchi.S1G694100"
Phchi.S1	AUGUSTUS	start_codon	43656616	43656618	.	-	0	transcript_id "Phchi.S1G694100.t1"; gene_id "Phchi.S1G694100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15476.t1 is derived from g13944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19369764	19371453	.	+	.	Phchi.S3G279500
Phchi.S3	AUGUSTUS	transcript	19369764	19371453	.	+	.	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	start_codon	19369764	19369766	.	+	0	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	CDS	19369764	19370741	0.75	+	0	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	exon	19369764	19370741	.	+	.	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	intron	19370742	19370831	.	+	.	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	CDS	19370832	19371097	1	+	0	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	exon	19370832	19371097	.	+	.	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	intron	19371098	19371191	.	+	.	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	CDS	19371192	19371453	1	+	1	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	exon	19371192	19371453	.	+	.	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
Phchi.S3	AUGUSTUS	stop_codon	19371454	19371456	.	+	0	transcript_id "Phchi.S3G279500.t1"; gene_id "Phchi.S3G279500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9161.t1 is derived from g6336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40150589	40152171	.	+	.	Phchi.S1G632000
Phchi.S1	AUGUSTUS	transcript	40150589	40152171	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	start_codon	40150589	40150591	.	+	0	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	CDS	40150589	40150825	0.71	+	0	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	exon	40150589	40150825	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	intron	40150826	40151022	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	CDS	40151023	40151490	1	+	0	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	exon	40151023	40151490	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	intron	40151491	40151588	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	CDS	40151589	40151924	1	+	0	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	exon	40151589	40151924	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	intron	40151925	40152045	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	CDS	40152046	40152171	1	+	0	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	exon	40152046	40152171	.	+	.	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
Phchi.S1	AUGUSTUS	stop_codon	40152172	40152174	.	+	0	transcript_id "Phchi.S1G632000.t1"; gene_id "Phchi.S1G632000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9796.t1 is derived from g6972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43734853	43735422	.	-	.	Phchi.S1G695500
Phchi.S1	AUGUSTUS	transcript	43734853	43735422	.	-	.	transcript_id "Phchi.S1G695500.t1"; gene_id "Phchi.S1G695500"
Phchi.S1	AUGUSTUS	stop_codon	43734850	43734852	.	-	0	transcript_id "Phchi.S1G695500.t1"; gene_id "Phchi.S1G695500"
Phchi.S1	AUGUSTUS	CDS	43734853	43735422	0.43	-	0	transcript_id "Phchi.S1G695500.t1"; gene_id "Phchi.S1G695500"
Phchi.S1	AUGUSTUS	exon	43734853	43735422	.	-	.	transcript_id "Phchi.S1G695500.t1"; gene_id "Phchi.S1G695500"
Phchi.S1	AUGUSTUS	start_codon	43735420	43735422	.	-	0	transcript_id "Phchi.S1G695500.t1"; gene_id "Phchi.S1G695500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14328.t1 is derived from g12795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12108579	12109490	.	-	.	Phchi.S3G164700
Phchi.S3	AUGUSTUS	transcript	12108579	12109490	.	-	.	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	stop_codon	12108576	12108578	.	-	0	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	CDS	12108579	12108692	0.7	-	0	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	exon	12108579	12108692	.	-	.	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	intron	12108693	12108784	.	-	.	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	CDS	12108785	12108853	0.97	-	0	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	exon	12108785	12108853	.	-	.	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	intron	12108854	12109235	.	-	.	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	CDS	12109236	12109490	0.89	-	0	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	exon	12109236	12109490	.	-	.	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
Phchi.S3	AUGUSTUS	start_codon	12109488	12109490	.	-	0	transcript_id "Phchi.S3G164700.t1"; gene_id "Phchi.S3G164700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4089.t1 is derived from g1258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7751353	7752442	.	+	.	Phchi.S1G124800
Phchi.S1	AUGUSTUS	transcript	7751353	7752442	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	start_codon	7751353	7751355	.	+	0	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	CDS	7751353	7751759	0.36	+	0	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	exon	7751353	7751759	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	intron	7751760	7751872	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	CDS	7751873	7752044	1	+	1	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	exon	7751873	7752044	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	intron	7752045	7752138	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	CDS	7752139	7752255	1	+	0	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	exon	7752139	7752255	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	intron	7752256	7752340	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	CDS	7752341	7752442	1	+	0	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	exon	7752341	7752442	.	+	.	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
Phchi.S1	AUGUSTUS	stop_codon	7752443	7752445	.	+	0	transcript_id "Phchi.S1G124800.t1"; gene_id "Phchi.S1G124800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14231.t1 is derived from g12698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11670669	11674097	.	-	.	Phchi.S3G155000
Phchi.S3	AUGUSTUS	transcript	11670669	11674097	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	stop_codon	11670666	11670668	.	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	CDS	11670669	11671630	1	-	2	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	exon	11670669	11671630	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	intron	11671631	11671723	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	CDS	11671724	11671913	1	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	exon	11671724	11671913	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	intron	11671914	11672147	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	CDS	11672148	11672396	0.94	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	exon	11672148	11672396	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	intron	11672397	11672548	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	CDS	11672549	11672602	0.41	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	exon	11672549	11672602	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	intron	11672603	11672693	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	CDS	11672694	11673569	0.92	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	exon	11672694	11673569	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	intron	11673570	11673701	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	CDS	11673702	11674097	0.76	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	exon	11673702	11674097	.	-	.	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
Phchi.S3	AUGUSTUS	start_codon	11674095	11674097	.	-	0	transcript_id "Phchi.S3G155000.t1"; gene_id "Phchi.S3G155000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14986.t1 is derived from g13454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15898566	15898796	.	+	.	Phchi.S3G230500
Phchi.S3	AUGUSTUS	transcript	15898566	15898796	.	+	.	transcript_id "Phchi.S3G230500.t1"; gene_id "Phchi.S3G230500"
Phchi.S3	AUGUSTUS	start_codon	15898566	15898568	.	+	0	transcript_id "Phchi.S3G230500.t1"; gene_id "Phchi.S3G230500"
Phchi.S3	AUGUSTUS	CDS	15898566	15898796	0.4	+	0	transcript_id "Phchi.S3G230500.t1"; gene_id "Phchi.S3G230500"
Phchi.S3	AUGUSTUS	exon	15898566	15898796	.	+	.	transcript_id "Phchi.S3G230500.t1"; gene_id "Phchi.S3G230500"
Phchi.S3	AUGUSTUS	stop_codon	15898797	15898799	.	+	0	transcript_id "Phchi.S3G230500.t1"; gene_id "Phchi.S3G230500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7891.t1 is derived from g5065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31775505	31776855	.	-	.	Phchi.S1G505000
Phchi.S1	AUGUSTUS	transcript	31775505	31776855	.	-	.	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	stop_codon	31775502	31775504	.	-	0	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	CDS	31775505	31775573	1	-	0	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	exon	31775505	31775573	.	-	.	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	intron	31775574	31775657	.	-	.	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	CDS	31775658	31775975	0.46	-	0	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	exon	31775658	31775975	.	-	.	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	intron	31775976	31776381	.	-	.	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	CDS	31776382	31776855	0.84	-	0	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	exon	31776382	31776855	.	-	.	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
Phchi.S1	AUGUSTUS	start_codon	31776853	31776855	.	-	0	transcript_id "Phchi.S1G505000.t1"; gene_id "Phchi.S1G505000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4874.t1 is derived from g2044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13182364	13184867	.	-	.	Phchi.S1G203300
Phchi.S1	AUGUSTUS	transcript	13182364	13184867	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	stop_codon	13182361	13182363	.	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13182364	13182774	0.98	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13182364	13182774	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13182775	13182870	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13182871	13182990	1	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13182871	13182990	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13182991	13183069	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13183070	13183188	1	-	2	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13183070	13183188	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13183189	13183281	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13183282	13183390	1	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13183282	13183390	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13183391	13183488	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13183489	13183527	1	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13183489	13183527	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13183528	13183658	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13183659	13183737	1	-	1	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13183659	13183737	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13183738	13183827	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13183828	13183902	1	-	1	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13183828	13183902	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13183903	13184057	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13184058	13184122	0.97	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13184058	13184122	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13184123	13184225	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13184226	13184281	1	-	2	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13184226	13184281	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13184282	13184381	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13184382	13184474	1	-	2	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13184382	13184474	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	intron	13184475	13184557	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	CDS	13184558	13184867	0.69	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	exon	13184558	13184867	.	-	.	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
Phchi.S1	AUGUSTUS	start_codon	13184865	13184867	.	-	0	transcript_id "Phchi.S1G203300.t1"; gene_id "Phchi.S1G203300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5394.t1 is derived from g2564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16656454	16660445	.	+	.	Phchi.S1G255300
Phchi.S1	AUGUSTUS	transcript	16656454	16660445	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	start_codon	16656454	16656456	.	+	0	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16656454	16656552	1	+	0	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16656454	16656552	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16656553	16656690	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16656691	16656782	1	+	0	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16656691	16656782	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16656783	16656939	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16656940	16657037	1	+	1	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16656940	16657037	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16657038	16657168	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16657169	16657339	0.99	+	2	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16657169	16657339	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16657340	16657485	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16657486	16657597	1	+	2	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16657486	16657597	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16657598	16657732	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16657733	16657914	0.99	+	1	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16657733	16657914	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16657915	16658000	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16658001	16658356	1	+	2	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16658001	16658356	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16658357	16658488	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16658489	16658586	1	+	0	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16658489	16658586	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16658587	16658732	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16658733	16658972	1	+	1	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16658733	16658972	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16658973	16659166	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16659167	16659281	0.76	+	1	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16659167	16659281	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16659282	16659388	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16659389	16659578	1	+	0	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16659389	16659578	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16659579	16659719	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16659720	16659929	1	+	2	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16659720	16659929	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	intron	16659930	16660071	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	CDS	16660072	16660445	1	+	2	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	exon	16660072	16660445	.	+	.	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
Phchi.S1	AUGUSTUS	stop_codon	16660446	16660448	.	+	0	transcript_id "Phchi.S1G255300.t1"; gene_id "Phchi.S1G255300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2095.t1 is derived from g9015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4843597	4845836	.	-	.	Phchi.S5G070400
Phchi.S5	AUGUSTUS	transcript	4843597	4845836	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	stop_codon	4843594	4843596	.	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4843597	4843729	1	-	1	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4843597	4843729	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4843730	4843824	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4843825	4843943	0.99	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4843825	4843943	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4843944	4844044	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4844045	4844151	0.99	-	2	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4844045	4844151	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4844152	4844239	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4844240	4844318	1	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4844240	4844318	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4844319	4844415	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4844416	4844505	1	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4844416	4844505	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4844506	4844595	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4844596	4844844	1	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4844596	4844844	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4844845	4844917	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4844918	4845070	1	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4844918	4845070	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4845071	4845165	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4845166	4845490	1	-	1	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4845166	4845490	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	intron	4845491	4845639	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	CDS	4845640	4845836	1	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	exon	4845640	4845836	.	-	.	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
Phchi.S5	AUGUSTUS	start_codon	4845834	4845836	.	-	0	transcript_id "Phchi.S5G070400.t1"; gene_id "Phchi.S5G070400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14596.t1 is derived from g13064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13651638	13655897	.	+	.	Phchi.S3G191500
Phchi.S3	AUGUSTUS	transcript	13651638	13655897	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	start_codon	13651638	13651640	.	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13651638	13651724	0.97	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13651638	13651724	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13651725	13651805	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13651806	13651984	1	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13651806	13651984	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13651985	13652065	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13652066	13652128	1	+	1	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13652066	13652128	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13652129	13652215	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13652216	13652345	1	+	1	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13652216	13652345	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13652346	13652428	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13652429	13652516	0.99	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13652429	13652516	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13652517	13652619	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13652620	13652762	1	+	2	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13652620	13652762	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13652763	13652852	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13652853	13652940	1	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13652853	13652940	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13652941	13653019	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13653020	13653132	1	+	2	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13653020	13653132	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13653133	13653224	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13653225	13653417	1	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13653225	13653417	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13653418	13653500	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13653501	13653604	1	+	2	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13653501	13653604	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13653605	13653695	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13653696	13653803	1	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13653696	13653803	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13653804	13653898	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13653899	13654069	1	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13653899	13654069	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13654070	13654162	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13654163	13654305	1	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13654163	13654305	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13654306	13654397	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13654398	13654569	1	+	1	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13654398	13654569	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13654570	13654653	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13654654	13654830	0.67	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13654654	13654830	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13654831	13655193	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13655194	13655260	0.85	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13655194	13655260	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13655261	13655353	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13655354	13655452	1	+	2	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13655354	13655452	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13655453	13655624	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13655625	13655784	1	+	2	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13655625	13655784	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	intron	13655785	13655872	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	CDS	13655873	13655897	0.86	+	1	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	exon	13655873	13655897	.	+	.	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
Phchi.S3	AUGUSTUS	stop_codon	13655898	13655900	.	+	0	transcript_id "Phchi.S3G191500.t1"; gene_id "Phchi.S3G191500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4778.t1 is derived from g1948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12778312	12778782	.	-	.	Phchi.S1G193700
Phchi.S1	AUGUSTUS	transcript	12778312	12778782	.	-	.	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	stop_codon	12778309	12778311	.	-	0	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	CDS	12778312	12778482	0.95	-	0	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	exon	12778312	12778482	.	-	.	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	intron	12778483	12778620	.	-	.	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	CDS	12778621	12778782	0.99	-	0	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	exon	12778621	12778782	.	-	.	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
Phchi.S1	AUGUSTUS	start_codon	12778780	12778782	.	-	0	transcript_id "Phchi.S1G193700.t1"; gene_id "Phchi.S1G193700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2441.t1 is derived from g9361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6644917	6646434	.	-	.	Phchi.S5G105000
Phchi.S5	AUGUSTUS	transcript	6644917	6646434	.	-	.	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	stop_codon	6644914	6644916	.	-	0	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	CDS	6644917	6645196	0.3	-	1	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	exon	6644917	6645196	.	-	.	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	intron	6645197	6645520	.	-	.	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	CDS	6645521	6646434	0.91	-	0	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	exon	6645521	6646434	.	-	.	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
Phchi.S5	AUGUSTUS	start_codon	6646432	6646434	.	-	0	transcript_id "Phchi.S5G105000.t1"; gene_id "Phchi.S5G105000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11273.t1 is derived from g15323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5135961	5137891	.	+	.	Phchi.S4G085500
Phchi.S4	AUGUSTUS	transcript	5135961	5137891	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	start_codon	5135961	5135963	.	+	0	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5135961	5135973	0.99	+	0	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5135961	5135973	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	intron	5135974	5136044	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5136045	5136115	0.99	+	2	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5136045	5136115	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	intron	5136116	5136212	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5136213	5136304	1	+	0	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5136213	5136304	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	intron	5136305	5136448	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5136449	5136476	0.47	+	1	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5136449	5136476	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	intron	5136477	5136596	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5136597	5136657	0.23	+	0	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5136597	5136657	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	intron	5136658	5136891	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5136892	5137767	0.33	+	2	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5136892	5137767	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	intron	5137768	5137874	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	CDS	5137875	5137891	0.53	+	2	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	exon	5137875	5137891	.	+	.	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
Phchi.S4	AUGUSTUS	stop_codon	5137892	5137894	.	+	0	transcript_id "Phchi.S4G085500.t1"; gene_id "Phchi.S4G085500"
# This transcript jg8565.t2 is derived from g5740.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8566.t1 is derived from g5741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36638173	36640040	.	+	.	Phchi.S1G572500
Phchi.S1	AUGUSTUS	transcript	36638173	36640040	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	start_codon	36638173	36638175	.	+	0	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36638173	36638268	0.81	+	0	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36638173	36638268	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36638269	36638341	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36638342	36638443	0.91	+	0	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36638342	36638443	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36638444	36638547	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36638548	36638698	0.91	+	0	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36638548	36638698	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36638699	36638829	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36638830	36638912	1	+	2	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36638830	36638912	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36638913	36639034	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36639035	36639092	1	+	0	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36639035	36639092	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36639093	36639232	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36639233	36639334	1	+	2	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36639233	36639334	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36639335	36639421	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36639422	36639593	1	+	2	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36639422	36639593	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36639594	36639681	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36639682	36639752	0.98	+	1	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36639682	36639752	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	intron	36639753	36639858	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	CDS	36639859	36640040	0.63	+	2	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	exon	36639859	36640040	.	+	.	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
Phchi.S1	AUGUSTUS	stop_codon	36640041	36640043	.	+	0	transcript_id "Phchi.S1G572500.t1"; gene_id "Phchi.S1G572500"
# This transcript jg4092.t2 is derived from g1261.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4093.t1 is derived from g1262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7790108	7790710	.	+	.	Phchi.S1G125200
Phchi.S1	AUGUSTUS	transcript	7790108	7790710	.	+	.	transcript_id "Phchi.S1G125200.t1"; gene_id "Phchi.S1G125200"
Phchi.S1	AUGUSTUS	start_codon	7790108	7790110	.	+	0	transcript_id "Phchi.S1G125200.t1"; gene_id "Phchi.S1G125200"
Phchi.S1	AUGUSTUS	CDS	7790108	7790710	0.72	+	0	transcript_id "Phchi.S1G125200.t1"; gene_id "Phchi.S1G125200"
Phchi.S1	AUGUSTUS	exon	7790108	7790710	.	+	.	transcript_id "Phchi.S1G125200.t1"; gene_id "Phchi.S1G125200"
Phchi.S1	AUGUSTUS	stop_codon	7790711	7790713	.	+	0	transcript_id "Phchi.S1G125200.t1"; gene_id "Phchi.S1G125200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10289.t1 is derived from g7465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46831065	46836240	.	-	.	Phchi.S1G744800
Phchi.S1	AUGUSTUS	transcript	46831065	46836240	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	stop_codon	46831062	46831064	.	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46831065	46831347	0.67	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46831065	46831347	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46831348	46831436	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46831437	46832064	0.78	-	2	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46831437	46832064	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46832065	46832249	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46832250	46832830	0.85	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46832250	46832830	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46832831	46832904	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46832905	46832993	0.87	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46832905	46832993	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46832994	46833088	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46833089	46833149	1	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46833089	46833149	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46833150	46833374	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46833375	46833447	0.92	-	2	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46833375	46833447	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46833448	46833553	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46833554	46833621	1	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46833554	46833621	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46833622	46833714	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46833715	46833899	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46833715	46833899	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46833900	46833998	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46833999	46834140	1	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46833999	46834140	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46834141	46834355	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46834356	46834394	1	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46834356	46834394	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46834395	46834509	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46834510	46834565	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46834510	46834565	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46834566	46834651	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46834652	46834705	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46834652	46834705	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46834706	46834782	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46834783	46834886	1	-	2	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46834783	46834886	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46834887	46835001	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46835002	46835105	0.85	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46835002	46835105	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46835106	46835210	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46835211	46835293	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46835211	46835293	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46835294	46835415	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46835416	46835515	0.87	-	1	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46835416	46835515	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46835516	46835629	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46835630	46835700	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46835630	46835700	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46835701	46835786	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46835787	46835843	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46835787	46835843	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46835844	46835936	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46835937	46836047	1	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46835937	46836047	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	intron	46836048	46836159	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	CDS	46836160	46836240	0.6	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	exon	46836160	46836240	.	-	.	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
Phchi.S1	AUGUSTUS	start_codon	46836238	46836240	.	-	0	transcript_id "Phchi.S1G744800.t1"; gene_id "Phchi.S1G744800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15832.t1 is derived from g14302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21652284	21654152	.	+	.	Phchi.S3G315100
Phchi.S3	AUGUSTUS	transcript	21652284	21654152	.	+	.	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	start_codon	21652284	21652286	.	+	0	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	CDS	21652284	21653081	0.48	+	0	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	exon	21652284	21653081	.	+	.	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	intron	21653082	21653205	.	+	.	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	CDS	21653206	21653589	0.81	+	0	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	exon	21653206	21653589	.	+	.	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	intron	21653590	21653651	.	+	.	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	CDS	21653652	21654152	0.8	+	0	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	exon	21653652	21654152	.	+	.	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
Phchi.S3	AUGUSTUS	stop_codon	21654153	21654155	.	+	0	transcript_id "Phchi.S3G315100.t1"; gene_id "Phchi.S3G315100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13563.t1 is derived from g12030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7512477	7515132	.	-	.	Phchi.S3G088200
Phchi.S3	AUGUSTUS	transcript	7512477	7515132	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	stop_codon	7512474	7512476	.	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7512477	7512483	1	-	1	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7512477	7512483	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7512484	7512637	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7512638	7512801	1	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7512638	7512801	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7512802	7512883	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7512884	7513072	1	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7512884	7513072	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7513073	7513158	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7513159	7513276	1	-	1	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7513159	7513276	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7513277	7513366	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7513367	7513455	1	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7513367	7513455	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7513456	7513544	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7513545	7514106	1	-	1	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7513545	7514106	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7514107	7514271	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7514272	7514435	1	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7514272	7514435	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	intron	7514436	7514703	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	CDS	7514704	7515132	1	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	exon	7514704	7515132	.	-	.	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
Phchi.S3	AUGUSTUS	start_codon	7515130	7515132	.	-	0	transcript_id "Phchi.S3G088200.t1"; gene_id "Phchi.S3G088200"
# This transcript jg4900.t2 is derived from g2070.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4900.t3 is derived from g2070.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4901.t1 is derived from g2071.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13325508	13327730	.	+	.	Phchi.S1G206000
Phchi.S1	AUGUSTUS	transcript	13325508	13327730	.	+	.	transcript_id "Phchi.S1G206000.t1"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	start_codon	13325508	13325510	.	+	0	transcript_id "Phchi.S1G206000.t1"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	CDS	13325508	13327730	1	+	0	transcript_id "Phchi.S1G206000.t1"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	exon	13325508	13327730	.	+	.	transcript_id "Phchi.S1G206000.t1"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	stop_codon	13327731	13327733	.	+	0	transcript_id "Phchi.S1G206000.t1"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	transcript	13326714	13327730	.	+	.	transcript_id "Phchi.S1G206000.t2"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	start_codon	13326714	13326716	.	+	0	transcript_id "Phchi.S1G206000.t2"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	CDS	13326714	13327730	1	+	0	transcript_id "Phchi.S1G206000.t2"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	exon	13326714	13327730	.	+	.	transcript_id "Phchi.S1G206000.t2"; gene_id "Phchi.S1G206000"
Phchi.S1	AUGUSTUS	stop_codon	13327731	13327733	.	+	0	transcript_id "Phchi.S1G206000.t2"; gene_id "Phchi.S1G206000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6167.t1 is derived from g3338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21272625	21274385	.	-	.	Phchi.S1G332600
Phchi.S1	AUGUSTUS	transcript	21272625	21274385	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	stop_codon	21272622	21272624	.	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	CDS	21272625	21272672	0.53	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	exon	21272625	21272672	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	intron	21272673	21272783	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	CDS	21272784	21272840	0.53	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	exon	21272784	21272840	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	intron	21272841	21272931	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	CDS	21272932	21273165	0.7	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	exon	21272932	21273165	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	intron	21273166	21273292	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	CDS	21273293	21273486	1	-	2	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	exon	21273293	21273486	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	intron	21273487	21273716	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	CDS	21273717	21273834	1	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	exon	21273717	21273834	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	intron	21273835	21274193	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	CDS	21274194	21274385	1	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	exon	21274194	21274385	.	-	.	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
Phchi.S1	AUGUSTUS	start_codon	21274383	21274385	.	-	0	transcript_id "Phchi.S1G332600.t1"; gene_id "Phchi.S1G332600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13717.t1 is derived from g12184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8494738	8496329	.	+	.	Phchi.S3G103600
Phchi.S3	AUGUSTUS	transcript	8494738	8496329	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	start_codon	8494738	8494740	.	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8494738	8494800	1	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8494738	8494800	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8494801	8494943	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8494944	8495020	1	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8494944	8495020	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8495021	8495094	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8495095	8495182	0.86	+	1	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8495095	8495182	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8495183	8495306	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8495307	8495405	0.99	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8495307	8495405	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8495406	8495554	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8495555	8495572	0.97	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8495555	8495572	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8495573	8495686	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8495687	8495757	0.98	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8495687	8495757	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8495758	8495849	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8495850	8495976	1	+	1	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8495850	8495976	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8495977	8496074	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8496075	8496135	1	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8496075	8496135	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	intron	8496136	8496234	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	CDS	8496235	8496329	0.97	+	2	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	exon	8496235	8496329	.	+	.	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
Phchi.S3	AUGUSTUS	stop_codon	8496330	8496332	.	+	0	transcript_id "Phchi.S3G103600.t1"; gene_id "Phchi.S3G103600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15409.t1 is derived from g13877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18864538	18867228	.	-	.	Phchi.S3G272800
Phchi.S3	AUGUSTUS	transcript	18864538	18867228	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	stop_codon	18864535	18864537	.	-	0	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	CDS	18864538	18864576	0.95	-	0	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	exon	18864538	18864576	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	intron	18864577	18864669	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	CDS	18864670	18864725	0.87	-	2	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	exon	18864670	18864725	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	intron	18864726	18864906	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	CDS	18864907	18864971	0.94	-	1	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	exon	18864907	18864971	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	intron	18864972	18865082	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	CDS	18865083	18865413	0.37	-	2	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	exon	18865083	18865413	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	intron	18865414	18865521	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	CDS	18865522	18865680	0.26	-	2	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	exon	18865522	18865680	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	intron	18865681	18865865	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	CDS	18865866	18867228	0.22	-	0	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	exon	18865866	18867228	.	-	.	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
Phchi.S3	AUGUSTUS	start_codon	18867226	18867228	.	-	0	transcript_id "Phchi.S3G272800.t1"; gene_id "Phchi.S3G272800"
# This transcript jg12560.t2 is derived from g8237.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12560.t3 is derived from g8237.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12561.t1 is derived from g8238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34767281	34769579	.	+	.	Phchi.S2G064100
Phchi.S2	AUGUSTUS	transcript	34767281	34769579	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	start_codon	34767281	34767283	.	+	0	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34767281	34767319	0.55	+	0	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34767281	34767319	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34767320	34767447	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34767448	34767500	0.53	+	0	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34767448	34767500	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34767501	34767582	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34767583	34767922	0.96	+	1	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34767583	34767922	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34767923	34768020	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34768021	34768141	1	+	0	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34768021	34768141	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34768142	34768324	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34768325	34768499	1	+	2	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34768325	34768499	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34768500	34768597	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34768598	34768668	1	+	1	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34768598	34768668	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34768669	34768739	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34768740	34768930	0.69	+	2	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34768740	34768930	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34768931	34769007	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34769008	34769089	0.69	+	0	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34769008	34769089	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34769090	34769184	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34769185	34769382	0.78	+	2	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34769185	34769382	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	intron	34769383	34769478	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	CDS	34769479	34769579	0.57	+	2	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	exon	34769479	34769579	.	+	.	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
Phchi.S2	AUGUSTUS	stop_codon	34769580	34769582	.	+	0	transcript_id "Phchi.S2G064100.t1"; gene_id "Phchi.S2G064100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12700.t1 is derived from g11165.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	628148	629485	.	+	.	Phchi.S3G001900
Phchi.S3	AUGUSTUS	transcript	628148	629207	.	+	.	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	start_codon	628148	628150	.	+	0	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	CDS	628148	629111	0.87	+	0	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	exon	628148	629111	.	+	.	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	intron	629112	629199	.	+	.	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	CDS	629200	629207	0.99	+	2	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	exon	629200	629207	.	+	.	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	stop_codon	629208	629210	.	+	0	transcript_id "Phchi.S3G001900.t1"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	transcript	628148	629399	.	+	.	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	start_codon	628148	628150	.	+	0	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	CDS	628148	629329	0.62	+	0	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	exon	628148	629329	.	+	.	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	intron	629330	629396	.	+	.	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	CDS	629397	629399	0.9	+	0	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	exon	629397	629399	.	+	.	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	stop_codon	629400	629402	.	+	0	transcript_id "Phchi.S3G001900.t2"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	transcript	628148	629485	.	+	.	transcript_id "Phchi.S3G001900.t3"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	start_codon	628148	628150	.	+	0	transcript_id "Phchi.S3G001900.t3"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	CDS	628148	629485	1	+	0	transcript_id "Phchi.S3G001900.t3"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	exon	628148	629485	.	+	.	transcript_id "Phchi.S3G001900.t3"; gene_id "Phchi.S3G001900"
Phchi.S3	AUGUSTUS	stop_codon	629486	629488	.	+	0	transcript_id "Phchi.S3G001900.t3"; gene_id "Phchi.S3G001900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1428.t1 is derived from g8347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	798803	800609	.	+	.	Phchi.S5G003700
Phchi.S5	AUGUSTUS	transcript	798803	800609	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	start_codon	798803	798805	.	+	0	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	798803	799049	1	+	0	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	798803	799049	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	799050	799231	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	799232	799351	1	+	2	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	799232	799351	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	799352	799449	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	799450	799670	1	+	2	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	799450	799670	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	799671	799752	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	799753	799911	1	+	0	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	799753	799911	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	799912	800038	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	800039	800069	1	+	0	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	800039	800069	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	800070	800168	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	800169	800304	1	+	2	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	800169	800304	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	800305	800378	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	800379	800462	1	+	1	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	800379	800462	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	intron	800463	800545	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	CDS	800546	800609	1	+	1	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	exon	800546	800609	.	+	.	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
Phchi.S5	AUGUSTUS	stop_codon	800610	800612	.	+	0	transcript_id "Phchi.S5G003700.t1"; gene_id "Phchi.S5G003700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12473.t1 is derived from g8150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	26444198	26445664	.	-	.	Phchi.S2G055300
Phchi.S2	AUGUSTUS	transcript	26444198	26445664	.	-	.	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	stop_codon	26444195	26444197	.	-	0	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	CDS	26444198	26444675	1	-	1	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	exon	26444198	26444675	.	-	.	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	intron	26444676	26444798	.	-	.	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	CDS	26444799	26445168	1	-	2	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	exon	26444799	26445168	.	-	.	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	intron	26445169	26445315	.	-	.	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	CDS	26445316	26445664	1	-	0	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	exon	26445316	26445664	.	-	.	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
Phchi.S2	AUGUSTUS	start_codon	26445662	26445664	.	-	0	transcript_id "Phchi.S2G055300.t1"; gene_id "Phchi.S2G055300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13552.t1 is derived from g12019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7469056	7471258	.	+	.	Phchi.S3G087100
Phchi.S3	AUGUSTUS	transcript	7469056	7471258	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	start_codon	7469056	7469058	.	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7469056	7469136	0.99	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7469056	7469136	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7469137	7469237	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7469238	7469360	0.94	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7469238	7469360	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7469361	7469462	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7469463	7469502	0.95	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7469463	7469502	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7469503	7469632	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7469633	7469706	1	+	2	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7469633	7469706	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7469707	7469826	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7469827	7469886	1	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7469827	7469886	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7469887	7470021	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7470022	7470099	1	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7470022	7470099	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7470100	7470207	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7470208	7470366	1	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7470208	7470366	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7470367	7470456	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7470457	7470582	1	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7470457	7470582	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7470583	7470662	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7470663	7470755	1	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7470663	7470755	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7470756	7470847	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7470848	7470934	1	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7470848	7470934	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	intron	7470935	7471021	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	CDS	7471022	7471258	0.93	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	exon	7471022	7471258	.	+	.	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
Phchi.S3	AUGUSTUS	stop_codon	7471259	7471261	.	+	0	transcript_id "Phchi.S3G087100.t1"; gene_id "Phchi.S3G087100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6034.t1 is derived from g3205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20524724	20525038	.	+	.	Phchi.S1G319300
Phchi.S1	AUGUSTUS	transcript	20524724	20525038	.	+	.	transcript_id "Phchi.S1G319300.t1"; gene_id "Phchi.S1G319300"
Phchi.S1	AUGUSTUS	start_codon	20524724	20524726	.	+	0	transcript_id "Phchi.S1G319300.t1"; gene_id "Phchi.S1G319300"
Phchi.S1	AUGUSTUS	CDS	20524724	20525038	0.58	+	0	transcript_id "Phchi.S1G319300.t1"; gene_id "Phchi.S1G319300"
Phchi.S1	AUGUSTUS	exon	20524724	20525038	.	+	.	transcript_id "Phchi.S1G319300.t1"; gene_id "Phchi.S1G319300"
Phchi.S1	AUGUSTUS	stop_codon	20525039	20525041	.	+	0	transcript_id "Phchi.S1G319300.t1"; gene_id "Phchi.S1G319300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7127.t1 is derived from g4299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27090445	27093078	.	+	.	Phchi.S1G428600
Phchi.S1	AUGUSTUS	transcript	27090445	27093078	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	start_codon	27090445	27090447	.	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27090445	27090610	0.39	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27090445	27090610	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27090611	27090706	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27090707	27090814	1	+	2	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27090707	27090814	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27090815	27090962	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27090963	27090970	1	+	2	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27090963	27090970	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27090971	27091112	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091113	27091196	1	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091113	27091196	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091197	27091347	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091348	27091488	1	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091348	27091488	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091489	27091570	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091571	27091605	1	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091571	27091605	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091606	27091723	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091724	27091807	0.99	+	1	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091724	27091807	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091808	27091917	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091918	27092006	1	+	1	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091918	27092006	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092007	27092164	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092165	27092317	1	+	2	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092165	27092317	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092318	27092444	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092445	27092545	0.7	+	2	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092445	27092545	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092546	27092646	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092647	27092747	0.86	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092647	27092747	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092748	27092840	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092841	27092990	0.91	+	1	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092841	27092990	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092991	27093068	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27093069	27093078	0.91	+	1	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27093069	27093078	.	+	.	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	stop_codon	27093079	27093081	.	+	0	transcript_id "Phchi.S1G428600.t1"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	transcript	27090445	27093078	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	start_codon	27090445	27090447	.	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27090445	27090610	0.39	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27090445	27090610	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27090611	27090706	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27090707	27090814	0.69	+	2	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27090707	27090814	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27090815	27091001	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091002	27091036	0.6	+	2	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091002	27091036	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091037	27091112	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091113	27091196	0.7	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091113	27091196	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091197	27091347	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091348	27091488	1	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091348	27091488	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091489	27091570	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091571	27091605	1	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091571	27091605	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091606	27091723	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091724	27091807	1	+	1	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091724	27091807	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27091808	27091917	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27091918	27092006	1	+	1	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27091918	27092006	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092007	27092164	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092165	27092317	1	+	2	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092165	27092317	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092318	27092444	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092445	27092545	0.71	+	2	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092445	27092545	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092546	27092646	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092647	27092747	0.76	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092647	27092747	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092748	27092840	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27092841	27092990	0.78	+	1	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27092841	27092990	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	intron	27092991	27093068	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	CDS	27093069	27093078	0.78	+	1	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	exon	27093069	27093078	.	+	.	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
Phchi.S1	AUGUSTUS	stop_codon	27093079	27093081	.	+	0	transcript_id "Phchi.S1G428600.t2"; gene_id "Phchi.S1G428600"
# This transcript jg3967.t2 is derived from g1136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3968.t1 is derived from g1137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6790734	6793676	.	-	.	Phchi.S1G112700
Phchi.S1	AUGUSTUS	transcript	6790734	6793676	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	stop_codon	6790731	6790733	.	-	0	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	CDS	6790734	6790901	0.99	-	0	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	exon	6790734	6790901	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	intron	6790902	6790995	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	CDS	6790996	6791508	1	-	0	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	exon	6790996	6791508	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	intron	6791509	6791633	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	CDS	6791634	6793045	1	-	2	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	exon	6791634	6793045	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	intron	6793046	6793135	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	CDS	6793136	6793314	0.89	-	1	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	exon	6793136	6793314	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	intron	6793315	6793398	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	CDS	6793399	6793406	1	-	0	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	exon	6793399	6793406	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	intron	6793407	6793622	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	CDS	6793623	6793676	0.53	-	0	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	exon	6793623	6793676	.	-	.	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
Phchi.S1	AUGUSTUS	start_codon	6793674	6793676	.	-	0	transcript_id "Phchi.S1G112700.t1"; gene_id "Phchi.S1G112700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8792.t1 is derived from g5967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37974416	37976449	.	+	.	Phchi.S1G595100
Phchi.S1	AUGUSTUS	transcript	37974416	37976449	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	start_codon	37974416	37974418	.	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37974416	37974937	0.99	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37974416	37974937	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	intron	37974938	37975068	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37975069	37975185	1	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37975069	37975185	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	intron	37975186	37975289	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37975290	37975468	1	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37975290	37975468	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	intron	37975469	37975580	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37975581	37975674	1	+	1	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37975581	37975674	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	intron	37975675	37975782	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37975783	37975860	1	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37975783	37975860	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	intron	37975861	37975964	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37975965	37976066	1	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37975965	37976066	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	intron	37976067	37976299	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	CDS	37976300	37976449	0.96	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	exon	37976300	37976449	.	+	.	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
Phchi.S1	AUGUSTUS	stop_codon	37976450	37976452	.	+	0	transcript_id "Phchi.S1G595100.t1"; gene_id "Phchi.S1G595100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg981.t1 is derived from g10764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6833159	6834669	.	-	.	Phchi.S6G094000
Phchi.S6	AUGUSTUS	transcript	6833159	6834669	.	-	.	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	stop_codon	6833156	6833158	.	-	0	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	CDS	6833159	6834018	0.98	-	2	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	exon	6833159	6834018	.	-	.	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	intron	6834019	6834155	.	-	.	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	CDS	6834156	6834669	0.59	-	0	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	exon	6834156	6834669	.	-	.	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
Phchi.S6	AUGUSTUS	start_codon	6834667	6834669	.	-	0	transcript_id "Phchi.S6G094000.t1"; gene_id "Phchi.S6G094000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15823.t1 is derived from g14293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21591305	21591982	.	+	.	Phchi.S3G314200
Phchi.S3	AUGUSTUS	transcript	21591305	21591982	.	+	.	transcript_id "Phchi.S3G314200.t1"; gene_id "Phchi.S3G314200"
Phchi.S3	AUGUSTUS	start_codon	21591305	21591307	.	+	0	transcript_id "Phchi.S3G314200.t1"; gene_id "Phchi.S3G314200"
Phchi.S3	AUGUSTUS	CDS	21591305	21591982	0.77	+	0	transcript_id "Phchi.S3G314200.t1"; gene_id "Phchi.S3G314200"
Phchi.S3	AUGUSTUS	exon	21591305	21591982	.	+	.	transcript_id "Phchi.S3G314200.t1"; gene_id "Phchi.S3G314200"
Phchi.S3	AUGUSTUS	stop_codon	21591983	21591985	.	+	0	transcript_id "Phchi.S3G314200.t1"; gene_id "Phchi.S3G314200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1831.t1 is derived from g8751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3409653	3410632	.	-	.	Phchi.S5G044000
Phchi.S5	AUGUSTUS	transcript	3409653	3410632	.	-	.	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	stop_codon	3409650	3409652	.	-	0	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	CDS	3409653	3410025	0.64	-	1	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	exon	3409653	3410025	.	-	.	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	intron	3410026	3410393	.	-	.	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	CDS	3410394	3410632	0.53	-	0	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	exon	3410394	3410632	.	-	.	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
Phchi.S5	AUGUSTUS	start_codon	3410630	3410632	.	-	0	transcript_id "Phchi.S5G044000.t1"; gene_id "Phchi.S5G044000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8190.t1 is derived from g5365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34351791	34353497	.	+	.	Phchi.S1G534900
Phchi.S1	AUGUSTUS	transcript	34351791	34353497	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	start_codon	34351791	34351793	.	+	0	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	CDS	34351791	34351918	1	+	0	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	exon	34351791	34351918	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	intron	34351919	34352093	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	CDS	34352094	34352144	0.67	+	1	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	exon	34352094	34352144	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	intron	34352145	34352505	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	CDS	34352506	34352524	0.99	+	1	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	exon	34352506	34352524	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	intron	34352525	34352609	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	CDS	34352610	34352727	0.99	+	0	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	exon	34352610	34352727	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	intron	34352728	34352814	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	CDS	34352815	34352917	1	+	2	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	exon	34352815	34352917	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	intron	34352918	34353010	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	CDS	34353011	34353497	0.84	+	1	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	exon	34353011	34353497	.	+	.	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
Phchi.S1	AUGUSTUS	stop_codon	34353498	34353500	.	+	0	transcript_id "Phchi.S1G534900.t1"; gene_id "Phchi.S1G534900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10905.t1 is derived from g14955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2857236	2857747	.	+	.	Phchi.S4G048700
Phchi.S4	AUGUSTUS	transcript	2857236	2857747	.	+	.	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	start_codon	2857236	2857238	.	+	0	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	CDS	2857236	2857303	0.6	+	0	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	exon	2857236	2857303	.	+	.	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	intron	2857304	2857575	.	+	.	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	CDS	2857576	2857747	0.66	+	1	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	exon	2857576	2857747	.	+	.	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
Phchi.S4	AUGUSTUS	stop_codon	2857748	2857750	.	+	0	transcript_id "Phchi.S4G048700.t1"; gene_id "Phchi.S4G048700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13217.t1 is derived from g11682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4733378	4734310	.	-	.	Phchi.S3G053600
Phchi.S3	AUGUSTUS	transcript	4733378	4734310	.	-	.	transcript_id "Phchi.S3G053600.t1"; gene_id "Phchi.S3G053600"
Phchi.S3	AUGUSTUS	stop_codon	4733375	4733377	.	-	0	transcript_id "Phchi.S3G053600.t1"; gene_id "Phchi.S3G053600"
Phchi.S3	AUGUSTUS	CDS	4733378	4734310	0.64	-	0	transcript_id "Phchi.S3G053600.t1"; gene_id "Phchi.S3G053600"
Phchi.S3	AUGUSTUS	exon	4733378	4734310	.	-	.	transcript_id "Phchi.S3G053600.t1"; gene_id "Phchi.S3G053600"
Phchi.S3	AUGUSTUS	start_codon	4734308	4734310	.	-	0	transcript_id "Phchi.S3G053600.t1"; gene_id "Phchi.S3G053600"
# This transcript jg1465.t2 is derived from g8384.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1466.t1 is derived from g8385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1079622	1080610	.	+	.	Phchi.S5G007500
Phchi.S5	AUGUSTUS	transcript	1079622	1080610	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	start_codon	1079622	1079624	.	+	0	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	CDS	1079622	1079651	1	+	0	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	exon	1079622	1079651	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	intron	1079652	1079736	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	CDS	1079737	1079808	1	+	0	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	exon	1079737	1079808	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	intron	1079809	1079923	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	CDS	1079924	1080090	1	+	0	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	exon	1079924	1080090	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	intron	1080091	1080174	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	CDS	1080175	1080286	1	+	1	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	exon	1080175	1080286	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	intron	1080287	1080445	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	CDS	1080446	1080610	0.91	+	0	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	exon	1080446	1080610	.	+	.	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
Phchi.S5	AUGUSTUS	stop_codon	1080611	1080613	.	+	0	transcript_id "Phchi.S5G007500.t1"; gene_id "Phchi.S5G007500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15992.t1 is derived from g14435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C220	AUGUSTUS	gene	13466	19803	.	-	.	Phchi.C220G000100
Phchi.C220	AUGUSTUS	transcript	13466	19803	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	stop_codon	13463	13465	.	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	13466	13612	0.99	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	13466	13612	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	13613	13697	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	13698	13764	1	-	1	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	13698	13764	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	13765	13916	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	13917	14007	0.99	-	2	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	13917	14007	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	14008	14127	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	14128	14229	0.99	-	2	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	14128	14229	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	14230	14308	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	14309	14375	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	14309	14375	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	14376	14514	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	14515	14581	1	-	1	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	14515	14581	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	14582	14656	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	14657	14742	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	14657	14742	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	14743	14882	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	14883	14975	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	14883	14975	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	14976	15193	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	15194	15379	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	15194	15379	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	15380	15682	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	15683	15739	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	15683	15739	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	15740	15828	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	15829	15956	1	-	2	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	15829	15956	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	15957	16041	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	16042	16111	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	16042	16111	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	16112	16196	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	16197	16332	1	-	1	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	16197	16332	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	16333	16430	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	16431	16582	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	16431	16582	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	16583	16672	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	16673	16747	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	16673	16747	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	16748	16842	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	16843	17007	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	16843	17007	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	17008	17120	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	17121	17186	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	17121	17186	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	17187	17314	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	17315	17419	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	17315	17419	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	17420	17598	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	17599	17802	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	17599	17802	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	17803	18354	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	18355	18747	1	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	18355	18747	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	18748	18984	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	18985	19457	0.55	-	2	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	18985	19457	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	19458	19539	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	19540	19597	0.61	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	19540	19597	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	intron	19598	19782	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	CDS	19783	19803	0.78	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	exon	19783	19803	.	-	.	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
Phchi.C220	AUGUSTUS	start_codon	19801	19803	.	-	0	transcript_id "Phchi.C220G000100.t1"; gene_id "Phchi.C220G000100"
# This transcript jg14543.t2 is derived from g13011.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14544.t1 is derived from g13012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13409317	13410888	.	+	.	Phchi.S3G186300
Phchi.S3	AUGUSTUS	transcript	13409317	13410888	.	+	.	transcript_id "Phchi.S3G186300.t1"; gene_id "Phchi.S3G186300"
Phchi.S3	AUGUSTUS	start_codon	13409317	13409319	.	+	0	transcript_id "Phchi.S3G186300.t1"; gene_id "Phchi.S3G186300"
Phchi.S3	AUGUSTUS	CDS	13409317	13410888	0.6	+	0	transcript_id "Phchi.S3G186300.t1"; gene_id "Phchi.S3G186300"
Phchi.S3	AUGUSTUS	exon	13409317	13410888	.	+	.	transcript_id "Phchi.S3G186300.t1"; gene_id "Phchi.S3G186300"
Phchi.S3	AUGUSTUS	stop_codon	13410889	13410891	.	+	0	transcript_id "Phchi.S3G186300.t1"; gene_id "Phchi.S3G186300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13122.t1 is derived from g11587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4227340	4236999	.	-	.	Phchi.S3G044100
Phchi.S3	AUGUSTUS	transcript	4227340	4236999	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	stop_codon	4227337	4227339	.	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4227340	4227685	0.62	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4227340	4227685	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4227686	4227790	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4227791	4228165	0.63	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4227791	4228165	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4228166	4228323	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4228324	4228509	0.93	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4228324	4228509	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4228510	4228627	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4228628	4228913	0.97	-	2	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4228628	4228913	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4228914	4229006	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4229007	4229109	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4229007	4229109	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4229110	4229184	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4229185	4230456	0.96	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4229185	4230456	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4230457	4230533	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4230534	4230689	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4230534	4230689	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4230690	4230781	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4230782	4231033	0.96	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4230782	4231033	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4231034	4231126	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4231127	4231215	1	-	2	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4231127	4231215	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4231216	4231353	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4231354	4231426	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4231354	4231426	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4231427	4231515	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4231516	4231614	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4231516	4231614	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4231615	4231738	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4231739	4231842	0.95	-	2	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4231739	4231842	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4231843	4231968	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4231969	4232074	0.86	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4231969	4232074	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4232075	4232201	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4232202	4232403	0.95	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4232202	4232403	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4232404	4232499	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4232500	4232627	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4232500	4232627	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4232628	4232707	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4232708	4233016	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4232708	4233016	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4233017	4233113	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4233114	4233230	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4233114	4233230	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4233231	4233306	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4233307	4233421	1	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4233307	4233421	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4233422	4233509	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4233510	4233531	1	-	2	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4233510	4233531	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4233532	4233622	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4233623	4233781	1	-	2	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4233623	4233781	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4233782	4233882	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4233883	4234091	1	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4233883	4234091	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4234092	4234174	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4234175	4234266	0.99	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4234175	4234266	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4234267	4234357	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4234358	4234480	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4234358	4234480	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4234481	4234564	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4234565	4234687	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4234565	4234687	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4234688	4234765	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4234766	4234851	1	-	2	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4234766	4234851	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4234852	4234949	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4234950	4235064	0.99	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4234950	4235064	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4235065	4235181	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4235182	4235346	0.58	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4235182	4235346	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4235347	4235443	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4235444	4235512	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4235444	4235512	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4235513	4235591	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4235592	4235706	1	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4235592	4235706	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4235707	4235785	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4235786	4235841	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4235786	4235841	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4235842	4235926	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4235927	4236008	1	-	1	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4235927	4236008	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4236009	4236103	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4236104	4236243	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4236104	4236243	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4236244	4236341	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4236342	4236461	1	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4236342	4236461	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	intron	4236462	4236555	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	CDS	4236556	4236999	0.99	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	exon	4236556	4236999	.	-	.	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
Phchi.S3	AUGUSTUS	start_codon	4236997	4236999	.	-	0	transcript_id "Phchi.S3G044100.t1"; gene_id "Phchi.S3G044100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6621.t1 is derived from g3793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24034988	24035338	.	+	.	Phchi.S1G378000
Phchi.S1	AUGUSTUS	transcript	24034988	24035338	.	+	.	transcript_id "Phchi.S1G378000.t1"; gene_id "Phchi.S1G378000"
Phchi.S1	AUGUSTUS	start_codon	24034988	24034990	.	+	0	transcript_id "Phchi.S1G378000.t1"; gene_id "Phchi.S1G378000"
Phchi.S1	AUGUSTUS	CDS	24034988	24035338	0.87	+	0	transcript_id "Phchi.S1G378000.t1"; gene_id "Phchi.S1G378000"
Phchi.S1	AUGUSTUS	exon	24034988	24035338	.	+	.	transcript_id "Phchi.S1G378000.t1"; gene_id "Phchi.S1G378000"
Phchi.S1	AUGUSTUS	stop_codon	24035339	24035341	.	+	0	transcript_id "Phchi.S1G378000.t1"; gene_id "Phchi.S1G378000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5889.t1 is derived from g3059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19615873	19618498	.	+	.	Phchi.S1G304800
Phchi.S1	AUGUSTUS	transcript	19615873	19618498	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	start_codon	19615873	19615875	.	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19615873	19616892	0.76	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19615873	19616892	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	intron	19616893	19617037	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19617038	19617150	1	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19617038	19617150	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	intron	19617151	19617270	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19617271	19617530	1	+	1	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19617271	19617530	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	intron	19617531	19617611	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19617612	19617733	1	+	2	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19617612	19617733	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	intron	19617734	19617890	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19617891	19617959	1	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19617891	19617959	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	intron	19617960	19618163	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19618164	19618217	1	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19618164	19618217	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	intron	19618218	19618306	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	CDS	19618307	19618498	0.72	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	exon	19618307	19618498	.	+	.	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
Phchi.S1	AUGUSTUS	stop_codon	19618499	19618501	.	+	0	transcript_id "Phchi.S1G304800.t1"; gene_id "Phchi.S1G304800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5691.t1 is derived from g2861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18332885	18334099	.	+	.	Phchi.S1G285000
Phchi.S1	AUGUSTUS	transcript	18332885	18334099	.	+	.	transcript_id "Phchi.S1G285000.t1"; gene_id "Phchi.S1G285000"
Phchi.S1	AUGUSTUS	start_codon	18332885	18332887	.	+	0	transcript_id "Phchi.S1G285000.t1"; gene_id "Phchi.S1G285000"
Phchi.S1	AUGUSTUS	CDS	18332885	18334099	1	+	0	transcript_id "Phchi.S1G285000.t1"; gene_id "Phchi.S1G285000"
Phchi.S1	AUGUSTUS	exon	18332885	18334099	.	+	.	transcript_id "Phchi.S1G285000.t1"; gene_id "Phchi.S1G285000"
Phchi.S1	AUGUSTUS	stop_codon	18334100	18334102	.	+	0	transcript_id "Phchi.S1G285000.t1"; gene_id "Phchi.S1G285000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10812.t1 is derived from g14862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2208278	2210305	.	+	.	Phchi.S4G039400
Phchi.S4	AUGUSTUS	transcript	2208278	2210305	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	start_codon	2208278	2208280	.	+	0	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	CDS	2208278	2209010	0.97	+	0	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	exon	2208278	2209010	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	intron	2209011	2209190	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	CDS	2209191	2209958	0.44	+	2	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	exon	2209191	2209958	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	intron	2209959	2210160	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	CDS	2210161	2210206	0.56	+	2	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	exon	2210161	2210206	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	intron	2210207	2210304	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	CDS	2210305	2210305	1	+	1	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	exon	2210305	2210305	.	+	.	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
Phchi.S4	AUGUSTUS	stop_codon	2210306	2210308	.	+	0	transcript_id "Phchi.S4G039400.t1"; gene_id "Phchi.S4G039400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1171.t1 is derived from g10954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8261525	8262537	.	+	.	Phchi.S6G113000
Phchi.S6	AUGUSTUS	transcript	8261525	8262537	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	start_codon	8261525	8261527	.	+	0	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	CDS	8261525	8261672	0.9	+	0	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	exon	8261525	8261672	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	intron	8261673	8261749	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	CDS	8261750	8261820	1	+	2	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	exon	8261750	8261820	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	intron	8261821	8261978	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	CDS	8261979	8262098	1	+	0	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	exon	8261979	8262098	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	intron	8262099	8262238	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	CDS	8262239	8262357	1	+	0	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	exon	8262239	8262357	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	intron	8262358	8262443	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	CDS	8262444	8262537	1	+	1	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	exon	8262444	8262537	.	+	.	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
Phchi.S6	AUGUSTUS	stop_codon	8262538	8262540	.	+	0	transcript_id "Phchi.S6G113000.t1"; gene_id "Phchi.S6G113000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8422.t1 is derived from g5597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35878565	35880172	.	+	.	Phchi.S1G558100
Phchi.S1	AUGUSTUS	transcript	35878565	35880172	.	+	.	transcript_id "Phchi.S1G558100.t1"; gene_id "Phchi.S1G558100"
Phchi.S1	AUGUSTUS	start_codon	35878565	35878567	.	+	0	transcript_id "Phchi.S1G558100.t1"; gene_id "Phchi.S1G558100"
Phchi.S1	AUGUSTUS	CDS	35878565	35880172	0.99	+	0	transcript_id "Phchi.S1G558100.t1"; gene_id "Phchi.S1G558100"
Phchi.S1	AUGUSTUS	exon	35878565	35880172	.	+	.	transcript_id "Phchi.S1G558100.t1"; gene_id "Phchi.S1G558100"
Phchi.S1	AUGUSTUS	stop_codon	35880173	35880175	.	+	0	transcript_id "Phchi.S1G558100.t1"; gene_id "Phchi.S1G558100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4423.t1 is derived from g1592.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10429959	10432185	.	+	.	Phchi.S1G158200
Phchi.S1	AUGUSTUS	transcript	10429959	10432185	.	+	.	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	start_codon	10429959	10429961	.	+	0	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	CDS	10429959	10430207	0.49	+	0	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	exon	10429959	10430207	.	+	.	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	intron	10430208	10430356	.	+	.	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	CDS	10430357	10430478	0.45	+	0	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	exon	10430357	10430478	.	+	.	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	intron	10430479	10430558	.	+	.	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	CDS	10430559	10432185	0.9	+	1	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	exon	10430559	10432185	.	+	.	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	stop_codon	10432186	10432188	.	+	0	transcript_id "Phchi.S1G158200.t1"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	transcript	10430659	10432185	.	+	.	transcript_id "Phchi.S1G158200.t2"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	start_codon	10430659	10430661	.	+	0	transcript_id "Phchi.S1G158200.t2"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	CDS	10430659	10432185	0.98	+	0	transcript_id "Phchi.S1G158200.t2"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	exon	10430659	10432185	.	+	.	transcript_id "Phchi.S1G158200.t2"; gene_id "Phchi.S1G158200"
Phchi.S1	AUGUSTUS	stop_codon	10432186	10432188	.	+	0	transcript_id "Phchi.S1G158200.t2"; gene_id "Phchi.S1G158200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1559.t1 is derived from g8478.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1761444	1771312	.	+	.	Phchi.S5G016800
Phchi.S5	AUGUSTUS	transcript	1761444	1771312	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	start_codon	1761444	1761446	.	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1761444	1761688	0.99	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1761444	1761688	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1761689	1761824	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1761825	1761888	1	+	1	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1761825	1761888	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1761889	1762144	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762145	1762229	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762145	1762229	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1762230	1762363	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762364	1762680	0.87	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762364	1762680	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1762681	1762753	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762754	1762859	0.57	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762754	1762859	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1762860	1762967	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762968	1763113	0.52	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762968	1763113	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763114	1763219	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1763220	1763398	0.54	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1763220	1763398	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763399	1763557	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1763558	1763627	1	+	1	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1763558	1763627	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763628	1763764	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1763765	1763983	0.91	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1763765	1763983	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763984	1764154	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1764155	1764464	0.8	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1764155	1764464	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1764465	1764542	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1764543	1764666	0.77	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1764543	1764666	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1764667	1764928	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1764929	1765112	0.47	+	1	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1764929	1765112	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1765113	1765237	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1765238	1765396	0.7	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1765238	1765396	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1765397	1765496	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1765497	1765859	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1765497	1765859	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1765860	1765963	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1765964	1766056	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1765964	1766056	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766057	1766138	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766139	1766231	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766139	1766231	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766232	1766321	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766322	1766381	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766322	1766381	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766382	1766480	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766481	1766579	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766481	1766579	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766580	1766771	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766772	1766912	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766772	1766912	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766913	1767046	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767047	1767127	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767047	1767127	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767128	1767240	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767241	1767316	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767241	1767316	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767317	1767514	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767515	1767582	1	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767515	1767582	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767583	1767701	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767702	1767795	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767702	1767795	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767796	1767979	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767980	1768068	1	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767980	1768068	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768069	1768229	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768230	1768313	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768230	1768313	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768314	1768398	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768399	1768476	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768399	1768476	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768477	1768566	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768567	1768688	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768567	1768688	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768689	1768787	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768788	1768957	0.98	+	1	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768788	1768957	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768958	1769073	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769074	1769150	1	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769074	1769150	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769151	1769234	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769235	1769348	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769235	1769348	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769349	1769446	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769447	1769548	0.99	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769447	1769548	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769549	1769652	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769653	1769793	0.75	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769653	1769793	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769794	1769916	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769917	1770090	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769917	1770090	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770091	1770171	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770172	1770235	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770172	1770235	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770236	1770392	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770393	1770532	0.99	+	2	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770393	1770532	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770533	1770639	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770640	1770785	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770640	1770785	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770786	1770875	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770876	1770957	1	+	1	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770876	1770957	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770958	1771050	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1771051	1771161	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1771051	1771161	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1771162	1771240	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1771241	1771312	1	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1771241	1771312	.	+	.	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	stop_codon	1771313	1771315	.	+	0	transcript_id "Phchi.S5G016800.t1"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	transcript	1761444	1771312	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	start_codon	1761444	1761446	.	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1761444	1761688	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1761444	1761688	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1761689	1761824	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1761825	1761888	1	+	1	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1761825	1761888	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1761889	1762144	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762145	1762229	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762145	1762229	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1762230	1762363	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762364	1762680	0.86	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762364	1762680	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1762681	1762753	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762754	1762859	0.57	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762754	1762859	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1762860	1762967	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1762968	1763113	0.51	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1762968	1763113	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763114	1763219	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1763220	1763398	0.54	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1763220	1763398	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763399	1763557	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1763558	1763627	1	+	1	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1763558	1763627	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763628	1763764	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1763765	1763983	0.9	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1763765	1763983	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1763984	1764154	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1764155	1764464	0.67	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1764155	1764464	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1764465	1764542	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1764543	1764666	0.59	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1764543	1764666	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1764667	1764928	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1764929	1765112	0.53	+	1	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1764929	1765112	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1765113	1765237	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1765238	1765396	0.65	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1765238	1765396	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1765397	1765496	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1765497	1765859	0.99	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1765497	1765859	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1765860	1765963	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1765964	1766056	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1765964	1766056	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766057	1766138	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766139	1766231	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766139	1766231	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766232	1766321	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766322	1766381	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766322	1766381	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766382	1766480	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766481	1766579	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766481	1766579	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766580	1766771	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1766772	1766912	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1766772	1766912	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1766913	1767046	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767047	1767127	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767047	1767127	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767128	1767240	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767241	1767316	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767241	1767316	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767317	1767514	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767515	1767582	1	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767515	1767582	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767583	1767701	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767702	1767795	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767702	1767795	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1767796	1767979	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1767980	1768068	1	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1767980	1768068	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768069	1768229	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768230	1768313	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768230	1768313	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768314	1768398	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768399	1768476	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768399	1768476	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768477	1768566	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768567	1768688	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768567	1768688	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768689	1768787	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1768788	1768957	1	+	1	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1768788	1768957	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1768958	1769073	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769074	1769150	0.99	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769074	1769150	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769151	1769234	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769235	1769348	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769235	1769348	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769349	1769446	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769447	1769548	0.99	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769447	1769548	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769549	1769652	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769653	1769793	0.88	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769653	1769793	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1769794	1769916	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1769917	1770090	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1769917	1770090	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770091	1770171	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770172	1770235	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770172	1770235	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770236	1770389	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770390	1770532	1	+	2	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770390	1770532	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770533	1770639	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770640	1770785	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770640	1770785	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770786	1770875	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1770876	1770957	1	+	1	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1770876	1770957	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1770958	1771050	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1771051	1771161	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1771051	1771161	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	intron	1771162	1771240	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	CDS	1771241	1771312	1	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	exon	1771241	1771312	.	+	.	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
Phchi.S5	AUGUSTUS	stop_codon	1771313	1771315	.	+	0	transcript_id "Phchi.S5G016800.t2"; gene_id "Phchi.S5G016800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3781.t1 is derived from g950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5662636	5663080	.	-	.	Phchi.S1G094000
Phchi.S1	AUGUSTUS	transcript	5662636	5663080	.	-	.	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	stop_codon	5662633	5662635	.	-	0	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	CDS	5662636	5662782	1	-	0	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	exon	5662636	5662782	.	-	.	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	intron	5662783	5662870	.	-	.	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	CDS	5662871	5663080	0.99	-	0	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	exon	5662871	5663080	.	-	.	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
Phchi.S1	AUGUSTUS	start_codon	5663078	5663080	.	-	0	transcript_id "Phchi.S1G094000.t1"; gene_id "Phchi.S1G094000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5972.t1 is derived from g3143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20163207	20165675	.	-	.	Phchi.S1G313100
Phchi.S1	AUGUSTUS	transcript	20163207	20165675	.	-	.	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	stop_codon	20163204	20163206	.	-	0	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	CDS	20163207	20165254	0.99	-	2	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	exon	20163207	20165254	.	-	.	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	intron	20165255	20165389	.	-	.	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	CDS	20165390	20165675	0.35	-	0	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	exon	20165390	20165675	.	-	.	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
Phchi.S1	AUGUSTUS	start_codon	20165673	20165675	.	-	0	transcript_id "Phchi.S1G313100.t1"; gene_id "Phchi.S1G313100"
# This transcript jg4106.t2 is derived from g1275.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4107.t1 is derived from g1276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7866734	7869835	.	+	.	Phchi.S1G126600
Phchi.S1	AUGUSTUS	transcript	7866734	7869835	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	start_codon	7866734	7866736	.	+	0	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7866734	7866754	0.72	+	0	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7866734	7866754	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	intron	7866755	7866858	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7866859	7866888	0.91	+	0	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7866859	7866888	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	intron	7866889	7866974	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7866975	7867048	1	+	0	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7866975	7867048	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	intron	7867049	7867206	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7867207	7867333	1	+	1	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7867207	7867333	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	intron	7867334	7867487	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7867488	7867855	1	+	0	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7867488	7867855	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	intron	7867856	7868321	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7868322	7869232	0.87	+	1	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7868322	7869232	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	intron	7869233	7869317	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	CDS	7869318	7869835	0.22	+	2	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	exon	7869318	7869835	.	+	.	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
Phchi.S1	AUGUSTUS	stop_codon	7869836	7869838	.	+	0	transcript_id "Phchi.S1G126600.t1"; gene_id "Phchi.S1G126600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15983.t1 is derived from g9772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C16	AUGUSTUS	gene	27208	27759	.	-	.	Phchi.C16G000100
Phchi.C16	AUGUSTUS	transcript	27208	27759	.	-	.	transcript_id "Phchi.C16G000100.t1"; gene_id "Phchi.C16G000100"
Phchi.C16	AUGUSTUS	stop_codon	27205	27207	.	-	0	transcript_id "Phchi.C16G000100.t1"; gene_id "Phchi.C16G000100"
Phchi.C16	AUGUSTUS	CDS	27208	27759	0.38	-	0	transcript_id "Phchi.C16G000100.t1"; gene_id "Phchi.C16G000100"
Phchi.C16	AUGUSTUS	exon	27208	27759	.	-	.	transcript_id "Phchi.C16G000100.t1"; gene_id "Phchi.C16G000100"
Phchi.C16	AUGUSTUS	start_codon	27757	27759	.	-	0	transcript_id "Phchi.C16G000100.t1"; gene_id "Phchi.C16G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13889.t1 is derived from g12356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9469347	9472463	.	+	.	Phchi.S3G120800
Phchi.S3	AUGUSTUS	transcript	9469347	9472463	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	start_codon	9469347	9469349	.	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9469347	9469370	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9469347	9469370	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9469371	9469456	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9469457	9469531	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9469457	9469531	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9469532	9469703	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9469704	9469734	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9469704	9469734	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9469735	9469924	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9469925	9469968	1	+	2	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9469925	9469968	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9469969	9470069	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9470070	9470168	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9470070	9470168	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9470169	9470266	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9470267	9470328	0.98	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9470267	9470328	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9470329	9470428	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9470429	9470446	1	+	1	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9470429	9470446	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9470447	9470655	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9470656	9470857	0.99	+	1	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9470656	9470857	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9470858	9470969	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9470970	9471059	0.97	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9470970	9471059	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9471060	9471153	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9471154	9471253	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9471154	9471253	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9471254	9471359	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9471360	9471511	0.98	+	2	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9471360	9471511	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9471512	9471618	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9471619	9471722	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9471619	9471722	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9471723	9471845	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9471846	9471999	0.96	+	1	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9471846	9471999	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9472000	9472108	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9472109	9472207	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9472109	9472207	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	intron	9472208	9472298	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	CDS	9472299	9472463	1	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	exon	9472299	9472463	.	+	.	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
Phchi.S3	AUGUSTUS	stop_codon	9472464	9472466	.	+	0	transcript_id "Phchi.S3G120800.t1"; gene_id "Phchi.S3G120800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2017.t1 is derived from g8937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4468972	4472608	.	-	.	Phchi.S5G062600
Phchi.S5	AUGUSTUS	transcript	4468972	4472608	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	stop_codon	4468969	4468971	.	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4468972	4469311	0.96	-	1	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4468972	4469311	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4469312	4469404	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4469405	4469606	1	-	2	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4469405	4469606	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4469607	4469743	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4469744	4469879	1	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4469744	4469879	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4469880	4469962	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4469963	4470064	1	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4469963	4470064	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4470065	4470143	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4470144	4470368	1	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4470144	4470368	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4470369	4470443	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4470444	4470602	1	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4470444	4470602	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4470603	4470699	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4470700	4470832	1	-	1	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4470700	4470832	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4470833	4470970	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4470971	4471998	0.99	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4470971	4471998	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4471999	4472204	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4472205	4472350	1	-	2	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4472205	4472350	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	intron	4472351	4472427	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	CDS	4472428	4472608	0.99	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	exon	4472428	4472608	.	-	.	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
Phchi.S5	AUGUSTUS	start_codon	4472606	4472608	.	-	0	transcript_id "Phchi.S5G062600.t1"; gene_id "Phchi.S5G062600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1467.t1 is derived from g8386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1081096	1082425	.	+	.	Phchi.S5G007600
Phchi.S5	AUGUSTUS	transcript	1081096	1082425	.	+	.	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	start_codon	1081096	1081098	.	+	0	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	CDS	1081096	1081460	0.7	+	0	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	exon	1081096	1081460	.	+	.	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	intron	1081461	1081585	.	+	.	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	CDS	1081586	1081946	0.4	+	1	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	exon	1081586	1081946	.	+	.	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	intron	1081947	1082041	.	+	.	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	CDS	1082042	1082425	0.55	+	0	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	exon	1082042	1082425	.	+	.	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
Phchi.S5	AUGUSTUS	stop_codon	1082426	1082428	.	+	0	transcript_id "Phchi.S5G007600.t1"; gene_id "Phchi.S5G007600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3807.t1 is derived from g976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5821309	5822737	.	+	.	Phchi.S1G096600
Phchi.S1	AUGUSTUS	transcript	5821309	5822737	.	+	.	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	start_codon	5821309	5821311	.	+	0	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	CDS	5821309	5821737	0.24	+	0	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	exon	5821309	5821737	.	+	.	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	intron	5821738	5821969	.	+	.	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	CDS	5821970	5822737	0.38	+	0	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	exon	5821970	5822737	.	+	.	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
Phchi.S1	AUGUSTUS	stop_codon	5822738	5822740	.	+	0	transcript_id "Phchi.S1G096600.t1"; gene_id "Phchi.S1G096600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4659.t1 is derived from g1829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11671004	11672736	.	+	.	Phchi.S1G181800
Phchi.S1	AUGUSTUS	transcript	11671004	11672736	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	start_codon	11671004	11671006	.	+	0	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	CDS	11671004	11671125	0.47	+	0	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	exon	11671004	11671125	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	intron	11671126	11671289	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	CDS	11671290	11671461	1	+	1	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	exon	11671290	11671461	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	intron	11671462	11671604	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	CDS	11671605	11671868	0.83	+	0	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	exon	11671605	11671868	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	intron	11671869	11671970	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	CDS	11671971	11672052	0.79	+	0	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	exon	11671971	11672052	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	intron	11672053	11672140	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	CDS	11672141	11672325	1	+	2	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	exon	11672141	11672325	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	intron	11672326	11672445	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	CDS	11672446	11672736	0.81	+	0	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	exon	11672446	11672736	.	+	.	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
Phchi.S1	AUGUSTUS	stop_codon	11672737	11672739	.	+	0	transcript_id "Phchi.S1G181800.t1"; gene_id "Phchi.S1G181800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2191.t1 is derived from g9111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5291804	5292333	.	+	.	Phchi.S5G080000
Phchi.S5	AUGUSTUS	transcript	5291804	5292333	.	+	.	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	start_codon	5291804	5291806	.	+	0	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	CDS	5291804	5291880	0.43	+	0	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	exon	5291804	5291880	.	+	.	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	intron	5291881	5291978	.	+	.	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	CDS	5291979	5292057	0.64	+	1	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	exon	5291979	5292057	.	+	.	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	intron	5292058	5292162	.	+	.	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	CDS	5292163	5292333	0.61	+	0	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	exon	5292163	5292333	.	+	.	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
Phchi.S5	AUGUSTUS	stop_codon	5292334	5292336	.	+	0	transcript_id "Phchi.S5G080000.t1"; gene_id "Phchi.S5G080000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg488.t1 is derived from g10270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3411267	3412675	.	+	.	Phchi.S6G044700
Phchi.S6	AUGUSTUS	transcript	3411267	3412675	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	start_codon	3411267	3411269	.	+	0	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3411267	3411370	0.97	+	0	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3411267	3411370	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	intron	3411371	3411458	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3411459	3411590	1	+	1	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3411459	3411590	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	intron	3411591	3411678	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3411679	3411723	0.99	+	1	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3411679	3411723	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	intron	3411724	3411825	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3411826	3411995	1	+	1	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3411826	3411995	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	intron	3411996	3412168	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3412169	3412254	0.95	+	2	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3412169	3412254	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	intron	3412255	3412448	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3412449	3412472	1	+	0	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3412449	3412472	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	intron	3412473	3412555	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	CDS	3412556	3412675	0.87	+	0	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	exon	3412556	3412675	.	+	.	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
Phchi.S6	AUGUSTUS	stop_codon	3412676	3412678	.	+	0	transcript_id "Phchi.S6G044700.t1"; gene_id "Phchi.S6G044700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15660.t1 is derived from g14129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20529970	20530748	.	+	.	Phchi.S3G297900
Phchi.S3	AUGUSTUS	transcript	20529970	20530748	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	start_codon	20529970	20529972	.	+	0	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	CDS	20529970	20530033	0.85	+	0	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	exon	20529970	20530033	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	intron	20530034	20530134	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	CDS	20530135	20530256	0.85	+	2	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	exon	20530135	20530256	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	intron	20530257	20530368	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	CDS	20530369	20530573	1	+	0	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	exon	20530369	20530573	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	intron	20530574	20530641	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	CDS	20530642	20530748	1	+	2	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	exon	20530642	20530748	.	+	.	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
Phchi.S3	AUGUSTUS	stop_codon	20530749	20530751	.	+	0	transcript_id "Phchi.S3G297900.t1"; gene_id "Phchi.S3G297900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7562.t1 is derived from g4736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30050515	30051984	.	-	.	Phchi.S1G472100
Phchi.S1	AUGUSTUS	transcript	30050515	30051984	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	stop_codon	30050512	30050514	.	-	0	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	CDS	30050515	30050735	0.96	-	2	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	exon	30050515	30050735	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	intron	30050736	30050847	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	CDS	30050848	30051100	0.87	-	0	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	exon	30050848	30051100	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	intron	30051101	30051193	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	CDS	30051194	30051433	1	-	0	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	exon	30051194	30051433	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	intron	30051434	30051548	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	CDS	30051549	30051676	1	-	2	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	exon	30051549	30051676	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	intron	30051677	30051755	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	CDS	30051756	30051984	1	-	0	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	exon	30051756	30051984	.	-	.	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
Phchi.S1	AUGUSTUS	start_codon	30051982	30051984	.	-	0	transcript_id "Phchi.S1G472100.t1"; gene_id "Phchi.S1G472100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3183.t1 is derived from g352.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2127588	2128861	.	-	.	Phchi.S1G034200
Phchi.S1	AUGUSTUS	transcript	2127588	2128861	.	-	.	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	stop_codon	2127585	2127587	.	-	0	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	CDS	2127588	2128577	0.89	-	0	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	exon	2127588	2128577	.	-	.	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	intron	2128578	2128687	.	-	.	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	CDS	2128688	2128861	0.84	-	0	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	exon	2128688	2128861	.	-	.	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	start_codon	2128859	2128861	.	-	0	transcript_id "Phchi.S1G034200.t1"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	transcript	2127588	2128574	.	-	.	transcript_id "Phchi.S1G034200.t2"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	stop_codon	2127585	2127587	.	-	0	transcript_id "Phchi.S1G034200.t2"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	CDS	2127588	2128574	0.94	-	0	transcript_id "Phchi.S1G034200.t2"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	exon	2127588	2128574	.	-	.	transcript_id "Phchi.S1G034200.t2"; gene_id "Phchi.S1G034200"
Phchi.S1	AUGUSTUS	start_codon	2128572	2128574	.	-	0	transcript_id "Phchi.S1G034200.t2"; gene_id "Phchi.S1G034200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3777.t1 is derived from g946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5650814	5651902	.	+	.	Phchi.S1G093600
Phchi.S1	AUGUSTUS	transcript	5650814	5651902	.	+	.	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	start_codon	5650814	5650816	.	+	0	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	CDS	5650814	5651140	0.95	+	0	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	exon	5650814	5651140	.	+	.	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	intron	5651141	5651326	.	+	.	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	CDS	5651327	5651902	1	+	0	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	exon	5651327	5651902	.	+	.	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
Phchi.S1	AUGUSTUS	stop_codon	5651903	5651905	.	+	0	transcript_id "Phchi.S1G093600.t1"; gene_id "Phchi.S1G093600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12153.t1 is derived from g7829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4964253	4965414	.	-	.	Phchi.S2G023300
Phchi.S2	AUGUSTUS	transcript	4964253	4965414	.	-	.	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	stop_codon	4964250	4964252	.	-	0	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	CDS	4964253	4965103	0.89	-	2	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	exon	4964253	4965103	.	-	.	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	intron	4965104	4965200	.	-	.	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	CDS	4965201	4965414	0.69	-	0	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	exon	4965201	4965414	.	-	.	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
Phchi.S2	AUGUSTUS	start_codon	4965412	4965414	.	-	0	transcript_id "Phchi.S2G023300.t1"; gene_id "Phchi.S2G023300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4561.t1 is derived from g1731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11121418	11121858	.	-	.	Phchi.S1G172000
Phchi.S1	AUGUSTUS	transcript	11121418	11121858	.	-	.	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	stop_codon	11121415	11121417	.	-	0	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	CDS	11121418	11121582	0.79	-	0	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	exon	11121418	11121582	.	-	.	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	intron	11121583	11121666	.	-	.	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	CDS	11121667	11121858	0.44	-	0	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	exon	11121667	11121858	.	-	.	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
Phchi.S1	AUGUSTUS	start_codon	11121856	11121858	.	-	0	transcript_id "Phchi.S1G172000.t1"; gene_id "Phchi.S1G172000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4713.t1 is derived from g1883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12433298	12434108	.	-	.	Phchi.S1G187200
Phchi.S1	AUGUSTUS	transcript	12433298	12434108	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	stop_codon	12433295	12433297	.	-	0	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	CDS	12433298	12433374	0.26	-	2	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	exon	12433298	12433374	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	intron	12433375	12433483	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	CDS	12433484	12433586	0.59	-	0	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	exon	12433484	12433586	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	intron	12433587	12433668	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	CDS	12433669	12433746	0.73	-	0	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	exon	12433669	12433746	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	intron	12433747	12433826	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	CDS	12433827	12433915	0.68	-	2	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	exon	12433827	12433915	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	intron	12433916	12434002	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	CDS	12434003	12434108	0.65	-	0	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	exon	12434003	12434108	.	-	.	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
Phchi.S1	AUGUSTUS	start_codon	12434106	12434108	.	-	0	transcript_id "Phchi.S1G187200.t1"; gene_id "Phchi.S1G187200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg742.t1 is derived from g10524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5283300	5284609	.	-	.	Phchi.S6G070100
Phchi.S6	AUGUSTUS	transcript	5283300	5284609	.	-	.	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	stop_codon	5283297	5283299	.	-	0	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	CDS	5283300	5284044	0.44	-	1	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	exon	5283300	5284044	.	-	.	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	intron	5284045	5284181	.	-	.	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	CDS	5284182	5284609	0.64	-	0	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	exon	5284182	5284609	.	-	.	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
Phchi.S6	AUGUSTUS	start_codon	5284607	5284609	.	-	0	transcript_id "Phchi.S6G070100.t1"; gene_id "Phchi.S6G070100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8070.t1 is derived from g5245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32800098	32800393	.	-	.	Phchi.S1G522900
Phchi.S1	AUGUSTUS	transcript	32800098	32800393	.	-	.	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	stop_codon	32800095	32800097	.	-	0	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	CDS	32800098	32800249	0.57	-	2	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	exon	32800098	32800249	.	-	.	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	intron	32800250	32800338	.	-	.	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	CDS	32800339	32800393	0.48	-	0	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	exon	32800339	32800393	.	-	.	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
Phchi.S1	AUGUSTUS	start_codon	32800391	32800393	.	-	0	transcript_id "Phchi.S1G522900.t1"; gene_id "Phchi.S1G522900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg817.t1 is derived from g10599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5705984	5707974	.	+	.	Phchi.S6G077600
Phchi.S6	AUGUSTUS	transcript	5705984	5707974	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	start_codon	5705984	5705986	.	+	0	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5705984	5706333	0.96	+	0	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5705984	5706333	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	intron	5706334	5706532	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5706533	5706557	1	+	1	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5706533	5706557	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	intron	5706558	5707061	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5707062	5707191	1	+	0	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5707062	5707191	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	intron	5707192	5707282	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5707283	5707413	1	+	2	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5707283	5707413	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	intron	5707414	5707492	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5707493	5707581	1	+	0	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5707493	5707581	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	intron	5707582	5707660	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5707661	5707737	0.98	+	1	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5707661	5707737	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	intron	5707738	5707843	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	CDS	5707844	5707974	1	+	2	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	exon	5707844	5707974	.	+	.	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
Phchi.S6	AUGUSTUS	stop_codon	5707975	5707977	.	+	0	transcript_id "Phchi.S6G077600.t1"; gene_id "Phchi.S6G077600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11823.t1 is derived from g15875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8403656	8406259	.	-	.	Phchi.S4G140500
Phchi.S4	AUGUSTUS	transcript	8403656	8406259	.	-	.	transcript_id "Phchi.S4G140500.t1"; gene_id "Phchi.S4G140500"
Phchi.S4	AUGUSTUS	stop_codon	8403653	8403655	.	-	0	transcript_id "Phchi.S4G140500.t1"; gene_id "Phchi.S4G140500"
Phchi.S4	AUGUSTUS	CDS	8403656	8406259	1	-	0	transcript_id "Phchi.S4G140500.t1"; gene_id "Phchi.S4G140500"
Phchi.S4	AUGUSTUS	exon	8403656	8406259	.	-	.	transcript_id "Phchi.S4G140500.t1"; gene_id "Phchi.S4G140500"
Phchi.S4	AUGUSTUS	start_codon	8406257	8406259	.	-	0	transcript_id "Phchi.S4G140500.t1"; gene_id "Phchi.S4G140500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10167.t1 is derived from g7343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46072195	46072619	.	+	.	Phchi.S1G732600
Phchi.S1	AUGUSTUS	transcript	46072195	46072619	.	+	.	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	start_codon	46072195	46072197	.	+	0	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	CDS	46072195	46072285	0.95	+	0	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	exon	46072195	46072285	.	+	.	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	intron	46072286	46072461	.	+	.	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	CDS	46072462	46072619	1	+	2	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	exon	46072462	46072619	.	+	.	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
Phchi.S1	AUGUSTUS	stop_codon	46072620	46072622	.	+	0	transcript_id "Phchi.S1G732600.t1"; gene_id "Phchi.S1G732600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4096.t1 is derived from g1265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7799642	7801488	.	-	.	Phchi.S1G125500
Phchi.S1	AUGUSTUS	transcript	7799642	7801488	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	stop_codon	7799639	7799641	.	-	0	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	CDS	7799642	7799719	0.67	-	0	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	exon	7799642	7799719	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	intron	7799720	7799842	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	CDS	7799843	7799897	1	-	1	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	exon	7799843	7799897	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	intron	7799898	7800012	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	CDS	7800013	7800208	0.83	-	2	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	exon	7800013	7800208	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	intron	7800209	7800295	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	CDS	7800296	7800533	1	-	0	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	exon	7800296	7800533	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	intron	7800534	7800669	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	CDS	7800670	7800888	1	-	0	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	exon	7800670	7800888	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	intron	7800889	7801119	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	CDS	7801120	7801488	0.99	-	0	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	exon	7801120	7801488	.	-	.	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
Phchi.S1	AUGUSTUS	start_codon	7801486	7801488	.	-	0	transcript_id "Phchi.S1G125500.t1"; gene_id "Phchi.S1G125500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9982.t1 is derived from g7158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44778931	44781393	.	-	.	Phchi.S1G714100
Phchi.S1	AUGUSTUS	transcript	44778931	44781393	.	-	.	transcript_id "Phchi.S1G714100.t1"; gene_id "Phchi.S1G714100"
Phchi.S1	AUGUSTUS	stop_codon	44778928	44778930	.	-	0	transcript_id "Phchi.S1G714100.t1"; gene_id "Phchi.S1G714100"
Phchi.S1	AUGUSTUS	CDS	44778931	44781393	0.62	-	0	transcript_id "Phchi.S1G714100.t1"; gene_id "Phchi.S1G714100"
Phchi.S1	AUGUSTUS	exon	44778931	44781393	.	-	.	transcript_id "Phchi.S1G714100.t1"; gene_id "Phchi.S1G714100"
Phchi.S1	AUGUSTUS	start_codon	44781391	44781393	.	-	0	transcript_id "Phchi.S1G714100.t1"; gene_id "Phchi.S1G714100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7543.t1 is derived from g4717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29972217	29973019	.	-	.	Phchi.S1G470200
Phchi.S1	AUGUSTUS	transcript	29972217	29973019	.	-	.	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	stop_codon	29972214	29972216	.	-	0	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	CDS	29972217	29972333	1	-	0	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	exon	29972217	29972333	.	-	.	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	intron	29972334	29972440	.	-	.	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	CDS	29972441	29972586	0.98	-	2	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	exon	29972441	29972586	.	-	.	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	intron	29972587	29972685	.	-	.	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	CDS	29972686	29973019	0.99	-	0	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	exon	29972686	29973019	.	-	.	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
Phchi.S1	AUGUSTUS	start_codon	29973017	29973019	.	-	0	transcript_id "Phchi.S1G470200.t1"; gene_id "Phchi.S1G470200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11914.t1 is derived from g15966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9299464	9300176	.	+	.	Phchi.S4G149600
Phchi.S4	AUGUSTUS	transcript	9299464	9300176	.	+	.	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	start_codon	9299464	9299466	.	+	0	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	CDS	9299464	9299596	0.68	+	0	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	exon	9299464	9299596	.	+	.	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	intron	9299597	9299665	.	+	.	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	CDS	9299666	9299872	0.99	+	2	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	exon	9299666	9299872	.	+	.	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	intron	9299873	9299982	.	+	.	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	CDS	9299983	9300176	0.99	+	2	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	exon	9299983	9300176	.	+	.	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
Phchi.S4	AUGUSTUS	stop_codon	9300177	9300179	.	+	0	transcript_id "Phchi.S4G149600.t1"; gene_id "Phchi.S4G149600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14722.t1 is derived from g13190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14363362	14365315	.	+	.	Phchi.S3G204100
Phchi.S3	AUGUSTUS	transcript	14363362	14365315	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	start_codon	14363362	14363364	.	+	0	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	CDS	14363362	14363387	0.37	+	0	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	exon	14363362	14363387	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	intron	14363388	14363533	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	CDS	14363534	14363928	0.6	+	1	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	exon	14363534	14363928	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	intron	14363929	14364159	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	CDS	14364160	14365080	0.18	+	2	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	exon	14364160	14365080	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	intron	14365081	14365226	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	CDS	14365227	14365315	0.45	+	2	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	exon	14365227	14365315	.	+	.	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
Phchi.S3	AUGUSTUS	stop_codon	14365316	14365318	.	+	0	transcript_id "Phchi.S3G204100.t1"; gene_id "Phchi.S3G204100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5497.t1 is derived from g2667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17124431	17125452	.	+	.	Phchi.S1G265600
Phchi.S1	AUGUSTUS	transcript	17124431	17125452	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	start_codon	17124431	17124433	.	+	0	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	CDS	17124431	17124549	1	+	0	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	exon	17124431	17124549	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	intron	17124550	17124635	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	CDS	17124636	17124708	1	+	1	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	exon	17124636	17124708	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	intron	17124709	17124792	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	CDS	17124793	17124948	0.93	+	0	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	exon	17124793	17124948	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	intron	17124949	17125082	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	CDS	17125083	17125168	0.56	+	0	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	exon	17125083	17125168	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	intron	17125169	17125319	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	CDS	17125320	17125452	1	+	1	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	exon	17125320	17125452	.	+	.	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
Phchi.S1	AUGUSTUS	stop_codon	17125453	17125455	.	+	0	transcript_id "Phchi.S1G265600.t1"; gene_id "Phchi.S1G265600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8143.t1 is derived from g5318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34057003	34058143	.	+	.	Phchi.S1G530200
Phchi.S1	AUGUSTUS	transcript	34057003	34058143	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	start_codon	34057003	34057005	.	+	0	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	CDS	34057003	34057161	0.83	+	0	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	exon	34057003	34057161	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	intron	34057162	34057251	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	CDS	34057252	34057467	1	+	0	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	exon	34057252	34057467	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	intron	34057468	34057599	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	CDS	34057600	34057903	0.66	+	0	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	exon	34057600	34057903	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	intron	34057904	34058006	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	CDS	34058007	34058143	0.63	+	2	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	exon	34058007	34058143	.	+	.	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
Phchi.S1	AUGUSTUS	stop_codon	34058144	34058146	.	+	0	transcript_id "Phchi.S1G530200.t1"; gene_id "Phchi.S1G530200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4702.t1 is derived from g1872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12365798	12366775	.	+	.	Phchi.S1G186100
Phchi.S1	AUGUSTUS	transcript	12365798	12366775	.	+	.	transcript_id "Phchi.S1G186100.t1"; gene_id "Phchi.S1G186100"
Phchi.S1	AUGUSTUS	start_codon	12365798	12365800	.	+	0	transcript_id "Phchi.S1G186100.t1"; gene_id "Phchi.S1G186100"
Phchi.S1	AUGUSTUS	CDS	12365798	12366775	0.27	+	0	transcript_id "Phchi.S1G186100.t1"; gene_id "Phchi.S1G186100"
Phchi.S1	AUGUSTUS	exon	12365798	12366775	.	+	.	transcript_id "Phchi.S1G186100.t1"; gene_id "Phchi.S1G186100"
Phchi.S1	AUGUSTUS	stop_codon	12366776	12366778	.	+	0	transcript_id "Phchi.S1G186100.t1"; gene_id "Phchi.S1G186100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4354.t1 is derived from g1523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9944817	9945119	.	-	.	Phchi.S1G151300
Phchi.S1	AUGUSTUS	transcript	9944817	9945119	.	-	.	transcript_id "Phchi.S1G151300.t1"; gene_id "Phchi.S1G151300"
Phchi.S1	AUGUSTUS	stop_codon	9944814	9944816	.	-	0	transcript_id "Phchi.S1G151300.t1"; gene_id "Phchi.S1G151300"
Phchi.S1	AUGUSTUS	CDS	9944817	9945119	0.56	-	0	transcript_id "Phchi.S1G151300.t1"; gene_id "Phchi.S1G151300"
Phchi.S1	AUGUSTUS	exon	9944817	9945119	.	-	.	transcript_id "Phchi.S1G151300.t1"; gene_id "Phchi.S1G151300"
Phchi.S1	AUGUSTUS	start_codon	9945117	9945119	.	-	0	transcript_id "Phchi.S1G151300.t1"; gene_id "Phchi.S1G151300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10888.t1 is derived from g14938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2766526	2767754	.	-	.	Phchi.S4G047000
Phchi.S4	AUGUSTUS	transcript	2766526	2767754	.	-	.	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	stop_codon	2766523	2766525	.	-	0	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	CDS	2766526	2766914	0.99	-	2	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	exon	2766526	2766914	.	-	.	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	intron	2766915	2767042	.	-	.	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	CDS	2767043	2767174	1	-	2	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	exon	2767043	2767174	.	-	.	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	intron	2767175	2767252	.	-	.	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	CDS	2767253	2767754	0.95	-	0	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	exon	2767253	2767754	.	-	.	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
Phchi.S4	AUGUSTUS	start_codon	2767752	2767754	.	-	0	transcript_id "Phchi.S4G047000.t1"; gene_id "Phchi.S4G047000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12767.t1 is derived from g11232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1953834	1954808	.	+	.	Phchi.S3G008600
Phchi.S3	AUGUSTUS	transcript	1953834	1954808	.	+	.	transcript_id "Phchi.S3G008600.t1"; gene_id "Phchi.S3G008600"
Phchi.S3	AUGUSTUS	start_codon	1953834	1953836	.	+	0	transcript_id "Phchi.S3G008600.t1"; gene_id "Phchi.S3G008600"
Phchi.S3	AUGUSTUS	CDS	1953834	1954808	0.72	+	0	transcript_id "Phchi.S3G008600.t1"; gene_id "Phchi.S3G008600"
Phchi.S3	AUGUSTUS	exon	1953834	1954808	.	+	.	transcript_id "Phchi.S3G008600.t1"; gene_id "Phchi.S3G008600"
Phchi.S3	AUGUSTUS	stop_codon	1954809	1954811	.	+	0	transcript_id "Phchi.S3G008600.t1"; gene_id "Phchi.S3G008600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15849.t1 is derived from g14319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21805183	21811598	.	+	.	Phchi.S3G316800
Phchi.S3	AUGUSTUS	transcript	21805183	21811598	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	start_codon	21805183	21805185	.	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21805183	21805371	0.84	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21805183	21805371	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21805372	21805448	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21805449	21805498	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21805449	21805498	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21805499	21805581	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21805582	21805642	0.97	+	1	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21805582	21805642	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21805643	21805748	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21805749	21805844	0.97	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21805749	21805844	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21805845	21805925	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21805926	21806066	0.98	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21805926	21806066	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21806067	21806178	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21806179	21806310	0.98	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21806179	21806310	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21806311	21806475	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21806476	21806603	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21806476	21806603	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21806604	21806769	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21806770	21806812	1	+	1	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21806770	21806812	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21806813	21806981	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21806982	21807065	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21806982	21807065	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21807066	21807160	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21807161	21807202	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21807161	21807202	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21807203	21807338	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21807339	21807409	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21807339	21807409	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21807410	21807588	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21807589	21807642	1	+	1	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21807589	21807642	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21807643	21807857	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21807858	21807963	0.99	+	1	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21807858	21807963	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21807964	21808064	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21808065	21808133	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21808065	21808133	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21808134	21808244	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21808245	21808388	0.99	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21808245	21808388	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21808389	21808493	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21808494	21808550	0.67	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21808494	21808550	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21808551	21808699	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21808700	21809070	0.81	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21808700	21809070	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21809071	21809145	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21809146	21809327	0.71	+	1	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21809146	21809327	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21809328	21809403	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21809404	21809537	0.65	+	2	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21809404	21809537	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21809538	21809631	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21809632	21809776	0.65	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21809632	21809776	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21809777	21809859	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21809860	21810053	0.84	+	2	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21809860	21810053	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21810054	21810168	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21810169	21810284	0.87	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21810169	21810284	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21810285	21810360	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21810361	21810703	0.95	+	1	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21810361	21810703	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21810704	21810793	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21810794	21811037	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21810794	21811037	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21811038	21811133	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21811134	21811267	1	+	2	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21811134	21811267	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	intron	21811268	21811343	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	CDS	21811344	21811598	1	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	exon	21811344	21811598	.	+	.	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
Phchi.S3	AUGUSTUS	stop_codon	21811599	21811601	.	+	0	transcript_id "Phchi.S3G316800.t1"; gene_id "Phchi.S3G316800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1436.t1 is derived from g8355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	831035	831845	.	+	.	Phchi.S5G004500
Phchi.S5	AUGUSTUS	transcript	831035	831845	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	start_codon	831035	831037	.	+	0	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	CDS	831035	831073	1	+	0	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	exon	831035	831073	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	intron	831074	831164	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	CDS	831165	831267	1	+	0	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	exon	831165	831267	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	intron	831268	831359	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	CDS	831360	831435	1	+	2	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	exon	831360	831435	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	intron	831436	831525	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	CDS	831526	831607	1	+	1	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	exon	831526	831607	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	intron	831608	831707	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	CDS	831708	831845	0.99	+	0	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	exon	831708	831845	.	+	.	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
Phchi.S5	AUGUSTUS	stop_codon	831846	831848	.	+	0	transcript_id "Phchi.S5G004500.t1"; gene_id "Phchi.S5G004500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13967.t1 is derived from g12434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9965525	9967421	.	+	.	Phchi.S3G128600
Phchi.S3	AUGUSTUS	transcript	9965525	9967421	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	start_codon	9965525	9965527	.	+	0	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	CDS	9965525	9965680	0.99	+	0	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	exon	9965525	9965680	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	intron	9965681	9965806	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	CDS	9965807	9966097	0.93	+	0	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	exon	9965807	9966097	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	intron	9966098	9966213	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	CDS	9966214	9966550	1	+	0	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	exon	9966214	9966550	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	intron	9966551	9966763	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	CDS	9966764	9967083	1	+	2	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	exon	9966764	9967083	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	intron	9967084	9967166	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	CDS	9967167	9967421	0.98	+	0	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	exon	9967167	9967421	.	+	.	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
Phchi.S3	AUGUSTUS	stop_codon	9967422	9967424	.	+	0	transcript_id "Phchi.S3G128600.t1"; gene_id "Phchi.S3G128600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13719.t1 is derived from g12186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8499361	8502118	.	-	.	Phchi.S3G103800
Phchi.S3	AUGUSTUS	transcript	8499361	8502118	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	stop_codon	8499358	8499360	.	-	0	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	CDS	8499361	8501175	0.99	-	0	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	exon	8499361	8501175	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	intron	8501176	8501311	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	CDS	8501312	8501581	1	-	0	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	exon	8501312	8501581	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	intron	8501582	8501679	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	CDS	8501680	8501909	1	-	2	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	exon	8501680	8501909	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	intron	8501910	8502075	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	CDS	8502076	8502118	1	-	0	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	exon	8502076	8502118	.	-	.	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
Phchi.S3	AUGUSTUS	start_codon	8502116	8502118	.	-	0	transcript_id "Phchi.S3G103800.t1"; gene_id "Phchi.S3G103800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10591.t1 is derived from g14641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1092776	1094694	.	-	.	Phchi.S4G017300
Phchi.S4	AUGUSTUS	transcript	1092776	1094694	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	stop_codon	1092773	1092775	.	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1092776	1093127	0.97	-	1	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1092776	1093127	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1093128	1093211	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1093212	1093449	1	-	2	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1093212	1093449	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1093450	1093592	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1093593	1093686	1	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1093593	1093686	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1093687	1093808	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1093809	1093904	1	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1093809	1093904	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1093905	1094038	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1094039	1094139	1	-	2	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1094039	1094139	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1094140	1094255	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1094256	1094313	1	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1094256	1094313	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1094314	1094465	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1094466	1094552	0.97	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1094466	1094552	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	intron	1094553	1094658	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	CDS	1094659	1094694	0.97	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	exon	1094659	1094694	.	-	.	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
Phchi.S4	AUGUSTUS	start_codon	1094692	1094694	.	-	0	transcript_id "Phchi.S4G017300.t1"; gene_id "Phchi.S4G017300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12754.t1 is derived from g11219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1898615	1900291	.	+	.	Phchi.S3G007300
Phchi.S3	AUGUSTUS	transcript	1898615	1900291	.	+	.	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	start_codon	1898615	1898617	.	+	0	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	CDS	1898615	1899120	0.66	+	0	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	exon	1898615	1899120	.	+	.	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	intron	1899121	1899339	.	+	.	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	CDS	1899340	1900291	0.71	+	1	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	exon	1899340	1900291	.	+	.	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	stop_codon	1900292	1900294	.	+	0	transcript_id "Phchi.S3G007300.t1"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	transcript	1899464	1900291	.	+	.	transcript_id "Phchi.S3G007300.t2"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	start_codon	1899464	1899466	.	+	0	transcript_id "Phchi.S3G007300.t2"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	CDS	1899464	1900291	0.47	+	0	transcript_id "Phchi.S3G007300.t2"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	exon	1899464	1900291	.	+	.	transcript_id "Phchi.S3G007300.t2"; gene_id "Phchi.S3G007300"
Phchi.S3	AUGUSTUS	stop_codon	1900292	1900294	.	+	0	transcript_id "Phchi.S3G007300.t2"; gene_id "Phchi.S3G007300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1744.t1 is derived from g8664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2835557	2837211	.	+	.	Phchi.S5G035300
Phchi.S5	AUGUSTUS	transcript	2835557	2837211	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	start_codon	2835557	2835559	.	+	0	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	CDS	2835557	2836051	0.94	+	0	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	exon	2835557	2836051	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	intron	2836052	2836124	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	CDS	2836125	2836411	0.99	+	0	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	exon	2836125	2836411	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	intron	2836412	2836539	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	CDS	2836540	2836631	0.72	+	1	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	exon	2836540	2836631	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	intron	2836632	2836712	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	CDS	2836713	2836772	0.72	+	2	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	exon	2836713	2836772	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	intron	2836773	2836857	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	CDS	2836858	2837015	1	+	2	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	exon	2836858	2837015	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	intron	2837016	2837112	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	CDS	2837113	2837211	1	+	0	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	exon	2837113	2837211	.	+	.	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
Phchi.S5	AUGUSTUS	stop_codon	2837212	2837214	.	+	0	transcript_id "Phchi.S5G035300.t1"; gene_id "Phchi.S5G035300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13558.t1 is derived from g12025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7487096	7488505	.	+	.	Phchi.S3G087700
Phchi.S3	AUGUSTUS	transcript	7487096	7488505	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	start_codon	7487096	7487098	.	+	0	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	CDS	7487096	7487196	0.46	+	0	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	exon	7487096	7487196	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	intron	7487197	7487350	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	CDS	7487351	7487449	0.5	+	1	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	exon	7487351	7487449	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	intron	7487450	7487684	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	CDS	7487685	7487753	0.38	+	1	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	exon	7487685	7487753	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	intron	7487754	7487839	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	CDS	7487840	7487993	0.6	+	1	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	exon	7487840	7487993	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	intron	7487994	7488099	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	CDS	7488100	7488213	0.71	+	0	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	exon	7488100	7488213	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	intron	7488214	7488478	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	CDS	7488479	7488505	0.74	+	0	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	exon	7488479	7488505	.	+	.	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
Phchi.S3	AUGUSTUS	stop_codon	7488506	7488508	.	+	0	transcript_id "Phchi.S3G087700.t1"; gene_id "Phchi.S3G087700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7097.t1 is derived from g4269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26888355	26893836	.	-	.	Phchi.S1G425600
Phchi.S1	AUGUSTUS	transcript	26888355	26893836	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	stop_codon	26888352	26888354	.	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26888355	26888465	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26888355	26888465	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26888466	26888560	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26888561	26888722	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26888561	26888722	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26888723	26888806	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26888807	26888989	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26888807	26888989	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26888990	26889092	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26889093	26889218	0.95	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26889093	26889218	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26889219	26889321	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26889322	26889453	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26889322	26889453	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26889454	26889547	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26889548	26889632	1	-	1	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26889548	26889632	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26889633	26889712	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26889713	26889829	0.94	-	1	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26889713	26889829	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26889830	26889931	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26889932	26890120	0.79	-	1	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26889932	26890120	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26890121	26890235	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26890236	26890408	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26890236	26890408	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26890409	26890497	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26890498	26890689	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26890498	26890689	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26890690	26890786	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26890787	26890921	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26890787	26890921	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26890922	26891031	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26891032	26891239	0.56	-	1	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26891032	26891239	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26891240	26891316	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26891317	26891560	0.56	-	2	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26891317	26891560	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26891561	26891764	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26891765	26891933	1	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26891765	26891933	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26891934	26892031	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26892032	26892153	1	-	2	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26892032	26892153	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26892154	26892253	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26892254	26892435	1	-	1	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26892254	26892435	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26892436	26892543	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26892544	26892660	0.96	-	1	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26892544	26892660	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26892661	26892783	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26892784	26892935	0.69	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26892784	26892935	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26892936	26893037	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26893038	26893114	0.23	-	2	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26893038	26893114	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26893115	26893544	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26893545	26893560	0.24	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26893545	26893560	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	intron	26893561	26893728	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	CDS	26893729	26893836	0.54	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	exon	26893729	26893836	.	-	.	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
Phchi.S1	AUGUSTUS	start_codon	26893834	26893836	.	-	0	transcript_id "Phchi.S1G425600.t1"; gene_id "Phchi.S1G425600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12668.t1 is derived from g14466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C42	AUGUSTUS	gene	40301	40804	.	+	.	Phchi.C42G000300
Phchi.C42	AUGUSTUS	transcript	40301	40804	.	+	.	transcript_id "Phchi.C42G000300.t1"; gene_id "Phchi.C42G000300"
Phchi.C42	AUGUSTUS	start_codon	40301	40303	.	+	0	transcript_id "Phchi.C42G000300.t1"; gene_id "Phchi.C42G000300"
Phchi.C42	AUGUSTUS	CDS	40301	40804	0.95	+	0	transcript_id "Phchi.C42G000300.t1"; gene_id "Phchi.C42G000300"
Phchi.C42	AUGUSTUS	exon	40301	40804	.	+	.	transcript_id "Phchi.C42G000300.t1"; gene_id "Phchi.C42G000300"
Phchi.C42	AUGUSTUS	stop_codon	40805	40807	.	+	0	transcript_id "Phchi.C42G000300.t1"; gene_id "Phchi.C42G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg416.t1 is derived from g10198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2959083	2960822	.	-	.	Phchi.S6G037500
Phchi.S6	AUGUSTUS	transcript	2959083	2960822	.	-	.	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	stop_codon	2959080	2959082	.	-	0	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	CDS	2959083	2960009	0.92	-	0	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	exon	2959083	2960009	.	-	.	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	intron	2960010	2960136	.	-	.	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	CDS	2960137	2960322	0.5	-	0	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	exon	2960137	2960322	.	-	.	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	intron	2960323	2960606	.	-	.	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	CDS	2960607	2960822	0.56	-	0	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	exon	2960607	2960822	.	-	.	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
Phchi.S6	AUGUSTUS	start_codon	2960820	2960822	.	-	0	transcript_id "Phchi.S6G037500.t1"; gene_id "Phchi.S6G037500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12881.t1 is derived from g11346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2903829	2906137	.	+	.	Phchi.S3G020000
Phchi.S3	AUGUSTUS	transcript	2903829	2906137	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	start_codon	2903829	2903831	.	+	0	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2903829	2903927	0.78	+	0	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2903829	2903927	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2903928	2903993	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2903994	2904111	0.47	+	0	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2903994	2904111	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2904112	2904191	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2904192	2904442	0.43	+	2	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2904192	2904442	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2904443	2904534	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2904535	2905133	0.41	+	0	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2904535	2905133	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2905134	2905224	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2905225	2905317	0.41	+	1	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2905225	2905317	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2905318	2905449	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2905450	2905631	1	+	1	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2905450	2905631	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2905632	2905740	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2905741	2905862	0.96	+	2	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2905741	2905862	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	intron	2905863	2905951	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	CDS	2905952	2906137	0.9	+	0	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	exon	2905952	2906137	.	+	.	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
Phchi.S3	AUGUSTUS	stop_codon	2906138	2906140	.	+	0	transcript_id "Phchi.S3G020000.t1"; gene_id "Phchi.S3G020000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2663.t1 is derived from g9583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8107383	8109158	.	+	.	Phchi.S5G127200
Phchi.S5	AUGUSTUS	transcript	8107383	8109158	.	+	.	transcript_id "Phchi.S5G127200.t1"; gene_id "Phchi.S5G127200"
Phchi.S5	AUGUSTUS	start_codon	8107383	8107385	.	+	0	transcript_id "Phchi.S5G127200.t1"; gene_id "Phchi.S5G127200"
Phchi.S5	AUGUSTUS	CDS	8107383	8109158	0.9	+	0	transcript_id "Phchi.S5G127200.t1"; gene_id "Phchi.S5G127200"
Phchi.S5	AUGUSTUS	exon	8107383	8109158	.	+	.	transcript_id "Phchi.S5G127200.t1"; gene_id "Phchi.S5G127200"
Phchi.S5	AUGUSTUS	stop_codon	8109159	8109161	.	+	0	transcript_id "Phchi.S5G127200.t1"; gene_id "Phchi.S5G127200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13784.t1 is derived from g12251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8882871	8885432	.	+	.	Phchi.S3G110300
Phchi.S3	AUGUSTUS	transcript	8882871	8885432	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	start_codon	8882871	8882873	.	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8882871	8883011	0.99	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8882871	8883011	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8883012	8883095	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8883096	8883310	1	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8883096	8883310	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8883311	8883441	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8883442	8883550	1	+	1	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8883442	8883550	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8883551	8883684	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8883685	8884065	1	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8883685	8884065	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8884066	8884153	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8884154	8884227	1	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8884154	8884227	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8884228	8884349	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8884350	8884417	1	+	1	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8884350	8884417	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8884418	8884545	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8884546	8884661	1	+	2	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8884546	8884661	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8884662	8884756	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8884757	8884863	1	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8884757	8884863	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8884864	8884972	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8884973	8885124	0.99	+	1	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8884973	8885124	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	intron	8885125	8885196	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	CDS	8885197	8885432	1	+	2	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	exon	8885197	8885432	.	+	.	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
Phchi.S3	AUGUSTUS	stop_codon	8885433	8885435	.	+	0	transcript_id "Phchi.S3G110300.t1"; gene_id "Phchi.S3G110300"
# This transcript jg6337.t2 is derived from g3509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6338.t1 is derived from g3510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22393864	22395213	.	+	.	Phchi.S1G349700
Phchi.S1	AUGUSTUS	transcript	22393864	22395213	.	+	.	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	start_codon	22393864	22393866	.	+	0	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	CDS	22393864	22394818	0.43	+	0	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	exon	22393864	22394818	.	+	.	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	intron	22394819	22394995	.	+	.	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	CDS	22394996	22395213	0.52	+	2	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	exon	22394996	22395213	.	+	.	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
Phchi.S1	AUGUSTUS	stop_codon	22395214	22395216	.	+	0	transcript_id "Phchi.S1G349700.t1"; gene_id "Phchi.S1G349700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5212.t1 is derived from g2382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15497818	15500063	.	-	.	Phchi.S1G237100
Phchi.S1	AUGUSTUS	transcript	15497818	15500063	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	stop_codon	15497815	15497817	.	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15497818	15497913	0.99	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15497818	15497913	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	intron	15497914	15498001	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15498002	15498070	0.99	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15498002	15498070	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	intron	15498071	15498196	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15498197	15498334	0.99	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15498197	15498334	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	intron	15498335	15498451	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15498452	15498493	0.47	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15498452	15498493	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	intron	15498494	15498616	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15498617	15499013	0.87	-	1	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15498617	15499013	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	intron	15499014	15499153	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15499154	15499555	0.97	-	1	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15499154	15499555	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	intron	15499556	15499689	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	CDS	15499690	15500063	0.98	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	exon	15499690	15500063	.	-	.	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
Phchi.S1	AUGUSTUS	start_codon	15500061	15500063	.	-	0	transcript_id "Phchi.S1G237100.t1"; gene_id "Phchi.S1G237100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4525.t1 is derived from g1695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10946241	10946465	.	-	.	Phchi.S1G168400
Phchi.S1	AUGUSTUS	transcript	10946241	10946465	.	-	.	transcript_id "Phchi.S1G168400.t1"; gene_id "Phchi.S1G168400"
Phchi.S1	AUGUSTUS	stop_codon	10946238	10946240	.	-	0	transcript_id "Phchi.S1G168400.t1"; gene_id "Phchi.S1G168400"
Phchi.S1	AUGUSTUS	CDS	10946241	10946465	0.55	-	0	transcript_id "Phchi.S1G168400.t1"; gene_id "Phchi.S1G168400"
Phchi.S1	AUGUSTUS	exon	10946241	10946465	.	-	.	transcript_id "Phchi.S1G168400.t1"; gene_id "Phchi.S1G168400"
Phchi.S1	AUGUSTUS	start_codon	10946463	10946465	.	-	0	transcript_id "Phchi.S1G168400.t1"; gene_id "Phchi.S1G168400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8151.t1 is derived from g5326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34107037	34110083	.	+	.	Phchi.S1G531000
Phchi.S1	AUGUSTUS	transcript	34107037	34110083	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	start_codon	34107037	34107039	.	+	0	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	CDS	34107037	34107102	0.66	+	0	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	exon	34107037	34107102	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	intron	34107103	34107231	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	CDS	34107232	34107677	1	+	0	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	exon	34107232	34107677	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	intron	34107678	34107858	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	CDS	34107859	34108349	0.99	+	1	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	exon	34107859	34108349	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	intron	34108350	34108457	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	CDS	34108458	34108651	0.66	+	2	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	exon	34108458	34108651	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	intron	34108652	34108782	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	CDS	34108783	34109367	0.27	+	0	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	exon	34108783	34109367	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	intron	34109368	34109483	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	CDS	34109484	34110083	0.31	+	0	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	exon	34109484	34110083	.	+	.	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
Phchi.S1	AUGUSTUS	stop_codon	34110084	34110086	.	+	0	transcript_id "Phchi.S1G531000.t1"; gene_id "Phchi.S1G531000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg908.t1 is derived from g10690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6379612	6380377	.	+	.	Phchi.S6G086700
Phchi.S6	AUGUSTUS	transcript	6379612	6380377	.	+	.	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	start_codon	6379612	6379614	.	+	0	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	CDS	6379612	6380235	0.97	+	0	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	exon	6379612	6380235	.	+	.	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	intron	6380236	6380326	.	+	.	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	CDS	6380327	6380377	1	+	0	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	exon	6380327	6380377	.	+	.	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
Phchi.S6	AUGUSTUS	stop_codon	6380378	6380380	.	+	0	transcript_id "Phchi.S6G086700.t1"; gene_id "Phchi.S6G086700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15390.t1 is derived from g13858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18802984	18807102	.	-	.	Phchi.S3G270900
Phchi.S3	AUGUSTUS	transcript	18802984	18807102	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	stop_codon	18802981	18802983	.	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18802984	18803083	1	-	1	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18802984	18803083	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18803084	18803156	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18803157	18803284	1	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18803157	18803284	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18803285	18803392	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18803393	18803499	1	-	2	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18803393	18803499	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18803500	18803627	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18803628	18803706	1	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18803628	18803706	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18803707	18803806	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18803807	18803893	1	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18803807	18803893	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18803894	18803987	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18803988	18804245	1	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18803988	18804245	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18804246	18804325	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18804326	18804475	0.95	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18804326	18804475	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18804476	18804580	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18804581	18804902	0.99	-	1	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18804581	18804902	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18804903	18804993	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18804994	18805161	0.89	-	1	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18804994	18805161	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18805162	18805259	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18805260	18805386	0.89	-	2	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18805260	18805386	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18805387	18805632	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18805633	18805657	0.9	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18805633	18805657	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18805658	18805748	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18805749	18805765	0.84	-	2	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18805749	18805765	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18805766	18805847	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18805848	18805898	1	-	2	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18805848	18805898	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18805899	18806212	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18806213	18806347	1	-	2	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18806213	18806347	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18806348	18806420	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18806421	18806539	0.66	-	1	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18806421	18806539	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18806540	18806664	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18806665	18806768	0.66	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18806665	18806768	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	intron	18806769	18807081	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	CDS	18807082	18807102	0.99	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	exon	18807082	18807102	.	-	.	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
Phchi.S3	AUGUSTUS	start_codon	18807100	18807102	.	-	0	transcript_id "Phchi.S3G270900.t1"; gene_id "Phchi.S3G270900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4194.t1 is derived from g1363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8866768	8867295	.	-	.	Phchi.S1G135300
Phchi.S1	AUGUSTUS	transcript	8866768	8867295	.	-	.	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	stop_codon	8866765	8866767	.	-	0	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	CDS	8866768	8866800	0.89	-	0	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	exon	8866768	8866800	.	-	.	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	intron	8866801	8866935	.	-	.	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	CDS	8866936	8867175	0.79	-	0	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	exon	8866936	8867175	.	-	.	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	intron	8867176	8867250	.	-	.	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	CDS	8867251	8867295	0.47	-	0	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	exon	8867251	8867295	.	-	.	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
Phchi.S1	AUGUSTUS	start_codon	8867293	8867295	.	-	0	transcript_id "Phchi.S1G135300.t1"; gene_id "Phchi.S1G135300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9230.t1 is derived from g6405.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40516918	40519504	.	-	.	Phchi.S1G638900
Phchi.S1	AUGUSTUS	transcript	40516918	40519504	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	stop_codon	40516915	40516917	.	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40516918	40517010	1	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40516918	40517010	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517011	40517137	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517138	40517278	1	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517138	40517278	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517279	40517352	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517353	40517411	1	-	2	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517353	40517411	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517412	40517489	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517490	40517580	1	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517490	40517580	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517581	40517663	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517664	40517746	1	-	2	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517664	40517746	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517747	40517857	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517858	40517922	0.67	-	1	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517858	40517922	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517923	40518027	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518028	40518111	1	-	1	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518028	40518111	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518112	40518206	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518207	40518272	1	-	1	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518207	40518272	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518273	40518354	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518355	40518413	1	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518355	40518413	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518414	40518498	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518499	40518574	1	-	1	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518499	40518574	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518575	40518674	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518675	40518778	1	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518675	40518778	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518779	40518864	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518865	40518899	1	-	2	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518865	40518899	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518900	40519019	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519020	40519076	1	-	2	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519020	40519076	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40519077	40519193	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519194	40519252	1	-	1	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519194	40519252	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40519253	40519349	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519350	40519504	0.86	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519350	40519504	.	-	.	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	start_codon	40519502	40519504	.	-	0	transcript_id "Phchi.S1G638900.t1"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	transcript	40516918	40519504	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	stop_codon	40516915	40516917	.	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40516918	40517010	1	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40516918	40517010	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517011	40517137	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517138	40517278	1	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517138	40517278	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517279	40517352	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517353	40517411	1	-	2	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517353	40517411	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517412	40517489	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517490	40517592	1	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517490	40517592	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517593	40517663	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517664	40517746	1	-	2	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517664	40517746	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517747	40517857	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517858	40517922	0.62	-	1	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517858	40517922	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517923	40518027	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518028	40518111	1	-	1	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518028	40518111	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518112	40518206	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518207	40518272	1	-	1	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518207	40518272	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518273	40518354	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518355	40518413	1	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518355	40518413	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518414	40518498	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518499	40518574	1	-	1	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518499	40518574	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518575	40518674	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518675	40518778	1	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518675	40518778	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518779	40518864	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518865	40518899	1	-	2	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518865	40518899	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518900	40519019	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519020	40519076	1	-	2	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519020	40519076	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40519077	40519193	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519194	40519252	1	-	1	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519194	40519252	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40519253	40519349	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519350	40519504	0.88	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519350	40519504	.	-	.	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	start_codon	40519502	40519504	.	-	0	transcript_id "Phchi.S1G638900.t2"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	transcript	40516918	40519504	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	stop_codon	40516915	40516917	.	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40516918	40517010	1	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40516918	40517010	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517011	40517137	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517138	40517278	1	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517138	40517278	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517279	40517352	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517353	40517411	1	-	2	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517353	40517411	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517412	40517489	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517490	40517580	1	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517490	40517580	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517581	40517663	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517664	40517746	1	-	2	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517664	40517746	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517747	40517857	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40517858	40517922	0.64	-	1	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40517858	40517922	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40517923	40518027	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518028	40518111	1	-	1	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518028	40518111	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518112	40518206	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518207	40518272	1	-	1	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518207	40518272	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518273	40518354	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518355	40518413	1	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518355	40518413	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518414	40518498	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518499	40518574	1	-	1	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518499	40518574	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518575	40518674	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518675	40518781	0.92	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518675	40518781	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518782	40518864	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40518865	40518899	1	-	2	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40518865	40518899	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40518900	40519019	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519020	40519076	1	-	2	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519020	40519076	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40519077	40519193	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519194	40519252	1	-	1	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519194	40519252	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	intron	40519253	40519349	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	CDS	40519350	40519504	0.84	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	exon	40519350	40519504	.	-	.	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
Phchi.S1	AUGUSTUS	start_codon	40519502	40519504	.	-	0	transcript_id "Phchi.S1G638900.t3"; gene_id "Phchi.S1G638900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1188.t1 is derived from g10971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8348373	8351279	.	-	.	Phchi.S6G114700
Phchi.S6	AUGUSTUS	transcript	8348373	8351279	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	stop_codon	8348370	8348372	.	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8348373	8348519	0.89	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8348373	8348519	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	intron	8348520	8348655	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8348656	8349087	0.93	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8348656	8349087	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	intron	8349088	8349196	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8349197	8349467	0.27	-	1	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8349197	8349467	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	intron	8349468	8349678	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8349679	8350014	0.36	-	1	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8349679	8350014	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	intron	8350015	8350106	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8350107	8350588	0.65	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8350107	8350588	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	intron	8350589	8350707	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8350708	8351157	0.97	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8350708	8351157	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	intron	8351158	8351231	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	CDS	8351232	8351279	0.79	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	exon	8351232	8351279	.	-	.	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
Phchi.S6	AUGUSTUS	start_codon	8351277	8351279	.	-	0	transcript_id "Phchi.S6G114700.t1"; gene_id "Phchi.S6G114700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg855.t1 is derived from g10637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5952581	5953419	.	-	.	Phchi.S6G081400
Phchi.S6	AUGUSTUS	transcript	5952619	5953419	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	stop_codon	5952616	5952618	.	-	0	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5952619	5952620	1	-	2	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5952619	5952620	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	intron	5952621	5952703	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5952704	5952762	1	-	1	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5952704	5952762	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	intron	5952763	5952861	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5952862	5953280	0.79	-	0	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5952862	5953280	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	intron	5953281	5953353	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5953354	5953419	0.97	-	0	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5953354	5953419	.	-	.	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	start_codon	5953417	5953419	.	-	0	transcript_id "Phchi.S6G081400.t1"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	transcript	5952581	5953419	.	-	.	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	stop_codon	5952578	5952580	.	-	0	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5952581	5952620	0.86	-	1	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5952581	5952620	.	-	.	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	intron	5952621	5952762	.	-	.	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5952763	5953280	0.76	-	0	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5952763	5953280	.	-	.	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	intron	5953281	5953353	.	-	.	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	CDS	5953354	5953419	0.98	-	0	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	exon	5953354	5953419	.	-	.	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
Phchi.S6	AUGUSTUS	start_codon	5953417	5953419	.	-	0	transcript_id "Phchi.S6G081400.t2"; gene_id "Phchi.S6G081400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2590.t1 is derived from g9510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7531753	7535796	.	+	.	Phchi.S5G119900
Phchi.S5	AUGUSTUS	transcript	7531753	7535796	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	start_codon	7531753	7531755	.	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7531753	7532023	1	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7531753	7532023	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7532024	7532107	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7532108	7532153	0.99	+	2	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7532108	7532153	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7532154	7532236	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7532237	7533200	0.82	+	1	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7532237	7533200	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7533201	7533285	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7533286	7533462	1	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7533286	7533462	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7533463	7533553	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7533554	7533670	0.96	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7533554	7533670	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7533671	7533787	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7533788	7533892	0.96	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7533788	7533892	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7533893	7534015	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7534016	7534150	1	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7534016	7534150	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7534151	7534247	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7534248	7534303	1	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7534248	7534303	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7534304	7534388	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7534389	7534494	1	+	1	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7534389	7534494	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7534495	7534594	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7534595	7534711	1	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7534595	7534711	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7534712	7534807	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7534808	7534931	1	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7534808	7534931	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7534932	7535006	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7535007	7535137	1	+	2	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7535007	7535137	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	intron	7535138	7535226	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	CDS	7535227	7535796	0.98	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	exon	7535227	7535796	.	+	.	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
Phchi.S5	AUGUSTUS	stop_codon	7535797	7535799	.	+	0	transcript_id "Phchi.S5G119900.t1"; gene_id "Phchi.S5G119900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5744.t1 is derived from g2914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18690034	18691888	.	-	.	Phchi.S1G290300
Phchi.S1	AUGUSTUS	transcript	18690034	18691888	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	stop_codon	18690031	18690033	.	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18690034	18690210	0.59	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18690034	18690210	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18690211	18690658	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18690659	18690687	0.43	-	2	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18690659	18690687	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18690688	18690772	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18690773	18690797	0.43	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18690773	18690797	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18690798	18690927	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18690928	18691035	1	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18690928	18691035	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18691036	18691189	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18691190	18691195	0.61	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18691190	18691195	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18691196	18691257	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18691258	18691262	0.61	-	2	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18691258	18691262	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18691263	18691412	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18691413	18691519	1	-	1	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18691413	18691519	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18691520	18691750	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18691751	18691762	0.93	-	1	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18691751	18691762	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	intron	18691763	18691844	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	CDS	18691845	18691888	0.3	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	exon	18691845	18691888	.	-	.	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
Phchi.S1	AUGUSTUS	start_codon	18691886	18691888	.	-	0	transcript_id "Phchi.S1G290300.t1"; gene_id "Phchi.S1G290300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11738.t1 is derived from g15790.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7929033	7930892	.	+	.	Phchi.S4G132000
Phchi.S4	AUGUSTUS	transcript	7929033	7930892	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	start_codon	7929033	7929035	.	+	0	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7929033	7929311	0.96	+	0	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7929033	7929311	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7929312	7929426	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7929427	7929768	1	+	0	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7929427	7929768	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7929769	7929952	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7929953	7930119	1	+	0	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7929953	7930119	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7930120	7930234	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7930235	7930463	1	+	1	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7930235	7930463	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7930464	7930553	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7930554	7930892	0.96	+	0	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7930554	7930892	.	+	.	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	stop_codon	7930893	7930895	.	+	0	transcript_id "Phchi.S4G132000.t1"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	transcript	7929033	7930892	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	start_codon	7929033	7929035	.	+	0	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7929033	7929311	0.97	+	0	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7929033	7929311	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7929312	7929426	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7929427	7929768	1	+	0	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7929427	7929768	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7929769	7929859	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7929860	7930119	1	+	0	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7929860	7930119	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7930120	7930234	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7930235	7930463	1	+	1	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7930235	7930463	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	intron	7930464	7930553	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	CDS	7930554	7930892	0.95	+	0	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	exon	7930554	7930892	.	+	.	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
Phchi.S4	AUGUSTUS	stop_codon	7930893	7930895	.	+	0	transcript_id "Phchi.S4G132000.t2"; gene_id "Phchi.S4G132000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg43.t1 is derived from g9825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	43852	45488	.	+	.	Phchi.S6G000200
Phchi.S6	AUGUSTUS	transcript	43852	45488	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	start_codon	43852	43854	.	+	0	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	CDS	43852	44208	0.89	+	0	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	exon	43852	44208	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	intron	44209	44376	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	CDS	44377	44406	0.42	+	0	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	exon	44377	44406	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	intron	44407	44544	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	CDS	44545	44626	0.44	+	0	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	exon	44545	44626	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	intron	44627	44785	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	CDS	44786	45020	0.25	+	2	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	exon	44786	45020	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	intron	45021	45214	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	CDS	45215	45488	0.56	+	1	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	exon	45215	45488	.	+	.	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
Phchi.S6	AUGUSTUS	stop_codon	45489	45491	.	+	0	transcript_id "Phchi.S6G000200.t1"; gene_id "Phchi.S6G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11870.t1 is derived from g15922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8932526	8934683	.	-	.	Phchi.S4G145200
Phchi.S4	AUGUSTUS	transcript	8932526	8934683	.	-	.	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	stop_codon	8932523	8932525	.	-	0	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	CDS	8932526	8933034	0.96	-	2	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	exon	8932526	8933034	.	-	.	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	intron	8933035	8933123	.	-	.	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	CDS	8933124	8933224	1	-	1	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	exon	8933124	8933224	.	-	.	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	intron	8933225	8933301	.	-	.	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	CDS	8933302	8934683	0.63	-	0	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	exon	8933302	8934683	.	-	.	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
Phchi.S4	AUGUSTUS	start_codon	8934681	8934683	.	-	0	transcript_id "Phchi.S4G145200.t1"; gene_id "Phchi.S4G145200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11666.t1 is derived from g15717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7586630	7587349	.	+	.	Phchi.S4G124800
Phchi.S4	AUGUSTUS	transcript	7586630	7587349	.	+	.	transcript_id "Phchi.S4G124800.t1"; gene_id "Phchi.S4G124800"
Phchi.S4	AUGUSTUS	start_codon	7586630	7586632	.	+	0	transcript_id "Phchi.S4G124800.t1"; gene_id "Phchi.S4G124800"
Phchi.S4	AUGUSTUS	CDS	7586630	7587349	1	+	0	transcript_id "Phchi.S4G124800.t1"; gene_id "Phchi.S4G124800"
Phchi.S4	AUGUSTUS	exon	7586630	7587349	.	+	.	transcript_id "Phchi.S4G124800.t1"; gene_id "Phchi.S4G124800"
Phchi.S4	AUGUSTUS	stop_codon	7587350	7587352	.	+	0	transcript_id "Phchi.S4G124800.t1"; gene_id "Phchi.S4G124800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4256.t1 is derived from g1425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9179718	9180099	.	+	.	Phchi.S1G141500
Phchi.S1	AUGUSTUS	transcript	9179718	9180099	.	+	.	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	start_codon	9179718	9179720	.	+	0	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	CDS	9179718	9179853	0.47	+	0	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	exon	9179718	9179853	.	+	.	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	intron	9179854	9179950	.	+	.	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	CDS	9179951	9180099	0.98	+	2	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	exon	9179951	9180099	.	+	.	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
Phchi.S1	AUGUSTUS	stop_codon	9180100	9180102	.	+	0	transcript_id "Phchi.S1G141500.t1"; gene_id "Phchi.S1G141500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7871.t1 is derived from g5045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31643052	31643442	.	+	.	Phchi.S1G503000
Phchi.S1	AUGUSTUS	transcript	31643052	31643442	.	+	.	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	start_codon	31643052	31643054	.	+	0	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	CDS	31643052	31643115	0.2	+	0	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	exon	31643052	31643115	.	+	.	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	intron	31643116	31643209	.	+	.	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	CDS	31643210	31643442	0.58	+	2	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	exon	31643210	31643442	.	+	.	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
Phchi.S1	AUGUSTUS	stop_codon	31643443	31643445	.	+	0	transcript_id "Phchi.S1G503000.t1"; gene_id "Phchi.S1G503000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11148.t1 is derived from g15198.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4385306	4387288	.	+	.	Phchi.S4G073000
Phchi.S4	AUGUSTUS	transcript	4385306	4387288	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	start_codon	4385306	4385308	.	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385306	4385407	1	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385306	4385407	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4385408	4385489	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385490	4385651	1	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385490	4385651	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4385652	4385789	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385790	4385842	1	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385790	4385842	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4385843	4385942	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385943	4386035	1	+	1	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385943	4386035	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386036	4386128	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386129	4386191	1	+	1	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386129	4386191	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386192	4386341	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386342	4386431	1	+	1	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386342	4386431	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386432	4386502	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386503	4386590	1	+	1	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386503	4386590	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386591	4386676	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386677	4386719	1	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386677	4386719	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386720	4386816	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386817	4386934	0.63	+	2	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386817	4386934	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386935	4387026	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4387027	4387090	1	+	1	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4387027	4387090	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4387091	4387165	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4387166	4387288	1	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4387166	4387288	.	+	.	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	stop_codon	4387289	4387291	.	+	0	transcript_id "Phchi.S4G073000.t1"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	transcript	4385306	4387288	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	start_codon	4385306	4385308	.	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385306	4385407	1	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385306	4385407	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4385408	4385489	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385490	4385651	1	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385490	4385651	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4385652	4385755	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385756	4385823	0.99	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385756	4385823	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4385824	4385942	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4385943	4386035	0.59	+	1	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4385943	4386035	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386036	4386128	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386129	4386191	1	+	1	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386129	4386191	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386192	4386341	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386342	4386431	1	+	1	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386342	4386431	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386432	4386502	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386503	4386590	1	+	1	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386503	4386590	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386591	4386676	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386677	4386719	1	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386677	4386719	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386720	4386816	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4386817	4386934	0.59	+	2	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4386817	4386934	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4386935	4387026	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4387027	4387090	1	+	1	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4387027	4387090	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	intron	4387091	4387165	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	CDS	4387166	4387288	0.99	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	exon	4387166	4387288	.	+	.	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
Phchi.S4	AUGUSTUS	stop_codon	4387289	4387291	.	+	0	transcript_id "Phchi.S4G073000.t2"; gene_id "Phchi.S4G073000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11697.t1 is derived from g15748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7744638	7745633	.	-	.	Phchi.S4G127900
Phchi.S4	AUGUSTUS	transcript	7744638	7745633	.	-	.	transcript_id "Phchi.S4G127900.t1"; gene_id "Phchi.S4G127900"
Phchi.S4	AUGUSTUS	stop_codon	7744635	7744637	.	-	0	transcript_id "Phchi.S4G127900.t1"; gene_id "Phchi.S4G127900"
Phchi.S4	AUGUSTUS	CDS	7744638	7745633	0.99	-	0	transcript_id "Phchi.S4G127900.t1"; gene_id "Phchi.S4G127900"
Phchi.S4	AUGUSTUS	exon	7744638	7745633	.	-	.	transcript_id "Phchi.S4G127900.t1"; gene_id "Phchi.S4G127900"
Phchi.S4	AUGUSTUS	start_codon	7745631	7745633	.	-	0	transcript_id "Phchi.S4G127900.t1"; gene_id "Phchi.S4G127900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10709.t1 is derived from g14759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1705041	1707347	.	+	.	Phchi.S4G029100
Phchi.S4	AUGUSTUS	transcript	1705041	1707347	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	start_codon	1705041	1705043	.	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1705041	1705349	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1705041	1705349	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1705350	1705491	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1705492	1705601	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1705492	1705601	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1705602	1705711	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1705712	1705769	1	+	1	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1705712	1705769	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1705770	1705862	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1705863	1706126	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1705863	1706126	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1706127	1706241	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1706242	1706379	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1706242	1706379	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1706380	1706489	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1706490	1706541	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1706490	1706541	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1706542	1706659	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1706660	1706739	1	+	2	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1706660	1706739	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1706740	1706938	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1706939	1706998	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1706939	1706998	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1706999	1707086	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1707087	1707167	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1707087	1707167	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	intron	1707168	1707257	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	CDS	1707258	1707347	1	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	exon	1707258	1707347	.	+	.	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
Phchi.S4	AUGUSTUS	stop_codon	1707348	1707350	.	+	0	transcript_id "Phchi.S4G029100.t1"; gene_id "Phchi.S4G029100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8279.t1 is derived from g5454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35075328	35076458	.	-	.	Phchi.S1G543800
Phchi.S1	AUGUSTUS	transcript	35075328	35076458	.	-	.	transcript_id "Phchi.S1G543800.t1"; gene_id "Phchi.S1G543800"
Phchi.S1	AUGUSTUS	stop_codon	35075325	35075327	.	-	0	transcript_id "Phchi.S1G543800.t1"; gene_id "Phchi.S1G543800"
Phchi.S1	AUGUSTUS	CDS	35075328	35076458	1	-	0	transcript_id "Phchi.S1G543800.t1"; gene_id "Phchi.S1G543800"
Phchi.S1	AUGUSTUS	exon	35075328	35076458	.	-	.	transcript_id "Phchi.S1G543800.t1"; gene_id "Phchi.S1G543800"
Phchi.S1	AUGUSTUS	start_codon	35076456	35076458	.	-	0	transcript_id "Phchi.S1G543800.t1"; gene_id "Phchi.S1G543800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6614.t1 is derived from g3786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24011541	24012960	.	+	.	Phchi.S1G377300
Phchi.S1	AUGUSTUS	transcript	24011541	24012960	.	+	.	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	start_codon	24011541	24011543	.	+	0	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	CDS	24011541	24012062	0.98	+	0	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	exon	24011541	24012062	.	+	.	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	intron	24012063	24012149	.	+	.	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	CDS	24012150	24012323	1	+	0	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	exon	24012150	24012323	.	+	.	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	intron	24012324	24012414	.	+	.	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	CDS	24012415	24012960	1	+	0	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	exon	24012415	24012960	.	+	.	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
Phchi.S1	AUGUSTUS	stop_codon	24012961	24012963	.	+	0	transcript_id "Phchi.S1G377300.t1"; gene_id "Phchi.S1G377300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12817.t1 is derived from g11282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2490847	2492587	.	-	.	Phchi.S3G013600
Phchi.S3	AUGUSTUS	transcript	2490847	2492587	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	stop_codon	2490844	2490846	.	-	0	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	CDS	2490847	2491029	1	-	0	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	exon	2490847	2491029	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	intron	2491030	2491124	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	CDS	2491125	2491317	1	-	1	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	exon	2491125	2491317	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	intron	2491318	2491422	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	CDS	2491423	2491658	1	-	0	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	exon	2491423	2491658	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	intron	2491659	2491741	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	CDS	2491742	2491914	1	-	2	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	exon	2491742	2491914	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	intron	2491915	2492004	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	CDS	2492005	2492055	1	-	2	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	exon	2492005	2492055	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	intron	2492056	2492136	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	CDS	2492137	2492587	1	-	0	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	exon	2492137	2492587	.	-	.	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
Phchi.S3	AUGUSTUS	start_codon	2492585	2492587	.	-	0	transcript_id "Phchi.S3G013600.t1"; gene_id "Phchi.S3G013600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15637.t1 is derived from g14106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20413792	20420974	.	-	.	Phchi.S3G295600
Phchi.S3	AUGUSTUS	transcript	20413792	20420974	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	stop_codon	20413789	20413791	.	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20413792	20414180	0.98	-	2	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20413792	20414180	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20414181	20414260	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20414261	20414670	0.8	-	1	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20414261	20414670	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20414671	20414755	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20414756	20414907	0.44	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20414756	20414907	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20414908	20415179	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20415180	20415308	0.37	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20415180	20415308	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20415309	20415417	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20415418	20415447	0.33	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20415418	20415447	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20415448	20415634	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20415635	20415729	0.6	-	2	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20415635	20415729	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20415730	20415876	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20415877	20416039	0.33	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20415877	20416039	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20416040	20416221	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20416222	20416332	0.95	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20416222	20416332	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20416333	20416404	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20416405	20417306	0.99	-	2	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20416405	20417306	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20417307	20417392	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20417393	20417795	0.93	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20417393	20417795	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20417796	20417892	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20417893	20418552	0.52	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20417893	20418552	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20418553	20418731	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20418732	20418917	0.52	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20418732	20418917	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20418918	20419058	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20419059	20419391	0.71	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20419059	20419391	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20419392	20419491	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20419492	20420078	0.96	-	2	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20419492	20420078	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20420079	20420190	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20420191	20420343	1	-	2	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20420191	20420343	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	intron	20420344	20420643	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	CDS	20420644	20420974	0.64	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	exon	20420644	20420974	.	-	.	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
Phchi.S3	AUGUSTUS	start_codon	20420972	20420974	.	-	0	transcript_id "Phchi.S3G295600.t1"; gene_id "Phchi.S3G295600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10647.t1 is derived from g14697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1401690	1407862	.	-	.	Phchi.S4G022900
Phchi.S4	AUGUSTUS	transcript	1401690	1407862	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	stop_codon	1401687	1401689	.	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1401690	1401715	0.83	-	2	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1401690	1401715	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1401716	1401834	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1401835	1401901	0.83	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1401835	1401901	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1401902	1401984	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1401985	1402080	1	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1401985	1402080	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1402081	1402156	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1402157	1402219	1	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1402157	1402219	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1402220	1402323	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1402324	1402489	0.62	-	1	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1402324	1402489	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1402490	1402592	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1402593	1406581	0.96	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1402593	1406581	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1406582	1406813	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1406814	1406892	1	-	1	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1406814	1406892	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1406893	1407055	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1407056	1407116	1	-	2	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1407056	1407116	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1407117	1407226	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1407227	1407298	1	-	2	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1407227	1407298	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1407299	1407510	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1407511	1407547	0.87	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1407511	1407547	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	intron	1407548	1407625	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	CDS	1407626	1407862	0.89	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	exon	1407626	1407862	.	-	.	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
Phchi.S4	AUGUSTUS	start_codon	1407860	1407862	.	-	0	transcript_id "Phchi.S4G022900.t1"; gene_id "Phchi.S4G022900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5628.t1 is derived from g2798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17958347	17962927	.	-	.	Phchi.S1G278700
Phchi.S1	AUGUSTUS	transcript	17958347	17962927	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	stop_codon	17958344	17958346	.	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17958347	17958505	0.55	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17958347	17958505	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17958506	17958639	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17958640	17958719	0.97	-	2	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17958640	17958719	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17958720	17958876	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17958877	17959144	0.82	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17958877	17959144	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17959145	17959257	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17959258	17959432	0.92	-	1	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17959258	17959432	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17959433	17959560	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17959561	17959691	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17959561	17959691	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17959692	17959778	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17959779	17959898	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17959779	17959898	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17959899	17959978	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17959979	17960055	1	-	2	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17959979	17960055	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17960056	17960150	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17960151	17960397	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17960151	17960397	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17960398	17960534	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17960535	17960697	1	-	1	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17960535	17960697	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17960698	17960792	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17960793	17960911	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17960793	17960911	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17960912	17961031	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17961032	17961151	0.99	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17961032	17961151	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17961152	17961294	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17961295	17961580	0.66	-	1	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17961295	17961580	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17961581	17961682	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17961683	17961891	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17961683	17961891	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17961892	17962116	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17962117	17962266	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17962117	17962266	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17962267	17962345	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17962346	17962528	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17962346	17962528	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	intron	17962529	17962627	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	CDS	17962628	17962927	1	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	exon	17962628	17962927	.	-	.	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
Phchi.S1	AUGUSTUS	start_codon	17962925	17962927	.	-	0	transcript_id "Phchi.S1G278700.t1"; gene_id "Phchi.S1G278700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13710.t1 is derived from g12177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8311220	8313632	.	+	.	Phchi.S3G102900
Phchi.S3	AUGUSTUS	transcript	8311220	8313632	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	start_codon	8311220	8311222	.	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8311220	8311744	0.91	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8311220	8311744	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8311745	8311878	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8311879	8312025	0.69	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8311879	8312025	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312026	8312137	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8312138	8312270	0.99	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8312138	8312270	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312271	8312350	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8312351	8312760	0.99	+	2	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8312351	8312760	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312761	8312848	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8312849	8312925	1	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8312849	8312925	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312926	8313014	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8313015	8313150	1	+	1	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8313015	8313150	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8313151	8313232	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8313233	8313436	1	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8313233	8313436	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8313437	8313512	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8313513	8313632	1	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8313513	8313632	.	+	.	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	stop_codon	8313633	8313635	.	+	0	transcript_id "Phchi.S3G102900.t1"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	transcript	8311220	8313632	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	start_codon	8311220	8311222	.	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8311220	8311744	0.91	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8311220	8311744	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8311745	8311835	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8311836	8311868	0.43	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8311836	8311868	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8311869	8312137	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8312138	8312270	0.88	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8312138	8312270	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312271	8312350	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8312351	8312760	0.99	+	2	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8312351	8312760	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312761	8312848	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8312849	8312925	1	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8312849	8312925	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8312926	8313014	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8313015	8313150	1	+	1	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8313015	8313150	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8313151	8313232	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8313233	8313436	1	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8313233	8313436	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	intron	8313437	8313512	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	CDS	8313513	8313632	1	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	exon	8313513	8313632	.	+	.	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
Phchi.S3	AUGUSTUS	stop_codon	8313633	8313635	.	+	0	transcript_id "Phchi.S3G102900.t2"; gene_id "Phchi.S3G102900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15545.t1 is derived from g14014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19821441	19823191	.	-	.	Phchi.S3G286400
Phchi.S3	AUGUSTUS	transcript	19821441	19823191	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	stop_codon	19821438	19821440	.	-	0	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19821441	19821652	0.99	-	2	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19821441	19821652	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19821653	19821797	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19821798	19821844	0.99	-	1	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19821798	19821844	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19821845	19821942	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19821943	19821980	1	-	0	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19821943	19821980	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19821981	19822101	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19822102	19822164	1	-	0	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19822102	19822164	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19822165	19822316	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19822317	19822403	1	-	0	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19822317	19822403	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19822404	19822520	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19822521	19822621	1	-	2	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19822521	19822621	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19822622	19822798	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19822799	19822882	1	-	2	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19822799	19822882	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	intron	19822883	19823004	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	CDS	19823005	19823191	0.67	-	0	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	exon	19823005	19823191	.	-	.	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
Phchi.S3	AUGUSTUS	start_codon	19823189	19823191	.	-	0	transcript_id "Phchi.S3G286400.t1"; gene_id "Phchi.S3G286400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15299.t1 is derived from g13767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18287294	18287761	.	-	.	Phchi.S3G261800
Phchi.S3	AUGUSTUS	transcript	18287294	18287761	.	-	.	transcript_id "Phchi.S3G261800.t1"; gene_id "Phchi.S3G261800"
Phchi.S3	AUGUSTUS	stop_codon	18287291	18287293	.	-	0	transcript_id "Phchi.S3G261800.t1"; gene_id "Phchi.S3G261800"
Phchi.S3	AUGUSTUS	CDS	18287294	18287761	0.79	-	0	transcript_id "Phchi.S3G261800.t1"; gene_id "Phchi.S3G261800"
Phchi.S3	AUGUSTUS	exon	18287294	18287761	.	-	.	transcript_id "Phchi.S3G261800.t1"; gene_id "Phchi.S3G261800"
Phchi.S3	AUGUSTUS	start_codon	18287759	18287761	.	-	0	transcript_id "Phchi.S3G261800.t1"; gene_id "Phchi.S3G261800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5153.t1 is derived from g2323.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15173237	15174139	.	-	.	Phchi.S1G231200
Phchi.S1	AUGUSTUS	transcript	15173237	15174139	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	stop_codon	15173234	15173236	.	-	0	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173237	15173280	0.7	-	2	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173237	15173280	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	intron	15173281	15173372	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173373	15173569	0.96	-	1	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173373	15173569	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	intron	15173570	15173779	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173780	15173901	0.98	-	0	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173780	15173901	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	intron	15173902	15174085	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15174086	15174139	0.98	-	0	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15174086	15174139	.	-	.	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	start_codon	15174137	15174139	.	-	0	transcript_id "Phchi.S1G231200.t1"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	transcript	15173237	15173933	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	stop_codon	15173234	15173236	.	-	0	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173237	15173280	0.43	-	2	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173237	15173280	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	intron	15173281	15173372	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173373	15173569	0.39	-	1	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173373	15173569	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	intron	15173570	15173634	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173635	15173692	0.42	-	2	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173635	15173692	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	intron	15173693	15173779	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	CDS	15173780	15173933	0.9	-	0	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	exon	15173780	15173933	.	-	.	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
Phchi.S1	AUGUSTUS	start_codon	15173931	15173933	.	-	0	transcript_id "Phchi.S1G231200.t2"; gene_id "Phchi.S1G231200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13145.t1 is derived from g11610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4387812	4388529	.	+	.	Phchi.S3G046400
Phchi.S3	AUGUSTUS	transcript	4387812	4388529	.	+	.	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	start_codon	4387812	4387814	.	+	0	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	CDS	4387812	4388075	0.76	+	0	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	exon	4387812	4388075	.	+	.	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	intron	4388076	4388154	.	+	.	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	CDS	4388155	4388343	1	+	0	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	exon	4388155	4388343	.	+	.	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	intron	4388344	4388436	.	+	.	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	CDS	4388437	4388529	1	+	0	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	exon	4388437	4388529	.	+	.	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
Phchi.S3	AUGUSTUS	stop_codon	4388530	4388532	.	+	0	transcript_id "Phchi.S3G046400.t1"; gene_id "Phchi.S3G046400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8515.t1 is derived from g5690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36401149	36401872	.	-	.	Phchi.S1G567400
Phchi.S1	AUGUSTUS	transcript	36401149	36401872	.	-	.	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	stop_codon	36401146	36401148	.	-	0	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	CDS	36401149	36401230	1	-	1	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	exon	36401149	36401230	.	-	.	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	intron	36401231	36401336	.	-	.	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	CDS	36401337	36401694	1	-	2	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	exon	36401337	36401694	.	-	.	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	intron	36401695	36401856	.	-	.	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	CDS	36401857	36401872	1	-	0	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	exon	36401857	36401872	.	-	.	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
Phchi.S1	AUGUSTUS	start_codon	36401870	36401872	.	-	0	transcript_id "Phchi.S1G567400.t1"; gene_id "Phchi.S1G567400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8378.t1 is derived from g5553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35594673	35595721	.	-	.	Phchi.S1G553700
Phchi.S1	AUGUSTUS	transcript	35594673	35595721	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	stop_codon	35594670	35594672	.	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	CDS	35594673	35594819	0.99	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	exon	35594673	35594819	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	intron	35594820	35594910	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	CDS	35594911	35594997	1	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	exon	35594911	35594997	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	intron	35594998	35595078	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	CDS	35595079	35595132	1	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	exon	35595079	35595132	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	intron	35595133	35595219	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	CDS	35595220	35595282	1	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	exon	35595220	35595282	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	intron	35595283	35595390	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	CDS	35595391	35595441	1	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	exon	35595391	35595441	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	intron	35595442	35595595	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	CDS	35595596	35595721	0.98	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	exon	35595596	35595721	.	-	.	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
Phchi.S1	AUGUSTUS	start_codon	35595719	35595721	.	-	0	transcript_id "Phchi.S1G553700.t1"; gene_id "Phchi.S1G553700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2804.t1 is derived from g9724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8961004	8962872	.	-	.	Phchi.S5G141300
Phchi.S5	AUGUSTUS	transcript	8961004	8962872	.	-	.	transcript_id "Phchi.S5G141300.t1"; gene_id "Phchi.S5G141300"
Phchi.S5	AUGUSTUS	stop_codon	8961001	8961003	.	-	0	transcript_id "Phchi.S5G141300.t1"; gene_id "Phchi.S5G141300"
Phchi.S5	AUGUSTUS	CDS	8961004	8962872	0.33	-	0	transcript_id "Phchi.S5G141300.t1"; gene_id "Phchi.S5G141300"
Phchi.S5	AUGUSTUS	exon	8961004	8962872	.	-	.	transcript_id "Phchi.S5G141300.t1"; gene_id "Phchi.S5G141300"
Phchi.S5	AUGUSTUS	start_codon	8962870	8962872	.	-	0	transcript_id "Phchi.S5G141300.t1"; gene_id "Phchi.S5G141300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg257.t1 is derived from g10039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1733893	1746201	.	-	.	Phchi.S6G021600
Phchi.S6	AUGUSTUS	transcript	1733893	1746201	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	stop_codon	1733890	1733892	.	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1733893	1733941	1	-	1	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1733893	1733941	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1733942	1734025	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1734026	1734129	0.92	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1734026	1734129	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1734130	1734365	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1734366	1734422	0.82	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1734366	1734422	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1734423	1734509	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1734510	1734638	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1734510	1734638	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1734639	1734724	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1734725	1734898	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1734725	1734898	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1734899	1734967	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1734968	1735147	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1734968	1735147	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1735148	1735249	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1735250	1735417	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1735250	1735417	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1735418	1735509	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1735510	1735605	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1735510	1735605	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1735606	1735704	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1735705	1735767	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1735705	1735767	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1735768	1735843	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1735844	1736012	1	-	1	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1735844	1736012	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1736013	1736110	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1736111	1736178	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1736111	1736178	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1736179	1736350	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1736351	1736494	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1736351	1736494	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1736495	1736586	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1736587	1736626	1	-	1	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1736587	1736626	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1736627	1736709	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1736710	1736741	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1736710	1736741	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1736742	1736834	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1736835	1736900	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1736835	1736900	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1736901	1737026	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1737027	1737218	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1737027	1737218	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1737219	1737363	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1737364	1737513	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1737364	1737513	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1737514	1737596	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1737597	1737687	0.98	-	1	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1737597	1737687	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1737688	1737802	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1737803	1737891	0.98	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1737803	1737891	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1737892	1737981	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1737982	1738044	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1737982	1738044	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1738045	1738235	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1738236	1738361	0.93	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1738236	1738361	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1738362	1738468	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1738469	1738558	0.98	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1738469	1738558	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1738559	1738644	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1738645	1738767	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1738645	1738767	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1738768	1738872	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1738873	1738989	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1738873	1738989	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1738990	1739082	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1739083	1739286	0.96	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1739083	1739286	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1739287	1739374	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1739375	1739455	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1739375	1739455	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1739456	1739573	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1739574	1739654	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1739574	1739654	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1739655	1739754	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1739755	1739856	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1739755	1739856	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1739857	1739958	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1739959	1740183	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1739959	1740183	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1740184	1740324	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1740325	1740480	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1740325	1740480	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1740481	1740600	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1740601	1740813	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1740601	1740813	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1740814	1740977	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1740978	1741127	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1740978	1741127	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1741128	1741241	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1741242	1741364	0.92	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1741242	1741364	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1741365	1741445	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1741446	1741511	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1741446	1741511	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1741512	1741609	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1741610	1741675	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1741610	1741675	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1741676	1741756	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1741757	1741888	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1741757	1741888	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1741889	1742038	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1742039	1742113	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1742039	1742113	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1742114	1742200	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1742201	1742284	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1742201	1742284	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1742285	1742370	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1742371	1742523	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1742371	1742523	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1742524	1742649	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1742650	1742715	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1742650	1742715	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1742716	1742831	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1742832	1742993	0.97	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1742832	1742993	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1742994	1743078	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1743079	1743195	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1743079	1743195	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1743196	1743276	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1743277	1743348	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1743277	1743348	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1743349	1743499	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1743500	1743559	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1743500	1743559	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1743560	1743686	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1743687	1743803	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1743687	1743803	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1743804	1743911	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1743912	1744235	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1743912	1744235	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1744236	1744437	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1744438	1744542	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1744438	1744542	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1744543	1744633	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1744634	1744699	1	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1744634	1744699	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1744700	1744859	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1744860	1744937	0.64	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1744860	1744937	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1744938	1745041	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1745042	1745339	0.76	-	1	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1745042	1745339	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1745340	1745473	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1745474	1745642	1	-	2	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1745474	1745642	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1745643	1745729	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1745730	1745794	1	-	1	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1745730	1745794	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	intron	1745795	1746076	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	CDS	1746077	1746201	0.48	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	exon	1746077	1746201	.	-	.	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
Phchi.S6	AUGUSTUS	start_codon	1746199	1746201	.	-	0	transcript_id "Phchi.S6G021600.t1"; gene_id "Phchi.S6G021600"
# This transcript jg1717.t2 is derived from g8637.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1718.t1 is derived from g8638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2684922	2689146	.	+	.	Phchi.S5G032700
Phchi.S5	AUGUSTUS	transcript	2684922	2689146	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	start_codon	2684922	2684924	.	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2684922	2685213	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2684922	2685213	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685214	2685381	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685382	2685437	1	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685382	2685437	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685438	2685519	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685520	2685624	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685520	2685624	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685625	2685717	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685718	2685820	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685718	2685820	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685821	2685946	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685947	2686063	1	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685947	2686063	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686064	2686162	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686163	2686351	0.91	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686163	2686351	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686352	2686459	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686460	2686521	0.86	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686460	2686521	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686522	2686622	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686623	2686716	0.9	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686623	2686716	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686717	2686856	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686857	2686965	1	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686857	2686965	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686966	2687041	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687042	2687104	1	+	1	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687042	2687104	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687105	2687203	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687204	2687284	1	+	1	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687204	2687284	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687285	2687416	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687417	2687523	0.5	+	1	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687417	2687523	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687524	2687698	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687699	2687868	0.39	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687699	2687868	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687869	2688061	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688062	2688127	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688062	2688127	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688128	2688204	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688205	2688309	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688205	2688309	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688310	2688399	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688400	2688447	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688400	2688447	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688448	2688548	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688549	2688683	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688549	2688683	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688684	2688860	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688861	2688930	1	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688861	2688930	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688931	2689090	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2689091	2689146	0.69	+	2	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2689091	2689146	.	+	.	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	stop_codon	2689147	2689149	.	+	0	transcript_id "Phchi.S5G032700.t1"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	transcript	2684922	2689146	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	start_codon	2684922	2684924	.	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2684922	2685213	0.99	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2684922	2685213	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685214	2685381	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685382	2685437	1	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685382	2685437	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685438	2685519	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685520	2685624	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685520	2685624	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685625	2685717	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685718	2685820	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685718	2685820	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2685821	2685946	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2685947	2686063	1	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2685947	2686063	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686064	2686162	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686163	2686351	0.72	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686163	2686351	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686352	2686459	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686460	2686521	0.63	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686460	2686521	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686522	2686662	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686663	2686681	0.42	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686663	2686681	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686682	2686856	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2686857	2686965	0.59	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2686857	2686965	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2686966	2687041	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687042	2687104	1	+	1	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687042	2687104	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687105	2687203	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687204	2687284	1	+	1	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687204	2687284	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687285	2687416	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687417	2687523	0.47	+	1	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687417	2687523	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687524	2687698	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2687699	2687868	0.37	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2687699	2687868	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2687869	2688061	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688062	2688127	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688062	2688127	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688128	2688204	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688205	2688309	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688205	2688309	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688310	2688399	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688400	2688447	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688400	2688447	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688448	2688548	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688549	2688683	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688549	2688683	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688684	2688860	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2688861	2688930	1	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2688861	2688930	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	intron	2688931	2689090	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	CDS	2689091	2689146	0.55	+	2	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	exon	2689091	2689146	.	+	.	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
Phchi.S5	AUGUSTUS	stop_codon	2689147	2689149	.	+	0	transcript_id "Phchi.S5G032700.t2"; gene_id "Phchi.S5G032700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7908.t1 is derived from g5082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31840593	31842231	.	-	.	Phchi.S1G506700
Phchi.S1	AUGUSTUS	transcript	31840593	31842231	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	stop_codon	31840590	31840592	.	-	0	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	CDS	31840593	31841110	0.93	-	2	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	exon	31840593	31841110	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	intron	31841111	31841229	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	CDS	31841230	31841345	1	-	1	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	exon	31841230	31841345	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	intron	31841346	31841431	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	CDS	31841432	31841507	1	-	2	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	exon	31841432	31841507	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	intron	31841508	31841636	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	CDS	31841637	31842231	0.87	-	0	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	exon	31841637	31842231	.	-	.	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
Phchi.S1	AUGUSTUS	start_codon	31842229	31842231	.	-	0	transcript_id "Phchi.S1G506700.t1"; gene_id "Phchi.S1G506700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4126.t1 is derived from g1295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8380299	8383459	.	+	.	Phchi.S1G128500
Phchi.S1	AUGUSTUS	transcript	8380299	8383459	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	start_codon	8380299	8380301	.	+	0	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	CDS	8380299	8380301	1	+	0	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	exon	8380299	8380301	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	intron	8380302	8380384	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	CDS	8380385	8380602	0.06	+	0	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	exon	8380385	8380602	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	intron	8380603	8380892	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	CDS	8380893	8381014	0.01	+	1	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	exon	8380893	8381014	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	intron	8381015	8383133	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	CDS	8383134	8383459	0.01	+	2	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	exon	8383134	8383459	.	+	.	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
Phchi.S1	AUGUSTUS	stop_codon	8383460	8383462	.	+	0	transcript_id "Phchi.S1G128500.t1"; gene_id "Phchi.S1G128500"
# This transcript jg12545.t2 is derived from g8222.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12546.t1 is derived from g8223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34310343	34311234	.	+	.	Phchi.S2G062600
Phchi.S2	AUGUSTUS	transcript	34310343	34311234	.	+	.	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	start_codon	34310343	34310345	.	+	0	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	CDS	34310343	34310533	0.9	+	0	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	exon	34310343	34310533	.	+	.	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	intron	34310534	34310873	.	+	.	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	CDS	34310874	34310958	0.44	+	1	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	exon	34310874	34310958	.	+	.	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	intron	34310959	34311114	.	+	.	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	CDS	34311115	34311234	0.83	+	0	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	exon	34311115	34311234	.	+	.	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
Phchi.S2	AUGUSTUS	stop_codon	34311235	34311237	.	+	0	transcript_id "Phchi.S2G062600.t1"; gene_id "Phchi.S2G062600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14994.t1 is derived from g13462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16151007	16153311	.	+	.	Phchi.S3G231300
Phchi.S3	AUGUSTUS	transcript	16151007	16153311	.	+	.	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	start_codon	16151007	16151009	.	+	0	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	CDS	16151007	16151513	0.97	+	0	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	exon	16151007	16151513	.	+	.	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	intron	16151514	16151655	.	+	.	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	CDS	16151656	16151896	0.99	+	0	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	exon	16151656	16151896	.	+	.	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	intron	16151897	16152253	.	+	.	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	CDS	16152254	16153311	1	+	2	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	exon	16152254	16153311	.	+	.	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
Phchi.S3	AUGUSTUS	stop_codon	16153312	16153314	.	+	0	transcript_id "Phchi.S3G231300.t1"; gene_id "Phchi.S3G231300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9112.t1 is derived from g6287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39882499	39883994	.	+	.	Phchi.S1G627100
Phchi.S1	AUGUSTUS	transcript	39882499	39883994	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	start_codon	39882499	39882501	.	+	0	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	CDS	39882499	39883114	0.47	+	0	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	exon	39882499	39883114	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	intron	39883115	39883348	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	CDS	39883349	39883459	0.51	+	2	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	exon	39883349	39883459	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	intron	39883460	39883570	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	CDS	39883571	39883826	0.5	+	2	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	exon	39883571	39883826	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	intron	39883827	39883918	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	CDS	39883919	39883994	0.64	+	1	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	exon	39883919	39883994	.	+	.	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
Phchi.S1	AUGUSTUS	stop_codon	39883995	39883997	.	+	0	transcript_id "Phchi.S1G627100.t1"; gene_id "Phchi.S1G627100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11455.t1 is derived from g15505.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6453267	6453757	.	+	.	Phchi.S4G103700
Phchi.S4	AUGUSTUS	transcript	6453267	6453757	.	+	.	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	start_codon	6453267	6453269	.	+	0	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	CDS	6453267	6453437	0.35	+	0	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	exon	6453267	6453437	.	+	.	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	intron	6453438	6453544	.	+	.	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	CDS	6453545	6453757	0.56	+	0	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	exon	6453545	6453757	.	+	.	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
Phchi.S4	AUGUSTUS	stop_codon	6453758	6453760	.	+	0	transcript_id "Phchi.S4G103700.t1"; gene_id "Phchi.S4G103700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8023.t1 is derived from g5198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32523019	32523499	.	+	.	Phchi.S1G518200
Phchi.S1	AUGUSTUS	transcript	32523019	32523499	.	+	.	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	start_codon	32523019	32523021	.	+	0	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	CDS	32523019	32523151	0.61	+	0	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	exon	32523019	32523151	.	+	.	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	intron	32523152	32523254	.	+	.	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	CDS	32523255	32523305	0.78	+	2	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	exon	32523255	32523305	.	+	.	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	intron	32523306	32523389	.	+	.	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	CDS	32523390	32523499	0.77	+	2	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	exon	32523390	32523499	.	+	.	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
Phchi.S1	AUGUSTUS	stop_codon	32523500	32523502	.	+	0	transcript_id "Phchi.S1G518200.t1"; gene_id "Phchi.S1G518200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14385.t1 is derived from g12853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12548929	12553696	.	-	.	Phchi.S3G170400
Phchi.S3	AUGUSTUS	transcript	12548929	12553696	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	stop_codon	12548926	12548928	.	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12548929	12549222	1	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12548929	12549222	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12549223	12549300	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12549301	12549442	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12549301	12549442	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12549443	12549527	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12549528	12549656	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12549528	12549656	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12549657	12549756	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12549757	12549802	1	-	2	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12549757	12549802	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12549803	12549869	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12549870	12549938	1	-	2	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12549870	12549938	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12549939	12550027	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12550028	12550154	1	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12550028	12550154	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12550155	12550237	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12550238	12550446	1	-	2	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12550238	12550446	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12550447	12550553	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12550554	12550837	0.94	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12550554	12550837	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12550838	12550934	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12550935	12551006	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12550935	12551006	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12551007	12551090	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12551091	12551162	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12551091	12551162	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12551163	12551254	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12551255	12551326	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12551255	12551326	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12551327	12551407	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12551408	12551478	1	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12551408	12551478	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12551479	12551576	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12551577	12551598	0.99	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12551577	12551598	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12551599	12551675	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12551676	12551712	0.61	-	2	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12551676	12551712	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12551713	12551801	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12551802	12552040	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12551802	12552040	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12552041	12552129	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12552130	12552393	1	-	1	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12552130	12552393	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12552394	12552486	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12552487	12552752	1	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12552487	12552752	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12552753	12552828	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12552829	12553130	0.95	-	2	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12552829	12553130	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12553131	12553231	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12553232	12553304	1	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12553232	12553304	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	intron	12553305	12553414	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	CDS	12553415	12553696	0.49	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	exon	12553415	12553696	.	-	.	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
Phchi.S3	AUGUSTUS	start_codon	12553694	12553696	.	-	0	transcript_id "Phchi.S3G170400.t1"; gene_id "Phchi.S3G170400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9937.t1 is derived from g7113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44567420	44567760	.	-	.	Phchi.S1G709600
Phchi.S1	AUGUSTUS	transcript	44567420	44567760	.	-	.	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	stop_codon	44567417	44567419	.	-	0	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	CDS	44567420	44567580	0.94	-	2	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	exon	44567420	44567580	.	-	.	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	intron	44567581	44567657	.	-	.	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	CDS	44567658	44567760	0.91	-	0	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	exon	44567658	44567760	.	-	.	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
Phchi.S1	AUGUSTUS	start_codon	44567758	44567760	.	-	0	transcript_id "Phchi.S1G709600.t1"; gene_id "Phchi.S1G709600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8842.t1 is derived from g6017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38246980	38248227	.	-	.	Phchi.S1G600100
Phchi.S1	AUGUSTUS	transcript	38246980	38248227	.	-	.	transcript_id "Phchi.S1G600100.t1"; gene_id "Phchi.S1G600100"
Phchi.S1	AUGUSTUS	stop_codon	38246977	38246979	.	-	0	transcript_id "Phchi.S1G600100.t1"; gene_id "Phchi.S1G600100"
Phchi.S1	AUGUSTUS	CDS	38246980	38248227	0.6	-	0	transcript_id "Phchi.S1G600100.t1"; gene_id "Phchi.S1G600100"
Phchi.S1	AUGUSTUS	exon	38246980	38248227	.	-	.	transcript_id "Phchi.S1G600100.t1"; gene_id "Phchi.S1G600100"
Phchi.S1	AUGUSTUS	start_codon	38248225	38248227	.	-	0	transcript_id "Phchi.S1G600100.t1"; gene_id "Phchi.S1G600100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9370.t1 is derived from g6546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41194797	41203803	.	+	.	Phchi.S1G652900
Phchi.S1	AUGUSTUS	transcript	41194797	41203803	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	start_codon	41194797	41194799	.	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41194797	41194866	0.99	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41194797	41194866	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41194867	41195147	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41195148	41195212	1	+	2	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41195148	41195212	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41195213	41195357	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41195358	41195450	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41195358	41195450	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41195451	41195581	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41195582	41195654	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41195582	41195654	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41195655	41195742	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41195743	41195994	0.95	+	2	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41195743	41195994	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41195995	41196152	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41196153	41196197	0.95	+	2	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41196153	41196197	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41196198	41196315	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41196316	41196383	1	+	2	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41196316	41196383	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41196384	41196471	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41196472	41196603	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41196472	41196603	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41196604	41196784	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41196785	41196826	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41196785	41196826	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41196827	41196917	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41196918	41197074	0.46	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41196918	41197074	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41197075	41197187	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41197188	41197450	0.92	+	2	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41197188	41197450	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41197451	41197534	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41197535	41197692	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41197535	41197692	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41197693	41197784	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41197785	41198268	0.48	+	1	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41197785	41198268	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41198269	41198353	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41198354	41198416	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41198354	41198416	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41198417	41198508	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41198509	41198610	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41198509	41198610	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41198611	41198730	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41198731	41199051	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41198731	41199051	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41199052	41199149	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41199150	41199242	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41199150	41199242	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41199243	41199326	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41199327	41199428	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41199327	41199428	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41199429	41199524	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41199525	41199629	0.99	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41199525	41199629	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41199630	41199740	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41199741	41199874	0.99	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41199741	41199874	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41199875	41199979	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41199980	41200163	1	+	1	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41199980	41200163	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41200164	41200252	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41200253	41200497	1	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41200253	41200497	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41200498	41200592	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41200593	41200674	1	+	1	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41200593	41200674	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41200675	41200755	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41200756	41201961	0.93	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41200756	41201961	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41201962	41202021	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41202022	41203192	0.9	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41202022	41203192	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	intron	41203193	41203342	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	CDS	41203343	41203803	0.92	+	2	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	exon	41203343	41203803	.	+	.	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
Phchi.S1	AUGUSTUS	stop_codon	41203804	41203806	.	+	0	transcript_id "Phchi.S1G652900.t1"; gene_id "Phchi.S1G652900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5637.t1 is derived from g2807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17989776	17991891	.	+	.	Phchi.S1G279600
Phchi.S1	AUGUSTUS	transcript	17989776	17991891	.	+	.	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	start_codon	17989776	17989778	.	+	0	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	CDS	17989776	17989956	0.92	+	0	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	exon	17989776	17989956	.	+	.	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	intron	17989957	17990045	.	+	.	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	CDS	17990046	17990334	0.7	+	2	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	exon	17990046	17990334	.	+	.	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	intron	17990335	17990420	.	+	.	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	CDS	17990421	17991891	0.79	+	1	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	exon	17990421	17991891	.	+	.	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
Phchi.S1	AUGUSTUS	stop_codon	17991892	17991894	.	+	0	transcript_id "Phchi.S1G279600.t1"; gene_id "Phchi.S1G279600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg315.t1 is derived from g10097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2231999	2233458	.	-	.	Phchi.S6G027400
Phchi.S6	AUGUSTUS	transcript	2231999	2233458	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	stop_codon	2231996	2231998	.	-	0	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	CDS	2231999	2232057	0.9	-	2	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	exon	2231999	2232057	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	intron	2232058	2232419	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	CDS	2232420	2232711	0.33	-	0	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	exon	2232420	2232711	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	intron	2232712	2232823	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	CDS	2232824	2232946	0.41	-	0	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	exon	2232824	2232946	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	intron	2232947	2233049	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	CDS	2233050	2233137	0.67	-	1	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	exon	2233050	2233137	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	intron	2233138	2233250	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	CDS	2233251	2233288	0.66	-	0	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	exon	2233251	2233288	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	intron	2233289	2233386	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	CDS	2233387	2233458	0.6	-	0	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	exon	2233387	2233458	.	-	.	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
Phchi.S6	AUGUSTUS	start_codon	2233456	2233458	.	-	0	transcript_id "Phchi.S6G027400.t1"; gene_id "Phchi.S6G027400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2614.t1 is derived from g9534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7789690	7790127	.	-	.	Phchi.S5G122300
Phchi.S5	AUGUSTUS	transcript	7789690	7790127	.	-	.	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	stop_codon	7789687	7789689	.	-	0	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	CDS	7789690	7789841	0.97	-	2	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	exon	7789690	7789841	.	-	.	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	intron	7789842	7789979	.	-	.	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	CDS	7789980	7790127	0.47	-	0	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	exon	7789980	7790127	.	-	.	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
Phchi.S5	AUGUSTUS	start_codon	7790125	7790127	.	-	0	transcript_id "Phchi.S5G122300.t1"; gene_id "Phchi.S5G122300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2962.t1 is derived from g131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	834396	837869	.	+	.	Phchi.S1G012100
Phchi.S1	AUGUSTUS	transcript	834396	837869	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	start_codon	834396	834398	.	+	0	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	834396	834633	0.66	+	0	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	834396	834633	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	834634	834747	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	834748	834862	0.53	+	2	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	834748	834862	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	834863	835022	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	835023	835091	0.69	+	1	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	835023	835091	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	835092	835181	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	835182	835253	0.99	+	1	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	835182	835253	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	835254	835337	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	835338	835406	1	+	1	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	835338	835406	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	835407	835539	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	835540	835763	0.71	+	1	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	835540	835763	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	835764	835871	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	835872	836095	0.97	+	2	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	835872	836095	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	836096	836205	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	836206	836332	1	+	0	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	836206	836332	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	836333	836449	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	836450	836518	1	+	2	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	836450	836518	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	836519	836602	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	836603	836652	1	+	2	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	836603	836652	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	836653	836749	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	836750	837228	0.72	+	0	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	836750	837228	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	837229	837589	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	837590	837612	0.65	+	1	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	837590	837612	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	837613	837703	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	837704	837767	0.65	+	2	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	837704	837767	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	intron	837768	837853	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	CDS	837854	837869	1	+	1	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	exon	837854	837869	.	+	.	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
Phchi.S1	AUGUSTUS	stop_codon	837870	837872	.	+	0	transcript_id "Phchi.S1G012100.t1"; gene_id "Phchi.S1G012100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8121.t1 is derived from g5296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33449833	33450723	.	-	.	Phchi.S1G528000
Phchi.S1	AUGUSTUS	transcript	33449833	33450723	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	stop_codon	33449830	33449832	.	-	0	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	CDS	33449833	33449834	0.76	-	2	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	exon	33449833	33449834	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	intron	33449835	33449908	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	CDS	33449909	33450065	0.76	-	0	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	exon	33449909	33450065	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	intron	33450066	33450162	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	CDS	33450163	33450238	0.86	-	1	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	exon	33450163	33450238	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	intron	33450239	33450353	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	CDS	33450354	33450521	0.64	-	1	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	exon	33450354	33450521	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	intron	33450522	33450637	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	CDS	33450638	33450723	0.62	-	0	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	exon	33450638	33450723	.	-	.	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
Phchi.S1	AUGUSTUS	start_codon	33450721	33450723	.	-	0	transcript_id "Phchi.S1G528000.t1"; gene_id "Phchi.S1G528000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13380.t1 is derived from g11846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6435162	6437756	.	+	.	Phchi.S3G069900
Phchi.S3	AUGUSTUS	transcript	6435162	6437756	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	start_codon	6435162	6435164	.	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6435162	6435311	1	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6435162	6435311	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6435312	6435530	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6435531	6435851	0.98	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6435531	6435851	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6435852	6435974	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6435975	6436169	0.99	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6435975	6436169	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6436170	6436256	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6436257	6436328	1	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6436257	6436328	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6436329	6436428	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6436429	6436476	1	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6436429	6436476	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6436477	6436593	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6436594	6436719	1	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6436594	6436719	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6436720	6436883	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6436884	6437003	1	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6436884	6437003	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6437004	6437087	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6437088	6437296	0.57	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6437088	6437296	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6437297	6437386	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6437387	6437478	1	+	1	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6437387	6437478	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	intron	6437479	6437577	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	CDS	6437578	6437756	0.78	+	2	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	exon	6437578	6437756	.	+	.	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
Phchi.S3	AUGUSTUS	stop_codon	6437757	6437759	.	+	0	transcript_id "Phchi.S3G069900.t1"; gene_id "Phchi.S3G069900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5909.t1 is derived from g3080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19744170	19744854	.	-	.	Phchi.S1G306800
Phchi.S1	AUGUSTUS	transcript	19744170	19744854	.	-	.	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	stop_codon	19744167	19744169	.	-	0	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	CDS	19744170	19744340	0.91	-	0	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	exon	19744170	19744340	.	-	.	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	intron	19744341	19744415	.	-	.	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	CDS	19744416	19744628	1	-	0	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	exon	19744416	19744628	.	-	.	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	intron	19744629	19744716	.	-	.	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	CDS	19744717	19744854	0.98	-	0	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	exon	19744717	19744854	.	-	.	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
Phchi.S1	AUGUSTUS	start_codon	19744852	19744854	.	-	0	transcript_id "Phchi.S1G306800.t1"; gene_id "Phchi.S1G306800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7064.t1 is derived from g4236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26692968	26695936	.	-	.	Phchi.S1G422300
Phchi.S1	AUGUSTUS	transcript	26692968	26695936	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	stop_codon	26692965	26692967	.	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26692968	26693111	0.91	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26692968	26693111	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26693112	26693249	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26693250	26693396	0.99	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26693250	26693396	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26693397	26693478	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26693479	26693566	0.8	-	1	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26693479	26693566	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26693567	26693657	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26693658	26693725	0.99	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26693658	26693725	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26693726	26693818	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26693819	26694005	1	-	1	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26693819	26694005	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26694006	26694085	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26694086	26694273	1	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26694086	26694273	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26694274	26694355	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26694356	26694488	1	-	1	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26694356	26694488	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26694489	26694572	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26694573	26694681	1	-	2	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26694573	26694681	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26694682	26694763	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26694764	26694869	0.96	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26694764	26694869	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26694870	26694952	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26694953	26695219	0.94	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26694953	26695219	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26695220	26695308	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26695309	26695396	1	-	1	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26695309	26695396	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	intron	26695397	26695532	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	CDS	26695533	26695936	1	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	exon	26695533	26695936	.	-	.	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
Phchi.S1	AUGUSTUS	start_codon	26695934	26695936	.	-	0	transcript_id "Phchi.S1G422300.t1"; gene_id "Phchi.S1G422300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15398.t1 is derived from g13866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18820088	18820483	.	-	.	Phchi.S3G271700
Phchi.S3	AUGUSTUS	transcript	18820088	18820483	.	-	.	transcript_id "Phchi.S3G271700.t1"; gene_id "Phchi.S3G271700"
Phchi.S3	AUGUSTUS	stop_codon	18820085	18820087	.	-	0	transcript_id "Phchi.S3G271700.t1"; gene_id "Phchi.S3G271700"
Phchi.S3	AUGUSTUS	CDS	18820088	18820483	0.48	-	0	transcript_id "Phchi.S3G271700.t1"; gene_id "Phchi.S3G271700"
Phchi.S3	AUGUSTUS	exon	18820088	18820483	.	-	.	transcript_id "Phchi.S3G271700.t1"; gene_id "Phchi.S3G271700"
Phchi.S3	AUGUSTUS	start_codon	18820481	18820483	.	-	0	transcript_id "Phchi.S3G271700.t1"; gene_id "Phchi.S3G271700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2820.t1 is derived from g9740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9030623	9032455	.	+	.	Phchi.S5G142900
Phchi.S5	AUGUSTUS	transcript	9030623	9032455	.	+	.	transcript_id "Phchi.S5G142900.t1"; gene_id "Phchi.S5G142900"
Phchi.S5	AUGUSTUS	start_codon	9030623	9030625	.	+	0	transcript_id "Phchi.S5G142900.t1"; gene_id "Phchi.S5G142900"
Phchi.S5	AUGUSTUS	CDS	9030623	9032455	1	+	0	transcript_id "Phchi.S5G142900.t1"; gene_id "Phchi.S5G142900"
Phchi.S5	AUGUSTUS	exon	9030623	9032455	.	+	.	transcript_id "Phchi.S5G142900.t1"; gene_id "Phchi.S5G142900"
Phchi.S5	AUGUSTUS	stop_codon	9032456	9032458	.	+	0	transcript_id "Phchi.S5G142900.t1"; gene_id "Phchi.S5G142900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12498.t1 is derived from g8175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30844040	30844372	.	-	.	Phchi.S2G057800
Phchi.S2	AUGUSTUS	transcript	30844040	30844372	.	-	.	transcript_id "Phchi.S2G057800.t1"; gene_id "Phchi.S2G057800"
Phchi.S2	AUGUSTUS	stop_codon	30844037	30844039	.	-	0	transcript_id "Phchi.S2G057800.t1"; gene_id "Phchi.S2G057800"
Phchi.S2	AUGUSTUS	CDS	30844040	30844372	0.69	-	0	transcript_id "Phchi.S2G057800.t1"; gene_id "Phchi.S2G057800"
Phchi.S2	AUGUSTUS	exon	30844040	30844372	.	-	.	transcript_id "Phchi.S2G057800.t1"; gene_id "Phchi.S2G057800"
Phchi.S2	AUGUSTUS	start_codon	30844370	30844372	.	-	0	transcript_id "Phchi.S2G057800.t1"; gene_id "Phchi.S2G057800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10957.t1 is derived from g15007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3275117	3275679	.	+	.	Phchi.S4G053900
Phchi.S4	AUGUSTUS	transcript	3275117	3275679	.	+	.	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	start_codon	3275117	3275119	.	+	0	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	CDS	3275117	3275321	1	+	0	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	exon	3275117	3275321	.	+	.	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	intron	3275322	3275410	.	+	.	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	CDS	3275411	3275679	0.97	+	2	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	exon	3275411	3275679	.	+	.	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
Phchi.S4	AUGUSTUS	stop_codon	3275680	3275682	.	+	0	transcript_id "Phchi.S4G053900.t1"; gene_id "Phchi.S4G053900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8587.t1 is derived from g5762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36771613	36776719	.	-	.	Phchi.S1G574600
Phchi.S1	AUGUSTUS	transcript	36771613	36776719	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	stop_codon	36771610	36771612	.	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36771613	36771731	0.55	-	2	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36771613	36771731	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36771732	36771858	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36771859	36771868	0.34	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36771859	36771868	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36771869	36771965	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36771966	36771990	0.31	-	1	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36771966	36771990	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36771991	36772079	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36772080	36772116	0.44	-	2	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36772080	36772116	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36772117	36772220	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36772221	36772491	0.71	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36772221	36772491	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36772492	36772573	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36772574	36772749	1	-	2	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36772574	36772749	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36772750	36772830	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36772831	36772981	1	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36772831	36772981	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36772982	36773056	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36773057	36773207	1	-	1	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36773057	36773207	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36773208	36773332	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36773333	36773481	1	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36773333	36773481	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36773482	36773571	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36773572	36773833	0.99	-	1	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36773572	36773833	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36773834	36773922	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36773923	36774151	1	-	2	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36773923	36774151	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36774152	36774225	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36774226	36774374	1	-	1	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36774226	36774374	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36774375	36774449	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36774450	36774553	1	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36774450	36774553	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36774554	36774637	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36774638	36774715	0.92	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36774638	36774715	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36774716	36774821	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36774822	36774968	1	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36774822	36774968	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36774969	36775053	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36775054	36775147	1	-	1	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36775054	36775147	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36775148	36775217	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36775218	36775404	1	-	2	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36775218	36775404	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36775405	36775494	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36775495	36775666	1	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36775495	36775666	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36775667	36775745	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36775746	36775820	1	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36775746	36775820	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36775821	36775927	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36775928	36776054	1	-	1	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36775928	36776054	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	intron	36776055	36776141	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	CDS	36776142	36776719	0.79	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	exon	36776142	36776719	.	-	.	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
Phchi.S1	AUGUSTUS	start_codon	36776717	36776719	.	-	0	transcript_id "Phchi.S1G574600.t1"; gene_id "Phchi.S1G574600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg714.t1 is derived from g10496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5046271	5047325	.	-	.	Phchi.S6G067300
Phchi.S6	AUGUSTUS	transcript	5046271	5047325	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	stop_codon	5046268	5046270	.	-	0	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	CDS	5046271	5046423	0.77	-	0	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	exon	5046271	5046423	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	intron	5046424	5046563	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	CDS	5046564	5046742	0.96	-	2	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	exon	5046564	5046742	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	intron	5046743	5046818	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	CDS	5046819	5046942	1	-	0	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	exon	5046819	5046942	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	intron	5046943	5047037	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	CDS	5047038	5047325	0.72	-	0	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	exon	5047038	5047325	.	-	.	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
Phchi.S6	AUGUSTUS	start_codon	5047323	5047325	.	-	0	transcript_id "Phchi.S6G067300.t1"; gene_id "Phchi.S6G067300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7608.t1 is derived from g4782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30228605	30229810	.	+	.	Phchi.S1G476700
Phchi.S1	AUGUSTUS	transcript	30228605	30229810	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	start_codon	30228605	30228607	.	+	0	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30228605	30228664	1	+	0	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30228605	30228664	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	intron	30228665	30228740	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30228741	30228836	1	+	0	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30228741	30228836	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	intron	30228837	30228916	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30228917	30229020	0.97	+	0	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30228917	30229020	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	intron	30229021	30229128	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30229129	30229265	0.71	+	1	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30229129	30229265	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	intron	30229266	30229368	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30229369	30229432	0.6	+	2	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30229369	30229432	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	intron	30229433	30229599	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30229600	30229650	0.72	+	1	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30229600	30229650	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	intron	30229651	30229800	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	CDS	30229801	30229810	1	+	1	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	exon	30229801	30229810	.	+	.	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
Phchi.S1	AUGUSTUS	stop_codon	30229811	30229813	.	+	0	transcript_id "Phchi.S1G476700.t1"; gene_id "Phchi.S1G476700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12033.t1 is derived from g7708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	710903	714361	.	+	.	Phchi.S2G011300
Phchi.S2	AUGUSTUS	transcript	710903	714361	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	start_codon	710903	710905	.	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	710903	711081	1	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	710903	711081	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	711082	711570	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	711571	711645	1	+	1	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	711571	711645	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	711646	711796	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	711797	711888	0.99	+	1	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	711797	711888	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	711889	711989	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	711990	712036	0.99	+	2	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	711990	712036	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	712037	712151	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	712152	712232	1	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	712152	712232	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	712233	712361	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	712362	712518	1	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	712362	712518	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	712519	712656	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	712657	712706	1	+	2	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	712657	712706	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	712707	712774	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	712775	712819	0.92	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	712775	712819	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	712820	712903	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	712904	712977	1	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	712904	712977	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	712978	713071	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	713072	713203	1	+	1	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	713072	713203	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	713204	713291	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	713292	713364	1	+	1	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	713292	713364	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	713365	713455	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	713456	713470	0.78	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	713456	713470	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	713471	713594	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	713595	713679	0.78	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	713595	713679	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	713680	713768	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	713769	713798	1	+	2	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	713769	713798	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	713799	713851	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	713852	713857	1	+	2	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	713852	713857	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	intron	713858	714098	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	CDS	714099	714361	1	+	2	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	exon	714099	714361	.	+	.	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
Phchi.S2	AUGUSTUS	stop_codon	714362	714364	.	+	0	transcript_id "Phchi.S2G011300.t1"; gene_id "Phchi.S2G011300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15699.t1 is derived from g14168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20754600	20762067	.	-	.	Phchi.S3G301800
Phchi.S3	AUGUSTUS	transcript	20754600	20762067	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	stop_codon	20754597	20754599	.	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20754600	20754935	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20754600	20754935	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20754936	20755028	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20755029	20755409	0.97	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20755029	20755409	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20755410	20755533	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20755534	20755850	0.97	-	2	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20755534	20755850	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20755851	20755929	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20755930	20756104	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20755930	20756104	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20756105	20756211	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20756212	20756325	0.99	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20756212	20756325	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20756326	20756429	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20756430	20757017	0.98	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20756430	20757017	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20757018	20757121	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20757122	20757205	0.91	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20757122	20757205	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20757206	20757295	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20757296	20757379	0.85	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20757296	20757379	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20757380	20757482	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20757483	20757599	0.98	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20757483	20757599	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20757600	20757773	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20757774	20758021	0.98	-	2	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20757774	20758021	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20758022	20758210	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20758211	20758355	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20758211	20758355	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20758356	20758490	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20758491	20758706	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20758491	20758706	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20758707	20758787	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20758788	20758991	0.97	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20758788	20758991	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20758992	20759114	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20759115	20759219	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20759115	20759219	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20759220	20759412	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20759413	20759601	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20759413	20759601	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20759602	20759782	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20759783	20760055	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20759783	20760055	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20760056	20760142	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20760143	20760350	1	-	1	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20760143	20760350	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20760351	20760440	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20760441	20760559	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20760441	20760559	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20760560	20760700	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20760701	20760844	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20760701	20760844	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20760845	20760982	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20760983	20761141	1	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20760983	20761141	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20761142	20761228	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20761229	20761352	0.99	-	1	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20761229	20761352	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20761353	20761458	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20761459	20761592	0.99	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20761459	20761592	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	intron	20761593	20762061	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	CDS	20762062	20762067	0.6	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	exon	20762062	20762067	.	-	.	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
Phchi.S3	AUGUSTUS	start_codon	20762065	20762067	.	-	0	transcript_id "Phchi.S3G301800.t1"; gene_id "Phchi.S3G301800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4073.t1 is derived from g1242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7634212	7634586	.	+	.	Phchi.S1G123200
Phchi.S1	AUGUSTUS	transcript	7634212	7634586	.	+	.	transcript_id "Phchi.S1G123200.t1"; gene_id "Phchi.S1G123200"
Phchi.S1	AUGUSTUS	start_codon	7634212	7634214	.	+	0	transcript_id "Phchi.S1G123200.t1"; gene_id "Phchi.S1G123200"
Phchi.S1	AUGUSTUS	CDS	7634212	7634586	0.98	+	0	transcript_id "Phchi.S1G123200.t1"; gene_id "Phchi.S1G123200"
Phchi.S1	AUGUSTUS	exon	7634212	7634586	.	+	.	transcript_id "Phchi.S1G123200.t1"; gene_id "Phchi.S1G123200"
Phchi.S1	AUGUSTUS	stop_codon	7634587	7634589	.	+	0	transcript_id "Phchi.S1G123200.t1"; gene_id "Phchi.S1G123200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15174.t1 is derived from g13642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17363758	17365240	.	-	.	Phchi.S3G249300
Phchi.S3	AUGUSTUS	transcript	17363758	17365240	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	stop_codon	17363755	17363757	.	-	0	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	CDS	17363758	17364093	1	-	0	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	exon	17363758	17364093	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	intron	17364094	17364173	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	CDS	17364174	17364365	1	-	0	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	exon	17364174	17364365	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	intron	17364366	17364452	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	CDS	17364453	17364523	1	-	2	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	exon	17364453	17364523	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	intron	17364524	17364638	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	CDS	17364639	17364984	0.97	-	0	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	exon	17364639	17364984	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	intron	17364985	17365075	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	CDS	17365076	17365240	0.39	-	0	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	exon	17365076	17365240	.	-	.	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
Phchi.S3	AUGUSTUS	start_codon	17365238	17365240	.	-	0	transcript_id "Phchi.S3G249300.t1"; gene_id "Phchi.S3G249300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5546.t1 is derived from g2716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17477875	17478899	.	+	.	Phchi.S1G270500
Phchi.S1	AUGUSTUS	transcript	17477875	17478899	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	start_codon	17477875	17477877	.	+	0	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	CDS	17477875	17478103	0.8	+	0	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	exon	17477875	17478103	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	intron	17478104	17478181	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	CDS	17478182	17478297	0.64	+	2	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	exon	17478182	17478297	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	intron	17478298	17478391	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	CDS	17478392	17478564	0.42	+	0	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	exon	17478392	17478564	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	intron	17478565	17478690	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	CDS	17478691	17478755	0.53	+	1	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	exon	17478691	17478755	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	intron	17478756	17478831	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	CDS	17478832	17478899	0.45	+	2	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	exon	17478832	17478899	.	+	.	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
Phchi.S1	AUGUSTUS	stop_codon	17478900	17478902	.	+	0	transcript_id "Phchi.S1G270500.t1"; gene_id "Phchi.S1G270500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8386.t1 is derived from g5561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35661709	35664781	.	+	.	Phchi.S1G554500
Phchi.S1	AUGUSTUS	transcript	35661709	35664781	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	start_codon	35661709	35661711	.	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35661709	35662438	1	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35661709	35662438	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35662439	35662920	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35662921	35663000	1	+	2	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35662921	35663000	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35663001	35663156	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35663157	35663234	1	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35663157	35663234	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35663235	35663353	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35663354	35663449	1	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35663354	35663449	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35663450	35663541	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35663542	35663613	1	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35663542	35663613	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35663614	35663687	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35663688	35663741	1	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35663688	35663741	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35663742	35663880	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35663881	35663946	1	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35663881	35663946	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35663947	35664038	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35664039	35664079	0.76	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35664039	35664079	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	intron	35664080	35664720	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	CDS	35664721	35664781	0.76	+	1	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	exon	35664721	35664781	.	+	.	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
Phchi.S1	AUGUSTUS	stop_codon	35664782	35664784	.	+	0	transcript_id "Phchi.S1G554500.t1"; gene_id "Phchi.S1G554500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13962.t1 is derived from g12429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9941398	9943116	.	+	.	Phchi.S3G128100
Phchi.S3	AUGUSTUS	transcript	9941398	9943116	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	start_codon	9941398	9941400	.	+	0	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9941398	9941489	0.93	+	0	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9941398	9941489	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	intron	9941490	9941606	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9941607	9941704	0.93	+	1	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9941607	9941704	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	intron	9941705	9941828	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9941829	9941959	1	+	2	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9941829	9941959	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	intron	9941960	9942099	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9942100	9942130	1	+	0	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9942100	9942130	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	intron	9942131	9942235	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9942236	9942339	0.99	+	2	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9942236	9942339	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	intron	9942340	9942429	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9942430	9942551	1	+	0	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9942430	9942551	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	intron	9942552	9942680	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	CDS	9942681	9943116	0.97	+	1	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	exon	9942681	9943116	.	+	.	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
Phchi.S3	AUGUSTUS	stop_codon	9943117	9943119	.	+	0	transcript_id "Phchi.S3G128100.t1"; gene_id "Phchi.S3G128100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1371.t1 is derived from g9816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C217	AUGUSTUS	gene	25307	25954	.	-	.	Phchi.C217G000500
Phchi.C217	AUGUSTUS	transcript	25307	25954	.	-	.	transcript_id "Phchi.C217G000500.t1"; gene_id "Phchi.C217G000500"
Phchi.C217	AUGUSTUS	stop_codon	25304	25306	.	-	0	transcript_id "Phchi.C217G000500.t1"; gene_id "Phchi.C217G000500"
Phchi.C217	AUGUSTUS	CDS	25307	25954	0.48	-	0	transcript_id "Phchi.C217G000500.t1"; gene_id "Phchi.C217G000500"
Phchi.C217	AUGUSTUS	exon	25307	25954	.	-	.	transcript_id "Phchi.C217G000500.t1"; gene_id "Phchi.C217G000500"
Phchi.C217	AUGUSTUS	start_codon	25952	25954	.	-	0	transcript_id "Phchi.C217G000500.t1"; gene_id "Phchi.C217G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7446.t1 is derived from g4618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29182573	29183148	.	+	.	Phchi.S1G460500
Phchi.S1	AUGUSTUS	transcript	29182573	29183148	.	+	.	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	start_codon	29182573	29182575	.	+	0	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	CDS	29182573	29182634	0.35	+	0	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	exon	29182573	29182634	.	+	.	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	intron	29182635	29182727	.	+	.	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	CDS	29182728	29183148	1	+	1	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	exon	29182728	29183148	.	+	.	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
Phchi.S1	AUGUSTUS	stop_codon	29183149	29183151	.	+	0	transcript_id "Phchi.S1G460500.t1"; gene_id "Phchi.S1G460500"
# This transcript jg14373.t2 is derived from g12840.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14374.t1 is derived from g12841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12419466	12420033	.	+	.	Phchi.S3G169300
Phchi.S3	AUGUSTUS	transcript	12419466	12420033	.	+	.	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	start_codon	12419466	12419468	.	+	0	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	CDS	12419466	12419771	0.97	+	0	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	exon	12419466	12419771	.	+	.	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	intron	12419772	12419886	.	+	.	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	CDS	12419887	12420033	0.58	+	0	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	exon	12419887	12420033	.	+	.	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
Phchi.S3	AUGUSTUS	stop_codon	12420034	12420036	.	+	0	transcript_id "Phchi.S3G169300.t1"; gene_id "Phchi.S3G169300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3897.t1 is derived from g1066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6302252	6302649	.	+	.	Phchi.S1G105600
Phchi.S1	AUGUSTUS	transcript	6302252	6302649	.	+	.	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	start_codon	6302252	6302254	.	+	0	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	CDS	6302252	6302523	0.53	+	0	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	exon	6302252	6302523	.	+	.	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	intron	6302524	6302615	.	+	.	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	CDS	6302616	6302649	0.9	+	1	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	exon	6302616	6302649	.	+	.	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
Phchi.S1	AUGUSTUS	stop_codon	6302650	6302652	.	+	0	transcript_id "Phchi.S1G105600.t1"; gene_id "Phchi.S1G105600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6133.t1 is derived from g3304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21091734	21093211	.	+	.	Phchi.S1G329200
Phchi.S1	AUGUSTUS	transcript	21091734	21093211	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	start_codon	21091734	21091736	.	+	0	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	CDS	21091734	21092087	0.93	+	0	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	exon	21091734	21092087	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	intron	21092088	21092211	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	CDS	21092212	21092438	0.99	+	0	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	exon	21092212	21092438	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	intron	21092439	21092590	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	CDS	21092591	21092691	1	+	1	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	exon	21092591	21092691	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	intron	21092692	21092771	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	CDS	21092772	21092813	0.75	+	2	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	exon	21092772	21092813	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	intron	21092814	21092910	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	CDS	21092911	21092920	0.52	+	2	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	exon	21092911	21092920	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	intron	21092921	21093105	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	CDS	21093106	21093211	0.72	+	1	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	exon	21093106	21093211	.	+	.	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
Phchi.S1	AUGUSTUS	stop_codon	21093212	21093214	.	+	0	transcript_id "Phchi.S1G329200.t1"; gene_id "Phchi.S1G329200"
# This transcript jg6901.t2 is derived from g4073.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6902.t1 is derived from g4074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25902708	25904929	.	-	.	Phchi.S1G406100
Phchi.S1	AUGUSTUS	transcript	25902708	25904929	.	-	.	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	stop_codon	25902705	25902707	.	-	0	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	CDS	25902708	25903264	1	-	2	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	exon	25902708	25903264	.	-	.	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	intron	25903265	25903358	.	-	.	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	CDS	25903359	25904381	0.97	-	2	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	exon	25903359	25904381	.	-	.	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	intron	25904382	25904460	.	-	.	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	CDS	25904461	25904929	0.99	-	0	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	exon	25904461	25904929	.	-	.	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
Phchi.S1	AUGUSTUS	start_codon	25904927	25904929	.	-	0	transcript_id "Phchi.S1G406100.t1"; gene_id "Phchi.S1G406100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3798.t1 is derived from g967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5801334	5803152	.	+	.	Phchi.S1G095700
Phchi.S1	AUGUSTUS	transcript	5801334	5803152	.	+	.	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	start_codon	5801334	5801336	.	+	0	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	CDS	5801334	5801497	0.44	+	0	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	exon	5801334	5801497	.	+	.	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	intron	5801498	5801636	.	+	.	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	CDS	5801637	5803152	0.48	+	1	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	exon	5801637	5803152	.	+	.	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	stop_codon	5803153	5803155	.	+	0	transcript_id "Phchi.S1G095700.t1"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	transcript	5801692	5803152	.	+	.	transcript_id "Phchi.S1G095700.t2"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	start_codon	5801692	5801694	.	+	0	transcript_id "Phchi.S1G095700.t2"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	CDS	5801692	5803152	0.35	+	0	transcript_id "Phchi.S1G095700.t2"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	exon	5801692	5803152	.	+	.	transcript_id "Phchi.S1G095700.t2"; gene_id "Phchi.S1G095700"
Phchi.S1	AUGUSTUS	stop_codon	5803153	5803155	.	+	0	transcript_id "Phchi.S1G095700.t2"; gene_id "Phchi.S1G095700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1254.t1 is derived from g11037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8655988	8657923	.	+	.	Phchi.S6G121300
Phchi.S6	AUGUSTUS	transcript	8655988	8657923	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	start_codon	8655988	8655990	.	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8655988	8656099	0.98	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8655988	8656099	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8656100	8656295	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8656296	8656399	0.7	+	2	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8656296	8656399	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8656400	8656541	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8656542	8656673	0.99	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8656542	8656673	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8656674	8656848	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8656849	8656923	1	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8656849	8656923	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8656924	8657210	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8657211	8657341	1	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8657211	8657341	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8657342	8657438	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8657439	8657493	0.98	+	1	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8657439	8657493	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8657494	8657703	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8657704	8657717	0.98	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8657704	8657717	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	intron	8657718	8657892	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	CDS	8657893	8657923	1	+	1	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	exon	8657893	8657923	.	+	.	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
Phchi.S6	AUGUSTUS	stop_codon	8657924	8657926	.	+	0	transcript_id "Phchi.S6G121300.t1"; gene_id "Phchi.S6G121300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11094.t1 is derived from g15144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4088773	4090904	.	+	.	Phchi.S4G067600
Phchi.S4	AUGUSTUS	transcript	4088773	4090904	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	start_codon	4088773	4088775	.	+	0	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	CDS	4088773	4089761	0.78	+	0	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	exon	4088773	4089761	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	intron	4089762	4089866	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	CDS	4089867	4090215	1	+	1	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	exon	4089867	4090215	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	intron	4090216	4090284	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	CDS	4090285	4090481	0.56	+	0	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	exon	4090285	4090481	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	intron	4090482	4090534	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	CDS	4090535	4090614	0.47	+	1	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	exon	4090535	4090614	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	intron	4090615	4090836	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	CDS	4090837	4090904	0.49	+	2	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	exon	4090837	4090904	.	+	.	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
Phchi.S4	AUGUSTUS	stop_codon	4090905	4090907	.	+	0	transcript_id "Phchi.S4G067600.t1"; gene_id "Phchi.S4G067600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1808.t1 is derived from g8728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3147283	3148072	.	+	.	Phchi.S5G041700
Phchi.S5	AUGUSTUS	transcript	3147283	3148072	.	+	.	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	start_codon	3147283	3147285	.	+	0	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	CDS	3147283	3147411	0.66	+	0	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	exon	3147283	3147411	.	+	.	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	intron	3147412	3147672	.	+	.	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	CDS	3147673	3147714	0.72	+	0	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	exon	3147673	3147714	.	+	.	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	intron	3147715	3147868	.	+	.	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	CDS	3147869	3148072	0.89	+	0	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	exon	3147869	3148072	.	+	.	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
Phchi.S5	AUGUSTUS	stop_codon	3148073	3148075	.	+	0	transcript_id "Phchi.S5G041700.t1"; gene_id "Phchi.S5G041700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8364.t1 is derived from g5539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35523025	35524413	.	+	.	Phchi.S1G552300
Phchi.S1	AUGUSTUS	transcript	35523025	35524413	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	start_codon	35523025	35523027	.	+	0	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	CDS	35523025	35523203	0.88	+	0	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	exon	35523025	35523203	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	intron	35523204	35523292	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	CDS	35523293	35523426	1	+	1	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	exon	35523293	35523426	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	intron	35523427	35523517	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	CDS	35523518	35523596	1	+	2	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	exon	35523518	35523596	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	intron	35523597	35523719	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	CDS	35523720	35523858	1	+	1	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	exon	35523720	35523858	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	intron	35523859	35524013	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	CDS	35524014	35524127	1	+	0	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	exon	35524014	35524127	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	intron	35524128	35524224	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	CDS	35524225	35524413	0.98	+	0	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	exon	35524225	35524413	.	+	.	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
Phchi.S1	AUGUSTUS	stop_codon	35524414	35524416	.	+	0	transcript_id "Phchi.S1G552300.t1"; gene_id "Phchi.S1G552300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6506.t1 is derived from g3678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23361236	23362702	.	-	.	Phchi.S1G366500
Phchi.S1	AUGUSTUS	transcript	23361236	23362117	.	-	.	transcript_id "Phchi.S1G366500.t1"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	stop_codon	23361233	23361235	.	-	0	transcript_id "Phchi.S1G366500.t1"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	CDS	23361236	23362117	0.91	-	0	transcript_id "Phchi.S1G366500.t1"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	exon	23361236	23362117	.	-	.	transcript_id "Phchi.S1G366500.t1"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	start_codon	23362115	23362117	.	-	0	transcript_id "Phchi.S1G366500.t1"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	transcript	23361236	23362702	.	-	.	transcript_id "Phchi.S1G366500.t2"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	stop_codon	23361233	23361235	.	-	0	transcript_id "Phchi.S1G366500.t2"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	CDS	23361236	23362702	0.82	-	0	transcript_id "Phchi.S1G366500.t2"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	exon	23361236	23362702	.	-	.	transcript_id "Phchi.S1G366500.t2"; gene_id "Phchi.S1G366500"
Phchi.S1	AUGUSTUS	start_codon	23362700	23362702	.	-	0	transcript_id "Phchi.S1G366500.t2"; gene_id "Phchi.S1G366500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14898.t1 is derived from g13366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15430306	15432300	.	-	.	Phchi.S3G221700
Phchi.S3	AUGUSTUS	transcript	15430306	15432300	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	stop_codon	15430303	15430305	.	-	0	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	CDS	15430306	15430483	1	-	1	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	exon	15430306	15430483	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	intron	15430484	15430566	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	CDS	15430567	15430784	1	-	0	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	exon	15430567	15430784	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	intron	15430785	15430898	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	CDS	15430899	15431306	0.83	-	0	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	exon	15430899	15431306	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	intron	15431307	15431398	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	CDS	15431399	15431589	0.85	-	2	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	exon	15431399	15431589	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	intron	15431590	15431675	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	CDS	15431676	15432300	0.66	-	0	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	exon	15431676	15432300	.	-	.	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
Phchi.S3	AUGUSTUS	start_codon	15432298	15432300	.	-	0	transcript_id "Phchi.S3G221700.t1"; gene_id "Phchi.S3G221700"
# This transcript jg9406.t2 is derived from g6582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9407.t1 is derived from g6583.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41356217	41360316	.	-	.	Phchi.S1G656600
Phchi.S1	AUGUSTUS	transcript	41356348	41360316	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	stop_codon	41356345	41356347	.	-	0	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356348	41356372	0.99	-	1	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356348	41356372	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356373	41356454	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356455	41356565	0.94	-	1	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356455	41356565	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356566	41356656	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356657	41356706	0.95	-	0	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356657	41356706	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356707	41357222	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41357223	41357437	0.99	-	2	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41357223	41357437	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41357438	41357791	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41357792	41357909	0.47	-	0	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41357792	41357909	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41357910	41358319	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41358320	41359176	0.35	-	2	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41358320	41359176	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41359177	41359241	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41359242	41360316	0.39	-	0	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41359242	41360316	.	-	.	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	start_codon	41360314	41360316	.	-	0	transcript_id "Phchi.S1G656600.t1"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	transcript	41356217	41360316	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	stop_codon	41356214	41356216	.	-	0	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356217	41356355	0.84	-	1	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356217	41356355	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356356	41356454	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356455	41356565	0.77	-	1	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356455	41356565	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356566	41356656	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356657	41356706	0.81	-	0	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356657	41356706	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356707	41357222	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41357223	41357440	1	-	2	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41357223	41357440	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41357441	41357791	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41357792	41357909	0.41	-	0	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41357792	41357909	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41357910	41358319	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41358320	41359176	0.36	-	2	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41358320	41359176	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41359177	41359241	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41359242	41360316	0.3	-	0	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41359242	41360316	.	-	.	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	start_codon	41360314	41360316	.	-	0	transcript_id "Phchi.S1G656600.t2"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	transcript	41356217	41360316	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	stop_codon	41356214	41356216	.	-	0	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356217	41356355	0.84	-	1	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356217	41356355	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356356	41356454	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356455	41356565	0.69	-	1	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356455	41356565	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356566	41356656	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356657	41356706	0.72	-	0	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356657	41356706	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356707	41356904	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41356905	41356952	0.93	-	0	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41356905	41356952	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41356953	41357222	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41357223	41357437	0.87	-	2	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41357223	41357437	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41357438	41357791	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41357792	41357909	0.3	-	0	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41357792	41357909	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41357910	41358319	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41358320	41359176	0.23	-	2	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41358320	41359176	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	intron	41359177	41359241	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	CDS	41359242	41360316	0.29	-	0	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	exon	41359242	41360316	.	-	.	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
Phchi.S1	AUGUSTUS	start_codon	41360314	41360316	.	-	0	transcript_id "Phchi.S1G656600.t3"; gene_id "Phchi.S1G656600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14850.t1 is derived from g13318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15047753	15048492	.	-	.	Phchi.S3G216900
Phchi.S3	AUGUSTUS	transcript	15047753	15048492	.	-	.	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	stop_codon	15047750	15047752	.	-	0	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	CDS	15047753	15048210	0.99	-	2	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	exon	15047753	15048210	.	-	.	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	intron	15048211	15048286	.	-	.	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	CDS	15048287	15048315	0.99	-	1	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	exon	15048287	15048315	.	-	.	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	intron	15048316	15048463	.	-	.	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	CDS	15048464	15048492	0.98	-	0	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	exon	15048464	15048492	.	-	.	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
Phchi.S3	AUGUSTUS	start_codon	15048490	15048492	.	-	0	transcript_id "Phchi.S3G216900.t1"; gene_id "Phchi.S3G216900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3965.t1 is derived from g1134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6772399	6773361	.	-	.	Phchi.S1G112400
Phchi.S1	AUGUSTUS	transcript	6772399	6773361	.	-	.	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	stop_codon	6772396	6772398	.	-	0	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	CDS	6772399	6772566	0.98	-	0	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	exon	6772399	6772566	.	-	.	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	intron	6772567	6772660	.	-	.	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	CDS	6772661	6773173	1	-	0	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	exon	6772661	6773173	.	-	.	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	intron	6773174	6773307	.	-	.	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	CDS	6773308	6773361	0.6	-	0	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	exon	6773308	6773361	.	-	.	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
Phchi.S1	AUGUSTUS	start_codon	6773359	6773361	.	-	0	transcript_id "Phchi.S1G112400.t1"; gene_id "Phchi.S1G112400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10537.t1 is derived from g14587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	869659	870648	.	-	.	Phchi.S4G011900
Phchi.S4	AUGUSTUS	transcript	869659	870648	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	stop_codon	869656	869658	.	-	0	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	CDS	869659	869745	1	-	0	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	exon	869659	869745	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	intron	869746	869838	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	CDS	869839	869923	1	-	1	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	exon	869839	869923	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	intron	869924	870103	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	CDS	870104	870162	1	-	0	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	exon	870104	870162	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	intron	870163	870260	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	CDS	870261	870409	1	-	2	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	exon	870261	870409	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	intron	870410	870494	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	CDS	870495	870648	1	-	0	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	exon	870495	870648	.	-	.	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
Phchi.S4	AUGUSTUS	start_codon	870646	870648	.	-	0	transcript_id "Phchi.S4G011900.t1"; gene_id "Phchi.S4G011900"
# This transcript jg7186.t2 is derived from g4358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7187.t1 is derived from g4359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27459659	27464289	.	-	.	Phchi.S1G434600
Phchi.S1	AUGUSTUS	transcript	27459659	27464289	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	stop_codon	27459656	27459658	.	-	0	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	CDS	27459659	27463486	0.98	-	0	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	exon	27459659	27463486	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	intron	27463487	27463731	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	CDS	27463732	27463817	0.99	-	2	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	exon	27463732	27463817	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	intron	27463818	27464013	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	CDS	27464014	27464021	0.91	-	1	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	exon	27464014	27464021	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	intron	27464022	27464194	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	CDS	27464195	27464289	0.6	-	0	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	exon	27464195	27464289	.	-	.	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
Phchi.S1	AUGUSTUS	start_codon	27464287	27464289	.	-	0	transcript_id "Phchi.S1G434600.t1"; gene_id "Phchi.S1G434600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8859.t1 is derived from g6034.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38314076	38317911	.	+	.	Phchi.S1G601800
Phchi.S1	AUGUSTUS	transcript	38314076	38317911	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	start_codon	38314076	38314078	.	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314076	38314126	1	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314076	38314126	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38314127	38314202	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314203	38314300	1	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314203	38314300	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38314301	38314392	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314393	38314439	1	+	1	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314393	38314439	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38314440	38314530	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314531	38314580	1	+	2	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314531	38314580	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38314581	38314665	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314666	38314755	1	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314666	38314755	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38314756	38314833	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314834	38314887	1	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314834	38314887	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38314888	38314995	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38314996	38315043	1	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38314996	38315043	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38315044	38315191	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38315192	38316282	0.36	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38315192	38316282	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	intron	38316283	38316422	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	CDS	38316423	38317911	0.37	+	1	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	exon	38316423	38317911	.	+	.	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
Phchi.S1	AUGUSTUS	stop_codon	38317912	38317914	.	+	0	transcript_id "Phchi.S1G601800.t1"; gene_id "Phchi.S1G601800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5704.t1 is derived from g2874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18442825	18444899	.	+	.	Phchi.S1G286300
Phchi.S1	AUGUSTUS	transcript	18442825	18444899	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	start_codon	18442825	18442827	.	+	0	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	CDS	18442825	18442899	0.98	+	0	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	exon	18442825	18442899	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	intron	18442900	18443012	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	CDS	18443013	18443289	0.99	+	0	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	exon	18443013	18443289	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	intron	18443290	18443387	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	CDS	18443388	18443568	1	+	2	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	exon	18443388	18443568	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	intron	18443569	18443675	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	CDS	18443676	18443967	0.87	+	1	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	exon	18443676	18443967	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	intron	18443968	18444137	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	CDS	18444138	18444531	0.92	+	0	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	exon	18444138	18444531	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	intron	18444532	18444612	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	CDS	18444613	18444899	1	+	2	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	exon	18444613	18444899	.	+	.	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
Phchi.S1	AUGUSTUS	stop_codon	18444900	18444902	.	+	0	transcript_id "Phchi.S1G286300.t1"; gene_id "Phchi.S1G286300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11867.t1 is derived from g15919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8865166	8866731	.	+	.	Phchi.S4G144900
Phchi.S4	AUGUSTUS	transcript	8865166	8866731	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	start_codon	8865166	8865168	.	+	0	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8865166	8865283	1	+	0	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8865166	8865283	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8865284	8865354	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8865355	8865481	1	+	2	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8865355	8865481	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8865482	8865568	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8865569	8865630	1	+	1	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8865569	8865630	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8865631	8865727	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8865728	8865892	1	+	2	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8865728	8865892	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8865893	8865983	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8865984	8866128	1	+	2	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8865984	8866128	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8866129	8866266	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8866267	8866335	0.99	+	1	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8866267	8866335	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8866336	8866443	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8866444	8866552	1	+	1	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8866444	8866552	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	intron	8866553	8866632	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	CDS	8866633	8866731	1	+	0	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	exon	8866633	8866731	.	+	.	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
Phchi.S4	AUGUSTUS	stop_codon	8866732	8866734	.	+	0	transcript_id "Phchi.S4G144900.t1"; gene_id "Phchi.S4G144900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1650.t1 is derived from g8569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2216154	2219108	.	-	.	Phchi.S5G025900
Phchi.S5	AUGUSTUS	transcript	2216154	2219108	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	stop_codon	2216151	2216153	.	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2216154	2216249	1	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2216154	2216249	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2216250	2216399	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2216400	2216504	1	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2216400	2216504	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2216505	2216585	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2216586	2216636	0.99	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2216586	2216636	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2216637	2216753	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2216754	2216840	0.62	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2216754	2216840	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2216841	2216979	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2216980	2217212	1	-	2	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2216980	2217212	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2217213	2217327	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2217328	2217519	1	-	2	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2217328	2217519	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2217520	2217642	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2217643	2217823	1	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2217643	2217823	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2217824	2218000	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2218001	2218200	1	-	2	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2218001	2218200	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	intron	2218201	2218372	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	CDS	2218373	2219108	0.99	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	exon	2218373	2219108	.	-	.	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
Phchi.S5	AUGUSTUS	start_codon	2219106	2219108	.	-	0	transcript_id "Phchi.S5G025900.t1"; gene_id "Phchi.S5G025900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7515.t1 is derived from g4689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29797313	29798590	.	+	.	Phchi.S1G467400
Phchi.S1	AUGUSTUS	transcript	29797313	29798590	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	start_codon	29797313	29797315	.	+	0	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	CDS	29797313	29797673	0.66	+	0	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	exon	29797313	29797673	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	intron	29797674	29797913	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	CDS	29797914	29798017	1	+	2	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	exon	29797914	29798017	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	intron	29798018	29798099	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	CDS	29798100	29798207	1	+	0	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	exon	29798100	29798207	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	intron	29798208	29798325	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	CDS	29798326	29798427	0.99	+	0	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	exon	29798326	29798427	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	intron	29798428	29798545	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	CDS	29798546	29798590	0.99	+	0	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	exon	29798546	29798590	.	+	.	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
Phchi.S1	AUGUSTUS	stop_codon	29798591	29798593	.	+	0	transcript_id "Phchi.S1G467400.t1"; gene_id "Phchi.S1G467400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12792.t1 is derived from g11257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2393558	2394347	.	+	.	Phchi.S3G011100
Phchi.S3	AUGUSTUS	transcript	2393558	2394347	.	+	.	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	start_codon	2393558	2393560	.	+	0	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	CDS	2393558	2393898	0.98	+	0	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	exon	2393558	2393898	.	+	.	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	intron	2393899	2394013	.	+	.	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	CDS	2394014	2394347	0.95	+	1	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	exon	2394014	2394347	.	+	.	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
Phchi.S3	AUGUSTUS	stop_codon	2394348	2394350	.	+	0	transcript_id "Phchi.S3G011100.t1"; gene_id "Phchi.S3G011100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10165.t1 is derived from g7341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46056531	46057036	.	+	.	Phchi.S1G732400
Phchi.S1	AUGUSTUS	transcript	46056531	46057036	.	+	.	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	start_codon	46056531	46056533	.	+	0	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	CDS	46056531	46056818	0.68	+	0	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	exon	46056531	46056818	.	+	.	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	intron	46056819	46056928	.	+	.	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	CDS	46056929	46057036	1	+	0	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	exon	46056929	46057036	.	+	.	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
Phchi.S1	AUGUSTUS	stop_codon	46057037	46057039	.	+	0	transcript_id "Phchi.S1G732400.t1"; gene_id "Phchi.S1G732400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11223.t1 is derived from g15273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4869654	4870214	.	-	.	Phchi.S4G080500
Phchi.S4	AUGUSTUS	transcript	4869654	4870214	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	stop_codon	4869651	4869653	.	-	0	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	CDS	4869654	4869693	1	-	1	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	exon	4869654	4869693	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	intron	4869694	4869799	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	CDS	4869800	4869867	1	-	0	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	exon	4869800	4869867	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	intron	4869868	4869957	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	CDS	4869958	4870009	0.62	-	1	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	exon	4869958	4870009	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	intron	4870010	4870131	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	CDS	4870132	4870214	0.62	-	0	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	exon	4870132	4870214	.	-	.	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
Phchi.S4	AUGUSTUS	start_codon	4870212	4870214	.	-	0	transcript_id "Phchi.S4G080500.t1"; gene_id "Phchi.S4G080500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg789.t1 is derived from g10571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5592497	5595008	.	+	.	Phchi.S6G074800
Phchi.S6	AUGUSTUS	transcript	5592497	5595008	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	start_codon	5592497	5592499	.	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5592497	5592629	1	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5592497	5592629	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5592630	5592756	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5592757	5592827	1	+	2	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5592757	5592827	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5592828	5592930	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5592931	5593092	1	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5592931	5593092	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5593093	5593181	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5593182	5593193	1	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5593182	5593193	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5593194	5593258	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5593259	5593286	1	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5593259	5593286	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5593287	5593433	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5593434	5593627	1	+	2	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5593434	5593627	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5593628	5593715	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5593716	5593819	1	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5593716	5593819	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5593820	5593936	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5593937	5594120	1	+	1	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5593937	5594120	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5594121	5594200	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5594201	5594380	1	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5594201	5594380	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5594381	5594461	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5594462	5594564	0.88	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5594462	5594564	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5594565	5594644	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5594645	5594662	0.87	+	2	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5594645	5594662	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	intron	5594663	5594949	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	CDS	5594950	5595008	0.98	+	2	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	exon	5594950	5595008	.	+	.	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
Phchi.S6	AUGUSTUS	stop_codon	5595009	5595011	.	+	0	transcript_id "Phchi.S6G074800.t1"; gene_id "Phchi.S6G074800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6650.t1 is derived from g3822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24294326	24294859	.	+	.	Phchi.S1G380900
Phchi.S1	AUGUSTUS	transcript	24294326	24294859	.	+	.	transcript_id "Phchi.S1G380900.t1"; gene_id "Phchi.S1G380900"
Phchi.S1	AUGUSTUS	start_codon	24294326	24294328	.	+	0	transcript_id "Phchi.S1G380900.t1"; gene_id "Phchi.S1G380900"
Phchi.S1	AUGUSTUS	CDS	24294326	24294859	0.95	+	0	transcript_id "Phchi.S1G380900.t1"; gene_id "Phchi.S1G380900"
Phchi.S1	AUGUSTUS	exon	24294326	24294859	.	+	.	transcript_id "Phchi.S1G380900.t1"; gene_id "Phchi.S1G380900"
Phchi.S1	AUGUSTUS	stop_codon	24294860	24294862	.	+	0	transcript_id "Phchi.S1G380900.t1"; gene_id "Phchi.S1G380900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14224.t1 is derived from g12691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11640914	11642566	.	-	.	Phchi.S3G154300
Phchi.S3	AUGUSTUS	transcript	11640914	11642566	.	-	.	transcript_id "Phchi.S3G154300.t1"; gene_id "Phchi.S3G154300"
Phchi.S3	AUGUSTUS	stop_codon	11640911	11640913	.	-	0	transcript_id "Phchi.S3G154300.t1"; gene_id "Phchi.S3G154300"
Phchi.S3	AUGUSTUS	CDS	11640914	11642566	0.48	-	0	transcript_id "Phchi.S3G154300.t1"; gene_id "Phchi.S3G154300"
Phchi.S3	AUGUSTUS	exon	11640914	11642566	.	-	.	transcript_id "Phchi.S3G154300.t1"; gene_id "Phchi.S3G154300"
Phchi.S3	AUGUSTUS	start_codon	11642564	11642566	.	-	0	transcript_id "Phchi.S3G154300.t1"; gene_id "Phchi.S3G154300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg757.t1 is derived from g10539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5358226	5359065	.	-	.	Phchi.S6G071600
Phchi.S6	AUGUSTUS	transcript	5358226	5359065	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	stop_codon	5358223	5358225	.	-	0	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	CDS	5358226	5358245	0.99	-	2	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	exon	5358226	5358245	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	intron	5358246	5358435	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	CDS	5358436	5358459	0.71	-	2	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	exon	5358436	5358459	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	intron	5358460	5358531	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	CDS	5358532	5358633	0.97	-	2	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	exon	5358532	5358633	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	intron	5358634	5358770	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	CDS	5358771	5359065	0.95	-	0	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	exon	5358771	5359065	.	-	.	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
Phchi.S6	AUGUSTUS	start_codon	5359063	5359065	.	-	0	transcript_id "Phchi.S6G071600.t1"; gene_id "Phchi.S6G071600"
# This transcript jg8520.t2 is derived from g5695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8521.t1 is derived from g5696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36419267	36419743	.	-	.	Phchi.S1G568000
Phchi.S1	AUGUSTUS	transcript	36419267	36419743	.	-	.	transcript_id "Phchi.S1G568000.t1"; gene_id "Phchi.S1G568000"
Phchi.S1	AUGUSTUS	stop_codon	36419264	36419266	.	-	0	transcript_id "Phchi.S1G568000.t1"; gene_id "Phchi.S1G568000"
Phchi.S1	AUGUSTUS	CDS	36419267	36419743	0.46	-	0	transcript_id "Phchi.S1G568000.t1"; gene_id "Phchi.S1G568000"
Phchi.S1	AUGUSTUS	exon	36419267	36419743	.	-	.	transcript_id "Phchi.S1G568000.t1"; gene_id "Phchi.S1G568000"
Phchi.S1	AUGUSTUS	start_codon	36419741	36419743	.	-	0	transcript_id "Phchi.S1G568000.t1"; gene_id "Phchi.S1G568000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg521.t1 is derived from g10303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3739511	3741945	.	+	.	Phchi.S6G048000
Phchi.S6	AUGUSTUS	transcript	3739511	3741945	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	start_codon	3739511	3739513	.	+	0	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3739511	3739544	0.5	+	0	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3739511	3739544	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3739545	3739708	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3739709	3739714	0.89	+	2	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3739709	3739714	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3739715	3739913	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3739914	3740089	0.89	+	2	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3739914	3740089	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3740090	3740168	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3740169	3740248	1	+	0	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3740169	3740248	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3740249	3740324	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3740325	3740525	1	+	1	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3740325	3740525	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3740526	3740628	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3740629	3740642	1	+	1	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3740629	3740642	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3740643	3740780	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3740781	3740995	1	+	2	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3740781	3740995	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3740996	3741078	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3741079	3741273	1	+	0	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3741079	3741273	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	intron	3741274	3741354	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	CDS	3741355	3741945	0.93	+	0	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	exon	3741355	3741945	.	+	.	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
Phchi.S6	AUGUSTUS	stop_codon	3741946	3741948	.	+	0	transcript_id "Phchi.S6G048000.t1"; gene_id "Phchi.S6G048000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg365.t1 is derived from g10147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2666520	2668073	.	-	.	Phchi.S6G032400
Phchi.S6	AUGUSTUS	transcript	2666520	2668073	.	-	.	transcript_id "Phchi.S6G032400.t1"; gene_id "Phchi.S6G032400"
Phchi.S6	AUGUSTUS	stop_codon	2666517	2666519	.	-	0	transcript_id "Phchi.S6G032400.t1"; gene_id "Phchi.S6G032400"
Phchi.S6	AUGUSTUS	CDS	2666520	2668073	1	-	0	transcript_id "Phchi.S6G032400.t1"; gene_id "Phchi.S6G032400"
Phchi.S6	AUGUSTUS	exon	2666520	2668073	.	-	.	transcript_id "Phchi.S6G032400.t1"; gene_id "Phchi.S6G032400"
Phchi.S6	AUGUSTUS	start_codon	2668071	2668073	.	-	0	transcript_id "Phchi.S6G032400.t1"; gene_id "Phchi.S6G032400"
# This transcript jg3825.t2 is derived from g994.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3826.t1 is derived from g995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5899669	5901190	.	+	.	Phchi.S1G098500
Phchi.S1	AUGUSTUS	transcript	5899669	5901190	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	start_codon	5899669	5899671	.	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5899669	5899803	0.97	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5899669	5899803	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5899804	5899876	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5899877	5899950	1	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5899877	5899950	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5899951	5900038	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5900039	5900120	0.99	+	1	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5900039	5900120	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5900121	5900225	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5900226	5900276	0.89	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5900226	5900276	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5900277	5900347	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5900348	5900448	1	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5900348	5900448	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5900449	5900533	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5900534	5900687	1	+	1	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5900534	5900687	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5900688	5900780	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5900781	5901002	1	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5900781	5901002	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	intron	5901003	5901079	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	CDS	5901080	5901190	1	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	exon	5901080	5901190	.	+	.	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
Phchi.S1	AUGUSTUS	stop_codon	5901191	5901193	.	+	0	transcript_id "Phchi.S1G098500.t1"; gene_id "Phchi.S1G098500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3242.t1 is derived from g411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2406650	2408407	.	-	.	Phchi.S1G040100
Phchi.S1	AUGUSTUS	transcript	2406650	2408407	.	-	.	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	stop_codon	2406647	2406649	.	-	0	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	CDS	2406650	2407288	1	-	0	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	exon	2406650	2407288	.	-	.	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	intron	2407289	2407379	.	-	.	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	CDS	2407380	2407838	1	-	0	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	exon	2407380	2407838	.	-	.	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	intron	2407839	2407924	.	-	.	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	CDS	2407925	2408407	0.93	-	0	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	exon	2407925	2408407	.	-	.	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
Phchi.S1	AUGUSTUS	start_codon	2408405	2408407	.	-	0	transcript_id "Phchi.S1G040100.t1"; gene_id "Phchi.S1G040100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16006.t1 is derived from g14430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	100992	101429	.	-	.	Phchi.C10G000400
Phchi.C10	AUGUSTUS	transcript	100992	101429	.	-	.	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	stop_codon	100989	100991	.	-	0	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	CDS	100992	101211	0.68	-	1	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	exon	100992	101211	.	-	.	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	intron	101212	101304	.	-	.	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	CDS	101305	101429	0.71	-	0	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	exon	101305	101429	.	-	.	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
Phchi.C10	AUGUSTUS	start_codon	101427	101429	.	-	0	transcript_id "Phchi.C10G000400.t1"; gene_id "Phchi.C10G000400"
# This transcript jg3149.t2 is derived from g318.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3150.t1 is derived from g319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1987548	1987958	.	-	.	Phchi.S1G030900
Phchi.S1	AUGUSTUS	transcript	1987548	1987958	.	-	.	transcript_id "Phchi.S1G030900.t1"; gene_id "Phchi.S1G030900"
Phchi.S1	AUGUSTUS	stop_codon	1987545	1987547	.	-	0	transcript_id "Phchi.S1G030900.t1"; gene_id "Phchi.S1G030900"
Phchi.S1	AUGUSTUS	CDS	1987548	1987958	0.61	-	0	transcript_id "Phchi.S1G030900.t1"; gene_id "Phchi.S1G030900"
Phchi.S1	AUGUSTUS	exon	1987548	1987958	.	-	.	transcript_id "Phchi.S1G030900.t1"; gene_id "Phchi.S1G030900"
Phchi.S1	AUGUSTUS	start_codon	1987956	1987958	.	-	0	transcript_id "Phchi.S1G030900.t1"; gene_id "Phchi.S1G030900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4361.t1 is derived from g1530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10017497	10018156	.	-	.	Phchi.S1G152000
Phchi.S1	AUGUSTUS	transcript	10017497	10018156	.	-	.	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	stop_codon	10017494	10017496	.	-	0	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	CDS	10017497	10017539	0.81	-	1	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	exon	10017497	10017539	.	-	.	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	intron	10017540	10017685	.	-	.	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	CDS	10017686	10017926	0.34	-	2	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	exon	10017686	10017926	.	-	.	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	intron	10017927	10018029	.	-	.	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	CDS	10018030	10018156	0.69	-	0	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	exon	10018030	10018156	.	-	.	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
Phchi.S1	AUGUSTUS	start_codon	10018154	10018156	.	-	0	transcript_id "Phchi.S1G152000.t1"; gene_id "Phchi.S1G152000"
# This transcript jg9771.t2 is derived from g6947.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9772.t1 is derived from g6948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43614328	43615107	.	-	.	Phchi.S1G693100
Phchi.S1	AUGUSTUS	transcript	43614328	43615107	.	-	.	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	stop_codon	43614325	43614327	.	-	0	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	CDS	43614328	43614872	1	-	2	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	exon	43614328	43614872	.	-	.	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	intron	43614873	43615016	.	-	.	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	CDS	43615017	43615107	0.99	-	0	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	exon	43615017	43615107	.	-	.	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
Phchi.S1	AUGUSTUS	start_codon	43615105	43615107	.	-	0	transcript_id "Phchi.S1G693100.t1"; gene_id "Phchi.S1G693100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10564.t1 is derived from g14614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	996376	997218	.	-	.	Phchi.S4G014600
Phchi.S4	AUGUSTUS	transcript	996376	997218	.	-	.	transcript_id "Phchi.S4G014600.t1"; gene_id "Phchi.S4G014600"
Phchi.S4	AUGUSTUS	stop_codon	996373	996375	.	-	0	transcript_id "Phchi.S4G014600.t1"; gene_id "Phchi.S4G014600"
Phchi.S4	AUGUSTUS	CDS	996376	997218	0.98	-	0	transcript_id "Phchi.S4G014600.t1"; gene_id "Phchi.S4G014600"
Phchi.S4	AUGUSTUS	exon	996376	997218	.	-	.	transcript_id "Phchi.S4G014600.t1"; gene_id "Phchi.S4G014600"
Phchi.S4	AUGUSTUS	start_codon	997216	997218	.	-	0	transcript_id "Phchi.S4G014600.t1"; gene_id "Phchi.S4G014600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6025.t1 is derived from g3196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20490587	20491653	.	+	.	Phchi.S1G318400
Phchi.S1	AUGUSTUS	transcript	20490587	20491653	.	+	.	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	start_codon	20490587	20490589	.	+	0	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	CDS	20490587	20490844	1	+	0	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	exon	20490587	20490844	.	+	.	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	intron	20490845	20491011	.	+	.	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	CDS	20491012	20491218	1	+	0	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	exon	20491012	20491218	.	+	.	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	intron	20491219	20491299	.	+	.	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	CDS	20491300	20491653	1	+	0	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	exon	20491300	20491653	.	+	.	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
Phchi.S1	AUGUSTUS	stop_codon	20491654	20491656	.	+	0	transcript_id "Phchi.S1G318400.t1"; gene_id "Phchi.S1G318400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9533.t1 is derived from g6709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42351961	42355330	.	+	.	Phchi.S1G669200
Phchi.S1	AUGUSTUS	transcript	42351961	42355330	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	start_codon	42351961	42351963	.	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42351961	42352285	0.97	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42351961	42352285	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42352286	42352367	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42352368	42352869	0.43	+	2	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42352368	42352869	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42352870	42352995	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42352996	42353167	0.94	+	1	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42352996	42353167	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42353168	42353450	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42353451	42353588	1	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42353451	42353588	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42353589	42353693	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42353694	42353900	0.91	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42353694	42353900	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42353901	42354043	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42354044	42354130	0.61	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42354044	42354130	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42354131	42354341	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42354342	42354614	0.47	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42354342	42354614	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42354615	42354857	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42354858	42354996	0.6	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42354858	42354996	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42354997	42355085	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42355086	42355330	0.65	+	2	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42355086	42355330	.	+	.	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	stop_codon	42355331	42355333	.	+	0	transcript_id "Phchi.S1G669200.t1"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	transcript	42353272	42355330	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	start_codon	42353272	42353274	.	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42353272	42353334	0.86	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42353272	42353334	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42353335	42353450	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42353451	42353588	0.85	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42353451	42353588	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42353589	42353693	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42353694	42353900	0.83	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42353694	42353900	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42353901	42354043	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42354044	42354130	0.57	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42354044	42354130	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42354131	42354341	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42354342	42354614	0.52	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42354342	42354614	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42354615	42354857	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42354858	42354996	0.5	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42354858	42354996	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	intron	42354997	42355085	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	CDS	42355086	42355330	0.58	+	2	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	exon	42355086	42355330	.	+	.	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
Phchi.S1	AUGUSTUS	stop_codon	42355331	42355333	.	+	0	transcript_id "Phchi.S1G669200.t2"; gene_id "Phchi.S1G669200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8450.t1 is derived from g5625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35989284	35993376	.	+	.	Phchi.S1G560900
Phchi.S1	AUGUSTUS	transcript	35989284	35993376	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	start_codon	35989284	35989286	.	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35989284	35989336	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35989284	35989336	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35989337	35989433	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35989434	35989473	1	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35989434	35989473	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35989474	35989629	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35989630	35989710	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35989630	35989710	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35989711	35989787	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35989788	35989985	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35989788	35989985	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35989986	35990076	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35990077	35990187	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35990077	35990187	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35990188	35990319	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35990320	35990385	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35990320	35990385	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35990386	35990508	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35990509	35990616	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35990509	35990616	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35990617	35990758	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35990759	35990803	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35990759	35990803	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35990804	35990896	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35990897	35990953	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35990897	35990953	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35990954	35991091	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35991092	35991186	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35991092	35991186	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35991187	35991301	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35991302	35991353	0.81	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35991302	35991353	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35991354	35991638	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35991639	35991710	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35991639	35991710	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35991711	35991825	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35991826	35991932	0.93	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35991826	35991932	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35991933	35992034	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35992035	35992157	0.96	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35992035	35992157	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35992158	35992247	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35992248	35992329	1	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35992248	35992329	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35992330	35992465	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35992466	35992536	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35992466	35992536	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35992537	35992643	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35992644	35992724	1	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35992644	35992724	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35992725	35992805	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35992806	35992863	1	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35992806	35992863	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35992864	35992959	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35992960	35993021	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35992960	35993021	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35993022	35993112	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35993113	35993212	1	+	1	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35993113	35993212	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	intron	35993213	35993289	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	CDS	35993290	35993376	1	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	exon	35993290	35993376	.	+	.	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
Phchi.S1	AUGUSTUS	stop_codon	35993377	35993379	.	+	0	transcript_id "Phchi.S1G560900.t1"; gene_id "Phchi.S1G560900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6579.t1 is derived from g3751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23838395	23839711	.	+	.	Phchi.S1G373800
Phchi.S1	AUGUSTUS	transcript	23838395	23839711	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	start_codon	23838395	23838397	.	+	0	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	CDS	23838395	23838558	0.97	+	0	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	exon	23838395	23838558	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	intron	23838559	23838774	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	CDS	23838775	23838898	1	+	1	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	exon	23838775	23838898	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	intron	23838899	23839013	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	CDS	23839014	23839140	1	+	0	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	exon	23839014	23839140	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	intron	23839141	23839269	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	CDS	23839270	23839329	1	+	2	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	exon	23839270	23839329	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	intron	23839330	23839452	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	CDS	23839453	23839562	0.42	+	2	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	exon	23839453	23839562	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	intron	23839563	23839648	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	CDS	23839649	23839711	0.74	+	0	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	exon	23839649	23839711	.	+	.	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
Phchi.S1	AUGUSTUS	stop_codon	23839712	23839714	.	+	0	transcript_id "Phchi.S1G373800.t1"; gene_id "Phchi.S1G373800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14619.t1 is derived from g13087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13806999	13807592	.	+	.	Phchi.S3G193800
Phchi.S3	AUGUSTUS	transcript	13806999	13807592	.	+	.	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	start_codon	13806999	13807001	.	+	0	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	CDS	13806999	13807179	0.96	+	0	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	exon	13806999	13807179	.	+	.	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	intron	13807180	13807260	.	+	.	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	CDS	13807261	13807592	1	+	2	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	exon	13807261	13807592	.	+	.	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
Phchi.S3	AUGUSTUS	stop_codon	13807593	13807595	.	+	0	transcript_id "Phchi.S3G193800.t1"; gene_id "Phchi.S3G193800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4510.t1 is derived from g1680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10887566	10890780	.	+	.	Phchi.S1G166900
Phchi.S1	AUGUSTUS	transcript	10887566	10890780	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	start_codon	10887566	10887568	.	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10887566	10887775	0.84	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10887566	10887775	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10887776	10887935	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10887936	10888982	0.74	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10887936	10888982	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10888983	10889079	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10889080	10889102	0.9	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10889080	10889102	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10889103	10889411	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10889412	10889431	0.9	+	1	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10889412	10889431	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10889432	10889649	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10889650	10889684	0.99	+	2	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10889650	10889684	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10889685	10889854	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10889855	10889972	0.56	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10889855	10889972	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10889973	10890189	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10890190	10890533	0.43	+	2	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10890190	10890533	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	intron	10890534	10890750	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	CDS	10890751	10890780	0.87	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	exon	10890751	10890780	.	+	.	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
Phchi.S1	AUGUSTUS	stop_codon	10890781	10890783	.	+	0	transcript_id "Phchi.S1G166900.t1"; gene_id "Phchi.S1G166900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10261.t1 is derived from g7437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46728989	46730244	.	-	.	Phchi.S1G742000
Phchi.S1	AUGUSTUS	transcript	46728989	46730244	.	-	.	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	stop_codon	46728986	46728988	.	-	0	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	CDS	46728989	46729243	0.82	-	0	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	exon	46728989	46729243	.	-	.	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	intron	46729244	46729347	.	-	.	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	CDS	46729348	46730244	0.8	-	0	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	exon	46729348	46730244	.	-	.	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
Phchi.S1	AUGUSTUS	start_codon	46730242	46730244	.	-	0	transcript_id "Phchi.S1G742000.t1"; gene_id "Phchi.S1G742000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13919.t1 is derived from g12386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9658065	9661037	.	+	.	Phchi.S3G123800
Phchi.S3	AUGUSTUS	transcript	9658065	9661037	.	+	.	transcript_id "Phchi.S3G123800.t1"; gene_id "Phchi.S3G123800"
Phchi.S3	AUGUSTUS	start_codon	9658065	9658067	.	+	0	transcript_id "Phchi.S3G123800.t1"; gene_id "Phchi.S3G123800"
Phchi.S3	AUGUSTUS	CDS	9658065	9661037	0.77	+	0	transcript_id "Phchi.S3G123800.t1"; gene_id "Phchi.S3G123800"
Phchi.S3	AUGUSTUS	exon	9658065	9661037	.	+	.	transcript_id "Phchi.S3G123800.t1"; gene_id "Phchi.S3G123800"
Phchi.S3	AUGUSTUS	stop_codon	9661038	9661040	.	+	0	transcript_id "Phchi.S3G123800.t1"; gene_id "Phchi.S3G123800"
# This transcript jg10508.t2 is derived from g14557.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10509.t1 is derived from g14558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	758692	759967	.	+	.	Phchi.S4G009100
Phchi.S4	AUGUSTUS	transcript	758692	759967	.	+	.	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	start_codon	758692	758694	.	+	0	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	CDS	758692	759196	0.46	+	0	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	exon	758692	759196	.	+	.	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	intron	759197	759430	.	+	.	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	CDS	759431	759860	0.7	+	2	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	exon	759431	759860	.	+	.	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	intron	759861	759963	.	+	.	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	CDS	759964	759967	0.57	+	1	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	exon	759964	759967	.	+	.	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
Phchi.S4	AUGUSTUS	stop_codon	759968	759970	.	+	0	transcript_id "Phchi.S4G009100.t1"; gene_id "Phchi.S4G009100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13213.t1 is derived from g11678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4712177	4714953	.	-	.	Phchi.S3G053200
Phchi.S3	AUGUSTUS	transcript	4712177	4714953	.	-	.	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	stop_codon	4712174	4712176	.	-	0	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	CDS	4712177	4712658	1	-	2	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	exon	4712177	4712658	.	-	.	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	intron	4712659	4712799	.	-	.	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	CDS	4712800	4713934	0.82	-	0	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	exon	4712800	4713934	.	-	.	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	intron	4713935	4714188	.	-	.	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	CDS	4714189	4714953	0.27	-	0	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	exon	4714189	4714953	.	-	.	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
Phchi.S3	AUGUSTUS	start_codon	4714951	4714953	.	-	0	transcript_id "Phchi.S3G053200.t1"; gene_id "Phchi.S3G053200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10144.t1 is derived from g7320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45974047	45978640	.	-	.	Phchi.S1G730300
Phchi.S1	AUGUSTUS	transcript	45974047	45978640	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	stop_codon	45974044	45974046	.	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45974047	45974148	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45974047	45974148	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45974149	45974245	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45974246	45974299	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45974246	45974299	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45974300	45974414	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45974415	45974475	0.99	-	1	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45974415	45974475	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45974476	45974611	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45974612	45974712	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45974612	45974712	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45974713	45974827	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45974828	45974948	1	-	1	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45974828	45974948	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45974949	45975059	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45975060	45975185	1	-	1	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45975060	45975185	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45975186	45975296	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45975297	45975418	0.6	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45975297	45975418	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45975419	45975524	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45975525	45975593	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45975525	45975593	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45975594	45975680	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45975681	45975755	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45975681	45975755	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45975756	45975916	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45975917	45976026	1	-	2	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45975917	45976026	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45976027	45976119	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45976120	45976180	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45976120	45976180	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45976181	45976287	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45976288	45976326	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45976288	45976326	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45976327	45976420	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45976421	45976487	1	-	1	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45976421	45976487	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45976488	45976568	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45976569	45976657	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45976569	45976657	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45976658	45976756	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45976757	45976852	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45976757	45976852	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45976853	45977034	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45977035	45977106	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45977035	45977106	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45977107	45977217	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45977218	45977368	1	-	1	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45977218	45977368	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45977369	45977461	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45977462	45977583	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45977462	45977583	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45977584	45977954	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45977955	45978176	1	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45977955	45978176	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	intron	45978177	45978274	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	CDS	45978275	45978640	0.71	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	exon	45978275	45978640	.	-	.	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
Phchi.S1	AUGUSTUS	start_codon	45978638	45978640	.	-	0	transcript_id "Phchi.S1G730300.t1"; gene_id "Phchi.S1G730300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13942.t1 is derived from g12409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9829623	9832498	.	-	.	Phchi.S3G126100
Phchi.S3	AUGUSTUS	transcript	9829623	9832498	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	stop_codon	9829620	9829622	.	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9829623	9829845	1	-	1	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9829623	9829845	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9829846	9829931	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9829932	9830064	1	-	2	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9829932	9830064	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9830065	9830159	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9830160	9830261	1	-	2	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9830160	9830261	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9830262	9830337	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9830338	9830434	1	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9830338	9830434	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9830435	9830516	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9830517	9830624	0.99	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9830517	9830624	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9830625	9830729	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9830730	9830873	0.98	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9830730	9830873	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9830874	9831001	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9831002	9831104	1	-	1	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9831002	9831104	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9831105	9831201	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9831202	9831312	1	-	1	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9831202	9831312	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9831313	9831443	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9831444	9831579	1	-	2	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9831444	9831579	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9831580	9831814	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9831815	9831986	1	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9831815	9831986	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	intron	9831987	9832102	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	CDS	9832103	9832498	0.33	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	exon	9832103	9832498	.	-	.	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
Phchi.S3	AUGUSTUS	start_codon	9832496	9832498	.	-	0	transcript_id "Phchi.S3G126100.t1"; gene_id "Phchi.S3G126100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10694.t1 is derived from g14744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1623454	1623855	.	-	.	Phchi.S4G027600
Phchi.S4	AUGUSTUS	transcript	1623454	1623855	.	-	.	transcript_id "Phchi.S4G027600.t1"; gene_id "Phchi.S4G027600"
Phchi.S4	AUGUSTUS	stop_codon	1623451	1623453	.	-	0	transcript_id "Phchi.S4G027600.t1"; gene_id "Phchi.S4G027600"
Phchi.S4	AUGUSTUS	CDS	1623454	1623855	0.64	-	0	transcript_id "Phchi.S4G027600.t1"; gene_id "Phchi.S4G027600"
Phchi.S4	AUGUSTUS	exon	1623454	1623855	.	-	.	transcript_id "Phchi.S4G027600.t1"; gene_id "Phchi.S4G027600"
Phchi.S4	AUGUSTUS	start_codon	1623853	1623855	.	-	0	transcript_id "Phchi.S4G027600.t1"; gene_id "Phchi.S4G027600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1716.t1 is derived from g8636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2678299	2678556	.	+	.	Phchi.S5G032500
Phchi.S5	AUGUSTUS	transcript	2678299	2678556	.	+	.	transcript_id "Phchi.S5G032500.t1"; gene_id "Phchi.S5G032500"
Phchi.S5	AUGUSTUS	start_codon	2678299	2678301	.	+	0	transcript_id "Phchi.S5G032500.t1"; gene_id "Phchi.S5G032500"
Phchi.S5	AUGUSTUS	CDS	2678299	2678556	0.71	+	0	transcript_id "Phchi.S5G032500.t1"; gene_id "Phchi.S5G032500"
Phchi.S5	AUGUSTUS	exon	2678299	2678556	.	+	.	transcript_id "Phchi.S5G032500.t1"; gene_id "Phchi.S5G032500"
Phchi.S5	AUGUSTUS	stop_codon	2678557	2678559	.	+	0	transcript_id "Phchi.S5G032500.t1"; gene_id "Phchi.S5G032500"
# This transcript jg6070.t2 is derived from g3241.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6071.t1 is derived from g3242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20737354	20737905	.	-	.	Phchi.S1G323000
Phchi.S1	AUGUSTUS	transcript	20737354	20737905	.	-	.	transcript_id "Phchi.S1G323000.t1"; gene_id "Phchi.S1G323000"
Phchi.S1	AUGUSTUS	stop_codon	20737351	20737353	.	-	0	transcript_id "Phchi.S1G323000.t1"; gene_id "Phchi.S1G323000"
Phchi.S1	AUGUSTUS	CDS	20737354	20737905	0.72	-	0	transcript_id "Phchi.S1G323000.t1"; gene_id "Phchi.S1G323000"
Phchi.S1	AUGUSTUS	exon	20737354	20737905	.	-	.	transcript_id "Phchi.S1G323000.t1"; gene_id "Phchi.S1G323000"
Phchi.S1	AUGUSTUS	start_codon	20737903	20737905	.	-	0	transcript_id "Phchi.S1G323000.t1"; gene_id "Phchi.S1G323000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11096.t1 is derived from g15146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4100614	4101384	.	-	.	Phchi.S4G067800
Phchi.S4	AUGUSTUS	transcript	4100614	4101384	.	-	.	transcript_id "Phchi.S4G067800.t1"; gene_id "Phchi.S4G067800"
Phchi.S4	AUGUSTUS	stop_codon	4100611	4100613	.	-	0	transcript_id "Phchi.S4G067800.t1"; gene_id "Phchi.S4G067800"
Phchi.S4	AUGUSTUS	CDS	4100614	4101384	0.74	-	0	transcript_id "Phchi.S4G067800.t1"; gene_id "Phchi.S4G067800"
Phchi.S4	AUGUSTUS	exon	4100614	4101384	.	-	.	transcript_id "Phchi.S4G067800.t1"; gene_id "Phchi.S4G067800"
Phchi.S4	AUGUSTUS	start_codon	4101382	4101384	.	-	0	transcript_id "Phchi.S4G067800.t1"; gene_id "Phchi.S4G067800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1021.t1 is derived from g10804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7156415	7161517	.	-	.	Phchi.S6G098000
Phchi.S6	AUGUSTUS	transcript	7156415	7161517	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	stop_codon	7156412	7156414	.	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7156415	7157021	0.99	-	1	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7156415	7157021	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7157022	7157196	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7157197	7157231	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7157197	7157231	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7157232	7157361	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7157362	7157535	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7157362	7157535	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7157536	7157672	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7157673	7158149	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7157673	7158149	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7158150	7158322	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7158323	7158383	1	-	1	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7158323	7158383	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7158384	7158505	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7158506	7158575	1	-	2	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7158506	7158575	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7158576	7158716	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7158717	7158775	0.97	-	1	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7158717	7158775	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7158776	7158825	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7158826	7158841	0.95	-	2	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7158826	7158841	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7158842	7158961	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7158962	7159280	0.9	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7158962	7159280	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7159281	7159388	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7159389	7159541	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7159389	7159541	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7159542	7159694	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7159695	7159790	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7159695	7159790	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7159791	7159967	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7159968	7160099	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7159968	7160099	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7160100	7160192	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7160193	7160417	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7160193	7160417	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7160418	7160489	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7160490	7160633	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7160490	7160633	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7160634	7160734	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7160735	7160818	0.99	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7160735	7160818	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7160819	7161106	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7161107	7161274	1	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7161107	7161274	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	intron	7161275	7161361	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	CDS	7161362	7161517	0.9	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	exon	7161362	7161517	.	-	.	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
Phchi.S6	AUGUSTUS	start_codon	7161515	7161517	.	-	0	transcript_id "Phchi.S6G098000.t1"; gene_id "Phchi.S6G098000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3533.t1 is derived from g702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4311470	4311872	.	+	.	Phchi.S1G069200
Phchi.S1	AUGUSTUS	transcript	4311470	4311872	.	+	.	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	start_codon	4311470	4311472	.	+	0	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	CDS	4311470	4311645	0.86	+	0	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	exon	4311470	4311645	.	+	.	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	intron	4311646	4311754	.	+	.	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	CDS	4311755	4311872	0.84	+	1	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	exon	4311755	4311872	.	+	.	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
Phchi.S1	AUGUSTUS	stop_codon	4311873	4311875	.	+	0	transcript_id "Phchi.S1G069200.t1"; gene_id "Phchi.S1G069200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2244.t1 is derived from g9164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5626356	5626835	.	+	.	Phchi.S5G085300
Phchi.S5	AUGUSTUS	transcript	5626356	5626835	.	+	.	transcript_id "Phchi.S5G085300.t1"; gene_id "Phchi.S5G085300"
Phchi.S5	AUGUSTUS	start_codon	5626356	5626358	.	+	0	transcript_id "Phchi.S5G085300.t1"; gene_id "Phchi.S5G085300"
Phchi.S5	AUGUSTUS	CDS	5626356	5626835	0.73	+	0	transcript_id "Phchi.S5G085300.t1"; gene_id "Phchi.S5G085300"
Phchi.S5	AUGUSTUS	exon	5626356	5626835	.	+	.	transcript_id "Phchi.S5G085300.t1"; gene_id "Phchi.S5G085300"
Phchi.S5	AUGUSTUS	stop_codon	5626836	5626838	.	+	0	transcript_id "Phchi.S5G085300.t1"; gene_id "Phchi.S5G085300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9944.t1 is derived from g7120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44602761	44607120	.	-	.	Phchi.S1G710300
Phchi.S1	AUGUSTUS	transcript	44602761	44607120	.	-	.	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	stop_codon	44602758	44602760	.	-	0	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	CDS	44602761	44603894	0.73	-	0	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	exon	44602761	44603894	.	-	.	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	intron	44603895	44604007	.	-	.	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	CDS	44604008	44605377	0.96	-	2	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	exon	44604008	44605377	.	-	.	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	intron	44605378	44605493	.	-	.	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	CDS	44605494	44607120	0.62	-	0	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	exon	44605494	44607120	.	-	.	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
Phchi.S1	AUGUSTUS	start_codon	44607118	44607120	.	-	0	transcript_id "Phchi.S1G710300.t1"; gene_id "Phchi.S1G710300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9938.t1 is derived from g7114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44570653	44571377	.	-	.	Phchi.S1G709700
Phchi.S1	AUGUSTUS	transcript	44570653	44571377	.	-	.	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	stop_codon	44570650	44570652	.	-	0	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	CDS	44570653	44570996	0.26	-	2	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	exon	44570653	44570996	.	-	.	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	intron	44570997	44571100	.	-	.	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	CDS	44571101	44571377	0.66	-	0	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	exon	44571101	44571377	.	-	.	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
Phchi.S1	AUGUSTUS	start_codon	44571375	44571377	.	-	0	transcript_id "Phchi.S1G709700.t1"; gene_id "Phchi.S1G709700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1922.t1 is derived from g8842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3857547	3858550	.	+	.	Phchi.S5G053100
Phchi.S5	AUGUSTUS	transcript	3857547	3858550	.	+	.	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	start_codon	3857547	3857549	.	+	0	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	CDS	3857547	3858138	0.68	+	0	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	exon	3857547	3858138	.	+	.	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	intron	3858139	3858224	.	+	.	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	CDS	3858225	3858550	0.99	+	2	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	exon	3858225	3858550	.	+	.	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
Phchi.S5	AUGUSTUS	stop_codon	3858551	3858553	.	+	0	transcript_id "Phchi.S5G053100.t1"; gene_id "Phchi.S5G053100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15413.t1 is derived from g13881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18933293	18934173	.	+	.	Phchi.S3G273200
Phchi.S3	AUGUSTUS	transcript	18933293	18934173	.	+	.	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	start_codon	18933293	18933295	.	+	0	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	CDS	18933293	18933559	0.64	+	0	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	exon	18933293	18933559	.	+	.	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	intron	18933560	18933639	.	+	.	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	CDS	18933640	18934173	0.91	+	0	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	exon	18933640	18934173	.	+	.	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
Phchi.S3	AUGUSTUS	stop_codon	18934174	18934176	.	+	0	transcript_id "Phchi.S3G273200.t1"; gene_id "Phchi.S3G273200"
# This transcript jg12101.t2 is derived from g7776.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12101.t3 is derived from g7776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12102.t1 is derived from g7778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3291616	3292231	.	-	.	Phchi.S2G018200
Phchi.S2	AUGUSTUS	transcript	3291616	3292231	.	-	.	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	stop_codon	3291613	3291615	.	-	0	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	CDS	3291616	3291930	0.99	-	0	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	exon	3291616	3291930	.	-	.	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	intron	3291931	3292000	.	-	.	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	CDS	3292001	3292089	1	-	2	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	exon	3292001	3292089	.	-	.	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	intron	3292090	3292209	.	-	.	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	CDS	3292210	3292231	0.99	-	0	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	exon	3292210	3292231	.	-	.	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
Phchi.S2	AUGUSTUS	start_codon	3292229	3292231	.	-	0	transcript_id "Phchi.S2G018200.t1"; gene_id "Phchi.S2G018200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13366.t1 is derived from g11832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6365817	6367850	.	-	.	Phchi.S3G068500
Phchi.S3	AUGUSTUS	transcript	6365817	6367850	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	stop_codon	6365814	6365816	.	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6365817	6366062	0.61	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6365817	6366062	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	intron	6366063	6366146	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6366147	6366263	1	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6366147	6366263	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	intron	6366264	6366357	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6366358	6366459	1	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6366358	6366459	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	intron	6366460	6366549	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6366550	6366576	1	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6366550	6366576	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	intron	6366577	6366837	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6366838	6367047	1	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6366838	6367047	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	intron	6367048	6367203	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6367204	6367437	0.95	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6367204	6367437	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	intron	6367438	6367541	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	CDS	6367542	6367850	0.48	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	exon	6367542	6367850	.	-	.	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
Phchi.S3	AUGUSTUS	start_codon	6367848	6367850	.	-	0	transcript_id "Phchi.S3G068500.t1"; gene_id "Phchi.S3G068500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8935.t1 is derived from g6110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38744250	38748894	.	+	.	Phchi.S1G609400
Phchi.S1	AUGUSTUS	transcript	38744250	38748894	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	start_codon	38744250	38744252	.	+	0	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38744250	38744370	0.68	+	0	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38744250	38744370	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38744371	38744449	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38744450	38744754	1	+	2	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38744450	38744754	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38744755	38744838	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38744839	38745104	1	+	0	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38744839	38745104	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38745105	38745193	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38745194	38745469	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38745194	38745469	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38745470	38745547	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38745548	38745816	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38745548	38745816	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38745817	38745938	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38745939	38746056	1	+	2	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38745939	38746056	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38746057	38746145	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38746146	38746217	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38746146	38746217	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38746218	38746299	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38746300	38746371	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38746300	38746371	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38746372	38746499	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38746500	38746568	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38746500	38746568	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38746569	38746670	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38746671	38746739	0.91	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38746671	38746739	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38746740	38746849	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38746850	38747082	0.98	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38746850	38747082	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38747083	38747171	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38747172	38747204	0.95	+	2	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38747172	38747204	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38747205	38747320	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38747321	38747391	0.95	+	2	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38747321	38747391	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38747392	38747510	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38747511	38747637	1	+	0	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38747511	38747637	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38747638	38747852	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38747853	38747921	1	+	2	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38747853	38747921	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38747922	38748009	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38748010	38748055	1	+	2	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38748010	38748055	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38748056	38748138	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38748139	38748279	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38748139	38748279	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38748280	38748364	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38748365	38748506	1	+	1	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38748365	38748506	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	intron	38748507	38748588	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	CDS	38748589	38748894	0.99	+	0	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	exon	38748589	38748894	.	+	.	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
Phchi.S1	AUGUSTUS	stop_codon	38748895	38748897	.	+	0	transcript_id "Phchi.S1G609400.t1"; gene_id "Phchi.S1G609400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg494.t1 is derived from g10276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3439209	3439660	.	+	.	Phchi.S6G045300
Phchi.S6	AUGUSTUS	transcript	3439209	3439660	.	+	.	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	start_codon	3439209	3439211	.	+	0	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	CDS	3439209	3439443	0.93	+	0	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	exon	3439209	3439443	.	+	.	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	intron	3439444	3439544	.	+	.	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	CDS	3439545	3439660	0.99	+	2	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	exon	3439545	3439660	.	+	.	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
Phchi.S6	AUGUSTUS	stop_codon	3439661	3439663	.	+	0	transcript_id "Phchi.S6G045300.t1"; gene_id "Phchi.S6G045300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12069.t1 is derived from g7744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1877320	1879963	.	-	.	Phchi.S2G014900
Phchi.S2	AUGUSTUS	transcript	1877320	1879963	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	stop_codon	1877317	1877319	.	-	0	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	CDS	1877320	1877525	1	-	2	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	exon	1877320	1877525	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	intron	1877526	1877861	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	CDS	1877862	1877999	1	-	2	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	exon	1877862	1877999	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	intron	1878000	1878098	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	CDS	1878099	1878544	0.82	-	1	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	exon	1878099	1878544	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	intron	1878545	1878623	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	CDS	1878624	1878751	1	-	0	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	exon	1878624	1878751	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	intron	1878752	1878943	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	CDS	1878944	1879057	1	-	0	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	exon	1878944	1879057	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	intron	1879058	1879174	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	CDS	1879175	1879963	0.65	-	0	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	exon	1879175	1879963	.	-	.	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
Phchi.S2	AUGUSTUS	start_codon	1879961	1879963	.	-	0	transcript_id "Phchi.S2G014900.t1"; gene_id "Phchi.S2G014900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5593.t1 is derived from g2763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17801181	17803355	.	+	.	Phchi.S1G275200
Phchi.S1	AUGUSTUS	transcript	17801181	17803355	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	start_codon	17801181	17801183	.	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17801181	17801348	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17801181	17801348	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17801349	17801468	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17801469	17801528	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17801469	17801528	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17801529	17801608	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17801609	17801692	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17801609	17801692	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17801693	17801780	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17801781	17801893	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17801781	17801893	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17801894	17802006	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17802007	17802082	1	+	1	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17802007	17802082	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17802083	17802214	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17802215	17802285	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17802215	17802285	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17802286	17802369	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17802370	17802456	1	+	1	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17802370	17802456	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17802457	17802607	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17802608	17802680	1	+	1	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17802608	17802680	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17802681	17802790	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17802791	17802858	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17802791	17802858	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17802859	17802944	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17802945	17803013	1	+	1	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17802945	17803013	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17803014	17803104	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17803105	17803210	1	+	1	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17803105	17803210	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	intron	17803211	17803292	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	CDS	17803293	17803355	1	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	exon	17803293	17803355	.	+	.	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
Phchi.S1	AUGUSTUS	stop_codon	17803356	17803358	.	+	0	transcript_id "Phchi.S1G275200.t1"; gene_id "Phchi.S1G275200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12909.t1 is derived from g11374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3093003	3096130	.	+	.	Phchi.S3G022800
Phchi.S3	AUGUSTUS	transcript	3093003	3096130	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	start_codon	3093003	3093005	.	+	0	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	CDS	3093003	3093582	0.73	+	0	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	exon	3093003	3093582	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	intron	3093583	3093677	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	CDS	3093678	3093823	1	+	2	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	exon	3093678	3093823	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	intron	3093824	3093936	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	CDS	3093937	3094011	1	+	0	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	exon	3093937	3094011	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	intron	3094012	3094356	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	CDS	3094357	3095838	1	+	0	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	exon	3094357	3095838	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	intron	3095839	3095920	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	CDS	3095921	3096130	1	+	0	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	exon	3095921	3096130	.	+	.	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
Phchi.S3	AUGUSTUS	stop_codon	3096131	3096133	.	+	0	transcript_id "Phchi.S3G022800.t1"; gene_id "Phchi.S3G022800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14208.t1 is derived from g12675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11507762	11509044	.	+	.	Phchi.S3G152700
Phchi.S3	AUGUSTUS	transcript	11507762	11509044	.	+	.	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	start_codon	11507762	11507764	.	+	0	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	CDS	11507762	11508079	0.44	+	0	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	exon	11507762	11508079	.	+	.	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	intron	11508080	11508212	.	+	.	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	CDS	11508213	11508285	0.61	+	0	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	exon	11508213	11508285	.	+	.	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	intron	11508286	11508412	.	+	.	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	CDS	11508413	11509044	0.54	+	2	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	exon	11508413	11509044	.	+	.	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
Phchi.S3	AUGUSTUS	stop_codon	11509045	11509047	.	+	0	transcript_id "Phchi.S3G152700.t1"; gene_id "Phchi.S3G152700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg395.t1 is derived from g10177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2872144	2873448	.	+	.	Phchi.S6G035400
Phchi.S6	AUGUSTUS	transcript	2872144	2873448	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	start_codon	2872144	2872146	.	+	0	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2872144	2872235	1	+	0	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2872144	2872235	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	intron	2872236	2872315	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2872316	2872397	1	+	1	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2872316	2872397	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	intron	2872398	2872503	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2872504	2872578	0.42	+	0	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2872504	2872578	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	intron	2872579	2872680	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2872681	2872820	0.87	+	0	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2872681	2872820	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	intron	2872821	2872931	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2872932	2873027	1	+	1	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2872932	2873027	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	intron	2873028	2873105	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2873106	2873184	1	+	1	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2873106	2873184	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	intron	2873185	2873304	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	CDS	2873305	2873448	1	+	0	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	exon	2873305	2873448	.	+	.	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
Phchi.S6	AUGUSTUS	stop_codon	2873449	2873451	.	+	0	transcript_id "Phchi.S6G035400.t1"; gene_id "Phchi.S6G035400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8823.t1 is derived from g5998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38145528	38146655	.	-	.	Phchi.S1G598200
Phchi.S1	AUGUSTUS	transcript	38145528	38146655	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	stop_codon	38145525	38145527	.	-	0	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	CDS	38145528	38145818	1	-	0	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	exon	38145528	38145818	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	intron	38145819	38145897	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	CDS	38145898	38145975	1	-	0	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	exon	38145898	38145975	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	intron	38145976	38146183	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	CDS	38146184	38146407	1	-	2	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	exon	38146184	38146407	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	intron	38146408	38146576	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	CDS	38146577	38146655	0.65	-	0	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	exon	38146577	38146655	.	-	.	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
Phchi.S1	AUGUSTUS	start_codon	38146653	38146655	.	-	0	transcript_id "Phchi.S1G598200.t1"; gene_id "Phchi.S1G598200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13469.t1 is derived from g11936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7052092	7059921	.	-	.	Phchi.S3G078800
Phchi.S3	AUGUSTUS	transcript	7052092	7059921	.	-	.	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	stop_codon	7052089	7052091	.	-	0	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	CDS	7052092	7056344	1	-	2	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	exon	7052092	7056344	.	-	.	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	intron	7056345	7056512	.	-	.	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	CDS	7056513	7059921	0.97	-	0	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	exon	7056513	7059921	.	-	.	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
Phchi.S3	AUGUSTUS	start_codon	7059919	7059921	.	-	0	transcript_id "Phchi.S3G078800.t1"; gene_id "Phchi.S3G078800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9628.t1 is derived from g6804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42976178	42976886	.	-	.	Phchi.S1G678700
Phchi.S1	AUGUSTUS	transcript	42976178	42976886	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	stop_codon	42976175	42976177	.	-	0	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	CDS	42976178	42976255	1	-	0	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	exon	42976178	42976255	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	intron	42976256	42976337	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	CDS	42976338	42976404	1	-	1	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	exon	42976338	42976404	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	intron	42976405	42976482	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	CDS	42976483	42976538	1	-	0	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	exon	42976483	42976538	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	intron	42976539	42976760	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	CDS	42976761	42976886	1	-	0	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	exon	42976761	42976886	.	-	.	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
Phchi.S1	AUGUSTUS	start_codon	42976884	42976886	.	-	0	transcript_id "Phchi.S1G678700.t1"; gene_id "Phchi.S1G678700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10436.t1 is derived from g14485.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	333879	334759	.	+	.	Phchi.S4G001800
Phchi.S4	AUGUSTUS	transcript	333879	334759	.	+	.	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	start_codon	333879	333881	.	+	0	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	CDS	333879	334454	1	+	0	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	exon	333879	334454	.	+	.	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	intron	334455	334534	.	+	.	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	CDS	334535	334759	1	+	0	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	exon	334535	334759	.	+	.	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	stop_codon	334760	334762	.	+	0	transcript_id "Phchi.S4G001800.t1"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	transcript	333879	334759	.	+	.	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	start_codon	333879	333881	.	+	0	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	CDS	333879	334454	0.99	+	0	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	exon	333879	334454	.	+	.	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	intron	334455	334531	.	+	.	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	CDS	334532	334759	1	+	0	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	exon	334532	334759	.	+	.	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
Phchi.S4	AUGUSTUS	stop_codon	334760	334762	.	+	0	transcript_id "Phchi.S4G001800.t2"; gene_id "Phchi.S4G001800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11350.t1 is derived from g15400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5691015	5693688	.	-	.	Phchi.S4G093200
Phchi.S4	AUGUSTUS	transcript	5691015	5693688	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	stop_codon	5691012	5691014	.	-	0	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	CDS	5691015	5692574	0.98	-	0	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	exon	5691015	5692574	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	intron	5692575	5692717	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	CDS	5692718	5692998	1	-	2	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	exon	5692718	5692998	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	intron	5692999	5693098	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	CDS	5693099	5693240	1	-	0	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	exon	5693099	5693240	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	intron	5693241	5693520	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	CDS	5693521	5693688	0.3	-	0	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	exon	5693521	5693688	.	-	.	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
Phchi.S4	AUGUSTUS	start_codon	5693686	5693688	.	-	0	transcript_id "Phchi.S4G093200.t1"; gene_id "Phchi.S4G093200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8804.t1 is derived from g5979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38070052	38070927	.	+	.	Phchi.S1G596300
Phchi.S1	AUGUSTUS	transcript	38070052	38070927	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	start_codon	38070052	38070054	.	+	0	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	CDS	38070052	38070109	0.59	+	0	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	exon	38070052	38070109	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	intron	38070110	38070275	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	CDS	38070276	38070385	1	+	2	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	exon	38070276	38070385	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	intron	38070386	38070481	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	CDS	38070482	38070616	1	+	0	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	exon	38070482	38070616	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	intron	38070617	38070795	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	CDS	38070796	38070927	1	+	0	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	exon	38070796	38070927	.	+	.	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
Phchi.S1	AUGUSTUS	stop_codon	38070928	38070930	.	+	0	transcript_id "Phchi.S1G596300.t1"; gene_id "Phchi.S1G596300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8236.t1 is derived from g5411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34576553	34577089	.	-	.	Phchi.S1G539500
Phchi.S1	AUGUSTUS	transcript	34576553	34577089	.	-	.	transcript_id "Phchi.S1G539500.t1"; gene_id "Phchi.S1G539500"
Phchi.S1	AUGUSTUS	stop_codon	34576550	34576552	.	-	0	transcript_id "Phchi.S1G539500.t1"; gene_id "Phchi.S1G539500"
Phchi.S1	AUGUSTUS	CDS	34576553	34577089	0.97	-	0	transcript_id "Phchi.S1G539500.t1"; gene_id "Phchi.S1G539500"
Phchi.S1	AUGUSTUS	exon	34576553	34577089	.	-	.	transcript_id "Phchi.S1G539500.t1"; gene_id "Phchi.S1G539500"
Phchi.S1	AUGUSTUS	start_codon	34577087	34577089	.	-	0	transcript_id "Phchi.S1G539500.t1"; gene_id "Phchi.S1G539500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2336.t1 is derived from g9256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6224624	6225058	.	-	.	Phchi.S5G094500
Phchi.S5	AUGUSTUS	transcript	6224624	6225058	.	-	.	transcript_id "Phchi.S5G094500.t1"; gene_id "Phchi.S5G094500"
Phchi.S5	AUGUSTUS	stop_codon	6224621	6224623	.	-	0	transcript_id "Phchi.S5G094500.t1"; gene_id "Phchi.S5G094500"
Phchi.S5	AUGUSTUS	CDS	6224624	6225058	0.89	-	0	transcript_id "Phchi.S5G094500.t1"; gene_id "Phchi.S5G094500"
Phchi.S5	AUGUSTUS	exon	6224624	6225058	.	-	.	transcript_id "Phchi.S5G094500.t1"; gene_id "Phchi.S5G094500"
Phchi.S5	AUGUSTUS	start_codon	6225056	6225058	.	-	0	transcript_id "Phchi.S5G094500.t1"; gene_id "Phchi.S5G094500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11442.t1 is derived from g15492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6388670	6391884	.	-	.	Phchi.S4G102400
Phchi.S4	AUGUSTUS	transcript	6388670	6391884	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	stop_codon	6388667	6388669	.	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6388670	6388802	0.96	-	1	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6388670	6388802	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6388803	6388901	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6388902	6388981	1	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6388902	6388981	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6388982	6389067	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6389068	6389203	1	-	1	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6389068	6389203	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6389204	6389317	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6389318	6389493	0.39	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6389318	6389493	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6389494	6389581	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6389582	6389699	0.69	-	1	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6389582	6389699	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6389700	6389783	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6389784	6389902	1	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6389784	6389902	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6389903	6390012	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6390013	6390126	1	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6390013	6390126	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6390127	6390212	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6390213	6390296	1	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6390213	6390296	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6390297	6390430	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6390431	6390510	1	-	2	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6390431	6390510	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6390511	6390609	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6390610	6390664	1	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6390610	6390664	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6390665	6390812	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6390813	6390880	1	-	2	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6390813	6390880	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6390881	6391032	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6391033	6391077	1	-	2	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6391033	6391077	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6391078	6391160	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6391161	6391272	1	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6391161	6391272	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6391273	6391373	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6391374	6391488	1	-	1	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6391374	6391488	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	intron	6391489	6391633	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	CDS	6391634	6391884	0.99	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	exon	6391634	6391884	.	-	.	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
Phchi.S4	AUGUSTUS	start_codon	6391882	6391884	.	-	0	transcript_id "Phchi.S4G102400.t1"; gene_id "Phchi.S4G102400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4404.t1 is derived from g1573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10251856	10254578	.	-	.	Phchi.S1G156300
Phchi.S1	AUGUSTUS	transcript	10251856	10254578	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	stop_codon	10251853	10251855	.	-	0	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10251856	10251999	0.97	-	0	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10251856	10251999	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	intron	10252000	10252104	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10252105	10252932	0.99	-	0	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10252105	10252932	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	intron	10252933	10253011	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10253012	10253190	1	-	2	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10253012	10253190	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	intron	10253191	10253310	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10253311	10253466	0.92	-	2	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10253311	10253466	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	intron	10253467	10253563	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10253564	10253698	0.83	-	2	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10253564	10253698	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	intron	10253699	10253789	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10253790	10254067	0.6	-	1	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10253790	10254067	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	intron	10254068	10254243	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	CDS	10254244	10254578	0.36	-	0	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	exon	10254244	10254578	.	-	.	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
Phchi.S1	AUGUSTUS	start_codon	10254576	10254578	.	-	0	transcript_id "Phchi.S1G156300.t1"; gene_id "Phchi.S1G156300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8954.t1 is derived from g6129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38838568	38840671	.	+	.	Phchi.S1G611300
Phchi.S1	AUGUSTUS	transcript	38838568	38840671	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	start_codon	38838568	38838570	.	+	0	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	CDS	38838568	38838889	0.99	+	0	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	exon	38838568	38838889	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	intron	38838890	38838969	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	CDS	38838970	38839851	0.95	+	2	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	exon	38838970	38839851	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	intron	38839852	38839972	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	CDS	38839973	38840067	1	+	2	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	exon	38839973	38840067	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	intron	38840068	38840145	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	CDS	38840146	38840254	1	+	0	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	exon	38840146	38840254	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	intron	38840255	38840341	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	CDS	38840342	38840401	1	+	2	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	exon	38840342	38840401	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	intron	38840402	38840477	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	CDS	38840478	38840671	0.99	+	2	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	exon	38840478	38840671	.	+	.	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
Phchi.S1	AUGUSTUS	stop_codon	38840672	38840674	.	+	0	transcript_id "Phchi.S1G611300.t1"; gene_id "Phchi.S1G611300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5848.t1 is derived from g3018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19319765	19326211	.	-	.	Phchi.S1G300700
Phchi.S1	AUGUSTUS	transcript	19319765	19326211	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	stop_codon	19319762	19319764	.	-	0	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	CDS	19319765	19319875	0.01	-	0	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	exon	19319765	19319875	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	intron	19319876	19321236	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	CDS	19321237	19321441	0.97	-	1	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	exon	19321237	19321441	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	intron	19321442	19322642	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	CDS	19322643	19322725	0.44	-	0	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	exon	19322643	19322725	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	intron	19322726	19326202	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	CDS	19326203	19326211	0.01	-	0	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	exon	19326203	19326211	.	-	.	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
Phchi.S1	AUGUSTUS	start_codon	19326209	19326211	.	-	0	transcript_id "Phchi.S1G300700.t1"; gene_id "Phchi.S1G300700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1448.t1 is derived from g8367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	952423	952854	.	-	.	Phchi.S5G005700
Phchi.S5	AUGUSTUS	transcript	952423	952854	.	-	.	transcript_id "Phchi.S5G005700.t1"; gene_id "Phchi.S5G005700"
Phchi.S5	AUGUSTUS	stop_codon	952420	952422	.	-	0	transcript_id "Phchi.S5G005700.t1"; gene_id "Phchi.S5G005700"
Phchi.S5	AUGUSTUS	CDS	952423	952854	0.95	-	0	transcript_id "Phchi.S5G005700.t1"; gene_id "Phchi.S5G005700"
Phchi.S5	AUGUSTUS	exon	952423	952854	.	-	.	transcript_id "Phchi.S5G005700.t1"; gene_id "Phchi.S5G005700"
Phchi.S5	AUGUSTUS	start_codon	952852	952854	.	-	0	transcript_id "Phchi.S5G005700.t1"; gene_id "Phchi.S5G005700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12299.t1 is derived from g7975.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9604190	9605899	.	+	.	Phchi.S2G037900
Phchi.S2	AUGUSTUS	transcript	9604190	9605899	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	start_codon	9604190	9604192	.	+	0	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604190	9604375	0.68	+	0	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604190	9604375	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9604376	9604473	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604474	9604646	0.81	+	0	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604474	9604646	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9604647	9604738	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604739	9604854	0.92	+	1	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604739	9604854	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9604855	9604965	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604966	9605086	0.63	+	2	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604966	9605086	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9605087	9605161	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9605162	9605414	0.79	+	1	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9605162	9605414	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9605415	9605565	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9605566	9605588	0.55	+	0	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9605566	9605588	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9605589	9605736	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9605737	9605899	0.52	+	1	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9605737	9605899	.	+	.	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	stop_codon	9605900	9605902	.	+	0	transcript_id "Phchi.S2G037900.t1"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	transcript	9604190	9605899	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	start_codon	9604190	9604192	.	+	0	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604190	9604375	0.76	+	0	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604190	9604375	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9604376	9604473	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604474	9604646	0.88	+	0	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604474	9604646	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9604647	9604738	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604739	9604854	0.96	+	1	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604739	9604854	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9604855	9604965	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9604966	9605020	0.38	+	2	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9604966	9605020	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9605021	9605161	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9605162	9605414	0.8	+	1	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9605162	9605414	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9605415	9605565	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9605566	9605588	0.5	+	0	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9605566	9605588	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	intron	9605589	9605736	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	CDS	9605737	9605899	0.46	+	1	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	exon	9605737	9605899	.	+	.	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
Phchi.S2	AUGUSTUS	stop_codon	9605900	9605902	.	+	0	transcript_id "Phchi.S2G037900.t2"; gene_id "Phchi.S2G037900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4067.t1 is derived from g1236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7619572	7620591	.	+	.	Phchi.S1G122600
Phchi.S1	AUGUSTUS	transcript	7619572	7620591	.	+	.	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	start_codon	7619572	7619574	.	+	0	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	CDS	7619572	7620095	1	+	0	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	exon	7619572	7620095	.	+	.	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	intron	7620096	7620179	.	+	.	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	CDS	7620180	7620591	1	+	1	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	exon	7620180	7620591	.	+	.	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
Phchi.S1	AUGUSTUS	stop_codon	7620592	7620594	.	+	0	transcript_id "Phchi.S1G122600.t1"; gene_id "Phchi.S1G122600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7048.t1 is derived from g4220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26596689	26597636	.	+	.	Phchi.S1G420700
Phchi.S1	AUGUSTUS	transcript	26596689	26597636	.	+	.	transcript_id "Phchi.S1G420700.t1"; gene_id "Phchi.S1G420700"
Phchi.S1	AUGUSTUS	start_codon	26596689	26596691	.	+	0	transcript_id "Phchi.S1G420700.t1"; gene_id "Phchi.S1G420700"
Phchi.S1	AUGUSTUS	CDS	26596689	26597636	0.86	+	0	transcript_id "Phchi.S1G420700.t1"; gene_id "Phchi.S1G420700"
Phchi.S1	AUGUSTUS	exon	26596689	26597636	.	+	.	transcript_id "Phchi.S1G420700.t1"; gene_id "Phchi.S1G420700"
Phchi.S1	AUGUSTUS	stop_codon	26597637	26597639	.	+	0	transcript_id "Phchi.S1G420700.t1"; gene_id "Phchi.S1G420700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg656.t1 is derived from g10438.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4609460	4614682	.	-	.	Phchi.S6G061500
Phchi.S6	AUGUSTUS	transcript	4611286	4614682	.	-	.	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	stop_codon	4611283	4611285	.	-	0	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	CDS	4611286	4611425	0.95	-	2	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	exon	4611286	4611425	.	-	.	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	intron	4611426	4611513	.	-	.	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	CDS	4611514	4614682	0.91	-	0	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	exon	4611514	4614682	.	-	.	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	start_codon	4614680	4614682	.	-	0	transcript_id "Phchi.S6G061500.t1"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	transcript	4609460	4614682	.	-	.	transcript_id "Phchi.S6G061500.t2"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	stop_codon	4609457	4609459	.	-	0	transcript_id "Phchi.S6G061500.t2"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	CDS	4609460	4614682	0.99	-	0	transcript_id "Phchi.S6G061500.t2"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	exon	4609460	4614682	.	-	.	transcript_id "Phchi.S6G061500.t2"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	start_codon	4614680	4614682	.	-	0	transcript_id "Phchi.S6G061500.t2"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	transcript	4609460	4611076	.	-	.	transcript_id "Phchi.S6G061500.t3"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	stop_codon	4609457	4609459	.	-	0	transcript_id "Phchi.S6G061500.t3"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	CDS	4609460	4611076	0.83	-	0	transcript_id "Phchi.S6G061500.t3"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	exon	4609460	4611076	.	-	.	transcript_id "Phchi.S6G061500.t3"; gene_id "Phchi.S6G061500"
Phchi.S6	AUGUSTUS	start_codon	4611074	4611076	.	-	0	transcript_id "Phchi.S6G061500.t3"; gene_id "Phchi.S6G061500"
# This transcript jg15790.t2 is derived from g14260.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15791.t1 is derived from g14261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21359804	21360691	.	-	.	Phchi.S3G311000
Phchi.S3	AUGUSTUS	transcript	21359804	21360691	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	stop_codon	21359801	21359803	.	-	0	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	CDS	21359804	21359811	1	-	2	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	exon	21359804	21359811	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	intron	21359812	21360141	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	CDS	21360142	21360241	1	-	0	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	exon	21360142	21360241	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	intron	21360242	21360323	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	CDS	21360324	21360383	0.99	-	0	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	exon	21360324	21360383	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	intron	21360384	21360490	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	CDS	21360491	21360557	0.99	-	1	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	exon	21360491	21360557	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	intron	21360558	21360647	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	CDS	21360648	21360691	0.39	-	0	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	exon	21360648	21360691	.	-	.	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
Phchi.S3	AUGUSTUS	start_codon	21360689	21360691	.	-	0	transcript_id "Phchi.S3G311000.t1"; gene_id "Phchi.S3G311000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6988.t1 is derived from g4160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26293918	26294822	.	-	.	Phchi.S1G414700
Phchi.S1	AUGUSTUS	transcript	26293918	26294822	.	-	.	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	stop_codon	26293915	26293917	.	-	0	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	CDS	26293918	26294175	0.72	-	0	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	exon	26293918	26294175	.	-	.	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	intron	26294176	26294270	.	-	.	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	CDS	26294271	26294822	0.22	-	0	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	exon	26294271	26294822	.	-	.	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
Phchi.S1	AUGUSTUS	start_codon	26294820	26294822	.	-	0	transcript_id "Phchi.S1G414700.t1"; gene_id "Phchi.S1G414700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5884.t1 is derived from g3054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19576792	19579150	.	+	.	Phchi.S1G304300
Phchi.S1	AUGUSTUS	transcript	19576792	19579150	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	start_codon	19576792	19576794	.	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19576792	19577573	0.55	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19576792	19577573	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19577574	19577679	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19577680	19577731	1	+	1	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19577680	19577731	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19577732	19577812	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19577813	19578021	1	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19577813	19578021	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19578022	19578267	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19578268	19578355	1	+	1	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19578268	19578355	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19578356	19578608	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19578609	19578670	1	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19578609	19578670	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19578671	19578753	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19578754	19578793	0.95	+	1	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19578754	19578793	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19578794	19578876	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19578877	19578921	0.7	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19578877	19578921	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	intron	19578922	19579009	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	CDS	19579010	19579150	1	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	exon	19579010	19579150	.	+	.	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
Phchi.S1	AUGUSTUS	stop_codon	19579151	19579153	.	+	0	transcript_id "Phchi.S1G304300.t1"; gene_id "Phchi.S1G304300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5747.t1 is derived from g2917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18697457	18700742	.	-	.	Phchi.S1G290600
Phchi.S1	AUGUSTUS	transcript	18697457	18700742	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	stop_codon	18697454	18697456	.	-	0	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	CDS	18697457	18698625	0.71	-	2	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	exon	18697457	18698625	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	intron	18698626	18698717	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	CDS	18698718	18699294	0.67	-	0	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	exon	18698718	18699294	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	intron	18699295	18699439	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	CDS	18699440	18699598	1	-	0	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	exon	18699440	18699598	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	intron	18699599	18699681	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	CDS	18699682	18699840	0.98	-	0	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	exon	18699682	18699840	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	intron	18699841	18700108	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	CDS	18700109	18700241	0.71	-	1	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	exon	18700109	18700241	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	intron	18700242	18700344	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	CDS	18700345	18700742	0.69	-	0	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	exon	18700345	18700742	.	-	.	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
Phchi.S1	AUGUSTUS	start_codon	18700740	18700742	.	-	0	transcript_id "Phchi.S1G290600.t1"; gene_id "Phchi.S1G290600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4642.t1 is derived from g1812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11605698	11607706	.	+	.	Phchi.S1G180100
Phchi.S1	AUGUSTUS	transcript	11605698	11607706	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	start_codon	11605698	11605700	.	+	0	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	CDS	11605698	11606223	0.48	+	0	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	exon	11605698	11606223	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	intron	11606224	11606557	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	CDS	11606558	11606832	0.98	+	2	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	exon	11606558	11606832	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	intron	11606833	11606946	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	CDS	11606947	11607137	0.97	+	0	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	exon	11606947	11607137	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	intron	11607138	11607217	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	CDS	11607218	11607354	0.97	+	1	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	exon	11607218	11607354	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	intron	11607355	11607431	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	CDS	11607432	11607706	0.99	+	2	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	exon	11607432	11607706	.	+	.	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
Phchi.S1	AUGUSTUS	stop_codon	11607707	11607709	.	+	0	transcript_id "Phchi.S1G180100.t1"; gene_id "Phchi.S1G180100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14129.t1 is derived from g12596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11039049	11040112	.	-	.	Phchi.S3G144800
Phchi.S3	AUGUSTUS	transcript	11039049	11040112	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	stop_codon	11039046	11039048	.	-	0	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	CDS	11039049	11039312	1	-	0	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	exon	11039049	11039312	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	intron	11039313	11039530	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	CDS	11039531	11039603	1	-	1	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	exon	11039531	11039603	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	intron	11039604	11039776	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	CDS	11039777	11039903	1	-	2	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	exon	11039777	11039903	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	intron	11039904	11040048	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	CDS	11040049	11040112	1	-	0	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	exon	11040049	11040112	.	-	.	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
Phchi.S3	AUGUSTUS	start_codon	11040110	11040112	.	-	0	transcript_id "Phchi.S3G144800.t1"; gene_id "Phchi.S3G144800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12308.t1 is derived from g7984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9927860	9929118	.	+	.	Phchi.S2G038800
Phchi.S2	AUGUSTUS	transcript	9927860	9929118	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	start_codon	9927860	9927862	.	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9927860	9927931	0.36	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9927860	9927931	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	intron	9927932	9928014	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9928015	9928119	0.61	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9928015	9928119	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	intron	9928120	9928206	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9928207	9928288	1	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9928207	9928288	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	intron	9928289	9928418	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9928419	9928528	0.97	+	2	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9928419	9928528	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	intron	9928529	9928631	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9928632	9928709	1	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9928632	9928709	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	intron	9928710	9928854	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9928855	9928971	1	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9928855	9928971	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	intron	9928972	9929058	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	CDS	9929059	9929118	0.68	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	exon	9929059	9929118	.	+	.	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
Phchi.S2	AUGUSTUS	stop_codon	9929119	9929121	.	+	0	transcript_id "Phchi.S2G038800.t1"; gene_id "Phchi.S2G038800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg408.t1 is derived from g10190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2939122	2940742	.	-	.	Phchi.S6G036700
Phchi.S6	AUGUSTUS	transcript	2939122	2940742	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	stop_codon	2939119	2939121	.	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2939122	2939146	1	-	1	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2939122	2939146	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2939147	2939239	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2939240	2939349	1	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2939240	2939349	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2939350	2939422	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2939423	2939485	1	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2939423	2939485	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2939486	2939623	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2939624	2939698	1	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2939624	2939698	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2939699	2939787	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2939788	2939880	0.99	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2939788	2939880	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2939881	2939983	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2939984	2940088	1	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2939984	2940088	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2940089	2940227	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2940228	2940349	1	-	2	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2940228	2940349	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	intron	2940350	2940435	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	CDS	2940436	2940742	0.94	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	exon	2940436	2940742	.	-	.	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
Phchi.S6	AUGUSTUS	start_codon	2940740	2940742	.	-	0	transcript_id "Phchi.S6G036700.t1"; gene_id "Phchi.S6G036700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5247.t1 is derived from g2417.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15850068	15852819	.	-	.	Phchi.S1G240600
Phchi.S1	AUGUSTUS	transcript	15850068	15852819	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	stop_codon	15850065	15850067	.	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15850068	15850205	1	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15850068	15850205	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15850206	15850307	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15850308	15850449	1	-	1	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15850308	15850449	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15850450	15850571	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15850572	15850720	1	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15850572	15850720	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15850721	15850817	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15850818	15850952	1	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15850818	15850952	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15850953	15851052	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15851053	15851235	0.58	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15851053	15851235	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15851236	15851510	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15851511	15851588	0.68	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15851511	15851588	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15851589	15851953	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15851954	15852234	1	-	2	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15851954	15852234	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15852235	15852370	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15852371	15852457	1	-	2	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15852371	15852457	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15852458	15852776	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15852777	15852819	0.49	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15852777	15852819	.	-	.	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	start_codon	15852817	15852819	.	-	0	transcript_id "Phchi.S1G240600.t1"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	transcript	15851703	15852819	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	stop_codon	15851700	15851702	.	-	0	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15851703	15851801	0.36	-	0	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15851703	15851801	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15851802	15851953	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15851954	15852234	0.95	-	2	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15851954	15852234	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15852235	15852370	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15852371	15852457	1	-	2	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15852371	15852457	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	intron	15852458	15852776	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	CDS	15852777	15852819	0.51	-	0	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	exon	15852777	15852819	.	-	.	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
Phchi.S1	AUGUSTUS	start_codon	15852817	15852819	.	-	0	transcript_id "Phchi.S1G240600.t2"; gene_id "Phchi.S1G240600"
# This transcript jg11123.t2 is derived from g15173.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11124.t1 is derived from g15174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4271205	4272776	.	+	.	Phchi.S4G070600
Phchi.S4	AUGUSTUS	transcript	4271205	4272776	.	+	.	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	start_codon	4271205	4271207	.	+	0	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	CDS	4271205	4271508	0.96	+	0	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	exon	4271205	4271508	.	+	.	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	intron	4271509	4271710	.	+	.	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	CDS	4271711	4272087	0.97	+	2	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	exon	4271711	4272087	.	+	.	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	intron	4272088	4272335	.	+	.	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	CDS	4272336	4272776	1	+	0	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	exon	4272336	4272776	.	+	.	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
Phchi.S4	AUGUSTUS	stop_codon	4272777	4272779	.	+	0	transcript_id "Phchi.S4G070600.t1"; gene_id "Phchi.S4G070600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9377.t1 is derived from g6553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41225790	41228158	.	+	.	Phchi.S1G653600
Phchi.S1	AUGUSTUS	transcript	41225790	41228158	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	start_codon	41225790	41225792	.	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41225790	41226075	0.96	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41225790	41226075	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41226076	41226194	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41226195	41226304	1	+	2	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41226195	41226304	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41226305	41226398	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41226399	41226454	1	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41226399	41226454	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41226455	41226556	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41226557	41226641	1	+	1	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41226557	41226641	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41226642	41226743	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41226744	41226791	1	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41226744	41226791	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41226792	41226897	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41226898	41226972	1	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41226898	41226972	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41226973	41227057	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41227058	41227187	0.59	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41227058	41227187	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41227188	41227275	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41227276	41227327	1	+	2	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41227276	41227327	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41227328	41227488	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41227489	41227540	1	+	1	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41227489	41227540	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41227541	41227627	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41227628	41227685	1	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41227628	41227685	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41227686	41227794	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41227795	41227893	1	+	2	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41227795	41227893	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	intron	41227894	41227991	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	CDS	41227992	41228158	1	+	2	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	exon	41227992	41228158	.	+	.	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
Phchi.S1	AUGUSTUS	stop_codon	41228159	41228161	.	+	0	transcript_id "Phchi.S1G653600.t1"; gene_id "Phchi.S1G653600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7298.t1 is derived from g4470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28379361	28382229	.	-	.	Phchi.S1G445700
Phchi.S1	AUGUSTUS	transcript	28379361	28382229	.	-	.	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	stop_codon	28379358	28379360	.	-	0	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	CDS	28379361	28379788	1	-	2	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	exon	28379361	28379788	.	-	.	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	intron	28379789	28379934	.	-	.	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	CDS	28379935	28381828	0.94	-	0	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	exon	28379935	28381828	.	-	.	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	intron	28381829	28382121	.	-	.	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	CDS	28382122	28382229	1	-	0	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	exon	28382122	28382229	.	-	.	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
Phchi.S1	AUGUSTUS	start_codon	28382227	28382229	.	-	0	transcript_id "Phchi.S1G445700.t1"; gene_id "Phchi.S1G445700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7811.t1 is derived from g4985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31302902	31307678	.	+	.	Phchi.S1G497000
Phchi.S1	AUGUSTUS	transcript	31302902	31307678	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	start_codon	31302902	31302904	.	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31302902	31303105	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31302902	31303105	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31303106	31303498	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31303499	31303638	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31303499	31303638	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31303639	31303735	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31303736	31303898	1	+	1	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31303736	31303898	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31303899	31303998	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31303999	31304097	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31303999	31304097	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304098	31304290	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304291	31304368	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304291	31304368	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304369	31304471	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304472	31304549	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304472	31304549	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304550	31304715	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304716	31304868	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304716	31304868	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304869	31304980	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304981	31305081	0.79	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304981	31305081	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305082	31305368	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305369	31305445	1	+	1	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305369	31305445	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305446	31305541	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305542	31305615	1	+	2	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305542	31305615	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305616	31305695	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305696	31305762	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305696	31305762	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305763	31305848	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305849	31305961	1	+	2	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305849	31305961	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305962	31306057	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306058	31306309	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306058	31306309	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306310	31306408	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306409	31306525	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306409	31306525	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306526	31306654	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306655	31306726	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306655	31306726	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306727	31306807	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306808	31306858	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306808	31306858	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306859	31306943	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306944	31307180	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306944	31307180	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31307181	31307297	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31307298	31307474	1	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31307298	31307474	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31307475	31307561	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31307562	31307678	0.99	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31307562	31307678	.	+	.	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	stop_codon	31307679	31307681	.	+	0	transcript_id "Phchi.S1G497000.t1"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	transcript	31302902	31307678	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	start_codon	31302902	31302904	.	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31302902	31303105	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31302902	31303105	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31303106	31303498	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31303499	31303638	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31303499	31303638	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31303639	31303735	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31303736	31303898	1	+	1	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31303736	31303898	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31303899	31303998	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31303999	31304097	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31303999	31304097	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304098	31304253	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304254	31304292	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304254	31304292	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304293	31304471	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304472	31304549	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304472	31304549	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304550	31304715	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304716	31304868	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304716	31304868	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31304869	31304980	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31304981	31305081	0.72	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31304981	31305081	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305082	31305368	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305369	31305445	1	+	1	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305369	31305445	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305446	31305541	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305542	31305615	1	+	2	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305542	31305615	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305616	31305695	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305696	31305762	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305696	31305762	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305763	31305848	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31305849	31305961	1	+	2	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31305849	31305961	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31305962	31306057	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306058	31306309	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306058	31306309	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306310	31306408	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306409	31306525	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306409	31306525	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306526	31306654	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306655	31306726	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306655	31306726	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306727	31306807	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306808	31306858	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306808	31306858	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31306859	31306943	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31306944	31307180	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31306944	31307180	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31307181	31307297	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31307298	31307474	1	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31307298	31307474	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	intron	31307475	31307561	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	CDS	31307562	31307678	0.97	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	exon	31307562	31307678	.	+	.	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
Phchi.S1	AUGUSTUS	stop_codon	31307679	31307681	.	+	0	transcript_id "Phchi.S1G497000.t2"; gene_id "Phchi.S1G497000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9363.t1 is derived from g6539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41163629	41165368	.	+	.	Phchi.S1G652200
Phchi.S1	AUGUSTUS	transcript	41163629	41165368	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	start_codon	41163629	41163631	.	+	0	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	CDS	41163629	41163721	1	+	0	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	exon	41163629	41163721	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	intron	41163722	41163803	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	CDS	41163804	41164038	1	+	0	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	exon	41163804	41164038	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	intron	41164039	41164134	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	CDS	41164135	41164505	1	+	2	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	exon	41164135	41164505	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	intron	41164506	41164594	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	CDS	41164595	41164991	0.99	+	0	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	exon	41164595	41164991	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	intron	41164992	41165114	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	CDS	41165115	41165368	0.99	+	2	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	exon	41165115	41165368	.	+	.	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
Phchi.S1	AUGUSTUS	stop_codon	41165369	41165371	.	+	0	transcript_id "Phchi.S1G652200.t1"; gene_id "Phchi.S1G652200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14119.t1 is derived from g12586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10963744	10964558	.	-	.	Phchi.S3G143800
Phchi.S3	AUGUSTUS	transcript	10963744	10964558	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	stop_codon	10963741	10963743	.	-	0	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	CDS	10963744	10963864	0.64	-	1	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	exon	10963744	10963864	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	intron	10963865	10964035	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	CDS	10964036	10964202	0.84	-	0	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	exon	10964036	10964202	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	intron	10964203	10964302	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	CDS	10964303	10964335	0.41	-	0	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	exon	10964303	10964335	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	intron	10964336	10964540	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	CDS	10964541	10964558	0.25	-	0	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	exon	10964541	10964558	.	-	.	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
Phchi.S3	AUGUSTUS	start_codon	10964556	10964558	.	-	0	transcript_id "Phchi.S3G143800.t1"; gene_id "Phchi.S3G143800"
# This transcript jg13829.t2 is derived from g12296.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13830.t1 is derived from g12297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9097749	9098711	.	+	.	Phchi.S3G114900
Phchi.S3	AUGUSTUS	transcript	9097749	9098711	.	+	.	transcript_id "Phchi.S3G114900.t1"; gene_id "Phchi.S3G114900"
Phchi.S3	AUGUSTUS	start_codon	9097749	9097751	.	+	0	transcript_id "Phchi.S3G114900.t1"; gene_id "Phchi.S3G114900"
Phchi.S3	AUGUSTUS	CDS	9097749	9098711	0.99	+	0	transcript_id "Phchi.S3G114900.t1"; gene_id "Phchi.S3G114900"
Phchi.S3	AUGUSTUS	exon	9097749	9098711	.	+	.	transcript_id "Phchi.S3G114900.t1"; gene_id "Phchi.S3G114900"
Phchi.S3	AUGUSTUS	stop_codon	9098712	9098714	.	+	0	transcript_id "Phchi.S3G114900.t1"; gene_id "Phchi.S3G114900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14395.t1 is derived from g12863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12594559	12595513	.	-	.	Phchi.S3G171400
Phchi.S3	AUGUSTUS	transcript	12594559	12595513	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	stop_codon	12594556	12594558	.	-	0	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12594559	12594606	1	-	0	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12594559	12594606	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	intron	12594607	12594693	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12594694	12594744	1	-	0	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12594694	12594744	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	intron	12594745	12594815	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12594816	12594904	1	-	2	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12594816	12594904	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	intron	12594905	12594987	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12594988	12595071	1	-	2	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12594988	12595071	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	intron	12595072	12595152	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12595153	12595209	1	-	2	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12595153	12595209	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	intron	12595210	12595305	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12595306	12595337	0.95	-	1	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12595306	12595337	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	intron	12595338	12595442	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	CDS	12595443	12595513	0.95	-	0	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	exon	12595443	12595513	.	-	.	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
Phchi.S3	AUGUSTUS	start_codon	12595511	12595513	.	-	0	transcript_id "Phchi.S3G171400.t1"; gene_id "Phchi.S3G171400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6677.t1 is derived from g3849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24454617	24456033	.	+	.	Phchi.S1G383600
Phchi.S1	AUGUSTUS	transcript	24454617	24456033	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	start_codon	24454617	24454619	.	+	0	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	CDS	24454617	24454784	1	+	0	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	exon	24454617	24454784	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	intron	24454785	24455015	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	CDS	24455016	24455062	0.56	+	0	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	exon	24455016	24455062	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	intron	24455063	24455178	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	CDS	24455179	24455194	0.56	+	1	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	exon	24455179	24455194	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	intron	24455195	24455277	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	CDS	24455278	24456033	0.88	+	0	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	exon	24455278	24456033	.	+	.	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
Phchi.S1	AUGUSTUS	stop_codon	24456034	24456036	.	+	0	transcript_id "Phchi.S1G383600.t1"; gene_id "Phchi.S1G383600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15315.t1 is derived from g13783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18358094	18359998	.	-	.	Phchi.S3G263400
Phchi.S3	AUGUSTUS	transcript	18358094	18359998	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	stop_codon	18358091	18358093	.	-	0	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	CDS	18358094	18358565	0.91	-	1	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	exon	18358094	18358565	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	intron	18358566	18358701	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	CDS	18358702	18359151	0.91	-	1	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	exon	18358702	18359151	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	intron	18359152	18359291	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	CDS	18359292	18359632	1	-	0	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	exon	18359292	18359632	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	intron	18359633	18359704	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	CDS	18359705	18359998	0.98	-	0	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	exon	18359705	18359998	.	-	.	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
Phchi.S3	AUGUSTUS	start_codon	18359996	18359998	.	-	0	transcript_id "Phchi.S3G263400.t1"; gene_id "Phchi.S3G263400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5001.t1 is derived from g2171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13957551	13959625	.	+	.	Phchi.S1G216000
Phchi.S1	AUGUSTUS	transcript	13957551	13959625	.	+	.	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	start_codon	13957551	13957553	.	+	0	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	CDS	13957551	13959297	0.84	+	0	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	exon	13957551	13959297	.	+	.	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	intron	13959298	13959395	.	+	.	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	CDS	13959396	13959625	1	+	2	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	exon	13959396	13959625	.	+	.	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
Phchi.S1	AUGUSTUS	stop_codon	13959626	13959628	.	+	0	transcript_id "Phchi.S1G216000.t1"; gene_id "Phchi.S1G216000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7904.t1 is derived from g5078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31823757	31826471	.	+	.	Phchi.S1G506300
Phchi.S1	AUGUSTUS	transcript	31823757	31826471	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	start_codon	31823757	31823759	.	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31823757	31823893	1	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31823757	31823893	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31823894	31823984	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31823985	31824087	0.61	+	1	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31823985	31824087	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31824088	31824206	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31824207	31824287	0.8	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31824207	31824287	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31824288	31824391	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31824392	31824556	0.74	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31824392	31824556	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31824557	31824826	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31824827	31824931	1	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31824827	31824931	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31824932	31825021	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31825022	31825132	0.96	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31825022	31825132	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31825133	31825283	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31825284	31825472	0.86	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31825284	31825472	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31825473	31825551	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31825552	31825665	0.86	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31825552	31825665	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	intron	31825666	31825751	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	CDS	31825752	31826471	0.65	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	exon	31825752	31826471	.	+	.	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
Phchi.S1	AUGUSTUS	stop_codon	31826472	31826474	.	+	0	transcript_id "Phchi.S1G506300.t1"; gene_id "Phchi.S1G506300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6109.t1 is derived from g3280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20979592	20980695	.	+	.	Phchi.S1G326800
Phchi.S1	AUGUSTUS	transcript	20979592	20980695	.	+	.	transcript_id "Phchi.S1G326800.t1"; gene_id "Phchi.S1G326800"
Phchi.S1	AUGUSTUS	start_codon	20979592	20979594	.	+	0	transcript_id "Phchi.S1G326800.t1"; gene_id "Phchi.S1G326800"
Phchi.S1	AUGUSTUS	CDS	20979592	20980695	0.6	+	0	transcript_id "Phchi.S1G326800.t1"; gene_id "Phchi.S1G326800"
Phchi.S1	AUGUSTUS	exon	20979592	20980695	.	+	.	transcript_id "Phchi.S1G326800.t1"; gene_id "Phchi.S1G326800"
Phchi.S1	AUGUSTUS	stop_codon	20980696	20980698	.	+	0	transcript_id "Phchi.S1G326800.t1"; gene_id "Phchi.S1G326800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12624.t1 is derived from g8301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37616606	37621492	.	-	.	Phchi.S2G070400
Phchi.S2	AUGUSTUS	transcript	37616606	37617892	.	-	.	transcript_id "Phchi.S2G070400.t1"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	stop_codon	37616603	37616605	.	-	0	transcript_id "Phchi.S2G070400.t1"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	CDS	37616606	37617892	0.89	-	0	transcript_id "Phchi.S2G070400.t1"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	exon	37616606	37617892	.	-	.	transcript_id "Phchi.S2G070400.t1"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	start_codon	37617890	37617892	.	-	0	transcript_id "Phchi.S2G070400.t1"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	transcript	37616606	37621492	.	-	.	transcript_id "Phchi.S2G070400.t2"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	stop_codon	37616603	37616605	.	-	0	transcript_id "Phchi.S2G070400.t2"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	CDS	37616606	37621492	0.81	-	0	transcript_id "Phchi.S2G070400.t2"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	exon	37616606	37621492	.	-	.	transcript_id "Phchi.S2G070400.t2"; gene_id "Phchi.S2G070400"
Phchi.S2	AUGUSTUS	start_codon	37621490	37621492	.	-	0	transcript_id "Phchi.S2G070400.t2"; gene_id "Phchi.S2G070400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4592.t1 is derived from g1762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11240502	11242334	.	+	.	Phchi.S1G175100
Phchi.S1	AUGUSTUS	transcript	11240502	11242334	.	+	.	transcript_id "Phchi.S1G175100.t1"; gene_id "Phchi.S1G175100"
Phchi.S1	AUGUSTUS	start_codon	11240502	11240504	.	+	0	transcript_id "Phchi.S1G175100.t1"; gene_id "Phchi.S1G175100"
Phchi.S1	AUGUSTUS	CDS	11240502	11242334	0.53	+	0	transcript_id "Phchi.S1G175100.t1"; gene_id "Phchi.S1G175100"
Phchi.S1	AUGUSTUS	exon	11240502	11242334	.	+	.	transcript_id "Phchi.S1G175100.t1"; gene_id "Phchi.S1G175100"
Phchi.S1	AUGUSTUS	stop_codon	11242335	11242337	.	+	0	transcript_id "Phchi.S1G175100.t1"; gene_id "Phchi.S1G175100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5933.t1 is derived from g3104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19927623	19928504	.	+	.	Phchi.S1G309200
Phchi.S1	AUGUSTUS	transcript	19927623	19928504	.	+	.	transcript_id "Phchi.S1G309200.t1"; gene_id "Phchi.S1G309200"
Phchi.S1	AUGUSTUS	start_codon	19927623	19927625	.	+	0	transcript_id "Phchi.S1G309200.t1"; gene_id "Phchi.S1G309200"
Phchi.S1	AUGUSTUS	CDS	19927623	19928504	0.96	+	0	transcript_id "Phchi.S1G309200.t1"; gene_id "Phchi.S1G309200"
Phchi.S1	AUGUSTUS	exon	19927623	19928504	.	+	.	transcript_id "Phchi.S1G309200.t1"; gene_id "Phchi.S1G309200"
Phchi.S1	AUGUSTUS	stop_codon	19928505	19928507	.	+	0	transcript_id "Phchi.S1G309200.t1"; gene_id "Phchi.S1G309200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14521.t1 is derived from g12989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13299553	13300788	.	+	.	Phchi.S3G184000
Phchi.S3	AUGUSTUS	transcript	13299553	13300788	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	start_codon	13299553	13299555	.	+	0	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	CDS	13299553	13299622	1	+	0	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	exon	13299553	13299622	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	intron	13299623	13299721	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	CDS	13299722	13299801	1	+	2	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	exon	13299722	13299801	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	intron	13299802	13300037	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	CDS	13300038	13300191	1	+	0	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	exon	13300038	13300191	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	intron	13300192	13300345	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	CDS	13300346	13300549	0.96	+	2	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	exon	13300346	13300549	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	intron	13300550	13300636	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	CDS	13300637	13300788	0.96	+	2	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	exon	13300637	13300788	.	+	.	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
Phchi.S3	AUGUSTUS	stop_codon	13300789	13300791	.	+	0	transcript_id "Phchi.S3G184000.t1"; gene_id "Phchi.S3G184000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10089.t1 is derived from g7265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45698048	45699206	.	+	.	Phchi.S1G724800
Phchi.S1	AUGUSTUS	transcript	45698048	45699206	.	+	.	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	start_codon	45698048	45698050	.	+	0	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	CDS	45698048	45698529	0.37	+	0	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	exon	45698048	45698529	.	+	.	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	intron	45698530	45698641	.	+	.	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	CDS	45698642	45699206	0.65	+	1	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	exon	45698642	45699206	.	+	.	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
Phchi.S1	AUGUSTUS	stop_codon	45699207	45699209	.	+	0	transcript_id "Phchi.S1G724800.t1"; gene_id "Phchi.S1G724800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14740.t1 is derived from g13208.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14467210	14468564	.	-	.	Phchi.S3G205900
Phchi.S3	AUGUSTUS	transcript	14467210	14468564	.	-	.	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	stop_codon	14467207	14467209	.	-	0	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	CDS	14467210	14467680	0.92	-	0	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	exon	14467210	14467680	.	-	.	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	intron	14467681	14467787	.	-	.	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	CDS	14467788	14468564	0.55	-	0	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	exon	14467788	14468564	.	-	.	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	start_codon	14468562	14468564	.	-	0	transcript_id "Phchi.S3G205900.t1"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	transcript	14467210	14467524	.	-	.	transcript_id "Phchi.S3G205900.t2"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	stop_codon	14467207	14467209	.	-	0	transcript_id "Phchi.S3G205900.t2"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	CDS	14467210	14467524	1	-	0	transcript_id "Phchi.S3G205900.t2"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	exon	14467210	14467524	.	-	.	transcript_id "Phchi.S3G205900.t2"; gene_id "Phchi.S3G205900"
Phchi.S3	AUGUSTUS	start_codon	14467522	14467524	.	-	0	transcript_id "Phchi.S3G205900.t2"; gene_id "Phchi.S3G205900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8526.t1 is derived from g5701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36439890	36441747	.	+	.	Phchi.S1G568500
Phchi.S1	AUGUSTUS	transcript	36439890	36441747	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	start_codon	36439890	36439892	.	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36439890	36440025	0.4	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36439890	36440025	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36440026	36440143	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36440144	36440244	1	+	2	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36440144	36440244	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36440245	36440335	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36440336	36440467	1	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36440336	36440467	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36440468	36440615	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36440616	36440716	1	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36440616	36440716	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36440717	36440806	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36440807	36440912	1	+	1	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36440807	36440912	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36440913	36441022	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36441023	36441091	1	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36441023	36441091	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36441092	36441178	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36441179	36441243	1	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36441179	36441243	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36441244	36441329	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36441330	36441428	1	+	1	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36441330	36441428	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36441429	36441509	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36441510	36441609	1	+	1	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36441510	36441609	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	intron	36441610	36441687	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	CDS	36441688	36441747	1	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	exon	36441688	36441747	.	+	.	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
Phchi.S1	AUGUSTUS	stop_codon	36441748	36441750	.	+	0	transcript_id "Phchi.S1G568500.t1"; gene_id "Phchi.S1G568500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2319.t1 is derived from g9239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6157153	6160361	.	-	.	Phchi.S5G092800
Phchi.S5	AUGUSTUS	transcript	6157153	6160361	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	stop_codon	6157150	6157152	.	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6157153	6157231	1	-	1	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6157153	6157231	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6157232	6157321	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6157322	6157377	1	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6157322	6157377	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6157378	6157484	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6157485	6157545	1	-	1	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6157485	6157545	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6157546	6157662	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6157663	6157736	1	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6157663	6157736	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6157737	6157908	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6157909	6158069	0.79	-	2	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6157909	6158069	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6158070	6158172	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6158173	6158293	0.76	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6158173	6158293	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6158294	6158382	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6158383	6158463	1	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6158383	6158463	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6158464	6158561	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6158562	6158630	0.97	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6158562	6158630	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6158631	6158753	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6158754	6158825	0.67	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6158754	6158825	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6158826	6159180	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6159181	6159321	0.65	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6159181	6159321	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6159322	6159450	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6159451	6159574	1	-	1	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6159451	6159574	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6159575	6159743	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6159744	6160117	0.97	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6159744	6160117	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	intron	6160118	6160235	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	CDS	6160236	6160361	0.56	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	exon	6160236	6160361	.	-	.	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
Phchi.S5	AUGUSTUS	start_codon	6160359	6160361	.	-	0	transcript_id "Phchi.S5G092800.t1"; gene_id "Phchi.S5G092800"
# This transcript jg14682.t2 is derived from g13150.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14683.t1 is derived from g13151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14155570	14156058	.	-	.	Phchi.S3G200200
Phchi.S3	AUGUSTUS	transcript	14155570	14156058	.	-	.	transcript_id "Phchi.S3G200200.t1"; gene_id "Phchi.S3G200200"
Phchi.S3	AUGUSTUS	stop_codon	14155567	14155569	.	-	0	transcript_id "Phchi.S3G200200.t1"; gene_id "Phchi.S3G200200"
Phchi.S3	AUGUSTUS	CDS	14155570	14156058	0.95	-	0	transcript_id "Phchi.S3G200200.t1"; gene_id "Phchi.S3G200200"
Phchi.S3	AUGUSTUS	exon	14155570	14156058	.	-	.	transcript_id "Phchi.S3G200200.t1"; gene_id "Phchi.S3G200200"
Phchi.S3	AUGUSTUS	start_codon	14156056	14156058	.	-	0	transcript_id "Phchi.S3G200200.t1"; gene_id "Phchi.S3G200200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9268.t1 is derived from g6443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40672961	40680877	.	-	.	Phchi.S1G642700
Phchi.S1	AUGUSTUS	transcript	40672961	40680877	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	stop_codon	40672958	40672960	.	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40672961	40673017	0.99	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40672961	40673017	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40673018	40673186	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40673187	40673363	1	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40673187	40673363	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40673364	40673440	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40673441	40673740	0.87	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40673441	40673740	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40673741	40674220	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40674221	40674536	0.65	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40674221	40674536	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40674537	40674612	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40674613	40674666	1	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40674613	40674666	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40674667	40674762	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40674763	40674836	0.79	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40674763	40674836	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40674837	40674939	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40674940	40675032	1	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40674940	40675032	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40675033	40675132	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40675133	40675277	1	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40675133	40675277	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40675278	40675409	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40675410	40675531	1	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40675410	40675531	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40675532	40675674	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40675675	40676021	0.99	-	2	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40675675	40676021	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40676022	40676203	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40676204	40676411	0.99	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40676204	40676411	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40676412	40676514	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40676515	40676629	1	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40676515	40676629	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40676630	40676815	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40676816	40676976	1	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40676816	40676976	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40676977	40677077	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40677078	40677260	1	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40677078	40677260	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40677261	40677350	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40677351	40677423	1	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40677351	40677423	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40677424	40677544	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40677545	40677644	1	-	2	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40677545	40677644	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40677645	40677827	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40677828	40678047	0.73	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40677828	40678047	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40678048	40678193	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40678194	40678230	0.87	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40678194	40678230	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40678231	40678310	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40678311	40678537	0.73	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40678311	40678537	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40678538	40678664	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40678665	40678735	0.62	-	2	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40678665	40678735	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40678736	40678820	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40678821	40678908	1	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40678821	40678908	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40678909	40679048	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40679049	40679183	0.57	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40679049	40679183	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40679184	40679279	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40679280	40679532	0.56	-	1	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40679280	40679532	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	intron	40679533	40679867	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	CDS	40679868	40680877	0.63	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	exon	40679868	40680877	.	-	.	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
Phchi.S1	AUGUSTUS	start_codon	40680875	40680877	.	-	0	transcript_id "Phchi.S1G642700.t1"; gene_id "Phchi.S1G642700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1333.t1 is derived from g11116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9082924	9084513	.	+	.	Phchi.S6G129200
Phchi.S6	AUGUSTUS	transcript	9082924	9084513	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	start_codon	9082924	9082926	.	+	0	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	CDS	9082924	9083018	0.93	+	0	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	exon	9082924	9083018	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	intron	9083019	9083336	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	CDS	9083337	9083423	0.99	+	1	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	exon	9083337	9083423	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	intron	9083424	9083511	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	CDS	9083512	9083566	1	+	1	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	exon	9083512	9083566	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	intron	9083567	9083723	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	CDS	9083724	9083920	0.48	+	0	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	exon	9083724	9083920	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	intron	9083921	9084118	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	CDS	9084119	9084239	0.43	+	1	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	exon	9084119	9084239	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	intron	9084240	9084330	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	CDS	9084331	9084513	0.99	+	0	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	exon	9084331	9084513	.	+	.	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
Phchi.S6	AUGUSTUS	stop_codon	9084514	9084516	.	+	0	transcript_id "Phchi.S6G129200.t1"; gene_id "Phchi.S6G129200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3963.t1 is derived from g1132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6766946	6767752	.	-	.	Phchi.S1G112200
Phchi.S1	AUGUSTUS	transcript	6766946	6767752	.	-	.	transcript_id "Phchi.S1G112200.t1"; gene_id "Phchi.S1G112200"
Phchi.S1	AUGUSTUS	stop_codon	6766943	6766945	.	-	0	transcript_id "Phchi.S1G112200.t1"; gene_id "Phchi.S1G112200"
Phchi.S1	AUGUSTUS	CDS	6766946	6767752	0.86	-	0	transcript_id "Phchi.S1G112200.t1"; gene_id "Phchi.S1G112200"
Phchi.S1	AUGUSTUS	exon	6766946	6767752	.	-	.	transcript_id "Phchi.S1G112200.t1"; gene_id "Phchi.S1G112200"
Phchi.S1	AUGUSTUS	start_codon	6767750	6767752	.	-	0	transcript_id "Phchi.S1G112200.t1"; gene_id "Phchi.S1G112200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2513.t1 is derived from g9433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7081508	7083360	.	-	.	Phchi.S5G112200
Phchi.S5	AUGUSTUS	transcript	7081508	7083360	.	-	.	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	stop_codon	7081505	7081507	.	-	0	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	CDS	7081508	7081971	0.97	-	2	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	exon	7081508	7081971	.	-	.	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	intron	7081972	7082045	.	-	.	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	CDS	7082046	7082794	0.95	-	1	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	exon	7082046	7082794	.	-	.	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	intron	7082795	7082995	.	-	.	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	CDS	7082996	7083360	0.52	-	0	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	exon	7082996	7083360	.	-	.	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
Phchi.S5	AUGUSTUS	start_codon	7083358	7083360	.	-	0	transcript_id "Phchi.S5G112200.t1"; gene_id "Phchi.S5G112200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4840.t1 is derived from g2010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13056249	13057677	.	+	.	Phchi.S1G199900
Phchi.S1	AUGUSTUS	transcript	13056249	13057677	.	+	.	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	start_codon	13056249	13056251	.	+	0	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	CDS	13056249	13056344	0.04	+	0	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	exon	13056249	13056344	.	+	.	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	intron	13056345	13057464	.	+	.	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	CDS	13057465	13057677	0.01	+	0	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	exon	13057465	13057677	.	+	.	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
Phchi.S1	AUGUSTUS	stop_codon	13057678	13057680	.	+	0	transcript_id "Phchi.S1G199900.t1"; gene_id "Phchi.S1G199900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10651.t1 is derived from g14701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1430998	1433053	.	-	.	Phchi.S4G023300
Phchi.S4	AUGUSTUS	transcript	1430998	1433053	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	stop_codon	1430995	1430997	.	-	0	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	CDS	1430998	1431004	0.68	-	1	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	exon	1430998	1431004	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	intron	1431005	1431093	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	CDS	1431094	1431201	0.62	-	1	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	exon	1431094	1431201	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	intron	1431202	1431502	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	CDS	1431503	1431550	0.4	-	1	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	exon	1431503	1431550	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	intron	1431551	1431640	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	CDS	1431641	1431871	1	-	1	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	exon	1431641	1431871	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	intron	1431872	1431968	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	CDS	1431969	1433053	0.52	-	0	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	exon	1431969	1433053	.	-	.	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
Phchi.S4	AUGUSTUS	start_codon	1433051	1433053	.	-	0	transcript_id "Phchi.S4G023300.t1"; gene_id "Phchi.S4G023300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9294.t1 is derived from g6469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40820622	40822120	.	+	.	Phchi.S1G645300
Phchi.S1	AUGUSTUS	transcript	40820622	40822120	.	+	.	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	start_codon	40820622	40820624	.	+	0	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	CDS	40820622	40821233	0.86	+	0	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	exon	40820622	40821233	.	+	.	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	intron	40821234	40821319	.	+	.	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	CDS	40821320	40821512	0.94	+	0	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	exon	40821320	40821512	.	+	.	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	intron	40821513	40821656	.	+	.	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	CDS	40821657	40822120	1	+	2	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	exon	40821657	40822120	.	+	.	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	stop_codon	40822121	40822123	.	+	0	transcript_id "Phchi.S1G645300.t1"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	transcript	40820622	40822120	.	+	.	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	start_codon	40820622	40820624	.	+	0	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	CDS	40820622	40821233	0.7	+	0	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	exon	40820622	40821233	.	+	.	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	intron	40821234	40821319	.	+	.	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	CDS	40821320	40821598	0.79	+	0	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	exon	40821320	40821598	.	+	.	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	intron	40821599	40821697	.	+	.	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	CDS	40821698	40822120	0.94	+	0	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	exon	40821698	40822120	.	+	.	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
Phchi.S1	AUGUSTUS	stop_codon	40822121	40822123	.	+	0	transcript_id "Phchi.S1G645300.t2"; gene_id "Phchi.S1G645300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14902.t1 is derived from g13370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15445824	15446806	.	-	.	Phchi.S3G222100
Phchi.S3	AUGUSTUS	transcript	15445824	15446806	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	stop_codon	15445821	15445823	.	-	0	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	CDS	15445824	15446129	0.99	-	0	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	exon	15445824	15446129	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	intron	15446130	15446227	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	CDS	15446228	15446382	1	-	2	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	exon	15446228	15446382	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	intron	15446383	15446469	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	CDS	15446470	15446611	1	-	0	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	exon	15446470	15446611	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	intron	15446612	15446755	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	CDS	15446756	15446806	1	-	0	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	exon	15446756	15446806	.	-	.	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
Phchi.S3	AUGUSTUS	start_codon	15446804	15446806	.	-	0	transcript_id "Phchi.S3G222100.t1"; gene_id "Phchi.S3G222100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2354.t1 is derived from g9274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6322902	6323648	.	+	.	Phchi.S5G096300
Phchi.S5	AUGUSTUS	transcript	6322902	6323648	.	+	.	transcript_id "Phchi.S5G096300.t1"; gene_id "Phchi.S5G096300"
Phchi.S5	AUGUSTUS	start_codon	6322902	6322904	.	+	0	transcript_id "Phchi.S5G096300.t1"; gene_id "Phchi.S5G096300"
Phchi.S5	AUGUSTUS	CDS	6322902	6323648	0.6	+	0	transcript_id "Phchi.S5G096300.t1"; gene_id "Phchi.S5G096300"
Phchi.S5	AUGUSTUS	exon	6322902	6323648	.	+	.	transcript_id "Phchi.S5G096300.t1"; gene_id "Phchi.S5G096300"
Phchi.S5	AUGUSTUS	stop_codon	6323649	6323651	.	+	0	transcript_id "Phchi.S5G096300.t1"; gene_id "Phchi.S5G096300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg881.t1 is derived from g10663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6244733	6250827	.	+	.	Phchi.S6G084000
Phchi.S6	AUGUSTUS	transcript	6244733	6250827	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	start_codon	6244733	6244735	.	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6244733	6244754	0.97	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6244733	6244754	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6244755	6245122	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6245123	6245223	1	+	2	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6245123	6245223	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6245224	6245406	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6245407	6245505	1	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6245407	6245505	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6245506	6245599	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6245600	6245737	1	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6245600	6245737	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6245738	6245829	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6245830	6246370	0.79	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6245830	6246370	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6246371	6246457	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6246458	6247465	0.91	+	2	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6246458	6247465	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6247466	6247583	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6247584	6247978	0.97	+	2	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6247584	6247978	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6247979	6248082	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6248083	6248541	1	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6248083	6248541	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6248542	6248662	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6248663	6248767	1	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6248663	6248767	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6248768	6249214	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6249215	6249307	0.62	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6249215	6249307	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6249308	6249427	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6249428	6249565	1	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6249428	6249565	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6249566	6249656	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6249657	6249758	0.76	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6249657	6249758	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6249759	6249836	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6249837	6249908	0.76	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6249837	6249908	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6249909	6250127	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6250128	6250260	1	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6250128	6250260	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6250261	6250484	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6250485	6250523	0.53	+	2	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6250485	6250523	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	intron	6250524	6250672	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	CDS	6250673	6250827	0.54	+	2	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	exon	6250673	6250827	.	+	.	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
Phchi.S6	AUGUSTUS	stop_codon	6250828	6250830	.	+	0	transcript_id "Phchi.S6G084000.t1"; gene_id "Phchi.S6G084000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2326.t1 is derived from g9246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6190938	6191631	.	-	.	Phchi.S5G093500
Phchi.S5	AUGUSTUS	transcript	6190938	6191631	.	-	.	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	stop_codon	6190935	6190937	.	-	0	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	CDS	6190938	6191057	0.92	-	0	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	exon	6190938	6191057	.	-	.	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	intron	6191058	6191202	.	-	.	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	CDS	6191203	6191362	0.59	-	1	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	exon	6191203	6191362	.	-	.	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	intron	6191363	6191482	.	-	.	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	CDS	6191483	6191631	0.58	-	0	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	exon	6191483	6191631	.	-	.	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	start_codon	6191629	6191631	.	-	0	transcript_id "Phchi.S5G093500.t1"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	transcript	6190955	6191631	.	-	.	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	stop_codon	6190952	6190954	.	-	0	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	CDS	6190955	6191050	0.47	-	0	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	exon	6190955	6191050	.	-	.	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	intron	6191051	6191202	.	-	.	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	CDS	6191203	6191362	0.55	-	1	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	exon	6191203	6191362	.	-	.	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	intron	6191363	6191482	.	-	.	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	CDS	6191483	6191631	0.54	-	0	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	exon	6191483	6191631	.	-	.	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
Phchi.S5	AUGUSTUS	start_codon	6191629	6191631	.	-	0	transcript_id "Phchi.S5G093500.t2"; gene_id "Phchi.S5G093500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10068.t1 is derived from g7244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45618813	45619481	.	-	.	Phchi.S1G722700
Phchi.S1	AUGUSTUS	transcript	45618813	45619481	.	-	.	transcript_id "Phchi.S1G722700.t1"; gene_id "Phchi.S1G722700"
Phchi.S1	AUGUSTUS	stop_codon	45618810	45618812	.	-	0	transcript_id "Phchi.S1G722700.t1"; gene_id "Phchi.S1G722700"
Phchi.S1	AUGUSTUS	CDS	45618813	45619481	1	-	0	transcript_id "Phchi.S1G722700.t1"; gene_id "Phchi.S1G722700"
Phchi.S1	AUGUSTUS	exon	45618813	45619481	.	-	.	transcript_id "Phchi.S1G722700.t1"; gene_id "Phchi.S1G722700"
Phchi.S1	AUGUSTUS	start_codon	45619479	45619481	.	-	0	transcript_id "Phchi.S1G722700.t1"; gene_id "Phchi.S1G722700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2765.t1 is derived from g9685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8719586	8720515	.	-	.	Phchi.S5G137400
Phchi.S5	AUGUSTUS	transcript	8719586	8720515	.	-	.	transcript_id "Phchi.S5G137400.t1"; gene_id "Phchi.S5G137400"
Phchi.S5	AUGUSTUS	stop_codon	8719583	8719585	.	-	0	transcript_id "Phchi.S5G137400.t1"; gene_id "Phchi.S5G137400"
Phchi.S5	AUGUSTUS	CDS	8719586	8720515	0.52	-	0	transcript_id "Phchi.S5G137400.t1"; gene_id "Phchi.S5G137400"
Phchi.S5	AUGUSTUS	exon	8719586	8720515	.	-	.	transcript_id "Phchi.S5G137400.t1"; gene_id "Phchi.S5G137400"
Phchi.S5	AUGUSTUS	start_codon	8720513	8720515	.	-	0	transcript_id "Phchi.S5G137400.t1"; gene_id "Phchi.S5G137400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13739.t1 is derived from g12206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8661732	8662793	.	+	.	Phchi.S3G105800
Phchi.S3	AUGUSTUS	transcript	8661732	8662793	.	+	.	transcript_id "Phchi.S3G105800.t1"; gene_id "Phchi.S3G105800"
Phchi.S3	AUGUSTUS	start_codon	8661732	8661734	.	+	0	transcript_id "Phchi.S3G105800.t1"; gene_id "Phchi.S3G105800"
Phchi.S3	AUGUSTUS	CDS	8661732	8662793	0.89	+	0	transcript_id "Phchi.S3G105800.t1"; gene_id "Phchi.S3G105800"
Phchi.S3	AUGUSTUS	exon	8661732	8662793	.	+	.	transcript_id "Phchi.S3G105800.t1"; gene_id "Phchi.S3G105800"
Phchi.S3	AUGUSTUS	stop_codon	8662794	8662796	.	+	0	transcript_id "Phchi.S3G105800.t1"; gene_id "Phchi.S3G105800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11815.t1 is derived from g15867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8371282	8371740	.	-	.	Phchi.S4G139700
Phchi.S4	AUGUSTUS	transcript	8371282	8371740	.	-	.	transcript_id "Phchi.S4G139700.t1"; gene_id "Phchi.S4G139700"
Phchi.S4	AUGUSTUS	stop_codon	8371279	8371281	.	-	0	transcript_id "Phchi.S4G139700.t1"; gene_id "Phchi.S4G139700"
Phchi.S4	AUGUSTUS	CDS	8371282	8371740	0.71	-	0	transcript_id "Phchi.S4G139700.t1"; gene_id "Phchi.S4G139700"
Phchi.S4	AUGUSTUS	exon	8371282	8371740	.	-	.	transcript_id "Phchi.S4G139700.t1"; gene_id "Phchi.S4G139700"
Phchi.S4	AUGUSTUS	start_codon	8371738	8371740	.	-	0	transcript_id "Phchi.S4G139700.t1"; gene_id "Phchi.S4G139700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11382.t1 is derived from g15432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6008482	6010472	.	+	.	Phchi.S4G096400
Phchi.S4	AUGUSTUS	transcript	6008482	6010472	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	start_codon	6008482	6008484	.	+	0	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	CDS	6008482	6008578	1	+	0	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	exon	6008482	6008578	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	intron	6008579	6008724	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	CDS	6008725	6009094	1	+	2	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	exon	6008725	6009094	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	intron	6009095	6009211	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	CDS	6009212	6010003	0.94	+	1	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	exon	6009212	6010003	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	intron	6010004	6010114	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	CDS	6010115	6010329	0.66	+	1	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	exon	6010115	6010329	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	intron	6010330	6010443	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	CDS	6010444	6010472	0.94	+	2	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	exon	6010444	6010472	.	+	.	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
Phchi.S4	AUGUSTUS	stop_codon	6010473	6010475	.	+	0	transcript_id "Phchi.S4G096400.t1"; gene_id "Phchi.S4G096400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5811.t1 is derived from g2981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19068564	19070676	.	-	.	Phchi.S1G297000
Phchi.S1	AUGUSTUS	transcript	19068564	19070676	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	stop_codon	19068561	19068563	.	-	0	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19068564	19068695	1	-	0	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19068564	19068695	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19068696	19068793	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19068794	19068908	1	-	1	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19068794	19068908	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19068909	19068998	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19068999	19069150	1	-	0	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19068999	19069150	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19069151	19069236	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19069237	19069385	1	-	2	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19069237	19069385	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19069386	19069535	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19069536	19069683	1	-	0	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19069536	19069683	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19069684	19069897	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19069898	19070015	1	-	1	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19069898	19070015	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19070016	19070098	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19070099	19070287	0.99	-	1	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19070099	19070287	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	intron	19070288	19070368	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	CDS	19070369	19070676	0.92	-	0	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	exon	19070369	19070676	.	-	.	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
Phchi.S1	AUGUSTUS	start_codon	19070674	19070676	.	-	0	transcript_id "Phchi.S1G297000.t1"; gene_id "Phchi.S1G297000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3931.t1 is derived from g1100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6511878	6512343	.	+	.	Phchi.S1G109000
Phchi.S1	AUGUSTUS	transcript	6511878	6512343	.	+	.	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	start_codon	6511878	6511880	.	+	0	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	CDS	6511878	6512061	0.38	+	0	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	exon	6511878	6512061	.	+	.	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	intron	6512062	6512179	.	+	.	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	CDS	6512180	6512343	0.38	+	2	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	exon	6512180	6512343	.	+	.	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
Phchi.S1	AUGUSTUS	stop_codon	6512344	6512346	.	+	0	transcript_id "Phchi.S1G109000.t1"; gene_id "Phchi.S1G109000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9760.t1 is derived from g6936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43538825	43539598	.	+	.	Phchi.S1G691900
Phchi.S1	AUGUSTUS	transcript	43538825	43539598	.	+	.	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	start_codon	43538825	43538827	.	+	0	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	CDS	43538825	43539353	0.68	+	0	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	exon	43538825	43539353	.	+	.	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	intron	43539354	43539467	.	+	.	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	CDS	43539468	43539598	0.51	+	2	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	exon	43539468	43539598	.	+	.	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
Phchi.S1	AUGUSTUS	stop_codon	43539599	43539601	.	+	0	transcript_id "Phchi.S1G691900.t1"; gene_id "Phchi.S1G691900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1880.t1 is derived from g8800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3689418	3690101	.	-	.	Phchi.S5G048900
Phchi.S5	AUGUSTUS	transcript	3689418	3690101	.	-	.	transcript_id "Phchi.S5G048900.t1"; gene_id "Phchi.S5G048900"
Phchi.S5	AUGUSTUS	stop_codon	3689415	3689417	.	-	0	transcript_id "Phchi.S5G048900.t1"; gene_id "Phchi.S5G048900"
Phchi.S5	AUGUSTUS	CDS	3689418	3690101	0.65	-	0	transcript_id "Phchi.S5G048900.t1"; gene_id "Phchi.S5G048900"
Phchi.S5	AUGUSTUS	exon	3689418	3690101	.	-	.	transcript_id "Phchi.S5G048900.t1"; gene_id "Phchi.S5G048900"
Phchi.S5	AUGUSTUS	start_codon	3690099	3690101	.	-	0	transcript_id "Phchi.S5G048900.t1"; gene_id "Phchi.S5G048900"
# This transcript jg5540.t1 is derived from g2710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17459614	17463336	.	-	.	Phchi.S1G269900
Phchi.S1	AUGUSTUS	transcript	17459614	17463336	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	stop_codon	17459611	17459613	.	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17459614	17460219	0.6	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17459614	17460219	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17460220	17460518	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17460519	17460611	0.52	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17460519	17460611	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17460612	17460714	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17460715	17460791	0.61	-	2	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17460715	17460791	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17460792	17460891	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17460892	17460961	0.64	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17460892	17460961	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17460962	17461030	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17461031	17461166	1	-	1	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17461031	17461166	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17461167	17461249	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17461250	17461347	1	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17461250	17461347	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17461348	17461441	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17461442	17461519	1	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17461442	17461519	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17461520	17461597	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17461598	17461667	1	-	1	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17461598	17461667	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17461668	17461767	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17461768	17461832	1	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17461768	17461832	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17461833	17461978	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17461979	17462014	0.47	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17461979	17462014	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17462015	17462125	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17462126	17462230	0.99	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17462126	17462230	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17462231	17462313	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17462314	17462397	1	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17462314	17462397	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17462398	17462478	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17462479	17462554	1	-	1	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17462479	17462554	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17462555	17462739	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17462740	17462818	1	-	2	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17462740	17462818	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17462819	17462896	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17462897	17463002	1	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17462897	17463002	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	intron	17463003	17463246	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	CDS	17463247	17463336	1	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	exon	17463247	17463336	.	-	.	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
Phchi.S1	AUGUSTUS	start_codon	17463334	17463336	.	-	0	transcript_id "Phchi.S1G269900.t1"; gene_id "Phchi.S1G269900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11371.t1 is derived from g15421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5938467	5938679	.	-	.	Phchi.S4G095300
Phchi.S4	AUGUSTUS	transcript	5938467	5938679	.	-	.	transcript_id "Phchi.S4G095300.t1"; gene_id "Phchi.S4G095300"
Phchi.S4	AUGUSTUS	stop_codon	5938464	5938466	.	-	0	transcript_id "Phchi.S4G095300.t1"; gene_id "Phchi.S4G095300"
Phchi.S4	AUGUSTUS	CDS	5938467	5938679	0.84	-	0	transcript_id "Phchi.S4G095300.t1"; gene_id "Phchi.S4G095300"
Phchi.S4	AUGUSTUS	exon	5938467	5938679	.	-	.	transcript_id "Phchi.S4G095300.t1"; gene_id "Phchi.S4G095300"
Phchi.S4	AUGUSTUS	start_codon	5938677	5938679	.	-	0	transcript_id "Phchi.S4G095300.t1"; gene_id "Phchi.S4G095300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10390.t1 is derived from g7566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47515786	47516199	.	-	.	Phchi.S1G754900
Phchi.S1	AUGUSTUS	transcript	47515786	47516199	.	-	.	transcript_id "Phchi.S1G754900.t1"; gene_id "Phchi.S1G754900"
Phchi.S1	AUGUSTUS	stop_codon	47515783	47515785	.	-	0	transcript_id "Phchi.S1G754900.t1"; gene_id "Phchi.S1G754900"
Phchi.S1	AUGUSTUS	CDS	47515786	47516199	0.79	-	0	transcript_id "Phchi.S1G754900.t1"; gene_id "Phchi.S1G754900"
Phchi.S1	AUGUSTUS	exon	47515786	47516199	.	-	.	transcript_id "Phchi.S1G754900.t1"; gene_id "Phchi.S1G754900"
Phchi.S1	AUGUSTUS	start_codon	47516197	47516199	.	-	0	transcript_id "Phchi.S1G754900.t1"; gene_id "Phchi.S1G754900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8569.t1 is derived from g5744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36691025	36691762	.	+	.	Phchi.S1G572800
Phchi.S1	AUGUSTUS	transcript	36691025	36691762	.	+	.	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	start_codon	36691025	36691027	.	+	0	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	CDS	36691025	36691063	0.93	+	0	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	exon	36691025	36691063	.	+	.	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	intron	36691064	36691502	.	+	.	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	CDS	36691503	36691599	1	+	0	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	exon	36691503	36691599	.	+	.	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	intron	36691600	36691682	.	+	.	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	CDS	36691683	36691762	1	+	2	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	exon	36691683	36691762	.	+	.	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
Phchi.S1	AUGUSTUS	stop_codon	36691763	36691765	.	+	0	transcript_id "Phchi.S1G572800.t1"; gene_id "Phchi.S1G572800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6864.t1 is derived from g4036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25655136	25659748	.	+	.	Phchi.S1G402300
Phchi.S1	AUGUSTUS	transcript	25655136	25659748	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	start_codon	25655136	25655138	.	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25655136	25655156	0.97	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25655136	25655156	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25655157	25655334	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25655335	25655391	1	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25655335	25655391	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25655392	25655584	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25655585	25655688	1	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25655585	25655688	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25655689	25655855	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25655856	25655949	0.91	+	1	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25655856	25655949	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25655950	25656054	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25656055	25656154	0.91	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25656055	25656154	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25656155	25656283	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25656284	25656533	1	+	2	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25656284	25656533	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25656534	25656686	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25656687	25656724	1	+	1	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25656687	25656724	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25656725	25656818	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25656819	25656850	1	+	2	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25656819	25656850	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25656851	25656942	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25656943	25657062	1	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25656943	25657062	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25657063	25657189	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25657190	25657269	1	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25657190	25657269	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25657270	25657416	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25657417	25657665	1	+	1	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25657417	25657665	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25657666	25657812	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25657813	25657981	1	+	1	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25657813	25657981	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25657982	25658074	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25658075	25658203	1	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25658075	25658203	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25658204	25658295	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25658296	25658508	0.98	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25658296	25658508	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25658509	25658619	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25658620	25658799	0.98	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25658620	25658799	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25658800	25658912	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25658913	25659428	0.61	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25658913	25659428	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	intron	25659429	25659643	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	CDS	25659644	25659748	0.92	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	exon	25659644	25659748	.	+	.	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
Phchi.S1	AUGUSTUS	stop_codon	25659749	25659751	.	+	0	transcript_id "Phchi.S1G402300.t1"; gene_id "Phchi.S1G402300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11075.t1 is derived from g15125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3975316	3976266	.	-	.	Phchi.S4G065700
Phchi.S4	AUGUSTUS	transcript	3975316	3976266	.	-	.	transcript_id "Phchi.S4G065700.t1"; gene_id "Phchi.S4G065700"
Phchi.S4	AUGUSTUS	stop_codon	3975313	3975315	.	-	0	transcript_id "Phchi.S4G065700.t1"; gene_id "Phchi.S4G065700"
Phchi.S4	AUGUSTUS	CDS	3975316	3976266	1	-	0	transcript_id "Phchi.S4G065700.t1"; gene_id "Phchi.S4G065700"
Phchi.S4	AUGUSTUS	exon	3975316	3976266	.	-	.	transcript_id "Phchi.S4G065700.t1"; gene_id "Phchi.S4G065700"
Phchi.S4	AUGUSTUS	start_codon	3976264	3976266	.	-	0	transcript_id "Phchi.S4G065700.t1"; gene_id "Phchi.S4G065700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14482.t1 is derived from g12950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13060817	13061068	.	-	.	Phchi.S3G180100
Phchi.S3	AUGUSTUS	transcript	13060817	13061068	.	-	.	transcript_id "Phchi.S3G180100.t1"; gene_id "Phchi.S3G180100"
Phchi.S3	AUGUSTUS	stop_codon	13060814	13060816	.	-	0	transcript_id "Phchi.S3G180100.t1"; gene_id "Phchi.S3G180100"
Phchi.S3	AUGUSTUS	CDS	13060817	13061068	0.93	-	0	transcript_id "Phchi.S3G180100.t1"; gene_id "Phchi.S3G180100"
Phchi.S3	AUGUSTUS	exon	13060817	13061068	.	-	.	transcript_id "Phchi.S3G180100.t1"; gene_id "Phchi.S3G180100"
Phchi.S3	AUGUSTUS	start_codon	13061066	13061068	.	-	0	transcript_id "Phchi.S3G180100.t1"; gene_id "Phchi.S3G180100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1003.t1 is derived from g10786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7046668	7048149	.	-	.	Phchi.S6G096200
Phchi.S6	AUGUSTUS	transcript	7046668	7048149	.	-	.	transcript_id "Phchi.S6G096200.t1"; gene_id "Phchi.S6G096200"
Phchi.S6	AUGUSTUS	stop_codon	7046665	7046667	.	-	0	transcript_id "Phchi.S6G096200.t1"; gene_id "Phchi.S6G096200"
Phchi.S6	AUGUSTUS	CDS	7046668	7048149	1	-	0	transcript_id "Phchi.S6G096200.t1"; gene_id "Phchi.S6G096200"
Phchi.S6	AUGUSTUS	exon	7046668	7048149	.	-	.	transcript_id "Phchi.S6G096200.t1"; gene_id "Phchi.S6G096200"
Phchi.S6	AUGUSTUS	start_codon	7048147	7048149	.	-	0	transcript_id "Phchi.S6G096200.t1"; gene_id "Phchi.S6G096200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2132.t1 is derived from g9052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4995726	4997591	.	-	.	Phchi.S5G074100
Phchi.S5	AUGUSTUS	transcript	4995726	4997591	.	-	.	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	stop_codon	4995723	4995725	.	-	0	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	CDS	4995726	4996638	0.48	-	1	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	exon	4995726	4996638	.	-	.	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	intron	4996639	4996724	.	-	.	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	CDS	4996725	4997174	1	-	1	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	exon	4996725	4997174	.	-	.	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	intron	4997175	4997352	.	-	.	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	CDS	4997353	4997591	0.52	-	0	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	exon	4997353	4997591	.	-	.	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
Phchi.S5	AUGUSTUS	start_codon	4997589	4997591	.	-	0	transcript_id "Phchi.S5G074100.t1"; gene_id "Phchi.S5G074100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12502.t1 is derived from g8179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30855547	30855948	.	-	.	Phchi.S2G058200
Phchi.S2	AUGUSTUS	transcript	30855547	30855948	.	-	.	transcript_id "Phchi.S2G058200.t1"; gene_id "Phchi.S2G058200"
Phchi.S2	AUGUSTUS	stop_codon	30855544	30855546	.	-	0	transcript_id "Phchi.S2G058200.t1"; gene_id "Phchi.S2G058200"
Phchi.S2	AUGUSTUS	CDS	30855547	30855948	0.36	-	0	transcript_id "Phchi.S2G058200.t1"; gene_id "Phchi.S2G058200"
Phchi.S2	AUGUSTUS	exon	30855547	30855948	.	-	.	transcript_id "Phchi.S2G058200.t1"; gene_id "Phchi.S2G058200"
Phchi.S2	AUGUSTUS	start_codon	30855946	30855948	.	-	0	transcript_id "Phchi.S2G058200.t1"; gene_id "Phchi.S2G058200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9544.t1 is derived from g6720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42401628	42402593	.	+	.	Phchi.S1G670300
Phchi.S1	AUGUSTUS	transcript	42401628	42402593	.	+	.	transcript_id "Phchi.S1G670300.t1"; gene_id "Phchi.S1G670300"
Phchi.S1	AUGUSTUS	start_codon	42401628	42401630	.	+	0	transcript_id "Phchi.S1G670300.t1"; gene_id "Phchi.S1G670300"
Phchi.S1	AUGUSTUS	CDS	42401628	42402593	0.65	+	0	transcript_id "Phchi.S1G670300.t1"; gene_id "Phchi.S1G670300"
Phchi.S1	AUGUSTUS	exon	42401628	42402593	.	+	.	transcript_id "Phchi.S1G670300.t1"; gene_id "Phchi.S1G670300"
Phchi.S1	AUGUSTUS	stop_codon	42402594	42402596	.	+	0	transcript_id "Phchi.S1G670300.t1"; gene_id "Phchi.S1G670300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10587.t1 is derived from g14637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1071353	1072218	.	-	.	Phchi.S4G016900
Phchi.S4	AUGUSTUS	transcript	1071353	1072218	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	stop_codon	1071350	1071352	.	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	CDS	1071353	1071472	0.6	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	exon	1071353	1071472	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	intron	1071473	1071545	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	CDS	1071546	1071611	0.67	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	exon	1071546	1071611	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	intron	1071612	1071687	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	CDS	1071688	1071708	1	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	exon	1071688	1071708	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	intron	1071709	1071788	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	CDS	1071789	1071887	0.56	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	exon	1071789	1071887	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	intron	1071888	1071993	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	CDS	1071994	1072218	0.5	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	exon	1071994	1072218	.	-	.	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
Phchi.S4	AUGUSTUS	start_codon	1072216	1072218	.	-	0	transcript_id "Phchi.S4G016900.t1"; gene_id "Phchi.S4G016900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15213.t1 is derived from g13681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17685903	17688010	.	+	.	Phchi.S3G253200
Phchi.S3	AUGUSTUS	transcript	17685903	17688010	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	start_codon	17685903	17685905	.	+	0	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	CDS	17685903	17686593	0.85	+	0	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	exon	17685903	17686593	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	intron	17686594	17686698	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	CDS	17686699	17686892	0.88	+	2	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	exon	17686699	17686892	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	intron	17686893	17686982	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	CDS	17686983	17687405	1	+	0	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	exon	17686983	17687405	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	intron	17687406	17687522	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	CDS	17687523	17687740	0.99	+	0	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	exon	17687523	17687740	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	intron	17687741	17687832	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	CDS	17687833	17688010	1	+	1	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	exon	17687833	17688010	.	+	.	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	stop_codon	17688011	17688013	.	+	0	transcript_id "Phchi.S3G253200.t1"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	transcript	17685903	17686646	.	+	.	transcript_id "Phchi.S3G253200.t2"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	start_codon	17685903	17685905	.	+	0	transcript_id "Phchi.S3G253200.t2"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	CDS	17685903	17686646	0.9	+	0	transcript_id "Phchi.S3G253200.t2"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	exon	17685903	17686646	.	+	.	transcript_id "Phchi.S3G253200.t2"; gene_id "Phchi.S3G253200"
Phchi.S3	AUGUSTUS	stop_codon	17686647	17686649	.	+	0	transcript_id "Phchi.S3G253200.t2"; gene_id "Phchi.S3G253200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8778.t1 is derived from g5953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37917038	37918278	.	+	.	Phchi.S1G593700
Phchi.S1	AUGUSTUS	transcript	37917038	37918278	.	+	.	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	start_codon	37917038	37917040	.	+	0	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	CDS	37917038	37917277	0.9	+	0	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	exon	37917038	37917277	.	+	.	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	intron	37917278	37917384	.	+	.	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	CDS	37917385	37918278	0.88	+	0	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	exon	37917385	37918278	.	+	.	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
Phchi.S1	AUGUSTUS	stop_codon	37918279	37918281	.	+	0	transcript_id "Phchi.S1G593700.t1"; gene_id "Phchi.S1G593700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2795.t1 is derived from g9715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8932536	8934207	.	-	.	Phchi.S5G140400
Phchi.S5	AUGUSTUS	transcript	8932536	8934207	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	stop_codon	8932533	8932535	.	-	0	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	CDS	8932536	8932667	1	-	0	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	exon	8932536	8932667	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	intron	8932668	8932805	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	CDS	8932806	8932904	1	-	0	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	exon	8932806	8932904	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	intron	8932905	8933001	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	CDS	8933002	8933179	1	-	1	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	exon	8933002	8933179	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	intron	8933180	8933263	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	CDS	8933264	8933461	1	-	1	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	exon	8933264	8933461	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	intron	8933462	8933535	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	CDS	8933536	8933750	1	-	0	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	exon	8933536	8933750	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	intron	8933751	8933832	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	CDS	8933833	8934207	0.65	-	0	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	exon	8933833	8934207	.	-	.	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
Phchi.S5	AUGUSTUS	start_codon	8934205	8934207	.	-	0	transcript_id "Phchi.S5G140400.t1"; gene_id "Phchi.S5G140400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3133.t1 is derived from g302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1889196	1889537	.	+	.	Phchi.S1G029200
Phchi.S1	AUGUSTUS	transcript	1889196	1889537	.	+	.	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	start_codon	1889196	1889198	.	+	0	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	CDS	1889196	1889300	0.62	+	0	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	exon	1889196	1889300	.	+	.	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	intron	1889301	1889393	.	+	.	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	CDS	1889394	1889537	0.78	+	0	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	exon	1889394	1889537	.	+	.	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
Phchi.S1	AUGUSTUS	stop_codon	1889538	1889540	.	+	0	transcript_id "Phchi.S1G029200.t1"; gene_id "Phchi.S1G029200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2808.t1 is derived from g9728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8969336	8971895	.	+	.	Phchi.S5G141700
Phchi.S5	AUGUSTUS	transcript	8969336	8971895	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	start_codon	8969336	8969338	.	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8969336	8969539	1	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8969336	8969539	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8969540	8969638	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8969639	8969680	1	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8969639	8969680	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8969681	8969757	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8969758	8969851	1	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8969758	8969851	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8969852	8969941	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8969942	8970018	0.99	+	2	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8969942	8970018	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8970019	8970120	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8970121	8970209	1	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8970121	8970209	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8970210	8970299	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8970300	8970477	1	+	1	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8970300	8970477	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8970478	8970607	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8970608	8970789	1	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8970608	8970789	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8970790	8970875	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8970876	8970978	1	+	1	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8970876	8970978	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8970979	8971084	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8971085	8971416	1	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8971085	8971416	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	intron	8971417	8971489	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	CDS	8971490	8971895	1	+	1	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	exon	8971490	8971895	.	+	.	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
Phchi.S5	AUGUSTUS	stop_codon	8971896	8971898	.	+	0	transcript_id "Phchi.S5G141700.t1"; gene_id "Phchi.S5G141700"
# This transcript jg4448.t2 is derived from g1617.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4448.t3 is derived from g1617.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4448.t4 is derived from g1617.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4449.t1 is derived from g1619.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10559385	10561403	.	+	.	Phchi.S1G160800
Phchi.S1	AUGUSTUS	transcript	10559385	10560847	.	+	.	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	start_codon	10559385	10559387	.	+	0	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	CDS	10559385	10560528	0.27	+	0	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	exon	10559385	10560528	.	+	.	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	intron	10560529	10560800	.	+	.	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	CDS	10560801	10560847	0.45	+	2	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	exon	10560801	10560847	.	+	.	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	stop_codon	10560848	10560850	.	+	0	transcript_id "Phchi.S1G160800.t1"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	transcript	10559385	10561403	.	+	.	transcript_id "Phchi.S1G160800.t2"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	start_codon	10559385	10559387	.	+	0	transcript_id "Phchi.S1G160800.t2"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	CDS	10559385	10561403	0.49	+	0	transcript_id "Phchi.S1G160800.t2"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	exon	10559385	10561403	.	+	.	transcript_id "Phchi.S1G160800.t2"; gene_id "Phchi.S1G160800"
Phchi.S1	AUGUSTUS	stop_codon	10561404	10561406	.	+	0	transcript_id "Phchi.S1G160800.t2"; gene_id "Phchi.S1G160800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14192.t1 is derived from g12659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11403419	11403835	.	+	.	Phchi.S3G151100
Phchi.S3	AUGUSTUS	transcript	11403419	11403835	.	+	.	transcript_id "Phchi.S3G151100.t1"; gene_id "Phchi.S3G151100"
Phchi.S3	AUGUSTUS	start_codon	11403419	11403421	.	+	0	transcript_id "Phchi.S3G151100.t1"; gene_id "Phchi.S3G151100"
Phchi.S3	AUGUSTUS	CDS	11403419	11403835	0.84	+	0	transcript_id "Phchi.S3G151100.t1"; gene_id "Phchi.S3G151100"
Phchi.S3	AUGUSTUS	exon	11403419	11403835	.	+	.	transcript_id "Phchi.S3G151100.t1"; gene_id "Phchi.S3G151100"
Phchi.S3	AUGUSTUS	stop_codon	11403836	11403838	.	+	0	transcript_id "Phchi.S3G151100.t1"; gene_id "Phchi.S3G151100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2740.t1 is derived from g9660.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8512036	8514246	.	+	.	Phchi.S5G134900
Phchi.S5	AUGUSTUS	transcript	8512036	8514246	.	+	.	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	start_codon	8512036	8512038	.	+	0	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	CDS	8512036	8512612	0.24	+	0	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	exon	8512036	8512612	.	+	.	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	intron	8512613	8512874	.	+	.	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	CDS	8512875	8512964	0.28	+	2	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	exon	8512875	8512964	.	+	.	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	intron	8512965	8513056	.	+	.	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	CDS	8513057	8514246	0.74	+	2	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	exon	8513057	8514246	.	+	.	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	stop_codon	8514247	8514249	.	+	0	transcript_id "Phchi.S5G134900.t1"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	transcript	8513107	8514246	.	+	.	transcript_id "Phchi.S5G134900.t2"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	start_codon	8513107	8513109	.	+	0	transcript_id "Phchi.S5G134900.t2"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	CDS	8513107	8514246	0.54	+	0	transcript_id "Phchi.S5G134900.t2"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	exon	8513107	8514246	.	+	.	transcript_id "Phchi.S5G134900.t2"; gene_id "Phchi.S5G134900"
Phchi.S5	AUGUSTUS	stop_codon	8514247	8514249	.	+	0	transcript_id "Phchi.S5G134900.t2"; gene_id "Phchi.S5G134900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7280.t1 is derived from g4452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28125149	28127858	.	+	.	Phchi.S1G443900
Phchi.S1	AUGUSTUS	transcript	28125149	28127858	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	start_codon	28125149	28125151	.	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28125149	28125358	0.82	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28125149	28125358	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28125359	28125451	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28125452	28125827	0.99	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28125452	28125827	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28125828	28126029	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28126030	28126142	0.96	+	2	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28126030	28126142	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28126143	28126241	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28126242	28126364	0.95	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28126242	28126364	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28126365	28126445	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28126446	28126500	1	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28126446	28126500	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28126501	28126591	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28126592	28126771	1	+	2	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28126592	28126771	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28126772	28126865	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28126866	28126960	0.78	+	2	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28126866	28126960	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28126961	28127126	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28127127	28127257	0.73	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28127127	28127257	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	intron	28127258	28127590	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	CDS	28127591	28127858	0.96	+	1	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	exon	28127591	28127858	.	+	.	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
Phchi.S1	AUGUSTUS	stop_codon	28127859	28127861	.	+	0	transcript_id "Phchi.S1G443900.t1"; gene_id "Phchi.S1G443900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6021.t1 is derived from g3192.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20474007	20478386	.	-	.	Phchi.S1G318000
Phchi.S1	AUGUSTUS	transcript	20474007	20478386	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	stop_codon	20474004	20474006	.	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474007	20474093	0.96	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474007	20474093	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474094	20474219	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474220	20474297	0.79	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474220	20474297	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474298	20474391	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474392	20474487	0.89	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474392	20474487	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474488	20474580	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474581	20474637	1	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474581	20474637	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474638	20474735	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474736	20475047	0.98	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474736	20475047	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20475048	20475136	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20475137	20475268	1	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20475137	20475268	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20475269	20475398	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20475399	20476547	0.52	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20475399	20476547	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20476548	20476686	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20476687	20476745	1	-	2	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20476687	20476745	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20476746	20476992	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20476993	20477188	1	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20476993	20477188	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20477189	20477548	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20477549	20477629	0.57	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20477549	20477629	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20477630	20477698	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20477699	20477712	0.56	-	2	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20477699	20477712	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20477713	20478247	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20478248	20478386	0.57	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20478248	20478386	.	-	.	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	start_codon	20478384	20478386	.	-	0	transcript_id "Phchi.S1G318000.t1"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	transcript	20474007	20478386	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	stop_codon	20474004	20474006	.	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474007	20474093	0.97	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474007	20474093	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474094	20474219	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474220	20474297	0.78	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474220	20474297	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474298	20474391	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474392	20474487	0.82	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474392	20474487	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474488	20474580	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474581	20474637	1	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474581	20474637	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20474638	20474735	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20474736	20475047	0.99	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20474736	20475047	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20475048	20475136	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20475137	20475265	0.79	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20475137	20475265	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20475266	20475398	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20475399	20476547	0.71	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20475399	20476547	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20476548	20476686	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20476687	20476745	1	-	2	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20476687	20476745	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20476746	20476992	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20476993	20477188	1	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20476993	20477188	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20477189	20477548	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20477549	20477629	0.59	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20477549	20477629	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20477630	20477698	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20477699	20477712	0.58	-	2	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20477699	20477712	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	intron	20477713	20478247	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	CDS	20478248	20478386	0.6	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	exon	20478248	20478386	.	-	.	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
Phchi.S1	AUGUSTUS	start_codon	20478384	20478386	.	-	0	transcript_id "Phchi.S1G318000.t2"; gene_id "Phchi.S1G318000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15596.t1 is derived from g14065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20190478	20191929	.	+	.	Phchi.S3G291500
Phchi.S3	AUGUSTUS	transcript	20190478	20191929	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	start_codon	20190478	20190480	.	+	0	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	CDS	20190478	20190684	0.5	+	0	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	exon	20190478	20190684	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	intron	20190685	20190938	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	CDS	20190939	20191115	0.55	+	0	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	exon	20190939	20191115	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	intron	20191116	20191393	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	CDS	20191394	20191501	0.9	+	0	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	exon	20191394	20191501	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	intron	20191502	20191614	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	CDS	20191615	20191929	0.71	+	0	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	exon	20191615	20191929	.	+	.	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
Phchi.S3	AUGUSTUS	stop_codon	20191930	20191932	.	+	0	transcript_id "Phchi.S3G291500.t1"; gene_id "Phchi.S3G291500"
# This transcript jg3328.t2 is derived from g497.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3329.t1 is derived from g498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2940220	2940631	.	-	.	Phchi.S1G048800
Phchi.S1	AUGUSTUS	transcript	2940220	2940631	.	-	.	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	stop_codon	2940217	2940219	.	-	0	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	CDS	2940220	2940342	0.95	-	0	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	exon	2940220	2940342	.	-	.	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	intron	2940343	2940502	.	-	.	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	CDS	2940503	2940631	0.49	-	0	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	exon	2940503	2940631	.	-	.	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
Phchi.S1	AUGUSTUS	start_codon	2940629	2940631	.	-	0	transcript_id "Phchi.S1G048800.t1"; gene_id "Phchi.S1G048800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7357.t1 is derived from g4529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28753734	28758952	.	+	.	Phchi.S1G451600
Phchi.S1	AUGUSTUS	transcript	28753734	28758952	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	start_codon	28753734	28753736	.	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28753734	28754717	0.95	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28753734	28754717	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28754718	28754801	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28754802	28754867	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28754802	28754867	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28754868	28754953	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28754954	28754966	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28754954	28754966	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28754967	28755037	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28755038	28755084	0.87	+	2	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28755038	28755084	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28755085	28755208	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28755209	28755274	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28755209	28755274	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28755275	28755360	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28755361	28755546	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28755361	28755546	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28755547	28755632	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28755633	28755719	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28755633	28755719	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28755720	28755801	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28755802	28755915	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28755802	28755915	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28755916	28756045	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28756046	28756170	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28756046	28756170	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28756171	28756291	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28756292	28756400	1	+	1	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28756292	28756400	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28756401	28756485	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28756486	28756611	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28756486	28756611	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28756612	28756737	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28756738	28757061	0.92	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28756738	28757061	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28757062	28757188	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28757189	28757312	1	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28757189	28757312	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28757313	28757404	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28757405	28757429	0.96	+	2	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28757405	28757429	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28757430	28757523	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28757524	28757547	0.99	+	1	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28757524	28757547	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28757548	28757640	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28757641	28757695	0.47	+	1	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28757641	28757695	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	intron	28757696	28757854	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	CDS	28757855	28758952	0.47	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	exon	28757855	28758952	.	+	.	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
Phchi.S1	AUGUSTUS	stop_codon	28758953	28758955	.	+	0	transcript_id "Phchi.S1G451600.t1"; gene_id "Phchi.S1G451600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11312.t1 is derived from g15362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5320982	5323994	.	-	.	Phchi.S4G089400
Phchi.S4	AUGUSTUS	transcript	5320982	5323994	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	stop_codon	5320979	5320981	.	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5320982	5321158	0.93	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5320982	5321158	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5321159	5321256	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5321257	5321330	0.93	-	2	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5321257	5321330	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5321331	5321418	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5321419	5321454	0.93	-	2	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5321419	5321454	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5321455	5321819	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5321820	5321880	0.74	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5321820	5321880	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5321881	5321971	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5321972	5322007	1	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5321972	5322007	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5322008	5322171	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5322172	5322236	1	-	2	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5322172	5322236	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5322237	5322359	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5322360	5322438	1	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5322360	5322438	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5322439	5322604	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5322605	5322679	1	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5322605	5322679	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5322680	5322858	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5322859	5322935	0.71	-	2	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5322859	5322935	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5322936	5323325	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5323326	5323449	0.55	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5323326	5323449	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	intron	5323450	5323526	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	CDS	5323527	5323994	0.65	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	exon	5323527	5323994	.	-	.	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
Phchi.S4	AUGUSTUS	start_codon	5323992	5323994	.	-	0	transcript_id "Phchi.S4G089400.t1"; gene_id "Phchi.S4G089400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9113.t1 is derived from g6288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39885692	39887604	.	+	.	Phchi.S1G627200
Phchi.S1	AUGUSTUS	transcript	39885692	39887604	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	start_codon	39885692	39885694	.	+	0	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	CDS	39885692	39886342	1	+	0	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	exon	39885692	39886342	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	intron	39886343	39886508	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	CDS	39886509	39886646	1	+	0	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	exon	39886509	39886646	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	intron	39886647	39886775	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	CDS	39886776	39886910	1	+	0	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	exon	39886776	39886910	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	intron	39886911	39887003	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	CDS	39887004	39887197	1	+	0	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	exon	39887004	39887197	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	intron	39887198	39887285	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	CDS	39887286	39887604	0.49	+	1	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	exon	39887286	39887604	.	+	.	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
Phchi.S1	AUGUSTUS	stop_codon	39887605	39887607	.	+	0	transcript_id "Phchi.S1G627200.t1"; gene_id "Phchi.S1G627200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3017.t1 is derived from g186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1165924	1166675	.	+	.	Phchi.S1G017600
Phchi.S1	AUGUSTUS	transcript	1165924	1166675	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	start_codon	1165924	1165926	.	+	0	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	CDS	1165924	1166030	1	+	0	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	exon	1165924	1166030	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	intron	1166031	1166149	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	CDS	1166150	1166345	1	+	1	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	exon	1166150	1166345	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	intron	1166346	1166509	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	CDS	1166510	1166529	0.99	+	0	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	exon	1166510	1166529	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	intron	1166530	1166647	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	CDS	1166648	1166675	0.99	+	1	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	exon	1166648	1166675	.	+	.	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
Phchi.S1	AUGUSTUS	stop_codon	1166676	1166678	.	+	0	transcript_id "Phchi.S1G017600.t1"; gene_id "Phchi.S1G017600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2411.t1 is derived from g9331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6527858	6528598	.	-	.	Phchi.S5G102000
Phchi.S5	AUGUSTUS	transcript	6527858	6528598	.	-	.	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	stop_codon	6527855	6527857	.	-	0	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	CDS	6527858	6528067	1	-	0	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	exon	6527858	6528067	.	-	.	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	intron	6528068	6528152	.	-	.	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	CDS	6528153	6528288	1	-	1	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	exon	6528153	6528288	.	-	.	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	intron	6528289	6528377	.	-	.	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	CDS	6528378	6528598	1	-	0	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	exon	6528378	6528598	.	-	.	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
Phchi.S5	AUGUSTUS	start_codon	6528596	6528598	.	-	0	transcript_id "Phchi.S5G102000.t1"; gene_id "Phchi.S5G102000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2646.t1 is derived from g9566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7955353	7955613	.	-	.	Phchi.S5G125500
Phchi.S5	AUGUSTUS	transcript	7955353	7955613	.	-	.	transcript_id "Phchi.S5G125500.t1"; gene_id "Phchi.S5G125500"
Phchi.S5	AUGUSTUS	stop_codon	7955350	7955352	.	-	0	transcript_id "Phchi.S5G125500.t1"; gene_id "Phchi.S5G125500"
Phchi.S5	AUGUSTUS	CDS	7955353	7955613	0.41	-	0	transcript_id "Phchi.S5G125500.t1"; gene_id "Phchi.S5G125500"
Phchi.S5	AUGUSTUS	exon	7955353	7955613	.	-	.	transcript_id "Phchi.S5G125500.t1"; gene_id "Phchi.S5G125500"
Phchi.S5	AUGUSTUS	start_codon	7955611	7955613	.	-	0	transcript_id "Phchi.S5G125500.t1"; gene_id "Phchi.S5G125500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10103.t1 is derived from g7279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45753341	45754354	.	+	.	Phchi.S1G726200
Phchi.S1	AUGUSTUS	transcript	45753341	45754354	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	start_codon	45753341	45753343	.	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	CDS	45753341	45753343	1	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	exon	45753341	45753343	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	intron	45753344	45753432	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	CDS	45753433	45753540	1	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	exon	45753433	45753540	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	intron	45753541	45753648	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	CDS	45753649	45753711	1	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	exon	45753649	45753711	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	intron	45753712	45753823	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	CDS	45753824	45753895	0.9	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	exon	45753824	45753895	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	intron	45753896	45754008	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	CDS	45754009	45754203	0.68	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	exon	45754009	45754203	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	intron	45754204	45754294	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	CDS	45754295	45754354	0.36	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	exon	45754295	45754354	.	+	.	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
Phchi.S1	AUGUSTUS	stop_codon	45754355	45754357	.	+	0	transcript_id "Phchi.S1G726200.t1"; gene_id "Phchi.S1G726200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3135.t1 is derived from g304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1906694	1907763	.	+	.	Phchi.S1G029400
Phchi.S1	AUGUSTUS	transcript	1906694	1907763	.	+	.	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	start_codon	1906694	1906696	.	+	0	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	CDS	1906694	1907243	0.87	+	0	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	exon	1906694	1907243	.	+	.	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	intron	1907244	1907365	.	+	.	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	CDS	1907366	1907763	0.81	+	2	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	exon	1907366	1907763	.	+	.	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
Phchi.S1	AUGUSTUS	stop_codon	1907764	1907766	.	+	0	transcript_id "Phchi.S1G029400.t1"; gene_id "Phchi.S1G029400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7257.t1 is derived from g4429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27889130	27891549	.	-	.	Phchi.S1G441600
Phchi.S1	AUGUSTUS	transcript	27889130	27891549	.	-	.	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	stop_codon	27889127	27889129	.	-	0	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	CDS	27889130	27889737	0.95	-	2	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	exon	27889130	27889737	.	-	.	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	intron	27889738	27889833	.	-	.	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	CDS	27889834	27891458	0.76	-	1	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	exon	27889834	27891458	.	-	.	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	intron	27891459	27891535	.	-	.	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	CDS	27891536	27891549	1	-	0	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	exon	27891536	27891549	.	-	.	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
Phchi.S1	AUGUSTUS	start_codon	27891547	27891549	.	-	0	transcript_id "Phchi.S1G441600.t1"; gene_id "Phchi.S1G441600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10141.t1 is derived from g7317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45960887	45961462	.	-	.	Phchi.S1G730000
Phchi.S1	AUGUSTUS	transcript	45960887	45961462	.	-	.	transcript_id "Phchi.S1G730000.t1"; gene_id "Phchi.S1G730000"
Phchi.S1	AUGUSTUS	stop_codon	45960884	45960886	.	-	0	transcript_id "Phchi.S1G730000.t1"; gene_id "Phchi.S1G730000"
Phchi.S1	AUGUSTUS	CDS	45960887	45961462	0.71	-	0	transcript_id "Phchi.S1G730000.t1"; gene_id "Phchi.S1G730000"
Phchi.S1	AUGUSTUS	exon	45960887	45961462	.	-	.	transcript_id "Phchi.S1G730000.t1"; gene_id "Phchi.S1G730000"
Phchi.S1	AUGUSTUS	start_codon	45961460	45961462	.	-	0	transcript_id "Phchi.S1G730000.t1"; gene_id "Phchi.S1G730000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4258.t1 is derived from g1427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9201105	9203014	.	-	.	Phchi.S1G141700
Phchi.S1	AUGUSTUS	transcript	9201105	9203014	.	-	.	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	stop_codon	9201102	9201104	.	-	0	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	CDS	9201105	9201445	0.52	-	2	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	exon	9201105	9201445	.	-	.	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	intron	9201446	9201602	.	-	.	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	CDS	9201603	9202298	0.66	-	2	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	exon	9201603	9202298	.	-	.	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	intron	9202299	9202419	.	-	.	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	CDS	9202420	9203014	1	-	0	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	exon	9202420	9203014	.	-	.	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
Phchi.S1	AUGUSTUS	start_codon	9203012	9203014	.	-	0	transcript_id "Phchi.S1G141700.t1"; gene_id "Phchi.S1G141700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10545.t1 is derived from g14595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	891895	895853	.	+	.	Phchi.S4G012700
Phchi.S4	AUGUSTUS	transcript	891895	895853	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	start_codon	891895	891897	.	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	891895	892825	0.3	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	891895	892825	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	892826	893007	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	893008	893069	0.4	+	2	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	893008	893069	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	893070	893151	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	893152	893274	1	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	893152	893274	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	893275	893401	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	893402	893475	1	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	893402	893475	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	893476	893557	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	893558	893630	1	+	1	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	893558	893630	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	893631	893719	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	893720	893794	0.96	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	893720	893794	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	893795	893982	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	893983	894068	0.98	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	893983	894068	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	894069	894186	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	894187	894256	1	+	1	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	894187	894256	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	894257	894352	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	894353	894511	0.99	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	894353	894511	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	894512	894618	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	894619	894846	0.97	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	894619	894846	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	894847	894931	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	894932	895036	1	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	894932	895036	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	895037	895123	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	895124	895216	1	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	895124	895216	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	895217	895291	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	895292	895351	1	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	895292	895351	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	895352	895451	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	895452	895540	1	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	895452	895540	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	895541	895624	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	895625	895705	1	+	1	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	895625	895705	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	intron	895706	895783	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	CDS	895784	895853	1	+	1	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	exon	895784	895853	.	+	.	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
Phchi.S4	AUGUSTUS	stop_codon	895854	895856	.	+	0	transcript_id "Phchi.S4G012700.t1"; gene_id "Phchi.S4G012700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8607.t1 is derived from g5782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36895639	36896543	.	+	.	Phchi.S1G576600
Phchi.S1	AUGUSTUS	transcript	36895639	36896543	.	+	.	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	start_codon	36895639	36895641	.	+	0	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	CDS	36895639	36895668	0.49	+	0	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	exon	36895639	36895668	.	+	.	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	intron	36895669	36896015	.	+	.	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	CDS	36896016	36896543	0.98	+	0	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	exon	36896016	36896543	.	+	.	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
Phchi.S1	AUGUSTUS	stop_codon	36896544	36896546	.	+	0	transcript_id "Phchi.S1G576600.t1"; gene_id "Phchi.S1G576600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13873.t1 is derived from g12340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9404040	9405281	.	+	.	Phchi.S3G119200
Phchi.S3	AUGUSTUS	transcript	9404040	9405281	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	start_codon	9404040	9404042	.	+	0	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	CDS	9404040	9404219	0.93	+	0	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	exon	9404040	9404219	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	intron	9404220	9404320	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	CDS	9404321	9404455	1	+	0	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	exon	9404321	9404455	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	intron	9404456	9404534	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	CDS	9404535	9404766	1	+	0	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	exon	9404535	9404766	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	intron	9404767	9404842	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	CDS	9404843	9405046	1	+	2	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	exon	9404843	9405046	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	intron	9405047	9405123	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	CDS	9405124	9405281	0.9	+	2	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	exon	9405124	9405281	.	+	.	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
Phchi.S3	AUGUSTUS	stop_codon	9405282	9405284	.	+	0	transcript_id "Phchi.S3G119200.t1"; gene_id "Phchi.S3G119200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7370.t1 is derived from g4542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28803790	28811009	.	-	.	Phchi.S1G452900
Phchi.S1	AUGUSTUS	transcript	28803790	28811009	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	stop_codon	28803787	28803789	.	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28803790	28804037	0.84	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28803790	28804037	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28804038	28804119	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28804120	28804539	1	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28804120	28804539	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28804540	28804623	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28804624	28805296	0.78	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28804624	28805296	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28805297	28805376	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28805377	28805577	1	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28805377	28805577	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28805578	28805657	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28805658	28806270	0.99	-	1	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28805658	28806270	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28806271	28806374	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28806375	28806565	1	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28806375	28806565	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28806566	28806657	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28806658	28806842	0.94	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28806658	28806842	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28806843	28807086	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28807087	28807093	0.76	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28807087	28807093	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28807094	28807316	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28807317	28807478	1	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28807317	28807478	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28807479	28807566	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28807567	28807653	1	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28807567	28807653	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28807654	28807761	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28807762	28807900	0.91	-	1	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28807762	28807900	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28807901	28808018	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28808019	28808120	1	-	1	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28808019	28808120	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28808121	28808238	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28808239	28808375	0.67	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28808239	28808375	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28808376	28808532	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28808533	28808705	0.63	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28808533	28808705	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28808706	28808843	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28808844	28808947	0.27	-	1	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28808844	28808947	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28808948	28809129	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28809130	28809197	0.41	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28809130	28809197	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28809198	28809310	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28809311	28809366	0.93	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28809311	28809366	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28809367	28809501	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28809502	28809751	0.94	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28809502	28809751	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28809752	28809849	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28809850	28809905	0.78	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28809850	28809905	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28809906	28810065	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28810066	28810434	0.98	-	2	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28810066	28810434	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28810435	28810523	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28810524	28810632	0.98	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28810524	28810632	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	intron	28810633	28810766	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	CDS	28810767	28811009	0.86	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	exon	28810767	28811009	.	-	.	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
Phchi.S1	AUGUSTUS	start_codon	28811007	28811009	.	-	0	transcript_id "Phchi.S1G452900.t1"; gene_id "Phchi.S1G452900"
# This transcript jg11011.t2 is derived from g15061.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11012.t1 is derived from g15062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3629120	3638104	.	+	.	Phchi.S4G059400
Phchi.S4	AUGUSTUS	transcript	3629120	3638104	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	start_codon	3629120	3629122	.	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629120	3629139	0.99	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629120	3629139	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629140	3629234	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629235	3629426	0.95	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629235	3629426	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629427	3629573	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629574	3629593	0.67	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629574	3629593	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629594	3629689	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629690	3629778	1	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629690	3629778	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629779	3629870	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629871	3630032	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629871	3630032	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3630033	3630167	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3630168	3630490	0.69	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3630168	3630490	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3630491	3630588	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3630589	3631020	0.58	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3630589	3631020	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631021	3631104	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631105	3631234	1	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631105	3631234	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631235	3631364	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631365	3631478	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631365	3631478	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631479	3631574	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631575	3631740	0.98	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631575	3631740	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631741	3631862	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631863	3631986	0.9	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631863	3631986	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631987	3632184	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3632185	3632402	1	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3632185	3632402	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3632403	3632499	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3632500	3632597	1	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3632500	3632597	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3632598	3632753	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3632754	3632898	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3632754	3632898	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3632899	3633051	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633052	3633175	1	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633052	3633175	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633176	3633254	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633255	3633351	1	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633255	3633351	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633352	3633444	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633445	3633552	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633445	3633552	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633553	3633625	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633626	3633704	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633626	3633704	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633705	3633804	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633805	3634074	0.97	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633805	3634074	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3634075	3634171	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3634172	3634515	1	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3634172	3634515	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3634516	3634997	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3634998	3635113	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3634998	3635113	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635114	3635224	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635225	3635411	1	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635225	3635411	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635412	3635500	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635501	3635632	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635501	3635632	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635633	3635712	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635713	3635883	0.9	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635713	3635883	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635884	3635991	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635992	3636137	0.84	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635992	3636137	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636138	3636225	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636226	3636274	1	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636226	3636274	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636275	3636408	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636409	3636468	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636409	3636468	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636469	3636552	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636553	3636733	0.77	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636553	3636733	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636734	3636837	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636838	3637016	0.92	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636838	3637016	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637017	3637096	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637097	3637232	1	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637097	3637232	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637233	3637308	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637309	3637378	1	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637309	3637378	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637379	3637473	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637474	3637646	1	+	1	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637474	3637646	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637647	3637764	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637765	3637842	0.62	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637765	3637842	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637843	3637955	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637956	3638104	0.63	+	2	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637956	3638104	.	+	.	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	stop_codon	3638105	3638107	.	+	0	transcript_id "Phchi.S4G059400.t1"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	transcript	3629120	3638104	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	start_codon	3629120	3629122	.	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629120	3629139	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629120	3629139	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629140	3629234	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629235	3629426	0.92	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629235	3629426	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629427	3629573	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629574	3629593	0.57	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629574	3629593	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629594	3629689	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629690	3629778	1	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629690	3629778	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3629779	3629870	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3629871	3630032	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3629871	3630032	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3630033	3630167	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3630168	3630490	0.59	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3630168	3630490	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3630491	3630588	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3630589	3631020	0.4	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3630589	3631020	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631021	3631104	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631105	3631234	1	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631105	3631234	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631235	3631364	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631365	3631478	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631365	3631478	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631479	3631574	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631575	3631740	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631575	3631740	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631741	3631862	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3631863	3631986	0.88	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3631863	3631986	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3631987	3632184	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3632185	3632402	1	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3632185	3632402	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3632403	3632499	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3632500	3632597	1	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3632500	3632597	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3632598	3632753	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3632754	3632898	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3632754	3632898	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3632899	3633051	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633052	3633175	1	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633052	3633175	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633176	3633254	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633255	3633351	1	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633255	3633351	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633352	3633444	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633445	3633552	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633445	3633552	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633553	3633625	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633626	3633704	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633626	3633704	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3633705	3633804	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3633805	3634074	0.97	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3633805	3634074	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3634075	3634198	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3634199	3634515	0.88	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3634199	3634515	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3634516	3634997	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3634998	3635113	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3634998	3635113	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635114	3635224	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635225	3635411	1	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635225	3635411	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635412	3635500	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635501	3635632	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635501	3635632	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635633	3635712	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635713	3635883	0.83	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635713	3635883	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3635884	3635991	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3635992	3636137	0.77	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3635992	3636137	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636138	3636225	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636226	3636274	1	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636226	3636274	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636275	3636408	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636409	3636468	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636409	3636468	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636469	3636552	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636553	3636733	0.77	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636553	3636733	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3636734	3636837	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3636838	3637016	0.95	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3636838	3637016	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637017	3637096	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637097	3637232	1	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637097	3637232	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637233	3637308	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637309	3637378	1	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637309	3637378	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637379	3637473	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637474	3637646	1	+	1	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637474	3637646	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637647	3637764	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637765	3637842	0.55	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637765	3637842	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	intron	3637843	3637955	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	CDS	3637956	3638104	0.57	+	2	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	exon	3637956	3638104	.	+	.	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
Phchi.S4	AUGUSTUS	stop_codon	3638105	3638107	.	+	0	transcript_id "Phchi.S4G059400.t2"; gene_id "Phchi.S4G059400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10052.t1 is derived from g7228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45484441	45486235	.	+	.	Phchi.S1G721100
Phchi.S1	AUGUSTUS	transcript	45484441	45486235	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	start_codon	45484441	45484443	.	+	0	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	CDS	45484441	45484507	0.46	+	0	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	exon	45484441	45484507	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	intron	45484508	45484604	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	CDS	45484605	45485116	0.56	+	2	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	exon	45484605	45485116	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	intron	45485117	45485209	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	CDS	45485210	45485431	0.46	+	0	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	exon	45485210	45485431	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	intron	45485432	45485551	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	CDS	45485552	45486235	0.44	+	0	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	exon	45485552	45486235	.	+	.	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
Phchi.S1	AUGUSTUS	stop_codon	45486236	45486238	.	+	0	transcript_id "Phchi.S1G721100.t1"; gene_id "Phchi.S1G721100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9729.t1 is derived from g6905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43430408	43431052	.	-	.	Phchi.S1G688800
Phchi.S1	AUGUSTUS	transcript	43430408	43431052	.	-	.	transcript_id "Phchi.S1G688800.t1"; gene_id "Phchi.S1G688800"
Phchi.S1	AUGUSTUS	stop_codon	43430405	43430407	.	-	0	transcript_id "Phchi.S1G688800.t1"; gene_id "Phchi.S1G688800"
Phchi.S1	AUGUSTUS	CDS	43430408	43431052	0.74	-	0	transcript_id "Phchi.S1G688800.t1"; gene_id "Phchi.S1G688800"
Phchi.S1	AUGUSTUS	exon	43430408	43431052	.	-	.	transcript_id "Phchi.S1G688800.t1"; gene_id "Phchi.S1G688800"
Phchi.S1	AUGUSTUS	start_codon	43431050	43431052	.	-	0	transcript_id "Phchi.S1G688800.t1"; gene_id "Phchi.S1G688800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7712.t1 is derived from g4886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30752222	30756742	.	-	.	Phchi.S1G487100
Phchi.S1	AUGUSTUS	transcript	30752222	30756742	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	stop_codon	30752219	30752221	.	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30752222	30752311	0.93	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30752222	30752311	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30752312	30752398	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30752399	30752524	0.61	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30752399	30752524	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30752525	30752600	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30752601	30752762	0.82	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30752601	30752762	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30752763	30752880	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30752881	30752917	0.86	-	1	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30752881	30752917	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30752918	30752988	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30752989	30753074	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30752989	30753074	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30753075	30753172	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30753173	30753265	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30753173	30753265	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30753266	30753339	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30753340	30753414	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30753340	30753414	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30753415	30753499	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30753500	30753595	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30753500	30753595	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30753596	30753745	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30753746	30753892	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30753746	30753892	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30753893	30754055	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30754056	30754103	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30754056	30754103	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30754104	30754183	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30754184	30754284	1	-	2	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30754184	30754284	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30754285	30754373	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30754374	30754485	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30754374	30754485	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30754486	30754601	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30754602	30754686	0.93	-	1	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30754602	30754686	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30754687	30754845	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30754846	30755001	0.62	-	1	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30754846	30755001	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30755002	30755108	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30755109	30755200	0.49	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30755109	30755200	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30755201	30755317	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30755318	30755401	0.99	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30755318	30755401	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30755402	30755490	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30755491	30755541	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30755491	30755541	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30755542	30755635	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30755636	30755728	0.88	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30755636	30755728	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30755729	30755838	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30755839	30755907	0.7	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30755839	30755907	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30755908	30755995	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30755996	30756055	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30755996	30756055	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30756056	30756192	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30756193	30756217	1	-	1	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30756193	30756217	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30756218	30756391	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30756392	30756471	1	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30756392	30756471	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	intron	30756472	30756565	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	CDS	30756566	30756742	0.98	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	exon	30756566	30756742	.	-	.	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
Phchi.S1	AUGUSTUS	start_codon	30756740	30756742	.	-	0	transcript_id "Phchi.S1G487100.t1"; gene_id "Phchi.S1G487100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7884.t1 is derived from g5058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31750605	31753261	.	-	.	Phchi.S1G504300
Phchi.S1	AUGUSTUS	transcript	31750605	31753261	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	stop_codon	31750602	31750604	.	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31750605	31750654	1	-	2	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31750605	31750654	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31750655	31750754	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31750755	31750926	0.74	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31750755	31750926	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31750927	31751148	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31751149	31751211	0.63	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31751149	31751211	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31751212	31751334	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31751335	31751403	0.99	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31751335	31751403	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31751404	31751516	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31751517	31751579	0.87	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31751517	31751579	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31751580	31751687	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31751688	31751902	0.87	-	2	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31751688	31751902	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31751903	31752019	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31752020	31752259	0.99	-	2	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31752020	31752259	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31752260	31752360	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31752361	31752537	0.92	-	2	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31752361	31752537	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31752538	31752676	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31752677	31752804	0.68	-	1	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31752677	31752804	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31752805	31752872	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31752873	31752909	0.7	-	2	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31752873	31752909	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	intron	31752910	31753008	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	CDS	31753009	31753261	0.73	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	exon	31753009	31753261	.	-	.	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
Phchi.S1	AUGUSTUS	start_codon	31753259	31753261	.	-	0	transcript_id "Phchi.S1G504300.t1"; gene_id "Phchi.S1G504300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5728.t1 is derived from g2898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18583072	18584457	.	+	.	Phchi.S1G288700
Phchi.S1	AUGUSTUS	transcript	18583072	18584457	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	start_codon	18583072	18583074	.	+	0	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	CDS	18583072	18583368	0.38	+	0	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	exon	18583072	18583368	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	intron	18583369	18583529	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	CDS	18583530	18583970	0.24	+	0	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	exon	18583530	18583970	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	intron	18583971	18584037	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	CDS	18584038	18584238	0.5	+	0	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	exon	18584038	18584238	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	intron	18584239	18584352	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	CDS	18584353	18584457	0.81	+	0	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	exon	18584353	18584457	.	+	.	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
Phchi.S1	AUGUSTUS	stop_codon	18584458	18584460	.	+	0	transcript_id "Phchi.S1G288700.t1"; gene_id "Phchi.S1G288700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15131.t1 is derived from g13599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17203249	17204279	.	-	.	Phchi.S3G245000
Phchi.S3	AUGUSTUS	transcript	17203249	17204279	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	stop_codon	17203246	17203248	.	-	0	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	CDS	17203249	17203508	0.99	-	2	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	exon	17203249	17203508	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	intron	17203509	17203604	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	CDS	17203605	17203696	1	-	1	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	exon	17203605	17203696	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	intron	17203697	17203790	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	CDS	17203791	17204065	1	-	0	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	exon	17203791	17204065	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	intron	17204066	17204213	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	CDS	17204214	17204279	1	-	0	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	exon	17204214	17204279	.	-	.	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
Phchi.S3	AUGUSTUS	start_codon	17204277	17204279	.	-	0	transcript_id "Phchi.S3G245000.t1"; gene_id "Phchi.S3G245000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1314.t1 is derived from g11097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8958197	8965421	.	+	.	Phchi.S6G127300
Phchi.S6	AUGUSTUS	transcript	8958197	8965421	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	start_codon	8958197	8958199	.	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8958197	8958232	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8958197	8958232	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8958233	8958448	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8958449	8958618	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8958449	8958618	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8958619	8958797	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8958798	8959005	1	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8958798	8959005	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8959006	8959129	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8959130	8959295	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8959130	8959295	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8959296	8959381	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8959382	8959511	0.95	+	2	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8959382	8959511	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8959512	8959621	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8959622	8959736	0.91	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8959622	8959736	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8959737	8959834	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8959835	8959844	0.85	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8959835	8959844	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8959845	8959954	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8959955	8959994	0.81	+	2	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8959955	8959994	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8959995	8960151	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8960152	8960275	1	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8960152	8960275	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8960276	8960476	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8960477	8960527	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8960477	8960527	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8960528	8960612	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8960613	8960695	0.96	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8960613	8960695	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8960696	8960813	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8960814	8960902	1	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8960814	8960902	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8960903	8961001	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8961002	8961099	1	+	2	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8961002	8961099	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8961100	8961200	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8961201	8961299	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8961201	8961299	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8961300	8961398	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8961399	8961515	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8961399	8961515	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8961516	8961682	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8961683	8961766	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8961683	8961766	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8961767	8961886	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8961887	8962027	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8961887	8962027	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8962028	8962172	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8962173	8962265	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8962173	8962265	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8962266	8962395	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8962396	8962517	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8962396	8962517	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8962518	8962603	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8962604	8962766	1	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8962604	8962766	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8962767	8962849	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8962850	8963095	0.94	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8962850	8963095	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8963096	8963185	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8963186	8963431	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8963186	8963431	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8963432	8963516	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8963517	8963702	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8963517	8963702	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8963703	8963799	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8963800	8963946	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8963800	8963946	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8963947	8964058	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8964059	8964175	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8964059	8964175	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8964176	8964263	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8964264	8964432	1	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8964264	8964432	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8964433	8964570	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8964571	8964648	1	+	2	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8964571	8964648	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8964649	8964740	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8964741	8964879	1	+	2	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8964741	8964879	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8964880	8964967	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8964968	8965110	0.86	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8964968	8965110	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8965111	8965228	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8965229	8965310	0.59	+	2	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8965229	8965310	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	intron	8965311	8965393	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	CDS	8965394	8965421	0.93	+	1	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	exon	8965394	8965421	.	+	.	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
Phchi.S6	AUGUSTUS	stop_codon	8965422	8965424	.	+	0	transcript_id "Phchi.S6G127300.t1"; gene_id "Phchi.S6G127300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6276.t1 is derived from g3448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22038126	22041019	.	+	.	Phchi.S1G343500
Phchi.S1	AUGUSTUS	transcript	22038126	22041019	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	start_codon	22038126	22038128	.	+	0	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	CDS	22038126	22038231	0.89	+	0	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	exon	22038126	22038231	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	intron	22038232	22038531	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	CDS	22038532	22038544	0.55	+	2	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	exon	22038532	22038544	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	intron	22038545	22038733	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	CDS	22038734	22039601	0.66	+	1	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	exon	22038734	22039601	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	intron	22039602	22040743	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	CDS	22040744	22041019	1	+	0	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	exon	22040744	22041019	.	+	.	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
Phchi.S1	AUGUSTUS	stop_codon	22041020	22041022	.	+	0	transcript_id "Phchi.S1G343500.t1"; gene_id "Phchi.S1G343500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7521.t1 is derived from g4695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29822042	29824051	.	-	.	Phchi.S1G468000
Phchi.S1	AUGUSTUS	transcript	29822042	29824051	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	stop_codon	29822039	29822041	.	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	CDS	29822042	29822311	1	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	exon	29822042	29822311	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	intron	29822312	29822411	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	CDS	29822412	29822542	1	-	2	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	exon	29822412	29822542	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	intron	29822543	29822647	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	CDS	29822648	29822849	0.94	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	exon	29822648	29822849	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	intron	29822850	29822958	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	CDS	29822959	29823057	1	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	exon	29822959	29823057	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	intron	29823058	29823162	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	CDS	29823163	29823249	1	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	exon	29823163	29823249	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	intron	29823250	29823766	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	CDS	29823767	29824051	1	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	exon	29823767	29824051	.	-	.	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
Phchi.S1	AUGUSTUS	start_codon	29824049	29824051	.	-	0	transcript_id "Phchi.S1G468000.t1"; gene_id "Phchi.S1G468000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10178.t1 is derived from g7354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46160865	46162336	.	-	.	Phchi.S1G733700
Phchi.S1	AUGUSTUS	transcript	46160865	46162336	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	stop_codon	46160862	46160864	.	-	0	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	CDS	46160865	46161227	0.81	-	0	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	exon	46160865	46161227	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	intron	46161228	46161304	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	CDS	46161305	46161739	0.39	-	0	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	exon	46161305	46161739	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	intron	46161740	46161825	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	CDS	46161826	46161966	0.52	-	0	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	exon	46161826	46161966	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	intron	46161967	46162058	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	CDS	46162059	46162126	0.33	-	2	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	exon	46162059	46162126	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	intron	46162127	46162290	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	CDS	46162291	46162336	0.38	-	0	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	exon	46162291	46162336	.	-	.	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
Phchi.S1	AUGUSTUS	start_codon	46162334	46162336	.	-	0	transcript_id "Phchi.S1G733700.t1"; gene_id "Phchi.S1G733700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7485.t1 is derived from g4658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29583702	29585563	.	+	.	Phchi.S1G464400
Phchi.S1	AUGUSTUS	transcript	29583702	29585563	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	start_codon	29583702	29583704	.	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29583702	29583759	1	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29583702	29583759	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29583760	29583852	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29583853	29583968	1	+	2	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29583853	29583968	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29583969	29584123	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29584124	29584183	1	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29584124	29584183	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29584184	29584326	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29584327	29584512	0.92	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29584327	29584512	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29584513	29584617	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29584618	29584722	1	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29584618	29584722	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29584723	29584809	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29584810	29584906	1	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29584810	29584906	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29584907	29585030	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29585031	29585138	1	+	2	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29585031	29585138	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29585139	29585224	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29585225	29585360	1	+	2	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29585225	29585360	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	intron	29585361	29585454	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	CDS	29585455	29585563	1	+	1	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	exon	29585455	29585563	.	+	.	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
Phchi.S1	AUGUSTUS	stop_codon	29585564	29585566	.	+	0	transcript_id "Phchi.S1G464400.t1"; gene_id "Phchi.S1G464400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg636.t1 is derived from g10418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4534915	4535351	.	+	.	Phchi.S6G059500
Phchi.S6	AUGUSTUS	transcript	4534915	4535351	.	+	.	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	start_codon	4534915	4534917	.	+	0	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	CDS	4534915	4535107	0.96	+	0	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	exon	4534915	4535107	.	+	.	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	intron	4535108	4535319	.	+	.	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	CDS	4535320	4535351	0.94	+	2	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	exon	4535320	4535351	.	+	.	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
Phchi.S6	AUGUSTUS	stop_codon	4535352	4535354	.	+	0	transcript_id "Phchi.S6G059500.t1"; gene_id "Phchi.S6G059500"
# This transcript jg12309.t2 is derived from g7985.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12310.t1 is derived from g7986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10144263	10145320	.	-	.	Phchi.S2G039000
Phchi.S2	AUGUSTUS	transcript	10144263	10145320	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	stop_codon	10144260	10144262	.	-	0	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	CDS	10144263	10144392	0.53	-	1	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	exon	10144263	10144392	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	intron	10144393	10144535	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	CDS	10144536	10144742	0.92	-	1	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	exon	10144536	10144742	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	intron	10144743	10144853	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	CDS	10144854	10145044	0.92	-	0	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	exon	10144854	10145044	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	intron	10145045	10145173	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	CDS	10145174	10145320	0.48	-	0	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	exon	10145174	10145320	.	-	.	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
Phchi.S2	AUGUSTUS	start_codon	10145318	10145320	.	-	0	transcript_id "Phchi.S2G039000.t1"; gene_id "Phchi.S2G039000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6838.t1 is derived from g4010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25489309	25490377	.	-	.	Phchi.S1G399700
Phchi.S1	AUGUSTUS	transcript	25489309	25490377	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	stop_codon	25489306	25489308	.	-	0	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	CDS	25489309	25489316	0.84	-	2	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	exon	25489309	25489316	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	intron	25489317	25489449	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	CDS	25489450	25489553	0.84	-	1	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	exon	25489450	25489553	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	intron	25489554	25489964	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	CDS	25489965	25490064	1	-	2	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	exon	25489965	25490064	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	intron	25490065	25490208	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	CDS	25490209	25490377	1	-	0	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	exon	25490209	25490377	.	-	.	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
Phchi.S1	AUGUSTUS	start_codon	25490375	25490377	.	-	0	transcript_id "Phchi.S1G399700.t1"; gene_id "Phchi.S1G399700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8302.t1 is derived from g5477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35162064	35162758	.	+	.	Phchi.S1G546100
Phchi.S1	AUGUSTUS	transcript	35162064	35162758	.	+	.	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	start_codon	35162064	35162066	.	+	0	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	CDS	35162064	35162195	0.88	+	0	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	exon	35162064	35162195	.	+	.	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	intron	35162196	35162354	.	+	.	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	CDS	35162355	35162543	0.45	+	0	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	exon	35162355	35162543	.	+	.	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	intron	35162544	35162668	.	+	.	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	CDS	35162669	35162758	0.72	+	0	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	exon	35162669	35162758	.	+	.	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
Phchi.S1	AUGUSTUS	stop_codon	35162759	35162761	.	+	0	transcript_id "Phchi.S1G546100.t1"; gene_id "Phchi.S1G546100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10839.t1 is derived from g14889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2410679	2411926	.	+	.	Phchi.S4G042100
Phchi.S4	AUGUSTUS	transcript	2410679	2411926	.	+	.	transcript_id "Phchi.S4G042100.t1"; gene_id "Phchi.S4G042100"
Phchi.S4	AUGUSTUS	start_codon	2410679	2410681	.	+	0	transcript_id "Phchi.S4G042100.t1"; gene_id "Phchi.S4G042100"
Phchi.S4	AUGUSTUS	CDS	2410679	2411926	1	+	0	transcript_id "Phchi.S4G042100.t1"; gene_id "Phchi.S4G042100"
Phchi.S4	AUGUSTUS	exon	2410679	2411926	.	+	.	transcript_id "Phchi.S4G042100.t1"; gene_id "Phchi.S4G042100"
Phchi.S4	AUGUSTUS	stop_codon	2411927	2411929	.	+	0	transcript_id "Phchi.S4G042100.t1"; gene_id "Phchi.S4G042100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13371.t1 is derived from g11837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6390024	6390963	.	+	.	Phchi.S3G069000
Phchi.S3	AUGUSTUS	transcript	6390024	6390963	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	start_codon	6390024	6390026	.	+	0	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	CDS	6390024	6390220	1	+	0	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	exon	6390024	6390220	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	intron	6390221	6390312	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	CDS	6390313	6390567	0.98	+	1	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	exon	6390313	6390567	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	intron	6390568	6390675	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	CDS	6390676	6390741	0.86	+	1	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	exon	6390676	6390741	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	intron	6390742	6390842	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	CDS	6390843	6390963	0.86	+	1	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	exon	6390843	6390963	.	+	.	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
Phchi.S3	AUGUSTUS	stop_codon	6390964	6390966	.	+	0	transcript_id "Phchi.S3G069000.t1"; gene_id "Phchi.S3G069000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6685.t1 is derived from g3857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24506650	24508014	.	-	.	Phchi.S1G384400
Phchi.S1	AUGUSTUS	transcript	24506650	24508014	.	-	.	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	stop_codon	24506647	24506649	.	-	0	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	CDS	24506650	24507027	0.97	-	0	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	exon	24506650	24507027	.	-	.	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	intron	24507028	24507136	.	-	.	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	CDS	24507137	24507385	1	-	0	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	exon	24507137	24507385	.	-	.	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	intron	24507386	24507474	.	-	.	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	CDS	24507475	24508014	0.44	-	0	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	exon	24507475	24508014	.	-	.	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
Phchi.S1	AUGUSTUS	start_codon	24508012	24508014	.	-	0	transcript_id "Phchi.S1G384400.t1"; gene_id "Phchi.S1G384400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8798.t1 is derived from g5973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38045237	38046577	.	+	.	Phchi.S1G595700
Phchi.S1	AUGUSTUS	transcript	38045237	38046577	.	+	.	transcript_id "Phchi.S1G595700.t1"; gene_id "Phchi.S1G595700"
Phchi.S1	AUGUSTUS	start_codon	38045237	38045239	.	+	0	transcript_id "Phchi.S1G595700.t1"; gene_id "Phchi.S1G595700"
Phchi.S1	AUGUSTUS	CDS	38045237	38046577	0.96	+	0	transcript_id "Phchi.S1G595700.t1"; gene_id "Phchi.S1G595700"
Phchi.S1	AUGUSTUS	exon	38045237	38046577	.	+	.	transcript_id "Phchi.S1G595700.t1"; gene_id "Phchi.S1G595700"
Phchi.S1	AUGUSTUS	stop_codon	38046578	38046580	.	+	0	transcript_id "Phchi.S1G595700.t1"; gene_id "Phchi.S1G595700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1986.t1 is derived from g8906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4287433	4288770	.	-	.	Phchi.S5G059500
Phchi.S5	AUGUSTUS	transcript	4287433	4288770	.	-	.	transcript_id "Phchi.S5G059500.t1"; gene_id "Phchi.S5G059500"
Phchi.S5	AUGUSTUS	stop_codon	4287430	4287432	.	-	0	transcript_id "Phchi.S5G059500.t1"; gene_id "Phchi.S5G059500"
Phchi.S5	AUGUSTUS	CDS	4287433	4288770	0.95	-	0	transcript_id "Phchi.S5G059500.t1"; gene_id "Phchi.S5G059500"
Phchi.S5	AUGUSTUS	exon	4287433	4288770	.	-	.	transcript_id "Phchi.S5G059500.t1"; gene_id "Phchi.S5G059500"
Phchi.S5	AUGUSTUS	start_codon	4288768	4288770	.	-	0	transcript_id "Phchi.S5G059500.t1"; gene_id "Phchi.S5G059500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2302.t1 is derived from g9222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5948013	5948640	.	-	.	Phchi.S5G091100
Phchi.S5	AUGUSTUS	transcript	5948013	5948640	.	-	.	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	stop_codon	5948010	5948012	.	-	0	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	CDS	5948013	5948126	0.8	-	0	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	exon	5948013	5948126	.	-	.	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	intron	5948127	5948205	.	-	.	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	CDS	5948206	5948285	0.88	-	2	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	exon	5948206	5948285	.	-	.	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	intron	5948286	5948429	.	-	.	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	CDS	5948430	5948640	0.83	-	0	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	exon	5948430	5948640	.	-	.	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
Phchi.S5	AUGUSTUS	start_codon	5948638	5948640	.	-	0	transcript_id "Phchi.S5G091100.t1"; gene_id "Phchi.S5G091100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg830.t1 is derived from g10612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5772543	5773410	.	+	.	Phchi.S6G078900
Phchi.S6	AUGUSTUS	transcript	5772543	5773410	.	+	.	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	start_codon	5772543	5772545	.	+	0	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	CDS	5772543	5772553	0.55	+	0	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	exon	5772543	5772553	.	+	.	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	intron	5772554	5773046	.	+	.	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	CDS	5773047	5773410	0.64	+	1	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	exon	5773047	5773410	.	+	.	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
Phchi.S6	AUGUSTUS	stop_codon	5773411	5773413	.	+	0	transcript_id "Phchi.S6G078900.t1"; gene_id "Phchi.S6G078900"
# This transcript jg15964.t1 is derived from g16003.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	4745	6332	.	-	.	Phchi.C133G000300
Phchi.C133	AUGUSTUS	transcript	5618	6332	.	-	.	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	stop_codon	5615	5617	.	-	0	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	5618	5963	1	-	1	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	5618	5963	.	-	.	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	intron	5964	6054	.	-	.	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	6055	6332	0.69	-	0	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	6055	6332	.	-	.	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	start_codon	6330	6332	.	-	0	transcript_id "Phchi.C133G000300.t1"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	transcript	4745	6332	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	stop_codon	4742	4744	.	-	0	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	4745	4864	0.89	-	0	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	4745	4864	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	intron	4865	4994	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	4995	5255	0.84	-	0	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	4995	5255	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	intron	5256	5359	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	5360	5509	0.9	-	0	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	5360	5509	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	intron	5510	5635	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	5636	5963	1	-	1	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	5636	5963	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	intron	5964	6054	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	CDS	6055	6332	0.83	-	0	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	exon	6055	6332	.	-	.	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
Phchi.C133	AUGUSTUS	start_codon	6330	6332	.	-	0	transcript_id "Phchi.C133G000300.t2"; gene_id "Phchi.C133G000300"
# This transcript jg8501.t2 is derived from g5676.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8501.t3 is derived from g5676.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8502.t1 is derived from g5677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36350151	36350636	.	+	.	Phchi.S1G566100
Phchi.S1	AUGUSTUS	transcript	36350151	36350636	.	+	.	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	start_codon	36350151	36350153	.	+	0	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	CDS	36350151	36350153	1	+	0	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	exon	36350151	36350153	.	+	.	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	intron	36350154	36350316	.	+	.	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	CDS	36350317	36350421	1	+	0	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	exon	36350317	36350421	.	+	.	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	intron	36350422	36350504	.	+	.	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	CDS	36350505	36350636	1	+	0	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	exon	36350505	36350636	.	+	.	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
Phchi.S1	AUGUSTUS	stop_codon	36350637	36350639	.	+	0	transcript_id "Phchi.S1G566100.t1"; gene_id "Phchi.S1G566100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4526.t1 is derived from g1696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10968967	10972524	.	-	.	Phchi.S1G168500
Phchi.S1	AUGUSTUS	transcript	10968967	10972524	.	-	.	transcript_id "Phchi.S1G168500.t1"; gene_id "Phchi.S1G168500"
Phchi.S1	AUGUSTUS	stop_codon	10968964	10968966	.	-	0	transcript_id "Phchi.S1G168500.t1"; gene_id "Phchi.S1G168500"
Phchi.S1	AUGUSTUS	CDS	10968967	10972524	0.99	-	0	transcript_id "Phchi.S1G168500.t1"; gene_id "Phchi.S1G168500"
Phchi.S1	AUGUSTUS	exon	10968967	10972524	.	-	.	transcript_id "Phchi.S1G168500.t1"; gene_id "Phchi.S1G168500"
Phchi.S1	AUGUSTUS	start_codon	10972522	10972524	.	-	0	transcript_id "Phchi.S1G168500.t1"; gene_id "Phchi.S1G168500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14548.t1 is derived from g13016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13426942	13430689	.	+	.	Phchi.S3G186700
Phchi.S3	AUGUSTUS	transcript	13426942	13430689	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	start_codon	13426942	13426944	.	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13426942	13427488	0.64	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13426942	13427488	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13427489	13427595	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13427596	13427918	1	+	2	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13427596	13427918	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13427919	13428092	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13428093	13428500	0.99	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13428093	13428500	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13428501	13428617	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13428618	13429004	0.99	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13428618	13429004	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13429005	13429090	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13429091	13429186	1	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13429091	13429186	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13429187	13429273	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13429274	13429389	1	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13429274	13429389	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13429390	13429483	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13429484	13429657	1	+	1	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13429484	13429657	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13429658	13429739	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13429740	13429899	1	+	1	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13429740	13429899	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13429900	13430004	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13430005	13430313	1	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13430005	13430313	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13430314	13430391	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13430392	13430470	1	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13430392	13430470	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	intron	13430471	13430582	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	CDS	13430583	13430689	1	+	2	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	exon	13430583	13430689	.	+	.	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
Phchi.S3	AUGUSTUS	stop_codon	13430690	13430692	.	+	0	transcript_id "Phchi.S3G186700.t1"; gene_id "Phchi.S3G186700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6112.t1 is derived from g3283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20989106	20990108	.	-	.	Phchi.S1G327100
Phchi.S1	AUGUSTUS	transcript	20989106	20990108	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	stop_codon	20989103	20989105	.	-	0	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	CDS	20989106	20989250	0.99	-	1	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	exon	20989106	20989250	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	intron	20989251	20989324	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	CDS	20989325	20989357	0.96	-	1	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	exon	20989325	20989357	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	intron	20989358	20989487	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	CDS	20989488	20989600	0.39	-	0	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	exon	20989488	20989600	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	intron	20989601	20989931	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	CDS	20989932	20990108	0.4	-	0	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	exon	20989932	20990108	.	-	.	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
Phchi.S1	AUGUSTUS	start_codon	20990106	20990108	.	-	0	transcript_id "Phchi.S1G327100.t1"; gene_id "Phchi.S1G327100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12867.t1 is derived from g11332.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2825991	2828000	.	+	.	Phchi.S3G018600
Phchi.S3	AUGUSTUS	transcript	2825991	2828000	.	+	.	transcript_id "Phchi.S3G018600.t1"; gene_id "Phchi.S3G018600"
Phchi.S3	AUGUSTUS	start_codon	2825991	2825993	.	+	0	transcript_id "Phchi.S3G018600.t1"; gene_id "Phchi.S3G018600"
Phchi.S3	AUGUSTUS	CDS	2825991	2828000	0.6	+	0	transcript_id "Phchi.S3G018600.t1"; gene_id "Phchi.S3G018600"
Phchi.S3	AUGUSTUS	exon	2825991	2828000	.	+	.	transcript_id "Phchi.S3G018600.t1"; gene_id "Phchi.S3G018600"
Phchi.S3	AUGUSTUS	stop_codon	2828001	2828003	.	+	0	transcript_id "Phchi.S3G018600.t1"; gene_id "Phchi.S3G018600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4052.t1 is derived from g1221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7542294	7545279	.	-	.	Phchi.S1G121100
Phchi.S1	AUGUSTUS	transcript	7542294	7545279	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	stop_codon	7542291	7542293	.	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7542294	7542353	0.96	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7542294	7542353	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7542354	7542440	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7542441	7542518	1	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7542441	7542518	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7542519	7542603	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7542604	7542648	1	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7542604	7542648	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7542649	7542742	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7542743	7542874	0.49	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7542743	7542874	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7542875	7543105	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7543106	7543130	0.5	-	1	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7543106	7543130	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7543131	7543260	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7543261	7543312	0.75	-	2	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7543261	7543312	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7543313	7543896	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7543897	7543909	0.9	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7543897	7543909	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7543910	7543997	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7543998	7544084	1	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7543998	7544084	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7544085	7544176	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7544177	7544185	1	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7544177	7544185	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7544186	7544479	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7544480	7544529	0.9	-	2	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7544480	7544529	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7544530	7544782	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7544783	7544887	1	-	2	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7544783	7544887	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7544888	7544967	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7544968	7545056	1	-	1	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7544968	7545056	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	intron	7545057	7545238	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	CDS	7545239	7545279	0.64	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	exon	7545239	7545279	.	-	.	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
Phchi.S1	AUGUSTUS	start_codon	7545277	7545279	.	-	0	transcript_id "Phchi.S1G121100.t1"; gene_id "Phchi.S1G121100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1250.t1 is derived from g11033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8647132	8649454	.	-	.	Phchi.S6G120900
Phchi.S6	AUGUSTUS	transcript	8647132	8649454	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	stop_codon	8647129	8647131	.	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8647132	8647179	1	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8647132	8647179	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8647180	8647367	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8647368	8647436	1	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8647368	8647436	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8647437	8647547	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8647548	8647637	1	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8647548	8647637	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8647638	8647762	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8647763	8647917	1	-	2	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8647763	8647917	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8647918	8648024	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8648025	8648214	0.98	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8648025	8648214	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8648215	8648330	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8648331	8648515	1	-	2	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8648331	8648515	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8648516	8648705	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8648706	8648865	1	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8648706	8648865	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8648866	8648952	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8648953	8649213	1	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8648953	8649213	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	intron	8649214	8649304	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	CDS	8649305	8649454	1	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	exon	8649305	8649454	.	-	.	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
Phchi.S6	AUGUSTUS	start_codon	8649452	8649454	.	-	0	transcript_id "Phchi.S6G120900.t1"; gene_id "Phchi.S6G120900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3441.t1 is derived from g610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3707602	3708279	.	+	.	Phchi.S1G060000
Phchi.S1	AUGUSTUS	transcript	3707602	3708279	.	+	.	transcript_id "Phchi.S1G060000.t1"; gene_id "Phchi.S1G060000"
Phchi.S1	AUGUSTUS	start_codon	3707602	3707604	.	+	0	transcript_id "Phchi.S1G060000.t1"; gene_id "Phchi.S1G060000"
Phchi.S1	AUGUSTUS	CDS	3707602	3708279	0.98	+	0	transcript_id "Phchi.S1G060000.t1"; gene_id "Phchi.S1G060000"
Phchi.S1	AUGUSTUS	exon	3707602	3708279	.	+	.	transcript_id "Phchi.S1G060000.t1"; gene_id "Phchi.S1G060000"
Phchi.S1	AUGUSTUS	stop_codon	3708280	3708282	.	+	0	transcript_id "Phchi.S1G060000.t1"; gene_id "Phchi.S1G060000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11885.t1 is derived from g15937.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8996248	9004041	.	+	.	Phchi.S4G146700
Phchi.S4	AUGUSTUS	transcript	8996248	9004041	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	start_codon	8996248	8996250	.	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8996248	8996895	0.47	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8996248	8996895	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	8996896	8997297	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8997298	8997436	0.57	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8997298	8997436	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	8997437	8998150	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8998151	8998236	1	+	2	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8998151	8998236	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	8998237	8998505	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8998506	8999019	0.74	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8998506	8999019	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	8999020	8999157	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8999158	8999318	0.81	+	2	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8999158	8999318	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	8999319	8999481	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8999482	8999701	1	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8999482	8999701	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	8999702	8999908	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	8999909	9000188	1	+	2	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	8999909	9000188	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9000189	9000299	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9000300	9000802	0.99	+	1	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9000300	9000802	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9000803	9000935	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9000936	9001516	0.99	+	2	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9000936	9001516	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9001517	9001628	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9001629	9001853	0.96	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9001629	9001853	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9001854	9001940	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9001941	9001994	0.99	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9001941	9001994	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9001995	9002239	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9002240	9002311	0.78	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9002240	9002311	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9002312	9002409	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9002410	9002480	0.53	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9002410	9002480	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9002481	9002666	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9002667	9002853	0.33	+	1	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9002667	9002853	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9002854	9003029	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9003030	9003086	1	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9003030	9003086	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9003087	9003258	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9003259	9003318	1	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9003259	9003318	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9003319	9003417	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9003418	9003583	1	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9003418	9003583	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9003584	9003674	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9003675	9003778	1	+	2	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9003675	9003778	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	intron	9003779	9003894	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	CDS	9003895	9004041	0.81	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	exon	9003895	9004041	.	+	.	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
Phchi.S4	AUGUSTUS	stop_codon	9004042	9004044	.	+	0	transcript_id "Phchi.S4G146700.t1"; gene_id "Phchi.S4G146700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8914.t1 is derived from g6089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38610792	38613142	.	+	.	Phchi.S1G607300
Phchi.S1	AUGUSTUS	transcript	38610792	38613142	.	+	.	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	start_codon	38610792	38610794	.	+	0	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	CDS	38610792	38611016	0.56	+	0	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	exon	38610792	38611016	.	+	.	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	intron	38611017	38611095	.	+	.	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	CDS	38611096	38612949	0.33	+	0	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	exon	38611096	38612949	.	+	.	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	intron	38612950	38613133	.	+	.	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	CDS	38613134	38613142	0.65	+	0	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	exon	38613134	38613142	.	+	.	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
Phchi.S1	AUGUSTUS	stop_codon	38613143	38613145	.	+	0	transcript_id "Phchi.S1G607300.t1"; gene_id "Phchi.S1G607300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11337.t1 is derived from g15387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5619956	5623022	.	-	.	Phchi.S4G091900
Phchi.S4	AUGUSTUS	transcript	5619956	5623022	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	stop_codon	5619953	5619955	.	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5619956	5620073	0.9	-	1	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5619956	5620073	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5620074	5620295	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5620296	5620660	1	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5620296	5620660	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5620661	5620758	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5620759	5620980	1	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5620759	5620980	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5620981	5621077	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5621078	5621194	0.96	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5621078	5621194	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5621195	5621301	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5621302	5621407	0.9	-	1	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5621302	5621407	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5621408	5621518	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5621519	5621687	0.99	-	2	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5621519	5621687	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5621688	5621778	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5621779	5622028	1	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5621779	5622028	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5622029	5622172	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5622173	5622555	0.95	-	2	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5622173	5622555	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5622556	5622659	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5622660	5622742	0.62	-	1	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5622660	5622742	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5622743	5622845	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5622846	5622880	0.64	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5622846	5622880	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	intron	5622881	5623016	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	CDS	5623017	5623022	0.81	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	exon	5623017	5623022	.	-	.	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
Phchi.S4	AUGUSTUS	start_codon	5623020	5623022	.	-	0	transcript_id "Phchi.S4G091900.t1"; gene_id "Phchi.S4G091900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4852.t1 is derived from g2022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13108122	13108901	.	-	.	Phchi.S1G201100
Phchi.S1	AUGUSTUS	transcript	13108122	13108901	.	-	.	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	stop_codon	13108119	13108121	.	-	0	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	CDS	13108122	13108292	0.99	-	0	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	exon	13108122	13108292	.	-	.	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	intron	13108293	13108598	.	-	.	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	CDS	13108599	13108901	1	-	0	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	exon	13108599	13108901	.	-	.	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
Phchi.S1	AUGUSTUS	start_codon	13108899	13108901	.	-	0	transcript_id "Phchi.S1G201100.t1"; gene_id "Phchi.S1G201100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10938.t1 is derived from g14988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3185862	3186131	.	-	.	Phchi.S4G052000
Phchi.S4	AUGUSTUS	transcript	3185862	3186131	.	-	.	transcript_id "Phchi.S4G052000.t1"; gene_id "Phchi.S4G052000"
Phchi.S4	AUGUSTUS	stop_codon	3185859	3185861	.	-	0	transcript_id "Phchi.S4G052000.t1"; gene_id "Phchi.S4G052000"
Phchi.S4	AUGUSTUS	CDS	3185862	3186131	0.01	-	0	transcript_id "Phchi.S4G052000.t1"; gene_id "Phchi.S4G052000"
Phchi.S4	AUGUSTUS	exon	3185862	3186131	.	-	.	transcript_id "Phchi.S4G052000.t1"; gene_id "Phchi.S4G052000"
Phchi.S4	AUGUSTUS	start_codon	3186129	3186131	.	-	0	transcript_id "Phchi.S4G052000.t1"; gene_id "Phchi.S4G052000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15987.t1 is derived from g9776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C16	AUGUSTUS	gene	77660	78091	.	-	.	Phchi.C16G000500
Phchi.C16	AUGUSTUS	transcript	77660	78091	.	-	.	transcript_id "Phchi.C16G000500.t1"; gene_id "Phchi.C16G000500"
Phchi.C16	AUGUSTUS	stop_codon	77657	77659	.	-	0	transcript_id "Phchi.C16G000500.t1"; gene_id "Phchi.C16G000500"
Phchi.C16	AUGUSTUS	CDS	77660	78091	1	-	0	transcript_id "Phchi.C16G000500.t1"; gene_id "Phchi.C16G000500"
Phchi.C16	AUGUSTUS	exon	77660	78091	.	-	.	transcript_id "Phchi.C16G000500.t1"; gene_id "Phchi.C16G000500"
Phchi.C16	AUGUSTUS	start_codon	78089	78091	.	-	0	transcript_id "Phchi.C16G000500.t1"; gene_id "Phchi.C16G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg316.t1 is derived from g10098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2238093	2239753	.	-	.	Phchi.S6G027500
Phchi.S6	AUGUSTUS	transcript	2238093	2239753	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	stop_codon	2238090	2238092	.	-	0	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	CDS	2238093	2238131	0.57	-	0	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	exon	2238093	2238131	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	intron	2238132	2238764	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	CDS	2238765	2238792	0.57	-	1	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	exon	2238765	2238792	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	intron	2238793	2238928	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	CDS	2238929	2238945	0.49	-	0	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	exon	2238929	2238945	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	intron	2238946	2239080	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	CDS	2239081	2239392	0.3	-	0	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	exon	2239081	2239392	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	intron	2239393	2239615	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	CDS	2239616	2239753	0.79	-	0	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	exon	2239616	2239753	.	-	.	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
Phchi.S6	AUGUSTUS	start_codon	2239751	2239753	.	-	0	transcript_id "Phchi.S6G027500.t1"; gene_id "Phchi.S6G027500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5148.t1 is derived from g2318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15144656	15146392	.	+	.	Phchi.S1G230700
Phchi.S1	AUGUSTUS	transcript	15144656	15145598	.	+	.	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	start_codon	15144656	15144658	.	+	0	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	CDS	15144656	15145429	0.5	+	0	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	exon	15144656	15145429	.	+	.	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	intron	15145430	15145544	.	+	.	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	CDS	15145545	15145598	0.93	+	0	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	exon	15145545	15145598	.	+	.	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	stop_codon	15145599	15145601	.	+	0	transcript_id "Phchi.S1G230700.t1"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	transcript	15144656	15146392	.	+	.	transcript_id "Phchi.S1G230700.t2"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	start_codon	15144656	15144658	.	+	0	transcript_id "Phchi.S1G230700.t2"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	CDS	15144656	15146392	0.58	+	0	transcript_id "Phchi.S1G230700.t2"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	exon	15144656	15146392	.	+	.	transcript_id "Phchi.S1G230700.t2"; gene_id "Phchi.S1G230700"
Phchi.S1	AUGUSTUS	stop_codon	15146393	15146395	.	+	0	transcript_id "Phchi.S1G230700.t2"; gene_id "Phchi.S1G230700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9475.t1 is derived from g6651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41727179	41729485	.	-	.	Phchi.S1G663400
Phchi.S1	AUGUSTUS	transcript	41727179	41729485	.	-	.	transcript_id "Phchi.S1G663400.t1"; gene_id "Phchi.S1G663400"
Phchi.S1	AUGUSTUS	stop_codon	41727176	41727178	.	-	0	transcript_id "Phchi.S1G663400.t1"; gene_id "Phchi.S1G663400"
Phchi.S1	AUGUSTUS	CDS	41727179	41729485	0.55	-	0	transcript_id "Phchi.S1G663400.t1"; gene_id "Phchi.S1G663400"
Phchi.S1	AUGUSTUS	exon	41727179	41729485	.	-	.	transcript_id "Phchi.S1G663400.t1"; gene_id "Phchi.S1G663400"
Phchi.S1	AUGUSTUS	start_codon	41729483	41729485	.	-	0	transcript_id "Phchi.S1G663400.t1"; gene_id "Phchi.S1G663400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5142.t1 is derived from g2312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15131943	15133591	.	+	.	Phchi.S1G230100
Phchi.S1	AUGUSTUS	transcript	15131943	15133591	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	start_codon	15131943	15131945	.	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15131943	15132011	1	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15131943	15132011	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	intron	15132012	15132103	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15132104	15132313	1	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15132104	15132313	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	intron	15132314	15132407	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15132408	15132653	1	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15132408	15132653	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	intron	15132654	15132793	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15132794	15132859	1	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15132794	15132859	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	intron	15132860	15132938	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15132939	15133112	1	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15132939	15133112	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	intron	15133113	15133254	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15133255	15133320	0.9	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15133255	15133320	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	intron	15133321	15133429	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	CDS	15133430	15133591	0.91	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	exon	15133430	15133591	.	+	.	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
Phchi.S1	AUGUSTUS	stop_codon	15133592	15133594	.	+	0	transcript_id "Phchi.S1G230100.t1"; gene_id "Phchi.S1G230100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14731.t1 is derived from g13199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14409557	14410350	.	+	.	Phchi.S3G205000
Phchi.S3	AUGUSTUS	transcript	14409557	14410350	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	start_codon	14409557	14409559	.	+	0	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	CDS	14409557	14409815	0.98	+	0	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	exon	14409557	14409815	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	intron	14409816	14409929	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	CDS	14409930	14409945	1	+	2	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	exon	14409930	14409945	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	intron	14409946	14410037	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	CDS	14410038	14410096	1	+	1	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	exon	14410038	14410096	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	intron	14410097	14410306	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	CDS	14410307	14410350	1	+	2	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	exon	14410307	14410350	.	+	.	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
Phchi.S3	AUGUSTUS	stop_codon	14410351	14410353	.	+	0	transcript_id "Phchi.S3G205000.t1"; gene_id "Phchi.S3G205000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6965.t1 is derived from g4137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26159322	26161211	.	+	.	Phchi.S1G412400
Phchi.S1	AUGUSTUS	transcript	26159322	26161211	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	start_codon	26159322	26159324	.	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26159322	26159525	0.33	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26159322	26159525	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	intron	26159526	26159697	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26159698	26159803	1	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26159698	26159803	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	intron	26159804	26159898	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26159899	26159966	1	+	2	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26159899	26159966	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	intron	26159967	26160118	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26160119	26160313	1	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26160119	26160313	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	intron	26160314	26160730	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26160731	26160847	1	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26160731	26160847	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	intron	26160848	26160931	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26160932	26160988	1	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26160932	26160988	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	intron	26160989	26161178	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	CDS	26161179	26161211	1	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	exon	26161179	26161211	.	+	.	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
Phchi.S1	AUGUSTUS	stop_codon	26161212	26161214	.	+	0	transcript_id "Phchi.S1G412400.t1"; gene_id "Phchi.S1G412400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8613.t1 is derived from g5788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36913931	36914878	.	-	.	Phchi.S1G577200
Phchi.S1	AUGUSTUS	transcript	36913931	36914878	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	stop_codon	36913928	36913930	.	-	0	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	CDS	36913931	36913945	0.99	-	0	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	exon	36913931	36913945	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	intron	36913946	36914132	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	CDS	36914133	36914158	0.79	-	2	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	exon	36914133	36914158	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	intron	36914159	36914371	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	CDS	36914372	36914626	0.26	-	2	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	exon	36914372	36914626	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	intron	36914627	36914853	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	CDS	36914854	36914878	0.5	-	0	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	exon	36914854	36914878	.	-	.	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
Phchi.S1	AUGUSTUS	start_codon	36914876	36914878	.	-	0	transcript_id "Phchi.S1G577200.t1"; gene_id "Phchi.S1G577200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg239.t1 is derived from g10021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1643551	1644474	.	-	.	Phchi.S6G019800
Phchi.S6	AUGUSTUS	transcript	1643551	1644474	.	-	.	transcript_id "Phchi.S6G019800.t1"; gene_id "Phchi.S6G019800"
Phchi.S6	AUGUSTUS	stop_codon	1643548	1643550	.	-	0	transcript_id "Phchi.S6G019800.t1"; gene_id "Phchi.S6G019800"
Phchi.S6	AUGUSTUS	CDS	1643551	1644474	1	-	0	transcript_id "Phchi.S6G019800.t1"; gene_id "Phchi.S6G019800"
Phchi.S6	AUGUSTUS	exon	1643551	1644474	.	-	.	transcript_id "Phchi.S6G019800.t1"; gene_id "Phchi.S6G019800"
Phchi.S6	AUGUSTUS	start_codon	1644472	1644474	.	-	0	transcript_id "Phchi.S6G019800.t1"; gene_id "Phchi.S6G019800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4833.t1 is derived from g2003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13047283	13047594	.	+	.	Phchi.S1G199200
Phchi.S1	AUGUSTUS	transcript	13047283	13047594	.	+	.	transcript_id "Phchi.S1G199200.t1"; gene_id "Phchi.S1G199200"
Phchi.S1	AUGUSTUS	start_codon	13047283	13047285	.	+	0	transcript_id "Phchi.S1G199200.t1"; gene_id "Phchi.S1G199200"
Phchi.S1	AUGUSTUS	CDS	13047283	13047594	0.85	+	0	transcript_id "Phchi.S1G199200.t1"; gene_id "Phchi.S1G199200"
Phchi.S1	AUGUSTUS	exon	13047283	13047594	.	+	.	transcript_id "Phchi.S1G199200.t1"; gene_id "Phchi.S1G199200"
Phchi.S1	AUGUSTUS	stop_codon	13047595	13047597	.	+	0	transcript_id "Phchi.S1G199200.t1"; gene_id "Phchi.S1G199200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8750.t1 is derived from g5925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37788503	37790385	.	-	.	Phchi.S1G590900
Phchi.S1	AUGUSTUS	transcript	37788503	37790385	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	stop_codon	37788500	37788502	.	-	0	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	CDS	37788503	37788608	0.97	-	1	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	exon	37788503	37788608	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	intron	37788609	37788856	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	CDS	37788857	37789256	0.98	-	2	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	exon	37788857	37789256	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	intron	37789257	37789372	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	CDS	37789373	37789439	0.95	-	0	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	exon	37789373	37789439	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	intron	37789440	37789517	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	CDS	37789518	37789541	1	-	0	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	exon	37789518	37789541	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	intron	37789542	37790034	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	CDS	37790035	37790385	0.33	-	0	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	exon	37790035	37790385	.	-	.	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
Phchi.S1	AUGUSTUS	start_codon	37790383	37790385	.	-	0	transcript_id "Phchi.S1G590900.t1"; gene_id "Phchi.S1G590900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8876.t1 is derived from g6051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38413524	38417844	.	+	.	Phchi.S1G603500
Phchi.S1	AUGUSTUS	transcript	38413524	38417844	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	start_codon	38413524	38413526	.	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38413524	38413676	0.96	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38413524	38413676	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38413677	38413781	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38413782	38414271	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38413782	38414271	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38414272	38414349	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38414350	38414483	1	+	2	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38414350	38414483	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38414484	38414570	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38414571	38414671	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38414571	38414671	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38414672	38414768	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38414769	38414901	1	+	1	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38414769	38414901	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38414902	38414995	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38414996	38415112	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38414996	38415112	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38415113	38415245	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38415246	38415413	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38415246	38415413	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38415414	38415488	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38415489	38415611	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38415489	38415611	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38415612	38415695	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38415696	38415855	0.97	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38415696	38415855	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38415856	38415956	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38415957	38416090	0.99	+	2	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38415957	38416090	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38416091	38416170	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38416171	38416308	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38416171	38416308	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38416309	38416390	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38416391	38416533	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38416391	38416533	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38416534	38416625	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38416626	38416688	1	+	1	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38416626	38416688	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38416689	38416782	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38416783	38416846	1	+	1	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38416783	38416846	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38416847	38416938	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38416939	38417110	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38416939	38417110	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38417111	38417193	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38417194	38417267	1	+	2	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38417194	38417267	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38417268	38417351	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38417352	38417446	1	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38417352	38417446	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38417447	38417525	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38417526	38417557	1	+	1	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38417526	38417557	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	intron	38417558	38417641	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	CDS	38417642	38417844	1	+	2	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	exon	38417642	38417844	.	+	.	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
Phchi.S1	AUGUSTUS	stop_codon	38417845	38417847	.	+	0	transcript_id "Phchi.S1G603500.t1"; gene_id "Phchi.S1G603500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9223.t1 is derived from g6398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40474101	40474495	.	+	.	Phchi.S1G638200
Phchi.S1	AUGUSTUS	transcript	40474101	40474495	.	+	.	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	start_codon	40474101	40474103	.	+	0	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	CDS	40474101	40474103	1	+	0	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	exon	40474101	40474103	.	+	.	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	intron	40474104	40474255	.	+	.	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	CDS	40474256	40474495	1	+	0	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	exon	40474256	40474495	.	+	.	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
Phchi.S1	AUGUSTUS	stop_codon	40474496	40474498	.	+	0	transcript_id "Phchi.S1G638200.t1"; gene_id "Phchi.S1G638200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12266.t1 is derived from g7942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7271425	7277557	.	+	.	Phchi.S2G034600
Phchi.S2	AUGUSTUS	transcript	7271425	7277557	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	start_codon	7271425	7271427	.	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7271425	7271483	0.86	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7271425	7271483	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7271484	7271754	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7271755	7271854	1	+	1	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7271755	7271854	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7271855	7271941	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7271942	7272010	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7271942	7272010	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7272011	7272173	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7272174	7272410	0.96	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7272174	7272410	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7272411	7272493	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7272494	7272671	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7272494	7272671	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7272672	7272761	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7272762	7272894	1	+	2	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7272762	7272894	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7272895	7273046	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7273047	7273236	0.9	+	1	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7273047	7273236	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7273237	7273331	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7273332	7273479	0.73	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7273332	7273479	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7273480	7273601	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7273602	7273702	1	+	2	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7273602	7273702	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7273703	7273887	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7273888	7274046	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7273888	7274046	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7274047	7274185	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7274186	7274254	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7274186	7274254	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7274255	7274349	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7274350	7274418	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7274350	7274418	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7274419	7274595	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7274596	7274715	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7274596	7274715	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7274716	7274985	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7274986	7275114	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7274986	7275114	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7275115	7275461	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7275462	7275609	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7275462	7275609	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7275610	7275824	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7275825	7275832	1	+	2	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7275825	7275832	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7275833	7275915	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7275916	7276056	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7275916	7276056	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7276057	7276143	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7276144	7276269	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7276144	7276269	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7276270	7276350	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7276351	7276416	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7276351	7276416	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7276417	7276582	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7276583	7277023	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7276583	7277023	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7277024	7277160	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7277161	7277250	0.94	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7277161	7277250	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	intron	7277251	7277446	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	CDS	7277447	7277557	1	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	exon	7277447	7277557	.	+	.	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
Phchi.S2	AUGUSTUS	stop_codon	7277558	7277560	.	+	0	transcript_id "Phchi.S2G034600.t1"; gene_id "Phchi.S2G034600"
# This transcript jg15829.t2 is derived from g14299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15830.t1 is derived from g14300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21645476	21647293	.	+	.	Phchi.S3G314900
Phchi.S3	AUGUSTUS	transcript	21645476	21647293	.	+	.	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	start_codon	21645476	21645478	.	+	0	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	CDS	21645476	21645982	0.43	+	0	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	exon	21645476	21645982	.	+	.	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	intron	21645983	21646096	.	+	.	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	CDS	21646097	21646910	0.73	+	0	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	exon	21646097	21646910	.	+	.	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	intron	21646911	21646994	.	+	.	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	CDS	21646995	21647293	1	+	2	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	exon	21646995	21647293	.	+	.	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
Phchi.S3	AUGUSTUS	stop_codon	21647294	21647296	.	+	0	transcript_id "Phchi.S3G314900.t1"; gene_id "Phchi.S3G314900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3155.t1 is derived from g324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2011287	2011779	.	+	.	Phchi.S1G031400
Phchi.S1	AUGUSTUS	transcript	2011287	2011779	.	+	.	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	start_codon	2011287	2011289	.	+	0	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	CDS	2011287	2011455	0.65	+	0	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	exon	2011287	2011455	.	+	.	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	intron	2011456	2011609	.	+	.	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	CDS	2011610	2011657	1	+	2	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	exon	2011610	2011657	.	+	.	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	intron	2011658	2011741	.	+	.	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	CDS	2011742	2011779	1	+	2	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	exon	2011742	2011779	.	+	.	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
Phchi.S1	AUGUSTUS	stop_codon	2011780	2011782	.	+	0	transcript_id "Phchi.S1G031400.t1"; gene_id "Phchi.S1G031400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8184.t1 is derived from g5359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34331856	34333318	.	-	.	Phchi.S1G534300
Phchi.S1	AUGUSTUS	transcript	34331856	34333318	.	-	.	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	stop_codon	34331853	34331855	.	-	0	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	CDS	34331856	34332518	0.86	-	0	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	exon	34331856	34332518	.	-	.	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	intron	34332519	34332654	.	-	.	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	CDS	34332655	34332939	1	-	0	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	exon	34332655	34332939	.	-	.	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	intron	34332940	34333051	.	-	.	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	CDS	34333052	34333318	0.99	-	0	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	exon	34333052	34333318	.	-	.	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
Phchi.S1	AUGUSTUS	start_codon	34333316	34333318	.	-	0	transcript_id "Phchi.S1G534300.t1"; gene_id "Phchi.S1G534300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4767.t1 is derived from g1937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12732320	12733155	.	-	.	Phchi.S1G192600
Phchi.S1	AUGUSTUS	transcript	12732320	12733155	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	stop_codon	12732317	12732319	.	-	0	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	CDS	12732320	12732372	0.78	-	2	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	exon	12732320	12732372	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	intron	12732373	12732458	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	CDS	12732459	12732479	0.79	-	2	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	exon	12732459	12732479	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	intron	12732480	12732575	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	CDS	12732576	12732590	0.73	-	2	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	exon	12732576	12732590	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	intron	12732591	12732770	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	CDS	12732771	12733155	0.72	-	0	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	exon	12732771	12733155	.	-	.	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
Phchi.S1	AUGUSTUS	start_codon	12733153	12733155	.	-	0	transcript_id "Phchi.S1G192600.t1"; gene_id "Phchi.S1G192600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15260.t1 is derived from g13728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17961716	17967508	.	-	.	Phchi.S3G257900
Phchi.S3	AUGUSTUS	transcript	17961716	17967508	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	stop_codon	17961713	17961715	.	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17961716	17961952	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17961716	17961952	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17961953	17962031	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17962032	17962279	0.97	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17962032	17962279	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17962280	17962344	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17962345	17962416	0.86	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17962345	17962416	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17962417	17962502	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17962503	17962590	0.86	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17962503	17962590	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17962591	17962727	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17962728	17962934	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17962728	17962934	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17962935	17963003	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17963004	17963222	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17963004	17963222	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17963223	17963319	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17963320	17963451	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17963320	17963451	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17963452	17963530	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17963531	17963628	1	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17963531	17963628	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17963629	17963826	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17963827	17963935	0.91	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17963827	17963935	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17963936	17964043	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17964044	17964141	0.94	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17964044	17964141	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17964142	17964241	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17964242	17964479	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17964242	17964479	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17964480	17964628	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17964629	17964736	0.98	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17964629	17964736	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17964737	17964868	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17964869	17964913	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17964869	17964913	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17964914	17965005	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17965006	17965190	1	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17965006	17965190	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17965191	17965345	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17965346	17965395	1	-	1	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17965346	17965395	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17965396	17965548	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17965549	17965593	1	-	1	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17965549	17965593	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17965594	17965701	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17965702	17965767	1	-	1	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17965702	17965767	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17965768	17965950	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17965951	17966003	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17965951	17966003	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17966004	17966109	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17966110	17966227	1	-	1	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17966110	17966227	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17966228	17966331	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17966332	17966433	1	-	1	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17966332	17966433	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17966434	17966614	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17966615	17966772	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17966615	17966772	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17966773	17966857	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17966858	17966935	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17966858	17966935	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17966936	17967018	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17967019	17967110	1	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17967019	17967110	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17967111	17967205	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17967206	17967253	1	-	2	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17967206	17967253	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	intron	17967254	17967333	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	CDS	17967334	17967508	1	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	exon	17967334	17967508	.	-	.	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
Phchi.S3	AUGUSTUS	start_codon	17967506	17967508	.	-	0	transcript_id "Phchi.S3G257900.t1"; gene_id "Phchi.S3G257900"
# This transcript jg16000.t2 is derived from g15978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16001.t1 is derived from g14446.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C104	AUGUSTUS	gene	31789	32028	.	-	.	Phchi.C104G000100
Phchi.C104	AUGUSTUS	transcript	31789	32028	.	-	.	transcript_id "Phchi.C104G000100.t1"; gene_id "Phchi.C104G000100"
Phchi.C104	AUGUSTUS	stop_codon	31786	31788	.	-	0	transcript_id "Phchi.C104G000100.t1"; gene_id "Phchi.C104G000100"
Phchi.C104	AUGUSTUS	CDS	31789	32028	0.4	-	0	transcript_id "Phchi.C104G000100.t1"; gene_id "Phchi.C104G000100"
Phchi.C104	AUGUSTUS	exon	31789	32028	.	-	.	transcript_id "Phchi.C104G000100.t1"; gene_id "Phchi.C104G000100"
Phchi.C104	AUGUSTUS	start_codon	32026	32028	.	-	0	transcript_id "Phchi.C104G000100.t1"; gene_id "Phchi.C104G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9097.t1 is derived from g6272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39822526	39823280	.	+	.	Phchi.S1G625600
Phchi.S1	AUGUSTUS	transcript	39822526	39823280	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	start_codon	39822526	39822528	.	+	0	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	CDS	39822526	39822669	0.62	+	0	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	exon	39822526	39822669	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	intron	39822670	39822746	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	CDS	39822747	39822835	1	+	0	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	exon	39822747	39822835	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	intron	39822836	39822974	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	CDS	39822975	39823104	1	+	1	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	exon	39822975	39823104	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	intron	39823105	39823196	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	CDS	39823197	39823280	0.73	+	0	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	exon	39823197	39823280	.	+	.	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
Phchi.S1	AUGUSTUS	stop_codon	39823281	39823283	.	+	0	transcript_id "Phchi.S1G625600.t1"; gene_id "Phchi.S1G625600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1191.t1 is derived from g10974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8355865	8356770	.	+	.	Phchi.S6G115000
Phchi.S6	AUGUSTUS	transcript	8355865	8356770	.	+	.	transcript_id "Phchi.S6G115000.t1"; gene_id "Phchi.S6G115000"
Phchi.S6	AUGUSTUS	start_codon	8355865	8355867	.	+	0	transcript_id "Phchi.S6G115000.t1"; gene_id "Phchi.S6G115000"
Phchi.S6	AUGUSTUS	CDS	8355865	8356770	0.94	+	0	transcript_id "Phchi.S6G115000.t1"; gene_id "Phchi.S6G115000"
Phchi.S6	AUGUSTUS	exon	8355865	8356770	.	+	.	transcript_id "Phchi.S6G115000.t1"; gene_id "Phchi.S6G115000"
Phchi.S6	AUGUSTUS	stop_codon	8356771	8356773	.	+	0	transcript_id "Phchi.S6G115000.t1"; gene_id "Phchi.S6G115000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8437.t1 is derived from g5612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35934552	35935736	.	-	.	Phchi.S1G559600
Phchi.S1	AUGUSTUS	transcript	35934552	35935736	.	-	.	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	stop_codon	35934549	35934551	.	-	0	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	CDS	35934552	35935195	0.94	-	2	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	exon	35934552	35935195	.	-	.	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	intron	35935196	35935306	.	-	.	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	CDS	35935307	35935736	1	-	0	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	exon	35935307	35935736	.	-	.	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
Phchi.S1	AUGUSTUS	start_codon	35935734	35935736	.	-	0	transcript_id "Phchi.S1G559600.t1"; gene_id "Phchi.S1G559600"
# This transcript jg3362.t2 is derived from g531.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3363.t1 is derived from g532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3151706	3152682	.	+	.	Phchi.S1G052200
Phchi.S1	AUGUSTUS	transcript	3151706	3152682	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	start_codon	3151706	3151708	.	+	0	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	CDS	3151706	3151746	0.66	+	0	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	exon	3151706	3151746	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	intron	3151747	3151872	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	CDS	3151873	3151893	1	+	1	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	exon	3151873	3151893	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	intron	3151894	3152093	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	CDS	3152094	3152156	1	+	1	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	exon	3152094	3152156	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	intron	3152157	3152263	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	CDS	3152264	3152361	1	+	1	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	exon	3152264	3152361	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	intron	3152362	3152459	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	CDS	3152460	3152492	1	+	2	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	exon	3152460	3152492	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	intron	3152493	3152617	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	CDS	3152618	3152682	1	+	2	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	exon	3152618	3152682	.	+	.	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
Phchi.S1	AUGUSTUS	stop_codon	3152683	3152685	.	+	0	transcript_id "Phchi.S1G052200.t1"; gene_id "Phchi.S1G052200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9617.t1 is derived from g6793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42943987	42946345	.	-	.	Phchi.S1G677600
Phchi.S1	AUGUSTUS	transcript	42943987	42946345	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	stop_codon	42943984	42943986	.	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42943987	42944091	1	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42943987	42944091	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944092	42944206	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944207	42944357	1	-	1	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944207	42944357	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944358	42944433	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944434	42944645	1	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944434	42944645	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944646	42944790	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944791	42944880	1	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944791	42944880	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944881	42944962	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944963	42945043	0.99	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944963	42945043	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945044	42945146	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945147	42945188	0.98	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945147	42945188	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945189	42945295	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945296	42945397	0.99	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945296	42945397	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945398	42945492	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945493	42945552	0.96	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945493	42945552	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945553	42945683	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945684	42945728	0.86	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945684	42945728	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945729	42945813	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945814	42946014	1	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945814	42946014	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42946015	42946108	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42946109	42946345	0.98	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42946109	42946345	.	-	.	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	start_codon	42946343	42946345	.	-	0	transcript_id "Phchi.S1G677600.t1"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	transcript	42943987	42946345	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	stop_codon	42943984	42943986	.	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42943987	42944091	0.99	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42943987	42944091	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944092	42944206	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944207	42944357	1	-	1	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944207	42944357	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944358	42944433	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944434	42944645	1	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944434	42944645	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944646	42944790	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944791	42944880	1	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944791	42944880	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42944881	42944962	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42944963	42945075	0.89	-	2	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42944963	42945075	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945076	42945146	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945147	42945188	0.98	-	2	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945147	42945188	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945189	42945285	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945286	42945397	1	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945286	42945397	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945398	42945492	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945493	42945552	0.95	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945493	42945552	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945553	42945683	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945684	42945728	0.84	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945684	42945728	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42945729	42945813	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42945814	42946014	1	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42945814	42946014	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	intron	42946015	42946108	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	CDS	42946109	42946345	0.98	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	exon	42946109	42946345	.	-	.	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
Phchi.S1	AUGUSTUS	start_codon	42946343	42946345	.	-	0	transcript_id "Phchi.S1G677600.t2"; gene_id "Phchi.S1G677600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7275.t1 is derived from g4447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28092165	28094834	.	-	.	Phchi.S1G443400
Phchi.S1	AUGUSTUS	transcript	28092165	28094834	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	stop_codon	28092162	28092164	.	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28092165	28092285	0.81	-	1	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28092165	28092285	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28092286	28092401	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28092402	28092460	1	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28092402	28092460	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28092461	28092574	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28092575	28092595	1	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28092575	28092595	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28092596	28092711	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28092712	28092858	1	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28092712	28092858	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28092859	28093028	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28093029	28093145	1	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28093029	28093145	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28093146	28093299	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28093300	28093364	0.79	-	2	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28093300	28093364	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28093365	28093477	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28093478	28093497	0.43	-	1	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28093478	28093497	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28093498	28093633	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28093634	28093821	0.96	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28093634	28093821	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28093822	28093929	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28093930	28094049	1	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28093930	28094049	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28094050	28094162	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28094163	28094189	1	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28094163	28094189	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28094190	28094343	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28094344	28094386	1	-	1	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28094344	28094386	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	intron	28094387	28094607	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	CDS	28094608	28094834	0.89	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	exon	28094608	28094834	.	-	.	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
Phchi.S1	AUGUSTUS	start_codon	28094832	28094834	.	-	0	transcript_id "Phchi.S1G443400.t1"; gene_id "Phchi.S1G443400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14545.t1 is derived from g13013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13410983	13413277	.	-	.	Phchi.S3G186400
Phchi.S3	AUGUSTUS	transcript	13410983	13413277	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	stop_codon	13410980	13410982	.	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13410983	13411189	0.99	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13410983	13411189	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13411190	13411280	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13411281	13411358	0.99	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13411281	13411358	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13411359	13411449	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13411450	13411525	0.85	-	1	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13411450	13411525	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13411526	13411630	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13411631	13412042	0.98	-	2	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13411631	13412042	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13412043	13412173	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13412174	13412287	0.99	-	2	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13412174	13412287	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13412288	13412378	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13412379	13412522	0.91	-	2	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13412379	13412522	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13412523	13412605	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13412606	13412732	1	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13412606	13412732	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13412733	13412831	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13412832	13412954	0.99	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13412832	13412954	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13412955	13413044	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13413045	13413140	0.65	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13413045	13413140	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	intron	13413141	13413235	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	CDS	13413236	13413277	0.65	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	exon	13413236	13413277	.	-	.	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
Phchi.S3	AUGUSTUS	start_codon	13413275	13413277	.	-	0	transcript_id "Phchi.S3G186400.t1"; gene_id "Phchi.S3G186400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8881.t1 is derived from g6056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38463289	38463822	.	+	.	Phchi.S1G604000
Phchi.S1	AUGUSTUS	transcript	38463289	38463822	.	+	.	transcript_id "Phchi.S1G604000.t1"; gene_id "Phchi.S1G604000"
Phchi.S1	AUGUSTUS	start_codon	38463289	38463291	.	+	0	transcript_id "Phchi.S1G604000.t1"; gene_id "Phchi.S1G604000"
Phchi.S1	AUGUSTUS	CDS	38463289	38463822	0.81	+	0	transcript_id "Phchi.S1G604000.t1"; gene_id "Phchi.S1G604000"
Phchi.S1	AUGUSTUS	exon	38463289	38463822	.	+	.	transcript_id "Phchi.S1G604000.t1"; gene_id "Phchi.S1G604000"
Phchi.S1	AUGUSTUS	stop_codon	38463823	38463825	.	+	0	transcript_id "Phchi.S1G604000.t1"; gene_id "Phchi.S1G604000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9241.t1 is derived from g6416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40562171	40563510	.	-	.	Phchi.S1G640000
Phchi.S1	AUGUSTUS	transcript	40562171	40563510	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	stop_codon	40562168	40562170	.	-	0	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	CDS	40562171	40562375	1	-	1	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	exon	40562171	40562375	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	intron	40562376	40562453	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	CDS	40562454	40562513	1	-	1	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	exon	40562454	40562513	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	intron	40562514	40562604	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	CDS	40562605	40562792	1	-	0	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	exon	40562605	40562792	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	intron	40562793	40562930	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	CDS	40562931	40563014	1	-	0	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	exon	40562931	40563014	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	intron	40563015	40563169	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	CDS	40563170	40563353	0.87	-	1	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	exon	40563170	40563353	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	intron	40563354	40563445	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	CDS	40563446	40563510	0.49	-	0	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	exon	40563446	40563510	.	-	.	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
Phchi.S1	AUGUSTUS	start_codon	40563508	40563510	.	-	0	transcript_id "Phchi.S1G640000.t1"; gene_id "Phchi.S1G640000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1237.t1 is derived from g11020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8548141	8550352	.	+	.	Phchi.S6G119600
Phchi.S6	AUGUSTUS	transcript	8548141	8550352	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	start_codon	8548141	8548143	.	+	0	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	CDS	8548141	8548876	0.38	+	0	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	exon	8548141	8548876	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	intron	8548877	8549120	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	CDS	8549121	8549149	0.26	+	2	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	exon	8549121	8549149	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	intron	8549150	8549378	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	CDS	8549379	8549435	0.57	+	0	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	exon	8549379	8549435	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	intron	8549436	8549531	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	CDS	8549532	8549717	0.59	+	0	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	exon	8549532	8549717	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	intron	8549718	8550061	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	CDS	8550062	8550352	0.7	+	0	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	exon	8550062	8550352	.	+	.	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
Phchi.S6	AUGUSTUS	stop_codon	8550353	8550355	.	+	0	transcript_id "Phchi.S6G119600.t1"; gene_id "Phchi.S6G119600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10754.t1 is derived from g14804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1940967	1944621	.	+	.	Phchi.S4G033600
Phchi.S4	AUGUSTUS	transcript	1940967	1944621	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	start_codon	1940967	1940969	.	+	0	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1940967	1941769	0.78	+	0	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1940967	1941769	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1941770	1941840	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1941841	1942660	1	+	1	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1941841	1942660	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1942661	1942752	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1942753	1942803	0.88	+	0	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1942753	1942803	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1942804	1942974	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1942975	1943256	1	+	0	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1942975	1943256	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1943257	1943427	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1943428	1943752	0.86	+	0	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1943428	1943752	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1943753	1943919	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1943920	1944016	0.77	+	2	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1943920	1944016	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1944017	1944133	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1944134	1944274	1	+	1	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1944134	1944274	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	intron	1944275	1944464	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	CDS	1944465	1944621	1	+	1	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	exon	1944465	1944621	.	+	.	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
Phchi.S4	AUGUSTUS	stop_codon	1944622	1944624	.	+	0	transcript_id "Phchi.S4G033600.t1"; gene_id "Phchi.S4G033600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12050.t1 is derived from g7725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1016306	1020296	.	+	.	Phchi.S2G013000
Phchi.S2	AUGUSTUS	transcript	1016306	1020296	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	start_codon	1016306	1016308	.	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1016306	1016409	0.85	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1016306	1016409	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1016410	1016486	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1016487	1016571	1	+	1	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1016487	1016571	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1016572	1016652	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1016653	1016952	1	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1016653	1016952	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1016953	1017038	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1017039	1017197	1	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1017039	1017197	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1017198	1017765	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1017766	1017906	1	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1017766	1017906	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1017907	1018224	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1018225	1018281	1	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1018225	1018281	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1018282	1018421	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1018422	1018560	1	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1018422	1018560	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1018561	1018895	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1018896	1018993	0.82	+	2	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1018896	1018993	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1018994	1019321	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1019322	1019373	0.67	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1019322	1019373	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1019374	1019484	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1019485	1019702	0.9	+	2	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1019485	1019702	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1019703	1019874	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1019875	1019913	1	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1019875	1019913	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	intron	1019914	1020152	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	CDS	1020153	1020296	0.98	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	exon	1020153	1020296	.	+	.	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
Phchi.S2	AUGUSTUS	stop_codon	1020297	1020299	.	+	0	transcript_id "Phchi.S2G013000.t1"; gene_id "Phchi.S2G013000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg792.t1 is derived from g10574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5604506	5605925	.	-	.	Phchi.S6G075100
Phchi.S6	AUGUSTUS	transcript	5604506	5605925	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	stop_codon	5604503	5604505	.	-	0	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	CDS	5604506	5604903	1	-	2	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	exon	5604506	5604903	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	intron	5604904	5605036	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	CDS	5605037	5605205	1	-	0	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	exon	5605037	5605205	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	intron	5605206	5605304	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	CDS	5605305	5605493	1	-	0	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	exon	5605305	5605493	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	intron	5605494	5605583	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	CDS	5605584	5605925	0.74	-	0	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	exon	5605584	5605925	.	-	.	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
Phchi.S6	AUGUSTUS	start_codon	5605923	5605925	.	-	0	transcript_id "Phchi.S6G075100.t1"; gene_id "Phchi.S6G075100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7376.t1 is derived from g4548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28825742	28827569	.	+	.	Phchi.S1G453500
Phchi.S1	AUGUSTUS	transcript	28825742	28827569	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	start_codon	28825742	28825744	.	+	0	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	CDS	28825742	28825768	0.76	+	0	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	exon	28825742	28825768	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	intron	28825769	28825957	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	CDS	28825958	28826092	0.76	+	0	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	exon	28825958	28826092	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	intron	28826093	28826235	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	CDS	28826236	28826390	1	+	0	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	exon	28826236	28826390	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	intron	28826391	28826499	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	CDS	28826500	28826637	1	+	1	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	exon	28826500	28826637	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	intron	28826638	28826728	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	CDS	28826729	28827569	1	+	1	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	exon	28826729	28827569	.	+	.	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
Phchi.S1	AUGUSTUS	stop_codon	28827570	28827572	.	+	0	transcript_id "Phchi.S1G453500.t1"; gene_id "Phchi.S1G453500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13413.t1 is derived from g11879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6591576	6593473	.	+	.	Phchi.S3G073200
Phchi.S3	AUGUSTUS	transcript	6591576	6593473	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	start_codon	6591576	6591578	.	+	0	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6591576	6591759	0.95	+	0	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6591576	6591759	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6591760	6591833	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6591834	6591939	1	+	2	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6591834	6591939	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6591940	6592020	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6592021	6592359	1	+	1	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6592021	6592359	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6592360	6592449	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6592450	6592683	0.68	+	1	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6592450	6592683	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6592684	6592818	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6592819	6592873	0.87	+	1	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6592819	6592873	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6592874	6592967	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6592968	6593066	1	+	0	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6592968	6593066	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6593067	6593185	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6593186	6593268	1	+	0	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6593186	6593268	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	intron	6593269	6593367	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	CDS	6593368	6593473	1	+	1	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	exon	6593368	6593473	.	+	.	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
Phchi.S3	AUGUSTUS	stop_codon	6593474	6593476	.	+	0	transcript_id "Phchi.S3G073200.t1"; gene_id "Phchi.S3G073200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2695.t1 is derived from g9615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8236415	8238223	.	+	.	Phchi.S5G130400
Phchi.S5	AUGUSTUS	transcript	8236415	8238223	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	start_codon	8236415	8236417	.	+	0	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8236415	8236563	1	+	0	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8236415	8236563	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	intron	8236564	8236770	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8236771	8236900	1	+	1	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8236771	8236900	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	intron	8236901	8237078	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8237079	8237216	1	+	0	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8237079	8237216	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	intron	8237217	8237320	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8237321	8237460	1	+	0	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8237321	8237460	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	intron	8237461	8237535	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8237536	8237653	1	+	1	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8237536	8237653	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	intron	8237654	8237778	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8237779	8237962	1	+	0	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8237779	8237962	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	intron	8237963	8238059	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	CDS	8238060	8238223	0.93	+	2	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	exon	8238060	8238223	.	+	.	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
Phchi.S5	AUGUSTUS	stop_codon	8238224	8238226	.	+	0	transcript_id "Phchi.S5G130400.t1"; gene_id "Phchi.S5G130400"
# This transcript jg11810.t2 is derived from g15862.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11811.t1 is derived from g15863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8342668	8343135	.	+	.	Phchi.S4G139300
Phchi.S4	AUGUSTUS	transcript	8342668	8343135	.	+	.	transcript_id "Phchi.S4G139300.t1"; gene_id "Phchi.S4G139300"
Phchi.S4	AUGUSTUS	start_codon	8342668	8342670	.	+	0	transcript_id "Phchi.S4G139300.t1"; gene_id "Phchi.S4G139300"
Phchi.S4	AUGUSTUS	CDS	8342668	8343135	1	+	0	transcript_id "Phchi.S4G139300.t1"; gene_id "Phchi.S4G139300"
Phchi.S4	AUGUSTUS	exon	8342668	8343135	.	+	.	transcript_id "Phchi.S4G139300.t1"; gene_id "Phchi.S4G139300"
Phchi.S4	AUGUSTUS	stop_codon	8343136	8343138	.	+	0	transcript_id "Phchi.S4G139300.t1"; gene_id "Phchi.S4G139300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14931.t1 is derived from g13399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15574169	15575803	.	-	.	Phchi.S3G225000
Phchi.S3	AUGUSTUS	transcript	15574169	15575803	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	stop_codon	15574166	15574168	.	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574169	15574216	0.53	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574169	15574216	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574217	15574293	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574294	15574354	1	-	1	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574294	15574354	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574355	15574472	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574473	15574538	1	-	1	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574473	15574538	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574539	15574616	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574617	15574708	1	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574617	15574708	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574709	15574843	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574844	15574918	1	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574844	15574918	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574919	15575150	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15575151	15575246	1	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15575151	15575246	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15575247	15575334	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15575335	15575479	1	-	1	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15575335	15575479	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15575480	15575558	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15575559	15575803	0.98	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15575559	15575803	.	-	.	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	start_codon	15575801	15575803	.	-	0	transcript_id "Phchi.S3G225000.t1"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	transcript	15574169	15575803	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	stop_codon	15574166	15574168	.	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574169	15574216	0.48	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574169	15574216	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574217	15574293	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574294	15574354	1	-	1	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574294	15574354	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574355	15574472	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574473	15574538	1	-	1	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574473	15574538	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574539	15574616	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574617	15574708	1	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574617	15574708	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574709	15574843	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15574844	15574918	1	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15574844	15574918	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15574919	15575150	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15575151	15575246	1	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15575151	15575246	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15575247	15575334	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15575335	15575422	1	-	1	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15575335	15575422	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	intron	15575423	15575558	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	CDS	15575559	15575803	1	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	exon	15575559	15575803	.	-	.	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
Phchi.S3	AUGUSTUS	start_codon	15575801	15575803	.	-	0	transcript_id "Phchi.S3G225000.t2"; gene_id "Phchi.S3G225000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11620.t1 is derived from g15671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7353283	7354439	.	-	.	Phchi.S4G120200
Phchi.S4	AUGUSTUS	transcript	7353283	7354439	.	-	.	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	stop_codon	7353280	7353282	.	-	0	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	CDS	7353283	7353506	0.98	-	2	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	exon	7353283	7353506	.	-	.	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	intron	7353507	7353622	.	-	.	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	CDS	7353623	7354439	0.99	-	0	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	exon	7353623	7354439	.	-	.	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
Phchi.S4	AUGUSTUS	start_codon	7354437	7354439	.	-	0	transcript_id "Phchi.S4G120200.t1"; gene_id "Phchi.S4G120200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8510.t1 is derived from g5685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36382598	36383398	.	+	.	Phchi.S1G566900
Phchi.S1	AUGUSTUS	transcript	36382598	36383398	.	+	.	transcript_id "Phchi.S1G566900.t1"; gene_id "Phchi.S1G566900"
Phchi.S1	AUGUSTUS	start_codon	36382598	36382600	.	+	0	transcript_id "Phchi.S1G566900.t1"; gene_id "Phchi.S1G566900"
Phchi.S1	AUGUSTUS	CDS	36382598	36383398	0.96	+	0	transcript_id "Phchi.S1G566900.t1"; gene_id "Phchi.S1G566900"
Phchi.S1	AUGUSTUS	exon	36382598	36383398	.	+	.	transcript_id "Phchi.S1G566900.t1"; gene_id "Phchi.S1G566900"
Phchi.S1	AUGUSTUS	stop_codon	36383399	36383401	.	+	0	transcript_id "Phchi.S1G566900.t1"; gene_id "Phchi.S1G566900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2077.t1 is derived from g8997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4735235	4737857	.	+	.	Phchi.S5G068600
Phchi.S5	AUGUSTUS	transcript	4735235	4737857	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	start_codon	4735235	4735237	.	+	0	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	CDS	4735235	4735397	0.95	+	0	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	exon	4735235	4735397	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	intron	4735398	4735483	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	CDS	4735484	4735701	0.96	+	2	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	exon	4735484	4735701	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	intron	4735702	4735805	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	CDS	4735806	4736365	0.95	+	0	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	exon	4735806	4736365	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	intron	4736366	4736462	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	CDS	4736463	4737329	0.72	+	1	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	exon	4736463	4737329	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	intron	4737330	4737577	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	CDS	4737578	4737692	0.64	+	1	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	exon	4737578	4737692	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	intron	4737693	4737854	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	CDS	4737855	4737857	0.76	+	0	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	exon	4737855	4737857	.	+	.	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
Phchi.S5	AUGUSTUS	stop_codon	4737858	4737860	.	+	0	transcript_id "Phchi.S5G068600.t1"; gene_id "Phchi.S5G068600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10524.t1 is derived from g14574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	831609	832954	.	+	.	Phchi.S4G010600
Phchi.S4	AUGUSTUS	transcript	831609	832954	.	+	.	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	start_codon	831609	831611	.	+	0	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	CDS	831609	832097	0.55	+	0	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	exon	831609	832097	.	+	.	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	intron	832098	832186	.	+	.	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	CDS	832187	832954	0.64	+	0	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	exon	832187	832954	.	+	.	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	stop_codon	832955	832957	.	+	0	transcript_id "Phchi.S4G010600.t1"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	transcript	831609	832821	.	+	.	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	start_codon	831609	831611	.	+	0	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	CDS	831609	832216	0.47	+	0	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	exon	831609	832216	.	+	.	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	intron	832217	832296	.	+	.	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	CDS	832297	832532	0.39	+	1	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	exon	832297	832532	.	+	.	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	intron	832533	832696	.	+	.	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	CDS	832697	832821	0.78	+	2	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	exon	832697	832821	.	+	.	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
Phchi.S4	AUGUSTUS	stop_codon	832822	832824	.	+	0	transcript_id "Phchi.S4G010600.t2"; gene_id "Phchi.S4G010600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9411.t1 is derived from g6587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41369110	41370069	.	-	.	Phchi.S1G657000
Phchi.S1	AUGUSTUS	transcript	41369110	41370069	.	-	.	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	stop_codon	41369107	41369109	.	-	0	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	CDS	41369110	41369765	1	-	2	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	exon	41369110	41369765	.	-	.	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	intron	41369766	41369852	.	-	.	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	CDS	41369853	41370069	0.99	-	0	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	exon	41369853	41370069	.	-	.	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
Phchi.S1	AUGUSTUS	start_codon	41370067	41370069	.	-	0	transcript_id "Phchi.S1G657000.t1"; gene_id "Phchi.S1G657000"
# This transcript jg337.t2 is derived from g10119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg338.t1 is derived from g10120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2477125	2477810	.	-	.	Phchi.S6G029700
Phchi.S6	AUGUSTUS	transcript	2477125	2477810	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	stop_codon	2477122	2477124	.	-	0	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	CDS	2477125	2477158	1	-	1	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	exon	2477125	2477158	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	intron	2477159	2477234	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	CDS	2477235	2477298	1	-	2	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	exon	2477235	2477298	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	intron	2477299	2477475	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	CDS	2477476	2477595	1	-	2	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	exon	2477476	2477595	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	intron	2477596	2477728	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	CDS	2477729	2477810	1	-	0	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	exon	2477729	2477810	.	-	.	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
Phchi.S6	AUGUSTUS	start_codon	2477808	2477810	.	-	0	transcript_id "Phchi.S6G029700.t1"; gene_id "Phchi.S6G029700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6900.t1 is derived from g4072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25897821	25898258	.	-	.	Phchi.S1G405900
Phchi.S1	AUGUSTUS	transcript	25897821	25898258	.	-	.	transcript_id "Phchi.S1G405900.t1"; gene_id "Phchi.S1G405900"
Phchi.S1	AUGUSTUS	stop_codon	25897818	25897820	.	-	0	transcript_id "Phchi.S1G405900.t1"; gene_id "Phchi.S1G405900"
Phchi.S1	AUGUSTUS	CDS	25897821	25898258	0.83	-	0	transcript_id "Phchi.S1G405900.t1"; gene_id "Phchi.S1G405900"
Phchi.S1	AUGUSTUS	exon	25897821	25898258	.	-	.	transcript_id "Phchi.S1G405900.t1"; gene_id "Phchi.S1G405900"
Phchi.S1	AUGUSTUS	start_codon	25898256	25898258	.	-	0	transcript_id "Phchi.S1G405900.t1"; gene_id "Phchi.S1G405900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2150.t1 is derived from g9070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5078240	5078726	.	+	.	Phchi.S5G075900
Phchi.S5	AUGUSTUS	transcript	5078240	5078726	.	+	.	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	start_codon	5078240	5078242	.	+	0	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	CDS	5078240	5078401	1	+	0	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	exon	5078240	5078401	.	+	.	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	intron	5078402	5078540	.	+	.	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	CDS	5078541	5078726	1	+	0	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	exon	5078541	5078726	.	+	.	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
Phchi.S5	AUGUSTUS	stop_codon	5078727	5078729	.	+	0	transcript_id "Phchi.S5G075900.t1"; gene_id "Phchi.S5G075900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg162.t1 is derived from g9944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	932568	936258	.	+	.	Phchi.S6G012100
Phchi.S6	AUGUSTUS	transcript	932568	936258	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	start_codon	932568	932570	.	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	932568	932751	0.98	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	932568	932751	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	932752	932833	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	932834	932916	1	+	2	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	932834	932916	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	932917	933012	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	933013	933107	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	933013	933107	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	933108	933186	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	933187	933290	1	+	1	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	933187	933290	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	933291	933435	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	933436	933605	1	+	2	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	933436	933605	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	933606	933745	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	933746	933860	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	933746	933860	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	933861	933995	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	933996	934054	1	+	2	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	933996	934054	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	934055	934168	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	934169	934228	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	934169	934228	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	934229	934395	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	934396	934494	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	934396	934494	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	934495	934587	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	934588	934650	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	934588	934650	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	934651	934733	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	934734	934796	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	934734	934796	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	934797	934868	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	934869	934951	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	934869	934951	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	934952	935061	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	935062	935170	1	+	1	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	935062	935170	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	935171	935254	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	935255	935308	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	935255	935308	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	935309	935429	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	935430	935517	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	935430	935517	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	935518	935611	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	935612	935649	1	+	2	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	935612	935649	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	935650	935743	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	935744	935849	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	935744	935849	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	935850	935939	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	935940	936106	1	+	2	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	935940	936106	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	intron	936107	936189	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	CDS	936190	936258	1	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	exon	936190	936258	.	+	.	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
Phchi.S6	AUGUSTUS	stop_codon	936259	936261	.	+	0	transcript_id "Phchi.S6G012100.t1"; gene_id "Phchi.S6G012100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13644.t1 is derived from g12111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7993425	7994336	.	-	.	Phchi.S3G096300
Phchi.S3	AUGUSTUS	transcript	7993425	7994336	.	-	.	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	stop_codon	7993422	7993424	.	-	0	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	CDS	7993425	7993595	1	-	0	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	exon	7993425	7993595	.	-	.	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	intron	7993596	7993699	.	-	.	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	CDS	7993700	7994030	1	-	1	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	exon	7993700	7994030	.	-	.	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	intron	7994031	7994118	.	-	.	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	CDS	7994119	7994336	0.93	-	0	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	exon	7994119	7994336	.	-	.	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
Phchi.S3	AUGUSTUS	start_codon	7994334	7994336	.	-	0	transcript_id "Phchi.S3G096300.t1"; gene_id "Phchi.S3G096300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6154.t1 is derived from g3325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21215792	21216531	.	-	.	Phchi.S1G331300
Phchi.S1	AUGUSTUS	transcript	21215792	21216531	.	-	.	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	stop_codon	21215789	21215791	.	-	0	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	CDS	21215792	21216204	0.99	-	2	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	exon	21215792	21216204	.	-	.	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	intron	21216205	21216308	.	-	.	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	CDS	21216309	21216531	0.73	-	0	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	exon	21216309	21216531	.	-	.	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
Phchi.S1	AUGUSTUS	start_codon	21216529	21216531	.	-	0	transcript_id "Phchi.S1G331300.t1"; gene_id "Phchi.S1G331300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6654.t1 is derived from g3826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24317113	24319266	.	+	.	Phchi.S1G381300
Phchi.S1	AUGUSTUS	transcript	24317113	24319266	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	start_codon	24317113	24317115	.	+	0	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	CDS	24317113	24317143	0.61	+	0	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	exon	24317113	24317143	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	intron	24317144	24317390	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	CDS	24317391	24317699	0.54	+	2	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	exon	24317391	24317699	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	intron	24317700	24317817	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	CDS	24317818	24318398	1	+	2	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	exon	24317818	24318398	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	intron	24318399	24318534	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	CDS	24318535	24318783	1	+	0	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	exon	24318535	24318783	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	intron	24318784	24318894	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	CDS	24318895	24319266	0.89	+	0	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	exon	24318895	24319266	.	+	.	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
Phchi.S1	AUGUSTUS	stop_codon	24319267	24319269	.	+	0	transcript_id "Phchi.S1G381300.t1"; gene_id "Phchi.S1G381300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7425.t1 is derived from g4597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29081962	29084540	.	+	.	Phchi.S1G458400
Phchi.S1	AUGUSTUS	transcript	29081962	29084540	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	start_codon	29081962	29081964	.	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29081962	29082045	1	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29081962	29082045	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29082046	29082143	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29082144	29082190	1	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29082144	29082190	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29082191	29082345	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29082346	29082416	1	+	1	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29082346	29082416	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29082417	29082507	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29082508	29082621	1	+	2	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29082508	29082621	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29082622	29082707	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29082708	29082883	1	+	2	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29082708	29082883	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29082884	29082999	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29083000	29083088	0.99	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29083000	29083088	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29083089	29083263	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29083264	29083381	0.99	+	1	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29083264	29083381	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29083382	29083495	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29083496	29083569	1	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29083496	29083569	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29083570	29083656	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29083657	29083704	1	+	1	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29083657	29083704	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29083705	29083825	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29083826	29083967	1	+	1	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29083826	29083967	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29083968	29084055	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29084056	29084265	1	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29084056	29084265	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	intron	29084266	29084351	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	CDS	29084352	29084540	0.85	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	exon	29084352	29084540	.	+	.	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
Phchi.S1	AUGUSTUS	stop_codon	29084541	29084543	.	+	0	transcript_id "Phchi.S1G458400.t1"; gene_id "Phchi.S1G458400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11519.t1 is derived from g15569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6885740	6886408	.	+	.	Phchi.S4G110100
Phchi.S4	AUGUSTUS	transcript	6885740	6886408	.	+	.	transcript_id "Phchi.S4G110100.t1"; gene_id "Phchi.S4G110100"
Phchi.S4	AUGUSTUS	start_codon	6885740	6885742	.	+	0	transcript_id "Phchi.S4G110100.t1"; gene_id "Phchi.S4G110100"
Phchi.S4	AUGUSTUS	CDS	6885740	6886408	0.79	+	0	transcript_id "Phchi.S4G110100.t1"; gene_id "Phchi.S4G110100"
Phchi.S4	AUGUSTUS	exon	6885740	6886408	.	+	.	transcript_id "Phchi.S4G110100.t1"; gene_id "Phchi.S4G110100"
Phchi.S4	AUGUSTUS	stop_codon	6886409	6886411	.	+	0	transcript_id "Phchi.S4G110100.t1"; gene_id "Phchi.S4G110100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12902.t1 is derived from g11367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3077468	3079431	.	+	.	Phchi.S3G022100
Phchi.S3	AUGUSTUS	transcript	3077468	3079431	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	start_codon	3077468	3077470	.	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3077468	3077497	0.58	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3077468	3077497	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3077498	3077622	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3077623	3077922	1	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3077623	3077922	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3077923	3078026	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3078027	3078128	0.96	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3078027	3078128	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3078129	3078256	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3078257	3078427	0.64	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3078257	3078427	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3078428	3078547	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3078548	3078627	0.88	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3078548	3078627	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3078628	3078734	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3078735	3078864	0.9	+	1	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3078735	3078864	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3078865	3078968	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3078969	3079155	0.99	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3078969	3079155	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3079156	3079240	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3079241	3079287	1	+	2	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3079241	3079287	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	intron	3079288	3079374	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	CDS	3079375	3079431	1	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	exon	3079375	3079431	.	+	.	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
Phchi.S3	AUGUSTUS	stop_codon	3079432	3079434	.	+	0	transcript_id "Phchi.S3G022100.t1"; gene_id "Phchi.S3G022100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2879.t1 is derived from g48.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	242556	245954	.	-	.	Phchi.S1G003800
Phchi.S1	AUGUSTUS	transcript	242556	245954	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	stop_codon	242553	242555	.	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	242556	242672	0.86	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	242556	242672	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	242673	242777	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	242778	242844	1	-	1	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	242778	242844	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	242845	242935	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	242936	243075	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	242936	243075	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	243076	243163	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	243164	243256	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	243164	243256	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	243257	243420	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	243421	243603	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	243421	243603	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	243604	243684	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	243685	243789	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	243685	243789	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	243790	243947	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	243948	244028	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	243948	244028	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	244029	244123	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	244124	244265	1	-	1	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	244124	244265	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	244266	244406	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	244407	244486	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	244407	244486	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	244487	244578	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	244579	244691	0.98	-	2	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	244579	244691	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	244692	244793	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	244794	245040	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	244794	245040	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	245041	245189	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	245190	245614	1	-	2	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	245190	245614	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	intron	245615	245926	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	CDS	245927	245954	1	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	exon	245927	245954	.	-	.	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
Phchi.S1	AUGUSTUS	start_codon	245952	245954	.	-	0	transcript_id "Phchi.S1G003800.t1"; gene_id "Phchi.S1G003800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13870.t1 is derived from g12337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9394090	9395409	.	+	.	Phchi.S3G118900
Phchi.S3	AUGUSTUS	transcript	9394090	9395409	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	start_codon	9394090	9394092	.	+	0	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	CDS	9394090	9394269	1	+	0	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	exon	9394090	9394269	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	intron	9394270	9394373	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	CDS	9394374	9394508	0.95	+	0	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	exon	9394374	9394508	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	intron	9394509	9394612	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	CDS	9394613	9394844	0.99	+	0	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	exon	9394613	9394844	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	intron	9394845	9394942	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	CDS	9394943	9395146	1	+	2	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	exon	9394943	9395146	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	intron	9395147	9395248	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	CDS	9395249	9395409	0.88	+	2	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	exon	9395249	9395409	.	+	.	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
Phchi.S3	AUGUSTUS	stop_codon	9395410	9395412	.	+	0	transcript_id "Phchi.S3G118900.t1"; gene_id "Phchi.S3G118900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11410.t1 is derived from g15460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6226553	6227053	.	-	.	Phchi.S4G099200
Phchi.S4	AUGUSTUS	transcript	6226553	6227053	.	-	.	transcript_id "Phchi.S4G099200.t1"; gene_id "Phchi.S4G099200"
Phchi.S4	AUGUSTUS	stop_codon	6226550	6226552	.	-	0	transcript_id "Phchi.S4G099200.t1"; gene_id "Phchi.S4G099200"
Phchi.S4	AUGUSTUS	CDS	6226553	6227053	0.79	-	0	transcript_id "Phchi.S4G099200.t1"; gene_id "Phchi.S4G099200"
Phchi.S4	AUGUSTUS	exon	6226553	6227053	.	-	.	transcript_id "Phchi.S4G099200.t1"; gene_id "Phchi.S4G099200"
Phchi.S4	AUGUSTUS	start_codon	6227051	6227053	.	-	0	transcript_id "Phchi.S4G099200.t1"; gene_id "Phchi.S4G099200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3440.t1 is derived from g609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3687691	3688368	.	-	.	Phchi.S1G059900
Phchi.S1	AUGUSTUS	transcript	3687691	3688368	.	-	.	transcript_id "Phchi.S1G059900.t1"; gene_id "Phchi.S1G059900"
Phchi.S1	AUGUSTUS	stop_codon	3687688	3687690	.	-	0	transcript_id "Phchi.S1G059900.t1"; gene_id "Phchi.S1G059900"
Phchi.S1	AUGUSTUS	CDS	3687691	3688368	0.98	-	0	transcript_id "Phchi.S1G059900.t1"; gene_id "Phchi.S1G059900"
Phchi.S1	AUGUSTUS	exon	3687691	3688368	.	-	.	transcript_id "Phchi.S1G059900.t1"; gene_id "Phchi.S1G059900"
Phchi.S1	AUGUSTUS	start_codon	3688366	3688368	.	-	0	transcript_id "Phchi.S1G059900.t1"; gene_id "Phchi.S1G059900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5723.t1 is derived from g2893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18550317	18550793	.	-	.	Phchi.S1G288200
Phchi.S1	AUGUSTUS	transcript	18550317	18550793	.	-	.	transcript_id "Phchi.S1G288200.t1"; gene_id "Phchi.S1G288200"
Phchi.S1	AUGUSTUS	stop_codon	18550314	18550316	.	-	0	transcript_id "Phchi.S1G288200.t1"; gene_id "Phchi.S1G288200"
Phchi.S1	AUGUSTUS	CDS	18550317	18550793	0.94	-	0	transcript_id "Phchi.S1G288200.t1"; gene_id "Phchi.S1G288200"
Phchi.S1	AUGUSTUS	exon	18550317	18550793	.	-	.	transcript_id "Phchi.S1G288200.t1"; gene_id "Phchi.S1G288200"
Phchi.S1	AUGUSTUS	start_codon	18550791	18550793	.	-	0	transcript_id "Phchi.S1G288200.t1"; gene_id "Phchi.S1G288200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5014.t1 is derived from g2184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14057221	14059949	.	+	.	Phchi.S1G217300
Phchi.S1	AUGUSTUS	transcript	14057221	14059949	.	+	.	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	start_codon	14057221	14057223	.	+	0	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	CDS	14057221	14058729	1	+	0	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	exon	14057221	14058729	.	+	.	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	intron	14058730	14058851	.	+	.	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	CDS	14058852	14059949	0.99	+	0	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	exon	14058852	14059949	.	+	.	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
Phchi.S1	AUGUSTUS	stop_codon	14059950	14059952	.	+	0	transcript_id "Phchi.S1G217300.t1"; gene_id "Phchi.S1G217300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2757.t1 is derived from g9677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8678417	8682564	.	+	.	Phchi.S5G136600
Phchi.S5	AUGUSTUS	transcript	8678417	8682564	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	start_codon	8678417	8678419	.	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8678417	8678608	0.47	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8678417	8678608	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8678609	8678717	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8678718	8678792	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8678718	8678792	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8678793	8678922	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8678923	8679030	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8678923	8679030	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8679031	8679191	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8679192	8679224	0.99	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8679192	8679224	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8679225	8679330	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8679331	8679414	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8679331	8679414	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8679415	8679625	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8679626	8679754	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8679626	8679754	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8679755	8679895	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8679896	8680039	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8679896	8680039	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8680040	8680159	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8680160	8680567	0.95	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8680160	8680567	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8680568	8680667	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8680668	8680802	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8680668	8680802	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8680803	8680955	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8680956	8681180	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8680956	8681180	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8681181	8681303	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8681304	8681579	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8681304	8681579	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8681580	8681660	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8681661	8681813	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8681661	8681813	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8681814	8681940	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8681941	8682264	0.93	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8681941	8682264	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	intron	8682265	8682372	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	CDS	8682373	8682564	1	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	exon	8682373	8682564	.	+	.	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
Phchi.S5	AUGUSTUS	stop_codon	8682565	8682567	.	+	0	transcript_id "Phchi.S5G136600.t1"; gene_id "Phchi.S5G136600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9051.t1 is derived from g6226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39399005	39401944	.	+	.	Phchi.S1G621000
Phchi.S1	AUGUSTUS	transcript	39399005	39401944	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	start_codon	39399005	39399007	.	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39399005	39399397	0.94	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39399005	39399397	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39399398	39399506	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39399507	39399554	0.93	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39399507	39399554	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39399555	39399687	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39399688	39399738	1	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39399688	39399738	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39399739	39399967	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39399968	39400011	1	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39399968	39400011	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39400012	39400092	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39400093	39400156	1	+	1	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39400093	39400156	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39400157	39400291	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39400292	39400381	0.97	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39400292	39400381	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39400382	39400455	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39400456	39400547	1	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39400456	39400547	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39400548	39400664	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39400665	39400749	0.99	+	1	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39400665	39400749	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39400750	39400839	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39400840	39400925	0.99	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39400840	39400925	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39400926	39401046	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39401047	39401156	0.99	+	1	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39401047	39401156	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39401157	39401244	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39401245	39401337	0.99	+	2	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39401245	39401337	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39401338	39401451	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39401452	39401516	0.99	+	2	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39401452	39401516	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39401517	39401633	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39401634	39401774	0.67	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39401634	39401774	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	intron	39401775	39401905	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	CDS	39401906	39401944	0.64	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	exon	39401906	39401944	.	+	.	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
Phchi.S1	AUGUSTUS	stop_codon	39401945	39401947	.	+	0	transcript_id "Phchi.S1G621000.t1"; gene_id "Phchi.S1G621000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11468.t1 is derived from g15518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6506302	6507443	.	+	.	Phchi.S4G105000
Phchi.S4	AUGUSTUS	transcript	6506302	6507443	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	start_codon	6506302	6506304	.	+	0	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	CDS	6506302	6506480	0.48	+	0	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	exon	6506302	6506480	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	intron	6506481	6506570	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	CDS	6506571	6506703	0.91	+	1	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	exon	6506571	6506703	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	intron	6506704	6506968	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	CDS	6506969	6507279	0.27	+	0	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	exon	6506969	6507279	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	intron	6507280	6507379	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	CDS	6507380	6507443	0.41	+	1	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	exon	6507380	6507443	.	+	.	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
Phchi.S4	AUGUSTUS	stop_codon	6507444	6507446	.	+	0	transcript_id "Phchi.S4G105000.t1"; gene_id "Phchi.S4G105000"
# This transcript jg3782.t2 is derived from g951.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3783.t1 is derived from g952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5667426	5670041	.	+	.	Phchi.S1G094200
Phchi.S1	AUGUSTUS	transcript	5667426	5670041	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	start_codon	5667426	5667428	.	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5667426	5667492	0.52	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5667426	5667492	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5667493	5667670	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5667671	5667870	0.51	+	2	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5667671	5667870	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5667871	5668030	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5668031	5668142	1	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5668031	5668142	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5668143	5668246	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5668247	5668375	0.74	+	2	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5668247	5668375	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5668376	5668469	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5668470	5668519	0.93	+	2	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5668470	5668519	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5668520	5668623	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5668624	5668782	0.98	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5668624	5668782	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5668783	5669059	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5669060	5669175	1	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5669060	5669175	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5669176	5669313	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5669314	5669437	1	+	1	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5669314	5669437	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5669438	5669516	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5669517	5669710	0.59	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5669517	5669710	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	intron	5669711	5669932	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	CDS	5669933	5670041	0.59	+	1	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	exon	5669933	5670041	.	+	.	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
Phchi.S1	AUGUSTUS	stop_codon	5670042	5670044	.	+	0	transcript_id "Phchi.S1G094200.t1"; gene_id "Phchi.S1G094200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15501.t1 is derived from g13970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19559929	19561424	.	-	.	Phchi.S3G282000
Phchi.S3	AUGUSTUS	transcript	19559929	19561424	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	stop_codon	19559926	19559928	.	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	CDS	19559929	19560009	1	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	exon	19559929	19560009	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	intron	19560010	19560106	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	CDS	19560107	19560221	1	-	1	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	exon	19560107	19560221	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	intron	19560222	19560399	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	CDS	19560400	19560494	1	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	exon	19560400	19560494	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	intron	19560495	19560692	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	CDS	19560693	19560785	1	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	exon	19560693	19560785	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	intron	19560786	19560966	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	CDS	19560967	19561017	1	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	exon	19560967	19561017	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	intron	19561018	19561193	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	CDS	19561194	19561424	0.86	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	exon	19561194	19561424	.	-	.	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
Phchi.S3	AUGUSTUS	start_codon	19561422	19561424	.	-	0	transcript_id "Phchi.S3G282000.t1"; gene_id "Phchi.S3G282000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10901.t1 is derived from g14952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2816526	2817341	.	+	.	Phchi.S4G048400
Phchi.S4	AUGUSTUS	transcript	2816526	2817341	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	start_codon	2816526	2816528	.	+	0	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	CDS	2816526	2816666	0.99	+	0	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	exon	2816526	2816666	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	intron	2816667	2816762	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	CDS	2816763	2816863	1	+	0	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	exon	2816763	2816863	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	intron	2816864	2816998	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	CDS	2816999	2817140	1	+	1	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	exon	2816999	2817140	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	intron	2817141	2817227	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	CDS	2817228	2817341	1	+	0	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	exon	2817228	2817341	.	+	.	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
Phchi.S4	AUGUSTUS	stop_codon	2817342	2817344	.	+	0	transcript_id "Phchi.S4G048400.t1"; gene_id "Phchi.S4G048400"
# This transcript jg4025.t2 is derived from g1194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4026.t1 is derived from g1195.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7224544	7225498	.	+	.	Phchi.S1G118500
Phchi.S1	AUGUSTUS	transcript	7224544	7225498	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	start_codon	7224544	7224546	.	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7224544	7224642	0.94	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7224544	7224642	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7224643	7224738	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7224739	7224853	1	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7224739	7224853	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7224854	7224944	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7224945	7225012	1	+	2	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7224945	7225012	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7225013	7225095	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7225096	7225161	1	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7225096	7225161	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7225162	7225259	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7225260	7225316	1	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7225260	7225316	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7225317	7225393	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7225394	7225498	0.73	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7225394	7225498	.	+	.	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	stop_codon	7225499	7225501	.	+	0	transcript_id "Phchi.S1G118500.t1"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	transcript	7224544	7225498	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	start_codon	7224544	7224546	.	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7224544	7224642	0.94	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7224544	7224642	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7224643	7224738	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7224739	7224853	1	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7224739	7224853	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7224854	7224944	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7224945	7225012	1	+	2	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7224945	7225012	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7225013	7225098	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7225099	7225161	1	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7225099	7225161	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7225162	7225259	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7225260	7225316	1	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7225260	7225316	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	intron	7225317	7225393	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	CDS	7225394	7225498	0.71	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	exon	7225394	7225498	.	+	.	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
Phchi.S1	AUGUSTUS	stop_codon	7225499	7225501	.	+	0	transcript_id "Phchi.S1G118500.t2"; gene_id "Phchi.S1G118500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1289.t1 is derived from g11072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8858232	8859619	.	+	.	Phchi.S6G124800
Phchi.S6	AUGUSTUS	transcript	8858232	8859619	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	start_codon	8858232	8858234	.	+	0	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	CDS	8858232	8858318	1	+	0	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	exon	8858232	8858318	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	intron	8858319	8858395	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	CDS	8858396	8858470	1	+	0	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	exon	8858396	8858470	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	intron	8858471	8858567	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	CDS	8858568	8858698	1	+	0	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	exon	8858568	8858698	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	intron	8858699	8858784	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	CDS	8858785	8859308	0.94	+	1	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	exon	8858785	8859308	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	intron	8859309	8859446	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	CDS	8859447	8859619	0.94	+	2	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	exon	8859447	8859619	.	+	.	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
Phchi.S6	AUGUSTUS	stop_codon	8859620	8859622	.	+	0	transcript_id "Phchi.S6G124800.t1"; gene_id "Phchi.S6G124800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11156.t1 is derived from g15206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4412191	4416712	.	+	.	Phchi.S4G073800
Phchi.S4	AUGUSTUS	transcript	4412191	4416712	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	start_codon	4412191	4412193	.	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4412191	4412379	0.99	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4412191	4412379	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4412380	4412499	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4412500	4412589	1	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4412500	4412589	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4412590	4412736	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4412737	4412960	1	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4412737	4412960	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4412961	4413050	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4413051	4413114	1	+	1	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4413051	4413114	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4413115	4413257	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4413258	4413826	0.99	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4413258	4413826	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4413827	4414185	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4414186	4414237	1	+	1	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4414186	4414237	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4414238	4414370	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4414371	4414502	1	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4414371	4414502	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4414503	4414590	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4414591	4414767	1	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4414591	4414767	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4414768	4414848	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4414849	4414902	1	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4414849	4414902	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4414903	4414996	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4414997	4415059	1	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4414997	4415059	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4415060	4415159	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4415160	4415880	0.85	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4415160	4415880	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4415881	4416005	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4416006	4416112	0.76	+	2	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4416006	4416112	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4416113	4416193	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4416194	4416321	0.97	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4416194	4416321	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	intron	4416322	4416441	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	CDS	4416442	4416712	1	+	1	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	exon	4416442	4416712	.	+	.	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
Phchi.S4	AUGUSTUS	stop_codon	4416713	4416715	.	+	0	transcript_id "Phchi.S4G073800.t1"; gene_id "Phchi.S4G073800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15777.t1 is derived from g14247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21293547	21295744	.	-	.	Phchi.S3G309600
Phchi.S3	AUGUSTUS	transcript	21293547	21295744	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	stop_codon	21293544	21293546	.	-	0	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	CDS	21293547	21293759	0.55	-	0	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	exon	21293547	21293759	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	intron	21293760	21293865	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	CDS	21293866	21294043	0.58	-	1	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	exon	21293866	21294043	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	intron	21294044	21294390	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	CDS	21294391	21294668	0.76	-	0	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	exon	21294391	21294668	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	intron	21294669	21294771	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	CDS	21294772	21295016	0.97	-	2	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	exon	21294772	21295016	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	intron	21295017	21295170	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	CDS	21295171	21295744	0.92	-	0	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	exon	21295171	21295744	.	-	.	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
Phchi.S3	AUGUSTUS	start_codon	21295742	21295744	.	-	0	transcript_id "Phchi.S3G309600.t1"; gene_id "Phchi.S3G309600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13099.t1 is derived from g11564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4134103	4135433	.	+	.	Phchi.S3G041800
Phchi.S3	AUGUSTUS	transcript	4134103	4135433	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	start_codon	4134103	4134105	.	+	0	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	CDS	4134103	4134366	0.81	+	0	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	exon	4134103	4134366	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	intron	4134367	4134448	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	CDS	4134449	4134637	0.87	+	0	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	exon	4134449	4134637	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	intron	4134638	4134752	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	CDS	4134753	4134921	0.91	+	0	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	exon	4134753	4134921	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	intron	4134922	4135026	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	CDS	4135027	4135433	0.68	+	2	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	exon	4135027	4135433	.	+	.	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
Phchi.S3	AUGUSTUS	stop_codon	4135434	4135436	.	+	0	transcript_id "Phchi.S3G041800.t1"; gene_id "Phchi.S3G041800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5858.t1 is derived from g3028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19386017	19386424	.	-	.	Phchi.S1G301700
Phchi.S1	AUGUSTUS	transcript	19386017	19386424	.	-	.	transcript_id "Phchi.S1G301700.t1"; gene_id "Phchi.S1G301700"
Phchi.S1	AUGUSTUS	stop_codon	19386014	19386016	.	-	0	transcript_id "Phchi.S1G301700.t1"; gene_id "Phchi.S1G301700"
Phchi.S1	AUGUSTUS	CDS	19386017	19386424	0.47	-	0	transcript_id "Phchi.S1G301700.t1"; gene_id "Phchi.S1G301700"
Phchi.S1	AUGUSTUS	exon	19386017	19386424	.	-	.	transcript_id "Phchi.S1G301700.t1"; gene_id "Phchi.S1G301700"
Phchi.S1	AUGUSTUS	start_codon	19386422	19386424	.	-	0	transcript_id "Phchi.S1G301700.t1"; gene_id "Phchi.S1G301700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8807.t1 is derived from g5982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38083053	38084441	.	-	.	Phchi.S1G596600
Phchi.S1	AUGUSTUS	transcript	38083053	38084441	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	stop_codon	38083050	38083052	.	-	0	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	CDS	38083053	38083118	0.57	-	0	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	exon	38083053	38083118	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	intron	38083119	38083287	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	CDS	38083288	38083412	1	-	2	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	exon	38083288	38083412	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	intron	38083413	38083561	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	CDS	38083562	38083780	0.9	-	2	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	exon	38083562	38083780	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	intron	38083781	38083874	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	CDS	38083875	38083935	1	-	0	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	exon	38083875	38083935	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	intron	38083936	38084029	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	CDS	38084030	38084294	1	-	1	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	exon	38084030	38084294	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	intron	38084295	38084427	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	CDS	38084428	38084441	1	-	0	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	exon	38084428	38084441	.	-	.	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
Phchi.S1	AUGUSTUS	start_codon	38084439	38084441	.	-	0	transcript_id "Phchi.S1G596600.t1"; gene_id "Phchi.S1G596600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5258.t1 is derived from g2428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15899624	15900580	.	-	.	Phchi.S1G241700
Phchi.S1	AUGUSTUS	transcript	15899624	15900580	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	stop_codon	15899621	15899623	.	-	0	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	CDS	15899624	15899647	1	-	0	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	exon	15899624	15899647	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	intron	15899648	15899787	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	CDS	15899788	15899805	1	-	0	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	exon	15899788	15899805	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	intron	15899806	15899956	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	CDS	15899957	15900043	1	-	0	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	exon	15899957	15900043	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	intron	15900044	15900120	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	CDS	15900121	15900313	0.73	-	1	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	exon	15900121	15900313	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	intron	15900314	15900479	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	CDS	15900480	15900580	1	-	0	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	exon	15900480	15900580	.	-	.	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
Phchi.S1	AUGUSTUS	start_codon	15900578	15900580	.	-	0	transcript_id "Phchi.S1G241700.t1"; gene_id "Phchi.S1G241700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9320.t1 is derived from g6495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40932360	40933526	.	-	.	Phchi.S1G647900
Phchi.S1	AUGUSTUS	transcript	40932360	40933526	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	stop_codon	40932357	40932359	.	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	CDS	40932360	40932485	1	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	exon	40932360	40932485	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	intron	40932486	40932569	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	CDS	40932570	40932692	1	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	exon	40932570	40932692	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	intron	40932693	40932811	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	CDS	40932812	40932916	1	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	exon	40932812	40932916	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	intron	40932917	40933011	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	CDS	40933012	40933116	1	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	exon	40933012	40933116	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	intron	40933117	40933301	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	CDS	40933302	40933380	0.89	-	1	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	exon	40933302	40933380	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	intron	40933381	40933494	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	CDS	40933495	40933526	0.87	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	exon	40933495	40933526	.	-	.	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
Phchi.S1	AUGUSTUS	start_codon	40933524	40933526	.	-	0	transcript_id "Phchi.S1G647900.t1"; gene_id "Phchi.S1G647900"
# This transcript jg4942.t2 is derived from g2112.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4943.t1 is derived from g2113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13674674	13676652	.	+	.	Phchi.S1G210200
Phchi.S1	AUGUSTUS	transcript	13674674	13676652	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	start_codon	13674674	13674676	.	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	CDS	13674674	13674799	0.99	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	exon	13674674	13674799	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	intron	13674800	13675045	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	CDS	13675046	13675129	0.45	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	exon	13675046	13675129	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	intron	13675130	13675212	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	CDS	13675213	13675302	0.41	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	exon	13675213	13675302	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	intron	13675303	13675405	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	CDS	13675406	13675633	1	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	exon	13675406	13675633	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	intron	13675634	13675713	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	CDS	13675714	13675827	1	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	exon	13675714	13675827	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	intron	13675828	13675926	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	CDS	13675927	13676652	0.96	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	exon	13675927	13676652	.	+	.	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
Phchi.S1	AUGUSTUS	stop_codon	13676653	13676655	.	+	0	transcript_id "Phchi.S1G210200.t1"; gene_id "Phchi.S1G210200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2648.t1 is derived from g9568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7986396	7988823	.	-	.	Phchi.S5G125700
Phchi.S5	AUGUSTUS	transcript	7986396	7988823	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	stop_codon	7986393	7986395	.	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7986396	7986473	0.59	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7986396	7986473	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7986474	7986584	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7986585	7986671	0.34	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7986585	7986671	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7986672	7986779	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7986780	7986863	0.97	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7986780	7986863	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7986864	7986950	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7986951	7987003	1	-	2	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7986951	7987003	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7987004	7987145	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7987146	7987230	1	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7987146	7987230	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7987231	7987358	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7987359	7987454	1	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7987359	7987454	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7987455	7987568	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7987569	7987667	0.85	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7987569	7987667	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7987668	7987751	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7987752	7987808	1	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7987752	7987808	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7987809	7987953	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7987954	7988334	0.97	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7987954	7988334	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	intron	7988335	7988559	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	CDS	7988560	7988823	0.99	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	exon	7988560	7988823	.	-	.	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
Phchi.S5	AUGUSTUS	start_codon	7988821	7988823	.	-	0	transcript_id "Phchi.S5G125700.t1"; gene_id "Phchi.S5G125700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8307.t1 is derived from g5482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35200005	35201672	.	-	.	Phchi.S1G546600
Phchi.S1	AUGUSTUS	transcript	35200005	35201672	.	-	.	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	stop_codon	35200002	35200004	.	-	0	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	CDS	35200005	35200632	0.98	-	1	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	exon	35200005	35200632	.	-	.	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	intron	35200633	35200894	.	-	.	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	CDS	35200895	35201155	0.97	-	1	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	exon	35200895	35201155	.	-	.	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	intron	35201156	35201289	.	-	.	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	CDS	35201290	35201672	1	-	0	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	exon	35201290	35201672	.	-	.	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
Phchi.S1	AUGUSTUS	start_codon	35201670	35201672	.	-	0	transcript_id "Phchi.S1G546600.t1"; gene_id "Phchi.S1G546600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9149.t1 is derived from g6324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40099489	40100127	.	+	.	Phchi.S1G630800
Phchi.S1	AUGUSTUS	transcript	40099489	40100127	.	+	.	transcript_id "Phchi.S1G630800.t1"; gene_id "Phchi.S1G630800"
Phchi.S1	AUGUSTUS	start_codon	40099489	40099491	.	+	0	transcript_id "Phchi.S1G630800.t1"; gene_id "Phchi.S1G630800"
Phchi.S1	AUGUSTUS	CDS	40099489	40100127	1	+	0	transcript_id "Phchi.S1G630800.t1"; gene_id "Phchi.S1G630800"
Phchi.S1	AUGUSTUS	exon	40099489	40100127	.	+	.	transcript_id "Phchi.S1G630800.t1"; gene_id "Phchi.S1G630800"
Phchi.S1	AUGUSTUS	stop_codon	40100128	40100130	.	+	0	transcript_id "Phchi.S1G630800.t1"; gene_id "Phchi.S1G630800"
# This transcript jg1414.t2 is derived from g8333.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1415.t1 is derived from g8334.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	641216	647356	.	-	.	Phchi.S5G002400
Phchi.S5	AUGUSTUS	transcript	641216	647356	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	stop_codon	641213	641215	.	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641216	641302	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641216	641302	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641303	641380	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641381	641496	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641381	641496	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641497	641592	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641593	641616	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641593	641616	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641617	641711	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641712	641743	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641712	641743	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641744	641817	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641818	641906	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641818	641906	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641907	642014	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642015	642068	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642015	642068	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642069	642213	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642214	642275	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642214	642275	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642276	642358	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642359	642420	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642359	642420	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642421	642551	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642552	642641	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642552	642641	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642642	642719	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642720	642796	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642720	642796	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642797	642878	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642879	642937	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642879	642937	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642938	643037	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643038	643102	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643038	643102	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643103	643194	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643195	643284	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643195	643284	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643285	643383	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643384	643480	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643384	643480	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643481	643575	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643576	643675	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643576	643675	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643676	643862	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643863	643936	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643863	643936	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643937	644016	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644017	644098	0.99	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644017	644098	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644099	644207	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644208	644258	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644208	644258	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644259	644477	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644478	644546	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644478	644546	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644547	644645	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644646	644690	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644646	644690	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644691	644826	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644827	644928	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644827	644928	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644929	645053	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645054	645110	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645054	645110	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645111	645259	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645260	645346	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645260	645346	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645347	645440	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645441	645498	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645441	645498	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645499	645580	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645581	645612	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645581	645612	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645613	645687	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645688	645715	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645688	645715	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645716	645830	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645831	645877	0.78	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645831	645877	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645878	646065	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646066	646194	0.8	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646066	646194	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646195	646273	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646274	646337	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646274	646337	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646338	646439	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646440	646512	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646440	646512	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646513	646662	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646663	646743	1	-	2	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646663	646743	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646744	646934	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646935	647029	1	-	1	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646935	647029	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	647030	647125	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	647126	647157	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	647126	647157	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	647158	647230	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	647231	647356	1	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	647231	647356	.	-	.	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	start_codon	647354	647356	.	-	0	transcript_id "Phchi.S5G002400.t1"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	transcript	641216	647356	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	stop_codon	641213	641215	.	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641216	641302	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641216	641302	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641303	641380	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641381	641496	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641381	641496	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641497	641592	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641593	641616	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641593	641616	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641617	641711	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641712	641743	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641712	641743	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641744	641817	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641818	641906	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641818	641906	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641907	642014	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642015	642068	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642015	642068	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642069	642213	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642214	642275	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642214	642275	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642276	642358	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642359	642420	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642359	642420	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642421	642551	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642552	642641	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642552	642641	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642642	642719	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642720	642796	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642720	642796	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642797	642878	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642879	642937	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642879	642937	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642938	643013	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643014	643102	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643014	643102	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643103	643194	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643195	643284	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643195	643284	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643285	643383	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643384	643480	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643384	643480	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643481	643575	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643576	643675	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643576	643675	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643676	643862	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643863	643936	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643863	643936	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643937	644016	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644017	644098	0.97	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644017	644098	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644099	644207	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644208	644258	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644208	644258	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644259	644477	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644478	644546	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644478	644546	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644547	644645	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644646	644690	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644646	644690	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644691	644826	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644827	644928	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644827	644928	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644929	645053	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645054	645110	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645054	645110	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645111	645259	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645260	645346	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645260	645346	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645347	645440	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645441	645498	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645441	645498	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645499	645580	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645581	645612	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645581	645612	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645613	645687	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645688	645715	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645688	645715	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645716	645830	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645831	645877	0.74	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645831	645877	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645878	646065	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646066	646194	0.67	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646066	646194	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646195	646273	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646274	646337	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646274	646337	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646338	646439	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646440	646512	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646440	646512	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646513	646662	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646663	646743	1	-	2	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646663	646743	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646744	646934	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646935	647029	1	-	1	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646935	647029	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	647030	647125	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	647126	647157	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	647126	647157	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	647158	647230	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	647231	647356	1	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	647231	647356	.	-	.	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	start_codon	647354	647356	.	-	0	transcript_id "Phchi.S5G002400.t2"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	transcript	641216	647356	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	stop_codon	641213	641215	.	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641216	641302	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641216	641302	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641303	641380	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641381	641496	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641381	641496	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641497	641592	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641593	641616	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641593	641616	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641617	641711	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641712	641743	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641712	641743	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641744	641817	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	641818	641906	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	641818	641906	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	641907	642014	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642015	642068	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642015	642068	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642069	642183	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642184	642275	0.98	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642184	642275	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642276	642358	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642359	642420	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642359	642420	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642421	642551	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642552	642641	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642552	642641	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642642	642719	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642720	642796	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642720	642796	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642797	642878	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	642879	642937	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	642879	642937	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	642938	643037	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643038	643102	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643038	643102	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643103	643194	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643195	643284	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643195	643284	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643285	643383	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643384	643480	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643384	643480	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643481	643575	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643576	643675	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643576	643675	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643676	643862	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	643863	643936	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	643863	643936	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	643937	644016	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644017	644098	0.99	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644017	644098	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644099	644207	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644208	644258	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644208	644258	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644259	644477	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644478	644546	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644478	644546	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644547	644645	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644646	644690	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644646	644690	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644691	644826	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	644827	644928	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	644827	644928	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	644929	645053	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645054	645110	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645054	645110	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645111	645259	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645260	645346	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645260	645346	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645347	645440	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645441	645498	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645441	645498	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645499	645580	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645581	645612	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645581	645612	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645613	645687	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645688	645715	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645688	645715	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645716	645830	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	645831	645877	0.71	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	645831	645877	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	645878	646065	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646066	646194	0.72	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646066	646194	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646195	646273	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646274	646337	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646274	646337	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646338	646439	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646440	646512	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646440	646512	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646513	646662	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646663	646743	1	-	2	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646663	646743	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	646744	646934	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	646935	647029	1	-	1	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	646935	647029	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	647030	647125	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	647126	647157	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	647126	647157	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	intron	647158	647230	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	CDS	647231	647356	1	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	exon	647231	647356	.	-	.	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
Phchi.S5	AUGUSTUS	start_codon	647354	647356	.	-	0	transcript_id "Phchi.S5G002400.t3"; gene_id "Phchi.S5G002400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3078.t1 is derived from g247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1487896	1490085	.	-	.	Phchi.S1G023700
Phchi.S1	AUGUSTUS	transcript	1487896	1490085	.	-	.	transcript_id "Phchi.S1G023700.t1"; gene_id "Phchi.S1G023700"
Phchi.S1	AUGUSTUS	stop_codon	1487893	1487895	.	-	0	transcript_id "Phchi.S1G023700.t1"; gene_id "Phchi.S1G023700"
Phchi.S1	AUGUSTUS	CDS	1487896	1490085	0.92	-	0	transcript_id "Phchi.S1G023700.t1"; gene_id "Phchi.S1G023700"
Phchi.S1	AUGUSTUS	exon	1487896	1490085	.	-	.	transcript_id "Phchi.S1G023700.t1"; gene_id "Phchi.S1G023700"
Phchi.S1	AUGUSTUS	start_codon	1490083	1490085	.	-	0	transcript_id "Phchi.S1G023700.t1"; gene_id "Phchi.S1G023700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg758.t1 is derived from g10540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5359668	5362261	.	+	.	Phchi.S6G071700
Phchi.S6	AUGUSTUS	transcript	5359668	5362261	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	start_codon	5359668	5359670	.	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5359668	5359774	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5359668	5359774	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5359775	5359854	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5359855	5359967	1	+	1	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5359855	5359967	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5359968	5360044	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5360045	5360080	1	+	2	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5360045	5360080	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5360081	5360248	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5360249	5360322	1	+	2	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5360249	5360322	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5360323	5360411	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5360412	5360452	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5360412	5360452	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5360453	5360624	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5360625	5360696	1	+	1	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5360625	5360696	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5360697	5360840	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5360841	5361024	1	+	1	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5360841	5361024	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5361025	5361104	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5361105	5361200	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5361105	5361200	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5361201	5361275	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5361276	5361343	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5361276	5361343	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5361344	5361446	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5361447	5361552	1	+	1	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5361447	5361552	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5361553	5361647	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5361648	5361722	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5361648	5361722	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5361723	5361832	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5361833	5361916	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5361833	5361916	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5361917	5362040	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5362041	5362096	1	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5362041	5362096	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	intron	5362097	5362239	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	CDS	5362240	5362261	0.99	+	1	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	exon	5362240	5362261	.	+	.	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
Phchi.S6	AUGUSTUS	stop_codon	5362262	5362264	.	+	0	transcript_id "Phchi.S6G071700.t1"; gene_id "Phchi.S6G071700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15182.t1 is derived from g13650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17433297	17435271	.	+	.	Phchi.S3G250100
Phchi.S3	AUGUSTUS	transcript	17433297	17435271	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	start_codon	17433297	17433299	.	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17433297	17433659	0.95	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17433297	17433659	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17433660	17433740	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17433741	17433833	1	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17433741	17433833	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17433834	17433929	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17433930	17434019	1	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17433930	17434019	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17434020	17434117	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17434118	17434212	1	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17434118	17434212	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17434213	17434295	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17434296	17434356	1	+	1	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17434296	17434356	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17434357	17434452	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17434453	17434542	1	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17434453	17434542	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17434543	17434645	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17434646	17434708	1	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17434646	17434708	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17434709	17434854	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17434855	17434910	1	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17434855	17434910	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17434911	17435055	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17435056	17435151	1	+	1	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17435056	17435151	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	intron	17435152	17435237	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	CDS	17435238	17435271	1	+	1	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	exon	17435238	17435271	.	+	.	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
Phchi.S3	AUGUSTUS	stop_codon	17435272	17435274	.	+	0	transcript_id "Phchi.S3G250100.t1"; gene_id "Phchi.S3G250100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15735.t1 is derived from g14205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20961094	20961925	.	-	.	Phchi.S3G305400
Phchi.S3	AUGUSTUS	transcript	20961094	20961925	.	-	.	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	stop_codon	20961091	20961093	.	-	0	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	CDS	20961094	20961140	0.99	-	2	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	exon	20961094	20961140	.	-	.	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	intron	20961141	20961308	.	-	.	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	CDS	20961309	20961380	0.66	-	2	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	exon	20961309	20961380	.	-	.	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	intron	20961381	20961534	.	-	.	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	CDS	20961535	20961925	0.79	-	0	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	exon	20961535	20961925	.	-	.	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
Phchi.S3	AUGUSTUS	start_codon	20961923	20961925	.	-	0	transcript_id "Phchi.S3G305400.t1"; gene_id "Phchi.S3G305400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13800.t1 is derived from g12267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8952111	8953339	.	+	.	Phchi.S3G111900
Phchi.S3	AUGUSTUS	transcript	8952111	8953339	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	start_codon	8952111	8952113	.	+	0	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	CDS	8952111	8952566	0.94	+	0	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	exon	8952111	8952566	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	intron	8952567	8952703	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	CDS	8952704	8952779	0.93	+	0	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	exon	8952704	8952779	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	intron	8952780	8952918	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	CDS	8952919	8953031	0.61	+	2	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	exon	8952919	8953031	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	intron	8953032	8953336	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	CDS	8953337	8953339	0.49	+	0	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	exon	8953337	8953339	.	+	.	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
Phchi.S3	AUGUSTUS	stop_codon	8953340	8953342	.	+	0	transcript_id "Phchi.S3G111900.t1"; gene_id "Phchi.S3G111900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10848.t1 is derived from g14898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2468213	2469460	.	+	.	Phchi.S4G043000
Phchi.S4	AUGUSTUS	transcript	2468213	2469460	.	+	.	transcript_id "Phchi.S4G043000.t1"; gene_id "Phchi.S4G043000"
Phchi.S4	AUGUSTUS	start_codon	2468213	2468215	.	+	0	transcript_id "Phchi.S4G043000.t1"; gene_id "Phchi.S4G043000"
Phchi.S4	AUGUSTUS	CDS	2468213	2469460	1	+	0	transcript_id "Phchi.S4G043000.t1"; gene_id "Phchi.S4G043000"
Phchi.S4	AUGUSTUS	exon	2468213	2469460	.	+	.	transcript_id "Phchi.S4G043000.t1"; gene_id "Phchi.S4G043000"
Phchi.S4	AUGUSTUS	stop_codon	2469461	2469463	.	+	0	transcript_id "Phchi.S4G043000.t1"; gene_id "Phchi.S4G043000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12871.t1 is derived from g11336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2844804	2846535	.	+	.	Phchi.S3G019000
Phchi.S3	AUGUSTUS	transcript	2844804	2846535	.	+	.	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	start_codon	2844804	2844806	.	+	0	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	CDS	2844804	2844923	0.99	+	0	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	exon	2844804	2844923	.	+	.	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	intron	2844924	2845198	.	+	.	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	CDS	2845199	2845564	1	+	0	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	exon	2845199	2845564	.	+	.	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	intron	2845565	2845728	.	+	.	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	CDS	2845729	2846535	0.98	+	0	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	exon	2845729	2846535	.	+	.	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
Phchi.S3	AUGUSTUS	stop_codon	2846536	2846538	.	+	0	transcript_id "Phchi.S3G019000.t1"; gene_id "Phchi.S3G019000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9106.t1 is derived from g6281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39851330	39852533	.	+	.	Phchi.S1G626500
Phchi.S1	AUGUSTUS	transcript	39851330	39852533	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	start_codon	39851330	39851332	.	+	0	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	CDS	39851330	39851354	0.58	+	0	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	exon	39851330	39851354	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	intron	39851355	39851438	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	CDS	39851439	39851545	0.58	+	2	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	exon	39851439	39851545	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	intron	39851546	39851725	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	CDS	39851726	39851776	0.94	+	0	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	exon	39851726	39851776	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	intron	39851777	39851987	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	CDS	39851988	39852120	0.88	+	0	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	exon	39851988	39852120	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	intron	39852121	39852292	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	CDS	39852293	39852362	0.44	+	2	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	exon	39852293	39852362	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	intron	39852363	39852445	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	CDS	39852446	39852533	0.7	+	1	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	exon	39852446	39852533	.	+	.	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
Phchi.S1	AUGUSTUS	stop_codon	39852534	39852536	.	+	0	transcript_id "Phchi.S1G626500.t1"; gene_id "Phchi.S1G626500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5105.t1 is derived from g2275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14772431	14773262	.	-	.	Phchi.S1G226400
Phchi.S1	AUGUSTUS	transcript	14772431	14773262	.	-	.	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	stop_codon	14772428	14772430	.	-	0	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	CDS	14772431	14772651	1	-	2	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	exon	14772431	14772651	.	-	.	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	intron	14772652	14772738	.	-	.	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	CDS	14772739	14772943	0.87	-	0	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	exon	14772739	14772943	.	-	.	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	intron	14772944	14773034	.	-	.	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	CDS	14773035	14773262	0.82	-	0	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	exon	14773035	14773262	.	-	.	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
Phchi.S1	AUGUSTUS	start_codon	14773260	14773262	.	-	0	transcript_id "Phchi.S1G226400.t1"; gene_id "Phchi.S1G226400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4268.t1 is derived from g1437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9315750	9317411	.	-	.	Phchi.S1G142700
Phchi.S1	AUGUSTUS	transcript	9315750	9317411	.	-	.	transcript_id "Phchi.S1G142700.t1"; gene_id "Phchi.S1G142700"
Phchi.S1	AUGUSTUS	stop_codon	9315747	9315749	.	-	0	transcript_id "Phchi.S1G142700.t1"; gene_id "Phchi.S1G142700"
Phchi.S1	AUGUSTUS	CDS	9315750	9317411	1	-	0	transcript_id "Phchi.S1G142700.t1"; gene_id "Phchi.S1G142700"
Phchi.S1	AUGUSTUS	exon	9315750	9317411	.	-	.	transcript_id "Phchi.S1G142700.t1"; gene_id "Phchi.S1G142700"
Phchi.S1	AUGUSTUS	start_codon	9317409	9317411	.	-	0	transcript_id "Phchi.S1G142700.t1"; gene_id "Phchi.S1G142700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6367.t1 is derived from g3539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22592898	22594339	.	+	.	Phchi.S1G352600
Phchi.S1	AUGUSTUS	transcript	22592898	22594339	.	+	.	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	start_codon	22592898	22592900	.	+	0	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	CDS	22592898	22593239	1	+	0	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	exon	22592898	22593239	.	+	.	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	intron	22593240	22593352	.	+	.	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	CDS	22593353	22594339	0.85	+	0	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	exon	22593353	22594339	.	+	.	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
Phchi.S1	AUGUSTUS	stop_codon	22594340	22594342	.	+	0	transcript_id "Phchi.S1G352600.t1"; gene_id "Phchi.S1G352600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6858.t1 is derived from g4030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25608093	25609823	.	+	.	Phchi.S1G401700
Phchi.S1	AUGUSTUS	transcript	25608093	25609823	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	start_codon	25608093	25608095	.	+	0	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	CDS	25608093	25609041	0.28	+	0	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	exon	25608093	25609041	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	intron	25609042	25609201	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	CDS	25609202	25609265	0.3	+	2	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	exon	25609202	25609265	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	intron	25609266	25609354	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	CDS	25609355	25609412	0.3	+	1	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	exon	25609355	25609412	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	intron	25609413	25609570	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	CDS	25609571	25609617	0.3	+	0	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	exon	25609571	25609617	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	intron	25609618	25609753	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	CDS	25609754	25609823	0.95	+	1	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	exon	25609754	25609823	.	+	.	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
Phchi.S1	AUGUSTUS	stop_codon	25609824	25609826	.	+	0	transcript_id "Phchi.S1G401700.t1"; gene_id "Phchi.S1G401700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4278.t1 is derived from g1447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9375858	9376136	.	-	.	Phchi.S1G143700
Phchi.S1	AUGUSTUS	transcript	9375858	9376136	.	-	.	transcript_id "Phchi.S1G143700.t1"; gene_id "Phchi.S1G143700"
Phchi.S1	AUGUSTUS	stop_codon	9375855	9375857	.	-	0	transcript_id "Phchi.S1G143700.t1"; gene_id "Phchi.S1G143700"
Phchi.S1	AUGUSTUS	CDS	9375858	9376136	0.26	-	0	transcript_id "Phchi.S1G143700.t1"; gene_id "Phchi.S1G143700"
Phchi.S1	AUGUSTUS	exon	9375858	9376136	.	-	.	transcript_id "Phchi.S1G143700.t1"; gene_id "Phchi.S1G143700"
Phchi.S1	AUGUSTUS	start_codon	9376134	9376136	.	-	0	transcript_id "Phchi.S1G143700.t1"; gene_id "Phchi.S1G143700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3835.t1 is derived from g1004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5944355	5946117	.	+	.	Phchi.S1G099400
Phchi.S1	AUGUSTUS	transcript	5944355	5946117	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	start_codon	5944355	5944357	.	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5944355	5944399	0.99	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5944355	5944399	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5944400	5944495	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5944496	5944663	1	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5944496	5944663	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5944664	5944740	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5944741	5945002	1	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5944741	5945002	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5945003	5945081	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5945082	5945120	1	+	2	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5945082	5945120	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5945121	5945239	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5945240	5945247	1	+	2	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5945240	5945247	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5945248	5945335	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5945336	5945485	1	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5945336	5945485	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5945486	5945670	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5945671	5945815	1	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5945671	5945815	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	intron	5945816	5945914	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	CDS	5945915	5946117	1	+	2	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	exon	5945915	5946117	.	+	.	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
Phchi.S1	AUGUSTUS	stop_codon	5946118	5946120	.	+	0	transcript_id "Phchi.S1G099400.t1"; gene_id "Phchi.S1G099400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14576.t1 is derived from g13044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13549076	13551340	.	-	.	Phchi.S3G189500
Phchi.S3	AUGUSTUS	transcript	13549076	13551340	.	-	.	transcript_id "Phchi.S3G189500.t1"; gene_id "Phchi.S3G189500"
Phchi.S3	AUGUSTUS	stop_codon	13549073	13549075	.	-	0	transcript_id "Phchi.S3G189500.t1"; gene_id "Phchi.S3G189500"
Phchi.S3	AUGUSTUS	CDS	13549076	13551340	0.85	-	0	transcript_id "Phchi.S3G189500.t1"; gene_id "Phchi.S3G189500"
Phchi.S3	AUGUSTUS	exon	13549076	13551340	.	-	.	transcript_id "Phchi.S3G189500.t1"; gene_id "Phchi.S3G189500"
Phchi.S3	AUGUSTUS	start_codon	13551338	13551340	.	-	0	transcript_id "Phchi.S3G189500.t1"; gene_id "Phchi.S3G189500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12271.t1 is derived from g7947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7400192	7401891	.	-	.	Phchi.S2G035100
Phchi.S2	AUGUSTUS	transcript	7400192	7401891	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	stop_codon	7400189	7400191	.	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7400192	7400276	1	-	1	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7400192	7400276	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7400277	7400383	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7400384	7400553	1	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7400384	7400553	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7400554	7400651	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7400652	7400786	1	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7400652	7400786	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7400787	7400901	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7400902	7401018	0.97	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7400902	7401018	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7401019	7401124	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7401125	7401204	0.95	-	2	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7401125	7401204	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7401205	7401295	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7401296	7401422	1	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7401296	7401422	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7401423	7401517	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7401518	7401609	1	-	2	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7401518	7401609	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7401610	7401732	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7401733	7401802	1	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7401733	7401802	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	intron	7401803	7401888	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	CDS	7401889	7401891	0.99	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	exon	7401889	7401891	.	-	.	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
Phchi.S2	AUGUSTUS	start_codon	7401889	7401891	.	-	0	transcript_id "Phchi.S2G035100.t1"; gene_id "Phchi.S2G035100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11669.t1 is derived from g15720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7592613	7593333	.	-	.	Phchi.S4G125100
Phchi.S4	AUGUSTUS	transcript	7592613	7593333	.	-	.	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	stop_codon	7592610	7592612	.	-	0	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	CDS	7592613	7592750	0.76	-	0	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	exon	7592613	7592750	.	-	.	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	intron	7592751	7593193	.	-	.	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	CDS	7593194	7593224	0.66	-	1	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	exon	7593194	7593224	.	-	.	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	intron	7593225	7593289	.	-	.	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	CDS	7593290	7593333	0.39	-	0	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	exon	7593290	7593333	.	-	.	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
Phchi.S4	AUGUSTUS	start_codon	7593331	7593333	.	-	0	transcript_id "Phchi.S4G125100.t1"; gene_id "Phchi.S4G125100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12484.t1 is derived from g8161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28763328	28763767	.	+	.	Phchi.S2G056400
Phchi.S2	AUGUSTUS	transcript	28763328	28763767	.	+	.	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	start_codon	28763328	28763330	.	+	0	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	CDS	28763328	28763451	0.73	+	0	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	exon	28763328	28763451	.	+	.	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	intron	28763452	28763600	.	+	.	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	CDS	28763601	28763767	0.73	+	2	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	exon	28763601	28763767	.	+	.	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
Phchi.S2	AUGUSTUS	stop_codon	28763768	28763770	.	+	0	transcript_id "Phchi.S2G056400.t1"; gene_id "Phchi.S2G056400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7817.t1 is derived from g4991.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31348214	31349482	.	-	.	Phchi.S1G497600
Phchi.S1	AUGUSTUS	transcript	31348214	31349482	.	-	.	transcript_id "Phchi.S1G497600.t1"; gene_id "Phchi.S1G497600"
Phchi.S1	AUGUSTUS	stop_codon	31348211	31348213	.	-	0	transcript_id "Phchi.S1G497600.t1"; gene_id "Phchi.S1G497600"
Phchi.S1	AUGUSTUS	CDS	31348214	31349482	0.81	-	0	transcript_id "Phchi.S1G497600.t1"; gene_id "Phchi.S1G497600"
Phchi.S1	AUGUSTUS	exon	31348214	31349482	.	-	.	transcript_id "Phchi.S1G497600.t1"; gene_id "Phchi.S1G497600"
Phchi.S1	AUGUSTUS	start_codon	31349480	31349482	.	-	0	transcript_id "Phchi.S1G497600.t1"; gene_id "Phchi.S1G497600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13528.t1 is derived from g11995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7385339	7386214	.	+	.	Phchi.S3G084700
Phchi.S3	AUGUSTUS	transcript	7385339	7386214	.	+	.	transcript_id "Phchi.S3G084700.t1"; gene_id "Phchi.S3G084700"
Phchi.S3	AUGUSTUS	start_codon	7385339	7385341	.	+	0	transcript_id "Phchi.S3G084700.t1"; gene_id "Phchi.S3G084700"
Phchi.S3	AUGUSTUS	CDS	7385339	7386214	0.93	+	0	transcript_id "Phchi.S3G084700.t1"; gene_id "Phchi.S3G084700"
Phchi.S3	AUGUSTUS	exon	7385339	7386214	.	+	.	transcript_id "Phchi.S3G084700.t1"; gene_id "Phchi.S3G084700"
Phchi.S3	AUGUSTUS	stop_codon	7386215	7386217	.	+	0	transcript_id "Phchi.S3G084700.t1"; gene_id "Phchi.S3G084700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13112.t1 is derived from g11577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4190759	4192975	.	-	.	Phchi.S3G043100
Phchi.S3	AUGUSTUS	transcript	4190759	4192975	.	-	.	transcript_id "Phchi.S3G043100.t1"; gene_id "Phchi.S3G043100"
Phchi.S3	AUGUSTUS	stop_codon	4190756	4190758	.	-	0	transcript_id "Phchi.S3G043100.t1"; gene_id "Phchi.S3G043100"
Phchi.S3	AUGUSTUS	CDS	4190759	4192975	0.35	-	0	transcript_id "Phchi.S3G043100.t1"; gene_id "Phchi.S3G043100"
Phchi.S3	AUGUSTUS	exon	4190759	4192975	.	-	.	transcript_id "Phchi.S3G043100.t1"; gene_id "Phchi.S3G043100"
Phchi.S3	AUGUSTUS	start_codon	4192973	4192975	.	-	0	transcript_id "Phchi.S3G043100.t1"; gene_id "Phchi.S3G043100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15120.t1 is derived from g13588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17165335	17167826	.	-	.	Phchi.S3G243900
Phchi.S3	AUGUSTUS	transcript	17165335	17167826	.	-	.	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	stop_codon	17165332	17165334	.	-	0	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	CDS	17165335	17166194	0.95	-	2	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	exon	17165335	17166194	.	-	.	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	intron	17166195	17166283	.	-	.	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	CDS	17166284	17167619	0.98	-	0	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	exon	17166284	17167619	.	-	.	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	intron	17167620	17167739	.	-	.	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	CDS	17167740	17167826	0.79	-	0	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	exon	17167740	17167826	.	-	.	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
Phchi.S3	AUGUSTUS	start_codon	17167824	17167826	.	-	0	transcript_id "Phchi.S3G243900.t1"; gene_id "Phchi.S3G243900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9063.t1 is derived from g6238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39542977	39544429	.	+	.	Phchi.S1G622200
Phchi.S1	AUGUSTUS	transcript	39542977	39544429	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	start_codon	39542977	39542979	.	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39542977	39543156	0.79	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39542977	39543156	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	intron	39543157	39543375	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39543376	39543405	1	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39543376	39543405	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	intron	39543406	39543497	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39543498	39543656	1	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39543498	39543656	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	intron	39543657	39543752	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39543753	39543847	1	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39543753	39543847	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	intron	39543848	39543928	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39543929	39543962	0.88	+	1	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39543929	39543962	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	intron	39543963	39544037	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39544038	39544069	0.88	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39544038	39544069	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	intron	39544070	39544254	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	CDS	39544255	39544429	0.85	+	1	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	exon	39544255	39544429	.	+	.	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
Phchi.S1	AUGUSTUS	stop_codon	39544430	39544432	.	+	0	transcript_id "Phchi.S1G622200.t1"; gene_id "Phchi.S1G622200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8880.t1 is derived from g6055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38447779	38449981	.	-	.	Phchi.S1G603900
Phchi.S1	AUGUSTUS	transcript	38447779	38449981	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	stop_codon	38447776	38447778	.	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38447779	38447967	1	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38447779	38447967	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38447968	38448061	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38448062	38448174	1	-	2	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38448062	38448174	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38448175	38448271	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38448272	38448440	1	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38448272	38448440	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38448441	38448532	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38448533	38448631	1	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38448533	38448631	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38448632	38448774	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38448775	38448816	1	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38448775	38448816	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38448817	38448927	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38448928	38449017	0.99	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38448928	38449017	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38449018	38449104	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38449105	38449176	1	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38449105	38449176	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38449177	38449312	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38449313	38449546	0.88	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38449313	38449546	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38449547	38449666	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38449667	38449680	0.88	-	2	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38449667	38449680	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38449681	38449790	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38449791	38449893	0.48	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38449791	38449893	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	intron	38449894	38449978	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	CDS	38449979	38449981	0.42	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	exon	38449979	38449981	.	-	.	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
Phchi.S1	AUGUSTUS	start_codon	38449979	38449981	.	-	0	transcript_id "Phchi.S1G603900.t1"; gene_id "Phchi.S1G603900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4710.t1 is derived from g1880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12423837	12424120	.	-	.	Phchi.S1G186900
Phchi.S1	AUGUSTUS	transcript	12423837	12424120	.	-	.	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	stop_codon	12423834	12423836	.	-	0	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	CDS	12423837	12423958	0.72	-	2	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	exon	12423837	12423958	.	-	.	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	intron	12423959	12424032	.	-	.	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	CDS	12424033	12424120	0.92	-	0	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	exon	12424033	12424120	.	-	.	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
Phchi.S1	AUGUSTUS	start_codon	12424118	12424120	.	-	0	transcript_id "Phchi.S1G186900.t1"; gene_id "Phchi.S1G186900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9704.t1 is derived from g6880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43343908	43345908	.	-	.	Phchi.S1G686300
Phchi.S1	AUGUSTUS	transcript	43343908	43345908	.	-	.	transcript_id "Phchi.S1G686300.t1"; gene_id "Phchi.S1G686300"
Phchi.S1	AUGUSTUS	stop_codon	43343905	43343907	.	-	0	transcript_id "Phchi.S1G686300.t1"; gene_id "Phchi.S1G686300"
Phchi.S1	AUGUSTUS	CDS	43343908	43345908	1	-	0	transcript_id "Phchi.S1G686300.t1"; gene_id "Phchi.S1G686300"
Phchi.S1	AUGUSTUS	exon	43343908	43345908	.	-	.	transcript_id "Phchi.S1G686300.t1"; gene_id "Phchi.S1G686300"
Phchi.S1	AUGUSTUS	start_codon	43345906	43345908	.	-	0	transcript_id "Phchi.S1G686300.t1"; gene_id "Phchi.S1G686300"
# This transcript jg8899.t2 is derived from g6074.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8900.t1 is derived from g6075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38552055	38552582	.	+	.	Phchi.S1G605900
Phchi.S1	AUGUSTUS	transcript	38552055	38552582	.	+	.	transcript_id "Phchi.S1G605900.t1"; gene_id "Phchi.S1G605900"
Phchi.S1	AUGUSTUS	start_codon	38552055	38552057	.	+	0	transcript_id "Phchi.S1G605900.t1"; gene_id "Phchi.S1G605900"
Phchi.S1	AUGUSTUS	CDS	38552055	38552582	0.86	+	0	transcript_id "Phchi.S1G605900.t1"; gene_id "Phchi.S1G605900"
Phchi.S1	AUGUSTUS	exon	38552055	38552582	.	+	.	transcript_id "Phchi.S1G605900.t1"; gene_id "Phchi.S1G605900"
Phchi.S1	AUGUSTUS	stop_codon	38552583	38552585	.	+	0	transcript_id "Phchi.S1G605900.t1"; gene_id "Phchi.S1G605900"
# This transcript jg2053.t2 is derived from g8973.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2054.t1 is derived from g8974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4628487	4629460	.	-	.	Phchi.S5G066300
Phchi.S5	AUGUSTUS	transcript	4628487	4629460	.	-	.	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	stop_codon	4628484	4628486	.	-	0	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	CDS	4628487	4628900	0.99	-	0	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	exon	4628487	4628900	.	-	.	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	intron	4628901	4628988	.	-	.	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	CDS	4628989	4629201	1	-	0	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	exon	4628989	4629201	.	-	.	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	intron	4629202	4629346	.	-	.	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	CDS	4629347	4629460	0.96	-	0	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	exon	4629347	4629460	.	-	.	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
Phchi.S5	AUGUSTUS	start_codon	4629458	4629460	.	-	0	transcript_id "Phchi.S5G066300.t1"; gene_id "Phchi.S5G066300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4331.t1 is derived from g1500.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9819347	9820563	.	+	.	Phchi.S1G149000
Phchi.S1	AUGUSTUS	transcript	9819347	9820563	.	+	.	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	start_codon	9819347	9819349	.	+	0	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	CDS	9819347	9819556	0.77	+	0	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	exon	9819347	9819556	.	+	.	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	intron	9819557	9819750	.	+	.	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	CDS	9819751	9820563	0.89	+	0	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	exon	9819751	9820563	.	+	.	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	stop_codon	9820564	9820566	.	+	0	transcript_id "Phchi.S1G149000.t1"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	transcript	9819658	9820563	.	+	.	transcript_id "Phchi.S1G149000.t2"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	start_codon	9819658	9819660	.	+	0	transcript_id "Phchi.S1G149000.t2"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	CDS	9819658	9820563	0.9	+	0	transcript_id "Phchi.S1G149000.t2"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	exon	9819658	9820563	.	+	.	transcript_id "Phchi.S1G149000.t2"; gene_id "Phchi.S1G149000"
Phchi.S1	AUGUSTUS	stop_codon	9820564	9820566	.	+	0	transcript_id "Phchi.S1G149000.t2"; gene_id "Phchi.S1G149000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5033.t1 is derived from g2203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14185025	14187706	.	+	.	Phchi.S1G219200
Phchi.S1	AUGUSTUS	transcript	14185025	14187706	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	start_codon	14185025	14185027	.	+	0	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	CDS	14185025	14185667	0.8	+	0	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	exon	14185025	14185667	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	intron	14185668	14185920	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	CDS	14185921	14185971	0.67	+	2	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	exon	14185921	14185971	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	intron	14185972	14186257	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	CDS	14186258	14186445	0.81	+	2	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	exon	14186258	14186445	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	intron	14186446	14186759	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	CDS	14186760	14186825	0.56	+	0	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	exon	14186760	14186825	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	intron	14186826	14186925	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	CDS	14186926	14187569	0.12	+	0	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	exon	14186926	14187569	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	intron	14187570	14187672	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	CDS	14187673	14187706	0.24	+	1	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	exon	14187673	14187706	.	+	.	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
Phchi.S1	AUGUSTUS	stop_codon	14187707	14187709	.	+	0	transcript_id "Phchi.S1G219200.t1"; gene_id "Phchi.S1G219200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15021.t1 is derived from g13489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16564686	16567542	.	-	.	Phchi.S3G234000
Phchi.S3	AUGUSTUS	transcript	16564686	16567542	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	stop_codon	16564683	16564685	.	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16564686	16564874	1	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16564686	16564874	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16564875	16564957	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16564958	16565152	1	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16564958	16565152	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16565153	16565258	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16565259	16565369	1	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16565259	16565369	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16565370	16565469	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16565470	16565560	1	-	1	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16565470	16565560	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16565561	16565775	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16565776	16565870	0.93	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16565776	16565870	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16565871	16566016	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16566017	16566247	0.93	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16566017	16566247	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16566248	16566379	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16566380	16566424	1	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16566380	16566424	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16566425	16566509	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16566510	16566565	1	-	2	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16566510	16566565	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16566566	16566718	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16566719	16566793	1	-	2	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16566719	16566793	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16566794	16566914	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16566915	16566982	1	-	1	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16566915	16566982	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16566983	16567189	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16567190	16567217	1	-	2	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16567190	16567217	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16567218	16567323	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16567324	16567378	1	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16567324	16567378	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	intron	16567379	16567470	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	CDS	16567471	16567542	1	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	exon	16567471	16567542	.	-	.	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
Phchi.S3	AUGUSTUS	start_codon	16567540	16567542	.	-	0	transcript_id "Phchi.S3G234000.t1"; gene_id "Phchi.S3G234000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg967.t1 is derived from g10749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6709914	6711671	.	+	.	Phchi.S6G092600
Phchi.S6	AUGUSTUS	transcript	6709914	6711671	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	start_codon	6709914	6709916	.	+	0	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6709914	6710217	0.74	+	0	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6709914	6710217	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	intron	6710218	6710388	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6710389	6710495	1	+	2	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6710389	6710495	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	intron	6710496	6710599	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6710600	6710700	1	+	0	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6710600	6710700	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	intron	6710701	6710779	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6710780	6710857	1	+	1	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6710780	6710857	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	intron	6710858	6710956	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6710957	6711106	1	+	1	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6710957	6711106	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	intron	6711107	6711215	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6711216	6711389	1	+	1	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6711216	6711389	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	intron	6711390	6711511	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	CDS	6711512	6711671	0.86	+	1	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	exon	6711512	6711671	.	+	.	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
Phchi.S6	AUGUSTUS	stop_codon	6711672	6711674	.	+	0	transcript_id "Phchi.S6G092600.t1"; gene_id "Phchi.S6G092600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg25.t1 is derived from g9823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C43	AUGUSTUS	gene	43698	44924	.	+	.	Phchi.C43G000200
Phchi.C43	AUGUSTUS	transcript	43698	44924	.	+	.	transcript_id "Phchi.C43G000200.t1"; gene_id "Phchi.C43G000200"
Phchi.C43	AUGUSTUS	start_codon	43698	43700	.	+	0	transcript_id "Phchi.C43G000200.t1"; gene_id "Phchi.C43G000200"
Phchi.C43	AUGUSTUS	CDS	43698	44924	0.95	+	0	transcript_id "Phchi.C43G000200.t1"; gene_id "Phchi.C43G000200"
Phchi.C43	AUGUSTUS	exon	43698	44924	.	+	.	transcript_id "Phchi.C43G000200.t1"; gene_id "Phchi.C43G000200"
Phchi.C43	AUGUSTUS	stop_codon	44925	44927	.	+	0	transcript_id "Phchi.C43G000200.t1"; gene_id "Phchi.C43G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11720.t1 is derived from g15772.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7837743	7839097	.	-	.	Phchi.S4G130200
Phchi.S4	AUGUSTUS	transcript	7838510	7839097	.	-	.	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	stop_codon	7838507	7838509	.	-	0	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	CDS	7838510	7838513	1	-	1	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	exon	7838510	7838513	.	-	.	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	intron	7838514	7838590	.	-	.	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	CDS	7838591	7838697	1	-	0	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	exon	7838591	7838697	.	-	.	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	intron	7838698	7838773	.	-	.	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	CDS	7838774	7839097	0.96	-	0	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	exon	7838774	7839097	.	-	.	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	start_codon	7839095	7839097	.	-	0	transcript_id "Phchi.S4G130200.t1"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	transcript	7837743	7839097	.	-	.	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	stop_codon	7837740	7837742	.	-	0	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	CDS	7837743	7838523	0.94	-	1	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	exon	7837743	7838523	.	-	.	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	intron	7838524	7838590	.	-	.	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	CDS	7838591	7838697	1	-	0	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	exon	7838591	7838697	.	-	.	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	intron	7838698	7838773	.	-	.	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	CDS	7838774	7839097	0.98	-	0	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	exon	7838774	7839097	.	-	.	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
Phchi.S4	AUGUSTUS	start_codon	7839095	7839097	.	-	0	transcript_id "Phchi.S4G130200.t2"; gene_id "Phchi.S4G130200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11217.t1 is derived from g15267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4811607	4812563	.	-	.	Phchi.S4G079900
Phchi.S4	AUGUSTUS	transcript	4811607	4812563	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	stop_codon	4811604	4811606	.	-	0	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	CDS	4811607	4811646	1	-	1	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	exon	4811607	4811646	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	intron	4811647	4811752	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	CDS	4811753	4811820	1	-	0	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	exon	4811753	4811820	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	intron	4811821	4811910	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	CDS	4811911	4811962	1	-	1	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	exon	4811911	4811962	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	intron	4811963	4812084	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	CDS	4812085	4812251	1	-	0	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	exon	4812085	4812251	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	intron	4812252	4812332	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	CDS	4812333	4812366	1	-	1	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	exon	4812333	4812366	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	intron	4812367	4812516	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	CDS	4812517	4812563	1	-	0	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	exon	4812517	4812563	.	-	.	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
Phchi.S4	AUGUSTUS	start_codon	4812561	4812563	.	-	0	transcript_id "Phchi.S4G079900.t1"; gene_id "Phchi.S4G079900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7796.t1 is derived from g4970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31206025	31207214	.	+	.	Phchi.S1G495500
Phchi.S1	AUGUSTUS	transcript	31206025	31207214	.	+	.	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	start_codon	31206025	31206027	.	+	0	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	CDS	31206025	31206459	0.88	+	0	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	exon	31206025	31206459	.	+	.	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	intron	31206460	31206737	.	+	.	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	CDS	31206738	31207214	0.96	+	0	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	exon	31206738	31207214	.	+	.	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	stop_codon	31207215	31207217	.	+	0	transcript_id "Phchi.S1G495500.t1"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	transcript	31206025	31206534	.	+	.	transcript_id "Phchi.S1G495500.t2"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	start_codon	31206025	31206027	.	+	0	transcript_id "Phchi.S1G495500.t2"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	CDS	31206025	31206534	0.45	+	0	transcript_id "Phchi.S1G495500.t2"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	exon	31206025	31206534	.	+	.	transcript_id "Phchi.S1G495500.t2"; gene_id "Phchi.S1G495500"
Phchi.S1	AUGUSTUS	stop_codon	31206535	31206537	.	+	0	transcript_id "Phchi.S1G495500.t2"; gene_id "Phchi.S1G495500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15635.t1 is derived from g14104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20397408	20404242	.	-	.	Phchi.S3G295400
Phchi.S3	AUGUSTUS	transcript	20397408	20404242	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	stop_codon	20397405	20397407	.	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20397408	20397587	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20397408	20397587	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20397588	20397666	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20397667	20397752	1	-	2	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20397667	20397752	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20397753	20397849	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20397850	20397952	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20397850	20397952	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20397953	20398026	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20398027	20398080	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20398027	20398080	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20398081	20398171	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20398172	20398319	1	-	1	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20398172	20398319	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20398320	20398448	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20398449	20398579	0.99	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20398449	20398579	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20398580	20398664	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20398665	20398742	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20398665	20398742	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20398743	20398831	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20398832	20399119	0.96	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20398832	20399119	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20399120	20399230	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20399231	20399419	0.96	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20399231	20399419	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20399420	20399682	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20399683	20399755	1	-	1	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20399683	20399755	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20399756	20399901	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20399902	20400026	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20399902	20400026	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20400027	20400132	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20400133	20400228	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20400133	20400228	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20400229	20400395	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20400396	20400509	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20400396	20400509	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20400510	20400622	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20400623	20400738	1	-	2	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20400623	20400738	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20400739	20400842	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20400843	20400912	0.99	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20400843	20400912	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20400913	20401068	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20401069	20401179	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20401069	20401179	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20401180	20401268	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20401269	20401397	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20401269	20401397	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20401398	20401526	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20401527	20401610	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20401527	20401610	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20401611	20401725	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20401726	20401818	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20401726	20401818	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20401819	20401905	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20401906	20401945	1	-	1	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20401906	20401945	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20401946	20402108	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20402109	20402185	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20402109	20402185	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20402186	20402280	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20402281	20402346	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20402281	20402346	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20402347	20402422	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20402423	20402557	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20402423	20402557	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20402558	20402746	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20402747	20402818	0.9	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20402747	20402818	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20402819	20402987	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20402988	20403029	1	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20402988	20403029	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20403030	20403224	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20403225	20403374	0.96	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20403225	20403374	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20403375	20403455	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20403456	20403491	0.79	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20403456	20403491	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20403492	20403593	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20403594	20403678	0.92	-	1	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20403594	20403678	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20403679	20403775	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20403776	20403873	0.46	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20403776	20403873	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	intron	20403874	20403951	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	CDS	20403952	20404242	0.49	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	exon	20403952	20404242	.	-	.	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
Phchi.S3	AUGUSTUS	start_codon	20404240	20404242	.	-	0	transcript_id "Phchi.S3G295400.t1"; gene_id "Phchi.S3G295400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11995.t1 is derived from g7670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	437471	439608	.	+	.	Phchi.S2G007500
Phchi.S2	AUGUSTUS	transcript	438635	439608	.	+	.	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	start_codon	438635	438637	.	+	0	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	CDS	438635	439235	0.26	+	0	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	exon	438635	439235	.	+	.	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	intron	439236	439353	.	+	.	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	CDS	439354	439454	0.46	+	2	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	exon	439354	439454	.	+	.	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	intron	439455	439551	.	+	.	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	CDS	439552	439608	0.43	+	0	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	exon	439552	439608	.	+	.	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	stop_codon	439609	439611	.	+	0	transcript_id "Phchi.S2G007500.t1"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	transcript	437471	439363	.	+	.	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	start_codon	437471	437473	.	+	0	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	CDS	437471	438058	0.16	+	0	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	exon	437471	438058	.	+	.	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	intron	438059	438520	.	+	.	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	CDS	438521	439363	0.26	+	0	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	exon	438521	439363	.	+	.	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
Phchi.S2	AUGUSTUS	stop_codon	439364	439366	.	+	0	transcript_id "Phchi.S2G007500.t2"; gene_id "Phchi.S2G007500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8468.t1 is derived from g5643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36071294	36073141	.	-	.	Phchi.S1G562700
Phchi.S1	AUGUSTUS	transcript	36071294	36073141	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	stop_codon	36071291	36071293	.	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36071294	36071486	1	-	1	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36071294	36071486	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36071487	36071568	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36071569	36071636	1	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36071569	36071636	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36071637	36071723	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36071724	36071852	1	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36071724	36071852	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36071853	36071947	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36071948	36072077	0.42	-	1	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36071948	36072077	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36072078	36072267	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36072268	36072323	0.57	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36072268	36072323	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36072324	36072416	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36072417	36072572	0.94	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36072417	36072572	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36072573	36072695	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36072696	36072920	1	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36072696	36072920	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	intron	36072921	36073075	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	CDS	36073076	36073141	0.9	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	exon	36073076	36073141	.	-	.	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
Phchi.S1	AUGUSTUS	start_codon	36073139	36073141	.	-	0	transcript_id "Phchi.S1G562700.t1"; gene_id "Phchi.S1G562700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15286.t1 is derived from g13754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18166646	18185027	.	-	.	Phchi.S3G260500
Phchi.S3	AUGUSTUS	transcript	18166646	18185027	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	stop_codon	18166643	18166645	.	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18166646	18166720	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18166646	18166720	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18166721	18166794	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18166795	18166947	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18166795	18166947	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18166948	18167033	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167034	18167099	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167034	18167099	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167100	18167179	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167180	18167314	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167180	18167314	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167315	18167411	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167412	18167543	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167412	18167543	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167544	18167713	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167714	18167813	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167714	18167813	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167814	18167948	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167949	18167995	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167949	18167995	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167996	18168142	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168143	18168224	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168143	18168224	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168225	18168306	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168307	18168386	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168307	18168386	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168387	18168512	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168513	18168602	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168513	18168602	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168603	18168731	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168732	18168840	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168732	18168840	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168841	18168923	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168924	18169021	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168924	18169021	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169022	18169102	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169103	18169162	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169103	18169162	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169163	18169257	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169258	18169314	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169258	18169314	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169315	18169433	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169434	18169574	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169434	18169574	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169575	18169665	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169666	18169728	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169666	18169728	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169729	18169878	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169879	18169967	1	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169879	18169967	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169968	18170113	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170114	18170194	0.96	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170114	18170194	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170195	18170360	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170361	18170382	0.88	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170361	18170382	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170383	18170582	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170583	18170666	0.99	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170583	18170666	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170667	18170781	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170782	18170829	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170782	18170829	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170830	18170959	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170960	18171176	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170960	18171176	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18171177	18171338	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18171339	18171490	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18171339	18171490	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18171491	18171570	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18171571	18171699	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18171571	18171699	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18171700	18171857	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18171858	18172022	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18171858	18172022	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172023	18172114	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172115	18172249	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172115	18172249	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172250	18172347	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172348	18172422	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172348	18172422	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172423	18172535	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172536	18172602	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172536	18172602	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172603	18172701	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172702	18172814	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172702	18172814	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172815	18172898	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172899	18172940	0.59	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172899	18172940	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172941	18173050	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173051	18173173	0.99	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173051	18173173	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173174	18173326	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173327	18173413	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173327	18173413	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173414	18173566	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173567	18173671	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173567	18173671	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173672	18173823	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173824	18173871	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173824	18173871	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173872	18173973	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173974	18174090	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173974	18174090	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174091	18174170	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174171	18174317	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174171	18174317	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174318	18174393	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174394	18174517	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174394	18174517	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174518	18174657	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174658	18174775	1	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174658	18174775	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174776	18174869	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174870	18174939	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174870	18174939	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174940	18175040	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175041	18175112	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175041	18175112	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175113	18175192	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175193	18175372	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175193	18175372	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175373	18175484	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175485	18175674	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175485	18175674	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175675	18175783	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175784	18175830	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175784	18175830	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175831	18175921	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175922	18176008	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175922	18176008	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176009	18176112	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176113	18176262	0.99	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176113	18176262	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176263	18176368	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176369	18176510	0.97	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176369	18176510	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176511	18176601	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176602	18176729	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176602	18176729	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176730	18176830	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176831	18176900	0.98	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176831	18176900	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176901	18176985	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176986	18177107	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176986	18177107	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177108	18177218	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177219	18177407	0.82	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177219	18177407	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177408	18177495	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177496	18177615	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177496	18177615	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177616	18177681	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177682	18177756	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177682	18177756	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177757	18177888	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177889	18177952	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177889	18177952	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177953	18178060	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178061	18178107	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178061	18178107	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18178108	18178282	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178283	18178445	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178283	18178445	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18178446	18178645	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178646	18178773	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178646	18178773	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18178774	18178914	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178915	18179040	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178915	18179040	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179041	18179193	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18179194	18179355	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18179194	18179355	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179356	18179498	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18179499	18179570	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18179499	18179570	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179571	18179659	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18179660	18179931	0.81	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18179660	18179931	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179932	18180149	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180150	18180252	0.64	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180150	18180252	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18180253	18180342	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180343	18180567	0.63	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180343	18180567	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18180568	18180650	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180651	18180746	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180651	18180746	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18180747	18180863	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180864	18181031	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180864	18181031	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181032	18181104	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181105	18181176	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181105	18181176	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181177	18181283	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181284	18181332	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181284	18181332	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181333	18181476	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181477	18181547	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181477	18181547	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181548	18181638	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181639	18181680	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181639	18181680	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181681	18181838	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181839	18181913	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181839	18181913	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181914	18182011	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182012	18182093	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182012	18182093	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182094	18182191	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182192	18182248	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182192	18182248	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182249	18182331	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182332	18182430	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182332	18182430	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182431	18182598	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182599	18182702	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182599	18182702	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182703	18182884	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182885	18182957	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182885	18182957	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182958	18183144	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18183145	18183287	1	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18183145	18183287	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18183288	18183360	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18183361	18183517	1	-	1	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18183361	18183517	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18183518	18183714	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18183715	18183898	1	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18183715	18183898	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18183899	18184043	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184044	18184205	1	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184044	18184205	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18184206	18184410	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184411	18184554	1	-	2	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184411	18184554	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18184555	18184727	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184728	18184827	0.92	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184728	18184827	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18184828	18184943	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184944	18185027	0.94	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184944	18185027	.	-	.	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	start_codon	18185025	18185027	.	-	0	transcript_id "Phchi.S3G260500.t1"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	transcript	18166646	18185027	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	stop_codon	18166643	18166645	.	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18166646	18166720	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18166646	18166720	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18166721	18166794	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18166795	18166947	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18166795	18166947	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18166948	18167033	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167034	18167099	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167034	18167099	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167100	18167179	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167180	18167314	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167180	18167314	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167315	18167411	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167412	18167543	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167412	18167543	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167544	18167713	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167714	18167813	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167714	18167813	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167814	18167948	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18167949	18167995	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18167949	18167995	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18167996	18168142	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168143	18168224	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168143	18168224	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168225	18168306	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168307	18168386	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168307	18168386	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168387	18168512	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168513	18168602	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168513	18168602	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168603	18168731	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168732	18168840	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168732	18168840	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18168841	18168923	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18168924	18169021	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18168924	18169021	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169022	18169102	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169103	18169162	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169103	18169162	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169163	18169257	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169258	18169314	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169258	18169314	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169315	18169433	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169434	18169574	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169434	18169574	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169575	18169665	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169666	18169728	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169666	18169728	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169729	18169878	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18169879	18169967	1	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18169879	18169967	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18169968	18170113	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170114	18170194	0.96	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170114	18170194	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170195	18170360	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170361	18170382	0.89	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170361	18170382	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170383	18170582	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170583	18170666	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170583	18170666	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170667	18170781	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170782	18170829	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170782	18170829	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18170830	18170959	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18170960	18171176	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18170960	18171176	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18171177	18171338	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18171339	18171490	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18171339	18171490	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18171491	18171570	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18171571	18171699	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18171571	18171699	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18171700	18171857	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18171858	18172022	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18171858	18172022	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172023	18172114	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172115	18172249	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172115	18172249	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172250	18172347	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172348	18172422	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172348	18172422	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172423	18172535	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172536	18172602	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172536	18172602	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172603	18172701	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172702	18172814	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172702	18172814	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172815	18172898	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18172899	18172940	0.63	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18172899	18172940	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18172941	18173050	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173051	18173173	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173051	18173173	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173174	18173326	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173327	18173413	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173327	18173413	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173414	18173566	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173567	18173671	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173567	18173671	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173672	18173823	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173824	18173871	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173824	18173871	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18173872	18173973	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18173974	18174093	0.94	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18173974	18174093	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174094	18174170	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174171	18174317	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174171	18174317	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174318	18174393	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174394	18174517	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174394	18174517	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174518	18174657	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174658	18174775	1	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174658	18174775	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174776	18174869	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18174870	18174939	0.98	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18174870	18174939	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18174940	18175040	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175041	18175112	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175041	18175112	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175113	18175192	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175193	18175372	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175193	18175372	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175373	18175484	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175485	18175674	0.97	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175485	18175674	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175675	18175783	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175784	18175830	0.99	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175784	18175830	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18175831	18175921	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18175922	18176008	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18175922	18176008	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176009	18176112	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176113	18176262	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176113	18176262	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176263	18176368	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176369	18176510	0.95	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176369	18176510	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176511	18176601	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176602	18176729	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176602	18176729	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176730	18176830	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176831	18176900	0.99	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176831	18176900	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18176901	18176985	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18176986	18177107	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18176986	18177107	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177108	18177218	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177219	18177407	0.82	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177219	18177407	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177408	18177495	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177496	18177615	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177496	18177615	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177616	18177681	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177682	18177756	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177682	18177756	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177757	18177888	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18177889	18177952	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18177889	18177952	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18177953	18178060	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178061	18178107	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178061	18178107	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18178108	18178282	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178283	18178445	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178283	18178445	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18178446	18178645	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178646	18178773	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178646	18178773	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18178774	18178914	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18178915	18179040	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18178915	18179040	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179041	18179193	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18179194	18179355	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18179194	18179355	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179356	18179498	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18179499	18179570	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18179499	18179570	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179571	18179659	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18179660	18179931	0.76	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18179660	18179931	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18179932	18180149	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180150	18180252	0.47	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180150	18180252	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18180253	18180342	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180343	18180567	0.48	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180343	18180567	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18180568	18180650	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180651	18180746	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180651	18180746	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18180747	18180863	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18180864	18181031	0.98	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18180864	18181031	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181032	18181104	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181105	18181176	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181105	18181176	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181177	18181283	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181284	18181332	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181284	18181332	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181333	18181476	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181477	18181547	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181477	18181547	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181548	18181638	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181639	18181680	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181639	18181680	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181681	18181838	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18181839	18181913	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18181839	18181913	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18181914	18182011	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182012	18182093	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182012	18182093	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182094	18182191	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182192	18182248	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182192	18182248	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182249	18182331	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182332	18182430	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182332	18182430	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182431	18182598	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182599	18182702	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182599	18182702	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182703	18182884	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18182885	18182957	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18182885	18182957	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18182958	18183144	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18183145	18183287	1	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18183145	18183287	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18183288	18183360	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18183361	18183517	1	-	1	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18183361	18183517	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18183518	18183714	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18183715	18183898	1	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18183715	18183898	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18183899	18184043	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184044	18184205	1	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184044	18184205	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18184206	18184410	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184411	18184554	1	-	2	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184411	18184554	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18184555	18184727	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184728	18184827	0.86	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184728	18184827	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	intron	18184828	18184943	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	CDS	18184944	18185027	0.97	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	exon	18184944	18185027	.	-	.	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
Phchi.S3	AUGUSTUS	start_codon	18185025	18185027	.	-	0	transcript_id "Phchi.S3G260500.t2"; gene_id "Phchi.S3G260500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8902.t1 is derived from g6077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38575506	38576279	.	+	.	Phchi.S1G606100
Phchi.S1	AUGUSTUS	transcript	38575506	38576279	.	+	.	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	start_codon	38575506	38575508	.	+	0	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	CDS	38575506	38575701	1	+	0	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	exon	38575506	38575701	.	+	.	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	intron	38575702	38575953	.	+	.	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	CDS	38575954	38576279	0.93	+	2	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	exon	38575954	38576279	.	+	.	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
Phchi.S1	AUGUSTUS	stop_codon	38576280	38576282	.	+	0	transcript_id "Phchi.S1G606100.t1"; gene_id "Phchi.S1G606100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15758.t1 is derived from g14228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21094682	21096894	.	+	.	Phchi.S3G307700
Phchi.S3	AUGUSTUS	transcript	21094682	21096894	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	start_codon	21094682	21094684	.	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21094682	21094745	1	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21094682	21094745	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21094746	21094910	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21094911	21095019	1	+	2	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21094911	21095019	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21095020	21095112	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21095113	21095202	1	+	1	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21095113	21095202	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21095203	21095289	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21095290	21095382	1	+	1	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21095290	21095382	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21095383	21095462	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21095463	21095535	1	+	1	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21095463	21095535	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21095536	21095630	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21095631	21095695	1	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21095631	21095695	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21095696	21095794	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21095795	21095888	1	+	1	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21095795	21095888	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21095889	21095968	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21095969	21096061	1	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21095969	21096061	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21096062	21096142	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21096143	21096178	0.98	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21096143	21096178	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21096179	21096291	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21096292	21096332	0.99	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21096292	21096332	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21096333	21096446	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21096447	21096535	0.99	+	1	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21096447	21096535	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21096536	21096607	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21096608	21096696	1	+	2	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21096608	21096696	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	intron	21096697	21096783	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	CDS	21096784	21096894	0.99	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	exon	21096784	21096894	.	+	.	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
Phchi.S3	AUGUSTUS	stop_codon	21096895	21096897	.	+	0	transcript_id "Phchi.S3G307700.t1"; gene_id "Phchi.S3G307700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12406.t1 is derived from g8083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18391841	18395893	.	-	.	Phchi.S2G048600
Phchi.S2	AUGUSTUS	transcript	18391841	18395893	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	stop_codon	18391838	18391840	.	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18391841	18391939	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18391841	18391939	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18391940	18392036	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392037	18392088	1	-	1	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392037	18392088	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392089	18392190	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392191	18392264	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392191	18392264	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392265	18392349	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392350	18392400	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392350	18392400	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392401	18392512	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392513	18392620	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392513	18392620	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392621	18392804	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392805	18392906	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392805	18392906	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392907	18393009	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18393010	18393096	0.94	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18393010	18393096	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18393097	18393901	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18393902	18393979	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18393902	18393979	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18393980	18394256	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394257	18394339	1	-	2	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394257	18394339	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394340	18394427	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394428	18394491	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394428	18394491	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394492	18394578	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394579	18394611	0.85	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394579	18394611	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394612	18394750	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394751	18394864	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394751	18394864	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394865	18395030	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395031	18395096	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395031	18395096	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395097	18395312	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395313	18395378	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395313	18395378	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395379	18395523	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395524	18395565	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395524	18395565	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395566	18395642	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395643	18395708	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395643	18395708	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395709	18395839	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395840	18395893	1	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395840	18395893	.	-	.	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	start_codon	18395891	18395893	.	-	0	transcript_id "Phchi.S2G048600.t1"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	transcript	18391841	18395893	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	stop_codon	18391838	18391840	.	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18391841	18391939	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18391841	18391939	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18391940	18392036	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392037	18392088	1	-	1	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392037	18392088	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392089	18392190	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392191	18392264	0.98	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392191	18392264	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392265	18392349	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392350	18392400	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392350	18392400	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392401	18392512	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392513	18392620	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392513	18392620	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392621	18392804	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18392805	18392906	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18392805	18392906	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18392907	18393009	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18393010	18393096	0.95	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18393010	18393096	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18393097	18393226	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18393227	18393269	0.94	-	1	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18393227	18393269	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18393270	18393549	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18393550	18393678	0.95	-	1	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18393550	18393678	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18393679	18393829	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18393830	18393979	0.52	-	1	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18393830	18393979	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18393980	18394082	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394083	18394114	0.59	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394083	18394114	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394115	18394256	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394257	18394339	0.95	-	2	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394257	18394339	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394340	18394427	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394428	18394491	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394428	18394491	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394492	18394578	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394579	18394611	0.84	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394579	18394611	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394612	18394750	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18394751	18394864	0.99	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18394751	18394864	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18394865	18395030	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395031	18395096	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395031	18395096	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395097	18395312	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395313	18395378	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395313	18395378	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395379	18395523	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395524	18395565	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395524	18395565	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395566	18395642	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395643	18395708	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395643	18395708	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	intron	18395709	18395839	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	CDS	18395840	18395893	1	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	exon	18395840	18395893	.	-	.	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
Phchi.S2	AUGUSTUS	start_codon	18395891	18395893	.	-	0	transcript_id "Phchi.S2G048600.t2"; gene_id "Phchi.S2G048600"
# This transcript jg8454.t1 is derived from g5628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36010496	36010759	.	-	.	Phchi.S1G561200
Phchi.S1	AUGUSTUS	transcript	36010496	36010759	.	-	.	transcript_id "Phchi.S1G561200.t1"; gene_id "Phchi.S1G561200"
Phchi.S1	AUGUSTUS	stop_codon	36010493	36010495	.	-	0	transcript_id "Phchi.S1G561200.t1"; gene_id "Phchi.S1G561200"
Phchi.S1	AUGUSTUS	CDS	36010496	36010759	0.21	-	0	transcript_id "Phchi.S1G561200.t1"; gene_id "Phchi.S1G561200"
Phchi.S1	AUGUSTUS	exon	36010496	36010759	.	-	.	transcript_id "Phchi.S1G561200.t1"; gene_id "Phchi.S1G561200"
Phchi.S1	AUGUSTUS	start_codon	36010757	36010759	.	-	0	transcript_id "Phchi.S1G561200.t1"; gene_id "Phchi.S1G561200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11287.t1 is derived from g15337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5219235	5219748	.	-	.	Phchi.S4G086900
Phchi.S4	AUGUSTUS	transcript	5219235	5219748	.	-	.	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	stop_codon	5219232	5219234	.	-	0	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	CDS	5219235	5219360	0.63	-	0	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	exon	5219235	5219360	.	-	.	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	intron	5219361	5219502	.	-	.	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	CDS	5219503	5219748	0.98	-	0	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	exon	5219503	5219748	.	-	.	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
Phchi.S4	AUGUSTUS	start_codon	5219746	5219748	.	-	0	transcript_id "Phchi.S4G086900.t1"; gene_id "Phchi.S4G086900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8759.t1 is derived from g5934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37843704	37845477	.	+	.	Phchi.S1G591800
Phchi.S1	AUGUSTUS	transcript	37843704	37845477	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	start_codon	37843704	37843706	.	+	0	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	CDS	37843704	37843854	0.68	+	0	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	exon	37843704	37843854	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	intron	37843855	37844002	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	CDS	37844003	37844132	1	+	2	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	exon	37844003	37844132	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	intron	37844133	37844254	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	CDS	37844255	37844451	0.79	+	1	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	exon	37844255	37844451	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	intron	37844452	37844548	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	CDS	37844549	37845477	0.24	+	2	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	exon	37844549	37845477	.	+	.	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
Phchi.S1	AUGUSTUS	stop_codon	37845478	37845480	.	+	0	transcript_id "Phchi.S1G591800.t1"; gene_id "Phchi.S1G591800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11853.t1 is derived from g15905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8627053	8628177	.	+	.	Phchi.S4G143500
Phchi.S4	AUGUSTUS	transcript	8627053	8628177	.	+	.	transcript_id "Phchi.S4G143500.t1"; gene_id "Phchi.S4G143500"
Phchi.S4	AUGUSTUS	start_codon	8627053	8627055	.	+	0	transcript_id "Phchi.S4G143500.t1"; gene_id "Phchi.S4G143500"
Phchi.S4	AUGUSTUS	CDS	8627053	8628177	0.82	+	0	transcript_id "Phchi.S4G143500.t1"; gene_id "Phchi.S4G143500"
Phchi.S4	AUGUSTUS	exon	8627053	8628177	.	+	.	transcript_id "Phchi.S4G143500.t1"; gene_id "Phchi.S4G143500"
Phchi.S4	AUGUSTUS	stop_codon	8628178	8628180	.	+	0	transcript_id "Phchi.S4G143500.t1"; gene_id "Phchi.S4G143500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg139.t1 is derived from g9921.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	767407	770634	.	+	.	Phchi.S6G009800
Phchi.S6	AUGUSTUS	transcript	767407	769004	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	start_codon	767407	767409	.	+	0	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	767407	767737	0.97	+	0	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	767407	767737	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	767738	767807	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	767808	768007	1	+	2	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	767808	768007	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	768008	768095	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	768096	768579	0.99	+	0	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	768096	768579	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	768580	768674	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	768675	768793	0.78	+	2	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	768675	768793	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	768794	768977	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	768978	769004	0.78	+	0	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	768978	769004	.	+	.	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	stop_codon	769005	769007	.	+	0	transcript_id "Phchi.S6G009800.t1"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	transcript	767407	770634	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	start_codon	767407	767409	.	+	0	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	767407	767737	0.98	+	0	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	767407	767737	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	767738	767807	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	767808	768007	1	+	2	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	767808	768007	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	768008	768095	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	768096	768579	0.98	+	0	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	768096	768579	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	768580	768674	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	768675	768837	1	+	2	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	768675	768837	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	768838	768977	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	768978	769066	1	+	1	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	768978	769066	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	769067	769174	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	769175	769431	0.56	+	2	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	769175	769431	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	769432	769521	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	769522	769564	0.67	+	0	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	769522	769564	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	769565	769799	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	769800	769929	0.57	+	2	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	769800	769929	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	769930	770251	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	770252	770357	0.7	+	1	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	770252	770357	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	intron	770358	770589	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	CDS	770590	770634	1	+	0	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	exon	770590	770634	.	+	.	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
Phchi.S6	AUGUSTUS	stop_codon	770635	770637	.	+	0	transcript_id "Phchi.S6G009800.t2"; gene_id "Phchi.S6G009800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7490.t1 is derived from g4663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29625012	29625745	.	+	.	Phchi.S1G464900
Phchi.S1	AUGUSTUS	transcript	29625012	29625745	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	start_codon	29625012	29625014	.	+	0	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	CDS	29625012	29625040	0.65	+	0	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	exon	29625012	29625040	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	intron	29625041	29625117	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	CDS	29625118	29625284	0.66	+	1	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	exon	29625118	29625284	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	intron	29625285	29625368	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	CDS	29625369	29625442	0.72	+	2	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	exon	29625369	29625442	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	intron	29625443	29625512	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	CDS	29625513	29625582	0.62	+	0	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	exon	29625513	29625582	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	intron	29625583	29625662	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	CDS	29625663	29625745	0.83	+	2	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	exon	29625663	29625745	.	+	.	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
Phchi.S1	AUGUSTUS	stop_codon	29625746	29625748	.	+	0	transcript_id "Phchi.S1G464900.t1"; gene_id "Phchi.S1G464900"
# This transcript jg10880.t2 is derived from g14930.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10880.t3 is derived from g14930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10881.t1 is derived from g14931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2742334	2742606	.	-	.	Phchi.S4G046300
Phchi.S4	AUGUSTUS	transcript	2742334	2742606	.	-	.	transcript_id "Phchi.S4G046300.t1"; gene_id "Phchi.S4G046300"
Phchi.S4	AUGUSTUS	stop_codon	2742331	2742333	.	-	0	transcript_id "Phchi.S4G046300.t1"; gene_id "Phchi.S4G046300"
Phchi.S4	AUGUSTUS	CDS	2742334	2742606	1	-	0	transcript_id "Phchi.S4G046300.t1"; gene_id "Phchi.S4G046300"
Phchi.S4	AUGUSTUS	exon	2742334	2742606	.	-	.	transcript_id "Phchi.S4G046300.t1"; gene_id "Phchi.S4G046300"
Phchi.S4	AUGUSTUS	start_codon	2742604	2742606	.	-	0	transcript_id "Phchi.S4G046300.t1"; gene_id "Phchi.S4G046300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15557.t1 is derived from g14026.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19911932	19914575	.	-	.	Phchi.S3G287600
Phchi.S3	AUGUSTUS	transcript	19911932	19914575	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	stop_codon	19911929	19911931	.	-	0	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19911932	19912043	0.99	-	1	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19911932	19912043	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19912044	19912305	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19912306	19912428	1	-	1	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19912306	19912428	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19912429	19912634	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19912635	19912691	0.83	-	1	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19912635	19912691	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19912692	19912836	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19912837	19912943	0.28	-	0	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19912837	19912943	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19912944	19913062	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19913063	19913977	0.72	-	0	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19913063	19913977	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19913978	19914061	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19914062	19914148	1	-	0	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19914062	19914148	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19914149	19914240	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19914241	19914433	1	-	1	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19914241	19914433	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	intron	19914434	19914516	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	CDS	19914517	19914575	0.59	-	0	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	exon	19914517	19914575	.	-	.	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
Phchi.S3	AUGUSTUS	start_codon	19914573	19914575	.	-	0	transcript_id "Phchi.S3G287600.t1"; gene_id "Phchi.S3G287600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6091.t1 is derived from g3262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20919915	20921777	.	+	.	Phchi.S1G325000
Phchi.S1	AUGUSTUS	transcript	20919915	20921777	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	start_codon	20919915	20919917	.	+	0	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	CDS	20919915	20920102	0.33	+	0	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	exon	20919915	20920102	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	intron	20920103	20920222	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	CDS	20920223	20920344	0.56	+	1	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	exon	20920223	20920344	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	intron	20920345	20920437	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	CDS	20920438	20920504	0.66	+	2	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	exon	20920438	20920504	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	intron	20920505	20920580	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	CDS	20920581	20920675	0.89	+	1	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	exon	20920581	20920675	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	intron	20920676	20920758	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	CDS	20920759	20921777	0.81	+	2	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	exon	20920759	20921777	.	+	.	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
Phchi.S1	AUGUSTUS	stop_codon	20921778	20921780	.	+	0	transcript_id "Phchi.S1G325000.t1"; gene_id "Phchi.S1G325000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12542.t1 is derived from g8219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34114171	34115589	.	-	.	Phchi.S2G062200
Phchi.S2	AUGUSTUS	transcript	34114171	34115589	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	stop_codon	34114168	34114170	.	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34114171	34114293	0.51	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34114171	34114293	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34114294	34114391	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34114392	34114427	0.97	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34114392	34114427	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34114428	34114529	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34114530	34114613	0.98	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34114530	34114613	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34114614	34114754	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34114755	34114814	1	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34114755	34114814	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34114815	34114945	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34114946	34115002	1	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34114946	34115002	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34115003	34115138	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34115139	34115213	1	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34115139	34115213	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34115214	34115317	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34115318	34115380	0.99	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34115318	34115380	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34115381	34115461	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34115462	34115492	1	-	1	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34115462	34115492	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	intron	34115493	34115569	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	CDS	34115570	34115589	0.98	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	exon	34115570	34115589	.	-	.	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
Phchi.S2	AUGUSTUS	start_codon	34115587	34115589	.	-	0	transcript_id "Phchi.S2G062200.t1"; gene_id "Phchi.S2G062200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5629.t1 is derived from g2799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17963547	17964187	.	-	.	Phchi.S1G278800
Phchi.S1	AUGUSTUS	transcript	17963547	17964187	.	-	.	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	stop_codon	17963544	17963546	.	-	0	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	CDS	17963547	17963708	1	-	0	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	exon	17963547	17963708	.	-	.	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	intron	17963709	17963788	.	-	.	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	CDS	17963789	17964187	0.44	-	0	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	exon	17963789	17964187	.	-	.	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
Phchi.S1	AUGUSTUS	start_codon	17964185	17964187	.	-	0	transcript_id "Phchi.S1G278800.t1"; gene_id "Phchi.S1G278800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7602.t1 is derived from g4776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30213476	30214331	.	+	.	Phchi.S1G476100
Phchi.S1	AUGUSTUS	transcript	30213476	30214331	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	start_codon	30213476	30213478	.	+	0	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	CDS	30213476	30213550	0.55	+	0	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	exon	30213476	30213550	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	intron	30213551	30213635	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	CDS	30213636	30213760	1	+	0	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	exon	30213636	30213760	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	intron	30213761	30213845	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	CDS	30213846	30213956	1	+	1	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	exon	30213846	30213956	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	intron	30213957	30214046	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	CDS	30214047	30214137	1	+	1	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	exon	30214047	30214137	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	intron	30214138	30214223	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	CDS	30214224	30214331	1	+	0	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	exon	30214224	30214331	.	+	.	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
Phchi.S1	AUGUSTUS	stop_codon	30214332	30214334	.	+	0	transcript_id "Phchi.S1G476100.t1"; gene_id "Phchi.S1G476100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13905.t1 is derived from g12372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9603058	9604003	.	-	.	Phchi.S3G122400
Phchi.S3	AUGUSTUS	transcript	9603058	9604003	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	stop_codon	9603055	9603057	.	-	0	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	CDS	9603058	9603219	1	-	0	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	exon	9603058	9603219	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	intron	9603220	9603307	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	CDS	9603308	9603379	1	-	0	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	exon	9603308	9603379	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	intron	9603380	9603457	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	CDS	9603458	9603571	1	-	0	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	exon	9603458	9603571	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	intron	9603572	9603655	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	CDS	9603656	9604003	0.72	-	0	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	exon	9603656	9604003	.	-	.	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
Phchi.S3	AUGUSTUS	start_codon	9604001	9604003	.	-	0	transcript_id "Phchi.S3G122400.t1"; gene_id "Phchi.S3G122400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3660.t1 is derived from g829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5007173	5008522	.	+	.	Phchi.S1G081900
Phchi.S1	AUGUSTUS	transcript	5007173	5008522	.	+	.	transcript_id "Phchi.S1G081900.t1"; gene_id "Phchi.S1G081900"
Phchi.S1	AUGUSTUS	start_codon	5007173	5007175	.	+	0	transcript_id "Phchi.S1G081900.t1"; gene_id "Phchi.S1G081900"
Phchi.S1	AUGUSTUS	CDS	5007173	5008522	0.92	+	0	transcript_id "Phchi.S1G081900.t1"; gene_id "Phchi.S1G081900"
Phchi.S1	AUGUSTUS	exon	5007173	5008522	.	+	.	transcript_id "Phchi.S1G081900.t1"; gene_id "Phchi.S1G081900"
Phchi.S1	AUGUSTUS	stop_codon	5008523	5008525	.	+	0	transcript_id "Phchi.S1G081900.t1"; gene_id "Phchi.S1G081900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7455.t1 is derived from g4627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29373422	29376476	.	+	.	Phchi.S1G461400
Phchi.S1	AUGUSTUS	transcript	29373422	29376476	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	start_codon	29373422	29373424	.	+	0	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	CDS	29373422	29374520	0.86	+	0	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	exon	29373422	29374520	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	intron	29374521	29374683	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	CDS	29374684	29374736	0.84	+	2	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	exon	29374684	29374736	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	intron	29374737	29374816	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	CDS	29374817	29376048	0.26	+	0	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	exon	29374817	29376048	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	intron	29376049	29376158	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	CDS	29376159	29376233	0.35	+	1	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	exon	29376159	29376233	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	intron	29376234	29376328	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	CDS	29376329	29376476	1	+	1	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	exon	29376329	29376476	.	+	.	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
Phchi.S1	AUGUSTUS	stop_codon	29376477	29376479	.	+	0	transcript_id "Phchi.S1G461400.t1"; gene_id "Phchi.S1G461400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg460.t1 is derived from g10242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3237649	3242870	.	+	.	Phchi.S6G041900
Phchi.S6	AUGUSTUS	transcript	3237649	3242870	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	start_codon	3237649	3237651	.	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3237649	3237696	1	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3237649	3237696	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3237697	3237795	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3237796	3237885	1	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3237796	3237885	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3237886	3237971	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3237972	3238024	1	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3237972	3238024	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3238025	3238109	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3238110	3238185	1	+	1	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3238110	3238185	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3238186	3238283	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3238284	3238345	1	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3238284	3238345	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3238346	3238471	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3238472	3238550	1	+	1	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3238472	3238550	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3238551	3238644	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3238645	3238704	1	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3238645	3238704	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3238705	3238786	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3238787	3240535	1	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3238787	3240535	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3240536	3240680	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3240681	3241562	0.98	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3240681	3241562	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	intron	3241563	3241715	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	CDS	3241716	3242870	0.99	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	exon	3241716	3242870	.	+	.	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
Phchi.S6	AUGUSTUS	stop_codon	3242871	3242873	.	+	0	transcript_id "Phchi.S6G041900.t1"; gene_id "Phchi.S6G041900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11091.t1 is derived from g15141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4081673	4082760	.	-	.	Phchi.S4G067300
Phchi.S4	AUGUSTUS	transcript	4081673	4082760	.	-	.	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	stop_codon	4081670	4081672	.	-	0	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	CDS	4081673	4081748	0.62	-	1	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	exon	4081673	4081748	.	-	.	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	intron	4081749	4081900	.	-	.	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	CDS	4081901	4082760	0.4	-	0	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	exon	4081901	4082760	.	-	.	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
Phchi.S4	AUGUSTUS	start_codon	4082758	4082760	.	-	0	transcript_id "Phchi.S4G067300.t1"; gene_id "Phchi.S4G067300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7325.t1 is derived from g4497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28523739	28524764	.	-	.	Phchi.S1G448400
Phchi.S1	AUGUSTUS	transcript	28523739	28524764	.	-	.	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	stop_codon	28523736	28523738	.	-	0	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	CDS	28523739	28524035	1	-	0	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	exon	28523739	28524035	.	-	.	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	intron	28524036	28524124	.	-	.	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	CDS	28524125	28524482	1	-	1	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	exon	28524125	28524482	.	-	.	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	intron	28524483	28524567	.	-	.	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	CDS	28524568	28524764	0.82	-	0	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	exon	28524568	28524764	.	-	.	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
Phchi.S1	AUGUSTUS	start_codon	28524762	28524764	.	-	0	transcript_id "Phchi.S1G448400.t1"; gene_id "Phchi.S1G448400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg607.t1 is derived from g10389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4382324	4384151	.	-	.	Phchi.S6G056600
Phchi.S6	AUGUSTUS	transcript	4382324	4383274	.	-	.	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	stop_codon	4382321	4382323	.	-	0	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4382324	4382569	0.99	-	0	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4382324	4382569	.	-	.	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4382570	4382637	.	-	.	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4382638	4382841	0.97	-	0	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4382638	4382841	.	-	.	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4382842	4382935	.	-	.	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4382936	4383274	0.5	-	0	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4382936	4383274	.	-	.	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	start_codon	4383272	4383274	.	-	0	transcript_id "Phchi.S6G056600.t1"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	transcript	4382324	4384151	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	stop_codon	4382321	4382323	.	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4382324	4382569	1	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4382324	4382569	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4382570	4382637	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4382638	4382841	0.93	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4382638	4382841	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4382842	4382935	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4382936	4383262	0.83	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4382936	4383262	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4383263	4383356	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4383357	4383560	0.46	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4383357	4383560	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4383561	4383650	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4383651	4383920	0.93	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4383651	4383920	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	intron	4383921	4384034	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	CDS	4384035	4384151	1	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	exon	4384035	4384151	.	-	.	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
Phchi.S6	AUGUSTUS	start_codon	4384149	4384151	.	-	0	transcript_id "Phchi.S6G056600.t2"; gene_id "Phchi.S6G056600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13983.t1 is derived from g12450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10042230	10045765	.	-	.	Phchi.S3G130200
Phchi.S3	AUGUSTUS	transcript	10042230	10045765	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	stop_codon	10042227	10042229	.	-	0	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10042230	10042992	0.68	-	1	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10042230	10042992	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	intron	10042993	10043101	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10043102	10043351	0.98	-	2	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10043102	10043351	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	intron	10043352	10043449	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10043450	10043654	0.77	-	0	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10043450	10043654	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	intron	10043655	10043751	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10043752	10043793	0.63	-	0	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10043752	10043793	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	intron	10043794	10043883	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10043884	10044298	0.95	-	1	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10043884	10044298	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	intron	10044299	10044376	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10044377	10044729	0.65	-	0	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10044377	10044729	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	intron	10044730	10044811	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	CDS	10044812	10045765	0.65	-	0	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	exon	10044812	10045765	.	-	.	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
Phchi.S3	AUGUSTUS	start_codon	10045763	10045765	.	-	0	transcript_id "Phchi.S3G130200.t1"; gene_id "Phchi.S3G130200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11086.t1 is derived from g15136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4023011	4026141	.	-	.	Phchi.S4G066800
Phchi.S4	AUGUSTUS	transcript	4023011	4026141	.	-	.	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	stop_codon	4023008	4023010	.	-	0	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	CDS	4023011	4025113	0.89	-	0	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	exon	4023011	4025113	.	-	.	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	intron	4025114	4025199	.	-	.	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	CDS	4025200	4026141	0.7	-	0	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	exon	4025200	4026141	.	-	.	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
Phchi.S4	AUGUSTUS	start_codon	4026139	4026141	.	-	0	transcript_id "Phchi.S4G066800.t1"; gene_id "Phchi.S4G066800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12993.t1 is derived from g11458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3542145	3545853	.	+	.	Phchi.S3G031200
Phchi.S3	AUGUSTUS	transcript	3542145	3545853	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	start_codon	3542145	3542147	.	+	0	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	CDS	3542145	3543034	0.89	+	0	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	exon	3542145	3543034	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	intron	3543035	3543260	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	CDS	3543261	3543541	0.44	+	1	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	exon	3543261	3543541	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	intron	3543542	3543594	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	CDS	3543595	3545176	0.51	+	2	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	exon	3543595	3545176	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	intron	3545177	3545355	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	CDS	3545356	3545441	0.66	+	1	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	exon	3545356	3545441	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	intron	3545442	3545851	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	CDS	3545852	3545853	1	+	2	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	exon	3545852	3545853	.	+	.	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
Phchi.S3	AUGUSTUS	stop_codon	3545854	3545856	.	+	0	transcript_id "Phchi.S3G031200.t1"; gene_id "Phchi.S3G031200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5647.t1 is derived from g2817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18049572	18052382	.	-	.	Phchi.S1G280600
Phchi.S1	AUGUSTUS	transcript	18049572	18052382	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	stop_codon	18049569	18049571	.	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18049572	18049652	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18049572	18049652	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18049653	18049739	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18049740	18050074	1	-	2	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18049740	18050074	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18050075	18050202	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18050203	18050380	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18050203	18050380	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18050381	18050497	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18050498	18050578	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18050498	18050578	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18050579	18050667	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18050668	18050779	1	-	1	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18050668	18050779	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18050780	18050862	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18050863	18050963	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18050863	18050963	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18050964	18051059	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18051060	18051233	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18051060	18051233	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18051234	18051318	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18051319	18051492	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18051319	18051492	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18051493	18051573	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18051574	18051656	1	-	2	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18051574	18051656	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18051657	18051753	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18051754	18051814	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18051754	18051814	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18051815	18051895	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18051896	18052078	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18051896	18052078	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	intron	18052079	18052163	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	CDS	18052164	18052382	1	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	exon	18052164	18052382	.	-	.	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
Phchi.S1	AUGUSTUS	start_codon	18052380	18052382	.	-	0	transcript_id "Phchi.S1G280600.t1"; gene_id "Phchi.S1G280600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3070.t1 is derived from g239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1433173	1433847	.	-	.	Phchi.S1G022900
Phchi.S1	AUGUSTUS	transcript	1433173	1433847	.	-	.	transcript_id "Phchi.S1G022900.t1"; gene_id "Phchi.S1G022900"
Phchi.S1	AUGUSTUS	stop_codon	1433170	1433172	.	-	0	transcript_id "Phchi.S1G022900.t1"; gene_id "Phchi.S1G022900"
Phchi.S1	AUGUSTUS	CDS	1433173	1433847	0.62	-	0	transcript_id "Phchi.S1G022900.t1"; gene_id "Phchi.S1G022900"
Phchi.S1	AUGUSTUS	exon	1433173	1433847	.	-	.	transcript_id "Phchi.S1G022900.t1"; gene_id "Phchi.S1G022900"
Phchi.S1	AUGUSTUS	start_codon	1433845	1433847	.	-	0	transcript_id "Phchi.S1G022900.t1"; gene_id "Phchi.S1G022900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1713.t1 is derived from g8633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2663399	2666307	.	+	.	Phchi.S5G032200
Phchi.S5	AUGUSTUS	transcript	2663399	2666307	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	start_codon	2663399	2663401	.	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2663399	2663627	0.97	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2663399	2663627	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2663628	2663716	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2663717	2663850	1	+	2	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2663717	2663850	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2663851	2663930	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2663931	2664060	0.82	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2663931	2664060	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2664061	2664171	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2664172	2664332	0.83	+	2	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2664172	2664332	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2664333	2664419	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2664420	2664521	1	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2664420	2664521	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2664522	2664617	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2664618	2664722	1	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2664618	2664722	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2664723	2664818	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2664819	2664947	1	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2664819	2664947	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2664948	2665050	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2665051	2665191	1	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2665051	2665191	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2665192	2665277	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2665278	2665378	1	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2665278	2665378	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2665379	2665457	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2665458	2665515	0.91	+	1	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2665458	2665515	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	intron	2665516	2665620	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	CDS	2665621	2666307	0.91	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	exon	2665621	2666307	.	+	.	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
Phchi.S5	AUGUSTUS	stop_codon	2666308	2666310	.	+	0	transcript_id "Phchi.S5G032200.t1"; gene_id "Phchi.S5G032200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5334.t1 is derived from g2504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16351965	16352661	.	-	.	Phchi.S1G249300
Phchi.S1	AUGUSTUS	transcript	16351965	16352661	.	-	.	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	stop_codon	16351962	16351964	.	-	0	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	CDS	16351965	16352057	0.37	-	0	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	exon	16351965	16352057	.	-	.	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	intron	16352058	16352216	.	-	.	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	CDS	16352217	16352337	0.39	-	1	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	exon	16352217	16352337	.	-	.	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	intron	16352338	16352608	.	-	.	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	CDS	16352609	16352661	0.55	-	0	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	exon	16352609	16352661	.	-	.	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
Phchi.S1	AUGUSTUS	start_codon	16352659	16352661	.	-	0	transcript_id "Phchi.S1G249300.t1"; gene_id "Phchi.S1G249300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13496.t1 is derived from g11963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7164042	7164572	.	+	.	Phchi.S3G081500
Phchi.S3	AUGUSTUS	transcript	7164042	7164572	.	+	.	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	start_codon	7164042	7164044	.	+	0	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	CDS	7164042	7164247	0.31	+	0	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	exon	7164042	7164247	.	+	.	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	intron	7164248	7164556	.	+	.	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	CDS	7164557	7164572	0.8	+	1	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	exon	7164557	7164572	.	+	.	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
Phchi.S3	AUGUSTUS	stop_codon	7164573	7164575	.	+	0	transcript_id "Phchi.S3G081500.t1"; gene_id "Phchi.S3G081500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1902.t1 is derived from g8822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3783239	3783948	.	-	.	Phchi.S5G051100
Phchi.S5	AUGUSTUS	transcript	3783239	3783948	.	-	.	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	stop_codon	3783236	3783238	.	-	0	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	CDS	3783239	3783337	0.66	-	0	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	exon	3783239	3783337	.	-	.	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	intron	3783338	3783532	.	-	.	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	CDS	3783533	3783723	0.7	-	2	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	exon	3783533	3783723	.	-	.	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	intron	3783724	3783884	.	-	.	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	CDS	3783885	3783948	0.51	-	0	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	exon	3783885	3783948	.	-	.	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
Phchi.S5	AUGUSTUS	start_codon	3783946	3783948	.	-	0	transcript_id "Phchi.S5G051100.t1"; gene_id "Phchi.S5G051100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg48.t1 is derived from g9830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	80020	81506	.	+	.	Phchi.S6G000700
Phchi.S6	AUGUSTUS	transcript	80020	81506	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	start_codon	80020	80022	.	+	0	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	CDS	80020	80265	0.7	+	0	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	exon	80020	80265	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	intron	80266	80565	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	CDS	80566	80614	0.59	+	0	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	exon	80566	80614	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	intron	80615	80827	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	CDS	80828	81029	0.55	+	2	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	exon	80828	81029	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	intron	81030	81271	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	CDS	81272	81366	0.44	+	1	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	exon	81272	81366	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	intron	81367	81447	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	CDS	81448	81506	0.74	+	2	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	exon	81448	81506	.	+	.	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
Phchi.S6	AUGUSTUS	stop_codon	81507	81509	.	+	0	transcript_id "Phchi.S6G000700.t1"; gene_id "Phchi.S6G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14269.t1 is derived from g12736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11864195	11864719	.	-	.	Phchi.S3G158800
Phchi.S3	AUGUSTUS	transcript	11864195	11864719	.	-	.	transcript_id "Phchi.S3G158800.t1"; gene_id "Phchi.S3G158800"
Phchi.S3	AUGUSTUS	stop_codon	11864192	11864194	.	-	0	transcript_id "Phchi.S3G158800.t1"; gene_id "Phchi.S3G158800"
Phchi.S3	AUGUSTUS	CDS	11864195	11864719	0.34	-	0	transcript_id "Phchi.S3G158800.t1"; gene_id "Phchi.S3G158800"
Phchi.S3	AUGUSTUS	exon	11864195	11864719	.	-	.	transcript_id "Phchi.S3G158800.t1"; gene_id "Phchi.S3G158800"
Phchi.S3	AUGUSTUS	start_codon	11864717	11864719	.	-	0	transcript_id "Phchi.S3G158800.t1"; gene_id "Phchi.S3G158800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2072.t1 is derived from g8992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4716413	4716973	.	+	.	Phchi.S5G068100
Phchi.S5	AUGUSTUS	transcript	4716413	4716973	.	+	.	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	start_codon	4716413	4716415	.	+	0	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	CDS	4716413	4716508	0.37	+	0	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	exon	4716413	4716508	.	+	.	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	intron	4716509	4716642	.	+	.	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	CDS	4716643	4716750	1	+	0	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	exon	4716643	4716750	.	+	.	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	intron	4716751	4716874	.	+	.	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	CDS	4716875	4716973	1	+	0	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	exon	4716875	4716973	.	+	.	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
Phchi.S5	AUGUSTUS	stop_codon	4716974	4716976	.	+	0	transcript_id "Phchi.S5G068100.t1"; gene_id "Phchi.S5G068100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10130.t1 is derived from g7306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45872430	45874240	.	+	.	Phchi.S1G728900
Phchi.S1	AUGUSTUS	transcript	45872430	45874240	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	start_codon	45872430	45872432	.	+	0	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	CDS	45872430	45872740	1	+	0	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	exon	45872430	45872740	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	intron	45872741	45872820	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	CDS	45872821	45872922	1	+	1	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	exon	45872821	45872922	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	intron	45872923	45873020	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	CDS	45873021	45873516	0.66	+	1	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	exon	45873021	45873516	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	intron	45873517	45873690	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	CDS	45873691	45873730	0.97	+	0	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	exon	45873691	45873730	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	intron	45873731	45873851	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	CDS	45873852	45874240	0.99	+	2	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	exon	45873852	45874240	.	+	.	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
Phchi.S1	AUGUSTUS	stop_codon	45874241	45874243	.	+	0	transcript_id "Phchi.S1G728900.t1"; gene_id "Phchi.S1G728900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg283.t1 is derived from g10065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2021025	2022183	.	+	.	Phchi.S6G024200
Phchi.S6	AUGUSTUS	transcript	2021025	2022183	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	start_codon	2021025	2021027	.	+	0	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	CDS	2021025	2021225	0.51	+	0	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	exon	2021025	2021225	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	intron	2021226	2021317	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	CDS	2021318	2021571	0.99	+	0	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	exon	2021318	2021571	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	intron	2021572	2021652	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	CDS	2021653	2021776	1	+	1	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	exon	2021653	2021776	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	intron	2021777	2021888	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	CDS	2021889	2021993	0.99	+	0	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	exon	2021889	2021993	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	intron	2021994	2022102	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	CDS	2022103	2022183	0.99	+	0	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	exon	2022103	2022183	.	+	.	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
Phchi.S6	AUGUSTUS	stop_codon	2022184	2022186	.	+	0	transcript_id "Phchi.S6G024200.t1"; gene_id "Phchi.S6G024200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15164.t1 is derived from g13632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17329831	17331178	.	+	.	Phchi.S3G248300
Phchi.S3	AUGUSTUS	transcript	17329831	17331178	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	start_codon	17329831	17329833	.	+	0	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17329831	17329906	1	+	0	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17329831	17329906	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	intron	17329907	17330039	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17330040	17330102	1	+	2	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17330040	17330102	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	intron	17330103	17330208	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17330209	17330300	1	+	2	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17330209	17330300	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	intron	17330301	17330432	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17330433	17330546	1	+	0	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17330433	17330546	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	intron	17330547	17330714	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17330715	17330782	1	+	0	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17330715	17330782	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	intron	17330783	17330871	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17330872	17330983	0.99	+	1	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17330872	17330983	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	intron	17330984	17331085	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	CDS	17331086	17331178	0.99	+	0	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	exon	17331086	17331178	.	+	.	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
Phchi.S3	AUGUSTUS	stop_codon	17331179	17331181	.	+	0	transcript_id "Phchi.S3G248300.t1"; gene_id "Phchi.S3G248300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12794.t1 is derived from g11259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2419187	2420845	.	-	.	Phchi.S3G011300
Phchi.S3	AUGUSTUS	transcript	2419187	2420845	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	stop_codon	2419184	2419186	.	-	0	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2419187	2419287	1	-	2	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2419187	2419287	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2419288	2419384	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2419385	2419541	1	-	0	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2419385	2419541	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2419542	2419636	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2419637	2419730	1	-	1	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2419637	2419730	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2419731	2419942	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2419943	2420146	1	-	1	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2419943	2420146	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2420147	2420247	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2420248	2420351	1	-	0	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2420248	2420351	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2420352	2420431	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2420432	2420466	1	-	2	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2420432	2420466	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2420467	2420564	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2420565	2420686	1	-	1	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2420565	2420686	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	intron	2420687	2420759	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	CDS	2420760	2420845	0.99	-	0	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	exon	2420760	2420845	.	-	.	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
Phchi.S3	AUGUSTUS	start_codon	2420843	2420845	.	-	0	transcript_id "Phchi.S3G011300.t1"; gene_id "Phchi.S3G011300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7406.t1 is derived from g4578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28977112	28977708	.	-	.	Phchi.S1G456500
Phchi.S1	AUGUSTUS	transcript	28977112	28977708	.	-	.	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	stop_codon	28977109	28977111	.	-	0	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	CDS	28977112	28977199	1	-	1	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	exon	28977112	28977199	.	-	.	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	intron	28977200	28977296	.	-	.	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	CDS	28977297	28977403	1	-	0	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	exon	28977297	28977403	.	-	.	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	intron	28977404	28977669	.	-	.	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	CDS	28977670	28977708	1	-	0	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	exon	28977670	28977708	.	-	.	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
Phchi.S1	AUGUSTUS	start_codon	28977706	28977708	.	-	0	transcript_id "Phchi.S1G456500.t1"; gene_id "Phchi.S1G456500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg334.t1 is derived from g10116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2443125	2443585	.	-	.	Phchi.S6G029300
Phchi.S6	AUGUSTUS	transcript	2443125	2443585	.	-	.	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	stop_codon	2443122	2443124	.	-	0	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	CDS	2443125	2443125	0.98	-	1	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	exon	2443125	2443125	.	-	.	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	intron	2443126	2443267	.	-	.	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	CDS	2443268	2443471	0.98	-	1	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	exon	2443268	2443471	.	-	.	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	intron	2443472	2443547	.	-	.	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	CDS	2443548	2443585	0.98	-	0	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	exon	2443548	2443585	.	-	.	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
Phchi.S6	AUGUSTUS	start_codon	2443583	2443585	.	-	0	transcript_id "Phchi.S6G029300.t1"; gene_id "Phchi.S6G029300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2723.t1 is derived from g9643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8446679	8447998	.	+	.	Phchi.S5G133200
Phchi.S5	AUGUSTUS	transcript	8446679	8447998	.	+	.	transcript_id "Phchi.S5G133200.t1"; gene_id "Phchi.S5G133200"
Phchi.S5	AUGUSTUS	start_codon	8446679	8446681	.	+	0	transcript_id "Phchi.S5G133200.t1"; gene_id "Phchi.S5G133200"
Phchi.S5	AUGUSTUS	CDS	8446679	8447998	0.99	+	0	transcript_id "Phchi.S5G133200.t1"; gene_id "Phchi.S5G133200"
Phchi.S5	AUGUSTUS	exon	8446679	8447998	.	+	.	transcript_id "Phchi.S5G133200.t1"; gene_id "Phchi.S5G133200"
Phchi.S5	AUGUSTUS	stop_codon	8447999	8448001	.	+	0	transcript_id "Phchi.S5G133200.t1"; gene_id "Phchi.S5G133200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg274.t1 is derived from g10056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1956607	1960259	.	+	.	Phchi.S6G023300
Phchi.S6	AUGUSTUS	transcript	1956607	1960259	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	start_codon	1956607	1956609	.	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1956607	1956612	0.98	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1956607	1956612	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1956613	1956776	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1956777	1956899	0.59	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1956777	1956899	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1956900	1957185	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1957186	1957377	0.75	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1957186	1957377	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1957378	1957593	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1957594	1957692	1	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1957594	1957692	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1957693	1957821	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1957822	1957953	1	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1957822	1957953	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1957954	1958048	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1958049	1958288	1	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1958049	1958288	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1958289	1958388	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1958389	1958416	0.67	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1958389	1958416	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1958417	1958575	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1958576	1958679	0.66	+	2	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1958576	1958679	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1958680	1958795	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1958796	1958941	0.98	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1958796	1958941	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1958942	1959062	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1959063	1959140	0.94	+	1	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1959063	1959140	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1959141	1959263	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1959264	1959396	1	+	1	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1959264	1959396	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1959397	1959514	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1959515	1959776	1	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1959515	1959776	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1959777	1959875	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1959876	1960053	1	+	2	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1959876	1960053	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	intron	1960054	1960147	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	CDS	1960148	1960259	0.88	+	1	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	exon	1960148	1960259	.	+	.	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
Phchi.S6	AUGUSTUS	stop_codon	1960260	1960262	.	+	0	transcript_id "Phchi.S6G023300.t1"; gene_id "Phchi.S6G023300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13411.t1 is derived from g11877.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6568376	6571088	.	+	.	Phchi.S3G073000
Phchi.S3	AUGUSTUS	transcript	6568376	6571088	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	start_codon	6568376	6568378	.	+	0	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6568376	6568433	0.88	+	0	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6568376	6568433	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6568434	6568549	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6568550	6568603	0.91	+	2	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6568550	6568603	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6568604	6569295	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6569296	6569415	0.92	+	2	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6569296	6569415	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6569416	6569870	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6569871	6569981	1	+	2	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6569871	6569981	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6569982	6570080	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570081	6570112	1	+	2	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570081	6570112	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570113	6570201	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570202	6570306	1	+	0	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570202	6570306	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570307	6570442	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570443	6570566	1	+	0	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570443	6570566	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570567	6570682	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570683	6570754	1	+	2	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570683	6570754	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570755	6570841	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570842	6570915	1	+	2	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570842	6570915	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570916	6571007	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6571008	6571088	1	+	0	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6571008	6571088	.	+	.	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	stop_codon	6571089	6571091	.	+	0	transcript_id "Phchi.S3G073000.t1"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	transcript	6569479	6571088	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	start_codon	6569479	6569481	.	+	0	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6569479	6569536	0.38	+	0	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6569479	6569536	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6569537	6569870	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6569871	6569981	0.98	+	2	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6569871	6569981	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6569982	6570080	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570081	6570112	1	+	2	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570081	6570112	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570113	6570201	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570202	6570306	1	+	0	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570202	6570306	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570307	6570442	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570443	6570566	1	+	0	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570443	6570566	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570567	6570682	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570683	6570754	1	+	2	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570683	6570754	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570755	6570841	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6570842	6570915	1	+	2	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6570842	6570915	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	intron	6570916	6571007	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	CDS	6571008	6571088	1	+	0	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	exon	6571008	6571088	.	+	.	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
Phchi.S3	AUGUSTUS	stop_codon	6571089	6571091	.	+	0	transcript_id "Phchi.S3G073000.t2"; gene_id "Phchi.S3G073000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14712.t1 is derived from g13180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14327754	14331327	.	+	.	Phchi.S3G203100
Phchi.S3	AUGUSTUS	transcript	14327754	14331327	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	start_codon	14327754	14327756	.	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14327754	14327793	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14327754	14327793	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14327794	14327998	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14327999	14328099	1	+	2	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14327999	14328099	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14328100	14328199	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14328200	14328256	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14328200	14328256	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14328257	14328333	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14328334	14328399	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14328334	14328399	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14328400	14328494	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14328495	14328628	0.88	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14328495	14328628	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14328629	14328730	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14328731	14328800	1	+	1	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14328731	14328800	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14328801	14328896	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14328897	14329017	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14328897	14329017	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14329018	14329176	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14329177	14329314	1	+	2	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14329177	14329314	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14329315	14329446	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14329447	14329514	1	+	2	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14329447	14329514	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14329515	14329608	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14329609	14329668	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14329609	14329668	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14329669	14329816	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14329817	14329872	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14329817	14329872	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14329873	14330025	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14330026	14330086	1	+	1	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14330026	14330086	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14330087	14330169	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14330170	14330262	0.52	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14330170	14330262	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14330263	14330363	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14330364	14330439	0.83	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14330364	14330439	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14330440	14330513	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14330514	14330698	1	+	2	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14330514	14330698	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14330699	14330779	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14330780	14331075	1	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14330780	14331075	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	intron	14331076	14331185	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	CDS	14331186	14331327	0.99	+	1	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	exon	14331186	14331327	.	+	.	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
Phchi.S3	AUGUSTUS	stop_codon	14331328	14331330	.	+	0	transcript_id "Phchi.S3G203100.t1"; gene_id "Phchi.S3G203100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5169.t1 is derived from g2339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15293824	15295104	.	+	.	Phchi.S1G232800
Phchi.S1	AUGUSTUS	transcript	15293824	15295104	.	+	.	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	start_codon	15293824	15293826	.	+	0	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	CDS	15293824	15294312	0.31	+	0	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	exon	15293824	15294312	.	+	.	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	intron	15294313	15294488	.	+	.	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	CDS	15294489	15294712	0.81	+	0	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	exon	15294489	15294712	.	+	.	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	intron	15294713	15295019	.	+	.	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	CDS	15295020	15295104	0.93	+	1	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	exon	15295020	15295104	.	+	.	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
Phchi.S1	AUGUSTUS	stop_codon	15295105	15295107	.	+	0	transcript_id "Phchi.S1G232800.t1"; gene_id "Phchi.S1G232800"
# This transcript jg8106.t2 is derived from g5281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8107.t1 is derived from g5282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33154146	33160909	.	-	.	Phchi.S1G526600
Phchi.S1	AUGUSTUS	transcript	33154146	33160909	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	stop_codon	33154143	33154145	.	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33154146	33154256	0.27	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33154146	33154256	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33154257	33154331	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33154332	33154463	0.84	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33154332	33154463	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33154464	33154583	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33154584	33154694	0.81	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33154584	33154694	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33154695	33154812	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33154813	33154977	0.98	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33154813	33154977	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33154978	33155096	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33155097	33155279	0.74	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33155097	33155279	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33155280	33155383	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33155384	33155521	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33155384	33155521	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33155522	33155774	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33155775	33155861	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33155775	33155861	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33155862	33155952	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33155953	33156025	1	-	1	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33155953	33156025	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33156026	33156163	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33156164	33156358	1	-	1	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33156164	33156358	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33156359	33156820	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33156821	33156897	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33156821	33156897	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33156898	33156995	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33156996	33157067	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33156996	33157067	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33157068	33157148	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33157149	33157309	1	-	2	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33157149	33157309	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33157310	33158147	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33158148	33158334	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33158148	33158334	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33158335	33158421	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33158422	33158535	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33158422	33158535	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33158536	33158636	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33158637	33158720	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33158637	33158720	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33158721	33158850	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33158851	33159032	1	-	2	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33158851	33159032	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33159033	33159156	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33159157	33159324	1	-	2	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33159157	33159324	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33159325	33159827	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33159828	33160039	1	-	1	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33159828	33160039	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33160040	33160328	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33160329	33160420	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33160329	33160420	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33160421	33160512	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33160513	33160674	1	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33160513	33160674	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	intron	33160675	33160798	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	CDS	33160799	33160909	0.97	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	exon	33160799	33160909	.	-	.	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
Phchi.S1	AUGUSTUS	start_codon	33160907	33160909	.	-	0	transcript_id "Phchi.S1G526600.t1"; gene_id "Phchi.S1G526600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1218.t1 is derived from g11001.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8447075	8448467	.	+	.	Phchi.S6G117700
Phchi.S6	AUGUSTUS	transcript	8447075	8448467	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	start_codon	8447075	8447077	.	+	0	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447075	8447113	1	+	0	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447075	8447113	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447114	8447300	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447301	8447414	1	+	0	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447301	8447414	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447415	8447557	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447558	8447607	1	+	0	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447558	8447607	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447608	8447740	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447741	8447851	1	+	1	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447741	8447851	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447852	8447938	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447939	8448024	0.78	+	1	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447939	8448024	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8448025	8448224	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8448225	8448253	0.8	+	2	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8448225	8448253	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8448254	8448341	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8448342	8448467	0.99	+	0	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8448342	8448467	.	+	.	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	stop_codon	8448468	8448470	.	+	0	transcript_id "Phchi.S6G117700.t1"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	transcript	8447075	8448467	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	start_codon	8447075	8447077	.	+	0	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447075	8447113	1	+	0	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447075	8447113	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447114	8447300	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447301	8447414	1	+	0	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447301	8447414	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447415	8447554	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447555	8447607	1	+	0	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447555	8447607	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447608	8447740	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447741	8447851	1	+	1	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447741	8447851	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8447852	8447938	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8447939	8448024	0.76	+	1	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8447939	8448024	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8448025	8448224	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8448225	8448253	0.73	+	2	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8448225	8448253	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	intron	8448254	8448341	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	CDS	8448342	8448467	0.98	+	0	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	exon	8448342	8448467	.	+	.	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
Phchi.S6	AUGUSTUS	stop_codon	8448468	8448470	.	+	0	transcript_id "Phchi.S6G117700.t2"; gene_id "Phchi.S6G117700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2066.t1 is derived from g8986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4675609	4676058	.	-	.	Phchi.S5G067500
Phchi.S5	AUGUSTUS	transcript	4675609	4676058	.	-	.	transcript_id "Phchi.S5G067500.t1"; gene_id "Phchi.S5G067500"
Phchi.S5	AUGUSTUS	stop_codon	4675606	4675608	.	-	0	transcript_id "Phchi.S5G067500.t1"; gene_id "Phchi.S5G067500"
Phchi.S5	AUGUSTUS	CDS	4675609	4676058	0.85	-	0	transcript_id "Phchi.S5G067500.t1"; gene_id "Phchi.S5G067500"
Phchi.S5	AUGUSTUS	exon	4675609	4676058	.	-	.	transcript_id "Phchi.S5G067500.t1"; gene_id "Phchi.S5G067500"
Phchi.S5	AUGUSTUS	start_codon	4676056	4676058	.	-	0	transcript_id "Phchi.S5G067500.t1"; gene_id "Phchi.S5G067500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14335.t1 is derived from g12802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12291332	12292587	.	-	.	Phchi.S3G165400
Phchi.S3	AUGUSTUS	transcript	12291332	12292587	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	stop_codon	12291329	12291331	.	-	0	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	CDS	12291332	12291470	0.62	-	1	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	exon	12291332	12291470	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	intron	12291471	12291562	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	CDS	12291563	12291724	1	-	1	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	exon	12291563	12291724	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	intron	12291725	12291840	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	CDS	12291841	12292051	1	-	2	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	exon	12291841	12292051	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	intron	12292052	12292255	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	CDS	12292256	12292356	1	-	1	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	exon	12292256	12292356	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	intron	12292357	12292450	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	CDS	12292451	12292587	0.5	-	0	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	exon	12292451	12292587	.	-	.	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
Phchi.S3	AUGUSTUS	start_codon	12292585	12292587	.	-	0	transcript_id "Phchi.S3G165400.t1"; gene_id "Phchi.S3G165400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15364.t1 is derived from g13832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18599892	18602344	.	-	.	Phchi.S3G268300
Phchi.S3	AUGUSTUS	transcript	18599892	18602344	.	-	.	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	stop_codon	18599889	18599891	.	-	0	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	CDS	18599892	18600868	1	-	2	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	exon	18599892	18600868	.	-	.	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	intron	18600869	18601053	.	-	.	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	CDS	18601054	18601851	1	-	2	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	exon	18601054	18601851	.	-	.	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	intron	18601852	18602085	.	-	.	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	CDS	18602086	18602344	0.9	-	0	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	exon	18602086	18602344	.	-	.	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
Phchi.S3	AUGUSTUS	start_codon	18602342	18602344	.	-	0	transcript_id "Phchi.S3G268300.t1"; gene_id "Phchi.S3G268300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8796.t1 is derived from g5971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38011401	38012075	.	+	.	Phchi.S1G595500
Phchi.S1	AUGUSTUS	transcript	38011401	38012075	.	+	.	transcript_id "Phchi.S1G595500.t1"; gene_id "Phchi.S1G595500"
Phchi.S1	AUGUSTUS	start_codon	38011401	38011403	.	+	0	transcript_id "Phchi.S1G595500.t1"; gene_id "Phchi.S1G595500"
Phchi.S1	AUGUSTUS	CDS	38011401	38012075	0.93	+	0	transcript_id "Phchi.S1G595500.t1"; gene_id "Phchi.S1G595500"
Phchi.S1	AUGUSTUS	exon	38011401	38012075	.	+	.	transcript_id "Phchi.S1G595500.t1"; gene_id "Phchi.S1G595500"
Phchi.S1	AUGUSTUS	stop_codon	38012076	38012078	.	+	0	transcript_id "Phchi.S1G595500.t1"; gene_id "Phchi.S1G595500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6102.t1 is derived from g3273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20954594	20955547	.	+	.	Phchi.S1G326100
Phchi.S1	AUGUSTUS	transcript	20954594	20955547	.	+	.	transcript_id "Phchi.S1G326100.t1"; gene_id "Phchi.S1G326100"
Phchi.S1	AUGUSTUS	start_codon	20954594	20954596	.	+	0	transcript_id "Phchi.S1G326100.t1"; gene_id "Phchi.S1G326100"
Phchi.S1	AUGUSTUS	CDS	20954594	20955547	0.28	+	0	transcript_id "Phchi.S1G326100.t1"; gene_id "Phchi.S1G326100"
Phchi.S1	AUGUSTUS	exon	20954594	20955547	.	+	.	transcript_id "Phchi.S1G326100.t1"; gene_id "Phchi.S1G326100"
Phchi.S1	AUGUSTUS	stop_codon	20955548	20955550	.	+	0	transcript_id "Phchi.S1G326100.t1"; gene_id "Phchi.S1G326100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg217.t1 is derived from g9999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1406780	1407088	.	-	.	Phchi.S6G017600
Phchi.S6	AUGUSTUS	transcript	1406780	1407088	.	-	.	transcript_id "Phchi.S6G017600.t1"; gene_id "Phchi.S6G017600"
Phchi.S6	AUGUSTUS	stop_codon	1406777	1406779	.	-	0	transcript_id "Phchi.S6G017600.t1"; gene_id "Phchi.S6G017600"
Phchi.S6	AUGUSTUS	CDS	1406780	1407088	0.92	-	0	transcript_id "Phchi.S6G017600.t1"; gene_id "Phchi.S6G017600"
Phchi.S6	AUGUSTUS	exon	1406780	1407088	.	-	.	transcript_id "Phchi.S6G017600.t1"; gene_id "Phchi.S6G017600"
Phchi.S6	AUGUSTUS	start_codon	1407086	1407088	.	-	0	transcript_id "Phchi.S6G017600.t1"; gene_id "Phchi.S6G017600"
# This transcript jg7384.t2 is derived from g4556.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7385.t1 is derived from g4557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28873416	28874346	.	+	.	Phchi.S1G454400
Phchi.S1	AUGUSTUS	transcript	28873416	28874346	.	+	.	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	start_codon	28873416	28873418	.	+	0	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	CDS	28873416	28873637	1	+	0	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	exon	28873416	28873637	.	+	.	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	intron	28873638	28873812	.	+	.	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	CDS	28873813	28873870	0.36	+	0	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	exon	28873813	28873870	.	+	.	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	intron	28873871	28874059	.	+	.	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	CDS	28874060	28874346	0.51	+	2	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	exon	28874060	28874346	.	+	.	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
Phchi.S1	AUGUSTUS	stop_codon	28874347	28874349	.	+	0	transcript_id "Phchi.S1G454400.t1"; gene_id "Phchi.S1G454400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13017.t1 is derived from g11482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3641514	3641942	.	+	.	Phchi.S3G033600
Phchi.S3	AUGUSTUS	transcript	3641514	3641942	.	+	.	transcript_id "Phchi.S3G033600.t1"; gene_id "Phchi.S3G033600"
Phchi.S3	AUGUSTUS	start_codon	3641514	3641516	.	+	0	transcript_id "Phchi.S3G033600.t1"; gene_id "Phchi.S3G033600"
Phchi.S3	AUGUSTUS	CDS	3641514	3641942	0.75	+	0	transcript_id "Phchi.S3G033600.t1"; gene_id "Phchi.S3G033600"
Phchi.S3	AUGUSTUS	exon	3641514	3641942	.	+	.	transcript_id "Phchi.S3G033600.t1"; gene_id "Phchi.S3G033600"
Phchi.S3	AUGUSTUS	stop_codon	3641943	3641945	.	+	0	transcript_id "Phchi.S3G033600.t1"; gene_id "Phchi.S3G033600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13530.t1 is derived from g11997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7388858	7389079	.	-	.	Phchi.S3G084900
Phchi.S3	AUGUSTUS	transcript	7388858	7389079	.	-	.	transcript_id "Phchi.S3G084900.t1"; gene_id "Phchi.S3G084900"
Phchi.S3	AUGUSTUS	stop_codon	7388855	7388857	.	-	0	transcript_id "Phchi.S3G084900.t1"; gene_id "Phchi.S3G084900"
Phchi.S3	AUGUSTUS	CDS	7388858	7389079	0.88	-	0	transcript_id "Phchi.S3G084900.t1"; gene_id "Phchi.S3G084900"
Phchi.S3	AUGUSTUS	exon	7388858	7389079	.	-	.	transcript_id "Phchi.S3G084900.t1"; gene_id "Phchi.S3G084900"
Phchi.S3	AUGUSTUS	start_codon	7389077	7389079	.	-	0	transcript_id "Phchi.S3G084900.t1"; gene_id "Phchi.S3G084900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9963.t1 is derived from g7139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44685108	44689443	.	+	.	Phchi.S1G712200
Phchi.S1	AUGUSTUS	transcript	44685108	44689443	.	+	.	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	start_codon	44685108	44685110	.	+	0	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	CDS	44685108	44686623	0.32	+	0	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	exon	44685108	44686623	.	+	.	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	intron	44686624	44686735	.	+	.	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	CDS	44686736	44688183	1	+	2	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	exon	44686736	44688183	.	+	.	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	intron	44688184	44688303	.	+	.	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	CDS	44688304	44689443	0.99	+	0	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	exon	44688304	44689443	.	+	.	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
Phchi.S1	AUGUSTUS	stop_codon	44689444	44689446	.	+	0	transcript_id "Phchi.S1G712200.t1"; gene_id "Phchi.S1G712200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10305.t1 is derived from g7481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47054786	47055085	.	+	.	Phchi.S1G746400
Phchi.S1	AUGUSTUS	transcript	47054786	47055085	.	+	.	transcript_id "Phchi.S1G746400.t1"; gene_id "Phchi.S1G746400"
Phchi.S1	AUGUSTUS	start_codon	47054786	47054788	.	+	0	transcript_id "Phchi.S1G746400.t1"; gene_id "Phchi.S1G746400"
Phchi.S1	AUGUSTUS	CDS	47054786	47055085	0.8	+	0	transcript_id "Phchi.S1G746400.t1"; gene_id "Phchi.S1G746400"
Phchi.S1	AUGUSTUS	exon	47054786	47055085	.	+	.	transcript_id "Phchi.S1G746400.t1"; gene_id "Phchi.S1G746400"
Phchi.S1	AUGUSTUS	stop_codon	47055086	47055088	.	+	0	transcript_id "Phchi.S1G746400.t1"; gene_id "Phchi.S1G746400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13379.t1 is derived from g11845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6433864	6434309	.	-	.	Phchi.S3G069800
Phchi.S3	AUGUSTUS	transcript	6433864	6434309	.	-	.	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	stop_codon	6433861	6433863	.	-	0	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	CDS	6433864	6433920	0.9	-	0	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	exon	6433864	6433920	.	-	.	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	intron	6433921	6434013	.	-	.	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	CDS	6434014	6434057	0.86	-	2	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	exon	6434014	6434057	.	-	.	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	intron	6434058	6434209	.	-	.	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	CDS	6434210	6434309	0.46	-	0	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	exon	6434210	6434309	.	-	.	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
Phchi.S3	AUGUSTUS	start_codon	6434307	6434309	.	-	0	transcript_id "Phchi.S3G069800.t1"; gene_id "Phchi.S3G069800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14400.t1 is derived from g12868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12628518	12629675	.	+	.	Phchi.S3G171900
Phchi.S3	AUGUSTUS	transcript	12628518	12629675	.	+	.	transcript_id "Phchi.S3G171900.t1"; gene_id "Phchi.S3G171900"
Phchi.S3	AUGUSTUS	start_codon	12628518	12628520	.	+	0	transcript_id "Phchi.S3G171900.t1"; gene_id "Phchi.S3G171900"
Phchi.S3	AUGUSTUS	CDS	12628518	12629675	0.86	+	0	transcript_id "Phchi.S3G171900.t1"; gene_id "Phchi.S3G171900"
Phchi.S3	AUGUSTUS	exon	12628518	12629675	.	+	.	transcript_id "Phchi.S3G171900.t1"; gene_id "Phchi.S3G171900"
Phchi.S3	AUGUSTUS	stop_codon	12629676	12629678	.	+	0	transcript_id "Phchi.S3G171900.t1"; gene_id "Phchi.S3G171900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11373.t1 is derived from g15423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5943383	5943766	.	-	.	Phchi.S4G095500
Phchi.S4	AUGUSTUS	transcript	5943383	5943766	.	-	.	transcript_id "Phchi.S4G095500.t1"; gene_id "Phchi.S4G095500"
Phchi.S4	AUGUSTUS	stop_codon	5943380	5943382	.	-	0	transcript_id "Phchi.S4G095500.t1"; gene_id "Phchi.S4G095500"
Phchi.S4	AUGUSTUS	CDS	5943383	5943766	0.93	-	0	transcript_id "Phchi.S4G095500.t1"; gene_id "Phchi.S4G095500"
Phchi.S4	AUGUSTUS	exon	5943383	5943766	.	-	.	transcript_id "Phchi.S4G095500.t1"; gene_id "Phchi.S4G095500"
Phchi.S4	AUGUSTUS	start_codon	5943764	5943766	.	-	0	transcript_id "Phchi.S4G095500.t1"; gene_id "Phchi.S4G095500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12061.t1 is derived from g7736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1282355	1287293	.	+	.	Phchi.S2G014100
Phchi.S2	AUGUSTUS	transcript	1282355	1287293	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	start_codon	1282355	1282357	.	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1282355	1282622	0.95	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1282355	1282622	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1282623	1282717	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1282718	1282816	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1282718	1282816	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1282817	1282985	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1282986	1283044	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1282986	1283044	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283045	1283211	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283212	1283372	0.96	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283212	1283372	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283373	1283479	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283480	1283619	0.99	+	1	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283480	1283619	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283620	1283733	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283734	1283845	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283734	1283845	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283846	1283934	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283935	1284037	1	+	1	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283935	1284037	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284038	1284173	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284174	1284219	1	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284174	1284219	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284220	1284307	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284308	1284346	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284308	1284346	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284347	1284466	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284467	1284623	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284467	1284623	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284624	1284757	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284758	1284872	1	+	1	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284758	1284872	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284873	1285023	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285024	1285110	0.27	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285024	1285110	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285111	1285258	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285259	1285336	0.99	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285259	1285336	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285337	1285414	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285415	1285516	1	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285415	1285516	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285517	1285608	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285609	1285714	1	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285609	1285714	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285715	1285794	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285795	1285923	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285795	1285923	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285924	1286011	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286012	1286076	1	+	2	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286012	1286076	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286077	1286221	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286222	1286361	1	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286222	1286361	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286362	1286489	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286490	1286558	0.88	+	1	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286490	1286558	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286559	1286705	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286706	1286865	0.63	+	1	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286706	1286865	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286866	1286986	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286987	1287097	1	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286987	1287097	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1287098	1287185	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1287186	1287293	0.98	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1287186	1287293	.	+	.	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	stop_codon	1287294	1287296	.	+	0	transcript_id "Phchi.S2G014100.t1"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	transcript	1282355	1287293	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	start_codon	1282355	1282357	.	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1282355	1282622	0.97	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1282355	1282622	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1282623	1282717	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1282718	1282816	1	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1282718	1282816	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1282817	1282985	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1282986	1283044	1	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1282986	1283044	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283045	1283211	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283212	1283372	0.99	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283212	1283372	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283373	1283479	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283480	1283619	1	+	1	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283480	1283619	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283620	1283733	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283734	1283845	1	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283734	1283845	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1283846	1283934	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1283935	1284037	1	+	1	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1283935	1284037	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284038	1284173	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284174	1284219	1	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284174	1284219	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284220	1284307	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284308	1284346	1	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284308	1284346	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284347	1284432	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284433	1284471	0.45	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284433	1284471	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284472	1284559	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284560	1284623	0.86	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284560	1284623	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284624	1284757	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1284758	1284872	1	+	1	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1284758	1284872	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1284873	1285023	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285024	1285110	0.31	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285024	1285110	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285111	1285258	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285259	1285336	1	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285259	1285336	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285337	1285414	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285415	1285516	1	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285415	1285516	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285517	1285608	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285609	1285714	1	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285609	1285714	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285715	1285794	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1285795	1285923	1	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1285795	1285923	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1285924	1286011	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286012	1286076	1	+	2	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286012	1286076	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286077	1286221	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286222	1286361	1	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286222	1286361	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286362	1286489	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286490	1286558	0.9	+	1	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286490	1286558	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286559	1286705	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286706	1286865	0.69	+	1	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286706	1286865	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1286866	1286986	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1286987	1287097	1	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1286987	1287097	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	intron	1287098	1287185	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	CDS	1287186	1287293	0.96	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	exon	1287186	1287293	.	+	.	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
Phchi.S2	AUGUSTUS	stop_codon	1287294	1287296	.	+	0	transcript_id "Phchi.S2G014100.t2"; gene_id "Phchi.S2G014100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7852.t1 is derived from g5026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31524636	31526725	.	-	.	Phchi.S1G501100
Phchi.S1	AUGUSTUS	transcript	31524636	31526725	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	stop_codon	31524633	31524635	.	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31524636	31524689	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31524636	31524689	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31524690	31524757	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31524758	31524826	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31524758	31524826	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31524827	31524920	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31524921	31525034	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31524921	31525034	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525035	31525123	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31525124	31525213	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31525124	31525213	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525214	31525293	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31525294	31525371	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31525294	31525371	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525372	31525464	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31525465	31525516	1	-	1	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31525465	31525516	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525517	31525611	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31525612	31525682	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31525612	31525682	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525683	31525758	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31525759	31525813	1	-	1	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31525759	31525813	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525814	31525939	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31525940	31525990	1	-	1	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31525940	31525990	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31525991	31526071	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31526072	31526131	1	-	1	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31526072	31526131	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31526132	31526209	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31526210	31526285	1	-	2	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31526210	31526285	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31526286	31526384	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31526385	31526430	1	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31526385	31526430	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	intron	31526431	31526566	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	CDS	31526567	31526725	0.91	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	exon	31526567	31526725	.	-	.	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
Phchi.S1	AUGUSTUS	start_codon	31526723	31526725	.	-	0	transcript_id "Phchi.S1G501100.t1"; gene_id "Phchi.S1G501100"
# This transcript jg661.t2 is derived from g10443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg662.t1 is derived from g10444.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4627379	4629800	.	-	.	Phchi.S6G062100
Phchi.S6	AUGUSTUS	transcript	4627379	4629568	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	stop_codon	4627376	4627378	.	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4627379	4627519	0.67	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4627379	4627519	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4627520	4627610	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4627611	4627724	0.98	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4627611	4627724	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4627725	4627812	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4627813	4627950	1	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4627813	4627950	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4627951	4628073	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628074	4628124	1	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628074	4628124	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628125	4628208	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628209	4628316	1	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628209	4628316	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628317	4628428	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628429	4628584	0.97	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628429	4628584	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628585	4628670	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628671	4628826	0.52	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628671	4628826	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628827	4628960	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628961	4629012	0.99	-	1	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628961	4629012	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4629013	4629128	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4629129	4629568	0.23	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4629129	4629568	.	-	.	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	start_codon	4629566	4629568	.	-	0	transcript_id "Phchi.S6G062100.t1"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	transcript	4627379	4629800	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	stop_codon	4627376	4627378	.	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4627379	4627519	0.67	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4627379	4627519	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4627520	4627610	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4627611	4627724	0.99	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4627611	4627724	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4627725	4627812	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4627813	4627950	0.99	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4627813	4627950	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4627951	4628073	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628074	4628124	0.96	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628074	4628124	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628125	4628208	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628209	4628316	0.98	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628209	4628316	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628317	4628428	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628429	4628584	0.93	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628429	4628584	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628585	4628670	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628671	4628826	0.48	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628671	4628826	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4628827	4628960	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4628961	4629012	0.99	-	1	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4628961	4629012	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4629013	4629128	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4629129	4629561	0.47	-	2	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4629129	4629561	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	intron	4629562	4629643	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	CDS	4629644	4629800	0.98	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	exon	4629644	4629800	.	-	.	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
Phchi.S6	AUGUSTUS	start_codon	4629798	4629800	.	-	0	transcript_id "Phchi.S6G062100.t2"; gene_id "Phchi.S6G062100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1040.t1 is derived from g10823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7261633	7262547	.	-	.	Phchi.S6G099900
Phchi.S6	AUGUSTUS	transcript	7261633	7262547	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	stop_codon	7261630	7261632	.	-	0	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	CDS	7261633	7261720	0.99	-	1	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	exon	7261633	7261720	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	intron	7261721	7261819	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	CDS	7261820	7261947	0.87	-	0	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	exon	7261820	7261947	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	intron	7261948	7262071	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	CDS	7262072	7262295	0.81	-	2	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	exon	7262072	7262295	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	intron	7262296	7262393	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	CDS	7262394	7262547	1	-	0	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	exon	7262394	7262547	.	-	.	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
Phchi.S6	AUGUSTUS	start_codon	7262545	7262547	.	-	0	transcript_id "Phchi.S6G099900.t1"; gene_id "Phchi.S6G099900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5993.t1 is derived from g3164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20282728	20285185	.	+	.	Phchi.S1G315200
Phchi.S1	AUGUSTUS	transcript	20282728	20285185	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	start_codon	20282728	20282730	.	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20282728	20282929	0.5	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20282728	20282929	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20282930	20283052	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20283053	20283138	1	+	2	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20283053	20283138	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20283139	20283344	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20283345	20283443	1	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20283345	20283443	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20283444	20283524	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20283525	20283591	1	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20283525	20283591	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20283592	20283676	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20283677	20283752	1	+	2	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20283677	20283752	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20283753	20283863	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20283864	20283930	1	+	1	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20283864	20283930	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20283931	20284055	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20284056	20284273	1	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20284056	20284273	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20284274	20284361	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20284362	20284429	0.99	+	1	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20284362	20284429	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20284430	20284535	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20284536	20284615	0.99	+	2	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20284536	20284615	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20284616	20284702	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20284703	20284789	1	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20284703	20284789	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20284790	20284877	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20284878	20284985	1	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20284878	20284985	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	intron	20284986	20285059	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	CDS	20285060	20285185	1	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	exon	20285060	20285185	.	+	.	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
Phchi.S1	AUGUSTUS	stop_codon	20285186	20285188	.	+	0	transcript_id "Phchi.S1G315200.t1"; gene_id "Phchi.S1G315200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9488.t1 is derived from g6664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41991398	41992354	.	+	.	Phchi.S1G664700
Phchi.S1	AUGUSTUS	transcript	41991398	41992354	.	+	.	transcript_id "Phchi.S1G664700.t1"; gene_id "Phchi.S1G664700"
Phchi.S1	AUGUSTUS	start_codon	41991398	41991400	.	+	0	transcript_id "Phchi.S1G664700.t1"; gene_id "Phchi.S1G664700"
Phchi.S1	AUGUSTUS	CDS	41991398	41992354	0.69	+	0	transcript_id "Phchi.S1G664700.t1"; gene_id "Phchi.S1G664700"
Phchi.S1	AUGUSTUS	exon	41991398	41992354	.	+	.	transcript_id "Phchi.S1G664700.t1"; gene_id "Phchi.S1G664700"
Phchi.S1	AUGUSTUS	stop_codon	41992355	41992357	.	+	0	transcript_id "Phchi.S1G664700.t1"; gene_id "Phchi.S1G664700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15451.t1 is derived from g13919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19227735	19232671	.	-	.	Phchi.S3G277000
Phchi.S3	AUGUSTUS	transcript	19227735	19232671	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	stop_codon	19227732	19227734	.	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19227735	19227800	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19227735	19227800	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19227801	19227883	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19227884	19227949	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19227884	19227949	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19227950	19228032	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19228033	19228140	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19228033	19228140	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19228141	19228230	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19228231	19228365	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19228231	19228365	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19228366	19228443	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19228444	19228521	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19228444	19228521	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19228522	19228604	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19228605	19228655	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19228605	19228655	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19228656	19228760	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19228761	19228835	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19228761	19228835	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19228836	19228945	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19228946	19229008	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19228946	19229008	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19229009	19229130	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19229131	19229220	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19229131	19229220	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19229221	19229382	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19229383	19229580	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19229383	19229580	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19229581	19229712	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19229713	19229824	1	-	1	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19229713	19229824	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19229825	19230053	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19230054	19230611	0.96	-	1	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19230054	19230611	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19230612	19230728	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19230729	19230928	0.96	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19230729	19230928	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19230929	19231063	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19231064	19231108	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19231064	19231108	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19231109	19231215	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19231216	19231275	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19231216	19231275	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19231276	19231450	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19231451	19231534	1	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19231451	19231534	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19231535	19231883	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19231884	19231946	0.85	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19231884	19231946	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19231947	19232040	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19232041	19232088	0.95	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19232041	19232088	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	intron	19232089	19232362	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	CDS	19232363	19232671	0.92	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	exon	19232363	19232671	.	-	.	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
Phchi.S3	AUGUSTUS	start_codon	19232669	19232671	.	-	0	transcript_id "Phchi.S3G277000.t1"; gene_id "Phchi.S3G277000"
# This transcript jg10367.t2 is derived from g7543.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10368.t1 is derived from g7544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47404801	47406227	.	-	.	Phchi.S1G752700
Phchi.S1	AUGUSTUS	transcript	47404801	47406227	.	-	.	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	stop_codon	47404798	47404800	.	-	0	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	CDS	47404801	47405589	0.73	-	0	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	exon	47404801	47405589	.	-	.	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	intron	47405590	47405690	.	-	.	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	CDS	47405691	47406227	0.51	-	0	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	exon	47405691	47406227	.	-	.	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
Phchi.S1	AUGUSTUS	start_codon	47406225	47406227	.	-	0	transcript_id "Phchi.S1G752700.t1"; gene_id "Phchi.S1G752700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15649.t1 is derived from g14118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20481870	20483150	.	+	.	Phchi.S3G296800
Phchi.S3	AUGUSTUS	transcript	20481870	20483150	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	start_codon	20481870	20481872	.	+	0	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	CDS	20481870	20481872	1	+	0	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	exon	20481870	20481872	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	intron	20481873	20482139	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	CDS	20482140	20482299	1	+	0	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	exon	20482140	20482299	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	intron	20482300	20482445	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	CDS	20482446	20482593	1	+	2	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	exon	20482446	20482593	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	intron	20482594	20482705	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	CDS	20482706	20482783	1	+	1	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	exon	20482706	20482783	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	intron	20482784	20482913	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	CDS	20482914	20482998	1	+	1	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	exon	20482914	20482998	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	intron	20482999	20483093	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	CDS	20483094	20483150	1	+	0	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	exon	20483094	20483150	.	+	.	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
Phchi.S3	AUGUSTUS	stop_codon	20483151	20483153	.	+	0	transcript_id "Phchi.S3G296800.t1"; gene_id "Phchi.S3G296800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12021.t1 is derived from g7696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	614413	614865	.	+	.	Phchi.S2G010100
Phchi.S2	AUGUSTUS	transcript	614413	614865	.	+	.	transcript_id "Phchi.S2G010100.t1"; gene_id "Phchi.S2G010100"
Phchi.S2	AUGUSTUS	start_codon	614413	614415	.	+	0	transcript_id "Phchi.S2G010100.t1"; gene_id "Phchi.S2G010100"
Phchi.S2	AUGUSTUS	CDS	614413	614865	1	+	0	transcript_id "Phchi.S2G010100.t1"; gene_id "Phchi.S2G010100"
Phchi.S2	AUGUSTUS	exon	614413	614865	.	+	.	transcript_id "Phchi.S2G010100.t1"; gene_id "Phchi.S2G010100"
Phchi.S2	AUGUSTUS	stop_codon	614866	614868	.	+	0	transcript_id "Phchi.S2G010100.t1"; gene_id "Phchi.S2G010100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11387.t1 is derived from g15437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6054461	6054763	.	-	.	Phchi.S4G096900
Phchi.S4	AUGUSTUS	transcript	6054461	6054763	.	-	.	transcript_id "Phchi.S4G096900.t1"; gene_id "Phchi.S4G096900"
Phchi.S4	AUGUSTUS	stop_codon	6054458	6054460	.	-	0	transcript_id "Phchi.S4G096900.t1"; gene_id "Phchi.S4G096900"
Phchi.S4	AUGUSTUS	CDS	6054461	6054763	0.39	-	0	transcript_id "Phchi.S4G096900.t1"; gene_id "Phchi.S4G096900"
Phchi.S4	AUGUSTUS	exon	6054461	6054763	.	-	.	transcript_id "Phchi.S4G096900.t1"; gene_id "Phchi.S4G096900"
Phchi.S4	AUGUSTUS	start_codon	6054761	6054763	.	-	0	transcript_id "Phchi.S4G096900.t1"; gene_id "Phchi.S4G096900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1430.t1 is derived from g8349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	808559	811074	.	+	.	Phchi.S5G003900
Phchi.S5	AUGUSTUS	transcript	808559	811074	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	start_codon	808559	808561	.	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	808559	808609	0.55	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	808559	808609	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	808610	808868	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	808869	808948	0.93	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	808869	808948	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	808949	809074	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	809075	809153	1	+	1	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	809075	809153	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	809154	809291	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	809292	809373	1	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	809292	809373	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	809374	809495	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	809496	809643	1	+	2	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	809496	809643	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	809644	809804	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	809805	809895	1	+	1	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	809805	809895	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	809896	809981	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	809982	810065	1	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	809982	810065	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	810066	810310	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	810311	810357	1	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	810311	810357	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	810358	810449	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	810450	810581	1	+	1	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	810450	810581	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	810582	810681	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	810682	810766	1	+	1	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	810682	810766	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	810767	810880	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	810881	810961	1	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	810881	810961	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	intron	810962	811056	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	CDS	811057	811074	1	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	exon	811057	811074	.	+	.	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
Phchi.S5	AUGUSTUS	stop_codon	811075	811077	.	+	0	transcript_id "Phchi.S5G003900.t1"; gene_id "Phchi.S5G003900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12549.t1 is derived from g8226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34445417	34450693	.	-	.	Phchi.S2G062900
Phchi.S2	AUGUSTUS	transcript	34445417	34450693	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	stop_codon	34445414	34445416	.	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34445417	34445516	1	-	1	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34445417	34445516	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34445517	34445593	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34445594	34445700	1	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34445594	34445700	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34445701	34445778	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34445779	34445918	1	-	2	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34445779	34445918	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34445919	34446040	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34446041	34446266	1	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34446041	34446266	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34446267	34446362	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34446363	34446443	1	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34446363	34446443	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34446444	34446542	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34446543	34446689	1	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34446543	34446689	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34446690	34446772	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34446773	34447928	0.89	-	1	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34446773	34447928	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34447929	34448013	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34448014	34448128	0.94	-	2	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34448014	34448128	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34448129	34448229	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34448230	34448344	1	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34448230	34448344	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34448345	34448426	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34448427	34448725	1	-	2	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34448427	34448725	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34448726	34448822	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34448823	34449030	1	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34448823	34449030	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34449031	34449113	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34449114	34449455	0.99	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34449114	34449455	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	intron	34449456	34449565	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	CDS	34449566	34450693	0.88	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	exon	34449566	34450693	.	-	.	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
Phchi.S2	AUGUSTUS	start_codon	34450691	34450693	.	-	0	transcript_id "Phchi.S2G062900.t1"; gene_id "Phchi.S2G062900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14642.t1 is derived from g13110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13896007	13902033	.	+	.	Phchi.S3G196100
Phchi.S3	AUGUSTUS	transcript	13896007	13902033	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	start_codon	13896007	13896009	.	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13896007	13896114	0.92	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13896007	13896114	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13896115	13896241	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13896242	13896349	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13896242	13896349	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13896350	13896480	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13896481	13896549	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13896481	13896549	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13896550	13896690	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13896691	13896774	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13896691	13896774	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13896775	13896919	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13896920	13896996	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13896920	13896996	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13896997	13897125	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13897126	13897192	1	+	1	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13897126	13897192	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13897193	13897330	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13897331	13897388	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13897331	13897388	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13897389	13897520	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13897521	13897588	1	+	2	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13897521	13897588	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13897589	13897683	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13897684	13897746	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13897684	13897746	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13897747	13897859	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13897860	13897913	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13897860	13897913	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13897914	13897985	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13897986	13898079	0.55	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13897986	13898079	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13898080	13898191	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13898192	13898301	1	+	2	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13898192	13898301	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13898302	13898430	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13898431	13898550	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13898431	13898550	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13898551	13898640	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13898641	13898697	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13898641	13898697	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13898698	13898771	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13898772	13898959	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13898772	13898959	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13898960	13899038	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13899039	13899213	1	+	1	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13899039	13899213	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13899214	13899298	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13899299	13899382	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13899299	13899382	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13899383	13899503	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13899504	13899629	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13899504	13899629	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13899630	13899816	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13899817	13899950	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13899817	13899950	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13899951	13900069	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13900070	13900151	1	+	1	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13900070	13900151	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13900152	13900232	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13900233	13900320	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13900233	13900320	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13900321	13900434	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13900435	13900478	1	+	2	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13900435	13900478	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13900479	13900570	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13900571	13900666	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13900571	13900666	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13900667	13900761	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13900762	13900838	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13900762	13900838	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13900839	13900937	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13900938	13901141	1	+	1	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13900938	13901141	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13901142	13901213	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13901214	13901379	1	+	1	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13901214	13901379	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13901380	13901463	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13901464	13901535	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13901464	13901535	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13901536	13901627	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13901628	13901825	1	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13901628	13901825	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	intron	13901826	13901919	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	CDS	13901920	13902033	0.98	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	exon	13901920	13902033	.	+	.	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
Phchi.S3	AUGUSTUS	stop_codon	13902034	13902036	.	+	0	transcript_id "Phchi.S3G196100.t1"; gene_id "Phchi.S3G196100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg356.t1 is derived from g10139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2622114	2623121	.	+	.	Phchi.S6G031600
Phchi.S6	AUGUSTUS	transcript	2622114	2623121	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	start_codon	2622114	2622116	.	+	0	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	CDS	2622114	2622170	0.87	+	0	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	exon	2622114	2622170	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	intron	2622171	2622242	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	CDS	2622243	2622304	1	+	0	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	exon	2622243	2622304	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	intron	2622305	2622535	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	CDS	2622536	2622565	0.75	+	1	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	exon	2622536	2622565	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	intron	2622566	2622635	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	CDS	2622636	2622642	0.75	+	1	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	exon	2622636	2622642	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	intron	2622643	2622735	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	CDS	2622736	2622854	1	+	0	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	exon	2622736	2622854	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	intron	2622855	2622952	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	CDS	2622953	2623121	1	+	1	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	exon	2622953	2623121	.	+	.	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
Phchi.S6	AUGUSTUS	stop_codon	2623122	2623124	.	+	0	transcript_id "Phchi.S6G031600.t1"; gene_id "Phchi.S6G031600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13820.t1 is derived from g12287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9061973	9063917	.	+	.	Phchi.S3G113900
Phchi.S3	AUGUSTUS	transcript	9061973	9063917	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	start_codon	9061973	9061975	.	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9061973	9062136	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9061973	9062136	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062137	9062238	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062239	9062320	1	+	1	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062239	9062320	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062321	9062476	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062477	9062647	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062477	9062647	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062648	9062732	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062733	9062933	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062733	9062933	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062934	9063069	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063070	9063252	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063070	9063252	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063253	9063345	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063346	9063433	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063346	9063433	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063434	9063526	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063527	9063585	1	+	2	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063527	9063585	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063586	9063679	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063680	9063745	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063680	9063745	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063746	9063830	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063831	9063917	1	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063831	9063917	.	+	.	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	stop_codon	9063918	9063920	.	+	0	transcript_id "Phchi.S3G113900.t1"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	transcript	9061973	9063917	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	start_codon	9061973	9061975	.	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9061973	9062136	0.99	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9061973	9062136	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062137	9062238	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062239	9062320	0.99	+	1	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062239	9062320	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062321	9062447	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062448	9062476	0.77	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062448	9062476	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062477	9062616	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062617	9062647	0.95	+	1	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062617	9062647	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062648	9062732	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9062733	9062933	1	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9062733	9062933	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9062934	9063069	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063070	9063252	1	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063070	9063252	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063253	9063345	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063346	9063433	1	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063346	9063433	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063434	9063526	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063527	9063585	1	+	2	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063527	9063585	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063586	9063679	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063680	9063745	1	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063680	9063745	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	intron	9063746	9063830	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	CDS	9063831	9063917	1	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	exon	9063831	9063917	.	+	.	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
Phchi.S3	AUGUSTUS	stop_codon	9063918	9063920	.	+	0	transcript_id "Phchi.S3G113900.t2"; gene_id "Phchi.S3G113900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12366.t1 is derived from g8042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13079625	13082206	.	-	.	Phchi.S2G044600
Phchi.S2	AUGUSTUS	transcript	13079625	13082206	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	stop_codon	13079622	13079624	.	-	0	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	CDS	13079625	13080846	0.94	-	1	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	exon	13079625	13080846	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	intron	13080847	13080950	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	CDS	13080951	13081012	0.98	-	0	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	exon	13080951	13081012	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	intron	13081013	13081116	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	CDS	13081117	13081272	0.98	-	0	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	exon	13081117	13081272	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	intron	13081273	13081412	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	CDS	13081413	13081625	1	-	0	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	exon	13081413	13081625	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	intron	13081626	13081909	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	CDS	13081910	13082206	0.93	-	0	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	exon	13081910	13082206	.	-	.	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
Phchi.S2	AUGUSTUS	start_codon	13082204	13082206	.	-	0	transcript_id "Phchi.S2G044600.t1"; gene_id "Phchi.S2G044600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg42.t1 is derived from g9824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4468	6768	.	-	.	Phchi.S6G000100
Phchi.S6	AUGUSTUS	transcript	4468	6768	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	stop_codon	4465	4467	.	-	0	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	CDS	4468	4503	1	-	0	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	exon	4468	4503	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	intron	4504	4588	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	CDS	4589	5403	0.83	-	2	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	exon	4589	5403	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	intron	5404	6129	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	CDS	6130	6169	0.99	-	0	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	exon	6130	6169	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	intron	6170	6478	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	CDS	6479	6552	0.95	-	2	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	exon	6479	6552	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	intron	6553	6635	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	CDS	6636	6768	0.78	-	0	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	exon	6636	6768	.	-	.	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
Phchi.S6	AUGUSTUS	start_codon	6766	6768	.	-	0	transcript_id "Phchi.S6G000100.t1"; gene_id "Phchi.S6G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9283.t1 is derived from g6458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40752448	40754179	.	+	.	Phchi.S1G644200
Phchi.S1	AUGUSTUS	transcript	40752448	40754179	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	start_codon	40752448	40752450	.	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	CDS	40752448	40753185	0.65	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	exon	40752448	40753185	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	intron	40753186	40753304	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	CDS	40753305	40753373	1	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	exon	40753305	40753373	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	intron	40753374	40753455	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	CDS	40753456	40753524	1	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	exon	40753456	40753524	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	intron	40753525	40753677	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	CDS	40753678	40753764	1	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	exon	40753678	40753764	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	intron	40753765	40753864	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	CDS	40753865	40753932	0.99	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	exon	40753865	40753932	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	intron	40753933	40754040	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	CDS	40754041	40754179	0.96	+	1	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	exon	40754041	40754179	.	+	.	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
Phchi.S1	AUGUSTUS	stop_codon	40754180	40754182	.	+	0	transcript_id "Phchi.S1G644200.t1"; gene_id "Phchi.S1G644200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5111.t1 is derived from g2281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14779003	14787435	.	+	.	Phchi.S1G227000
Phchi.S1	AUGUSTUS	transcript	14779003	14787435	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	start_codon	14779003	14779005	.	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14779003	14779053	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14779003	14779053	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14779054	14779273	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14779274	14779338	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14779274	14779338	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14779339	14779437	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14779438	14779534	0.98	+	1	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14779438	14779534	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14779535	14779636	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14779637	14779744	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14779637	14779744	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14779745	14779941	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14779942	14780058	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14779942	14780058	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14780059	14780218	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14780219	14780369	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14780219	14780369	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14780370	14780526	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14780527	14780774	0.98	+	2	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14780527	14780774	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14780775	14780901	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14780902	14781093	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14780902	14781093	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14781094	14781299	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14781300	14781367	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14781300	14781367	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14781368	14781459	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14781460	14781577	1	+	1	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14781460	14781577	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14781578	14781664	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14781665	14781748	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14781665	14781748	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14781749	14781892	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14781893	14781988	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14781893	14781988	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14781989	14782124	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14782125	14782226	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14782125	14782226	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14782227	14782307	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14782308	14782376	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14782308	14782376	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14782377	14782488	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14782489	14782584	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14782489	14782584	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14782585	14782708	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14782709	14782816	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14782709	14782816	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14782817	14782907	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14782908	14783021	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14782908	14783021	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14783022	14783109	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14783110	14783196	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14783110	14783196	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14783197	14783332	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14783333	14783461	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14783333	14783461	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14783462	14783547	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14783548	14783746	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14783548	14783746	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14783747	14783826	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14783827	14783976	1	+	2	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14783827	14783976	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14783977	14784106	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14784107	14784159	1	+	2	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14784107	14784159	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14784160	14784326	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14784327	14784410	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14784327	14784410	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14784411	14784506	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14784507	14784575	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14784507	14784575	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14784576	14784660	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14784661	14784737	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14784661	14784737	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14784738	14784867	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14784868	14784937	1	+	1	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14784868	14784937	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14784938	14785079	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14785080	14785229	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14785080	14785229	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14785230	14785353	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14785354	14785419	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14785354	14785419	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14785420	14785501	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14785502	14785646	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14785502	14785646	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14785647	14785740	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14785741	14785805	1	+	2	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14785741	14785805	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14785806	14785928	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14785929	14785994	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14785929	14785994	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14785995	14786078	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14786079	14786172	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14786079	14786172	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14786173	14786278	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14786279	14786315	1	+	2	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14786279	14786315	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14786316	14786427	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14786428	14786485	1	+	1	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14786428	14786485	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14786486	14786565	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14786566	14786676	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14786566	14786676	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14786677	14786775	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14786776	14786843	1	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14786776	14786843	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14786844	14786982	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14786983	14787049	0.92	+	1	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14786983	14787049	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14787050	14787151	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14787152	14787220	0.89	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14787152	14787220	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	intron	14787221	14787324	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	CDS	14787325	14787435	0.88	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	exon	14787325	14787435	.	+	.	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
Phchi.S1	AUGUSTUS	stop_codon	14787436	14787438	.	+	0	transcript_id "Phchi.S1G227000.t1"; gene_id "Phchi.S1G227000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12176.t1 is derived from g7852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6092074	6094476	.	-	.	Phchi.S2G025600
Phchi.S2	AUGUSTUS	transcript	6092074	6094476	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	stop_codon	6092071	6092073	.	-	0	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6092074	6092150	1	-	2	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6092074	6092150	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6092151	6092230	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6092231	6092275	1	-	2	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6092231	6092275	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6092276	6092354	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6092355	6092558	1	-	2	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6092355	6092558	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6092559	6092676	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6092677	6092767	1	-	0	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6092677	6092767	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6092768	6092894	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6092895	6092969	1	-	0	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6092895	6092969	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6092970	6093092	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6093093	6093232	1	-	2	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6093093	6093232	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6093233	6093313	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6093314	6093609	1	-	1	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6093314	6093609	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6093610	6093767	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6093768	6093828	1	-	2	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6093768	6093828	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6093829	6093961	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6093962	6094073	1	-	0	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6093962	6094073	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	intron	6094074	6094275	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	CDS	6094276	6094476	0.99	-	0	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	exon	6094276	6094476	.	-	.	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
Phchi.S2	AUGUSTUS	start_codon	6094474	6094476	.	-	0	transcript_id "Phchi.S2G025600.t1"; gene_id "Phchi.S2G025600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10607.t1 is derived from g14657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1167654	1171995	.	+	.	Phchi.S4G018900
Phchi.S4	AUGUSTUS	transcript	1167654	1171995	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	start_codon	1167654	1167656	.	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1167654	1167747	0.58	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1167654	1167747	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1167748	1167829	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1167830	1167956	1	+	2	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1167830	1167956	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1167957	1168034	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1168035	1168208	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1168035	1168208	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1168209	1168289	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1168290	1168361	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1168290	1168361	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1168362	1168450	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1168451	1168522	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1168451	1168522	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1168523	1168616	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1168617	1168700	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1168617	1168700	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1168701	1168786	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1168787	1168858	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1168787	1168858	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1168859	1168972	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1168973	1169044	0.99	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1168973	1169044	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1169045	1169130	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1169131	1169202	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1169131	1169202	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1169203	1169301	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1169302	1169376	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1169302	1169376	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1169377	1169458	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1169459	1169554	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1169459	1169554	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1169555	1169658	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1169659	1169730	0.65	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1169659	1169730	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1169731	1169841	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1169842	1169854	0.43	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1169842	1169854	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1169855	1169946	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1169947	1170076	0.99	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1169947	1170076	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1170077	1170178	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1170179	1170352	0.51	+	2	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1170179	1170352	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1170353	1170435	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1170436	1170719	0.99	+	2	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1170436	1170719	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1170720	1170873	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1170874	1170925	1	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1170874	1170925	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1170926	1171012	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1171013	1171098	1	+	2	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1171013	1171098	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1171099	1171173	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1171174	1171319	1	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1171174	1171319	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1171320	1171392	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1171393	1171537	1	+	1	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1171393	1171537	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1171538	1171623	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1171624	1171770	1	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1171624	1171770	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	intron	1171771	1171848	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	CDS	1171849	1171995	0.65	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	exon	1171849	1171995	.	+	.	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
Phchi.S4	AUGUSTUS	stop_codon	1171996	1171998	.	+	0	transcript_id "Phchi.S4G018900.t1"; gene_id "Phchi.S4G018900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10505.t1 is derived from g14554.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	743585	746908	.	-	.	Phchi.S4G008700
Phchi.S4	AUGUSTUS	transcript	743585	746908	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	stop_codon	743582	743584	.	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	743585	743641	0.95	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	743585	743641	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	743642	743743	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	743744	743845	0.9	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	743744	743845	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	743846	744239	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744240	744336	1	-	1	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744240	744336	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744337	744434	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744435	744526	1	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744435	744526	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744527	744594	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744595	744762	1	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744595	744762	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744763	744868	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744869	744946	1	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744869	744946	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744947	745017	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	745018	745975	0.96	-	1	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	745018	745975	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	745976	746145	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	746146	746483	0.66	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	746146	746483	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	746484	746605	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	746606	746657	0.44	-	1	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	746606	746657	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	746658	746819	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	746820	746908	0.91	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	746820	746908	.	-	.	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	start_codon	746906	746908	.	-	0	transcript_id "Phchi.S4G008700.t1"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	transcript	743585	746908	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	stop_codon	743582	743584	.	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	743585	743641	0.97	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	743585	743641	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	743642	743743	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	743744	743845	0.94	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	743744	743845	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	743846	744239	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744240	744336	1	-	1	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744240	744336	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744337	744434	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744435	744526	1	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744435	744526	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744527	744594	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744595	744762	1	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744595	744762	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744763	744868	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	744869	744946	0.99	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	744869	744946	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	744947	745017	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	745018	745975	0.99	-	1	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	745018	745975	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	745976	746145	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	746146	746483	0.59	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	746146	746483	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	746484	746605	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	746606	746657	0.43	-	1	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	746606	746657	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	intron	746658	746870	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	CDS	746871	746908	0.88	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	exon	746871	746908	.	-	.	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
Phchi.S4	AUGUSTUS	start_codon	746906	746908	.	-	0	transcript_id "Phchi.S4G008700.t2"; gene_id "Phchi.S4G008700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4965.t1 is derived from g2135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13792074	13793865	.	-	.	Phchi.S1G212400
Phchi.S1	AUGUSTUS	transcript	13792074	13793865	.	-	.	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	stop_codon	13792071	13792073	.	-	0	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	CDS	13792074	13792129	0.43	-	2	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	exon	13792074	13792129	.	-	.	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	intron	13792130	13792350	.	-	.	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	CDS	13792351	13793647	0.43	-	0	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	exon	13792351	13793647	.	-	.	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	intron	13793648	13793733	.	-	.	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	CDS	13793734	13793865	0.94	-	0	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	exon	13793734	13793865	.	-	.	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
Phchi.S1	AUGUSTUS	start_codon	13793863	13793865	.	-	0	transcript_id "Phchi.S1G212400.t1"; gene_id "Phchi.S1G212400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4887.t1 is derived from g2057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13236178	13240012	.	-	.	Phchi.S1G204600
Phchi.S1	AUGUSTUS	transcript	13236178	13240012	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	stop_codon	13236175	13236177	.	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13236178	13236217	0.99	-	1	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13236178	13236217	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13236218	13236350	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13236351	13236380	0.99	-	1	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13236351	13236380	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13236381	13236456	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13236457	13236524	0.74	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13236457	13236524	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13236525	13236609	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13236610	13236857	1	-	2	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13236610	13236857	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13236858	13237005	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13237006	13237226	1	-	1	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13237006	13237226	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13237227	13237378	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13237379	13237509	1	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13237379	13237509	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13237510	13237646	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13237647	13237768	1	-	2	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13237647	13237768	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13237769	13237896	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13237897	13237929	1	-	2	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13237897	13237929	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13237930	13238193	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13238194	13238218	0.87	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13238194	13238218	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13238219	13238333	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13238334	13238447	0.55	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13238334	13238447	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	intron	13238448	13238821	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	CDS	13238822	13240012	0.67	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	exon	13238822	13240012	.	-	.	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
Phchi.S1	AUGUSTUS	start_codon	13240010	13240012	.	-	0	transcript_id "Phchi.S1G204600.t1"; gene_id "Phchi.S1G204600"
# This transcript jg2651.t2 is derived from g9571.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2651.t3 is derived from g9571.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2652.t1 is derived from g9572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8009428	8010055	.	-	.	Phchi.S5G126100
Phchi.S5	AUGUSTUS	transcript	8009428	8010055	.	-	.	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	stop_codon	8009425	8009427	.	-	0	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	CDS	8009428	8009435	0.95	-	2	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	exon	8009428	8009435	.	-	.	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	intron	8009436	8009571	.	-	.	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	CDS	8009572	8010055	0.88	-	0	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	exon	8009572	8010055	.	-	.	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
Phchi.S5	AUGUSTUS	start_codon	8010053	8010055	.	-	0	transcript_id "Phchi.S5G126100.t1"; gene_id "Phchi.S5G126100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12328.t1 is derived from g8004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10986844	10988315	.	-	.	Phchi.S2G040800
Phchi.S2	AUGUSTUS	transcript	10986844	10988315	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	stop_codon	10986841	10986843	.	-	0	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	CDS	10986844	10987077	0.99	-	0	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	exon	10986844	10987077	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	intron	10987078	10987156	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	CDS	10987157	10987256	1	-	1	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	exon	10987157	10987256	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	intron	10987257	10987350	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	CDS	10987351	10987520	1	-	0	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	exon	10987351	10987520	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	intron	10987521	10987609	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	CDS	10987610	10987714	1	-	0	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	exon	10987610	10987714	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	intron	10987715	10987796	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	CDS	10987797	10988315	0.85	-	0	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	exon	10987797	10988315	.	-	.	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
Phchi.S2	AUGUSTUS	start_codon	10988313	10988315	.	-	0	transcript_id "Phchi.S2G040800.t1"; gene_id "Phchi.S2G040800"
# This transcript jg5794.t2 is derived from g2964.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5795.t1 is derived from g2965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18986089	18987063	.	-	.	Phchi.S1G295400
Phchi.S1	AUGUSTUS	transcript	18986089	18987063	.	-	.	transcript_id "Phchi.S1G295400.t1"; gene_id "Phchi.S1G295400"
Phchi.S1	AUGUSTUS	stop_codon	18986086	18986088	.	-	0	transcript_id "Phchi.S1G295400.t1"; gene_id "Phchi.S1G295400"
Phchi.S1	AUGUSTUS	CDS	18986089	18987063	0.96	-	0	transcript_id "Phchi.S1G295400.t1"; gene_id "Phchi.S1G295400"
Phchi.S1	AUGUSTUS	exon	18986089	18987063	.	-	.	transcript_id "Phchi.S1G295400.t1"; gene_id "Phchi.S1G295400"
Phchi.S1	AUGUSTUS	start_codon	18987061	18987063	.	-	0	transcript_id "Phchi.S1G295400.t1"; gene_id "Phchi.S1G295400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13540.t1 is derived from g12007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7427116	7428297	.	+	.	Phchi.S3G085900
Phchi.S3	AUGUSTUS	transcript	7427116	7428297	.	+	.	transcript_id "Phchi.S3G085900.t1"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	start_codon	7427116	7427118	.	+	0	transcript_id "Phchi.S3G085900.t1"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	CDS	7427116	7428297	1	+	0	transcript_id "Phchi.S3G085900.t1"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	exon	7427116	7428297	.	+	.	transcript_id "Phchi.S3G085900.t1"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	stop_codon	7428298	7428300	.	+	0	transcript_id "Phchi.S3G085900.t1"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	transcript	7427860	7428297	.	+	.	transcript_id "Phchi.S3G085900.t2"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	start_codon	7427860	7427862	.	+	0	transcript_id "Phchi.S3G085900.t2"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	CDS	7427860	7428297	0.9	+	0	transcript_id "Phchi.S3G085900.t2"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	exon	7427860	7428297	.	+	.	transcript_id "Phchi.S3G085900.t2"; gene_id "Phchi.S3G085900"
Phchi.S3	AUGUSTUS	stop_codon	7428298	7428300	.	+	0	transcript_id "Phchi.S3G085900.t2"; gene_id "Phchi.S3G085900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7915.t1 is derived from g5089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31887054	31888072	.	-	.	Phchi.S1G507400
Phchi.S1	AUGUSTUS	transcript	31887054	31888072	.	-	.	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	stop_codon	31887051	31887053	.	-	0	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	CDS	31887054	31887794	1	-	0	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	exon	31887054	31887794	.	-	.	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	intron	31887795	31887898	.	-	.	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	CDS	31887899	31888072	1	-	0	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	exon	31887899	31888072	.	-	.	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
Phchi.S1	AUGUSTUS	start_codon	31888070	31888072	.	-	0	transcript_id "Phchi.S1G507400.t1"; gene_id "Phchi.S1G507400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12888.t1 is derived from g11353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3002771	3003502	.	-	.	Phchi.S3G020700
Phchi.S3	AUGUSTUS	transcript	3002771	3003502	.	-	.	transcript_id "Phchi.S3G020700.t1"; gene_id "Phchi.S3G020700"
Phchi.S3	AUGUSTUS	stop_codon	3002768	3002770	.	-	0	transcript_id "Phchi.S3G020700.t1"; gene_id "Phchi.S3G020700"
Phchi.S3	AUGUSTUS	CDS	3002771	3003502	0.59	-	0	transcript_id "Phchi.S3G020700.t1"; gene_id "Phchi.S3G020700"
Phchi.S3	AUGUSTUS	exon	3002771	3003502	.	-	.	transcript_id "Phchi.S3G020700.t1"; gene_id "Phchi.S3G020700"
Phchi.S3	AUGUSTUS	start_codon	3003500	3003502	.	-	0	transcript_id "Phchi.S3G020700.t1"; gene_id "Phchi.S3G020700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6807.t1 is derived from g3979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25142983	25144398	.	+	.	Phchi.S1G396600
Phchi.S1	AUGUSTUS	transcript	25142983	25144398	.	+	.	transcript_id "Phchi.S1G396600.t1"; gene_id "Phchi.S1G396600"
Phchi.S1	AUGUSTUS	start_codon	25142983	25142985	.	+	0	transcript_id "Phchi.S1G396600.t1"; gene_id "Phchi.S1G396600"
Phchi.S1	AUGUSTUS	CDS	25142983	25144398	0.95	+	0	transcript_id "Phchi.S1G396600.t1"; gene_id "Phchi.S1G396600"
Phchi.S1	AUGUSTUS	exon	25142983	25144398	.	+	.	transcript_id "Phchi.S1G396600.t1"; gene_id "Phchi.S1G396600"
Phchi.S1	AUGUSTUS	stop_codon	25144399	25144401	.	+	0	transcript_id "Phchi.S1G396600.t1"; gene_id "Phchi.S1G396600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10992.t1 is derived from g15042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3563379	3564461	.	+	.	Phchi.S4G057400
Phchi.S4	AUGUSTUS	transcript	3563379	3564461	.	+	.	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	start_codon	3563379	3563381	.	+	0	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	CDS	3563379	3564113	0.94	+	0	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	exon	3563379	3564113	.	+	.	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	intron	3564114	3564285	.	+	.	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	CDS	3564286	3564375	0.53	+	0	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	exon	3564286	3564375	.	+	.	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	intron	3564376	3564458	.	+	.	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	CDS	3564459	3564461	0.85	+	0	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	exon	3564459	3564461	.	+	.	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
Phchi.S4	AUGUSTUS	stop_codon	3564462	3564464	.	+	0	transcript_id "Phchi.S4G057400.t1"; gene_id "Phchi.S4G057400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7807.t1 is derived from g4981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31275617	31276340	.	+	.	Phchi.S1G496600
Phchi.S1	AUGUSTUS	transcript	31275617	31276340	.	+	.	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	start_codon	31275617	31275619	.	+	0	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	CDS	31275617	31275871	0.74	+	0	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	exon	31275617	31275871	.	+	.	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	intron	31275872	31276033	.	+	.	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	CDS	31276034	31276102	1	+	0	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	exon	31276034	31276102	.	+	.	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	intron	31276103	31276190	.	+	.	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	CDS	31276191	31276340	1	+	0	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	exon	31276191	31276340	.	+	.	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
Phchi.S1	AUGUSTUS	stop_codon	31276341	31276343	.	+	0	transcript_id "Phchi.S1G496600.t1"; gene_id "Phchi.S1G496600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14655.t1 is derived from g13123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13981117	13986305	.	+	.	Phchi.S3G197400
Phchi.S3	AUGUSTUS	transcript	13981117	13986305	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	start_codon	13981117	13981119	.	+	0	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13981117	13981762	1	+	0	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13981117	13981762	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	intron	13981763	13981938	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13981939	13982055	1	+	2	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13981939	13982055	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	intron	13982056	13982177	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13982178	13982384	1	+	2	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13982178	13982384	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	intron	13982385	13982494	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13982495	13983886	0.86	+	2	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13982495	13983886	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	intron	13983887	13984033	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13984034	13985158	0.86	+	2	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13984034	13985158	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	intron	13985159	13985290	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13985291	13985602	1	+	2	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13985291	13985602	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	intron	13985603	13985691	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	CDS	13985692	13986305	0.83	+	2	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	exon	13985692	13986305	.	+	.	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
Phchi.S3	AUGUSTUS	stop_codon	13986306	13986308	.	+	0	transcript_id "Phchi.S3G197400.t1"; gene_id "Phchi.S3G197400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg22.t1 is derived from g9784.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C19	AUGUSTUS	gene	84935	85708	.	-	.	Phchi.C19G000200
Phchi.C19	AUGUSTUS	transcript	84935	85708	.	-	.	transcript_id "Phchi.C19G000200.t1"; gene_id "Phchi.C19G000200"
Phchi.C19	AUGUSTUS	stop_codon	84932	84934	.	-	0	transcript_id "Phchi.C19G000200.t1"; gene_id "Phchi.C19G000200"
Phchi.C19	AUGUSTUS	CDS	84935	85708	0.85	-	0	transcript_id "Phchi.C19G000200.t1"; gene_id "Phchi.C19G000200"
Phchi.C19	AUGUSTUS	exon	84935	85708	.	-	.	transcript_id "Phchi.C19G000200.t1"; gene_id "Phchi.C19G000200"
Phchi.C19	AUGUSTUS	start_codon	85706	85708	.	-	0	transcript_id "Phchi.C19G000200.t1"; gene_id "Phchi.C19G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12075.t1 is derived from g7750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2126490	2131205	.	-	.	Phchi.S2G015500
Phchi.S2	AUGUSTUS	transcript	2126490	2131205	.	-	.	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	stop_codon	2126487	2126489	.	-	0	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	CDS	2126490	2127470	0.02	-	0	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	exon	2126490	2127470	.	-	.	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	intron	2127471	2128080	.	-	.	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	CDS	2128081	2128405	0.99	-	1	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	exon	2128081	2128405	.	-	.	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	intron	2128406	2131059	.	-	.	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	CDS	2131060	2131205	0.01	-	0	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	exon	2131060	2131205	.	-	.	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
Phchi.S2	AUGUSTUS	start_codon	2131203	2131205	.	-	0	transcript_id "Phchi.S2G015500.t1"; gene_id "Phchi.S2G015500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9883.t1 is derived from g7059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44248470	44250845	.	+	.	Phchi.S1G704200
Phchi.S1	AUGUSTUS	transcript	44248470	44250845	.	+	.	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	start_codon	44248470	44248472	.	+	0	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	CDS	44248470	44248492	0.31	+	0	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	exon	44248470	44248492	.	+	.	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	intron	44248493	44250814	.	+	.	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	CDS	44250815	44250845	0.01	+	1	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	exon	44250815	44250845	.	+	.	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
Phchi.S1	AUGUSTUS	stop_codon	44250846	44250848	.	+	0	transcript_id "Phchi.S1G704200.t1"; gene_id "Phchi.S1G704200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10594.t1 is derived from g14644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1118132	1118587	.	-	.	Phchi.S4G017600
Phchi.S4	AUGUSTUS	transcript	1118132	1118587	.	-	.	transcript_id "Phchi.S4G017600.t1"; gene_id "Phchi.S4G017600"
Phchi.S4	AUGUSTUS	stop_codon	1118129	1118131	.	-	0	transcript_id "Phchi.S4G017600.t1"; gene_id "Phchi.S4G017600"
Phchi.S4	AUGUSTUS	CDS	1118132	1118587	0.28	-	0	transcript_id "Phchi.S4G017600.t1"; gene_id "Phchi.S4G017600"
Phchi.S4	AUGUSTUS	exon	1118132	1118587	.	-	.	transcript_id "Phchi.S4G017600.t1"; gene_id "Phchi.S4G017600"
Phchi.S4	AUGUSTUS	start_codon	1118585	1118587	.	-	0	transcript_id "Phchi.S4G017600.t1"; gene_id "Phchi.S4G017600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4164.t1 is derived from g1333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8699818	8700993	.	-	.	Phchi.S1G132300
Phchi.S1	AUGUSTUS	transcript	8699818	8700993	.	-	.	transcript_id "Phchi.S1G132300.t1"; gene_id "Phchi.S1G132300"
Phchi.S1	AUGUSTUS	stop_codon	8699815	8699817	.	-	0	transcript_id "Phchi.S1G132300.t1"; gene_id "Phchi.S1G132300"
Phchi.S1	AUGUSTUS	CDS	8699818	8700993	0.69	-	0	transcript_id "Phchi.S1G132300.t1"; gene_id "Phchi.S1G132300"
Phchi.S1	AUGUSTUS	exon	8699818	8700993	.	-	.	transcript_id "Phchi.S1G132300.t1"; gene_id "Phchi.S1G132300"
Phchi.S1	AUGUSTUS	start_codon	8700991	8700993	.	-	0	transcript_id "Phchi.S1G132300.t1"; gene_id "Phchi.S1G132300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11401.t1 is derived from g15451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6145905	6147298	.	-	.	Phchi.S4G098300
Phchi.S4	AUGUSTUS	transcript	6145905	6147298	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	stop_codon	6145902	6145904	.	-	0	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6145905	6146269	1	-	2	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6145905	6146269	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	intron	6146270	6146354	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6146355	6146451	0.96	-	0	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6146355	6146451	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	intron	6146452	6146555	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6146556	6146647	0.99	-	2	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6146556	6146647	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	intron	6146648	6146750	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6146751	6146871	0.98	-	0	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6146751	6146871	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	intron	6146872	6146973	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6146974	6147013	0.85	-	1	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6146974	6147013	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	intron	6147014	6147135	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6147136	6147174	0.78	-	1	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6147136	6147174	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	intron	6147175	6147266	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	CDS	6147267	6147298	0.65	-	0	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	exon	6147267	6147298	.	-	.	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
Phchi.S4	AUGUSTUS	start_codon	6147296	6147298	.	-	0	transcript_id "Phchi.S4G098300.t1"; gene_id "Phchi.S4G098300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9298.t1 is derived from g6473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40829524	40830446	.	+	.	Phchi.S1G645700
Phchi.S1	AUGUSTUS	transcript	40829524	40830446	.	+	.	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	start_codon	40829524	40829526	.	+	0	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	CDS	40829524	40829700	1	+	0	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	exon	40829524	40829700	.	+	.	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	intron	40829701	40829790	.	+	.	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	CDS	40829791	40829898	0.61	+	0	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	exon	40829791	40829898	.	+	.	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	intron	40829899	40830068	.	+	.	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	CDS	40830069	40830446	0.41	+	0	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	exon	40830069	40830446	.	+	.	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
Phchi.S1	AUGUSTUS	stop_codon	40830447	40830449	.	+	0	transcript_id "Phchi.S1G645700.t1"; gene_id "Phchi.S1G645700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12903.t1 is derived from g11368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3079934	3083367	.	-	.	Phchi.S3G022200
Phchi.S3	AUGUSTUS	transcript	3079934	3083367	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	stop_codon	3079931	3079933	.	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3079934	3080063	0.69	-	1	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3079934	3080063	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3080064	3080147	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3080148	3080227	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3080148	3080227	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3080228	3080372	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3080373	3080439	1	-	1	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3080373	3080439	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3080440	3080528	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3080529	3080578	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3080529	3080578	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3080579	3080693	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3080694	3080827	1	-	2	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3080694	3080827	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3080828	3080910	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3080911	3081013	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3080911	3081013	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3081014	3081087	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3081088	3081351	0.7	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3081088	3081351	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3081352	3081551	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3081552	3081668	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3081552	3081668	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3081669	3081757	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3081758	3081832	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3081758	3081832	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3081833	3081954	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3081955	3082001	1	-	2	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3081955	3082001	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3082002	3082086	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3082087	3082198	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3082087	3082198	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3082199	3082371	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3082372	3082453	1	-	1	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3082372	3082453	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3082454	3082542	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3082543	3082649	1	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3082543	3082649	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3082650	3082731	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3082732	3082808	1	-	2	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3082732	3082808	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	intron	3082809	3082964	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	CDS	3082965	3083367	0.95	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	exon	3082965	3083367	.	-	.	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
Phchi.S3	AUGUSTUS	start_codon	3083365	3083367	.	-	0	transcript_id "Phchi.S3G022200.t1"; gene_id "Phchi.S3G022200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7882.t1 is derived from g5056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31744278	31747752	.	-	.	Phchi.S1G504100
Phchi.S1	AUGUSTUS	transcript	31744278	31747752	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	stop_codon	31744275	31744277	.	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31744278	31744508	1	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31744278	31744508	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31744509	31744599	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31744600	31744716	1	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31744600	31744716	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31744717	31744810	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31744811	31745365	0.93	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31744811	31745365	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31745366	31745452	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31745453	31745560	1	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31745453	31745560	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31745561	31745717	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31745718	31745800	0.97	-	2	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31745718	31745800	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31745801	31745891	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31745892	31745903	0.93	-	2	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31745892	31745903	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31745904	31746001	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31746002	31746218	0.63	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31746002	31746218	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31746219	31746474	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31746475	31746604	1	-	1	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31746475	31746604	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31746605	31746725	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31746726	31746853	1	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31746726	31746853	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	intron	31746854	31746999	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	CDS	31747000	31747752	0.8	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	exon	31747000	31747752	.	-	.	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
Phchi.S1	AUGUSTUS	start_codon	31747750	31747752	.	-	0	transcript_id "Phchi.S1G504100.t1"; gene_id "Phchi.S1G504100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9686.t1 is derived from g6862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43284590	43286274	.	-	.	Phchi.S1G684500
Phchi.S1	AUGUSTUS	transcript	43284590	43286274	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	stop_codon	43284587	43284589	.	-	0	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	CDS	43284590	43285197	1	-	2	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	exon	43284590	43285197	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	intron	43285198	43285294	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	CDS	43285295	43285477	1	-	2	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	exon	43285295	43285477	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	intron	43285478	43285592	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	CDS	43285593	43285723	1	-	1	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	exon	43285593	43285723	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	intron	43285724	43285815	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	CDS	43285816	43285959	1	-	1	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	exon	43285816	43285959	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	intron	43285960	43286056	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	CDS	43286057	43286274	0.99	-	0	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	exon	43286057	43286274	.	-	.	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
Phchi.S1	AUGUSTUS	start_codon	43286272	43286274	.	-	0	transcript_id "Phchi.S1G684500.t1"; gene_id "Phchi.S1G684500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2039.t1 is derived from g8959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4553597	4559641	.	+	.	Phchi.S5G064800
Phchi.S5	AUGUSTUS	transcript	4553597	4559641	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	start_codon	4553597	4553599	.	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4553597	4553759	0.86	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4553597	4553759	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4553760	4554013	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4554014	4554080	1	+	2	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4554014	4554080	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4554081	4554206	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4554207	4554381	1	+	1	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4554207	4554381	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4554382	4554481	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4554482	4554649	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4554482	4554649	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4554650	4554741	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4554742	4554852	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4554742	4554852	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4554853	4555029	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4555030	4555239	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4555030	4555239	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4555240	4555399	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4555400	4555501	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4555400	4555501	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4555502	4555640	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4555641	4555871	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4555641	4555871	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4555872	4555998	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4555999	4556079	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4555999	4556079	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4556080	4556228	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4556229	4556321	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4556229	4556321	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4556322	4556415	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4556416	4556601	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4556416	4556601	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4556602	4556744	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4556745	4556903	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4556745	4556903	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4556904	4556985	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4556986	4557078	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4556986	4557078	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4557079	4557161	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4557162	4557233	0.99	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4557162	4557233	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4557234	4557336	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4557337	4557454	0.95	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4557337	4557454	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4557455	4557860	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4557861	4557941	0.43	+	2	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4557861	4557941	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4557942	4558055	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4558056	4558190	0.89	+	2	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4558056	4558190	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4558191	4558331	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4558332	4558438	1	+	2	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4558332	4558438	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4558439	4558553	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4558554	4558631	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4558554	4558631	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4558632	4558723	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4558724	4558819	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4558724	4558819	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4558820	4558975	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4558976	4559071	1	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4558976	4559071	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4559072	4559184	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4559185	4559295	0.52	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4559185	4559295	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4559296	4559427	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4559428	4559555	0.47	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4559428	4559555	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	intron	4559556	4559631	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	CDS	4559632	4559641	1	+	1	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	exon	4559632	4559641	.	+	.	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
Phchi.S5	AUGUSTUS	stop_codon	4559642	4559644	.	+	0	transcript_id "Phchi.S5G064800.t1"; gene_id "Phchi.S5G064800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4016.t1 is derived from g1185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7187652	7189241	.	+	.	Phchi.S1G117500
Phchi.S1	AUGUSTUS	transcript	7187652	7189241	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	start_codon	7187652	7187654	.	+	0	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7187652	7187798	0.99	+	0	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7187652	7187798	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7187799	7187970	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7187971	7188033	1	+	0	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7187971	7188033	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7188034	7188118	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7188119	7188198	0.22	+	0	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7188119	7188198	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7188199	7188287	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7188288	7189148	0.22	+	1	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7188288	7189148	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7189149	7189237	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7189238	7189241	1	+	1	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7189238	7189241	.	+	.	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	stop_codon	7189242	7189244	.	+	0	transcript_id "Phchi.S1G117500.t1"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	transcript	7187652	7189241	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	start_codon	7187652	7187654	.	+	0	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7187652	7187798	0.56	+	0	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7187652	7187798	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7187799	7187963	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7187964	7188033	0.48	+	0	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7187964	7188033	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7188034	7188118	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7188119	7188181	0.36	+	2	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7188119	7188181	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7188182	7188358	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7188359	7189148	0.2	+	2	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7188359	7189148	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	intron	7189149	7189237	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	CDS	7189238	7189241	1	+	1	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	exon	7189238	7189241	.	+	.	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
Phchi.S1	AUGUSTUS	stop_codon	7189242	7189244	.	+	0	transcript_id "Phchi.S1G117500.t2"; gene_id "Phchi.S1G117500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg874.t1 is derived from g10656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6058826	6063720	.	+	.	Phchi.S6G083300
Phchi.S6	AUGUSTUS	transcript	6058826	6063720	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	start_codon	6058826	6058828	.	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6058826	6058953	1	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6058826	6058953	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6058954	6059153	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6059154	6059264	1	+	1	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6059154	6059264	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6059265	6059420	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6059421	6059479	1	+	1	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6059421	6059479	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6059480	6059578	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6059579	6059718	1	+	2	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6059579	6059718	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6059719	6059841	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6059842	6060039	1	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6059842	6060039	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6060040	6060168	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6060169	6060365	1	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6060169	6060365	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6060366	6060537	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6060538	6060637	0.91	+	1	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6060538	6060637	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6060638	6060748	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6060749	6061342	0.99	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6060749	6061342	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6061343	6061440	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6061441	6061563	1	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6061441	6061563	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6061564	6061746	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6061747	6061827	1	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6061747	6061827	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6061828	6061947	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6061948	6062264	0.72	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6061948	6062264	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6062265	6062357	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6062358	6062735	1	+	1	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6062358	6062735	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6062736	6062852	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6062853	6062934	1	+	1	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6062853	6062934	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6062935	6063014	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6063015	6063192	0.98	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6063015	6063192	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6063193	6063298	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6063299	6063428	1	+	2	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6063299	6063428	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	intron	6063429	6063548	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	CDS	6063549	6063720	1	+	1	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	exon	6063549	6063720	.	+	.	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
Phchi.S6	AUGUSTUS	stop_codon	6063721	6063723	.	+	0	transcript_id "Phchi.S6G083300.t1"; gene_id "Phchi.S6G083300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2485.t1 is derived from g9405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6912886	6914136	.	-	.	Phchi.S5G109400
Phchi.S5	AUGUSTUS	transcript	6912886	6914136	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	stop_codon	6912883	6912885	.	-	0	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	CDS	6912886	6913205	0.67	-	2	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	exon	6912886	6913205	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	intron	6913206	6913379	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	CDS	6913380	6913491	0.34	-	0	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	exon	6913380	6913491	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	intron	6913492	6913615	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	CDS	6913616	6913687	0.35	-	0	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	exon	6913616	6913687	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	intron	6913688	6913854	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	CDS	6913855	6914018	0.81	-	2	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	exon	6913855	6914018	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	intron	6914019	6914105	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	CDS	6914106	6914136	0.76	-	0	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	exon	6914106	6914136	.	-	.	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
Phchi.S5	AUGUSTUS	start_codon	6914134	6914136	.	-	0	transcript_id "Phchi.S5G109400.t1"; gene_id "Phchi.S5G109400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3867.t1 is derived from g1036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6131358	6134637	.	+	.	Phchi.S1G102600
Phchi.S1	AUGUSTUS	transcript	6131358	6134637	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	start_codon	6131358	6131360	.	+	0	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6131358	6131380	0.34	+	0	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6131358	6131380	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	intron	6131381	6131541	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6131542	6131630	0.72	+	1	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6131542	6131630	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	intron	6131631	6131741	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6131742	6132901	0.62	+	2	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6131742	6132901	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	intron	6132902	6132989	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6132990	6133199	1	+	0	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6132990	6133199	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	intron	6133200	6133296	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6133297	6133387	1	+	0	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6133297	6133387	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	intron	6133388	6133463	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6133464	6133484	0.46	+	2	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6133464	6133484	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	intron	6133485	6133597	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	CDS	6133598	6134637	0.7	+	2	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	exon	6133598	6134637	.	+	.	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
Phchi.S1	AUGUSTUS	stop_codon	6134638	6134640	.	+	0	transcript_id "Phchi.S1G102600.t1"; gene_id "Phchi.S1G102600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8546.t1 is derived from g5721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36572523	36574481	.	-	.	Phchi.S1G570500
Phchi.S1	AUGUSTUS	transcript	36572523	36574481	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	stop_codon	36572520	36572522	.	-	0	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	CDS	36572523	36572523	1	-	1	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	exon	36572523	36572523	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	intron	36572524	36573152	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	CDS	36573153	36573370	1	-	0	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	exon	36573153	36573370	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	intron	36573371	36573443	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	CDS	36573444	36573543	1	-	1	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	exon	36573444	36573543	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	intron	36573544	36573714	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	CDS	36573715	36573899	1	-	0	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	exon	36573715	36573899	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	intron	36573900	36573977	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	CDS	36573978	36574102	1	-	2	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	exon	36573978	36574102	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	intron	36574103	36574231	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	CDS	36574232	36574481	1	-	0	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	exon	36574232	36574481	.	-	.	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
Phchi.S1	AUGUSTUS	start_codon	36574479	36574481	.	-	0	transcript_id "Phchi.S1G570500.t1"; gene_id "Phchi.S1G570500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2557.t1 is derived from g9477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7339514	7342416	.	-	.	Phchi.S5G116600
Phchi.S5	AUGUSTUS	transcript	7339514	7342416	.	-	.	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	stop_codon	7339511	7339513	.	-	0	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	CDS	7339514	7341428	0.67	-	1	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	exon	7339514	7341428	.	-	.	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	intron	7341429	7341683	.	-	.	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	CDS	7341684	7341755	0.99	-	1	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	exon	7341684	7341755	.	-	.	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	intron	7341756	7341850	.	-	.	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	CDS	7341851	7342416	0.69	-	0	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	exon	7341851	7342416	.	-	.	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
Phchi.S5	AUGUSTUS	start_codon	7342414	7342416	.	-	0	transcript_id "Phchi.S5G116600.t1"; gene_id "Phchi.S5G116600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1305.t1 is derived from g11088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8923731	8924677	.	-	.	Phchi.S6G126400
Phchi.S6	AUGUSTUS	transcript	8923731	8924677	.	-	.	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	stop_codon	8923728	8923730	.	-	0	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	CDS	8923731	8924487	0.77	-	1	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	exon	8923731	8924487	.	-	.	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	intron	8924488	8924612	.	-	.	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	CDS	8924613	8924677	0.72	-	0	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	exon	8924613	8924677	.	-	.	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
Phchi.S6	AUGUSTUS	start_codon	8924675	8924677	.	-	0	transcript_id "Phchi.S6G126400.t1"; gene_id "Phchi.S6G126400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13581.t1 is derived from g12048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7570728	7571627	.	-	.	Phchi.S3G090000
Phchi.S3	AUGUSTUS	transcript	7570728	7571627	.	-	.	transcript_id "Phchi.S3G090000.t1"; gene_id "Phchi.S3G090000"
Phchi.S3	AUGUSTUS	stop_codon	7570725	7570727	.	-	0	transcript_id "Phchi.S3G090000.t1"; gene_id "Phchi.S3G090000"
Phchi.S3	AUGUSTUS	CDS	7570728	7571627	0.39	-	0	transcript_id "Phchi.S3G090000.t1"; gene_id "Phchi.S3G090000"
Phchi.S3	AUGUSTUS	exon	7570728	7571627	.	-	.	transcript_id "Phchi.S3G090000.t1"; gene_id "Phchi.S3G090000"
Phchi.S3	AUGUSTUS	start_codon	7571625	7571627	.	-	0	transcript_id "Phchi.S3G090000.t1"; gene_id "Phchi.S3G090000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2489.t1 is derived from g9409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6926405	6927291	.	-	.	Phchi.S5G109800
Phchi.S5	AUGUSTUS	transcript	6926405	6927291	.	-	.	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	stop_codon	6926402	6926404	.	-	0	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	CDS	6926405	6926420	0.4	-	1	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	exon	6926405	6926420	.	-	.	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	intron	6926421	6926635	.	-	.	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	CDS	6926636	6927291	0.43	-	0	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	exon	6926636	6927291	.	-	.	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
Phchi.S5	AUGUSTUS	start_codon	6927289	6927291	.	-	0	transcript_id "Phchi.S5G109800.t1"; gene_id "Phchi.S5G109800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2880.t1 is derived from g49.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	256303	259063	.	+	.	Phchi.S1G003900
Phchi.S1	AUGUSTUS	transcript	256303	259063	.	+	.	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	start_codon	256303	256305	.	+	0	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	CDS	256303	258027	0.99	+	0	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	exon	256303	258027	.	+	.	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	intron	258028	258247	.	+	.	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	CDS	258248	258408	1	+	0	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	exon	258248	258408	.	+	.	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	intron	258409	258564	.	+	.	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	CDS	258565	259063	0.99	+	1	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	exon	258565	259063	.	+	.	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
Phchi.S1	AUGUSTUS	stop_codon	259064	259066	.	+	0	transcript_id "Phchi.S1G003900.t1"; gene_id "Phchi.S1G003900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15093.t1 is derived from g13561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16985390	16988847	.	+	.	Phchi.S3G241200
Phchi.S3	AUGUSTUS	transcript	16985390	16988847	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	start_codon	16985390	16985392	.	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16985390	16985411	0.57	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16985390	16985411	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16985412	16985790	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16985791	16986128	1	+	2	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16985791	16986128	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16986129	16986451	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16986452	16986526	0.68	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16986452	16986526	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16986527	16986603	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16986604	16986660	0.94	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16986604	16986660	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16986661	16986769	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16986770	16986983	0.28	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16986770	16986983	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16986984	16987126	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16987127	16987267	0.38	+	2	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16987127	16987267	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16987268	16987385	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16987386	16987390	0.41	+	2	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16987386	16987390	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16987391	16988002	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16988003	16988092	0.46	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16988003	16988092	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16988093	16988185	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16988186	16988217	0.58	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16988186	16988217	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	intron	16988218	16988501	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	CDS	16988502	16988847	0.7	+	1	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	exon	16988502	16988847	.	+	.	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
Phchi.S3	AUGUSTUS	stop_codon	16988848	16988850	.	+	0	transcript_id "Phchi.S3G241200.t1"; gene_id "Phchi.S3G241200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5561.t1 is derived from g2731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17598026	17601892	.	+	.	Phchi.S1G272000
Phchi.S1	AUGUSTUS	transcript	17598026	17601892	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	start_codon	17598026	17598028	.	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17598026	17598388	0.83	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17598026	17598388	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17598389	17598564	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17598565	17598743	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17598565	17598743	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17598744	17598864	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17598865	17598949	1	+	1	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17598865	17598949	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17598950	17599026	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17599027	17599343	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17599027	17599343	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17599344	17599458	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17599459	17599582	1	+	1	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17599459	17599582	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17599583	17599702	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17599703	17599795	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17599703	17599795	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17599796	17599910	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17599911	17600006	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17599911	17600006	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17600007	17600118	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17600119	17600250	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17600119	17600250	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17600251	17600338	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17600339	17600548	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17600339	17600548	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17600549	17600629	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17600630	17600791	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17600630	17600791	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17600792	17600875	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17600876	17600983	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17600876	17600983	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17600984	17601110	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17601111	17601245	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17601111	17601245	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17601246	17601338	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17601339	17601500	1	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17601339	17601500	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17601501	17601603	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17601604	17601724	0.98	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17601604	17601724	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	intron	17601725	17601809	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	CDS	17601810	17601892	0.93	+	2	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	exon	17601810	17601892	.	+	.	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
Phchi.S1	AUGUSTUS	stop_codon	17601893	17601895	.	+	0	transcript_id "Phchi.S1G272000.t1"; gene_id "Phchi.S1G272000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4147.t1 is derived from g1316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8639605	8641464	.	+	.	Phchi.S1G130600
Phchi.S1	AUGUSTUS	transcript	8639605	8641464	.	+	.	transcript_id "Phchi.S1G130600.t1"; gene_id "Phchi.S1G130600"
Phchi.S1	AUGUSTUS	start_codon	8639605	8639607	.	+	0	transcript_id "Phchi.S1G130600.t1"; gene_id "Phchi.S1G130600"
Phchi.S1	AUGUSTUS	CDS	8639605	8641464	1	+	0	transcript_id "Phchi.S1G130600.t1"; gene_id "Phchi.S1G130600"
Phchi.S1	AUGUSTUS	exon	8639605	8641464	.	+	.	transcript_id "Phchi.S1G130600.t1"; gene_id "Phchi.S1G130600"
Phchi.S1	AUGUSTUS	stop_codon	8641465	8641467	.	+	0	transcript_id "Phchi.S1G130600.t1"; gene_id "Phchi.S1G130600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4020.t1 is derived from g1189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7201565	7201967	.	+	.	Phchi.S1G117900
Phchi.S1	AUGUSTUS	transcript	7201565	7201967	.	+	.	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	start_codon	7201565	7201567	.	+	0	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	CDS	7201565	7201703	0.98	+	0	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	exon	7201565	7201703	.	+	.	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	intron	7201704	7201884	.	+	.	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	CDS	7201885	7201967	0.96	+	2	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	exon	7201885	7201967	.	+	.	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
Phchi.S1	AUGUSTUS	stop_codon	7201968	7201970	.	+	0	transcript_id "Phchi.S1G117900.t1"; gene_id "Phchi.S1G117900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9663.t1 is derived from g6839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43126430	43128531	.	-	.	Phchi.S1G682200
Phchi.S1	AUGUSTUS	transcript	43126430	43128531	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	stop_codon	43126427	43126429	.	-	0	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	CDS	43126430	43127644	0.81	-	0	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	exon	43126430	43127644	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	intron	43127645	43127805	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	CDS	43127806	43127950	0.67	-	1	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	exon	43127806	43127950	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	intron	43127951	43128046	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	CDS	43128047	43128285	0.6	-	0	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	exon	43128047	43128285	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	intron	43128286	43128396	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	CDS	43128397	43128531	0.51	-	0	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	exon	43128397	43128531	.	-	.	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
Phchi.S1	AUGUSTUS	start_codon	43128529	43128531	.	-	0	transcript_id "Phchi.S1G682200.t1"; gene_id "Phchi.S1G682200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10002.t1 is derived from g7178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44999144	45001253	.	-	.	Phchi.S1G716100
Phchi.S1	AUGUSTUS	transcript	44999144	45001253	.	-	.	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	stop_codon	44999141	44999143	.	-	0	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	CDS	44999144	44999502	0.31	-	2	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	exon	44999144	44999502	.	-	.	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	intron	44999503	44999600	.	-	.	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	CDS	44999601	45000279	0.35	-	0	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	exon	44999601	45000279	.	-	.	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	intron	45000280	45000398	.	-	.	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	CDS	45000399	45001253	0.68	-	0	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	exon	45000399	45001253	.	-	.	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
Phchi.S1	AUGUSTUS	start_codon	45001251	45001253	.	-	0	transcript_id "Phchi.S1G716100.t1"; gene_id "Phchi.S1G716100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7230.t1 is derived from g4402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27730374	27731318	.	-	.	Phchi.S1G438900
Phchi.S1	AUGUSTUS	transcript	27730374	27731318	.	-	.	transcript_id "Phchi.S1G438900.t1"; gene_id "Phchi.S1G438900"
Phchi.S1	AUGUSTUS	stop_codon	27730371	27730373	.	-	0	transcript_id "Phchi.S1G438900.t1"; gene_id "Phchi.S1G438900"
Phchi.S1	AUGUSTUS	CDS	27730374	27731318	1	-	0	transcript_id "Phchi.S1G438900.t1"; gene_id "Phchi.S1G438900"
Phchi.S1	AUGUSTUS	exon	27730374	27731318	.	-	.	transcript_id "Phchi.S1G438900.t1"; gene_id "Phchi.S1G438900"
Phchi.S1	AUGUSTUS	start_codon	27731316	27731318	.	-	0	transcript_id "Phchi.S1G438900.t1"; gene_id "Phchi.S1G438900"
# This transcript jg11825.t2 is derived from g15877.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11826.t1 is derived from g15878.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8455012	8456289	.	+	.	Phchi.S4G140800
Phchi.S4	AUGUSTUS	transcript	8455204	8456289	.	+	.	transcript_id "Phchi.S4G140800.t1"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	start_codon	8455204	8455206	.	+	0	transcript_id "Phchi.S4G140800.t1"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	CDS	8455204	8456289	0.66	+	0	transcript_id "Phchi.S4G140800.t1"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	exon	8455204	8456289	.	+	.	transcript_id "Phchi.S4G140800.t1"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	stop_codon	8456290	8456292	.	+	0	transcript_id "Phchi.S4G140800.t1"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	transcript	8455012	8456289	.	+	.	transcript_id "Phchi.S4G140800.t2"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	start_codon	8455012	8455014	.	+	0	transcript_id "Phchi.S4G140800.t2"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	CDS	8455012	8456289	0.32	+	0	transcript_id "Phchi.S4G140800.t2"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	exon	8455012	8456289	.	+	.	transcript_id "Phchi.S4G140800.t2"; gene_id "Phchi.S4G140800"
Phchi.S4	AUGUSTUS	stop_codon	8456290	8456292	.	+	0	transcript_id "Phchi.S4G140800.t2"; gene_id "Phchi.S4G140800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3299.t1 is derived from g468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2732253	2738981	.	-	.	Phchi.S1G045800
Phchi.S1	AUGUSTUS	transcript	2732253	2738981	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	stop_codon	2732250	2732252	.	-	0	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	CDS	2732253	2734460	0.31	-	0	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	exon	2732253	2734460	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	intron	2734461	2734594	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	CDS	2734595	2735014	0.46	-	0	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	exon	2734595	2735014	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	intron	2735015	2735145	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	CDS	2735146	2738455	0.36	-	1	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	exon	2735146	2738455	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	intron	2738456	2738616	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	CDS	2738617	2738981	0.3	-	0	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	exon	2738617	2738981	.	-	.	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
Phchi.S1	AUGUSTUS	start_codon	2738979	2738981	.	-	0	transcript_id "Phchi.S1G045800.t1"; gene_id "Phchi.S1G045800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8232.t1 is derived from g5407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34567305	34567769	.	+	.	Phchi.S1G539100
Phchi.S1	AUGUSTUS	transcript	34567305	34567769	.	+	.	transcript_id "Phchi.S1G539100.t1"; gene_id "Phchi.S1G539100"
Phchi.S1	AUGUSTUS	start_codon	34567305	34567307	.	+	0	transcript_id "Phchi.S1G539100.t1"; gene_id "Phchi.S1G539100"
Phchi.S1	AUGUSTUS	CDS	34567305	34567769	0.99	+	0	transcript_id "Phchi.S1G539100.t1"; gene_id "Phchi.S1G539100"
Phchi.S1	AUGUSTUS	exon	34567305	34567769	.	+	.	transcript_id "Phchi.S1G539100.t1"; gene_id "Phchi.S1G539100"
Phchi.S1	AUGUSTUS	stop_codon	34567770	34567772	.	+	0	transcript_id "Phchi.S1G539100.t1"; gene_id "Phchi.S1G539100"
# This transcript jg12945.t2 is derived from g11410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12946.t1 is derived from g11411.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3269434	3274367	.	-	.	Phchi.S3G026500
Phchi.S3	AUGUSTUS	transcript	3269434	3274367	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	stop_codon	3269431	3269433	.	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269434	3269463	1	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269434	3269463	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269464	3269610	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269611	3269688	1	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269611	3269688	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269689	3269768	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269769	3269813	0.57	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269769	3269813	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269814	3269898	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269899	3270102	1	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269899	3270102	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270103	3270202	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270203	3270343	1	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270203	3270343	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270344	3270437	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270438	3270569	0.48	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270438	3270569	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270570	3270696	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270697	3270847	0.48	-	1	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270697	3270847	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270848	3271156	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3271157	3271325	0.32	-	2	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3271157	3271325	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3271326	3271510	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3271511	3271613	0.4	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3271511	3271613	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3271614	3271820	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3271821	3271928	0.99	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3271821	3271928	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3271929	3272034	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272035	3272149	1	-	1	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272035	3272149	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272150	3272359	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272360	3272516	0.98	-	2	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272360	3272516	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272517	3272896	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272897	3272904	0.98	-	1	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272897	3272904	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272905	3273044	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273045	3273130	0.88	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273045	3273130	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3273131	3273275	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273276	3273416	0.86	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273276	3273416	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3273417	3273605	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273606	3274367	0.56	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273606	3274367	.	-	.	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	start_codon	3274365	3274367	.	-	0	transcript_id "Phchi.S3G026500.t1"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	transcript	3269434	3274367	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	stop_codon	3269431	3269433	.	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269434	3269463	1	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269434	3269463	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269464	3269610	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269611	3269688	1	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269611	3269688	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269689	3269768	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269769	3269813	0.52	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269769	3269813	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269814	3269898	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269899	3270102	1	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269899	3270102	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270103	3270202	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270203	3270343	1	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270203	3270343	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270344	3270437	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270438	3270569	0.45	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270438	3270569	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270570	3270696	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270697	3270847	0.44	-	1	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270697	3270847	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270848	3271156	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3271157	3271325	0.28	-	2	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3271157	3271325	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3271326	3271510	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3271511	3271613	0.38	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3271511	3271613	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3271614	3271820	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3271821	3271928	0.97	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3271821	3271928	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3271929	3272034	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272035	3272149	0.99	-	1	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272035	3272149	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272150	3272359	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272360	3272505	1	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272360	3272505	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272506	3272896	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272897	3273130	0.98	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272897	3273130	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3273131	3273275	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273276	3273416	0.88	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273276	3273416	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3273417	3273605	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273606	3274367	0.46	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273606	3274367	.	-	.	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	start_codon	3274365	3274367	.	-	0	transcript_id "Phchi.S3G026500.t2"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	transcript	3269434	3274367	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	stop_codon	3269431	3269433	.	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269434	3269463	1	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269434	3269463	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269464	3269610	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269611	3269688	1	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269611	3269688	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269689	3269768	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269769	3269813	0.47	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269769	3269813	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3269814	3269898	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3269899	3270102	0.99	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3269899	3270102	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270103	3270202	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270203	3270343	1	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270203	3270343	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270344	3270437	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270438	3270729	0.33	-	1	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270438	3270729	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270730	3270806	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3270807	3270847	0.33	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3270807	3270847	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3270848	3272034	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272035	3272149	0.93	-	1	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272035	3272149	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272150	3272359	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272360	3272516	0.98	-	2	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272360	3272516	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272517	3272896	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3272897	3272904	0.98	-	1	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3272897	3272904	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3272905	3273044	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273045	3273130	0.85	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273045	3273130	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3273131	3273275	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273276	3273416	0.86	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273276	3273416	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	intron	3273417	3273605	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	CDS	3273606	3274367	0.4	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	exon	3273606	3274367	.	-	.	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
Phchi.S3	AUGUSTUS	start_codon	3274365	3274367	.	-	0	transcript_id "Phchi.S3G026500.t3"; gene_id "Phchi.S3G026500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1949.t1 is derived from g8869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3958341	3960463	.	-	.	Phchi.S5G055800
Phchi.S5	AUGUSTUS	transcript	3958341	3960463	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	stop_codon	3958338	3958340	.	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3958341	3958439	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3958341	3958439	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3958440	3958534	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3958535	3958610	1	-	1	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3958535	3958610	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3958611	3958719	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3958720	3958806	1	-	1	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3958720	3958806	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3958807	3958909	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3958910	3958975	1	-	1	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3958910	3958975	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3958976	3959078	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3959079	3959149	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3959079	3959149	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3959150	3959271	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3959272	3959358	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3959272	3959358	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3959359	3959449	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3959450	3959563	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3959450	3959563	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3959564	3959646	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3959647	3959713	1	-	1	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3959647	3959713	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3959714	3959806	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3959807	3959868	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3959807	3959868	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3959869	3959954	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3959955	3960029	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3959955	3960029	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3960030	3960160	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3960161	3960208	1	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3960161	3960208	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	intron	3960209	3960307	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	CDS	3960308	3960463	0.98	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	exon	3960308	3960463	.	-	.	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
Phchi.S5	AUGUSTUS	start_codon	3960461	3960463	.	-	0	transcript_id "Phchi.S5G055800.t1"; gene_id "Phchi.S5G055800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12958.t1 is derived from g11423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3331367	3332030	.	-	.	Phchi.S3G027700
Phchi.S3	AUGUSTUS	transcript	3331367	3332030	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	stop_codon	3331364	3331366	.	-	0	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	CDS	3331367	3331492	0.99	-	0	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	exon	3331367	3331492	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	intron	3331493	3331585	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	CDS	3331586	3331630	1	-	0	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	exon	3331586	3331630	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	intron	3331631	3331735	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	CDS	3331736	3331836	1	-	2	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	exon	3331736	3331836	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	intron	3331837	3332020	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	CDS	3332021	3332030	0.76	-	0	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	exon	3332021	3332030	.	-	.	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
Phchi.S3	AUGUSTUS	start_codon	3332028	3332030	.	-	0	transcript_id "Phchi.S3G027700.t1"; gene_id "Phchi.S3G027700"
# This transcript jg1016.t1 is derived from g10798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7122924	7124420	.	+	.	Phchi.S6G097500
Phchi.S6	AUGUSTUS	transcript	7122924	7124420	.	+	.	transcript_id "Phchi.S6G097500.t1"; gene_id "Phchi.S6G097500"
Phchi.S6	AUGUSTUS	start_codon	7122924	7122926	.	+	0	transcript_id "Phchi.S6G097500.t1"; gene_id "Phchi.S6G097500"
Phchi.S6	AUGUSTUS	CDS	7122924	7124420	0.9	+	0	transcript_id "Phchi.S6G097500.t1"; gene_id "Phchi.S6G097500"
Phchi.S6	AUGUSTUS	exon	7122924	7124420	.	+	.	transcript_id "Phchi.S6G097500.t1"; gene_id "Phchi.S6G097500"
Phchi.S6	AUGUSTUS	stop_codon	7124421	7124423	.	+	0	transcript_id "Phchi.S6G097500.t1"; gene_id "Phchi.S6G097500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3789.t1 is derived from g958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5743212	5750615	.	-	.	Phchi.S1G094800
Phchi.S1	AUGUSTUS	transcript	5743212	5750615	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	stop_codon	5743209	5743211	.	-	0	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5743212	5743276	0.82	-	2	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5743212	5743276	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5743277	5743420	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5743421	5743507	1	-	2	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5743421	5743507	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5743508	5743632	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5743633	5743776	0.45	-	2	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5743633	5743776	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5743777	5743913	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5743914	5745762	0.42	-	0	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5743914	5745762	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5745763	5745963	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5745964	5748694	0.99	-	1	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5745964	5748694	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5748695	5748867	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5748868	5749020	1	-	1	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5748868	5749020	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5749021	5749137	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5749138	5749190	1	-	0	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5749138	5749190	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5749191	5749347	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5749348	5749400	1	-	2	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5749348	5749400	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5749401	5749547	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5749548	5749590	1	-	0	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5749548	5749590	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5749591	5749681	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5749682	5749793	1	-	1	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5749682	5749793	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5749794	5749870	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5749871	5750062	1	-	1	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5749871	5750062	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5750063	5750309	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5750310	5750381	0.77	-	1	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5750310	5750381	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	intron	5750382	5750514	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	CDS	5750515	5750615	0.38	-	0	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	exon	5750515	5750615	.	-	.	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
Phchi.S1	AUGUSTUS	start_codon	5750613	5750615	.	-	0	transcript_id "Phchi.S1G094800.t1"; gene_id "Phchi.S1G094800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3354.t1 is derived from g523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3096870	3097604	.	+	.	Phchi.S1G051300
Phchi.S1	AUGUSTUS	transcript	3096870	3097604	.	+	.	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	start_codon	3096870	3096872	.	+	0	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	CDS	3096870	3096909	0.93	+	0	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	exon	3096870	3096909	.	+	.	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	intron	3096910	3097014	.	+	.	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	CDS	3097015	3097604	0.95	+	2	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	exon	3097015	3097604	.	+	.	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
Phchi.S1	AUGUSTUS	stop_codon	3097605	3097607	.	+	0	transcript_id "Phchi.S1G051300.t1"; gene_id "Phchi.S1G051300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8111.t1 is derived from g5286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33168653	33170731	.	+	.	Phchi.S1G527000
Phchi.S1	AUGUSTUS	transcript	33168653	33170731	.	+	.	transcript_id "Phchi.S1G527000.t1"; gene_id "Phchi.S1G527000"
Phchi.S1	AUGUSTUS	start_codon	33168653	33168655	.	+	0	transcript_id "Phchi.S1G527000.t1"; gene_id "Phchi.S1G527000"
Phchi.S1	AUGUSTUS	CDS	33168653	33170731	0.61	+	0	transcript_id "Phchi.S1G527000.t1"; gene_id "Phchi.S1G527000"
Phchi.S1	AUGUSTUS	exon	33168653	33170731	.	+	.	transcript_id "Phchi.S1G527000.t1"; gene_id "Phchi.S1G527000"
Phchi.S1	AUGUSTUS	stop_codon	33170732	33170734	.	+	0	transcript_id "Phchi.S1G527000.t1"; gene_id "Phchi.S1G527000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6389.t1 is derived from g3561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22698213	22702302	.	-	.	Phchi.S1G354800
Phchi.S1	AUGUSTUS	transcript	22698213	22702302	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	stop_codon	22698210	22698212	.	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22698213	22698362	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22698213	22698362	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22698363	22698446	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22698447	22698668	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22698447	22698668	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22698669	22698758	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22698759	22698887	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22698759	22698887	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22698888	22698975	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22698976	22699048	1	-	1	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22698976	22699048	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22699049	22699143	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22699144	22699394	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22699144	22699394	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22699395	22699507	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22699508	22699613	1	-	1	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22699508	22699613	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22699614	22699707	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22699708	22699874	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22699708	22699874	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22699875	22699975	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22699976	22700056	0.99	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22699976	22700056	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22700057	22700227	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22700228	22700391	1	-	2	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22700228	22700391	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22700392	22700485	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22700486	22700688	1	-	1	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22700486	22700688	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22700689	22700810	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22700811	22701002	1	-	1	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22700811	22701002	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22701003	22701140	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22701141	22701268	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22701141	22701268	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22701269	22701384	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22701385	22701472	1	-	1	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22701385	22701472	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22701473	22701551	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22701552	22701913	1	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22701552	22701913	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	intron	22701914	22702296	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	CDS	22702297	22702302	0.39	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	exon	22702297	22702302	.	-	.	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
Phchi.S1	AUGUSTUS	start_codon	22702300	22702302	.	-	0	transcript_id "Phchi.S1G354800.t1"; gene_id "Phchi.S1G354800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6888.t1 is derived from g4060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25830281	25830886	.	+	.	Phchi.S1G404700
Phchi.S1	AUGUSTUS	transcript	25830281	25830886	.	+	.	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	start_codon	25830281	25830283	.	+	0	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	CDS	25830281	25830338	0.78	+	0	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	exon	25830281	25830338	.	+	.	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	intron	25830339	25830501	.	+	.	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	CDS	25830502	25830539	0.69	+	2	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	exon	25830502	25830539	.	+	.	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	intron	25830540	25830760	.	+	.	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	CDS	25830761	25830886	0.83	+	0	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	exon	25830761	25830886	.	+	.	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
Phchi.S1	AUGUSTUS	stop_codon	25830887	25830889	.	+	0	transcript_id "Phchi.S1G404700.t1"; gene_id "Phchi.S1G404700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10534.t1 is derived from g14584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	857648	860650	.	-	.	Phchi.S4G011600
Phchi.S4	AUGUSTUS	transcript	857648	860650	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	stop_codon	857645	857647	.	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	857648	857872	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	857648	857872	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	857873	857945	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	857946	858053	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	857946	858053	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	858054	858149	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	858150	858236	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	858150	858236	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	858237	858333	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	858334	858408	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	858334	858408	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	858409	858480	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	858481	858615	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	858481	858615	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	858616	858705	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	858706	858927	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	858706	858927	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	858928	859021	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	859022	859102	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	859022	859102	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	859103	859183	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	859184	859345	0.93	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	859184	859345	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	859346	859458	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	859459	859553	0.93	-	2	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	859459	859553	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	859554	859628	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	859629	859724	1	-	2	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	859629	859724	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	859725	859848	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	859849	859990	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	859849	859990	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	859991	860153	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	860154	860249	1	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	860154	860249	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	860250	860346	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	860347	860485	1	-	1	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	860347	860485	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	intron	860486	860570	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	CDS	860571	860650	0.99	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	exon	860571	860650	.	-	.	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
Phchi.S4	AUGUSTUS	start_codon	860648	860650	.	-	0	transcript_id "Phchi.S4G011600.t1"; gene_id "Phchi.S4G011600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3343.t1 is derived from g512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3044148	3045676	.	-	.	Phchi.S1G050200
Phchi.S1	AUGUSTUS	transcript	3044148	3045676	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	stop_codon	3044145	3044147	.	-	0	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	CDS	3044148	3044451	1	-	1	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	exon	3044148	3044451	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	intron	3044452	3044611	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	CDS	3044612	3044820	1	-	0	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	exon	3044612	3044820	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	intron	3044821	3045065	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	CDS	3045066	3045152	1	-	0	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	exon	3045066	3045152	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	intron	3045153	3045267	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	CDS	3045268	3045378	1	-	0	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	exon	3045268	3045378	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	intron	3045379	3045475	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	CDS	3045476	3045543	1	-	2	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	exon	3045476	3045543	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	intron	3045544	3045627	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	CDS	3045628	3045676	1	-	0	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	exon	3045628	3045676	.	-	.	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
Phchi.S1	AUGUSTUS	start_codon	3045674	3045676	.	-	0	transcript_id "Phchi.S1G050200.t1"; gene_id "Phchi.S1G050200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3439.t1 is derived from g608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3671774	3672451	.	+	.	Phchi.S1G059800
Phchi.S1	AUGUSTUS	transcript	3671774	3672451	.	+	.	transcript_id "Phchi.S1G059800.t1"; gene_id "Phchi.S1G059800"
Phchi.S1	AUGUSTUS	start_codon	3671774	3671776	.	+	0	transcript_id "Phchi.S1G059800.t1"; gene_id "Phchi.S1G059800"
Phchi.S1	AUGUSTUS	CDS	3671774	3672451	0.97	+	0	transcript_id "Phchi.S1G059800.t1"; gene_id "Phchi.S1G059800"
Phchi.S1	AUGUSTUS	exon	3671774	3672451	.	+	.	transcript_id "Phchi.S1G059800.t1"; gene_id "Phchi.S1G059800"
Phchi.S1	AUGUSTUS	stop_codon	3672452	3672454	.	+	0	transcript_id "Phchi.S1G059800.t1"; gene_id "Phchi.S1G059800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8511.t1 is derived from g5686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36383567	36384490	.	-	.	Phchi.S1G567000
Phchi.S1	AUGUSTUS	transcript	36383567	36384490	.	-	.	transcript_id "Phchi.S1G567000.t1"; gene_id "Phchi.S1G567000"
Phchi.S1	AUGUSTUS	stop_codon	36383564	36383566	.	-	0	transcript_id "Phchi.S1G567000.t1"; gene_id "Phchi.S1G567000"
Phchi.S1	AUGUSTUS	CDS	36383567	36384490	0.83	-	0	transcript_id "Phchi.S1G567000.t1"; gene_id "Phchi.S1G567000"
Phchi.S1	AUGUSTUS	exon	36383567	36384490	.	-	.	transcript_id "Phchi.S1G567000.t1"; gene_id "Phchi.S1G567000"
Phchi.S1	AUGUSTUS	start_codon	36384488	36384490	.	-	0	transcript_id "Phchi.S1G567000.t1"; gene_id "Phchi.S1G567000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2709.t1 is derived from g9629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8290738	8292087	.	-	.	Phchi.S5G131800
Phchi.S5	AUGUSTUS	transcript	8290738	8292087	.	-	.	transcript_id "Phchi.S5G131800.t1"; gene_id "Phchi.S5G131800"
Phchi.S5	AUGUSTUS	stop_codon	8290735	8290737	.	-	0	transcript_id "Phchi.S5G131800.t1"; gene_id "Phchi.S5G131800"
Phchi.S5	AUGUSTUS	CDS	8290738	8292087	0.78	-	0	transcript_id "Phchi.S5G131800.t1"; gene_id "Phchi.S5G131800"
Phchi.S5	AUGUSTUS	exon	8290738	8292087	.	-	.	transcript_id "Phchi.S5G131800.t1"; gene_id "Phchi.S5G131800"
Phchi.S5	AUGUSTUS	start_codon	8292085	8292087	.	-	0	transcript_id "Phchi.S5G131800.t1"; gene_id "Phchi.S5G131800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5026.t1 is derived from g2196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14104263	14106064	.	+	.	Phchi.S1G218500
Phchi.S1	AUGUSTUS	transcript	14104263	14106064	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	start_codon	14104263	14104265	.	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	CDS	14104263	14104543	1	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	exon	14104263	14104543	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	intron	14104544	14104694	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	CDS	14104695	14105016	1	+	1	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	exon	14104695	14105016	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	intron	14105017	14105167	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	CDS	14105168	14105317	1	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	exon	14105168	14105317	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	intron	14105318	14105413	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	CDS	14105414	14105668	1	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	exon	14105414	14105668	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	intron	14105669	14105763	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	CDS	14105764	14105850	0.77	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	exon	14105764	14105850	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	intron	14105851	14105956	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	CDS	14105957	14106064	0.34	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	exon	14105957	14106064	.	+	.	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
Phchi.S1	AUGUSTUS	stop_codon	14106065	14106067	.	+	0	transcript_id "Phchi.S1G218500.t1"; gene_id "Phchi.S1G218500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12140.t1 is derived from g7816.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4835304	4836343	.	-	.	Phchi.S2G022000
Phchi.S2	AUGUSTUS	transcript	4835304	4836343	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	stop_codon	4835301	4835303	.	-	0	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835304	4835386	0.95	-	2	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835304	4835386	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4835387	4835462	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835463	4835599	1	-	1	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835463	4835599	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4835600	4835745	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835746	4835858	0.99	-	0	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835746	4835858	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4835859	4835929	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835930	4836052	0.99	-	0	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835930	4836052	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4836053	4836220	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4836221	4836343	0.62	-	0	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4836221	4836343	.	-	.	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	start_codon	4836341	4836343	.	-	0	transcript_id "Phchi.S2G022000.t1"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	transcript	4835304	4836343	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	stop_codon	4835301	4835303	.	-	0	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835304	4835386	0.92	-	2	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835304	4835386	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4835387	4835462	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835463	4835599	1	-	1	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835463	4835599	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4835600	4835693	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835694	4835858	0.87	-	1	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835694	4835858	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4835859	4835939	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4835940	4836052	0.88	-	0	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4835940	4836052	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	intron	4836053	4836220	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	CDS	4836221	4836343	0.68	-	0	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	exon	4836221	4836343	.	-	.	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
Phchi.S2	AUGUSTUS	start_codon	4836341	4836343	.	-	0	transcript_id "Phchi.S2G022000.t2"; gene_id "Phchi.S2G022000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14058.t1 is derived from g12525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10542115	10549794	.	-	.	Phchi.S3G137700
Phchi.S3	AUGUSTUS	transcript	10542115	10549794	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	stop_codon	10542112	10542114	.	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10542115	10542260	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10542115	10542260	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10542261	10542414	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10542415	10544289	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10542415	10544289	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10544290	10544379	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10544380	10544484	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10544380	10544484	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10544485	10544666	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10544667	10544943	0.84	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10544667	10544943	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10544944	10545045	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10545046	10545412	0.99	-	1	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10545046	10545412	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10545413	10545499	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10545500	10545618	1	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10545500	10545618	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10545619	10545712	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10545713	10545846	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10545713	10545846	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10545847	10546012	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10546013	10546070	1	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10546013	10546070	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10546071	10546268	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10546269	10546427	1	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10546269	10546427	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10546428	10546517	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10546518	10547520	0.99	-	1	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10546518	10547520	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10547521	10547624	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10547625	10547790	0.99	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10547625	10547790	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10547791	10547907	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10547908	10548044	1	-	1	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10547908	10548044	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10548045	10548172	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10548173	10548285	1	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10548173	10548285	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10548286	10548447	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10548448	10548578	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10548448	10548578	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10548579	10548829	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10548830	10548970	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10548830	10548970	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10548971	10549050	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10549051	10549225	1	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10549051	10549225	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10549226	10549309	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10549310	10549521	1	-	2	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10549310	10549521	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	intron	10549522	10549625	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	CDS	10549626	10549794	0.64	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	exon	10549626	10549794	.	-	.	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
Phchi.S3	AUGUSTUS	start_codon	10549792	10549794	.	-	0	transcript_id "Phchi.S3G137700.t1"; gene_id "Phchi.S3G137700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13797.t1 is derived from g12264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8943800	8945152	.	+	.	Phchi.S3G111600
Phchi.S3	AUGUSTUS	transcript	8943800	8945152	.	+	.	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	start_codon	8943800	8943802	.	+	0	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	CDS	8943800	8944849	0.84	+	0	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	exon	8943800	8944849	.	+	.	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	intron	8944850	8945017	.	+	.	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	CDS	8945018	8945152	0.69	+	0	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	exon	8945018	8945152	.	+	.	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
Phchi.S3	AUGUSTUS	stop_codon	8945153	8945155	.	+	0	transcript_id "Phchi.S3G111600.t1"; gene_id "Phchi.S3G111600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8662.t1 is derived from g5837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37340208	37345208	.	+	.	Phchi.S1G582100
Phchi.S1	AUGUSTUS	transcript	37340208	37345208	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	start_codon	37340208	37340210	.	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37340208	37340837	0.58	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37340208	37340837	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37340838	37340946	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37340947	37341192	1	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37340947	37341192	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37341193	37341277	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37341278	37342021	0.93	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37341278	37342021	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37342022	37342129	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37342130	37342508	0.99	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37342130	37342508	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37342509	37342623	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37342624	37343198	0.62	+	2	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37342624	37343198	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37343199	37343419	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37343420	37343518	0.84	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37343420	37343518	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37343519	37343604	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37343605	37344882	0.63	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37343605	37344882	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	intron	37344883	37344989	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	CDS	37344990	37345208	0.92	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	exon	37344990	37345208	.	+	.	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
Phchi.S1	AUGUSTUS	stop_codon	37345209	37345211	.	+	0	transcript_id "Phchi.S1G582100.t1"; gene_id "Phchi.S1G582100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3663.t1 is derived from g832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5038888	5039325	.	+	.	Phchi.S1G082200
Phchi.S1	AUGUSTUS	transcript	5038888	5039325	.	+	.	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	start_codon	5038888	5038890	.	+	0	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	CDS	5038888	5039012	0.73	+	0	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	exon	5038888	5039012	.	+	.	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	intron	5039013	5039105	.	+	.	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	CDS	5039106	5039325	0.72	+	1	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	exon	5039106	5039325	.	+	.	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
Phchi.S1	AUGUSTUS	stop_codon	5039326	5039328	.	+	0	transcript_id "Phchi.S1G082200.t1"; gene_id "Phchi.S1G082200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13667.t1 is derived from g12134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8070119	8072326	.	+	.	Phchi.S3G098600
Phchi.S3	AUGUSTUS	transcript	8070119	8072326	.	+	.	transcript_id "Phchi.S3G098600.t1"; gene_id "Phchi.S3G098600"
Phchi.S3	AUGUSTUS	start_codon	8070119	8070121	.	+	0	transcript_id "Phchi.S3G098600.t1"; gene_id "Phchi.S3G098600"
Phchi.S3	AUGUSTUS	CDS	8070119	8072326	0.98	+	0	transcript_id "Phchi.S3G098600.t1"; gene_id "Phchi.S3G098600"
Phchi.S3	AUGUSTUS	exon	8070119	8072326	.	+	.	transcript_id "Phchi.S3G098600.t1"; gene_id "Phchi.S3G098600"
Phchi.S3	AUGUSTUS	stop_codon	8072327	8072329	.	+	0	transcript_id "Phchi.S3G098600.t1"; gene_id "Phchi.S3G098600"
# This transcript jg11826.t2 is derived from g15878.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11827.t1 is derived from g15879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8461862	8462209	.	+	.	Phchi.S4G140900
Phchi.S4	AUGUSTUS	transcript	8461862	8462209	.	+	.	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	start_codon	8461862	8461864	.	+	0	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	CDS	8461862	8461950	0.97	+	0	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	exon	8461862	8461950	.	+	.	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	intron	8461951	8462100	.	+	.	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	CDS	8462101	8462209	0.9	+	1	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	exon	8462101	8462209	.	+	.	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
Phchi.S4	AUGUSTUS	stop_codon	8462210	8462212	.	+	0	transcript_id "Phchi.S4G140900.t1"; gene_id "Phchi.S4G140900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg397.t1 is derived from g10179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2876414	2879763	.	+	.	Phchi.S6G035600
Phchi.S6	AUGUSTUS	transcript	2876414	2879398	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	start_codon	2876414	2876416	.	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2876414	2877123	0.99	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2876414	2877123	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877124	2877228	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2877229	2877451	1	+	1	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2877229	2877451	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877452	2877531	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2877532	2877684	1	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2877532	2877684	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877685	2877822	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2877823	2877981	1	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2877823	2877981	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877982	2878074	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878075	2878234	0.98	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878075	2878234	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2878235	2878326	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878327	2878436	1	+	2	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878327	2878436	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2878437	2878537	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878538	2878654	0.98	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878538	2878654	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2878655	2878759	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878760	2879089	0.95	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878760	2879089	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2879090	2879362	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2879363	2879398	0.99	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2879363	2879398	.	+	.	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	stop_codon	2879399	2879401	.	+	0	transcript_id "Phchi.S6G035600.t1"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	transcript	2876414	2879763	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	start_codon	2876414	2876416	.	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2876414	2877123	1	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2876414	2877123	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877124	2877228	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2877229	2877451	1	+	1	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2877229	2877451	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877452	2877531	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2877532	2877684	1	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2877532	2877684	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877685	2877822	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2877823	2877981	1	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2877823	2877981	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2877982	2878074	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878075	2878234	0.95	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878075	2878234	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2878235	2878326	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878327	2878436	1	+	2	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878327	2878436	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2878437	2878537	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878538	2878654	1	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878538	2878654	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2878655	2878759	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2878760	2879162	0.97	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2878760	2879162	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2879163	2879362	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2879363	2879403	0.97	+	2	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2879363	2879403	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	intron	2879404	2879646	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	CDS	2879647	2879763	0.96	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	exon	2879647	2879763	.	+	.	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
Phchi.S6	AUGUSTUS	stop_codon	2879764	2879766	.	+	0	transcript_id "Phchi.S6G035600.t2"; gene_id "Phchi.S6G035600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15877.t1 is derived from g14347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22008687	22010433	.	-	.	Phchi.S3G319600
Phchi.S3	AUGUSTUS	transcript	22008687	22010433	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	stop_codon	22008684	22008686	.	-	0	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	CDS	22008687	22008896	0.87	-	0	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	exon	22008687	22008896	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	intron	22008897	22009015	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	CDS	22009016	22009381	0.98	-	0	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	exon	22009016	22009381	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	intron	22009382	22009503	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	CDS	22009504	22010150	1	-	2	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	exon	22009504	22010150	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	intron	22010151	22010273	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	CDS	22010274	22010433	0.55	-	0	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	exon	22010274	22010433	.	-	.	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
Phchi.S3	AUGUSTUS	start_codon	22010431	22010433	.	-	0	transcript_id "Phchi.S3G319600.t1"; gene_id "Phchi.S3G319600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3453.t1 is derived from g622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3821881	3822557	.	-	.	Phchi.S1G061200
Phchi.S1	AUGUSTUS	transcript	3821881	3822557	.	-	.	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	stop_codon	3821878	3821880	.	-	0	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	CDS	3821881	3822013	0.42	-	1	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	exon	3821881	3822013	.	-	.	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	intron	3822014	3822156	.	-	.	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	CDS	3822157	3822557	0.4	-	0	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	exon	3822157	3822557	.	-	.	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
Phchi.S1	AUGUSTUS	start_codon	3822555	3822557	.	-	0	transcript_id "Phchi.S1G061200.t1"; gene_id "Phchi.S1G061200"
# This transcript jg15632.t2 is derived from g14101.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15633.t1 is derived from g14102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20389445	20390492	.	+	.	Phchi.S3G295200
Phchi.S3	AUGUSTUS	transcript	20389445	20390492	.	+	.	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	start_codon	20389445	20389447	.	+	0	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	CDS	20389445	20389858	0.31	+	0	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	exon	20389445	20389858	.	+	.	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	intron	20389859	20390120	.	+	.	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	CDS	20390121	20390492	0.56	+	0	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	exon	20390121	20390492	.	+	.	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	stop_codon	20390493	20390495	.	+	0	transcript_id "Phchi.S3G295200.t1"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	transcript	20389445	20389873	.	+	.	transcript_id "Phchi.S3G295200.t2"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	start_codon	20389445	20389447	.	+	0	transcript_id "Phchi.S3G295200.t2"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	CDS	20389445	20389873	0.4	+	0	transcript_id "Phchi.S3G295200.t2"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	exon	20389445	20389873	.	+	.	transcript_id "Phchi.S3G295200.t2"; gene_id "Phchi.S3G295200"
Phchi.S3	AUGUSTUS	stop_codon	20389874	20389876	.	+	0	transcript_id "Phchi.S3G295200.t2"; gene_id "Phchi.S3G295200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1341.t1 is derived from g11124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9104250	9106100	.	-	.	Phchi.S6G130000
Phchi.S6	AUGUSTUS	transcript	9104250	9104879	.	-	.	transcript_id "Phchi.S6G130000.t1"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	stop_codon	9104247	9104249	.	-	0	transcript_id "Phchi.S6G130000.t1"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	CDS	9104250	9104879	0.88	-	0	transcript_id "Phchi.S6G130000.t1"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	exon	9104250	9104879	.	-	.	transcript_id "Phchi.S6G130000.t1"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	start_codon	9104877	9104879	.	-	0	transcript_id "Phchi.S6G130000.t1"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	transcript	9104250	9106100	.	-	.	transcript_id "Phchi.S6G130000.t2"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	stop_codon	9104247	9104249	.	-	0	transcript_id "Phchi.S6G130000.t2"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	CDS	9104250	9106100	0.78	-	0	transcript_id "Phchi.S6G130000.t2"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	exon	9104250	9106100	.	-	.	transcript_id "Phchi.S6G130000.t2"; gene_id "Phchi.S6G130000"
Phchi.S6	AUGUSTUS	start_codon	9106098	9106100	.	-	0	transcript_id "Phchi.S6G130000.t2"; gene_id "Phchi.S6G130000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6678.t1 is derived from g3850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24456441	24460009	.	+	.	Phchi.S1G383700
Phchi.S1	AUGUSTUS	transcript	24456441	24460009	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	start_codon	24456441	24456443	.	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24456441	24456548	0.94	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24456441	24456548	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24456549	24456668	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24456669	24456841	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24456669	24456841	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24456842	24457162	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24457163	24457391	1	+	1	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24457163	24457391	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24457392	24457643	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24457644	24457736	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24457644	24457736	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24457737	24457950	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24457951	24458091	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24457951	24458091	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24458092	24458192	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24458193	24458285	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24458193	24458285	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24458286	24458418	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24458419	24458626	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24458419	24458626	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24458627	24458718	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24458719	24458804	1	+	2	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24458719	24458804	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24458805	24458970	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24458971	24459059	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24458971	24459059	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24459060	24459152	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24459153	24459204	1	+	1	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24459153	24459204	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24459205	24459299	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24459300	24459356	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24459300	24459356	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24459357	24459434	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24459435	24459617	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24459435	24459617	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24459618	24459791	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24459792	24459869	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24459792	24459869	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	intron	24459870	24459946	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	CDS	24459947	24460009	1	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	exon	24459947	24460009	.	+	.	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
Phchi.S1	AUGUSTUS	stop_codon	24460010	24460012	.	+	0	transcript_id "Phchi.S1G383700.t1"; gene_id "Phchi.S1G383700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10997.t1 is derived from g15047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3572465	3573348	.	+	.	Phchi.S4G057900
Phchi.S4	AUGUSTUS	transcript	3572465	3573348	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	start_codon	3572465	3572467	.	+	0	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	CDS	3572465	3572488	0.42	+	0	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	exon	3572465	3572488	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	intron	3572489	3572565	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	CDS	3572566	3572754	0.93	+	0	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	exon	3572566	3572754	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	intron	3572755	3572862	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	CDS	3572863	3572916	0.99	+	0	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	exon	3572863	3572916	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	intron	3572917	3573033	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	CDS	3573034	3573348	1	+	0	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	exon	3573034	3573348	.	+	.	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
Phchi.S4	AUGUSTUS	stop_codon	3573349	3573351	.	+	0	transcript_id "Phchi.S4G057900.t1"; gene_id "Phchi.S4G057900"
# This transcript jg5785.t2 is derived from g2955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5786.t1 is derived from g2956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18950383	18958602	.	-	.	Phchi.S1G294500
Phchi.S1	AUGUSTUS	transcript	18950383	18958602	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	stop_codon	18950380	18950382	.	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18950383	18950784	0.71	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18950383	18950784	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18950785	18950872	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18950873	18951097	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18950873	18951097	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951098	18951176	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18951177	18951336	1	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18951177	18951336	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951337	18951421	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18951422	18951556	1	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18951422	18951556	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951557	18951640	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18951641	18951927	0.96	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18951641	18951927	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951928	18952051	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18952052	18952177	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18952052	18952177	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18952178	18952275	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18952276	18952486	0.99	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18952276	18952486	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18952487	18952566	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18952567	18953654	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18952567	18953654	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18953655	18953758	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18953759	18953836	0.99	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18953759	18953836	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18953837	18953958	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18953959	18954078	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18953959	18954078	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954079	18954150	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954151	18954378	0.99	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954151	18954378	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954379	18954465	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954466	18954549	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954466	18954549	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954550	18954650	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954651	18954722	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954651	18954722	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954723	18954811	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954812	18954867	0.6	-	2	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954812	18954867	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954868	18955152	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955153	18955209	0.61	-	2	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955153	18955209	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955210	18955353	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955354	18955421	1	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955354	18955421	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955422	18955533	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955534	18955776	1	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955534	18955776	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955777	18955884	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955885	18955952	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955885	18955952	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955953	18956029	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956030	18956197	0.94	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956030	18956197	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956198	18956395	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956396	18956443	0.77	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956396	18956443	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956444	18956542	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956543	18956630	1	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956543	18956630	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956631	18956787	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956788	18956903	1	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956788	18956903	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956904	18956985	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956986	18957113	1	-	2	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956986	18957113	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957114	18957208	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18957209	18957302	0.99	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18957209	18957302	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957303	18957410	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18957411	18957706	0.33	-	2	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18957411	18957706	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957707	18957831	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18957832	18957982	0.94	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18957832	18957982	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957983	18958065	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18958066	18958186	1	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18958066	18958186	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18958187	18958282	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18958283	18958372	0.97	-	1	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18958283	18958372	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18958373	18958489	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18958490	18958602	0.75	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18958490	18958602	.	-	.	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	start_codon	18958600	18958602	.	-	0	transcript_id "Phchi.S1G294500.t1"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	transcript	18950383	18958602	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	stop_codon	18950380	18950382	.	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18950383	18950784	0.67	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18950383	18950784	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18950785	18950872	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18950873	18951097	1	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18950873	18951097	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951098	18951176	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18951177	18951336	0.99	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18951177	18951336	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951337	18951421	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18951422	18951556	1	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18951422	18951556	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951557	18951640	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18951641	18951927	0.93	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18951641	18951927	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18951928	18952051	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18952052	18952177	0.99	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18952052	18952177	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18952178	18952275	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18952276	18952486	0.99	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18952276	18952486	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18952487	18952566	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18952567	18953654	1	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18952567	18953654	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18953655	18953758	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18953759	18953836	0.99	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18953759	18953836	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18953837	18953958	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18953959	18954078	0.97	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18953959	18954078	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954079	18954150	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954151	18954378	1	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954151	18954378	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954379	18954465	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954466	18954549	1	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954466	18954549	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954550	18954650	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954651	18954722	0.99	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954651	18954722	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954723	18954811	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954812	18954867	0.61	-	2	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954812	18954867	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954868	18954935	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18954936	18954959	0.39	-	2	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18954936	18954959	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18954960	18955353	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955354	18955421	0.91	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955354	18955421	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955422	18955533	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955534	18955776	1	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955534	18955776	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955777	18955884	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18955885	18955952	1	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18955885	18955952	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18955953	18956029	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956030	18956197	0.9	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956030	18956197	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956198	18956395	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956396	18956443	0.74	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956396	18956443	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956444	18956542	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956543	18956630	1	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956543	18956630	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956631	18956787	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956788	18956903	1	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956788	18956903	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18956904	18956985	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18956986	18957113	1	-	2	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18956986	18957113	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957114	18957208	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18957209	18957302	0.99	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18957209	18957302	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957303	18957410	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18957411	18957706	0.31	-	2	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18957411	18957706	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957707	18957831	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18957832	18957982	0.97	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18957832	18957982	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18957983	18958065	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18958066	18958186	1	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18958066	18958186	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18958187	18958282	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18958283	18958372	1	-	1	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18958283	18958372	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	intron	18958373	18958489	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	CDS	18958490	18958602	0.77	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	exon	18958490	18958602	.	-	.	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
Phchi.S1	AUGUSTUS	start_codon	18958600	18958602	.	-	0	transcript_id "Phchi.S1G294500.t2"; gene_id "Phchi.S1G294500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4443.t1 is derived from g1612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10543367	10544095	.	-	.	Phchi.S1G160200
Phchi.S1	AUGUSTUS	transcript	10543367	10544095	.	-	.	transcript_id "Phchi.S1G160200.t1"; gene_id "Phchi.S1G160200"
Phchi.S1	AUGUSTUS	stop_codon	10543364	10543366	.	-	0	transcript_id "Phchi.S1G160200.t1"; gene_id "Phchi.S1G160200"
Phchi.S1	AUGUSTUS	CDS	10543367	10544095	0.43	-	0	transcript_id "Phchi.S1G160200.t1"; gene_id "Phchi.S1G160200"
Phchi.S1	AUGUSTUS	exon	10543367	10544095	.	-	.	transcript_id "Phchi.S1G160200.t1"; gene_id "Phchi.S1G160200"
Phchi.S1	AUGUSTUS	start_codon	10544093	10544095	.	-	0	transcript_id "Phchi.S1G160200.t1"; gene_id "Phchi.S1G160200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15797.t1 is derived from g14267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21379645	21381051	.	-	.	Phchi.S3G311600
Phchi.S3	AUGUSTUS	transcript	21379645	21381051	.	-	.	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	stop_codon	21379642	21379644	.	-	0	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	CDS	21379645	21380507	0.56	-	2	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	exon	21379645	21380507	.	-	.	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	intron	21380508	21380626	.	-	.	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	CDS	21380627	21380787	0.98	-	1	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	exon	21380627	21380787	.	-	.	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	intron	21380788	21380878	.	-	.	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	CDS	21380879	21381051	1	-	0	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	exon	21380879	21381051	.	-	.	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
Phchi.S3	AUGUSTUS	start_codon	21381049	21381051	.	-	0	transcript_id "Phchi.S3G311600.t1"; gene_id "Phchi.S3G311600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10333.t1 is derived from g7509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47222013	47225585	.	+	.	Phchi.S1G749200
Phchi.S1	AUGUSTUS	transcript	47222013	47225585	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	start_codon	47222013	47222015	.	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47222013	47222108	0.84	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47222013	47222108	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47222109	47222640	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47222641	47222766	1	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47222641	47222766	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47222767	47222889	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47222890	47223192	0.99	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47222890	47223192	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47223193	47223380	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47223381	47223489	1	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47223381	47223489	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47223490	47223599	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47223600	47224321	0.96	+	2	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47223600	47224321	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47224322	47224576	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47224577	47224741	1	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47224577	47224741	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47224742	47224820	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47224821	47225051	1	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47224821	47225051	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47225052	47225187	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47225188	47225418	0.95	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47225188	47225418	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	intron	47225419	47225525	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	CDS	47225526	47225585	0.75	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	exon	47225526	47225585	.	+	.	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
Phchi.S1	AUGUSTUS	stop_codon	47225586	47225588	.	+	0	transcript_id "Phchi.S1G749200.t1"; gene_id "Phchi.S1G749200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14361.t1 is derived from g12828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12362617	12364496	.	+	.	Phchi.S3G168000
Phchi.S3	AUGUSTUS	transcript	12362617	12364496	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	start_codon	12362617	12362619	.	+	0	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12362617	12362687	0.81	+	0	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12362617	12362687	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	intron	12362688	12362773	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12362774	12362842	1	+	1	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12362774	12362842	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	intron	12362843	12363007	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12363008	12363082	1	+	1	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12363008	12363082	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	intron	12363083	12363170	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12363171	12363221	1	+	1	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12363171	12363221	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	intron	12363222	12363300	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12363301	12363368	1	+	1	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12363301	12363368	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	intron	12363369	12363450	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12363451	12364001	0.95	+	2	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12363451	12364001	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	intron	12364002	12364112	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	CDS	12364113	12364496	1	+	0	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	exon	12364113	12364496	.	+	.	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
Phchi.S3	AUGUSTUS	stop_codon	12364497	12364499	.	+	0	transcript_id "Phchi.S3G168000.t1"; gene_id "Phchi.S3G168000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9263.t1 is derived from g6438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40649103	40651595	.	-	.	Phchi.S1G642200
Phchi.S1	AUGUSTUS	transcript	40649103	40651595	.	-	.	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	stop_codon	40649100	40649102	.	-	0	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	CDS	40649103	40651036	0.5	-	2	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	exon	40649103	40651036	.	-	.	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	intron	40651037	40651138	.	-	.	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	CDS	40651139	40651190	0.5	-	0	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	exon	40651139	40651190	.	-	.	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	intron	40651191	40651307	.	-	.	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	CDS	40651308	40651595	0.92	-	0	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	exon	40651308	40651595	.	-	.	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
Phchi.S1	AUGUSTUS	start_codon	40651593	40651595	.	-	0	transcript_id "Phchi.S1G642200.t1"; gene_id "Phchi.S1G642200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6266.t1 is derived from g3438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21931462	21932099	.	-	.	Phchi.S1G342500
Phchi.S1	AUGUSTUS	transcript	21931462	21932099	.	-	.	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	stop_codon	21931459	21931461	.	-	0	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	CDS	21931462	21931567	0.77	-	1	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	exon	21931462	21931567	.	-	.	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	intron	21931568	21931651	.	-	.	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	CDS	21931652	21931911	1	-	0	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	exon	21931652	21931911	.	-	.	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	intron	21931912	21932006	.	-	.	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	CDS	21932007	21932099	0.99	-	0	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	exon	21932007	21932099	.	-	.	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
Phchi.S1	AUGUSTUS	start_codon	21932097	21932099	.	-	0	transcript_id "Phchi.S1G342500.t1"; gene_id "Phchi.S1G342500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9349.t1 is derived from g6525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41075242	41075808	.	+	.	Phchi.S1G650800
Phchi.S1	AUGUSTUS	transcript	41075242	41075808	.	+	.	transcript_id "Phchi.S1G650800.t1"; gene_id "Phchi.S1G650800"
Phchi.S1	AUGUSTUS	start_codon	41075242	41075244	.	+	0	transcript_id "Phchi.S1G650800.t1"; gene_id "Phchi.S1G650800"
Phchi.S1	AUGUSTUS	CDS	41075242	41075808	0.65	+	0	transcript_id "Phchi.S1G650800.t1"; gene_id "Phchi.S1G650800"
Phchi.S1	AUGUSTUS	exon	41075242	41075808	.	+	.	transcript_id "Phchi.S1G650800.t1"; gene_id "Phchi.S1G650800"
Phchi.S1	AUGUSTUS	stop_codon	41075809	41075811	.	+	0	transcript_id "Phchi.S1G650800.t1"; gene_id "Phchi.S1G650800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13954.t1 is derived from g12421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9908052	9910218	.	+	.	Phchi.S3G127300
Phchi.S3	AUGUSTUS	transcript	9908052	9910218	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	start_codon	9908052	9908054	.	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	CDS	9908052	9908099	0.58	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	exon	9908052	9908099	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	intron	9908100	9908458	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	CDS	9908459	9908509	0.5	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	exon	9908459	9908509	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	intron	9908510	9908588	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	CDS	9908589	9908636	0.57	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	exon	9908589	9908636	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	intron	9908637	9908759	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	CDS	9908760	9908994	0.89	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	exon	9908760	9908994	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	intron	9908995	9909098	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	CDS	9909099	9909469	0.99	+	2	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	exon	9909099	9909469	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	intron	9909470	9909570	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	CDS	9909571	9910218	0.97	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	exon	9909571	9910218	.	+	.	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
Phchi.S3	AUGUSTUS	stop_codon	9910219	9910221	.	+	0	transcript_id "Phchi.S3G127300.t1"; gene_id "Phchi.S3G127300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5710.t1 is derived from g2880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18479805	18480481	.	-	.	Phchi.S1G286900
Phchi.S1	AUGUSTUS	transcript	18479805	18480481	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	stop_codon	18479802	18479804	.	-	0	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	CDS	18479805	18479846	1	-	0	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	exon	18479805	18479846	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	intron	18479847	18479931	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	CDS	18479932	18479993	1	-	2	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	exon	18479932	18479993	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	intron	18479994	18480090	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	CDS	18480091	18480146	1	-	1	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	exon	18480091	18480146	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	intron	18480147	18480229	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	CDS	18480230	18480321	1	-	0	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	exon	18480230	18480321	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	intron	18480322	18480394	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	CDS	18480395	18480481	1	-	0	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	exon	18480395	18480481	.	-	.	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
Phchi.S1	AUGUSTUS	start_codon	18480479	18480481	.	-	0	transcript_id "Phchi.S1G286900.t1"; gene_id "Phchi.S1G286900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15806.t1 is derived from g14276.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21482745	21485078	.	+	.	Phchi.S3G312500
Phchi.S3	AUGUSTUS	transcript	21482745	21485078	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	start_codon	21482745	21482747	.	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21482745	21482985	0.87	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21482745	21482985	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21482986	21483209	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21483210	21483547	1	+	2	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21483210	21483547	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21483548	21483647	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21483648	21483742	1	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21483648	21483742	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21483743	21483824	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21483825	21483900	1	+	1	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21483825	21483900	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21483901	21484015	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484016	21484103	1	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484016	21484103	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484104	21484185	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484186	21484349	1	+	2	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484186	21484349	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484350	21484459	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484460	21484597	1	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484460	21484597	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484598	21484710	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484711	21484842	1	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484711	21484842	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484843	21484928	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484929	21485078	0.97	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484929	21485078	.	+	.	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	stop_codon	21485079	21485081	.	+	0	transcript_id "Phchi.S3G312500.t1"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	transcript	21482745	21485078	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	start_codon	21482745	21482747	.	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21482745	21482985	0.81	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21482745	21482985	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21482986	21483209	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21483210	21483547	0.95	+	2	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21483210	21483547	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21483548	21483653	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21483654	21483742	0.81	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21483654	21483742	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21483743	21483824	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21483825	21483900	1	+	1	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21483825	21483900	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21483901	21484015	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484016	21484103	1	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484016	21484103	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484104	21484185	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484186	21484349	1	+	2	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484186	21484349	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484350	21484459	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484460	21484597	1	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484460	21484597	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484598	21484710	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484711	21484842	1	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484711	21484842	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	intron	21484843	21484928	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	CDS	21484929	21485078	1	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	exon	21484929	21485078	.	+	.	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
Phchi.S3	AUGUSTUS	stop_codon	21485079	21485081	.	+	0	transcript_id "Phchi.S3G312500.t2"; gene_id "Phchi.S3G312500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg181.t1 is derived from g9963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1034454	1039261	.	+	.	Phchi.S6G014000
Phchi.S6	AUGUSTUS	transcript	1034454	1039261	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	start_codon	1034454	1034456	.	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1034454	1034924	0.88	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1034454	1034924	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1034925	1035070	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1035071	1035232	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1035071	1035232	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1035233	1035345	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1035346	1035521	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1035346	1035521	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1035522	1035721	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1035722	1035797	1	+	1	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1035722	1035797	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1035798	1035927	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1035928	1036056	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1035928	1036056	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1036057	1036143	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1036144	1036263	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1036144	1036263	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1036264	1036411	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1036412	1036480	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1036412	1036480	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1036481	1036666	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1036667	1036748	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1036667	1036748	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1036749	1036828	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1036829	1036923	1	+	2	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1036829	1036923	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1036924	1037007	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1037008	1037072	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1037008	1037072	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1037073	1037159	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1037160	1037358	1	+	1	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1037160	1037358	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1037359	1037473	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1037474	1037668	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1037474	1037668	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1037669	1037838	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1037839	1037933	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1037839	1037933	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1037934	1038024	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1038025	1038160	1	+	1	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1038025	1038160	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1038161	1038238	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1038239	1038456	1	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1038239	1038456	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1038457	1038592	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1038593	1038720	1	+	1	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1038593	1038720	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	intron	1038721	1038812	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	CDS	1038813	1039261	1	+	2	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	exon	1038813	1039261	.	+	.	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
Phchi.S6	AUGUSTUS	stop_codon	1039262	1039264	.	+	0	transcript_id "Phchi.S6G014000.t1"; gene_id "Phchi.S6G014000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15267.t1 is derived from g13735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18033621	18035333	.	-	.	Phchi.S3G258600
Phchi.S3	AUGUSTUS	transcript	18033621	18035333	.	-	.	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	stop_codon	18033618	18033620	.	-	0	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	CDS	18033621	18034685	1	-	0	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	exon	18033621	18034685	.	-	.	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	intron	18034686	18034797	.	-	.	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	CDS	18034798	18034971	1	-	0	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	exon	18034798	18034971	.	-	.	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	intron	18034972	18035126	.	-	.	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	CDS	18035127	18035333	0.99	-	0	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	exon	18035127	18035333	.	-	.	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
Phchi.S3	AUGUSTUS	start_codon	18035331	18035333	.	-	0	transcript_id "Phchi.S3G258600.t1"; gene_id "Phchi.S3G258600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12744.t1 is derived from g11209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1551278	1551520	.	+	.	Phchi.S3G006300
Phchi.S3	AUGUSTUS	transcript	1551278	1551520	.	+	.	transcript_id "Phchi.S3G006300.t1"; gene_id "Phchi.S3G006300"
Phchi.S3	AUGUSTUS	start_codon	1551278	1551280	.	+	0	transcript_id "Phchi.S3G006300.t1"; gene_id "Phchi.S3G006300"
Phchi.S3	AUGUSTUS	CDS	1551278	1551520	0.58	+	0	transcript_id "Phchi.S3G006300.t1"; gene_id "Phchi.S3G006300"
Phchi.S3	AUGUSTUS	exon	1551278	1551520	.	+	.	transcript_id "Phchi.S3G006300.t1"; gene_id "Phchi.S3G006300"
Phchi.S3	AUGUSTUS	stop_codon	1551521	1551523	.	+	0	transcript_id "Phchi.S3G006300.t1"; gene_id "Phchi.S3G006300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1578.t1 is derived from g8497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1854773	1855675	.	+	.	Phchi.S5G018700
Phchi.S5	AUGUSTUS	transcript	1854773	1855675	.	+	.	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	start_codon	1854773	1854775	.	+	0	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	CDS	1854773	1855305	0.38	+	0	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	exon	1854773	1855305	.	+	.	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	intron	1855306	1855381	.	+	.	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	CDS	1855382	1855411	0.57	+	1	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	exon	1855382	1855411	.	+	.	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	intron	1855412	1855584	.	+	.	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	CDS	1855585	1855675	1	+	1	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	exon	1855585	1855675	.	+	.	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
Phchi.S5	AUGUSTUS	stop_codon	1855676	1855678	.	+	0	transcript_id "Phchi.S5G018700.t1"; gene_id "Phchi.S5G018700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11488.t1 is derived from g15538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6622068	6623099	.	-	.	Phchi.S4G107000
Phchi.S4	AUGUSTUS	transcript	6622068	6623099	.	-	.	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	stop_codon	6622065	6622067	.	-	0	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	CDS	6622068	6622251	0.99	-	1	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	exon	6622068	6622251	.	-	.	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	intron	6622252	6622752	.	-	.	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	CDS	6622753	6623099	0.94	-	0	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	exon	6622753	6623099	.	-	.	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
Phchi.S4	AUGUSTUS	start_codon	6623097	6623099	.	-	0	transcript_id "Phchi.S4G107000.t1"; gene_id "Phchi.S4G107000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11513.t1 is derived from g15563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6853916	6854741	.	-	.	Phchi.S4G109500
Phchi.S4	AUGUSTUS	transcript	6853916	6854741	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	stop_codon	6853913	6853915	.	-	0	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	CDS	6853916	6853920	0.98	-	2	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	exon	6853916	6853920	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	intron	6853921	6854058	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	CDS	6854059	6854134	0.98	-	0	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	exon	6854059	6854134	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	intron	6854135	6854241	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	CDS	6854242	6854381	0.98	-	2	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	exon	6854242	6854381	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	intron	6854382	6854466	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	CDS	6854467	6854604	1	-	2	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	exon	6854467	6854604	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	intron	6854605	6854677	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	CDS	6854678	6854741	0.88	-	0	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	exon	6854678	6854741	.	-	.	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
Phchi.S4	AUGUSTUS	start_codon	6854739	6854741	.	-	0	transcript_id "Phchi.S4G109500.t1"; gene_id "Phchi.S4G109500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg128.t1 is derived from g9910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	705689	707352	.	+	.	Phchi.S6G008700
Phchi.S6	AUGUSTUS	transcript	705689	707352	.	+	.	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	start_codon	705689	705691	.	+	0	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	CDS	705689	706963	0.96	+	0	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	exon	705689	706963	.	+	.	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	intron	706964	707052	.	+	.	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	CDS	707053	707352	0.93	+	0	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	exon	707053	707352	.	+	.	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
Phchi.S6	AUGUSTUS	stop_codon	707353	707355	.	+	0	transcript_id "Phchi.S6G008700.t1"; gene_id "Phchi.S6G008700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8498.t1 is derived from g5673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36257617	36258543	.	+	.	Phchi.S1G565700
Phchi.S1	AUGUSTUS	transcript	36257617	36258543	.	+	.	transcript_id "Phchi.S1G565700.t1"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	start_codon	36257617	36257619	.	+	0	transcript_id "Phchi.S1G565700.t1"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	CDS	36257617	36258543	0.88	+	0	transcript_id "Phchi.S1G565700.t1"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	exon	36257617	36258543	.	+	.	transcript_id "Phchi.S1G565700.t1"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	stop_codon	36258544	36258546	.	+	0	transcript_id "Phchi.S1G565700.t1"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	transcript	36257617	36258079	.	+	.	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	start_codon	36257617	36257619	.	+	0	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	CDS	36257617	36258009	0.39	+	0	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	exon	36257617	36258009	.	+	.	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	intron	36258010	36258067	.	+	.	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	CDS	36258068	36258079	0.43	+	0	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	exon	36258068	36258079	.	+	.	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
Phchi.S1	AUGUSTUS	stop_codon	36258080	36258082	.	+	0	transcript_id "Phchi.S1G565700.t2"; gene_id "Phchi.S1G565700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10927.t1 is derived from g14977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3014212	3016261	.	-	.	Phchi.S4G050900
Phchi.S4	AUGUSTUS	transcript	3014212	3016261	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	stop_codon	3014209	3014211	.	-	0	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3014212	3014318	0.98	-	2	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3014212	3014318	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3014319	3014417	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3014418	3014710	1	-	1	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3014418	3014710	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3014711	3014794	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3014795	3014838	1	-	0	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3014795	3014838	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3014839	3014940	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3014941	3015055	1	-	1	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3014941	3015055	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3015056	3015133	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3015134	3015274	1	-	1	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3015134	3015274	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3015275	3015363	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3015364	3015440	1	-	0	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3015364	3015440	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3015441	3015538	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3015539	3015568	1	-	0	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3015539	3015568	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3015569	3015678	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3015679	3015802	1	-	1	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3015679	3015802	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3015803	3015953	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3015954	3016002	1	-	2	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3015954	3016002	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	intron	3016003	3016176	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	CDS	3016177	3016261	1	-	0	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	exon	3016177	3016261	.	-	.	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
Phchi.S4	AUGUSTUS	start_codon	3016259	3016261	.	-	0	transcript_id "Phchi.S4G050900.t1"; gene_id "Phchi.S4G050900"
# This transcript jg13417.t2 is derived from g11883.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13418.t1 is derived from g11884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6609860	6611444	.	+	.	Phchi.S3G073700
Phchi.S3	AUGUSTUS	transcript	6609860	6611444	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	start_codon	6609860	6609862	.	+	0	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6609860	6609891	0.47	+	0	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6609860	6609891	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6609892	6609969	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6609970	6610027	1	+	1	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6609970	6610027	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610028	6610107	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6610108	6610216	0.95	+	0	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6610108	6610216	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610217	6610328	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6610329	6610476	1	+	2	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6610329	6610476	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610477	6610579	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6610580	6610631	1	+	1	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6610580	6610631	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610632	6610778	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6610779	6610934	1	+	0	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6610779	6610934	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610935	6611085	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6611086	6611197	0.77	+	0	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6611086	6611197	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6611198	6611298	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6611299	6611444	0.72	+	2	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6611299	6611444	.	+	.	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	stop_codon	6611445	6611447	.	+	0	transcript_id "Phchi.S3G073700.t1"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	transcript	6610587	6611444	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	start_codon	6610587	6610589	.	+	0	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6610587	6610631	0.52	+	0	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6610587	6610631	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610632	6610778	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6610779	6610934	1	+	0	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6610779	6610934	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6610935	6611085	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6611086	6611197	0.86	+	0	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6611086	6611197	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	intron	6611198	6611298	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	CDS	6611299	6611444	0.75	+	2	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	exon	6611299	6611444	.	+	.	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
Phchi.S3	AUGUSTUS	stop_codon	6611445	6611447	.	+	0	transcript_id "Phchi.S3G073700.t2"; gene_id "Phchi.S3G073700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1032.t1 is derived from g10815.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7219283	7222317	.	-	.	Phchi.S6G099100
Phchi.S6	AUGUSTUS	transcript	7219283	7222317	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	stop_codon	7219280	7219282	.	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7219283	7219408	0.8	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7219283	7219408	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7219409	7219851	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7219852	7220039	1	-	2	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7219852	7220039	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7220040	7220160	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7220161	7220221	1	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7220161	7220221	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7220222	7220358	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7220359	7220436	1	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7220359	7220436	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7220437	7220530	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7220531	7220626	1	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7220531	7220626	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7220627	7220815	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7220816	7220942	1	-	1	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7220816	7220942	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7220943	7221062	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7221063	7221285	0.95	-	2	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7221063	7221285	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7221286	7221385	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7221386	7221580	1	-	2	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7221386	7221580	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7221581	7221674	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7221675	7222086	1	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7221675	7222086	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	intron	7222087	7222173	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	CDS	7222174	7222317	0.73	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	exon	7222174	7222317	.	-	.	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
Phchi.S6	AUGUSTUS	start_codon	7222315	7222317	.	-	0	transcript_id "Phchi.S6G099100.t1"; gene_id "Phchi.S6G099100"
# This transcript jg8396.t2 is derived from g5571.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8396.t3 is derived from g5571.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8397.t1 is derived from g5572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35743771	35744712	.	+	.	Phchi.S1G555600
Phchi.S1	AUGUSTUS	transcript	35743771	35744712	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	start_codon	35743771	35743773	.	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	CDS	35743771	35743896	0.98	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	exon	35743771	35743896	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	intron	35743897	35743982	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	CDS	35743983	35744030	1	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	exon	35743983	35744030	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	intron	35744031	35744124	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	CDS	35744125	35744187	1	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	exon	35744125	35744187	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	intron	35744188	35744285	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	CDS	35744286	35744339	1	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	exon	35744286	35744339	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	intron	35744340	35744417	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	CDS	35744418	35744504	1	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	exon	35744418	35744504	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	intron	35744505	35744589	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	CDS	35744590	35744712	0.99	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	exon	35744590	35744712	.	+	.	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
Phchi.S1	AUGUSTUS	stop_codon	35744713	35744715	.	+	0	transcript_id "Phchi.S1G555600.t1"; gene_id "Phchi.S1G555600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1550.t1 is derived from g8469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1714159	1716841	.	-	.	Phchi.S5G015900
Phchi.S5	AUGUSTUS	transcript	1714159	1716841	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	stop_codon	1714156	1714158	.	-	0	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	CDS	1714159	1714278	0.95	-	0	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	exon	1714159	1714278	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	intron	1714279	1714382	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	CDS	1714383	1716023	0.94	-	0	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	exon	1714383	1716023	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	intron	1716024	1716162	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	CDS	1716163	1716404	0.99	-	2	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	exon	1716163	1716404	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	intron	1716405	1716576	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	CDS	1716577	1716841	0.95	-	0	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	exon	1716577	1716841	.	-	.	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
Phchi.S5	AUGUSTUS	start_codon	1716839	1716841	.	-	0	transcript_id "Phchi.S5G015900.t1"; gene_id "Phchi.S5G015900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8137.t1 is derived from g5312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33820793	33821217	.	+	.	Phchi.S1G529600
Phchi.S1	AUGUSTUS	transcript	33820793	33821217	.	+	.	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	start_codon	33820793	33820795	.	+	0	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	CDS	33820793	33820822	0.97	+	0	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	exon	33820793	33820822	.	+	.	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	intron	33820823	33820917	.	+	.	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	CDS	33820918	33821217	0.89	+	0	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	exon	33820918	33821217	.	+	.	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
Phchi.S1	AUGUSTUS	stop_codon	33821218	33821220	.	+	0	transcript_id "Phchi.S1G529600.t1"; gene_id "Phchi.S1G529600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12171.t1 is derived from g7847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5845228	5850743	.	+	.	Phchi.S2G025100
Phchi.S2	AUGUSTUS	transcript	5845228	5850743	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	start_codon	5845228	5845230	.	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5845228	5845402	0.85	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5845228	5845402	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5845403	5845504	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5845505	5845554	0.99	+	2	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5845505	5845554	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5845555	5845794	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5845795	5846002	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5845795	5846002	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5846003	5846081	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5846082	5846207	1	+	2	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5846082	5846207	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5846208	5846369	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5846370	5846468	1	+	2	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5846370	5846468	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5846469	5846697	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5846698	5846852	1	+	2	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5846698	5846852	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5846853	5846989	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5846990	5847302	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5846990	5847302	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5847303	5847381	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5847382	5847488	1	+	2	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5847382	5847488	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5847489	5847637	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5847638	5847889	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5847638	5847889	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5847890	5847985	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5847986	5848114	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5847986	5848114	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5848115	5848214	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5848215	5848283	0.89	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5848215	5848283	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5848284	5848402	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5848403	5848498	0.98	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5848403	5848498	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5848499	5848825	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5848826	5848930	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5848826	5848930	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5848931	5849191	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5849192	5849299	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5849192	5849299	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5849300	5849396	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5849397	5849471	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5849397	5849471	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5849472	5849611	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5849612	5849719	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5849612	5849719	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5849720	5849903	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5849904	5850083	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5849904	5850083	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5850084	5850408	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5850409	5850480	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5850409	5850480	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	intron	5850481	5850665	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	CDS	5850666	5850743	1	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	exon	5850666	5850743	.	+	.	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
Phchi.S2	AUGUSTUS	stop_codon	5850744	5850746	.	+	0	transcript_id "Phchi.S2G025100.t1"; gene_id "Phchi.S2G025100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3808.t1 is derived from g977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5823757	5824276	.	+	.	Phchi.S1G096700
Phchi.S1	AUGUSTUS	transcript	5823757	5824276	.	+	.	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	start_codon	5823757	5823759	.	+	0	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	CDS	5823757	5824110	0.57	+	0	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	exon	5823757	5824110	.	+	.	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	intron	5824111	5824210	.	+	.	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	CDS	5824211	5824276	0.95	+	0	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	exon	5824211	5824276	.	+	.	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
Phchi.S1	AUGUSTUS	stop_codon	5824277	5824279	.	+	0	transcript_id "Phchi.S1G096700.t1"; gene_id "Phchi.S1G096700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13353.t1 is derived from g11819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6291523	6293099	.	+	.	Phchi.S3G067200
Phchi.S3	AUGUSTUS	transcript	6291523	6293099	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	start_codon	6291523	6291525	.	+	0	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6291523	6291534	0.36	+	0	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6291523	6291534	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	intron	6291535	6291701	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6291702	6292187	0.97	+	0	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6291702	6292187	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	intron	6292188	6292372	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6292373	6292450	1	+	0	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6292373	6292450	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	intron	6292451	6292549	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6292550	6292584	1	+	0	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6292550	6292584	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	intron	6292585	6292707	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6292708	6292763	1	+	1	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6292708	6292763	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	intron	6292764	6292843	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6292844	6292954	1	+	2	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6292844	6292954	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	intron	6292955	6293037	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	CDS	6293038	6293099	0.99	+	2	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	exon	6293038	6293099	.	+	.	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
Phchi.S3	AUGUSTUS	stop_codon	6293100	6293102	.	+	0	transcript_id "Phchi.S3G067200.t1"; gene_id "Phchi.S3G067200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2016.t1 is derived from g8936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4467471	4468790	.	+	.	Phchi.S5G062500
Phchi.S5	AUGUSTUS	transcript	4467471	4468790	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	start_codon	4467471	4467473	.	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4467471	4467553	0.72	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4467471	4467553	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	intron	4467554	4467819	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4467820	4467843	1	+	1	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4467820	4467843	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	intron	4467844	4467961	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4467962	4468049	0.74	+	1	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4467962	4468049	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	intron	4468050	4468162	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4468163	4468255	1	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4468163	4468255	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	intron	4468256	4468378	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4468379	4468411	1	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4468379	4468411	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	intron	4468412	4468502	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4468503	4468559	1	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4468503	4468559	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	intron	4468560	4468682	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	CDS	4468683	4468790	0.98	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	exon	4468683	4468790	.	+	.	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
Phchi.S5	AUGUSTUS	stop_codon	4468791	4468793	.	+	0	transcript_id "Phchi.S5G062500.t1"; gene_id "Phchi.S5G062500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4251.t1 is derived from g1420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9170277	9171807	.	-	.	Phchi.S1G141000
Phchi.S1	AUGUSTUS	transcript	9170277	9171807	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	stop_codon	9170274	9170276	.	-	0	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	CDS	9170277	9170406	0.71	-	1	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	exon	9170277	9170406	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	intron	9170407	9170580	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	CDS	9170581	9170711	1	-	0	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	exon	9170581	9170711	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	intron	9170712	9170797	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	CDS	9170798	9171152	0.96	-	1	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	exon	9170798	9171152	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	intron	9171153	9171243	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	CDS	9171244	9171471	1	-	1	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	exon	9171244	9171471	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	intron	9171472	9171565	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	CDS	9171566	9171807	0.86	-	0	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	exon	9171566	9171807	.	-	.	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
Phchi.S1	AUGUSTUS	start_codon	9171805	9171807	.	-	0	transcript_id "Phchi.S1G141000.t1"; gene_id "Phchi.S1G141000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg882.t1 is derived from g10664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6255610	6256651	.	+	.	Phchi.S6G084100
Phchi.S6	AUGUSTUS	transcript	6255610	6256651	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	start_codon	6255610	6255612	.	+	0	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	CDS	6255610	6255727	0.71	+	0	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	exon	6255610	6255727	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	intron	6255728	6255812	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	CDS	6255813	6255918	1	+	2	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	exon	6255813	6255918	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	intron	6255919	6256000	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	CDS	6256001	6256100	1	+	1	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	exon	6256001	6256100	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	intron	6256101	6256181	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	CDS	6256182	6256227	0.66	+	0	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	exon	6256182	6256227	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	intron	6256228	6256361	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	CDS	6256362	6256434	0.52	+	2	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	exon	6256362	6256434	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	intron	6256435	6256608	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	CDS	6256609	6256651	1	+	1	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	exon	6256609	6256651	.	+	.	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
Phchi.S6	AUGUSTUS	stop_codon	6256652	6256654	.	+	0	transcript_id "Phchi.S6G084100.t1"; gene_id "Phchi.S6G084100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9083.t1 is derived from g6258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39770458	39771809	.	+	.	Phchi.S1G624200
Phchi.S1	AUGUSTUS	transcript	39770750	39771809	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	start_codon	39770750	39770752	.	+	0	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39770750	39770783	0.88	+	0	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39770750	39770783	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39770784	39771090	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771091	39771148	1	+	2	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771091	39771148	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39771149	39771285	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771286	39771434	1	+	1	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771286	39771434	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39771435	39771756	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771757	39771809	1	+	2	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771757	39771809	.	+	.	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	stop_codon	39771810	39771812	.	+	0	transcript_id "Phchi.S1G624200.t1"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	transcript	39770676	39771809	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	start_codon	39770676	39770678	.	+	0	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39770676	39770783	0.79	+	0	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39770676	39770783	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39770784	39771090	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771091	39771137	1	+	0	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771091	39771137	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39771138	39771285	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771286	39771434	1	+	1	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771286	39771434	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39771435	39771756	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771757	39771809	1	+	2	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771757	39771809	.	+	.	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	stop_codon	39771810	39771812	.	+	0	transcript_id "Phchi.S1G624200.t2"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	transcript	39770458	39771809	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	start_codon	39770458	39770460	.	+	0	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39770458	39770512	0.61	+	0	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39770458	39770512	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39770513	39771090	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771091	39771148	1	+	2	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771091	39771148	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39771149	39771285	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771286	39771434	1	+	1	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771286	39771434	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	intron	39771435	39771756	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	CDS	39771757	39771809	1	+	2	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	exon	39771757	39771809	.	+	.	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
Phchi.S1	AUGUSTUS	stop_codon	39771810	39771812	.	+	0	transcript_id "Phchi.S1G624200.t3"; gene_id "Phchi.S1G624200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13168.t1 is derived from g11633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4471575	4477685	.	-	.	Phchi.S3G048700
Phchi.S3	AUGUSTUS	transcript	4471575	4477685	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	stop_codon	4471572	4471574	.	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4471575	4471811	0.95	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4471575	4471811	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4471812	4471923	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4471924	4472059	1	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4471924	4472059	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4472060	4472218	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4472219	4472349	1	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4472219	4472349	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4472350	4472440	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4472441	4472795	0.98	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4472441	4472795	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4472796	4472879	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4472880	4473107	1	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4472880	4473107	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4473108	4473191	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4473192	4473546	0.55	-	2	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4473192	4473546	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4473547	4474158	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4474159	4474309	0.55	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4474159	4474309	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4474310	4474380	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4474381	4474591	1	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4474381	4474591	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4474592	4474690	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4474691	4474848	0.99	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4474691	4474848	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4474849	4474961	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4474962	4475048	0.97	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4474962	4475048	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4475049	4475134	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4475135	4475325	1	-	2	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4475135	4475325	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4475326	4475460	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4475461	4475636	1	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4475461	4475636	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4475637	4475727	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4475728	4475843	1	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4475728	4475843	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4475844	4475941	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4475942	4476488	1	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4475942	4476488	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4476489	4476667	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4476668	4477276	0.96	-	1	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4476668	4477276	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	intron	4477277	4477371	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	CDS	4477372	4477685	0.91	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	exon	4477372	4477685	.	-	.	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
Phchi.S3	AUGUSTUS	start_codon	4477683	4477685	.	-	0	transcript_id "Phchi.S3G048700.t1"; gene_id "Phchi.S3G048700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6321.t1 is derived from g3493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22250977	22251529	.	-	.	Phchi.S1G348000
Phchi.S1	AUGUSTUS	transcript	22250977	22251529	.	-	.	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	stop_codon	22250974	22250976	.	-	0	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	CDS	22250977	22251167	0.99	-	2	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	exon	22250977	22251167	.	-	.	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	intron	22251168	22251291	.	-	.	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	CDS	22251292	22251359	1	-	1	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	exon	22251292	22251359	.	-	.	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	intron	22251360	22251515	.	-	.	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	CDS	22251516	22251529	1	-	0	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	exon	22251516	22251529	.	-	.	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
Phchi.S1	AUGUSTUS	start_codon	22251527	22251529	.	-	0	transcript_id "Phchi.S1G348000.t1"; gene_id "Phchi.S1G348000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4483.t1 is derived from g1653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10716715	10720002	.	-	.	Phchi.S1G164200
Phchi.S1	AUGUSTUS	transcript	10716715	10720002	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	stop_codon	10716712	10716714	.	-	0	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	CDS	10716715	10717110	0.76	-	0	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	exon	10716715	10717110	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	intron	10717111	10717436	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	CDS	10717437	10718221	0.42	-	2	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	exon	10717437	10718221	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	intron	10718222	10718370	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	CDS	10718371	10718671	1	-	0	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	exon	10718371	10718671	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	intron	10718672	10718770	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	CDS	10718771	10719270	0.7	-	2	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	exon	10718771	10719270	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	intron	10719271	10719356	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	CDS	10719357	10720002	0.37	-	0	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	exon	10719357	10720002	.	-	.	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
Phchi.S1	AUGUSTUS	start_codon	10720000	10720002	.	-	0	transcript_id "Phchi.S1G164200.t1"; gene_id "Phchi.S1G164200"
# This transcript jg7211.t1 is derived from g4383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27646141	27646401	.	-	.	Phchi.S1G437000
Phchi.S1	AUGUSTUS	transcript	27646141	27646401	.	-	.	transcript_id "Phchi.S1G437000.t1"; gene_id "Phchi.S1G437000"
Phchi.S1	AUGUSTUS	stop_codon	27646138	27646140	.	-	0	transcript_id "Phchi.S1G437000.t1"; gene_id "Phchi.S1G437000"
Phchi.S1	AUGUSTUS	CDS	27646141	27646401	0.59	-	0	transcript_id "Phchi.S1G437000.t1"; gene_id "Phchi.S1G437000"
Phchi.S1	AUGUSTUS	exon	27646141	27646401	.	-	.	transcript_id "Phchi.S1G437000.t1"; gene_id "Phchi.S1G437000"
Phchi.S1	AUGUSTUS	start_codon	27646399	27646401	.	-	0	transcript_id "Phchi.S1G437000.t1"; gene_id "Phchi.S1G437000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10536.t1 is derived from g14586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	868230	869084	.	+	.	Phchi.S4G011800
Phchi.S4	AUGUSTUS	transcript	868230	869084	.	+	.	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	start_codon	868230	868232	.	+	0	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	CDS	868230	868305	0.82	+	0	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	exon	868230	868305	.	+	.	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	intron	868306	868713	.	+	.	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	CDS	868714	869084	1	+	2	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	exon	868714	869084	.	+	.	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
Phchi.S4	AUGUSTUS	stop_codon	869085	869087	.	+	0	transcript_id "Phchi.S4G011800.t1"; gene_id "Phchi.S4G011800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1731.t1 is derived from g8651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2753344	2754372	.	-	.	Phchi.S5G034000
Phchi.S5	AUGUSTUS	transcript	2753344	2754372	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	stop_codon	2753341	2753343	.	-	0	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	CDS	2753344	2753363	1	-	2	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	exon	2753344	2753363	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	intron	2753364	2753453	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	CDS	2753454	2753538	1	-	0	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	exon	2753454	2753538	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	intron	2753539	2753622	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	CDS	2753623	2753684	1	-	2	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	exon	2753623	2753684	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	intron	2753685	2753783	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	CDS	2753784	2753856	1	-	0	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	exon	2753784	2753856	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	intron	2753857	2753984	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	CDS	2753985	2754094	1	-	2	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	exon	2753985	2754094	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	intron	2754095	2754161	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	CDS	2754162	2754372	0.99	-	0	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	exon	2754162	2754372	.	-	.	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
Phchi.S5	AUGUSTUS	start_codon	2754370	2754372	.	-	0	transcript_id "Phchi.S5G034000.t1"; gene_id "Phchi.S5G034000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14746.t1 is derived from g13214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14511435	14518493	.	-	.	Phchi.S3G206500
Phchi.S3	AUGUSTUS	transcript	14511435	14518493	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	stop_codon	14511432	14511434	.	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14511435	14511617	0.98	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14511435	14511617	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14511618	14511731	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14511732	14511992	1	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14511732	14511992	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14511993	14512473	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14512474	14512689	1	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14512474	14512689	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14512690	14512785	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14512786	14513587	0.99	-	1	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14512786	14513587	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14513588	14513676	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14513677	14513729	0.8	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14513677	14513729	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14513730	14513826	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14513827	14513988	0.97	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14513827	14513988	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14513989	14514101	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14514102	14514380	0.97	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14514102	14514380	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14514381	14514513	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14514514	14514648	0.57	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14514514	14514648	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14514649	14514783	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14514784	14514888	0.45	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14514784	14514888	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14514889	14514968	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14514969	14515295	0.9	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14514969	14515295	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14515296	14515380	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14515381	14515682	0.97	-	2	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14515381	14515682	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14515683	14516131	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14516132	14516611	0.98	-	2	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14516132	14516611	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14516612	14516995	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14516996	14517611	0.53	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14516996	14517611	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14517612	14517708	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14517709	14517942	0.3	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14517709	14517942	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14517943	14518095	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14518096	14518274	0.34	-	2	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14518096	14518274	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	intron	14518275	14518372	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	CDS	14518373	14518493	0.97	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	exon	14518373	14518493	.	-	.	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
Phchi.S3	AUGUSTUS	start_codon	14518491	14518493	.	-	0	transcript_id "Phchi.S3G206500.t1"; gene_id "Phchi.S3G206500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11860.t1 is derived from g15912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8806197	8806542	.	-	.	Phchi.S4G144200
Phchi.S4	AUGUSTUS	transcript	8806197	8806542	.	-	.	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	stop_codon	8806194	8806196	.	-	0	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	CDS	8806197	8806332	1	-	1	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	exon	8806197	8806332	.	-	.	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	intron	8806333	8806471	.	-	.	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	CDS	8806472	8806542	0.56	-	0	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	exon	8806472	8806542	.	-	.	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
Phchi.S4	AUGUSTUS	start_codon	8806540	8806542	.	-	0	transcript_id "Phchi.S4G144200.t1"; gene_id "Phchi.S4G144200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13249.t1 is derived from g11714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4922277	4923415	.	+	.	Phchi.S3G056800
Phchi.S3	AUGUSTUS	transcript	4922277	4923415	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	start_codon	4922277	4922279	.	+	0	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	CDS	4922277	4922327	0.82	+	0	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	exon	4922277	4922327	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	intron	4922328	4922416	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	CDS	4922417	4922650	1	+	0	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	exon	4922417	4922650	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	intron	4922651	4922751	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	CDS	4922752	4922838	0.93	+	0	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	exon	4922752	4922838	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	intron	4922839	4922941	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	CDS	4922942	4923415	0.99	+	0	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	exon	4922942	4923415	.	+	.	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
Phchi.S3	AUGUSTUS	stop_codon	4923416	4923418	.	+	0	transcript_id "Phchi.S3G056800.t1"; gene_id "Phchi.S3G056800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14550.t1 is derived from g13018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13434257	13438044	.	-	.	Phchi.S3G186900
Phchi.S3	AUGUSTUS	transcript	13434257	13438044	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	stop_codon	13434254	13434256	.	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13434257	13434283	1	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13434257	13434283	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13434284	13434365	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13434366	13435168	1	-	2	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13434366	13435168	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13435169	13435250	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13435251	13435492	1	-	1	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13435251	13435492	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13435493	13435629	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13435630	13435763	1	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13435630	13435763	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13435764	13435849	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13435850	13435963	1	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13435850	13435963	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13435964	13436100	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13436101	13436196	1	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13436101	13436196	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13436197	13436336	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13436337	13436498	0.99	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13436337	13436498	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13436499	13436601	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13436602	13436650	0.99	-	1	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13436602	13436650	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13436651	13436916	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13436917	13436972	1	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13436917	13436972	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13436973	13437098	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13437099	13437178	1	-	2	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13437099	13437178	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13437179	13437275	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13437276	13437361	1	-	1	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13437276	13437361	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	intron	13437362	13437484	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	CDS	13437485	13438044	0.96	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	exon	13437485	13438044	.	-	.	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
Phchi.S3	AUGUSTUS	start_codon	13438042	13438044	.	-	0	transcript_id "Phchi.S3G186900.t1"; gene_id "Phchi.S3G186900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2642.t1 is derived from g9562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7921381	7922397	.	+	.	Phchi.S5G125100
Phchi.S5	AUGUSTUS	transcript	7921381	7922397	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	start_codon	7921381	7921383	.	+	0	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	CDS	7921381	7921803	0.4	+	0	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	exon	7921381	7921803	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	intron	7921804	7921945	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	CDS	7921946	7922132	0.73	+	0	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	exon	7921946	7922132	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	intron	7922133	7922229	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	CDS	7922230	7922274	0.44	+	2	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	exon	7922230	7922274	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	intron	7922275	7922356	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	CDS	7922357	7922397	1	+	2	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	exon	7922357	7922397	.	+	.	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
Phchi.S5	AUGUSTUS	stop_codon	7922398	7922400	.	+	0	transcript_id "Phchi.S5G125100.t1"; gene_id "Phchi.S5G125100"
# This transcript jg12188.t2 is derived from g7864.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12189.t1 is derived from g7865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6319146	6319664	.	+	.	Phchi.S2G026900
Phchi.S2	AUGUSTUS	transcript	6319146	6319664	.	+	.	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	start_codon	6319146	6319148	.	+	0	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	CDS	6319146	6319248	0.63	+	0	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	exon	6319146	6319248	.	+	.	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	intron	6319249	6319361	.	+	.	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	CDS	6319362	6319437	1	+	2	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	exon	6319362	6319437	.	+	.	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	intron	6319438	6319522	.	+	.	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	CDS	6319523	6319664	1	+	1	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	exon	6319523	6319664	.	+	.	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
Phchi.S2	AUGUSTUS	stop_codon	6319665	6319667	.	+	0	transcript_id "Phchi.S2G026900.t1"; gene_id "Phchi.S2G026900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14950.t1 is derived from g13418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15672893	15674158	.	-	.	Phchi.S3G226900
Phchi.S3	AUGUSTUS	transcript	15672893	15674158	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	stop_codon	15672890	15672892	.	-	0	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	CDS	15672893	15672928	0.68	-	0	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	exon	15672893	15672928	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	intron	15672929	15673224	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	CDS	15673225	15673306	1	-	1	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	exon	15673225	15673306	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	intron	15673307	15673406	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	CDS	15673407	15673504	1	-	0	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	exon	15673407	15673504	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	intron	15673505	15673722	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	CDS	15673723	15673803	1	-	0	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	exon	15673723	15673803	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	intron	15673804	15673911	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	CDS	15673912	15674003	1	-	2	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	exon	15673912	15674003	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	intron	15674004	15674142	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	CDS	15674143	15674158	0.47	-	0	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	exon	15674143	15674158	.	-	.	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
Phchi.S3	AUGUSTUS	start_codon	15674156	15674158	.	-	0	transcript_id "Phchi.S3G226900.t1"; gene_id "Phchi.S3G226900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5522.t1 is derived from g2692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17399758	17401012	.	-	.	Phchi.S1G268100
Phchi.S1	AUGUSTUS	transcript	17399758	17401012	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	stop_codon	17399755	17399757	.	-	0	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	CDS	17399758	17400006	0.97	-	0	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	exon	17399758	17400006	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	intron	17400007	17400122	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	CDS	17400123	17400282	0.67	-	1	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	exon	17400123	17400282	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	intron	17400283	17400402	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	CDS	17400403	17400417	0.97	-	1	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	exon	17400403	17400417	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	intron	17400418	17400515	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	CDS	17400516	17400643	0.56	-	0	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	exon	17400516	17400643	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	intron	17400644	17400817	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	CDS	17400818	17401012	0.39	-	0	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	exon	17400818	17401012	.	-	.	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
Phchi.S1	AUGUSTUS	start_codon	17401010	17401012	.	-	0	transcript_id "Phchi.S1G268100.t1"; gene_id "Phchi.S1G268100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg272.t1 is derived from g10054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1947308	1947903	.	+	.	Phchi.S6G023100
Phchi.S6	AUGUSTUS	transcript	1947308	1947903	.	+	.	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	start_codon	1947308	1947310	.	+	0	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	CDS	1947308	1947479	0.99	+	0	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	exon	1947308	1947479	.	+	.	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	intron	1947480	1947610	.	+	.	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	CDS	1947611	1947903	1	+	2	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	exon	1947611	1947903	.	+	.	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
Phchi.S6	AUGUSTUS	stop_codon	1947904	1947906	.	+	0	transcript_id "Phchi.S6G023100.t1"; gene_id "Phchi.S6G023100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1343.t1 is derived from g11126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9117769	9119577	.	-	.	Phchi.S6G130200
Phchi.S6	AUGUSTUS	transcript	9117769	9119577	.	-	.	transcript_id "Phchi.S6G130200.t1"; gene_id "Phchi.S6G130200"
Phchi.S6	AUGUSTUS	stop_codon	9117766	9117768	.	-	0	transcript_id "Phchi.S6G130200.t1"; gene_id "Phchi.S6G130200"
Phchi.S6	AUGUSTUS	CDS	9117769	9119577	0.86	-	0	transcript_id "Phchi.S6G130200.t1"; gene_id "Phchi.S6G130200"
Phchi.S6	AUGUSTUS	exon	9117769	9119577	.	-	.	transcript_id "Phchi.S6G130200.t1"; gene_id "Phchi.S6G130200"
Phchi.S6	AUGUSTUS	start_codon	9119575	9119577	.	-	0	transcript_id "Phchi.S6G130200.t1"; gene_id "Phchi.S6G130200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9465.t1 is derived from g6641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41581229	41583169	.	-	.	Phchi.S1G662400
Phchi.S1	AUGUSTUS	transcript	41581229	41583169	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	stop_codon	41581226	41581228	.	-	0	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	CDS	41581229	41581504	0.4	-	0	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	exon	41581229	41581504	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	intron	41581505	41581587	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	CDS	41581588	41581641	1	-	0	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	exon	41581588	41581641	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	intron	41581642	41581724	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	CDS	41581725	41582802	0.99	-	1	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	exon	41581725	41582802	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	intron	41582803	41582891	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	CDS	41582892	41583169	0.47	-	0	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	exon	41582892	41583169	.	-	.	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
Phchi.S1	AUGUSTUS	start_codon	41583167	41583169	.	-	0	transcript_id "Phchi.S1G662400.t1"; gene_id "Phchi.S1G662400"
# This transcript jg11720.t2 is derived from g15772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11721.t1 is derived from g15773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7839176	7840634	.	+	.	Phchi.S4G130300
Phchi.S4	AUGUSTUS	transcript	7839176	7840634	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	start_codon	7839176	7839178	.	+	0	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	CDS	7839176	7839445	0.9	+	0	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	exon	7839176	7839445	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	intron	7839446	7839528	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	CDS	7839529	7839756	1	+	0	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	exon	7839529	7839756	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	intron	7839757	7839844	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	CDS	7839845	7840102	1	+	0	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	exon	7839845	7840102	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	intron	7840103	7840194	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	CDS	7840195	7840291	1	+	0	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	exon	7840195	7840291	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	intron	7840292	7840380	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	CDS	7840381	7840425	0.98	+	2	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	exon	7840381	7840425	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	intron	7840426	7840515	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	CDS	7840516	7840634	0.97	+	2	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	exon	7840516	7840634	.	+	.	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
Phchi.S4	AUGUSTUS	stop_codon	7840635	7840637	.	+	0	transcript_id "Phchi.S4G130300.t1"; gene_id "Phchi.S4G130300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3201.t1 is derived from g370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2224854	2225925	.	-	.	Phchi.S1G036000
Phchi.S1	AUGUSTUS	transcript	2224854	2225925	.	-	.	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	stop_codon	2224851	2224853	.	-	0	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	CDS	2224854	2225282	1	-	0	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	exon	2224854	2225282	.	-	.	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	intron	2225283	2225379	.	-	.	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	CDS	2225380	2225925	0.59	-	0	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	exon	2225380	2225925	.	-	.	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
Phchi.S1	AUGUSTUS	start_codon	2225923	2225925	.	-	0	transcript_id "Phchi.S1G036000.t1"; gene_id "Phchi.S1G036000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5584.t1 is derived from g2754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17741842	17743738	.	+	.	Phchi.S1G274300
Phchi.S1	AUGUSTUS	transcript	17741842	17743738	.	+	.	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	start_codon	17741842	17741844	.	+	0	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	CDS	17741842	17742135	0.99	+	0	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	exon	17741842	17742135	.	+	.	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	intron	17742136	17742418	.	+	.	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	CDS	17742419	17742436	1	+	0	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	exon	17742419	17742436	.	+	.	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	intron	17742437	17742487	.	+	.	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	CDS	17742488	17743738	0.85	+	0	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	exon	17742488	17743738	.	+	.	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
Phchi.S1	AUGUSTUS	stop_codon	17743739	17743741	.	+	0	transcript_id "Phchi.S1G274300.t1"; gene_id "Phchi.S1G274300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6359.t1 is derived from g3531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22551224	22553872	.	+	.	Phchi.S1G351800
Phchi.S1	AUGUSTUS	transcript	22551224	22553872	.	+	.	transcript_id "Phchi.S1G351800.t1"; gene_id "Phchi.S1G351800"
Phchi.S1	AUGUSTUS	start_codon	22551224	22551226	.	+	0	transcript_id "Phchi.S1G351800.t1"; gene_id "Phchi.S1G351800"
Phchi.S1	AUGUSTUS	CDS	22551224	22553872	1	+	0	transcript_id "Phchi.S1G351800.t1"; gene_id "Phchi.S1G351800"
Phchi.S1	AUGUSTUS	exon	22551224	22553872	.	+	.	transcript_id "Phchi.S1G351800.t1"; gene_id "Phchi.S1G351800"
Phchi.S1	AUGUSTUS	stop_codon	22553873	22553875	.	+	0	transcript_id "Phchi.S1G351800.t1"; gene_id "Phchi.S1G351800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5374.t1 is derived from g2544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16554811	16555257	.	-	.	Phchi.S1G253300
Phchi.S1	AUGUSTUS	transcript	16554811	16555257	.	-	.	transcript_id "Phchi.S1G253300.t1"; gene_id "Phchi.S1G253300"
Phchi.S1	AUGUSTUS	stop_codon	16554808	16554810	.	-	0	transcript_id "Phchi.S1G253300.t1"; gene_id "Phchi.S1G253300"
Phchi.S1	AUGUSTUS	CDS	16554811	16555257	0.63	-	0	transcript_id "Phchi.S1G253300.t1"; gene_id "Phchi.S1G253300"
Phchi.S1	AUGUSTUS	exon	16554811	16555257	.	-	.	transcript_id "Phchi.S1G253300.t1"; gene_id "Phchi.S1G253300"
Phchi.S1	AUGUSTUS	start_codon	16555255	16555257	.	-	0	transcript_id "Phchi.S1G253300.t1"; gene_id "Phchi.S1G253300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1431.t1 is derived from g8350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	811664	813520	.	-	.	Phchi.S5G004000
Phchi.S5	AUGUSTUS	transcript	811664	813520	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	stop_codon	811661	811663	.	-	0	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	CDS	811664	811775	0.99	-	1	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	exon	811664	811775	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	intron	811776	811915	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	CDS	811916	811943	0.99	-	2	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	exon	811916	811943	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	intron	811944	812046	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	CDS	812047	813303	0.99	-	2	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	exon	812047	813303	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	intron	813304	813438	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	CDS	813439	813520	1	-	0	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	exon	813439	813520	.	-	.	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
Phchi.S5	AUGUSTUS	start_codon	813518	813520	.	-	0	transcript_id "Phchi.S5G004000.t1"; gene_id "Phchi.S5G004000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10237.t1 is derived from g7413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46511983	46513515	.	+	.	Phchi.S1G739600
Phchi.S1	AUGUSTUS	transcript	46511983	46513515	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	start_codon	46511983	46511985	.	+	0	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	CDS	46511983	46512451	0.83	+	0	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	exon	46511983	46512451	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	intron	46512452	46512566	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	CDS	46512567	46512761	0.93	+	2	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	exon	46512567	46512761	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	intron	46512762	46512931	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	CDS	46512932	46513186	1	+	2	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	exon	46512932	46513186	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	intron	46513187	46513306	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	CDS	46513307	46513515	1	+	2	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	exon	46513307	46513515	.	+	.	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
Phchi.S1	AUGUSTUS	stop_codon	46513516	46513518	.	+	0	transcript_id "Phchi.S1G739600.t1"; gene_id "Phchi.S1G739600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14688.t1 is derived from g13156.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14178742	14181253	.	-	.	Phchi.S3G200700
Phchi.S3	AUGUSTUS	transcript	14178742	14181253	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	stop_codon	14178739	14178741	.	-	0	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14178742	14179091	0.37	-	2	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14178742	14179091	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179092	14179237	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14179238	14179426	1	-	2	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14179238	14179426	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179427	14179569	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14179570	14179669	1	-	0	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14179570	14179669	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179670	14179833	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14179834	14179949	1	-	2	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14179834	14179949	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179950	14180115	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14180116	14180203	1	-	0	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14180116	14180203	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14180204	14180425	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14180426	14180667	1	-	2	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14180426	14180667	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14180668	14180900	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14180901	14180981	1	-	2	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14180901	14180981	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14180982	14181198	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14181199	14181253	1	-	0	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14181199	14181253	.	-	.	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	start_codon	14181251	14181253	.	-	0	transcript_id "Phchi.S3G200700.t1"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	transcript	14178742	14181253	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	stop_codon	14178739	14178741	.	-	0	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14178742	14179091	0.44	-	2	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14178742	14179091	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179092	14179237	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14179238	14179426	1	-	2	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14179238	14179426	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179427	14179569	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14179570	14179669	1	-	0	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14179570	14179669	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179670	14179833	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14179834	14179949	1	-	2	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14179834	14179949	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14179950	14180115	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14180116	14180203	1	-	0	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14180116	14180203	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14180204	14180425	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14180426	14180667	0.99	-	2	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14180426	14180667	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14180668	14180900	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14180901	14180981	1	-	2	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14180901	14180981	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	intron	14180982	14181120	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	CDS	14181121	14181253	0.96	-	0	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	exon	14181121	14181253	.	-	.	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
Phchi.S3	AUGUSTUS	start_codon	14181251	14181253	.	-	0	transcript_id "Phchi.S3G200700.t2"; gene_id "Phchi.S3G200700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10208.t1 is derived from g7384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46388357	46389703	.	+	.	Phchi.S1G736700
Phchi.S1	AUGUSTUS	transcript	46388357	46389703	.	+	.	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	start_codon	46388357	46388359	.	+	0	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	CDS	46388357	46388797	0.95	+	0	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	exon	46388357	46388797	.	+	.	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	intron	46388798	46388962	.	+	.	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	CDS	46388963	46389703	1	+	0	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	exon	46388963	46389703	.	+	.	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
Phchi.S1	AUGUSTUS	stop_codon	46389704	46389706	.	+	0	transcript_id "Phchi.S1G736700.t1"; gene_id "Phchi.S1G736700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13871.t1 is derived from g12338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9396515	9401602	.	-	.	Phchi.S3G119000
Phchi.S3	AUGUSTUS	transcript	9396515	9401602	.	-	.	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	stop_codon	9396512	9396514	.	-	0	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	CDS	9396515	9401176	0.99	-	0	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	exon	9396515	9401176	.	-	.	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	intron	9401177	9401259	.	-	.	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	CDS	9401260	9401360	0.98	-	2	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	exon	9401260	9401360	.	-	.	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	intron	9401361	9401532	.	-	.	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	CDS	9401533	9401602	0.83	-	0	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	exon	9401533	9401602	.	-	.	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
Phchi.S3	AUGUSTUS	start_codon	9401600	9401602	.	-	0	transcript_id "Phchi.S3G119000.t1"; gene_id "Phchi.S3G119000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5535.t1 is derived from g2705.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17441140	17447797	.	-	.	Phchi.S1G269400
Phchi.S1	AUGUSTUS	transcript	17441140	17447797	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	stop_codon	17441137	17441139	.	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441140	17441243	0.94	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441140	17441243	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17441244	17441318	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441319	17441470	1	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441319	17441470	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17441471	17441549	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441550	17441722	1	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441550	17441722	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17441723	17441817	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441818	17442079	0.99	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441818	17442079	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442080	17442261	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442262	17442451	1	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442262	17442451	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442452	17442536	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442537	17442614	1	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442537	17442614	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442615	17442746	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442747	17442804	1	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442747	17442804	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442805	17442949	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442950	17443071	1	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442950	17443071	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17443072	17443334	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17443335	17443562	0.97	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17443335	17443562	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17443563	17443738	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17443739	17443857	0.92	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17443739	17443857	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17443858	17443995	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17443996	17444203	1	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17443996	17444203	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17444204	17444445	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17444446	17444660	1	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17444446	17444660	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17444661	17444739	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17444740	17445014	1	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17444740	17445014	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445015	17445110	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445111	17445234	0.99	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445111	17445234	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445235	17445340	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445341	17445460	1	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445341	17445460	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445461	17445551	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445552	17445667	0.99	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445552	17445667	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445668	17445772	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445773	17445854	1	-	1	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445773	17445854	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445855	17445986	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445987	17446141	1	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445987	17446141	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446142	17446226	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17446227	17446372	1	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17446227	17446372	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446373	17446468	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17446469	17446655	1	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17446469	17446655	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446656	17446777	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17446778	17446950	0.94	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17446778	17446950	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446951	17447061	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17447062	17447115	0.94	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17447062	17447115	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17447116	17447202	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17447203	17447271	1	-	2	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17447203	17447271	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17447272	17447469	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17447470	17447797	0.97	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17447470	17447797	.	-	.	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	start_codon	17447795	17447797	.	-	0	transcript_id "Phchi.S1G269400.t1"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	transcript	17441140	17447797	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	stop_codon	17441137	17441139	.	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441140	17441243	0.86	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441140	17441243	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17441244	17441318	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441319	17441470	1	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441319	17441470	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17441471	17441549	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441550	17441722	1	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441550	17441722	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17441723	17441817	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17441818	17442079	0.99	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17441818	17442079	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442080	17442261	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442262	17442451	1	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442262	17442451	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442452	17442536	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442537	17442614	1	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442537	17442614	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442615	17442746	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442747	17442804	1	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442747	17442804	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17442805	17442949	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17442950	17443071	1	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17442950	17443071	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17443072	17443334	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17443335	17443556	0.52	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17443335	17443556	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17443557	17443738	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17443739	17443857	0.49	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17443739	17443857	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17443858	17443995	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17443996	17444203	0.56	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17443996	17444203	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17444204	17444445	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17444446	17444660	1	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17444446	17444660	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17444661	17444739	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17444740	17445014	1	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17444740	17445014	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445015	17445110	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445111	17445234	1	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445111	17445234	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445235	17445340	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445341	17445460	1	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445341	17445460	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445461	17445551	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445552	17445667	1	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445552	17445667	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445668	17445772	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445773	17445854	1	-	1	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445773	17445854	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17445855	17445986	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17445987	17446141	1	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17445987	17446141	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446142	17446226	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17446227	17446372	1	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17446227	17446372	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446373	17446468	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17446469	17446655	1	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17446469	17446655	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446656	17446777	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17446778	17446950	0.97	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17446778	17446950	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17446951	17447061	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17447062	17447115	0.97	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17447062	17447115	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17447116	17447202	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17447203	17447271	1	-	2	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17447203	17447271	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	intron	17447272	17447469	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	CDS	17447470	17447797	0.96	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	exon	17447470	17447797	.	-	.	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
Phchi.S1	AUGUSTUS	start_codon	17447795	17447797	.	-	0	transcript_id "Phchi.S1G269400.t2"; gene_id "Phchi.S1G269400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2589.t1 is derived from g9509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7529037	7531391	.	-	.	Phchi.S5G119800
Phchi.S5	AUGUSTUS	transcript	7529037	7531391	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	stop_codon	7529034	7529036	.	-	0	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7529037	7529065	1	-	2	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7529037	7529065	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7529066	7529165	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7529166	7529296	1	-	1	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7529166	7529296	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7529297	7529425	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7529426	7529464	0.97	-	1	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7529426	7529464	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7529465	7529536	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7529537	7529617	0.84	-	1	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7529537	7529617	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7529618	7529708	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7529709	7529771	1	-	1	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7529709	7529771	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7529772	7529861	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7529862	7529912	1	-	1	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7529862	7529912	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7529913	7530031	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7530032	7530116	1	-	2	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7530032	7530116	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7530117	7530211	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7530212	7530275	1	-	0	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7530212	7530275	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7530276	7530356	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7530357	7530594	1	-	1	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7530357	7530594	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7530595	7530685	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7530686	7530869	0.99	-	2	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7530686	7530869	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7530870	7531008	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7531009	7531027	0.92	-	0	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7531009	7531027	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	intron	7531028	7531118	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	CDS	7531119	7531391	0.73	-	0	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	exon	7531119	7531391	.	-	.	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
Phchi.S5	AUGUSTUS	start_codon	7531389	7531391	.	-	0	transcript_id "Phchi.S5G119800.t1"; gene_id "Phchi.S5G119800"
# This transcript jg12740.t2 is derived from g11205.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12741.t1 is derived from g11206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1472870	1473343	.	-	.	Phchi.S3G006000
Phchi.S3	AUGUSTUS	transcript	1472870	1473343	.	-	.	transcript_id "Phchi.S3G006000.t1"; gene_id "Phchi.S3G006000"
Phchi.S3	AUGUSTUS	stop_codon	1472867	1472869	.	-	0	transcript_id "Phchi.S3G006000.t1"; gene_id "Phchi.S3G006000"
Phchi.S3	AUGUSTUS	CDS	1472870	1473343	0.01	-	0	transcript_id "Phchi.S3G006000.t1"; gene_id "Phchi.S3G006000"
Phchi.S3	AUGUSTUS	exon	1472870	1473343	.	-	.	transcript_id "Phchi.S3G006000.t1"; gene_id "Phchi.S3G006000"
Phchi.S3	AUGUSTUS	start_codon	1473341	1473343	.	-	0	transcript_id "Phchi.S3G006000.t1"; gene_id "Phchi.S3G006000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7202.t1 is derived from g4374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27621676	27624173	.	-	.	Phchi.S1G436100
Phchi.S1	AUGUSTUS	transcript	27621676	27624173	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	stop_codon	27621673	27621675	.	-	0	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	CDS	27621676	27622071	0.99	-	0	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	exon	27621676	27622071	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	intron	27622072	27622152	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	CDS	27622153	27622228	1	-	1	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	exon	27622153	27622228	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	intron	27622229	27622569	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	CDS	27622570	27622766	1	-	0	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	exon	27622570	27622766	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	intron	27622767	27622856	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	CDS	27622857	27623000	1	-	0	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	exon	27622857	27623000	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	intron	27623001	27623321	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	CDS	27623322	27623442	1	-	1	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	exon	27623322	27623442	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	intron	27623443	27624009	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	CDS	27624010	27624173	0.99	-	0	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	exon	27624010	27624173	.	-	.	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
Phchi.S1	AUGUSTUS	start_codon	27624171	27624173	.	-	0	transcript_id "Phchi.S1G436100.t1"; gene_id "Phchi.S1G436100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5557.t1 is derived from g2727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17582415	17584822	.	+	.	Phchi.S1G271600
Phchi.S1	AUGUSTUS	transcript	17582415	17584822	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	start_codon	17582415	17582417	.	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17582415	17582492	1	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17582415	17582492	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17582493	17582610	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17582611	17582816	1	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17582611	17582816	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17582817	17582941	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17582942	17583355	0.84	+	1	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17582942	17583355	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17583356	17583455	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17583456	17583711	0.98	+	1	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17583456	17583711	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17583712	17583796	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17583797	17583988	1	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17583797	17583988	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17583989	17584096	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17584097	17584232	0.96	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17584097	17584232	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17584233	17584332	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17584333	17584424	1	+	2	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17584333	17584424	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17584425	17584505	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17584506	17584574	1	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17584506	17584574	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	intron	17584575	17584666	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	CDS	17584667	17584822	0.96	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	exon	17584667	17584822	.	+	.	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
Phchi.S1	AUGUSTUS	stop_codon	17584823	17584825	.	+	0	transcript_id "Phchi.S1G271600.t1"; gene_id "Phchi.S1G271600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13474.t1 is derived from g11941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7072150	7075859	.	+	.	Phchi.S3G079300
Phchi.S3	AUGUSTUS	transcript	7072150	7075859	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	start_codon	7072150	7072152	.	+	0	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7072150	7072216	0.44	+	0	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7072150	7072216	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7072217	7072367	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7072368	7073795	0.73	+	2	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7072368	7073795	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7073796	7073941	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7073942	7073999	1	+	2	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7073942	7073999	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7074000	7074156	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7074157	7074296	0.98	+	1	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7074157	7074296	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7074297	7074410	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7074411	7074498	1	+	2	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7074411	7074498	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7074499	7074644	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7074645	7074942	1	+	1	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7074645	7074942	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7074943	7075032	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7075033	7075137	1	+	0	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7075033	7075137	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7075138	7075269	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7075270	7075352	1	+	0	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7075270	7075352	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7075353	7075450	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7075451	7075493	1	+	1	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7075451	7075493	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	intron	7075494	7075709	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	CDS	7075710	7075859	0.4	+	0	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	exon	7075710	7075859	.	+	.	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
Phchi.S3	AUGUSTUS	stop_codon	7075860	7075862	.	+	0	transcript_id "Phchi.S3G079300.t1"; gene_id "Phchi.S3G079300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9226.t1 is derived from g6401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40494224	40495656	.	+	.	Phchi.S1G638500
Phchi.S1	AUGUSTUS	transcript	40494224	40495656	.	+	.	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	start_codon	40494224	40494226	.	+	0	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	CDS	40494224	40494760	1	+	0	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	exon	40494224	40494760	.	+	.	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	intron	40494761	40494850	.	+	.	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	CDS	40494851	40495156	1	+	0	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	exon	40494851	40495156	.	+	.	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	intron	40495157	40495293	.	+	.	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	CDS	40495294	40495656	1	+	0	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	exon	40495294	40495656	.	+	.	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
Phchi.S1	AUGUSTUS	stop_codon	40495657	40495659	.	+	0	transcript_id "Phchi.S1G638500.t1"; gene_id "Phchi.S1G638500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9570.t1 is derived from g6746.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42719394	42721074	.	+	.	Phchi.S1G672900
Phchi.S1	AUGUSTUS	transcript	42719394	42721074	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	start_codon	42719394	42719396	.	+	0	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	CDS	42719394	42719688	0.58	+	0	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	exon	42719394	42719688	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	intron	42719689	42719823	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	CDS	42719824	42720223	0.95	+	2	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	exon	42719824	42720223	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	intron	42720224	42720340	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	CDS	42720341	42720433	1	+	1	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	exon	42720341	42720433	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	intron	42720434	42720549	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	CDS	42720550	42720673	0.93	+	1	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	exon	42720550	42720673	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	intron	42720674	42720744	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	CDS	42720745	42721074	0.93	+	0	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	exon	42720745	42721074	.	+	.	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
Phchi.S1	AUGUSTUS	stop_codon	42721075	42721077	.	+	0	transcript_id "Phchi.S1G672900.t1"; gene_id "Phchi.S1G672900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5467.t1 is derived from g2637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16981942	16983506	.	+	.	Phchi.S1G262600
Phchi.S1	AUGUSTUS	transcript	16981942	16983506	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	start_codon	16981942	16981944	.	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16981942	16982099	1	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16981942	16982099	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	intron	16982100	16982173	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16982174	16982275	1	+	1	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16982174	16982275	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	intron	16982276	16982423	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16982424	16982469	1	+	1	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16982424	16982469	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	intron	16982470	16982603	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16982604	16982693	1	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16982604	16982693	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	intron	16982694	16982781	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16982782	16982847	1	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16982782	16982847	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	intron	16982848	16982932	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16982933	16983001	1	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16982933	16983001	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	intron	16983002	16983107	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	CDS	16983108	16983506	1	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	exon	16983108	16983506	.	+	.	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
Phchi.S1	AUGUSTUS	stop_codon	16983507	16983509	.	+	0	transcript_id "Phchi.S1G262600.t1"; gene_id "Phchi.S1G262600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg689.t1 is derived from g10471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4911014	4911304	.	+	.	Phchi.S6G064800
Phchi.S6	AUGUSTUS	transcript	4911014	4911304	.	+	.	transcript_id "Phchi.S6G064800.t1"; gene_id "Phchi.S6G064800"
Phchi.S6	AUGUSTUS	start_codon	4911014	4911016	.	+	0	transcript_id "Phchi.S6G064800.t1"; gene_id "Phchi.S6G064800"
Phchi.S6	AUGUSTUS	CDS	4911014	4911304	0.99	+	0	transcript_id "Phchi.S6G064800.t1"; gene_id "Phchi.S6G064800"
Phchi.S6	AUGUSTUS	exon	4911014	4911304	.	+	.	transcript_id "Phchi.S6G064800.t1"; gene_id "Phchi.S6G064800"
Phchi.S6	AUGUSTUS	stop_codon	4911305	4911307	.	+	0	transcript_id "Phchi.S6G064800.t1"; gene_id "Phchi.S6G064800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13114.t1 is derived from g11579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4194253	4198559	.	+	.	Phchi.S3G043300
Phchi.S3	AUGUSTUS	transcript	4194253	4198559	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	start_codon	4194253	4194255	.	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4194253	4194480	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4194253	4194480	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4194481	4194589	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4194590	4194666	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4194590	4194666	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4194667	4194779	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4194780	4194991	1	+	1	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4194780	4194991	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4194992	4195178	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4195179	4195300	0.96	+	2	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4195179	4195300	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4195301	4195411	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4195412	4195503	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4195412	4195503	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4195504	4195612	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4195613	4195707	1	+	1	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4195613	4195707	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4195708	4195795	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4195796	4195877	1	+	2	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4195796	4195877	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4195878	4195974	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4195975	4196081	1	+	1	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4195975	4196081	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4196082	4196178	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4196179	4196209	1	+	2	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4196179	4196209	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4196210	4196298	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4196299	4196416	1	+	1	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4196299	4196416	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4196417	4196525	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4196526	4196576	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4196526	4196576	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4196577	4196703	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4196704	4196813	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4196704	4196813	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4196814	4196904	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4196905	4197007	1	+	1	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4196905	4197007	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4197008	4197101	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4197102	4197200	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4197102	4197200	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4197201	4197282	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4197283	4197393	0.92	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4197283	4197393	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4197394	4197494	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4197495	4197724	0.98	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4197495	4197724	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4197725	4197808	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4197809	4198046	1	+	1	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4197809	4198046	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4198047	4198123	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4198124	4198202	1	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4198124	4198202	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	intron	4198203	4198302	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	CDS	4198303	4198559	1	+	2	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	exon	4198303	4198559	.	+	.	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
Phchi.S3	AUGUSTUS	stop_codon	4198560	4198562	.	+	0	transcript_id "Phchi.S3G043300.t1"; gene_id "Phchi.S3G043300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg470.t1 is derived from g10252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3302052	3302894	.	-	.	Phchi.S6G042900
Phchi.S6	AUGUSTUS	transcript	3302052	3302894	.	-	.	transcript_id "Phchi.S6G042900.t1"; gene_id "Phchi.S6G042900"
Phchi.S6	AUGUSTUS	stop_codon	3302049	3302051	.	-	0	transcript_id "Phchi.S6G042900.t1"; gene_id "Phchi.S6G042900"
Phchi.S6	AUGUSTUS	CDS	3302052	3302894	0.94	-	0	transcript_id "Phchi.S6G042900.t1"; gene_id "Phchi.S6G042900"
Phchi.S6	AUGUSTUS	exon	3302052	3302894	.	-	.	transcript_id "Phchi.S6G042900.t1"; gene_id "Phchi.S6G042900"
Phchi.S6	AUGUSTUS	start_codon	3302892	3302894	.	-	0	transcript_id "Phchi.S6G042900.t1"; gene_id "Phchi.S6G042900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3263.t1 is derived from g432.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2581007	2583430	.	+	.	Phchi.S1G042200
Phchi.S1	AUGUSTUS	transcript	2581007	2583430	.	+	.	transcript_id "Phchi.S1G042200.t1"; gene_id "Phchi.S1G042200"
Phchi.S1	AUGUSTUS	start_codon	2581007	2581009	.	+	0	transcript_id "Phchi.S1G042200.t1"; gene_id "Phchi.S1G042200"
Phchi.S1	AUGUSTUS	CDS	2581007	2583430	0.99	+	0	transcript_id "Phchi.S1G042200.t1"; gene_id "Phchi.S1G042200"
Phchi.S1	AUGUSTUS	exon	2581007	2583430	.	+	.	transcript_id "Phchi.S1G042200.t1"; gene_id "Phchi.S1G042200"
Phchi.S1	AUGUSTUS	stop_codon	2583431	2583433	.	+	0	transcript_id "Phchi.S1G042200.t1"; gene_id "Phchi.S1G042200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9168.t1 is derived from g6343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40190745	40193775	.	+	.	Phchi.S1G632700
Phchi.S1	AUGUSTUS	transcript	40190745	40193775	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	start_codon	40190745	40190747	.	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40190745	40190918	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40190745	40190918	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40190919	40191022	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191023	40191136	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191023	40191136	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191137	40191273	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191274	40191378	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191274	40191378	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191379	40191498	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191499	40191641	0.79	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191499	40191641	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191642	40191744	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191745	40191841	1	+	1	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191745	40191841	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191842	40191999	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192000	40192167	0.98	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192000	40192167	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192168	40192276	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192277	40192348	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192277	40192348	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192349	40192671	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192672	40192830	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192672	40192830	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192831	40193019	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193020	40193097	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193020	40193097	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40193098	40193190	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193191	40193319	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193191	40193319	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40193320	40193397	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193398	40193544	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193398	40193544	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40193545	40193631	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193632	40193775	1	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193632	40193775	.	+	.	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	stop_codon	40193776	40193778	.	+	0	transcript_id "Phchi.S1G632700.t1"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	transcript	40190745	40193775	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	start_codon	40190745	40190747	.	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40190745	40190918	0.99	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40190745	40190918	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40190919	40191022	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191023	40191136	1	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191023	40191136	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191137	40191273	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191274	40191378	0.97	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191274	40191378	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191379	40191498	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191499	40191641	0.78	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191499	40191641	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191642	40191744	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40191745	40191841	1	+	1	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40191745	40191841	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40191842	40191999	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192000	40192167	1	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192000	40192167	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192168	40192276	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192277	40192348	0.98	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192277	40192348	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192349	40192493	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192494	40192539	0.72	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192494	40192539	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192540	40192630	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40192631	40192830	0.73	+	2	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40192631	40192830	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40192831	40193019	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193020	40193097	1	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193020	40193097	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40193098	40193190	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193191	40193319	1	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193191	40193319	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40193320	40193397	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193398	40193544	1	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193398	40193544	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	intron	40193545	40193631	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	CDS	40193632	40193775	1	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	exon	40193632	40193775	.	+	.	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
Phchi.S1	AUGUSTUS	stop_codon	40193776	40193778	.	+	0	transcript_id "Phchi.S1G632700.t2"; gene_id "Phchi.S1G632700"
# This transcript jg5535.t2 is derived from g2705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5536.t1 is derived from g2706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17449659	17451254	.	+	.	Phchi.S1G269500
Phchi.S1	AUGUSTUS	transcript	17449659	17451254	.	+	.	transcript_id "Phchi.S1G269500.t1"; gene_id "Phchi.S1G269500"
Phchi.S1	AUGUSTUS	start_codon	17449659	17449661	.	+	0	transcript_id "Phchi.S1G269500.t1"; gene_id "Phchi.S1G269500"
Phchi.S1	AUGUSTUS	CDS	17449659	17451254	1	+	0	transcript_id "Phchi.S1G269500.t1"; gene_id "Phchi.S1G269500"
Phchi.S1	AUGUSTUS	exon	17449659	17451254	.	+	.	transcript_id "Phchi.S1G269500.t1"; gene_id "Phchi.S1G269500"
Phchi.S1	AUGUSTUS	stop_codon	17451255	17451257	.	+	0	transcript_id "Phchi.S1G269500.t1"; gene_id "Phchi.S1G269500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6335.t1 is derived from g3507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22383414	22384004	.	-	.	Phchi.S1G349400
Phchi.S1	AUGUSTUS	transcript	22383414	22384004	.	-	.	transcript_id "Phchi.S1G349400.t1"; gene_id "Phchi.S1G349400"
Phchi.S1	AUGUSTUS	stop_codon	22383411	22383413	.	-	0	transcript_id "Phchi.S1G349400.t1"; gene_id "Phchi.S1G349400"
Phchi.S1	AUGUSTUS	CDS	22383414	22384004	0.77	-	0	transcript_id "Phchi.S1G349400.t1"; gene_id "Phchi.S1G349400"
Phchi.S1	AUGUSTUS	exon	22383414	22384004	.	-	.	transcript_id "Phchi.S1G349400.t1"; gene_id "Phchi.S1G349400"
Phchi.S1	AUGUSTUS	start_codon	22384002	22384004	.	-	0	transcript_id "Phchi.S1G349400.t1"; gene_id "Phchi.S1G349400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8259.t1 is derived from g5434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34911233	34912980	.	-	.	Phchi.S1G541800
Phchi.S1	AUGUSTUS	transcript	34911233	34912980	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	stop_codon	34911230	34911232	.	-	0	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34911233	34911451	0.92	-	0	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34911233	34911451	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34911452	34911561	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34911562	34911667	0.94	-	1	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34911562	34911667	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34911668	34911746	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34911747	34911940	1	-	0	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34911747	34911940	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34911941	34912013	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34912014	34912114	1	-	2	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34912014	34912114	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34912115	34912199	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34912200	34912320	1	-	0	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34912200	34912320	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34912321	34912389	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34912390	34912628	1	-	2	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34912390	34912628	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34912629	34912711	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34912712	34912879	0.93	-	2	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34912712	34912879	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	intron	34912880	34912973	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	CDS	34912974	34912980	0.93	-	0	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	exon	34912974	34912980	.	-	.	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
Phchi.S1	AUGUSTUS	start_codon	34912978	34912980	.	-	0	transcript_id "Phchi.S1G541800.t1"; gene_id "Phchi.S1G541800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4019.t1 is derived from g1188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7200984	7201538	.	+	.	Phchi.S1G117800
Phchi.S1	AUGUSTUS	transcript	7200984	7201538	.	+	.	transcript_id "Phchi.S1G117800.t1"; gene_id "Phchi.S1G117800"
Phchi.S1	AUGUSTUS	start_codon	7200984	7200986	.	+	0	transcript_id "Phchi.S1G117800.t1"; gene_id "Phchi.S1G117800"
Phchi.S1	AUGUSTUS	CDS	7200984	7201538	1	+	0	transcript_id "Phchi.S1G117800.t1"; gene_id "Phchi.S1G117800"
Phchi.S1	AUGUSTUS	exon	7200984	7201538	.	+	.	transcript_id "Phchi.S1G117800.t1"; gene_id "Phchi.S1G117800"
Phchi.S1	AUGUSTUS	stop_codon	7201539	7201541	.	+	0	transcript_id "Phchi.S1G117800.t1"; gene_id "Phchi.S1G117800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10073.t1 is derived from g7249.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45629427	45630488	.	-	.	Phchi.S1G723200
Phchi.S1	AUGUSTUS	transcript	45629427	45630488	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	stop_codon	45629424	45629426	.	-	0	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	CDS	45629427	45629510	0.86	-	0	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	exon	45629427	45629510	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	intron	45629511	45629605	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	CDS	45629606	45629625	0.85	-	2	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	exon	45629606	45629625	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	intron	45629626	45629732	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	CDS	45629733	45630225	0.75	-	0	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	exon	45629733	45630225	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	intron	45630226	45630317	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	CDS	45630318	45630488	0.81	-	0	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	exon	45630318	45630488	.	-	.	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
Phchi.S1	AUGUSTUS	start_codon	45630486	45630488	.	-	0	transcript_id "Phchi.S1G723200.t1"; gene_id "Phchi.S1G723200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5590.t1 is derived from g2760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17784103	17785559	.	+	.	Phchi.S1G274900
Phchi.S1	AUGUSTUS	transcript	17784103	17785559	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	start_codon	17784103	17784105	.	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17784103	17784174	1	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17784103	17784174	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	intron	17784175	17784339	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17784340	17784442	1	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17784340	17784442	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	intron	17784443	17784521	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17784522	17784601	1	+	2	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17784522	17784601	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	intron	17784602	17784735	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17784736	17785071	1	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17784736	17785071	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	intron	17785072	17785203	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17785204	17785280	1	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17785204	17785280	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	intron	17785281	17785366	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17785367	17785409	1	+	1	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17785367	17785409	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	intron	17785410	17785490	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	CDS	17785491	17785559	1	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	exon	17785491	17785559	.	+	.	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
Phchi.S1	AUGUSTUS	stop_codon	17785691	17785693	.	+	0	transcript_id "Phchi.S1G274900.t1"; gene_id "Phchi.S1G274900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8981.t1 is derived from g6156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38956269	38956652	.	+	.	Phchi.S1G614000
Phchi.S1	AUGUSTUS	transcript	38956269	38956652	.	+	.	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	start_codon	38956269	38956271	.	+	0	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	CDS	38956269	38956508	0.99	+	0	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	exon	38956269	38956508	.	+	.	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	intron	38956509	38956577	.	+	.	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	CDS	38956578	38956652	1	+	0	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	exon	38956578	38956652	.	+	.	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
Phchi.S1	AUGUSTUS	stop_codon	38956653	38956655	.	+	0	transcript_id "Phchi.S1G614000.t1"; gene_id "Phchi.S1G614000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg116.t1 is derived from g9898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	609914	611439	.	-	.	Phchi.S6G007500
Phchi.S6	AUGUSTUS	transcript	609914	611439	.	-	.	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	stop_codon	609911	609913	.	-	0	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	CDS	609914	610480	0.91	-	0	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	exon	609914	610480	.	-	.	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	intron	610481	610606	.	-	.	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	CDS	610607	611132	1	-	1	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	exon	610607	611132	.	-	.	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	intron	611133	611257	.	-	.	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	CDS	611258	611439	1	-	0	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	exon	611258	611439	.	-	.	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
Phchi.S6	AUGUSTUS	start_codon	611437	611439	.	-	0	transcript_id "Phchi.S6G007500.t1"; gene_id "Phchi.S6G007500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3358.t1 is derived from g527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3135066	3137242	.	-	.	Phchi.S1G051700
Phchi.S1	AUGUSTUS	transcript	3135066	3137242	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	stop_codon	3135063	3135065	.	-	0	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3135066	3135103	1	-	2	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3135066	3135103	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3135104	3135338	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3135339	3135491	1	-	2	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3135339	3135491	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3135492	3135666	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3135667	3135826	1	-	0	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3135667	3135826	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3135827	3135952	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3135953	3136050	1	-	2	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3135953	3136050	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3136051	3136131	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3136132	3136194	1	-	2	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3136132	3136194	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3136195	3136497	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3136498	3136699	0.89	-	0	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3136498	3136699	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3136700	3136815	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3136816	3136915	0.8	-	1	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3136816	3136915	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	intron	3136916	3137117	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	CDS	3137118	3137242	0.73	-	0	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	exon	3137118	3137242	.	-	.	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
Phchi.S1	AUGUSTUS	start_codon	3137240	3137242	.	-	0	transcript_id "Phchi.S1G051700.t1"; gene_id "Phchi.S1G051700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7339.t1 is derived from g4511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28596231	28597178	.	-	.	Phchi.S1G449800
Phchi.S1	AUGUSTUS	transcript	28596231	28597178	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	stop_codon	28596228	28596230	.	-	0	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	CDS	28596231	28596569	1	-	0	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	exon	28596231	28596569	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	intron	28596570	28596682	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	CDS	28596683	28596746	1	-	1	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	exon	28596683	28596746	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	intron	28596747	28596900	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	CDS	28596901	28597016	1	-	0	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	exon	28596901	28597016	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	intron	28597017	28597166	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	CDS	28597167	28597178	1	-	0	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	exon	28597167	28597178	.	-	.	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
Phchi.S1	AUGUSTUS	start_codon	28597176	28597178	.	-	0	transcript_id "Phchi.S1G449800.t1"; gene_id "Phchi.S1G449800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10959.t1 is derived from g15009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3303288	3306216	.	+	.	Phchi.S4G054100
Phchi.S4	AUGUSTUS	transcript	3303288	3306216	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	start_codon	3303288	3303290	.	+	0	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3303288	3303290	1	+	0	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3303288	3303290	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3303291	3303535	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3303536	3303830	1	+	0	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3303536	3303830	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3303831	3303956	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3303957	3304174	0.97	+	2	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3303957	3304174	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3304175	3304275	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3304276	3304520	0.99	+	0	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3304276	3304520	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3304521	3304629	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3304630	3304959	0.98	+	1	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3304630	3304959	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3304960	3305060	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3305061	3305244	1	+	1	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3305061	3305244	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3305245	3305381	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3305382	3305830	1	+	0	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3305382	3305830	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	intron	3305831	3305921	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	CDS	3305922	3306216	1	+	1	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	exon	3305922	3306216	.	+	.	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
Phchi.S4	AUGUSTUS	stop_codon	3306217	3306219	.	+	0	transcript_id "Phchi.S4G054100.t1"; gene_id "Phchi.S4G054100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13664.t1 is derived from g12131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8061052	8062820	.	+	.	Phchi.S3G098300
Phchi.S3	AUGUSTUS	transcript	8061052	8062820	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	start_codon	8061052	8061054	.	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	CDS	8061052	8061377	1	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	exon	8061052	8061377	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	intron	8061378	8061458	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	CDS	8061459	8061774	0.64	+	1	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	exon	8061459	8061774	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	intron	8061775	8062152	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	CDS	8062153	8062251	0.64	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	exon	8062153	8062251	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	intron	8062252	8062402	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	CDS	8062403	8062435	0.68	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	exon	8062403	8062435	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	intron	8062436	8062579	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	CDS	8062580	8062633	0.69	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	exon	8062580	8062633	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	intron	8062634	8062718	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	CDS	8062719	8062820	1	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	exon	8062719	8062820	.	+	.	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
Phchi.S3	AUGUSTUS	stop_codon	8062821	8062823	.	+	0	transcript_id "Phchi.S3G098300.t1"; gene_id "Phchi.S3G098300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6502.t1 is derived from g3674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23343150	23345579	.	-	.	Phchi.S1G366100
Phchi.S1	AUGUSTUS	transcript	23343150	23345579	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	stop_codon	23343147	23343149	.	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23343150	23343218	0.74	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23343150	23343218	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23343219	23343370	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23343371	23343451	0.39	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23343371	23343451	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23343452	23343525	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23343526	23343757	0.76	-	1	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23343526	23343757	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23343758	23343856	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23343857	23343964	1	-	1	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23343857	23343964	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23343965	23344106	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23344107	23344209	0.32	-	2	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23344107	23344209	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23344210	23344337	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23344338	23344458	0.43	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23344338	23344458	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23344459	23344634	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23344635	23344743	1	-	1	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23344635	23344743	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23344744	23344874	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23344875	23344937	1	-	1	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23344875	23344937	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23344938	23345074	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23345075	23345121	1	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23345075	23345121	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	intron	23345122	23345477	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	CDS	23345478	23345579	1	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	exon	23345478	23345579	.	-	.	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
Phchi.S1	AUGUSTUS	start_codon	23345577	23345579	.	-	0	transcript_id "Phchi.S1G366100.t1"; gene_id "Phchi.S1G366100"
# This transcript jg7306.t2 is derived from g4478.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7307.t1 is derived from g4479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28433025	28434112	.	-	.	Phchi.S1G446600
Phchi.S1	AUGUSTUS	transcript	28433025	28434112	.	-	.	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	stop_codon	28433022	28433024	.	-	0	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	CDS	28433025	28433789	0.97	-	0	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	exon	28433025	28433789	.	-	.	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	intron	28433790	28433902	.	-	.	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	CDS	28433903	28434112	0.98	-	0	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	exon	28433903	28434112	.	-	.	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
Phchi.S1	AUGUSTUS	start_codon	28434110	28434112	.	-	0	transcript_id "Phchi.S1G446600.t1"; gene_id "Phchi.S1G446600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5493.t1 is derived from g2663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17118472	17119549	.	-	.	Phchi.S1G265200
Phchi.S1	AUGUSTUS	transcript	17118472	17119549	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	stop_codon	17118469	17118471	.	-	0	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17118472	17118537	1	-	0	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17118472	17118537	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17118538	17118661	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17118662	17118721	1	-	0	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17118662	17118721	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17118722	17118808	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17118809	17118875	1	-	1	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17118809	17118875	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17118876	17119013	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17119014	17119066	1	-	0	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17119014	17119066	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17119067	17119390	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17119391	17119549	1	-	0	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17119391	17119549	.	-	.	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	start_codon	17119547	17119549	.	-	0	transcript_id "Phchi.S1G265200.t1"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	transcript	17118472	17119549	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	stop_codon	17118469	17118471	.	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17118472	17118537	1	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17118472	17118537	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17118538	17118661	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17118662	17118721	1	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17118662	17118721	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17118722	17118808	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17118809	17118875	1	-	1	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17118809	17118875	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17118876	17119013	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17119014	17119066	1	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17119014	17119066	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17119067	17119150	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17119151	17119165	0.91	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17119151	17119165	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	intron	17119166	17119279	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	CDS	17119280	17119549	0.94	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	exon	17119280	17119549	.	-	.	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
Phchi.S1	AUGUSTUS	start_codon	17119547	17119549	.	-	0	transcript_id "Phchi.S1G265200.t2"; gene_id "Phchi.S1G265200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9892.t1 is derived from g7068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44305232	44306879	.	-	.	Phchi.S1G705100
Phchi.S1	AUGUSTUS	transcript	44305528	44306879	.	-	.	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	stop_codon	44305525	44305527	.	-	0	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	CDS	44305528	44305538	0.45	-	2	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	exon	44305528	44305538	.	-	.	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	intron	44305539	44305717	.	-	.	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	CDS	44305718	44305975	0.5	-	2	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	exon	44305718	44305975	.	-	.	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	intron	44305976	44306266	.	-	.	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	CDS	44306267	44306879	0.87	-	0	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	exon	44306267	44306879	.	-	.	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	start_codon	44306877	44306879	.	-	0	transcript_id "Phchi.S1G705100.t1"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	transcript	44305232	44305985	.	-	.	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	stop_codon	44305229	44305231	.	-	0	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	CDS	44305232	44305292	0.45	-	1	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	exon	44305232	44305292	.	-	.	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	intron	44305293	44305530	.	-	.	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	CDS	44305531	44305985	0.24	-	0	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	exon	44305531	44305985	.	-	.	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
Phchi.S1	AUGUSTUS	start_codon	44305983	44305985	.	-	0	transcript_id "Phchi.S1G705100.t2"; gene_id "Phchi.S1G705100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14534.t1 is derived from g13002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13333395	13335882	.	+	.	Phchi.S3G185300
Phchi.S3	AUGUSTUS	transcript	13333395	13335882	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	start_codon	13333395	13333397	.	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13333395	13333523	0.95	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13333395	13333523	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13333524	13333616	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13333617	13333682	1	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13333617	13333682	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13333683	13333786	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13333787	13333875	1	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13333787	13333875	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13333876	13333968	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13333969	13334114	1	+	1	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13333969	13334114	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13334115	13334214	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13334215	13334339	1	+	2	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13334215	13334339	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13334340	13334463	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13334464	13334557	1	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13334464	13334557	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13334558	13334633	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13334634	13334783	0.55	+	2	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13334634	13334783	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13334784	13334920	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13334921	13335060	0.82	+	2	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13334921	13335060	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13335061	13335142	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13335143	13335269	1	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13335143	13335269	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13335270	13335351	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13335352	13335518	1	+	2	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13335352	13335518	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13335519	13335604	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13335605	13335712	1	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13335605	13335712	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	intron	13335713	13335789	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	CDS	13335790	13335882	0.98	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	exon	13335790	13335882	.	+	.	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
Phchi.S3	AUGUSTUS	stop_codon	13335883	13335885	.	+	0	transcript_id "Phchi.S3G185300.t1"; gene_id "Phchi.S3G185300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12106.t1 is derived from g7782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3485918	3487780	.	+	.	Phchi.S2G018600
Phchi.S2	AUGUSTUS	transcript	3485918	3487780	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	start_codon	3485918	3485920	.	+	0	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	CDS	3485918	3486044	0.65	+	0	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	exon	3485918	3486044	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	intron	3486045	3486169	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	CDS	3486170	3486557	0.9	+	2	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	exon	3486170	3486557	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	intron	3486558	3486654	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	CDS	3486655	3486750	1	+	1	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	exon	3486655	3486750	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	intron	3486751	3486939	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	CDS	3486940	3487246	1	+	1	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	exon	3486940	3487246	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	intron	3487247	3487334	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	CDS	3487335	3487595	0.6	+	0	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	exon	3487335	3487595	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	intron	3487596	3487690	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	CDS	3487691	3487780	0.68	+	0	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	exon	3487691	3487780	.	+	.	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
Phchi.S2	AUGUSTUS	stop_codon	3487781	3487783	.	+	0	transcript_id "Phchi.S2G018600.t1"; gene_id "Phchi.S2G018600"
# This transcript jg5946.t2 is derived from g3117.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5947.t1 is derived from g3118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19980215	19981859	.	-	.	Phchi.S1G310600
Phchi.S1	AUGUSTUS	transcript	19980215	19981859	.	-	.	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	stop_codon	19980212	19980214	.	-	0	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	CDS	19980215	19980397	0.34	-	0	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	exon	19980215	19980397	.	-	.	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	intron	19980398	19980483	.	-	.	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	CDS	19980484	19981286	0.71	-	2	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	exon	19980484	19981286	.	-	.	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	intron	19981287	19981513	.	-	.	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	CDS	19981514	19981859	0.86	-	0	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	exon	19981514	19981859	.	-	.	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
Phchi.S1	AUGUSTUS	start_codon	19981857	19981859	.	-	0	transcript_id "Phchi.S1G310600.t1"; gene_id "Phchi.S1G310600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8412.t1 is derived from g5587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35835782	35837312	.	+	.	Phchi.S1G557100
Phchi.S1	AUGUSTUS	transcript	35835782	35837312	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	start_codon	35835782	35835784	.	+	0	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35835782	35835906	0.75	+	0	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35835782	35835906	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	intron	35835907	35836005	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35836006	35836157	0.48	+	1	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35836006	35836157	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	intron	35836158	35836256	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35836257	35836406	0.48	+	2	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35836257	35836406	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	intron	35836407	35836539	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35836540	35836622	1	+	2	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35836540	35836622	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	intron	35836623	35836740	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35836741	35836827	1	+	0	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35836741	35836827	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	intron	35836828	35836925	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35836926	35837057	1	+	0	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35836926	35837057	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	intron	35837058	35837162	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	CDS	35837163	35837312	0.9	+	0	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	exon	35837163	35837312	.	+	.	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
Phchi.S1	AUGUSTUS	stop_codon	35837313	35837315	.	+	0	transcript_id "Phchi.S1G557100.t1"; gene_id "Phchi.S1G557100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2307.t1 is derived from g9227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5984471	5986753	.	-	.	Phchi.S5G091600
Phchi.S5	AUGUSTUS	transcript	5984471	5986753	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	stop_codon	5984468	5984470	.	-	0	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	CDS	5984471	5984712	0.6	-	2	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	exon	5984471	5984712	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	intron	5984713	5985039	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	CDS	5985040	5985250	0.21	-	0	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	exon	5985040	5985250	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	intron	5985251	5985332	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	CDS	5985333	5985558	0.48	-	1	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	exon	5985333	5985558	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	intron	5985559	5985714	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	CDS	5985715	5986277	0.42	-	0	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	exon	5985715	5986277	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	intron	5986278	5986501	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	CDS	5986502	5986753	0.17	-	0	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	exon	5986502	5986753	.	-	.	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
Phchi.S5	AUGUSTUS	start_codon	5986751	5986753	.	-	0	transcript_id "Phchi.S5G091600.t1"; gene_id "Phchi.S5G091600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2675.t1 is derived from g9595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8150401	8150950	.	+	.	Phchi.S5G128400
Phchi.S5	AUGUSTUS	transcript	8150401	8150950	.	+	.	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	start_codon	8150401	8150403	.	+	0	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	CDS	8150401	8150505	0.31	+	0	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	exon	8150401	8150505	.	+	.	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	intron	8150506	8150604	.	+	.	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	CDS	8150605	8150796	0.72	+	0	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	exon	8150605	8150796	.	+	.	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	intron	8150797	8150890	.	+	.	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	CDS	8150891	8150950	0.94	+	0	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	exon	8150891	8150950	.	+	.	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
Phchi.S5	AUGUSTUS	stop_codon	8150951	8150953	.	+	0	transcript_id "Phchi.S5G128400.t1"; gene_id "Phchi.S5G128400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14738.t1 is derived from g13206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14457006	14459468	.	+	.	Phchi.S3G205700
Phchi.S3	AUGUSTUS	transcript	14457006	14459468	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	start_codon	14457006	14457008	.	+	0	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	CDS	14457006	14457264	0.71	+	0	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	exon	14457006	14457264	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	intron	14457265	14457345	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	CDS	14457346	14458573	1	+	2	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	exon	14457346	14458573	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	intron	14458574	14458780	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	CDS	14458781	14458898	1	+	1	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	exon	14458781	14458898	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	intron	14458899	14458971	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	CDS	14458972	14459073	1	+	0	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	exon	14458972	14459073	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	intron	14459074	14459160	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	CDS	14459161	14459242	0.95	+	0	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	exon	14459161	14459242	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	intron	14459243	14459382	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	CDS	14459383	14459468	0.89	+	2	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	exon	14459383	14459468	.	+	.	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
Phchi.S3	AUGUSTUS	stop_codon	14459469	14459471	.	+	0	transcript_id "Phchi.S3G205700.t1"; gene_id "Phchi.S3G205700"
# This transcript jg7291.t2 is derived from g4463.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7292.t1 is derived from g4464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28362953	28364914	.	-	.	Phchi.S1G445100
Phchi.S1	AUGUSTUS	transcript	28362953	28364914	.	-	.	transcript_id "Phchi.S1G445100.t1"; gene_id "Phchi.S1G445100"
Phchi.S1	AUGUSTUS	stop_codon	28362950	28362952	.	-	0	transcript_id "Phchi.S1G445100.t1"; gene_id "Phchi.S1G445100"
Phchi.S1	AUGUSTUS	CDS	28362953	28364914	0.52	-	0	transcript_id "Phchi.S1G445100.t1"; gene_id "Phchi.S1G445100"
Phchi.S1	AUGUSTUS	exon	28362953	28364914	.	-	.	transcript_id "Phchi.S1G445100.t1"; gene_id "Phchi.S1G445100"
Phchi.S1	AUGUSTUS	start_codon	28364912	28364914	.	-	0	transcript_id "Phchi.S1G445100.t1"; gene_id "Phchi.S1G445100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15629.t1 is derived from g14098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20374064	20376427	.	-	.	Phchi.S3G294800
Phchi.S3	AUGUSTUS	transcript	20374064	20376427	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	stop_codon	20374061	20374063	.	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20374064	20374210	1	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20374064	20374210	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20374211	20374339	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20374340	20374453	1	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20374340	20374453	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20374454	20374551	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20374552	20374722	1	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20374552	20374722	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20374723	20374808	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20374809	20374892	1	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20374809	20374892	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20374893	20374972	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20374973	20375086	1	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20374973	20375086	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20375087	20375201	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20375202	20375450	1	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20375202	20375450	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20375451	20375555	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20375556	20375659	1	-	2	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20375556	20375659	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20375660	20375767	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20375768	20375861	0.97	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20375768	20375861	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20375862	20375961	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20375962	20376199	1	-	1	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20375962	20376199	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	intron	20376200	20376275	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	CDS	20376276	20376427	0.97	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	exon	20376276	20376427	.	-	.	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
Phchi.S3	AUGUSTUS	start_codon	20376425	20376427	.	-	0	transcript_id "Phchi.S3G294800.t1"; gene_id "Phchi.S3G294800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14238.t1 is derived from g12705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11691775	11694560	.	+	.	Phchi.S3G155700
Phchi.S3	AUGUSTUS	transcript	11691775	11694560	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	start_codon	11691775	11691777	.	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11691775	11691852	1	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11691775	11691852	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11691853	11691972	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11691973	11692014	1	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11691973	11692014	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11692015	11692092	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11692093	11692272	0.92	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11692093	11692272	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11692273	11692384	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11692385	11692549	0.97	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11692385	11692549	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11692550	11692656	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11692657	11692857	0.98	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11692657	11692857	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11692858	11693020	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11693021	11693317	1	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11693021	11693317	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11693318	11693458	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11693459	11693659	1	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11693459	11693659	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11693660	11693757	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11693758	11693892	1	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11693758	11693892	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11693893	11693973	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11693974	11694049	1	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11693974	11694049	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11694050	11694113	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11694114	11694221	0.92	+	2	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11694114	11694221	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11694222	11694331	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11694332	11694391	1	+	2	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11694332	11694391	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	intron	11694392	11694483	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	CDS	11694484	11694560	0.97	+	2	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	exon	11694484	11694560	.	+	.	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
Phchi.S3	AUGUSTUS	stop_codon	11694561	11694563	.	+	0	transcript_id "Phchi.S3G155700.t1"; gene_id "Phchi.S3G155700"
# This transcript jg1670.t2 is derived from g8589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1671.t1 is derived from g8590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2330535	2331721	.	-	.	Phchi.S5G028000
Phchi.S5	AUGUSTUS	transcript	2330535	2331721	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	stop_codon	2330532	2330534	.	-	0	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	CDS	2330535	2330555	1	-	0	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	exon	2330535	2330555	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	intron	2330556	2330688	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	CDS	2330689	2330754	1	-	0	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	exon	2330689	2330754	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	intron	2330755	2330856	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	CDS	2330857	2330928	1	-	0	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	exon	2330857	2330928	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	intron	2330929	2331030	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	CDS	2331031	2331355	1	-	1	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	exon	2331031	2331355	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	intron	2331356	2331437	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	CDS	2331438	2331721	0.87	-	0	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	exon	2331438	2331721	.	-	.	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
Phchi.S5	AUGUSTUS	start_codon	2331719	2331721	.	-	0	transcript_id "Phchi.S5G028000.t1"; gene_id "Phchi.S5G028000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3600.t1 is derived from g769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4675749	4676819	.	-	.	Phchi.S1G075900
Phchi.S1	AUGUSTUS	transcript	4675749	4676819	.	-	.	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	stop_codon	4675746	4675748	.	-	0	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	CDS	4675749	4675924	1	-	2	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	exon	4675749	4675924	.	-	.	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	intron	4675925	4676037	.	-	.	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	CDS	4676038	4676156	1	-	1	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	exon	4676038	4676156	.	-	.	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	intron	4676157	4676334	.	-	.	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	CDS	4676335	4676819	0.47	-	0	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	exon	4676335	4676819	.	-	.	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
Phchi.S1	AUGUSTUS	start_codon	4676817	4676819	.	-	0	transcript_id "Phchi.S1G075900.t1"; gene_id "Phchi.S1G075900"
# This transcript jg14124.t2 is derived from g12591.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14125.t1 is derived from g12592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11008836	11009813	.	+	.	Phchi.S3G144400
Phchi.S3	AUGUSTUS	transcript	11008836	11009813	.	+	.	transcript_id "Phchi.S3G144400.t1"; gene_id "Phchi.S3G144400"
Phchi.S3	AUGUSTUS	start_codon	11008836	11008838	.	+	0	transcript_id "Phchi.S3G144400.t1"; gene_id "Phchi.S3G144400"
Phchi.S3	AUGUSTUS	CDS	11008836	11009813	1	+	0	transcript_id "Phchi.S3G144400.t1"; gene_id "Phchi.S3G144400"
Phchi.S3	AUGUSTUS	exon	11008836	11009813	.	+	.	transcript_id "Phchi.S3G144400.t1"; gene_id "Phchi.S3G144400"
Phchi.S3	AUGUSTUS	stop_codon	11009814	11009816	.	+	0	transcript_id "Phchi.S3G144400.t1"; gene_id "Phchi.S3G144400"
# This transcript jg12921.t2 is derived from g11386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12922.t1 is derived from g11387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3171980	3174477	.	+	.	Phchi.S3G024100
Phchi.S3	AUGUSTUS	transcript	3171980	3174477	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	start_codon	3171980	3171982	.	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3171980	3172113	0.75	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3171980	3172113	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3172114	3172260	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3172261	3172323	1	+	1	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3172261	3172323	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3172324	3172442	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3172443	3172502	0.95	+	1	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3172443	3172502	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3172503	3172589	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3172590	3172680	0.94	+	1	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3172590	3172680	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3172681	3172783	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3172784	3172838	0.99	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3172784	3172838	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3172839	3172920	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3172921	3173000	1	+	2	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3172921	3173000	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3173001	3173085	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3173086	3173202	1	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3173086	3173202	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3173203	3173319	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3173320	3173404	1	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3173320	3173404	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3173405	3173532	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3173533	3173624	1	+	2	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3173533	3173624	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3173625	3173766	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3173767	3174020	1	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3173767	3174020	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3174021	3174136	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3174137	3174225	1	+	1	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3174137	3174225	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	intron	3174226	3174340	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	CDS	3174341	3174477	0.99	+	2	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	exon	3174341	3174477	.	+	.	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
Phchi.S3	AUGUSTUS	stop_codon	3174478	3174480	.	+	0	transcript_id "Phchi.S3G024100.t1"; gene_id "Phchi.S3G024100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg1410.t1 is derived from g8329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	297978	304411	.	-	.	Phchi.S5G001900
Phchi.S5	AUGUSTUS	transcript	298073	304411	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	stop_codon	298070	298072	.	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	298073	298095	0.63	-	2	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	298073	298095	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	298096	299580	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299581	299736	0.28	-	2	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299581	299736	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299737	299880	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299881	299949	0.39	-	2	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299881	299949	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299950	300365	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300366	300512	1	-	2	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300366	300512	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300513	300659	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300660	301195	1	-	1	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300660	301195	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	301196	301387	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	301388	302035	0.9	-	1	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	301388	302035	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302036	302179	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302180	302520	1	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302180	302520	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302521	302619	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302620	302670	0.92	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302620	302670	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302671	302806	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302807	302916	0.97	-	2	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302807	302916	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302917	302984	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302985	303051	1	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302985	303051	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303052	303270	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303271	303624	0.95	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303271	303624	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303625	303749	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303750	303852	0.95	-	1	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303750	303852	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303853	303942	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303943	303949	0.95	-	2	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303943	303949	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303950	304404	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	304405	304411	0.95	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	304405	304411	.	-	.	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	start_codon	304409	304411	.	-	0	transcript_id "Phchi.S5G001900.t1"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	transcript	297978	304411	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	stop_codon	297975	297977	.	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	297978	298095	0.98	-	1	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	297978	298095	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	298096	299580	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299581	299658	0.51	-	1	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299581	299658	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299659	299787	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299788	299949	0.6	-	1	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299788	299949	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299950	300233	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300234	300255	0.29	-	2	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300234	300255	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300256	300365	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300366	300512	0.81	-	2	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300366	300512	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300513	300659	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300660	301195	0.99	-	1	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300660	301195	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	301196	301387	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	301388	302035	0.91	-	1	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	301388	302035	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302036	302179	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302180	302520	0.99	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302180	302520	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302521	302619	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302620	302670	0.86	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302620	302670	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302671	302806	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302807	302916	1	-	2	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302807	302916	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302917	302984	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302985	303051	1	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302985	303051	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303052	303270	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303271	303624	0.94	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303271	303624	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303625	303749	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303750	303852	0.94	-	1	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303750	303852	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303853	303942	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303943	303949	0.94	-	2	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303943	303949	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303950	304404	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	304405	304411	0.94	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	304405	304411	.	-	.	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	start_codon	304409	304411	.	-	0	transcript_id "Phchi.S5G001900.t2"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	transcript	297978	304411	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	stop_codon	297975	297977	.	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	297978	298095	0.66	-	1	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	297978	298095	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	298096	299580	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299581	299658	0.32	-	1	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299581	299658	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299659	299787	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299788	299949	0.33	-	1	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299788	299949	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299950	300120	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300121	300233	0.46	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300121	300233	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300234	300342	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300343	300512	0.6	-	2	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300343	300512	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300513	300659	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300660	301195	1	-	1	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300660	301195	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	301196	301387	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	301388	302035	0.91	-	1	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	301388	302035	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302036	302179	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302180	302520	0.99	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302180	302520	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302521	302619	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302620	302670	0.95	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302620	302670	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302671	302806	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302807	302916	1	-	2	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302807	302916	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302917	302984	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302985	303051	1	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302985	303051	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303052	303270	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303271	303624	0.97	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303271	303624	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303625	303749	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303750	303852	0.97	-	1	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303750	303852	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303853	303942	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303943	303949	0.97	-	2	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303943	303949	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303950	304404	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	304405	304411	0.94	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	304405	304411	.	-	.	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	start_codon	304409	304411	.	-	0	transcript_id "Phchi.S5G001900.t3"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	transcript	297978	304411	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	stop_codon	297975	297977	.	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	297978	298095	0.79	-	1	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	297978	298095	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	298096	299580	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299581	299658	0.35	-	1	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299581	299658	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299659	299787	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	299788	299949	0.41	-	1	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	299788	299949	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	299950	300130	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300131	300222	0.16	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300131	300222	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300223	300342	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300343	300512	0.48	-	2	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300343	300512	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	300513	300659	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	300660	301195	1	-	1	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	300660	301195	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	301196	301387	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	301388	302035	0.91	-	1	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	301388	302035	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302036	302179	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302180	302520	0.99	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302180	302520	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302521	302619	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302620	302670	0.92	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302620	302670	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302671	302806	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302807	302916	0.99	-	2	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302807	302916	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	302917	302984	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	302985	303051	1	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	302985	303051	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303052	303270	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303271	303624	0.93	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303271	303624	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303625	303749	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303750	303852	0.93	-	1	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303750	303852	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303853	303942	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	303943	303949	0.93	-	2	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	303943	303949	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	intron	303950	304404	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	CDS	304405	304411	0.92	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	exon	304405	304411	.	-	.	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
Phchi.S5	AUGUSTUS	start_codon	304409	304411	.	-	0	transcript_id "Phchi.S5G001900.t4"; gene_id "Phchi.S5G001900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4383.t1 is derived from g1552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10171847	10172683	.	-	.	Phchi.S1G154200
Phchi.S1	AUGUSTUS	transcript	10171847	10172683	.	-	.	transcript_id "Phchi.S1G154200.t1"; gene_id "Phchi.S1G154200"
Phchi.S1	AUGUSTUS	stop_codon	10171844	10171846	.	-	0	transcript_id "Phchi.S1G154200.t1"; gene_id "Phchi.S1G154200"
Phchi.S1	AUGUSTUS	CDS	10171847	10172683	0.76	-	0	transcript_id "Phchi.S1G154200.t1"; gene_id "Phchi.S1G154200"
Phchi.S1	AUGUSTUS	exon	10171847	10172683	.	-	.	transcript_id "Phchi.S1G154200.t1"; gene_id "Phchi.S1G154200"
Phchi.S1	AUGUSTUS	start_codon	10172681	10172683	.	-	0	transcript_id "Phchi.S1G154200.t1"; gene_id "Phchi.S1G154200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5524.t1 is derived from g2694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17408385	17409613	.	-	.	Phchi.S1G268300
Phchi.S1	AUGUSTUS	transcript	17408385	17409613	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	stop_codon	17408382	17408384	.	-	0	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	CDS	17408385	17408560	0.6	-	2	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	exon	17408385	17408560	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	intron	17408561	17408702	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	CDS	17408703	17408732	0.64	-	2	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	exon	17408703	17408732	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	intron	17408733	17408827	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	CDS	17408828	17408844	0.56	-	1	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	exon	17408828	17408844	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	intron	17408845	17409016	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	CDS	17409017	17409117	0.73	-	0	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	exon	17409017	17409117	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	intron	17409118	17409436	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	CDS	17409437	17409613	0.22	-	0	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	exon	17409437	17409613	.	-	.	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
Phchi.S1	AUGUSTUS	start_codon	17409611	17409613	.	-	0	transcript_id "Phchi.S1G268300.t1"; gene_id "Phchi.S1G268300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12852.t1 is derived from g11317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2724823	2725329	.	+	.	Phchi.S3G017100
Phchi.S3	AUGUSTUS	transcript	2724823	2725329	.	+	.	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	start_codon	2724823	2724825	.	+	0	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	CDS	2724823	2725143	0.48	+	0	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	exon	2724823	2725143	.	+	.	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	intron	2725144	2725242	.	+	.	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	CDS	2725243	2725329	0.74	+	0	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	exon	2725243	2725329	.	+	.	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	stop_codon	2725330	2725332	.	+	0	transcript_id "Phchi.S3G017100.t1"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	transcript	2724823	2725329	.	+	.	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	start_codon	2724823	2724825	.	+	0	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	CDS	2724823	2725143	0.5	+	0	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	exon	2724823	2725143	.	+	.	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	intron	2725144	2725224	.	+	.	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	CDS	2725225	2725329	0.67	+	0	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	exon	2725225	2725329	.	+	.	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
Phchi.S3	AUGUSTUS	stop_codon	2725330	2725332	.	+	0	transcript_id "Phchi.S3G017100.t2"; gene_id "Phchi.S3G017100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11328.t1 is derived from g15378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5587917	5588405	.	-	.	Phchi.S4G091000
Phchi.S4	AUGUSTUS	transcript	5587917	5588405	.	-	.	transcript_id "Phchi.S4G091000.t1"; gene_id "Phchi.S4G091000"
Phchi.S4	AUGUSTUS	stop_codon	5587914	5587916	.	-	0	transcript_id "Phchi.S4G091000.t1"; gene_id "Phchi.S4G091000"
Phchi.S4	AUGUSTUS	CDS	5587917	5588405	0.87	-	0	transcript_id "Phchi.S4G091000.t1"; gene_id "Phchi.S4G091000"
Phchi.S4	AUGUSTUS	exon	5587917	5588405	.	-	.	transcript_id "Phchi.S4G091000.t1"; gene_id "Phchi.S4G091000"
Phchi.S4	AUGUSTUS	start_codon	5588403	5588405	.	-	0	transcript_id "Phchi.S4G091000.t1"; gene_id "Phchi.S4G091000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6846.t1 is derived from g4018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25520920	25525299	.	-	.	Phchi.S1G400500
Phchi.S1	AUGUSTUS	transcript	25520920	25525299	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	stop_codon	25520917	25520919	.	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25520920	25521708	1	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25520920	25521708	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	intron	25521709	25521824	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25521825	25521921	1	-	1	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25521825	25521921	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	intron	25521922	25522005	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25522006	25522463	1	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25522006	25522463	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	intron	25522464	25522584	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25522585	25524548	1	-	2	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25522585	25524548	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	intron	25524549	25524640	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25524641	25524821	1	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25524641	25524821	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	intron	25524822	25524933	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25524934	25525095	1	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25524934	25525095	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	intron	25525096	25525284	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	CDS	25525285	25525299	1	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	exon	25525285	25525299	.	-	.	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
Phchi.S1	AUGUSTUS	start_codon	25525297	25525299	.	-	0	transcript_id "Phchi.S1G400500.t1"; gene_id "Phchi.S1G400500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6920.t1 is derived from g4092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25990200	25992106	.	-	.	Phchi.S1G407900
Phchi.S1	AUGUSTUS	transcript	25990200	25992106	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	stop_codon	25990197	25990199	.	-	0	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	CDS	25990200	25990320	1	-	1	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	exon	25990200	25990320	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	intron	25990321	25990505	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	CDS	25990506	25990742	1	-	1	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	exon	25990506	25990742	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	intron	25990743	25990924	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	CDS	25990925	25990998	1	-	0	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	exon	25990925	25990998	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	intron	25990999	25991200	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	CDS	25991201	25992106	0.56	-	0	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	exon	25991201	25992106	.	-	.	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
Phchi.S1	AUGUSTUS	start_codon	25992104	25992106	.	-	0	transcript_id "Phchi.S1G407900.t1"; gene_id "Phchi.S1G407900"
# This transcript jg151.t2 is derived from g9933.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg152.t1 is derived from g9934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	856105	857056	.	-	.	Phchi.S6G011100
Phchi.S6	AUGUSTUS	transcript	856105	857056	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	stop_codon	856102	856104	.	-	0	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	CDS	856105	856250	0.57	-	2	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	exon	856105	856250	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	intron	856251	856324	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	CDS	856325	856396	0.56	-	2	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	exon	856325	856396	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	intron	856397	856631	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	CDS	856632	856656	0.51	-	0	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	exon	856632	856656	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	intron	856657	856924	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	CDS	856925	857056	0.54	-	0	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	exon	856925	857056	.	-	.	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
Phchi.S6	AUGUSTUS	start_codon	857054	857056	.	-	0	transcript_id "Phchi.S6G011100.t1"; gene_id "Phchi.S6G011100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1186.t1 is derived from g10969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8342091	8343287	.	-	.	Phchi.S6G114500
Phchi.S6	AUGUSTUS	transcript	8342091	8343287	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	stop_codon	8342088	8342090	.	-	0	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	CDS	8342091	8342388	0.83	-	1	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	exon	8342091	8342388	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	intron	8342389	8342518	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	CDS	8342519	8342646	0.71	-	0	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	exon	8342519	8342646	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	intron	8342647	8342732	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	CDS	8342733	8342820	0.71	-	1	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	exon	8342733	8342820	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	intron	8342821	8342937	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	CDS	8342938	8343287	0.62	-	0	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	exon	8342938	8343287	.	-	.	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
Phchi.S6	AUGUSTUS	start_codon	8343285	8343287	.	-	0	transcript_id "Phchi.S6G114500.t1"; gene_id "Phchi.S6G114500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15688.t1 is derived from g14157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20667795	20669197	.	+	.	Phchi.S3G300700
Phchi.S3	AUGUSTUS	transcript	20667795	20669197	.	+	.	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	start_codon	20667795	20667797	.	+	0	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	CDS	20667795	20667984	0.98	+	0	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	exon	20667795	20667984	.	+	.	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	intron	20667985	20668065	.	+	.	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	CDS	20668066	20668131	0.63	+	2	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	exon	20668066	20668131	.	+	.	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	intron	20668132	20668223	.	+	.	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	CDS	20668224	20669197	0.98	+	2	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	exon	20668224	20669197	.	+	.	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
Phchi.S3	AUGUSTUS	stop_codon	20669198	20669200	.	+	0	transcript_id "Phchi.S3G300700.t1"; gene_id "Phchi.S3G300700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8615.t1 is derived from g5790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36933235	36933973	.	-	.	Phchi.S1G577400
Phchi.S1	AUGUSTUS	transcript	36933235	36933973	.	-	.	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	stop_codon	36933232	36933234	.	-	0	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	CDS	36933235	36933375	0.89	-	0	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	exon	36933235	36933375	.	-	.	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	intron	36933376	36933501	.	-	.	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	CDS	36933502	36933760	0.8	-	1	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	exon	36933502	36933760	.	-	.	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	intron	36933761	36933917	.	-	.	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	CDS	36933918	36933973	0.7	-	0	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	exon	36933918	36933973	.	-	.	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
Phchi.S1	AUGUSTUS	start_codon	36933971	36933973	.	-	0	transcript_id "Phchi.S1G577400.t1"; gene_id "Phchi.S1G577400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2959.t1 is derived from g128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	791719	792027	.	-	.	Phchi.S1G011800
Phchi.S1	AUGUSTUS	transcript	791719	792027	.	-	.	transcript_id "Phchi.S1G011800.t1"; gene_id "Phchi.S1G011800"
Phchi.S1	AUGUSTUS	stop_codon	791716	791718	.	-	0	transcript_id "Phchi.S1G011800.t1"; gene_id "Phchi.S1G011800"
Phchi.S1	AUGUSTUS	CDS	791719	792027	0.98	-	0	transcript_id "Phchi.S1G011800.t1"; gene_id "Phchi.S1G011800"
Phchi.S1	AUGUSTUS	exon	791719	792027	.	-	.	transcript_id "Phchi.S1G011800.t1"; gene_id "Phchi.S1G011800"
Phchi.S1	AUGUSTUS	start_codon	792025	792027	.	-	0	transcript_id "Phchi.S1G011800.t1"; gene_id "Phchi.S1G011800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg496.t1 is derived from g10278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3445686	3446845	.	+	.	Phchi.S6G045500
Phchi.S6	AUGUSTUS	transcript	3445686	3446845	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	start_codon	3445686	3445688	.	+	0	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	CDS	3445686	3445730	0.97	+	0	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	exon	3445686	3445730	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	intron	3445731	3445853	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	CDS	3445854	3445925	0.98	+	0	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	exon	3445854	3445925	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	intron	3445926	3446053	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	CDS	3446054	3446154	0.75	+	0	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	exon	3446054	3446154	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	intron	3446155	3446239	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	CDS	3446240	3446332	1	+	1	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	exon	3446240	3446332	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	intron	3446333	3446457	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	CDS	3446458	3446593	0.78	+	1	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	exon	3446458	3446593	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	intron	3446594	3446677	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	CDS	3446678	3446845	0.73	+	0	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	exon	3446678	3446845	.	+	.	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
Phchi.S6	AUGUSTUS	stop_codon	3446846	3446848	.	+	0	transcript_id "Phchi.S6G045500.t1"; gene_id "Phchi.S6G045500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2529.t1 is derived from g9449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7174194	7175078	.	+	.	Phchi.S5G113800
Phchi.S5	AUGUSTUS	transcript	7174194	7175078	.	+	.	transcript_id "Phchi.S5G113800.t1"; gene_id "Phchi.S5G113800"
Phchi.S5	AUGUSTUS	start_codon	7174194	7174196	.	+	0	transcript_id "Phchi.S5G113800.t1"; gene_id "Phchi.S5G113800"
Phchi.S5	AUGUSTUS	CDS	7174194	7175078	1	+	0	transcript_id "Phchi.S5G113800.t1"; gene_id "Phchi.S5G113800"
Phchi.S5	AUGUSTUS	exon	7174194	7175078	.	+	.	transcript_id "Phchi.S5G113800.t1"; gene_id "Phchi.S5G113800"
Phchi.S5	AUGUSTUS	stop_codon	7175079	7175081	.	+	0	transcript_id "Phchi.S5G113800.t1"; gene_id "Phchi.S5G113800"
# This transcript jg1283.t2 is derived from g11066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1284.t1 is derived from g11067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8807279	8808571	.	-	.	Phchi.S6G124300
Phchi.S6	AUGUSTUS	transcript	8807279	8808571	.	-	.	transcript_id "Phchi.S6G124300.t1"; gene_id "Phchi.S6G124300"
Phchi.S6	AUGUSTUS	stop_codon	8807276	8807278	.	-	0	transcript_id "Phchi.S6G124300.t1"; gene_id "Phchi.S6G124300"
Phchi.S6	AUGUSTUS	CDS	8807279	8808571	0.54	-	0	transcript_id "Phchi.S6G124300.t1"; gene_id "Phchi.S6G124300"
Phchi.S6	AUGUSTUS	exon	8807279	8808571	.	-	.	transcript_id "Phchi.S6G124300.t1"; gene_id "Phchi.S6G124300"
Phchi.S6	AUGUSTUS	start_codon	8808569	8808571	.	-	0	transcript_id "Phchi.S6G124300.t1"; gene_id "Phchi.S6G124300"
# This transcript jg9351.t2 is derived from g6527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9351.t3 is derived from g6527.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9352.t1 is derived from g6528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41097153	41098300	.	-	.	Phchi.S1G651100
Phchi.S1	AUGUSTUS	transcript	41097153	41098300	.	-	.	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	stop_codon	41097150	41097152	.	-	0	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	CDS	41097153	41097929	0.52	-	0	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	exon	41097153	41097929	.	-	.	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	intron	41097930	41098102	.	-	.	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	CDS	41098103	41098300	0.47	-	0	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	exon	41098103	41098300	.	-	.	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
Phchi.S1	AUGUSTUS	start_codon	41098298	41098300	.	-	0	transcript_id "Phchi.S1G651100.t1"; gene_id "Phchi.S1G651100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg136.t1 is derived from g9918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	759864	761388	.	-	.	Phchi.S6G009500
Phchi.S6	AUGUSTUS	transcript	759864	761388	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	stop_codon	759861	759863	.	-	0	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	759864	759936	1	-	1	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	759864	759936	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	intron	759937	760111	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	760112	760238	1	-	2	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	760112	760238	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	intron	760239	760322	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	760323	760395	1	-	0	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	760323	760395	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	intron	760396	760512	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	760513	760644	1	-	0	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	760513	760644	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	intron	760645	760808	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	760809	760861	1	-	2	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	760809	760861	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	intron	760862	760946	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	760947	761052	0.93	-	0	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	760947	761052	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	intron	761053	761157	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	CDS	761158	761388	0.52	-	0	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	exon	761158	761388	.	-	.	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
Phchi.S6	AUGUSTUS	start_codon	761386	761388	.	-	0	transcript_id "Phchi.S6G009500.t1"; gene_id "Phchi.S6G009500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14198.t1 is derived from g12665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11433049	11435140	.	+	.	Phchi.S3G151700
Phchi.S3	AUGUSTUS	transcript	11433049	11435140	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	start_codon	11433049	11433051	.	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433049	11433300	0.37	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433049	11433300	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433301	11433402	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433403	11433542	0.95	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433403	11433542	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433543	11433634	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433635	11433890	1	+	1	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433635	11433890	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433891	11433977	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433978	11434110	1	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433978	11434110	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11434111	11434269	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11434270	11434358	1	+	2	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11434270	11434358	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11434359	11434477	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11434478	11434825	1	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11434478	11434825	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11434826	11434915	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11434916	11435140	0.9	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11434916	11435140	.	+	.	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	stop_codon	11435141	11435143	.	+	0	transcript_id "Phchi.S3G151700.t1"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	transcript	11433049	11435140	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	start_codon	11433049	11433051	.	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433049	11433135	0.39	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433049	11433135	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433136	11433280	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433281	11433300	0.77	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433281	11433300	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433301	11433398	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433399	11433542	1	+	1	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433399	11433542	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433543	11433634	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433635	11433890	1	+	1	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433635	11433890	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11433891	11433977	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11433978	11434110	1	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11433978	11434110	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11434111	11434269	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11434270	11434358	1	+	2	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11434270	11434358	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11434359	11434477	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11434478	11434825	1	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11434478	11434825	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	intron	11434826	11434915	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	CDS	11434916	11435140	0.9	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	exon	11434916	11435140	.	+	.	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
Phchi.S3	AUGUSTUS	stop_codon	11435141	11435143	.	+	0	transcript_id "Phchi.S3G151700.t2"; gene_id "Phchi.S3G151700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14889.t1 is derived from g13357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15290611	15292062	.	-	.	Phchi.S3G220800
Phchi.S3	AUGUSTUS	transcript	15290611	15292062	.	-	.	transcript_id "Phchi.S3G220800.t1"; gene_id "Phchi.S3G220800"
Phchi.S3	AUGUSTUS	stop_codon	15290608	15290610	.	-	0	transcript_id "Phchi.S3G220800.t1"; gene_id "Phchi.S3G220800"
Phchi.S3	AUGUSTUS	CDS	15290611	15292062	0.86	-	0	transcript_id "Phchi.S3G220800.t1"; gene_id "Phchi.S3G220800"
Phchi.S3	AUGUSTUS	exon	15290611	15292062	.	-	.	transcript_id "Phchi.S3G220800.t1"; gene_id "Phchi.S3G220800"
Phchi.S3	AUGUSTUS	start_codon	15292060	15292062	.	-	0	transcript_id "Phchi.S3G220800.t1"; gene_id "Phchi.S3G220800"
# This transcript jg1411.t2 is derived from g8330.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1412.t1 is derived from g8331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	500762	501276	.	+	.	Phchi.S5G002100
Phchi.S5	AUGUSTUS	transcript	500762	501276	.	+	.	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	start_codon	500762	500764	.	+	0	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	CDS	500762	500780	1	+	0	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	exon	500762	500780	.	+	.	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	intron	500781	500857	.	+	.	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	CDS	500858	500964	1	+	2	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	exon	500858	500964	.	+	.	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	intron	500965	501195	.	+	.	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	CDS	501196	501276	0.76	+	0	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	exon	501196	501276	.	+	.	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
Phchi.S5	AUGUSTUS	stop_codon	501277	501279	.	+	0	transcript_id "Phchi.S5G002100.t1"; gene_id "Phchi.S5G002100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14847.t1 is derived from g13315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15041114	15042703	.	+	.	Phchi.S3G216600
Phchi.S3	AUGUSTUS	transcript	15041114	15042703	.	+	.	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	start_codon	15041114	15041116	.	+	0	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	CDS	15041114	15041421	0.42	+	0	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	exon	15041114	15041421	.	+	.	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	intron	15041422	15041572	.	+	.	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	CDS	15041573	15041587	0.34	+	1	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	exon	15041573	15041587	.	+	.	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	intron	15041588	15041745	.	+	.	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	CDS	15041746	15042703	1	+	1	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	exon	15041746	15042703	.	+	.	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
Phchi.S3	AUGUSTUS	stop_codon	15042704	15042706	.	+	0	transcript_id "Phchi.S3G216600.t1"; gene_id "Phchi.S3G216600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5427.t1 is derived from g2597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16820362	16821755	.	-	.	Phchi.S1G258600
Phchi.S1	AUGUSTUS	transcript	16820362	16821755	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	stop_codon	16820359	16820361	.	-	0	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16820362	16820535	0.99	-	0	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16820362	16820535	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	intron	16820536	16820663	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16820664	16820763	1	-	1	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16820664	16820763	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	intron	16820764	16820873	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16820874	16820966	1	-	1	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16820874	16820966	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	intron	16820967	16821093	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16821094	16821251	1	-	0	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16821094	16821251	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	intron	16821252	16821344	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16821345	16821420	1	-	1	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16821345	16821420	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	intron	16821421	16821502	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16821503	16821567	1	-	0	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16821503	16821567	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	intron	16821568	16821671	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	CDS	16821672	16821755	0.99	-	0	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	exon	16821672	16821755	.	-	.	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
Phchi.S1	AUGUSTUS	start_codon	16821753	16821755	.	-	0	transcript_id "Phchi.S1G258600.t1"; gene_id "Phchi.S1G258600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5329.t1 is derived from g2499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16315283	16317852	.	-	.	Phchi.S1G248800
Phchi.S1	AUGUSTUS	transcript	16315283	16317852	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	stop_codon	16315280	16315282	.	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	CDS	16315283	16315480	1	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	exon	16315283	16315480	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	intron	16315481	16315637	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	CDS	16315638	16315907	1	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	exon	16315638	16315907	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	intron	16315908	16316025	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	CDS	16316026	16316262	1	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	exon	16316026	16316262	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	intron	16316263	16316375	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	CDS	16316376	16316537	1	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	exon	16316376	16316537	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	intron	16316538	16316628	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	CDS	16316629	16317852	1	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	exon	16316629	16317852	.	-	.	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
Phchi.S1	AUGUSTUS	start_codon	16317850	16317852	.	-	0	transcript_id "Phchi.S1G248800.t1"; gene_id "Phchi.S1G248800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15423.t1 is derived from g13891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19013037	19015351	.	+	.	Phchi.S3G274200
Phchi.S3	AUGUSTUS	transcript	19013037	19015351	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	start_codon	19013037	19013039	.	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19013037	19013198	0.89	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19013037	19013198	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19013199	19013278	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19013279	19013332	1	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19013279	19013332	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19013333	19013412	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19013413	19013543	1	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19013413	19013543	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19013544	19013627	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19013628	19013744	0.79	+	1	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19013628	19013744	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19013745	19013855	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19013856	19013972	0.94	+	1	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19013856	19013972	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19013973	19014116	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19014117	19014220	1	+	1	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19014117	19014220	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19014221	19014311	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19014312	19014481	1	+	2	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19014312	19014481	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19014482	19014620	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19014621	19014674	1	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19014621	19014674	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19014675	19014767	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19014768	19014791	1	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19014768	19014791	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19014792	19014877	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19014878	19014927	1	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19014878	19014927	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19014928	19015043	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19015044	19015157	1	+	1	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19015044	19015157	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	intron	19015158	19015239	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	CDS	19015240	19015351	0.83	+	1	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	exon	19015240	19015351	.	+	.	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
Phchi.S3	AUGUSTUS	stop_codon	19015352	19015354	.	+	0	transcript_id "Phchi.S3G274200.t1"; gene_id "Phchi.S3G274200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11490.t1 is derived from g15540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6627697	6629657	.	-	.	Phchi.S4G107200
Phchi.S4	AUGUSTUS	transcript	6627697	6629657	.	-	.	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	stop_codon	6627694	6627696	.	-	0	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	CDS	6627697	6628156	0.97	-	1	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	exon	6627697	6628156	.	-	.	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	intron	6628157	6628254	.	-	.	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	CDS	6628255	6629657	0.97	-	0	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	exon	6628255	6629657	.	-	.	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	start_codon	6629655	6629657	.	-	0	transcript_id "Phchi.S4G107200.t1"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	transcript	6627697	6628550	.	-	.	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	stop_codon	6627694	6627696	.	-	0	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	CDS	6627697	6628156	0.95	-	1	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	exon	6627697	6628156	.	-	.	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	intron	6628157	6628254	.	-	.	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	CDS	6628255	6628550	0.9	-	0	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	exon	6628255	6628550	.	-	.	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
Phchi.S4	AUGUSTUS	start_codon	6628548	6628550	.	-	0	transcript_id "Phchi.S4G107200.t2"; gene_id "Phchi.S4G107200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12635.t1 is derived from g15984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C86	AUGUSTUS	gene	25288	26091	.	-	.	Phchi.C86G000400
Phchi.C86	AUGUSTUS	transcript	25288	26091	.	-	.	transcript_id "Phchi.C86G000400.t1"; gene_id "Phchi.C86G000400"
Phchi.C86	AUGUSTUS	stop_codon	25285	25287	.	-	0	transcript_id "Phchi.C86G000400.t1"; gene_id "Phchi.C86G000400"
Phchi.C86	AUGUSTUS	CDS	25288	26091	0.96	-	0	transcript_id "Phchi.C86G000400.t1"; gene_id "Phchi.C86G000400"
Phchi.C86	AUGUSTUS	exon	25288	26091	.	-	.	transcript_id "Phchi.C86G000400.t1"; gene_id "Phchi.C86G000400"
Phchi.C86	AUGUSTUS	start_codon	26089	26091	.	-	0	transcript_id "Phchi.C86G000400.t1"; gene_id "Phchi.C86G000400"
# This transcript jg2881.t2 is derived from g50.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2882.t1 is derived from g51.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	262405	264405	.	+	.	Phchi.S1G004100
Phchi.S1	AUGUSTUS	transcript	262405	264405	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	start_codon	262405	262407	.	+	0	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	CDS	262405	262943	0.66	+	0	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	exon	262405	262943	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	intron	262944	263023	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	CDS	263024	263122	1	+	1	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	exon	263024	263122	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	intron	263123	263219	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	CDS	263220	263435	1	+	1	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	exon	263220	263435	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	intron	263436	263529	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	CDS	263530	263668	1	+	1	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	exon	263530	263668	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	intron	263669	263765	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	CDS	263766	264011	1	+	0	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	exon	263766	264011	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	intron	264012	264120	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	CDS	264121	264405	0.94	+	0	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	exon	264121	264405	.	+	.	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
Phchi.S1	AUGUSTUS	stop_codon	264406	264408	.	+	0	transcript_id "Phchi.S1G004100.t1"; gene_id "Phchi.S1G004100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2951.t1 is derived from g120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	722496	725429	.	+	.	Phchi.S1G011000
Phchi.S1	AUGUSTUS	transcript	722496	725429	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	start_codon	722496	722498	.	+	0	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	CDS	722496	723941	0.72	+	0	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	exon	722496	723941	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	intron	723942	724086	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	CDS	724087	724257	0.64	+	0	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	exon	724087	724257	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	intron	724258	724366	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	CDS	724367	724426	0.56	+	0	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	exon	724367	724426	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	intron	724427	724665	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	CDS	724666	724874	0.45	+	0	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	exon	724666	724874	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	intron	724875	724978	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	CDS	724979	725429	0.65	+	1	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	exon	724979	725429	.	+	.	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
Phchi.S1	AUGUSTUS	stop_codon	725430	725432	.	+	0	transcript_id "Phchi.S1G011000.t1"; gene_id "Phchi.S1G011000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10288.t1 is derived from g7464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46829443	46830402	.	-	.	Phchi.S1G744700
Phchi.S1	AUGUSTUS	transcript	46829443	46830402	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	stop_codon	46829440	46829442	.	-	0	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	CDS	46829443	46829450	1	-	2	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	exon	46829443	46829450	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	intron	46829451	46829623	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	CDS	46829624	46829998	0.54	-	2	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	exon	46829624	46829998	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	intron	46829999	46830081	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	CDS	46830082	46830140	0.52	-	1	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	exon	46830082	46830140	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	intron	46830141	46830232	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	CDS	46830233	46830402	0.77	-	0	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	exon	46830233	46830402	.	-	.	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
Phchi.S1	AUGUSTUS	start_codon	46830400	46830402	.	-	0	transcript_id "Phchi.S1G744700.t1"; gene_id "Phchi.S1G744700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13937.t1 is derived from g12404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9808952	9810036	.	-	.	Phchi.S3G125600
Phchi.S3	AUGUSTUS	transcript	9808952	9810036	.	-	.	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	stop_codon	9808949	9808951	.	-	0	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	CDS	9808952	9809352	1	-	2	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	exon	9808952	9809352	.	-	.	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	intron	9809353	9809487	.	-	.	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	CDS	9809488	9809653	1	-	0	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	exon	9809488	9809653	.	-	.	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	intron	9809654	9809745	.	-	.	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	CDS	9809746	9810036	0.98	-	0	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	exon	9809746	9810036	.	-	.	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
Phchi.S3	AUGUSTUS	start_codon	9810034	9810036	.	-	0	transcript_id "Phchi.S3G125600.t1"; gene_id "Phchi.S3G125600"
# This transcript jg3109.t2 is derived from g278.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3110.t1 is derived from g279.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1769966	1773330	.	-	.	Phchi.S1G026900
Phchi.S1	AUGUSTUS	transcript	1769966	1771893	.	-	.	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	stop_codon	1769963	1769965	.	-	0	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	CDS	1769966	1770561	0.49	-	2	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	exon	1769966	1770561	.	-	.	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	intron	1770562	1770659	.	-	.	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	CDS	1770660	1771893	0.46	-	0	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	exon	1770660	1771893	.	-	.	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	start_codon	1771891	1771893	.	-	0	transcript_id "Phchi.S1G026900.t1"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	transcript	1769966	1770517	.	-	.	transcript_id "Phchi.S1G026900.t2"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	stop_codon	1769963	1769965	.	-	0	transcript_id "Phchi.S1G026900.t2"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	CDS	1769966	1770517	0.66	-	0	transcript_id "Phchi.S1G026900.t2"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	exon	1769966	1770517	.	-	.	transcript_id "Phchi.S1G026900.t2"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	start_codon	1770515	1770517	.	-	0	transcript_id "Phchi.S1G026900.t2"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	transcript	1770571	1773330	.	-	.	transcript_id "Phchi.S1G026900.t3"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	stop_codon	1770568	1770570	.	-	0	transcript_id "Phchi.S1G026900.t3"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	CDS	1770571	1773330	0.58	-	0	transcript_id "Phchi.S1G026900.t3"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	exon	1770571	1773330	.	-	.	transcript_id "Phchi.S1G026900.t3"; gene_id "Phchi.S1G026900"
Phchi.S1	AUGUSTUS	start_codon	1773328	1773330	.	-	0	transcript_id "Phchi.S1G026900.t3"; gene_id "Phchi.S1G026900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12654.t1 is derived from g14453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	7715	9146	.	-	.	Phchi.C12G000400
Phchi.C12	AUGUSTUS	transcript	7715	9146	.	-	.	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	stop_codon	7712	7714	.	-	0	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	CDS	7715	8446	0.9	-	0	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	exon	7715	8446	.	-	.	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	intron	8447	8535	.	-	.	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	CDS	8536	8742	0.95	-	0	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	exon	8536	8742	.	-	.	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	intron	8743	9110	.	-	.	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	CDS	9111	9146	0.76	-	0	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	exon	9111	9146	.	-	.	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
Phchi.C12	AUGUSTUS	start_codon	9144	9146	.	-	0	transcript_id "Phchi.C12G000400.t1"; gene_id "Phchi.C12G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8008.t1 is derived from g5183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32456512	32462307	.	-	.	Phchi.S1G516700
Phchi.S1	AUGUSTUS	transcript	32456512	32462307	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	stop_codon	32456509	32456511	.	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32456512	32456568	0.66	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32456512	32456568	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32456569	32456644	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32456645	32456706	0.57	-	2	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32456645	32456706	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32456707	32456930	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32456931	32456998	0.62	-	1	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32456931	32456998	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32456999	32457088	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32457089	32458290	0.25	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32457089	32458290	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32458291	32458408	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32458409	32458650	0.63	-	2	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32458409	32458650	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32458651	32458772	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32458773	32459554	0.99	-	1	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32458773	32459554	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32459555	32459639	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32459640	32459980	1	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32459640	32459980	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32459981	32460091	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32460092	32460315	1	-	2	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32460092	32460315	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32460316	32460413	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32460414	32460724	1	-	1	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32460414	32460724	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32460725	32460895	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32460896	32461155	0.98	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32460896	32461155	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32461156	32461274	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32461275	32461475	1	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32461275	32461475	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32461476	32461628	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32461629	32461804	1	-	2	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32461629	32461804	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32461805	32461901	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32461902	32461956	1	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32461902	32461956	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	intron	32461957	32462055	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	CDS	32462056	32462307	0.54	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	exon	32462056	32462307	.	-	.	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
Phchi.S1	AUGUSTUS	start_codon	32462305	32462307	.	-	0	transcript_id "Phchi.S1G516700.t1"; gene_id "Phchi.S1G516700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11197.t1 is derived from g15247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4645336	4653267	.	+	.	Phchi.S4G077900
Phchi.S4	AUGUSTUS	transcript	4645336	4653267	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	start_codon	4645336	4645338	.	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4645336	4645583	0.54	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4645336	4645583	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4645584	4645668	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4645669	4645849	1	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4645669	4645849	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4645850	4645939	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4645940	4646053	1	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4645940	4646053	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4646054	4646137	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4646138	4646272	1	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4646138	4646272	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4646273	4646363	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4646364	4646430	1	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4646364	4646430	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4646431	4646587	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4646588	4646652	0.72	+	2	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4646588	4646652	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4646653	4646753	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4646754	4646888	0.73	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4646754	4646888	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4646889	4646967	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4646968	4647126	1	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4646968	4647126	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4647127	4647211	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4647212	4647353	0.99	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4647212	4647353	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4647354	4647464	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4647465	4647531	1	+	2	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4647465	4647531	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4647532	4647650	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4647651	4647855	0.99	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4647651	4647855	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4647856	4647939	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4647940	4648100	1	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4647940	4648100	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4648101	4648197	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4648198	4648419	0.7	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4648198	4648419	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4648420	4648522	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4648523	4648791	0.72	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4648523	4648791	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4648792	4648877	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4648878	4649149	1	+	2	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4648878	4649149	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4649150	4649304	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4649305	4649368	0.67	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4649305	4649368	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4649369	4649556	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4649557	4649797	0.77	+	2	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4649557	4649797	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4649798	4649914	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4649915	4650009	1	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4649915	4650009	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4650010	4650108	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4650109	4650317	1	+	2	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4650109	4650317	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4650318	4650407	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4650408	4650617	0.99	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4650408	4650617	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4650618	4650720	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4650721	4651221	0.94	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4650721	4651221	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4651222	4651358	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4651359	4651459	0.57	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4651359	4651459	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4651460	4651573	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4651574	4651637	0.57	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4651574	4651637	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4651638	4651742	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4651743	4652075	0.99	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4651743	4652075	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4652076	4652180	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4652181	4653037	0.94	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4652181	4653037	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	intron	4653038	4653125	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	CDS	4653126	4653267	1	+	1	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	exon	4653126	4653267	.	+	.	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
Phchi.S4	AUGUSTUS	stop_codon	4653268	4653270	.	+	0	transcript_id "Phchi.S4G077900.t1"; gene_id "Phchi.S4G077900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11651.t1 is derived from g15702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7515467	7517073	.	+	.	Phchi.S4G123300
Phchi.S4	AUGUSTUS	transcript	7515467	7517073	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	start_codon	7515467	7515469	.	+	0	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	CDS	7515467	7515546	0.78	+	0	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	exon	7515467	7515546	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	intron	7515547	7515641	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	CDS	7515642	7515706	0.78	+	1	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	exon	7515642	7515706	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	intron	7515707	7516100	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	CDS	7516101	7516148	0.99	+	2	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	exon	7516101	7516148	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	intron	7516149	7516216	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	CDS	7516217	7517073	0.74	+	2	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	exon	7516217	7517073	.	+	.	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
Phchi.S4	AUGUSTUS	stop_codon	7517074	7517076	.	+	0	transcript_id "Phchi.S4G123300.t1"; gene_id "Phchi.S4G123300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg270.t1 is derived from g10052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1921984	1923343	.	+	.	Phchi.S6G022900
Phchi.S6	AUGUSTUS	transcript	1921984	1923343	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	start_codon	1921984	1921986	.	+	0	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	CDS	1921984	1922157	1	+	0	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	exon	1921984	1922157	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	intron	1922158	1922266	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	CDS	1922267	1922401	1	+	0	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	exon	1922267	1922401	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	intron	1922402	1922504	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	CDS	1922505	1922739	1	+	0	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	exon	1922505	1922739	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	intron	1922740	1922849	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	CDS	1922850	1923053	1	+	2	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	exon	1922850	1923053	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	intron	1923054	1923173	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	CDS	1923174	1923343	1	+	2	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	exon	1923174	1923343	.	+	.	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
Phchi.S6	AUGUSTUS	stop_codon	1923344	1923346	.	+	0	transcript_id "Phchi.S6G022900.t1"; gene_id "Phchi.S6G022900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6936.t1 is derived from g4108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26053376	26055519	.	-	.	Phchi.S1G409500
Phchi.S1	AUGUSTUS	transcript	26053376	26055519	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	stop_codon	26053373	26053375	.	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26053376	26053421	0.99	-	1	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26053376	26053421	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26053422	26053549	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26053550	26053675	1	-	1	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26053550	26053675	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26053676	26053805	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26053806	26053945	1	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26053806	26053945	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26053946	26054071	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26054072	26054116	1	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26054072	26054116	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26054117	26054223	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26054224	26054277	1	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26054224	26054277	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26054278	26054401	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26054402	26054533	1	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26054402	26054533	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26054534	26054647	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26054648	26054716	1	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26054648	26054716	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26054717	26054911	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26054912	26055123	1	-	2	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26054912	26055123	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	intron	26055124	26055245	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	CDS	26055246	26055519	0.56	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	exon	26055246	26055519	.	-	.	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
Phchi.S1	AUGUSTUS	start_codon	26055517	26055519	.	-	0	transcript_id "Phchi.S1G409500.t1"; gene_id "Phchi.S1G409500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7569.t1 is derived from g4743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30082854	30084287	.	+	.	Phchi.S1G472800
Phchi.S1	AUGUSTUS	transcript	30082854	30084287	.	+	.	transcript_id "Phchi.S1G472800.t1"; gene_id "Phchi.S1G472800"
Phchi.S1	AUGUSTUS	start_codon	30082854	30082856	.	+	0	transcript_id "Phchi.S1G472800.t1"; gene_id "Phchi.S1G472800"
Phchi.S1	AUGUSTUS	CDS	30082854	30084287	0.6	+	0	transcript_id "Phchi.S1G472800.t1"; gene_id "Phchi.S1G472800"
Phchi.S1	AUGUSTUS	exon	30082854	30084287	.	+	.	transcript_id "Phchi.S1G472800.t1"; gene_id "Phchi.S1G472800"
Phchi.S1	AUGUSTUS	stop_codon	30084288	30084290	.	+	0	transcript_id "Phchi.S1G472800.t1"; gene_id "Phchi.S1G472800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1709.t1 is derived from g8629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2644270	2644950	.	+	.	Phchi.S5G031800
Phchi.S5	AUGUSTUS	transcript	2644270	2644950	.	+	.	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	start_codon	2644270	2644272	.	+	0	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	CDS	2644270	2644295	0.38	+	0	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	exon	2644270	2644295	.	+	.	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	intron	2644296	2644614	.	+	.	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	CDS	2644615	2644677	0.71	+	1	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	exon	2644615	2644677	.	+	.	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	intron	2644678	2644769	.	+	.	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	CDS	2644770	2644950	0.86	+	1	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	exon	2644770	2644950	.	+	.	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
Phchi.S5	AUGUSTUS	stop_codon	2644951	2644953	.	+	0	transcript_id "Phchi.S5G031800.t1"; gene_id "Phchi.S5G031800"
# This transcript jg6624.t2 is derived from g3796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6625.t1 is derived from g3797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24144590	24147641	.	-	.	Phchi.S1G378400
Phchi.S1	AUGUSTUS	transcript	24144590	24147641	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	stop_codon	24144587	24144589	.	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24144590	24144655	1	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24144590	24144655	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24144656	24144750	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24144751	24144808	1	-	1	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24144751	24144808	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24144809	24144890	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24144891	24145100	1	-	1	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24144891	24145100	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24145101	24145299	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24145300	24145394	1	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24145300	24145394	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24145395	24145480	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24145481	24145600	0.61	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24145481	24145600	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24145601	24145704	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24145705	24145782	0.61	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24145705	24145782	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24145783	24145907	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24145908	24145980	1	-	1	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24145908	24145980	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24145981	24146066	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24146067	24146200	1	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24146067	24146200	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24146201	24146294	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24146295	24146372	0.99	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24146295	24146372	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24146373	24146484	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24146485	24146646	0.99	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24146485	24146646	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24146647	24146746	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24146747	24146893	1	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24146747	24146893	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24146894	24146983	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24146984	24147246	1	-	2	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24146984	24147246	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	intron	24147247	24147490	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	CDS	24147491	24147641	0.86	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	exon	24147491	24147641	.	-	.	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
Phchi.S1	AUGUSTUS	start_codon	24147639	24147641	.	-	0	transcript_id "Phchi.S1G378400.t1"; gene_id "Phchi.S1G378400"
# This transcript jg3798.t2 is derived from g967.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3799.t1 is derived from g968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5803500	5804227	.	-	.	Phchi.S1G095800
Phchi.S1	AUGUSTUS	transcript	5803500	5804227	.	-	.	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	stop_codon	5803497	5803499	.	-	0	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	CDS	5803500	5803611	1	-	1	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	exon	5803500	5803611	.	-	.	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	intron	5803612	5803717	.	-	.	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	CDS	5803718	5803808	1	-	2	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	exon	5803718	5803808	.	-	.	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	intron	5803809	5804139	.	-	.	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	CDS	5804140	5804227	1	-	0	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	exon	5804140	5804227	.	-	.	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
Phchi.S1	AUGUSTUS	start_codon	5804225	5804227	.	-	0	transcript_id "Phchi.S1G095800.t1"; gene_id "Phchi.S1G095800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1509.t1 is derived from g8428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1291361	1295186	.	+	.	Phchi.S5G011800
Phchi.S5	AUGUSTUS	transcript	1291361	1295186	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	start_codon	1291361	1291363	.	+	0	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1291361	1291457	0.83	+	0	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1291361	1291457	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1291458	1292132	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1292133	1292265	1	+	2	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1292133	1292265	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1292266	1292398	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1292399	1292470	1	+	1	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1292399	1292470	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1292471	1292588	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1292589	1292732	1	+	1	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1292589	1292732	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1292733	1292937	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1292938	1293009	1	+	1	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1292938	1293009	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1293010	1293112	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1293113	1293184	0.99	+	1	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1293113	1293184	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1293185	1293339	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1293340	1293458	1	+	1	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1293340	1293458	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1293459	1293553	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1293554	1293691	1	+	2	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1293554	1293691	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1293692	1293828	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1293829	1294170	0.99	+	2	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1293829	1294170	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1294171	1294340	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1294341	1294735	1	+	2	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1294341	1294735	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	intron	1294736	1294871	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	CDS	1294872	1295186	0.97	+	0	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	exon	1294872	1295186	.	+	.	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
Phchi.S5	AUGUSTUS	stop_codon	1295187	1295189	.	+	0	transcript_id "Phchi.S5G011800.t1"; gene_id "Phchi.S5G011800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8763.t1 is derived from g5938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37858198	37862098	.	+	.	Phchi.S1G592200
Phchi.S1	AUGUSTUS	transcript	37858198	37862098	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	start_codon	37858198	37858200	.	+	0	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37858198	37858220	0.99	+	0	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37858198	37858220	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	intron	37858221	37858373	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37858374	37858604	0.76	+	1	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37858374	37858604	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	intron	37858605	37858690	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37858691	37858791	0.75	+	1	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37858691	37858791	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	intron	37858792	37858901	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37858902	37859301	0.6	+	2	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37858902	37859301	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	intron	37859302	37859393	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37859394	37859414	0.56	+	1	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37859394	37859414	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	intron	37859415	37859505	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37859506	37861604	0.39	+	1	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37859506	37861604	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	intron	37861605	37861691	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	CDS	37861692	37862098	0.47	+	2	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	exon	37861692	37862098	.	+	.	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
Phchi.S1	AUGUSTUS	stop_codon	37862099	37862101	.	+	0	transcript_id "Phchi.S1G592200.t1"; gene_id "Phchi.S1G592200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12397.t1 is derived from g8074.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17441295	17445283	.	-	.	Phchi.S2G047700
Phchi.S2	AUGUSTUS	transcript	17441295	17445283	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	stop_codon	17441292	17441294	.	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17441295	17441460	1	-	1	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17441295	17441460	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17441461	17441552	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17441553	17441771	1	-	1	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17441553	17441771	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17441772	17441889	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17441890	17442026	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17441890	17442026	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442027	17442145	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442146	17442223	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442146	17442223	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442224	17442315	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442316	17442474	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442316	17442474	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442475	17442551	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442552	17442725	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442552	17442725	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442726	17442808	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442809	17443021	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442809	17443021	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443022	17443228	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17443229	17443409	1	-	1	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17443229	17443409	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443410	17443482	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17443483	17443733	0.97	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17443483	17443733	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443734	17443817	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17443818	17443858	1	-	2	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17443818	17443858	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443859	17444019	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17444020	17444137	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17444020	17444137	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17444138	17444308	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17444309	17444481	1	-	2	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17444309	17444481	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17444482	17444586	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17444587	17445283	1	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17444587	17445283	.	-	.	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	start_codon	17445281	17445283	.	-	0	transcript_id "Phchi.S2G047700.t1"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	transcript	17441295	17445283	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	stop_codon	17441292	17441294	.	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17441295	17441460	0.99	-	1	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17441295	17441460	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17441461	17441552	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17441553	17441771	1	-	1	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17441553	17441771	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17441772	17441889	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17441890	17442026	1	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17441890	17442026	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442027	17442145	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442146	17442223	1	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442146	17442223	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442224	17442315	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442316	17442474	1	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442316	17442474	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442475	17442551	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442552	17442728	0.7	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442552	17442728	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17442729	17442808	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17442809	17443021	0.88	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17442809	17443021	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443022	17443228	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17443229	17443409	1	-	1	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17443229	17443409	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443410	17443482	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17443483	17443733	0.97	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17443483	17443733	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443734	17443817	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17443818	17443858	1	-	2	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17443818	17443858	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17443859	17444019	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17444020	17444137	1	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17444020	17444137	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17444138	17444308	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17444309	17444481	1	-	2	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17444309	17444481	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	intron	17444482	17444586	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	CDS	17444587	17445283	0.96	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	exon	17444587	17445283	.	-	.	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
Phchi.S2	AUGUSTUS	start_codon	17445281	17445283	.	-	0	transcript_id "Phchi.S2G047700.t2"; gene_id "Phchi.S2G047700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12559.t1 is derived from g8236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34757100	34757796	.	-	.	Phchi.S2G063900
Phchi.S2	AUGUSTUS	transcript	34757100	34757796	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	stop_codon	34757097	34757099	.	-	0	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	CDS	34757100	34757246	0.9	-	0	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	exon	34757100	34757246	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	intron	34757247	34757329	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	CDS	34757330	34757493	0.68	-	2	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	exon	34757330	34757493	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	intron	34757494	34757575	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	CDS	34757576	34757656	0.93	-	2	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	exon	34757576	34757656	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	intron	34757657	34757750	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	CDS	34757751	34757796	0.37	-	0	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	exon	34757751	34757796	.	-	.	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
Phchi.S2	AUGUSTUS	start_codon	34757794	34757796	.	-	0	transcript_id "Phchi.S2G063900.t1"; gene_id "Phchi.S2G063900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13227.t1 is derived from g11692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4784389	4785013	.	+	.	Phchi.S3G054600
Phchi.S3	AUGUSTUS	transcript	4784389	4785013	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	start_codon	4784389	4784391	.	+	0	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	CDS	4784389	4784431	0.62	+	0	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	exon	4784389	4784431	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	intron	4784432	4784527	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	CDS	4784528	4784573	0.4	+	2	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	exon	4784528	4784573	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	intron	4784574	4784638	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	CDS	4784639	4784702	0.4	+	1	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	exon	4784639	4784702	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	intron	4784703	4784848	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	CDS	4784849	4785013	0.79	+	0	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	exon	4784849	4785013	.	+	.	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
Phchi.S3	AUGUSTUS	stop_codon	4785014	4785016	.	+	0	transcript_id "Phchi.S3G054600.t1"; gene_id "Phchi.S3G054600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4971.t1 is derived from g2141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13814120	13814530	.	-	.	Phchi.S1G213000
Phchi.S1	AUGUSTUS	transcript	13814120	13814530	.	-	.	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	stop_codon	13814117	13814119	.	-	0	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	CDS	13814120	13814265	0.56	-	2	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	exon	13814120	13814265	.	-	.	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	intron	13814266	13814412	.	-	.	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	CDS	13814413	13814530	1	-	0	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	exon	13814413	13814530	.	-	.	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
Phchi.S1	AUGUSTUS	start_codon	13814528	13814530	.	-	0	transcript_id "Phchi.S1G213000.t1"; gene_id "Phchi.S1G213000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7605.t1 is derived from g4779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30222057	30224641	.	-	.	Phchi.S1G476400
Phchi.S1	AUGUSTUS	transcript	30222057	30224641	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	stop_codon	30222054	30222056	.	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30222057	30222170	0.49	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30222057	30222170	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30222171	30222317	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30222318	30222596	0.95	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30222318	30222596	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30222597	30222767	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30222768	30223043	1	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30222768	30223043	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30223044	30223120	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30223121	30223339	0.99	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30223121	30223339	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30223340	30223444	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30223445	30223610	0.79	-	1	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30223445	30223610	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30223611	30223712	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30223713	30223887	1	-	2	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30223713	30223887	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30223888	30224003	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30224004	30224115	1	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30224004	30224115	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	intron	30224116	30224398	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	CDS	30224399	30224641	1	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	exon	30224399	30224641	.	-	.	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
Phchi.S1	AUGUSTUS	start_codon	30224639	30224641	.	-	0	transcript_id "Phchi.S1G476400.t1"; gene_id "Phchi.S1G476400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14106.t1 is derived from g12573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10881577	10883067	.	+	.	Phchi.S3G142500
Phchi.S3	AUGUSTUS	transcript	10881577	10883067	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	start_codon	10881577	10881579	.	+	0	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	CDS	10881577	10881579	1	+	0	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	exon	10881577	10881579	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	intron	10881580	10881880	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	CDS	10881881	10881958	1	+	0	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	exon	10881881	10881958	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	intron	10881959	10882125	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	CDS	10882126	10882306	1	+	0	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	exon	10882126	10882306	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	intron	10882307	10882434	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	CDS	10882435	10882532	1	+	2	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	exon	10882435	10882532	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	intron	10882533	10882641	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	CDS	10882642	10883067	0.99	+	0	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	exon	10882642	10883067	.	+	.	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
Phchi.S3	AUGUSTUS	stop_codon	10883068	10883070	.	+	0	transcript_id "Phchi.S3G142500.t1"; gene_id "Phchi.S3G142500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13310.t1 is derived from g11776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5747061	5750357	.	-	.	Phchi.S3G062900
Phchi.S3	AUGUSTUS	transcript	5747061	5750357	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	stop_codon	5747058	5747060	.	-	0	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5747061	5747342	1	-	0	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5747061	5747342	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	intron	5747343	5747462	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5747463	5747708	0.98	-	0	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5747463	5747708	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	intron	5747709	5747822	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5747823	5747961	1	-	1	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5747823	5747961	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	intron	5747962	5748050	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5748051	5748278	1	-	1	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5748051	5748278	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	intron	5748279	5748379	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5748380	5748478	1	-	1	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5748380	5748478	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	intron	5748479	5748615	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5748616	5748964	1	-	2	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5748616	5748964	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	intron	5748965	5749063	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	CDS	5749064	5750357	0.96	-	0	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	exon	5749064	5750357	.	-	.	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
Phchi.S3	AUGUSTUS	start_codon	5750355	5750357	.	-	0	transcript_id "Phchi.S3G062900.t1"; gene_id "Phchi.S3G062900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9448.t1 is derived from g6624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41515144	41521256	.	-	.	Phchi.S1G660700
Phchi.S1	AUGUSTUS	transcript	41515144	41521256	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	stop_codon	41515141	41515143	.	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41515144	41515465	0.57	-	1	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41515144	41515465	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41515466	41515670	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41515671	41515801	0.88	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41515671	41515801	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41515802	41515957	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41515958	41516152	0.96	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41515958	41516152	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41516153	41516270	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41516271	41516468	0.84	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41516271	41516468	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41516469	41516715	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41516716	41516856	1	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41516716	41516856	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41516857	41516951	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41516952	41517083	0.97	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41516952	41517083	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517084	41517190	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41517191	41517410	0.83	-	1	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41517191	41517410	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517411	41517559	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41517560	41517728	0.94	-	2	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41517560	41517728	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517729	41517817	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41517818	41517920	0.93	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41517818	41517920	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517921	41518201	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41518202	41518312	1	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41518202	41518312	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41518313	41518450	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41518451	41518565	0.9	-	1	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41518451	41518565	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41518566	41518680	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41518681	41518817	1	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41518681	41518817	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41518818	41519138	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41519139	41519366	0.81	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41519139	41519366	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41519367	41519446	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41519447	41519593	0.73	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41519447	41519593	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41519594	41519744	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41519745	41521256	0.74	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41519745	41521256	.	-	.	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	start_codon	41521254	41521256	.	-	0	transcript_id "Phchi.S1G660700.t1"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	transcript	41515144	41521256	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	stop_codon	41515141	41515143	.	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41515144	41515465	0.52	-	1	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41515144	41515465	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41515466	41515670	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41515671	41515798	0.78	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41515671	41515798	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41515799	41515957	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41515958	41516152	0.94	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41515958	41516152	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41516153	41516270	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41516271	41516468	0.92	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41516271	41516468	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41516469	41516715	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41516716	41516856	1	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41516716	41516856	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41516857	41516951	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41516952	41517083	1	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41516952	41517083	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517084	41517190	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41517191	41517410	0.83	-	1	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41517191	41517410	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517411	41517559	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41517560	41517728	0.97	-	2	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41517560	41517728	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517729	41517817	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41517818	41517920	0.96	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41517818	41517920	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41517921	41518201	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41518202	41518312	1	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41518202	41518312	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41518313	41518450	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41518451	41518565	0.93	-	1	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41518451	41518565	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41518566	41518680	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41518681	41518817	1	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41518681	41518817	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41518818	41519138	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41519139	41519366	0.77	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41519139	41519366	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41519367	41519446	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41519447	41519593	0.71	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41519447	41519593	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	intron	41519594	41519744	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	CDS	41519745	41521256	0.61	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	exon	41519745	41521256	.	-	.	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
Phchi.S1	AUGUSTUS	start_codon	41521254	41521256	.	-	0	transcript_id "Phchi.S1G660700.t2"; gene_id "Phchi.S1G660700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15846.t1 is derived from g14316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21793795	21799730	.	-	.	Phchi.S3G316500
Phchi.S3	AUGUSTUS	transcript	21793795	21799730	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	stop_codon	21793792	21793794	.	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21793795	21794056	0.85	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21793795	21794056	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21794057	21794139	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21794140	21794244	1	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21794140	21794244	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21794245	21794347	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21794348	21794493	0.95	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21794348	21794493	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21794494	21794592	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21794593	21794656	1	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21794593	21794656	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21794657	21794746	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21794747	21794920	1	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21794747	21794920	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21794921	21795044	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21795045	21795125	0.86	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21795045	21795125	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21795126	21795226	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21795227	21795417	0.95	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21795227	21795417	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21795418	21795516	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21795517	21795633	1	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21795517	21795633	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21795634	21795914	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21795915	21795993	1	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21795915	21795993	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21795994	21796199	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21796200	21796264	0.61	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21796200	21796264	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21796265	21796425	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21796426	21796503	0.61	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21796426	21796503	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21796504	21796594	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21796595	21797005	0.85	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21796595	21797005	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21797006	21797096	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21797097	21797168	1	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21797097	21797168	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21797169	21797243	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21797244	21797334	1	-	1	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21797244	21797334	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21797335	21797701	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21797702	21797828	1	-	2	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21797702	21797828	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21797829	21798217	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21798218	21798692	1	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21798218	21798692	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	intron	21798693	21798941	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	CDS	21798942	21799730	1	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	exon	21798942	21799730	.	-	.	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
Phchi.S3	AUGUSTUS	start_codon	21799728	21799730	.	-	0	transcript_id "Phchi.S3G316500.t1"; gene_id "Phchi.S3G316500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13622.t1 is derived from g12089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7812160	7812519	.	+	.	Phchi.S3G094100
Phchi.S3	AUGUSTUS	transcript	7812160	7812519	.	+	.	transcript_id "Phchi.S3G094100.t1"; gene_id "Phchi.S3G094100"
Phchi.S3	AUGUSTUS	start_codon	7812160	7812162	.	+	0	transcript_id "Phchi.S3G094100.t1"; gene_id "Phchi.S3G094100"
Phchi.S3	AUGUSTUS	CDS	7812160	7812519	0.53	+	0	transcript_id "Phchi.S3G094100.t1"; gene_id "Phchi.S3G094100"
Phchi.S3	AUGUSTUS	exon	7812160	7812519	.	+	.	transcript_id "Phchi.S3G094100.t1"; gene_id "Phchi.S3G094100"
Phchi.S3	AUGUSTUS	stop_codon	7812520	7812522	.	+	0	transcript_id "Phchi.S3G094100.t1"; gene_id "Phchi.S3G094100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7016.t1 is derived from g4188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26410437	26412274	.	+	.	Phchi.S1G417500
Phchi.S1	AUGUSTUS	transcript	26410437	26412274	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	start_codon	26410437	26410439	.	+	0	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	CDS	26410437	26410535	0.48	+	0	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	exon	26410437	26410535	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	intron	26410536	26410669	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	CDS	26410670	26411134	0.5	+	0	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	exon	26410670	26411134	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	intron	26411135	26411210	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	CDS	26411211	26411447	0.67	+	0	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	exon	26411211	26411447	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	intron	26411448	26411525	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	CDS	26411526	26411818	0.95	+	0	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	exon	26411526	26411818	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	intron	26411819	26411910	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	CDS	26411911	26412274	1	+	1	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	exon	26411911	26412274	.	+	.	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
Phchi.S1	AUGUSTUS	stop_codon	26412275	26412277	.	+	0	transcript_id "Phchi.S1G417500.t1"; gene_id "Phchi.S1G417500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6368.t1 is derived from g3540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22594640	22595642	.	+	.	Phchi.S1G352700
Phchi.S1	AUGUSTUS	transcript	22594640	22595642	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	start_codon	22594640	22594642	.	+	0	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	CDS	22594640	22594845	0.73	+	0	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	exon	22594640	22594845	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	intron	22594846	22594993	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	CDS	22594994	22595147	1	+	1	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	exon	22594994	22595147	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	intron	22595148	22595261	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	CDS	22595262	22595392	1	+	0	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	exon	22595262	22595392	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	intron	22595393	22595485	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	CDS	22595486	22595642	0.99	+	1	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	exon	22595486	22595642	.	+	.	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
Phchi.S1	AUGUSTUS	stop_codon	22595643	22595645	.	+	0	transcript_id "Phchi.S1G352700.t1"; gene_id "Phchi.S1G352700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14754.t1 is derived from g13222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14555940	14558551	.	+	.	Phchi.S3G207300
Phchi.S3	AUGUSTUS	transcript	14555940	14558551	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	start_codon	14555940	14555942	.	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14555940	14556047	1	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14555940	14556047	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14556048	14556149	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14556150	14556256	0.99	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14556150	14556256	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14556257	14556337	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14556338	14556416	1	+	1	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14556338	14556416	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14556417	14556512	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14556513	14556698	1	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14556513	14556698	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14556699	14556894	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14556895	14556993	1	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14556895	14556993	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14556994	14557084	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14557085	14557253	1	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14557085	14557253	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14557254	14557377	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14557378	14557484	0.99	+	2	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14557378	14557484	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14557485	14557592	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14557593	14557732	0.99	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14557593	14557732	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14557733	14557879	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14557880	14557952	1	+	1	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14557880	14557952	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14557953	14558030	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14558031	14558143	1	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14558031	14558143	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14558144	14558226	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14558227	14558344	1	+	1	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14558227	14558344	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	intron	14558345	14558428	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	CDS	14558429	14558551	1	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	exon	14558429	14558551	.	+	.	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
Phchi.S3	AUGUSTUS	stop_codon	14558552	14558554	.	+	0	transcript_id "Phchi.S3G207300.t1"; gene_id "Phchi.S3G207300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3414.t1 is derived from g583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3386240	3387787	.	-	.	Phchi.S1G057300
Phchi.S1	AUGUSTUS	transcript	3386240	3387787	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	stop_codon	3386237	3386239	.	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386240	3386289	0.64	-	2	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386240	3386289	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386290	3386373	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386374	3386454	0.93	-	2	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386374	3386454	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386455	3386529	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386530	3386548	0.95	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386530	3386548	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386549	3386824	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386825	3386875	1	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386825	3386875	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386876	3386961	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386962	3387054	1	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386962	3387054	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3387055	3387137	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3387138	3387380	1	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3387138	3387380	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3387381	3387535	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3387536	3387787	0.98	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3387536	3387787	.	-	.	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	start_codon	3387785	3387787	.	-	0	transcript_id "Phchi.S1G057300.t1"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	transcript	3386240	3387787	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	stop_codon	3386237	3386239	.	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386240	3386289	0.69	-	2	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386240	3386289	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386290	3386373	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386374	3386454	0.88	-	2	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386374	3386454	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386455	3386529	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386530	3386539	0.93	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386530	3386539	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386540	3386824	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386825	3386875	1	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386825	3386875	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3386876	3386961	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3386962	3387054	1	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3386962	3387054	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3387055	3387137	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3387138	3387380	0.97	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3387138	3387380	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	intron	3387381	3387535	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	CDS	3387536	3387787	0.95	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	exon	3387536	3387787	.	-	.	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
Phchi.S1	AUGUSTUS	start_codon	3387785	3387787	.	-	0	transcript_id "Phchi.S1G057300.t2"; gene_id "Phchi.S1G057300"
# This transcript jg918.t2 is derived from g10700.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg918.t3 is derived from g10700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg919.t1 is derived from g10701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6452108	6452660	.	-	.	Phchi.S6G087800
Phchi.S6	AUGUSTUS	transcript	6452108	6452660	.	-	.	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	stop_codon	6452105	6452107	.	-	0	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	CDS	6452108	6452214	0.64	-	2	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	exon	6452108	6452214	.	-	.	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	intron	6452215	6452341	.	-	.	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	CDS	6452342	6452660	0.85	-	0	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	exon	6452342	6452660	.	-	.	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
Phchi.S6	AUGUSTUS	start_codon	6452658	6452660	.	-	0	transcript_id "Phchi.S6G087800.t1"; gene_id "Phchi.S6G087800"
# This transcript jg6017.t2 is derived from g3188.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6018.t1 is derived from g3189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20461979	20466091	.	-	.	Phchi.S1G317700
Phchi.S1	AUGUSTUS	transcript	20461979	20466091	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	stop_codon	20461976	20461978	.	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20461979	20462014	0.99	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20461979	20462014	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462015	20462164	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462165	20462290	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462165	20462290	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462291	20462374	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462375	20462446	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462375	20462446	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462447	20462545	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462546	20462628	1	-	2	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462546	20462628	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462629	20462855	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462856	20462947	1	-	1	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462856	20462947	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462948	20463096	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463097	20463176	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463097	20463176	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463177	20463244	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463245	20463484	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463245	20463484	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463485	20463578	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463579	20463652	1	-	2	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463579	20463652	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463653	20463821	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463822	20463963	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463822	20463963	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463964	20464079	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20464080	20464342	1	-	2	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20464080	20464342	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20464343	20464493	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20464494	20464692	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20464494	20464692	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20464693	20464844	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20464845	20464952	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20464845	20464952	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20464953	20465073	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20465074	20465403	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20465074	20465403	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20465404	20465589	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20465590	20465820	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20465590	20465820	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20465821	20465962	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20465963	20466091	1	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20465963	20466091	.	-	.	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	start_codon	20466089	20466091	.	-	0	transcript_id "Phchi.S1G317700.t1"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	transcript	20461979	20466091	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	stop_codon	20461976	20461978	.	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20461979	20462014	0.95	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20461979	20462014	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462015	20462164	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462165	20462290	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462165	20462290	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462291	20462374	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462375	20462446	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462375	20462446	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462447	20462545	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462546	20462628	1	-	2	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462546	20462628	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462629	20462855	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20462856	20462947	1	-	1	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20462856	20462947	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20462948	20463096	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463097	20463176	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463097	20463176	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463177	20463244	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463245	20463484	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463245	20463484	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463485	20463578	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463579	20463649	1	-	2	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463579	20463649	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463650	20463821	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20463822	20463963	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20463822	20463963	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20463964	20464079	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20464080	20464342	0.99	-	2	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20464080	20464342	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20464343	20464493	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20464494	20464692	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20464494	20464692	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20464693	20464844	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20464845	20464952	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20464845	20464952	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20464953	20465073	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20465074	20465403	0.99	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20465074	20465403	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20465404	20465589	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20465590	20465820	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20465590	20465820	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	intron	20465821	20465962	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	CDS	20465963	20466091	1	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	exon	20465963	20466091	.	-	.	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
Phchi.S1	AUGUSTUS	start_codon	20466089	20466091	.	-	0	transcript_id "Phchi.S1G317700.t2"; gene_id "Phchi.S1G317700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10454.t1 is derived from g14503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	406738	407406	.	-	.	Phchi.S4G003600
Phchi.S4	AUGUSTUS	transcript	406738	407406	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	stop_codon	406735	406737	.	-	0	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	CDS	406738	406855	1	-	1	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	exon	406738	406855	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	intron	406856	406990	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	CDS	406991	407046	1	-	0	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	exon	406991	407046	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	intron	407047	407121	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	CDS	407122	407194	0.95	-	1	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	exon	407122	407194	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	intron	407195	407305	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	CDS	407306	407406	0.95	-	0	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	exon	407306	407406	.	-	.	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
Phchi.S4	AUGUSTUS	start_codon	407404	407406	.	-	0	transcript_id "Phchi.S4G003600.t1"; gene_id "Phchi.S4G003600"
# This transcript jg10057.t2 is derived from g7233.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg10058.t1 is derived from g7234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45570260	45571000	.	+	.	Phchi.S1G721700
Phchi.S1	AUGUSTUS	transcript	45570425	45571000	.	+	.	transcript_id "Phchi.S1G721700.t1"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	start_codon	45570425	45570427	.	+	0	transcript_id "Phchi.S1G721700.t1"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	CDS	45570425	45571000	1	+	0	transcript_id "Phchi.S1G721700.t1"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	exon	45570425	45571000	.	+	.	transcript_id "Phchi.S1G721700.t1"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	stop_codon	45571001	45571003	.	+	0	transcript_id "Phchi.S1G721700.t1"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	transcript	45570488	45571000	.	+	.	transcript_id "Phchi.S1G721700.t2"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	start_codon	45570488	45570490	.	+	0	transcript_id "Phchi.S1G721700.t2"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	CDS	45570488	45571000	0.96	+	0	transcript_id "Phchi.S1G721700.t2"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	exon	45570488	45571000	.	+	.	transcript_id "Phchi.S1G721700.t2"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	stop_codon	45571001	45571003	.	+	0	transcript_id "Phchi.S1G721700.t2"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	transcript	45570260	45571000	.	+	.	transcript_id "Phchi.S1G721700.t3"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	start_codon	45570260	45570262	.	+	0	transcript_id "Phchi.S1G721700.t3"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	CDS	45570260	45571000	0.82	+	0	transcript_id "Phchi.S1G721700.t3"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	exon	45570260	45571000	.	+	.	transcript_id "Phchi.S1G721700.t3"; gene_id "Phchi.S1G721700"
Phchi.S1	AUGUSTUS	stop_codon	45571001	45571003	.	+	0	transcript_id "Phchi.S1G721700.t3"; gene_id "Phchi.S1G721700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg327.t1 is derived from g10109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2275944	2278098	.	+	.	Phchi.S6G028600
Phchi.S6	AUGUSTUS	transcript	2275944	2278098	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	start_codon	2275944	2275946	.	+	0	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	CDS	2275944	2276160	0.96	+	0	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	exon	2275944	2276160	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	intron	2276161	2276273	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	CDS	2276274	2276408	0.63	+	2	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	exon	2276274	2276408	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	intron	2276409	2276509	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	CDS	2276510	2276613	0.76	+	2	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	exon	2276510	2276613	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	intron	2276614	2276703	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	CDS	2276704	2276788	1	+	0	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	exon	2276704	2276788	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	intron	2276789	2276891	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	CDS	2276892	2277517	1	+	2	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	exon	2276892	2277517	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	intron	2277518	2277609	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	CDS	2277610	2278098	0.99	+	0	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	exon	2277610	2278098	.	+	.	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
Phchi.S6	AUGUSTUS	stop_codon	2278099	2278101	.	+	0	transcript_id "Phchi.S6G028600.t1"; gene_id "Phchi.S6G028600"
# This transcript jg1907.t2 is derived from g8827.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1908.t1 is derived from g8828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3819219	3819755	.	-	.	Phchi.S5G051700
Phchi.S5	AUGUSTUS	transcript	3819219	3819755	.	-	.	transcript_id "Phchi.S5G051700.t1"; gene_id "Phchi.S5G051700"
Phchi.S5	AUGUSTUS	stop_codon	3819216	3819218	.	-	0	transcript_id "Phchi.S5G051700.t1"; gene_id "Phchi.S5G051700"
Phchi.S5	AUGUSTUS	CDS	3819219	3819755	0.95	-	0	transcript_id "Phchi.S5G051700.t1"; gene_id "Phchi.S5G051700"
Phchi.S5	AUGUSTUS	exon	3819219	3819755	.	-	.	transcript_id "Phchi.S5G051700.t1"; gene_id "Phchi.S5G051700"
Phchi.S5	AUGUSTUS	start_codon	3819753	3819755	.	-	0	transcript_id "Phchi.S5G051700.t1"; gene_id "Phchi.S5G051700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15353.t1 is derived from g13821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18560411	18563756	.	+	.	Phchi.S3G267200
Phchi.S3	AUGUSTUS	transcript	18560411	18563756	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	start_codon	18560411	18560413	.	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18560411	18560536	0.84	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18560411	18560536	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18560537	18560620	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18560621	18560697	1	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18560621	18560697	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18560698	18560796	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18560797	18560854	1	+	1	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18560797	18560854	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18560855	18560938	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18560939	18561036	1	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18560939	18561036	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18561037	18561160	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18561161	18561212	1	+	1	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18561161	18561212	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18561213	18561346	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18561347	18561475	0.68	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18561347	18561475	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18561476	18561591	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18561592	18561651	0.93	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18561592	18561651	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18561652	18561746	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18561747	18561791	1	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18561747	18561791	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18561792	18561888	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18561889	18561984	0.98	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18561889	18561984	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18561985	18562092	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18562093	18562153	0.59	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18562093	18562153	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18562154	18562287	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18562288	18562349	0.61	+	2	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18562288	18562349	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18562350	18562444	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18562445	18562512	0.91	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18562445	18562512	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18562513	18562599	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18562600	18562714	0.57	+	1	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18562600	18562714	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18562715	18562942	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18562943	18563020	0.89	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18562943	18563020	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18563021	18563132	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18563133	18563186	0.92	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18563133	18563186	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18563187	18563275	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18563276	18563362	0.67	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18563276	18563362	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18563363	18563597	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18563598	18563609	0.7	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18563598	18563609	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	intron	18563610	18563696	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	CDS	18563697	18563756	0.9	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	exon	18563697	18563756	.	+	.	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
Phchi.S3	AUGUSTUS	stop_codon	18563757	18563759	.	+	0	transcript_id "Phchi.S3G267200.t1"; gene_id "Phchi.S3G267200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg623.t1 is derived from g10405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4451126	4452983	.	+	.	Phchi.S6G058200
Phchi.S6	AUGUSTUS	transcript	4451126	4452983	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	start_codon	4451126	4451128	.	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4451126	4451326	0.96	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4451126	4451326	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4451327	4451481	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4451482	4451979	0.99	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4451482	4451979	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4451980	4452049	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4452050	4452137	1	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4452050	4452137	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4452138	4452241	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4452242	4452294	1	+	2	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4452242	4452294	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4452295	4452403	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4452404	4452508	1	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4452404	4452508	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4452509	4452619	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4452620	4452695	1	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4452620	4452695	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4452696	4452809	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4452810	4452847	1	+	2	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4452810	4452847	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	intron	4452848	4452932	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	CDS	4452933	4452983	1	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	exon	4452933	4452983	.	+	.	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
Phchi.S6	AUGUSTUS	stop_codon	4452984	4452986	.	+	0	transcript_id "Phchi.S6G058200.t1"; gene_id "Phchi.S6G058200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8286.t1 is derived from g5461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35101439	35102447	.	-	.	Phchi.S1G544500
Phchi.S1	AUGUSTUS	transcript	35101439	35102447	.	-	.	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	stop_codon	35101436	35101438	.	-	0	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	CDS	35101439	35102070	0.89	-	2	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	exon	35101439	35102070	.	-	.	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	intron	35102071	35102168	.	-	.	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	CDS	35102169	35102216	0.74	-	2	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	exon	35102169	35102216	.	-	.	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	intron	35102217	35102380	.	-	.	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	CDS	35102381	35102447	0.98	-	0	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	exon	35102381	35102447	.	-	.	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
Phchi.S1	AUGUSTUS	start_codon	35102445	35102447	.	-	0	transcript_id "Phchi.S1G544500.t1"; gene_id "Phchi.S1G544500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11808.t1 is derived from g15860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8227160	8228112	.	+	.	Phchi.S4G139000
Phchi.S4	AUGUSTUS	transcript	8227160	8228112	.	+	.	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	start_codon	8227160	8227162	.	+	0	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	CDS	8227160	8227497	0.81	+	0	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	exon	8227160	8227497	.	+	.	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	intron	8227498	8227670	.	+	.	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	CDS	8227671	8228112	0.35	+	1	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	exon	8227671	8228112	.	+	.	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
Phchi.S4	AUGUSTUS	stop_codon	8228113	8228115	.	+	0	transcript_id "Phchi.S4G139000.t1"; gene_id "Phchi.S4G139000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8744.t1 is derived from g5919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37770890	37773267	.	+	.	Phchi.S1G590300
Phchi.S1	AUGUSTUS	transcript	37770890	37773267	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	start_codon	37770890	37770892	.	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37770890	37771069	0.88	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37770890	37771069	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37771070	37771220	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37771221	37771280	1	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37771221	37771280	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37771281	37771374	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37771375	37771446	1	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37771375	37771446	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37771447	37771595	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37771596	37771717	1	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37771596	37771717	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37771718	37771860	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37771861	37772001	1	+	1	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37771861	37772001	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37772002	37772083	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37772084	37772194	1	+	1	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37772084	37772194	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37772195	37772367	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37772368	37772638	1	+	1	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37772368	37772638	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37772639	37772869	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37772870	37772895	0.56	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37772870	37772895	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	intron	37772896	37773086	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	CDS	37773087	37773267	1	+	1	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	exon	37773087	37773267	.	+	.	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
Phchi.S1	AUGUSTUS	stop_codon	37773268	37773270	.	+	0	transcript_id "Phchi.S1G590300.t1"; gene_id "Phchi.S1G590300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14527.t1 is derived from g12995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13320102	13320760	.	-	.	Phchi.S3G184600
Phchi.S3	AUGUSTUS	transcript	13320102	13320760	.	-	.	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	stop_codon	13320099	13320101	.	-	0	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	CDS	13320102	13320236	1	-	0	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	exon	13320102	13320236	.	-	.	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	intron	13320237	13320316	.	-	.	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	CDS	13320317	13320760	0.87	-	0	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	exon	13320317	13320760	.	-	.	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
Phchi.S3	AUGUSTUS	start_codon	13320758	13320760	.	-	0	transcript_id "Phchi.S3G184600.t1"; gene_id "Phchi.S3G184600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6852.t1 is derived from g4024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25573072	25575186	.	+	.	Phchi.S1G401100
Phchi.S1	AUGUSTUS	transcript	25573072	25575186	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	start_codon	25573072	25573074	.	+	0	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	CDS	25573072	25573677	0.62	+	0	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	exon	25573072	25573677	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	intron	25573678	25573809	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	CDS	25573810	25574052	1	+	0	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	exon	25573810	25574052	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	intron	25574053	25574214	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	CDS	25574215	25574601	1	+	0	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	exon	25574215	25574601	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	intron	25574602	25574697	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	CDS	25574698	25575186	0.94	+	0	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	exon	25574698	25575186	.	+	.	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
Phchi.S1	AUGUSTUS	stop_codon	25575187	25575189	.	+	0	transcript_id "Phchi.S1G401100.t1"; gene_id "Phchi.S1G401100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7286.t1 is derived from g4458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28144264	28145272	.	-	.	Phchi.S1G444500
Phchi.S1	AUGUSTUS	transcript	28144264	28145272	.	-	.	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	stop_codon	28144261	28144263	.	-	0	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	CDS	28144264	28145046	0.8	-	0	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	exon	28144264	28145046	.	-	.	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	intron	28145047	28145125	.	-	.	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	CDS	28145126	28145272	0.81	-	0	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	exon	28145126	28145272	.	-	.	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
Phchi.S1	AUGUSTUS	start_codon	28145270	28145272	.	-	0	transcript_id "Phchi.S1G444500.t1"; gene_id "Phchi.S1G444500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11101.t1 is derived from g15151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4134557	4137537	.	-	.	Phchi.S4G068300
Phchi.S4	AUGUSTUS	transcript	4134557	4137537	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	stop_codon	4134554	4134556	.	-	0	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4134557	4135340	1	-	1	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4134557	4135340	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4135341	4135422	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4135423	4135507	0.75	-	2	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4135423	4135507	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4135508	4135806	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4135807	4135964	0.86	-	1	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4135807	4135964	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4135965	4136058	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4136059	4136106	0.96	-	1	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4136059	4136106	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4136107	4136204	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4136205	4136275	0.74	-	0	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4136205	4136275	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4136276	4136365	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4136366	4136806	1	-	0	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4136366	4136806	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4136807	4136901	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4136902	4137086	1	-	2	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4136902	4137086	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4137087	4137186	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4137187	4137243	0.99	-	2	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4137187	4137243	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	intron	4137244	4137413	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	CDS	4137414	4137537	0.65	-	0	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	exon	4137414	4137537	.	-	.	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
Phchi.S4	AUGUSTUS	start_codon	4137535	4137537	.	-	0	transcript_id "Phchi.S4G068300.t1"; gene_id "Phchi.S4G068300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12359.t1 is derived from g8035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12713215	12717149	.	+	.	Phchi.S2G043900
Phchi.S2	AUGUSTUS	transcript	12713215	12717149	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	start_codon	12713215	12713217	.	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12713215	12713313	0.98	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12713215	12713313	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12713314	12713639	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12713640	12713709	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12713640	12713709	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12713710	12713945	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12713946	12714043	1	+	2	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12713946	12714043	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12714044	12714227	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12714228	12714369	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12714228	12714369	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12714370	12714467	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12714468	12714571	1	+	2	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12714468	12714571	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12714572	12714671	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12714672	12714764	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12714672	12714764	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12714765	12714875	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12714876	12714926	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12714876	12714926	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12714927	12715146	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12715147	12715212	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12715147	12715212	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12715213	12715305	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12715306	12715371	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12715306	12715371	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12715372	12715551	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12715552	12715632	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12715552	12715632	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12715633	12715726	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12715727	12715807	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12715727	12715807	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12715808	12715962	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12715963	12715986	0.95	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12715963	12715986	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12715987	12716075	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12716076	12716120	0.95	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12716076	12716120	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12716121	12716247	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12716248	12716326	0.99	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12716248	12716326	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12716327	12716428	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12716429	12716562	0.95	+	2	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12716429	12716562	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	intron	12716563	12716750	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	CDS	12716751	12717149	1	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	exon	12716751	12717149	.	+	.	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
Phchi.S2	AUGUSTUS	stop_codon	12717150	12717152	.	+	0	transcript_id "Phchi.S2G043900.t1"; gene_id "Phchi.S2G043900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15218.t1 is derived from g13686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17745854	17747596	.	+	.	Phchi.S3G253700
Phchi.S3	AUGUSTUS	transcript	17745854	17747596	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	start_codon	17745854	17745856	.	+	0	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	CDS	17745854	17746351	0.93	+	0	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	exon	17745854	17746351	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	intron	17746352	17746473	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	CDS	17746474	17746965	1	+	0	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	exon	17746474	17746965	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	intron	17746966	17747050	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	CDS	17747051	17747268	0.99	+	0	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	exon	17747051	17747268	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	intron	17747269	17747349	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	CDS	17747350	17747596	1	+	1	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	exon	17747350	17747596	.	+	.	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
Phchi.S3	AUGUSTUS	stop_codon	17747597	17747599	.	+	0	transcript_id "Phchi.S3G253700.t1"; gene_id "Phchi.S3G253700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3945.t1 is derived from g1114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6589762	6590592	.	-	.	Phchi.S1G110400
Phchi.S1	AUGUSTUS	transcript	6589762	6590592	.	-	.	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	stop_codon	6589759	6589761	.	-	0	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	CDS	6589762	6589807	0.99	-	1	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	exon	6589762	6589807	.	-	.	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	intron	6589808	6589939	.	-	.	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	CDS	6589940	6590592	0.86	-	0	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	exon	6589940	6590592	.	-	.	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
Phchi.S1	AUGUSTUS	start_codon	6590590	6590592	.	-	0	transcript_id "Phchi.S1G110400.t1"; gene_id "Phchi.S1G110400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13115.t1 is derived from g11580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4198653	4199225	.	-	.	Phchi.S3G043400
Phchi.S3	AUGUSTUS	transcript	4198653	4199225	.	-	.	transcript_id "Phchi.S3G043400.t1"; gene_id "Phchi.S3G043400"
Phchi.S3	AUGUSTUS	stop_codon	4198650	4198652	.	-	0	transcript_id "Phchi.S3G043400.t1"; gene_id "Phchi.S3G043400"
Phchi.S3	AUGUSTUS	CDS	4198653	4199225	1	-	0	transcript_id "Phchi.S3G043400.t1"; gene_id "Phchi.S3G043400"
Phchi.S3	AUGUSTUS	exon	4198653	4199225	.	-	.	transcript_id "Phchi.S3G043400.t1"; gene_id "Phchi.S3G043400"
Phchi.S3	AUGUSTUS	start_codon	4199223	4199225	.	-	0	transcript_id "Phchi.S3G043400.t1"; gene_id "Phchi.S3G043400"
# This transcript jg12495.t2 is derived from g8172.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12496.t1 is derived from g8173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	30136893	30139747	.	-	.	Phchi.S2G057600
Phchi.S2	AUGUSTUS	transcript	30136893	30139747	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	stop_codon	30136890	30136892	.	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30136893	30137363	0.89	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30136893	30137363	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	intron	30137364	30137460	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30137461	30137574	1	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30137461	30137574	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	intron	30137575	30137667	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30137668	30137832	1	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30137668	30137832	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	intron	30137833	30138067	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30138068	30138136	1	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30138068	30138136	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	intron	30138137	30138217	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30138218	30138310	1	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30138218	30138310	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	intron	30138311	30138471	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30138472	30138555	1	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30138472	30138555	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	intron	30138556	30138877	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	CDS	30138878	30139747	0.98	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	exon	30138878	30139747	.	-	.	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
Phchi.S2	AUGUSTUS	start_codon	30139745	30139747	.	-	0	transcript_id "Phchi.S2G057600.t1"; gene_id "Phchi.S2G057600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13463.t1 is derived from g11930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7016942	7019908	.	+	.	Phchi.S3G078200
Phchi.S3	AUGUSTUS	transcript	7016942	7019908	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	start_codon	7016942	7016944	.	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7016942	7017079	0.73	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7016942	7017079	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7017080	7017362	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7017363	7017463	1	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7017363	7017463	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7017464	7017589	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7017590	7017707	0.78	+	1	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7017590	7017707	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7017708	7017855	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7017856	7018020	0.32	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7017856	7018020	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7018021	7018108	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7018109	7018161	0.68	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7018109	7018161	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7018162	7018251	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7018252	7018448	0.99	+	1	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7018252	7018448	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7018449	7018548	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7018549	7019462	1	+	2	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7018549	7019462	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7019463	7019583	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7019584	7019700	1	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7019584	7019700	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	intron	7019701	7019839	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	CDS	7019840	7019908	0.99	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	exon	7019840	7019908	.	+	.	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
Phchi.S3	AUGUSTUS	stop_codon	7019909	7019911	.	+	0	transcript_id "Phchi.S3G078200.t1"; gene_id "Phchi.S3G078200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6165.t1 is derived from g3336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21264389	21267061	.	-	.	Phchi.S1G332400
Phchi.S1	AUGUSTUS	transcript	21264389	21267061	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	stop_codon	21264386	21264388	.	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21264389	21264486	1	-	2	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21264389	21264486	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21264487	21264569	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21264570	21264690	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21264570	21264690	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21264691	21264788	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21264789	21264863	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21264789	21264863	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21264864	21264978	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21264979	21265106	1	-	2	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21264979	21265106	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21265107	21265196	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21265197	21265413	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21265197	21265413	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21265414	21265497	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21265498	21265580	1	-	2	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21265498	21265580	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21265581	21265694	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21265695	21265821	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21265695	21265821	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21265822	21265913	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21265914	21265973	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21265914	21265973	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21265974	21266122	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21266123	21266233	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21266123	21266233	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21266234	21266316	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21266317	21266433	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21266317	21266433	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21266434	21266528	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21266529	21266678	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21266529	21266678	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21266679	21266771	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21266772	21266876	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21266772	21266876	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	intron	21266877	21266953	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	CDS	21266954	21267061	1	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	exon	21266954	21267061	.	-	.	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
Phchi.S1	AUGUSTUS	start_codon	21267059	21267061	.	-	0	transcript_id "Phchi.S1G332400.t1"; gene_id "Phchi.S1G332400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11849.t1 is derived from g15901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8617222	8618666	.	-	.	Phchi.S4G143100
Phchi.S4	AUGUSTUS	transcript	8617222	8618666	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	stop_codon	8617219	8617221	.	-	0	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	CDS	8617222	8617560	0.98	-	0	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	exon	8617222	8617560	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	intron	8617561	8617651	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	CDS	8617652	8618299	0.74	-	0	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	exon	8617652	8618299	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	intron	8618300	8618382	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	CDS	8618383	8618411	0.81	-	2	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	exon	8618383	8618411	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	intron	8618412	8618623	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	CDS	8618624	8618666	0.83	-	0	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	exon	8618624	8618666	.	-	.	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
Phchi.S4	AUGUSTUS	start_codon	8618664	8618666	.	-	0	transcript_id "Phchi.S4G143100.t1"; gene_id "Phchi.S4G143100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2195.t1 is derived from g9115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5330676	5339595	.	-	.	Phchi.S5G080400
Phchi.S5	AUGUSTUS	transcript	5330676	5339595	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	stop_codon	5330673	5330675	.	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5330676	5330773	1	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5330676	5330773	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5330774	5330845	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5330846	5330888	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5330846	5330888	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5330889	5330984	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5330985	5331053	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5330985	5331053	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5331054	5331140	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5331141	5331233	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5331141	5331233	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5331234	5331319	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5331320	5331467	1	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5331320	5331467	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5331468	5331544	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5331545	5331661	1	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5331545	5331661	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5331662	5331753	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5331754	5331802	1	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5331754	5331802	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5331803	5331875	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5331876	5331966	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5331876	5331966	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5331967	5332048	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5332049	5332141	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5332049	5332141	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5332142	5332233	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5332234	5332280	1	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5332234	5332280	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5332281	5332359	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5332360	5332420	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5332360	5332420	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5332421	5332502	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5332503	5332581	1	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5332503	5332581	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5332582	5332666	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5332667	5332767	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5332667	5332767	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5332768	5332847	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5332848	5332945	1	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5332848	5332945	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5332946	5333263	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5333264	5333341	0.8	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5333264	5333341	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5333342	5333472	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5333473	5333569	0.83	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5333473	5333569	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5333570	5333797	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5333798	5333904	0.37	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5333798	5333904	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5333905	5334115	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5334116	5334210	0.44	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5334116	5334210	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5334211	5334330	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5334331	5334470	0.92	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5334331	5334470	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5334471	5334619	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5334620	5335102	0.93	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5334620	5335102	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5335103	5335182	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5335183	5335446	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5335183	5335446	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5335447	5335551	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5335552	5335818	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5335552	5335818	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5335819	5335911	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5335912	5336140	1	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5335912	5336140	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5336141	5336235	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5336236	5336739	1	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5336236	5336739	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5336740	5336823	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5336824	5337004	1	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5336824	5337004	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5337005	5337082	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5337083	5337356	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5337083	5337356	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5337357	5337464	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5337465	5337990	1	-	1	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5337465	5337990	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5337991	5338105	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5338106	5338344	0.99	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5338106	5338344	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5338345	5338437	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5338438	5338659	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5338438	5338659	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5338660	5338739	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5338740	5338915	1	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5338740	5338915	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5338916	5339026	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5339027	5339081	1	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5339027	5339081	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5339082	5339176	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5339177	5339274	0.92	-	2	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5339177	5339274	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	intron	5339275	5339345	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	CDS	5339346	5339595	0.66	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	exon	5339346	5339595	.	-	.	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
Phchi.S5	AUGUSTUS	start_codon	5339593	5339595	.	-	0	transcript_id "Phchi.S5G080400.t1"; gene_id "Phchi.S5G080400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2989.t1 is derived from g158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1024326	1024896	.	-	.	Phchi.S1G014800
Phchi.S1	AUGUSTUS	transcript	1024326	1024896	.	-	.	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	stop_codon	1024323	1024325	.	-	0	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	CDS	1024326	1024701	0.93	-	1	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	exon	1024326	1024701	.	-	.	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	intron	1024702	1024876	.	-	.	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	CDS	1024877	1024896	0.54	-	0	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	exon	1024877	1024896	.	-	.	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
Phchi.S1	AUGUSTUS	start_codon	1024894	1024896	.	-	0	transcript_id "Phchi.S1G014800.t1"; gene_id "Phchi.S1G014800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6198.t1 is derived from g3369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21444268	21447345	.	-	.	Phchi.S1G335700
Phchi.S1	AUGUSTUS	transcript	21444268	21447345	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	stop_codon	21444265	21444267	.	-	0	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	CDS	21444268	21444287	1	-	2	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	exon	21444268	21444287	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	intron	21444288	21444369	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	CDS	21444370	21444716	0.99	-	1	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	exon	21444370	21444716	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	intron	21444717	21444821	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	CDS	21444822	21445033	1	-	0	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	exon	21444822	21445033	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	intron	21445034	21445139	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	CDS	21445140	21445907	0.94	-	0	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	exon	21445140	21445907	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	intron	21445908	21446008	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	CDS	21446009	21446734	1	-	0	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	exon	21446009	21446734	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	intron	21446735	21447081	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	CDS	21447082	21447345	1	-	0	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	exon	21447082	21447345	.	-	.	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
Phchi.S1	AUGUSTUS	start_codon	21447343	21447345	.	-	0	transcript_id "Phchi.S1G335700.t1"; gene_id "Phchi.S1G335700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11988.t1 is derived from g7663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	390689	392147	.	-	.	Phchi.S2G006800
Phchi.S2	AUGUSTUS	transcript	390689	392147	.	-	.	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	stop_codon	390686	390688	.	-	0	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	CDS	390689	390963	0.17	-	2	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	exon	390689	390963	.	-	.	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	intron	390964	391078	.	-	.	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	CDS	391079	391199	0.26	-	0	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	exon	391079	391199	.	-	.	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	intron	391200	392069	.	-	.	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	CDS	392070	392147	0.02	-	0	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	exon	392070	392147	.	-	.	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
Phchi.S2	AUGUSTUS	start_codon	392145	392147	.	-	0	transcript_id "Phchi.S2G006800.t1"; gene_id "Phchi.S2G006800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2824.t1 is derived from g9744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9060397	9061856	.	+	.	Phchi.S5G143300
Phchi.S5	AUGUSTUS	transcript	9060397	9061856	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	start_codon	9060397	9060399	.	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	CDS	9060397	9060771	0.63	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	exon	9060397	9060771	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	intron	9060772	9060864	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	CDS	9060865	9060915	1	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	exon	9060865	9060915	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	intron	9060916	9061000	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	CDS	9061001	9061222	1	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	exon	9061001	9061222	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	intron	9061223	9061295	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	CDS	9061296	9061418	1	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	exon	9061296	9061418	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	intron	9061419	9061506	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	CDS	9061507	9061683	1	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	exon	9061507	9061683	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	intron	9061684	9061769	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	CDS	9061770	9061856	1	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	exon	9061770	9061856	.	+	.	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
Phchi.S5	AUGUSTUS	stop_codon	9061857	9061859	.	+	0	transcript_id "Phchi.S5G143300.t1"; gene_id "Phchi.S5G143300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11893.t1 is derived from g15945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9058656	9060552	.	+	.	Phchi.S4G147500
Phchi.S4	AUGUSTUS	transcript	9058656	9060552	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	start_codon	9058656	9058658	.	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9058656	9058895	1	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9058656	9058895	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9058896	9058978	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9058979	9059053	1	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9058979	9059053	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059054	9059149	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059150	9059293	1	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059150	9059293	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059294	9059495	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059496	9059762	1	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059496	9059762	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059763	9059860	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059861	9060096	1	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059861	9060096	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9060097	9060188	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9060189	9060310	0.98	+	1	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9060189	9060310	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9060311	9060541	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9060542	9060552	0.98	+	2	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9060542	9060552	.	+	.	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	stop_codon	9060553	9060555	.	+	0	transcript_id "Phchi.S4G147500.t1"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	transcript	9058656	9060552	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	start_codon	9058656	9058658	.	+	0	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9058656	9058895	1	+	0	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9058656	9058895	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9058896	9058978	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9058979	9059053	1	+	0	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9058979	9059053	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059054	9059149	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059150	9059249	0.37	+	0	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059150	9059249	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059250	9059363	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059364	9059403	0.37	+	2	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059364	9059403	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059404	9059495	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059496	9059534	0.34	+	1	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059496	9059534	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059535	9059587	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059588	9059762	0.35	+	1	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059588	9059762	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9059763	9059860	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9059861	9060096	1	+	0	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9059861	9060096	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9060097	9060188	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9060189	9060310	1	+	1	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9060189	9060310	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	intron	9060311	9060541	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	CDS	9060542	9060552	1	+	2	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	exon	9060542	9060552	.	+	.	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
Phchi.S4	AUGUSTUS	stop_codon	9060553	9060555	.	+	0	transcript_id "Phchi.S4G147500.t2"; gene_id "Phchi.S4G147500"
# This transcript jg15251.t2 is derived from g13719.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15252.t1 is derived from g13720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17909753	17911956	.	+	.	Phchi.S3G257100
Phchi.S3	AUGUSTUS	transcript	17909753	17911956	.	+	.	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	start_codon	17909753	17909755	.	+	0	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	CDS	17909753	17910193	0.86	+	0	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	exon	17909753	17910193	.	+	.	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	intron	17910194	17910299	.	+	.	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	CDS	17910300	17910532	0.96	+	0	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	exon	17910300	17910532	.	+	.	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	intron	17910533	17910743	.	+	.	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	CDS	17910744	17911956	1	+	1	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	exon	17910744	17911956	.	+	.	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
Phchi.S3	AUGUSTUS	stop_codon	17911957	17911959	.	+	0	transcript_id "Phchi.S3G257100.t1"; gene_id "Phchi.S3G257100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg730.t1 is derived from g10512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5202734	5205522	.	+	.	Phchi.S6G068900
Phchi.S6	AUGUSTUS	transcript	5202734	5205522	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	start_codon	5202734	5202736	.	+	0	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	CDS	5202734	5203694	0.41	+	0	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	exon	5202734	5203694	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	intron	5203695	5204025	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	CDS	5204026	5204047	0.79	+	2	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	exon	5204026	5204047	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	intron	5204048	5204189	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	CDS	5204190	5204264	1	+	1	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	exon	5204190	5204264	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	intron	5204265	5204378	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	CDS	5204379	5204465	1	+	1	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	exon	5204379	5204465	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	intron	5204466	5204855	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	CDS	5204856	5204884	1	+	1	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	exon	5204856	5204884	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	intron	5204885	5205082	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	CDS	5205083	5205522	1	+	2	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	exon	5205083	5205522	.	+	.	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
Phchi.S6	AUGUSTUS	stop_codon	5205523	5205525	.	+	0	transcript_id "Phchi.S6G068900.t1"; gene_id "Phchi.S6G068900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5336.t1 is derived from g2506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16354723	16357248	.	-	.	Phchi.S1G249500
Phchi.S1	AUGUSTUS	transcript	16354723	16357248	.	-	.	transcript_id "Phchi.S1G249500.t1"; gene_id "Phchi.S1G249500"
Phchi.S1	AUGUSTUS	stop_codon	16354720	16354722	.	-	0	transcript_id "Phchi.S1G249500.t1"; gene_id "Phchi.S1G249500"
Phchi.S1	AUGUSTUS	CDS	16354723	16357248	0.97	-	0	transcript_id "Phchi.S1G249500.t1"; gene_id "Phchi.S1G249500"
Phchi.S1	AUGUSTUS	exon	16354723	16357248	.	-	.	transcript_id "Phchi.S1G249500.t1"; gene_id "Phchi.S1G249500"
Phchi.S1	AUGUSTUS	start_codon	16357246	16357248	.	-	0	transcript_id "Phchi.S1G249500.t1"; gene_id "Phchi.S1G249500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8852.t1 is derived from g6027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38287021	38287967	.	+	.	Phchi.S1G601100
Phchi.S1	AUGUSTUS	transcript	38287021	38287967	.	+	.	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	start_codon	38287021	38287023	.	+	0	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	CDS	38287021	38287036	0.88	+	0	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	exon	38287021	38287036	.	+	.	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	intron	38287037	38287184	.	+	.	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	CDS	38287185	38287437	0.88	+	2	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	exon	38287185	38287437	.	+	.	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	intron	38287438	38287510	.	+	.	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	CDS	38287511	38287967	0.83	+	1	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	exon	38287511	38287967	.	+	.	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
Phchi.S1	AUGUSTUS	stop_codon	38287968	38287970	.	+	0	transcript_id "Phchi.S1G601100.t1"; gene_id "Phchi.S1G601100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13069.t1 is derived from g11534.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3996855	3998823	.	-	.	Phchi.S3G038800
Phchi.S3	AUGUSTUS	transcript	3996855	3998823	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	stop_codon	3996852	3996854	.	-	0	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3996855	3996982	1	-	2	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3996855	3996982	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	intron	3996983	3997114	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3997115	3997243	1	-	2	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3997115	3997243	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	intron	3997244	3997388	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3997389	3997441	1	-	1	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3997389	3997441	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	intron	3997442	3997837	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3997838	3997952	1	-	2	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3997838	3997952	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	intron	3997953	3998285	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3998286	3998365	1	-	1	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3998286	3998365	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	intron	3998366	3998555	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3998556	3998664	0.51	-	2	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3998556	3998664	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	intron	3998665	3998753	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	CDS	3998754	3998823	0.51	-	0	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	exon	3998754	3998823	.	-	.	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
Phchi.S3	AUGUSTUS	start_codon	3998821	3998823	.	-	0	transcript_id "Phchi.S3G038800.t1"; gene_id "Phchi.S3G038800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14211.t1 is derived from g12678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11522540	11523997	.	+	.	Phchi.S3G153000
Phchi.S3	AUGUSTUS	transcript	11522540	11523997	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	start_codon	11522540	11522542	.	+	0	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11522540	11522610	0.99	+	0	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11522540	11522610	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	intron	11522611	11522828	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11522829	11522902	1	+	1	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11522829	11522902	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	intron	11522903	11522988	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11522989	11523049	1	+	2	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11522989	11523049	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	intron	11523050	11523136	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11523137	11523190	1	+	1	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11523137	11523190	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	intron	11523191	11523303	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11523304	11523383	0.99	+	1	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11523304	11523383	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	intron	11523384	11523494	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11523495	11523700	1	+	2	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11523495	11523700	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	intron	11523701	11523790	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	CDS	11523791	11523997	1	+	0	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	exon	11523791	11523997	.	+	.	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
Phchi.S3	AUGUSTUS	stop_codon	11523998	11524000	.	+	0	transcript_id "Phchi.S3G153000.t1"; gene_id "Phchi.S3G153000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13003.t1 is derived from g11468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3594328	3597867	.	+	.	Phchi.S3G032200
Phchi.S3	AUGUSTUS	transcript	3594328	3597867	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	start_codon	3594328	3594330	.	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3594328	3594424	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3594328	3594424	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3594425	3594518	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3594519	3594799	1	+	2	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3594519	3594799	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3594800	3594935	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3594936	3595169	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3594936	3595169	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3595170	3595277	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3595278	3595376	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3595278	3595376	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3595377	3595462	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3595463	3595612	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3595463	3595612	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3595613	3595690	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3595691	3595837	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3595691	3595837	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3595838	3595923	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3595924	3595974	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3595924	3595974	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3595975	3596080	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3596081	3596277	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3596081	3596277	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3596278	3596363	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3596364	3596499	1	+	1	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3596364	3596499	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3596500	3596628	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3596629	3596726	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3596629	3596726	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3596727	3596807	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3596808	3597042	1	+	1	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3596808	3597042	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3597043	3597113	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3597114	3597317	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3597114	3597317	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3597318	3597385	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3597386	3597466	0.99	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3597386	3597466	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	intron	3597467	3597570	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	CDS	3597571	3597867	1	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	exon	3597571	3597867	.	+	.	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
Phchi.S3	AUGUSTUS	stop_codon	3597868	3597870	.	+	0	transcript_id "Phchi.S3G032200.t1"; gene_id "Phchi.S3G032200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9250.t1 is derived from g6425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40588029	40590139	.	+	.	Phchi.S1G640900
Phchi.S1	AUGUSTUS	transcript	40588029	40590139	.	+	.	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	start_codon	40588029	40588031	.	+	0	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	CDS	40588029	40588523	0.98	+	0	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	exon	40588029	40588523	.	+	.	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	intron	40588524	40588603	.	+	.	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	CDS	40588604	40590139	0.96	+	0	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	exon	40588604	40590139	.	+	.	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
Phchi.S1	AUGUSTUS	stop_codon	40590140	40590142	.	+	0	transcript_id "Phchi.S1G640900.t1"; gene_id "Phchi.S1G640900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2722.t1 is derived from g9642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8440250	8442475	.	-	.	Phchi.S5G133100
Phchi.S5	AUGUSTUS	transcript	8440250	8442475	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	stop_codon	8440247	8440249	.	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8440250	8440318	0.85	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8440250	8440318	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8440319	8440433	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8440434	8440556	1	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8440434	8440556	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8440557	8440661	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8440662	8440727	1	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8440662	8440727	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8440728	8440846	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8440847	8440967	0.97	-	1	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8440847	8440967	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8440968	8441077	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8441078	8441145	1	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8441078	8441145	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8441146	8441264	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8441265	8441336	1	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8441265	8441336	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8441337	8441446	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8441447	8441622	1	-	2	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8441447	8441622	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8441623	8441809	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8441810	8442045	1	-	1	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8441810	8442045	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	intron	8442046	8442134	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	CDS	8442135	8442475	1	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	exon	8442135	8442475	.	-	.	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
Phchi.S5	AUGUSTUS	start_codon	8442473	8442475	.	-	0	transcript_id "Phchi.S5G133100.t1"; gene_id "Phchi.S5G133100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7554.t1 is derived from g4728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30012251	30015296	.	-	.	Phchi.S1G471300
Phchi.S1	AUGUSTUS	transcript	30012251	30015296	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	stop_codon	30012248	30012250	.	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30012251	30012319	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30012251	30012319	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30012320	30012478	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30012479	30012526	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30012479	30012526	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30012527	30012753	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30012754	30012831	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30012754	30012831	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30012832	30012920	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30012921	30012977	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30012921	30012977	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30012978	30013062	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30013063	30013128	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30013063	30013128	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30013129	30013207	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30013208	30013297	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30013208	30013297	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30013298	30013402	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30013403	30013510	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30013403	30013510	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30013511	30013592	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30013593	30013697	0.99	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30013593	30013697	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30013698	30013801	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30013802	30013937	0.99	-	1	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30013802	30013937	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30013938	30014007	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30014008	30014083	1	-	2	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30014008	30014083	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30014084	30014196	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30014197	30014401	0.97	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30014197	30014401	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30014402	30014506	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30014507	30014719	1	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30014507	30014719	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	intron	30014720	30014837	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	CDS	30014838	30015296	0.91	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	exon	30014838	30015296	.	-	.	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
Phchi.S1	AUGUSTUS	start_codon	30015294	30015296	.	-	0	transcript_id "Phchi.S1G471300.t1"; gene_id "Phchi.S1G471300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9360.t1 is derived from g6536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41158371	41159344	.	-	.	Phchi.S1G651900
Phchi.S1	AUGUSTUS	transcript	41158371	41159344	.	-	.	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	stop_codon	41158368	41158370	.	-	0	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	CDS	41158371	41158383	0.49	-	1	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	exon	41158371	41158383	.	-	.	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	intron	41158384	41158598	.	-	.	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	CDS	41158599	41159344	0.43	-	0	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	exon	41158599	41159344	.	-	.	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
Phchi.S1	AUGUSTUS	start_codon	41159342	41159344	.	-	0	transcript_id "Phchi.S1G651900.t1"; gene_id "Phchi.S1G651900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4837.t1 is derived from g2007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13051909	13053089	.	-	.	Phchi.S1G199600
Phchi.S1	AUGUSTUS	transcript	13051909	13053089	.	-	.	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	stop_codon	13051906	13051908	.	-	0	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	CDS	13051909	13052226	0.95	-	0	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	exon	13051909	13052226	.	-	.	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	intron	13052227	13052316	.	-	.	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	CDS	13052317	13052691	0.52	-	0	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	exon	13052317	13052691	.	-	.	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	intron	13052692	13052798	.	-	.	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	CDS	13052799	13053089	0.88	-	0	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	exon	13052799	13053089	.	-	.	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
Phchi.S1	AUGUSTUS	start_codon	13053087	13053089	.	-	0	transcript_id "Phchi.S1G199600.t1"; gene_id "Phchi.S1G199600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15516.t1 is derived from g13985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19638278	19642316	.	-	.	Phchi.S3G283500
Phchi.S3	AUGUSTUS	transcript	19638278	19642316	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	stop_codon	19638275	19638277	.	-	0	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19638278	19638338	0.69	-	1	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19638278	19638338	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	intron	19638339	19638424	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19638425	19638525	0.96	-	0	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19638425	19638525	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	intron	19638526	19638616	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19638617	19638624	1	-	2	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19638617	19638624	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	intron	19638625	19638819	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19638820	19640544	0.97	-	2	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19638820	19640544	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	intron	19640545	19640654	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19640655	19641548	0.65	-	2	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19640655	19641548	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	intron	19641549	19641632	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19641633	19641746	0.5	-	2	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19641633	19641746	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	intron	19641747	19641871	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	CDS	19641872	19642316	0.34	-	0	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	exon	19641872	19642316	.	-	.	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
Phchi.S3	AUGUSTUS	start_codon	19642314	19642316	.	-	0	transcript_id "Phchi.S3G283500.t1"; gene_id "Phchi.S3G283500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11216.t1 is derived from g15266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4811185	4811576	.	-	.	Phchi.S4G079800
Phchi.S4	AUGUSTUS	transcript	4811185	4811576	.	-	.	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	stop_codon	4811182	4811184	.	-	0	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	CDS	4811185	4811253	0.95	-	0	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	exon	4811185	4811253	.	-	.	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	intron	4811254	4811447	.	-	.	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	CDS	4811448	4811576	0.96	-	0	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	exon	4811448	4811576	.	-	.	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
Phchi.S4	AUGUSTUS	start_codon	4811574	4811576	.	-	0	transcript_id "Phchi.S4G079800.t1"; gene_id "Phchi.S4G079800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10953.t1 is derived from g15003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3266959	3267532	.	+	.	Phchi.S4G053500
Phchi.S4	AUGUSTUS	transcript	3266959	3267532	.	+	.	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	start_codon	3266959	3266961	.	+	0	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	CDS	3266959	3267151	0.98	+	0	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	exon	3266959	3267151	.	+	.	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	intron	3267152	3267260	.	+	.	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	CDS	3267261	3267532	0.92	+	2	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	exon	3267261	3267532	.	+	.	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
Phchi.S4	AUGUSTUS	stop_codon	3267533	3267535	.	+	0	transcript_id "Phchi.S4G053500.t1"; gene_id "Phchi.S4G053500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5801.t1 is derived from g2971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19012705	19013933	.	-	.	Phchi.S1G296000
Phchi.S1	AUGUSTUS	transcript	19012705	19013933	.	-	.	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	stop_codon	19012702	19012704	.	-	0	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	CDS	19012705	19013663	0.53	-	2	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	exon	19012705	19013663	.	-	.	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	intron	19013664	19013728	.	-	.	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	CDS	19013729	19013933	0.54	-	0	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	exon	19013729	19013933	.	-	.	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
Phchi.S1	AUGUSTUS	start_codon	19013931	19013933	.	-	0	transcript_id "Phchi.S1G296000.t1"; gene_id "Phchi.S1G296000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1044.t1 is derived from g10827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7273349	7274513	.	-	.	Phchi.S6G100300
Phchi.S6	AUGUSTUS	transcript	7273349	7274513	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	stop_codon	7273346	7273348	.	-	0	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	CDS	7273349	7273557	0.65	-	2	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	exon	7273349	7273557	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	intron	7273558	7273660	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	CDS	7273661	7273940	1	-	0	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	exon	7273661	7273940	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	intron	7273941	7274046	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	CDS	7274047	7274198	1	-	2	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	exon	7274047	7274198	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	intron	7274199	7274305	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	CDS	7274306	7274513	0.33	-	0	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	exon	7274306	7274513	.	-	.	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
Phchi.S6	AUGUSTUS	start_codon	7274511	7274513	.	-	0	transcript_id "Phchi.S6G100300.t1"; gene_id "Phchi.S6G100300"
# This transcript jg15317.t2 is derived from g13785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15318.t1 is derived from g13786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18372054	18375116	.	-	.	Phchi.S3G263700
Phchi.S3	AUGUSTUS	transcript	18372054	18375116	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	stop_codon	18372051	18372053	.	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18372054	18372290	0.99	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18372054	18372290	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18372291	18372419	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18372420	18372718	1	-	2	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18372420	18372718	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18372719	18372818	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18372819	18372903	1	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18372819	18372903	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18372904	18373001	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18373002	18373066	0.71	-	2	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18373002	18373066	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18373067	18373251	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18373252	18373393	0.58	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18373252	18373393	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18373394	18373476	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18373477	18373633	0.75	-	1	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18373477	18373633	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18373634	18373752	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18373753	18373892	1	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18373753	18373892	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18373893	18374099	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18374100	18374165	1	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18374100	18374165	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18374166	18374491	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18374492	18374941	1	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18374492	18374941	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	intron	18374942	18375029	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	CDS	18375030	18375116	0.32	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	exon	18375030	18375116	.	-	.	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
Phchi.S3	AUGUSTUS	start_codon	18375114	18375116	.	-	0	transcript_id "Phchi.S3G263700.t1"; gene_id "Phchi.S3G263700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15679.t1 is derived from g14148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20629725	20630756	.	+	.	Phchi.S3G299800
Phchi.S3	AUGUSTUS	transcript	20629725	20630756	.	+	.	transcript_id "Phchi.S3G299800.t1"; gene_id "Phchi.S3G299800"
Phchi.S3	AUGUSTUS	start_codon	20629725	20629727	.	+	0	transcript_id "Phchi.S3G299800.t1"; gene_id "Phchi.S3G299800"
Phchi.S3	AUGUSTUS	CDS	20629725	20630756	0.61	+	0	transcript_id "Phchi.S3G299800.t1"; gene_id "Phchi.S3G299800"
Phchi.S3	AUGUSTUS	exon	20629725	20630756	.	+	.	transcript_id "Phchi.S3G299800.t1"; gene_id "Phchi.S3G299800"
Phchi.S3	AUGUSTUS	stop_codon	20630757	20630759	.	+	0	transcript_id "Phchi.S3G299800.t1"; gene_id "Phchi.S3G299800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg712.t1 is derived from g10494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5020011	5044302	.	+	.	Phchi.S6G067100
Phchi.S6	AUGUSTUS	transcript	5020011	5044302	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	start_codon	5020011	5020013	.	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020011	5020045	0.92	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020011	5020045	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020046	5020198	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020199	5020355	0.54	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020199	5020355	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020356	5020526	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020527	5020692	0.72	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020527	5020692	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020693	5020806	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020807	5020919	0.9	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020807	5020919	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020920	5021014	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021015	5021134	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021015	5021134	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021135	5021231	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021232	5021316	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021232	5021316	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021317	5021456	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021457	5021579	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021457	5021579	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021580	5021733	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021734	5021818	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021734	5021818	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021819	5022019	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022020	5022119	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022020	5022119	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022120	5022268	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022269	5022403	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022269	5022403	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022404	5022475	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022476	5022532	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022476	5022532	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022533	5022642	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022643	5022822	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022643	5022822	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022823	5022920	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022921	5023046	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022921	5023046	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5023047	5023123	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5023124	5024980	0.95	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5023124	5024980	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5024981	5025075	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025076	5025149	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025076	5025149	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025150	5025262	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025263	5025458	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025263	5025458	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025459	5025532	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025533	5025637	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025533	5025637	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025638	5025782	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025783	5025860	0.78	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025783	5025860	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025861	5025952	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025953	5026102	0.79	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025953	5026102	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026103	5026190	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026191	5026384	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026191	5026384	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026385	5026541	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026542	5026596	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026542	5026596	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026597	5026683	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026684	5026837	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026684	5026837	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026838	5026975	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026976	5027052	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026976	5027052	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027053	5027197	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027198	5027315	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027198	5027315	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027316	5027402	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027403	5027501	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027403	5027501	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027502	5027583	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027584	5027684	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027584	5027684	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027685	5027756	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027757	5027846	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027757	5027846	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027847	5027932	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027933	5027998	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027933	5027998	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027999	5028086	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5028087	5028251	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5028087	5028251	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5028252	5028328	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5028329	5028536	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5028329	5028536	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5028537	5028640	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5028641	5029581	0.59	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5028641	5029581	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5029582	5029680	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5029681	5031288	0.84	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5029681	5031288	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5031289	5031371	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5031372	5031561	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5031372	5031561	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5031562	5031696	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5031697	5031765	0.94	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5031697	5031765	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5031766	5031878	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5031879	5032006	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5031879	5032006	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032007	5032087	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032088	5032387	0.97	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032088	5032387	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032388	5032486	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032487	5032616	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032487	5032616	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032617	5032733	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032734	5032822	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032734	5032822	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032823	5032913	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032914	5032990	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032914	5032990	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032991	5033064	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033065	5033209	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033065	5033209	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033210	5033293	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033294	5033380	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033294	5033380	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033381	5033478	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033479	5033644	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033479	5033644	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033645	5033789	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033790	5033944	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033790	5033944	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033945	5034110	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034111	5034224	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034111	5034224	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5034225	5034331	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034332	5034508	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034332	5034508	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5034509	5034683	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034684	5034866	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034684	5034866	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5034867	5034948	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034949	5035140	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034949	5035140	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035141	5035243	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035244	5035345	0.95	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035244	5035345	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035346	5035427	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035428	5035649	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035428	5035649	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035650	5035745	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035746	5035892	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035746	5035892	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035893	5035989	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035990	5036059	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035990	5036059	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036060	5036272	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036273	5036394	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036273	5036394	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036395	5036470	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036471	5036635	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036471	5036635	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036636	5036806	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036807	5036885	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036807	5036885	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036886	5036981	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036982	5037094	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036982	5037094	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037095	5037181	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037182	5037261	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037182	5037261	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037262	5037350	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037351	5037476	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037351	5037476	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037477	5037581	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037582	5037650	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037582	5037650	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037651	5037749	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037750	5037906	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037750	5037906	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037907	5038019	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038020	5038180	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038020	5038180	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038181	5038286	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038287	5038369	1	+	1	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038287	5038369	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038370	5038447	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038448	5038534	0.85	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038448	5038534	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038535	5038618	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038619	5038716	0.88	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038619	5038716	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038717	5038795	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038796	5039047	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038796	5039047	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039048	5039133	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039134	5039260	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039134	5039260	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039261	5039392	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039393	5039463	1	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039393	5039463	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039464	5039573	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039574	5039735	0.98	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039574	5039735	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039736	5039860	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039861	5040085	0.99	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039861	5040085	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5040086	5040172	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5040173	5040508	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5040173	5040508	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5040509	5040662	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5040663	5040791	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5040663	5040791	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5040792	5040886	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5040887	5041093	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5040887	5041093	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5041094	5041174	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5041175	5041643	0.72	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5041175	5041643	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5041644	5041750	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5041751	5043084	0.65	+	2	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5041751	5043084	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043085	5043181	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5043182	5043463	0.94	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5043182	5043463	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043464	5043570	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5043571	5043750	0.96	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5043571	5043750	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043751	5043842	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5043843	5043941	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5043843	5043941	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043942	5044050	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5044051	5044176	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5044051	5044176	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5044177	5044272	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5044273	5044302	1	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5044273	5044302	.	+	.	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	stop_codon	5044303	5044305	.	+	0	transcript_id "Phchi.S6G067100.t1"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	transcript	5020011	5044302	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	start_codon	5020011	5020013	.	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020011	5020045	0.92	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020011	5020045	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020046	5020198	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020199	5020355	0.42	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020199	5020355	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020356	5020526	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020527	5020692	0.65	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020527	5020692	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020693	5020806	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5020807	5020919	0.93	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5020807	5020919	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5020920	5021014	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021015	5021134	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021015	5021134	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021135	5021231	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021232	5021316	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021232	5021316	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021317	5021456	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021457	5021579	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021457	5021579	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021580	5021733	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5021734	5021818	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5021734	5021818	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5021819	5022019	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022020	5022119	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022020	5022119	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022120	5022268	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022269	5022403	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022269	5022403	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022404	5022475	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022476	5022532	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022476	5022532	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022533	5022642	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022643	5022822	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022643	5022822	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5022823	5022920	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5022921	5023046	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5022921	5023046	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5023047	5023123	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5023124	5024980	0.96	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5023124	5024980	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5024981	5025075	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025076	5025149	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025076	5025149	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025150	5025262	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025263	5025458	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025263	5025458	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025459	5025532	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025533	5025637	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025533	5025637	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025638	5025782	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025783	5025860	0.66	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025783	5025860	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5025861	5025952	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5025953	5026102	0.68	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5025953	5026102	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026103	5026190	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026191	5026384	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026191	5026384	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026385	5026541	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026542	5026596	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026542	5026596	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026597	5026683	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026684	5026837	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026684	5026837	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5026838	5026975	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5026976	5027052	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5026976	5027052	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027053	5027197	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027198	5027315	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027198	5027315	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027316	5027402	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027403	5027501	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027403	5027501	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027502	5027583	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027584	5027684	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027584	5027684	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027685	5027756	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027757	5027846	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027757	5027846	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027847	5027932	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5027933	5027998	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5027933	5027998	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5027999	5028086	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5028087	5028251	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5028087	5028251	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5028252	5028328	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5028329	5028536	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5028329	5028536	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5028537	5028640	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5028641	5029581	0.63	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5028641	5029581	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5029582	5029680	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5029681	5031288	0.84	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5029681	5031288	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5031289	5031371	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5031372	5031561	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5031372	5031561	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5031562	5031693	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5031694	5031765	0.99	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5031694	5031765	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5031766	5031878	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5031879	5032006	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5031879	5032006	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032007	5032087	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032088	5032387	0.97	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032088	5032387	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032388	5032486	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032487	5032616	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032487	5032616	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032617	5032733	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032734	5032822	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032734	5032822	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032823	5032913	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5032914	5032990	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5032914	5032990	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5032991	5033064	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033065	5033209	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033065	5033209	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033210	5033293	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033294	5033380	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033294	5033380	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033381	5033478	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033479	5033644	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033479	5033644	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033645	5033789	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5033790	5033944	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5033790	5033944	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5033945	5034110	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034111	5034224	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034111	5034224	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5034225	5034331	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034332	5034508	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034332	5034508	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5034509	5034683	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034684	5034866	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034684	5034866	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5034867	5034948	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5034949	5035140	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5034949	5035140	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035141	5035243	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035244	5035345	0.96	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035244	5035345	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035346	5035427	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035428	5035649	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035428	5035649	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035650	5035745	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035746	5035892	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035746	5035892	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5035893	5035989	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5035990	5036059	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5035990	5036059	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036060	5036272	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036273	5036394	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036273	5036394	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036395	5036470	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036471	5036635	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036471	5036635	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036636	5036806	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036807	5036885	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036807	5036885	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5036886	5036981	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5036982	5037094	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5036982	5037094	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037095	5037181	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037182	5037261	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037182	5037261	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037262	5037350	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037351	5037476	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037351	5037476	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037477	5037581	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037582	5037650	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037582	5037650	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037651	5037749	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5037750	5037906	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5037750	5037906	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5037907	5038019	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038020	5038180	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038020	5038180	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038181	5038286	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038287	5038369	1	+	1	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038287	5038369	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038370	5038447	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038448	5038534	0.91	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038448	5038534	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038535	5038618	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038619	5038716	0.91	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038619	5038716	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5038717	5038795	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5038796	5039047	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5038796	5039047	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039048	5039133	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039134	5039260	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039134	5039260	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039261	5039392	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039393	5039463	1	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039393	5039463	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039464	5039573	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039574	5039735	0.99	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039574	5039735	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5039736	5039860	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5039861	5040085	0.98	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5039861	5040085	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5040086	5040172	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5040173	5040508	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5040173	5040508	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5040509	5040662	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5040663	5040791	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5040663	5040791	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5040792	5040886	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5040887	5041093	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5040887	5041093	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5041094	5041174	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5041175	5041643	0.78	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5041175	5041643	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5041644	5041750	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5041751	5043084	0.53	+	2	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5041751	5043084	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043085	5043181	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5043182	5043463	0.98	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5043182	5043463	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043464	5043570	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5043571	5043750	0.99	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5043571	5043750	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043751	5043842	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5043843	5043941	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5043843	5043941	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5043942	5044050	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5044051	5044176	0.99	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5044051	5044176	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	intron	5044177	5044272	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	CDS	5044273	5044302	1	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	exon	5044273	5044302	.	+	.	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
Phchi.S6	AUGUSTUS	stop_codon	5044303	5044305	.	+	0	transcript_id "Phchi.S6G067100.t2"; gene_id "Phchi.S6G067100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13291.t1 is derived from g11757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5219349	5219900	.	+	.	Phchi.S3G061000
Phchi.S3	AUGUSTUS	transcript	5219349	5219900	.	+	.	transcript_id "Phchi.S3G061000.t1"; gene_id "Phchi.S3G061000"
Phchi.S3	AUGUSTUS	start_codon	5219349	5219351	.	+	0	transcript_id "Phchi.S3G061000.t1"; gene_id "Phchi.S3G061000"
Phchi.S3	AUGUSTUS	CDS	5219349	5219900	1	+	0	transcript_id "Phchi.S3G061000.t1"; gene_id "Phchi.S3G061000"
Phchi.S3	AUGUSTUS	exon	5219349	5219900	.	+	.	transcript_id "Phchi.S3G061000.t1"; gene_id "Phchi.S3G061000"
Phchi.S3	AUGUSTUS	stop_codon	5219901	5219903	.	+	0	transcript_id "Phchi.S3G061000.t1"; gene_id "Phchi.S3G061000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13403.t1 is derived from g11869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6540216	6542501	.	-	.	Phchi.S3G072200
Phchi.S3	AUGUSTUS	transcript	6540216	6542501	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	stop_codon	6540213	6540215	.	-	0	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	CDS	6540216	6540600	1	-	1	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	exon	6540216	6540600	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	intron	6540601	6540686	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	CDS	6540687	6540883	1	-	0	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	exon	6540687	6540883	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	intron	6540884	6540971	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	CDS	6540972	6541428	1	-	1	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	exon	6540972	6541428	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	intron	6541429	6541504	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	CDS	6541505	6541538	0.48	-	2	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	exon	6541505	6541538	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	intron	6541539	6541618	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	CDS	6541619	6541630	0.48	-	2	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	exon	6541619	6541630	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	intron	6541631	6541783	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	CDS	6541784	6542501	0.33	-	0	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	exon	6541784	6542501	.	-	.	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
Phchi.S3	AUGUSTUS	start_codon	6542499	6542501	.	-	0	transcript_id "Phchi.S3G072200.t1"; gene_id "Phchi.S3G072200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12382.t1 is derived from g8058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14543492	14543923	.	-	.	Phchi.S2G046200
Phchi.S2	AUGUSTUS	transcript	14543492	14543923	.	-	.	transcript_id "Phchi.S2G046200.t1"; gene_id "Phchi.S2G046200"
Phchi.S2	AUGUSTUS	stop_codon	14543489	14543491	.	-	0	transcript_id "Phchi.S2G046200.t1"; gene_id "Phchi.S2G046200"
Phchi.S2	AUGUSTUS	CDS	14543492	14543923	0.36	-	0	transcript_id "Phchi.S2G046200.t1"; gene_id "Phchi.S2G046200"
Phchi.S2	AUGUSTUS	exon	14543492	14543923	.	-	.	transcript_id "Phchi.S2G046200.t1"; gene_id "Phchi.S2G046200"
Phchi.S2	AUGUSTUS	start_codon	14543921	14543923	.	-	0	transcript_id "Phchi.S2G046200.t1"; gene_id "Phchi.S2G046200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12186.t1 is derived from g7862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6266332	6266762	.	-	.	Phchi.S2G026600
Phchi.S2	AUGUSTUS	transcript	6266332	6266762	.	-	.	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	stop_codon	6266329	6266331	.	-	0	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	CDS	6266332	6266545	0.07	-	1	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	exon	6266332	6266545	.	-	.	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	intron	6266546	6266679	.	-	.	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	CDS	6266680	6266762	0.02	-	0	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	exon	6266680	6266762	.	-	.	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
Phchi.S2	AUGUSTUS	start_codon	6266760	6266762	.	-	0	transcript_id "Phchi.S2G026600.t1"; gene_id "Phchi.S2G026600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1687.t1 is derived from g8606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2502322	2503290	.	+	.	Phchi.S5G029600
Phchi.S5	AUGUSTUS	transcript	2502322	2503290	.	+	.	transcript_id "Phchi.S5G029600.t1"; gene_id "Phchi.S5G029600"
Phchi.S5	AUGUSTUS	start_codon	2502322	2502324	.	+	0	transcript_id "Phchi.S5G029600.t1"; gene_id "Phchi.S5G029600"
Phchi.S5	AUGUSTUS	CDS	2502322	2503290	1	+	0	transcript_id "Phchi.S5G029600.t1"; gene_id "Phchi.S5G029600"
Phchi.S5	AUGUSTUS	exon	2502322	2503290	.	+	.	transcript_id "Phchi.S5G029600.t1"; gene_id "Phchi.S5G029600"
Phchi.S5	AUGUSTUS	stop_codon	2503291	2503293	.	+	0	transcript_id "Phchi.S5G029600.t1"; gene_id "Phchi.S5G029600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10042.t1 is derived from g7218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45221429	45222043	.	-	.	Phchi.S1G720100
Phchi.S1	AUGUSTUS	transcript	45221429	45222043	.	-	.	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	stop_codon	45221426	45221428	.	-	0	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	CDS	45221429	45221770	0.5	-	0	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	exon	45221429	45221770	.	-	.	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	intron	45221771	45221965	.	-	.	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	CDS	45221966	45222043	0.56	-	0	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	exon	45221966	45222043	.	-	.	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
Phchi.S1	AUGUSTUS	start_codon	45222041	45222043	.	-	0	transcript_id "Phchi.S1G720100.t1"; gene_id "Phchi.S1G720100"
# This transcript jg15728.t2 is derived from g14198.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15729.t1 is derived from g14199.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20914272	20916354	.	+	.	Phchi.S3G304800
Phchi.S3	AUGUSTUS	transcript	20914272	20916354	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	start_codon	20914272	20914274	.	+	0	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	CDS	20914272	20914419	0.99	+	0	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	exon	20914272	20914419	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	intron	20914420	20914506	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	CDS	20914507	20914646	1	+	2	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	exon	20914507	20914646	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	intron	20914647	20914738	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	CDS	20914739	20915836	1	+	0	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	exon	20914739	20915836	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	intron	20915837	20915931	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	CDS	20915932	20916354	1	+	0	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	exon	20915932	20916354	.	+	.	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
Phchi.S3	AUGUSTUS	stop_codon	20916355	20916357	.	+	0	transcript_id "Phchi.S3G304800.t1"; gene_id "Phchi.S3G304800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7666.t1 is derived from g4840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30501816	30507088	.	+	.	Phchi.S1G482500
Phchi.S1	AUGUSTUS	transcript	30501816	30507088	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	start_codon	30501816	30501818	.	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30501816	30501947	0.36	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30501816	30501947	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30501948	30502245	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30502246	30502567	0.98	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30502246	30502567	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30502568	30502915	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30502916	30503166	1	+	2	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30502916	30503166	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30503167	30503398	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30503399	30503500	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30503399	30503500	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30503501	30503581	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30503582	30503758	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30503582	30503758	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30503759	30503860	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30503861	30504136	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30503861	30504136	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30504137	30504303	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30504304	30504575	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30504304	30504575	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30504576	30504783	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30504784	30504901	1	+	1	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30504784	30504901	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30504902	30504984	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30504985	30505296	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30504985	30505296	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30505297	30505379	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30505380	30505532	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30505380	30505532	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30505533	30505655	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30505656	30505784	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30505656	30505784	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30505785	30505865	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30505866	30506102	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30505866	30506102	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30506103	30506187	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30506188	30506264	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30506188	30506264	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30506265	30506377	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30506378	30506564	1	+	1	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30506378	30506564	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30506565	30506688	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30506689	30506889	1	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30506689	30506889	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	intron	30506890	30506974	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	CDS	30506975	30507088	0.96	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	exon	30506975	30507088	.	+	.	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
Phchi.S1	AUGUSTUS	stop_codon	30507089	30507091	.	+	0	transcript_id "Phchi.S1G482500.t1"; gene_id "Phchi.S1G482500"
# This transcript jg4824.t2 is derived from g1995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4825.t1 is derived from g1994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13013499	13018292	.	-	.	Phchi.S1G198300
Phchi.S1	AUGUSTUS	transcript	13013499	13018292	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	stop_codon	13013496	13013498	.	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13013499	13013923	0.93	-	2	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13013499	13013923	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13013924	13014140	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13014141	13014289	0.92	-	1	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13014141	13014289	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13014290	13014381	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13014382	13014605	1	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13014382	13014605	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13014606	13014697	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13014698	13014958	0.99	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13014698	13014958	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13014959	13015038	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13015039	13015149	1	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13015039	13015149	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13015150	13015252	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13015253	13016092	1	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13015253	13016092	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13016093	13016224	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13016225	13016377	0.97	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13016225	13016377	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13016378	13016480	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13016481	13017649	0.73	-	2	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13016481	13017649	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13017650	13017761	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13017762	13017981	0.59	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13017762	13017981	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13017982	13018149	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13018150	13018180	0.72	-	1	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13018150	13018180	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	intron	13018181	13018269	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	CDS	13018270	13018292	0.72	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	exon	13018270	13018292	.	-	.	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
Phchi.S1	AUGUSTUS	start_codon	13018290	13018292	.	-	0	transcript_id "Phchi.S1G198300.t1"; gene_id "Phchi.S1G198300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3221.t1 is derived from g390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2328290	2329410	.	-	.	Phchi.S1G038000
Phchi.S1	AUGUSTUS	transcript	2328290	2329410	.	-	.	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	stop_codon	2328287	2328289	.	-	0	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	CDS	2328290	2329218	0.98	-	2	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	exon	2328290	2329218	.	-	.	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	intron	2329219	2329304	.	-	.	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	CDS	2329305	2329410	0.8	-	0	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	exon	2329305	2329410	.	-	.	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
Phchi.S1	AUGUSTUS	start_codon	2329408	2329410	.	-	0	transcript_id "Phchi.S1G038000.t1"; gene_id "Phchi.S1G038000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg700.t1 is derived from g10482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4969694	4970655	.	+	.	Phchi.S6G065900
Phchi.S6	AUGUSTUS	transcript	4969694	4970655	.	+	.	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	start_codon	4969694	4969696	.	+	0	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	CDS	4969694	4969787	0.5	+	0	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	exon	4969694	4969787	.	+	.	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	intron	4969788	4969878	.	+	.	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	CDS	4969879	4970492	1	+	2	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	exon	4969879	4970492	.	+	.	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	intron	4970493	4970592	.	+	.	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	CDS	4970593	4970655	1	+	0	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	exon	4970593	4970655	.	+	.	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
Phchi.S6	AUGUSTUS	stop_codon	4970656	4970658	.	+	0	transcript_id "Phchi.S6G065900.t1"; gene_id "Phchi.S6G065900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5015.t1 is derived from g2185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14061406	14063825	.	-	.	Phchi.S1G217400
Phchi.S1	AUGUSTUS	transcript	14061406	14063825	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	stop_codon	14061403	14061405	.	-	0	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	CDS	14061406	14062463	1	-	2	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	exon	14061406	14062463	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	intron	14062464	14062607	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	CDS	14062608	14062851	1	-	0	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	exon	14062608	14062851	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	intron	14062852	14063045	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	CDS	14063046	14063546	1	-	0	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	exon	14063046	14063546	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	intron	14063547	14063632	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	CDS	14063633	14063653	1	-	0	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	exon	14063633	14063653	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	intron	14063654	14063762	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	CDS	14063763	14063825	0.21	-	0	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	exon	14063763	14063825	.	-	.	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
Phchi.S1	AUGUSTUS	start_codon	14063823	14063825	.	-	0	transcript_id "Phchi.S1G217400.t1"; gene_id "Phchi.S1G217400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13910.t1 is derived from g12377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9631547	9633241	.	-	.	Phchi.S3G122900
Phchi.S3	AUGUSTUS	transcript	9631547	9633241	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	stop_codon	9631544	9631546	.	-	0	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	CDS	9631547	9631572	0.76	-	2	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	exon	9631547	9631572	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	intron	9631573	9631849	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	CDS	9631850	9631911	0.74	-	1	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	exon	9631850	9631911	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	intron	9631912	9632295	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	CDS	9632296	9632498	0.7	-	0	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	exon	9632296	9632498	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	intron	9632499	9632683	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	CDS	9632684	9633241	0.47	-	0	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	exon	9632684	9633241	.	-	.	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
Phchi.S3	AUGUSTUS	start_codon	9633239	9633241	.	-	0	transcript_id "Phchi.S3G122900.t1"; gene_id "Phchi.S3G122900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14438.t1 is derived from g12906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12819199	12821783	.	-	.	Phchi.S3G175700
Phchi.S3	AUGUSTUS	transcript	12819199	12821783	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	stop_codon	12819196	12819198	.	-	0	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	CDS	12819199	12819340	1	-	1	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	exon	12819199	12819340	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	intron	12819341	12819439	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	CDS	12819440	12819777	0.99	-	0	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	exon	12819440	12819777	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	intron	12819778	12819857	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	CDS	12819858	12820686	0.55	-	1	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	exon	12819858	12820686	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	intron	12820687	12820788	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	CDS	12820789	12820951	0.59	-	2	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	exon	12820789	12820951	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	intron	12820952	12821038	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	CDS	12821039	12821418	0.35	-	1	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	exon	12821039	12821418	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	intron	12821419	12821778	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	CDS	12821779	12821783	0.76	-	0	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	exon	12821779	12821783	.	-	.	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
Phchi.S3	AUGUSTUS	start_codon	12821781	12821783	.	-	0	transcript_id "Phchi.S3G175700.t1"; gene_id "Phchi.S3G175700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2109.t1 is derived from g9029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4915166	4916025	.	-	.	Phchi.S5G071800
Phchi.S5	AUGUSTUS	transcript	4915166	4916025	.	-	.	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	stop_codon	4915163	4915165	.	-	0	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	CDS	4915166	4915243	0.75	-	0	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	exon	4915166	4915243	.	-	.	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	intron	4915244	4915710	.	-	.	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	CDS	4915711	4915869	0.68	-	0	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	exon	4915711	4915869	.	-	.	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	intron	4915870	4915998	.	-	.	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	CDS	4915999	4916025	0.45	-	0	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	exon	4915999	4916025	.	-	.	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
Phchi.S5	AUGUSTUS	start_codon	4916023	4916025	.	-	0	transcript_id "Phchi.S5G071800.t1"; gene_id "Phchi.S5G071800"
# This transcript jg14194.t2 is derived from g12661.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14194.t3 is derived from g12661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14195.t1 is derived from g12662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11420773	11427389	.	-	.	Phchi.S3G151400
Phchi.S3	AUGUSTUS	transcript	11420773	11427389	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	stop_codon	11420770	11420772	.	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11420773	11421390	0.96	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11420773	11421390	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11421391	11421512	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11421513	11422186	1	-	2	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11421513	11422186	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11422187	11422357	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11422358	11422730	1	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11422358	11422730	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11422731	11422855	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11422856	11423177	1	-	1	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11422856	11423177	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11423178	11423258	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11423259	11423282	1	-	1	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11423259	11423282	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11423283	11423428	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11423429	11423763	0.89	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11423429	11423763	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11423764	11423941	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11423942	11424215	1	-	1	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11423942	11424215	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11424216	11424297	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11424298	11424590	1	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11424298	11424590	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11424591	11424682	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11424683	11425105	1	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11424683	11425105	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11425106	11425199	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11425200	11425542	0.94	-	1	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11425200	11425542	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11425543	11425692	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11425693	11426010	0.98	-	1	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11425693	11426010	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11426011	11426158	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11426159	11426917	0.66	-	1	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11426159	11426917	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	intron	11426918	11427051	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	CDS	11427052	11427389	0.63	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	exon	11427052	11427389	.	-	.	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
Phchi.S3	AUGUSTUS	start_codon	11427387	11427389	.	-	0	transcript_id "Phchi.S3G151400.t1"; gene_id "Phchi.S3G151400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg671.t1 is derived from g10453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4652156	4653440	.	+	.	Phchi.S6G063000
Phchi.S6	AUGUSTUS	transcript	4652156	4653440	.	+	.	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	start_codon	4652156	4652158	.	+	0	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	CDS	4652156	4652346	0.9	+	0	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	exon	4652156	4652346	.	+	.	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	intron	4652347	4652443	.	+	.	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	CDS	4652444	4653440	1	+	1	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	exon	4652444	4653440	.	+	.	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
Phchi.S6	AUGUSTUS	stop_codon	4653441	4653443	.	+	0	transcript_id "Phchi.S6G063000.t1"; gene_id "Phchi.S6G063000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5920.t1 is derived from g3091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19877188	19878822	.	-	.	Phchi.S1G307900
Phchi.S1	AUGUSTUS	transcript	19877188	19878822	.	-	.	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	stop_codon	19877185	19877187	.	-	0	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	CDS	19877188	19878531	0.96	-	0	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	exon	19877188	19878531	.	-	.	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	intron	19878532	19878690	.	-	.	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	CDS	19878691	19878822	0.54	-	0	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	exon	19878691	19878822	.	-	.	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
Phchi.S1	AUGUSTUS	start_codon	19878820	19878822	.	-	0	transcript_id "Phchi.S1G307900.t1"; gene_id "Phchi.S1G307900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5778.t1 is derived from g2948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18903740	18908539	.	-	.	Phchi.S1G293700
Phchi.S1	AUGUSTUS	transcript	18903740	18908539	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	stop_codon	18903737	18903739	.	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18903740	18903868	1	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18903740	18903868	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18903869	18903992	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18903993	18904191	1	-	1	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18903993	18904191	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18904192	18904277	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18904278	18904809	0.75	-	2	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18904278	18904809	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18904810	18904913	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18904914	18905190	0.9	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18904914	18905190	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18905191	18905333	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18905334	18905851	0.55	-	2	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18905334	18905851	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18905852	18905979	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18905980	18906078	0.87	-	2	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18905980	18906078	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18906079	18906187	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18906188	18906402	0.92	-	1	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18906188	18906402	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18906403	18906507	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18906508	18906766	0.98	-	2	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18906508	18906766	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18906767	18906891	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18906892	18907043	0.98	-	1	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18906892	18907043	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18907044	18907136	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18907137	18907364	1	-	1	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18907137	18907364	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18907365	18907478	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18907479	18907659	0.98	-	2	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18907479	18907659	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18907660	18907752	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18907753	18907876	1	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18907753	18907876	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18907877	18907964	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18907965	18908002	1	-	2	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18907965	18908002	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18908003	18908102	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18908103	18908298	0.61	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18908103	18908298	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	intron	18908299	18908395	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	CDS	18908396	18908539	0.61	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	exon	18908396	18908539	.	-	.	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
Phchi.S1	AUGUSTUS	start_codon	18908537	18908539	.	-	0	transcript_id "Phchi.S1G293700.t1"; gene_id "Phchi.S1G293700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15508.t1 is derived from g13977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19601646	19603787	.	-	.	Phchi.S3G282700
Phchi.S3	AUGUSTUS	transcript	19601646	19603787	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	stop_codon	19601643	19601645	.	-	0	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	CDS	19601646	19601667	0.7	-	1	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	exon	19601646	19601667	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	intron	19601668	19601759	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	CDS	19601760	19603153	0.71	-	0	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	exon	19601760	19603153	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	intron	19603154	19603240	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	CDS	19603241	19603438	0.99	-	0	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	exon	19603241	19603438	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	intron	19603439	19603509	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	CDS	19603510	19603568	1	-	2	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	exon	19603510	19603568	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	intron	19603569	19603651	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	CDS	19603652	19603787	0.99	-	0	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	exon	19603652	19603787	.	-	.	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
Phchi.S3	AUGUSTUS	start_codon	19603785	19603787	.	-	0	transcript_id "Phchi.S3G282700.t1"; gene_id "Phchi.S3G282700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12893.t1 is derived from g11358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3022163	3022807	.	+	.	Phchi.S3G021200
Phchi.S3	AUGUSTUS	transcript	3022163	3022807	.	+	.	transcript_id "Phchi.S3G021200.t1"; gene_id "Phchi.S3G021200"
Phchi.S3	AUGUSTUS	start_codon	3022163	3022165	.	+	0	transcript_id "Phchi.S3G021200.t1"; gene_id "Phchi.S3G021200"
Phchi.S3	AUGUSTUS	CDS	3022163	3022807	0.44	+	0	transcript_id "Phchi.S3G021200.t1"; gene_id "Phchi.S3G021200"
Phchi.S3	AUGUSTUS	exon	3022163	3022807	.	+	.	transcript_id "Phchi.S3G021200.t1"; gene_id "Phchi.S3G021200"
Phchi.S3	AUGUSTUS	stop_codon	3022808	3022810	.	+	0	transcript_id "Phchi.S3G021200.t1"; gene_id "Phchi.S3G021200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10293.t1 is derived from g7469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46853037	46853974	.	-	.	Phchi.S1G745200
Phchi.S1	AUGUSTUS	transcript	46853037	46853974	.	-	.	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	stop_codon	46853034	46853036	.	-	0	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	CDS	46853037	46853105	0.98	-	0	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	exon	46853037	46853105	.	-	.	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	intron	46853106	46853184	.	-	.	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	CDS	46853185	46853379	0.62	-	0	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	exon	46853185	46853379	.	-	.	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	intron	46853380	46853728	.	-	.	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	CDS	46853729	46853974	0.2	-	0	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	exon	46853729	46853974	.	-	.	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
Phchi.S1	AUGUSTUS	start_codon	46853972	46853974	.	-	0	transcript_id "Phchi.S1G745200.t1"; gene_id "Phchi.S1G745200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9805.t1 is derived from g6981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43790945	43791729	.	-	.	Phchi.S1G696400
Phchi.S1	AUGUSTUS	transcript	43790945	43791729	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	stop_codon	43790942	43790944	.	-	0	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	CDS	43790945	43790994	0.84	-	2	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	exon	43790945	43790994	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	intron	43790995	43791079	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	CDS	43791080	43791223	0.88	-	2	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	exon	43791080	43791223	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	intron	43791224	43791315	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	CDS	43791316	43791462	0.98	-	2	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	exon	43791316	43791462	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	intron	43791463	43791557	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	CDS	43791558	43791729	0.98	-	0	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	exon	43791558	43791729	.	-	.	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
Phchi.S1	AUGUSTUS	start_codon	43791727	43791729	.	-	0	transcript_id "Phchi.S1G696400.t1"; gene_id "Phchi.S1G696400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12887.t1 is derived from g11352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3002071	3002625	.	+	.	Phchi.S3G020600
Phchi.S3	AUGUSTUS	transcript	3002071	3002625	.	+	.	transcript_id "Phchi.S3G020600.t1"; gene_id "Phchi.S3G020600"
Phchi.S3	AUGUSTUS	start_codon	3002071	3002073	.	+	0	transcript_id "Phchi.S3G020600.t1"; gene_id "Phchi.S3G020600"
Phchi.S3	AUGUSTUS	CDS	3002071	3002625	0.18	+	0	transcript_id "Phchi.S3G020600.t1"; gene_id "Phchi.S3G020600"
Phchi.S3	AUGUSTUS	exon	3002071	3002625	.	+	.	transcript_id "Phchi.S3G020600.t1"; gene_id "Phchi.S3G020600"
Phchi.S3	AUGUSTUS	stop_codon	3002626	3002628	.	+	0	transcript_id "Phchi.S3G020600.t1"; gene_id "Phchi.S3G020600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg92.t1 is derived from g9874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	468608	470888	.	-	.	Phchi.S6G005100
Phchi.S6	AUGUSTUS	transcript	468608	470888	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	stop_codon	468605	468607	.	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	468608	468686	1	-	1	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	468608	468686	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	468687	468785	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	468786	468853	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	468786	468853	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	468854	469016	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	469017	469103	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	469017	469103	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	469104	469181	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	469182	469283	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	469182	469283	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	469284	469370	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	469371	469466	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	469371	469466	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	469467	469590	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	469591	469635	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	469591	469635	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	469636	469737	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	469738	469824	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	469738	469824	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	469825	470026	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	470027	470149	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	470027	470149	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	470150	470273	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	470274	470373	1	-	1	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	470274	470373	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	470374	470468	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	470469	470554	1	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	470469	470554	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	intron	470555	470729	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	CDS	470730	470888	0.96	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	exon	470730	470888	.	-	.	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
Phchi.S6	AUGUSTUS	start_codon	470886	470888	.	-	0	transcript_id "Phchi.S6G005100.t1"; gene_id "Phchi.S6G005100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8313.t1 is derived from g5488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35250398	35251762	.	+	.	Phchi.S1G547200
Phchi.S1	AUGUSTUS	transcript	35250398	35251762	.	+	.	transcript_id "Phchi.S1G547200.t1"; gene_id "Phchi.S1G547200"
Phchi.S1	AUGUSTUS	start_codon	35250398	35250400	.	+	0	transcript_id "Phchi.S1G547200.t1"; gene_id "Phchi.S1G547200"
Phchi.S1	AUGUSTUS	CDS	35250398	35251762	0.8	+	0	transcript_id "Phchi.S1G547200.t1"; gene_id "Phchi.S1G547200"
Phchi.S1	AUGUSTUS	exon	35250398	35251762	.	+	.	transcript_id "Phchi.S1G547200.t1"; gene_id "Phchi.S1G547200"
Phchi.S1	AUGUSTUS	stop_codon	35251763	35251765	.	+	0	transcript_id "Phchi.S1G547200.t1"; gene_id "Phchi.S1G547200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6476.t1 is derived from g3648.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23190603	23191495	.	-	.	Phchi.S1G363500
Phchi.S1	AUGUSTUS	transcript	23190603	23191495	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	stop_codon	23190600	23190602	.	-	0	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	CDS	23190603	23190691	1	-	2	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	exon	23190603	23190691	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	intron	23190692	23190785	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	CDS	23190786	23190864	1	-	0	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	exon	23190786	23190864	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	intron	23190865	23190946	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	CDS	23190947	23191075	0.59	-	0	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	exon	23190947	23191075	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	intron	23191076	23191191	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	CDS	23191192	23191278	0.43	-	0	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	exon	23191192	23191278	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	intron	23191279	23191372	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	CDS	23191373	23191495	0.15	-	0	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	exon	23191373	23191495	.	-	.	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
Phchi.S1	AUGUSTUS	start_codon	23191493	23191495	.	-	0	transcript_id "Phchi.S1G363500.t1"; gene_id "Phchi.S1G363500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13499.t1 is derived from g11966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7195473	7196655	.	+	.	Phchi.S3G081800
Phchi.S3	AUGUSTUS	transcript	7195473	7196655	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	start_codon	7195473	7195475	.	+	0	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	CDS	7195473	7195609	1	+	0	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	exon	7195473	7195609	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	intron	7195610	7195727	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	CDS	7195728	7195807	0.65	+	1	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	exon	7195728	7195807	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	intron	7195808	7195895	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	CDS	7195896	7196191	1	+	2	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	exon	7195896	7196191	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	intron	7196192	7196314	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	CDS	7196315	7196455	0.99	+	0	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	exon	7196315	7196455	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	intron	7196456	7196562	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	CDS	7196563	7196655	1	+	0	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	exon	7196563	7196655	.	+	.	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
Phchi.S3	AUGUSTUS	stop_codon	7196656	7196658	.	+	0	transcript_id "Phchi.S3G081800.t1"; gene_id "Phchi.S3G081800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14573.t1 is derived from g13041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13542742	13543790	.	+	.	Phchi.S3G189200
Phchi.S3	AUGUSTUS	transcript	13542742	13543790	.	+	.	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	start_codon	13542742	13542744	.	+	0	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	CDS	13542742	13543643	0.55	+	0	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	exon	13542742	13543643	.	+	.	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	intron	13543644	13543711	.	+	.	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	CDS	13543712	13543790	0.94	+	1	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	exon	13543712	13543790	.	+	.	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
Phchi.S3	AUGUSTUS	stop_codon	13543791	13543793	.	+	0	transcript_id "Phchi.S3G189200.t1"; gene_id "Phchi.S3G189200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg382.t1 is derived from g10164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2741195	2747949	.	+	.	Phchi.S6G034100
Phchi.S6	AUGUSTUS	transcript	2741195	2747949	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	start_codon	2741195	2741197	.	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2741195	2741364	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2741195	2741364	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2741365	2741718	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2741719	2741841	1	+	1	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2741719	2741841	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2741842	2741929	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2741930	2741993	1	+	1	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2741930	2741993	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2741994	2742086	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2742087	2742218	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2742087	2742218	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2742219	2742390	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2742391	2742629	0.97	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2742391	2742629	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2742630	2742713	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2742714	2743041	1	+	1	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2742714	2743041	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2743042	2743131	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2743132	2743231	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2743132	2743231	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2743232	2743328	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2743329	2743510	1	+	2	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2743329	2743510	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2743511	2743635	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2743636	2743751	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2743636	2743751	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2743752	2743855	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2743856	2743962	0.85	+	1	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2743856	2743962	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2743963	2744065	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2744066	2744217	0.94	+	2	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2744066	2744217	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2744218	2744359	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2744360	2744506	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2744360	2744506	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2744507	2744618	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2744619	2744822	0.97	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2744619	2744822	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2744823	2744935	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2744936	2745100	0.87	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2744936	2745100	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2745101	2745177	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2745178	2745342	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2745178	2745342	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2745343	2745444	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2745445	2745582	0.98	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2745445	2745582	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2745583	2745690	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2745691	2745885	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2745691	2745885	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2745886	2745977	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2745978	2746104	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2745978	2746104	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2746105	2746231	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2746232	2746431	1	+	2	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2746232	2746431	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2746432	2746560	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2746561	2746743	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2746561	2746743	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2746744	2746894	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2746895	2747020	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2746895	2747020	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2747021	2747111	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2747112	2747309	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2747112	2747309	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2747310	2747401	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2747402	2747673	1	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2747402	2747673	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	intron	2747674	2747780	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	CDS	2747781	2747949	1	+	1	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	exon	2747781	2747949	.	+	.	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
Phchi.S6	AUGUSTUS	stop_codon	2747950	2747952	.	+	0	transcript_id "Phchi.S6G034100.t1"; gene_id "Phchi.S6G034100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2794.t1 is derived from g9714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8930777	8932480	.	-	.	Phchi.S5G140300
Phchi.S5	AUGUSTUS	transcript	8930777	8932480	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	stop_codon	8930774	8930776	.	-	0	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8930777	8930998	0.99	-	0	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8930777	8930998	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	intron	8930999	8931076	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8931077	8931318	1	-	2	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8931077	8931318	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	intron	8931319	8931405	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8931406	8931540	1	-	2	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8931406	8931540	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	intron	8931541	8931661	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8931662	8931770	1	-	0	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8931662	8931770	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	intron	8931771	8931853	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8931854	8932030	1	-	0	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8931854	8932030	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	intron	8932031	8932128	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8932129	8932295	1	-	2	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8932129	8932295	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	intron	8932296	8932434	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	CDS	8932435	8932480	1	-	0	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	exon	8932435	8932480	.	-	.	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
Phchi.S5	AUGUSTUS	start_codon	8932478	8932480	.	-	0	transcript_id "Phchi.S5G140300.t1"; gene_id "Phchi.S5G140300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg478.t1 is derived from g10260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3349578	3350931	.	+	.	Phchi.S6G043700
Phchi.S6	AUGUSTUS	transcript	3349578	3350931	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	start_codon	3349578	3349580	.	+	0	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	CDS	3349578	3349626	0.3	+	0	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	exon	3349578	3349626	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	intron	3349627	3349736	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	CDS	3349737	3349906	0.98	+	2	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	exon	3349737	3349906	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	intron	3349907	3350274	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	CDS	3350275	3350437	0.72	+	0	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	exon	3350275	3350437	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	intron	3350438	3350521	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	CDS	3350522	3350717	1	+	2	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	exon	3350522	3350717	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	intron	3350718	3350792	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	CDS	3350793	3350931	1	+	1	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	exon	3350793	3350931	.	+	.	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
Phchi.S6	AUGUSTUS	stop_codon	3350932	3350934	.	+	0	transcript_id "Phchi.S6G043700.t1"; gene_id "Phchi.S6G043700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9273.t1 is derived from g6448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40721386	40722749	.	-	.	Phchi.S1G643200
Phchi.S1	AUGUSTUS	transcript	40721386	40722749	.	-	.	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	stop_codon	40721383	40721385	.	-	0	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	CDS	40721386	40722505	0.87	-	1	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	exon	40721386	40722505	.	-	.	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	intron	40722506	40722636	.	-	.	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	CDS	40722637	40722749	0.89	-	0	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	exon	40722637	40722749	.	-	.	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
Phchi.S1	AUGUSTUS	start_codon	40722747	40722749	.	-	0	transcript_id "Phchi.S1G643200.t1"; gene_id "Phchi.S1G643200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8199.t1 is derived from g5374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34380450	34389186	.	+	.	Phchi.S1G535800
Phchi.S1	AUGUSTUS	transcript	34380450	34389186	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	start_codon	34380450	34380452	.	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34380450	34380489	0.68	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34380450	34380489	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34380490	34380610	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34380611	34380673	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34380611	34380673	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34380674	34380758	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34380759	34380929	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34380759	34380929	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34380930	34381089	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381090	34381224	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381090	34381224	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34381225	34381304	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381305	34381444	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381305	34381444	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34381445	34381644	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381645	34381731	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381645	34381731	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34381732	34381891	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381892	34382017	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381892	34382017	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382018	34382155	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382156	34382308	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382156	34382308	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382309	34382486	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382487	34382561	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382487	34382561	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382562	34382660	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382661	34382762	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382661	34382762	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382763	34382837	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382838	34383008	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382838	34383008	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34383009	34383109	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34383110	34383215	0.97	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34383110	34383215	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34383216	34383299	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34383300	34383378	0.39	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34383300	34383378	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34383379	34383780	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34383781	34385398	0.24	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34383781	34385398	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34385399	34385651	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34385652	34385796	0.26	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34385652	34385796	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34385797	34385896	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34385897	34385954	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34385897	34385954	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34385955	34386046	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386047	34386120	0.88	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386047	34386120	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386121	34386221	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386222	34386286	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386222	34386286	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386287	34386381	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386382	34386426	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386382	34386426	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386427	34386518	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386519	34386599	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386519	34386599	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386600	34386708	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386709	34386776	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386709	34386776	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386777	34386866	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386867	34386945	1	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386867	34386945	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386946	34387032	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387033	34387193	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387033	34387193	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387194	34387278	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387279	34387342	0.99	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387279	34387342	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387343	34387668	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387669	34387681	1	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387669	34387681	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387682	34387777	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387778	34387832	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387778	34387832	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387833	34387998	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387999	34388265	1	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387999	34388265	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388266	34388362	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388363	34388419	1	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388363	34388419	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388420	34388527	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388528	34388592	1	+	1	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388528	34388592	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388593	34388678	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388679	34388809	1	+	2	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388679	34388809	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388810	34388910	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388911	34389186	0.99	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388911	34389186	.	+	.	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	stop_codon	34389187	34389189	.	+	0	transcript_id "Phchi.S1G535800.t1"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	transcript	34380450	34389186	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	start_codon	34380450	34380452	.	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34380450	34380489	0.64	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34380450	34380489	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34380490	34380610	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34380611	34380673	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34380611	34380673	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34380674	34380758	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34380759	34380929	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34380759	34380929	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34380930	34381089	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381090	34381224	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381090	34381224	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34381225	34381304	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381305	34381444	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381305	34381444	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34381445	34381644	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381645	34381731	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381645	34381731	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34381732	34381891	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34381892	34382017	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34381892	34382017	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382018	34382155	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382156	34382308	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382156	34382308	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382309	34382486	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382487	34382561	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382487	34382561	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382562	34382660	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382661	34382762	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382661	34382762	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34382763	34382837	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34382838	34383008	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34382838	34383008	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34383009	34383109	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34383110	34383215	0.94	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34383110	34383215	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34383216	34383299	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34383300	34383378	0.24	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34383300	34383378	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34383379	34383780	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34383781	34385398	0.13	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34383781	34385398	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34385399	34385651	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34385652	34385796	0.28	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34385652	34385796	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34385797	34385896	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34385897	34385954	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34385897	34385954	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34385955	34386046	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386047	34386120	0.89	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386047	34386120	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386121	34386221	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386222	34386286	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386222	34386286	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386287	34386381	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386382	34386426	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386382	34386426	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386427	34386518	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386519	34386599	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386519	34386599	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386600	34386708	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386709	34386776	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386709	34386776	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386777	34386866	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34386867	34386945	1	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34386867	34386945	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34386946	34387032	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387033	34387193	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387033	34387193	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387194	34387278	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387279	34387342	0.98	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387279	34387342	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387343	34387668	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387669	34387681	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387669	34387681	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387682	34387777	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34387778	34387832	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34387778	34387832	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34387833	34388079	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388080	34388265	0.92	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388080	34388265	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388266	34388362	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388363	34388419	1	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388363	34388419	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388420	34388527	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388528	34388592	1	+	1	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388528	34388592	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388593	34388678	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388679	34388809	1	+	2	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388679	34388809	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	intron	34388810	34388910	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	CDS	34388911	34389186	1	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	exon	34388911	34389186	.	+	.	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
Phchi.S1	AUGUSTUS	stop_codon	34389187	34389189	.	+	0	transcript_id "Phchi.S1G535800.t2"; gene_id "Phchi.S1G535800"
# This transcript jg7551.t2 is derived from g4725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7552.t1 is derived from g4726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30007427	30007792	.	-	.	Phchi.S1G471100
Phchi.S1	AUGUSTUS	transcript	30007427	30007792	.	-	.	transcript_id "Phchi.S1G471100.t1"; gene_id "Phchi.S1G471100"
Phchi.S1	AUGUSTUS	stop_codon	30007424	30007426	.	-	0	transcript_id "Phchi.S1G471100.t1"; gene_id "Phchi.S1G471100"
Phchi.S1	AUGUSTUS	CDS	30007427	30007792	0.96	-	0	transcript_id "Phchi.S1G471100.t1"; gene_id "Phchi.S1G471100"
Phchi.S1	AUGUSTUS	exon	30007427	30007792	.	-	.	transcript_id "Phchi.S1G471100.t1"; gene_id "Phchi.S1G471100"
Phchi.S1	AUGUSTUS	start_codon	30007790	30007792	.	-	0	transcript_id "Phchi.S1G471100.t1"; gene_id "Phchi.S1G471100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2566.t1 is derived from g9486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7418509	7420104	.	-	.	Phchi.S5G117500
Phchi.S5	AUGUSTUS	transcript	7418509	7420104	.	-	.	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	stop_codon	7418506	7418508	.	-	0	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	CDS	7418509	7418535	0.34	-	0	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	exon	7418509	7418535	.	-	.	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	intron	7418536	7418687	.	-	.	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	CDS	7418688	7419576	0.58	-	1	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	exon	7418688	7419576	.	-	.	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	intron	7419577	7419712	.	-	.	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	CDS	7419713	7420104	0.4	-	0	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	exon	7419713	7420104	.	-	.	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
Phchi.S5	AUGUSTUS	start_codon	7420102	7420104	.	-	0	transcript_id "Phchi.S5G117500.t1"; gene_id "Phchi.S5G117500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11339.t1 is derived from g15389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5635902	5636396	.	+	.	Phchi.S4G092100
Phchi.S4	AUGUSTUS	transcript	5635902	5636396	.	+	.	transcript_id "Phchi.S4G092100.t1"; gene_id "Phchi.S4G092100"
Phchi.S4	AUGUSTUS	start_codon	5635902	5635904	.	+	0	transcript_id "Phchi.S4G092100.t1"; gene_id "Phchi.S4G092100"
Phchi.S4	AUGUSTUS	CDS	5635902	5636396	1	+	0	transcript_id "Phchi.S4G092100.t1"; gene_id "Phchi.S4G092100"
Phchi.S4	AUGUSTUS	exon	5635902	5636396	.	+	.	transcript_id "Phchi.S4G092100.t1"; gene_id "Phchi.S4G092100"
Phchi.S4	AUGUSTUS	stop_codon	5636397	5636399	.	+	0	transcript_id "Phchi.S4G092100.t1"; gene_id "Phchi.S4G092100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13378.t1 is derived from g11844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6427062	6430822	.	+	.	Phchi.S3G069700
Phchi.S3	AUGUSTUS	transcript	6427062	6430822	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	start_codon	6427062	6427064	.	+	0	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	CDS	6427062	6427389	0.41	+	0	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	exon	6427062	6427389	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	intron	6427390	6427501	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	CDS	6427502	6427580	0.25	+	2	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	exon	6427502	6427580	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	intron	6427581	6427675	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	CDS	6427676	6429733	0.23	+	1	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	exon	6427676	6429733	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	intron	6429734	6429871	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	CDS	6429872	6430402	0.79	+	1	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	exon	6429872	6430402	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	intron	6430403	6430496	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	CDS	6430497	6430551	0.88	+	1	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	exon	6430497	6430551	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	intron	6430552	6430705	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	CDS	6430706	6430822	0.85	+	0	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	exon	6430706	6430822	.	+	.	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
Phchi.S3	AUGUSTUS	stop_codon	6430823	6430825	.	+	0	transcript_id "Phchi.S3G069700.t1"; gene_id "Phchi.S3G069700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10413.t1 is derived from g7589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47728192	47729189	.	+	.	Phchi.S1G757200
Phchi.S1	AUGUSTUS	transcript	47728192	47729189	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	start_codon	47728192	47728194	.	+	0	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	CDS	47728192	47728256	0.77	+	0	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	exon	47728192	47728256	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	intron	47728257	47728348	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	CDS	47728349	47728369	0.97	+	1	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	exon	47728349	47728369	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	intron	47728370	47728535	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	CDS	47728536	47728555	0.97	+	1	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	exon	47728536	47728555	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	intron	47728556	47728792	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	CDS	47728793	47728801	1	+	2	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	exon	47728793	47728801	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	intron	47728802	47728887	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	CDS	47728888	47729189	0.99	+	2	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	exon	47728888	47729189	.	+	.	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
Phchi.S1	AUGUSTUS	stop_codon	47729190	47729192	.	+	0	transcript_id "Phchi.S1G757200.t1"; gene_id "Phchi.S1G757200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4199.t1 is derived from g1368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8879701	8880576	.	+	.	Phchi.S1G135800
Phchi.S1	AUGUSTUS	transcript	8879701	8880576	.	+	.	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	start_codon	8879701	8879703	.	+	0	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	CDS	8879701	8879891	0.36	+	0	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	exon	8879701	8879891	.	+	.	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	intron	8879892	8880344	.	+	.	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	CDS	8880345	8880576	0.07	+	1	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	exon	8880345	8880576	.	+	.	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
Phchi.S1	AUGUSTUS	stop_codon	8880577	8880579	.	+	0	transcript_id "Phchi.S1G135800.t1"; gene_id "Phchi.S1G135800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5760.t1 is derived from g2930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18836359	18836796	.	-	.	Phchi.S1G291900
Phchi.S1	AUGUSTUS	transcript	18836359	18836796	.	-	.	transcript_id "Phchi.S1G291900.t1"; gene_id "Phchi.S1G291900"
Phchi.S1	AUGUSTUS	stop_codon	18836356	18836358	.	-	0	transcript_id "Phchi.S1G291900.t1"; gene_id "Phchi.S1G291900"
Phchi.S1	AUGUSTUS	CDS	18836359	18836796	0.6	-	0	transcript_id "Phchi.S1G291900.t1"; gene_id "Phchi.S1G291900"
Phchi.S1	AUGUSTUS	exon	18836359	18836796	.	-	.	transcript_id "Phchi.S1G291900.t1"; gene_id "Phchi.S1G291900"
Phchi.S1	AUGUSTUS	start_codon	18836794	18836796	.	-	0	transcript_id "Phchi.S1G291900.t1"; gene_id "Phchi.S1G291900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2779.t1 is derived from g9699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8834692	8835139	.	-	.	Phchi.S5G138800
Phchi.S5	AUGUSTUS	transcript	8834692	8835139	.	-	.	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	stop_codon	8834689	8834691	.	-	0	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	CDS	8834692	8834714	0.28	-	2	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	exon	8834692	8834714	.	-	.	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	intron	8834715	8834788	.	-	.	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	CDS	8834789	8834869	0.4	-	2	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	exon	8834789	8834869	.	-	.	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	intron	8834870	8834949	.	-	.	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	CDS	8834950	8835139	0.58	-	0	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	exon	8834950	8835139	.	-	.	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
Phchi.S5	AUGUSTUS	start_codon	8835137	8835139	.	-	0	transcript_id "Phchi.S5G138800.t1"; gene_id "Phchi.S5G138800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5562.t1 is derived from g2732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17602320	17603018	.	+	.	Phchi.S1G272100
Phchi.S1	AUGUSTUS	transcript	17602320	17603018	.	+	.	transcript_id "Phchi.S1G272100.t1"; gene_id "Phchi.S1G272100"
Phchi.S1	AUGUSTUS	start_codon	17602320	17602322	.	+	0	transcript_id "Phchi.S1G272100.t1"; gene_id "Phchi.S1G272100"
Phchi.S1	AUGUSTUS	CDS	17602320	17603018	0.82	+	0	transcript_id "Phchi.S1G272100.t1"; gene_id "Phchi.S1G272100"
Phchi.S1	AUGUSTUS	exon	17602320	17603018	.	+	.	transcript_id "Phchi.S1G272100.t1"; gene_id "Phchi.S1G272100"
Phchi.S1	AUGUSTUS	stop_codon	17603019	17603021	.	+	0	transcript_id "Phchi.S1G272100.t1"; gene_id "Phchi.S1G272100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9566.t1 is derived from g6742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42689465	42693768	.	-	.	Phchi.S1G672500
Phchi.S1	AUGUSTUS	transcript	42689465	42693768	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	stop_codon	42689462	42689464	.	-	0	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	CDS	42689465	42689753	0.45	-	1	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	exon	42689465	42689753	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	intron	42689754	42689937	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	CDS	42689938	42690269	0.27	-	0	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	exon	42689938	42690269	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	intron	42690270	42690389	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	CDS	42690390	42690602	0.43	-	0	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	exon	42690390	42690602	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	intron	42690603	42690716	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	CDS	42690717	42692080	0.96	-	2	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	exon	42690717	42692080	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	intron	42692081	42692201	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	CDS	42692202	42693768	0.72	-	0	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	exon	42692202	42693768	.	-	.	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
Phchi.S1	AUGUSTUS	start_codon	42693766	42693768	.	-	0	transcript_id "Phchi.S1G672500.t1"; gene_id "Phchi.S1G672500"
# This transcript jg15872.t2 is derived from g14342.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15873.t1 is derived from g14343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21986798	21987733	.	-	.	Phchi.S3G319200
Phchi.S3	AUGUSTUS	transcript	21986798	21987733	.	-	.	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	stop_codon	21986795	21986797	.	-	0	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	CDS	21986798	21987283	1	-	0	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	exon	21986798	21987283	.	-	.	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	intron	21987284	21987382	.	-	.	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	CDS	21987383	21987733	1	-	0	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	exon	21987383	21987733	.	-	.	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
Phchi.S3	AUGUSTUS	start_codon	21987731	21987733	.	-	0	transcript_id "Phchi.S3G319200.t1"; gene_id "Phchi.S3G319200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15785.t1 is derived from g14255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21331375	21341127	.	+	.	Phchi.S3G310400
Phchi.S3	AUGUSTUS	transcript	21331375	21341127	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	start_codon	21331375	21331377	.	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21331375	21331391	0.94	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21331375	21331391	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21331392	21331532	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21331533	21331767	0.99	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21331533	21331767	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21331768	21331859	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21331860	21332027	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21331860	21332027	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21332028	21332120	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21332121	21332210	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21332121	21332210	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21332211	21332346	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21332347	21332483	0.99	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21332347	21332483	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21332484	21332605	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21332606	21332699	0.99	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21332606	21332699	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21332700	21332822	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21332823	21332905	0.97	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21332823	21332905	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21332906	21333015	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21333016	21333122	1	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21333016	21333122	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21333123	21333222	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21333223	21333375	0.76	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21333223	21333375	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21333376	21333485	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21333486	21333550	0.99	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21333486	21333550	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21333551	21333693	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21333694	21333781	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21333694	21333781	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21333782	21333895	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21333896	21333974	1	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21333896	21333974	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21333975	21334083	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21334084	21334192	0.91	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21334084	21334192	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21334193	21334296	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21334297	21334356	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21334297	21334356	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21334357	21334520	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21334521	21334639	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21334521	21334639	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21334640	21334729	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21334730	21335126	1	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21334730	21335126	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21335127	21335253	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21335254	21335435	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21335254	21335435	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21335436	21335530	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21335531	21335603	1	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21335531	21335603	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21335604	21335697	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21335698	21336159	0.98	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21335698	21336159	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21336160	21336361	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21336362	21336709	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21336362	21336709	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21336710	21336830	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21336831	21336998	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21336831	21336998	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21336999	21337084	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21337085	21337378	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21337085	21337378	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21337379	21337518	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21337519	21337695	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21337519	21337695	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21337696	21337788	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21337789	21337867	0.73	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21337789	21337867	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21337868	21338031	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21338032	21338052	1	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21338032	21338052	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21338053	21338146	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21338147	21338244	1	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21338147	21338244	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21338245	21338469	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21338470	21338654	0.72	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21338470	21338654	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21338655	21338771	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21338772	21339113	1	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21338772	21339113	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21339114	21339298	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21339299	21339452	1	+	1	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21339299	21339452	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21339453	21339649	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21339650	21339760	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21339650	21339760	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21339761	21339841	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21339842	21340009	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21339842	21340009	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21340010	21340093	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21340094	21340226	0.96	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21340094	21340226	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21340227	21340334	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21340335	21340493	0.9	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21340335	21340493	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21340494	21340594	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21340595	21340686	0.9	+	2	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21340595	21340686	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21340687	21340786	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21340787	21340846	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21340787	21340846	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	intron	21340847	21340929	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	CDS	21340930	21341127	1	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	exon	21340930	21341127	.	+	.	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
Phchi.S3	AUGUSTUS	stop_codon	21341128	21341130	.	+	0	transcript_id "Phchi.S3G310400.t1"; gene_id "Phchi.S3G310400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4673.t1 is derived from g1843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11750308	11751409	.	+	.	Phchi.S1G183200
Phchi.S1	AUGUSTUS	transcript	11750308	11751409	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	start_codon	11750308	11750310	.	+	0	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	CDS	11750308	11750348	0.67	+	0	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	exon	11750308	11750348	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	intron	11750349	11750422	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	CDS	11750423	11750783	0.54	+	1	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	exon	11750423	11750783	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	intron	11750784	11750886	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	CDS	11750887	11751227	0.69	+	0	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	exon	11750887	11751227	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	intron	11751228	11751327	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	CDS	11751328	11751409	0.73	+	1	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	exon	11751328	11751409	.	+	.	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
Phchi.S1	AUGUSTUS	stop_codon	11751410	11751412	.	+	0	transcript_id "Phchi.S1G183200.t1"; gene_id "Phchi.S1G183200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1012.t1 is derived from g10795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7116436	7117603	.	-	.	Phchi.S6G097100
Phchi.S6	AUGUSTUS	transcript	7116436	7117603	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	stop_codon	7116433	7116435	.	-	0	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	CDS	7116436	7116543	1	-	0	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	exon	7116436	7116543	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	intron	7116544	7116692	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	CDS	7116693	7117186	1	-	2	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	exon	7116693	7117186	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	intron	7117187	7117273	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	CDS	7117274	7117322	1	-	0	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	exon	7117274	7117322	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	intron	7117323	7117447	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	CDS	7117448	7117603	0.6	-	0	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	exon	7117448	7117603	.	-	.	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
Phchi.S6	AUGUSTUS	start_codon	7117601	7117603	.	-	0	transcript_id "Phchi.S6G097100.t1"; gene_id "Phchi.S6G097100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11767.t1 is derived from g15819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8081877	8084921	.	-	.	Phchi.S4G134900
Phchi.S4	AUGUSTUS	transcript	8081877	8084921	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	stop_codon	8081874	8081876	.	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8081877	8082029	0.89	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8081877	8082029	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082030	8082118	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8082119	8082169	1	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8082119	8082169	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082170	8082280	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8082281	8082326	1	-	1	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8082281	8082326	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082327	8082413	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8082414	8082463	1	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8082414	8082463	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082464	8082557	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8082558	8082601	1	-	2	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8082558	8082601	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082602	8082755	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8082756	8082786	0.86	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8082756	8082786	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082787	8082893	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8082894	8082981	0.68	-	1	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8082894	8082981	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8082982	8083096	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8083097	8083167	0.99	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8083097	8083167	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8083168	8083314	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8083315	8083404	1	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8083315	8083404	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8083405	8083613	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8083614	8083745	0.99	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8083614	8083745	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8083746	8083861	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8083862	8083912	1	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8083862	8083912	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8083913	8084002	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8084003	8084092	1	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8084003	8084092	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8084093	8084323	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8084324	8084388	1	-	2	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8084324	8084388	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8084389	8084580	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8084581	8084701	1	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8084581	8084701	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	intron	8084702	8084873	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	CDS	8084874	8084921	0.96	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	exon	8084874	8084921	.	-	.	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
Phchi.S4	AUGUSTUS	start_codon	8084919	8084921	.	-	0	transcript_id "Phchi.S4G134900.t1"; gene_id "Phchi.S4G134900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5706.t1 is derived from g2876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18454280	18456629	.	+	.	Phchi.S1G286500
Phchi.S1	AUGUSTUS	transcript	18454280	18456629	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	start_codon	18454280	18454282	.	+	0	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	CDS	18454280	18455749	0.31	+	0	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	exon	18454280	18455749	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	intron	18455750	18455932	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	CDS	18455933	18456133	0.54	+	0	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	exon	18455933	18456133	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	intron	18456134	18456240	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	CDS	18456241	18456321	0.73	+	0	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	exon	18456241	18456321	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	intron	18456322	18456578	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	CDS	18456579	18456629	0.74	+	0	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	exon	18456579	18456629	.	+	.	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
Phchi.S1	AUGUSTUS	stop_codon	18456630	18456632	.	+	0	transcript_id "Phchi.S1G286500.t1"; gene_id "Phchi.S1G286500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14010.t1 is derived from g12477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10301967	10302323	.	+	.	Phchi.S3G132900
Phchi.S3	AUGUSTUS	transcript	10301967	10302323	.	+	.	transcript_id "Phchi.S3G132900.t1"; gene_id "Phchi.S3G132900"
Phchi.S3	AUGUSTUS	start_codon	10301967	10301969	.	+	0	transcript_id "Phchi.S3G132900.t1"; gene_id "Phchi.S3G132900"
Phchi.S3	AUGUSTUS	CDS	10301967	10302323	0.57	+	0	transcript_id "Phchi.S3G132900.t1"; gene_id "Phchi.S3G132900"
Phchi.S3	AUGUSTUS	exon	10301967	10302323	.	+	.	transcript_id "Phchi.S3G132900.t1"; gene_id "Phchi.S3G132900"
Phchi.S3	AUGUSTUS	stop_codon	10302324	10302326	.	+	0	transcript_id "Phchi.S3G132900.t1"; gene_id "Phchi.S3G132900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12877.t1 is derived from g11342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2878631	2879734	.	-	.	Phchi.S3G019600
Phchi.S3	AUGUSTUS	transcript	2878631	2879734	.	-	.	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	stop_codon	2878628	2878630	.	-	0	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	CDS	2878631	2879627	1	-	1	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	exon	2878631	2879627	.	-	.	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	intron	2879628	2879711	.	-	.	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	CDS	2879712	2879734	0.92	-	0	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	exon	2879712	2879734	.	-	.	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
Phchi.S3	AUGUSTUS	start_codon	2879732	2879734	.	-	0	transcript_id "Phchi.S3G019600.t1"; gene_id "Phchi.S3G019600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg157.t1 is derived from g9939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	894798	896482	.	-	.	Phchi.S6G011600
Phchi.S6	AUGUSTUS	transcript	894798	896482	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	stop_codon	894795	894797	.	-	0	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	894798	894887	0.98	-	0	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	894798	894887	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	894888	895019	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	895020	895075	0.75	-	2	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	895020	895075	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	895076	895170	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	895171	895277	0.97	-	1	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	895171	895277	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	895278	895391	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	895392	895479	0.44	-	2	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	895392	895479	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	895480	895637	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	895638	895651	0.97	-	1	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	895638	895651	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	895652	895751	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	895752	895873	0.92	-	0	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	895752	895873	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	895874	896081	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	896082	896380	0.65	-	2	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	896082	896380	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	intron	896381	896472	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	CDS	896473	896482	1	-	0	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	exon	896473	896482	.	-	.	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
Phchi.S6	AUGUSTUS	start_codon	896480	896482	.	-	0	transcript_id "Phchi.S6G011600.t1"; gene_id "Phchi.S6G011600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8198.t1 is derived from g5373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34378990	34380164	.	-	.	Phchi.S1G535700
Phchi.S1	AUGUSTUS	transcript	34378990	34380164	.	-	.	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	stop_codon	34378987	34378989	.	-	0	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	CDS	34378990	34379433	0.99	-	0	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	exon	34378990	34379433	.	-	.	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	intron	34379434	34379525	.	-	.	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	CDS	34379526	34380164	0.73	-	0	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	exon	34379526	34380164	.	-	.	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
Phchi.S1	AUGUSTUS	start_codon	34380162	34380164	.	-	0	transcript_id "Phchi.S1G535700.t1"; gene_id "Phchi.S1G535700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4224.t1 is derived from g1393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9001905	9002904	.	+	.	Phchi.S1G138300
Phchi.S1	AUGUSTUS	transcript	9001905	9002904	.	+	.	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	start_codon	9001905	9001907	.	+	0	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	CDS	9001905	9002038	0.98	+	0	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	exon	9001905	9002038	.	+	.	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	intron	9002039	9002216	.	+	.	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	CDS	9002217	9002904	0.53	+	1	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	exon	9002217	9002904	.	+	.	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
Phchi.S1	AUGUSTUS	stop_codon	9002905	9002907	.	+	0	transcript_id "Phchi.S1G138300.t1"; gene_id "Phchi.S1G138300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2470.t1 is derived from g9390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6821825	6822832	.	-	.	Phchi.S5G107900
Phchi.S5	AUGUSTUS	transcript	6821825	6822832	.	-	.	transcript_id "Phchi.S5G107900.t1"; gene_id "Phchi.S5G107900"
Phchi.S5	AUGUSTUS	stop_codon	6821822	6821824	.	-	0	transcript_id "Phchi.S5G107900.t1"; gene_id "Phchi.S5G107900"
Phchi.S5	AUGUSTUS	CDS	6821825	6822832	0.89	-	0	transcript_id "Phchi.S5G107900.t1"; gene_id "Phchi.S5G107900"
Phchi.S5	AUGUSTUS	exon	6821825	6822832	.	-	.	transcript_id "Phchi.S5G107900.t1"; gene_id "Phchi.S5G107900"
Phchi.S5	AUGUSTUS	start_codon	6822830	6822832	.	-	0	transcript_id "Phchi.S5G107900.t1"; gene_id "Phchi.S5G107900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4001.t1 is derived from g1170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6931795	6933602	.	+	.	Phchi.S1G116000
Phchi.S1	AUGUSTUS	transcript	6931795	6933602	.	+	.	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	start_codon	6931795	6931797	.	+	0	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	CDS	6931795	6933128	0.73	+	0	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	exon	6931795	6933128	.	+	.	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	intron	6933129	6933266	.	+	.	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	CDS	6933267	6933378	0.75	+	1	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	exon	6933267	6933378	.	+	.	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	intron	6933379	6933587	.	+	.	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	CDS	6933588	6933602	1	+	0	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	exon	6933588	6933602	.	+	.	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
Phchi.S1	AUGUSTUS	stop_codon	6933603	6933605	.	+	0	transcript_id "Phchi.S1G116000.t1"; gene_id "Phchi.S1G116000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10143.t1 is derived from g7319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45971964	45973707	.	+	.	Phchi.S1G730200
Phchi.S1	AUGUSTUS	transcript	45971964	45973707	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	start_codon	45971964	45971966	.	+	0	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	CDS	45971964	45972056	0.98	+	0	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	exon	45971964	45972056	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	intron	45972057	45972146	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	CDS	45972147	45972381	0.98	+	0	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	exon	45972147	45972381	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	intron	45972382	45972506	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	CDS	45972507	45973106	1	+	2	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	exon	45972507	45973106	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	intron	45973107	45973195	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	CDS	45973196	45973363	1	+	2	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	exon	45973196	45973363	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	intron	45973364	45973453	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	CDS	45973454	45973707	1	+	2	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	exon	45973454	45973707	.	+	.	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
Phchi.S1	AUGUSTUS	stop_codon	45973708	45973710	.	+	0	transcript_id "Phchi.S1G730200.t1"; gene_id "Phchi.S1G730200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14953.t1 is derived from g13421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15680165	15681923	.	-	.	Phchi.S3G227200
Phchi.S3	AUGUSTUS	transcript	15680165	15681923	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	stop_codon	15680162	15680164	.	-	0	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	CDS	15680165	15680392	0.68	-	0	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	exon	15680165	15680392	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	intron	15680393	15680537	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	CDS	15680538	15680657	1	-	0	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	exon	15680538	15680657	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	intron	15680658	15680806	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	CDS	15680807	15680974	0.97	-	0	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	exon	15680807	15680974	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	intron	15680975	15681121	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	CDS	15681122	15681335	0.9	-	1	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	exon	15681122	15681335	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	intron	15681336	15681580	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	CDS	15681581	15681617	0.86	-	2	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	exon	15681581	15681617	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	intron	15681618	15681763	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	CDS	15681764	15681923	0.4	-	0	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	exon	15681764	15681923	.	-	.	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
Phchi.S3	AUGUSTUS	start_codon	15681921	15681923	.	-	0	transcript_id "Phchi.S3G227200.t1"; gene_id "Phchi.S3G227200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9868.t1 is derived from g7044.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44148862	44154007	.	-	.	Phchi.S1G702700
Phchi.S1	AUGUSTUS	transcript	44148862	44154007	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	stop_codon	44148859	44148861	.	-	0	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44148862	44148926	0.99	-	2	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44148862	44148926	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44148927	44149178	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44149179	44149283	1	-	2	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44149179	44149283	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44149284	44149429	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44149430	44149546	0.7	-	2	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44149430	44149546	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44149547	44149635	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44149636	44149878	0.58	-	2	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44149636	44149878	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44149879	44150075	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44150076	44150361	0.31	-	0	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44150076	44150361	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44150362	44150438	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44150439	44151206	0.92	-	0	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44150439	44151206	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44151207	44151319	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44151320	44152698	0.97	-	2	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44151320	44152698	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44152699	44152792	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44152793	44152994	0.54	-	0	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44152793	44152994	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44152995	44153107	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44153108	44154007	0.17	-	0	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44153108	44154007	.	-	.	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	start_codon	44154005	44154007	.	-	0	transcript_id "Phchi.S1G702700.t1"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	transcript	44148862	44154007	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	stop_codon	44148859	44148861	.	-	0	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44148862	44148926	1	-	2	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44148862	44148926	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44148927	44149178	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44149179	44149283	0.99	-	2	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44149179	44149283	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44149284	44149420	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44149421	44149546	0.58	-	2	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44149421	44149546	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44149547	44149635	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44149636	44149878	0.52	-	2	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44149636	44149878	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44149879	44150075	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44150076	44150361	0.24	-	0	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44150076	44150361	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44150362	44150438	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44150439	44151206	0.93	-	0	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44150439	44151206	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44151207	44151319	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44151320	44152698	0.99	-	2	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44151320	44152698	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44152699	44152792	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44152793	44152994	0.67	-	0	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44152793	44152994	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	intron	44152995	44153107	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	CDS	44153108	44154007	0.23	-	0	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	exon	44153108	44154007	.	-	.	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
Phchi.S1	AUGUSTUS	start_codon	44154005	44154007	.	-	0	transcript_id "Phchi.S1G702700.t2"; gene_id "Phchi.S1G702700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5468.t1 is derived from g2638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16983545	16985720	.	-	.	Phchi.S1G262700
Phchi.S1	AUGUSTUS	transcript	16983545	16985720	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	stop_codon	16983542	16983544	.	-	0	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16983545	16983959	1	-	1	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16983545	16983959	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	intron	16983960	16984038	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16984039	16984239	1	-	1	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16984039	16984239	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	intron	16984240	16984316	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16984317	16984399	1	-	0	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16984317	16984399	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	intron	16984400	16984487	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16984488	16984646	1	-	0	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16984488	16984646	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	intron	16984647	16984774	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16984775	16985107	1	-	0	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16984775	16985107	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	intron	16985108	16985258	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16985259	16985428	1	-	2	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16985259	16985428	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	intron	16985429	16985518	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	CDS	16985519	16985720	0.97	-	0	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	exon	16985519	16985720	.	-	.	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
Phchi.S1	AUGUSTUS	start_codon	16985718	16985720	.	-	0	transcript_id "Phchi.S1G262700.t1"; gene_id "Phchi.S1G262700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14599.t1 is derived from g13067.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13663026	13671551	.	+	.	Phchi.S3G191800
Phchi.S3	AUGUSTUS	transcript	13663026	13671551	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	start_codon	13663026	13663028	.	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13663026	13663422	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13663026	13663422	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13663423	13663568	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13663569	13663811	0.99	+	2	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13663569	13663811	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13663812	13663892	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13663893	13664278	0.99	+	2	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13663893	13664278	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13664279	13664523	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13664524	13666493	0.68	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13664524	13666493	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13666494	13666617	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13666618	13667083	0.99	+	1	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13666618	13667083	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13667084	13667292	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13667293	13667339	0.98	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13667293	13667339	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13667340	13667512	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13667513	13667594	1	+	1	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13667513	13667594	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13667595	13667684	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13667685	13667735	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13667685	13667735	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13667736	13667878	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13667879	13667982	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13667879	13667982	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13667983	13668614	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13668615	13668725	0.94	+	1	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13668615	13668725	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13668726	13668958	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13668959	13668991	0.97	+	1	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13668959	13668991	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13668992	13669130	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13669131	13669218	0.97	+	1	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13669131	13669218	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13669219	13669317	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13669318	13669434	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13669318	13669434	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13669435	13669532	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13669533	13669736	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13669533	13669736	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13669737	13669826	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13669827	13670021	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13669827	13670021	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13670022	13670120	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13670121	13670285	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13670121	13670285	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13670286	13670379	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13670380	13670640	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13670380	13670640	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13670641	13670727	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13670728	13670946	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13670728	13670946	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13670947	13671037	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13671038	13671257	1	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13671038	13671257	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	intron	13671258	13671522	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	CDS	13671523	13671551	1	+	2	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	exon	13671523	13671551	.	+	.	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
Phchi.S3	AUGUSTUS	stop_codon	13671552	13671554	.	+	0	transcript_id "Phchi.S3G191800.t1"; gene_id "Phchi.S3G191800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3833.t1 is derived from g1002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5934147	5935204	.	-	.	Phchi.S1G099200
Phchi.S1	AUGUSTUS	transcript	5934147	5935204	.	-	.	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	stop_codon	5934144	5934146	.	-	0	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	CDS	5934147	5934260	0.47	-	0	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	exon	5934147	5934260	.	-	.	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	intron	5934261	5934497	.	-	.	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	CDS	5934498	5934554	0.47	-	0	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	exon	5934498	5934554	.	-	.	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	intron	5934555	5934679	.	-	.	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	CDS	5934680	5935204	0.46	-	0	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	exon	5934680	5935204	.	-	.	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
Phchi.S1	AUGUSTUS	start_codon	5935202	5935204	.	-	0	transcript_id "Phchi.S1G099200.t1"; gene_id "Phchi.S1G099200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9401.t1 is derived from g6577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41343988	41346888	.	-	.	Phchi.S1G656000
Phchi.S1	AUGUSTUS	transcript	41343988	41346888	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	stop_codon	41343985	41343987	.	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41343988	41344101	0.86	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41343988	41344101	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41344102	41344194	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41344195	41344292	1	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41344195	41344292	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41344293	41344408	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41344409	41344453	1	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41344409	41344453	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41344454	41344545	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41344546	41344630	1	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41344546	41344630	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41344631	41344718	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41344719	41344768	1	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41344719	41344768	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41344769	41344851	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41344852	41344975	1	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41344852	41344975	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41344976	41345068	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41345069	41345149	1	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41345069	41345149	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41345150	41345232	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41345233	41345348	1	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41345233	41345348	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41345349	41345458	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41345459	41345554	0.95	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41345459	41345554	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41345555	41345680	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41345681	41345960	1	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41345681	41345960	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41345961	41346086	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41346087	41346100	1	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41346087	41346100	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41346101	41346208	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41346209	41346291	0.99	-	1	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41346209	41346291	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41346292	41346470	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41346471	41346621	0.94	-	2	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41346471	41346621	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	intron	41346622	41346698	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	CDS	41346699	41346888	0.99	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	exon	41346699	41346888	.	-	.	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
Phchi.S1	AUGUSTUS	start_codon	41346886	41346888	.	-	0	transcript_id "Phchi.S1G656000.t1"; gene_id "Phchi.S1G656000"
# This transcript jg426.t2 is derived from g10208.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg427.t1 is derived from g10209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3037407	3038527	.	+	.	Phchi.S6G038600
Phchi.S6	AUGUSTUS	transcript	3037407	3038527	.	+	.	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	start_codon	3037407	3037409	.	+	0	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	CDS	3037407	3037814	0.53	+	0	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	exon	3037407	3037814	.	+	.	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	intron	3037815	3037915	.	+	.	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	CDS	3037916	3038527	1	+	0	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	exon	3037916	3038527	.	+	.	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
Phchi.S6	AUGUSTUS	stop_codon	3038528	3038530	.	+	0	transcript_id "Phchi.S6G038600.t1"; gene_id "Phchi.S6G038600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3154.t1 is derived from g323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1992664	1993994	.	+	.	Phchi.S1G031300
Phchi.S1	AUGUSTUS	transcript	1992664	1993994	.	+	.	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	start_codon	1992664	1992666	.	+	0	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	CDS	1992664	1993377	0.86	+	0	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	exon	1992664	1993377	.	+	.	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	intron	1993378	1993493	.	+	.	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	CDS	1993494	1993994	0.99	+	0	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	exon	1993494	1993994	.	+	.	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
Phchi.S1	AUGUSTUS	stop_codon	1993995	1993997	.	+	0	transcript_id "Phchi.S1G031300.t1"; gene_id "Phchi.S1G031300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg50.t1 is derived from g9832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	103396	105280	.	-	.	Phchi.S6G000900
Phchi.S6	AUGUSTUS	transcript	103396	105280	.	-	.	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	stop_codon	103393	103395	.	-	0	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	CDS	103396	103399	0.69	-	1	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	exon	103396	103399	.	-	.	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	intron	103400	103538	.	-	.	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	CDS	103539	105280	0.73	-	0	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	exon	103539	105280	.	-	.	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
Phchi.S6	AUGUSTUS	start_codon	105278	105280	.	-	0	transcript_id "Phchi.S6G000900.t1"; gene_id "Phchi.S6G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4288.t1 is derived from g1457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9425780	9426396	.	-	.	Phchi.S1G144700
Phchi.S1	AUGUSTUS	transcript	9425780	9426396	.	-	.	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	stop_codon	9425777	9425779	.	-	0	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	CDS	9425780	9425926	0.73	-	0	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	exon	9425780	9425926	.	-	.	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	intron	9425927	9426012	.	-	.	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	CDS	9426013	9426396	0.73	-	0	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	exon	9426013	9426396	.	-	.	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
Phchi.S1	AUGUSTUS	start_codon	9426394	9426396	.	-	0	transcript_id "Phchi.S1G144700.t1"; gene_id "Phchi.S1G144700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3948.t1 is derived from g1117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6614255	6615085	.	-	.	Phchi.S1G110700
Phchi.S1	AUGUSTUS	transcript	6614255	6615085	.	-	.	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	stop_codon	6614252	6614254	.	-	0	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	CDS	6614255	6614300	0.99	-	1	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	exon	6614255	6614300	.	-	.	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	intron	6614301	6614432	.	-	.	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	CDS	6614433	6615085	0.87	-	0	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	exon	6614433	6615085	.	-	.	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
Phchi.S1	AUGUSTUS	start_codon	6615083	6615085	.	-	0	transcript_id "Phchi.S1G110700.t1"; gene_id "Phchi.S1G110700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1832.t1 is derived from g8752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3472616	3475004	.	-	.	Phchi.S5G044100
Phchi.S5	AUGUSTUS	transcript	3472616	3475004	.	-	.	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	stop_codon	3472613	3472615	.	-	0	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	CDS	3472616	3472644	0.45	-	2	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	exon	3472616	3472644	.	-	.	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	intron	3472645	3472867	.	-	.	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	CDS	3472868	3475004	0.37	-	0	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	exon	3472868	3475004	.	-	.	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
Phchi.S5	AUGUSTUS	start_codon	3475002	3475004	.	-	0	transcript_id "Phchi.S5G044100.t1"; gene_id "Phchi.S5G044100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2334.t1 is derived from g9254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6215925	6218168	.	+	.	Phchi.S5G094300
Phchi.S5	AUGUSTUS	transcript	6215925	6218168	.	+	.	transcript_id "Phchi.S5G094300.t1"; gene_id "Phchi.S5G094300"
Phchi.S5	AUGUSTUS	start_codon	6215925	6215927	.	+	0	transcript_id "Phchi.S5G094300.t1"; gene_id "Phchi.S5G094300"
Phchi.S5	AUGUSTUS	CDS	6215925	6218168	0.48	+	0	transcript_id "Phchi.S5G094300.t1"; gene_id "Phchi.S5G094300"
Phchi.S5	AUGUSTUS	exon	6215925	6218168	.	+	.	transcript_id "Phchi.S5G094300.t1"; gene_id "Phchi.S5G094300"
Phchi.S5	AUGUSTUS	stop_codon	6218169	6218171	.	+	0	transcript_id "Phchi.S5G094300.t1"; gene_id "Phchi.S5G094300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6829.t1 is derived from g4001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25439132	25440596	.	+	.	Phchi.S1G398800
Phchi.S1	AUGUSTUS	transcript	25439474	25440596	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	start_codon	25439474	25439476	.	+	0	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439474	25439497	0.78	+	0	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439474	25439497	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439498	25439688	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439689	25439756	0.99	+	0	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439689	25439756	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439757	25439837	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439838	25439986	1	+	1	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439838	25439986	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439987	25440115	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25440116	25440172	1	+	2	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25440116	25440172	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25440173	25440303	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25440304	25440342	0.99	+	2	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25440304	25440342	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25440343	25440450	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25440451	25440596	1	+	2	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25440451	25440596	.	+	.	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	stop_codon	25440597	25440599	.	+	0	transcript_id "Phchi.S1G398800.t1"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	transcript	25439132	25440596	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	start_codon	25439132	25439134	.	+	0	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439132	25439214	0.68	+	0	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439132	25439214	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439215	25439293	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439294	25439384	0.65	+	1	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439294	25439384	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439385	25439688	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439689	25439756	1	+	0	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439689	25439756	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439757	25439837	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25439838	25439986	1	+	1	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25439838	25439986	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25439987	25440115	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25440116	25440172	1	+	2	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25440116	25440172	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25440173	25440303	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25440304	25440342	1	+	2	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25440304	25440342	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	intron	25440343	25440450	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	CDS	25440451	25440596	1	+	2	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	exon	25440451	25440596	.	+	.	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
Phchi.S1	AUGUSTUS	stop_codon	25440597	25440599	.	+	0	transcript_id "Phchi.S1G398800.t2"; gene_id "Phchi.S1G398800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9691.t1 is derived from g6867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43301249	43302252	.	+	.	Phchi.S1G685000
Phchi.S1	AUGUSTUS	transcript	43301249	43302252	.	+	.	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	start_codon	43301249	43301251	.	+	0	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	CDS	43301249	43301638	0.79	+	0	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	exon	43301249	43301638	.	+	.	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	intron	43301639	43301724	.	+	.	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	CDS	43301725	43302252	1	+	0	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	exon	43301725	43302252	.	+	.	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
Phchi.S1	AUGUSTUS	stop_codon	43302253	43302255	.	+	0	transcript_id "Phchi.S1G685000.t1"; gene_id "Phchi.S1G685000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13193.t1 is derived from g11658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4627581	4628624	.	-	.	Phchi.S3G051200
Phchi.S3	AUGUSTUS	transcript	4627581	4628624	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	stop_codon	4627578	4627580	.	-	0	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	CDS	4627581	4627626	1	-	1	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	exon	4627581	4627626	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	intron	4627627	4627720	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	CDS	4627721	4627806	1	-	0	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	exon	4627721	4627806	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	intron	4627807	4627915	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	CDS	4627916	4628032	1	-	0	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	exon	4627916	4628032	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	intron	4628033	4628186	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	CDS	4628187	4628624	0.62	-	0	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	exon	4628187	4628624	.	-	.	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
Phchi.S3	AUGUSTUS	start_codon	4628622	4628624	.	-	0	transcript_id "Phchi.S3G051200.t1"; gene_id "Phchi.S3G051200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10630.t1 is derived from g14680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1331541	1333028	.	+	.	Phchi.S4G021200
Phchi.S4	AUGUSTUS	transcript	1331541	1333028	.	+	.	transcript_id "Phchi.S4G021200.t1"; gene_id "Phchi.S4G021200"
Phchi.S4	AUGUSTUS	start_codon	1331541	1331543	.	+	0	transcript_id "Phchi.S4G021200.t1"; gene_id "Phchi.S4G021200"
Phchi.S4	AUGUSTUS	CDS	1331541	1333028	0.54	+	0	transcript_id "Phchi.S4G021200.t1"; gene_id "Phchi.S4G021200"
Phchi.S4	AUGUSTUS	exon	1331541	1333028	.	+	.	transcript_id "Phchi.S4G021200.t1"; gene_id "Phchi.S4G021200"
Phchi.S4	AUGUSTUS	stop_codon	1333029	1333031	.	+	0	transcript_id "Phchi.S4G021200.t1"; gene_id "Phchi.S4G021200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15932.t1 is derived from g16033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C71	AUGUSTUS	gene	36796	37470	.	-	.	Phchi.C71G000300
Phchi.C71	AUGUSTUS	transcript	36796	37470	.	-	.	transcript_id "Phchi.C71G000300.t1"; gene_id "Phchi.C71G000300"
Phchi.C71	AUGUSTUS	stop_codon	36793	36795	.	-	0	transcript_id "Phchi.C71G000300.t1"; gene_id "Phchi.C71G000300"
Phchi.C71	AUGUSTUS	CDS	36796	37470	0.79	-	0	transcript_id "Phchi.C71G000300.t1"; gene_id "Phchi.C71G000300"
Phchi.C71	AUGUSTUS	exon	36796	37470	.	-	.	transcript_id "Phchi.C71G000300.t1"; gene_id "Phchi.C71G000300"
Phchi.C71	AUGUSTUS	start_codon	37468	37470	.	-	0	transcript_id "Phchi.C71G000300.t1"; gene_id "Phchi.C71G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13164.t1 is derived from g11629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4453656	4454306	.	+	.	Phchi.S3G048300
Phchi.S3	AUGUSTUS	transcript	4453656	4454306	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	start_codon	4453656	4453658	.	+	0	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	CDS	4453656	4453728	1	+	0	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	exon	4453656	4453728	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	intron	4453729	4453814	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	CDS	4453815	4453880	0.98	+	2	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	exon	4453815	4453880	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	intron	4453881	4453981	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	CDS	4453982	4454108	1	+	2	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	exon	4453982	4454108	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	intron	4454109	4454176	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	CDS	4454177	4454306	1	+	1	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	exon	4454177	4454306	.	+	.	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
Phchi.S3	AUGUSTUS	stop_codon	4454307	4454309	.	+	0	transcript_id "Phchi.S3G048300.t1"; gene_id "Phchi.S3G048300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7865.t1 is derived from g5039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31591860	31592659	.	+	.	Phchi.S1G502400
Phchi.S1	AUGUSTUS	transcript	31591860	31592659	.	+	.	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	start_codon	31591860	31591862	.	+	0	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	CDS	31591860	31592070	0.24	+	0	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	exon	31591860	31592070	.	+	.	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	intron	31592071	31592290	.	+	.	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	CDS	31592291	31592309	0.28	+	2	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	exon	31592291	31592309	.	+	.	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	intron	31592310	31592475	.	+	.	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	CDS	31592476	31592659	0.26	+	1	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	exon	31592476	31592659	.	+	.	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
Phchi.S1	AUGUSTUS	stop_codon	31592660	31592662	.	+	0	transcript_id "Phchi.S1G502400.t1"; gene_id "Phchi.S1G502400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7461.t1 is derived from g4634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29393128	29396027	.	-	.	Phchi.S1G462000
Phchi.S1	AUGUSTUS	transcript	29393128	29396027	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	stop_codon	29393125	29393127	.	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29393128	29393482	1	-	1	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29393128	29393482	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29393483	29393622	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29393623	29393714	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29393623	29393714	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29393715	29393974	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29393975	29394082	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29393975	29394082	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29394083	29394263	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29394264	29394377	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29394264	29394377	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29394378	29394516	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29394517	29394684	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29394517	29394684	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29394685	29394818	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29394819	29394956	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29394819	29394956	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29394957	29395094	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29395095	29395313	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29395095	29395313	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29395314	29395522	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29395523	29395789	1	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29395523	29395789	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	intron	29395790	29395925	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	CDS	29395926	29396027	0.88	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	exon	29395926	29396027	.	-	.	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
Phchi.S1	AUGUSTUS	start_codon	29396025	29396027	.	-	0	transcript_id "Phchi.S1G462000.t1"; gene_id "Phchi.S1G462000"
# This transcript jg6059.t1 is derived from g3229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20678133	20678587	.	-	.	Phchi.S1G321700
Phchi.S1	AUGUSTUS	transcript	20678133	20678587	.	-	.	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	stop_codon	20678130	20678132	.	-	0	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	CDS	20678133	20678290	0.48	-	2	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	exon	20678133	20678290	.	-	.	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	intron	20678291	20678502	.	-	.	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	CDS	20678503	20678587	0.41	-	0	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	exon	20678503	20678587	.	-	.	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
Phchi.S1	AUGUSTUS	start_codon	20678585	20678587	.	-	0	transcript_id "Phchi.S1G321700.t1"; gene_id "Phchi.S1G321700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10856.t1 is derived from g14906.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2569437	2570069	.	-	.	Phchi.S4G043800
Phchi.S4	AUGUSTUS	transcript	2569437	2570069	.	-	.	transcript_id "Phchi.S4G043800.t1"; gene_id "Phchi.S4G043800"
Phchi.S4	AUGUSTUS	stop_codon	2569434	2569436	.	-	0	transcript_id "Phchi.S4G043800.t1"; gene_id "Phchi.S4G043800"
Phchi.S4	AUGUSTUS	CDS	2569437	2570069	0.55	-	0	transcript_id "Phchi.S4G043800.t1"; gene_id "Phchi.S4G043800"
Phchi.S4	AUGUSTUS	exon	2569437	2570069	.	-	.	transcript_id "Phchi.S4G043800.t1"; gene_id "Phchi.S4G043800"
Phchi.S4	AUGUSTUS	start_codon	2570067	2570069	.	-	0	transcript_id "Phchi.S4G043800.t1"; gene_id "Phchi.S4G043800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5439.t1 is derived from g2609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16874482	16875855	.	+	.	Phchi.S1G259800
Phchi.S1	AUGUSTUS	transcript	16874482	16875855	.	+	.	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	start_codon	16874482	16874484	.	+	0	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	CDS	16874482	16874538	0.88	+	0	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	exon	16874482	16874538	.	+	.	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	intron	16874539	16874721	.	+	.	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	CDS	16874722	16875855	0.88	+	0	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	exon	16874722	16875855	.	+	.	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
Phchi.S1	AUGUSTUS	stop_codon	16875856	16875858	.	+	0	transcript_id "Phchi.S1G259800.t1"; gene_id "Phchi.S1G259800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4860.t1 is derived from g2030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13138419	13142971	.	-	.	Phchi.S1G201900
Phchi.S1	AUGUSTUS	transcript	13138419	13142971	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	stop_codon	13138416	13138418	.	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13138419	13138655	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13138419	13138655	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13138656	13138773	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13138774	13138950	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13138774	13138950	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13138951	13139059	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13139060	13139263	0.98	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13139060	13139263	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13139264	13139385	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13139386	13139610	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13139386	13139610	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13139611	13139747	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13139748	13139858	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13139748	13139858	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13139859	13139948	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13139949	13140215	0.99	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13139949	13140215	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13140216	13140301	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13140302	13140543	0.91	-	2	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13140302	13140543	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13140544	13140737	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13140738	13140757	0.91	-	1	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13140738	13140757	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13140758	13140888	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13140889	13140977	0.58	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13140889	13140977	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13140978	13141056	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13141057	13141213	1	-	1	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13141057	13141213	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13141214	13141301	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13141302	13141450	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13141302	13141450	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13141451	13141634	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13141635	13141667	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13141635	13141667	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13141668	13141794	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13141795	13141873	1	-	1	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13141795	13141873	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13141874	13142013	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13142014	13142035	1	-	2	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13142014	13142035	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13142036	13142186	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13142187	13142259	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13142187	13142259	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13142260	13142404	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13142405	13142642	1	-	1	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13142405	13142642	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	intron	13142643	13142792	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	CDS	13142793	13142971	1	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	exon	13142793	13142971	.	-	.	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
Phchi.S1	AUGUSTUS	start_codon	13142969	13142971	.	-	0	transcript_id "Phchi.S1G201900.t1"; gene_id "Phchi.S1G201900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15893.t1 is derived from g14363.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22051895	22052253	.	-	.	Phchi.S3G321200
Phchi.S3	AUGUSTUS	transcript	22051895	22052253	.	-	.	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	stop_codon	22051892	22051894	.	-	0	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	CDS	22051895	22052032	1	-	0	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	exon	22051895	22052032	.	-	.	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	intron	22052033	22052115	.	-	.	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	CDS	22052116	22052253	0.43	-	0	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	exon	22052116	22052253	.	-	.	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
Phchi.S3	AUGUSTUS	start_codon	22052251	22052253	.	-	0	transcript_id "Phchi.S3G321200.t1"; gene_id "Phchi.S3G321200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3522.t1 is derived from g691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4203709	4204310	.	+	.	Phchi.S1G068100
Phchi.S1	AUGUSTUS	transcript	4203709	4204310	.	+	.	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	start_codon	4203709	4203711	.	+	0	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	CDS	4203709	4203852	0.88	+	0	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	exon	4203709	4203852	.	+	.	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	intron	4203853	4204157	.	+	.	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	CDS	4204158	4204310	0.61	+	0	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	exon	4204158	4204310	.	+	.	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
Phchi.S1	AUGUSTUS	stop_codon	4204311	4204313	.	+	0	transcript_id "Phchi.S1G068100.t1"; gene_id "Phchi.S1G068100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14701.t1 is derived from g13169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14254583	14256259	.	+	.	Phchi.S3G202000
Phchi.S3	AUGUSTUS	transcript	14254583	14256259	.	+	.	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	start_codon	14254583	14254585	.	+	0	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	CDS	14254583	14254748	0.98	+	0	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	exon	14254583	14254748	.	+	.	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	intron	14254749	14254875	.	+	.	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	CDS	14254876	14255028	1	+	2	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	exon	14254876	14255028	.	+	.	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	intron	14255029	14255162	.	+	.	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	CDS	14255163	14256259	0.8	+	2	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	exon	14255163	14256259	.	+	.	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
Phchi.S3	AUGUSTUS	stop_codon	14256260	14256262	.	+	0	transcript_id "Phchi.S3G202000.t1"; gene_id "Phchi.S3G202000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12098.t1 is derived from g7773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2730842	2731428	.	+	.	Phchi.S2G017800
Phchi.S2	AUGUSTUS	transcript	2730842	2731428	.	+	.	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	start_codon	2730842	2730844	.	+	0	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	CDS	2730842	2731085	0.77	+	0	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	exon	2730842	2731085	.	+	.	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	intron	2731086	2731192	.	+	.	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	CDS	2731193	2731428	0.51	+	2	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	exon	2731193	2731428	.	+	.	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
Phchi.S2	AUGUSTUS	stop_codon	2731429	2731431	.	+	0	transcript_id "Phchi.S2G017800.t1"; gene_id "Phchi.S2G017800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10216.t1 is derived from g7392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46421305	46422632	.	+	.	Phchi.S1G737500
Phchi.S1	AUGUSTUS	transcript	46421305	46422632	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	start_codon	46421305	46421307	.	+	0	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	CDS	46421305	46421488	0.99	+	0	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	exon	46421305	46421488	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	intron	46421489	46421701	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	CDS	46421702	46421852	0.97	+	2	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	exon	46421702	46421852	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	intron	46421853	46421982	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	CDS	46421983	46422172	1	+	1	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	exon	46421983	46422172	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	intron	46422173	46422314	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	CDS	46422315	46422632	0.92	+	0	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	exon	46422315	46422632	.	+	.	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
Phchi.S1	AUGUSTUS	stop_codon	46422633	46422635	.	+	0	transcript_id "Phchi.S1G737500.t1"; gene_id "Phchi.S1G737500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10010.t1 is derived from g7186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45032278	45032816	.	+	.	Phchi.S1G716900
Phchi.S1	AUGUSTUS	transcript	45032278	45032816	.	+	.	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	start_codon	45032278	45032280	.	+	0	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	CDS	45032278	45032627	0.41	+	0	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	exon	45032278	45032627	.	+	.	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	intron	45032628	45032782	.	+	.	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	CDS	45032783	45032816	0.87	+	1	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	exon	45032783	45032816	.	+	.	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
Phchi.S1	AUGUSTUS	stop_codon	45032817	45032819	.	+	0	transcript_id "Phchi.S1G716900.t1"; gene_id "Phchi.S1G716900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2112.t1 is derived from g9032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4919363	4921116	.	-	.	Phchi.S5G072100
Phchi.S5	AUGUSTUS	transcript	4919363	4921116	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	stop_codon	4919360	4919362	.	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4919363	4919386	1	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4919363	4919386	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4919387	4919467	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4919468	4919593	1	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4919468	4919593	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4919594	4919673	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4919674	4919721	1	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4919674	4919721	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4919722	4919801	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4919802	4919936	1	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4919802	4919936	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4919937	4920053	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4920054	4920209	1	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4920054	4920209	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4920210	4920339	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4920340	4920415	1	-	1	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4920340	4920415	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4920416	4920495	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4920496	4920812	1	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4920496	4920812	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	intron	4920813	4920972	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	CDS	4920973	4921116	0.99	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	exon	4920973	4921116	.	-	.	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
Phchi.S5	AUGUSTUS	start_codon	4921114	4921116	.	-	0	transcript_id "Phchi.S5G072100.t1"; gene_id "Phchi.S5G072100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11524.t1 is derived from g15574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6896868	6900314	.	-	.	Phchi.S4G110600
Phchi.S4	AUGUSTUS	transcript	6896868	6900314	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	stop_codon	6896865	6896867	.	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6896868	6896996	1	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6896868	6896996	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6896997	6897091	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6897092	6897221	1	-	1	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6897092	6897221	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6897222	6897297	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6897298	6897391	0.77	-	2	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6897298	6897391	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6897392	6897471	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6897472	6897492	0.77	-	2	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6897472	6897492	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6897493	6897611	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6897612	6897771	1	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6897612	6897771	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6897772	6897906	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6897907	6898092	1	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6897907	6898092	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6898093	6898194	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6898195	6898404	1	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6898195	6898404	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6898405	6898514	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6898515	6898676	1	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6898515	6898676	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6898677	6898772	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6898773	6898923	1	-	1	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6898773	6898923	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6898924	6899068	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6899069	6899253	0.62	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6899069	6899253	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6899254	6899339	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6899340	6899361	0.71	-	1	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6899340	6899361	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6899362	6899521	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6899522	6899608	0.84	-	1	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6899522	6899608	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	intron	6899609	6899706	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	CDS	6899707	6900314	0.87	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	exon	6899707	6900314	.	-	.	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
Phchi.S4	AUGUSTUS	start_codon	6900312	6900314	.	-	0	transcript_id "Phchi.S4G110600.t1"; gene_id "Phchi.S4G110600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4060.t1 is derived from g1229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7584132	7585069	.	-	.	Phchi.S1G121900
Phchi.S1	AUGUSTUS	transcript	7584132	7585069	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	stop_codon	7584129	7584131	.	-	0	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	CDS	7584132	7584276	0.39	-	1	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	exon	7584132	7584276	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	intron	7584277	7584392	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	CDS	7584393	7584511	0.9	-	0	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	exon	7584393	7584511	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	intron	7584512	7584621	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	CDS	7584622	7584746	1	-	2	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	exon	7584622	7584746	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	intron	7584747	7584867	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	CDS	7584868	7585069	0.87	-	0	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	exon	7584868	7585069	.	-	.	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
Phchi.S1	AUGUSTUS	start_codon	7585067	7585069	.	-	0	transcript_id "Phchi.S1G121900.t1"; gene_id "Phchi.S1G121900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3818.t1 is derived from g987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5881425	5886247	.	+	.	Phchi.S1G097700
Phchi.S1	AUGUSTUS	transcript	5881425	5886247	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	start_codon	5881425	5881427	.	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5881425	5881580	1	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5881425	5881580	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5881581	5881665	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5881666	5881850	1	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5881666	5881850	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5881851	5881958	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5881959	5882277	0.95	+	1	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5881959	5882277	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5882278	5882377	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5882378	5882630	1	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5882378	5882630	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5882631	5882707	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5882708	5883420	0.8	+	2	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5882708	5883420	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5883421	5883556	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5883557	5884600	0.88	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5883557	5884600	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5884601	5884684	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5884685	5885084	0.56	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5884685	5885084	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5885085	5885172	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5885173	5885222	0.79	+	2	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5885173	5885222	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5885223	5885430	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5885431	5885799	0.4	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5885431	5885799	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5885800	5885893	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5885894	5885946	1	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5885894	5885946	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5885947	5886038	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5886039	5886083	1	+	1	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5886039	5886083	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	intron	5886084	5886162	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	CDS	5886163	5886247	0.99	+	1	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	exon	5886163	5886247	.	+	.	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
Phchi.S1	AUGUSTUS	stop_codon	5886248	5886250	.	+	0	transcript_id "Phchi.S1G097700.t1"; gene_id "Phchi.S1G097700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5228.t1 is derived from g2398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15730638	15730955	.	-	.	Phchi.S1G238700
Phchi.S1	AUGUSTUS	transcript	15730638	15730955	.	-	.	transcript_id "Phchi.S1G238700.t1"; gene_id "Phchi.S1G238700"
Phchi.S1	AUGUSTUS	stop_codon	15730635	15730637	.	-	0	transcript_id "Phchi.S1G238700.t1"; gene_id "Phchi.S1G238700"
Phchi.S1	AUGUSTUS	CDS	15730638	15730955	0.69	-	0	transcript_id "Phchi.S1G238700.t1"; gene_id "Phchi.S1G238700"
Phchi.S1	AUGUSTUS	exon	15730638	15730955	.	-	.	transcript_id "Phchi.S1G238700.t1"; gene_id "Phchi.S1G238700"
Phchi.S1	AUGUSTUS	start_codon	15730953	15730955	.	-	0	transcript_id "Phchi.S1G238700.t1"; gene_id "Phchi.S1G238700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13293.t1 is derived from g11759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5291708	5292669	.	-	.	Phchi.S3G061200
Phchi.S3	AUGUSTUS	transcript	5291708	5292669	.	-	.	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	stop_codon	5291705	5291707	.	-	0	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	CDS	5291708	5291733	0.54	-	2	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	exon	5291708	5291733	.	-	.	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	intron	5291734	5291816	.	-	.	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	CDS	5291817	5292669	0.54	-	0	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	exon	5291817	5292669	.	-	.	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
Phchi.S3	AUGUSTUS	start_codon	5292667	5292669	.	-	0	transcript_id "Phchi.S3G061200.t1"; gene_id "Phchi.S3G061200"
# This transcript jg7121.t2 is derived from g4293.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg7122.t1 is derived from g4294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27068131	27070204	.	-	.	Phchi.S1G428100
Phchi.S1	AUGUSTUS	transcript	27069050	27070204	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	stop_codon	27069047	27069049	.	-	0	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069050	27069066	1	-	2	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069050	27069066	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27069067	27069142	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069143	27069509	0.99	-	0	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069143	27069509	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27069510	27069635	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069636	27069775	1	-	2	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069636	27069775	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27069776	27069862	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069863	27070010	1	-	0	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069863	27070010	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27070011	27070186	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27070187	27070204	0.74	-	0	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27070187	27070204	.	-	.	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	start_codon	27070202	27070204	.	-	0	transcript_id "Phchi.S1G428100.t1"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	transcript	27068131	27070204	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	stop_codon	27068128	27068130	.	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068131	27068207	0.99	-	2	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068131	27068207	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068208	27068425	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068426	27068524	0.93	-	2	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068426	27068524	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068525	27068660	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068661	27068672	0.64	-	2	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068661	27068672	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068673	27068743	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068744	27068915	0.61	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068744	27068915	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068916	27069003	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069004	27069066	1	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069004	27069066	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27069067	27069146	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069147	27069509	1	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069147	27069509	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27069510	27069635	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069636	27069775	1	-	2	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069636	27069775	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27069776	27069862	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069863	27070010	1	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069863	27070010	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27070011	27070186	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27070187	27070204	0.7	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27070187	27070204	.	-	.	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	start_codon	27070202	27070204	.	-	0	transcript_id "Phchi.S1G428100.t2"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	transcript	27068131	27069006	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	stop_codon	27068128	27068130	.	-	0	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068131	27068207	1	-	2	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068131	27068207	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068208	27068425	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068426	27068524	0.95	-	2	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068426	27068524	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068525	27068660	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068661	27068672	0.56	-	2	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068661	27068672	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068673	27068743	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27068744	27068915	0.52	-	0	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27068744	27068915	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	intron	27068916	27069003	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	CDS	27069004	27069006	1	-	0	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	exon	27069004	27069006	.	-	.	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
Phchi.S1	AUGUSTUS	start_codon	27069004	27069006	.	-	0	transcript_id "Phchi.S1G428100.t3"; gene_id "Phchi.S1G428100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7518.t1 is derived from g4692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29805012	29810926	.	-	.	Phchi.S1G467700
Phchi.S1	AUGUSTUS	transcript	29805012	29810926	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	stop_codon	29805009	29805011	.	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29805012	29805147	0.76	-	1	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29805012	29805147	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29805148	29805244	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29805245	29805325	1	-	1	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29805245	29805325	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29805326	29805480	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29805481	29805548	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29805481	29805548	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29805549	29805689	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29805690	29805851	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29805690	29805851	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29805852	29806008	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29806009	29806088	1	-	2	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29806009	29806088	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29806089	29806159	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29806160	29806241	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29806160	29806241	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29806242	29806362	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29806363	29806516	1	-	1	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29806363	29806516	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29806517	29806630	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29806631	29807073	0.98	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29806631	29807073	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29807074	29807153	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29807154	29807236	0.84	-	2	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29807154	29807236	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29807237	29807452	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29807453	29807514	0.53	-	1	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29807453	29807514	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29807515	29807613	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29807614	29807870	0.98	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29807614	29807870	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29807871	29807980	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29807981	29808069	1	-	2	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29807981	29808069	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29808070	29808242	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29808243	29808399	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29808243	29808399	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29808400	29808724	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29808725	29808799	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29808725	29808799	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29808800	29809110	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29809111	29809243	1	-	1	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29809111	29809243	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29809244	29809410	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29809411	29809490	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29809411	29809490	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29809491	29809675	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29809676	29809738	1	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29809676	29809738	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	intron	29809739	29809936	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	CDS	29809937	29810926	0.43	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	exon	29809937	29810926	.	-	.	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
Phchi.S1	AUGUSTUS	start_codon	29810924	29810926	.	-	0	transcript_id "Phchi.S1G467700.t1"; gene_id "Phchi.S1G467700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12856.t1 is derived from g11321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2752457	2753023	.	-	.	Phchi.S3G017500
Phchi.S3	AUGUSTUS	transcript	2752457	2753023	.	-	.	transcript_id "Phchi.S3G017500.t1"; gene_id "Phchi.S3G017500"
Phchi.S3	AUGUSTUS	stop_codon	2752454	2752456	.	-	0	transcript_id "Phchi.S3G017500.t1"; gene_id "Phchi.S3G017500"
Phchi.S3	AUGUSTUS	CDS	2752457	2753023	1	-	0	transcript_id "Phchi.S3G017500.t1"; gene_id "Phchi.S3G017500"
Phchi.S3	AUGUSTUS	exon	2752457	2753023	.	-	.	transcript_id "Phchi.S3G017500.t1"; gene_id "Phchi.S3G017500"
Phchi.S3	AUGUSTUS	start_codon	2753021	2753023	.	-	0	transcript_id "Phchi.S3G017500.t1"; gene_id "Phchi.S3G017500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10281.t1 is derived from g7457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46801983	46804564	.	-	.	Phchi.S1G744000
Phchi.S1	AUGUSTUS	transcript	46801983	46804564	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	stop_codon	46801980	46801982	.	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46801983	46802150	1	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46801983	46802150	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46802151	46802250	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46802251	46802364	1	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46802251	46802364	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46802365	46802461	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46802462	46802628	1	-	2	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46802462	46802628	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46802629	46802760	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46802761	46802863	1	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46802761	46802863	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46802864	46802984	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46802985	46803037	1	-	2	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46802985	46803037	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46803038	46803149	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46803150	46803282	1	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46803150	46803282	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46803283	46803381	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46803382	46803730	1	-	1	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46803382	46803730	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46803731	46803879	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46803880	46804198	1	-	2	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46803880	46804198	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	intron	46804199	46804365	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	CDS	46804366	46804564	0.99	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	exon	46804366	46804564	.	-	.	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
Phchi.S1	AUGUSTUS	start_codon	46804562	46804564	.	-	0	transcript_id "Phchi.S1G744000.t1"; gene_id "Phchi.S1G744000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4005.t1 is derived from g1174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6986604	6987082	.	-	.	Phchi.S1G116400
Phchi.S1	AUGUSTUS	transcript	6986604	6987082	.	-	.	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	stop_codon	6986601	6986603	.	-	0	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	CDS	6986604	6986843	0.98	-	0	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	exon	6986604	6986843	.	-	.	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	intron	6986844	6986974	.	-	.	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	CDS	6986975	6987082	1	-	0	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	exon	6986975	6987082	.	-	.	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
Phchi.S1	AUGUSTUS	start_codon	6987080	6987082	.	-	0	transcript_id "Phchi.S1G116400.t1"; gene_id "Phchi.S1G116400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5041.t1 is derived from g2211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14220762	14223039	.	+	.	Phchi.S1G220000
Phchi.S1	AUGUSTUS	transcript	14220762	14223039	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	start_codon	14220762	14220764	.	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14220762	14220842	0.8	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14220762	14220842	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14220843	14220922	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14220923	14221080	0.82	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14220923	14221080	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14221081	14221170	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14221171	14221407	1	+	1	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14221171	14221407	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14221408	14221501	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14221502	14221661	1	+	1	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14221502	14221661	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14221662	14221758	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14221759	14221828	0.49	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14221759	14221828	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14221829	14221938	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14221939	14222159	0.94	+	2	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14221939	14222159	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14222160	14222308	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14222309	14222695	1	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14222309	14222695	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	intron	14222696	14222787	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	CDS	14222788	14223039	1	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	exon	14222788	14223039	.	+	.	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
Phchi.S1	AUGUSTUS	stop_codon	14223040	14223042	.	+	0	transcript_id "Phchi.S1G220000.t1"; gene_id "Phchi.S1G220000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9196.t1 is derived from g6371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40303153	40304044	.	+	.	Phchi.S1G635500
Phchi.S1	AUGUSTUS	transcript	40303153	40304044	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	start_codon	40303153	40303155	.	+	0	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	CDS	40303153	40303155	0.54	+	0	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	exon	40303153	40303155	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	intron	40303156	40303443	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	CDS	40303444	40303519	1	+	0	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	exon	40303444	40303519	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	intron	40303520	40303792	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	CDS	40303793	40303879	0.99	+	2	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	exon	40303793	40303879	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	intron	40303880	40304009	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	CDS	40304010	40304044	0.98	+	2	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	exon	40304010	40304044	.	+	.	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
Phchi.S1	AUGUSTUS	stop_codon	40304045	40304047	.	+	0	transcript_id "Phchi.S1G635500.t1"; gene_id "Phchi.S1G635500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8535.t1 is derived from g5710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36529434	36531094	.	+	.	Phchi.S1G569400
Phchi.S1	AUGUSTUS	transcript	36529434	36531094	.	+	.	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	start_codon	36529434	36529436	.	+	0	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	CDS	36529434	36530129	0.77	+	0	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	exon	36529434	36530129	.	+	.	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	intron	36530130	36530242	.	+	.	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	CDS	36530243	36531094	0.79	+	0	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	exon	36530243	36531094	.	+	.	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
Phchi.S1	AUGUSTUS	stop_codon	36531095	36531097	.	+	0	transcript_id "Phchi.S1G569400.t1"; gene_id "Phchi.S1G569400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9778.t1 is derived from g6954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43624612	43625799	.	-	.	Phchi.S1G693700
Phchi.S1	AUGUSTUS	transcript	43624612	43625799	.	-	.	transcript_id "Phchi.S1G693700.t1"; gene_id "Phchi.S1G693700"
Phchi.S1	AUGUSTUS	stop_codon	43624609	43624611	.	-	0	transcript_id "Phchi.S1G693700.t1"; gene_id "Phchi.S1G693700"
Phchi.S1	AUGUSTUS	CDS	43624612	43625799	1	-	0	transcript_id "Phchi.S1G693700.t1"; gene_id "Phchi.S1G693700"
Phchi.S1	AUGUSTUS	exon	43624612	43625799	.	-	.	transcript_id "Phchi.S1G693700.t1"; gene_id "Phchi.S1G693700"
Phchi.S1	AUGUSTUS	start_codon	43625797	43625799	.	-	0	transcript_id "Phchi.S1G693700.t1"; gene_id "Phchi.S1G693700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5651.t1 is derived from g2821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18060905	18061647	.	+	.	Phchi.S1G281000
Phchi.S1	AUGUSTUS	transcript	18060905	18061647	.	+	.	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	start_codon	18060905	18060907	.	+	0	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	CDS	18060905	18061048	0.47	+	0	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	exon	18060905	18061048	.	+	.	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	intron	18061049	18061128	.	+	.	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	CDS	18061129	18061239	0.66	+	0	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	exon	18061129	18061239	.	+	.	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	intron	18061240	18061479	.	+	.	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	CDS	18061480	18061647	0.61	+	0	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	exon	18061480	18061647	.	+	.	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
Phchi.S1	AUGUSTUS	stop_codon	18061648	18061650	.	+	0	transcript_id "Phchi.S1G281000.t1"; gene_id "Phchi.S1G281000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15470.t1 is derived from g13938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19345497	19346608	.	-	.	Phchi.S3G278900
Phchi.S3	AUGUSTUS	transcript	19345497	19346608	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	stop_codon	19345494	19345496	.	-	0	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19345497	19345531	1	-	2	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19345497	19345531	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	intron	19345532	19345612	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19345613	19345746	1	-	1	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19345613	19345746	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	intron	19345747	19345832	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19345833	19345935	1	-	2	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19345833	19345935	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	intron	19345936	19346019	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19346020	19346185	1	-	0	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19346020	19346185	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	intron	19346186	19346275	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19346276	19346342	1	-	1	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19346276	19346342	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	intron	19346343	19346424	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19346425	19346462	1	-	0	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19346425	19346462	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	intron	19346463	19346533	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	CDS	19346534	19346608	0.92	-	0	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	exon	19346534	19346608	.	-	.	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
Phchi.S3	AUGUSTUS	start_codon	19346606	19346608	.	-	0	transcript_id "Phchi.S3G278900.t1"; gene_id "Phchi.S3G278900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10600.t1 is derived from g14650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1139914	1142792	.	+	.	Phchi.S4G018200
Phchi.S4	AUGUSTUS	transcript	1139914	1142792	.	+	.	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	start_codon	1139914	1139916	.	+	0	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	CDS	1139914	1140347	0.36	+	0	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	exon	1139914	1140347	.	+	.	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	intron	1140348	1140442	.	+	.	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	CDS	1140443	1142792	0.35	+	1	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	exon	1140443	1142792	.	+	.	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
Phchi.S4	AUGUSTUS	stop_codon	1142793	1142795	.	+	0	transcript_id "Phchi.S4G018200.t1"; gene_id "Phchi.S4G018200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4643.t1 is derived from g1813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11609134	11610600	.	-	.	Phchi.S1G180200
Phchi.S1	AUGUSTUS	transcript	11609134	11610600	.	-	.	transcript_id "Phchi.S1G180200.t1"; gene_id "Phchi.S1G180200"
Phchi.S1	AUGUSTUS	stop_codon	11609131	11609133	.	-	0	transcript_id "Phchi.S1G180200.t1"; gene_id "Phchi.S1G180200"
Phchi.S1	AUGUSTUS	CDS	11609134	11610600	0.87	-	0	transcript_id "Phchi.S1G180200.t1"; gene_id "Phchi.S1G180200"
Phchi.S1	AUGUSTUS	exon	11609134	11610600	.	-	.	transcript_id "Phchi.S1G180200.t1"; gene_id "Phchi.S1G180200"
Phchi.S1	AUGUSTUS	start_codon	11610598	11610600	.	-	0	transcript_id "Phchi.S1G180200.t1"; gene_id "Phchi.S1G180200"
# This transcript jg3259.t2 is derived from g428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3260.t1 is derived from g429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2573742	2574527	.	+	.	Phchi.S1G041900
Phchi.S1	AUGUSTUS	transcript	2573742	2574527	.	+	.	transcript_id "Phchi.S1G041900.t1"; gene_id "Phchi.S1G041900"
Phchi.S1	AUGUSTUS	start_codon	2573742	2573744	.	+	0	transcript_id "Phchi.S1G041900.t1"; gene_id "Phchi.S1G041900"
Phchi.S1	AUGUSTUS	CDS	2573742	2574527	0.49	+	0	transcript_id "Phchi.S1G041900.t1"; gene_id "Phchi.S1G041900"
Phchi.S1	AUGUSTUS	exon	2573742	2574527	.	+	.	transcript_id "Phchi.S1G041900.t1"; gene_id "Phchi.S1G041900"
Phchi.S1	AUGUSTUS	stop_codon	2574528	2574530	.	+	0	transcript_id "Phchi.S1G041900.t1"; gene_id "Phchi.S1G041900"
# This transcript jg13169.t2 is derived from g11634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13170.t1 is derived from g11635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4480586	4483498	.	-	.	Phchi.S3G048900
Phchi.S3	AUGUSTUS	transcript	4480586	4483498	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	stop_codon	4480583	4480585	.	-	0	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	CDS	4480586	4480670	0.43	-	1	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	exon	4480586	4480670	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	intron	4480671	4480863	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	CDS	4480864	4482152	0.16	-	0	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	exon	4480864	4482152	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	intron	4482153	4482332	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	CDS	4482333	4482473	0.69	-	0	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	exon	4482333	4482473	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	intron	4482474	4482665	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	CDS	4482666	4483205	0.35	-	0	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	exon	4482666	4483205	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	intron	4483206	4483303	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	CDS	4483304	4483498	0.52	-	0	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	exon	4483304	4483498	.	-	.	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
Phchi.S3	AUGUSTUS	start_codon	4483496	4483498	.	-	0	transcript_id "Phchi.S3G048900.t1"; gene_id "Phchi.S3G048900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg616.t1 is derived from g10398.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4421885	4423192	.	-	.	Phchi.S6G057500
Phchi.S6	AUGUSTUS	transcript	4421885	4423192	.	-	.	transcript_id "Phchi.S6G057500.t1"; gene_id "Phchi.S6G057500"
Phchi.S6	AUGUSTUS	stop_codon	4421882	4421884	.	-	0	transcript_id "Phchi.S6G057500.t1"; gene_id "Phchi.S6G057500"
Phchi.S6	AUGUSTUS	CDS	4421885	4423192	0.71	-	0	transcript_id "Phchi.S6G057500.t1"; gene_id "Phchi.S6G057500"
Phchi.S6	AUGUSTUS	exon	4421885	4423192	.	-	.	transcript_id "Phchi.S6G057500.t1"; gene_id "Phchi.S6G057500"
Phchi.S6	AUGUSTUS	start_codon	4423190	4423192	.	-	0	transcript_id "Phchi.S6G057500.t1"; gene_id "Phchi.S6G057500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11427.t1 is derived from g15477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6283960	6286911	.	-	.	Phchi.S4G100900
Phchi.S4	AUGUSTUS	transcript	6283960	6286911	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	stop_codon	6283957	6283959	.	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6283960	6284178	1	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6283960	6284178	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284179	6284295	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284296	6284381	1	-	2	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284296	6284381	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284382	6284472	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284473	6284602	1	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284473	6284602	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284603	6284678	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284679	6284786	1	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284679	6284786	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284787	6284946	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284947	6285028	1	-	1	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284947	6285028	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285029	6285192	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285193	6285245	1	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285193	6285245	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285246	6285371	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285372	6285455	1	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285372	6285455	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285456	6285560	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285561	6285718	1	-	2	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285561	6285718	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285719	6285859	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285860	6286175	0.91	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285860	6286175	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6286176	6286282	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6286283	6286329	0.91	-	2	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6286283	6286329	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6286330	6286502	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6286503	6286911	0.87	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6286503	6286911	.	-	.	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	start_codon	6286909	6286911	.	-	0	transcript_id "Phchi.S4G100900.t1"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	transcript	6283960	6286911	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	stop_codon	6283957	6283959	.	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6283960	6284178	1	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6283960	6284178	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284179	6284295	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284296	6284381	1	-	2	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284296	6284381	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284382	6284472	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284473	6284602	1	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284473	6284602	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284603	6284678	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284679	6284786	1	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284679	6284786	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6284787	6284946	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6284947	6285028	1	-	1	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6284947	6285028	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285029	6285192	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285193	6285245	0.99	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285193	6285245	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285246	6285371	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285372	6285455	0.84	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285372	6285455	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285456	6285737	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285738	6285778	0.7	-	2	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285738	6285778	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6285779	6285859	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6285860	6286175	0.9	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6285860	6286175	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6286176	6286282	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6286283	6286329	0.9	-	2	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6286283	6286329	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	intron	6286330	6286502	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	CDS	6286503	6286911	0.83	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	exon	6286503	6286911	.	-	.	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
Phchi.S4	AUGUSTUS	start_codon	6286909	6286911	.	-	0	transcript_id "Phchi.S4G100900.t2"; gene_id "Phchi.S4G100900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10596.t1 is derived from g14646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1129035	1129678	.	+	.	Phchi.S4G017800
Phchi.S4	AUGUSTUS	transcript	1129035	1129678	.	+	.	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	start_codon	1129035	1129037	.	+	0	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	CDS	1129035	1129548	0.54	+	0	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	exon	1129035	1129548	.	+	.	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	intron	1129549	1129649	.	+	.	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	CDS	1129650	1129678	0.54	+	2	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	exon	1129650	1129678	.	+	.	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
Phchi.S4	AUGUSTUS	stop_codon	1129679	1129681	.	+	0	transcript_id "Phchi.S4G017800.t1"; gene_id "Phchi.S4G017800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7930.t1 is derived from g5104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31961595	31966458	.	+	.	Phchi.S1G508900
Phchi.S1	AUGUSTUS	transcript	31961595	31966458	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	start_codon	31961595	31961597	.	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31961595	31961722	0.96	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31961595	31961722	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31961723	31961957	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31961958	31962039	1	+	1	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31961958	31962039	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31962040	31962172	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31962173	31962280	1	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31962173	31962280	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31962281	31962426	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31962427	31962526	1	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31962427	31962526	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31962527	31962638	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31962639	31962726	0.89	+	2	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31962639	31962726	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31962727	31962880	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31962881	31962975	1	+	1	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31962881	31962975	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31962976	31963053	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31963054	31963177	0.99	+	2	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31963054	31963177	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31963178	31963280	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31963281	31963377	0.91	+	1	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31963281	31963377	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31963378	31963462	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31963463	31963637	1	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31963463	31963637	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31963638	31963862	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31963863	31963945	1	+	2	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31963863	31963945	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31963946	31964113	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31964114	31964476	1	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31964114	31964476	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31964477	31964594	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31964595	31964647	1	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31964595	31964647	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31964648	31964771	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31964772	31964819	1	+	1	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31964772	31964819	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31964820	31964910	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31964911	31965024	0.97	+	1	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31964911	31965024	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31965025	31965135	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31965136	31965200	0.96	+	1	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31965136	31965200	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	intron	31965201	31965397	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	CDS	31965398	31966458	0.78	+	2	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	exon	31965398	31966458	.	+	.	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
Phchi.S1	AUGUSTUS	stop_codon	31966459	31966461	.	+	0	transcript_id "Phchi.S1G508900.t1"; gene_id "Phchi.S1G508900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2958.t1 is derived from g127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	787517	788641	.	+	.	Phchi.S1G011700
Phchi.S1	AUGUSTUS	transcript	787517	788641	.	+	.	transcript_id "Phchi.S1G011700.t1"; gene_id "Phchi.S1G011700"
Phchi.S1	AUGUSTUS	start_codon	787517	787519	.	+	0	transcript_id "Phchi.S1G011700.t1"; gene_id "Phchi.S1G011700"
Phchi.S1	AUGUSTUS	CDS	787517	788641	1	+	0	transcript_id "Phchi.S1G011700.t1"; gene_id "Phchi.S1G011700"
Phchi.S1	AUGUSTUS	exon	787517	788641	.	+	.	transcript_id "Phchi.S1G011700.t1"; gene_id "Phchi.S1G011700"
Phchi.S1	AUGUSTUS	stop_codon	788642	788644	.	+	0	transcript_id "Phchi.S1G011700.t1"; gene_id "Phchi.S1G011700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6438.t1 is derived from g3610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23033154	23034404	.	-	.	Phchi.S1G359700
Phchi.S1	AUGUSTUS	transcript	23033154	23034404	.	-	.	transcript_id "Phchi.S1G359700.t1"; gene_id "Phchi.S1G359700"
Phchi.S1	AUGUSTUS	stop_codon	23033151	23033153	.	-	0	transcript_id "Phchi.S1G359700.t1"; gene_id "Phchi.S1G359700"
Phchi.S1	AUGUSTUS	CDS	23033154	23034404	0.91	-	0	transcript_id "Phchi.S1G359700.t1"; gene_id "Phchi.S1G359700"
Phchi.S1	AUGUSTUS	exon	23033154	23034404	.	-	.	transcript_id "Phchi.S1G359700.t1"; gene_id "Phchi.S1G359700"
Phchi.S1	AUGUSTUS	start_codon	23034402	23034404	.	-	0	transcript_id "Phchi.S1G359700.t1"; gene_id "Phchi.S1G359700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12886.t1 is derived from g11351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2940069	2942954	.	+	.	Phchi.S3G020500
Phchi.S3	AUGUSTUS	transcript	2940069	2942954	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	start_codon	2940069	2940071	.	+	0	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	CDS	2940069	2940089	0.83	+	0	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	exon	2940069	2940089	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	intron	2940090	2940167	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	CDS	2940168	2940199	0.83	+	0	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	exon	2940168	2940199	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	intron	2940200	2940508	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	CDS	2940509	2940549	1	+	1	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	exon	2940509	2940549	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	intron	2940550	2940756	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	CDS	2940757	2942954	0.56	+	2	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	exon	2940757	2942954	.	+	.	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
Phchi.S3	AUGUSTUS	stop_codon	2942955	2942957	.	+	0	transcript_id "Phchi.S3G020500.t1"; gene_id "Phchi.S3G020500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7692.t1 is derived from g4866.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30651178	30652895	.	+	.	Phchi.S1G485100
Phchi.S1	AUGUSTUS	transcript	30651178	30652895	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	start_codon	30651178	30651180	.	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30651178	30651258	1	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30651178	30651258	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30651259	30651403	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30651404	30651499	1	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30651404	30651499	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30651500	30651629	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30651630	30651851	1	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30651630	30651851	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30651852	30652009	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30652010	30652050	1	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30652010	30652050	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30652051	30652144	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30652145	30652173	0.7	+	1	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30652145	30652173	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30652174	30652285	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30652286	30652308	0.7	+	2	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30652286	30652308	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30652309	30652391	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30652392	30652895	0.95	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30652392	30652895	.	+	.	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	stop_codon	30652896	30652898	.	+	0	transcript_id "Phchi.S1G485100.t1"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	transcript	30651178	30652895	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	start_codon	30651178	30651180	.	+	0	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30651178	30651258	1	+	0	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30651178	30651258	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30651259	30651403	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30651404	30651499	1	+	0	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30651404	30651499	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30651500	30651629	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30651630	30651855	0.73	+	0	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30651630	30651855	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30651856	30652009	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30652010	30652308	0.37	+	2	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30652010	30652308	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	intron	30652309	30652391	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	CDS	30652392	30652895	0.96	+	0	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	exon	30652392	30652895	.	+	.	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
Phchi.S1	AUGUSTUS	stop_codon	30652896	30652898	.	+	0	transcript_id "Phchi.S1G485100.t2"; gene_id "Phchi.S1G485100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11592.t1 is derived from g15643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7252218	7258668	.	+	.	Phchi.S4G117400
Phchi.S4	AUGUSTUS	transcript	7252218	7258668	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	start_codon	7252218	7252220	.	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7252218	7252307	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7252218	7252307	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7252308	7252390	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7252391	7252465	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7252391	7252465	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7252466	7252582	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7252583	7252675	0.98	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7252583	7252675	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7252676	7252770	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7252771	7252845	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7252771	7252845	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7252846	7252993	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7252994	7253086	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7252994	7253086	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7253087	7253184	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7253185	7253248	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7253185	7253248	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7253249	7253350	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7253351	7253435	1	+	2	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7253351	7253435	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7253436	7253584	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7253585	7253657	1	+	1	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7253585	7253657	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7253658	7253748	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7253749	7253817	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7253749	7253817	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7253818	7253968	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7253969	7254049	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7253969	7254049	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7254050	7254127	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7254128	7254260	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7254128	7254260	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7254261	7254342	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7254343	7254510	1	+	2	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7254343	7254510	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7254511	7254587	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7254588	7254729	1	+	2	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7254588	7254729	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7254730	7254900	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7254901	7255072	0.86	+	1	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7254901	7255072	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7255073	7255186	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7255187	7255285	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7255187	7255285	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7255286	7255373	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7255374	7255931	0.52	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7255374	7255931	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7255932	7256055	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7256056	7256701	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7256056	7256701	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7256702	7256796	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7256797	7257245	0.84	+	2	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7256797	7257245	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7257246	7257355	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7257356	7257592	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7257356	7257592	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7257593	7257715	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7257716	7257859	1	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7257716	7257859	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7257860	7257945	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7257946	7257980	0.54	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7257946	7257980	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7257981	7258077	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7258078	7258127	0.47	+	1	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7258078	7258127	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7258128	7258248	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7258249	7258319	0.32	+	2	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7258249	7258319	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7258320	7258408	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7258409	7258443	0.64	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7258409	7258443	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	intron	7258444	7258541	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	CDS	7258542	7258668	0.54	+	1	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	exon	7258542	7258668	.	+	.	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
Phchi.S4	AUGUSTUS	stop_codon	7258669	7258671	.	+	0	transcript_id "Phchi.S4G117400.t1"; gene_id "Phchi.S4G117400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8866.t1 is derived from g6041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38376593	38377246	.	+	.	Phchi.S1G602500
Phchi.S1	AUGUSTUS	transcript	38376593	38377246	.	+	.	transcript_id "Phchi.S1G602500.t1"; gene_id "Phchi.S1G602500"
Phchi.S1	AUGUSTUS	start_codon	38376593	38376595	.	+	0	transcript_id "Phchi.S1G602500.t1"; gene_id "Phchi.S1G602500"
Phchi.S1	AUGUSTUS	CDS	38376593	38377246	0.96	+	0	transcript_id "Phchi.S1G602500.t1"; gene_id "Phchi.S1G602500"
Phchi.S1	AUGUSTUS	exon	38376593	38377246	.	+	.	transcript_id "Phchi.S1G602500.t1"; gene_id "Phchi.S1G602500"
Phchi.S1	AUGUSTUS	stop_codon	38377247	38377249	.	+	0	transcript_id "Phchi.S1G602500.t1"; gene_id "Phchi.S1G602500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11764.t1 is derived from g15816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8046649	8049400	.	-	.	Phchi.S4G134600
Phchi.S4	AUGUSTUS	transcript	8046649	8049400	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	stop_codon	8046646	8046648	.	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8046649	8047098	1	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8046649	8047098	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8047099	8047177	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8047178	8047286	1	-	1	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8047178	8047286	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8047287	8047413	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8047414	8047472	1	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8047414	8047472	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8047473	8047568	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8047569	8047681	1	-	2	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8047569	8047681	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8047682	8047788	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8047789	8047945	1	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8047789	8047945	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8047946	8048091	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8048092	8048151	1	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8048092	8048151	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8048152	8048329	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8048330	8048458	1	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8048330	8048458	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8048459	8048580	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8048581	8048628	1	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8048581	8048628	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	intron	8048629	8049289	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	CDS	8049290	8049400	0.4	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	exon	8049290	8049400	.	-	.	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
Phchi.S4	AUGUSTUS	start_codon	8049398	8049400	.	-	0	transcript_id "Phchi.S4G134600.t1"; gene_id "Phchi.S4G134600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4386.t1 is derived from g1555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10179583	10180201	.	-	.	Phchi.S1G154500
Phchi.S1	AUGUSTUS	transcript	10179583	10180201	.	-	.	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	stop_codon	10179580	10179582	.	-	0	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	CDS	10179583	10179621	0.99	-	0	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	exon	10179583	10179621	.	-	.	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	intron	10179622	10179714	.	-	.	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	CDS	10179715	10179756	0.99	-	0	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	exon	10179715	10179756	.	-	.	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	intron	10179757	10179970	.	-	.	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	CDS	10179971	10180201	0.81	-	0	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	exon	10179971	10180201	.	-	.	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
Phchi.S1	AUGUSTUS	start_codon	10180199	10180201	.	-	0	transcript_id "Phchi.S1G154500.t1"; gene_id "Phchi.S1G154500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1027.t1 is derived from g10810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7206775	7208892	.	+	.	Phchi.S6G098600
Phchi.S6	AUGUSTUS	transcript	7206775	7208892	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	start_codon	7206775	7206777	.	+	0	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7206775	7206866	0.66	+	0	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7206775	7206866	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	intron	7206867	7207074	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7207075	7207116	0.7	+	1	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7207075	7207116	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	intron	7207117	7207322	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7207323	7207723	0.61	+	1	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7207323	7207723	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	intron	7207724	7207861	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7207862	7208082	0.96	+	2	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7207862	7208082	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	intron	7208083	7208199	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7208200	7208252	1	+	0	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7208200	7208252	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	intron	7208253	7208406	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7208407	7208577	1	+	1	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7208407	7208577	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	intron	7208578	7208660	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	CDS	7208661	7208892	0.96	+	1	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	exon	7208661	7208892	.	+	.	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
Phchi.S6	AUGUSTUS	stop_codon	7208893	7208895	.	+	0	transcript_id "Phchi.S6G098600.t1"; gene_id "Phchi.S6G098600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10304.t1 is derived from g7480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47053962	47054457	.	-	.	Phchi.S1G746300
Phchi.S1	AUGUSTUS	transcript	47053962	47054457	.	-	.	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	stop_codon	47053959	47053961	.	-	0	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	CDS	47053962	47053972	1	-	2	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	exon	47053962	47053972	.	-	.	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	intron	47053973	47054068	.	-	.	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	CDS	47054069	47054206	1	-	2	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	exon	47054069	47054206	.	-	.	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	intron	47054207	47054366	.	-	.	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	CDS	47054367	47054457	0.95	-	0	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	exon	47054367	47054457	.	-	.	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
Phchi.S1	AUGUSTUS	start_codon	47054455	47054457	.	-	0	transcript_id "Phchi.S1G746300.t1"; gene_id "Phchi.S1G746300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1256.t1 is derived from g11039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8658884	8663006	.	-	.	Phchi.S6G121500
Phchi.S6	AUGUSTUS	transcript	8658884	8663006	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	stop_codon	8658881	8658883	.	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8658884	8659087	0.9	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8658884	8659087	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8659088	8659182	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8659183	8659290	1	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8659183	8659290	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8659291	8659399	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8659400	8659486	1	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8659400	8659486	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8659487	8659603	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8659604	8659715	0.97	-	1	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8659604	8659715	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8659716	8659829	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8659830	8659925	0.99	-	1	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8659830	8659925	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8659926	8660076	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8660077	8660153	1	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8660077	8660153	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8660154	8660233	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8660234	8660347	1	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8660234	8660347	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8660348	8660435	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8660436	8660529	1	-	1	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8660436	8660529	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8660530	8660647	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8660648	8660768	0.9	-	2	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8660648	8660768	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8660769	8660952	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8660953	8661065	0.81	-	1	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8660953	8661065	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8661066	8661196	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8661197	8661275	1	-	2	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8661197	8661275	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8661276	8661349	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8661350	8661897	0.85	-	1	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8661350	8661897	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8661898	8662013	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8662014	8662093	0.99	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8662014	8662093	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8662094	8662212	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8662213	8662282	1	-	1	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8662213	8662282	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8662283	8662498	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8662499	8662614	1	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8662499	8662614	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8662615	8662758	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8662759	8662803	0.59	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8662759	8662803	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	intron	8662804	8662943	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	CDS	8662944	8663006	0.49	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	exon	8662944	8663006	.	-	.	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
Phchi.S6	AUGUSTUS	start_codon	8663004	8663006	.	-	0	transcript_id "Phchi.S6G121500.t1"; gene_id "Phchi.S6G121500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9521.t1 is derived from g6697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42249788	42251270	.	-	.	Phchi.S1G668000
Phchi.S1	AUGUSTUS	transcript	42249788	42251270	.	-	.	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	stop_codon	42249785	42249787	.	-	0	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	CDS	42249788	42249941	0.92	-	1	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	exon	42249788	42249941	.	-	.	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	intron	42249942	42250041	.	-	.	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	CDS	42250042	42250095	1	-	1	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	exon	42250042	42250095	.	-	.	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	intron	42250096	42250191	.	-	.	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	CDS	42250192	42251270	0.67	-	0	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	exon	42250192	42251270	.	-	.	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
Phchi.S1	AUGUSTUS	start_codon	42251268	42251270	.	-	0	transcript_id "Phchi.S1G668000.t1"; gene_id "Phchi.S1G668000"
# This transcript jg15697.t2 is derived from g14166.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15697.t3 is derived from g14166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15698.t1 is derived from g14167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20749992	20754278	.	+	.	Phchi.S3G301700
Phchi.S3	AUGUSTUS	transcript	20749992	20754278	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	start_codon	20749992	20749994	.	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20749992	20750258	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20749992	20750258	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20750259	20750445	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20750446	20750625	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20750446	20750625	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20750626	20750721	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20750722	20750898	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20750722	20750898	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20750899	20751018	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20751019	20751104	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20751019	20751104	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20751105	20751338	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20751339	20751528	1	+	1	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20751339	20751528	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20751529	20751647	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20751648	20751740	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20751648	20751740	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20751741	20751819	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20751820	20752233	0.24	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20751820	20752233	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20752234	20752332	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20752333	20752464	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20752333	20752464	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20752465	20752581	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20752582	20752800	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20752582	20752800	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20752801	20752891	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20752892	20753095	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20752892	20753095	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20753096	20753200	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20753201	20753359	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20753201	20753359	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20753360	20753472	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20753473	20753736	1	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20753473	20753736	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20753737	20753862	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20753863	20754053	0.98	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20753863	20754053	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	intron	20754054	20754154	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	CDS	20754155	20754278	0.97	+	1	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	exon	20754155	20754278	.	+	.	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
Phchi.S3	AUGUSTUS	stop_codon	20754279	20754281	.	+	0	transcript_id "Phchi.S3G301700.t1"; gene_id "Phchi.S3G301700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8602.t1 is derived from g5777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36853045	36856656	.	-	.	Phchi.S1G576100
Phchi.S1	AUGUSTUS	transcript	36853045	36856656	.	-	.	transcript_id "Phchi.S1G576100.t1"; gene_id "Phchi.S1G576100"
Phchi.S1	AUGUSTUS	stop_codon	36853042	36853044	.	-	0	transcript_id "Phchi.S1G576100.t1"; gene_id "Phchi.S1G576100"
Phchi.S1	AUGUSTUS	CDS	36853045	36856656	0.62	-	0	transcript_id "Phchi.S1G576100.t1"; gene_id "Phchi.S1G576100"
Phchi.S1	AUGUSTUS	exon	36853045	36856656	.	-	.	transcript_id "Phchi.S1G576100.t1"; gene_id "Phchi.S1G576100"
Phchi.S1	AUGUSTUS	start_codon	36856654	36856656	.	-	0	transcript_id "Phchi.S1G576100.t1"; gene_id "Phchi.S1G576100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5426.t1 is derived from g2596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16817982	16819881	.	+	.	Phchi.S1G258500
Phchi.S1	AUGUSTUS	transcript	16817982	16819881	.	+	.	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	start_codon	16817982	16817984	.	+	0	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	CDS	16817982	16818727	0.68	+	0	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	exon	16817982	16818727	.	+	.	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	intron	16818728	16818865	.	+	.	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	CDS	16818866	16819417	0.49	+	1	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	exon	16818866	16819417	.	+	.	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	intron	16819418	16819607	.	+	.	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	CDS	16819608	16819881	0.54	+	1	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	exon	16819608	16819881	.	+	.	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
Phchi.S1	AUGUSTUS	stop_codon	16819882	16819884	.	+	0	transcript_id "Phchi.S1G258500.t1"; gene_id "Phchi.S1G258500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1688.t1 is derived from g8607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2503903	2506402	.	+	.	Phchi.S5G029700
Phchi.S5	AUGUSTUS	transcript	2503903	2506402	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	start_codon	2503903	2503905	.	+	0	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2503903	2504368	0.8	+	0	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2503903	2504368	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2504369	2504481	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2504482	2504626	1	+	2	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2504482	2504626	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2504627	2504721	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2504722	2504881	0.98	+	1	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2504722	2504881	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2504882	2504982	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2504983	2505209	0.99	+	0	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2504983	2505209	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2505210	2505420	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2505421	2505511	1	+	1	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2505421	2505511	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2505512	2505651	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2505652	2505780	1	+	0	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2505652	2505780	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2505781	2505942	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2505943	2506079	0.95	+	0	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2505943	2506079	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	intron	2506080	2506182	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	CDS	2506183	2506402	0.93	+	1	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	exon	2506183	2506402	.	+	.	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
Phchi.S5	AUGUSTUS	stop_codon	2506403	2506405	.	+	0	transcript_id "Phchi.S5G029700.t1"; gene_id "Phchi.S5G029700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13464.t1 is derived from g11931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7020004	7020528	.	+	.	Phchi.S3G078300
Phchi.S3	AUGUSTUS	transcript	7020004	7020528	.	+	.	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	start_codon	7020004	7020006	.	+	0	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	CDS	7020004	7020128	0.78	+	0	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	exon	7020004	7020128	.	+	.	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	intron	7020129	7020263	.	+	.	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	CDS	7020264	7020351	1	+	1	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	exon	7020264	7020351	.	+	.	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	intron	7020352	7020441	.	+	.	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	CDS	7020442	7020528	1	+	0	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	exon	7020442	7020528	.	+	.	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
Phchi.S3	AUGUSTUS	stop_codon	7020529	7020531	.	+	0	transcript_id "Phchi.S3G078300.t1"; gene_id "Phchi.S3G078300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11392.t1 is derived from g15442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6116509	6119155	.	-	.	Phchi.S4G097400
Phchi.S4	AUGUSTUS	transcript	6116509	6119155	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	stop_codon	6116506	6116508	.	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6116509	6116919	1	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6116509	6116919	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6116920	6117023	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6117024	6117125	0.97	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6117024	6117125	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6117126	6117200	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6117201	6117396	1	-	1	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6117201	6117396	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6117397	6117504	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6117505	6117584	1	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6117505	6117584	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6117585	6117657	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6117658	6117732	1	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6117658	6117732	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6117733	6117868	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6117869	6117970	1	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6117869	6117970	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6117971	6118048	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6118049	6118173	0.98	-	2	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6118049	6118173	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6118174	6118274	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6118275	6118395	0.97	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6118275	6118395	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6118396	6118498	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6118499	6118549	1	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6118499	6118549	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6118550	6118649	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6118650	6118751	1	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6118650	6118751	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	intron	6118752	6118930	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	CDS	6118931	6119155	0.75	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	exon	6118931	6119155	.	-	.	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
Phchi.S4	AUGUSTUS	start_codon	6119153	6119155	.	-	0	transcript_id "Phchi.S4G097400.t1"; gene_id "Phchi.S4G097400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1011.t1 is derived from g10794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7106650	7107810	.	-	.	Phchi.S6G097000
Phchi.S6	AUGUSTUS	transcript	7106650	7107810	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	stop_codon	7106647	7106649	.	-	0	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	CDS	7106650	7106757	1	-	0	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	exon	7106650	7106757	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	intron	7106758	7106906	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	CDS	7106907	7107006	0.83	-	1	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	exon	7106907	7107006	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	intron	7107007	7107080	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	CDS	7107081	7107402	0.78	-	2	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	exon	7107081	7107402	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	intron	7107403	7107489	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	CDS	7107490	7107538	1	-	0	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	exon	7107490	7107538	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	intron	7107539	7107663	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	CDS	7107664	7107810	0.98	-	0	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	exon	7107664	7107810	.	-	.	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
Phchi.S6	AUGUSTUS	start_codon	7107808	7107810	.	-	0	transcript_id "Phchi.S6G097000.t1"; gene_id "Phchi.S6G097000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14288.t1 is derived from g12755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11932349	11932681	.	+	.	Phchi.S3G160700
Phchi.S3	AUGUSTUS	transcript	11932349	11932681	.	+	.	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	start_codon	11932349	11932351	.	+	0	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	CDS	11932349	11932566	0.91	+	0	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	exon	11932349	11932566	.	+	.	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	intron	11932567	11932659	.	+	.	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	CDS	11932660	11932681	1	+	1	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	exon	11932660	11932681	.	+	.	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
Phchi.S3	AUGUSTUS	stop_codon	11932682	11932684	.	+	0	transcript_id "Phchi.S3G160700.t1"; gene_id "Phchi.S3G160700"
# This transcript jg9151.t2 is derived from g6326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9152.t1 is derived from g6327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40111001	40113784	.	-	.	Phchi.S1G631100
Phchi.S1	AUGUSTUS	transcript	40111001	40113784	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	stop_codon	40110998	40111000	.	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111001	40111017	1	-	2	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111001	40111017	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40111018	40111166	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111167	40111186	0.84	-	1	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111167	40111186	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40111187	40111265	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111266	40111469	0.81	-	1	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111266	40111469	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40111470	40111552	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111553	40111605	1	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111553	40111605	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40111606	40111682	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111683	40111733	1	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111683	40111733	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40111734	40111809	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111810	40111879	1	-	1	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111810	40111879	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40111880	40111965	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40111966	40112144	1	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40111966	40112144	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40112145	40112241	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40112242	40112347	1	-	1	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40112242	40112347	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40112348	40112431	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40112432	40112499	0.72	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40112432	40112499	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40112500	40112708	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40112709	40112971	0.61	-	2	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40112709	40112971	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40112972	40113126	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40113127	40113145	0.99	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40113127	40113145	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40113146	40113265	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40113266	40113373	0.97	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40113266	40113373	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40113374	40113465	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40113466	40113551	1	-	2	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40113466	40113551	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	intron	40113552	40113645	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	CDS	40113646	40113784	1	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	exon	40113646	40113784	.	-	.	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
Phchi.S1	AUGUSTUS	start_codon	40113782	40113784	.	-	0	transcript_id "Phchi.S1G631100.t1"; gene_id "Phchi.S1G631100"
# This transcript jg2145.t2 is derived from g9065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2145.t3 is derived from g9065.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2146.t1 is derived from g9066.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5056865	5059110	.	-	.	Phchi.S5G075500
Phchi.S5	AUGUSTUS	transcript	5056865	5059110	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	stop_codon	5056862	5056864	.	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5056865	5056912	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5056865	5056912	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5056913	5056995	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5056996	5057070	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5056996	5057070	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5057071	5057192	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5057193	5057258	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5057193	5057258	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5057259	5057352	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5057353	5057406	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5057353	5057406	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5057407	5057544	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5057545	5057676	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5057545	5057676	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5057677	5057751	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5057752	5057813	1	-	2	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5057752	5057813	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5057814	5057913	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5057914	5057990	1	-	1	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5057914	5057990	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5057991	5058125	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5058126	5058201	1	-	2	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5058126	5058201	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5058202	5058309	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5058310	5058425	1	-	1	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5058310	5058425	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5058426	5058632	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5058633	5058697	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5058633	5058697	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5058698	5058798	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5058799	5058864	1	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5058799	5058864	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	intron	5058865	5058945	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	CDS	5058946	5059110	0.76	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	exon	5058946	5059110	.	-	.	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
Phchi.S5	AUGUSTUS	start_codon	5059108	5059110	.	-	0	transcript_id "Phchi.S5G075500.t1"; gene_id "Phchi.S5G075500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7038.t1 is derived from g4210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26530492	26531400	.	+	.	Phchi.S1G419700
Phchi.S1	AUGUSTUS	transcript	26530492	26531400	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	start_codon	26530492	26530494	.	+	0	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	CDS	26530492	26530569	0.66	+	0	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	exon	26530492	26530569	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	intron	26530570	26530703	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	CDS	26530704	26530799	0.66	+	0	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	exon	26530704	26530799	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	intron	26530800	26530888	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	CDS	26530889	26530969	0.64	+	0	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	exon	26530889	26530969	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	intron	26530970	26531133	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	CDS	26531134	26531400	0.54	+	0	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	exon	26531134	26531400	.	+	.	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
Phchi.S1	AUGUSTUS	stop_codon	26531401	26531403	.	+	0	transcript_id "Phchi.S1G419700.t1"; gene_id "Phchi.S1G419700"
# This transcript jg11201.t2 is derived from g15251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11202.t1 is derived from g15252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4662457	4666620	.	-	.	Phchi.S4G078400
Phchi.S4	AUGUSTUS	transcript	4662457	4666620	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	stop_codon	4662454	4662456	.	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4662457	4662552	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4662457	4662552	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4662553	4662688	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4662689	4662835	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4662689	4662835	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4662836	4662947	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4662948	4663047	1	-	1	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4662948	4663047	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4663048	4663211	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4663212	4663432	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4663212	4663432	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4663433	4663519	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4663520	4663606	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4663520	4663606	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4663607	4663687	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4663688	4663737	0.97	-	2	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4663688	4663737	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4663738	4663862	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4663863	4663962	0.9	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4663863	4663962	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4663963	4664078	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4664079	4664678	0.93	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4664079	4664678	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4664679	4664763	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4664764	4664938	1	-	1	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4664764	4664938	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4664939	4665040	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4665041	4665159	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4665041	4665159	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4665160	4665251	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4665252	4665338	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4665252	4665338	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4665339	4665554	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4665555	4665663	1	-	1	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4665555	4665663	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4665664	4665763	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4665764	4665877	1	-	1	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4665764	4665877	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4665878	4665970	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4665971	4666146	1	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4665971	4666146	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	intron	4666147	4666236	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	CDS	4666237	4666620	0.55	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	exon	4666237	4666620	.	-	.	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
Phchi.S4	AUGUSTUS	start_codon	4666618	4666620	.	-	0	transcript_id "Phchi.S4G078400.t1"; gene_id "Phchi.S4G078400"
# This transcript jg3801.t2 is derived from g970.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3802.t1 is derived from g971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5809103	5810605	.	-	.	Phchi.S1G096100
Phchi.S1	AUGUSTUS	transcript	5809103	5810605	.	-	.	transcript_id "Phchi.S1G096100.t1"; gene_id "Phchi.S1G096100"
Phchi.S1	AUGUSTUS	stop_codon	5809100	5809102	.	-	0	transcript_id "Phchi.S1G096100.t1"; gene_id "Phchi.S1G096100"
Phchi.S1	AUGUSTUS	CDS	5809103	5810605	1	-	0	transcript_id "Phchi.S1G096100.t1"; gene_id "Phchi.S1G096100"
Phchi.S1	AUGUSTUS	exon	5809103	5810605	.	-	.	transcript_id "Phchi.S1G096100.t1"; gene_id "Phchi.S1G096100"
Phchi.S1	AUGUSTUS	start_codon	5810603	5810605	.	-	0	transcript_id "Phchi.S1G096100.t1"; gene_id "Phchi.S1G096100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3220.t1 is derived from g389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2324819	2327319	.	+	.	Phchi.S1G037900
Phchi.S1	AUGUSTUS	transcript	2324819	2327319	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	start_codon	2324819	2324821	.	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2324819	2325028	0.99	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2324819	2325028	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2325029	2325383	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2325384	2325474	0.67	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2325384	2325474	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2325475	2325642	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2325643	2325802	0.63	+	2	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2325643	2325802	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2325803	2325925	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2325926	2326109	1	+	1	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2325926	2326109	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2326110	2326196	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2326197	2326294	1	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2326197	2326294	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2326295	2326511	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2326512	2326725	1	+	1	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2326512	2326725	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2326726	2326800	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2326801	2327055	1	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2326801	2327055	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	intron	2327056	2327136	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	CDS	2327137	2327319	0.49	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	exon	2327137	2327319	.	+	.	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
Phchi.S1	AUGUSTUS	stop_codon	2327320	2327322	.	+	0	transcript_id "Phchi.S1G037900.t1"; gene_id "Phchi.S1G037900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13455.t1 is derived from g11922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6938958	6939320	.	+	.	Phchi.S3G077400
Phchi.S3	AUGUSTUS	transcript	6938958	6939320	.	+	.	transcript_id "Phchi.S3G077400.t1"; gene_id "Phchi.S3G077400"
Phchi.S3	AUGUSTUS	start_codon	6938958	6938960	.	+	0	transcript_id "Phchi.S3G077400.t1"; gene_id "Phchi.S3G077400"
Phchi.S3	AUGUSTUS	CDS	6938958	6939320	0.9	+	0	transcript_id "Phchi.S3G077400.t1"; gene_id "Phchi.S3G077400"
Phchi.S3	AUGUSTUS	exon	6938958	6939320	.	+	.	transcript_id "Phchi.S3G077400.t1"; gene_id "Phchi.S3G077400"
Phchi.S3	AUGUSTUS	stop_codon	6939321	6939323	.	+	0	transcript_id "Phchi.S3G077400.t1"; gene_id "Phchi.S3G077400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11361.t1 is derived from g15411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5758365	5760548	.	+	.	Phchi.S4G094300
Phchi.S4	AUGUSTUS	transcript	5758365	5760548	.	+	.	transcript_id "Phchi.S4G094300.t1"; gene_id "Phchi.S4G094300"
Phchi.S4	AUGUSTUS	start_codon	5758365	5758367	.	+	0	transcript_id "Phchi.S4G094300.t1"; gene_id "Phchi.S4G094300"
Phchi.S4	AUGUSTUS	CDS	5758365	5760548	0.74	+	0	transcript_id "Phchi.S4G094300.t1"; gene_id "Phchi.S4G094300"
Phchi.S4	AUGUSTUS	exon	5758365	5760548	.	+	.	transcript_id "Phchi.S4G094300.t1"; gene_id "Phchi.S4G094300"
Phchi.S4	AUGUSTUS	stop_codon	5760549	5760551	.	+	0	transcript_id "Phchi.S4G094300.t1"; gene_id "Phchi.S4G094300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5486.t1 is derived from g2656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17089464	17093847	.	-	.	Phchi.S1G264500
Phchi.S1	AUGUSTUS	transcript	17089464	17093847	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	stop_codon	17089461	17089463	.	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17089464	17089547	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17089464	17089547	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17089548	17089675	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17089676	17089783	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17089676	17089783	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17089784	17089870	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17089871	17089960	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17089871	17089960	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17089961	17090050	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17090051	17090119	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17090051	17090119	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17090120	17090220	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17090221	17090274	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17090221	17090274	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17090275	17090412	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17090413	17090486	1	-	2	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17090413	17090486	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17090487	17090591	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17090592	17090655	0.99	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17090592	17090655	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17090656	17090728	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17090729	17090857	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17090729	17090857	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17090858	17091055	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17091056	17091109	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17091056	17091109	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17091110	17091294	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17091295	17091351	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17091295	17091351	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17091352	17091493	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17091494	17091560	1	-	1	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17091494	17091560	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17091561	17091649	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17091650	17091710	1	-	2	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17091650	17091710	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17091711	17091841	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17091842	17091914	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17091842	17091914	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17091915	17092011	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17092012	17092060	1	-	1	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17092012	17092060	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17092061	17092143	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17092144	17092228	1	-	2	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17092144	17092228	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17092229	17092323	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17092324	17092391	1	-	1	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17092324	17092391	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17092392	17092515	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17092516	17092558	0.98	-	2	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17092516	17092558	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17092559	17092663	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17092664	17092760	0.99	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17092664	17092760	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17092761	17092845	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17092846	17093001	0.87	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17092846	17093001	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17093002	17093110	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17093111	17093158	0.88	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17093111	17093158	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17093159	17093237	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17093238	17093319	0.95	-	1	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17093238	17093319	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17093320	17093427	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17093428	17093504	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17093428	17093504	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17093505	17093680	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17093681	17093749	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17093681	17093749	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	intron	17093750	17093844	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	CDS	17093845	17093847	1	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	exon	17093845	17093847	.	-	.	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
Phchi.S1	AUGUSTUS	start_codon	17093845	17093847	.	-	0	transcript_id "Phchi.S1G264500.t1"; gene_id "Phchi.S1G264500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6916.t1 is derived from g4088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25979649	25981625	.	-	.	Phchi.S1G407500
Phchi.S1	AUGUSTUS	transcript	25979649	25981625	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	stop_codon	25979646	25979648	.	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	CDS	25979649	25979840	1	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	exon	25979649	25979840	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	intron	25979841	25979926	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	CDS	25979927	25980133	0.89	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	exon	25979927	25980133	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	intron	25980134	25980313	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	CDS	25980314	25980487	1	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	exon	25980314	25980487	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	intron	25980488	25980710	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	CDS	25980711	25980866	1	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	exon	25980711	25980866	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	intron	25980867	25980966	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	CDS	25980967	25981310	0.41	-	2	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	exon	25980967	25981310	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	intron	25981311	25981420	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	CDS	25981421	25981625	0.56	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	exon	25981421	25981625	.	-	.	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
Phchi.S1	AUGUSTUS	start_codon	25981623	25981625	.	-	0	transcript_id "Phchi.S1G407500.t1"; gene_id "Phchi.S1G407500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12928.t1 is derived from g11393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3188334	3194008	.	-	.	Phchi.S3G024700
Phchi.S3	AUGUSTUS	transcript	3188334	3194008	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	stop_codon	3188331	3188333	.	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3188334	3188483	1	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3188334	3188483	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3188484	3188567	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3188568	3188876	0.59	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3188568	3188876	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3188877	3189185	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3189186	3189362	1	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3189186	3189362	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3189363	3189498	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3189499	3189584	1	-	2	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3189499	3189584	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3189585	3189664	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3189665	3189985	0.82	-	2	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3189665	3189985	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3189986	3190112	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3190113	3190281	1	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3190113	3190281	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3190282	3190399	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3190400	3190636	0.99	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3190400	3190636	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3190637	3190739	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3190740	3190822	0.99	-	2	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3190740	3190822	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3190823	3190973	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3190974	3191053	1	-	1	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3190974	3191053	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3191054	3191288	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3191289	3191844	0.97	-	2	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3191289	3191844	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3191845	3191979	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3191980	3192130	0.83	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3191980	3192130	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3192131	3192309	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3192310	3192572	0.38	-	2	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3192310	3192572	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3192573	3192868	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3192869	3192941	0.98	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3192869	3192941	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3192942	3193044	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3193045	3193146	0.99	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3193045	3193146	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3193147	3193275	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3193276	3193388	1	-	2	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3193276	3193388	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3193389	3193489	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3193490	3193578	1	-	1	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3193490	3193578	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3193579	3193695	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3193696	3193764	1	-	1	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3193696	3193764	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	intron	3193765	3193847	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	CDS	3193848	3194008	0.82	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	exon	3193848	3194008	.	-	.	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
Phchi.S3	AUGUSTUS	start_codon	3194006	3194008	.	-	0	transcript_id "Phchi.S3G024700.t1"; gene_id "Phchi.S3G024700"
# This transcript jg12910.t2 is derived from g11375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12911.t1 is derived from g11376.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3106095	3108107	.	+	.	Phchi.S3G023000
Phchi.S3	AUGUSTUS	transcript	3106095	3107104	.	+	.	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	start_codon	3106095	3106097	.	+	0	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	CDS	3106095	3106956	0.75	+	0	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	exon	3106095	3106956	.	+	.	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	intron	3106957	3107057	.	+	.	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	CDS	3107058	3107104	0.83	+	2	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	exon	3107058	3107104	.	+	.	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	stop_codon	3107105	3107107	.	+	0	transcript_id "Phchi.S3G023000.t1"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	transcript	3106095	3108107	.	+	.	transcript_id "Phchi.S3G023000.t2"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	start_codon	3106095	3106097	.	+	0	transcript_id "Phchi.S3G023000.t2"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	CDS	3106095	3108107	0.98	+	0	transcript_id "Phchi.S3G023000.t2"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	exon	3106095	3108107	.	+	.	transcript_id "Phchi.S3G023000.t2"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	stop_codon	3108108	3108110	.	+	0	transcript_id "Phchi.S3G023000.t2"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	transcript	3106095	3107905	.	+	.	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	start_codon	3106095	3106097	.	+	0	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	CDS	3106095	3107716	0.43	+	0	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	exon	3106095	3107716	.	+	.	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	intron	3107717	3107820	.	+	.	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	CDS	3107821	3107905	0.55	+	1	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	exon	3107821	3107905	.	+	.	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
Phchi.S3	AUGUSTUS	stop_codon	3107906	3107908	.	+	0	transcript_id "Phchi.S3G023000.t3"; gene_id "Phchi.S3G023000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2232.t1 is derived from g9152.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5565260	5567996	.	-	.	Phchi.S5G084100
Phchi.S5	AUGUSTUS	transcript	5565260	5567996	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	stop_codon	5565257	5565259	.	-	0	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5565260	5565496	1	-	0	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5565260	5565496	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5565497	5565585	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5565586	5565842	1	-	2	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5565586	5565842	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5565843	5565934	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5565935	5566129	1	-	2	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5565935	5566129	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5566130	5566216	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5566217	5566711	0.73	-	2	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5566217	5566711	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5566712	5566798	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5566799	5566885	1	-	2	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5566799	5566885	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5566886	5566986	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5566987	5567295	1	-	2	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5566987	5567295	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5567296	5567471	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5567472	5567530	0.37	-	1	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5567472	5567530	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5567531	5567720	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5567721	5567771	0.68	-	1	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5567721	5567771	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5567772	5567910	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5567911	5567996	0.74	-	0	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5567911	5567996	.	-	.	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	start_codon	5567994	5567996	.	-	0	transcript_id "Phchi.S5G084100.t1"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	transcript	5565260	5567996	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	stop_codon	5565257	5565259	.	-	0	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5565260	5565496	1	-	0	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5565260	5565496	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5565497	5565585	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5565586	5565842	1	-	2	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5565586	5565842	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5565843	5565934	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5565935	5566129	1	-	2	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5565935	5566129	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5566130	5566216	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5566217	5566711	0.62	-	2	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5566217	5566711	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5566712	5566798	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5566799	5566885	0.99	-	2	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5566799	5566885	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5566886	5566986	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5566987	5567295	1	-	2	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5566987	5567295	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5567296	5567471	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5567472	5567530	0.26	-	1	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5567472	5567530	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5567531	5567720	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5567721	5567771	0.56	-	1	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5567721	5567771	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	intron	5567772	5567940	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	CDS	5567941	5567996	0.6	-	0	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	exon	5567941	5567996	.	-	.	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
Phchi.S5	AUGUSTUS	start_codon	5567994	5567996	.	-	0	transcript_id "Phchi.S5G084100.t2"; gene_id "Phchi.S5G084100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12641.t1 is derived from g16008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	126	1981	.	+	.	Phchi.C136G000100
Phchi.C136	AUGUSTUS	transcript	126	1981	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	126	360	0.49	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	126	360	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	361	466	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	467	588	0.96	+	2	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	467	588	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	589	762	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	763	954	1	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	763	954	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	955	1047	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	1048	1131	1	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	1048	1131	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	1132	1228	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	1229	1315	1	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	1229	1315	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	1316	1398	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	1399	1452	1	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	1399	1452	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	1453	1578	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	1579	1661	1	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	1579	1661	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	1662	1755	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	1756	1866	0.87	+	1	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	1756	1866	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	intron	1867	1947	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	CDS	1948	1981	0.86	+	1	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	exon	1948	1981	.	+	.	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
Phchi.C136	AUGUSTUS	stop_codon	1982	1984	.	+	0	transcript_id "Phchi.C136G000100.t1"; gene_id "Phchi.C136G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11504.t1 is derived from g15554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6757673	6759890	.	+	.	Phchi.S4G108600
Phchi.S4	AUGUSTUS	transcript	6757673	6759890	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	start_codon	6757673	6757675	.	+	0	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6757673	6757973	0.76	+	0	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6757673	6757973	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6757974	6758075	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6758076	6758267	0.98	+	2	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6758076	6758267	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6758268	6758367	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6758368	6758704	1	+	2	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6758368	6758704	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6758705	6758795	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6758796	6759013	1	+	1	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6758796	6759013	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759014	6759101	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759102	6759292	1	+	2	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759102	6759292	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759293	6759385	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759386	6759529	0.54	+	0	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759386	6759529	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759530	6759615	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759616	6759666	0.81	+	0	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759616	6759666	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759667	6759749	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759750	6759890	0.99	+	0	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759750	6759890	.	+	.	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	stop_codon	6759891	6759893	.	+	0	transcript_id "Phchi.S4G108600.t1"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	transcript	6757673	6759890	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	start_codon	6757673	6757675	.	+	0	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6757673	6757973	0.76	+	0	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6757673	6757973	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6757974	6758075	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6758076	6758267	1	+	2	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6758076	6758267	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6758268	6758367	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6758368	6758704	1	+	2	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6758368	6758704	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6758705	6758795	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6758796	6759013	1	+	1	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6758796	6759013	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759014	6759101	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759102	6759162	0.59	+	2	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759102	6759162	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759163	6759287	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759288	6759296	0.94	+	1	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759288	6759296	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759297	6759385	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759386	6759414	0.86	+	1	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759386	6759414	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759415	6759538	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759539	6759666	0.65	+	2	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759539	6759666	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	intron	6759667	6759749	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	CDS	6759750	6759890	0.91	+	0	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	exon	6759750	6759890	.	+	.	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
Phchi.S4	AUGUSTUS	stop_codon	6759891	6759893	.	+	0	transcript_id "Phchi.S4G108600.t2"; gene_id "Phchi.S4G108600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13047.t1 is derived from g11512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3871325	3872484	.	+	.	Phchi.S3G036600
Phchi.S3	AUGUSTUS	transcript	3871325	3872484	.	+	.	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	start_codon	3871325	3871327	.	+	0	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	CDS	3871325	3871500	0.82	+	0	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	exon	3871325	3871500	.	+	.	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	intron	3871501	3871586	.	+	.	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	CDS	3871587	3871993	0.96	+	1	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	exon	3871587	3871993	.	+	.	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	intron	3871994	3872071	.	+	.	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	CDS	3872072	3872484	1	+	2	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	exon	3872072	3872484	.	+	.	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
Phchi.S3	AUGUSTUS	stop_codon	3872485	3872487	.	+	0	transcript_id "Phchi.S3G036600.t1"; gene_id "Phchi.S3G036600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6446.t1 is derived from g3618.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23061794	23064038	.	+	.	Phchi.S1G360500
Phchi.S1	AUGUSTUS	transcript	23061794	23064038	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	start_codon	23061794	23061796	.	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23061794	23061843	0.99	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23061794	23061843	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23061844	23061983	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23061984	23062113	1	+	1	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23061984	23062113	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062114	23062203	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062204	23062410	1	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062204	23062410	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062411	23062552	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062553	23062655	1	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062553	23062655	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062656	23062786	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062787	23062866	1	+	2	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062787	23062866	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062867	23062994	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062995	23063072	1	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062995	23063072	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063073	23063214	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063215	23063306	1	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063215	23063306	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063307	23063399	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063400	23063511	1	+	1	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063400	23063511	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063512	23063715	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063716	23063844	1	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063716	23063844	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063845	23063930	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063931	23064038	0.98	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063931	23064038	.	+	.	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	stop_codon	23064039	23064041	.	+	0	transcript_id "Phchi.S1G360500.t1"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	transcript	23061794	23064038	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	start_codon	23061794	23061796	.	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23061794	23061843	1	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23061794	23061843	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23061844	23061983	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23061984	23062113	1	+	1	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23061984	23062113	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062114	23062203	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062204	23062410	0.99	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062204	23062410	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062411	23062552	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062553	23062655	1	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062553	23062655	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062656	23062786	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062787	23062866	1	+	2	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062787	23062866	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23062867	23062994	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23062995	23063072	1	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23062995	23063072	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063073	23063214	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063215	23063306	1	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063215	23063306	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063307	23063399	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063400	23063562	1	+	1	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063400	23063562	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063563	23063715	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063716	23063844	1	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063716	23063844	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	intron	23063845	23063930	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	CDS	23063931	23064038	0.97	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	exon	23063931	23064038	.	+	.	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
Phchi.S1	AUGUSTUS	stop_codon	23064039	23064041	.	+	0	transcript_id "Phchi.S1G360500.t2"; gene_id "Phchi.S1G360500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8133.t1 is derived from g5308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33726383	33730299	.	+	.	Phchi.S1G529200
Phchi.S1	AUGUSTUS	transcript	33726383	33730299	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	start_codon	33726383	33726385	.	+	0	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	CDS	33726383	33727113	0.64	+	0	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	exon	33726383	33727113	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	intron	33727114	33727206	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	CDS	33727207	33727239	0.84	+	1	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	exon	33727207	33727239	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	intron	33727240	33727360	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	CDS	33727361	33727487	0.88	+	1	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	exon	33727361	33727487	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	intron	33727488	33727568	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	CDS	33727569	33728140	0.89	+	0	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	exon	33727569	33728140	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	intron	33728141	33728661	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	CDS	33728662	33728881	1	+	1	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	exon	33728662	33728881	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	intron	33728882	33728985	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	CDS	33728986	33730299	0.79	+	0	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	exon	33728986	33730299	.	+	.	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
Phchi.S1	AUGUSTUS	stop_codon	33730300	33730302	.	+	0	transcript_id "Phchi.S1G529200.t1"; gene_id "Phchi.S1G529200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14617.t1 is derived from g13085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13795956	13798188	.	-	.	Phchi.S3G193600
Phchi.S3	AUGUSTUS	transcript	13795956	13798188	.	-	.	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	stop_codon	13795953	13795955	.	-	0	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	CDS	13795956	13795976	1	-	0	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	exon	13795956	13795976	.	-	.	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	intron	13795977	13798170	.	-	.	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	CDS	13798171	13798188	0.07	-	0	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	exon	13798171	13798188	.	-	.	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
Phchi.S3	AUGUSTUS	start_codon	13798186	13798188	.	-	0	transcript_id "Phchi.S3G193600.t1"; gene_id "Phchi.S3G193600"
# This transcript jg8001.t2 is derived from g5176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8002.t1 is derived from g5177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32375677	32380323	.	+	.	Phchi.S1G516100
Phchi.S1	AUGUSTUS	transcript	32375677	32380323	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	start_codon	32375677	32375679	.	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32375677	32375920	1	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32375677	32375920	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32375921	32376626	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32376627	32376763	1	+	2	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32376627	32376763	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32376764	32376863	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32376864	32376961	1	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32376864	32376961	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32376962	32377186	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32377187	32377671	0.99	+	1	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32377187	32377671	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32377672	32377816	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32377817	32377921	1	+	2	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32377817	32377921	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32377922	32378079	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32378080	32378829	0.92	+	2	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32378080	32378829	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32378830	32378975	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32378976	32379136	1	+	2	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32378976	32379136	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32379137	32379352	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32379353	32379429	1	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32379353	32379429	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32379430	32379517	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32379518	32379665	1	+	1	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32379518	32379665	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32379666	32379885	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32379886	32380041	1	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32379886	32380041	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32380042	32380132	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32380133	32380232	1	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32380133	32380232	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	intron	32380233	32380318	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	CDS	32380319	32380323	1	+	2	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	exon	32380319	32380323	.	+	.	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
Phchi.S1	AUGUSTUS	stop_codon	32380324	32380326	.	+	0	transcript_id "Phchi.S1G516100.t1"; gene_id "Phchi.S1G516100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13504.t1 is derived from g11971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7204519	7204973	.	-	.	Phchi.S3G082300
Phchi.S3	AUGUSTUS	transcript	7204519	7204973	.	-	.	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	stop_codon	7204516	7204518	.	-	0	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	CDS	7204519	7204540	0.96	-	1	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	exon	7204519	7204540	.	-	.	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	intron	7204541	7204707	.	-	.	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	CDS	7204708	7204973	1	-	0	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	exon	7204708	7204973	.	-	.	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
Phchi.S3	AUGUSTUS	start_codon	7204971	7204973	.	-	0	transcript_id "Phchi.S3G082300.t1"; gene_id "Phchi.S3G082300"
# This transcript jg14931.t2 is derived from g13399.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14932.t1 is derived from g13400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15576088	15577307	.	+	.	Phchi.S3G225100
Phchi.S3	AUGUSTUS	transcript	15576088	15577307	.	+	.	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	start_codon	15576088	15576090	.	+	0	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	CDS	15576088	15576357	0.74	+	0	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	exon	15576088	15576357	.	+	.	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	intron	15576358	15576522	.	+	.	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	CDS	15576523	15576768	1	+	0	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	exon	15576523	15576768	.	+	.	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	intron	15576769	15576992	.	+	.	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	CDS	15576993	15577307	1	+	0	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	exon	15576993	15577307	.	+	.	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
Phchi.S3	AUGUSTUS	stop_codon	15577308	15577310	.	+	0	transcript_id "Phchi.S3G225100.t1"; gene_id "Phchi.S3G225100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1726.t1 is derived from g8646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2726020	2728358	.	-	.	Phchi.S5G033500
Phchi.S5	AUGUSTUS	transcript	2726020	2728358	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	stop_codon	2726017	2726019	.	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2726020	2726161	0.52	-	1	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2726020	2726161	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2726162	2726288	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2726289	2726462	0.57	-	1	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2726289	2726462	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2726463	2726549	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2726550	2726746	0.47	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2726550	2726746	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2726747	2726877	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2726878	2726991	0.74	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2726878	2726991	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2726992	2727090	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2727091	2727212	0.55	-	2	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2727091	2727212	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2727213	2727293	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2727294	2727404	0.86	-	2	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2727294	2727404	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2727405	2727492	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2727493	2727745	0.98	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2727493	2727745	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2727746	2727855	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2727856	2727954	0.95	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2727856	2727954	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	intron	2727955	2728064	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	CDS	2728065	2728358	0.8	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	exon	2728065	2728358	.	-	.	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
Phchi.S5	AUGUSTUS	start_codon	2728356	2728358	.	-	0	transcript_id "Phchi.S5G033500.t1"; gene_id "Phchi.S5G033500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9713.t1 is derived from g6889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43381243	43382097	.	+	.	Phchi.S1G687200
Phchi.S1	AUGUSTUS	transcript	43381243	43382097	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	start_codon	43381243	43381245	.	+	0	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	CDS	43381243	43381245	0.94	+	0	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	exon	43381243	43381245	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	intron	43381246	43381327	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	CDS	43381328	43381473	0.99	+	0	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	exon	43381328	43381473	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	intron	43381474	43381582	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	CDS	43381583	43381640	1	+	1	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	exon	43381583	43381640	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	intron	43381641	43381742	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	CDS	43381743	43381877	0.93	+	0	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	exon	43381743	43381877	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	intron	43381878	43381986	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	CDS	43381987	43382097	0.88	+	0	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	exon	43381987	43382097	.	+	.	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
Phchi.S1	AUGUSTUS	stop_codon	43382098	43382100	.	+	0	transcript_id "Phchi.S1G687200.t1"; gene_id "Phchi.S1G687200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7506.t1 is derived from g4680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29708196	29708897	.	+	.	Phchi.S1G466500
Phchi.S1	AUGUSTUS	transcript	29708196	29708897	.	+	.	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	start_codon	29708196	29708198	.	+	0	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	CDS	29708196	29708290	0.47	+	0	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	exon	29708196	29708290	.	+	.	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	intron	29708291	29708401	.	+	.	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	CDS	29708402	29708897	0.51	+	1	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	exon	29708402	29708897	.	+	.	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
Phchi.S1	AUGUSTUS	stop_codon	29708898	29708900	.	+	0	transcript_id "Phchi.S1G466500.t1"; gene_id "Phchi.S1G466500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5630.t1 is derived from g2800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17964690	17966185	.	+	.	Phchi.S1G278900
Phchi.S1	AUGUSTUS	transcript	17964690	17966185	.	+	.	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	start_codon	17964690	17964692	.	+	0	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	CDS	17964690	17965289	0.7	+	0	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	exon	17964690	17965289	.	+	.	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	intron	17965290	17965390	.	+	.	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	CDS	17965391	17966185	1	+	0	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	exon	17965391	17966185	.	+	.	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
Phchi.S1	AUGUSTUS	stop_codon	17966186	17966188	.	+	0	transcript_id "Phchi.S1G278900.t1"; gene_id "Phchi.S1G278900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5600.t1 is derived from g2770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17827944	17829033	.	-	.	Phchi.S1G275900
Phchi.S1	AUGUSTUS	transcript	17827944	17829033	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	stop_codon	17827941	17827943	.	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17827944	17827986	0.59	-	1	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17827944	17827986	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	intron	17827987	17828073	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17828074	17828123	0.47	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17828074	17828123	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	intron	17828124	17828254	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17828255	17828323	1	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17828255	17828323	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	intron	17828324	17828415	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17828416	17828461	0.93	-	1	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17828416	17828461	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	intron	17828462	17828635	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17828636	17828706	1	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17828636	17828706	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	intron	17828707	17828794	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17828795	17828881	1	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17828795	17828881	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	intron	17828882	17828961	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	CDS	17828962	17829033	0.99	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	exon	17828962	17829033	.	-	.	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
Phchi.S1	AUGUSTUS	start_codon	17829031	17829033	.	-	0	transcript_id "Phchi.S1G275900.t1"; gene_id "Phchi.S1G275900"
# This transcript jg6483.t2 is derived from g3655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6484.t1 is derived from g3656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23218317	23218811	.	-	.	Phchi.S1G364300
Phchi.S1	AUGUSTUS	transcript	23218317	23218811	.	-	.	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	stop_codon	23218314	23218316	.	-	0	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	CDS	23218317	23218518	0.98	-	1	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	exon	23218317	23218518	.	-	.	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	intron	23218519	23218734	.	-	.	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	CDS	23218735	23218811	0.97	-	0	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	exon	23218735	23218811	.	-	.	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
Phchi.S1	AUGUSTUS	start_codon	23218809	23218811	.	-	0	transcript_id "Phchi.S1G364300.t1"; gene_id "Phchi.S1G364300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4862.t1 is derived from g2032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13147732	13148214	.	-	.	Phchi.S1G202100
Phchi.S1	AUGUSTUS	transcript	13147732	13148214	.	-	.	transcript_id "Phchi.S1G202100.t1"; gene_id "Phchi.S1G202100"
Phchi.S1	AUGUSTUS	stop_codon	13147729	13147731	.	-	0	transcript_id "Phchi.S1G202100.t1"; gene_id "Phchi.S1G202100"
Phchi.S1	AUGUSTUS	CDS	13147732	13148214	0.71	-	0	transcript_id "Phchi.S1G202100.t1"; gene_id "Phchi.S1G202100"
Phchi.S1	AUGUSTUS	exon	13147732	13148214	.	-	.	transcript_id "Phchi.S1G202100.t1"; gene_id "Phchi.S1G202100"
Phchi.S1	AUGUSTUS	start_codon	13148212	13148214	.	-	0	transcript_id "Phchi.S1G202100.t1"; gene_id "Phchi.S1G202100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8128.t1 is derived from g5303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33629082	33630152	.	-	.	Phchi.S1G528700
Phchi.S1	AUGUSTUS	transcript	33629082	33630152	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	stop_codon	33629079	33629081	.	-	0	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	CDS	33629082	33629111	0.88	-	0	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	exon	33629082	33629111	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	intron	33629112	33629217	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	CDS	33629218	33629316	1	-	0	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	exon	33629218	33629316	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	intron	33629317	33629399	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	CDS	33629400	33629570	1	-	0	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	exon	33629400	33629570	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	intron	33629571	33629667	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	CDS	33629668	33629740	1	-	1	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	exon	33629668	33629740	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	intron	33629741	33629825	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	CDS	33629826	33629966	1	-	1	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	exon	33629826	33629966	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	intron	33629967	33630108	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	CDS	33630109	33630152	1	-	0	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	exon	33630109	33630152	.	-	.	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
Phchi.S1	AUGUSTUS	start_codon	33630150	33630152	.	-	0	transcript_id "Phchi.S1G528700.t1"; gene_id "Phchi.S1G528700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9243.t1 is derived from g6418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40567940	40568763	.	+	.	Phchi.S1G640200
Phchi.S1	AUGUSTUS	transcript	40567940	40568763	.	+	.	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	start_codon	40567940	40567942	.	+	0	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	CDS	40567940	40568029	1	+	0	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	exon	40567940	40568029	.	+	.	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	intron	40568030	40568322	.	+	.	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	CDS	40568323	40568504	1	+	0	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	exon	40568323	40568504	.	+	.	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	intron	40568505	40568636	.	+	.	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	CDS	40568637	40568763	1	+	1	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	exon	40568637	40568763	.	+	.	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
Phchi.S1	AUGUSTUS	stop_codon	40568764	40568766	.	+	0	transcript_id "Phchi.S1G640200.t1"; gene_id "Phchi.S1G640200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15715.t1 is derived from g14185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20819204	20823044	.	-	.	Phchi.S3G303400
Phchi.S3	AUGUSTUS	transcript	20819204	20823044	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	stop_codon	20819201	20819203	.	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20819204	20819368	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20819204	20819368	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20819369	20819446	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20819447	20819560	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20819447	20819560	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20819561	20819634	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20819635	20819865	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20819635	20819865	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20819866	20819959	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20819960	20820100	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20819960	20820100	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20820101	20820243	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20820244	20820306	0.88	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20820244	20820306	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20820307	20820392	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20820393	20820410	0.79	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20820393	20820410	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20820411	20820506	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20820507	20820662	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20820507	20820662	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20820663	20820747	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20820748	20821202	1	-	2	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20820748	20821202	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20821203	20821447	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20821448	20821547	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20821448	20821547	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20821548	20821631	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20821632	20821988	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20821632	20821988	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20821989	20822208	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20822209	20822796	1	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20822209	20822796	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	intron	20822797	20822942	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	CDS	20822943	20823044	0.99	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	exon	20822943	20823044	.	-	.	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
Phchi.S3	AUGUSTUS	start_codon	20823042	20823044	.	-	0	transcript_id "Phchi.S3G303400.t1"; gene_id "Phchi.S3G303400"
# This transcript jg12670.t2 is derived from g14404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12671.t1 is derived from g14405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	5182	6024	.	-	.	Phchi.C62G000200
Phchi.C62	AUGUSTUS	transcript	5182	6024	.	-	.	transcript_id "Phchi.C62G000200.t1"; gene_id "Phchi.C62G000200"
Phchi.C62	AUGUSTUS	stop_codon	5179	5181	.	-	0	transcript_id "Phchi.C62G000200.t1"; gene_id "Phchi.C62G000200"
Phchi.C62	AUGUSTUS	CDS	5182	6024	0.88	-	0	transcript_id "Phchi.C62G000200.t1"; gene_id "Phchi.C62G000200"
Phchi.C62	AUGUSTUS	exon	5182	6024	.	-	.	transcript_id "Phchi.C62G000200.t1"; gene_id "Phchi.C62G000200"
Phchi.C62	AUGUSTUS	start_codon	6022	6024	.	-	0	transcript_id "Phchi.C62G000200.t1"; gene_id "Phchi.C62G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15655.t1 is derived from g14124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20500971	20503121	.	+	.	Phchi.S3G297400
Phchi.S3	AUGUSTUS	transcript	20500971	20503121	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	start_codon	20500971	20500973	.	+	0	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	CDS	20500971	20500988	1	+	0	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	exon	20500971	20500988	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	intron	20500989	20501098	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	CDS	20501099	20501426	1	+	0	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	exon	20501099	20501426	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	intron	20501427	20501562	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	CDS	20501563	20501831	0.92	+	2	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	exon	20501563	20501831	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	intron	20501832	20501933	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	CDS	20501934	20502182	0.94	+	0	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	exon	20501934	20502182	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	intron	20502183	20502287	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	CDS	20502288	20503005	1	+	0	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	exon	20502288	20503005	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	intron	20503006	20503083	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	CDS	20503084	20503121	1	+	2	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	exon	20503084	20503121	.	+	.	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
Phchi.S3	AUGUSTUS	stop_codon	20503122	20503124	.	+	0	transcript_id "Phchi.S3G297400.t1"; gene_id "Phchi.S3G297400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14538.t1 is derived from g13006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13393517	13395024	.	-	.	Phchi.S3G185700
Phchi.S3	AUGUSTUS	transcript	13393517	13395024	.	-	.	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	stop_codon	13393514	13393516	.	-	0	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	CDS	13393517	13393649	1	-	1	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	exon	13393517	13393649	.	-	.	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	intron	13393650	13393760	.	-	.	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	CDS	13393761	13394793	0.85	-	2	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	exon	13393761	13394793	.	-	.	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	intron	13394794	13394936	.	-	.	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	CDS	13394937	13395024	0.61	-	0	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	exon	13394937	13395024	.	-	.	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
Phchi.S3	AUGUSTUS	start_codon	13395022	13395024	.	-	0	transcript_id "Phchi.S3G185700.t1"; gene_id "Phchi.S3G185700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5919.t1 is derived from g3090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19871385	19876981	.	+	.	Phchi.S1G307800
Phchi.S1	AUGUSTUS	transcript	19871385	19876981	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	start_codon	19871385	19871387	.	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19871385	19872645	0.63	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19871385	19872645	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19872646	19872817	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19872818	19872927	0.4	+	2	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19872818	19872927	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19872928	19873115	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19873116	19873191	0.47	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19873116	19873191	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19873192	19873416	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19873417	19874377	0.62	+	2	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19873417	19874377	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19874378	19874569	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19874570	19874652	1	+	1	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19874570	19874652	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19874653	19874838	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19874839	19875242	1	+	2	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19874839	19875242	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19875243	19875339	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19875340	19875533	1	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19875340	19875533	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19875534	19875621	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19875622	19875802	1	+	1	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19875622	19875802	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19875803	19875900	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19875901	19876025	1	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19875901	19876025	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19876026	19876111	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19876112	19876201	1	+	1	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19876112	19876201	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19876202	19876317	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19876318	19876396	0.93	+	1	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19876318	19876396	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19876397	19876486	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19876487	19876563	1	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19876487	19876563	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19876564	19876678	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19876679	19876787	1	+	1	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19876679	19876787	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	intron	19876788	19876873	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	CDS	19876874	19876981	1	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	exon	19876874	19876981	.	+	.	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
Phchi.S1	AUGUSTUS	stop_codon	19876982	19876984	.	+	0	transcript_id "Phchi.S1G307800.t1"; gene_id "Phchi.S1G307800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg253.t1 is derived from g10035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1720871	1724584	.	-	.	Phchi.S6G021200
Phchi.S6	AUGUSTUS	transcript	1720871	1724584	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	stop_codon	1720868	1720870	.	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1720871	1720992	1	-	2	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1720871	1720992	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1720993	1721200	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1721201	1721288	1	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1721201	1721288	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1721289	1721431	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1721432	1721475	1	-	2	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1721432	1721475	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1721476	1721557	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1721558	1721688	1	-	1	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1721558	1721688	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1721689	1721763	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1721764	1721843	1	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1721764	1721843	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1721844	1721921	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1721922	1721984	1	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1721922	1721984	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1721985	1722125	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1722126	1722235	1	-	2	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1722126	1722235	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1722236	1722376	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1722377	1722485	0.99	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1722377	1722485	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1722486	1722586	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1722587	1722661	0.99	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1722587	1722661	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1722662	1722751	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1722752	1722848	1	-	1	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1722752	1722848	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1722849	1722937	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1722938	1722999	0.82	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1722938	1722999	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1723000	1723103	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1723104	1723140	0.94	-	1	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1723104	1723140	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1723141	1723235	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1723236	1723296	1	-	2	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1723236	1723296	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1723297	1723393	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1723394	1723508	1	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1723394	1723508	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1723509	1723590	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1723591	1723683	1	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1723591	1723683	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1723684	1723794	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1723795	1723843	1	-	1	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1723795	1723843	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1723844	1723935	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1723936	1724039	1	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1723936	1724039	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1724040	1724139	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1724140	1724206	1	-	1	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1724140	1724206	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	intron	1724207	1724303	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	CDS	1724304	1724584	0.59	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	exon	1724304	1724584	.	-	.	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
Phchi.S6	AUGUSTUS	start_codon	1724582	1724584	.	-	0	transcript_id "Phchi.S6G021200.t1"; gene_id "Phchi.S6G021200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13080.t1 is derived from g11545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4062084	4062465	.	+	.	Phchi.S3G039900
Phchi.S3	AUGUSTUS	transcript	4062084	4062465	.	+	.	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	start_codon	4062084	4062086	.	+	0	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	CDS	4062084	4062182	0.98	+	0	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	exon	4062084	4062182	.	+	.	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	intron	4062183	4062294	.	+	.	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	CDS	4062295	4062465	0.98	+	0	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	exon	4062295	4062465	.	+	.	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
Phchi.S3	AUGUSTUS	stop_codon	4062466	4062468	.	+	0	transcript_id "Phchi.S3G039900.t1"; gene_id "Phchi.S3G039900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3049.t1 is derived from g218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1358325	1358752	.	+	.	Phchi.S1G020800
Phchi.S1	AUGUSTUS	transcript	1358325	1358752	.	+	.	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	start_codon	1358325	1358327	.	+	0	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	CDS	1358325	1358487	0.83	+	0	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	exon	1358325	1358487	.	+	.	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	intron	1358488	1358573	.	+	.	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	CDS	1358574	1358752	0.89	+	2	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	exon	1358574	1358752	.	+	.	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
Phchi.S1	AUGUSTUS	stop_codon	1358753	1358755	.	+	0	transcript_id "Phchi.S1G020800.t1"; gene_id "Phchi.S1G020800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2511.t1 is derived from g9431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7073240	7075045	.	-	.	Phchi.S5G112000
Phchi.S5	AUGUSTUS	transcript	7073240	7075045	.	-	.	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	stop_codon	7073237	7073239	.	-	0	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	CDS	7073240	7074066	0.6	-	2	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	exon	7073240	7074066	.	-	.	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	intron	7074067	7074208	.	-	.	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	CDS	7074209	7074917	0.56	-	0	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	exon	7074209	7074917	.	-	.	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	intron	7074918	7075012	.	-	.	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	CDS	7075013	7075045	0.92	-	0	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	exon	7075013	7075045	.	-	.	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
Phchi.S5	AUGUSTUS	start_codon	7075043	7075045	.	-	0	transcript_id "Phchi.S5G112000.t1"; gene_id "Phchi.S5G112000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15520.t1 is derived from g13989.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19686213	19687633	.	+	.	Phchi.S3G283900
Phchi.S3	AUGUSTUS	transcript	19686213	19687633	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	start_codon	19686213	19686215	.	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686213	19686281	1	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686213	19686281	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686282	19686377	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686378	19686460	0.98	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686378	19686460	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686461	19686737	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686738	19686792	0.93	+	1	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686738	19686792	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686793	19686880	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686881	19686973	0.74	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686881	19686973	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686974	19687068	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687069	19687097	0.72	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687069	19687097	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19687098	19687180	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687181	19687312	1	+	1	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687181	19687312	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19687313	19687408	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687409	19687511	1	+	1	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687409	19687511	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19687512	19687594	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687595	19687633	1	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687595	19687633	.	+	.	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	stop_codon	19687634	19687636	.	+	0	transcript_id "Phchi.S3G283900.t1"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	transcript	19686213	19687633	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	start_codon	19686213	19686215	.	+	0	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686213	19686281	0.99	+	0	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686213	19686281	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686282	19686377	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686378	19686460	0.85	+	0	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686378	19686460	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686461	19686557	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686558	19686619	0.75	+	1	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686558	19686619	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686620	19686880	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19686881	19686915	0.78	+	2	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19686881	19686915	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19686916	19687026	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687027	19687097	0.94	+	0	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687027	19687097	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19687098	19687180	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687181	19687312	1	+	1	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687181	19687312	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19687313	19687408	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687409	19687511	0.98	+	1	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687409	19687511	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	intron	19687512	19687594	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	CDS	19687595	19687633	1	+	0	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	exon	19687595	19687633	.	+	.	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
Phchi.S3	AUGUSTUS	stop_codon	19687634	19687636	.	+	0	transcript_id "Phchi.S3G283900.t2"; gene_id "Phchi.S3G283900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15242.t1 is derived from g13710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17879266	17879816	.	-	.	Phchi.S3G256100
Phchi.S3	AUGUSTUS	transcript	17879266	17879816	.	-	.	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	stop_codon	17879263	17879265	.	-	0	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	CDS	17879266	17879272	0.57	-	1	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	exon	17879266	17879272	.	-	.	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	intron	17879273	17879373	.	-	.	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	CDS	17879374	17879615	0.46	-	0	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	exon	17879374	17879615	.	-	.	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	intron	17879616	17879699	.	-	.	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	CDS	17879700	17879816	0.99	-	0	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	exon	17879700	17879816	.	-	.	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
Phchi.S3	AUGUSTUS	start_codon	17879814	17879816	.	-	0	transcript_id "Phchi.S3G256100.t1"; gene_id "Phchi.S3G256100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1013.t1 is derived from g10796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7118825	7120984	.	+	.	Phchi.S6G097200
Phchi.S6	AUGUSTUS	transcript	7118825	7120984	.	+	.	transcript_id "Phchi.S6G097200.t1"; gene_id "Phchi.S6G097200"
Phchi.S6	AUGUSTUS	start_codon	7118825	7118827	.	+	0	transcript_id "Phchi.S6G097200.t1"; gene_id "Phchi.S6G097200"
Phchi.S6	AUGUSTUS	CDS	7118825	7120984	0.44	+	0	transcript_id "Phchi.S6G097200.t1"; gene_id "Phchi.S6G097200"
Phchi.S6	AUGUSTUS	exon	7118825	7120984	.	+	.	transcript_id "Phchi.S6G097200.t1"; gene_id "Phchi.S6G097200"
Phchi.S6	AUGUSTUS	stop_codon	7120985	7120987	.	+	0	transcript_id "Phchi.S6G097200.t1"; gene_id "Phchi.S6G097200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6514.t1 is derived from g3686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23412914	23416429	.	+	.	Phchi.S1G367300
Phchi.S1	AUGUSTUS	transcript	23412914	23416429	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	start_codon	23412914	23412916	.	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23412914	23413060	1	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23412914	23413060	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	intron	23413061	23413176	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23413177	23413505	1	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23413177	23413505	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	intron	23413506	23413665	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23413666	23414647	0.98	+	1	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23413666	23414647	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	intron	23414648	23414805	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23414806	23414836	0.99	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23414806	23414836	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	intron	23414837	23414902	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23414903	23414946	1	+	2	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23414903	23414946	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	intron	23414947	23415081	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23415082	23415351	0.97	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23415082	23415351	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	intron	23415352	23415457	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	CDS	23415458	23416429	0.87	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	exon	23415458	23416429	.	+	.	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
Phchi.S1	AUGUSTUS	stop_codon	23416430	23416432	.	+	0	transcript_id "Phchi.S1G367300.t1"; gene_id "Phchi.S1G367300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3707.t1 is derived from g876.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5254969	5255568	.	+	.	Phchi.S1G086600
Phchi.S1	AUGUSTUS	transcript	5254969	5255568	.	+	.	transcript_id "Phchi.S1G086600.t1"; gene_id "Phchi.S1G086600"
Phchi.S1	AUGUSTUS	start_codon	5254969	5254971	.	+	0	transcript_id "Phchi.S1G086600.t1"; gene_id "Phchi.S1G086600"
Phchi.S1	AUGUSTUS	CDS	5254969	5255568	0.75	+	0	transcript_id "Phchi.S1G086600.t1"; gene_id "Phchi.S1G086600"
Phchi.S1	AUGUSTUS	exon	5254969	5255568	.	+	.	transcript_id "Phchi.S1G086600.t1"; gene_id "Phchi.S1G086600"
Phchi.S1	AUGUSTUS	stop_codon	5255569	5255571	.	+	0	transcript_id "Phchi.S1G086600.t1"; gene_id "Phchi.S1G086600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6142.t1 is derived from g3313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21137301	21139289	.	+	.	Phchi.S1G330100
Phchi.S1	AUGUSTUS	transcript	21137301	21139289	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	start_codon	21137301	21137303	.	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21137301	21137674	0.64	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21137301	21137674	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21137675	21137772	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21137773	21137888	1	+	1	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21137773	21137888	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21137889	21137968	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21137969	21138018	1	+	2	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21137969	21138018	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21138019	21138207	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21138208	21138438	1	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21138208	21138438	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21138439	21138536	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21138537	21138701	1	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21138537	21138701	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21138702	21138794	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21138795	21138890	1	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21138795	21138890	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21138891	21139006	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21139007	21139027	1	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21139007	21139027	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	intron	21139028	21139124	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	CDS	21139125	21139289	0.99	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	exon	21139125	21139289	.	+	.	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
Phchi.S1	AUGUSTUS	stop_codon	21139290	21139292	.	+	0	transcript_id "Phchi.S1G330100.t1"; gene_id "Phchi.S1G330100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3366.t1 is derived from g535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3180591	3181663	.	+	.	Phchi.S1G052500
Phchi.S1	AUGUSTUS	transcript	3180591	3181663	.	+	.	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	start_codon	3180591	3180593	.	+	0	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	CDS	3180591	3181282	0.68	+	0	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	exon	3180591	3181282	.	+	.	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	intron	3181283	3181401	.	+	.	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	CDS	3181402	3181663	0.91	+	1	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	exon	3181402	3181663	.	+	.	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
Phchi.S1	AUGUSTUS	stop_codon	3181664	3181666	.	+	0	transcript_id "Phchi.S1G052500.t1"; gene_id "Phchi.S1G052500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6423.t1 is derived from g3595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22934210	22935821	.	-	.	Phchi.S1G358200
Phchi.S1	AUGUSTUS	transcript	22934210	22935821	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	stop_codon	22934207	22934209	.	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22934210	22934246	1	-	1	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22934210	22934246	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22934247	22934388	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22934389	22934457	1	-	1	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22934389	22934457	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22934458	22934555	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22934556	22934626	1	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22934556	22934626	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22934627	22934715	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22934716	22934778	0.45	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22934716	22934778	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22934779	22934877	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22934878	22934912	0.59	-	2	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22934878	22934912	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22934913	22935001	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22935002	22935095	0.55	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22935002	22935095	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22935096	22935194	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22935195	22935276	0.86	-	1	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22935195	22935276	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22935277	22935404	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22935405	22935463	0.88	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22935405	22935463	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22935464	22935578	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22935579	22935689	1	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22935579	22935689	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	intron	22935690	22935785	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	CDS	22935786	22935821	0.4	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	exon	22935786	22935821	.	-	.	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
Phchi.S1	AUGUSTUS	start_codon	22935819	22935821	.	-	0	transcript_id "Phchi.S1G358200.t1"; gene_id "Phchi.S1G358200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2400.t1 is derived from g9320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6481972	6482748	.	-	.	Phchi.S5G100900
Phchi.S5	AUGUSTUS	transcript	6481972	6482748	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	stop_codon	6481969	6481971	.	-	0	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	CDS	6481972	6482126	0.51	-	2	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	exon	6481972	6482126	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	intron	6482127	6482266	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	CDS	6482267	6482342	1	-	0	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	exon	6482267	6482342	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	intron	6482343	6482420	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	CDS	6482421	6482609	1	-	0	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	exon	6482421	6482609	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	intron	6482610	6482721	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	CDS	6482722	6482748	0.81	-	0	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	exon	6482722	6482748	.	-	.	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
Phchi.S5	AUGUSTUS	start_codon	6482746	6482748	.	-	0	transcript_id "Phchi.S5G100900.t1"; gene_id "Phchi.S5G100900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11950.t1 is derived from g7625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	164776	166995	.	-	.	Phchi.S2G003000
Phchi.S2	AUGUSTUS	transcript	164776	166995	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	stop_codon	164773	164775	.	-	0	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	CDS	164776	164794	0.39	-	1	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	exon	164776	164794	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	intron	164795	164886	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	CDS	164887	166694	0.52	-	0	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	exon	164887	166694	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	intron	166695	166782	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	CDS	166783	166877	0.96	-	2	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	exon	166783	166877	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	intron	166878	166976	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	CDS	166977	166995	0.92	-	0	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	exon	166977	166995	.	-	.	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
Phchi.S2	AUGUSTUS	start_codon	166993	166995	.	-	0	transcript_id "Phchi.S2G003000.t1"; gene_id "Phchi.S2G003000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8997.t1 is derived from g6172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39035520	39036776	.	-	.	Phchi.S1G615600
Phchi.S1	AUGUSTUS	transcript	39035520	39036776	.	-	.	transcript_id "Phchi.S1G615600.t1"; gene_id "Phchi.S1G615600"
Phchi.S1	AUGUSTUS	stop_codon	39035517	39035519	.	-	0	transcript_id "Phchi.S1G615600.t1"; gene_id "Phchi.S1G615600"
Phchi.S1	AUGUSTUS	CDS	39035520	39036776	1	-	0	transcript_id "Phchi.S1G615600.t1"; gene_id "Phchi.S1G615600"
Phchi.S1	AUGUSTUS	exon	39035520	39036776	.	-	.	transcript_id "Phchi.S1G615600.t1"; gene_id "Phchi.S1G615600"
Phchi.S1	AUGUSTUS	start_codon	39036774	39036776	.	-	0	transcript_id "Phchi.S1G615600.t1"; gene_id "Phchi.S1G615600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10720.t1 is derived from g14770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1751244	1751558	.	+	.	Phchi.S4G030200
Phchi.S4	AUGUSTUS	transcript	1751244	1751558	.	+	.	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	start_codon	1751244	1751246	.	+	0	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	CDS	1751244	1751287	0.32	+	0	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	exon	1751244	1751287	.	+	.	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	intron	1751288	1751365	.	+	.	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	CDS	1751366	1751558	0.95	+	1	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	exon	1751366	1751558	.	+	.	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
Phchi.S4	AUGUSTUS	stop_codon	1751559	1751561	.	+	0	transcript_id "Phchi.S4G030200.t1"; gene_id "Phchi.S4G030200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14812.t1 is derived from g13280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14817629	14819104	.	+	.	Phchi.S3G213100
Phchi.S3	AUGUSTUS	transcript	14817629	14819104	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	start_codon	14817629	14817631	.	+	0	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	CDS	14817629	14817911	0.72	+	0	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	exon	14817629	14817911	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	intron	14817912	14817994	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	CDS	14817995	14818203	1	+	2	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	exon	14817995	14818203	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	intron	14818204	14818438	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	CDS	14818439	14818546	1	+	0	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	exon	14818439	14818546	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	intron	14818547	14818733	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	CDS	14818734	14818872	0.64	+	0	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	exon	14818734	14818872	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	intron	14818873	14819015	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	CDS	14819016	14819104	0.65	+	2	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	exon	14819016	14819104	.	+	.	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
Phchi.S3	AUGUSTUS	stop_codon	14819105	14819107	.	+	0	transcript_id "Phchi.S3G213100.t1"; gene_id "Phchi.S3G213100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3273.t1 is derived from g442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2642407	2643327	.	-	.	Phchi.S1G043200
Phchi.S1	AUGUSTUS	transcript	2642407	2643327	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	stop_codon	2642404	2642406	.	-	0	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	CDS	2642407	2642434	0.83	-	1	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	exon	2642407	2642434	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	intron	2642435	2642713	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	CDS	2642714	2642798	0.84	-	2	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	exon	2642714	2642798	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	intron	2642799	2642886	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	CDS	2642887	2642985	0.59	-	2	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	exon	2642887	2642985	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	intron	2642986	2643170	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	CDS	2643171	2643327	0.79	-	0	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	exon	2643171	2643327	.	-	.	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
Phchi.S1	AUGUSTUS	start_codon	2643325	2643327	.	-	0	transcript_id "Phchi.S1G043200.t1"; gene_id "Phchi.S1G043200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2303.t1 is derived from g9223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5948712	5949332	.	-	.	Phchi.S5G091200
Phchi.S5	AUGUSTUS	transcript	5948712	5949332	.	-	.	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	stop_codon	5948709	5948711	.	-	0	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	CDS	5948712	5948947	0.51	-	2	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	exon	5948712	5948947	.	-	.	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	intron	5948948	5949045	.	-	.	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	CDS	5949046	5949171	0.57	-	2	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	exon	5949046	5949171	.	-	.	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	intron	5949172	5949268	.	-	.	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	CDS	5949269	5949332	0.47	-	0	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	exon	5949269	5949332	.	-	.	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
Phchi.S5	AUGUSTUS	start_codon	5949330	5949332	.	-	0	transcript_id "Phchi.S5G091200.t1"; gene_id "Phchi.S5G091200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15765.t1 is derived from g14235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21123279	21129733	.	+	.	Phchi.S3G308400
Phchi.S3	AUGUSTUS	transcript	21123279	21129733	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	start_codon	21123279	21123281	.	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21123279	21124281	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21123279	21124281	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21124282	21124447	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21124448	21124866	0.98	+	2	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21124448	21124866	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21124867	21125049	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21125050	21125313	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21125050	21125313	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21125314	21125407	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21125408	21125651	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21125408	21125651	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21125652	21125746	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21125747	21125991	1	+	2	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21125747	21125991	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21125992	21126069	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21126070	21126205	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21126070	21126205	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21126206	21126313	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21126314	21126566	1	+	2	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21126314	21126566	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21126567	21126667	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21126668	21126920	1	+	1	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21126668	21126920	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21126921	21127070	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21127071	21127223	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21127071	21127223	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21127224	21127373	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21127374	21127483	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21127374	21127483	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21127484	21127775	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21127776	21127835	0.87	+	1	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21127776	21127835	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21127836	21128042	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21128043	21128110	0.74	+	1	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21128043	21128110	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21128111	21128271	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21128272	21128346	1	+	2	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21128272	21128346	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21128347	21128456	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21128457	21128515	0.98	+	2	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21128457	21128515	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21128516	21128625	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21128626	21128733	0.99	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21128626	21128733	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21128734	21128833	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21128834	21128956	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21128834	21128956	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21128957	21129118	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21129119	21129265	1	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21129119	21129265	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21129266	21129354	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21129355	21129462	0.74	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21129355	21129462	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	intron	21129463	21129568	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	CDS	21129569	21129733	0.43	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	exon	21129569	21129733	.	+	.	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
Phchi.S3	AUGUSTUS	stop_codon	21129734	21129736	.	+	0	transcript_id "Phchi.S3G308400.t1"; gene_id "Phchi.S3G308400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10210.t1 is derived from g7386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46393724	46394151	.	+	.	Phchi.S1G736900
Phchi.S1	AUGUSTUS	transcript	46393724	46394151	.	+	.	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	start_codon	46393724	46393726	.	+	0	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	CDS	46393724	46393841	0.85	+	0	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	exon	46393724	46393841	.	+	.	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	intron	46393842	46393979	.	+	.	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	CDS	46393980	46394024	0.97	+	2	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	exon	46393980	46394024	.	+	.	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	intron	46394025	46394104	.	+	.	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	CDS	46394105	46394151	0.82	+	2	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	exon	46394105	46394151	.	+	.	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
Phchi.S1	AUGUSTUS	stop_codon	46394152	46394154	.	+	0	transcript_id "Phchi.S1G736900.t1"; gene_id "Phchi.S1G736900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7953.t1 is derived from g5127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32079261	32081784	.	-	.	Phchi.S1G511200
Phchi.S1	AUGUSTUS	transcript	32079261	32081784	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	stop_codon	32079258	32079260	.	-	0	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	CDS	32079261	32079596	1	-	0	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	exon	32079261	32079596	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	intron	32079597	32079740	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	CDS	32079741	32079866	1	-	0	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	exon	32079741	32079866	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	intron	32079867	32080002	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	CDS	32080003	32080093	1	-	1	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	exon	32080003	32080093	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	intron	32080094	32080224	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	CDS	32080225	32080301	1	-	0	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	exon	32080225	32080301	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	intron	32080302	32080392	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	CDS	32080393	32081784	1	-	0	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	exon	32080393	32081784	.	-	.	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
Phchi.S1	AUGUSTUS	start_codon	32081782	32081784	.	-	0	transcript_id "Phchi.S1G511200.t1"; gene_id "Phchi.S1G511200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12535.t1 is derived from g8212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33634282	33635575	.	-	.	Phchi.S2G061500
Phchi.S2	AUGUSTUS	transcript	33634282	33635575	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	stop_codon	33634279	33634281	.	-	0	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	CDS	33634282	33634365	1	-	0	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	exon	33634282	33634365	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	intron	33634366	33634484	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	CDS	33634485	33634610	0.99	-	0	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	exon	33634485	33634610	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	intron	33634611	33634732	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	CDS	33634733	33634790	0.99	-	1	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	exon	33634733	33634790	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	intron	33634791	33634938	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	CDS	33634939	33635269	0.97	-	2	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	exon	33634939	33635269	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	intron	33635270	33635373	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	CDS	33635374	33635575	1	-	0	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	exon	33635374	33635575	.	-	.	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
Phchi.S2	AUGUSTUS	start_codon	33635573	33635575	.	-	0	transcript_id "Phchi.S2G061500.t1"; gene_id "Phchi.S2G061500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3216.t1 is derived from g385.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2280174	2280580	.	+	.	Phchi.S1G037500
Phchi.S1	AUGUSTUS	transcript	2280174	2280580	.	+	.	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	start_codon	2280174	2280176	.	+	0	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	CDS	2280174	2280277	0.66	+	0	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	exon	2280174	2280277	.	+	.	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	intron	2280278	2280369	.	+	.	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	CDS	2280370	2280418	0.69	+	1	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	exon	2280370	2280418	.	+	.	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	intron	2280419	2280517	.	+	.	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	CDS	2280518	2280580	0.69	+	0	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	exon	2280518	2280580	.	+	.	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
Phchi.S1	AUGUSTUS	stop_codon	2280581	2280583	.	+	0	transcript_id "Phchi.S1G037500.t1"; gene_id "Phchi.S1G037500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14484.t1 is derived from g12952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13075784	13078957	.	+	.	Phchi.S3G180300
Phchi.S3	AUGUSTUS	transcript	13075784	13078957	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	start_codon	13075784	13075786	.	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13075784	13075807	0.89	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13075784	13075807	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13075808	13076087	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13076088	13076218	1	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13076088	13076218	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13076219	13076390	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13076391	13076478	1	+	1	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13076391	13076478	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13076479	13076558	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13076559	13076618	1	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13076559	13076618	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13076619	13076743	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13076744	13076776	1	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13076744	13076776	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13076777	13076911	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13076912	13076989	1	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13076912	13076989	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13076990	13077152	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13077153	13077196	1	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13077153	13077196	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13077197	13077276	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13077277	13077317	1	+	1	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13077277	13077317	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13077318	13077602	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13077603	13077685	1	+	2	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13077603	13077685	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13077686	13077788	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13077789	13077880	0.99	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13077789	13077880	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13077881	13077981	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13077982	13078060	1	+	1	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13077982	13078060	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13078061	13078141	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13078142	13078183	0.97	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13078142	13078183	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13078184	13078293	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13078294	13078392	0.32	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13078294	13078392	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13078393	13078473	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13078474	13078502	0.6	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13078474	13078502	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	intron	13078503	13078854	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	CDS	13078855	13078957	0.96	+	1	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	exon	13078855	13078957	.	+	.	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
Phchi.S3	AUGUSTUS	stop_codon	13078958	13078960	.	+	0	transcript_id "Phchi.S3G180300.t1"; gene_id "Phchi.S3G180300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2582.t1 is derived from g9502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7484795	7486447	.	-	.	Phchi.S5G119100
Phchi.S5	AUGUSTUS	transcript	7484795	7486447	.	-	.	transcript_id "Phchi.S5G119100.t1"; gene_id "Phchi.S5G119100"
Phchi.S5	AUGUSTUS	stop_codon	7484792	7484794	.	-	0	transcript_id "Phchi.S5G119100.t1"; gene_id "Phchi.S5G119100"
Phchi.S5	AUGUSTUS	CDS	7484795	7486447	1	-	0	transcript_id "Phchi.S5G119100.t1"; gene_id "Phchi.S5G119100"
Phchi.S5	AUGUSTUS	exon	7484795	7486447	.	-	.	transcript_id "Phchi.S5G119100.t1"; gene_id "Phchi.S5G119100"
Phchi.S5	AUGUSTUS	start_codon	7486445	7486447	.	-	0	transcript_id "Phchi.S5G119100.t1"; gene_id "Phchi.S5G119100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3928.t1 is derived from g1097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6471391	6471899	.	-	.	Phchi.S1G108700
Phchi.S1	AUGUSTUS	transcript	6471391	6471899	.	-	.	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	stop_codon	6471388	6471390	.	-	0	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	CDS	6471391	6471434	0.98	-	2	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	exon	6471391	6471434	.	-	.	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	intron	6471435	6471691	.	-	.	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	CDS	6471692	6471899	0.92	-	0	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	exon	6471692	6471899	.	-	.	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
Phchi.S1	AUGUSTUS	start_codon	6471897	6471899	.	-	0	transcript_id "Phchi.S1G108700.t1"; gene_id "Phchi.S1G108700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2143.t1 is derived from g9063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5040099	5040416	.	+	.	Phchi.S5G075200
Phchi.S5	AUGUSTUS	transcript	5040099	5040416	.	+	.	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	start_codon	5040099	5040101	.	+	0	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	CDS	5040099	5040249	0.81	+	0	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	exon	5040099	5040249	.	+	.	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	intron	5040250	5040342	.	+	.	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	CDS	5040343	5040416	1	+	2	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	exon	5040343	5040416	.	+	.	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
Phchi.S5	AUGUSTUS	stop_codon	5040417	5040419	.	+	0	transcript_id "Phchi.S5G075200.t1"; gene_id "Phchi.S5G075200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1172.t1 is derived from g10955.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8266984	8269850	.	+	.	Phchi.S6G113100
Phchi.S6	AUGUSTUS	transcript	8266984	8269850	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	start_codon	8266984	8266986	.	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8266984	8267109	0.99	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8266984	8267109	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267110	8267197	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267198	8267270	1	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267198	8267270	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267271	8267463	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267464	8267538	1	+	2	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267464	8267538	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267539	8267693	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267694	8267755	0.89	+	2	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267694	8267755	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267756	8267861	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267862	8267930	0.91	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267862	8267930	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267931	8268020	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268021	8268049	1	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268021	8268049	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8268050	8268140	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268141	8268345	1	+	1	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268141	8268345	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8268346	8268476	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268477	8268650	1	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268477	8268650	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8268651	8268731	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268732	8269850	0.97	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268732	8269850	.	+	.	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	stop_codon	8269851	8269853	.	+	0	transcript_id "Phchi.S6G113100.t1"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	transcript	8266984	8269850	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	start_codon	8266984	8266986	.	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8266984	8267109	0.94	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8266984	8267109	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267110	8267197	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267198	8267270	1	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267198	8267270	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267271	8267463	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267464	8267538	1	+	2	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267464	8267538	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267539	8267693	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267694	8267755	0.89	+	2	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267694	8267755	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267756	8267861	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8267862	8267930	0.9	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8267862	8267930	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8267931	8268020	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268021	8268049	1	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268021	8268049	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8268050	8268140	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268141	8268345	1	+	1	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268141	8268345	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8268346	8268476	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268477	8268650	1	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268477	8268650	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	intron	8268651	8268728	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	CDS	8268729	8269850	0.99	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	exon	8268729	8269850	.	+	.	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
Phchi.S6	AUGUSTUS	stop_codon	8269851	8269853	.	+	0	transcript_id "Phchi.S6G113100.t2"; gene_id "Phchi.S6G113100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg499.t1 is derived from g10281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3454667	3457939	.	+	.	Phchi.S6G045800
Phchi.S6	AUGUSTUS	transcript	3454667	3457939	.	+	.	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	start_codon	3454667	3454669	.	+	0	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	CDS	3454667	3455833	0.99	+	0	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	exon	3454667	3455833	.	+	.	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	intron	3455834	3456119	.	+	.	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	CDS	3456120	3456200	1	+	0	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	exon	3456120	3456200	.	+	.	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	intron	3456201	3456307	.	+	.	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	CDS	3456308	3457939	0.33	+	0	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	exon	3456308	3457939	.	+	.	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
Phchi.S6	AUGUSTUS	stop_codon	3457940	3457942	.	+	0	transcript_id "Phchi.S6G045800.t1"; gene_id "Phchi.S6G045800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15015.t1 is derived from g13483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16534634	16535128	.	+	.	Phchi.S3G233400
Phchi.S3	AUGUSTUS	transcript	16534634	16535128	.	+	.	transcript_id "Phchi.S3G233400.t1"; gene_id "Phchi.S3G233400"
Phchi.S3	AUGUSTUS	start_codon	16534634	16534636	.	+	0	transcript_id "Phchi.S3G233400.t1"; gene_id "Phchi.S3G233400"
Phchi.S3	AUGUSTUS	CDS	16534634	16535128	0.99	+	0	transcript_id "Phchi.S3G233400.t1"; gene_id "Phchi.S3G233400"
Phchi.S3	AUGUSTUS	exon	16534634	16535128	.	+	.	transcript_id "Phchi.S3G233400.t1"; gene_id "Phchi.S3G233400"
Phchi.S3	AUGUSTUS	stop_codon	16535129	16535131	.	+	0	transcript_id "Phchi.S3G233400.t1"; gene_id "Phchi.S3G233400"
# This transcript jg3147.t2 is derived from g316.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3148.t1 is derived from g317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1983435	1984169	.	+	.	Phchi.S1G030700
Phchi.S1	AUGUSTUS	transcript	1983435	1984169	.	+	.	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	start_codon	1983435	1983437	.	+	0	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	CDS	1983435	1983462	0.51	+	0	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	exon	1983435	1983462	.	+	.	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	intron	1983463	1983642	.	+	.	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	CDS	1983643	1983649	1	+	2	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	exon	1983643	1983649	.	+	.	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	intron	1983650	1983733	.	+	.	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	CDS	1983734	1984169	0.99	+	1	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	exon	1983734	1984169	.	+	.	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
Phchi.S1	AUGUSTUS	stop_codon	1984170	1984172	.	+	0	transcript_id "Phchi.S1G030700.t1"; gene_id "Phchi.S1G030700"
# This transcript jg1758.t2 is derived from g8678.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1759.t1 is derived from g8679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2908504	2909257	.	-	.	Phchi.S5G036800
Phchi.S5	AUGUSTUS	transcript	2908504	2909257	.	-	.	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	stop_codon	2908501	2908503	.	-	0	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	CDS	2908504	2909111	1	-	2	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	exon	2908504	2909111	.	-	.	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	intron	2909112	2909187	.	-	.	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	CDS	2909188	2909257	1	-	0	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	exon	2909188	2909257	.	-	.	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
Phchi.S5	AUGUSTUS	start_codon	2909255	2909257	.	-	0	transcript_id "Phchi.S5G036800.t1"; gene_id "Phchi.S5G036800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg864.t1 is derived from g10646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5989185	5990233	.	+	.	Phchi.S6G082300
Phchi.S6	AUGUSTUS	transcript	5989185	5990233	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	start_codon	5989185	5989187	.	+	0	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	CDS	5989185	5989272	0.85	+	0	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	exon	5989185	5989272	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	intron	5989273	5989379	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	CDS	5989380	5989480	1	+	2	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	exon	5989380	5989480	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	intron	5989481	5989624	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	CDS	5989625	5989708	1	+	0	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	exon	5989625	5989708	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	intron	5989709	5989809	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	CDS	5989810	5989920	1	+	0	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	exon	5989810	5989920	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	intron	5989921	5990191	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	CDS	5990192	5990233	1	+	0	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	exon	5990192	5990233	.	+	.	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
Phchi.S6	AUGUSTUS	stop_codon	5990234	5990236	.	+	0	transcript_id "Phchi.S6G082300.t1"; gene_id "Phchi.S6G082300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3407.t1 is derived from g576.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3373767	3375246	.	+	.	Phchi.S1G056600
Phchi.S1	AUGUSTUS	transcript	3373767	3375246	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	start_codon	3373767	3373769	.	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3373767	3374041	1	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3373767	3374041	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3374042	3374268	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3374269	3374353	1	+	1	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3374269	3374353	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3374354	3374429	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3374430	3374495	0.99	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3374430	3374495	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3374496	3374672	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3374673	3374717	0.67	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3374673	3374717	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3374718	3374808	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3374809	3374850	0.95	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3374809	3374850	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3374851	3374947	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3374948	3375007	1	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3374948	3375007	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3375008	3375091	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3375092	3375103	1	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3375092	3375103	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	intron	3375104	3375195	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	CDS	3375196	3375246	1	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	exon	3375196	3375246	.	+	.	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
Phchi.S1	AUGUSTUS	stop_codon	3375247	3375249	.	+	0	transcript_id "Phchi.S1G056600.t1"; gene_id "Phchi.S1G056600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8021.t1 is derived from g5196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32500144	32502069	.	-	.	Phchi.S1G518000
Phchi.S1	AUGUSTUS	transcript	32500144	32502069	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	stop_codon	32500141	32500143	.	-	0	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32500144	32500515	0.85	-	0	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32500144	32500515	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	intron	32500516	32500598	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32500599	32500649	0.85	-	0	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32500599	32500649	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	intron	32500650	32500771	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32500772	32500835	1	-	1	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32500772	32500835	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	intron	32500836	32501022	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32501023	32501136	1	-	1	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32501023	32501136	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	intron	32501137	32501502	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32501503	32501596	1	-	2	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32501503	32501596	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	intron	32501597	32501706	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32501707	32501779	1	-	0	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32501707	32501779	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	intron	32501780	32501883	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	CDS	32501884	32502069	0.82	-	0	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	exon	32501884	32502069	.	-	.	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
Phchi.S1	AUGUSTUS	start_codon	32502067	32502069	.	-	0	transcript_id "Phchi.S1G518000.t1"; gene_id "Phchi.S1G518000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7985.t1 is derived from g5160.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32258106	32260943	.	+	.	Phchi.S1G514400
Phchi.S1	AUGUSTUS	transcript	32258106	32260943	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	start_codon	32258106	32258108	.	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32258106	32258264	0.96	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32258106	32258264	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32258265	32258457	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32258458	32258892	0.78	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32258458	32258892	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32258893	32259022	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259023	32259060	0.92	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259023	32259060	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259061	32259131	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259132	32259211	0.92	+	1	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259132	32259211	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259212	32259350	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259351	32259621	0.91	+	2	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259351	32259621	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259622	32259720	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259721	32259793	1	+	1	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259721	32259793	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259794	32259987	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259988	32260108	1	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259988	32260108	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32260109	32260354	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32260355	32260434	1	+	2	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32260355	32260434	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32260435	32260658	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32260659	32260943	0.99	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32260659	32260943	.	+	.	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	stop_codon	32260944	32260946	.	+	0	transcript_id "Phchi.S1G514400.t1"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	transcript	32258106	32260943	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	start_codon	32258106	32258108	.	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32258106	32258264	0.96	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32258106	32258264	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32258265	32258457	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32258458	32258892	0.67	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32258458	32258892	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32258893	32259022	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259023	32259060	0.91	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259023	32259060	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259061	32259131	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259132	32259211	0.91	+	1	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259132	32259211	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259212	32259350	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259351	32259621	0.91	+	2	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259351	32259621	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259622	32259720	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259721	32259793	1	+	1	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259721	32259793	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32259794	32259987	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32259988	32260078	1	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32259988	32260078	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32260079	32260354	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32260355	32260434	1	+	2	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32260355	32260434	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	intron	32260435	32260658	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	CDS	32260659	32260943	1	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	exon	32260659	32260943	.	+	.	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
Phchi.S1	AUGUSTUS	stop_codon	32260944	32260946	.	+	0	transcript_id "Phchi.S1G514400.t2"; gene_id "Phchi.S1G514400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10952.t1 is derived from g15002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3265179	3266285	.	+	.	Phchi.S4G053400
Phchi.S4	AUGUSTUS	transcript	3265179	3266285	.	+	.	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	start_codon	3265179	3265181	.	+	0	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	CDS	3265179	3265818	0.96	+	0	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	exon	3265179	3265818	.	+	.	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	intron	3265819	3265906	.	+	.	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	CDS	3265907	3266077	0.54	+	2	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	exon	3265907	3266077	.	+	.	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	intron	3266078	3266214	.	+	.	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	CDS	3266215	3266285	0.53	+	2	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	exon	3266215	3266285	.	+	.	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
Phchi.S4	AUGUSTUS	stop_codon	3266286	3266288	.	+	0	transcript_id "Phchi.S4G053400.t1"; gene_id "Phchi.S4G053400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4831.t1 is derived from g2001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13039536	13041073	.	-	.	Phchi.S1G199000
Phchi.S1	AUGUSTUS	transcript	13039536	13041073	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	stop_codon	13039533	13039535	.	-	0	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	CDS	13039536	13039715	0.63	-	0	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	exon	13039536	13039715	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	intron	13039716	13039929	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	CDS	13039930	13040305	0.45	-	1	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	exon	13039930	13040305	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	intron	13040306	13040397	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	CDS	13040398	13040684	0.71	-	0	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	exon	13040398	13040684	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	intron	13040685	13040794	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	CDS	13040795	13041073	0.3	-	0	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	exon	13040795	13041073	.	-	.	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
Phchi.S1	AUGUSTUS	start_codon	13041071	13041073	.	-	0	transcript_id "Phchi.S1G199000.t1"; gene_id "Phchi.S1G199000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5927.t1 is derived from g3098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19893017	19896386	.	-	.	Phchi.S1G308600
Phchi.S1	AUGUSTUS	transcript	19893017	19896386	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	stop_codon	19893014	19893016	.	-	0	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	CDS	19893017	19893044	0.02	-	1	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	exon	19893017	19893044	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	intron	19893045	19893508	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	CDS	19893509	19893598	1	-	1	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	exon	19893509	19893598	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	intron	19893599	19895287	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	CDS	19895288	19895374	0.01	-	1	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	exon	19895288	19895374	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	intron	19895375	19895577	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	CDS	19895578	19895899	0.01	-	2	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	exon	19895578	19895899	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	intron	19895900	19896160	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	CDS	19896161	19896386	0.03	-	0	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	exon	19896161	19896386	.	-	.	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
Phchi.S1	AUGUSTUS	start_codon	19896384	19896386	.	-	0	transcript_id "Phchi.S1G308600.t1"; gene_id "Phchi.S1G308600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2466.t1 is derived from g9386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6803694	6807150	.	-	.	Phchi.S5G107500
Phchi.S5	AUGUSTUS	transcript	6803694	6807150	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	stop_codon	6803691	6803693	.	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6803694	6803948	0.22	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6803694	6803948	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6803949	6804023	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6804024	6804242	0.82	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6804024	6804242	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6804243	6804316	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6804317	6804388	0.64	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6804317	6804388	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6804389	6804480	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6804481	6804717	0.98	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6804481	6804717	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6804718	6804849	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6804850	6804929	0.98	-	2	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6804850	6804929	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6804930	6805006	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6805007	6805082	0.96	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6805007	6805082	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6805083	6805225	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6805226	6805416	1	-	2	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6805226	6805416	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6805417	6805495	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6805496	6805610	1	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6805496	6805610	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6805611	6805844	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6805845	6805958	1	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6805845	6805958	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6805959	6806084	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6806085	6806191	1	-	2	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6806085	6806191	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6806192	6806272	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6806273	6806347	1	-	2	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6806273	6806347	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6806348	6806447	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6806448	6806649	0.51	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6806448	6806649	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6806650	6806755	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6806756	6806836	0.51	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6806756	6806836	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	intron	6806837	6807015	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	CDS	6807016	6807150	0.65	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	exon	6807016	6807150	.	-	.	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
Phchi.S5	AUGUSTUS	start_codon	6807148	6807150	.	-	0	transcript_id "Phchi.S5G107500.t1"; gene_id "Phchi.S5G107500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14411.t1 is derived from g12879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12692727	12695786	.	-	.	Phchi.S3G173000
Phchi.S3	AUGUSTUS	transcript	12692727	12695786	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	stop_codon	12692724	12692726	.	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12692727	12692796	1	-	1	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12692727	12692796	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12692797	12692875	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12692876	12692994	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12692876	12692994	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12692995	12693090	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12693091	12693198	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12693091	12693198	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12693199	12693321	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12693322	12693390	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12693322	12693390	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12693391	12693476	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12693477	12693571	1	-	2	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12693477	12693571	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12693572	12693690	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12693691	12693895	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12693691	12693895	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12693896	12694038	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12694039	12694125	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12694039	12694125	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12694126	12694211	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12694212	12694326	1	-	1	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12694212	12694326	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12694327	12694422	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12694423	12694529	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12694423	12694529	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12694530	12694636	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12694637	12694729	0.99	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12694637	12694729	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12694730	12694820	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12694821	12694868	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12694821	12694868	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12694869	12695003	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12695004	12695155	1	-	2	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12695004	12695155	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12695156	12695260	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12695261	12695396	0.99	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12695261	12695396	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12695397	12695510	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12695511	12695574	1	-	1	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12695511	12695574	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	intron	12695575	12695652	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	CDS	12695653	12695786	1	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	exon	12695653	12695786	.	-	.	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
Phchi.S3	AUGUSTUS	start_codon	12695784	12695786	.	-	0	transcript_id "Phchi.S3G173000.t1"; gene_id "Phchi.S3G173000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4993.t1 is derived from g2163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13930774	13931832	.	-	.	Phchi.S1G215200
Phchi.S1	AUGUSTUS	transcript	13930774	13931832	.	-	.	transcript_id "Phchi.S1G215200.t1"; gene_id "Phchi.S1G215200"
Phchi.S1	AUGUSTUS	stop_codon	13930771	13930773	.	-	0	transcript_id "Phchi.S1G215200.t1"; gene_id "Phchi.S1G215200"
Phchi.S1	AUGUSTUS	CDS	13930774	13931832	0.54	-	0	transcript_id "Phchi.S1G215200.t1"; gene_id "Phchi.S1G215200"
Phchi.S1	AUGUSTUS	exon	13930774	13931832	.	-	.	transcript_id "Phchi.S1G215200.t1"; gene_id "Phchi.S1G215200"
Phchi.S1	AUGUSTUS	start_codon	13931830	13931832	.	-	0	transcript_id "Phchi.S1G215200.t1"; gene_id "Phchi.S1G215200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4776.t1 is derived from g1946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12776550	12777437	.	-	.	Phchi.S1G193500
Phchi.S1	AUGUSTUS	transcript	12776550	12777437	.	-	.	transcript_id "Phchi.S1G193500.t1"; gene_id "Phchi.S1G193500"
Phchi.S1	AUGUSTUS	stop_codon	12776547	12776549	.	-	0	transcript_id "Phchi.S1G193500.t1"; gene_id "Phchi.S1G193500"
Phchi.S1	AUGUSTUS	CDS	12776550	12777437	0.41	-	0	transcript_id "Phchi.S1G193500.t1"; gene_id "Phchi.S1G193500"
Phchi.S1	AUGUSTUS	exon	12776550	12777437	.	-	.	transcript_id "Phchi.S1G193500.t1"; gene_id "Phchi.S1G193500"
Phchi.S1	AUGUSTUS	start_codon	12777435	12777437	.	-	0	transcript_id "Phchi.S1G193500.t1"; gene_id "Phchi.S1G193500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12822.t1 is derived from g11287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2569019	2571168	.	+	.	Phchi.S3G014100
Phchi.S3	AUGUSTUS	transcript	2569019	2571168	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	start_codon	2569019	2569021	.	+	0	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	CDS	2569019	2569135	0.84	+	0	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	exon	2569019	2569135	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	intron	2569136	2569244	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	CDS	2569245	2569761	0.39	+	0	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	exon	2569245	2569761	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	intron	2569762	2570064	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	CDS	2570065	2570256	0.51	+	2	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	exon	2570065	2570256	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	intron	2570257	2570475	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	CDS	2570476	2570860	0.5	+	2	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	exon	2570476	2570860	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	intron	2570861	2571164	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	CDS	2571165	2571168	0.62	+	1	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	exon	2571165	2571168	.	+	.	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
Phchi.S3	AUGUSTUS	stop_codon	2571169	2571171	.	+	0	transcript_id "Phchi.S3G014100.t1"; gene_id "Phchi.S3G014100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5143.t1 is derived from g2313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15133965	15135811	.	-	.	Phchi.S1G230200
Phchi.S1	AUGUSTUS	transcript	15133965	15135811	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	stop_codon	15133962	15133964	.	-	0	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15133965	15134347	1	-	2	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15133965	15134347	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	intron	15134348	15134430	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15134431	15134534	1	-	1	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15134431	15134534	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	intron	15134535	15134636	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15134637	15134762	0.99	-	1	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15134637	15134762	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	intron	15134763	15134864	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15134865	15134998	1	-	0	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15134865	15134998	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	intron	15134999	15135133	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15135134	15135271	1	-	0	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15135134	15135271	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	intron	15135272	15135374	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15135375	15135504	1	-	1	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15135375	15135504	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	intron	15135505	15135599	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	CDS	15135600	15135811	0.84	-	0	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	exon	15135600	15135811	.	-	.	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
Phchi.S1	AUGUSTUS	start_codon	15135809	15135811	.	-	0	transcript_id "Phchi.S1G230200.t1"; gene_id "Phchi.S1G230200"
# This transcript jg8064.t2 is derived from g5239.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8065.t1 is derived from g5240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32761565	32765256	.	+	.	Phchi.S1G522400
Phchi.S1	AUGUSTUS	transcript	32761565	32765256	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	start_codon	32761565	32761567	.	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32761565	32761649	0.73	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32761565	32761649	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32761650	32761781	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32761782	32762084	1	+	2	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32761782	32762084	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32762085	32762181	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32762182	32762281	0.51	+	2	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32762182	32762281	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32762282	32762364	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32762365	32762522	0.51	+	1	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32762365	32762522	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32762523	32762613	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32762614	32762720	1	+	2	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32762614	32762720	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32762721	32763088	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32763089	32763238	0.33	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32763089	32763238	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32763239	32763372	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32763373	32763478	0.52	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32763373	32763478	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32763479	32763567	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32763568	32763918	0.93	+	2	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32763568	32763918	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32763919	32764115	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32764116	32764291	1	+	2	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32764116	32764291	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32764292	32764440	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32764441	32764541	1	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32764441	32764541	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32764542	32764676	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32764677	32764713	0.72	+	1	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32764677	32764713	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32764714	32764882	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32764883	32765113	0.62	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32764883	32765113	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	intron	32765114	32765253	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	CDS	32765254	32765256	0.95	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	exon	32765254	32765256	.	+	.	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
Phchi.S1	AUGUSTUS	stop_codon	32765257	32765259	.	+	0	transcript_id "Phchi.S1G522400.t1"; gene_id "Phchi.S1G522400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8243.t1 is derived from g5418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34673264	34674378	.	+	.	Phchi.S1G540200
Phchi.S1	AUGUSTUS	transcript	34673264	34674378	.	+	.	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	start_codon	34673264	34673266	.	+	0	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	CDS	34673264	34673791	0.7	+	0	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	exon	34673264	34673791	.	+	.	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	intron	34673792	34673868	.	+	.	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	CDS	34673869	34674378	0.98	+	0	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	exon	34673869	34674378	.	+	.	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
Phchi.S1	AUGUSTUS	stop_codon	34674379	34674381	.	+	0	transcript_id "Phchi.S1G540200.t1"; gene_id "Phchi.S1G540200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6442.t1 is derived from g3614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23041567	23042507	.	-	.	Phchi.S1G360100
Phchi.S1	AUGUSTUS	transcript	23041911	23042507	.	-	.	transcript_id "Phchi.S1G360100.t1"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	stop_codon	23041908	23041910	.	-	0	transcript_id "Phchi.S1G360100.t1"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	CDS	23041911	23042507	1	-	0	transcript_id "Phchi.S1G360100.t1"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	exon	23041911	23042507	.	-	.	transcript_id "Phchi.S1G360100.t1"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	start_codon	23042505	23042507	.	-	0	transcript_id "Phchi.S1G360100.t1"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	transcript	23041567	23042507	.	-	.	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	stop_codon	23041564	23041566	.	-	0	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	CDS	23041567	23041941	0.52	-	0	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	exon	23041567	23041941	.	-	.	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	intron	23041942	23042081	.	-	.	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	CDS	23042082	23042507	0.49	-	0	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	exon	23042082	23042507	.	-	.	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
Phchi.S1	AUGUSTUS	start_codon	23042505	23042507	.	-	0	transcript_id "Phchi.S1G360100.t2"; gene_id "Phchi.S1G360100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5841.t1 is derived from g3011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19286439	19288097	.	-	.	Phchi.S1G300000
Phchi.S1	AUGUSTUS	transcript	19286439	19288097	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	stop_codon	19286436	19286438	.	-	0	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	CDS	19286439	19286497	0.98	-	2	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	exon	19286439	19286497	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	intron	19286498	19286574	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	CDS	19286575	19286652	0.98	-	2	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	exon	19286575	19286652	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	intron	19286653	19286780	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	CDS	19286781	19286919	0.89	-	0	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	exon	19286781	19286919	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	intron	19286920	19287002	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	CDS	19287003	19287341	0.68	-	0	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	exon	19287003	19287341	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	intron	19287342	19287466	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	CDS	19287467	19287633	0.97	-	2	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	exon	19287467	19287633	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	intron	19287634	19287847	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	CDS	19287848	19288097	0.79	-	0	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	exon	19287848	19288097	.	-	.	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
Phchi.S1	AUGUSTUS	start_codon	19288095	19288097	.	-	0	transcript_id "Phchi.S1G300000.t1"; gene_id "Phchi.S1G300000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg797.t1 is derived from g10579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5624450	5625619	.	+	.	Phchi.S6G075600
Phchi.S6	AUGUSTUS	transcript	5624450	5625619	.	+	.	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	start_codon	5624450	5624452	.	+	0	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	CDS	5624450	5624874	0.56	+	0	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	exon	5624450	5624874	.	+	.	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	intron	5624875	5625070	.	+	.	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	CDS	5625071	5625304	1	+	1	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	exon	5625071	5625304	.	+	.	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	intron	5625305	5625402	.	+	.	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	CDS	5625403	5625619	0.99	+	1	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	exon	5625403	5625619	.	+	.	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
Phchi.S6	AUGUSTUS	stop_codon	5625620	5625622	.	+	0	transcript_id "Phchi.S6G075600.t1"; gene_id "Phchi.S6G075600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14561.t1 is derived from g13029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13473449	13474198	.	+	.	Phchi.S3G188000
Phchi.S3	AUGUSTUS	transcript	13473449	13474198	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	start_codon	13473449	13473451	.	+	0	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	CDS	13473449	13473488	0.97	+	0	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	exon	13473449	13473488	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	intron	13473489	13473770	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	CDS	13473771	13473897	0.97	+	2	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	exon	13473771	13473897	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	intron	13473898	13473993	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	CDS	13473994	13474030	0.97	+	1	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	exon	13473994	13474030	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	intron	13474031	13474129	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	CDS	13474130	13474198	0.69	+	0	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	exon	13474130	13474198	.	+	.	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
Phchi.S3	AUGUSTUS	stop_codon	13474199	13474201	.	+	0	transcript_id "Phchi.S3G188000.t1"; gene_id "Phchi.S3G188000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14261.t1 is derived from g12728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11792272	11794663	.	-	.	Phchi.S3G158000
Phchi.S3	AUGUSTUS	transcript	11792272	11794663	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	stop_codon	11792269	11792271	.	-	0	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11792272	11792275	1	-	1	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11792272	11792275	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11792276	11792395	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11792396	11792967	0.55	-	0	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11792396	11792967	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11792968	11793173	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11793174	11793234	0.64	-	1	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11793174	11793234	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11793235	11793368	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11793369	11793452	1	-	1	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11793369	11793452	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11793453	11793547	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11793548	11793595	1	-	1	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11793548	11793595	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11793596	11793718	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11793719	11793761	1	-	2	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11793719	11793761	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11793762	11794168	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11794169	11794226	1	-	0	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11794169	11794226	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11794227	11794326	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11794327	11794453	1	-	1	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11794327	11794453	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	intron	11794454	11794538	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	CDS	11794539	11794663	0.95	-	0	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	exon	11794539	11794663	.	-	.	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
Phchi.S3	AUGUSTUS	start_codon	11794661	11794663	.	-	0	transcript_id "Phchi.S3G158000.t1"; gene_id "Phchi.S3G158000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8955.t1 is derived from g6130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38841185	38841848	.	-	.	Phchi.S1G611400
Phchi.S1	AUGUSTUS	transcript	38841185	38841848	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	stop_codon	38841182	38841184	.	-	0	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	CDS	38841185	38841271	1	-	0	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	exon	38841185	38841271	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	intron	38841272	38841366	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	CDS	38841367	38841419	1	-	2	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	exon	38841367	38841419	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	intron	38841420	38841510	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	CDS	38841511	38841582	1	-	2	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	exon	38841511	38841582	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	intron	38841583	38841679	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	CDS	38841680	38841761	1	-	0	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	exon	38841680	38841761	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	intron	38841762	38841845	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	CDS	38841846	38841848	0.96	-	0	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	exon	38841846	38841848	.	-	.	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
Phchi.S1	AUGUSTUS	start_codon	38841846	38841848	.	-	0	transcript_id "Phchi.S1G611400.t1"; gene_id "Phchi.S1G611400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2724.t1 is derived from g9644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8448546	8450328	.	+	.	Phchi.S5G133300
Phchi.S5	AUGUSTUS	transcript	8448546	8450328	.	+	.	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	start_codon	8448546	8448548	.	+	0	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	CDS	8448546	8448805	0.98	+	0	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	exon	8448546	8448805	.	+	.	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	intron	8448806	8448899	.	+	.	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	CDS	8448900	8450328	1	+	1	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	exon	8448900	8450328	.	+	.	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
Phchi.S5	AUGUSTUS	stop_codon	8450329	8450331	.	+	0	transcript_id "Phchi.S5G133300.t1"; gene_id "Phchi.S5G133300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4175.t1 is derived from g1344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8761923	8763908	.	+	.	Phchi.S1G133400
Phchi.S1	AUGUSTUS	transcript	8761923	8763908	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	start_codon	8761923	8761925	.	+	0	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	CDS	8761923	8761967	0.89	+	0	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	exon	8761923	8761967	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	intron	8761968	8762045	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	CDS	8762046	8762246	0.97	+	0	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	exon	8762046	8762246	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	intron	8762247	8762370	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	CDS	8762371	8763255	0.79	+	0	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	exon	8762371	8763255	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	intron	8763256	8763338	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	CDS	8763339	8763908	0.78	+	0	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	exon	8763339	8763908	.	+	.	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
Phchi.S1	AUGUSTUS	stop_codon	8763909	8763911	.	+	0	transcript_id "Phchi.S1G133400.t1"; gene_id "Phchi.S1G133400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10253.t1 is derived from g7429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46683105	46684842	.	-	.	Phchi.S1G741200
Phchi.S1	AUGUSTUS	transcript	46683105	46684842	.	-	.	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	stop_codon	46683102	46683104	.	-	0	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	CDS	46683105	46683691	1	-	2	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	exon	46683105	46683691	.	-	.	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	intron	46683692	46683783	.	-	.	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	CDS	46683784	46683899	1	-	1	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	exon	46683784	46683899	.	-	.	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	intron	46683900	46684030	.	-	.	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	CDS	46684031	46684842	0.77	-	0	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	exon	46684031	46684842	.	-	.	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
Phchi.S1	AUGUSTUS	start_codon	46684840	46684842	.	-	0	transcript_id "Phchi.S1G741200.t1"; gene_id "Phchi.S1G741200"
# This transcript jg8196.t2 is derived from g5371.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8197.t1 is derived from g5372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34376997	34378186	.	+	.	Phchi.S1G535600
Phchi.S1	AUGUSTUS	transcript	34376997	34378186	.	+	.	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	start_codon	34376997	34376999	.	+	0	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	CDS	34376997	34377762	0.41	+	0	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	exon	34376997	34377762	.	+	.	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	intron	34377763	34377842	.	+	.	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	CDS	34377843	34378186	0.35	+	2	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	exon	34377843	34378186	.	+	.	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
Phchi.S1	AUGUSTUS	stop_codon	34378187	34378189	.	+	0	transcript_id "Phchi.S1G535600.t1"; gene_id "Phchi.S1G535600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg703.t1 is derived from g10485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4976782	4977347	.	-	.	Phchi.S6G066200
Phchi.S6	AUGUSTUS	transcript	4976782	4977347	.	-	.	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	stop_codon	4976779	4976781	.	-	0	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	CDS	4976782	4976862	1	-	0	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	exon	4976782	4976862	.	-	.	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	intron	4976863	4977044	.	-	.	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	CDS	4977045	4977347	0.58	-	0	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	exon	4977045	4977347	.	-	.	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
Phchi.S6	AUGUSTUS	start_codon	4977345	4977347	.	-	0	transcript_id "Phchi.S6G066200.t1"; gene_id "Phchi.S6G066200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12391.t1 is derived from g8068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	16401642	16401962	.	+	.	Phchi.S2G047100
Phchi.S2	AUGUSTUS	transcript	16401642	16401962	.	+	.	transcript_id "Phchi.S2G047100.t1"; gene_id "Phchi.S2G047100"
Phchi.S2	AUGUSTUS	start_codon	16401642	16401644	.	+	0	transcript_id "Phchi.S2G047100.t1"; gene_id "Phchi.S2G047100"
Phchi.S2	AUGUSTUS	CDS	16401642	16401962	0.75	+	0	transcript_id "Phchi.S2G047100.t1"; gene_id "Phchi.S2G047100"
Phchi.S2	AUGUSTUS	exon	16401642	16401962	.	+	.	transcript_id "Phchi.S2G047100.t1"; gene_id "Phchi.S2G047100"
Phchi.S2	AUGUSTUS	stop_codon	16401963	16401965	.	+	0	transcript_id "Phchi.S2G047100.t1"; gene_id "Phchi.S2G047100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12385.t1 is derived from g8062.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15344095	15345667	.	+	.	Phchi.S2G046500
Phchi.S2	AUGUSTUS	transcript	15344095	15345667	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	start_codon	15344095	15344097	.	+	0	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15344095	15344181	1	+	0	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15344095	15344181	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15344182	15344792	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15344793	15345011	1	+	0	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15344793	15345011	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345012	15345110	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345111	15345259	0.99	+	0	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345111	15345259	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345260	15345403	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345404	15345532	1	+	1	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345404	15345532	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345533	15345624	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345625	15345667	0.99	+	1	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345625	15345667	.	+	.	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	stop_codon	15345668	15345670	.	+	0	transcript_id "Phchi.S2G046500.t1"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	transcript	15344095	15345667	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	start_codon	15344095	15344097	.	+	0	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15344095	15344235	1	+	0	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15344095	15344235	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15344236	15344792	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15344793	15345011	1	+	0	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15344793	15345011	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345012	15345110	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345111	15345259	0.96	+	0	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345111	15345259	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345260	15345403	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345404	15345532	0.99	+	1	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345404	15345532	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345533	15345624	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345625	15345667	0.98	+	1	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345625	15345667	.	+	.	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	stop_codon	15345668	15345670	.	+	0	transcript_id "Phchi.S2G046500.t2"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	transcript	15344095	15345432	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	start_codon	15344095	15344097	.	+	0	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15344095	15344181	0.99	+	0	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15344095	15344181	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15344182	15344792	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15344793	15345011	1	+	0	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15344793	15345011	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345012	15345110	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345111	15345259	0.95	+	0	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345111	15345259	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	intron	15345260	15345425	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	CDS	15345426	15345432	0.78	+	1	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	exon	15345426	15345432	.	+	.	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
Phchi.S2	AUGUSTUS	stop_codon	15345433	15345435	.	+	0	transcript_id "Phchi.S2G046500.t3"; gene_id "Phchi.S2G046500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11219.t1 is derived from g15269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4843060	4843620	.	-	.	Phchi.S4G080100
Phchi.S4	AUGUSTUS	transcript	4843060	4843620	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	stop_codon	4843057	4843059	.	-	0	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	CDS	4843060	4843099	1	-	1	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	exon	4843060	4843099	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	intron	4843100	4843205	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	CDS	4843206	4843273	1	-	0	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	exon	4843206	4843273	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	intron	4843274	4843363	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	CDS	4843364	4843415	0.58	-	1	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	exon	4843364	4843415	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	intron	4843416	4843537	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	CDS	4843538	4843620	0.54	-	0	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	exon	4843538	4843620	.	-	.	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
Phchi.S4	AUGUSTUS	start_codon	4843618	4843620	.	-	0	transcript_id "Phchi.S4G080100.t1"; gene_id "Phchi.S4G080100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6898.t1 is derived from g4070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25876739	25882244	.	-	.	Phchi.S1G405700
Phchi.S1	AUGUSTUS	transcript	25876739	25882244	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	stop_codon	25876736	25876738	.	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25876739	25877053	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25876739	25877053	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25877054	25877162	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25877163	25877362	1	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25877163	25877362	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25877363	25877478	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25877479	25877671	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25877479	25877671	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25877672	25877773	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25877774	25878051	0.8	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25877774	25878051	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25878052	25878144	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25878145	25878190	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25878145	25878190	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25878191	25878312	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25878313	25878387	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25878313	25878387	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25878388	25878535	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25878536	25878656	1	-	1	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25878536	25878656	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25878657	25878771	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25878772	25878896	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25878772	25878896	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25878897	25878970	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25878971	25879063	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25878971	25879063	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25879064	25879205	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25879206	25879339	0.99	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25879206	25879339	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25879340	25879441	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25879442	25879570	0.97	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25879442	25879570	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25879571	25879648	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25879649	25879741	1	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25879649	25879741	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25879742	25879823	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25879824	25879933	1	-	1	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25879824	25879933	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25879934	25880024	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25880025	25880151	1	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25880025	25880151	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25880152	25880281	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25880282	25880501	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25880282	25880501	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25880502	25880597	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25880598	25880769	1	-	1	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25880598	25880769	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25880770	25880942	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25880943	25881040	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25880943	25881040	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25881041	25881176	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25881177	25881244	1	-	2	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25881177	25881244	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25881245	25881336	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25881337	25881454	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25881337	25881454	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25881455	25881602	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25881603	25881666	1	-	1	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25881603	25881666	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25881667	25881772	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25881773	25881816	1	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25881773	25881816	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	intron	25881817	25882187	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	CDS	25882188	25882244	0.73	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	exon	25882188	25882244	.	-	.	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
Phchi.S1	AUGUSTUS	start_codon	25882242	25882244	.	-	0	transcript_id "Phchi.S1G405700.t1"; gene_id "Phchi.S1G405700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11817.t1 is derived from g15869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8386790	8390139	.	+	.	Phchi.S4G139900
Phchi.S4	AUGUSTUS	transcript	8386790	8390139	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	start_codon	8386790	8386792	.	+	0	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	CDS	8386790	8386887	0.93	+	0	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	exon	8386790	8386887	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	intron	8386888	8387098	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	CDS	8387099	8387124	0.99	+	1	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	exon	8387099	8387124	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	intron	8387125	8387192	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	CDS	8387193	8387265	0.86	+	2	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	exon	8387193	8387265	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	intron	8387266	8387365	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	CDS	8387366	8388626	0.58	+	1	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	exon	8387366	8388626	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	intron	8388627	8388730	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	CDS	8388731	8389147	0.36	+	0	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	exon	8388731	8389147	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	intron	8389148	8389236	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	CDS	8389237	8390139	0.61	+	0	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	exon	8389237	8390139	.	+	.	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
Phchi.S4	AUGUSTUS	stop_codon	8390140	8390142	.	+	0	transcript_id "Phchi.S4G139900.t1"; gene_id "Phchi.S4G139900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8465.t1 is derived from g5640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36060411	36061283	.	+	.	Phchi.S1G562400
Phchi.S1	AUGUSTUS	transcript	36060411	36061283	.	+	.	transcript_id "Phchi.S1G562400.t1"; gene_id "Phchi.S1G562400"
Phchi.S1	AUGUSTUS	start_codon	36060411	36060413	.	+	0	transcript_id "Phchi.S1G562400.t1"; gene_id "Phchi.S1G562400"
Phchi.S1	AUGUSTUS	CDS	36060411	36061283	0.94	+	0	transcript_id "Phchi.S1G562400.t1"; gene_id "Phchi.S1G562400"
Phchi.S1	AUGUSTUS	exon	36060411	36061283	.	+	.	transcript_id "Phchi.S1G562400.t1"; gene_id "Phchi.S1G562400"
Phchi.S1	AUGUSTUS	stop_codon	36061284	36061286	.	+	0	transcript_id "Phchi.S1G562400.t1"; gene_id "Phchi.S1G562400"
# This transcript jg13254.t2 is derived from g11719.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13255.t1 is derived from g11720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4938078	4941236	.	-	.	Phchi.S3G057400
Phchi.S3	AUGUSTUS	transcript	4938078	4941236	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	stop_codon	4938075	4938077	.	-	0	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4938078	4938143	1	-	0	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4938078	4938143	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4938144	4938235	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4938236	4938371	1	-	1	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4938236	4938371	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4938372	4938596	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4938597	4938694	1	-	0	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4938597	4938694	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4938695	4938946	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4938947	4939062	1	-	2	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4938947	4939062	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4939063	4939328	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4939329	4939501	1	-	1	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4939329	4939501	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4939502	4939642	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4939643	4939728	1	-	0	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4939643	4939728	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4939729	4939895	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4939896	4940905	0.6	-	2	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4939896	4940905	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4940906	4941084	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4941085	4941122	0.61	-	1	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4941085	4941122	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	intron	4941123	4941219	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	CDS	4941220	4941236	0.93	-	0	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	exon	4941220	4941236	.	-	.	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
Phchi.S3	AUGUSTUS	start_codon	4941234	4941236	.	-	0	transcript_id "Phchi.S3G057400.t1"; gene_id "Phchi.S3G057400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4616.t1 is derived from g1786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11423312	11423704	.	-	.	Phchi.S1G177500
Phchi.S1	AUGUSTUS	transcript	11423312	11423704	.	-	.	transcript_id "Phchi.S1G177500.t1"; gene_id "Phchi.S1G177500"
Phchi.S1	AUGUSTUS	stop_codon	11423309	11423311	.	-	0	transcript_id "Phchi.S1G177500.t1"; gene_id "Phchi.S1G177500"
Phchi.S1	AUGUSTUS	CDS	11423312	11423704	0.56	-	0	transcript_id "Phchi.S1G177500.t1"; gene_id "Phchi.S1G177500"
Phchi.S1	AUGUSTUS	exon	11423312	11423704	.	-	.	transcript_id "Phchi.S1G177500.t1"; gene_id "Phchi.S1G177500"
Phchi.S1	AUGUSTUS	start_codon	11423702	11423704	.	-	0	transcript_id "Phchi.S1G177500.t1"; gene_id "Phchi.S1G177500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2644.t1 is derived from g9564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7941646	7941984	.	-	.	Phchi.S5G125300
Phchi.S5	AUGUSTUS	transcript	7941646	7941984	.	-	.	transcript_id "Phchi.S5G125300.t1"; gene_id "Phchi.S5G125300"
Phchi.S5	AUGUSTUS	stop_codon	7941643	7941645	.	-	0	transcript_id "Phchi.S5G125300.t1"; gene_id "Phchi.S5G125300"
Phchi.S5	AUGUSTUS	CDS	7941646	7941984	0.85	-	0	transcript_id "Phchi.S5G125300.t1"; gene_id "Phchi.S5G125300"
Phchi.S5	AUGUSTUS	exon	7941646	7941984	.	-	.	transcript_id "Phchi.S5G125300.t1"; gene_id "Phchi.S5G125300"
Phchi.S5	AUGUSTUS	start_codon	7941982	7941984	.	-	0	transcript_id "Phchi.S5G125300.t1"; gene_id "Phchi.S5G125300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2510.t1 is derived from g9430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7069598	7071740	.	-	.	Phchi.S5G111900
Phchi.S5	AUGUSTUS	transcript	7069598	7071740	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	stop_codon	7069595	7069597	.	-	0	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7069598	7069750	0.65	-	0	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7069598	7069750	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	intron	7069751	7069904	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7069905	7069943	0.31	-	0	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7069905	7069943	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	intron	7069944	7070152	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7070153	7070218	0.3	-	0	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7070153	7070218	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	intron	7070219	7070360	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7070361	7070769	0.25	-	1	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7070361	7070769	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	intron	7070770	7070906	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7070907	7070955	0.9	-	2	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7070907	7070955	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	intron	7070956	7071049	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7071050	7071487	0.86	-	2	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7071050	7071487	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	intron	7071488	7071655	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	CDS	7071656	7071740	0.2	-	0	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	exon	7071656	7071740	.	-	.	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
Phchi.S5	AUGUSTUS	start_codon	7071738	7071740	.	-	0	transcript_id "Phchi.S5G111900.t1"; gene_id "Phchi.S5G111900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8413.t1 is derived from g5588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35837536	35838096	.	-	.	Phchi.S1G557200
Phchi.S1	AUGUSTUS	transcript	35837536	35838096	.	-	.	transcript_id "Phchi.S1G557200.t1"; gene_id "Phchi.S1G557200"
Phchi.S1	AUGUSTUS	stop_codon	35837533	35837535	.	-	0	transcript_id "Phchi.S1G557200.t1"; gene_id "Phchi.S1G557200"
Phchi.S1	AUGUSTUS	CDS	35837536	35838096	0.52	-	0	transcript_id "Phchi.S1G557200.t1"; gene_id "Phchi.S1G557200"
Phchi.S1	AUGUSTUS	exon	35837536	35838096	.	-	.	transcript_id "Phchi.S1G557200.t1"; gene_id "Phchi.S1G557200"
Phchi.S1	AUGUSTUS	start_codon	35838094	35838096	.	-	0	transcript_id "Phchi.S1G557200.t1"; gene_id "Phchi.S1G557200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13148.t1 is derived from g11613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4402028	4404056	.	+	.	Phchi.S3G046700
Phchi.S3	AUGUSTUS	transcript	4402028	4404056	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	start_codon	4402028	4402030	.	+	0	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	CDS	4402028	4402141	0.49	+	0	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	exon	4402028	4402141	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	intron	4402142	4402218	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	CDS	4402219	4402387	1	+	0	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	exon	4402219	4402387	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	intron	4402388	4402594	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	CDS	4402595	4402668	1	+	2	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	exon	4402595	4402668	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	intron	4402669	4402765	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	CDS	4402766	4402851	1	+	0	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	exon	4402766	4402851	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	intron	4402852	4402999	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	CDS	4403000	4403600	0.98	+	1	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	exon	4403000	4403600	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	intron	4403601	4403735	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	CDS	4403736	4404056	0.98	+	0	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	exon	4403736	4404056	.	+	.	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
Phchi.S3	AUGUSTUS	stop_codon	4404057	4404059	.	+	0	transcript_id "Phchi.S3G046700.t1"; gene_id "Phchi.S3G046700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9928.t1 is derived from g7104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44521033	44522583	.	+	.	Phchi.S1G708700
Phchi.S1	AUGUSTUS	transcript	44521033	44522583	.	+	.	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	start_codon	44521033	44521035	.	+	0	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	CDS	44521033	44521371	0.44	+	0	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	exon	44521033	44521371	.	+	.	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	intron	44521372	44521533	.	+	.	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	CDS	44521534	44522583	0.56	+	0	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	exon	44521534	44522583	.	+	.	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
Phchi.S1	AUGUSTUS	stop_codon	44522584	44522586	.	+	0	transcript_id "Phchi.S1G708700.t1"; gene_id "Phchi.S1G708700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11805.t1 is derived from g15857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8219799	8221339	.	+	.	Phchi.S4G138700
Phchi.S4	AUGUSTUS	transcript	8219799	8220903	.	+	.	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	start_codon	8219799	8219801	.	+	0	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	CDS	8219799	8220371	0.64	+	0	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	exon	8219799	8220371	.	+	.	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	intron	8220372	8220513	.	+	.	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	CDS	8220514	8220903	0.96	+	0	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	exon	8220514	8220903	.	+	.	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	stop_codon	8220904	8220906	.	+	0	transcript_id "Phchi.S4G138700.t1"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	transcript	8219799	8221339	.	+	.	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	start_codon	8219799	8219801	.	+	0	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	CDS	8219799	8220371	0.61	+	0	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	exon	8219799	8220371	.	+	.	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	intron	8220372	8220513	.	+	.	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	CDS	8220514	8220791	0.38	+	0	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	exon	8220514	8220791	.	+	.	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	intron	8220792	8220969	.	+	.	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	CDS	8220970	8221339	0.41	+	1	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	exon	8220970	8221339	.	+	.	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
Phchi.S4	AUGUSTUS	stop_codon	8221340	8221342	.	+	0	transcript_id "Phchi.S4G138700.t2"; gene_id "Phchi.S4G138700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7768.t1 is derived from g4942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31169032	31169283	.	+	.	Phchi.S1G492700
Phchi.S1	AUGUSTUS	transcript	31169032	31169283	.	+	.	transcript_id "Phchi.S1G492700.t1"; gene_id "Phchi.S1G492700"
Phchi.S1	AUGUSTUS	start_codon	31169032	31169034	.	+	0	transcript_id "Phchi.S1G492700.t1"; gene_id "Phchi.S1G492700"
Phchi.S1	AUGUSTUS	CDS	31169032	31169283	0.96	+	0	transcript_id "Phchi.S1G492700.t1"; gene_id "Phchi.S1G492700"
Phchi.S1	AUGUSTUS	exon	31169032	31169283	.	+	.	transcript_id "Phchi.S1G492700.t1"; gene_id "Phchi.S1G492700"
Phchi.S1	AUGUSTUS	stop_codon	31169284	31169286	.	+	0	transcript_id "Phchi.S1G492700.t1"; gene_id "Phchi.S1G492700"
# This transcript jg266.t2 is derived from g10048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg267.t1 is derived from g10049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1911666	1914055	.	+	.	Phchi.S6G022600
Phchi.S6	AUGUSTUS	transcript	1911666	1914055	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	start_codon	1911666	1911668	.	+	0	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	CDS	1911666	1912710	0.58	+	0	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	exon	1911666	1912710	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	intron	1912711	1912875	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	CDS	1912876	1913216	0.93	+	2	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	exon	1912876	1913216	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	intron	1913217	1913299	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	CDS	1913300	1913505	0.37	+	0	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	exon	1913300	1913505	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	intron	1913506	1913694	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	CDS	1913695	1913843	1	+	1	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	exon	1913695	1913843	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	intron	1913844	1914041	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	CDS	1914042	1914055	0.95	+	2	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	exon	1914042	1914055	.	+	.	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
Phchi.S6	AUGUSTUS	stop_codon	1914056	1914058	.	+	0	transcript_id "Phchi.S6G022600.t1"; gene_id "Phchi.S6G022600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6693.t1 is derived from g3865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24553139	24555329	.	+	.	Phchi.S1G385200
Phchi.S1	AUGUSTUS	transcript	24553139	24555329	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	start_codon	24553139	24553141	.	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24553139	24553402	0.54	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24553139	24553402	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24553403	24553591	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24553592	24553707	1	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24553592	24553707	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24553708	24553844	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24553845	24553898	1	+	1	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24553845	24553898	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24553899	24554030	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24554031	24554055	1	+	1	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24554031	24554055	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24554056	24554178	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24554179	24554301	1	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24554179	24554301	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24554302	24554487	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24554488	24554657	1	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24554488	24554657	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24554658	24554741	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24554742	24554823	1	+	1	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24554742	24554823	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24554824	24554935	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24554936	24555034	1	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24554936	24555034	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	intron	24555035	24555218	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	CDS	24555219	24555329	1	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	exon	24555219	24555329	.	+	.	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
Phchi.S1	AUGUSTUS	stop_codon	24555330	24555332	.	+	0	transcript_id "Phchi.S1G385200.t1"; gene_id "Phchi.S1G385200"
# This transcript jg248.t2 is derived from g10030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg249.t1 is derived from g10031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1706041	1706417	.	+	.	Phchi.S6G020800
Phchi.S6	AUGUSTUS	transcript	1706041	1706417	.	+	.	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	start_codon	1706041	1706043	.	+	0	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	CDS	1706041	1706077	1	+	0	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	exon	1706041	1706077	.	+	.	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	intron	1706078	1706244	.	+	.	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	CDS	1706245	1706417	0.87	+	2	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	exon	1706245	1706417	.	+	.	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
Phchi.S6	AUGUSTUS	stop_codon	1706418	1706420	.	+	0	transcript_id "Phchi.S6G020800.t1"; gene_id "Phchi.S6G020800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1203.t1 is derived from g10986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8405353	8408119	.	-	.	Phchi.S6G116200
Phchi.S6	AUGUSTUS	transcript	8405353	8408119	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	stop_codon	8405350	8405352	.	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8405353	8405473	1	-	1	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8405353	8405473	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8405474	8405559	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8405560	8405654	1	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8405560	8405654	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8405655	8405776	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8405777	8405863	0.98	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8405777	8405863	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8405864	8405970	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8405971	8406155	0.93	-	2	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8405971	8406155	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8406156	8406260	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8406261	8406273	1	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8406261	8406273	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8406274	8406493	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8406494	8406594	1	-	2	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8406494	8406594	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8406595	8406686	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8406687	8406754	1	-	1	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8406687	8406754	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8406755	8406859	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8406860	8406909	1	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8406860	8406909	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8406910	8407028	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8407029	8407114	1	-	2	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8407029	8407114	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8407115	8407267	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8407268	8407437	1	-	1	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8407268	8407437	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	intron	8407438	8407619	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	CDS	8407620	8408119	0.98	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	exon	8407620	8408119	.	-	.	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
Phchi.S6	AUGUSTUS	start_codon	8408117	8408119	.	-	0	transcript_id "Phchi.S6G116200.t1"; gene_id "Phchi.S6G116200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9362.t1 is derived from g6538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41161842	41162763	.	+	.	Phchi.S1G652100
Phchi.S1	AUGUSTUS	transcript	41161842	41162763	.	+	.	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	start_codon	41161842	41161844	.	+	0	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	CDS	41161842	41161961	0.99	+	0	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	exon	41161842	41161961	.	+	.	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	intron	41161962	41162358	.	+	.	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	CDS	41162359	41162508	1	+	0	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	exon	41162359	41162508	.	+	.	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	intron	41162509	41162700	.	+	.	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	CDS	41162701	41162763	1	+	0	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	exon	41162701	41162763	.	+	.	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
Phchi.S1	AUGUSTUS	stop_codon	41162764	41162766	.	+	0	transcript_id "Phchi.S1G652100.t1"; gene_id "Phchi.S1G652100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg475.t1 is derived from g10257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3338391	3341810	.	-	.	Phchi.S6G043400
Phchi.S6	AUGUSTUS	transcript	3338391	3341810	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	stop_codon	3338388	3338390	.	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3338391	3338564	1	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3338391	3338564	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3338565	3338686	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3338687	3338815	0.91	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3338687	3338815	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3338816	3338904	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3338905	3338924	0.7	-	2	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3338905	3338924	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3338925	3339010	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3339011	3339059	0.91	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3339011	3339059	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3339060	3339148	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3339149	3339264	1	-	2	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3339149	3339264	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3339265	3339352	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3339353	3339533	0.99	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3339353	3339533	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3339534	3339637	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3339638	3339736	0.99	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3339638	3339736	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3339737	3339918	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3339919	3340012	1	-	1	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3339919	3340012	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3340013	3340107	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3340108	3340232	1	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3340108	3340232	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3340233	3340330	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3340331	3340498	1	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3340331	3340498	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3340499	3340612	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3340613	3340762	1	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3340613	3340762	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3340763	3340895	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3340896	3341039	1	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3340896	3341039	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3341040	3341155	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3341156	3341327	0.57	-	1	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3341156	3341327	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3341328	3341449	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3341450	3341549	0.88	-	2	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3341450	3341549	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	intron	3341550	3341710	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	CDS	3341711	3341810	0.86	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	exon	3341711	3341810	.	-	.	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
Phchi.S6	AUGUSTUS	start_codon	3341808	3341810	.	-	0	transcript_id "Phchi.S6G043400.t1"; gene_id "Phchi.S6G043400"
# This transcript jg13630.t2 is derived from g12097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13631.t1 is derived from g12098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7837755	7838509	.	+	.	Phchi.S3G095000
Phchi.S3	AUGUSTUS	transcript	7837755	7838509	.	+	.	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	start_codon	7837755	7837757	.	+	0	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	CDS	7837755	7837914	0.97	+	0	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	exon	7837755	7837914	.	+	.	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	intron	7837915	7838005	.	+	.	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	CDS	7838006	7838235	0.99	+	2	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	exon	7838006	7838235	.	+	.	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	intron	7838236	7838350	.	+	.	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	CDS	7838351	7838509	0.98	+	0	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	exon	7838351	7838509	.	+	.	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
Phchi.S3	AUGUSTUS	stop_codon	7838510	7838512	.	+	0	transcript_id "Phchi.S3G095000.t1"; gene_id "Phchi.S3G095000"
# This transcript jg6450.t2 is derived from g3622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6451.t1 is derived from g3623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23076968	23079082	.	+	.	Phchi.S1G361000
Phchi.S1	AUGUSTUS	transcript	23076968	23079082	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	start_codon	23076968	23076970	.	+	0	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	CDS	23076968	23077413	0.59	+	0	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	exon	23076968	23077413	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	intron	23077414	23077518	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	CDS	23077519	23077943	0.91	+	1	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	exon	23077519	23077943	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	intron	23077944	23078084	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	CDS	23078085	23078471	1	+	2	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	exon	23078085	23078471	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	intron	23078472	23078552	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	CDS	23078553	23078674	1	+	2	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	exon	23078553	23078674	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	intron	23078675	23078774	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	CDS	23078775	23078887	1	+	0	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	exon	23078775	23078887	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	intron	23078888	23078985	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	CDS	23078986	23079082	0.77	+	1	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	exon	23078986	23079082	.	+	.	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
Phchi.S1	AUGUSTUS	stop_codon	23079083	23079085	.	+	0	transcript_id "Phchi.S1G361000.t1"; gene_id "Phchi.S1G361000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9807.t1 is derived from g6983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43833384	43834688	.	+	.	Phchi.S1G696600
Phchi.S1	AUGUSTUS	transcript	43833384	43834688	.	+	.	transcript_id "Phchi.S1G696600.t1"; gene_id "Phchi.S1G696600"
Phchi.S1	AUGUSTUS	start_codon	43833384	43833386	.	+	0	transcript_id "Phchi.S1G696600.t1"; gene_id "Phchi.S1G696600"
Phchi.S1	AUGUSTUS	CDS	43833384	43834688	0.88	+	0	transcript_id "Phchi.S1G696600.t1"; gene_id "Phchi.S1G696600"
Phchi.S1	AUGUSTUS	exon	43833384	43834688	.	+	.	transcript_id "Phchi.S1G696600.t1"; gene_id "Phchi.S1G696600"
Phchi.S1	AUGUSTUS	stop_codon	43834689	43834691	.	+	0	transcript_id "Phchi.S1G696600.t1"; gene_id "Phchi.S1G696600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5202.t1 is derived from g2372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15441422	15442624	.	-	.	Phchi.S1G236100
Phchi.S1	AUGUSTUS	transcript	15441422	15442624	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	stop_codon	15441419	15441421	.	-	0	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	CDS	15441422	15441544	0.96	-	0	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	exon	15441422	15441544	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	intron	15441545	15441639	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	CDS	15441640	15442050	1	-	0	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	exon	15441640	15442050	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	intron	15442051	15442198	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	CDS	15442199	15442414	0.99	-	0	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	exon	15442199	15442414	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	intron	15442415	15442519	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	CDS	15442520	15442624	1	-	0	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	exon	15442520	15442624	.	-	.	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
Phchi.S1	AUGUSTUS	start_codon	15442622	15442624	.	-	0	transcript_id "Phchi.S1G236100.t1"; gene_id "Phchi.S1G236100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16.t1 is derived from g14436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C282	AUGUSTUS	gene	13581	13859	.	+	.	Phchi.C282G000100
Phchi.C282	AUGUSTUS	transcript	13581	13859	.	+	.	transcript_id "Phchi.C282G000100.t1"; gene_id "Phchi.C282G000100"
Phchi.C282	AUGUSTUS	start_codon	13581	13583	.	+	0	transcript_id "Phchi.C282G000100.t1"; gene_id "Phchi.C282G000100"
Phchi.C282	AUGUSTUS	CDS	13581	13859	0.5	+	0	transcript_id "Phchi.C282G000100.t1"; gene_id "Phchi.C282G000100"
Phchi.C282	AUGUSTUS	exon	13581	13859	.	+	.	transcript_id "Phchi.C282G000100.t1"; gene_id "Phchi.C282G000100"
Phchi.C282	AUGUSTUS	stop_codon	13860	13862	.	+	0	transcript_id "Phchi.C282G000100.t1"; gene_id "Phchi.C282G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4413.t1 is derived from g1582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10332748	10354684	.	-	.	Phchi.S1G157200
Phchi.S1	AUGUSTUS	transcript	10332748	10354684	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	stop_codon	10332745	10332747	.	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10332748	10333065	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10332748	10333065	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10333066	10333157	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10333158	10333266	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10333158	10333266	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10333267	10333440	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10333441	10333493	0.66	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10333441	10333493	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10333494	10333594	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10333595	10333680	0.95	-	2	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10333595	10333680	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10333681	10333749	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10333750	10333843	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10333750	10333843	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10333844	10334012	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10334013	10334145	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10334013	10334145	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10334146	10334229	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10334230	10334303	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10334230	10334303	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10334304	10334389	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10334390	10334542	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10334390	10334542	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10334543	10334641	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10334642	10334656	0.74	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10334642	10334656	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10334657	10334835	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10334836	10335000	0.29	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10334836	10335000	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10335001	10335255	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10335256	10335330	0.54	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10335256	10335330	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10335331	10335448	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10335449	10335575	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10335449	10335575	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10335576	10335670	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10335671	10335819	0.36	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10335671	10335819	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10335820	10335918	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10335919	10335955	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10335919	10335955	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10335956	10336201	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10336202	10336762	0.85	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10336202	10336762	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10336763	10336837	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10336838	10337019	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10336838	10337019	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10337020	10337149	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10337150	10337305	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10337150	10337305	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10337306	10337373	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10337374	10337472	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10337374	10337472	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10337473	10337589	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10337590	10337941	0.99	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10337590	10337941	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10337942	10338023	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10338024	10338097	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10338024	10338097	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10338098	10338195	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10338196	10338978	0.72	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10338196	10338978	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10338979	10339131	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10339132	10339665	0.97	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10339132	10339665	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10339666	10339740	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10339741	10339889	1	-	2	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10339741	10339889	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10339890	10340091	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10340092	10340134	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10340092	10340134	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10340135	10340289	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10340290	10340496	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10340290	10340496	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10340497	10340580	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10340581	10340847	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10340581	10340847	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10340848	10340991	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10340992	10341175	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10340992	10341175	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10341176	10341309	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10341310	10341473	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10341310	10341473	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10341474	10341557	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10341558	10341595	0.6	-	2	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10341558	10341595	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10341596	10341693	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10341694	10341715	0.6	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10341694	10341715	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10341716	10341799	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10341800	10342133	0.6	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10341800	10342133	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10342134	10342307	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10342308	10342682	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10342308	10342682	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10342683	10342776	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10342777	10343088	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10342777	10343088	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10343089	10343186	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10343187	10343274	1	-	2	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10343187	10343274	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10343275	10343399	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10343400	10343692	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10343400	10343692	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10343693	10343828	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10343829	10343929	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10343829	10343929	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10343930	10344016	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10344017	10344220	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10344017	10344220	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10344221	10344330	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10344331	10344975	0.99	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10344331	10344975	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10344976	10345096	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10345097	10345396	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10345097	10345396	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10345397	10345482	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10345483	10345626	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10345483	10345626	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10345627	10345739	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10345740	10345848	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10345740	10345848	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10345849	10345993	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10345994	10346178	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10345994	10346178	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10346179	10346352	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10346353	10346466	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10346353	10346466	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10346467	10346609	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10346610	10346741	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10346610	10346741	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10346742	10346914	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10346915	10347277	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10346915	10347277	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10347278	10347351	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10347352	10347873	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10347352	10347873	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10347874	10347986	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10347987	10348061	0.94	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10347987	10348061	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10348062	10348151	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10348152	10348328	0.99	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10348152	10348328	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10348329	10348439	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10348440	10348538	0.99	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10348440	10348538	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10348539	10348621	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10348622	10348718	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10348622	10348718	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10348719	10348808	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10348809	10348918	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10348809	10348918	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10348919	10349001	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10349002	10349208	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10349002	10349208	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10349209	10349740	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10349741	10349950	0.73	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10349741	10349950	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10349951	10350066	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10350067	10350196	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10350067	10350196	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10350197	10350354	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10350355	10350422	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10350355	10350422	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10350423	10350551	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10350552	10350647	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10350552	10350647	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10350648	10350738	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10350739	10350843	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10350739	10350843	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10350844	10350982	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10350983	10351307	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10350983	10351307	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10351308	10351395	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10351396	10351485	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10351396	10351485	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10351486	10351578	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10351579	10351749	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10351579	10351749	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10351750	10351964	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10351965	10352125	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10351965	10352125	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10352126	10352344	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10352345	10352557	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10352345	10352557	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10352558	10352659	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10352660	10352761	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10352660	10352761	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10352762	10352895	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10352896	10353013	1	-	1	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10352896	10353013	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10353014	10353132	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10353133	10353230	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10353133	10353230	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10353231	10353325	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10353326	10353385	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10353326	10353385	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10353386	10353600	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10353601	10353735	1	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10353601	10353735	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10353736	10353892	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10353893	10353996	1	-	2	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10353893	10353996	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	intron	10353997	10354587	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	CDS	10354588	10354684	0.94	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	exon	10354588	10354684	.	-	.	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
Phchi.S1	AUGUSTUS	start_codon	10354682	10354684	.	-	0	transcript_id "Phchi.S1G157200.t1"; gene_id "Phchi.S1G157200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5820.t1 is derived from g2990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19107423	19108310	.	+	.	Phchi.S1G297900
Phchi.S1	AUGUSTUS	transcript	19107423	19108310	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	start_codon	19107423	19107425	.	+	0	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	CDS	19107423	19107616	1	+	0	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	exon	19107423	19107616	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	intron	19107617	19107698	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	CDS	19107699	19107879	1	+	1	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	exon	19107699	19107879	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	intron	19107880	19107998	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	CDS	19107999	19108125	1	+	0	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	exon	19107999	19108125	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	intron	19108126	19108248	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	CDS	19108249	19108310	1	+	2	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	exon	19108249	19108310	.	+	.	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
Phchi.S1	AUGUSTUS	stop_codon	19108311	19108313	.	+	0	transcript_id "Phchi.S1G297900.t1"; gene_id "Phchi.S1G297900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8095.t1 is derived from g5270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32919724	32920411	.	-	.	Phchi.S1G525400
Phchi.S1	AUGUSTUS	transcript	32919724	32920411	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	stop_codon	32919721	32919723	.	-	0	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	CDS	32919724	32919799	1	-	1	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	exon	32919724	32919799	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	intron	32919800	32919888	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	CDS	32919889	32920009	1	-	2	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	exon	32919889	32920009	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	intron	32920010	32920103	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	CDS	32920104	32920162	1	-	1	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	exon	32920104	32920162	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	intron	32920163	32920247	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	CDS	32920248	32920411	0.35	-	0	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	exon	32920248	32920411	.	-	.	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
Phchi.S1	AUGUSTUS	start_codon	32920409	32920411	.	-	0	transcript_id "Phchi.S1G525400.t1"; gene_id "Phchi.S1G525400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9307.t1 is derived from g6482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40889565	40891245	.	-	.	Phchi.S1G646600
Phchi.S1	AUGUSTUS	transcript	40889565	40891245	.	-	.	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	stop_codon	40889562	40889564	.	-	0	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	CDS	40889565	40890197	1	-	0	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	exon	40889565	40890197	.	-	.	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	intron	40890198	40890290	.	-	.	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	CDS	40890291	40890522	1	-	1	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	exon	40890291	40890522	.	-	.	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	intron	40890523	40890610	.	-	.	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	CDS	40890611	40891245	1	-	0	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	exon	40890611	40891245	.	-	.	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
Phchi.S1	AUGUSTUS	start_codon	40891243	40891245	.	-	0	transcript_id "Phchi.S1G646600.t1"; gene_id "Phchi.S1G646600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15389.t1 is derived from g13857.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18769532	18770776	.	-	.	Phchi.S3G270800
Phchi.S3	AUGUSTUS	transcript	18769532	18770776	.	-	.	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	stop_codon	18769529	18769531	.	-	0	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	CDS	18769532	18769602	0.55	-	2	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	exon	18769532	18769602	.	-	.	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	intron	18769603	18769788	.	-	.	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	CDS	18769789	18770101	1	-	0	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	exon	18769789	18770101	.	-	.	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	intron	18770102	18770197	.	-	.	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	CDS	18770198	18770776	0.99	-	0	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	exon	18770198	18770776	.	-	.	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
Phchi.S3	AUGUSTUS	start_codon	18770774	18770776	.	-	0	transcript_id "Phchi.S3G270800.t1"; gene_id "Phchi.S3G270800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg880.t1 is derived from g10662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6239195	6240391	.	+	.	Phchi.S6G083900
Phchi.S6	AUGUSTUS	transcript	6239195	6240391	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	start_codon	6239195	6239197	.	+	0	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	CDS	6239195	6239384	1	+	0	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	exon	6239195	6239384	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	intron	6239385	6239602	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	CDS	6239603	6239744	1	+	2	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	exon	6239603	6239744	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	intron	6239745	6239852	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	CDS	6239853	6239973	1	+	1	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	exon	6239853	6239973	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	intron	6239974	6240091	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	CDS	6240092	6240154	1	+	0	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	exon	6240092	6240154	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	intron	6240155	6240247	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	CDS	6240248	6240391	1	+	0	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	exon	6240248	6240391	.	+	.	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
Phchi.S6	AUGUSTUS	stop_codon	6240392	6240394	.	+	0	transcript_id "Phchi.S6G083900.t1"; gene_id "Phchi.S6G083900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9119.t1 is derived from g6294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39920720	39921100	.	-	.	Phchi.S1G627800
Phchi.S1	AUGUSTUS	transcript	39920720	39921100	.	-	.	transcript_id "Phchi.S1G627800.t1"; gene_id "Phchi.S1G627800"
Phchi.S1	AUGUSTUS	stop_codon	39920717	39920719	.	-	0	transcript_id "Phchi.S1G627800.t1"; gene_id "Phchi.S1G627800"
Phchi.S1	AUGUSTUS	CDS	39920720	39921100	0.27	-	0	transcript_id "Phchi.S1G627800.t1"; gene_id "Phchi.S1G627800"
Phchi.S1	AUGUSTUS	exon	39920720	39921100	.	-	.	transcript_id "Phchi.S1G627800.t1"; gene_id "Phchi.S1G627800"
Phchi.S1	AUGUSTUS	start_codon	39921098	39921100	.	-	0	transcript_id "Phchi.S1G627800.t1"; gene_id "Phchi.S1G627800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3274.t1 is derived from g443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2643597	2645496	.	+	.	Phchi.S1G043300
Phchi.S1	AUGUSTUS	transcript	2643597	2645496	.	+	.	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	start_codon	2643597	2643599	.	+	0	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	CDS	2643597	2645358	0.83	+	0	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	exon	2643597	2645358	.	+	.	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	intron	2645359	2645494	.	+	.	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	CDS	2645495	2645496	0.98	+	2	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	exon	2645495	2645496	.	+	.	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
Phchi.S1	AUGUSTUS	stop_codon	2645497	2645499	.	+	0	transcript_id "Phchi.S1G043300.t1"; gene_id "Phchi.S1G043300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4255.t1 is derived from g1424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9179168	9179676	.	+	.	Phchi.S1G141400
Phchi.S1	AUGUSTUS	transcript	9179168	9179676	.	+	.	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	start_codon	9179168	9179170	.	+	0	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	CDS	9179168	9179211	0.99	+	0	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	exon	9179168	9179211	.	+	.	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	intron	9179212	9179435	.	+	.	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	CDS	9179436	9179481	1	+	1	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	exon	9179436	9179481	.	+	.	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	intron	9179482	9179568	.	+	.	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	CDS	9179569	9179676	0.62	+	0	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	exon	9179569	9179676	.	+	.	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
Phchi.S1	AUGUSTUS	stop_codon	9179677	9179679	.	+	0	transcript_id "Phchi.S1G141400.t1"; gene_id "Phchi.S1G141400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11355.t1 is derived from g15405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5716447	5717048	.	-	.	Phchi.S4G093700
Phchi.S4	AUGUSTUS	transcript	5716447	5717048	.	-	.	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	stop_codon	5716444	5716446	.	-	0	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	CDS	5716447	5716589	1	-	2	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	exon	5716447	5716589	.	-	.	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	intron	5716590	5716662	.	-	.	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	CDS	5716663	5716879	0.96	-	0	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	exon	5716663	5716879	.	-	.	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	intron	5716880	5717045	.	-	.	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	CDS	5717046	5717048	0.97	-	0	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	exon	5717046	5717048	.	-	.	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
Phchi.S4	AUGUSTUS	start_codon	5717046	5717048	.	-	0	transcript_id "Phchi.S4G093700.t1"; gene_id "Phchi.S4G093700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14717.t1 is derived from g13185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14346936	14352209	.	+	.	Phchi.S3G203600
Phchi.S3	AUGUSTUS	transcript	14346936	14352209	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	start_codon	14346936	14346938	.	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14346936	14347216	0.16	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14346936	14347216	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14347217	14347295	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14347296	14347936	0.18	+	1	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14347296	14347936	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14347937	14348067	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14348068	14348393	0.74	+	2	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14348068	14348393	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14348394	14348696	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14348697	14348867	1	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14348697	14348867	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14348868	14348982	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14348983	14349280	0.9	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14348983	14349280	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14349281	14349389	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14349390	14349505	0.96	+	2	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14349390	14349505	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14349506	14349627	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14349628	14349911	1	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14349628	14349911	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14349912	14350000	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14350001	14350067	1	+	1	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14350001	14350067	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14350068	14350161	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14350162	14350395	0.98	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14350162	14350395	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14350396	14350583	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14350584	14350712	1	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14350584	14350712	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14350713	14351260	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14351261	14351386	1	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14351261	14351386	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14351387	14351485	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14351486	14351674	1	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14351486	14351674	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14351675	14351770	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14351771	14351890	0.95	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14351771	14351890	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	intron	14351891	14351993	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	CDS	14351994	14352209	0.82	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	exon	14351994	14352209	.	+	.	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
Phchi.S3	AUGUSTUS	stop_codon	14352210	14352212	.	+	0	transcript_id "Phchi.S3G203600.t1"; gene_id "Phchi.S3G203600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14715.t1 is derived from g13183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14342002	14345453	.	+	.	Phchi.S3G203400
Phchi.S3	AUGUSTUS	transcript	14342002	14345453	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	start_codon	14342002	14342004	.	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14342002	14342100	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14342002	14342100	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14342101	14342199	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14342200	14342336	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14342200	14342336	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14342337	14342466	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14342467	14342565	1	+	1	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14342467	14342565	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14342566	14342664	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14342665	14342785	1	+	1	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14342665	14342785	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14342786	14342888	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14342889	14343143	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14342889	14343143	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14343144	14343257	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14343258	14343338	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14343258	14343338	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14343339	14343421	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14343422	14343505	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14343422	14343505	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14343506	14343601	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14343602	14343688	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14343602	14343688	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14343689	14343816	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14343817	14343872	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14343817	14343872	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14343873	14343979	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14343980	14344174	0.99	+	1	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14343980	14344174	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14344175	14344300	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14344301	14344526	1	+	1	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14344301	14344526	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14344527	14344749	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14344750	14344838	1	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14344750	14344838	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14344839	14344927	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14344928	14345081	1	+	1	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14344928	14345081	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14345082	14345164	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14345165	14345287	0.63	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14345165	14345287	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	intron	14345288	14345390	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	CDS	14345391	14345453	0.63	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	exon	14345391	14345453	.	+	.	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
Phchi.S3	AUGUSTUS	stop_codon	14345454	14345456	.	+	0	transcript_id "Phchi.S3G203400.t1"; gene_id "Phchi.S3G203400"
# This transcript jg23.t2 is derived from g15992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg24.t1 is derived from g9822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C43	AUGUSTUS	gene	38557	39115	.	+	.	Phchi.C43G000100
Phchi.C43	AUGUSTUS	transcript	38557	39115	.	+	.	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	start_codon	38557	38559	.	+	0	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	CDS	38557	38673	0.4	+	0	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	exon	38557	38673	.	+	.	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	intron	38674	38749	.	+	.	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	CDS	38750	39115	0.52	+	0	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	exon	38750	39115	.	+	.	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
Phchi.C43	AUGUSTUS	stop_codon	39116	39118	.	+	0	transcript_id "Phchi.C43G000100.t1"; gene_id "Phchi.C43G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15134.t1 is derived from g13602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17207226	17208716	.	-	.	Phchi.S3G245300
Phchi.S3	AUGUSTUS	transcript	17207226	17208716	.	-	.	transcript_id "Phchi.S3G245300.t1"; gene_id "Phchi.S3G245300"
Phchi.S3	AUGUSTUS	stop_codon	17207223	17207225	.	-	0	transcript_id "Phchi.S3G245300.t1"; gene_id "Phchi.S3G245300"
Phchi.S3	AUGUSTUS	CDS	17207226	17208716	0.84	-	0	transcript_id "Phchi.S3G245300.t1"; gene_id "Phchi.S3G245300"
Phchi.S3	AUGUSTUS	exon	17207226	17208716	.	-	.	transcript_id "Phchi.S3G245300.t1"; gene_id "Phchi.S3G245300"
Phchi.S3	AUGUSTUS	start_codon	17208714	17208716	.	-	0	transcript_id "Phchi.S3G245300.t1"; gene_id "Phchi.S3G245300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13884.t1 is derived from g12351.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9453593	9457320	.	+	.	Phchi.S3G120300
Phchi.S3	AUGUSTUS	transcript	9453593	9457320	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	start_codon	9453593	9453595	.	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9453593	9453791	0.4	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9453593	9453791	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9453792	9453962	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9453963	9454024	0.96	+	2	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9453963	9454024	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9454025	9454384	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9454385	9454451	0.91	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9454385	9454451	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9454452	9454543	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9454544	9454721	0.75	+	2	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9454544	9454721	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9454722	9454792	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9454793	9454916	1	+	1	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9454793	9454916	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9454917	9455093	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9455094	9455176	1	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9455094	9455176	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9455177	9455258	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9455259	9455370	1	+	1	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9455259	9455370	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9455371	9455485	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9455486	9455590	1	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9455486	9455590	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9455591	9455731	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9455732	9455782	1	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9455732	9455782	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9455783	9455933	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9455934	9456023	1	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9455934	9456023	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9456024	9456178	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9456179	9456287	1	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9456179	9456287	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9456288	9456360	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9456361	9456508	0.95	+	2	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9456361	9456508	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9456509	9456626	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9456627	9456669	0.95	+	1	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9456627	9456669	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9456670	9456753	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9456754	9456982	0.93	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9456754	9456982	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	intron	9456983	9457303	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	CDS	9457304	9457320	0.9	+	2	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	exon	9457304	9457320	.	+	.	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
Phchi.S3	AUGUSTUS	stop_codon	9457321	9457323	.	+	0	transcript_id "Phchi.S3G120300.t1"; gene_id "Phchi.S3G120300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11239.t1 is derived from g15289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4954944	4955667	.	+	.	Phchi.S4G082100
Phchi.S4	AUGUSTUS	transcript	4954944	4955667	.	+	.	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	start_codon	4954944	4954946	.	+	0	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	CDS	4954944	4955508	0.7	+	0	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	exon	4954944	4955508	.	+	.	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	intron	4955509	4955617	.	+	.	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	CDS	4955618	4955667	0.99	+	2	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	exon	4955618	4955667	.	+	.	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
Phchi.S4	AUGUSTUS	stop_codon	4955668	4955670	.	+	0	transcript_id "Phchi.S4G082100.t1"; gene_id "Phchi.S4G082100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7556.t1 is derived from g4730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30022733	30024612	.	+	.	Phchi.S1G471500
Phchi.S1	AUGUSTUS	transcript	30022733	30024612	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	start_codon	30022733	30022735	.	+	0	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	CDS	30022733	30023227	0.8	+	0	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	exon	30022733	30023227	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	intron	30023228	30023312	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	CDS	30023313	30024172	0.11	+	0	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	exon	30023313	30024172	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	intron	30024173	30024258	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	CDS	30024259	30024359	0.33	+	1	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	exon	30024259	30024359	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	intron	30024360	30024433	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	CDS	30024434	30024612	0.99	+	2	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	exon	30024434	30024612	.	+	.	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
Phchi.S1	AUGUSTUS	stop_codon	30024613	30024615	.	+	0	transcript_id "Phchi.S1G471500.t1"; gene_id "Phchi.S1G471500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3977.t1 is derived from g1146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6831069	6833490	.	-	.	Phchi.S1G113600
Phchi.S1	AUGUSTUS	transcript	6831069	6833490	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	stop_codon	6831066	6831068	.	-	0	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	CDS	6831069	6832297	0.76	-	2	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	exon	6831069	6832297	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	intron	6832298	6832494	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	CDS	6832495	6832627	1	-	0	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	exon	6832495	6832627	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	intron	6832628	6832724	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	CDS	6832725	6833308	0.97	-	2	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	exon	6832725	6833308	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	intron	6833309	6833474	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	CDS	6833475	6833490	0.41	-	0	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	exon	6833475	6833490	.	-	.	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
Phchi.S1	AUGUSTUS	start_codon	6833488	6833490	.	-	0	transcript_id "Phchi.S1G113600.t1"; gene_id "Phchi.S1G113600"
# This transcript jg10419.t2 is derived from g14468.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10420.t1 is derived from g14469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	112982	113338	.	+	.	Phchi.S4G000200
Phchi.S4	AUGUSTUS	transcript	112982	113338	.	+	.	transcript_id "Phchi.S4G000200.t1"; gene_id "Phchi.S4G000200"
Phchi.S4	AUGUSTUS	start_codon	112982	112984	.	+	0	transcript_id "Phchi.S4G000200.t1"; gene_id "Phchi.S4G000200"
Phchi.S4	AUGUSTUS	CDS	112982	113338	0.61	+	0	transcript_id "Phchi.S4G000200.t1"; gene_id "Phchi.S4G000200"
Phchi.S4	AUGUSTUS	exon	112982	113338	.	+	.	transcript_id "Phchi.S4G000200.t1"; gene_id "Phchi.S4G000200"
Phchi.S4	AUGUSTUS	stop_codon	113339	113341	.	+	0	transcript_id "Phchi.S4G000200.t1"; gene_id "Phchi.S4G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3300.t1 is derived from g469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2739313	2744433	.	+	.	Phchi.S1G045900
Phchi.S1	AUGUSTUS	transcript	2739313	2744433	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	start_codon	2739313	2739315	.	+	0	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2739313	2739348	0.4	+	0	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2739313	2739348	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2739349	2739515	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2739516	2739532	0.4	+	0	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2739516	2739532	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2739533	2739632	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2739633	2739784	0.23	+	1	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2739633	2739784	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2739785	2739887	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2739888	2739971	0.23	+	2	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2739888	2739971	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2739972	2740074	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2740075	2740101	0.87	+	2	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2740075	2740101	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2740102	2740175	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2740176	2741569	0.71	+	2	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2740176	2741569	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2741570	2741760	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2741761	2742406	0.99	+	0	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2741761	2742406	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2742407	2742499	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2742500	2743602	1	+	2	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2742500	2743602	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2743603	2743724	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2743725	2744286	0.99	+	0	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2743725	2744286	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	intron	2744287	2744386	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	CDS	2744387	2744433	0.82	+	2	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	exon	2744387	2744433	.	+	.	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
Phchi.S1	AUGUSTUS	stop_codon	2744434	2744436	.	+	0	transcript_id "Phchi.S1G045900.t1"; gene_id "Phchi.S1G045900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14945.t1 is derived from g13413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15654197	15655488	.	+	.	Phchi.S3G226400
Phchi.S3	AUGUSTUS	transcript	15654197	15655488	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	start_codon	15654197	15654199	.	+	0	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	CDS	15654197	15654317	0.88	+	0	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	exon	15654197	15654317	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	intron	15654318	15654461	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	CDS	15654462	15654558	1	+	2	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	exon	15654462	15654558	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	intron	15654559	15654648	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	CDS	15654649	15654721	1	+	1	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	exon	15654649	15654721	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	intron	15654722	15654805	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	CDS	15654806	15654907	1	+	0	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	exon	15654806	15654907	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	intron	15654908	15654999	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	CDS	15655000	15655249	1	+	0	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	exon	15655000	15655249	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	intron	15655250	15655336	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	CDS	15655337	15655488	1	+	2	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	exon	15655337	15655488	.	+	.	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
Phchi.S3	AUGUSTUS	stop_codon	15655489	15655491	.	+	0	transcript_id "Phchi.S3G226400.t1"; gene_id "Phchi.S3G226400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2659.t1 is derived from g9579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8069889	8070863	.	-	.	Phchi.S5G126800
Phchi.S5	AUGUSTUS	transcript	8069889	8070863	.	-	.	transcript_id "Phchi.S5G126800.t1"; gene_id "Phchi.S5G126800"
Phchi.S5	AUGUSTUS	stop_codon	8069886	8069888	.	-	0	transcript_id "Phchi.S5G126800.t1"; gene_id "Phchi.S5G126800"
Phchi.S5	AUGUSTUS	CDS	8069889	8070863	0.7	-	0	transcript_id "Phchi.S5G126800.t1"; gene_id "Phchi.S5G126800"
Phchi.S5	AUGUSTUS	exon	8069889	8070863	.	-	.	transcript_id "Phchi.S5G126800.t1"; gene_id "Phchi.S5G126800"
Phchi.S5	AUGUSTUS	start_codon	8070861	8070863	.	-	0	transcript_id "Phchi.S5G126800.t1"; gene_id "Phchi.S5G126800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg987.t1 is derived from g10771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6896415	6897162	.	-	.	Phchi.S6G094700
Phchi.S6	AUGUSTUS	transcript	6896415	6897162	.	-	.	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	stop_codon	6896412	6896414	.	-	0	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	CDS	6896415	6896530	0.99	-	2	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	exon	6896415	6896530	.	-	.	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	intron	6896531	6896690	.	-	.	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	CDS	6896691	6896815	1	-	1	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	exon	6896691	6896815	.	-	.	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	intron	6896816	6897091	.	-	.	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	CDS	6897092	6897162	0.97	-	0	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	exon	6897092	6897162	.	-	.	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
Phchi.S6	AUGUSTUS	start_codon	6897160	6897162	.	-	0	transcript_id "Phchi.S6G094700.t1"; gene_id "Phchi.S6G094700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13361.t1 is derived from g11827.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6352340	6354466	.	-	.	Phchi.S3G068000
Phchi.S3	AUGUSTUS	transcript	6352340	6354466	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	stop_codon	6352337	6352339	.	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6352340	6352585	0.67	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6352340	6352585	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6352586	6352669	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6352670	6352786	1	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6352670	6352786	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6352787	6352880	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6352881	6352982	1	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6352881	6352982	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6352983	6353072	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353073	6353099	0.96	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353073	6353099	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353100	6353157	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353158	6353166	1	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353158	6353166	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353167	6353360	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353361	6353570	0.98	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353361	6353570	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353571	6353726	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353727	6353960	0.94	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353727	6353960	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353961	6354064	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6354065	6354466	0.61	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6354065	6354466	.	-	.	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	start_codon	6354464	6354466	.	-	0	transcript_id "Phchi.S3G068000.t1"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	transcript	6352340	6354466	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	stop_codon	6352337	6352339	.	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6352340	6352585	0.65	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6352340	6352585	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6352586	6352669	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6352670	6352786	1	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6352670	6352786	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6352787	6352880	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6352881	6352982	1	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6352881	6352982	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6352983	6353072	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353073	6353099	0.95	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353073	6353099	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353100	6353157	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353158	6353166	1	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353158	6353166	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353167	6353360	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353361	6353612	0.99	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353361	6353612	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353613	6353726	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6353727	6353960	0.91	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6353727	6353960	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	intron	6353961	6354064	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	CDS	6354065	6354466	0.52	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	exon	6354065	6354466	.	-	.	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
Phchi.S3	AUGUSTUS	start_codon	6354464	6354466	.	-	0	transcript_id "Phchi.S3G068000.t2"; gene_id "Phchi.S3G068000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5613.t1 is derived from g2783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17892628	17896949	.	+	.	Phchi.S1G277200
Phchi.S1	AUGUSTUS	transcript	17892628	17896949	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	start_codon	17892628	17892630	.	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17892628	17892711	0.97	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17892628	17892711	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17892712	17892801	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17892802	17892927	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17892802	17892927	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17892928	17893012	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17893013	17893229	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17893013	17893229	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17893230	17893495	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17893496	17893617	0.76	+	2	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17893496	17893617	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17893618	17893737	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17893738	17893819	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17893738	17893819	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17893820	17893894	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17893895	17894163	0.74	+	2	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17893895	17894163	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17894164	17894243	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17894244	17894373	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17894244	17894373	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17894374	17894614	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17894615	17894670	1	+	2	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17894615	17894670	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17894671	17894739	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17894740	17894813	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17894740	17894813	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17894814	17895043	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17895044	17895090	1	+	1	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17895044	17895090	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17895091	17895174	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17895175	17895224	1	+	2	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17895175	17895224	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17895225	17895350	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17895351	17895416	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17895351	17895416	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17895417	17895529	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17895530	17895613	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17895530	17895613	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17895614	17895760	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17895761	17895871	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17895761	17895871	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17895872	17896067	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17896068	17896143	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17896068	17896143	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17896144	17896229	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17896230	17896372	1	+	2	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17896230	17896372	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17896373	17896463	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17896464	17896537	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17896464	17896537	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17896538	17896665	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17896666	17896771	1	+	1	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17896666	17896771	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	intron	17896772	17896853	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	CDS	17896854	17896949	1	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	exon	17896854	17896949	.	+	.	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
Phchi.S1	AUGUSTUS	stop_codon	17896950	17896952	.	+	0	transcript_id "Phchi.S1G277200.t1"; gene_id "Phchi.S1G277200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg702.t1 is derived from g10484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4975080	4976705	.	+	.	Phchi.S6G066100
Phchi.S6	AUGUSTUS	transcript	4975080	4976705	.	+	.	transcript_id "Phchi.S6G066100.t1"; gene_id "Phchi.S6G066100"
Phchi.S6	AUGUSTUS	start_codon	4975080	4975082	.	+	0	transcript_id "Phchi.S6G066100.t1"; gene_id "Phchi.S6G066100"
Phchi.S6	AUGUSTUS	CDS	4975080	4976705	0.99	+	0	transcript_id "Phchi.S6G066100.t1"; gene_id "Phchi.S6G066100"
Phchi.S6	AUGUSTUS	exon	4975080	4976705	.	+	.	transcript_id "Phchi.S6G066100.t1"; gene_id "Phchi.S6G066100"
Phchi.S6	AUGUSTUS	stop_codon	4976706	4976708	.	+	0	transcript_id "Phchi.S6G066100.t1"; gene_id "Phchi.S6G066100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14935.t1 is derived from g13403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15604670	15607910	.	+	.	Phchi.S3G225400
Phchi.S3	AUGUSTUS	transcript	15604670	15607910	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	start_codon	15604670	15604672	.	+	0	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15604670	15605416	0.48	+	0	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15604670	15605416	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	intron	15605417	15605521	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15605522	15605608	0.51	+	0	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15605522	15605608	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	intron	15605609	15605775	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15605776	15605935	1	+	0	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15605776	15605935	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	intron	15605936	15606069	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15606070	15606887	0.99	+	2	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15606070	15606887	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	intron	15606888	15606985	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15606986	15607155	1	+	0	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15606986	15607155	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	intron	15607156	15607245	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15607246	15607503	1	+	1	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15607246	15607503	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	intron	15607504	15607588	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	CDS	15607589	15607910	0.85	+	1	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	exon	15607589	15607910	.	+	.	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
Phchi.S3	AUGUSTUS	stop_codon	15607911	15607913	.	+	0	transcript_id "Phchi.S3G225400.t1"; gene_id "Phchi.S3G225400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15010.t1 is derived from g13478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16473616	16474284	.	-	.	Phchi.S3G232900
Phchi.S3	AUGUSTUS	transcript	16473616	16474284	.	-	.	transcript_id "Phchi.S3G232900.t1"; gene_id "Phchi.S3G232900"
Phchi.S3	AUGUSTUS	stop_codon	16473613	16473615	.	-	0	transcript_id "Phchi.S3G232900.t1"; gene_id "Phchi.S3G232900"
Phchi.S3	AUGUSTUS	CDS	16473616	16474284	0.99	-	0	transcript_id "Phchi.S3G232900.t1"; gene_id "Phchi.S3G232900"
Phchi.S3	AUGUSTUS	exon	16473616	16474284	.	-	.	transcript_id "Phchi.S3G232900.t1"; gene_id "Phchi.S3G232900"
Phchi.S3	AUGUSTUS	start_codon	16474282	16474284	.	-	0	transcript_id "Phchi.S3G232900.t1"; gene_id "Phchi.S3G232900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15234.t1 is derived from g13702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17857239	17862689	.	-	.	Phchi.S3G255300
Phchi.S3	AUGUSTUS	transcript	17857239	17862689	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	stop_codon	17857236	17857238	.	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17857239	17857504	0.89	-	2	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17857239	17857504	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17857505	17857639	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17857640	17857921	1	-	2	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17857640	17857921	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17857922	17858045	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17858046	17858161	1	-	1	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17858046	17858161	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17858162	17858307	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17858308	17858387	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17858308	17858387	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17858388	17858475	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17858476	17858545	0.91	-	1	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17858476	17858545	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17858546	17858645	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17858646	17858718	0.83	-	2	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17858646	17858718	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17858719	17858801	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17858802	17858877	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17858802	17858877	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17858878	17858977	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17858978	17859052	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17858978	17859052	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17859053	17859241	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17859242	17859295	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17859242	17859295	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17859296	17859435	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17859436	17859525	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17859436	17859525	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17859526	17859620	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17859621	17859737	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17859621	17859737	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17859738	17859813	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17859814	17859924	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17859814	17859924	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17859925	17860010	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17860011	17860044	0.92	-	1	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17860011	17860044	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17860045	17860115	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17860116	17860149	0.92	-	2	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17860116	17860149	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17860150	17860335	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17860336	17860417	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17860336	17860417	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17860418	17860610	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17860611	17860690	1	-	2	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17860611	17860690	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17860691	17860899	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17860900	17861008	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17860900	17861008	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17861009	17861133	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17861134	17861256	1	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17861134	17861256	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17861257	17861404	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17861405	17861477	1	-	1	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17861405	17861477	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17861478	17861673	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17861674	17861679	0.89	-	1	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17861674	17861679	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17861680	17861762	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17861763	17861824	0.87	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17861763	17861824	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17861825	17861922	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17861923	17862021	0.97	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17861923	17862021	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17862022	17862349	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17862350	17862494	0.65	-	1	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17862350	17862494	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	intron	17862495	17862651	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	CDS	17862652	17862689	0.49	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	exon	17862652	17862689	.	-	.	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
Phchi.S3	AUGUSTUS	start_codon	17862687	17862689	.	-	0	transcript_id "Phchi.S3G255300.t1"; gene_id "Phchi.S3G255300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12658.t1 is derived from g14457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	26038	30419	.	+	.	Phchi.C12G000800
Phchi.C12	AUGUSTUS	transcript	26038	30419	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	start_codon	26038	26040	.	+	0	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	CDS	26038	27565	0.63	+	0	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	exon	26038	27565	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	intron	27566	27672	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	CDS	27673	28297	0.64	+	2	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	exon	27673	28297	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	intron	28298	28481	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	CDS	28482	29163	0.81	+	1	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	exon	28482	29163	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	intron	29164	29282	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	CDS	29283	30419	1	+	0	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	exon	29283	30419	.	+	.	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
Phchi.C12	AUGUSTUS	stop_codon	30420	30422	.	+	0	transcript_id "Phchi.C12G000800.t1"; gene_id "Phchi.C12G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12980.t1 is derived from g11445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3437457	3439028	.	-	.	Phchi.S3G029900
Phchi.S3	AUGUSTUS	transcript	3437457	3439028	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	stop_codon	3437454	3437456	.	-	0	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	CDS	3437457	3437717	1	-	0	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	exon	3437457	3437717	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	intron	3437718	3437806	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	CDS	3437807	3438192	0.96	-	2	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	exon	3437807	3438192	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	intron	3438193	3438256	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	CDS	3438257	3438455	0.67	-	0	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	exon	3438257	3438455	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	intron	3438456	3438533	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	CDS	3438534	3439028	1	-	0	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	exon	3438534	3439028	.	-	.	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
Phchi.S3	AUGUSTUS	start_codon	3439026	3439028	.	-	0	transcript_id "Phchi.S3G029900.t1"; gene_id "Phchi.S3G029900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11876.t1 is derived from g15928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8947827	8948099	.	+	.	Phchi.S4G145800
Phchi.S4	AUGUSTUS	transcript	8947827	8948099	.	+	.	transcript_id "Phchi.S4G145800.t1"; gene_id "Phchi.S4G145800"
Phchi.S4	AUGUSTUS	start_codon	8947827	8947829	.	+	0	transcript_id "Phchi.S4G145800.t1"; gene_id "Phchi.S4G145800"
Phchi.S4	AUGUSTUS	CDS	8947827	8948099	0.93	+	0	transcript_id "Phchi.S4G145800.t1"; gene_id "Phchi.S4G145800"
Phchi.S4	AUGUSTUS	exon	8947827	8948099	.	+	.	transcript_id "Phchi.S4G145800.t1"; gene_id "Phchi.S4G145800"
Phchi.S4	AUGUSTUS	stop_codon	8948100	8948102	.	+	0	transcript_id "Phchi.S4G145800.t1"; gene_id "Phchi.S4G145800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3703.t1 is derived from g872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5239470	5239973	.	+	.	Phchi.S1G086200
Phchi.S1	AUGUSTUS	transcript	5239470	5239973	.	+	.	transcript_id "Phchi.S1G086200.t1"; gene_id "Phchi.S1G086200"
Phchi.S1	AUGUSTUS	start_codon	5239470	5239472	.	+	0	transcript_id "Phchi.S1G086200.t1"; gene_id "Phchi.S1G086200"
Phchi.S1	AUGUSTUS	CDS	5239470	5239973	0.95	+	0	transcript_id "Phchi.S1G086200.t1"; gene_id "Phchi.S1G086200"
Phchi.S1	AUGUSTUS	exon	5239470	5239973	.	+	.	transcript_id "Phchi.S1G086200.t1"; gene_id "Phchi.S1G086200"
Phchi.S1	AUGUSTUS	stop_codon	5239974	5239976	.	+	0	transcript_id "Phchi.S1G086200.t1"; gene_id "Phchi.S1G086200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2520.t1 is derived from g9440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7116121	7116960	.	-	.	Phchi.S5G112900
Phchi.S5	AUGUSTUS	transcript	7116121	7116960	.	-	.	transcript_id "Phchi.S5G112900.t1"; gene_id "Phchi.S5G112900"
Phchi.S5	AUGUSTUS	stop_codon	7116118	7116120	.	-	0	transcript_id "Phchi.S5G112900.t1"; gene_id "Phchi.S5G112900"
Phchi.S5	AUGUSTUS	CDS	7116121	7116960	0.98	-	0	transcript_id "Phchi.S5G112900.t1"; gene_id "Phchi.S5G112900"
Phchi.S5	AUGUSTUS	exon	7116121	7116960	.	-	.	transcript_id "Phchi.S5G112900.t1"; gene_id "Phchi.S5G112900"
Phchi.S5	AUGUSTUS	start_codon	7116958	7116960	.	-	0	transcript_id "Phchi.S5G112900.t1"; gene_id "Phchi.S5G112900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8273.t1 is derived from g5448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35058761	35060363	.	-	.	Phchi.S1G543200
Phchi.S1	AUGUSTUS	transcript	35058761	35060363	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	stop_codon	35058758	35058760	.	-	0	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	CDS	35058761	35058875	1	-	1	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	exon	35058761	35058875	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	intron	35058876	35058964	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	CDS	35058965	35059011	1	-	0	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	exon	35058965	35059011	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	intron	35059012	35059110	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	CDS	35059111	35059268	1	-	2	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	exon	35059111	35059268	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	intron	35059269	35059448	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	CDS	35059449	35059526	0.58	-	2	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	exon	35059449	35059526	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	intron	35059527	35059766	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	CDS	35059767	35059981	0.49	-	1	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	exon	35059767	35059981	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	intron	35059982	35060166	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	CDS	35060167	35060363	0.45	-	0	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	exon	35060167	35060363	.	-	.	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
Phchi.S1	AUGUSTUS	start_codon	35060361	35060363	.	-	0	transcript_id "Phchi.S1G543200.t1"; gene_id "Phchi.S1G543200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10053.t1 is derived from g7229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45488266	45489816	.	-	.	Phchi.S1G721200
Phchi.S1	AUGUSTUS	transcript	45488266	45489816	.	-	.	transcript_id "Phchi.S1G721200.t1"; gene_id "Phchi.S1G721200"
Phchi.S1	AUGUSTUS	stop_codon	45488263	45488265	.	-	0	transcript_id "Phchi.S1G721200.t1"; gene_id "Phchi.S1G721200"
Phchi.S1	AUGUSTUS	CDS	45488266	45489816	0.27	-	0	transcript_id "Phchi.S1G721200.t1"; gene_id "Phchi.S1G721200"
Phchi.S1	AUGUSTUS	exon	45488266	45489816	.	-	.	transcript_id "Phchi.S1G721200.t1"; gene_id "Phchi.S1G721200"
Phchi.S1	AUGUSTUS	start_codon	45489814	45489816	.	-	0	transcript_id "Phchi.S1G721200.t1"; gene_id "Phchi.S1G721200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9021.t1 is derived from g6196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39182245	39184125	.	+	.	Phchi.S1G618000
Phchi.S1	AUGUSTUS	transcript	39182245	39184125	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	start_codon	39182245	39182247	.	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39182245	39182415	0.93	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39182245	39182415	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39182416	39182512	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39182513	39182530	0.45	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39182513	39182530	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39182531	39182622	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39182623	39182699	0.99	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39182623	39182699	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39182700	39182791	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39182792	39182978	0.98	+	1	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39182792	39182978	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39182979	39183081	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39183082	39183243	1	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39183082	39183243	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39183244	39183338	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39183339	39183413	1	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39183339	39183413	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39183414	39183492	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39183493	39183714	1	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39183493	39183714	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39183715	39183820	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39183821	39183990	1	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39183821	39183990	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	intron	39183991	39184073	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	CDS	39184074	39184125	1	+	1	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	exon	39184074	39184125	.	+	.	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
Phchi.S1	AUGUSTUS	stop_codon	39184126	39184128	.	+	0	transcript_id "Phchi.S1G618000.t1"; gene_id "Phchi.S1G618000"
# This transcript jg12604.t2 is derived from g8281.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12605.t1 is derived from g8282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37473093	37473928	.	+	.	Phchi.S2G068500
Phchi.S2	AUGUSTUS	transcript	37473093	37473928	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	start_codon	37473093	37473095	.	+	0	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	CDS	37473093	37473193	1	+	0	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	exon	37473093	37473193	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	intron	37473194	37473272	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	CDS	37473273	37473529	1	+	1	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	exon	37473273	37473529	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	intron	37473530	37473607	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	CDS	37473608	37473685	1	+	2	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	exon	37473608	37473685	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	intron	37473686	37473770	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	CDS	37473771	37473928	1	+	2	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	exon	37473771	37473928	.	+	.	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
Phchi.S2	AUGUSTUS	stop_codon	37473929	37473931	.	+	0	transcript_id "Phchi.S2G068500.t1"; gene_id "Phchi.S2G068500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7086.t1 is derived from g4258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26817552	26818680	.	+	.	Phchi.S1G424500
Phchi.S1	AUGUSTUS	transcript	26817552	26818680	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	start_codon	26817552	26817554	.	+	0	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26817552	26817648	0.59	+	0	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26817552	26817648	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	intron	26817649	26817745	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26817746	26817844	0.56	+	2	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26817746	26817844	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	intron	26817845	26817990	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26817991	26818455	0.62	+	2	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26817991	26818455	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	intron	26818456	26818552	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26818553	26818680	0.98	+	2	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26818553	26818680	.	+	.	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	stop_codon	26818681	26818683	.	+	0	transcript_id "Phchi.S1G424500.t1"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	transcript	26817552	26818680	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	start_codon	26817552	26817554	.	+	0	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26817552	26817692	0.27	+	0	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26817552	26817692	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	intron	26817693	26817824	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26817825	26817844	0.45	+	0	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26817825	26817844	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	intron	26817845	26817976	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26817977	26818455	0.32	+	1	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26817977	26818455	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	intron	26818456	26818552	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	CDS	26818553	26818680	0.91	+	2	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	exon	26818553	26818680	.	+	.	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
Phchi.S1	AUGUSTUS	stop_codon	26818681	26818683	.	+	0	transcript_id "Phchi.S1G424500.t2"; gene_id "Phchi.S1G424500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11403.t1 is derived from g15454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6181225	6182714	.	-	.	Phchi.S4G098600
Phchi.S4	AUGUSTUS	transcript	6181296	6182714	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	stop_codon	6181293	6181295	.	-	0	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6181296	6181349	0.85	-	0	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6181296	6181349	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6181350	6182089	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182090	6182140	1	-	0	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182090	6182140	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6182141	6182377	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182378	6182444	1	-	1	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182378	6182444	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6182445	6182688	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182689	6182714	0.74	-	0	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182689	6182714	.	-	.	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	start_codon	6182712	6182714	.	-	0	transcript_id "Phchi.S4G098600.t1"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	transcript	6181225	6182714	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	stop_codon	6181222	6181224	.	-	0	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6181225	6181349	0.57	-	2	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6181225	6181349	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6181350	6182089	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182090	6182103	0.57	-	1	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182090	6182103	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6182104	6182161	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182162	6182175	0.57	-	0	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182162	6182175	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6182176	6182377	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182378	6182444	0.93	-	1	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182378	6182444	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	intron	6182445	6182688	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	CDS	6182689	6182714	0.61	-	0	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	exon	6182689	6182714	.	-	.	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
Phchi.S4	AUGUSTUS	start_codon	6182712	6182714	.	-	0	transcript_id "Phchi.S4G098600.t2"; gene_id "Phchi.S4G098600"
# This transcript jg6086.t2 is derived from g3257.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 5 different transcripts
# This transcript jg6087.t1 is derived from g3258.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20892440	20895559	.	+	.	Phchi.S1G324600
Phchi.S1	AUGUSTUS	transcript	20894404	20895559	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	start_codon	20894404	20894406	.	+	0	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894404	20894497	0.54	+	0	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894404	20894497	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894498	20894572	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894573	20894658	1	+	2	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894573	20894658	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894659	20894763	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894764	20894871	1	+	0	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894764	20894871	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894872	20894959	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894960	20895004	1	+	0	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894960	20895004	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20895005	20895133	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20895134	20895222	1	+	0	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20895134	20895222	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20895223	20895329	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20895330	20895370	1	+	1	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20895330	20895370	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20895371	20895452	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20895453	20895559	0.98	+	2	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20895453	20895559	.	+	.	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	stop_codon	20895560	20895562	.	+	0	transcript_id "Phchi.S1G324600.t1"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	transcript	20892440	20895559	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	start_codon	20892440	20892442	.	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892440	20892578	0.66	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892440	20892578	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892579	20892679	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892680	20892720	0.66	+	2	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892680	20892720	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892721	20892813	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892814	20892874	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892814	20892874	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892875	20892951	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892952	20893054	0.88	+	2	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892952	20893054	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893055	20893161	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893162	20893267	0.92	+	1	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893162	20893267	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893268	20893397	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893398	20893451	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893398	20893451	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893452	20893559	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893560	20893622	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893560	20893622	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893623	20893741	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893742	20893791	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893742	20893791	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893792	20893888	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893889	20893964	1	+	1	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893889	20893964	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893965	20894066	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894067	20894303	0.94	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894067	20894303	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894304	20894409	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894410	20894497	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894410	20894497	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894498	20894572	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894573	20894658	1	+	2	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894573	20894658	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894659	20894763	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894764	20894871	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894764	20894871	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20894872	20894959	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894960	20895004	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894960	20895004	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20895005	20895133	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20895134	20895222	1	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20895134	20895222	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20895223	20895329	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20895330	20895370	1	+	1	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20895330	20895370	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20895371	20895452	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20895453	20895559	0.99	+	2	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20895453	20895559	.	+	.	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	stop_codon	20895560	20895562	.	+	0	transcript_id "Phchi.S1G324600.t2"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	transcript	20892440	20894063	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	start_codon	20892440	20892442	.	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892440	20892472	0.97	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892440	20892472	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892473	20892611	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892612	20892720	0.98	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892612	20892720	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892721	20892951	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892952	20893054	0.85	+	2	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892952	20893054	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893055	20893161	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893162	20893267	0.93	+	1	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893162	20893267	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893268	20893397	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893398	20893451	0.99	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893398	20893451	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893452	20893559	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893560	20893622	0.99	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893560	20893622	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893623	20893741	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893742	20893791	1	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893742	20893791	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893792	20893888	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893889	20893964	0.99	+	1	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893889	20893964	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893965	20894048	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894049	20894063	0.81	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894049	20894063	.	+	.	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	stop_codon	20894064	20894066	.	+	0	transcript_id "Phchi.S1G324600.t3"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	transcript	20892440	20894063	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	start_codon	20892440	20892442	.	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892440	20892578	0.73	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892440	20892578	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892579	20892679	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892680	20892720	0.74	+	2	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892680	20892720	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892721	20892813	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892814	20892874	1	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892814	20892874	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892875	20892951	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892952	20893054	0.92	+	2	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892952	20893054	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893055	20893161	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893162	20893267	0.95	+	1	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893162	20893267	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893268	20893397	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893398	20893451	1	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893398	20893451	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893452	20893559	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893560	20893622	1	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893560	20893622	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893623	20893741	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893742	20893791	1	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893742	20893791	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893792	20893888	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893889	20893964	1	+	1	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893889	20893964	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893965	20894048	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894049	20894063	0.89	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894049	20894063	.	+	.	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	stop_codon	20894064	20894066	.	+	0	transcript_id "Phchi.S1G324600.t4"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	transcript	20892440	20894063	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	start_codon	20892440	20892442	.	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892440	20892578	0.72	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892440	20892578	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892579	20892679	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892680	20892720	0.72	+	2	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892680	20892720	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892721	20892813	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892814	20892874	1	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892814	20892874	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20892875	20892951	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20892952	20893054	0.86	+	2	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20892952	20893054	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893055	20893161	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893162	20893267	0.91	+	1	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893162	20893267	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893268	20893397	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893398	20893451	0.99	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893398	20893451	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893452	20893559	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893560	20893622	0.99	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893560	20893622	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893623	20893775	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893776	20893795	0.75	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893776	20893795	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893796	20893888	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20893889	20893964	0.79	+	1	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20893889	20893964	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	intron	20893965	20894048	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	CDS	20894049	20894063	0.7	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	exon	20894049	20894063	.	+	.	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
Phchi.S1	AUGUSTUS	stop_codon	20894064	20894066	.	+	0	transcript_id "Phchi.S1G324600.t5"; gene_id "Phchi.S1G324600"
# This transcript jg12942.t2 is derived from g11407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12943.t1 is derived from g11408.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3259879	3261584	.	-	.	Phchi.S3G026200
Phchi.S3	AUGUSTUS	transcript	3259879	3261584	.	-	.	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	stop_codon	3259876	3259878	.	-	0	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	CDS	3259879	3260954	0.94	-	2	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	exon	3259879	3260954	.	-	.	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	intron	3260955	3261107	.	-	.	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	CDS	3261108	3261121	0.98	-	1	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	exon	3261108	3261121	.	-	.	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	intron	3261122	3261564	.	-	.	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	CDS	3261565	3261584	1	-	0	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	exon	3261565	3261584	.	-	.	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
Phchi.S3	AUGUSTUS	start_codon	3261582	3261584	.	-	0	transcript_id "Phchi.S3G026200.t1"; gene_id "Phchi.S3G026200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9576.t1 is derived from g6752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42739389	42740822	.	-	.	Phchi.S1G673500
Phchi.S1	AUGUSTUS	transcript	42739389	42740822	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	stop_codon	42739386	42739388	.	-	0	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	CDS	42739389	42739647	1	-	1	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	exon	42739389	42739647	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	intron	42739648	42739735	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	CDS	42739736	42739885	1	-	1	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	exon	42739736	42739885	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	intron	42739886	42739976	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	CDS	42739977	42740089	1	-	0	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	exon	42739977	42740089	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	intron	42740090	42740248	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	CDS	42740249	42740487	1	-	2	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	exon	42740249	42740487	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	intron	42740488	42740578	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	CDS	42740579	42740822	0.87	-	0	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	exon	42740579	42740822	.	-	.	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
Phchi.S1	AUGUSTUS	start_codon	42740820	42740822	.	-	0	transcript_id "Phchi.S1G673500.t1"; gene_id "Phchi.S1G673500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7045.t1 is derived from g4217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26576560	26578833	.	+	.	Phchi.S1G420400
Phchi.S1	AUGUSTUS	transcript	26576560	26578833	.	+	.	transcript_id "Phchi.S1G420400.t1"; gene_id "Phchi.S1G420400"
Phchi.S1	AUGUSTUS	start_codon	26576560	26576562	.	+	0	transcript_id "Phchi.S1G420400.t1"; gene_id "Phchi.S1G420400"
Phchi.S1	AUGUSTUS	CDS	26576560	26578833	0.83	+	0	transcript_id "Phchi.S1G420400.t1"; gene_id "Phchi.S1G420400"
Phchi.S1	AUGUSTUS	exon	26576560	26578833	.	+	.	transcript_id "Phchi.S1G420400.t1"; gene_id "Phchi.S1G420400"
Phchi.S1	AUGUSTUS	stop_codon	26578834	26578836	.	+	0	transcript_id "Phchi.S1G420400.t1"; gene_id "Phchi.S1G420400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5646.t1 is derived from g2816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18045103	18045947	.	+	.	Phchi.S1G280500
Phchi.S1	AUGUSTUS	transcript	18045103	18045947	.	+	.	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	start_codon	18045103	18045105	.	+	0	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	CDS	18045103	18045219	0.75	+	0	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	exon	18045103	18045219	.	+	.	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	intron	18045220	18045491	.	+	.	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	CDS	18045492	18045602	1	+	0	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	exon	18045492	18045602	.	+	.	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	intron	18045603	18045872	.	+	.	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	CDS	18045873	18045947	0.82	+	0	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	exon	18045873	18045947	.	+	.	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
Phchi.S1	AUGUSTUS	stop_codon	18045948	18045950	.	+	0	transcript_id "Phchi.S1G280500.t1"; gene_id "Phchi.S1G280500"
# This transcript jg2934.t2 is derived from g103.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2935.t1 is derived from g104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	640576	642381	.	+	.	Phchi.S1G009400
Phchi.S1	AUGUSTUS	transcript	640576	642381	.	+	.	transcript_id "Phchi.S1G009400.t1"; gene_id "Phchi.S1G009400"
Phchi.S1	AUGUSTUS	start_codon	640576	640578	.	+	0	transcript_id "Phchi.S1G009400.t1"; gene_id "Phchi.S1G009400"
Phchi.S1	AUGUSTUS	CDS	640576	642381	0.81	+	0	transcript_id "Phchi.S1G009400.t1"; gene_id "Phchi.S1G009400"
Phchi.S1	AUGUSTUS	exon	640576	642381	.	+	.	transcript_id "Phchi.S1G009400.t1"; gene_id "Phchi.S1G009400"
Phchi.S1	AUGUSTUS	stop_codon	642382	642384	.	+	0	transcript_id "Phchi.S1G009400.t1"; gene_id "Phchi.S1G009400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14529.t1 is derived from g12997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13324486	13325738	.	-	.	Phchi.S3G184800
Phchi.S3	AUGUSTUS	transcript	13324486	13325738	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	stop_codon	13324483	13324485	.	-	0	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13324486	13324773	0.73	-	0	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13324486	13324773	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	intron	13324774	13324868	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13324869	13325118	0.88	-	1	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13324869	13325118	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	intron	13325119	13325219	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13325220	13325360	1	-	1	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13325220	13325360	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	intron	13325361	13325469	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13325470	13325738	0.48	-	0	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13325470	13325738	.	-	.	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	start_codon	13325736	13325738	.	-	0	transcript_id "Phchi.S3G184800.t1"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	transcript	13324760	13325738	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	stop_codon	13324757	13324759	.	-	0	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13324760	13324773	0.71	-	2	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13324760	13324773	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	intron	13324774	13324924	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13324925	13325118	0.74	-	1	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13324925	13325118	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	intron	13325119	13325219	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13325220	13325360	1	-	1	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13325220	13325360	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	intron	13325361	13325469	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	CDS	13325470	13325738	0.49	-	0	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	exon	13325470	13325738	.	-	.	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
Phchi.S3	AUGUSTUS	start_codon	13325736	13325738	.	-	0	transcript_id "Phchi.S3G184800.t2"; gene_id "Phchi.S3G184800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8252.t1 is derived from g5427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34715117	34716775	.	+	.	Phchi.S1G541100
Phchi.S1	AUGUSTUS	transcript	34715117	34716775	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	start_codon	34715117	34715119	.	+	0	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	CDS	34715117	34715305	0.99	+	0	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	exon	34715117	34715305	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	intron	34715306	34715477	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	CDS	34715478	34715670	1	+	0	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	exon	34715478	34715670	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	intron	34715671	34715824	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	CDS	34715825	34715911	1	+	2	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	exon	34715825	34715911	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	intron	34715912	34715997	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	CDS	34715998	34716133	0.75	+	2	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	exon	34715998	34716133	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	intron	34716134	34716214	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	CDS	34716215	34716422	1	+	1	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	exon	34716215	34716422	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	intron	34716423	34716499	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	CDS	34716500	34716775	1	+	0	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	exon	34716500	34716775	.	+	.	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
Phchi.S1	AUGUSTUS	stop_codon	34716776	34716778	.	+	0	transcript_id "Phchi.S1G541100.t1"; gene_id "Phchi.S1G541100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7367.t1 is derived from g4539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28794397	28797708	.	-	.	Phchi.S1G452600
Phchi.S1	AUGUSTUS	transcript	28794397	28797708	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	stop_codon	28794394	28794396	.	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28794397	28794507	1	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28794397	28794507	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	intron	28794508	28794629	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28794630	28794737	1	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28794630	28794737	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	intron	28794738	28794863	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28794864	28794953	1	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28794864	28794953	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	intron	28794954	28795040	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28795041	28795157	1	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28795041	28795157	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	intron	28795158	28795304	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28795305	28795424	1	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28795305	28795424	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	intron	28795425	28795570	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28795571	28797037	0.78	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28795571	28797037	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	intron	28797038	28797165	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	CDS	28797166	28797708	0.93	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	exon	28797166	28797708	.	-	.	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
Phchi.S1	AUGUSTUS	start_codon	28797706	28797708	.	-	0	transcript_id "Phchi.S1G452600.t1"; gene_id "Phchi.S1G452600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6834.t1 is derived from g4006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25473090	25475140	.	-	.	Phchi.S1G399300
Phchi.S1	AUGUSTUS	transcript	25473090	25475140	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	stop_codon	25473087	25473089	.	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25473090	25473200	1	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25473090	25473200	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25473201	25473285	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25473286	25473345	1	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25473286	25473345	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25473346	25473427	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25473428	25473494	1	-	1	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25473428	25473494	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25473495	25473585	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25473586	25473638	1	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25473586	25473638	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25473639	25473726	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25473727	25473897	1	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25473727	25473897	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25473898	25474060	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25474061	25474146	1	-	2	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25474061	25474146	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25474147	25474277	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25474278	25474566	1	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25474278	25474566	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	intron	25474567	25474717	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	CDS	25474718	25475140	0.96	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	exon	25474718	25475140	.	-	.	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
Phchi.S1	AUGUSTUS	start_codon	25475138	25475140	.	-	0	transcript_id "Phchi.S1G399300.t1"; gene_id "Phchi.S1G399300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8765.t1 is derived from g5940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37863291	37863974	.	+	.	Phchi.S1G592400
Phchi.S1	AUGUSTUS	transcript	37863291	37863974	.	+	.	transcript_id "Phchi.S1G592400.t1"; gene_id "Phchi.S1G592400"
Phchi.S1	AUGUSTUS	start_codon	37863291	37863293	.	+	0	transcript_id "Phchi.S1G592400.t1"; gene_id "Phchi.S1G592400"
Phchi.S1	AUGUSTUS	CDS	37863291	37863974	0.42	+	0	transcript_id "Phchi.S1G592400.t1"; gene_id "Phchi.S1G592400"
Phchi.S1	AUGUSTUS	exon	37863291	37863974	.	+	.	transcript_id "Phchi.S1G592400.t1"; gene_id "Phchi.S1G592400"
Phchi.S1	AUGUSTUS	stop_codon	37863975	37863977	.	+	0	transcript_id "Phchi.S1G592400.t1"; gene_id "Phchi.S1G592400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8716.t1 is derived from g5891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37630773	37631643	.	+	.	Phchi.S1G587500
Phchi.S1	AUGUSTUS	transcript	37630773	37631643	.	+	.	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	start_codon	37630773	37630775	.	+	0	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	CDS	37630773	37631270	0.66	+	0	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	exon	37630773	37631270	.	+	.	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	intron	37631271	37631385	.	+	.	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	CDS	37631386	37631643	1	+	0	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	exon	37631386	37631643	.	+	.	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
Phchi.S1	AUGUSTUS	stop_codon	37631644	37631646	.	+	0	transcript_id "Phchi.S1G587500.t1"; gene_id "Phchi.S1G587500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8076.t1 is derived from g5251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32831169	32834951	.	-	.	Phchi.S1G523500
Phchi.S1	AUGUSTUS	transcript	32831169	32834951	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	stop_codon	32831166	32831168	.	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32831169	32831285	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32831169	32831285	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32831286	32831380	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32831381	32831471	1	-	1	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32831381	32831471	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32831472	32831585	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32831586	32831686	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32831586	32831686	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32831687	32831780	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32831781	32831879	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32831781	32831879	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32831880	32831969	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32831970	32832107	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32831970	32832107	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32832108	32832187	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32832188	32832856	0.99	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32832188	32832856	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32832857	32832958	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32832959	32833138	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32832959	32833138	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32833139	32833248	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32833249	32833381	1	-	1	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32833249	32833381	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32833382	32833473	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32833474	32833505	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32833474	32833505	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32833506	32833680	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32833681	32833737	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32833681	32833737	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32833738	32833904	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32833905	32833918	0.76	-	2	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32833905	32833918	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32833919	32834113	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32834114	32834190	0.39	-	1	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32834114	32834190	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32834191	32834302	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32834303	32834394	0.76	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32834303	32834394	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32834395	32834490	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32834491	32834538	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32834491	32834538	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32834539	32834659	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32834660	32834845	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32834660	32834845	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	intron	32834846	32834945	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	CDS	32834946	32834951	1	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	exon	32834946	32834951	.	-	.	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
Phchi.S1	AUGUSTUS	start_codon	32834949	32834951	.	-	0	transcript_id "Phchi.S1G523500.t1"; gene_id "Phchi.S1G523500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6206.t1 is derived from g3377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21470052	21471431	.	+	.	Phchi.S1G336500
Phchi.S1	AUGUSTUS	transcript	21470052	21471431	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	start_codon	21470052	21470054	.	+	0	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21470052	21470057	0.93	+	0	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21470052	21470057	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	intron	21470058	21470201	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21470202	21470214	0.63	+	0	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21470202	21470214	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	intron	21470215	21470380	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21470381	21470576	0.56	+	2	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21470381	21470576	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	intron	21470577	21470663	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21470664	21470788	1	+	1	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21470664	21470788	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	intron	21470789	21470920	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21470921	21471033	1	+	2	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21470921	21471033	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	intron	21471034	21471130	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21471131	21471322	1	+	0	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21471131	21471322	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	intron	21471323	21471404	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	CDS	21471405	21471431	1	+	0	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	exon	21471405	21471431	.	+	.	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
Phchi.S1	AUGUSTUS	stop_codon	21471432	21471434	.	+	0	transcript_id "Phchi.S1G336500.t1"; gene_id "Phchi.S1G336500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6111.t1 is derived from g3282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20987629	20988702	.	+	.	Phchi.S1G327000
Phchi.S1	AUGUSTUS	transcript	20987629	20988702	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	start_codon	20987629	20987631	.	+	0	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	CDS	20987629	20987650	0.89	+	0	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	exon	20987629	20987650	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	intron	20987651	20987778	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	CDS	20987779	20987889	0.66	+	2	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	exon	20987779	20987889	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	intron	20987890	20988078	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	CDS	20988079	20988254	0.65	+	2	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	exon	20988079	20988254	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	intron	20988255	20988343	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	CDS	20988344	20988361	0.47	+	0	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	exon	20988344	20988361	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	intron	20988362	20988438	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	CDS	20988439	20988702	0.24	+	0	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	exon	20988439	20988702	.	+	.	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
Phchi.S1	AUGUSTUS	stop_codon	20988703	20988705	.	+	0	transcript_id "Phchi.S1G327000.t1"; gene_id "Phchi.S1G327000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2484.t1 is derived from g9404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6877087	6878482	.	-	.	Phchi.S5G109300
Phchi.S5	AUGUSTUS	transcript	6877087	6878482	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	stop_codon	6877084	6877086	.	-	0	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	CDS	6877087	6877236	1	-	0	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	exon	6877087	6877236	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	intron	6877237	6877331	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	CDS	6877332	6877502	1	-	0	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	exon	6877332	6877502	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	intron	6877503	6877604	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	CDS	6877605	6877713	1	-	1	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	exon	6877605	6877713	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	intron	6877714	6877809	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	CDS	6877810	6877916	1	-	0	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	exon	6877810	6877916	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	intron	6877917	6878019	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	CDS	6878020	6878240	0.49	-	2	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	exon	6878020	6878240	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	intron	6878241	6878397	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	CDS	6878398	6878482	0.76	-	0	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	exon	6878398	6878482	.	-	.	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
Phchi.S5	AUGUSTUS	start_codon	6878480	6878482	.	-	0	transcript_id "Phchi.S5G109300.t1"; gene_id "Phchi.S5G109300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1974.t1 is derived from g8894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4090669	4092934	.	+	.	Phchi.S5G058300
Phchi.S5	AUGUSTUS	transcript	4090669	4092934	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	start_codon	4090669	4090671	.	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4090669	4090932	0.99	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4090669	4090932	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4090933	4091151	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4091152	4091256	1	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4091152	4091256	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4091257	4091350	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4091351	4091422	1	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4091351	4091422	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4091423	4091522	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4091523	4092206	0.95	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4091523	4092206	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4092207	4092287	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4092288	4092404	1	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4092288	4092404	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4092405	4092493	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4092494	4092528	0.99	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4092494	4092528	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4092529	4092641	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4092642	4092684	1	+	1	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4092642	4092684	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	intron	4092685	4092778	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	CDS	4092779	4092934	1	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	exon	4092779	4092934	.	+	.	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
Phchi.S5	AUGUSTUS	stop_codon	4092935	4092937	.	+	0	transcript_id "Phchi.S5G058300.t1"; gene_id "Phchi.S5G058300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7082.t1 is derived from g4254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26801918	26803480	.	-	.	Phchi.S1G424100
Phchi.S1	AUGUSTUS	transcript	26801918	26803480	.	-	.	transcript_id "Phchi.S1G424100.t1"; gene_id "Phchi.S1G424100"
Phchi.S1	AUGUSTUS	stop_codon	26801915	26801917	.	-	0	transcript_id "Phchi.S1G424100.t1"; gene_id "Phchi.S1G424100"
Phchi.S1	AUGUSTUS	CDS	26801918	26803480	1	-	0	transcript_id "Phchi.S1G424100.t1"; gene_id "Phchi.S1G424100"
Phchi.S1	AUGUSTUS	exon	26801918	26803480	.	-	.	transcript_id "Phchi.S1G424100.t1"; gene_id "Phchi.S1G424100"
Phchi.S1	AUGUSTUS	start_codon	26803478	26803480	.	-	0	transcript_id "Phchi.S1G424100.t1"; gene_id "Phchi.S1G424100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11884.t1 is derived from g15936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8994517	8995008	.	+	.	Phchi.S4G146600
Phchi.S4	AUGUSTUS	transcript	8994517	8995008	.	+	.	transcript_id "Phchi.S4G146600.t1"; gene_id "Phchi.S4G146600"
Phchi.S4	AUGUSTUS	start_codon	8994517	8994519	.	+	0	transcript_id "Phchi.S4G146600.t1"; gene_id "Phchi.S4G146600"
Phchi.S4	AUGUSTUS	CDS	8994517	8995008	0.67	+	0	transcript_id "Phchi.S4G146600.t1"; gene_id "Phchi.S4G146600"
Phchi.S4	AUGUSTUS	exon	8994517	8995008	.	+	.	transcript_id "Phchi.S4G146600.t1"; gene_id "Phchi.S4G146600"
Phchi.S4	AUGUSTUS	stop_codon	8995009	8995011	.	+	0	transcript_id "Phchi.S4G146600.t1"; gene_id "Phchi.S4G146600"
# This transcript jg6018.t2 is derived from g3189.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6019.t1 is derived from g3190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20466506	20468075	.	+	.	Phchi.S1G317800
Phchi.S1	AUGUSTUS	transcript	20466506	20468075	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	start_codon	20466506	20466508	.	+	0	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	CDS	20466506	20466662	0.28	+	0	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	exon	20466506	20466662	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	intron	20466663	20466750	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	CDS	20466751	20466959	0.82	+	2	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	exon	20466751	20466959	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	intron	20466960	20467033	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	CDS	20467034	20467332	1	+	0	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	exon	20467034	20467332	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	intron	20467333	20467423	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	CDS	20467424	20468075	0.99	+	1	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	exon	20467424	20468075	.	+	.	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
Phchi.S1	AUGUSTUS	stop_codon	20468076	20468078	.	+	0	transcript_id "Phchi.S1G317800.t1"; gene_id "Phchi.S1G317800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7754.t1 is derived from g4928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31148674	31150687	.	+	.	Phchi.S1G491300
Phchi.S1	AUGUSTUS	transcript	31148674	31150687	.	+	.	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	start_codon	31148674	31148676	.	+	0	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	CDS	31148674	31148928	1	+	0	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	exon	31148674	31148928	.	+	.	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	intron	31148929	31149229	.	+	.	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	CDS	31149230	31150687	1	+	0	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	exon	31149230	31150687	.	+	.	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
Phchi.S1	AUGUSTUS	stop_codon	31150688	31150690	.	+	0	transcript_id "Phchi.S1G491300.t1"; gene_id "Phchi.S1G491300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2703.t1 is derived from g9623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8256329	8258817	.	-	.	Phchi.S5G131200
Phchi.S5	AUGUSTUS	transcript	8256329	8258817	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	stop_codon	8256326	8256328	.	-	0	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8256329	8257622	0.56	-	1	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8256329	8257622	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	intron	8257623	8257732	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8257733	8257812	1	-	0	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8257733	8257812	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	intron	8257813	8257946	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8257947	8258003	1	-	0	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8257947	8258003	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	intron	8258004	8258146	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8258147	8258240	1	-	1	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8258147	8258240	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	intron	8258241	8258320	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8258321	8258407	0.98	-	1	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8258321	8258407	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	intron	8258408	8258516	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8258517	8258615	0.98	-	1	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8258517	8258615	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	intron	8258616	8258686	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	CDS	8258687	8258817	0.97	-	0	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	exon	8258687	8258817	.	-	.	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
Phchi.S5	AUGUSTUS	start_codon	8258815	8258817	.	-	0	transcript_id "Phchi.S5G131200.t1"; gene_id "Phchi.S5G131200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4760.t1 is derived from g1930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12685616	12687382	.	-	.	Phchi.S1G191900
Phchi.S1	AUGUSTUS	transcript	12685616	12687382	.	-	.	transcript_id "Phchi.S1G191900.t1"; gene_id "Phchi.S1G191900"
Phchi.S1	AUGUSTUS	stop_codon	12685613	12685615	.	-	0	transcript_id "Phchi.S1G191900.t1"; gene_id "Phchi.S1G191900"
Phchi.S1	AUGUSTUS	CDS	12685616	12687382	0.74	-	0	transcript_id "Phchi.S1G191900.t1"; gene_id "Phchi.S1G191900"
Phchi.S1	AUGUSTUS	exon	12685616	12687382	.	-	.	transcript_id "Phchi.S1G191900.t1"; gene_id "Phchi.S1G191900"
Phchi.S1	AUGUSTUS	start_codon	12687380	12687382	.	-	0	transcript_id "Phchi.S1G191900.t1"; gene_id "Phchi.S1G191900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10391.t1 is derived from g7567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47516894	47518029	.	-	.	Phchi.S1G755000
Phchi.S1	AUGUSTUS	transcript	47516894	47518029	.	-	.	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	stop_codon	47516891	47516893	.	-	0	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	CDS	47516894	47516895	0.6	-	2	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	exon	47516894	47516895	.	-	.	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	intron	47516896	47517011	.	-	.	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	CDS	47517012	47517219	0.54	-	0	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	exon	47517012	47517219	.	-	.	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	intron	47517220	47517387	.	-	.	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	CDS	47517388	47518029	0.58	-	0	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	exon	47517388	47518029	.	-	.	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
Phchi.S1	AUGUSTUS	start_codon	47518027	47518029	.	-	0	transcript_id "Phchi.S1G755000.t1"; gene_id "Phchi.S1G755000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14091.t1 is derived from g12558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10803795	10806160	.	+	.	Phchi.S3G141000
Phchi.S3	AUGUSTUS	transcript	10803795	10806160	.	+	.	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	start_codon	10803795	10803797	.	+	0	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	CDS	10803795	10804881	0.88	+	0	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	exon	10803795	10804881	.	+	.	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	intron	10804882	10805219	.	+	.	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	CDS	10805220	10805407	1	+	2	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	exon	10805220	10805407	.	+	.	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	intron	10805408	10805521	.	+	.	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	CDS	10805522	10806160	1	+	0	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	exon	10805522	10806160	.	+	.	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
Phchi.S3	AUGUSTUS	stop_codon	10806161	10806163	.	+	0	transcript_id "Phchi.S3G141000.t1"; gene_id "Phchi.S3G141000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9600.t1 is derived from g6776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42883412	42884518	.	-	.	Phchi.S1G675900
Phchi.S1	AUGUSTUS	transcript	42883412	42884518	.	-	.	transcript_id "Phchi.S1G675900.t1"; gene_id "Phchi.S1G675900"
Phchi.S1	AUGUSTUS	stop_codon	42883409	42883411	.	-	0	transcript_id "Phchi.S1G675900.t1"; gene_id "Phchi.S1G675900"
Phchi.S1	AUGUSTUS	CDS	42883412	42884518	0.87	-	0	transcript_id "Phchi.S1G675900.t1"; gene_id "Phchi.S1G675900"
Phchi.S1	AUGUSTUS	exon	42883412	42884518	.	-	.	transcript_id "Phchi.S1G675900.t1"; gene_id "Phchi.S1G675900"
Phchi.S1	AUGUSTUS	start_codon	42884516	42884518	.	-	0	transcript_id "Phchi.S1G675900.t1"; gene_id "Phchi.S1G675900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7822.t1 is derived from g4996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31373987	31377960	.	-	.	Phchi.S1G498100
Phchi.S1	AUGUSTUS	transcript	31373987	31377960	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	stop_codon	31373984	31373986	.	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	CDS	31373987	31374910	0.99	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	exon	31373987	31374910	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	intron	31374911	31375000	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	CDS	31375001	31375114	0.94	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	exon	31375001	31375114	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	intron	31375115	31375219	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	CDS	31375220	31375771	1	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	exon	31375220	31375771	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	intron	31375772	31375862	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	CDS	31375863	31376045	0.99	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	exon	31375863	31376045	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	intron	31376046	31377222	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	CDS	31377223	31377960	0.96	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	exon	31377223	31377960	.	-	.	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
Phchi.S1	AUGUSTUS	start_codon	31377958	31377960	.	-	0	transcript_id "Phchi.S1G498100.t1"; gene_id "Phchi.S1G498100"
# This transcript jg1539.t2 is derived from g8458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1540.t1 is derived from g8459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1675799	1677245	.	-	.	Phchi.S5G014900
Phchi.S5	AUGUSTUS	transcript	1675799	1677245	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	stop_codon	1675796	1675798	.	-	0	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	CDS	1675799	1675897	0.21	-	0	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	exon	1675799	1675897	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	intron	1675898	1676141	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	CDS	1676142	1676200	0.85	-	2	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	exon	1676142	1676200	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	intron	1676201	1676434	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	CDS	1676435	1676527	0.39	-	2	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	exon	1676435	1676527	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	intron	1676528	1676761	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	CDS	1676762	1677245	0.59	-	0	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	exon	1676762	1677245	.	-	.	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
Phchi.S5	AUGUSTUS	start_codon	1677243	1677245	.	-	0	transcript_id "Phchi.S5G014900.t1"; gene_id "Phchi.S5G014900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12307.t1 is derived from g7983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9920677	9927488	.	-	.	Phchi.S2G038700
Phchi.S2	AUGUSTUS	transcript	9920677	9927488	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	stop_codon	9920674	9920676	.	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9920677	9920809	0.46	-	1	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9920677	9920809	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9920810	9920902	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9920903	9920979	0.52	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9920903	9920979	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9920980	9921100	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9921101	9921190	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9921101	9921190	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9921191	9921280	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9921281	9921448	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9921281	9921448	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9921449	9921767	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9921768	9921860	0.96	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9921768	9921860	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9921861	9921971	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9921972	9922094	0.96	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9921972	9922094	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9922095	9922323	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9922324	9922419	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9922324	9922419	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9922420	9922500	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9922501	9922704	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9922501	9922704	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9922705	9923002	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9923003	9923092	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9923003	9923092	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9923093	9923311	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9923312	9923438	1	-	1	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9923312	9923438	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9923439	9923544	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9923545	9923657	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9923545	9923657	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9923658	9923757	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9923758	9923961	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9923758	9923961	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9923962	9924526	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9924527	9924655	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9924527	9924655	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9924656	9924932	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9924933	9925200	0.98	-	1	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9924933	9925200	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9925201	9926006	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9926007	9926158	1	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9926007	9926158	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9926159	9926239	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9926240	9926444	1	-	1	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9926240	9926444	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	intron	9926445	9926634	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	CDS	9926635	9927488	0.98	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	exon	9926635	9927488	.	-	.	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
Phchi.S2	AUGUSTUS	start_codon	9927486	9927488	.	-	0	transcript_id "Phchi.S2G038700.t1"; gene_id "Phchi.S2G038700"
# This transcript jg15579.t2 is derived from g14048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15580.t1 is derived from g14049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20117057	20120213	.	-	.	Phchi.S3G289900
Phchi.S3	AUGUSTUS	transcript	20117057	20120213	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	stop_codon	20117054	20117056	.	-	0	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20117057	20117094	1	-	2	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20117057	20117094	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20117095	20117363	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20117364	20118423	1	-	0	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20117364	20118423	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20118424	20118515	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20118516	20118802	0.99	-	2	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20118516	20118802	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20118803	20118903	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20118904	20119055	0.99	-	1	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20118904	20119055	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20119056	20119202	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20119203	20119378	1	-	0	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20119203	20119378	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20119379	20119499	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20119500	20119640	1	-	0	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20119500	20119640	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20119641	20119795	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20119796	20119877	1	-	1	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20119796	20119877	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	intron	20119878	20119983	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	CDS	20119984	20120213	1	-	0	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	exon	20119984	20120213	.	-	.	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
Phchi.S3	AUGUSTUS	start_codon	20120211	20120213	.	-	0	transcript_id "Phchi.S3G289900.t1"; gene_id "Phchi.S3G289900"
# This transcript jg1761.t2 is derived from g8681.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1762.t1 is derived from g8682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2922432	2925601	.	-	.	Phchi.S5G037100
Phchi.S5	AUGUSTUS	transcript	2922432	2925601	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	stop_codon	2922429	2922431	.	-	0	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	CDS	2922432	2922517	1	-	2	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	exon	2922432	2922517	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	intron	2922518	2922599	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	CDS	2922600	2922672	0.99	-	0	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	exon	2922600	2922672	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	intron	2922673	2922846	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	CDS	2922847	2922987	0.99	-	0	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	exon	2922847	2922987	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	intron	2922988	2923180	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	CDS	2923181	2924105	0.43	-	1	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	exon	2923181	2924105	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	intron	2924106	2924648	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	CDS	2924649	2925601	0.68	-	0	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	exon	2924649	2925601	.	-	.	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
Phchi.S5	AUGUSTUS	start_codon	2925599	2925601	.	-	0	transcript_id "Phchi.S5G037100.t1"; gene_id "Phchi.S5G037100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8844.t1 is derived from g6019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38251907	38254246	.	+	.	Phchi.S1G600300
Phchi.S1	AUGUSTUS	transcript	38251907	38254246	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	start_codon	38251907	38251909	.	+	0	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38251907	38252041	0.49	+	0	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38251907	38252041	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	intron	38252042	38252149	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38252150	38252318	0.54	+	0	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38252150	38252318	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	intron	38252319	38252458	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38252459	38252491	0.78	+	2	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38252459	38252491	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	intron	38252492	38252586	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38252587	38252741	0.62	+	2	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38252587	38252741	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	intron	38252742	38252918	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38252919	38253411	0.91	+	0	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38252919	38253411	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	intron	38253412	38253519	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38253520	38253596	0.92	+	2	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38253520	38253596	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	intron	38253597	38253706	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	CDS	38253707	38254246	0.89	+	0	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	exon	38253707	38254246	.	+	.	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
Phchi.S1	AUGUSTUS	stop_codon	38254247	38254249	.	+	0	transcript_id "Phchi.S1G600300.t1"; gene_id "Phchi.S1G600300"
# This transcript jg11174.t2 is derived from g15224.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11175.t1 is derived from g15225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4498483	4500760	.	+	.	Phchi.S4G075700
Phchi.S4	AUGUSTUS	transcript	4498483	4500760	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	start_codon	4498483	4498485	.	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4498483	4499334	1	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4498483	4499334	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4499335	4499421	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4499422	4499483	1	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4499422	4499483	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4499484	4499578	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4499579	4499630	1	+	1	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4499579	4499630	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4499631	4499706	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4499707	4499821	1	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4499707	4499821	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4499822	4499900	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4499901	4499995	0.62	+	2	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4499901	4499995	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4499996	4500096	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4500097	4500203	1	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4500097	4500203	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4500204	4500351	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4500352	4500466	1	+	1	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4500352	4500466	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4500467	4500563	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4500564	4500608	1	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4500564	4500608	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	intron	4500609	4500691	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	CDS	4500692	4500760	1	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	exon	4500692	4500760	.	+	.	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
Phchi.S4	AUGUSTUS	stop_codon	4500761	4500763	.	+	0	transcript_id "Phchi.S4G075700.t1"; gene_id "Phchi.S4G075700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9353.t1 is derived from g6529.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41099291	41102375	.	+	.	Phchi.S1G651200
Phchi.S1	AUGUSTUS	transcript	41099291	41102375	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	start_codon	41099291	41099293	.	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41099291	41099467	1	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41099291	41099467	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41099468	41099590	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41099591	41099735	1	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41099591	41099735	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41099736	41099830	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41099831	41099966	0.97	+	2	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41099831	41099966	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41099967	41100068	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100069	41100183	0.96	+	1	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100069	41100183	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100184	41100346	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100347	41100413	0.99	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100347	41100413	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100414	41100521	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100522	41100613	0.99	+	2	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100522	41100613	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100614	41100742	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100743	41100805	1	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100743	41100805	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100806	41100885	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100886	41100956	1	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100886	41100956	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100957	41101040	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101041	41101093	1	+	1	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101041	41101093	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41101094	41101208	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101209	41101349	0.98	+	2	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101209	41101349	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41101350	41101475	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101476	41101636	1	+	2	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101476	41101636	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41101637	41101935	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101936	41102058	1	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101936	41102058	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41102059	41102330	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41102331	41102375	1	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41102331	41102375	.	+	.	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	stop_codon	41102376	41102378	.	+	0	transcript_id "Phchi.S1G651200.t1"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	transcript	41099291	41102241	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	start_codon	41099291	41099293	.	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41099291	41099467	1	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41099291	41099467	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41099468	41099590	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41099591	41099735	1	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41099591	41099735	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41099736	41099830	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41099831	41099966	0.93	+	2	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41099831	41099966	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41099967	41100068	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100069	41100183	0.94	+	1	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100069	41100183	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100184	41100346	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100347	41100413	0.97	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100347	41100413	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100414	41100521	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100522	41100613	0.97	+	2	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100522	41100613	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100614	41100742	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100743	41100805	1	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100743	41100805	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100806	41100885	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41100886	41100956	1	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41100886	41100956	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41100957	41101040	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101041	41101093	1	+	1	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101041	41101093	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41101094	41101208	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101209	41101349	0.99	+	2	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101209	41101349	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41101350	41101475	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101476	41101636	1	+	2	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101476	41101636	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41101637	41101935	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41101936	41102058	1	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41101936	41102058	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	intron	41102059	41102145	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	CDS	41102146	41102241	1	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	exon	41102146	41102241	.	+	.	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
Phchi.S1	AUGUSTUS	stop_codon	41102242	41102244	.	+	0	transcript_id "Phchi.S1G651200.t2"; gene_id "Phchi.S1G651200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4132.t1 is derived from g1301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8431089	8432957	.	+	.	Phchi.S1G129100
Phchi.S1	AUGUSTUS	transcript	8431089	8432957	.	+	.	transcript_id "Phchi.S1G129100.t1"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	start_codon	8431089	8431091	.	+	0	transcript_id "Phchi.S1G129100.t1"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	CDS	8431089	8432957	0.6	+	0	transcript_id "Phchi.S1G129100.t1"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	exon	8431089	8432957	.	+	.	transcript_id "Phchi.S1G129100.t1"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	stop_codon	8432958	8432960	.	+	0	transcript_id "Phchi.S1G129100.t1"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	transcript	8431644	8432957	.	+	.	transcript_id "Phchi.S1G129100.t2"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	start_codon	8431644	8431646	.	+	0	transcript_id "Phchi.S1G129100.t2"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	CDS	8431644	8432957	0.42	+	0	transcript_id "Phchi.S1G129100.t2"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	exon	8431644	8432957	.	+	.	transcript_id "Phchi.S1G129100.t2"; gene_id "Phchi.S1G129100"
Phchi.S1	AUGUSTUS	stop_codon	8432958	8432960	.	+	0	transcript_id "Phchi.S1G129100.t2"; gene_id "Phchi.S1G129100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5944.t1 is derived from g3115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19962969	19964282	.	-	.	Phchi.S1G310300
Phchi.S1	AUGUSTUS	transcript	19962969	19964282	.	-	.	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	stop_codon	19962966	19962968	.	-	0	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	CDS	19962969	19963385	0.98	-	0	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	exon	19962969	19963385	.	-	.	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	intron	19963386	19963577	.	-	.	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	CDS	19963578	19964282	0.98	-	0	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	exon	19963578	19964282	.	-	.	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
Phchi.S1	AUGUSTUS	start_codon	19964280	19964282	.	-	0	transcript_id "Phchi.S1G310300.t1"; gene_id "Phchi.S1G310300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6931.t1 is derived from g4103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26038760	26039904	.	+	.	Phchi.S1G409000
Phchi.S1	AUGUSTUS	transcript	26038760	26039904	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	start_codon	26038760	26038762	.	+	0	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	CDS	26038760	26038825	0.79	+	0	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	exon	26038760	26038825	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	intron	26038826	26038943	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	CDS	26038944	26039071	1	+	0	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	exon	26038944	26039071	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	intron	26039072	26039271	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	CDS	26039272	26039415	1	+	1	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	exon	26039272	26039415	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	intron	26039416	26039544	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	CDS	26039545	26039748	1	+	1	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	exon	26039545	26039748	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	intron	26039749	26039852	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	CDS	26039853	26039904	1	+	1	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	exon	26039853	26039904	.	+	.	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
Phchi.S1	AUGUSTUS	stop_codon	26039905	26039907	.	+	0	transcript_id "Phchi.S1G409000.t1"; gene_id "Phchi.S1G409000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12951.t1 is derived from g11416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3286646	3288122	.	-	.	Phchi.S3G027000
Phchi.S3	AUGUSTUS	transcript	3286646	3288122	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	stop_codon	3286643	3286645	.	-	0	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	CDS	3286646	3287486	1	-	1	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	exon	3286646	3287486	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	intron	3287487	3287563	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	CDS	3287564	3287833	1	-	1	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	exon	3287564	3287833	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	intron	3287834	3287913	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	CDS	3287914	3288011	1	-	0	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	exon	3287914	3288011	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	intron	3288012	3288110	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	CDS	3288111	3288122	1	-	0	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	exon	3288111	3288122	.	-	.	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
Phchi.S3	AUGUSTUS	start_codon	3288120	3288122	.	-	0	transcript_id "Phchi.S3G027000.t1"; gene_id "Phchi.S3G027000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15127.t1 is derived from g13595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17192712	17194568	.	+	.	Phchi.S3G244600
Phchi.S3	AUGUSTUS	transcript	17192712	17194568	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	start_codon	17192712	17192714	.	+	0	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	CDS	17192712	17193191	0.99	+	0	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	exon	17192712	17193191	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	intron	17193192	17193470	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	CDS	17193471	17193596	0.82	+	0	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	exon	17193471	17193596	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	intron	17193597	17193733	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	CDS	17193734	17193915	0.87	+	0	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	exon	17193734	17193915	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	intron	17193916	17194012	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	CDS	17194013	17194568	0.99	+	1	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	exon	17194013	17194568	.	+	.	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
Phchi.S3	AUGUSTUS	stop_codon	17194569	17194571	.	+	0	transcript_id "Phchi.S3G244600.t1"; gene_id "Phchi.S3G244600"
# This transcript jg4948.t2 is derived from g2118.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4949.t1 is derived from g2119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13690342	13691778	.	-	.	Phchi.S1G210800
Phchi.S1	AUGUSTUS	transcript	13690342	13691778	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	stop_codon	13690339	13690341	.	-	0	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13690342	13690571	1	-	2	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13690342	13690571	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	intron	13690572	13690656	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13690657	13690751	1	-	1	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13690657	13690751	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	intron	13690752	13690827	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13690828	13690997	0.92	-	0	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13690828	13690997	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	intron	13690998	13691148	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13691149	13691247	0.75	-	0	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13691149	13691247	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	intron	13691248	13691323	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13691324	13691397	1	-	2	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13691324	13691397	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	intron	13691398	13691512	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13691513	13691554	0.92	-	2	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13691513	13691554	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	intron	13691555	13691630	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	CDS	13691631	13691778	0.79	-	0	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	exon	13691631	13691778	.	-	.	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
Phchi.S1	AUGUSTUS	start_codon	13691776	13691778	.	-	0	transcript_id "Phchi.S1G210800.t1"; gene_id "Phchi.S1G210800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9155.t1 is derived from g6330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40124291	40126557	.	-	.	Phchi.S1G631400
Phchi.S1	AUGUSTUS	transcript	40124291	40126557	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	stop_codon	40124288	40124290	.	-	0	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124291	40124306	0.94	-	1	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124291	40124306	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40124307	40124437	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124438	40124516	0.95	-	2	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124438	40124516	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40124517	40124718	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124719	40124746	1	-	0	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124719	40124746	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40124747	40125149	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40125150	40125374	1	-	0	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40125150	40125374	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40125375	40125543	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40125544	40126557	0.92	-	0	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40125544	40126557	.	-	.	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	start_codon	40126555	40126557	.	-	0	transcript_id "Phchi.S1G631400.t1"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	transcript	40124291	40126557	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	stop_codon	40124288	40124290	.	-	0	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124291	40124306	0.96	-	1	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124291	40124306	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40124307	40124437	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124438	40124516	0.96	-	2	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124438	40124516	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40124517	40124718	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124719	40124746	1	-	0	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124719	40124746	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40124747	40124926	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40124927	40125015	0.87	-	2	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40124927	40125015	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40125016	40125268	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40125269	40125374	0.85	-	0	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40125269	40125374	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	intron	40125375	40125543	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	CDS	40125544	40126557	0.97	-	0	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	exon	40125544	40126557	.	-	.	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
Phchi.S1	AUGUSTUS	start_codon	40126555	40126557	.	-	0	transcript_id "Phchi.S1G631400.t2"; gene_id "Phchi.S1G631400"
# This transcript jg3946.t2 is derived from g1115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3947.t1 is derived from g1116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6593780	6594784	.	+	.	Phchi.S1G110600
Phchi.S1	AUGUSTUS	transcript	6593780	6594784	.	+	.	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	start_codon	6593780	6593782	.	+	0	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	CDS	6593780	6593855	0.28	+	0	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	exon	6593780	6593855	.	+	.	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	intron	6593856	6593951	.	+	.	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	CDS	6593952	6594071	0.66	+	2	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	exon	6593952	6594071	.	+	.	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	intron	6594072	6594278	.	+	.	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	CDS	6594279	6594784	0.73	+	2	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	exon	6594279	6594784	.	+	.	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
Phchi.S1	AUGUSTUS	stop_codon	6594785	6594787	.	+	0	transcript_id "Phchi.S1G110600.t1"; gene_id "Phchi.S1G110600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg906.t1 is derived from g10688.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6373691	6374818	.	-	.	Phchi.S6G086500
Phchi.S6	AUGUSTUS	transcript	6373691	6374818	.	-	.	transcript_id "Phchi.S6G086500.t1"; gene_id "Phchi.S6G086500"
Phchi.S6	AUGUSTUS	stop_codon	6373688	6373690	.	-	0	transcript_id "Phchi.S6G086500.t1"; gene_id "Phchi.S6G086500"
Phchi.S6	AUGUSTUS	CDS	6373691	6374818	0.95	-	0	transcript_id "Phchi.S6G086500.t1"; gene_id "Phchi.S6G086500"
Phchi.S6	AUGUSTUS	exon	6373691	6374818	.	-	.	transcript_id "Phchi.S6G086500.t1"; gene_id "Phchi.S6G086500"
Phchi.S6	AUGUSTUS	start_codon	6374816	6374818	.	-	0	transcript_id "Phchi.S6G086500.t1"; gene_id "Phchi.S6G086500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6349.t1 is derived from g3521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22440395	22442806	.	+	.	Phchi.S1G350800
Phchi.S1	AUGUSTUS	transcript	22440395	22441425	.	+	.	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	start_codon	22440395	22440397	.	+	0	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22440395	22440582	0.99	+	0	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22440395	22440582	.	+	.	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	intron	22440583	22440654	.	+	.	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22440655	22441142	0.93	+	1	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22440655	22441142	.	+	.	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	intron	22441143	22441417	.	+	.	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22441418	22441425	1	+	2	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22441418	22441425	.	+	.	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	stop_codon	22441426	22441428	.	+	0	transcript_id "Phchi.S1G350800.t1"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	transcript	22440395	22442806	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	start_codon	22440395	22440397	.	+	0	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22440395	22440582	1	+	0	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22440395	22440582	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	intron	22440583	22440654	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22440655	22441142	0.96	+	1	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22440655	22441142	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	intron	22441143	22441310	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22441311	22441358	0.93	+	2	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22441311	22441358	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	intron	22441359	22441742	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22441743	22441754	0.61	+	2	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22441743	22441754	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	intron	22441755	22441931	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	CDS	22441932	22442806	0.97	+	2	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	exon	22441932	22442806	.	+	.	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
Phchi.S1	AUGUSTUS	stop_codon	22442807	22442809	.	+	0	transcript_id "Phchi.S1G350800.t2"; gene_id "Phchi.S1G350800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12702.t1 is derived from g11167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	631271	632103	.	+	.	Phchi.S3G002100
Phchi.S3	AUGUSTUS	transcript	631271	632103	.	+	.	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	start_codon	631271	631273	.	+	0	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	CDS	631271	631664	0.45	+	0	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	exon	631271	631664	.	+	.	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	intron	631665	631765	.	+	.	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	CDS	631766	631897	1	+	2	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	exon	631766	631897	.	+	.	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	intron	631898	632026	.	+	.	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	CDS	632027	632103	0.83	+	2	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	exon	632027	632103	.	+	.	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
Phchi.S3	AUGUSTUS	stop_codon	632104	632106	.	+	0	transcript_id "Phchi.S3G002100.t1"; gene_id "Phchi.S3G002100"
# This transcript jg9028.t2 is derived from g6203.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9028.t3 is derived from g6203.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9029.t1 is derived from g6204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39216248	39219232	.	-	.	Phchi.S1G618800
Phchi.S1	AUGUSTUS	transcript	39216248	39219232	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	stop_codon	39216245	39216247	.	-	0	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	CDS	39216248	39217289	1	-	1	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	exon	39216248	39217289	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	intron	39217290	39217371	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	CDS	39217372	39217959	1	-	1	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	exon	39217372	39217959	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	intron	39217960	39218056	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	CDS	39218057	39218325	1	-	0	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	exon	39218057	39218325	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	intron	39218326	39218399	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	CDS	39218400	39218534	1	-	0	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	exon	39218400	39218534	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	intron	39218535	39218631	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	CDS	39218632	39218954	1	-	2	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	exon	39218632	39218954	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	intron	39218955	39219036	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	CDS	39219037	39219232	1	-	0	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	exon	39219037	39219232	.	-	.	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
Phchi.S1	AUGUSTUS	start_codon	39219230	39219232	.	-	0	transcript_id "Phchi.S1G618800.t1"; gene_id "Phchi.S1G618800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3926.t1 is derived from g1095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6455387	6457462	.	+	.	Phchi.S1G108500
Phchi.S1	AUGUSTUS	transcript	6455387	6457462	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	start_codon	6455387	6455389	.	+	0	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	CDS	6455387	6455795	0.52	+	0	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	exon	6455387	6455795	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	intron	6455796	6455900	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	CDS	6455901	6456193	0.7	+	2	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	exon	6455901	6456193	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	intron	6456194	6456317	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	CDS	6456318	6456463	0.36	+	0	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	exon	6456318	6456463	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	intron	6456464	6456558	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	CDS	6456559	6456604	0.37	+	1	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	exon	6456559	6456604	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	intron	6456605	6456700	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	CDS	6456701	6457068	0.64	+	0	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	exon	6456701	6457068	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	intron	6457069	6457206	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	CDS	6457207	6457462	1	+	1	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	exon	6457207	6457462	.	+	.	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
Phchi.S1	AUGUSTUS	stop_codon	6457463	6457465	.	+	0	transcript_id "Phchi.S1G108500.t1"; gene_id "Phchi.S1G108500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8833.t1 is derived from g6008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38199498	38201159	.	-	.	Phchi.S1G599200
Phchi.S1	AUGUSTUS	transcript	38199498	38201159	.	-	.	transcript_id "Phchi.S1G599200.t1"; gene_id "Phchi.S1G599200"
Phchi.S1	AUGUSTUS	stop_codon	38199495	38199497	.	-	0	transcript_id "Phchi.S1G599200.t1"; gene_id "Phchi.S1G599200"
Phchi.S1	AUGUSTUS	CDS	38199498	38201159	0.83	-	0	transcript_id "Phchi.S1G599200.t1"; gene_id "Phchi.S1G599200"
Phchi.S1	AUGUSTUS	exon	38199498	38201159	.	-	.	transcript_id "Phchi.S1G599200.t1"; gene_id "Phchi.S1G599200"
Phchi.S1	AUGUSTUS	start_codon	38201157	38201159	.	-	0	transcript_id "Phchi.S1G599200.t1"; gene_id "Phchi.S1G599200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5901.t1 is derived from g3071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19668910	19671432	.	+	.	Phchi.S1G306000
Phchi.S1	AUGUSTUS	transcript	19668910	19671432	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	start_codon	19668910	19668912	.	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19668910	19668966	0.9	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19668910	19668966	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19668967	19669119	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19669120	19669209	1	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19669120	19669209	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19669210	19669293	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19669294	19669360	1	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19669294	19669360	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19669361	19669435	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19669436	19669501	1	+	2	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19669436	19669501	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19669502	19669600	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19669601	19669685	1	+	2	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19669601	19669685	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19669686	19669906	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19669907	19669952	1	+	1	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19669907	19669952	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19669953	19670058	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19670059	19670113	1	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19670059	19670113	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19670114	19670220	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19670221	19670297	1	+	2	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19670221	19670297	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19670298	19670398	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19670399	19670654	0.73	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19670399	19670654	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19670655	19670724	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19670725	19670795	0.73	+	2	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19670725	19670795	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19670796	19670888	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19670889	19670993	1	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19670889	19670993	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19670994	19671078	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19671079	19671255	1	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19671079	19671255	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	intron	19671256	19671342	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	CDS	19671343	19671432	0.99	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	exon	19671343	19671432	.	+	.	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
Phchi.S1	AUGUSTUS	stop_codon	19671433	19671435	.	+	0	transcript_id "Phchi.S1G306000.t1"; gene_id "Phchi.S1G306000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12316.t1 is derived from g7992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10421519	10421956	.	-	.	Phchi.S2G039600
Phchi.S2	AUGUSTUS	transcript	10421519	10421956	.	-	.	transcript_id "Phchi.S2G039600.t1"; gene_id "Phchi.S2G039600"
Phchi.S2	AUGUSTUS	stop_codon	10421516	10421518	.	-	0	transcript_id "Phchi.S2G039600.t1"; gene_id "Phchi.S2G039600"
Phchi.S2	AUGUSTUS	CDS	10421519	10421956	0.68	-	0	transcript_id "Phchi.S2G039600.t1"; gene_id "Phchi.S2G039600"
Phchi.S2	AUGUSTUS	exon	10421519	10421956	.	-	.	transcript_id "Phchi.S2G039600.t1"; gene_id "Phchi.S2G039600"
Phchi.S2	AUGUSTUS	start_codon	10421954	10421956	.	-	0	transcript_id "Phchi.S2G039600.t1"; gene_id "Phchi.S2G039600"
# This transcript jg7684.t2 is derived from g4858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7684.t3 is derived from g4858.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7685.t1 is derived from g4859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30615844	30617593	.	-	.	Phchi.S1G484400
Phchi.S1	AUGUSTUS	transcript	30615844	30617593	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	stop_codon	30615841	30615843	.	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30615844	30616108	1	-	1	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30615844	30616108	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616109	30616200	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616201	30616305	1	-	1	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616201	30616305	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616306	30616403	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616404	30616462	1	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616404	30616462	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616463	30616536	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616537	30616710	0.66	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616537	30616710	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616711	30616820	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616821	30616934	0.89	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616821	30616934	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616935	30617113	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30617114	30617178	1	-	2	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30617114	30617178	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30617179	30617271	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30617272	30617437	1	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30617272	30617437	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30617438	30617524	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30617525	30617593	0.97	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30617525	30617593	.	-	.	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	start_codon	30617591	30617593	.	-	0	transcript_id "Phchi.S1G484400.t1"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	transcript	30615844	30617593	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	stop_codon	30615841	30615843	.	-	0	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30615844	30616108	1	-	1	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30615844	30616108	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616109	30616200	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616201	30616305	1	-	1	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616201	30616305	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616306	30616403	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616404	30616462	1	-	0	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616404	30616462	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616463	30616536	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616537	30616634	0.49	-	2	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616537	30616634	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616635	30616787	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30616788	30616923	0.72	-	0	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30616788	30616923	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30616924	30617113	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30617114	30617178	1	-	2	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30617114	30617178	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30617179	30617271	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30617272	30617437	1	-	0	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30617272	30617437	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	intron	30617438	30617524	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	CDS	30617525	30617593	0.96	-	0	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	exon	30617525	30617593	.	-	.	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
Phchi.S1	AUGUSTUS	start_codon	30617591	30617593	.	-	0	transcript_id "Phchi.S1G484400.t2"; gene_id "Phchi.S1G484400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1285.t1 is derived from g11068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8811244	8813102	.	+	.	Phchi.S6G124400
Phchi.S6	AUGUSTUS	transcript	8811244	8813102	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	start_codon	8811244	8811246	.	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8811244	8811519	0.96	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8811244	8811519	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8811520	8811620	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8811621	8811686	1	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8811621	8811686	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8811687	8811822	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8811823	8811897	0.99	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8811823	8811897	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8811898	8812004	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8812005	8812067	1	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8812005	8812067	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8812068	8812175	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8812176	8812235	1	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8812176	8812235	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8812236	8812322	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8812323	8812412	1	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8812323	8812412	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8812413	8812536	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8812537	8812644	1	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8812537	8812644	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8812645	8812756	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8812757	8812879	1	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8812757	8812879	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	intron	8812880	8812964	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	CDS	8812965	8813102	0.99	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	exon	8812965	8813102	.	+	.	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
Phchi.S6	AUGUSTUS	stop_codon	8813103	8813105	.	+	0	transcript_id "Phchi.S6G124400.t1"; gene_id "Phchi.S6G124400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5429.t1 is derived from g2599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16829803	16836125	.	+	.	Phchi.S1G258800
Phchi.S1	AUGUSTUS	transcript	16829803	16836125	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	start_codon	16829803	16829805	.	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16829803	16830995	1	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16829803	16830995	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16830996	16831161	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16831162	16831220	1	+	1	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16831162	16831220	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16831221	16831681	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16831682	16832883	1	+	2	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16831682	16832883	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16832884	16832990	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16832991	16833704	0.98	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16832991	16833704	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16833705	16833849	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16833850	16833958	0.83	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16833850	16833958	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16833959	16834062	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16834063	16834204	0.74	+	2	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16834063	16834204	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16834205	16834354	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16834355	16834422	1	+	1	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16834355	16834422	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16834423	16834507	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16834508	16834605	1	+	2	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16834508	16834605	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16834606	16834731	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16834732	16834968	1	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16834732	16834968	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16834969	16835123	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16835124	16835843	1	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16835124	16835843	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	intron	16835844	16835987	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	CDS	16835988	16836125	1	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	exon	16835988	16836125	.	+	.	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
Phchi.S1	AUGUSTUS	stop_codon	16836126	16836128	.	+	0	transcript_id "Phchi.S1G258800.t1"; gene_id "Phchi.S1G258800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15899.t1 is derived from g14369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22062207	22065367	.	-	.	Phchi.S3G321800
Phchi.S3	AUGUSTUS	transcript	22062207	22065367	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	stop_codon	22062204	22062206	.	-	0	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	CDS	22062207	22064634	0.76	-	1	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	exon	22062207	22064634	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	intron	22064635	22064724	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	CDS	22064725	22064777	0.61	-	0	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	exon	22064725	22064777	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	intron	22064778	22064893	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	CDS	22064894	22064974	0.61	-	0	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	exon	22064894	22064974	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	intron	22064975	22065060	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	CDS	22065061	22065140	1	-	2	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	exon	22065061	22065140	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	intron	22065141	22065216	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	CDS	22065217	22065367	1	-	0	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	exon	22065217	22065367	.	-	.	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
Phchi.S3	AUGUSTUS	start_codon	22065365	22065367	.	-	0	transcript_id "Phchi.S3G321800.t1"; gene_id "Phchi.S3G321800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4703.t1 is derived from g1873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12367836	12370603	.	-	.	Phchi.S1G186200
Phchi.S1	AUGUSTUS	transcript	12367836	12370603	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	stop_codon	12367833	12367835	.	-	0	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	CDS	12367836	12368147	0.98	-	0	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	exon	12367836	12368147	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	intron	12368148	12368241	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	CDS	12368242	12369521	0.7	-	2	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	exon	12368242	12369521	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	intron	12369522	12369707	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	CDS	12369708	12370201	0.89	-	1	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	exon	12369708	12370201	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	intron	12370202	12370301	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	CDS	12370302	12370603	0.94	-	0	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	exon	12370302	12370603	.	-	.	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
Phchi.S1	AUGUSTUS	start_codon	12370601	12370603	.	-	0	transcript_id "Phchi.S1G186200.t1"; gene_id "Phchi.S1G186200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1258.t1 is derived from g11041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8667405	8669756	.	-	.	Phchi.S6G121700
Phchi.S6	AUGUSTUS	transcript	8667405	8669756	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	stop_codon	8667402	8667404	.	-	0	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8667405	8667577	1	-	2	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8667405	8667577	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8667578	8667667	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8667668	8667794	1	-	0	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8667668	8667794	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8667795	8668001	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8668002	8668058	1	-	0	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8668002	8668058	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8668059	8668210	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8668211	8668310	1	-	1	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8668211	8668310	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8668311	8668404	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8668405	8668516	1	-	2	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8668405	8668516	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8668517	8668602	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8668603	8668683	0.63	-	2	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8668603	8668683	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8668684	8668794	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8668795	8669030	0.64	-	1	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8668795	8669030	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8669031	8669129	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8669130	8669254	1	-	0	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8669130	8669254	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	intron	8669255	8669378	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	CDS	8669379	8669756	0.36	-	0	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	exon	8669379	8669756	.	-	.	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
Phchi.S6	AUGUSTUS	start_codon	8669754	8669756	.	-	0	transcript_id "Phchi.S6G121700.t1"; gene_id "Phchi.S6G121700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4074.t1 is derived from g1243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7636088	7638814	.	+	.	Phchi.S1G123300
Phchi.S1	AUGUSTUS	transcript	7636088	7638814	.	+	.	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	start_codon	7636088	7636090	.	+	0	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	CDS	7636088	7637444	1	+	0	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	exon	7636088	7637444	.	+	.	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	intron	7637445	7638024	.	+	.	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	CDS	7638025	7638200	1	+	2	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	exon	7638025	7638200	.	+	.	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	intron	7638201	7638283	.	+	.	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	CDS	7638284	7638814	0.99	+	0	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	exon	7638284	7638814	.	+	.	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
Phchi.S1	AUGUSTUS	stop_codon	7638815	7638817	.	+	0	transcript_id "Phchi.S1G123300.t1"; gene_id "Phchi.S1G123300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6466.t1 is derived from g3638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23135285	23137771	.	-	.	Phchi.S1G362500
Phchi.S1	AUGUSTUS	transcript	23135285	23137771	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	stop_codon	23135282	23135284	.	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23135285	23135296	1	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23135285	23135296	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23135297	23135475	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23135476	23135679	1	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23135476	23135679	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23135680	23135843	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23135844	23135975	1	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23135844	23135975	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23135976	23136128	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23136129	23136425	0.99	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23136129	23136425	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23136426	23136559	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23136560	23136679	1	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23136560	23136679	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23136680	23136767	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23136768	23136982	1	-	2	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23136768	23136982	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23136983	23137095	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23137096	23137124	0.96	-	1	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23137096	23137124	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23137125	23137211	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23137212	23137537	0.99	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23137212	23137537	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	intron	23137538	23137624	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	CDS	23137625	23137771	0.75	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	exon	23137625	23137771	.	-	.	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
Phchi.S1	AUGUSTUS	start_codon	23137769	23137771	.	-	0	transcript_id "Phchi.S1G362500.t1"; gene_id "Phchi.S1G362500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14926.t1 is derived from g13394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15545537	15548582	.	+	.	Phchi.S3G224500
Phchi.S3	AUGUSTUS	transcript	15545537	15548582	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	start_codon	15545537	15545539	.	+	0	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15545537	15546267	0.65	+	0	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15545537	15546267	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	intron	15546268	15546416	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15546417	15546561	1	+	1	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15546417	15546561	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	intron	15546562	15546636	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15546637	15547869	0.92	+	0	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15546637	15547869	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	intron	15547870	15547962	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15547963	15548047	1	+	0	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15547963	15548047	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	intron	15548048	15548127	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15548128	15548186	1	+	2	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15548128	15548186	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	intron	15548187	15548319	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15548320	15548377	1	+	0	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15548320	15548377	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	intron	15548378	15548469	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	CDS	15548470	15548582	1	+	2	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	exon	15548470	15548582	.	+	.	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
Phchi.S3	AUGUSTUS	stop_codon	15548583	15548585	.	+	0	transcript_id "Phchi.S3G224500.t1"; gene_id "Phchi.S3G224500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15145.t1 is derived from g13613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17257180	17258474	.	-	.	Phchi.S3G246400
Phchi.S3	AUGUSTUS	transcript	17257180	17258474	.	-	.	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	stop_codon	17257177	17257179	.	-	0	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	CDS	17257180	17257740	0.6	-	0	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	exon	17257180	17257740	.	-	.	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	intron	17257741	17257877	.	-	.	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	CDS	17257878	17258474	0.16	-	0	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	exon	17257878	17258474	.	-	.	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
Phchi.S3	AUGUSTUS	start_codon	17258472	17258474	.	-	0	transcript_id "Phchi.S3G246400.t1"; gene_id "Phchi.S3G246400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3667.t1 is derived from g836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5072360	5073562	.	+	.	Phchi.S1G082600
Phchi.S1	AUGUSTUS	transcript	5072360	5073562	.	+	.	transcript_id "Phchi.S1G082600.t1"; gene_id "Phchi.S1G082600"
Phchi.S1	AUGUSTUS	start_codon	5072360	5072362	.	+	0	transcript_id "Phchi.S1G082600.t1"; gene_id "Phchi.S1G082600"
Phchi.S1	AUGUSTUS	CDS	5072360	5073562	0.52	+	0	transcript_id "Phchi.S1G082600.t1"; gene_id "Phchi.S1G082600"
Phchi.S1	AUGUSTUS	exon	5072360	5073562	.	+	.	transcript_id "Phchi.S1G082600.t1"; gene_id "Phchi.S1G082600"
Phchi.S1	AUGUSTUS	stop_codon	5073563	5073565	.	+	0	transcript_id "Phchi.S1G082600.t1"; gene_id "Phchi.S1G082600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8576.t1 is derived from g5751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36707936	36710180	.	-	.	Phchi.S1G573500
Phchi.S1	AUGUSTUS	transcript	36707936	36710180	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	stop_codon	36707933	36707935	.	-	0	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	CDS	36707936	36708531	0.79	-	2	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	exon	36707936	36708531	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	intron	36708532	36708667	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	CDS	36708668	36708912	0.77	-	1	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	exon	36708668	36708912	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	intron	36708913	36709196	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	CDS	36709197	36709252	0.98	-	0	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	exon	36709197	36709252	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	intron	36709253	36709345	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	CDS	36709346	36709423	1	-	0	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	exon	36709346	36709423	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	intron	36709424	36709675	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	CDS	36709676	36709803	1	-	2	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	exon	36709676	36709803	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	intron	36709804	36710062	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	CDS	36710063	36710180	1	-	0	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	exon	36710063	36710180	.	-	.	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
Phchi.S1	AUGUSTUS	start_codon	36710178	36710180	.	-	0	transcript_id "Phchi.S1G573500.t1"; gene_id "Phchi.S1G573500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10945.t1 is derived from g14995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3219250	3219870	.	-	.	Phchi.S4G052700
Phchi.S4	AUGUSTUS	transcript	3219250	3219870	.	-	.	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	stop_codon	3219247	3219249	.	-	0	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	CDS	3219250	3219716	0.99	-	2	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	exon	3219250	3219716	.	-	.	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	intron	3219717	3219803	.	-	.	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	CDS	3219804	3219870	0.81	-	0	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	exon	3219804	3219870	.	-	.	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
Phchi.S4	AUGUSTUS	start_codon	3219868	3219870	.	-	0	transcript_id "Phchi.S4G052700.t1"; gene_id "Phchi.S4G052700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2785.t1 is derived from g9705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8857220	8858744	.	+	.	Phchi.S5G139400
Phchi.S5	AUGUSTUS	transcript	8857220	8858744	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	start_codon	8857220	8857222	.	+	0	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	CDS	8857220	8857484	0.95	+	0	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	exon	8857220	8857484	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	intron	8857485	8857591	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	CDS	8857592	8857728	0.98	+	2	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	exon	8857592	8857728	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	intron	8857729	8857813	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	CDS	8857814	8858053	0.96	+	0	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	exon	8857814	8858053	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	intron	8858054	8858174	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	CDS	8858175	8858427	1	+	0	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	exon	8858175	8858427	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	intron	8858428	8858520	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	CDS	8858521	8858744	1	+	2	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	exon	8858521	8858744	.	+	.	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
Phchi.S5	AUGUSTUS	stop_codon	8858745	8858747	.	+	0	transcript_id "Phchi.S5G139400.t1"; gene_id "Phchi.S5G139400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12020.t1 is derived from g7695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	611883	613190	.	-	.	Phchi.S2G010000
Phchi.S2	AUGUSTUS	transcript	611883	613190	.	-	.	transcript_id "Phchi.S2G010000.t1"; gene_id "Phchi.S2G010000"
Phchi.S2	AUGUSTUS	stop_codon	611880	611882	.	-	0	transcript_id "Phchi.S2G010000.t1"; gene_id "Phchi.S2G010000"
Phchi.S2	AUGUSTUS	CDS	611883	613190	1	-	0	transcript_id "Phchi.S2G010000.t1"; gene_id "Phchi.S2G010000"
Phchi.S2	AUGUSTUS	exon	611883	613190	.	-	.	transcript_id "Phchi.S2G010000.t1"; gene_id "Phchi.S2G010000"
Phchi.S2	AUGUSTUS	start_codon	613188	613190	.	-	0	transcript_id "Phchi.S2G010000.t1"; gene_id "Phchi.S2G010000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2982.t1 is derived from g151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	960011	964298	.	-	.	Phchi.S1G014100
Phchi.S1	AUGUSTUS	transcript	960011	964298	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	stop_codon	960008	960010	.	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	960011	960021	0.73	-	2	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	960011	960021	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	960022	960317	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	960318	960324	0.73	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	960318	960324	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	960325	960498	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	960499	960617	0.34	-	2	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	960499	960617	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	960618	960715	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	960716	960902	0.8	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	960716	960902	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	960903	961042	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	961043	961147	0.62	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	961043	961147	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	961148	961224	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	961225	961396	1	-	1	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	961225	961396	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	961397	961487	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	961488	961633	1	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	961488	961633	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	961634	961723	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	961724	961894	1	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	961724	961894	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	961895	962020	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	962021	962128	0.98	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	962021	962128	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	962129	962245	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	962246	962349	0.86	-	2	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	962246	962349	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	962350	962462	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	962463	962655	0.62	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	962463	962655	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	962656	962768	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	962769	962969	0.62	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	962769	962969	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	962970	963053	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	963054	963196	1	-	2	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	963054	963196	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	963197	963347	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	963348	963435	1	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	963348	963435	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	963436	963520	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	963521	963650	1	-	1	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	963521	963650	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	963651	963748	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	963749	963811	1	-	1	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	963749	963811	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	963812	963925	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	963926	964104	1	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	963926	964104	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	intron	964105	964211	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	CDS	964212	964298	0.99	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	exon	964212	964298	.	-	.	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
Phchi.S1	AUGUSTUS	start_codon	964296	964298	.	-	0	transcript_id "Phchi.S1G014100.t1"; gene_id "Phchi.S1G014100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3508.t1 is derived from g677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4132109	4132621	.	-	.	Phchi.S1G066700
Phchi.S1	AUGUSTUS	transcript	4132109	4132621	.	-	.	transcript_id "Phchi.S1G066700.t1"; gene_id "Phchi.S1G066700"
Phchi.S1	AUGUSTUS	stop_codon	4132106	4132108	.	-	0	transcript_id "Phchi.S1G066700.t1"; gene_id "Phchi.S1G066700"
Phchi.S1	AUGUSTUS	CDS	4132109	4132621	0.66	-	0	transcript_id "Phchi.S1G066700.t1"; gene_id "Phchi.S1G066700"
Phchi.S1	AUGUSTUS	exon	4132109	4132621	.	-	.	transcript_id "Phchi.S1G066700.t1"; gene_id "Phchi.S1G066700"
Phchi.S1	AUGUSTUS	start_codon	4132619	4132621	.	-	0	transcript_id "Phchi.S1G066700.t1"; gene_id "Phchi.S1G066700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12518.t1 is derived from g8195.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32799854	32803324	.	-	.	Phchi.S2G059800
Phchi.S2	AUGUSTUS	transcript	32799854	32803324	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	stop_codon	32799851	32799853	.	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32799854	32800102	1	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32799854	32800102	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32800103	32800181	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32800182	32800646	0.99	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32800182	32800646	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32800647	32800733	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32800734	32800819	0.99	-	2	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32800734	32800819	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32800820	32800970	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32800971	32801417	0.67	-	2	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32800971	32801417	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32801418	32801555	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32801556	32801654	0.39	-	2	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32801556	32801654	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32801655	32801766	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32801767	32801891	0.54	-	1	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32801767	32801891	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32801892	32802086	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32802087	32802364	1	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32802087	32802364	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32802365	32802635	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32802636	32802788	1	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32802636	32802788	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32802789	32802876	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32802877	32803199	1	-	2	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32802877	32803199	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32803200	32803299	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32803300	32803324	0.98	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32803300	32803324	.	-	.	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	start_codon	32803322	32803324	.	-	0	transcript_id "Phchi.S2G059800.t1"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	transcript	32799854	32803324	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	stop_codon	32799851	32799853	.	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32799854	32800102	1	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32799854	32800102	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32800103	32800181	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32800182	32800646	0.95	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32800182	32800646	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32800647	32800733	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32800734	32800822	0.95	-	2	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32800734	32800822	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32800823	32800970	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32800971	32801417	0.6	-	2	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32800971	32801417	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32801418	32801555	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32801556	32801654	0.41	-	2	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32801556	32801654	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32801655	32801766	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32801767	32801891	0.58	-	1	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32801767	32801891	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32801892	32802086	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32802087	32802364	1	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32802087	32802364	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32802365	32802635	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32802636	32802788	1	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32802636	32802788	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32802789	32802876	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32802877	32803199	0.98	-	2	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32802877	32803199	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	intron	32803200	32803299	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	CDS	32803300	32803324	0.95	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	exon	32803300	32803324	.	-	.	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
Phchi.S2	AUGUSTUS	start_codon	32803322	32803324	.	-	0	transcript_id "Phchi.S2G059800.t2"; gene_id "Phchi.S2G059800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7755.t1 is derived from g4929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31151137	31152451	.	+	.	Phchi.S1G491400
Phchi.S1	AUGUSTUS	transcript	31151137	31152451	.	+	.	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	start_codon	31151137	31151139	.	+	0	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	CDS	31151137	31151764	0.41	+	0	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	exon	31151137	31151764	.	+	.	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	intron	31151765	31151936	.	+	.	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	CDS	31151937	31152451	0.25	+	2	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	exon	31151937	31152451	.	+	.	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
Phchi.S1	AUGUSTUS	stop_codon	31152452	31152454	.	+	0	transcript_id "Phchi.S1G491400.t1"; gene_id "Phchi.S1G491400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1844.t1 is derived from g8764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3531248	3533022	.	-	.	Phchi.S5G045300
Phchi.S5	AUGUSTUS	transcript	3531248	3533022	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	stop_codon	3531245	3531247	.	-	0	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3531248	3531591	0.94	-	2	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3531248	3531591	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3531592	3531698	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3531699	3531743	1	-	2	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3531699	3531743	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3531744	3531832	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3531833	3532321	1	-	2	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3531833	3532321	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3532322	3532417	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3532418	3532680	0.79	-	1	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3532418	3532680	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3532681	3532763	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3532764	3532906	0.98	-	0	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3532764	3532906	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3532907	3532989	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3532990	3533022	0.61	-	0	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3532990	3533022	.	-	.	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	start_codon	3533020	3533022	.	-	0	transcript_id "Phchi.S5G045300.t1"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	transcript	3531248	3533022	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	stop_codon	3531245	3531247	.	-	0	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3531248	3531591	0.91	-	2	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3531248	3531591	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3531592	3531698	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3531699	3531743	1	-	2	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3531699	3531743	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3531744	3531832	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3531833	3532336	1	-	2	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3531833	3532336	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3532337	3532417	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3532418	3532680	0.76	-	1	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3532418	3532680	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3532681	3532763	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3532764	3532906	0.97	-	0	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3532764	3532906	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	intron	3532907	3532989	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	CDS	3532990	3533022	0.69	-	0	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	exon	3532990	3533022	.	-	.	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
Phchi.S5	AUGUSTUS	start_codon	3533020	3533022	.	-	0	transcript_id "Phchi.S5G045300.t2"; gene_id "Phchi.S5G045300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10566.t1 is derived from g14616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1001546	1004338	.	+	.	Phchi.S4G014800
Phchi.S4	AUGUSTUS	transcript	1001546	1004338	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	start_codon	1001546	1001548	.	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1001546	1001875	0.78	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1001546	1001875	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1001876	1002012	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1002013	1002105	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1002013	1002105	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1002106	1002199	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1002200	1002265	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1002200	1002265	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1002266	1002342	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1002343	1002483	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1002343	1002483	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1002484	1002591	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1002592	1002819	0.98	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1002592	1002819	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1002820	1002934	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1002935	1003052	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1002935	1003052	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1003053	1003139	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1003140	1003279	1	+	2	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1003140	1003279	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1003280	1003364	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1003365	1003532	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1003365	1003532	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1003533	1003617	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1003618	1003773	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1003618	1003773	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1003774	1003891	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1003892	1004083	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1003892	1004083	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	intron	1004084	1004173	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	CDS	1004174	1004338	1	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	exon	1004174	1004338	.	+	.	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
Phchi.S4	AUGUSTUS	stop_codon	1004339	1004341	.	+	0	transcript_id "Phchi.S4G014800.t1"; gene_id "Phchi.S4G014800"
# This transcript jg8086.t2 is derived from g5261.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8087.t1 is derived from g5262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32884683	32886796	.	-	.	Phchi.S1G524600
Phchi.S1	AUGUSTUS	transcript	32884683	32886796	.	-	.	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	stop_codon	32884680	32884682	.	-	0	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	CDS	32884683	32885428	0.98	-	2	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	exon	32884683	32885428	.	-	.	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	intron	32885429	32885554	.	-	.	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	CDS	32885555	32885604	0.99	-	1	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	exon	32885555	32885604	.	-	.	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	intron	32885605	32885774	.	-	.	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	CDS	32885775	32886796	0.97	-	0	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	exon	32885775	32886796	.	-	.	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
Phchi.S1	AUGUSTUS	start_codon	32886794	32886796	.	-	0	transcript_id "Phchi.S1G524600.t1"; gene_id "Phchi.S1G524600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14358.t1 is derived from g12825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12353381	12353828	.	+	.	Phchi.S3G167700
Phchi.S3	AUGUSTUS	transcript	12353381	12353828	.	+	.	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	start_codon	12353381	12353383	.	+	0	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	CDS	12353381	12353462	1	+	0	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	exon	12353381	12353462	.	+	.	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	intron	12353463	12353616	.	+	.	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	CDS	12353617	12353828	0.99	+	2	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	exon	12353617	12353828	.	+	.	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
Phchi.S3	AUGUSTUS	stop_codon	12353829	12353831	.	+	0	transcript_id "Phchi.S3G167700.t1"; gene_id "Phchi.S3G167700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1642.t1 is derived from g8561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2164533	2170721	.	+	.	Phchi.S5G025100
Phchi.S5	AUGUSTUS	transcript	2164533	2170721	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	start_codon	2164533	2164535	.	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2164533	2164609	0.99	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2164533	2164609	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2164610	2165114	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2165115	2165708	0.97	+	1	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2165115	2165708	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2165709	2165997	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2165998	2166253	0.84	+	1	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2165998	2166253	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2166254	2166383	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2166384	2167144	0.96	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2166384	2167144	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2167145	2167283	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2167284	2167395	1	+	1	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2167284	2167395	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2167396	2167807	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2167808	2167989	1	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2167808	2167989	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2167990	2168149	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2168150	2168434	1	+	1	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2168150	2168434	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2168435	2168540	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2168541	2168748	1	+	1	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2168541	2168748	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2168749	2168839	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2168840	2168914	1	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2168840	2168914	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2168915	2169080	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2169081	2169359	0.99	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2169081	2169359	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2169360	2169474	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2169475	2169744	0.93	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2169475	2169744	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2169745	2170009	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2170010	2170151	1	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2170010	2170151	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	intron	2170152	2170245	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	CDS	2170246	2170721	0.98	+	2	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	exon	2170246	2170721	.	+	.	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
Phchi.S5	AUGUSTUS	stop_codon	2170722	2170724	.	+	0	transcript_id "Phchi.S5G025100.t1"; gene_id "Phchi.S5G025100"
# This transcript jg15292.t2 is derived from g13760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15293.t1 is derived from g13761.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18233999	18237340	.	+	.	Phchi.S3G261200
Phchi.S3	AUGUSTUS	transcript	18233999	18237283	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	start_codon	18233999	18234001	.	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18233999	18234189	0.81	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18233999	18234189	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18234190	18234308	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18234309	18234449	0.96	+	1	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18234309	18234449	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18234450	18234624	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18234625	18235583	0.94	+	1	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18234625	18235583	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18235584	18235739	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18235740	18235765	0.6	+	2	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18235740	18235765	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18235766	18235852	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18235853	18235862	0.95	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18235853	18235862	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18235863	18235936	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18235937	18236103	0.94	+	2	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18235937	18236103	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18236104	18236231	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18236232	18236420	1	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18236232	18236420	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18236421	18236501	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18236502	18236720	1	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18236502	18236720	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18236721	18236867	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18236868	18237162	1	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18236868	18237162	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18237163	18237245	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18237246	18237283	1	+	2	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18237246	18237283	.	+	.	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	stop_codon	18237284	18237286	.	+	0	transcript_id "Phchi.S3G261200.t1"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	transcript	18233999	18237340	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	start_codon	18233999	18234001	.	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18233999	18234189	0.82	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18233999	18234189	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18234190	18234308	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18234309	18234449	0.93	+	1	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18234309	18234449	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18234450	18234624	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18234625	18235583	0.93	+	1	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18234625	18235583	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18235584	18235739	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18235740	18235765	0.57	+	2	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18235740	18235765	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18235766	18235852	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18235853	18235862	0.96	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18235853	18235862	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18235863	18235936	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18235937	18236103	0.94	+	2	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18235937	18236103	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18236104	18236231	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18236232	18236420	1	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18236232	18236420	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18236421	18236501	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18236502	18236720	1	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18236502	18236720	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18236721	18236867	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18236868	18237162	1	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18236868	18237162	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	intron	18237163	18237308	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	CDS	18237309	18237340	1	+	2	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	exon	18237309	18237340	.	+	.	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
Phchi.S3	AUGUSTUS	stop_codon	18237341	18237343	.	+	0	transcript_id "Phchi.S3G261200.t2"; gene_id "Phchi.S3G261200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14890.t1 is derived from g13358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15293854	15299152	.	-	.	Phchi.S3G220900
Phchi.S3	AUGUSTUS	transcript	15293854	15299152	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	stop_codon	15293851	15293853	.	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15293854	15294819	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15293854	15294819	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15294820	15294937	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15294938	15295123	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15294938	15295123	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15295124	15295205	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15295206	15295376	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15295206	15295376	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15295377	15295479	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15295480	15295698	0.99	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15295480	15295698	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15295699	15295842	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15295843	15296094	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15295843	15296094	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15296095	15296325	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15296326	15296427	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15296326	15296427	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15296428	15296532	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15296533	15296730	0.99	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15296533	15296730	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15296731	15296945	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15296946	15297251	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15296946	15297251	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15297252	15297325	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15297326	15297419	1	-	1	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15297326	15297419	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15297420	15297604	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15297605	15297781	1	-	1	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15297605	15297781	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15297782	15297935	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15297936	15298063	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15297936	15298063	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15298064	15298163	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15298164	15298268	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15298164	15298268	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15298269	15298356	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15298357	15298704	1	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15298357	15298704	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15298705	15298830	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15298831	15299033	1	-	2	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15298831	15299033	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	intron	15299034	15299109	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	CDS	15299110	15299152	0.76	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	exon	15299110	15299152	.	-	.	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
Phchi.S3	AUGUSTUS	start_codon	15299150	15299152	.	-	0	transcript_id "Phchi.S3G220900.t1"; gene_id "Phchi.S3G220900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg165.t1 is derived from g9947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	942798	943574	.	-	.	Phchi.S6G012400
Phchi.S6	AUGUSTUS	transcript	942798	943574	.	-	.	transcript_id "Phchi.S6G012400.t1"; gene_id "Phchi.S6G012400"
Phchi.S6	AUGUSTUS	stop_codon	942795	942797	.	-	0	transcript_id "Phchi.S6G012400.t1"; gene_id "Phchi.S6G012400"
Phchi.S6	AUGUSTUS	CDS	942798	943574	0.84	-	0	transcript_id "Phchi.S6G012400.t1"; gene_id "Phchi.S6G012400"
Phchi.S6	AUGUSTUS	exon	942798	943574	.	-	.	transcript_id "Phchi.S6G012400.t1"; gene_id "Phchi.S6G012400"
Phchi.S6	AUGUSTUS	start_codon	943572	943574	.	-	0	transcript_id "Phchi.S6G012400.t1"; gene_id "Phchi.S6G012400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg974.t1 is derived from g10757.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6740545	6744546	.	+	.	Phchi.S6G093300
Phchi.S6	AUGUSTUS	transcript	6740545	6744546	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	start_codon	6740545	6740547	.	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6740545	6740674	0.85	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6740545	6740674	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6740675	6740773	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6740774	6740843	0.83	+	2	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6740774	6740843	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6740844	6740918	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6740919	6741015	0.68	+	1	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6740919	6741015	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6741016	6741283	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6741284	6741383	1	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6741284	6741383	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6741384	6741511	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6741512	6741597	1	+	2	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6741512	6741597	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6741598	6741776	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6741777	6741868	1	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6741777	6741868	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6741869	6742039	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6742040	6742154	1	+	1	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6742040	6742154	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6742155	6742238	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6742239	6742436	0.41	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6742239	6742436	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6742437	6742641	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6742642	6742684	0.79	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6742642	6742684	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6742685	6742907	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6742908	6743031	0.7	+	2	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6742908	6743031	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6743032	6743488	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6743489	6743598	0.73	+	1	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6743489	6743598	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6743599	6743682	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6743683	6743736	0.48	+	2	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6743683	6743736	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6743737	6743959	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6743960	6744025	0.74	+	2	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6743960	6744025	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6744026	6744226	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6744227	6744293	0.69	+	2	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6744227	6744293	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	intron	6744294	6744383	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	CDS	6744384	6744546	0.63	+	1	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	exon	6744384	6744546	.	+	.	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
Phchi.S6	AUGUSTUS	stop_codon	6744547	6744549	.	+	0	transcript_id "Phchi.S6G093300.t1"; gene_id "Phchi.S6G093300"
# This transcript jg11472.t2 is derived from g15522.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11473.t1 is derived from g15523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6520650	6522757	.	-	.	Phchi.S4G105500
Phchi.S4	AUGUSTUS	transcript	6520650	6522757	.	-	.	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	stop_codon	6520647	6520649	.	-	0	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	CDS	6520650	6521002	0.59	-	2	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	exon	6520650	6521002	.	-	.	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	intron	6521003	6521248	.	-	.	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	CDS	6521249	6522071	0.72	-	0	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	exon	6521249	6522071	.	-	.	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	intron	6522072	6522313	.	-	.	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	CDS	6522314	6522757	0.97	-	0	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	exon	6522314	6522757	.	-	.	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
Phchi.S4	AUGUSTUS	start_codon	6522755	6522757	.	-	0	transcript_id "Phchi.S4G105500.t1"; gene_id "Phchi.S4G105500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10462.t1 is derived from g14511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	449178	450404	.	+	.	Phchi.S4G004400
Phchi.S4	AUGUSTUS	transcript	449178	450404	.	+	.	transcript_id "Phchi.S4G004400.t1"; gene_id "Phchi.S4G004400"
Phchi.S4	AUGUSTUS	start_codon	449178	449180	.	+	0	transcript_id "Phchi.S4G004400.t1"; gene_id "Phchi.S4G004400"
Phchi.S4	AUGUSTUS	CDS	449178	450404	0.5	+	0	transcript_id "Phchi.S4G004400.t1"; gene_id "Phchi.S4G004400"
Phchi.S4	AUGUSTUS	exon	449178	450404	.	+	.	transcript_id "Phchi.S4G004400.t1"; gene_id "Phchi.S4G004400"
Phchi.S4	AUGUSTUS	stop_codon	450405	450407	.	+	0	transcript_id "Phchi.S4G004400.t1"; gene_id "Phchi.S4G004400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11230.t1 is derived from g15280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4907909	4908439	.	+	.	Phchi.S4G081200
Phchi.S4	AUGUSTUS	transcript	4907909	4908439	.	+	.	transcript_id "Phchi.S4G081200.t1"; gene_id "Phchi.S4G081200"
Phchi.S4	AUGUSTUS	start_codon	4907909	4907911	.	+	0	transcript_id "Phchi.S4G081200.t1"; gene_id "Phchi.S4G081200"
Phchi.S4	AUGUSTUS	CDS	4907909	4908439	0.59	+	0	transcript_id "Phchi.S4G081200.t1"; gene_id "Phchi.S4G081200"
Phchi.S4	AUGUSTUS	exon	4907909	4908439	.	+	.	transcript_id "Phchi.S4G081200.t1"; gene_id "Phchi.S4G081200"
Phchi.S4	AUGUSTUS	stop_codon	4908440	4908442	.	+	0	transcript_id "Phchi.S4G081200.t1"; gene_id "Phchi.S4G081200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2348.t1 is derived from g9268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6287215	6289410	.	-	.	Phchi.S5G095700
Phchi.S5	AUGUSTUS	transcript	6287215	6289410	.	-	.	transcript_id "Phchi.S5G095700.t1"; gene_id "Phchi.S5G095700"
Phchi.S5	AUGUSTUS	stop_codon	6287212	6287214	.	-	0	transcript_id "Phchi.S5G095700.t1"; gene_id "Phchi.S5G095700"
Phchi.S5	AUGUSTUS	CDS	6287215	6289410	0.76	-	0	transcript_id "Phchi.S5G095700.t1"; gene_id "Phchi.S5G095700"
Phchi.S5	AUGUSTUS	exon	6287215	6289410	.	-	.	transcript_id "Phchi.S5G095700.t1"; gene_id "Phchi.S5G095700"
Phchi.S5	AUGUSTUS	start_codon	6289408	6289410	.	-	0	transcript_id "Phchi.S5G095700.t1"; gene_id "Phchi.S5G095700"
# This transcript jg6087.t2 is derived from g3258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6087.t3 is derived from g3258.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6087.t4 is derived from g3258.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6087.t5 is derived from g3258.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6088.t1 is derived from g3259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20901386	20904487	.	-	.	Phchi.S1G324700
Phchi.S1	AUGUSTUS	transcript	20901386	20904487	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	stop_codon	20901383	20901385	.	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20901386	20901486	0.9	-	2	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20901386	20901486	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20901487	20901568	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20901569	20901609	0.9	-	1	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20901569	20901609	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20901610	20901710	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20901711	20901799	0.9	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20901711	20901799	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20901800	20901882	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20901883	20901927	1	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20901883	20901927	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20901928	20902004	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20902005	20902112	0.99	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20902005	20902112	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20902113	20902230	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20902231	20902316	0.94	-	2	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20902231	20902316	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20902317	20902389	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20902390	20902477	1	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20902390	20902477	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20902478	20902588	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20902589	20902825	1	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20902589	20902825	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20902826	20902916	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20902917	20902992	1	-	1	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20902917	20902992	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20902993	20903084	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20903085	20903134	0.93	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20903085	20903134	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20903135	20903245	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20903246	20903308	1	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20903246	20903308	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20903309	20903408	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20903409	20903462	1	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20903409	20903462	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20903463	20903596	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20903597	20903702	0.99	-	1	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20903597	20903702	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20903703	20903829	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20903830	20903932	0.99	-	2	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20903830	20903932	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20903933	20904013	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20904014	20904074	1	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20904014	20904074	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20904075	20904168	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20904169	20904209	0.99	-	2	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20904169	20904209	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	intron	20904210	20904336	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	CDS	20904337	20904487	0.97	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	exon	20904337	20904487	.	-	.	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
Phchi.S1	AUGUSTUS	start_codon	20904485	20904487	.	-	0	transcript_id "Phchi.S1G324700.t1"; gene_id "Phchi.S1G324700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9637.t1 is derived from g6813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43010606	43012898	.	-	.	Phchi.S1G679600
Phchi.S1	AUGUSTUS	transcript	43010606	43012898	.	-	.	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	stop_codon	43010603	43010605	.	-	0	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	CDS	43010606	43011143	0.92	-	1	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	exon	43010606	43011143	.	-	.	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	intron	43011144	43011222	.	-	.	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	CDS	43011223	43012898	0.4	-	0	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	exon	43011223	43012898	.	-	.	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
Phchi.S1	AUGUSTUS	start_codon	43012896	43012898	.	-	0	transcript_id "Phchi.S1G679600.t1"; gene_id "Phchi.S1G679600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12303.t1 is derived from g7979.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9873299	9877966	.	+	.	Phchi.S2G038300
Phchi.S2	AUGUSTUS	transcript	9873299	9877966	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	start_codon	9873299	9873301	.	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9873299	9873391	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9873299	9873391	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9873392	9873472	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9873473	9873604	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9873473	9873604	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9873605	9874252	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874253	9874369	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874253	9874369	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874370	9874451	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874452	9874502	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874452	9874502	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874503	9874591	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874592	9874681	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874592	9874681	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874682	9874850	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874851	9874997	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874851	9874997	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874998	9875102	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875103	9875228	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875103	9875228	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9875229	9875321	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875322	9875390	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875322	9875390	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9875391	9875535	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875536	9876187	0.61	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875536	9876187	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876188	9876314	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876315	9876535	0.7	+	2	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876315	9876535	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876536	9876653	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876654	9876882	0.96	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876654	9876882	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876883	9876963	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876964	9877142	0.98	+	2	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876964	9877142	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877143	9877239	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877240	9877494	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877240	9877494	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877495	9877579	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877580	9877699	1	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877580	9877699	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877700	9877783	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877784	9877966	0.67	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877784	9877966	.	+	.	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	stop_codon	9877967	9877969	.	+	0	transcript_id "Phchi.S2G038300.t1"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	transcript	9873299	9877966	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	start_codon	9873299	9873301	.	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9873299	9873391	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9873299	9873391	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9873392	9873472	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9873473	9873604	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9873473	9873604	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9873605	9874231	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874232	9874369	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874232	9874369	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874370	9874451	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874452	9874502	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874452	9874502	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874503	9874591	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874592	9874681	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874592	9874681	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874682	9874850	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874851	9874997	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874851	9874997	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874998	9875102	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875103	9875228	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875103	9875228	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9875229	9875321	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875322	9875390	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875322	9875390	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9875391	9875535	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875536	9876187	0.58	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875536	9876187	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876188	9876314	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876315	9876535	0.66	+	2	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876315	9876535	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876536	9876653	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876654	9876882	0.94	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876654	9876882	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876883	9876963	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876964	9877142	0.96	+	2	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876964	9877142	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877143	9877239	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877240	9877494	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877240	9877494	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877495	9877579	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877580	9877699	1	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877580	9877699	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877700	9877783	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877784	9877966	0.67	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877784	9877966	.	+	.	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	stop_codon	9877967	9877969	.	+	0	transcript_id "Phchi.S2G038300.t2"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	transcript	9873299	9877966	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	start_codon	9873299	9873301	.	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9873299	9873391	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9873299	9873391	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9873392	9873472	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9873473	9873604	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9873473	9873604	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9873605	9874252	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874253	9874369	0.89	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874253	9874369	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874370	9874451	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874452	9874502	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874452	9874502	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874503	9874591	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874592	9874681	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874592	9874681	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874682	9874850	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9874851	9874997	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9874851	9874997	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9874998	9875102	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875103	9875228	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875103	9875228	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9875229	9875321	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875322	9875390	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875322	9875390	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9875391	9875535	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9875536	9876187	0.55	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9875536	9876187	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876188	9876314	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876315	9876535	0.63	+	2	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876315	9876535	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876536	9876653	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876654	9876882	0.99	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876654	9876882	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9876883	9876963	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9876964	9877142	1	+	2	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9876964	9877142	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877143	9877239	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877240	9877494	1	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877240	9877494	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877495	9877582	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877583	9877699	0.59	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877583	9877699	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	intron	9877700	9877783	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	CDS	9877784	9877966	0.62	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	exon	9877784	9877966	.	+	.	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
Phchi.S2	AUGUSTUS	stop_codon	9877967	9877969	.	+	0	transcript_id "Phchi.S2G038300.t3"; gene_id "Phchi.S2G038300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6966.t1 is derived from g4138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26161741	26162637	.	-	.	Phchi.S1G412500
Phchi.S1	AUGUSTUS	transcript	26161741	26162637	.	-	.	transcript_id "Phchi.S1G412500.t1"; gene_id "Phchi.S1G412500"
Phchi.S1	AUGUSTUS	stop_codon	26161738	26161740	.	-	0	transcript_id "Phchi.S1G412500.t1"; gene_id "Phchi.S1G412500"
Phchi.S1	AUGUSTUS	CDS	26161741	26162637	0.99	-	0	transcript_id "Phchi.S1G412500.t1"; gene_id "Phchi.S1G412500"
Phchi.S1	AUGUSTUS	exon	26161741	26162637	.	-	.	transcript_id "Phchi.S1G412500.t1"; gene_id "Phchi.S1G412500"
Phchi.S1	AUGUSTUS	start_codon	26162635	26162637	.	-	0	transcript_id "Phchi.S1G412500.t1"; gene_id "Phchi.S1G412500"
# This transcript jg12110.t2 is derived from g7786.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12111.t1 is derived from g7787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3570350	3571695	.	+	.	Phchi.S2G019100
Phchi.S2	AUGUSTUS	transcript	3570350	3571695	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	start_codon	3570350	3570352	.	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	CDS	3570350	3570451	0.96	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	exon	3570350	3570451	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	intron	3570452	3570613	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	CDS	3570614	3570692	1	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	exon	3570614	3570692	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	intron	3570693	3570885	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	CDS	3570886	3571055	1	+	2	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	exon	3570886	3571055	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	intron	3571056	3571167	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	CDS	3571168	3571215	1	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	exon	3571168	3571215	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	intron	3571216	3571380	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	CDS	3571381	3571476	1	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	exon	3571381	3571476	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	intron	3571477	3571563	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	CDS	3571564	3571695	0.36	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	exon	3571564	3571695	.	+	.	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
Phchi.S2	AUGUSTUS	stop_codon	3571696	3571698	.	+	0	transcript_id "Phchi.S2G019100.t1"; gene_id "Phchi.S2G019100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9518.t1 is derived from g6694.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42233888	42244411	.	+	.	Phchi.S1G667700
Phchi.S1	AUGUSTUS	transcript	42233888	42244358	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	start_codon	42233888	42233890	.	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42233888	42234130	0.74	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42233888	42234130	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42234131	42234208	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42234209	42234296	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42234209	42234296	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42234297	42234429	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42234430	42234638	0.99	+	2	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42234430	42234638	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42234639	42234936	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42234937	42235038	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42234937	42235038	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42235039	42235192	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42235193	42235255	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42235193	42235255	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42235256	42235416	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42235417	42237642	0.88	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42235417	42237642	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42237643	42237805	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42237806	42238168	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42237806	42238168	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42238169	42238324	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42238325	42238465	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42238325	42238465	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42238466	42238559	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42238560	42238952	0.96	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42238560	42238952	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42238953	42239054	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42239055	42239591	0.99	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42239055	42239591	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42239592	42239747	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42239748	42239971	0.99	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42239748	42239971	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42239972	42240087	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240088	42240167	0.87	+	1	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240088	42240167	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42240168	42240248	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240249	42240432	0.87	+	2	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240249	42240432	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42240433	42240552	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240553	42240847	1	+	1	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240553	42240847	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42240848	42240941	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240942	42241433	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240942	42241433	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42241434	42241519	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42241520	42241865	0.95	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42241520	42241865	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42241866	42241955	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42241956	42242299	1	+	2	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42241956	42242299	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42242300	42242409	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42242410	42242874	0.93	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42242410	42242874	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42242875	42242988	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42242989	42243113	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42242989	42243113	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243114	42243199	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243200	42243323	1	+	1	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243200	42243323	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243324	42243494	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243495	42243563	1	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243495	42243563	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243564	42243683	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243684	42243817	0.94	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243684	42243817	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243818	42243887	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243888	42243916	0.94	+	1	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243888	42243916	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243917	42244010	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42244011	42244090	0.99	+	2	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42244011	42244090	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42244091	42244304	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42244305	42244358	0.93	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42244305	42244358	.	+	.	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	stop_codon	42244359	42244361	.	+	0	transcript_id "Phchi.S1G667700.t1"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	transcript	42233888	42244411	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	start_codon	42233888	42233890	.	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42233888	42234130	0.77	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42233888	42234130	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42234131	42234208	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42234209	42234296	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42234209	42234296	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42234297	42234429	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42234430	42234638	0.99	+	2	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42234430	42234638	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42234639	42234936	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42234937	42235038	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42234937	42235038	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42235039	42235192	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42235193	42235255	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42235193	42235255	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42235256	42235416	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42235417	42237642	0.93	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42235417	42237642	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42237643	42237805	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42237806	42238168	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42237806	42238168	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42238169	42238324	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42238325	42238465	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42238325	42238465	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42238466	42238559	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42238560	42238952	0.87	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42238560	42238952	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42238953	42239054	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42239055	42239591	0.99	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42239055	42239591	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42239592	42239747	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42239748	42239971	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42239748	42239971	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42239972	42240087	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240088	42240167	0.88	+	1	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240088	42240167	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42240168	42240248	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240249	42240432	0.83	+	2	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240249	42240432	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42240433	42240552	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240553	42240847	1	+	1	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240553	42240847	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42240848	42240941	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42240942	42241433	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42240942	42241433	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42241434	42241519	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42241520	42241865	0.94	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42241520	42241865	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42241866	42241955	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42241956	42242299	1	+	2	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42241956	42242299	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42242300	42242409	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42242410	42242874	0.97	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42242410	42242874	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42242875	42242988	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42242989	42243113	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42242989	42243113	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243114	42243199	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243200	42243323	1	+	1	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243200	42243323	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243324	42243494	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243495	42243563	1	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243495	42243563	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243564	42243683	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243684	42243817	0.93	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243684	42243817	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243818	42243887	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42243888	42243916	0.92	+	1	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42243888	42243916	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42243917	42244010	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42244011	42244090	0.99	+	2	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42244011	42244090	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	intron	42244091	42244186	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	CDS	42244187	42244411	0.73	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	exon	42244187	42244411	.	+	.	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
Phchi.S1	AUGUSTUS	stop_codon	42244412	42244414	.	+	0	transcript_id "Phchi.S1G667700.t2"; gene_id "Phchi.S1G667700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1378.t1 is derived from g15986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C149	AUGUSTUS	gene	9028	10652	.	-	.	Phchi.C149G000100
Phchi.C149	AUGUSTUS	transcript	9028	10652	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	stop_codon	9025	9027	.	-	0	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	CDS	9028	9181	1	-	1	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	exon	9028	9181	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	intron	9182	9276	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	CDS	9277	9497	1	-	0	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	exon	9277	9497	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	intron	9498	9595	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	CDS	9596	9925	0.8	-	0	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	exon	9596	9925	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	intron	9926	10038	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	CDS	10039	10223	1	-	2	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	exon	10039	10223	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	intron	10224	10324	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	CDS	10325	10652	1	-	0	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	exon	10325	10652	.	-	.	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
Phchi.C149	AUGUSTUS	start_codon	10650	10652	.	-	0	transcript_id "Phchi.C149G000100.t1"; gene_id "Phchi.C149G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3379.t1 is derived from g548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3253771	3255209	.	+	.	Phchi.S1G053800
Phchi.S1	AUGUSTUS	transcript	3253771	3255209	.	+	.	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	start_codon	3253771	3253773	.	+	0	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	CDS	3253771	3254025	0.51	+	0	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	exon	3253771	3254025	.	+	.	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	intron	3254026	3254120	.	+	.	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	CDS	3254121	3255209	0.47	+	0	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	exon	3254121	3255209	.	+	.	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
Phchi.S1	AUGUSTUS	stop_codon	3255210	3255212	.	+	0	transcript_id "Phchi.S1G053800.t1"; gene_id "Phchi.S1G053800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3879.t1 is derived from g1048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6185439	6189320	.	+	.	Phchi.S1G103800
Phchi.S1	AUGUSTUS	transcript	6185439	6189320	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	start_codon	6185439	6185441	.	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6185439	6185819	0.99	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6185439	6185819	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6185820	6185893	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6185894	6185989	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6185894	6185989	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6185990	6186086	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6186087	6186275	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6186087	6186275	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6186276	6186405	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6186406	6186546	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6186406	6186546	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6186547	6186638	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6186639	6186779	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6186639	6186779	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6186780	6186862	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6186863	6187005	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6186863	6187005	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6187006	6187121	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6187122	6187254	0.98	+	1	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6187122	6187254	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6187255	6187364	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6187365	6187413	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6187365	6187413	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6187414	6187494	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6187495	6187832	0.25	+	2	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6187495	6187832	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6187833	6188110	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6188111	6188323	0.68	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6188111	6188323	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6188324	6188470	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6188471	6188650	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6188471	6188650	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6188651	6188726	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6188727	6188882	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6188727	6188882	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6188883	6188981	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6188982	6189059	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6188982	6189059	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	intron	6189060	6189149	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	CDS	6189150	6189320	1	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	exon	6189150	6189320	.	+	.	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
Phchi.S1	AUGUSTUS	stop_codon	6189321	6189323	.	+	0	transcript_id "Phchi.S1G103800.t1"; gene_id "Phchi.S1G103800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11896.t1 is derived from g15948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9072497	9080228	.	+	.	Phchi.S4G147800
Phchi.S4	AUGUSTUS	transcript	9072497	9080228	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	start_codon	9072497	9072499	.	+	0	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	CDS	9072497	9075039	0.45	+	0	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	exon	9072497	9075039	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	intron	9075040	9075137	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	CDS	9075138	9076362	1	+	1	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	exon	9075138	9076362	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	intron	9076363	9076458	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	CDS	9076459	9076742	1	+	0	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	exon	9076459	9076742	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	intron	9076743	9076858	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	CDS	9076859	9077032	0.98	+	1	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	exon	9076859	9077032	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	intron	9077033	9077117	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	CDS	9077118	9077471	0.7	+	1	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	exon	9077118	9077471	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	intron	9077472	9077554	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	CDS	9077555	9080228	0.91	+	1	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	exon	9077555	9080228	.	+	.	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
Phchi.S4	AUGUSTUS	stop_codon	9080229	9080231	.	+	0	transcript_id "Phchi.S4G147800.t1"; gene_id "Phchi.S4G147800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15518.t1 is derived from g13987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19671481	19673315	.	-	.	Phchi.S3G283700
Phchi.S3	AUGUSTUS	transcript	19671481	19673315	.	-	.	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	stop_codon	19671478	19671480	.	-	0	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	CDS	19671481	19673128	0.82	-	1	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	exon	19671481	19673128	.	-	.	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	intron	19673129	19673310	.	-	.	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	CDS	19673311	19673315	0.98	-	0	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	exon	19673311	19673315	.	-	.	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
Phchi.S3	AUGUSTUS	start_codon	19673313	19673315	.	-	0	transcript_id "Phchi.S3G283700.t1"; gene_id "Phchi.S3G283700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4252.t1 is derived from g1421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9173091	9176546	.	-	.	Phchi.S1G141100
Phchi.S1	AUGUSTUS	transcript	9173091	9176546	.	-	.	transcript_id "Phchi.S1G141100.t1"; gene_id "Phchi.S1G141100"
Phchi.S1	AUGUSTUS	stop_codon	9173088	9173090	.	-	0	transcript_id "Phchi.S1G141100.t1"; gene_id "Phchi.S1G141100"
Phchi.S1	AUGUSTUS	CDS	9173091	9176546	0.5	-	0	transcript_id "Phchi.S1G141100.t1"; gene_id "Phchi.S1G141100"
Phchi.S1	AUGUSTUS	exon	9173091	9176546	.	-	.	transcript_id "Phchi.S1G141100.t1"; gene_id "Phchi.S1G141100"
Phchi.S1	AUGUSTUS	start_codon	9176544	9176546	.	-	0	transcript_id "Phchi.S1G141100.t1"; gene_id "Phchi.S1G141100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14174.t1 is derived from g12641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11276736	11277872	.	-	.	Phchi.S3G149300
Phchi.S3	AUGUSTUS	transcript	11276736	11277872	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	stop_codon	11276733	11276735	.	-	0	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	CDS	11276736	11276921	0.97	-	0	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	exon	11276736	11276921	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	intron	11276922	11277017	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	CDS	11277018	11277637	0.53	-	2	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	exon	11277018	11277637	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	intron	11277638	11277735	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	CDS	11277736	11277769	0.46	-	0	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	exon	11277736	11277769	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	intron	11277770	11277869	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	CDS	11277870	11277872	0.36	-	0	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	exon	11277870	11277872	.	-	.	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
Phchi.S3	AUGUSTUS	start_codon	11277870	11277872	.	-	0	transcript_id "Phchi.S3G149300.t1"; gene_id "Phchi.S3G149300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10920.t1 is derived from g14970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2967001	2968157	.	+	.	Phchi.S4G050200
Phchi.S4	AUGUSTUS	transcript	2967001	2968157	.	+	.	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	start_codon	2967001	2967003	.	+	0	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	CDS	2967001	2967081	0.8	+	0	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	exon	2967001	2967081	.	+	.	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	intron	2967082	2967467	.	+	.	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	CDS	2967468	2967515	1	+	0	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	exon	2967468	2967515	.	+	.	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	intron	2967516	2967602	.	+	.	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	CDS	2967603	2968157	0.99	+	0	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	exon	2967603	2968157	.	+	.	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
Phchi.S4	AUGUSTUS	stop_codon	2968158	2968160	.	+	0	transcript_id "Phchi.S4G050200.t1"; gene_id "Phchi.S4G050200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9640.t1 is derived from g6816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43022719	43023419	.	+	.	Phchi.S1G679900
Phchi.S1	AUGUSTUS	transcript	43022719	43023419	.	+	.	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	start_codon	43022719	43022721	.	+	0	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	CDS	43022719	43023074	0.99	+	0	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	exon	43022719	43023074	.	+	.	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	intron	43023075	43023175	.	+	.	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	CDS	43023176	43023419	0.99	+	1	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	exon	43023176	43023419	.	+	.	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
Phchi.S1	AUGUSTUS	stop_codon	43023420	43023422	.	+	0	transcript_id "Phchi.S1G679900.t1"; gene_id "Phchi.S1G679900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13259.t1 is derived from g11724.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4960868	4962532	.	-	.	Phchi.S3G057800
Phchi.S3	AUGUSTUS	transcript	4960868	4962532	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	stop_codon	4960865	4960867	.	-	0	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4960868	4961068	0.99	-	0	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4960868	4961068	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	intron	4961069	4961141	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4961142	4961519	0.99	-	0	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4961142	4961519	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	intron	4961520	4961609	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4961610	4961915	1	-	0	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4961610	4961915	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	intron	4961916	4962016	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4962017	4962532	0.52	-	0	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4962017	4962532	.	-	.	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	start_codon	4962530	4962532	.	-	0	transcript_id "Phchi.S3G057800.t1"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	transcript	4961014	4962532	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	stop_codon	4961011	4961013	.	-	0	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4961014	4961068	0.99	-	1	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4961014	4961068	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	intron	4961069	4961151	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4961152	4961519	0.99	-	0	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4961152	4961519	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	intron	4961520	4961609	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4961610	4961915	1	-	0	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4961610	4961915	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	intron	4961916	4962016	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	CDS	4962017	4962532	0.43	-	0	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	exon	4962017	4962532	.	-	.	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
Phchi.S3	AUGUSTUS	start_codon	4962530	4962532	.	-	0	transcript_id "Phchi.S3G057800.t2"; gene_id "Phchi.S3G057800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg391.t1 is derived from g10173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2854402	2858520	.	+	.	Phchi.S6G035000
Phchi.S6	AUGUSTUS	transcript	2854402	2858520	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	start_codon	2854402	2854404	.	+	0	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	CDS	2854402	2856732	0.86	+	0	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	exon	2854402	2856732	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	intron	2856733	2856924	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	CDS	2856925	2857307	0.94	+	0	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	exon	2856925	2857307	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	intron	2857308	2857553	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	CDS	2857554	2857614	1	+	1	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	exon	2857554	2857614	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	intron	2857615	2857959	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	CDS	2857960	2858520	0.99	+	0	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	exon	2857960	2858520	.	+	.	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
Phchi.S6	AUGUSTUS	stop_codon	2858521	2858523	.	+	0	transcript_id "Phchi.S6G035000.t1"; gene_id "Phchi.S6G035000"
# This transcript jg8431.t2 is derived from g5606.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8431.t3 is derived from g5606.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8432.t1 is derived from g5607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35914082	35916632	.	-	.	Phchi.S1G559100
Phchi.S1	AUGUSTUS	transcript	35914082	35916632	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	stop_codon	35914079	35914081	.	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35914082	35914168	0.99	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35914082	35914168	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35914169	35914618	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35914619	35914705	1	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35914619	35914705	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35914706	35915016	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35915017	35915277	1	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35915017	35915277	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35915278	35915568	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35915569	35915623	0.73	-	1	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35915569	35915623	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35915624	35915724	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35915725	35915801	0.74	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35915725	35915801	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35915802	35916113	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35916114	35916632	0.79	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35916114	35916632	.	-	.	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	start_codon	35916630	35916632	.	-	0	transcript_id "Phchi.S1G559100.t1"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	transcript	35914082	35916632	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	stop_codon	35914079	35914081	.	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35914082	35914168	1	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35914082	35914168	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35914169	35914618	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35914619	35914708	0.97	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35914619	35914708	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35914709	35915016	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35915017	35915277	1	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35915017	35915277	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35915278	35915568	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35915569	35915623	0.66	-	1	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35915569	35915623	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35915624	35915724	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35915725	35915801	0.67	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35915725	35915801	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	intron	35915802	35916113	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	CDS	35916114	35916632	0.75	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	exon	35916114	35916632	.	-	.	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
Phchi.S1	AUGUSTUS	start_codon	35916630	35916632	.	-	0	transcript_id "Phchi.S1G559100.t2"; gene_id "Phchi.S1G559100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3860.t1 is derived from g1029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6078402	6079415	.	+	.	Phchi.S1G101900
Phchi.S1	AUGUSTUS	transcript	6078402	6079415	.	+	.	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	start_codon	6078402	6078404	.	+	0	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	CDS	6078402	6078845	0.69	+	0	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	exon	6078402	6078845	.	+	.	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	intron	6078846	6078952	.	+	.	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	CDS	6078953	6079075	1	+	0	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	exon	6078953	6079075	.	+	.	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	intron	6079076	6079157	.	+	.	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	CDS	6079158	6079415	0.97	+	0	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	exon	6079158	6079415	.	+	.	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
Phchi.S1	AUGUSTUS	stop_codon	6079416	6079418	.	+	0	transcript_id "Phchi.S1G101900.t1"; gene_id "Phchi.S1G101900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15717.t1 is derived from g14187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20853041	20854341	.	+	.	Phchi.S3G303600
Phchi.S3	AUGUSTUS	transcript	20853041	20854341	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	start_codon	20853041	20853043	.	+	0	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	CDS	20853041	20853088	0.87	+	0	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	exon	20853041	20853088	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	intron	20853089	20853187	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	CDS	20853188	20853268	1	+	0	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	exon	20853188	20853268	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	intron	20853269	20853371	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	CDS	20853372	20853506	0.99	+	0	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	exon	20853372	20853506	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	intron	20853507	20853617	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	CDS	20853618	20853790	1	+	0	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	exon	20853618	20853790	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	intron	20853791	20853944	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	CDS	20853945	20854096	1	+	1	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	exon	20853945	20854096	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	intron	20854097	20854240	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	CDS	20854241	20854341	1	+	2	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	exon	20854241	20854341	.	+	.	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
Phchi.S3	AUGUSTUS	stop_codon	20854342	20854344	.	+	0	transcript_id "Phchi.S3G303600.t1"; gene_id "Phchi.S3G303600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13916.t1 is derived from g12383.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9644803	9645770	.	+	.	Phchi.S3G123500
Phchi.S3	AUGUSTUS	transcript	9644803	9645770	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	start_codon	9644803	9644805	.	+	0	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	CDS	9644803	9644887	1	+	0	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	exon	9644803	9644887	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	intron	9644888	9645191	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	CDS	9645192	9645297	1	+	2	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	exon	9645192	9645297	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	intron	9645298	9645436	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	CDS	9645437	9645499	1	+	1	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	exon	9645437	9645499	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	intron	9645500	9645643	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	CDS	9645644	9645770	0.97	+	1	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	exon	9645644	9645770	.	+	.	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
Phchi.S3	AUGUSTUS	stop_codon	9645771	9645773	.	+	0	transcript_id "Phchi.S3G123500.t1"; gene_id "Phchi.S3G123500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10577.t1 is derived from g14627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1040341	1041645	.	-	.	Phchi.S4G015900
Phchi.S4	AUGUSTUS	transcript	1040341	1041645	.	-	.	transcript_id "Phchi.S4G015900.t1"; gene_id "Phchi.S4G015900"
Phchi.S4	AUGUSTUS	stop_codon	1040338	1040340	.	-	0	transcript_id "Phchi.S4G015900.t1"; gene_id "Phchi.S4G015900"
Phchi.S4	AUGUSTUS	CDS	1040341	1041645	0.96	-	0	transcript_id "Phchi.S4G015900.t1"; gene_id "Phchi.S4G015900"
Phchi.S4	AUGUSTUS	exon	1040341	1041645	.	-	.	transcript_id "Phchi.S4G015900.t1"; gene_id "Phchi.S4G015900"
Phchi.S4	AUGUSTUS	start_codon	1041643	1041645	.	-	0	transcript_id "Phchi.S4G015900.t1"; gene_id "Phchi.S4G015900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13814.t1 is derived from g12281.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9039609	9040811	.	+	.	Phchi.S3G113300
Phchi.S3	AUGUSTUS	transcript	9039609	9040811	.	+	.	transcript_id "Phchi.S3G113300.t1"; gene_id "Phchi.S3G113300"
Phchi.S3	AUGUSTUS	start_codon	9039609	9039611	.	+	0	transcript_id "Phchi.S3G113300.t1"; gene_id "Phchi.S3G113300"
Phchi.S3	AUGUSTUS	CDS	9039609	9040811	0.44	+	0	transcript_id "Phchi.S3G113300.t1"; gene_id "Phchi.S3G113300"
Phchi.S3	AUGUSTUS	exon	9039609	9040811	.	+	.	transcript_id "Phchi.S3G113300.t1"; gene_id "Phchi.S3G113300"
Phchi.S3	AUGUSTUS	stop_codon	9040812	9040814	.	+	0	transcript_id "Phchi.S3G113300.t1"; gene_id "Phchi.S3G113300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1717.t1 is derived from g8637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2680970	2684471	.	+	.	Phchi.S5G032600
Phchi.S5	AUGUSTUS	transcript	2680970	2684471	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	start_codon	2680970	2680972	.	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2680970	2681203	0.83	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2680970	2681203	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2681204	2681831	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2681832	2681897	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2681832	2681897	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2681898	2682201	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682202	2682270	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682202	2682270	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682271	2682397	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682398	2682433	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682398	2682433	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682434	2682547	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682548	2682613	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682548	2682613	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682614	2682694	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682695	2682763	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682695	2682763	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682764	2682888	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682889	2682966	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682889	2682966	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682967	2683068	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683069	2683147	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683069	2683147	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2683148	2683385	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683386	2683480	1	+	2	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683386	2683480	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2683481	2683625	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683626	2683710	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683626	2683710	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2683711	2683854	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683855	2684057	1	+	2	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683855	2684057	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2684058	2684185	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2684186	2684304	1	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2684186	2684304	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2684305	2684431	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2684432	2684471	0.99	+	1	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2684432	2684471	.	+	.	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	stop_codon	2684472	2684474	.	+	0	transcript_id "Phchi.S5G032600.t1"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	transcript	2680970	2684471	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	start_codon	2680970	2680972	.	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2680970	2681282	0.55	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2680970	2681282	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2681283	2681492	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2681493	2681545	0.88	+	2	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2681493	2681545	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2681546	2681831	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2681832	2681897	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2681832	2681897	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2681898	2682201	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682202	2682270	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682202	2682270	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682271	2682397	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682398	2682433	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682398	2682433	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682434	2682547	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682548	2682613	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682548	2682613	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682614	2682694	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682695	2682763	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682695	2682763	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682764	2682888	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2682889	2682966	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2682889	2682966	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2682967	2683068	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683069	2683147	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683069	2683147	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2683148	2683385	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683386	2683480	1	+	2	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683386	2683480	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2683481	2683625	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683626	2683710	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683626	2683710	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2683711	2683854	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2683855	2684057	1	+	2	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2683855	2684057	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2684058	2684185	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2684186	2684304	1	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2684186	2684304	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	intron	2684305	2684431	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	CDS	2684432	2684471	1	+	1	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	exon	2684432	2684471	.	+	.	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
Phchi.S5	AUGUSTUS	stop_codon	2684472	2684474	.	+	0	transcript_id "Phchi.S5G032600.t2"; gene_id "Phchi.S5G032600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8104.t1 is derived from g5279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33099491	33100840	.	+	.	Phchi.S1G526300
Phchi.S1	AUGUSTUS	transcript	33099491	33100840	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	start_codon	33099491	33099493	.	+	0	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	CDS	33099491	33099912	0.74	+	0	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	exon	33099491	33099912	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	intron	33099913	33099991	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	CDS	33099992	33100487	0.88	+	1	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	exon	33099992	33100487	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	intron	33100488	33100646	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	CDS	33100647	33100698	0.98	+	0	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	exon	33100647	33100698	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	intron	33100699	33100784	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	CDS	33100785	33100840	0.95	+	2	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	exon	33100785	33100840	.	+	.	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
Phchi.S1	AUGUSTUS	stop_codon	33100841	33100843	.	+	0	transcript_id "Phchi.S1G526300.t1"; gene_id "Phchi.S1G526300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10668.t1 is derived from g14718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1509475	1510232	.	+	.	Phchi.S4G025000
Phchi.S4	AUGUSTUS	transcript	1509475	1510232	.	+	.	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	start_codon	1509475	1509477	.	+	0	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	CDS	1509475	1509539	0.72	+	0	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	exon	1509475	1509539	.	+	.	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	intron	1509540	1509849	.	+	.	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	CDS	1509850	1509977	0.64	+	1	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	exon	1509850	1509977	.	+	.	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	intron	1509978	1510182	.	+	.	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	CDS	1510183	1510232	0.62	+	2	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	exon	1510183	1510232	.	+	.	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
Phchi.S4	AUGUSTUS	stop_codon	1510233	1510235	.	+	0	transcript_id "Phchi.S4G025000.t1"; gene_id "Phchi.S4G025000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10090.t1 is derived from g7266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45699848	45700520	.	-	.	Phchi.S1G724900
Phchi.S1	AUGUSTUS	transcript	45699848	45700520	.	-	.	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	stop_codon	45699845	45699847	.	-	0	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	CDS	45699848	45699951	0.98	-	2	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	exon	45699848	45699951	.	-	.	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	intron	45699952	45700084	.	-	.	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	CDS	45700085	45700216	0.98	-	2	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	exon	45700085	45700216	.	-	.	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	intron	45700217	45700414	.	-	.	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	CDS	45700415	45700520	0.75	-	0	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	exon	45700415	45700520	.	-	.	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
Phchi.S1	AUGUSTUS	start_codon	45700518	45700520	.	-	0	transcript_id "Phchi.S1G724900.t1"; gene_id "Phchi.S1G724900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9736.t1 is derived from g6912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43454370	43455024	.	+	.	Phchi.S1G689500
Phchi.S1	AUGUSTUS	transcript	43454370	43455024	.	+	.	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	start_codon	43454370	43454372	.	+	0	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	CDS	43454370	43454514	1	+	0	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	exon	43454370	43454514	.	+	.	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	intron	43454515	43454784	.	+	.	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	CDS	43454785	43454853	0.54	+	2	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	exon	43454785	43454853	.	+	.	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	intron	43454854	43454992	.	+	.	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	CDS	43454993	43455024	0.55	+	2	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	exon	43454993	43455024	.	+	.	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
Phchi.S1	AUGUSTUS	stop_codon	43455025	43455027	.	+	0	transcript_id "Phchi.S1G689500.t1"; gene_id "Phchi.S1G689500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1271.t1 is derived from g11054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8766778	8767993	.	-	.	Phchi.S6G123000
Phchi.S6	AUGUSTUS	transcript	8766778	8767993	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	stop_codon	8766775	8766777	.	-	0	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	CDS	8766778	8766865	1	-	1	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	exon	8766778	8766865	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	intron	8766866	8767046	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	CDS	8767047	8767091	0.87	-	1	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	exon	8767047	8767091	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	intron	8767092	8767166	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	CDS	8767167	8767220	0.87	-	1	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	exon	8767167	8767220	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	intron	8767221	8767417	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	CDS	8767418	8767498	0.9	-	1	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	exon	8767418	8767498	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	intron	8767499	8767620	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	CDS	8767621	8767691	0.87	-	0	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	exon	8767621	8767691	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	intron	8767692	8767939	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	CDS	8767940	8767993	0.65	-	0	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	exon	8767940	8767993	.	-	.	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
Phchi.S6	AUGUSTUS	start_codon	8767991	8767993	.	-	0	transcript_id "Phchi.S6G123000.t1"; gene_id "Phchi.S6G123000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2721.t1 is derived from g9641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8417155	8419576	.	-	.	Phchi.S5G133000
Phchi.S5	AUGUSTUS	transcript	8417155	8419576	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	stop_codon	8417152	8417154	.	-	0	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8417155	8417282	1	-	2	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8417155	8417282	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	intron	8417283	8417411	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8417412	8417775	0.9	-	0	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8417412	8417775	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	intron	8417776	8417859	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8417860	8418449	1	-	2	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8417860	8418449	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	intron	8418450	8418532	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8418533	8418661	1	-	2	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8418533	8418661	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	intron	8418662	8418778	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8418779	8419026	1	-	1	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8418779	8419026	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	intron	8419027	8419161	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8419162	8419313	1	-	0	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8419162	8419313	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	intron	8419314	8419405	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	CDS	8419406	8419576	1	-	0	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	exon	8419406	8419576	.	-	.	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
Phchi.S5	AUGUSTUS	start_codon	8419574	8419576	.	-	0	transcript_id "Phchi.S5G133000.t1"; gene_id "Phchi.S5G133000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg143.t1 is derived from g9925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	786883	787095	.	+	.	Phchi.S6G010200
Phchi.S6	AUGUSTUS	transcript	786883	787095	.	+	.	transcript_id "Phchi.S6G010200.t1"; gene_id "Phchi.S6G010200"
Phchi.S6	AUGUSTUS	start_codon	786883	786885	.	+	0	transcript_id "Phchi.S6G010200.t1"; gene_id "Phchi.S6G010200"
Phchi.S6	AUGUSTUS	CDS	786883	787095	0.55	+	0	transcript_id "Phchi.S6G010200.t1"; gene_id "Phchi.S6G010200"
Phchi.S6	AUGUSTUS	exon	786883	787095	.	+	.	transcript_id "Phchi.S6G010200.t1"; gene_id "Phchi.S6G010200"
Phchi.S6	AUGUSTUS	stop_codon	787096	787098	.	+	0	transcript_id "Phchi.S6G010200.t1"; gene_id "Phchi.S6G010200"
# This transcript jg9872.t2 is derived from g7048.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9873.t1 is derived from g7049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44192409	44192777	.	+	.	Phchi.S1G703200
Phchi.S1	AUGUSTUS	transcript	44192409	44192777	.	+	.	transcript_id "Phchi.S1G703200.t1"; gene_id "Phchi.S1G703200"
Phchi.S1	AUGUSTUS	start_codon	44192409	44192411	.	+	0	transcript_id "Phchi.S1G703200.t1"; gene_id "Phchi.S1G703200"
Phchi.S1	AUGUSTUS	CDS	44192409	44192777	0.71	+	0	transcript_id "Phchi.S1G703200.t1"; gene_id "Phchi.S1G703200"
Phchi.S1	AUGUSTUS	exon	44192409	44192777	.	+	.	transcript_id "Phchi.S1G703200.t1"; gene_id "Phchi.S1G703200"
Phchi.S1	AUGUSTUS	stop_codon	44192778	44192780	.	+	0	transcript_id "Phchi.S1G703200.t1"; gene_id "Phchi.S1G703200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14603.t1 is derived from g13071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13696114	13697992	.	+	.	Phchi.S3G192200
Phchi.S3	AUGUSTUS	transcript	13696114	13697992	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	start_codon	13696114	13696116	.	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13696114	13696314	0.83	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13696114	13696314	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13696315	13696421	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13696422	13696551	0.97	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13696422	13696551	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13696552	13696635	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13696636	13696792	1	+	2	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13696636	13696792	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13696793	13696870	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13696871	13696949	0.97	+	1	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13696871	13696949	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13696950	13697054	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13697055	13697214	0.55	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13697055	13697214	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13697215	13697315	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13697316	13697407	1	+	2	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13697316	13697407	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13697408	13697496	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13697497	13697602	0.97	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13697497	13697602	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13697603	13697702	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13697703	13697728	0.98	+	2	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13697703	13697728	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	intron	13697729	13697947	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	CDS	13697948	13697992	0.97	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	exon	13697948	13697992	.	+	.	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
Phchi.S3	AUGUSTUS	stop_codon	13697993	13697995	.	+	0	transcript_id "Phchi.S3G192200.t1"; gene_id "Phchi.S3G192200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3287.t1 is derived from g456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2694393	2694903	.	-	.	Phchi.S1G044600
Phchi.S1	AUGUSTUS	transcript	2694393	2694903	.	-	.	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	stop_codon	2694390	2694392	.	-	0	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	CDS	2694393	2694724	1	-	2	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	exon	2694393	2694724	.	-	.	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	intron	2694725	2694815	.	-	.	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	CDS	2694816	2694903	0.6	-	0	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	exon	2694816	2694903	.	-	.	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
Phchi.S1	AUGUSTUS	start_codon	2694901	2694903	.	-	0	transcript_id "Phchi.S1G044600.t1"; gene_id "Phchi.S1G044600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13235.t1 is derived from g11700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4854391	4855465	.	-	.	Phchi.S3G055400
Phchi.S3	AUGUSTUS	transcript	4854391	4855465	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	stop_codon	4854388	4854390	.	-	0	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	CDS	4854391	4854444	0.95	-	0	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	exon	4854391	4854444	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	intron	4854445	4854531	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	CDS	4854532	4854685	0.96	-	1	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	exon	4854532	4854685	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	intron	4854686	4854769	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	CDS	4854770	4854921	1	-	0	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	exon	4854770	4854921	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	intron	4854922	4855023	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	CDS	4855024	4855185	0.99	-	0	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	exon	4855024	4855185	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	intron	4855186	4855288	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	CDS	4855289	4855465	0.63	-	0	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	exon	4855289	4855465	.	-	.	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
Phchi.S3	AUGUSTUS	start_codon	4855463	4855465	.	-	0	transcript_id "Phchi.S3G055400.t1"; gene_id "Phchi.S3G055400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1531.t1 is derived from g8450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1612294	1614612	.	-	.	Phchi.S5G014000
Phchi.S5	AUGUSTUS	transcript	1612294	1614612	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	stop_codon	1612291	1612293	.	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1612294	1612603	0.79	-	1	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1612294	1612603	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1612604	1612710	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1612711	1612763	0.96	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1612711	1612763	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1612764	1612900	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1612901	1612981	1	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1612901	1612981	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1612982	1613160	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1613161	1613242	1	-	1	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1613161	1613242	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1613243	1613405	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1613406	1613509	1	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1613406	1613509	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1613510	1613600	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1613601	1613660	1	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1613601	1613660	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1613661	1614101	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1614102	1614164	1	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1614102	1614164	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1614165	1614244	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1614245	1614340	1	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1614245	1614340	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	intron	1614341	1614492	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	CDS	1614493	1614612	0.66	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	exon	1614493	1614612	.	-	.	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
Phchi.S5	AUGUSTUS	start_codon	1614610	1614612	.	-	0	transcript_id "Phchi.S5G014000.t1"; gene_id "Phchi.S5G014000"
# This transcript jg5095.t2 is derived from g2265.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5096.t1 is derived from g2266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14722357	14723514	.	-	.	Phchi.S1G225500
Phchi.S1	AUGUSTUS	transcript	14722357	14723514	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	stop_codon	14722354	14722356	.	-	0	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	CDS	14722357	14722447	1	-	1	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	exon	14722357	14722447	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	intron	14722448	14722520	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	CDS	14722521	14722610	1	-	1	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	exon	14722521	14722610	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	intron	14722611	14722707	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	CDS	14722708	14722852	1	-	2	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	exon	14722708	14722852	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	intron	14722853	14722935	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	CDS	14722936	14723036	1	-	1	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	exon	14722936	14723036	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	intron	14723037	14723278	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	CDS	14723279	14723319	1	-	0	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	exon	14723279	14723319	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	intron	14723320	14723502	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	CDS	14723503	14723514	0.92	-	0	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	exon	14723503	14723514	.	-	.	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
Phchi.S1	AUGUSTUS	start_codon	14723512	14723514	.	-	0	transcript_id "Phchi.S1G225500.t1"; gene_id "Phchi.S1G225500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1377.t1 is derived from g11136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C13	AUGUSTUS	gene	61651	62274	.	+	.	Phchi.C13G000400
Phchi.C13	AUGUSTUS	transcript	61651	62274	.	+	.	transcript_id "Phchi.C13G000400.t1"; gene_id "Phchi.C13G000400"
Phchi.C13	AUGUSTUS	start_codon	61651	61653	.	+	0	transcript_id "Phchi.C13G000400.t1"; gene_id "Phchi.C13G000400"
Phchi.C13	AUGUSTUS	CDS	61651	62274	0.66	+	0	transcript_id "Phchi.C13G000400.t1"; gene_id "Phchi.C13G000400"
Phchi.C13	AUGUSTUS	exon	61651	62274	.	+	.	transcript_id "Phchi.C13G000400.t1"; gene_id "Phchi.C13G000400"
Phchi.C13	AUGUSTUS	stop_codon	62275	62277	.	+	0	transcript_id "Phchi.C13G000400.t1"; gene_id "Phchi.C13G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3473.t1 is derived from g642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3960477	3961538	.	+	.	Phchi.S1G063200
Phchi.S1	AUGUSTUS	transcript	3960477	3961538	.	+	.	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	start_codon	3960477	3960479	.	+	0	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	CDS	3960477	3960876	0.55	+	0	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	exon	3960477	3960876	.	+	.	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	intron	3960877	3960972	.	+	.	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	CDS	3960973	3961538	0.98	+	2	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	exon	3960973	3961538	.	+	.	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
Phchi.S1	AUGUSTUS	stop_codon	3961539	3961541	.	+	0	transcript_id "Phchi.S1G063200.t1"; gene_id "Phchi.S1G063200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12761.t1 is derived from g11226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1938585	1940108	.	+	.	Phchi.S3G008000
Phchi.S3	AUGUSTUS	transcript	1939479	1940108	.	+	.	transcript_id "Phchi.S3G008000.t1"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	start_codon	1939479	1939481	.	+	0	transcript_id "Phchi.S3G008000.t1"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	CDS	1939479	1940108	1	+	0	transcript_id "Phchi.S3G008000.t1"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	exon	1939479	1940108	.	+	.	transcript_id "Phchi.S3G008000.t1"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	stop_codon	1940109	1940111	.	+	0	transcript_id "Phchi.S3G008000.t1"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	transcript	1939224	1940108	.	+	.	transcript_id "Phchi.S3G008000.t2"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	start_codon	1939224	1939226	.	+	0	transcript_id "Phchi.S3G008000.t2"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	CDS	1939224	1940108	0.98	+	0	transcript_id "Phchi.S3G008000.t2"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	exon	1939224	1940108	.	+	.	transcript_id "Phchi.S3G008000.t2"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	stop_codon	1940109	1940111	.	+	0	transcript_id "Phchi.S3G008000.t2"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	transcript	1938585	1940108	.	+	.	transcript_id "Phchi.S3G008000.t3"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	start_codon	1938585	1938587	.	+	0	transcript_id "Phchi.S3G008000.t3"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	CDS	1938585	1940108	0.75	+	0	transcript_id "Phchi.S3G008000.t3"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	exon	1938585	1940108	.	+	.	transcript_id "Phchi.S3G008000.t3"; gene_id "Phchi.S3G008000"
Phchi.S3	AUGUSTUS	stop_codon	1940109	1940111	.	+	0	transcript_id "Phchi.S3G008000.t3"; gene_id "Phchi.S3G008000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5200.t1 is derived from g2370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15437731	15438840	.	-	.	Phchi.S1G235900
Phchi.S1	AUGUSTUS	transcript	15437731	15438840	.	-	.	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	stop_codon	15437728	15437730	.	-	0	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	CDS	15437731	15437977	1	-	1	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	exon	15437731	15437977	.	-	.	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	intron	15437978	15438190	.	-	.	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	CDS	15438191	15438840	0.92	-	0	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	exon	15438191	15438840	.	-	.	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
Phchi.S1	AUGUSTUS	start_codon	15438838	15438840	.	-	0	transcript_id "Phchi.S1G235900.t1"; gene_id "Phchi.S1G235900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg294.t1 is derived from g10076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2102152	2102670	.	+	.	Phchi.S6G025300
Phchi.S6	AUGUSTUS	transcript	2102152	2102670	.	+	.	transcript_id "Phchi.S6G025300.t1"; gene_id "Phchi.S6G025300"
Phchi.S6	AUGUSTUS	start_codon	2102152	2102154	.	+	0	transcript_id "Phchi.S6G025300.t1"; gene_id "Phchi.S6G025300"
Phchi.S6	AUGUSTUS	CDS	2102152	2102670	0.82	+	0	transcript_id "Phchi.S6G025300.t1"; gene_id "Phchi.S6G025300"
Phchi.S6	AUGUSTUS	exon	2102152	2102670	.	+	.	transcript_id "Phchi.S6G025300.t1"; gene_id "Phchi.S6G025300"
Phchi.S6	AUGUSTUS	stop_codon	2102671	2102673	.	+	0	transcript_id "Phchi.S6G025300.t1"; gene_id "Phchi.S6G025300"
# This transcript jg15571.t2 is derived from g14040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15572.t1 is derived from g14041.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20072902	20076364	.	+	.	Phchi.S3G289100
Phchi.S3	AUGUSTUS	transcript	20072902	20076364	.	+	.	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	start_codon	20072902	20072904	.	+	0	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	CDS	20072902	20075586	0.3	+	0	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	exon	20072902	20075586	.	+	.	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	intron	20075587	20075666	.	+	.	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	CDS	20075667	20075955	0.21	+	0	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	exon	20075667	20075955	.	+	.	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	intron	20075956	20076086	.	+	.	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	CDS	20076087	20076364	0.63	+	2	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	exon	20076087	20076364	.	+	.	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	stop_codon	20076365	20076367	.	+	0	transcript_id "Phchi.S3G289100.t1"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	transcript	20072902	20075739	.	+	.	transcript_id "Phchi.S3G289100.t2"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	start_codon	20072902	20072904	.	+	0	transcript_id "Phchi.S3G289100.t2"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	CDS	20072902	20075739	0.58	+	0	transcript_id "Phchi.S3G289100.t2"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	exon	20072902	20075739	.	+	.	transcript_id "Phchi.S3G289100.t2"; gene_id "Phchi.S3G289100"
Phchi.S3	AUGUSTUS	stop_codon	20075740	20075742	.	+	0	transcript_id "Phchi.S3G289100.t2"; gene_id "Phchi.S3G289100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg985.t1 is derived from g10768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6884241	6884903	.	-	.	Phchi.S6G094400
Phchi.S6	AUGUSTUS	transcript	6884241	6884903	.	-	.	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	stop_codon	6884238	6884240	.	-	0	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	CDS	6884241	6884352	0.88	-	1	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	exon	6884241	6884352	.	-	.	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	intron	6884353	6884517	.	-	.	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	CDS	6884518	6884903	0.54	-	0	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	exon	6884518	6884903	.	-	.	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
Phchi.S6	AUGUSTUS	start_codon	6884901	6884903	.	-	0	transcript_id "Phchi.S6G094400.t1"; gene_id "Phchi.S6G094400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10958.t1 is derived from g15008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3282025	3284300	.	-	.	Phchi.S4G054000
Phchi.S4	AUGUSTUS	transcript	3282025	3284300	.	-	.	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	stop_codon	3282022	3282024	.	-	0	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	CDS	3282025	3283668	0.99	-	0	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	exon	3282025	3283668	.	-	.	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	intron	3283669	3283772	.	-	.	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	CDS	3283773	3284300	0.68	-	0	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	exon	3283773	3284300	.	-	.	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
Phchi.S4	AUGUSTUS	start_codon	3284298	3284300	.	-	0	transcript_id "Phchi.S4G054000.t1"; gene_id "Phchi.S4G054000"
# This transcript jg12596.t2 is derived from g8273.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12597.t1 is derived from g8274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37084838	37086184	.	-	.	Phchi.S2G067700
Phchi.S2	AUGUSTUS	transcript	37084838	37086184	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	stop_codon	37084835	37084837	.	-	0	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	CDS	37084838	37085032	0.99	-	0	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	exon	37084838	37085032	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	intron	37085033	37085402	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	CDS	37085403	37085492	1	-	0	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	exon	37085403	37085492	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	intron	37085493	37085652	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	CDS	37085653	37085696	1	-	2	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	exon	37085653	37085696	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	intron	37085697	37085846	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	CDS	37085847	37085970	1	-	0	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	exon	37085847	37085970	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	intron	37085971	37086049	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	CDS	37086050	37086184	0.97	-	0	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	exon	37086050	37086184	.	-	.	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
Phchi.S2	AUGUSTUS	start_codon	37086182	37086184	.	-	0	transcript_id "Phchi.S2G067700.t1"; gene_id "Phchi.S2G067700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15319.t1 is derived from g13787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18376681	18380423	.	+	.	Phchi.S3G263800
Phchi.S3	AUGUSTUS	transcript	18376681	18380423	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	start_codon	18376681	18376683	.	+	0	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	CDS	18376681	18378082	0.74	+	0	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	exon	18376681	18378082	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	intron	18378083	18378175	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	CDS	18378176	18378230	0.85	+	2	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	exon	18378176	18378230	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	intron	18378231	18378530	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	CDS	18378531	18379111	0.7	+	1	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	exon	18378531	18379111	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	intron	18379112	18379209	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	CDS	18379210	18380247	1	+	2	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	exon	18379210	18380247	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	intron	18380248	18380346	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	CDS	18380347	18380423	1	+	2	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	exon	18380347	18380423	.	+	.	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
Phchi.S3	AUGUSTUS	stop_codon	18380424	18380426	.	+	0	transcript_id "Phchi.S3G263800.t1"; gene_id "Phchi.S3G263800"
# This transcript jg2473.t2 is derived from g9393.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2473.t3 is derived from g9393.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2474.t1 is derived from g9394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6834253	6835433	.	+	.	Phchi.S5G108300
Phchi.S5	AUGUSTUS	transcript	6834253	6835433	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	start_codon	6834253	6834255	.	+	0	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	CDS	6834253	6834335	1	+	0	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	exon	6834253	6834335	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	intron	6834336	6834418	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	CDS	6834419	6834524	1	+	1	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	exon	6834419	6834524	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	intron	6834525	6834611	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	CDS	6834612	6834874	1	+	0	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	exon	6834612	6834874	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	intron	6834875	6834955	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	CDS	6834956	6835433	0.98	+	1	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	exon	6834956	6835433	.	+	.	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
Phchi.S5	AUGUSTUS	stop_codon	6835434	6835436	.	+	0	transcript_id "Phchi.S5G108300.t1"; gene_id "Phchi.S5G108300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6790.t1 is derived from g3962.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25093855	25096212	.	-	.	Phchi.S1G394900
Phchi.S1	AUGUSTUS	transcript	25093855	25096212	.	-	.	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	stop_codon	25093852	25093854	.	-	0	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	CDS	25093855	25093919	0.13	-	2	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	exon	25093855	25093919	.	-	.	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	intron	25093920	25095075	.	-	.	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	CDS	25095076	25095306	0.06	-	2	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	exon	25095076	25095306	.	-	.	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	intron	25095307	25096010	.	-	.	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	CDS	25096011	25096212	0.04	-	0	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	exon	25096011	25096212	.	-	.	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
Phchi.S1	AUGUSTUS	start_codon	25096210	25096212	.	-	0	transcript_id "Phchi.S1G394900.t1"; gene_id "Phchi.S1G394900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6651.t1 is derived from g3823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24297032	24297727	.	-	.	Phchi.S1G381000
Phchi.S1	AUGUSTUS	transcript	24297032	24297727	.	-	.	transcript_id "Phchi.S1G381000.t1"; gene_id "Phchi.S1G381000"
Phchi.S1	AUGUSTUS	stop_codon	24297029	24297031	.	-	0	transcript_id "Phchi.S1G381000.t1"; gene_id "Phchi.S1G381000"
Phchi.S1	AUGUSTUS	CDS	24297032	24297727	0.69	-	0	transcript_id "Phchi.S1G381000.t1"; gene_id "Phchi.S1G381000"
Phchi.S1	AUGUSTUS	exon	24297032	24297727	.	-	.	transcript_id "Phchi.S1G381000.t1"; gene_id "Phchi.S1G381000"
Phchi.S1	AUGUSTUS	start_codon	24297725	24297727	.	-	0	transcript_id "Phchi.S1G381000.t1"; gene_id "Phchi.S1G381000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14671.t1 is derived from g13139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14116426	14119464	.	+	.	Phchi.S3G199000
Phchi.S3	AUGUSTUS	transcript	14116426	14119464	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	start_codon	14116426	14116428	.	+	0	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	CDS	14116426	14116491	0.64	+	0	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	exon	14116426	14116491	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	intron	14116492	14116572	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	CDS	14116573	14116682	0.74	+	0	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	exon	14116573	14116682	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	intron	14116683	14116763	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	CDS	14116764	14118530	0.44	+	1	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	exon	14116764	14118530	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	intron	14118531	14118845	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	CDS	14118846	14119464	0.73	+	1	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	exon	14118846	14119464	.	+	.	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
Phchi.S3	AUGUSTUS	stop_codon	14119465	14119467	.	+	0	transcript_id "Phchi.S3G199000.t1"; gene_id "Phchi.S3G199000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg628.t1 is derived from g10410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4465922	4468867	.	-	.	Phchi.S6G058700
Phchi.S6	AUGUSTUS	transcript	4465922	4468867	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	stop_codon	4465919	4465921	.	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4465922	4466043	0.5	-	2	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4465922	4466043	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4466044	4466152	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4466153	4466193	0.97	-	1	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4466153	4466193	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4466194	4466283	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4466284	4466372	0.98	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4466284	4466372	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4466373	4466442	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4466443	4466520	0.62	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4466443	4466520	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4466521	4466600	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4466601	4466707	0.59	-	2	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4466601	4466707	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4466708	4466806	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4466807	4466896	0.59	-	2	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4466807	4466896	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4466897	4466996	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4466997	4467084	1	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4466997	4467084	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4467085	4467174	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4467175	4467390	1	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4467175	4467390	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4467391	4467481	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4467482	4467557	1	-	1	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4467482	4467557	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4467558	4467676	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4467677	4467726	1	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4467677	4467726	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4467727	4467816	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4467817	4467879	1	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4467817	4467879	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4467880	4467995	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4467996	4468049	0.99	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4467996	4468049	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4468050	4468131	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4468132	4468233	1	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4468132	4468233	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4468234	4468318	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4468319	4468421	1	-	1	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4468319	4468421	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4468422	4468509	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4468510	4468564	1	-	2	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4468510	4468564	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4468565	4468652	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4468653	4468693	1	-	1	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4468653	4468693	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	intron	4468694	4468772	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	CDS	4468773	4468867	0.44	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	exon	4468773	4468867	.	-	.	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
Phchi.S6	AUGUSTUS	start_codon	4468865	4468867	.	-	0	transcript_id "Phchi.S6G058700.t1"; gene_id "Phchi.S6G058700"
# This transcript jg1586.t2 is derived from g8505.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1587.t1 is derived from g8506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1897310	1900107	.	-	.	Phchi.S5G019600
Phchi.S5	AUGUSTUS	transcript	1897310	1900107	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	stop_codon	1897307	1897309	.	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1897310	1897492	0.98	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1897310	1897492	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1897493	1897624	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1897625	1897758	1	-	2	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1897625	1897758	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1897759	1898270	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1898271	1898436	1	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1898271	1898436	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1898437	1898516	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1898517	1898696	1	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1898517	1898696	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1898697	1898774	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1898775	1899220	1	-	2	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1898775	1899220	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1899221	1899316	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1899317	1899475	1	-	2	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1899317	1899475	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1899476	1899562	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1899563	1899744	0.33	-	1	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1899563	1899744	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1899745	1899824	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1899825	1899883	0.7	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1899825	1899883	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	intron	1899884	1899966	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	CDS	1899967	1900107	0.79	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	exon	1899967	1900107	.	-	.	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
Phchi.S5	AUGUSTUS	start_codon	1900105	1900107	.	-	0	transcript_id "Phchi.S5G019600.t1"; gene_id "Phchi.S5G019600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15488.t1 is derived from g13957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19447689	19449187	.	-	.	Phchi.S3G280700
Phchi.S3	AUGUSTUS	transcript	19447689	19449187	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	stop_codon	19447686	19447688	.	-	0	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	CDS	19447689	19447736	1	-	0	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	exon	19447689	19447736	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	intron	19447737	19447875	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	CDS	19447876	19447948	0.99	-	1	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	exon	19447876	19447948	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	intron	19447949	19448050	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	CDS	19448051	19448122	0.98	-	1	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	exon	19448051	19448122	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	intron	19448123	19448231	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	CDS	19448232	19448300	1	-	1	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	exon	19448232	19448300	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	intron	19448301	19448484	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	CDS	19448485	19448615	1	-	0	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	exon	19448485	19448615	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	intron	19448616	19449127	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	CDS	19449128	19449187	0.6	-	0	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	exon	19449128	19449187	.	-	.	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
Phchi.S3	AUGUSTUS	start_codon	19449185	19449187	.	-	0	transcript_id "Phchi.S3G280700.t1"; gene_id "Phchi.S3G280700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14744.t1 is derived from g13212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14503599	14504209	.	-	.	Phchi.S3G206300
Phchi.S3	AUGUSTUS	transcript	14503599	14504209	.	-	.	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	stop_codon	14503596	14503598	.	-	0	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	CDS	14503599	14503907	0.92	-	0	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	exon	14503599	14503907	.	-	.	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	intron	14503908	14504029	.	-	.	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	CDS	14504030	14504209	0.99	-	0	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	exon	14504030	14504209	.	-	.	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
Phchi.S3	AUGUSTUS	start_codon	14504207	14504209	.	-	0	transcript_id "Phchi.S3G206300.t1"; gene_id "Phchi.S3G206300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10634.t1 is derived from g14684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1356145	1358033	.	-	.	Phchi.S4G021600
Phchi.S4	AUGUSTUS	transcript	1356145	1358033	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	stop_codon	1356142	1356144	.	-	0	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1356145	1356316	0.99	-	1	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1356145	1356316	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1356317	1356465	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1356466	1356634	1	-	2	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1356466	1356634	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1356635	1356758	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1356759	1356867	1	-	0	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1356759	1356867	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1356868	1356965	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1356966	1357185	1	-	1	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1356966	1357185	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1357186	1357268	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1357269	1357414	1	-	0	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1357269	1357414	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1357415	1357502	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1357503	1357560	0.98	-	1	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1357503	1357560	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1357561	1357641	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1357642	1357810	0.97	-	2	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1357642	1357810	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	intron	1357811	1357897	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	CDS	1357898	1358033	1	-	0	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	exon	1357898	1358033	.	-	.	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
Phchi.S4	AUGUSTUS	start_codon	1358031	1358033	.	-	0	transcript_id "Phchi.S4G021600.t1"; gene_id "Phchi.S4G021600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2368.t1 is derived from g9288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6375661	6377205	.	+	.	Phchi.S5G097700
Phchi.S5	AUGUSTUS	transcript	6375661	6377205	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	start_codon	6375661	6375663	.	+	0	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	CDS	6375661	6375782	0.86	+	0	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	exon	6375661	6375782	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	intron	6375783	6375878	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	CDS	6375879	6376022	1	+	1	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	exon	6375879	6376022	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	intron	6376023	6376121	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	CDS	6376122	6376252	1	+	1	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	exon	6376122	6376252	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	intron	6376253	6376342	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	CDS	6376343	6376501	1	+	2	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	exon	6376343	6376501	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	intron	6376502	6376582	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	CDS	6376583	6377205	1	+	2	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	exon	6376583	6377205	.	+	.	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
Phchi.S5	AUGUSTUS	stop_codon	6377206	6377208	.	+	0	transcript_id "Phchi.S5G097700.t1"; gene_id "Phchi.S5G097700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg948.t1 is derived from g10730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6619427	6620905	.	-	.	Phchi.S6G090700
Phchi.S6	AUGUSTUS	transcript	6619427	6620905	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	stop_codon	6619424	6619426	.	-	0	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	CDS	6619427	6619510	0.94	-	0	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	exon	6619427	6619510	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	intron	6619511	6619618	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	CDS	6619619	6619709	0.96	-	1	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	exon	6619619	6619709	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	intron	6619710	6619786	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	CDS	6619787	6620290	0.95	-	1	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	exon	6619787	6620290	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	intron	6620291	6620372	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	CDS	6620373	6620443	1	-	0	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	exon	6620373	6620443	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	intron	6620444	6620563	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	CDS	6620564	6620628	1	-	2	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	exon	6620564	6620628	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	intron	6620629	6620763	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	CDS	6620764	6620905	0.99	-	0	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	exon	6620764	6620905	.	-	.	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
Phchi.S6	AUGUSTUS	start_codon	6620903	6620905	.	-	0	transcript_id "Phchi.S6G090700.t1"; gene_id "Phchi.S6G090700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13839.t1 is derived from g12306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9147680	9150311	.	+	.	Phchi.S3G115800
Phchi.S3	AUGUSTUS	transcript	9147680	9150311	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	start_codon	9147680	9147682	.	+	0	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	CDS	9147680	9149137	0.56	+	0	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	exon	9147680	9149137	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	intron	9149138	9149248	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	CDS	9149249	9149505	0.89	+	0	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	exon	9149249	9149505	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	intron	9149506	9149721	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	CDS	9149722	9149750	0.92	+	1	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	exon	9149722	9149750	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	intron	9149751	9149870	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	CDS	9149871	9149911	0.9	+	2	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	exon	9149871	9149911	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	intron	9149912	9150010	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	CDS	9150011	9150057	0.98	+	0	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	exon	9150011	9150057	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	intron	9150058	9150139	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	CDS	9150140	9150311	1	+	1	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	exon	9150140	9150311	.	+	.	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
Phchi.S3	AUGUSTUS	stop_codon	9150312	9150314	.	+	0	transcript_id "Phchi.S3G115800.t1"; gene_id "Phchi.S3G115800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13586.t1 is derived from g12053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7587874	7590936	.	-	.	Phchi.S3G090500
Phchi.S3	AUGUSTUS	transcript	7587874	7590936	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	stop_codon	7587871	7587873	.	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7587874	7588185	0.74	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7587874	7588185	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7588186	7588279	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7588280	7588387	0.99	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7588280	7588387	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7588388	7588520	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7588521	7588793	0.99	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7588521	7588793	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7588794	7588876	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7588877	7588963	0.84	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7588877	7588963	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7588964	7589070	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7589071	7589265	0.98	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7589071	7589265	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7589266	7589425	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7589426	7589557	0.87	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7589426	7589557	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7589558	7589667	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7589668	7589778	0.96	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7589668	7589778	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7589779	7589887	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7589888	7590059	1	-	1	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7589888	7590059	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7590060	7590164	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7590165	7590454	1	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7590165	7590454	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7590455	7590541	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7590542	7590621	1	-	2	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7590542	7590621	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	intron	7590622	7590707	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	CDS	7590708	7590936	0.66	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	exon	7590708	7590936	.	-	.	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
Phchi.S3	AUGUSTUS	start_codon	7590934	7590936	.	-	0	transcript_id "Phchi.S3G090500.t1"; gene_id "Phchi.S3G090500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11372.t1 is derived from g15422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5941066	5942734	.	+	.	Phchi.S4G095400
Phchi.S4	AUGUSTUS	transcript	5941066	5942734	.	+	.	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	start_codon	5941066	5941068	.	+	0	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	CDS	5941066	5941162	1	+	0	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	exon	5941066	5941162	.	+	.	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	intron	5941163	5941306	.	+	.	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	CDS	5941307	5941676	1	+	2	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	exon	5941307	5941676	.	+	.	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	intron	5941677	5941800	.	+	.	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	CDS	5941801	5942734	0.53	+	1	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	exon	5941801	5942734	.	+	.	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
Phchi.S4	AUGUSTUS	stop_codon	5942735	5942737	.	+	0	transcript_id "Phchi.S4G095400.t1"; gene_id "Phchi.S4G095400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9031.t1 is derived from g6206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39221829	39223190	.	-	.	Phchi.S1G619000
Phchi.S1	AUGUSTUS	transcript	39221829	39223190	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	stop_codon	39221826	39221828	.	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	CDS	39221829	39221915	1	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	exon	39221829	39221915	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	intron	39221916	39221995	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	CDS	39221996	39222166	1	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	exon	39221996	39222166	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	intron	39222167	39222263	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	CDS	39222264	39222344	1	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	exon	39222264	39222344	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	intron	39222345	39222466	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	CDS	39222467	39222580	1	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	exon	39222467	39222580	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	intron	39222581	39222663	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	CDS	39222664	39222708	1	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	exon	39222664	39222708	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	intron	39222709	39222842	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	CDS	39222843	39223190	0.69	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	exon	39222843	39223190	.	-	.	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
Phchi.S1	AUGUSTUS	start_codon	39223188	39223190	.	-	0	transcript_id "Phchi.S1G619000.t1"; gene_id "Phchi.S1G619000"
# This transcript jg199.t2 is derived from g9981.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg200.t1 is derived from g9982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1122537	1123730	.	+	.	Phchi.S6G015900
Phchi.S6	AUGUSTUS	transcript	1122537	1123730	.	+	.	transcript_id "Phchi.S6G015900.t1"; gene_id "Phchi.S6G015900"
Phchi.S6	AUGUSTUS	start_codon	1122537	1122539	.	+	0	transcript_id "Phchi.S6G015900.t1"; gene_id "Phchi.S6G015900"
Phchi.S6	AUGUSTUS	CDS	1122537	1123730	0.62	+	0	transcript_id "Phchi.S6G015900.t1"; gene_id "Phchi.S6G015900"
Phchi.S6	AUGUSTUS	exon	1122537	1123730	.	+	.	transcript_id "Phchi.S6G015900.t1"; gene_id "Phchi.S6G015900"
Phchi.S6	AUGUSTUS	stop_codon	1123731	1123733	.	+	0	transcript_id "Phchi.S6G015900.t1"; gene_id "Phchi.S6G015900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1324.t1 is derived from g11107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9026089	9026792	.	+	.	Phchi.S6G128300
Phchi.S6	AUGUSTUS	transcript	9026089	9026792	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	start_codon	9026089	9026091	.	+	0	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	CDS	9026089	9026197	1	+	0	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	exon	9026089	9026197	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	intron	9026198	9026310	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	CDS	9026311	9026362	1	+	2	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	exon	9026311	9026362	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	intron	9026363	9026499	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	CDS	9026500	9026659	1	+	1	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	exon	9026500	9026659	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	intron	9026660	9026747	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	CDS	9026748	9026792	1	+	0	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	exon	9026748	9026792	.	+	.	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
Phchi.S6	AUGUSTUS	stop_codon	9026793	9026795	.	+	0	transcript_id "Phchi.S6G128300.t1"; gene_id "Phchi.S6G128300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3975.t1 is derived from g1144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6825732	6826646	.	+	.	Phchi.S1G113400
Phchi.S1	AUGUSTUS	transcript	6825732	6826646	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	start_codon	6825732	6825734	.	+	0	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	CDS	6825732	6825795	0.39	+	0	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	exon	6825732	6825795	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	intron	6825796	6825942	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	CDS	6825943	6825948	0.54	+	2	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	exon	6825943	6825948	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	intron	6825949	6826041	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	CDS	6826042	6826070	0.65	+	2	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	exon	6826042	6826070	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	intron	6826071	6826145	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	CDS	6826146	6826646	0.6	+	0	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	exon	6826146	6826646	.	+	.	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
Phchi.S1	AUGUSTUS	stop_codon	6826647	6826649	.	+	0	transcript_id "Phchi.S1G113400.t1"; gene_id "Phchi.S1G113400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11515.t1 is derived from g15565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6858195	6859696	.	-	.	Phchi.S4G109700
Phchi.S4	AUGUSTUS	transcript	6858195	6859696	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	stop_codon	6858192	6858194	.	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6858195	6858272	1	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6858195	6858272	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6858273	6858371	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6858372	6858444	1	-	1	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6858372	6858444	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6858445	6858524	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6858525	6858592	1	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6858525	6858592	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6858593	6858673	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6858674	6858761	1	-	1	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6858674	6858761	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6858762	6858838	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6858839	6858913	1	-	1	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6858839	6858913	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6858914	6858997	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6858998	6859037	1	-	2	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6858998	6859037	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6859038	6859166	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6859167	6859263	1	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6859167	6859263	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6859264	6859352	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6859353	6859460	1	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6859353	6859460	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	intron	6859461	6859549	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	CDS	6859550	6859696	0.3	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	exon	6859550	6859696	.	-	.	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
Phchi.S4	AUGUSTUS	start_codon	6859694	6859696	.	-	0	transcript_id "Phchi.S4G109700.t1"; gene_id "Phchi.S4G109700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8309.t1 is derived from g5484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35223498	35225378	.	-	.	Phchi.S1G546800
Phchi.S1	AUGUSTUS	transcript	35223498	35225378	.	-	.	transcript_id "Phchi.S1G546800.t1"; gene_id "Phchi.S1G546800"
Phchi.S1	AUGUSTUS	stop_codon	35223495	35223497	.	-	0	transcript_id "Phchi.S1G546800.t1"; gene_id "Phchi.S1G546800"
Phchi.S1	AUGUSTUS	CDS	35223498	35225378	0.79	-	0	transcript_id "Phchi.S1G546800.t1"; gene_id "Phchi.S1G546800"
Phchi.S1	AUGUSTUS	exon	35223498	35225378	.	-	.	transcript_id "Phchi.S1G546800.t1"; gene_id "Phchi.S1G546800"
Phchi.S1	AUGUSTUS	start_codon	35225376	35225378	.	-	0	transcript_id "Phchi.S1G546800.t1"; gene_id "Phchi.S1G546800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6130.t1 is derived from g3301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21071611	21073809	.	-	.	Phchi.S1G328900
Phchi.S1	AUGUSTUS	transcript	21071611	21073809	.	-	.	transcript_id "Phchi.S1G328900.t1"; gene_id "Phchi.S1G328900"
Phchi.S1	AUGUSTUS	stop_codon	21071608	21071610	.	-	0	transcript_id "Phchi.S1G328900.t1"; gene_id "Phchi.S1G328900"
Phchi.S1	AUGUSTUS	CDS	21071611	21073809	0.83	-	0	transcript_id "Phchi.S1G328900.t1"; gene_id "Phchi.S1G328900"
Phchi.S1	AUGUSTUS	exon	21071611	21073809	.	-	.	transcript_id "Phchi.S1G328900.t1"; gene_id "Phchi.S1G328900"
Phchi.S1	AUGUSTUS	start_codon	21073807	21073809	.	-	0	transcript_id "Phchi.S1G328900.t1"; gene_id "Phchi.S1G328900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg853.t1 is derived from g10635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5920744	5922099	.	-	.	Phchi.S6G081200
Phchi.S6	AUGUSTUS	transcript	5920744	5922099	.	-	.	transcript_id "Phchi.S6G081200.t1"; gene_id "Phchi.S6G081200"
Phchi.S6	AUGUSTUS	stop_codon	5920741	5920743	.	-	0	transcript_id "Phchi.S6G081200.t1"; gene_id "Phchi.S6G081200"
Phchi.S6	AUGUSTUS	CDS	5920744	5922099	0.95	-	0	transcript_id "Phchi.S6G081200.t1"; gene_id "Phchi.S6G081200"
Phchi.S6	AUGUSTUS	exon	5920744	5922099	.	-	.	transcript_id "Phchi.S6G081200.t1"; gene_id "Phchi.S6G081200"
Phchi.S6	AUGUSTUS	start_codon	5922097	5922099	.	-	0	transcript_id "Phchi.S6G081200.t1"; gene_id "Phchi.S6G081200"
# This transcript jg12304.t2 is derived from g7980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12304.t3 is derived from g7980.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12305.t1 is derived from g7981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9905330	9908111	.	+	.	Phchi.S2G038500
Phchi.S2	AUGUSTUS	transcript	9905330	9908111	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	start_codon	9905330	9905332	.	+	0	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9905330	9905418	0.39	+	0	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9905330	9905418	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	intron	9905419	9905627	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9905628	9905772	1	+	1	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9905628	9905772	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	intron	9905773	9905913	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9905914	9906588	0.99	+	0	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9905914	9906588	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	intron	9906589	9906742	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9906743	9906815	1	+	0	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9906743	9906815	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	intron	9906816	9906988	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9906989	9907340	0.57	+	2	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9906989	9907340	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	intron	9907341	9907426	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9907427	9907613	0.38	+	1	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9907427	9907613	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	intron	9907614	9907718	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	CDS	9907719	9908111	0.43	+	0	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	exon	9907719	9908111	.	+	.	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
Phchi.S2	AUGUSTUS	stop_codon	9908112	9908114	.	+	0	transcript_id "Phchi.S2G038500.t1"; gene_id "Phchi.S2G038500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2080.t1 is derived from g9000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4760398	4760613	.	-	.	Phchi.S5G068900
Phchi.S5	AUGUSTUS	transcript	4760398	4760613	.	-	.	transcript_id "Phchi.S5G068900.t1"; gene_id "Phchi.S5G068900"
Phchi.S5	AUGUSTUS	stop_codon	4760395	4760397	.	-	0	transcript_id "Phchi.S5G068900.t1"; gene_id "Phchi.S5G068900"
Phchi.S5	AUGUSTUS	CDS	4760398	4760613	0.74	-	0	transcript_id "Phchi.S5G068900.t1"; gene_id "Phchi.S5G068900"
Phchi.S5	AUGUSTUS	exon	4760398	4760613	.	-	.	transcript_id "Phchi.S5G068900.t1"; gene_id "Phchi.S5G068900"
Phchi.S5	AUGUSTUS	start_codon	4760611	4760613	.	-	0	transcript_id "Phchi.S5G068900.t1"; gene_id "Phchi.S5G068900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7759.t1 is derived from g4933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31154953	31156298	.	+	.	Phchi.S1G491800
Phchi.S1	AUGUSTUS	transcript	31154953	31156298	.	+	.	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	start_codon	31154953	31154955	.	+	0	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	CDS	31154953	31155057	0.99	+	0	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	exon	31154953	31155057	.	+	.	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	intron	31155058	31155886	.	+	.	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	CDS	31155887	31155968	0.02	+	0	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	exon	31155887	31155968	.	+	.	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	intron	31155969	31156209	.	+	.	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	CDS	31156210	31156298	0.02	+	2	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	exon	31156210	31156298	.	+	.	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
Phchi.S1	AUGUSTUS	stop_codon	31156299	31156301	.	+	0	transcript_id "Phchi.S1G491800.t1"; gene_id "Phchi.S1G491800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15669.t1 is derived from g14138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20590403	20592307	.	-	.	Phchi.S3G298800
Phchi.S3	AUGUSTUS	transcript	20590403	20592307	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	stop_codon	20590400	20590402	.	-	0	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	CDS	20590403	20590662	0.99	-	2	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	exon	20590403	20590662	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	intron	20590663	20590757	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	CDS	20590758	20590989	1	-	0	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	exon	20590758	20590989	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	intron	20590990	20591124	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	CDS	20591125	20591851	1	-	1	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	exon	20591125	20591851	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	intron	20591852	20592278	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	CDS	20592279	20592307	0.99	-	0	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	exon	20592279	20592307	.	-	.	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
Phchi.S3	AUGUSTUS	start_codon	20592305	20592307	.	-	0	transcript_id "Phchi.S3G298800.t1"; gene_id "Phchi.S3G298800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8794.t1 is derived from g5969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37997367	37998041	.	+	.	Phchi.S1G595300
Phchi.S1	AUGUSTUS	transcript	37997367	37998041	.	+	.	transcript_id "Phchi.S1G595300.t1"; gene_id "Phchi.S1G595300"
Phchi.S1	AUGUSTUS	start_codon	37997367	37997369	.	+	0	transcript_id "Phchi.S1G595300.t1"; gene_id "Phchi.S1G595300"
Phchi.S1	AUGUSTUS	CDS	37997367	37998041	0.87	+	0	transcript_id "Phchi.S1G595300.t1"; gene_id "Phchi.S1G595300"
Phchi.S1	AUGUSTUS	exon	37997367	37998041	.	+	.	transcript_id "Phchi.S1G595300.t1"; gene_id "Phchi.S1G595300"
Phchi.S1	AUGUSTUS	stop_codon	37998042	37998044	.	+	0	transcript_id "Phchi.S1G595300.t1"; gene_id "Phchi.S1G595300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15613.t1 is derived from g14082.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20295247	20297058	.	-	.	Phchi.S3G293200
Phchi.S3	AUGUSTUS	transcript	20295247	20297058	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	stop_codon	20295244	20295246	.	-	0	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	CDS	20295247	20295576	1	-	0	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	exon	20295247	20295576	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	intron	20295577	20295683	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	CDS	20295684	20295899	1	-	0	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	exon	20295684	20295899	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	intron	20295900	20295983	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	CDS	20295984	20296083	0.54	-	1	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	exon	20295984	20296083	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	intron	20296084	20296232	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	CDS	20296233	20296512	0.67	-	2	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	exon	20296233	20296512	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	intron	20296513	20296602	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	CDS	20296603	20296654	1	-	0	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	exon	20296603	20296654	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	intron	20296655	20296740	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	CDS	20296741	20297058	1	-	0	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	exon	20296741	20297058	.	-	.	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
Phchi.S3	AUGUSTUS	start_codon	20297056	20297058	.	-	0	transcript_id "Phchi.S3G293200.t1"; gene_id "Phchi.S3G293200"
# This transcript jg962.t2 is derived from g10744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg963.t1 is derived from g10745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6690182	6692778	.	+	.	Phchi.S6G092200
Phchi.S6	AUGUSTUS	transcript	6690182	6692778	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	start_codon	6690182	6690184	.	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6690182	6690318	0.78	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6690182	6690318	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6690319	6690437	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6690438	6690670	0.8	+	1	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6690438	6690670	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6690671	6690748	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6690749	6690968	1	+	2	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6690749	6690968	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6690969	6691060	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6691061	6691182	1	+	1	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6691061	6691182	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6691183	6691331	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6691332	6691585	1	+	2	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6691332	6691585	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6691586	6691667	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6691668	6691775	1	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6691668	6691775	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6691776	6691868	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6691869	6692075	1	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6691869	6692075	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6692076	6692168	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6692169	6692279	1	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6692169	6692279	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6692280	6692365	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6692366	6692539	1	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6692366	6692539	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	intron	6692540	6692625	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	CDS	6692626	6692778	1	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	exon	6692626	6692778	.	+	.	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
Phchi.S6	AUGUSTUS	stop_codon	6692779	6692781	.	+	0	transcript_id "Phchi.S6G092200.t1"; gene_id "Phchi.S6G092200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5062.t1 is derived from g2232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14492073	14494208	.	+	.	Phchi.S1G222100
Phchi.S1	AUGUSTUS	transcript	14492073	14494208	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	start_codon	14492073	14492075	.	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	CDS	14492073	14492219	0.78	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	exon	14492073	14492219	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	intron	14492220	14492309	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	CDS	14492310	14492564	1	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	exon	14492310	14492564	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	intron	14492565	14492874	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	CDS	14492875	14493606	1	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	exon	14492875	14493606	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	intron	14493607	14493909	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	CDS	14493910	14494098	0.67	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	exon	14493910	14494098	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	intron	14494099	14494175	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	CDS	14494176	14494208	0.59	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	exon	14494176	14494208	.	+	.	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
Phchi.S1	AUGUSTUS	stop_codon	14494209	14494211	.	+	0	transcript_id "Phchi.S1G222100.t1"; gene_id "Phchi.S1G222100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1485.t1 is derived from g8404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1148186	1149158	.	+	.	Phchi.S5G009400
Phchi.S5	AUGUSTUS	transcript	1148186	1149158	.	+	.	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	start_codon	1148186	1148188	.	+	0	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	CDS	1148186	1148615	0.53	+	0	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	exon	1148186	1148615	.	+	.	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	intron	1148616	1148709	.	+	.	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	CDS	1148710	1149158	0.54	+	2	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	exon	1148710	1149158	.	+	.	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
Phchi.S5	AUGUSTUS	stop_codon	1149159	1149161	.	+	0	transcript_id "Phchi.S5G009400.t1"; gene_id "Phchi.S5G009400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8906.t1 is derived from g6081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38584024	38584995	.	+	.	Phchi.S1G606500
Phchi.S1	AUGUSTUS	transcript	38584024	38584995	.	+	.	transcript_id "Phchi.S1G606500.t1"; gene_id "Phchi.S1G606500"
Phchi.S1	AUGUSTUS	start_codon	38584024	38584026	.	+	0	transcript_id "Phchi.S1G606500.t1"; gene_id "Phchi.S1G606500"
Phchi.S1	AUGUSTUS	CDS	38584024	38584995	0.55	+	0	transcript_id "Phchi.S1G606500.t1"; gene_id "Phchi.S1G606500"
Phchi.S1	AUGUSTUS	exon	38584024	38584995	.	+	.	transcript_id "Phchi.S1G606500.t1"; gene_id "Phchi.S1G606500"
Phchi.S1	AUGUSTUS	stop_codon	38584996	38584998	.	+	0	transcript_id "Phchi.S1G606500.t1"; gene_id "Phchi.S1G606500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10372.t1 is derived from g7548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47414633	47415949	.	-	.	Phchi.S1G753100
Phchi.S1	AUGUSTUS	transcript	47414633	47415949	.	-	.	transcript_id "Phchi.S1G753100.t1"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	stop_codon	47414630	47414632	.	-	0	transcript_id "Phchi.S1G753100.t1"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	CDS	47414633	47415949	1	-	0	transcript_id "Phchi.S1G753100.t1"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	exon	47414633	47415949	.	-	.	transcript_id "Phchi.S1G753100.t1"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	start_codon	47415947	47415949	.	-	0	transcript_id "Phchi.S1G753100.t1"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	transcript	47414633	47414992	.	-	.	transcript_id "Phchi.S1G753100.t2"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	stop_codon	47414630	47414632	.	-	0	transcript_id "Phchi.S1G753100.t2"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	CDS	47414633	47414992	0.75	-	0	transcript_id "Phchi.S1G753100.t2"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	exon	47414633	47414992	.	-	.	transcript_id "Phchi.S1G753100.t2"; gene_id "Phchi.S1G753100"
Phchi.S1	AUGUSTUS	start_codon	47414990	47414992	.	-	0	transcript_id "Phchi.S1G753100.t2"; gene_id "Phchi.S1G753100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3337.t1 is derived from g506.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2979505	2980668	.	-	.	Phchi.S1G049600
Phchi.S1	AUGUSTUS	transcript	2979505	2980668	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	stop_codon	2979502	2979504	.	-	0	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	CDS	2979505	2979565	0.92	-	1	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	exon	2979505	2979565	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	intron	2979566	2979970	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	CDS	2979971	2980092	0.91	-	0	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	exon	2979971	2980092	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	intron	2980093	2980202	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	CDS	2980203	2980301	0.86	-	0	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	exon	2980203	2980301	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	intron	2980302	2980443	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	CDS	2980444	2980668	0.75	-	0	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	exon	2980444	2980668	.	-	.	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
Phchi.S1	AUGUSTUS	start_codon	2980666	2980668	.	-	0	transcript_id "Phchi.S1G049600.t1"; gene_id "Phchi.S1G049600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8089.t1 is derived from g5264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32893305	32895105	.	+	.	Phchi.S1G524800
Phchi.S1	AUGUSTUS	transcript	32893305	32895105	.	+	.	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	start_codon	32893305	32893307	.	+	0	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	CDS	32893305	32894967	0.63	+	0	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	exon	32893305	32894967	.	+	.	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	intron	32894968	32895061	.	+	.	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	CDS	32895062	32895105	1	+	2	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	exon	32895062	32895105	.	+	.	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
Phchi.S1	AUGUSTUS	stop_codon	32895106	32895108	.	+	0	transcript_id "Phchi.S1G524800.t1"; gene_id "Phchi.S1G524800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3333.t1 is derived from g502.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2960979	2963088	.	-	.	Phchi.S1G049200
Phchi.S1	AUGUSTUS	transcript	2960979	2963088	.	-	.	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	stop_codon	2960976	2960978	.	-	0	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	CDS	2960979	2962592	0.83	-	0	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	exon	2960979	2962592	.	-	.	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	intron	2962593	2962710	.	-	.	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	CDS	2962711	2963088	0.71	-	0	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	exon	2962711	2963088	.	-	.	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
Phchi.S1	AUGUSTUS	start_codon	2963086	2963088	.	-	0	transcript_id "Phchi.S1G049200.t1"; gene_id "Phchi.S1G049200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14237.t1 is derived from g12704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11687947	11691603	.	-	.	Phchi.S3G155600
Phchi.S3	AUGUSTUS	transcript	11687947	11691603	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	stop_codon	11687944	11687946	.	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11687947	11688005	1	-	2	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11687947	11688005	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11688006	11688086	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11688087	11688161	1	-	2	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11688087	11688161	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11688162	11688244	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11688245	11688346	1	-	2	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11688245	11688346	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11688347	11688540	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11688541	11688601	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11688541	11688601	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11688602	11688676	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11688677	11688820	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11688677	11688820	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11688821	11688897	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11688898	11688978	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11688898	11688978	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11688979	11689062	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11689063	11689132	1	-	1	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11689063	11689132	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11689133	11689251	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11689252	11689340	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11689252	11689340	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11689341	11689469	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11689470	11689578	1	-	1	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11689470	11689578	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11689579	11689669	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11689670	11689720	1	-	1	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11689670	11689720	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11689721	11689802	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11689803	11689873	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11689803	11689873	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11689874	11689964	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11689965	11690024	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11689965	11690024	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11690025	11690136	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11690137	11690260	1	-	1	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11690137	11690260	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11690261	11690522	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11690523	11690623	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11690523	11690623	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11690624	11690892	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11690893	11691003	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11690893	11691003	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11691004	11691088	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11691089	11691124	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11691089	11691124	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11691125	11691208	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11691209	11691354	1	-	2	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11691209	11691354	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	intron	11691355	11691593	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	CDS	11691594	11691603	1	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	exon	11691594	11691603	.	-	.	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
Phchi.S3	AUGUSTUS	start_codon	11691601	11691603	.	-	0	transcript_id "Phchi.S3G155600.t1"; gene_id "Phchi.S3G155600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5376.t1 is derived from g2546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16564739	16567476	.	-	.	Phchi.S1G253500
Phchi.S1	AUGUSTUS	transcript	16564739	16567476	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	stop_codon	16564736	16564738	.	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16564739	16564830	1	-	2	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16564739	16564830	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16564831	16564923	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16564924	16565040	1	-	2	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16564924	16565040	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565041	16565124	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16565125	16565198	1	-	1	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16565125	16565198	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565199	16565275	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16565276	16565358	0.77	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16565276	16565358	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565359	16565442	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16565443	16565553	1	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16565443	16565553	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565554	16565662	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16565663	16565707	0.51	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16565663	16565707	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565708	16565796	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16565797	16565822	0.75	-	2	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16565797	16565822	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565823	16565892	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16565893	16565989	0.49	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16565893	16565989	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16565990	16566505	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16566506	16566755	0.49	-	1	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16566506	16566755	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	intron	16566756	16566970	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	CDS	16566971	16567476	0.86	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	exon	16566971	16567476	.	-	.	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
Phchi.S1	AUGUSTUS	start_codon	16567474	16567476	.	-	0	transcript_id "Phchi.S1G253500.t1"; gene_id "Phchi.S1G253500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4344.t1 is derived from g1513.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9870356	9871801	.	-	.	Phchi.S1G150300
Phchi.S1	AUGUSTUS	transcript	9870356	9871801	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	stop_codon	9870353	9870355	.	-	0	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	CDS	9870356	9870655	0.99	-	0	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	exon	9870356	9870655	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	intron	9870656	9870757	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	CDS	9870758	9871064	0.57	-	1	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	exon	9870758	9871064	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	intron	9871065	9871156	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	CDS	9871157	9871422	0.99	-	0	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	exon	9871157	9871422	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	intron	9871423	9871540	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	CDS	9871541	9871801	0.99	-	0	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	exon	9871541	9871801	.	-	.	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	start_codon	9871799	9871801	.	-	0	transcript_id "Phchi.S1G150300.t1"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	transcript	9871410	9871801	.	-	.	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	stop_codon	9871407	9871409	.	-	0	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	CDS	9871410	9871422	0.61	-	1	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	exon	9871410	9871422	.	-	.	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	intron	9871423	9871529	.	-	.	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	CDS	9871530	9871801	0.64	-	0	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	exon	9871530	9871801	.	-	.	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
Phchi.S1	AUGUSTUS	start_codon	9871799	9871801	.	-	0	transcript_id "Phchi.S1G150300.t2"; gene_id "Phchi.S1G150300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg326.t1 is derived from g10108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2274622	2275213	.	+	.	Phchi.S6G028500
Phchi.S6	AUGUSTUS	transcript	2274622	2275213	.	+	.	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	start_codon	2274622	2274624	.	+	0	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	CDS	2274622	2274730	0.8	+	0	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	exon	2274622	2274730	.	+	.	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	intron	2274731	2274836	.	+	.	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	CDS	2274837	2274950	1	+	2	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	exon	2274837	2274950	.	+	.	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	intron	2274951	2275073	.	+	.	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	CDS	2275074	2275213	1	+	2	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	exon	2275074	2275213	.	+	.	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
Phchi.S6	AUGUSTUS	stop_codon	2275214	2275216	.	+	0	transcript_id "Phchi.S6G028500.t1"; gene_id "Phchi.S6G028500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg343.t1 is derived from g10125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2489249	2490514	.	+	.	Phchi.S6G030200
Phchi.S6	AUGUSTUS	transcript	2489249	2490514	.	+	.	transcript_id "Phchi.S6G030200.t1"; gene_id "Phchi.S6G030200"
Phchi.S6	AUGUSTUS	start_codon	2489249	2489251	.	+	0	transcript_id "Phchi.S6G030200.t1"; gene_id "Phchi.S6G030200"
Phchi.S6	AUGUSTUS	CDS	2489249	2490514	0.96	+	0	transcript_id "Phchi.S6G030200.t1"; gene_id "Phchi.S6G030200"
Phchi.S6	AUGUSTUS	exon	2489249	2490514	.	+	.	transcript_id "Phchi.S6G030200.t1"; gene_id "Phchi.S6G030200"
Phchi.S6	AUGUSTUS	stop_codon	2490515	2490517	.	+	0	transcript_id "Phchi.S6G030200.t1"; gene_id "Phchi.S6G030200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11568.t1 is derived from g15619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7091256	7092437	.	-	.	Phchi.S4G115000
Phchi.S4	AUGUSTUS	transcript	7091256	7092437	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	stop_codon	7091253	7091255	.	-	0	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	CDS	7091256	7091461	1	-	2	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	exon	7091256	7091461	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	intron	7091462	7091558	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	CDS	7091559	7091622	1	-	0	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	exon	7091559	7091622	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	intron	7091623	7091744	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	CDS	7091745	7091917	1	-	2	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	exon	7091745	7091917	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	intron	7091918	7092166	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	CDS	7092167	7092437	0.51	-	0	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	exon	7092167	7092437	.	-	.	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
Phchi.S4	AUGUSTUS	start_codon	7092435	7092437	.	-	0	transcript_id "Phchi.S4G115000.t1"; gene_id "Phchi.S4G115000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg659.t1 is derived from g10441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4619200	4620432	.	+	.	Phchi.S6G061800
Phchi.S6	AUGUSTUS	transcript	4619200	4620432	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	start_codon	4619200	4619202	.	+	0	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	CDS	4619200	4619406	1	+	0	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	exon	4619200	4619406	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	intron	4619407	4619506	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	CDS	4619507	4619830	1	+	0	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	exon	4619507	4619830	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	intron	4619831	4619923	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	CDS	4619924	4620083	1	+	0	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	exon	4619924	4620083	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	intron	4620084	4620157	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	CDS	4620158	4620432	1	+	2	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	exon	4620158	4620432	.	+	.	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
Phchi.S6	AUGUSTUS	stop_codon	4620433	4620435	.	+	0	transcript_id "Phchi.S6G061800.t1"; gene_id "Phchi.S6G061800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8895.t1 is derived from g6070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38536077	38538778	.	+	.	Phchi.S1G605400
Phchi.S1	AUGUSTUS	transcript	38536077	38538778	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	start_codon	38536077	38536079	.	+	0	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38536077	38536230	1	+	0	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38536077	38536230	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38536231	38536309	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38536310	38536408	1	+	2	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38536310	38536408	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38536409	38536486	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38536487	38537175	0.97	+	2	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38536487	38537175	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38537176	38537319	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38537320	38537386	1	+	0	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38537320	38537386	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38537387	38537475	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38537476	38537828	0.99	+	2	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38537476	38537828	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38537829	38537928	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38537929	38538140	1	+	0	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38537929	38538140	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38538141	38538289	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38538290	38538546	1	+	1	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38538290	38538546	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	intron	38538547	38538674	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	CDS	38538675	38538778	1	+	2	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	exon	38538675	38538778	.	+	.	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
Phchi.S1	AUGUSTUS	stop_codon	38538779	38538781	.	+	0	transcript_id "Phchi.S1G605400.t1"; gene_id "Phchi.S1G605400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg95.t1 is derived from g9877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	483862	484437	.	-	.	Phchi.S6G005400
Phchi.S6	AUGUSTUS	transcript	483862	484437	.	-	.	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	stop_codon	483859	483861	.	-	0	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	CDS	483862	483984	0.95	-	0	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	exon	483862	483984	.	-	.	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	intron	483985	484125	.	-	.	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	CDS	484126	484152	0.35	-	0	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	exon	484126	484152	.	-	.	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	intron	484153	484317	.	-	.	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	CDS	484318	484437	0.69	-	0	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	exon	484318	484437	.	-	.	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
Phchi.S6	AUGUSTUS	start_codon	484435	484437	.	-	0	transcript_id "Phchi.S6G005400.t1"; gene_id "Phchi.S6G005400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7429.t1 is derived from g4601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29091120	29091930	.	-	.	Phchi.S1G458800
Phchi.S1	AUGUSTUS	transcript	29091120	29091930	.	-	.	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	stop_codon	29091117	29091119	.	-	0	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	CDS	29091120	29091410	0.98	-	0	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	exon	29091120	29091410	.	-	.	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	intron	29091411	29091516	.	-	.	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	CDS	29091517	29091745	0.8	-	1	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	exon	29091517	29091745	.	-	.	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	intron	29091746	29091853	.	-	.	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	CDS	29091854	29091930	0.81	-	0	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	exon	29091854	29091930	.	-	.	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
Phchi.S1	AUGUSTUS	start_codon	29091928	29091930	.	-	0	transcript_id "Phchi.S1G458800.t1"; gene_id "Phchi.S1G458800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg167.t1 is derived from g9949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	948377	949153	.	-	.	Phchi.S6G012600
Phchi.S6	AUGUSTUS	transcript	948377	949153	.	-	.	transcript_id "Phchi.S6G012600.t1"; gene_id "Phchi.S6G012600"
Phchi.S6	AUGUSTUS	stop_codon	948374	948376	.	-	0	transcript_id "Phchi.S6G012600.t1"; gene_id "Phchi.S6G012600"
Phchi.S6	AUGUSTUS	CDS	948377	949153	0.85	-	0	transcript_id "Phchi.S6G012600.t1"; gene_id "Phchi.S6G012600"
Phchi.S6	AUGUSTUS	exon	948377	949153	.	-	.	transcript_id "Phchi.S6G012600.t1"; gene_id "Phchi.S6G012600"
Phchi.S6	AUGUSTUS	start_codon	949151	949153	.	-	0	transcript_id "Phchi.S6G012600.t1"; gene_id "Phchi.S6G012600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14290.t1 is derived from g12757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11958301	11962170	.	-	.	Phchi.S3G160900
Phchi.S3	AUGUSTUS	transcript	11958301	11962170	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	stop_codon	11958298	11958300	.	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11958301	11958393	0.98	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11958301	11958393	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11958394	11958501	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11958502	11958570	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11958502	11958570	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11958571	11958647	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11958648	11958764	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11958648	11958764	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11958765	11958860	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11958861	11958947	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11958861	11958947	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11958948	11959076	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11959077	11959148	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11959077	11959148	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11959149	11959266	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11959267	11959353	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11959267	11959353	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11959354	11959453	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11959454	11959525	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11959454	11959525	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11959526	11959604	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11959605	11959718	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11959605	11959718	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11959719	11959808	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11959809	11959868	0.8	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11959809	11959868	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11959869	11960026	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11960027	11960113	1	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11960027	11960113	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11960114	11960263	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11960264	11960359	0.86	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11960264	11960359	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11960360	11960463	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11960464	11960686	1	-	1	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11960464	11960686	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11960687	11960875	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11960876	11961528	0.85	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11960876	11961528	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11961529	11961626	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11961627	11961779	0.89	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11961627	11961779	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	intron	11961780	11961864	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	CDS	11961865	11962170	0.7	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	exon	11961865	11962170	.	-	.	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
Phchi.S3	AUGUSTUS	start_codon	11962168	11962170	.	-	0	transcript_id "Phchi.S3G160900.t1"; gene_id "Phchi.S3G160900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7795.t1 is derived from g4969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31203967	31205348	.	+	.	Phchi.S1G495400
Phchi.S1	AUGUSTUS	transcript	31203967	31205348	.	+	.	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	start_codon	31203967	31203969	.	+	0	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	CDS	31203967	31204071	0.51	+	0	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	exon	31203967	31204071	.	+	.	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	intron	31204072	31204319	.	+	.	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	CDS	31204320	31204644	0.92	+	0	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	exon	31204320	31204644	.	+	.	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	intron	31204645	31204845	.	+	.	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	CDS	31204846	31205348	0.68	+	2	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	exon	31204846	31205348	.	+	.	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
Phchi.S1	AUGUSTUS	stop_codon	31205349	31205351	.	+	0	transcript_id "Phchi.S1G495400.t1"; gene_id "Phchi.S1G495400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 5 different transcripts
# This transcript jg6089.t1 is derived from g3260.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20905329	20908448	.	-	.	Phchi.S1G324800
Phchi.S1	AUGUSTUS	transcript	20906825	20908448	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	stop_codon	20906822	20906824	.	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906825	20906839	0.95	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906825	20906839	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906840	20906923	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906924	20906999	1	-	1	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906924	20906999	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907000	20907096	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907097	20907146	1	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907097	20907146	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907147	20907265	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907266	20907328	1	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907266	20907328	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907329	20907436	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907437	20907490	1	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907437	20907490	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907491	20907620	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907621	20907726	0.92	-	1	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907621	20907726	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907727	20907833	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907834	20907936	0.91	-	2	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907834	20907936	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907937	20908167	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908168	20908276	0.98	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908168	20908276	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908277	20908415	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908416	20908448	0.94	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908416	20908448	.	-	.	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	start_codon	20908446	20908448	.	-	0	transcript_id "Phchi.S1G324800.t1"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	transcript	20905329	20906484	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	stop_codon	20905326	20905328	.	-	0	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905329	20905435	0.93	-	2	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905329	20905435	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905436	20905517	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905518	20905558	1	-	1	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905518	20905558	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905559	20905665	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905666	20905754	1	-	0	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905666	20905754	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905755	20905883	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905884	20905928	1	-	0	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905884	20905928	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905929	20906016	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906017	20906124	1	-	0	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906017	20906124	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906125	20906229	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906230	20906315	1	-	2	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906230	20906315	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906316	20906390	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906391	20906484	0.64	-	0	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906391	20906484	.	-	.	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	start_codon	20906482	20906484	.	-	0	transcript_id "Phchi.S1G324800.t2"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	transcript	20905329	20908448	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	stop_codon	20905326	20905328	.	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905329	20905435	0.97	-	2	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905329	20905435	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905436	20905517	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905518	20905558	1	-	1	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905518	20905558	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905559	20905665	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905666	20905754	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905666	20905754	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905755	20905883	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20905884	20905928	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20905884	20905928	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20905929	20906016	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906017	20906124	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906017	20906124	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906125	20906229	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906230	20906315	1	-	2	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906230	20906315	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906316	20906390	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906391	20906478	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906391	20906478	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906479	20906584	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906585	20906821	0.92	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906585	20906821	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906822	20906923	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906924	20906999	0.97	-	1	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906924	20906999	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907000	20907096	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907097	20907146	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907097	20907146	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907147	20907265	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907266	20907328	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907266	20907328	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907329	20907436	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907437	20907490	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907437	20907490	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907491	20907620	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907621	20907726	0.97	-	1	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907621	20907726	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907727	20907833	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907834	20907936	0.94	-	2	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907834	20907936	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907937	20908013	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908014	20908074	1	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908014	20908074	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908075	20908167	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908168	20908208	0.63	-	2	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908168	20908208	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908209	20908309	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908310	20908448	0.63	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908310	20908448	.	-	.	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	start_codon	20908446	20908448	.	-	0	transcript_id "Phchi.S1G324800.t3"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	transcript	20906825	20908448	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	stop_codon	20906822	20906824	.	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906825	20906839	0.99	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906825	20906839	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906840	20906923	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906924	20906999	1	-	1	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906924	20906999	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907000	20907096	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907097	20907146	1	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907097	20907146	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907147	20907265	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907266	20907328	0.99	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907266	20907328	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907329	20907436	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907437	20907490	0.98	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907437	20907490	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907491	20907620	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907621	20907726	0.93	-	1	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907621	20907726	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907727	20907833	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907834	20907936	0.87	-	2	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907834	20907936	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907937	20908013	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908014	20908074	1	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908014	20908074	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908075	20908167	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908168	20908208	0.76	-	2	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908168	20908208	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908209	20908309	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908310	20908448	0.76	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908310	20908448	.	-	.	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	start_codon	20908446	20908448	.	-	0	transcript_id "Phchi.S1G324800.t4"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	transcript	20906825	20908448	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	stop_codon	20906822	20906824	.	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906825	20906839	0.55	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906825	20906839	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20906840	20906923	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20906924	20906999	0.58	-	1	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20906924	20906999	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907000	20907092	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907093	20907112	0.52	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907093	20907112	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907113	20907265	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907266	20907328	1	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907266	20907328	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907329	20907436	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907437	20907490	1	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907437	20907490	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907491	20907620	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907621	20907726	0.95	-	1	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907621	20907726	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907727	20907833	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20907834	20907936	0.93	-	2	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20907834	20907936	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20907937	20908013	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908014	20908074	1	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908014	20908074	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908075	20908167	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908168	20908208	0.67	-	2	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908168	20908208	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	intron	20908209	20908309	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	CDS	20908310	20908448	0.67	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	exon	20908310	20908448	.	-	.	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
Phchi.S1	AUGUSTUS	start_codon	20908446	20908448	.	-	0	transcript_id "Phchi.S1G324800.t5"; gene_id "Phchi.S1G324800"
# This transcript jg6617.t2 is derived from g3789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6618.t1 is derived from g3790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24018361	24020496	.	-	.	Phchi.S1G377700
Phchi.S1	AUGUSTUS	transcript	24018361	24020496	.	-	.	transcript_id "Phchi.S1G377700.t1"; gene_id "Phchi.S1G377700"
Phchi.S1	AUGUSTUS	stop_codon	24018358	24018360	.	-	0	transcript_id "Phchi.S1G377700.t1"; gene_id "Phchi.S1G377700"
Phchi.S1	AUGUSTUS	CDS	24018361	24020496	0.97	-	0	transcript_id "Phchi.S1G377700.t1"; gene_id "Phchi.S1G377700"
Phchi.S1	AUGUSTUS	exon	24018361	24020496	.	-	.	transcript_id "Phchi.S1G377700.t1"; gene_id "Phchi.S1G377700"
Phchi.S1	AUGUSTUS	start_codon	24020494	24020496	.	-	0	transcript_id "Phchi.S1G377700.t1"; gene_id "Phchi.S1G377700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13321.t1 is derived from g11787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6095748	6096929	.	-	.	Phchi.S3G064000
Phchi.S3	AUGUSTUS	transcript	6095748	6096929	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	stop_codon	6095745	6095747	.	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	CDS	6095748	6095901	0.79	-	1	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	exon	6095748	6095901	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	intron	6095902	6096027	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	CDS	6096028	6096134	1	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	exon	6096028	6096134	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	intron	6096135	6096253	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	CDS	6096254	6096343	1	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	exon	6096254	6096343	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	intron	6096344	6096437	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	CDS	6096438	6096581	1	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	exon	6096438	6096581	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	intron	6096582	6096663	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	CDS	6096664	6096714	1	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	exon	6096664	6096714	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	intron	6096715	6096821	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	CDS	6096822	6096929	1	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	exon	6096822	6096929	.	-	.	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
Phchi.S3	AUGUSTUS	start_codon	6096927	6096929	.	-	0	transcript_id "Phchi.S3G064000.t1"; gene_id "Phchi.S3G064000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6286.t1 is derived from g3458.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22091714	22092355	.	+	.	Phchi.S1G344500
Phchi.S1	AUGUSTUS	transcript	22091714	22092355	.	+	.	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	start_codon	22091714	22091716	.	+	0	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	CDS	22091714	22091731	0.86	+	0	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	exon	22091714	22091731	.	+	.	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	intron	22091732	22091880	.	+	.	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	CDS	22091881	22092144	0.78	+	0	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	exon	22091881	22092144	.	+	.	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	intron	22092145	22092274	.	+	.	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	CDS	22092275	22092355	0.97	+	0	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	exon	22092275	22092355	.	+	.	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
Phchi.S1	AUGUSTUS	stop_codon	22092356	22092358	.	+	0	transcript_id "Phchi.S1G344500.t1"; gene_id "Phchi.S1G344500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1486.t1 is derived from g8405.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1149367	1151311	.	-	.	Phchi.S5G009500
Phchi.S5	AUGUSTUS	transcript	1149367	1151311	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	stop_codon	1149364	1149366	.	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1149367	1149410	1	-	2	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1149367	1149410	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1149411	1149492	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1149493	1149634	1	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1149493	1149634	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1149635	1149718	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1149719	1149898	0.96	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1149719	1149898	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1149899	1150025	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1150026	1150142	0.97	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1150026	1150142	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1150143	1150237	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1150238	1150360	1	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1150238	1150360	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1150361	1150454	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1150455	1150696	0.57	-	2	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1150455	1150696	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1150697	1150852	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1150853	1151065	0.6	-	2	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1150853	1151065	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	intron	1151066	1151151	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	CDS	1151152	1151311	0.43	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	exon	1151152	1151311	.	-	.	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
Phchi.S5	AUGUSTUS	start_codon	1151309	1151311	.	-	0	transcript_id "Phchi.S5G009500.t1"; gene_id "Phchi.S5G009500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2580.t1 is derived from g9500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7479210	7480926	.	+	.	Phchi.S5G118900
Phchi.S5	AUGUSTUS	transcript	7479210	7480926	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	start_codon	7479210	7479212	.	+	0	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	CDS	7479210	7480187	0.36	+	0	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	exon	7479210	7480187	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	intron	7480188	7480583	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	CDS	7480584	7480591	0.28	+	0	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	exon	7480584	7480591	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	intron	7480592	7480713	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	CDS	7480714	7480788	0.86	+	1	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	exon	7480714	7480788	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	intron	7480789	7480871	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	CDS	7480872	7480926	0.96	+	1	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	exon	7480872	7480926	.	+	.	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
Phchi.S5	AUGUSTUS	stop_codon	7480927	7480929	.	+	0	transcript_id "Phchi.S5G118900.t1"; gene_id "Phchi.S5G118900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12858.t1 is derived from g11323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2756666	2757100	.	+	.	Phchi.S3G017700
Phchi.S3	AUGUSTUS	transcript	2756666	2757100	.	+	.	transcript_id "Phchi.S3G017700.t1"; gene_id "Phchi.S3G017700"
Phchi.S3	AUGUSTUS	start_codon	2756666	2756668	.	+	0	transcript_id "Phchi.S3G017700.t1"; gene_id "Phchi.S3G017700"
Phchi.S3	AUGUSTUS	CDS	2756666	2757100	0.98	+	0	transcript_id "Phchi.S3G017700.t1"; gene_id "Phchi.S3G017700"
Phchi.S3	AUGUSTUS	exon	2756666	2757100	.	+	.	transcript_id "Phchi.S3G017700.t1"; gene_id "Phchi.S3G017700"
Phchi.S3	AUGUSTUS	stop_codon	2757101	2757103	.	+	0	transcript_id "Phchi.S3G017700.t1"; gene_id "Phchi.S3G017700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7818.t1 is derived from g4992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31350078	31353674	.	+	.	Phchi.S1G497700
Phchi.S1	AUGUSTUS	transcript	31350078	31353674	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	start_codon	31350078	31350080	.	+	0	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31350078	31350211	0.98	+	0	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31350078	31350211	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31350212	31350399	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31350400	31350982	0.82	+	1	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31350400	31350982	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31350983	31351156	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31351157	31352347	0.28	+	0	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31351157	31352347	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31352348	31352565	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31352566	31353117	0.82	+	0	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31352566	31353117	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31353118	31353207	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31353208	31353280	1	+	0	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31353208	31353280	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31353281	31353350	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31353351	31353431	1	+	2	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31353351	31353431	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31353432	31353508	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31353509	31353574	0.99	+	2	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31353509	31353574	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	intron	31353575	31353651	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	CDS	31353652	31353674	0.99	+	2	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	exon	31353652	31353674	.	+	.	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
Phchi.S1	AUGUSTUS	stop_codon	31353675	31353677	.	+	0	transcript_id "Phchi.S1G497700.t1"; gene_id "Phchi.S1G497700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4151.t1 is derived from g1320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8653948	8654877	.	+	.	Phchi.S1G131000
Phchi.S1	AUGUSTUS	transcript	8653948	8654877	.	+	.	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	start_codon	8653948	8653950	.	+	0	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	CDS	8653948	8654025	0.76	+	0	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	exon	8653948	8654025	.	+	.	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	intron	8654026	8654127	.	+	.	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	CDS	8654128	8654283	0.47	+	0	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	exon	8654128	8654283	.	+	.	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	intron	8654284	8654430	.	+	.	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	CDS	8654431	8654877	1	+	0	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	exon	8654431	8654877	.	+	.	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
Phchi.S1	AUGUSTUS	stop_codon	8654878	8654880	.	+	0	transcript_id "Phchi.S1G131000.t1"; gene_id "Phchi.S1G131000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6571.t1 is derived from g3743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23769174	23773952	.	+	.	Phchi.S1G373000
Phchi.S1	AUGUSTUS	transcript	23769174	23773952	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	start_codon	23769174	23769176	.	+	0	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23769174	23769633	0.36	+	0	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23769174	23769633	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23769634	23769772	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23769773	23771379	0.36	+	2	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23769773	23771379	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23771380	23771490	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23771491	23771710	1	+	0	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23771491	23771710	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23771711	23771853	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23771854	23772519	1	+	2	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23771854	23772519	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23772520	23772592	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23772593	23773352	0.97	+	2	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23772593	23773352	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23773353	23773498	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23773499	23773565	0.98	+	1	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23773499	23773565	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23773566	23773677	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23773678	23773705	0.34	+	0	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23773678	23773705	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23773706	23773805	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23773806	23773836	0.36	+	2	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23773806	23773836	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	intron	23773837	23773909	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	CDS	23773910	23773952	0.95	+	1	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	exon	23773910	23773952	.	+	.	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
Phchi.S1	AUGUSTUS	stop_codon	23773953	23773955	.	+	0	transcript_id "Phchi.S1G373000.t1"; gene_id "Phchi.S1G373000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7501.t1 is derived from g4675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29681919	29685660	.	+	.	Phchi.S1G466000
Phchi.S1	AUGUSTUS	transcript	29681919	29685660	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	start_codon	29681919	29681921	.	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29681919	29682086	0.69	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29681919	29682086	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29682087	29682206	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29682207	29682283	0.98	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29682207	29682283	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29682284	29682470	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29682471	29682632	1	+	1	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29682471	29682632	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29682633	29682730	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29682731	29682941	1	+	1	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29682731	29682941	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29682942	29683070	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29683071	29683157	1	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29683071	29683157	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29683158	29683247	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29683248	29683387	1	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29683248	29683387	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29683388	29683521	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29683522	29683593	1	+	1	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29683522	29683593	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29683594	29683798	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29683799	29683863	1	+	1	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29683799	29683863	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29683864	29684014	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29684015	29684187	1	+	2	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29684015	29684187	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29684188	29684326	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29684327	29684457	1	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29684327	29684457	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29684458	29684585	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29684586	29684667	1	+	1	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29684586	29684667	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29684668	29684839	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29684840	29685059	1	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29684840	29685059	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29685060	29685182	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29685183	29685292	1	+	2	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29685183	29685292	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	intron	29685293	29685381	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	CDS	29685382	29685660	0.96	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	exon	29685382	29685660	.	+	.	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
Phchi.S1	AUGUSTUS	stop_codon	29685661	29685663	.	+	0	transcript_id "Phchi.S1G466000.t1"; gene_id "Phchi.S1G466000"
# This transcript jg485.t2 is derived from g10267.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg486.t1 is derived from g10268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3395523	3396135	.	-	.	Phchi.S6G044500
Phchi.S6	AUGUSTUS	transcript	3395523	3396135	.	-	.	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	stop_codon	3395520	3395522	.	-	0	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	CDS	3395523	3395635	0.96	-	2	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	exon	3395523	3395635	.	-	.	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	intron	3395636	3395719	.	-	.	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	CDS	3395720	3395782	0.99	-	2	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	exon	3395720	3395782	.	-	.	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	intron	3395783	3395888	.	-	.	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	CDS	3395889	3396135	0.98	-	0	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	exon	3395889	3396135	.	-	.	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
Phchi.S6	AUGUSTUS	start_codon	3396133	3396135	.	-	0	transcript_id "Phchi.S6G044500.t1"; gene_id "Phchi.S6G044500"
# This transcript jg4790.t2 is derived from g1960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4791.t1 is derived from g1961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12824787	12825402	.	+	.	Phchi.S1G195000
Phchi.S1	AUGUSTUS	transcript	12824787	12825402	.	+	.	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	start_codon	12824787	12824789	.	+	0	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	CDS	12824787	12824967	1	+	0	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	exon	12824787	12824967	.	+	.	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	intron	12824968	12825047	.	+	.	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	CDS	12825048	12825279	0.72	+	2	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	exon	12825048	12825279	.	+	.	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	intron	12825280	12825365	.	+	.	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	CDS	12825366	12825402	0.72	+	1	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	exon	12825366	12825402	.	+	.	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	stop_codon	12825403	12825405	.	+	0	transcript_id "Phchi.S1G195000.t1"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	transcript	12824915	12825402	.	+	.	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	start_codon	12824915	12824917	.	+	0	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	CDS	12824915	12824967	0.52	+	0	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	exon	12824915	12824967	.	+	.	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	intron	12824968	12825042	.	+	.	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	CDS	12825043	12825279	0.66	+	1	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	exon	12825043	12825279	.	+	.	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	intron	12825280	12825365	.	+	.	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	CDS	12825366	12825402	0.71	+	1	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	exon	12825366	12825402	.	+	.	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
Phchi.S1	AUGUSTUS	stop_codon	12825403	12825405	.	+	0	transcript_id "Phchi.S1G195000.t2"; gene_id "Phchi.S1G195000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4521.t1 is derived from g1691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10937737	10938142	.	-	.	Phchi.S1G168000
Phchi.S1	AUGUSTUS	transcript	10937737	10938142	.	-	.	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	stop_codon	10937734	10937736	.	-	0	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	CDS	10937737	10937813	1	-	2	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	exon	10937737	10937813	.	-	.	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	intron	10937814	10937898	.	-	.	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	CDS	10937899	10938142	0.95	-	0	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	exon	10937899	10938142	.	-	.	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
Phchi.S1	AUGUSTUS	start_codon	10938140	10938142	.	-	0	transcript_id "Phchi.S1G168000.t1"; gene_id "Phchi.S1G168000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6823.t1 is derived from g3995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25222426	25223937	.	+	.	Phchi.S1G398200
Phchi.S1	AUGUSTUS	transcript	25222426	25223937	.	+	.	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	start_codon	25222426	25222428	.	+	0	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	CDS	25222426	25222917	1	+	0	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	exon	25222426	25222917	.	+	.	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	intron	25222918	25223034	.	+	.	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	CDS	25223035	25223937	1	+	0	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	exon	25223035	25223937	.	+	.	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
Phchi.S1	AUGUSTUS	stop_codon	25223938	25223940	.	+	0	transcript_id "Phchi.S1G398200.t1"; gene_id "Phchi.S1G398200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9334.t1 is derived from g6509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40969362	40970724	.	-	.	Phchi.S1G649300
Phchi.S1	AUGUSTUS	transcript	40969362	40970724	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	stop_codon	40969359	40969361	.	-	0	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	CDS	40969362	40969568	1	-	0	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	exon	40969362	40969568	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	intron	40969569	40969693	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	CDS	40969694	40970121	0.6	-	2	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	exon	40969694	40970121	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	intron	40970122	40970244	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	CDS	40970245	40970257	0.93	-	0	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	exon	40970245	40970257	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	intron	40970258	40970349	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	CDS	40970350	40970724	0.91	-	0	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	exon	40970350	40970724	.	-	.	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
Phchi.S1	AUGUSTUS	start_codon	40970722	40970724	.	-	0	transcript_id "Phchi.S1G649300.t1"; gene_id "Phchi.S1G649300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5890.t1 is derived from g3060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19619730	19621950	.	-	.	Phchi.S1G304900
Phchi.S1	AUGUSTUS	transcript	19619730	19621950	.	-	.	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	stop_codon	19619727	19619729	.	-	0	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	CDS	19619730	19619783	1	-	0	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	exon	19619730	19619783	.	-	.	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	intron	19619784	19619921	.	-	.	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	CDS	19619922	19619988	0.34	-	1	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	exon	19619922	19619988	.	-	.	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	intron	19619989	19620109	.	-	.	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	CDS	19620110	19621950	0.32	-	0	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	exon	19620110	19621950	.	-	.	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
Phchi.S1	AUGUSTUS	start_codon	19621948	19621950	.	-	0	transcript_id "Phchi.S1G304900.t1"; gene_id "Phchi.S1G304900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10763.t1 is derived from g14813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1996540	1997001	.	+	.	Phchi.S4G034500
Phchi.S4	AUGUSTUS	transcript	1996540	1997001	.	+	.	transcript_id "Phchi.S4G034500.t1"; gene_id "Phchi.S4G034500"
Phchi.S4	AUGUSTUS	start_codon	1996540	1996542	.	+	0	transcript_id "Phchi.S4G034500.t1"; gene_id "Phchi.S4G034500"
Phchi.S4	AUGUSTUS	CDS	1996540	1997001	0.54	+	0	transcript_id "Phchi.S4G034500.t1"; gene_id "Phchi.S4G034500"
Phchi.S4	AUGUSTUS	exon	1996540	1997001	.	+	.	transcript_id "Phchi.S4G034500.t1"; gene_id "Phchi.S4G034500"
Phchi.S4	AUGUSTUS	stop_codon	1997002	1997004	.	+	0	transcript_id "Phchi.S4G034500.t1"; gene_id "Phchi.S4G034500"
# This transcript jg5216.t2 is derived from g2386.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5217.t1 is derived from g2387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15541671	15545096	.	+	.	Phchi.S1G237600
Phchi.S1	AUGUSTUS	transcript	15541671	15545096	.	+	.	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	start_codon	15541671	15541673	.	+	0	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	CDS	15541671	15542460	0.31	+	0	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	exon	15541671	15542460	.	+	.	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	intron	15542461	15542669	.	+	.	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	CDS	15542670	15544616	0.74	+	2	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	exon	15542670	15544616	.	+	.	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	intron	15544617	15544764	.	+	.	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	CDS	15544765	15545096	0.67	+	2	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	exon	15544765	15545096	.	+	.	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
Phchi.S1	AUGUSTUS	stop_codon	15545097	15545099	.	+	0	transcript_id "Phchi.S1G237600.t1"; gene_id "Phchi.S1G237600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg109.t1 is derived from g9891.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	583317	584256	.	+	.	Phchi.S6G006800
Phchi.S6	AUGUSTUS	transcript	583317	584256	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	start_codon	583317	583319	.	+	0	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	CDS	583317	583358	0.98	+	0	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	exon	583317	583358	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	intron	583359	583461	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	CDS	583462	583548	1	+	0	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	exon	583462	583548	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	intron	583549	583710	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	CDS	583711	583767	1	+	0	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	exon	583711	583767	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	intron	583768	583921	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	CDS	583922	583997	1	+	0	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	exon	583922	583997	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	intron	583998	584095	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	CDS	584096	584256	1	+	2	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	exon	584096	584256	.	+	.	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
Phchi.S6	AUGUSTUS	stop_codon	584257	584259	.	+	0	transcript_id "Phchi.S6G006800.t1"; gene_id "Phchi.S6G006800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3058.t1 is derived from g227.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1381524	1383405	.	-	.	Phchi.S1G021700
Phchi.S1	AUGUSTUS	transcript	1381524	1383405	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	stop_codon	1381521	1381523	.	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1381524	1381780	1	-	2	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1381524	1381780	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1381781	1381873	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1381874	1381928	1	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1381874	1381928	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1381929	1382063	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382064	1382129	1	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382064	1382129	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1382130	1382308	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382309	1382410	1	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382309	1382410	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1382411	1382497	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382498	1382560	0.84	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382498	1382560	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1382561	1382661	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382662	1383405	0.98	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382662	1383405	.	-	.	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	start_codon	1383403	1383405	.	-	0	transcript_id "Phchi.S1G021700.t1"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	transcript	1381524	1383405	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	stop_codon	1381521	1381523	.	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1381524	1381780	1	-	2	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1381524	1381780	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1381781	1381873	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1381874	1381928	1	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1381874	1381928	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1381929	1382063	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382064	1382222	0.99	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382064	1382222	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1382223	1382308	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382309	1382410	1	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382309	1382410	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1382411	1382497	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382498	1382560	0.72	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382498	1382560	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	intron	1382561	1382661	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	CDS	1382662	1383405	0.94	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	exon	1382662	1383405	.	-	.	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
Phchi.S1	AUGUSTUS	start_codon	1383403	1383405	.	-	0	transcript_id "Phchi.S1G021700.t2"; gene_id "Phchi.S1G021700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4823.t1 is derived from g1993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13008736	13011110	.	+	.	Phchi.S1G198200
Phchi.S1	AUGUSTUS	transcript	13008736	13011110	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	start_codon	13008736	13008738	.	+	0	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	CDS	13008736	13009479	0.73	+	0	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	exon	13008736	13009479	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	intron	13009480	13009578	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	CDS	13009579	13009725	1	+	0	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	exon	13009579	13009725	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	intron	13009726	13009825	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	CDS	13009826	13010858	0.47	+	0	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	exon	13009826	13010858	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	intron	13010859	13011057	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	CDS	13011058	13011110	0.54	+	2	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	exon	13011058	13011110	.	+	.	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
Phchi.S1	AUGUSTUS	stop_codon	13011111	13011113	.	+	0	transcript_id "Phchi.S1G198200.t1"; gene_id "Phchi.S1G198200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2144.t1 is derived from g9064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5043005	5044528	.	-	.	Phchi.S5G075300
Phchi.S5	AUGUSTUS	transcript	5043005	5044528	.	-	.	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	stop_codon	5043002	5043004	.	-	0	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	CDS	5043005	5044295	1	-	1	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	exon	5043005	5044295	.	-	.	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	intron	5044296	5044517	.	-	.	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	CDS	5044518	5044528	1	-	0	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	exon	5044518	5044528	.	-	.	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
Phchi.S5	AUGUSTUS	start_codon	5044526	5044528	.	-	0	transcript_id "Phchi.S5G075300.t1"; gene_id "Phchi.S5G075300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12974.t1 is derived from g11439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3397999	3398502	.	+	.	Phchi.S3G029300
Phchi.S3	AUGUSTUS	transcript	3397999	3398502	.	+	.	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	start_codon	3397999	3398001	.	+	0	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	CDS	3397999	3398093	0.99	+	0	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	exon	3397999	3398093	.	+	.	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	intron	3398094	3398177	.	+	.	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	CDS	3398178	3398254	1	+	1	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	exon	3398178	3398254	.	+	.	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	intron	3398255	3398329	.	+	.	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	CDS	3398330	3398502	0.99	+	2	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	exon	3398330	3398502	.	+	.	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
Phchi.S3	AUGUSTUS	stop_codon	3398503	3398505	.	+	0	transcript_id "Phchi.S3G029300.t1"; gene_id "Phchi.S3G029300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10137.t1 is derived from g7313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45939645	45940085	.	+	.	Phchi.S1G729600
Phchi.S1	AUGUSTUS	transcript	45939645	45940085	.	+	.	transcript_id "Phchi.S1G729600.t1"; gene_id "Phchi.S1G729600"
Phchi.S1	AUGUSTUS	start_codon	45939645	45939647	.	+	0	transcript_id "Phchi.S1G729600.t1"; gene_id "Phchi.S1G729600"
Phchi.S1	AUGUSTUS	CDS	45939645	45940085	0.54	+	0	transcript_id "Phchi.S1G729600.t1"; gene_id "Phchi.S1G729600"
Phchi.S1	AUGUSTUS	exon	45939645	45940085	.	+	.	transcript_id "Phchi.S1G729600.t1"; gene_id "Phchi.S1G729600"
Phchi.S1	AUGUSTUS	stop_codon	45940086	45940088	.	+	0	transcript_id "Phchi.S1G729600.t1"; gene_id "Phchi.S1G729600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6588.t1 is derived from g3760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23894488	23895661	.	+	.	Phchi.S1G374700
Phchi.S1	AUGUSTUS	transcript	23894488	23895661	.	+	.	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	start_codon	23894488	23894490	.	+	0	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	CDS	23894488	23895054	0.34	+	0	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	exon	23894488	23895054	.	+	.	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	intron	23895055	23895178	.	+	.	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	CDS	23895179	23895661	0.7	+	0	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	exon	23895179	23895661	.	+	.	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
Phchi.S1	AUGUSTUS	stop_codon	23895662	23895664	.	+	0	transcript_id "Phchi.S1G374700.t1"; gene_id "Phchi.S1G374700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8492.t1 is derived from g5667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36239237	36239623	.	-	.	Phchi.S1G565100
Phchi.S1	AUGUSTUS	transcript	36239237	36239623	.	-	.	transcript_id "Phchi.S1G565100.t1"; gene_id "Phchi.S1G565100"
Phchi.S1	AUGUSTUS	stop_codon	36239234	36239236	.	-	0	transcript_id "Phchi.S1G565100.t1"; gene_id "Phchi.S1G565100"
Phchi.S1	AUGUSTUS	CDS	36239237	36239623	0.64	-	0	transcript_id "Phchi.S1G565100.t1"; gene_id "Phchi.S1G565100"
Phchi.S1	AUGUSTUS	exon	36239237	36239623	.	-	.	transcript_id "Phchi.S1G565100.t1"; gene_id "Phchi.S1G565100"
Phchi.S1	AUGUSTUS	start_codon	36239621	36239623	.	-	0	transcript_id "Phchi.S1G565100.t1"; gene_id "Phchi.S1G565100"
# This transcript jg11209.t2 is derived from g15259.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11209.t3 is derived from g15259.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11210.t1 is derived from g15260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4798569	4799040	.	-	.	Phchi.S4G079200
Phchi.S4	AUGUSTUS	transcript	4798569	4799040	.	-	.	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	stop_codon	4798566	4798568	.	-	0	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	CDS	4798569	4798640	0.99	-	0	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	exon	4798569	4798640	.	-	.	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	intron	4798641	4798718	.	-	.	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	CDS	4798719	4798848	1	-	1	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	exon	4798719	4798848	.	-	.	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	intron	4798849	4798924	.	-	.	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	CDS	4798925	4799040	0.95	-	0	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	exon	4798925	4799040	.	-	.	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
Phchi.S4	AUGUSTUS	start_codon	4799038	4799040	.	-	0	transcript_id "Phchi.S4G079200.t1"; gene_id "Phchi.S4G079200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3896.t1 is derived from g1065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6293933	6295263	.	-	.	Phchi.S1G105500
Phchi.S1	AUGUSTUS	transcript	6293933	6295263	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	stop_codon	6293930	6293932	.	-	0	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	CDS	6293933	6294154	0.94	-	0	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	exon	6293933	6294154	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	intron	6294155	6294252	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	CDS	6294253	6294551	0.99	-	2	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	exon	6294253	6294551	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	intron	6294552	6294663	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	CDS	6294664	6294731	0.98	-	1	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	exon	6294664	6294731	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	intron	6294732	6294835	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	CDS	6294836	6295263	0.8	-	0	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	exon	6294836	6295263	.	-	.	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
Phchi.S1	AUGUSTUS	start_codon	6295261	6295263	.	-	0	transcript_id "Phchi.S1G105500.t1"; gene_id "Phchi.S1G105500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11555.t1 is derived from g15606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7018475	7021754	.	-	.	Phchi.S4G113700
Phchi.S4	AUGUSTUS	transcript	7018475	7021754	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	stop_codon	7018472	7018474	.	-	0	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	CDS	7018475	7018893	1	-	2	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	exon	7018475	7018893	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	intron	7018894	7018976	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	CDS	7018977	7019133	1	-	0	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	exon	7018977	7019133	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	intron	7019134	7019257	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	CDS	7019258	7020854	0.5	-	1	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	exon	7019258	7020854	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	intron	7020855	7020942	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	CDS	7020943	7021754	0.98	-	0	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	exon	7020943	7021754	.	-	.	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
Phchi.S4	AUGUSTUS	start_codon	7021752	7021754	.	-	0	transcript_id "Phchi.S4G113700.t1"; gene_id "Phchi.S4G113700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9852.t1 is derived from g7028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44087371	44089387	.	-	.	Phchi.S1G701100
Phchi.S1	AUGUSTUS	transcript	44087371	44089387	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	stop_codon	44087368	44087370	.	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087371	44087423	0.9	-	2	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087371	44087423	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44087424	44087575	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087576	44087614	0.9	-	2	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087576	44087614	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44087615	44087773	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087774	44087860	1	-	2	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087774	44087860	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44087861	44087939	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087940	44088002	1	-	2	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087940	44088002	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088003	44088082	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088083	44088179	1	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088083	44088179	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088180	44088259	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088260	44088478	1	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088260	44088478	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088479	44088570	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088571	44088666	1	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088571	44088666	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088667	44088756	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088757	44089009	0.81	-	1	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088757	44089009	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44089010	44089208	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44089209	44089243	0.93	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44089209	44089243	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44089244	44089384	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44089385	44089387	0.89	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44089385	44089387	.	-	.	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	start_codon	44089385	44089387	.	-	0	transcript_id "Phchi.S1G701100.t1"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	transcript	44087371	44089387	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	stop_codon	44087368	44087370	.	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087371	44087423	0.94	-	2	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087371	44087423	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44087424	44087575	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087576	44087614	0.94	-	2	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087576	44087614	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44087615	44087773	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087774	44087860	1	-	2	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087774	44087860	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44087861	44087939	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44087940	44088002	1	-	2	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44087940	44088002	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088003	44088082	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088083	44088179	1	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088083	44088179	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088180	44088259	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088260	44088478	1	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088260	44088478	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088479	44088570	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088571	44088666	1	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088571	44088666	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088667	44088756	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44088757	44088838	0.79	-	1	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44088757	44088838	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44088839	44089208	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44089209	44089243	0.71	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44089209	44089243	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	intron	44089244	44089384	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	CDS	44089385	44089387	0.69	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	exon	44089385	44089387	.	-	.	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
Phchi.S1	AUGUSTUS	start_codon	44089385	44089387	.	-	0	transcript_id "Phchi.S1G701100.t2"; gene_id "Phchi.S1G701100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14751.t1 is derived from g13219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14537456	14538550	.	+	.	Phchi.S3G207000
Phchi.S3	AUGUSTUS	transcript	14537456	14538550	.	+	.	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	start_codon	14537456	14537458	.	+	0	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	CDS	14537456	14538223	0.47	+	0	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	exon	14537456	14538223	.	+	.	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	intron	14538224	14538293	.	+	.	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	CDS	14538294	14538373	0.47	+	0	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	exon	14538294	14538373	.	+	.	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	intron	14538374	14538459	.	+	.	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	CDS	14538460	14538550	0.31	+	1	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	exon	14538460	14538550	.	+	.	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
Phchi.S3	AUGUSTUS	stop_codon	14538551	14538553	.	+	0	transcript_id "Phchi.S3G207000.t1"; gene_id "Phchi.S3G207000"
# This transcript jg13541.t2 is derived from g12008.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13542.t1 is derived from g12009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7431472	7432341	.	-	.	Phchi.S3G086100
Phchi.S3	AUGUSTUS	transcript	7431472	7432341	.	-	.	transcript_id "Phchi.S3G086100.t1"; gene_id "Phchi.S3G086100"
Phchi.S3	AUGUSTUS	stop_codon	7431469	7431471	.	-	0	transcript_id "Phchi.S3G086100.t1"; gene_id "Phchi.S3G086100"
Phchi.S3	AUGUSTUS	CDS	7431472	7432341	0.74	-	0	transcript_id "Phchi.S3G086100.t1"; gene_id "Phchi.S3G086100"
Phchi.S3	AUGUSTUS	exon	7431472	7432341	.	-	.	transcript_id "Phchi.S3G086100.t1"; gene_id "Phchi.S3G086100"
Phchi.S3	AUGUSTUS	start_codon	7432339	7432341	.	-	0	transcript_id "Phchi.S3G086100.t1"; gene_id "Phchi.S3G086100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9754.t1 is derived from g6930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43517408	43519316	.	-	.	Phchi.S1G691300
Phchi.S1	AUGUSTUS	transcript	43517408	43519316	.	-	.	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	stop_codon	43517405	43517407	.	-	0	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	CDS	43517408	43517628	0.98	-	2	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	exon	43517408	43517628	.	-	.	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	intron	43517629	43517725	.	-	.	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	CDS	43517726	43519316	0.7	-	0	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	exon	43517726	43519316	.	-	.	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
Phchi.S1	AUGUSTUS	start_codon	43519314	43519316	.	-	0	transcript_id "Phchi.S1G691300.t1"; gene_id "Phchi.S1G691300"
# This transcript jg13201.t2 is derived from g11666.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13202.t1 is derived from g11667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4652368	4654268	.	+	.	Phchi.S3G052100
Phchi.S3	AUGUSTUS	transcript	4652368	4654268	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	start_codon	4652368	4652370	.	+	0	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4652368	4652672	0.94	+	0	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4652368	4652672	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	intron	4652673	4652765	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4652766	4652864	0.44	+	1	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4652766	4652864	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	intron	4652865	4652961	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4652962	4653076	0.52	+	1	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4652962	4653076	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	intron	4653077	4653178	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4653179	4653300	0.96	+	0	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4653179	4653300	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	intron	4653301	4653474	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4653475	4653661	1	+	1	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4653475	4653661	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	intron	4653662	4653744	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4653745	4653891	1	+	0	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4653745	4653891	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	intron	4653892	4653980	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	CDS	4653981	4654268	1	+	0	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	exon	4653981	4654268	.	+	.	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
Phchi.S3	AUGUSTUS	stop_codon	4654269	4654271	.	+	0	transcript_id "Phchi.S3G052100.t1"; gene_id "Phchi.S3G052100"
# This transcript jg2154.t2 is derived from g9074.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2155.t1 is derived from g9075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5092585	5093626	.	-	.	Phchi.S5G076400
Phchi.S5	AUGUSTUS	transcript	5092585	5093626	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	stop_codon	5092582	5092584	.	-	0	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	CDS	5092585	5092585	1	-	1	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	exon	5092585	5092585	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	intron	5092586	5092679	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	CDS	5092680	5092737	1	-	2	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	exon	5092680	5092737	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	intron	5092738	5092816	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	CDS	5092817	5092997	0.74	-	0	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	exon	5092817	5092997	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	intron	5092998	5093115	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	CDS	5093116	5093382	0.71	-	0	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	exon	5093116	5093382	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	intron	5093383	5093470	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	CDS	5093471	5093626	1	-	0	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	exon	5093471	5093626	.	-	.	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
Phchi.S5	AUGUSTUS	start_codon	5093624	5093626	.	-	0	transcript_id "Phchi.S5G076400.t1"; gene_id "Phchi.S5G076400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2731.t1 is derived from g9651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8479470	8481592	.	+	.	Phchi.S5G134000
Phchi.S5	AUGUSTUS	transcript	8479470	8481592	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	start_codon	8479470	8479472	.	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8479470	8479646	0.6	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8479470	8479646	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8479647	8479721	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8479722	8479907	0.96	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8479722	8479907	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8479908	8480038	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8480039	8480151	1	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8480039	8480151	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8480152	8480247	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8480248	8480431	0.99	+	1	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8480248	8480431	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8480432	8480529	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8480530	8480561	0.85	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8480530	8480561	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8480562	8480667	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8480668	8480935	0.69	+	1	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8480668	8480935	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8480936	8481048	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8481049	8481312	1	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8481049	8481312	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	intron	8481313	8481403	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	CDS	8481404	8481592	0.99	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	exon	8481404	8481592	.	+	.	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
Phchi.S5	AUGUSTUS	stop_codon	8481593	8481595	.	+	0	transcript_id "Phchi.S5G134000.t1"; gene_id "Phchi.S5G134000"
# This transcript jg13414.t2 is derived from g11880.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13415.t1 is derived from g11881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6597201	6599717	.	+	.	Phchi.S3G073400
Phchi.S3	AUGUSTUS	transcript	6597201	6599717	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	start_codon	6597201	6597203	.	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6597201	6597395	1	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6597201	6597395	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6597396	6597509	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6597510	6597552	1	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6597510	6597552	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6597553	6597638	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6597639	6597728	1	+	2	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6597639	6597728	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6597729	6597822	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6597823	6597898	1	+	2	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6597823	6597898	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6597899	6597995	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6597996	6598065	1	+	1	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6597996	6598065	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6598066	6598219	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6598220	6598363	1	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6598220	6598363	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6598364	6598498	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6598499	6598603	0.62	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6598499	6598603	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6598604	6598706	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6598707	6598853	0.62	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6598707	6598853	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6598854	6598953	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6598954	6599029	1	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6598954	6599029	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6599030	6599112	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6599113	6599201	0.52	+	2	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6599113	6599201	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6599202	6599310	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6599311	6599402	1	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6599311	6599402	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6599403	6599501	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6599502	6599547	1	+	1	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6599502	6599547	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	intron	6599548	6599663	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	CDS	6599664	6599717	0.9	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	exon	6599664	6599717	.	+	.	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
Phchi.S3	AUGUSTUS	stop_codon	6599718	6599720	.	+	0	transcript_id "Phchi.S3G073400.t1"; gene_id "Phchi.S3G073400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4437.t1 is derived from g1606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10496031	10499070	.	-	.	Phchi.S1G159600
Phchi.S1	AUGUSTUS	transcript	10496031	10499070	.	-	.	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	stop_codon	10496028	10496030	.	-	0	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	CDS	10496031	10498049	0.88	-	0	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	exon	10496031	10498049	.	-	.	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	intron	10498050	10498173	.	-	.	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	CDS	10498174	10498256	0.86	-	2	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	exon	10498174	10498256	.	-	.	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	intron	10498257	10498988	.	-	.	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	CDS	10498989	10499070	0.51	-	0	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	exon	10498989	10499070	.	-	.	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
Phchi.S1	AUGUSTUS	start_codon	10499068	10499070	.	-	0	transcript_id "Phchi.S1G159600.t1"; gene_id "Phchi.S1G159600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1815.t1 is derived from g8735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3284503	3286720	.	-	.	Phchi.S5G042400
Phchi.S5	AUGUSTUS	transcript	3284503	3286720	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	stop_codon	3284500	3284502	.	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3284503	3284622	0.9	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3284503	3284622	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3284623	3284772	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3284773	3284879	1	-	2	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3284773	3284879	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3284880	3284967	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3284968	3285046	0.63	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3284968	3285046	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3285047	3285160	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3285161	3285250	0.97	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3285161	3285250	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3285251	3285363	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3285364	3285642	0.97	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3285364	3285642	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3285643	3285786	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3285787	3285942	1	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3285787	3285942	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3285943	3286056	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3286057	3286390	0.97	-	1	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3286057	3286390	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	intron	3286391	3286493	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	CDS	3286494	3286720	1	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	exon	3286494	3286720	.	-	.	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
Phchi.S5	AUGUSTUS	start_codon	3286718	3286720	.	-	0	transcript_id "Phchi.S5G042400.t1"; gene_id "Phchi.S5G042400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7244.t1 is derived from g4416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27808835	27809252	.	-	.	Phchi.S1G440300
Phchi.S1	AUGUSTUS	transcript	27808835	27809252	.	-	.	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	stop_codon	27808832	27808834	.	-	0	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	CDS	27808835	27808971	0.5	-	2	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	exon	27808835	27808971	.	-	.	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	intron	27808972	27809041	.	-	.	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	CDS	27809042	27809252	0.72	-	0	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	exon	27809042	27809252	.	-	.	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
Phchi.S1	AUGUSTUS	start_codon	27809250	27809252	.	-	0	transcript_id "Phchi.S1G440300.t1"; gene_id "Phchi.S1G440300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4982.t1 is derived from g2152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13872087	13872512	.	-	.	Phchi.S1G214100
Phchi.S1	AUGUSTUS	transcript	13872087	13872512	.	-	.	transcript_id "Phchi.S1G214100.t1"; gene_id "Phchi.S1G214100"
Phchi.S1	AUGUSTUS	stop_codon	13872084	13872086	.	-	0	transcript_id "Phchi.S1G214100.t1"; gene_id "Phchi.S1G214100"
Phchi.S1	AUGUSTUS	CDS	13872087	13872512	0.31	-	0	transcript_id "Phchi.S1G214100.t1"; gene_id "Phchi.S1G214100"
Phchi.S1	AUGUSTUS	exon	13872087	13872512	.	-	.	transcript_id "Phchi.S1G214100.t1"; gene_id "Phchi.S1G214100"
Phchi.S1	AUGUSTUS	start_codon	13872510	13872512	.	-	0	transcript_id "Phchi.S1G214100.t1"; gene_id "Phchi.S1G214100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2337.t1 is derived from g9257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6225356	6225736	.	-	.	Phchi.S5G094600
Phchi.S5	AUGUSTUS	transcript	6225356	6225736	.	-	.	transcript_id "Phchi.S5G094600.t1"; gene_id "Phchi.S5G094600"
Phchi.S5	AUGUSTUS	stop_codon	6225353	6225355	.	-	0	transcript_id "Phchi.S5G094600.t1"; gene_id "Phchi.S5G094600"
Phchi.S5	AUGUSTUS	CDS	6225356	6225736	0.99	-	0	transcript_id "Phchi.S5G094600.t1"; gene_id "Phchi.S5G094600"
Phchi.S5	AUGUSTUS	exon	6225356	6225736	.	-	.	transcript_id "Phchi.S5G094600.t1"; gene_id "Phchi.S5G094600"
Phchi.S5	AUGUSTUS	start_codon	6225734	6225736	.	-	0	transcript_id "Phchi.S5G094600.t1"; gene_id "Phchi.S5G094600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1048.t1 is derived from g10831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7282166	7282685	.	-	.	Phchi.S6G100700
Phchi.S6	AUGUSTUS	transcript	7282166	7282685	.	-	.	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	stop_codon	7282163	7282165	.	-	0	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	CDS	7282166	7282213	0.98	-	0	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	exon	7282166	7282213	.	-	.	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	intron	7282214	7282300	.	-	.	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	CDS	7282301	7282368	0.98	-	2	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	exon	7282301	7282368	.	-	.	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	intron	7282369	7282456	.	-	.	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	CDS	7282457	7282685	0.9	-	0	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	exon	7282457	7282685	.	-	.	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	start_codon	7282683	7282685	.	-	0	transcript_id "Phchi.S6G100700.t1"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	transcript	7282166	7282685	.	-	.	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	stop_codon	7282163	7282165	.	-	0	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	CDS	7282166	7282213	0.23	-	0	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	exon	7282166	7282213	.	-	.	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	intron	7282214	7282300	.	-	.	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	CDS	7282301	7282371	0.23	-	2	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	exon	7282301	7282371	.	-	.	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	intron	7282372	7282456	.	-	.	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	CDS	7282457	7282685	0.27	-	0	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	exon	7282457	7282685	.	-	.	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
Phchi.S6	AUGUSTUS	start_codon	7282683	7282685	.	-	0	transcript_id "Phchi.S6G100700.t2"; gene_id "Phchi.S6G100700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6298.t1 is derived from g3470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22159466	22160392	.	-	.	Phchi.S1G345700
Phchi.S1	AUGUSTUS	transcript	22159466	22160392	.	-	.	transcript_id "Phchi.S1G345700.t1"; gene_id "Phchi.S1G345700"
Phchi.S1	AUGUSTUS	stop_codon	22159463	22159465	.	-	0	transcript_id "Phchi.S1G345700.t1"; gene_id "Phchi.S1G345700"
Phchi.S1	AUGUSTUS	CDS	22159466	22160392	1	-	0	transcript_id "Phchi.S1G345700.t1"; gene_id "Phchi.S1G345700"
Phchi.S1	AUGUSTUS	exon	22159466	22160392	.	-	.	transcript_id "Phchi.S1G345700.t1"; gene_id "Phchi.S1G345700"
Phchi.S1	AUGUSTUS	start_codon	22160390	22160392	.	-	0	transcript_id "Phchi.S1G345700.t1"; gene_id "Phchi.S1G345700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6458.t1 is derived from g3630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23118751	23121237	.	+	.	Phchi.S1G361700
Phchi.S1	AUGUSTUS	transcript	23118751	23121237	.	+	.	transcript_id "Phchi.S1G361700.t1"; gene_id "Phchi.S1G361700"
Phchi.S1	AUGUSTUS	start_codon	23118751	23118753	.	+	0	transcript_id "Phchi.S1G361700.t1"; gene_id "Phchi.S1G361700"
Phchi.S1	AUGUSTUS	CDS	23118751	23121237	1	+	0	transcript_id "Phchi.S1G361700.t1"; gene_id "Phchi.S1G361700"
Phchi.S1	AUGUSTUS	exon	23118751	23121237	.	+	.	transcript_id "Phchi.S1G361700.t1"; gene_id "Phchi.S1G361700"
Phchi.S1	AUGUSTUS	stop_codon	23121238	23121240	.	+	0	transcript_id "Phchi.S1G361700.t1"; gene_id "Phchi.S1G361700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11393.t1 is derived from g15443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6129274	6130403	.	-	.	Phchi.S4G097500
Phchi.S4	AUGUSTUS	transcript	6129274	6130403	.	-	.	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	stop_codon	6129271	6129273	.	-	0	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	CDS	6129274	6129421	1	-	1	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	exon	6129274	6129421	.	-	.	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	intron	6129422	6129511	.	-	.	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	CDS	6129512	6129713	1	-	2	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	exon	6129512	6129713	.	-	.	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	intron	6129714	6130300	.	-	.	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	CDS	6130301	6130403	0.93	-	0	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	exon	6130301	6130403	.	-	.	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
Phchi.S4	AUGUSTUS	start_codon	6130401	6130403	.	-	0	transcript_id "Phchi.S4G097500.t1"; gene_id "Phchi.S4G097500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15956.t1 is derived from g11139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	19720	23043	.	+	.	Phchi.C91G000300
Phchi.C91	AUGUSTUS	transcript	19720	23043	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	start_codon	19720	19722	.	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	19720	19877	0.99	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	19720	19877	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	19878	20191	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	20192	20276	1	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	20192	20276	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	20277	20416	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	20417	20514	1	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	20417	20514	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	20515	20629	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	20630	20685	1	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	20630	20685	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	20686	20798	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	20799	20916	1	+	2	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	20799	20916	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	20917	21029	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	21030	21057	1	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	21030	21057	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	21058	21141	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	21142	21233	1	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	21142	21233	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	21234	21325	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	21326	21482	1	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	21326	21482	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	21483	21565	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	21566	21690	1	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	21566	21690	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	21691	21795	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	21796	21895	1	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	21796	21895	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	21896	21983	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	21984	22075	0.95	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	21984	22075	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	22076	22376	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	22377	22527	1	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	22377	22527	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	22528	22656	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	22657	22716	1	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	22657	22716	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	22717	22816	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	22817	22863	1	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	22817	22863	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	intron	22864	22952	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	CDS	22953	23043	0.99	+	1	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	exon	22953	23043	.	+	.	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
Phchi.C91	AUGUSTUS	stop_codon	23044	23046	.	+	0	transcript_id "Phchi.C91G000300.t1"; gene_id "Phchi.C91G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14977.t1 is derived from g13445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15825259	15827538	.	-	.	Phchi.S3G229600
Phchi.S3	AUGUSTUS	transcript	15825259	15827538	.	-	.	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	stop_codon	15825256	15825258	.	-	0	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	CDS	15825259	15826304	0.95	-	2	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	exon	15825259	15826304	.	-	.	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	intron	15826305	15826635	.	-	.	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	CDS	15826636	15826843	0.82	-	0	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	exon	15826636	15826843	.	-	.	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	intron	15826844	15827028	.	-	.	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	CDS	15827029	15827538	0.94	-	0	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	exon	15827029	15827538	.	-	.	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
Phchi.S3	AUGUSTUS	start_codon	15827536	15827538	.	-	0	transcript_id "Phchi.S3G229600.t1"; gene_id "Phchi.S3G229600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14499.t1 is derived from g12967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13191747	13193798	.	-	.	Phchi.S3G181800
Phchi.S3	AUGUSTUS	transcript	13191747	13193798	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	stop_codon	13191744	13191746	.	-	0	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13191747	13192007	0.98	-	0	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13191747	13192007	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	intron	13192008	13192105	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13192106	13192241	1	-	1	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13192106	13192241	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	intron	13192242	13192315	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13192316	13192453	1	-	1	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13192316	13192453	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	intron	13192454	13192573	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13192574	13192749	1	-	0	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13192574	13192749	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	intron	13192750	13192930	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13192931	13193012	1	-	1	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13192931	13193012	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	intron	13193013	13193099	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13193100	13193235	1	-	2	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13193100	13193235	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	intron	13193236	13193680	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	CDS	13193681	13193798	1	-	0	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	exon	13193681	13193798	.	-	.	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
Phchi.S3	AUGUSTUS	start_codon	13193796	13193798	.	-	0	transcript_id "Phchi.S3G181800.t1"; gene_id "Phchi.S3G181800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2435.t1 is derived from g9355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6627620	6628457	.	-	.	Phchi.S5G104400
Phchi.S5	AUGUSTUS	transcript	6627620	6628457	.	-	.	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	stop_codon	6627617	6627619	.	-	0	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	CDS	6627620	6627643	0.86	-	0	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	exon	6627620	6627643	.	-	.	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	intron	6627644	6627815	.	-	.	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	CDS	6627816	6628457	0.45	-	0	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	exon	6627816	6628457	.	-	.	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
Phchi.S5	AUGUSTUS	start_codon	6628455	6628457	.	-	0	transcript_id "Phchi.S5G104400.t1"; gene_id "Phchi.S5G104400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9054.t1 is derived from g6229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39415303	39418873	.	+	.	Phchi.S1G621300
Phchi.S1	AUGUSTUS	transcript	39415897	39418873	.	+	.	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	start_codon	39415897	39415899	.	+	0	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	CDS	39415897	39416834	0.88	+	0	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	exon	39415897	39416834	.	+	.	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	intron	39416835	39416919	.	+	.	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	CDS	39416920	39417189	0.25	+	1	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	exon	39416920	39417189	.	+	.	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	intron	39417190	39417399	.	+	.	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	CDS	39417400	39418873	0.63	+	1	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	exon	39417400	39418873	.	+	.	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	stop_codon	39418874	39418876	.	+	0	transcript_id "Phchi.S1G621300.t1"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	transcript	39415303	39418873	.	+	.	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	start_codon	39415303	39415305	.	+	0	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	CDS	39415303	39416834	0.72	+	0	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	exon	39415303	39416834	.	+	.	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	intron	39416835	39416919	.	+	.	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	CDS	39416920	39417189	0.18	+	1	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	exon	39416920	39417189	.	+	.	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	intron	39417190	39417399	.	+	.	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	CDS	39417400	39418873	0.28	+	1	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	exon	39417400	39418873	.	+	.	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
Phchi.S1	AUGUSTUS	stop_codon	39418874	39418876	.	+	0	transcript_id "Phchi.S1G621300.t2"; gene_id "Phchi.S1G621300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg799.t1 is derived from g10581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5668808	5670227	.	-	.	Phchi.S6G075800
Phchi.S6	AUGUSTUS	transcript	5668808	5670227	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	stop_codon	5668805	5668807	.	-	0	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	CDS	5668808	5669205	1	-	2	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	exon	5668808	5669205	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	intron	5669206	5669338	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	CDS	5669339	5669507	1	-	0	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	exon	5669339	5669507	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	intron	5669508	5669606	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	CDS	5669607	5669795	0.99	-	0	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	exon	5669607	5669795	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	intron	5669796	5669885	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	CDS	5669886	5670227	0.79	-	0	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	exon	5669886	5670227	.	-	.	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
Phchi.S6	AUGUSTUS	start_codon	5670225	5670227	.	-	0	transcript_id "Phchi.S6G075800.t1"; gene_id "Phchi.S6G075800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7174.t1 is derived from g4346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27397394	27400445	.	-	.	Phchi.S1G433300
Phchi.S1	AUGUSTUS	transcript	27397394	27400445	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	stop_codon	27397391	27397393	.	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27397394	27397540	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27397394	27397540	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27397541	27397631	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27397632	27397916	0.96	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27397632	27397916	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27397917	27398002	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27398003	27398284	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27398003	27398284	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27398285	27398392	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27398393	27398700	0.89	-	2	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27398393	27398700	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27398701	27398795	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27398796	27399069	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27398796	27399069	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27399070	27399164	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27399165	27399222	0.66	-	1	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27399165	27399222	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27399223	27399326	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27399327	27399435	0.86	-	2	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27399327	27399435	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27399436	27399547	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27399548	27399698	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27399548	27399698	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27399699	27399775	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27399776	27399940	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27399776	27399940	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27399941	27400038	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27400039	27400164	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27400039	27400164	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	intron	27400165	27400244	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	CDS	27400245	27400445	1	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	exon	27400245	27400445	.	-	.	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
Phchi.S1	AUGUSTUS	start_codon	27400443	27400445	.	-	0	transcript_id "Phchi.S1G433300.t1"; gene_id "Phchi.S1G433300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10499.t1 is derived from g14548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	719462	721510	.	-	.	Phchi.S4G008100
Phchi.S4	AUGUSTUS	transcript	719462	721510	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	stop_codon	719459	719461	.	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	CDS	719462	719473	1	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	exon	719462	719473	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	intron	719474	719553	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	CDS	719554	719715	1	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	exon	719554	719715	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	intron	719716	719890	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	CDS	719891	719956	0.8	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	exon	719891	719956	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	intron	719957	720034	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	CDS	720035	720109	0.48	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	exon	720035	720109	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	intron	720110	720228	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	CDS	720229	720471	0.95	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	exon	720229	720471	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	intron	720472	720649	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	CDS	720650	721510	0.98	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	exon	720650	721510	.	-	.	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
Phchi.S4	AUGUSTUS	start_codon	721508	721510	.	-	0	transcript_id "Phchi.S4G008100.t1"; gene_id "Phchi.S4G008100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2453.t1 is derived from g9373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6730491	6731809	.	+	.	Phchi.S5G106200
Phchi.S5	AUGUSTUS	transcript	6730491	6731809	.	+	.	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	start_codon	6730491	6730493	.	+	0	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	CDS	6730491	6730680	0.32	+	0	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	exon	6730491	6730680	.	+	.	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	intron	6730681	6730782	.	+	.	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	CDS	6730783	6731411	0.76	+	2	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	exon	6730783	6731411	.	+	.	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	intron	6731412	6731491	.	+	.	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	CDS	6731492	6731809	0.97	+	0	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	exon	6731492	6731809	.	+	.	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
Phchi.S5	AUGUSTUS	stop_codon	6731810	6731812	.	+	0	transcript_id "Phchi.S5G106200.t1"; gene_id "Phchi.S5G106200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9988.t1 is derived from g7164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44807109	44808185	.	-	.	Phchi.S1G714700
Phchi.S1	AUGUSTUS	transcript	44807109	44808185	.	-	.	transcript_id "Phchi.S1G714700.t1"; gene_id "Phchi.S1G714700"
Phchi.S1	AUGUSTUS	stop_codon	44807106	44807108	.	-	0	transcript_id "Phchi.S1G714700.t1"; gene_id "Phchi.S1G714700"
Phchi.S1	AUGUSTUS	CDS	44807109	44808185	0.38	-	0	transcript_id "Phchi.S1G714700.t1"; gene_id "Phchi.S1G714700"
Phchi.S1	AUGUSTUS	exon	44807109	44808185	.	-	.	transcript_id "Phchi.S1G714700.t1"; gene_id "Phchi.S1G714700"
Phchi.S1	AUGUSTUS	start_codon	44808183	44808185	.	-	0	transcript_id "Phchi.S1G714700.t1"; gene_id "Phchi.S1G714700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12614.t1 is derived from g8291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37578359	37579534	.	+	.	Phchi.S2G069400
Phchi.S2	AUGUSTUS	transcript	37578359	37579534	.	+	.	transcript_id "Phchi.S2G069400.t1"; gene_id "Phchi.S2G069400"
Phchi.S2	AUGUSTUS	start_codon	37578359	37578361	.	+	0	transcript_id "Phchi.S2G069400.t1"; gene_id "Phchi.S2G069400"
Phchi.S2	AUGUSTUS	CDS	37578359	37579534	0.33	+	0	transcript_id "Phchi.S2G069400.t1"; gene_id "Phchi.S2G069400"
Phchi.S2	AUGUSTUS	exon	37578359	37579534	.	+	.	transcript_id "Phchi.S2G069400.t1"; gene_id "Phchi.S2G069400"
Phchi.S2	AUGUSTUS	stop_codon	37579535	37579537	.	+	0	transcript_id "Phchi.S2G069400.t1"; gene_id "Phchi.S2G069400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3452.t1 is derived from g621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3818552	3819541	.	+	.	Phchi.S1G061100
Phchi.S1	AUGUSTUS	transcript	3818552	3819541	.	+	.	transcript_id "Phchi.S1G061100.t1"; gene_id "Phchi.S1G061100"
Phchi.S1	AUGUSTUS	start_codon	3818552	3818554	.	+	0	transcript_id "Phchi.S1G061100.t1"; gene_id "Phchi.S1G061100"
Phchi.S1	AUGUSTUS	CDS	3818552	3819541	1	+	0	transcript_id "Phchi.S1G061100.t1"; gene_id "Phchi.S1G061100"
Phchi.S1	AUGUSTUS	exon	3818552	3819541	.	+	.	transcript_id "Phchi.S1G061100.t1"; gene_id "Phchi.S1G061100"
Phchi.S1	AUGUSTUS	stop_codon	3819542	3819544	.	+	0	transcript_id "Phchi.S1G061100.t1"; gene_id "Phchi.S1G061100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4389.t1 is derived from g1558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10190777	10192084	.	-	.	Phchi.S1G154800
Phchi.S1	AUGUSTUS	transcript	10190777	10192084	.	-	.	transcript_id "Phchi.S1G154800.t1"; gene_id "Phchi.S1G154800"
Phchi.S1	AUGUSTUS	stop_codon	10190774	10190776	.	-	0	transcript_id "Phchi.S1G154800.t1"; gene_id "Phchi.S1G154800"
Phchi.S1	AUGUSTUS	CDS	10190777	10192084	0.94	-	0	transcript_id "Phchi.S1G154800.t1"; gene_id "Phchi.S1G154800"
Phchi.S1	AUGUSTUS	exon	10190777	10192084	.	-	.	transcript_id "Phchi.S1G154800.t1"; gene_id "Phchi.S1G154800"
Phchi.S1	AUGUSTUS	start_codon	10192082	10192084	.	-	0	transcript_id "Phchi.S1G154800.t1"; gene_id "Phchi.S1G154800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6784.t1 is derived from g3956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25081855	25082331	.	-	.	Phchi.S1G394300
Phchi.S1	AUGUSTUS	transcript	25081855	25082331	.	-	.	transcript_id "Phchi.S1G394300.t1"; gene_id "Phchi.S1G394300"
Phchi.S1	AUGUSTUS	stop_codon	25081852	25081854	.	-	0	transcript_id "Phchi.S1G394300.t1"; gene_id "Phchi.S1G394300"
Phchi.S1	AUGUSTUS	CDS	25081855	25082331	0.5	-	0	transcript_id "Phchi.S1G394300.t1"; gene_id "Phchi.S1G394300"
Phchi.S1	AUGUSTUS	exon	25081855	25082331	.	-	.	transcript_id "Phchi.S1G394300.t1"; gene_id "Phchi.S1G394300"
Phchi.S1	AUGUSTUS	start_codon	25082329	25082331	.	-	0	transcript_id "Phchi.S1G394300.t1"; gene_id "Phchi.S1G394300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15149.t1 is derived from g13617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17269863	17270782	.	+	.	Phchi.S3G246800
Phchi.S3	AUGUSTUS	transcript	17269863	17270782	.	+	.	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	start_codon	17269863	17269865	.	+	0	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	CDS	17269863	17270030	0.73	+	0	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	exon	17269863	17270030	.	+	.	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	intron	17270031	17270101	.	+	.	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	CDS	17270102	17270416	0.93	+	0	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	exon	17270102	17270416	.	+	.	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	intron	17270417	17270557	.	+	.	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	CDS	17270558	17270782	1	+	0	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	exon	17270558	17270782	.	+	.	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
Phchi.S3	AUGUSTUS	stop_codon	17270783	17270785	.	+	0	transcript_id "Phchi.S3G246800.t1"; gene_id "Phchi.S3G246800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1666.t1 is derived from g8585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2303531	2306051	.	+	.	Phchi.S5G027500
Phchi.S5	AUGUSTUS	transcript	2303531	2306051	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	start_codon	2303531	2303533	.	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2303531	2303773	0.99	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2303531	2303773	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2303774	2303851	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2303852	2303965	1	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2303852	2303965	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2303966	2304062	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2304063	2304197	0.95	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2304063	2304197	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2304198	2304460	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2304461	2304502	0.98	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2304461	2304502	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2304503	2304657	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2304658	2304792	0.99	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2304658	2304792	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2304793	2304883	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2304884	2305027	1	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2304884	2305027	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2305028	2305190	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2305191	2305295	1	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2305191	2305295	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2305296	2305399	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2305400	2305489	1	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2305400	2305489	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	intron	2305490	2305577	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	CDS	2305578	2306051	1	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	exon	2305578	2306051	.	+	.	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
Phchi.S5	AUGUSTUS	stop_codon	2306052	2306054	.	+	0	transcript_id "Phchi.S5G027500.t1"; gene_id "Phchi.S5G027500"
# This transcript jg7686.t2 is derived from g4860.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7686.t3 is derived from g4860.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7686.t4 is derived from g4860.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7686.t5 is derived from g4860.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7687.t1 is derived from g4861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30624726	30626932	.	-	.	Phchi.S1G484600
Phchi.S1	AUGUSTUS	transcript	30624726	30626932	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	stop_codon	30624723	30624725	.	-	0	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	CDS	30624726	30625695	1	-	1	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	exon	30624726	30625695	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	intron	30625696	30625822	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	CDS	30625823	30625863	1	-	0	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	exon	30625823	30625863	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	intron	30625864	30625950	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	CDS	30625951	30626051	1	-	2	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	exon	30625951	30626051	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	intron	30626052	30626591	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	CDS	30626592	30626663	0.89	-	2	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	exon	30626592	30626663	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	intron	30626664	30626742	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	CDS	30626743	30626811	0.89	-	2	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	exon	30626743	30626811	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	intron	30626812	30626913	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	CDS	30626914	30626932	0.86	-	0	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	exon	30626914	30626932	.	-	.	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
Phchi.S1	AUGUSTUS	start_codon	30626930	30626932	.	-	0	transcript_id "Phchi.S1G484600.t1"; gene_id "Phchi.S1G484600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9065.t1 is derived from g6240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39610491	39611786	.	-	.	Phchi.S1G622400
Phchi.S1	AUGUSTUS	transcript	39610491	39611786	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	stop_codon	39610488	39610490	.	-	0	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	CDS	39610491	39610857	0.67	-	1	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	exon	39610491	39610857	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	intron	39610858	39610941	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	CDS	39610942	39611058	0.96	-	1	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	exon	39610942	39611058	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	intron	39611059	39611146	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	CDS	39611147	39611478	0.45	-	0	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	exon	39611147	39611478	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	intron	39611479	39611590	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	CDS	39611591	39611617	0.84	-	0	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	exon	39611591	39611617	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	intron	39611618	39611765	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	CDS	39611766	39611786	1	-	0	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	exon	39611766	39611786	.	-	.	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
Phchi.S1	AUGUSTUS	start_codon	39611784	39611786	.	-	0	transcript_id "Phchi.S1G622400.t1"; gene_id "Phchi.S1G622400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2439.t1 is derived from g9359.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6641339	6642902	.	+	.	Phchi.S5G104800
Phchi.S5	AUGUSTUS	transcript	6641339	6642902	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	start_codon	6641339	6641341	.	+	0	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6641339	6641352	0.94	+	0	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6641339	6641352	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	intron	6641353	6641573	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6641574	6641650	1	+	1	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6641574	6641650	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	intron	6641651	6641733	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6641734	6641958	0.69	+	2	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6641734	6641958	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	intron	6641959	6642059	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6642060	6642094	0.35	+	2	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6642060	6642094	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	intron	6642095	6642451	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6642452	6642461	0.33	+	0	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6642452	6642461	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	intron	6642462	6642649	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6642650	6642755	0.33	+	2	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6642650	6642755	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	intron	6642756	6642901	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	CDS	6642902	6642902	0.99	+	1	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	exon	6642902	6642902	.	+	.	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
Phchi.S5	AUGUSTUS	stop_codon	6642903	6642905	.	+	0	transcript_id "Phchi.S5G104800.t1"; gene_id "Phchi.S5G104800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9057.t1 is derived from g6232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39426143	39428208	.	+	.	Phchi.S1G621600
Phchi.S1	AUGUSTUS	transcript	39426143	39428208	.	+	.	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	start_codon	39426143	39426145	.	+	0	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	CDS	39426143	39426294	0.86	+	0	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	exon	39426143	39426294	.	+	.	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	intron	39426295	39426395	.	+	.	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	CDS	39426396	39428208	0.86	+	1	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	exon	39426396	39428208	.	+	.	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
Phchi.S1	AUGUSTUS	stop_codon	39428209	39428211	.	+	0	transcript_id "Phchi.S1G621600.t1"; gene_id "Phchi.S1G621600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14644.t1 is derived from g13112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13908197	13908671	.	-	.	Phchi.S3G196300
Phchi.S3	AUGUSTUS	transcript	13908197	13908671	.	-	.	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	stop_codon	13908194	13908196	.	-	0	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	CDS	13908197	13908297	1	-	2	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	exon	13908197	13908297	.	-	.	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	intron	13908298	13908535	.	-	.	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	CDS	13908536	13908671	0.63	-	0	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	exon	13908536	13908671	.	-	.	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
Phchi.S3	AUGUSTUS	start_codon	13908669	13908671	.	-	0	transcript_id "Phchi.S3G196300.t1"; gene_id "Phchi.S3G196300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15340.t1 is derived from g13808.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18457927	18459799	.	-	.	Phchi.S3G265900
Phchi.S3	AUGUSTUS	transcript	18457927	18459799	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	stop_codon	18457924	18457926	.	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18457927	18458003	0.91	-	2	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18457927	18458003	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458004	18458082	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458083	18458221	0.55	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458083	18458221	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458222	18458370	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458371	18458424	1	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458371	18458424	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458425	18458518	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458519	18458590	1	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458519	18458590	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458591	18458741	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458742	18459023	0.95	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458742	18459023	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18459024	18459233	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18459234	18459452	1	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18459234	18459452	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18459453	18459541	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18459542	18459799	1	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18459542	18459799	.	-	.	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	start_codon	18459797	18459799	.	-	0	transcript_id "Phchi.S3G265900.t1"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	transcript	18457927	18459799	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	stop_codon	18457924	18457926	.	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18457927	18458003	0.89	-	2	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18457927	18458003	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458004	18458082	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458083	18458221	0.54	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458083	18458221	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458222	18458370	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458371	18458424	1	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458371	18458424	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458425	18458518	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458519	18458590	1	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458519	18458590	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18458591	18458741	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18458742	18459080	0.94	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18458742	18459080	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18459081	18459233	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18459234	18459452	1	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18459234	18459452	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	intron	18459453	18459541	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	CDS	18459542	18459799	1	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	exon	18459542	18459799	.	-	.	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
Phchi.S3	AUGUSTUS	start_codon	18459797	18459799	.	-	0	transcript_id "Phchi.S3G265900.t2"; gene_id "Phchi.S3G265900"
# This transcript jg12642.t2 is derived from g16010.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12643.t1 is derived from g16009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	3909	5606	.	+	.	Phchi.C136G000200
Phchi.C136	AUGUSTUS	transcript	3909	5606	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	start_codon	3909	3911	.	+	0	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	3909	3962	1	+	0	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	3909	3962	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	intron	3963	4142	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	4143	4254	0.75	+	0	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	4143	4254	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	intron	4255	4562	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	4563	4679	0.89	+	2	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	4563	4679	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	intron	4680	4880	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	4881	4900	0.6	+	2	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	4881	4900	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	intron	4901	5001	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	5002	5238	0.55	+	0	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	5002	5238	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	intron	5239	5392	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	5393	5504	0.99	+	0	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	5393	5504	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	intron	5505	5595	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	CDS	5596	5606	1	+	2	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	exon	5596	5606	.	+	.	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
Phchi.C136	AUGUSTUS	stop_codon	5607	5609	.	+	0	transcript_id "Phchi.C136G000200.t1"; gene_id "Phchi.C136G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15870.t1 is derived from g14340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21978841	21979311	.	-	.	Phchi.S3G318900
Phchi.S3	AUGUSTUS	transcript	21978841	21979311	.	-	.	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	stop_codon	21978838	21978840	.	-	0	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	CDS	21978841	21978980	0.49	-	2	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	exon	21978841	21978980	.	-	.	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	intron	21978981	21979117	.	-	.	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	CDS	21979118	21979193	0.3	-	0	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	exon	21979118	21979193	.	-	.	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	intron	21979194	21979308	.	-	.	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	CDS	21979309	21979311	0.28	-	0	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	exon	21979309	21979311	.	-	.	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
Phchi.S3	AUGUSTUS	start_codon	21979309	21979311	.	-	0	transcript_id "Phchi.S3G318900.t1"; gene_id "Phchi.S3G318900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11159.t1 is derived from g15209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4425409	4426425	.	+	.	Phchi.S4G074100
Phchi.S4	AUGUSTUS	transcript	4425409	4426425	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	start_codon	4425409	4425411	.	+	0	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	CDS	4425409	4425582	0.97	+	0	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	exon	4425409	4425582	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	intron	4425583	4425763	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	CDS	4425764	4425813	1	+	0	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	exon	4425764	4425813	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	intron	4425814	4425908	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	CDS	4425909	4426014	1	+	1	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	exon	4425909	4426014	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	intron	4426015	4426085	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	CDS	4426086	4426146	0.4	+	0	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	exon	4426086	4426146	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	intron	4426147	4426255	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	CDS	4426256	4426425	0.65	+	2	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	exon	4426256	4426425	.	+	.	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
Phchi.S4	AUGUSTUS	stop_codon	4426426	4426428	.	+	0	transcript_id "Phchi.S4G074100.t1"; gene_id "Phchi.S4G074100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10449.t1 is derived from g14498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	387726	389752	.	-	.	Phchi.S4G003100
Phchi.S4	AUGUSTUS	transcript	387726	389752	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	stop_codon	387723	387725	.	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	387726	387837	0.95	-	1	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	387726	387837	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	387838	387939	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	387940	388022	0.95	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	387940	388022	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	388023	388114	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	388115	388199	1	-	1	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	388115	388199	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	388200	388294	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	388295	388437	1	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	388295	388437	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	388438	388555	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	388556	388651	1	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	388556	388651	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	388652	388739	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	388740	388831	1	-	2	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	388740	388831	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	388832	388925	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	388926	389076	1	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	388926	389076	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	389077	389209	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	389210	389324	0.95	-	1	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	389210	389324	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	389325	389434	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	389435	389523	0.88	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	389435	389523	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	intron	389524	389647	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	CDS	389648	389752	0.9	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	exon	389648	389752	.	-	.	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
Phchi.S4	AUGUSTUS	start_codon	389750	389752	.	-	0	transcript_id "Phchi.S4G003100.t1"; gene_id "Phchi.S4G003100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5266.t1 is derived from g2436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15955322	15955601	.	-	.	Phchi.S1G242500
Phchi.S1	AUGUSTUS	transcript	15955322	15955601	.	-	.	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	stop_codon	15955319	15955321	.	-	0	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	CDS	15955322	15955360	1	-	0	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	exon	15955322	15955360	.	-	.	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	intron	15955361	15955427	.	-	.	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	CDS	15955428	15955601	1	-	0	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	exon	15955428	15955601	.	-	.	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
Phchi.S1	AUGUSTUS	start_codon	15955599	15955601	.	-	0	transcript_id "Phchi.S1G242500.t1"; gene_id "Phchi.S1G242500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8745.t1 is derived from g5920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37774057	37774978	.	+	.	Phchi.S1G590400
Phchi.S1	AUGUSTUS	transcript	37774057	37774978	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	start_codon	37774057	37774059	.	+	0	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	CDS	37774057	37774249	1	+	0	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	exon	37774057	37774249	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	intron	37774250	37774345	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	CDS	37774346	37774401	1	+	2	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	exon	37774346	37774401	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	intron	37774402	37774505	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	CDS	37774506	37774560	1	+	0	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	exon	37774506	37774560	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	intron	37774561	37774657	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	CDS	37774658	37774738	1	+	2	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	exon	37774658	37774738	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	intron	37774739	37774811	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	CDS	37774812	37774978	1	+	2	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	exon	37774812	37774978	.	+	.	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
Phchi.S1	AUGUSTUS	stop_codon	37774979	37774981	.	+	0	transcript_id "Phchi.S1G590400.t1"; gene_id "Phchi.S1G590400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11638.t1 is derived from g15689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7414928	7417669	.	+	.	Phchi.S4G122000
Phchi.S4	AUGUSTUS	transcript	7414928	7417669	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	start_codon	7414928	7414930	.	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7414928	7415838	0.9	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7414928	7415838	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7415839	7416052	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7416053	7416251	1	+	1	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7416053	7416251	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7416252	7416370	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7416371	7416463	1	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7416371	7416463	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7416464	7416551	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7416552	7416680	1	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7416552	7416680	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7416681	7416810	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7416811	7416864	1	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7416811	7416864	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7416865	7416989	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7416990	7417070	0.92	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7416990	7417070	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7417071	7417173	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7417174	7417236	0.92	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7417174	7417236	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7417237	7417358	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7417359	7417480	1	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7417359	7417480	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	intron	7417481	7417563	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	CDS	7417564	7417669	0.88	+	1	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	exon	7417564	7417669	.	+	.	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
Phchi.S4	AUGUSTUS	stop_codon	7417670	7417672	.	+	0	transcript_id "Phchi.S4G122000.t1"; gene_id "Phchi.S4G122000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5387.t1 is derived from g2557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16631303	16631681	.	-	.	Phchi.S1G254600
Phchi.S1	AUGUSTUS	transcript	16631303	16631681	.	-	.	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	stop_codon	16631300	16631302	.	-	0	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	CDS	16631303	16631338	0.96	-	0	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	exon	16631303	16631338	.	-	.	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	intron	16631339	16631432	.	-	.	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	CDS	16631433	16631681	0.93	-	0	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	exon	16631433	16631681	.	-	.	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
Phchi.S1	AUGUSTUS	start_codon	16631679	16631681	.	-	0	transcript_id "Phchi.S1G254600.t1"; gene_id "Phchi.S1G254600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10916.t1 is derived from g14966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2932321	2933860	.	-	.	Phchi.S4G049800
Phchi.S4	AUGUSTUS	transcript	2932321	2933860	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	stop_codon	2932318	2932320	.	-	0	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2932321	2932325	0.96	-	2	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2932321	2932325	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2932326	2932515	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2932516	2932561	1	-	0	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2932516	2932561	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2932562	2932642	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2932643	2932708	1	-	0	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2932643	2932708	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2932709	2932786	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2932787	2932899	1	-	2	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2932787	2932899	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2932900	2932992	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2932993	2933058	1	-	2	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2932993	2933058	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2933059	2933141	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2933142	2933254	1	-	1	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2933142	2933254	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2933255	2933354	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2933355	2933440	1	-	0	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2933355	2933440	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2933441	2933522	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2933523	2933679	1	-	1	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2933523	2933679	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	intron	2933680	2933768	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	CDS	2933769	2933860	1	-	0	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	exon	2933769	2933860	.	-	.	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
Phchi.S4	AUGUSTUS	start_codon	2933858	2933860	.	-	0	transcript_id "Phchi.S4G049800.t1"; gene_id "Phchi.S4G049800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12067.t1 is derived from g7742.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1779822	1781602	.	+	.	Phchi.S2G014700
Phchi.S2	AUGUSTUS	transcript	1779822	1781602	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	start_codon	1779822	1779824	.	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1779822	1779845	0.78	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1779822	1779845	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1779846	1779934	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1779935	1780072	1	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1779935	1780072	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780073	1780162	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780163	1780279	1	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780163	1780279	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780280	1780389	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780390	1780533	0.99	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780390	1780533	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780534	1780666	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780667	1780753	1	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780667	1780753	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780754	1780839	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780840	1780955	1	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780840	1780955	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780956	1781077	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1781078	1781259	1	+	1	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1781078	1781259	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1781260	1781339	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1781340	1781397	1	+	2	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1781340	1781397	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1781398	1781481	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1781482	1781602	1	+	1	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1781482	1781602	.	+	.	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	stop_codon	1781603	1781605	.	+	0	transcript_id "Phchi.S2G014700.t1"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	transcript	1779836	1781602	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	start_codon	1779836	1779838	.	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1779836	1779850	0.38	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1779836	1779850	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1779851	1779934	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1779935	1780072	0.38	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1779935	1780072	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780073	1780162	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780163	1780279	0.97	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780163	1780279	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780280	1780389	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780390	1780533	1	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780390	1780533	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780534	1780666	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780667	1780753	1	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780667	1780753	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780754	1780839	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1780840	1780955	1	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1780840	1780955	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1780956	1781077	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1781078	1781259	1	+	1	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1781078	1781259	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1781260	1781339	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1781340	1781397	1	+	2	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1781340	1781397	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	intron	1781398	1781481	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	CDS	1781482	1781602	1	+	1	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	exon	1781482	1781602	.	+	.	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
Phchi.S2	AUGUSTUS	stop_codon	1781603	1781605	.	+	0	transcript_id "Phchi.S2G014700.t2"; gene_id "Phchi.S2G014700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6681.t1 is derived from g3853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24469479	24471235	.	+	.	Phchi.S1G384000
Phchi.S1	AUGUSTUS	transcript	24469479	24471235	.	+	.	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	start_codon	24469479	24469481	.	+	0	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	CDS	24469479	24470790	0.9	+	0	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	exon	24469479	24470790	.	+	.	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	intron	24470791	24471077	.	+	.	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	CDS	24471078	24471235	0.92	+	2	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	exon	24471078	24471235	.	+	.	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
Phchi.S1	AUGUSTUS	stop_codon	24471236	24471238	.	+	0	transcript_id "Phchi.S1G384000.t1"; gene_id "Phchi.S1G384000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11754.t1 is derived from g15806.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8011232	8012358	.	-	.	Phchi.S4G133600
Phchi.S4	AUGUSTUS	transcript	8011232	8012358	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	stop_codon	8011229	8011231	.	-	0	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8011232	8011502	1	-	1	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8011232	8011502	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	intron	8011503	8011618	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8011619	8011810	1	-	1	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8011619	8011810	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	intron	8011811	8011907	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8011908	8012142	0.99	-	2	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8011908	8012142	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	intron	8012143	8012240	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8012241	8012358	0.83	-	0	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8012241	8012358	.	-	.	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	start_codon	8012356	8012358	.	-	0	transcript_id "Phchi.S4G133600.t1"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	transcript	8011232	8012358	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	stop_codon	8011229	8011231	.	-	0	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8011232	8011502	1	-	1	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8011232	8011502	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	intron	8011503	8011618	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8011619	8011810	1	-	1	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8011619	8011810	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	intron	8011811	8011907	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8011908	8012145	0.98	-	2	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8011908	8012145	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	intron	8012146	8012240	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	CDS	8012241	8012358	0.8	-	0	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	exon	8012241	8012358	.	-	.	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
Phchi.S4	AUGUSTUS	start_codon	8012356	8012358	.	-	0	transcript_id "Phchi.S4G133600.t2"; gene_id "Phchi.S4G133600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4718.t1 is derived from g1889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12455093	12457137	.	-	.	Phchi.S1G187800
Phchi.S1	AUGUSTUS	transcript	12455093	12457137	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	stop_codon	12455090	12455092	.	-	0	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	CDS	12455093	12455135	0.99	-	1	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	exon	12455093	12455135	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	intron	12455136	12455285	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	CDS	12455286	12455815	1	-	0	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	exon	12455286	12455815	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	intron	12455816	12455897	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	CDS	12455898	12455975	1	-	0	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	exon	12455898	12455975	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	intron	12455976	12456055	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	CDS	12456056	12456634	0.72	-	0	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	exon	12456056	12456634	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	intron	12456635	12456756	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	CDS	12456757	12457137	0.68	-	0	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	exon	12456757	12457137	.	-	.	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
Phchi.S1	AUGUSTUS	start_codon	12457135	12457137	.	-	0	transcript_id "Phchi.S1G187800.t1"; gene_id "Phchi.S1G187800"
# This transcript jg10652.t2 is derived from g14702.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10652.t3 is derived from g14702.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10653.t1 is derived from g14703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1436199	1437200	.	-	.	Phchi.S4G023500
Phchi.S4	AUGUSTUS	transcript	1436199	1437200	.	-	.	transcript_id "Phchi.S4G023500.t1"; gene_id "Phchi.S4G023500"
Phchi.S4	AUGUSTUS	stop_codon	1436196	1436198	.	-	0	transcript_id "Phchi.S4G023500.t1"; gene_id "Phchi.S4G023500"
Phchi.S4	AUGUSTUS	CDS	1436199	1437200	0.82	-	0	transcript_id "Phchi.S4G023500.t1"; gene_id "Phchi.S4G023500"
Phchi.S4	AUGUSTUS	exon	1436199	1437200	.	-	.	transcript_id "Phchi.S4G023500.t1"; gene_id "Phchi.S4G023500"
Phchi.S4	AUGUSTUS	start_codon	1437198	1437200	.	-	0	transcript_id "Phchi.S4G023500.t1"; gene_id "Phchi.S4G023500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14207.t1 is derived from g12674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11501852	11502544	.	+	.	Phchi.S3G152600
Phchi.S3	AUGUSTUS	transcript	11501852	11502544	.	+	.	transcript_id "Phchi.S3G152600.t1"; gene_id "Phchi.S3G152600"
Phchi.S3	AUGUSTUS	start_codon	11501852	11501854	.	+	0	transcript_id "Phchi.S3G152600.t1"; gene_id "Phchi.S3G152600"
Phchi.S3	AUGUSTUS	CDS	11501852	11502544	0.94	+	0	transcript_id "Phchi.S3G152600.t1"; gene_id "Phchi.S3G152600"
Phchi.S3	AUGUSTUS	exon	11501852	11502544	.	+	.	transcript_id "Phchi.S3G152600.t1"; gene_id "Phchi.S3G152600"
Phchi.S3	AUGUSTUS	stop_codon	11502545	11502547	.	+	0	transcript_id "Phchi.S3G152600.t1"; gene_id "Phchi.S3G152600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11916.t1 is derived from g15968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9301361	9307008	.	+	.	Phchi.S4G149800
Phchi.S4	AUGUSTUS	transcript	9301361	9307008	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	start_codon	9301361	9301363	.	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9301361	9301705	0.61	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9301361	9301705	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9301706	9301793	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9301794	9301865	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9301794	9301865	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9301866	9301946	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9301947	9301990	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9301947	9301990	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9301991	9302102	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9302103	9302214	1	+	1	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9302103	9302214	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9302215	9302309	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9302310	9302381	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9302310	9302381	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9302382	9302469	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9302470	9302568	0.92	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9302470	9302568	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9302569	9302643	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9302644	9302721	0.98	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9302644	9302721	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9302722	9302820	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9302821	9302913	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9302821	9302913	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9302914	9303113	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9303114	9303230	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9303114	9303230	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9303231	9303345	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9303346	9303423	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9303346	9303423	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9303424	9303544	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9303545	9303769	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9303545	9303769	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9303770	9303904	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9303905	9303952	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9303905	9303952	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9303953	9304056	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9304057	9304296	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9304057	9304296	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9304297	9304416	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9304417	9304493	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9304417	9304493	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9304494	9304582	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9304583	9304827	1	+	1	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9304583	9304827	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9304828	9304960	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9304961	9305029	1	+	2	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9304961	9305029	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9305030	9305119	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9305120	9305184	1	+	2	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9305120	9305184	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9305185	9305457	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9305458	9305654	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9305458	9305654	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9305655	9305877	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9305878	9305956	1	+	1	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9305878	9305956	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9305957	9306048	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9306049	9306313	1	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9306049	9306313	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9306314	9306449	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9306450	9306495	1	+	2	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9306450	9306495	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9306496	9306577	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9306578	9306686	1	+	1	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9306578	9306686	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9306687	9306759	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9306760	9306822	0.89	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9306760	9306822	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	intron	9306823	9306924	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	CDS	9306925	9307008	0.94	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	exon	9306925	9307008	.	+	.	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
Phchi.S4	AUGUSTUS	stop_codon	9307009	9307011	.	+	0	transcript_id "Phchi.S4G149800.t1"; gene_id "Phchi.S4G149800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4237.t1 is derived from g1406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9047876	9051993	.	-	.	Phchi.S1G139600
Phchi.S1	AUGUSTUS	transcript	9047876	9051993	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	stop_codon	9047873	9047875	.	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9047876	9047992	0.96	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9047876	9047992	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9047993	9048098	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9048099	9048182	0.98	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9048099	9048182	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9048183	9048287	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9048288	9048435	1	-	1	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9048288	9048435	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9048436	9048528	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9048529	9048678	1	-	1	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9048529	9048678	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9048679	9048766	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9048767	9048969	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9048767	9048969	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9048970	9049101	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9049102	9049221	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9049102	9049221	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9049222	9049337	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9049338	9049502	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9049338	9049502	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9049503	9049599	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9049600	9049686	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9049600	9049686	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9049687	9049796	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9049797	9049946	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9049797	9049946	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9049947	9050034	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9050035	9050127	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9050035	9050127	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9050128	9050216	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9050217	9050249	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9050217	9050249	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9050250	9050323	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9050324	9050386	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9050324	9050386	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9050387	9050484	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9050485	9050561	1	-	2	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9050485	9050561	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9050562	9050656	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9050657	9050897	0.94	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9050657	9050897	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9050898	9051045	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9051046	9051309	0.99	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9051046	9051309	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9051310	9051422	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9051423	9051510	1	-	1	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9051423	9051510	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9051511	9051604	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9051605	9051666	1	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9051605	9051666	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	intron	9051667	9051768	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	CDS	9051769	9051993	0.73	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	exon	9051769	9051993	.	-	.	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
Phchi.S1	AUGUSTUS	start_codon	9051991	9051993	.	-	0	transcript_id "Phchi.S1G139600.t1"; gene_id "Phchi.S1G139600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7314.t1 is derived from g4486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28467545	28467994	.	-	.	Phchi.S1G447300
Phchi.S1	AUGUSTUS	transcript	28467545	28467994	.	-	.	transcript_id "Phchi.S1G447300.t1"; gene_id "Phchi.S1G447300"
Phchi.S1	AUGUSTUS	stop_codon	28467542	28467544	.	-	0	transcript_id "Phchi.S1G447300.t1"; gene_id "Phchi.S1G447300"
Phchi.S1	AUGUSTUS	CDS	28467545	28467994	0.57	-	0	transcript_id "Phchi.S1G447300.t1"; gene_id "Phchi.S1G447300"
Phchi.S1	AUGUSTUS	exon	28467545	28467994	.	-	.	transcript_id "Phchi.S1G447300.t1"; gene_id "Phchi.S1G447300"
Phchi.S1	AUGUSTUS	start_codon	28467992	28467994	.	-	0	transcript_id "Phchi.S1G447300.t1"; gene_id "Phchi.S1G447300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8169.t1 is derived from g5344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34260147	34263298	.	-	.	Phchi.S1G532800
Phchi.S1	AUGUSTUS	transcript	34260147	34263298	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	stop_codon	34260144	34260146	.	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	CDS	34260147	34260469	0.51	-	2	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	exon	34260147	34260469	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	intron	34260470	34260562	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	CDS	34260563	34260695	0.52	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	exon	34260563	34260695	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	intron	34260696	34260874	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	CDS	34260875	34261984	0.79	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	exon	34260875	34261984	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	intron	34261985	34262092	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	CDS	34262093	34262122	0.79	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	exon	34262093	34262122	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	intron	34262123	34262500	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	CDS	34262501	34262695	1	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	exon	34262501	34262695	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	intron	34262696	34262791	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	CDS	34262792	34263298	1	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	exon	34262792	34263298	.	-	.	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
Phchi.S1	AUGUSTUS	start_codon	34263296	34263298	.	-	0	transcript_id "Phchi.S1G532800.t1"; gene_id "Phchi.S1G532800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9696.t1 is derived from g6872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43320288	43322532	.	+	.	Phchi.S1G685500
Phchi.S1	AUGUSTUS	transcript	43320288	43322532	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	start_codon	43320288	43320290	.	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43320288	43320581	0.85	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43320288	43320581	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43320582	43320749	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43320750	43320916	1	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43320750	43320916	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43320917	43321015	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43321016	43321355	0.97	+	1	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43321016	43321355	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43321356	43321457	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43321458	43321676	0.97	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43321458	43321676	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43321677	43321785	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43321786	43321845	1	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43321786	43321845	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43321846	43321970	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43321971	43322126	1	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43321971	43322126	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43322127	43322208	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43322209	43322302	1	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43322209	43322302	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	intron	43322303	43322413	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	CDS	43322414	43322532	1	+	2	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	exon	43322414	43322532	.	+	.	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
Phchi.S1	AUGUSTUS	stop_codon	43322533	43322535	.	+	0	transcript_id "Phchi.S1G685500.t1"; gene_id "Phchi.S1G685500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg820.t1 is derived from g10602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5714716	5716575	.	-	.	Phchi.S6G077900
Phchi.S6	AUGUSTUS	transcript	5714716	5716575	.	-	.	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	stop_codon	5714713	5714715	.	-	0	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	CDS	5714716	5716074	0.93	-	0	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	exon	5714716	5716074	.	-	.	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	intron	5716075	5716236	.	-	.	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	CDS	5716237	5716575	0.83	-	0	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	exon	5716237	5716575	.	-	.	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
Phchi.S6	AUGUSTUS	start_codon	5716573	5716575	.	-	0	transcript_id "Phchi.S6G077900.t1"; gene_id "Phchi.S6G077900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10511.t1 is derived from g14560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	765721	767896	.	-	.	Phchi.S4G009300
Phchi.S4	AUGUSTUS	transcript	765721	767896	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	stop_codon	765718	765720	.	-	0	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	765721	766004	0.68	-	2	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	765721	766004	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	766005	766179	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	766180	766205	0.91	-	1	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	766180	766205	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	766206	766302	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	766303	766424	0.99	-	0	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	766303	766424	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	766425	766771	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	766772	766908	0.8	-	2	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	766772	766908	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	766909	767068	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	767069	767141	0.55	-	0	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	767069	767141	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	767142	767220	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	767221	767395	0.81	-	1	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	767221	767395	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	767396	767505	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	767506	767617	0.76	-	2	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	767506	767617	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	intron	767618	767724	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	CDS	767725	767896	0.62	-	0	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	exon	767725	767896	.	-	.	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
Phchi.S4	AUGUSTUS	start_codon	767894	767896	.	-	0	transcript_id "Phchi.S4G009300.t1"; gene_id "Phchi.S4G009300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4439.t1 is derived from g1608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10509286	10509606	.	+	.	Phchi.S1G159800
Phchi.S1	AUGUSTUS	transcript	10509286	10509606	.	+	.	transcript_id "Phchi.S1G159800.t1"; gene_id "Phchi.S1G159800"
Phchi.S1	AUGUSTUS	start_codon	10509286	10509288	.	+	0	transcript_id "Phchi.S1G159800.t1"; gene_id "Phchi.S1G159800"
Phchi.S1	AUGUSTUS	CDS	10509286	10509606	0.57	+	0	transcript_id "Phchi.S1G159800.t1"; gene_id "Phchi.S1G159800"
Phchi.S1	AUGUSTUS	exon	10509286	10509606	.	+	.	transcript_id "Phchi.S1G159800.t1"; gene_id "Phchi.S1G159800"
Phchi.S1	AUGUSTUS	stop_codon	10509607	10509609	.	+	0	transcript_id "Phchi.S1G159800.t1"; gene_id "Phchi.S1G159800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14001.t1 is derived from g12468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10184385	10185082	.	-	.	Phchi.S3G132000
Phchi.S3	AUGUSTUS	transcript	10184385	10185082	.	-	.	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	stop_codon	10184382	10184384	.	-	0	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	CDS	10184385	10184468	0.95	-	0	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	exon	10184385	10184468	.	-	.	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	intron	10184469	10184713	.	-	.	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	CDS	10184714	10184769	1	-	2	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	exon	10184714	10184769	.	-	.	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	intron	10184770	10184895	.	-	.	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	CDS	10184896	10185082	0.48	-	0	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	exon	10184896	10185082	.	-	.	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
Phchi.S3	AUGUSTUS	start_codon	10185080	10185082	.	-	0	transcript_id "Phchi.S3G132000.t1"; gene_id "Phchi.S3G132000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9455.t1 is derived from g6631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41556049	41556814	.	-	.	Phchi.S1G661400
Phchi.S1	AUGUSTUS	transcript	41556049	41556814	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	stop_codon	41556046	41556048	.	-	0	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	CDS	41556049	41556258	1	-	0	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	exon	41556049	41556258	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	intron	41556259	41556336	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	CDS	41556337	41556517	0.9	-	1	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	exon	41556337	41556517	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	intron	41556518	41556613	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	CDS	41556614	41556661	0.89	-	1	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	exon	41556614	41556661	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	intron	41556662	41556755	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	CDS	41556756	41556814	0.57	-	0	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	exon	41556756	41556814	.	-	.	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
Phchi.S1	AUGUSTUS	start_codon	41556812	41556814	.	-	0	transcript_id "Phchi.S1G661400.t1"; gene_id "Phchi.S1G661400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg565.t1 is derived from g10347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4077131	4077733	.	+	.	Phchi.S6G052400
Phchi.S6	AUGUSTUS	transcript	4077131	4077733	.	+	.	transcript_id "Phchi.S6G052400.t1"; gene_id "Phchi.S6G052400"
Phchi.S6	AUGUSTUS	start_codon	4077131	4077133	.	+	0	transcript_id "Phchi.S6G052400.t1"; gene_id "Phchi.S6G052400"
Phchi.S6	AUGUSTUS	CDS	4077131	4077733	0.87	+	0	transcript_id "Phchi.S6G052400.t1"; gene_id "Phchi.S6G052400"
Phchi.S6	AUGUSTUS	exon	4077131	4077733	.	+	.	transcript_id "Phchi.S6G052400.t1"; gene_id "Phchi.S6G052400"
Phchi.S6	AUGUSTUS	stop_codon	4077734	4077736	.	+	0	transcript_id "Phchi.S6G052400.t1"; gene_id "Phchi.S6G052400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6554.t1 is derived from g3726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23685888	23686822	.	+	.	Phchi.S1G371300
Phchi.S1	AUGUSTUS	transcript	23685888	23686822	.	+	.	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	start_codon	23685888	23685890	.	+	0	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	CDS	23685888	23685923	1	+	0	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	exon	23685888	23685923	.	+	.	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	intron	23685924	23686327	.	+	.	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	CDS	23686328	23686822	1	+	0	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	exon	23686328	23686822	.	+	.	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
Phchi.S1	AUGUSTUS	stop_codon	23686823	23686825	.	+	0	transcript_id "Phchi.S1G371300.t1"; gene_id "Phchi.S1G371300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7510.t1 is derived from g4684.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29755614	29756589	.	-	.	Phchi.S1G466900
Phchi.S1	AUGUSTUS	transcript	29755614	29756589	.	-	.	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	stop_codon	29755611	29755613	.	-	0	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	CDS	29755614	29755773	1	-	1	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	exon	29755614	29755773	.	-	.	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	intron	29755774	29755871	.	-	.	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	CDS	29755872	29756183	1	-	1	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	exon	29755872	29756183	.	-	.	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	intron	29756184	29756278	.	-	.	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	CDS	29756279	29756589	0.99	-	0	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	exon	29756279	29756589	.	-	.	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
Phchi.S1	AUGUSTUS	start_codon	29756587	29756589	.	-	0	transcript_id "Phchi.S1G466900.t1"; gene_id "Phchi.S1G466900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2190.t1 is derived from g9110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5291255	5291756	.	-	.	Phchi.S5G079900
Phchi.S5	AUGUSTUS	transcript	5291255	5291756	.	-	.	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	stop_codon	5291252	5291254	.	-	0	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	CDS	5291255	5291338	0.22	-	0	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	exon	5291255	5291338	.	-	.	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	intron	5291339	5291430	.	-	.	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	CDS	5291431	5291523	1	-	0	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	exon	5291431	5291523	.	-	.	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	intron	5291524	5291609	.	-	.	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	CDS	5291610	5291756	0.92	-	0	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	exon	5291610	5291756	.	-	.	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
Phchi.S5	AUGUSTUS	start_codon	5291754	5291756	.	-	0	transcript_id "Phchi.S5G079900.t1"; gene_id "Phchi.S5G079900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2409.t1 is derived from g9329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6523576	6524163	.	+	.	Phchi.S5G101800
Phchi.S5	AUGUSTUS	transcript	6523576	6524163	.	+	.	transcript_id "Phchi.S5G101800.t1"; gene_id "Phchi.S5G101800"
Phchi.S5	AUGUSTUS	start_codon	6523576	6523578	.	+	0	transcript_id "Phchi.S5G101800.t1"; gene_id "Phchi.S5G101800"
Phchi.S5	AUGUSTUS	CDS	6523576	6524163	0.44	+	0	transcript_id "Phchi.S5G101800.t1"; gene_id "Phchi.S5G101800"
Phchi.S5	AUGUSTUS	exon	6523576	6524163	.	+	.	transcript_id "Phchi.S5G101800.t1"; gene_id "Phchi.S5G101800"
Phchi.S5	AUGUSTUS	stop_codon	6524164	6524166	.	+	0	transcript_id "Phchi.S5G101800.t1"; gene_id "Phchi.S5G101800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2613.t1 is derived from g9533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7786993	7789106	.	-	.	Phchi.S5G122200
Phchi.S5	AUGUSTUS	transcript	7786993	7789106	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	stop_codon	7786990	7786992	.	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	CDS	7786993	7787172	0.72	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	exon	7786993	7787172	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	intron	7787173	7787318	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	CDS	7787319	7787519	0.98	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	exon	7787319	7787519	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	intron	7787520	7787636	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	CDS	7787637	7787993	0.98	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	exon	7787637	7787993	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	intron	7787994	7788085	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	CDS	7788086	7788379	1	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	exon	7788086	7788379	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	intron	7788380	7788483	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	CDS	7788484	7788705	0.96	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	exon	7788484	7788705	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	intron	7788706	7788818	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	CDS	7788819	7789106	0.62	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	exon	7788819	7789106	.	-	.	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
Phchi.S5	AUGUSTUS	start_codon	7789104	7789106	.	-	0	transcript_id "Phchi.S5G122200.t1"; gene_id "Phchi.S5G122200"
# This transcript jg10263.t2 is derived from g7439.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10264.t1 is derived from g7440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46737350	46744862	.	+	.	Phchi.S1G742300
Phchi.S1	AUGUSTUS	transcript	46737350	46744862	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	start_codon	46737350	46737352	.	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46737350	46737486	0.84	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46737350	46737486	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46737487	46737573	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46737574	46737706	1	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46737574	46737706	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46737707	46737801	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46737802	46737951	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46737802	46737951	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46737952	46738132	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46738133	46738292	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46738133	46738292	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46738293	46738503	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46738504	46738703	1	+	2	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46738504	46738703	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46738704	46738808	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46738809	46738921	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46738809	46738921	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46738922	46739010	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46739011	46739110	1	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46739011	46739110	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46739111	46739194	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46739195	46739407	0.98	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46739195	46739407	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46739408	46739558	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46739559	46739707	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46739559	46739707	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46739708	46739789	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46739790	46739931	1	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46739790	46739931	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46739932	46740056	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46740057	46740197	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46740057	46740197	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46740198	46740284	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46740285	46740473	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46740285	46740473	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46740474	46740575	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46740576	46740768	0.95	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46740576	46740768	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46740769	46740884	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46740885	46740978	1	+	2	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46740885	46740978	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46740979	46741161	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46741162	46741396	1	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46741162	46741396	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46741397	46741483	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46741484	46741675	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46741484	46741675	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46741676	46741809	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46741810	46741908	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46741810	46741908	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46741909	46742011	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46742012	46742215	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46742012	46742215	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46742216	46742354	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46742355	46742630	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46742355	46742630	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46742631	46742770	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46742771	46742912	0.46	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46742771	46742912	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46742913	46743019	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46743020	46743171	0.83	+	2	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46743020	46743171	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46743172	46743257	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46743258	46743413	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46743258	46743413	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46743414	46743516	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46743517	46743633	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46743517	46743633	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46743634	46743733	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46743734	46743801	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46743734	46743801	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46743802	46743963	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46743964	46744168	1	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46743964	46744168	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46744169	46744249	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46744250	46744452	1	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46744250	46744452	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46744453	46744546	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46744547	46744594	0.63	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46744547	46744594	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	intron	46744595	46744807	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	CDS	46744808	46744862	0.68	+	1	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	exon	46744808	46744862	.	+	.	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
Phchi.S1	AUGUSTUS	stop_codon	46744950	46744952	.	+	0	transcript_id "Phchi.S1G742300.t1"; gene_id "Phchi.S1G742300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3820.t1 is derived from g989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5888147	5890015	.	-	.	Phchi.S1G097900
Phchi.S1	AUGUSTUS	transcript	5888147	5890015	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	stop_codon	5888144	5888146	.	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5888147	5888272	0.9	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5888147	5888272	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5888273	5888378	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5888379	5888510	1	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5888379	5888510	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5888511	5888585	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5888586	5888675	1	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5888586	5888675	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5888676	5888804	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5888805	5888914	1	-	2	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5888805	5888914	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5888915	5889003	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5889004	5889079	1	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5889004	5889079	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5889080	5889188	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5889189	5889251	0.99	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5889189	5889251	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5889252	5889348	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5889349	5889409	1	-	1	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5889349	5889409	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5889410	5889556	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5889557	5889814	0.65	-	1	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5889557	5889814	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	intron	5889815	5889968	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	CDS	5889969	5890015	0.55	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	exon	5889969	5890015	.	-	.	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
Phchi.S1	AUGUSTUS	start_codon	5890013	5890015	.	-	0	transcript_id "Phchi.S1G097900.t1"; gene_id "Phchi.S1G097900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9282.t1 is derived from g6457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40750825	40752343	.	-	.	Phchi.S1G644100
Phchi.S1	AUGUSTUS	transcript	40750825	40752343	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	stop_codon	40750822	40750824	.	-	0	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40750825	40750994	0.95	-	2	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40750825	40750994	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	intron	40750995	40751099	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40751100	40751211	0.67	-	0	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40751100	40751211	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	intron	40751212	40751309	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40751310	40751398	1	-	2	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40751310	40751398	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	intron	40751399	40751534	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40751535	40751628	1	-	0	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40751535	40751628	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	intron	40751629	40751740	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40751741	40751824	1	-	0	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40751741	40751824	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	intron	40751825	40751966	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40751967	40752036	0.97	-	1	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40751967	40752036	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	intron	40752037	40752110	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	CDS	40752111	40752343	0.97	-	0	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	exon	40752111	40752343	.	-	.	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
Phchi.S1	AUGUSTUS	start_codon	40752341	40752343	.	-	0	transcript_id "Phchi.S1G644100.t1"; gene_id "Phchi.S1G644100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15707.t1 is derived from g14177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20798256	20800362	.	+	.	Phchi.S3G302600
Phchi.S3	AUGUSTUS	transcript	20798256	20800362	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	start_codon	20798256	20798258	.	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20798256	20798744	0.98	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20798256	20798744	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20798745	20798872	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20798873	20799114	0.98	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20798873	20799114	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20799115	20799221	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20799222	20799318	1	+	1	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20799222	20799318	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20799319	20799412	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20799413	20799596	1	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20799413	20799596	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20799597	20799753	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20799754	20799835	1	+	2	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20799754	20799835	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20799836	20799915	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20799916	20800024	1	+	1	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20799916	20800024	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20800025	20800117	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20800118	20800207	1	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20800118	20800207	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	intron	20800208	20800308	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	CDS	20800309	20800362	1	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	exon	20800309	20800362	.	+	.	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
Phchi.S3	AUGUSTUS	stop_codon	20800363	20800365	.	+	0	transcript_id "Phchi.S3G302600.t1"; gene_id "Phchi.S3G302600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14266.t1 is derived from g12733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11841076	11842320	.	+	.	Phchi.S3G158500
Phchi.S3	AUGUSTUS	transcript	11841076	11842320	.	+	.	transcript_id "Phchi.S3G158500.t1"; gene_id "Phchi.S3G158500"
Phchi.S3	AUGUSTUS	start_codon	11841076	11841078	.	+	0	transcript_id "Phchi.S3G158500.t1"; gene_id "Phchi.S3G158500"
Phchi.S3	AUGUSTUS	CDS	11841076	11842320	1	+	0	transcript_id "Phchi.S3G158500.t1"; gene_id "Phchi.S3G158500"
Phchi.S3	AUGUSTUS	exon	11841076	11842320	.	+	.	transcript_id "Phchi.S3G158500.t1"; gene_id "Phchi.S3G158500"
Phchi.S3	AUGUSTUS	stop_codon	11842321	11842323	.	+	0	transcript_id "Phchi.S3G158500.t1"; gene_id "Phchi.S3G158500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14104.t1 is derived from g12571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10849639	10852746	.	+	.	Phchi.S3G142300
Phchi.S3	AUGUSTUS	transcript	10849639	10852746	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	start_codon	10849639	10849641	.	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10849639	10849896	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10849639	10849896	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10849897	10850113	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10850114	10850239	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10850114	10850239	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10850240	10850330	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10850331	10850528	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10850331	10850528	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10850529	10850698	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10850699	10850868	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10850699	10850868	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10850869	10850970	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10850971	10851106	1	+	1	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10850971	10851106	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10851107	10851255	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10851256	10851372	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10851256	10851372	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10851373	10851469	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10851470	10851589	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10851470	10851589	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10851590	10851699	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10851700	10851798	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10851700	10851798	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10851799	10851914	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10851915	10852004	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10851915	10852004	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10852005	10852091	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10852092	10852179	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10852092	10852179	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10852180	10852300	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10852301	10852389	1	+	2	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10852301	10852389	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10852390	10852466	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10852467	10852541	1	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10852467	10852541	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	intron	10852542	10852641	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	CDS	10852642	10852746	0.95	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	exon	10852642	10852746	.	+	.	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
Phchi.S3	AUGUSTUS	stop_codon	10852747	10852749	.	+	0	transcript_id "Phchi.S3G142300.t1"; gene_id "Phchi.S3G142300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14160.t1 is derived from g12627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11218766	11222442	.	+	.	Phchi.S3G147900
Phchi.S3	AUGUSTUS	transcript	11218766	11222442	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	start_codon	11218766	11218768	.	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11218766	11219409	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11218766	11219409	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11219410	11219528	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11219529	11219691	1	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11219529	11219691	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11219692	11219778	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11219779	11219853	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11219779	11219853	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11219854	11219954	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11219955	11220055	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11219955	11220055	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11220056	11220137	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11220138	11220253	1	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11220138	11220253	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11220254	11220366	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11220367	11220578	1	+	2	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11220367	11220578	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11220579	11220670	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11220671	11220759	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11220671	11220759	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11220760	11220844	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11220845	11220959	1	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11220845	11220959	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11220960	11221053	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11221054	11221157	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11221054	11221157	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11221158	11221317	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11221318	11221366	1	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11221318	11221366	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11221367	11221462	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11221463	11221527	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11221463	11221527	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11221528	11221614	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11221615	11221725	0.99	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11221615	11221725	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11221726	11221837	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11221838	11221892	1	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11221838	11221892	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11221893	11221990	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11221991	11222079	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11221991	11222079	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11222080	11222157	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11222158	11222245	0.99	+	1	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11222158	11222245	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	intron	11222246	11222352	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	CDS	11222353	11222442	1	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	exon	11222353	11222442	.	+	.	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
Phchi.S3	AUGUSTUS	stop_codon	11222443	11222445	.	+	0	transcript_id "Phchi.S3G147900.t1"; gene_id "Phchi.S3G147900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9865.t1 is derived from g7041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44138662	44139876	.	-	.	Phchi.S1G702400
Phchi.S1	AUGUSTUS	transcript	44138662	44139876	.	-	.	transcript_id "Phchi.S1G702400.t1"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	stop_codon	44138659	44138661	.	-	0	transcript_id "Phchi.S1G702400.t1"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	CDS	44138662	44139876	1	-	0	transcript_id "Phchi.S1G702400.t1"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	exon	44138662	44139876	.	-	.	transcript_id "Phchi.S1G702400.t1"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	start_codon	44139874	44139876	.	-	0	transcript_id "Phchi.S1G702400.t1"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	transcript	44138662	44139240	.	-	.	transcript_id "Phchi.S1G702400.t2"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	stop_codon	44138659	44138661	.	-	0	transcript_id "Phchi.S1G702400.t2"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	CDS	44138662	44139240	0.9	-	0	transcript_id "Phchi.S1G702400.t2"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	exon	44138662	44139240	.	-	.	transcript_id "Phchi.S1G702400.t2"; gene_id "Phchi.S1G702400"
Phchi.S1	AUGUSTUS	start_codon	44139238	44139240	.	-	0	transcript_id "Phchi.S1G702400.t2"; gene_id "Phchi.S1G702400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4482.t1 is derived from g1652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10714388	10715641	.	+	.	Phchi.S1G164100
Phchi.S1	AUGUSTUS	transcript	10714388	10715641	.	+	.	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	start_codon	10714388	10714390	.	+	0	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	CDS	10714388	10715107	0.91	+	0	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	exon	10714388	10715107	.	+	.	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	intron	10715108	10715215	.	+	.	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	CDS	10715216	10715641	0.71	+	0	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	exon	10715216	10715641	.	+	.	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
Phchi.S1	AUGUSTUS	stop_codon	10715642	10715644	.	+	0	transcript_id "Phchi.S1G164100.t1"; gene_id "Phchi.S1G164100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6996.t1 is derived from g4168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26314132	26315100	.	+	.	Phchi.S1G415500
Phchi.S1	AUGUSTUS	transcript	26314132	26315100	.	+	.	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	start_codon	26314132	26314134	.	+	0	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	CDS	26314132	26314278	0.61	+	0	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	exon	26314132	26314278	.	+	.	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	intron	26314279	26314383	.	+	.	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	CDS	26314384	26315100	0.98	+	0	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	exon	26314384	26315100	.	+	.	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
Phchi.S1	AUGUSTUS	stop_codon	26315101	26315103	.	+	0	transcript_id "Phchi.S1G415500.t1"; gene_id "Phchi.S1G415500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5043.t1 is derived from g2213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14226499	14228812	.	+	.	Phchi.S1G220200
Phchi.S1	AUGUSTUS	transcript	14226499	14228812	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	start_codon	14226499	14226501	.	+	0	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	CDS	14226499	14226590	0.83	+	0	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	exon	14226499	14226590	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	intron	14226591	14226726	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	CDS	14226727	14226820	1	+	1	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	exon	14226727	14226820	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	intron	14226821	14226894	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	CDS	14226895	14228622	0.73	+	0	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	exon	14226895	14228622	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	intron	14228623	14228773	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	CDS	14228774	14228812	0.84	+	0	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	exon	14228774	14228812	.	+	.	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
Phchi.S1	AUGUSTUS	stop_codon	14228813	14228815	.	+	0	transcript_id "Phchi.S1G220200.t1"; gene_id "Phchi.S1G220200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12410.t1 is derived from g8087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18427426	18428760	.	+	.	Phchi.S2G049000
Phchi.S2	AUGUSTUS	transcript	18427426	18428760	.	+	.	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	start_codon	18427426	18427428	.	+	0	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	CDS	18427426	18427951	0.66	+	0	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	exon	18427426	18427951	.	+	.	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	intron	18427952	18428119	.	+	.	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	CDS	18428120	18428760	0.89	+	2	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	exon	18428120	18428760	.	+	.	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
Phchi.S2	AUGUSTUS	stop_codon	18428761	18428763	.	+	0	transcript_id "Phchi.S2G049000.t1"; gene_id "Phchi.S2G049000"
# This transcript jg12072.t2 is derived from g7747.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12073.t1 is derived from g7748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2068670	2070348	.	+	.	Phchi.S2G015300
Phchi.S2	AUGUSTUS	transcript	2068670	2070348	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	start_codon	2068670	2068672	.	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2068670	2068834	0.8	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2068670	2068834	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2068835	2068959	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2068960	2069016	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2068960	2069016	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069017	2069097	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069098	2069157	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069098	2069157	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069158	2069268	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069269	2069337	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069269	2069337	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069338	2069417	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069418	2069510	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069418	2069510	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069511	2069610	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069611	2069715	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069611	2069715	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069716	2069893	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069894	2069971	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069894	2069971	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069972	2070069	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2070070	2070204	1	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2070070	2070204	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2070205	2070294	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2070295	2070348	0.98	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2070295	2070348	.	+	.	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	stop_codon	2070349	2070351	.	+	0	transcript_id "Phchi.S2G015300.t1"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	transcript	2068670	2069878	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	start_codon	2068670	2068672	.	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2068670	2068834	0.75	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2068670	2068834	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2068835	2068959	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2068960	2069016	1	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2068960	2069016	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069017	2069097	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069098	2069157	0.99	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069098	2069157	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069158	2069268	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069269	2069337	0.99	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069269	2069337	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069338	2069417	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069418	2069510	1	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069418	2069510	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069511	2069610	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069611	2069715	0.96	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069611	2069715	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	intron	2069716	2069866	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	CDS	2069867	2069878	0.88	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	exon	2069867	2069878	.	+	.	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
Phchi.S2	AUGUSTUS	stop_codon	2069879	2069881	.	+	0	transcript_id "Phchi.S2G015300.t2"; gene_id "Phchi.S2G015300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13095.t1 is derived from g11560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4129129	4130020	.	-	.	Phchi.S3G041400
Phchi.S3	AUGUSTUS	transcript	4129129	4130020	.	-	.	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	stop_codon	4129126	4129128	.	-	0	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	CDS	4129129	4129377	0.99	-	0	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	exon	4129129	4129377	.	-	.	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	intron	4129378	4129513	.	-	.	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	CDS	4129514	4129735	1	-	0	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	exon	4129514	4129735	.	-	.	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	intron	4129736	4129984	.	-	.	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	CDS	4129985	4130020	1	-	0	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	exon	4129985	4130020	.	-	.	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
Phchi.S3	AUGUSTUS	start_codon	4130018	4130020	.	-	0	transcript_id "Phchi.S3G041400.t1"; gene_id "Phchi.S3G041400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9003.t1 is derived from g6178.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39116203	39117036	.	-	.	Phchi.S1G616200
Phchi.S1	AUGUSTUS	transcript	39116203	39117036	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	stop_codon	39116200	39116202	.	-	0	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	CDS	39116203	39116241	1	-	0	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	exon	39116203	39116241	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	intron	39116242	39116364	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	CDS	39116365	39116420	1	-	2	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	exon	39116365	39116420	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	intron	39116421	39116583	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	CDS	39116584	39116665	1	-	0	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	exon	39116584	39116665	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	intron	39116666	39116782	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	CDS	39116783	39116824	1	-	0	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	exon	39116783	39116824	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	intron	39116825	39116910	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	CDS	39116911	39117036	1	-	0	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	exon	39116911	39117036	.	-	.	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
Phchi.S1	AUGUSTUS	start_codon	39117034	39117036	.	-	0	transcript_id "Phchi.S1G616200.t1"; gene_id "Phchi.S1G616200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11461.t1 is derived from g15511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6481096	6482394	.	+	.	Phchi.S4G104300
Phchi.S4	AUGUSTUS	transcript	6481096	6482394	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	start_codon	6481096	6481098	.	+	0	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	CDS	6481096	6481168	0.98	+	0	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	exon	6481096	6481168	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	intron	6481169	6481338	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	CDS	6481339	6481442	1	+	2	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	exon	6481339	6481442	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	intron	6481443	6481540	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	CDS	6481541	6481667	1	+	0	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	exon	6481541	6481667	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	intron	6481668	6481913	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	CDS	6481914	6482160	1	+	2	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	exon	6481914	6482160	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	intron	6482161	6482282	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	CDS	6482283	6482394	0.97	+	1	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	exon	6482283	6482394	.	+	.	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
Phchi.S4	AUGUSTUS	stop_codon	6482395	6482397	.	+	0	transcript_id "Phchi.S4G104300.t1"; gene_id "Phchi.S4G104300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10609.t1 is derived from g14659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1185212	1185994	.	-	.	Phchi.S4G019100
Phchi.S4	AUGUSTUS	transcript	1185212	1185994	.	-	.	transcript_id "Phchi.S4G019100.t1"; gene_id "Phchi.S4G019100"
Phchi.S4	AUGUSTUS	stop_codon	1185209	1185211	.	-	0	transcript_id "Phchi.S4G019100.t1"; gene_id "Phchi.S4G019100"
Phchi.S4	AUGUSTUS	CDS	1185212	1185994	0.25	-	0	transcript_id "Phchi.S4G019100.t1"; gene_id "Phchi.S4G019100"
Phchi.S4	AUGUSTUS	exon	1185212	1185994	.	-	.	transcript_id "Phchi.S4G019100.t1"; gene_id "Phchi.S4G019100"
Phchi.S4	AUGUSTUS	start_codon	1185992	1185994	.	-	0	transcript_id "Phchi.S4G019100.t1"; gene_id "Phchi.S4G019100"
# This transcript jg12082.t2 is derived from g7757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12082.t3 is derived from g7757.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12083.t1 is derived from g7758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2171499	2173102	.	-	.	Phchi.S2G016300
Phchi.S2	AUGUSTUS	transcript	2171499	2173102	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	stop_codon	2171496	2171498	.	-	0	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	CDS	2171499	2172078	0.85	-	1	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	exon	2171499	2172078	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	intron	2172079	2172208	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	CDS	2172209	2172429	1	-	0	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	exon	2172209	2172429	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	intron	2172430	2172522	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	CDS	2172523	2172830	0.9	-	2	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	exon	2172523	2172830	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	intron	2172831	2172930	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	CDS	2172931	2173102	0.64	-	0	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	exon	2172931	2173102	.	-	.	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
Phchi.S2	AUGUSTUS	start_codon	2173100	2173102	.	-	0	transcript_id "Phchi.S2G016300.t1"; gene_id "Phchi.S2G016300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15507.t1 is derived from g13976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19596702	19599839	.	-	.	Phchi.S3G282600
Phchi.S3	AUGUSTUS	transcript	19596702	19599839	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	stop_codon	19596699	19596701	.	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19596702	19596823	0.97	-	2	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19596702	19596823	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19596824	19596917	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19596918	19596992	0.93	-	2	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19596918	19596992	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19596993	19597089	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19597090	19597115	0.99	-	1	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19597090	19597115	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19597116	19597192	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19597193	19597422	1	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19597193	19597422	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19597423	19597545	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19597546	19597701	1	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19597546	19597701	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19597702	19597837	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19597838	19598314	1	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19597838	19598314	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19598315	19598494	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19598495	19598593	1	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19598495	19598593	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19598594	19598717	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19598718	19598827	1	-	2	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19598718	19598827	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19598828	19599084	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19599085	19599268	1	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19599085	19599268	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19599269	19599416	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19599417	19599510	1	-	1	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19599417	19599510	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	intron	19599511	19599672	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	CDS	19599673	19599839	0.68	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	exon	19599673	19599839	.	-	.	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
Phchi.S3	AUGUSTUS	start_codon	19599837	19599839	.	-	0	transcript_id "Phchi.S3G282600.t1"; gene_id "Phchi.S3G282600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6616.t1 is derived from g3788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24014933	24016201	.	+	.	Phchi.S1G377500
Phchi.S1	AUGUSTUS	transcript	24014933	24016201	.	+	.	transcript_id "Phchi.S1G377500.t1"; gene_id "Phchi.S1G377500"
Phchi.S1	AUGUSTUS	start_codon	24014933	24014935	.	+	0	transcript_id "Phchi.S1G377500.t1"; gene_id "Phchi.S1G377500"
Phchi.S1	AUGUSTUS	CDS	24014933	24016201	0.93	+	0	transcript_id "Phchi.S1G377500.t1"; gene_id "Phchi.S1G377500"
Phchi.S1	AUGUSTUS	exon	24014933	24016201	.	+	.	transcript_id "Phchi.S1G377500.t1"; gene_id "Phchi.S1G377500"
Phchi.S1	AUGUSTUS	stop_codon	24016202	24016204	.	+	0	transcript_id "Phchi.S1G377500.t1"; gene_id "Phchi.S1G377500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13812.t1 is derived from g12279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9034318	9036994	.	+	.	Phchi.S3G113100
Phchi.S3	AUGUSTUS	transcript	9034318	9036994	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	start_codon	9034318	9034320	.	+	0	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	CDS	9034318	9034476	0.84	+	0	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	exon	9034318	9034476	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	intron	9034477	9034596	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	CDS	9034597	9035598	1	+	0	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	exon	9034597	9035598	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	intron	9035599	9035704	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	CDS	9035705	9036356	0.88	+	0	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	exon	9035705	9036356	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	intron	9036357	9036455	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	CDS	9036456	9036994	0.86	+	2	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	exon	9036456	9036994	.	+	.	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
Phchi.S3	AUGUSTUS	stop_codon	9036995	9036997	.	+	0	transcript_id "Phchi.S3G113100.t1"; gene_id "Phchi.S3G113100"
# This transcript jg9633.t2 is derived from g6809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9634.t1 is derived from g6810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43002298	43003121	.	-	.	Phchi.S1G679300
Phchi.S1	AUGUSTUS	transcript	43002298	43003121	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	stop_codon	43002295	43002297	.	-	0	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	CDS	43002298	43002320	0.69	-	2	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	exon	43002298	43002320	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	intron	43002321	43002652	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	CDS	43002653	43002783	0.78	-	1	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	exon	43002653	43002783	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	intron	43002784	43002864	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	CDS	43002865	43002911	0.76	-	0	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	exon	43002865	43002911	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	intron	43002912	43003079	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	CDS	43003080	43003121	0.91	-	0	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	exon	43003080	43003121	.	-	.	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
Phchi.S1	AUGUSTUS	start_codon	43003119	43003121	.	-	0	transcript_id "Phchi.S1G679300.t1"; gene_id "Phchi.S1G679300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4819.t1 is derived from g1989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12994580	12997522	.	-	.	Phchi.S1G197800
Phchi.S1	AUGUSTUS	transcript	12994580	12997522	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	stop_codon	12994577	12994579	.	-	0	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12994580	12994657	1	-	0	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12994580	12994657	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	intron	12994658	12994731	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12994732	12994751	1	-	2	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12994732	12994751	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	intron	12994752	12995170	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12995171	12995262	0.7	-	1	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12995171	12995262	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	intron	12995263	12995368	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12995369	12995544	0.96	-	0	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12995369	12995544	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	intron	12995545	12995633	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12995634	12995912	1	-	0	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12995634	12995912	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	intron	12995913	12996011	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12996012	12996675	0.69	-	1	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12996012	12996675	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	intron	12996676	12996923	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	CDS	12996924	12997522	0.65	-	0	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	exon	12996924	12997522	.	-	.	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
Phchi.S1	AUGUSTUS	start_codon	12997520	12997522	.	-	0	transcript_id "Phchi.S1G197800.t1"; gene_id "Phchi.S1G197800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4127.t1 is derived from g1296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8390735	8393197	.	+	.	Phchi.S1G128600
Phchi.S1	AUGUSTUS	transcript	8390735	8393197	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	start_codon	8390735	8390737	.	+	0	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8390735	8390737	0.94	+	0	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8390735	8390737	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	intron	8390738	8390824	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8390825	8390963	1	+	0	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8390825	8390963	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	intron	8390964	8391039	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8391040	8391369	0.98	+	2	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8391040	8391369	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	intron	8391370	8391505	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8391506	8391660	0.56	+	2	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8391506	8391660	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	intron	8391661	8391762	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8391763	8392025	1	+	0	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8391763	8392025	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	intron	8392026	8392126	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8392127	8392461	0.99	+	1	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8392127	8392461	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	intron	8392462	8392556	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	CDS	8392557	8393197	1	+	2	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	exon	8392557	8393197	.	+	.	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
Phchi.S1	AUGUSTUS	stop_codon	8393198	8393200	.	+	0	transcript_id "Phchi.S1G128600.t1"; gene_id "Phchi.S1G128600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7033.t1 is derived from g4205.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26514162	26514740	.	+	.	Phchi.S1G419200
Phchi.S1	AUGUSTUS	transcript	26514162	26514740	.	+	.	transcript_id "Phchi.S1G419200.t1"; gene_id "Phchi.S1G419200"
Phchi.S1	AUGUSTUS	start_codon	26514162	26514164	.	+	0	transcript_id "Phchi.S1G419200.t1"; gene_id "Phchi.S1G419200"
Phchi.S1	AUGUSTUS	CDS	26514162	26514740	0.55	+	0	transcript_id "Phchi.S1G419200.t1"; gene_id "Phchi.S1G419200"
Phchi.S1	AUGUSTUS	exon	26514162	26514740	.	+	.	transcript_id "Phchi.S1G419200.t1"; gene_id "Phchi.S1G419200"
Phchi.S1	AUGUSTUS	stop_codon	26514741	26514743	.	+	0	transcript_id "Phchi.S1G419200.t1"; gene_id "Phchi.S1G419200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15309.t1 is derived from g13777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18332042	18332978	.	-	.	Phchi.S3G262800
Phchi.S3	AUGUSTUS	transcript	18332042	18332978	.	-	.	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	stop_codon	18332039	18332041	.	-	0	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	CDS	18332042	18332520	0.96	-	2	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	exon	18332042	18332520	.	-	.	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	intron	18332521	18332618	.	-	.	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	CDS	18332619	18332667	1	-	0	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	exon	18332619	18332667	.	-	.	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	intron	18332668	18332828	.	-	.	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	CDS	18332829	18332978	0.91	-	0	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	exon	18332829	18332978	.	-	.	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
Phchi.S3	AUGUSTUS	start_codon	18332976	18332978	.	-	0	transcript_id "Phchi.S3G262800.t1"; gene_id "Phchi.S3G262800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9068.t1 is derived from g6243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39648097	39648591	.	+	.	Phchi.S1G622700
Phchi.S1	AUGUSTUS	transcript	39648097	39648591	.	+	.	transcript_id "Phchi.S1G622700.t1"; gene_id "Phchi.S1G622700"
Phchi.S1	AUGUSTUS	start_codon	39648097	39648099	.	+	0	transcript_id "Phchi.S1G622700.t1"; gene_id "Phchi.S1G622700"
Phchi.S1	AUGUSTUS	CDS	39648097	39648591	0.88	+	0	transcript_id "Phchi.S1G622700.t1"; gene_id "Phchi.S1G622700"
Phchi.S1	AUGUSTUS	exon	39648097	39648591	.	+	.	transcript_id "Phchi.S1G622700.t1"; gene_id "Phchi.S1G622700"
Phchi.S1	AUGUSTUS	stop_codon	39648592	39648594	.	+	0	transcript_id "Phchi.S1G622700.t1"; gene_id "Phchi.S1G622700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12892.t1 is derived from g11357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3019083	3019496	.	+	.	Phchi.S3G021100
Phchi.S3	AUGUSTUS	transcript	3019083	3019496	.	+	.	transcript_id "Phchi.S3G021100.t1"; gene_id "Phchi.S3G021100"
Phchi.S3	AUGUSTUS	start_codon	3019083	3019085	.	+	0	transcript_id "Phchi.S3G021100.t1"; gene_id "Phchi.S3G021100"
Phchi.S3	AUGUSTUS	CDS	3019083	3019496	0.78	+	0	transcript_id "Phchi.S3G021100.t1"; gene_id "Phchi.S3G021100"
Phchi.S3	AUGUSTUS	exon	3019083	3019496	.	+	.	transcript_id "Phchi.S3G021100.t1"; gene_id "Phchi.S3G021100"
Phchi.S3	AUGUSTUS	stop_codon	3019497	3019499	.	+	0	transcript_id "Phchi.S3G021100.t1"; gene_id "Phchi.S3G021100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8354.t1 is derived from g5529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35472099	35473000	.	+	.	Phchi.S1G551300
Phchi.S1	AUGUSTUS	transcript	35472099	35473000	.	+	.	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	start_codon	35472099	35472101	.	+	0	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	CDS	35472099	35472263	1	+	0	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	exon	35472099	35472263	.	+	.	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	intron	35472264	35472508	.	+	.	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	CDS	35472509	35473000	1	+	0	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	exon	35472509	35473000	.	+	.	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
Phchi.S1	AUGUSTUS	stop_codon	35473001	35473003	.	+	0	transcript_id "Phchi.S1G551300.t1"; gene_id "Phchi.S1G551300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11863.t1 is derived from g15915.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8811390	8813030	.	+	.	Phchi.S4G144500
Phchi.S4	AUGUSTUS	transcript	8811390	8812464	.	+	.	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	start_codon	8811390	8811392	.	+	0	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	CDS	8811390	8812333	0.97	+	0	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	exon	8811390	8812333	.	+	.	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	intron	8812334	8812427	.	+	.	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	CDS	8812428	8812464	0.96	+	1	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	exon	8812428	8812464	.	+	.	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	stop_codon	8812465	8812467	.	+	0	transcript_id "Phchi.S4G144500.t1"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	transcript	8811390	8813030	.	+	.	transcript_id "Phchi.S4G144500.t2"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	start_codon	8811390	8811392	.	+	0	transcript_id "Phchi.S4G144500.t2"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	CDS	8811390	8813030	0.98	+	0	transcript_id "Phchi.S4G144500.t2"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	exon	8811390	8813030	.	+	.	transcript_id "Phchi.S4G144500.t2"; gene_id "Phchi.S4G144500"
Phchi.S4	AUGUSTUS	stop_codon	8813031	8813033	.	+	0	transcript_id "Phchi.S4G144500.t2"; gene_id "Phchi.S4G144500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9660.t1 is derived from g6836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43116193	43117398	.	+	.	Phchi.S1G681900
Phchi.S1	AUGUSTUS	transcript	43116193	43117398	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	start_codon	43116193	43116195	.	+	0	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	CDS	43116193	43116195	1	+	0	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	exon	43116193	43116195	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	intron	43116196	43116473	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	CDS	43116474	43116657	0.94	+	0	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	exon	43116474	43116657	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	intron	43116658	43116764	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	CDS	43116765	43116790	0.81	+	2	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	exon	43116765	43116790	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	intron	43116791	43116890	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	CDS	43116891	43117040	0.79	+	0	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	exon	43116891	43117040	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	intron	43117041	43117293	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	CDS	43117294	43117398	0.81	+	0	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	exon	43117294	43117398	.	+	.	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
Phchi.S1	AUGUSTUS	stop_codon	43117399	43117401	.	+	0	transcript_id "Phchi.S1G681900.t1"; gene_id "Phchi.S1G681900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2707.t1 is derived from g9627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8285357	8285644	.	-	.	Phchi.S5G131600
Phchi.S5	AUGUSTUS	transcript	8285357	8285644	.	-	.	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	stop_codon	8285354	8285356	.	-	0	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	CDS	8285357	8285373	1	-	2	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	exon	8285357	8285373	.	-	.	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	intron	8285374	8285457	.	-	.	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	CDS	8285458	8285644	0.86	-	0	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	exon	8285458	8285644	.	-	.	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
Phchi.S5	AUGUSTUS	start_codon	8285642	8285644	.	-	0	transcript_id "Phchi.S5G131600.t1"; gene_id "Phchi.S5G131600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8949.t1 is derived from g6124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38808041	38810227	.	-	.	Phchi.S1G610800
Phchi.S1	AUGUSTUS	transcript	38808041	38810227	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	stop_codon	38808038	38808040	.	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38808041	38808070	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38808041	38808070	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38808071	38808165	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38808166	38808252	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38808166	38808252	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38808253	38808336	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38808337	38808414	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38808337	38808414	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38808415	38808513	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38808514	38808618	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38808514	38808618	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38808619	38808706	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38808707	38808808	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38808707	38808808	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38808809	38808905	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38808906	38809039	1	-	2	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38808906	38809039	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38809040	38809184	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38809185	38809263	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38809185	38809263	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38809264	38809362	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38809363	38809575	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38809363	38809575	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	intron	38809576	38810140	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	CDS	38810141	38810227	1	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	exon	38810141	38810227	.	-	.	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
Phchi.S1	AUGUSTUS	start_codon	38810225	38810227	.	-	0	transcript_id "Phchi.S1G610800.t1"; gene_id "Phchi.S1G610800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg45.t1 is derived from g9827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	50290	51225	.	-	.	Phchi.S6G000400
Phchi.S6	AUGUSTUS	transcript	50290	51225	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	stop_codon	50287	50289	.	-	0	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	CDS	50290	50389	0.8	-	1	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	exon	50290	50389	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	intron	50390	50726	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	CDS	50727	50805	0.82	-	2	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	exon	50727	50805	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	intron	50806	50902	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	CDS	50903	50966	0.8	-	0	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	exon	50903	50966	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	intron	50967	51222	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	CDS	51223	51225	0.79	-	0	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	exon	51223	51225	.	-	.	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
Phchi.S6	AUGUSTUS	start_codon	51223	51225	.	-	0	transcript_id "Phchi.S6G000400.t1"; gene_id "Phchi.S6G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8846.t1 is derived from g6021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38257756	38259423	.	+	.	Phchi.S1G600500
Phchi.S1	AUGUSTUS	transcript	38257756	38259423	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	start_codon	38257756	38257758	.	+	0	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38257756	38258094	1	+	0	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38257756	38258094	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258095	38258192	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38258193	38258398	1	+	0	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38258193	38258398	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258399	38258614	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38258615	38258969	1	+	1	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38258615	38258969	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258970	38259159	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38259160	38259423	0.96	+	0	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38259160	38259423	.	+	.	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	stop_codon	38259424	38259426	.	+	0	transcript_id "Phchi.S1G600500.t1"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	transcript	38257756	38259423	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	start_codon	38257756	38257758	.	+	0	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38257756	38258094	1	+	0	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38257756	38258094	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258095	38258192	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38258193	38258227	0.89	+	0	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38258193	38258227	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258228	38258340	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38258341	38258394	0.89	+	1	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38258341	38258394	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258395	38258614	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38258615	38258969	0.99	+	1	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38258615	38258969	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	intron	38258970	38259159	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	CDS	38259160	38259423	0.93	+	0	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	exon	38259160	38259423	.	+	.	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
Phchi.S1	AUGUSTUS	stop_codon	38259424	38259426	.	+	0	transcript_id "Phchi.S1G600500.t2"; gene_id "Phchi.S1G600500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4059.t1 is derived from g1228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7579612	7580954	.	+	.	Phchi.S1G121800
Phchi.S1	AUGUSTUS	transcript	7579612	7580954	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	start_codon	7579612	7579614	.	+	0	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7579612	7579732	0.53	+	0	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7579612	7579732	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	intron	7579733	7579827	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7579828	7579861	0.97	+	2	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7579828	7579861	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	intron	7579862	7580009	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7580010	7580223	0.93	+	1	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7580010	7580223	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	intron	7580224	7580315	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7580316	7580375	1	+	0	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7580316	7580375	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	intron	7580376	7580465	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7580466	7580558	1	+	0	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7580466	7580558	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	intron	7580559	7580642	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7580643	7580727	1	+	0	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7580643	7580727	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	intron	7580728	7580892	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	CDS	7580893	7580954	0.99	+	2	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	exon	7580893	7580954	.	+	.	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
Phchi.S1	AUGUSTUS	stop_codon	7580955	7580957	.	+	0	transcript_id "Phchi.S1G121800.t1"; gene_id "Phchi.S1G121800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2858.t1 is derived from g27.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	103789	105399	.	+	.	Phchi.S1G001700
Phchi.S1	AUGUSTUS	transcript	103789	105399	.	+	.	transcript_id "Phchi.S1G001700.t1"; gene_id "Phchi.S1G001700"
Phchi.S1	AUGUSTUS	start_codon	103789	103791	.	+	0	transcript_id "Phchi.S1G001700.t1"; gene_id "Phchi.S1G001700"
Phchi.S1	AUGUSTUS	CDS	103789	105399	0.79	+	0	transcript_id "Phchi.S1G001700.t1"; gene_id "Phchi.S1G001700"
Phchi.S1	AUGUSTUS	exon	103789	105399	.	+	.	transcript_id "Phchi.S1G001700.t1"; gene_id "Phchi.S1G001700"
Phchi.S1	AUGUSTUS	stop_codon	105400	105402	.	+	0	transcript_id "Phchi.S1G001700.t1"; gene_id "Phchi.S1G001700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg749.t1 is derived from g10531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5322269	5323887	.	-	.	Phchi.S6G070800
Phchi.S6	AUGUSTUS	transcript	5322269	5323887	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	stop_codon	5322266	5322268	.	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	CDS	5322269	5322436	1	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	exon	5322269	5322436	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	intron	5322437	5322544	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	CDS	5322545	5322613	1	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	exon	5322545	5322613	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	intron	5322614	5322848	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	CDS	5322849	5323025	1	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	exon	5322849	5323025	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	intron	5323026	5323145	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	CDS	5323146	5323223	1	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	exon	5323146	5323223	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	intron	5323224	5323327	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	CDS	5323328	5323423	1	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	exon	5323328	5323423	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	intron	5323424	5323530	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	CDS	5323531	5323887	0.99	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	exon	5323531	5323887	.	-	.	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
Phchi.S6	AUGUSTUS	start_codon	5323885	5323887	.	-	0	transcript_id "Phchi.S6G070800.t1"; gene_id "Phchi.S6G070800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6205.t1 is derived from g3376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21468048	21468901	.	+	.	Phchi.S1G336400
Phchi.S1	AUGUSTUS	transcript	21468048	21468901	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	start_codon	21468048	21468050	.	+	0	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	CDS	21468048	21468155	0.65	+	0	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	exon	21468048	21468155	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	intron	21468156	21468238	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	CDS	21468239	21468273	0.79	+	0	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	exon	21468239	21468273	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	intron	21468274	21468469	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	CDS	21468470	21468576	0.97	+	1	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	exon	21468470	21468576	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	intron	21468577	21468748	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	CDS	21468749	21468807	0.97	+	2	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	exon	21468749	21468807	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	intron	21468808	21468892	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	CDS	21468893	21468901	0.97	+	0	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	exon	21468893	21468901	.	+	.	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
Phchi.S1	AUGUSTUS	stop_codon	21468902	21468904	.	+	0	transcript_id "Phchi.S1G336400.t1"; gene_id "Phchi.S1G336400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12312.t1 is derived from g7988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10165039	10165443	.	-	.	Phchi.S2G039200
Phchi.S2	AUGUSTUS	transcript	10165039	10165443	.	-	.	transcript_id "Phchi.S2G039200.t1"; gene_id "Phchi.S2G039200"
Phchi.S2	AUGUSTUS	stop_codon	10165036	10165038	.	-	0	transcript_id "Phchi.S2G039200.t1"; gene_id "Phchi.S2G039200"
Phchi.S2	AUGUSTUS	CDS	10165039	10165443	0.89	-	0	transcript_id "Phchi.S2G039200.t1"; gene_id "Phchi.S2G039200"
Phchi.S2	AUGUSTUS	exon	10165039	10165443	.	-	.	transcript_id "Phchi.S2G039200.t1"; gene_id "Phchi.S2G039200"
Phchi.S2	AUGUSTUS	start_codon	10165441	10165443	.	-	0	transcript_id "Phchi.S2G039200.t1"; gene_id "Phchi.S2G039200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10259.t1 is derived from g7435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46720313	46721317	.	+	.	Phchi.S1G741800
Phchi.S1	AUGUSTUS	transcript	46720313	46721317	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	start_codon	46720313	46720315	.	+	0	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	CDS	46720313	46720424	0.4	+	0	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	exon	46720313	46720424	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	intron	46720425	46720629	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	CDS	46720630	46720725	0.82	+	2	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	exon	46720630	46720725	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	intron	46720726	46720983	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	CDS	46720984	46721162	0.95	+	2	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	exon	46720984	46721162	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	intron	46721163	46721272	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	CDS	46721273	46721317	0.98	+	0	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	exon	46721273	46721317	.	+	.	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
Phchi.S1	AUGUSTUS	stop_codon	46721318	46721320	.	+	0	transcript_id "Phchi.S1G741800.t1"; gene_id "Phchi.S1G741800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3074.t1 is derived from g243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1440753	1441309	.	-	.	Phchi.S1G023300
Phchi.S1	AUGUSTUS	transcript	1440753	1441309	.	-	.	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	stop_codon	1440750	1440752	.	-	0	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	CDS	1440753	1440830	0.5	-	0	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	exon	1440753	1440830	.	-	.	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	intron	1440831	1441071	.	-	.	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	CDS	1441072	1441170	0.95	-	0	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	exon	1441072	1441170	.	-	.	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	intron	1441171	1441258	.	-	.	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	CDS	1441259	1441309	0.99	-	0	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	exon	1441259	1441309	.	-	.	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
Phchi.S1	AUGUSTUS	start_codon	1441307	1441309	.	-	0	transcript_id "Phchi.S1G023300.t1"; gene_id "Phchi.S1G023300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12324.t1 is derived from g8000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10897520	10897819	.	-	.	Phchi.S2G040400
Phchi.S2	AUGUSTUS	transcript	10897520	10897819	.	-	.	transcript_id "Phchi.S2G040400.t1"; gene_id "Phchi.S2G040400"
Phchi.S2	AUGUSTUS	stop_codon	10897517	10897519	.	-	0	transcript_id "Phchi.S2G040400.t1"; gene_id "Phchi.S2G040400"
Phchi.S2	AUGUSTUS	CDS	10897520	10897819	0.79	-	0	transcript_id "Phchi.S2G040400.t1"; gene_id "Phchi.S2G040400"
Phchi.S2	AUGUSTUS	exon	10897520	10897819	.	-	.	transcript_id "Phchi.S2G040400.t1"; gene_id "Phchi.S2G040400"
Phchi.S2	AUGUSTUS	start_codon	10897817	10897819	.	-	0	transcript_id "Phchi.S2G040400.t1"; gene_id "Phchi.S2G040400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5939.t1 is derived from g3110.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19955599	19957312	.	+	.	Phchi.S1G309800
Phchi.S1	AUGUSTUS	transcript	19955599	19957312	.	+	.	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	start_codon	19955599	19955601	.	+	0	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	CDS	19955599	19955979	1	+	0	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	exon	19955599	19955979	.	+	.	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	intron	19955980	19956064	.	+	.	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	CDS	19956065	19956565	0.75	+	0	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	exon	19956065	19956565	.	+	.	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	intron	19956566	19956664	.	+	.	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	CDS	19956665	19957312	1	+	0	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	exon	19956665	19957312	.	+	.	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
Phchi.S1	AUGUSTUS	stop_codon	19957313	19957315	.	+	0	transcript_id "Phchi.S1G309800.t1"; gene_id "Phchi.S1G309800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2310.t1 is derived from g9230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6008405	6009407	.	-	.	Phchi.S5G091900
Phchi.S5	AUGUSTUS	transcript	6008405	6009407	.	-	.	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	stop_codon	6008402	6008404	.	-	0	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	CDS	6008405	6008592	0.32	-	2	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	exon	6008405	6008592	.	-	.	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	intron	6008593	6008674	.	-	.	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	CDS	6008675	6009407	0.05	-	0	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	exon	6008675	6009407	.	-	.	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
Phchi.S5	AUGUSTUS	start_codon	6009405	6009407	.	-	0	transcript_id "Phchi.S5G091900.t1"; gene_id "Phchi.S5G091900"
# This transcript jg4152.t2 is derived from g1321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4153.t1 is derived from g1322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8656348	8657610	.	+	.	Phchi.S1G131200
Phchi.S1	AUGUSTUS	transcript	8656348	8657610	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	start_codon	8656348	8656350	.	+	0	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	CDS	8656348	8656618	0.97	+	0	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	exon	8656348	8656618	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	intron	8656619	8656714	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	CDS	8656715	8656851	1	+	2	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	exon	8656715	8656851	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	intron	8656852	8656966	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	CDS	8656967	8657112	1	+	0	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	exon	8656967	8657112	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	intron	8657113	8657201	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	CDS	8657202	8657228	0.47	+	1	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	exon	8657202	8657228	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	intron	8657229	8657290	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	CDS	8657291	8657427	0.47	+	1	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	exon	8657291	8657427	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	intron	8657428	8657518	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	CDS	8657519	8657610	0.99	+	2	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	exon	8657519	8657610	.	+	.	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
Phchi.S1	AUGUSTUS	stop_codon	8657611	8657613	.	+	0	transcript_id "Phchi.S1G131200.t1"; gene_id "Phchi.S1G131200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11324.t1 is derived from g15374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5369951	5371001	.	-	.	Phchi.S4G090600
Phchi.S4	AUGUSTUS	transcript	5369951	5371001	.	-	.	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	stop_codon	5369948	5369950	.	-	0	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	CDS	5369951	5370631	0.62	-	0	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	exon	5369951	5370631	.	-	.	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	intron	5370632	5370744	.	-	.	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	CDS	5370745	5370788	0.96	-	2	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	exon	5370745	5370788	.	-	.	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	intron	5370789	5370883	.	-	.	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	CDS	5370884	5371001	0.94	-	0	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	exon	5370884	5371001	.	-	.	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
Phchi.S4	AUGUSTUS	start_codon	5370999	5371001	.	-	0	transcript_id "Phchi.S4G090600.t1"; gene_id "Phchi.S4G090600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5089.t1 is derived from g2259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14701531	14701812	.	+	.	Phchi.S1G224800
Phchi.S1	AUGUSTUS	transcript	14701531	14701812	.	+	.	transcript_id "Phchi.S1G224800.t1"; gene_id "Phchi.S1G224800"
Phchi.S1	AUGUSTUS	start_codon	14701531	14701533	.	+	0	transcript_id "Phchi.S1G224800.t1"; gene_id "Phchi.S1G224800"
Phchi.S1	AUGUSTUS	CDS	14701531	14701812	0.56	+	0	transcript_id "Phchi.S1G224800.t1"; gene_id "Phchi.S1G224800"
Phchi.S1	AUGUSTUS	exon	14701531	14701812	.	+	.	transcript_id "Phchi.S1G224800.t1"; gene_id "Phchi.S1G224800"
Phchi.S1	AUGUSTUS	stop_codon	14701813	14701815	.	+	0	transcript_id "Phchi.S1G224800.t1"; gene_id "Phchi.S1G224800"
# This transcript jg1341.t2 is derived from g11124.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1342.t1 is derived from g11125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9115607	9117283	.	+	.	Phchi.S6G130100
Phchi.S6	AUGUSTUS	transcript	9115607	9117283	.	+	.	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	start_codon	9115607	9115609	.	+	0	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	CDS	9115607	9116344	0.85	+	0	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	exon	9115607	9116344	.	+	.	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	intron	9116345	9116647	.	+	.	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	CDS	9116648	9117283	1	+	0	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	exon	9116648	9117283	.	+	.	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
Phchi.S6	AUGUSTUS	stop_codon	9117284	9117286	.	+	0	transcript_id "Phchi.S6G130100.t1"; gene_id "Phchi.S6G130100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg973.t1 is derived from g10756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6738778	6740467	.	-	.	Phchi.S6G093200
Phchi.S6	AUGUSTUS	transcript	6738778	6740467	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	stop_codon	6738775	6738777	.	-	0	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	CDS	6738778	6739272	1	-	0	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	exon	6738778	6739272	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	intron	6739273	6739357	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	CDS	6739358	6739711	1	-	0	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	exon	6739358	6739711	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	intron	6739712	6739841	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	CDS	6739842	6739985	1	-	0	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	exon	6739842	6739985	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	intron	6739986	6740095	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	CDS	6740096	6740467	1	-	0	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	exon	6740096	6740467	.	-	.	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
Phchi.S6	AUGUSTUS	start_codon	6740465	6740467	.	-	0	transcript_id "Phchi.S6G093200.t1"; gene_id "Phchi.S6G093200"
# This transcript jg3957.t2 is derived from g1126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3958.t1 is derived from g1127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6706467	6707183	.	+	.	Phchi.S1G111700
Phchi.S1	AUGUSTUS	transcript	6706467	6707183	.	+	.	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	start_codon	6706467	6706469	.	+	0	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	CDS	6706467	6706685	0.81	+	0	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	exon	6706467	6706685	.	+	.	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	intron	6706686	6706892	.	+	.	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	CDS	6706893	6707183	0.99	+	0	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	exon	6706893	6707183	.	+	.	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
Phchi.S1	AUGUSTUS	stop_codon	6707184	6707186	.	+	0	transcript_id "Phchi.S1G111700.t1"; gene_id "Phchi.S1G111700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4556.t1 is derived from g1726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11104097	11104615	.	-	.	Phchi.S1G171500
Phchi.S1	AUGUSTUS	transcript	11104097	11104615	.	-	.	transcript_id "Phchi.S1G171500.t1"; gene_id "Phchi.S1G171500"
Phchi.S1	AUGUSTUS	stop_codon	11104094	11104096	.	-	0	transcript_id "Phchi.S1G171500.t1"; gene_id "Phchi.S1G171500"
Phchi.S1	AUGUSTUS	CDS	11104097	11104615	0.8	-	0	transcript_id "Phchi.S1G171500.t1"; gene_id "Phchi.S1G171500"
Phchi.S1	AUGUSTUS	exon	11104097	11104615	.	-	.	transcript_id "Phchi.S1G171500.t1"; gene_id "Phchi.S1G171500"
Phchi.S1	AUGUSTUS	start_codon	11104613	11104615	.	-	0	transcript_id "Phchi.S1G171500.t1"; gene_id "Phchi.S1G171500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10431.t1 is derived from g14480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	239732	239992	.	+	.	Phchi.S4G001300
Phchi.S4	AUGUSTUS	transcript	239732	239992	.	+	.	transcript_id "Phchi.S4G001300.t1"; gene_id "Phchi.S4G001300"
Phchi.S4	AUGUSTUS	start_codon	239732	239734	.	+	0	transcript_id "Phchi.S4G001300.t1"; gene_id "Phchi.S4G001300"
Phchi.S4	AUGUSTUS	CDS	239732	239992	0.64	+	0	transcript_id "Phchi.S4G001300.t1"; gene_id "Phchi.S4G001300"
Phchi.S4	AUGUSTUS	exon	239732	239992	.	+	.	transcript_id "Phchi.S4G001300.t1"; gene_id "Phchi.S4G001300"
Phchi.S4	AUGUSTUS	stop_codon	239993	239995	.	+	0	transcript_id "Phchi.S4G001300.t1"; gene_id "Phchi.S4G001300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg879.t1 is derived from g10661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6236537	6238635	.	+	.	Phchi.S6G083800
Phchi.S6	AUGUSTUS	transcript	6236537	6238635	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	start_codon	6236537	6236539	.	+	0	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	CDS	6236537	6236708	0.8	+	0	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	exon	6236537	6236708	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	intron	6236709	6236793	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	CDS	6236794	6236848	1	+	2	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	exon	6236794	6236848	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	intron	6236849	6236983	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	CDS	6236984	6237529	0.78	+	1	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	exon	6236984	6237529	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	intron	6237530	6237617	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	CDS	6237618	6238477	0.4	+	1	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	exon	6237618	6238477	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	intron	6238478	6238525	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	CDS	6238526	6238635	1	+	2	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	exon	6238526	6238635	.	+	.	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
Phchi.S6	AUGUSTUS	stop_codon	6238636	6238638	.	+	0	transcript_id "Phchi.S6G083800.t1"; gene_id "Phchi.S6G083800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2052.t1 is derived from g8972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4623824	4625758	.	-	.	Phchi.S5G066100
Phchi.S5	AUGUSTUS	transcript	4623824	4625758	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	stop_codon	4623821	4623823	.	-	0	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4623824	4623865	1	-	0	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4623824	4623865	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4623866	4623957	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4623958	4624057	1	-	1	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4623958	4624057	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4624058	4624179	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4624180	4624352	1	-	0	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4624180	4624352	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4624353	4624448	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4624449	4624605	1	-	1	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4624449	4624605	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4624606	4624700	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4624701	4624801	1	-	0	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4624701	4624801	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4624802	4624911	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4624912	4625054	0.67	-	2	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4624912	4625054	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4625055	4625275	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4625276	4625310	0.67	-	1	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4625276	4625310	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4625311	4625434	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4625435	4625495	0.52	-	2	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4625435	4625495	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	intron	4625496	4625634	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	CDS	4625635	4625758	0.6	-	0	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	exon	4625635	4625758	.	-	.	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
Phchi.S5	AUGUSTUS	start_codon	4625756	4625758	.	-	0	transcript_id "Phchi.S5G066100.t1"; gene_id "Phchi.S5G066100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7730.t1 is derived from g4904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30878302	30880964	.	+	.	Phchi.S1G488900
Phchi.S1	AUGUSTUS	transcript	30878302	30880964	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	start_codon	30878302	30878304	.	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30878302	30878314	0.99	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30878302	30878314	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30878315	30878392	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30878393	30878448	0.78	+	2	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30878393	30878448	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30878449	30878584	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30878585	30878721	0.42	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30878585	30878721	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30878722	30878865	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30878866	30879100	1	+	1	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30878866	30879100	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30879101	30879189	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30879190	30879444	1	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30879190	30879444	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30879445	30879583	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30879584	30879720	1	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30879584	30879720	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30879721	30879801	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30879802	30879985	1	+	1	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30879802	30879985	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30879986	30880065	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30880066	30880253	1	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30880066	30880253	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30880254	30880337	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30880338	30880542	1	+	1	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30880338	30880542	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30880543	30880625	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30880626	30880731	1	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30880626	30880731	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	intron	30880732	30880815	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	CDS	30880816	30880964	1	+	2	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	exon	30880816	30880964	.	+	.	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
Phchi.S1	AUGUSTUS	stop_codon	30880965	30880967	.	+	0	transcript_id "Phchi.S1G488900.t1"; gene_id "Phchi.S1G488900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9709.t1 is derived from g6885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43363657	43365416	.	-	.	Phchi.S1G686800
Phchi.S1	AUGUSTUS	transcript	43363657	43365416	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	stop_codon	43363654	43363656	.	-	0	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	CDS	43363657	43364001	1	-	0	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	exon	43363657	43364001	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	intron	43364002	43364102	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	CDS	43364103	43364507	1	-	0	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	exon	43364103	43364507	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	intron	43364508	43364595	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	CDS	43364596	43364769	1	-	0	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	exon	43364596	43364769	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	intron	43364770	43364891	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	CDS	43364892	43365416	0.78	-	0	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	exon	43364892	43365416	.	-	.	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
Phchi.S1	AUGUSTUS	start_codon	43365414	43365416	.	-	0	transcript_id "Phchi.S1G686800.t1"; gene_id "Phchi.S1G686800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7468.t1 is derived from g4641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29525172	29526570	.	+	.	Phchi.S1G462700
Phchi.S1	AUGUSTUS	transcript	29525172	29526570	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	start_codon	29525172	29525174	.	+	0	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	CDS	29525172	29525608	0.98	+	0	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	exon	29525172	29525608	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	intron	29525609	29525936	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	CDS	29525937	29526273	0.97	+	1	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	exon	29525937	29526273	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	intron	29526274	29526357	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	CDS	29526358	29526410	0.98	+	0	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	exon	29526358	29526410	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	intron	29526411	29526515	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	CDS	29526516	29526570	0.99	+	1	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	exon	29526516	29526570	.	+	.	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
Phchi.S1	AUGUSTUS	stop_codon	29526571	29526573	.	+	0	transcript_id "Phchi.S1G462700.t1"; gene_id "Phchi.S1G462700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4816.t1 is derived from g1986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12973137	12973973	.	+	.	Phchi.S1G197500
Phchi.S1	AUGUSTUS	transcript	12973137	12973973	.	+	.	transcript_id "Phchi.S1G197500.t1"; gene_id "Phchi.S1G197500"
Phchi.S1	AUGUSTUS	start_codon	12973137	12973139	.	+	0	transcript_id "Phchi.S1G197500.t1"; gene_id "Phchi.S1G197500"
Phchi.S1	AUGUSTUS	CDS	12973137	12973973	0.5	+	0	transcript_id "Phchi.S1G197500.t1"; gene_id "Phchi.S1G197500"
Phchi.S1	AUGUSTUS	exon	12973137	12973973	.	+	.	transcript_id "Phchi.S1G197500.t1"; gene_id "Phchi.S1G197500"
Phchi.S1	AUGUSTUS	stop_codon	12973974	12973976	.	+	0	transcript_id "Phchi.S1G197500.t1"; gene_id "Phchi.S1G197500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2806.t1 is derived from g9726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8964069	8964626	.	+	.	Phchi.S5G141500
Phchi.S5	AUGUSTUS	transcript	8964069	8964626	.	+	.	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	start_codon	8964069	8964071	.	+	0	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	CDS	8964069	8964210	0.41	+	0	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	exon	8964069	8964210	.	+	.	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	intron	8964211	8964350	.	+	.	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	CDS	8964351	8964501	0.43	+	2	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	exon	8964351	8964501	.	+	.	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	intron	8964502	8964592	.	+	.	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	CDS	8964593	8964626	0.9	+	1	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	exon	8964593	8964626	.	+	.	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
Phchi.S5	AUGUSTUS	stop_codon	8964627	8964629	.	+	0	transcript_id "Phchi.S5G141500.t1"; gene_id "Phchi.S5G141500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg339.t1 is derived from g10121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2478075	2478740	.	+	.	Phchi.S6G029800
Phchi.S6	AUGUSTUS	transcript	2478075	2478740	.	+	.	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	start_codon	2478075	2478077	.	+	0	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	CDS	2478075	2478329	0.98	+	0	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	exon	2478075	2478329	.	+	.	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	intron	2478330	2478449	.	+	.	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	CDS	2478450	2478740	0.98	+	0	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	exon	2478450	2478740	.	+	.	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
Phchi.S6	AUGUSTUS	stop_codon	2478741	2478743	.	+	0	transcript_id "Phchi.S6G029800.t1"; gene_id "Phchi.S6G029800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12217.t1 is derived from g7893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6805588	6810244	.	-	.	Phchi.S2G029700
Phchi.S2	AUGUSTUS	transcript	6805588	6810244	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	stop_codon	6805585	6805587	.	-	0	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6805588	6805601	0.9	-	2	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6805588	6805601	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6805602	6805684	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6805685	6805707	0.86	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6805685	6805707	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6805708	6805790	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6805791	6806119	0.89	-	0	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6805791	6806119	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6806120	6806283	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6806284	6806416	1	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6806284	6806416	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6806417	6806525	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6806526	6806715	1	-	2	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6806526	6806715	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6806716	6806847	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6806848	6806916	1	-	2	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6806848	6806916	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6806917	6807001	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6807002	6807013	1	-	2	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6807002	6807013	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6807014	6807078	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6807079	6807127	1	-	0	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6807079	6807127	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6807128	6807224	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6807225	6807457	1	-	2	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6807225	6807457	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6807458	6807542	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6807543	6807712	1	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6807543	6807712	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6807713	6807786	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6807787	6807867	1	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6807787	6807867	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6807868	6807963	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6807964	6808035	1	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6807964	6808035	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6808036	6808135	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6808136	6808207	0.99	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6808136	6808207	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6808208	6808314	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6808315	6808386	1	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6808315	6808386	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6808387	6808643	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6808644	6808788	1	-	2	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6808644	6808788	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6808789	6808995	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6808996	6809465	0.99	-	1	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6808996	6809465	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	intron	6809466	6809675	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	CDS	6809676	6810244	0.88	-	0	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	exon	6809676	6810244	.	-	.	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
Phchi.S2	AUGUSTUS	start_codon	6810242	6810244	.	-	0	transcript_id "Phchi.S2G029700.t1"; gene_id "Phchi.S2G029700"
# This transcript jg6002.t2 is derived from g3173.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6003.t1 is derived from g3174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20346323	20347676	.	-	.	Phchi.S1G316200
Phchi.S1	AUGUSTUS	transcript	20346323	20347676	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	stop_codon	20346320	20346322	.	-	0	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	CDS	20346323	20346586	0.96	-	0	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	exon	20346323	20346586	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	intron	20346587	20346684	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	CDS	20346685	20346864	1	-	0	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	exon	20346685	20346864	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	intron	20346865	20347094	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	CDS	20347095	20347172	0.96	-	0	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	exon	20347095	20347172	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	intron	20347173	20347251	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	CDS	20347252	20347510	0.96	-	1	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	exon	20347252	20347510	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	intron	20347511	20347656	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	CDS	20347657	20347676	0.91	-	0	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	exon	20347657	20347676	.	-	.	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
Phchi.S1	AUGUSTUS	start_codon	20347674	20347676	.	-	0	transcript_id "Phchi.S1G316200.t1"; gene_id "Phchi.S1G316200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2543.t1 is derived from g9463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7254070	7254811	.	+	.	Phchi.S5G115200
Phchi.S5	AUGUSTUS	transcript	7254070	7254811	.	+	.	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	start_codon	7254070	7254072	.	+	0	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	CDS	7254070	7254158	0.91	+	0	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	exon	7254070	7254158	.	+	.	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	intron	7254159	7254535	.	+	.	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	CDS	7254536	7254613	1	+	1	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	exon	7254536	7254613	.	+	.	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	intron	7254614	7254708	.	+	.	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	CDS	7254709	7254811	1	+	1	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	exon	7254709	7254811	.	+	.	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
Phchi.S5	AUGUSTUS	stop_codon	7254812	7254814	.	+	0	transcript_id "Phchi.S5G115200.t1"; gene_id "Phchi.S5G115200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13392.t1 is derived from g11858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6514160	6515401	.	+	.	Phchi.S3G071100
Phchi.S3	AUGUSTUS	transcript	6514160	6515401	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	start_codon	6514160	6514162	.	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6514160	6514162	0.98	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6514160	6514162	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	intron	6514163	6514322	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6514323	6514359	1	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6514323	6514359	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	intron	6514360	6514449	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6514450	6514490	1	+	2	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6514450	6514490	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	intron	6514491	6514626	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6514627	6514857	1	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6514627	6514857	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	intron	6514858	6514973	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6514974	6515076	1	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6514974	6515076	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	intron	6515077	6515169	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6515170	6515237	1	+	2	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6515170	6515237	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	intron	6515238	6515335	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	CDS	6515336	6515401	1	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	exon	6515336	6515401	.	+	.	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
Phchi.S3	AUGUSTUS	stop_codon	6515402	6515404	.	+	0	transcript_id "Phchi.S3G071100.t1"; gene_id "Phchi.S3G071100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5716.t1 is derived from g2886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18497942	18499746	.	-	.	Phchi.S1G287500
Phchi.S1	AUGUSTUS	transcript	18497942	18499746	.	-	.	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	stop_codon	18497939	18497941	.	-	0	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	CDS	18497942	18498163	1	-	0	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	exon	18497942	18498163	.	-	.	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	intron	18498164	18498783	.	-	.	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	CDS	18498784	18499746	1	-	0	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	exon	18498784	18499746	.	-	.	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
Phchi.S1	AUGUSTUS	start_codon	18499744	18499746	.	-	0	transcript_id "Phchi.S1G287500.t1"; gene_id "Phchi.S1G287500"
# This transcript jg8573.t2 is derived from g5748.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8573.t3 is derived from g5748.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8574.t1 is derived from g5749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36702288	36703204	.	+	.	Phchi.S1G573300
Phchi.S1	AUGUSTUS	transcript	36702288	36703204	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	start_codon	36702288	36702290	.	+	0	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	CDS	36702288	36702291	1	+	0	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	exon	36702288	36702291	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	intron	36702292	36702372	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	CDS	36702373	36702410	1	+	2	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	exon	36702373	36702410	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	intron	36702411	36702500	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	CDS	36702501	36702608	1	+	0	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	exon	36702501	36702608	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	intron	36702609	36702804	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	CDS	36702805	36702859	1	+	0	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	exon	36702805	36702859	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	intron	36702860	36702939	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	CDS	36702940	36703072	1	+	2	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	exon	36702940	36703072	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	intron	36703073	36703167	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	CDS	36703168	36703204	0.98	+	1	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	exon	36703168	36703204	.	+	.	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
Phchi.S1	AUGUSTUS	stop_codon	36703205	36703207	.	+	0	transcript_id "Phchi.S1G573300.t1"; gene_id "Phchi.S1G573300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10787.t1 is derived from g14837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2117656	2118412	.	-	.	Phchi.S4G036900
Phchi.S4	AUGUSTUS	transcript	2117656	2118412	.	-	.	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	stop_codon	2117653	2117655	.	-	0	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	CDS	2117656	2117701	1	-	1	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	exon	2117656	2117701	.	-	.	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	intron	2117702	2118242	.	-	.	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	CDS	2118243	2118412	1	-	0	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	exon	2118243	2118412	.	-	.	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
Phchi.S4	AUGUSTUS	start_codon	2118410	2118412	.	-	0	transcript_id "Phchi.S4G036900.t1"; gene_id "Phchi.S4G036900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9046.t1 is derived from g6221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39367698	39368378	.	-	.	Phchi.S1G620500
Phchi.S1	AUGUSTUS	transcript	39367698	39368378	.	-	.	transcript_id "Phchi.S1G620500.t1"; gene_id "Phchi.S1G620500"
Phchi.S1	AUGUSTUS	stop_codon	39367695	39367697	.	-	0	transcript_id "Phchi.S1G620500.t1"; gene_id "Phchi.S1G620500"
Phchi.S1	AUGUSTUS	CDS	39367698	39368378	0.99	-	0	transcript_id "Phchi.S1G620500.t1"; gene_id "Phchi.S1G620500"
Phchi.S1	AUGUSTUS	exon	39367698	39368378	.	-	.	transcript_id "Phchi.S1G620500.t1"; gene_id "Phchi.S1G620500"
Phchi.S1	AUGUSTUS	start_codon	39368376	39368378	.	-	0	transcript_id "Phchi.S1G620500.t1"; gene_id "Phchi.S1G620500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6026.t1 is derived from g3197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20499370	20500468	.	+	.	Phchi.S1G318500
Phchi.S1	AUGUSTUS	transcript	20499370	20500468	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	start_codon	20499370	20499372	.	+	0	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	CDS	20499370	20499389	0.74	+	0	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	exon	20499370	20499389	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	intron	20499390	20499489	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	CDS	20499490	20499751	1	+	1	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	exon	20499490	20499751	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	intron	20499752	20499853	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	CDS	20499854	20500027	1	+	0	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	exon	20499854	20500027	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	intron	20500028	20500096	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	CDS	20500097	20500468	1	+	0	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	exon	20500097	20500468	.	+	.	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
Phchi.S1	AUGUSTUS	stop_codon	20500469	20500471	.	+	0	transcript_id "Phchi.S1G318500.t1"; gene_id "Phchi.S1G318500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4644.t1 is derived from g1814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11614996	11615625	.	+	.	Phchi.S1G180300
Phchi.S1	AUGUSTUS	transcript	11614996	11615625	.	+	.	transcript_id "Phchi.S1G180300.t1"; gene_id "Phchi.S1G180300"
Phchi.S1	AUGUSTUS	start_codon	11614996	11614998	.	+	0	transcript_id "Phchi.S1G180300.t1"; gene_id "Phchi.S1G180300"
Phchi.S1	AUGUSTUS	CDS	11614996	11615625	0.62	+	0	transcript_id "Phchi.S1G180300.t1"; gene_id "Phchi.S1G180300"
Phchi.S1	AUGUSTUS	exon	11614996	11615625	.	+	.	transcript_id "Phchi.S1G180300.t1"; gene_id "Phchi.S1G180300"
Phchi.S1	AUGUSTUS	stop_codon	11615626	11615628	.	+	0	transcript_id "Phchi.S1G180300.t1"; gene_id "Phchi.S1G180300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6745.t1 is derived from g3918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24829115	24829621	.	+	.	Phchi.S1G390400
Phchi.S1	AUGUSTUS	transcript	24829115	24829621	.	+	.	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	start_codon	24829115	24829117	.	+	0	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	CDS	24829115	24829328	0.74	+	0	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	exon	24829115	24829328	.	+	.	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	intron	24829329	24829417	.	+	.	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	CDS	24829418	24829524	1	+	2	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	exon	24829418	24829524	.	+	.	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	intron	24829525	24829600	.	+	.	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	CDS	24829601	24829621	0.74	+	0	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	exon	24829601	24829621	.	+	.	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
Phchi.S1	AUGUSTUS	stop_codon	24829622	24829624	.	+	0	transcript_id "Phchi.S1G390400.t1"; gene_id "Phchi.S1G390400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7279.t1 is derived from g4451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28109135	28110036	.	+	.	Phchi.S1G443800
Phchi.S1	AUGUSTUS	transcript	28109135	28110036	.	+	.	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	start_codon	28109135	28109137	.	+	0	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	CDS	28109135	28109539	0.52	+	0	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	exon	28109135	28109539	.	+	.	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	intron	28109540	28109751	.	+	.	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	CDS	28109752	28110036	1	+	0	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	exon	28109752	28110036	.	+	.	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
Phchi.S1	AUGUSTUS	stop_codon	28110037	28110039	.	+	0	transcript_id "Phchi.S1G443800.t1"; gene_id "Phchi.S1G443800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12042.t1 is derived from g7717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	903255	904476	.	-	.	Phchi.S2G012200
Phchi.S2	AUGUSTUS	transcript	903255	904476	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	stop_codon	903252	903254	.	-	0	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	CDS	903255	903505	1	-	2	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	exon	903255	903505	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	intron	903506	903663	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	CDS	903664	903777	1	-	2	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	exon	903664	903777	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	intron	903778	903867	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	CDS	903868	903956	1	-	1	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	exon	903868	903956	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	intron	903957	904053	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	CDS	904054	904109	0.58	-	0	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	exon	904054	904109	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	intron	904110	904266	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	CDS	904267	904476	0.61	-	0	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	exon	904267	904476	.	-	.	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
Phchi.S2	AUGUSTUS	start_codon	904474	904476	.	-	0	transcript_id "Phchi.S2G012200.t1"; gene_id "Phchi.S2G012200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10693.t1 is derived from g14743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1621435	1622388	.	-	.	Phchi.S4G027500
Phchi.S4	AUGUSTUS	transcript	1621435	1622388	.	-	.	transcript_id "Phchi.S4G027500.t1"; gene_id "Phchi.S4G027500"
Phchi.S4	AUGUSTUS	stop_codon	1621432	1621434	.	-	0	transcript_id "Phchi.S4G027500.t1"; gene_id "Phchi.S4G027500"
Phchi.S4	AUGUSTUS	CDS	1621435	1622388	0.6	-	0	transcript_id "Phchi.S4G027500.t1"; gene_id "Phchi.S4G027500"
Phchi.S4	AUGUSTUS	exon	1621435	1622388	.	-	.	transcript_id "Phchi.S4G027500.t1"; gene_id "Phchi.S4G027500"
Phchi.S4	AUGUSTUS	start_codon	1622386	1622388	.	-	0	transcript_id "Phchi.S4G027500.t1"; gene_id "Phchi.S4G027500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13302.t1 is derived from g11768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5596923	5597620	.	+	.	Phchi.S3G062100
Phchi.S3	AUGUSTUS	transcript	5596923	5597620	.	+	.	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	start_codon	5596923	5596925	.	+	0	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	CDS	5596923	5597414	0.83	+	0	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	exon	5596923	5597414	.	+	.	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	intron	5597415	5597602	.	+	.	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	CDS	5597603	5597620	1	+	0	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	exon	5597603	5597620	.	+	.	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
Phchi.S3	AUGUSTUS	stop_codon	5597621	5597623	.	+	0	transcript_id "Phchi.S3G062100.t1"; gene_id "Phchi.S3G062100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8244.t1 is derived from g5419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34674774	34676283	.	+	.	Phchi.S1G540300
Phchi.S1	AUGUSTUS	transcript	34674774	34676283	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	start_codon	34674774	34674776	.	+	0	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34674774	34674881	0.95	+	0	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34674774	34674881	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	intron	34674882	34675039	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34675040	34675121	1	+	0	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34675040	34675121	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	intron	34675122	34675325	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34675326	34675385	1	+	2	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34675326	34675385	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	intron	34675386	34675493	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34675494	34675581	1	+	2	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34675494	34675581	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	intron	34675582	34675660	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34675661	34675736	1	+	1	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34675661	34675736	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	intron	34675737	34675813	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34675814	34675878	1	+	0	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34675814	34675878	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	intron	34675879	34675958	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	CDS	34675959	34676283	0.99	+	1	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	exon	34675959	34676283	.	+	.	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
Phchi.S1	AUGUSTUS	stop_codon	34676284	34676286	.	+	0	transcript_id "Phchi.S1G540300.t1"; gene_id "Phchi.S1G540300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12661.t1 is derived from g14460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	44535	45091	.	-	.	Phchi.C12G001100
Phchi.C12	AUGUSTUS	transcript	44535	45091	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	stop_codon	44532	44534	.	-	0	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	CDS	44535	44648	1	-	0	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	exon	44535	44648	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	intron	44649	44730	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	CDS	44731	44845	0.98	-	1	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	exon	44731	44845	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	intron	44846	44983	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	CDS	44984	44988	0.98	-	0	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	exon	44984	44988	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	intron	44989	45067	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	CDS	45068	45091	0.5	-	0	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	exon	45068	45091	.	-	.	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
Phchi.C12	AUGUSTUS	start_codon	45089	45091	.	-	0	transcript_id "Phchi.C12G001100.t1"; gene_id "Phchi.C12G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11601.t1 is derived from g15652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7283937	7285843	.	-	.	Phchi.S4G118300
Phchi.S4	AUGUSTUS	transcript	7283937	7285843	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	stop_codon	7283934	7283936	.	-	0	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7283937	7284040	1	-	2	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7283937	7284040	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	intron	7284041	7284164	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7284165	7284341	1	-	2	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7284165	7284341	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	intron	7284342	7284430	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7284431	7284657	1	-	1	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7284431	7284657	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	intron	7284658	7284746	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7284747	7284838	1	-	0	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7284747	7284838	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	intron	7284839	7284958	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7284959	7285012	1	-	0	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7284959	7285012	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	intron	7285013	7285091	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7285092	7285242	1	-	1	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7285092	7285242	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	intron	7285243	7285460	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	CDS	7285461	7285843	0.57	-	0	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	exon	7285461	7285843	.	-	.	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
Phchi.S4	AUGUSTUS	start_codon	7285841	7285843	.	-	0	transcript_id "Phchi.S4G118300.t1"; gene_id "Phchi.S4G118300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7018.t1 is derived from g4190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26414625	26416158	.	-	.	Phchi.S1G417700
Phchi.S1	AUGUSTUS	transcript	26414625	26416158	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	stop_codon	26414622	26414624	.	-	0	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	CDS	26414625	26414689	0.29	-	2	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	exon	26414625	26414689	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	intron	26414690	26414889	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	CDS	26414890	26415028	1	-	0	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	exon	26414890	26415028	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	intron	26415029	26415167	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	CDS	26415168	26415228	0.81	-	1	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	exon	26415168	26415228	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	intron	26415229	26415487	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	CDS	26415488	26415498	0.49	-	0	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	exon	26415488	26415498	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	intron	26415499	26415640	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	CDS	26415641	26415746	0.92	-	1	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	exon	26415641	26415746	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	intron	26415747	26416045	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	CDS	26416046	26416158	0.91	-	0	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	exon	26416046	26416158	.	-	.	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
Phchi.S1	AUGUSTUS	start_codon	26416156	26416158	.	-	0	transcript_id "Phchi.S1G417700.t1"; gene_id "Phchi.S1G417700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13590.t1 is derived from g12057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7609806	7610577	.	-	.	Phchi.S3G090900
Phchi.S3	AUGUSTUS	transcript	7609806	7610577	.	-	.	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	stop_codon	7609803	7609805	.	-	0	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	CDS	7609806	7609918	0.59	-	2	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	exon	7609806	7609918	.	-	.	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	intron	7609919	7610019	.	-	.	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	CDS	7610020	7610155	0.53	-	0	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	exon	7610020	7610155	.	-	.	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	intron	7610156	7610283	.	-	.	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	CDS	7610284	7610577	0.53	-	0	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	exon	7610284	7610577	.	-	.	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
Phchi.S3	AUGUSTUS	start_codon	7610575	7610577	.	-	0	transcript_id "Phchi.S3G090900.t1"; gene_id "Phchi.S3G090900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2383.t1 is derived from g9303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6439994	6442489	.	+	.	Phchi.S5G099200
Phchi.S5	AUGUSTUS	transcript	6439994	6442489	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	start_codon	6439994	6439996	.	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6439994	6440060	0.97	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6439994	6440060	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6440061	6440149	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6440150	6440274	1	+	2	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6440150	6440274	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6440275	6440363	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6440364	6440492	0.66	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6440364	6440492	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6440493	6440599	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6440600	6440707	1	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6440600	6440707	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6440708	6440796	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6440797	6440888	1	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6440797	6440888	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6440889	6440988	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6440989	6441130	1	+	1	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6440989	6441130	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6441131	6441264	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6441265	6441359	1	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6441265	6441359	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6441360	6441456	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6441457	6441586	1	+	1	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6441457	6441586	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6441587	6441675	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6441676	6441820	1	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6441676	6441820	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6441821	6441973	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6441974	6442070	0.92	+	2	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6441974	6442070	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6442071	6442351	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6442352	6442396	0.88	+	1	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6442352	6442396	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	intron	6442397	6442482	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	CDS	6442483	6442489	0.99	+	1	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	exon	6442483	6442489	.	+	.	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
Phchi.S5	AUGUSTUS	stop_codon	6442490	6442492	.	+	0	transcript_id "Phchi.S5G099200.t1"; gene_id "Phchi.S5G099200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13964.t1 is derived from g12431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9951713	9953080	.	+	.	Phchi.S3G128300
Phchi.S3	AUGUSTUS	transcript	9951713	9953080	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	start_codon	9951713	9951715	.	+	0	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	CDS	9951713	9951910	0.59	+	0	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	exon	9951713	9951910	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	intron	9951911	9952021	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	CDS	9952022	9952284	1	+	0	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	exon	9952022	9952284	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	intron	9952285	9952379	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	CDS	9952380	9952707	1	+	1	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	exon	9952380	9952707	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	intron	9952708	9952795	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	CDS	9952796	9953080	1	+	0	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	exon	9952796	9953080	.	+	.	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
Phchi.S3	AUGUSTUS	stop_codon	9953081	9953083	.	+	0	transcript_id "Phchi.S3G128300.t1"; gene_id "Phchi.S3G128300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6001.t1 is derived from g3172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20340476	20341701	.	-	.	Phchi.S1G316000
Phchi.S1	AUGUSTUS	transcript	20340476	20341701	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	stop_codon	20340473	20340475	.	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	CDS	20340476	20340487	0.92	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	exon	20340476	20340487	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	intron	20340488	20340614	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	CDS	20340615	20340680	0.92	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	exon	20340615	20340680	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	intron	20340681	20341065	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	CDS	20341066	20341152	0.99	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	exon	20341066	20341152	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	intron	20341153	20341244	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	CDS	20341245	20341266	0.97	-	1	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	exon	20341245	20341266	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	intron	20341267	20341396	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	CDS	20341397	20341494	0.95	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	exon	20341397	20341494	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	intron	20341495	20341662	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	CDS	20341663	20341701	0.56	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	exon	20341663	20341701	.	-	.	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
Phchi.S1	AUGUSTUS	start_codon	20341699	20341701	.	-	0	transcript_id "Phchi.S1G316000.t1"; gene_id "Phchi.S1G316000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10032.t1 is derived from g7208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45172933	45174674	.	-	.	Phchi.S1G719100
Phchi.S1	AUGUSTUS	transcript	45172933	45174674	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	stop_codon	45172930	45172932	.	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	CDS	45172933	45173163	1	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	exon	45172933	45173163	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	intron	45173164	45173252	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	CDS	45173253	45173324	1	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	exon	45173253	45173324	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	intron	45173325	45173412	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	CDS	45173413	45173988	0.97	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	exon	45173413	45173988	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	intron	45173989	45174071	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	CDS	45174072	45174119	1	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	exon	45174072	45174119	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	intron	45174120	45174233	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	CDS	45174234	45174338	1	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	exon	45174234	45174338	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	intron	45174339	45174548	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	CDS	45174549	45174674	1	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	exon	45174549	45174674	.	-	.	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
Phchi.S1	AUGUSTUS	start_codon	45174672	45174674	.	-	0	transcript_id "Phchi.S1G719100.t1"; gene_id "Phchi.S1G719100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1519.t1 is derived from g8438.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1510095	1518586	.	-	.	Phchi.S5G012800
Phchi.S5	AUGUSTUS	transcript	1510095	1518586	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	stop_codon	1510092	1510094	.	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510095	1510175	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510095	1510175	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510176	1510252	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510253	1510375	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510253	1510375	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510376	1510467	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510468	1510560	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510468	1510560	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510561	1510637	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510638	1510853	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510638	1510853	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510854	1510957	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510958	1511044	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510958	1511044	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511045	1511134	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511135	1511195	1	-	1	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511135	1511195	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511196	1511285	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511286	1511356	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511286	1511356	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511357	1511490	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511491	1511634	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511491	1511634	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511635	1511731	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511732	1511830	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511732	1511830	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511831	1511927	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511928	1512011	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511928	1512011	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512012	1512094	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512095	1512151	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512095	1512151	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512152	1512239	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512240	1512329	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512240	1512329	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512330	1512452	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512453	1512593	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512453	1512593	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512594	1512680	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512681	1512785	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512681	1512785	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512786	1512915	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512916	1513068	0.99	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512916	1513068	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1513069	1513175	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1513176	1513277	0.98	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1513176	1513277	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1513278	1513665	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1513666	1513818	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1513666	1513818	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1513819	1513911	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1513912	1514089	1	-	1	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1513912	1514089	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514090	1514223	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514224	1514303	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514224	1514303	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514304	1514403	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514404	1514469	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514404	1514469	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514470	1514649	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514650	1514707	1	-	1	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514650	1514707	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514708	1514783	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514784	1514884	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514784	1514884	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514885	1515056	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515057	1515143	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515057	1515143	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515144	1515243	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515244	1515366	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515244	1515366	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515367	1515500	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515501	1515580	0.99	-	2	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515501	1515580	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515581	1515690	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515691	1515873	1	-	2	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515691	1515873	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515874	1515998	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515999	1516113	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515999	1516113	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1516114	1516228	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1516229	1516453	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1516229	1516453	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1516454	1516555	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1516556	1517013	0.95	-	2	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1516556	1517013	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517014	1517124	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517125	1517275	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517125	1517275	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517276	1517470	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517471	1517518	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517471	1517518	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517519	1517656	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517657	1517713	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517657	1517713	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517714	1517798	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517799	1518013	0.95	-	2	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517799	1518013	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1518014	1518093	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1518094	1518199	0.96	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1518094	1518199	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1518200	1518304	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1518305	1518586	1	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1518305	1518586	.	-	.	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	start_codon	1518584	1518586	.	-	0	transcript_id "Phchi.S5G012800.t1"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	transcript	1510095	1516398	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	stop_codon	1510092	1510094	.	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510095	1510175	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510095	1510175	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510176	1510252	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510253	1510375	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510253	1510375	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510376	1510467	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510468	1510560	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510468	1510560	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510561	1510637	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510638	1510853	0.98	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510638	1510853	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1510854	1510957	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1510958	1511044	0.98	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1510958	1511044	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511045	1511134	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511135	1511195	1	-	1	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511135	1511195	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511196	1511285	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511286	1511356	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511286	1511356	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511357	1511490	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511491	1511634	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511491	1511634	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511635	1511731	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511732	1511830	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511732	1511830	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1511831	1511927	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1511928	1512011	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1511928	1512011	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512012	1512094	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512095	1512151	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512095	1512151	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512152	1512239	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512240	1512329	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512240	1512329	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512330	1512452	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512453	1512593	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512453	1512593	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512594	1512680	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512681	1512785	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512681	1512785	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1512786	1512915	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1512916	1513068	0.94	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1512916	1513068	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1513069	1513175	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1513176	1513277	0.99	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1513176	1513277	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1513278	1513665	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1513666	1513818	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1513666	1513818	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1513819	1513911	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1513912	1514089	1	-	1	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1513912	1514089	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514090	1514223	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514224	1514303	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514224	1514303	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514304	1514403	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514404	1514469	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514404	1514469	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514470	1514649	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514650	1514707	1	-	1	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514650	1514707	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514708	1514783	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1514784	1514884	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1514784	1514884	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1514885	1515056	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515057	1515143	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515057	1515143	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515144	1515243	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515244	1515366	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515244	1515366	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515367	1515500	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515501	1515580	1	-	2	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515501	1515580	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515581	1515690	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515691	1515873	1	-	2	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515691	1515873	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1515874	1515998	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1515999	1516113	1	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1515999	1516113	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1516114	1516362	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1516363	1516398	0.5	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1516363	1516398	.	-	.	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	start_codon	1516396	1516398	.	-	0	transcript_id "Phchi.S5G012800.t2"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	transcript	1516517	1518586	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	stop_codon	1516514	1516516	.	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1516517	1517013	0.42	-	2	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1516517	1517013	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517014	1517124	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517125	1517275	1	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517125	1517275	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517276	1517470	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517471	1517518	1	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517471	1517518	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517519	1517656	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517657	1517713	1	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517657	1517713	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1517714	1517798	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1517799	1518013	0.91	-	2	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1517799	1518013	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1518014	1518093	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1518094	1518199	0.95	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1518094	1518199	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	intron	1518200	1518304	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	CDS	1518305	1518586	0.99	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	exon	1518305	1518586	.	-	.	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
Phchi.S5	AUGUSTUS	start_codon	1518584	1518586	.	-	0	transcript_id "Phchi.S5G012800.t3"; gene_id "Phchi.S5G012800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5187.t1 is derived from g2357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15393290	15394159	.	+	.	Phchi.S1G234600
Phchi.S1	AUGUSTUS	transcript	15393290	15394159	.	+	.	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	start_codon	15393290	15393292	.	+	0	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	CDS	15393290	15393319	0.86	+	0	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	exon	15393290	15393319	.	+	.	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	intron	15393320	15393499	.	+	.	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	CDS	15393500	15394159	1	+	0	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	exon	15393500	15394159	.	+	.	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
Phchi.S1	AUGUSTUS	stop_codon	15394160	15394162	.	+	0	transcript_id "Phchi.S1G234600.t1"; gene_id "Phchi.S1G234600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1037.t1 is derived from g10820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7230444	7232341	.	-	.	Phchi.S6G099600
Phchi.S6	AUGUSTUS	transcript	7230444	7232341	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	stop_codon	7230441	7230443	.	-	0	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7230444	7230549	1	-	1	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7230444	7230549	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	intron	7230550	7230662	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7230663	7230800	1	-	1	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7230663	7230800	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	intron	7230801	7230901	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7230902	7231044	1	-	0	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7230902	7231044	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	intron	7231045	7231136	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7231137	7231356	1	-	1	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7231137	7231356	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	intron	7231357	7231452	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7231453	7231574	1	-	0	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7231453	7231574	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	intron	7231575	7231672	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7231673	7232055	1	-	2	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7231673	7232055	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	intron	7232056	7232133	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	CDS	7232134	7232341	0.99	-	0	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	exon	7232134	7232341	.	-	.	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
Phchi.S6	AUGUSTUS	start_codon	7232339	7232341	.	-	0	transcript_id "Phchi.S6G099600.t1"; gene_id "Phchi.S6G099600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9036.t1 is derived from g6211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39236916	39237609	.	+	.	Phchi.S1G619500
Phchi.S1	AUGUSTUS	transcript	39236916	39237609	.	+	.	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	start_codon	39236916	39236918	.	+	0	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	CDS	39236916	39237000	1	+	0	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	exon	39236916	39237000	.	+	.	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	intron	39237001	39237409	.	+	.	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	CDS	39237410	39237609	0.98	+	2	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	exon	39237410	39237609	.	+	.	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
Phchi.S1	AUGUSTUS	stop_codon	39237610	39237612	.	+	0	transcript_id "Phchi.S1G619500.t1"; gene_id "Phchi.S1G619500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7718.t1 is derived from g4892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30788342	30788785	.	+	.	Phchi.S1G487700
Phchi.S1	AUGUSTUS	transcript	30788342	30788785	.	+	.	transcript_id "Phchi.S1G487700.t1"; gene_id "Phchi.S1G487700"
Phchi.S1	AUGUSTUS	start_codon	30788342	30788344	.	+	0	transcript_id "Phchi.S1G487700.t1"; gene_id "Phchi.S1G487700"
Phchi.S1	AUGUSTUS	CDS	30788342	30788785	0.93	+	0	transcript_id "Phchi.S1G487700.t1"; gene_id "Phchi.S1G487700"
Phchi.S1	AUGUSTUS	exon	30788342	30788785	.	+	.	transcript_id "Phchi.S1G487700.t1"; gene_id "Phchi.S1G487700"
Phchi.S1	AUGUSTUS	stop_codon	30788786	30788788	.	+	0	transcript_id "Phchi.S1G487700.t1"; gene_id "Phchi.S1G487700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2601.t1 is derived from g9521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7711844	7712518	.	-	.	Phchi.S5G121000
Phchi.S5	AUGUSTUS	transcript	7711844	7712518	.	-	.	transcript_id "Phchi.S5G121000.t1"; gene_id "Phchi.S5G121000"
Phchi.S5	AUGUSTUS	stop_codon	7711841	7711843	.	-	0	transcript_id "Phchi.S5G121000.t1"; gene_id "Phchi.S5G121000"
Phchi.S5	AUGUSTUS	CDS	7711844	7712518	0.81	-	0	transcript_id "Phchi.S5G121000.t1"; gene_id "Phchi.S5G121000"
Phchi.S5	AUGUSTUS	exon	7711844	7712518	.	-	.	transcript_id "Phchi.S5G121000.t1"; gene_id "Phchi.S5G121000"
Phchi.S5	AUGUSTUS	start_codon	7712516	7712518	.	-	0	transcript_id "Phchi.S5G121000.t1"; gene_id "Phchi.S5G121000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4108.t1 is derived from g1277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7871267	7871709	.	-	.	Phchi.S1G126700
Phchi.S1	AUGUSTUS	transcript	7871267	7871709	.	-	.	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	stop_codon	7871264	7871266	.	-	0	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	CDS	7871267	7871377	1	-	0	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	exon	7871267	7871377	.	-	.	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	intron	7871378	7871468	.	-	.	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	CDS	7871469	7871548	1	-	2	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	exon	7871469	7871548	.	-	.	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	intron	7871549	7871639	.	-	.	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	CDS	7871640	7871709	0.57	-	0	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	exon	7871640	7871709	.	-	.	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
Phchi.S1	AUGUSTUS	start_codon	7871707	7871709	.	-	0	transcript_id "Phchi.S1G126700.t1"; gene_id "Phchi.S1G126700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg945.t1 is derived from g10727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6606177	6609906	.	+	.	Phchi.S6G090400
Phchi.S6	AUGUSTUS	transcript	6606177	6609906	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	start_codon	6606177	6606179	.	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6606177	6606662	0.82	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6606177	6606662	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6606663	6606876	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6606877	6607007	1	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6606877	6607007	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6607008	6607168	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6607169	6607212	1	+	1	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6607169	6607212	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6607213	6607311	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6607312	6607418	1	+	2	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6607312	6607418	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6607419	6607536	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6607537	6607615	1	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6607537	6607615	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6607616	6607710	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6607711	6608007	1	+	2	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6607711	6608007	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6608008	6608104	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6608105	6608214	0.98	+	2	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6608105	6608214	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6608215	6608320	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6608321	6608428	1	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6608321	6608428	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6608429	6608529	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6608530	6608592	0.97	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6608530	6608592	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6608593	6608700	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6608701	6608868	1	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6608701	6608868	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6608869	6608960	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6608961	6609011	0.76	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6608961	6609011	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6609012	6609139	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6609140	6609203	0.56	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6609140	6609203	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6609204	6609347	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6609348	6609446	0.4	+	2	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6609348	6609446	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6609447	6609594	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6609595	6609712	0.28	+	2	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6609595	6609712	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	intron	6609713	6609806	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	CDS	6609807	6609906	0.56	+	1	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	exon	6609807	6609906	.	+	.	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
Phchi.S6	AUGUSTUS	stop_codon	6609907	6609909	.	+	0	transcript_id "Phchi.S6G090400.t1"; gene_id "Phchi.S6G090400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13176.t1 is derived from g11641.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4505316	4507690	.	-	.	Phchi.S3G049500
Phchi.S3	AUGUSTUS	transcript	4505316	4507690	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	stop_codon	4505313	4505315	.	-	0	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	CDS	4505316	4505337	0.57	-	1	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	exon	4505316	4505337	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	intron	4505338	4505429	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	CDS	4505430	4507307	0.36	-	1	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	exon	4505430	4507307	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	intron	4507308	4507504	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	CDS	4507505	4507530	0.38	-	0	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	exon	4507505	4507530	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	intron	4507531	4507615	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	CDS	4507616	4507690	1	-	0	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	exon	4507616	4507690	.	-	.	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
Phchi.S3	AUGUSTUS	start_codon	4507688	4507690	.	-	0	transcript_id "Phchi.S3G049500.t1"; gene_id "Phchi.S3G049500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg995.t1 is derived from g10778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6957684	6958587	.	-	.	Phchi.S6G095400
Phchi.S6	AUGUSTUS	transcript	6957684	6958587	.	-	.	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	stop_codon	6957681	6957683	.	-	0	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	CDS	6957684	6957985	0.92	-	2	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	exon	6957684	6957985	.	-	.	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	intron	6957986	6958106	.	-	.	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	CDS	6958107	6958191	0.84	-	0	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	exon	6958107	6958191	.	-	.	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	intron	6958192	6958389	.	-	.	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	CDS	6958390	6958587	0.86	-	0	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	exon	6958390	6958587	.	-	.	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
Phchi.S6	AUGUSTUS	start_codon	6958585	6958587	.	-	0	transcript_id "Phchi.S6G095400.t1"; gene_id "Phchi.S6G095400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12523.t1 is derived from g8200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32858800	32863145	.	+	.	Phchi.S2G060300
Phchi.S2	AUGUSTUS	transcript	32858800	32863145	.	+	.	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	start_codon	32858800	32858802	.	+	0	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	CDS	32858800	32862234	0.99	+	0	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	exon	32858800	32862234	.	+	.	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	intron	32862235	32862401	.	+	.	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	CDS	32862402	32863145	0.95	+	0	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	exon	32862402	32863145	.	+	.	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
Phchi.S2	AUGUSTUS	stop_codon	32863146	32863148	.	+	0	transcript_id "Phchi.S2G060300.t1"; gene_id "Phchi.S2G060300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15753.t1 is derived from g14223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21074579	21076036	.	+	.	Phchi.S3G307200
Phchi.S3	AUGUSTUS	transcript	21074579	21076036	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	start_codon	21074579	21074581	.	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21074579	21074697	1	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21074579	21074697	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	intron	21074698	21075012	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21075013	21075058	1	+	1	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21075013	21075058	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	intron	21075059	21075151	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21075152	21075245	1	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21075152	21075245	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	intron	21075246	21075344	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21075345	21075418	1	+	2	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21075345	21075418	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	intron	21075419	21075561	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21075562	21075648	1	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21075562	21075648	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	intron	21075649	21075760	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21075761	21075871	1	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21075761	21075871	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	intron	21075872	21075967	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	CDS	21075968	21076036	1	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	exon	21075968	21076036	.	+	.	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
Phchi.S3	AUGUSTUS	stop_codon	21076037	21076039	.	+	0	transcript_id "Phchi.S3G307200.t1"; gene_id "Phchi.S3G307200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2137.t1 is derived from g9057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5018475	5019240	.	-	.	Phchi.S5G074600
Phchi.S5	AUGUSTUS	transcript	5018475	5019240	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	stop_codon	5018472	5018474	.	-	0	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	CDS	5018475	5018594	1	-	0	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	exon	5018475	5018594	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	intron	5018595	5018682	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	CDS	5018683	5018850	1	-	0	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	exon	5018683	5018850	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	intron	5018851	5018940	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	CDS	5018941	5019048	1	-	0	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	exon	5018941	5019048	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	intron	5019049	5019138	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	CDS	5019139	5019240	1	-	0	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	exon	5019139	5019240	.	-	.	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
Phchi.S5	AUGUSTUS	start_codon	5019238	5019240	.	-	0	transcript_id "Phchi.S5G074600.t1"; gene_id "Phchi.S5G074600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14024.t1 is derived from g12491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10349271	10350248	.	+	.	Phchi.S3G134300
Phchi.S3	AUGUSTUS	transcript	10349271	10350248	.	+	.	transcript_id "Phchi.S3G134300.t1"; gene_id "Phchi.S3G134300"
Phchi.S3	AUGUSTUS	start_codon	10349271	10349273	.	+	0	transcript_id "Phchi.S3G134300.t1"; gene_id "Phchi.S3G134300"
Phchi.S3	AUGUSTUS	CDS	10349271	10350248	0.72	+	0	transcript_id "Phchi.S3G134300.t1"; gene_id "Phchi.S3G134300"
Phchi.S3	AUGUSTUS	exon	10349271	10350248	.	+	.	transcript_id "Phchi.S3G134300.t1"; gene_id "Phchi.S3G134300"
Phchi.S3	AUGUSTUS	stop_codon	10350249	10350251	.	+	0	transcript_id "Phchi.S3G134300.t1"; gene_id "Phchi.S3G134300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12095.t1 is derived from g7770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2594659	2599101	.	-	.	Phchi.S2G017500
Phchi.S2	AUGUSTUS	transcript	2594659	2599101	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	stop_codon	2594656	2594658	.	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2594659	2594739	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2594659	2594739	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2594740	2594818	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2594819	2594869	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2594819	2594869	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2594870	2594972	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2594973	2595056	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2594973	2595056	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2595057	2595147	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2595148	2595198	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2595148	2595198	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2595199	2595295	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2595296	2595382	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2595296	2595382	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2595383	2595458	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2595459	2595508	1	-	2	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2595459	2595508	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2595509	2595663	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2595664	2595680	1	-	1	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2595664	2595680	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2595681	2595844	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2595845	2595969	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2595845	2595969	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2595970	2596159	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2596160	2596214	1	-	1	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2596160	2596214	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2596215	2596307	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2596308	2596371	1	-	2	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2596308	2596371	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2596372	2596448	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2596449	2596572	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2596449	2596572	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2596573	2596709	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2596710	2596808	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2596710	2596808	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2596809	2596917	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2596918	2597043	0.97	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2596918	2597043	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2597044	2597119	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2597120	2597124	0.53	-	2	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2597120	2597124	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2597125	2597225	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2597226	2597256	0.81	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2597226	2597256	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2597257	2597414	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2597415	2597584	1	-	2	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2597415	2597584	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2597585	2597755	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2597756	2597824	1	-	2	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2597756	2597824	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2597825	2597961	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2597962	2598112	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2597962	2598112	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2598113	2598223	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2598224	2598298	1	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2598224	2598298	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2598299	2598438	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2598439	2598721	0.47	-	1	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2598439	2598721	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2598722	2598838	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2598839	2598851	0.82	-	2	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2598839	2598851	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	intron	2598852	2598944	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	CDS	2598945	2599101	0.84	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	exon	2598945	2599101	.	-	.	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
Phchi.S2	AUGUSTUS	start_codon	2599099	2599101	.	-	0	transcript_id "Phchi.S2G017500.t1"; gene_id "Phchi.S2G017500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10755.t1 is derived from g14805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1954578	1958587	.	+	.	Phchi.S4G033700
Phchi.S4	AUGUSTUS	transcript	1954578	1958587	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	start_codon	1954578	1954580	.	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1954578	1954634	0.37	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1954578	1954634	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1954635	1954708	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1954709	1954825	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1954709	1954825	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1954826	1955046	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1955047	1955223	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1955047	1955223	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1955224	1955355	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1955356	1955404	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1955356	1955404	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1955405	1955515	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1955516	1955616	1	+	2	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1955516	1955616	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1955617	1955697	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1955698	1955829	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1955698	1955829	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1955830	1955915	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1955916	1956005	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1955916	1956005	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1956006	1956248	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1956249	1956318	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1956249	1956318	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1956319	1956420	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1956421	1956491	1	+	2	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1956421	1956491	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1956492	1956584	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1956585	1956668	0.99	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1956585	1956668	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1956669	1956782	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1956783	1956860	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1956783	1956860	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1956861	1956971	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1956972	1957043	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1956972	1957043	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1957044	1957231	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1957232	1957315	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1957232	1957315	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1957316	1957424	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1957425	1957507	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1957425	1957507	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1957508	1957592	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1957593	1957692	1	+	1	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1957593	1957692	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1957693	1957793	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1957794	1957849	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1957794	1957849	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1957850	1957944	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1957945	1957987	1	+	1	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1957945	1957987	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1957988	1958065	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1958066	1958149	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1958066	1958149	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1958150	1958339	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1958340	1958381	0.85	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1958340	1958381	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1958382	1958454	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1958455	1958477	1	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1958455	1958477	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	intron	1958478	1958553	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	CDS	1958554	1958587	1	+	1	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	exon	1958554	1958587	.	+	.	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
Phchi.S4	AUGUSTUS	stop_codon	1958588	1958590	.	+	0	transcript_id "Phchi.S4G033700.t1"; gene_id "Phchi.S4G033700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9707.t1 is derived from g6883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43355824	43356875	.	-	.	Phchi.S1G686600
Phchi.S1	AUGUSTUS	transcript	43355824	43356875	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	stop_codon	43355821	43355823	.	-	0	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	CDS	43355824	43355826	0.98	-	0	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	exon	43355824	43355826	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	intron	43355827	43355926	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	CDS	43355927	43356155	0.81	-	1	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	exon	43355927	43356155	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	intron	43356156	43356239	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	CDS	43356240	43356316	1	-	0	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	exon	43356240	43356316	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	intron	43356317	43356482	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	CDS	43356483	43356538	1	-	2	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	exon	43356483	43356538	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	intron	43356539	43356619	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	CDS	43356620	43356875	0.55	-	0	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	exon	43356620	43356875	.	-	.	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
Phchi.S1	AUGUSTUS	start_codon	43356873	43356875	.	-	0	transcript_id "Phchi.S1G686600.t1"; gene_id "Phchi.S1G686600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7568.t1 is derived from g4742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30078850	30080838	.	+	.	Phchi.S1G472700
Phchi.S1	AUGUSTUS	transcript	30078850	30080838	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	start_codon	30078850	30078852	.	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30078850	30079052	0.99	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30078850	30079052	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30079053	30079136	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30079137	30079169	1	+	1	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30079137	30079169	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30079170	30079627	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30079628	30079697	1	+	1	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30079628	30079697	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30079698	30079811	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30079812	30079871	1	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30079812	30079871	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30079872	30079966	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30079967	30080094	1	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30079967	30080094	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30080095	30080245	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30080246	30080300	1	+	1	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30080246	30080300	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30080301	30080409	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30080410	30080490	0.86	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30080410	30080490	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30080491	30080597	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30080598	30080651	0.86	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30080598	30080651	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	intron	30080652	30080802	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	CDS	30080803	30080838	0.86	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	exon	30080803	30080838	.	+	.	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
Phchi.S1	AUGUSTUS	stop_codon	30080839	30080841	.	+	0	transcript_id "Phchi.S1G472700.t1"; gene_id "Phchi.S1G472700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15556.t1 is derived from g14025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19909314	19909541	.	+	.	Phchi.S3G287500
Phchi.S3	AUGUSTUS	transcript	19909314	19909541	.	+	.	transcript_id "Phchi.S3G287500.t1"; gene_id "Phchi.S3G287500"
Phchi.S3	AUGUSTUS	start_codon	19909314	19909316	.	+	0	transcript_id "Phchi.S3G287500.t1"; gene_id "Phchi.S3G287500"
Phchi.S3	AUGUSTUS	CDS	19909314	19909541	0.98	+	0	transcript_id "Phchi.S3G287500.t1"; gene_id "Phchi.S3G287500"
Phchi.S3	AUGUSTUS	exon	19909314	19909541	.	+	.	transcript_id "Phchi.S3G287500.t1"; gene_id "Phchi.S3G287500"
Phchi.S3	AUGUSTUS	stop_codon	19909542	19909544	.	+	0	transcript_id "Phchi.S3G287500.t1"; gene_id "Phchi.S3G287500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9006.t1 is derived from g6181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39121629	39122414	.	-	.	Phchi.S1G616500
Phchi.S1	AUGUSTUS	transcript	39121629	39122414	.	-	.	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	stop_codon	39121626	39121628	.	-	0	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	CDS	39121629	39121802	0.98	-	0	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	exon	39121629	39121802	.	-	.	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	intron	39121803	39121911	.	-	.	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	CDS	39121912	39122037	0.99	-	0	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	exon	39121912	39122037	.	-	.	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	intron	39122038	39122165	.	-	.	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	CDS	39122166	39122414	0.52	-	0	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	exon	39122166	39122414	.	-	.	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
Phchi.S1	AUGUSTUS	start_codon	39122412	39122414	.	-	0	transcript_id "Phchi.S1G616500.t1"; gene_id "Phchi.S1G616500"
# This transcript jg11935.t2 is derived from g7610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11936.t1 is derived from g7611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	99018	100360	.	+	.	Phchi.S2G001600
Phchi.S2	AUGUSTUS	transcript	99018	100360	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	start_codon	99018	99020	.	+	0	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	99018	99037	0.63	+	0	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	99018	99037	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	intron	99038	99156	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	99157	99239	1	+	1	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	99157	99239	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	intron	99240	99330	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	99331	99434	1	+	2	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	99331	99434	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	intron	99435	99514	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	99515	99585	1	+	0	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	99515	99585	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	intron	99586	99683	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	99684	99907	1	+	1	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	99684	99907	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	intron	99908	100003	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	100004	100140	0.85	+	2	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	100004	100140	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	intron	100141	100315	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	CDS	100316	100360	0.39	+	0	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	exon	100316	100360	.	+	.	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
Phchi.S2	AUGUSTUS	stop_codon	100361	100363	.	+	0	transcript_id "Phchi.S2G001600.t1"; gene_id "Phchi.S2G001600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7017.t1 is derived from g4189.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26412532	26414123	.	-	.	Phchi.S1G417600
Phchi.S1	AUGUSTUS	transcript	26412532	26414123	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	stop_codon	26412529	26412531	.	-	0	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	CDS	26412532	26412558	0.99	-	0	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	exon	26412532	26412558	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	intron	26412559	26412704	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	CDS	26412705	26412847	0.99	-	2	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	exon	26412705	26412847	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	intron	26412848	26413009	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	CDS	26413010	26413114	1	-	2	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	exon	26413010	26413114	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	intron	26413115	26413305	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	CDS	26413306	26413547	0.87	-	1	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	exon	26413306	26413547	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	intron	26413548	26413669	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	CDS	26413670	26413817	0.82	-	2	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	exon	26413670	26413817	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	intron	26413818	26413915	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	CDS	26413916	26414123	0.32	-	0	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	exon	26413916	26414123	.	-	.	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
Phchi.S1	AUGUSTUS	start_codon	26414121	26414123	.	-	0	transcript_id "Phchi.S1G417600.t1"; gene_id "Phchi.S1G417600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5051.t1 is derived from g2221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14367172	14367976	.	-	.	Phchi.S1G221000
Phchi.S1	AUGUSTUS	transcript	14367172	14367976	.	-	.	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	stop_codon	14367169	14367171	.	-	0	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	CDS	14367172	14367410	0.86	-	2	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	exon	14367172	14367410	.	-	.	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	intron	14367411	14367579	.	-	.	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	CDS	14367580	14367976	0.85	-	0	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	exon	14367580	14367976	.	-	.	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
Phchi.S1	AUGUSTUS	start_codon	14367974	14367976	.	-	0	transcript_id "Phchi.S1G221000.t1"; gene_id "Phchi.S1G221000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3302.t1 is derived from g471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2746805	2747338	.	-	.	Phchi.S1G046100
Phchi.S1	AUGUSTUS	transcript	2746805	2747338	.	-	.	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	stop_codon	2746802	2746804	.	-	0	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	CDS	2746805	2746978	1	-	0	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	exon	2746805	2746978	.	-	.	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	intron	2746979	2747067	.	-	.	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	CDS	2747068	2747205	1	-	0	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	exon	2747068	2747205	.	-	.	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	intron	2747206	2747296	.	-	.	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	CDS	2747297	2747338	1	-	0	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	exon	2747297	2747338	.	-	.	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
Phchi.S1	AUGUSTUS	start_codon	2747336	2747338	.	-	0	transcript_id "Phchi.S1G046100.t1"; gene_id "Phchi.S1G046100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3574.t1 is derived from g743.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4586820	4588639	.	-	.	Phchi.S1G073300
Phchi.S1	AUGUSTUS	transcript	4586820	4588639	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	stop_codon	4586817	4586819	.	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4586820	4587101	1	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4586820	4587101	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	intron	4587102	4587205	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4587206	4587316	0.94	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4587206	4587316	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	intron	4587317	4587422	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4587423	4587641	0.99	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4587423	4587641	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	intron	4587642	4587728	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4587729	4588126	1	-	2	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4587729	4588126	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	intron	4588127	4588221	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4588222	4588285	1	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4588222	4588285	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	intron	4588286	4588430	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4588431	4588490	0.93	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4588431	4588490	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	intron	4588491	4588576	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	CDS	4588577	4588639	0.93	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	exon	4588577	4588639	.	-	.	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
Phchi.S1	AUGUSTUS	start_codon	4588637	4588639	.	-	0	transcript_id "Phchi.S1G073300.t1"; gene_id "Phchi.S1G073300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10542.t1 is derived from g14592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	881523	882740	.	-	.	Phchi.S4G012400
Phchi.S4	AUGUSTUS	transcript	881523	882740	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	stop_codon	881520	881522	.	-	0	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	CDS	881523	881805	1	-	1	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	exon	881523	881805	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	intron	881806	881891	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	CDS	881892	882142	1	-	0	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	exon	881892	882142	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	intron	882143	882264	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	CDS	882265	882435	0.57	-	0	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	exon	882265	882435	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	intron	882436	882515	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	CDS	882516	882740	0.33	-	0	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	exon	882516	882740	.	-	.	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
Phchi.S4	AUGUSTUS	start_codon	882738	882740	.	-	0	transcript_id "Phchi.S4G012400.t1"; gene_id "Phchi.S4G012400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11833.t1 is derived from g15885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8480000	8482320	.	+	.	Phchi.S4G141500
Phchi.S4	AUGUSTUS	transcript	8480000	8482320	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	start_codon	8480000	8480002	.	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8480000	8480093	0.96	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8480000	8480093	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8480094	8480309	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8480310	8480530	1	+	2	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8480310	8480530	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8480531	8480648	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8480649	8480711	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8480649	8480711	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8480712	8480833	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8480834	8480944	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8480834	8480944	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8480945	8481064	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8481065	8481139	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8481065	8481139	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8481140	8481210	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8481211	8481279	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8481211	8481279	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8481280	8481365	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8481366	8481431	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8481366	8481431	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8481432	8481540	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8481541	8481618	0.98	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8481541	8481618	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8481619	8481760	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8481761	8481859	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8481761	8481859	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8481860	8481957	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8481958	8482092	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8481958	8482092	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	intron	8482093	8482185	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	CDS	8482186	8482320	1	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	exon	8482186	8482320	.	+	.	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
Phchi.S4	AUGUSTUS	stop_codon	8482321	8482323	.	+	0	transcript_id "Phchi.S4G141500.t1"; gene_id "Phchi.S4G141500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7626.t1 is derived from g4800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30307185	30308601	.	+	.	Phchi.S1G478500
Phchi.S1	AUGUSTUS	transcript	30307185	30308601	.	+	.	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	start_codon	30307185	30307187	.	+	0	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	CDS	30307185	30307304	0.79	+	0	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	exon	30307185	30307304	.	+	.	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	intron	30307305	30307402	.	+	.	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	CDS	30307403	30307440	0.81	+	0	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	exon	30307403	30307440	.	+	.	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	intron	30307441	30307625	.	+	.	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	CDS	30307626	30308601	0.8	+	1	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	exon	30307626	30308601	.	+	.	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
Phchi.S1	AUGUSTUS	stop_codon	30308602	30308604	.	+	0	transcript_id "Phchi.S1G478500.t1"; gene_id "Phchi.S1G478500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15196.t1 is derived from g13664.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17512972	17514252	.	-	.	Phchi.S3G251500
Phchi.S3	AUGUSTUS	transcript	17512972	17514252	.	-	.	transcript_id "Phchi.S3G251500.t1"; gene_id "Phchi.S3G251500"
Phchi.S3	AUGUSTUS	stop_codon	17512969	17512971	.	-	0	transcript_id "Phchi.S3G251500.t1"; gene_id "Phchi.S3G251500"
Phchi.S3	AUGUSTUS	CDS	17512972	17514252	0.88	-	0	transcript_id "Phchi.S3G251500.t1"; gene_id "Phchi.S3G251500"
Phchi.S3	AUGUSTUS	exon	17512972	17514252	.	-	.	transcript_id "Phchi.S3G251500.t1"; gene_id "Phchi.S3G251500"
Phchi.S3	AUGUSTUS	start_codon	17514250	17514252	.	-	0	transcript_id "Phchi.S3G251500.t1"; gene_id "Phchi.S3G251500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9556.t1 is derived from g6732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42651892	42652806	.	-	.	Phchi.S1G671500
Phchi.S1	AUGUSTUS	transcript	42651892	42652806	.	-	.	transcript_id "Phchi.S1G671500.t1"; gene_id "Phchi.S1G671500"
Phchi.S1	AUGUSTUS	stop_codon	42651889	42651891	.	-	0	transcript_id "Phchi.S1G671500.t1"; gene_id "Phchi.S1G671500"
Phchi.S1	AUGUSTUS	CDS	42651892	42652806	0.99	-	0	transcript_id "Phchi.S1G671500.t1"; gene_id "Phchi.S1G671500"
Phchi.S1	AUGUSTUS	exon	42651892	42652806	.	-	.	transcript_id "Phchi.S1G671500.t1"; gene_id "Phchi.S1G671500"
Phchi.S1	AUGUSTUS	start_codon	42652804	42652806	.	-	0	transcript_id "Phchi.S1G671500.t1"; gene_id "Phchi.S1G671500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6556.t1 is derived from g3728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23704068	23705850	.	-	.	Phchi.S1G371500
Phchi.S1	AUGUSTUS	transcript	23704068	23705850	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	stop_codon	23704065	23704067	.	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	CDS	23704068	23704200	1	-	1	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	exon	23704068	23704200	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	intron	23704201	23704329	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	CDS	23704330	23704388	1	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	exon	23704330	23704388	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	intron	23704389	23704466	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	CDS	23704467	23704616	1	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	exon	23704467	23704616	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	intron	23704617	23704725	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	CDS	23704726	23704842	1	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	exon	23704726	23704842	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	intron	23704843	23705014	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	CDS	23705015	23705437	0.99	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	exon	23705015	23705437	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	intron	23705438	23705691	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	CDS	23705692	23705850	0.75	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	exon	23705692	23705850	.	-	.	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
Phchi.S1	AUGUSTUS	start_codon	23705848	23705850	.	-	0	transcript_id "Phchi.S1G371500.t1"; gene_id "Phchi.S1G371500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15590.t1 is derived from g14059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20154201	20158317	.	-	.	Phchi.S3G290900
Phchi.S3	AUGUSTUS	transcript	20154201	20158317	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	stop_codon	20154198	20154200	.	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20154201	20154251	0.49	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20154201	20154251	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20154252	20154353	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20154354	20154440	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20154354	20154440	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20154441	20154529	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20154530	20154616	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20154530	20154616	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20154617	20154814	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20154815	20154892	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20154815	20154892	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20154893	20155007	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20155008	20155136	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20155008	20155136	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20155137	20155235	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20155236	20155355	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20155236	20155355	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20155356	20155433	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20155434	20155505	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20155434	20155505	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20155506	20155585	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20155586	20155681	0.99	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20155586	20155681	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20155682	20155786	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20155787	20155894	0.98	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20155787	20155894	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20155895	20155965	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20155966	20156043	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20155966	20156043	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20156044	20156249	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20156250	20156376	1	-	1	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20156250	20156376	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20156377	20156496	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20156497	20156698	1	-	2	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20156497	20156698	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20156699	20156862	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20156863	20156950	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20156863	20156950	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20156951	20157121	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20157122	20157198	1	-	2	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20157122	20157198	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20157199	20157371	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20157372	20157477	1	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20157372	20157477	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20157478	20157644	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20157645	20157829	1	-	2	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20157645	20157829	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20157830	20157997	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20157998	20158162	1	-	2	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20157998	20158162	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	intron	20158163	20158262	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	CDS	20158263	20158317	0.97	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	exon	20158263	20158317	.	-	.	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
Phchi.S3	AUGUSTUS	start_codon	20158315	20158317	.	-	0	transcript_id "Phchi.S3G290900.t1"; gene_id "Phchi.S3G290900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9417.t1 is derived from g6593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41390044	41390648	.	-	.	Phchi.S1G657600
Phchi.S1	AUGUSTUS	transcript	41390044	41390648	.	-	.	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	stop_codon	41390041	41390043	.	-	0	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	CDS	41390044	41390438	0.4	-	2	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	exon	41390044	41390438	.	-	.	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	intron	41390439	41390587	.	-	.	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	CDS	41390588	41390648	0.37	-	0	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	exon	41390588	41390648	.	-	.	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
Phchi.S1	AUGUSTUS	start_codon	41390646	41390648	.	-	0	transcript_id "Phchi.S1G657600.t1"; gene_id "Phchi.S1G657600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7689.t1 is derived from g4863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30631647	30635044	.	+	.	Phchi.S1G484800
Phchi.S1	AUGUSTUS	transcript	30631647	30635044	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	start_codon	30631647	30631649	.	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30631647	30632018	0.95	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30631647	30632018	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30632019	30632236	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30632237	30632455	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30632237	30632455	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30632456	30632555	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30632556	30632667	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30632556	30632667	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30632668	30632793	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30632794	30632902	1	+	2	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30632794	30632902	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30632903	30632997	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30632998	30633055	1	+	1	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30632998	30633055	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30633056	30633169	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30633170	30633238	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30633170	30633238	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30633239	30633333	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30633334	30633441	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30633334	30633441	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30633442	30633528	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30633529	30633621	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30633529	30633621	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30633622	30633750	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30633751	30633855	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30633751	30633855	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30633856	30633940	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30633941	30634129	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30633941	30634129	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30634130	30634236	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30634237	30634331	1	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30634237	30634331	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30634332	30634435	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30634436	30634526	0.86	+	1	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30634436	30634526	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30634527	30634630	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30634631	30634810	0.84	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30634631	30634810	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	intron	30634811	30634957	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	CDS	30634958	30635044	0.81	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	exon	30634958	30635044	.	+	.	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
Phchi.S1	AUGUSTUS	stop_codon	30635045	30635047	.	+	0	transcript_id "Phchi.S1G484800.t1"; gene_id "Phchi.S1G484800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9343.t1 is derived from g6518.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41062610	41063931	.	+	.	Phchi.S1G650200
Phchi.S1	AUGUSTUS	transcript	41062610	41063931	.	+	.	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	start_codon	41062610	41062612	.	+	0	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	CDS	41062610	41063009	0.57	+	0	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	exon	41062610	41063009	.	+	.	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	intron	41063010	41063101	.	+	.	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	CDS	41063102	41063931	0.62	+	2	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	exon	41063102	41063931	.	+	.	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	stop_codon	41063932	41063934	.	+	0	transcript_id "Phchi.S1G650200.t1"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	transcript	41062963	41063931	.	+	.	transcript_id "Phchi.S1G650200.t2"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	start_codon	41062963	41062965	.	+	0	transcript_id "Phchi.S1G650200.t2"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	CDS	41062963	41063931	1	+	0	transcript_id "Phchi.S1G650200.t2"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	exon	41062963	41063931	.	+	.	transcript_id "Phchi.S1G650200.t2"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	stop_codon	41063932	41063934	.	+	0	transcript_id "Phchi.S1G650200.t2"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	transcript	41063668	41063931	.	+	.	transcript_id "Phchi.S1G650200.t3"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	start_codon	41063668	41063670	.	+	0	transcript_id "Phchi.S1G650200.t3"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	CDS	41063668	41063931	0.99	+	0	transcript_id "Phchi.S1G650200.t3"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	exon	41063668	41063931	.	+	.	transcript_id "Phchi.S1G650200.t3"; gene_id "Phchi.S1G650200"
Phchi.S1	AUGUSTUS	stop_codon	41063932	41063934	.	+	0	transcript_id "Phchi.S1G650200.t3"; gene_id "Phchi.S1G650200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13737.t1 is derived from g12204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8650032	8653208	.	+	.	Phchi.S3G105600
Phchi.S3	AUGUSTUS	transcript	8650032	8653208	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	start_codon	8650032	8650034	.	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8650032	8650326	1	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8650032	8650326	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8650327	8650442	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8650443	8651132	0.94	+	2	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8650443	8651132	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8651133	8651216	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8651217	8651368	1	+	2	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8651217	8651368	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8651369	8651492	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8651493	8651791	0.41	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8651493	8651791	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8651792	8651910	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8651911	8651977	0.83	+	1	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8651911	8651977	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8651978	8652143	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8652144	8652326	1	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8652144	8652326	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8652327	8652414	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8652415	8652576	1	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8652415	8652576	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	intron	8652577	8652656	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	CDS	8652657	8653208	0.99	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	exon	8652657	8653208	.	+	.	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
Phchi.S3	AUGUSTUS	stop_codon	8653209	8653211	.	+	0	transcript_id "Phchi.S3G105600.t1"; gene_id "Phchi.S3G105600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6721.t1 is derived from g3893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24742608	24743280	.	-	.	Phchi.S1G388000
Phchi.S1	AUGUSTUS	transcript	24742608	24743280	.	-	.	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	stop_codon	24742605	24742607	.	-	0	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	CDS	24742608	24742775	0.96	-	0	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	exon	24742608	24742775	.	-	.	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	intron	24742776	24742869	.	-	.	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	CDS	24742870	24743280	0.94	-	0	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	exon	24742870	24743280	.	-	.	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
Phchi.S1	AUGUSTUS	start_codon	24743278	24743280	.	-	0	transcript_id "Phchi.S1G388000.t1"; gene_id "Phchi.S1G388000"
# This transcript jg9083.t2 is derived from g6258.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9083.t3 is derived from g6258.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9084.t1 is derived from g6259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39782721	39785715	.	+	.	Phchi.S1G624300
Phchi.S1	AUGUSTUS	transcript	39782721	39785715	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	start_codon	39782721	39782723	.	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39782721	39782783	0.88	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39782721	39782783	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39782784	39782859	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39782860	39782879	0.87	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39782860	39782879	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39782880	39783089	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39783090	39783261	0.6	+	1	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39783090	39783261	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39783262	39783401	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39783402	39783458	1	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39783402	39783458	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39783459	39783557	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39783558	39783620	1	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39783558	39783620	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39783621	39783746	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39783747	39783836	1	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39783747	39783836	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39783837	39783953	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39783954	39784086	1	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39783954	39784086	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39784087	39784180	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39784181	39784299	0.99	+	2	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39784181	39784299	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39784300	39784404	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39784405	39784472	1	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39784405	39784472	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39784473	39784556	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39784557	39784605	1	+	1	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39784557	39784605	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	intron	39784606	39784686	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	CDS	39784687	39785715	1	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	exon	39784687	39785715	.	+	.	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
Phchi.S1	AUGUSTUS	stop_codon	39785716	39785718	.	+	0	transcript_id "Phchi.S1G624300.t1"; gene_id "Phchi.S1G624300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg201.t1 is derived from g9983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1123738	1126128	.	-	.	Phchi.S6G016000
Phchi.S6	AUGUSTUS	transcript	1123738	1124809	.	-	.	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	stop_codon	1123735	1123737	.	-	0	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1123738	1123957	1	-	1	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1123738	1123957	.	-	.	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	intron	1123958	1124039	.	-	.	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1124040	1124809	0.99	-	0	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1124040	1124809	.	-	.	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	start_codon	1124807	1124809	.	-	0	transcript_id "Phchi.S6G016000.t1"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	transcript	1123738	1126128	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	stop_codon	1123735	1123737	.	-	0	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1123738	1123957	1	-	1	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1123738	1123957	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	intron	1123958	1124039	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1124040	1124678	0.96	-	1	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1124040	1124678	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	intron	1124679	1124895	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1124896	1125083	0.94	-	0	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1124896	1125083	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	intron	1125084	1125173	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1125174	1125271	0.92	-	2	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1125174	1125271	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	intron	1125272	1125342	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1125343	1125562	0.95	-	0	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1125343	1125562	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	intron	1125563	1125639	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	CDS	1125640	1126128	0.82	-	0	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	exon	1125640	1126128	.	-	.	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
Phchi.S6	AUGUSTUS	start_codon	1126126	1126128	.	-	0	transcript_id "Phchi.S6G016000.t2"; gene_id "Phchi.S6G016000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg73.t1 is derived from g9855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	361872	362278	.	+	.	Phchi.S6G003200
Phchi.S6	AUGUSTUS	transcript	361872	362278	.	+	.	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	start_codon	361872	361874	.	+	0	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	CDS	361872	361974	0.57	+	0	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	exon	361872	361974	.	+	.	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	intron	361975	362057	.	+	.	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	CDS	362058	362278	1	+	2	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	exon	362058	362278	.	+	.	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
Phchi.S6	AUGUSTUS	stop_codon	362279	362281	.	+	0	transcript_id "Phchi.S6G003200.t1"; gene_id "Phchi.S6G003200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14780.t1 is derived from g13248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14663389	14665377	.	+	.	Phchi.S3G209900
Phchi.S3	AUGUSTUS	transcript	14663389	14665377	.	+	.	transcript_id "Phchi.S3G209900.t1"; gene_id "Phchi.S3G209900"
Phchi.S3	AUGUSTUS	start_codon	14663389	14663391	.	+	0	transcript_id "Phchi.S3G209900.t1"; gene_id "Phchi.S3G209900"
Phchi.S3	AUGUSTUS	CDS	14663389	14665377	0.66	+	0	transcript_id "Phchi.S3G209900.t1"; gene_id "Phchi.S3G209900"
Phchi.S3	AUGUSTUS	exon	14663389	14665377	.	+	.	transcript_id "Phchi.S3G209900.t1"; gene_id "Phchi.S3G209900"
Phchi.S3	AUGUSTUS	stop_codon	14665378	14665380	.	+	0	transcript_id "Phchi.S3G209900.t1"; gene_id "Phchi.S3G209900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5069.t1 is derived from g2239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14525696	14527933	.	+	.	Phchi.S1G222800
Phchi.S1	AUGUSTUS	transcript	14525696	14527933	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	start_codon	14525696	14525698	.	+	0	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	CDS	14525696	14526646	0.95	+	0	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	exon	14525696	14526646	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	intron	14526647	14526768	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	CDS	14526769	14527206	1	+	0	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	exon	14526769	14527206	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	intron	14527207	14527300	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	CDS	14527301	14527473	1	+	0	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	exon	14527301	14527473	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	intron	14527474	14527565	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	CDS	14527566	14527752	1	+	1	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	exon	14527566	14527752	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	intron	14527753	14527834	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	CDS	14527835	14527933	1	+	0	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	exon	14527835	14527933	.	+	.	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
Phchi.S1	AUGUSTUS	stop_codon	14527934	14527936	.	+	0	transcript_id "Phchi.S1G222800.t1"; gene_id "Phchi.S1G222800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2895.t1 is derived from g64.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	373084	373749	.	+	.	Phchi.S1G005400
Phchi.S1	AUGUSTUS	transcript	373084	373749	.	+	.	transcript_id "Phchi.S1G005400.t1"; gene_id "Phchi.S1G005400"
Phchi.S1	AUGUSTUS	start_codon	373084	373086	.	+	0	transcript_id "Phchi.S1G005400.t1"; gene_id "Phchi.S1G005400"
Phchi.S1	AUGUSTUS	CDS	373084	373749	0.59	+	0	transcript_id "Phchi.S1G005400.t1"; gene_id "Phchi.S1G005400"
Phchi.S1	AUGUSTUS	exon	373084	373749	.	+	.	transcript_id "Phchi.S1G005400.t1"; gene_id "Phchi.S1G005400"
Phchi.S1	AUGUSTUS	stop_codon	373750	373752	.	+	0	transcript_id "Phchi.S1G005400.t1"; gene_id "Phchi.S1G005400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7711.t1 is derived from g4885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30748986	30751266	.	+	.	Phchi.S1G487000
Phchi.S1	AUGUSTUS	transcript	30748986	30751266	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	start_codon	30748986	30748988	.	+	0	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	CDS	30748986	30748998	1	+	0	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	exon	30748986	30748998	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	intron	30748999	30749169	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	CDS	30749170	30749301	1	+	2	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	exon	30749170	30749301	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	intron	30749302	30749508	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	CDS	30749509	30750999	1	+	2	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	exon	30749509	30750999	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	intron	30751000	30751126	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	CDS	30751127	30751266	0.97	+	2	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	exon	30751127	30751266	.	+	.	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
Phchi.S1	AUGUSTUS	stop_codon	30751267	30751269	.	+	0	transcript_id "Phchi.S1G487000.t1"; gene_id "Phchi.S1G487000"
# This transcript jg13460.t2 is derived from g11927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13461.t1 is derived from g11928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7013055	7013837	.	-	.	Phchi.S3G078000
Phchi.S3	AUGUSTUS	transcript	7013055	7013837	.	-	.	transcript_id "Phchi.S3G078000.t1"; gene_id "Phchi.S3G078000"
Phchi.S3	AUGUSTUS	stop_codon	7013052	7013054	.	-	0	transcript_id "Phchi.S3G078000.t1"; gene_id "Phchi.S3G078000"
Phchi.S3	AUGUSTUS	CDS	7013055	7013837	0.91	-	0	transcript_id "Phchi.S3G078000.t1"; gene_id "Phchi.S3G078000"
Phchi.S3	AUGUSTUS	exon	7013055	7013837	.	-	.	transcript_id "Phchi.S3G078000.t1"; gene_id "Phchi.S3G078000"
Phchi.S3	AUGUSTUS	start_codon	7013835	7013837	.	-	0	transcript_id "Phchi.S3G078000.t1"; gene_id "Phchi.S3G078000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5942.t1 is derived from g3113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19960112	19960996	.	-	.	Phchi.S1G310100
Phchi.S1	AUGUSTUS	transcript	19960112	19960996	.	-	.	transcript_id "Phchi.S1G310100.t1"; gene_id "Phchi.S1G310100"
Phchi.S1	AUGUSTUS	stop_codon	19960109	19960111	.	-	0	transcript_id "Phchi.S1G310100.t1"; gene_id "Phchi.S1G310100"
Phchi.S1	AUGUSTUS	CDS	19960112	19960996	0.73	-	0	transcript_id "Phchi.S1G310100.t1"; gene_id "Phchi.S1G310100"
Phchi.S1	AUGUSTUS	exon	19960112	19960996	.	-	.	transcript_id "Phchi.S1G310100.t1"; gene_id "Phchi.S1G310100"
Phchi.S1	AUGUSTUS	start_codon	19960994	19960996	.	-	0	transcript_id "Phchi.S1G310100.t1"; gene_id "Phchi.S1G310100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6538.t1 is derived from g3710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23532391	23534481	.	+	.	Phchi.S1G369700
Phchi.S1	AUGUSTUS	transcript	23532391	23534481	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	start_codon	23532391	23532393	.	+	0	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	CDS	23532391	23533578	0.59	+	0	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	exon	23532391	23533578	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	intron	23533579	23533675	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	CDS	23533676	23533736	0.97	+	0	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	exon	23533676	23533736	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	intron	23533737	23533981	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	CDS	23533982	23534059	0.9	+	2	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	exon	23533982	23534059	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	intron	23534060	23534392	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	CDS	23534393	23534481	0.9	+	2	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	exon	23534393	23534481	.	+	.	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
Phchi.S1	AUGUSTUS	stop_codon	23534482	23534484	.	+	0	transcript_id "Phchi.S1G369700.t1"; gene_id "Phchi.S1G369700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1525.t1 is derived from g8444.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1583883	1584207	.	-	.	Phchi.S5G013400
Phchi.S5	AUGUSTUS	transcript	1583883	1584207	.	-	.	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	stop_codon	1583880	1583882	.	-	0	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	CDS	1583883	1584042	0.49	-	1	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	exon	1583883	1584042	.	-	.	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	intron	1584043	1584124	.	-	.	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	CDS	1584125	1584207	0.44	-	0	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	exon	1584125	1584207	.	-	.	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
Phchi.S5	AUGUSTUS	start_codon	1584205	1584207	.	-	0	transcript_id "Phchi.S5G013400.t1"; gene_id "Phchi.S5G013400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9280.t1 is derived from g6455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40742113	40743218	.	+	.	Phchi.S1G643900
Phchi.S1	AUGUSTUS	transcript	40742113	40742826	.	+	.	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	start_codon	40742113	40742115	.	+	0	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40742113	40742224	1	+	0	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40742113	40742224	.	+	.	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	intron	40742225	40742322	.	+	.	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40742323	40742453	1	+	2	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40742323	40742453	.	+	.	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	intron	40742454	40742544	.	+	.	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40742545	40742826	1	+	0	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40742545	40742826	.	+	.	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	stop_codon	40743185	40743187	.	+	0	transcript_id "Phchi.S1G643900.t1"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	transcript	40742113	40743218	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	start_codon	40742113	40742115	.	+	0	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40742113	40742224	1	+	0	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40742113	40742224	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	intron	40742225	40742322	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40742323	40742453	1	+	2	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40742323	40742453	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	intron	40742454	40742544	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40742545	40742826	1	+	0	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40742545	40742826	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	intron	40742827	40743206	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	CDS	40743207	40743218	0.99	+	0	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	exon	40743207	40743218	.	+	.	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
Phchi.S1	AUGUSTUS	stop_codon	40743219	40743221	.	+	0	transcript_id "Phchi.S1G643900.t2"; gene_id "Phchi.S1G643900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1213.t1 is derived from g10996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8434001	8437382	.	-	.	Phchi.S6G117200
Phchi.S6	AUGUSTUS	transcript	8434001	8437382	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	stop_codon	8433998	8434000	.	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434001	8434013	0.91	-	1	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434001	8434013	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434014	8434259	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434260	8434404	0.92	-	2	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434260	8434404	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434405	8434494	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434495	8434651	1	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434495	8434651	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434652	8434778	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434779	8434952	1	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434779	8434952	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434953	8435058	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435059	8435196	0.6	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435059	8435196	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8435197	8435335	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435336	8435425	1	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435336	8435425	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8435426	8435555	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435556	8435626	1	-	2	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435556	8435626	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8435627	8435856	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435857	8436557	1	-	1	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435857	8436557	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8436558	8436766	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8436767	8436858	1	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8436767	8436858	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8436859	8437007	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8437008	8437382	0.98	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8437008	8437382	.	-	.	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	start_codon	8437380	8437382	.	-	0	transcript_id "Phchi.S6G117200.t1"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	transcript	8434001	8437382	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	stop_codon	8433998	8434000	.	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434001	8434013	0.91	-	1	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434001	8434013	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434014	8434259	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434260	8434404	0.91	-	2	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434260	8434404	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434405	8434494	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434495	8434651	0.78	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434495	8434651	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434652	8434889	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8434890	8434952	0.59	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8434890	8434952	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8434953	8435058	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435059	8435196	0.57	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435059	8435196	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8435197	8435335	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435336	8435425	1	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435336	8435425	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8435426	8435555	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435556	8435626	1	-	2	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435556	8435626	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8435627	8435856	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8435857	8436557	0.99	-	1	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8435857	8436557	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8436558	8436766	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8436767	8436858	1	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8436767	8436858	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	intron	8436859	8437007	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	CDS	8437008	8437382	0.97	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	exon	8437008	8437382	.	-	.	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
Phchi.S6	AUGUSTUS	start_codon	8437380	8437382	.	-	0	transcript_id "Phchi.S6G117200.t2"; gene_id "Phchi.S6G117200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5953.t1 is derived from g3124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20056335	20057825	.	-	.	Phchi.S1G311200
Phchi.S1	AUGUSTUS	transcript	20056335	20057825	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	stop_codon	20056332	20056334	.	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20056335	20056578	1	-	1	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20056335	20056578	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	intron	20056579	20056693	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20056694	20056764	1	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20056694	20056764	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	intron	20056765	20056856	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20056857	20056976	1	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20056857	20056976	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	intron	20056977	20057064	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20057065	20057191	1	-	1	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20057065	20057191	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	intron	20057192	20057311	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20057312	20057466	1	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20057312	20057466	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	intron	20057467	20057554	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20057555	20057644	1	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20057555	20057644	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	intron	20057645	20057732	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	CDS	20057733	20057825	1	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	exon	20057733	20057825	.	-	.	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
Phchi.S1	AUGUSTUS	start_codon	20057823	20057825	.	-	0	transcript_id "Phchi.S1G311200.t1"; gene_id "Phchi.S1G311200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10890.t1 is derived from g14940.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2780724	2781728	.	+	.	Phchi.S4G047200
Phchi.S4	AUGUSTUS	transcript	2780724	2781728	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	start_codon	2780724	2780726	.	+	0	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2780724	2780848	0.38	+	0	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2780724	2780848	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	intron	2780849	2781033	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2781034	2781313	0.81	+	1	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2781034	2781313	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	intron	2781314	2781468	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2781469	2781550	0.99	+	0	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2781469	2781550	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	intron	2781551	2781645	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2781646	2781728	0.74	+	2	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2781646	2781728	.	+	.	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	stop_codon	2781729	2781731	.	+	0	transcript_id "Phchi.S4G047200.t1"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	transcript	2780724	2781688	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	start_codon	2780724	2780726	.	+	0	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2780724	2780848	0.24	+	0	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2780724	2780848	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	intron	2780849	2781016	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2781017	2781178	0.59	+	1	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2781017	2781178	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	intron	2781179	2781268	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2781269	2781313	0.59	+	1	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2781269	2781313	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	intron	2781314	2781468	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	CDS	2781469	2781688	0.69	+	1	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	exon	2781469	2781688	.	+	.	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
Phchi.S4	AUGUSTUS	stop_codon	2781689	2781691	.	+	0	transcript_id "Phchi.S4G047200.t2"; gene_id "Phchi.S4G047200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11082.t1 is derived from g15132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3999786	4000229	.	-	.	Phchi.S4G066400
Phchi.S4	AUGUSTUS	transcript	3999786	4000229	.	-	.	transcript_id "Phchi.S4G066400.t1"; gene_id "Phchi.S4G066400"
Phchi.S4	AUGUSTUS	stop_codon	3999783	3999785	.	-	0	transcript_id "Phchi.S4G066400.t1"; gene_id "Phchi.S4G066400"
Phchi.S4	AUGUSTUS	CDS	3999786	4000229	0.98	-	0	transcript_id "Phchi.S4G066400.t1"; gene_id "Phchi.S4G066400"
Phchi.S4	AUGUSTUS	exon	3999786	4000229	.	-	.	transcript_id "Phchi.S4G066400.t1"; gene_id "Phchi.S4G066400"
Phchi.S4	AUGUSTUS	start_codon	4000227	4000229	.	-	0	transcript_id "Phchi.S4G066400.t1"; gene_id "Phchi.S4G066400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg774.t1 is derived from g10556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5452229	5453974	.	-	.	Phchi.S6G073300
Phchi.S6	AUGUSTUS	transcript	5452229	5453974	.	-	.	transcript_id "Phchi.S6G073300.t1"; gene_id "Phchi.S6G073300"
Phchi.S6	AUGUSTUS	stop_codon	5452226	5452228	.	-	0	transcript_id "Phchi.S6G073300.t1"; gene_id "Phchi.S6G073300"
Phchi.S6	AUGUSTUS	CDS	5452229	5453974	1	-	0	transcript_id "Phchi.S6G073300.t1"; gene_id "Phchi.S6G073300"
Phchi.S6	AUGUSTUS	exon	5452229	5453974	.	-	.	transcript_id "Phchi.S6G073300.t1"; gene_id "Phchi.S6G073300"
Phchi.S6	AUGUSTUS	start_codon	5453972	5453974	.	-	0	transcript_id "Phchi.S6G073300.t1"; gene_id "Phchi.S6G073300"
# This transcript jg15526.t2 is derived from g13995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15527.t1 is derived from g13996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19727633	19728878	.	+	.	Phchi.S3G284600
Phchi.S3	AUGUSTUS	transcript	19727633	19728878	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	start_codon	19727633	19727635	.	+	0	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	CDS	19727633	19727944	1	+	0	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	exon	19727633	19727944	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	intron	19727945	19728043	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	CDS	19728044	19728241	0.9	+	0	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	exon	19728044	19728241	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	intron	19728242	19728350	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	CDS	19728351	19728579	0.74	+	0	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	exon	19728351	19728579	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	intron	19728580	19728867	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	CDS	19728868	19728878	1	+	2	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	exon	19728868	19728878	.	+	.	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
Phchi.S3	AUGUSTUS	stop_codon	19728879	19728881	.	+	0	transcript_id "Phchi.S3G284600.t1"; gene_id "Phchi.S3G284600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6907.t1 is derived from g4079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25932772	25933717	.	-	.	Phchi.S1G406600
Phchi.S1	AUGUSTUS	transcript	25932772	25933717	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	stop_codon	25932769	25932771	.	-	0	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	CDS	25932772	25932851	1	-	2	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	exon	25932772	25932851	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	intron	25932852	25932967	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	CDS	25932968	25933072	1	-	2	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	exon	25932968	25933072	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	intron	25933073	25933168	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	CDS	25933169	25933259	1	-	0	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	exon	25933169	25933259	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	intron	25933260	25933356	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	CDS	25933357	25933419	1	-	0	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	exon	25933357	25933419	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	intron	25933420	25933510	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	CDS	25933511	25933560	1	-	2	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	exon	25933511	25933560	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	intron	25933561	25933659	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	CDS	25933660	25933717	1	-	0	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	exon	25933660	25933717	.	-	.	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
Phchi.S1	AUGUSTUS	start_codon	25933715	25933717	.	-	0	transcript_id "Phchi.S1G406600.t1"; gene_id "Phchi.S1G406600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15359.t1 is derived from g13827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18583915	18584262	.	-	.	Phchi.S3G267800
Phchi.S3	AUGUSTUS	transcript	18583915	18584262	.	-	.	transcript_id "Phchi.S3G267800.t1"; gene_id "Phchi.S3G267800"
Phchi.S3	AUGUSTUS	stop_codon	18583912	18583914	.	-	0	transcript_id "Phchi.S3G267800.t1"; gene_id "Phchi.S3G267800"
Phchi.S3	AUGUSTUS	CDS	18583915	18584262	0.82	-	0	transcript_id "Phchi.S3G267800.t1"; gene_id "Phchi.S3G267800"
Phchi.S3	AUGUSTUS	exon	18583915	18584262	.	-	.	transcript_id "Phchi.S3G267800.t1"; gene_id "Phchi.S3G267800"
Phchi.S3	AUGUSTUS	start_codon	18584260	18584262	.	-	0	transcript_id "Phchi.S3G267800.t1"; gene_id "Phchi.S3G267800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2950.t1 is derived from g119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	721668	722323	.	+	.	Phchi.S1G010900
Phchi.S1	AUGUSTUS	transcript	721668	722323	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	start_codon	721668	721670	.	+	0	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	CDS	721668	721773	0.93	+	0	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	exon	721668	721773	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	intron	721774	721858	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	CDS	721859	721930	1	+	2	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	exon	721859	721930	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	intron	721931	722019	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	CDS	722020	722100	1	+	2	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	exon	722020	722100	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	intron	722101	722183	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	CDS	722184	722323	1	+	2	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	exon	722184	722323	.	+	.	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
Phchi.S1	AUGUSTUS	stop_codon	722324	722326	.	+	0	transcript_id "Phchi.S1G010900.t1"; gene_id "Phchi.S1G010900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg13913.t1 is derived from g12380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9635529	9637449	.	+	.	Phchi.S3G123200
Phchi.S3	AUGUSTUS	transcript	9635529	9637449	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	start_codon	9635529	9635531	.	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9635529	9635573	0.93	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9635529	9635573	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9635574	9635675	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9635676	9635746	0.99	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9635676	9635746	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9635747	9636188	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636189	9636240	0.98	+	1	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636189	9636240	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636241	9636427	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636428	9636494	0.99	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636428	9636494	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636495	9636580	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636581	9636666	1	+	2	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636581	9636666	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636667	9636750	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636751	9636816	1	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636751	9636816	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636817	9636909	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636910	9636957	1	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636910	9636957	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636958	9637109	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9637110	9637252	1	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9637110	9637252	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9637253	9637415	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9637416	9637449	1	+	1	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9637416	9637449	.	+	.	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	stop_codon	9637450	9637452	.	+	0	transcript_id "Phchi.S3G123200.t1"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	transcript	9635529	9637449	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	start_codon	9635529	9635531	.	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9635529	9635573	0.9	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9635529	9635573	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9635574	9635675	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9635676	9635746	1	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9635676	9635746	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9635747	9636188	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636189	9636240	1	+	1	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636189	9636240	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636241	9636427	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636428	9636494	1	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636428	9636494	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636495	9636580	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636581	9636666	1	+	2	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636581	9636666	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636667	9636765	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636766	9636816	1	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636766	9636816	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636817	9636909	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636910	9636957	1	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636910	9636957	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636958	9637109	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9637110	9637252	1	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9637110	9637252	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9637253	9637415	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9637416	9637449	1	+	1	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9637416	9637449	.	+	.	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	stop_codon	9637450	9637452	.	+	0	transcript_id "Phchi.S3G123200.t2"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	transcript	9635529	9637449	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	start_codon	9635529	9635531	.	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9635529	9635573	0.93	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9635529	9635573	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9635574	9635675	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9635676	9635746	1	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9635676	9635746	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9635747	9636167	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636168	9636240	0.73	+	1	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636168	9636240	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636241	9636427	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636428	9636494	1	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636428	9636494	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636495	9636580	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636581	9636666	1	+	2	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636581	9636666	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636667	9636765	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636766	9636816	1	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636766	9636816	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636817	9636909	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9636910	9636957	1	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9636910	9636957	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9636958	9637109	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9637110	9637252	1	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9637110	9637252	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	intron	9637253	9637415	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	CDS	9637416	9637449	1	+	1	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	exon	9637416	9637449	.	+	.	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
Phchi.S3	AUGUSTUS	stop_codon	9637450	9637452	.	+	0	transcript_id "Phchi.S3G123200.t3"; gene_id "Phchi.S3G123200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2853.t1 is derived from g22.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30009	34781	.	-	.	Phchi.S1G001200
Phchi.S1	AUGUSTUS	transcript	30009	34781	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	stop_codon	30006	30008	.	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	30009	30047	1	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	30009	30047	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	30048	30136	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	30137	30356	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	30137	30356	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	30357	30445	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	30446	30514	0.95	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	30446	30514	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	30515	30616	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	30617	30654	1	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	30617	30654	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	30655	30787	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	30788	30848	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	30788	30848	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	30849	31013	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	31014	31081	1	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	31014	31081	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	31082	31194	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	31195	31376	1	-	2	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	31195	31376	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	31377	31472	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	31473	31537	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	31473	31537	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	31538	31637	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	31638	31710	1	-	2	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	31638	31710	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	31711	31877	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	31878	31888	0.95	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	31878	31888	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	31889	32117	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	32118	32194	0.86	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	32118	32194	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	32195	32454	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	32455	32542	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	32455	32542	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	32543	32653	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	32654	32716	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	32654	32716	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	32717	32802	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	32803	32882	1	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	32803	32882	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	32883	33068	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	33069	33125	1	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	33069	33125	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	33126	33224	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	33225	33297	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	33225	33297	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	33298	33374	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	33375	33640	1	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	33375	33640	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	33641	33778	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	33779	34036	0.98	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	33779	34036	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	34037	34113	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	34114	34192	1	-	1	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	34114	34192	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	intron	34193	34422	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	CDS	34423	34781	0.8	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	exon	34423	34781	.	-	.	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
Phchi.S1	AUGUSTUS	start_codon	34779	34781	.	-	0	transcript_id "Phchi.S1G001200.t1"; gene_id "Phchi.S1G001200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9216.t1 is derived from g6391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40458082	40458492	.	+	.	Phchi.S1G637500
Phchi.S1	AUGUSTUS	transcript	40458082	40458492	.	+	.	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	start_codon	40458082	40458084	.	+	0	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	CDS	40458082	40458156	0.97	+	0	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	exon	40458082	40458156	.	+	.	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	intron	40458157	40458252	.	+	.	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	CDS	40458253	40458492	1	+	0	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	exon	40458253	40458492	.	+	.	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
Phchi.S1	AUGUSTUS	stop_codon	40458493	40458495	.	+	0	transcript_id "Phchi.S1G637500.t1"; gene_id "Phchi.S1G637500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12065.t1 is derived from g7740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1619628	1620952	.	-	.	Phchi.S2G014500
Phchi.S2	AUGUSTUS	transcript	1619628	1620952	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	stop_codon	1619625	1619627	.	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	CDS	1619628	1619789	1	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	exon	1619628	1619789	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	intron	1619790	1619902	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	CDS	1619903	1619956	1	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	exon	1619903	1619956	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	intron	1619957	1620070	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	CDS	1620071	1620166	0.52	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	exon	1620071	1620166	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	intron	1620167	1620262	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	CDS	1620263	1620477	0.96	-	2	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	exon	1620263	1620477	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	intron	1620478	1620632	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	CDS	1620633	1620732	1	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	exon	1620633	1620732	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	intron	1620733	1620853	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	CDS	1620854	1620952	0.53	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	exon	1620854	1620952	.	-	.	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
Phchi.S2	AUGUSTUS	start_codon	1620950	1620952	.	-	0	transcript_id "Phchi.S2G014500.t1"; gene_id "Phchi.S2G014500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5050.t1 is derived from g2220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14340509	14341675	.	+	.	Phchi.S1G220900
Phchi.S1	AUGUSTUS	transcript	14340509	14341675	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	start_codon	14340509	14340511	.	+	0	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	CDS	14340509	14340688	0.69	+	0	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	exon	14340509	14340688	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	intron	14340689	14340860	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	CDS	14340861	14340890	1	+	0	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	exon	14340861	14340890	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	intron	14340891	14341070	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	CDS	14341071	14341119	0.97	+	0	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	exon	14341071	14341119	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	intron	14341120	14341274	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	CDS	14341275	14341411	0.98	+	2	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	exon	14341275	14341411	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	intron	14341412	14341546	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	CDS	14341547	14341675	0.98	+	0	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	exon	14341547	14341675	.	+	.	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
Phchi.S1	AUGUSTUS	stop_codon	14341676	14341678	.	+	0	transcript_id "Phchi.S1G220900.t1"; gene_id "Phchi.S1G220900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1760.t1 is derived from g8680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2919710	2920477	.	+	.	Phchi.S5G036900
Phchi.S5	AUGUSTUS	transcript	2919710	2920477	.	+	.	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	start_codon	2919710	2919712	.	+	0	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	CDS	2919710	2920189	0.62	+	0	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	exon	2919710	2920189	.	+	.	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	intron	2920190	2920267	.	+	.	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	CDS	2920268	2920477	1	+	0	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	exon	2920268	2920477	.	+	.	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
Phchi.S5	AUGUSTUS	stop_codon	2920478	2920480	.	+	0	transcript_id "Phchi.S5G036900.t1"; gene_id "Phchi.S5G036900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11964.t1 is derived from g7639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	224712	228147	.	+	.	Phchi.S2G004400
Phchi.S2	AUGUSTUS	transcript	224712	228147	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	start_codon	224712	224714	.	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	224712	225839	0.84	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	224712	225839	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	225840	225942	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	225943	226083	0.99	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	225943	226083	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	226084	226224	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	226225	226572	1	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	226225	226572	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	226573	226667	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	226668	226731	1	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	226668	226731	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	226732	226819	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	226820	227037	0.94	+	2	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	226820	227037	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	227038	227118	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	227119	227232	0.91	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	227119	227232	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	227233	227321	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	227322	227427	0.85	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	227322	227427	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	227428	227517	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	227518	227729	0.75	+	2	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	227518	227729	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	227730	227804	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	227805	227908	0.89	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	227805	227908	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	intron	227909	227999	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	CDS	228000	228147	0.95	+	1	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	exon	228000	228147	.	+	.	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
Phchi.S2	AUGUSTUS	stop_codon	228148	228150	.	+	0	transcript_id "Phchi.S2G004400.t1"; gene_id "Phchi.S2G004400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12764.t1 is derived from g11229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1947640	1948746	.	+	.	Phchi.S3G008300
Phchi.S3	AUGUSTUS	transcript	1947640	1948746	.	+	.	transcript_id "Phchi.S3G008300.t1"; gene_id "Phchi.S3G008300"
Phchi.S3	AUGUSTUS	start_codon	1947640	1947642	.	+	0	transcript_id "Phchi.S3G008300.t1"; gene_id "Phchi.S3G008300"
Phchi.S3	AUGUSTUS	CDS	1947640	1948746	0.98	+	0	transcript_id "Phchi.S3G008300.t1"; gene_id "Phchi.S3G008300"
Phchi.S3	AUGUSTUS	exon	1947640	1948746	.	+	.	transcript_id "Phchi.S3G008300.t1"; gene_id "Phchi.S3G008300"
Phchi.S3	AUGUSTUS	stop_codon	1948747	1948749	.	+	0	transcript_id "Phchi.S3G008300.t1"; gene_id "Phchi.S3G008300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7364.t1 is derived from g4536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28781777	28783247	.	+	.	Phchi.S1G452300
Phchi.S1	AUGUSTUS	transcript	28781777	28783247	.	+	.	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	start_codon	28781777	28781779	.	+	0	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	CDS	28781777	28782217	0.56	+	0	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	exon	28781777	28782217	.	+	.	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	intron	28782218	28782362	.	+	.	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	CDS	28782363	28783247	0.79	+	0	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	exon	28782363	28783247	.	+	.	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
Phchi.S1	AUGUSTUS	stop_codon	28783248	28783250	.	+	0	transcript_id "Phchi.S1G452300.t1"; gene_id "Phchi.S1G452300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4722.t1 is derived from g1892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12479679	12481067	.	-	.	Phchi.S1G188100
Phchi.S1	AUGUSTUS	transcript	12479679	12481067	.	-	.	transcript_id "Phchi.S1G188100.t1"; gene_id "Phchi.S1G188100"
Phchi.S1	AUGUSTUS	stop_codon	12479676	12479678	.	-	0	transcript_id "Phchi.S1G188100.t1"; gene_id "Phchi.S1G188100"
Phchi.S1	AUGUSTUS	CDS	12479679	12481067	1	-	0	transcript_id "Phchi.S1G188100.t1"; gene_id "Phchi.S1G188100"
Phchi.S1	AUGUSTUS	exon	12479679	12481067	.	-	.	transcript_id "Phchi.S1G188100.t1"; gene_id "Phchi.S1G188100"
Phchi.S1	AUGUSTUS	start_codon	12481065	12481067	.	-	0	transcript_id "Phchi.S1G188100.t1"; gene_id "Phchi.S1G188100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12636.t1 is derived from g15985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C86	AUGUSTUS	gene	29077	30480	.	-	.	Phchi.C86G000500
Phchi.C86	AUGUSTUS	transcript	29077	30480	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	stop_codon	29074	29076	.	-	0	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	CDS	29077	29167	0.97	-	1	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	exon	29077	29167	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	intron	29168	29275	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	CDS	29276	29394	0.98	-	0	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	exon	29276	29394	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	intron	29395	29570	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	CDS	29571	29677	1	-	2	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	exon	29571	29677	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	intron	29678	29769	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	CDS	29770	29994	0.72	-	2	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	exon	29770	29994	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	intron	29995	30161	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	CDS	30162	30480	0.71	-	0	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	exon	30162	30480	.	-	.	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
Phchi.C86	AUGUSTUS	start_codon	30478	30480	.	-	0	transcript_id "Phchi.C86G000500.t1"; gene_id "Phchi.C86G000500"
# This transcript jg12330.t2 is derived from g8006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12331.t1 is derived from g8007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10995950	10998913	.	+	.	Phchi.S2G041100
Phchi.S2	AUGUSTUS	transcript	10995950	10998913	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	start_codon	10995950	10995952	.	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10995950	10996090	0.86	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10995950	10996090	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10996091	10996180	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10996181	10996240	0.99	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10996181	10996240	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10996241	10996317	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10996318	10996584	0.99	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10996318	10996584	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10996585	10996719	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10996720	10996818	0.99	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10996720	10996818	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10996819	10996929	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10996930	10997025	0.99	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10996930	10997025	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10997026	10997117	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10997118	10997207	0.6	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10997118	10997207	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10997208	10997325	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10997326	10997480	0.76	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10997326	10997480	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10997481	10997587	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10997588	10997708	0.67	+	1	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10997588	10997708	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10997709	10997936	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10997937	10998032	0.62	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10997937	10998032	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10998033	10998139	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10998140	10998236	0.45	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10998140	10998236	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10998237	10998344	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10998345	10998619	0.6	+	2	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10998345	10998619	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	intron	10998620	10998688	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	CDS	10998689	10998913	0.95	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	exon	10998689	10998913	.	+	.	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
Phchi.S2	AUGUSTUS	stop_codon	10998914	10998916	.	+	0	transcript_id "Phchi.S2G041100.t1"; gene_id "Phchi.S2G041100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg812.t1 is derived from g10594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5697626	5700509	.	+	.	Phchi.S6G077100
Phchi.S6	AUGUSTUS	transcript	5697626	5700509	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	start_codon	5697626	5697628	.	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5697626	5697796	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5697626	5697796	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5697797	5697910	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5697911	5698067	0.99	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5697911	5698067	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5698068	5698158	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5698159	5698226	1	+	2	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5698159	5698226	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5698227	5698327	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5698328	5698429	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5698328	5698429	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5698430	5698519	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5698520	5698672	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5698520	5698672	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5698673	5698747	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5698748	5698825	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5698748	5698825	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5698826	5698993	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5698994	5699119	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5698994	5699119	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5699120	5699244	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5699245	5699347	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5699245	5699347	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5699348	5699464	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5699465	5699565	1	+	2	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5699465	5699565	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5699566	5699654	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5699655	5700098	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5699655	5700098	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5700099	5700194	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5700195	5700308	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5700195	5700308	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	intron	5700309	5700401	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	CDS	5700402	5700509	1	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	exon	5700402	5700509	.	+	.	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
Phchi.S6	AUGUSTUS	stop_codon	5700510	5700512	.	+	0	transcript_id "Phchi.S6G077100.t1"; gene_id "Phchi.S6G077100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10512.t1 is derived from g14562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	770853	771668	.	+	.	Phchi.S4G009400
Phchi.S4	AUGUSTUS	transcript	770853	771668	.	+	.	transcript_id "Phchi.S4G009400.t1"; gene_id "Phchi.S4G009400"
Phchi.S4	AUGUSTUS	start_codon	770853	770855	.	+	0	transcript_id "Phchi.S4G009400.t1"; gene_id "Phchi.S4G009400"
Phchi.S4	AUGUSTUS	CDS	770853	771668	0.99	+	0	transcript_id "Phchi.S4G009400.t1"; gene_id "Phchi.S4G009400"
Phchi.S4	AUGUSTUS	exon	770853	771668	.	+	.	transcript_id "Phchi.S4G009400.t1"; gene_id "Phchi.S4G009400"
Phchi.S4	AUGUSTUS	stop_codon	771669	771671	.	+	0	transcript_id "Phchi.S4G009400.t1"; gene_id "Phchi.S4G009400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13721.t1 is derived from g12188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8505478	8507048	.	+	.	Phchi.S3G104000
Phchi.S3	AUGUSTUS	transcript	8505478	8507048	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	start_codon	8505478	8505480	.	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8505478	8505507	0.92	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8505478	8505507	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	intron	8505508	8505696	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8505697	8505927	0.99	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8505697	8505927	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	intron	8505928	8506057	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8506058	8506208	1	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8506058	8506208	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	intron	8506209	8506386	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8506387	8506475	1	+	2	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8506387	8506475	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	intron	8506476	8506575	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8506576	8506630	1	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8506576	8506630	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	intron	8506631	8506727	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8506728	8506813	1	+	2	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8506728	8506813	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	intron	8506814	8506907	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	CDS	8506908	8507048	0.99	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	exon	8506908	8507048	.	+	.	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
Phchi.S3	AUGUSTUS	stop_codon	8507049	8507051	.	+	0	transcript_id "Phchi.S3G104000.t1"; gene_id "Phchi.S3G104000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9.t1 is derived from g14437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C123	AUGUSTUS	gene	28805	30656	.	+	.	Phchi.C123G000100
Phchi.C123	AUGUSTUS	transcript	28805	30656	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	start_codon	28805	28807	.	+	0	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	CDS	28805	28979	0.98	+	0	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	exon	28805	28979	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	intron	28980	29139	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	CDS	29140	29245	0.5	+	2	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	exon	29140	29245	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	intron	29246	29390	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	CDS	29391	29501	0.51	+	1	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	exon	29391	29501	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	intron	29502	29821	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	CDS	29822	30656	1	+	1	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	exon	29822	30656	.	+	.	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
Phchi.C123	AUGUSTUS	stop_codon	30657	30659	.	+	0	transcript_id "Phchi.C123G000100.t1"; gene_id "Phchi.C123G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1481.t1 is derived from g8400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1134522	1138119	.	-	.	Phchi.S5G009000
Phchi.S5	AUGUSTUS	transcript	1134522	1138119	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	stop_codon	1134519	1134521	.	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1134522	1134655	0.97	-	2	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1134522	1134655	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1134656	1134736	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1134737	1134932	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1134737	1134932	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1134933	1135020	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1135021	1135186	1	-	1	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1135021	1135186	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1135187	1135273	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1135274	1135368	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1135274	1135368	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1135369	1135446	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1135447	1135531	1	-	1	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1135447	1135531	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1135532	1135662	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1135663	1135814	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1135663	1135814	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1135815	1135922	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1135923	1136039	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1135923	1136039	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1136040	1136185	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1136186	1136320	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1136186	1136320	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1136321	1136403	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1136404	1136493	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1136404	1136493	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1136494	1136639	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1136640	1136792	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1136640	1136792	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1136793	1136924	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1136925	1137101	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1136925	1137101	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1137102	1137227	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1137228	1137431	1	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1137228	1137431	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1137432	1137578	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1137579	1137688	1	-	2	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1137579	1137688	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	intron	1137689	1137866	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	CDS	1137867	1138119	0.96	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	exon	1137867	1138119	.	-	.	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
Phchi.S5	AUGUSTUS	start_codon	1138117	1138119	.	-	0	transcript_id "Phchi.S5G009000.t1"; gene_id "Phchi.S5G009000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5115.t1 is derived from g2285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14800250	14803204	.	-	.	Phchi.S1G227400
Phchi.S1	AUGUSTUS	transcript	14800250	14803204	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	stop_codon	14800247	14800249	.	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14800250	14800403	0.98	-	1	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14800250	14800403	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14800404	14800506	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14800507	14800637	0.99	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14800507	14800637	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14800638	14800757	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14800758	14800826	1	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14800758	14800826	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14800827	14801040	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801041	14801133	1	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801041	14801133	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801134	14801271	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801272	14801298	1	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801272	14801298	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801299	14801388	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801389	14801481	1	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801389	14801481	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801482	14801658	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801659	14801747	1	-	2	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801659	14801747	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801748	14801846	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801847	14801925	1	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801847	14801925	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801926	14802050	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802051	14802171	1	-	1	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802051	14802171	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802172	14802328	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802329	14802449	1	-	2	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802329	14802449	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802450	14802565	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802566	14802673	0.97	-	2	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802566	14802673	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802674	14802774	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802775	14802875	0.84	-	1	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802775	14802875	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802876	14802980	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802981	14803204	0.86	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802981	14803204	.	-	.	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	start_codon	14803202	14803204	.	-	0	transcript_id "Phchi.S1G227400.t1"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	transcript	14800250	14803204	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	stop_codon	14800247	14800249	.	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14800250	14800403	0.95	-	1	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14800250	14800403	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14800404	14800506	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14800507	14800637	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14800507	14800637	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14800638	14800757	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14800758	14800826	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14800758	14800826	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14800827	14801040	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801041	14801133	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801041	14801133	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801134	14801271	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801272	14801298	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801272	14801298	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801299	14801388	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801389	14801481	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801389	14801481	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801482	14801658	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801659	14801747	1	-	2	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801659	14801747	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801748	14801846	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14801847	14801925	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14801847	14801925	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14801926	14802050	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802051	14802185	1	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802051	14802185	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802186	14802328	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802329	14802365	0.78	-	1	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802329	14802365	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802366	14802459	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802460	14802673	0.51	-	2	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802460	14802673	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802674	14802774	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802775	14802875	0.77	-	1	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802775	14802875	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	intron	14802876	14802980	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	CDS	14802981	14803204	0.72	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	exon	14802981	14803204	.	-	.	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
Phchi.S1	AUGUSTUS	start_codon	14803202	14803204	.	-	0	transcript_id "Phchi.S1G227400.t2"; gene_id "Phchi.S1G227400"
# This transcript jg2097.t2 is derived from g9017.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2097.t3 is derived from g9017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2098.t1 is derived from g9018.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4857758	4858994	.	+	.	Phchi.S5G070700
Phchi.S5	AUGUSTUS	transcript	4857758	4858994	.	+	.	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	start_codon	4857758	4857760	.	+	0	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	CDS	4857758	4858360	0.83	+	0	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	exon	4857758	4858360	.	+	.	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	intron	4858361	4858502	.	+	.	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	CDS	4858503	4858994	1	+	0	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	exon	4858503	4858994	.	+	.	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
Phchi.S5	AUGUSTUS	stop_codon	4858995	4858997	.	+	0	transcript_id "Phchi.S5G070700.t1"; gene_id "Phchi.S5G070700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15681.t1 is derived from g14150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20634927	20635784	.	+	.	Phchi.S3G300000
Phchi.S3	AUGUSTUS	transcript	20634927	20635784	.	+	.	transcript_id "Phchi.S3G300000.t1"; gene_id "Phchi.S3G300000"
Phchi.S3	AUGUSTUS	start_codon	20634927	20634929	.	+	0	transcript_id "Phchi.S3G300000.t1"; gene_id "Phchi.S3G300000"
Phchi.S3	AUGUSTUS	CDS	20634927	20635784	0.43	+	0	transcript_id "Phchi.S3G300000.t1"; gene_id "Phchi.S3G300000"
Phchi.S3	AUGUSTUS	exon	20634927	20635784	.	+	.	transcript_id "Phchi.S3G300000.t1"; gene_id "Phchi.S3G300000"
Phchi.S3	AUGUSTUS	stop_codon	20635785	20635787	.	+	0	transcript_id "Phchi.S3G300000.t1"; gene_id "Phchi.S3G300000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1761.t1 is derived from g8681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2921344	2922255	.	-	.	Phchi.S5G037000
Phchi.S5	AUGUSTUS	transcript	2921344	2922255	.	-	.	transcript_id "Phchi.S5G037000.t1"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	stop_codon	2921341	2921343	.	-	0	transcript_id "Phchi.S5G037000.t1"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	CDS	2921344	2922255	0.96	-	0	transcript_id "Phchi.S5G037000.t1"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	exon	2921344	2922255	.	-	.	transcript_id "Phchi.S5G037000.t1"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	start_codon	2922253	2922255	.	-	0	transcript_id "Phchi.S5G037000.t1"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	transcript	2921344	2921970	.	-	.	transcript_id "Phchi.S5G037000.t2"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	stop_codon	2921341	2921343	.	-	0	transcript_id "Phchi.S5G037000.t2"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	CDS	2921344	2921970	0.47	-	0	transcript_id "Phchi.S5G037000.t2"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	exon	2921344	2921970	.	-	.	transcript_id "Phchi.S5G037000.t2"; gene_id "Phchi.S5G037000"
Phchi.S5	AUGUSTUS	start_codon	2921968	2921970	.	-	0	transcript_id "Phchi.S5G037000.t2"; gene_id "Phchi.S5G037000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14259.t1 is derived from g12726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11788463	11789361	.	-	.	Phchi.S3G157800
Phchi.S3	AUGUSTUS	transcript	11788463	11789361	.	-	.	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	stop_codon	11788460	11788462	.	-	0	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	CDS	11788463	11788702	0.94	-	0	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	exon	11788463	11788702	.	-	.	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	intron	11788703	11788809	.	-	.	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	CDS	11788810	11788945	0.97	-	1	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	exon	11788810	11788945	.	-	.	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	intron	11788946	11789074	.	-	.	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	CDS	11789075	11789361	1	-	0	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	exon	11789075	11789361	.	-	.	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
Phchi.S3	AUGUSTUS	start_codon	11789359	11789361	.	-	0	transcript_id "Phchi.S3G157800.t1"; gene_id "Phchi.S3G157800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2944.t1 is derived from g113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	706055	708051	.	+	.	Phchi.S1G010300
Phchi.S1	AUGUSTUS	transcript	706055	708051	.	+	.	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	start_codon	706055	706057	.	+	0	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	CDS	706055	706075	0.33	+	0	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	exon	706055	706075	.	+	.	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	intron	706076	706165	.	+	.	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	CDS	706166	706247	0.46	+	0	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	exon	706166	706247	.	+	.	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	intron	706248	706504	.	+	.	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	CDS	706505	708051	0.99	+	2	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	exon	706505	708051	.	+	.	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
Phchi.S1	AUGUSTUS	stop_codon	708052	708054	.	+	0	transcript_id "Phchi.S1G010300.t1"; gene_id "Phchi.S1G010300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11624.t1 is derived from g15675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7372644	7375001	.	+	.	Phchi.S4G120600
Phchi.S4	AUGUSTUS	transcript	7372644	7375001	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	start_codon	7372644	7372646	.	+	0	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	CDS	7372644	7373615	0.6	+	0	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	exon	7372644	7373615	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	intron	7373616	7373824	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	CDS	7373825	7373874	1	+	0	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	exon	7373825	7373874	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	intron	7373875	7373955	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	CDS	7373956	7373996	1	+	1	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	exon	7373956	7373996	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	intron	7373997	7374090	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	CDS	7374091	7375001	0.99	+	2	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	exon	7374091	7375001	.	+	.	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
Phchi.S4	AUGUSTUS	stop_codon	7375002	7375004	.	+	0	transcript_id "Phchi.S4G120600.t1"; gene_id "Phchi.S4G120600"
# This transcript jg553.t2 is derived from g10335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg554.t1 is derived from g10336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4024428	4030840	.	-	.	Phchi.S6G051300
Phchi.S6	AUGUSTUS	transcript	4024428	4030840	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	stop_codon	4024425	4024427	.	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4024428	4024580	0.91	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4024428	4024580	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4024581	4024655	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4024656	4024692	1	-	1	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4024656	4024692	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4024693	4024787	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4024788	4024846	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4024788	4024846	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4024847	4024954	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4024955	4025080	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4024955	4025080	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4025081	4025161	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4025162	4025266	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4025162	4025266	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4025267	4025341	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4025342	4025410	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4025342	4025410	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4025411	4025492	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4025493	4025558	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4025493	4025558	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4025559	4025636	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4025637	4025723	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4025637	4025723	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4025724	4025820	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4025821	4025877	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4025821	4025877	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4025878	4025975	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4025976	4026104	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4025976	4026104	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4026105	4026229	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4026230	4026295	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4026230	4026295	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4026296	4026382	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4026383	4026451	0.98	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4026383	4026451	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4026452	4026566	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4026567	4026644	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4026567	4026644	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4026645	4026728	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4026729	4026884	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4026729	4026884	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4026885	4026974	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4026975	4027016	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4026975	4027016	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027017	4027105	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4027106	4027189	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4027106	4027189	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027190	4027273	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4027274	4027340	1	-	1	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4027274	4027340	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027341	4027415	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4027416	4027482	1	-	2	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4027416	4027482	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027483	4027582	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4027583	4027649	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4027583	4027649	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027650	4027724	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4027725	4027769	0.87	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4027725	4027769	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027770	4027927	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4027928	4027987	0.93	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4027928	4027987	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4027988	4028064	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4028065	4028261	0.99	-	2	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4028065	4028261	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4028262	4028344	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4028345	4028396	0.97	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4028345	4028396	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4028397	4028501	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4028502	4028577	0.94	-	1	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4028502	4028577	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4028578	4028695	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4028696	4028751	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4028696	4028751	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4028752	4028891	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4028892	4029076	1	-	2	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4028892	4029076	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4029077	4029150	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4029151	4029202	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4029151	4029202	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4029203	4029298	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4029299	4029377	1	-	1	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4029299	4029377	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4029378	4029556	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4029557	4029612	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4029557	4029612	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4029613	4029705	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4029706	4029869	0.95	-	2	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4029706	4029869	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4029870	4029984	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4029985	4030039	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4029985	4030039	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4030040	4030129	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4030130	4030205	1	-	1	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4030130	4030205	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4030206	4030285	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4030286	4030341	1	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4030286	4030341	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	intron	4030342	4030438	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	CDS	4030439	4030840	0.62	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	exon	4030439	4030840	.	-	.	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
Phchi.S6	AUGUSTUS	start_codon	4030838	4030840	.	-	0	transcript_id "Phchi.S6G051300.t1"; gene_id "Phchi.S6G051300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11862.t1 is derived from g15914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8809526	8810787	.	+	.	Phchi.S4G144400
Phchi.S4	AUGUSTUS	transcript	8809526	8810787	.	+	.	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	start_codon	8809526	8809528	.	+	0	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	CDS	8809526	8809985	0.81	+	0	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	exon	8809526	8809985	.	+	.	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	intron	8809986	8810104	.	+	.	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	CDS	8810105	8810787	0.92	+	2	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	exon	8810105	8810787	.	+	.	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
Phchi.S4	AUGUSTUS	stop_codon	8810788	8810790	.	+	0	transcript_id "Phchi.S4G144400.t1"; gene_id "Phchi.S4G144400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9195.t1 is derived from g6370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40298048	40298885	.	-	.	Phchi.S1G635400
Phchi.S1	AUGUSTUS	transcript	40298048	40298885	.	-	.	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	stop_codon	40298045	40298047	.	-	0	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	CDS	40298048	40298183	1	-	1	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	exon	40298048	40298183	.	-	.	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	intron	40298184	40298270	.	-	.	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	CDS	40298271	40298621	1	-	1	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	exon	40298271	40298621	.	-	.	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	intron	40298622	40298712	.	-	.	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	CDS	40298713	40298885	0.97	-	0	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	exon	40298713	40298885	.	-	.	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
Phchi.S1	AUGUSTUS	start_codon	40298883	40298885	.	-	0	transcript_id "Phchi.S1G635400.t1"; gene_id "Phchi.S1G635400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2454.t1 is derived from g9374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6733013	6733964	.	+	.	Phchi.S5G106300
Phchi.S5	AUGUSTUS	transcript	6733013	6733964	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	start_codon	6733013	6733015	.	+	0	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	CDS	6733013	6733207	0.48	+	0	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	exon	6733013	6733207	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	intron	6733208	6733288	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	CDS	6733289	6733367	0.39	+	0	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	exon	6733289	6733367	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	intron	6733368	6733648	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	CDS	6733649	6733727	0.47	+	2	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	exon	6733649	6733727	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	intron	6733728	6733804	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	CDS	6733805	6733964	0.63	+	1	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	exon	6733805	6733964	.	+	.	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
Phchi.S5	AUGUSTUS	stop_codon	6733965	6733967	.	+	0	transcript_id "Phchi.S5G106300.t1"; gene_id "Phchi.S5G106300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7474.t1 is derived from g4647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29540609	29544087	.	+	.	Phchi.S1G463300
Phchi.S1	AUGUSTUS	transcript	29540609	29544087	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	start_codon	29540609	29540611	.	+	0	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29540609	29540816	0.84	+	0	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29540609	29540816	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	intron	29540817	29540894	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29540895	29540962	1	+	2	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29540895	29540962	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	intron	29540963	29541042	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29541043	29541154	1	+	0	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29541043	29541154	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	intron	29541155	29541319	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29541320	29541399	1	+	2	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29541320	29541399	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	intron	29541400	29541707	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29541708	29541895	1	+	0	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29541708	29541895	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	intron	29541896	29542005	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29542006	29542517	0.95	+	1	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29542006	29542517	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	intron	29542518	29542609	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	CDS	29542610	29544087	0.8	+	2	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	exon	29542610	29544087	.	+	.	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
Phchi.S1	AUGUSTUS	stop_codon	29544088	29544090	.	+	0	transcript_id "Phchi.S1G463300.t1"; gene_id "Phchi.S1G463300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2509.t1 is derived from g9429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7062126	7065732	.	-	.	Phchi.S5G111800
Phchi.S5	AUGUSTUS	transcript	7062126	7065732	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	stop_codon	7062123	7062125	.	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7062126	7062250	1	-	2	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7062126	7062250	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7062251	7062346	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7062347	7062430	1	-	2	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7062347	7062430	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7062431	7062537	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7062538	7062608	1	-	1	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7062538	7062608	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7062609	7062695	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7062696	7062838	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7062696	7062838	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7062839	7062961	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7062962	7063054	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7062962	7063054	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7063055	7063139	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7063140	7063193	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7063140	7063193	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7063194	7063271	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7063272	7063428	1	-	1	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7063272	7063428	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7063429	7063571	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7063572	7063606	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7063572	7063606	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7063607	7063763	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7063764	7063943	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7063764	7063943	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7063944	7064494	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7064495	7064645	0.6	-	1	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7064495	7064645	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7064646	7064732	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7064733	7064741	0.34	-	1	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7064733	7064741	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7064742	7064960	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7064961	7065073	0.51	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7064961	7065073	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7065074	7065211	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7065212	7065370	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7065212	7065370	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	intron	7065371	7065558	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	CDS	7065559	7065732	1	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	exon	7065559	7065732	.	-	.	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
Phchi.S5	AUGUSTUS	start_codon	7065730	7065732	.	-	0	transcript_id "Phchi.S5G111800.t1"; gene_id "Phchi.S5G111800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg583.t1 is derived from g10365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4293257	4293502	.	-	.	Phchi.S6G054200
Phchi.S6	AUGUSTUS	transcript	4293257	4293502	.	-	.	transcript_id "Phchi.S6G054200.t1"; gene_id "Phchi.S6G054200"
Phchi.S6	AUGUSTUS	stop_codon	4293254	4293256	.	-	0	transcript_id "Phchi.S6G054200.t1"; gene_id "Phchi.S6G054200"
Phchi.S6	AUGUSTUS	CDS	4293257	4293502	0.49	-	0	transcript_id "Phchi.S6G054200.t1"; gene_id "Phchi.S6G054200"
Phchi.S6	AUGUSTUS	exon	4293257	4293502	.	-	.	transcript_id "Phchi.S6G054200.t1"; gene_id "Phchi.S6G054200"
Phchi.S6	AUGUSTUS	start_codon	4293500	4293502	.	-	0	transcript_id "Phchi.S6G054200.t1"; gene_id "Phchi.S6G054200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5378.t1 is derived from g2548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16582627	16583768	.	-	.	Phchi.S1G253700
Phchi.S1	AUGUSTUS	transcript	16582627	16583768	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	stop_codon	16582624	16582626	.	-	0	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	CDS	16582627	16582779	1	-	0	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	exon	16582627	16582779	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	intron	16582780	16582870	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	CDS	16582871	16583132	1	-	1	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	exon	16582871	16583132	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	intron	16583133	16583236	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	CDS	16583237	16583391	1	-	0	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	exon	16583237	16583391	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	intron	16583392	16583488	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	CDS	16583489	16583610	1	-	2	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	exon	16583489	16583610	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	intron	16583611	16583698	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	CDS	16583699	16583768	0.45	-	0	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	exon	16583699	16583768	.	-	.	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
Phchi.S1	AUGUSTUS	start_codon	16583766	16583768	.	-	0	transcript_id "Phchi.S1G253700.t1"; gene_id "Phchi.S1G253700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14022.t1 is derived from g12489.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10344609	10345571	.	-	.	Phchi.S3G134100
Phchi.S3	AUGUSTUS	transcript	10344609	10345571	.	-	.	transcript_id "Phchi.S3G134100.t1"; gene_id "Phchi.S3G134100"
Phchi.S3	AUGUSTUS	stop_codon	10344606	10344608	.	-	0	transcript_id "Phchi.S3G134100.t1"; gene_id "Phchi.S3G134100"
Phchi.S3	AUGUSTUS	CDS	10344609	10345571	0.63	-	0	transcript_id "Phchi.S3G134100.t1"; gene_id "Phchi.S3G134100"
Phchi.S3	AUGUSTUS	exon	10344609	10345571	.	-	.	transcript_id "Phchi.S3G134100.t1"; gene_id "Phchi.S3G134100"
Phchi.S3	AUGUSTUS	start_codon	10345569	10345571	.	-	0	transcript_id "Phchi.S3G134100.t1"; gene_id "Phchi.S3G134100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5222.t1 is derived from g2392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15568702	15569928	.	-	.	Phchi.S1G238100
Phchi.S1	AUGUSTUS	transcript	15568702	15569928	.	-	.	transcript_id "Phchi.S1G238100.t1"; gene_id "Phchi.S1G238100"
Phchi.S1	AUGUSTUS	stop_codon	15568699	15568701	.	-	0	transcript_id "Phchi.S1G238100.t1"; gene_id "Phchi.S1G238100"
Phchi.S1	AUGUSTUS	CDS	15568702	15569928	0.89	-	0	transcript_id "Phchi.S1G238100.t1"; gene_id "Phchi.S1G238100"
Phchi.S1	AUGUSTUS	exon	15568702	15569928	.	-	.	transcript_id "Phchi.S1G238100.t1"; gene_id "Phchi.S1G238100"
Phchi.S1	AUGUSTUS	start_codon	15569926	15569928	.	-	0	transcript_id "Phchi.S1G238100.t1"; gene_id "Phchi.S1G238100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8342.t1 is derived from g5517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35404632	35406315	.	-	.	Phchi.S1G550100
Phchi.S1	AUGUSTUS	transcript	35404632	35406315	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	stop_codon	35404629	35404631	.	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35404632	35404777	1	-	2	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35404632	35404777	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35404778	35404854	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35404855	35404972	1	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35404855	35404972	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35404973	35405064	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405065	35405202	0.99	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405065	35405202	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405203	35405317	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405318	35405410	1	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405318	35405410	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405411	35405488	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405489	35405738	0.99	-	1	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405489	35405738	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405739	35405846	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405847	35405977	0.99	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405847	35405977	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405978	35406060	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35406061	35406315	0.69	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35406061	35406315	.	-	.	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	start_codon	35406313	35406315	.	-	0	transcript_id "Phchi.S1G550100.t1"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	transcript	35404632	35406315	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	stop_codon	35404629	35404631	.	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35404632	35404777	1	-	2	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35404632	35404777	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35404778	35404854	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35404855	35404972	1	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35404855	35404972	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35404973	35405064	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405065	35405202	1	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405065	35405202	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405203	35405317	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405318	35405410	1	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405318	35405410	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405411	35405488	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405489	35405775	0.41	-	2	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405489	35405775	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405776	35405893	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405894	35405981	0.31	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405894	35405981	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405982	35406060	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35406061	35406315	0.66	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35406061	35406315	.	-	.	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	start_codon	35406313	35406315	.	-	0	transcript_id "Phchi.S1G550100.t2"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	transcript	35404632	35406315	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	stop_codon	35404629	35404631	.	-	0	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35404632	35404777	0.99	-	2	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35404632	35404777	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35404778	35404854	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35404855	35404972	1	-	0	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35404855	35404972	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35404973	35405064	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405065	35405202	1	-	0	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405065	35405202	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405203	35405317	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405318	35405402	0.53	-	1	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405318	35405402	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405403	35405488	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405489	35405495	0.51	-	2	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405489	35405495	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405496	35405622	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405623	35405738	0.48	-	1	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405623	35405738	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405739	35405846	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35405847	35405977	0.94	-	0	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35405847	35405977	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	intron	35405978	35406060	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	CDS	35406061	35406315	0.65	-	0	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	exon	35406061	35406315	.	-	.	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
Phchi.S1	AUGUSTUS	start_codon	35406313	35406315	.	-	0	transcript_id "Phchi.S1G550100.t3"; gene_id "Phchi.S1G550100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7757.t1 is derived from g4931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31153093	31153509	.	+	.	Phchi.S1G491600
Phchi.S1	AUGUSTUS	transcript	31153093	31153509	.	+	.	transcript_id "Phchi.S1G491600.t1"; gene_id "Phchi.S1G491600"
Phchi.S1	AUGUSTUS	start_codon	31153093	31153095	.	+	0	transcript_id "Phchi.S1G491600.t1"; gene_id "Phchi.S1G491600"
Phchi.S1	AUGUSTUS	CDS	31153093	31153509	0.28	+	0	transcript_id "Phchi.S1G491600.t1"; gene_id "Phchi.S1G491600"
Phchi.S1	AUGUSTUS	exon	31153093	31153509	.	+	.	transcript_id "Phchi.S1G491600.t1"; gene_id "Phchi.S1G491600"
Phchi.S1	AUGUSTUS	stop_codon	31153510	31153512	.	+	0	transcript_id "Phchi.S1G491600.t1"; gene_id "Phchi.S1G491600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3437.t1 is derived from g606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3644019	3644695	.	-	.	Phchi.S1G059600
Phchi.S1	AUGUSTUS	transcript	3644019	3644695	.	-	.	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	stop_codon	3644016	3644018	.	-	0	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	CDS	3644019	3644151	0.43	-	1	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	exon	3644019	3644151	.	-	.	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	intron	3644152	3644294	.	-	.	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	CDS	3644295	3644695	0.4	-	0	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	exon	3644295	3644695	.	-	.	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
Phchi.S1	AUGUSTUS	start_codon	3644693	3644695	.	-	0	transcript_id "Phchi.S1G059600.t1"; gene_id "Phchi.S1G059600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5144.t1 is derived from g2314.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15136202	15137464	.	+	.	Phchi.S1G230300
Phchi.S1	AUGUSTUS	transcript	15136202	15137464	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	start_codon	15136202	15136204	.	+	0	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136202	15136229	0.98	+	0	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136202	15136229	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136230	15136321	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136322	15136393	1	+	2	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136322	15136393	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136394	15136484	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136485	15136672	1	+	2	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136485	15136672	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136673	15136781	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136782	15136845	1	+	0	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136782	15136845	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136846	15136951	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136952	15137036	0.99	+	2	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136952	15137036	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15137037	15137136	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15137137	15137260	1	+	1	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15137137	15137260	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15137261	15137356	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15137357	15137464	1	+	0	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15137357	15137464	.	+	.	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	stop_codon	15137465	15137467	.	+	0	transcript_id "Phchi.S1G230300.t1"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	transcript	15136224	15137464	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	start_codon	15136224	15136226	.	+	0	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136224	15136229	0.97	+	0	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136224	15136229	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136230	15136311	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136312	15136393	1	+	0	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136312	15136393	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136394	15136484	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136485	15136672	0.99	+	2	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136485	15136672	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136673	15136781	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136782	15136845	1	+	0	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136782	15136845	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15136846	15136951	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15136952	15137036	0.98	+	2	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15136952	15137036	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15137037	15137136	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15137137	15137260	1	+	1	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15137137	15137260	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	intron	15137261	15137356	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	CDS	15137357	15137464	1	+	0	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	exon	15137357	15137464	.	+	.	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
Phchi.S1	AUGUSTUS	stop_codon	15137465	15137467	.	+	0	transcript_id "Phchi.S1G230300.t2"; gene_id "Phchi.S1G230300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg970.t1 is derived from g10753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6716093	6717753	.	-	.	Phchi.S6G092900
Phchi.S6	AUGUSTUS	transcript	6716093	6717753	.	-	.	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	stop_codon	6716090	6716092	.	-	0	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	CDS	6716093	6716859	0.43	-	2	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	exon	6716093	6716859	.	-	.	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	intron	6716860	6716986	.	-	.	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	CDS	6716987	6717028	0.89	-	2	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	exon	6716987	6717028	.	-	.	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	intron	6717029	6717176	.	-	.	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	CDS	6717177	6717753	0.46	-	0	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	exon	6717177	6717753	.	-	.	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
Phchi.S6	AUGUSTUS	start_codon	6717751	6717753	.	-	0	transcript_id "Phchi.S6G092900.t1"; gene_id "Phchi.S6G092900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9632.t1 is derived from g6808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42994348	42996828	.	+	.	Phchi.S1G679100
Phchi.S1	AUGUSTUS	transcript	42994348	42996828	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	start_codon	42994348	42994350	.	+	0	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	CDS	42994348	42994765	0.75	+	0	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	exon	42994348	42994765	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	intron	42994766	42994867	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	CDS	42994868	42995827	0.29	+	2	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	exon	42994868	42995827	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	intron	42995828	42995981	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	CDS	42995982	42996051	0.18	+	2	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	exon	42995982	42996051	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	intron	42996052	42996315	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	CDS	42996316	42996413	0.32	+	1	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	exon	42996316	42996413	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	intron	42996414	42996622	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	CDS	42996623	42996704	0.42	+	2	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	exon	42996623	42996704	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	intron	42996705	42996827	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	CDS	42996828	42996828	0.42	+	1	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	exon	42996828	42996828	.	+	.	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
Phchi.S1	AUGUSTUS	stop_codon	42996829	42996831	.	+	0	transcript_id "Phchi.S1G679100.t1"; gene_id "Phchi.S1G679100"
# This transcript jg1035.t2 is derived from g10818.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1036.t1 is derived from g10819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7228405	7229513	.	+	.	Phchi.S6G099500
Phchi.S6	AUGUSTUS	transcript	7228405	7229513	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	start_codon	7228405	7228407	.	+	0	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	CDS	7228405	7228536	0.76	+	0	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	exon	7228405	7228536	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	intron	7228537	7228621	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	CDS	7228622	7228765	0.91	+	0	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	exon	7228622	7228765	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	intron	7228766	7228840	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	CDS	7228841	7228972	0.49	+	0	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	exon	7228841	7228972	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	intron	7228973	7229069	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	CDS	7229070	7229513	0.89	+	0	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	exon	7229070	7229513	.	+	.	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
Phchi.S6	AUGUSTUS	stop_codon	7229514	7229516	.	+	0	transcript_id "Phchi.S6G099500.t1"; gene_id "Phchi.S6G099500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5538.t1 is derived from g2708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17456772	17457537	.	-	.	Phchi.S1G269700
Phchi.S1	AUGUSTUS	transcript	17456772	17457537	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	stop_codon	17456769	17456771	.	-	0	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	CDS	17456772	17456840	0.73	-	0	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	exon	17456772	17456840	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	intron	17456841	17456932	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	CDS	17456933	17457063	0.73	-	2	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	exon	17456933	17457063	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	intron	17457064	17457177	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	CDS	17457178	17457262	0.91	-	0	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	exon	17457178	17457262	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	intron	17457263	17457353	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	CDS	17457354	17457446	1	-	0	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	exon	17457354	17457446	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	intron	17457447	17457534	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	CDS	17457535	17457537	1	-	0	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	exon	17457535	17457537	.	-	.	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
Phchi.S1	AUGUSTUS	start_codon	17457535	17457537	.	-	0	transcript_id "Phchi.S1G269700.t1"; gene_id "Phchi.S1G269700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15711.t1 is derived from g14181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20808415	20809842	.	+	.	Phchi.S3G303000
Phchi.S3	AUGUSTUS	transcript	20808415	20809842	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	start_codon	20808415	20808417	.	+	0	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	CDS	20808415	20808861	0.61	+	0	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	exon	20808415	20808861	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	intron	20808862	20808970	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	CDS	20808971	20809106	0.96	+	0	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	exon	20808971	20809106	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	intron	20809107	20809188	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	CDS	20809189	20809280	1	+	2	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	exon	20809189	20809280	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	intron	20809281	20809383	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	CDS	20809384	20809486	0.99	+	0	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	exon	20809384	20809486	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	intron	20809487	20809579	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	CDS	20809580	20809842	0.95	+	2	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	exon	20809580	20809842	.	+	.	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
Phchi.S3	AUGUSTUS	stop_codon	20809843	20809845	.	+	0	transcript_id "Phchi.S3G303000.t1"; gene_id "Phchi.S3G303000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9234.t1 is derived from g6409.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40529537	40531218	.	-	.	Phchi.S1G639300
Phchi.S1	AUGUSTUS	transcript	40529537	40531218	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	stop_codon	40529534	40529536	.	-	0	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	CDS	40529537	40530495	0.96	-	2	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	exon	40529537	40530495	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	intron	40530496	40530590	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	CDS	40530591	40530606	0.98	-	0	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	exon	40530591	40530606	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	intron	40530607	40530710	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	CDS	40530711	40530814	0.98	-	2	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	exon	40530711	40530814	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	intron	40530815	40530902	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	CDS	40530903	40531218	1	-	0	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	exon	40530903	40531218	.	-	.	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
Phchi.S1	AUGUSTUS	start_codon	40531216	40531218	.	-	0	transcript_id "Phchi.S1G639300.t1"; gene_id "Phchi.S1G639300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15701.t1 is derived from g14170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20764048	20775433	.	-	.	Phchi.S3G302000
Phchi.S3	AUGUSTUS	transcript	20764048	20775433	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	stop_codon	20764045	20764047	.	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20764048	20764135	0.79	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20764048	20764135	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20764136	20764223	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20764224	20764445	1	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20764224	20764445	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20764446	20764532	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20764533	20764864	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20764533	20764864	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20764865	20765002	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20765003	20765145	1	-	2	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20765003	20765145	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20765146	20765239	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20765240	20765306	0.98	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20765240	20765306	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20765307	20765426	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20765427	20765735	0.5	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20765427	20765735	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20765736	20765846	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20765847	20766039	0.99	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20765847	20766039	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20766040	20766124	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20766125	20766369	0.96	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20766125	20766369	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20766370	20766651	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20766652	20766843	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20766652	20766843	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20766844	20767014	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20767015	20767114	1	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20767015	20767114	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20767115	20767206	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20767207	20767562	0.98	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20767207	20767562	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20767563	20767649	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20767650	20767844	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20767650	20767844	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20767845	20767935	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20767936	20768100	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20767936	20768100	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20768101	20768203	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20768204	20768404	0.99	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20768204	20768404	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20768405	20768552	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20768553	20768924	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20768553	20768924	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20768925	20769046	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20769047	20769235	0.67	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20769047	20769235	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20769236	20769358	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20769359	20769517	0.87	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20769359	20769517	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20769518	20769817	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20769818	20769931	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20769818	20769931	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20769932	20770034	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20770035	20770132	0.92	-	2	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20770035	20770132	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20770133	20770255	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20770256	20770403	0.7	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20770256	20770403	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20770404	20770524	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20770525	20770752	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20770525	20770752	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20770753	20770828	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20770829	20770904	1	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20770829	20770904	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20770905	20771002	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20771003	20771487	0.76	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20771003	20771487	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20771488	20771582	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20771583	20771870	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20771583	20771870	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20771871	20771977	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20771978	20772284	0.45	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20771978	20772284	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20772285	20772402	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20772403	20773076	0.78	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20772403	20773076	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20773077	20773175	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20773176	20773576	0.93	-	2	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20773176	20773576	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20773577	20773692	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20773693	20774093	0.75	-	1	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20773693	20774093	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20774094	20774424	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20774425	20774555	0.89	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20774425	20774555	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20774556	20774739	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20774740	20774802	1	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20774740	20774802	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	intron	20774803	20774950	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	CDS	20774951	20775433	0.69	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	exon	20774951	20775433	.	-	.	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
Phchi.S3	AUGUSTUS	start_codon	20775431	20775433	.	-	0	transcript_id "Phchi.S3G302000.t1"; gene_id "Phchi.S3G302000"
# This transcript jg11857.t2 is derived from g15909.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11858.t1 is derived from g15910.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8795517	8797504	.	+	.	Phchi.S4G144000
Phchi.S4	AUGUSTUS	transcript	8795517	8797504	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	start_codon	8795517	8795519	.	+	0	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	CDS	8795517	8795839	1	+	0	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	exon	8795517	8795839	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	intron	8795840	8796003	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	CDS	8796004	8796283	0.98	+	1	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	exon	8796004	8796283	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	intron	8796284	8796405	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	CDS	8796406	8796617	0.77	+	0	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	exon	8796406	8796617	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	intron	8796618	8796766	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	CDS	8796767	8797078	0.69	+	1	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	exon	8796767	8797078	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	intron	8797079	8797164	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	CDS	8797165	8797504	1	+	1	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	exon	8797165	8797504	.	+	.	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
Phchi.S4	AUGUSTUS	stop_codon	8797505	8797507	.	+	0	transcript_id "Phchi.S4G144000.t1"; gene_id "Phchi.S4G144000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7798.t1 is derived from g4972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31208519	31209058	.	+	.	Phchi.S1G495700
Phchi.S1	AUGUSTUS	transcript	31208519	31209058	.	+	.	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	start_codon	31208519	31208521	.	+	0	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	CDS	31208519	31208624	0.81	+	0	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	exon	31208519	31208624	.	+	.	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	intron	31208625	31208717	.	+	.	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	CDS	31208718	31209058	0.45	+	2	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	exon	31208718	31209058	.	+	.	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
Phchi.S1	AUGUSTUS	stop_codon	31209059	31209061	.	+	0	transcript_id "Phchi.S1G495700.t1"; gene_id "Phchi.S1G495700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4601.t1 is derived from g1771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11291415	11292536	.	-	.	Phchi.S1G176000
Phchi.S1	AUGUSTUS	transcript	11291415	11292536	.	-	.	transcript_id "Phchi.S1G176000.t1"; gene_id "Phchi.S1G176000"
Phchi.S1	AUGUSTUS	stop_codon	11291412	11291414	.	-	0	transcript_id "Phchi.S1G176000.t1"; gene_id "Phchi.S1G176000"
Phchi.S1	AUGUSTUS	CDS	11291415	11292536	0.95	-	0	transcript_id "Phchi.S1G176000.t1"; gene_id "Phchi.S1G176000"
Phchi.S1	AUGUSTUS	exon	11291415	11292536	.	-	.	transcript_id "Phchi.S1G176000.t1"; gene_id "Phchi.S1G176000"
Phchi.S1	AUGUSTUS	start_codon	11292534	11292536	.	-	0	transcript_id "Phchi.S1G176000.t1"; gene_id "Phchi.S1G176000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10074.t1 is derived from g7250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45632109	45632522	.	-	.	Phchi.S1G723300
Phchi.S1	AUGUSTUS	transcript	45632109	45632522	.	-	.	transcript_id "Phchi.S1G723300.t1"; gene_id "Phchi.S1G723300"
Phchi.S1	AUGUSTUS	stop_codon	45632106	45632108	.	-	0	transcript_id "Phchi.S1G723300.t1"; gene_id "Phchi.S1G723300"
Phchi.S1	AUGUSTUS	CDS	45632109	45632522	1	-	0	transcript_id "Phchi.S1G723300.t1"; gene_id "Phchi.S1G723300"
Phchi.S1	AUGUSTUS	exon	45632109	45632522	.	-	.	transcript_id "Phchi.S1G723300.t1"; gene_id "Phchi.S1G723300"
Phchi.S1	AUGUSTUS	start_codon	45632520	45632522	.	-	0	transcript_id "Phchi.S1G723300.t1"; gene_id "Phchi.S1G723300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1769.t1 is derived from g8689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2937953	2940318	.	+	.	Phchi.S5G037800
Phchi.S5	AUGUSTUS	transcript	2937953	2940318	.	+	.	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	start_codon	2937953	2937955	.	+	0	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	CDS	2937953	2938405	0.93	+	0	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	exon	2937953	2938405	.	+	.	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	intron	2938406	2938506	.	+	.	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	CDS	2938507	2940318	0.99	+	0	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	exon	2938507	2940318	.	+	.	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
Phchi.S5	AUGUSTUS	stop_codon	2940319	2940321	.	+	0	transcript_id "Phchi.S5G037800.t1"; gene_id "Phchi.S5G037800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5665.t1 is derived from g2835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18192193	18193989	.	+	.	Phchi.S1G282400
Phchi.S1	AUGUSTUS	transcript	18192193	18193989	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	start_codon	18192193	18192195	.	+	0	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	CDS	18192193	18192558	1	+	0	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	exon	18192193	18192558	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	intron	18192559	18192684	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	CDS	18192685	18192797	1	+	0	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	exon	18192685	18192797	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	intron	18192798	18192936	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	CDS	18192937	18193024	1	+	1	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	exon	18192937	18193024	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	intron	18193025	18193122	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	CDS	18193123	18193196	1	+	0	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	exon	18193123	18193196	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	intron	18193197	18193328	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	CDS	18193329	18193499	1	+	1	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	exon	18193329	18193499	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	intron	18193500	18193586	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	CDS	18193587	18193989	0.98	+	1	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	exon	18193587	18193989	.	+	.	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
Phchi.S1	AUGUSTUS	stop_codon	18193990	18193992	.	+	0	transcript_id "Phchi.S1G282400.t1"; gene_id "Phchi.S1G282400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6586.t1 is derived from g3758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23884665	23885207	.	-	.	Phchi.S1G374500
Phchi.S1	AUGUSTUS	transcript	23884665	23885207	.	-	.	transcript_id "Phchi.S1G374500.t1"; gene_id "Phchi.S1G374500"
Phchi.S1	AUGUSTUS	stop_codon	23884662	23884664	.	-	0	transcript_id "Phchi.S1G374500.t1"; gene_id "Phchi.S1G374500"
Phchi.S1	AUGUSTUS	CDS	23884665	23885207	1	-	0	transcript_id "Phchi.S1G374500.t1"; gene_id "Phchi.S1G374500"
Phchi.S1	AUGUSTUS	exon	23884665	23885207	.	-	.	transcript_id "Phchi.S1G374500.t1"; gene_id "Phchi.S1G374500"
Phchi.S1	AUGUSTUS	start_codon	23885205	23885207	.	-	0	transcript_id "Phchi.S1G374500.t1"; gene_id "Phchi.S1G374500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7524.t1 is derived from g4698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29870688	29873198	.	+	.	Phchi.S1G468300
Phchi.S1	AUGUSTUS	transcript	29870688	29873198	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	start_codon	29870688	29870690	.	+	0	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	CDS	29870688	29871770	0.15	+	0	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	exon	29870688	29871770	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	intron	29871771	29871900	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	CDS	29871901	29872342	0.22	+	0	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	exon	29871901	29872342	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	intron	29872343	29872441	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	CDS	29872442	29872685	0.56	+	2	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	exon	29872442	29872685	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	intron	29872686	29872783	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	CDS	29872784	29873198	0.37	+	1	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	exon	29872784	29873198	.	+	.	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
Phchi.S1	AUGUSTUS	stop_codon	29873199	29873201	.	+	0	transcript_id "Phchi.S1G468300.t1"; gene_id "Phchi.S1G468300"
# This transcript jg4734.t2 is derived from g1904.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4735.t1 is derived from g1905.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12531232	12532260	.	+	.	Phchi.S1G189400
Phchi.S1	AUGUSTUS	transcript	12531232	12531930	.	+	.	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	start_codon	12531232	12531234	.	+	0	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	CDS	12531232	12531409	0.86	+	0	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	exon	12531232	12531409	.	+	.	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	intron	12531410	12531511	.	+	.	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	CDS	12531512	12531930	0.95	+	2	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	exon	12531512	12531930	.	+	.	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	stop_codon	12531931	12531933	.	+	0	transcript_id "Phchi.S1G189400.t1"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	transcript	12531232	12532260	.	+	.	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	start_codon	12531232	12531234	.	+	0	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	CDS	12531232	12531409	0.83	+	0	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	exon	12531232	12531409	.	+	.	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	intron	12531410	12531511	.	+	.	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	CDS	12531512	12531877	0.72	+	2	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	exon	12531512	12531877	.	+	.	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	intron	12531878	12531997	.	+	.	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	CDS	12531998	12532260	0.76	+	2	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	exon	12531998	12532260	.	+	.	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
Phchi.S1	AUGUSTUS	stop_codon	12532261	12532263	.	+	0	transcript_id "Phchi.S1G189400.t2"; gene_id "Phchi.S1G189400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12383.t1 is derived from g8059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15191533	15193107	.	+	.	Phchi.S2G046300
Phchi.S2	AUGUSTUS	transcript	15191533	15193107	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	start_codon	15191533	15191535	.	+	0	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15191533	15191619	0.97	+	0	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15191533	15191619	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15191620	15192230	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192231	15192449	1	+	0	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192231	15192449	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192450	15192548	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192549	15192697	0.98	+	0	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192549	15192697	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192698	15192843	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192844	15192972	1	+	1	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192844	15192972	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192973	15193064	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15193065	15193107	0.99	+	1	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15193065	15193107	.	+	.	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	stop_codon	15193108	15193110	.	+	0	transcript_id "Phchi.S2G046300.t1"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	transcript	15191533	15192872	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	start_codon	15191533	15191535	.	+	0	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15191533	15191619	0.99	+	0	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15191533	15191619	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15191620	15192230	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192231	15192449	1	+	0	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192231	15192449	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192450	15192548	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192549	15192697	0.93	+	0	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192549	15192697	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192698	15192865	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192866	15192872	0.8	+	1	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192866	15192872	.	+	.	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	stop_codon	15192873	15192875	.	+	0	transcript_id "Phchi.S2G046300.t2"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	transcript	15191533	15192872	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	start_codon	15191533	15191535	.	+	0	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15191533	15191673	1	+	0	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15191533	15191673	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15191674	15192230	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192231	15192449	1	+	0	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192231	15192449	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192450	15192548	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192549	15192697	0.95	+	0	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192549	15192697	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	intron	15192698	15192865	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	CDS	15192866	15192872	0.5	+	1	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	exon	15192866	15192872	.	+	.	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
Phchi.S2	AUGUSTUS	stop_codon	15192873	15192875	.	+	0	transcript_id "Phchi.S2G046300.t3"; gene_id "Phchi.S2G046300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1608.t1 is derived from g8527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2016103	2017118	.	+	.	Phchi.S5G021700
Phchi.S5	AUGUSTUS	transcript	2016103	2017118	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	start_codon	2016103	2016105	.	+	0	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	CDS	2016103	2016238	1	+	0	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	exon	2016103	2016238	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	intron	2016239	2016308	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	CDS	2016309	2016466	0.72	+	2	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	exon	2016309	2016466	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	intron	2016467	2016575	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	CDS	2016576	2016719	0.71	+	0	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	exon	2016576	2016719	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	intron	2016720	2016798	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	CDS	2016799	2016858	1	+	0	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	exon	2016799	2016858	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	intron	2016859	2016944	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	CDS	2016945	2017118	1	+	0	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	exon	2016945	2017118	.	+	.	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
Phchi.S5	AUGUSTUS	stop_codon	2017119	2017121	.	+	0	transcript_id "Phchi.S5G021700.t1"; gene_id "Phchi.S5G021700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9959.t1 is derived from g7135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44667717	44668025	.	-	.	Phchi.S1G711800
Phchi.S1	AUGUSTUS	transcript	44667717	44668025	.	-	.	transcript_id "Phchi.S1G711800.t1"; gene_id "Phchi.S1G711800"
Phchi.S1	AUGUSTUS	stop_codon	44667714	44667716	.	-	0	transcript_id "Phchi.S1G711800.t1"; gene_id "Phchi.S1G711800"
Phchi.S1	AUGUSTUS	CDS	44667717	44668025	1	-	0	transcript_id "Phchi.S1G711800.t1"; gene_id "Phchi.S1G711800"
Phchi.S1	AUGUSTUS	exon	44667717	44668025	.	-	.	transcript_id "Phchi.S1G711800.t1"; gene_id "Phchi.S1G711800"
Phchi.S1	AUGUSTUS	start_codon	44668023	44668025	.	-	0	transcript_id "Phchi.S1G711800.t1"; gene_id "Phchi.S1G711800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13096.t1 is derived from g11561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4130418	4131335	.	+	.	Phchi.S3G041500
Phchi.S3	AUGUSTUS	transcript	4130418	4131335	.	+	.	transcript_id "Phchi.S3G041500.t1"; gene_id "Phchi.S3G041500"
Phchi.S3	AUGUSTUS	start_codon	4130418	4130420	.	+	0	transcript_id "Phchi.S3G041500.t1"; gene_id "Phchi.S3G041500"
Phchi.S3	AUGUSTUS	CDS	4130418	4131335	1	+	0	transcript_id "Phchi.S3G041500.t1"; gene_id "Phchi.S3G041500"
Phchi.S3	AUGUSTUS	exon	4130418	4131335	.	+	.	transcript_id "Phchi.S3G041500.t1"; gene_id "Phchi.S3G041500"
Phchi.S3	AUGUSTUS	stop_codon	4131336	4131338	.	+	0	transcript_id "Phchi.S3G041500.t1"; gene_id "Phchi.S3G041500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9287.t1 is derived from g6462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40767986	40770112	.	-	.	Phchi.S1G644600
Phchi.S1	AUGUSTUS	transcript	40767986	40770112	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	stop_codon	40767983	40767985	.	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	CDS	40767986	40768306	0.99	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	exon	40767986	40768306	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	intron	40768307	40768402	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	CDS	40768403	40768510	1	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	exon	40768403	40768510	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	intron	40768511	40768587	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	CDS	40768588	40768761	1	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	exon	40768588	40768761	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	intron	40768762	40768862	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	CDS	40768863	40768983	1	-	1	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	exon	40768863	40768983	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	intron	40768984	40769070	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	CDS	40769071	40769153	1	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	exon	40769071	40769153	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	intron	40769154	40769377	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	CDS	40769378	40770112	0.92	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	exon	40769378	40770112	.	-	.	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
Phchi.S1	AUGUSTUS	start_codon	40770110	40770112	.	-	0	transcript_id "Phchi.S1G644600.t1"; gene_id "Phchi.S1G644600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8235.t1 is derived from g5410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34572997	34576035	.	+	.	Phchi.S1G539400
Phchi.S1	AUGUSTUS	transcript	34572997	34576035	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	start_codon	34572997	34572999	.	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34572997	34573053	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34572997	34573053	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34573054	34573151	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34573152	34573223	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34573152	34573223	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34573224	34573359	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34573360	34573436	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34573360	34573436	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34573437	34573518	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34573519	34573609	1	+	1	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34573519	34573609	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34573610	34573855	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34573856	34573988	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34573856	34573988	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34573989	34574197	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34574198	34574262	1	+	2	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34574198	34574262	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34574263	34574389	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34574390	34574439	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34574390	34574439	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34574440	34574527	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34574528	34574569	1	+	1	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34574528	34574569	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34574570	34574662	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34574663	34574735	1	+	1	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34574663	34574735	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34574736	34574824	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34574825	34574894	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34574825	34574894	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34574895	34575025	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34575026	34575081	1	+	2	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34575026	34575081	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34575082	34575208	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34575209	34575328	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34575209	34575328	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34575329	34575417	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34575418	34575561	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34575418	34575561	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	intron	34575562	34575648	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	CDS	34575649	34576035	1	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	exon	34575649	34576035	.	+	.	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
Phchi.S1	AUGUSTUS	stop_codon	34576036	34576038	.	+	0	transcript_id "Phchi.S1G539400.t1"; gene_id "Phchi.S1G539400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4990.t1 is derived from g2160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13915615	13916647	.	+	.	Phchi.S1G214900
Phchi.S1	AUGUSTUS	transcript	13915615	13916647	.	+	.	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	start_codon	13915615	13915617	.	+	0	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	CDS	13915615	13916316	0.77	+	0	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	exon	13915615	13916316	.	+	.	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	intron	13916317	13916539	.	+	.	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	CDS	13916540	13916647	0.94	+	0	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	exon	13916540	13916647	.	+	.	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
Phchi.S1	AUGUSTUS	stop_codon	13916648	13916650	.	+	0	transcript_id "Phchi.S1G214900.t1"; gene_id "Phchi.S1G214900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11925.t1 is derived from g7600.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	49143	50554	.	+	.	Phchi.S2G000500
Phchi.S2	AUGUSTUS	transcript	49143	50554	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	start_codon	49143	49145	.	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49143	49167	0.8	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49143	49167	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49168	49267	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49268	49350	1	+	2	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49268	49350	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49351	49444	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49445	49517	1	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49445	49517	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49518	49603	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49604	49662	1	+	2	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49604	49662	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49663	49782	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49783	49911	1	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49783	49911	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49912	49998	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49999	50085	0.64	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49999	50085	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	50086	50186	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	50187	50231	0.69	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	50187	50231	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	50232	50329	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	50330	50554	0.4	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	50330	50554	.	+	.	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	stop_codon	50555	50557	.	+	0	transcript_id "Phchi.S2G000500.t1"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	transcript	49143	50554	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	start_codon	49143	49145	.	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49143	49167	0.84	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49143	49167	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49168	49267	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49268	49370	1	+	2	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49268	49370	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49371	49505	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49506	49662	1	+	1	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49506	49662	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49663	49782	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49783	49911	1	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49783	49911	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	49912	49998	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	49999	50085	0.62	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	49999	50085	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	50086	50186	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	50187	50231	0.65	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	50187	50231	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	intron	50232	50329	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	CDS	50330	50554	0.39	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	exon	50330	50554	.	+	.	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
Phchi.S2	AUGUSTUS	stop_codon	50555	50557	.	+	0	transcript_id "Phchi.S2G000500.t2"; gene_id "Phchi.S2G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg81.t1 is derived from g9863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	416420	418452	.	+	.	Phchi.S6G004000
Phchi.S6	AUGUSTUS	transcript	416420	418452	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	start_codon	416420	416422	.	+	0	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	CDS	416420	416859	0.56	+	0	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	exon	416420	416859	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	intron	416860	416976	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	CDS	416977	417222	0.53	+	1	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	exon	416977	417222	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	intron	417223	417329	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	CDS	417330	418148	0.59	+	1	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	exon	417330	418148	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	intron	418149	418229	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	CDS	418230	418452	0.98	+	1	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	exon	418230	418452	.	+	.	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
Phchi.S6	AUGUSTUS	stop_codon	418453	418455	.	+	0	transcript_id "Phchi.S6G004000.t1"; gene_id "Phchi.S6G004000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7308.t1 is derived from g4480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28448530	28450602	.	+	.	Phchi.S1G446700
Phchi.S1	AUGUSTUS	transcript	28448530	28450602	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	start_codon	28448530	28448532	.	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28448530	28448760	1	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28448530	28448760	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28448761	28448859	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28448860	28449048	0.82	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28448860	28449048	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449049	28449191	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28449192	28449488	0.94	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28449192	28449488	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449489	28449581	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28449582	28449679	0.99	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28449582	28449679	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449680	28449765	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28449766	28449973	1	+	1	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28449766	28449973	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449974	28450070	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28450071	28450331	0.93	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28450071	28450331	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28450332	28450416	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28450417	28450602	0.92	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28450417	28450602	.	+	.	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	stop_codon	28450603	28450605	.	+	0	transcript_id "Phchi.S1G446700.t1"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	transcript	28449255	28450602	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	start_codon	28449255	28449257	.	+	0	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28449255	28449488	0.8	+	0	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28449255	28449488	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449489	28449581	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28449582	28449679	0.93	+	0	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28449582	28449679	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449680	28449765	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28449766	28449973	1	+	1	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28449766	28449973	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28449974	28450070	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28450071	28450331	0.95	+	0	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28450071	28450331	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	intron	28450332	28450416	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	CDS	28450417	28450602	0.94	+	0	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	exon	28450417	28450602	.	+	.	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
Phchi.S1	AUGUSTUS	stop_codon	28450603	28450605	.	+	0	transcript_id "Phchi.S1G446700.t2"; gene_id "Phchi.S1G446700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2206.t1 is derived from g9126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5415935	5416951	.	-	.	Phchi.S5G081500
Phchi.S5	AUGUSTUS	transcript	5415935	5416951	.	-	.	transcript_id "Phchi.S5G081500.t1"; gene_id "Phchi.S5G081500"
Phchi.S5	AUGUSTUS	stop_codon	5415932	5415934	.	-	0	transcript_id "Phchi.S5G081500.t1"; gene_id "Phchi.S5G081500"
Phchi.S5	AUGUSTUS	CDS	5415935	5416951	0.7	-	0	transcript_id "Phchi.S5G081500.t1"; gene_id "Phchi.S5G081500"
Phchi.S5	AUGUSTUS	exon	5415935	5416951	.	-	.	transcript_id "Phchi.S5G081500.t1"; gene_id "Phchi.S5G081500"
Phchi.S5	AUGUSTUS	start_codon	5416949	5416951	.	-	0	transcript_id "Phchi.S5G081500.t1"; gene_id "Phchi.S5G081500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13352.t1 is derived from g11818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6289147	6290891	.	-	.	Phchi.S3G067100
Phchi.S3	AUGUSTUS	transcript	6289147	6290891	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	stop_codon	6289144	6289146	.	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6289147	6289251	0.89	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6289147	6289251	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	intron	6289252	6289335	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6289336	6289413	1	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6289336	6289413	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	intron	6289414	6289517	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6289518	6289603	0.99	-	2	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6289518	6289603	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	intron	6289604	6289704	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6289705	6289852	1	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6289705	6289852	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	intron	6289853	6289953	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6289954	6290235	0.99	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6289954	6290235	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	intron	6290236	6290505	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6290506	6290553	0.88	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6290506	6290553	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	intron	6290554	6290684	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	CDS	6290685	6290891	0.86	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	exon	6290685	6290891	.	-	.	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
Phchi.S3	AUGUSTUS	start_codon	6290889	6290891	.	-	0	transcript_id "Phchi.S3G067100.t1"; gene_id "Phchi.S3G067100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6067.t1 is derived from g3238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20714112	20714603	.	+	.	Phchi.S1G322600
Phchi.S1	AUGUSTUS	transcript	20714112	20714603	.	+	.	transcript_id "Phchi.S1G322600.t1"; gene_id "Phchi.S1G322600"
Phchi.S1	AUGUSTUS	start_codon	20714112	20714114	.	+	0	transcript_id "Phchi.S1G322600.t1"; gene_id "Phchi.S1G322600"
Phchi.S1	AUGUSTUS	CDS	20714112	20714603	1	+	0	transcript_id "Phchi.S1G322600.t1"; gene_id "Phchi.S1G322600"
Phchi.S1	AUGUSTUS	exon	20714112	20714603	.	+	.	transcript_id "Phchi.S1G322600.t1"; gene_id "Phchi.S1G322600"
Phchi.S1	AUGUSTUS	stop_codon	20714604	20714606	.	+	0	transcript_id "Phchi.S1G322600.t1"; gene_id "Phchi.S1G322600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8818.t1 is derived from g5993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38121171	38122921	.	-	.	Phchi.S1G597700
Phchi.S1	AUGUSTUS	transcript	38121171	38122921	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	stop_codon	38121168	38121170	.	-	0	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38121171	38121178	0.55	-	2	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38121171	38121178	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	intron	38121179	38121267	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38121268	38121361	0.84	-	0	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38121268	38121361	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	intron	38121362	38121544	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38121545	38121635	1	-	1	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38121545	38121635	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	intron	38121636	38121730	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38121731	38121826	0.46	-	1	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38121731	38121826	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	intron	38121827	38121907	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38121908	38122008	0.84	-	0	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38121908	38122008	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	intron	38122009	38122191	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38122192	38122299	1	-	0	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38122192	38122299	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	intron	38122300	38122645	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	CDS	38122646	38122921	0.72	-	0	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	exon	38122646	38122921	.	-	.	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
Phchi.S1	AUGUSTUS	start_codon	38122919	38122921	.	-	0	transcript_id "Phchi.S1G597700.t1"; gene_id "Phchi.S1G597700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2053.t1 is derived from g8973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4625817	4627827	.	+	.	Phchi.S5G066200
Phchi.S5	AUGUSTUS	transcript	4625817	4627827	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	start_codon	4625817	4625819	.	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4625817	4625988	0.6	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4625817	4625988	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4625989	4626076	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626077	4626138	1	+	2	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626077	4626138	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626139	4626220	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626221	4626277	1	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626221	4626277	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626278	4626380	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626381	4626440	1	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626381	4626440	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626441	4626531	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626532	4626635	0.93	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626532	4626635	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626636	4626840	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626841	4626938	1	+	1	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626841	4626938	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626939	4627035	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4627036	4627366	0.98	+	2	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4627036	4627366	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4627367	4627472	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4627473	4627641	0.97	+	1	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4627473	4627641	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4627642	4627740	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4627741	4627827	1	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4627741	4627827	.	+	.	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	stop_codon	4627828	4627830	.	+	0	transcript_id "Phchi.S5G066200.t1"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	transcript	4625817	4627827	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	start_codon	4625817	4625819	.	+	0	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4625817	4625988	0.68	+	0	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4625817	4625988	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4625989	4626076	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626077	4626138	1	+	2	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626077	4626138	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626139	4626236	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626237	4626440	1	+	0	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626237	4626440	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626441	4626531	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626532	4626635	0.91	+	0	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626532	4626635	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626636	4626840	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4626841	4626938	1	+	1	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4626841	4626938	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4626939	4627035	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4627036	4627366	1	+	2	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4627036	4627366	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4627367	4627472	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4627473	4627641	0.97	+	1	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4627473	4627641	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	intron	4627642	4627740	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	CDS	4627741	4627827	1	+	0	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	exon	4627741	4627827	.	+	.	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
Phchi.S5	AUGUSTUS	stop_codon	4627828	4627830	.	+	0	transcript_id "Phchi.S5G066200.t2"; gene_id "Phchi.S5G066200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5236.t1 is derived from g2406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15787050	15788753	.	-	.	Phchi.S1G239500
Phchi.S1	AUGUSTUS	transcript	15787050	15788753	.	-	.	transcript_id "Phchi.S1G239500.t1"; gene_id "Phchi.S1G239500"
Phchi.S1	AUGUSTUS	stop_codon	15787047	15787049	.	-	0	transcript_id "Phchi.S1G239500.t1"; gene_id "Phchi.S1G239500"
Phchi.S1	AUGUSTUS	CDS	15787050	15788753	0.89	-	0	transcript_id "Phchi.S1G239500.t1"; gene_id "Phchi.S1G239500"
Phchi.S1	AUGUSTUS	exon	15787050	15788753	.	-	.	transcript_id "Phchi.S1G239500.t1"; gene_id "Phchi.S1G239500"
Phchi.S1	AUGUSTUS	start_codon	15788751	15788753	.	-	0	transcript_id "Phchi.S1G239500.t1"; gene_id "Phchi.S1G239500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11582.t1 is derived from g15633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7194541	7195862	.	+	.	Phchi.S4G116400
Phchi.S4	AUGUSTUS	transcript	7194541	7195862	.	+	.	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	start_codon	7194541	7194543	.	+	0	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	CDS	7194541	7194877	1	+	0	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	exon	7194541	7194877	.	+	.	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	intron	7194878	7194963	.	+	.	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	CDS	7194964	7195862	1	+	2	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	exon	7194964	7195862	.	+	.	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
Phchi.S4	AUGUSTUS	stop_codon	7195863	7195865	.	+	0	transcript_id "Phchi.S4G116400.t1"; gene_id "Phchi.S4G116400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1675.t1 is derived from g8594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2430289	2430945	.	-	.	Phchi.S5G028400
Phchi.S5	AUGUSTUS	transcript	2430289	2430945	.	-	.	transcript_id "Phchi.S5G028400.t1"; gene_id "Phchi.S5G028400"
Phchi.S5	AUGUSTUS	stop_codon	2430286	2430288	.	-	0	transcript_id "Phchi.S5G028400.t1"; gene_id "Phchi.S5G028400"
Phchi.S5	AUGUSTUS	CDS	2430289	2430945	0.97	-	0	transcript_id "Phchi.S5G028400.t1"; gene_id "Phchi.S5G028400"
Phchi.S5	AUGUSTUS	exon	2430289	2430945	.	-	.	transcript_id "Phchi.S5G028400.t1"; gene_id "Phchi.S5G028400"
Phchi.S5	AUGUSTUS	start_codon	2430943	2430945	.	-	0	transcript_id "Phchi.S5G028400.t1"; gene_id "Phchi.S5G028400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3195.t1 is derived from g364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2196874	2198801	.	+	.	Phchi.S1G035400
Phchi.S1	AUGUSTUS	transcript	2196874	2198801	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	start_codon	2196874	2196876	.	+	0	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2196874	2197025	0.53	+	0	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2196874	2197025	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2197026	2197174	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2197175	2197260	1	+	1	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2197175	2197260	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2197261	2197434	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2197435	2197556	1	+	2	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2197435	2197556	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2197557	2197677	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2197678	2197760	1	+	0	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2197678	2197760	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2197761	2197901	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2197902	2198023	1	+	1	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2197902	2198023	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2198024	2198175	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2198176	2198340	1	+	2	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2198176	2198340	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2198341	2198434	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2198435	2198522	1	+	2	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2198435	2198522	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	intron	2198523	2198602	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	CDS	2198603	2198801	1	+	1	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	exon	2198603	2198801	.	+	.	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
Phchi.S1	AUGUSTUS	stop_codon	2198802	2198804	.	+	0	transcript_id "Phchi.S1G035400.t1"; gene_id "Phchi.S1G035400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg345.t1 is derived from g10127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2514991	2518396	.	+	.	Phchi.S6G030400
Phchi.S6	AUGUSTUS	transcript	2514991	2518396	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	start_codon	2514991	2514993	.	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2514991	2515005	0.78	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2514991	2515005	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2515006	2515158	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2515159	2515230	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2515159	2515230	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2515231	2515373	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2515374	2515514	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2515374	2515514	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2515515	2515600	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2515601	2515684	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2515601	2515684	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2515685	2515878	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2515879	2515936	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2515879	2515936	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2515937	2516123	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2516124	2516248	1	+	2	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2516124	2516248	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2516249	2516380	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2516381	2516425	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2516381	2516425	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2516426	2516555	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2516556	2516604	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2516556	2516604	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2516605	2516682	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2516683	2516792	0.99	+	2	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2516683	2516792	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2516793	2516903	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2516904	2516980	0.97	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2516904	2516980	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2516981	2517101	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2517102	2517152	1	+	1	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2517102	2517152	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2517153	2517281	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2517282	2517346	1	+	1	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2517282	2517346	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2517347	2517505	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2517506	2517660	1	+	2	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2517506	2517660	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2517661	2517778	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2517779	2517819	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2517779	2517819	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2517820	2517919	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2517920	2517974	1	+	1	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2517920	2517974	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2517975	2518069	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2518070	2518126	1	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2518070	2518126	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	intron	2518127	2518246	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	CDS	2518247	2518396	0.99	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	exon	2518247	2518396	.	+	.	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
Phchi.S6	AUGUSTUS	stop_codon	2518397	2518399	.	+	0	transcript_id "Phchi.S6G030400.t1"; gene_id "Phchi.S6G030400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1101.t1 is derived from g10884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7603804	7604728	.	-	.	Phchi.S6G106000
Phchi.S6	AUGUSTUS	transcript	7603804	7604728	.	-	.	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	stop_codon	7603801	7603803	.	-	0	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	CDS	7603804	7604460	0.99	-	0	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	exon	7603804	7604460	.	-	.	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	intron	7604461	7604602	.	-	.	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	CDS	7604603	7604728	0.76	-	0	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	exon	7604603	7604728	.	-	.	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
Phchi.S6	AUGUSTUS	start_codon	7604726	7604728	.	-	0	transcript_id "Phchi.S6G106000.t1"; gene_id "Phchi.S6G106000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12827.t1 is derived from g11292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2585557	2586975	.	-	.	Phchi.S3G014600
Phchi.S3	AUGUSTUS	transcript	2585557	2586975	.	-	.	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	stop_codon	2585554	2585556	.	-	0	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	CDS	2585557	2585847	1	-	0	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	exon	2585557	2585847	.	-	.	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	intron	2585848	2585936	.	-	.	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	CDS	2585937	2586311	1	-	0	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	exon	2585937	2586311	.	-	.	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	intron	2586312	2586471	.	-	.	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	CDS	2586472	2586975	0.41	-	0	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	exon	2586472	2586975	.	-	.	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
Phchi.S3	AUGUSTUS	start_codon	2586973	2586975	.	-	0	transcript_id "Phchi.S3G014600.t1"; gene_id "Phchi.S3G014600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12962.t1 is derived from g11427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3339705	3343352	.	+	.	Phchi.S3G028100
Phchi.S3	AUGUSTUS	transcript	3339705	3343352	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	start_codon	3339705	3339707	.	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3339705	3339762	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3339705	3339762	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3339763	3339838	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3339839	3339894	1	+	2	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3339839	3339894	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3339895	3339974	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3339975	3340072	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3339975	3340072	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3340073	3340153	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3340154	3340337	0.73	+	1	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3340154	3340337	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3340338	3340447	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3340448	3340503	0.77	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3340448	3340503	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3340504	3340591	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3340592	3340658	1	+	1	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3340592	3340658	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3340659	3340815	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3340816	3340857	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3340816	3340857	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3340858	3340944	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3340945	3340986	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3340945	3340986	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3340987	3341117	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3341118	3341194	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3341118	3341194	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3341195	3341298	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3341299	3341425	1	+	1	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3341299	3341425	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3341426	3341510	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3341511	3341678	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3341511	3341678	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3341679	3341782	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3341783	3341911	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3341783	3341911	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3341912	3341989	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3341990	3342100	0.98	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3341990	3342100	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3342101	3342201	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3342202	3342336	0.99	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3342202	3342336	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3342337	3342449	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3342450	3342524	0.97	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3342450	3342524	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3342525	3342614	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3342615	3342725	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3342615	3342725	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3342726	3342837	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3342838	3342933	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3342838	3342933	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3342934	3343082	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3343083	3343166	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3343083	3343166	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	intron	3343167	3343259	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	CDS	3343260	3343352	1	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	exon	3343260	3343352	.	+	.	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
Phchi.S3	AUGUSTUS	stop_codon	3343353	3343355	.	+	0	transcript_id "Phchi.S3G028100.t1"; gene_id "Phchi.S3G028100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9138.t1 is derived from g6313.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40037629	40038700	.	-	.	Phchi.S1G629700
Phchi.S1	AUGUSTUS	transcript	40037629	40038700	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	stop_codon	40037626	40037628	.	-	0	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40037629	40037696	0.79	-	2	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40037629	40037696	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40037697	40037795	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40037796	40037922	1	-	0	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40037796	40037922	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40037923	40038076	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40038077	40038220	1	-	0	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40038077	40038220	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40038221	40038303	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40038304	40038325	1	-	1	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40038304	40038325	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40038326	40038405	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40038406	40038453	1	-	1	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40038406	40038453	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40038454	40038593	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40038594	40038700	1	-	0	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40038594	40038700	.	-	.	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	start_codon	40038698	40038700	.	-	0	transcript_id "Phchi.S1G629700.t1"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	transcript	40037629	40038059	.	-	.	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	stop_codon	40037626	40037628	.	-	0	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40037629	40037696	0.83	-	2	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40037629	40037696	.	-	.	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40037697	40037795	.	-	.	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40037796	40037922	1	-	0	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40037796	40037922	.	-	.	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	intron	40037923	40038008	.	-	.	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	CDS	40038009	40038059	1	-	0	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	exon	40038009	40038059	.	-	.	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
Phchi.S1	AUGUSTUS	start_codon	40038057	40038059	.	-	0	transcript_id "Phchi.S1G629700.t2"; gene_id "Phchi.S1G629700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3966.t1 is derived from g1135.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6785298	6786104	.	-	.	Phchi.S1G112500
Phchi.S1	AUGUSTUS	transcript	6785298	6786104	.	-	.	transcript_id "Phchi.S1G112500.t1"; gene_id "Phchi.S1G112500"
Phchi.S1	AUGUSTUS	stop_codon	6785295	6785297	.	-	0	transcript_id "Phchi.S1G112500.t1"; gene_id "Phchi.S1G112500"
Phchi.S1	AUGUSTUS	CDS	6785298	6786104	0.86	-	0	transcript_id "Phchi.S1G112500.t1"; gene_id "Phchi.S1G112500"
Phchi.S1	AUGUSTUS	exon	6785298	6786104	.	-	.	transcript_id "Phchi.S1G112500.t1"; gene_id "Phchi.S1G112500"
Phchi.S1	AUGUSTUS	start_codon	6786102	6786104	.	-	0	transcript_id "Phchi.S1G112500.t1"; gene_id "Phchi.S1G112500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9490.t1 is derived from g6666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41994636	41999113	.	+	.	Phchi.S1G664900
Phchi.S1	AUGUSTUS	transcript	41994636	41999113	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	start_codon	41994636	41994638	.	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41994636	41994697	0.78	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41994636	41994697	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41994698	41994880	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41994881	41994930	0.85	+	1	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41994881	41994930	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41994931	41995053	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41995054	41996352	1	+	2	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41995054	41996352	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41996353	41996450	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41996451	41997046	0.78	+	2	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41996451	41997046	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41997047	41997382	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41997383	41997456	1	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41997383	41997456	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41997457	41997585	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41997586	41997670	1	+	1	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41997586	41997670	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41997671	41997839	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41997840	41997926	1	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41997840	41997926	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41997927	41998033	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41998034	41998106	1	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41998034	41998106	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41998107	41998225	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41998226	41998269	1	+	2	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41998226	41998269	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41998270	41998385	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41998386	41998514	0.86	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41998386	41998514	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41998515	41998622	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41998623	41998721	1	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41998623	41998721	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41998722	41998894	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41998895	41998965	0.91	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41998895	41998965	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	intron	41998966	41999076	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	CDS	41999077	41999113	0.22	+	1	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	exon	41999077	41999113	.	+	.	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
Phchi.S1	AUGUSTUS	stop_codon	41999114	41999116	.	+	0	transcript_id "Phchi.S1G664900.t1"; gene_id "Phchi.S1G664900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4281.t1 is derived from g1450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9391100	9392476	.	-	.	Phchi.S1G144000
Phchi.S1	AUGUSTUS	transcript	9391100	9392476	.	-	.	transcript_id "Phchi.S1G144000.t1"; gene_id "Phchi.S1G144000"
Phchi.S1	AUGUSTUS	stop_codon	9391097	9391099	.	-	0	transcript_id "Phchi.S1G144000.t1"; gene_id "Phchi.S1G144000"
Phchi.S1	AUGUSTUS	CDS	9391100	9392476	0.99	-	0	transcript_id "Phchi.S1G144000.t1"; gene_id "Phchi.S1G144000"
Phchi.S1	AUGUSTUS	exon	9391100	9392476	.	-	.	transcript_id "Phchi.S1G144000.t1"; gene_id "Phchi.S1G144000"
Phchi.S1	AUGUSTUS	start_codon	9392474	9392476	.	-	0	transcript_id "Phchi.S1G144000.t1"; gene_id "Phchi.S1G144000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9192.t1 is derived from g6367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40278688	40281019	.	-	.	Phchi.S1G635100
Phchi.S1	AUGUSTUS	transcript	40278688	40281019	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	stop_codon	40278685	40278687	.	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40278688	40278780	1	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40278688	40278780	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40278781	40278865	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40278866	40278944	1	-	1	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40278866	40278944	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40278945	40279062	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40279063	40279108	1	-	2	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40279063	40279108	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40279109	40279279	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40279280	40279525	0.99	-	2	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40279280	40279525	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40279526	40279745	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40279746	40279895	1	-	2	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40279746	40279895	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40279896	40279989	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40279990	40280056	1	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40279990	40280056	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40280057	40280153	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40280154	40280213	1	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40280154	40280213	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40280214	40280430	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40280431	40280499	1	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40280431	40280499	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	intron	40280500	40280737	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	CDS	40280738	40281019	0.82	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	exon	40280738	40281019	.	-	.	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
Phchi.S1	AUGUSTUS	start_codon	40281017	40281019	.	-	0	transcript_id "Phchi.S1G635100.t1"; gene_id "Phchi.S1G635100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg788.t1 is derived from g10570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5591777	5592325	.	-	.	Phchi.S6G074700
Phchi.S6	AUGUSTUS	transcript	5591777	5592325	.	-	.	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	stop_codon	5591774	5591776	.	-	0	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	CDS	5591777	5591877	0.33	-	2	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	exon	5591777	5591877	.	-	.	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	intron	5591878	5592036	.	-	.	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	CDS	5592037	5592325	0.99	-	0	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	exon	5592037	5592325	.	-	.	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
Phchi.S6	AUGUSTUS	start_codon	5592323	5592325	.	-	0	transcript_id "Phchi.S6G074700.t1"; gene_id "Phchi.S6G074700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10154.t1 is derived from g7330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46004074	46005626	.	-	.	Phchi.S1G731300
Phchi.S1	AUGUSTUS	transcript	46004074	46005626	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	stop_codon	46004071	46004073	.	-	0	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	CDS	46004074	46004124	0.44	-	0	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	exon	46004074	46004124	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	intron	46004125	46004208	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	CDS	46004209	46004321	0.44	-	2	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	exon	46004209	46004321	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	intron	46004322	46004394	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	CDS	46004395	46004420	0.44	-	1	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	exon	46004395	46004420	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	intron	46004421	46004576	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	CDS	46004577	46005274	0.63	-	0	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	exon	46004577	46005274	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	intron	46005275	46005617	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	CDS	46005618	46005626	1	-	0	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	exon	46005618	46005626	.	-	.	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
Phchi.S1	AUGUSTUS	start_codon	46005624	46005626	.	-	0	transcript_id "Phchi.S1G731300.t1"; gene_id "Phchi.S1G731300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11820.t1 is derived from g15872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8392887	8393580	.	-	.	Phchi.S4G140200
Phchi.S4	AUGUSTUS	transcript	8392887	8393580	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	stop_codon	8392884	8392886	.	-	0	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	CDS	8392887	8392910	1	-	0	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	exon	8392887	8392910	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	intron	8392911	8393092	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	CDS	8393093	8393251	1	-	0	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	exon	8393093	8393251	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	intron	8393252	8393387	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	CDS	8393388	8393463	1	-	1	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	exon	8393388	8393463	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	intron	8393464	8393551	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	CDS	8393552	8393580	0.67	-	0	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	exon	8393552	8393580	.	-	.	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
Phchi.S4	AUGUSTUS	start_codon	8393578	8393580	.	-	0	transcript_id "Phchi.S4G140200.t1"; gene_id "Phchi.S4G140200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13863.t1 is derived from g12330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9299887	9300382	.	-	.	Phchi.S3G118200
Phchi.S3	AUGUSTUS	transcript	9299887	9300382	.	-	.	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	stop_codon	9299884	9299886	.	-	0	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	CDS	9299887	9299975	0.53	-	2	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	exon	9299887	9299975	.	-	.	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	intron	9299976	9300072	.	-	.	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	CDS	9300073	9300106	0.52	-	0	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	exon	9300073	9300106	.	-	.	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	intron	9300107	9300196	.	-	.	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	CDS	9300197	9300382	0.26	-	0	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	exon	9300197	9300382	.	-	.	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
Phchi.S3	AUGUSTUS	start_codon	9300380	9300382	.	-	0	transcript_id "Phchi.S3G118200.t1"; gene_id "Phchi.S3G118200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2801.t1 is derived from g9721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8944084	8945216	.	+	.	Phchi.S5G141000
Phchi.S5	AUGUSTUS	transcript	8944084	8945216	.	+	.	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	start_codon	8944084	8944086	.	+	0	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	CDS	8944084	8944753	0.69	+	0	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	exon	8944084	8944753	.	+	.	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	intron	8944754	8944950	.	+	.	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	CDS	8944951	8944995	0.67	+	2	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	exon	8944951	8944995	.	+	.	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	intron	8944996	8945121	.	+	.	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	CDS	8945122	8945216	0.67	+	2	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	exon	8945122	8945216	.	+	.	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
Phchi.S5	AUGUSTUS	stop_codon	8945217	8945219	.	+	0	transcript_id "Phchi.S5G141000.t1"; gene_id "Phchi.S5G141000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11020.t1 is derived from g15070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3664825	3665864	.	+	.	Phchi.S4G060200
Phchi.S4	AUGUSTUS	transcript	3664825	3665864	.	+	.	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	start_codon	3664825	3664827	.	+	0	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	CDS	3664825	3664972	0.99	+	0	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	exon	3664825	3664972	.	+	.	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	intron	3664973	3665119	.	+	.	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	CDS	3665120	3665429	1	+	2	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	exon	3665120	3665429	.	+	.	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	intron	3665430	3665563	.	+	.	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	CDS	3665564	3665864	0.97	+	1	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	exon	3665564	3665864	.	+	.	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
Phchi.S4	AUGUSTUS	stop_codon	3665865	3665867	.	+	0	transcript_id "Phchi.S4G060200.t1"; gene_id "Phchi.S4G060200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10341.t1 is derived from g7517.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47253094	47255683	.	+	.	Phchi.S1G750000
Phchi.S1	AUGUSTUS	transcript	47253094	47255683	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	start_codon	47253094	47253096	.	+	0	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253094	47253178	1	+	0	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253094	47253178	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47253179	47253264	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253265	47253329	1	+	2	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253265	47253329	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47253330	47253406	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253407	47253495	0.98	+	0	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253407	47253495	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47253496	47253669	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253670	47254150	0.99	+	1	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253670	47254150	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47254151	47254534	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47254535	47255683	0.99	+	0	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47254535	47255683	.	+	.	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	stop_codon	47255684	47255686	.	+	0	transcript_id "Phchi.S1G750000.t1"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	transcript	47253162	47255683	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	start_codon	47253162	47253164	.	+	0	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253162	47253178	1	+	0	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253162	47253178	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47253179	47253264	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253265	47253329	1	+	1	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253265	47253329	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47253330	47253425	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253426	47253495	1	+	2	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253426	47253495	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47253496	47253669	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47253670	47254150	0.95	+	1	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47253670	47254150	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	intron	47254151	47254534	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	CDS	47254535	47255683	0.98	+	0	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	exon	47254535	47255683	.	+	.	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
Phchi.S1	AUGUSTUS	stop_codon	47255684	47255686	.	+	0	transcript_id "Phchi.S1G750000.t2"; gene_id "Phchi.S1G750000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14278.t1 is derived from g12745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11895073	11899008	.	+	.	Phchi.S3G159700
Phchi.S3	AUGUSTUS	transcript	11895073	11899008	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	start_codon	11895073	11895075	.	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895073	11895191	0.9	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895073	11895191	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895192	11895278	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895279	11895396	1	+	1	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895279	11895396	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895397	11895476	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895477	11895520	1	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895477	11895520	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895521	11895613	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895614	11895724	1	+	1	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895614	11895724	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895725	11895802	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895803	11895883	1	+	1	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895803	11895883	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895884	11895965	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895966	11896105	0.69	+	1	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895966	11896105	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11896106	11896186	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11896187	11896291	0.38	+	2	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11896187	11896291	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11896292	11896466	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11896467	11896729	0.35	+	2	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11896467	11896729	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11896730	11896812	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11896813	11897010	1	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11896813	11897010	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897011	11897178	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897179	11897395	0.87	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897179	11897395	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897396	11897515	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897516	11897588	0.84	+	2	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897516	11897588	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897589	11897709	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897710	11897782	0.99	+	1	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897710	11897782	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897783	11897920	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897921	11898040	1	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897921	11898040	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11898041	11898179	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11898180	11898578	0.95	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11898180	11898578	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11898579	11898672	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11898673	11898768	1	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11898673	11898768	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11898769	11898846	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11898847	11899008	1	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11898847	11899008	.	+	.	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	stop_codon	11899009	11899011	.	+	0	transcript_id "Phchi.S3G159700.t1"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	transcript	11895073	11899008	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	start_codon	11895073	11895075	.	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895073	11895191	0.97	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895073	11895191	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895192	11895278	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895279	11895396	1	+	1	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895279	11895396	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895397	11895476	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895477	11895520	1	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895477	11895520	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895521	11895598	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895599	11895724	0.83	+	1	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895599	11895724	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895725	11895802	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895803	11895883	1	+	1	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895803	11895883	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11895884	11895965	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11895966	11896105	0.65	+	1	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11895966	11896105	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11896106	11896186	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11896187	11896291	0.4	+	2	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11896187	11896291	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11896292	11896466	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11896467	11896729	0.46	+	2	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11896467	11896729	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11896730	11896812	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11896813	11897010	1	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11896813	11897010	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897011	11897178	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897179	11897395	0.86	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897179	11897395	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897396	11897515	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897516	11897588	0.81	+	2	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897516	11897588	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897589	11897709	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897710	11897782	1	+	1	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897710	11897782	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11897783	11897920	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11897921	11898040	1	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11897921	11898040	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11898041	11898179	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11898180	11898578	0.96	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11898180	11898578	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11898579	11898672	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11898673	11898768	1	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11898673	11898768	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	intron	11898769	11898846	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	CDS	11898847	11899008	1	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	exon	11898847	11899008	.	+	.	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
Phchi.S3	AUGUSTUS	stop_codon	11899009	11899011	.	+	0	transcript_id "Phchi.S3G159700.t2"; gene_id "Phchi.S3G159700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2833.t1 is derived from g9753.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9097612	9098244	.	+	.	Phchi.S5G144200
Phchi.S5	AUGUSTUS	transcript	9097612	9098244	.	+	.	transcript_id "Phchi.S5G144200.t1"; gene_id "Phchi.S5G144200"
Phchi.S5	AUGUSTUS	start_codon	9097612	9097614	.	+	0	transcript_id "Phchi.S5G144200.t1"; gene_id "Phchi.S5G144200"
Phchi.S5	AUGUSTUS	CDS	9097612	9098244	0.51	+	0	transcript_id "Phchi.S5G144200.t1"; gene_id "Phchi.S5G144200"
Phchi.S5	AUGUSTUS	exon	9097612	9098244	.	+	.	transcript_id "Phchi.S5G144200.t1"; gene_id "Phchi.S5G144200"
Phchi.S5	AUGUSTUS	stop_codon	9098245	9098247	.	+	0	transcript_id "Phchi.S5G144200.t1"; gene_id "Phchi.S5G144200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3732.t1 is derived from g901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5432898	5433430	.	-	.	Phchi.S1G089100
Phchi.S1	AUGUSTUS	transcript	5432898	5433430	.	-	.	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	stop_codon	5432895	5432897	.	-	0	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	CDS	5432898	5432914	1	-	2	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	exon	5432898	5432914	.	-	.	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	intron	5432915	5433189	.	-	.	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	CDS	5433190	5433430	1	-	0	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	exon	5433190	5433430	.	-	.	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
Phchi.S1	AUGUSTUS	start_codon	5433428	5433430	.	-	0	transcript_id "Phchi.S1G089100.t1"; gene_id "Phchi.S1G089100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13356.t1 is derived from g11822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6302934	6304789	.	-	.	Phchi.S3G067500
Phchi.S3	AUGUSTUS	transcript	6302934	6304789	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	stop_codon	6302931	6302933	.	-	0	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6302934	6303099	0.99	-	1	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6302934	6303099	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6303100	6303183	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6303184	6303275	1	-	0	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6303184	6303275	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6303276	6303383	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6303384	6303630	1	-	1	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6303384	6303630	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6303631	6303764	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6303765	6303935	1	-	1	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6303765	6303935	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6303936	6304024	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6304025	6304163	1	-	2	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6304025	6304163	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6304164	6304271	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6304272	6304391	1	-	2	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6304272	6304391	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6304392	6304557	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6304558	6304630	0.39	-	0	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6304558	6304630	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	intron	6304631	6304753	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	CDS	6304754	6304789	0.38	-	0	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	exon	6304754	6304789	.	-	.	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
Phchi.S3	AUGUSTUS	start_codon	6304787	6304789	.	-	0	transcript_id "Phchi.S3G067500.t1"; gene_id "Phchi.S3G067500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3000.t1 is derived from g169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1079894	1080392	.	-	.	Phchi.S1G015900
Phchi.S1	AUGUSTUS	transcript	1079894	1080392	.	-	.	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	stop_codon	1079891	1079893	.	-	0	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	CDS	1079894	1079911	0.95	-	0	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	exon	1079894	1079911	.	-	.	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	intron	1079912	1080057	.	-	.	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	CDS	1080058	1080228	0.95	-	0	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	exon	1080058	1080228	.	-	.	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	intron	1080229	1080374	.	-	.	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	CDS	1080375	1080392	1	-	0	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	exon	1080375	1080392	.	-	.	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
Phchi.S1	AUGUSTUS	start_codon	1080390	1080392	.	-	0	transcript_id "Phchi.S1G015900.t1"; gene_id "Phchi.S1G015900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9120.t1 is derived from g6295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39924759	39925427	.	-	.	Phchi.S1G627900
Phchi.S1	AUGUSTUS	transcript	39924759	39925427	.	-	.	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	stop_codon	39924756	39924758	.	-	0	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	CDS	39924759	39924906	1	-	1	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	exon	39924759	39924906	.	-	.	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	intron	39924907	39925020	.	-	.	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	CDS	39925021	39925427	0.57	-	0	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	exon	39925021	39925427	.	-	.	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
Phchi.S1	AUGUSTUS	start_codon	39925425	39925427	.	-	0	transcript_id "Phchi.S1G627900.t1"; gene_id "Phchi.S1G627900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8285.t1 is derived from g5460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35097926	35100783	.	+	.	Phchi.S1G544400
Phchi.S1	AUGUSTUS	transcript	35097926	35100783	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	start_codon	35097926	35097928	.	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35097926	35098008	0.98	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35097926	35098008	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35098009	35098245	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35098246	35098423	1	+	1	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35098246	35098423	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35098424	35098535	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35098536	35098626	1	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35098536	35098626	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35098627	35098768	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35098769	35098863	1	+	2	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35098769	35098863	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35098864	35098954	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35098955	35099047	1	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35098955	35099047	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35099048	35099138	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35099139	35099187	1	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35099139	35099187	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35099188	35099307	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35099308	35099446	1	+	2	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35099308	35099446	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35099447	35099643	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35099644	35099760	1	+	1	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35099644	35099760	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35099761	35099856	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35099857	35099947	1	+	1	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35099857	35099947	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35099948	35100072	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35100073	35100215	1	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35100073	35100215	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35100216	35100352	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35100353	35100467	1	+	1	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35100353	35100467	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35100468	35100548	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35100549	35100593	0.77	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35100549	35100593	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	intron	35100594	35100705	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	CDS	35100706	35100783	0.79	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	exon	35100706	35100783	.	+	.	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
Phchi.S1	AUGUSTUS	stop_codon	35100784	35100786	.	+	0	transcript_id "Phchi.S1G544400.t1"; gene_id "Phchi.S1G544400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg800.t1 is derived from g10582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5670785	5671954	.	+	.	Phchi.S6G075900
Phchi.S6	AUGUSTUS	transcript	5670785	5671954	.	+	.	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	start_codon	5670785	5670787	.	+	0	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	CDS	5670785	5671209	0.64	+	0	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	exon	5670785	5671209	.	+	.	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	intron	5671210	5671405	.	+	.	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	CDS	5671406	5671639	1	+	1	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	exon	5671406	5671639	.	+	.	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	intron	5671640	5671737	.	+	.	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	CDS	5671738	5671954	1	+	1	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	exon	5671738	5671954	.	+	.	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
Phchi.S6	AUGUSTUS	stop_codon	5671955	5671957	.	+	0	transcript_id "Phchi.S6G075900.t1"; gene_id "Phchi.S6G075900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14824.t1 is derived from g13292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14897263	14898744	.	+	.	Phchi.S3G214300
Phchi.S3	AUGUSTUS	transcript	14897263	14898744	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	start_codon	14897263	14897265	.	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14897263	14897403	0.92	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14897263	14897403	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14897404	14897485	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14897486	14897627	0.99	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14897486	14897627	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14897628	14897710	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14897711	14897807	1	+	2	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14897711	14897807	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14897808	14897934	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14897935	14898004	0.99	+	1	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14897935	14898004	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14898005	14898108	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14898109	14898213	1	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14898109	14898213	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14898214	14898314	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14898315	14898413	1	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14898315	14898413	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14898414	14898490	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14898491	14898581	1	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14898491	14898581	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	intron	14898582	14898673	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	CDS	14898674	14898744	1	+	2	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	exon	14898674	14898744	.	+	.	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
Phchi.S3	AUGUSTUS	stop_codon	14898745	14898747	.	+	0	transcript_id "Phchi.S3G214300.t1"; gene_id "Phchi.S3G214300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9386.t1 is derived from g6562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41273737	41274144	.	-	.	Phchi.S1G654500
Phchi.S1	AUGUSTUS	transcript	41273737	41274144	.	-	.	transcript_id "Phchi.S1G654500.t1"; gene_id "Phchi.S1G654500"
Phchi.S1	AUGUSTUS	stop_codon	41273734	41273736	.	-	0	transcript_id "Phchi.S1G654500.t1"; gene_id "Phchi.S1G654500"
Phchi.S1	AUGUSTUS	CDS	41273737	41274144	0.54	-	0	transcript_id "Phchi.S1G654500.t1"; gene_id "Phchi.S1G654500"
Phchi.S1	AUGUSTUS	exon	41273737	41274144	.	-	.	transcript_id "Phchi.S1G654500.t1"; gene_id "Phchi.S1G654500"
Phchi.S1	AUGUSTUS	start_codon	41274142	41274144	.	-	0	transcript_id "Phchi.S1G654500.t1"; gene_id "Phchi.S1G654500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2350.t1 is derived from g9270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6311355	6312400	.	+	.	Phchi.S5G095900
Phchi.S5	AUGUSTUS	transcript	6311355	6312400	.	+	.	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	start_codon	6311355	6311357	.	+	0	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	CDS	6311355	6311393	0.99	+	0	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	exon	6311355	6311393	.	+	.	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	intron	6311394	6311569	.	+	.	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	CDS	6311570	6311740	1	+	0	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	exon	6311570	6311740	.	+	.	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	intron	6311741	6312103	.	+	.	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	CDS	6312104	6312400	1	+	0	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	exon	6312104	6312400	.	+	.	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
Phchi.S5	AUGUSTUS	stop_codon	6312401	6312403	.	+	0	transcript_id "Phchi.S5G095900.t1"; gene_id "Phchi.S5G095900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5783.t1 is derived from g2953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18936555	18940313	.	-	.	Phchi.S1G294200
Phchi.S1	AUGUSTUS	transcript	18936555	18940313	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	stop_codon	18936552	18936554	.	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18936555	18936685	0.99	-	2	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18936555	18936685	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18936686	18936801	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18936802	18936873	1	-	2	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18936802	18936873	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18936874	18936963	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18936964	18937076	1	-	1	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18936964	18937076	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18937077	18937271	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18937272	18937409	1	-	1	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18937272	18937409	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18937410	18937580	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18937581	18937761	1	-	2	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18937581	18937761	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18937762	18937924	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18937925	18938066	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18937925	18938066	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18938067	18938198	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18938199	18938246	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18938199	18938246	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18938247	18938343	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18938344	18938394	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18938344	18938394	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18938395	18938494	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18938495	18938580	1	-	2	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18938495	18938580	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18938581	18938666	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18938667	18938733	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18938667	18938733	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18938734	18938926	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18938927	18939004	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18938927	18939004	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18939005	18939099	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18939100	18939193	1	-	1	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18939100	18939193	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18939194	18939436	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18939437	18939507	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18939437	18939507	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18939508	18939636	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18939637	18939777	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18939637	18939777	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18939778	18939864	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18939865	18939948	1	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18939865	18939948	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	intron	18939949	18940034	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	CDS	18940035	18940313	0.97	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	exon	18940035	18940313	.	-	.	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
Phchi.S1	AUGUSTUS	start_codon	18940311	18940313	.	-	0	transcript_id "Phchi.S1G294200.t1"; gene_id "Phchi.S1G294200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2734.t1 is derived from g9654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8492141	8494262	.	-	.	Phchi.S5G134300
Phchi.S5	AUGUSTUS	transcript	8492141	8494262	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	stop_codon	8492138	8492140	.	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8492141	8492338	0.99	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8492141	8492338	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8492339	8492437	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8492438	8492695	1	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8492438	8492695	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8492696	8492791	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8492792	8492999	0.99	-	1	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8492792	8492999	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8493000	8493119	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8493120	8493217	1	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8493120	8493217	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8493218	8493292	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8493293	8493476	1	-	1	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8493293	8493476	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8493477	8493560	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8493561	8493673	1	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8493561	8493673	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8493674	8493771	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8493772	8493957	1	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8493772	8493957	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	intron	8493958	8494070	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	CDS	8494071	8494262	0.39	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	exon	8494071	8494262	.	-	.	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
Phchi.S5	AUGUSTUS	start_codon	8494260	8494262	.	-	0	transcript_id "Phchi.S5G134300.t1"; gene_id "Phchi.S5G134300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2871.t1 is derived from g40.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	201742	205210	.	-	.	Phchi.S1G003000
Phchi.S1	AUGUSTUS	transcript	201742	205210	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	stop_codon	201739	201741	.	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	201742	201899	1	-	2	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	201742	201899	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	201900	201999	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	202000	202075	1	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	202000	202075	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	202076	202171	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	202172	202213	0.59	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	202172	202213	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	202214	202425	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	202426	203382	0.59	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	202426	203382	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	203383	203465	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	203466	203619	1	-	1	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	203466	203619	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	203620	203719	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	203720	203871	1	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	203720	203871	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	203872	203968	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	203969	204254	0.99	-	1	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	203969	204254	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	204255	204363	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	204364	204469	1	-	2	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	204364	204469	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	204470	204565	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	204566	204656	1	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	204566	204656	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	intron	204657	204769	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	CDS	204770	205210	0.46	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	exon	204770	205210	.	-	.	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
Phchi.S1	AUGUSTUS	start_codon	205208	205210	.	-	0	transcript_id "Phchi.S1G003000.t1"; gene_id "Phchi.S1G003000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3253.t1 is derived from g422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2520767	2523373	.	+	.	Phchi.S1G041200
Phchi.S1	AUGUSTUS	transcript	2520767	2523373	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	start_codon	2520767	2520769	.	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2520767	2520949	0.99	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2520767	2520949	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2520950	2521124	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2521125	2521149	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2521125	2521149	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2521150	2521324	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2521325	2521437	1	+	2	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2521325	2521437	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2521438	2521523	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2521524	2521835	0.74	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2521524	2521835	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2521836	2521936	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2521937	2522025	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2521937	2522025	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2522026	2522117	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2522118	2522169	1	+	1	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2522118	2522169	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2522170	2522273	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2522274	2522369	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2522274	2522369	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2522370	2522468	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2522469	2522513	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2522469	2522513	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2522514	2522610	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2522611	2522700	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2522611	2522700	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2522701	2522794	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2522795	2522866	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2522795	2522866	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2522867	2523172	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2523173	2523253	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2523173	2523253	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	intron	2523254	2523328	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	CDS	2523329	2523373	1	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	exon	2523329	2523373	.	+	.	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
Phchi.S1	AUGUSTUS	stop_codon	2523374	2523376	.	+	0	transcript_id "Phchi.S1G041200.t1"; gene_id "Phchi.S1G041200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12277.t1 is derived from g7953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8055625	8055843	.	+	.	Phchi.S2G035700
Phchi.S2	AUGUSTUS	transcript	8055625	8055843	.	+	.	transcript_id "Phchi.S2G035700.t1"; gene_id "Phchi.S2G035700"
Phchi.S2	AUGUSTUS	start_codon	8055625	8055627	.	+	0	transcript_id "Phchi.S2G035700.t1"; gene_id "Phchi.S2G035700"
Phchi.S2	AUGUSTUS	CDS	8055625	8055843	0.9	+	0	transcript_id "Phchi.S2G035700.t1"; gene_id "Phchi.S2G035700"
Phchi.S2	AUGUSTUS	exon	8055625	8055843	.	+	.	transcript_id "Phchi.S2G035700.t1"; gene_id "Phchi.S2G035700"
Phchi.S2	AUGUSTUS	stop_codon	8055844	8055846	.	+	0	transcript_id "Phchi.S2G035700.t1"; gene_id "Phchi.S2G035700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9943.t1 is derived from g7119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44598385	44599127	.	-	.	Phchi.S1G710200
Phchi.S1	AUGUSTUS	transcript	44598385	44599127	.	-	.	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	stop_codon	44598382	44598384	.	-	0	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	CDS	44598385	44598728	0.22	-	2	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	exon	44598385	44598728	.	-	.	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	intron	44598729	44598832	.	-	.	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	CDS	44598833	44599127	0.51	-	0	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	exon	44598833	44599127	.	-	.	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
Phchi.S1	AUGUSTUS	start_codon	44599125	44599127	.	-	0	transcript_id "Phchi.S1G710200.t1"; gene_id "Phchi.S1G710200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4087.t1 is derived from g1256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7748761	7750298	.	+	.	Phchi.S1G124600
Phchi.S1	AUGUSTUS	transcript	7748761	7750298	.	+	.	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	start_codon	7748761	7748763	.	+	0	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	CDS	7748761	7748885	0.64	+	0	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	exon	7748761	7748885	.	+	.	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	intron	7748886	7749301	.	+	.	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	CDS	7749302	7750298	0.79	+	1	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	exon	7749302	7750298	.	+	.	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
Phchi.S1	AUGUSTUS	stop_codon	7750299	7750301	.	+	0	transcript_id "Phchi.S1G124600.t1"; gene_id "Phchi.S1G124600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13816.t1 is derived from g12283.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9046709	9048269	.	-	.	Phchi.S3G113500
Phchi.S3	AUGUSTUS	transcript	9046709	9048269	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	stop_codon	9046706	9046708	.	-	0	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9046709	9046789	1	-	0	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9046709	9046789	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9046790	9046886	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9046887	9046975	1	-	2	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9046887	9046975	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9046976	9047132	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047133	9047206	1	-	1	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047133	9047206	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047207	9047288	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047289	9047383	1	-	0	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047289	9047383	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047384	9047520	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047521	9047613	1	-	0	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047521	9047613	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047614	9047688	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047689	9047783	1	-	2	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047689	9047783	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047784	9047872	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047873	9048003	1	-	1	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047873	9048003	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9048004	9048216	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9048217	9048269	1	-	0	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9048217	9048269	.	-	.	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	start_codon	9048267	9048269	.	-	0	transcript_id "Phchi.S3G113500.t1"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	transcript	9046709	9048269	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	stop_codon	9046706	9046708	.	-	0	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9046709	9046789	1	-	0	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9046709	9046789	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9046790	9046886	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9046887	9046975	1	-	2	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9046887	9046975	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9046976	9047132	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047133	9047206	1	-	1	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047133	9047206	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047207	9047288	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047289	9047383	1	-	0	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047289	9047383	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047384	9047520	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047521	9047613	1	-	0	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047521	9047613	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047614	9047688	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047689	9047780	1	-	2	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047689	9047780	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9047781	9047872	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9047873	9048003	1	-	1	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9047873	9048003	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	intron	9048004	9048216	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	CDS	9048217	9048269	0.99	-	0	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	exon	9048217	9048269	.	-	.	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
Phchi.S3	AUGUSTUS	start_codon	9048267	9048269	.	-	0	transcript_id "Phchi.S3G113500.t2"; gene_id "Phchi.S3G113500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12722.t1 is derived from g11187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1120447	1120998	.	-	.	Phchi.S3G004100
Phchi.S3	AUGUSTUS	transcript	1120447	1120998	.	-	.	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	stop_codon	1120444	1120446	.	-	0	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	CDS	1120447	1120566	0.91	-	0	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	exon	1120447	1120566	.	-	.	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	intron	1120567	1120650	.	-	.	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	CDS	1120651	1120770	0.98	-	0	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	exon	1120651	1120770	.	-	.	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	intron	1120771	1120866	.	-	.	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	CDS	1120867	1120998	0.52	-	0	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	exon	1120867	1120998	.	-	.	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
Phchi.S3	AUGUSTUS	start_codon	1120996	1120998	.	-	0	transcript_id "Phchi.S3G004100.t1"; gene_id "Phchi.S3G004100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9416.t1 is derived from g6592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41386330	41389441	.	+	.	Phchi.S1G657500
Phchi.S1	AUGUSTUS	transcript	41386330	41389441	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	start_codon	41386330	41386332	.	+	0	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	CDS	41386330	41386945	0.96	+	0	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	exon	41386330	41386945	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	intron	41386946	41387067	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	CDS	41387068	41388296	1	+	2	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	exon	41387068	41388296	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	intron	41388297	41388403	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	CDS	41388404	41388449	1	+	0	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	exon	41388404	41388449	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	intron	41388450	41388552	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	CDS	41388553	41389025	0.28	+	2	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	exon	41388553	41389025	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	intron	41389026	41389145	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	CDS	41389146	41389245	0.51	+	0	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	exon	41389146	41389245	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	intron	41389246	41389349	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	CDS	41389350	41389441	0.51	+	2	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	exon	41389350	41389441	.	+	.	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
Phchi.S1	AUGUSTUS	stop_codon	41389442	41389444	.	+	0	transcript_id "Phchi.S1G657500.t1"; gene_id "Phchi.S1G657500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2870.t1 is derived from g39.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	199758	201685	.	+	.	Phchi.S1G002900
Phchi.S1	AUGUSTUS	transcript	199758	201685	.	+	.	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	start_codon	199758	199760	.	+	0	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	CDS	199758	199830	0.01	+	0	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	exon	199758	199830	.	+	.	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	intron	199831	200600	.	+	.	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	CDS	200601	200634	0.27	+	2	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	exon	200601	200634	.	+	.	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	intron	200635	201642	.	+	.	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	CDS	201643	201685	0.01	+	1	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	exon	201643	201685	.	+	.	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
Phchi.S1	AUGUSTUS	stop_codon	201686	201688	.	+	0	transcript_id "Phchi.S1G002900.t1"; gene_id "Phchi.S1G002900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15760.t1 is derived from g14230.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21098712	21100454	.	+	.	Phchi.S3G307900
Phchi.S3	AUGUSTUS	transcript	21098712	21100454	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	start_codon	21098712	21098714	.	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	CDS	21098712	21099152	1	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	exon	21098712	21099152	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	intron	21099153	21099267	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	CDS	21099268	21099396	0.99	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	exon	21099268	21099396	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	intron	21099397	21099523	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	CDS	21099524	21099544	0.96	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	exon	21099524	21099544	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	intron	21099545	21099789	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	CDS	21099790	21100278	0.99	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	exon	21099790	21100278	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	intron	21100279	21100397	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	CDS	21100398	21100454	0.99	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	exon	21100398	21100454	.	+	.	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
Phchi.S3	AUGUSTUS	stop_codon	21100455	21100457	.	+	0	transcript_id "Phchi.S3G307900.t1"; gene_id "Phchi.S3G307900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1348.t1 is derived from g11131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9128938	9131120	.	+	.	Phchi.S6G130700
Phchi.S6	AUGUSTUS	transcript	9128938	9131120	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	start_codon	9128938	9128940	.	+	0	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9128938	9128992	1	+	0	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9128938	9128992	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9128993	9129246	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129247	9129356	1	+	2	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129247	9129356	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129357	9129473	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129474	9129531	1	+	0	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129474	9129531	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129532	9129613	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129614	9129763	1	+	2	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129614	9129763	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129764	9129930	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129931	9129989	0.93	+	2	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129931	9129989	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129990	9130114	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130115	9130140	0.95	+	0	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130115	9130140	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130141	9130305	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130306	9130351	1	+	1	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130306	9130351	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130352	9130437	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130438	9130564	1	+	0	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130438	9130564	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130565	9130717	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130718	9130790	1	+	2	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130718	9130790	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130791	9130867	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130868	9130957	0.99	+	1	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130868	9130957	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130958	9131050	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9131051	9131120	0.99	+	1	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9131051	9131120	.	+	.	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	stop_codon	9131121	9131123	.	+	0	transcript_id "Phchi.S6G130700.t1"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	transcript	9128938	9131120	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	start_codon	9128938	9128940	.	+	0	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9128938	9128992	1	+	0	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9128938	9128992	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9128993	9129246	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129247	9129356	1	+	2	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129247	9129356	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129357	9129473	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129474	9129531	1	+	0	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129474	9129531	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129532	9129613	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129614	9129730	0.42	+	2	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129614	9129730	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129731	9129930	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9129931	9129989	0.4	+	2	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9129931	9129989	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9129990	9130114	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130115	9130140	0.41	+	0	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130115	9130140	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130141	9130305	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130306	9130351	1	+	1	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130306	9130351	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130352	9130437	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130438	9130564	1	+	0	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130438	9130564	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130565	9130717	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130718	9130790	1	+	2	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130718	9130790	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130791	9130867	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9130868	9130957	0.97	+	1	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9130868	9130957	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	intron	9130958	9131050	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	CDS	9131051	9131120	0.97	+	1	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	exon	9131051	9131120	.	+	.	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
Phchi.S6	AUGUSTUS	stop_codon	9131121	9131123	.	+	0	transcript_id "Phchi.S6G130700.t2"; gene_id "Phchi.S6G130700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg939.t1 is derived from g10721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6538473	6541299	.	-	.	Phchi.S6G089800
Phchi.S6	AUGUSTUS	transcript	6538473	6541299	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	stop_codon	6538470	6538472	.	-	0	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	CDS	6538473	6539020	1	-	2	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	exon	6538473	6539020	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	intron	6539021	6539113	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	CDS	6539114	6539528	1	-	0	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	exon	6539114	6539528	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	intron	6539529	6539623	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	CDS	6539624	6540744	0.98	-	2	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	exon	6539624	6540744	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	intron	6540745	6540954	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	CDS	6540955	6541057	0.74	-	0	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	exon	6540955	6541057	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	intron	6541058	6541167	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	CDS	6541168	6541299	0.64	-	0	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	exon	6541168	6541299	.	-	.	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
Phchi.S6	AUGUSTUS	start_codon	6541297	6541299	.	-	0	transcript_id "Phchi.S6G089800.t1"; gene_id "Phchi.S6G089800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12789.t1 is derived from g11254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2378833	2379850	.	+	.	Phchi.S3G010800
Phchi.S3	AUGUSTUS	transcript	2378833	2379850	.	+	.	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	start_codon	2378833	2378835	.	+	0	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	CDS	2378833	2379138	0.66	+	0	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	exon	2378833	2379138	.	+	.	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	intron	2379139	2379277	.	+	.	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	CDS	2379278	2379850	1	+	0	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	exon	2379278	2379850	.	+	.	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
Phchi.S3	AUGUSTUS	stop_codon	2379851	2379853	.	+	0	transcript_id "Phchi.S3G010800.t1"; gene_id "Phchi.S3G010800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7623.t1 is derived from g4797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30303577	30304650	.	+	.	Phchi.S1G478200
Phchi.S1	AUGUSTUS	transcript	30303577	30304650	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	start_codon	30303577	30303579	.	+	0	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	CDS	30303577	30303816	0.73	+	0	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	exon	30303577	30303816	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	intron	30303817	30304094	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	CDS	30304095	30304275	1	+	0	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	exon	30304095	30304275	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	intron	30304276	30304371	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	CDS	30304372	30304479	1	+	2	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	exon	30304372	30304479	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	intron	30304480	30304594	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	CDS	30304595	30304650	1	+	2	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	exon	30304595	30304650	.	+	.	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
Phchi.S1	AUGUSTUS	stop_codon	30304651	30304653	.	+	0	transcript_id "Phchi.S1G478200.t1"; gene_id "Phchi.S1G478200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1669.t1 is derived from g8588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2326626	2327126	.	+	.	Phchi.S5G027800
Phchi.S5	AUGUSTUS	transcript	2326626	2327126	.	+	.	transcript_id "Phchi.S5G027800.t1"; gene_id "Phchi.S5G027800"
Phchi.S5	AUGUSTUS	start_codon	2326626	2326628	.	+	0	transcript_id "Phchi.S5G027800.t1"; gene_id "Phchi.S5G027800"
Phchi.S5	AUGUSTUS	CDS	2326626	2327126	1	+	0	transcript_id "Phchi.S5G027800.t1"; gene_id "Phchi.S5G027800"
Phchi.S5	AUGUSTUS	exon	2326626	2327126	.	+	.	transcript_id "Phchi.S5G027800.t1"; gene_id "Phchi.S5G027800"
Phchi.S5	AUGUSTUS	stop_codon	2327127	2327129	.	+	0	transcript_id "Phchi.S5G027800.t1"; gene_id "Phchi.S5G027800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8767.t1 is derived from g5942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37866009	37867786	.	+	.	Phchi.S1G592600
Phchi.S1	AUGUSTUS	transcript	37866009	37867786	.	+	.	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	start_codon	37866009	37866011	.	+	0	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	CDS	37866009	37866958	0.24	+	0	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	exon	37866009	37866958	.	+	.	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	intron	37866959	37867036	.	+	.	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	CDS	37867037	37867235	0.73	+	1	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	exon	37867037	37867235	.	+	.	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	intron	37867236	37867372	.	+	.	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	CDS	37867373	37867786	0.55	+	0	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	exon	37867373	37867786	.	+	.	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
Phchi.S1	AUGUSTUS	stop_codon	37867787	37867789	.	+	0	transcript_id "Phchi.S1G592600.t1"; gene_id "Phchi.S1G592600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8691.t1 is derived from g5866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37456894	37458266	.	+	.	Phchi.S1G585000
Phchi.S1	AUGUSTUS	transcript	37456894	37458266	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	start_codon	37456894	37456896	.	+	0	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	CDS	37456894	37457266	0.94	+	0	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	exon	37456894	37457266	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	intron	37457267	37457358	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	CDS	37457359	37457765	1	+	2	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	exon	37457359	37457765	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	intron	37457766	37457847	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	CDS	37457848	37457949	1	+	0	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	exon	37457848	37457949	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	intron	37457950	37458041	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	CDS	37458042	37458266	1	+	0	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	exon	37458042	37458266	.	+	.	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
Phchi.S1	AUGUSTUS	stop_codon	37458267	37458269	.	+	0	transcript_id "Phchi.S1G585000.t1"; gene_id "Phchi.S1G585000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3745.t1 is derived from g914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5471294	5473360	.	+	.	Phchi.S1G090400
Phchi.S1	AUGUSTUS	transcript	5471294	5473360	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	start_codon	5471294	5471296	.	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5471294	5471335	0.92	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5471294	5471335	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5471336	5471462	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5471463	5471516	1	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5471463	5471516	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5471517	5471619	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5471620	5471793	1	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5471620	5471793	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5471794	5471908	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5471909	5471980	1	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5471909	5471980	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5471981	5472139	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5472140	5472199	1	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5472140	5472199	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5472200	5472275	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5472276	5472385	1	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5472276	5472385	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5472386	5472504	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5472505	5472804	0.97	+	1	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5472505	5472804	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5472805	5472905	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5472906	5473097	1	+	1	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5472906	5473097	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5473098	5473176	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5473177	5473228	1	+	1	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5473177	5473228	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	intron	5473229	5473312	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	CDS	5473313	5473360	1	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	exon	5473313	5473360	.	+	.	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
Phchi.S1	AUGUSTUS	stop_codon	5473361	5473363	.	+	0	transcript_id "Phchi.S1G090400.t1"; gene_id "Phchi.S1G090400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4128.t1 is derived from g1297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8394290	8395350	.	-	.	Phchi.S1G128700
Phchi.S1	AUGUSTUS	transcript	8394290	8395350	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	stop_codon	8394287	8394289	.	-	0	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	CDS	8394290	8394330	0.3	-	2	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	exon	8394290	8394330	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	intron	8394331	8394454	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	CDS	8394455	8394565	0.56	-	2	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	exon	8394455	8394565	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	intron	8394566	8394658	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	CDS	8394659	8394842	1	-	0	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	exon	8394659	8394842	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	intron	8394843	8395075	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	CDS	8395076	8395184	1	-	1	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	exon	8395076	8395184	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	intron	8395185	8395282	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	CDS	8395283	8395350	1	-	0	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	exon	8395283	8395350	.	-	.	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
Phchi.S1	AUGUSTUS	start_codon	8395348	8395350	.	-	0	transcript_id "Phchi.S1G128700.t1"; gene_id "Phchi.S1G128700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12210.t1 is derived from g7886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6746949	6750380	.	-	.	Phchi.S2G029000
Phchi.S2	AUGUSTUS	transcript	6746949	6750380	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	stop_codon	6746946	6746948	.	-	0	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	CDS	6746949	6747025	0.7	-	2	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	exon	6746949	6747025	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	intron	6747026	6747160	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	CDS	6747161	6747274	0.53	-	2	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	exon	6747161	6747274	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	intron	6747275	6747348	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	CDS	6747349	6747691	0.69	-	0	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	exon	6747349	6747691	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	intron	6747692	6747783	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	CDS	6747784	6748075	1	-	1	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	exon	6747784	6748075	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	intron	6748076	6748216	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	CDS	6748217	6749965	0.99	-	1	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	exon	6748217	6749965	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	intron	6749966	6750255	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	CDS	6750256	6750380	0.73	-	0	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	exon	6750256	6750380	.	-	.	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
Phchi.S2	AUGUSTUS	start_codon	6750378	6750380	.	-	0	transcript_id "Phchi.S2G029000.t1"; gene_id "Phchi.S2G029000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8052.t1 is derived from g5227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32721165	32721852	.	-	.	Phchi.S1G521100
Phchi.S1	AUGUSTUS	transcript	32721165	32721852	.	-	.	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	stop_codon	32721162	32721164	.	-	0	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	CDS	32721165	32721191	1	-	0	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	exon	32721165	32721191	.	-	.	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	intron	32721192	32721416	.	-	.	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	CDS	32721417	32721518	1	-	0	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	exon	32721417	32721518	.	-	.	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	intron	32721519	32721738	.	-	.	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	CDS	32721739	32721852	1	-	0	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	exon	32721739	32721852	.	-	.	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
Phchi.S1	AUGUSTUS	start_codon	32721850	32721852	.	-	0	transcript_id "Phchi.S1G521100.t1"; gene_id "Phchi.S1G521100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3593.t1 is derived from g762.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4648873	4649409	.	-	.	Phchi.S1G075200
Phchi.S1	AUGUSTUS	transcript	4648873	4649409	.	-	.	transcript_id "Phchi.S1G075200.t1"; gene_id "Phchi.S1G075200"
Phchi.S1	AUGUSTUS	stop_codon	4648870	4648872	.	-	0	transcript_id "Phchi.S1G075200.t1"; gene_id "Phchi.S1G075200"
Phchi.S1	AUGUSTUS	CDS	4648873	4649409	0.96	-	0	transcript_id "Phchi.S1G075200.t1"; gene_id "Phchi.S1G075200"
Phchi.S1	AUGUSTUS	exon	4648873	4649409	.	-	.	transcript_id "Phchi.S1G075200.t1"; gene_id "Phchi.S1G075200"
Phchi.S1	AUGUSTUS	start_codon	4649407	4649409	.	-	0	transcript_id "Phchi.S1G075200.t1"; gene_id "Phchi.S1G075200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4488.t1 is derived from g1658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10771159	10775493	.	-	.	Phchi.S1G164700
Phchi.S1	AUGUSTUS	transcript	10771159	10775493	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	stop_codon	10771156	10771158	.	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10771159	10771245	0.57	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10771159	10771245	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10771246	10771355	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10771356	10771396	0.28	-	2	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10771356	10771396	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10771397	10771478	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10771479	10773486	0.5	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10771479	10773486	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10773487	10773572	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10773573	10773727	1	-	2	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10773573	10773727	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10773728	10773850	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10773851	10774193	1	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10773851	10774193	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10774194	10774286	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10774287	10774355	1	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10774287	10774355	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10774356	10774452	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10774453	10774551	1	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10774453	10774551	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10774552	10774654	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10774655	10774700	1	-	1	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10774655	10774700	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10774701	10774820	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10774821	10774887	1	-	2	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10774821	10774887	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10774888	10775020	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10775021	10775069	1	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10775021	10775069	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	intron	10775070	10775364	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	CDS	10775365	10775493	0.85	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	exon	10775365	10775493	.	-	.	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
Phchi.S1	AUGUSTUS	start_codon	10775491	10775493	.	-	0	transcript_id "Phchi.S1G164700.t1"; gene_id "Phchi.S1G164700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4407.t1 is derived from g1576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10259604	10261572	.	-	.	Phchi.S1G156600
Phchi.S1	AUGUSTUS	transcript	10259604	10261572	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	stop_codon	10259601	10259603	.	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	CDS	10259604	10260017	0.86	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	exon	10259604	10260017	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	intron	10260018	10260239	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	CDS	10260240	10260326	1	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	exon	10260240	10260326	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	intron	10260327	10260419	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	CDS	10260420	10260494	1	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	exon	10260420	10260494	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	intron	10260495	10260611	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	CDS	10260612	10260710	0.97	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	exon	10260612	10260710	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	intron	10260711	10260916	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	CDS	10260917	10261036	0.87	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	exon	10260917	10261036	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	intron	10261037	10261305	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	CDS	10261306	10261572	0.86	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	exon	10261306	10261572	.	-	.	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
Phchi.S1	AUGUSTUS	start_codon	10261570	10261572	.	-	0	transcript_id "Phchi.S1G156600.t1"; gene_id "Phchi.S1G156600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8196.t1 is derived from g5371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34375676	34376674	.	+	.	Phchi.S1G535500
Phchi.S1	AUGUSTUS	transcript	34375676	34376674	.	+	.	transcript_id "Phchi.S1G535500.t1"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	start_codon	34375676	34375678	.	+	0	transcript_id "Phchi.S1G535500.t1"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	CDS	34375676	34376674	0.97	+	0	transcript_id "Phchi.S1G535500.t1"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	exon	34375676	34376674	.	+	.	transcript_id "Phchi.S1G535500.t1"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	stop_codon	34376675	34376677	.	+	0	transcript_id "Phchi.S1G535500.t1"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	transcript	34375832	34376674	.	+	.	transcript_id "Phchi.S1G535500.t2"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	start_codon	34375832	34375834	.	+	0	transcript_id "Phchi.S1G535500.t2"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	CDS	34375832	34376674	0.89	+	0	transcript_id "Phchi.S1G535500.t2"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	exon	34375832	34376674	.	+	.	transcript_id "Phchi.S1G535500.t2"; gene_id "Phchi.S1G535500"
Phchi.S1	AUGUSTUS	stop_codon	34376675	34376677	.	+	0	transcript_id "Phchi.S1G535500.t2"; gene_id "Phchi.S1G535500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10626.t1 is derived from g14676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1320907	1321595	.	+	.	Phchi.S4G020800
Phchi.S4	AUGUSTUS	transcript	1320907	1321595	.	+	.	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	start_codon	1320907	1320909	.	+	0	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	CDS	1320907	1320916	0.92	+	0	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	exon	1320907	1320916	.	+	.	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	intron	1320917	1321074	.	+	.	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	CDS	1321075	1321595	0.93	+	2	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	exon	1321075	1321595	.	+	.	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
Phchi.S4	AUGUSTUS	stop_codon	1321596	1321598	.	+	0	transcript_id "Phchi.S4G020800.t1"; gene_id "Phchi.S4G020800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14417.t1 is derived from g12885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12719871	12720672	.	+	.	Phchi.S3G173600
Phchi.S3	AUGUSTUS	transcript	12719871	12720672	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	start_codon	12719871	12719873	.	+	0	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	CDS	12719871	12720128	0.88	+	0	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	exon	12719871	12720128	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	intron	12720129	12720231	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	CDS	12720232	12720344	1	+	0	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	exon	12720232	12720344	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	intron	12720345	12720427	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	CDS	12720428	12720571	1	+	1	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	exon	12720428	12720571	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	intron	12720572	12720662	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	CDS	12720663	12720672	1	+	1	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	exon	12720663	12720672	.	+	.	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
Phchi.S3	AUGUSTUS	stop_codon	12720673	12720675	.	+	0	transcript_id "Phchi.S3G173600.t1"; gene_id "Phchi.S3G173600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6422.t1 is derived from g3594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22925450	22925986	.	+	.	Phchi.S1G358100
Phchi.S1	AUGUSTUS	transcript	22925450	22925986	.	+	.	transcript_id "Phchi.S1G358100.t1"; gene_id "Phchi.S1G358100"
Phchi.S1	AUGUSTUS	start_codon	22925450	22925452	.	+	0	transcript_id "Phchi.S1G358100.t1"; gene_id "Phchi.S1G358100"
Phchi.S1	AUGUSTUS	CDS	22925450	22925986	0.55	+	0	transcript_id "Phchi.S1G358100.t1"; gene_id "Phchi.S1G358100"
Phchi.S1	AUGUSTUS	exon	22925450	22925986	.	+	.	transcript_id "Phchi.S1G358100.t1"; gene_id "Phchi.S1G358100"
Phchi.S1	AUGUSTUS	stop_codon	22925987	22925989	.	+	0	transcript_id "Phchi.S1G358100.t1"; gene_id "Phchi.S1G358100"
# This transcript jg14504.t2 is derived from g12972.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14505.t1 is derived from g12973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13223375	13224106	.	+	.	Phchi.S3G182400
Phchi.S3	AUGUSTUS	transcript	13223375	13224106	.	+	.	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	start_codon	13223375	13223377	.	+	0	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	CDS	13223375	13223494	0.99	+	0	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	exon	13223375	13223494	.	+	.	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	intron	13223495	13223677	.	+	.	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	CDS	13223678	13224106	1	+	0	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	exon	13223678	13224106	.	+	.	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
Phchi.S3	AUGUSTUS	stop_codon	13224107	13224109	.	+	0	transcript_id "Phchi.S3G182400.t1"; gene_id "Phchi.S3G182400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9568.t1 is derived from g6744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42714963	42717167	.	+	.	Phchi.S1G672700
Phchi.S1	AUGUSTUS	transcript	42715053	42717167	.	+	.	transcript_id "Phchi.S1G672700.t1"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	start_codon	42715053	42715055	.	+	0	transcript_id "Phchi.S1G672700.t1"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	CDS	42715053	42717167	0.95	+	0	transcript_id "Phchi.S1G672700.t1"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	exon	42715053	42717167	.	+	.	transcript_id "Phchi.S1G672700.t1"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	stop_codon	42717168	42717170	.	+	0	transcript_id "Phchi.S1G672700.t1"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	transcript	42714963	42717167	.	+	.	transcript_id "Phchi.S1G672700.t2"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	start_codon	42714963	42714965	.	+	0	transcript_id "Phchi.S1G672700.t2"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	CDS	42714963	42717167	0.84	+	0	transcript_id "Phchi.S1G672700.t2"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	exon	42714963	42717167	.	+	.	transcript_id "Phchi.S1G672700.t2"; gene_id "Phchi.S1G672700"
Phchi.S1	AUGUSTUS	stop_codon	42717168	42717170	.	+	0	transcript_id "Phchi.S1G672700.t2"; gene_id "Phchi.S1G672700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12002.t1 is derived from g7677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	492036	492689	.	+	.	Phchi.S2G008200
Phchi.S2	AUGUSTUS	transcript	492036	492689	.	+	.	transcript_id "Phchi.S2G008200.t1"; gene_id "Phchi.S2G008200"
Phchi.S2	AUGUSTUS	start_codon	492036	492038	.	+	0	transcript_id "Phchi.S2G008200.t1"; gene_id "Phchi.S2G008200"
Phchi.S2	AUGUSTUS	CDS	492036	492689	0.99	+	0	transcript_id "Phchi.S2G008200.t1"; gene_id "Phchi.S2G008200"
Phchi.S2	AUGUSTUS	exon	492036	492689	.	+	.	transcript_id "Phchi.S2G008200.t1"; gene_id "Phchi.S2G008200"
Phchi.S2	AUGUSTUS	stop_codon	492690	492692	.	+	0	transcript_id "Phchi.S2G008200.t1"; gene_id "Phchi.S2G008200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8360.t1 is derived from g5535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35507927	35508950	.	-	.	Phchi.S1G551900
Phchi.S1	AUGUSTUS	transcript	35507927	35508950	.	-	.	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	stop_codon	35507924	35507926	.	-	0	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	CDS	35507927	35508066	1	-	2	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	exon	35507927	35508066	.	-	.	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	intron	35508067	35508232	.	-	.	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	CDS	35508233	35508950	0.98	-	0	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	exon	35508233	35508950	.	-	.	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
Phchi.S1	AUGUSTUS	start_codon	35508948	35508950	.	-	0	transcript_id "Phchi.S1G551900.t1"; gene_id "Phchi.S1G551900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14300.t1 is derived from g12767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11994497	11995147	.	+	.	Phchi.S3G161900
Phchi.S3	AUGUSTUS	transcript	11994497	11995147	.	+	.	transcript_id "Phchi.S3G161900.t1"; gene_id "Phchi.S3G161900"
Phchi.S3	AUGUSTUS	start_codon	11994497	11994499	.	+	0	transcript_id "Phchi.S3G161900.t1"; gene_id "Phchi.S3G161900"
Phchi.S3	AUGUSTUS	CDS	11994497	11995147	0.65	+	0	transcript_id "Phchi.S3G161900.t1"; gene_id "Phchi.S3G161900"
Phchi.S3	AUGUSTUS	exon	11994497	11995147	.	+	.	transcript_id "Phchi.S3G161900.t1"; gene_id "Phchi.S3G161900"
Phchi.S3	AUGUSTUS	stop_codon	11995148	11995150	.	+	0	transcript_id "Phchi.S3G161900.t1"; gene_id "Phchi.S3G161900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15622.t1 is derived from g14091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20337214	20340208	.	+	.	Phchi.S3G294100
Phchi.S3	AUGUSTUS	transcript	20337214	20340208	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	start_codon	20337214	20337216	.	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20337214	20337310	0.62	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20337214	20337310	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20337311	20337404	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20337405	20337481	1	+	2	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20337405	20337481	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20337482	20337573	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20337574	20337657	1	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20337574	20337657	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20337658	20337756	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20337757	20337870	1	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20337757	20337870	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20337871	20338091	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20338092	20338178	1	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20338092	20338178	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20338179	20338298	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20338299	20338438	1	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20338299	20338438	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20338439	20338556	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20338557	20338644	1	+	1	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20338557	20338644	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20338645	20338769	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20338770	20338843	1	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20338770	20338843	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20338844	20339004	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20339005	20339180	1	+	1	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20339005	20339180	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20339181	20339375	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20339376	20339695	1	+	2	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20339376	20339695	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20339696	20339773	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20339774	20339820	1	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20339774	20339820	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	intron	20339821	20339913	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	CDS	20339914	20340208	0.99	+	1	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	exon	20339914	20340208	.	+	.	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
Phchi.S3	AUGUSTUS	stop_codon	20340209	20340211	.	+	0	transcript_id "Phchi.S3G294100.t1"; gene_id "Phchi.S3G294100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7934.t1 is derived from g5108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31994907	31996604	.	-	.	Phchi.S1G509300
Phchi.S1	AUGUSTUS	transcript	31994907	31996604	.	-	.	transcript_id "Phchi.S1G509300.t1"; gene_id "Phchi.S1G509300"
Phchi.S1	AUGUSTUS	stop_codon	31994904	31994906	.	-	0	transcript_id "Phchi.S1G509300.t1"; gene_id "Phchi.S1G509300"
Phchi.S1	AUGUSTUS	CDS	31994907	31996604	0.58	-	0	transcript_id "Phchi.S1G509300.t1"; gene_id "Phchi.S1G509300"
Phchi.S1	AUGUSTUS	exon	31994907	31996604	.	-	.	transcript_id "Phchi.S1G509300.t1"; gene_id "Phchi.S1G509300"
Phchi.S1	AUGUSTUS	start_codon	31996602	31996604	.	-	0	transcript_id "Phchi.S1G509300.t1"; gene_id "Phchi.S1G509300"
# This transcript jg14199.t2 is derived from g12666.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14200.t1 is derived from g12667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11451003	11452704	.	-	.	Phchi.S3G151900
Phchi.S3	AUGUSTUS	transcript	11451003	11452704	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	stop_codon	11451000	11451002	.	-	0	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11451003	11451032	0.97	-	0	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11451003	11451032	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	intron	11451033	11451174	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11451175	11451312	1	-	0	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11451175	11451312	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	intron	11451313	11451478	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11451479	11451555	1	-	2	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11451479	11451555	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	intron	11451556	11451648	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11451649	11451825	1	-	2	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11451649	11451825	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	intron	11451826	11451923	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11451924	11452035	0.48	-	0	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11451924	11452035	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	intron	11452036	11452174	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11452175	11452451	0.24	-	1	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11452175	11452451	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	intron	11452452	11452528	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	CDS	11452529	11452704	0.6	-	0	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	exon	11452529	11452704	.	-	.	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
Phchi.S3	AUGUSTUS	start_codon	11452702	11452704	.	-	0	transcript_id "Phchi.S3G151900.t1"; gene_id "Phchi.S3G151900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5420.t1 is derived from g2590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16795944	16798581	.	+	.	Phchi.S1G257900
Phchi.S1	AUGUSTUS	transcript	16795944	16798581	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	start_codon	16795944	16795946	.	+	0	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	CDS	16795944	16796004	0.19	+	0	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	exon	16795944	16796004	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	intron	16796005	16796280	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	CDS	16796281	16796956	0.35	+	2	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	exon	16796281	16796956	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	intron	16796957	16797142	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	CDS	16797143	16797282	0.75	+	1	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	exon	16797143	16797282	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	intron	16797283	16797378	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	CDS	16797379	16797969	0.64	+	2	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	exon	16797379	16797969	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	intron	16797970	16798137	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	CDS	16798138	16798345	0.61	+	2	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	exon	16798138	16798345	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	intron	16798346	16798541	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	CDS	16798542	16798581	0.83	+	1	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	exon	16798542	16798581	.	+	.	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
Phchi.S1	AUGUSTUS	stop_codon	16798582	16798584	.	+	0	transcript_id "Phchi.S1G257900.t1"; gene_id "Phchi.S1G257900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10482.t1 is derived from g14531.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	582170	582986	.	-	.	Phchi.S4G006400
Phchi.S4	AUGUSTUS	transcript	582170	582986	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	stop_codon	582167	582169	.	-	0	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582170	582211	0.98	-	0	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582170	582211	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582212	582476	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582477	582585	1	-	1	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582477	582585	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582586	582658	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582659	582711	1	-	0	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582659	582711	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582712	582859	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582860	582886	1	-	0	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582860	582886	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582887	582977	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582978	582986	0.96	-	0	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582978	582986	.	-	.	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	start_codon	582984	582986	.	-	0	transcript_id "Phchi.S4G006400.t1"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	transcript	582170	582986	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	stop_codon	582167	582169	.	-	0	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582170	582211	0.98	-	0	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582170	582211	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582212	582476	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582477	582576	1	-	1	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582477	582576	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582577	582658	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582659	582711	1	-	0	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582659	582711	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582712	582859	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582860	582886	1	-	0	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582860	582886	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	intron	582887	582977	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	CDS	582978	582986	0.9	-	0	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	exon	582978	582986	.	-	.	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
Phchi.S4	AUGUSTUS	start_codon	582984	582986	.	-	0	transcript_id "Phchi.S4G006400.t2"; gene_id "Phchi.S4G006400"
# This transcript jg1179.t2 is derived from g10962.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1180.t1 is derived from g10963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8316661	8318256	.	-	.	Phchi.S6G113900
Phchi.S6	AUGUSTUS	transcript	8316661	8318256	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	stop_codon	8316658	8316660	.	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8316661	8316885	1	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8316661	8316885	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	intron	8316886	8317008	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8317009	8317188	1	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8317009	8317188	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	intron	8317189	8317268	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8317269	8317319	1	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8317269	8317319	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	intron	8317320	8317411	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8317412	8317498	1	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8317412	8317498	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	intron	8317499	8317627	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8317628	8317822	1	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8317628	8317822	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	intron	8317823	8317912	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8317913	8318027	1	-	1	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8317913	8318027	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	intron	8318028	8318107	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	CDS	8318108	8318256	0.76	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	exon	8318108	8318256	.	-	.	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
Phchi.S6	AUGUSTUS	start_codon	8318254	8318256	.	-	0	transcript_id "Phchi.S6G113900.t1"; gene_id "Phchi.S6G113900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15460.t1 is derived from g13928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19292638	19293855	.	+	.	Phchi.S3G277900
Phchi.S3	AUGUSTUS	transcript	19292638	19293855	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	start_codon	19292638	19292640	.	+	0	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	CDS	19292638	19292710	1	+	0	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	exon	19292638	19292710	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	intron	19292711	19292910	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	CDS	19292911	19293012	1	+	2	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	exon	19292911	19293012	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	intron	19293013	19293220	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	CDS	19293221	19293399	1	+	2	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	exon	19293221	19293399	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	intron	19293400	19293513	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	CDS	19293514	19293855	0.98	+	0	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	exon	19293514	19293855	.	+	.	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
Phchi.S3	AUGUSTUS	stop_codon	19293856	19293858	.	+	0	transcript_id "Phchi.S3G277900.t1"; gene_id "Phchi.S3G277900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7809.t1 is derived from g4983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31298662	31299009	.	+	.	Phchi.S1G496800
Phchi.S1	AUGUSTUS	transcript	31298662	31299009	.	+	.	transcript_id "Phchi.S1G496800.t1"; gene_id "Phchi.S1G496800"
Phchi.S1	AUGUSTUS	start_codon	31298662	31298664	.	+	0	transcript_id "Phchi.S1G496800.t1"; gene_id "Phchi.S1G496800"
Phchi.S1	AUGUSTUS	CDS	31298662	31299009	0.73	+	0	transcript_id "Phchi.S1G496800.t1"; gene_id "Phchi.S1G496800"
Phchi.S1	AUGUSTUS	exon	31298662	31299009	.	+	.	transcript_id "Phchi.S1G496800.t1"; gene_id "Phchi.S1G496800"
Phchi.S1	AUGUSTUS	stop_codon	31299010	31299012	.	+	0	transcript_id "Phchi.S1G496800.t1"; gene_id "Phchi.S1G496800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1146.t1 is derived from g10929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7996616	7997110	.	-	.	Phchi.S6G110500
Phchi.S6	AUGUSTUS	transcript	7996616	7997110	.	-	.	transcript_id "Phchi.S6G110500.t1"; gene_id "Phchi.S6G110500"
Phchi.S6	AUGUSTUS	stop_codon	7996613	7996615	.	-	0	transcript_id "Phchi.S6G110500.t1"; gene_id "Phchi.S6G110500"
Phchi.S6	AUGUSTUS	CDS	7996616	7997110	0.81	-	0	transcript_id "Phchi.S6G110500.t1"; gene_id "Phchi.S6G110500"
Phchi.S6	AUGUSTUS	exon	7996616	7997110	.	-	.	transcript_id "Phchi.S6G110500.t1"; gene_id "Phchi.S6G110500"
Phchi.S6	AUGUSTUS	start_codon	7997108	7997110	.	-	0	transcript_id "Phchi.S6G110500.t1"; gene_id "Phchi.S6G110500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13637.t1 is derived from g12104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7926971	7928385	.	+	.	Phchi.S3G095600
Phchi.S3	AUGUSTUS	transcript	7926971	7928385	.	+	.	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	start_codon	7926971	7926973	.	+	0	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	CDS	7926971	7927384	0.33	+	0	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	exon	7926971	7927384	.	+	.	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	intron	7927385	7927536	.	+	.	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	CDS	7927537	7928385	0.8	+	0	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	exon	7927537	7928385	.	+	.	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
Phchi.S3	AUGUSTUS	stop_codon	7928386	7928388	.	+	0	transcript_id "Phchi.S3G095600.t1"; gene_id "Phchi.S3G095600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4085.t1 is derived from g1254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7729365	7730474	.	-	.	Phchi.S1G124400
Phchi.S1	AUGUSTUS	transcript	7729365	7730474	.	-	.	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	stop_codon	7729362	7729364	.	-	0	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	CDS	7729365	7729939	0.51	-	2	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	exon	7729365	7729939	.	-	.	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	intron	7729940	7730119	.	-	.	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	CDS	7730120	7730474	0.46	-	0	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	exon	7730120	7730474	.	-	.	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
Phchi.S1	AUGUSTUS	start_codon	7730472	7730474	.	-	0	transcript_id "Phchi.S1G124400.t1"; gene_id "Phchi.S1G124400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4562.t1 is derived from g1732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11123779	11124318	.	-	.	Phchi.S1G172100
Phchi.S1	AUGUSTUS	transcript	11123779	11124318	.	-	.	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	stop_codon	11123776	11123778	.	-	0	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	CDS	11123779	11123937	0.54	-	0	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	exon	11123779	11123937	.	-	.	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	intron	11123938	11124117	.	-	.	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	CDS	11124118	11124318	0.29	-	0	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	exon	11124118	11124318	.	-	.	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
Phchi.S1	AUGUSTUS	start_codon	11124316	11124318	.	-	0	transcript_id "Phchi.S1G172100.t1"; gene_id "Phchi.S1G172100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7010.t1 is derived from g4182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26391465	26392020	.	+	.	Phchi.S1G416900
Phchi.S1	AUGUSTUS	transcript	26391465	26392020	.	+	.	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	start_codon	26391465	26391467	.	+	0	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	CDS	26391465	26391871	0.92	+	0	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	exon	26391465	26391871	.	+	.	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	intron	26391872	26391989	.	+	.	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	CDS	26391990	26392020	0.92	+	1	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	exon	26391990	26392020	.	+	.	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
Phchi.S1	AUGUSTUS	stop_codon	26392021	26392023	.	+	0	transcript_id "Phchi.S1G416900.t1"; gene_id "Phchi.S1G416900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3492.t1 is derived from g661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4037790	4038931	.	+	.	Phchi.S1G065100
Phchi.S1	AUGUSTUS	transcript	4037790	4038931	.	+	.	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	start_codon	4037790	4037792	.	+	0	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	CDS	4037790	4037933	0.61	+	0	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	exon	4037790	4037933	.	+	.	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	intron	4037934	4038083	.	+	.	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	CDS	4038084	4038155	0.92	+	0	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	exon	4038084	4038155	.	+	.	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	intron	4038156	4038328	.	+	.	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	CDS	4038329	4038931	0.38	+	0	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	exon	4038329	4038931	.	+	.	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
Phchi.S1	AUGUSTUS	stop_codon	4038932	4038934	.	+	0	transcript_id "Phchi.S1G065100.t1"; gene_id "Phchi.S1G065100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10303.t1 is derived from g7479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47050885	47053401	.	-	.	Phchi.S1G746200
Phchi.S1	AUGUSTUS	transcript	47050885	47053401	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	stop_codon	47050882	47050884	.	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47050885	47050984	1	-	1	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47050885	47050984	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47050985	47051078	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47051079	47051150	1	-	1	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47051079	47051150	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47051151	47051237	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47051238	47051284	1	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47051238	47051284	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47051285	47051404	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47051405	47051511	1	-	2	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47051405	47051511	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47051512	47051592	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47051593	47051671	1	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47051593	47051671	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47051672	47051761	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47051762	47051851	1	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47051762	47051851	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47051852	47051941	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47051942	47052138	1	-	2	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47051942	47052138	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47052139	47052251	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47052252	47052312	1	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47052252	47052312	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47052313	47052410	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47052411	47052560	1	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47052411	47052560	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47052561	47052679	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47052680	47052998	0.98	-	1	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47052680	47052998	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	intron	47052999	47053150	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	CDS	47053151	47053401	0.87	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	exon	47053151	47053401	.	-	.	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
Phchi.S1	AUGUSTUS	start_codon	47053399	47053401	.	-	0	transcript_id "Phchi.S1G746200.t1"; gene_id "Phchi.S1G746200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15489.t1 is derived from g13958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19456426	19457656	.	-	.	Phchi.S3G280800
Phchi.S3	AUGUSTUS	transcript	19456426	19457656	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	stop_codon	19456423	19456425	.	-	0	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	CDS	19456426	19456510	0.78	-	1	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	exon	19456426	19456510	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	intron	19456511	19456688	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	CDS	19456689	19456746	0.9	-	2	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	exon	19456689	19456746	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	intron	19456747	19456923	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	CDS	19456924	19456986	0.52	-	2	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	exon	19456924	19456986	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	intron	19456987	19457316	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	CDS	19457317	19457656	0.99	-	0	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	exon	19457317	19457656	.	-	.	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
Phchi.S3	AUGUSTUS	start_codon	19457654	19457656	.	-	0	transcript_id "Phchi.S3G280800.t1"; gene_id "Phchi.S3G280800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13307.t1 is derived from g11773.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5665206	5667291	.	+	.	Phchi.S3G062600
Phchi.S3	AUGUSTUS	transcript	5665206	5667291	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	start_codon	5665206	5665208	.	+	0	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	CDS	5665206	5665594	0.99	+	0	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	exon	5665206	5665594	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	intron	5665595	5665686	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	CDS	5665687	5665975	0.98	+	1	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	exon	5665687	5665975	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	intron	5665976	5666117	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	CDS	5666118	5666411	1	+	0	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	exon	5666118	5666411	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	intron	5666412	5666557	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	CDS	5666558	5666925	1	+	0	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	exon	5666558	5666925	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	intron	5666926	5667035	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	CDS	5667036	5667291	1	+	1	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	exon	5667036	5667291	.	+	.	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
Phchi.S3	AUGUSTUS	stop_codon	5667292	5667294	.	+	0	transcript_id "Phchi.S3G062600.t1"; gene_id "Phchi.S3G062600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6865.t1 is derived from g4037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25665094	25667231	.	+	.	Phchi.S1G402400
Phchi.S1	AUGUSTUS	transcript	25665094	25667231	.	+	.	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	start_codon	25665094	25665096	.	+	0	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	CDS	25665094	25666579	0.96	+	0	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	exon	25665094	25666579	.	+	.	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	intron	25666580	25666710	.	+	.	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	CDS	25666711	25667231	0.87	+	2	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	exon	25666711	25667231	.	+	.	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
Phchi.S1	AUGUSTUS	stop_codon	25667232	25667234	.	+	0	transcript_id "Phchi.S1G402400.t1"; gene_id "Phchi.S1G402400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8460.t1 is derived from g5635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36048697	36049235	.	-	.	Phchi.S1G561900
Phchi.S1	AUGUSTUS	transcript	36048697	36049235	.	-	.	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	stop_codon	36048694	36048696	.	-	0	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	CDS	36048697	36048704	0.68	-	2	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	exon	36048697	36048704	.	-	.	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	intron	36048705	36048841	.	-	.	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	CDS	36048842	36049235	0.74	-	0	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	exon	36048842	36049235	.	-	.	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
Phchi.S1	AUGUSTUS	start_codon	36049233	36049235	.	-	0	transcript_id "Phchi.S1G561900.t1"; gene_id "Phchi.S1G561900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg344.t1 is derived from g10126.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2512540	2514843	.	+	.	Phchi.S6G030300
Phchi.S6	AUGUSTUS	transcript	2512540	2514843	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	start_codon	2512540	2512542	.	+	0	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	CDS	2512540	2512578	0.93	+	0	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	exon	2512540	2512578	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	intron	2512579	2512723	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	CDS	2512724	2513456	0.87	+	0	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	exon	2512724	2513456	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	intron	2513457	2513543	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	CDS	2513544	2514367	0.76	+	2	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	exon	2513544	2514367	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	intron	2514368	2514605	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	CDS	2514606	2514664	0.75	+	0	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	exon	2514606	2514664	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	intron	2514665	2514833	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	CDS	2514834	2514843	0.76	+	1	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	exon	2514834	2514843	.	+	.	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
Phchi.S6	AUGUSTUS	stop_codon	2514844	2514846	.	+	0	transcript_id "Phchi.S6G030300.t1"; gene_id "Phchi.S6G030300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1599.t1 is derived from g8518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1949777	1951435	.	+	.	Phchi.S5G020800
Phchi.S5	AUGUSTUS	transcript	1949777	1951435	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	start_codon	1949777	1949779	.	+	0	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1949777	1949809	0.92	+	0	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1949777	1949809	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1949810	1949998	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1949999	1950057	1	+	0	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1949999	1950057	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1950058	1950173	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1950174	1950271	1	+	1	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1950174	1950271	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1950272	1950404	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1950405	1950456	1	+	2	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1950405	1950456	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1950457	1950604	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1950605	1950668	1	+	1	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1950605	1950668	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1950669	1950769	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1950770	1950865	1	+	0	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1950770	1950865	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1950866	1951018	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1951019	1951091	1	+	0	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1951019	1951091	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	intron	1951092	1951214	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	CDS	1951215	1951435	1	+	2	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	exon	1951215	1951435	.	+	.	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
Phchi.S5	AUGUSTUS	stop_codon	1951436	1951438	.	+	0	transcript_id "Phchi.S5G020800.t1"; gene_id "Phchi.S5G020800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1403.t1 is derived from g8322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	148702	152311	.	+	.	Phchi.S5G001200
Phchi.S5	AUGUSTUS	transcript	148702	152311	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	start_codon	148702	148704	.	+	0	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	148702	149092	0.49	+	0	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	148702	149092	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	149093	149214	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	149215	149489	0.99	+	2	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	149215	149489	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	149490	149571	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	149572	149812	1	+	0	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	149572	149812	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	149813	149893	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	149894	150253	1	+	2	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	149894	150253	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	150254	150348	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	150349	150434	1	+	2	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	150349	150434	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	150435	150521	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	150522	150626	1	+	0	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	150522	150626	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	150627	150721	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	150722	151041	1	+	0	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	150722	151041	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	151042	151158	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	151159	151425	1	+	1	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	151159	151425	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	intron	151426	151554	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	CDS	151555	152311	0.68	+	1	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	exon	151555	152311	.	+	.	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
Phchi.S5	AUGUSTUS	stop_codon	152312	152314	.	+	0	transcript_id "Phchi.S5G001200.t1"; gene_id "Phchi.S5G001200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg12900.t1 is derived from g11365.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3070931	3073789	.	+	.	Phchi.S3G021900
Phchi.S3	AUGUSTUS	transcript	3070931	3073789	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	start_codon	3070931	3070933	.	+	0	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3070931	3071182	0.59	+	0	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3070931	3071182	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071183	3071715	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071716	3071773	1	+	0	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071716	3071773	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071774	3071854	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071855	3071970	1	+	2	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071855	3071970	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071971	3072100	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072101	3072347	1	+	0	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072101	3072347	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072348	3072447	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072448	3072536	1	+	2	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072448	3072536	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072537	3072621	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072622	3072685	1	+	0	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072622	3072685	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072686	3072800	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072801	3072830	0.93	+	2	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072801	3072830	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072831	3073032	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073033	3073078	0.98	+	2	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073033	3073078	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073079	3073279	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073280	3073356	0.98	+	1	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073280	3073356	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073357	3073589	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073590	3073789	0.99	+	2	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073590	3073789	.	+	.	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	stop_codon	3073790	3073792	.	+	0	transcript_id "Phchi.S3G021900.t1"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	transcript	3070931	3073789	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	start_codon	3070931	3070933	.	+	0	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3070931	3071182	0.66	+	0	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3070931	3071182	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071183	3071715	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071716	3071773	1	+	0	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071716	3071773	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071774	3071854	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071855	3071970	0.99	+	2	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071855	3071970	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071971	3072100	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072101	3072347	1	+	0	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072101	3072347	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072348	3072447	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072448	3072536	1	+	2	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072448	3072536	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072537	3072615	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072616	3072685	1	+	0	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072616	3072685	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072686	3072800	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072801	3072830	0.91	+	2	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072801	3072830	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072831	3073032	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073033	3073078	0.95	+	2	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073033	3073078	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073079	3073279	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073280	3073356	0.98	+	1	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073280	3073356	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073357	3073589	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073590	3073789	0.98	+	2	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073590	3073789	.	+	.	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	stop_codon	3073790	3073792	.	+	0	transcript_id "Phchi.S3G021900.t2"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	transcript	3070931	3073789	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	start_codon	3070931	3070933	.	+	0	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3070931	3071182	0.66	+	0	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3070931	3071182	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071183	3071715	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071716	3071773	1	+	0	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071716	3071773	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071774	3071854	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071855	3071970	1	+	2	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071855	3071970	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071971	3072100	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072101	3072347	1	+	0	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072101	3072347	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072348	3072465	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072466	3072536	0.87	+	2	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072466	3072536	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072537	3072615	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072616	3072685	1	+	0	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072616	3072685	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072686	3072800	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072801	3072830	0.85	+	2	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072801	3072830	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072831	3073032	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073033	3073078	0.91	+	2	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073033	3073078	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073079	3073279	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073280	3073356	0.97	+	1	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073280	3073356	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073357	3073589	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073590	3073789	0.97	+	2	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073590	3073789	.	+	.	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	stop_codon	3073790	3073792	.	+	0	transcript_id "Phchi.S3G021900.t3"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	transcript	3070931	3073789	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	start_codon	3070931	3070933	.	+	0	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3070931	3071182	0.63	+	0	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3070931	3071182	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071183	3071715	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071716	3071773	1	+	0	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071716	3071773	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071774	3071854	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3071855	3071970	1	+	2	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3071855	3071970	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3071971	3072100	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072101	3072347	1	+	0	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072101	3072347	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072348	3072447	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072448	3072536	1	+	2	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072448	3072536	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072537	3072615	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072616	3072685	1	+	0	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072616	3072685	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072686	3072800	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3072801	3072830	0.66	+	2	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3072801	3072830	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3072831	3073032	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073033	3073078	0.68	+	2	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073033	3073078	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073079	3073279	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073280	3073332	0.75	+	1	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073280	3073332	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	intron	3073333	3073589	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	CDS	3073590	3073789	0.75	+	2	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	exon	3073590	3073789	.	+	.	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
Phchi.S3	AUGUSTUS	stop_codon	3073790	3073792	.	+	0	transcript_id "Phchi.S3G021900.t4"; gene_id "Phchi.S3G021900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12264.t1 is derived from g7940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7261832	7263885	.	-	.	Phchi.S2G034400
Phchi.S2	AUGUSTUS	transcript	7261832	7263885	.	-	.	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	stop_codon	7261829	7261831	.	-	0	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	CDS	7261832	7263022	0.69	-	0	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	exon	7261832	7263022	.	-	.	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	intron	7263023	7263105	.	-	.	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	CDS	7263106	7263885	0.61	-	0	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	exon	7263106	7263885	.	-	.	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
Phchi.S2	AUGUSTUS	start_codon	7263883	7263885	.	-	0	transcript_id "Phchi.S2G034400.t1"; gene_id "Phchi.S2G034400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11830.t1 is derived from g15882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8470814	8473343	.	+	.	Phchi.S4G141200
Phchi.S4	AUGUSTUS	transcript	8470814	8473343	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	start_codon	8470814	8470816	.	+	0	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8470814	8471068	0.61	+	0	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8470814	8471068	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8471069	8471167	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8471168	8471284	1	+	0	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8471168	8471284	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8471285	8471381	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8471382	8471563	0.93	+	0	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8471382	8471563	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8471564	8471683	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8471684	8471953	0.91	+	1	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8471684	8471953	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8471954	8472026	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8472027	8472085	0.52	+	1	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8472027	8472085	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8472086	8472286	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8472287	8472323	0.38	+	2	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8472287	8472323	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8472324	8472434	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8472435	8472506	0.28	+	1	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8472435	8472506	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8472507	8472592	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8472593	8472917	0.47	+	1	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8472593	8472917	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	intron	8472918	8473001	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	CDS	8473002	8473343	0.43	+	0	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	exon	8473002	8473343	.	+	.	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
Phchi.S4	AUGUSTUS	stop_codon	8473344	8473346	.	+	0	transcript_id "Phchi.S4G141200.t1"; gene_id "Phchi.S4G141200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg545.t1 is derived from g10327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3994715	3999554	.	+	.	Phchi.S6G050400
Phchi.S6	AUGUSTUS	transcript	3994715	3999554	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	start_codon	3994715	3994717	.	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3994715	3995170	0.95	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3994715	3995170	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3995171	3995255	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3995256	3995339	0.93	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3995256	3995339	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3995340	3995450	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3995451	3995585	0.93	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3995451	3995585	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3995586	3995664	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3995665	3995982	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3995665	3995982	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3995983	3996171	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3996172	3996261	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3996172	3996261	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3996262	3996341	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3996342	3996398	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3996342	3996398	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3996399	3996477	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3996478	3996549	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3996478	3996549	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3996550	3996717	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3996718	3996801	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3996718	3996801	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3996802	3997023	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3997024	3997167	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3997024	3997167	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3997168	3997262	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3997263	3997406	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3997263	3997406	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3997407	3997497	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3997498	3997578	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3997498	3997578	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3997579	3997682	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3997683	3997773	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3997683	3997773	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3997774	3997854	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3997855	3997937	0.89	+	2	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3997855	3997937	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3997938	3998042	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3998043	3998098	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3998043	3998098	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3998099	3998258	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3998259	3998354	1	+	1	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3998259	3998354	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3998355	3998501	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3998502	3998586	1	+	1	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3998502	3998586	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3998587	3998863	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3998864	3998968	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3998864	3998968	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3998969	3999050	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3999051	3999217	1	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3999051	3999217	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	intron	3999218	3999349	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	CDS	3999350	3999554	0.91	+	1	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	exon	3999350	3999554	.	+	.	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
Phchi.S6	AUGUSTUS	stop_codon	3999555	3999557	.	+	0	transcript_id "Phchi.S6G050400.t1"; gene_id "Phchi.S6G050400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2434.t1 is derived from g9354.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6625428	6627578	.	-	.	Phchi.S5G104300
Phchi.S5	AUGUSTUS	transcript	6625428	6627578	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	stop_codon	6625425	6625427	.	-	0	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	CDS	6625428	6625659	1	-	1	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	exon	6625428	6625659	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	intron	6625660	6625795	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	CDS	6625796	6625874	1	-	2	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	exon	6625796	6625874	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	intron	6625875	6625964	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	CDS	6625965	6626121	1	-	0	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	exon	6625965	6626121	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	intron	6626122	6626208	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	CDS	6626209	6626493	1	-	0	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	exon	6626209	6626493	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	intron	6626494	6626630	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	CDS	6626631	6626781	0.93	-	1	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	exon	6626631	6626781	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	intron	6626782	6627315	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	CDS	6627316	6627578	0.83	-	0	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	exon	6627316	6627578	.	-	.	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
Phchi.S5	AUGUSTUS	start_codon	6627576	6627578	.	-	0	transcript_id "Phchi.S5G104300.t1"; gene_id "Phchi.S5G104300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13238.t1 is derived from g11703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4865527	4866380	.	-	.	Phchi.S3G055700
Phchi.S3	AUGUSTUS	transcript	4865527	4866380	.	-	.	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	stop_codon	4865524	4865526	.	-	0	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	CDS	4865527	4865569	0.44	-	1	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	exon	4865527	4865569	.	-	.	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	intron	4865570	4865661	.	-	.	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	CDS	4865662	4866380	0.4	-	0	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	exon	4865662	4866380	.	-	.	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
Phchi.S3	AUGUSTUS	start_codon	4866378	4866380	.	-	0	transcript_id "Phchi.S3G055700.t1"; gene_id "Phchi.S3G055700"
# This transcript jg10571.t2 is derived from g14621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10572.t1 is derived from g14622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1019518	1020129	.	+	.	Phchi.S4G015400
Phchi.S4	AUGUSTUS	transcript	1019518	1020129	.	+	.	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	start_codon	1019518	1019520	.	+	0	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	CDS	1019518	1019552	0.74	+	0	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	exon	1019518	1019552	.	+	.	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	intron	1019553	1019691	.	+	.	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	CDS	1019692	1019854	0.75	+	1	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	exon	1019692	1019854	.	+	.	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	intron	1019855	1020021	.	+	.	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	CDS	1020022	1020129	0.74	+	0	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	exon	1020022	1020129	.	+	.	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
Phchi.S4	AUGUSTUS	stop_codon	1020130	1020132	.	+	0	transcript_id "Phchi.S4G015400.t1"; gene_id "Phchi.S4G015400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg819.t1 is derived from g10601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5712943	5714088	.	+	.	Phchi.S6G077800
Phchi.S6	AUGUSTUS	transcript	5712943	5714088	.	+	.	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	start_codon	5712943	5712945	.	+	0	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	CDS	5712943	5713269	0.41	+	0	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	exon	5712943	5713269	.	+	.	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	intron	5713270	5713360	.	+	.	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	CDS	5713361	5713454	0.7	+	0	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	exon	5713361	5713454	.	+	.	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	intron	5713455	5713624	.	+	.	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	CDS	5713625	5714088	0.39	+	2	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	exon	5713625	5714088	.	+	.	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
Phchi.S6	AUGUSTUS	stop_codon	5714089	5714091	.	+	0	transcript_id "Phchi.S6G077800.t1"; gene_id "Phchi.S6G077800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2214.t1 is derived from g9134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5440974	5443914	.	-	.	Phchi.S5G082300
Phchi.S5	AUGUSTUS	transcript	5440974	5443914	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	stop_codon	5440971	5440973	.	-	0	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	CDS	5440974	5442211	1	-	2	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	exon	5440974	5442211	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	intron	5442212	5442305	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	CDS	5442306	5442374	1	-	2	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	exon	5442306	5442374	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	intron	5442375	5442518	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	CDS	5442519	5442776	0.96	-	2	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	exon	5442519	5442776	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	intron	5442777	5442880	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	CDS	5442881	5443315	0.99	-	2	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	exon	5442881	5443315	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	intron	5443316	5443525	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	CDS	5443526	5443756	0.41	-	2	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	exon	5443526	5443756	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	intron	5443757	5443862	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	CDS	5443863	5443914	0.34	-	0	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	exon	5443863	5443914	.	-	.	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
Phchi.S5	AUGUSTUS	start_codon	5443912	5443914	.	-	0	transcript_id "Phchi.S5G082300.t1"; gene_id "Phchi.S5G082300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12422.t1 is derived from g8099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19537521	19538199	.	+	.	Phchi.S2G050200
Phchi.S2	AUGUSTUS	transcript	19537521	19538199	.	+	.	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	start_codon	19537521	19537523	.	+	0	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	CDS	19537521	19537735	0.48	+	0	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	exon	19537521	19537735	.	+	.	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	intron	19537736	19537874	.	+	.	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	CDS	19537875	19538199	0.54	+	1	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	exon	19537875	19538199	.	+	.	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
Phchi.S2	AUGUSTUS	stop_codon	19538200	19538202	.	+	0	transcript_id "Phchi.S2G050200.t1"; gene_id "Phchi.S2G050200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10477.t1 is derived from g14526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	569088	570612	.	+	.	Phchi.S4G005900
Phchi.S4	AUGUSTUS	transcript	569088	570612	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	start_codon	569088	569090	.	+	0	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	CDS	569088	569122	0.93	+	0	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	exon	569088	569122	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	intron	569123	569262	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	CDS	569263	569425	0.39	+	1	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	exon	569263	569425	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	intron	569426	569662	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	CDS	569663	569869	0.22	+	0	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	exon	569663	569869	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	intron	569870	569990	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	CDS	569991	570040	0.77	+	0	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	exon	569991	570040	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	intron	570041	570183	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	CDS	570184	570277	1	+	1	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	exon	570184	570277	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	intron	570278	570435	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	CDS	570436	570612	0.98	+	0	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	exon	570436	570612	.	+	.	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
Phchi.S4	AUGUSTUS	stop_codon	570613	570615	.	+	0	transcript_id "Phchi.S4G005900.t1"; gene_id "Phchi.S4G005900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9342.t1 is derived from g6517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41025211	41025543	.	+	.	Phchi.S1G650100
Phchi.S1	AUGUSTUS	transcript	41025211	41025543	.	+	.	transcript_id "Phchi.S1G650100.t1"; gene_id "Phchi.S1G650100"
Phchi.S1	AUGUSTUS	start_codon	41025211	41025213	.	+	0	transcript_id "Phchi.S1G650100.t1"; gene_id "Phchi.S1G650100"
Phchi.S1	AUGUSTUS	CDS	41025211	41025543	0.47	+	0	transcript_id "Phchi.S1G650100.t1"; gene_id "Phchi.S1G650100"
Phchi.S1	AUGUSTUS	exon	41025211	41025543	.	+	.	transcript_id "Phchi.S1G650100.t1"; gene_id "Phchi.S1G650100"
Phchi.S1	AUGUSTUS	stop_codon	41025544	41025546	.	+	0	transcript_id "Phchi.S1G650100.t1"; gene_id "Phchi.S1G650100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9005.t1 is derived from g6180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39119622	39121402	.	+	.	Phchi.S1G616400
Phchi.S1	AUGUSTUS	transcript	39119622	39121402	.	+	.	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	start_codon	39119622	39119624	.	+	0	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	CDS	39119622	39120715	0.77	+	0	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	exon	39119622	39120715	.	+	.	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	intron	39120716	39120786	.	+	.	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	CDS	39120787	39121402	0.88	+	1	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	exon	39120787	39121402	.	+	.	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
Phchi.S1	AUGUSTUS	stop_codon	39121403	39121405	.	+	0	transcript_id "Phchi.S1G616400.t1"; gene_id "Phchi.S1G616400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15506.t1 is derived from g13975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19591468	19596174	.	+	.	Phchi.S3G282500
Phchi.S3	AUGUSTUS	transcript	19591468	19596174	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	start_codon	19591468	19591470	.	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19591468	19591535	0.99	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19591468	19591535	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19591536	19591648	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19591649	19591828	0.96	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19591649	19591828	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19591829	19591946	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19591947	19592024	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19591947	19592024	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19592025	19592103	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19592104	19592200	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19592104	19592200	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19592201	19592438	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19592439	19592575	0.71	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19592439	19592575	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19592576	19592679	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19592680	19592761	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19592680	19592761	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19592762	19592916	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19592917	19593003	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19592917	19593003	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19593004	19593100	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19593101	19593207	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19593101	19593207	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19593208	19593295	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19593296	19593467	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19593296	19593467	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19593468	19593557	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19593558	19593754	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19593558	19593754	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19593755	19593867	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19593868	19593949	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19593868	19593949	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19593950	19594098	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19594099	19594164	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19594099	19594164	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19594165	19594311	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19594312	19594389	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19594312	19594389	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19594390	19594571	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19594572	19594667	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19594572	19594667	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19594668	19594776	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19594777	19594883	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19594777	19594883	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19594884	19594998	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19594999	19595167	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19594999	19595167	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19595168	19595358	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19595359	19595442	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19595359	19595442	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19595443	19595520	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19595521	19595615	0.98	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19595521	19595615	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19595616	19595718	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19595719	19595809	1	+	1	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19595719	19595809	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19595810	19595896	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19595897	19596043	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19595897	19596043	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	intron	19596044	19596123	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	CDS	19596124	19596174	1	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	exon	19596124	19596174	.	+	.	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
Phchi.S3	AUGUSTUS	stop_codon	19596175	19596177	.	+	0	transcript_id "Phchi.S3G282500.t1"; gene_id "Phchi.S3G282500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1589.t1 is derived from g8508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1905799	1907507	.	+	.	Phchi.S5G019800
Phchi.S5	AUGUSTUS	transcript	1905799	1907507	.	+	.	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	start_codon	1905799	1905801	.	+	0	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	CDS	1905799	1906403	0.74	+	0	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	exon	1905799	1906403	.	+	.	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	intron	1906404	1906495	.	+	.	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	CDS	1906496	1907507	0.82	+	1	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	exon	1906496	1907507	.	+	.	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
Phchi.S5	AUGUSTUS	stop_codon	1907508	1907510	.	+	0	transcript_id "Phchi.S5G019800.t1"; gene_id "Phchi.S5G019800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1379.t1 is derived from g15987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C149	AUGUSTUS	gene	12227	13098	.	-	.	Phchi.C149G000200
Phchi.C149	AUGUSTUS	transcript	12227	13098	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	stop_codon	12224	12226	.	-	0	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12227	12445	0.88	-	0	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12227	12445	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	intron	12446	12573	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12574	12706	1	-	1	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12574	12706	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	intron	12707	12806	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12807	12891	1	-	2	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12807	12891	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	intron	12892	12965	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12966	13098	0.55	-	0	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12966	13098	.	-	.	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	start_codon	13096	13098	.	-	0	transcript_id "Phchi.C149G000200.t1"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	transcript	12227	13098	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	stop_codon	12224	12226	.	-	0	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12227	12445	0.81	-	0	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12227	12445	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	intron	12446	12573	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12574	12706	1	-	1	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12574	12706	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	intron	12707	12806	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12807	12885	0.97	-	2	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12807	12885	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	intron	12886	12965	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	CDS	12966	13098	0.55	-	0	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	exon	12966	13098	.	-	.	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
Phchi.C149	AUGUSTUS	start_codon	13096	13098	.	-	0	transcript_id "Phchi.C149G000200.t2"; gene_id "Phchi.C149G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9145.t1 is derived from g6320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40070466	40070822	.	+	.	Phchi.S1G630400
Phchi.S1	AUGUSTUS	transcript	40070466	40070822	.	+	.	transcript_id "Phchi.S1G630400.t1"; gene_id "Phchi.S1G630400"
Phchi.S1	AUGUSTUS	start_codon	40070466	40070468	.	+	0	transcript_id "Phchi.S1G630400.t1"; gene_id "Phchi.S1G630400"
Phchi.S1	AUGUSTUS	CDS	40070466	40070822	0.42	+	0	transcript_id "Phchi.S1G630400.t1"; gene_id "Phchi.S1G630400"
Phchi.S1	AUGUSTUS	exon	40070466	40070822	.	+	.	transcript_id "Phchi.S1G630400.t1"; gene_id "Phchi.S1G630400"
Phchi.S1	AUGUSTUS	stop_codon	40070823	40070825	.	+	0	transcript_id "Phchi.S1G630400.t1"; gene_id "Phchi.S1G630400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7840.t1 is derived from g5014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31472416	31474004	.	+	.	Phchi.S1G499900
Phchi.S1	AUGUSTUS	transcript	31472416	31474004	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	start_codon	31472416	31472418	.	+	0	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31472416	31472757	0.46	+	0	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31472416	31472757	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31472758	31472936	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31472937	31473061	1	+	0	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31472937	31473061	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473062	31473139	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473140	31473177	1	+	1	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473140	31473177	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473178	31473260	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473261	31473265	0.63	+	2	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473261	31473265	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473266	31473339	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473340	31473373	0.47	+	0	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473340	31473373	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473374	31473473	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473474	31473553	1	+	2	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473474	31473553	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473554	31473649	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473650	31473686	1	+	0	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473650	31473686	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473687	31473769	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473770	31473811	1	+	2	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473770	31473811	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	intron	31473812	31473891	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	CDS	31473892	31474004	1	+	2	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	exon	31473892	31474004	.	+	.	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
Phchi.S1	AUGUSTUS	stop_codon	31474005	31474007	.	+	0	transcript_id "Phchi.S1G499900.t1"; gene_id "Phchi.S1G499900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15638.t1 is derived from g14107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20422147	20423497	.	-	.	Phchi.S3G295700
Phchi.S3	AUGUSTUS	transcript	20422147	20423497	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	stop_codon	20422144	20422146	.	-	0	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	CDS	20422147	20422189	0.97	-	1	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	exon	20422147	20422189	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	intron	20422190	20422275	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	CDS	20422276	20422348	0.7	-	2	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	exon	20422276	20422348	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	intron	20422349	20422529	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	CDS	20422530	20422612	0.54	-	1	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	exon	20422530	20422612	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	intron	20422613	20422709	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	CDS	20422710	20422774	1	-	0	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	exon	20422710	20422774	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	intron	20422775	20422874	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	CDS	20422875	20422944	0.89	-	1	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	exon	20422875	20422944	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	intron	20422945	20423171	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	CDS	20423172	20423497	0.56	-	0	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	exon	20423172	20423497	.	-	.	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
Phchi.S3	AUGUSTUS	start_codon	20423495	20423497	.	-	0	transcript_id "Phchi.S3G295700.t1"; gene_id "Phchi.S3G295700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2980.t1 is derived from g149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	948124	948750	.	-	.	Phchi.S1G013900
Phchi.S1	AUGUSTUS	transcript	948124	948750	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	stop_codon	948121	948123	.	-	0	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	CDS	948124	948244	1	-	1	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	exon	948124	948244	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	intron	948245	948358	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	CDS	948359	948477	1	-	0	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	exon	948359	948477	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	intron	948478	948566	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	CDS	948567	948662	1	-	0	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	exon	948567	948662	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	intron	948663	948732	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	CDS	948733	948750	0.8	-	0	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	exon	948733	948750	.	-	.	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
Phchi.S1	AUGUSTUS	start_codon	948748	948750	.	-	0	transcript_id "Phchi.S1G013900.t1"; gene_id "Phchi.S1G013900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6521.t1 is derived from g3693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23468653	23472055	.	-	.	Phchi.S1G368000
Phchi.S1	AUGUSTUS	transcript	23468653	23472055	.	-	.	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	stop_codon	23468650	23468652	.	-	0	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	CDS	23468653	23471180	0.54	-	2	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	exon	23468653	23471180	.	-	.	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	intron	23471181	23471280	.	-	.	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	CDS	23471281	23472055	0.43	-	0	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	exon	23471281	23472055	.	-	.	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
Phchi.S1	AUGUSTUS	start_codon	23472053	23472055	.	-	0	transcript_id "Phchi.S1G368000.t1"; gene_id "Phchi.S1G368000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13833.t1 is derived from g12300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9116026	9119412	.	+	.	Phchi.S3G115200
Phchi.S3	AUGUSTUS	transcript	9116026	9119412	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	start_codon	9116026	9116028	.	+	0	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9116026	9116345	0.87	+	0	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9116026	9116345	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9116346	9116419	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9116420	9116628	1	+	1	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9116420	9116628	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9116629	9116937	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9116938	9117327	0.98	+	2	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9116938	9117327	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9117328	9117466	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9117467	9117731	0.98	+	2	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9117467	9117731	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9117732	9117852	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9117853	9118114	1	+	1	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9117853	9118114	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9118115	9118206	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9118207	9118332	1	+	0	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9118207	9118332	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9118333	9118465	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9118466	9118529	1	+	0	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9118466	9118529	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9118530	9118614	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9118615	9118781	1	+	2	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9118615	9118781	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	intron	9118782	9118863	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	CDS	9118864	9119412	1	+	0	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	exon	9118864	9119412	.	+	.	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
Phchi.S3	AUGUSTUS	stop_codon	9119413	9119415	.	+	0	transcript_id "Phchi.S3G115200.t1"; gene_id "Phchi.S3G115200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14836.t1 is derived from g13304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14930207	14933240	.	-	.	Phchi.S3G215500
Phchi.S3	AUGUSTUS	transcript	14930207	14933240	.	-	.	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	stop_codon	14930204	14930206	.	-	0	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	CDS	14930207	14930555	1	-	1	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	exon	14930207	14930555	.	-	.	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	intron	14930556	14930771	.	-	.	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	CDS	14930772	14932909	1	-	0	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	exon	14930772	14932909	.	-	.	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	intron	14932910	14933081	.	-	.	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	CDS	14933082	14933240	0.99	-	0	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	exon	14933082	14933240	.	-	.	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
Phchi.S3	AUGUSTUS	start_codon	14933238	14933240	.	-	0	transcript_id "Phchi.S3G215500.t1"; gene_id "Phchi.S3G215500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15833.t1 is derived from g14303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21654898	21655790	.	+	.	Phchi.S3G315200
Phchi.S3	AUGUSTUS	transcript	21654898	21655790	.	+	.	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	start_codon	21654898	21654900	.	+	0	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	CDS	21654898	21655274	0.48	+	0	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	exon	21654898	21655274	.	+	.	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	intron	21655275	21655426	.	+	.	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	CDS	21655427	21655790	0.54	+	1	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	exon	21655427	21655790	.	+	.	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
Phchi.S3	AUGUSTUS	stop_codon	21655791	21655793	.	+	0	transcript_id "Phchi.S3G315200.t1"; gene_id "Phchi.S3G315200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9076.t1 is derived from g6251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39732057	39736464	.	+	.	Phchi.S1G623500
Phchi.S1	AUGUSTUS	transcript	39732057	39736464	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	start_codon	39732057	39732059	.	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39732057	39732233	0.99	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39732057	39732233	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39732234	39732575	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39732576	39732827	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39732576	39732827	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39732828	39732904	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39732905	39732975	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39732905	39732975	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39732976	39733059	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39733060	39733172	1	+	1	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39733060	39733172	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39733173	39733246	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39733247	39733355	1	+	2	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39733247	39733355	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39733356	39733432	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39733433	39733589	1	+	1	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39733433	39733589	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39733590	39733706	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39733707	39733802	0.99	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39733707	39733802	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39733803	39733915	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39733916	39733964	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39733916	39733964	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39733965	39734114	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39734115	39734392	1	+	2	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39734115	39734392	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39734393	39734465	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39734466	39734638	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39734466	39734638	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39734639	39734716	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39734717	39734837	1	+	1	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39734717	39734837	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39734838	39735011	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39735012	39735064	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39735012	39735064	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39735065	39735166	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39735167	39735287	1	+	1	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39735167	39735287	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39735288	39735377	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39735378	39735523	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39735378	39735523	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39735524	39735601	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39735602	39735799	1	+	1	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39735602	39735799	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39735800	39735883	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39735884	39735926	0.23	+	1	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39735884	39735926	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39735927	39736009	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39736010	39736115	0.23	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39736010	39736115	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39736116	39736189	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39736190	39736335	1	+	2	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39736190	39736335	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	intron	39736336	39736410	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	CDS	39736411	39736464	1	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	exon	39736411	39736464	.	+	.	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
Phchi.S1	AUGUSTUS	stop_codon	39736465	39736467	.	+	0	transcript_id "Phchi.S1G623500.t1"; gene_id "Phchi.S1G623500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15646.t1 is derived from g14115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20468091	20469060	.	-	.	Phchi.S3G296500
Phchi.S3	AUGUSTUS	transcript	20468091	20469060	.	-	.	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	stop_codon	20468088	20468090	.	-	0	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	CDS	20468091	20468872	0.56	-	2	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	exon	20468091	20468872	.	-	.	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	intron	20468873	20469020	.	-	.	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	CDS	20469021	20469060	0.43	-	0	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	exon	20469021	20469060	.	-	.	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
Phchi.S3	AUGUSTUS	start_codon	20469058	20469060	.	-	0	transcript_id "Phchi.S3G296500.t1"; gene_id "Phchi.S3G296500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10824.t1 is derived from g14874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2303728	2304971	.	+	.	Phchi.S4G040600
Phchi.S4	AUGUSTUS	transcript	2303728	2304971	.	+	.	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	start_codon	2303728	2303730	.	+	0	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	CDS	2303728	2303775	0.44	+	0	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	exon	2303728	2303775	.	+	.	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	intron	2303776	2303852	.	+	.	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	CDS	2303853	2304971	0.58	+	0	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	exon	2303853	2304971	.	+	.	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
Phchi.S4	AUGUSTUS	stop_codon	2304972	2304974	.	+	0	transcript_id "Phchi.S4G040600.t1"; gene_id "Phchi.S4G040600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1970.t1 is derived from g8890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4080379	4083062	.	-	.	Phchi.S5G057900
Phchi.S5	AUGUSTUS	transcript	4080379	4083062	.	-	.	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	stop_codon	4080376	4080378	.	-	0	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	CDS	4080379	4080394	0.37	-	1	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	exon	4080379	4080394	.	-	.	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	intron	4080395	4080582	.	-	.	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	CDS	4080583	4083062	0.19	-	0	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	exon	4080583	4083062	.	-	.	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
Phchi.S5	AUGUSTUS	start_codon	4083060	4083062	.	-	0	transcript_id "Phchi.S5G057900.t1"; gene_id "Phchi.S5G057900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14398.t1 is derived from g12866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12622928	12625169	.	+	.	Phchi.S3G171700
Phchi.S3	AUGUSTUS	transcript	12622928	12625169	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	start_codon	12622928	12622930	.	+	0	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12622928	12623072	0.48	+	0	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12622928	12623072	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12623073	12623268	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12623269	12623488	0.99	+	2	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12623269	12623488	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12623489	12623612	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12623613	12623719	1	+	1	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12623613	12623719	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12623720	12623838	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12623839	12624038	1	+	2	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12623839	12624038	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12624039	12624321	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12624322	12624425	1	+	0	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12624322	12624425	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12624426	12624500	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12624501	12624688	0.99	+	1	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12624501	12624688	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12624689	12624808	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12624809	12625008	1	+	2	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12624809	12625008	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	intron	12625009	12625103	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	CDS	12625104	12625169	0.95	+	0	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	exon	12625104	12625169	.	+	.	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
Phchi.S3	AUGUSTUS	stop_codon	12625170	12625172	.	+	0	transcript_id "Phchi.S3G171700.t1"; gene_id "Phchi.S3G171700"
# This transcript jg3303.t2 is derived from g472.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3304.t1 is derived from g473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2750394	2755941	.	-	.	Phchi.S1G046300
Phchi.S1	AUGUSTUS	transcript	2750394	2755941	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	stop_codon	2750391	2750393	.	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2750394	2750499	1	-	1	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2750394	2750499	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2750500	2750589	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2750590	2750697	1	-	1	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2750590	2750697	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2750698	2750792	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2750793	2750979	0.99	-	2	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2750793	2750979	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2750980	2751071	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2751072	2751231	1	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2751072	2751231	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2751232	2751336	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2751337	2751453	1	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2751337	2751453	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2751454	2751582	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2751583	2751740	1	-	2	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2751583	2751740	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2751741	2751815	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2751816	2751940	1	-	1	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2751816	2751940	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2751941	2752040	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2752041	2752169	0.98	-	1	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2752041	2752169	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2752170	2752287	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2752288	2752444	0.88	-	2	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2752288	2752444	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2752445	2752583	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2752584	2752653	0.99	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2752584	2752653	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2752654	2752798	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2752799	2752921	1	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2752799	2752921	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2752922	2753017	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2753018	2753124	0.99	-	2	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2753018	2753124	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2753125	2753246	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2753247	2753411	1	-	2	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2753247	2753411	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2753412	2753500	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2753501	2753587	1	-	2	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2753501	2753587	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2753588	2753679	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2753680	2753761	1	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2753680	2753761	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2753762	2753911	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2753912	2754046	0.97	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2753912	2754046	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2754047	2754170	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2754171	2754251	0.52	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2754171	2754251	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2754252	2754358	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2754359	2754415	0.54	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2754359	2754415	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2754416	2754519	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2754520	2755107	0.99	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2754520	2755107	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2755108	2755246	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2755247	2755465	1	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2755247	2755465	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	intron	2755466	2755755	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	CDS	2755756	2755941	0.48	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	exon	2755756	2755941	.	-	.	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
Phchi.S1	AUGUSTUS	start_codon	2755939	2755941	.	-	0	transcript_id "Phchi.S1G046300.t1"; gene_id "Phchi.S1G046300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5256.t1 is derived from g2426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15883111	15883533	.	+	.	Phchi.S1G241500
Phchi.S1	AUGUSTUS	transcript	15883111	15883533	.	+	.	transcript_id "Phchi.S1G241500.t1"; gene_id "Phchi.S1G241500"
Phchi.S1	AUGUSTUS	start_codon	15883111	15883113	.	+	0	transcript_id "Phchi.S1G241500.t1"; gene_id "Phchi.S1G241500"
Phchi.S1	AUGUSTUS	CDS	15883111	15883533	0.79	+	0	transcript_id "Phchi.S1G241500.t1"; gene_id "Phchi.S1G241500"
Phchi.S1	AUGUSTUS	exon	15883111	15883533	.	+	.	transcript_id "Phchi.S1G241500.t1"; gene_id "Phchi.S1G241500"
Phchi.S1	AUGUSTUS	stop_codon	15883534	15883536	.	+	0	transcript_id "Phchi.S1G241500.t1"; gene_id "Phchi.S1G241500"
# This transcript jg15866.t2 is derived from g14336.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15867.t1 is derived from g14337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21948893	21951944	.	+	.	Phchi.S3G318600
Phchi.S3	AUGUSTUS	transcript	21948893	21951944	.	+	.	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	start_codon	21948893	21948895	.	+	0	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	CDS	21948893	21949100	0.76	+	0	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	exon	21948893	21949100	.	+	.	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	intron	21949101	21949180	.	+	.	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	CDS	21949181	21949320	0.76	+	2	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	exon	21949181	21949320	.	+	.	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	intron	21949321	21949475	.	+	.	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	CDS	21949476	21951944	0.88	+	0	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	exon	21949476	21951944	.	+	.	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
Phchi.S3	AUGUSTUS	stop_codon	21951945	21951947	.	+	0	transcript_id "Phchi.S3G318600.t1"; gene_id "Phchi.S3G318600"
# This transcript jg8524.t2 is derived from g5699.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8525.t1 is derived from g5700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36436158	36436885	.	+	.	Phchi.S1G568400
Phchi.S1	AUGUSTUS	transcript	36436158	36436885	.	+	.	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	start_codon	36436158	36436160	.	+	0	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	CDS	36436158	36436675	0.22	+	0	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	exon	36436158	36436675	.	+	.	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	intron	36436676	36436809	.	+	.	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	CDS	36436810	36436885	0.46	+	1	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	exon	36436810	36436885	.	+	.	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
Phchi.S1	AUGUSTUS	stop_codon	36436886	36436888	.	+	0	transcript_id "Phchi.S1G568400.t1"; gene_id "Phchi.S1G568400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14552.t1 is derived from g13020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13443552	13443803	.	-	.	Phchi.S3G187100
Phchi.S3	AUGUSTUS	transcript	13443552	13443803	.	-	.	transcript_id "Phchi.S3G187100.t1"; gene_id "Phchi.S3G187100"
Phchi.S3	AUGUSTUS	stop_codon	13443549	13443551	.	-	0	transcript_id "Phchi.S3G187100.t1"; gene_id "Phchi.S3G187100"
Phchi.S3	AUGUSTUS	CDS	13443552	13443803	0.37	-	0	transcript_id "Phchi.S3G187100.t1"; gene_id "Phchi.S3G187100"
Phchi.S3	AUGUSTUS	exon	13443552	13443803	.	-	.	transcript_id "Phchi.S3G187100.t1"; gene_id "Phchi.S3G187100"
Phchi.S3	AUGUSTUS	start_codon	13443801	13443803	.	-	0	transcript_id "Phchi.S3G187100.t1"; gene_id "Phchi.S3G187100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7628.t1 is derived from g4802.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30319650	30321593	.	+	.	Phchi.S1G478700
Phchi.S1	AUGUSTUS	transcript	30319650	30321593	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	start_codon	30319650	30319652	.	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30319650	30319718	0.77	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30319650	30319718	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	intron	30319719	30319882	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30319883	30320053	0.8	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30319883	30320053	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	intron	30320054	30320245	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30320246	30320773	1	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30320246	30320773	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	intron	30320774	30320902	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30320903	30320980	1	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30320903	30320980	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	intron	30320981	30321064	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30321065	30321142	1	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30321065	30321142	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	intron	30321143	30321226	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30321227	30321322	0.7	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30321227	30321322	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	intron	30321323	30321455	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	CDS	30321456	30321593	0.7	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	exon	30321456	30321593	.	+	.	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
Phchi.S1	AUGUSTUS	stop_codon	30321594	30321596	.	+	0	transcript_id "Phchi.S1G478700.t1"; gene_id "Phchi.S1G478700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10219.t1 is derived from g7395.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46451480	46454001	.	+	.	Phchi.S1G737800
Phchi.S1	AUGUSTUS	transcript	46451480	46454001	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	start_codon	46451480	46451482	.	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46451480	46451657	0.59	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46451480	46451657	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46451658	46451751	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46451752	46451911	1	+	2	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46451752	46451911	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46451912	46451996	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46451997	46452162	1	+	1	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46451997	46452162	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46452163	46452259	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46452260	46452520	1	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46452260	46452520	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46452521	46452649	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46452650	46452820	1	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46452650	46452820	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46452821	46452966	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46452967	46453294	0.98	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46452967	46453294	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46453295	46453380	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46453381	46453547	0.89	+	2	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46453381	46453547	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	intron	46453548	46453656	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	CDS	46453657	46454001	0.95	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	exon	46453657	46454001	.	+	.	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
Phchi.S1	AUGUSTUS	stop_codon	46454002	46454004	.	+	0	transcript_id "Phchi.S1G737800.t1"; gene_id "Phchi.S1G737800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4598.t1 is derived from g1768.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11280429	11284209	.	+	.	Phchi.S1G175700
Phchi.S1	AUGUSTUS	transcript	11280429	11284209	.	+	.	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	start_codon	11280429	11280431	.	+	0	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	CDS	11280429	11282175	0.67	+	0	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	exon	11280429	11282175	.	+	.	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	intron	11282176	11282269	.	+	.	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	CDS	11282270	11284209	1	+	2	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	exon	11282270	11284209	.	+	.	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
Phchi.S1	AUGUSTUS	stop_codon	11284210	11284212	.	+	0	transcript_id "Phchi.S1G175700.t1"; gene_id "Phchi.S1G175700"
# This transcript jg9375.t2 is derived from g6551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9376.t1 is derived from g6552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41224658	41225218	.	-	.	Phchi.S1G653500
Phchi.S1	AUGUSTUS	transcript	41224658	41225218	.	-	.	transcript_id "Phchi.S1G653500.t1"; gene_id "Phchi.S1G653500"
Phchi.S1	AUGUSTUS	stop_codon	41224655	41224657	.	-	0	transcript_id "Phchi.S1G653500.t1"; gene_id "Phchi.S1G653500"
Phchi.S1	AUGUSTUS	CDS	41224658	41225218	0.84	-	0	transcript_id "Phchi.S1G653500.t1"; gene_id "Phchi.S1G653500"
Phchi.S1	AUGUSTUS	exon	41224658	41225218	.	-	.	transcript_id "Phchi.S1G653500.t1"; gene_id "Phchi.S1G653500"
Phchi.S1	AUGUSTUS	start_codon	41225216	41225218	.	-	0	transcript_id "Phchi.S1G653500.t1"; gene_id "Phchi.S1G653500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15854.t1 is derived from g14324.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21828619	21830350	.	-	.	Phchi.S3G317300
Phchi.S3	AUGUSTUS	transcript	21828619	21830350	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	stop_codon	21828616	21828618	.	-	0	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	CDS	21828619	21829014	0.87	-	0	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	exon	21828619	21829014	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	intron	21829015	21829132	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	CDS	21829133	21829275	0.93	-	2	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	exon	21829133	21829275	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	intron	21829276	21829361	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	CDS	21829362	21829613	0.99	-	2	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	exon	21829362	21829613	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	intron	21829614	21829708	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	CDS	21829709	21829859	1	-	0	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	exon	21829709	21829859	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	intron	21829860	21830009	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	CDS	21830010	21830203	1	-	2	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	exon	21830010	21830203	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	intron	21830204	21830289	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	CDS	21830290	21830350	1	-	0	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	exon	21830290	21830350	.	-	.	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
Phchi.S3	AUGUSTUS	start_codon	21830348	21830350	.	-	0	transcript_id "Phchi.S3G317300.t1"; gene_id "Phchi.S3G317300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg756.t1 is derived from g10538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5354977	5356025	.	+	.	Phchi.S6G071500
Phchi.S6	AUGUSTUS	transcript	5354977	5356025	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	start_codon	5354977	5354979	.	+	0	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	CDS	5354977	5355028	0.99	+	0	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	exon	5354977	5355028	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	intron	5355029	5355123	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	CDS	5355124	5355194	1	+	2	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	exon	5355124	5355194	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	intron	5355195	5355277	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	CDS	5355278	5355411	1	+	0	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	exon	5355278	5355411	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	intron	5355412	5355492	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	CDS	5355493	5355822	0.75	+	1	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	exon	5355493	5355822	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	intron	5355823	5355958	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	CDS	5355959	5356025	0.4	+	1	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	exon	5355959	5356025	.	+	.	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
Phchi.S6	AUGUSTUS	stop_codon	5356026	5356028	.	+	0	transcript_id "Phchi.S6G071500.t1"; gene_id "Phchi.S6G071500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12056.t1 is derived from g7731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1062750	1065273	.	+	.	Phchi.S2G013600
Phchi.S2	AUGUSTUS	transcript	1062750	1065273	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	start_codon	1062750	1062752	.	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1062750	1062848	0.97	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1062750	1062848	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	intron	1062849	1063367	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1063368	1063555	1	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1063368	1063555	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	intron	1063556	1063727	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1063728	1063902	1	+	1	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1063728	1063902	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	intron	1063903	1064118	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1064119	1064292	1	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1064119	1064292	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	intron	1064293	1064407	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1064408	1064551	1	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1064408	1064551	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	intron	1064552	1064752	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1064753	1064808	1	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1064753	1064808	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	intron	1064809	1064927	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	CDS	1064928	1065273	0.62	+	1	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	exon	1064928	1065273	.	+	.	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
Phchi.S2	AUGUSTUS	stop_codon	1065274	1065276	.	+	0	transcript_id "Phchi.S2G013600.t1"; gene_id "Phchi.S2G013600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8531.t1 is derived from g5706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36515820	36517692	.	-	.	Phchi.S1G569000
Phchi.S1	AUGUSTUS	transcript	36515820	36517692	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	stop_codon	36515817	36515819	.	-	0	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36515820	36515832	0.32	-	1	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36515820	36515832	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36515833	36516053	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36516054	36516245	0.39	-	1	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36516054	36516245	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36516246	36516367	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36516368	36516429	0.81	-	0	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36516368	36516429	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36516430	36516592	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36516593	36516671	1	-	1	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36516593	36516671	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36516672	36516840	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36516841	36517039	0.99	-	2	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36516841	36517039	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36517040	36517141	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36517142	36517295	0.98	-	0	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36517142	36517295	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36517296	36517394	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36517395	36517487	0.99	-	0	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36517395	36517487	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	intron	36517488	36517617	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	CDS	36517618	36517692	0.22	-	0	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	exon	36517618	36517692	.	-	.	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
Phchi.S1	AUGUSTUS	start_codon	36517690	36517692	.	-	0	transcript_id "Phchi.S1G569000.t1"; gene_id "Phchi.S1G569000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6983.t1 is derived from g4155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26265895	26266638	.	-	.	Phchi.S1G414200
Phchi.S1	AUGUSTUS	transcript	26265895	26266638	.	-	.	transcript_id "Phchi.S1G414200.t1"; gene_id "Phchi.S1G414200"
Phchi.S1	AUGUSTUS	stop_codon	26265892	26265894	.	-	0	transcript_id "Phchi.S1G414200.t1"; gene_id "Phchi.S1G414200"
Phchi.S1	AUGUSTUS	CDS	26265895	26266638	0.68	-	0	transcript_id "Phchi.S1G414200.t1"; gene_id "Phchi.S1G414200"
Phchi.S1	AUGUSTUS	exon	26265895	26266638	.	-	.	transcript_id "Phchi.S1G414200.t1"; gene_id "Phchi.S1G414200"
Phchi.S1	AUGUSTUS	start_codon	26266636	26266638	.	-	0	transcript_id "Phchi.S1G414200.t1"; gene_id "Phchi.S1G414200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7533.t1 is derived from g4707.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29935276	29935674	.	-	.	Phchi.S1G469200
Phchi.S1	AUGUSTUS	transcript	29935276	29935674	.	-	.	transcript_id "Phchi.S1G469200.t1"; gene_id "Phchi.S1G469200"
Phchi.S1	AUGUSTUS	stop_codon	29935273	29935275	.	-	0	transcript_id "Phchi.S1G469200.t1"; gene_id "Phchi.S1G469200"
Phchi.S1	AUGUSTUS	CDS	29935276	29935674	0.57	-	0	transcript_id "Phchi.S1G469200.t1"; gene_id "Phchi.S1G469200"
Phchi.S1	AUGUSTUS	exon	29935276	29935674	.	-	.	transcript_id "Phchi.S1G469200.t1"; gene_id "Phchi.S1G469200"
Phchi.S1	AUGUSTUS	start_codon	29935672	29935674	.	-	0	transcript_id "Phchi.S1G469200.t1"; gene_id "Phchi.S1G469200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15425.t1 is derived from g13893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19020522	19027152	.	-	.	Phchi.S3G274400
Phchi.S3	AUGUSTUS	transcript	19020522	19027152	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	stop_codon	19020519	19020521	.	-	0	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19020522	19022342	0.97	-	0	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19020522	19022342	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19022343	19022504	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19022505	19022700	1	-	1	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19022505	19022700	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19022701	19022855	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19022856	19023346	0.98	-	0	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19022856	19023346	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19023347	19023576	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19023577	19023727	1	-	1	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19023577	19023727	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19023728	19024039	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19024040	19024152	1	-	0	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19024040	19024152	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19024153	19024339	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19024340	19024691	1	-	1	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19024340	19024691	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19024692	19024816	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19024817	19024975	1	-	1	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19024817	19024975	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19024976	19025133	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19025134	19025263	1	-	2	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19025134	19025263	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19025264	19025404	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19025405	19025473	1	-	2	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19025405	19025473	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19025474	19025602	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19025603	19025691	1	-	1	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19025603	19025691	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19025692	19025809	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19025810	19025921	1	-	2	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19025810	19025921	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	intron	19025922	19026950	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	CDS	19026951	19027152	1	-	0	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	exon	19026951	19027152	.	-	.	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
Phchi.S3	AUGUSTUS	start_codon	19027150	19027152	.	-	0	transcript_id "Phchi.S3G274400.t1"; gene_id "Phchi.S3G274400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15611.t1 is derived from g14080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20284978	20286366	.	+	.	Phchi.S3G293000
Phchi.S3	AUGUSTUS	transcript	20284978	20286366	.	+	.	transcript_id "Phchi.S3G293000.t1"; gene_id "Phchi.S3G293000"
Phchi.S3	AUGUSTUS	start_codon	20284978	20284980	.	+	0	transcript_id "Phchi.S3G293000.t1"; gene_id "Phchi.S3G293000"
Phchi.S3	AUGUSTUS	CDS	20284978	20286366	0.96	+	0	transcript_id "Phchi.S3G293000.t1"; gene_id "Phchi.S3G293000"
Phchi.S3	AUGUSTUS	exon	20284978	20286366	.	+	.	transcript_id "Phchi.S3G293000.t1"; gene_id "Phchi.S3G293000"
Phchi.S3	AUGUSTUS	stop_codon	20286367	20286369	.	+	0	transcript_id "Phchi.S3G293000.t1"; gene_id "Phchi.S3G293000"
# This transcript jg15336.t2 is derived from g13804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15337.t1 is derived from g13805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18451576	18452588	.	+	.	Phchi.S3G265600
Phchi.S3	AUGUSTUS	transcript	18451576	18452588	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	start_codon	18451576	18451578	.	+	0	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	CDS	18451576	18451639	0.78	+	0	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	exon	18451576	18451639	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	intron	18451640	18451798	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	CDS	18451799	18451917	0.78	+	2	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	exon	18451799	18451917	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	intron	18451918	18452123	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	CDS	18452124	18452219	1	+	0	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	exon	18452124	18452219	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	intron	18452220	18452306	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	CDS	18452307	18452326	0.71	+	0	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	exon	18452307	18452326	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	intron	18452327	18452431	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	CDS	18452432	18452450	0.71	+	1	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	exon	18452432	18452450	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	intron	18452451	18452543	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	CDS	18452544	18452588	0.71	+	0	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	exon	18452544	18452588	.	+	.	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
Phchi.S3	AUGUSTUS	stop_codon	18452589	18452591	.	+	0	transcript_id "Phchi.S3G265600.t1"; gene_id "Phchi.S3G265600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13760.t1 is derived from g12227.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8744854	8748686	.	+	.	Phchi.S3G107900
Phchi.S3	AUGUSTUS	transcript	8744854	8748686	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	start_codon	8744854	8744856	.	+	0	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8744854	8744962	1	+	0	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8744854	8744962	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8744963	8745051	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8745052	8745102	1	+	2	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8745052	8745102	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8745103	8745311	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8745312	8745627	1	+	2	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8745312	8745627	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8745628	8745722	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8745723	8746276	1	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8745723	8746276	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8746277	8746366	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8746367	8746502	1	+	2	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8746367	8746502	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8746503	8746603	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8746604	8746675	0.64	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8746604	8746675	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8746676	8746781	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8746782	8746853	1	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8746782	8746853	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8746854	8746942	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8746943	8747014	1	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8746943	8747014	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8747015	8747105	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8747106	8747595	0.57	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8747106	8747595	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8747596	8747686	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8747687	8747813	1	+	0	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8747687	8747813	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8747814	8747898	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8747899	8747967	1	+	2	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8747899	8747967	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8747968	8748062	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8748063	8748095	1	+	2	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8748063	8748095	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8748096	8748187	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8748188	8748350	1	+	2	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8748188	8748350	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8748351	8748426	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8748427	8748558	1	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8748427	8748558	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	intron	8748559	8748658	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	CDS	8748659	8748686	1	+	1	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	exon	8748659	8748686	.	+	.	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
Phchi.S3	AUGUSTUS	stop_codon	8748687	8748689	.	+	0	transcript_id "Phchi.S3G107900.t1"; gene_id "Phchi.S3G107900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3204.t1 is derived from g373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2232203	2233389	.	+	.	Phchi.S1G036300
Phchi.S1	AUGUSTUS	transcript	2232203	2233389	.	+	.	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	start_codon	2232203	2232205	.	+	0	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	CDS	2232203	2232601	0.39	+	0	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	exon	2232203	2232601	.	+	.	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	intron	2232602	2232744	.	+	.	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	CDS	2232745	2233029	0.71	+	0	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	exon	2232745	2233029	.	+	.	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	intron	2233030	2233113	.	+	.	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	CDS	2233114	2233389	0.96	+	0	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	exon	2233114	2233389	.	+	.	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
Phchi.S1	AUGUSTUS	stop_codon	2233390	2233392	.	+	0	transcript_id "Phchi.S1G036300.t1"; gene_id "Phchi.S1G036300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6384.t1 is derived from g3556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22659616	22661581	.	+	.	Phchi.S1G354300
Phchi.S1	AUGUSTUS	transcript	22659616	22661581	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	start_codon	22659616	22659618	.	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22659616	22659971	1	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22659616	22659971	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	intron	22659972	22660110	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22660111	22660342	0.97	+	1	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22660111	22660342	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	intron	22660343	22660453	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22660454	22660599	1	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22660454	22660599	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	intron	22660600	22660752	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22660753	22660840	1	+	1	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22660753	22660840	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	intron	22660841	22661002	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22661003	22661149	1	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22661003	22661149	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	intron	22661150	22661276	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22661277	22661432	0.85	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22661277	22661432	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	intron	22661433	22661533	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	CDS	22661534	22661581	0.85	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	exon	22661534	22661581	.	+	.	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
Phchi.S1	AUGUSTUS	stop_codon	22661582	22661584	.	+	0	transcript_id "Phchi.S1G354300.t1"; gene_id "Phchi.S1G354300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5587.t1 is derived from g2757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17754460	17754933	.	+	.	Phchi.S1G274600
Phchi.S1	AUGUSTUS	transcript	17754460	17754933	.	+	.	transcript_id "Phchi.S1G274600.t1"; gene_id "Phchi.S1G274600"
Phchi.S1	AUGUSTUS	start_codon	17754460	17754462	.	+	0	transcript_id "Phchi.S1G274600.t1"; gene_id "Phchi.S1G274600"
Phchi.S1	AUGUSTUS	CDS	17754460	17754933	1	+	0	transcript_id "Phchi.S1G274600.t1"; gene_id "Phchi.S1G274600"
Phchi.S1	AUGUSTUS	exon	17754460	17754933	.	+	.	transcript_id "Phchi.S1G274600.t1"; gene_id "Phchi.S1G274600"
Phchi.S1	AUGUSTUS	stop_codon	17754934	17754936	.	+	0	transcript_id "Phchi.S1G274600.t1"; gene_id "Phchi.S1G274600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11557.t1 is derived from g15608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7037641	7040013	.	-	.	Phchi.S4G113900
Phchi.S4	AUGUSTUS	transcript	7037641	7040013	.	-	.	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	stop_codon	7037638	7037640	.	-	0	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	CDS	7037641	7039775	0.99	-	2	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	exon	7037641	7039775	.	-	.	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	intron	7039776	7039937	.	-	.	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	CDS	7039938	7040013	0.69	-	0	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	exon	7039938	7040013	.	-	.	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
Phchi.S4	AUGUSTUS	start_codon	7040011	7040013	.	-	0	transcript_id "Phchi.S4G113900.t1"; gene_id "Phchi.S4G113900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14158.t1 is derived from g12625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11195615	11196811	.	+	.	Phchi.S3G147700
Phchi.S3	AUGUSTUS	transcript	11195615	11196811	.	+	.	transcript_id "Phchi.S3G147700.t1"; gene_id "Phchi.S3G147700"
Phchi.S3	AUGUSTUS	start_codon	11195615	11195617	.	+	0	transcript_id "Phchi.S3G147700.t1"; gene_id "Phchi.S3G147700"
Phchi.S3	AUGUSTUS	CDS	11195615	11196811	0.84	+	0	transcript_id "Phchi.S3G147700.t1"; gene_id "Phchi.S3G147700"
Phchi.S3	AUGUSTUS	exon	11195615	11196811	.	+	.	transcript_id "Phchi.S3G147700.t1"; gene_id "Phchi.S3G147700"
Phchi.S3	AUGUSTUS	stop_codon	11196812	11196814	.	+	0	transcript_id "Phchi.S3G147700.t1"; gene_id "Phchi.S3G147700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7950.t1 is derived from g5124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32065999	32068207	.	+	.	Phchi.S1G510900
Phchi.S1	AUGUSTUS	transcript	32065999	32068207	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	start_codon	32065999	32066001	.	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32065999	32066115	0.95	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32065999	32066115	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32066116	32066581	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32066582	32066704	0.99	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32066582	32066704	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32066705	32066808	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32066809	32066859	1	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32066809	32066859	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32066860	32067006	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32067007	32067078	1	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32067007	32067078	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32067079	32067200	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32067201	32067314	1	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32067201	32067314	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32067315	32067467	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32067468	32067532	1	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32067468	32067532	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32067533	32067673	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32067674	32067734	1	+	1	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32067674	32067734	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32067735	32067821	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32067822	32067878	1	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32067822	32067878	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32067879	32067951	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32067952	32068011	0.66	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32067952	32068011	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	intron	32068012	32068123	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	CDS	32068124	32068207	0.82	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	exon	32068124	32068207	.	+	.	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
Phchi.S1	AUGUSTUS	stop_codon	32068208	32068210	.	+	0	transcript_id "Phchi.S1G510900.t1"; gene_id "Phchi.S1G510900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg753.t1 is derived from g10535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5339105	5340163	.	+	.	Phchi.S6G071200
Phchi.S6	AUGUSTUS	transcript	5339105	5340163	.	+	.	transcript_id "Phchi.S6G071200.t1"; gene_id "Phchi.S6G071200"
Phchi.S6	AUGUSTUS	start_codon	5339105	5339107	.	+	0	transcript_id "Phchi.S6G071200.t1"; gene_id "Phchi.S6G071200"
Phchi.S6	AUGUSTUS	CDS	5339105	5340163	0.95	+	0	transcript_id "Phchi.S6G071200.t1"; gene_id "Phchi.S6G071200"
Phchi.S6	AUGUSTUS	exon	5339105	5340163	.	+	.	transcript_id "Phchi.S6G071200.t1"; gene_id "Phchi.S6G071200"
Phchi.S6	AUGUSTUS	stop_codon	5340164	5340166	.	+	0	transcript_id "Phchi.S6G071200.t1"; gene_id "Phchi.S6G071200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9204.t1 is derived from g6379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40366506	40369609	.	+	.	Phchi.S1G636300
Phchi.S1	AUGUSTUS	transcript	40366506	40369609	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	start_codon	40366506	40366508	.	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40366506	40367529	0.92	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40366506	40367529	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40367530	40367921	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40367922	40368008	0.86	+	2	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40367922	40368008	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40368009	40368086	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40368087	40368346	0.94	+	2	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40368087	40368346	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40368347	40368482	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40368483	40368603	1	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40368483	40368603	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40368604	40368755	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40368756	40368880	0.65	+	2	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40368756	40368880	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40368881	40368950	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40368951	40368998	1	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40368951	40368998	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40368999	40369097	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40369098	40369238	1	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40369098	40369238	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40369239	40369305	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40369306	40369388	1	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40369306	40369388	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	intron	40369389	40369479	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	CDS	40369480	40369609	1	+	1	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	exon	40369480	40369609	.	+	.	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
Phchi.S1	AUGUSTUS	stop_codon	40369610	40369612	.	+	0	transcript_id "Phchi.S1G636300.t1"; gene_id "Phchi.S1G636300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10786.t1 is derived from g14836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2112190	2117298	.	+	.	Phchi.S4G036800
Phchi.S4	AUGUSTUS	transcript	2112190	2117298	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	start_codon	2112190	2112192	.	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2112190	2112282	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2112190	2112282	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2112283	2112422	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2112423	2112482	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2112423	2112482	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2112483	2112607	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2112608	2112664	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2112608	2112664	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2112665	2112752	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2112753	2112824	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2112753	2112824	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2112825	2112925	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2112926	2112988	0.99	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2112926	2112988	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2112989	2113190	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2113191	2113367	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2113191	2113367	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2113368	2113505	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2113506	2113622	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2113506	2113622	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2113623	2113750	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2113751	2113817	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2113751	2113817	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2113818	2113992	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2113993	2114195	1	+	2	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2113993	2114195	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2114196	2114307	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2114308	2114378	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2114308	2114378	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2114379	2114511	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2114512	2114596	1	+	1	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2114512	2114596	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2114597	2114798	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2114799	2114867	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2114799	2114867	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2114868	2115256	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2115257	2115375	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2115257	2115375	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2115376	2115512	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2115513	2115651	1	+	1	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2115513	2115651	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2115652	2115755	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2115756	2116259	0.98	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2115756	2116259	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2116260	2116353	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2116354	2116653	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2116354	2116653	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2116654	2116738	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2116739	2116911	1	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2116739	2116911	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2116912	2117011	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2117012	2117123	1	+	1	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2117012	2117123	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	intron	2117124	2117199	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	CDS	2117200	2117298	0.99	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	exon	2117200	2117298	.	+	.	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
Phchi.S4	AUGUSTUS	stop_codon	2117299	2117301	.	+	0	transcript_id "Phchi.S4G036800.t1"; gene_id "Phchi.S4G036800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14233.t1 is derived from g12700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11679772	11680528	.	-	.	Phchi.S3G155200
Phchi.S3	AUGUSTUS	transcript	11679772	11680528	.	-	.	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	stop_codon	11679769	11679771	.	-	0	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	CDS	11679772	11679838	0.94	-	1	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	exon	11679772	11679838	.	-	.	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	intron	11679839	11680169	.	-	.	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	CDS	11680170	11680528	0.72	-	0	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	exon	11680170	11680528	.	-	.	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
Phchi.S3	AUGUSTUS	start_codon	11680526	11680528	.	-	0	transcript_id "Phchi.S3G155200.t1"; gene_id "Phchi.S3G155200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3917.t1 is derived from g1086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6424643	6427632	.	+	.	Phchi.S1G107600
Phchi.S1	AUGUSTUS	transcript	6424643	6427632	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	start_codon	6424643	6424645	.	+	0	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6424643	6425825	0.88	+	0	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6424643	6425825	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6425826	6425939	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6425940	6425981	0.99	+	2	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6425940	6425981	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6425982	6426118	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6426119	6426221	0.88	+	2	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6426119	6426221	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6426222	6426327	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6426328	6426402	0.99	+	1	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6426328	6426402	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6426403	6426529	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6426530	6426671	1	+	1	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6426530	6426671	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6426672	6426802	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6426803	6426872	1	+	0	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6426803	6426872	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6426873	6426964	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6426965	6427060	0.49	+	2	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6426965	6427060	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6427061	6427150	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6427151	6427273	1	+	2	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6427151	6427273	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	intron	6427274	6427525	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	CDS	6427526	6427632	0.9	+	2	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	exon	6427526	6427632	.	+	.	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
Phchi.S1	AUGUSTUS	stop_codon	6427633	6427635	.	+	0	transcript_id "Phchi.S1G107600.t1"; gene_id "Phchi.S1G107600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3426.t1 is derived from g595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3583072	3585363	.	+	.	Phchi.S1G058500
Phchi.S1	AUGUSTUS	transcript	3583072	3585363	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	start_codon	3583072	3583074	.	+	0	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	CDS	3583072	3583094	0.98	+	0	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	exon	3583072	3583094	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	intron	3583095	3583190	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	CDS	3583191	3584301	0.93	+	1	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	exon	3583191	3584301	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	intron	3584302	3584384	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	CDS	3584385	3584474	1	+	0	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	exon	3584385	3584474	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	intron	3584475	3584712	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	CDS	3584713	3584769	1	+	0	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	exon	3584713	3584769	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	intron	3584770	3585327	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	CDS	3585328	3585363	1	+	0	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	exon	3585328	3585363	.	+	.	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
Phchi.S1	AUGUSTUS	stop_codon	3585364	3585366	.	+	0	transcript_id "Phchi.S1G058500.t1"; gene_id "Phchi.S1G058500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1460.t1 is derived from g8379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1011175	1012746	.	+	.	Phchi.S5G006900
Phchi.S5	AUGUSTUS	transcript	1011175	1012746	.	+	.	transcript_id "Phchi.S5G006900.t1"; gene_id "Phchi.S5G006900"
Phchi.S5	AUGUSTUS	start_codon	1011175	1011177	.	+	0	transcript_id "Phchi.S5G006900.t1"; gene_id "Phchi.S5G006900"
Phchi.S5	AUGUSTUS	CDS	1011175	1012746	1	+	0	transcript_id "Phchi.S5G006900.t1"; gene_id "Phchi.S5G006900"
Phchi.S5	AUGUSTUS	exon	1011175	1012746	.	+	.	transcript_id "Phchi.S5G006900.t1"; gene_id "Phchi.S5G006900"
Phchi.S5	AUGUSTUS	stop_codon	1012747	1012749	.	+	0	transcript_id "Phchi.S5G006900.t1"; gene_id "Phchi.S5G006900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5579.t1 is derived from g2749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17709785	17710264	.	-	.	Phchi.S1G273800
Phchi.S1	AUGUSTUS	transcript	17709785	17710264	.	-	.	transcript_id "Phchi.S1G273800.t1"; gene_id "Phchi.S1G273800"
Phchi.S1	AUGUSTUS	stop_codon	17709782	17709784	.	-	0	transcript_id "Phchi.S1G273800.t1"; gene_id "Phchi.S1G273800"
Phchi.S1	AUGUSTUS	CDS	17709785	17710264	0.51	-	0	transcript_id "Phchi.S1G273800.t1"; gene_id "Phchi.S1G273800"
Phchi.S1	AUGUSTUS	exon	17709785	17710264	.	-	.	transcript_id "Phchi.S1G273800.t1"; gene_id "Phchi.S1G273800"
Phchi.S1	AUGUSTUS	start_codon	17710262	17710264	.	-	0	transcript_id "Phchi.S1G273800.t1"; gene_id "Phchi.S1G273800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2342.t1 is derived from g9262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6257444	6259900	.	+	.	Phchi.S5G095100
Phchi.S5	AUGUSTUS	transcript	6257444	6259900	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	start_codon	6257444	6257446	.	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6257444	6257517	0.42	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6257444	6257517	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6257518	6257659	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6257660	6258488	0.4	+	1	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6257660	6258488	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6258489	6258597	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6258598	6258630	1	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6258598	6258630	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6258631	6258759	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6258760	6258850	1	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6258760	6258850	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6258851	6258932	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6258933	6259196	1	+	2	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6258933	6259196	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6259197	6259278	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6259279	6259349	0.89	+	2	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6259279	6259349	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6259350	6259452	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6259453	6259494	0.62	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6259453	6259494	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6259495	6259629	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6259630	6259655	0.87	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6259630	6259655	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	intron	6259656	6259800	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	CDS	6259801	6259900	0.83	+	1	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	exon	6259801	6259900	.	+	.	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
Phchi.S5	AUGUSTUS	stop_codon	6259901	6259903	.	+	0	transcript_id "Phchi.S5G095100.t1"; gene_id "Phchi.S5G095100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5313.t1 is derived from g2483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16248849	16251861	.	-	.	Phchi.S1G247200
Phchi.S1	AUGUSTUS	transcript	16248849	16251861	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	stop_codon	16248846	16248848	.	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16248849	16249604	0.93	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16248849	16249604	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16249605	16249687	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16249688	16249753	1	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16249688	16249753	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16249754	16249841	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16249842	16249920	1	-	1	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16249842	16249920	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16249921	16250021	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250022	16250155	0.99	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250022	16250155	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250156	16250265	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250266	16250356	1	-	1	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250266	16250356	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250357	16250442	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250443	16250585	1	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250443	16250585	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250586	16250793	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250794	16251234	0.72	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250794	16251234	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16251235	16251330	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16251331	16251861	0.95	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16251331	16251861	.	-	.	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	start_codon	16251859	16251861	.	-	0	transcript_id "Phchi.S1G247200.t1"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	transcript	16248849	16251861	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	stop_codon	16248846	16248848	.	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16248849	16249604	0.95	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16248849	16249604	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16249605	16249687	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16249688	16249753	1	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16249688	16249753	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16249754	16249841	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16249842	16249920	1	-	1	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16249842	16249920	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16249921	16250021	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250022	16250155	0.99	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250022	16250155	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250156	16250265	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250266	16250356	1	-	1	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250266	16250356	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250357	16250442	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250443	16250593	1	-	2	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250443	16250593	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250594	16250793	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250794	16250881	0.81	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250794	16250881	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16250882	16250997	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16250998	16251234	0.77	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16250998	16251234	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	intron	16251235	16251330	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	CDS	16251331	16251861	0.92	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	exon	16251331	16251861	.	-	.	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
Phchi.S1	AUGUSTUS	start_codon	16251859	16251861	.	-	0	transcript_id "Phchi.S1G247200.t2"; gene_id "Phchi.S1G247200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg632.t1 is derived from g10414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4482935	4484992	.	+	.	Phchi.S6G059100
Phchi.S6	AUGUSTUS	transcript	4482935	4484992	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	start_codon	4482935	4482937	.	+	0	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	CDS	4482935	4483121	0.94	+	0	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	exon	4482935	4483121	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	intron	4483122	4483208	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	CDS	4483209	4483665	0.87	+	2	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	exon	4483209	4483665	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	intron	4483666	4483774	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	CDS	4483775	4483900	1	+	1	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	exon	4483775	4483900	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	intron	4483901	4484275	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	CDS	4484276	4484582	1	+	1	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	exon	4484276	4484582	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	intron	4484583	4484752	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	CDS	4484753	4484992	1	+	0	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	exon	4484753	4484992	.	+	.	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
Phchi.S6	AUGUSTUS	stop_codon	4484993	4484995	.	+	0	transcript_id "Phchi.S6G059100.t1"; gene_id "Phchi.S6G059100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14831.t1 is derived from g13299.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14918217	14919209	.	-	.	Phchi.S3G215000
Phchi.S3	AUGUSTUS	transcript	14918217	14919209	.	-	.	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	stop_codon	14918214	14918216	.	-	0	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	CDS	14918217	14918355	0.55	-	1	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	exon	14918217	14918355	.	-	.	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	intron	14918356	14918469	.	-	.	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	CDS	14918470	14919209	0.99	-	0	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	exon	14918470	14919209	.	-	.	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
Phchi.S3	AUGUSTUS	start_codon	14919207	14919209	.	-	0	transcript_id "Phchi.S3G215000.t1"; gene_id "Phchi.S3G215000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5246.t1 is derived from g2416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15848282	15849745	.	+	.	Phchi.S1G240500
Phchi.S1	AUGUSTUS	transcript	15848282	15849745	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	start_codon	15848282	15848284	.	+	0	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	CDS	15848282	15848420	0.79	+	0	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	exon	15848282	15848420	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	intron	15848421	15848506	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	CDS	15848507	15848665	0.96	+	2	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	exon	15848507	15848665	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	intron	15848666	15848748	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	CDS	15848749	15848882	1	+	2	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	exon	15848749	15848882	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	intron	15848883	15848965	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	CDS	15848966	15849175	1	+	0	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	exon	15848966	15849175	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	intron	15849176	15849286	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	CDS	15849287	15849397	1	+	0	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	exon	15849287	15849397	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	intron	15849398	15849487	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	CDS	15849488	15849745	1	+	0	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	exon	15849488	15849745	.	+	.	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
Phchi.S1	AUGUSTUS	stop_codon	15849746	15849748	.	+	0	transcript_id "Phchi.S1G240500.t1"; gene_id "Phchi.S1G240500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5877.t1 is derived from g3047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19530034	19535914	.	+	.	Phchi.S1G303600
Phchi.S1	AUGUSTUS	transcript	19530034	19535914	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	start_codon	19530034	19530036	.	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19530034	19531662	0.98	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19530034	19531662	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19531663	19531795	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19531796	19532032	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19531796	19532032	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19532033	19532216	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19532217	19532265	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19532217	19532265	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19532266	19532387	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19532388	19532520	1	+	2	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19532388	19532520	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19532521	19532699	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19532700	19533351	0.98	+	1	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19532700	19533351	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19533352	19533487	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19533488	19533571	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19533488	19533571	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19533572	19533664	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19533665	19533787	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19533665	19533787	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19533788	19533871	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19533872	19533941	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19533872	19533941	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19533942	19534047	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19534048	19534145	1	+	2	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19534048	19534145	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19534146	19534257	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19534258	19534362	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19534258	19534362	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19534363	19534666	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19534667	19534720	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19534667	19534720	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19534721	19534831	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19534832	19534975	1	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19534832	19534975	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19534976	19535067	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19535068	19535121	0.83	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19535068	19535121	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19535122	19535224	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19535225	19535299	0.69	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19535225	19535299	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19535300	19535404	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19535405	19535488	0.72	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19535405	19535488	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19535489	19535619	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19535620	19535681	0.37	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19535620	19535681	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19535682	19535757	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19535758	19535818	0.44	+	1	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19535758	19535818	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	intron	19535819	19535902	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	CDS	19535903	19535914	0.89	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	exon	19535903	19535914	.	+	.	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
Phchi.S1	AUGUSTUS	stop_codon	19535915	19535917	.	+	0	transcript_id "Phchi.S1G303600.t1"; gene_id "Phchi.S1G303600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7031.t1 is derived from g4203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26493139	26494018	.	+	.	Phchi.S1G419000
Phchi.S1	AUGUSTUS	transcript	26493139	26494018	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	start_codon	26493139	26493141	.	+	0	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	CDS	26493139	26493196	1	+	0	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	exon	26493139	26493196	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	intron	26493197	26493267	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	CDS	26493268	26493330	0.37	+	2	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	exon	26493268	26493330	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	intron	26493331	26493423	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	CDS	26493424	26493483	0.61	+	2	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	exon	26493424	26493483	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	intron	26493484	26493565	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	CDS	26493566	26493700	0.89	+	2	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	exon	26493566	26493700	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	intron	26493701	26493806	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	CDS	26493807	26493930	1	+	2	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	exon	26493807	26493930	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	intron	26493931	26494014	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	CDS	26494015	26494018	1	+	1	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	exon	26494015	26494018	.	+	.	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
Phchi.S1	AUGUSTUS	stop_codon	26494019	26494021	.	+	0	transcript_id "Phchi.S1G419000.t1"; gene_id "Phchi.S1G419000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9539.t1 is derived from g6715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42390029	42391542	.	+	.	Phchi.S1G669800
Phchi.S1	AUGUSTUS	transcript	42390029	42391542	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	start_codon	42390029	42390031	.	+	0	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	CDS	42390029	42390214	1	+	0	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	exon	42390029	42390214	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	intron	42390215	42390352	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	CDS	42390353	42390489	1	+	0	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	exon	42390353	42390489	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	intron	42390490	42390588	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	CDS	42390589	42391015	1	+	1	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	exon	42390589	42391015	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	intron	42391016	42391518	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	CDS	42391519	42391542	1	+	0	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	exon	42391519	42391542	.	+	.	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
Phchi.S1	AUGUSTUS	stop_codon	42391543	42391545	.	+	0	transcript_id "Phchi.S1G669800.t1"; gene_id "Phchi.S1G669800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2364.t1 is derived from g9284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6356742	6357190	.	+	.	Phchi.S5G097300
Phchi.S5	AUGUSTUS	transcript	6356742	6357190	.	+	.	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	start_codon	6356742	6356744	.	+	0	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	CDS	6356742	6356965	0.68	+	0	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	exon	6356742	6356965	.	+	.	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	intron	6356966	6357171	.	+	.	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	CDS	6357172	6357190	0.98	+	1	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	exon	6357172	6357190	.	+	.	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
Phchi.S5	AUGUSTUS	stop_codon	6357191	6357193	.	+	0	transcript_id "Phchi.S5G097300.t1"; gene_id "Phchi.S5G097300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9650.t1 is derived from g6826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43054812	43056700	.	+	.	Phchi.S1G680900
Phchi.S1	AUGUSTUS	transcript	43054812	43056700	.	+	.	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	start_codon	43054812	43054814	.	+	0	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	CDS	43054812	43055921	1	+	0	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	exon	43054812	43055921	.	+	.	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	intron	43055922	43056000	.	+	.	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	CDS	43056001	43056166	1	+	0	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	exon	43056001	43056166	.	+	.	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	intron	43056167	43056257	.	+	.	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	CDS	43056258	43056700	1	+	2	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	exon	43056258	43056700	.	+	.	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
Phchi.S1	AUGUSTUS	stop_codon	43056701	43056703	.	+	0	transcript_id "Phchi.S1G680900.t1"; gene_id "Phchi.S1G680900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5754.t1 is derived from g2924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18740209	18741848	.	-	.	Phchi.S1G291300
Phchi.S1	AUGUSTUS	transcript	18740209	18741848	.	-	.	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	stop_codon	18740206	18740208	.	-	0	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	CDS	18740209	18740385	0.97	-	0	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	exon	18740209	18740385	.	-	.	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	intron	18740386	18740561	.	-	.	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	CDS	18740562	18741848	0.35	-	0	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	exon	18740562	18741848	.	-	.	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
Phchi.S1	AUGUSTUS	start_codon	18741846	18741848	.	-	0	transcript_id "Phchi.S1G291300.t1"; gene_id "Phchi.S1G291300"
# This transcript jg1169.t2 is derived from g10952.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1170.t1 is derived from g10953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8259139	8261487	.	+	.	Phchi.S6G112900
Phchi.S6	AUGUSTUS	transcript	8259139	8261487	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	start_codon	8259139	8259141	.	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8259139	8259141	1	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8259139	8259141	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8259142	8259338	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8259339	8259380	1	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8259339	8259380	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8259381	8259535	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8259536	8259634	1	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8259536	8259634	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8259635	8259813	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8259814	8259891	1	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8259814	8259891	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8259892	8260008	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8260009	8260048	1	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8260009	8260048	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8260049	8260204	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8260205	8260257	0.61	+	2	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8260205	8260257	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8260258	8260342	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8260343	8260390	0.61	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8260343	8260390	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8260391	8260477	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8260478	8260499	0.51	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8260478	8260499	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8260500	8261065	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8261066	8261175	0.93	+	2	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8261066	8261175	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	intron	8261176	8261484	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	CDS	8261485	8261487	1	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	exon	8261485	8261487	.	+	.	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
Phchi.S6	AUGUSTUS	stop_codon	8261488	8261490	.	+	0	transcript_id "Phchi.S6G112900.t1"; gene_id "Phchi.S6G112900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12332.t1 is derived from g8008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10999263	11000703	.	-	.	Phchi.S2G041200
Phchi.S2	AUGUSTUS	transcript	10999263	11000703	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	stop_codon	10999260	10999262	.	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	CDS	10999263	10999436	0.97	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	exon	10999263	10999436	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	intron	10999437	10999524	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	CDS	10999525	10999623	1	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	exon	10999525	10999623	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	intron	10999624	10999727	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	CDS	10999728	11000222	0.98	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	exon	10999728	11000222	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	intron	11000223	11000307	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	CDS	11000308	11000550	1	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	exon	11000308	11000550	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	intron	11000551	11000643	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	CDS	11000644	11000703	1	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	exon	11000644	11000703	.	-	.	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
Phchi.S2	AUGUSTUS	start_codon	11000701	11000703	.	-	0	transcript_id "Phchi.S2G041200.t1"; gene_id "Phchi.S2G041200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14117.t1 is derived from g12584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10956535	10957745	.	-	.	Phchi.S3G143600
Phchi.S3	AUGUSTUS	transcript	10956535	10957745	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	stop_codon	10956532	10956534	.	-	0	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	CDS	10956535	10956675	1	-	0	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	exon	10956535	10956675	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	intron	10956676	10956752	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	CDS	10956753	10956804	1	-	1	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	exon	10956753	10956804	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	intron	10956805	10956894	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	CDS	10956895	10956963	1	-	1	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	exon	10956895	10956963	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	intron	10956964	10957053	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	CDS	10957054	10957166	1	-	0	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	exon	10957054	10957166	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	intron	10957167	10957249	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	CDS	10957250	10957309	1	-	0	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	exon	10957250	10957309	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	intron	10957310	10957430	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	CDS	10957431	10957745	0.57	-	0	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	exon	10957431	10957745	.	-	.	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
Phchi.S3	AUGUSTUS	start_codon	10957743	10957745	.	-	0	transcript_id "Phchi.S3G143600.t1"; gene_id "Phchi.S3G143600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12696.t1 is derived from g11161.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	609066	611201	.	-	.	Phchi.S3G001500
Phchi.S3	AUGUSTUS	transcript	609619	611201	.	-	.	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	stop_codon	609616	609618	.	-	0	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609619	609634	0.94	-	1	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609619	609634	.	-	.	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609635	609816	.	-	.	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609817	609999	0.93	-	1	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609817	609999	.	-	.	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	610000	610182	.	-	.	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	610183	611201	0.76	-	0	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	610183	611201	.	-	.	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	start_codon	611199	611201	.	-	0	transcript_id "Phchi.S3G001500.t1"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	transcript	609066	611201	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	stop_codon	609063	609065	.	-	0	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609066	609086	0.61	-	0	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609066	609086	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609087	609442	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609443	609647	0.61	-	1	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609443	609647	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609648	609816	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609817	609999	0.95	-	1	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609817	609999	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	610000	610182	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	610183	611201	0.67	-	0	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	610183	611201	.	-	.	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	start_codon	611199	611201	.	-	0	transcript_id "Phchi.S3G001500.t2"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	transcript	609066	611201	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	stop_codon	609063	609065	.	-	0	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609066	609086	0.87	-	0	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609066	609086	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609087	609166	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609167	609267	0.32	-	2	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609167	609267	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609268	609442	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609443	609461	0.28	-	0	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609443	609461	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609462	609550	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609551	609647	0.28	-	1	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609551	609647	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	609648	609816	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	609817	609999	0.98	-	1	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	609817	609999	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	intron	610000	610182	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	CDS	610183	611201	0.84	-	0	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	exon	610183	611201	.	-	.	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
Phchi.S3	AUGUSTUS	start_codon	611199	611201	.	-	0	transcript_id "Phchi.S3G001500.t3"; gene_id "Phchi.S3G001500"
# This transcript jg8912.t2 is derived from g6087.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8913.t1 is derived from g6088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38599957	38601857	.	+	.	Phchi.S1G607200
Phchi.S1	AUGUSTUS	transcript	38599957	38601857	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	start_codon	38599957	38599959	.	+	0	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	CDS	38599957	38600098	0.76	+	0	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	exon	38599957	38600098	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	intron	38600099	38600338	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	CDS	38600339	38600761	1	+	2	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	exon	38600339	38600761	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	intron	38600762	38600853	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	CDS	38600854	38601026	1	+	2	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	exon	38600854	38601026	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	intron	38601027	38601162	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	CDS	38601163	38601281	1	+	0	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	exon	38601163	38601281	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	intron	38601282	38601448	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	CDS	38601449	38601857	1	+	1	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	exon	38601449	38601857	.	+	.	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
Phchi.S1	AUGUSTUS	stop_codon	38601858	38601860	.	+	0	transcript_id "Phchi.S1G607200.t1"; gene_id "Phchi.S1G607200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14007.t1 is derived from g12474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10259408	10260916	.	+	.	Phchi.S3G132600
Phchi.S3	AUGUSTUS	transcript	10259408	10260916	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	start_codon	10259408	10259410	.	+	0	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	CDS	10259408	10259511	0.75	+	0	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	exon	10259408	10259511	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	intron	10259512	10259607	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	CDS	10259608	10259751	1	+	1	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	exon	10259608	10259751	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	intron	10259752	10259836	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	CDS	10259837	10259967	1	+	1	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	exon	10259837	10259967	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	intron	10259968	10260059	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	CDS	10260060	10260200	1	+	2	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	exon	10260060	10260200	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	intron	10260201	10260290	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	CDS	10260291	10260916	1	+	2	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	exon	10260291	10260916	.	+	.	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
Phchi.S3	AUGUSTUS	stop_codon	10260917	10260919	.	+	0	transcript_id "Phchi.S3G132600.t1"; gene_id "Phchi.S3G132600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5990.t1 is derived from g3161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20273613	20279023	.	+	.	Phchi.S1G314900
Phchi.S1	AUGUSTUS	transcript	20273613	20279023	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	start_codon	20273613	20273615	.	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20273613	20273884	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20273613	20273884	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20273885	20274010	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20274011	20274143	1	+	1	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20274011	20274143	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20274144	20274244	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20274245	20274381	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20274245	20274381	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20274382	20274504	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20274505	20274550	1	+	1	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20274505	20274550	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20274551	20274640	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20274641	20274853	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20274641	20274853	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20274854	20274946	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20274947	20275450	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20274947	20275450	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20275451	20275557	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20275558	20275692	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20275558	20275692	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20275693	20275799	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20275800	20276015	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20275800	20276015	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20276016	20276136	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20276137	20276226	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20276137	20276226	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20276227	20276331	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20276332	20276582	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20276332	20276582	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20276583	20276699	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20276700	20276788	1	+	1	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20276700	20276788	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20276789	20276988	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20276989	20277029	1	+	2	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20276989	20277029	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20277030	20277136	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20277137	20277167	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20277137	20277167	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20277168	20277271	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20277272	20277394	0.99	+	2	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20277272	20277394	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20277395	20277496	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20277497	20277717	0.99	+	2	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20277497	20277717	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20277718	20277937	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20277938	20278033	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20277938	20278033	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20278034	20278187	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20278188	20278300	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20278188	20278300	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20278301	20278392	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20278393	20278528	1	+	1	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20278393	20278528	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20278529	20278635	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20278636	20278740	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20278636	20278740	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	intron	20278741	20278825	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	CDS	20278826	20279023	1	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	exon	20278826	20279023	.	+	.	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
Phchi.S1	AUGUSTUS	stop_codon	20279024	20279026	.	+	0	transcript_id "Phchi.S1G314900.t1"; gene_id "Phchi.S1G314900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10762.t1 is derived from g14812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1991137	1993889	.	-	.	Phchi.S4G034400
Phchi.S4	AUGUSTUS	transcript	1991137	1993889	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	stop_codon	1991134	1991136	.	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1991137	1991187	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1991137	1991187	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1991188	1991271	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1991272	1991326	1	-	1	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1991272	1991326	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1991327	1991417	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1991418	1991503	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1991418	1991503	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1991504	1991590	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1991591	1991724	1	-	2	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1991591	1991724	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1991725	1991915	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1991916	1992023	1	-	2	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1991916	1992023	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1992024	1992110	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1992111	1992180	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1992111	1992180	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1992181	1992259	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1992260	1992337	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1992260	1992337	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1992338	1992486	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1992487	1992606	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1992487	1992606	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1992607	1992783	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1992784	1992843	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1992784	1992843	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1992844	1992935	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1992936	1992980	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1992936	1992980	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1992981	1993103	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1993104	1993181	0.99	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1993104	1993181	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1993182	1993295	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1993296	1993352	0.99	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1993296	1993352	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1993353	1993447	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1993448	1993564	1	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1993448	1993564	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	intron	1993565	1993736	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	CDS	1993737	1993889	0.37	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	exon	1993737	1993889	.	-	.	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
Phchi.S4	AUGUSTUS	start_codon	1993887	1993889	.	-	0	transcript_id "Phchi.S4G034400.t1"; gene_id "Phchi.S4G034400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15621.t1 is derived from g14090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20333632	20336020	.	+	.	Phchi.S3G294000
Phchi.S3	AUGUSTUS	transcript	20333632	20336020	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	start_codon	20333632	20333634	.	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20333632	20333678	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20333632	20333678	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20333679	20333816	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20333817	20334014	1	+	1	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20333817	20334014	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20334015	20334104	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20334105	20334189	1	+	1	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20334105	20334189	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20334190	20334331	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20334332	20334406	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20334332	20334406	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20334407	20334491	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20334492	20334569	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20334492	20334569	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20334570	20334723	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20334724	20334777	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20334724	20334777	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20334778	20334872	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20334873	20334949	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20334873	20334949	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20334950	20335085	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20335086	20335167	1	+	1	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20335086	20335167	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20335168	20335237	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20335238	20335354	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20335238	20335354	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20335355	20335436	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20335437	20335552	1	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20335437	20335552	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20335553	20335658	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20335659	20335728	0.99	+	1	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20335659	20335728	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	intron	20335729	20335831	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	CDS	20335832	20336020	0.98	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	exon	20335832	20336020	.	+	.	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
Phchi.S3	AUGUSTUS	stop_codon	20336021	20336023	.	+	0	transcript_id "Phchi.S3G294000.t1"; gene_id "Phchi.S3G294000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1967.t1 is derived from g8887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4069408	4071167	.	+	.	Phchi.S5G057600
Phchi.S5	AUGUSTUS	transcript	4069530	4071167	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	start_codon	4069530	4069532	.	+	0	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4069530	4069565	0.99	+	0	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4069530	4069565	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4069566	4069866	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4069867	4069995	1	+	0	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4069867	4069995	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4069996	4070088	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070089	4070181	1	+	0	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070089	4070181	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4070182	4070329	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070330	4070429	1	+	0	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070330	4070429	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4070430	4070580	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070581	4070706	1	+	2	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070581	4070706	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4070707	4070853	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070854	4071167	0.78	+	2	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070854	4071167	.	+	.	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	stop_codon	4071168	4071170	.	+	0	transcript_id "Phchi.S5G057600.t1"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	transcript	4069408	4071167	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	start_codon	4069408	4069410	.	+	0	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4069408	4069565	0.75	+	0	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4069408	4069565	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4069566	4069657	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4069658	4069721	0.31	+	1	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4069658	4069721	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4069722	4069866	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4069867	4069995	0.34	+	0	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4069867	4069995	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4069996	4070088	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070089	4070181	1	+	0	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070089	4070181	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4070182	4070329	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070330	4070429	1	+	0	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070330	4070429	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4070430	4070580	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070581	4070706	1	+	2	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070581	4070706	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	intron	4070707	4070853	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	CDS	4070854	4071167	0.73	+	2	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	exon	4070854	4071167	.	+	.	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
Phchi.S5	AUGUSTUS	stop_codon	4071168	4071170	.	+	0	transcript_id "Phchi.S5G057600.t2"; gene_id "Phchi.S5G057600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3861.t1 is derived from g1030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6080182	6082146	.	-	.	Phchi.S1G102000
Phchi.S1	AUGUSTUS	transcript	6080182	6082146	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	stop_codon	6080179	6080181	.	-	0	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6080182	6080699	1	-	2	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6080182	6080699	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	intron	6080700	6080794	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6080795	6080970	1	-	1	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6080795	6080970	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	intron	6080971	6081147	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6081148	6081302	1	-	0	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6081148	6081302	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	intron	6081303	6081459	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6081460	6081629	1	-	2	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6081460	6081629	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	intron	6081630	6081723	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6081724	6081788	1	-	1	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6081724	6081788	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	intron	6081789	6081870	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6081871	6081890	1	-	0	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6081871	6081890	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	intron	6081891	6082131	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	CDS	6082132	6082146	1	-	0	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	exon	6082132	6082146	.	-	.	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
Phchi.S1	AUGUSTUS	start_codon	6082144	6082146	.	-	0	transcript_id "Phchi.S1G102000.t1"; gene_id "Phchi.S1G102000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6716.t1 is derived from g3888.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24691936	24693756	.	-	.	Phchi.S1G387500
Phchi.S1	AUGUSTUS	transcript	24691936	24693756	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	stop_codon	24691933	24691935	.	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24691936	24691940	0.94	-	2	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24691936	24691940	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24691941	24692270	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692271	24692393	0.94	-	2	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692271	24692393	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692394	24692479	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692480	24692504	0.96	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692480	24692504	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692505	24692642	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692643	24692687	0.99	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692643	24692687	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692688	24692808	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692809	24692878	1	-	1	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692809	24692878	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692879	24692972	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692973	24693000	0.99	-	2	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692973	24693000	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693001	24693085	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693086	24693134	0.99	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693086	24693134	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693135	24693298	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693299	24693358	1	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693299	24693358	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693359	24693456	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693457	24693528	1	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693457	24693528	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693529	24693624	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693625	24693756	0.9	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693625	24693756	.	-	.	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	start_codon	24693754	24693756	.	-	0	transcript_id "Phchi.S1G387500.t1"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	transcript	24691936	24693756	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	stop_codon	24691933	24691935	.	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24691936	24691940	0.91	-	2	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24691936	24691940	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24691941	24692270	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692271	24692393	0.91	-	2	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692271	24692393	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692394	24692479	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692480	24692504	0.93	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692480	24692504	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692505	24692642	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692643	24692687	0.98	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692643	24692687	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692688	24692808	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692809	24692878	1	-	1	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692809	24692878	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24692879	24692972	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24692973	24693067	1	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24692973	24693067	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693068	24693298	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693299	24693358	1	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693299	24693358	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693359	24693456	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693457	24693528	1	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693457	24693528	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	intron	24693529	24693624	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	CDS	24693625	24693756	0.88	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	exon	24693625	24693756	.	-	.	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
Phchi.S1	AUGUSTUS	start_codon	24693754	24693756	.	-	0	transcript_id "Phchi.S1G387500.t2"; gene_id "Phchi.S1G387500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13337.t1 is derived from g11803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6144357	6147293	.	+	.	Phchi.S3G065600
Phchi.S3	AUGUSTUS	transcript	6144357	6147293	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	start_codon	6144357	6144359	.	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6144357	6144591	0.52	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6144357	6144591	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6144592	6144700	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6144701	6144777	1	+	2	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6144701	6144777	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6144778	6144862	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6144863	6144946	1	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6144863	6144946	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6144947	6145042	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6145043	6145156	1	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6145043	6145156	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6145157	6145253	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6145254	6145337	1	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6145254	6145337	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6145338	6145464	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6145465	6145536	1	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6145465	6145536	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6145537	6145642	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6145643	6145710	0.99	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6145643	6145710	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6145711	6145921	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6145922	6146009	0.99	+	1	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6145922	6146009	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6146010	6146123	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6146124	6146197	1	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6146124	6146197	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6146198	6146286	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6146287	6146677	1	+	1	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6146287	6146677	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6146678	6146849	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6146850	6146896	0.95	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6146850	6146896	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6146897	6146997	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6146998	6147088	1	+	1	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6146998	6147088	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	intron	6147089	6147167	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	CDS	6147168	6147293	1	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	exon	6147168	6147293	.	+	.	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
Phchi.S3	AUGUSTUS	stop_codon	6147294	6147296	.	+	0	transcript_id "Phchi.S3G065600.t1"; gene_id "Phchi.S3G065600"
# This transcript jg3175.t2 is derived from g344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3176.t1 is derived from g345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2111286	2112871	.	+	.	Phchi.S1G033500
Phchi.S1	AUGUSTUS	transcript	2111286	2112871	.	+	.	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	start_codon	2111286	2111288	.	+	0	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	CDS	2111286	2112067	0.74	+	0	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	exon	2111286	2112067	.	+	.	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	intron	2112068	2112237	.	+	.	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	CDS	2112238	2112871	1	+	1	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	exon	2112238	2112871	.	+	.	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
Phchi.S1	AUGUSTUS	stop_codon	2112872	2112874	.	+	0	transcript_id "Phchi.S1G033500.t1"; gene_id "Phchi.S1G033500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg264.t1 is derived from g10046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1855945	1856785	.	-	.	Phchi.S6G022300
Phchi.S6	AUGUSTUS	transcript	1855945	1856785	.	-	.	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	stop_codon	1855942	1855944	.	-	0	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	CDS	1855945	1856034	0.76	-	0	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	exon	1855945	1856034	.	-	.	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	intron	1856035	1856128	.	-	.	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	CDS	1856129	1856785	0.82	-	0	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	exon	1856129	1856785	.	-	.	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
Phchi.S6	AUGUSTUS	start_codon	1856783	1856785	.	-	0	transcript_id "Phchi.S6G022300.t1"; gene_id "Phchi.S6G022300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6927.t1 is derived from g4099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26028701	26029787	.	-	.	Phchi.S1G408600
Phchi.S1	AUGUSTUS	transcript	26028701	26029787	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	stop_codon	26028698	26028700	.	-	0	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	CDS	26028701	26028730	0.99	-	0	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	exon	26028701	26028730	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	intron	26028731	26028990	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	CDS	26028991	26029080	0.99	-	0	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	exon	26028991	26029080	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	intron	26029081	26029197	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	CDS	26029198	26029285	0.99	-	1	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	exon	26029198	26029285	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	intron	26029286	26029639	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	CDS	26029640	26029678	0.99	-	1	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	exon	26029640	26029678	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	intron	26029679	26029782	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	CDS	26029783	26029787	0.99	-	0	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	exon	26029783	26029787	.	-	.	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
Phchi.S1	AUGUSTUS	start_codon	26029785	26029787	.	-	0	transcript_id "Phchi.S1G408600.t1"; gene_id "Phchi.S1G408600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4786.t1 is derived from g1956.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12811690	12813138	.	+	.	Phchi.S1G194500
Phchi.S1	AUGUSTUS	transcript	12811690	12813138	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	start_codon	12811690	12811692	.	+	0	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	CDS	12811690	12811737	0.64	+	0	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	exon	12811690	12811737	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	intron	12811738	12811844	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	CDS	12811845	12811941	0.98	+	0	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	exon	12811845	12811941	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	intron	12811942	12812464	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	CDS	12812465	12812569	1	+	2	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	exon	12812465	12812569	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	intron	12812570	12812655	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	CDS	12812656	12812813	1	+	2	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	exon	12812656	12812813	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	intron	12812814	12812908	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	CDS	12812909	12813010	1	+	0	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	exon	12812909	12813010	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	intron	12813011	12813096	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	CDS	12813097	12813138	1	+	0	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	exon	12813097	12813138	.	+	.	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
Phchi.S1	AUGUSTUS	stop_codon	12813139	12813141	.	+	0	transcript_id "Phchi.S1G194500.t1"; gene_id "Phchi.S1G194500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg374.t1 is derived from g10156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2699551	2701850	.	+	.	Phchi.S6G033300
Phchi.S6	AUGUSTUS	transcript	2699551	2701850	.	+	.	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	start_codon	2699551	2699553	.	+	0	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	CDS	2699551	2700541	0.49	+	0	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	exon	2699551	2700541	.	+	.	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	intron	2700542	2700648	.	+	.	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	CDS	2700649	2701850	0.85	+	2	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	exon	2700649	2701850	.	+	.	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	stop_codon	2701851	2701853	.	+	0	transcript_id "Phchi.S6G033300.t1"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	transcript	2699551	2701269	.	+	.	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	start_codon	2699551	2699553	.	+	0	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	CDS	2699551	2700541	0.51	+	0	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	exon	2699551	2700541	.	+	.	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	intron	2700542	2700648	.	+	.	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	CDS	2700649	2701166	0.51	+	2	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	exon	2700649	2701166	.	+	.	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	intron	2701167	2701254	.	+	.	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	CDS	2701255	2701269	0.78	+	0	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	exon	2701255	2701269	.	+	.	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	stop_codon	2701270	2701272	.	+	0	transcript_id "Phchi.S6G033300.t2"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	transcript	2699551	2700702	.	+	.	transcript_id "Phchi.S6G033300.t3"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	start_codon	2699551	2699553	.	+	0	transcript_id "Phchi.S6G033300.t3"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	CDS	2699551	2700702	0.69	+	0	transcript_id "Phchi.S6G033300.t3"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	exon	2699551	2700702	.	+	.	transcript_id "Phchi.S6G033300.t3"; gene_id "Phchi.S6G033300"
Phchi.S6	AUGUSTUS	stop_codon	2700703	2700705	.	+	0	transcript_id "Phchi.S6G033300.t3"; gene_id "Phchi.S6G033300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9911.t1 is derived from g7087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44397051	44398094	.	-	.	Phchi.S1G707000
Phchi.S1	AUGUSTUS	transcript	44397051	44398094	.	-	.	transcript_id "Phchi.S1G707000.t1"; gene_id "Phchi.S1G707000"
Phchi.S1	AUGUSTUS	stop_codon	44397048	44397050	.	-	0	transcript_id "Phchi.S1G707000.t1"; gene_id "Phchi.S1G707000"
Phchi.S1	AUGUSTUS	CDS	44397051	44398094	0.83	-	0	transcript_id "Phchi.S1G707000.t1"; gene_id "Phchi.S1G707000"
Phchi.S1	AUGUSTUS	exon	44397051	44398094	.	-	.	transcript_id "Phchi.S1G707000.t1"; gene_id "Phchi.S1G707000"
Phchi.S1	AUGUSTUS	start_codon	44398092	44398094	.	-	0	transcript_id "Phchi.S1G707000.t1"; gene_id "Phchi.S1G707000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9547.t1 is derived from g6723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42411623	42413317	.	+	.	Phchi.S1G670600
Phchi.S1	AUGUSTUS	transcript	42411623	42413317	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	start_codon	42411623	42411625	.	+	0	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	CDS	42411623	42412245	0.31	+	0	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	exon	42411623	42412245	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	intron	42412246	42412319	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	CDS	42412320	42412921	0.69	+	1	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	exon	42412320	42412921	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	intron	42412922	42413005	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	CDS	42413006	42413184	1	+	2	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	exon	42413006	42413184	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	intron	42413185	42413311	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	CDS	42413312	42413317	1	+	0	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	exon	42413312	42413317	.	+	.	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
Phchi.S1	AUGUSTUS	stop_codon	42413318	42413320	.	+	0	transcript_id "Phchi.S1G670600.t1"; gene_id "Phchi.S1G670600"
# This transcript jg2266.t2 is derived from g9186.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2267.t1 is derived from g9187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5772029	5772298	.	-	.	Phchi.S5G087600
Phchi.S5	AUGUSTUS	transcript	5772029	5772298	.	-	.	transcript_id "Phchi.S5G087600.t1"; gene_id "Phchi.S5G087600"
Phchi.S5	AUGUSTUS	stop_codon	5772026	5772028	.	-	0	transcript_id "Phchi.S5G087600.t1"; gene_id "Phchi.S5G087600"
Phchi.S5	AUGUSTUS	CDS	5772029	5772298	0.72	-	0	transcript_id "Phchi.S5G087600.t1"; gene_id "Phchi.S5G087600"
Phchi.S5	AUGUSTUS	exon	5772029	5772298	.	-	.	transcript_id "Phchi.S5G087600.t1"; gene_id "Phchi.S5G087600"
Phchi.S5	AUGUSTUS	start_codon	5772296	5772298	.	-	0	transcript_id "Phchi.S5G087600.t1"; gene_id "Phchi.S5G087600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14418.t1 is derived from g12886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12721166	12723546	.	-	.	Phchi.S3G173700
Phchi.S3	AUGUSTUS	transcript	12721166	12723546	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	stop_codon	12721163	12721165	.	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12721166	12721301	0.99	-	1	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12721166	12721301	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12721302	12721412	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12721413	12721576	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12721413	12721576	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12721577	12721668	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12721669	12721797	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12721669	12721797	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12721798	12721884	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12721885	12721938	0.77	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12721885	12721938	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12721939	12722017	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12722018	12722128	0.47	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12722018	12722128	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12722129	12722222	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12722223	12722246	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12722223	12722246	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12722247	12722367	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12722368	12722442	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12722368	12722442	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12722443	12722534	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12722535	12722627	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12722535	12722627	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12722628	12722754	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12722755	12722881	1	-	1	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12722755	12722881	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12722882	12722982	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12722983	12723071	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12722983	12723071	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12723072	12723181	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12723182	12723277	1	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12723182	12723277	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12723278	12723362	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12723363	12723419	0.97	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12723363	12723419	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	intron	12723420	12723498	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	CDS	12723499	12723546	0.77	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	exon	12723499	12723546	.	-	.	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
Phchi.S3	AUGUSTUS	start_codon	12723544	12723546	.	-	0	transcript_id "Phchi.S3G173700.t1"; gene_id "Phchi.S3G173700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2550.t1 is derived from g9470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7288076	7290285	.	-	.	Phchi.S5G115900
Phchi.S5	AUGUSTUS	transcript	7288076	7290285	.	-	.	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	stop_codon	7288073	7288075	.	-	0	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	CDS	7288076	7289752	0.83	-	0	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	exon	7288076	7289752	.	-	.	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	intron	7289753	7289841	.	-	.	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	CDS	7289842	7290285	0.68	-	0	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	exon	7289842	7290285	.	-	.	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	start_codon	7290283	7290285	.	-	0	transcript_id "Phchi.S5G115900.t1"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	transcript	7288076	7289839	.	-	.	transcript_id "Phchi.S5G115900.t2"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	stop_codon	7288073	7288075	.	-	0	transcript_id "Phchi.S5G115900.t2"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	CDS	7288076	7289839	0.66	-	0	transcript_id "Phchi.S5G115900.t2"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	exon	7288076	7289839	.	-	.	transcript_id "Phchi.S5G115900.t2"; gene_id "Phchi.S5G115900"
Phchi.S5	AUGUSTUS	start_codon	7289837	7289839	.	-	0	transcript_id "Phchi.S5G115900.t2"; gene_id "Phchi.S5G115900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6020.t1 is derived from g3191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20468286	20471818	.	-	.	Phchi.S1G317900
Phchi.S1	AUGUSTUS	transcript	20468286	20471818	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	stop_codon	20468283	20468285	.	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	CDS	20468286	20468723	0.9	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	exon	20468286	20468723	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	intron	20468724	20468825	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	CDS	20468826	20469311	0.88	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	exon	20468826	20469311	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	intron	20469312	20469398	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	CDS	20469399	20469521	1	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	exon	20469399	20469521	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	intron	20469522	20469605	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	CDS	20469606	20469860	1	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	exon	20469606	20469860	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	intron	20469861	20469955	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	CDS	20469956	20471353	1	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	exon	20469956	20471353	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	intron	20471354	20471470	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	CDS	20471471	20471818	0.4	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	exon	20471471	20471818	.	-	.	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
Phchi.S1	AUGUSTUS	start_codon	20471816	20471818	.	-	0	transcript_id "Phchi.S1G317900.t1"; gene_id "Phchi.S1G317900"
# This transcript jg13993.t2 is derived from g12460.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13993.t3 is derived from g12460.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13994.t1 is derived from g12461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10142259	10143672	.	-	.	Phchi.S3G131300
Phchi.S3	AUGUSTUS	transcript	10142259	10143672	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	stop_codon	10142256	10142258	.	-	0	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	CDS	10142259	10142639	0.42	-	0	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	exon	10142259	10142639	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	intron	10142640	10142736	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	CDS	10142737	10143047	0.97	-	2	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	exon	10142737	10143047	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	intron	10143048	10143152	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	CDS	10143153	10143279	0.97	-	0	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	exon	10143153	10143279	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	intron	10143280	10143361	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	CDS	10143362	10143474	1	-	2	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	exon	10143362	10143474	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	intron	10143475	10143572	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	CDS	10143573	10143672	0.69	-	0	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	exon	10143573	10143672	.	-	.	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
Phchi.S3	AUGUSTUS	start_codon	10143670	10143672	.	-	0	transcript_id "Phchi.S3G131300.t1"; gene_id "Phchi.S3G131300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5386.t1 is derived from g2556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16630930	16631249	.	-	.	Phchi.S1G254500
Phchi.S1	AUGUSTUS	transcript	16630930	16631249	.	-	.	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	stop_codon	16630927	16630929	.	-	0	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	CDS	16630930	16630965	0.83	-	0	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	exon	16630930	16630965	.	-	.	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	intron	16630966	16631057	.	-	.	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	CDS	16631058	16631249	0.99	-	0	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	exon	16631058	16631249	.	-	.	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
Phchi.S1	AUGUSTUS	start_codon	16631247	16631249	.	-	0	transcript_id "Phchi.S1G254500.t1"; gene_id "Phchi.S1G254500"
# This transcript jg2328.t2 is derived from g9248.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2329.t1 is derived from g9249.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6197909	6199987	.	-	.	Phchi.S5G093800
Phchi.S5	AUGUSTUS	transcript	6197909	6199987	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	stop_codon	6197906	6197908	.	-	0	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6197909	6197921	0.94	-	1	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6197909	6197921	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6197922	6198090	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6198091	6198759	0.9	-	1	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6198091	6198759	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6198760	6198886	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6198887	6199053	0.97	-	0	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6198887	6199053	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199054	6199226	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199227	6199335	0.97	-	1	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199227	6199335	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199336	6199565	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199566	6199595	0.96	-	1	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199566	6199595	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199596	6199677	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199678	6199713	0.87	-	1	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199678	6199713	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199714	6199859	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199860	6199987	0.96	-	0	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199860	6199987	.	-	.	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	start_codon	6199985	6199987	.	-	0	transcript_id "Phchi.S5G093800.t1"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	transcript	6197909	6199901	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	stop_codon	6197906	6197908	.	-	0	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6197909	6197921	0.97	-	1	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6197909	6197921	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6197922	6198090	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6198091	6198759	0.95	-	1	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6198091	6198759	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6198760	6198886	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6198887	6199053	0.87	-	0	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6198887	6199053	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199054	6199226	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199227	6199335	0.87	-	1	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199227	6199335	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199336	6199565	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199566	6199595	0.88	-	1	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199566	6199595	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199596	6199685	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199686	6199708	0.88	-	0	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199686	6199708	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	intron	6199709	6199859	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	CDS	6199860	6199901	0.73	-	0	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	exon	6199860	6199901	.	-	.	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
Phchi.S5	AUGUSTUS	start_codon	6199899	6199901	.	-	0	transcript_id "Phchi.S5G093800.t2"; gene_id "Phchi.S5G093800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12461.t1 is derived from g8138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	24371388	24373024	.	-	.	Phchi.S2G054100
Phchi.S2	AUGUSTUS	transcript	24371388	24373024	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	stop_codon	24371385	24371387	.	-	0	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	CDS	24371388	24372563	0.26	-	0	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	exon	24371388	24372563	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	intron	24372564	24372689	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	CDS	24372690	24372745	0.27	-	2	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	exon	24372690	24372745	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	intron	24372746	24372889	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	CDS	24372890	24372929	0.15	-	0	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	exon	24372890	24372929	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	intron	24372930	24373021	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	CDS	24373022	24373024	0.14	-	0	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	exon	24373022	24373024	.	-	.	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
Phchi.S2	AUGUSTUS	start_codon	24373022	24373024	.	-	0	transcript_id "Phchi.S2G054100.t1"; gene_id "Phchi.S2G054100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8779.t1 is derived from g5954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37919878	37921392	.	-	.	Phchi.S1G593800
Phchi.S1	AUGUSTUS	transcript	37919878	37921392	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	stop_codon	37919875	37919877	.	-	0	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37919878	37919949	1	-	0	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37919878	37919949	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	intron	37919950	37920070	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37920071	37920157	1	-	0	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37920071	37920157	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	intron	37920158	37920271	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37920272	37920414	1	-	2	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37920272	37920414	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	intron	37920415	37920568	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37920569	37920698	1	-	0	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37920569	37920698	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	intron	37920699	37920814	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37920815	37920896	1	-	1	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37920815	37920896	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	intron	37920897	37920992	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37920993	37921100	1	-	1	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37920993	37921100	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	intron	37921101	37921306	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	CDS	37921307	37921392	0.51	-	0	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	exon	37921307	37921392	.	-	.	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
Phchi.S1	AUGUSTUS	start_codon	37921390	37921392	.	-	0	transcript_id "Phchi.S1G593800.t1"; gene_id "Phchi.S1G593800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6301.t1 is derived from g3473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22167091	22167609	.	+	.	Phchi.S1G346000
Phchi.S1	AUGUSTUS	transcript	22167091	22167609	.	+	.	transcript_id "Phchi.S1G346000.t1"; gene_id "Phchi.S1G346000"
Phchi.S1	AUGUSTUS	start_codon	22167091	22167093	.	+	0	transcript_id "Phchi.S1G346000.t1"; gene_id "Phchi.S1G346000"
Phchi.S1	AUGUSTUS	CDS	22167091	22167609	0.84	+	0	transcript_id "Phchi.S1G346000.t1"; gene_id "Phchi.S1G346000"
Phchi.S1	AUGUSTUS	exon	22167091	22167609	.	+	.	transcript_id "Phchi.S1G346000.t1"; gene_id "Phchi.S1G346000"
Phchi.S1	AUGUSTUS	stop_codon	22167610	22167612	.	+	0	transcript_id "Phchi.S1G346000.t1"; gene_id "Phchi.S1G346000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg204.t1 is derived from g9986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1131630	1133071	.	+	.	Phchi.S6G016300
Phchi.S6	AUGUSTUS	transcript	1131630	1133071	.	+	.	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	start_codon	1131630	1131632	.	+	0	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	CDS	1131630	1132262	0.97	+	0	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	exon	1131630	1132262	.	+	.	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	intron	1132263	1132425	.	+	.	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	CDS	1132426	1132680	1	+	0	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	exon	1132426	1132680	.	+	.	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	intron	1132681	1132771	.	+	.	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	CDS	1132772	1133071	1	+	0	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	exon	1132772	1133071	.	+	.	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
Phchi.S6	AUGUSTUS	stop_codon	1133072	1133074	.	+	0	transcript_id "Phchi.S6G016300.t1"; gene_id "Phchi.S6G016300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4445.t1 is derived from g1614.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10546920	10547120	.	-	.	Phchi.S1G160400
Phchi.S1	AUGUSTUS	transcript	10546920	10547120	.	-	.	transcript_id "Phchi.S1G160400.t1"; gene_id "Phchi.S1G160400"
Phchi.S1	AUGUSTUS	stop_codon	10546917	10546919	.	-	0	transcript_id "Phchi.S1G160400.t1"; gene_id "Phchi.S1G160400"
Phchi.S1	AUGUSTUS	CDS	10546920	10547120	0.34	-	0	transcript_id "Phchi.S1G160400.t1"; gene_id "Phchi.S1G160400"
Phchi.S1	AUGUSTUS	exon	10546920	10547120	.	-	.	transcript_id "Phchi.S1G160400.t1"; gene_id "Phchi.S1G160400"
Phchi.S1	AUGUSTUS	start_codon	10547118	10547120	.	-	0	transcript_id "Phchi.S1G160400.t1"; gene_id "Phchi.S1G160400"
# This transcript jg2158.t2 is derived from g9078.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2159.t1 is derived from g9079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5102148	5103839	.	-	.	Phchi.S5G076800
Phchi.S5	AUGUSTUS	transcript	5102148	5103839	.	-	.	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	stop_codon	5102145	5102147	.	-	0	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	CDS	5102148	5103587	1	-	0	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	exon	5102148	5103587	.	-	.	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	intron	5103588	5103743	.	-	.	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	CDS	5103744	5103839	1	-	0	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	exon	5103744	5103839	.	-	.	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
Phchi.S5	AUGUSTUS	start_codon	5103837	5103839	.	-	0	transcript_id "Phchi.S5G076800.t1"; gene_id "Phchi.S5G076800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2464.t1 is derived from g9384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6791091	6792923	.	-	.	Phchi.S5G107300
Phchi.S5	AUGUSTUS	transcript	6791091	6792923	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	stop_codon	6791088	6791090	.	-	0	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	CDS	6791091	6791889	0.76	-	1	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	exon	6791091	6791889	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	intron	6791890	6791978	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	CDS	6791979	6792211	0.99	-	0	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	exon	6791979	6792211	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	intron	6792212	6792313	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	CDS	6792314	6792534	0.79	-	2	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	exon	6792314	6792534	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	intron	6792535	6792637	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	CDS	6792638	6792923	0.41	-	0	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	exon	6792638	6792923	.	-	.	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
Phchi.S5	AUGUSTUS	start_codon	6792921	6792923	.	-	0	transcript_id "Phchi.S5G107300.t1"; gene_id "Phchi.S5G107300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3886.t1 is derived from g1055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6206012	6207199	.	-	.	Phchi.S1G104500
Phchi.S1	AUGUSTUS	transcript	6206012	6207199	.	-	.	transcript_id "Phchi.S1G104500.t1"; gene_id "Phchi.S1G104500"
Phchi.S1	AUGUSTUS	stop_codon	6206009	6206011	.	-	0	transcript_id "Phchi.S1G104500.t1"; gene_id "Phchi.S1G104500"
Phchi.S1	AUGUSTUS	CDS	6206012	6207199	0.94	-	0	transcript_id "Phchi.S1G104500.t1"; gene_id "Phchi.S1G104500"
Phchi.S1	AUGUSTUS	exon	6206012	6207199	.	-	.	transcript_id "Phchi.S1G104500.t1"; gene_id "Phchi.S1G104500"
Phchi.S1	AUGUSTUS	start_codon	6207197	6207199	.	-	0	transcript_id "Phchi.S1G104500.t1"; gene_id "Phchi.S1G104500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4711.t1 is derived from g1881.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12424785	12425583	.	+	.	Phchi.S1G187000
Phchi.S1	AUGUSTUS	transcript	12424785	12425583	.	+	.	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	start_codon	12424785	12424787	.	+	0	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	CDS	12424785	12425313	0.34	+	0	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	exon	12424785	12425313	.	+	.	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	intron	12425314	12425554	.	+	.	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	CDS	12425555	12425583	0.52	+	2	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	exon	12425555	12425583	.	+	.	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	stop_codon	12425584	12425586	.	+	0	transcript_id "Phchi.S1G187000.t1"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	transcript	12424785	12425453	.	+	.	transcript_id "Phchi.S1G187000.t2"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	start_codon	12424785	12424787	.	+	0	transcript_id "Phchi.S1G187000.t2"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	CDS	12424785	12425453	0.52	+	0	transcript_id "Phchi.S1G187000.t2"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	exon	12424785	12425453	.	+	.	transcript_id "Phchi.S1G187000.t2"; gene_id "Phchi.S1G187000"
Phchi.S1	AUGUSTUS	stop_codon	12425454	12425456	.	+	0	transcript_id "Phchi.S1G187000.t2"; gene_id "Phchi.S1G187000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14525.t1 is derived from g12993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13310094	13310950	.	-	.	Phchi.S3G184400
Phchi.S3	AUGUSTUS	transcript	13310094	13310950	.	-	.	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	stop_codon	13310091	13310093	.	-	0	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	CDS	13310094	13310562	1	-	1	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	exon	13310094	13310562	.	-	.	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	intron	13310563	13310765	.	-	.	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	CDS	13310766	13310950	1	-	0	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	exon	13310766	13310950	.	-	.	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
Phchi.S3	AUGUSTUS	start_codon	13310948	13310950	.	-	0	transcript_id "Phchi.S3G184400.t1"; gene_id "Phchi.S3G184400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4572.t1 is derived from g1742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11164889	11167204	.	-	.	Phchi.S1G173100
Phchi.S1	AUGUSTUS	transcript	11164889	11167204	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	stop_codon	11164886	11164888	.	-	0	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11164889	11165296	0.72	-	0	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11164889	11165296	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11165297	11165395	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11165396	11165525	1	-	1	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11165396	11165525	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11165526	11165608	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11165609	11165898	0.59	-	0	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11165609	11165898	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11165899	11165986	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11165987	11166168	1	-	2	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11165987	11166168	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11166169	11166307	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11166308	11166527	1	-	0	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11166308	11166527	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11166528	11166668	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11166669	11166687	0.98	-	1	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11166669	11166687	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11166688	11166781	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11166782	11167042	0.93	-	1	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11166782	11167042	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11167043	11167127	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11167128	11167204	0.97	-	0	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11167128	11167204	.	-	.	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	start_codon	11167202	11167204	.	-	0	transcript_id "Phchi.S1G173100.t1"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	transcript	11164889	11165524	.	-	.	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	stop_codon	11164886	11164888	.	-	0	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11164889	11165296	0.8	-	0	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11164889	11165296	.	-	.	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	intron	11165297	11165395	.	-	.	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	CDS	11165396	11165524	0.55	-	0	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	exon	11165396	11165524	.	-	.	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
Phchi.S1	AUGUSTUS	start_codon	11165522	11165524	.	-	0	transcript_id "Phchi.S1G173100.t2"; gene_id "Phchi.S1G173100"
# This transcript jg4290.t2 is derived from g1459.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4291.t1 is derived from g1460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9448114	9448543	.	+	.	Phchi.S1G145000
Phchi.S1	AUGUSTUS	transcript	9448114	9448543	.	+	.	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	start_codon	9448114	9448116	.	+	0	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	CDS	9448114	9448122	0.99	+	0	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	exon	9448114	9448122	.	+	.	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	intron	9448123	9448220	.	+	.	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	CDS	9448221	9448277	1	+	0	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	exon	9448221	9448277	.	+	.	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	intron	9448278	9448369	.	+	.	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	CDS	9448370	9448543	1	+	0	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	exon	9448370	9448543	.	+	.	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
Phchi.S1	AUGUSTUS	stop_codon	9448544	9448546	.	+	0	transcript_id "Phchi.S1G145000.t1"; gene_id "Phchi.S1G145000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2916.t1 is derived from g85.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	477840	479641	.	-	.	Phchi.S1G007500
Phchi.S1	AUGUSTUS	transcript	477840	479641	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	stop_codon	477837	477839	.	-	0	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	477840	478060	1	-	2	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	477840	478060	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478061	478156	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478157	478271	1	-	0	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478157	478271	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478272	478376	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478377	478475	1	-	0	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478377	478475	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478476	478587	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478588	478694	1	-	2	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478588	478694	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478695	478793	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478794	478925	1	-	2	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478794	478925	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478926	479073	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	479074	479128	0.9	-	0	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	479074	479128	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	479129	479386	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	479387	479641	0.85	-	0	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	479387	479641	.	-	.	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	start_codon	479639	479641	.	-	0	transcript_id "Phchi.S1G007500.t1"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	transcript	477840	479641	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	stop_codon	477837	477839	.	-	0	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	477840	478060	1	-	2	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	477840	478060	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478061	478156	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478157	478271	1	-	0	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478157	478271	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478272	478376	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478377	478475	1	-	0	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478377	478475	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478476	478587	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478588	478694	1	-	2	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478588	478694	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478695	478793	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	478794	478918	1	-	1	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	478794	478918	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	478919	479073	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	479074	479279	0.76	-	0	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	479074	479279	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	intron	479280	479386	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	CDS	479387	479641	0.75	-	0	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	exon	479387	479641	.	-	.	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
Phchi.S1	AUGUSTUS	start_codon	479639	479641	.	-	0	transcript_id "Phchi.S1G007500.t2"; gene_id "Phchi.S1G007500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg401.t1 is derived from g10183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2888790	2890901	.	+	.	Phchi.S6G036000
Phchi.S6	AUGUSTUS	transcript	2888790	2890901	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	start_codon	2888790	2888792	.	+	0	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	CDS	2888790	2888800	0.96	+	0	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	exon	2888790	2888800	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	intron	2888801	2888897	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	CDS	2888898	2890606	0.86	+	1	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	exon	2888898	2890606	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	intron	2890607	2890749	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	CDS	2890750	2890797	0.57	+	2	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	exon	2890750	2890797	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	intron	2890798	2890884	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	CDS	2890885	2890901	0.14	+	2	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	exon	2890885	2890901	.	+	.	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
Phchi.S6	AUGUSTUS	stop_codon	2890902	2890904	.	+	0	transcript_id "Phchi.S6G036000.t1"; gene_id "Phchi.S6G036000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3128.t1 is derived from g297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1871086	1873474	.	+	.	Phchi.S1G028700
Phchi.S1	AUGUSTUS	transcript	1871086	1873474	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	start_codon	1871086	1871088	.	+	0	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	CDS	1871086	1871215	1	+	0	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	exon	1871086	1871215	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	intron	1871216	1871437	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	CDS	1871438	1871634	1	+	2	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	exon	1871438	1871634	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	intron	1871635	1871739	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	CDS	1871740	1871929	0.99	+	0	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	exon	1871740	1871929	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	intron	1871930	1872071	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	CDS	1872072	1872463	1	+	2	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	exon	1872072	1872463	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	intron	1872464	1872800	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	CDS	1872801	1873067	0.73	+	0	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	exon	1872801	1873067	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	intron	1873068	1873177	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	CDS	1873178	1873474	0.72	+	0	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	exon	1873178	1873474	.	+	.	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
Phchi.S1	AUGUSTUS	stop_codon	1873475	1873477	.	+	0	transcript_id "Phchi.S1G028700.t1"; gene_id "Phchi.S1G028700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11606.t1 is derived from g15657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7303341	7307099	.	-	.	Phchi.S4G118800
Phchi.S4	AUGUSTUS	transcript	7303341	7307099	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	stop_codon	7303338	7303340	.	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7303341	7303454	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7303341	7303454	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7303455	7303534	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7303535	7303663	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7303535	7303663	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7303664	7303738	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7303739	7303825	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7303739	7303825	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7303826	7303922	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7303923	7304114	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7303923	7304114	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7304115	7304207	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7304208	7304384	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7304208	7304384	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7304385	7304492	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7304493	7304736	1	-	1	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7304493	7304736	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7304737	7304822	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7304823	7304932	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7304823	7304932	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7304933	7305038	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7305039	7305139	1	-	2	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7305039	7305139	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7305140	7305224	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7305225	7305288	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7305225	7305288	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7305289	7305389	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7305390	7305479	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7305390	7305479	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7305480	7305558	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7305559	7305657	1	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7305559	7305657	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7305658	7305806	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7305807	7305886	1	-	2	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7305807	7305886	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7305887	7306159	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7306160	7306179	0.98	-	1	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7306160	7306179	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7306180	7306328	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7306329	7306416	0.33	-	2	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7306329	7306416	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7306417	7306612	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7306613	7306622	0.6	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7306613	7306622	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	intron	7306623	7306949	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	CDS	7306950	7307099	0.47	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	exon	7306950	7307099	.	-	.	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
Phchi.S4	AUGUSTUS	start_codon	7307097	7307099	.	-	0	transcript_id "Phchi.S4G118800.t1"; gene_id "Phchi.S4G118800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9808.t1 is derived from g6984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43835078	43835530	.	-	.	Phchi.S1G696700
Phchi.S1	AUGUSTUS	transcript	43835078	43835530	.	-	.	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	stop_codon	43835075	43835077	.	-	0	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	CDS	43835078	43835191	1	-	0	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	exon	43835078	43835191	.	-	.	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	intron	43835192	43835329	.	-	.	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	CDS	43835330	43835372	0.88	-	1	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	exon	43835330	43835372	.	-	.	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	intron	43835373	43835486	.	-	.	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	CDS	43835487	43835530	0.9	-	0	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	exon	43835487	43835530	.	-	.	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
Phchi.S1	AUGUSTUS	start_codon	43835528	43835530	.	-	0	transcript_id "Phchi.S1G696700.t1"; gene_id "Phchi.S1G696700"
# This transcript jg15306.t2 is derived from g13774.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15307.t1 is derived from g13775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18320516	18321456	.	+	.	Phchi.S3G262600
Phchi.S3	AUGUSTUS	transcript	18320516	18321456	.	+	.	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	start_codon	18320516	18320518	.	+	0	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	CDS	18320516	18320665	1	+	0	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	exon	18320516	18320665	.	+	.	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	intron	18320666	18320821	.	+	.	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	CDS	18320822	18320870	1	+	0	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	exon	18320822	18320870	.	+	.	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	intron	18320871	18320971	.	+	.	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	CDS	18320972	18321456	0.9	+	2	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	exon	18320972	18321456	.	+	.	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
Phchi.S3	AUGUSTUS	stop_codon	18321457	18321459	.	+	0	transcript_id "Phchi.S3G262600.t1"; gene_id "Phchi.S3G262600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg462.t1 is derived from g10244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3249646	3250620	.	+	.	Phchi.S6G042100
Phchi.S6	AUGUSTUS	transcript	3249646	3250620	.	+	.	transcript_id "Phchi.S6G042100.t1"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	start_codon	3249646	3249648	.	+	0	transcript_id "Phchi.S6G042100.t1"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	CDS	3249646	3250620	0.98	+	0	transcript_id "Phchi.S6G042100.t1"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	exon	3249646	3250620	.	+	.	transcript_id "Phchi.S6G042100.t1"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	stop_codon	3250621	3250623	.	+	0	transcript_id "Phchi.S6G042100.t1"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	transcript	3249646	3250544	.	+	.	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	start_codon	3249646	3249648	.	+	0	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	CDS	3249646	3250433	0.4	+	0	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	exon	3249646	3250433	.	+	.	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	intron	3250434	3250492	.	+	.	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	CDS	3250493	3250544	0.39	+	1	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	exon	3250493	3250544	.	+	.	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
Phchi.S6	AUGUSTUS	stop_codon	3250545	3250547	.	+	0	transcript_id "Phchi.S6G042100.t2"; gene_id "Phchi.S6G042100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14077.t1 is derived from g12544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10677238	10680028	.	-	.	Phchi.S3G139600
Phchi.S3	AUGUSTUS	transcript	10677238	10680028	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	stop_codon	10677235	10677237	.	-	0	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10677238	10677304	1	-	1	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10677238	10677304	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	intron	10677305	10677379	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10677380	10677584	1	-	2	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10677380	10677584	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	intron	10677585	10677778	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10677779	10677837	1	-	1	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10677779	10677837	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	intron	10677838	10677950	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10677951	10678111	1	-	0	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10677951	10678111	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	intron	10678112	10678202	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10678203	10678685	0.95	-	0	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10678203	10678685	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	intron	10678686	10678802	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10678803	10679314	0.94	-	2	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10678803	10679314	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	intron	10679315	10679415	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	CDS	10679416	10680028	1	-	0	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	exon	10679416	10680028	.	-	.	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
Phchi.S3	AUGUSTUS	start_codon	10680026	10680028	.	-	0	transcript_id "Phchi.S3G139600.t1"; gene_id "Phchi.S3G139600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15839.t1 is derived from g14309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21692181	21693761	.	+	.	Phchi.S3G315800
Phchi.S3	AUGUSTUS	transcript	21692181	21693761	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	start_codon	21692181	21692183	.	+	0	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	CDS	21692181	21692278	1	+	0	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	exon	21692181	21692278	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	intron	21692279	21692364	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	CDS	21692365	21692478	0.99	+	1	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	exon	21692365	21692478	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	intron	21692479	21692587	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	CDS	21692588	21692818	0.97	+	1	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	exon	21692588	21692818	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	intron	21692819	21692910	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	CDS	21692911	21693196	1	+	1	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	exon	21692911	21693196	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	intron	21693197	21693284	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	CDS	21693285	21693435	1	+	0	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	exon	21693285	21693435	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	intron	21693436	21693564	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	CDS	21693565	21693761	1	+	2	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	exon	21693565	21693761	.	+	.	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
Phchi.S3	AUGUSTUS	stop_codon	21693762	21693764	.	+	0	transcript_id "Phchi.S3G315800.t1"; gene_id "Phchi.S3G315800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5692.t1 is derived from g2862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18334159	18346164	.	+	.	Phchi.S1G285100
Phchi.S1	AUGUSTUS	transcript	18334159	18346164	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	start_codon	18334159	18334161	.	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18334159	18336981	0.4	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18334159	18336981	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18336982	18337236	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18337237	18337885	0.51	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18337237	18337885	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18337886	18337974	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18337975	18341054	0.76	+	2	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18337975	18341054	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18341055	18341146	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18341147	18341432	1	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18341147	18341432	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18341433	18341509	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18341510	18341970	0.55	+	2	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18341510	18341970	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18341971	18342053	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18342054	18342116	0.9	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18342054	18342116	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18342117	18342211	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18342212	18342987	0.49	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18342212	18342987	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18342988	18343106	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18343107	18343966	0.45	+	1	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18343107	18343966	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18343967	18344139	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18344140	18346074	0.64	+	2	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18344140	18346074	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	intron	18346075	18346162	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	CDS	18346163	18346164	0.91	+	2	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	exon	18346163	18346164	.	+	.	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
Phchi.S1	AUGUSTUS	stop_codon	18346165	18346167	.	+	0	transcript_id "Phchi.S1G285100.t1"; gene_id "Phchi.S1G285100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15060.t1 is derived from g13528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16787937	16790245	.	+	.	Phchi.S3G237900
Phchi.S3	AUGUSTUS	transcript	16787937	16790245	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	start_codon	16787937	16787939	.	+	0	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	CDS	16787937	16787985	0.99	+	0	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	exon	16787937	16787985	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	intron	16787986	16788212	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	CDS	16788213	16788316	0.88	+	2	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	exon	16788213	16788316	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	intron	16788317	16788459	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	CDS	16788460	16788542	0.54	+	0	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	exon	16788460	16788542	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	intron	16788543	16788637	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	CDS	16788638	16788737	0.58	+	1	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	exon	16788638	16788737	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	intron	16788738	16788845	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	CDS	16788846	16789167	0.36	+	0	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	exon	16788846	16789167	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	intron	16789168	16789283	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	CDS	16789284	16790245	0.3	+	2	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	exon	16789284	16790245	.	+	.	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
Phchi.S3	AUGUSTUS	stop_codon	16790246	16790248	.	+	0	transcript_id "Phchi.S3G237900.t1"; gene_id "Phchi.S3G237900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3088.t1 is derived from g257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1673027	1674988	.	-	.	Phchi.S1G024700
Phchi.S1	AUGUSTUS	transcript	1673027	1674988	.	-	.	transcript_id "Phchi.S1G024700.t1"; gene_id "Phchi.S1G024700"
Phchi.S1	AUGUSTUS	stop_codon	1673024	1673026	.	-	0	transcript_id "Phchi.S1G024700.t1"; gene_id "Phchi.S1G024700"
Phchi.S1	AUGUSTUS	CDS	1673027	1674988	1	-	0	transcript_id "Phchi.S1G024700.t1"; gene_id "Phchi.S1G024700"
Phchi.S1	AUGUSTUS	exon	1673027	1674988	.	-	.	transcript_id "Phchi.S1G024700.t1"; gene_id "Phchi.S1G024700"
Phchi.S1	AUGUSTUS	start_codon	1674986	1674988	.	-	0	transcript_id "Phchi.S1G024700.t1"; gene_id "Phchi.S1G024700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15084.t1 is derived from g13552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16947624	16948692	.	-	.	Phchi.S3G240300
Phchi.S3	AUGUSTUS	transcript	16947624	16948692	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	stop_codon	16947621	16947623	.	-	0	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	CDS	16947624	16947698	1	-	0	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	exon	16947624	16947698	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	intron	16947699	16947785	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	CDS	16947786	16947848	1	-	0	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	exon	16947786	16947848	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	intron	16947849	16947966	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	CDS	16947967	16947983	0.5	-	2	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	exon	16947967	16947983	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	intron	16947984	16948063	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	CDS	16948064	16948081	0.57	-	2	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	exon	16948064	16948081	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	intron	16948082	16948227	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	CDS	16948228	16948296	1	-	2	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	exon	16948228	16948296	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	intron	16948297	16948634	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	CDS	16948635	16948692	1	-	0	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	exon	16948635	16948692	.	-	.	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
Phchi.S3	AUGUSTUS	start_codon	16948690	16948692	.	-	0	transcript_id "Phchi.S3G240300.t1"; gene_id "Phchi.S3G240300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2653.t1 is derived from g9573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8040906	8043518	.	-	.	Phchi.S5G126200
Phchi.S5	AUGUSTUS	transcript	8040906	8043518	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	stop_codon	8040903	8040905	.	-	0	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	CDS	8040906	8040941	0.37	-	0	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	exon	8040906	8040941	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	intron	8040942	8041081	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	CDS	8041082	8041103	0.37	-	1	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	exon	8041082	8041103	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	intron	8041104	8041200	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	CDS	8041201	8041606	0.28	-	2	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	exon	8041201	8041606	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	intron	8041607	8041768	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	CDS	8041769	8042792	0.5	-	0	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	exon	8041769	8042792	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	intron	8042793	8042893	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	CDS	8042894	8042898	0.73	-	2	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	exon	8042894	8042898	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	intron	8042899	8043034	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	CDS	8043035	8043518	0.89	-	0	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	exon	8043035	8043518	.	-	.	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
Phchi.S5	AUGUSTUS	start_codon	8043516	8043518	.	-	0	transcript_id "Phchi.S5G126200.t1"; gene_id "Phchi.S5G126200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6099.t1 is derived from g3270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20948631	20949284	.	+	.	Phchi.S1G325800
Phchi.S1	AUGUSTUS	transcript	20948631	20949284	.	+	.	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	start_codon	20948631	20948633	.	+	0	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	CDS	20948631	20948878	0.69	+	0	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	exon	20948631	20948878	.	+	.	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	intron	20948879	20948977	.	+	.	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	CDS	20948978	20949284	0.91	+	1	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	exon	20948978	20949284	.	+	.	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
Phchi.S1	AUGUSTUS	stop_codon	20949285	20949287	.	+	0	transcript_id "Phchi.S1G325800.t1"; gene_id "Phchi.S1G325800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6240.t1 is derived from g3412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21815758	21820263	.	-	.	Phchi.S1G339900
Phchi.S1	AUGUSTUS	transcript	21815758	21820263	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	stop_codon	21815755	21815757	.	-	0	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	CDS	21815758	21815985	1	-	0	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	exon	21815758	21815985	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	intron	21815986	21816302	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	CDS	21816303	21816405	0.02	-	1	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	exon	21816303	21816405	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	intron	21816406	21817635	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	CDS	21817636	21817853	1	-	0	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	exon	21817636	21817853	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	intron	21817854	21820095	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	CDS	21820096	21820263	0.63	-	0	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	exon	21820096	21820263	.	-	.	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
Phchi.S1	AUGUSTUS	start_codon	21820261	21820263	.	-	0	transcript_id "Phchi.S1G339900.t1"; gene_id "Phchi.S1G339900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4609.t1 is derived from g1779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11381470	11381764	.	-	.	Phchi.S1G176800
Phchi.S1	AUGUSTUS	transcript	11381470	11381764	.	-	.	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	stop_codon	11381467	11381469	.	-	0	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	CDS	11381470	11381507	0.93	-	2	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	exon	11381470	11381507	.	-	.	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	intron	11381508	11381586	.	-	.	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	CDS	11381587	11381764	0.66	-	0	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	exon	11381587	11381764	.	-	.	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
Phchi.S1	AUGUSTUS	start_codon	11381762	11381764	.	-	0	transcript_id "Phchi.S1G176800.t1"; gene_id "Phchi.S1G176800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2760.t1 is derived from g9680.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8706256	8707714	.	-	.	Phchi.S5G136900
Phchi.S5	AUGUSTUS	transcript	8706256	8707714	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	stop_codon	8706253	8706255	.	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706256	8706402	0.94	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706256	8706402	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8706403	8706484	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706485	8706512	0.98	-	1	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706485	8706512	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8706513	8706597	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706598	8706635	0.98	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706598	8706635	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8706636	8706812	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706813	8707004	0.99	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706813	8707004	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8707005	8707094	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8707095	8707301	1	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8707095	8707301	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8707302	8707393	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8707394	8707714	0.92	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8707394	8707714	.	-	.	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	start_codon	8707712	8707714	.	-	0	transcript_id "Phchi.S5G136900.t1"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	transcript	8706256	8707714	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	stop_codon	8706253	8706255	.	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706256	8706402	0.96	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706256	8706402	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8706403	8706484	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706485	8706691	0.92	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706485	8706691	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8706692	8706812	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8706813	8707004	1	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8706813	8707004	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8707005	8707094	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8707095	8707301	1	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8707095	8707301	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	intron	8707302	8707393	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	CDS	8707394	8707714	0.92	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	exon	8707394	8707714	.	-	.	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
Phchi.S5	AUGUSTUS	start_codon	8707712	8707714	.	-	0	transcript_id "Phchi.S5G136900.t2"; gene_id "Phchi.S5G136900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14053.t1 is derived from g12520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10504063	10506520	.	+	.	Phchi.S3G137200
Phchi.S3	AUGUSTUS	transcript	10504063	10506520	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	start_codon	10504063	10504065	.	+	0	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	CDS	10504063	10504247	0.74	+	0	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	exon	10504063	10504247	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	intron	10504248	10504660	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	CDS	10504661	10504678	0.82	+	1	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	exon	10504661	10504678	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	intron	10504679	10504836	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	CDS	10504837	10505671	0.75	+	1	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	exon	10504837	10505671	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	intron	10505672	10505797	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	CDS	10505798	10505899	0.8	+	0	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	exon	10505798	10505899	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	intron	10505900	10506117	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	CDS	10506118	10506227	1	+	0	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	exon	10506118	10506227	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	intron	10506228	10506318	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	CDS	10506319	10506520	1	+	1	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	exon	10506319	10506520	.	+	.	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
Phchi.S3	AUGUSTUS	stop_codon	10506521	10506523	.	+	0	transcript_id "Phchi.S3G137200.t1"; gene_id "Phchi.S3G137200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7324.t1 is derived from g4496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28522882	28523286	.	+	.	Phchi.S1G448300
Phchi.S1	AUGUSTUS	transcript	28522882	28523286	.	+	.	transcript_id "Phchi.S1G448300.t1"; gene_id "Phchi.S1G448300"
Phchi.S1	AUGUSTUS	start_codon	28522882	28522884	.	+	0	transcript_id "Phchi.S1G448300.t1"; gene_id "Phchi.S1G448300"
Phchi.S1	AUGUSTUS	CDS	28522882	28523286	0.65	+	0	transcript_id "Phchi.S1G448300.t1"; gene_id "Phchi.S1G448300"
Phchi.S1	AUGUSTUS	exon	28522882	28523286	.	+	.	transcript_id "Phchi.S1G448300.t1"; gene_id "Phchi.S1G448300"
Phchi.S1	AUGUSTUS	stop_codon	28523287	28523289	.	+	0	transcript_id "Phchi.S1G448300.t1"; gene_id "Phchi.S1G448300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1890.t1 is derived from g8810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3717569	3718511	.	-	.	Phchi.S5G049900
Phchi.S5	AUGUSTUS	transcript	3717569	3718511	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	stop_codon	3717566	3717568	.	-	0	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	CDS	3717569	3717629	0.94	-	1	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	exon	3717569	3717629	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	intron	3717630	3717718	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	CDS	3717719	3717801	1	-	0	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	exon	3717719	3717801	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	intron	3717802	3718112	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	CDS	3718113	3718201	1	-	2	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	exon	3718113	3718201	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	intron	3718202	3718312	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	CDS	3718313	3718352	1	-	0	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	exon	3718313	3718352	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	intron	3718353	3718508	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	CDS	3718509	3718511	1	-	0	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	exon	3718509	3718511	.	-	.	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
Phchi.S5	AUGUSTUS	start_codon	3718509	3718511	.	-	0	transcript_id "Phchi.S5G049900.t1"; gene_id "Phchi.S5G049900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15773.t1 is derived from g14243.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21278300	21286379	.	+	.	Phchi.S3G309200
Phchi.S3	AUGUSTUS	transcript	21278300	21286379	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	start_codon	21278300	21278302	.	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21278300	21278553	0.95	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21278300	21278553	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21278554	21279306	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21279307	21279388	0.99	+	1	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21279307	21279388	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21279389	21279492	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21279493	21279609	1	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21279493	21279609	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21279610	21279698	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21279699	21279889	1	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21279699	21279889	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21279890	21279995	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21279996	21280570	0.5	+	1	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21279996	21280570	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21280571	21280647	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21280648	21280949	0.69	+	2	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21280648	21280949	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21280950	21281127	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21281128	21281225	1	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21281128	21281225	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21281226	21281315	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21281316	21281754	0.97	+	1	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21281316	21281754	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21281755	21281860	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21281861	21282466	0.97	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21281861	21282466	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21282467	21282560	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21282561	21282740	1	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21282561	21282740	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21282741	21282828	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21282829	21283341	0.7	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21282829	21283341	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21283342	21283430	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21283431	21283559	1	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21283431	21283559	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21283560	21283642	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21283643	21283761	1	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21283643	21283761	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21283762	21283881	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21283882	21285586	0.96	+	1	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21283882	21285586	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	intron	21285587	21285677	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	CDS	21285678	21286379	0.97	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	exon	21285678	21286379	.	+	.	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
Phchi.S3	AUGUSTUS	stop_codon	21286380	21286382	.	+	0	transcript_id "Phchi.S3G309200.t1"; gene_id "Phchi.S3G309200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10573.t1 is derived from g14623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1023071	1023361	.	+	.	Phchi.S4G015500
Phchi.S4	AUGUSTUS	transcript	1023071	1023361	.	+	.	transcript_id "Phchi.S4G015500.t1"; gene_id "Phchi.S4G015500"
Phchi.S4	AUGUSTUS	start_codon	1023071	1023073	.	+	0	transcript_id "Phchi.S4G015500.t1"; gene_id "Phchi.S4G015500"
Phchi.S4	AUGUSTUS	CDS	1023071	1023361	0.46	+	0	transcript_id "Phchi.S4G015500.t1"; gene_id "Phchi.S4G015500"
Phchi.S4	AUGUSTUS	exon	1023071	1023361	.	+	.	transcript_id "Phchi.S4G015500.t1"; gene_id "Phchi.S4G015500"
Phchi.S4	AUGUSTUS	stop_codon	1023362	1023364	.	+	0	transcript_id "Phchi.S4G015500.t1"; gene_id "Phchi.S4G015500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5396.t1 is derived from g2566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16676123	16677037	.	-	.	Phchi.S1G255500
Phchi.S1	AUGUSTUS	transcript	16676123	16677037	.	-	.	transcript_id "Phchi.S1G255500.t1"; gene_id "Phchi.S1G255500"
Phchi.S1	AUGUSTUS	stop_codon	16676120	16676122	.	-	0	transcript_id "Phchi.S1G255500.t1"; gene_id "Phchi.S1G255500"
Phchi.S1	AUGUSTUS	CDS	16676123	16677037	1	-	0	transcript_id "Phchi.S1G255500.t1"; gene_id "Phchi.S1G255500"
Phchi.S1	AUGUSTUS	exon	16676123	16677037	.	-	.	transcript_id "Phchi.S1G255500.t1"; gene_id "Phchi.S1G255500"
Phchi.S1	AUGUSTUS	start_codon	16677035	16677037	.	-	0	transcript_id "Phchi.S1G255500.t1"; gene_id "Phchi.S1G255500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1363.t1 is derived from g15999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C81	AUGUSTUS	gene	24722	26849	.	+	.	Phchi.C81G000500
Phchi.C81	AUGUSTUS	transcript	24722	26849	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	start_codon	24722	24724	.	+	0	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	CDS	24722	25475	0.49	+	0	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	exon	24722	25475	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	intron	25476	25580	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	CDS	25581	25771	0.65	+	2	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	exon	25581	25771	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	intron	25772	25834	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	CDS	25835	26272	0.73	+	0	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	exon	25835	26272	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	intron	26273	26359	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	CDS	26360	26577	0.99	+	0	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	exon	26360	26577	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	intron	26578	26665	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	CDS	26666	26849	1	+	1	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	exon	26666	26849	.	+	.	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
Phchi.C81	AUGUSTUS	stop_codon	26850	26852	.	+	0	transcript_id "Phchi.C81G000500.t1"; gene_id "Phchi.C81G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4618.t1 is derived from g1788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11426260	11428469	.	+	.	Phchi.S1G177700
Phchi.S1	AUGUSTUS	transcript	11426260	11428469	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	start_codon	11426260	11426262	.	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11426260	11426411	0.68	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11426260	11426411	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11426412	11426516	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11426517	11426610	0.67	+	1	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11426517	11426610	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11426611	11426713	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11426714	11426833	1	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11426714	11426833	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11426834	11426912	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11426913	11426961	1	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11426913	11426961	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11426962	11427112	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11427113	11427212	1	+	2	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11427113	11427212	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11427213	11427336	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11427337	11427398	1	+	1	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11427337	11427398	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11427399	11427528	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11427529	11427593	1	+	2	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11427529	11427593	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11427594	11427675	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11427676	11427795	1	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11427676	11427795	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11427796	11428072	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11428073	11428153	1	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11428073	11428153	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11428154	11428232	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11428233	11428324	1	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11428233	11428324	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	intron	11428325	11428405	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	CDS	11428406	11428469	1	+	1	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	exon	11428406	11428469	.	+	.	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
Phchi.S1	AUGUSTUS	stop_codon	11428470	11428472	.	+	0	transcript_id "Phchi.S1G177700.t1"; gene_id "Phchi.S1G177700"
# This transcript jg3535.t2 is derived from g704.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3536.t1 is derived from g705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4349392	4351931	.	+	.	Phchi.S1G069500
Phchi.S1	AUGUSTUS	transcript	4349392	4351931	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	start_codon	4349392	4349394	.	+	0	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	CDS	4349392	4349478	0.59	+	0	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	exon	4349392	4349478	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	intron	4349479	4349554	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	CDS	4349555	4349634	1	+	0	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	exon	4349555	4349634	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	intron	4349635	4349763	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	CDS	4349764	4349842	1	+	1	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	exon	4349764	4349842	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	intron	4349843	4349998	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	CDS	4349999	4350568	1	+	0	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	exon	4349999	4350568	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	intron	4350569	4350659	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	CDS	4350660	4351931	0.26	+	0	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	exon	4350660	4351931	.	+	.	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
Phchi.S1	AUGUSTUS	stop_codon	4351932	4351934	.	+	0	transcript_id "Phchi.S1G069500.t1"; gene_id "Phchi.S1G069500"
# This transcript jg8563.t2 is derived from g5738.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8563.t3 is derived from g5738.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8564.t1 is derived from g5739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36632570	36633413	.	+	.	Phchi.S1G572300
Phchi.S1	AUGUSTUS	transcript	36632570	36633413	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	start_codon	36632570	36632572	.	+	0	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	CDS	36632570	36632649	0.78	+	0	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	exon	36632570	36632649	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	intron	36632650	36632757	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	CDS	36632758	36632815	1	+	1	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	exon	36632758	36632815	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	intron	36632816	36632899	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	CDS	36632900	36632989	1	+	0	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	exon	36632900	36632989	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	intron	36632990	36633071	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	CDS	36633072	36633189	1	+	0	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	exon	36633072	36633189	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	intron	36633190	36633348	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	CDS	36633349	36633413	0.56	+	2	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	exon	36633349	36633413	.	+	.	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
Phchi.S1	AUGUSTUS	stop_codon	36633414	36633416	.	+	0	transcript_id "Phchi.S1G572300.t1"; gene_id "Phchi.S1G572300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6889.t1 is derived from g4061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25832251	25834697	.	+	.	Phchi.S1G404800
Phchi.S1	AUGUSTUS	transcript	25832251	25834697	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	start_codon	25832251	25832253	.	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25832251	25832440	0.84	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25832251	25832440	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25832441	25832579	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25832580	25832672	1	+	2	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25832580	25832672	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25832673	25832771	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25832772	25832953	1	+	2	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25832772	25832953	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25832954	25833084	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25833085	25833144	1	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25833085	25833144	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25833145	25833285	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25833286	25833357	1	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25833286	25833357	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25833358	25833470	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25833471	25833671	0.99	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25833471	25833671	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25833672	25833769	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25833770	25833869	1	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25833770	25833869	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25833870	25833960	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25833961	25834047	0.96	+	2	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25833961	25834047	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25834048	25834334	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25834335	25834443	1	+	2	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25834335	25834443	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	intron	25834444	25834528	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	CDS	25834529	25834697	0.97	+	1	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	exon	25834529	25834697	.	+	.	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
Phchi.S1	AUGUSTUS	stop_codon	25834698	25834700	.	+	0	transcript_id "Phchi.S1G404800.t1"; gene_id "Phchi.S1G404800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8594.t1 is derived from g5769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36799318	36800394	.	-	.	Phchi.S1G575300
Phchi.S1	AUGUSTUS	transcript	36799318	36800394	.	-	.	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	stop_codon	36799315	36799317	.	-	0	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	CDS	36799318	36799530	0.65	-	0	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	exon	36799318	36799530	.	-	.	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	intron	36799531	36799605	.	-	.	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	CDS	36799606	36799762	0.36	-	1	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	exon	36799606	36799762	.	-	.	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	intron	36799763	36800068	.	-	.	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	CDS	36800069	36800394	0.19	-	0	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	exon	36800069	36800394	.	-	.	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
Phchi.S1	AUGUSTUS	start_codon	36800392	36800394	.	-	0	transcript_id "Phchi.S1G575300.t1"; gene_id "Phchi.S1G575300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8270.t1 is derived from g5445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35048640	35049345	.	+	.	Phchi.S1G542900
Phchi.S1	AUGUSTUS	transcript	35048640	35049345	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	start_codon	35048640	35048642	.	+	0	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	CDS	35048640	35048853	0.59	+	0	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	exon	35048640	35048853	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	intron	35048854	35048932	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	CDS	35048933	35049062	1	+	2	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	exon	35048933	35049062	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	intron	35049063	35049157	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	CDS	35049158	35049202	1	+	1	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	exon	35049158	35049202	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	intron	35049203	35049290	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	CDS	35049291	35049345	0.99	+	1	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	exon	35049291	35049345	.	+	.	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
Phchi.S1	AUGUSTUS	stop_codon	35049346	35049348	.	+	0	transcript_id "Phchi.S1G542900.t1"; gene_id "Phchi.S1G542900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12367.t1 is derived from g8043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13083220	13084228	.	-	.	Phchi.S2G044700
Phchi.S2	AUGUSTUS	transcript	13083220	13084228	.	-	.	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	stop_codon	13083217	13083219	.	-	0	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	CDS	13083220	13083576	0.99	-	0	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	exon	13083220	13083576	.	-	.	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	intron	13083577	13083659	.	-	.	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	CDS	13083660	13083893	1	-	0	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	exon	13083660	13083893	.	-	.	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	intron	13083894	13083982	.	-	.	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	CDS	13083983	13084228	0.73	-	0	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	exon	13083983	13084228	.	-	.	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
Phchi.S2	AUGUSTUS	start_codon	13084226	13084228	.	-	0	transcript_id "Phchi.S2G044700.t1"; gene_id "Phchi.S2G044700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2713.t1 is derived from g9633.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8304601	8306119	.	+	.	Phchi.S5G132200
Phchi.S5	AUGUSTUS	transcript	8304601	8306119	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	start_codon	8304601	8304603	.	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8304601	8304759	0.96	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8304601	8304759	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	intron	8304760	8304845	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8304846	8304944	1	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8304846	8304944	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	intron	8304945	8305096	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8305097	8305210	1	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8305097	8305210	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	intron	8305211	8305298	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8305299	8305377	1	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8305299	8305377	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	intron	8305378	8305462	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8305463	8305657	0.44	+	2	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8305463	8305657	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	intron	8305658	8305823	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8305824	8305936	0.43	+	2	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8305824	8305936	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	intron	8305937	8306023	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	CDS	8306024	8306119	1	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	exon	8306024	8306119	.	+	.	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
Phchi.S5	AUGUSTUS	stop_codon	8306120	8306122	.	+	0	transcript_id "Phchi.S5G132200.t1"; gene_id "Phchi.S5G132200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10595.t1 is derived from g14645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1119539	1120213	.	+	.	Phchi.S4G017700
Phchi.S4	AUGUSTUS	transcript	1119539	1120213	.	+	.	transcript_id "Phchi.S4G017700.t1"; gene_id "Phchi.S4G017700"
Phchi.S4	AUGUSTUS	start_codon	1119539	1119541	.	+	0	transcript_id "Phchi.S4G017700.t1"; gene_id "Phchi.S4G017700"
Phchi.S4	AUGUSTUS	CDS	1119539	1120213	0.96	+	0	transcript_id "Phchi.S4G017700.t1"; gene_id "Phchi.S4G017700"
Phchi.S4	AUGUSTUS	exon	1119539	1120213	.	+	.	transcript_id "Phchi.S4G017700.t1"; gene_id "Phchi.S4G017700"
Phchi.S4	AUGUSTUS	stop_codon	1120214	1120216	.	+	0	transcript_id "Phchi.S4G017700.t1"; gene_id "Phchi.S4G017700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1152.t1 is derived from g10935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8034707	8039355	.	-	.	Phchi.S6G111100
Phchi.S6	AUGUSTUS	transcript	8034707	8039355	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	stop_codon	8034704	8034706	.	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8034707	8034868	0.86	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8034707	8034868	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8034869	8034946	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8034947	8035083	1	-	2	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8034947	8035083	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8035084	8035178	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8035179	8035257	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8035179	8035257	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8035258	8035338	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8035339	8035419	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8035339	8035419	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8035420	8035494	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8035495	8035656	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8035495	8035656	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8035657	8035779	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8035780	8035876	1	-	1	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8035780	8035876	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8035877	8035977	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8035978	8036138	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8035978	8036138	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8036139	8036267	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8036268	8036366	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8036268	8036366	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8036367	8036455	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8036456	8036502	0.71	-	2	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8036456	8036502	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8036503	8036580	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8036581	8036668	0.43	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8036581	8036668	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8036669	8036776	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8036777	8036890	0.58	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8036777	8036890	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8036891	8037053	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8037054	8037191	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8037054	8037191	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8037192	8037304	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8037305	8037376	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8037305	8037376	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8037377	8037448	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8037449	8037581	0.88	-	1	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8037449	8037581	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8037582	8037761	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8037762	8037783	0.68	-	2	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8037762	8037783	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8037784	8037909	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8037910	8038041	1	-	2	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8037910	8038041	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8038042	8038118	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8038119	8038173	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8038119	8038173	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8038174	8038312	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8038313	8038516	0.77	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8038313	8038516	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8038517	8038588	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8038589	8038753	1	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8038589	8038753	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8038754	8038833	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8038834	8038933	1	-	1	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8038834	8038933	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8038934	8039073	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8039074	8039215	0.98	-	2	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8039074	8039215	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	intron	8039216	8039336	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	CDS	8039337	8039355	0.74	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	exon	8039337	8039355	.	-	.	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
Phchi.S6	AUGUSTUS	start_codon	8039353	8039355	.	-	0	transcript_id "Phchi.S6G111100.t1"; gene_id "Phchi.S6G111100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11923.t1 is derived from g7598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	46736	47161	.	+	.	Phchi.S2G000300
Phchi.S2	AUGUSTUS	transcript	46736	47161	.	+	.	transcript_id "Phchi.S2G000300.t1"; gene_id "Phchi.S2G000300"
Phchi.S2	AUGUSTUS	start_codon	46736	46738	.	+	0	transcript_id "Phchi.S2G000300.t1"; gene_id "Phchi.S2G000300"
Phchi.S2	AUGUSTUS	CDS	46736	47161	0.64	+	0	transcript_id "Phchi.S2G000300.t1"; gene_id "Phchi.S2G000300"
Phchi.S2	AUGUSTUS	exon	46736	47161	.	+	.	transcript_id "Phchi.S2G000300.t1"; gene_id "Phchi.S2G000300"
Phchi.S2	AUGUSTUS	stop_codon	47162	47164	.	+	0	transcript_id "Phchi.S2G000300.t1"; gene_id "Phchi.S2G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5395.t1 is derived from g2565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16674348	16675562	.	+	.	Phchi.S1G255400
Phchi.S1	AUGUSTUS	transcript	16674348	16675562	.	+	.	transcript_id "Phchi.S1G255400.t1"; gene_id "Phchi.S1G255400"
Phchi.S1	AUGUSTUS	start_codon	16674348	16674350	.	+	0	transcript_id "Phchi.S1G255400.t1"; gene_id "Phchi.S1G255400"
Phchi.S1	AUGUSTUS	CDS	16674348	16675562	1	+	0	transcript_id "Phchi.S1G255400.t1"; gene_id "Phchi.S1G255400"
Phchi.S1	AUGUSTUS	exon	16674348	16675562	.	+	.	transcript_id "Phchi.S1G255400.t1"; gene_id "Phchi.S1G255400"
Phchi.S1	AUGUSTUS	stop_codon	16675563	16675565	.	+	0	transcript_id "Phchi.S1G255400.t1"; gene_id "Phchi.S1G255400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10571.t1 is derived from g14621.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1015928	1019121	.	-	.	Phchi.S4G015300
Phchi.S4	AUGUSTUS	transcript	1015928	1019121	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	stop_codon	1015925	1015927	.	-	0	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1015928	1015991	0.93	-	1	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1015928	1015991	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1015992	1016068	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1016069	1016207	1	-	2	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1016069	1016207	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1016208	1016576	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1016577	1018136	0.77	-	2	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1016577	1018136	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018137	1018216	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018217	1018274	0.98	-	0	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018217	1018274	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018275	1018371	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018372	1018466	1	-	2	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018372	1018466	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018467	1018558	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018559	1018709	1	-	0	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018559	1018709	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018710	1018793	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018794	1018879	0.77	-	2	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018794	1018879	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018880	1018988	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018989	1019121	0.97	-	0	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018989	1019121	.	-	.	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	start_codon	1019119	1019121	.	-	0	transcript_id "Phchi.S4G015300.t1"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	transcript	1015928	1019121	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	stop_codon	1015925	1015927	.	-	0	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1015928	1015991	0.91	-	1	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1015928	1015991	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1015992	1016068	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1016069	1016207	1	-	2	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1016069	1016207	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1016208	1016576	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1016577	1018293	0.71	-	0	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1016577	1018293	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018294	1018371	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018372	1018466	1	-	2	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018372	1018466	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018467	1018558	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018559	1018709	1	-	0	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018559	1018709	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018710	1018793	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018794	1018879	0.72	-	2	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018794	1018879	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	intron	1018880	1018988	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	CDS	1018989	1019121	0.99	-	0	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	exon	1018989	1019121	.	-	.	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
Phchi.S4	AUGUSTUS	start_codon	1019119	1019121	.	-	0	transcript_id "Phchi.S4G015300.t2"; gene_id "Phchi.S4G015300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2138.t1 is derived from g9058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5020094	5021899	.	+	.	Phchi.S5G074700
Phchi.S5	AUGUSTUS	transcript	5020094	5021899	.	+	.	transcript_id "Phchi.S5G074700.t1"; gene_id "Phchi.S5G074700"
Phchi.S5	AUGUSTUS	start_codon	5020094	5020096	.	+	0	transcript_id "Phchi.S5G074700.t1"; gene_id "Phchi.S5G074700"
Phchi.S5	AUGUSTUS	CDS	5020094	5021899	0.86	+	0	transcript_id "Phchi.S5G074700.t1"; gene_id "Phchi.S5G074700"
Phchi.S5	AUGUSTUS	exon	5020094	5021899	.	+	.	transcript_id "Phchi.S5G074700.t1"; gene_id "Phchi.S5G074700"
Phchi.S5	AUGUSTUS	stop_codon	5021900	5021902	.	+	0	transcript_id "Phchi.S5G074700.t1"; gene_id "Phchi.S5G074700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8851.t1 is derived from g6026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38279227	38280130	.	+	.	Phchi.S1G601000
Phchi.S1	AUGUSTUS	transcript	38279227	38280130	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	start_codon	38279227	38279229	.	+	0	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	CDS	38279227	38279520	0.46	+	0	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	exon	38279227	38279520	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	intron	38279521	38279634	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	CDS	38279635	38279784	0.78	+	0	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	exon	38279635	38279784	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	intron	38279785	38279864	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	CDS	38279865	38279884	0.65	+	0	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	exon	38279865	38279884	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	intron	38279885	38280075	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	CDS	38280076	38280130	0.64	+	1	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	exon	38280076	38280130	.	+	.	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
Phchi.S1	AUGUSTUS	stop_codon	38280131	38280133	.	+	0	transcript_id "Phchi.S1G601000.t1"; gene_id "Phchi.S1G601000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9058.t1 is derived from g6233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39519681	39520719	.	+	.	Phchi.S1G621700
Phchi.S1	AUGUSTUS	transcript	39519681	39520719	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	start_codon	39519681	39519683	.	+	0	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	CDS	39519681	39519954	0.59	+	0	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	exon	39519681	39519954	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	intron	39519955	39520051	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	CDS	39520052	39520176	0.56	+	2	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	exon	39520052	39520176	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	intron	39520177	39520298	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	CDS	39520299	39520445	0.46	+	0	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	exon	39520299	39520445	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	intron	39520446	39520650	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	CDS	39520651	39520719	0.58	+	0	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	exon	39520651	39520719	.	+	.	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
Phchi.S1	AUGUSTUS	stop_codon	39520720	39520722	.	+	0	transcript_id "Phchi.S1G621700.t1"; gene_id "Phchi.S1G621700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6399.t1 is derived from g3571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22765332	22766314	.	+	.	Phchi.S1G355800
Phchi.S1	AUGUSTUS	transcript	22765332	22766314	.	+	.	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	start_codon	22765332	22765334	.	+	0	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	CDS	22765332	22765741	1	+	0	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	exon	22765332	22765741	.	+	.	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	intron	22765742	22765815	.	+	.	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	CDS	22765816	22766314	0.87	+	1	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	exon	22765816	22766314	.	+	.	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
Phchi.S1	AUGUSTUS	stop_codon	22766315	22766317	.	+	0	transcript_id "Phchi.S1G355800.t1"; gene_id "Phchi.S1G355800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14189.t1 is derived from g12656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11397899	11398719	.	-	.	Phchi.S3G150800
Phchi.S3	AUGUSTUS	transcript	11397899	11398719	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	stop_codon	11397896	11397898	.	-	0	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	CDS	11397899	11397933	0.77	-	2	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	exon	11397899	11397933	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	intron	11397934	11398033	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	CDS	11398034	11398061	0.98	-	0	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	exon	11398034	11398061	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	intron	11398062	11398141	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	CDS	11398142	11398291	1	-	0	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	exon	11398142	11398291	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	intron	11398292	11398488	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	CDS	11398489	11398719	0.99	-	0	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	exon	11398489	11398719	.	-	.	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
Phchi.S3	AUGUSTUS	start_codon	11398717	11398719	.	-	0	transcript_id "Phchi.S3G150800.t1"; gene_id "Phchi.S3G150800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2891.t1 is derived from g60.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	340845	341474	.	+	.	Phchi.S1G005000
Phchi.S1	AUGUSTUS	transcript	340845	341474	.	+	.	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	start_codon	340845	340847	.	+	0	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	CDS	340845	340868	0.98	+	0	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	exon	340845	340868	.	+	.	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	intron	340869	341011	.	+	.	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	CDS	341012	341029	1	+	0	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	exon	341012	341029	.	+	.	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	intron	341030	341162	.	+	.	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	CDS	341163	341474	1	+	0	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	exon	341163	341474	.	+	.	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
Phchi.S1	AUGUSTUS	stop_codon	341475	341477	.	+	0	transcript_id "Phchi.S1G005000.t1"; gene_id "Phchi.S1G005000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg935.t1 is derived from g10717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6503654	6505649	.	+	.	Phchi.S6G089400
Phchi.S6	AUGUSTUS	transcript	6503654	6505649	.	+	.	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	start_codon	6503654	6503656	.	+	0	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	CDS	6503654	6505059	0.74	+	0	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	exon	6503654	6505059	.	+	.	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	intron	6505060	6505241	.	+	.	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	CDS	6505242	6505365	0.46	+	1	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	exon	6505242	6505365	.	+	.	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	intron	6505366	6505556	.	+	.	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	CDS	6505557	6505649	0.85	+	0	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	exon	6505557	6505649	.	+	.	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
Phchi.S6	AUGUSTUS	stop_codon	6505650	6505652	.	+	0	transcript_id "Phchi.S6G089400.t1"; gene_id "Phchi.S6G089400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7051.t1 is derived from g4223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26625380	26627653	.	-	.	Phchi.S1G421000
Phchi.S1	AUGUSTUS	transcript	26625380	26625886	.	-	.	transcript_id "Phchi.S1G421000.t1"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	stop_codon	26625377	26625379	.	-	0	transcript_id "Phchi.S1G421000.t1"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	CDS	26625380	26625886	0.99	-	0	transcript_id "Phchi.S1G421000.t1"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	exon	26625380	26625886	.	-	.	transcript_id "Phchi.S1G421000.t1"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	start_codon	26625884	26625886	.	-	0	transcript_id "Phchi.S1G421000.t1"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	transcript	26625380	26627653	.	-	.	transcript_id "Phchi.S1G421000.t2"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	stop_codon	26625377	26625379	.	-	0	transcript_id "Phchi.S1G421000.t2"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	CDS	26625380	26627653	0.73	-	0	transcript_id "Phchi.S1G421000.t2"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	exon	26625380	26627653	.	-	.	transcript_id "Phchi.S1G421000.t2"; gene_id "Phchi.S1G421000"
Phchi.S1	AUGUSTUS	start_codon	26627651	26627653	.	-	0	transcript_id "Phchi.S1G421000.t2"; gene_id "Phchi.S1G421000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1150.t1 is derived from g10933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8024291	8029536	.	-	.	Phchi.S6G110900
Phchi.S6	AUGUSTUS	transcript	8024291	8029536	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	stop_codon	8024288	8024290	.	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8024291	8024315	0.93	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8024291	8024315	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8024316	8024396	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8024397	8024612	0.46	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8024397	8024612	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8024613	8024728	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8024729	8024782	0.83	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8024729	8024782	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8024783	8024882	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8024883	8024898	0.65	-	2	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8024883	8024898	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8024899	8024977	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8024978	8024993	0.78	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8024978	8024993	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8024994	8025080	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8025081	8025247	1	-	2	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8025081	8025247	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8025248	8025384	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8025385	8025459	0.89	-	2	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8025385	8025459	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8025460	8025553	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8025554	8025741	0.65	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8025554	8025741	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8025742	8025868	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8025869	8025955	0.9	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8025869	8025955	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8025956	8026031	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8026032	8026327	0.93	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8026032	8026327	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8026328	8026409	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8026410	8026515	1	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8026410	8026515	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8026516	8026637	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8026638	8026695	0.44	-	2	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8026638	8026695	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8026696	8026802	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8026803	8026962	1	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8026803	8026962	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8026963	8027050	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8027051	8027224	1	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8027051	8027224	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8027225	8027438	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8027439	8027613	1	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8027439	8027613	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8027614	8027698	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8027699	8027757	1	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8027699	8027757	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8027758	8027847	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8027848	8027949	1	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8027848	8027949	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8027950	8028144	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8028145	8028182	1	-	2	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8028145	8028182	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8028183	8028278	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8028279	8028376	0.99	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8028279	8028376	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8028377	8028477	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8028478	8028523	1	-	2	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8028478	8028523	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8028524	8028617	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8028618	8028676	1	-	1	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8028618	8028676	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8028677	8028756	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8028757	8028827	1	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8028757	8028827	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8028828	8028914	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8028915	8029007	1	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8028915	8029007	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	intron	8029008	8029080	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	CDS	8029081	8029536	0.99	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	exon	8029081	8029536	.	-	.	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
Phchi.S6	AUGUSTUS	start_codon	8029534	8029536	.	-	0	transcript_id "Phchi.S6G110900.t1"; gene_id "Phchi.S6G110900"
# This transcript jg9294.t2 is derived from g6469.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9295.t1 is derived from g6470.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40822445	40824426	.	-	.	Phchi.S1G645400
Phchi.S1	AUGUSTUS	transcript	40822445	40824426	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	stop_codon	40822442	40822444	.	-	0	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40822445	40822523	1	-	1	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40822445	40822523	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	intron	40822524	40822613	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40822614	40822873	1	-	0	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40822614	40822873	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	intron	40822874	40822972	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40822973	40823206	1	-	0	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40822973	40823206	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	intron	40823207	40823345	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40823346	40823518	1	-	2	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40823346	40823518	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	intron	40823519	40823607	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40823608	40823757	1	-	2	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40823608	40823757	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	intron	40823758	40823898	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40823899	40824035	1	-	1	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40823899	40824035	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	intron	40824036	40824226	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	CDS	40824227	40824426	0.41	-	0	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	exon	40824227	40824426	.	-	.	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
Phchi.S1	AUGUSTUS	start_codon	40824424	40824426	.	-	0	transcript_id "Phchi.S1G645400.t1"; gene_id "Phchi.S1G645400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7863.t1 is derived from g5037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31576038	31583090	.	+	.	Phchi.S1G502200
Phchi.S1	AUGUSTUS	transcript	31576038	31583090	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	start_codon	31576038	31576040	.	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31576038	31577390	0.94	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31576038	31577390	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31577391	31577562	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31577563	31577790	1	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31577563	31577790	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31577791	31577901	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31577902	31578009	1	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31577902	31578009	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31578010	31578093	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31578094	31578276	1	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31578094	31578276	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31578277	31578392	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31578393	31578641	1	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31578393	31578641	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31578642	31578730	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31578731	31578895	0.46	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31578731	31578895	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31578896	31579086	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31579087	31579307	0.93	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31579087	31579307	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31579308	31579409	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31579410	31579617	0.78	+	1	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31579410	31579617	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31579618	31579722	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31579723	31579966	0.78	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31579723	31579966	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31579967	31580046	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31580047	31580109	1	+	2	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31580047	31580109	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31580110	31580346	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31580347	31580620	1	+	2	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31580347	31580620	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31580621	31581222	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31581223	31581352	1	+	1	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31581223	31581352	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31581353	31581560	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31581561	31581756	1	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31581561	31581756	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31581757	31581895	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31581896	31582020	1	+	2	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31581896	31582020	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31582021	31582348	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31582349	31582507	1	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31582349	31582507	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	intron	31582508	31582712	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	CDS	31582713	31583090	0.84	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	exon	31582713	31583090	.	+	.	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
Phchi.S1	AUGUSTUS	stop_codon	31583091	31583093	.	+	0	transcript_id "Phchi.S1G502200.t1"; gene_id "Phchi.S1G502200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3916.t1 is derived from g1085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6420223	6423421	.	+	.	Phchi.S1G107500
Phchi.S1	AUGUSTUS	transcript	6420223	6423421	.	+	.	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	start_codon	6420223	6420225	.	+	0	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	CDS	6420223	6420352	1	+	0	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	exon	6420223	6420352	.	+	.	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	intron	6420353	6420439	.	+	.	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	CDS	6420440	6420505	1	+	2	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	exon	6420440	6420505	.	+	.	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	intron	6420506	6420602	.	+	.	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	CDS	6420603	6423421	0.99	+	2	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	exon	6420603	6423421	.	+	.	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
Phchi.S1	AUGUSTUS	stop_codon	6423422	6423424	.	+	0	transcript_id "Phchi.S1G107500.t1"; gene_id "Phchi.S1G107500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3967.t1 is derived from g1136.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6788548	6790082	.	+	.	Phchi.S1G112600
Phchi.S1	AUGUSTUS	transcript	6788627	6790082	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	start_codon	6788627	6788629	.	+	0	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6788627	6788728	1	+	0	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6788627	6788728	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6788729	6788911	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6788912	6789035	0.96	+	0	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6788912	6789035	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6789036	6789108	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6789109	6789173	0.95	+	2	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6789109	6789173	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6789174	6789422	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6789423	6789584	0.93	+	0	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6789423	6789584	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6789585	6789791	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6789792	6790082	0.96	+	0	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6789792	6790082	.	+	.	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	stop_codon	6790083	6790085	.	+	0	transcript_id "Phchi.S1G112600.t1"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	transcript	6788548	6790082	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	start_codon	6788548	6788550	.	+	0	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6788548	6788748	0.59	+	0	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6788548	6788748	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6788749	6788911	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6788912	6789035	0.75	+	0	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6788912	6789035	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6789036	6789108	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6789109	6789173	0.89	+	2	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6789109	6789173	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6789174	6789422	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6789423	6789584	0.9	+	0	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6789423	6789584	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	intron	6789585	6789791	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	CDS	6789792	6790082	0.97	+	0	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	exon	6789792	6790082	.	+	.	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
Phchi.S1	AUGUSTUS	stop_codon	6790083	6790085	.	+	0	transcript_id "Phchi.S1G112600.t2"; gene_id "Phchi.S1G112600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9697.t1 is derived from g6873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43323714	43325535	.	-	.	Phchi.S1G685600
Phchi.S1	AUGUSTUS	transcript	43323714	43325535	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	stop_codon	43323711	43323713	.	-	0	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	CDS	43323714	43323891	0.7	-	1	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	exon	43323714	43323891	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	intron	43323892	43324061	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	CDS	43324062	43324346	0.51	-	1	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	exon	43324062	43324346	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	intron	43324347	43324472	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	CDS	43324473	43324725	0.61	-	2	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	exon	43324473	43324725	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	intron	43324726	43324917	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	CDS	43324918	43324991	0.68	-	1	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	exon	43324918	43324991	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	intron	43324992	43325485	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	CDS	43325486	43325535	0.98	-	0	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	exon	43325486	43325535	.	-	.	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
Phchi.S1	AUGUSTUS	start_codon	43325533	43325535	.	-	0	transcript_id "Phchi.S1G685600.t1"; gene_id "Phchi.S1G685600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15950.t1 is derived from g14443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	23587	24342	.	-	.	Phchi.C116G000600
Phchi.C116	AUGUSTUS	transcript	23587	24342	.	-	.	transcript_id "Phchi.C116G000600.t1"; gene_id "Phchi.C116G000600"
Phchi.C116	AUGUSTUS	stop_codon	23584	23586	.	-	0	transcript_id "Phchi.C116G000600.t1"; gene_id "Phchi.C116G000600"
Phchi.C116	AUGUSTUS	CDS	23587	24342	0.46	-	0	transcript_id "Phchi.C116G000600.t1"; gene_id "Phchi.C116G000600"
Phchi.C116	AUGUSTUS	exon	23587	24342	.	-	.	transcript_id "Phchi.C116G000600.t1"; gene_id "Phchi.C116G000600"
Phchi.C116	AUGUSTUS	start_codon	24340	24342	.	-	0	transcript_id "Phchi.C116G000600.t1"; gene_id "Phchi.C116G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11194.t1 is derived from g15244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4634797	4639311	.	+	.	Phchi.S4G077600
Phchi.S4	AUGUSTUS	transcript	4634797	4639311	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	start_codon	4634797	4634799	.	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4634797	4635037	0.95	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4634797	4635037	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4635038	4635691	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4635692	4635807	1	+	2	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4635692	4635807	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4635808	4635894	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4635895	4635957	0.96	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4635895	4635957	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4635958	4636049	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4636050	4636240	0.75	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4636050	4636240	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4636241	4636393	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4636394	4636574	1	+	1	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4636394	4636574	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4636575	4636651	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4636652	4636774	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4636652	4636774	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4636775	4636871	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4636872	4637159	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4636872	4637159	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4637160	4637250	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4637251	4637376	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4637251	4637376	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4637377	4637490	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4637491	4637592	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4637491	4637592	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4637593	4637670	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4637671	4637724	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4637671	4637724	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4637725	4637828	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4637829	4637935	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4637829	4637935	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4637936	4638040	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4638041	4638101	0.98	+	1	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4638041	4638101	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4638102	4638212	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4638213	4638344	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4638213	4638344	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4638345	4638439	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4638440	4638577	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4638440	4638577	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4638578	4638665	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4638666	4638746	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4638666	4638746	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4638747	4638833	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4638834	4638914	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4638834	4638914	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4638915	4639018	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4639019	4639099	1	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4639019	4639099	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	intron	4639100	4639200	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	CDS	4639201	4639311	0.95	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	exon	4639201	4639311	.	+	.	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
Phchi.S4	AUGUSTUS	stop_codon	4639312	4639314	.	+	0	transcript_id "Phchi.S4G077600.t1"; gene_id "Phchi.S4G077600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10979.t1 is derived from g15029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3499941	3501176	.	-	.	Phchi.S4G056100
Phchi.S4	AUGUSTUS	transcript	3499941	3501176	.	-	.	transcript_id "Phchi.S4G056100.t1"; gene_id "Phchi.S4G056100"
Phchi.S4	AUGUSTUS	stop_codon	3499938	3499940	.	-	0	transcript_id "Phchi.S4G056100.t1"; gene_id "Phchi.S4G056100"
Phchi.S4	AUGUSTUS	CDS	3499941	3501176	0.5	-	0	transcript_id "Phchi.S4G056100.t1"; gene_id "Phchi.S4G056100"
Phchi.S4	AUGUSTUS	exon	3499941	3501176	.	-	.	transcript_id "Phchi.S4G056100.t1"; gene_id "Phchi.S4G056100"
Phchi.S4	AUGUSTUS	start_codon	3501174	3501176	.	-	0	transcript_id "Phchi.S4G056100.t1"; gene_id "Phchi.S4G056100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13576.t1 is derived from g12043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7556108	7557543	.	-	.	Phchi.S3G089500
Phchi.S3	AUGUSTUS	transcript	7556108	7557543	.	-	.	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	stop_codon	7556105	7556107	.	-	0	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	CDS	7556108	7556836	0.99	-	0	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	exon	7556108	7556836	.	-	.	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	intron	7556837	7556941	.	-	.	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	CDS	7556942	7557249	0.97	-	2	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	exon	7556942	7557249	.	-	.	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	intron	7557250	7557344	.	-	.	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	CDS	7557345	7557543	0.99	-	0	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	exon	7557345	7557543	.	-	.	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
Phchi.S3	AUGUSTUS	start_codon	7557541	7557543	.	-	0	transcript_id "Phchi.S3G089500.t1"; gene_id "Phchi.S3G089500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13334.t1 is derived from g11800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6139989	6141314	.	+	.	Phchi.S3G065300
Phchi.S3	AUGUSTUS	transcript	6139989	6141070	.	+	.	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	start_codon	6139989	6139991	.	+	0	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	CDS	6139989	6140300	1	+	0	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	exon	6139989	6140300	.	+	.	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	intron	6140301	6140598	.	+	.	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	CDS	6140599	6140695	1	+	0	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	exon	6140599	6140695	.	+	.	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	intron	6140696	6141053	.	+	.	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	CDS	6141054	6141070	1	+	2	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	exon	6141054	6141070	.	+	.	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	stop_codon	6141071	6141073	.	+	0	transcript_id "Phchi.S3G065300.t1"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	transcript	6139989	6141314	.	+	.	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	start_codon	6139989	6139991	.	+	0	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	CDS	6139989	6140300	0.98	+	0	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	exon	6139989	6140300	.	+	.	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	intron	6140301	6141053	.	+	.	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	CDS	6141054	6141314	0.43	+	0	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	exon	6141054	6141314	.	+	.	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
Phchi.S3	AUGUSTUS	stop_codon	6141315	6141317	.	+	0	transcript_id "Phchi.S3G065300.t2"; gene_id "Phchi.S3G065300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10804.t1 is derived from g14854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2181217	2182006	.	+	.	Phchi.S4G038600
Phchi.S4	AUGUSTUS	transcript	2181217	2182006	.	+	.	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	start_codon	2181217	2181219	.	+	0	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	CDS	2181217	2181345	0.63	+	0	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	exon	2181217	2181345	.	+	.	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	intron	2181346	2181473	.	+	.	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	CDS	2181474	2181837	0.95	+	0	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	exon	2181474	2181837	.	+	.	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	intron	2181838	2181995	.	+	.	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	CDS	2181996	2182006	0.92	+	2	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	exon	2181996	2182006	.	+	.	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
Phchi.S4	AUGUSTUS	stop_codon	2182007	2182009	.	+	0	transcript_id "Phchi.S4G038600.t1"; gene_id "Phchi.S4G038600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5549.t1 is derived from g2719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17494591	17495888	.	+	.	Phchi.S1G270800
Phchi.S1	AUGUSTUS	transcript	17494591	17495888	.	+	.	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	start_codon	17494591	17494593	.	+	0	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	CDS	17494591	17494715	0.6	+	0	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	exon	17494591	17494715	.	+	.	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	intron	17494716	17494867	.	+	.	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	CDS	17494868	17495678	0.34	+	1	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	exon	17494868	17495678	.	+	.	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	intron	17495679	17495783	.	+	.	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	CDS	17495784	17495888	0.51	+	0	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	exon	17495784	17495888	.	+	.	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
Phchi.S1	AUGUSTUS	stop_codon	17495889	17495891	.	+	0	transcript_id "Phchi.S1G270800.t1"; gene_id "Phchi.S1G270800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5843.t1 is derived from g3013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19294808	19296043	.	-	.	Phchi.S1G300200
Phchi.S1	AUGUSTUS	transcript	19294808	19296043	.	-	.	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	stop_codon	19294805	19294807	.	-	0	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	CDS	19294808	19295205	0.7	-	2	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	exon	19294808	19295205	.	-	.	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	intron	19295206	19295286	.	-	.	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	CDS	19295287	19295417	0.88	-	1	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	exon	19295287	19295417	.	-	.	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	intron	19295418	19295534	.	-	.	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	CDS	19295535	19296043	0.64	-	0	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	exon	19295535	19296043	.	-	.	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
Phchi.S1	AUGUSTUS	start_codon	19296041	19296043	.	-	0	transcript_id "Phchi.S1G300200.t1"; gene_id "Phchi.S1G300200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8426.t1 is derived from g5601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35889263	35889943	.	+	.	Phchi.S1G558500
Phchi.S1	AUGUSTUS	transcript	35889263	35889943	.	+	.	transcript_id "Phchi.S1G558500.t1"; gene_id "Phchi.S1G558500"
Phchi.S1	AUGUSTUS	start_codon	35889263	35889265	.	+	0	transcript_id "Phchi.S1G558500.t1"; gene_id "Phchi.S1G558500"
Phchi.S1	AUGUSTUS	CDS	35889263	35889943	0.89	+	0	transcript_id "Phchi.S1G558500.t1"; gene_id "Phchi.S1G558500"
Phchi.S1	AUGUSTUS	exon	35889263	35889943	.	+	.	transcript_id "Phchi.S1G558500.t1"; gene_id "Phchi.S1G558500"
Phchi.S1	AUGUSTUS	stop_codon	35889944	35889946	.	+	0	transcript_id "Phchi.S1G558500.t1"; gene_id "Phchi.S1G558500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7222.t1 is derived from g4394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27703919	27705082	.	+	.	Phchi.S1G438100
Phchi.S1	AUGUSTUS	transcript	27703919	27705082	.	+	.	transcript_id "Phchi.S1G438100.t1"; gene_id "Phchi.S1G438100"
Phchi.S1	AUGUSTUS	start_codon	27703919	27703921	.	+	0	transcript_id "Phchi.S1G438100.t1"; gene_id "Phchi.S1G438100"
Phchi.S1	AUGUSTUS	CDS	27703919	27705082	0.95	+	0	transcript_id "Phchi.S1G438100.t1"; gene_id "Phchi.S1G438100"
Phchi.S1	AUGUSTUS	exon	27703919	27705082	.	+	.	transcript_id "Phchi.S1G438100.t1"; gene_id "Phchi.S1G438100"
Phchi.S1	AUGUSTUS	stop_codon	27705083	27705085	.	+	0	transcript_id "Phchi.S1G438100.t1"; gene_id "Phchi.S1G438100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg159.t1 is derived from g9941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	904959	906644	.	-	.	Phchi.S6G011800
Phchi.S6	AUGUSTUS	transcript	904959	906644	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	stop_codon	904956	904958	.	-	0	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	904959	905048	0.99	-	0	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	904959	905048	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	905049	905180	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	905181	905236	0.87	-	2	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	905181	905236	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	905237	905331	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	905332	905438	0.97	-	1	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	905332	905438	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	905439	905552	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	905553	905640	0.46	-	2	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	905553	905640	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	905641	905798	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	905799	905812	0.96	-	1	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	905799	905812	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	905813	905912	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	905913	906034	0.98	-	0	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	905913	906034	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	906035	906243	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	906244	906542	0.68	-	2	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	906244	906542	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	intron	906543	906634	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	CDS	906635	906644	0.98	-	0	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	exon	906635	906644	.	-	.	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
Phchi.S6	AUGUSTUS	start_codon	906642	906644	.	-	0	transcript_id "Phchi.S6G011800.t1"; gene_id "Phchi.S6G011800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9920.t1 is derived from g7096.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44469692	44475788	.	+	.	Phchi.S1G707900
Phchi.S1	AUGUSTUS	transcript	44469692	44475788	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	start_codon	44469692	44469694	.	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44469692	44471249	0.74	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44469692	44471249	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44471250	44471365	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44471366	44472738	1	+	2	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44471366	44472738	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44472739	44472852	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44472853	44473065	0.53	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44472853	44473065	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44473066	44473185	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44473186	44473568	0.63	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44473186	44473568	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44473569	44473702	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44473703	44473990	0.65	+	1	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44473703	44473990	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44473991	44474570	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44474571	44474706	0.48	+	1	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44474571	44474706	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44474707	44474812	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44474813	44474886	0.92	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44474813	44474886	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44474887	44475008	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44475009	44475102	0.99	+	1	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44475009	44475102	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44475103	44475204	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44475205	44475336	1	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44475205	44475336	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44475337	44475419	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44475420	44475580	1	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44475420	44475580	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	intron	44475581	44475670	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	CDS	44475671	44475788	1	+	1	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	exon	44475671	44475788	.	+	.	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
Phchi.S1	AUGUSTUS	stop_codon	44475789	44475791	.	+	0	transcript_id "Phchi.S1G707900.t1"; gene_id "Phchi.S1G707900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13355.t1 is derived from g11821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6299484	6301350	.	-	.	Phchi.S3G067400
Phchi.S3	AUGUSTUS	transcript	6299484	6301350	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	stop_codon	6299481	6299483	.	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6299484	6299663	0.9	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6299484	6299663	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	intron	6299664	6299785	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6299786	6299891	0.93	-	1	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6299786	6299891	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	intron	6299892	6299984	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6299985	6300181	1	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6299985	6300181	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	intron	6300182	6300284	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6300285	6300377	1	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6300285	6300377	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	intron	6300378	6300465	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6300466	6300583	1	-	1	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6300466	6300583	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	intron	6300584	6300693	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6300694	6300905	1	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6300694	6300905	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	intron	6300906	6301044	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	CDS	6301045	6301350	0.93	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	exon	6301045	6301350	.	-	.	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
Phchi.S3	AUGUSTUS	start_codon	6301348	6301350	.	-	0	transcript_id "Phchi.S3G067400.t1"; gene_id "Phchi.S3G067400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13726.t1 is derived from g12193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8551672	8555044	.	+	.	Phchi.S3G104500
Phchi.S3	AUGUSTUS	transcript	8551672	8555044	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	start_codon	8551672	8551674	.	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8551672	8552089	0.92	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8551672	8552089	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8552090	8552179	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8552180	8552463	1	+	2	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8552180	8552463	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8552464	8552554	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8552555	8552791	1	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8552555	8552791	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8552792	8552879	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8552880	8552899	0.85	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8552880	8552899	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8552900	8553012	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8553013	8553176	0.57	+	1	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8553013	8553176	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8553177	8553261	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8553262	8553347	1	+	2	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8553262	8553347	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8553348	8553444	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8553445	8553522	1	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8553445	8553522	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8553523	8553636	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8553637	8553766	1	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8553637	8553766	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8553767	8553858	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8553859	8553943	1	+	2	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8553859	8553943	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	intron	8553944	8554026	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	CDS	8554027	8555044	1	+	1	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	exon	8554027	8555044	.	+	.	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
Phchi.S3	AUGUSTUS	stop_codon	8555045	8555047	.	+	0	transcript_id "Phchi.S3G104500.t1"; gene_id "Phchi.S3G104500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14461.t1 is derived from g12929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12990961	12993114	.	-	.	Phchi.S3G178000
Phchi.S3	AUGUSTUS	transcript	12990961	12993114	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	stop_codon	12990958	12990960	.	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12990961	12991027	0.99	-	1	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12990961	12991027	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991028	12991253	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991254	12991281	0.98	-	2	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991254	12991281	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991282	12991369	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991370	12991466	0.98	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991370	12991466	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991467	12991560	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991561	12991647	1	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991561	12991647	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991648	12991731	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991732	12991830	1	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991732	12991830	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991831	12991981	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991982	12992141	1	-	1	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991982	12992141	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992142	12992217	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992218	12992291	1	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992218	12992291	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992292	12992395	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992396	12992546	0.83	-	1	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992396	12992546	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992547	12992737	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992738	12992859	1	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992738	12992859	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992860	12992958	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992959	12993114	0.86	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992959	12993114	.	-	.	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	start_codon	12993112	12993114	.	-	0	transcript_id "Phchi.S3G178000.t1"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	transcript	12990961	12993114	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	stop_codon	12990958	12990960	.	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12990961	12991027	0.99	-	1	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12990961	12991027	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991028	12991253	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991254	12991281	0.97	-	2	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991254	12991281	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991282	12991369	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991370	12991466	0.97	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991370	12991466	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991467	12991560	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991561	12991647	1	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991561	12991647	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991648	12991731	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991732	12991830	1	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991732	12991830	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991831	12991981	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991982	12992141	1	-	1	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991982	12992141	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992142	12992217	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992218	12992291	0.91	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992218	12992291	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992292	12992436	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992437	12992521	0.49	-	1	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992437	12992521	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992522	12992737	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992738	12992859	1	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992738	12992859	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992860	12992958	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992959	12993114	0.78	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992959	12993114	.	-	.	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	start_codon	12993112	12993114	.	-	0	transcript_id "Phchi.S3G178000.t2"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	transcript	12990961	12993114	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	stop_codon	12990958	12990960	.	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12990961	12991027	0.98	-	1	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12990961	12991027	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991028	12991253	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991254	12991281	0.96	-	2	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991254	12991281	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991282	12991369	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991370	12991466	0.96	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991370	12991466	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991467	12991560	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991561	12991647	1	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991561	12991647	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991648	12991731	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991732	12991830	1	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991732	12991830	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12991831	12991981	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12991982	12992141	1	-	1	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12991982	12992141	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992142	12992217	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992218	12992262	0.41	-	1	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992218	12992262	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992263	12992347	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992348	12992395	0.32	-	1	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992348	12992395	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992396	12992737	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992738	12992859	1	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992738	12992859	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	intron	12992860	12992958	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	CDS	12992959	12993114	0.85	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	exon	12992959	12993114	.	-	.	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
Phchi.S3	AUGUSTUS	start_codon	12993112	12993114	.	-	0	transcript_id "Phchi.S3G178000.t3"; gene_id "Phchi.S3G178000"
# This transcript jg8452.t2 is derived from g5627.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8453.t1 is derived from g5629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36010593	36012288	.	+	.	Phchi.S1G561300
Phchi.S1	AUGUSTUS	transcript	36010593	36012288	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	start_codon	36010593	36010595	.	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	CDS	36010593	36010925	0.73	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	exon	36010593	36010925	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	intron	36010926	36011326	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	CDS	36011327	36011509	1	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	exon	36011327	36011509	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	intron	36011510	36011677	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	CDS	36011678	36011842	1	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	exon	36011678	36011842	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	intron	36011843	36011928	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	CDS	36011929	36012024	0.97	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	exon	36011929	36012024	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	intron	36012025	36012264	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	CDS	36012265	36012288	0.74	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	exon	36012265	36012288	.	+	.	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
Phchi.S1	AUGUSTUS	stop_codon	36012289	36012291	.	+	0	transcript_id "Phchi.S1G561300.t1"; gene_id "Phchi.S1G561300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10108.t1 is derived from g7284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45763822	45764968	.	-	.	Phchi.S1G726700
Phchi.S1	AUGUSTUS	transcript	45763822	45764968	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	stop_codon	45763819	45763821	.	-	0	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	CDS	45763822	45763938	0.97	-	0	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	exon	45763822	45763938	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	intron	45763939	45764041	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	CDS	45764042	45764212	1	-	0	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	exon	45764042	45764212	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	intron	45764213	45764392	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	CDS	45764393	45764578	1	-	0	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	exon	45764393	45764578	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	intron	45764579	45764659	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	CDS	45764660	45764968	0.4	-	0	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	exon	45764660	45764968	.	-	.	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
Phchi.S1	AUGUSTUS	start_codon	45764966	45764968	.	-	0	transcript_id "Phchi.S1G726700.t1"; gene_id "Phchi.S1G726700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9193.t1 is derived from g6368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40288570	40290351	.	-	.	Phchi.S1G635200
Phchi.S1	AUGUSTUS	transcript	40288570	40290351	.	-	.	transcript_id "Phchi.S1G635200.t1"; gene_id "Phchi.S1G635200"
Phchi.S1	AUGUSTUS	stop_codon	40288567	40288569	.	-	0	transcript_id "Phchi.S1G635200.t1"; gene_id "Phchi.S1G635200"
Phchi.S1	AUGUSTUS	CDS	40288570	40290351	0.98	-	0	transcript_id "Phchi.S1G635200.t1"; gene_id "Phchi.S1G635200"
Phchi.S1	AUGUSTUS	exon	40288570	40290351	.	-	.	transcript_id "Phchi.S1G635200.t1"; gene_id "Phchi.S1G635200"
Phchi.S1	AUGUSTUS	start_codon	40290349	40290351	.	-	0	transcript_id "Phchi.S1G635200.t1"; gene_id "Phchi.S1G635200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11495.t1 is derived from g15545.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6642791	6643405	.	-	.	Phchi.S4G107700
Phchi.S4	AUGUSTUS	transcript	6642867	6643318	.	-	.	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	stop_codon	6642864	6642866	.	-	0	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	CDS	6642867	6642995	0.6	-	0	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	exon	6642867	6642995	.	-	.	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	intron	6642996	6643078	.	-	.	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	CDS	6643079	6643318	0.6	-	0	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	exon	6643079	6643318	.	-	.	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	start_codon	6643316	6643318	.	-	0	transcript_id "Phchi.S4G107700.t1"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	transcript	6642791	6643405	.	-	.	transcript_id "Phchi.S4G107700.t2"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	stop_codon	6642788	6642790	.	-	0	transcript_id "Phchi.S4G107700.t2"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	CDS	6642791	6643405	0.75	-	0	transcript_id "Phchi.S4G107700.t2"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	exon	6642791	6643405	.	-	.	transcript_id "Phchi.S4G107700.t2"; gene_id "Phchi.S4G107700"
Phchi.S4	AUGUSTUS	start_codon	6643403	6643405	.	-	0	transcript_id "Phchi.S4G107700.t2"; gene_id "Phchi.S4G107700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15247.t1 is derived from g13715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17891314	17891903	.	+	.	Phchi.S3G256600
Phchi.S3	AUGUSTUS	transcript	17891314	17891903	.	+	.	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	start_codon	17891314	17891316	.	+	0	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	CDS	17891314	17891627	0.39	+	0	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	exon	17891314	17891627	.	+	.	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	intron	17891628	17891728	.	+	.	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	CDS	17891729	17891903	0.64	+	1	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	exon	17891729	17891903	.	+	.	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
Phchi.S3	AUGUSTUS	stop_codon	17891904	17891906	.	+	0	transcript_id "Phchi.S3G256600.t1"; gene_id "Phchi.S3G256600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11957.t1 is derived from g7632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	190459	193939	.	-	.	Phchi.S2G003700
Phchi.S2	AUGUSTUS	transcript	190459	193939	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	stop_codon	190456	190458	.	-	0	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	CDS	190459	190504	0.51	-	1	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	exon	190459	190504	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	intron	190505	190637	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	CDS	190638	190856	0.51	-	1	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	exon	190638	190856	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	intron	190857	191054	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	CDS	191055	191755	0.92	-	0	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	exon	191055	191755	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	intron	191756	191948	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	CDS	191949	192847	0.89	-	2	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	exon	191949	192847	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	intron	192848	192963	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	CDS	192964	193939	0.92	-	0	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	exon	192964	193939	.	-	.	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
Phchi.S2	AUGUSTUS	start_codon	193937	193939	.	-	0	transcript_id "Phchi.S2G003700.t1"; gene_id "Phchi.S2G003700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg911.t1 is derived from g10693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6406614	6407186	.	+	.	Phchi.S6G087000
Phchi.S6	AUGUSTUS	transcript	6406614	6407186	.	+	.	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	start_codon	6406614	6406616	.	+	0	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	CDS	6406614	6406845	0.7	+	0	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	exon	6406614	6406845	.	+	.	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	intron	6406846	6407172	.	+	.	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	CDS	6407173	6407186	0.99	+	2	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	exon	6407173	6407186	.	+	.	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
Phchi.S6	AUGUSTUS	stop_codon	6407187	6407189	.	+	0	transcript_id "Phchi.S6G087000.t1"; gene_id "Phchi.S6G087000"
# This transcript jg6799.t2 is derived from g3971.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6800.t1 is derived from g3972.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25121132	25123202	.	+	.	Phchi.S1G395900
Phchi.S1	AUGUSTUS	transcript	25121132	25123202	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	start_codon	25121132	25121134	.	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25121132	25121159	0.43	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25121132	25121159	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	intron	25121160	25121283	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25121284	25121522	0.99	+	2	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25121284	25121522	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	intron	25121523	25121694	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25121695	25121876	0.98	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25121695	25121876	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	intron	25121877	25121984	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25121985	25122096	0.98	+	1	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25121985	25122096	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	intron	25122097	25122182	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25122183	25122332	0.98	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25122183	25122332	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	intron	25122333	25122445	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25122446	25122769	0.99	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25122446	25122769	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	intron	25122770	25122863	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	CDS	25122864	25123202	1	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	exon	25122864	25123202	.	+	.	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
Phchi.S1	AUGUSTUS	stop_codon	25123203	25123205	.	+	0	transcript_id "Phchi.S1G395900.t1"; gene_id "Phchi.S1G395900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14982.t1 is derived from g13450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15863381	15865063	.	-	.	Phchi.S3G230100
Phchi.S3	AUGUSTUS	transcript	15863381	15865063	.	-	.	transcript_id "Phchi.S3G230100.t1"; gene_id "Phchi.S3G230100"
Phchi.S3	AUGUSTUS	stop_codon	15863378	15863380	.	-	0	transcript_id "Phchi.S3G230100.t1"; gene_id "Phchi.S3G230100"
Phchi.S3	AUGUSTUS	CDS	15863381	15865063	0.93	-	0	transcript_id "Phchi.S3G230100.t1"; gene_id "Phchi.S3G230100"
Phchi.S3	AUGUSTUS	exon	15863381	15865063	.	-	.	transcript_id "Phchi.S3G230100.t1"; gene_id "Phchi.S3G230100"
Phchi.S3	AUGUSTUS	start_codon	15865061	15865063	.	-	0	transcript_id "Phchi.S3G230100.t1"; gene_id "Phchi.S3G230100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4809.t1 is derived from g1979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12926982	12928805	.	-	.	Phchi.S1G196800
Phchi.S1	AUGUSTUS	transcript	12926982	12928805	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	stop_codon	12926979	12926981	.	-	0	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12926982	12927041	1	-	0	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12926982	12927041	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12927042	12927117	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12927118	12927517	0.92	-	1	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12927118	12927517	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12927518	12927598	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12927599	12927647	0.84	-	2	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12927599	12927647	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12927648	12927751	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12927752	12927829	0.28	-	2	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12927752	12927829	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12927830	12927946	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12927947	12928046	0.72	-	0	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12927947	12928046	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12928047	12928193	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12928194	12928241	1	-	0	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12928194	12928241	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12928242	12928326	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12928327	12928453	0.96	-	1	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12928327	12928453	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	intron	12928454	12928557	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	CDS	12928558	12928805	0.94	-	0	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	exon	12928558	12928805	.	-	.	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
Phchi.S1	AUGUSTUS	start_codon	12928803	12928805	.	-	0	transcript_id "Phchi.S1G196800.t1"; gene_id "Phchi.S1G196800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11829.t1 is derived from g15881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8466169	8468709	.	-	.	Phchi.S4G141100
Phchi.S4	AUGUSTUS	transcript	8466169	8468709	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	stop_codon	8466166	8466168	.	-	0	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	CDS	8466169	8466345	0.9	-	0	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	exon	8466169	8466345	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	intron	8466346	8466435	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	CDS	8466436	8467053	0.93	-	0	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	exon	8466436	8467053	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	intron	8467054	8467160	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	CDS	8467161	8467625	0.9	-	0	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	exon	8467161	8467625	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	intron	8467626	8467830	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	CDS	8467831	8468709	0.92	-	0	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	exon	8467831	8468709	.	-	.	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
Phchi.S4	AUGUSTUS	start_codon	8468707	8468709	.	-	0	transcript_id "Phchi.S4G141100.t1"; gene_id "Phchi.S4G141100"
# This transcript jg9407.t2 is derived from g6583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9407.t3 is derived from g6583.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9408.t1 is derived from g6584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41362412	41363161	.	-	.	Phchi.S1G656700
Phchi.S1	AUGUSTUS	transcript	41362412	41363161	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	stop_codon	41362409	41362411	.	-	0	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	CDS	41362412	41362500	1	-	2	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	exon	41362412	41362500	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	intron	41362501	41362604	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	CDS	41362605	41362817	1	-	2	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	exon	41362605	41362817	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	intron	41362818	41362902	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	CDS	41362903	41362974	1	-	2	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	exon	41362903	41362974	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	intron	41362975	41363058	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	CDS	41363059	41363161	1	-	0	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	exon	41363059	41363161	.	-	.	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
Phchi.S1	AUGUSTUS	start_codon	41363159	41363161	.	-	0	transcript_id "Phchi.S1G656700.t1"; gene_id "Phchi.S1G656700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5845.t1 is derived from g3015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19303061	19306383	.	+	.	Phchi.S1G300400
Phchi.S1	AUGUSTUS	transcript	19303061	19306383	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	start_codon	19303061	19303063	.	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19303061	19303218	0.99	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19303061	19303218	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19303219	19303532	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19303533	19303617	1	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19303533	19303617	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19303618	19303757	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19303758	19303855	1	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19303758	19303855	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19303856	19303970	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19303971	19304026	1	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19303971	19304026	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19304027	19304139	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19304140	19304257	1	+	2	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19304140	19304257	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19304258	19304370	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19304371	19304398	1	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19304371	19304398	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19304399	19304482	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19304483	19304574	1	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19304483	19304574	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19304575	19304665	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19304666	19304822	0.99	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19304666	19304822	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19304823	19304905	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19304906	19305030	1	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19304906	19305030	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19305031	19305135	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19305136	19305235	1	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19305136	19305235	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19305236	19305323	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19305324	19305415	0.95	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19305324	19305415	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19305416	19305716	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19305717	19305867	0.99	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19305717	19305867	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19305868	19305996	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19305997	19306056	1	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19305997	19306056	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19306057	19306156	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19306157	19306203	1	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19306157	19306203	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	intron	19306204	19306292	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	CDS	19306293	19306383	1	+	1	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	exon	19306293	19306383	.	+	.	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
Phchi.S1	AUGUSTUS	stop_codon	19306384	19306386	.	+	0	transcript_id "Phchi.S1G300400.t1"; gene_id "Phchi.S1G300400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11407.t1 is derived from g15457.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6210506	6211800	.	-	.	Phchi.S4G098900
Phchi.S4	AUGUSTUS	transcript	6210506	6211800	.	-	.	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	stop_codon	6210503	6210505	.	-	0	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	CDS	6210506	6210586	0.93	-	0	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	exon	6210506	6210586	.	-	.	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	intron	6210587	6210797	.	-	.	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	CDS	6210798	6211160	0.98	-	0	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	exon	6210798	6211160	.	-	.	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	intron	6211161	6211647	.	-	.	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	CDS	6211648	6211800	0.85	-	0	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	exon	6211648	6211800	.	-	.	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	start_codon	6211798	6211800	.	-	0	transcript_id "Phchi.S4G098900.t1"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	transcript	6210506	6211800	.	-	.	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	stop_codon	6210503	6210505	.	-	0	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	CDS	6210506	6210586	0.93	-	0	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	exon	6210506	6210586	.	-	.	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	intron	6210587	6210809	.	-	.	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	CDS	6210810	6211160	0.98	-	0	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	exon	6210810	6211160	.	-	.	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	intron	6211161	6211647	.	-	.	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	CDS	6211648	6211800	0.81	-	0	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	exon	6211648	6211800	.	-	.	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
Phchi.S4	AUGUSTUS	start_codon	6211798	6211800	.	-	0	transcript_id "Phchi.S4G098900.t2"; gene_id "Phchi.S4G098900"
# This transcript jg15744.t2 is derived from g14214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15745.t1 is derived from g14215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21031437	21035288	.	+	.	Phchi.S3G306400
Phchi.S3	AUGUSTUS	transcript	21031437	21035288	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	start_codon	21031437	21031439	.	+	0	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21031437	21031750	0.76	+	0	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21031437	21031750	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21031751	21032059	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21032060	21032617	0.8	+	1	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21032060	21032617	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21032618	21032748	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21032749	21032954	1	+	1	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21032749	21032954	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21032955	21033435	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21033436	21033928	0.36	+	2	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21033436	21033928	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21033929	21034023	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21034024	21034381	0.42	+	1	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21034024	21034381	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21034382	21034478	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21034479	21034550	1	+	0	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21034479	21034550	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21034551	21034636	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21034637	21034741	1	+	0	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21034637	21034741	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21034742	21034874	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21034875	21035061	1	+	0	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21034875	21035061	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	intron	21035062	21035214	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	CDS	21035215	21035288	0.8	+	2	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	exon	21035215	21035288	.	+	.	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
Phchi.S3	AUGUSTUS	stop_codon	21035289	21035291	.	+	0	transcript_id "Phchi.S3G306400.t1"; gene_id "Phchi.S3G306400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9308.t1 is derived from g6483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40893320	40893869	.	-	.	Phchi.S1G646700
Phchi.S1	AUGUSTUS	transcript	40893320	40893869	.	-	.	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	stop_codon	40893317	40893319	.	-	0	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	CDS	40893320	40893408	0.45	-	2	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	exon	40893320	40893408	.	-	.	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	intron	40893409	40893493	.	-	.	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	CDS	40893494	40893614	0.88	-	0	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	exon	40893494	40893614	.	-	.	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	intron	40893615	40893734	.	-	.	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	CDS	40893735	40893869	0.74	-	0	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	exon	40893735	40893869	.	-	.	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
Phchi.S1	AUGUSTUS	start_codon	40893867	40893869	.	-	0	transcript_id "Phchi.S1G646700.t1"; gene_id "Phchi.S1G646700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14326.t1 is derived from g12793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12104523	12105543	.	-	.	Phchi.S3G164500
Phchi.S3	AUGUSTUS	transcript	12104523	12105543	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	stop_codon	12104520	12104522	.	-	0	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	CDS	12104523	12104581	0.72	-	2	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	exon	12104523	12104581	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	intron	12104582	12104723	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	CDS	12104724	12104760	0.53	-	0	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	exon	12104724	12104760	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	intron	12104761	12104855	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	CDS	12104856	12104874	0.75	-	1	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	exon	12104856	12104874	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	intron	12104875	12105284	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	CDS	12105285	12105403	0.79	-	0	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	exon	12105285	12105403	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	intron	12105404	12105528	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	CDS	12105529	12105543	0.48	-	0	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	exon	12105529	12105543	.	-	.	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
Phchi.S3	AUGUSTUS	start_codon	12105541	12105543	.	-	0	transcript_id "Phchi.S3G164500.t1"; gene_id "Phchi.S3G164500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8811.t1 is derived from g5986.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38096508	38096798	.	-	.	Phchi.S1G597000
Phchi.S1	AUGUSTUS	transcript	38096508	38096798	.	-	.	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	stop_codon	38096505	38096507	.	-	0	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	CDS	38096508	38096524	0.99	-	2	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	exon	38096508	38096524	.	-	.	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	intron	38096525	38096605	.	-	.	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	CDS	38096606	38096798	0.92	-	0	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	exon	38096606	38096798	.	-	.	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
Phchi.S1	AUGUSTUS	start_codon	38096796	38096798	.	-	0	transcript_id "Phchi.S1G597000.t1"; gene_id "Phchi.S1G597000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2061.t1 is derived from g8981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4661733	4663538	.	+	.	Phchi.S5G067000
Phchi.S5	AUGUSTUS	transcript	4661733	4663538	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	start_codon	4661733	4661735	.	+	0	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	CDS	4661733	4661915	0.87	+	0	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	exon	4661733	4661915	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	intron	4661916	4662034	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	CDS	4662035	4662071	0.53	+	0	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	exon	4662035	4662071	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	intron	4662072	4662266	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	CDS	4662267	4662310	1	+	2	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	exon	4662267	4662310	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	intron	4662311	4662401	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	CDS	4662402	4663538	0.59	+	0	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	exon	4662402	4663538	.	+	.	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
Phchi.S5	AUGUSTUS	stop_codon	4663539	4663541	.	+	0	transcript_id "Phchi.S5G067000.t1"; gene_id "Phchi.S5G067000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8934.t1 is derived from g6109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38737632	38739200	.	-	.	Phchi.S1G609300
Phchi.S1	AUGUSTUS	transcript	38737632	38739200	.	-	.	transcript_id "Phchi.S1G609300.t1"; gene_id "Phchi.S1G609300"
Phchi.S1	AUGUSTUS	stop_codon	38737629	38737631	.	-	0	transcript_id "Phchi.S1G609300.t1"; gene_id "Phchi.S1G609300"
Phchi.S1	AUGUSTUS	CDS	38737632	38739200	0.97	-	0	transcript_id "Phchi.S1G609300.t1"; gene_id "Phchi.S1G609300"
Phchi.S1	AUGUSTUS	exon	38737632	38739200	.	-	.	transcript_id "Phchi.S1G609300.t1"; gene_id "Phchi.S1G609300"
Phchi.S1	AUGUSTUS	start_codon	38739198	38739200	.	-	0	transcript_id "Phchi.S1G609300.t1"; gene_id "Phchi.S1G609300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14285.t1 is derived from g12752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11917329	11919534	.	-	.	Phchi.S3G160400
Phchi.S3	AUGUSTUS	transcript	11917329	11919534	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	stop_codon	11917326	11917328	.	-	0	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11917329	11917444	0.99	-	2	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11917329	11917444	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11917445	11917524	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11917525	11917768	0.73	-	0	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11917525	11917768	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11917769	11917857	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11917858	11917922	0.99	-	2	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11917858	11917922	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11917923	11918000	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11918001	11918101	1	-	1	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11918001	11918101	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11918102	11918231	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11918232	11918390	0.98	-	1	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11918232	11918390	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11918391	11918600	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11918601	11918656	1	-	0	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11918601	11918656	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11918657	11918740	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11918741	11918813	0.66	-	1	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11918741	11918813	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11918814	11918917	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11918918	11918974	1	-	1	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11918918	11918974	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11918975	11919127	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11919128	11919174	1	-	0	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11919128	11919174	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11919175	11919279	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11919280	11919437	1	-	2	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11919280	11919437	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	intron	11919438	11919527	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	CDS	11919528	11919534	1	-	0	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	exon	11919528	11919534	.	-	.	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
Phchi.S3	AUGUSTUS	start_codon	11919532	11919534	.	-	0	transcript_id "Phchi.S3G160400.t1"; gene_id "Phchi.S3G160400"
# This transcript jg1252.t2 is derived from g11035.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1253.t1 is derived from g11036.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8653263	8655384	.	+	.	Phchi.S6G121200
Phchi.S6	AUGUSTUS	transcript	8653263	8655384	.	+	.	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	start_codon	8653263	8653265	.	+	0	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	CDS	8653263	8654126	0.53	+	0	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	exon	8653263	8654126	.	+	.	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	intron	8654127	8654257	.	+	.	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	CDS	8654258	8654805	0.37	+	0	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	exon	8654258	8654805	.	+	.	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	intron	8654806	8654879	.	+	.	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	CDS	8654880	8655384	0.75	+	1	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	exon	8654880	8655384	.	+	.	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
Phchi.S6	AUGUSTUS	stop_codon	8655385	8655387	.	+	0	transcript_id "Phchi.S6G121200.t1"; gene_id "Phchi.S6G121200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5610.t1 is derived from g2780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17887692	17888256	.	-	.	Phchi.S1G276900
Phchi.S1	AUGUSTUS	transcript	17887692	17888256	.	-	.	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	stop_codon	17887689	17887691	.	-	0	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	CDS	17887692	17887793	0.74	-	0	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	exon	17887692	17887793	.	-	.	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	intron	17887794	17887896	.	-	.	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	CDS	17887897	17888256	0.59	-	0	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	exon	17887897	17888256	.	-	.	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
Phchi.S1	AUGUSTUS	start_codon	17888254	17888256	.	-	0	transcript_id "Phchi.S1G276900.t1"; gene_id "Phchi.S1G276900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14987.t1 is derived from g13455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15945117	15947397	.	-	.	Phchi.S3G230600
Phchi.S3	AUGUSTUS	transcript	15945117	15947397	.	-	.	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	stop_codon	15945114	15945116	.	-	0	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	CDS	15945117	15946162	1	-	2	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	exon	15945117	15946162	.	-	.	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	intron	15946163	15946461	.	-	.	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	CDS	15946462	15946702	1	-	0	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	exon	15946462	15946702	.	-	.	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	intron	15946703	15946887	.	-	.	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	CDS	15946888	15947397	0.94	-	0	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	exon	15946888	15947397	.	-	.	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
Phchi.S3	AUGUSTUS	start_codon	15947395	15947397	.	-	0	transcript_id "Phchi.S3G230600.t1"; gene_id "Phchi.S3G230600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3124.t1 is derived from g293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1852533	1853367	.	-	.	Phchi.S1G028300
Phchi.S1	AUGUSTUS	transcript	1852533	1853367	.	-	.	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	stop_codon	1852530	1852532	.	-	0	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	CDS	1852533	1852751	0.96	-	0	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	exon	1852533	1852751	.	-	.	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	intron	1852752	1852893	.	-	.	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	CDS	1852894	1853111	0.97	-	2	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	exon	1852894	1853111	.	-	.	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	intron	1853112	1853192	.	-	.	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	CDS	1853193	1853367	0.7	-	0	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	exon	1853193	1853367	.	-	.	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
Phchi.S1	AUGUSTUS	start_codon	1853365	1853367	.	-	0	transcript_id "Phchi.S1G028300.t1"; gene_id "Phchi.S1G028300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13135.t1 is derived from g11600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4316991	4318454	.	+	.	Phchi.S3G045400
Phchi.S3	AUGUSTUS	transcript	4316991	4318454	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	start_codon	4316991	4316993	.	+	0	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	CDS	4316991	4317138	0.65	+	0	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	exon	4316991	4317138	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	intron	4317139	4317275	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	CDS	4317276	4317371	1	+	2	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	exon	4317276	4317371	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	intron	4317372	4317531	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	CDS	4317532	4317590	1	+	2	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	exon	4317532	4317590	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	intron	4317591	4317671	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	CDS	4317672	4317857	1	+	0	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	exon	4317672	4317857	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	intron	4317858	4317994	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	CDS	4317995	4318165	1	+	0	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	exon	4317995	4318165	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	intron	4318166	4318301	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	CDS	4318302	4318454	0.97	+	0	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	exon	4318302	4318454	.	+	.	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
Phchi.S3	AUGUSTUS	stop_codon	4318455	4318457	.	+	0	transcript_id "Phchi.S3G045400.t1"; gene_id "Phchi.S3G045400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9720.t1 is derived from g6896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43396520	43397867	.	+	.	Phchi.S1G687900
Phchi.S1	AUGUSTUS	transcript	43396520	43397867	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	start_codon	43396520	43396522	.	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	CDS	43396520	43396735	0.96	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	exon	43396520	43396735	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	intron	43396736	43396833	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	CDS	43396834	43397010	1	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	exon	43396834	43397010	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	intron	43397011	43397108	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	CDS	43397109	43397333	1	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	exon	43397109	43397333	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	intron	43397334	43397424	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	CDS	43397425	43397553	1	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	exon	43397425	43397553	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	intron	43397554	43397639	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	CDS	43397640	43397867	0.78	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	exon	43397640	43397867	.	+	.	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
Phchi.S1	AUGUSTUS	stop_codon	43397868	43397870	.	+	0	transcript_id "Phchi.S1G687900.t1"; gene_id "Phchi.S1G687900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4758.t1 is derived from g1928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12681173	12681794	.	+	.	Phchi.S1G191700
Phchi.S1	AUGUSTUS	transcript	12681173	12681794	.	+	.	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	start_codon	12681173	12681175	.	+	0	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	CDS	12681173	12681290	0.86	+	0	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	exon	12681173	12681290	.	+	.	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	intron	12681291	12681418	.	+	.	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	CDS	12681419	12681477	0.97	+	2	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	exon	12681419	12681477	.	+	.	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	intron	12681478	12681587	.	+	.	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	CDS	12681588	12681794	1	+	0	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	exon	12681588	12681794	.	+	.	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
Phchi.S1	AUGUSTUS	stop_codon	12681795	12681797	.	+	0	transcript_id "Phchi.S1G191700.t1"; gene_id "Phchi.S1G191700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6750.t1 is derived from g3922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24844166	24845000	.	+	.	Phchi.S1G390900
Phchi.S1	AUGUSTUS	transcript	24844166	24845000	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	start_codon	24844166	24844168	.	+	0	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	CDS	24844166	24844238	0.49	+	0	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	exon	24844166	24844238	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	intron	24844239	24844352	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	CDS	24844353	24844554	0.75	+	2	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	exon	24844353	24844554	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	intron	24844555	24844627	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	CDS	24844628	24844782	0.86	+	1	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	exon	24844628	24844782	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	intron	24844783	24844917	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	CDS	24844918	24845000	0.85	+	2	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	exon	24844918	24845000	.	+	.	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
Phchi.S1	AUGUSTUS	stop_codon	24845001	24845003	.	+	0	transcript_id "Phchi.S1G390900.t1"; gene_id "Phchi.S1G390900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2881.t1 is derived from g50.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	260682	262226	.	+	.	Phchi.S1G004000
Phchi.S1	AUGUSTUS	transcript	260682	262226	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	start_codon	260682	260684	.	+	0	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	260682	260886	0.98	+	0	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	260682	260886	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	260887	261126	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	261127	261180	1	+	2	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	261127	261180	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	261181	261292	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	261293	261694	1	+	2	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	261293	261694	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	261695	261769	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	261770	261953	1	+	2	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	261770	261953	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	261954	262042	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	262043	262226	0.83	+	1	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	262043	262226	.	+	.	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	stop_codon	262227	262229	.	+	0	transcript_id "Phchi.S1G004000.t1"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	transcript	260682	262226	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	start_codon	260682	260684	.	+	0	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	260682	260886	0.98	+	0	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	260682	260886	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	260887	260972	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	260973	260982	0.61	+	2	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	260973	260982	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	260983	261067	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	261068	261180	0.61	+	1	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	261068	261180	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	261181	261292	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	261293	261694	0.98	+	2	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	261293	261694	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	261695	261769	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	261770	261953	0.99	+	2	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	261770	261953	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	intron	261954	262042	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	CDS	262043	262226	0.74	+	1	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	exon	262043	262226	.	+	.	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
Phchi.S1	AUGUSTUS	stop_codon	262227	262229	.	+	0	transcript_id "Phchi.S1G004000.t2"; gene_id "Phchi.S1G004000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14025.t1 is derived from g12492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10351400	10353839	.	-	.	Phchi.S3G134400
Phchi.S3	AUGUSTUS	transcript	10351400	10353839	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	stop_codon	10351397	10351399	.	-	0	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10351400	10351421	0.63	-	1	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10351400	10351421	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	intron	10351422	10351504	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10351505	10352592	0.47	-	0	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10351505	10352592	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	intron	10352593	10352690	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10352691	10352785	1	-	2	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10352691	10352785	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	intron	10352786	10352868	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10352869	10352994	1	-	2	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10352869	10352994	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	intron	10352995	10353148	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10353149	10353373	0.94	-	2	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10353149	10353373	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	intron	10353374	10353587	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10353588	10353644	0.51	-	2	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10353588	10353644	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	intron	10353645	10353790	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	CDS	10353791	10353839	0.82	-	0	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	exon	10353791	10353839	.	-	.	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
Phchi.S3	AUGUSTUS	start_codon	10353837	10353839	.	-	0	transcript_id "Phchi.S3G134400.t1"; gene_id "Phchi.S3G134400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12504.t1 is derived from g8181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	31025546	31026560	.	+	.	Phchi.S2G058400
Phchi.S2	AUGUSTUS	transcript	31025546	31026560	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	start_codon	31025546	31025548	.	+	0	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	CDS	31025546	31025641	1	+	0	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	exon	31025546	31025641	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	intron	31025642	31025817	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	CDS	31025818	31025865	1	+	0	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	exon	31025818	31025865	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	intron	31025866	31025949	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	CDS	31025950	31026014	1	+	0	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	exon	31025950	31026014	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	intron	31026015	31026100	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	CDS	31026101	31026170	0.97	+	1	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	exon	31026101	31026170	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	intron	31026171	31026282	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	CDS	31026283	31026328	0.91	+	0	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	exon	31026283	31026328	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	intron	31026329	31026426	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	CDS	31026427	31026560	0.91	+	2	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	exon	31026427	31026560	.	+	.	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
Phchi.S2	AUGUSTUS	stop_codon	31026561	31026563	.	+	0	transcript_id "Phchi.S2G058400.t1"; gene_id "Phchi.S2G058400"
# This transcript jg2559.t2 is derived from g9479.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2560.t1 is derived from g9480.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7390841	7391551	.	-	.	Phchi.S5G116900
Phchi.S5	AUGUSTUS	transcript	7390841	7391551	.	-	.	transcript_id "Phchi.S5G116900.t1"; gene_id "Phchi.S5G116900"
Phchi.S5	AUGUSTUS	stop_codon	7390838	7390840	.	-	0	transcript_id "Phchi.S5G116900.t1"; gene_id "Phchi.S5G116900"
Phchi.S5	AUGUSTUS	CDS	7390841	7391551	0.77	-	0	transcript_id "Phchi.S5G116900.t1"; gene_id "Phchi.S5G116900"
Phchi.S5	AUGUSTUS	exon	7390841	7391551	.	-	.	transcript_id "Phchi.S5G116900.t1"; gene_id "Phchi.S5G116900"
Phchi.S5	AUGUSTUS	start_codon	7391549	7391551	.	-	0	transcript_id "Phchi.S5G116900.t1"; gene_id "Phchi.S5G116900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2359.t1 is derived from g9279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6332816	6335420	.	+	.	Phchi.S5G096800
Phchi.S5	AUGUSTUS	transcript	6332816	6335420	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	start_codon	6332816	6332818	.	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6332816	6332871	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6332816	6332871	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6332872	6332974	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6332975	6333063	1	+	1	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6332975	6333063	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6333064	6333268	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6333269	6333414	1	+	2	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6333269	6333414	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6333415	6333513	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6333514	6333561	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6333514	6333561	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6333562	6333642	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6333643	6333724	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6333643	6333724	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6333725	6333938	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6333939	6334041	1	+	2	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6333939	6334041	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6334042	6334193	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6334194	6334314	1	+	1	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6334194	6334314	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6334315	6334602	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6334603	6334650	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6334603	6334650	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6334651	6334768	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6334769	6334852	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6334769	6334852	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6334853	6334938	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6334939	6335003	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6334939	6335003	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6335004	6335072	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6335073	6335124	1	+	1	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6335073	6335124	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6335125	6335210	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6335211	6335249	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6335211	6335249	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	intron	6335250	6335363	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	CDS	6335364	6335420	1	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	exon	6335364	6335420	.	+	.	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
Phchi.S5	AUGUSTUS	stop_codon	6335421	6335423	.	+	0	transcript_id "Phchi.S5G096800.t1"; gene_id "Phchi.S5G096800"
# This transcript jg5921.t2 is derived from g3092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5922.t1 is derived from g3093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19881948	19882371	.	-	.	Phchi.S1G308100
Phchi.S1	AUGUSTUS	transcript	19881948	19882371	.	-	.	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	stop_codon	19881945	19881947	.	-	0	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	CDS	19881948	19882005	0.74	-	1	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	exon	19881948	19882005	.	-	.	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	intron	19882006	19882084	.	-	.	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	CDS	19882085	19882152	0.76	-	0	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	exon	19882085	19882152	.	-	.	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	intron	19882153	19882251	.	-	.	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	CDS	19882252	19882371	0.6	-	0	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	exon	19882252	19882371	.	-	.	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
Phchi.S1	AUGUSTUS	start_codon	19882369	19882371	.	-	0	transcript_id "Phchi.S1G308100.t1"; gene_id "Phchi.S1G308100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4818.t1 is derived from g1988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12987946	12988799	.	-	.	Phchi.S1G197700
Phchi.S1	AUGUSTUS	transcript	12987946	12988799	.	-	.	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	stop_codon	12987943	12987945	.	-	0	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	CDS	12987946	12988180	0.99	-	1	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	exon	12987946	12988180	.	-	.	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	intron	12988181	12988257	.	-	.	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	CDS	12988258	12988582	0.94	-	2	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	exon	12988258	12988582	.	-	.	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	intron	12988583	12988660	.	-	.	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	CDS	12988661	12988799	0.99	-	0	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	exon	12988661	12988799	.	-	.	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
Phchi.S1	AUGUSTUS	start_codon	12988797	12988799	.	-	0	transcript_id "Phchi.S1G197700.t1"; gene_id "Phchi.S1G197700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5047.t1 is derived from g2217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14285247	14286403	.	+	.	Phchi.S1G220600
Phchi.S1	AUGUSTUS	transcript	14285247	14286403	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	start_codon	14285247	14285249	.	+	0	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	CDS	14285247	14285329	0.93	+	0	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	exon	14285247	14285329	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	intron	14285330	14285471	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	CDS	14285472	14285487	0.9	+	1	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	exon	14285472	14285487	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	intron	14285488	14285959	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	CDS	14285960	14286025	0.75	+	0	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	exon	14285960	14286025	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	intron	14286026	14286334	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	CDS	14286335	14286403	0.58	+	0	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	exon	14286335	14286403	.	+	.	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
Phchi.S1	AUGUSTUS	stop_codon	14286404	14286406	.	+	0	transcript_id "Phchi.S1G220600.t1"; gene_id "Phchi.S1G220600"
# This transcript jg8947.t2 is derived from g6122.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8947.t3 is derived from g6122.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8948.t1 is derived from g6123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38805517	38807029	.	-	.	Phchi.S1G610700
Phchi.S1	AUGUSTUS	transcript	38805517	38807029	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	stop_codon	38805514	38805516	.	-	0	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	CDS	38805517	38805582	0.7	-	0	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	exon	38805517	38805582	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	intron	38805583	38805696	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	CDS	38805697	38806448	0.75	-	2	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	exon	38805697	38806448	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	intron	38806449	38806535	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	CDS	38806536	38806575	1	-	0	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	exon	38806536	38806575	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	intron	38806576	38806780	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	CDS	38806781	38806859	0.9	-	1	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	exon	38806781	38806859	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	intron	38806860	38806943	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	CDS	38806944	38807029	0.93	-	0	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	exon	38806944	38807029	.	-	.	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
Phchi.S1	AUGUSTUS	start_codon	38807027	38807029	.	-	0	transcript_id "Phchi.S1G610700.t1"; gene_id "Phchi.S1G610700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4633.t1 is derived from g1803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11485618	11487290	.	+	.	Phchi.S1G179200
Phchi.S1	AUGUSTUS	transcript	11485618	11487290	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	start_codon	11485618	11485620	.	+	0	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	CDS	11485618	11485822	0.99	+	0	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	exon	11485618	11485822	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	intron	11485823	11486032	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	CDS	11486033	11486317	1	+	2	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	exon	11486033	11486317	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	intron	11486318	11486413	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	CDS	11486414	11486780	1	+	2	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	exon	11486414	11486780	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	intron	11486781	11486860	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	CDS	11486861	11487071	1	+	1	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	exon	11486861	11487071	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	intron	11487072	11487155	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	CDS	11487156	11487290	0.96	+	0	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	exon	11487156	11487290	.	+	.	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
Phchi.S1	AUGUSTUS	stop_codon	11487291	11487293	.	+	0	transcript_id "Phchi.S1G179200.t1"; gene_id "Phchi.S1G179200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg12195.t1 is derived from g7871.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6669855	6672952	.	-	.	Phchi.S2G027500
Phchi.S2	AUGUSTUS	transcript	6669913	6672952	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	stop_codon	6669910	6669912	.	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6669913	6669941	0.85	-	2	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6669913	6669941	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6669942	6670022	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670023	6670073	1	-	2	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670023	6670073	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670074	6670225	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670226	6670264	1	-	2	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670226	6670264	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670265	6670360	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670361	6670458	1	-	1	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670361	6670458	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670459	6670551	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670552	6670646	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670552	6670646	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670647	6670718	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670719	6670901	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670719	6670901	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670902	6670990	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670991	6671239	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670991	6671239	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671240	6671331	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671332	6671376	0.98	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671332	6671376	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671377	6671486	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671487	6671652	0.84	-	1	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671487	6671652	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671653	6671780	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671781	6671905	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671781	6671905	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671906	6672088	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672089	6672304	0.95	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672089	6672304	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672305	6672441	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672442	6672594	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672442	6672594	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672595	6672727	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672728	6672820	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672728	6672820	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672821	6672910	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672911	6672952	1	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672911	6672952	.	-	.	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	start_codon	6672950	6672952	.	-	0	transcript_id "Phchi.S2G027500.t1"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	transcript	6669855	6672952	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	stop_codon	6669852	6669854	.	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6669855	6669941	0.99	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6669855	6669941	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6669942	6670022	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670023	6670027	0.99	-	2	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670023	6670027	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670028	6670101	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670102	6670125	0.88	-	2	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670102	6670125	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670126	6670225	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670226	6670264	1	-	2	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670226	6670264	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670265	6670360	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670361	6670458	1	-	1	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670361	6670458	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670459	6670551	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670552	6670646	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670552	6670646	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670647	6670718	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670719	6670901	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670719	6670901	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670902	6670990	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670991	6671239	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670991	6671239	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671240	6671331	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671332	6671376	0.99	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671332	6671376	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671377	6671486	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671487	6671652	0.87	-	1	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671487	6671652	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671653	6671780	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671781	6671905	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671781	6671905	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671906	6672088	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672089	6672304	0.82	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672089	6672304	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672305	6672441	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672442	6672594	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672442	6672594	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672595	6672727	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672728	6672820	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672728	6672820	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672821	6672910	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672911	6672952	1	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672911	6672952	.	-	.	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	start_codon	6672950	6672952	.	-	0	transcript_id "Phchi.S2G027500.t2"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	transcript	6669913	6672952	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	stop_codon	6669910	6669912	.	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6669913	6669941	0.84	-	2	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6669913	6669941	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6669942	6670022	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670023	6670073	1	-	2	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670023	6670073	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670074	6670225	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670226	6670264	1	-	2	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670226	6670264	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670265	6670360	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670361	6670458	1	-	1	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670361	6670458	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670459	6670551	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670552	6670646	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670552	6670646	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670647	6670718	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670719	6670904	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670719	6670904	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670905	6670990	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670991	6671239	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670991	6671239	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671240	6671331	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671332	6671376	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671332	6671376	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671377	6671486	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671487	6671652	0.75	-	1	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671487	6671652	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671653	6671780	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671781	6671905	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671781	6671905	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671906	6672088	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672089	6672304	0.88	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672089	6672304	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672305	6672441	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672442	6672594	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672442	6672594	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672595	6672727	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672728	6672820	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672728	6672820	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672821	6672910	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672911	6672952	1	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672911	6672952	.	-	.	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	start_codon	6672950	6672952	.	-	0	transcript_id "Phchi.S2G027500.t3"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	transcript	6669913	6672952	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	stop_codon	6669910	6669912	.	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6669913	6669941	0.84	-	2	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6669913	6669941	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6669942	6670022	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670023	6670073	1	-	2	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670023	6670073	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670074	6670225	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670226	6670264	1	-	2	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670226	6670264	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670265	6670360	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670361	6670458	1	-	1	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670361	6670458	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670459	6670551	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670552	6670646	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670552	6670646	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670647	6670718	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670719	6670901	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670719	6670901	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6670902	6670990	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6670991	6671239	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6670991	6671239	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671240	6671331	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671332	6671376	0.95	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671332	6671376	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671377	6671486	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671487	6671652	0.89	-	1	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671487	6671652	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671653	6671780	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6671781	6671905	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6671781	6671905	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6671906	6672088	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672089	6672322	0.66	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672089	6672322	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672323	6672441	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672442	6672594	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672442	6672594	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672595	6672727	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672728	6672820	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672728	6672820	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	intron	6672821	6672910	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	CDS	6672911	6672952	1	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	exon	6672911	6672952	.	-	.	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
Phchi.S2	AUGUSTUS	start_codon	6672950	6672952	.	-	0	transcript_id "Phchi.S2G027500.t4"; gene_id "Phchi.S2G027500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15536.t1 is derived from g14005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19766029	19767890	.	+	.	Phchi.S3G285500
Phchi.S3	AUGUSTUS	transcript	19766029	19767890	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	start_codon	19766029	19766031	.	+	0	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	CDS	19766029	19766531	0.3	+	0	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	exon	19766029	19766531	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	intron	19766532	19766617	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	CDS	19766618	19767318	0.84	+	1	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	exon	19766618	19767318	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	intron	19767319	19767451	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	CDS	19767452	19767569	1	+	2	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	exon	19767452	19767569	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	intron	19767570	19767671	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	CDS	19767672	19767733	1	+	1	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	exon	19767672	19767733	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	intron	19767734	19767849	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	CDS	19767850	19767890	1	+	2	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	exon	19767850	19767890	.	+	.	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
Phchi.S3	AUGUSTUS	stop_codon	19767891	19767893	.	+	0	transcript_id "Phchi.S3G285500.t1"; gene_id "Phchi.S3G285500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4299.t1 is derived from g1468.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9507265	9509819	.	+	.	Phchi.S1G145800
Phchi.S1	AUGUSTUS	transcript	9507265	9509819	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	start_codon	9507265	9507267	.	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9507265	9507469	0.96	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9507265	9507469	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9507470	9507569	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9507570	9507640	1	+	2	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9507570	9507640	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9507641	9507785	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9507786	9507870	0.97	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9507786	9507870	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9507871	9507971	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9507972	9508523	0.77	+	2	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9507972	9508523	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9508524	9508656	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9508657	9508860	1	+	2	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9508657	9508860	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9508861	9508945	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9508946	9508989	1	+	2	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9508946	9508989	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9508990	9509073	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9509074	9509256	1	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9509074	9509256	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9509257	9509342	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9509343	9509430	1	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9509343	9509430	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9509431	9509520	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9509521	9509564	1	+	2	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9509521	9509564	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	intron	9509565	9509657	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	CDS	9509658	9509819	1	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	exon	9509658	9509819	.	+	.	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
Phchi.S1	AUGUSTUS	stop_codon	9509820	9509822	.	+	0	transcript_id "Phchi.S1G145800.t1"; gene_id "Phchi.S1G145800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1680.t1 is derived from g8599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2478357	2479607	.	+	.	Phchi.S5G028900
Phchi.S5	AUGUSTUS	transcript	2478357	2479607	.	+	.	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	start_codon	2478357	2478359	.	+	0	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	CDS	2478357	2478836	0.87	+	0	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	exon	2478357	2478836	.	+	.	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	intron	2478837	2479025	.	+	.	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	CDS	2479026	2479607	0.95	+	0	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	exon	2479026	2479607	.	+	.	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
Phchi.S5	AUGUSTUS	stop_codon	2479608	2479610	.	+	0	transcript_id "Phchi.S5G028900.t1"; gene_id "Phchi.S5G028900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg402.t1 is derived from g10184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2899325	2900101	.	-	.	Phchi.S6G036100
Phchi.S6	AUGUSTUS	transcript	2899325	2900101	.	-	.	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	stop_codon	2899322	2899324	.	-	0	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	CDS	2899325	2899481	1	-	1	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	exon	2899325	2899481	.	-	.	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	intron	2899482	2899662	.	-	.	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	CDS	2899663	2899803	1	-	1	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	exon	2899663	2899803	.	-	.	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	intron	2899804	2899886	.	-	.	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	CDS	2899887	2900101	0.93	-	0	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	exon	2899887	2900101	.	-	.	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
Phchi.S6	AUGUSTUS	start_codon	2900099	2900101	.	-	0	transcript_id "Phchi.S6G036100.t1"; gene_id "Phchi.S6G036100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7136.t1 is derived from g4308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27126534	27128018	.	+	.	Phchi.S1G429500
Phchi.S1	AUGUSTUS	transcript	27126534	27128018	.	+	.	transcript_id "Phchi.S1G429500.t1"; gene_id "Phchi.S1G429500"
Phchi.S1	AUGUSTUS	start_codon	27126534	27126536	.	+	0	transcript_id "Phchi.S1G429500.t1"; gene_id "Phchi.S1G429500"
Phchi.S1	AUGUSTUS	CDS	27126534	27128018	0.29	+	0	transcript_id "Phchi.S1G429500.t1"; gene_id "Phchi.S1G429500"
Phchi.S1	AUGUSTUS	exon	27126534	27128018	.	+	.	transcript_id "Phchi.S1G429500.t1"; gene_id "Phchi.S1G429500"
Phchi.S1	AUGUSTUS	stop_codon	27128019	27128021	.	+	0	transcript_id "Phchi.S1G429500.t1"; gene_id "Phchi.S1G429500"
# This transcript jg15169.t2 is derived from g13637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15170.t1 is derived from g13638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17351466	17356240	.	+	.	Phchi.S3G248900
Phchi.S3	AUGUSTUS	transcript	17351466	17356240	.	+	.	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	start_codon	17351466	17351468	.	+	0	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	CDS	17351466	17355658	0.65	+	0	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	exon	17351466	17355658	.	+	.	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	intron	17355659	17355759	.	+	.	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	CDS	17355760	17356240	1	+	1	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	exon	17355760	17356240	.	+	.	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
Phchi.S3	AUGUSTUS	stop_codon	17356241	17356243	.	+	0	transcript_id "Phchi.S3G248900.t1"; gene_id "Phchi.S3G248900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13672.t1 is derived from g12139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8085418	8090183	.	-	.	Phchi.S3G099100
Phchi.S3	AUGUSTUS	transcript	8085418	8090183	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	stop_codon	8085415	8085417	.	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8085418	8085438	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8085418	8085438	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8085439	8085580	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8085581	8085639	0.8	-	2	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8085581	8085639	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8085640	8085933	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8085934	8086012	0.49	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8085934	8086012	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8086013	8086099	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8086100	8086257	1	-	2	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8086100	8086257	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8086258	8086424	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8086425	8086497	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8086425	8086497	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8086498	8086651	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8086652	8086726	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8086652	8086726	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8086727	8086848	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8086849	8087172	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8086849	8087172	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8087173	8087309	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8087310	8087467	1	-	2	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8087310	8087467	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8087468	8087582	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8087583	8087766	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8087583	8087766	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8087767	8087861	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8087862	8088003	1	-	1	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8087862	8088003	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8088004	8088120	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8088121	8088228	0.96	-	1	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8088121	8088228	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8088229	8088312	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8088313	8088569	0.99	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8088313	8088569	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8088570	8088683	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8088684	8088809	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8088684	8088809	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8088810	8088947	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8088948	8089164	1	-	1	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8088948	8089164	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8089165	8089254	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8089255	8089379	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8089255	8089379	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8089380	8089479	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8089480	8089731	1	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8089480	8089731	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	intron	8089732	8089916	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	CDS	8089917	8090183	0.98	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	exon	8089917	8090183	.	-	.	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
Phchi.S3	AUGUSTUS	start_codon	8090181	8090183	.	-	0	transcript_id "Phchi.S3G099100.t1"; gene_id "Phchi.S3G099100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1627.t1 is derived from g8546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2084527	2086354	.	+	.	Phchi.S5G023600
Phchi.S5	AUGUSTUS	transcript	2084527	2086354	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	start_codon	2084527	2084529	.	+	0	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	CDS	2084527	2084637	1	+	0	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	exon	2084527	2084637	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	intron	2084638	2084727	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	CDS	2084728	2084856	1	+	0	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	exon	2084728	2084856	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	intron	2084857	2084937	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	CDS	2084938	2085009	1	+	0	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	exon	2084938	2085009	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	intron	2085010	2085158	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	CDS	2085159	2085334	1	+	0	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	exon	2085159	2085334	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	intron	2085335	2085458	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	CDS	2085459	2086165	1	+	1	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	exon	2085459	2086165	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	intron	2086166	2086256	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	CDS	2086257	2086354	1	+	2	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	exon	2086257	2086354	.	+	.	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
Phchi.S5	AUGUSTUS	stop_codon	2086355	2086357	.	+	0	transcript_id "Phchi.S5G023600.t1"; gene_id "Phchi.S5G023600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13008.t1 is derived from g11473.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3615329	3618445	.	-	.	Phchi.S3G032700
Phchi.S3	AUGUSTUS	transcript	3615329	3618445	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	stop_codon	3615326	3615328	.	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3615329	3615676	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3615329	3615676	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3615677	3615762	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3615763	3615894	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3615763	3615894	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3615895	3615990	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3615991	3616110	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3615991	3616110	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3616111	3616196	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3616197	3616261	1	-	2	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3616197	3616261	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3616262	3616441	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3616442	3616670	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3616442	3616670	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3616671	3616754	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3616755	3616859	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3616755	3616859	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3616860	3616975	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3616976	3617119	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3616976	3617119	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3617120	3617284	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3617285	3617588	0.98	-	1	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3617285	3617588	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3617589	3617748	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3617749	3617863	0.7	-	2	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3617749	3617863	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3617864	3618016	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3618017	3618133	0.3	-	2	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3618017	3618133	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	intron	3618134	3618405	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	CDS	3618406	3618445	1	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	exon	3618406	3618445	.	-	.	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
Phchi.S3	AUGUSTUS	start_codon	3618443	3618445	.	-	0	transcript_id "Phchi.S3G032700.t1"; gene_id "Phchi.S3G032700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1840.t1 is derived from g8760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3524160	3525781	.	-	.	Phchi.S5G044900
Phchi.S5	AUGUSTUS	transcript	3524160	3525781	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	stop_codon	3524157	3524159	.	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3524160	3524191	0.95	-	2	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3524160	3524191	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3524192	3524275	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3524276	3524390	0.95	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3524276	3524390	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3524391	3524470	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3524471	3524608	1	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3524471	3524608	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3524609	3524712	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3524713	3524836	1	-	1	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3524713	3524836	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3524837	3524918	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3524919	3524983	1	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3524919	3524983	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3524984	3525064	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3525065	3525121	1	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3525065	3525121	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3525122	3525204	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3525205	3525329	0.99	-	2	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3525205	3525329	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3525330	3525471	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3525472	3525535	0.99	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3525472	3525535	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	intron	3525536	3525634	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	CDS	3525635	3525781	0.71	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	exon	3525635	3525781	.	-	.	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
Phchi.S5	AUGUSTUS	start_codon	3525779	3525781	.	-	0	transcript_id "Phchi.S5G044900.t1"; gene_id "Phchi.S5G044900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15562.t1 is derived from g14031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19924744	19925913	.	-	.	Phchi.S3G288100
Phchi.S3	AUGUSTUS	transcript	19924744	19925913	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	stop_codon	19924741	19924743	.	-	0	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	CDS	19924744	19924989	1	-	0	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	exon	19924744	19924989	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	intron	19924990	19925084	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	CDS	19925085	19925141	1	-	0	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	exon	19925085	19925141	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	intron	19925142	19925225	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	CDS	19925226	19925254	1	-	2	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	exon	19925226	19925254	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	intron	19925255	19925339	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	CDS	19925340	19925913	0.95	-	0	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	exon	19925340	19925913	.	-	.	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
Phchi.S3	AUGUSTUS	start_codon	19925911	19925913	.	-	0	transcript_id "Phchi.S3G288100.t1"; gene_id "Phchi.S3G288100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6421.t1 is derived from g3593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22913560	22915381	.	+	.	Phchi.S1G358000
Phchi.S1	AUGUSTUS	transcript	22913560	22915381	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	start_codon	22913560	22913562	.	+	0	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	CDS	22913560	22914584	0.35	+	0	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	exon	22913560	22914584	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	intron	22914585	22914759	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	CDS	22914760	22914868	1	+	1	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	exon	22914760	22914868	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	intron	22914869	22914955	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	CDS	22914956	22915091	1	+	0	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	exon	22914956	22915091	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	intron	22915092	22915250	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	CDS	22915251	22915381	1	+	2	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	exon	22915251	22915381	.	+	.	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
Phchi.S1	AUGUSTUS	stop_codon	22915382	22915384	.	+	0	transcript_id "Phchi.S1G358000.t1"; gene_id "Phchi.S1G358000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11186.t1 is derived from g15236.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4542076	4544799	.	+	.	Phchi.S4G076800
Phchi.S4	AUGUSTUS	transcript	4542076	4544799	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	start_codon	4542076	4542078	.	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4542076	4542137	0.6	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4542076	4542137	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4542138	4542291	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4542292	4542330	0.84	+	1	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4542292	4542330	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4542331	4542485	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4542486	4542630	1	+	1	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4542486	4542630	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4542631	4542715	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4542716	4542778	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4542716	4542778	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4542779	4542906	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4542907	4542984	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4542907	4542984	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4542985	4543130	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4543131	4543351	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4543131	4543351	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4543352	4543442	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4543443	4543515	1	+	1	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4543443	4543515	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4543516	4543599	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4543600	4543884	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4543600	4543884	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4543885	4543999	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4544000	4544143	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4544000	4544143	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4544144	4544233	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4544234	4544284	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4544234	4544284	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4544285	4544372	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4544373	4544556	1	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4544373	4544556	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	intron	4544557	4544632	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	CDS	4544633	4544799	0.46	+	2	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	exon	4544633	4544799	.	+	.	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
Phchi.S4	AUGUSTUS	stop_codon	4544800	4544802	.	+	0	transcript_id "Phchi.S4G076800.t1"; gene_id "Phchi.S4G076800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9965.t1 is derived from g7141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44692276	44694627	.	+	.	Phchi.S1G712400
Phchi.S1	AUGUSTUS	transcript	44694319	44694627	.	+	.	transcript_id "Phchi.S1G712400.t1"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	start_codon	44694319	44694321	.	+	0	transcript_id "Phchi.S1G712400.t1"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	CDS	44694319	44694627	0.66	+	0	transcript_id "Phchi.S1G712400.t1"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	exon	44694319	44694627	.	+	.	transcript_id "Phchi.S1G712400.t1"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	stop_codon	44694628	44694630	.	+	0	transcript_id "Phchi.S1G712400.t1"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	transcript	44692276	44694627	.	+	.	transcript_id "Phchi.S1G712400.t2"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	start_codon	44692276	44692278	.	+	0	transcript_id "Phchi.S1G712400.t2"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	CDS	44692276	44694627	0.51	+	0	transcript_id "Phchi.S1G712400.t2"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	exon	44692276	44694627	.	+	.	transcript_id "Phchi.S1G712400.t2"; gene_id "Phchi.S1G712400"
Phchi.S1	AUGUSTUS	stop_codon	44694628	44694630	.	+	0	transcript_id "Phchi.S1G712400.t2"; gene_id "Phchi.S1G712400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14949.t1 is derived from g13417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15663699	15667023	.	-	.	Phchi.S3G226800
Phchi.S3	AUGUSTUS	transcript	15663699	15667023	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	stop_codon	15663696	15663698	.	-	0	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15663699	15663862	0.96	-	2	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15663699	15663862	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15663863	15664029	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15664030	15664754	0.97	-	1	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15664030	15664754	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15664755	15664862	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15664863	15665142	0.99	-	2	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15664863	15665142	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15665143	15665232	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15665233	15665560	0.98	-	0	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15665233	15665560	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15665561	15665649	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15665650	15665887	0.92	-	1	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15665650	15665887	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15665888	15666043	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15666044	15666238	0.85	-	1	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15666044	15666238	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15666239	15666341	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15666342	15666438	0.99	-	2	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15666342	15666438	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	intron	15666439	15666842	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	CDS	15666843	15667023	0.7	-	0	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	exon	15666843	15667023	.	-	.	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
Phchi.S3	AUGUSTUS	start_codon	15667021	15667023	.	-	0	transcript_id "Phchi.S3G226800.t1"; gene_id "Phchi.S3G226800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14896.t1 is derived from g13364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15346041	15346409	.	+	.	Phchi.S3G221500
Phchi.S3	AUGUSTUS	transcript	15346041	15346409	.	+	.	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	start_codon	15346041	15346043	.	+	0	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	CDS	15346041	15346118	0.99	+	0	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	exon	15346041	15346118	.	+	.	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	intron	15346119	15346205	.	+	.	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	CDS	15346206	15346409	1	+	0	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	exon	15346206	15346409	.	+	.	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
Phchi.S3	AUGUSTUS	stop_codon	15346410	15346412	.	+	0	transcript_id "Phchi.S3G221500.t1"; gene_id "Phchi.S3G221500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9090.t1 is derived from g6265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39799311	39800279	.	+	.	Phchi.S1G624900
Phchi.S1	AUGUSTUS	transcript	39799311	39800279	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	start_codon	39799311	39799313	.	+	0	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	CDS	39799311	39799607	0.55	+	0	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	exon	39799311	39799607	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	intron	39799608	39799705	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	CDS	39799706	39799864	1	+	0	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	exon	39799706	39799864	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	intron	39799865	39800000	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	CDS	39800001	39800126	0.9	+	0	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	exon	39800001	39800126	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	intron	39800127	39800237	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	CDS	39800238	39800279	0.82	+	0	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	exon	39800238	39800279	.	+	.	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
Phchi.S1	AUGUSTUS	stop_codon	39800280	39800282	.	+	0	transcript_id "Phchi.S1G624900.t1"; gene_id "Phchi.S1G624900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13727.t1 is derived from g12194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8555169	8556488	.	-	.	Phchi.S3G104600
Phchi.S3	AUGUSTUS	transcript	8555169	8556488	.	-	.	transcript_id "Phchi.S3G104600.t1"; gene_id "Phchi.S3G104600"
Phchi.S3	AUGUSTUS	stop_codon	8555166	8555168	.	-	0	transcript_id "Phchi.S3G104600.t1"; gene_id "Phchi.S3G104600"
Phchi.S3	AUGUSTUS	CDS	8555169	8556488	0.83	-	0	transcript_id "Phchi.S3G104600.t1"; gene_id "Phchi.S3G104600"
Phchi.S3	AUGUSTUS	exon	8555169	8556488	.	-	.	transcript_id "Phchi.S3G104600.t1"; gene_id "Phchi.S3G104600"
Phchi.S3	AUGUSTUS	start_codon	8556486	8556488	.	-	0	transcript_id "Phchi.S3G104600.t1"; gene_id "Phchi.S3G104600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4461.t1 is derived from g1631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10616270	10617796	.	-	.	Phchi.S1G162000
Phchi.S1	AUGUSTUS	transcript	10616270	10617796	.	-	.	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	stop_codon	10616267	10616269	.	-	0	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	CDS	10616270	10617018	1	-	2	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	exon	10616270	10617018	.	-	.	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	intron	10617019	10617124	.	-	.	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	CDS	10617125	10617373	1	-	2	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	exon	10617125	10617373	.	-	.	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	intron	10617374	10617474	.	-	.	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	CDS	10617475	10617796	0.8	-	0	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	exon	10617475	10617796	.	-	.	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
Phchi.S1	AUGUSTUS	start_codon	10617794	10617796	.	-	0	transcript_id "Phchi.S1G162000.t1"; gene_id "Phchi.S1G162000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5323.t1 is derived from g2493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16282432	16285693	.	-	.	Phchi.S1G248200
Phchi.S1	AUGUSTUS	transcript	16282432	16285693	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	stop_codon	16282429	16282431	.	-	0	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	CDS	16282432	16284306	1	-	0	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	exon	16282432	16284306	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	intron	16284307	16284484	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	CDS	16284485	16284628	1	-	0	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	exon	16284485	16284628	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	intron	16284629	16284807	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	CDS	16284808	16285336	0.8	-	1	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	exon	16284808	16285336	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	intron	16285337	16285613	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	CDS	16285614	16285693	0.83	-	0	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	exon	16285614	16285693	.	-	.	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
Phchi.S1	AUGUSTUS	start_codon	16285691	16285693	.	-	0	transcript_id "Phchi.S1G248200.t1"; gene_id "Phchi.S1G248200"
# This transcript jg7104.t2 is derived from g4276.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7105.t1 is derived from g4277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26964800	26969846	.	-	.	Phchi.S1G426400
Phchi.S1	AUGUSTUS	transcript	26964800	26969846	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	stop_codon	26964797	26964799	.	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26964800	26965069	0.86	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26964800	26965069	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26965070	26965163	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26965164	26965232	1	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26965164	26965232	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26965233	26965322	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26965323	26965457	1	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26965323	26965457	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26965458	26965705	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26965706	26965782	1	-	2	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26965706	26965782	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26965783	26965893	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26965894	26966008	0.52	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26965894	26966008	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26966009	26966123	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26966124	26966245	0.54	-	2	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26966124	26966245	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26966246	26966332	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26966333	26966438	1	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26966333	26966438	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26966439	26966534	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26966535	26966579	1	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26966535	26966579	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26966580	26966691	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26966692	26966789	1	-	2	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26966692	26966789	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26966790	26966942	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26966943	26967075	1	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26966943	26967075	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26967076	26967224	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26967225	26967256	1	-	2	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26967225	26967256	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26967257	26967368	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26967369	26968908	0.99	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26967369	26968908	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26968909	26968984	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26968985	26969054	1	-	1	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26968985	26969054	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26969055	26969135	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26969136	26969323	0.97	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26969136	26969323	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	intron	26969324	26969813	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	CDS	26969814	26969846	0.92	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	exon	26969814	26969846	.	-	.	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
Phchi.S1	AUGUSTUS	start_codon	26969844	26969846	.	-	0	transcript_id "Phchi.S1G426400.t1"; gene_id "Phchi.S1G426400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2238.t1 is derived from g9158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5603501	5604619	.	-	.	Phchi.S5G084700
Phchi.S5	AUGUSTUS	transcript	5603501	5604619	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	stop_codon	5603498	5603500	.	-	0	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	CDS	5603501	5603725	0.99	-	0	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	exon	5603501	5603725	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	intron	5603726	5603875	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	CDS	5603876	5604012	1	-	2	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	exon	5603876	5604012	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	intron	5604013	5604124	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	CDS	5604125	5604365	1	-	0	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	exon	5604125	5604365	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	intron	5604366	5604502	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	CDS	5604503	5604619	0.77	-	0	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	exon	5604503	5604619	.	-	.	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
Phchi.S5	AUGUSTUS	start_codon	5604617	5604619	.	-	0	transcript_id "Phchi.S5G084700.t1"; gene_id "Phchi.S5G084700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10142.t1 is derived from g7318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45961884	45966023	.	-	.	Phchi.S1G730100
Phchi.S1	AUGUSTUS	transcript	45961884	45966023	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	stop_codon	45961881	45961883	.	-	0	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	CDS	45961884	45962202	0.32	-	1	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	exon	45961884	45962202	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	intron	45962203	45962335	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	CDS	45962336	45962667	1	-	0	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	exon	45962336	45962667	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	intron	45962668	45962799	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	CDS	45962800	45964169	1	-	2	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	exon	45962800	45964169	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	intron	45964170	45964264	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	CDS	45964265	45964844	0.96	-	0	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	exon	45964265	45964844	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	intron	45964845	45964921	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	CDS	45964922	45965706	0.59	-	2	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	exon	45964922	45965706	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	intron	45965707	45965875	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	CDS	45965876	45966023	0.32	-	0	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	exon	45965876	45966023	.	-	.	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
Phchi.S1	AUGUSTUS	start_codon	45966021	45966023	.	-	0	transcript_id "Phchi.S1G730100.t1"; gene_id "Phchi.S1G730100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg282.t1 is derived from g10064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2018133	2019110	.	-	.	Phchi.S6G024100
Phchi.S6	AUGUSTUS	transcript	2018133	2019110	.	-	.	transcript_id "Phchi.S6G024100.t1"; gene_id "Phchi.S6G024100"
Phchi.S6	AUGUSTUS	stop_codon	2018130	2018132	.	-	0	transcript_id "Phchi.S6G024100.t1"; gene_id "Phchi.S6G024100"
Phchi.S6	AUGUSTUS	CDS	2018133	2019110	0.8	-	0	transcript_id "Phchi.S6G024100.t1"; gene_id "Phchi.S6G024100"
Phchi.S6	AUGUSTUS	exon	2018133	2019110	.	-	.	transcript_id "Phchi.S6G024100.t1"; gene_id "Phchi.S6G024100"
Phchi.S6	AUGUSTUS	start_codon	2019108	2019110	.	-	0	transcript_id "Phchi.S6G024100.t1"; gene_id "Phchi.S6G024100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13852.t1 is derived from g12319.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9242420	9246321	.	+	.	Phchi.S3G117100
Phchi.S3	AUGUSTUS	transcript	9242420	9246321	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	start_codon	9242420	9242422	.	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9242420	9242500	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9242420	9242500	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9242501	9242631	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9242632	9242713	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9242632	9242713	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9242714	9242814	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9242815	9242888	1	+	2	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9242815	9242888	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9242889	9243028	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9243029	9243089	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9243029	9243089	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9243090	9243256	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9243257	9243390	1	+	2	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9243257	9243390	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9243391	9243467	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9243468	9243539	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9243468	9243539	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9243540	9243642	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9243643	9243738	0.98	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9243643	9243738	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9243739	9243840	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9243841	9243885	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9243841	9243885	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9243886	9243984	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9243985	9244041	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9243985	9244041	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9244042	9244144	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9244145	9244300	0.98	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9244145	9244300	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9244301	9244436	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9244437	9244502	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9244437	9244502	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9244503	9244588	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9244589	9244712	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9244589	9244712	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9244713	9244865	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9244866	9244922	1	+	2	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9244866	9244922	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9244923	9245086	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9245087	9245208	1	+	2	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9245087	9245208	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9245209	9245286	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9245287	9245439	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9245287	9245439	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9245440	9245563	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9245564	9245677	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9245564	9245677	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9245678	9245766	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9245767	9245844	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9245767	9245844	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9245845	9245929	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9245930	9245977	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9245930	9245977	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9245978	9246055	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9246056	9246124	1	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9246056	9246124	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	intron	9246125	9246207	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	CDS	9246208	9246321	0.7	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	exon	9246208	9246321	.	+	.	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
Phchi.S3	AUGUSTUS	stop_codon	9246322	9246324	.	+	0	transcript_id "Phchi.S3G117100.t1"; gene_id "Phchi.S3G117100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11037.t1 is derived from g15087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3764016	3764643	.	+	.	Phchi.S4G061900
Phchi.S4	AUGUSTUS	transcript	3764016	3764643	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	start_codon	3764016	3764018	.	+	0	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	CDS	3764016	3764049	0.78	+	0	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	exon	3764016	3764049	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	intron	3764050	3764238	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	CDS	3764239	3764362	1	+	2	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	exon	3764239	3764362	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	intron	3764363	3764467	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	CDS	3764468	3764540	1	+	1	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	exon	3764468	3764540	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	intron	3764541	3764619	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	CDS	3764620	3764643	1	+	0	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	exon	3764620	3764643	.	+	.	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
Phchi.S4	AUGUSTUS	stop_codon	3764644	3764646	.	+	0	transcript_id "Phchi.S4G061900.t1"; gene_id "Phchi.S4G061900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8988.t1 is derived from g6163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38987821	38990870	.	-	.	Phchi.S1G614700
Phchi.S1	AUGUSTUS	transcript	38987821	38990870	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	stop_codon	38987818	38987820	.	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38987821	38987888	1	-	2	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38987821	38987888	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	intron	38987889	38988022	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38988023	38988192	0.75	-	1	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38988023	38988192	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	intron	38988193	38988300	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38988301	38989640	0.33	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38988301	38989640	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	intron	38989641	38989726	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38989727	38989879	0.46	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38989727	38989879	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	intron	38989880	38990027	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38990028	38990195	1	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38990028	38990195	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	intron	38990196	38990311	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38990312	38990434	0.72	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38990312	38990434	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	intron	38990435	38990540	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	CDS	38990541	38990870	0.71	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	exon	38990541	38990870	.	-	.	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
Phchi.S1	AUGUSTUS	start_codon	38990868	38990870	.	-	0	transcript_id "Phchi.S1G614700.t1"; gene_id "Phchi.S1G614700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8417.t1 is derived from g5592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35847263	35852745	.	-	.	Phchi.S1G557600
Phchi.S1	AUGUSTUS	transcript	35847263	35852745	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	stop_codon	35847260	35847262	.	-	0	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	CDS	35847263	35847322	1	-	0	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	exon	35847263	35847322	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	intron	35847323	35848246	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	CDS	35848247	35848503	1	-	2	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	exon	35848247	35848503	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	intron	35848504	35850439	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	CDS	35850440	35850638	0.04	-	0	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	exon	35850440	35850638	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	intron	35850639	35850976	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	CDS	35850977	35851411	0.08	-	0	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	exon	35850977	35851411	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	intron	35851412	35852694	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	CDS	35852695	35852745	0.01	-	0	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	exon	35852695	35852745	.	-	.	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
Phchi.S1	AUGUSTUS	start_codon	35852743	35852745	.	-	0	transcript_id "Phchi.S1G557600.t1"; gene_id "Phchi.S1G557600"
# This transcript jg9537.t2 is derived from g6713.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9538.t1 is derived from g6714.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42385065	42387200	.	+	.	Phchi.S1G669700
Phchi.S1	AUGUSTUS	transcript	42385065	42387200	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	start_codon	42385065	42385067	.	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42385065	42385276	0.97	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42385065	42385276	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42385277	42385371	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42385372	42385696	1	+	1	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42385372	42385696	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42385697	42385770	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42385771	42385932	0.96	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42385771	42385932	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42385933	42386051	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42386052	42386312	1	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42386052	42386312	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42386313	42386425	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42386426	42386518	1	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42386426	42386518	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42386519	42386598	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42386599	42386677	1	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42386599	42386677	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42386678	42386771	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42386772	42386997	1	+	2	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42386772	42386997	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	intron	42386998	42387097	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	CDS	42387098	42387200	1	+	1	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	exon	42387098	42387200	.	+	.	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
Phchi.S1	AUGUSTUS	stop_codon	42387201	42387203	.	+	0	transcript_id "Phchi.S1G669700.t1"; gene_id "Phchi.S1G669700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6064.t1 is derived from g3235.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20698088	20702902	.	-	.	Phchi.S1G322300
Phchi.S1	AUGUSTUS	transcript	20698088	20702902	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	stop_codon	20698085	20698087	.	-	0	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20698088	20698685	0.94	-	1	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20698088	20698685	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	intron	20698686	20698811	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20698812	20702469	0.94	-	2	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20698812	20702469	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	intron	20702470	20702553	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20702554	20702599	0.99	-	0	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20702554	20702599	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	intron	20702600	20702827	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20702828	20702902	0.99	-	0	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20702828	20702902	.	-	.	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	start_codon	20702900	20702902	.	-	0	transcript_id "Phchi.S1G322300.t1"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	transcript	20698088	20702902	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	stop_codon	20698085	20698087	.	-	0	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20698088	20698685	0.85	-	1	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20698088	20698685	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	intron	20698686	20698811	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20698812	20702469	0.75	-	2	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20698812	20702469	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	intron	20702470	20702553	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20702554	20702599	0.84	-	0	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20702554	20702599	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	intron	20702600	20702833	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	CDS	20702834	20702902	0.85	-	0	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	exon	20702834	20702902	.	-	.	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
Phchi.S1	AUGUSTUS	start_codon	20702900	20702902	.	-	0	transcript_id "Phchi.S1G322300.t2"; gene_id "Phchi.S1G322300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11277.t1 is derived from g15327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5175617	5177309	.	-	.	Phchi.S4G085900
Phchi.S4	AUGUSTUS	transcript	5175617	5177309	.	-	.	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	stop_codon	5175614	5175616	.	-	0	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	CDS	5175617	5176206	1	-	2	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	exon	5175617	5176206	.	-	.	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	intron	5176207	5176350	.	-	.	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	CDS	5176351	5176526	1	-	1	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	exon	5176351	5176526	.	-	.	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	intron	5176527	5176692	.	-	.	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	CDS	5176693	5177309	0.86	-	0	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	exon	5176693	5177309	.	-	.	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
Phchi.S4	AUGUSTUS	start_codon	5177307	5177309	.	-	0	transcript_id "Phchi.S4G085900.t1"; gene_id "Phchi.S4G085900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg281.t1 is derived from g10063.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2016365	2017838	.	+	.	Phchi.S6G024000
Phchi.S6	AUGUSTUS	transcript	2016365	2017838	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	start_codon	2016365	2016367	.	+	0	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2016365	2016439	0.5	+	0	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2016365	2016439	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	intron	2016440	2016672	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2016673	2016732	0.99	+	0	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2016673	2016732	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	intron	2016733	2016875	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2016876	2017037	0.32	+	0	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2016876	2017037	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	intron	2017038	2017165	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2017166	2017203	0.68	+	0	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2017166	2017203	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	intron	2017204	2017354	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2017355	2017462	1	+	1	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2017355	2017462	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	intron	2017463	2017548	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2017549	2017683	1	+	1	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2017549	2017683	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	intron	2017684	2017762	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	CDS	2017763	2017838	0.98	+	1	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	exon	2017763	2017838	.	+	.	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
Phchi.S6	AUGUSTUS	stop_codon	2017839	2017841	.	+	0	transcript_id "Phchi.S6G024000.t1"; gene_id "Phchi.S6G024000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6504.t1 is derived from g3676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23355689	23359104	.	+	.	Phchi.S1G366300
Phchi.S1	AUGUSTUS	transcript	23355689	23359104	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	start_codon	23355689	23355691	.	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23355689	23355784	0.25	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23355689	23355784	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23355785	23355965	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23355966	23356066	0.57	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23355966	23356066	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23356067	23356152	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23356153	23356231	0.58	+	1	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23356153	23356231	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23356232	23356321	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23356322	23356333	0.95	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23356322	23356333	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23356334	23356657	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23356658	23356726	1	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23356658	23356726	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23356727	23356814	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23356815	23356958	1	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23356815	23356958	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23356959	23357066	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23357067	23357168	0.27	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23357067	23357168	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23357169	23357296	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23357297	23357369	0.65	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23357297	23357369	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23357370	23357478	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23357479	23357774	0.78	+	2	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23357479	23357774	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23357775	23357869	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23357870	23358050	1	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23357870	23358050	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23358051	23358155	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23358156	23358277	1	+	2	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23358156	23358277	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23358278	23358365	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23358366	23358431	1	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23358366	23358431	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23358432	23358584	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23358585	23358651	1	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23358585	23358651	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23358652	23358735	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23358736	23358762	0.85	+	2	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23358736	23358762	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	intron	23358763	23358859	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	CDS	23358860	23359104	0.83	+	2	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	exon	23358860	23359104	.	+	.	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
Phchi.S1	AUGUSTUS	stop_codon	23359105	23359107	.	+	0	transcript_id "Phchi.S1G366300.t1"; gene_id "Phchi.S1G366300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7954.t1 is derived from g5128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32082318	32085773	.	-	.	Phchi.S1G511300
Phchi.S1	AUGUSTUS	transcript	32082318	32085773	.	-	.	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	stop_codon	32082315	32082317	.	-	0	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	CDS	32082318	32083397	0.97	-	0	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	exon	32082318	32083397	.	-	.	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	intron	32083398	32083506	.	-	.	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	CDS	32083507	32085366	0.95	-	0	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	exon	32083507	32085366	.	-	.	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	intron	32085367	32085746	.	-	.	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	CDS	32085747	32085773	1	-	0	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	exon	32085747	32085773	.	-	.	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
Phchi.S1	AUGUSTUS	start_codon	32085771	32085773	.	-	0	transcript_id "Phchi.S1G511300.t1"; gene_id "Phchi.S1G511300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14973.t1 is derived from g13441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15805036	15806100	.	+	.	Phchi.S3G229200
Phchi.S3	AUGUSTUS	transcript	15805036	15806100	.	+	.	transcript_id "Phchi.S3G229200.t1"; gene_id "Phchi.S3G229200"
Phchi.S3	AUGUSTUS	start_codon	15805036	15805038	.	+	0	transcript_id "Phchi.S3G229200.t1"; gene_id "Phchi.S3G229200"
Phchi.S3	AUGUSTUS	CDS	15805036	15806100	0.72	+	0	transcript_id "Phchi.S3G229200.t1"; gene_id "Phchi.S3G229200"
Phchi.S3	AUGUSTUS	exon	15805036	15806100	.	+	.	transcript_id "Phchi.S3G229200.t1"; gene_id "Phchi.S3G229200"
Phchi.S3	AUGUSTUS	stop_codon	15806101	15806103	.	+	0	transcript_id "Phchi.S3G229200.t1"; gene_id "Phchi.S3G229200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2456.t1 is derived from g9376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6742017	6742641	.	+	.	Phchi.S5G106500
Phchi.S5	AUGUSTUS	transcript	6742017	6742641	.	+	.	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	start_codon	6742017	6742019	.	+	0	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	CDS	6742017	6742145	0.28	+	0	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	exon	6742017	6742145	.	+	.	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	intron	6742146	6742233	.	+	.	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	CDS	6742234	6742641	0.76	+	0	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	exon	6742234	6742641	.	+	.	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
Phchi.S5	AUGUSTUS	stop_codon	6742642	6742644	.	+	0	transcript_id "Phchi.S5G106500.t1"; gene_id "Phchi.S5G106500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6225.t1 is derived from g3397.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21766443	21768255	.	+	.	Phchi.S1G338400
Phchi.S1	AUGUSTUS	transcript	21766443	21768255	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	start_codon	21766443	21766445	.	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21766443	21766514	0.98	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21766443	21766514	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	intron	21766515	21766643	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21766644	21766743	1	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21766644	21766743	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	intron	21766744	21766847	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21766848	21766933	1	+	2	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21766848	21766933	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	intron	21766934	21767032	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21767033	21767095	0.27	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21767033	21767095	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	intron	21767096	21767631	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21767632	21767723	0.42	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21767632	21767723	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	intron	21767724	21767825	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21767826	21767940	1	+	1	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21767826	21767940	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	intron	21767941	21768033	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	CDS	21768034	21768255	1	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	exon	21768034	21768255	.	+	.	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
Phchi.S1	AUGUSTUS	stop_codon	21768256	21768258	.	+	0	transcript_id "Phchi.S1G338400.t1"; gene_id "Phchi.S1G338400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9575.t1 is derived from g6751.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42736322	42738381	.	-	.	Phchi.S1G673400
Phchi.S1	AUGUSTUS	transcript	42736322	42738381	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	stop_codon	42736319	42736321	.	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42736322	42736369	1	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42736322	42736369	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42736370	42736459	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42736460	42736638	1	-	2	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42736460	42736638	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42736639	42736828	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42736829	42736925	1	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42736829	42736925	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42736926	42737004	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42737005	42737142	1	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42737005	42737142	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42737143	42737240	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42737241	42737328	1	-	1	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42737241	42737328	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42737329	42737445	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42737446	42737543	1	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42737446	42737543	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42737544	42737657	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42737658	42737776	0.99	-	2	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42737658	42737776	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42737777	42737978	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42737979	42738088	1	-	1	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42737979	42738088	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	intron	42738089	42738319	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	CDS	42738320	42738381	1	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	exon	42738320	42738381	.	-	.	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
Phchi.S1	AUGUSTUS	start_codon	42738379	42738381	.	-	0	transcript_id "Phchi.S1G673400.t1"; gene_id "Phchi.S1G673400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg809.t1 is derived from g10591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5689954	5690542	.	+	.	Phchi.S6G076800
Phchi.S6	AUGUSTUS	transcript	5689954	5690542	.	+	.	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	start_codon	5689954	5689956	.	+	0	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	CDS	5689954	5690181	1	+	0	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	exon	5689954	5690181	.	+	.	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	intron	5690182	5690263	.	+	.	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	CDS	5690264	5690378	1	+	0	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	exon	5690264	5690378	.	+	.	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	intron	5690379	5690465	.	+	.	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	CDS	5690466	5690542	1	+	2	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	exon	5690466	5690542	.	+	.	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
Phchi.S6	AUGUSTUS	stop_codon	5690543	5690545	.	+	0	transcript_id "Phchi.S6G076800.t1"; gene_id "Phchi.S6G076800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg552.t1 is derived from g10334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4020581	4021330	.	-	.	Phchi.S6G051100
Phchi.S6	AUGUSTUS	transcript	4020581	4021330	.	-	.	transcript_id "Phchi.S6G051100.t1"; gene_id "Phchi.S6G051100"
Phchi.S6	AUGUSTUS	stop_codon	4020578	4020580	.	-	0	transcript_id "Phchi.S6G051100.t1"; gene_id "Phchi.S6G051100"
Phchi.S6	AUGUSTUS	CDS	4020581	4021330	0.52	-	0	transcript_id "Phchi.S6G051100.t1"; gene_id "Phchi.S6G051100"
Phchi.S6	AUGUSTUS	exon	4020581	4021330	.	-	.	transcript_id "Phchi.S6G051100.t1"; gene_id "Phchi.S6G051100"
Phchi.S6	AUGUSTUS	start_codon	4021328	4021330	.	-	0	transcript_id "Phchi.S6G051100.t1"; gene_id "Phchi.S6G051100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9777.t1 is derived from g6953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43623503	43624480	.	-	.	Phchi.S1G693600
Phchi.S1	AUGUSTUS	transcript	43623503	43624480	.	-	.	transcript_id "Phchi.S1G693600.t1"; gene_id "Phchi.S1G693600"
Phchi.S1	AUGUSTUS	stop_codon	43623500	43623502	.	-	0	transcript_id "Phchi.S1G693600.t1"; gene_id "Phchi.S1G693600"
Phchi.S1	AUGUSTUS	CDS	43623503	43624480	0.9	-	0	transcript_id "Phchi.S1G693600.t1"; gene_id "Phchi.S1G693600"
Phchi.S1	AUGUSTUS	exon	43623503	43624480	.	-	.	transcript_id "Phchi.S1G693600.t1"; gene_id "Phchi.S1G693600"
Phchi.S1	AUGUSTUS	start_codon	43624478	43624480	.	-	0	transcript_id "Phchi.S1G693600.t1"; gene_id "Phchi.S1G693600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14636.t1 is derived from g13104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13859934	13860994	.	-	.	Phchi.S3G195500
Phchi.S3	AUGUSTUS	transcript	13859934	13860994	.	-	.	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	stop_codon	13859931	13859933	.	-	0	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	CDS	13859934	13860688	1	-	2	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	exon	13859934	13860688	.	-	.	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	intron	13860689	13860789	.	-	.	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	CDS	13860790	13860994	0.94	-	0	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	exon	13860790	13860994	.	-	.	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
Phchi.S3	AUGUSTUS	start_codon	13860992	13860994	.	-	0	transcript_id "Phchi.S3G195500.t1"; gene_id "Phchi.S3G195500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9909.t1 is derived from g7085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44393865	44395861	.	+	.	Phchi.S1G706800
Phchi.S1	AUGUSTUS	transcript	44393865	44395861	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	start_codon	44393865	44393867	.	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44393865	44394275	0.98	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44393865	44394275	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44394276	44394363	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44394364	44394426	1	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44394364	44394426	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44394427	44394524	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44394525	44394611	1	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44394525	44394611	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44394612	44394747	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44394748	44394958	0.57	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44394748	44394958	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44394959	44395101	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44395102	44395175	1	+	2	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44395102	44395175	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44395176	44395310	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44395311	44395406	0.95	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44395311	44395406	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44395407	44395627	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44395628	44395658	0.75	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44395628	44395658	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	intron	44395659	44395757	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	CDS	44395758	44395861	0.99	+	2	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	exon	44395758	44395861	.	+	.	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
Phchi.S1	AUGUSTUS	stop_codon	44395862	44395864	.	+	0	transcript_id "Phchi.S1G706800.t1"; gene_id "Phchi.S1G706800"
# This transcript jg12971.t2 is derived from g11436.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12972.t1 is derived from g11437.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3395964	3396350	.	-	.	Phchi.S3G029100
Phchi.S3	AUGUSTUS	transcript	3395964	3396350	.	-	.	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	stop_codon	3395961	3395963	.	-	0	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	CDS	3395964	3396034	0.98	-	2	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	exon	3395964	3396034	.	-	.	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	intron	3396035	3396113	.	-	.	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	CDS	3396114	3396228	1	-	0	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	exon	3396114	3396228	.	-	.	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	intron	3396229	3396305	.	-	.	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	CDS	3396306	3396350	0.67	-	0	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	exon	3396306	3396350	.	-	.	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
Phchi.S3	AUGUSTUS	start_codon	3396348	3396350	.	-	0	transcript_id "Phchi.S3G029100.t1"; gene_id "Phchi.S3G029100"
# This transcript jg10688.t2 is derived from g14738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10689.t1 is derived from g14739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1591424	1594073	.	-	.	Phchi.S4G027100
Phchi.S4	AUGUSTUS	transcript	1591424	1594073	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	stop_codon	1591421	1591423	.	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1591424	1591576	0.99	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1591424	1591576	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1591577	1591672	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1591673	1591759	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1591673	1591759	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1591760	1591849	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1591850	1592038	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1591850	1592038	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1592039	1592156	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1592157	1592228	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1592157	1592228	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1592229	1592320	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1592321	1592620	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1592321	1592620	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1592621	1592749	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1592750	1592917	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1592750	1592917	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1592918	1593033	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1593034	1593162	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1593034	1593162	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1593163	1593250	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1593251	1593334	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1593251	1593334	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1593335	1593454	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1593455	1593567	1	-	2	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1593455	1593567	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1593568	1593656	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1593657	1593741	1	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1593657	1593741	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	intron	1593742	1593845	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	CDS	1593846	1594073	0.57	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	exon	1593846	1594073	.	-	.	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
Phchi.S4	AUGUSTUS	start_codon	1594071	1594073	.	-	0	transcript_id "Phchi.S4G027100.t1"; gene_id "Phchi.S4G027100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2189.t1 is derived from g9109.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5289721	5290801	.	+	.	Phchi.S5G079800
Phchi.S5	AUGUSTUS	transcript	5289721	5290801	.	+	.	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	start_codon	5289721	5289723	.	+	0	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	CDS	5289721	5290042	1	+	0	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	exon	5289721	5290042	.	+	.	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	intron	5290043	5290130	.	+	.	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	CDS	5290131	5290801	0.97	+	2	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	exon	5290131	5290801	.	+	.	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
Phchi.S5	AUGUSTUS	stop_codon	5290802	5290804	.	+	0	transcript_id "Phchi.S5G079800.t1"; gene_id "Phchi.S5G079800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11838.t1 is derived from g15890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8504062	8505852	.	+	.	Phchi.S4G142000
Phchi.S4	AUGUSTUS	transcript	8504062	8505852	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	start_codon	8504062	8504064	.	+	0	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	CDS	8504062	8504926	0.59	+	0	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	exon	8504062	8504926	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	intron	8504927	8505037	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	CDS	8505038	8505113	0.36	+	2	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	exon	8505038	8505113	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	intron	8505114	8505221	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	CDS	8505222	8505261	0.45	+	1	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	exon	8505222	8505261	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	intron	8505262	8505579	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	CDS	8505580	8505723	0.85	+	0	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	exon	8505580	8505723	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	intron	8505724	8505849	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	CDS	8505850	8505852	0.85	+	0	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	exon	8505850	8505852	.	+	.	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
Phchi.S4	AUGUSTUS	stop_codon	8505853	8505855	.	+	0	transcript_id "Phchi.S4G142000.t1"; gene_id "Phchi.S4G142000"
# This transcript jg14848.t2 is derived from g13316.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14849.t1 is derived from g13317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15045990	15047169	.	+	.	Phchi.S3G216800
Phchi.S3	AUGUSTUS	transcript	15045990	15047169	.	+	.	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	start_codon	15045990	15045992	.	+	0	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	CDS	15045990	15046944	0.2	+	0	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	exon	15045990	15046944	.	+	.	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	intron	15046945	15047040	.	+	.	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	CDS	15047041	15047073	0.61	+	2	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	exon	15047041	15047073	.	+	.	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	intron	15047074	15047167	.	+	.	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	CDS	15047168	15047169	1	+	2	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	exon	15047168	15047169	.	+	.	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
Phchi.S3	AUGUSTUS	stop_codon	15047170	15047172	.	+	0	transcript_id "Phchi.S3G216800.t1"; gene_id "Phchi.S3G216800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10844.t1 is derived from g14894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2441561	2442808	.	+	.	Phchi.S4G042600
Phchi.S4	AUGUSTUS	transcript	2441561	2442808	.	+	.	transcript_id "Phchi.S4G042600.t1"; gene_id "Phchi.S4G042600"
Phchi.S4	AUGUSTUS	start_codon	2441561	2441563	.	+	0	transcript_id "Phchi.S4G042600.t1"; gene_id "Phchi.S4G042600"
Phchi.S4	AUGUSTUS	CDS	2441561	2442808	1	+	0	transcript_id "Phchi.S4G042600.t1"; gene_id "Phchi.S4G042600"
Phchi.S4	AUGUSTUS	exon	2441561	2442808	.	+	.	transcript_id "Phchi.S4G042600.t1"; gene_id "Phchi.S4G042600"
Phchi.S4	AUGUSTUS	stop_codon	2442809	2442811	.	+	0	transcript_id "Phchi.S4G042600.t1"; gene_id "Phchi.S4G042600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14803.t1 is derived from g13271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14786823	14792262	.	-	.	Phchi.S3G212200
Phchi.S3	AUGUSTUS	transcript	14786823	14792262	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	stop_codon	14786820	14786822	.	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14786823	14787077	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14786823	14787077	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14787078	14787185	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14787186	14787282	1	-	1	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14787186	14787282	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14787283	14787404	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14787405	14787499	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14787405	14787499	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14787500	14787600	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14787601	14787705	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14787601	14787705	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14787706	14787789	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14787790	14787963	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14787790	14787963	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14787964	14788100	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14788101	14788197	1	-	1	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14788101	14788197	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14788198	14788294	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14788295	14788557	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14788295	14788557	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14788558	14788721	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14788722	14788834	0.97	-	2	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14788722	14788834	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14788835	14788946	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14788947	14789115	0.95	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14788947	14789115	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14789116	14789211	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14789212	14789290	1	-	1	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14789212	14789290	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14789291	14789419	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14789420	14789511	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14789420	14789511	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14789512	14789601	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14789602	14789670	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14789602	14789670	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14789671	14789788	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14789789	14789947	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14789789	14789947	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14789948	14790023	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14790024	14790080	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14790024	14790080	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14790081	14790184	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14790185	14790247	0.99	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14790185	14790247	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14790248	14790335	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14790336	14790452	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14790336	14790452	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14790453	14790536	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14790537	14790600	1	-	1	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14790537	14790600	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14790601	14790687	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14790688	14790758	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14790688	14790758	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14790759	14791049	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14791050	14791152	1	-	1	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14791050	14791152	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14791153	14791252	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14791253	14791319	1	-	2	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14791253	14791319	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14791320	14791617	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14791618	14791878	0.55	-	2	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14791618	14791878	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14791879	14791976	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14791977	14792040	0.68	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14791977	14792040	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	intron	14792041	14792193	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	CDS	14792194	14792262	1	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	exon	14792194	14792262	.	-	.	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
Phchi.S3	AUGUSTUS	start_codon	14792260	14792262	.	-	0	transcript_id "Phchi.S3G212200.t1"; gene_id "Phchi.S3G212200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11512.t1 is derived from g15562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6845618	6850008	.	-	.	Phchi.S4G109400
Phchi.S4	AUGUSTUS	transcript	6845618	6850008	.	-	.	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	stop_codon	6845615	6845617	.	-	0	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	CDS	6845618	6847995	0.71	-	2	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	exon	6845618	6847995	.	-	.	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	intron	6847996	6848184	.	-	.	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	CDS	6848185	6849712	0.24	-	0	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	exon	6848185	6849712	.	-	.	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	intron	6849713	6849882	.	-	.	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	CDS	6849883	6850008	0.22	-	0	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	exon	6849883	6850008	.	-	.	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
Phchi.S4	AUGUSTUS	start_codon	6850006	6850008	.	-	0	transcript_id "Phchi.S4G109400.t1"; gene_id "Phchi.S4G109400"
# This transcript jg1308.t2 is derived from g11091.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1309.t1 is derived from g11092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8943106	8945548	.	-	.	Phchi.S6G126800
Phchi.S6	AUGUSTUS	transcript	8943106	8945548	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	stop_codon	8943103	8943105	.	-	0	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8943106	8943237	1	-	0	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8943106	8943237	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8943238	8943318	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8943319	8943664	1	-	1	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8943319	8943664	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8943665	8943749	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8943750	8943906	1	-	2	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8943750	8943906	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8943907	8943996	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8943997	8944131	1	-	2	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8943997	8944131	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8944132	8944231	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8944232	8944619	0.99	-	0	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8944232	8944619	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8944620	8944737	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8944738	8945038	1	-	1	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8944738	8945038	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8945039	8945125	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8945126	8945364	1	-	0	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8945126	8945364	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	intron	8945365	8945443	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	CDS	8945444	8945548	0.76	-	0	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	exon	8945444	8945548	.	-	.	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
Phchi.S6	AUGUSTUS	start_codon	8945546	8945548	.	-	0	transcript_id "Phchi.S6G126800.t1"; gene_id "Phchi.S6G126800"
# This transcript jg1909.t2 is derived from g8829.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1910.t1 is derived from g8830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3821643	3824732	.	-	.	Phchi.S5G051900
Phchi.S5	AUGUSTUS	transcript	3821643	3824732	.	-	.	transcript_id "Phchi.S5G051900.t1"; gene_id "Phchi.S5G051900"
Phchi.S5	AUGUSTUS	stop_codon	3821640	3821642	.	-	0	transcript_id "Phchi.S5G051900.t1"; gene_id "Phchi.S5G051900"
Phchi.S5	AUGUSTUS	CDS	3821643	3824732	0.34	-	0	transcript_id "Phchi.S5G051900.t1"; gene_id "Phchi.S5G051900"
Phchi.S5	AUGUSTUS	exon	3821643	3824732	.	-	.	transcript_id "Phchi.S5G051900.t1"; gene_id "Phchi.S5G051900"
Phchi.S5	AUGUSTUS	start_codon	3824730	3824732	.	-	0	transcript_id "Phchi.S5G051900.t1"; gene_id "Phchi.S5G051900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4653.t1 is derived from g1823.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11649481	11650026	.	-	.	Phchi.S1G181200
Phchi.S1	AUGUSTUS	transcript	11649481	11650026	.	-	.	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	stop_codon	11649478	11649480	.	-	0	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	CDS	11649481	11649773	1	-	2	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	exon	11649481	11649773	.	-	.	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	intron	11649774	11649911	.	-	.	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	CDS	11649912	11650026	0.8	-	0	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	exon	11649912	11650026	.	-	.	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
Phchi.S1	AUGUSTUS	start_codon	11650024	11650026	.	-	0	transcript_id "Phchi.S1G181200.t1"; gene_id "Phchi.S1G181200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2492.t1 is derived from g9412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6935137	6936916	.	-	.	Phchi.S5G110100
Phchi.S5	AUGUSTUS	transcript	6935137	6936916	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	stop_codon	6935134	6935136	.	-	0	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6935137	6935195	0.63	-	2	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6935137	6935195	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6935196	6935371	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6935372	6935681	0.84	-	0	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6935372	6935681	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6935682	6935777	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6935778	6935874	0.99	-	1	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6935778	6935874	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6935875	6936082	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936083	6936137	0.86	-	2	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936083	6936137	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6936138	6936211	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936212	6936220	0.86	-	2	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936212	6936220	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6936221	6936432	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936433	6936529	0.71	-	0	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936433	6936529	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6936530	6936676	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936677	6936916	0.74	-	0	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936677	6936916	.	-	.	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	start_codon	6936914	6936916	.	-	0	transcript_id "Phchi.S5G110100.t1"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	transcript	6935137	6936916	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	stop_codon	6935134	6935136	.	-	0	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6935137	6935195	0.48	-	2	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6935137	6935195	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6935196	6935371	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6935372	6935681	0.71	-	0	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6935372	6935681	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6935682	6935777	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6935778	6935871	0.47	-	1	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6935778	6935871	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6935872	6936082	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936083	6936137	0.38	-	2	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936083	6936137	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6936138	6936211	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936212	6936220	0.41	-	2	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936212	6936220	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6936221	6936432	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936433	6936529	0.77	-	0	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936433	6936529	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	intron	6936530	6936676	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	CDS	6936677	6936916	0.84	-	0	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	exon	6936677	6936916	.	-	.	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
Phchi.S5	AUGUSTUS	start_codon	6936914	6936916	.	-	0	transcript_id "Phchi.S5G110100.t2"; gene_id "Phchi.S5G110100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4105.t1 is derived from g1274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7856698	7858305	.	+	.	Phchi.S1G126400
Phchi.S1	AUGUSTUS	transcript	7856698	7858305	.	+	.	transcript_id "Phchi.S1G126400.t1"; gene_id "Phchi.S1G126400"
Phchi.S1	AUGUSTUS	start_codon	7856698	7856700	.	+	0	transcript_id "Phchi.S1G126400.t1"; gene_id "Phchi.S1G126400"
Phchi.S1	AUGUSTUS	CDS	7856698	7858305	0.69	+	0	transcript_id "Phchi.S1G126400.t1"; gene_id "Phchi.S1G126400"
Phchi.S1	AUGUSTUS	exon	7856698	7858305	.	+	.	transcript_id "Phchi.S1G126400.t1"; gene_id "Phchi.S1G126400"
Phchi.S1	AUGUSTUS	stop_codon	7858306	7858308	.	+	0	transcript_id "Phchi.S1G126400.t1"; gene_id "Phchi.S1G126400"
# This transcript jg12029.t2 is derived from g7704.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12030.t1 is derived from g7705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	647604	649925	.	-	.	Phchi.S2G011000
Phchi.S2	AUGUSTUS	transcript	647604	649925	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	stop_codon	647601	647603	.	-	0	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	CDS	647604	647808	0.73	-	1	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	exon	647604	647808	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	intron	647809	647883	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	CDS	647884	648011	0.93	-	0	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	exon	647884	648011	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	intron	648012	648098	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	CDS	648099	648188	1	-	0	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	exon	648099	648188	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	intron	648189	648273	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	CDS	648274	648374	1	-	2	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	exon	648274	648374	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	intron	648375	648487	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	CDS	648488	649019	1	-	0	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	exon	648488	649019	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	intron	649020	649133	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	CDS	649134	649925	1	-	0	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	exon	649134	649925	.	-	.	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
Phchi.S2	AUGUSTUS	start_codon	649923	649925	.	-	0	transcript_id "Phchi.S2G011000.t1"; gene_id "Phchi.S2G011000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2471.t1 is derived from g9391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6825015	6828427	.	-	.	Phchi.S5G108000
Phchi.S5	AUGUSTUS	transcript	6825015	6828427	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	stop_codon	6825012	6825014	.	-	0	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	CDS	6825015	6826222	0.32	-	2	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	exon	6825015	6826222	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	intron	6826223	6826307	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	CDS	6826308	6827082	1	-	0	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	exon	6826308	6827082	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	intron	6827083	6827330	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	CDS	6827331	6827750	0.97	-	0	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	exon	6827331	6827750	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	intron	6827751	6827830	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	CDS	6827831	6828427	0.78	-	0	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	exon	6827831	6828427	.	-	.	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
Phchi.S5	AUGUSTUS	start_codon	6828425	6828427	.	-	0	transcript_id "Phchi.S5G108000.t1"; gene_id "Phchi.S5G108000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11136.t1 is derived from g15186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4353084	4357478	.	-	.	Phchi.S4G071800
Phchi.S4	AUGUSTUS	transcript	4353084	4357478	.	-	.	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	stop_codon	4353081	4353083	.	-	0	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	CDS	4353084	4353358	1	-	2	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	exon	4353084	4353358	.	-	.	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	intron	4353359	4353583	.	-	.	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	CDS	4353584	4353680	0.5	-	0	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	exon	4353584	4353680	.	-	.	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	intron	4353681	4353896	.	-	.	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	CDS	4353897	4357478	0.48	-	0	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	exon	4353897	4357478	.	-	.	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
Phchi.S4	AUGUSTUS	start_codon	4357476	4357478	.	-	0	transcript_id "Phchi.S4G071800.t1"; gene_id "Phchi.S4G071800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7387.t1 is derived from g4559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28885137	28889055	.	+	.	Phchi.S1G454600
Phchi.S1	AUGUSTUS	transcript	28885137	28889055	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	start_codon	28885137	28885139	.	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28885137	28885391	0.45	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28885137	28885391	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28885392	28885550	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28885551	28885605	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28885551	28885605	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28885606	28885727	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28885728	28885939	0.62	+	2	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28885728	28885939	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28885940	28886047	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28886048	28886169	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28886048	28886169	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28886170	28886256	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28886257	28886410	1	+	1	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28886257	28886410	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28886411	28886547	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28886548	28886617	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28886548	28886617	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28886618	28886732	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28886733	28886878	1	+	2	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28886733	28886878	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28886879	28887028	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28887029	28887074	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28887029	28887074	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28887075	28887186	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28887187	28887239	1	+	2	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28887187	28887239	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28887240	28887312	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28887313	28887457	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28887313	28887457	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28887458	28887583	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28887584	28887702	1	+	2	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28887584	28887702	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28887703	28887787	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28887788	28887859	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28887788	28887859	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28887860	28887940	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28887941	28888044	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28887941	28888044	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28888045	28888142	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28888143	28888199	1	+	1	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28888143	28888199	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28888200	28888308	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28888309	28888516	0.98	+	1	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28888309	28888516	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28888517	28888700	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28888701	28888847	1	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28888701	28888847	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	intron	28888848	28888938	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	CDS	28888939	28889055	0.99	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	exon	28888939	28889055	.	+	.	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
Phchi.S1	AUGUSTUS	stop_codon	28889056	28889058	.	+	0	transcript_id "Phchi.S1G454600.t1"; gene_id "Phchi.S1G454600"
# This transcript jg7692.t2 is derived from g4866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7693.t1 is derived from g4867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30653603	30659563	.	+	.	Phchi.S1G485200
Phchi.S1	AUGUSTUS	transcript	30653603	30659563	.	+	.	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	start_codon	30653603	30653605	.	+	0	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	CDS	30653603	30655800	0.48	+	0	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	exon	30653603	30655800	.	+	.	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	intron	30655801	30655883	.	+	.	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	CDS	30655884	30656377	0.17	+	1	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	exon	30655884	30656377	.	+	.	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	intron	30656378	30659528	.	+	.	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	CDS	30659529	30659563	0.03	+	2	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	exon	30659529	30659563	.	+	.	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
Phchi.S1	AUGUSTUS	stop_codon	30659564	30659566	.	+	0	transcript_id "Phchi.S1G485200.t1"; gene_id "Phchi.S1G485200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2410.t1 is derived from g9330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6525396	6525888	.	-	.	Phchi.S5G101900
Phchi.S5	AUGUSTUS	transcript	6525396	6525888	.	-	.	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	stop_codon	6525393	6525395	.	-	0	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	CDS	6525396	6525422	0.67	-	0	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	exon	6525396	6525422	.	-	.	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	intron	6525423	6525621	.	-	.	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	CDS	6525622	6525888	0.65	-	0	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	exon	6525622	6525888	.	-	.	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
Phchi.S5	AUGUSTUS	start_codon	6525886	6525888	.	-	0	transcript_id "Phchi.S5G101900.t1"; gene_id "Phchi.S5G101900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4202.t1 is derived from g1371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8886803	8888380	.	+	.	Phchi.S1G136100
Phchi.S1	AUGUSTUS	transcript	8886803	8888380	.	+	.	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	start_codon	8886803	8886805	.	+	0	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	CDS	8886803	8887110	0.96	+	0	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	exon	8886803	8887110	.	+	.	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	intron	8887111	8887224	.	+	.	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	CDS	8887225	8888148	0.47	+	1	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	exon	8887225	8888148	.	+	.	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	intron	8888149	8888262	.	+	.	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	CDS	8888263	8888380	0.48	+	1	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	exon	8888263	8888380	.	+	.	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
Phchi.S1	AUGUSTUS	stop_codon	8888381	8888383	.	+	0	transcript_id "Phchi.S1G136100.t1"; gene_id "Phchi.S1G136100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13236.t1 is derived from g11701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4859330	4859962	.	+	.	Phchi.S3G055500
Phchi.S3	AUGUSTUS	transcript	4859330	4859962	.	+	.	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	start_codon	4859330	4859332	.	+	0	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	CDS	4859330	4859484	0.76	+	0	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	exon	4859330	4859484	.	+	.	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	intron	4859485	4859584	.	+	.	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	CDS	4859585	4859675	0.76	+	1	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	exon	4859585	4859675	.	+	.	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	intron	4859676	4859791	.	+	.	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	CDS	4859792	4859962	0.73	+	0	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	exon	4859792	4859962	.	+	.	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
Phchi.S3	AUGUSTUS	stop_codon	4859963	4859965	.	+	0	transcript_id "Phchi.S3G055500.t1"; gene_id "Phchi.S3G055500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10093.t1 is derived from g7269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45722033	45724049	.	+	.	Phchi.S1G725200
Phchi.S1	AUGUSTUS	transcript	45722033	45724049	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	start_codon	45722033	45722035	.	+	0	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	CDS	45722033	45722433	0.61	+	0	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	exon	45722033	45722433	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	intron	45722434	45722592	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	CDS	45722593	45722851	0.92	+	1	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	exon	45722593	45722851	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	intron	45722852	45722931	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	CDS	45722932	45723021	1	+	0	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	exon	45722932	45723021	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	intron	45723022	45723109	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	CDS	45723110	45723280	1	+	0	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	exon	45723110	45723280	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	intron	45723281	45723404	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	CDS	45723405	45724049	0.96	+	0	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	exon	45723405	45724049	.	+	.	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
Phchi.S1	AUGUSTUS	stop_codon	45724050	45724052	.	+	0	transcript_id "Phchi.S1G725200.t1"; gene_id "Phchi.S1G725200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3125.t1 is derived from g294.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1854528	1855073	.	+	.	Phchi.S1G028400
Phchi.S1	AUGUSTUS	transcript	1854528	1855073	.	+	.	transcript_id "Phchi.S1G028400.t1"; gene_id "Phchi.S1G028400"
Phchi.S1	AUGUSTUS	start_codon	1854528	1854530	.	+	0	transcript_id "Phchi.S1G028400.t1"; gene_id "Phchi.S1G028400"
Phchi.S1	AUGUSTUS	CDS	1854528	1855073	0.98	+	0	transcript_id "Phchi.S1G028400.t1"; gene_id "Phchi.S1G028400"
Phchi.S1	AUGUSTUS	exon	1854528	1855073	.	+	.	transcript_id "Phchi.S1G028400.t1"; gene_id "Phchi.S1G028400"
Phchi.S1	AUGUSTUS	stop_codon	1855074	1855076	.	+	0	transcript_id "Phchi.S1G028400.t1"; gene_id "Phchi.S1G028400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7154.t1 is derived from g4326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27315400	27316691	.	-	.	Phchi.S1G431300
Phchi.S1	AUGUSTUS	transcript	27315400	27316691	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	stop_codon	27315397	27315399	.	-	0	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27315400	27315501	0.99	-	0	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27315400	27315501	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	intron	27315502	27315608	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27315609	27315706	0.89	-	2	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27315609	27315706	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	intron	27315707	27315797	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27315798	27315972	1	-	0	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27315798	27315972	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	intron	27315973	27316131	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27316132	27316184	1	-	2	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27316132	27316184	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	intron	27316185	27316261	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27316262	27316317	1	-	1	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27316262	27316317	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	intron	27316318	27316420	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27316421	27316584	1	-	0	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27316421	27316584	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	intron	27316585	27316667	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	CDS	27316668	27316691	0.86	-	0	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	exon	27316668	27316691	.	-	.	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
Phchi.S1	AUGUSTUS	start_codon	27316689	27316691	.	-	0	transcript_id "Phchi.S1G431300.t1"; gene_id "Phchi.S1G431300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1975.t1 is derived from g8895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4094773	4097628	.	+	.	Phchi.S5G058400
Phchi.S5	AUGUSTUS	transcript	4094773	4097628	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	start_codon	4094773	4094775	.	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4094773	4094887	0.95	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4094773	4094887	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4094888	4095075	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4095076	4095167	1	+	2	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4095076	4095167	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4095168	4095257	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4095258	4095361	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4095258	4095361	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4095362	4095460	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4095461	4095545	1	+	1	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4095461	4095545	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4095546	4095627	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4095628	4095744	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4095628	4095744	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4095745	4095887	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4095888	4095997	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4095888	4095997	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4095998	4096141	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4096142	4096247	1	+	1	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4096142	4096247	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4096248	4096372	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4096373	4096459	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4096373	4096459	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4096460	4096581	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4096582	4096764	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4096582	4096764	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4096765	4096922	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4096923	4097048	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4096923	4097048	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4097049	4097234	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4097235	4097408	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4097235	4097408	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	intron	4097409	4097493	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	CDS	4097494	4097628	1	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	exon	4097494	4097628	.	+	.	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
Phchi.S5	AUGUSTUS	stop_codon	4097629	4097631	.	+	0	transcript_id "Phchi.S5G058400.t1"; gene_id "Phchi.S5G058400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14074.t1 is derived from g12541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10664556	10669094	.	-	.	Phchi.S3G139300
Phchi.S3	AUGUSTUS	transcript	10664556	10669094	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	stop_codon	10664553	10664555	.	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10664556	10664813	0.99	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10664556	10664813	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10664814	10664899	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10664900	10665046	1	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10664900	10665046	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10665047	10665116	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10665117	10665178	1	-	2	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10665117	10665178	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10665179	10665276	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10665277	10665368	1	-	1	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10665277	10665368	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10665369	10665475	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10665476	10666609	0.86	-	1	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10665476	10666609	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10666610	10666895	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10666896	10666984	1	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10666896	10666984	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10666985	10667065	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10667066	10667152	1	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10667066	10667152	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10667153	10667294	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10667295	10667354	1	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10667295	10667354	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10667355	10667434	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10667435	10667478	1	-	2	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10667435	10667478	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10667479	10667606	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10667607	10667784	0.97	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10667607	10667784	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10667785	10668034	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10668035	10668129	1	-	2	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10668035	10668129	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10668130	10668301	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10668302	10668386	1	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10668302	10668386	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10668387	10668478	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10668479	10668586	1	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10668479	10668586	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10668587	10668676	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10668677	10668857	1	-	1	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10668677	10668857	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	intron	10668858	10668945	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	CDS	10668946	10669094	0.98	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	exon	10668946	10669094	.	-	.	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
Phchi.S3	AUGUSTUS	start_codon	10669092	10669094	.	-	0	transcript_id "Phchi.S3G139300.t1"; gene_id "Phchi.S3G139300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9899.t1 is derived from g7075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44331410	44332474	.	+	.	Phchi.S1G705800
Phchi.S1	AUGUSTUS	transcript	44331410	44332474	.	+	.	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	start_codon	44331410	44331412	.	+	0	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	CDS	44331410	44331412	1	+	0	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	exon	44331410	44331412	.	+	.	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	intron	44331413	44332024	.	+	.	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	CDS	44332025	44332093	1	+	0	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	exon	44332025	44332093	.	+	.	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	intron	44332094	44332189	.	+	.	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	CDS	44332190	44332474	1	+	0	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	exon	44332190	44332474	.	+	.	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
Phchi.S1	AUGUSTUS	stop_codon	44332475	44332477	.	+	0	transcript_id "Phchi.S1G705800.t1"; gene_id "Phchi.S1G705800"
# This transcript jg11134.t2 is derived from g15184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11135.t1 is derived from g15185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4350985	4352493	.	+	.	Phchi.S4G071700
Phchi.S4	AUGUSTUS	transcript	4350985	4352493	.	+	.	transcript_id "Phchi.S4G071700.t1"; gene_id "Phchi.S4G071700"
Phchi.S4	AUGUSTUS	start_codon	4350985	4350987	.	+	0	transcript_id "Phchi.S4G071700.t1"; gene_id "Phchi.S4G071700"
Phchi.S4	AUGUSTUS	CDS	4350985	4352493	0.52	+	0	transcript_id "Phchi.S4G071700.t1"; gene_id "Phchi.S4G071700"
Phchi.S4	AUGUSTUS	exon	4350985	4352493	.	+	.	transcript_id "Phchi.S4G071700.t1"; gene_id "Phchi.S4G071700"
Phchi.S4	AUGUSTUS	stop_codon	4352494	4352496	.	+	0	transcript_id "Phchi.S4G071700.t1"; gene_id "Phchi.S4G071700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg293.t1 is derived from g10075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2100568	2102092	.	+	.	Phchi.S6G025200
Phchi.S6	AUGUSTUS	transcript	2100568	2102092	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	start_codon	2100568	2100570	.	+	0	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	CDS	2100568	2100647	1	+	0	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	exon	2100568	2100647	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	intron	2100648	2100745	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	CDS	2100746	2100824	0.99	+	1	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	exon	2100746	2100824	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	intron	2100825	2100983	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	CDS	2100984	2101352	0.25	+	0	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	exon	2100984	2101352	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	intron	2101353	2101735	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	CDS	2101736	2101806	0.7	+	0	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	exon	2101736	2101806	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	intron	2101807	2101902	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	CDS	2101903	2102092	0.72	+	1	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	exon	2101903	2102092	.	+	.	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
Phchi.S6	AUGUSTUS	stop_codon	2102093	2102095	.	+	0	transcript_id "Phchi.S6G025200.t1"; gene_id "Phchi.S6G025200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12425.t1 is derived from g8102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19553202	19554089	.	+	.	Phchi.S2G050500
Phchi.S2	AUGUSTUS	transcript	19553202	19554089	.	+	.	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	start_codon	19553202	19553204	.	+	0	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	CDS	19553202	19553420	0.97	+	0	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	exon	19553202	19553420	.	+	.	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	intron	19553421	19553572	.	+	.	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	CDS	19553573	19553678	1	+	0	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	exon	19553573	19553678	.	+	.	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	intron	19553679	19553775	.	+	.	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	CDS	19553776	19554089	1	+	2	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	exon	19553776	19554089	.	+	.	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
Phchi.S2	AUGUSTUS	stop_codon	19554090	19554092	.	+	0	transcript_id "Phchi.S2G050500.t1"; gene_id "Phchi.S2G050500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14132.t1 is derived from g12599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11069281	11074571	.	+	.	Phchi.S3G145100
Phchi.S3	AUGUSTUS	transcript	11069281	11074571	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	start_codon	11069281	11069283	.	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11069281	11069540	0.94	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11069281	11069540	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11069541	11069972	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11069973	11070261	1	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11069973	11070261	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11070262	11070425	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11070426	11070558	1	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11070426	11070558	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11070559	11070690	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11070691	11070793	1	+	2	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11070691	11070793	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11070794	11070888	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11070889	11071089	1	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11070889	11071089	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071090	11071231	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11071232	11071502	1	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11071232	11071502	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071503	11071619	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11071620	11071718	1	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11071620	11071718	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071719	11071898	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11071899	11071987	1	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11071899	11071987	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071988	11072071	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072072	11072171	1	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072072	11072171	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072172	11072256	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072257	11072297	0.55	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072257	11072297	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072298	11072383	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072384	11072426	0.87	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072384	11072426	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072427	11072506	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072507	11072659	0.98	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072507	11072659	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072660	11072800	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072801	11072961	1	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072801	11072961	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072962	11073092	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11073093	11073291	0.97	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11073093	11073291	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11073292	11073398	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11073399	11074012	0.76	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11073399	11074012	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11074013	11074102	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11074103	11074166	1	+	1	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11074103	11074166	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11074167	11074268	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11074269	11074355	0.94	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11074269	11074355	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11074356	11074496	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11074497	11074571	0.8	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11074497	11074571	.	+	.	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	stop_codon	11074572	11074574	.	+	0	transcript_id "Phchi.S3G145100.t1"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	transcript	11069281	11074571	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	start_codon	11069281	11069283	.	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11069281	11069660	0.79	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11069281	11069660	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11069661	11069972	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11069973	11070261	1	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11069973	11070261	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11070262	11070425	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11070426	11070558	1	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11070426	11070558	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11070559	11070690	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11070691	11070793	1	+	2	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11070691	11070793	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11070794	11070888	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11070889	11071089	1	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11070889	11071089	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071090	11071231	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11071232	11071502	0.99	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11071232	11071502	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071503	11071619	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11071620	11071718	1	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11071620	11071718	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071719	11071898	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11071899	11071987	1	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11071899	11071987	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11071988	11072071	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072072	11072171	1	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072072	11072171	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072172	11072256	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072257	11072297	0.57	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072257	11072297	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072298	11072383	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072384	11072426	0.88	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072384	11072426	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072427	11072506	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072507	11072659	0.99	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072507	11072659	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072660	11072800	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11072801	11072961	1	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11072801	11072961	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11072962	11073092	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11073093	11073291	0.88	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11073093	11073291	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11073292	11073398	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11073399	11074012	0.8	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11073399	11074012	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11074013	11074102	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11074103	11074166	1	+	1	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11074103	11074166	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11074167	11074268	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11074269	11074355	0.96	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11074269	11074355	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	intron	11074356	11074496	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	CDS	11074497	11074571	0.78	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	exon	11074497	11074571	.	+	.	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
Phchi.S3	AUGUSTUS	stop_codon	11074572	11074574	.	+	0	transcript_id "Phchi.S3G145100.t2"; gene_id "Phchi.S3G145100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13251.t1 is derived from g11716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4925714	4927365	.	+	.	Phchi.S3G057000
Phchi.S3	AUGUSTUS	transcript	4925714	4927365	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	start_codon	4925714	4925716	.	+	0	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4925714	4925814	1	+	0	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4925714	4925814	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	intron	4925815	4926066	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4926067	4926246	0.58	+	1	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4926067	4926246	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	intron	4926247	4926352	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4926353	4926413	1	+	1	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4926353	4926413	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	intron	4926414	4926514	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4926515	4926716	1	+	0	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4926515	4926716	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	intron	4926717	4926805	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4926806	4926927	1	+	2	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4926806	4926927	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	intron	4926928	4927068	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4927069	4927173	1	+	0	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4927069	4927173	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	intron	4927174	4927272	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	CDS	4927273	4927365	1	+	0	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	exon	4927273	4927365	.	+	.	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
Phchi.S3	AUGUSTUS	stop_codon	4927366	4927368	.	+	0	transcript_id "Phchi.S3G057000.t1"; gene_id "Phchi.S3G057000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4500.t1 is derived from g1670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10856622	10858680	.	+	.	Phchi.S1G165900
Phchi.S1	AUGUSTUS	transcript	10856622	10858680	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	start_codon	10856622	10856624	.	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10856622	10856670	0.95	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10856622	10856670	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10856671	10856772	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10856773	10856927	0.95	+	2	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10856773	10856927	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10856928	10857005	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857006	10857053	0.89	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857006	10857053	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857054	10857143	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857144	10857197	0.91	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857144	10857197	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857198	10857293	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857294	10857438	0.58	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857294	10857438	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857439	10857588	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857589	10857837	0.99	+	2	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857589	10857837	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857838	10857922	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857923	10858010	0.99	+	2	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857923	10858010	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10858011	10858112	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10858113	10858236	0.96	+	1	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10858113	10858236	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10858237	10858332	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10858333	10858680	0.79	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10858333	10858680	.	+	.	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	stop_codon	10858681	10858683	.	+	0	transcript_id "Phchi.S1G165900.t1"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	transcript	10856622	10858680	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	start_codon	10856622	10856624	.	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10856622	10856670	0.95	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10856622	10856670	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10856671	10856772	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10856773	10856927	0.95	+	2	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10856773	10856927	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10856928	10857005	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857006	10857053	0.84	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857006	10857053	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857054	10857143	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857144	10857197	0.86	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857144	10857197	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857198	10857293	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857294	10857438	0.62	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857294	10857438	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857439	10857588	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857589	10857837	0.99	+	2	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857589	10857837	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10857838	10857928	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10857929	10858010	0.66	+	2	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10857929	10858010	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10858011	10858112	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10858113	10858236	0.94	+	1	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10858113	10858236	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	intron	10858237	10858332	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	CDS	10858333	10858680	0.7	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	exon	10858333	10858680	.	+	.	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
Phchi.S1	AUGUSTUS	stop_codon	10858681	10858683	.	+	0	transcript_id "Phchi.S1G165900.t2"; gene_id "Phchi.S1G165900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2746.t1 is derived from g9666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8583698	8585166	.	+	.	Phchi.S5G135500
Phchi.S5	AUGUSTUS	transcript	8583698	8585166	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	start_codon	8583698	8583700	.	+	0	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8583698	8583931	1	+	0	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8583698	8583931	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8583932	8584024	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584025	8584147	1	+	0	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584025	8584147	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584148	8584230	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584231	8584367	1	+	0	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584231	8584367	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584368	8584481	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584482	8584579	1	+	1	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584482	8584579	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584580	8584698	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584699	8584790	1	+	2	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584699	8584790	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584791	8584874	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584875	8585017	1	+	0	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584875	8585017	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8585018	8585099	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8585100	8585166	0.79	+	1	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8585100	8585166	.	+	.	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	stop_codon	8585167	8585169	.	+	0	transcript_id "Phchi.S5G135500.t1"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	transcript	8583698	8585166	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	start_codon	8583698	8583700	.	+	0	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8583698	8583931	1	+	0	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8583698	8583931	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8583932	8584024	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584025	8584130	0.98	+	0	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584025	8584130	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584131	8584230	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584231	8584282	0.98	+	2	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584231	8584282	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584283	8584481	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584482	8584579	1	+	1	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584482	8584579	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584580	8584698	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584699	8584790	1	+	2	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584699	8584790	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8584791	8584874	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8584875	8585017	1	+	0	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8584875	8585017	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	intron	8585018	8585099	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	CDS	8585100	8585166	0.85	+	1	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	exon	8585100	8585166	.	+	.	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
Phchi.S5	AUGUSTUS	stop_codon	8585167	8585169	.	+	0	transcript_id "Phchi.S5G135500.t2"; gene_id "Phchi.S5G135500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15253.t1 is derived from g13721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17917722	17918640	.	-	.	Phchi.S3G257200
Phchi.S3	AUGUSTUS	transcript	17917722	17918640	.	-	.	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	stop_codon	17917719	17917721	.	-	0	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	CDS	17917722	17917851	1	-	1	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	exon	17917722	17917851	.	-	.	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	intron	17917852	17917990	.	-	.	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	CDS	17917991	17918640	0.45	-	0	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	exon	17917991	17918640	.	-	.	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
Phchi.S3	AUGUSTUS	start_codon	17918638	17918640	.	-	0	transcript_id "Phchi.S3G257200.t1"; gene_id "Phchi.S3G257200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3351.t1 is derived from g520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3067014	3071031	.	-	.	Phchi.S1G051000
Phchi.S1	AUGUSTUS	transcript	3067014	3071031	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	stop_codon	3067011	3067013	.	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3067014	3067135	1	-	2	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3067014	3067135	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3067136	3067218	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3067219	3068004	0.98	-	2	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3067219	3068004	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3068005	3068080	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3068081	3068156	0.73	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3068081	3068156	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3068157	3068266	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3068267	3068461	0.91	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3068267	3068461	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3068462	3068600	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3068601	3068786	1	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3068601	3068786	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3068787	3068887	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3068888	3068920	1	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3068888	3068920	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3068921	3069023	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3069024	3069122	1	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3069024	3069122	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3069123	3069210	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3069211	3069450	1	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3069211	3069450	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3069451	3069593	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3069594	3069911	1	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3069594	3069911	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3069912	3070018	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3070019	3070076	1	-	1	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3070019	3070076	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3070077	3070207	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3070208	3070366	1	-	1	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3070208	3070366	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3070367	3070485	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3070486	3070701	1	-	1	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3070486	3070701	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	intron	3070702	3070840	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	CDS	3070841	3071031	0.57	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	exon	3070841	3071031	.	-	.	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
Phchi.S1	AUGUSTUS	start_codon	3071029	3071031	.	-	0	transcript_id "Phchi.S1G051000.t1"; gene_id "Phchi.S1G051000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6171.t1 is derived from g3342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21288064	21290941	.	+	.	Phchi.S1G333000
Phchi.S1	AUGUSTUS	transcript	21288064	21290941	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	start_codon	21288064	21288066	.	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21288064	21288137	0.99	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21288064	21288137	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21288138	21288576	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21288577	21288669	0.99	+	1	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21288577	21288669	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21288670	21288793	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21288794	21288887	1	+	1	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21288794	21288887	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21288888	21289037	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21289038	21289075	1	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21289038	21289075	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21289076	21289914	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21289915	21290009	1	+	1	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21289915	21290009	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21290010	21290139	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21290140	21290219	0.81	+	2	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21290140	21290219	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21290220	21290325	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21290326	21290382	1	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21290326	21290382	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21290383	21290466	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21290467	21290559	1	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21290467	21290559	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21290560	21290654	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21290655	21290729	0.98	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21290655	21290729	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	intron	21290730	21290842	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	CDS	21290843	21290941	0.7	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	exon	21290843	21290941	.	+	.	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
Phchi.S1	AUGUSTUS	stop_codon	21290942	21290944	.	+	0	transcript_id "Phchi.S1G333000.t1"; gene_id "Phchi.S1G333000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2284.t1 is derived from g9204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5868403	5870231	.	+	.	Phchi.S5G089300
Phchi.S5	AUGUSTUS	transcript	5868403	5870231	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	start_codon	5868403	5868405	.	+	0	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	CDS	5868403	5868788	0.99	+	0	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	exon	5868403	5868788	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	intron	5868789	5868874	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	CDS	5868875	5868927	1	+	1	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	exon	5868875	5868927	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	intron	5868928	5869036	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	CDS	5869037	5869180	0.51	+	2	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	exon	5869037	5869180	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	intron	5869181	5869313	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	CDS	5869314	5869571	0.52	+	2	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	exon	5869314	5869571	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	intron	5869572	5869667	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	CDS	5869668	5869994	1	+	2	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	exon	5869668	5869994	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	intron	5869995	5870079	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	CDS	5870080	5870231	1	+	2	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	exon	5870080	5870231	.	+	.	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
Phchi.S5	AUGUSTUS	stop_codon	5870232	5870234	.	+	0	transcript_id "Phchi.S5G089300.t1"; gene_id "Phchi.S5G089300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg198.t1 is derived from g9980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1116885	1119910	.	-	.	Phchi.S6G015700
Phchi.S6	AUGUSTUS	transcript	1116885	1119910	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	stop_codon	1116882	1116884	.	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1116885	1116965	0.65	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1116885	1116965	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1116966	1117149	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1117150	1117161	0.65	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1117150	1117161	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1117162	1117261	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1117262	1117324	0.86	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1117262	1117324	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1117325	1117404	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1117405	1117498	1	-	1	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1117405	1117498	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1117499	1117621	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1117622	1117687	1	-	1	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1117622	1117687	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1117688	1117870	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1117871	1117962	1	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1117871	1117962	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1117963	1118103	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1118104	1118227	1	-	1	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1118104	1118227	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1118228	1118492	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1118493	1118575	1	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1118493	1118575	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1118576	1118803	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1118804	1118917	1	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1118804	1118917	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1118918	1119444	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1119445	1119532	1	-	1	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1119445	1119532	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	intron	1119533	1119623	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	CDS	1119624	1119910	0.99	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	exon	1119624	1119910	.	-	.	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
Phchi.S6	AUGUSTUS	start_codon	1119908	1119910	.	-	0	transcript_id "Phchi.S6G015700.t1"; gene_id "Phchi.S6G015700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5963.t1 is derived from g3134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20104234	20104986	.	-	.	Phchi.S1G312200
Phchi.S1	AUGUSTUS	transcript	20104234	20104986	.	-	.	transcript_id "Phchi.S1G312200.t1"; gene_id "Phchi.S1G312200"
Phchi.S1	AUGUSTUS	stop_codon	20104231	20104233	.	-	0	transcript_id "Phchi.S1G312200.t1"; gene_id "Phchi.S1G312200"
Phchi.S1	AUGUSTUS	CDS	20104234	20104986	0.53	-	0	transcript_id "Phchi.S1G312200.t1"; gene_id "Phchi.S1G312200"
Phchi.S1	AUGUSTUS	exon	20104234	20104986	.	-	.	transcript_id "Phchi.S1G312200.t1"; gene_id "Phchi.S1G312200"
Phchi.S1	AUGUSTUS	start_codon	20104984	20104986	.	-	0	transcript_id "Phchi.S1G312200.t1"; gene_id "Phchi.S1G312200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14490.t1 is derived from g12958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13116085	13118981	.	-	.	Phchi.S3G180900
Phchi.S3	AUGUSTUS	transcript	13116085	13118981	.	-	.	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	stop_codon	13116082	13116084	.	-	0	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	CDS	13116085	13117082	1	-	2	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	exon	13116085	13117082	.	-	.	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	intron	13117083	13117228	.	-	.	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	CDS	13117229	13118981	0.6	-	0	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	exon	13117229	13118981	.	-	.	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
Phchi.S3	AUGUSTUS	start_codon	13118979	13118981	.	-	0	transcript_id "Phchi.S3G180900.t1"; gene_id "Phchi.S3G180900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9383.t1 is derived from g6559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41259523	41260198	.	+	.	Phchi.S1G654200
Phchi.S1	AUGUSTUS	transcript	41259523	41260198	.	+	.	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	start_codon	41259523	41259525	.	+	0	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	CDS	41259523	41259657	0.95	+	0	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	exon	41259523	41259657	.	+	.	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	intron	41259658	41259828	.	+	.	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	CDS	41259829	41259900	1	+	0	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	exon	41259829	41259900	.	+	.	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	intron	41259901	41260042	.	+	.	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	CDS	41260043	41260198	0.87	+	0	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	exon	41260043	41260198	.	+	.	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
Phchi.S1	AUGUSTUS	stop_codon	41260199	41260201	.	+	0	transcript_id "Phchi.S1G654200.t1"; gene_id "Phchi.S1G654200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg295.t1 is derived from g10077.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2103243	2106608	.	-	.	Phchi.S6G025400
Phchi.S6	AUGUSTUS	transcript	2103243	2106608	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	stop_codon	2103240	2103242	.	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2103243	2103386	0.98	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2103243	2103386	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2103387	2103484	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2103485	2103590	1	-	1	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2103485	2103590	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2103591	2103838	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2103839	2103936	1	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2103839	2103936	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2103937	2104099	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2104100	2104164	1	-	2	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2104100	2104164	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2104165	2104298	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2104299	2104452	1	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2104299	2104452	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2104453	2104602	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2104603	2104694	1	-	2	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2104603	2104694	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2104695	2104901	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2104902	2105016	1	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2104902	2105016	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2105017	2105118	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2105119	2105170	1	-	1	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2105119	2105170	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2105171	2105279	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2105280	2105433	0.94	-	2	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2105280	2105433	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2105434	2106112	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2106113	2106139	1	-	2	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2106113	2106139	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2106140	2106230	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2106231	2106435	1	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2106231	2106435	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	intron	2106436	2106506	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	CDS	2106507	2106608	0.6	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	exon	2106507	2106608	.	-	.	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
Phchi.S6	AUGUSTUS	start_codon	2106606	2106608	.	-	0	transcript_id "Phchi.S6G025400.t1"; gene_id "Phchi.S6G025400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3094.t1 is derived from g263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1729466	1731912	.	+	.	Phchi.S1G025300
Phchi.S1	AUGUSTUS	transcript	1729466	1731912	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	start_codon	1729466	1729468	.	+	0	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1729466	1729571	0.77	+	0	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1729466	1729571	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1729572	1729780	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1729781	1729981	0.97	+	2	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1729781	1729981	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1729982	1730106	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1730107	1730387	1	+	2	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1730107	1730387	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1730388	1730485	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1730486	1730576	1	+	0	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1730486	1730576	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1730577	1730679	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1730680	1730750	0.55	+	2	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1730680	1730750	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1730751	1730965	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1730966	1731235	0.45	+	0	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1730966	1731235	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1731236	1731334	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1731335	1731521	0.97	+	0	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1731335	1731521	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	intron	1731522	1731637	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	CDS	1731638	1731912	0.94	+	2	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	exon	1731638	1731912	.	+	.	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
Phchi.S1	AUGUSTUS	stop_codon	1731913	1731915	.	+	0	transcript_id "Phchi.S1G025300.t1"; gene_id "Phchi.S1G025300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1491.t1 is derived from g8410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1177408	1179672	.	-	.	Phchi.S5G010000
Phchi.S5	AUGUSTUS	transcript	1177408	1179672	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	stop_codon	1177405	1177407	.	-	0	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	CDS	1177408	1177536	1	-	0	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	exon	1177408	1177536	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	intron	1177537	1177782	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	CDS	1177783	1177884	1	-	0	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	exon	1177783	1177884	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	intron	1177885	1178083	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	CDS	1178084	1179274	0.99	-	0	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	exon	1178084	1179274	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	intron	1179275	1179363	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	CDS	1179364	1179535	1	-	1	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	exon	1179364	1179535	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	intron	1179536	1179628	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	CDS	1179629	1179672	0.73	-	0	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	exon	1179629	1179672	.	-	.	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
Phchi.S5	AUGUSTUS	start_codon	1179670	1179672	.	-	0	transcript_id "Phchi.S5G010000.t1"; gene_id "Phchi.S5G010000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8642.t1 is derived from g5817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37198929	37199763	.	+	.	Phchi.S1G580100
Phchi.S1	AUGUSTUS	transcript	37198929	37199763	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	start_codon	37198929	37198931	.	+	0	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	CDS	37198929	37198984	0.98	+	0	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	exon	37198929	37198984	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	intron	37198985	37199140	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	CDS	37199141	37199205	1	+	1	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	exon	37199141	37199205	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	intron	37199206	37199287	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	CDS	37199288	37199379	1	+	2	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	exon	37199288	37199379	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	intron	37199380	37199493	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	CDS	37199494	37199565	1	+	0	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	exon	37199494	37199565	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	intron	37199566	37199730	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	CDS	37199731	37199763	1	+	0	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	exon	37199731	37199763	.	+	.	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
Phchi.S1	AUGUSTUS	stop_codon	37199764	37199766	.	+	0	transcript_id "Phchi.S1G580100.t1"; gene_id "Phchi.S1G580100"
# This transcript jg14559.t2 is derived from g13027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14560.t1 is derived from g13028.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13471143	13471586	.	+	.	Phchi.S3G187900
Phchi.S3	AUGUSTUS	transcript	13471143	13471586	.	+	.	transcript_id "Phchi.S3G187900.t1"; gene_id "Phchi.S3G187900"
Phchi.S3	AUGUSTUS	start_codon	13471143	13471145	.	+	0	transcript_id "Phchi.S3G187900.t1"; gene_id "Phchi.S3G187900"
Phchi.S3	AUGUSTUS	CDS	13471143	13471586	0.66	+	0	transcript_id "Phchi.S3G187900.t1"; gene_id "Phchi.S3G187900"
Phchi.S3	AUGUSTUS	exon	13471143	13471586	.	+	.	transcript_id "Phchi.S3G187900.t1"; gene_id "Phchi.S3G187900"
Phchi.S3	AUGUSTUS	stop_codon	13471587	13471589	.	+	0	transcript_id "Phchi.S3G187900.t1"; gene_id "Phchi.S3G187900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg62.t1 is derived from g9844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	314861	317065	.	-	.	Phchi.S6G002100
Phchi.S6	AUGUSTUS	transcript	314861	317065	.	-	.	transcript_id "Phchi.S6G002100.t1"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	stop_codon	314858	314860	.	-	0	transcript_id "Phchi.S6G002100.t1"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	CDS	314861	317065	0.94	-	0	transcript_id "Phchi.S6G002100.t1"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	exon	314861	317065	.	-	.	transcript_id "Phchi.S6G002100.t1"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	start_codon	317063	317065	.	-	0	transcript_id "Phchi.S6G002100.t1"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	transcript	314861	316228	.	-	.	transcript_id "Phchi.S6G002100.t2"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	stop_codon	314858	314860	.	-	0	transcript_id "Phchi.S6G002100.t2"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	CDS	314861	316228	0.85	-	0	transcript_id "Phchi.S6G002100.t2"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	exon	314861	316228	.	-	.	transcript_id "Phchi.S6G002100.t2"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	start_codon	316226	316228	.	-	0	transcript_id "Phchi.S6G002100.t2"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	transcript	314861	316003	.	-	.	transcript_id "Phchi.S6G002100.t3"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	stop_codon	314858	314860	.	-	0	transcript_id "Phchi.S6G002100.t3"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	CDS	314861	316003	0.77	-	0	transcript_id "Phchi.S6G002100.t3"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	exon	314861	316003	.	-	.	transcript_id "Phchi.S6G002100.t3"; gene_id "Phchi.S6G002100"
Phchi.S6	AUGUSTUS	start_codon	316001	316003	.	-	0	transcript_id "Phchi.S6G002100.t3"; gene_id "Phchi.S6G002100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15710.t1 is derived from g14180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20807523	20808179	.	+	.	Phchi.S3G302900
Phchi.S3	AUGUSTUS	transcript	20807523	20808179	.	+	.	transcript_id "Phchi.S3G302900.t1"; gene_id "Phchi.S3G302900"
Phchi.S3	AUGUSTUS	start_codon	20807523	20807525	.	+	0	transcript_id "Phchi.S3G302900.t1"; gene_id "Phchi.S3G302900"
Phchi.S3	AUGUSTUS	CDS	20807523	20808179	0.61	+	0	transcript_id "Phchi.S3G302900.t1"; gene_id "Phchi.S3G302900"
Phchi.S3	AUGUSTUS	exon	20807523	20808179	.	+	.	transcript_id "Phchi.S3G302900.t1"; gene_id "Phchi.S3G302900"
Phchi.S3	AUGUSTUS	stop_codon	20808180	20808182	.	+	0	transcript_id "Phchi.S3G302900.t1"; gene_id "Phchi.S3G302900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14271.t1 is derived from g12738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11875116	11875976	.	-	.	Phchi.S3G159000
Phchi.S3	AUGUSTUS	transcript	11875116	11875976	.	-	.	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	stop_codon	11875113	11875115	.	-	0	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	CDS	11875116	11875388	0.76	-	0	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	exon	11875116	11875388	.	-	.	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	intron	11875389	11875617	.	-	.	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	CDS	11875618	11875845	0.77	-	0	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	exon	11875618	11875845	.	-	.	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	intron	11875846	11875931	.	-	.	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	CDS	11875932	11875976	1	-	0	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	exon	11875932	11875976	.	-	.	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
Phchi.S3	AUGUSTUS	start_codon	11875974	11875976	.	-	0	transcript_id "Phchi.S3G159000.t1"; gene_id "Phchi.S3G159000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg14518.t1 is derived from g12986.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13279299	13281416	.	+	.	Phchi.S3G183700
Phchi.S3	AUGUSTUS	transcript	13279299	13280355	.	+	.	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	start_codon	13279299	13279301	.	+	0	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	CDS	13279299	13280238	0.08	+	0	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	exon	13279299	13280238	.	+	.	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	intron	13280239	13280335	.	+	.	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	CDS	13280336	13280355	0.91	+	2	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	exon	13280336	13280355	.	+	.	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	stop_codon	13280356	13280358	.	+	0	transcript_id "Phchi.S3G183700.t1"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	transcript	13279299	13280374	.	+	.	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	start_codon	13279299	13279301	.	+	0	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	CDS	13279299	13280284	0.06	+	0	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	exon	13279299	13280284	.	+	.	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	intron	13280285	13280373	.	+	.	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	CDS	13280374	13280374	0.82	+	1	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	exon	13280374	13280374	.	+	.	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	stop_codon	13280375	13280377	.	+	0	transcript_id "Phchi.S3G183700.t2"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	transcript	13279563	13281416	.	+	.	transcript_id "Phchi.S3G183700.t3"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	start_codon	13279563	13279565	.	+	0	transcript_id "Phchi.S3G183700.t3"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	CDS	13279563	13281416	0.36	+	0	transcript_id "Phchi.S3G183700.t3"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	exon	13279563	13281416	.	+	.	transcript_id "Phchi.S3G183700.t3"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	stop_codon	13281417	13281419	.	+	0	transcript_id "Phchi.S3G183700.t3"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	transcript	13279299	13281416	.	+	.	transcript_id "Phchi.S3G183700.t4"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	start_codon	13279299	13279301	.	+	0	transcript_id "Phchi.S3G183700.t4"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	CDS	13279299	13281416	0.32	+	0	transcript_id "Phchi.S3G183700.t4"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	exon	13279299	13281416	.	+	.	transcript_id "Phchi.S3G183700.t4"; gene_id "Phchi.S3G183700"
Phchi.S3	AUGUSTUS	stop_codon	13281417	13281419	.	+	0	transcript_id "Phchi.S3G183700.t4"; gene_id "Phchi.S3G183700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2710.t1 is derived from g9630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8292338	8292991	.	-	.	Phchi.S5G131900
Phchi.S5	AUGUSTUS	transcript	8292338	8292991	.	-	.	transcript_id "Phchi.S5G131900.t1"; gene_id "Phchi.S5G131900"
Phchi.S5	AUGUSTUS	stop_codon	8292335	8292337	.	-	0	transcript_id "Phchi.S5G131900.t1"; gene_id "Phchi.S5G131900"
Phchi.S5	AUGUSTUS	CDS	8292338	8292991	0.97	-	0	transcript_id "Phchi.S5G131900.t1"; gene_id "Phchi.S5G131900"
Phchi.S5	AUGUSTUS	exon	8292338	8292991	.	-	.	transcript_id "Phchi.S5G131900.t1"; gene_id "Phchi.S5G131900"
Phchi.S5	AUGUSTUS	start_codon	8292989	8292991	.	-	0	transcript_id "Phchi.S5G131900.t1"; gene_id "Phchi.S5G131900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6687.t1 is derived from g3859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24509537	24511202	.	-	.	Phchi.S1G384600
Phchi.S1	AUGUSTUS	transcript	24509537	24511202	.	-	.	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	stop_codon	24509534	24509536	.	-	0	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	CDS	24509537	24510475	1	-	0	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	exon	24509537	24510475	.	-	.	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	intron	24510476	24510612	.	-	.	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	CDS	24510613	24510816	0.7	-	0	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	exon	24510613	24510816	.	-	.	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	intron	24510817	24510917	.	-	.	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	CDS	24510918	24511202	0.8	-	0	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	exon	24510918	24511202	.	-	.	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
Phchi.S1	AUGUSTUS	start_codon	24511200	24511202	.	-	0	transcript_id "Phchi.S1G384600.t1"; gene_id "Phchi.S1G384600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8723.t1 is derived from g5898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37675028	37677580	.	+	.	Phchi.S1G588200
Phchi.S1	AUGUSTUS	transcript	37675028	37677580	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	start_codon	37675028	37675030	.	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37675028	37675216	0.29	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37675028	37675216	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37675217	37675310	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37675311	37675697	0.35	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37675311	37675697	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37675698	37675807	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37675808	37675945	1	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37675808	37675945	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37675946	37676058	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37676059	37676304	1	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37676059	37676304	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37676305	37676400	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37676401	37676514	1	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37676401	37676514	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37676515	37676591	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37676592	37676777	1	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37676592	37676777	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37676778	37676900	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37676901	37677118	1	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37676901	37677118	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	intron	37677119	37677255	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	CDS	37677256	37677580	1	+	1	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	exon	37677256	37677580	.	+	.	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
Phchi.S1	AUGUSTUS	stop_codon	37677581	37677583	.	+	0	transcript_id "Phchi.S1G588200.t1"; gene_id "Phchi.S1G588200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6617.t1 is derived from g3789.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24016904	24018325	.	-	.	Phchi.S1G377600
Phchi.S1	AUGUSTUS	transcript	24017114	24018325	.	-	.	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	stop_codon	24017111	24017113	.	-	0	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	CDS	24017114	24017121	0.98	-	2	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	exon	24017114	24017121	.	-	.	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	intron	24017122	24017493	.	-	.	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	CDS	24017494	24018325	0.73	-	0	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	exon	24017494	24018325	.	-	.	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	start_codon	24018323	24018325	.	-	0	transcript_id "Phchi.S1G377600.t1"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	transcript	24016904	24018325	.	-	.	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	stop_codon	24016901	24016903	.	-	0	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	CDS	24016904	24016917	0.91	-	2	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	exon	24016904	24016917	.	-	.	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	intron	24016918	24017493	.	-	.	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	CDS	24017494	24018325	0.66	-	0	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	exon	24017494	24018325	.	-	.	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
Phchi.S1	AUGUSTUS	start_codon	24018323	24018325	.	-	0	transcript_id "Phchi.S1G377600.t2"; gene_id "Phchi.S1G377600"
# This transcript jg1996.t2 is derived from g8916.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1997.t1 is derived from g8917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4356265	4360514	.	-	.	Phchi.S5G060600
Phchi.S5	AUGUSTUS	transcript	4356265	4360514	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	stop_codon	4356262	4356264	.	-	0	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	CDS	4356265	4356654	1	-	0	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	exon	4356265	4356654	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	intron	4356655	4356805	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	CDS	4356806	4357013	0.93	-	1	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	exon	4356806	4357013	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	intron	4357014	4357224	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	CDS	4357225	4357343	0.57	-	0	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	exon	4357225	4357343	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	intron	4357344	4357519	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	CDS	4357520	4359245	0.99	-	1	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	exon	4357520	4359245	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	intron	4359246	4359350	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	CDS	4359351	4360279	0.8	-	0	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	exon	4359351	4360279	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	intron	4360280	4360511	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	CDS	4360512	4360514	1	-	0	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	exon	4360512	4360514	.	-	.	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
Phchi.S5	AUGUSTUS	start_codon	4360512	4360514	.	-	0	transcript_id "Phchi.S5G060600.t1"; gene_id "Phchi.S5G060600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4672.t1 is derived from g1842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11745805	11747046	.	-	.	Phchi.S1G183100
Phchi.S1	AUGUSTUS	transcript	11745805	11747046	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	stop_codon	11745802	11745804	.	-	0	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	CDS	11745805	11746193	1	-	2	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	exon	11745805	11746193	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	intron	11746194	11746360	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	CDS	11746361	11746478	0.78	-	0	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	exon	11746361	11746478	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	intron	11746479	11746553	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	CDS	11746554	11746751	1	-	0	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	exon	11746554	11746751	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	intron	11746752	11746836	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	CDS	11746837	11747046	0.77	-	0	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	exon	11746837	11747046	.	-	.	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
Phchi.S1	AUGUSTUS	start_codon	11747044	11747046	.	-	0	transcript_id "Phchi.S1G183100.t1"; gene_id "Phchi.S1G183100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6955.t1 is derived from g4127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26125742	26127748	.	-	.	Phchi.S1G411400
Phchi.S1	AUGUSTUS	transcript	26125742	26127748	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	stop_codon	26125739	26125741	.	-	0	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	CDS	26125742	26125865	0.43	-	1	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	exon	26125742	26125865	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	intron	26125866	26126047	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	CDS	26126048	26126151	0.62	-	0	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	exon	26126048	26126151	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	intron	26126152	26126270	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	CDS	26126271	26126555	1	-	0	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	exon	26126271	26126555	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	intron	26126556	26126684	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	CDS	26126685	26127026	1	-	0	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	exon	26126685	26127026	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	intron	26127027	26127157	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	CDS	26127158	26127483	1	-	2	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	exon	26127158	26127483	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	intron	26127484	26127606	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	CDS	26127607	26127748	1	-	0	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	exon	26127607	26127748	.	-	.	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
Phchi.S1	AUGUSTUS	start_codon	26127746	26127748	.	-	0	transcript_id "Phchi.S1G411400.t1"; gene_id "Phchi.S1G411400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4765.t1 is derived from g1935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12712430	12713031	.	+	.	Phchi.S1G192400
Phchi.S1	AUGUSTUS	transcript	12712430	12713031	.	+	.	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	start_codon	12712430	12712432	.	+	0	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	CDS	12712430	12712493	0.53	+	0	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	exon	12712430	12712493	.	+	.	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	intron	12712494	12712590	.	+	.	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	CDS	12712591	12712629	0.47	+	2	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	exon	12712591	12712629	.	+	.	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	intron	12712630	12712729	.	+	.	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	CDS	12712730	12713031	0.78	+	2	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	exon	12712730	12713031	.	+	.	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
Phchi.S1	AUGUSTUS	stop_codon	12713032	12713034	.	+	0	transcript_id "Phchi.S1G192400.t1"; gene_id "Phchi.S1G192400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3864.t1 is derived from g1033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6087914	6088790	.	-	.	Phchi.S1G102300
Phchi.S1	AUGUSTUS	transcript	6087914	6088790	.	-	.	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	stop_codon	6087911	6087913	.	-	0	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	CDS	6087914	6088170	0.99	-	2	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	exon	6087914	6088170	.	-	.	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	intron	6088171	6088252	.	-	.	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	CDS	6088253	6088790	1	-	0	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	exon	6088253	6088790	.	-	.	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
Phchi.S1	AUGUSTUS	start_codon	6088788	6088790	.	-	0	transcript_id "Phchi.S1G102300.t1"; gene_id "Phchi.S1G102300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7224.t1 is derived from g4396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27706872	27708120	.	+	.	Phchi.S1G438300
Phchi.S1	AUGUSTUS	transcript	27706872	27708120	.	+	.	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	start_codon	27706872	27706874	.	+	0	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	CDS	27706872	27707024	0.99	+	0	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	exon	27706872	27707024	.	+	.	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	intron	27707025	27707209	.	+	.	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	CDS	27707210	27707286	0.96	+	0	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	exon	27707210	27707286	.	+	.	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	intron	27707287	27707372	.	+	.	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	CDS	27707373	27708120	0.54	+	1	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	exon	27707373	27708120	.	+	.	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
Phchi.S1	AUGUSTUS	stop_codon	27708121	27708123	.	+	0	transcript_id "Phchi.S1G438300.t1"; gene_id "Phchi.S1G438300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2755.t1 is derived from g9675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8650599	8652190	.	-	.	Phchi.S5G136400
Phchi.S5	AUGUSTUS	transcript	8650599	8652190	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	stop_codon	8650596	8650598	.	-	0	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8650599	8650710	0.99	-	1	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8650599	8650710	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8650711	8650837	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8650838	8650896	1	-	0	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8650838	8650896	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8650897	8651040	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8651041	8651178	1	-	0	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8651041	8651178	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8651179	8651321	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8651322	8651573	1	-	0	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8651322	8651573	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8651574	8651669	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8651670	8651926	1	-	2	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8651670	8651926	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8651927	8652006	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8652007	8652190	0.6	-	0	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8652007	8652190	.	-	.	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	start_codon	8652188	8652190	.	-	0	transcript_id "Phchi.S5G136400.t1"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	transcript	8650599	8652190	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	stop_codon	8650596	8650598	.	-	0	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8650599	8650710	1	-	1	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8650599	8650710	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8650711	8650837	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8650838	8650896	1	-	0	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8650838	8650896	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8650897	8651040	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8651041	8651178	1	-	0	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8651041	8651178	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8651179	8651321	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8651322	8651573	0.98	-	0	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8651322	8651573	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8651574	8651750	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8651751	8651926	0.72	-	2	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8651751	8651926	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	intron	8651927	8652006	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	CDS	8652007	8652190	0.54	-	0	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	exon	8652007	8652190	.	-	.	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
Phchi.S5	AUGUSTUS	start_codon	8652188	8652190	.	-	0	transcript_id "Phchi.S5G136400.t2"; gene_id "Phchi.S5G136400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4484.t1 is derived from g1654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10746795	10750082	.	-	.	Phchi.S1G164300
Phchi.S1	AUGUSTUS	transcript	10746795	10750082	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	stop_codon	10746792	10746794	.	-	0	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	CDS	10746795	10747190	0.74	-	0	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	exon	10746795	10747190	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	intron	10747191	10747516	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	CDS	10747517	10748301	0.38	-	2	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	exon	10747517	10748301	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	intron	10748302	10748450	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	CDS	10748451	10748751	1	-	0	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	exon	10748451	10748751	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	intron	10748752	10748850	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	CDS	10748851	10749350	0.63	-	2	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	exon	10748851	10749350	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	intron	10749351	10749436	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	CDS	10749437	10750082	0.35	-	0	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	exon	10749437	10750082	.	-	.	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
Phchi.S1	AUGUSTUS	start_codon	10750080	10750082	.	-	0	transcript_id "Phchi.S1G164300.t1"; gene_id "Phchi.S1G164300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7254.t1 is derived from g4426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27875579	27882194	.	-	.	Phchi.S1G441300
Phchi.S1	AUGUSTUS	transcript	27875579	27882194	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	stop_codon	27875576	27875578	.	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27875579	27876233	1	-	1	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27875579	27876233	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27876234	27876351	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27876352	27876498	1	-	1	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27876352	27876498	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27876499	27876634	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27876635	27876692	1	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27876635	27876692	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27876693	27876790	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27876791	27877246	0.58	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27876791	27877246	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27877247	27877506	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27877507	27878262	0.28	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27877507	27878262	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27878263	27878424	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27878425	27878694	0.84	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27878425	27878694	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27878695	27878824	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27878825	27879218	0.91	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27878825	27879218	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879219	27879332	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879333	27879460	0.92	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879333	27879460	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879461	27879544	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879545	27879661	0.96	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879545	27879661	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879662	27879822	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879823	27879872	0.96	-	1	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879823	27879872	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879873	27879968	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879969	27880036	1	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879969	27880036	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880037	27880121	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880122	27880181	0.73	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880122	27880181	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880182	27880366	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880367	27880433	0.56	-	1	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880367	27880433	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880434	27880627	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880628	27880824	0.99	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880628	27880824	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880825	27880959	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880960	27881073	1	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880960	27881073	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881074	27881168	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881169	27881290	1	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881169	27881290	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881291	27881383	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881384	27881438	1	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881384	27881438	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881439	27881614	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881615	27881706	0.99	-	2	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881615	27881706	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881707	27881830	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881831	27881945	0.9	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881831	27881945	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881946	27882047	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27882048	27882194	0.72	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27882048	27882194	.	-	.	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	start_codon	27882192	27882194	.	-	0	transcript_id "Phchi.S1G441300.t1"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	transcript	27875579	27882194	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	stop_codon	27875576	27875578	.	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27875579	27876233	0.99	-	1	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27875579	27876233	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27876234	27876351	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27876352	27876498	1	-	1	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27876352	27876498	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27876499	27876634	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27876635	27876692	1	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27876635	27876692	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27876693	27876787	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27876788	27877246	0.57	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27876788	27877246	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27877247	27877506	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27877507	27878262	0.29	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27877507	27878262	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27878263	27878424	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27878425	27878694	0.83	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27878425	27878694	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27878695	27878824	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27878825	27879218	0.95	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27878825	27879218	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879219	27879332	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879333	27879460	0.97	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879333	27879460	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879461	27879544	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879545	27879661	0.91	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879545	27879661	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879662	27879822	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879823	27879872	0.91	-	1	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879823	27879872	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27879873	27879968	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27879969	27880036	1	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27879969	27880036	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880037	27880121	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880122	27880181	0.7	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880122	27880181	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880182	27880366	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880367	27880433	0.52	-	1	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880367	27880433	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880434	27880627	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880628	27880824	1	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880628	27880824	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27880825	27880959	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27880960	27881073	1	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27880960	27881073	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881074	27881168	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881169	27881290	1	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881169	27881290	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881291	27881383	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881384	27881438	1	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881384	27881438	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881439	27881614	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881615	27881706	0.97	-	2	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881615	27881706	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881707	27881830	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27881831	27881945	0.93	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27881831	27881945	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	intron	27881946	27882047	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	CDS	27882048	27882194	0.65	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	exon	27882048	27882194	.	-	.	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
Phchi.S1	AUGUSTUS	start_codon	27882192	27882194	.	-	0	transcript_id "Phchi.S1G441300.t2"; gene_id "Phchi.S1G441300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15817.t1 is derived from g14287.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21540839	21547626	.	+	.	Phchi.S3G313600
Phchi.S3	AUGUSTUS	transcript	21540839	21547626	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	start_codon	21540839	21540841	.	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21540839	21541116	0.94	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21540839	21541116	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21541117	21541806	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21541807	21542012	0.97	+	1	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21541807	21542012	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542013	21542123	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542124	21542242	1	+	2	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542124	21542242	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542243	21542432	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542433	21542564	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542433	21542564	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542565	21542722	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542723	21543283	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542723	21543283	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543284	21543423	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543424	21543543	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543424	21543543	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543544	21543718	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543719	21543779	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543719	21543779	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543780	21543861	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543862	21543947	1	+	2	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543862	21543947	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543948	21544054	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544055	21544099	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544055	21544099	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544100	21544221	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544222	21544332	0.5	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544222	21544332	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544333	21544532	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544533	21544737	0.88	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544533	21544737	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544738	21544875	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544876	21545033	1	+	2	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544876	21545033	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545034	21545162	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545163	21545287	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545163	21545287	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545288	21545407	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545408	21545521	1	+	1	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545408	21545521	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545522	21545609	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545610	21545751	1	+	1	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545610	21545751	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545752	21545839	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545840	21546049	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545840	21546049	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546050	21546161	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546162	21546194	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546162	21546194	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546195	21546281	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546282	21546401	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546282	21546401	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546402	21546486	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546487	21546621	0.99	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546487	21546621	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546622	21546722	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546723	21546842	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546723	21546842	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546843	21547042	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547043	21547141	1	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547043	21547141	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547142	21547235	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547236	21547297	0.84	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547236	21547297	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547298	21547369	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547370	21547423	0.84	+	1	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547370	21547423	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547424	21547550	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547551	21547626	0.72	+	1	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547551	21547626	.	+	.	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	stop_codon	21547627	21547629	.	+	0	transcript_id "Phchi.S3G313600.t1"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	transcript	21540839	21547626	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	start_codon	21540839	21540841	.	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21540839	21541116	0.97	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21540839	21541116	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21541117	21541806	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21541807	21542012	0.99	+	1	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21541807	21542012	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542013	21542123	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542124	21542242	1	+	2	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542124	21542242	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542243	21542417	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542418	21542564	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542418	21542564	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542565	21542722	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542723	21543283	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542723	21543283	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543284	21543423	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543424	21543543	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543424	21543543	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543544	21543718	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543719	21543779	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543719	21543779	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543780	21543861	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543862	21543947	1	+	2	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543862	21543947	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543948	21544054	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544055	21544099	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544055	21544099	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544100	21544221	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544222	21544332	0.44	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544222	21544332	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544333	21544532	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544533	21544737	0.88	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544533	21544737	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544738	21544875	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544876	21545033	1	+	2	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544876	21545033	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545034	21545162	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545163	21545287	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545163	21545287	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545288	21545407	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545408	21545521	1	+	1	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545408	21545521	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545522	21545609	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545610	21545751	1	+	1	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545610	21545751	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545752	21545839	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545840	21546049	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545840	21546049	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546050	21546161	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546162	21546194	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546162	21546194	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546195	21546281	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546282	21546401	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546282	21546401	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546402	21546486	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546487	21546621	0.98	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546487	21546621	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546622	21546722	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546723	21546842	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546723	21546842	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546843	21547042	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547043	21547141	1	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547043	21547141	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547142	21547235	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547236	21547297	0.83	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547236	21547297	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547298	21547369	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547370	21547423	0.82	+	1	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547370	21547423	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547424	21547550	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547551	21547626	0.77	+	1	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547551	21547626	.	+	.	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	stop_codon	21547627	21547629	.	+	0	transcript_id "Phchi.S3G313600.t2"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	transcript	21541659	21547626	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	start_codon	21541659	21541661	.	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21541659	21541705	0.52	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21541659	21541705	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21541706	21541806	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21541807	21542012	0.8	+	1	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21541807	21542012	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542013	21542123	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542124	21542242	1	+	2	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542124	21542242	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542243	21542432	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542433	21542564	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542433	21542564	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21542565	21542722	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21542723	21543283	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21542723	21543283	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543284	21543423	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543424	21543543	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543424	21543543	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543544	21543718	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543719	21543779	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543719	21543779	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543780	21543861	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21543862	21543947	1	+	2	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21543862	21543947	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21543948	21544054	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544055	21544099	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544055	21544099	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544100	21544221	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544222	21544332	0.39	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544222	21544332	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544333	21544532	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544533	21544737	0.87	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544533	21544737	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21544738	21544875	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21544876	21545033	1	+	2	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21544876	21545033	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545034	21545162	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545163	21545287	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545163	21545287	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545288	21545407	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545408	21545521	1	+	1	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545408	21545521	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545522	21545609	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545610	21545751	1	+	1	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545610	21545751	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21545752	21545839	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21545840	21546049	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21545840	21546049	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546050	21546161	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546162	21546194	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546162	21546194	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546195	21546281	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546282	21546401	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546282	21546401	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546402	21546486	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546487	21546621	0.96	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546487	21546621	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546622	21546722	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21546723	21546842	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21546723	21546842	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21546843	21547042	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547043	21547141	1	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547043	21547141	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547142	21547235	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547236	21547297	0.75	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547236	21547297	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547298	21547369	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547370	21547423	0.75	+	1	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547370	21547423	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	intron	21547424	21547550	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	CDS	21547551	21547626	0.73	+	1	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	exon	21547551	21547626	.	+	.	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
Phchi.S3	AUGUSTUS	stop_codon	21547627	21547629	.	+	0	transcript_id "Phchi.S3G313600.t3"; gene_id "Phchi.S3G313600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1800.t1 is derived from g8720.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3110110	3111045	.	-	.	Phchi.S5G040900
Phchi.S5	AUGUSTUS	transcript	3110110	3111045	.	-	.	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	stop_codon	3109940	3109942	.	-	0	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	CDS	3110110	3110213	0.34	-	2	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	exon	3110110	3110213	.	-	.	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	intron	3110214	3110524	.	-	.	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	CDS	3110525	3110744	0.53	-	0	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	exon	3110525	3110744	.	-	.	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	intron	3110745	3110850	.	-	.	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	CDS	3110851	3111045	0.47	-	0	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	exon	3110851	3111045	.	-	.	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
Phchi.S5	AUGUSTUS	start_codon	3111043	3111045	.	-	0	transcript_id "Phchi.S5G040900.t1"; gene_id "Phchi.S5G040900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10857.t1 is derived from g14907.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2575044	2575727	.	-	.	Phchi.S4G043900
Phchi.S4	AUGUSTUS	transcript	2575044	2575727	.	-	.	transcript_id "Phchi.S4G043900.t1"; gene_id "Phchi.S4G043900"
Phchi.S4	AUGUSTUS	stop_codon	2575041	2575043	.	-	0	transcript_id "Phchi.S4G043900.t1"; gene_id "Phchi.S4G043900"
Phchi.S4	AUGUSTUS	CDS	2575044	2575727	1	-	0	transcript_id "Phchi.S4G043900.t1"; gene_id "Phchi.S4G043900"
Phchi.S4	AUGUSTUS	exon	2575044	2575727	.	-	.	transcript_id "Phchi.S4G043900.t1"; gene_id "Phchi.S4G043900"
Phchi.S4	AUGUSTUS	start_codon	2575725	2575727	.	-	0	transcript_id "Phchi.S4G043900.t1"; gene_id "Phchi.S4G043900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14159.t1 is derived from g12626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11216465	11216996	.	+	.	Phchi.S3G147800
Phchi.S3	AUGUSTUS	transcript	11216465	11216996	.	+	.	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	start_codon	11216465	11216467	.	+	0	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	CDS	11216465	11216611	1	+	0	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	exon	11216465	11216611	.	+	.	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	intron	11216612	11216709	.	+	.	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	CDS	11216710	11216799	1	+	0	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	exon	11216710	11216799	.	+	.	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	intron	11216800	11216885	.	+	.	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	CDS	11216886	11216996	0.98	+	0	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	exon	11216886	11216996	.	+	.	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
Phchi.S3	AUGUSTUS	stop_codon	11216997	11216999	.	+	0	transcript_id "Phchi.S3G147800.t1"; gene_id "Phchi.S3G147800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3118.t1 is derived from g287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1814009	1815357	.	-	.	Phchi.S1G027700
Phchi.S1	AUGUSTUS	transcript	1814009	1815357	.	-	.	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	stop_codon	1814006	1814008	.	-	0	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	CDS	1814009	1814017	0.52	-	0	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	exon	1814009	1814017	.	-	.	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	intron	1814018	1814346	.	-	.	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	CDS	1814347	1815357	0.65	-	0	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	exon	1814347	1815357	.	-	.	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
Phchi.S1	AUGUSTUS	start_codon	1815355	1815357	.	-	0	transcript_id "Phchi.S1G027700.t1"; gene_id "Phchi.S1G027700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11449.t1 is derived from g15499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6421856	6422346	.	+	.	Phchi.S4G103100
Phchi.S4	AUGUSTUS	transcript	6421856	6422346	.	+	.	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	start_codon	6421856	6421858	.	+	0	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	CDS	6421856	6422026	0.33	+	0	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	exon	6421856	6422026	.	+	.	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	intron	6422027	6422133	.	+	.	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	CDS	6422134	6422346	0.49	+	0	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	exon	6422134	6422346	.	+	.	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
Phchi.S4	AUGUSTUS	stop_codon	6422347	6422349	.	+	0	transcript_id "Phchi.S4G103100.t1"; gene_id "Phchi.S4G103100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7073.t1 is derived from g4245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26754288	26758137	.	+	.	Phchi.S1G423200
Phchi.S1	AUGUSTUS	transcript	26754288	26758137	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	start_codon	26754288	26754290	.	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26754288	26754512	0.58	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26754288	26754512	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26754513	26754632	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26754633	26754679	1	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26754633	26754679	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26754680	26754804	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26754805	26754844	1	+	1	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26754805	26754844	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26754845	26754955	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26754956	26755021	1	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26754956	26755021	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26755022	26755118	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26755119	26755256	0.98	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26755119	26755256	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26755257	26755435	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26755436	26755594	1	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26755436	26755594	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26755595	26755701	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26755702	26755755	1	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26755702	26755755	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26755756	26755832	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26755833	26755901	0.99	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26755833	26755901	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26755902	26756013	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26756014	26756143	1	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26756014	26756143	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26756144	26756259	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26756260	26756300	0.66	+	2	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26756260	26756300	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26756301	26756390	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26756391	26756618	0.7	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26756391	26756618	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26756619	26756739	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26756740	26756788	0.98	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26756740	26756788	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26756789	26756889	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26756890	26757044	0.92	+	2	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26756890	26757044	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26757045	26757150	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26757151	26757366	0.97	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26757151	26757366	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26757367	26757450	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26757451	26757647	0.89	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26757451	26757647	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26757648	26757813	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26757814	26757852	0.15	+	1	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26757814	26757852	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	intron	26757853	26758007	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	CDS	26758008	26758137	0.68	+	1	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	exon	26758008	26758137	.	+	.	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
Phchi.S1	AUGUSTUS	stop_codon	26758138	26758140	.	+	0	transcript_id "Phchi.S1G423200.t1"; gene_id "Phchi.S1G423200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8168.t1 is derived from g5343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34257551	34258012	.	-	.	Phchi.S1G532700
Phchi.S1	AUGUSTUS	transcript	34257551	34258012	.	-	.	transcript_id "Phchi.S1G532700.t1"; gene_id "Phchi.S1G532700"
Phchi.S1	AUGUSTUS	stop_codon	34257548	34257550	.	-	0	transcript_id "Phchi.S1G532700.t1"; gene_id "Phchi.S1G532700"
Phchi.S1	AUGUSTUS	CDS	34257551	34258012	0.64	-	0	transcript_id "Phchi.S1G532700.t1"; gene_id "Phchi.S1G532700"
Phchi.S1	AUGUSTUS	exon	34257551	34258012	.	-	.	transcript_id "Phchi.S1G532700.t1"; gene_id "Phchi.S1G532700"
Phchi.S1	AUGUSTUS	start_codon	34258010	34258012	.	-	0	transcript_id "Phchi.S1G532700.t1"; gene_id "Phchi.S1G532700"
# This transcript jg14539.t2 is derived from g13007.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14539.t3 is derived from g13007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14539.t4 is derived from g13007.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14540.t1 is derived from g13008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13399224	13402579	.	-	.	Phchi.S3G185900
Phchi.S3	AUGUSTUS	transcript	13399224	13402579	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	stop_codon	13399221	13399223	.	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13399224	13399559	0.99	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13399224	13399559	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13399560	13399642	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13399643	13399726	1	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13399643	13399726	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13399727	13399818	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13399819	13399881	1	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13399819	13399881	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13399882	13399986	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13399987	13400125	1	-	1	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13399987	13400125	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13400126	13400353	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13400354	13400455	1	-	1	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13400354	13400455	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13400456	13400534	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13400535	13400635	1	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13400535	13400635	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13400636	13400756	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13400757	13400823	0.99	-	1	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13400757	13400823	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13400824	13400944	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13400945	13400991	0.99	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13400945	13400991	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13400992	13401118	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13401119	13401313	1	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13401119	13401313	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13401314	13401412	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13401413	13401459	1	-	2	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13401413	13401459	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13401460	13401580	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13401581	13401640	1	-	2	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13401581	13401640	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13401641	13401733	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13401734	13401831	1	-	1	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13401734	13401831	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13401832	13402032	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13402033	13402151	1	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13402033	13402151	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	intron	13402152	13402378	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	CDS	13402379	13402579	0.35	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	exon	13402379	13402579	.	-	.	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
Phchi.S3	AUGUSTUS	start_codon	13402577	13402579	.	-	0	transcript_id "Phchi.S3G185900.t1"; gene_id "Phchi.S3G185900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15291.t1 is derived from g13759.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18225047	18228192	.	+	.	Phchi.S3G261000
Phchi.S3	AUGUSTUS	transcript	18225047	18228192	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	start_codon	18225047	18225049	.	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	CDS	18225047	18226543	0.34	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	exon	18225047	18226543	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	intron	18226544	18226662	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	CDS	18226663	18226953	0.55	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	exon	18226663	18226953	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	intron	18226954	18227080	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	CDS	18227081	18227449	0.88	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	exon	18227081	18227449	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	intron	18227450	18227548	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	CDS	18227549	18227602	0.54	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	exon	18227549	18227602	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	intron	18227603	18227709	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	CDS	18227710	18228192	0.33	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	exon	18227710	18228192	.	+	.	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
Phchi.S3	AUGUSTUS	stop_codon	18228193	18228195	.	+	0	transcript_id "Phchi.S3G261000.t1"; gene_id "Phchi.S3G261000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9104.t1 is derived from g6279.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39844526	39846211	.	-	.	Phchi.S1G626300
Phchi.S1	AUGUSTUS	transcript	39844526	39846211	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	stop_codon	39844523	39844525	.	-	0	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39844526	39844965	0.89	-	2	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39844526	39844965	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39844966	39845070	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39845071	39845280	0.64	-	2	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39845071	39845280	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39845281	39845508	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39845509	39845749	0.74	-	0	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39845509	39845749	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39845750	39845832	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39845833	39846061	1	-	1	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39845833	39846061	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39846062	39846152	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39846153	39846211	0.62	-	0	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39846153	39846211	.	-	.	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	start_codon	39846209	39846211	.	-	0	transcript_id "Phchi.S1G626300.t1"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	transcript	39844526	39846211	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	stop_codon	39844523	39844525	.	-	0	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39844526	39844965	0.85	-	2	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39844526	39844965	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39844966	39845070	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39845071	39845312	0.55	-	1	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39845071	39845312	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39845313	39845629	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39845630	39845749	0.66	-	1	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39845630	39845749	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39845750	39845836	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39845837	39846061	1	-	1	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39845837	39846061	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	intron	39846062	39846152	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	CDS	39846153	39846211	0.74	-	0	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	exon	39846153	39846211	.	-	.	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
Phchi.S1	AUGUSTUS	start_codon	39846209	39846211	.	-	0	transcript_id "Phchi.S1G626300.t2"; gene_id "Phchi.S1G626300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8850.t1 is derived from g6025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38271488	38272607	.	-	.	Phchi.S1G600900
Phchi.S1	AUGUSTUS	transcript	38271488	38272607	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	stop_codon	38271485	38271487	.	-	0	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	CDS	38271488	38271500	1	-	1	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	exon	38271488	38271500	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	intron	38271501	38271699	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	CDS	38271700	38271812	0.37	-	0	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	exon	38271700	38271812	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	intron	38271813	38271898	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	CDS	38271899	38271919	0.43	-	0	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	exon	38271899	38271919	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	intron	38271920	38272057	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	CDS	38272058	38272100	0.39	-	1	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	exon	38272058	38272100	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	intron	38272101	38272335	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	CDS	38272336	38272607	0.22	-	0	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	exon	38272336	38272607	.	-	.	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
Phchi.S1	AUGUSTUS	start_codon	38272605	38272607	.	-	0	transcript_id "Phchi.S1G600900.t1"; gene_id "Phchi.S1G600900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5998.t1 is derived from g3169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20322907	20324129	.	+	.	Phchi.S1G315700
Phchi.S1	AUGUSTUS	transcript	20322907	20324129	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	start_codon	20322907	20322909	.	+	0	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	CDS	20322907	20323526	0.6	+	0	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	exon	20322907	20323526	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	intron	20323527	20323712	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	CDS	20323713	20323834	0.61	+	1	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	exon	20323713	20323834	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	intron	20323835	20323970	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	CDS	20323971	20323999	0.87	+	2	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	exon	20323971	20323999	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	intron	20324000	20324093	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	CDS	20324094	20324129	0.87	+	0	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	exon	20324094	20324129	.	+	.	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
Phchi.S1	AUGUSTUS	stop_codon	20324130	20324132	.	+	0	transcript_id "Phchi.S1G315700.t1"; gene_id "Phchi.S1G315700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13638.t1 is derived from g12105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7946358	7946708	.	-	.	Phchi.S3G095700
Phchi.S3	AUGUSTUS	transcript	7946358	7946708	.	-	.	transcript_id "Phchi.S3G095700.t1"; gene_id "Phchi.S3G095700"
Phchi.S3	AUGUSTUS	stop_codon	7946355	7946357	.	-	0	transcript_id "Phchi.S3G095700.t1"; gene_id "Phchi.S3G095700"
Phchi.S3	AUGUSTUS	CDS	7946358	7946708	1	-	0	transcript_id "Phchi.S3G095700.t1"; gene_id "Phchi.S3G095700"
Phchi.S3	AUGUSTUS	exon	7946358	7946708	.	-	.	transcript_id "Phchi.S3G095700.t1"; gene_id "Phchi.S3G095700"
Phchi.S3	AUGUSTUS	start_codon	7946706	7946708	.	-	0	transcript_id "Phchi.S3G095700.t1"; gene_id "Phchi.S3G095700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7089.t1 is derived from g4261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26855714	26856610	.	-	.	Phchi.S1G424800
Phchi.S1	AUGUSTUS	transcript	26855714	26856610	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	stop_codon	26855711	26855713	.	-	0	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	CDS	26855714	26855799	1	-	2	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	exon	26855714	26855799	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	intron	26855800	26855969	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	CDS	26855970	26856099	1	-	0	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	exon	26855970	26856099	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	intron	26856100	26856211	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	CDS	26856212	26856340	1	-	0	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	exon	26856212	26856340	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	intron	26856341	26856406	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	CDS	26856407	26856529	1	-	0	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	exon	26856407	26856529	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	intron	26856530	26856607	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	CDS	26856608	26856610	1	-	0	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	exon	26856608	26856610	.	-	.	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
Phchi.S1	AUGUSTUS	start_codon	26856608	26856610	.	-	0	transcript_id "Phchi.S1G424800.t1"; gene_id "Phchi.S1G424800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5037.t1 is derived from g2207.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14197776	14200162	.	-	.	Phchi.S1G219600
Phchi.S1	AUGUSTUS	transcript	14197776	14200158	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	stop_codon	14197773	14197775	.	-	0	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14197776	14197922	1	-	0	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14197776	14197922	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14197923	14198003	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198004	14198090	1	-	0	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198004	14198090	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198091	14198176	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198177	14198295	1	-	2	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198177	14198295	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198296	14198379	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198380	14198489	0.69	-	1	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198380	14198489	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198490	14198728	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198729	14198785	1	-	1	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198729	14198785	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198786	14198907	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198908	14198994	1	-	1	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198908	14198994	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198995	14199132	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14199133	14199310	0.95	-	2	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14199133	14199310	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14199311	14199611	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14199612	14199677	0.91	-	2	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14199612	14199677	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14199678	14199950	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14199951	14199987	0.82	-	0	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14199951	14199987	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14199988	14200149	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14200150	14200158	0.82	-	0	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14200150	14200158	.	-	.	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	start_codon	14200156	14200158	.	-	0	transcript_id "Phchi.S1G219600.t1"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	transcript	14197776	14200162	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	stop_codon	14197773	14197775	.	-	0	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14197776	14197922	0.99	-	0	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14197776	14197922	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14197923	14198003	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198004	14198090	1	-	0	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198004	14198090	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198091	14198176	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198177	14198295	1	-	2	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198177	14198295	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198296	14198379	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198380	14198489	0.6	-	1	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198380	14198489	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198490	14198728	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198729	14198785	0.96	-	1	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198729	14198785	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198786	14198907	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14198908	14198994	1	-	1	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14198908	14198994	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14198995	14199132	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14199133	14199320	0.65	-	0	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14199133	14199320	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14199321	14199611	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14199612	14199810	0.49	-	1	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14199612	14199810	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14199811	14199950	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14199951	14199987	0.89	-	2	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14199951	14199987	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	intron	14199988	14200149	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	CDS	14200150	14200162	0.99	-	0	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	exon	14200150	14200162	.	-	.	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
Phchi.S1	AUGUSTUS	start_codon	14200160	14200162	.	-	0	transcript_id "Phchi.S1G219600.t2"; gene_id "Phchi.S1G219600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5106.t1 is derived from g2276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14773467	14774538	.	+	.	Phchi.S1G226500
Phchi.S1	AUGUSTUS	transcript	14773467	14774538	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	start_codon	14773467	14773469	.	+	0	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	CDS	14773467	14773710	0.65	+	0	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	exon	14773467	14773710	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	intron	14773711	14773792	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	CDS	14773793	14773853	1	+	2	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	exon	14773793	14773853	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	intron	14773854	14773947	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	CDS	14773948	14774094	1	+	1	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	exon	14773948	14774094	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	intron	14774095	14774229	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	CDS	14774230	14774253	0.99	+	1	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	exon	14774230	14774253	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	intron	14774254	14774420	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	CDS	14774421	14774538	0.94	+	1	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	exon	14774421	14774538	.	+	.	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
Phchi.S1	AUGUSTUS	stop_codon	14774539	14774541	.	+	0	transcript_id "Phchi.S1G226500.t1"; gene_id "Phchi.S1G226500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14791.t1 is derived from g13259.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14722705	14723822	.	-	.	Phchi.S3G211000
Phchi.S3	AUGUSTUS	transcript	14722705	14723822	.	-	.	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	stop_codon	14722702	14722704	.	-	0	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	CDS	14722705	14723427	0.99	-	0	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	exon	14722705	14723427	.	-	.	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	intron	14723428	14723573	.	-	.	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	CDS	14723574	14723822	0.86	-	0	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	exon	14723574	14723822	.	-	.	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
Phchi.S3	AUGUSTUS	start_codon	14723820	14723822	.	-	0	transcript_id "Phchi.S3G211000.t1"; gene_id "Phchi.S3G211000"
# This transcript jg6942.t2 is derived from g4114.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6943.t1 is derived from g4115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26085322	26086546	.	-	.	Phchi.S1G410200
Phchi.S1	AUGUSTUS	transcript	26085322	26086546	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	stop_codon	26085319	26085321	.	-	0	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	CDS	26085322	26085513	0.39	-	0	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	exon	26085322	26085513	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	intron	26085514	26085676	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	CDS	26085677	26085846	1	-	2	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	exon	26085677	26085846	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	intron	26085847	26086121	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	CDS	26086122	26086178	1	-	2	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	exon	26086122	26086178	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	intron	26086179	26086276	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	CDS	26086277	26086382	0.66	-	0	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	exon	26086277	26086382	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	intron	26086383	26086468	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	CDS	26086469	26086546	0.73	-	0	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	exon	26086469	26086546	.	-	.	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
Phchi.S1	AUGUSTUS	start_codon	26086544	26086546	.	-	0	transcript_id "Phchi.S1G410200.t1"; gene_id "Phchi.S1G410200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6342.t1 is derived from g3514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22415177	22416187	.	+	.	Phchi.S1G350100
Phchi.S1	AUGUSTUS	transcript	22415177	22416187	.	+	.	transcript_id "Phchi.S1G350100.t1"; gene_id "Phchi.S1G350100"
Phchi.S1	AUGUSTUS	start_codon	22415177	22415179	.	+	0	transcript_id "Phchi.S1G350100.t1"; gene_id "Phchi.S1G350100"
Phchi.S1	AUGUSTUS	CDS	22415177	22416187	0.59	+	0	transcript_id "Phchi.S1G350100.t1"; gene_id "Phchi.S1G350100"
Phchi.S1	AUGUSTUS	exon	22415177	22416187	.	+	.	transcript_id "Phchi.S1G350100.t1"; gene_id "Phchi.S1G350100"
Phchi.S1	AUGUSTUS	stop_codon	22416188	22416190	.	+	0	transcript_id "Phchi.S1G350100.t1"; gene_id "Phchi.S1G350100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7667.t1 is derived from g4841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30508095	30508811	.	+	.	Phchi.S1G482600
Phchi.S1	AUGUSTUS	transcript	30508095	30508811	.	+	.	transcript_id "Phchi.S1G482600.t1"; gene_id "Phchi.S1G482600"
Phchi.S1	AUGUSTUS	start_codon	30508095	30508097	.	+	0	transcript_id "Phchi.S1G482600.t1"; gene_id "Phchi.S1G482600"
Phchi.S1	AUGUSTUS	CDS	30508095	30508811	0.88	+	0	transcript_id "Phchi.S1G482600.t1"; gene_id "Phchi.S1G482600"
Phchi.S1	AUGUSTUS	exon	30508095	30508811	.	+	.	transcript_id "Phchi.S1G482600.t1"; gene_id "Phchi.S1G482600"
Phchi.S1	AUGUSTUS	stop_codon	30508812	30508814	.	+	0	transcript_id "Phchi.S1G482600.t1"; gene_id "Phchi.S1G482600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg380.t1 is derived from g10162.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2726985	2729714	.	+	.	Phchi.S6G033900
Phchi.S6	AUGUSTUS	transcript	2726985	2729714	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	start_codon	2726985	2726987	.	+	0	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2726985	2727024	0.87	+	0	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2726985	2727024	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2727025	2727752	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2727753	2727890	1	+	2	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2727753	2727890	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2727891	2728880	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2728881	2728996	1	+	2	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2728881	2728996	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2728997	2729079	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2729080	2729327	1	+	0	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2729080	2729327	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2729328	2729401	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2729402	2729566	1	+	1	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2729402	2729566	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2729567	2729650	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2729651	2729714	0.85	+	1	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2729651	2729714	.	+	.	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	stop_codon	2729715	2729717	.	+	0	transcript_id "Phchi.S6G033900.t1"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	transcript	2726985	2729714	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	start_codon	2726985	2726987	.	+	0	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2726985	2727024	0.78	+	0	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2726985	2727024	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2727025	2727752	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2727753	2727890	1	+	2	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2727753	2727890	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2727891	2728402	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2728403	2728630	0.94	+	2	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2728403	2728630	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2728631	2728880	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2728881	2728996	0.99	+	2	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2728881	2728996	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2728997	2729088	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2729089	2729327	1	+	0	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2729089	2729327	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2729328	2729401	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2729402	2729566	1	+	1	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2729402	2729566	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	intron	2729567	2729650	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	CDS	2729651	2729714	0.88	+	1	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	exon	2729651	2729714	.	+	.	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
Phchi.S6	AUGUSTUS	stop_codon	2729715	2729717	.	+	0	transcript_id "Phchi.S6G033900.t2"; gene_id "Phchi.S6G033900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15081.t1 is derived from g13549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16940737	16941687	.	+	.	Phchi.S3G240000
Phchi.S3	AUGUSTUS	transcript	16940737	16941687	.	+	.	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	start_codon	16940737	16940739	.	+	0	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	CDS	16940737	16940877	0.98	+	0	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	exon	16940737	16940877	.	+	.	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	intron	16940878	16941047	.	+	.	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	CDS	16941048	16941256	1	+	0	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	exon	16941048	16941256	.	+	.	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	intron	16941257	16941371	.	+	.	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	CDS	16941372	16941687	1	+	1	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	exon	16941372	16941687	.	+	.	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
Phchi.S3	AUGUSTUS	stop_codon	16941688	16941690	.	+	0	transcript_id "Phchi.S3G240000.t1"; gene_id "Phchi.S3G240000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8047.t1 is derived from g5222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32711466	32712389	.	+	.	Phchi.S1G520600
Phchi.S1	AUGUSTUS	transcript	32711466	32712389	.	+	.	transcript_id "Phchi.S1G520600.t1"; gene_id "Phchi.S1G520600"
Phchi.S1	AUGUSTUS	start_codon	32711466	32711468	.	+	0	transcript_id "Phchi.S1G520600.t1"; gene_id "Phchi.S1G520600"
Phchi.S1	AUGUSTUS	CDS	32711466	32712389	0.75	+	0	transcript_id "Phchi.S1G520600.t1"; gene_id "Phchi.S1G520600"
Phchi.S1	AUGUSTUS	exon	32711466	32712389	.	+	.	transcript_id "Phchi.S1G520600.t1"; gene_id "Phchi.S1G520600"
Phchi.S1	AUGUSTUS	stop_codon	32712390	32712392	.	+	0	transcript_id "Phchi.S1G520600.t1"; gene_id "Phchi.S1G520600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9094.t1 is derived from g6269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39814649	39816481	.	+	.	Phchi.S1G625300
Phchi.S1	AUGUSTUS	transcript	39814649	39816481	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	start_codon	39814649	39814651	.	+	0	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	CDS	39814649	39814879	1	+	0	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	exon	39814649	39814879	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	intron	39814880	39815021	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	CDS	39815022	39815143	0.47	+	0	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	exon	39815022	39815143	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	intron	39815144	39815264	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	CDS	39815265	39815309	1	+	1	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	exon	39815265	39815309	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	intron	39815310	39815572	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	CDS	39815573	39815896	0.99	+	1	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	exon	39815573	39815896	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	intron	39815897	39815998	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	CDS	39815999	39816114	1	+	1	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	exon	39815999	39816114	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	intron	39816115	39816227	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	CDS	39816228	39816481	0.71	+	2	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	exon	39816228	39816481	.	+	.	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
Phchi.S1	AUGUSTUS	stop_codon	39816482	39816484	.	+	0	transcript_id "Phchi.S1G625300.t1"; gene_id "Phchi.S1G625300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13834.t1 is derived from g12301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9119543	9122810	.	-	.	Phchi.S3G115300
Phchi.S3	AUGUSTUS	transcript	9119543	9122810	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	stop_codon	9119540	9119542	.	-	0	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9119543	9120003	1	-	2	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9119543	9120003	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9120004	9120090	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9120091	9120317	1	-	1	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9120091	9120317	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9120318	9120414	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9120415	9121023	0.98	-	1	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9120415	9121023	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9121024	9121106	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9121107	9121287	0.99	-	2	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9121107	9121287	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9121288	9121410	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9121411	9121482	0.97	-	2	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9121411	9121482	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9121483	9121595	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9121596	9121739	1	-	2	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9121596	9121739	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9121740	9121861	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9121862	9122005	0.9	-	2	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9121862	9122005	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9122006	9122107	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9122108	9122251	0.89	-	2	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9122108	9122251	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	intron	9122252	9122410	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	CDS	9122411	9122810	0.37	-	0	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	exon	9122411	9122810	.	-	.	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
Phchi.S3	AUGUSTUS	start_codon	9122808	9122810	.	-	0	transcript_id "Phchi.S3G115300.t1"; gene_id "Phchi.S3G115300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4210.t1 is derived from g1379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8917910	8919910	.	-	.	Phchi.S1G136900
Phchi.S1	AUGUSTUS	transcript	8917910	8919910	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	stop_codon	8917907	8917909	.	-	0	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8917910	8918089	0.69	-	0	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8917910	8918089	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	intron	8918090	8918222	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8918223	8918330	1	-	0	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8918223	8918330	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	intron	8918331	8918423	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8918424	8918601	1	-	1	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8918424	8918601	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	intron	8918602	8918721	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8918722	8918899	1	-	2	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8918722	8918899	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	intron	8918900	8918997	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8918998	8919148	1	-	0	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8918998	8919148	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	intron	8919149	8919287	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8919288	8919385	1	-	2	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8919288	8919385	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	intron	8919386	8919534	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	CDS	8919535	8919910	0.6	-	0	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	exon	8919535	8919910	.	-	.	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
Phchi.S1	AUGUSTUS	start_codon	8919908	8919910	.	-	0	transcript_id "Phchi.S1G136900.t1"; gene_id "Phchi.S1G136900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5982.t1 is derived from g3153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20231615	20232568	.	+	.	Phchi.S1G314100
Phchi.S1	AUGUSTUS	transcript	20231615	20232568	.	+	.	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	start_codon	20231615	20231617	.	+	0	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	CDS	20231615	20231741	1	+	0	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	exon	20231615	20231741	.	+	.	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	intron	20231742	20232027	.	+	.	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	CDS	20232028	20232236	0.99	+	2	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	exon	20232028	20232236	.	+	.	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	intron	20232237	20232346	.	+	.	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	CDS	20232347	20232568	0.66	+	0	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	exon	20232347	20232568	.	+	.	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
Phchi.S1	AUGUSTUS	stop_codon	20232569	20232571	.	+	0	transcript_id "Phchi.S1G314100.t1"; gene_id "Phchi.S1G314100"
# This transcript jg147.t2 is derived from g9929.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg147.t3 is derived from g9929.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg148.t1 is derived from g9930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	833273	835165	.	-	.	Phchi.S6G010700
Phchi.S6	AUGUSTUS	transcript	833273	835165	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	stop_codon	833270	833272	.	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	833273	833410	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	833273	833410	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	833411	833486	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	833487	833585	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	833487	833585	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	833586	833662	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	833663	833722	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	833663	833722	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	833723	833807	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	833808	834005	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	833808	834005	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	834006	834170	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	834171	834287	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	834171	834287	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	834288	834451	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	834452	834622	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	834452	834622	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	834623	834709	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	834710	834746	1	-	1	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	834710	834746	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	834747	834838	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	834839	834904	1	-	1	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	834839	834904	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	intron	834905	834986	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	CDS	834987	835165	1	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	exon	834987	835165	.	-	.	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
Phchi.S6	AUGUSTUS	start_codon	835163	835165	.	-	0	transcript_id "Phchi.S6G010700.t1"; gene_id "Phchi.S6G010700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15592.t1 is derived from g14061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20163987	20164447	.	-	.	Phchi.S3G291100
Phchi.S3	AUGUSTUS	transcript	20163987	20164447	.	-	.	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	stop_codon	20163984	20163986	.	-	0	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	CDS	20163987	20164063	0.9	-	2	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	exon	20163987	20164063	.	-	.	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	intron	20164064	20164165	.	-	.	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	CDS	20164166	20164268	1	-	0	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	exon	20164166	20164268	.	-	.	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	intron	20164269	20164351	.	-	.	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	CDS	20164352	20164447	1	-	0	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	exon	20164352	20164447	.	-	.	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
Phchi.S3	AUGUSTUS	start_codon	20164445	20164447	.	-	0	transcript_id "Phchi.S3G291100.t1"; gene_id "Phchi.S3G291100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9666.t1 is derived from g6842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43170423	43171913	.	-	.	Phchi.S1G682500
Phchi.S1	AUGUSTUS	transcript	43170423	43171913	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	stop_codon	43170420	43170422	.	-	0	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	CDS	43170423	43170529	0.9	-	2	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	exon	43170423	43170529	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	intron	43170530	43170751	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	CDS	43170752	43170839	0.57	-	0	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	exon	43170752	43170839	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	intron	43170840	43170956	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	CDS	43170957	43171004	1	-	0	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	exon	43170957	43171004	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	intron	43171005	43171102	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	CDS	43171103	43171339	1	-	0	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	exon	43171103	43171339	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	intron	43171340	43171433	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	CDS	43171434	43171470	1	-	1	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	exon	43171434	43171470	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	intron	43171471	43171611	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	CDS	43171612	43171913	1	-	0	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	exon	43171612	43171913	.	-	.	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
Phchi.S1	AUGUSTUS	start_codon	43171911	43171913	.	-	0	transcript_id "Phchi.S1G682500.t1"; gene_id "Phchi.S1G682500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4191.t1 is derived from g1360.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8845473	8846525	.	-	.	Phchi.S1G135000
Phchi.S1	AUGUSTUS	transcript	8845473	8846525	.	-	.	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	stop_codon	8845470	8845472	.	-	0	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	CDS	8845473	8845671	0.79	-	1	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	exon	8845473	8845671	.	-	.	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	intron	8845672	8846019	.	-	.	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	CDS	8846020	8846525	0.75	-	0	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	exon	8846020	8846525	.	-	.	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
Phchi.S1	AUGUSTUS	start_codon	8846523	8846525	.	-	0	transcript_id "Phchi.S1G135000.t1"; gene_id "Phchi.S1G135000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3919.t1 is derived from g1088.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6430883	6431681	.	+	.	Phchi.S1G107800
Phchi.S1	AUGUSTUS	transcript	6430883	6431681	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	start_codon	6430883	6430885	.	+	0	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	CDS	6430883	6430996	0.56	+	0	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	exon	6430883	6430996	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	intron	6430997	6431183	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	CDS	6431184	6431233	0.82	+	0	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	exon	6431184	6431233	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	intron	6431234	6431315	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	CDS	6431316	6431499	1	+	1	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	exon	6431316	6431499	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	intron	6431500	6431675	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	CDS	6431676	6431681	1	+	0	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	exon	6431676	6431681	.	+	.	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
Phchi.S1	AUGUSTUS	stop_codon	6431682	6431684	.	+	0	transcript_id "Phchi.S1G107800.t1"; gene_id "Phchi.S1G107800"
# This transcript jg12165.t2 is derived from g7841.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12166.t1 is derived from g7842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	5268362	5268942	.	+	.	Phchi.S2G024600
Phchi.S2	AUGUSTUS	transcript	5268362	5268942	.	+	.	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	start_codon	5268362	5268364	.	+	0	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	CDS	5268362	5268463	0.61	+	0	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	exon	5268362	5268463	.	+	.	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	intron	5268464	5268705	.	+	.	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	CDS	5268706	5268942	0.82	+	0	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	exon	5268706	5268942	.	+	.	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
Phchi.S2	AUGUSTUS	stop_codon	5268943	5268945	.	+	0	transcript_id "Phchi.S2G024600.t1"; gene_id "Phchi.S2G024600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11190.t1 is derived from g15240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4555352	4556071	.	-	.	Phchi.S4G077200
Phchi.S4	AUGUSTUS	transcript	4555352	4556071	.	-	.	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	stop_codon	4555349	4555351	.	-	0	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	CDS	4555352	4555479	0.39	-	2	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	exon	4555352	4555479	.	-	.	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	intron	4555480	4555585	.	-	.	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	CDS	4555586	4555619	0.79	-	0	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	exon	4555586	4555619	.	-	.	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	intron	4555620	4555735	.	-	.	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	CDS	4555736	4556071	0.73	-	0	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	exon	4555736	4556071	.	-	.	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
Phchi.S4	AUGUSTUS	start_codon	4556069	4556071	.	-	0	transcript_id "Phchi.S4G077200.t1"; gene_id "Phchi.S4G077200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15188.t1 is derived from g13656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17472671	17473304	.	-	.	Phchi.S3G250700
Phchi.S3	AUGUSTUS	transcript	17472671	17473304	.	-	.	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	stop_codon	17472668	17472670	.	-	0	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	CDS	17472671	17472673	0.96	-	0	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	exon	17472671	17472673	.	-	.	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	intron	17472674	17473010	.	-	.	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	CDS	17473011	17473132	0.95	-	2	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	exon	17473011	17473132	.	-	.	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	intron	17473133	17473231	.	-	.	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	CDS	17473232	17473304	0.91	-	0	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	exon	17473232	17473304	.	-	.	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
Phchi.S3	AUGUSTUS	start_codon	17473302	17473304	.	-	0	transcript_id "Phchi.S3G250700.t1"; gene_id "Phchi.S3G250700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13856.t1 is derived from g12323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9250535	9254391	.	+	.	Phchi.S3G117500
Phchi.S3	AUGUSTUS	transcript	9250535	9254391	.	+	.	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	start_codon	9250535	9250537	.	+	0	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	CDS	9250535	9250687	0.99	+	0	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	exon	9250535	9250687	.	+	.	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	intron	9250688	9250764	.	+	.	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	CDS	9250765	9254391	1	+	0	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	exon	9250765	9254391	.	+	.	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
Phchi.S3	AUGUSTUS	stop_codon	9254392	9254394	.	+	0	transcript_id "Phchi.S3G117500.t1"; gene_id "Phchi.S3G117500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12274.t1 is derived from g7950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7752196	7760165	.	+	.	Phchi.S2G035400
Phchi.S2	AUGUSTUS	transcript	7752196	7760165	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	start_codon	7752196	7752198	.	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7752196	7752288	1	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7752196	7752288	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7752289	7752609	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7752610	7752688	1	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7752610	7752688	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7752689	7753189	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7753190	7753317	0.94	+	2	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7753190	7753317	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7753318	7753423	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7753424	7753759	0.92	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7753424	7753759	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7753760	7753849	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7753850	7755552	1	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7753850	7755552	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7755553	7755706	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7755707	7755958	0.78	+	1	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7755707	7755958	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7755959	7756104	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7756105	7756139	0.79	+	1	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7756105	7756139	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7756140	7756262	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7756263	7758766	0.87	+	2	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7756263	7758766	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7758767	7758851	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7758852	7758870	0.91	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7758852	7758870	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7758871	7758943	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7758944	7759058	0.56	+	2	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7758944	7759058	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7759059	7759173	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7759174	7759433	1	+	1	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7759174	7759433	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7759434	7759614	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7759615	7759808	1	+	2	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7759615	7759808	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	intron	7759809	7759967	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	CDS	7759968	7760165	1	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	exon	7759968	7760165	.	+	.	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
Phchi.S2	AUGUSTUS	stop_codon	7760166	7760168	.	+	0	transcript_id "Phchi.S2G035400.t1"; gene_id "Phchi.S2G035400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13414.t1 is derived from g11880.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6594142	6596438	.	-	.	Phchi.S3G073300
Phchi.S3	AUGUSTUS	transcript	6594142	6596410	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	stop_codon	6594139	6594141	.	-	0	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6594142	6594429	0.51	-	0	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6594142	6594429	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6594430	6594521	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6594522	6594587	0.98	-	0	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6594522	6594587	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6594588	6594710	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6594711	6594813	0.74	-	1	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6594711	6594813	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6594814	6595136	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6595137	6595229	0.82	-	1	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6595137	6595229	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6595230	6595389	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6595390	6595532	1	-	0	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6595390	6595532	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6595533	6596091	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6596092	6596209	1	-	1	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6596092	6596209	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6596210	6596366	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6596367	6596410	0.52	-	0	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6596367	6596410	.	-	.	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	start_codon	6596408	6596410	.	-	0	transcript_id "Phchi.S3G073300.t1"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	transcript	6594142	6596438	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	stop_codon	6594139	6594141	.	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6594142	6594429	0.53	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6594142	6594429	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6594430	6594521	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6594522	6594587	0.99	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6594522	6594587	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6594588	6594710	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6594711	6594813	0.7	-	1	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6594711	6594813	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6594814	6595136	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6595137	6595229	0.81	-	1	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6595137	6595229	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6595230	6595389	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6595390	6595532	0.74	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6595390	6595532	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6595533	6595998	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6595999	6596044	0.29	-	1	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6595999	6596044	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6596045	6596108	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6596109	6596209	0.38	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6596109	6596209	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	intron	6596210	6596366	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	CDS	6596367	6596438	0.84	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	exon	6596367	6596438	.	-	.	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
Phchi.S3	AUGUSTUS	start_codon	6596436	6596438	.	-	0	transcript_id "Phchi.S3G073300.t2"; gene_id "Phchi.S3G073300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1811.t1 is derived from g8731.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3159180	3161233	.	-	.	Phchi.S5G042000
Phchi.S5	AUGUSTUS	transcript	3159180	3161233	.	-	.	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	stop_codon	3159177	3159179	.	-	0	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	CDS	3159180	3159618	0.79	-	1	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	exon	3159180	3159618	.	-	.	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	intron	3159619	3160292	.	-	.	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	CDS	3160293	3161233	0.73	-	0	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	exon	3160293	3161233	.	-	.	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
Phchi.S5	AUGUSTUS	start_codon	3161231	3161233	.	-	0	transcript_id "Phchi.S5G042000.t1"; gene_id "Phchi.S5G042000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9339.t1 is derived from g6514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41014838	41016069	.	+	.	Phchi.S1G649800
Phchi.S1	AUGUSTUS	transcript	41014838	41016069	.	+	.	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	start_codon	41014838	41014840	.	+	0	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	CDS	41014838	41015065	0.23	+	0	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	exon	41014838	41015065	.	+	.	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	intron	41015066	41015139	.	+	.	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	CDS	41015140	41016069	0.31	+	0	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	exon	41015140	41016069	.	+	.	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
Phchi.S1	AUGUSTUS	stop_codon	41016070	41016072	.	+	0	transcript_id "Phchi.S1G649800.t1"; gene_id "Phchi.S1G649800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1457.t1 is derived from g8376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	996534	1001028	.	-	.	Phchi.S5G006600
Phchi.S5	AUGUSTUS	transcript	996534	1001028	.	-	.	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	stop_codon	996531	996533	.	-	0	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	CDS	996534	997077	0.01	-	1	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	exon	996534	997077	.	-	.	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	intron	997078	1000993	.	-	.	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	CDS	1000994	1001028	0.87	-	0	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	exon	1000994	1001028	.	-	.	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
Phchi.S5	AUGUSTUS	start_codon	1001026	1001028	.	-	0	transcript_id "Phchi.S5G006600.t1"; gene_id "Phchi.S5G006600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12372.t1 is derived from g8048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13311275	13311568	.	-	.	Phchi.S2G045200
Phchi.S2	AUGUSTUS	transcript	13311275	13311568	.	-	.	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	stop_codon	13311272	13311274	.	-	0	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	CDS	13311275	13311351	0.49	-	2	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	exon	13311275	13311351	.	-	.	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	intron	13311352	13311441	.	-	.	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	CDS	13311442	13311568	0.67	-	0	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	exon	13311442	13311568	.	-	.	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
Phchi.S2	AUGUSTUS	start_codon	13311566	13311568	.	-	0	transcript_id "Phchi.S2G045200.t1"; gene_id "Phchi.S2G045200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1963.t1 is derived from g8883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4059570	4062195	.	+	.	Phchi.S5G057200
Phchi.S5	AUGUSTUS	transcript	4059570	4062195	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	start_codon	4059570	4059572	.	+	0	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4059570	4059710	0.5	+	0	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4059570	4059710	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4059711	4059855	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4059856	4059965	0.87	+	0	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4059856	4059965	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4059966	4060247	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4060248	4060518	0.89	+	1	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4060248	4060518	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4060519	4060645	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4060646	4060760	0.98	+	0	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4060646	4060760	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4060761	4060880	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4060881	4061229	0.81	+	2	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4060881	4061229	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4061230	4061340	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4061341	4061703	0.99	+	1	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4061341	4061703	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4061704	4061832	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4061833	4061911	1	+	1	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4061833	4061911	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	intron	4061912	4062003	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	CDS	4062004	4062195	0.56	+	0	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	exon	4062004	4062195	.	+	.	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
Phchi.S5	AUGUSTUS	stop_codon	4062196	4062198	.	+	0	transcript_id "Phchi.S5G057200.t1"; gene_id "Phchi.S5G057200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9260.t1 is derived from g6435.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40624467	40627367	.	+	.	Phchi.S1G641900
Phchi.S1	AUGUSTUS	transcript	40624467	40627367	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	start_codon	40624467	40624469	.	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	CDS	40624467	40625678	0.69	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	exon	40624467	40625678	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	intron	40625679	40625820	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	CDS	40625821	40625904	1	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	exon	40625821	40625904	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	intron	40625905	40626032	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	CDS	40626033	40626137	0.89	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	exon	40626033	40626137	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	intron	40626138	40626242	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	CDS	40626243	40626351	0.98	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	exon	40626243	40626351	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	intron	40626352	40626470	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	CDS	40626471	40626622	1	+	2	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	exon	40626471	40626622	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	intron	40626623	40626806	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	CDS	40626807	40627367	0.96	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	exon	40626807	40627367	.	+	.	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
Phchi.S1	AUGUSTUS	stop_codon	40627368	40627370	.	+	0	transcript_id "Phchi.S1G641900.t1"; gene_id "Phchi.S1G641900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4072.t1 is derived from g1241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7631369	7633190	.	+	.	Phchi.S1G123100
Phchi.S1	AUGUSTUS	transcript	7631369	7633190	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	start_codon	7631369	7631371	.	+	0	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	CDS	7631369	7631537	0.95	+	0	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	exon	7631369	7631537	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	intron	7631538	7631619	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	CDS	7631620	7631699	0.98	+	2	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	exon	7631620	7631699	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	intron	7631700	7632075	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	CDS	7632076	7632233	0.59	+	0	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	exon	7632076	7632233	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	intron	7632234	7632305	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	CDS	7632306	7632352	0.59	+	1	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	exon	7632306	7632352	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	intron	7632353	7632528	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	CDS	7632529	7633190	0.5	+	2	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	exon	7632529	7633190	.	+	.	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
Phchi.S1	AUGUSTUS	stop_codon	7633191	7633193	.	+	0	transcript_id "Phchi.S1G123100.t1"; gene_id "Phchi.S1G123100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1891.t1 is derived from g8811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3723416	3728352	.	-	.	Phchi.S5G050000
Phchi.S5	AUGUSTUS	transcript	3723416	3728352	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	stop_codon	3723413	3723415	.	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3723416	3723444	0.66	-	2	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3723416	3723444	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3723445	3723531	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3723532	3723580	1	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3723532	3723580	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3723581	3723672	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3723673	3723744	1	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3723673	3723744	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3723745	3723831	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3723832	3723839	1	-	2	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3723832	3723839	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3723840	3723971	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3723972	3724032	0.85	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3723972	3724032	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3724033	3724130	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3724131	3724246	0.99	-	2	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3724131	3724246	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3724247	3724335	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3724336	3724473	0.61	-	2	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3724336	3724473	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3724474	3724561	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3724562	3724683	0.35	-	1	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3724562	3724683	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3724684	3724806	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3724807	3725150	0.16	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3724807	3725150	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3725151	3725313	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3725314	3725375	1	-	2	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3725314	3725375	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3725376	3725461	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3725462	3725544	1	-	1	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3725462	3725544	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3725545	3725703	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3725704	3725952	0.8	-	1	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3725704	3725952	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3725953	3726100	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3726101	3726237	0.77	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3726101	3726237	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3726238	3726341	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3726342	3726404	0.93	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3726342	3726404	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3726405	3726561	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3726562	3726634	0.98	-	1	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3726562	3726634	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3726635	3726771	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3726772	3726887	0.98	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3726772	3726887	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3726888	3727006	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3727007	3727066	1	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3727007	3727066	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3727067	3727198	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3727199	3727366	0.99	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3727199	3727366	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3727367	3727493	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3727494	3727530	1	-	1	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3727494	3727530	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	intron	3727531	3727630	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	CDS	3727631	3728352	0.84	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	exon	3727631	3728352	.	-	.	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
Phchi.S5	AUGUSTUS	start_codon	3728350	3728352	.	-	0	transcript_id "Phchi.S5G050000.t1"; gene_id "Phchi.S5G050000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4541.t1 is derived from g1711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11021481	11023323	.	-	.	Phchi.S1G170000
Phchi.S1	AUGUSTUS	transcript	11021481	11023323	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	stop_codon	11021478	11021480	.	-	0	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11021481	11021699	0.55	-	0	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11021481	11021699	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11021700	11021795	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11021796	11021919	0.84	-	1	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11021796	11021919	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11021920	11022011	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11022012	11022099	1	-	2	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11022012	11022099	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11022100	11022184	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11022185	11022261	1	-	1	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11022185	11022261	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11022262	11022368	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11022369	11022531	1	-	2	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11022369	11022531	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11022532	11022617	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11022618	11022804	0.97	-	0	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11022618	11022804	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11022805	11022933	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11022934	11023083	1	-	0	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11022934	11023083	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	intron	11023084	11023167	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	CDS	11023168	11023323	0.74	-	0	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	exon	11023168	11023323	.	-	.	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
Phchi.S1	AUGUSTUS	start_codon	11023321	11023323	.	-	0	transcript_id "Phchi.S1G170000.t1"; gene_id "Phchi.S1G170000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3728.t1 is derived from g897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5420726	5421267	.	-	.	Phchi.S1G088700
Phchi.S1	AUGUSTUS	transcript	5420726	5421267	.	-	.	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	stop_codon	5420723	5420725	.	-	0	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	CDS	5420726	5420917	0.76	-	0	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	exon	5420726	5420917	.	-	.	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	intron	5420918	5421048	.	-	.	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	CDS	5421049	5421267	0.81	-	0	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	exon	5421049	5421267	.	-	.	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
Phchi.S1	AUGUSTUS	start_codon	5421265	5421267	.	-	0	transcript_id "Phchi.S1G088700.t1"; gene_id "Phchi.S1G088700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12253.t1 is derived from g7929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7021362	7021921	.	-	.	Phchi.S2G033300
Phchi.S2	AUGUSTUS	transcript	7021362	7021921	.	-	.	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	stop_codon	7021359	7021361	.	-	0	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	CDS	7021362	7021532	0.98	-	0	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	exon	7021362	7021532	.	-	.	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	intron	7021533	7021610	.	-	.	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	CDS	7021611	7021725	0.8	-	1	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	exon	7021611	7021725	.	-	.	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	intron	7021726	7021835	.	-	.	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	CDS	7021836	7021921	0.31	-	0	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	exon	7021836	7021921	.	-	.	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
Phchi.S2	AUGUSTUS	start_codon	7021919	7021921	.	-	0	transcript_id "Phchi.S2G033300.t1"; gene_id "Phchi.S2G033300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15276.t1 is derived from g13744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18114135	18115466	.	+	.	Phchi.S3G259500
Phchi.S3	AUGUSTUS	transcript	18114135	18115466	.	+	.	transcript_id "Phchi.S3G259500.t1"; gene_id "Phchi.S3G259500"
Phchi.S3	AUGUSTUS	start_codon	18114135	18114137	.	+	0	transcript_id "Phchi.S3G259500.t1"; gene_id "Phchi.S3G259500"
Phchi.S3	AUGUSTUS	CDS	18114135	18115466	0.99	+	0	transcript_id "Phchi.S3G259500.t1"; gene_id "Phchi.S3G259500"
Phchi.S3	AUGUSTUS	exon	18114135	18115466	.	+	.	transcript_id "Phchi.S3G259500.t1"; gene_id "Phchi.S3G259500"
Phchi.S3	AUGUSTUS	stop_codon	18115467	18115469	.	+	0	transcript_id "Phchi.S3G259500.t1"; gene_id "Phchi.S3G259500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13240.t1 is derived from g11705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4881878	4882709	.	+	.	Phchi.S3G055900
Phchi.S3	AUGUSTUS	transcript	4881878	4882709	.	+	.	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	start_codon	4881878	4881880	.	+	0	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	CDS	4881878	4882207	0.49	+	0	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	exon	4881878	4882207	.	+	.	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	intron	4882208	4882472	.	+	.	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	CDS	4882473	4882709	0.47	+	0	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	exon	4882473	4882709	.	+	.	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
Phchi.S3	AUGUSTUS	stop_codon	4882710	4882712	.	+	0	transcript_id "Phchi.S3G055900.t1"; gene_id "Phchi.S3G055900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1867.t1 is derived from g8787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3618516	3620491	.	-	.	Phchi.S5G047600
Phchi.S5	AUGUSTUS	transcript	3618516	3620491	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	stop_codon	3618513	3618515	.	-	0	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	CDS	3618516	3619559	0.9	-	0	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	exon	3618516	3619559	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	intron	3619560	3619633	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	CDS	3619634	3619713	1	-	2	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	exon	3619634	3619713	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	intron	3619714	3619795	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	CDS	3619796	3619900	0.9	-	2	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	exon	3619796	3619900	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	intron	3619901	3619990	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	CDS	3619991	3620219	0.9	-	0	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	exon	3619991	3620219	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	intron	3620220	3620365	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	CDS	3620366	3620491	0.73	-	0	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	exon	3620366	3620491	.	-	.	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
Phchi.S5	AUGUSTUS	start_codon	3620489	3620491	.	-	0	transcript_id "Phchi.S5G047600.t1"; gene_id "Phchi.S5G047600"
# This transcript jg5825.t2 is derived from g2995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5826.t1 is derived from g2996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19141262	19141954	.	+	.	Phchi.S1G298500
Phchi.S1	AUGUSTUS	transcript	19141262	19141954	.	+	.	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	start_codon	19141262	19141264	.	+	0	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	CDS	19141262	19141377	1	+	0	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	exon	19141262	19141377	.	+	.	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	intron	19141378	19141570	.	+	.	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	CDS	19141571	19141795	0.94	+	1	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	exon	19141571	19141795	.	+	.	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	intron	19141796	19141896	.	+	.	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	CDS	19141897	19141954	0.87	+	1	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	exon	19141897	19141954	.	+	.	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
Phchi.S1	AUGUSTUS	stop_codon	19141955	19141957	.	+	0	transcript_id "Phchi.S1G298500.t1"; gene_id "Phchi.S1G298500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8882.t1 is derived from g6057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38464230	38466432	.	-	.	Phchi.S1G604100
Phchi.S1	AUGUSTUS	transcript	38464230	38466432	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	stop_codon	38464227	38464229	.	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38464230	38464418	0.99	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38464230	38464418	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38464419	38464512	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38464513	38464625	1	-	2	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38464513	38464625	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38464626	38464722	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38464723	38464891	1	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38464723	38464891	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38464892	38464983	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38464984	38465082	1	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38464984	38465082	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38465083	38465225	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38465226	38465267	1	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38465226	38465267	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38465268	38465378	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38465379	38465468	1	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38465379	38465468	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38465469	38465555	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38465556	38465627	1	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38465556	38465627	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38465628	38465763	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38465764	38465997	0.99	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38465764	38465997	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38465998	38466117	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38466118	38466131	0.99	-	2	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38466118	38466131	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38466132	38466241	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38466242	38466344	0.6	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38466242	38466344	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	intron	38466345	38466429	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	CDS	38466430	38466432	0.53	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	exon	38466430	38466432	.	-	.	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
Phchi.S1	AUGUSTUS	start_codon	38466430	38466432	.	-	0	transcript_id "Phchi.S1G604100.t1"; gene_id "Phchi.S1G604100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14103.t1 is derived from g12570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10847633	10849437	.	-	.	Phchi.S3G142200
Phchi.S3	AUGUSTUS	transcript	10847633	10849437	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	stop_codon	10847630	10847632	.	-	0	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	CDS	10847633	10847917	0.69	-	0	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	exon	10847633	10847917	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	intron	10847918	10848180	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	CDS	10848181	10848430	1	-	1	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	exon	10848181	10848430	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	intron	10848431	10848506	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	CDS	10848507	10848644	1	-	1	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	exon	10848507	10848644	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	intron	10848645	10848781	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	CDS	10848782	10849437	0.35	-	0	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	exon	10848782	10849437	.	-	.	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
Phchi.S3	AUGUSTUS	start_codon	10849435	10849437	.	-	0	transcript_id "Phchi.S3G142200.t1"; gene_id "Phchi.S3G142200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12356.t1 is derived from g8032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12690552	12691478	.	-	.	Phchi.S2G043600
Phchi.S2	AUGUSTUS	transcript	12690552	12691478	.	-	.	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	stop_codon	12690549	12690551	.	-	0	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	CDS	12690552	12690757	0.87	-	2	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	exon	12690552	12690757	.	-	.	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	intron	12690758	12690856	.	-	.	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	CDS	12690857	12691161	0.78	-	1	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	exon	12690857	12691161	.	-	.	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	intron	12691162	12691278	.	-	.	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	CDS	12691279	12691478	0.65	-	0	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	exon	12691279	12691478	.	-	.	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
Phchi.S2	AUGUSTUS	start_codon	12691476	12691478	.	-	0	transcript_id "Phchi.S2G043600.t1"; gene_id "Phchi.S2G043600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9607.t1 is derived from g6783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42913027	42916362	.	-	.	Phchi.S1G676600
Phchi.S1	AUGUSTUS	transcript	42913027	42916362	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	stop_codon	42913024	42913026	.	-	0	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	CDS	42913027	42915721	0.99	-	1	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	exon	42913027	42915721	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	intron	42915722	42915818	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	CDS	42915819	42915985	1	-	0	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	exon	42915819	42915985	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	intron	42915986	42916066	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	CDS	42916067	42916146	1	-	2	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	exon	42916067	42916146	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	intron	42916147	42916223	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	CDS	42916224	42916362	0.99	-	0	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	exon	42916224	42916362	.	-	.	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
Phchi.S1	AUGUSTUS	start_codon	42916360	42916362	.	-	0	transcript_id "Phchi.S1G676600.t1"; gene_id "Phchi.S1G676600"
# This transcript jg2151.t2 is derived from g9071.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2152.t1 is derived from g9072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5085256	5087237	.	+	.	Phchi.S5G076100
Phchi.S5	AUGUSTUS	transcript	5085256	5087237	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	start_codon	5085256	5085258	.	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5085256	5085477	0.99	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5085256	5085477	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5085478	5085568	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5085569	5085758	1	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5085569	5085758	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5085759	5085838	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5085839	5085889	1	+	2	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5085839	5085889	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5085890	5086010	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5086011	5086157	1	+	2	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5086011	5086157	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5086158	5086246	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5086247	5086429	1	+	2	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5086247	5086429	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5086430	5086520	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5086521	5086618	1	+	2	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5086521	5086618	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5086619	5086708	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5086709	5086834	1	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5086709	5086834	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5086835	5086926	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5086927	5087016	1	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5086927	5087016	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	intron	5087017	5087114	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	CDS	5087115	5087237	1	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	exon	5087115	5087237	.	+	.	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
Phchi.S5	AUGUSTUS	stop_codon	5087238	5087240	.	+	0	transcript_id "Phchi.S5G076100.t1"; gene_id "Phchi.S5G076100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg669.t1 is derived from g10451.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4648887	4650313	.	-	.	Phchi.S6G062800
Phchi.S6	AUGUSTUS	transcript	4648887	4650313	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	stop_codon	4648884	4648886	.	-	0	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	CDS	4648887	4649146	1	-	2	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	exon	4648887	4649146	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	intron	4649147	4649229	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	CDS	4649230	4649389	1	-	0	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	exon	4649230	4649389	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	intron	4649390	4649472	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	CDS	4649473	4649796	1	-	0	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	exon	4649473	4649796	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	intron	4649797	4649878	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	CDS	4649879	4650313	0.56	-	0	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	exon	4649879	4650313	.	-	.	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
Phchi.S6	AUGUSTUS	start_codon	4650311	4650313	.	-	0	transcript_id "Phchi.S6G062800.t1"; gene_id "Phchi.S6G062800"
# This transcript jg12845.t2 is derived from g11310.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12845.t3 is derived from g11310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12846.t1 is derived from g11311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2678441	2681347	.	+	.	Phchi.S3G016500
Phchi.S3	AUGUSTUS	transcript	2678441	2681347	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	start_codon	2678441	2678443	.	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2678441	2678519	0.97	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2678441	2678519	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2678520	2678840	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2678841	2678884	1	+	2	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2678841	2678884	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2678885	2679007	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2679008	2679103	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2679008	2679103	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2679104	2679189	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2679190	2679282	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2679190	2679282	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2679283	2679416	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2679417	2679510	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2679417	2679510	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2679511	2679666	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2679667	2679728	1	+	2	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2679667	2679728	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2679729	2679857	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2679858	2679983	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2679858	2679983	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2679984	2680094	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2680095	2680153	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2680095	2680153	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2680154	2680317	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2680318	2680492	1	+	1	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2680318	2680492	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2680493	2680592	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2680593	2680636	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2680593	2680636	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2680637	2680723	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2680724	2680931	1	+	1	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2680724	2680931	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2680932	2681068	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2681069	2681086	1	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2681069	2681086	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	intron	2681087	2681281	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	CDS	2681282	2681347	0.84	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	exon	2681282	2681347	.	+	.	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
Phchi.S3	AUGUSTUS	stop_codon	2681348	2681350	.	+	0	transcript_id "Phchi.S3G016500.t1"; gene_id "Phchi.S3G016500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10494.t1 is derived from g14543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	688334	689409	.	-	.	Phchi.S4G007600
Phchi.S4	AUGUSTUS	transcript	688334	689409	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	stop_codon	688331	688333	.	-	0	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	CDS	688334	688409	0.97	-	1	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	exon	688334	688409	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	intron	688410	688666	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	CDS	688667	688838	1	-	2	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	exon	688667	688838	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	intron	688839	688937	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	CDS	688938	689259	0.55	-	0	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	exon	688938	689259	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	intron	689260	689364	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	CDS	689365	689409	0.33	-	0	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	exon	689365	689409	.	-	.	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
Phchi.S4	AUGUSTUS	start_codon	689407	689409	.	-	0	transcript_id "Phchi.S4G007600.t1"; gene_id "Phchi.S4G007600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4941.t1 is derived from g2111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13668720	13669175	.	-	.	Phchi.S1G210000
Phchi.S1	AUGUSTUS	transcript	13668720	13669175	.	-	.	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	stop_codon	13668717	13668719	.	-	0	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	CDS	13668720	13668903	1	-	1	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	exon	13668720	13668903	.	-	.	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	intron	13668904	13668993	.	-	.	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	CDS	13668994	13669175	0.99	-	0	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	exon	13668994	13669175	.	-	.	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
Phchi.S1	AUGUSTUS	start_codon	13669173	13669175	.	-	0	transcript_id "Phchi.S1G210000.t1"; gene_id "Phchi.S1G210000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9109.t1 is derived from g6284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39868533	39870520	.	-	.	Phchi.S1G626800
Phchi.S1	AUGUSTUS	transcript	39868533	39870520	.	-	.	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	stop_codon	39868530	39868532	.	-	0	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	CDS	39868533	39868763	0.9	-	0	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	exon	39868533	39868763	.	-	.	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	intron	39868764	39868879	.	-	.	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	CDS	39868880	39870520	0.62	-	0	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	exon	39868880	39870520	.	-	.	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
Phchi.S1	AUGUSTUS	start_codon	39870518	39870520	.	-	0	transcript_id "Phchi.S1G626800.t1"; gene_id "Phchi.S1G626800"
# This transcript jg13998.t2 is derived from g12465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13999.t1 is derived from g12466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10179808	10180283	.	+	.	Phchi.S3G131800
Phchi.S3	AUGUSTUS	transcript	10179808	10180283	.	+	.	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	start_codon	10179808	10179810	.	+	0	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	CDS	10179808	10180032	0.62	+	0	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	exon	10179808	10180032	.	+	.	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	intron	10180033	10180109	.	+	.	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	CDS	10180110	10180283	0.57	+	0	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	exon	10180110	10180283	.	+	.	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
Phchi.S3	AUGUSTUS	stop_codon	10180284	10180286	.	+	0	transcript_id "Phchi.S3G131800.t1"; gene_id "Phchi.S3G131800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9651.t1 is derived from g6827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43061676	43062466	.	-	.	Phchi.S1G681000
Phchi.S1	AUGUSTUS	transcript	43061676	43062466	.	-	.	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	stop_codon	43061673	43061675	.	-	0	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	CDS	43061676	43061914	1	-	2	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	exon	43061676	43061914	.	-	.	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	intron	43061915	43062065	.	-	.	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	CDS	43062066	43062145	1	-	1	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	exon	43062066	43062145	.	-	.	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	intron	43062146	43062353	.	-	.	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	CDS	43062354	43062466	0.6	-	0	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	exon	43062354	43062466	.	-	.	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
Phchi.S1	AUGUSTUS	start_codon	43062464	43062466	.	-	0	transcript_id "Phchi.S1G681000.t1"; gene_id "Phchi.S1G681000"
# This transcript jg374.t2 is derived from g10156.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg374.t3 is derived from g10156.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg375.t1 is derived from g10157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2709401	2711359	.	+	.	Phchi.S6G033400
Phchi.S6	AUGUSTUS	transcript	2709401	2711359	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	start_codon	2709401	2709403	.	+	0	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	CDS	2709401	2710032	0.45	+	0	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	exon	2709401	2710032	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	intron	2710033	2710186	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	CDS	2710187	2710362	1	+	1	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	exon	2710187	2710362	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	intron	2710363	2710453	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	CDS	2710454	2710611	0.97	+	2	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	exon	2710454	2710611	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	intron	2710612	2710723	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	CDS	2710724	2710773	1	+	0	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	exon	2710724	2710773	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	intron	2710774	2710871	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	CDS	2710872	2710946	1	+	1	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	exon	2710872	2710946	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	intron	2710947	2711040	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	CDS	2711041	2711359	0.21	+	1	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	exon	2711041	2711359	.	+	.	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
Phchi.S6	AUGUSTUS	stop_codon	2711360	2711362	.	+	0	transcript_id "Phchi.S6G033400.t1"; gene_id "Phchi.S6G033400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3847.t1 is derived from g1016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6020606	6021523	.	+	.	Phchi.S1G100600
Phchi.S1	AUGUSTUS	transcript	6020606	6021523	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	start_codon	6020606	6020608	.	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	CDS	6020606	6020713	0.89	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	exon	6020606	6020713	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	intron	6020714	6020838	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	CDS	6020839	6020937	0.99	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	exon	6020839	6020937	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	intron	6020938	6021039	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	CDS	6021040	6021093	0.79	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	exon	6021040	6021093	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	intron	6021094	6021199	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	CDS	6021200	6021262	0.96	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	exon	6021200	6021262	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	intron	6021263	6021336	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	CDS	6021337	6021399	1	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	exon	6021337	6021399	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	intron	6021400	6021490	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	CDS	6021491	6021523	1	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	exon	6021491	6021523	.	+	.	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
Phchi.S1	AUGUSTUS	stop_codon	6021524	6021526	.	+	0	transcript_id "Phchi.S1G100600.t1"; gene_id "Phchi.S1G100600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14150.t1 is derived from g12617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11172040	11172981	.	-	.	Phchi.S3G146900
Phchi.S3	AUGUSTUS	transcript	11172040	11172981	.	-	.	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	stop_codon	11172037	11172039	.	-	0	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	CDS	11172040	11172133	0.94	-	1	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	exon	11172040	11172133	.	-	.	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	intron	11172134	11172217	.	-	.	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	CDS	11172218	11172981	1	-	0	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	exon	11172218	11172981	.	-	.	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
Phchi.S3	AUGUSTUS	start_codon	11172979	11172981	.	-	0	transcript_id "Phchi.S3G146900.t1"; gene_id "Phchi.S3G146900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8827.t1 is derived from g6002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38154713	38155073	.	-	.	Phchi.S1G598600
Phchi.S1	AUGUSTUS	transcript	38154713	38155073	.	-	.	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	stop_codon	38154710	38154712	.	-	0	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	CDS	38154713	38154781	0.53	-	0	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	exon	38154713	38154781	.	-	.	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	intron	38154782	38154932	.	-	.	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	CDS	38154933	38155073	0.53	-	0	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	exon	38154933	38155073	.	-	.	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
Phchi.S1	AUGUSTUS	start_codon	38155071	38155073	.	-	0	transcript_id "Phchi.S1G598600.t1"; gene_id "Phchi.S1G598600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12378.t1 is derived from g8054.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14079674	14085344	.	-	.	Phchi.S2G045800
Phchi.S2	AUGUSTUS	transcript	14079674	14085344	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	stop_codon	14079671	14079673	.	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14079674	14079941	1	-	1	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14079674	14079941	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14079942	14080118	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080119	14080295	1	-	1	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080119	14080295	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080296	14080449	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080450	14080499	1	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080450	14080499	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080500	14080766	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080767	14080835	1	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080767	14080835	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080836	14080926	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080927	14081025	1	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080927	14081025	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14081026	14081120	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14081121	14081193	1	-	1	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14081121	14081193	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14081194	14081759	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14081760	14081860	1	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14081760	14081860	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14081861	14082023	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14082024	14082092	1	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14082024	14082092	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14082093	14082224	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14082225	14082265	1	-	2	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14082225	14082265	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14082266	14082477	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14082478	14083748	1	-	1	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14082478	14083748	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14083749	14083951	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14083952	14084055	1	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14083952	14084055	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14084056	14084190	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14084191	14084628	0.85	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14084191	14084628	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14084629	14085053	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14085054	14085344	0.59	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14085054	14085344	.	-	.	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	start_codon	14085342	14085344	.	-	0	transcript_id "Phchi.S2G045800.t1"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	transcript	14079674	14085344	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	stop_codon	14079671	14079673	.	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14079674	14079941	1	-	1	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14079674	14079941	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14079942	14080118	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080119	14080295	0.98	-	1	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080119	14080295	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080296	14080449	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080450	14080499	0.98	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080450	14080499	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080500	14080590	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080591	14080631	0.7	-	2	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080591	14080631	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080632	14080744	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080745	14080835	0.6	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080745	14080835	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14080836	14080926	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14080927	14081025	1	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14080927	14081025	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14081026	14081120	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14081121	14081193	1	-	1	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14081121	14081193	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14081194	14081759	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14081760	14081860	1	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14081760	14081860	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14081861	14082023	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14082024	14082092	1	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14082024	14082092	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14082093	14082224	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14082225	14082265	1	-	2	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14082225	14082265	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14082266	14082477	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14082478	14083748	1	-	1	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14082478	14083748	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14083749	14083951	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14083952	14084055	1	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14083952	14084055	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14084056	14084190	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14084191	14084628	0.87	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14084191	14084628	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	intron	14084629	14085053	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	CDS	14085054	14085344	0.59	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	exon	14085054	14085344	.	-	.	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
Phchi.S2	AUGUSTUS	start_codon	14085342	14085344	.	-	0	transcript_id "Phchi.S2G045800.t2"; gene_id "Phchi.S2G045800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15548.t1 is derived from g14017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19828982	19830778	.	+	.	Phchi.S3G286700
Phchi.S3	AUGUSTUS	transcript	19828982	19830778	.	+	.	transcript_id "Phchi.S3G286700.t1"; gene_id "Phchi.S3G286700"
Phchi.S3	AUGUSTUS	start_codon	19828982	19828984	.	+	0	transcript_id "Phchi.S3G286700.t1"; gene_id "Phchi.S3G286700"
Phchi.S3	AUGUSTUS	CDS	19828982	19830778	0.98	+	0	transcript_id "Phchi.S3G286700.t1"; gene_id "Phchi.S3G286700"
Phchi.S3	AUGUSTUS	exon	19828982	19830778	.	+	.	transcript_id "Phchi.S3G286700.t1"; gene_id "Phchi.S3G286700"
Phchi.S3	AUGUSTUS	stop_codon	19830779	19830781	.	+	0	transcript_id "Phchi.S3G286700.t1"; gene_id "Phchi.S3G286700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3645.t1 is derived from g814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4926188	4929194	.	-	.	Phchi.S1G080400
Phchi.S1	AUGUSTUS	transcript	4926188	4929194	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	stop_codon	4926185	4926187	.	-	0	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	CDS	4926188	4926288	0.22	-	2	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	exon	4926188	4926288	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	intron	4926289	4926464	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	CDS	4926465	4927469	0.79	-	2	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	exon	4926465	4927469	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	intron	4927470	4927576	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	CDS	4927577	4928549	0.69	-	0	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	exon	4927577	4928549	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	intron	4928550	4928646	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	CDS	4928647	4928741	0.81	-	2	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	exon	4928647	4928741	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	intron	4928742	4928890	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	CDS	4928891	4929008	0.57	-	0	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	exon	4928891	4929008	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	intron	4929009	4929086	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	CDS	4929087	4929194	0.5	-	0	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	exon	4929087	4929194	.	-	.	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
Phchi.S1	AUGUSTUS	start_codon	4929192	4929194	.	-	0	transcript_id "Phchi.S1G080400.t1"; gene_id "Phchi.S1G080400"
# This transcript jg10363.t2 is derived from g7539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10364.t1 is derived from g7540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47396373	47399820	.	-	.	Phchi.S1G752300
Phchi.S1	AUGUSTUS	transcript	47396373	47399820	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	stop_codon	47396370	47396372	.	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47396373	47396486	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47396373	47396486	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47396487	47396567	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47396568	47396771	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47396568	47396771	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47396772	47396854	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47396855	47396929	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47396855	47396929	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47396930	47397018	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47397019	47397173	1	-	2	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47397019	47397173	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47397174	47397416	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47397417	47397537	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47397417	47397537	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47397538	47397619	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47397620	47397694	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47397620	47397694	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47397695	47397850	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47397851	47397988	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47397851	47397988	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47397989	47398125	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47398126	47398236	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47398126	47398236	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47398237	47398350	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47398351	47398455	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47398351	47398455	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47398456	47398554	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47398555	47398633	1	-	1	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47398555	47398633	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47398634	47398815	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47398816	47398877	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47398816	47398877	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47398878	47399050	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47399051	47399116	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47399051	47399116	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47399117	47399206	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47399207	47399257	0.96	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47399207	47399257	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47399258	47399365	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47399366	47399416	1	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47399366	47399416	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	intron	47399417	47399538	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	CDS	47399539	47399820	0.61	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	exon	47399539	47399820	.	-	.	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
Phchi.S1	AUGUSTUS	start_codon	47399818	47399820	.	-	0	transcript_id "Phchi.S1G752300.t1"; gene_id "Phchi.S1G752300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2085.t1 is derived from g9005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4776653	4780482	.	-	.	Phchi.S5G069400
Phchi.S5	AUGUSTUS	transcript	4776653	4780482	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	stop_codon	4776650	4776652	.	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4776653	4776676	0.98	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4776653	4776676	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4776677	4776761	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4776762	4776806	0.96	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4776762	4776806	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4776807	4776930	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4776931	4776977	0.95	-	2	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4776931	4776977	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4776978	4777075	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4777076	4777476	0.96	-	1	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4777076	4777476	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4777477	4777640	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4777641	4777825	1	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4777641	4777825	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4777826	4777900	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4777901	4778752	0.89	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4777901	4778752	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4778753	4778867	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4778868	4778996	1	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4778868	4778996	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4778997	4779114	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4779115	4779469	1	-	1	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4779115	4779469	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4779470	4779645	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4779646	4780226	0.99	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4779646	4780226	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	intron	4780227	4780419	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	CDS	4780420	4780482	1	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	exon	4780420	4780482	.	-	.	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
Phchi.S5	AUGUSTUS	start_codon	4780480	4780482	.	-	0	transcript_id "Phchi.S5G069400.t1"; gene_id "Phchi.S5G069400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10279.t1 is derived from g7455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46797269	46798398	.	-	.	Phchi.S1G743800
Phchi.S1	AUGUSTUS	transcript	46797269	46798398	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	stop_codon	46797266	46797268	.	-	0	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	CDS	46797269	46797373	1	-	0	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	exon	46797269	46797373	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	intron	46797374	46797449	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	CDS	46797450	46797518	1	-	0	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	exon	46797450	46797518	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	intron	46797519	46797618	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	CDS	46797619	46797697	1	-	1	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	exon	46797619	46797697	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	intron	46797698	46797934	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	CDS	46797935	46798398	0.89	-	0	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	exon	46797935	46798398	.	-	.	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
Phchi.S1	AUGUSTUS	start_codon	46798396	46798398	.	-	0	transcript_id "Phchi.S1G743800.t1"; gene_id "Phchi.S1G743800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9563.t1 is derived from g6739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42678184	42681714	.	-	.	Phchi.S1G672200
Phchi.S1	AUGUSTUS	transcript	42678184	42681714	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	stop_codon	42678181	42678183	.	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42678184	42678459	1	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42678184	42678459	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42678460	42678583	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42678584	42678707	1	-	1	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42678584	42678707	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42678708	42678794	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42678795	42678868	1	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42678795	42678868	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42678869	42679023	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42679024	42679289	1	-	2	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42679024	42679289	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42679290	42679424	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42679425	42680946	0.64	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42679425	42680946	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42680947	42681033	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42681034	42681270	0.3	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42681034	42681270	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42681271	42681407	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42681408	42681552	0.89	-	1	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42681408	42681552	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	intron	42681553	42681652	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	CDS	42681653	42681714	0.88	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	exon	42681653	42681714	.	-	.	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
Phchi.S1	AUGUSTUS	start_codon	42681712	42681714	.	-	0	transcript_id "Phchi.S1G672200.t1"; gene_id "Phchi.S1G672200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2497.t1 is derived from g9417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6975673	6977527	.	+	.	Phchi.S5G110600
Phchi.S5	AUGUSTUS	transcript	6975673	6977527	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	start_codon	6975673	6975675	.	+	0	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6975673	6975731	0.23	+	0	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6975673	6975731	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	intron	6975732	6975835	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6975836	6975875	0.22	+	1	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6975836	6975875	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	intron	6975876	6976084	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6976085	6976170	0.7	+	0	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6976085	6976170	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	intron	6976171	6976251	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6976252	6976482	1	+	1	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6976252	6976482	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	intron	6976483	6976674	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6976675	6976748	1	+	1	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6976675	6976748	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	intron	6976749	6977000	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6977001	6977184	1	+	2	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6977001	6977184	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	intron	6977185	6977274	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	CDS	6977275	6977527	0.92	+	1	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	exon	6977275	6977527	.	+	.	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
Phchi.S5	AUGUSTUS	stop_codon	6977528	6977530	.	+	0	transcript_id "Phchi.S5G110600.t1"; gene_id "Phchi.S5G110600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9064.t1 is derived from g6239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39560500	39562488	.	+	.	Phchi.S1G622300
Phchi.S1	AUGUSTUS	transcript	39560500	39562488	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	start_codon	39560500	39560502	.	+	0	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	CDS	39560500	39560891	1	+	0	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	exon	39560500	39560891	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	intron	39560892	39560992	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	CDS	39560993	39561237	1	+	1	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	exon	39560993	39561237	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	intron	39561238	39561324	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	CDS	39561325	39561551	0.84	+	2	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	exon	39561325	39561551	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	intron	39561552	39561768	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	CDS	39561769	39562139	0.97	+	0	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	exon	39561769	39562139	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	intron	39562140	39562241	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	CDS	39562242	39562488	1	+	1	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	exon	39562242	39562488	.	+	.	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
Phchi.S1	AUGUSTUS	stop_codon	39562489	39562491	.	+	0	transcript_id "Phchi.S1G622300.t1"; gene_id "Phchi.S1G622300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4637.t1 is derived from g1807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11531246	11533939	.	-	.	Phchi.S1G179600
Phchi.S1	AUGUSTUS	transcript	11531246	11533939	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	stop_codon	11531243	11531245	.	-	0	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	CDS	11531246	11531411	1	-	1	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	exon	11531246	11531411	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	intron	11531412	11531870	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	CDS	11531871	11532664	1	-	0	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	exon	11531871	11532664	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	intron	11532665	11532785	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	CDS	11532786	11533199	0.92	-	0	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	exon	11532786	11533199	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	intron	11533200	11533305	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	CDS	11533306	11533398	1	-	0	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	exon	11533306	11533398	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	intron	11533399	11533687	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	CDS	11533688	11533939	1	-	0	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	exon	11533688	11533939	.	-	.	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
Phchi.S1	AUGUSTUS	start_codon	11533937	11533939	.	-	0	transcript_id "Phchi.S1G179600.t1"; gene_id "Phchi.S1G179600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14848.t1 is derived from g13316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15044070	15045810	.	+	.	Phchi.S3G216700
Phchi.S3	AUGUSTUS	transcript	15044070	15045810	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	start_codon	15044070	15044072	.	+	0	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044070	15044181	0.98	+	0	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044070	15044181	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044182	15044378	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044379	15044482	0.87	+	2	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044379	15044482	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044483	15044567	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044568	15044604	0.85	+	0	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044568	15044604	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044605	15044709	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044710	15044779	0.87	+	2	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044710	15044779	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044780	15044876	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044877	15045038	0.99	+	1	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044877	15045038	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15045039	15045130	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15045131	15045191	1	+	1	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15045131	15045191	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15045192	15045290	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15045291	15045617	0.59	+	0	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15045291	15045617	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15045618	15045777	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15045778	15045810	1	+	0	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15045778	15045810	.	+	.	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	stop_codon	15045811	15045813	.	+	0	transcript_id "Phchi.S3G216700.t1"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	transcript	15044070	15045810	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	start_codon	15044070	15044072	.	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044070	15044181	0.99	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044070	15044181	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044182	15044378	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044379	15044482	0.73	+	2	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044379	15044482	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044483	15044567	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044568	15044604	0.73	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044568	15044604	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044605	15044720	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044721	15044779	0.78	+	2	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044721	15044779	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15044780	15044865	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15044866	15045038	1	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15044866	15045038	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15045039	15045130	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15045131	15045191	1	+	1	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15045131	15045191	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15045192	15045290	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15045291	15045617	0.73	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15045291	15045617	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	intron	15045618	15045777	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	CDS	15045778	15045810	1	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	exon	15045778	15045810	.	+	.	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
Phchi.S3	AUGUSTUS	stop_codon	15045811	15045813	.	+	0	transcript_id "Phchi.S3G216700.t2"; gene_id "Phchi.S3G216700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3516.t1 is derived from g685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4159412	4160383	.	+	.	Phchi.S1G067500
Phchi.S1	AUGUSTUS	transcript	4159412	4160383	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	start_codon	4159412	4159414	.	+	0	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	CDS	4159412	4159458	0.54	+	0	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	exon	4159412	4159458	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	intron	4159459	4159805	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	CDS	4159806	4159830	0.44	+	1	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	exon	4159806	4159830	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	intron	4159831	4159955	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	CDS	4159956	4160128	0.31	+	0	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	exon	4159956	4160128	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	intron	4160129	4160220	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	CDS	4160221	4160383	0.89	+	1	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	exon	4160221	4160383	.	+	.	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
Phchi.S1	AUGUSTUS	stop_codon	4160384	4160386	.	+	0	transcript_id "Phchi.S1G067500.t1"; gene_id "Phchi.S1G067500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6377.t1 is derived from g3549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22643235	22644005	.	+	.	Phchi.S1G353600
Phchi.S1	AUGUSTUS	transcript	22643235	22644005	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	start_codon	22643235	22643237	.	+	0	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	CDS	22643235	22643531	1	+	0	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	exon	22643235	22643531	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	intron	22643532	22643623	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	CDS	22643624	22643708	0.99	+	0	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	exon	22643624	22643708	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	intron	22643709	22643820	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	CDS	22643821	22643862	1	+	2	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	exon	22643821	22643862	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	intron	22643863	22643946	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	CDS	22643947	22644005	1	+	2	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	exon	22643947	22644005	.	+	.	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
Phchi.S1	AUGUSTUS	stop_codon	22644006	22644008	.	+	0	transcript_id "Phchi.S1G353600.t1"; gene_id "Phchi.S1G353600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10831.t1 is derived from g14882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2331917	2332264	.	-	.	Phchi.S4G041400
Phchi.S4	AUGUSTUS	transcript	2331917	2332264	.	-	.	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	stop_codon	2331914	2331916	.	-	0	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	CDS	2331917	2332023	0.66	-	2	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	exon	2331917	2332023	.	-	.	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	intron	2332024	2332161	.	-	.	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	CDS	2332162	2332264	0.75	-	0	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	exon	2332162	2332264	.	-	.	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
Phchi.S4	AUGUSTUS	start_codon	2332262	2332264	.	-	0	transcript_id "Phchi.S4G041400.t1"; gene_id "Phchi.S4G041400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9913.t1 is derived from g7089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44420200	44421192	.	+	.	Phchi.S1G707200
Phchi.S1	AUGUSTUS	transcript	44420200	44421192	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	start_codon	44420200	44420202	.	+	0	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	CDS	44420200	44420500	0.45	+	0	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	exon	44420200	44420500	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	intron	44420501	44420640	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	CDS	44420641	44420702	1	+	2	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	exon	44420641	44420702	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	intron	44420703	44420799	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	CDS	44420800	44420904	1	+	0	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	exon	44420800	44420904	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	intron	44420905	44421000	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	CDS	44421001	44421192	0.99	+	0	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	exon	44421001	44421192	.	+	.	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
Phchi.S1	AUGUSTUS	stop_codon	44421193	44421195	.	+	0	transcript_id "Phchi.S1G707200.t1"; gene_id "Phchi.S1G707200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15204.t1 is derived from g13672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17539300	17544992	.	+	.	Phchi.S3G252300
Phchi.S3	AUGUSTUS	transcript	17539300	17544992	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	start_codon	17539300	17539302	.	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17539300	17539473	0.91	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17539300	17539473	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17539474	17540052	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17540053	17540115	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17540053	17540115	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17540116	17540188	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17540189	17540244	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17540189	17540244	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17540245	17540416	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17540417	17540488	1	+	1	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17540417	17540488	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17540489	17540596	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17540597	17540702	1	+	1	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17540597	17540702	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17540703	17540854	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17540855	17540905	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17540855	17540905	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17540906	17541024	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17541025	17541120	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17541025	17541120	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17541121	17541216	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17541217	17541276	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17541217	17541276	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17541277	17541367	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17541368	17541481	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17541368	17541481	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17541482	17541576	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17541577	17541663	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17541577	17541663	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17541664	17541755	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17541756	17541859	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17541756	17541859	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17541860	17542029	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17542030	17542125	1	+	1	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17542030	17542125	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17542126	17542382	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17542383	17542503	1	+	1	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17542383	17542503	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17542504	17542655	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17542656	17542736	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17542656	17542736	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17542737	17542878	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17542879	17543019	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17542879	17543019	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17543020	17543097	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17543098	17543346	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17543098	17543346	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17543347	17543443	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17543444	17543587	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17543444	17543587	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17543588	17543704	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17543705	17543891	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17543705	17543891	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17543892	17544070	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17544071	17544168	1	+	2	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17544071	17544168	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17544169	17544355	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17544356	17544435	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17544356	17544435	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17544436	17544558	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17544559	17544652	1	+	1	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17544559	17544652	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17544653	17544751	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17544752	17544841	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17544752	17544841	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	intron	17544842	17544953	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	CDS	17544954	17544992	1	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	exon	17544954	17544992	.	+	.	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
Phchi.S3	AUGUSTUS	stop_codon	17544993	17544995	.	+	0	transcript_id "Phchi.S3G252300.t1"; gene_id "Phchi.S3G252300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg318.t1 is derived from g10100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2241490	2243063	.	-	.	Phchi.S6G027700
Phchi.S6	AUGUSTUS	transcript	2241490	2243063	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	stop_codon	2241487	2241489	.	-	0	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	CDS	2241490	2241621	0.97	-	0	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	exon	2241490	2241621	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	intron	2241622	2241890	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	CDS	2241891	2242660	0.88	-	2	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	exon	2241891	2242660	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	intron	2242661	2242921	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	CDS	2242922	2242945	1	-	2	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	exon	2242922	2242945	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	intron	2242946	2243035	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	CDS	2243036	2243063	0.54	-	0	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	exon	2243036	2243063	.	-	.	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
Phchi.S6	AUGUSTUS	start_codon	2243061	2243063	.	-	0	transcript_id "Phchi.S6G027700.t1"; gene_id "Phchi.S6G027700"
# This transcript jg2448.t2 is derived from g9368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2449.t1 is derived from g9369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6668337	6670268	.	-	.	Phchi.S5G105800
Phchi.S5	AUGUSTUS	transcript	6668337	6670268	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	stop_codon	6668334	6668336	.	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6668337	6668396	1	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6668337	6668396	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6668397	6668606	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6668607	6668730	1	-	1	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6668607	6668730	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6668731	6668804	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6668805	6668922	1	-	2	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6668805	6668922	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6668923	6668997	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6668998	6669096	1	-	2	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6668998	6669096	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6669097	6669222	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6669223	6669424	1	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6669223	6669424	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6669425	6669524	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6669525	6669625	1	-	2	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6669525	6669625	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6669626	6669732	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6669733	6669772	1	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6669733	6669772	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6669773	6669857	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6669858	6669905	1	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6669858	6669905	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6669906	6669972	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6669973	6670110	1	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6669973	6670110	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	intron	6670111	6670199	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	CDS	6670200	6670268	0.92	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	exon	6670200	6670268	.	-	.	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
Phchi.S5	AUGUSTUS	start_codon	6670266	6670268	.	-	0	transcript_id "Phchi.S5G105800.t1"; gene_id "Phchi.S5G105800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5827.t1 is derived from g2997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19143193	19144776	.	-	.	Phchi.S1G298600
Phchi.S1	AUGUSTUS	transcript	19143193	19144776	.	-	.	transcript_id "Phchi.S1G298600.t1"; gene_id "Phchi.S1G298600"
Phchi.S1	AUGUSTUS	stop_codon	19143190	19143192	.	-	0	transcript_id "Phchi.S1G298600.t1"; gene_id "Phchi.S1G298600"
Phchi.S1	AUGUSTUS	CDS	19143193	19144776	1	-	0	transcript_id "Phchi.S1G298600.t1"; gene_id "Phchi.S1G298600"
Phchi.S1	AUGUSTUS	exon	19143193	19144776	.	-	.	transcript_id "Phchi.S1G298600.t1"; gene_id "Phchi.S1G298600"
Phchi.S1	AUGUSTUS	start_codon	19144774	19144776	.	-	0	transcript_id "Phchi.S1G298600.t1"; gene_id "Phchi.S1G298600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4400.t1 is derived from g1569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10238839	10240247	.	-	.	Phchi.S1G155900
Phchi.S1	AUGUSTUS	transcript	10238839	10240247	.	-	.	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	stop_codon	10238836	10238838	.	-	0	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	CDS	10238839	10238935	0.39	-	1	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	exon	10238839	10238935	.	-	.	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	intron	10238936	10239255	.	-	.	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	CDS	10239256	10240247	0.28	-	0	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	exon	10239256	10240247	.	-	.	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
Phchi.S1	AUGUSTUS	start_codon	10240245	10240247	.	-	0	transcript_id "Phchi.S1G155900.t1"; gene_id "Phchi.S1G155900"
# This transcript jg8129.t2 is derived from g5304.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8129.t3 is derived from g5304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8130.t1 is derived from g5305.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33634974	33637324	.	-	.	Phchi.S1G528900
Phchi.S1	AUGUSTUS	transcript	33634974	33637324	.	-	.	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	stop_codon	33634971	33634973	.	-	0	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	CDS	33634974	33636685	1	-	2	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	exon	33634974	33636685	.	-	.	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	intron	33636686	33636816	.	-	.	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	CDS	33636817	33637324	1	-	0	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	exon	33636817	33637324	.	-	.	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	start_codon	33637322	33637324	.	-	0	transcript_id "Phchi.S1G528900.t1"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	transcript	33635405	33637324	.	-	.	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	stop_codon	33635402	33635404	.	-	0	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	CDS	33635405	33635473	1	-	0	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	exon	33635405	33635473	.	-	.	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	intron	33635474	33635558	.	-	.	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	CDS	33635559	33636685	0.95	-	2	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	exon	33635559	33636685	.	-	.	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	intron	33636686	33636816	.	-	.	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	CDS	33636817	33637324	0.98	-	0	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	exon	33636817	33637324	.	-	.	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	start_codon	33637322	33637324	.	-	0	transcript_id "Phchi.S1G528900.t2"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	transcript	33634974	33636380	.	-	.	transcript_id "Phchi.S1G528900.t3"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	stop_codon	33634971	33634973	.	-	0	transcript_id "Phchi.S1G528900.t3"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	CDS	33634974	33636380	1	-	0	transcript_id "Phchi.S1G528900.t3"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	exon	33634974	33636380	.	-	.	transcript_id "Phchi.S1G528900.t3"; gene_id "Phchi.S1G528900"
Phchi.S1	AUGUSTUS	start_codon	33636378	33636380	.	-	0	transcript_id "Phchi.S1G528900.t3"; gene_id "Phchi.S1G528900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6841.t1 is derived from g4013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25505365	25508632	.	-	.	Phchi.S1G400000
Phchi.S1	AUGUSTUS	transcript	25505365	25508632	.	-	.	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	stop_codon	25505362	25505364	.	-	0	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	CDS	25505365	25507643	0.71	-	2	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	exon	25505365	25507643	.	-	.	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	intron	25507644	25508553	.	-	.	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	CDS	25508554	25508632	0.02	-	0	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	exon	25508554	25508632	.	-	.	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
Phchi.S1	AUGUSTUS	start_codon	25508630	25508632	.	-	0	transcript_id "Phchi.S1G400000.t1"; gene_id "Phchi.S1G400000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6659.t1 is derived from g3831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24353080	24355040	.	+	.	Phchi.S1G381800
Phchi.S1	AUGUSTUS	transcript	24353080	24355040	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	start_codon	24353080	24353082	.	+	0	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	CDS	24353080	24353473	0.92	+	0	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	exon	24353080	24353473	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	intron	24353474	24353591	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	CDS	24353592	24354172	1	+	2	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	exon	24353592	24354172	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	intron	24354173	24354308	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	CDS	24354309	24354557	1	+	0	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	exon	24354309	24354557	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	intron	24354558	24354668	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	CDS	24354669	24355040	0.91	+	0	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	exon	24354669	24355040	.	+	.	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
Phchi.S1	AUGUSTUS	stop_codon	24355041	24355043	.	+	0	transcript_id "Phchi.S1G381800.t1"; gene_id "Phchi.S1G381800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11336.t1 is derived from g15386.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5617330	5619748	.	-	.	Phchi.S4G091800
Phchi.S4	AUGUSTUS	transcript	5617330	5619748	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	stop_codon	5617327	5617329	.	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5617330	5617629	0.82	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5617330	5617629	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5617630	5617734	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5617735	5617953	0.96	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5617735	5617953	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5617954	5618031	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5618032	5618148	1	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5618032	5618148	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5618149	5618231	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5618232	5618334	1	-	1	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5618232	5618334	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5618335	5618434	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5618435	5618603	1	-	2	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5618435	5618603	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5618604	5618705	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5618706	5618955	0.99	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5618706	5618955	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5618956	5619039	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5619040	5619413	1	-	2	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5619040	5619413	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	intron	5619414	5619510	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	CDS	5619511	5619748	0.91	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	exon	5619511	5619748	.	-	.	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
Phchi.S4	AUGUSTUS	start_codon	5619746	5619748	.	-	0	transcript_id "Phchi.S4G091800.t1"; gene_id "Phchi.S4G091800"
# This transcript jg6655.t2 is derived from g3827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6656.t1 is derived from g3828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24327065	24328980	.	+	.	Phchi.S1G381500
Phchi.S1	AUGUSTUS	transcript	24327065	24328980	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	start_codon	24327065	24327067	.	+	0	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	CDS	24327065	24327443	0.36	+	0	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	exon	24327065	24327443	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	intron	24327444	24327554	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	CDS	24327555	24328150	0.82	+	2	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	exon	24327555	24328150	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	intron	24328151	24328238	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	CDS	24328239	24328487	0.98	+	0	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	exon	24328239	24328487	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	intron	24328488	24328602	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	CDS	24328603	24328980	0.86	+	0	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	exon	24328603	24328980	.	+	.	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
Phchi.S1	AUGUSTUS	stop_codon	24328981	24328983	.	+	0	transcript_id "Phchi.S1G381500.t1"; gene_id "Phchi.S1G381500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9771.t1 is derived from g6947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43608974	43611161	.	+	.	Phchi.S1G693000
Phchi.S1	AUGUSTUS	transcript	43608974	43611161	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	start_codon	43608974	43608976	.	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43608974	43609036	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43608974	43609036	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609037	43609134	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609135	43609205	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609135	43609205	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609206	43609341	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609342	43609390	1	+	1	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609342	43609390	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609391	43609495	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609496	43609602	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609496	43609602	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609603	43609739	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609740	43609785	1	+	1	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609740	43609785	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609786	43609891	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609892	43610026	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609892	43610026	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610027	43610174	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610175	43610264	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610175	43610264	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610265	43610417	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610418	43610540	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610418	43610540	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610541	43610625	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610626	43610709	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610626	43610709	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610710	43610805	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610806	43610870	1	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610806	43610870	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610871	43610962	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610963	43611161	0.93	+	1	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610963	43611161	.	+	.	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	stop_codon	43611162	43611164	.	+	0	transcript_id "Phchi.S1G693000.t1"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	transcript	43608974	43611161	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	start_codon	43608974	43608976	.	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43608974	43609036	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43608974	43609036	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609037	43609134	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609135	43609205	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609135	43609205	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609206	43609341	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609342	43609390	1	+	1	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609342	43609390	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609391	43609495	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609496	43609602	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609496	43609602	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609603	43609739	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609740	43609785	1	+	1	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609740	43609785	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43609786	43609891	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43609892	43610026	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43609892	43610026	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610027	43610174	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610175	43610264	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610175	43610264	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610265	43610361	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610362	43610373	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610362	43610373	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610374	43610489	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610490	43610540	0.95	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610490	43610540	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610541	43610625	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610626	43610709	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610626	43610709	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610710	43610805	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610806	43610870	1	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610806	43610870	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	intron	43610871	43610962	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	CDS	43610963	43611161	0.91	+	1	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	exon	43610963	43611161	.	+	.	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
Phchi.S1	AUGUSTUS	stop_codon	43611162	43611164	.	+	0	transcript_id "Phchi.S1G693000.t2"; gene_id "Phchi.S1G693000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7043.t1 is derived from g4215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26570227	26570714	.	+	.	Phchi.S1G420200
Phchi.S1	AUGUSTUS	transcript	26570227	26570714	.	+	.	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	start_codon	26570227	26570229	.	+	0	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	CDS	26570227	26570294	0.69	+	0	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	exon	26570227	26570294	.	+	.	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	intron	26570295	26570419	.	+	.	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	CDS	26570420	26570480	0.69	+	1	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	exon	26570420	26570480	.	+	.	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	intron	26570481	26570627	.	+	.	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	CDS	26570628	26570714	0.61	+	0	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	exon	26570628	26570714	.	+	.	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
Phchi.S1	AUGUSTUS	stop_codon	26570715	26570717	.	+	0	transcript_id "Phchi.S1G420200.t1"; gene_id "Phchi.S1G420200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14323.t1 is derived from g12790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12092865	12095068	.	+	.	Phchi.S3G164200
Phchi.S3	AUGUSTUS	transcript	12092865	12095068	.	+	.	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	start_codon	12092865	12092867	.	+	0	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	CDS	12092865	12092888	0.66	+	0	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	exon	12092865	12092888	.	+	.	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	intron	12092889	12092983	.	+	.	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	CDS	12092984	12095068	1	+	0	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	exon	12092984	12095068	.	+	.	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
Phchi.S3	AUGUSTUS	stop_codon	12095069	12095071	.	+	0	transcript_id "Phchi.S3G164200.t1"; gene_id "Phchi.S3G164200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9804.t1 is derived from g6980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43789099	43790211	.	-	.	Phchi.S1G696300
Phchi.S1	AUGUSTUS	transcript	43789099	43790211	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	stop_codon	43789096	43789098	.	-	0	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	CDS	43789099	43789197	0.88	-	0	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	exon	43789099	43789197	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	intron	43789198	43789282	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	CDS	43789283	43789613	0.84	-	1	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	exon	43789283	43789613	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	intron	43789614	43789746	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	CDS	43789747	43789854	0.59	-	1	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	exon	43789747	43789854	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	intron	43789855	43789996	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	CDS	43789997	43790211	0.55	-	0	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	exon	43789997	43790211	.	-	.	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
Phchi.S1	AUGUSTUS	start_codon	43790209	43790211	.	-	0	transcript_id "Phchi.S1G696300.t1"; gene_id "Phchi.S1G696300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6806.t1 is derived from g3978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25139788	25141663	.	+	.	Phchi.S1G396500
Phchi.S1	AUGUSTUS	transcript	25139788	25141663	.	+	.	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	start_codon	25139788	25139790	.	+	0	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	CDS	25139788	25140994	0.79	+	0	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	exon	25139788	25140994	.	+	.	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	intron	25140995	25141140	.	+	.	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	CDS	25141141	25141236	0.62	+	2	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	exon	25141141	25141236	.	+	.	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	intron	25141237	25141340	.	+	.	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	CDS	25141341	25141663	0.61	+	2	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	exon	25141341	25141663	.	+	.	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
Phchi.S1	AUGUSTUS	stop_codon	25141664	25141666	.	+	0	transcript_id "Phchi.S1G396500.t1"; gene_id "Phchi.S1G396500"
# This transcript jg7478.t2 is derived from g4651.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7478.t3 is derived from g4651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7479.t1 is derived from g4652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29553372	29554261	.	-	.	Phchi.S1G463800
Phchi.S1	AUGUSTUS	transcript	29553372	29554261	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	stop_codon	29553369	29553371	.	-	0	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	CDS	29553372	29553529	0.99	-	2	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	exon	29553372	29553529	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	intron	29553530	29553650	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	CDS	29553651	29553724	0.99	-	1	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	exon	29553651	29553724	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	intron	29553725	29553867	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	CDS	29553868	29553927	0.94	-	1	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	exon	29553868	29553927	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	intron	29553928	29554037	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	CDS	29554038	29554145	0.47	-	1	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	exon	29554038	29554145	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	intron	29554146	29554238	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	CDS	29554239	29554261	0.95	-	0	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	exon	29554239	29554261	.	-	.	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
Phchi.S1	AUGUSTUS	start_codon	29554259	29554261	.	-	0	transcript_id "Phchi.S1G463800.t1"; gene_id "Phchi.S1G463800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10109.t1 is derived from g7285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45765769	45771963	.	-	.	Phchi.S1G726800
Phchi.S1	AUGUSTUS	transcript	45765769	45771963	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	stop_codon	45765766	45765768	.	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45765769	45766502	0.94	-	2	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45765769	45766502	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45766503	45766673	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45766674	45766956	0.98	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45766674	45766956	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45766957	45767079	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45767080	45767137	1	-	1	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45767080	45767137	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45767138	45767286	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45767287	45767357	1	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45767287	45767357	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45767358	45767505	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45767506	45767568	1	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45767506	45767568	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45767569	45767668	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45767669	45768445	0.95	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45767669	45768445	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45768446	45768822	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45768823	45768888	1	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45768823	45768888	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45768889	45768965	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45768966	45769054	1	-	2	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45768966	45769054	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45769055	45769153	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45769154	45769216	0.94	-	2	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45769154	45769216	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45769217	45769314	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45769315	45769326	0.94	-	2	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45769315	45769326	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45769327	45769382	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45769383	45769420	0.94	-	1	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45769383	45769420	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45769421	45769587	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45769588	45770388	1	-	1	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45769588	45770388	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45770389	45770586	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45770587	45771147	1	-	1	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45770587	45771147	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	intron	45771148	45771478	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	CDS	45771479	45771963	0.99	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	exon	45771479	45771963	.	-	.	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
Phchi.S1	AUGUSTUS	start_codon	45771961	45771963	.	-	0	transcript_id "Phchi.S1G726800.t1"; gene_id "Phchi.S1G726800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2969.t1 is derived from g138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	890159	894101	.	-	.	Phchi.S1G012800
Phchi.S1	AUGUSTUS	transcript	890159	894101	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	stop_codon	890156	890158	.	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	890159	890376	1	-	2	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	890159	890376	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	890377	890459	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	890460	890529	1	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	890460	890529	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	890530	890623	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	890624	890671	0.97	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	890624	890671	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	890672	890799	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	890800	891036	1	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	890800	891036	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	891037	891121	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	891122	891390	0.97	-	2	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	891122	891390	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	891391	891498	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	891499	892557	0.76	-	2	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	891499	892557	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	892558	892628	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	892629	892655	0.56	-	2	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	892629	892655	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	892656	892741	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	892742	892815	0.96	-	1	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	892742	892815	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	892816	892906	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	892907	893124	0.93	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	892907	893124	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	893125	893216	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	893217	893306	0.94	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	893217	893306	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	893307	893397	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	893398	893601	0.91	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	893398	893601	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	893602	893710	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	893711	893743	0.99	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	893711	893743	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	893744	893818	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	893819	893872	0.99	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	893819	893872	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	intron	893873	893966	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	CDS	893967	894101	0.98	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	exon	893967	894101	.	-	.	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
Phchi.S1	AUGUSTUS	start_codon	894099	894101	.	-	0	transcript_id "Phchi.S1G012800.t1"; gene_id "Phchi.S1G012800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15009.t1 is derived from g13477.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16470771	16471742	.	+	.	Phchi.S3G232800
Phchi.S3	AUGUSTUS	transcript	16470771	16471742	.	+	.	transcript_id "Phchi.S3G232800.t1"; gene_id "Phchi.S3G232800"
Phchi.S3	AUGUSTUS	start_codon	16470771	16470773	.	+	0	transcript_id "Phchi.S3G232800.t1"; gene_id "Phchi.S3G232800"
Phchi.S3	AUGUSTUS	CDS	16470771	16471742	1	+	0	transcript_id "Phchi.S3G232800.t1"; gene_id "Phchi.S3G232800"
Phchi.S3	AUGUSTUS	exon	16470771	16471742	.	+	.	transcript_id "Phchi.S3G232800.t1"; gene_id "Phchi.S3G232800"
Phchi.S3	AUGUSTUS	stop_codon	16471743	16471745	.	+	0	transcript_id "Phchi.S3G232800.t1"; gene_id "Phchi.S3G232800"
# This transcript jg433.t2 is derived from g10215.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg434.t1 is derived from g10216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3064554	3064958	.	+	.	Phchi.S6G039300
Phchi.S6	AUGUSTUS	transcript	3064554	3064958	.	+	.	transcript_id "Phchi.S6G039300.t1"; gene_id "Phchi.S6G039300"
Phchi.S6	AUGUSTUS	start_codon	3064554	3064556	.	+	0	transcript_id "Phchi.S6G039300.t1"; gene_id "Phchi.S6G039300"
Phchi.S6	AUGUSTUS	CDS	3064554	3064958	0.99	+	0	transcript_id "Phchi.S6G039300.t1"; gene_id "Phchi.S6G039300"
Phchi.S6	AUGUSTUS	exon	3064554	3064958	.	+	.	transcript_id "Phchi.S6G039300.t1"; gene_id "Phchi.S6G039300"
Phchi.S6	AUGUSTUS	stop_codon	3064959	3064961	.	+	0	transcript_id "Phchi.S6G039300.t1"; gene_id "Phchi.S6G039300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4552.t1 is derived from g1722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11075211	11076289	.	-	.	Phchi.S1G171100
Phchi.S1	AUGUSTUS	transcript	11075211	11076289	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	stop_codon	11075208	11075210	.	-	0	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	CDS	11075211	11075235	0.42	-	1	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	exon	11075211	11075235	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	intron	11075236	11075330	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	CDS	11075331	11075512	0.4	-	0	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	exon	11075331	11075512	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	intron	11075513	11075608	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	CDS	11075609	11075716	0.9	-	0	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	exon	11075609	11075716	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	intron	11075717	11075878	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	CDS	11075879	11076023	0.85	-	1	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	exon	11075879	11076023	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	intron	11076024	11076167	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	CDS	11076168	11076289	0.28	-	0	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	exon	11076168	11076289	.	-	.	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
Phchi.S1	AUGUSTUS	start_codon	11076287	11076289	.	-	0	transcript_id "Phchi.S1G171100.t1"; gene_id "Phchi.S1G171100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13835.t1 is derived from g12302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9131595	9132813	.	-	.	Phchi.S3G115400
Phchi.S3	AUGUSTUS	transcript	9131595	9132813	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	stop_codon	9131592	9131594	.	-	0	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	CDS	9131595	9131929	1	-	2	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	exon	9131595	9131929	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	intron	9131930	9132020	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	CDS	9132021	9132261	1	-	0	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	exon	9132021	9132261	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	intron	9132262	9132342	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	CDS	9132343	9132438	1	-	0	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	exon	9132343	9132438	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	intron	9132439	9132570	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	CDS	9132571	9132813	0.99	-	0	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	exon	9132571	9132813	.	-	.	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
Phchi.S3	AUGUSTUS	start_codon	9132811	9132813	.	-	0	transcript_id "Phchi.S3G115400.t1"; gene_id "Phchi.S3G115400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg646.t1 is derived from g10428.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4568769	4569651	.	-	.	Phchi.S6G060500
Phchi.S6	AUGUSTUS	transcript	4568769	4569651	.	-	.	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	stop_codon	4568766	4568768	.	-	0	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	CDS	4568769	4568905	0.87	-	2	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	exon	4568769	4568905	.	-	.	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	intron	4568906	4569038	.	-	.	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	CDS	4569039	4569651	0.74	-	0	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	exon	4569039	4569651	.	-	.	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
Phchi.S6	AUGUSTUS	start_codon	4569649	4569651	.	-	0	transcript_id "Phchi.S6G060500.t1"; gene_id "Phchi.S6G060500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2367.t1 is derived from g9287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6372298	6373555	.	+	.	Phchi.S5G097600
Phchi.S5	AUGUSTUS	transcript	6372298	6373555	.	+	.	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	start_codon	6372298	6372300	.	+	0	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	CDS	6372298	6372440	0.78	+	0	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	exon	6372298	6372440	.	+	.	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	intron	6372441	6372535	.	+	.	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	CDS	6372536	6372661	1	+	1	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	exon	6372536	6372661	.	+	.	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	intron	6372662	6372828	.	+	.	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	CDS	6372829	6373555	0.98	+	1	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	exon	6372829	6373555	.	+	.	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
Phchi.S5	AUGUSTUS	stop_codon	6373556	6373558	.	+	0	transcript_id "Phchi.S5G097600.t1"; gene_id "Phchi.S5G097600"
# This transcript jg2027.t2 is derived from g8947.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2028.t1 is derived from g8948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4514299	4520112	.	+	.	Phchi.S5G063700
Phchi.S5	AUGUSTUS	transcript	4514299	4520112	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	start_codon	4514299	4514301	.	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4514299	4516401	0.92	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4514299	4516401	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4516402	4516482	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4516483	4516583	0.8	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4516483	4516583	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4516584	4516688	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4516689	4516803	0.78	+	1	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4516689	4516803	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4516804	4516905	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4516906	4516983	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4516906	4516983	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4516984	4517190	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4517191	4517283	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4517191	4517283	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4517284	4517393	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4517394	4517477	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4517394	4517477	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4517478	4517563	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4517564	4517662	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4517564	4517662	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4517663	4517780	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4517781	4517843	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4517781	4517843	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4517844	4517939	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4517940	4517970	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4517940	4517970	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4517971	4518089	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4518090	4518136	1	+	2	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4518090	4518136	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4518137	4518294	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4518295	4518353	1	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4518295	4518353	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4518354	4518442	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4518443	4518683	0.28	+	1	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4518443	4518683	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4518684	4519146	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4519147	4519184	0.28	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4519147	4519184	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4519185	4519428	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4519429	4519569	0.23	+	1	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4519429	4519569	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4519570	4519715	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4519716	4519797	0.47	+	1	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4519716	4519797	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4519798	4519891	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4519892	4519966	0.19	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4519892	4519966	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	intron	4519967	4520058	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	CDS	4520059	4520112	0.28	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	exon	4520059	4520112	.	+	.	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
Phchi.S5	AUGUSTUS	stop_codon	4520113	4520115	.	+	0	transcript_id "Phchi.S5G063700.t1"; gene_id "Phchi.S5G063700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2981.t1 is derived from g150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	948813	951108	.	-	.	Phchi.S1G014000
Phchi.S1	AUGUSTUS	transcript	948813	951108	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	stop_codon	948810	948812	.	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	948813	948840	0.8	-	1	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	948813	948840	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	948841	948927	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	948928	949013	1	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	948928	949013	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	949014	949143	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	949144	949347	1	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	949144	949347	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	949348	949445	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	949446	949505	1	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	949446	949505	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	949506	949584	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	949585	949646	0.71	-	2	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	949585	949646	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	949647	949712	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	949713	949753	0.71	-	1	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	949713	949753	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	949754	949848	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	949849	949922	1	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	949849	949922	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	949923	950072	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	950073	950176	1	-	2	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	950073	950176	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	intron	950177	950615	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	CDS	950616	951108	1	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	exon	950616	951108	.	-	.	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
Phchi.S1	AUGUSTUS	start_codon	951106	951108	.	-	0	transcript_id "Phchi.S1G014000.t1"; gene_id "Phchi.S1G014000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5030.t1 is derived from g2200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14151289	14154025	.	+	.	Phchi.S1G218900
Phchi.S1	AUGUSTUS	transcript	14151289	14154025	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	start_codon	14151289	14151291	.	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14151289	14151563	0.99	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14151289	14151563	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14151564	14151703	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14151704	14152024	0.97	+	1	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14151704	14152024	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14152025	14152177	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14152178	14152292	1	+	1	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14152178	14152292	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14152293	14152414	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14152415	14152669	1	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14152415	14152669	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14152670	14152822	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14152823	14152909	1	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14152823	14152909	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14152910	14153007	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14153008	14153086	1	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14153008	14153086	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14153087	14153327	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14153328	14153434	1	+	2	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14153328	14153434	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14153435	14153578	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14153579	14153697	1	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14153579	14153697	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	intron	14153698	14153928	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	CDS	14153929	14154025	1	+	1	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	exon	14153929	14154025	.	+	.	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
Phchi.S1	AUGUSTUS	stop_codon	14154026	14154028	.	+	0	transcript_id "Phchi.S1G218900.t1"; gene_id "Phchi.S1G218900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4524.t1 is derived from g1694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10944046	10945218	.	+	.	Phchi.S1G168300
Phchi.S1	AUGUSTUS	transcript	10944046	10945218	.	+	.	transcript_id "Phchi.S1G168300.t1"; gene_id "Phchi.S1G168300"
Phchi.S1	AUGUSTUS	start_codon	10944046	10944048	.	+	0	transcript_id "Phchi.S1G168300.t1"; gene_id "Phchi.S1G168300"
Phchi.S1	AUGUSTUS	CDS	10944046	10945218	0.93	+	0	transcript_id "Phchi.S1G168300.t1"; gene_id "Phchi.S1G168300"
Phchi.S1	AUGUSTUS	exon	10944046	10945218	.	+	.	transcript_id "Phchi.S1G168300.t1"; gene_id "Phchi.S1G168300"
Phchi.S1	AUGUSTUS	stop_codon	10945219	10945221	.	+	0	transcript_id "Phchi.S1G168300.t1"; gene_id "Phchi.S1G168300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4414.t1 is derived from g1583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10374129	10376370	.	-	.	Phchi.S1G157300
Phchi.S1	AUGUSTUS	transcript	10374129	10376370	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	stop_codon	10374126	10374128	.	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10374129	10374227	1	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10374129	10374227	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10374228	10374320	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10374321	10374422	1	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10374321	10374422	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10374423	10374500	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10374501	10374628	1	-	2	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10374501	10374628	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10374629	10374728	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10374729	10374907	1	-	1	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10374729	10374907	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10374908	10375052	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10375053	10375182	0.99	-	2	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10375053	10375182	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10375183	10375293	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10375294	10375390	1	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10375294	10375390	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10375391	10375485	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10375486	10375620	1	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10375486	10375620	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10375621	10375950	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10375951	10376015	1	-	2	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10375951	10376015	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10376016	10376099	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10376100	10376201	1	-	2	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10376100	10376201	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	intron	10376202	10376270	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	CDS	10376271	10376370	0.86	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	exon	10376271	10376370	.	-	.	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
Phchi.S1	AUGUSTUS	start_codon	10376368	10376370	.	-	0	transcript_id "Phchi.S1G157300.t1"; gene_id "Phchi.S1G157300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6877.t1 is derived from g4049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25770230	25771387	.	-	.	Phchi.S1G403600
Phchi.S1	AUGUSTUS	transcript	25770230	25771387	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	stop_codon	25770227	25770229	.	-	0	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	CDS	25770230	25770508	1	-	0	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	exon	25770230	25770508	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	intron	25770509	25770623	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	CDS	25770624	25770689	0.99	-	0	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	exon	25770624	25770689	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	intron	25770690	25770896	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	CDS	25770897	25771135	0.96	-	2	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	exon	25770897	25771135	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	intron	25771136	25771220	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	CDS	25771221	25771265	0.44	-	2	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	exon	25771221	25771265	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	intron	25771266	25771344	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	CDS	25771345	25771387	0.47	-	0	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	exon	25771345	25771387	.	-	.	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
Phchi.S1	AUGUSTUS	start_codon	25771385	25771387	.	-	0	transcript_id "Phchi.S1G403600.t1"; gene_id "Phchi.S1G403600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15282.t1 is derived from g13750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18150654	18152323	.	+	.	Phchi.S3G260100
Phchi.S3	AUGUSTUS	transcript	18150654	18152323	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	start_codon	18150654	18150656	.	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18150654	18150843	0.53	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18150654	18150843	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18150844	18151090	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18151091	18151177	1	+	2	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18151091	18151177	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18151178	18151311	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18151312	18151382	1	+	2	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18151312	18151382	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18151383	18151465	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18151466	18151567	1	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18151466	18151567	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18151568	18151646	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18151647	18151751	1	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18151647	18151751	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18151752	18151845	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18151846	18151978	1	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18151846	18151978	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18151979	18152061	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18152062	18152171	1	+	2	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18152062	18152171	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	intron	18152172	18152254	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	CDS	18152255	18152323	1	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	exon	18152255	18152323	.	+	.	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
Phchi.S3	AUGUSTUS	stop_codon	18152324	18152326	.	+	0	transcript_id "Phchi.S3G260100.t1"; gene_id "Phchi.S3G260100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5388.t1 is derived from g2558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16631954	16634551	.	-	.	Phchi.S1G254700
Phchi.S1	AUGUSTUS	transcript	16631954	16634551	.	-	.	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	stop_codon	16631951	16631953	.	-	0	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	CDS	16631954	16632329	0.76	-	1	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	exon	16631954	16632329	.	-	.	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	intron	16632330	16632412	.	-	.	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	CDS	16632413	16634217	0.43	-	0	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	exon	16632413	16634217	.	-	.	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	intron	16634218	16634431	.	-	.	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	CDS	16634432	16634551	1	-	0	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	exon	16634432	16634551	.	-	.	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
Phchi.S1	AUGUSTUS	start_codon	16634549	16634551	.	-	0	transcript_id "Phchi.S1G254700.t1"; gene_id "Phchi.S1G254700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11252.t1 is derived from g15302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5010424	5011752	.	-	.	Phchi.S4G083400
Phchi.S4	AUGUSTUS	transcript	5010424	5011752	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	stop_codon	5010421	5010423	.	-	0	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	CDS	5010424	5010462	0.9	-	0	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	exon	5010424	5010462	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	intron	5010463	5010869	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	CDS	5010870	5010950	0.9	-	0	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	exon	5010870	5010950	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	intron	5010951	5011206	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	CDS	5011207	5011221	0.86	-	0	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	exon	5011207	5011221	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	intron	5011222	5011321	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	CDS	5011322	5011362	0.56	-	2	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	exon	5011322	5011362	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	intron	5011363	5011468	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	CDS	5011469	5011575	0.69	-	1	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	exon	5011469	5011575	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	intron	5011576	5011666	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	CDS	5011667	5011752	1	-	0	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	exon	5011667	5011752	.	-	.	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
Phchi.S4	AUGUSTUS	start_codon	5011750	5011752	.	-	0	transcript_id "Phchi.S4G083400.t1"; gene_id "Phchi.S4G083400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14727.t1 is derived from g13195.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14388239	14389074	.	-	.	Phchi.S3G204600
Phchi.S3	AUGUSTUS	transcript	14388239	14389074	.	-	.	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	stop_codon	14388236	14388238	.	-	0	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	CDS	14388239	14388343	1	-	0	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	exon	14388239	14388343	.	-	.	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	intron	14388344	14388436	.	-	.	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	CDS	14388437	14388561	1	-	2	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	exon	14388437	14388561	.	-	.	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	intron	14388562	14388710	.	-	.	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	CDS	14388711	14389074	0.47	-	0	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	exon	14388711	14389074	.	-	.	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
Phchi.S3	AUGUSTUS	start_codon	14389072	14389074	.	-	0	transcript_id "Phchi.S3G204600.t1"; gene_id "Phchi.S3G204600"
# This transcript jg4842.t2 is derived from g2012.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4843.t1 is derived from g2013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13069033	13070385	.	-	.	Phchi.S1G200200
Phchi.S1	AUGUSTUS	transcript	13069033	13070385	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	stop_codon	13069030	13069032	.	-	0	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	CDS	13069033	13069062	1	-	0	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	exon	13069033	13069062	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	intron	13069063	13069198	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	CDS	13069199	13069357	1	-	0	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	exon	13069199	13069357	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	intron	13069358	13069552	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	CDS	13069553	13069595	1	-	1	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	exon	13069553	13069595	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	intron	13069596	13069732	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	CDS	13069733	13069781	1	-	2	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	exon	13069733	13069781	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	intron	13069782	13070180	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	CDS	13070181	13070252	1	-	2	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	exon	13070181	13070252	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	intron	13070253	13070339	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	CDS	13070340	13070385	1	-	0	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	exon	13070340	13070385	.	-	.	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
Phchi.S1	AUGUSTUS	start_codon	13070383	13070385	.	-	0	transcript_id "Phchi.S1G200200.t1"; gene_id "Phchi.S1G200200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4307.t1 is derived from g1476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9547678	9549547	.	+	.	Phchi.S1G146600
Phchi.S1	AUGUSTUS	transcript	9547678	9549547	.	+	.	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	start_codon	9547678	9547680	.	+	0	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	CDS	9547678	9547680	0.39	+	0	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	exon	9547678	9547680	.	+	.	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	intron	9547681	9547867	.	+	.	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	CDS	9547868	9549547	0.86	+	0	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	exon	9547868	9549547	.	+	.	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
Phchi.S1	AUGUSTUS	stop_codon	9549548	9549550	.	+	0	transcript_id "Phchi.S1G146600.t1"; gene_id "Phchi.S1G146600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15137.t1 is derived from g13605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17224619	17228022	.	-	.	Phchi.S3G245600
Phchi.S3	AUGUSTUS	transcript	17224619	17228022	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	stop_codon	17224616	17224618	.	-	0	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17224619	17225199	0.86	-	2	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17224619	17225199	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	intron	17225200	17225340	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17225341	17225482	1	-	0	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17225341	17225482	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	intron	17225483	17225581	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17225582	17227139	0.93	-	1	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17225582	17227139	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	intron	17227140	17227272	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17227273	17227278	0.93	-	1	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17227273	17227278	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	intron	17227279	17227486	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17227487	17227547	0.95	-	2	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17227487	17227547	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	intron	17227548	17227626	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17227627	17227722	1	-	2	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17227627	17227722	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	intron	17227723	17228003	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	CDS	17228004	17228022	0.86	-	0	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	exon	17228004	17228022	.	-	.	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
Phchi.S3	AUGUSTUS	start_codon	17228020	17228022	.	-	0	transcript_id "Phchi.S3G245600.t1"; gene_id "Phchi.S3G245600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3120.t1 is derived from g289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1835075	1837162	.	+	.	Phchi.S1G027900
Phchi.S1	AUGUSTUS	transcript	1835075	1837162	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	start_codon	1835075	1835077	.	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1835075	1835374	0.63	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1835075	1835374	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	intron	1835375	1835463	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1835464	1835596	1	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1835464	1835596	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	intron	1835597	1835719	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1835720	1835839	0.99	+	2	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1835720	1835839	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	intron	1835840	1835922	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1835923	1836140	0.99	+	2	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1835923	1836140	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	intron	1836141	1836250	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1836251	1836439	0.99	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1836251	1836439	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	intron	1836440	1836534	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1836535	1836660	1	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1836535	1836660	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	intron	1836661	1836793	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	CDS	1836794	1837162	1	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	exon	1836794	1837162	.	+	.	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
Phchi.S1	AUGUSTUS	stop_codon	1837163	1837165	.	+	0	transcript_id "Phchi.S1G027900.t1"; gene_id "Phchi.S1G027900"
# This transcript jg12536.t2 is derived from g8213.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12536.t3 is derived from g8213.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12537.t1 is derived from g8214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33716243	33717838	.	+	.	Phchi.S2G061700
Phchi.S2	AUGUSTUS	transcript	33716243	33717838	.	+	.	transcript_id "Phchi.S2G061700.t1"; gene_id "Phchi.S2G061700"
Phchi.S2	AUGUSTUS	start_codon	33716243	33716245	.	+	0	transcript_id "Phchi.S2G061700.t1"; gene_id "Phchi.S2G061700"
Phchi.S2	AUGUSTUS	CDS	33716243	33717838	1	+	0	transcript_id "Phchi.S2G061700.t1"; gene_id "Phchi.S2G061700"
Phchi.S2	AUGUSTUS	exon	33716243	33717838	.	+	.	transcript_id "Phchi.S2G061700.t1"; gene_id "Phchi.S2G061700"
Phchi.S2	AUGUSTUS	stop_codon	33717839	33717841	.	+	0	transcript_id "Phchi.S2G061700.t1"; gene_id "Phchi.S2G061700"
# This transcript jg450.t2 is derived from g10232.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg450.t3 is derived from g10232.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg451.t1 is derived from g10233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3171373	3173757	.	+	.	Phchi.S6G041000
Phchi.S6	AUGUSTUS	transcript	3171373	3173757	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	start_codon	3171373	3171375	.	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3171373	3171481	0.96	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3171373	3171481	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3171482	3171579	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3171580	3171860	1	+	2	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3171580	3171860	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3171861	3171942	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3171943	3172089	1	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3171943	3172089	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3172090	3172170	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3172171	3172235	1	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3172171	3172235	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3172236	3172453	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3172454	3172523	1	+	1	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3172454	3172523	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3172524	3172622	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3172623	3172850	1	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3172623	3172850	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3172851	3172934	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3172935	3173078	1	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3172935	3173078	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3173079	3173170	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3173171	3173306	1	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3173171	3173306	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3173307	3173402	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3173403	3173521	0.3	+	2	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3173403	3173521	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	intron	3173522	3173709	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	CDS	3173710	3173757	0.56	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	exon	3173710	3173757	.	+	.	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
Phchi.S6	AUGUSTUS	stop_codon	3173758	3173760	.	+	0	transcript_id "Phchi.S6G041000.t1"; gene_id "Phchi.S6G041000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4761.t1 is derived from g1931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12691558	12694076	.	-	.	Phchi.S1G192000
Phchi.S1	AUGUSTUS	transcript	12691558	12694076	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	stop_codon	12691555	12691557	.	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12691558	12692147	0.73	-	2	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12691558	12692147	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12692148	12692247	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12692248	12692488	0.72	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12692248	12692488	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12692489	12692783	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12692784	12692849	0.57	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12692784	12692849	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12692850	12693125	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12693126	12693173	0.57	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12693126	12693173	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12693174	12693255	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12693256	12693333	1	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12693256	12693333	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12693334	12693413	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12693414	12693503	1	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12693414	12693503	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12693504	12693612	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12693613	12693732	0.41	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12693613	12693732	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	intron	12693733	12693971	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	CDS	12693972	12694076	0.49	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	exon	12693972	12694076	.	-	.	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
Phchi.S1	AUGUSTUS	start_codon	12694074	12694076	.	-	0	transcript_id "Phchi.S1G192000.t1"; gene_id "Phchi.S1G192000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12666.t1 is derived from g14464.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C42	AUGUSTUS	gene	15064	16796	.	+	.	Phchi.C42G000100
Phchi.C42	AUGUSTUS	transcript	15064	16796	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	start_codon	15064	15066	.	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15064	15143	0.89	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15064	15143	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15144	15222	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15223	15244	1	+	1	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15223	15244	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15245	15397	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15398	15475	1	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15398	15475	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15476	15560	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15561	15635	1	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15561	15635	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15636	15777	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15778	15843	0.99	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15778	15843	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15844	15916	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15917	16181	0.99	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15917	16181	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	16182	16338	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16339	16607	0.99	+	2	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16339	16607	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	16608	16733	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16734	16796	1	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16734	16796	.	+	.	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	stop_codon	16797	16799	.	+	0	transcript_id "Phchi.C42G000100.t1"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	transcript	15064	16796	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	start_codon	15064	15066	.	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15064	15143	0.82	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15064	15143	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15144	15222	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15223	15244	0.99	+	1	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15223	15244	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15245	15397	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15398	15475	0.99	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15398	15475	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15476	15569	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15570	15635	0.99	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15570	15635	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15636	15777	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15778	15843	0.99	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15778	15843	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	15844	15916	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	15917	16181	0.99	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	15917	16181	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	16182	16338	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16339	16607	0.99	+	2	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16339	16607	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	16608	16733	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16734	16796	0.99	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16734	16796	.	+	.	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	stop_codon	16797	16799	.	+	0	transcript_id "Phchi.C42G000100.t2"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	transcript	16107	16796	.	+	.	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	start_codon	16107	16109	.	+	0	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16107	16181	0.42	+	0	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16107	16181	.	+	.	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	16182	16346	.	+	.	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16347	16607	0.82	+	0	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16347	16607	.	+	.	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	intron	16608	16733	.	+	.	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	CDS	16734	16796	0.96	+	0	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	exon	16734	16796	.	+	.	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
Phchi.C42	AUGUSTUS	stop_codon	16797	16799	.	+	0	transcript_id "Phchi.C42G000100.t3"; gene_id "Phchi.C42G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8803.t1 is derived from g5978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38060694	38064188	.	-	.	Phchi.S1G596200
Phchi.S1	AUGUSTUS	transcript	38060694	38064188	.	-	.	transcript_id "Phchi.S1G596200.t1"; gene_id "Phchi.S1G596200"
Phchi.S1	AUGUSTUS	stop_codon	38060691	38060693	.	-	0	transcript_id "Phchi.S1G596200.t1"; gene_id "Phchi.S1G596200"
Phchi.S1	AUGUSTUS	CDS	38060694	38064188	0.8	-	0	transcript_id "Phchi.S1G596200.t1"; gene_id "Phchi.S1G596200"
Phchi.S1	AUGUSTUS	exon	38060694	38064188	.	-	.	transcript_id "Phchi.S1G596200.t1"; gene_id "Phchi.S1G596200"
Phchi.S1	AUGUSTUS	start_codon	38064186	38064188	.	-	0	transcript_id "Phchi.S1G596200.t1"; gene_id "Phchi.S1G596200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1818.t1 is derived from g8738.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3307432	3308469	.	-	.	Phchi.S5G042700
Phchi.S5	AUGUSTUS	transcript	3307432	3308469	.	-	.	transcript_id "Phchi.S5G042700.t1"; gene_id "Phchi.S5G042700"
Phchi.S5	AUGUSTUS	stop_codon	3307429	3307431	.	-	0	transcript_id "Phchi.S5G042700.t1"; gene_id "Phchi.S5G042700"
Phchi.S5	AUGUSTUS	CDS	3307432	3308469	0.51	-	0	transcript_id "Phchi.S5G042700.t1"; gene_id "Phchi.S5G042700"
Phchi.S5	AUGUSTUS	exon	3307432	3308469	.	-	.	transcript_id "Phchi.S5G042700.t1"; gene_id "Phchi.S5G042700"
Phchi.S5	AUGUSTUS	start_codon	3308467	3308469	.	-	0	transcript_id "Phchi.S5G042700.t1"; gene_id "Phchi.S5G042700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3583.t1 is derived from g752.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4608141	4609092	.	+	.	Phchi.S1G074200
Phchi.S1	AUGUSTUS	transcript	4608141	4609092	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	start_codon	4608141	4608143	.	+	0	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	CDS	4608141	4608148	1	+	0	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	exon	4608141	4608148	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	intron	4608149	4608236	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	CDS	4608237	4608347	1	+	1	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	exon	4608237	4608347	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	intron	4608348	4608437	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	CDS	4608438	4608552	1	+	1	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	exon	4608438	4608552	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	intron	4608553	4608712	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	CDS	4608713	4608829	1	+	0	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	exon	4608713	4608829	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	intron	4608830	4608915	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	CDS	4608916	4609092	0.95	+	0	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	exon	4608916	4609092	.	+	.	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
Phchi.S1	AUGUSTUS	stop_codon	4609093	4609095	.	+	0	transcript_id "Phchi.S1G074200.t1"; gene_id "Phchi.S1G074200"
# This transcript jg6036.t2 is derived from g3207.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6037.t1 is derived from g3208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20535052	20535441	.	+	.	Phchi.S1G319600
Phchi.S1	AUGUSTUS	transcript	20535052	20535441	.	+	.	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	start_codon	20535052	20535054	.	+	0	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	CDS	20535052	20535237	0.56	+	0	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	exon	20535052	20535237	.	+	.	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	intron	20535238	20535414	.	+	.	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	CDS	20535415	20535441	0.96	+	0	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	exon	20535415	20535441	.	+	.	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
Phchi.S1	AUGUSTUS	stop_codon	20535442	20535444	.	+	0	transcript_id "Phchi.S1G319600.t1"; gene_id "Phchi.S1G319600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg796.t1 is derived from g10578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5621030	5622449	.	-	.	Phchi.S6G075500
Phchi.S6	AUGUSTUS	transcript	5621030	5622449	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	stop_codon	5621027	5621029	.	-	0	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	CDS	5621030	5621427	1	-	2	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	exon	5621030	5621427	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	intron	5621428	5621560	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	CDS	5621561	5621729	1	-	0	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	exon	5621561	5621729	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	intron	5621730	5621828	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	CDS	5621829	5622017	0.95	-	0	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	exon	5621829	5622017	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	intron	5622018	5622107	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	CDS	5622108	5622449	0.74	-	0	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	exon	5622108	5622449	.	-	.	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
Phchi.S6	AUGUSTUS	start_codon	5622447	5622449	.	-	0	transcript_id "Phchi.S6G075500.t1"; gene_id "Phchi.S6G075500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10479.t1 is derived from g14528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	573925	577976	.	-	.	Phchi.S4G006100
Phchi.S4	AUGUSTUS	transcript	573925	577976	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	stop_codon	573922	573924	.	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	573925	574031	0.94	-	2	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	573925	574031	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	574032	574127	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	574128	574201	1	-	1	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	574128	574201	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	574202	574299	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	574300	574382	1	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	574300	574382	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	574383	574460	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	574461	574566	1	-	1	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	574461	574566	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	574567	574690	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	574691	574731	1	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	574691	574731	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	574732	574837	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	574838	574911	1	-	2	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	574838	574911	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	574912	575003	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	575004	575068	1	-	1	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	575004	575068	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	575069	575177	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	575178	575205	1	-	2	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	575178	575205	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	575206	575288	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	575289	575368	1	-	1	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	575289	575368	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	575369	575477	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	575478	575555	1	-	1	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	575478	575555	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	575556	575730	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	575731	575813	1	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	575731	575813	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	575814	575907	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	575908	576035	0.76	-	2	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	575908	576035	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	576036	576207	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	576208	576346	0.7	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	576208	576346	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	576347	576473	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	576474	577028	0.57	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	576474	577028	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	intron	577029	577658	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	CDS	577659	577976	1	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	exon	577659	577976	.	-	.	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
Phchi.S4	AUGUSTUS	start_codon	577974	577976	.	-	0	transcript_id "Phchi.S4G006100.t1"; gene_id "Phchi.S4G006100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11329.t1 is derived from g15379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5593361	5595383	.	-	.	Phchi.S4G091100
Phchi.S4	AUGUSTUS	transcript	5593361	5595383	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	stop_codon	5593358	5593360	.	-	0	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5593361	5593648	0.98	-	0	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5593361	5593648	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	intron	5593649	5593743	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5593744	5593856	0.94	-	2	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5593744	5593856	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	intron	5593857	5593934	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5593935	5594201	0.97	-	2	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5593935	5594201	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	intron	5594202	5594303	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5594304	5594589	0.95	-	0	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5594304	5594589	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	intron	5594590	5594669	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5594670	5594953	1	-	2	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5594670	5594953	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	intron	5594954	5595036	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5595037	5595222	1	-	2	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5595037	5595222	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	intron	5595223	5595316	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	CDS	5595317	5595383	1	-	0	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	exon	5595317	5595383	.	-	.	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
Phchi.S4	AUGUSTUS	start_codon	5595381	5595383	.	-	0	transcript_id "Phchi.S4G091100.t1"; gene_id "Phchi.S4G091100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13383.t1 is derived from g11849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6474512	6477835	.	-	.	Phchi.S3G070200
Phchi.S3	AUGUSTUS	transcript	6474512	6477835	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	stop_codon	6474509	6474511	.	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6474512	6474541	1	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6474512	6474541	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6474542	6474634	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6474635	6474746	1	-	1	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6474635	6474746	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6474747	6474888	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6474889	6475128	1	-	1	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6474889	6475128	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6475129	6475237	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6475238	6475339	0.97	-	1	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6475238	6475339	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6475340	6475488	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6475489	6475567	0.77	-	2	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6475489	6475567	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6475568	6475657	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6475658	6475793	1	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6475658	6475793	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6475794	6475938	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6475939	6475982	1	-	2	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6475939	6475982	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6475983	6476077	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6476078	6476125	1	-	2	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6476078	6476125	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6476126	6476206	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6476207	6476317	1	-	2	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6476207	6476317	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6476318	6476412	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6476413	6476475	1	-	2	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6476413	6476475	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6476476	6476576	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6476577	6476676	0.78	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6476577	6476676	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6476677	6476838	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6476839	6476950	1	-	1	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6476839	6476950	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6476951	6477221	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6477222	6477236	1	-	1	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6477222	6477236	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6477237	6477431	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6477432	6477502	1	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6477432	6477502	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	intron	6477503	6477580	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	CDS	6477581	6477835	0.88	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	exon	6477581	6477835	.	-	.	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
Phchi.S3	AUGUSTUS	start_codon	6477833	6477835	.	-	0	transcript_id "Phchi.S3G070200.t1"; gene_id "Phchi.S3G070200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4619.t1 is derived from g1789.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11433562	11442179	.	+	.	Phchi.S1G177800
Phchi.S1	AUGUSTUS	transcript	11433562	11442179	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	start_codon	11433562	11433564	.	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11433562	11433644	0.98	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11433562	11433644	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11433645	11433737	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11433738	11433778	0.96	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11433738	11433778	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11433779	11433888	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11433889	11434018	0.96	+	2	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11433889	11434018	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11434019	11434194	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11434195	11434233	0.43	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11434195	11434233	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11434234	11434312	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11434313	11434361	0.43	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11434313	11434361	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11434362	11434465	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11434466	11437618	0.38	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11434466	11437618	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11437619	11437687	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11437688	11437837	1	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11437688	11437837	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11437838	11437994	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11437995	11438020	0.54	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11437995	11438020	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11438021	11438120	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11438121	11438156	0.32	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11438121	11438156	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11438157	11438239	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11438240	11439668	0.95	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11438240	11439668	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11439669	11440346	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11440347	11440455	0.55	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11440347	11440455	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11440456	11440649	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11440650	11440791	0.68	+	2	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11440650	11440791	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11440792	11440872	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11440873	11440921	1	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11440873	11440921	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11440922	11441118	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11441119	11441570	1	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11441119	11441570	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11441571	11441681	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11441682	11441780	0.98	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11441682	11441780	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11441781	11441887	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11441888	11442179	0.99	+	1	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11441888	11442179	.	+	.	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	stop_codon	11442180	11442182	.	+	0	transcript_id "Phchi.S1G177800.t1"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	transcript	11433562	11442179	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	start_codon	11433562	11433564	.	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11433562	11433644	1	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11433562	11433644	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11433645	11433737	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11433738	11433778	0.99	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11433738	11433778	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11433779	11433888	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11433889	11434018	0.99	+	2	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11433889	11434018	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11434019	11434203	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11434204	11434233	0.32	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11434204	11434233	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11434234	11434312	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11434313	11434361	0.32	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11434313	11434361	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11434362	11434465	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11434466	11437618	0.39	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11434466	11437618	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11437619	11437687	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11437688	11437837	1	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11437688	11437837	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11437838	11437994	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11437995	11438020	0.47	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11437995	11438020	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11438021	11438120	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11438121	11438156	0.29	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11438121	11438156	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11438157	11438239	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11438240	11439668	0.94	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11438240	11439668	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11439669	11440346	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11440347	11440455	0.51	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11440347	11440455	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11440456	11440649	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11440650	11440791	0.6	+	2	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11440650	11440791	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11440792	11440872	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11440873	11440921	1	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11440873	11440921	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11440922	11441118	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11441119	11441570	1	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11441119	11441570	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11441571	11441681	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11441682	11441780	0.95	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11441682	11441780	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	intron	11441781	11441887	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	CDS	11441888	11442179	1	+	1	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	exon	11441888	11442179	.	+	.	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
Phchi.S1	AUGUSTUS	stop_codon	11442180	11442182	.	+	0	transcript_id "Phchi.S1G177800.t2"; gene_id "Phchi.S1G177800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg534.t1 is derived from g10316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3878792	3879510	.	-	.	Phchi.S6G049300
Phchi.S6	AUGUSTUS	transcript	3878792	3879510	.	-	.	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	stop_codon	3878789	3878791	.	-	0	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	CDS	3878792	3879011	0.38	-	1	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	exon	3878792	3879011	.	-	.	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	intron	3879012	3879115	.	-	.	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	CDS	3879116	3879510	0.73	-	0	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	exon	3879116	3879510	.	-	.	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
Phchi.S6	AUGUSTUS	start_codon	3879508	3879510	.	-	0	transcript_id "Phchi.S6G049300.t1"; gene_id "Phchi.S6G049300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1355.t1 is derived from g14422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C23	AUGUSTUS	gene	63443	64555	.	+	.	Phchi.C23G000400
Phchi.C23	AUGUSTUS	transcript	63443	64555	.	+	.	transcript_id "Phchi.C23G000400.t1"; gene_id "Phchi.C23G000400"
Phchi.C23	AUGUSTUS	start_codon	63443	63445	.	+	0	transcript_id "Phchi.C23G000400.t1"; gene_id "Phchi.C23G000400"
Phchi.C23	AUGUSTUS	CDS	63443	64555	0.8	+	0	transcript_id "Phchi.C23G000400.t1"; gene_id "Phchi.C23G000400"
Phchi.C23	AUGUSTUS	exon	63443	64555	.	+	.	transcript_id "Phchi.C23G000400.t1"; gene_id "Phchi.C23G000400"
Phchi.C23	AUGUSTUS	stop_codon	64556	64558	.	+	0	transcript_id "Phchi.C23G000400.t1"; gene_id "Phchi.C23G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11596.t1 is derived from g15647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7270593	7271384	.	+	.	Phchi.S4G117800
Phchi.S4	AUGUSTUS	transcript	7270593	7271384	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	start_codon	7270593	7270595	.	+	0	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	CDS	7270593	7270650	0.59	+	0	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	exon	7270593	7270650	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	intron	7270651	7270728	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	CDS	7270729	7270834	1	+	2	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	exon	7270729	7270834	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	intron	7270835	7270921	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	CDS	7270922	7270987	1	+	1	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	exon	7270922	7270987	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	intron	7270988	7271074	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	CDS	7271075	7271272	1	+	1	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	exon	7271075	7271272	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	intron	7271273	7271353	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	CDS	7271354	7271384	1	+	1	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	exon	7271354	7271384	.	+	.	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
Phchi.S4	AUGUSTUS	stop_codon	7271385	7271387	.	+	0	transcript_id "Phchi.S4G117800.t1"; gene_id "Phchi.S4G117800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15100.t1 is derived from g13568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17066998	17069347	.	-	.	Phchi.S3G241900
Phchi.S3	AUGUSTUS	transcript	17066998	17069347	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	stop_codon	17066995	17066997	.	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17066998	17067129	1	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17066998	17067129	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17067130	17067247	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17067248	17067292	1	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17067248	17067292	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17067293	17067440	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17067441	17067575	1	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17067441	17067575	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17067576	17067675	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17067676	17068019	0.68	-	2	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17067676	17068019	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17068020	17068162	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17068163	17068372	0.75	-	2	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17068163	17068372	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17068373	17068490	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17068491	17068593	1	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17068491	17068593	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17068594	17068717	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17068718	17068834	1	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17068718	17068834	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	intron	17068835	17068942	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	CDS	17068943	17069347	0.99	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	exon	17068943	17069347	.	-	.	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
Phchi.S3	AUGUSTUS	start_codon	17069345	17069347	.	-	0	transcript_id "Phchi.S3G241900.t1"; gene_id "Phchi.S3G241900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14571.t1 is derived from g13039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13539175	13540060	.	-	.	Phchi.S3G189000
Phchi.S3	AUGUSTUS	transcript	13539175	13540060	.	-	.	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	stop_codon	13539172	13539174	.	-	0	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	CDS	13539175	13539522	1	-	0	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	exon	13539175	13539522	.	-	.	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	intron	13539523	13539600	.	-	.	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	CDS	13539601	13539882	1	-	0	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	exon	13539601	13539882	.	-	.	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	intron	13539883	13539973	.	-	.	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	CDS	13539974	13540060	0.99	-	0	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	exon	13539974	13540060	.	-	.	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
Phchi.S3	AUGUSTUS	start_codon	13540058	13540060	.	-	0	transcript_id "Phchi.S3G189000.t1"; gene_id "Phchi.S3G189000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15836.t1 is derived from g14306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21659179	21662460	.	-	.	Phchi.S3G315500
Phchi.S3	AUGUSTUS	transcript	21659179	21662460	.	-	.	transcript_id "Phchi.S3G315500.t1"; gene_id "Phchi.S3G315500"
Phchi.S3	AUGUSTUS	stop_codon	21659176	21659178	.	-	0	transcript_id "Phchi.S3G315500.t1"; gene_id "Phchi.S3G315500"
Phchi.S3	AUGUSTUS	CDS	21659179	21662460	0.56	-	0	transcript_id "Phchi.S3G315500.t1"; gene_id "Phchi.S3G315500"
Phchi.S3	AUGUSTUS	exon	21659179	21662460	.	-	.	transcript_id "Phchi.S3G315500.t1"; gene_id "Phchi.S3G315500"
Phchi.S3	AUGUSTUS	start_codon	21662458	21662460	.	-	0	transcript_id "Phchi.S3G315500.t1"; gene_id "Phchi.S3G315500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13280.t1 is derived from g11745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5144127	5144481	.	+	.	Phchi.S3G059900
Phchi.S3	AUGUSTUS	transcript	5144127	5144481	.	+	.	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	start_codon	5144127	5144129	.	+	0	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	CDS	5144127	5144274	0.94	+	0	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	exon	5144127	5144274	.	+	.	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	intron	5144275	5144395	.	+	.	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	CDS	5144396	5144481	0.38	+	2	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	exon	5144396	5144481	.	+	.	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
Phchi.S3	AUGUSTUS	stop_codon	5144482	5144484	.	+	0	transcript_id "Phchi.S3G059900.t1"; gene_id "Phchi.S3G059900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12333.t1 is derived from g8009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11000739	11003381	.	-	.	Phchi.S2G041300
Phchi.S2	AUGUSTUS	transcript	11000739	11003381	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	stop_codon	11000736	11000738	.	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11000739	11000870	1	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11000739	11000870	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	intron	11000871	11001018	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11001019	11001351	0.92	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11001019	11001351	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	intron	11001352	11001519	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11001520	11001910	1	-	1	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11001520	11001910	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	intron	11001911	11002119	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11002120	11002232	1	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11002120	11002232	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	intron	11002233	11002324	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11002325	11002468	1	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11002325	11002468	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	intron	11002469	11002550	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11002551	11002682	1	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11002551	11002682	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	intron	11002683	11002766	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	CDS	11002767	11003381	1	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	exon	11002767	11003381	.	-	.	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
Phchi.S2	AUGUSTUS	start_codon	11003379	11003381	.	-	0	transcript_id "Phchi.S2G041300.t1"; gene_id "Phchi.S2G041300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6703.t1 is derived from g3875.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24632235	24634758	.	+	.	Phchi.S1G386200
Phchi.S1	AUGUSTUS	transcript	24632235	24634758	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	start_codon	24632235	24632237	.	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24632235	24632742	0.85	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24632235	24632742	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24632743	24632872	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24632873	24633132	1	+	2	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24632873	24633132	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633133	24633250	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24633251	24633328	1	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24633251	24633328	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633329	24633422	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24633423	24633581	1	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24633423	24633581	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633582	24633739	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24633740	24633805	1	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24633740	24633805	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633806	24634007	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24634008	24634073	1	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24634008	24634073	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24634074	24634157	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24634158	24634229	1	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24634158	24634229	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24634230	24634317	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24634318	24634758	1	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24634318	24634758	.	+	.	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	stop_codon	24634759	24634761	.	+	0	transcript_id "Phchi.S1G386200.t1"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	transcript	24632235	24634758	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	start_codon	24632235	24632237	.	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24632235	24632742	0.83	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24632235	24632742	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24632743	24632872	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24632873	24633132	1	+	2	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24632873	24633132	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633133	24633250	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24633251	24633328	1	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24633251	24633328	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633329	24633422	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24633423	24633581	1	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24633423	24633581	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633582	24633739	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24633740	24633805	1	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24633740	24633805	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24633806	24634007	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24634008	24634073	1	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24634008	24634073	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24634074	24634157	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24634158	24634226	1	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24634158	24634226	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	intron	24634227	24634317	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	CDS	24634318	24634758	1	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	exon	24634318	24634758	.	+	.	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
Phchi.S1	AUGUSTUS	stop_codon	24634759	24634761	.	+	0	transcript_id "Phchi.S1G386200.t2"; gene_id "Phchi.S1G386200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12113.t1 is derived from g7789.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3573864	3579001	.	-	.	Phchi.S2G019300
Phchi.S2	AUGUSTUS	transcript	3573864	3579001	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	stop_codon	3573861	3573863	.	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3573864	3574007	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3573864	3574007	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3574008	3574125	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3574126	3574260	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3574126	3574260	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3574261	3574340	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3574341	3574523	0.99	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3574341	3574523	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3574524	3574627	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3574628	3574708	0.99	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3574628	3574708	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3574709	3574853	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3574854	3574934	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3574854	3574934	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3574935	3575055	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3575056	3575127	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3575056	3575127	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3575128	3575299	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3575300	3575364	1	-	2	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3575300	3575364	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3575365	3575505	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3575506	3575578	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3575506	3575578	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3575579	3575697	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3575698	3575790	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3575698	3575790	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3575791	3575871	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3575872	3575946	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3575872	3575946	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3575947	3576180	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3576181	3576213	0.7	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3576181	3576213	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3576214	3576295	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3576296	3576358	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3576296	3576358	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3576359	3576490	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3576491	3576580	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3576491	3576580	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3576581	3576764	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3576765	3576831	1	-	1	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3576765	3576831	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3576832	3577011	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3577012	3577139	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3577012	3577139	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3577140	3577219	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3577220	3577346	1	-	1	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3577220	3577346	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3577347	3577462	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3577463	3577561	1	-	1	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3577463	3577561	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3577562	3577673	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3577674	3577748	1	-	1	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3577674	3577748	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3577749	3577851	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3577852	3578063	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3577852	3578063	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3578064	3578189	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3578190	3578252	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3578190	3578252	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3578253	3578344	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3578345	3578401	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3578345	3578401	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3578402	3578502	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3578503	3578628	1	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3578503	3578628	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3578629	3578702	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3578703	3578800	1	-	2	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3578703	3578800	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	intron	3578801	3578892	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	CDS	3578893	3579001	0.52	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	exon	3578893	3579001	.	-	.	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
Phchi.S2	AUGUSTUS	start_codon	3578999	3579001	.	-	0	transcript_id "Phchi.S2G019300.t1"; gene_id "Phchi.S2G019300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12704.t1 is derived from g11169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	644235	651064	.	-	.	Phchi.S3G002300
Phchi.S3	AUGUSTUS	transcript	644235	651064	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	stop_codon	644232	644234	.	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	644235	644408	0.99	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	644235	644408	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	644409	644513	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	644514	644628	0.99	-	1	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	644514	644628	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	644629	644842	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	644843	645249	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	644843	645249	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	645250	645426	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	645427	645561	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	645427	645561	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	645562	645655	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	645656	645984	1	-	2	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	645656	645984	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	645985	646072	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	646073	646315	1	-	2	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	646073	646315	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	646316	646413	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	646414	646940	0.93	-	1	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	646414	646940	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	646941	647061	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	647062	647145	1	-	1	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	647062	647145	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	647146	647257	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	647258	647349	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	647258	647349	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	647350	647437	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	647438	647521	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	647438	647521	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	647522	647637	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	647638	647817	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	647638	647817	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	647818	647897	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	647898	647942	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	647898	647942	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	647943	648033	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	648034	648351	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	648034	648351	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	648352	648550	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	648551	648776	1	-	1	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	648551	648776	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	648777	648949	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	648950	649053	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	648950	649053	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	649054	649219	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	649220	649291	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	649220	649291	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	649292	649466	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	649467	649598	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	649467	649598	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	649599	649784	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	649785	649886	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	649785	649886	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	649887	650009	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	650010	650093	0.91	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	650010	650093	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	650094	650201	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	650202	650292	1	-	1	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	650202	650292	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	650293	650379	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	650380	650453	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	650380	650453	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	650454	650592	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	650593	650613	1	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	650593	650613	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	650614	650750	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	650751	650885	0.98	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	650751	650885	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	intron	650886	651004	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	CDS	651005	651064	0.98	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	exon	651005	651064	.	-	.	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
Phchi.S3	AUGUSTUS	start_codon	651062	651064	.	-	0	transcript_id "Phchi.S3G002300.t1"; gene_id "Phchi.S3G002300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8011.t1 is derived from g5186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32470458	32472798	.	+	.	Phchi.S1G517000
Phchi.S1	AUGUSTUS	transcript	32470458	32472798	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	start_codon	32470458	32470460	.	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32470458	32470487	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32470458	32470487	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32470488	32470643	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32470644	32470887	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32470644	32470887	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32470888	32470967	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32470968	32471097	1	+	2	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32470968	32471097	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32471098	32471248	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32471249	32471360	1	+	1	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32471249	32471360	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32471361	32471447	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32471448	32471699	0.98	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32471448	32471699	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32471700	32471812	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32471813	32471929	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32471813	32471929	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32471930	32472093	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32472094	32472201	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32472094	32472201	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32472202	32472322	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32472323	32472376	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32472323	32472376	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32472377	32472468	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32472469	32472621	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32472469	32472621	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	intron	32472622	32472720	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	CDS	32472721	32472798	1	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	exon	32472721	32472798	.	+	.	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
Phchi.S1	AUGUSTUS	stop_codon	32472799	32472801	.	+	0	transcript_id "Phchi.S1G517000.t1"; gene_id "Phchi.S1G517000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12146.t1 is derived from g7822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4901341	4903244	.	-	.	Phchi.S2G022600
Phchi.S2	AUGUSTUS	transcript	4901341	4903244	.	-	.	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	stop_codon	4901338	4901340	.	-	0	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	CDS	4901341	4902297	0.95	-	0	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	exon	4901341	4902297	.	-	.	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	intron	4902298	4902399	.	-	.	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	CDS	4902400	4902873	0.86	-	0	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	exon	4902400	4902873	.	-	.	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	intron	4902874	4903010	.	-	.	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	CDS	4903011	4903244	0.97	-	0	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	exon	4903011	4903244	.	-	.	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
Phchi.S2	AUGUSTUS	start_codon	4903242	4903244	.	-	0	transcript_id "Phchi.S2G022600.t1"; gene_id "Phchi.S2G022600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9619.t1 is derived from g6795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42949390	42951006	.	-	.	Phchi.S1G677800
Phchi.S1	AUGUSTUS	transcript	42949390	42951006	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	stop_codon	42949387	42949389	.	-	0	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42949390	42949435	0.82	-	1	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42949390	42949435	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42949436	42949539	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42949540	42949606	0.69	-	2	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42949540	42949606	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42949607	42949711	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42949712	42949889	0.71	-	0	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42949712	42949889	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42949890	42950052	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950053	42950099	1	-	2	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950053	42950099	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950100	42950180	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950181	42950342	1	-	2	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950181	42950342	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950343	42950517	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950518	42950638	1	-	0	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950518	42950638	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950639	42950799	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950800	42951006	0.97	-	0	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950800	42951006	.	-	.	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	start_codon	42951004	42951006	.	-	0	transcript_id "Phchi.S1G677800.t1"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	transcript	42949390	42951006	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	stop_codon	42949387	42949389	.	-	0	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42949390	42949435	0.87	-	1	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42949390	42949435	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42949436	42949539	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42949540	42949606	0.74	-	2	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42949540	42949606	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42949607	42949711	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42949712	42949889	0.74	-	0	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42949712	42949889	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42949890	42950052	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950053	42950099	1	-	2	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950053	42950099	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950100	42950180	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950181	42950228	0.59	-	2	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950181	42950228	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950229	42950322	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950323	42950342	0.93	-	1	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950323	42950342	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950343	42950471	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950472	42950638	0.99	-	0	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950472	42950638	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	intron	42950639	42950799	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	CDS	42950800	42951006	0.99	-	0	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	exon	42950800	42951006	.	-	.	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
Phchi.S1	AUGUSTUS	start_codon	42951004	42951006	.	-	0	transcript_id "Phchi.S1G677800.t2"; gene_id "Phchi.S1G677800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10791.t1 is derived from g14841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2136150	2136665	.	-	.	Phchi.S4G037300
Phchi.S4	AUGUSTUS	transcript	2136150	2136665	.	-	.	transcript_id "Phchi.S4G037300.t1"; gene_id "Phchi.S4G037300"
Phchi.S4	AUGUSTUS	stop_codon	2136147	2136149	.	-	0	transcript_id "Phchi.S4G037300.t1"; gene_id "Phchi.S4G037300"
Phchi.S4	AUGUSTUS	CDS	2136150	2136665	0.74	-	0	transcript_id "Phchi.S4G037300.t1"; gene_id "Phchi.S4G037300"
Phchi.S4	AUGUSTUS	exon	2136150	2136665	.	-	.	transcript_id "Phchi.S4G037300.t1"; gene_id "Phchi.S4G037300"
Phchi.S4	AUGUSTUS	start_codon	2136663	2136665	.	-	0	transcript_id "Phchi.S4G037300.t1"; gene_id "Phchi.S4G037300"
# This transcript jg5898.t2 is derived from g3068.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5899.t1 is derived from g3069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19661343	19663414	.	-	.	Phchi.S1G305800
Phchi.S1	AUGUSTUS	transcript	19661343	19663414	.	-	.	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	stop_codon	19661340	19661342	.	-	0	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	CDS	19661343	19663062	0.81	-	1	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	exon	19661343	19663062	.	-	.	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	intron	19663063	19663148	.	-	.	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	CDS	19663149	19663414	0.87	-	0	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	exon	19663149	19663414	.	-	.	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
Phchi.S1	AUGUSTUS	start_codon	19663412	19663414	.	-	0	transcript_id "Phchi.S1G305800.t1"; gene_id "Phchi.S1G305800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8575.t1 is derived from g5750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36703481	36706779	.	+	.	Phchi.S1G573400
Phchi.S1	AUGUSTUS	transcript	36703481	36706779	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	start_codon	36703481	36703483	.	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36703481	36703575	0.56	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36703481	36703575	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36703576	36703672	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36703673	36703745	1	+	1	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36703673	36703745	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36703746	36703819	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36703820	36703891	1	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36703820	36703891	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36703892	36703982	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36703983	36704024	0.93	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36703983	36704024	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36704025	36704127	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36704128	36704241	0.98	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36704128	36704241	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36704242	36704342	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36704343	36704414	0.87	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36704343	36704414	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36704415	36704537	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36704538	36704684	0.89	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36704538	36704684	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36704685	36704786	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36704787	36704942	0.92	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36704787	36704942	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36704943	36705134	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36705135	36705245	1	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36705135	36705245	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36705246	36705372	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36705373	36705462	1	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36705373	36705462	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36705463	36705622	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36705623	36705700	1	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36705623	36705700	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36705701	36705785	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36705786	36705881	1	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36705786	36705881	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36705882	36706021	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36706022	36706093	1	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36706022	36706093	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36706094	36706255	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36706256	36706368	0.6	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36706256	36706368	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36706369	36706450	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36706451	36706528	0.6	+	1	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36706451	36706528	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	intron	36706529	36706670	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	CDS	36706671	36706779	1	+	1	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	exon	36706671	36706779	.	+	.	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
Phchi.S1	AUGUSTUS	stop_codon	36706780	36706782	.	+	0	transcript_id "Phchi.S1G573400.t1"; gene_id "Phchi.S1G573400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15905.t1 is derived from g14375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22086997	22089208	.	+	.	Phchi.S3G322400
Phchi.S3	AUGUSTUS	transcript	22086997	22089208	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	start_codon	22086997	22086999	.	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22086997	22087398	0.99	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22086997	22087398	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22087399	22087519	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22087520	22087558	1	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22087520	22087558	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22087559	22087701	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22087702	22087825	1	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22087702	22087825	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22087826	22087947	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22087948	22088009	1	+	2	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22087948	22088009	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22088010	22088142	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22088143	22088210	1	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22088143	22088210	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22088211	22088309	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22088310	22088359	1	+	1	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22088310	22088359	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22088360	22088471	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22088472	22088541	1	+	2	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22088472	22088541	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22088542	22088678	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22088679	22088802	1	+	1	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22088679	22088802	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22088803	22088905	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22088906	22089022	1	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22088906	22089022	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	intron	22089023	22089097	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	CDS	22089098	22089208	1	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	exon	22089098	22089208	.	+	.	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
Phchi.S3	AUGUSTUS	stop_codon	22089209	22089211	.	+	0	transcript_id "Phchi.S3G322400.t1"; gene_id "Phchi.S3G322400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14825.t1 is derived from g13293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14899261	14902320	.	+	.	Phchi.S3G214400
Phchi.S3	AUGUSTUS	transcript	14899261	14902320	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	start_codon	14899261	14899263	.	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14899261	14899303	0.96	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14899261	14899303	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14899304	14899458	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14899459	14899480	0.97	+	2	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14899459	14899480	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14899481	14899575	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14899576	14899928	0.98	+	1	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14899576	14899928	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14899929	14900012	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14900013	14900347	1	+	2	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14900013	14900347	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14900348	14900539	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14900540	14900747	1	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14900540	14900747	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14900748	14900840	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14900841	14900941	1	+	2	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14900841	14900941	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14900942	14901029	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14901030	14901179	1	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14901030	14901179	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14901180	14901289	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14901290	14901353	1	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14901290	14901353	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14901354	14901486	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14901487	14901584	1	+	2	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14901487	14901584	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	intron	14901585	14901675	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	CDS	14901676	14902320	1	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	exon	14901676	14902320	.	+	.	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
Phchi.S3	AUGUSTUS	stop_codon	14902321	14902323	.	+	0	transcript_id "Phchi.S3G214400.t1"; gene_id "Phchi.S3G214400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12345.t1 is derived from g8021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12215805	12216920	.	-	.	Phchi.S2G042500
Phchi.S2	AUGUSTUS	transcript	12215805	12216920	.	-	.	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	stop_codon	12215802	12215804	.	-	0	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	CDS	12215805	12215894	0.82	-	0	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	exon	12215805	12215894	.	-	.	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	intron	12215895	12216057	.	-	.	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	CDS	12216058	12216328	0.87	-	1	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	exon	12216058	12216328	.	-	.	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	intron	12216329	12216516	.	-	.	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	CDS	12216517	12216920	0.79	-	0	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	exon	12216517	12216920	.	-	.	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
Phchi.S2	AUGUSTUS	start_codon	12216918	12216920	.	-	0	transcript_id "Phchi.S2G042500.t1"; gene_id "Phchi.S2G042500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12959.t1 is derived from g11424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3333074	3334441	.	+	.	Phchi.S3G027800
Phchi.S3	AUGUSTUS	transcript	3333074	3334441	.	+	.	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	start_codon	3333074	3333076	.	+	0	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	CDS	3333074	3333183	0.99	+	0	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	exon	3333074	3333183	.	+	.	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	intron	3333184	3333414	.	+	.	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	CDS	3333415	3334441	1	+	1	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	exon	3333415	3334441	.	+	.	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
Phchi.S3	AUGUSTUS	stop_codon	3334442	3334444	.	+	0	transcript_id "Phchi.S3G027800.t1"; gene_id "Phchi.S3G027800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg313.t1 is derived from g10095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2229027	2230634	.	-	.	Phchi.S6G027200
Phchi.S6	AUGUSTUS	transcript	2229027	2230634	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	stop_codon	2229024	2229026	.	-	0	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2229027	2229155	1	-	0	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2229027	2229155	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	intron	2229156	2229253	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2229254	2229451	0.92	-	0	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2229254	2229451	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	intron	2229452	2229546	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2229547	2229666	0.46	-	0	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2229547	2229666	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	intron	2229667	2229767	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2229768	2229885	1	-	1	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2229768	2229885	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	intron	2229886	2229999	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2230000	2230206	0.43	-	1	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2230000	2230206	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	intron	2230207	2230396	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2230397	2230508	0.25	-	2	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2230397	2230508	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	intron	2230509	2230591	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	CDS	2230592	2230634	0.31	-	0	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	exon	2230592	2230634	.	-	.	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
Phchi.S6	AUGUSTUS	start_codon	2230632	2230634	.	-	0	transcript_id "Phchi.S6G027200.t1"; gene_id "Phchi.S6G027200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3549.t1 is derived from g718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4427173	4427628	.	-	.	Phchi.S1G070800
Phchi.S1	AUGUSTUS	transcript	4427173	4427628	.	-	.	transcript_id "Phchi.S1G070800.t1"; gene_id "Phchi.S1G070800"
Phchi.S1	AUGUSTUS	stop_codon	4427170	4427172	.	-	0	transcript_id "Phchi.S1G070800.t1"; gene_id "Phchi.S1G070800"
Phchi.S1	AUGUSTUS	CDS	4427173	4427628	0.86	-	0	transcript_id "Phchi.S1G070800.t1"; gene_id "Phchi.S1G070800"
Phchi.S1	AUGUSTUS	exon	4427173	4427628	.	-	.	transcript_id "Phchi.S1G070800.t1"; gene_id "Phchi.S1G070800"
Phchi.S1	AUGUSTUS	start_codon	4427626	4427628	.	-	0	transcript_id "Phchi.S1G070800.t1"; gene_id "Phchi.S1G070800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10160.t1 is derived from g7336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46042393	46043985	.	+	.	Phchi.S1G731900
Phchi.S1	AUGUSTUS	transcript	46042393	46043985	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	start_codon	46042393	46042395	.	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46042393	46042476	1	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46042393	46042476	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46042477	46042562	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46042563	46042691	1	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46042563	46042691	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46042692	46042890	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46042891	46043027	1	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46042891	46043027	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46043028	46043177	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46043178	46043347	1	+	1	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46043178	46043347	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46043348	46043441	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46043442	46043471	1	+	2	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46043442	46043471	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46043472	46043566	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46043567	46043598	1	+	2	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46043567	46043598	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46043599	46043698	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46043699	46043818	1	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46043699	46043818	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	intron	46043819	46043895	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	CDS	46043896	46043985	1	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	exon	46043896	46043985	.	+	.	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
Phchi.S1	AUGUSTUS	stop_codon	46043986	46043988	.	+	0	transcript_id "Phchi.S1G731900.t1"; gene_id "Phchi.S1G731900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15322.t1 is derived from g13790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18384525	18385132	.	-	.	Phchi.S3G264100
Phchi.S3	AUGUSTUS	transcript	18384525	18385132	.	-	.	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	stop_codon	18384522	18384524	.	-	0	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	CDS	18384525	18384673	0.87	-	2	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	exon	18384525	18384673	.	-	.	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	intron	18384674	18384751	.	-	.	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	CDS	18384752	18384889	1	-	2	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	exon	18384752	18384889	.	-	.	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	intron	18384890	18384966	.	-	.	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	CDS	18384967	18385132	0.97	-	0	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	exon	18384967	18385132	.	-	.	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
Phchi.S3	AUGUSTUS	start_codon	18385130	18385132	.	-	0	transcript_id "Phchi.S3G264100.t1"; gene_id "Phchi.S3G264100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13085.t1 is derived from g11550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4086965	4089550	.	+	.	Phchi.S3G040400
Phchi.S3	AUGUSTUS	transcript	4086965	4089550	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	start_codon	4086965	4086967	.	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4086965	4087038	0.98	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4086965	4087038	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4087039	4087155	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4087156	4087249	0.99	+	1	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4087156	4087249	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4087250	4087330	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4087331	4087423	0.82	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4087331	4087423	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4087424	4087542	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4087543	4087613	1	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4087543	4087613	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4087614	4087747	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4087748	4087772	1	+	1	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4087748	4087772	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4087773	4087872	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4087873	4087940	1	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4087873	4087940	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4087941	4088021	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4088022	4088091	1	+	1	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4088022	4088091	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4088092	4088177	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4088178	4088279	1	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4088178	4088279	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4088280	4088369	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4088370	4088492	1	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4088370	4088492	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4088493	4088677	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4088678	4088800	1	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4088678	4088800	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	intron	4088801	4088893	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	CDS	4088894	4089550	1	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	exon	4088894	4089550	.	+	.	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
Phchi.S3	AUGUSTUS	stop_codon	4089551	4089553	.	+	0	transcript_id "Phchi.S3G040400.t1"; gene_id "Phchi.S3G040400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7139.t1 is derived from g4311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27139302	27140882	.	+	.	Phchi.S1G429800
Phchi.S1	AUGUSTUS	transcript	27139302	27140882	.	+	.	transcript_id "Phchi.S1G429800.t1"; gene_id "Phchi.S1G429800"
Phchi.S1	AUGUSTUS	start_codon	27139302	27139304	.	+	0	transcript_id "Phchi.S1G429800.t1"; gene_id "Phchi.S1G429800"
Phchi.S1	AUGUSTUS	CDS	27139302	27140882	0.66	+	0	transcript_id "Phchi.S1G429800.t1"; gene_id "Phchi.S1G429800"
Phchi.S1	AUGUSTUS	exon	27139302	27140882	.	+	.	transcript_id "Phchi.S1G429800.t1"; gene_id "Phchi.S1G429800"
Phchi.S1	AUGUSTUS	stop_codon	27140883	27140885	.	+	0	transcript_id "Phchi.S1G429800.t1"; gene_id "Phchi.S1G429800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15017.t1 is derived from g13485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16544655	16545005	.	-	.	Phchi.S3G233600
Phchi.S3	AUGUSTUS	transcript	16544655	16545005	.	-	.	transcript_id "Phchi.S3G233600.t1"; gene_id "Phchi.S3G233600"
Phchi.S3	AUGUSTUS	stop_codon	16544652	16544654	.	-	0	transcript_id "Phchi.S3G233600.t1"; gene_id "Phchi.S3G233600"
Phchi.S3	AUGUSTUS	CDS	16544655	16545005	0.48	-	0	transcript_id "Phchi.S3G233600.t1"; gene_id "Phchi.S3G233600"
Phchi.S3	AUGUSTUS	exon	16544655	16545005	.	-	.	transcript_id "Phchi.S3G233600.t1"; gene_id "Phchi.S3G233600"
Phchi.S3	AUGUSTUS	start_codon	16545003	16545005	.	-	0	transcript_id "Phchi.S3G233600.t1"; gene_id "Phchi.S3G233600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8488.t1 is derived from g5663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36203150	36208850	.	-	.	Phchi.S1G564700
Phchi.S1	AUGUSTUS	transcript	36203150	36208850	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	stop_codon	36203147	36203149	.	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36203150	36203284	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36203150	36203284	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36203285	36203366	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36203367	36203585	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36203367	36203585	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36203586	36203662	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36203663	36203824	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36203663	36203824	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36203825	36203909	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36203910	36204188	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36203910	36204188	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36204189	36204277	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36204278	36204475	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36204278	36204475	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36204476	36204564	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36204565	36204712	1	-	1	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36204565	36204712	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36204713	36204858	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36204859	36204970	1	-	2	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36204859	36204970	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36204971	36205053	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36205054	36205246	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36205054	36205246	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36205247	36205330	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36205331	36205495	0.9	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36205331	36205495	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36205496	36205611	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36205612	36207107	0.83	-	2	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36205612	36207107	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36207108	36207202	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36207203	36207238	0.76	-	2	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36207203	36207238	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36207239	36207328	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36207329	36207663	1	-	1	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36207329	36207663	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	intron	36207664	36207750	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	CDS	36207751	36208850	1	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	exon	36207751	36208850	.	-	.	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
Phchi.S1	AUGUSTUS	start_codon	36208848	36208850	.	-	0	transcript_id "Phchi.S1G564700.t1"; gene_id "Phchi.S1G564700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13662.t1 is derived from g12129.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8052862	8055096	.	+	.	Phchi.S3G098100
Phchi.S3	AUGUSTUS	transcript	8052862	8055096	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	start_codon	8052862	8052864	.	+	0	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	CDS	8052862	8052943	0.85	+	0	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	exon	8052862	8052943	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	intron	8052944	8053017	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	CDS	8053018	8053130	1	+	2	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	exon	8053018	8053130	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	intron	8053131	8053298	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	CDS	8053299	8053468	0.84	+	0	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	exon	8053299	8053468	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	intron	8053469	8053580	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	CDS	8053581	8054334	0.66	+	1	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	exon	8053581	8054334	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	intron	8054335	8054535	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	CDS	8054536	8055096	0.59	+	0	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	exon	8054536	8055096	.	+	.	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
Phchi.S3	AUGUSTUS	stop_codon	8055097	8055099	.	+	0	transcript_id "Phchi.S3G098100.t1"; gene_id "Phchi.S3G098100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11300.t1 is derived from g15350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5294646	5295506	.	-	.	Phchi.S4G088200
Phchi.S4	AUGUSTUS	transcript	5294646	5295506	.	-	.	transcript_id "Phchi.S4G088200.t1"; gene_id "Phchi.S4G088200"
Phchi.S4	AUGUSTUS	stop_codon	5294643	5294645	.	-	0	transcript_id "Phchi.S4G088200.t1"; gene_id "Phchi.S4G088200"
Phchi.S4	AUGUSTUS	CDS	5294646	5295506	1	-	0	transcript_id "Phchi.S4G088200.t1"; gene_id "Phchi.S4G088200"
Phchi.S4	AUGUSTUS	exon	5294646	5295506	.	-	.	transcript_id "Phchi.S4G088200.t1"; gene_id "Phchi.S4G088200"
Phchi.S4	AUGUSTUS	start_codon	5295504	5295506	.	-	0	transcript_id "Phchi.S4G088200.t1"; gene_id "Phchi.S4G088200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1899.t1 is derived from g8819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3775108	3777238	.	-	.	Phchi.S5G050800
Phchi.S5	AUGUSTUS	transcript	3775108	3777238	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	stop_codon	3775105	3775107	.	-	0	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	CDS	3775108	3775124	1	-	2	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	exon	3775108	3775124	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	intron	3775125	3775264	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	CDS	3775265	3775353	0.58	-	1	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	exon	3775265	3775353	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	intron	3775354	3775488	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	CDS	3775489	3775625	0.94	-	0	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	exon	3775489	3775625	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	intron	3775626	3775736	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	CDS	3775737	3776035	1	-	2	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	exon	3775737	3776035	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	intron	3776036	3776127	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	CDS	3776128	3776296	1	-	0	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	exon	3776128	3776296	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	intron	3776297	3776407	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	CDS	3776408	3777238	0.81	-	0	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	exon	3776408	3777238	.	-	.	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
Phchi.S5	AUGUSTUS	start_codon	3777236	3777238	.	-	0	transcript_id "Phchi.S5G050800.t1"; gene_id "Phchi.S5G050800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4346.t1 is derived from g1515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9899125	9900606	.	-	.	Phchi.S1G150500
Phchi.S1	AUGUSTUS	transcript	9899125	9900606	.	-	.	transcript_id "Phchi.S1G150500.t1"; gene_id "Phchi.S1G150500"
Phchi.S1	AUGUSTUS	stop_codon	9899122	9899124	.	-	0	transcript_id "Phchi.S1G150500.t1"; gene_id "Phchi.S1G150500"
Phchi.S1	AUGUSTUS	CDS	9899125	9900606	0.74	-	0	transcript_id "Phchi.S1G150500.t1"; gene_id "Phchi.S1G150500"
Phchi.S1	AUGUSTUS	exon	9899125	9900606	.	-	.	transcript_id "Phchi.S1G150500.t1"; gene_id "Phchi.S1G150500"
Phchi.S1	AUGUSTUS	start_codon	9900604	9900606	.	-	0	transcript_id "Phchi.S1G150500.t1"; gene_id "Phchi.S1G150500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12051.t1 is derived from g7726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1030880	1034614	.	-	.	Phchi.S2G013100
Phchi.S2	AUGUSTUS	transcript	1030880	1034614	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	stop_codon	1030877	1030879	.	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1030880	1030969	0.94	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1030880	1030969	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1030970	1031064	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1031065	1031156	0.94	-	2	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1031065	1031156	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1031157	1031275	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1031276	1031373	0.53	-	1	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1031276	1031373	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1031374	1031599	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1031600	1031635	0.48	-	1	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1031600	1031635	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1031636	1031729	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1031730	1031751	0.35	-	2	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1031730	1031751	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1031752	1031875	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1031876	1032075	1	-	1	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1031876	1032075	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1032076	1032233	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1032234	1032389	1	-	1	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1032234	1032389	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1032390	1032470	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1032471	1032682	1	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1032471	1032682	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1032683	1032826	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1032827	1032943	1	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1032827	1032943	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1032944	1033072	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1033073	1033141	0.99	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1033073	1033141	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1033142	1033245	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1033246	1033284	1	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1033246	1033284	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1033285	1033398	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1033399	1033550	0.52	-	2	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1033399	1033550	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1033551	1033653	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1033654	1033918	0.61	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1033654	1033918	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1033919	1034007	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1034008	1034178	1	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1034008	1034178	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	intron	1034179	1034527	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	CDS	1034528	1034614	0.79	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	exon	1034528	1034614	.	-	.	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
Phchi.S2	AUGUSTUS	start_codon	1034612	1034614	.	-	0	transcript_id "Phchi.S2G013100.t1"; gene_id "Phchi.S2G013100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3093.t1 is derived from g262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1726896	1727918	.	+	.	Phchi.S1G025200
Phchi.S1	AUGUSTUS	transcript	1726896	1727918	.	+	.	transcript_id "Phchi.S1G025200.t1"; gene_id "Phchi.S1G025200"
Phchi.S1	AUGUSTUS	start_codon	1726896	1726898	.	+	0	transcript_id "Phchi.S1G025200.t1"; gene_id "Phchi.S1G025200"
Phchi.S1	AUGUSTUS	CDS	1726896	1727918	0.88	+	0	transcript_id "Phchi.S1G025200.t1"; gene_id "Phchi.S1G025200"
Phchi.S1	AUGUSTUS	exon	1726896	1727918	.	+	.	transcript_id "Phchi.S1G025200.t1"; gene_id "Phchi.S1G025200"
Phchi.S1	AUGUSTUS	stop_codon	1727919	1727921	.	+	0	transcript_id "Phchi.S1G025200.t1"; gene_id "Phchi.S1G025200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15554.t1 is derived from g14023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19889834	19891942	.	+	.	Phchi.S3G287300
Phchi.S3	AUGUSTUS	transcript	19889834	19891942	.	+	.	transcript_id "Phchi.S3G287300.t1"; gene_id "Phchi.S3G287300"
Phchi.S3	AUGUSTUS	start_codon	19889834	19889836	.	+	0	transcript_id "Phchi.S3G287300.t1"; gene_id "Phchi.S3G287300"
Phchi.S3	AUGUSTUS	CDS	19889834	19891942	0.96	+	0	transcript_id "Phchi.S3G287300.t1"; gene_id "Phchi.S3G287300"
Phchi.S3	AUGUSTUS	exon	19889834	19891942	.	+	.	transcript_id "Phchi.S3G287300.t1"; gene_id "Phchi.S3G287300"
Phchi.S3	AUGUSTUS	stop_codon	19891943	19891945	.	+	0	transcript_id "Phchi.S3G287300.t1"; gene_id "Phchi.S3G287300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3447.t1 is derived from g616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3790028	3790705	.	+	.	Phchi.S1G060600
Phchi.S1	AUGUSTUS	transcript	3790028	3790705	.	+	.	transcript_id "Phchi.S1G060600.t1"; gene_id "Phchi.S1G060600"
Phchi.S1	AUGUSTUS	start_codon	3790028	3790030	.	+	0	transcript_id "Phchi.S1G060600.t1"; gene_id "Phchi.S1G060600"
Phchi.S1	AUGUSTUS	CDS	3790028	3790705	0.94	+	0	transcript_id "Phchi.S1G060600.t1"; gene_id "Phchi.S1G060600"
Phchi.S1	AUGUSTUS	exon	3790028	3790705	.	+	.	transcript_id "Phchi.S1G060600.t1"; gene_id "Phchi.S1G060600"
Phchi.S1	AUGUSTUS	stop_codon	3790706	3790708	.	+	0	transcript_id "Phchi.S1G060600.t1"; gene_id "Phchi.S1G060600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11055.t1 is derived from g15105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3872363	3874656	.	-	.	Phchi.S4G063700
Phchi.S4	AUGUSTUS	transcript	3872363	3874656	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	stop_codon	3872360	3872362	.	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3872363	3872695	0.98	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3872363	3872695	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	intron	3872696	3872854	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3872855	3872950	1	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3872855	3872950	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	intron	3872951	3873068	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3873069	3873425	1	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3873069	3873425	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	intron	3873426	3873571	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3873572	3873745	0.86	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3873572	3873745	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	intron	3873746	3873834	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3873835	3873994	0.88	-	1	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3873835	3873994	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	intron	3873995	3874145	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3874146	3874298	1	-	1	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3874146	3874298	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	intron	3874299	3874384	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	CDS	3874385	3874656	1	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	exon	3874385	3874656	.	-	.	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
Phchi.S4	AUGUSTUS	start_codon	3874654	3874656	.	-	0	transcript_id "Phchi.S4G063700.t1"; gene_id "Phchi.S4G063700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6828.t1 is derived from g4000.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25437178	25437566	.	-	.	Phchi.S1G398700
Phchi.S1	AUGUSTUS	transcript	25437178	25437566	.	-	.	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	stop_codon	25437175	25437177	.	-	0	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	CDS	25437178	25437267	0.8	-	0	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	exon	25437178	25437267	.	-	.	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	intron	25437268	25437353	.	-	.	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	CDS	25437354	25437566	0.81	-	0	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	exon	25437354	25437566	.	-	.	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
Phchi.S1	AUGUSTUS	start_codon	25437564	25437566	.	-	0	transcript_id "Phchi.S1G398700.t1"; gene_id "Phchi.S1G398700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13955.t1 is derived from g12422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9911817	9912684	.	+	.	Phchi.S3G127400
Phchi.S3	AUGUSTUS	transcript	9911817	9912684	.	+	.	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	start_codon	9911817	9911819	.	+	0	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	CDS	9911817	9912101	1	+	0	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	exon	9911817	9912101	.	+	.	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	intron	9912102	9912259	.	+	.	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	CDS	9912260	9912361	1	+	0	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	exon	9912260	9912361	.	+	.	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	intron	9912362	9912486	.	+	.	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	CDS	9912487	9912684	1	+	0	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	exon	9912487	9912684	.	+	.	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
Phchi.S3	AUGUSTUS	stop_codon	9912685	9912687	.	+	0	transcript_id "Phchi.S3G127400.t1"; gene_id "Phchi.S3G127400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6730.t1 is derived from g3902.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24761453	24764194	.	+	.	Phchi.S1G388900
Phchi.S1	AUGUSTUS	transcript	24761453	24764194	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	start_codon	24761453	24761455	.	+	0	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	CDS	24761453	24761557	0.78	+	0	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	exon	24761453	24761557	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	intron	24761558	24761666	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	CDS	24761667	24762619	0.97	+	0	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	exon	24761667	24762619	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	intron	24762620	24762712	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	CDS	24762713	24762846	0.88	+	1	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	exon	24762713	24762846	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	intron	24762847	24762945	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	CDS	24762946	24763370	0.82	+	2	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	exon	24762946	24763370	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	intron	24763371	24763464	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	CDS	24763465	24763596	0.88	+	0	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	exon	24763465	24763596	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	intron	24763597	24763687	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	CDS	24763688	24764194	0.92	+	0	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	exon	24763688	24764194	.	+	.	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
Phchi.S1	AUGUSTUS	stop_codon	24764195	24764197	.	+	0	transcript_id "Phchi.S1G388900.t1"; gene_id "Phchi.S1G388900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7589.t1 is derived from g4763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30171581	30175085	.	-	.	Phchi.S1G474800
Phchi.S1	AUGUSTUS	transcript	30171581	30175085	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	stop_codon	30171578	30171580	.	-	0	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30171581	30171648	0.98	-	2	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30171581	30171648	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30171649	30171764	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30171765	30171868	0.99	-	1	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30171765	30171868	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30171869	30172001	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30172002	30172176	0.95	-	2	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30172002	30172176	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30172177	30172265	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30172266	30172398	0.99	-	0	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30172266	30172398	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30172399	30172506	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30172507	30172640	0.91	-	2	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30172507	30172640	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30172641	30172751	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30172752	30172963	0.91	-	1	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30172752	30172963	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30172964	30173040	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30173041	30173201	1	-	0	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30173041	30173201	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30173202	30173292	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30173293	30173665	0.69	-	1	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30173293	30173665	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30173666	30173772	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30173773	30173954	0.72	-	0	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30173773	30173954	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30173955	30174067	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30174068	30174687	0.99	-	2	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30174068	30174687	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30174688	30174825	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30174826	30174903	1	-	2	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30174826	30174903	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	intron	30174904	30175024	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	CDS	30175025	30175085	0.7	-	0	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	exon	30175025	30175085	.	-	.	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
Phchi.S1	AUGUSTUS	start_codon	30175083	30175085	.	-	0	transcript_id "Phchi.S1G474800.t1"; gene_id "Phchi.S1G474800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5249.t1 is derived from g2419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15855621	15857366	.	+	.	Phchi.S1G240800
Phchi.S1	AUGUSTUS	transcript	15855621	15857366	.	+	.	transcript_id "Phchi.S1G240800.t1"; gene_id "Phchi.S1G240800"
Phchi.S1	AUGUSTUS	start_codon	15855621	15855623	.	+	0	transcript_id "Phchi.S1G240800.t1"; gene_id "Phchi.S1G240800"
Phchi.S1	AUGUSTUS	CDS	15855621	15857366	0.53	+	0	transcript_id "Phchi.S1G240800.t1"; gene_id "Phchi.S1G240800"
Phchi.S1	AUGUSTUS	exon	15855621	15857366	.	+	.	transcript_id "Phchi.S1G240800.t1"; gene_id "Phchi.S1G240800"
Phchi.S1	AUGUSTUS	stop_codon	15857367	15857369	.	+	0	transcript_id "Phchi.S1G240800.t1"; gene_id "Phchi.S1G240800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13927.t1 is derived from g12394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9724348	9727799	.	-	.	Phchi.S3G124600
Phchi.S3	AUGUSTUS	transcript	9724348	9727799	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	stop_codon	9724345	9724347	.	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9724348	9724432	0.85	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9724348	9724432	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9724433	9724534	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9724535	9724626	1	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9724535	9724626	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9724627	9724791	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9724792	9724866	1	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9724792	9724866	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9724867	9725004	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9725005	9725074	1	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9725005	9725074	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9725075	9725207	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9725208	9725275	1	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9725208	9725275	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9725276	9725385	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9725386	9725494	1	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9725386	9725494	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9725495	9725635	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9725636	9725884	0.99	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9725636	9725884	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9725885	9725960	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9725961	9725976	0.98	-	2	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9725961	9725976	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9725977	9726068	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9726069	9726175	0.98	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9726069	9726175	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9726176	9726443	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9726444	9726537	1	-	2	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9726444	9726537	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9726538	9726618	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9726619	9726689	1	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9726619	9726689	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9726690	9726796	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9726797	9726916	1	-	1	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9726797	9726916	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9726917	9727006	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9727007	9727062	1	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9727007	9727062	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9727063	9727156	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9727157	9727234	1	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9727157	9727234	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	intron	9727235	9727499	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	CDS	9727500	9727799	1	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	exon	9727500	9727799	.	-	.	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
Phchi.S3	AUGUSTUS	start_codon	9727797	9727799	.	-	0	transcript_id "Phchi.S3G124600.t1"; gene_id "Phchi.S3G124600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11347.t1 is derived from g15397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5671099	5672429	.	-	.	Phchi.S4G092900
Phchi.S4	AUGUSTUS	transcript	5671099	5672429	.	-	.	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	stop_codon	5671096	5671098	.	-	0	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	CDS	5671099	5671805	0.53	-	2	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	exon	5671099	5671805	.	-	.	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	intron	5671806	5671999	.	-	.	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	CDS	5672000	5672429	0.37	-	0	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	exon	5672000	5672429	.	-	.	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
Phchi.S4	AUGUSTUS	start_codon	5672427	5672429	.	-	0	transcript_id "Phchi.S4G092900.t1"; gene_id "Phchi.S4G092900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5741.t1 is derived from g2911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18680287	18682018	.	+	.	Phchi.S1G290000
Phchi.S1	AUGUSTUS	transcript	18680287	18682018	.	+	.	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	start_codon	18680287	18680289	.	+	0	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	CDS	18680287	18680943	0.47	+	0	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	exon	18680287	18680943	.	+	.	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	intron	18680944	18681131	.	+	.	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	CDS	18681132	18681321	0.96	+	0	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	exon	18681132	18681321	.	+	.	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	intron	18681322	18681428	.	+	.	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	CDS	18681429	18682018	0.97	+	2	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	exon	18681429	18682018	.	+	.	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
Phchi.S1	AUGUSTUS	stop_codon	18682019	18682021	.	+	0	transcript_id "Phchi.S1G290000.t1"; gene_id "Phchi.S1G290000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3432.t1 is derived from g601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3614455	3615131	.	+	.	Phchi.S1G059100
Phchi.S1	AUGUSTUS	transcript	3614455	3615131	.	+	.	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	start_codon	3614455	3614457	.	+	0	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	CDS	3614455	3614855	0.47	+	0	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	exon	3614455	3614855	.	+	.	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	intron	3614856	3614998	.	+	.	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	CDS	3614999	3615131	0.48	+	1	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	exon	3614999	3615131	.	+	.	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
Phchi.S1	AUGUSTUS	stop_codon	3615132	3615134	.	+	0	transcript_id "Phchi.S1G059100.t1"; gene_id "Phchi.S1G059100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6705.t1 is derived from g3877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24637422	24638639	.	+	.	Phchi.S1G386400
Phchi.S1	AUGUSTUS	transcript	24637422	24638639	.	+	.	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	start_codon	24637422	24637424	.	+	0	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	CDS	24637422	24638149	0.87	+	0	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	exon	24637422	24638149	.	+	.	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	intron	24638150	24638236	.	+	.	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	CDS	24638237	24638639	0.91	+	1	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	exon	24638237	24638639	.	+	.	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
Phchi.S1	AUGUSTUS	stop_codon	24638640	24638642	.	+	0	transcript_id "Phchi.S1G386400.t1"; gene_id "Phchi.S1G386400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3347.t1 is derived from g516.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3054214	3055970	.	+	.	Phchi.S1G050600
Phchi.S1	AUGUSTUS	transcript	3054214	3055970	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	start_codon	3054214	3054216	.	+	0	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	CDS	3054214	3054339	0.95	+	0	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	exon	3054214	3054339	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	intron	3054340	3054595	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	CDS	3054596	3054737	1	+	0	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	exon	3054596	3054737	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	intron	3054738	3054825	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	CDS	3054826	3055106	1	+	2	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	exon	3054826	3055106	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	intron	3055107	3055271	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	CDS	3055272	3055970	0.95	+	0	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	exon	3055272	3055970	.	+	.	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
Phchi.S1	AUGUSTUS	stop_codon	3055971	3055973	.	+	0	transcript_id "Phchi.S1G050600.t1"; gene_id "Phchi.S1G050600"
# This transcript jg14566.t2 is derived from g13034.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14567.t1 is derived from g13035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13505635	13507303	.	-	.	Phchi.S3G188600
Phchi.S3	AUGUSTUS	transcript	13505635	13507303	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	stop_codon	13505632	13505634	.	-	0	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	CDS	13505635	13505683	1	-	1	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	exon	13505635	13505683	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	intron	13505684	13505883	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	CDS	13505884	13505984	1	-	0	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	exon	13505884	13505984	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	intron	13505985	13506455	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	CDS	13506456	13506512	1	-	0	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	exon	13506456	13506512	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	intron	13506513	13506605	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	CDS	13506606	13506624	0.99	-	1	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	exon	13506606	13506624	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	intron	13506625	13506791	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	CDS	13506792	13507303	0.2	-	0	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	exon	13506792	13507303	.	-	.	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
Phchi.S3	AUGUSTUS	start_codon	13507301	13507303	.	-	0	transcript_id "Phchi.S3G188600.t1"; gene_id "Phchi.S3G188600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2679.t1 is derived from g9599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8167842	8168968	.	+	.	Phchi.S5G128800
Phchi.S5	AUGUSTUS	transcript	8167842	8168968	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	start_codon	8167842	8167844	.	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8167842	8167861	1	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8167842	8167861	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8167862	8167949	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8167950	8168037	1	+	1	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8167950	8168037	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168038	8168194	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168195	8168377	1	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168195	8168377	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168378	8168463	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168464	8168589	0.99	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168464	8168589	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168590	8168694	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168695	8168769	1	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168695	8168769	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168770	8168863	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168864	8168968	1	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168864	8168968	.	+	.	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	stop_codon	8168969	8168971	.	+	0	transcript_id "Phchi.S5G128800.t1"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	transcript	8167842	8168968	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	start_codon	8167842	8167844	.	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8167842	8167861	1	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8167842	8167861	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8167862	8167949	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8167950	8168037	1	+	1	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8167950	8168037	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168038	8168189	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168190	8168213	0.5	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168190	8168213	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168214	8168353	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168354	8168377	0.5	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168354	8168377	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168378	8168463	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168464	8168589	1	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168464	8168589	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168590	8168694	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168695	8168769	1	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168695	8168769	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	intron	8168770	8168863	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	CDS	8168864	8168968	1	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	exon	8168864	8168968	.	+	.	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
Phchi.S5	AUGUSTUS	stop_codon	8168969	8168971	.	+	0	transcript_id "Phchi.S5G128800.t2"; gene_id "Phchi.S5G128800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg86.t1 is derived from g9868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	441163	442285	.	+	.	Phchi.S6G004500
Phchi.S6	AUGUSTUS	transcript	441163	442285	.	+	.	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	start_codon	441163	441165	.	+	0	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	CDS	441163	441474	0.8	+	0	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	exon	441163	441474	.	+	.	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	intron	441475	441549	.	+	.	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	CDS	441550	441761	0.41	+	0	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	exon	441550	441761	.	+	.	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	intron	441762	442032	.	+	.	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	CDS	442033	442285	0.2	+	1	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	exon	442033	442285	.	+	.	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
Phchi.S6	AUGUSTUS	stop_codon	442286	442288	.	+	0	transcript_id "Phchi.S6G004500.t1"; gene_id "Phchi.S6G004500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12257.t1 is derived from g7933.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7053323	7055424	.	+	.	Phchi.S2G033700
Phchi.S2	AUGUSTUS	transcript	7054624	7055424	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	start_codon	7054624	7054626	.	+	0	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7054624	7054626	0.84	+	0	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7054624	7054626	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7054627	7054711	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7054712	7054931	0.86	+	0	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7054712	7054931	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7054932	7055086	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7055087	7055121	0.88	+	2	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7055087	7055121	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7055122	7055206	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7055207	7055242	0.57	+	0	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7055207	7055242	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7055243	7055346	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7055347	7055424	0.54	+	0	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7055347	7055424	.	+	.	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	stop_codon	7055425	7055427	.	+	0	transcript_id "Phchi.S2G033700.t1"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	transcript	7053323	7055424	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	start_codon	7053323	7053325	.	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7053323	7053508	0.78	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7053323	7053508	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7053509	7053621	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7053622	7053726	0.78	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7053622	7053726	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7053727	7054711	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7054712	7054931	0.7	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7054712	7054931	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7054932	7055086	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7055087	7055121	0.87	+	2	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7055087	7055121	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7055122	7055206	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7055207	7055242	0.63	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7055207	7055242	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	intron	7055243	7055346	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	CDS	7055347	7055424	0.51	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	exon	7055347	7055424	.	+	.	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
Phchi.S2	AUGUSTUS	stop_codon	7055425	7055427	.	+	0	transcript_id "Phchi.S2G033700.t2"; gene_id "Phchi.S2G033700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12321.t1 is derived from g7997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10712886	10714172	.	+	.	Phchi.S2G040100
Phchi.S2	AUGUSTUS	transcript	10712886	10714172	.	+	.	transcript_id "Phchi.S2G040100.t1"; gene_id "Phchi.S2G040100"
Phchi.S2	AUGUSTUS	start_codon	10712886	10712888	.	+	0	transcript_id "Phchi.S2G040100.t1"; gene_id "Phchi.S2G040100"
Phchi.S2	AUGUSTUS	CDS	10712886	10714172	0.75	+	0	transcript_id "Phchi.S2G040100.t1"; gene_id "Phchi.S2G040100"
Phchi.S2	AUGUSTUS	exon	10712886	10714172	.	+	.	transcript_id "Phchi.S2G040100.t1"; gene_id "Phchi.S2G040100"
Phchi.S2	AUGUSTUS	stop_codon	10714173	10714175	.	+	0	transcript_id "Phchi.S2G040100.t1"; gene_id "Phchi.S2G040100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11789.t1 is derived from g15841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8159617	8161527	.	-	.	Phchi.S4G137100
Phchi.S4	AUGUSTUS	transcript	8159617	8161527	.	-	.	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	stop_codon	8159614	8159616	.	-	0	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	CDS	8159617	8160436	0.79	-	1	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	exon	8159617	8160436	.	-	.	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	intron	8160437	8160742	.	-	.	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	CDS	8160743	8160812	0.92	-	2	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	exon	8160743	8160812	.	-	.	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	intron	8160813	8161109	.	-	.	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	CDS	8161110	8161527	0.71	-	0	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	exon	8161110	8161527	.	-	.	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
Phchi.S4	AUGUSTUS	start_codon	8161525	8161527	.	-	0	transcript_id "Phchi.S4G137100.t1"; gene_id "Phchi.S4G137100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9418.t1 is derived from g6594.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41397097	41399548	.	-	.	Phchi.S1G657700
Phchi.S1	AUGUSTUS	transcript	41397097	41399548	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	stop_codon	41397094	41397096	.	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397097	41397120	1	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397097	41397120	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397121	41397217	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397218	41397262	1	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397218	41397262	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397263	41397345	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397346	41397464	1	-	2	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397346	41397464	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397465	41397567	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397568	41397643	1	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397568	41397643	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397644	41397742	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397743	41397825	1	-	2	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397743	41397825	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397826	41397915	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397916	41397993	1	-	2	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397916	41397993	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397994	41398073	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398074	41398139	1	-	2	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398074	41398139	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398140	41398233	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398234	41398343	1	-	1	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398234	41398343	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398344	41398414	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398415	41398463	1	-	2	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398415	41398463	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398464	41398745	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398746	41398839	0.58	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398746	41398839	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398840	41398966	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398967	41399130	0.62	-	2	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398967	41399130	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399131	41399316	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399317	41399419	1	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399317	41399419	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399420	41399500	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399501	41399548	0.94	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399501	41399548	.	-	.	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	start_codon	41399546	41399548	.	-	0	transcript_id "Phchi.S1G657700.t1"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	transcript	41397097	41399548	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	stop_codon	41397094	41397096	.	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397097	41397120	1	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397097	41397120	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397121	41397217	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397218	41397262	1	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397218	41397262	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397263	41397345	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397346	41397464	0.99	-	2	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397346	41397464	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397465	41397567	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397568	41397643	1	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397568	41397643	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397644	41397742	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397743	41397825	1	-	2	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397743	41397825	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397826	41397915	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397916	41397993	1	-	2	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397916	41397993	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397994	41398073	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398074	41398139	1	-	2	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398074	41398139	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398140	41398233	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398234	41398343	1	-	1	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398234	41398343	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398344	41398414	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398415	41398463	1	-	2	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398415	41398463	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398464	41398745	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398746	41398839	0.55	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398746	41398839	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398840	41399022	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399023	41399130	0.48	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399023	41399130	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399131	41399272	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399273	41399419	0.61	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399273	41399419	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399420	41399500	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399501	41399548	0.95	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399501	41399548	.	-	.	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	start_codon	41399546	41399548	.	-	0	transcript_id "Phchi.S1G657700.t2"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	transcript	41397097	41399548	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	stop_codon	41397094	41397096	.	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397097	41397120	1	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397097	41397120	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397121	41397217	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397218	41397262	1	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397218	41397262	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397263	41397345	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397346	41397464	1	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397346	41397464	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397465	41397567	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397568	41397643	1	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397568	41397643	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397644	41397742	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397743	41397825	1	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397743	41397825	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397826	41397915	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41397916	41397993	1	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41397916	41397993	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41397994	41398073	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398074	41398139	1	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398074	41398139	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398140	41398233	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398234	41398343	1	-	1	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398234	41398343	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398344	41398414	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398415	41398463	1	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398415	41398463	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398464	41398745	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398746	41398839	0.46	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398746	41398839	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41398840	41398966	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41398967	41399130	0.46	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41398967	41399130	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399131	41399221	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399222	41399266	0.42	-	2	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399222	41399266	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399267	41399367	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399368	41399419	0.49	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399368	41399419	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	intron	41399420	41399500	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	CDS	41399501	41399548	0.92	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	exon	41399501	41399548	.	-	.	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
Phchi.S1	AUGUSTUS	start_codon	41399546	41399548	.	-	0	transcript_id "Phchi.S1G657700.t3"; gene_id "Phchi.S1G657700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg208.t1 is derived from g9990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1188052	1189716	.	+	.	Phchi.S6G016700
Phchi.S6	AUGUSTUS	transcript	1188052	1189716	.	+	.	transcript_id "Phchi.S6G016700.t1"; gene_id "Phchi.S6G016700"
Phchi.S6	AUGUSTUS	start_codon	1188052	1188054	.	+	0	transcript_id "Phchi.S6G016700.t1"; gene_id "Phchi.S6G016700"
Phchi.S6	AUGUSTUS	CDS	1188052	1189716	0.45	+	0	transcript_id "Phchi.S6G016700.t1"; gene_id "Phchi.S6G016700"
Phchi.S6	AUGUSTUS	exon	1188052	1189716	.	+	.	transcript_id "Phchi.S6G016700.t1"; gene_id "Phchi.S6G016700"
Phchi.S6	AUGUSTUS	stop_codon	1189717	1189719	.	+	0	transcript_id "Phchi.S6G016700.t1"; gene_id "Phchi.S6G016700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13104.t1 is derived from g11569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4145460	4147398	.	-	.	Phchi.S3G042300
Phchi.S3	AUGUSTUS	transcript	4145460	4147398	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	stop_codon	4145457	4145459	.	-	0	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	CDS	4145460	4145605	0.74	-	2	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	exon	4145460	4145605	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	intron	4145606	4145725	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	CDS	4145726	4145843	0.92	-	0	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	exon	4145726	4145843	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	intron	4145844	4145936	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	CDS	4145937	4146513	0.97	-	1	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	exon	4145937	4146513	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	intron	4146514	4146600	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	CDS	4146601	4146926	0.98	-	0	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	exon	4146601	4146926	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	intron	4146927	4147029	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	CDS	4147030	4147398	0.73	-	0	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	exon	4147030	4147398	.	-	.	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
Phchi.S3	AUGUSTUS	start_codon	4147396	4147398	.	-	0	transcript_id "Phchi.S3G042300.t1"; gene_id "Phchi.S3G042300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9517.t1 is derived from g6693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42232830	42233657	.	+	.	Phchi.S1G667600
Phchi.S1	AUGUSTUS	transcript	42232830	42233657	.	+	.	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	start_codon	42232830	42232832	.	+	0	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	CDS	42232830	42233010	0.58	+	0	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	exon	42232830	42233010	.	+	.	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	intron	42233011	42233096	.	+	.	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	CDS	42233097	42233396	0.65	+	2	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	exon	42233097	42233396	.	+	.	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	intron	42233397	42233640	.	+	.	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	CDS	42233641	42233657	0.99	+	2	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	exon	42233641	42233657	.	+	.	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
Phchi.S1	AUGUSTUS	stop_codon	42233658	42233660	.	+	0	transcript_id "Phchi.S1G667600.t1"; gene_id "Phchi.S1G667600"
# This transcript jg2609.t2 is derived from g9529.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2610.t1 is derived from g9530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7783145	7784040	.	+	.	Phchi.S5G121900
Phchi.S5	AUGUSTUS	transcript	7783145	7784040	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	start_codon	7783145	7783147	.	+	0	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	CDS	7783145	7783246	1	+	0	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	exon	7783145	7783246	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	intron	7783247	7783335	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	CDS	7783336	7783382	1	+	0	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	exon	7783336	7783382	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	intron	7783383	7783475	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	CDS	7783476	7783552	1	+	1	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	exon	7783476	7783552	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	intron	7783553	7783623	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	CDS	7783624	7783690	1	+	2	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	exon	7783624	7783690	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	intron	7783691	7783778	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	CDS	7783779	7783856	1	+	1	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	exon	7783779	7783856	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	intron	7783857	7783946	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	CDS	7783947	7784040	1	+	1	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	exon	7783947	7784040	.	+	.	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
Phchi.S5	AUGUSTUS	stop_codon	7784041	7784043	.	+	0	transcript_id "Phchi.S5G121900.t1"; gene_id "Phchi.S5G121900"
# This transcript jg7175.t2 is derived from g4347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7176.t1 is derived from g4348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27414535	27418991	.	-	.	Phchi.S1G433500
Phchi.S1	AUGUSTUS	transcript	27414535	27418991	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	stop_codon	27414532	27414534	.	-	0	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27414535	27414796	1	-	1	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27414535	27414796	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27414797	27414886	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27414887	27416564	0.97	-	2	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27414887	27416564	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27416565	27416664	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27416665	27417032	1	-	1	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27416665	27417032	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27417033	27417182	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27417183	27417243	1	-	2	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27417183	27417243	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27417244	27417546	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27417547	27417700	0.99	-	0	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27417547	27417700	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27417701	27417810	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27417811	27417933	1	-	0	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27417811	27417933	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27417934	27418031	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27418032	27418138	1	-	2	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27418032	27418138	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27418139	27418275	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27418276	27418372	1	-	0	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27418276	27418372	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27418373	27418515	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27418516	27418633	1	-	1	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27418516	27418633	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	intron	27418634	27418863	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	CDS	27418864	27418991	0.82	-	0	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	exon	27418864	27418991	.	-	.	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
Phchi.S1	AUGUSTUS	start_codon	27418989	27418991	.	-	0	transcript_id "Phchi.S1G433500.t1"; gene_id "Phchi.S1G433500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3250.t1 is derived from g419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2515065	2515685	.	-	.	Phchi.S1G040900
Phchi.S1	AUGUSTUS	transcript	2515065	2515685	.	-	.	transcript_id "Phchi.S1G040900.t1"; gene_id "Phchi.S1G040900"
Phchi.S1	AUGUSTUS	stop_codon	2515062	2515064	.	-	0	transcript_id "Phchi.S1G040900.t1"; gene_id "Phchi.S1G040900"
Phchi.S1	AUGUSTUS	CDS	2515065	2515685	0.89	-	0	transcript_id "Phchi.S1G040900.t1"; gene_id "Phchi.S1G040900"
Phchi.S1	AUGUSTUS	exon	2515065	2515685	.	-	.	transcript_id "Phchi.S1G040900.t1"; gene_id "Phchi.S1G040900"
Phchi.S1	AUGUSTUS	start_codon	2515683	2515685	.	-	0	transcript_id "Phchi.S1G040900.t1"; gene_id "Phchi.S1G040900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13272.t1 is derived from g11737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5046681	5047091	.	+	.	Phchi.S3G059100
Phchi.S3	AUGUSTUS	transcript	5046681	5047091	.	+	.	transcript_id "Phchi.S3G059100.t1"; gene_id "Phchi.S3G059100"
Phchi.S3	AUGUSTUS	start_codon	5046681	5046683	.	+	0	transcript_id "Phchi.S3G059100.t1"; gene_id "Phchi.S3G059100"
Phchi.S3	AUGUSTUS	CDS	5046681	5047091	0.58	+	0	transcript_id "Phchi.S3G059100.t1"; gene_id "Phchi.S3G059100"
Phchi.S3	AUGUSTUS	exon	5046681	5047091	.	+	.	transcript_id "Phchi.S3G059100.t1"; gene_id "Phchi.S3G059100"
Phchi.S3	AUGUSTUS	stop_codon	5047092	5047094	.	+	0	transcript_id "Phchi.S3G059100.t1"; gene_id "Phchi.S3G059100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15996.t1 is derived from g9803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C28	AUGUSTUS	gene	29765	30916	.	+	.	Phchi.C28G000100
Phchi.C28	AUGUSTUS	transcript	29765	30916	.	+	.	transcript_id "Phchi.C28G000100.t1"; gene_id "Phchi.C28G000100"
Phchi.C28	AUGUSTUS	start_codon	29765	29767	.	+	0	transcript_id "Phchi.C28G000100.t1"; gene_id "Phchi.C28G000100"
Phchi.C28	AUGUSTUS	CDS	29765	30916	1	+	0	transcript_id "Phchi.C28G000100.t1"; gene_id "Phchi.C28G000100"
Phchi.C28	AUGUSTUS	exon	29765	30916	.	+	.	transcript_id "Phchi.C28G000100.t1"; gene_id "Phchi.C28G000100"
Phchi.C28	AUGUSTUS	stop_codon	30917	30919	.	+	0	transcript_id "Phchi.C28G000100.t1"; gene_id "Phchi.C28G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8374.t1 is derived from g5549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35577524	35578411	.	-	.	Phchi.S1G553300
Phchi.S1	AUGUSTUS	transcript	35577524	35578411	.	-	.	transcript_id "Phchi.S1G553300.t1"; gene_id "Phchi.S1G553300"
Phchi.S1	AUGUSTUS	stop_codon	35577521	35577523	.	-	0	transcript_id "Phchi.S1G553300.t1"; gene_id "Phchi.S1G553300"
Phchi.S1	AUGUSTUS	CDS	35577524	35578411	1	-	0	transcript_id "Phchi.S1G553300.t1"; gene_id "Phchi.S1G553300"
Phchi.S1	AUGUSTUS	exon	35577524	35578411	.	-	.	transcript_id "Phchi.S1G553300.t1"; gene_id "Phchi.S1G553300"
Phchi.S1	AUGUSTUS	start_codon	35578409	35578411	.	-	0	transcript_id "Phchi.S1G553300.t1"; gene_id "Phchi.S1G553300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2220.t1 is derived from g9140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5483562	5486381	.	+	.	Phchi.S5G082900
Phchi.S5	AUGUSTUS	transcript	5483562	5486381	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	start_codon	5483562	5483564	.	+	0	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	CDS	5483562	5483778	1	+	0	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	exon	5483562	5483778	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	intron	5483779	5483857	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	CDS	5483858	5484430	0.97	+	2	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	exon	5483858	5484430	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	intron	5484431	5484524	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	CDS	5484525	5484758	0.86	+	2	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	exon	5484525	5484758	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	intron	5484759	5484843	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	CDS	5484844	5484897	1	+	2	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	exon	5484844	5484897	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	intron	5484898	5484997	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	CDS	5484998	5485998	1	+	2	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	exon	5484998	5485998	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	intron	5485999	5486093	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	CDS	5486094	5486381	1	+	0	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	exon	5486094	5486381	.	+	.	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
Phchi.S5	AUGUSTUS	stop_codon	5486382	5486384	.	+	0	transcript_id "Phchi.S5G082900.t1"; gene_id "Phchi.S5G082900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11266.t1 is derived from g15316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5088259	5088837	.	+	.	Phchi.S4G084800
Phchi.S4	AUGUSTUS	transcript	5088259	5088837	.	+	.	transcript_id "Phchi.S4G084800.t1"; gene_id "Phchi.S4G084800"
Phchi.S4	AUGUSTUS	start_codon	5088259	5088261	.	+	0	transcript_id "Phchi.S4G084800.t1"; gene_id "Phchi.S4G084800"
Phchi.S4	AUGUSTUS	CDS	5088259	5088837	1	+	0	transcript_id "Phchi.S4G084800.t1"; gene_id "Phchi.S4G084800"
Phchi.S4	AUGUSTUS	exon	5088259	5088837	.	+	.	transcript_id "Phchi.S4G084800.t1"; gene_id "Phchi.S4G084800"
Phchi.S4	AUGUSTUS	stop_codon	5088838	5088840	.	+	0	transcript_id "Phchi.S4G084800.t1"; gene_id "Phchi.S4G084800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8484.t1 is derived from g5659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36149682	36152264	.	-	.	Phchi.S1G564300
Phchi.S1	AUGUSTUS	transcript	36149682	36152264	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	stop_codon	36149679	36149681	.	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36149682	36149754	0.97	-	1	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36149682	36149754	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36149755	36149842	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36149843	36149870	0.97	-	2	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36149843	36149870	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36149871	36149979	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36149980	36150046	0.66	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36149980	36150046	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150047	36150139	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150140	36150226	0.95	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150140	36150226	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150227	36150310	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150311	36150448	0.96	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150311	36150448	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150449	36150651	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150652	36150717	0.84	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150652	36150717	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150718	36150816	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150817	36150848	0.57	-	2	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150817	36150848	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150849	36150931	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150932	36150950	0.99	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150932	36150950	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150951	36151036	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151037	36151101	0.97	-	2	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151037	36151101	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151102	36151293	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151294	36151372	1	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151294	36151372	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151373	36151523	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151524	36151597	1	-	2	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151524	36151597	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151598	36151879	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151880	36151920	0.73	-	1	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151880	36151920	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151921	36152160	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36152161	36152264	0.75	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36152161	36152264	.	-	.	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	start_codon	36152262	36152264	.	-	0	transcript_id "Phchi.S1G564300.t1"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	transcript	36149682	36152264	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	stop_codon	36149679	36149681	.	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36149682	36149754	0.97	-	1	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36149682	36149754	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36149755	36149842	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36149843	36149870	0.97	-	2	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36149843	36149870	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36149871	36149979	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36149980	36150046	0.78	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36149980	36150046	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150047	36150139	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150140	36150226	0.95	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150140	36150226	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150227	36150310	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150311	36150448	0.92	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150311	36150448	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150449	36150651	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150652	36150717	0.77	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150652	36150717	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150718	36150816	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150817	36150848	0.49	-	2	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150817	36150848	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150849	36150931	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36150932	36150950	0.98	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36150932	36150950	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36150951	36151036	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151037	36151101	0.98	-	2	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151037	36151101	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151102	36151293	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151294	36151370	0.36	-	1	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151294	36151370	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151371	36151462	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151463	36151484	0.36	-	2	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151463	36151484	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151485	36151570	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151571	36151597	1	-	2	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151571	36151597	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151598	36151879	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36151880	36151920	0.71	-	1	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36151880	36151920	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	intron	36151921	36152160	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	CDS	36152161	36152264	0.74	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	exon	36152161	36152264	.	-	.	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
Phchi.S1	AUGUSTUS	start_codon	36152262	36152264	.	-	0	transcript_id "Phchi.S1G564300.t2"; gene_id "Phchi.S1G564300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6310.t1 is derived from g3482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22208178	22210527	.	+	.	Phchi.S1G346900
Phchi.S1	AUGUSTUS	transcript	22208178	22210527	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	start_codon	22208178	22208180	.	+	0	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22208178	22208336	0.58	+	0	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22208178	22208336	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22208337	22208412	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22208413	22208498	1	+	0	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22208413	22208498	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22208499	22208580	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22208581	22208655	1	+	1	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22208581	22208655	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22208656	22208731	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22208732	22208860	1	+	1	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22208732	22208860	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22208861	22208943	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22208944	22209030	1	+	1	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22208944	22209030	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22209031	22209114	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22209115	22209317	1	+	1	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22209115	22209317	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22209318	22209402	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22209403	22209505	1	+	2	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22209403	22209505	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22209506	22209596	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22209597	22209688	1	+	1	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22209597	22209688	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22209689	22209776	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22209777	22209839	1	+	2	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22209777	22209839	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22209840	22209942	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22209943	22210183	0.97	+	2	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22209943	22210183	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22210184	22210290	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22210291	22210331	1	+	1	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22210291	22210331	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	intron	22210332	22210429	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	CDS	22210430	22210527	0.98	+	2	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	exon	22210430	22210527	.	+	.	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
Phchi.S1	AUGUSTUS	stop_codon	22210528	22210530	.	+	0	transcript_id "Phchi.S1G346900.t1"; gene_id "Phchi.S1G346900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11643.t1 is derived from g15694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7434547	7435321	.	-	.	Phchi.S4G122500
Phchi.S4	AUGUSTUS	transcript	7434547	7435321	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	stop_codon	7434544	7434546	.	-	0	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	CDS	7434547	7434664	0.75	-	1	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	exon	7434547	7434664	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	intron	7434665	7434753	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	CDS	7434754	7434807	0.78	-	1	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	exon	7434754	7434807	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	intron	7434808	7434898	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	CDS	7434899	7435086	1	-	0	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	exon	7434899	7435086	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	intron	7435087	7435291	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	CDS	7435292	7435321	0.99	-	0	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	exon	7435292	7435321	.	-	.	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
Phchi.S4	AUGUSTUS	start_codon	7435319	7435321	.	-	0	transcript_id "Phchi.S4G122500.t1"; gene_id "Phchi.S4G122500"
# This transcript jg3956.t2 is derived from g1125.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3957.t1 is derived from g1126.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6705649	6706315	.	+	.	Phchi.S1G111600
Phchi.S1	AUGUSTUS	transcript	6705728	6706315	.	+	.	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	start_codon	6705728	6705730	.	+	0	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	CDS	6705728	6705829	1	+	0	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	exon	6705728	6705829	.	+	.	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	intron	6705830	6706012	.	+	.	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	CDS	6706013	6706136	0.98	+	0	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	exon	6706013	6706136	.	+	.	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	intron	6706137	6706310	.	+	.	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	CDS	6706311	6706315	0.82	+	2	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	exon	6706311	6706315	.	+	.	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	stop_codon	6706316	6706318	.	+	0	transcript_id "Phchi.S1G111600.t1"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	transcript	6705649	6706315	.	+	.	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	start_codon	6705649	6705651	.	+	0	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	CDS	6705649	6705822	0.52	+	0	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	exon	6705649	6705822	.	+	.	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	intron	6705823	6706012	.	+	.	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	CDS	6706013	6706136	0.69	+	0	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	exon	6706013	6706136	.	+	.	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	intron	6706137	6706310	.	+	.	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	CDS	6706311	6706315	0.64	+	2	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	exon	6706311	6706315	.	+	.	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
Phchi.S1	AUGUSTUS	stop_codon	6706316	6706318	.	+	0	transcript_id "Phchi.S1G111600.t2"; gene_id "Phchi.S1G111600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12837.t1 is derived from g11302.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2633074	2634386	.	+	.	Phchi.S3G015600
Phchi.S3	AUGUSTUS	transcript	2633074	2634386	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	start_codon	2633074	2633076	.	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	CDS	2633074	2633295	1	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	exon	2633074	2633295	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	intron	2633296	2633437	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	CDS	2633438	2633521	1	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	exon	2633438	2633521	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	intron	2633522	2633614	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	CDS	2633615	2633680	1	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	exon	2633615	2633680	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	intron	2633681	2633800	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	CDS	2633801	2633863	1	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	exon	2633801	2633863	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	intron	2633864	2633987	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	CDS	2633988	2634228	1	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	exon	2633988	2634228	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	intron	2634229	2634318	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	CDS	2634319	2634386	1	+	2	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	exon	2634319	2634386	.	+	.	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
Phchi.S3	AUGUSTUS	stop_codon	2634387	2634389	.	+	0	transcript_id "Phchi.S3G015600.t1"; gene_id "Phchi.S3G015600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5415.t1 is derived from g2585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16774566	16777121	.	-	.	Phchi.S1G257400
Phchi.S1	AUGUSTUS	transcript	16774566	16777121	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	stop_codon	16774563	16774565	.	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16774566	16774567	1	-	2	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16774566	16774567	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16774568	16774956	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16774957	16774999	0.97	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16774957	16774999	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16775000	16775072	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16775073	16775097	0.68	-	1	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16775073	16775097	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16775098	16775192	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16775193	16775281	1	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16775193	16775281	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16775282	16775412	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16775413	16775538	1	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16775413	16775538	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16775539	16775648	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16775649	16775725	0.43	-	2	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16775649	16775725	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16775726	16775820	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16775821	16775838	0.8	-	2	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16775821	16775838	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16775839	16775933	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16775934	16776102	1	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16775934	16776102	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16776103	16776218	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16776219	16776308	1	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16776219	16776308	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16776309	16776625	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16776626	16776798	1	-	2	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16776626	16776798	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	intron	16776799	16776886	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	CDS	16776887	16777121	1	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	exon	16776887	16777121	.	-	.	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
Phchi.S1	AUGUSTUS	start_codon	16777119	16777121	.	-	0	transcript_id "Phchi.S1G257400.t1"; gene_id "Phchi.S1G257400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12288.t1 is derived from g7964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8847756	8850170	.	-	.	Phchi.S2G036800
Phchi.S2	AUGUSTUS	transcript	8847756	8850170	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	stop_codon	8847753	8847755	.	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8847756	8847817	1	-	2	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8847756	8847817	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8847818	8847904	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8847905	8848067	1	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8847905	8848067	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8848068	8848151	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8848152	8848559	0.99	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8848152	8848559	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8848560	8848654	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8848655	8848876	1	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8848655	8848876	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8848877	8848957	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8848958	8849068	1	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8848958	8849068	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8849069	8849149	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8849150	8849306	0.92	-	1	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8849150	8849306	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8849307	8849445	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8849446	8849607	0.56	-	1	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8849446	8849607	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8849608	8849699	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8849700	8849853	1	-	2	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8849700	8849853	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	intron	8849854	8849935	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	CDS	8849936	8850170	0.88	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	exon	8849936	8850170	.	-	.	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
Phchi.S2	AUGUSTUS	start_codon	8850168	8850170	.	-	0	transcript_id "Phchi.S2G036800.t1"; gene_id "Phchi.S2G036800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3297.t1 is derived from g466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2726317	2727551	.	+	.	Phchi.S1G045600
Phchi.S1	AUGUSTUS	transcript	2726317	2727551	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	start_codon	2726317	2726319	.	+	0	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2726317	2726440	0.48	+	0	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2726317	2726440	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	intron	2726441	2726537	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2726538	2726632	1	+	2	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2726538	2726632	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	intron	2726633	2726717	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2726718	2726818	1	+	0	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2726718	2726818	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	intron	2726819	2726937	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2726938	2727045	1	+	1	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2726938	2727045	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	intron	2727046	2727144	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2727145	2727253	1	+	1	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2727145	2727253	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	intron	2727254	2727332	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2727333	2727383	1	+	0	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2727333	2727383	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	intron	2727384	2727473	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	CDS	2727474	2727551	1	+	0	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	exon	2727474	2727551	.	+	.	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
Phchi.S1	AUGUSTUS	stop_codon	2727552	2727554	.	+	0	transcript_id "Phchi.S1G045600.t1"; gene_id "Phchi.S1G045600"
# This transcript jg2679.t2 is derived from g9599.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2680.t1 is derived from g9600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8169666	8172327	.	-	.	Phchi.S5G128900
Phchi.S5	AUGUSTUS	transcript	8169666	8172327	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	stop_codon	8169663	8169665	.	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8169666	8169806	1	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8169666	8169806	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8169807	8169891	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8169892	8169990	1	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8169892	8169990	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8169991	8170087	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8170088	8170184	1	-	1	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8170088	8170184	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8170185	8170260	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8170261	8170366	1	-	2	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8170261	8170366	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8170367	8170464	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8170465	8170537	1	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8170465	8170537	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8170538	8170635	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8170636	8170779	1	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8170636	8170779	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8170780	8170926	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8170927	8171927	0.34	-	2	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8170927	8171927	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8171928	8172021	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8172022	8172089	0.34	-	1	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8172022	8172089	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	intron	8172090	8172295	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	CDS	8172296	8172327	0.38	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	exon	8172296	8172327	.	-	.	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
Phchi.S5	AUGUSTUS	start_codon	8172325	8172327	.	-	0	transcript_id "Phchi.S5G128900.t1"; gene_id "Phchi.S5G128900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6658.t1 is derived from g3830.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24338403	24340630	.	+	.	Phchi.S1G381700
Phchi.S1	AUGUSTUS	transcript	24338403	24340630	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	start_codon	24338403	24338405	.	+	0	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	CDS	24338403	24338534	0.66	+	0	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	exon	24338403	24338534	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	intron	24338535	24338615	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	CDS	24338616	24338848	0.78	+	0	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	exon	24338616	24338848	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	intron	24338849	24339052	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	CDS	24339053	24339507	0.35	+	1	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	exon	24339053	24339507	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	intron	24339508	24339807	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	CDS	24339808	24340148	0.11	+	2	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	exon	24339808	24340148	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	intron	24340149	24340337	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	CDS	24340338	24340490	0.38	+	0	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	exon	24340338	24340490	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	intron	24340491	24340597	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	CDS	24340598	24340630	0.47	+	0	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	exon	24340598	24340630	.	+	.	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
Phchi.S1	AUGUSTUS	stop_codon	24340631	24340633	.	+	0	transcript_id "Phchi.S1G381700.t1"; gene_id "Phchi.S1G381700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2889.t1 is derived from g58.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	318038	320600	.	-	.	Phchi.S1G004800
Phchi.S1	AUGUSTUS	transcript	318038	320600	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	stop_codon	318035	318037	.	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	318038	318130	1	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	318038	318130	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	318131	318209	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	318210	318278	1	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	318210	318278	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	318279	318348	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	318349	318508	1	-	1	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	318349	318508	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	318509	318584	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	318585	318647	1	-	1	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	318585	318647	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	318648	318825	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	318826	319013	0.98	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	318826	319013	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	319014	319127	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	319128	319286	1	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	319128	319286	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	319287	319438	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	319439	319553	1	-	1	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	319439	319553	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	319554	319673	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	319674	319729	1	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	319674	319729	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	319730	319941	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	319942	320096	0.46	-	2	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	319942	320096	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	320097	320163	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	320164	320282	0.63	-	1	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	320164	320282	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	320283	320424	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	320425	320433	0.93	-	1	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	320425	320433	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	intron	320434	320514	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	CDS	320515	320600	0.47	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	exon	320515	320600	.	-	.	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
Phchi.S1	AUGUSTUS	start_codon	320598	320600	.	-	0	transcript_id "Phchi.S1G004800.t1"; gene_id "Phchi.S1G004800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13076.t1 is derived from g11541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4053902	4054603	.	-	.	Phchi.S3G039500
Phchi.S3	AUGUSTUS	transcript	4053902	4054603	.	-	.	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	stop_codon	4053899	4053901	.	-	0	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	CDS	4053902	4054161	0.9	-	2	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	exon	4053902	4054161	.	-	.	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	intron	4054162	4054270	.	-	.	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	CDS	4054271	4054380	0.97	-	1	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	exon	4054271	4054380	.	-	.	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	intron	4054381	4054481	.	-	.	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	CDS	4054482	4054603	0.44	-	0	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	exon	4054482	4054603	.	-	.	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
Phchi.S3	AUGUSTUS	start_codon	4054601	4054603	.	-	0	transcript_id "Phchi.S3G039500.t1"; gene_id "Phchi.S3G039500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3986.t1 is derived from g1155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6876768	6878622	.	+	.	Phchi.S1G114500
Phchi.S1	AUGUSTUS	transcript	6876768	6878622	.	+	.	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	start_codon	6876768	6876770	.	+	0	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	CDS	6876768	6878393	0.4	+	0	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	exon	6876768	6878393	.	+	.	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	intron	6878394	6878616	.	+	.	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	CDS	6878617	6878622	0.78	+	0	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	exon	6878617	6878622	.	+	.	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
Phchi.S1	AUGUSTUS	stop_codon	6878623	6878625	.	+	0	transcript_id "Phchi.S1G114500.t1"; gene_id "Phchi.S1G114500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11381.t1 is derived from g15431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5981926	5983458	.	+	.	Phchi.S4G096300
Phchi.S4	AUGUSTUS	transcript	5981926	5983458	.	+	.	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	start_codon	5981926	5981928	.	+	0	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	CDS	5981926	5982022	1	+	0	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	exon	5981926	5982022	.	+	.	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	intron	5982023	5982166	.	+	.	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	CDS	5982167	5982536	1	+	2	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	exon	5982167	5982536	.	+	.	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	intron	5982537	5982653	.	+	.	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	CDS	5982654	5983458	0.37	+	1	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	exon	5982654	5983458	.	+	.	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
Phchi.S4	AUGUSTUS	stop_codon	5983459	5983461	.	+	0	transcript_id "Phchi.S4G096300.t1"; gene_id "Phchi.S4G096300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3595.t1 is derived from g764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4658587	4661052	.	+	.	Phchi.S1G075400
Phchi.S1	AUGUSTUS	transcript	4658587	4661052	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	start_codon	4658587	4658589	.	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4658587	4658880	0.53	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4658587	4658880	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4658881	4658986	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4658987	4659059	0.66	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4658987	4659059	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4659060	4659214	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4659215	4659435	1	+	2	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4659215	4659435	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4659436	4659554	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4659555	4659642	1	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4659555	4659642	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4659643	4659735	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4659736	4659908	1	+	2	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4659736	4659908	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4659909	4660139	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4660140	4660286	1	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4660140	4660286	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4660287	4660403	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4660404	4660538	1	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4660404	4660538	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	intron	4660539	4660683	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	CDS	4660684	4661052	1	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	exon	4660684	4661052	.	+	.	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
Phchi.S1	AUGUSTUS	stop_codon	4661053	4661055	.	+	0	transcript_id "Phchi.S1G075400.t1"; gene_id "Phchi.S1G075400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8075.t1 is derived from g5250.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32829254	32830576	.	-	.	Phchi.S1G523400
Phchi.S1	AUGUSTUS	transcript	32829254	32830576	.	-	.	transcript_id "Phchi.S1G523400.t1"; gene_id "Phchi.S1G523400"
Phchi.S1	AUGUSTUS	stop_codon	32829251	32829253	.	-	0	transcript_id "Phchi.S1G523400.t1"; gene_id "Phchi.S1G523400"
Phchi.S1	AUGUSTUS	CDS	32829254	32830576	1	-	0	transcript_id "Phchi.S1G523400.t1"; gene_id "Phchi.S1G523400"
Phchi.S1	AUGUSTUS	exon	32829254	32830576	.	-	.	transcript_id "Phchi.S1G523400.t1"; gene_id "Phchi.S1G523400"
Phchi.S1	AUGUSTUS	start_codon	32830574	32830576	.	-	0	transcript_id "Phchi.S1G523400.t1"; gene_id "Phchi.S1G523400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6062.t1 is derived from g3233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20692047	20694197	.	-	.	Phchi.S1G322100
Phchi.S1	AUGUSTUS	transcript	20692047	20694197	.	-	.	transcript_id "Phchi.S1G322100.t1"; gene_id "Phchi.S1G322100"
Phchi.S1	AUGUSTUS	stop_codon	20692044	20692046	.	-	0	transcript_id "Phchi.S1G322100.t1"; gene_id "Phchi.S1G322100"
Phchi.S1	AUGUSTUS	CDS	20692047	20694197	0.52	-	0	transcript_id "Phchi.S1G322100.t1"; gene_id "Phchi.S1G322100"
Phchi.S1	AUGUSTUS	exon	20692047	20694197	.	-	.	transcript_id "Phchi.S1G322100.t1"; gene_id "Phchi.S1G322100"
Phchi.S1	AUGUSTUS	start_codon	20694195	20694197	.	-	0	transcript_id "Phchi.S1G322100.t1"; gene_id "Phchi.S1G322100"
# This transcript jg9535.t2 is derived from g6711.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9536.t1 is derived from g6712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42372100	42376786	.	+	.	Phchi.S1G669500
Phchi.S1	AUGUSTUS	transcript	42372100	42376786	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	start_codon	42372100	42372102	.	+	0	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	CDS	42372100	42373432	0.61	+	0	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	exon	42372100	42373432	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	intron	42373433	42373567	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	CDS	42373568	42374892	0.99	+	2	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	exon	42373568	42374892	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	intron	42374893	42375056	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	CDS	42375057	42375312	0.9	+	0	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	exon	42375057	42375312	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	intron	42375313	42375512	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	CDS	42375513	42376012	0.82	+	2	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	exon	42375513	42376012	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	intron	42376013	42376078	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	CDS	42376079	42376510	0.5	+	0	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	exon	42376079	42376510	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	intron	42376511	42376642	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	CDS	42376643	42376786	0.88	+	0	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	exon	42376643	42376786	.	+	.	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
Phchi.S1	AUGUSTUS	stop_codon	42376787	42376789	.	+	0	transcript_id "Phchi.S1G669500.t1"; gene_id "Phchi.S1G669500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9387.t1 is derived from g6563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41290741	41291163	.	+	.	Phchi.S1G654600
Phchi.S1	AUGUSTUS	transcript	41290741	41291163	.	+	.	transcript_id "Phchi.S1G654600.t1"; gene_id "Phchi.S1G654600"
Phchi.S1	AUGUSTUS	start_codon	41290741	41290743	.	+	0	transcript_id "Phchi.S1G654600.t1"; gene_id "Phchi.S1G654600"
Phchi.S1	AUGUSTUS	CDS	41290741	41291163	0.96	+	0	transcript_id "Phchi.S1G654600.t1"; gene_id "Phchi.S1G654600"
Phchi.S1	AUGUSTUS	exon	41290741	41291163	.	+	.	transcript_id "Phchi.S1G654600.t1"; gene_id "Phchi.S1G654600"
Phchi.S1	AUGUSTUS	stop_codon	41291164	41291166	.	+	0	transcript_id "Phchi.S1G654600.t1"; gene_id "Phchi.S1G654600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15532.t1 is derived from g14001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19742770	19743345	.	-	.	Phchi.S3G285100
Phchi.S3	AUGUSTUS	transcript	19742770	19743345	.	-	.	transcript_id "Phchi.S3G285100.t1"; gene_id "Phchi.S3G285100"
Phchi.S3	AUGUSTUS	stop_codon	19742767	19742769	.	-	0	transcript_id "Phchi.S3G285100.t1"; gene_id "Phchi.S3G285100"
Phchi.S3	AUGUSTUS	CDS	19742770	19743345	0.65	-	0	transcript_id "Phchi.S3G285100.t1"; gene_id "Phchi.S3G285100"
Phchi.S3	AUGUSTUS	exon	19742770	19743345	.	-	.	transcript_id "Phchi.S3G285100.t1"; gene_id "Phchi.S3G285100"
Phchi.S3	AUGUSTUS	start_codon	19743343	19743345	.	-	0	transcript_id "Phchi.S3G285100.t1"; gene_id "Phchi.S3G285100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13995.t1 is derived from g12462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10144198	10146119	.	-	.	Phchi.S3G131400
Phchi.S3	AUGUSTUS	transcript	10144198	10146119	.	-	.	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	stop_codon	10144195	10144197	.	-	0	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	CDS	10144198	10145358	1	-	0	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	exon	10144198	10145358	.	-	.	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	intron	10145359	10145449	.	-	.	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	CDS	10145450	10145777	1	-	1	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	exon	10145450	10145777	.	-	.	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	intron	10145778	10145973	.	-	.	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	CDS	10145974	10146119	0.98	-	0	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	exon	10145974	10146119	.	-	.	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
Phchi.S3	AUGUSTUS	start_codon	10146117	10146119	.	-	0	transcript_id "Phchi.S3G131400.t1"; gene_id "Phchi.S3G131400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4351.t1 is derived from g1520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9920594	9922414	.	+	.	Phchi.S1G151000
Phchi.S1	AUGUSTUS	transcript	9920594	9922414	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	start_codon	9920594	9920596	.	+	0	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9920594	9920802	1	+	0	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9920594	9920802	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	intron	9920803	9921206	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9921207	9921297	1	+	1	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9921207	9921297	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	intron	9921298	9921379	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9921380	9921468	1	+	0	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9921380	9921468	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	intron	9921469	9921543	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9921544	9921599	1	+	1	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9921544	9921599	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	intron	9921600	9921691	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9921692	9921838	1	+	2	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9921692	9921838	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	intron	9921839	9921923	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9921924	9922049	1	+	2	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9921924	9922049	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	intron	9922050	9922142	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	CDS	9922143	9922414	0.99	+	2	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	exon	9922143	9922414	.	+	.	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
Phchi.S1	AUGUSTUS	stop_codon	9922415	9922417	.	+	0	transcript_id "Phchi.S1G151000.t1"; gene_id "Phchi.S1G151000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3969.t1 is derived from g1138.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6794107	6795917	.	+	.	Phchi.S1G112800
Phchi.S1	AUGUSTUS	transcript	6794107	6795917	.	+	.	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	start_codon	6794107	6794109	.	+	0	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	CDS	6794107	6794379	0.49	+	0	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	exon	6794107	6794379	.	+	.	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	intron	6794380	6794432	.	+	.	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	CDS	6794433	6795917	0.41	+	0	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	exon	6794433	6795917	.	+	.	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
Phchi.S1	AUGUSTUS	stop_codon	6795918	6795920	.	+	0	transcript_id "Phchi.S1G112800.t1"; gene_id "Phchi.S1G112800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg7116.t1 is derived from g4288.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27055729	27058718	.	+	.	Phchi.S1G427500
Phchi.S1	AUGUSTUS	transcript	27055729	27058718	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	start_codon	27055729	27055731	.	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27055729	27055778	1	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27055729	27055778	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27055779	27056016	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056017	27056141	1	+	1	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056017	27056141	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056142	27056227	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056228	27056300	1	+	2	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056228	27056300	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056301	27056471	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056472	27056529	1	+	1	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056472	27056529	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056530	27056650	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056651	27056790	1	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056651	27056790	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056791	27056906	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056907	27057006	0.9	+	1	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056907	27057006	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057007	27057110	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057111	27057182	0.9	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057111	27057182	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057183	27057348	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057349	27057465	1	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057349	27057465	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057466	27057616	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057617	27057975	0.87	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057617	27057975	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057976	27058122	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058123	27058213	1	+	1	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058123	27058213	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27058214	27058309	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058310	27058504	1	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058310	27058504	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27058505	27058697	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058698	27058718	1	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058698	27058718	.	+	.	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	stop_codon	27058719	27058721	.	+	0	transcript_id "Phchi.S1G427500.t1"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	transcript	27055729	27058640	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	start_codon	27055729	27055731	.	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27055729	27055778	1	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27055729	27055778	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27055779	27056016	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056017	27056141	1	+	1	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056017	27056141	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056142	27056227	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056228	27056300	1	+	2	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056228	27056300	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056301	27056471	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056472	27056529	1	+	1	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056472	27056529	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056530	27056650	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056651	27056790	1	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056651	27056790	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056791	27056906	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056907	27057006	0.83	+	1	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056907	27057006	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057007	27057110	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057111	27057182	0.83	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057111	27057182	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057183	27057348	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057349	27057465	1	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057349	27057465	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057466	27057616	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057617	27057975	0.88	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057617	27057975	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057976	27058122	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058123	27058213	1	+	1	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058123	27058213	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27058214	27058309	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058310	27058504	0.98	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058310	27058504	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27058505	27058637	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058638	27058640	0.98	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058638	27058640	.	+	.	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	stop_codon	27058641	27058643	.	+	0	transcript_id "Phchi.S1G427500.t2"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	transcript	27055729	27058710	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	start_codon	27055729	27055731	.	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27055729	27055778	1	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27055729	27055778	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27055779	27056016	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056017	27056141	1	+	1	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056017	27056141	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056142	27056227	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056228	27056300	1	+	2	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056228	27056300	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056301	27056471	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056472	27056529	1	+	1	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056472	27056529	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056530	27056650	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056651	27056790	1	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056651	27056790	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27056791	27056906	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27056907	27057006	0.88	+	1	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27056907	27057006	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057007	27057110	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057111	27057182	0.88	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057111	27057182	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057183	27057348	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057349	27057465	1	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057349	27057465	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057466	27057616	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27057617	27057975	0.84	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27057617	27057975	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27057976	27058122	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058123	27058213	1	+	1	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058123	27058213	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27058214	27058309	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058310	27058551	0.66	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058310	27058551	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	intron	27058552	27058697	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	CDS	27058698	27058710	0.4	+	1	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	exon	27058698	27058710	.	+	.	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
Phchi.S1	AUGUSTUS	stop_codon	27058711	27058713	.	+	0	transcript_id "Phchi.S1G427500.t3"; gene_id "Phchi.S1G427500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2117.t1 is derived from g9037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4928973	4932265	.	+	.	Phchi.S5G072600
Phchi.S5	AUGUSTUS	transcript	4928973	4932265	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	start_codon	4928973	4928975	.	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4928973	4929110	0.86	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4928973	4929110	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4929111	4929229	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4929230	4929334	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4929230	4929334	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4929335	4929433	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4929434	4929502	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4929434	4929502	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4929503	4929581	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4929582	4929671	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4929582	4929671	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4929672	4929751	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4929752	4929835	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4929752	4929835	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4929836	4929926	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4929927	4930091	0.99	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4929927	4930091	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4930092	4930213	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4930214	4930401	0.99	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4930214	4930401	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4930402	4930487	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4930488	4930560	1	+	1	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4930488	4930560	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4930561	4930651	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4930652	4930705	0.99	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4930652	4930705	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4930706	4930820	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4930821	4931078	0.99	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4930821	4931078	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4931079	4931177	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4931178	4931384	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4931178	4931384	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4931385	4931458	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4931459	4931562	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4931459	4931562	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4931563	4931647	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4931648	4931792	1	+	1	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4931648	4931792	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4931793	4931884	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4931885	4932019	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4931885	4932019	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	intron	4932020	4932091	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	CDS	4932092	4932265	1	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	exon	4932092	4932265	.	+	.	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
Phchi.S5	AUGUSTUS	stop_codon	4932266	4932268	.	+	0	transcript_id "Phchi.S5G072600.t1"; gene_id "Phchi.S5G072600"
# This transcript jg12754.t2 is derived from g11219.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12755.t1 is derived from g11220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1901651	1906034	.	+	.	Phchi.S3G007400
Phchi.S3	AUGUSTUS	transcript	1901651	1906034	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	start_codon	1901651	1901653	.	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1901651	1901715	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1901651	1901715	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1901716	1901818	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1901819	1901900	1	+	1	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1901819	1901900	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1901901	1902009	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902010	1902121	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902010	1902121	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902122	1902288	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902289	1902374	1	+	2	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902289	1902374	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902375	1902455	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902456	1902532	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902456	1902532	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902533	1902624	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902625	1902681	1	+	1	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902625	1902681	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902682	1902782	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902783	1902895	0.97	+	1	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902783	1902895	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902896	1903038	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903039	1903121	1	+	2	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903039	1903121	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903122	1903277	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903278	1903364	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903278	1903364	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903365	1903443	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903444	1903524	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903444	1903524	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903525	1903777	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903778	1903945	0.94	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903778	1903945	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903946	1904050	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1904051	1904467	0.9	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1904051	1904467	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1904468	1904575	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1904576	1904848	0.96	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1904576	1904848	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1904849	1904961	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1904962	1905042	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1904962	1905042	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905043	1905177	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905178	1905315	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905178	1905315	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905316	1905456	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905457	1905546	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905457	1905546	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905547	1905644	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905645	1905698	1	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905645	1905698	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905699	1905782	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905783	1906034	0.97	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905783	1906034	.	+	.	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	stop_codon	1906035	1906037	.	+	0	transcript_id "Phchi.S3G007400.t1"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	transcript	1901651	1906034	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	start_codon	1901651	1901653	.	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1901651	1901715	0.99	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1901651	1901715	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1901716	1901818	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1901819	1901900	0.99	+	1	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1901819	1901900	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1901901	1902009	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902010	1902121	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902010	1902121	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902122	1902288	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902289	1902374	1	+	2	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902289	1902374	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902375	1902455	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902456	1902532	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902456	1902532	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902533	1902624	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902625	1902681	1	+	1	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902625	1902681	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902682	1902782	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1902783	1902895	0.98	+	1	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1902783	1902895	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1902896	1903038	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903039	1903121	1	+	2	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903039	1903121	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903122	1903277	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903278	1903364	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903278	1903364	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903365	1903443	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903444	1903524	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903444	1903524	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903525	1903618	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903619	1903706	0.84	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903619	1903706	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903707	1903793	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1903794	1903945	0.44	+	2	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1903794	1903945	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1903946	1904050	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1904051	1904467	0.91	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1904051	1904467	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1904468	1904575	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1904576	1904848	0.93	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1904576	1904848	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1904849	1904961	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1904962	1905042	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1904962	1905042	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905043	1905177	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905178	1905315	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905178	1905315	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905316	1905456	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905457	1905546	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905457	1905546	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905547	1905644	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905645	1905698	1	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905645	1905698	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	intron	1905699	1905782	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	CDS	1905783	1906034	0.96	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	exon	1905783	1906034	.	+	.	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
Phchi.S3	AUGUSTUS	stop_codon	1906035	1906037	.	+	0	transcript_id "Phchi.S3G007400.t2"; gene_id "Phchi.S3G007400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9835.t1 is derived from g7011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44006179	44008157	.	+	.	Phchi.S1G699400
Phchi.S1	AUGUSTUS	transcript	44006179	44008157	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	start_codon	44006179	44006181	.	+	0	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	CDS	44006179	44006716	0.79	+	0	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	exon	44006179	44006716	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	intron	44006717	44006804	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	CDS	44006805	44007040	1	+	2	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	exon	44006805	44007040	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	intron	44007041	44007132	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	CDS	44007133	44007579	0.9	+	0	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	exon	44007133	44007579	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	intron	44007580	44007692	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	CDS	44007693	44008157	0.86	+	0	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	exon	44007693	44008157	.	+	.	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
Phchi.S1	AUGUSTUS	stop_codon	44008158	44008160	.	+	0	transcript_id "Phchi.S1G699400.t1"; gene_id "Phchi.S1G699400"
# This transcript jg13151.t2 is derived from g11616.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg13152.t1 is derived from g11617.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4413286	4415871	.	-	.	Phchi.S3G047100
Phchi.S3	AUGUSTUS	transcript	4413286	4415871	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	stop_codon	4413283	4413285	.	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413286	4413411	0.97	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413286	4413411	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413412	4413491	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413492	4413576	1	-	1	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413492	4413576	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413577	4413660	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413661	4413758	1	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413661	4413758	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413759	4413852	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413853	4413957	1	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413853	4413957	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413958	4414040	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414041	4414106	1	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414041	4414106	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414107	4414189	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414190	4414255	1	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414190	4414255	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414256	4414395	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414396	4414432	0.74	-	1	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414396	4414432	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414433	4414636	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414637	4414698	0.98	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414637	4414698	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414699	4414798	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414799	4414933	1	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414799	4414933	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414934	4415098	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4415099	4415200	1	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4415099	4415200	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4415201	4415289	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4415290	4415871	0.83	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4415290	4415871	.	-	.	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	start_codon	4415869	4415871	.	-	0	transcript_id "Phchi.S3G047100.t1"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	transcript	4413286	4415871	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	stop_codon	4413283	4413285	.	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413286	4413411	0.98	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413286	4413411	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413412	4413491	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413492	4413576	1	-	1	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413492	4413576	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413577	4413660	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413661	4413758	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413661	4413758	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413759	4413852	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413853	4413957	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413853	4413957	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413958	4414040	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414041	4414106	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414041	4414106	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414107	4414189	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414190	4414255	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414190	4414255	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414256	4414395	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414396	4414432	0.63	-	1	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414396	4414432	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414433	4414636	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414637	4414701	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414637	4414701	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414702	4414798	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414799	4414933	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414799	4414933	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414934	4415098	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4415099	4415200	1	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4415099	4415200	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4415201	4415289	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4415290	4415871	0.87	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4415290	4415871	.	-	.	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	start_codon	4415869	4415871	.	-	0	transcript_id "Phchi.S3G047100.t2"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	transcript	4413286	4415871	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	stop_codon	4413283	4413285	.	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413286	4413411	0.97	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413286	4413411	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413412	4413491	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413492	4413576	1	-	1	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413492	4413576	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413577	4413660	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413661	4413758	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413661	4413758	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413759	4413852	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4413853	4413957	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4413853	4413957	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4413958	4414040	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414041	4414106	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414041	4414106	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414107	4414189	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414190	4414255	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414190	4414255	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414256	4414395	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414396	4414432	0.62	-	1	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414396	4414432	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414433	4414636	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414637	4414698	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414637	4414698	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414699	4414798	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4414799	4414933	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4414799	4414933	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4414934	4415152	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4415153	4415200	1	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4415153	4415200	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	intron	4415201	4415289	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	CDS	4415290	4415871	0.81	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	exon	4415290	4415871	.	-	.	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
Phchi.S3	AUGUSTUS	start_codon	4415869	4415871	.	-	0	transcript_id "Phchi.S3G047100.t3"; gene_id "Phchi.S3G047100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15997.t1 is derived from g15975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C244	AUGUSTUS	gene	4556	5386	.	-	.	Phchi.C244G000100
Phchi.C244	AUGUSTUS	transcript	4556	5386	.	-	.	transcript_id "Phchi.C244G000100.t1"; gene_id "Phchi.C244G000100"
Phchi.C244	AUGUSTUS	stop_codon	4553	4555	.	-	0	transcript_id "Phchi.C244G000100.t1"; gene_id "Phchi.C244G000100"
Phchi.C244	AUGUSTUS	CDS	4556	5386	0.82	-	0	transcript_id "Phchi.C244G000100.t1"; gene_id "Phchi.C244G000100"
Phchi.C244	AUGUSTUS	exon	4556	5386	.	-	.	transcript_id "Phchi.C244G000100.t1"; gene_id "Phchi.C244G000100"
Phchi.C244	AUGUSTUS	start_codon	5384	5386	.	-	0	transcript_id "Phchi.C244G000100.t1"; gene_id "Phchi.C244G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg88.t1 is derived from g9870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	456562	458594	.	-	.	Phchi.S6G004700
Phchi.S6	AUGUSTUS	transcript	456562	458594	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	stop_codon	456559	456561	.	-	0	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	CDS	456562	457269	1	-	0	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	exon	456562	457269	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	intron	457270	457352	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	CDS	457353	457631	1	-	0	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	exon	457353	457631	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	intron	457632	457700	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	CDS	457701	458253	1	-	1	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	exon	457701	458253	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	intron	458254	458343	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	CDS	458344	458594	1	-	0	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	exon	458344	458594	.	-	.	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
Phchi.S6	AUGUSTUS	start_codon	458592	458594	.	-	0	transcript_id "Phchi.S6G004700.t1"; gene_id "Phchi.S6G004700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4352.t1 is derived from g1521.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9925177	9928578	.	+	.	Phchi.S1G151100
Phchi.S1	AUGUSTUS	transcript	9925177	9928578	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	start_codon	9925177	9925179	.	+	0	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9925177	9925324	0.99	+	0	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9925177	9925324	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9925325	9925418	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9925419	9925464	1	+	2	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9925419	9925464	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9925465	9925570	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9925571	9925717	1	+	1	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9925571	9925717	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9925718	9925888	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9925889	9926049	1	+	1	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9925889	9926049	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9926050	9926158	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9926159	9926312	1	+	2	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9926159	9926312	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9926313	9926394	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9926395	9926479	1	+	1	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9926395	9926479	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9926480	9926591	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9926592	9926692	1	+	0	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9926592	9926692	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9926693	9926821	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9926822	9927120	1	+	1	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9926822	9927120	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9927121	9927215	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9927216	9927263	0.9	+	2	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9927216	9927263	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9927264	9927489	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9927490	9927555	0.9	+	2	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9927490	9927555	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9927556	9927658	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9927659	9927837	1	+	2	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9927659	9927837	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9927838	9927925	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9927926	9928095	1	+	0	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9927926	9928095	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9928096	9928182	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9928183	9928351	1	+	1	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9928183	9928351	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	intron	9928352	9928443	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	CDS	9928444	9928578	1	+	0	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	exon	9928444	9928578	.	+	.	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
Phchi.S1	AUGUSTUS	stop_codon	9928579	9928581	.	+	0	transcript_id "Phchi.S1G151100.t1"; gene_id "Phchi.S1G151100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg29.t1 is derived from g9807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C246	AUGUSTUS	gene	1310	2055	.	-	.	Phchi.C246G000200
Phchi.C246	AUGUSTUS	transcript	1310	2055	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	stop_codon	1307	1309	.	-	0	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	CDS	1310	1342	1	-	0	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	exon	1310	1342	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	intron	1343	1435	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	CDS	1436	1531	1	-	0	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	exon	1436	1531	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	intron	1532	1637	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	CDS	1638	1716	1	-	1	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	exon	1638	1716	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	intron	1717	1808	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	CDS	1809	1898	1	-	1	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	exon	1809	1898	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	intron	1899	2002	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	CDS	2003	2055	0.82	-	0	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	exon	2003	2055	.	-	.	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
Phchi.C246	AUGUSTUS	start_codon	2053	2055	.	-	0	transcript_id "Phchi.C246G000200.t1"; gene_id "Phchi.C246G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6400.t1 is derived from g3572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22766344	22767207	.	+	.	Phchi.S1G355900
Phchi.S1	AUGUSTUS	transcript	22766344	22767207	.	+	.	transcript_id "Phchi.S1G355900.t1"; gene_id "Phchi.S1G355900"
Phchi.S1	AUGUSTUS	start_codon	22766344	22766346	.	+	0	transcript_id "Phchi.S1G355900.t1"; gene_id "Phchi.S1G355900"
Phchi.S1	AUGUSTUS	CDS	22766344	22767207	0.6	+	0	transcript_id "Phchi.S1G355900.t1"; gene_id "Phchi.S1G355900"
Phchi.S1	AUGUSTUS	exon	22766344	22767207	.	+	.	transcript_id "Phchi.S1G355900.t1"; gene_id "Phchi.S1G355900"
Phchi.S1	AUGUSTUS	stop_codon	22767208	22767210	.	+	0	transcript_id "Phchi.S1G355900.t1"; gene_id "Phchi.S1G355900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3734.t1 is derived from g903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5447502	5448817	.	-	.	Phchi.S1G089300
Phchi.S1	AUGUSTUS	transcript	5447502	5448817	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	stop_codon	5447499	5447501	.	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	CDS	5447502	5447744	1	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	exon	5447502	5447744	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	intron	5447745	5447826	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	CDS	5447827	5447919	1	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	exon	5447827	5447919	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	intron	5447920	5448011	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	CDS	5448012	5448086	1	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	exon	5448012	5448086	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	intron	5448087	5448254	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	CDS	5448255	5448338	1	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	exon	5448255	5448338	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	intron	5448339	5448426	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	CDS	5448427	5448506	1	-	2	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	exon	5448427	5448506	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	intron	5448507	5448663	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	CDS	5448664	5448817	0.84	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	exon	5448664	5448817	.	-	.	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
Phchi.S1	AUGUSTUS	start_codon	5448815	5448817	.	-	0	transcript_id "Phchi.S1G089300.t1"; gene_id "Phchi.S1G089300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10367.t1 is derived from g7543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47403297	47404738	.	-	.	Phchi.S1G752600
Phchi.S1	AUGUSTUS	transcript	47403297	47404636	.	-	.	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	stop_codon	47403294	47403296	.	-	0	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	CDS	47403297	47404088	0.82	-	0	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	exon	47403297	47404088	.	-	.	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	intron	47404089	47404225	.	-	.	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	CDS	47404226	47404636	0.79	-	0	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	exon	47404226	47404636	.	-	.	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	start_codon	47404634	47404636	.	-	0	transcript_id "Phchi.S1G752600.t1"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	transcript	47403297	47404738	.	-	.	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	stop_codon	47403294	47403296	.	-	0	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	CDS	47403297	47404088	0.81	-	0	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	exon	47403297	47404088	.	-	.	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	intron	47404089	47404225	.	-	.	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	CDS	47404226	47404738	0.64	-	0	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	exon	47404226	47404738	.	-	.	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
Phchi.S1	AUGUSTUS	start_codon	47404736	47404738	.	-	0	transcript_id "Phchi.S1G752600.t2"; gene_id "Phchi.S1G752600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4417.t1 is derived from g1586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10380601	10383275	.	+	.	Phchi.S1G157600
Phchi.S1	AUGUSTUS	transcript	10380601	10383275	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	start_codon	10380601	10380603	.	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	CDS	10380601	10380705	0.53	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	exon	10380601	10380705	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	intron	10380706	10380805	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	CDS	10380806	10381057	1	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	exon	10380806	10381057	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	intron	10381058	10381176	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	CDS	10381177	10381320	1	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	exon	10381177	10381320	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	intron	10381321	10381910	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	CDS	10381911	10382624	1	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	exon	10381911	10382624	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	intron	10382625	10382795	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	CDS	10382796	10383000	1	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	exon	10382796	10383000	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	intron	10383001	10383225	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	CDS	10383226	10383275	0.76	+	2	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	exon	10383226	10383275	.	+	.	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
Phchi.S1	AUGUSTUS	stop_codon	10383276	10383278	.	+	0	transcript_id "Phchi.S1G157600.t1"; gene_id "Phchi.S1G157600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14526.t1 is derived from g12994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13314074	13318785	.	-	.	Phchi.S3G184500
Phchi.S3	AUGUSTUS	transcript	13314074	13318785	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	stop_codon	13314071	13314073	.	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13314074	13314319	0.91	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13314074	13314319	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13314320	13314399	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13314400	13314591	1	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13314400	13314591	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13314592	13314708	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13314709	13314823	1	-	1	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13314709	13314823	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13314824	13315013	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13315014	13315198	0.66	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13315014	13315198	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13315199	13315299	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13315300	13315320	0.89	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13315300	13315320	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13315321	13315405	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13315406	13315495	0.99	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13315406	13315495	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13315496	13315580	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13315581	13315821	0.93	-	1	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13315581	13315821	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13315822	13315968	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13315969	13316041	1	-	2	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13315969	13316041	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13316042	13316139	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13316140	13316244	1	-	2	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13316140	13316244	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13316245	13316341	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13316342	13316594	0.99	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13316342	13316594	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13316595	13316702	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13316703	13316972	0.98	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13316703	13316972	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13316973	13317109	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13317110	13317289	0.9	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13317110	13317289	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13317290	13317393	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13317394	13317518	0.88	-	2	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13317394	13317518	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13317519	13317608	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13317609	13317903	0.83	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13317609	13317903	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13317904	13318006	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13318007	13318392	0.7	-	2	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13318007	13318392	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	intron	13318393	13318538	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	CDS	13318539	13318785	0.9	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	exon	13318539	13318785	.	-	.	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
Phchi.S3	AUGUSTUS	start_codon	13318783	13318785	.	-	0	transcript_id "Phchi.S3G184500.t1"; gene_id "Phchi.S3G184500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2607.t1 is derived from g9527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7771404	7772742	.	-	.	Phchi.S5G121600
Phchi.S5	AUGUSTUS	transcript	7771404	7772742	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	stop_codon	7771401	7771403	.	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	CDS	7771404	7771422	0.51	-	1	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	exon	7771404	7771422	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	intron	7771423	7771668	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	CDS	7771669	7771751	0.38	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	exon	7771669	7771751	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	intron	7771752	7771897	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	CDS	7771898	7771960	0.61	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	exon	7771898	7771960	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	intron	7771961	7772091	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	CDS	7772092	7772193	1	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	exon	7772092	7772193	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	intron	7772194	7772265	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	CDS	7772266	7772406	1	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	exon	7772266	7772406	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	intron	7772407	7772499	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	CDS	7772500	7772742	0.95	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	exon	7772500	7772742	.	-	.	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
Phchi.S5	AUGUSTUS	start_codon	7772740	7772742	.	-	0	transcript_id "Phchi.S5G121600.t1"; gene_id "Phchi.S5G121600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15147.t1 is derived from g13615.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17262479	17264408	.	-	.	Phchi.S3G246600
Phchi.S3	AUGUSTUS	transcript	17262479	17264408	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	stop_codon	17262476	17262478	.	-	0	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17262479	17262549	0.63	-	2	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17262479	17262549	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17262550	17262685	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17262686	17262821	1	-	0	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17262686	17262821	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17262822	17262906	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17262907	17262986	1	-	2	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17262907	17262986	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17262987	17263065	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17263066	17263201	0.3	-	0	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17263066	17263201	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17263202	17263475	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17263476	17263540	0.52	-	2	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17263476	17263540	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17263541	17263718	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17263719	17263764	0.47	-	0	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17263719	17263764	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17263765	17263896	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17263897	17263946	0.4	-	2	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17263897	17263946	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	intron	17263947	17264146	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	CDS	17264147	17264408	0.55	-	0	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	exon	17264147	17264408	.	-	.	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
Phchi.S3	AUGUSTUS	start_codon	17264406	17264408	.	-	0	transcript_id "Phchi.S3G246600.t1"; gene_id "Phchi.S3G246600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14105.t1 is derived from g12572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10877798	10879150	.	+	.	Phchi.S3G142400
Phchi.S3	AUGUSTUS	transcript	10877798	10879150	.	+	.	transcript_id "Phchi.S3G142400.t1"; gene_id "Phchi.S3G142400"
Phchi.S3	AUGUSTUS	start_codon	10877798	10877800	.	+	0	transcript_id "Phchi.S3G142400.t1"; gene_id "Phchi.S3G142400"
Phchi.S3	AUGUSTUS	CDS	10877798	10879150	1	+	0	transcript_id "Phchi.S3G142400.t1"; gene_id "Phchi.S3G142400"
Phchi.S3	AUGUSTUS	exon	10877798	10879150	.	+	.	transcript_id "Phchi.S3G142400.t1"; gene_id "Phchi.S3G142400"
Phchi.S3	AUGUSTUS	stop_codon	10879151	10879153	.	+	0	transcript_id "Phchi.S3G142400.t1"; gene_id "Phchi.S3G142400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11665.t1 is derived from g15716.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7584865	7585554	.	-	.	Phchi.S4G124700
Phchi.S4	AUGUSTUS	transcript	7584865	7585554	.	-	.	transcript_id "Phchi.S4G124700.t1"; gene_id "Phchi.S4G124700"
Phchi.S4	AUGUSTUS	stop_codon	7584862	7584864	.	-	0	transcript_id "Phchi.S4G124700.t1"; gene_id "Phchi.S4G124700"
Phchi.S4	AUGUSTUS	CDS	7584865	7585554	0.89	-	0	transcript_id "Phchi.S4G124700.t1"; gene_id "Phchi.S4G124700"
Phchi.S4	AUGUSTUS	exon	7584865	7585554	.	-	.	transcript_id "Phchi.S4G124700.t1"; gene_id "Phchi.S4G124700"
Phchi.S4	AUGUSTUS	start_codon	7585552	7585554	.	-	0	transcript_id "Phchi.S4G124700.t1"; gene_id "Phchi.S4G124700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4905.t1 is derived from g2075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13335685	13340505	.	+	.	Phchi.S1G206400
Phchi.S1	AUGUSTUS	transcript	13335685	13340505	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	start_codon	13335685	13335687	.	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13335685	13336596	0.91	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13335685	13336596	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13336597	13336694	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13336695	13336878	0.86	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13336695	13336878	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13336879	13337101	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13337102	13337226	0.99	+	2	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13337102	13337226	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13337227	13337345	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13337346	13337453	0.99	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13337346	13337453	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13337454	13337559	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13337560	13337615	0.99	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13337560	13337615	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13337616	13337788	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13337789	13337879	1	+	1	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13337789	13337879	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13337880	13337977	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13337978	13338115	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13337978	13338115	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13338116	13338191	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13338192	13338275	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13338192	13338275	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13338276	13338395	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13338396	13338608	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13338396	13338608	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13338609	13338691	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13338692	13338763	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13338692	13338763	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13338764	13338845	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13338846	13338926	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13338846	13338926	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13338927	13339055	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13339056	13339174	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13339056	13339174	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13339175	13339300	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13339301	13339412	1	+	1	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13339301	13339412	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13339413	13339508	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13339509	13339577	1	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13339509	13339577	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13339578	13339692	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13339693	13339787	0.99	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13339693	13339787	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13339788	13339884	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13339885	13340007	1	+	1	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13339885	13340007	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13340008	13340137	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13340138	13340258	1	+	1	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13340138	13340258	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	intron	13340259	13340346	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	CDS	13340347	13340505	0.96	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	exon	13340347	13340505	.	+	.	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
Phchi.S1	AUGUSTUS	stop_codon	13340506	13340508	.	+	0	transcript_id "Phchi.S1G206400.t1"; gene_id "Phchi.S1G206400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13404.t1 is derived from g11870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6547682	6550404	.	-	.	Phchi.S3G072300
Phchi.S3	AUGUSTUS	transcript	6547682	6550404	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	stop_codon	6547679	6547681	.	-	0	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6547682	6547799	1	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6547682	6547799	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6547800	6547896	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6547897	6548111	1	-	0	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6547897	6548111	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6548112	6548200	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6548201	6548282	1	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6548201	6548282	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6548283	6548352	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6548353	6548598	1	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6548353	6548598	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6548599	6548687	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6548688	6548783	0.99	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6548688	6548783	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6548784	6549130	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6549131	6549250	0.91	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6549131	6549250	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6549251	6549353	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6549354	6549509	0.96	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6549354	6549509	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6549510	6549647	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6549648	6549718	1	-	0	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6549648	6549718	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6549719	6549816	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6549817	6550009	1	-	1	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6549817	6550009	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6550010	6550124	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6550125	6550215	0.96	-	2	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6550125	6550215	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	intron	6550216	6550340	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	CDS	6550341	6550404	0.81	-	0	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	exon	6550341	6550404	.	-	.	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
Phchi.S3	AUGUSTUS	start_codon	6550402	6550404	.	-	0	transcript_id "Phchi.S3G072300.t1"; gene_id "Phchi.S3G072300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8441.t1 is derived from g5616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35947132	35950410	.	+	.	Phchi.S1G560000
Phchi.S1	AUGUSTUS	transcript	35947132	35950410	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	start_codon	35947132	35947134	.	+	0	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35947132	35947172	0.86	+	0	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35947132	35947172	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	intron	35947173	35947253	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35947254	35947386	1	+	1	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35947254	35947386	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	intron	35947387	35947503	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35947504	35947607	1	+	0	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35947504	35947607	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	intron	35947608	35947728	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35947729	35947900	1	+	1	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35947729	35947900	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	intron	35947901	35948018	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35948019	35948159	1	+	0	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35948019	35948159	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	intron	35948160	35948263	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35948264	35950062	0.39	+	0	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35948264	35950062	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	intron	35950063	35950181	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	CDS	35950182	35950410	0.48	+	1	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	exon	35950182	35950410	.	+	.	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
Phchi.S1	AUGUSTUS	stop_codon	35950411	35950413	.	+	0	transcript_id "Phchi.S1G560000.t1"; gene_id "Phchi.S1G560000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6520.t1 is derived from g3692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23463081	23463695	.	+	.	Phchi.S1G367900
Phchi.S1	AUGUSTUS	transcript	23463081	23463695	.	+	.	transcript_id "Phchi.S1G367900.t1"; gene_id "Phchi.S1G367900"
Phchi.S1	AUGUSTUS	start_codon	23463081	23463083	.	+	0	transcript_id "Phchi.S1G367900.t1"; gene_id "Phchi.S1G367900"
Phchi.S1	AUGUSTUS	CDS	23463081	23463695	0.47	+	0	transcript_id "Phchi.S1G367900.t1"; gene_id "Phchi.S1G367900"
Phchi.S1	AUGUSTUS	exon	23463081	23463695	.	+	.	transcript_id "Phchi.S1G367900.t1"; gene_id "Phchi.S1G367900"
Phchi.S1	AUGUSTUS	stop_codon	23463696	23463698	.	+	0	transcript_id "Phchi.S1G367900.t1"; gene_id "Phchi.S1G367900"
# This transcript jg15216.t2 is derived from g13684.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15217.t1 is derived from g13685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17743382	17745489	.	-	.	Phchi.S3G253600
Phchi.S3	AUGUSTUS	transcript	17743382	17745489	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	stop_codon	17743379	17743381	.	-	0	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	CDS	17743382	17743559	1	-	1	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	exon	17743382	17743559	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	intron	17743560	17743651	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	CDS	17743652	17743869	0.98	-	0	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	exon	17743652	17743869	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	intron	17743870	17743986	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	CDS	17743987	17744409	1	-	0	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	exon	17743987	17744409	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	intron	17744410	17744499	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	CDS	17744500	17744693	0.97	-	2	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	exon	17744500	17744693	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	intron	17744694	17744798	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	CDS	17744799	17745489	0.86	-	0	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	exon	17744799	17745489	.	-	.	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
Phchi.S3	AUGUSTUS	start_codon	17745487	17745489	.	-	0	transcript_id "Phchi.S3G253600.t1"; gene_id "Phchi.S3G253600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11010.t1 is derived from g15060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3621476	3622266	.	-	.	Phchi.S4G059200
Phchi.S4	AUGUSTUS	transcript	3621476	3622266	.	-	.	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	stop_codon	3621473	3621475	.	-	0	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	CDS	3621476	3621596	0.57	-	1	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	exon	3621476	3621596	.	-	.	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	intron	3621597	3622011	.	-	.	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	CDS	3622012	3622069	0.61	-	2	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	exon	3622012	3622069	.	-	.	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	intron	3622070	3622238	.	-	.	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	CDS	3622239	3622266	0.43	-	0	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	exon	3622239	3622266	.	-	.	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
Phchi.S4	AUGUSTUS	start_codon	3622264	3622266	.	-	0	transcript_id "Phchi.S4G059200.t1"; gene_id "Phchi.S4G059200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6939.t1 is derived from g4111.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26070276	26072837	.	-	.	Phchi.S1G409800
Phchi.S1	AUGUSTUS	transcript	26070276	26072837	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	stop_codon	26070273	26070275	.	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070276	26070351	1	-	1	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070276	26070351	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26070352	26070449	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070450	26070520	1	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070450	26070520	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26070521	26070640	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070641	26070778	1	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070641	26070778	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26070779	26070865	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070866	26071102	1	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070866	26071102	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26071103	26071284	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26071285	26071985	0.81	-	2	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26071285	26071985	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26071986	26072146	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26072147	26072438	0.58	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26072147	26072438	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26072439	26072597	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26072598	26072837	0.46	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26072598	26072837	.	-	.	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	start_codon	26072835	26072837	.	-	0	transcript_id "Phchi.S1G409800.t1"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	transcript	26070276	26072837	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	stop_codon	26070273	26070275	.	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070276	26070351	0.99	-	1	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070276	26070351	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26070352	26070449	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070450	26070520	1	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070450	26070520	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26070521	26070640	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070641	26070778	1	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070641	26070778	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26070779	26070865	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26070866	26071102	1	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26070866	26071102	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26071103	26071284	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26071285	26071985	0.7	-	2	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26071285	26071985	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26071986	26072155	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26072156	26072438	0.56	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26072156	26072438	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	intron	26072439	26072597	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	CDS	26072598	26072837	0.39	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	exon	26072598	26072837	.	-	.	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
Phchi.S1	AUGUSTUS	start_codon	26072835	26072837	.	-	0	transcript_id "Phchi.S1G409800.t2"; gene_id "Phchi.S1G409800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11716.t1 is derived from g15767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7813638	7815054	.	-	.	Phchi.S4G129800
Phchi.S4	AUGUSTUS	transcript	7814394	7815054	.	-	.	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	stop_codon	7814391	7814393	.	-	0	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814394	7814478	0.3	-	1	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814394	7814478	.	-	.	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7814479	7814641	.	-	.	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814642	7814697	1	-	0	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814642	7814697	.	-	.	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7814698	7814967	.	-	.	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814968	7815054	1	-	0	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814968	7815054	.	-	.	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	start_codon	7815052	7815054	.	-	0	transcript_id "Phchi.S4G129800.t1"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	transcript	7813638	7815054	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	stop_codon	7813635	7813637	.	-	0	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7813638	7813728	0.3	-	1	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7813638	7813728	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7813729	7813856	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7813857	7813915	0.59	-	0	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7813857	7813915	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7813916	7814012	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814013	7814239	0.45	-	2	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814013	7814239	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7814240	7814403	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814404	7814478	0.42	-	2	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814404	7814478	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7814479	7814641	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814642	7814697	1	-	1	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814642	7814697	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7814698	7814775	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814776	7814867	1	-	0	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814776	7814867	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	intron	7814868	7814967	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	CDS	7814968	7815054	1	-	0	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	exon	7814968	7815054	.	-	.	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
Phchi.S4	AUGUSTUS	start_codon	7815052	7815054	.	-	0	transcript_id "Phchi.S4G129800.t2"; gene_id "Phchi.S4G129800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10949.t1 is derived from g14999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3232157	3233943	.	+	.	Phchi.S4G053100
Phchi.S4	AUGUSTUS	transcript	3232157	3233943	.	+	.	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	start_codon	3232157	3232159	.	+	0	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	CDS	3232157	3232244	0.9	+	0	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	exon	3232157	3232244	.	+	.	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	intron	3232245	3232381	.	+	.	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	CDS	3232382	3233943	0.98	+	2	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	exon	3232382	3233943	.	+	.	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	stop_codon	3233944	3233946	.	+	0	transcript_id "Phchi.S4G053100.t1"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	transcript	3232247	3233943	.	+	.	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	start_codon	3232247	3232249	.	+	0	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	CDS	3232247	3232262	0.57	+	0	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	exon	3232247	3232262	.	+	.	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	intron	3232263	3232381	.	+	.	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	CDS	3232382	3233943	0.65	+	2	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	exon	3232382	3233943	.	+	.	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
Phchi.S4	AUGUSTUS	stop_codon	3233944	3233946	.	+	0	transcript_id "Phchi.S4G053100.t2"; gene_id "Phchi.S4G053100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9942.t1 is derived from g7118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44594258	44594598	.	-	.	Phchi.S1G710100
Phchi.S1	AUGUSTUS	transcript	44594258	44594598	.	-	.	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	stop_codon	44594255	44594257	.	-	0	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	CDS	44594258	44594418	0.95	-	2	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	exon	44594258	44594418	.	-	.	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	intron	44594419	44594495	.	-	.	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	CDS	44594496	44594598	0.94	-	0	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	exon	44594496	44594598	.	-	.	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
Phchi.S1	AUGUSTUS	start_codon	44594596	44594598	.	-	0	transcript_id "Phchi.S1G710100.t1"; gene_id "Phchi.S1G710100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6853.t1 is derived from g4025.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25575871	25579104	.	+	.	Phchi.S1G401200
Phchi.S1	AUGUSTUS	transcript	25575871	25579104	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	start_codon	25575871	25575873	.	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25575871	25575957	0.57	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25575871	25575957	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25575958	25576051	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25576052	25576230	0.57	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25576052	25576230	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25576231	25576349	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25576350	25576412	0.99	+	1	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25576350	25576412	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25576413	25576487	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25576488	25576617	0.85	+	1	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25576488	25576617	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25576618	25576706	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25576707	25576794	0.97	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25576707	25576794	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25576795	25576870	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25576871	25577013	1	+	2	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25576871	25577013	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25577014	25577103	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25577104	25577191	1	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25577104	25577191	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25577192	25577265	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25577266	25577378	0.99	+	2	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25577266	25577378	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25577379	25577457	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25577458	25577650	1	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25577458	25577650	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25577651	25577737	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25577738	25577841	1	+	2	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25577738	25577841	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25577842	25577919	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25577920	25578027	1	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25577920	25578027	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25578028	25578116	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25578117	25578287	0.96	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25578117	25578287	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25578288	25578392	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25578393	25578538	1	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25578393	25578538	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25578539	25578614	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25578615	25578786	1	+	1	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25578615	25578786	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	intron	25578787	25578879	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	CDS	25578880	25579104	1	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	exon	25578880	25579104	.	+	.	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
Phchi.S1	AUGUSTUS	stop_codon	25579105	25579107	.	+	0	transcript_id "Phchi.S1G401200.t1"; gene_id "Phchi.S1G401200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12322.t1 is derived from g7998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10763303	10772294	.	-	.	Phchi.S2G040200
Phchi.S2	AUGUSTUS	transcript	10763303	10772294	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	stop_codon	10763300	10763302	.	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10763303	10763497	0.8	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10763303	10763497	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10763498	10763678	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10763679	10765052	0.9	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10763679	10765052	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10765053	10765227	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10765228	10765615	0.6	-	1	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10765228	10765615	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10765616	10765724	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10765725	10765776	0.92	-	2	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10765725	10765776	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10765777	10765862	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10765863	10765939	0.57	-	1	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10765863	10765939	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10765940	10766036	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10766037	10766128	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10766037	10766128	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10766129	10766238	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10766239	10766316	0.98	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10766239	10766316	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10766317	10766485	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10766486	10766557	0.95	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10766486	10766557	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10766558	10766718	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10766719	10766799	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10766719	10766799	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10766800	10766921	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10766922	10766975	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10766922	10766975	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10766976	10767070	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10767071	10767267	1	-	2	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10767071	10767267	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10767268	10767590	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10767591	10767675	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10767591	10767675	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10767676	10767852	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10767853	10768608	0.97	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10767853	10768608	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10768609	10768722	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10768723	10768806	0.98	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10768723	10768806	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10768807	10768987	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10768988	10769110	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10768988	10769110	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10769111	10769268	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10769269	10769523	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10769269	10769523	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10769524	10769612	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10769613	10769735	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10769613	10769735	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10769736	10769859	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10769860	10771336	0.77	-	1	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10769860	10771336	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10771337	10771585	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10771586	10771674	1	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10771586	10771674	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10771675	10771988	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10771989	10772043	1	-	1	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10771989	10772043	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	intron	10772044	10772205	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	CDS	10772206	10772294	0.83	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	exon	10772206	10772294	.	-	.	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
Phchi.S2	AUGUSTUS	start_codon	10772292	10772294	.	-	0	transcript_id "Phchi.S2G040200.t1"; gene_id "Phchi.S2G040200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7570.t1 is derived from g4744.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30087320	30087898	.	-	.	Phchi.S1G472900
Phchi.S1	AUGUSTUS	transcript	30087320	30087898	.	-	.	transcript_id "Phchi.S1G472900.t1"; gene_id "Phchi.S1G472900"
Phchi.S1	AUGUSTUS	stop_codon	30087317	30087319	.	-	0	transcript_id "Phchi.S1G472900.t1"; gene_id "Phchi.S1G472900"
Phchi.S1	AUGUSTUS	CDS	30087320	30087898	0.44	-	0	transcript_id "Phchi.S1G472900.t1"; gene_id "Phchi.S1G472900"
Phchi.S1	AUGUSTUS	exon	30087320	30087898	.	-	.	transcript_id "Phchi.S1G472900.t1"; gene_id "Phchi.S1G472900"
Phchi.S1	AUGUSTUS	start_codon	30087896	30087898	.	-	0	transcript_id "Phchi.S1G472900.t1"; gene_id "Phchi.S1G472900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3323.t1 is derived from g492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2903967	2904582	.	+	.	Phchi.S1G048200
Phchi.S1	AUGUSTUS	transcript	2903967	2904582	.	+	.	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	start_codon	2903967	2903969	.	+	0	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	CDS	2903967	2904335	0.43	+	0	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	exon	2903967	2904335	.	+	.	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	intron	2904336	2904411	.	+	.	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	CDS	2904412	2904582	0.5	+	0	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	exon	2904412	2904582	.	+	.	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
Phchi.S1	AUGUSTUS	stop_codon	2904583	2904585	.	+	0	transcript_id "Phchi.S1G048200.t1"; gene_id "Phchi.S1G048200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14458.t1 is derived from g12926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12975931	12976937	.	+	.	Phchi.S3G177700
Phchi.S3	AUGUSTUS	transcript	12975931	12976937	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	start_codon	12975931	12975933	.	+	0	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	CDS	12975931	12976023	0.44	+	0	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	exon	12975931	12976023	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	intron	12976024	12976103	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	CDS	12976104	12976191	0.93	+	0	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	exon	12976104	12976191	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	intron	12976192	12976272	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	CDS	12976273	12976337	1	+	2	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	exon	12976273	12976337	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	intron	12976338	12976521	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	CDS	12976522	12976590	1	+	0	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	exon	12976522	12976590	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	intron	12976591	12976674	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	CDS	12976675	12976724	0.99	+	0	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	exon	12976675	12976724	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	intron	12976725	12976828	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	CDS	12976829	12976937	0.99	+	1	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	exon	12976829	12976937	.	+	.	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
Phchi.S3	AUGUSTUS	stop_codon	12976938	12976940	.	+	0	transcript_id "Phchi.S3G177700.t1"; gene_id "Phchi.S3G177700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9181.t1 is derived from g6356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40240118	40241031	.	-	.	Phchi.S1G634000
Phchi.S1	AUGUSTUS	transcript	40240118	40241031	.	-	.	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	stop_codon	40240115	40240117	.	-	0	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	CDS	40240118	40240795	1	-	0	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	exon	40240118	40240795	.	-	.	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	intron	40240796	40240926	.	-	.	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	CDS	40240927	40241031	0.91	-	0	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	exon	40240927	40241031	.	-	.	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
Phchi.S1	AUGUSTUS	start_codon	40241029	40241031	.	-	0	transcript_id "Phchi.S1G634000.t1"; gene_id "Phchi.S1G634000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14297.t1 is derived from g12764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11987031	11988280	.	-	.	Phchi.S3G161600
Phchi.S3	AUGUSTUS	transcript	11987031	11988280	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	stop_codon	11987028	11987030	.	-	0	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11987031	11987094	0.87	-	1	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11987031	11987094	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11987095	11987196	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11987197	11987309	0.88	-	0	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11987197	11987309	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11987310	11987389	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11987390	11987470	1	-	0	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11987390	11987470	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11987471	11987556	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11987557	11987609	1	-	2	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11987557	11987609	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11987610	11987698	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11987699	11987807	1	-	0	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11987699	11987807	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11987808	11987878	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11987879	11987934	1	-	2	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11987879	11987934	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11987935	11988019	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11988020	11988106	1	-	2	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11988020	11988106	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	intron	11988107	11988186	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	CDS	11988187	11988280	1	-	0	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	exon	11988187	11988280	.	-	.	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
Phchi.S3	AUGUSTUS	start_codon	11988278	11988280	.	-	0	transcript_id "Phchi.S3G161600.t1"; gene_id "Phchi.S3G161600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1169.t1 is derived from g10952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8254682	8258503	.	+	.	Phchi.S6G112800
Phchi.S6	AUGUSTUS	transcript	8256473	8258503	.	+	.	transcript_id "Phchi.S6G112800.t1"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	start_codon	8256473	8256475	.	+	0	transcript_id "Phchi.S6G112800.t1"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	CDS	8256473	8258503	1	+	0	transcript_id "Phchi.S6G112800.t1"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	exon	8256473	8258503	.	+	.	transcript_id "Phchi.S6G112800.t1"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	stop_codon	8258504	8258506	.	+	0	transcript_id "Phchi.S6G112800.t1"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	transcript	8254682	8258503	.	+	.	transcript_id "Phchi.S6G112800.t2"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	start_codon	8254682	8254684	.	+	0	transcript_id "Phchi.S6G112800.t2"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	CDS	8254682	8258503	0.98	+	0	transcript_id "Phchi.S6G112800.t2"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	exon	8254682	8258503	.	+	.	transcript_id "Phchi.S6G112800.t2"; gene_id "Phchi.S6G112800"
Phchi.S6	AUGUSTUS	stop_codon	8258504	8258506	.	+	0	transcript_id "Phchi.S6G112800.t2"; gene_id "Phchi.S6G112800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg568.t1 is derived from g10350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4085234	4086472	.	-	.	Phchi.S6G052700
Phchi.S6	AUGUSTUS	transcript	4085234	4086472	.	-	.	transcript_id "Phchi.S6G052700.t1"; gene_id "Phchi.S6G052700"
Phchi.S6	AUGUSTUS	stop_codon	4085231	4085233	.	-	0	transcript_id "Phchi.S6G052700.t1"; gene_id "Phchi.S6G052700"
Phchi.S6	AUGUSTUS	CDS	4085234	4086472	0.7	-	0	transcript_id "Phchi.S6G052700.t1"; gene_id "Phchi.S6G052700"
Phchi.S6	AUGUSTUS	exon	4085234	4086472	.	-	.	transcript_id "Phchi.S6G052700.t1"; gene_id "Phchi.S6G052700"
Phchi.S6	AUGUSTUS	start_codon	4086470	4086472	.	-	0	transcript_id "Phchi.S6G052700.t1"; gene_id "Phchi.S6G052700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8333.t1 is derived from g5508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35365669	35367589	.	+	.	Phchi.S1G549200
Phchi.S1	AUGUSTUS	transcript	35365669	35367589	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	start_codon	35365669	35365671	.	+	0	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	CDS	35365669	35365747	0.46	+	0	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	exon	35365669	35365747	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	intron	35365748	35366056	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	CDS	35366057	35366133	0.92	+	2	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	exon	35366057	35366133	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	intron	35366134	35366228	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	CDS	35366229	35366516	0.91	+	0	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	exon	35366229	35366516	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	intron	35366517	35366644	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	CDS	35366645	35367589	0.56	+	0	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	exon	35366645	35367589	.	+	.	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
Phchi.S1	AUGUSTUS	stop_codon	35367590	35367592	.	+	0	transcript_id "Phchi.S1G549200.t1"; gene_id "Phchi.S1G549200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13611.t1 is derived from g12078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7684533	7686812	.	+	.	Phchi.S3G093000
Phchi.S3	AUGUSTUS	transcript	7684533	7686812	.	+	.	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	start_codon	7684533	7684535	.	+	0	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	CDS	7684533	7685372	0.42	+	0	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	exon	7684533	7685372	.	+	.	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	intron	7685373	7685591	.	+	.	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	CDS	7685592	7685717	0.3	+	0	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	exon	7685592	7685717	.	+	.	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	intron	7685718	7686029	.	+	.	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	CDS	7686030	7686812	0.49	+	0	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	exon	7686030	7686812	.	+	.	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
Phchi.S3	AUGUSTUS	stop_codon	7686813	7686815	.	+	0	transcript_id "Phchi.S3G093000.t1"; gene_id "Phchi.S3G093000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15528.t1 is derived from g13997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19729893	19732004	.	+	.	Phchi.S3G284700
Phchi.S3	AUGUSTUS	transcript	19729893	19732004	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	start_codon	19729893	19729895	.	+	0	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19729893	19730241	0.86	+	0	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19729893	19730241	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	intron	19730242	19730323	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19730324	19730460	1	+	2	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19730324	19730460	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	intron	19730461	19730540	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19730541	19730929	1	+	0	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19730541	19730929	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	intron	19730930	19731021	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19731022	19731121	1	+	1	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19731022	19731121	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	intron	19731122	19731228	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19731229	19731430	1	+	0	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19731229	19731430	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	intron	19731431	19731532	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19731533	19731590	0.99	+	2	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19731533	19731590	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	intron	19731591	19731691	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	CDS	19731692	19732004	0.85	+	1	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	exon	19731692	19732004	.	+	.	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
Phchi.S3	AUGUSTUS	stop_codon	19732005	19732007	.	+	0	transcript_id "Phchi.S3G284700.t1"; gene_id "Phchi.S3G284700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4667.t1 is derived from g1837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11708082	11709183	.	+	.	Phchi.S1G182600
Phchi.S1	AUGUSTUS	transcript	11708082	11709183	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	start_codon	11708082	11708084	.	+	0	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	CDS	11708082	11708122	0.69	+	0	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	exon	11708082	11708122	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	intron	11708123	11708196	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	CDS	11708197	11708557	0.54	+	1	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	exon	11708197	11708557	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	intron	11708558	11708660	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	CDS	11708661	11709001	0.7	+	0	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	exon	11708661	11709001	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	intron	11709002	11709101	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	CDS	11709102	11709183	0.71	+	1	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	exon	11709102	11709183	.	+	.	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
Phchi.S1	AUGUSTUS	stop_codon	11709184	11709186	.	+	0	transcript_id "Phchi.S1G182600.t1"; gene_id "Phchi.S1G182600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4312.t1 is derived from g1481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9573937	9575399	.	+	.	Phchi.S1G147100
Phchi.S1	AUGUSTUS	transcript	9573937	9575399	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	start_codon	9573937	9573939	.	+	0	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9573937	9574016	0.73	+	0	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9573937	9574016	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	intron	9574017	9574258	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9574259	9574315	1	+	1	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9574259	9574315	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	intron	9574316	9574412	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9574413	9574501	1	+	1	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9574413	9574501	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	intron	9574502	9574594	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9574595	9574668	1	+	2	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9574595	9574668	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	intron	9574669	9574855	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9574856	9575006	0.99	+	0	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9574856	9575006	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	intron	9575007	9575105	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9575106	9575273	0.99	+	2	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9575106	9575273	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	intron	9575274	9575364	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	CDS	9575365	9575399	1	+	2	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	exon	9575365	9575399	.	+	.	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
Phchi.S1	AUGUSTUS	stop_codon	9575400	9575402	.	+	0	transcript_id "Phchi.S1G147100.t1"; gene_id "Phchi.S1G147100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14714.t1 is derived from g13182.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14341557	14341831	.	+	.	Phchi.S3G203300
Phchi.S3	AUGUSTUS	transcript	14341557	14341831	.	+	.	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	start_codon	14341557	14341559	.	+	0	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	CDS	14341557	14341749	0.98	+	0	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	exon	14341557	14341749	.	+	.	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	intron	14341750	14341823	.	+	.	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	CDS	14341824	14341831	0.99	+	2	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	exon	14341824	14341831	.	+	.	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
Phchi.S3	AUGUSTUS	stop_codon	14341832	14341834	.	+	0	transcript_id "Phchi.S3G203300.t1"; gene_id "Phchi.S3G203300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7991.t1 is derived from g5166.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32276341	32283290	.	+	.	Phchi.S1G515000
Phchi.S1	AUGUSTUS	transcript	32276341	32283290	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	start_codon	32276341	32276343	.	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32276341	32276544	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32276341	32276544	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32276545	32276849	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32276850	32276952	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32276850	32276952	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32276953	32277076	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277077	32277153	1	+	2	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277077	32277153	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277154	32277236	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277237	32277428	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277237	32277428	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277429	32277584	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277585	32277704	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277585	32277704	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277705	32277791	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277792	32277854	0.99	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277792	32277854	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277855	32277958	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277959	32278108	0.98	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277959	32278108	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278109	32278287	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278288	32278452	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278288	32278452	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278453	32278582	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278583	32278660	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278583	32278660	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278661	32278789	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278790	32278876	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278790	32278876	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278877	32278980	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278981	32279343	0.98	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278981	32279343	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32279344	32279584	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32279585	32279683	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32279585	32279683	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32279684	32279766	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32279767	32279862	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32279767	32279862	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32279863	32279975	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32279976	32280046	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32279976	32280046	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280047	32280169	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280170	32280298	1	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280170	32280298	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280299	32280393	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280394	32280470	1	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280394	32280470	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280471	32280573	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280574	32280614	1	+	2	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280574	32280614	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280615	32280701	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280702	32280776	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280702	32280776	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280777	32280865	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280866	32281023	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280866	32281023	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281024	32281163	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281164	32281268	0.99	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281164	32281268	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281269	32281370	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281371	32281446	1	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281371	32281446	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281447	32281551	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281552	32281631	1	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281552	32281631	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281632	32281746	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281747	32282409	0.82	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281747	32282409	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32282410	32282775	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32282776	32282796	0.91	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32282776	32282796	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32282797	32283054	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32283055	32283095	0.97	+	1	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32283055	32283095	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32283096	32283285	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32283286	32283290	0.97	+	2	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32283286	32283290	.	+	.	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	stop_codon	32283291	32283293	.	+	0	transcript_id "Phchi.S1G515000.t1"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	transcript	32276341	32283290	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	start_codon	32276341	32276343	.	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32276341	32276544	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32276341	32276544	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32276545	32276849	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32276850	32276952	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32276850	32276952	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32276953	32277076	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277077	32277153	1	+	2	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277077	32277153	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277154	32277236	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277237	32277428	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277237	32277428	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277429	32277584	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277585	32277704	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277585	32277704	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277705	32277791	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277792	32277854	0.96	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277792	32277854	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32277855	32277958	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32277959	32278108	0.9	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32277959	32278108	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278109	32278287	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278288	32278452	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278288	32278452	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278453	32278582	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278583	32278660	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278583	32278660	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278661	32278789	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278790	32278876	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278790	32278876	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32278877	32278980	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32278981	32279070	0.98	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32278981	32279070	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32279071	32279584	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32279585	32279683	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32279585	32279683	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32279684	32279766	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32279767	32279862	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32279767	32279862	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32279863	32279975	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32279976	32280046	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32279976	32280046	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280047	32280169	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280170	32280298	1	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280170	32280298	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280299	32280393	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280394	32280470	1	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280394	32280470	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280471	32280573	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280574	32280614	1	+	2	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280574	32280614	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280615	32280701	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280702	32280776	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280702	32280776	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32280777	32280865	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32280866	32281023	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32280866	32281023	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281024	32281163	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281164	32281268	1	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281164	32281268	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281269	32281370	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281371	32281446	1	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281371	32281446	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281447	32281551	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281552	32281631	1	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281552	32281631	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32281632	32281746	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32281747	32282409	0.79	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32281747	32282409	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32282410	32282775	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32282776	32282796	0.91	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32282776	32282796	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32282797	32283054	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32283055	32283095	0.94	+	1	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32283055	32283095	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	intron	32283096	32283285	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	CDS	32283286	32283290	0.94	+	2	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	exon	32283286	32283290	.	+	.	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
Phchi.S1	AUGUSTUS	stop_codon	32283291	32283293	.	+	0	transcript_id "Phchi.S1G515000.t2"; gene_id "Phchi.S1G515000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15183.t1 is derived from g13651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17435450	17436738	.	-	.	Phchi.S3G250200
Phchi.S3	AUGUSTUS	transcript	17435450	17436738	.	-	.	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	stop_codon	17435447	17435449	.	-	0	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	CDS	17435450	17435753	1	-	1	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	exon	17435450	17435753	.	-	.	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	intron	17435754	17435833	.	-	.	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	CDS	17435834	17436146	1	-	2	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	exon	17435834	17436146	.	-	.	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	intron	17436147	17436239	.	-	.	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	CDS	17436240	17436738	1	-	0	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	exon	17436240	17436738	.	-	.	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
Phchi.S3	AUGUSTUS	start_codon	17436736	17436738	.	-	0	transcript_id "Phchi.S3G250200.t1"; gene_id "Phchi.S3G250200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11982.t1 is derived from g7657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	339265	340569	.	+	.	Phchi.S2G006200
Phchi.S2	AUGUSTUS	transcript	339265	340569	.	+	.	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	start_codon	339265	339267	.	+	0	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	CDS	339265	339516	0.54	+	0	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	exon	339265	339516	.	+	.	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	intron	339517	339609	.	+	.	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	CDS	339610	340569	0.93	+	0	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	exon	339610	340569	.	+	.	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
Phchi.S2	AUGUSTUS	stop_codon	340570	340572	.	+	0	transcript_id "Phchi.S2G006200.t1"; gene_id "Phchi.S2G006200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2711.t1 is derived from g9631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8295096	8296860	.	+	.	Phchi.S5G132000
Phchi.S5	AUGUSTUS	transcript	8295096	8296860	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	start_codon	8295096	8295098	.	+	0	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	CDS	8295096	8295461	0.76	+	0	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	exon	8295096	8295461	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	intron	8295462	8295531	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	CDS	8295532	8295581	0.72	+	0	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	exon	8295532	8295581	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	intron	8295582	8295772	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	CDS	8295773	8295827	0.5	+	1	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	exon	8295773	8295827	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	intron	8295828	8295907	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	CDS	8295908	8296032	0.55	+	0	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	exon	8295908	8296032	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	intron	8296033	8296814	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	CDS	8296815	8296860	0.97	+	1	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	exon	8296815	8296860	.	+	.	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
Phchi.S5	AUGUSTUS	stop_codon	8296861	8296863	.	+	0	transcript_id "Phchi.S5G132000.t1"; gene_id "Phchi.S5G132000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11566.t1 is derived from g15617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7085167	7089242	.	-	.	Phchi.S4G114800
Phchi.S4	AUGUSTUS	transcript	7085167	7089242	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	stop_codon	7085164	7085166	.	-	0	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7085167	7085470	0.59	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7085167	7085470	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7085471	7085609	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7085610	7085719	0.3	-	0	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7085610	7085719	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7085720	7085871	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7085872	7085914	0.39	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7085872	7085914	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7085915	7085993	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7085994	7086045	0.41	-	2	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7085994	7086045	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7086046	7086247	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7086248	7086873	0.88	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7086248	7086873	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7086874	7087000	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7087001	7087153	1	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7087001	7087153	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7087154	7087307	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7087308	7087466	1	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7087308	7087466	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7087467	7087604	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7087605	7087919	0.99	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7087605	7087919	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7087920	7088015	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7088016	7088180	1	-	1	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7088016	7088180	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	intron	7088181	7088262	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	CDS	7088263	7089242	0.98	-	0	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	exon	7088263	7089242	.	-	.	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
Phchi.S4	AUGUSTUS	start_codon	7089240	7089242	.	-	0	transcript_id "Phchi.S4G114800.t1"; gene_id "Phchi.S4G114800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15931.t1 is derived from g16032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C71	AUGUSTUS	gene	28021	28695	.	-	.	Phchi.C71G000200
Phchi.C71	AUGUSTUS	transcript	28021	28695	.	-	.	transcript_id "Phchi.C71G000200.t1"; gene_id "Phchi.C71G000200"
Phchi.C71	AUGUSTUS	stop_codon	28018	28020	.	-	0	transcript_id "Phchi.C71G000200.t1"; gene_id "Phchi.C71G000200"
Phchi.C71	AUGUSTUS	CDS	28021	28695	0.76	-	0	transcript_id "Phchi.C71G000200.t1"; gene_id "Phchi.C71G000200"
Phchi.C71	AUGUSTUS	exon	28021	28695	.	-	.	transcript_id "Phchi.C71G000200.t1"; gene_id "Phchi.C71G000200"
Phchi.C71	AUGUSTUS	start_codon	28693	28695	.	-	0	transcript_id "Phchi.C71G000200.t1"; gene_id "Phchi.C71G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12236.t1 is derived from g7912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6928277	6929764	.	-	.	Phchi.S2G031600
Phchi.S2	AUGUSTUS	transcript	6928277	6929764	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	stop_codon	6928274	6928276	.	-	0	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	CDS	6928277	6928474	0.99	-	0	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	exon	6928277	6928474	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	intron	6928475	6928566	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	CDS	6928567	6928690	1	-	1	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	exon	6928567	6928690	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	intron	6928691	6928774	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	CDS	6928775	6928900	1	-	1	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	exon	6928775	6928900	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	intron	6928901	6929009	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	CDS	6929010	6929090	0.97	-	1	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	exon	6929010	6929090	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	intron	6929091	6929162	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	CDS	6929163	6929764	0.77	-	0	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	exon	6929163	6929764	.	-	.	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
Phchi.S2	AUGUSTUS	start_codon	6929762	6929764	.	-	0	transcript_id "Phchi.S2G031600.t1"; gene_id "Phchi.S2G031600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13387.t1 is derived from g11853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6493007	6495415	.	-	.	Phchi.S3G070600
Phchi.S3	AUGUSTUS	transcript	6493007	6495415	.	-	.	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	stop_codon	6493004	6493006	.	-	0	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	CDS	6493007	6494945	0.55	-	1	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	exon	6493007	6494945	.	-	.	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	intron	6494946	6495229	.	-	.	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	CDS	6495230	6495261	0.36	-	0	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	exon	6495230	6495261	.	-	.	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	intron	6495262	6495397	.	-	.	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	CDS	6495398	6495415	0.42	-	0	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	exon	6495398	6495415	.	-	.	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
Phchi.S3	AUGUSTUS	start_codon	6495413	6495415	.	-	0	transcript_id "Phchi.S3G070600.t1"; gene_id "Phchi.S3G070600"
# This transcript jg1116.t2 is derived from g10899.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1117.t1 is derived from g10900.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7783108	7786051	.	-	.	Phchi.S6G107600
Phchi.S6	AUGUSTUS	transcript	7783108	7786051	.	-	.	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	stop_codon	7783105	7783107	.	-	0	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	CDS	7783108	7784540	0.77	-	2	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	exon	7783108	7784540	.	-	.	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	intron	7784541	7784656	.	-	.	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	CDS	7784657	7785611	0.4	-	0	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	exon	7784657	7785611	.	-	.	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	intron	7785612	7785727	.	-	.	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	CDS	7785728	7786051	0.37	-	0	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	exon	7785728	7786051	.	-	.	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	start_codon	7786049	7786051	.	-	0	transcript_id "Phchi.S6G107600.t1"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	transcript	7783108	7783725	.	-	.	transcript_id "Phchi.S6G107600.t2"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	stop_codon	7783105	7783107	.	-	0	transcript_id "Phchi.S6G107600.t2"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	CDS	7783108	7783725	0.75	-	0	transcript_id "Phchi.S6G107600.t2"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	exon	7783108	7783725	.	-	.	transcript_id "Phchi.S6G107600.t2"; gene_id "Phchi.S6G107600"
Phchi.S6	AUGUSTUS	start_codon	7783723	7783725	.	-	0	transcript_id "Phchi.S6G107600.t2"; gene_id "Phchi.S6G107600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6781.t1 is derived from g3953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25063291	25066692	.	-	.	Phchi.S1G394000
Phchi.S1	AUGUSTUS	transcript	25063291	25066692	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	stop_codon	25063288	25063290	.	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25063291	25063404	0.91	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25063291	25063404	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25063405	25063560	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25063561	25063669	1	-	1	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25063561	25063669	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25063670	25063771	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25063772	25063920	0.99	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25063772	25063920	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25063921	25064008	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25064009	25064111	1	-	1	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25064009	25064111	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25064112	25064254	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25064255	25064430	1	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25064255	25064430	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25064431	25064614	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25064615	25064677	1	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25064615	25064677	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25064678	25064755	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25064756	25064844	1	-	2	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25064756	25064844	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25064845	25065123	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25065124	25065234	1	-	2	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25065124	25065234	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25065235	25065336	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25065337	25065471	1	-	2	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25065337	25065471	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25065472	25065574	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25065575	25065740	0.99	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25065575	25065740	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25065741	25065875	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25065876	25066157	1	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25065876	25066157	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	intron	25066158	25066392	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	CDS	25066393	25066692	0.99	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	exon	25066393	25066692	.	-	.	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
Phchi.S1	AUGUSTUS	start_codon	25066690	25066692	.	-	0	transcript_id "Phchi.S1G394000.t1"; gene_id "Phchi.S1G394000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg612.t1 is derived from g10394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4400576	4403323	.	+	.	Phchi.S6G057100
Phchi.S6	AUGUSTUS	transcript	4400576	4403323	.	+	.	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	start_codon	4400576	4400578	.	+	0	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	CDS	4400576	4400709	0.48	+	0	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	exon	4400576	4400709	.	+	.	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	intron	4400710	4400823	.	+	.	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	CDS	4400824	4403323	0.59	+	1	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	exon	4400824	4403323	.	+	.	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
Phchi.S6	AUGUSTUS	stop_codon	4403324	4403326	.	+	0	transcript_id "Phchi.S6G057100.t1"; gene_id "Phchi.S6G057100"
# This transcript jg11925.t2 is derived from g7600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11926.t1 is derived from g7601.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	50731	51637	.	+	.	Phchi.S2G000600
Phchi.S2	AUGUSTUS	transcript	50731	51637	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	start_codon	50731	50733	.	+	0	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	CDS	50731	50765	0.52	+	0	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	exon	50731	50765	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	intron	50766	50838	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	CDS	50839	50919	1	+	1	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	exon	50839	50919	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	intron	50920	50997	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	CDS	50998	51114	1	+	1	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	exon	50998	51114	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	intron	51115	51197	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	CDS	51198	51232	1	+	1	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	exon	51198	51232	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	intron	51233	51340	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	CDS	51341	51441	1	+	2	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	exon	51341	51441	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	intron	51442	51559	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	CDS	51560	51637	1	+	0	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	exon	51560	51637	.	+	.	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
Phchi.S2	AUGUSTUS	stop_codon	51638	51640	.	+	0	transcript_id "Phchi.S2G000600.t1"; gene_id "Phchi.S2G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9787.t1 is derived from g6963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43685998	43687833	.	-	.	Phchi.S1G694600
Phchi.S1	AUGUSTUS	transcript	43685998	43687833	.	-	.	transcript_id "Phchi.S1G694600.t1"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	stop_codon	43685995	43685997	.	-	0	transcript_id "Phchi.S1G694600.t1"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	CDS	43685998	43687833	0.66	-	0	transcript_id "Phchi.S1G694600.t1"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	exon	43685998	43687833	.	-	.	transcript_id "Phchi.S1G694600.t1"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	start_codon	43687831	43687833	.	-	0	transcript_id "Phchi.S1G694600.t1"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	transcript	43685998	43687254	.	-	.	transcript_id "Phchi.S1G694600.t2"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	stop_codon	43685995	43685997	.	-	0	transcript_id "Phchi.S1G694600.t2"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	CDS	43685998	43687254	0.54	-	0	transcript_id "Phchi.S1G694600.t2"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	exon	43685998	43687254	.	-	.	transcript_id "Phchi.S1G694600.t2"; gene_id "Phchi.S1G694600"
Phchi.S1	AUGUSTUS	start_codon	43687252	43687254	.	-	0	transcript_id "Phchi.S1G694600.t2"; gene_id "Phchi.S1G694600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11875.t1 is derived from g15927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8946358	8947758	.	+	.	Phchi.S4G145700
Phchi.S4	AUGUSTUS	transcript	8946358	8947758	.	+	.	transcript_id "Phchi.S4G145700.t1"; gene_id "Phchi.S4G145700"
Phchi.S4	AUGUSTUS	start_codon	8946358	8946360	.	+	0	transcript_id "Phchi.S4G145700.t1"; gene_id "Phchi.S4G145700"
Phchi.S4	AUGUSTUS	CDS	8946358	8947758	0.98	+	0	transcript_id "Phchi.S4G145700.t1"; gene_id "Phchi.S4G145700"
Phchi.S4	AUGUSTUS	exon	8946358	8947758	.	+	.	transcript_id "Phchi.S4G145700.t1"; gene_id "Phchi.S4G145700"
Phchi.S4	AUGUSTUS	stop_codon	8947759	8947761	.	+	0	transcript_id "Phchi.S4G145700.t1"; gene_id "Phchi.S4G145700"
# This transcript jg1959.t2 is derived from g8879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1959.t3 is derived from g8879.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1959.t4 is derived from g8879.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1960.t1 is derived from g8880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4035025	4035676	.	-	.	Phchi.S5G056900
Phchi.S5	AUGUSTUS	transcript	4035025	4035676	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	stop_codon	4035022	4035024	.	-	0	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035025	4035205	1	-	1	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035025	4035205	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035206	4035298	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035299	4035371	1	-	2	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035299	4035371	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035372	4035457	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035458	4035497	1	-	0	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035458	4035497	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035498	4035577	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035578	4035676	0.93	-	0	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035578	4035676	.	-	.	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	start_codon	4035674	4035676	.	-	0	transcript_id "Phchi.S5G056900.t1"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	transcript	4035025	4035676	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	stop_codon	4035022	4035024	.	-	0	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035025	4035205	1	-	1	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035025	4035205	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035206	4035285	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035286	4035303	0.48	-	1	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035286	4035303	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035304	4035364	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035365	4035371	0.55	-	2	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035365	4035371	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035372	4035457	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035458	4035497	0.55	-	0	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035458	4035497	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	intron	4035498	4035577	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	CDS	4035578	4035676	0.51	-	0	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	exon	4035578	4035676	.	-	.	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
Phchi.S5	AUGUSTUS	start_codon	4035674	4035676	.	-	0	transcript_id "Phchi.S5G056900.t2"; gene_id "Phchi.S5G056900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8813.t1 is derived from g5988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38099864	38100685	.	-	.	Phchi.S1G597200
Phchi.S1	AUGUSTUS	transcript	38099864	38100685	.	-	.	transcript_id "Phchi.S1G597200.t1"; gene_id "Phchi.S1G597200"
Phchi.S1	AUGUSTUS	stop_codon	38099861	38099863	.	-	0	transcript_id "Phchi.S1G597200.t1"; gene_id "Phchi.S1G597200"
Phchi.S1	AUGUSTUS	CDS	38099864	38100685	0.78	-	0	transcript_id "Phchi.S1G597200.t1"; gene_id "Phchi.S1G597200"
Phchi.S1	AUGUSTUS	exon	38099864	38100685	.	-	.	transcript_id "Phchi.S1G597200.t1"; gene_id "Phchi.S1G597200"
Phchi.S1	AUGUSTUS	start_codon	38100683	38100685	.	-	0	transcript_id "Phchi.S1G597200.t1"; gene_id "Phchi.S1G597200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3596.t1 is derived from g765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4665563	4666890	.	+	.	Phchi.S1G075500
Phchi.S1	AUGUSTUS	transcript	4665563	4666890	.	+	.	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	start_codon	4665563	4665565	.	+	0	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	CDS	4665563	4665965	0.75	+	0	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	exon	4665563	4665965	.	+	.	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	intron	4665966	4666159	.	+	.	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	CDS	4666160	4666890	0.46	+	2	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	exon	4666160	4666890	.	+	.	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
Phchi.S1	AUGUSTUS	stop_codon	4666891	4666893	.	+	0	transcript_id "Phchi.S1G075500.t1"; gene_id "Phchi.S1G075500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10406.t1 is derived from g7582.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47676580	47677668	.	+	.	Phchi.S1G756500
Phchi.S1	AUGUSTUS	transcript	47676580	47677668	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	start_codon	47676580	47676582	.	+	0	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	CDS	47676580	47676640	0.8	+	0	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	exon	47676580	47676640	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	intron	47676641	47676938	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	CDS	47676939	47677072	1	+	2	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	exon	47676939	47677072	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	intron	47677073	47677279	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	CDS	47677280	47677348	0.93	+	0	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	exon	47677280	47677348	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	intron	47677349	47677623	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	CDS	47677624	47677668	0.55	+	0	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	exon	47677624	47677668	.	+	.	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
Phchi.S1	AUGUSTUS	stop_codon	47677669	47677671	.	+	0	transcript_id "Phchi.S1G756500.t1"; gene_id "Phchi.S1G756500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12320.t1 is derived from g7996.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10581591	10584638	.	+	.	Phchi.S2G040000
Phchi.S2	AUGUSTUS	transcript	10581591	10584638	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	start_codon	10581591	10581593	.	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10581591	10581912	0.68	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10581591	10581912	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10581913	10582001	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10582002	10582097	0.34	+	2	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10582002	10582097	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10582098	10582173	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10582174	10582385	0.53	+	2	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10582174	10582385	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10582386	10583011	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10583012	10583113	0.99	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10583012	10583113	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10583114	10583304	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10583305	10583319	0.99	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10583305	10583319	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10583320	10583583	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10583584	10584213	0.94	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10583584	10584213	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10584214	10584400	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10584401	10584472	1	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10584401	10584472	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	intron	10584473	10584554	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	CDS	10584555	10584638	0.66	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	exon	10584555	10584638	.	+	.	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
Phchi.S2	AUGUSTUS	stop_codon	10584639	10584641	.	+	0	transcript_id "Phchi.S2G040000.t1"; gene_id "Phchi.S2G040000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6463.t1 is derived from g3635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23129586	23129924	.	-	.	Phchi.S1G362200
Phchi.S1	AUGUSTUS	transcript	23129586	23129924	.	-	.	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	stop_codon	23129583	23129585	.	-	0	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	CDS	23129586	23129719	0.68	-	2	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	exon	23129586	23129719	.	-	.	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	intron	23129720	23129809	.	-	.	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	CDS	23129810	23129924	0.63	-	0	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	exon	23129810	23129924	.	-	.	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
Phchi.S1	AUGUSTUS	start_codon	23129922	23129924	.	-	0	transcript_id "Phchi.S1G362200.t1"; gene_id "Phchi.S1G362200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14911.t1 is derived from g13379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15472542	15476500	.	-	.	Phchi.S3G223000
Phchi.S3	AUGUSTUS	transcript	15472542	15476500	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	stop_codon	15472539	15472541	.	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15472542	15472870	1	-	2	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15472542	15472870	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15472871	15473002	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473003	15473083	0.8	-	2	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473003	15473083	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473084	15473242	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473243	15473354	0.93	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473243	15473354	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473355	15473469	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473470	15473610	0.99	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473470	15473610	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473611	15473736	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473737	15473842	1	-	1	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473737	15473842	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473843	15473975	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473976	15473984	1	-	1	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473976	15473984	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473985	15474140	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474141	15474183	1	-	2	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474141	15474183	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474184	15474270	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474271	15474403	0.58	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474271	15474403	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474404	15474482	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474483	15474600	1	-	1	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474483	15474600	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474601	15474686	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474687	15474928	1	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474687	15474928	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474929	15475025	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475026	15475190	1	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475026	15475190	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475191	15475344	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475345	15475554	1	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475345	15475554	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475555	15475699	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475700	15475774	1	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475700	15475774	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475775	15475857	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475858	15475986	1	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475858	15475986	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475987	15476075	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15476076	15476150	1	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15476076	15476150	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15476151	15476233	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15476234	15476500	0.99	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15476234	15476500	.	-	.	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	start_codon	15476498	15476500	.	-	0	transcript_id "Phchi.S3G223000.t1"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	transcript	15472542	15476500	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	stop_codon	15472539	15472541	.	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15472542	15472870	0.98	-	2	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15472542	15472870	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15472871	15473002	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473003	15473083	0.92	-	2	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473003	15473083	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473084	15473242	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473243	15473354	0.99	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473243	15473354	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473355	15473469	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473470	15473610	1	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473470	15473610	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473611	15473736	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473737	15473842	1	-	1	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473737	15473842	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473843	15473975	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15473976	15473984	0.99	-	1	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15473976	15473984	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15473985	15474140	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474141	15474183	0.99	-	2	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474141	15474183	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474184	15474270	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474271	15474403	0.57	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474271	15474403	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474404	15474482	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474483	15474600	1	-	1	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474483	15474600	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474601	15474686	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15474687	15474928	1	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15474687	15474928	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15474929	15475025	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475026	15475190	0.96	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475026	15475190	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475191	15475282	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475283	15475339	0.56	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475283	15475339	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475340	15475488	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475489	15475554	0.48	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475489	15475554	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475555	15475699	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475700	15475774	1	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475700	15475774	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475775	15475857	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15475858	15475986	1	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15475858	15475986	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15475987	15476075	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15476076	15476150	1	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15476076	15476150	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	intron	15476151	15476233	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	CDS	15476234	15476500	1	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	exon	15476234	15476500	.	-	.	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
Phchi.S3	AUGUSTUS	start_codon	15476498	15476500	.	-	0	transcript_id "Phchi.S3G223000.t2"; gene_id "Phchi.S3G223000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9180.t1 is derived from g6355.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40238557	40239422	.	-	.	Phchi.S1G633900
Phchi.S1	AUGUSTUS	transcript	40238557	40239422	.	-	.	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	stop_codon	40238554	40238556	.	-	0	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	CDS	40238557	40238575	0.9	-	1	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	exon	40238557	40238575	.	-	.	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	intron	40238576	40238667	.	-	.	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	CDS	40238668	40239422	0.54	-	0	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	exon	40238668	40239422	.	-	.	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
Phchi.S1	AUGUSTUS	start_codon	40239420	40239422	.	-	0	transcript_id "Phchi.S1G633900.t1"; gene_id "Phchi.S1G633900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14991.t1 is derived from g13459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16142200	16143641	.	-	.	Phchi.S3G231000
Phchi.S3	AUGUSTUS	transcript	16142200	16143641	.	-	.	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	stop_codon	16142197	16142199	.	-	0	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	CDS	16142200	16143245	1	-	2	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	exon	16142200	16143245	.	-	.	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	intron	16143246	16143481	.	-	.	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	CDS	16143482	16143641	0.53	-	0	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	exon	16143482	16143641	.	-	.	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
Phchi.S3	AUGUSTUS	start_codon	16143639	16143641	.	-	0	transcript_id "Phchi.S3G231000.t1"; gene_id "Phchi.S3G231000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8034.t1 is derived from g5209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32569212	32569869	.	-	.	Phchi.S1G519300
Phchi.S1	AUGUSTUS	transcript	32569212	32569869	.	-	.	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	stop_codon	32569209	32569211	.	-	0	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	CDS	32569212	32569331	1	-	0	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	exon	32569212	32569331	.	-	.	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	intron	32569332	32569476	.	-	.	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	CDS	32569477	32569869	0.45	-	0	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	exon	32569477	32569869	.	-	.	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
Phchi.S1	AUGUSTUS	start_codon	32569867	32569869	.	-	0	transcript_id "Phchi.S1G519300.t1"; gene_id "Phchi.S1G519300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg747.t1 is derived from g10529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5318177	5320081	.	-	.	Phchi.S6G070600
Phchi.S6	AUGUSTUS	transcript	5318177	5320081	.	-	.	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	stop_codon	5318174	5318176	.	-	0	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	CDS	5318177	5319399	0.98	-	2	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	exon	5318177	5319399	.	-	.	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	intron	5319400	5319530	.	-	.	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	CDS	5319531	5319683	0.92	-	2	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	exon	5319531	5319683	.	-	.	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	intron	5319684	5319879	.	-	.	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	CDS	5319880	5320081	1	-	0	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	exon	5319880	5320081	.	-	.	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
Phchi.S6	AUGUSTUS	start_codon	5320079	5320081	.	-	0	transcript_id "Phchi.S6G070600.t1"; gene_id "Phchi.S6G070600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5864.t1 is derived from g3034.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19477136	19477940	.	-	.	Phchi.S1G302300
Phchi.S1	AUGUSTUS	transcript	19477143	19477940	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	stop_codon	19477140	19477142	.	-	0	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477143	19477214	0.4	-	0	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477143	19477214	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	intron	19477215	19477361	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477362	19477471	0.91	-	2	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477362	19477471	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	intron	19477472	19477685	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477686	19477834	0.93	-	1	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477686	19477834	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	intron	19477835	19477920	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477921	19477940	0.97	-	0	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477921	19477940	.	-	.	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	start_codon	19477938	19477940	.	-	0	transcript_id "Phchi.S1G302300.t1"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	transcript	19477136	19477940	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	stop_codon	19477133	19477135	.	-	0	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477136	19477197	0.73	-	2	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477136	19477197	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	intron	19477198	19477361	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477362	19477385	0.54	-	2	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477362	19477385	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	intron	19477386	19477685	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477686	19477834	0.98	-	1	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477686	19477834	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	intron	19477835	19477920	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	CDS	19477921	19477940	0.97	-	0	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	exon	19477921	19477940	.	-	.	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
Phchi.S1	AUGUSTUS	start_codon	19477938	19477940	.	-	0	transcript_id "Phchi.S1G302300.t2"; gene_id "Phchi.S1G302300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4245.t1 is derived from g1414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9148830	9151353	.	-	.	Phchi.S1G140400
Phchi.S1	AUGUSTUS	transcript	9148830	9151353	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	stop_codon	9148827	9148829	.	-	0	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	CDS	9148830	9148899	1	-	1	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	exon	9148830	9148899	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	intron	9148900	9148977	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	CDS	9148978	9149131	0.59	-	2	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	exon	9148978	9149131	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	intron	9149132	9149645	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	CDS	9149646	9149741	0.78	-	2	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	exon	9149646	9149741	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	intron	9149742	9149891	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	CDS	9149892	9151353	0.36	-	0	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	exon	9149892	9151353	.	-	.	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
Phchi.S1	AUGUSTUS	start_codon	9151351	9151353	.	-	0	transcript_id "Phchi.S1G140400.t1"; gene_id "Phchi.S1G140400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8411.t1 is derived from g5586.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35834981	35835592	.	-	.	Phchi.S1G557000
Phchi.S1	AUGUSTUS	transcript	35834981	35835592	.	-	.	transcript_id "Phchi.S1G557000.t1"; gene_id "Phchi.S1G557000"
Phchi.S1	AUGUSTUS	stop_codon	35834978	35834980	.	-	0	transcript_id "Phchi.S1G557000.t1"; gene_id "Phchi.S1G557000"
Phchi.S1	AUGUSTUS	CDS	35834981	35835592	0.93	-	0	transcript_id "Phchi.S1G557000.t1"; gene_id "Phchi.S1G557000"
Phchi.S1	AUGUSTUS	exon	35834981	35835592	.	-	.	transcript_id "Phchi.S1G557000.t1"; gene_id "Phchi.S1G557000"
Phchi.S1	AUGUSTUS	start_codon	35835590	35835592	.	-	0	transcript_id "Phchi.S1G557000.t1"; gene_id "Phchi.S1G557000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4044.t1 is derived from g1213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7379991	7380608	.	+	.	Phchi.S1G120300
Phchi.S1	AUGUSTUS	transcript	7379991	7380608	.	+	.	transcript_id "Phchi.S1G120300.t1"; gene_id "Phchi.S1G120300"
Phchi.S1	AUGUSTUS	start_codon	7379991	7379993	.	+	0	transcript_id "Phchi.S1G120300.t1"; gene_id "Phchi.S1G120300"
Phchi.S1	AUGUSTUS	CDS	7379991	7380608	1	+	0	transcript_id "Phchi.S1G120300.t1"; gene_id "Phchi.S1G120300"
Phchi.S1	AUGUSTUS	exon	7379991	7380608	.	+	.	transcript_id "Phchi.S1G120300.t1"; gene_id "Phchi.S1G120300"
Phchi.S1	AUGUSTUS	stop_codon	7380609	7380611	.	+	0	transcript_id "Phchi.S1G120300.t1"; gene_id "Phchi.S1G120300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9582.t1 is derived from g6758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42773387	42775553	.	-	.	Phchi.S1G674100
Phchi.S1	AUGUSTUS	transcript	42773387	42775553	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	stop_codon	42773384	42773386	.	-	0	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	CDS	42773387	42773392	0.9	-	0	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	exon	42773387	42773392	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	intron	42773393	42773531	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	CDS	42773532	42773711	0.97	-	0	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	exon	42773532	42773711	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	intron	42773712	42773811	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	CDS	42773812	42774192	0.79	-	0	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	exon	42773812	42774192	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	intron	42774193	42774296	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	CDS	42774297	42774460	0.87	-	2	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	exon	42774297	42774460	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	intron	42774461	42774574	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	CDS	42774575	42774654	0.97	-	1	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	exon	42774575	42774654	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	intron	42774655	42774759	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	CDS	42774760	42775553	0.34	-	0	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	exon	42774760	42775553	.	-	.	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
Phchi.S1	AUGUSTUS	start_codon	42775551	42775553	.	-	0	transcript_id "Phchi.S1G674100.t1"; gene_id "Phchi.S1G674100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5285.t1 is derived from g2455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16023362	16023703	.	+	.	Phchi.S1G244400
Phchi.S1	AUGUSTUS	transcript	16023362	16023703	.	+	.	transcript_id "Phchi.S1G244400.t1"; gene_id "Phchi.S1G244400"
Phchi.S1	AUGUSTUS	start_codon	16023362	16023364	.	+	0	transcript_id "Phchi.S1G244400.t1"; gene_id "Phchi.S1G244400"
Phchi.S1	AUGUSTUS	CDS	16023362	16023703	0.9	+	0	transcript_id "Phchi.S1G244400.t1"; gene_id "Phchi.S1G244400"
Phchi.S1	AUGUSTUS	exon	16023362	16023703	.	+	.	transcript_id "Phchi.S1G244400.t1"; gene_id "Phchi.S1G244400"
Phchi.S1	AUGUSTUS	stop_codon	16023704	16023706	.	+	0	transcript_id "Phchi.S1G244400.t1"; gene_id "Phchi.S1G244400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11897.t1 is derived from g15949.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9081056	9082012	.	-	.	Phchi.S4G147900
Phchi.S4	AUGUSTUS	transcript	9081056	9082012	.	-	.	transcript_id "Phchi.S4G147900.t1"; gene_id "Phchi.S4G147900"
Phchi.S4	AUGUSTUS	stop_codon	9081053	9081055	.	-	0	transcript_id "Phchi.S4G147900.t1"; gene_id "Phchi.S4G147900"
Phchi.S4	AUGUSTUS	CDS	9081056	9082012	0.34	-	0	transcript_id "Phchi.S4G147900.t1"; gene_id "Phchi.S4G147900"
Phchi.S4	AUGUSTUS	exon	9081056	9082012	.	-	.	transcript_id "Phchi.S4G147900.t1"; gene_id "Phchi.S4G147900"
Phchi.S4	AUGUSTUS	start_codon	9082010	9082012	.	-	0	transcript_id "Phchi.S4G147900.t1"; gene_id "Phchi.S4G147900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14713.t1 is derived from g13181.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14340625	14341244	.	-	.	Phchi.S3G203200
Phchi.S3	AUGUSTUS	transcript	14340625	14341244	.	-	.	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	stop_codon	14340622	14340624	.	-	0	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	CDS	14340625	14340672	0.97	-	0	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	exon	14340625	14340672	.	-	.	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	intron	14340673	14340817	.	-	.	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	CDS	14340818	14340892	0.9	-	0	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	exon	14340818	14340892	.	-	.	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	intron	14340893	14340962	.	-	.	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	CDS	14340963	14341244	0.47	-	0	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	exon	14340963	14341244	.	-	.	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
Phchi.S3	AUGUSTUS	start_codon	14341242	14341244	.	-	0	transcript_id "Phchi.S3G203200.t1"; gene_id "Phchi.S3G203200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15995.t1 is derived from g10.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C194	AUGUSTUS	gene	271	612	.	+	.	Phchi.C194G000100
Phchi.C194	AUGUSTUS	transcript	271	612	.	+	.	transcript_id "Phchi.C194G000100.t1"; gene_id "Phchi.C194G000100"
Phchi.C194	AUGUSTUS	start_codon	271	273	.	+	0	transcript_id "Phchi.C194G000100.t1"; gene_id "Phchi.C194G000100"
Phchi.C194	AUGUSTUS	CDS	271	612	0.51	+	0	transcript_id "Phchi.C194G000100.t1"; gene_id "Phchi.C194G000100"
Phchi.C194	AUGUSTUS	exon	271	612	.	+	.	transcript_id "Phchi.C194G000100.t1"; gene_id "Phchi.C194G000100"
Phchi.C194	AUGUSTUS	stop_codon	613	615	.	+	0	transcript_id "Phchi.C194G000100.t1"; gene_id "Phchi.C194G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9141.t1 is derived from g6316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40060297	40060782	.	+	.	Phchi.S1G630000
Phchi.S1	AUGUSTUS	transcript	40060297	40060782	.	+	.	transcript_id "Phchi.S1G630000.t1"; gene_id "Phchi.S1G630000"
Phchi.S1	AUGUSTUS	start_codon	40060297	40060299	.	+	0	transcript_id "Phchi.S1G630000.t1"; gene_id "Phchi.S1G630000"
Phchi.S1	AUGUSTUS	CDS	40060297	40060782	0.85	+	0	transcript_id "Phchi.S1G630000.t1"; gene_id "Phchi.S1G630000"
Phchi.S1	AUGUSTUS	exon	40060297	40060782	.	+	.	transcript_id "Phchi.S1G630000.t1"; gene_id "Phchi.S1G630000"
Phchi.S1	AUGUSTUS	stop_codon	40060783	40060785	.	+	0	transcript_id "Phchi.S1G630000.t1"; gene_id "Phchi.S1G630000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15566.t1 is derived from g14035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20016679	20017160	.	-	.	Phchi.S3G288500
Phchi.S3	AUGUSTUS	transcript	20016679	20017160	.	-	.	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	stop_codon	20016676	20016678	.	-	0	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	CDS	20016679	20016779	0.98	-	2	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	exon	20016679	20016779	.	-	.	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	intron	20016780	20016925	.	-	.	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	CDS	20016926	20017016	0.93	-	0	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	exon	20016926	20017016	.	-	.	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	intron	20017017	20017091	.	-	.	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	CDS	20017092	20017160	0.65	-	0	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	exon	20017092	20017160	.	-	.	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
Phchi.S3	AUGUSTUS	start_codon	20017158	20017160	.	-	0	transcript_id "Phchi.S3G288500.t1"; gene_id "Phchi.S3G288500"
# This transcript jg14156.t2 is derived from g12623.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14156.t3 is derived from g12623.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14157.t1 is derived from g12624.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11193373	11194388	.	+	.	Phchi.S3G147600
Phchi.S3	AUGUSTUS	transcript	11193373	11194388	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	start_codon	11193373	11193375	.	+	0	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	CDS	11193373	11193477	1	+	0	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	exon	11193373	11193477	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	intron	11193478	11193600	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	CDS	11193601	11193690	1	+	0	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	exon	11193601	11193690	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	intron	11193691	11193781	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	CDS	11193782	11193866	1	+	0	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	exon	11193782	11193866	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	intron	11193867	11193984	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	CDS	11193985	11194388	1	+	2	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	exon	11193985	11194388	.	+	.	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
Phchi.S3	AUGUSTUS	stop_codon	11194389	11194391	.	+	0	transcript_id "Phchi.S3G147600.t1"; gene_id "Phchi.S3G147600"
# This transcript jg7157.t2 is derived from g4329.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7158.t1 is derived from g4330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27331757	27336739	.	-	.	Phchi.S1G431700
Phchi.S1	AUGUSTUS	transcript	27331757	27336739	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	stop_codon	27331754	27331756	.	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27331757	27331773	1	-	2	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27331757	27331773	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27331774	27331975	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27331976	27332160	1	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27331976	27332160	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27332161	27332259	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27332260	27332596	1	-	2	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27332260	27332596	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27332597	27332682	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27332683	27333658	0.88	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27332683	27333658	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27333659	27333766	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27333767	27333935	0.88	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27333767	27333935	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27333936	27334006	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27334007	27334200	1	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27334007	27334200	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27334201	27334315	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27334316	27334457	1	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27334316	27334457	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27334458	27334556	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27334557	27334593	0.46	-	2	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27334557	27334593	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27334594	27334758	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27334759	27334886	0.89	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27334759	27334886	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27334887	27334978	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27334979	27335112	1	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27334979	27335112	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27335113	27335336	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27335337	27335449	1	-	2	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27335337	27335449	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27335450	27335542	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27335543	27335631	1	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27335543	27335631	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27335632	27335832	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27335833	27335898	1	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27335833	27335898	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27335899	27335982	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27335983	27336066	1	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27335983	27336066	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27336067	27336164	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27336165	27336257	1	-	1	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27336165	27336257	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27336258	27336377	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27336378	27336427	1	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27336378	27336427	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	intron	27336428	27336508	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	CDS	27336509	27336739	0.7	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	exon	27336509	27336739	.	-	.	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
Phchi.S1	AUGUSTUS	start_codon	27336737	27336739	.	-	0	transcript_id "Phchi.S1G431700.t1"; gene_id "Phchi.S1G431700"
# This transcript jg5240.t2 is derived from g2410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5240.t3 is derived from g2410.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5241.t1 is derived from g2411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15815665	15817398	.	+	.	Phchi.S1G240000
Phchi.S1	AUGUSTUS	transcript	15815665	15817398	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	start_codon	15815665	15815667	.	+	0	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	CDS	15815665	15815970	1	+	0	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	exon	15815665	15815970	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	intron	15815971	15816063	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	CDS	15816064	15816197	1	+	0	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	exon	15816064	15816197	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	intron	15816198	15816289	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	CDS	15816290	15816479	1	+	1	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	exon	15816290	15816479	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	intron	15816480	15816589	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	CDS	15816590	15816796	0.99	+	0	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	exon	15816590	15816796	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	intron	15816797	15816903	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	CDS	15816904	15817139	0.91	+	0	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	exon	15816904	15817139	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	intron	15817140	15817256	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	CDS	15817257	15817398	0.98	+	1	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	exon	15817257	15817398	.	+	.	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
Phchi.S1	AUGUSTUS	stop_codon	15817399	15817401	.	+	0	transcript_id "Phchi.S1G240000.t1"; gene_id "Phchi.S1G240000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15420.t1 is derived from g13888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19005319	19006779	.	+	.	Phchi.S3G273900
Phchi.S3	AUGUSTUS	transcript	19005319	19006779	.	+	.	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	start_codon	19005319	19005321	.	+	0	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	CDS	19005319	19005593	1	+	0	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	exon	19005319	19005593	.	+	.	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	intron	19005594	19005806	.	+	.	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	CDS	19005807	19006779	0.97	+	1	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	exon	19005807	19006779	.	+	.	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
Phchi.S3	AUGUSTUS	stop_codon	19006780	19006782	.	+	0	transcript_id "Phchi.S3G273900.t1"; gene_id "Phchi.S3G273900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3215.t1 is derived from g384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2277483	2279203	.	-	.	Phchi.S1G037400
Phchi.S1	AUGUSTUS	transcript	2277483	2279203	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	stop_codon	2277480	2277482	.	-	0	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	CDS	2277483	2277728	0.99	-	0	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	exon	2277483	2277728	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	intron	2277729	2277809	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	CDS	2277810	2278130	1	-	0	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	exon	2277810	2278130	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	intron	2278131	2278242	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	CDS	2278243	2278301	0.49	-	2	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	exon	2278243	2278301	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	intron	2278302	2278396	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	CDS	2278397	2278776	0.48	-	1	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	exon	2278397	2278776	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	intron	2278777	2278994	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	CDS	2278995	2279203	0.75	-	0	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	exon	2278995	2279203	.	-	.	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
Phchi.S1	AUGUSTUS	start_codon	2279201	2279203	.	-	0	transcript_id "Phchi.S1G037400.t1"; gene_id "Phchi.S1G037400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1637.t1 is derived from g8556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2137563	2141721	.	-	.	Phchi.S5G024600
Phchi.S5	AUGUSTUS	transcript	2137563	2141721	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	stop_codon	2137560	2137562	.	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2137563	2137619	0.93	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2137563	2137619	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2137620	2137714	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2137715	2137827	0.86	-	2	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2137715	2137827	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2137828	2137917	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2137918	2138044	0.86	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2137918	2138044	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138045	2138208	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138209	2138346	1	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138209	2138346	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138347	2138432	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138433	2138634	0.65	-	1	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138433	2138634	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138635	2138706	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138707	2138738	0.62	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138707	2138738	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138739	2138923	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138924	2139720	1	-	2	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138924	2139720	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2139721	2139817	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2139818	2140054	1	-	2	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2139818	2140054	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2140055	2140146	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2140147	2140357	1	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2140147	2140357	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2140358	2140727	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2140728	2140807	0.96	-	2	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2140728	2140807	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2140808	2140929	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2140930	2141062	0.96	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2140930	2141062	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2141063	2141157	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2141158	2141721	0.52	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2141158	2141721	.	-	.	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	start_codon	2141719	2141721	.	-	0	transcript_id "Phchi.S5G024600.t1"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	transcript	2137563	2141721	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	stop_codon	2137560	2137562	.	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2137563	2137619	0.93	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2137563	2137619	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2137620	2137714	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2137715	2137827	0.92	-	2	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2137715	2137827	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2137828	2137917	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2137918	2138044	0.92	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2137918	2138044	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138045	2138208	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138209	2138346	1	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138209	2138346	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138347	2138432	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138433	2138634	0.61	-	1	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138433	2138634	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138635	2138706	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138707	2138738	0.55	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138707	2138738	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2138739	2138923	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2138924	2139720	1	-	2	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2138924	2139720	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2139721	2139817	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2139818	2140054	1	-	2	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2139818	2140054	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2140055	2140254	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2140255	2140357	1	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2140255	2140357	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2140358	2140727	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2140728	2140807	0.95	-	2	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2140728	2140807	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2140808	2140929	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2140930	2141062	0.95	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2140930	2141062	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	intron	2141063	2141157	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	CDS	2141158	2141721	0.5	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	exon	2141158	2141721	.	-	.	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
Phchi.S5	AUGUSTUS	start_codon	2141719	2141721	.	-	0	transcript_id "Phchi.S5G024600.t2"; gene_id "Phchi.S5G024600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8752.t1 is derived from g5927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37799193	37800332	.	+	.	Phchi.S1G591100
Phchi.S1	AUGUSTUS	transcript	37799193	37800332	.	+	.	transcript_id "Phchi.S1G591100.t1"; gene_id "Phchi.S1G591100"
Phchi.S1	AUGUSTUS	start_codon	37799193	37799195	.	+	0	transcript_id "Phchi.S1G591100.t1"; gene_id "Phchi.S1G591100"
Phchi.S1	AUGUSTUS	CDS	37799193	37800332	0.36	+	0	transcript_id "Phchi.S1G591100.t1"; gene_id "Phchi.S1G591100"
Phchi.S1	AUGUSTUS	exon	37799193	37800332	.	+	.	transcript_id "Phchi.S1G591100.t1"; gene_id "Phchi.S1G591100"
Phchi.S1	AUGUSTUS	stop_codon	37800333	37800335	.	+	0	transcript_id "Phchi.S1G591100.t1"; gene_id "Phchi.S1G591100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5772.t1 is derived from g2942.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18883102	18885260	.	-	.	Phchi.S1G293100
Phchi.S1	AUGUSTUS	transcript	18883102	18885260	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	stop_codon	18883099	18883101	.	-	0	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	CDS	18883102	18883275	0.98	-	0	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	exon	18883102	18883275	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	intron	18883276	18883511	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	CDS	18883512	18883574	0.73	-	0	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	exon	18883512	18883574	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	intron	18883575	18883884	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	CDS	18883885	18884076	0.94	-	0	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	exon	18883885	18884076	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	intron	18884077	18884280	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	CDS	18884281	18885020	0.99	-	2	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	exon	18884281	18885020	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	intron	18885021	18885148	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	CDS	18885149	18885260	0.92	-	0	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	exon	18885149	18885260	.	-	.	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
Phchi.S1	AUGUSTUS	start_codon	18885258	18885260	.	-	0	transcript_id "Phchi.S1G293100.t1"; gene_id "Phchi.S1G293100"
# This transcript jg3541.t2 is derived from g710.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3542.t1 is derived from g711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4369396	4370325	.	-	.	Phchi.S1G070100
Phchi.S1	AUGUSTUS	transcript	4369396	4370325	.	-	.	transcript_id "Phchi.S1G070100.t1"; gene_id "Phchi.S1G070100"
Phchi.S1	AUGUSTUS	stop_codon	4369393	4369395	.	-	0	transcript_id "Phchi.S1G070100.t1"; gene_id "Phchi.S1G070100"
Phchi.S1	AUGUSTUS	CDS	4369396	4370325	0.48	-	0	transcript_id "Phchi.S1G070100.t1"; gene_id "Phchi.S1G070100"
Phchi.S1	AUGUSTUS	exon	4369396	4370325	.	-	.	transcript_id "Phchi.S1G070100.t1"; gene_id "Phchi.S1G070100"
Phchi.S1	AUGUSTUS	start_codon	4370323	4370325	.	-	0	transcript_id "Phchi.S1G070100.t1"; gene_id "Phchi.S1G070100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5441.t1 is derived from g2611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16885144	16887916	.	+	.	Phchi.S1G260000
Phchi.S1	AUGUSTUS	transcript	16885144	16887916	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	start_codon	16885144	16885146	.	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16885144	16885229	0.78	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16885144	16885229	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16885230	16885360	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16885361	16885499	1	+	1	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16885361	16885499	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16885500	16885588	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16885589	16885701	1	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16885589	16885701	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16885702	16886151	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16886152	16886429	1	+	1	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16886152	16886429	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16886430	16886609	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16886610	16886677	0.52	+	2	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16886610	16886677	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16886678	16886847	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16886848	16887027	0.26	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16886848	16887027	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16887028	16887144	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16887145	16887255	0.97	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16887145	16887255	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16887256	16887350	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16887351	16887413	1	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16887351	16887413	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16887414	16887498	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16887499	16887552	1	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16887499	16887552	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16887553	16887643	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16887644	16887793	1	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16887644	16887793	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	intron	16887794	16887883	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	CDS	16887884	16887916	1	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	exon	16887884	16887916	.	+	.	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
Phchi.S1	AUGUSTUS	stop_codon	16887917	16887919	.	+	0	transcript_id "Phchi.S1G260000.t1"; gene_id "Phchi.S1G260000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5199.t1 is derived from g2369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15433608	15437590	.	+	.	Phchi.S1G235800
Phchi.S1	AUGUSTUS	transcript	15433608	15437590	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	start_codon	15433608	15433610	.	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15433608	15433963	0.41	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15433608	15433963	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15433964	15434068	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15434069	15434231	0.63	+	1	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15434069	15434231	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15434232	15434302	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15434303	15434643	1	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15434303	15434643	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15434644	15434890	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15434891	15435077	1	+	1	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15434891	15435077	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15435078	15435163	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15435164	15435477	0.71	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15435164	15435477	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15435478	15435569	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15435570	15435620	0.97	+	1	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15435570	15435620	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15435621	15435708	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15435709	15435748	0.94	+	1	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15435709	15435748	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15435749	15435879	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15435880	15436371	0.76	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15435880	15436371	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15436372	15436478	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15436479	15437021	0.84	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15436479	15437021	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	intron	15437022	15437137	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	CDS	15437138	15437590	0.92	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	exon	15437138	15437590	.	+	.	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
Phchi.S1	AUGUSTUS	stop_codon	15437591	15437593	.	+	0	transcript_id "Phchi.S1G235800.t1"; gene_id "Phchi.S1G235800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2574.t1 is derived from g9494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7437951	7440905	.	+	.	Phchi.S5G118300
Phchi.S5	AUGUSTUS	transcript	7437951	7440905	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	start_codon	7437951	7437953	.	+	0	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7437951	7438137	0.89	+	0	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7437951	7438137	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7438138	7438268	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7438269	7438388	0.5	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7438269	7438388	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7438389	7438525	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7438526	7438636	0.29	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7438526	7438636	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7438637	7438763	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7438764	7438931	1	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7438764	7438931	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7438932	7439020	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7439021	7439442	1	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7439021	7439442	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7439443	7439559	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7439560	7440280	0.4	+	0	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7439560	7440280	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7440281	7440372	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7440373	7440420	0.58	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7440373	7440420	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7440421	7440514	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7440515	7440745	0.76	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7440515	7440745	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	intron	7440746	7440831	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	CDS	7440832	7440905	0.48	+	2	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	exon	7440832	7440905	.	+	.	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
Phchi.S5	AUGUSTUS	stop_codon	7440906	7440908	.	+	0	transcript_id "Phchi.S5G118300.t1"; gene_id "Phchi.S5G118300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13849.t1 is derived from g12316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9235381	9236272	.	-	.	Phchi.S3G116800
Phchi.S3	AUGUSTUS	transcript	9235381	9236272	.	-	.	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	stop_codon	9235378	9235380	.	-	0	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	CDS	9235381	9235840	0.55	-	1	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	exon	9235381	9235840	.	-	.	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	intron	9235841	9235902	.	-	.	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	CDS	9235903	9235934	0.56	-	0	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	exon	9235903	9235934	.	-	.	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	intron	9235935	9236029	.	-	.	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	CDS	9236030	9236272	0.87	-	0	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	exon	9236030	9236272	.	-	.	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
Phchi.S3	AUGUSTUS	start_codon	9236270	9236272	.	-	0	transcript_id "Phchi.S3G116800.t1"; gene_id "Phchi.S3G116800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11578.t1 is derived from g15629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7172778	7175260	.	-	.	Phchi.S4G116000
Phchi.S4	AUGUSTUS	transcript	7172778	7175260	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	stop_codon	7172775	7172777	.	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7172778	7172966	1	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7172778	7172966	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7172967	7173043	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7173044	7173133	1	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7173044	7173133	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7173134	7173223	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7173224	7173342	1	-	2	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7173224	7173342	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7173343	7173425	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7173426	7173531	1	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7173426	7173531	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7173532	7173613	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7173614	7173710	1	-	1	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7173614	7173710	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7173711	7173808	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7173809	7173872	1	-	2	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7173809	7173872	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7173873	7173957	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7173958	7174090	1	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7173958	7174090	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7174091	7174222	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7174223	7174485	0.99	-	2	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7174223	7174485	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7174486	7174570	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7174571	7174753	1	-	2	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7174571	7174753	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	intron	7174754	7174857	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	CDS	7174858	7175260	0.89	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	exon	7174858	7175260	.	-	.	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
Phchi.S4	AUGUSTUS	start_codon	7175258	7175260	.	-	0	transcript_id "Phchi.S4G116000.t1"; gene_id "Phchi.S4G116000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7093.t1 is derived from g4265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26876198	26881415	.	-	.	Phchi.S1G425200
Phchi.S1	AUGUSTUS	transcript	26876198	26881415	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	stop_codon	26876195	26876197	.	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26876198	26876635	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26876198	26876635	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26876636	26876718	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26876719	26876817	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26876719	26876817	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26876818	26876908	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26876909	26877113	1	-	1	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26876909	26877113	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877114	26877191	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877192	26877250	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877192	26877250	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877251	26877349	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877350	26877427	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877350	26877427	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877428	26877512	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877513	26877596	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877513	26877596	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877597	26877699	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877700	26877813	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877700	26877813	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877814	26877911	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877912	26878031	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877912	26878031	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878032	26878192	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878193	26878319	1	-	1	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878193	26878319	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878320	26878460	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878461	26878552	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878461	26878552	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878553	26878700	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878701	26878787	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878701	26878787	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878788	26878893	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878894	26878968	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878894	26878968	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878969	26879064	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879065	26879115	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879065	26879115	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879116	26879207	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879208	26879303	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879208	26879303	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879304	26879395	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879396	26879482	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879396	26879482	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879483	26879581	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879582	26879638	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879582	26879638	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879639	26879737	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879738	26879863	1	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879738	26879863	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879864	26880044	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26880045	26880285	1	-	1	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26880045	26880285	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26880286	26880422	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26880423	26880515	1	-	1	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26880423	26880515	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26880516	26880601	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26880602	26880967	1	-	1	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26880602	26880967	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26880968	26881050	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26881051	26881415	0.69	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26881051	26881415	.	-	.	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	start_codon	26881413	26881415	.	-	0	transcript_id "Phchi.S1G425200.t1"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	transcript	26876198	26881415	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	stop_codon	26876195	26876197	.	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26876198	26876635	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26876198	26876635	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26876636	26876718	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26876719	26876817	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26876719	26876817	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26876818	26876908	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26876909	26877113	1	-	1	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26876909	26877113	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877114	26877191	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877192	26877250	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877192	26877250	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877251	26877349	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877350	26877427	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877350	26877427	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877428	26877512	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877513	26877596	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877513	26877596	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877597	26877699	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877700	26877813	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877700	26877813	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26877814	26877911	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26877912	26878031	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26877912	26878031	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878032	26878192	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878193	26878319	1	-	1	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878193	26878319	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878320	26878460	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878461	26878552	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878461	26878552	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878553	26878631	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878632	26878655	0.74	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878632	26878655	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878656	26878791	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26878792	26878968	0.5	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26878792	26878968	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26878969	26879064	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879065	26879115	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879065	26879115	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879116	26879207	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879208	26879303	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879208	26879303	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879304	26879395	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879396	26879482	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879396	26879482	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879483	26879581	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879582	26879638	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879582	26879638	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879639	26879737	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26879738	26879863	1	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26879738	26879863	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26879864	26880044	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26880045	26880285	1	-	1	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26880045	26880285	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26880286	26880422	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26880423	26880515	1	-	1	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26880423	26880515	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26880516	26880601	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26880602	26880967	1	-	1	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26880602	26880967	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	intron	26880968	26881050	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	CDS	26881051	26881415	0.72	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	exon	26881051	26881415	.	-	.	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
Phchi.S1	AUGUSTUS	start_codon	26881413	26881415	.	-	0	transcript_id "Phchi.S1G425200.t2"; gene_id "Phchi.S1G425200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13312.t1 is derived from g11778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5935771	5938276	.	-	.	Phchi.S3G063100
Phchi.S3	AUGUSTUS	transcript	5935771	5938276	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	stop_codon	5935768	5935770	.	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5935771	5935909	0.99	-	1	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5935771	5935909	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5935910	5936070	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5936071	5936189	0.99	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5936071	5936189	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5936190	5936292	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5936293	5936399	0.99	-	2	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5936293	5936399	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5936400	5936547	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5936548	5936626	1	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5936548	5936626	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5936627	5936747	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5936748	5936834	1	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5936748	5936834	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5936835	5936965	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5936966	5937226	1	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5936966	5937226	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5937227	5937316	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5937317	5937466	1	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5937317	5937466	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5937467	5937584	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5937585	5937909	1	-	1	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5937585	5937909	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	intron	5937910	5938058	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	CDS	5938059	5938276	1	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	exon	5938059	5938276	.	-	.	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
Phchi.S3	AUGUSTUS	start_codon	5938274	5938276	.	-	0	transcript_id "Phchi.S3G063100.t1"; gene_id "Phchi.S3G063100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2181.t1 is derived from g9101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5251523	5252016	.	-	.	Phchi.S5G079000
Phchi.S5	AUGUSTUS	transcript	5251523	5252016	.	-	.	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	stop_codon	5251520	5251522	.	-	0	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	CDS	5251523	5251553	0.61	-	1	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	exon	5251523	5251553	.	-	.	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	intron	5251554	5251636	.	-	.	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	CDS	5251637	5252016	0.6	-	0	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	exon	5251637	5252016	.	-	.	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
Phchi.S5	AUGUSTUS	start_codon	5252014	5252016	.	-	0	transcript_id "Phchi.S5G079000.t1"; gene_id "Phchi.S5G079000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13374.t1 is derived from g11840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6407275	6416540	.	+	.	Phchi.S3G069300
Phchi.S3	AUGUSTUS	transcript	6407275	6416540	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	start_codon	6407275	6407277	.	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6407275	6407364	0.55	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6407275	6407364	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6407365	6407441	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6407442	6407552	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6407442	6407552	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6407553	6407706	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6407707	6407841	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6407707	6407841	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6407842	6407967	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6407968	6408034	0.83	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6407968	6408034	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6408035	6408181	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6408182	6408252	1	+	2	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6408182	6408252	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6408253	6408428	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6408429	6408566	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6408429	6408566	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6408567	6408764	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6408765	6408911	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6408765	6408911	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6408912	6409057	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6409058	6409178	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6409058	6409178	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6409179	6409340	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6409341	6409419	1	+	2	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6409341	6409419	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6409420	6409640	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6409641	6409833	1	+	1	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6409641	6409833	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6409834	6409988	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6409989	6410149	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6409989	6410149	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6410150	6410407	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6410408	6410626	0.97	+	1	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6410408	6410626	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6410627	6410708	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6410709	6410929	0.95	+	1	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6410709	6410929	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6410930	6411060	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6411061	6411335	0.56	+	2	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6411061	6411335	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6411336	6411466	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6411467	6411966	0.98	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6411467	6411966	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6411967	6412303	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6412304	6412404	1	+	1	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6412304	6412404	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6412405	6412520	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6412521	6412726	1	+	2	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6412521	6412726	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6412727	6412917	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6412918	6413127	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6412918	6413127	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6413128	6413221	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6413222	6413659	0.93	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6413222	6413659	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6413660	6413811	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6413812	6414093	1	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6413812	6414093	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6414094	6414204	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6414205	6414531	0.92	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6414205	6414531	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6414532	6414608	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6414609	6416055	0.99	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6414609	6416055	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6416056	6416169	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6416170	6416302	1	+	2	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6416170	6416302	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	intron	6416303	6416401	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	CDS	6416402	6416540	1	+	1	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	exon	6416402	6416540	.	+	.	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
Phchi.S3	AUGUSTUS	stop_codon	6416541	6416543	.	+	0	transcript_id "Phchi.S3G069300.t1"; gene_id "Phchi.S3G069300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14055.t1 is derived from g12522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10531081	10532077	.	+	.	Phchi.S3G137400
Phchi.S3	AUGUSTUS	transcript	10531081	10532077	.	+	.	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	start_codon	10531081	10531083	.	+	0	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	CDS	10531081	10531153	0.58	+	0	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	exon	10531081	10531153	.	+	.	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	intron	10531154	10531307	.	+	.	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	CDS	10531308	10532077	1	+	2	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	exon	10531308	10532077	.	+	.	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
Phchi.S3	AUGUSTUS	stop_codon	10532078	10532080	.	+	0	transcript_id "Phchi.S3G137400.t1"; gene_id "Phchi.S3G137400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2241.t1 is derived from g9161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5613632	5614249	.	+	.	Phchi.S5G085000
Phchi.S5	AUGUSTUS	transcript	5613632	5614249	.	+	.	transcript_id "Phchi.S5G085000.t1"; gene_id "Phchi.S5G085000"
Phchi.S5	AUGUSTUS	start_codon	5613632	5613634	.	+	0	transcript_id "Phchi.S5G085000.t1"; gene_id "Phchi.S5G085000"
Phchi.S5	AUGUSTUS	CDS	5613632	5614249	1	+	0	transcript_id "Phchi.S5G085000.t1"; gene_id "Phchi.S5G085000"
Phchi.S5	AUGUSTUS	exon	5613632	5614249	.	+	.	transcript_id "Phchi.S5G085000.t1"; gene_id "Phchi.S5G085000"
Phchi.S5	AUGUSTUS	stop_codon	5614250	5614252	.	+	0	transcript_id "Phchi.S5G085000.t1"; gene_id "Phchi.S5G085000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11007.t1 is derived from g15057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3610852	3611759	.	-	.	Phchi.S4G058900
Phchi.S4	AUGUSTUS	transcript	3610852	3611759	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	stop_codon	3610849	3610851	.	-	0	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	CDS	3610852	3610884	1	-	0	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	exon	3610852	3610884	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	intron	3610885	3610962	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	CDS	3610963	3611142	1	-	0	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	exon	3610963	3611142	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	intron	3611143	3611267	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	CDS	3611268	3611369	0.99	-	0	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	exon	3611268	3611369	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	intron	3611370	3611489	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	CDS	3611490	3611759	0.95	-	0	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	exon	3611490	3611759	.	-	.	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
Phchi.S4	AUGUSTUS	start_codon	3611757	3611759	.	-	0	transcript_id "Phchi.S4G058900.t1"; gene_id "Phchi.S4G058900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8284.t1 is derived from g5459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35088261	35092377	.	-	.	Phchi.S1G544300
Phchi.S1	AUGUSTUS	transcript	35088261	35092377	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	stop_codon	35088258	35088260	.	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35088261	35088536	0.99	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35088261	35088536	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35088537	35088635	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35088636	35088791	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35088636	35088791	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35088792	35088975	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35088976	35089035	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35088976	35089035	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35089036	35089128	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35089129	35089179	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35089129	35089179	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35089180	35089266	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35089267	35089338	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35089267	35089338	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35089339	35089423	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35089424	35089490	0.45	-	1	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35089424	35089490	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35089491	35089608	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35089609	35089691	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35089609	35089691	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35089692	35089795	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35089796	35089912	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35089796	35089912	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35089913	35089999	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35090000	35090041	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35090000	35090041	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35090042	35090168	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35090169	35090234	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35090169	35090234	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35090235	35090448	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35090449	35090577	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35090449	35090577	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35090578	35090719	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35090720	35090791	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35090720	35090791	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35090792	35090898	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35090899	35090945	1	-	2	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35090899	35090945	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35090946	35091030	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35091031	35091099	0.99	-	2	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35091031	35091099	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35091100	35091200	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35091201	35091273	0.99	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35091201	35091273	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35091274	35091371	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35091372	35091443	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35091372	35091443	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35091444	35091553	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35091554	35091699	0.94	-	2	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35091554	35091699	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35091700	35091784	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35091785	35091878	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35091785	35091878	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35091879	35091993	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35091994	35092068	0.66	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35091994	35092068	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35092069	35092174	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35092175	35092258	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35092175	35092258	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	intron	35092259	35092344	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	CDS	35092345	35092377	1	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	exon	35092345	35092377	.	-	.	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
Phchi.S1	AUGUSTUS	start_codon	35092375	35092377	.	-	0	transcript_id "Phchi.S1G544300.t1"; gene_id "Phchi.S1G544300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12644.t1 is derived from g16011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C136	AUGUSTUS	gene	7861	8450	.	-	.	Phchi.C136G000400
Phchi.C136	AUGUSTUS	transcript	7861	8450	.	-	.	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	stop_codon	7858	7860	.	-	0	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	CDS	7861	8043	0.59	-	0	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	exon	7861	8043	.	-	.	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	intron	8044	8120	.	-	.	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	CDS	8121	8450	0.57	-	0	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	exon	8121	8450	.	-	.	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
Phchi.C136	AUGUSTUS	start_codon	8448	8450	.	-	0	transcript_id "Phchi.C136G000400.t1"; gene_id "Phchi.C136G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6962.t1 is derived from g4134.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26150163	26152093	.	+	.	Phchi.S1G412100
Phchi.S1	AUGUSTUS	transcript	26150163	26152093	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	start_codon	26150163	26150165	.	+	0	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	CDS	26150163	26150500	0.34	+	0	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	exon	26150163	26150500	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	intron	26150501	26150605	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	CDS	26150606	26150875	1	+	1	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	exon	26150606	26150875	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	intron	26150876	26150969	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	CDS	26150970	26151237	1	+	1	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	exon	26150970	26151237	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	intron	26151238	26151326	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	CDS	26151327	26151485	1	+	0	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	exon	26151327	26151485	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	intron	26151486	26151602	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	CDS	26151603	26151890	1	+	0	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	exon	26151603	26151890	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	intron	26151891	26151970	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	CDS	26151971	26152093	0.98	+	0	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	exon	26151971	26152093	.	+	.	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
Phchi.S1	AUGUSTUS	stop_codon	26152094	26152096	.	+	0	transcript_id "Phchi.S1G412100.t1"; gene_id "Phchi.S1G412100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2033.t1 is derived from g8953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4536580	4539598	.	-	.	Phchi.S5G064200
Phchi.S5	AUGUSTUS	transcript	4536580	4539598	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	stop_codon	4536577	4536579	.	-	0	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4536580	4536597	0.8	-	0	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4536580	4536597	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4536598	4536685	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4536686	4536792	0.58	-	2	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4536686	4536792	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4536793	4536885	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4536886	4536908	0.56	-	1	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4536886	4536908	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4536909	4536999	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4537000	4537020	0.58	-	1	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4537000	4537020	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4537021	4537112	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4537113	4537203	1	-	2	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4537113	4537203	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4537204	4537286	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4537287	4537326	1	-	0	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4537287	4537326	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4537327	4537543	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4537544	4539271	0.85	-	0	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4537544	4539271	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4539272	4539353	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4539354	4539433	1	-	2	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4539354	4539433	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	intron	4539434	4539510	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	CDS	4539511	4539598	0.93	-	0	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	exon	4539511	4539598	.	-	.	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
Phchi.S5	AUGUSTUS	start_codon	4539596	4539598	.	-	0	transcript_id "Phchi.S5G064200.t1"; gene_id "Phchi.S5G064200"
# This transcript jg10679.t2 is derived from g14729.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10680.t1 is derived from g14730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1565455	1566959	.	-	.	Phchi.S4G026200
Phchi.S4	AUGUSTUS	transcript	1565455	1566959	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	stop_codon	1565452	1565454	.	-	0	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	CDS	1565455	1566123	0.99	-	0	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	exon	1565455	1566123	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	intron	1566124	1566232	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	CDS	1566233	1566540	1	-	2	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	exon	1566233	1566540	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	intron	1566541	1566630	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	CDS	1566631	1566741	1	-	2	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	exon	1566631	1566741	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	intron	1566742	1566874	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	CDS	1566875	1566959	1	-	0	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	exon	1566875	1566959	.	-	.	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
Phchi.S4	AUGUSTUS	start_codon	1566957	1566959	.	-	0	transcript_id "Phchi.S4G026200.t1"; gene_id "Phchi.S4G026200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1609.t1 is derived from g8528.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2017976	2018372	.	-	.	Phchi.S5G021800
Phchi.S5	AUGUSTUS	transcript	2017976	2018372	.	-	.	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	stop_codon	2017973	2017975	.	-	0	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	CDS	2017976	2018094	0.48	-	2	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	exon	2017976	2018094	.	-	.	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	intron	2018095	2018170	.	-	.	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	CDS	2018171	2018372	0.46	-	0	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	exon	2018171	2018372	.	-	.	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
Phchi.S5	AUGUSTUS	start_codon	2018370	2018372	.	-	0	transcript_id "Phchi.S5G021800.t1"; gene_id "Phchi.S5G021800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6584.t1 is derived from g3756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23855139	23857407	.	-	.	Phchi.S1G374300
Phchi.S1	AUGUSTUS	transcript	23855139	23857407	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	stop_codon	23855136	23855138	.	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23855139	23855255	1	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23855139	23855255	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23855256	23855346	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23855347	23855433	1	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23855347	23855433	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23855434	23855516	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23855517	23855621	1	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23855517	23855621	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23855622	23855760	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23855761	23855844	0.99	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23855761	23855844	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23855845	23855945	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23855946	23856062	1	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23855946	23856062	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23856063	23856145	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23856146	23856238	1	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23856146	23856238	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23856239	23856431	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23856432	23856540	0.53	-	1	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23856432	23856540	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23856541	23856651	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23856652	23856776	0.63	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23856652	23856776	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23856777	23856865	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23856866	23857187	0.49	-	1	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23856866	23857187	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	intron	23857188	23857261	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	CDS	23857262	23857407	0.58	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	exon	23857262	23857407	.	-	.	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
Phchi.S1	AUGUSTUS	start_codon	23857405	23857407	.	-	0	transcript_id "Phchi.S1G374300.t1"; gene_id "Phchi.S1G374300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1034.t1 is derived from g10817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7224036	7224515	.	-	.	Phchi.S6G099300
Phchi.S6	AUGUSTUS	transcript	7224036	7224515	.	-	.	transcript_id "Phchi.S6G099300.t1"; gene_id "Phchi.S6G099300"
Phchi.S6	AUGUSTUS	stop_codon	7224033	7224035	.	-	0	transcript_id "Phchi.S6G099300.t1"; gene_id "Phchi.S6G099300"
Phchi.S6	AUGUSTUS	CDS	7224036	7224515	0.97	-	0	transcript_id "Phchi.S6G099300.t1"; gene_id "Phchi.S6G099300"
Phchi.S6	AUGUSTUS	exon	7224036	7224515	.	-	.	transcript_id "Phchi.S6G099300.t1"; gene_id "Phchi.S6G099300"
Phchi.S6	AUGUSTUS	start_codon	7224513	7224515	.	-	0	transcript_id "Phchi.S6G099300.t1"; gene_id "Phchi.S6G099300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg672.t1 is derived from g10454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4653526	4654080	.	-	.	Phchi.S6G063100
Phchi.S6	AUGUSTUS	transcript	4653526	4654080	.	-	.	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	stop_codon	4653523	4653525	.	-	0	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	CDS	4653526	4653653	1	-	2	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	exon	4653526	4653653	.	-	.	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	intron	4653654	4653737	.	-	.	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	CDS	4653738	4654080	0.81	-	0	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	exon	4653738	4654080	.	-	.	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
Phchi.S6	AUGUSTUS	start_codon	4654078	4654080	.	-	0	transcript_id "Phchi.S6G063100.t1"; gene_id "Phchi.S6G063100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14037.t1 is derived from g12504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10403394	10404316	.	+	.	Phchi.S3G135600
Phchi.S3	AUGUSTUS	transcript	10403394	10404316	.	+	.	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	start_codon	10403394	10403396	.	+	0	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	CDS	10403394	10403828	0.63	+	0	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	exon	10403394	10403828	.	+	.	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	intron	10403829	10404055	.	+	.	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	CDS	10404056	10404118	0.61	+	0	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	exon	10404056	10404118	.	+	.	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	intron	10404119	10404208	.	+	.	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	CDS	10404209	10404316	1	+	0	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	exon	10404209	10404316	.	+	.	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
Phchi.S3	AUGUSTUS	stop_codon	10404317	10404319	.	+	0	transcript_id "Phchi.S3G135600.t1"; gene_id "Phchi.S3G135600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8821.t1 is derived from g5996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38136047	38139206	.	+	.	Phchi.S1G598000
Phchi.S1	AUGUSTUS	transcript	38136047	38139206	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	start_codon	38136047	38136049	.	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38136047	38136286	0.53	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38136047	38136286	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38136287	38136420	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38136421	38136782	0.68	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38136421	38136782	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38136783	38136871	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38136872	38137063	1	+	1	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38136872	38137063	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38137064	38137147	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38137148	38137229	1	+	1	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38137148	38137229	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38137230	38137320	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38137321	38137512	1	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38137321	38137512	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38137513	38137629	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38137630	38137743	1	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38137630	38137743	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38137744	38137850	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38137851	38137944	1	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38137851	38137944	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38137945	38138036	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38138037	38138194	1	+	2	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38138037	38138194	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38138195	38138292	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38138293	38138467	0.59	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38138293	38138467	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38138468	38138554	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38138555	38138727	0.59	+	2	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38138555	38138727	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38138728	38138854	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38138855	38139073	0.94	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38138855	38139073	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	intron	38139074	38139170	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	CDS	38139171	38139206	0.92	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	exon	38139171	38139206	.	+	.	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
Phchi.S1	AUGUSTUS	stop_codon	38139207	38139209	.	+	0	transcript_id "Phchi.S1G598000.t1"; gene_id "Phchi.S1G598000"
# This transcript jg12255.t2 is derived from g7931.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12255.t3 is derived from g7931.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12256.t1 is derived from g7932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7033418	7034566	.	+	.	Phchi.S2G033600
Phchi.S2	AUGUSTUS	transcript	7033418	7034566	.	+	.	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	start_codon	7033418	7033420	.	+	0	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	CDS	7033418	7033981	0.99	+	0	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	exon	7033418	7033981	.	+	.	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	intron	7033982	7034068	.	+	.	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	CDS	7034069	7034566	0.75	+	0	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	exon	7034069	7034566	.	+	.	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
Phchi.S2	AUGUSTUS	stop_codon	7034567	7034569	.	+	0	transcript_id "Phchi.S2G033600.t1"; gene_id "Phchi.S2G033600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4159.t1 is derived from g1328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8682053	8682917	.	-	.	Phchi.S1G131800
Phchi.S1	AUGUSTUS	transcript	8682053	8682917	.	-	.	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	stop_codon	8682050	8682052	.	-	0	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	CDS	8682053	8682672	0.99	-	2	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	exon	8682053	8682672	.	-	.	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	intron	8682673	8682763	.	-	.	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	CDS	8682764	8682917	0.66	-	0	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	exon	8682764	8682917	.	-	.	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
Phchi.S1	AUGUSTUS	start_codon	8682915	8682917	.	-	0	transcript_id "Phchi.S1G131800.t1"; gene_id "Phchi.S1G131800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13591.t1 is derived from g12058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7611256	7616169	.	+	.	Phchi.S3G091000
Phchi.S3	AUGUSTUS	transcript	7611256	7616169	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	start_codon	7611256	7611258	.	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7611256	7611599	1	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7611256	7611599	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7611600	7611782	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7611783	7611847	1	+	1	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7611783	7611847	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7611848	7611930	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7611931	7612048	1	+	2	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7611931	7612048	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7612049	7612142	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7612143	7612266	1	+	1	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7612143	7612266	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7612267	7612481	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7612482	7612562	1	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7612482	7612562	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7612563	7612821	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7612822	7613163	0.93	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7612822	7613163	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7613164	7613294	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7613295	7613479	1	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7613295	7613479	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7613480	7613604	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7613605	7613722	0.97	+	1	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7613605	7613722	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7613723	7613799	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7613800	7614156	0.61	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7613800	7614156	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7614157	7614270	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7614271	7614472	0.89	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7614271	7614472	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7614473	7614593	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7614594	7614826	0.62	+	2	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7614594	7614826	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	intron	7614827	7614987	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	CDS	7614988	7616169	0.55	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	exon	7614988	7616169	.	+	.	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
Phchi.S3	AUGUSTUS	stop_codon	7616170	7616172	.	+	0	transcript_id "Phchi.S3G091000.t1"; gene_id "Phchi.S3G091000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15230.t1 is derived from g13698.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17841259	17843946	.	-	.	Phchi.S3G254900
Phchi.S3	AUGUSTUS	transcript	17841259	17843946	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	stop_codon	17841256	17841258	.	-	0	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17841259	17841293	0.98	-	2	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17841259	17841293	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17841294	17841383	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17841384	17841419	0.98	-	2	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17841384	17841419	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17841420	17841498	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17841499	17841557	1	-	1	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17841499	17841557	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17841558	17841636	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17841637	17841780	1	-	1	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17841637	17841780	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17841781	17841863	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17841864	17841948	1	-	2	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17841864	17841948	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17841949	17842036	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17842037	17842191	1	-	1	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17842037	17842191	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17842192	17842329	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17842330	17842410	1	-	1	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17842330	17842410	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17842411	17842542	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17842543	17842604	1	-	0	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17842543	17842604	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17842605	17842751	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17842752	17842820	1	-	0	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17842752	17842820	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17842821	17842928	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17842929	17842977	1	-	1	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17842929	17842977	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17842978	17843068	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17843069	17843132	1	-	2	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17843069	17843132	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17843133	17843337	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17843338	17843387	1	-	1	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17843338	17843387	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	intron	17843388	17843662	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	CDS	17843663	17843946	0.7	-	0	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	exon	17843663	17843946	.	-	.	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
Phchi.S3	AUGUSTUS	start_codon	17843944	17843946	.	-	0	transcript_id "Phchi.S3G254900.t1"; gene_id "Phchi.S3G254900"
# This transcript jg2864.t2 is derived from g33.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2865.t1 is derived from g34.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	158971	160619	.	-	.	Phchi.S1G002400
Phchi.S1	AUGUSTUS	transcript	158971	160619	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	stop_codon	158968	158970	.	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	158971	158985	1	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	158971	158985	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	intron	158986	159080	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	159081	159182	1	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	159081	159182	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	intron	159183	159315	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	159316	159450	1	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	159316	159450	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	intron	159451	159540	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	159541	159731	1	-	2	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	159541	159731	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	intron	159732	159930	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	159931	159955	1	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	159931	159955	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	intron	159956	160047	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	160048	160509	0.87	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	160048	160509	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	intron	160510	160613	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	CDS	160614	160619	0.88	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	exon	160614	160619	.	-	.	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
Phchi.S1	AUGUSTUS	start_codon	160617	160619	.	-	0	transcript_id "Phchi.S1G002400.t1"; gene_id "Phchi.S1G002400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10699.t1 is derived from g14749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1643732	1645379	.	+	.	Phchi.S4G028100
Phchi.S4	AUGUSTUS	transcript	1643732	1645379	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	start_codon	1643732	1643734	.	+	0	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1643732	1643817	1	+	0	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1643732	1643817	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1643818	1644081	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1644082	1644198	1	+	1	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1644082	1644198	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1644199	1644313	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1644314	1644470	1	+	1	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1644314	1644470	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1644471	1644573	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1644574	1644682	1	+	0	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1644574	1644682	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1644683	1644764	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1644765	1644878	1	+	2	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1644765	1644878	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1644879	1645016	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1645017	1645040	0.61	+	2	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1645017	1645040	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1645041	1645149	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1645150	1645178	0.61	+	2	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1645150	1645178	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	intron	1645179	1645271	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	CDS	1645272	1645379	1	+	0	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	exon	1645272	1645379	.	+	.	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
Phchi.S4	AUGUSTUS	stop_codon	1645380	1645382	.	+	0	transcript_id "Phchi.S4G028100.t1"; gene_id "Phchi.S4G028100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7658.t1 is derived from g4832.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30452554	30456985	.	+	.	Phchi.S1G481700
Phchi.S1	AUGUSTUS	transcript	30452554	30456985	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	start_codon	30452554	30452556	.	+	0	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30452554	30453026	0.87	+	0	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30452554	30453026	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30453027	30453121	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30453122	30453725	0.89	+	1	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30453122	30453725	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30453726	30453820	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30453821	30453868	1	+	0	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30453821	30453868	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30453869	30453960	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30453961	30455131	1	+	0	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30453961	30455131	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30455132	30455280	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30455281	30456263	0.93	+	2	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30455281	30456263	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30456264	30456333	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30456334	30456460	0.72	+	0	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30456334	30456460	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30456461	30456704	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30456705	30456747	0.72	+	2	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30456705	30456747	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30456748	30456843	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30456844	30456985	0.77	+	1	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30456844	30456985	.	+	.	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	stop_codon	30456986	30456988	.	+	0	transcript_id "Phchi.S1G481700.t1"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	transcript	30452554	30456985	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	start_codon	30452554	30452556	.	+	0	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30452554	30453026	0.87	+	0	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30452554	30453026	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30453027	30453121	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30453122	30453725	0.88	+	1	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30453122	30453725	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30453726	30453820	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30453821	30453868	1	+	0	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30453821	30453868	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30453869	30453960	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30453961	30455131	1	+	0	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30453961	30455131	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30455132	30455280	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30455281	30456263	0.68	+	2	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30455281	30456263	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30456264	30456333	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30456334	30456460	0.6	+	0	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30456334	30456460	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30456461	30456704	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30456705	30456747	0.62	+	2	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30456705	30456747	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	intron	30456748	30456846	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	CDS	30456847	30456985	0.61	+	1	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	exon	30456847	30456985	.	+	.	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
Phchi.S1	AUGUSTUS	stop_codon	30456986	30456988	.	+	0	transcript_id "Phchi.S1G481700.t2"; gene_id "Phchi.S1G481700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg795.t1 is derived from g10577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5616680	5617838	.	-	.	Phchi.S6G075400
Phchi.S6	AUGUSTUS	transcript	5616680	5617838	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	stop_codon	5616677	5616679	.	-	0	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	CDS	5616680	5616861	0.53	-	2	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	exon	5616680	5616861	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	intron	5616862	5616969	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	CDS	5616970	5617138	0.55	-	0	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	exon	5616970	5617138	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	intron	5617139	5617228	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	CDS	5617229	5617414	1	-	0	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	exon	5617229	5617414	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	intron	5617415	5617511	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	CDS	5617512	5617838	0.79	-	0	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	exon	5617512	5617838	.	-	.	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
Phchi.S6	AUGUSTUS	start_codon	5617836	5617838	.	-	0	transcript_id "Phchi.S6G075400.t1"; gene_id "Phchi.S6G075400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6566.t1 is derived from g3738.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23739412	23740945	.	-	.	Phchi.S1G372500
Phchi.S1	AUGUSTUS	transcript	23739412	23740945	.	-	.	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	stop_codon	23739409	23739411	.	-	0	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	CDS	23739412	23740046	1	-	2	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	exon	23739412	23740046	.	-	.	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	intron	23740047	23740146	.	-	.	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	CDS	23740147	23740945	1	-	0	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	exon	23740147	23740945	.	-	.	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	start_codon	23740943	23740945	.	-	0	transcript_id "Phchi.S1G372500.t1"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	transcript	23739412	23740140	.	-	.	transcript_id "Phchi.S1G372500.t2"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	stop_codon	23739409	23739411	.	-	0	transcript_id "Phchi.S1G372500.t2"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	CDS	23739412	23740140	1	-	0	transcript_id "Phchi.S1G372500.t2"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	exon	23739412	23740140	.	-	.	transcript_id "Phchi.S1G372500.t2"; gene_id "Phchi.S1G372500"
Phchi.S1	AUGUSTUS	start_codon	23740138	23740140	.	-	0	transcript_id "Phchi.S1G372500.t2"; gene_id "Phchi.S1G372500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3887.t1 is derived from g1056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6207377	6210097	.	+	.	Phchi.S1G104600
Phchi.S1	AUGUSTUS	transcript	6207377	6210097	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	start_codon	6207377	6207379	.	+	0	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6207377	6207395	1	+	0	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6207377	6207395	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6207396	6207474	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6207475	6207719	1	+	2	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6207475	6207719	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6207720	6207799	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6207800	6207929	1	+	0	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6207800	6207929	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6207930	6208124	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6208125	6208298	1	+	2	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6208125	6208298	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6208299	6208432	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6208433	6208659	0.99	+	2	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6208433	6208659	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6208660	6208768	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6208769	6209033	1	+	0	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6208769	6209033	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6209034	6209126	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6209127	6209306	1	+	2	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6209127	6209306	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6209307	6209439	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6209440	6209654	1	+	2	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6209440	6209654	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	intron	6209655	6209758	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	CDS	6209759	6210097	0.99	+	0	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	exon	6209759	6210097	.	+	.	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
Phchi.S1	AUGUSTUS	stop_codon	6210098	6210100	.	+	0	transcript_id "Phchi.S1G104600.t1"; gene_id "Phchi.S1G104600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3325.t1 is derived from g494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2916226	2922206	.	-	.	Phchi.S1G048400
Phchi.S1	AUGUSTUS	transcript	2916226	2922206	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	stop_codon	2916223	2916225	.	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2916226	2916318	0.86	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2916226	2916318	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2916319	2916436	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2916437	2916505	0.94	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2916437	2916505	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2916506	2916645	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2916646	2916706	1	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2916646	2916706	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2916707	2916880	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2916881	2917398	1	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2916881	2917398	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2917399	2917546	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2917547	2918155	0.98	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2917547	2918155	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2918156	2918269	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2918270	2918548	1	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2918270	2918548	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2918549	2918737	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2918738	2918929	0.99	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2918738	2918929	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2918930	2919037	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2919038	2919148	0.95	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2919038	2919148	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2919149	2919258	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2919259	2919567	1	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2919259	2919567	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2919568	2919662	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2919663	2919714	1	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2919663	2919714	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2919715	2919790	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2919791	2919982	0.99	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2919791	2919982	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2919983	2920256	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2920257	2920346	1	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2920257	2920346	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2920347	2920539	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2920540	2920803	0.97	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2920540	2920803	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2920804	2920948	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2920949	2921473	0.99	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2920949	2921473	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2921474	2921575	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2921576	2921626	1	-	1	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2921576	2921626	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2921627	2921713	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2921714	2921793	1	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2921714	2921793	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	intron	2921794	2921987	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	CDS	2921988	2922206	0.68	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	exon	2921988	2922206	.	-	.	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
Phchi.S1	AUGUSTUS	start_codon	2922204	2922206	.	-	0	transcript_id "Phchi.S1G048400.t1"; gene_id "Phchi.S1G048400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14447.t1 is derived from g12915.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12883466	12885035	.	-	.	Phchi.S3G176600
Phchi.S3	AUGUSTUS	transcript	12883466	12885035	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	stop_codon	12883463	12883465	.	-	0	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12883466	12883564	0.87	-	0	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12883466	12883564	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12883565	12883644	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12883645	12883753	1	-	1	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12883645	12883753	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12883754	12883872	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12883873	12883941	0.97	-	1	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12883873	12883941	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12883942	12884078	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884079	12884223	1	-	2	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884079	12884223	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884224	12884300	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884301	12884465	1	-	2	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884301	12884465	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884466	12884581	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884582	12884643	1	-	1	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884582	12884643	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884644	12884720	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884721	12884847	1	-	2	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884721	12884847	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884848	12884917	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884918	12885035	0.97	-	0	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884918	12885035	.	-	.	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	start_codon	12885033	12885035	.	-	0	transcript_id "Phchi.S3G176600.t1"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	transcript	12883466	12884920	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	stop_codon	12883463	12883465	.	-	0	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12883466	12883564	0.86	-	0	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12883466	12883564	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12883565	12883644	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12883645	12883753	0.99	-	1	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12883645	12883753	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12883754	12883872	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12883873	12883941	1	-	1	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12883873	12883941	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12883942	12884078	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884079	12884223	0.99	-	2	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884079	12884223	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884224	12884300	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884301	12884465	1	-	2	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884301	12884465	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884466	12884581	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884582	12884643	0.99	-	1	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884582	12884643	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884644	12884720	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884721	12884851	0.98	-	0	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884721	12884851	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	intron	12884852	12884917	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	CDS	12884918	12884920	0.98	-	0	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	exon	12884918	12884920	.	-	.	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
Phchi.S3	AUGUSTUS	start_codon	12884918	12884920	.	-	0	transcript_id "Phchi.S3G176600.t2"; gene_id "Phchi.S3G176600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10556.t1 is derived from g14606.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	971790	974842	.	+	.	Phchi.S4G013800
Phchi.S4	AUGUSTUS	transcript	971790	974842	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	start_codon	971790	971792	.	+	0	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	971790	972009	0.99	+	0	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	971790	972009	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972010	972097	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972098	972365	1	+	2	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972098	972365	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972366	972457	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972458	972547	0.43	+	1	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972458	972547	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972548	972600	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972601	972673	0.67	+	1	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972601	972673	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972674	972773	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972774	972889	1	+	0	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972774	972889	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972890	973001	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973002	973100	0.9	+	1	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973002	973100	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973101	973238	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973239	973369	0.72	+	1	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973239	973369	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973370	973596	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973597	973666	0.91	+	2	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973597	973666	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973667	973860	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973861	973933	1	+	1	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973861	973933	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973934	974071	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974072	974114	0.72	+	0	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974072	974114	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	974115	974165	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974166	974180	0.73	+	2	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974166	974180	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	974181	974517	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974518	974634	1	+	2	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974518	974634	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	974635	974792	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974793	974842	0.54	+	2	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974793	974842	.	+	.	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	stop_codon	974843	974845	.	+	0	transcript_id "Phchi.S4G013800.t1"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	transcript	971790	974842	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	start_codon	971790	971792	.	+	0	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	971790	972009	1	+	0	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	971790	972009	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972010	972097	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972098	972365	1	+	2	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972098	972365	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972366	972457	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972458	972547	0.29	+	1	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972458	972547	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972548	972600	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972601	972673	0.54	+	1	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972601	972673	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972674	972773	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	972774	972889	1	+	0	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	972774	972889	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	972890	973001	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973002	973100	0.91	+	1	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973002	973100	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973101	973238	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973239	973369	0.73	+	1	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973239	973369	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973370	973596	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973597	973666	0.96	+	2	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973597	973666	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973667	973860	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	973861	973933	1	+	1	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	973861	973933	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	973934	974009	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974010	974051	0.51	+	0	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974010	974051	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	974052	974143	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974144	974180	0.98	+	0	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974144	974180	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	974181	974517	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974518	974634	1	+	2	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974518	974634	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	intron	974635	974792	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	CDS	974793	974842	0.53	+	2	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	exon	974793	974842	.	+	.	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
Phchi.S4	AUGUSTUS	stop_codon	974843	974845	.	+	0	transcript_id "Phchi.S4G013800.t2"; gene_id "Phchi.S4G013800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9682.t1 is derived from g6858.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43262791	43264646	.	-	.	Phchi.S1G684100
Phchi.S1	AUGUSTUS	transcript	43262791	43264646	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	stop_codon	43262788	43262790	.	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43262791	43263058	0.96	-	1	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43262791	43263058	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43263059	43263146	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43263147	43263208	1	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43263147	43263208	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43263209	43263314	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43263315	43263452	0.98	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43263315	43263452	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43263453	43263575	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43263576	43263665	0.99	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43263576	43263665	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43263666	43263745	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43263746	43263831	0.38	-	2	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43263746	43263831	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43263832	43264059	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43264060	43264210	1	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43264060	43264210	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43264211	43264305	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43264306	43264448	1	-	2	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43264306	43264448	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	intron	43264449	43264540	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	CDS	43264541	43264646	1	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	exon	43264541	43264646	.	-	.	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
Phchi.S1	AUGUSTUS	start_codon	43264644	43264646	.	-	0	transcript_id "Phchi.S1G684100.t1"; gene_id "Phchi.S1G684100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3259.t1 is derived from g428.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2571230	2572988	.	-	.	Phchi.S1G041800
Phchi.S1	AUGUSTUS	transcript	2571230	2572988	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	stop_codon	2571227	2571229	.	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571230	2571325	0.62	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571230	2571325	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571326	2571432	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571433	2571479	0.63	-	2	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571433	2571479	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571480	2571586	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571587	2571704	0.89	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571587	2571704	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571705	2571881	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571882	2571956	1	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571882	2571956	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571957	2572095	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572096	2572150	1	-	1	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572096	2572150	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572151	2572233	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572234	2572256	0.95	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572234	2572256	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572257	2572411	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572412	2572478	0.98	-	1	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572412	2572478	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572479	2572613	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572614	2572738	0.98	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572614	2572738	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572739	2572844	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572845	2572988	0.98	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572845	2572988	.	-	.	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	start_codon	2572986	2572988	.	-	0	transcript_id "Phchi.S1G041800.t1"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	transcript	2571230	2572988	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	stop_codon	2571227	2571229	.	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571230	2571325	0.6	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571230	2571325	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571326	2571432	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571433	2571479	0.61	-	2	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571433	2571479	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571480	2571586	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571587	2571704	0.76	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571587	2571704	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571705	2571881	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2571882	2571956	1	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2571882	2571956	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2571957	2572095	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572096	2572150	1	-	1	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572096	2572150	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572151	2572256	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572257	2572309	1	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572257	2572309	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572310	2572411	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572412	2572478	0.96	-	1	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572412	2572478	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572479	2572613	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572614	2572738	0.97	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572614	2572738	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	intron	2572739	2572844	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	CDS	2572845	2572988	0.98	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	exon	2572845	2572988	.	-	.	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
Phchi.S1	AUGUSTUS	start_codon	2572986	2572988	.	-	0	transcript_id "Phchi.S1G041800.t2"; gene_id "Phchi.S1G041800"
# This transcript jg13418.t2 is derived from g11884.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13419.t1 is derived from g11886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6612124	6614514	.	-	.	Phchi.S3G073800
Phchi.S3	AUGUSTUS	transcript	6612124	6614514	.	-	.	transcript_id "Phchi.S3G073800.t1"; gene_id "Phchi.S3G073800"
Phchi.S3	AUGUSTUS	stop_codon	6612121	6612123	.	-	0	transcript_id "Phchi.S3G073800.t1"; gene_id "Phchi.S3G073800"
Phchi.S3	AUGUSTUS	CDS	6612124	6614514	0.89	-	0	transcript_id "Phchi.S3G073800.t1"; gene_id "Phchi.S3G073800"
Phchi.S3	AUGUSTUS	exon	6612124	6614514	.	-	.	transcript_id "Phchi.S3G073800.t1"; gene_id "Phchi.S3G073800"
Phchi.S3	AUGUSTUS	start_codon	6614512	6614514	.	-	0	transcript_id "Phchi.S3G073800.t1"; gene_id "Phchi.S3G073800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14962.t1 is derived from g13430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15774115	15775869	.	-	.	Phchi.S3G228100
Phchi.S3	AUGUSTUS	transcript	15774115	15775356	.	-	.	transcript_id "Phchi.S3G228100.t1"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	stop_codon	15774112	15774114	.	-	0	transcript_id "Phchi.S3G228100.t1"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	CDS	15774115	15775356	0.93	-	0	transcript_id "Phchi.S3G228100.t1"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	exon	15774115	15775356	.	-	.	transcript_id "Phchi.S3G228100.t1"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	start_codon	15775354	15775356	.	-	0	transcript_id "Phchi.S3G228100.t1"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	transcript	15774115	15775869	.	-	.	transcript_id "Phchi.S3G228100.t2"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	stop_codon	15774112	15774114	.	-	0	transcript_id "Phchi.S3G228100.t2"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	CDS	15774115	15775869	0.71	-	0	transcript_id "Phchi.S3G228100.t2"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	exon	15774115	15775869	.	-	.	transcript_id "Phchi.S3G228100.t2"; gene_id "Phchi.S3G228100"
Phchi.S3	AUGUSTUS	start_codon	15775867	15775869	.	-	0	transcript_id "Phchi.S3G228100.t2"; gene_id "Phchi.S3G228100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8340.t1 is derived from g5515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35401543	35402430	.	+	.	Phchi.S1G549900
Phchi.S1	AUGUSTUS	transcript	35401543	35402430	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	start_codon	35401543	35401545	.	+	0	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	CDS	35401543	35401632	1	+	0	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	exon	35401543	35401632	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	intron	35401633	35401755	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	CDS	35401756	35401857	1	+	0	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	exon	35401756	35401857	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	intron	35401858	35401968	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	CDS	35401969	35402049	1	+	0	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	exon	35401969	35402049	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	intron	35402050	35402190	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	CDS	35402191	35402430	0.91	+	0	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	exon	35402191	35402430	.	+	.	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
Phchi.S1	AUGUSTUS	stop_codon	35402431	35402433	.	+	0	transcript_id "Phchi.S1G549900.t1"; gene_id "Phchi.S1G549900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6255.t1 is derived from g3427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21895155	21896911	.	-	.	Phchi.S1G341400
Phchi.S1	AUGUSTUS	transcript	21895155	21896911	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	stop_codon	21895152	21895154	.	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21895155	21895391	1	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21895155	21895391	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	intron	21895392	21895535	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21895536	21895697	1	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21895536	21895697	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	intron	21895698	21895785	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21895786	21895845	1	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21895786	21895845	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	intron	21895846	21895945	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21895946	21896210	1	-	1	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21895946	21896210	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	intron	21896211	21896364	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21896365	21896438	0.96	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21896365	21896438	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	intron	21896439	21896571	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21896572	21896679	1	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21896572	21896679	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	intron	21896680	21896812	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	CDS	21896813	21896911	0.98	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	exon	21896813	21896911	.	-	.	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
Phchi.S1	AUGUSTUS	start_codon	21896909	21896911	.	-	0	transcript_id "Phchi.S1G341400.t1"; gene_id "Phchi.S1G341400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3169.t1 is derived from g338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2071819	2073723	.	-	.	Phchi.S1G032800
Phchi.S1	AUGUSTUS	transcript	2071819	2073723	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	stop_codon	2071816	2071818	.	-	0	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	CDS	2071819	2071862	1	-	2	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	exon	2071819	2071862	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	intron	2071863	2071945	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	CDS	2071946	2072330	0.99	-	0	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	exon	2071946	2072330	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	intron	2072331	2072473	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	CDS	2072474	2072563	1	-	0	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	exon	2072474	2072563	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	intron	2072564	2072818	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	CDS	2072819	2072903	1	-	1	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	exon	2072819	2072903	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	intron	2072904	2073101	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	CDS	2073102	2073331	1	-	0	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	exon	2073102	2073331	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	intron	2073332	2073573	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	CDS	2073574	2073723	1	-	0	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	exon	2073574	2073723	.	-	.	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
Phchi.S1	AUGUSTUS	start_codon	2073721	2073723	.	-	0	transcript_id "Phchi.S1G032800.t1"; gene_id "Phchi.S1G032800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10521.t1 is derived from g14571.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	814689	817499	.	+	.	Phchi.S4G010300
Phchi.S4	AUGUSTUS	transcript	814689	817499	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	start_codon	814689	814691	.	+	0	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	CDS	814689	815380	0.66	+	0	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	exon	814689	815380	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	intron	815381	815642	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	CDS	815643	815683	0.48	+	1	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	exon	815643	815683	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	intron	815684	815988	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	CDS	815989	816478	0.42	+	2	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	exon	815989	816478	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	intron	816479	816985	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	CDS	816986	817179	0.34	+	1	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	exon	816986	817179	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	intron	817180	817413	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	CDS	817414	817499	0.59	+	2	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	exon	817414	817499	.	+	.	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
Phchi.S4	AUGUSTUS	stop_codon	817500	817502	.	+	0	transcript_id "Phchi.S4G010300.t1"; gene_id "Phchi.S4G010300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11143.t1 is derived from g15193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4373412	4374829	.	+	.	Phchi.S4G072500
Phchi.S4	AUGUSTUS	transcript	4373412	4374829	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	start_codon	4373412	4373414	.	+	0	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	CDS	4373412	4373534	0.98	+	0	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	exon	4373412	4373534	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	intron	4373535	4373657	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	CDS	4373658	4373736	1	+	0	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	exon	4373658	4373736	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	intron	4373737	4373908	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	CDS	4373909	4374011	1	+	2	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	exon	4373909	4374011	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	intron	4374012	4374092	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	CDS	4374093	4374356	1	+	1	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	exon	4374093	4374356	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	intron	4374357	4374490	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	CDS	4374491	4374602	1	+	1	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	exon	4374491	4374602	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	intron	4374603	4374691	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	CDS	4374692	4374829	1	+	0	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	exon	4374692	4374829	.	+	.	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
Phchi.S4	AUGUSTUS	stop_codon	4374830	4374832	.	+	0	transcript_id "Phchi.S4G072500.t1"; gene_id "Phchi.S4G072500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5068.t1 is derived from g2238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14512607	14514289	.	+	.	Phchi.S1G222700
Phchi.S1	AUGUSTUS	transcript	14512607	14514289	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	start_codon	14512607	14512609	.	+	0	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	CDS	14512607	14512719	1	+	0	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	exon	14512607	14512719	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	intron	14512720	14512910	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	CDS	14512911	14512964	1	+	1	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	exon	14512911	14512964	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	intron	14512965	14513094	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	CDS	14513095	14513146	1	+	1	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	exon	14513095	14513146	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	intron	14513147	14513287	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	CDS	14513288	14513540	0.81	+	0	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	exon	14513288	14513540	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	intron	14513541	14513696	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	CDS	14513697	14514289	0.7	+	2	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	exon	14513697	14514289	.	+	.	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
Phchi.S1	AUGUSTUS	stop_codon	14514290	14514292	.	+	0	transcript_id "Phchi.S1G222700.t1"; gene_id "Phchi.S1G222700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9758.t1 is derived from g6934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43534176	43535118	.	+	.	Phchi.S1G691700
Phchi.S1	AUGUSTUS	transcript	43534176	43535118	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	start_codon	43534176	43534178	.	+	0	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	CDS	43534176	43534323	0.69	+	0	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	exon	43534176	43534323	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	intron	43534324	43534535	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	CDS	43534536	43534573	0.84	+	2	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	exon	43534536	43534573	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	intron	43534574	43534664	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	CDS	43534665	43534697	0.72	+	0	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	exon	43534665	43534697	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	intron	43534698	43534868	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	CDS	43534869	43534904	0.79	+	0	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	exon	43534869	43534904	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	intron	43534905	43535067	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	CDS	43535068	43535118	0.81	+	0	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	exon	43535068	43535118	.	+	.	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
Phchi.S1	AUGUSTUS	stop_codon	43535119	43535121	.	+	0	transcript_id "Phchi.S1G691700.t1"; gene_id "Phchi.S1G691700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5767.t1 is derived from g2937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18872122	18872827	.	+	.	Phchi.S1G292600
Phchi.S1	AUGUSTUS	transcript	18872122	18872827	.	+	.	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	start_codon	18872122	18872124	.	+	0	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	CDS	18872122	18872136	0.43	+	0	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	exon	18872122	18872136	.	+	.	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	intron	18872137	18872224	.	+	.	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	CDS	18872225	18872827	0.98	+	0	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	exon	18872225	18872827	.	+	.	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
Phchi.S1	AUGUSTUS	stop_codon	18872828	18872830	.	+	0	transcript_id "Phchi.S1G292600.t1"; gene_id "Phchi.S1G292600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10671.t1 is derived from g14721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1525070	1526807	.	+	.	Phchi.S4G025300
Phchi.S4	AUGUSTUS	transcript	1525070	1526807	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	start_codon	1525070	1525072	.	+	0	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	CDS	1525070	1525384	0.84	+	0	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	exon	1525070	1525384	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	intron	1525385	1525495	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	CDS	1525496	1525799	1	+	0	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	exon	1525496	1525799	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	intron	1525800	1525884	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	CDS	1525885	1526157	1	+	2	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	exon	1525885	1526157	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	intron	1526158	1526274	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	CDS	1526275	1526807	1	+	2	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	exon	1526275	1526807	.	+	.	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
Phchi.S4	AUGUSTUS	stop_codon	1526808	1526810	.	+	0	transcript_id "Phchi.S4G025300.t1"; gene_id "Phchi.S4G025300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9434.t1 is derived from g6610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41446141	41447256	.	+	.	Phchi.S1G659300
Phchi.S1	AUGUSTUS	transcript	41446141	41447256	.	+	.	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	start_codon	41446141	41446143	.	+	0	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	CDS	41446141	41446854	1	+	0	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	exon	41446141	41446854	.	+	.	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	intron	41446855	41446965	.	+	.	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	CDS	41446966	41447256	1	+	0	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	exon	41446966	41447256	.	+	.	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
Phchi.S1	AUGUSTUS	stop_codon	41447257	41447259	.	+	0	transcript_id "Phchi.S1G659300.t1"; gene_id "Phchi.S1G659300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10685.t1 is derived from g14735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1579454	1580524	.	-	.	Phchi.S4G026700
Phchi.S4	AUGUSTUS	transcript	1579454	1580524	.	-	.	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	stop_codon	1579451	1579453	.	-	0	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	CDS	1579454	1579751	0.48	-	1	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	exon	1579454	1579751	.	-	.	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	intron	1579752	1579859	.	-	.	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	CDS	1579860	1579943	0.71	-	1	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	exon	1579860	1579943	.	-	.	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	intron	1579944	1580054	.	-	.	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	CDS	1580055	1580524	0.73	-	0	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	exon	1580055	1580524	.	-	.	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
Phchi.S4	AUGUSTUS	start_codon	1580522	1580524	.	-	0	transcript_id "Phchi.S4G026700.t1"; gene_id "Phchi.S4G026700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9374.t1 is derived from g6550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41220545	41222725	.	+	.	Phchi.S1G653300
Phchi.S1	AUGUSTUS	transcript	41220545	41222725	.	+	.	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	start_codon	41220545	41220547	.	+	0	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	CDS	41220545	41220554	0.99	+	0	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	exon	41220545	41220554	.	+	.	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	intron	41220555	41220824	.	+	.	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	CDS	41220825	41222725	0.96	+	2	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	exon	41220825	41222725	.	+	.	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
Phchi.S1	AUGUSTUS	stop_codon	41222726	41222728	.	+	0	transcript_id "Phchi.S1G653300.t1"; gene_id "Phchi.S1G653300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12011.t1 is derived from g7686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	516379	517642	.	+	.	Phchi.S2G009100
Phchi.S2	AUGUSTUS	transcript	516379	517642	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	start_codon	516379	516381	.	+	0	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	CDS	516379	516405	0.4	+	0	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	exon	516379	516405	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	intron	516406	516782	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	CDS	516783	516846	1	+	0	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	exon	516783	516846	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	intron	516847	516936	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	CDS	516937	516992	1	+	2	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	exon	516937	516992	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	intron	516993	517200	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	CDS	517201	517253	1	+	0	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	exon	517201	517253	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	intron	517254	517347	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	CDS	517348	517466	1	+	1	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	exon	517348	517466	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	intron	517467	517547	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	CDS	517548	517642	1	+	2	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	exon	517548	517642	.	+	.	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
Phchi.S2	AUGUSTUS	stop_codon	517643	517645	.	+	0	transcript_id "Phchi.S2G009100.t1"; gene_id "Phchi.S2G009100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13113.t1 is derived from g11578.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4193569	4194141	.	-	.	Phchi.S3G043200
Phchi.S3	AUGUSTUS	transcript	4193569	4194141	.	-	.	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	stop_codon	4193566	4193568	.	-	0	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	CDS	4193569	4193645	0.5	-	2	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	exon	4193569	4193645	.	-	.	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	intron	4193646	4193732	.	-	.	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	CDS	4193733	4194141	1	-	0	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	exon	4193733	4194141	.	-	.	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
Phchi.S3	AUGUSTUS	start_codon	4194139	4194141	.	-	0	transcript_id "Phchi.S3G043200.t1"; gene_id "Phchi.S3G043200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15379.t1 is derived from g13847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18719452	18720322	.	+	.	Phchi.S3G269800
Phchi.S3	AUGUSTUS	transcript	18719452	18720322	.	+	.	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	start_codon	18719452	18719454	.	+	0	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	CDS	18719452	18719602	1	+	0	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	exon	18719452	18719602	.	+	.	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	intron	18719603	18719742	.	+	.	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	CDS	18719743	18719822	1	+	2	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	exon	18719743	18719822	.	+	.	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	intron	18719823	18719950	.	+	.	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	CDS	18719951	18720322	0.72	+	0	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	exon	18719951	18720322	.	+	.	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
Phchi.S3	AUGUSTUS	stop_codon	18720323	18720325	.	+	0	transcript_id "Phchi.S3G269800.t1"; gene_id "Phchi.S3G269800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10932.t1 is derived from g14982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3056682	3058330	.	+	.	Phchi.S4G051400
Phchi.S4	AUGUSTUS	transcript	3056682	3058330	.	+	.	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	start_codon	3056682	3056684	.	+	0	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	CDS	3056682	3056902	0.47	+	0	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	exon	3056682	3056902	.	+	.	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	intron	3056903	3057105	.	+	.	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	CDS	3057106	3057276	0.53	+	1	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	exon	3057106	3057276	.	+	.	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	intron	3057277	3057423	.	+	.	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	CDS	3057424	3058330	0.55	+	1	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	exon	3057424	3058330	.	+	.	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
Phchi.S4	AUGUSTUS	stop_codon	3058331	3058333	.	+	0	transcript_id "Phchi.S4G051400.t1"; gene_id "Phchi.S4G051400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13841.t1 is derived from g12308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9154201	9155702	.	+	.	Phchi.S3G116000
Phchi.S3	AUGUSTUS	transcript	9154201	9155702	.	+	.	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	start_codon	9154201	9154203	.	+	0	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	CDS	9154201	9154539	1	+	0	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	exon	9154201	9154539	.	+	.	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	intron	9154540	9154756	.	+	.	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	CDS	9154757	9155094	1	+	0	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	exon	9154757	9155094	.	+	.	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	intron	9155095	9155179	.	+	.	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	CDS	9155180	9155702	1	+	1	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	exon	9155180	9155702	.	+	.	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
Phchi.S3	AUGUSTUS	stop_codon	9155703	9155705	.	+	0	transcript_id "Phchi.S3G116000.t1"; gene_id "Phchi.S3G116000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12296.t1 is derived from g7972.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9204464	9205488	.	+	.	Phchi.S2G037600
Phchi.S2	AUGUSTUS	transcript	9204464	9205454	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	start_codon	9204464	9204466	.	+	0	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9204464	9204648	0.54	+	0	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9204464	9204648	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9204649	9204761	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9204762	9204816	0.48	+	1	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9204762	9204816	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9204817	9204903	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9204904	9204966	0.82	+	0	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9204904	9204966	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9204967	9205042	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9205043	9205166	1	+	0	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9205043	9205166	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9205167	9205305	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9205306	9205348	0.77	+	2	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9205306	9205348	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9205349	9205423	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9205424	9205454	0.74	+	1	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9205424	9205454	.	+	.	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	stop_codon	9205455	9205457	.	+	0	transcript_id "Phchi.S2G037600.t1"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	transcript	9204464	9205488	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	start_codon	9204464	9204466	.	+	0	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9204464	9204648	0.56	+	0	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9204464	9204648	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9204649	9204761	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9204762	9204816	0.45	+	1	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9204762	9204816	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9204817	9204903	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9204904	9204966	0.8	+	0	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9204904	9204966	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9204967	9205158	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9205159	9205203	0.88	+	0	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9205159	9205203	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9205204	9205305	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9205306	9205348	0.5	+	0	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9205306	9205348	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	intron	9205349	9205423	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	CDS	9205424	9205488	0.5	+	2	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	exon	9205424	9205488	.	+	.	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
Phchi.S2	AUGUSTUS	stop_codon	9205489	9205491	.	+	0	transcript_id "Phchi.S2G037600.t2"; gene_id "Phchi.S2G037600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9603.t1 is derived from g6779.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42891961	42894198	.	+	.	Phchi.S1G676200
Phchi.S1	AUGUSTUS	transcript	42891961	42894198	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	start_codon	42891961	42891963	.	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42891961	42892082	0.67	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42891961	42892082	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42892083	42892205	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42892206	42892476	0.96	+	1	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42892206	42892476	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42892477	42892551	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42892552	42892650	0.99	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42892552	42892650	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42892651	42892757	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42892758	42892960	1	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42892758	42892960	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42892961	42893045	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42893046	42893323	0.82	+	1	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42893046	42893323	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42893324	42893430	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42893431	42893618	0.46	+	2	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42893431	42893618	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42893619	42893741	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42893742	42893927	1	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42893742	42893927	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	intron	42893928	42894027	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	CDS	42894028	42894198	0.54	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	exon	42894028	42894198	.	+	.	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
Phchi.S1	AUGUSTUS	stop_codon	42894199	42894201	.	+	0	transcript_id "Phchi.S1G676200.t1"; gene_id "Phchi.S1G676200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9461.t1 is derived from g6637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41569183	41571700	.	-	.	Phchi.S1G662000
Phchi.S1	AUGUSTUS	transcript	41569183	41571700	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	stop_codon	41569180	41569182	.	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41569183	41569271	1	-	2	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41569183	41569271	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41569272	41569516	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41569517	41569634	1	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41569517	41569634	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41569635	41569741	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41569742	41569858	0.99	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41569742	41569858	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41569859	41569982	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41569983	41570120	1	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41569983	41570120	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41570121	41570205	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41570206	41570403	1	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41570206	41570403	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41570404	41570560	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41570561	41570773	1	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41570561	41570773	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41570774	41570858	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41570859	41571076	1	-	2	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41570859	41571076	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	intron	41571077	41571411	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	CDS	41571412	41571700	0.96	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	exon	41571412	41571700	.	-	.	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
Phchi.S1	AUGUSTUS	start_codon	41571698	41571700	.	-	0	transcript_id "Phchi.S1G662000.t1"; gene_id "Phchi.S1G662000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11011.t1 is derived from g15061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3622918	3624075	.	-	.	Phchi.S4G059300
Phchi.S4	AUGUSTUS	transcript	3622918	3624075	.	-	.	transcript_id "Phchi.S4G059300.t1"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	stop_codon	3622915	3622917	.	-	0	transcript_id "Phchi.S4G059300.t1"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	CDS	3622918	3624075	0.99	-	0	transcript_id "Phchi.S4G059300.t1"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	exon	3622918	3624075	.	-	.	transcript_id "Phchi.S4G059300.t1"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	start_codon	3624073	3624075	.	-	0	transcript_id "Phchi.S4G059300.t1"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	transcript	3622918	3623748	.	-	.	transcript_id "Phchi.S4G059300.t2"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	stop_codon	3622915	3622917	.	-	0	transcript_id "Phchi.S4G059300.t2"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	CDS	3622918	3623748	0.37	-	0	transcript_id "Phchi.S4G059300.t2"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	exon	3622918	3623748	.	-	.	transcript_id "Phchi.S4G059300.t2"; gene_id "Phchi.S4G059300"
Phchi.S4	AUGUSTUS	start_codon	3623746	3623748	.	-	0	transcript_id "Phchi.S4G059300.t2"; gene_id "Phchi.S4G059300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5411.t1 is derived from g2581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16739960	16743459	.	-	.	Phchi.S1G257000
Phchi.S1	AUGUSTUS	transcript	16739960	16743459	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	stop_codon	16739957	16739959	.	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16739960	16740013	0.38	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16739960	16740013	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16740014	16740098	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16740099	16740114	0.34	-	1	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16740099	16740114	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16740115	16740199	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16740200	16740333	0.31	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16740200	16740333	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16740334	16740541	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16740542	16740558	0.73	-	2	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16740542	16740558	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16740559	16740639	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16740640	16740654	0.53	-	2	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16740640	16740654	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16740655	16740846	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16740847	16740880	0.98	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16740847	16740880	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16740881	16741029	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16741030	16741096	0.62	-	1	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16741030	16741096	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16741097	16741254	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16741255	16741818	0.93	-	1	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16741255	16741818	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16741819	16741925	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16741926	16742269	0.97	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16741926	16742269	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16742270	16742399	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16742400	16742968	0.73	-	2	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16742400	16742968	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	intron	16742969	16743047	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	CDS	16743048	16743459	0.67	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	exon	16743048	16743459	.	-	.	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
Phchi.S1	AUGUSTUS	start_codon	16743457	16743459	.	-	0	transcript_id "Phchi.S1G257000.t1"; gene_id "Phchi.S1G257000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9399.t1 is derived from g6575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41338806	41342879	.	-	.	Phchi.S1G655800
Phchi.S1	AUGUSTUS	transcript	41338806	41342879	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	stop_codon	41338803	41338805	.	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41338806	41338831	0.97	-	2	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41338806	41338831	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41338832	41338943	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41338944	41339042	0.97	-	2	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41338944	41339042	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339043	41339167	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339168	41339418	0.97	-	1	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339168	41339418	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339419	41339502	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339503	41339594	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339503	41339594	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339595	41339699	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339700	41339787	0.95	-	1	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339700	41339787	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339788	41339895	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339896	41340005	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339896	41340005	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340006	41340084	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340085	41340202	1	-	1	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340085	41340202	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340203	41340300	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340301	41340389	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340301	41340389	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340390	41340474	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340475	41340624	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340475	41340624	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340625	41340750	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340751	41340888	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340751	41340888	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340889	41341017	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341018	41341287	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341018	41341287	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341288	41341688	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341689	41341805	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341689	41341805	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341806	41341884	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341885	41341995	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341885	41341995	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341996	41342147	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342148	41342267	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342148	41342267	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41342268	41342351	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342352	41342441	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342352	41342441	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41342442	41342539	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342540	41342639	1	-	1	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342540	41342639	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41342640	41342874	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342875	41342879	1	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342875	41342879	.	-	.	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	start_codon	41342877	41342879	.	-	0	transcript_id "Phchi.S1G655800.t1"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	transcript	41338806	41342879	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	stop_codon	41338803	41338805	.	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41338806	41338831	1	-	2	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41338806	41338831	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41338832	41338943	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41338944	41339042	1	-	2	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41338944	41339042	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339043	41339167	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339168	41339418	1	-	1	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339168	41339418	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339419	41339502	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339503	41339594	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339503	41339594	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339595	41339699	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339700	41339787	0.94	-	1	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339700	41339787	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41339788	41339895	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41339896	41340005	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41339896	41340005	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340006	41340084	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340085	41340202	1	-	1	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340085	41340202	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340203	41340300	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340301	41340389	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340301	41340389	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340390	41340474	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340475	41340624	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340475	41340624	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340625	41340750	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41340751	41340888	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41340751	41340888	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41340889	41341017	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341018	41341274	0.59	-	2	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341018	41341274	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341275	41341431	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341432	41341528	0.58	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341432	41341528	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341529	41341688	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341689	41341805	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341689	41341805	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341806	41341884	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41341885	41341995	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41341885	41341995	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41341996	41342147	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342148	41342267	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342148	41342267	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41342268	41342351	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342352	41342441	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342352	41342441	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41342442	41342539	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342540	41342639	1	-	1	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342540	41342639	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	intron	41342640	41342874	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	CDS	41342875	41342879	1	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	exon	41342875	41342879	.	-	.	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
Phchi.S1	AUGUSTUS	start_codon	41342877	41342879	.	-	0	transcript_id "Phchi.S1G655800.t2"; gene_id "Phchi.S1G655800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg873.t1 is derived from g10655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6057506	6058413	.	-	.	Phchi.S6G083200
Phchi.S6	AUGUSTUS	transcript	6057506	6058413	.	-	.	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	stop_codon	6057503	6057505	.	-	0	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	CDS	6057506	6058132	0.63	-	0	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	exon	6057506	6058132	.	-	.	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	intron	6058133	6058233	.	-	.	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	CDS	6058234	6058413	0.55	-	0	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	exon	6058234	6058413	.	-	.	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
Phchi.S6	AUGUSTUS	start_codon	6058411	6058413	.	-	0	transcript_id "Phchi.S6G083200.t1"; gene_id "Phchi.S6G083200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10585.t1 is derived from g14635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1065974	1068258	.	-	.	Phchi.S4G016700
Phchi.S4	AUGUSTUS	transcript	1065974	1068258	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	stop_codon	1065971	1065973	.	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1065974	1066045	0.89	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1065974	1066045	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1066046	1066154	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1066155	1066275	0.99	-	1	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1066155	1066275	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1066276	1066367	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1066368	1066453	1	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1066368	1066453	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1066454	1066609	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1066610	1066696	1	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1066610	1066696	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1066697	1066857	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1066858	1066938	1	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1066858	1066938	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1066939	1067013	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1067014	1067161	1	-	1	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1067014	1067161	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1067162	1067354	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1067355	1067422	1	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1067355	1067422	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1067423	1067517	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1067518	1067768	0.99	-	2	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1067518	1067768	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1067769	1067967	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1067968	1068059	1	-	1	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1067968	1068059	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	intron	1068060	1068253	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	CDS	1068254	1068258	0.78	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	exon	1068254	1068258	.	-	.	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
Phchi.S4	AUGUSTUS	start_codon	1068256	1068258	.	-	0	transcript_id "Phchi.S4G016700.t1"; gene_id "Phchi.S4G016700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2216.t1 is derived from g9136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5456113	5457204	.	-	.	Phchi.S5G082500
Phchi.S5	AUGUSTUS	transcript	5456113	5457204	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	stop_codon	5456110	5456112	.	-	0	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	CDS	5456113	5456240	0.9	-	2	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	exon	5456113	5456240	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	intron	5456241	5456322	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	CDS	5456323	5456410	1	-	0	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	exon	5456323	5456410	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	intron	5456411	5456492	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	CDS	5456493	5456570	0.91	-	0	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	exon	5456493	5456570	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	intron	5456571	5456868	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	CDS	5456869	5456921	0.84	-	2	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	exon	5456869	5456921	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	intron	5456922	5457149	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	CDS	5457150	5457204	0.71	-	0	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	exon	5457150	5457204	.	-	.	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
Phchi.S5	AUGUSTUS	start_codon	5457202	5457204	.	-	0	transcript_id "Phchi.S5G082500.t1"; gene_id "Phchi.S5G082500"
# This transcript jg7916.t2 is derived from g5090.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7917.t1 is derived from g5091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31900899	31903339	.	+	.	Phchi.S1G507600
Phchi.S1	AUGUSTUS	transcript	31900899	31903339	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	start_codon	31900899	31900901	.	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31900899	31901264	0.97	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31900899	31901264	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31901265	31901343	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31901344	31901419	1	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31901344	31901419	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31901420	31901577	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31901578	31901675	1	+	2	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31901578	31901675	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31901676	31901784	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31901785	31901886	1	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31901785	31901886	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31901887	31902042	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31902043	31902129	1	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31902043	31902129	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31902130	31902210	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31902211	31902327	1	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31902211	31902327	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31902328	31902519	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31902520	31902623	1	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31902520	31902623	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31902624	31902776	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31902777	31902916	1	+	1	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31902777	31902916	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31902917	31902987	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31902988	31903124	1	+	2	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31902988	31903124	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	intron	31903125	31903207	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	CDS	31903208	31903339	0.56	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	exon	31903208	31903339	.	+	.	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
Phchi.S1	AUGUSTUS	stop_codon	31903340	31903342	.	+	0	transcript_id "Phchi.S1G507600.t1"; gene_id "Phchi.S1G507600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7900.t1 is derived from g5074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31811340	31812449	.	-	.	Phchi.S1G505900
Phchi.S1	AUGUSTUS	transcript	31811340	31812449	.	-	.	transcript_id "Phchi.S1G505900.t1"; gene_id "Phchi.S1G505900"
Phchi.S1	AUGUSTUS	stop_codon	31811337	31811339	.	-	0	transcript_id "Phchi.S1G505900.t1"; gene_id "Phchi.S1G505900"
Phchi.S1	AUGUSTUS	CDS	31811340	31812449	1	-	0	transcript_id "Phchi.S1G505900.t1"; gene_id "Phchi.S1G505900"
Phchi.S1	AUGUSTUS	exon	31811340	31812449	.	-	.	transcript_id "Phchi.S1G505900.t1"; gene_id "Phchi.S1G505900"
Phchi.S1	AUGUSTUS	start_codon	31812447	31812449	.	-	0	transcript_id "Phchi.S1G505900.t1"; gene_id "Phchi.S1G505900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13907.t1 is derived from g12374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9622967	9624587	.	-	.	Phchi.S3G122600
Phchi.S3	AUGUSTUS	transcript	9622967	9624587	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	stop_codon	9622964	9622966	.	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	CDS	9622967	9623101	0.71	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	exon	9622967	9623101	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	intron	9623102	9623262	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	CDS	9623263	9623328	1	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	exon	9623263	9623328	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	intron	9623329	9623854	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	CDS	9623855	9623926	1	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	exon	9623855	9623926	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	intron	9623927	9624030	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	CDS	9624031	9624156	0.63	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	exon	9624031	9624156	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	intron	9624157	9624348	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	CDS	9624349	9624422	0.57	-	2	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	exon	9624349	9624422	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	intron	9624423	9624580	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	CDS	9624581	9624587	0.24	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	exon	9624581	9624587	.	-	.	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
Phchi.S3	AUGUSTUS	start_codon	9624585	9624587	.	-	0	transcript_id "Phchi.S3G122600.t1"; gene_id "Phchi.S3G122600"
# This transcript jg861.t2 is derived from g10643.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg862.t1 is derived from g10644.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5979111	5980180	.	+	.	Phchi.S6G082100
Phchi.S6	AUGUSTUS	transcript	5979111	5980180	.	+	.	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	start_codon	5979111	5979113	.	+	0	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	CDS	5979111	5979486	0.39	+	0	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	exon	5979111	5979486	.	+	.	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	intron	5979487	5979581	.	+	.	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	CDS	5979582	5980180	0.97	+	2	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	exon	5979582	5980180	.	+	.	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
Phchi.S6	AUGUSTUS	stop_codon	5980181	5980183	.	+	0	transcript_id "Phchi.S6G082100.t1"; gene_id "Phchi.S6G082100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7784.t1 is derived from g4958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31189295	31190009	.	+	.	Phchi.S1G494300
Phchi.S1	AUGUSTUS	transcript	31189295	31190009	.	+	.	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	start_codon	31189295	31189297	.	+	0	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	CDS	31189295	31189510	0.73	+	0	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	exon	31189295	31189510	.	+	.	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	intron	31189511	31189625	.	+	.	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	CDS	31189626	31190009	0.58	+	0	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	exon	31189626	31190009	.	+	.	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
Phchi.S1	AUGUSTUS	stop_codon	31190010	31190012	.	+	0	transcript_id "Phchi.S1G494300.t1"; gene_id "Phchi.S1G494300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10096.t1 is derived from g7272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45730040	45731429	.	-	.	Phchi.S1G725500
Phchi.S1	AUGUSTUS	transcript	45730040	45731429	.	-	.	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	stop_codon	45730037	45730039	.	-	0	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	CDS	45730040	45730303	0.99	-	0	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	exon	45730040	45730303	.	-	.	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	intron	45730304	45730376	.	-	.	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	CDS	45730377	45730707	1	-	1	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	exon	45730377	45730707	.	-	.	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	intron	45730708	45730803	.	-	.	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	CDS	45730804	45731429	0.93	-	0	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	exon	45730804	45731429	.	-	.	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
Phchi.S1	AUGUSTUS	start_codon	45731427	45731429	.	-	0	transcript_id "Phchi.S1G725500.t1"; gene_id "Phchi.S1G725500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg557.t1 is derived from g10339.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4040137	4041005	.	-	.	Phchi.S6G051600
Phchi.S6	AUGUSTUS	transcript	4040137	4041005	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	stop_codon	4040134	4040136	.	-	0	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	CDS	4040137	4040247	0.91	-	0	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	exon	4040137	4040247	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	intron	4040248	4040348	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	CDS	4040349	4040433	1	-	1	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	exon	4040349	4040433	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	intron	4040434	4040573	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	CDS	4040574	4040580	1	-	2	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	exon	4040574	4040580	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	intron	4040581	4040674	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	CDS	4040675	4040780	1	-	0	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	exon	4040675	4040780	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	intron	4040781	4040847	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	CDS	4040848	4040901	1	-	0	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	exon	4040848	4040901	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	intron	4040902	4040981	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	CDS	4040982	4041005	0.96	-	0	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	exon	4040982	4041005	.	-	.	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
Phchi.S6	AUGUSTUS	start_codon	4041003	4041005	.	-	0	transcript_id "Phchi.S6G051600.t1"; gene_id "Phchi.S6G051600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7864.t1 is derived from g5038.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31586707	31587437	.	+	.	Phchi.S1G502300
Phchi.S1	AUGUSTUS	transcript	31586707	31587437	.	+	.	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	start_codon	31586707	31586709	.	+	0	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	CDS	31586707	31586848	0.49	+	0	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	exon	31586707	31586848	.	+	.	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	intron	31586849	31587068	.	+	.	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	CDS	31587069	31587087	0.51	+	2	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	exon	31587069	31587087	.	+	.	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	intron	31587088	31587253	.	+	.	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	CDS	31587254	31587437	0.51	+	1	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	exon	31587254	31587437	.	+	.	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
Phchi.S1	AUGUSTUS	stop_codon	31587438	31587440	.	+	0	transcript_id "Phchi.S1G502300.t1"; gene_id "Phchi.S1G502300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1226.t1 is derived from g11009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8484982	8486454	.	-	.	Phchi.S6G118500
Phchi.S6	AUGUSTUS	transcript	8484982	8486454	.	-	.	transcript_id "Phchi.S6G118500.t1"; gene_id "Phchi.S6G118500"
Phchi.S6	AUGUSTUS	stop_codon	8484979	8484981	.	-	0	transcript_id "Phchi.S6G118500.t1"; gene_id "Phchi.S6G118500"
Phchi.S6	AUGUSTUS	CDS	8484982	8486454	0.79	-	0	transcript_id "Phchi.S6G118500.t1"; gene_id "Phchi.S6G118500"
Phchi.S6	AUGUSTUS	exon	8484982	8486454	.	-	.	transcript_id "Phchi.S6G118500.t1"; gene_id "Phchi.S6G118500"
Phchi.S6	AUGUSTUS	start_codon	8486452	8486454	.	-	0	transcript_id "Phchi.S6G118500.t1"; gene_id "Phchi.S6G118500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3246.t1 is derived from g415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2422993	2423595	.	+	.	Phchi.S1G040500
Phchi.S1	AUGUSTUS	transcript	2422993	2423595	.	+	.	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	start_codon	2422993	2422995	.	+	0	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	CDS	2422993	2423234	0.5	+	0	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	exon	2422993	2423234	.	+	.	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	intron	2423235	2423367	.	+	.	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	CDS	2423368	2423412	0.6	+	1	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	exon	2423368	2423412	.	+	.	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	intron	2423413	2423543	.	+	.	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	CDS	2423544	2423595	0.6	+	1	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	exon	2423544	2423595	.	+	.	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
Phchi.S1	AUGUSTUS	stop_codon	2423596	2423598	.	+	0	transcript_id "Phchi.S1G040500.t1"; gene_id "Phchi.S1G040500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14958.t1 is derived from g13426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15727814	15729191	.	-	.	Phchi.S3G227700
Phchi.S3	AUGUSTUS	transcript	15727814	15729191	.	-	.	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	stop_codon	15727811	15727813	.	-	0	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	CDS	15727814	15728957	0.97	-	1	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	exon	15727814	15728957	.	-	.	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	intron	15728958	15729042	.	-	.	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	CDS	15729043	15729191	0.96	-	0	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	exon	15729043	15729191	.	-	.	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
Phchi.S3	AUGUSTUS	start_codon	15729189	15729191	.	-	0	transcript_id "Phchi.S3G227700.t1"; gene_id "Phchi.S3G227700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2188.t1 is derived from g9108.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5287707	5288648	.	-	.	Phchi.S5G079700
Phchi.S5	AUGUSTUS	transcript	5287707	5288648	.	-	.	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	stop_codon	5287704	5287706	.	-	0	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	CDS	5287707	5288438	0.97	-	0	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	exon	5287707	5288438	.	-	.	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	intron	5288439	5288579	.	-	.	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	CDS	5288580	5288648	0.95	-	0	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	exon	5288580	5288648	.	-	.	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
Phchi.S5	AUGUSTUS	start_codon	5288646	5288648	.	-	0	transcript_id "Phchi.S5G079700.t1"; gene_id "Phchi.S5G079700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14431.t1 is derived from g12899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12768632	12770255	.	-	.	Phchi.S3G175000
Phchi.S3	AUGUSTUS	transcript	12768632	12770255	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	stop_codon	12768629	12768631	.	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	CDS	12768632	12768898	1	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	exon	12768632	12768898	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	intron	12768899	12769106	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	CDS	12769107	12769307	1	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	exon	12769107	12769307	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	intron	12769308	12769427	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	CDS	12769428	12769568	1	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	exon	12769428	12769568	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	intron	12769569	12769721	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	CDS	12769722	12769952	1	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	exon	12769722	12769952	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	intron	12769953	12770084	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	CDS	12770085	12770255	0.85	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	exon	12770085	12770255	.	-	.	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
Phchi.S3	AUGUSTUS	start_codon	12770253	12770255	.	-	0	transcript_id "Phchi.S3G175000.t1"; gene_id "Phchi.S3G175000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1113.t1 is derived from g10896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7677910	7678513	.	+	.	Phchi.S6G107200
Phchi.S6	AUGUSTUS	transcript	7677910	7678513	.	+	.	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	start_codon	7677910	7677912	.	+	0	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	CDS	7677910	7678223	0.39	+	0	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	exon	7677910	7678223	.	+	.	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	intron	7678224	7678404	.	+	.	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	CDS	7678405	7678513	1	+	1	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	exon	7678405	7678513	.	+	.	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
Phchi.S6	AUGUSTUS	stop_codon	7678514	7678516	.	+	0	transcript_id "Phchi.S6G107200.t1"; gene_id "Phchi.S6G107200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7924.t1 is derived from g5098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31925949	31929033	.	-	.	Phchi.S1G508300
Phchi.S1	AUGUSTUS	transcript	31925949	31929033	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	stop_codon	31925946	31925948	.	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31925949	31926014	1	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31925949	31926014	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31926015	31926283	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31926284	31926457	1	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31926284	31926457	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31926458	31926526	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31926527	31926649	0.93	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31926527	31926649	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31926650	31926750	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31926751	31926888	0.93	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31926751	31926888	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31926889	31926994	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31926995	31927049	1	-	1	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31926995	31927049	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31927050	31927150	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31927151	31927356	0.99	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31927151	31927356	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31927357	31927457	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31927458	31927519	0.99	-	2	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31927458	31927519	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31927520	31927597	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31927598	31927749	0.85	-	1	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31927598	31927749	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31927750	31927854	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31927855	31928031	0.89	-	1	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31927855	31928031	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31928032	31928120	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31928121	31928226	1	-	2	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31928121	31928226	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31928227	31928320	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31928321	31928482	0.87	-	2	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31928321	31928482	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31928483	31928732	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31928733	31928765	0.72	-	2	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31928733	31928765	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	intron	31928766	31928915	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	CDS	31928916	31929033	0.49	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	exon	31928916	31929033	.	-	.	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
Phchi.S1	AUGUSTUS	start_codon	31929031	31929033	.	-	0	transcript_id "Phchi.S1G508300.t1"; gene_id "Phchi.S1G508300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4955.t1 is derived from g2125.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13723958	13725248	.	+	.	Phchi.S1G211400
Phchi.S1	AUGUSTUS	transcript	13723958	13725248	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	start_codon	13723958	13723960	.	+	0	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	CDS	13723958	13724033	0.99	+	0	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	exon	13723958	13724033	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	intron	13724034	13724118	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	CDS	13724119	13724301	0.98	+	2	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	exon	13724119	13724301	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	intron	13724302	13724388	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	CDS	13724389	13724414	1	+	2	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	exon	13724389	13724414	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	intron	13724415	13724565	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	CDS	13724566	13724887	0.92	+	0	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	exon	13724566	13724887	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	intron	13724888	13725009	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	CDS	13725010	13725248	0.91	+	2	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	exon	13725010	13725248	.	+	.	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
Phchi.S1	AUGUSTUS	stop_codon	13725249	13725251	.	+	0	transcript_id "Phchi.S1G211400.t1"; gene_id "Phchi.S1G211400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4640.t1 is derived from g1810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11568926	11570680	.	+	.	Phchi.S1G179900
Phchi.S1	AUGUSTUS	transcript	11568926	11570680	.	+	.	transcript_id "Phchi.S1G179900.t1"; gene_id "Phchi.S1G179900"
Phchi.S1	AUGUSTUS	start_codon	11568926	11568928	.	+	0	transcript_id "Phchi.S1G179900.t1"; gene_id "Phchi.S1G179900"
Phchi.S1	AUGUSTUS	CDS	11568926	11570680	0.96	+	0	transcript_id "Phchi.S1G179900.t1"; gene_id "Phchi.S1G179900"
Phchi.S1	AUGUSTUS	exon	11568926	11570680	.	+	.	transcript_id "Phchi.S1G179900.t1"; gene_id "Phchi.S1G179900"
Phchi.S1	AUGUSTUS	stop_codon	11570681	11570683	.	+	0	transcript_id "Phchi.S1G179900.t1"; gene_id "Phchi.S1G179900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10452.t1 is derived from g14501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	402064	403540	.	-	.	Phchi.S4G003400
Phchi.S4	AUGUSTUS	transcript	402064	403540	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	stop_codon	402061	402063	.	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	CDS	402064	402399	0.99	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	exon	402064	402399	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	intron	402400	402508	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	CDS	402509	402605	1	-	1	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	exon	402509	402605	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	intron	402606	402689	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	CDS	402690	402862	1	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	exon	402690	402862	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	intron	402863	402943	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	CDS	402944	402979	0.61	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	exon	402944	402979	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	intron	402980	403065	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	CDS	403066	403146	0.61	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	exon	403066	403146	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	intron	403147	403327	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	CDS	403328	403540	0.99	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	exon	403328	403540	.	-	.	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
Phchi.S4	AUGUSTUS	start_codon	403538	403540	.	-	0	transcript_id "Phchi.S4G003400.t1"; gene_id "Phchi.S4G003400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4283.t1 is derived from g1452.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9395661	9396440	.	+	.	Phchi.S1G144200
Phchi.S1	AUGUSTUS	transcript	9395661	9396440	.	+	.	transcript_id "Phchi.S1G144200.t1"; gene_id "Phchi.S1G144200"
Phchi.S1	AUGUSTUS	start_codon	9395661	9395663	.	+	0	transcript_id "Phchi.S1G144200.t1"; gene_id "Phchi.S1G144200"
Phchi.S1	AUGUSTUS	CDS	9395661	9396440	0.43	+	0	transcript_id "Phchi.S1G144200.t1"; gene_id "Phchi.S1G144200"
Phchi.S1	AUGUSTUS	exon	9395661	9396440	.	+	.	transcript_id "Phchi.S1G144200.t1"; gene_id "Phchi.S1G144200"
Phchi.S1	AUGUSTUS	stop_codon	9396441	9396443	.	+	0	transcript_id "Phchi.S1G144200.t1"; gene_id "Phchi.S1G144200"
# This transcript jg11745.t2 is derived from g15797.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11745.t3 is derived from g15797.t5 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11745.t4 is derived from g15797.t6 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11745.t5 is derived from g15797.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11745.t6 is derived from g15797.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11746.t1 is derived from g15798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7983608	7985705	.	+	.	Phchi.S4G132800
Phchi.S4	AUGUSTUS	transcript	7983608	7985705	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	start_codon	7983608	7983610	.	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7983608	7983658	0.41	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7983608	7983658	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7983659	7983757	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7983758	7983862	1	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7983758	7983862	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7983863	7983984	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7983985	7984140	0.97	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7983985	7984140	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7984141	7984246	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7984247	7984390	1	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7984247	7984390	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7984391	7984530	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7984531	7984636	1	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7984531	7984636	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7984637	7984727	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7984728	7984903	1	+	2	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7984728	7984903	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7984904	7984980	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7984981	7985141	1	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7984981	7985141	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7985142	7985254	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7985255	7985513	1	+	1	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7985255	7985513	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	intron	7985514	7985600	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	CDS	7985601	7985705	1	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	exon	7985601	7985705	.	+	.	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
Phchi.S4	AUGUSTUS	stop_codon	7985706	7985708	.	+	0	transcript_id "Phchi.S4G132800.t1"; gene_id "Phchi.S4G132800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg690.t1 is derived from g10472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4916811	4917608	.	+	.	Phchi.S6G064900
Phchi.S6	AUGUSTUS	transcript	4916811	4917608	.	+	.	transcript_id "Phchi.S6G064900.t1"; gene_id "Phchi.S6G064900"
Phchi.S6	AUGUSTUS	start_codon	4916811	4916813	.	+	0	transcript_id "Phchi.S6G064900.t1"; gene_id "Phchi.S6G064900"
Phchi.S6	AUGUSTUS	CDS	4916811	4917608	0.74	+	0	transcript_id "Phchi.S6G064900.t1"; gene_id "Phchi.S6G064900"
Phchi.S6	AUGUSTUS	exon	4916811	4917608	.	+	.	transcript_id "Phchi.S6G064900.t1"; gene_id "Phchi.S6G064900"
Phchi.S6	AUGUSTUS	stop_codon	4917609	4917611	.	+	0	transcript_id "Phchi.S6G064900.t1"; gene_id "Phchi.S6G064900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6323.t1 is derived from g3495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22261154	22263313	.	+	.	Phchi.S1G348200
Phchi.S1	AUGUSTUS	transcript	22261154	22263313	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	start_codon	22261154	22261156	.	+	0	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	CDS	22261154	22262352	0.95	+	0	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	exon	22261154	22262352	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	intron	22262353	22262536	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	CDS	22262537	22262798	1	+	1	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	exon	22262537	22262798	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	intron	22262799	22262872	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	CDS	22262873	22263007	0.98	+	0	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	exon	22262873	22263007	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	intron	22263008	22263109	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	CDS	22263110	22263313	0.83	+	0	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	exon	22263110	22263313	.	+	.	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
Phchi.S1	AUGUSTUS	stop_codon	22263314	22263316	.	+	0	transcript_id "Phchi.S1G348200.t1"; gene_id "Phchi.S1G348200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9939.t1 is derived from g7115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44574109	44578563	.	-	.	Phchi.S1G709800
Phchi.S1	AUGUSTUS	transcript	44574109	44578563	.	-	.	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	stop_codon	44574106	44574108	.	-	0	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	CDS	44574109	44575248	0.69	-	0	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	exon	44574109	44575248	.	-	.	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	intron	44575249	44575362	.	-	.	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	CDS	44575363	44576726	0.92	-	2	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	exon	44575363	44576726	.	-	.	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	intron	44576727	44576834	.	-	.	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	CDS	44576835	44578563	0.78	-	0	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	exon	44576835	44578563	.	-	.	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
Phchi.S1	AUGUSTUS	start_codon	44578561	44578563	.	-	0	transcript_id "Phchi.S1G709800.t1"; gene_id "Phchi.S1G709800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7551.t1 is derived from g4725.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30003422	30006658	.	+	.	Phchi.S1G471000
Phchi.S1	AUGUSTUS	transcript	30003422	30006658	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	start_codon	30003422	30003424	.	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30003422	30003497	1	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30003422	30003497	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30003498	30003613	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30003614	30003734	1	+	2	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30003614	30003734	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30003735	30003829	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30003830	30003941	1	+	1	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30003830	30003941	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30003942	30004028	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004029	30004196	1	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004029	30004196	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004197	30004338	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004339	30004503	1	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004339	30004503	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004504	30004587	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004588	30004691	0.99	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004588	30004691	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004692	30004801	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004802	30004921	0.99	+	1	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004802	30004921	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004922	30005020	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005021	30005144	1	+	1	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005021	30005144	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005145	30005300	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005301	30005414	0.83	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005301	30005414	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005415	30005515	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005516	30005568	0.84	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005516	30005568	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005569	30005660	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005661	30005742	0.43	+	1	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005661	30005742	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005743	30005895	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005896	30006240	0.82	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005896	30006240	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30006241	30006328	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30006329	30006411	0.82	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30006329	30006411	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30006412	30006501	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30006502	30006658	0.57	+	1	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30006502	30006658	.	+	.	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	stop_codon	30006659	30006661	.	+	0	transcript_id "Phchi.S1G471000.t1"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	transcript	30003422	30006536	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	start_codon	30003422	30003424	.	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30003422	30003497	0.99	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30003422	30003497	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30003498	30003613	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30003614	30003734	0.98	+	2	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30003614	30003734	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30003735	30003829	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30003830	30003941	1	+	1	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30003830	30003941	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30003942	30004028	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004029	30004196	1	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004029	30004196	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004197	30004338	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004339	30004503	1	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004339	30004503	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004504	30004587	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004588	30004691	1	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004588	30004691	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004692	30004801	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30004802	30004921	1	+	1	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30004802	30004921	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30004922	30005020	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005021	30005144	1	+	1	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005021	30005144	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005145	30005300	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005301	30005414	0.87	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005301	30005414	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005415	30005515	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005516	30005568	0.89	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005516	30005568	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005569	30005660	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005661	30005742	0.41	+	1	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005661	30005742	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30005743	30005895	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30005896	30006240	0.71	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30005896	30006240	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30006241	30006328	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30006329	30006411	0.7	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30006329	30006411	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	intron	30006412	30006496	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	CDS	30006497	30006536	0.62	+	1	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	exon	30006497	30006536	.	+	.	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
Phchi.S1	AUGUSTUS	stop_codon	30006537	30006539	.	+	0	transcript_id "Phchi.S1G471000.t2"; gene_id "Phchi.S1G471000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3699.t1 is derived from g868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5231282	5231632	.	-	.	Phchi.S1G085800
Phchi.S1	AUGUSTUS	transcript	5231282	5231632	.	-	.	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	stop_codon	5231279	5231281	.	-	0	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	CDS	5231282	5231396	0.81	-	1	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	exon	5231282	5231396	.	-	.	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	intron	5231397	5231516	.	-	.	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	CDS	5231517	5231632	0.68	-	0	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	exon	5231517	5231632	.	-	.	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
Phchi.S1	AUGUSTUS	start_codon	5231630	5231632	.	-	0	transcript_id "Phchi.S1G085800.t1"; gene_id "Phchi.S1G085800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3083.t1 is derived from g252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1552803	1553843	.	+	.	Phchi.S1G024200
Phchi.S1	AUGUSTUS	transcript	1552803	1553843	.	+	.	transcript_id "Phchi.S1G024200.t1"; gene_id "Phchi.S1G024200"
Phchi.S1	AUGUSTUS	start_codon	1552803	1552805	.	+	0	transcript_id "Phchi.S1G024200.t1"; gene_id "Phchi.S1G024200"
Phchi.S1	AUGUSTUS	CDS	1552803	1553843	0.72	+	0	transcript_id "Phchi.S1G024200.t1"; gene_id "Phchi.S1G024200"
Phchi.S1	AUGUSTUS	exon	1552803	1553843	.	+	.	transcript_id "Phchi.S1G024200.t1"; gene_id "Phchi.S1G024200"
Phchi.S1	AUGUSTUS	stop_codon	1553844	1553846	.	+	0	transcript_id "Phchi.S1G024200.t1"; gene_id "Phchi.S1G024200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7063.t1 is derived from g4235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26689316	26692958	.	+	.	Phchi.S1G422200
Phchi.S1	AUGUSTUS	transcript	26689316	26692958	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	start_codon	26689316	26689318	.	+	0	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26689316	26689994	0.83	+	0	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26689316	26689994	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26689995	26690221	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26690222	26690352	1	+	2	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26690222	26690352	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26690353	26690498	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26690499	26690655	1	+	0	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26690499	26690655	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26690656	26690748	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26690749	26690866	1	+	2	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26690749	26690866	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26690867	26690963	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26690964	26692212	0.95	+	1	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26690964	26692212	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26692213	26692300	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26692301	26692386	1	+	0	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26692301	26692386	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26692387	26692517	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26692518	26692542	0.86	+	1	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26692518	26692542	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26692543	26692633	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26692634	26692728	0.58	+	0	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26692634	26692728	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	intron	26692729	26692882	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	CDS	26692883	26692958	0.68	+	1	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	exon	26692883	26692958	.	+	.	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
Phchi.S1	AUGUSTUS	stop_codon	26692959	26692961	.	+	0	transcript_id "Phchi.S1G422200.t1"; gene_id "Phchi.S1G422200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1367.t1 is derived from g9812.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C217	AUGUSTUS	gene	15793	17413	.	-	.	Phchi.C217G000100
Phchi.C217	AUGUSTUS	transcript	15793	17413	.	-	.	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	stop_codon	15790	15792	.	-	0	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	CDS	15793	15975	1	-	0	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	exon	15793	15975	.	-	.	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	intron	15976	16174	.	-	.	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	CDS	16175	17413	1	-	0	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	exon	16175	17413	.	-	.	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
Phchi.C217	AUGUSTUS	start_codon	17411	17413	.	-	0	transcript_id "Phchi.C217G000100.t1"; gene_id "Phchi.C217G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14256.t1 is derived from g12723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11780722	11782648	.	-	.	Phchi.S3G157500
Phchi.S3	AUGUSTUS	transcript	11780722	11782648	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	stop_codon	11780719	11780721	.	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11780722	11780767	1	-	1	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11780722	11780767	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11780768	11780844	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11780845	11780891	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11780845	11780891	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11780892	11780984	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11780985	11781044	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11780985	11781044	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781045	11781130	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11781131	11781190	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11781131	11781190	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781191	11781267	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11781268	11781323	1	-	2	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11781268	11781323	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781324	11781408	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11781409	11781442	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11781409	11781442	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781443	11781541	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11781542	11781616	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11781542	11781616	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781617	11781733	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11781734	11781784	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11781734	11781784	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781785	11781875	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11781876	11781920	1	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11781876	11781920	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11781921	11782014	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11782015	11782108	1	-	1	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11782015	11782108	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	intron	11782109	11782220	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	CDS	11782221	11782648	0.69	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	exon	11782221	11782648	.	-	.	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
Phchi.S3	AUGUSTUS	start_codon	11782646	11782648	.	-	0	transcript_id "Phchi.S3G157500.t1"; gene_id "Phchi.S3G157500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7951.t1 is derived from g5125.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32068785	32070539	.	-	.	Phchi.S1G511000
Phchi.S1	AUGUSTUS	transcript	32068785	32070539	.	-	.	transcript_id "Phchi.S1G511000.t1"; gene_id "Phchi.S1G511000"
Phchi.S1	AUGUSTUS	stop_codon	32068782	32068784	.	-	0	transcript_id "Phchi.S1G511000.t1"; gene_id "Phchi.S1G511000"
Phchi.S1	AUGUSTUS	CDS	32068785	32070539	1	-	0	transcript_id "Phchi.S1G511000.t1"; gene_id "Phchi.S1G511000"
Phchi.S1	AUGUSTUS	exon	32068785	32070539	.	-	.	transcript_id "Phchi.S1G511000.t1"; gene_id "Phchi.S1G511000"
Phchi.S1	AUGUSTUS	start_codon	32070537	32070539	.	-	0	transcript_id "Phchi.S1G511000.t1"; gene_id "Phchi.S1G511000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12657.t1 is derived from g14456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	23756	24261	.	+	.	Phchi.C12G000700
Phchi.C12	AUGUSTUS	transcript	23756	24261	.	+	.	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	start_codon	23756	23758	.	+	0	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	CDS	23756	24057	0.65	+	0	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	exon	23756	24057	.	+	.	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	intron	24058	24164	.	+	.	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	CDS	24165	24261	0.71	+	1	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	exon	24165	24261	.	+	.	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
Phchi.C12	AUGUSTUS	stop_codon	24262	24264	.	+	0	transcript_id "Phchi.C12G000700.t1"; gene_id "Phchi.C12G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13402.t1 is derived from g11868.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6537749	6540047	.	+	.	Phchi.S3G072100
Phchi.S3	AUGUSTUS	transcript	6537749	6540047	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	start_codon	6537749	6537751	.	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6537749	6537833	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6537749	6537833	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6537834	6537950	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6537951	6538000	1	+	2	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6537951	6538000	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6538001	6538101	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6538102	6538157	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6538102	6538157	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6538158	6538383	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6538384	6538399	1	+	1	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6538384	6538399	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6538400	6538527	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6538528	6538575	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6538528	6538575	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6538576	6538717	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6538718	6538782	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6538718	6538782	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6538783	6538904	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6538905	6538962	1	+	1	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6538905	6538962	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6538963	6539050	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6539051	6539155	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6539051	6539155	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6539156	6539236	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6539237	6539320	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6539237	6539320	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6539321	6539480	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6539481	6539615	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6539481	6539615	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6539616	6539730	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6539731	6539799	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6539731	6539799	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	intron	6539800	6539939	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	CDS	6539940	6540047	1	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	exon	6539940	6540047	.	+	.	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
Phchi.S3	AUGUSTUS	stop_codon	6540048	6540050	.	+	0	transcript_id "Phchi.S3G072100.t1"; gene_id "Phchi.S3G072100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9126.t1 is derived from g6301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39975206	39978266	.	+	.	Phchi.S1G628500
Phchi.S1	AUGUSTUS	transcript	39975206	39978266	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	start_codon	39975206	39975208	.	+	0	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975206	39975252	0.96	+	0	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975206	39975252	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39975253	39975400	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975401	39975429	1	+	1	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975401	39975429	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39975430	39975573	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975574	39975753	1	+	2	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975574	39975753	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39975754	39975877	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975878	39976542	0.3	+	2	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975878	39976542	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39976543	39976634	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39976635	39976914	0.28	+	0	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39976635	39976914	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39976915	39976995	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39976996	39977145	1	+	2	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39976996	39977145	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977146	39977290	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977291	39977494	0.99	+	2	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977291	39977494	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977495	39977609	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977610	39977695	0.99	+	2	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977610	39977695	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977696	39977801	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977802	39977857	0.92	+	0	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977802	39977857	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977858	39977980	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977981	39978102	0.96	+	1	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977981	39978102	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39978103	39978246	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39978247	39978266	1	+	2	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39978247	39978266	.	+	.	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	stop_codon	39978267	39978269	.	+	0	transcript_id "Phchi.S1G628500.t1"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	transcript	39975206	39978266	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	start_codon	39975206	39975208	.	+	0	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975206	39975252	0.97	+	0	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975206	39975252	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39975253	39975400	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975401	39975429	1	+	1	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975401	39975429	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39975430	39975573	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975574	39975753	1	+	2	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975574	39975753	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39975754	39975877	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39975878	39976542	0.22	+	2	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39975878	39976542	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39976543	39976634	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39976635	39976914	0.22	+	0	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39976635	39976914	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39976915	39976995	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39976996	39977145	1	+	2	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39976996	39977145	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977146	39977290	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977291	39977494	1	+	2	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977291	39977494	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977495	39977609	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977610	39977695	1	+	2	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977610	39977695	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977696	39977801	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977802	39977857	0.88	+	0	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977802	39977857	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39977858	39977980	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39977981	39978102	0.94	+	1	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39977981	39978102	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	intron	39978103	39978249	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	CDS	39978250	39978266	0.99	+	2	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	exon	39978250	39978266	.	+	.	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
Phchi.S1	AUGUSTUS	stop_codon	39978267	39978269	.	+	0	transcript_id "Phchi.S1G628500.t2"; gene_id "Phchi.S1G628500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15416.t1 is derived from g13884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18970869	18971855	.	+	.	Phchi.S3G273500
Phchi.S3	AUGUSTUS	transcript	18970869	18971855	.	+	.	transcript_id "Phchi.S3G273500.t1"; gene_id "Phchi.S3G273500"
Phchi.S3	AUGUSTUS	start_codon	18970869	18970871	.	+	0	transcript_id "Phchi.S3G273500.t1"; gene_id "Phchi.S3G273500"
Phchi.S3	AUGUSTUS	CDS	18970869	18971855	1	+	0	transcript_id "Phchi.S3G273500.t1"; gene_id "Phchi.S3G273500"
Phchi.S3	AUGUSTUS	exon	18970869	18971855	.	+	.	transcript_id "Phchi.S3G273500.t1"; gene_id "Phchi.S3G273500"
Phchi.S3	AUGUSTUS	stop_codon	18971856	18971858	.	+	0	transcript_id "Phchi.S3G273500.t1"; gene_id "Phchi.S3G273500"
# This transcript jg7234.t2 is derived from g4406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7235.t1 is derived from g4407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27761452	27762153	.	-	.	Phchi.S1G439400
Phchi.S1	AUGUSTUS	transcript	27761452	27762153	.	-	.	transcript_id "Phchi.S1G439400.t1"; gene_id "Phchi.S1G439400"
Phchi.S1	AUGUSTUS	stop_codon	27761449	27761451	.	-	0	transcript_id "Phchi.S1G439400.t1"; gene_id "Phchi.S1G439400"
Phchi.S1	AUGUSTUS	CDS	27761452	27762153	0.41	-	0	transcript_id "Phchi.S1G439400.t1"; gene_id "Phchi.S1G439400"
Phchi.S1	AUGUSTUS	exon	27761452	27762153	.	-	.	transcript_id "Phchi.S1G439400.t1"; gene_id "Phchi.S1G439400"
Phchi.S1	AUGUSTUS	start_codon	27762151	27762153	.	-	0	transcript_id "Phchi.S1G439400.t1"; gene_id "Phchi.S1G439400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4614.t1 is derived from g1784.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11418998	11420508	.	+	.	Phchi.S1G177300
Phchi.S1	AUGUSTUS	transcript	11418998	11419894	.	+	.	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	start_codon	11418998	11419000	.	+	0	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	CDS	11418998	11419249	1	+	0	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	exon	11418998	11419249	.	+	.	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	intron	11419250	11419366	.	+	.	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	CDS	11419367	11419894	0.58	+	0	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	exon	11419367	11419894	.	+	.	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	stop_codon	11420022	11420024	.	+	0	transcript_id "Phchi.S1G177300.t1"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	transcript	11418998	11420508	.	+	.	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	start_codon	11418998	11419000	.	+	0	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	CDS	11418998	11419249	0.99	+	0	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	exon	11418998	11419249	.	+	.	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	intron	11419250	11419366	.	+	.	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	CDS	11419367	11420147	1	+	0	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	exon	11419367	11420147	.	+	.	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	intron	11420148	11420233	.	+	.	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	CDS	11420234	11420508	0.94	+	2	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	exon	11420234	11420508	.	+	.	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
Phchi.S1	AUGUSTUS	stop_codon	11420509	11420511	.	+	0	transcript_id "Phchi.S1G177300.t2"; gene_id "Phchi.S1G177300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14145.t1 is derived from g12612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11158539	11159468	.	-	.	Phchi.S3G146400
Phchi.S3	AUGUSTUS	transcript	11158539	11159468	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	stop_codon	11158536	11158538	.	-	0	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	CDS	11158539	11158982	0.95	-	0	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	exon	11158539	11158982	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	intron	11158983	11159063	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	CDS	11159064	11159128	0.95	-	2	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	exon	11159064	11159128	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	intron	11159129	11159207	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	CDS	11159208	11159217	0.95	-	0	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	exon	11159208	11159217	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	intron	11159218	11159423	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	CDS	11159424	11159468	0.89	-	0	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	exon	11159424	11159468	.	-	.	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
Phchi.S3	AUGUSTUS	start_codon	11159466	11159468	.	-	0	transcript_id "Phchi.S3G146400.t1"; gene_id "Phchi.S3G146400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8027.t1 is derived from g5202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32551420	32553694	.	+	.	Phchi.S1G518600
Phchi.S1	AUGUSTUS	transcript	32551420	32553694	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	start_codon	32551420	32551422	.	+	0	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	CDS	32551420	32551884	0.85	+	0	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	exon	32551420	32551884	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	intron	32551885	32552023	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	CDS	32552024	32552716	0.98	+	0	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	exon	32552024	32552716	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	intron	32552717	32552860	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	CDS	32552861	32553172	1	+	0	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	exon	32552861	32553172	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	intron	32553173	32553267	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	CDS	32553268	32553437	1	+	0	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	exon	32553268	32553437	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	intron	32553438	32553597	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	CDS	32553598	32553694	1	+	1	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	exon	32553598	32553694	.	+	.	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
Phchi.S1	AUGUSTUS	stop_codon	32553695	32553697	.	+	0	transcript_id "Phchi.S1G518600.t1"; gene_id "Phchi.S1G518600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7512.t1 is derived from g4686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29762988	29764883	.	-	.	Phchi.S1G467100
Phchi.S1	AUGUSTUS	transcript	29762988	29763887	.	-	.	transcript_id "Phchi.S1G467100.t1"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	stop_codon	29762985	29762987	.	-	0	transcript_id "Phchi.S1G467100.t1"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	CDS	29762988	29763887	1	-	0	transcript_id "Phchi.S1G467100.t1"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	exon	29762988	29763887	.	-	.	transcript_id "Phchi.S1G467100.t1"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	start_codon	29763885	29763887	.	-	0	transcript_id "Phchi.S1G467100.t1"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	transcript	29762988	29764883	.	-	.	transcript_id "Phchi.S1G467100.t2"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	stop_codon	29762985	29762987	.	-	0	transcript_id "Phchi.S1G467100.t2"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	CDS	29762988	29764883	0.49	-	0	transcript_id "Phchi.S1G467100.t2"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	exon	29762988	29764883	.	-	.	transcript_id "Phchi.S1G467100.t2"; gene_id "Phchi.S1G467100"
Phchi.S1	AUGUSTUS	start_codon	29764881	29764883	.	-	0	transcript_id "Phchi.S1G467100.t2"; gene_id "Phchi.S1G467100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5286.t1 is derived from g2456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16028076	16029060	.	+	.	Phchi.S1G244500
Phchi.S1	AUGUSTUS	transcript	16028076	16029060	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	start_codon	16028076	16028078	.	+	0	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	CDS	16028076	16028176	0.93	+	0	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	exon	16028076	16028176	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	intron	16028177	16028264	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	CDS	16028265	16028364	1	+	1	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	exon	16028265	16028364	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	intron	16028365	16028454	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	CDS	16028455	16028853	0.99	+	0	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	exon	16028455	16028853	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	intron	16028854	16028937	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	CDS	16028938	16029060	1	+	0	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	exon	16028938	16029060	.	+	.	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
Phchi.S1	AUGUSTUS	stop_codon	16029061	16029063	.	+	0	transcript_id "Phchi.S1G244500.t1"; gene_id "Phchi.S1G244500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3790.t1 is derived from g959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5758643	5763320	.	-	.	Phchi.S1G094900
Phchi.S1	AUGUSTUS	transcript	5758643	5763320	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	stop_codon	5758640	5758642	.	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5758643	5758724	0.95	-	1	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5758643	5758724	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5758725	5758874	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5758875	5758941	1	-	2	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5758875	5758941	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5758942	5759029	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5759030	5759102	0.96	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5759030	5759102	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5759103	5759212	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5759213	5759692	0.56	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5759213	5759692	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5759693	5759801	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5759802	5759975	1	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5759802	5759975	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5759976	5760067	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5760068	5760959	0.99	-	1	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5760068	5760959	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5760960	5761085	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5761086	5761345	1	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5761086	5761345	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5761346	5761513	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5761514	5762980	0.94	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5761514	5762980	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5762981	5763063	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5763064	5763075	0.93	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5763064	5763075	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	intron	5763076	5763287	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	CDS	5763288	5763320	0.27	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	exon	5763288	5763320	.	-	.	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
Phchi.S1	AUGUSTUS	start_codon	5763318	5763320	.	-	0	transcript_id "Phchi.S1G094900.t1"; gene_id "Phchi.S1G094900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14818.t1 is derived from g13286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14840815	14843642	.	-	.	Phchi.S3G213700
Phchi.S3	AUGUSTUS	transcript	14840815	14843642	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	stop_codon	14840812	14840814	.	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14840815	14840982	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14840815	14840982	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14840983	14841103	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14841104	14841223	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14841104	14841223	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14841224	14841310	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14841311	14841388	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14841311	14841388	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14841389	14841484	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14841485	14841571	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14841485	14841571	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14841572	14841657	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14841658	14841739	1	-	1	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14841658	14841739	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14841740	14841984	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14841985	14842052	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14841985	14842052	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14842053	14842129	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14842130	14842190	1	-	1	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14842130	14842190	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14842191	14842330	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14842331	14842407	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14842331	14842407	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14842408	14842593	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14842594	14842670	1	-	2	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14842594	14842670	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14842671	14842757	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14842758	14842853	1	-	2	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14842758	14842853	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14842854	14842930	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14842931	14843075	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14842931	14843075	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14843076	14843171	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14843172	14843222	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14843172	14843222	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	intron	14843223	14843525	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	CDS	14843526	14843642	1	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	exon	14843526	14843642	.	-	.	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
Phchi.S3	AUGUSTUS	start_codon	14843640	14843642	.	-	0	transcript_id "Phchi.S3G213700.t1"; gene_id "Phchi.S3G213700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12261.t1 is derived from g7937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7063762	7065910	.	+	.	Phchi.S2G034100
Phchi.S2	AUGUSTUS	transcript	7063762	7065910	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	start_codon	7063762	7063764	.	+	0	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	CDS	7063762	7063806	0.91	+	0	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	exon	7063762	7063806	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	intron	7063807	7064249	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	CDS	7064250	7064313	0.95	+	0	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	exon	7064250	7064313	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	intron	7064314	7064469	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	CDS	7064470	7064668	0.94	+	2	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	exon	7064470	7064668	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	intron	7064669	7064793	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	CDS	7064794	7065910	0.37	+	1	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	exon	7064794	7065910	.	+	.	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
Phchi.S2	AUGUSTUS	stop_codon	7065911	7065913	.	+	0	transcript_id "Phchi.S2G034100.t1"; gene_id "Phchi.S2G034100"
# This transcript jg11863.t2 is derived from g15915.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11864.t1 is derived from g15916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8852787	8853465	.	+	.	Phchi.S4G144600
Phchi.S4	AUGUSTUS	transcript	8852787	8853465	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	start_codon	8852787	8852789	.	+	0	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	CDS	8852787	8852885	1	+	0	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	exon	8852787	8852885	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	intron	8852886	8853061	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	CDS	8853062	8853123	1	+	0	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	exon	8853062	8853123	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	intron	8853124	8853265	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	CDS	8853266	8853271	0.66	+	1	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	exon	8853266	8853271	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	intron	8853272	8853377	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	CDS	8853378	8853465	0.65	+	1	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	exon	8853378	8853465	.	+	.	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
Phchi.S4	AUGUSTUS	stop_codon	8853466	8853468	.	+	0	transcript_id "Phchi.S4G144600.t1"; gene_id "Phchi.S4G144600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4593.t1 is derived from g1763.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11243607	11245762	.	+	.	Phchi.S1G175200
Phchi.S1	AUGUSTUS	transcript	11243607	11245762	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	start_codon	11243607	11243609	.	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11243607	11243711	0.31	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11243607	11243711	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11243712	11243873	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11243874	11243909	0.99	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11243874	11243909	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11243910	11243992	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11243993	11244928	0.94	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11243993	11244928	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11244929	11245023	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245024	11245068	0.75	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245024	11245068	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11245069	11245413	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245414	11245478	0.77	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245414	11245478	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11245479	11245565	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245566	11245615	0.74	+	1	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245566	11245615	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11245616	11245697	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245698	11245762	0.39	+	2	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245698	11245762	.	+	.	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	stop_codon	11245763	11245765	.	+	0	transcript_id "Phchi.S1G175200.t1"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	transcript	11243607	11245585	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	start_codon	11243607	11243609	.	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11243607	11243711	0.24	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11243607	11243711	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11243712	11243873	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11243874	11243909	0.99	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11243874	11243909	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11243910	11243992	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11243993	11244928	0.75	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11243993	11244928	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11244929	11245023	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245024	11245068	0.58	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245024	11245068	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11245069	11245300	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245301	11245346	0.53	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245301	11245346	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11245347	11245421	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245422	11245478	0.39	+	2	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245422	11245478	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	intron	11245479	11245565	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	CDS	11245566	11245585	0.54	+	2	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	exon	11245566	11245585	.	+	.	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
Phchi.S1	AUGUSTUS	stop_codon	11245586	11245588	.	+	0	transcript_id "Phchi.S1G175200.t2"; gene_id "Phchi.S1G175200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1005.t1 is derived from g10788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7055312	7055884	.	-	.	Phchi.S6G096400
Phchi.S6	AUGUSTUS	transcript	7055312	7055884	.	-	.	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	stop_codon	7055309	7055311	.	-	0	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	CDS	7055312	7055405	0.9	-	1	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	exon	7055312	7055405	.	-	.	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	intron	7055406	7055585	.	-	.	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	CDS	7055586	7055884	0.48	-	0	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	exon	7055586	7055884	.	-	.	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	start_codon	7055882	7055884	.	-	0	transcript_id "Phchi.S6G096400.t1"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	transcript	7055312	7055884	.	-	.	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	stop_codon	7055309	7055311	.	-	0	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	CDS	7055312	7055405	0.8	-	1	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	exon	7055312	7055405	.	-	.	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	intron	7055406	7055594	.	-	.	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	CDS	7055595	7055884	0.51	-	0	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	exon	7055595	7055884	.	-	.	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
Phchi.S6	AUGUSTUS	start_codon	7055882	7055884	.	-	0	transcript_id "Phchi.S6G096400.t2"; gene_id "Phchi.S6G096400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5059.t1 is derived from g2229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14455602	14456903	.	-	.	Phchi.S1G221800
Phchi.S1	AUGUSTUS	transcript	14455602	14456903	.	-	.	transcript_id "Phchi.S1G221800.t1"; gene_id "Phchi.S1G221800"
Phchi.S1	AUGUSTUS	stop_codon	14455599	14455601	.	-	0	transcript_id "Phchi.S1G221800.t1"; gene_id "Phchi.S1G221800"
Phchi.S1	AUGUSTUS	CDS	14455602	14456903	0.96	-	0	transcript_id "Phchi.S1G221800.t1"; gene_id "Phchi.S1G221800"
Phchi.S1	AUGUSTUS	exon	14455602	14456903	.	-	.	transcript_id "Phchi.S1G221800.t1"; gene_id "Phchi.S1G221800"
Phchi.S1	AUGUSTUS	start_codon	14456901	14456903	.	-	0	transcript_id "Phchi.S1G221800.t1"; gene_id "Phchi.S1G221800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8530.t1 is derived from g5705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36511519	36515341	.	-	.	Phchi.S1G568900
Phchi.S1	AUGUSTUS	transcript	36511519	36515341	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	stop_codon	36511516	36511518	.	-	0	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36511519	36511886	1	-	2	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36511519	36511886	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36511887	36511991	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36511992	36512201	1	-	2	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36511992	36512201	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36512202	36512341	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36512342	36512546	1	-	0	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36512342	36512546	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36512547	36512643	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36512644	36512755	1	-	1	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36512644	36512755	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36512756	36512843	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36512844	36513113	0.93	-	1	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36512844	36513113	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36513114	36513221	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36513222	36513319	1	-	0	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36513222	36513319	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36513320	36513448	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36513449	36513807	1	-	2	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36513449	36513807	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36513808	36513893	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36513894	36514090	1	-	1	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36513894	36514090	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36514091	36514222	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36514223	36514334	0.97	-	2	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36514223	36514334	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36514335	36514406	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36514407	36514589	0.9	-	2	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36514407	36514589	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36514590	36514700	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36514701	36514798	0.95	-	1	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36514701	36514798	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36514799	36515027	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36515028	36515119	0.94	-	0	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36515028	36515119	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	intron	36515120	36515215	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	CDS	36515216	36515341	0.49	-	0	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	exon	36515216	36515341	.	-	.	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
Phchi.S1	AUGUSTUS	start_codon	36515339	36515341	.	-	0	transcript_id "Phchi.S1G568900.t1"; gene_id "Phchi.S1G568900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5301.t1 is derived from g2471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16100472	16102123	.	+	.	Phchi.S1G246000
Phchi.S1	AUGUSTUS	transcript	16100472	16102123	.	+	.	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	start_codon	16100472	16100474	.	+	0	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	CDS	16100472	16101098	0.9	+	0	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	exon	16100472	16101098	.	+	.	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	intron	16101099	16101199	.	+	.	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	CDS	16101200	16102123	0.54	+	0	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	exon	16101200	16102123	.	+	.	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
Phchi.S1	AUGUSTUS	stop_codon	16102124	16102126	.	+	0	transcript_id "Phchi.S1G246000.t1"; gene_id "Phchi.S1G246000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg13331.t1 is derived from g11797.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6134371	6136261	.	+	.	Phchi.S3G065000
Phchi.S3	AUGUSTUS	transcript	6134371	6136261	.	+	.	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	start_codon	6134371	6134373	.	+	0	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134371	6134588	0.98	+	0	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134371	6134588	.	+	.	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6134589	6134805	.	+	.	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134806	6135005	1	+	1	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134806	6135005	.	+	.	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6135006	6135101	.	+	.	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6135102	6136261	0.99	+	2	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6135102	6136261	.	+	.	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	stop_codon	6136262	6136264	.	+	0	transcript_id "Phchi.S3G065000.t1"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	transcript	6134371	6136261	.	+	.	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	start_codon	6134371	6134373	.	+	0	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134371	6134588	0.97	+	0	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134371	6134588	.	+	.	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6134589	6134805	.	+	.	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134806	6135005	1	+	1	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134806	6135005	.	+	.	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6135006	6135098	.	+	.	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6135099	6136261	0.98	+	2	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6135099	6136261	.	+	.	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	stop_codon	6136262	6136264	.	+	0	transcript_id "Phchi.S3G065000.t2"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	transcript	6134371	6136261	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	start_codon	6134371	6134373	.	+	0	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134371	6134650	0.59	+	0	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134371	6134650	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6134651	6134805	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134806	6134814	0.36	+	2	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134806	6134814	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6134815	6134930	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6134931	6135005	0.55	+	2	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6134931	6135005	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	intron	6135006	6135101	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	CDS	6135102	6136261	0.97	+	2	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	exon	6135102	6136261	.	+	.	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
Phchi.S3	AUGUSTUS	stop_codon	6136262	6136264	.	+	0	transcript_id "Phchi.S3G065000.t3"; gene_id "Phchi.S3G065000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9719.t1 is derived from g6895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43393951	43395125	.	-	.	Phchi.S1G687800
Phchi.S1	AUGUSTUS	transcript	43393951	43395125	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	stop_codon	43393948	43393950	.	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	CDS	43393951	43394271	0.98	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	exon	43393951	43394271	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	intron	43394272	43394356	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	CDS	43394357	43394494	1	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	exon	43394357	43394494	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	intron	43394495	43394573	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	CDS	43394574	43394717	1	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	exon	43394574	43394717	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	intron	43394718	43394792	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	CDS	43394793	43394930	0.73	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	exon	43394793	43394930	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	intron	43394931	43395074	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	CDS	43395075	43395125	0.46	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	exon	43395075	43395125	.	-	.	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
Phchi.S1	AUGUSTUS	start_codon	43395123	43395125	.	-	0	transcript_id "Phchi.S1G687800.t1"; gene_id "Phchi.S1G687800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12718.t1 is derived from g11183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1095460	1097249	.	-	.	Phchi.S3G003700
Phchi.S3	AUGUSTUS	transcript	1095460	1097249	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	stop_codon	1095457	1095459	.	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1095460	1095513	1	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1095460	1095513	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1095514	1095613	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1095614	1095742	0.98	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1095614	1095742	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1095743	1096180	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096181	1096300	1	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096181	1096300	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096301	1096396	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096397	1096534	1	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096397	1096534	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096535	1096673	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096674	1096755	1	-	1	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096674	1096755	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096756	1096848	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096849	1096962	0.99	-	1	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096849	1096962	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096963	1097065	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1097066	1097148	0.99	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1097066	1097148	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1097149	1097234	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1097235	1097249	0.96	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1097235	1097249	.	-	.	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	start_codon	1097247	1097249	.	-	0	transcript_id "Phchi.S3G003700.t1"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	transcript	1095977	1097249	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	stop_codon	1095974	1095976	.	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1095977	1096096	0.29	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1095977	1096096	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096097	1096180	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096181	1096300	0.98	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096181	1096300	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096301	1096396	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096397	1096534	1	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096397	1096534	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096535	1096673	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096674	1096755	1	-	1	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096674	1096755	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096756	1096848	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1096849	1096962	1	-	1	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1096849	1096962	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1096963	1097065	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1097066	1097148	1	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1097066	1097148	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1097149	1097234	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1097235	1097249	0.98	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1097235	1097249	.	-	.	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	start_codon	1097247	1097249	.	-	0	transcript_id "Phchi.S3G003700.t2"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	transcript	1095460	1095904	.	-	.	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	stop_codon	1095457	1095459	.	-	0	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1095460	1095513	1	-	0	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1095460	1095513	.	-	.	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1095514	1095613	.	-	.	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1095614	1095742	1	-	0	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1095614	1095742	.	-	.	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	intron	1095743	1095823	.	-	.	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	CDS	1095824	1095904	0.23	-	0	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	exon	1095824	1095904	.	-	.	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
Phchi.S3	AUGUSTUS	start_codon	1095902	1095904	.	-	0	transcript_id "Phchi.S3G003700.t3"; gene_id "Phchi.S3G003700"
# This transcript jg11616.t2 is derived from g15667.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11617.t1 is derived from g15668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7338936	7341655	.	-	.	Phchi.S4G119900
Phchi.S4	AUGUSTUS	transcript	7338936	7341655	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	stop_codon	7338933	7338935	.	-	0	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	CDS	7338936	7339363	1	-	2	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	exon	7338936	7339363	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	intron	7339364	7339449	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	CDS	7339450	7340198	0.51	-	1	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	exon	7339450	7340198	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	intron	7340199	7340387	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	CDS	7340388	7340659	0.57	-	0	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	exon	7340388	7340659	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	intron	7340660	7340754	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	CDS	7340755	7341157	0.93	-	1	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	exon	7340755	7341157	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	intron	7341158	7341258	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	CDS	7341259	7341350	0.87	-	0	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	exon	7341259	7341350	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	intron	7341351	7341544	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	CDS	7341545	7341655	1	-	0	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	exon	7341545	7341655	.	-	.	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
Phchi.S4	AUGUSTUS	start_codon	7341653	7341655	.	-	0	transcript_id "Phchi.S4G119900.t1"; gene_id "Phchi.S4G119900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7434.t1 is derived from g4606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29102005	29102946	.	+	.	Phchi.S1G459300
Phchi.S1	AUGUSTUS	transcript	29102005	29102946	.	+	.	transcript_id "Phchi.S1G459300.t1"; gene_id "Phchi.S1G459300"
Phchi.S1	AUGUSTUS	start_codon	29102005	29102007	.	+	0	transcript_id "Phchi.S1G459300.t1"; gene_id "Phchi.S1G459300"
Phchi.S1	AUGUSTUS	CDS	29102005	29102946	0.52	+	0	transcript_id "Phchi.S1G459300.t1"; gene_id "Phchi.S1G459300"
Phchi.S1	AUGUSTUS	exon	29102005	29102946	.	+	.	transcript_id "Phchi.S1G459300.t1"; gene_id "Phchi.S1G459300"
Phchi.S1	AUGUSTUS	stop_codon	29102947	29102949	.	+	0	transcript_id "Phchi.S1G459300.t1"; gene_id "Phchi.S1G459300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9125.t1 is derived from g6300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39959144	39966287	.	+	.	Phchi.S1G628400
Phchi.S1	AUGUSTUS	transcript	39959144	39966287	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	start_codon	39959144	39959146	.	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39959144	39959233	0.53	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39959144	39959233	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39959234	39959337	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39959338	39959368	0.92	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39959338	39959368	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39959369	39959847	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39959848	39960151	0.93	+	2	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39959848	39960151	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39960152	39960236	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39960237	39960411	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39960237	39960411	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39960412	39960536	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39960537	39960641	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39960537	39960641	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39960642	39960730	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39960731	39960866	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39960731	39960866	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39960867	39961009	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39961010	39961062	0.99	+	2	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39961010	39961062	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39961063	39961164	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39961165	39961273	0.99	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39961165	39961273	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39961274	39961403	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39961404	39961540	1	+	2	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39961404	39961540	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39961541	39961701	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39961702	39961901	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39961702	39961901	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39961902	39962032	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39962033	39962182	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39962033	39962182	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39962183	39962269	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39962270	39962330	0.93	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39962270	39962330	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39962331	39962432	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39962433	39962553	0.93	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39962433	39962553	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39962554	39962634	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39962635	39962725	1	+	2	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39962635	39962725	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39962726	39962825	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39962826	39962918	0.65	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39962826	39962918	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39962919	39963121	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39963122	39963155	0.94	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39963122	39963155	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39963156	39963248	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39963249	39963389	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39963249	39963389	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39963390	39963486	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39963487	39963537	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39963487	39963537	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39963538	39963620	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39963621	39963691	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39963621	39963691	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39963692	39963782	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39963783	39963875	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39963783	39963875	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39963876	39963980	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39963981	39964071	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39963981	39964071	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39964072	39964157	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39964158	39964229	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39964158	39964229	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39964230	39964328	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39964329	39964385	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39964329	39964385	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39964386	39964491	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39964492	39964560	0.97	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39964492	39964560	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39964561	39964648	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39964649	39964705	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39964649	39964705	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39964706	39964797	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39964798	39964872	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39964798	39964872	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39964873	39964947	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39964948	39965036	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39964948	39965036	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39965037	39965185	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39965186	39965263	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39965186	39965263	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39965264	39965335	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39965336	39965474	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39965336	39965474	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39965475	39965557	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39965558	39965661	0.76	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39965558	39965661	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39965662	39965770	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39965771	39965870	1	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39965771	39965870	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39965871	39965962	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39965963	39966066	1	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39965963	39966066	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	intron	39966067	39966226	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	CDS	39966227	39966287	0.99	+	1	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	exon	39966227	39966287	.	+	.	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
Phchi.S1	AUGUSTUS	stop_codon	39966288	39966290	.	+	0	transcript_id "Phchi.S1G628400.t1"; gene_id "Phchi.S1G628400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2822.t1 is derived from g9742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9037038	9038275	.	+	.	Phchi.S5G143100
Phchi.S5	AUGUSTUS	transcript	9037038	9038275	.	+	.	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	start_codon	9037038	9037040	.	+	0	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	CDS	9037038	9037258	0.89	+	0	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	exon	9037038	9037258	.	+	.	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	intron	9037259	9037359	.	+	.	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	CDS	9037360	9037643	0.78	+	1	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	exon	9037360	9037643	.	+	.	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	intron	9037644	9037808	.	+	.	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	CDS	9037809	9038275	0.45	+	2	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	exon	9037809	9038275	.	+	.	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
Phchi.S5	AUGUSTUS	stop_codon	9038276	9038278	.	+	0	transcript_id "Phchi.S5G143100.t1"; gene_id "Phchi.S5G143100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8204.t1 is derived from g5379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34426533	34429805	.	+	.	Phchi.S1G536300
Phchi.S1	AUGUSTUS	transcript	34426533	34429805	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	start_codon	34426533	34426535	.	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34426533	34426697	1	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34426533	34426697	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	intron	34426698	34426922	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34426923	34427212	1	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34426923	34427212	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	intron	34427213	34427432	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34427433	34427514	1	+	1	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34427433	34427514	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	intron	34427515	34427691	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34427692	34428204	1	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34427692	34428204	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	intron	34428205	34428357	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34428358	34429107	1	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34428358	34429107	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	intron	34429108	34429199	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34429200	34429316	1	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34429200	34429316	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	intron	34429317	34429418	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	CDS	34429419	34429805	0.98	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	exon	34429419	34429805	.	+	.	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
Phchi.S1	AUGUSTUS	stop_codon	34429806	34429808	.	+	0	transcript_id "Phchi.S1G536300.t1"; gene_id "Phchi.S1G536300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13806.t1 is derived from g12273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9007479	9011938	.	+	.	Phchi.S3G112500
Phchi.S3	AUGUSTUS	transcript	9007479	9011938	.	+	.	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	start_codon	9007479	9007481	.	+	0	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	CDS	9007479	9009696	0.91	+	0	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	exon	9007479	9009696	.	+	.	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	intron	9009697	9009764	.	+	.	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	CDS	9009765	9011938	0.7	+	2	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	exon	9009765	9011938	.	+	.	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
Phchi.S3	AUGUSTUS	stop_codon	9011939	9011941	.	+	0	transcript_id "Phchi.S3G112500.t1"; gene_id "Phchi.S3G112500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3387.t1 is derived from g556.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3294664	3297597	.	-	.	Phchi.S1G054600
Phchi.S1	AUGUSTUS	transcript	3294664	3297597	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	stop_codon	3294661	3294663	.	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3294664	3294675	0.83	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3294664	3294675	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3294676	3294874	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3294875	3294901	0.99	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3294875	3294901	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3294902	3295080	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3295081	3295140	1	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3295081	3295140	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3295141	3295237	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3295238	3295336	1	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3295238	3295336	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3295337	3295417	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3295418	3295468	1	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3295418	3295468	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3295469	3295566	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3295567	3295768	1	-	1	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3295567	3295768	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3295769	3295852	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3295853	3296055	1	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3295853	3296055	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3296056	3296178	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3296179	3296265	1	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3296179	3296265	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3296266	3296353	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3296354	3296472	1	-	2	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3296354	3296472	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3296473	3296608	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3296609	3296713	1	-	2	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3296609	3296713	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3296714	3296801	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3296802	3296905	1	-	1	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3296802	3296905	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3296906	3296992	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3296993	3297201	1	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3296993	3297201	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	intron	3297202	3297306	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	CDS	3297307	3297597	0.92	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	exon	3297307	3297597	.	-	.	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
Phchi.S1	AUGUSTUS	start_codon	3297595	3297597	.	-	0	transcript_id "Phchi.S1G054600.t1"; gene_id "Phchi.S1G054600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9464.t1 is derived from g6640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41579382	41580959	.	+	.	Phchi.S1G662300
Phchi.S1	AUGUSTUS	transcript	41579382	41580959	.	+	.	transcript_id "Phchi.S1G662300.t1"; gene_id "Phchi.S1G662300"
Phchi.S1	AUGUSTUS	start_codon	41579382	41579384	.	+	0	transcript_id "Phchi.S1G662300.t1"; gene_id "Phchi.S1G662300"
Phchi.S1	AUGUSTUS	CDS	41579382	41580959	0.71	+	0	transcript_id "Phchi.S1G662300.t1"; gene_id "Phchi.S1G662300"
Phchi.S1	AUGUSTUS	exon	41579382	41580959	.	+	.	transcript_id "Phchi.S1G662300.t1"; gene_id "Phchi.S1G662300"
Phchi.S1	AUGUSTUS	stop_codon	41580960	41580962	.	+	0	transcript_id "Phchi.S1G662300.t1"; gene_id "Phchi.S1G662300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14339.t1 is derived from g12806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12301481	12302542	.	+	.	Phchi.S3G165800
Phchi.S3	AUGUSTUS	transcript	12301481	12302542	.	+	.	transcript_id "Phchi.S3G165800.t1"; gene_id "Phchi.S3G165800"
Phchi.S3	AUGUSTUS	start_codon	12301481	12301483	.	+	0	transcript_id "Phchi.S3G165800.t1"; gene_id "Phchi.S3G165800"
Phchi.S3	AUGUSTUS	CDS	12301481	12302542	0.98	+	0	transcript_id "Phchi.S3G165800.t1"; gene_id "Phchi.S3G165800"
Phchi.S3	AUGUSTUS	exon	12301481	12302542	.	+	.	transcript_id "Phchi.S3G165800.t1"; gene_id "Phchi.S3G165800"
Phchi.S3	AUGUSTUS	stop_codon	12302543	12302545	.	+	0	transcript_id "Phchi.S3G165800.t1"; gene_id "Phchi.S3G165800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3406.t1 is derived from g575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3373073	3373420	.	-	.	Phchi.S1G056500
Phchi.S1	AUGUSTUS	transcript	3373073	3373420	.	-	.	transcript_id "Phchi.S1G056500.t1"; gene_id "Phchi.S1G056500"
Phchi.S1	AUGUSTUS	stop_codon	3373070	3373072	.	-	0	transcript_id "Phchi.S1G056500.t1"; gene_id "Phchi.S1G056500"
Phchi.S1	AUGUSTUS	CDS	3373073	3373420	0.95	-	0	transcript_id "Phchi.S1G056500.t1"; gene_id "Phchi.S1G056500"
Phchi.S1	AUGUSTUS	exon	3373073	3373420	.	-	.	transcript_id "Phchi.S1G056500.t1"; gene_id "Phchi.S1G056500"
Phchi.S1	AUGUSTUS	start_codon	3373418	3373420	.	-	0	transcript_id "Phchi.S1G056500.t1"; gene_id "Phchi.S1G056500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1619.t1 is derived from g8538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2051139	2051826	.	+	.	Phchi.S5G022800
Phchi.S5	AUGUSTUS	transcript	2051139	2051826	.	+	.	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	start_codon	2051139	2051141	.	+	0	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	CDS	2051139	2051472	0.94	+	0	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	exon	2051139	2051472	.	+	.	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	intron	2051473	2051584	.	+	.	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	CDS	2051585	2051826	1	+	2	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	exon	2051585	2051826	.	+	.	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
Phchi.S5	AUGUSTUS	stop_codon	2051827	2051829	.	+	0	transcript_id "Phchi.S5G022800.t1"; gene_id "Phchi.S5G022800"
# This transcript jg7270.t2 is derived from g4442.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg7271.t1 is derived from g4443.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28062134	28065652	.	+	.	Phchi.S1G443000
Phchi.S1	AUGUSTUS	transcript	28062134	28065652	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	start_codon	28062134	28062136	.	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062134	28062526	0.93	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062134	28062526	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28062527	28062628	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062629	28062684	1	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062629	28062684	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28062685	28062927	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062928	28063080	1	+	1	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062928	28063080	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063081	28063175	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063176	28063221	1	+	1	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063176	28063221	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063222	28063337	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063338	28063399	0.82	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063338	28063399	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063400	28063506	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063507	28064398	0.81	+	1	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063507	28064398	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064399	28064488	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064489	28064735	1	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064489	28064735	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064736	28064859	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064860	28064915	1	+	2	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064860	28064915	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064916	28064994	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064995	28065055	1	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064995	28065055	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065056	28065147	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065148	28065208	1	+	2	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065148	28065208	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065209	28065299	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065300	28065419	1	+	1	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065300	28065419	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065420	28065525	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065526	28065652	1	+	1	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065526	28065652	.	+	.	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	stop_codon	28065653	28065655	.	+	0	transcript_id "Phchi.S1G443000.t1"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	transcript	28062134	28065652	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	start_codon	28062134	28062136	.	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062134	28062526	0.95	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062134	28062526	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28062527	28062628	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062629	28062684	1	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062629	28062684	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28062685	28062927	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062928	28063080	1	+	1	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062928	28063080	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063081	28063175	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063176	28063221	1	+	1	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063176	28063221	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063222	28063337	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063338	28063399	0.78	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063338	28063399	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063400	28063506	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063507	28064398	0.76	+	1	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063507	28064398	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064399	28064485	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064486	28064735	1	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064486	28064735	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064736	28064859	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064860	28064915	1	+	2	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064860	28064915	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064916	28064994	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064995	28065055	1	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064995	28065055	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065056	28065147	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065148	28065208	1	+	2	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065148	28065208	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065209	28065299	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065300	28065419	1	+	1	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065300	28065419	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065420	28065525	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065526	28065652	1	+	1	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065526	28065652	.	+	.	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	stop_codon	28065653	28065655	.	+	0	transcript_id "Phchi.S1G443000.t2"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	transcript	28062134	28065652	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	start_codon	28062134	28062136	.	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062134	28062526	0.93	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062134	28062526	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28062527	28062628	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062629	28062684	1	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062629	28062684	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28062685	28062927	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28062928	28063080	1	+	1	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28062928	28063080	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063081	28063175	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063176	28063221	1	+	1	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063176	28063221	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063222	28063337	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063338	28063399	0.73	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063338	28063399	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28063400	28063506	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28063507	28064398	0.71	+	1	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28063507	28064398	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064399	28064488	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064489	28064735	1	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064489	28064735	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064736	28064859	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28064860	28064915	1	+	2	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28064860	28064915	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28064916	28065000	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065001	28065055	0.9	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065001	28065055	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065056	28065147	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065148	28065208	1	+	2	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065148	28065208	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065209	28065299	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065300	28065419	1	+	1	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065300	28065419	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	intron	28065420	28065525	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	CDS	28065526	28065652	1	+	1	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	exon	28065526	28065652	.	+	.	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
Phchi.S1	AUGUSTUS	stop_codon	28065653	28065655	.	+	0	transcript_id "Phchi.S1G443000.t3"; gene_id "Phchi.S1G443000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3392.t1 is derived from g561.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3322416	3326752	.	-	.	Phchi.S1G055100
Phchi.S1	AUGUSTUS	transcript	3322416	3326752	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	stop_codon	3322413	3322415	.	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3322416	3322565	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3322416	3322565	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3322566	3322649	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3322650	3322874	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3322650	3322874	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3322875	3322966	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3322967	3323029	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3322967	3323029	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323030	3323127	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3323128	3323364	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3323128	3323364	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323365	3323492	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3323493	3323636	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3323493	3323636	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323637	3323765	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3323766	3323908	1	-	2	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3323766	3323908	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323909	3324028	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324029	3324082	1	-	2	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324029	3324082	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324083	3324215	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324216	3324286	1	-	1	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324216	3324286	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324287	3324370	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324371	3324507	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324371	3324507	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324508	3324666	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324667	3324702	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324667	3324702	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324703	3324796	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324797	3324893	1	-	1	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324797	3324893	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324894	3324973	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324974	3325031	1	-	2	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324974	3325031	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325032	3325147	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325148	3325261	0.85	-	2	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325148	3325261	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325262	3325370	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325371	3325428	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325371	3325428	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325429	3325589	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325590	3325675	1	-	2	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325590	3325675	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325676	3325888	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325889	3325973	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325889	3325973	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325974	3326119	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326120	3326197	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326120	3326197	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3326198	3326273	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326274	3326322	1	-	1	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326274	3326322	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3326323	3326443	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326444	3326510	1	-	2	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326444	3326510	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3326511	3326643	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326644	3326752	1	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326644	3326752	.	-	.	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	start_codon	3326750	3326752	.	-	0	transcript_id "Phchi.S1G055100.t1"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	transcript	3322416	3326752	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	stop_codon	3322413	3322415	.	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3322416	3322565	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3322416	3322565	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3322566	3322649	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3322650	3322874	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3322650	3322874	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3322875	3322966	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3322967	3323029	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3322967	3323029	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323030	3323127	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3323128	3323364	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3323128	3323364	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323365	3323492	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3323493	3323636	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3323493	3323636	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323637	3323765	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3323766	3323908	1	-	2	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3323766	3323908	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3323909	3324028	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324029	3324082	1	-	2	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324029	3324082	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324083	3324215	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324216	3324286	1	-	1	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324216	3324286	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324287	3324370	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324371	3324507	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324371	3324507	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324508	3324666	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324667	3324702	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324667	3324702	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324703	3324796	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324797	3324893	1	-	1	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324797	3324893	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3324894	3324973	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3324974	3325031	0.99	-	2	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3324974	3325031	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325032	3325147	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325148	3325261	0.75	-	2	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325148	3325261	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325262	3325370	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325371	3325428	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325371	3325428	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325429	3325589	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325590	3325675	1	-	2	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325590	3325675	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325676	3325888	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3325889	3325976	0.94	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3325889	3325976	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3325977	3326119	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326120	3326197	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326120	3326197	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3326198	3326273	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326274	3326322	1	-	1	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326274	3326322	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3326323	3326443	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326444	3326510	1	-	2	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326444	3326510	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	intron	3326511	3326643	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	CDS	3326644	3326752	1	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	exon	3326644	3326752	.	-	.	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
Phchi.S1	AUGUSTUS	start_codon	3326750	3326752	.	-	0	transcript_id "Phchi.S1G055100.t2"; gene_id "Phchi.S1G055100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15693.t1 is derived from g14162.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20727066	20729468	.	-	.	Phchi.S3G301200
Phchi.S3	AUGUSTUS	transcript	20727066	20729468	.	-	.	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	stop_codon	20727063	20727065	.	-	0	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	CDS	20727066	20728127	0.64	-	0	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	exon	20727066	20728127	.	-	.	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	intron	20728128	20728298	.	-	.	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	CDS	20728299	20729468	0.41	-	0	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	exon	20728299	20729468	.	-	.	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	start_codon	20729466	20729468	.	-	0	transcript_id "Phchi.S3G301200.t1"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	transcript	20727066	20727905	.	-	.	transcript_id "Phchi.S3G301200.t2"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	stop_codon	20727063	20727065	.	-	0	transcript_id "Phchi.S3G301200.t2"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	CDS	20727066	20727905	0.78	-	0	transcript_id "Phchi.S3G301200.t2"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	exon	20727066	20727905	.	-	.	transcript_id "Phchi.S3G301200.t2"; gene_id "Phchi.S3G301200"
Phchi.S3	AUGUSTUS	start_codon	20727903	20727905	.	-	0	transcript_id "Phchi.S3G301200.t2"; gene_id "Phchi.S3G301200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3581.t1 is derived from g750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4602905	4603963	.	+	.	Phchi.S1G074000
Phchi.S1	AUGUSTUS	transcript	4602905	4603963	.	+	.	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	start_codon	4602905	4602907	.	+	0	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	CDS	4602905	4602963	0.84	+	0	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	exon	4602905	4602963	.	+	.	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	intron	4602964	4603460	.	+	.	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	CDS	4603461	4603523	0.98	+	1	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	exon	4603461	4603523	.	+	.	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	intron	4603524	4603824	.	+	.	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	CDS	4603825	4603963	0.95	+	1	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	exon	4603825	4603963	.	+	.	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
Phchi.S1	AUGUSTUS	stop_codon	4603964	4603966	.	+	0	transcript_id "Phchi.S1G074000.t1"; gene_id "Phchi.S1G074000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10817.t1 is derived from g14867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2251366	2252732	.	+	.	Phchi.S4G039900
Phchi.S4	AUGUSTUS	transcript	2251366	2252732	.	+	.	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	start_codon	2251366	2251368	.	+	0	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	CDS	2251366	2252204	0.6	+	0	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	exon	2251366	2252204	.	+	.	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	intron	2252205	2252432	.	+	.	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	CDS	2252433	2252521	0.95	+	1	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	exon	2252433	2252521	.	+	.	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	intron	2252522	2252703	.	+	.	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	CDS	2252704	2252732	1	+	2	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	exon	2252704	2252732	.	+	.	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
Phchi.S4	AUGUSTUS	stop_codon	2252733	2252735	.	+	0	transcript_id "Phchi.S4G039900.t1"; gene_id "Phchi.S4G039900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13805.t1 is derived from g12272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8965066	8968223	.	+	.	Phchi.S3G112400
Phchi.S3	AUGUSTUS	transcript	8965066	8968223	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	start_codon	8965066	8965068	.	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8965066	8965116	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8965066	8965116	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8965117	8965534	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8965535	8965659	0.71	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8965535	8965659	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8965660	8965760	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8965761	8965854	0.99	+	1	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8965761	8965854	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8965855	8965991	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8965992	8966217	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8965992	8966217	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8966218	8966301	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8966302	8966438	0.95	+	2	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8966302	8966438	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8966439	8966548	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8966549	8966674	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8966549	8966674	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8966675	8966794	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8966795	8966823	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8966795	8966823	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8966824	8966935	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8966936	8967065	1	+	1	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8966936	8967065	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8967066	8967183	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8967184	8967314	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8967184	8967314	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8967315	8967458	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8967459	8967552	1	+	1	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8967459	8967552	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8967553	8967670	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8967671	8967748	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8967671	8967748	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8967749	8967891	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8967892	8968025	1	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8967892	8968025	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	intron	8968026	8968102	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	CDS	8968103	8968223	1	+	1	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	exon	8968103	8968223	.	+	.	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
Phchi.S3	AUGUSTUS	stop_codon	8968224	8968226	.	+	0	transcript_id "Phchi.S3G112400.t1"; gene_id "Phchi.S3G112400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5863.t1 is derived from g3033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19473036	19476003	.	+	.	Phchi.S1G302200
Phchi.S1	AUGUSTUS	transcript	19473036	19476003	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	start_codon	19473036	19473038	.	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19473036	19473253	0.84	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19473036	19473253	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19473254	19473343	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19473344	19473470	1	+	1	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19473344	19473470	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19473471	19473607	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19473608	19473661	0.98	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19473608	19473661	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19473662	19473743	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19473744	19473890	1	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19473744	19473890	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19473891	19474005	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19474006	19474260	1	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19474006	19474260	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19474261	19474352	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19474353	19474442	1	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19474353	19474442	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19474443	19474534	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19474535	19474613	0.99	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19474535	19474613	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19474614	19474718	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19474719	19474825	0.99	+	2	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19474719	19474825	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19474826	19474918	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19474919	19475037	1	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19474919	19475037	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19475038	19475127	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19475128	19475217	0.7	+	1	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19475128	19475217	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19475218	19475628	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19475629	19475731	0.25	+	1	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19475629	19475731	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19475732	19475802	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19475803	19475847	0.54	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19475803	19475847	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	intron	19475848	19475943	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	CDS	19475944	19476003	1	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	exon	19475944	19476003	.	+	.	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
Phchi.S1	AUGUSTUS	stop_codon	19476004	19476006	.	+	0	transcript_id "Phchi.S1G302200.t1"; gene_id "Phchi.S1G302200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12554.t1 is derived from g8231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34743177	34743818	.	-	.	Phchi.S2G063400
Phchi.S2	AUGUSTUS	transcript	34743177	34743818	.	-	.	transcript_id "Phchi.S2G063400.t1"; gene_id "Phchi.S2G063400"
Phchi.S2	AUGUSTUS	stop_codon	34743174	34743176	.	-	0	transcript_id "Phchi.S2G063400.t1"; gene_id "Phchi.S2G063400"
Phchi.S2	AUGUSTUS	CDS	34743177	34743818	1	-	0	transcript_id "Phchi.S2G063400.t1"; gene_id "Phchi.S2G063400"
Phchi.S2	AUGUSTUS	exon	34743177	34743818	.	-	.	transcript_id "Phchi.S2G063400.t1"; gene_id "Phchi.S2G063400"
Phchi.S2	AUGUSTUS	start_codon	34743816	34743818	.	-	0	transcript_id "Phchi.S2G063400.t1"; gene_id "Phchi.S2G063400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5913.t1 is derived from g3084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19761467	19763039	.	-	.	Phchi.S1G307200
Phchi.S1	AUGUSTUS	transcript	19761467	19763039	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	stop_codon	19761464	19761466	.	-	0	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19761467	19761514	1	-	0	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19761467	19761514	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	intron	19761515	19761595	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19761596	19761717	1	-	2	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19761596	19761717	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	intron	19761718	19761851	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19761852	19761955	1	-	1	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19761852	19761955	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	intron	19761956	19762042	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19762043	19762163	1	-	2	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19762043	19762163	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	intron	19762164	19762318	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19762319	19762476	0.89	-	1	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19762319	19762476	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	intron	19762477	19762553	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19762554	19762569	1	-	2	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19762554	19762569	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	intron	19762570	19762963	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	CDS	19762964	19763039	0.73	-	0	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	exon	19762964	19763039	.	-	.	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
Phchi.S1	AUGUSTUS	start_codon	19763037	19763039	.	-	0	transcript_id "Phchi.S1G307200.t1"; gene_id "Phchi.S1G307200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8167.t1 is derived from g5342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34256625	34256843	.	-	.	Phchi.S1G532600
Phchi.S1	AUGUSTUS	transcript	34256625	34256843	.	-	.	transcript_id "Phchi.S1G532600.t1"; gene_id "Phchi.S1G532600"
Phchi.S1	AUGUSTUS	stop_codon	34256622	34256624	.	-	0	transcript_id "Phchi.S1G532600.t1"; gene_id "Phchi.S1G532600"
Phchi.S1	AUGUSTUS	CDS	34256625	34256843	0.76	-	0	transcript_id "Phchi.S1G532600.t1"; gene_id "Phchi.S1G532600"
Phchi.S1	AUGUSTUS	exon	34256625	34256843	.	-	.	transcript_id "Phchi.S1G532600.t1"; gene_id "Phchi.S1G532600"
Phchi.S1	AUGUSTUS	start_codon	34256841	34256843	.	-	0	transcript_id "Phchi.S1G532600.t1"; gene_id "Phchi.S1G532600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7910.t1 is derived from g5084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31848821	31850729	.	-	.	Phchi.S1G506900
Phchi.S1	AUGUSTUS	transcript	31848821	31850729	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	stop_codon	31848818	31848820	.	-	0	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	CDS	31848821	31849027	0.88	-	0	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	exon	31848821	31849027	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	intron	31849028	31849203	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	CDS	31849204	31849338	1	-	0	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	exon	31849204	31849338	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	intron	31849339	31849511	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	CDS	31849512	31849686	1	-	1	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	exon	31849512	31849686	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	intron	31849687	31849772	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	CDS	31849773	31849981	0.88	-	0	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	exon	31849773	31849981	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	intron	31849982	31850088	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	CDS	31850089	31850210	0.85	-	2	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	exon	31850089	31850210	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	intron	31850211	31850410	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	CDS	31850411	31850729	1	-	0	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	exon	31850411	31850729	.	-	.	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
Phchi.S1	AUGUSTUS	start_codon	31850727	31850729	.	-	0	transcript_id "Phchi.S1G506900.t1"; gene_id "Phchi.S1G506900"
# This transcript jg14032.t2 is derived from g12499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14033.t1 is derived from g12500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10397707	10400371	.	+	.	Phchi.S3G135200
Phchi.S3	AUGUSTUS	transcript	10397707	10400371	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	start_codon	10397707	10397709	.	+	0	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10397707	10397836	0.72	+	0	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10397707	10397836	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10397837	10398026	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10398027	10398065	0.43	+	2	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10398027	10398065	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10398066	10398169	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10398170	10398320	0.72	+	2	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10398170	10398320	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10398321	10398444	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10398445	10398584	1	+	1	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10398445	10398584	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10398585	10398755	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10398756	10398938	0.99	+	2	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10398756	10398938	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10398939	10399104	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10399105	10399161	0.79	+	2	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10399105	10399161	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10399162	10399469	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10399470	10399620	0.72	+	2	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10399470	10399620	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10399621	10399751	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10399752	10399983	1	+	1	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10399752	10399983	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10399984	10400208	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10400209	10400263	0.84	+	0	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10400209	10400263	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	intron	10400264	10400333	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	CDS	10400334	10400371	1	+	2	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	exon	10400334	10400371	.	+	.	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
Phchi.S3	AUGUSTUS	stop_codon	10400372	10400374	.	+	0	transcript_id "Phchi.S3G135200.t1"; gene_id "Phchi.S3G135200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2252.t1 is derived from g9172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5694743	5695274	.	-	.	Phchi.S5G086100
Phchi.S5	AUGUSTUS	transcript	5694743	5695274	.	-	.	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	stop_codon	5694740	5694742	.	-	0	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	CDS	5694743	5694781	0.97	-	0	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	exon	5694743	5694781	.	-	.	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	intron	5694782	5694909	.	-	.	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	CDS	5694910	5695013	1	-	2	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	exon	5694910	5695013	.	-	.	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	intron	5695014	5695096	.	-	.	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	CDS	5695097	5695274	1	-	0	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	exon	5695097	5695274	.	-	.	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
Phchi.S5	AUGUSTUS	start_codon	5695272	5695274	.	-	0	transcript_id "Phchi.S5G086100.t1"; gene_id "Phchi.S5G086100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10407.t1 is derived from g7583.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47677740	47679259	.	+	.	Phchi.S1G756600
Phchi.S1	AUGUSTUS	transcript	47677740	47679259	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	start_codon	47677740	47677742	.	+	0	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47677740	47677744	0.54	+	0	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47677740	47677744	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47677745	47677957	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47677958	47678084	1	+	1	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47677958	47678084	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678085	47678250	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678251	47678256	0.57	+	0	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678251	47678256	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678257	47678381	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678382	47678433	0.57	+	0	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678382	47678433	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678434	47678641	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678642	47678735	0.45	+	2	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678642	47678735	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678736	47678916	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678917	47679130	0.45	+	1	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678917	47679130	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47679131	47679217	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47679218	47679259	0.57	+	0	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47679218	47679259	.	+	.	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	stop_codon	47679260	47679262	.	+	0	transcript_id "Phchi.S1G756600.t1"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	transcript	47677740	47679259	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	start_codon	47677740	47677742	.	+	0	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47677740	47677744	0.49	+	0	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47677740	47677744	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47677745	47677957	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47677958	47678028	1	+	1	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47677958	47678028	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678029	47678250	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678251	47678285	0.62	+	2	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678251	47678285	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678286	47678381	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678382	47678433	0.62	+	0	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678382	47678433	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678434	47678641	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678642	47678735	0.56	+	2	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678642	47678735	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47678736	47678916	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47678917	47679130	0.55	+	1	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47678917	47679130	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	intron	47679131	47679217	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	CDS	47679218	47679259	0.26	+	0	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	exon	47679218	47679259	.	+	.	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
Phchi.S1	AUGUSTUS	stop_codon	47679260	47679262	.	+	0	transcript_id "Phchi.S1G756600.t2"; gene_id "Phchi.S1G756600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14637.t1 is derived from g13105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13861370	13862652	.	-	.	Phchi.S3G195600
Phchi.S3	AUGUSTUS	transcript	13861370	13862652	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	stop_codon	13861367	13861369	.	-	0	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	CDS	13861370	13861758	1	-	2	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	exon	13861370	13861758	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	intron	13861759	13861849	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	CDS	13861850	13861988	1	-	0	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	exon	13861850	13861988	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	intron	13861989	13862083	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	CDS	13862084	13862121	1	-	2	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	exon	13862084	13862121	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	intron	13862122	13862198	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	CDS	13862199	13862652	0.75	-	0	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	exon	13862199	13862652	.	-	.	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
Phchi.S3	AUGUSTUS	start_codon	13862650	13862652	.	-	0	transcript_id "Phchi.S3G195600.t1"; gene_id "Phchi.S3G195600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6235.t1 is derived from g3407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21803492	21804190	.	-	.	Phchi.S1G339400
Phchi.S1	AUGUSTUS	transcript	21803492	21804190	.	-	.	transcript_id "Phchi.S1G339400.t1"; gene_id "Phchi.S1G339400"
Phchi.S1	AUGUSTUS	stop_codon	21803489	21803491	.	-	0	transcript_id "Phchi.S1G339400.t1"; gene_id "Phchi.S1G339400"
Phchi.S1	AUGUSTUS	CDS	21803492	21804190	0.76	-	0	transcript_id "Phchi.S1G339400.t1"; gene_id "Phchi.S1G339400"
Phchi.S1	AUGUSTUS	exon	21803492	21804190	.	-	.	transcript_id "Phchi.S1G339400.t1"; gene_id "Phchi.S1G339400"
Phchi.S1	AUGUSTUS	start_codon	21804188	21804190	.	-	0	transcript_id "Phchi.S1G339400.t1"; gene_id "Phchi.S1G339400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6035.t1 is derived from g3206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20527082	20528209	.	-	.	Phchi.S1G319400
Phchi.S1	AUGUSTUS	transcript	20527082	20528209	.	-	.	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	stop_codon	20527079	20527081	.	-	0	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	CDS	20527082	20527110	0.3	-	2	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	exon	20527082	20527110	.	-	.	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	intron	20527111	20527235	.	-	.	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	CDS	20527236	20527914	0.36	-	0	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	exon	20527236	20527914	.	-	.	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	intron	20527915	20528008	.	-	.	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	CDS	20528009	20528209	0.76	-	0	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	exon	20528009	20528209	.	-	.	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
Phchi.S1	AUGUSTUS	start_codon	20528207	20528209	.	-	0	transcript_id "Phchi.S1G319400.t1"; gene_id "Phchi.S1G319400"
# This transcript jg5060.t2 is derived from g2230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5061.t1 is derived from g2231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14481840	14484048	.	-	.	Phchi.S1G222000
Phchi.S1	AUGUSTUS	transcript	14481840	14484048	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	stop_codon	14481837	14481839	.	-	0	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14481840	14481929	1	-	0	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14481840	14481929	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14481930	14482018	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14482019	14482094	1	-	1	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14482019	14482094	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14482095	14482258	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14482259	14482319	1	-	2	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14482259	14482319	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14482320	14482433	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14482434	14482532	1	-	2	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14482434	14482532	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14482533	14482647	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14482648	14482787	1	-	1	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14482648	14482787	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14482788	14482937	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14482938	14483021	1	-	1	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14482938	14483021	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14483022	14483192	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14483193	14483355	1	-	2	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14483193	14483355	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14483356	14483504	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14483505	14483658	0.95	-	0	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14483505	14483658	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14483659	14483806	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14483807	14483818	0.78	-	0	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14483807	14483818	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	intron	14483819	14484036	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	CDS	14484037	14484048	0.99	-	0	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	exon	14484037	14484048	.	-	.	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
Phchi.S1	AUGUSTUS	start_codon	14484046	14484048	.	-	0	transcript_id "Phchi.S1G222000.t1"; gene_id "Phchi.S1G222000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11710.t1 is derived from g15761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7787622	7789867	.	-	.	Phchi.S4G129200
Phchi.S4	AUGUSTUS	transcript	7787622	7789867	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	stop_codon	7787619	7787621	.	-	0	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	CDS	7787622	7788087	0.65	-	1	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	exon	7787622	7788087	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	intron	7788088	7788188	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	CDS	7788189	7788488	0.62	-	1	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	exon	7788189	7788488	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	intron	7788489	7788570	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	CDS	7788571	7788758	0.93	-	0	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	exon	7788571	7788758	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	intron	7788759	7788850	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	CDS	7788851	7788948	0.75	-	2	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	exon	7788851	7788948	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	intron	7788949	7789026	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	CDS	7789027	7789261	0.97	-	0	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	exon	7789027	7789261	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	intron	7789262	7789363	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	CDS	7789364	7789867	0.94	-	0	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	exon	7789364	7789867	.	-	.	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
Phchi.S4	AUGUSTUS	start_codon	7789865	7789867	.	-	0	transcript_id "Phchi.S4G129200.t1"; gene_id "Phchi.S4G129200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8292.t1 is derived from g5467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35117000	35118721	.	+	.	Phchi.S1G545100
Phchi.S1	AUGUSTUS	transcript	35117000	35118721	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	start_codon	35117000	35117002	.	+	0	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	CDS	35117000	35117812	0.45	+	0	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	exon	35117000	35117812	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	intron	35117813	35117897	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	CDS	35117898	35118098	0.83	+	0	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	exon	35117898	35118098	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	intron	35118099	35118225	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	CDS	35118226	35118421	0.85	+	0	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	exon	35118226	35118421	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	intron	35118422	35118524	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	CDS	35118525	35118721	0.57	+	2	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	exon	35118525	35118721	.	+	.	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
Phchi.S1	AUGUSTUS	stop_codon	35118722	35118724	.	+	0	transcript_id "Phchi.S1G545100.t1"; gene_id "Phchi.S1G545100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12627.t1 is derived from g8304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37649085	37650409	.	-	.	Phchi.S2G070700
Phchi.S2	AUGUSTUS	transcript	37649085	37650409	.	-	.	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	stop_codon	37649082	37649084	.	-	0	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	CDS	37649085	37649879	0.96	-	0	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	exon	37649085	37649879	.	-	.	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	intron	37649880	37649956	.	-	.	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	CDS	37649957	37650409	0.45	-	0	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	exon	37649957	37650409	.	-	.	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
Phchi.S2	AUGUSTUS	start_codon	37650407	37650409	.	-	0	transcript_id "Phchi.S2G070700.t1"; gene_id "Phchi.S2G070700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5835.t1 is derived from g3005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19192994	19195141	.	+	.	Phchi.S1G299400
Phchi.S1	AUGUSTUS	transcript	19192994	19195141	.	+	.	transcript_id "Phchi.S1G299400.t1"; gene_id "Phchi.S1G299400"
Phchi.S1	AUGUSTUS	start_codon	19192994	19192996	.	+	0	transcript_id "Phchi.S1G299400.t1"; gene_id "Phchi.S1G299400"
Phchi.S1	AUGUSTUS	CDS	19192994	19195141	0.92	+	0	transcript_id "Phchi.S1G299400.t1"; gene_id "Phchi.S1G299400"
Phchi.S1	AUGUSTUS	exon	19192994	19195141	.	+	.	transcript_id "Phchi.S1G299400.t1"; gene_id "Phchi.S1G299400"
Phchi.S1	AUGUSTUS	stop_codon	19195142	19195144	.	+	0	transcript_id "Phchi.S1G299400.t1"; gene_id "Phchi.S1G299400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10745.t1 is derived from g14795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1895694	1897669	.	-	.	Phchi.S4G032700
Phchi.S4	AUGUSTUS	transcript	1895694	1897669	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	stop_codon	1895691	1895693	.	-	0	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	CDS	1895694	1895791	0.46	-	2	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	exon	1895694	1895791	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	intron	1895792	1895891	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	CDS	1895892	1896463	0.95	-	1	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	exon	1895892	1896463	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	intron	1896464	1896619	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	CDS	1896620	1896791	0.78	-	2	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	exon	1896620	1896791	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	intron	1896792	1896885	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	CDS	1896886	1897006	0.49	-	0	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	exon	1896886	1897006	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	intron	1897007	1897122	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	CDS	1897123	1897225	0.56	-	1	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	exon	1897123	1897225	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	intron	1897226	1897358	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	CDS	1897359	1897669	0.97	-	0	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	exon	1897359	1897669	.	-	.	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
Phchi.S4	AUGUSTUS	start_codon	1897667	1897669	.	-	0	transcript_id "Phchi.S4G032700.t1"; gene_id "Phchi.S4G032700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5842.t1 is derived from g3012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19289302	19290485	.	+	.	Phchi.S1G300100
Phchi.S1	AUGUSTUS	transcript	19289302	19290485	.	+	.	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	start_codon	19289302	19289304	.	+	0	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	CDS	19289302	19289657	0.24	+	0	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	exon	19289302	19289657	.	+	.	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	intron	19289658	19290177	.	+	.	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	CDS	19290178	19290302	0.57	+	1	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	exon	19290178	19290302	.	+	.	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	intron	19290303	19290453	.	+	.	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	CDS	19290454	19290485	0.57	+	2	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	exon	19290454	19290485	.	+	.	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
Phchi.S1	AUGUSTUS	stop_codon	19290486	19290488	.	+	0	transcript_id "Phchi.S1G300100.t1"; gene_id "Phchi.S1G300100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2064.t1 is derived from g8984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4668819	4669237	.	+	.	Phchi.S5G067300
Phchi.S5	AUGUSTUS	transcript	4668819	4669237	.	+	.	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	start_codon	4668819	4668821	.	+	0	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	CDS	4668819	4668904	0.39	+	0	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	exon	4668819	4668904	.	+	.	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	intron	4668905	4668987	.	+	.	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	CDS	4668988	4669237	0.9	+	1	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	exon	4668988	4669237	.	+	.	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
Phchi.S5	AUGUSTUS	stop_codon	4669238	4669240	.	+	0	transcript_id "Phchi.S5G067300.t1"; gene_id "Phchi.S5G067300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12476.t1 is derived from g8153.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	27183290	27184067	.	+	.	Phchi.S2G055600
Phchi.S2	AUGUSTUS	transcript	27183290	27184067	.	+	.	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	start_codon	27183290	27183292	.	+	0	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	CDS	27183290	27183412	0.45	+	0	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	exon	27183290	27183412	.	+	.	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	intron	27183413	27183514	.	+	.	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	CDS	27183515	27183800	0.83	+	0	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	exon	27183515	27183800	.	+	.	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	intron	27183801	27183882	.	+	.	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	CDS	27183883	27184067	0.7	+	2	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	exon	27183883	27184067	.	+	.	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
Phchi.S2	AUGUSTUS	stop_codon	27184068	27184070	.	+	0	transcript_id "Phchi.S2G055600.t1"; gene_id "Phchi.S2G055600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6904.t1 is derived from g4076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25908558	25909389	.	-	.	Phchi.S1G406300
Phchi.S1	AUGUSTUS	transcript	25908558	25909389	.	-	.	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	stop_codon	25908555	25908557	.	-	0	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	CDS	25908558	25908953	0.99	-	0	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	exon	25908558	25908953	.	-	.	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	intron	25908954	25909173	.	-	.	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	CDS	25909174	25909389	0.99	-	0	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	exon	25909174	25909389	.	-	.	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
Phchi.S1	AUGUSTUS	start_codon	25909387	25909389	.	-	0	transcript_id "Phchi.S1G406300.t1"; gene_id "Phchi.S1G406300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5560.t1 is derived from g2730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17596507	17597609	.	-	.	Phchi.S1G271900
Phchi.S1	AUGUSTUS	transcript	17596507	17597609	.	-	.	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	stop_codon	17596504	17596506	.	-	0	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	CDS	17596507	17596594	1	-	1	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	exon	17596507	17596594	.	-	.	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	intron	17596595	17596746	.	-	.	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	CDS	17596747	17596843	0.7	-	2	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	exon	17596747	17596843	.	-	.	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	intron	17596844	17596930	.	-	.	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	CDS	17596931	17597609	0.95	-	0	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	exon	17596931	17597609	.	-	.	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
Phchi.S1	AUGUSTUS	start_codon	17597607	17597609	.	-	0	transcript_id "Phchi.S1G271900.t1"; gene_id "Phchi.S1G271900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6486.t1 is derived from g3658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23228231	23231741	.	+	.	Phchi.S1G364500
Phchi.S1	AUGUSTUS	transcript	23228231	23231741	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	start_codon	23228231	23228233	.	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23228231	23228458	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23228231	23228458	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23228459	23228607	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23228608	23228660	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23228608	23228660	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23228661	23228815	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23228816	23228963	1	+	1	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23228816	23228963	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23228964	23229055	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23229056	23229163	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23229056	23229163	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23229164	23229235	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23229236	23229303	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23229236	23229303	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23229304	23229515	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23229516	23229639	1	+	1	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23229516	23229639	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23229640	23229737	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23229738	23229884	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23229738	23229884	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23229885	23230033	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23230034	23230321	0.99	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23230034	23230321	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23230322	23230503	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23230504	23230788	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23230504	23230788	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23230789	23230909	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23230910	23231086	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23230910	23231086	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	intron	23231087	23231192	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	CDS	23231193	23231741	1	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	exon	23231193	23231741	.	+	.	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
Phchi.S1	AUGUSTUS	stop_codon	23231742	23231744	.	+	0	transcript_id "Phchi.S1G364500.t1"; gene_id "Phchi.S1G364500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14219.t1 is derived from g12686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11562641	11563525	.	-	.	Phchi.S3G153800
Phchi.S3	AUGUSTUS	transcript	11562641	11563525	.	-	.	transcript_id "Phchi.S3G153800.t1"; gene_id "Phchi.S3G153800"
Phchi.S3	AUGUSTUS	stop_codon	11562638	11562640	.	-	0	transcript_id "Phchi.S3G153800.t1"; gene_id "Phchi.S3G153800"
Phchi.S3	AUGUSTUS	CDS	11562641	11563525	0.71	-	0	transcript_id "Phchi.S3G153800.t1"; gene_id "Phchi.S3G153800"
Phchi.S3	AUGUSTUS	exon	11562641	11563525	.	-	.	transcript_id "Phchi.S3G153800.t1"; gene_id "Phchi.S3G153800"
Phchi.S3	AUGUSTUS	start_codon	11563523	11563525	.	-	0	transcript_id "Phchi.S3G153800.t1"; gene_id "Phchi.S3G153800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg26.t1 is derived from g15979.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C121	AUGUSTUS	gene	5760	7178	.	+	.	Phchi.C121G000100
Phchi.C121	AUGUSTUS	transcript	5760	7178	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	start_codon	5760	5762	.	+	0	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	CDS	5760	6116	0.99	+	0	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	exon	5760	6116	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	intron	6117	6273	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	CDS	6274	6436	0.47	+	0	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	exon	6274	6436	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	intron	6437	6606	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	CDS	6607	6860	0.55	+	2	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	exon	6607	6860	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	intron	6861	7106	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	CDS	7107	7178	1	+	0	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	exon	7107	7178	.	+	.	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
Phchi.C121	AUGUSTUS	stop_codon	7179	7181	.	+	0	transcript_id "Phchi.C121G000100.t1"; gene_id "Phchi.C121G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5088.t1 is derived from g2258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14682295	14684943	.	+	.	Phchi.S1G224700
Phchi.S1	AUGUSTUS	transcript	14682295	14684943	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	start_codon	14682295	14682297	.	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14682295	14682336	0.36	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14682295	14682336	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14682337	14682412	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14682413	14682644	0.88	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14682413	14682644	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14682645	14682814	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14682815	14683056	0.98	+	2	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14682815	14683056	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14683057	14683143	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14683144	14683235	0.7	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14683144	14683235	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14683236	14683364	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14683365	14683601	1	+	1	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14683365	14683601	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14683602	14683825	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14683826	14684036	1	+	1	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14683826	14684036	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14684037	14684118	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14684119	14684200	1	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14684119	14684200	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14684201	14684300	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14684301	14684470	1	+	2	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14684301	14684470	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14684471	14684565	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14684566	14684710	1	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14684566	14684710	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	intron	14684711	14684806	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	CDS	14684807	14684943	1	+	2	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	exon	14684807	14684943	.	+	.	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
Phchi.S1	AUGUSTUS	stop_codon	14684944	14684946	.	+	0	transcript_id "Phchi.S1G224700.t1"; gene_id "Phchi.S1G224700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11747.t1 is derived from g15799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7985860	7987403	.	-	.	Phchi.S4G132900
Phchi.S4	AUGUSTUS	transcript	7985860	7987403	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	stop_codon	7985857	7985859	.	-	0	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	CDS	7985860	7985959	1	-	1	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	exon	7985860	7985959	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	intron	7985960	7986030	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	CDS	7986031	7986258	1	-	1	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	exon	7986031	7986258	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	intron	7986259	7986336	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	CDS	7986337	7986425	1	-	0	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	exon	7986337	7986425	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	intron	7986426	7986499	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	CDS	7986500	7986951	0.74	-	2	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	exon	7986500	7986951	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	intron	7986952	7987062	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	CDS	7987063	7987202	0.72	-	1	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	exon	7987063	7987202	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	intron	7987203	7987275	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	CDS	7987276	7987403	0.98	-	0	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	exon	7987276	7987403	.	-	.	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
Phchi.S4	AUGUSTUS	start_codon	7987401	7987403	.	-	0	transcript_id "Phchi.S4G132900.t1"; gene_id "Phchi.S4G132900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15326.t1 is derived from g13794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18400560	18401142	.	+	.	Phchi.S3G264500
Phchi.S3	AUGUSTUS	transcript	18400560	18401142	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	start_codon	18400560	18400562	.	+	0	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	CDS	18400560	18400580	0.85	+	0	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	exon	18400560	18400580	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	intron	18400581	18400696	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	CDS	18400697	18400789	0.99	+	0	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	exon	18400697	18400789	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	intron	18400790	18400893	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	CDS	18400894	18401007	0.99	+	0	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	exon	18400894	18401007	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	intron	18401008	18401091	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	CDS	18401092	18401142	1	+	0	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	exon	18401092	18401142	.	+	.	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
Phchi.S3	AUGUSTUS	stop_codon	18401143	18401145	.	+	0	transcript_id "Phchi.S3G264500.t1"; gene_id "Phchi.S3G264500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4192.t1 is derived from g1361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8856333	8858738	.	+	.	Phchi.S1G135100
Phchi.S1	AUGUSTUS	transcript	8856333	8858738	.	+	.	transcript_id "Phchi.S1G135100.t1"; gene_id "Phchi.S1G135100"
Phchi.S1	AUGUSTUS	start_codon	8856333	8856335	.	+	0	transcript_id "Phchi.S1G135100.t1"; gene_id "Phchi.S1G135100"
Phchi.S1	AUGUSTUS	CDS	8856333	8858738	1	+	0	transcript_id "Phchi.S1G135100.t1"; gene_id "Phchi.S1G135100"
Phchi.S1	AUGUSTUS	exon	8856333	8858738	.	+	.	transcript_id "Phchi.S1G135100.t1"; gene_id "Phchi.S1G135100"
Phchi.S1	AUGUSTUS	stop_codon	8858739	8858741	.	+	0	transcript_id "Phchi.S1G135100.t1"; gene_id "Phchi.S1G135100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14643.t1 is derived from g13111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13904343	13906965	.	+	.	Phchi.S3G196200
Phchi.S3	AUGUSTUS	transcript	13904343	13906965	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	start_codon	13904343	13904345	.	+	0	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13904343	13904622	0.9	+	0	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13904343	13904622	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13904623	13904740	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13904741	13904925	1	+	2	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13904741	13904925	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13904926	13905124	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13905125	13905549	0.92	+	0	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13905125	13905549	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13905550	13905701	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13905702	13905789	1	+	1	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13905702	13905789	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13905790	13905905	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13905906	13906209	0.97	+	0	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13905906	13906209	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13906210	13906376	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13906377	13906465	0.96	+	2	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13906377	13906465	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13906466	13906650	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13906651	13906673	0.96	+	0	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13906651	13906673	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	intron	13906674	13906958	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	CDS	13906959	13906965	0.95	+	1	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	exon	13906959	13906965	.	+	.	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
Phchi.S3	AUGUSTUS	stop_codon	13906966	13906968	.	+	0	transcript_id "Phchi.S3G196200.t1"; gene_id "Phchi.S3G196200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6623.t1 is derived from g3795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24121369	24124752	.	+	.	Phchi.S1G378200
Phchi.S1	AUGUSTUS	transcript	24121369	24124752	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	start_codon	24121369	24121371	.	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24121369	24121386	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24121369	24121386	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24121387	24121468	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24121469	24121565	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24121469	24121565	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24121566	24121649	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24121650	24121761	1	+	2	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24121650	24121761	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24121762	24121939	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24121940	24122084	1	+	1	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24121940	24122084	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24122085	24122255	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24122256	24122333	0.99	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24122256	24122333	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24122334	24122435	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24122436	24122468	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24122436	24122468	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24122469	24122566	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24122567	24122627	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24122567	24122627	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24122628	24122801	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24122802	24122926	1	+	2	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24122802	24122926	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24122927	24123016	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24123017	24123102	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24123017	24123102	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24123103	24123179	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24123180	24123381	1	+	1	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24123180	24123381	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24123382	24123509	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24123510	24123566	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24123510	24123566	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24123567	24123692	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24123693	24123803	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24123693	24123803	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24123804	24123893	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24123894	24123950	1	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24123894	24123950	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24123951	24124041	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24124042	24124243	0.95	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24124042	24124243	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24124244	24124332	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24124333	24124337	0.98	+	2	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24124333	24124337	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	intron	24124338	24124746	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	CDS	24124747	24124752	0.98	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	exon	24124747	24124752	.	+	.	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
Phchi.S1	AUGUSTUS	stop_codon	24124753	24124755	.	+	0	transcript_id "Phchi.S1G378200.t1"; gene_id "Phchi.S1G378200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8715.t1 is derived from g5890.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37621558	37622717	.	+	.	Phchi.S1G587400
Phchi.S1	AUGUSTUS	transcript	37621558	37622717	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	start_codon	37621558	37621560	.	+	0	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	CDS	37621558	37621647	1	+	0	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	exon	37621558	37621647	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	intron	37621648	37621726	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	CDS	37621727	37621772	1	+	0	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	exon	37621727	37621772	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	intron	37621773	37621942	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	CDS	37621943	37622072	1	+	2	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	exon	37621943	37622072	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	intron	37622073	37622167	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	CDS	37622168	37622232	1	+	1	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	exon	37622168	37622232	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	intron	37622233	37622445	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	CDS	37622446	37622549	1	+	2	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	exon	37622446	37622549	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	intron	37622550	37622684	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	CDS	37622685	37622717	1	+	0	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	exon	37622685	37622717	.	+	.	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
Phchi.S1	AUGUSTUS	stop_codon	37622718	37622720	.	+	0	transcript_id "Phchi.S1G587400.t1"; gene_id "Phchi.S1G587400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11677.t1 is derived from g15728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7637262	7637839	.	-	.	Phchi.S4G125900
Phchi.S4	AUGUSTUS	transcript	7637262	7637839	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	stop_codon	7637259	7637261	.	-	0	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	CDS	7637262	7637312	1	-	0	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	exon	7637262	7637312	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	intron	7637313	7637393	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	CDS	7637394	7637471	1	-	0	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	exon	7637394	7637471	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	intron	7637472	7637553	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	CDS	7637554	7637709	1	-	0	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	exon	7637554	7637709	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	intron	7637710	7637785	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	CDS	7637786	7637839	0.9	-	0	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	exon	7637786	7637839	.	-	.	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
Phchi.S4	AUGUSTUS	start_codon	7637837	7637839	.	-	0	transcript_id "Phchi.S4G125900.t1"; gene_id "Phchi.S4G125900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9674.t1 is derived from g6850.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43228127	43231718	.	-	.	Phchi.S1G683300
Phchi.S1	AUGUSTUS	transcript	43228127	43231718	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	stop_codon	43228124	43228126	.	-	0	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43228127	43228152	1	-	2	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43228127	43228152	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43228153	43228245	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43228246	43230136	1	-	0	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43228246	43230136	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43230137	43230229	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43230230	43230369	1	-	2	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43230230	43230369	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43230370	43230515	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43230516	43230839	1	-	2	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43230516	43230839	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43230840	43231037	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43231038	43231122	1	-	0	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43231038	43231122	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43231123	43231240	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43231241	43231479	1	-	2	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43231241	43231479	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43231480	43231633	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43231634	43231718	1	-	0	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43231634	43231718	.	-	.	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	start_codon	43231716	43231718	.	-	0	transcript_id "Phchi.S1G683300.t1"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	transcript	43228127	43231718	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	stop_codon	43228124	43228126	.	-	0	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43228127	43228152	1	-	2	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43228127	43228152	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43228153	43228245	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43228246	43230136	1	-	0	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43228246	43230136	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43230137	43230229	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43230230	43230369	1	-	2	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43230230	43230369	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43230370	43230515	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43230516	43230731	1	-	2	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43230516	43230731	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43230732	43231037	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43231038	43231122	1	-	0	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43231038	43231122	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43231123	43231240	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43231241	43231479	1	-	2	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43231241	43231479	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	intron	43231480	43231633	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	CDS	43231634	43231718	1	-	0	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	exon	43231634	43231718	.	-	.	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
Phchi.S1	AUGUSTUS	start_codon	43231716	43231718	.	-	0	transcript_id "Phchi.S1G683300.t2"; gene_id "Phchi.S1G683300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5006.t1 is derived from g2176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13971679	13974296	.	-	.	Phchi.S1G216500
Phchi.S1	AUGUSTUS	transcript	13971679	13974296	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	stop_codon	13971676	13971678	.	-	0	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13971679	13971786	0.99	-	0	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13971679	13971786	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13971787	13971863	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13971864	13972081	1	-	2	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13971864	13972081	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13972082	13972176	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13972177	13972320	1	-	2	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13972177	13972320	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13972321	13972417	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13972418	13972514	1	-	0	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13972418	13972514	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13972515	13972642	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13972643	13972737	1	-	2	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13972643	13972737	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13972738	13972812	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13972813	13972904	1	-	1	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13972813	13972904	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13972905	13973048	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13973049	13973194	1	-	0	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13973049	13973194	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13973195	13973389	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13973390	13973489	1	-	1	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13973390	13973489	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13973490	13973630	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13973631	13973735	1	-	1	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13973631	13973735	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13973736	13973921	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13973922	13973958	1	-	2	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13973922	13973958	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	intron	13973959	13974187	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	CDS	13974188	13974296	0.99	-	0	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	exon	13974188	13974296	.	-	.	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
Phchi.S1	AUGUSTUS	start_codon	13974294	13974296	.	-	0	transcript_id "Phchi.S1G216500.t1"; gene_id "Phchi.S1G216500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6430.t1 is derived from g3602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22994495	22995236	.	+	.	Phchi.S1G358900
Phchi.S1	AUGUSTUS	transcript	22994495	22995236	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	start_codon	22994495	22994497	.	+	0	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	CDS	22994495	22994657	0.65	+	0	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	exon	22994495	22994657	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	intron	22994658	22994747	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	CDS	22994748	22994854	0.94	+	2	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	exon	22994748	22994854	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	intron	22994855	22994950	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	CDS	22994951	22995061	0.99	+	0	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	exon	22994951	22995061	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	intron	22995062	22995176	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	CDS	22995177	22995236	0.95	+	0	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	exon	22995177	22995236	.	+	.	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
Phchi.S1	AUGUSTUS	stop_codon	22995237	22995239	.	+	0	transcript_id "Phchi.S1G358900.t1"; gene_id "Phchi.S1G358900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12330.t1 is derived from g8006.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10990763	10994841	.	-	.	Phchi.S2G041000
Phchi.S2	AUGUSTUS	transcript	10990763	10994841	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	stop_codon	10990760	10990762	.	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10990763	10991082	0.89	-	2	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10990763	10991082	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10991083	10991172	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10991173	10991231	0.84	-	1	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10991173	10991231	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10991232	10991323	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10991324	10991403	0.93	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10991324	10991403	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10991404	10991487	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10991488	10991574	0.67	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10991488	10991574	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10991575	10991641	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10991642	10991749	0.44	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10991642	10991749	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10991750	10991837	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10991838	10991951	0.52	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10991838	10991951	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10991952	10992176	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10992177	10992224	0.93	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10992177	10992224	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10992225	10992319	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10992320	10992382	0.27	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10992320	10992382	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10992383	10992502	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10992503	10992640	0.97	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10992503	10992640	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10992641	10992784	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10992785	10993326	0.69	-	2	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10992785	10993326	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	intron	10993327	10993424	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10993425	10994841	0.58	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10993425	10994841	.	-	.	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	start_codon	10994839	10994841	.	-	0	transcript_id "Phchi.S2G041000.t1"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	transcript	10993351	10994841	.	-	.	transcript_id "Phchi.S2G041000.t2"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	stop_codon	10993348	10993350	.	-	0	transcript_id "Phchi.S2G041000.t2"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	CDS	10993351	10994841	0.99	-	0	transcript_id "Phchi.S2G041000.t2"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	exon	10993351	10994841	.	-	.	transcript_id "Phchi.S2G041000.t2"; gene_id "Phchi.S2G041000"
Phchi.S2	AUGUSTUS	start_codon	10994839	10994841	.	-	0	transcript_id "Phchi.S2G041000.t2"; gene_id "Phchi.S2G041000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4141.t1 is derived from g1310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8477996	8479012	.	-	.	Phchi.S1G130000
Phchi.S1	AUGUSTUS	transcript	8477996	8479012	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	stop_codon	8477993	8477995	.	-	0	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	CDS	8477996	8478163	0.98	-	0	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	exon	8477996	8478163	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	intron	8478164	8478265	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	CDS	8478266	8478356	1	-	1	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	exon	8478266	8478356	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	intron	8478357	8478445	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	CDS	8478446	8478599	0.98	-	2	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	exon	8478446	8478599	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	intron	8478600	8478735	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	CDS	8478736	8478744	0.98	-	2	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	exon	8478736	8478744	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	intron	8478745	8478978	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	CDS	8478979	8479012	0.92	-	0	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	exon	8478979	8479012	.	-	.	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
Phchi.S1	AUGUSTUS	start_codon	8479010	8479012	.	-	0	transcript_id "Phchi.S1G130000.t1"; gene_id "Phchi.S1G130000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2486.t1 is derived from g9406.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6914773	6916162	.	-	.	Phchi.S5G109500
Phchi.S5	AUGUSTUS	transcript	6914773	6916162	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	stop_codon	6914770	6914772	.	-	0	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	CDS	6914773	6914922	0.9	-	0	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	exon	6914773	6914922	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	intron	6914923	6915017	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	CDS	6915018	6915188	1	-	0	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	exon	6915018	6915188	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	intron	6915189	6915290	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	CDS	6915291	6915399	0.82	-	1	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	exon	6915291	6915399	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	intron	6915400	6915495	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	CDS	6915496	6915602	1	-	0	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	exon	6915496	6915602	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	intron	6915603	6915705	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	CDS	6915706	6915926	0.43	-	2	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	exon	6915706	6915926	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	intron	6915927	6916077	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	CDS	6916078	6916162	1	-	0	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	exon	6916078	6916162	.	-	.	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
Phchi.S5	AUGUSTUS	start_codon	6916160	6916162	.	-	0	transcript_id "Phchi.S5G109500.t1"; gene_id "Phchi.S5G109500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13720.t1 is derived from g12187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8503345	8505143	.	-	.	Phchi.S3G103900
Phchi.S3	AUGUSTUS	transcript	8503345	8505143	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	stop_codon	8503342	8503344	.	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8503345	8503404	1	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8503345	8503404	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8503405	8503490	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8503491	8503583	1	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8503491	8503583	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8503584	8503702	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8503703	8503803	1	-	2	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8503703	8503803	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8503804	8503926	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8503927	8503987	1	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8503927	8503987	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8503988	8504122	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8504123	8504142	1	-	2	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8504123	8504142	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8504143	8504279	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8504280	8504361	1	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8504280	8504361	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8504362	8504455	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8504456	8504554	1	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8504456	8504554	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	intron	8504555	8504708	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	CDS	8504709	8505143	1	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	exon	8504709	8505143	.	-	.	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
Phchi.S3	AUGUSTUS	start_codon	8505141	8505143	.	-	0	transcript_id "Phchi.S3G103900.t1"; gene_id "Phchi.S3G103900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6470.t1 is derived from g3642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23161735	23163105	.	-	.	Phchi.S1G362900
Phchi.S1	AUGUSTUS	transcript	23161735	23163105	.	-	.	transcript_id "Phchi.S1G362900.t1"; gene_id "Phchi.S1G362900"
Phchi.S1	AUGUSTUS	stop_codon	23161732	23161734	.	-	0	transcript_id "Phchi.S1G362900.t1"; gene_id "Phchi.S1G362900"
Phchi.S1	AUGUSTUS	CDS	23161735	23163105	1	-	0	transcript_id "Phchi.S1G362900.t1"; gene_id "Phchi.S1G362900"
Phchi.S1	AUGUSTUS	exon	23161735	23163105	.	-	.	transcript_id "Phchi.S1G362900.t1"; gene_id "Phchi.S1G362900"
Phchi.S1	AUGUSTUS	start_codon	23163103	23163105	.	-	0	transcript_id "Phchi.S1G362900.t1"; gene_id "Phchi.S1G362900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9513.t1 is derived from g6689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42164856	42165744	.	-	.	Phchi.S1G667200
Phchi.S1	AUGUSTUS	transcript	42164856	42165744	.	-	.	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	stop_codon	42164853	42164855	.	-	0	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	CDS	42164856	42165025	1	-	2	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	exon	42164856	42165025	.	-	.	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	intron	42165026	42165180	.	-	.	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	CDS	42165181	42165378	1	-	2	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	exon	42165181	42165378	.	-	.	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	intron	42165379	42165512	.	-	.	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	CDS	42165513	42165744	0.93	-	0	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	exon	42165513	42165744	.	-	.	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
Phchi.S1	AUGUSTUS	start_codon	42165742	42165744	.	-	0	transcript_id "Phchi.S1G667200.t1"; gene_id "Phchi.S1G667200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8263.t1 is derived from g5438.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35002776	35005284	.	+	.	Phchi.S1G542200
Phchi.S1	AUGUSTUS	transcript	35002776	35005284	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	start_codon	35002776	35002778	.	+	0	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35002776	35003423	1	+	0	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35002776	35003423	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35003424	35003584	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35003585	35003710	0.52	+	0	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35003585	35003710	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35003711	35003811	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35003812	35003899	1	+	0	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35003812	35003899	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35003900	35003998	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35003999	35004113	0.98	+	2	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35003999	35004113	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35004114	35004214	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35004215	35004330	1	+	1	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35004215	35004330	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35004331	35004419	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35004420	35004526	0.94	+	2	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35004420	35004526	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35004527	35004640	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35004641	35004717	0.99	+	0	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35004641	35004717	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35004718	35004814	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35004815	35004889	1	+	1	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35004815	35004889	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35004890	35004973	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35004974	35005036	1	+	1	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35004974	35005036	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	intron	35005037	35005127	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	CDS	35005128	35005284	0.94	+	1	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	exon	35005128	35005284	.	+	.	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
Phchi.S1	AUGUSTUS	stop_codon	35005285	35005287	.	+	0	transcript_id "Phchi.S1G542200.t1"; gene_id "Phchi.S1G542200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15589.t1 is derived from g14058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20151259	20153603	.	-	.	Phchi.S3G290800
Phchi.S3	AUGUSTUS	transcript	20151259	20153603	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	stop_codon	20151256	20151258	.	-	0	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20151259	20151472	0.26	-	1	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20151259	20151472	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	intron	20151473	20151554	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20151555	20151801	0.99	-	2	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20151555	20151801	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	intron	20151802	20151883	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20151884	20151978	1	-	1	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20151884	20151978	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	intron	20151979	20152133	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20152134	20152245	1	-	2	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20152134	20152245	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	intron	20152246	20152389	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20152390	20152540	1	-	0	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20152390	20152540	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	intron	20152541	20152646	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20152647	20152814	1	-	0	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20152647	20152814	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	intron	20152815	20152925	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	CDS	20152926	20153603	0.94	-	0	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	exon	20152926	20153603	.	-	.	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
Phchi.S3	AUGUSTUS	start_codon	20153601	20153603	.	-	0	transcript_id "Phchi.S3G290800.t1"; gene_id "Phchi.S3G290800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9066.t1 is derived from g6241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39612106	39613542	.	+	.	Phchi.S1G622500
Phchi.S1	AUGUSTUS	transcript	39612106	39613542	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	start_codon	39612106	39612108	.	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39612106	39612285	0.77	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39612106	39612285	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	intron	39612286	39612504	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39612505	39612534	1	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39612505	39612534	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	intron	39612535	39612626	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39612627	39612785	1	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39612627	39612785	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	intron	39612786	39612881	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39612882	39612976	1	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39612882	39612976	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	intron	39612977	39613057	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39613058	39613080	0.96	+	1	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39613058	39613080	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	intron	39613081	39613166	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39613167	39613198	0.96	+	2	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39613167	39613198	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	intron	39613199	39613383	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	CDS	39613384	39613542	0.96	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	exon	39613384	39613542	.	+	.	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
Phchi.S1	AUGUSTUS	stop_codon	39613543	39613545	.	+	0	transcript_id "Phchi.S1G622500.t1"; gene_id "Phchi.S1G622500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3844.t1 is derived from g1013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5995518	5996655	.	+	.	Phchi.S1G100300
Phchi.S1	AUGUSTUS	transcript	5995518	5996655	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	start_codon	5995518	5995520	.	+	0	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	CDS	5995518	5995607	0.45	+	0	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	exon	5995518	5995607	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	intron	5995608	5995696	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	CDS	5995697	5995933	0.64	+	0	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	exon	5995697	5995933	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	intron	5995934	5996064	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	CDS	5996065	5996355	0.71	+	0	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	exon	5996065	5996355	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	intron	5996356	5996481	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	CDS	5996482	5996655	0.72	+	0	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	exon	5996482	5996655	.	+	.	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
Phchi.S1	AUGUSTUS	stop_codon	5996656	5996658	.	+	0	transcript_id "Phchi.S1G100300.t1"; gene_id "Phchi.S1G100300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5499.t1 is derived from g2669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17137975	17138941	.	-	.	Phchi.S1G265800
Phchi.S1	AUGUSTUS	transcript	17137975	17138941	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	stop_codon	17137972	17137974	.	-	0	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	CDS	17137975	17138233	0.54	-	1	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	exon	17137975	17138233	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	intron	17138234	17138325	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	CDS	17138326	17138391	0.62	-	1	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	exon	17138326	17138391	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	intron	17138392	17138519	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	CDS	17138520	17138628	0.95	-	2	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	exon	17138520	17138628	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	intron	17138629	17138769	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	CDS	17138770	17138941	0.85	-	0	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	exon	17138770	17138941	.	-	.	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
Phchi.S1	AUGUSTUS	start_codon	17138939	17138941	.	-	0	transcript_id "Phchi.S1G265800.t1"; gene_id "Phchi.S1G265800"
# This transcript jg3972.t2 is derived from g1141.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3973.t1 is derived from g1142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6810913	6812112	.	+	.	Phchi.S1G113200
Phchi.S1	AUGUSTUS	transcript	6810913	6812112	.	+	.	transcript_id "Phchi.S1G113200.t1"; gene_id "Phchi.S1G113200"
Phchi.S1	AUGUSTUS	start_codon	6810913	6810915	.	+	0	transcript_id "Phchi.S1G113200.t1"; gene_id "Phchi.S1G113200"
Phchi.S1	AUGUSTUS	CDS	6810913	6812112	0.5	+	0	transcript_id "Phchi.S1G113200.t1"; gene_id "Phchi.S1G113200"
Phchi.S1	AUGUSTUS	exon	6810913	6812112	.	+	.	transcript_id "Phchi.S1G113200.t1"; gene_id "Phchi.S1G113200"
Phchi.S1	AUGUSTUS	stop_codon	6812113	6812115	.	+	0	transcript_id "Phchi.S1G113200.t1"; gene_id "Phchi.S1G113200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9515.t1 is derived from g6691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42167312	42170250	.	-	.	Phchi.S1G667400
Phchi.S1	AUGUSTUS	transcript	42167312	42170250	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	stop_codon	42167309	42167311	.	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42167312	42167509	0.91	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42167312	42167509	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42167510	42167617	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42167618	42167768	0.95	-	1	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42167618	42167768	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42167769	42167885	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42167886	42168079	0.99	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42167886	42168079	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42168080	42168199	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42168200	42168361	1	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42168200	42168361	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42168362	42168479	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42168480	42168662	1	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42168480	42168662	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42168663	42168826	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42168827	42168914	1	-	1	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42168827	42168914	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42168915	42169031	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42169032	42169171	1	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42169032	42169171	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42169172	42169259	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42169260	42169553	1	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42169260	42169553	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42169554	42169655	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42169656	42169739	1	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42169656	42169739	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42169740	42169847	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42169848	42169921	1	-	2	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42169848	42169921	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	intron	42169922	42170036	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	CDS	42170037	42170250	0.99	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	exon	42170037	42170250	.	-	.	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
Phchi.S1	AUGUSTUS	start_codon	42170248	42170250	.	-	0	transcript_id "Phchi.S1G667400.t1"; gene_id "Phchi.S1G667400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3467.t1 is derived from g636.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3899960	3901664	.	+	.	Phchi.S1G062600
Phchi.S1	AUGUSTUS	transcript	3899960	3901664	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	start_codon	3899960	3899962	.	+	0	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	CDS	3899960	3900212	0.47	+	0	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	exon	3899960	3900212	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	intron	3900213	3900429	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	CDS	3900430	3900458	0.49	+	2	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	exon	3900430	3900458	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	intron	3900459	3900629	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	CDS	3900630	3901002	0.59	+	0	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	exon	3900630	3901002	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	intron	3901003	3901098	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	CDS	3901099	3901664	0.95	+	2	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	exon	3901099	3901664	.	+	.	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
Phchi.S1	AUGUSTUS	stop_codon	3901665	3901667	.	+	0	transcript_id "Phchi.S1G062600.t1"; gene_id "Phchi.S1G062600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9347.t1 is derived from g6523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41073593	41074174	.	+	.	Phchi.S1G650600
Phchi.S1	AUGUSTUS	transcript	41073593	41074174	.	+	.	transcript_id "Phchi.S1G650600.t1"; gene_id "Phchi.S1G650600"
Phchi.S1	AUGUSTUS	start_codon	41073593	41073595	.	+	0	transcript_id "Phchi.S1G650600.t1"; gene_id "Phchi.S1G650600"
Phchi.S1	AUGUSTUS	CDS	41073593	41074174	1	+	0	transcript_id "Phchi.S1G650600.t1"; gene_id "Phchi.S1G650600"
Phchi.S1	AUGUSTUS	exon	41073593	41074174	.	+	.	transcript_id "Phchi.S1G650600.t1"; gene_id "Phchi.S1G650600"
Phchi.S1	AUGUSTUS	stop_codon	41074175	41074177	.	+	0	transcript_id "Phchi.S1G650600.t1"; gene_id "Phchi.S1G650600"
# This transcript jg4661.t2 is derived from g1831.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4661.t3 is derived from g1831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4662.t1 is derived from g1832.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11682815	11684778	.	+	.	Phchi.S1G182100
Phchi.S1	AUGUSTUS	transcript	11682815	11684558	.	+	.	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	start_codon	11682815	11682817	.	+	0	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	CDS	11682815	11683330	0.37	+	0	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	exon	11682815	11683330	.	+	.	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	intron	11683331	11683449	.	+	.	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	CDS	11683450	11684204	0.54	+	0	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	exon	11683450	11684204	.	+	.	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	intron	11684205	11684326	.	+	.	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	CDS	11684327	11684558	1	+	1	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	exon	11684327	11684558	.	+	.	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	stop_codon	11684559	11684561	.	+	0	transcript_id "Phchi.S1G182100.t1"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	transcript	11682815	11684778	.	+	.	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	start_codon	11682815	11682817	.	+	0	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	CDS	11682815	11683330	0.21	+	0	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	exon	11682815	11683330	.	+	.	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	intron	11683331	11683449	.	+	.	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	CDS	11683450	11684778	0.45	+	0	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	exon	11683450	11684778	.	+	.	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
Phchi.S1	AUGUSTUS	stop_codon	11684779	11684781	.	+	0	transcript_id "Phchi.S1G182100.t2"; gene_id "Phchi.S1G182100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15175.t1 is derived from g13643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17366517	17370644	.	+	.	Phchi.S3G249400
Phchi.S3	AUGUSTUS	transcript	17366517	17370644	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	start_codon	17366517	17366519	.	+	0	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	CDS	17366517	17366579	0.99	+	0	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	exon	17366517	17366579	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	intron	17366580	17366655	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	CDS	17366656	17366831	0.97	+	0	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	exon	17366656	17366831	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	intron	17366832	17366974	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	CDS	17366975	17367822	0.44	+	1	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	exon	17366975	17367822	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	intron	17367823	17368077	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	CDS	17368078	17368838	0.5	+	2	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	exon	17368078	17368838	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	intron	17368839	17369069	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	CDS	17369070	17369189	0.3	+	0	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	exon	17369070	17369189	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	intron	17369190	17369414	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	CDS	17369415	17370644	0.57	+	0	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	exon	17369415	17370644	.	+	.	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
Phchi.S3	AUGUSTUS	stop_codon	17370645	17370647	.	+	0	transcript_id "Phchi.S3G249400.t1"; gene_id "Phchi.S3G249400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4412.t1 is derived from g1581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10272829	10278069	.	-	.	Phchi.S1G157100
Phchi.S1	AUGUSTUS	transcript	10272829	10278069	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	stop_codon	10272826	10272828	.	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10272829	10272852	0.98	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10272829	10272852	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10272853	10272931	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10272932	10273102	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10272932	10273102	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10273103	10273189	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10273190	10273279	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10273190	10273279	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10273280	10273513	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10273514	10273625	1	-	1	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10273514	10273625	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10273626	10273801	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10273802	10273870	1	-	1	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10273802	10273870	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10273871	10273970	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10273971	10274026	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10273971	10274026	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10274027	10274119	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10274120	10274387	0.89	-	1	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10274120	10274387	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10274388	10274468	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10274469	10274517	1	-	2	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10274469	10274517	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10274518	10274636	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10274637	10274709	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10274637	10274709	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10274710	10274804	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10274805	10275086	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10274805	10275086	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10275087	10275503	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10275504	10275645	1	-	1	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10275504	10275645	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10275646	10275727	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10275728	10275918	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10275728	10275918	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10275919	10276003	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10276004	10276285	1	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10276004	10276285	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10276286	10276410	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10276411	10277561	0.99	-	2	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10276411	10277561	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	intron	10277562	10277750	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	CDS	10277751	10278069	0.99	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	exon	10277751	10278069	.	-	.	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
Phchi.S1	AUGUSTUS	start_codon	10278067	10278069	.	-	0	transcript_id "Phchi.S1G157100.t1"; gene_id "Phchi.S1G157100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11134.t1 is derived from g15184.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4347384	4349451	.	+	.	Phchi.S4G071600
Phchi.S4	AUGUSTUS	transcript	4347384	4349451	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	start_codon	4347384	4347386	.	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347384	4347460	0.95	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347384	4347460	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347461	4347587	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347588	4347655	0.93	+	1	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347588	4347655	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347656	4347723	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347724	4347821	1	+	2	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347724	4347821	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347822	4347902	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347903	4347992	0.96	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347903	4347992	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347993	4348104	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348105	4348192	1	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348105	4348192	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348193	4348314	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348315	4348406	1	+	2	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348315	4348406	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348407	4348523	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348524	4348628	1	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348524	4348628	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348629	4348824	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348825	4348934	1	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348825	4348934	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348935	4349030	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4349031	4349118	1	+	1	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4349031	4349118	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4349119	4349203	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4349204	4349239	1	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4349204	4349239	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4349240	4349376	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4349377	4349451	1	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4349377	4349451	.	+	.	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	stop_codon	4349452	4349454	.	+	0	transcript_id "Phchi.S4G071600.t1"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	transcript	4347384	4349451	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	start_codon	4347384	4347386	.	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347384	4347460	0.93	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347384	4347460	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347461	4347587	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347588	4347655	0.92	+	1	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347588	4347655	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347656	4347735	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347736	4347821	1	+	2	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347736	4347821	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347822	4347902	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4347903	4347992	0.98	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4347903	4347992	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4347993	4348104	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348105	4348192	0.99	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348105	4348192	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348193	4348314	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348315	4348406	0.99	+	2	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348315	4348406	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348407	4348523	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348524	4348628	1	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348524	4348628	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348629	4348824	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4348825	4348934	1	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4348825	4348934	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4348935	4349030	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4349031	4349118	1	+	1	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4349031	4349118	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4349119	4349203	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4349204	4349239	1	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4349204	4349239	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	intron	4349240	4349376	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	CDS	4349377	4349451	1	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	exon	4349377	4349451	.	+	.	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
Phchi.S4	AUGUSTUS	stop_codon	4349452	4349454	.	+	0	transcript_id "Phchi.S4G071600.t2"; gene_id "Phchi.S4G071600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5435.t1 is derived from g2605.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16852214	16853497	.	+	.	Phchi.S1G259400
Phchi.S1	AUGUSTUS	transcript	16852214	16853497	.	+	.	transcript_id "Phchi.S1G259400.t1"; gene_id "Phchi.S1G259400"
Phchi.S1	AUGUSTUS	start_codon	16852214	16852216	.	+	0	transcript_id "Phchi.S1G259400.t1"; gene_id "Phchi.S1G259400"
Phchi.S1	AUGUSTUS	CDS	16852214	16853497	0.5	+	0	transcript_id "Phchi.S1G259400.t1"; gene_id "Phchi.S1G259400"
Phchi.S1	AUGUSTUS	exon	16852214	16853497	.	+	.	transcript_id "Phchi.S1G259400.t1"; gene_id "Phchi.S1G259400"
Phchi.S1	AUGUSTUS	stop_codon	16853498	16853500	.	+	0	transcript_id "Phchi.S1G259400.t1"; gene_id "Phchi.S1G259400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8337.t1 is derived from g5512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35383749	35385185	.	+	.	Phchi.S1G549600
Phchi.S1	AUGUSTUS	transcript	35383749	35385185	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	start_codon	35383749	35383751	.	+	0	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	CDS	35383749	35384189	0.96	+	0	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	exon	35383749	35384189	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	intron	35384190	35384316	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	CDS	35384317	35384408	1	+	0	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	exon	35384317	35384408	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	intron	35384409	35384506	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	CDS	35384507	35384828	1	+	1	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	exon	35384507	35384828	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	intron	35384829	35384933	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	CDS	35384934	35385185	1	+	0	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	exon	35384934	35385185	.	+	.	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
Phchi.S1	AUGUSTUS	stop_codon	35385186	35385188	.	+	0	transcript_id "Phchi.S1G549600.t1"; gene_id "Phchi.S1G549600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5702.t1 is derived from g2872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18431358	18433597	.	-	.	Phchi.S1G286100
Phchi.S1	AUGUSTUS	transcript	18431358	18433597	.	-	.	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	stop_codon	18431355	18431357	.	-	0	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	CDS	18431358	18432218	0.43	-	0	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	exon	18431358	18432218	.	-	.	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	intron	18432219	18432350	.	-	.	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	CDS	18432351	18432500	0.97	-	0	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	exon	18432351	18432500	.	-	.	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	intron	18432501	18432616	.	-	.	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	CDS	18432617	18433597	0.5	-	0	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	exon	18432617	18433597	.	-	.	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
Phchi.S1	AUGUSTUS	start_codon	18433595	18433597	.	-	0	transcript_id "Phchi.S1G286100.t1"; gene_id "Phchi.S1G286100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7919.t1 is derived from g5093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31910035	31911135	.	+	.	Phchi.S1G507800
Phchi.S1	AUGUSTUS	transcript	31910035	31911135	.	+	.	transcript_id "Phchi.S1G507800.t1"; gene_id "Phchi.S1G507800"
Phchi.S1	AUGUSTUS	start_codon	31910035	31910037	.	+	0	transcript_id "Phchi.S1G507800.t1"; gene_id "Phchi.S1G507800"
Phchi.S1	AUGUSTUS	CDS	31910035	31911135	0.66	+	0	transcript_id "Phchi.S1G507800.t1"; gene_id "Phchi.S1G507800"
Phchi.S1	AUGUSTUS	exon	31910035	31911135	.	+	.	transcript_id "Phchi.S1G507800.t1"; gene_id "Phchi.S1G507800"
Phchi.S1	AUGUSTUS	stop_codon	31911136	31911138	.	+	0	transcript_id "Phchi.S1G507800.t1"; gene_id "Phchi.S1G507800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14923.t1 is derived from g13391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15536374	15541500	.	-	.	Phchi.S3G224200
Phchi.S3	AUGUSTUS	transcript	15536374	15541500	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	stop_codon	15536371	15536373	.	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	CDS	15536374	15537688	0.61	-	1	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	exon	15536374	15537688	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	intron	15537689	15537858	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	CDS	15537859	15538034	0.84	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	exon	15537859	15538034	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	intron	15538035	15538115	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	CDS	15538116	15538175	1	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	exon	15538116	15538175	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	intron	15538176	15538308	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	CDS	15538309	15538407	1	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	exon	15538309	15538407	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	intron	15538408	15538515	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	CDS	15538516	15538635	1	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	exon	15538516	15538635	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	intron	15538636	15538728	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	CDS	15538729	15541500	1	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	exon	15538729	15541500	.	-	.	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
Phchi.S3	AUGUSTUS	start_codon	15541498	15541500	.	-	0	transcript_id "Phchi.S3G224200.t1"; gene_id "Phchi.S3G224200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9318.t1 is derived from g6493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40928929	40929441	.	-	.	Phchi.S1G647700
Phchi.S1	AUGUSTUS	transcript	40928929	40929441	.	-	.	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	stop_codon	40928926	40928928	.	-	0	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	CDS	40928929	40929166	0.96	-	1	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	exon	40928929	40929166	.	-	.	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	intron	40929167	40929289	.	-	.	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	CDS	40929290	40929441	0.96	-	0	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	exon	40929290	40929441	.	-	.	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
Phchi.S1	AUGUSTUS	start_codon	40929439	40929441	.	-	0	transcript_id "Phchi.S1G647700.t1"; gene_id "Phchi.S1G647700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11531.t1 is derived from g15581.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6939138	6940490	.	-	.	Phchi.S4G111300
Phchi.S4	AUGUSTUS	transcript	6939138	6940490	.	-	.	transcript_id "Phchi.S4G111300.t1"; gene_id "Phchi.S4G111300"
Phchi.S4	AUGUSTUS	stop_codon	6939135	6939137	.	-	0	transcript_id "Phchi.S4G111300.t1"; gene_id "Phchi.S4G111300"
Phchi.S4	AUGUSTUS	CDS	6939138	6940490	0.97	-	0	transcript_id "Phchi.S4G111300.t1"; gene_id "Phchi.S4G111300"
Phchi.S4	AUGUSTUS	exon	6939138	6940490	.	-	.	transcript_id "Phchi.S4G111300.t1"; gene_id "Phchi.S4G111300"
Phchi.S4	AUGUSTUS	start_codon	6940488	6940490	.	-	0	transcript_id "Phchi.S4G111300.t1"; gene_id "Phchi.S4G111300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15721.t1 is derived from g14191.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20892439	20893426	.	+	.	Phchi.S3G304000
Phchi.S3	AUGUSTUS	transcript	20892439	20893426	.	+	.	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	start_codon	20892439	20892441	.	+	0	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	CDS	20892439	20892564	0.97	+	0	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	exon	20892439	20892564	.	+	.	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	intron	20892565	20893030	.	+	.	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	CDS	20893031	20893180	1	+	0	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	exon	20893031	20893180	.	+	.	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	intron	20893181	20893294	.	+	.	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	CDS	20893295	20893426	1	+	0	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	exon	20893295	20893426	.	+	.	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
Phchi.S3	AUGUSTUS	stop_codon	20893427	20893429	.	+	0	transcript_id "Phchi.S3G304000.t1"; gene_id "Phchi.S3G304000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13325.t1 is derived from g11791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6104429	6105722	.	+	.	Phchi.S3G064400
Phchi.S3	AUGUSTUS	transcript	6104429	6105722	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	start_codon	6104429	6104431	.	+	0	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	CDS	6104429	6104608	1	+	0	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	exon	6104429	6104608	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	intron	6104609	6104696	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	CDS	6104697	6104831	1	+	0	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	exon	6104697	6104831	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	intron	6104832	6104931	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	CDS	6104932	6105163	0.98	+	0	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	exon	6104932	6105163	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	intron	6105164	6105266	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	CDS	6105267	6105470	1	+	2	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	exon	6105267	6105470	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	intron	6105471	6105564	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	CDS	6105565	6105722	1	+	2	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	exon	6105565	6105722	.	+	.	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
Phchi.S3	AUGUSTUS	stop_codon	6105723	6105725	.	+	0	transcript_id "Phchi.S3G064400.t1"; gene_id "Phchi.S3G064400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4784.t1 is derived from g1954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12802182	12805991	.	+	.	Phchi.S1G194300
Phchi.S1	AUGUSTUS	transcript	12802182	12805991	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	start_codon	12802182	12802184	.	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12802182	12802211	0.49	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12802182	12802211	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12802212	12802291	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12802292	12802880	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12802292	12802880	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12802881	12803028	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12803029	12803165	1	+	2	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12803029	12803165	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12803166	12803289	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12803290	12803439	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12803290	12803439	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12803440	12803612	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12803613	12803714	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12803613	12803714	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12803715	12803848	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12803849	12804013	0.87	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12803849	12804013	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12804014	12804119	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12804120	12804230	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12804120	12804230	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12804231	12804334	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12804335	12804432	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12804335	12804432	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12804433	12804593	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12804594	12804717	1	+	1	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12804594	12804717	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12804718	12804817	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12804818	12804907	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12804818	12804907	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12804908	12805092	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12805093	12805137	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12805093	12805137	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12805138	12805269	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12805270	12805590	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12805270	12805590	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12805591	12805689	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12805690	12805733	1	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12805690	12805733	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	intron	12805734	12805951	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	CDS	12805952	12805991	1	+	1	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	exon	12805952	12805991	.	+	.	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
Phchi.S1	AUGUSTUS	stop_codon	12805992	12805994	.	+	0	transcript_id "Phchi.S1G194300.t1"; gene_id "Phchi.S1G194300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8245.t1 is derived from g5420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34676924	34678515	.	-	.	Phchi.S1G540400
Phchi.S1	AUGUSTUS	transcript	34676924	34678515	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	stop_codon	34676921	34676923	.	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34676924	34677037	1	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34676924	34677037	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	intron	34677038	34677144	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34677145	34677258	1	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34677145	34677258	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	intron	34677259	34677340	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34677341	34677466	1	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34677341	34677466	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	intron	34677467	34677591	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34677592	34677671	1	-	2	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34677592	34677671	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	intron	34677672	34677763	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34677764	34677845	1	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34677764	34677845	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	intron	34677846	34677964	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34677965	34678042	1	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34677965	34678042	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	intron	34678043	34678269	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	CDS	34678270	34678515	0.8	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	exon	34678270	34678515	.	-	.	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
Phchi.S1	AUGUSTUS	start_codon	34678513	34678515	.	-	0	transcript_id "Phchi.S1G540400.t1"; gene_id "Phchi.S1G540400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2257.t1 is derived from g9177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5712267	5712638	.	+	.	Phchi.S5G086600
Phchi.S5	AUGUSTUS	transcript	5712267	5712638	.	+	.	transcript_id "Phchi.S5G086600.t1"; gene_id "Phchi.S5G086600"
Phchi.S5	AUGUSTUS	start_codon	5712267	5712269	.	+	0	transcript_id "Phchi.S5G086600.t1"; gene_id "Phchi.S5G086600"
Phchi.S5	AUGUSTUS	CDS	5712267	5712638	0.78	+	0	transcript_id "Phchi.S5G086600.t1"; gene_id "Phchi.S5G086600"
Phchi.S5	AUGUSTUS	exon	5712267	5712638	.	+	.	transcript_id "Phchi.S5G086600.t1"; gene_id "Phchi.S5G086600"
Phchi.S5	AUGUSTUS	stop_codon	5712639	5712641	.	+	0	transcript_id "Phchi.S5G086600.t1"; gene_id "Phchi.S5G086600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2396.t1 is derived from g9316.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6475098	6475601	.	+	.	Phchi.S5G100500
Phchi.S5	AUGUSTUS	transcript	6475098	6475601	.	+	.	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	start_codon	6475098	6475100	.	+	0	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	CDS	6475098	6475100	1	+	0	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	exon	6475098	6475100	.	+	.	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	intron	6475101	6475173	.	+	.	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	CDS	6475174	6475355	1	+	0	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	exon	6475174	6475355	.	+	.	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	intron	6475356	6475447	.	+	.	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	CDS	6475448	6475601	1	+	1	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	exon	6475448	6475601	.	+	.	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
Phchi.S5	AUGUSTUS	stop_codon	6475602	6475604	.	+	0	transcript_id "Phchi.S5G100500.t1"; gene_id "Phchi.S5G100500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4700.t1 is derived from g1870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12349102	12350745	.	+	.	Phchi.S1G185900
Phchi.S1	AUGUSTUS	transcript	12349102	12350745	.	+	.	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	start_codon	12349102	12349104	.	+	0	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	CDS	12349102	12349395	0.99	+	0	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	exon	12349102	12349395	.	+	.	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	intron	12349396	12349510	.	+	.	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	CDS	12349511	12349819	0.98	+	0	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	exon	12349511	12349819	.	+	.	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	intron	12349820	12349950	.	+	.	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	CDS	12349951	12350745	1	+	0	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	exon	12349951	12350745	.	+	.	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
Phchi.S1	AUGUSTUS	stop_codon	12350746	12350748	.	+	0	transcript_id "Phchi.S1G185900.t1"; gene_id "Phchi.S1G185900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4314.t1 is derived from g1483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9585093	9585424	.	-	.	Phchi.S1G147300
Phchi.S1	AUGUSTUS	transcript	9585093	9585424	.	-	.	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	stop_codon	9585090	9585092	.	-	0	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	CDS	9585093	9585187	0.39	-	2	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	exon	9585093	9585187	.	-	.	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	intron	9585188	9585279	.	-	.	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	CDS	9585280	9585424	0.69	-	0	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	exon	9585280	9585424	.	-	.	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
Phchi.S1	AUGUSTUS	start_codon	9585422	9585424	.	-	0	transcript_id "Phchi.S1G147300.t1"; gene_id "Phchi.S1G147300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6765.t1 is derived from g3937.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24959593	24963325	.	+	.	Phchi.S1G392400
Phchi.S1	AUGUSTUS	transcript	24959593	24963325	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	start_codon	24959593	24959595	.	+	0	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24959593	24959617	0.94	+	0	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24959593	24959617	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	intron	24959618	24959811	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24959812	24959893	0.83	+	2	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24959812	24959893	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	intron	24959894	24959977	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24959978	24963039	0.48	+	1	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24959978	24963039	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	intron	24963040	24963143	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24963144	24963325	0.62	+	2	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24963144	24963325	.	+	.	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	stop_codon	24963326	24963328	.	+	0	transcript_id "Phchi.S1G392400.t1"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	transcript	24959593	24963325	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	start_codon	24959593	24959595	.	+	0	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24959593	24959617	0.83	+	0	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24959593	24959617	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	intron	24959618	24959740	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24959741	24959783	0.76	+	2	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24959741	24959783	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	intron	24959784	24959977	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24959978	24963039	0.59	+	1	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24959978	24963039	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	intron	24963040	24963143	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	CDS	24963144	24963325	0.69	+	2	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	exon	24963144	24963325	.	+	.	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
Phchi.S1	AUGUSTUS	stop_codon	24963326	24963328	.	+	0	transcript_id "Phchi.S1G392400.t2"; gene_id "Phchi.S1G392400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13614.t1 is derived from g12081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7694676	7696696	.	+	.	Phchi.S3G093300
Phchi.S3	AUGUSTUS	transcript	7694676	7696696	.	+	.	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	start_codon	7694676	7694678	.	+	0	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	CDS	7694676	7695055	0.95	+	0	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	exon	7694676	7695055	.	+	.	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	intron	7695056	7695156	.	+	.	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	CDS	7695157	7696293	0.46	+	1	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	exon	7695157	7696293	.	+	.	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	intron	7696294	7696392	.	+	.	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	CDS	7696393	7696696	0.72	+	1	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	exon	7696393	7696696	.	+	.	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
Phchi.S3	AUGUSTUS	stop_codon	7696697	7696699	.	+	0	transcript_id "Phchi.S3G093300.t1"; gene_id "Phchi.S3G093300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg261.t1 is derived from g10043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1754913	1756006	.	-	.	Phchi.S6G022000
Phchi.S6	AUGUSTUS	transcript	1754913	1756006	.	-	.	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	stop_codon	1754910	1754912	.	-	0	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	CDS	1754913	1755101	0.9	-	0	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	exon	1754913	1755101	.	-	.	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	intron	1755102	1755184	.	-	.	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	CDS	1755185	1756006	0.54	-	0	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	exon	1755185	1756006	.	-	.	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
Phchi.S6	AUGUSTUS	start_codon	1756004	1756006	.	-	0	transcript_id "Phchi.S6G022000.t1"; gene_id "Phchi.S6G022000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13545.t1 is derived from g12012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7437813	7439804	.	+	.	Phchi.S3G086400
Phchi.S3	AUGUSTUS	transcript	7437813	7439804	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	start_codon	7437813	7437815	.	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7437813	7437858	1	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7437813	7437858	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7437859	7437945	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7437946	7438082	1	+	2	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7437946	7438082	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7438083	7438177	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7438178	7438224	1	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7438178	7438224	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7438225	7438374	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7438375	7438709	1	+	1	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7438375	7438709	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7438710	7438789	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7438790	7438872	1	+	2	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7438790	7438872	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7438873	7438955	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7438956	7439031	1	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7438956	7439031	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7439032	7439118	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7439119	7439180	1	+	2	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7439119	7439180	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7439181	7439273	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7439274	7439369	1	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7439274	7439369	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7439370	7439446	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7439447	7439608	1	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7439447	7439608	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	intron	7439609	7439690	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	CDS	7439691	7439804	0.98	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	exon	7439691	7439804	.	+	.	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
Phchi.S3	AUGUSTUS	stop_codon	7439805	7439807	.	+	0	transcript_id "Phchi.S3G086400.t1"; gene_id "Phchi.S3G086400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14170.t1 is derived from g12637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11257854	11258267	.	+	.	Phchi.S3G148900
Phchi.S3	AUGUSTUS	transcript	11257854	11258267	.	+	.	transcript_id "Phchi.S3G148900.t1"; gene_id "Phchi.S3G148900"
Phchi.S3	AUGUSTUS	start_codon	11257854	11257856	.	+	0	transcript_id "Phchi.S3G148900.t1"; gene_id "Phchi.S3G148900"
Phchi.S3	AUGUSTUS	CDS	11257854	11258267	0.85	+	0	transcript_id "Phchi.S3G148900.t1"; gene_id "Phchi.S3G148900"
Phchi.S3	AUGUSTUS	exon	11257854	11258267	.	+	.	transcript_id "Phchi.S3G148900.t1"; gene_id "Phchi.S3G148900"
Phchi.S3	AUGUSTUS	stop_codon	11258268	11258270	.	+	0	transcript_id "Phchi.S3G148900.t1"; gene_id "Phchi.S3G148900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg950.t1 is derived from g10732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6625479	6625937	.	+	.	Phchi.S6G090900
Phchi.S6	AUGUSTUS	transcript	6625479	6625937	.	+	.	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	start_codon	6625479	6625481	.	+	0	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	CDS	6625479	6625756	0.22	+	0	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	exon	6625479	6625756	.	+	.	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	intron	6625757	6625876	.	+	.	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	CDS	6625877	6625937	0.26	+	1	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	exon	6625877	6625937	.	+	.	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
Phchi.S6	AUGUSTUS	stop_codon	6625938	6625940	.	+	0	transcript_id "Phchi.S6G090900.t1"; gene_id "Phchi.S6G090900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8871.t1 is derived from g6046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38391029	38391256	.	+	.	Phchi.S1G603000
Phchi.S1	AUGUSTUS	transcript	38391029	38391256	.	+	.	transcript_id "Phchi.S1G603000.t1"; gene_id "Phchi.S1G603000"
Phchi.S1	AUGUSTUS	start_codon	38391029	38391031	.	+	0	transcript_id "Phchi.S1G603000.t1"; gene_id "Phchi.S1G603000"
Phchi.S1	AUGUSTUS	CDS	38391029	38391256	0.59	+	0	transcript_id "Phchi.S1G603000.t1"; gene_id "Phchi.S1G603000"
Phchi.S1	AUGUSTUS	exon	38391029	38391256	.	+	.	transcript_id "Phchi.S1G603000.t1"; gene_id "Phchi.S1G603000"
Phchi.S1	AUGUSTUS	stop_codon	38391257	38391259	.	+	0	transcript_id "Phchi.S1G603000.t1"; gene_id "Phchi.S1G603000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10235.t1 is derived from g7411.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46508448	46509251	.	-	.	Phchi.S1G739400
Phchi.S1	AUGUSTUS	transcript	46508448	46509251	.	-	.	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	stop_codon	46508445	46508447	.	-	0	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	CDS	46508448	46508722	0.6	-	2	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	exon	46508448	46508722	.	-	.	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	intron	46508723	46508816	.	-	.	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	CDS	46508817	46508876	1	-	2	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	exon	46508817	46508876	.	-	.	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	intron	46508877	46508962	.	-	.	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	CDS	46508963	46509251	0.86	-	0	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	exon	46508963	46509251	.	-	.	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
Phchi.S1	AUGUSTUS	start_codon	46509249	46509251	.	-	0	transcript_id "Phchi.S1G739400.t1"; gene_id "Phchi.S1G739400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9585.t1 is derived from g6761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42785409	42790162	.	-	.	Phchi.S1G674400
Phchi.S1	AUGUSTUS	transcript	42785409	42790162	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	stop_codon	42785406	42785408	.	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42785409	42785474	0.98	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42785409	42785474	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42785475	42785615	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42785616	42785858	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42785616	42785858	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42785859	42785932	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42785933	42786031	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42785933	42786031	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42786032	42786113	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42786114	42786593	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42786114	42786593	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42786594	42786698	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42786699	42786797	0.99	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42786699	42786797	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42786798	42786967	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42786968	42787089	1	-	2	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42786968	42787089	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42787090	42787175	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42787176	42787294	1	-	1	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42787176	42787294	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42787295	42787382	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42787383	42787450	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42787383	42787450	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42787451	42787549	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42787550	42787735	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42787550	42787735	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42787736	42787832	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42787833	42787908	1	-	1	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42787833	42787908	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42787909	42787991	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42787992	42788071	0.99	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42787992	42788071	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42788072	42788175	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42788176	42788232	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42788176	42788232	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42788233	42788319	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42788320	42788462	1	-	2	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42788320	42788462	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42788463	42788562	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42788563	42788707	0.99	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42788563	42788707	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42788708	42788842	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42788843	42789004	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42788843	42789004	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42789005	42789148	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42789149	42789334	0.99	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42789149	42789334	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42789335	42789422	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42789423	42789515	1	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42789423	42789515	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42789516	42789608	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42789609	42789769	0.99	-	2	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42789609	42789769	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42789770	42789880	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42789881	42789991	0.99	-	2	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42789881	42789991	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	intron	42789992	42790089	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	CDS	42790090	42790162	0.87	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	exon	42790090	42790162	.	-	.	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
Phchi.S1	AUGUSTUS	start_codon	42790160	42790162	.	-	0	transcript_id "Phchi.S1G674400.t1"; gene_id "Phchi.S1G674400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11845.t1 is derived from g15897.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8557131	8558453	.	-	.	Phchi.S4G142700
Phchi.S4	AUGUSTUS	transcript	8557131	8558453	.	-	.	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	stop_codon	8557128	8557130	.	-	0	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	CDS	8557131	8557429	0.94	-	2	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	exon	8557131	8557429	.	-	.	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	intron	8557430	8557530	.	-	.	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	CDS	8557531	8557645	1	-	0	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	exon	8557531	8557645	.	-	.	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	intron	8557646	8557748	.	-	.	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	CDS	8557749	8558453	0.33	-	0	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	exon	8557749	8558453	.	-	.	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
Phchi.S4	AUGUSTUS	start_codon	8558451	8558453	.	-	0	transcript_id "Phchi.S4G142700.t1"; gene_id "Phchi.S4G142700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10049.t1 is derived from g7225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45279224	45282177	.	+	.	Phchi.S1G720800
Phchi.S1	AUGUSTUS	transcript	45279224	45282177	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	start_codon	45279224	45279226	.	+	0	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	CDS	45279224	45279464	0.55	+	0	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	exon	45279224	45279464	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	intron	45279465	45279569	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	CDS	45279570	45280738	0.31	+	2	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	exon	45279570	45280738	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	intron	45280739	45281047	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	CDS	45281048	45281269	0.58	+	0	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	exon	45281048	45281269	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	intron	45281270	45281457	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	CDS	45281458	45282177	0.84	+	0	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	exon	45281458	45282177	.	+	.	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
Phchi.S1	AUGUSTUS	stop_codon	45282178	45282180	.	+	0	transcript_id "Phchi.S1G720800.t1"; gene_id "Phchi.S1G720800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11537.t1 is derived from g15587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6958382	6958997	.	+	.	Phchi.S4G111900
Phchi.S4	AUGUSTUS	transcript	6958382	6958997	.	+	.	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	start_codon	6958382	6958384	.	+	0	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	CDS	6958382	6958642	0.78	+	0	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	exon	6958382	6958642	.	+	.	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	intron	6958643	6958723	.	+	.	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	CDS	6958724	6958779	0.99	+	0	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	exon	6958724	6958779	.	+	.	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	intron	6958780	6958879	.	+	.	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	CDS	6958880	6958997	0.94	+	1	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	exon	6958880	6958997	.	+	.	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
Phchi.S4	AUGUSTUS	stop_codon	6958998	6959000	.	+	0	transcript_id "Phchi.S4G111900.t1"; gene_id "Phchi.S4G111900"
# This transcript jg12406.t2 is derived from g8083.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12407.t1 is derived from g8084.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18396104	18397184	.	+	.	Phchi.S2G048700
Phchi.S2	AUGUSTUS	transcript	18396104	18396671	.	+	.	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	start_codon	18396104	18396106	.	+	0	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396104	18396312	0.83	+	0	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396104	18396312	.	+	.	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	intron	18396313	18396413	.	+	.	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396414	18396579	0.97	+	1	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396414	18396579	.	+	.	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	intron	18396580	18396665	.	+	.	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396666	18396671	0.99	+	0	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396666	18396671	.	+	.	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	stop_codon	18396672	18396674	.	+	0	transcript_id "Phchi.S2G048700.t1"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	transcript	18396104	18397184	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	start_codon	18396104	18396106	.	+	0	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396104	18396312	0.82	+	0	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396104	18396312	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	intron	18396313	18396413	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396414	18396579	1	+	1	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396414	18396579	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	intron	18396580	18396661	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396662	18396792	0.91	+	0	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396662	18396792	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	intron	18396793	18396874	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	CDS	18396875	18397184	0.86	+	1	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	exon	18396875	18397184	.	+	.	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
Phchi.S2	AUGUSTUS	stop_codon	18397185	18397187	.	+	0	transcript_id "Phchi.S2G048700.t2"; gene_id "Phchi.S2G048700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9246.t1 is derived from g6421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40575550	40576965	.	+	.	Phchi.S1G640500
Phchi.S1	AUGUSTUS	transcript	40575550	40576965	.	+	.	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	start_codon	40575550	40575552	.	+	0	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	CDS	40575550	40575950	0.44	+	0	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	exon	40575550	40575950	.	+	.	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	intron	40575951	40576044	.	+	.	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	CDS	40576045	40576261	0.99	+	1	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	exon	40576045	40576261	.	+	.	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	intron	40576262	40576359	.	+	.	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	CDS	40576360	40576965	0.98	+	0	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	exon	40576360	40576965	.	+	.	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
Phchi.S1	AUGUSTUS	stop_codon	40576966	40576968	.	+	0	transcript_id "Phchi.S1G640500.t1"; gene_id "Phchi.S1G640500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11398.t1 is derived from g15448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6140641	6141037	.	+	.	Phchi.S4G098000
Phchi.S4	AUGUSTUS	transcript	6140641	6141037	.	+	.	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	start_codon	6140641	6140643	.	+	0	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	CDS	6140641	6140824	0.01	+	0	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	exon	6140641	6140824	.	+	.	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	intron	6140825	6140966	.	+	.	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	CDS	6140967	6141037	0.01	+	2	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	exon	6140967	6141037	.	+	.	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
Phchi.S4	AUGUSTUS	stop_codon	6141038	6141040	.	+	0	transcript_id "Phchi.S4G098000.t1"; gene_id "Phchi.S4G098000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7940.t1 is derived from g5114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32020891	32024350	.	-	.	Phchi.S1G509900
Phchi.S1	AUGUSTUS	transcript	32020891	32024350	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	stop_codon	32020888	32020890	.	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32020891	32021205	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32020891	32021205	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021206	32021300	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32021301	32021384	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32021301	32021384	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021385	32021506	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32021507	32021659	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32021507	32021659	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021660	32021739	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32021740	32021892	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32021740	32021892	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021893	32022004	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022005	32022198	0.81	-	2	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022005	32022198	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32022199	32022464	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022465	32022588	0.5	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022465	32022588	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32022589	32022717	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022718	32022789	0.98	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022718	32022789	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32022790	32022896	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022897	32023094	0.97	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022897	32023094	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023095	32023210	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023211	32023351	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023211	32023351	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023352	32023435	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023436	32023612	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023436	32023612	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023613	32023721	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023722	32023850	0.98	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023722	32023850	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023851	32023936	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023937	32024053	1	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023937	32024053	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32024054	32024134	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32024135	32024350	0.93	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32024135	32024350	.	-	.	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	start_codon	32024348	32024350	.	-	0	transcript_id "Phchi.S1G509900.t1"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	transcript	32020891	32024350	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	stop_codon	32020888	32020890	.	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32020891	32021205	0.99	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32020891	32021205	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021206	32021300	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32021301	32021384	1	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32021301	32021384	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021385	32021506	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32021507	32021659	1	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32021507	32021659	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021660	32021739	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32021740	32021892	1	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32021740	32021892	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32021893	32022004	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022005	32022198	0.86	-	2	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022005	32022198	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32022199	32022464	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022465	32022588	0.48	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022465	32022588	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32022589	32022717	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022718	32022789	0.91	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022718	32022789	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32022790	32022896	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32022897	32023094	0.9	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32022897	32023094	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023095	32023210	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023211	32023351	1	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023211	32023351	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023352	32023435	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023436	32023500	0.64	-	2	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023436	32023500	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023501	32023604	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023605	32023629	0.75	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023605	32023629	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023630	32023721	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023722	32023850	1	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023722	32023850	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32023851	32023936	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32023937	32024053	1	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32023937	32024053	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	intron	32024054	32024134	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	CDS	32024135	32024350	0.93	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	exon	32024135	32024350	.	-	.	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
Phchi.S1	AUGUSTUS	start_codon	32024348	32024350	.	-	0	transcript_id "Phchi.S1G509900.t2"; gene_id "Phchi.S1G509900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1751.t1 is derived from g8671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2877974	2880430	.	-	.	Phchi.S5G036000
Phchi.S5	AUGUSTUS	transcript	2877974	2880430	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	stop_codon	2877971	2877973	.	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2877974	2878444	1	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2877974	2878444	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2878445	2878552	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2878553	2878713	0.77	-	2	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2878553	2878713	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2878714	2878795	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2878796	2878925	0.61	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2878796	2878925	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2878926	2879036	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2879037	2879397	0.59	-	1	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2879037	2879397	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2879398	2879477	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2879478	2879560	1	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2879478	2879560	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2879561	2879642	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2879643	2879809	1	-	2	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2879643	2879809	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2879810	2879928	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2879929	2880109	1	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2879929	2880109	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	intron	2880110	2880187	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	CDS	2880188	2880430	1	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	exon	2880188	2880430	.	-	.	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
Phchi.S5	AUGUSTUS	start_codon	2880428	2880430	.	-	0	transcript_id "Phchi.S5G036000.t1"; gene_id "Phchi.S5G036000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12639.t1 is derived from g9791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C183	AUGUSTUS	gene	19544	19939	.	+	.	Phchi.C183G000300
Phchi.C183	AUGUSTUS	transcript	19544	19939	.	+	.	transcript_id "Phchi.C183G000300.t1"; gene_id "Phchi.C183G000300"
Phchi.C183	AUGUSTUS	start_codon	19544	19546	.	+	0	transcript_id "Phchi.C183G000300.t1"; gene_id "Phchi.C183G000300"
Phchi.C183	AUGUSTUS	CDS	19544	19939	0.97	+	0	transcript_id "Phchi.C183G000300.t1"; gene_id "Phchi.C183G000300"
Phchi.C183	AUGUSTUS	exon	19544	19939	.	+	.	transcript_id "Phchi.C183G000300.t1"; gene_id "Phchi.C183G000300"
Phchi.C183	AUGUSTUS	stop_codon	19940	19942	.	+	0	transcript_id "Phchi.C183G000300.t1"; gene_id "Phchi.C183G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13132.t1 is derived from g11597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4302850	4304595	.	-	.	Phchi.S3G045100
Phchi.S3	AUGUSTUS	transcript	4302850	4304595	.	-	.	transcript_id "Phchi.S3G045100.t1"; gene_id "Phchi.S3G045100"
Phchi.S3	AUGUSTUS	stop_codon	4302847	4302849	.	-	0	transcript_id "Phchi.S3G045100.t1"; gene_id "Phchi.S3G045100"
Phchi.S3	AUGUSTUS	CDS	4302850	4304595	0.75	-	0	transcript_id "Phchi.S3G045100.t1"; gene_id "Phchi.S3G045100"
Phchi.S3	AUGUSTUS	exon	4302850	4304595	.	-	.	transcript_id "Phchi.S3G045100.t1"; gene_id "Phchi.S3G045100"
Phchi.S3	AUGUSTUS	start_codon	4304593	4304595	.	-	0	transcript_id "Phchi.S3G045100.t1"; gene_id "Phchi.S3G045100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12149.t1 is derived from g7825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4907573	4909841	.	-	.	Phchi.S2G022900
Phchi.S2	AUGUSTUS	transcript	4907573	4909841	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	stop_codon	4907570	4907572	.	-	0	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	CDS	4907573	4907816	0.68	-	1	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	exon	4907573	4907816	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	intron	4907817	4908327	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	CDS	4908328	4908408	0.22	-	1	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	exon	4908328	4908408	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	intron	4908409	4908506	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	CDS	4908507	4908933	0.41	-	2	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	exon	4908507	4908933	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	intron	4908934	4909081	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	CDS	4909082	4909294	1	-	2	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	exon	4909082	4909294	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	intron	4909295	4909506	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	CDS	4909507	4909672	1	-	0	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	exon	4909507	4909672	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	intron	4909673	4909790	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	CDS	4909791	4909841	1	-	0	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	exon	4909791	4909841	.	-	.	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
Phchi.S2	AUGUSTUS	start_codon	4909839	4909841	.	-	0	transcript_id "Phchi.S2G022900.t1"; gene_id "Phchi.S2G022900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3775.t1 is derived from g944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5644220	5646765	.	+	.	Phchi.S1G093400
Phchi.S1	AUGUSTUS	transcript	5644220	5646765	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	start_codon	5644220	5644222	.	+	0	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	CDS	5644220	5644392	1	+	0	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	exon	5644220	5644392	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	intron	5644393	5644471	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	CDS	5644472	5644511	1	+	1	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	exon	5644472	5644511	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	intron	5644512	5644632	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	CDS	5644633	5646475	1	+	0	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	exon	5644633	5646475	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	intron	5646476	5646555	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	CDS	5646556	5646643	1	+	2	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	exon	5646556	5646643	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	intron	5646644	5646728	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	CDS	5646729	5646765	1	+	1	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	exon	5646729	5646765	.	+	.	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
Phchi.S1	AUGUSTUS	stop_codon	5646766	5646768	.	+	0	transcript_id "Phchi.S1G093400.t1"; gene_id "Phchi.S1G093400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14026.t1 is derived from g12493.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10363979	10366812	.	+	.	Phchi.S3G134500
Phchi.S3	AUGUSTUS	transcript	10363979	10366812	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	start_codon	10363979	10363981	.	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10363979	10364083	0.9	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10363979	10364083	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10364084	10364222	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10364223	10364377	1	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10364223	10364377	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10364378	10364495	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10364496	10364670	1	+	1	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10364496	10364670	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10364671	10364838	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10364839	10364910	1	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10364839	10364910	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10364911	10365042	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10365043	10365159	1	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10365043	10365159	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10365160	10365259	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10365260	10365340	1	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10365260	10365340	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10365341	10365429	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10365430	10365506	1	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10365430	10365506	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10365507	10365595	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10365596	10365699	1	+	1	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10365596	10365699	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10365700	10365791	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10365792	10365893	1	+	2	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10365792	10365893	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10365894	10365990	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10365991	10366076	1	+	2	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10365991	10366076	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10366077	10366171	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10366172	10366258	1	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10366172	10366258	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	intron	10366259	10366341	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	CDS	10366342	10366812	0.63	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	exon	10366342	10366812	.	+	.	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
Phchi.S3	AUGUSTUS	stop_codon	10366813	10366815	.	+	0	transcript_id "Phchi.S3G134500.t1"; gene_id "Phchi.S3G134500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11125.t1 is derived from g15175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4281396	4283157	.	-	.	Phchi.S4G070700
Phchi.S4	AUGUSTUS	transcript	4281396	4283157	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	stop_codon	4281393	4281395	.	-	0	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	CDS	4281396	4281492	0.85	-	1	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	exon	4281396	4281492	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	intron	4281493	4281721	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	CDS	4281722	4281791	0.99	-	2	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	exon	4281722	4281791	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	intron	4281792	4281865	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	CDS	4281866	4282907	0.46	-	0	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	exon	4281866	4282907	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	intron	4282908	4283013	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	CDS	4283014	4283157	0.99	-	0	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	exon	4283014	4283157	.	-	.	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
Phchi.S4	AUGUSTUS	start_codon	4283155	4283157	.	-	0	transcript_id "Phchi.S4G070700.t1"; gene_id "Phchi.S4G070700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15834.t1 is derived from g14304.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21656002	21657076	.	-	.	Phchi.S3G315300
Phchi.S3	AUGUSTUS	transcript	21656002	21657076	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	stop_codon	21655999	21656001	.	-	0	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	CDS	21656002	21656244	0.97	-	0	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	exon	21656002	21656244	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	intron	21656245	21656345	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	CDS	21656346	21656429	0.96	-	0	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	exon	21656346	21656429	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	intron	21656430	21656594	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	CDS	21656595	21656668	0.96	-	2	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	exon	21656595	21656668	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	intron	21656669	21656778	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	CDS	21656779	21657076	0.34	-	0	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	exon	21656779	21657076	.	-	.	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
Phchi.S3	AUGUSTUS	start_codon	21657074	21657076	.	-	0	transcript_id "Phchi.S3G315300.t1"; gene_id "Phchi.S3G315300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4533.t1 is derived from g1703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10988265	10988870	.	-	.	Phchi.S1G169200
Phchi.S1	AUGUSTUS	transcript	10988265	10988870	.	-	.	transcript_id "Phchi.S1G169200.t1"; gene_id "Phchi.S1G169200"
Phchi.S1	AUGUSTUS	stop_codon	10988262	10988264	.	-	0	transcript_id "Phchi.S1G169200.t1"; gene_id "Phchi.S1G169200"
Phchi.S1	AUGUSTUS	CDS	10988265	10988870	0.89	-	0	transcript_id "Phchi.S1G169200.t1"; gene_id "Phchi.S1G169200"
Phchi.S1	AUGUSTUS	exon	10988265	10988870	.	-	.	transcript_id "Phchi.S1G169200.t1"; gene_id "Phchi.S1G169200"
Phchi.S1	AUGUSTUS	start_codon	10988868	10988870	.	-	0	transcript_id "Phchi.S1G169200.t1"; gene_id "Phchi.S1G169200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11822.t1 is derived from g15874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8401074	8403075	.	+	.	Phchi.S4G140400
Phchi.S4	AUGUSTUS	transcript	8401074	8403075	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	start_codon	8401074	8401076	.	+	0	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	CDS	8401074	8401707	0.4	+	0	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	exon	8401074	8401707	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	intron	8401708	8401829	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	CDS	8401830	8402181	1	+	2	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	exon	8401830	8402181	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	intron	8402182	8402277	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	CDS	8402278	8402416	1	+	1	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	exon	8402278	8402416	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	intron	8402417	8402545	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	CDS	8402546	8402607	1	+	0	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	exon	8402546	8402607	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	intron	8402608	8402681	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	CDS	8402682	8402820	1	+	1	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	exon	8402682	8402820	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	intron	8402821	8403003	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	CDS	8403004	8403075	1	+	0	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	exon	8403004	8403075	.	+	.	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
Phchi.S4	AUGUSTUS	stop_codon	8403076	8403078	.	+	0	transcript_id "Phchi.S4G140400.t1"; gene_id "Phchi.S4G140400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg386.t1 is derived from g10168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2801082	2801717	.	-	.	Phchi.S6G034500
Phchi.S6	AUGUSTUS	transcript	2801082	2801717	.	-	.	transcript_id "Phchi.S6G034500.t1"; gene_id "Phchi.S6G034500"
Phchi.S6	AUGUSTUS	stop_codon	2801079	2801081	.	-	0	transcript_id "Phchi.S6G034500.t1"; gene_id "Phchi.S6G034500"
Phchi.S6	AUGUSTUS	CDS	2801082	2801717	0.58	-	0	transcript_id "Phchi.S6G034500.t1"; gene_id "Phchi.S6G034500"
Phchi.S6	AUGUSTUS	exon	2801082	2801717	.	-	.	transcript_id "Phchi.S6G034500.t1"; gene_id "Phchi.S6G034500"
Phchi.S6	AUGUSTUS	start_codon	2801715	2801717	.	-	0	transcript_id "Phchi.S6G034500.t1"; gene_id "Phchi.S6G034500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13110.t1 is derived from g11575.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4187185	4188023	.	-	.	Phchi.S3G042900
Phchi.S3	AUGUSTUS	transcript	4187185	4188023	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	stop_codon	4187182	4187184	.	-	0	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	CDS	4187185	4187257	1	-	1	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	exon	4187185	4187257	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	intron	4187258	4187357	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	CDS	4187358	4187541	1	-	2	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	exon	4187358	4187541	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	intron	4187542	4187749	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	CDS	4187750	4187840	1	-	0	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	exon	4187750	4187840	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	intron	4187841	4187936	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	CDS	4187937	4188023	1	-	0	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	exon	4187937	4188023	.	-	.	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
Phchi.S3	AUGUSTUS	start_codon	4188021	4188023	.	-	0	transcript_id "Phchi.S3G042900.t1"; gene_id "Phchi.S3G042900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3420.t1 is derived from g589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3514330	3522134	.	+	.	Phchi.S1G057900
Phchi.S1	AUGUSTUS	transcript	3514330	3522134	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	start_codon	3514330	3514332	.	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3514330	3514399	0.44	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3514330	3514399	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3514400	3514683	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3514684	3515109	0.19	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3514684	3515109	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3515110	3515194	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3515195	3515289	0.8	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3515195	3515289	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3515290	3515423	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3515424	3515751	0.98	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3515424	3515751	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3515752	3515872	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3515873	3516128	0.95	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3515873	3516128	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516129	3516207	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516208	3516415	1	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516208	3516415	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516416	3516496	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516497	3516861	0.93	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516497	3516861	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516862	3516965	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516966	3517244	1	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516966	3517244	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3517245	3517464	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3517465	3517471	1	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3517465	3517471	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3517472	3517628	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3517629	3517695	1	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3517629	3517695	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3517696	3517859	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3517860	3518166	0.98	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3517860	3518166	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3518167	3518264	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3518265	3518406	0.96	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3518265	3518406	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3518407	3518594	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3518595	3518876	0.41	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3518595	3518876	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3518877	3518964	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3518965	3519330	0.58	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3518965	3519330	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519331	3519461	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3519462	3519523	0.94	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3519462	3519523	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519524	3519635	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3519636	3519691	0.94	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3519636	3519691	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519692	3519769	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3519770	3519922	0.71	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3519770	3519922	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519923	3520003	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3520004	3520214	0.2	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3520004	3520214	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3520215	3520374	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3520375	3520693	0.2	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3520375	3520693	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3520694	3520843	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3520844	3520890	0.32	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3520844	3520890	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3520891	3521106	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521107	3521129	0.33	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521107	3521129	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521130	3521246	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521247	3521302	0.73	+	2	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521247	3521302	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521303	3521475	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521476	3521622	1	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521476	3521622	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521623	3521712	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521713	3521954	0.98	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521713	3521954	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521955	3522040	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3522041	3522134	0.98	+	1	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3522041	3522134	.	+	.	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	stop_codon	3522135	3522137	.	+	0	transcript_id "Phchi.S1G057900.t1"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	transcript	3514330	3522134	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	start_codon	3514330	3514332	.	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3514330	3514399	0.4	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3514330	3514399	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3514400	3514683	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3514684	3515109	0.18	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3514684	3515109	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3515110	3515194	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3515195	3515289	0.82	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3515195	3515289	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3515290	3515423	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3515424	3515751	0.98	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3515424	3515751	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3515752	3515872	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3515873	3516128	0.87	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3515873	3516128	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516129	3516207	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516208	3516415	0.98	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516208	3516415	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516416	3516507	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516508	3516535	0.6	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516508	3516535	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516536	3516716	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516717	3516861	0.64	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516717	3516861	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3516862	3516965	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3516966	3517244	1	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3516966	3517244	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3517245	3517464	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3517465	3517471	1	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3517465	3517471	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3517472	3517628	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3517629	3517695	1	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3517629	3517695	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3517696	3517859	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3517860	3518166	0.99	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3517860	3518166	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3518167	3518264	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3518265	3518406	0.93	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3518265	3518406	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3518407	3518594	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3518595	3518876	0.5	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3518595	3518876	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3518877	3518964	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3518965	3519330	0.54	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3518965	3519330	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519331	3519461	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3519462	3519523	0.94	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3519462	3519523	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519524	3519635	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3519636	3519691	0.89	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3519636	3519691	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519692	3519769	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3519770	3519922	0.66	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3519770	3519922	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3519923	3520003	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3520004	3520214	0.28	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3520004	3520214	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3520215	3520374	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3520375	3520693	0.3	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3520375	3520693	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3520694	3520843	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3520844	3520890	0.41	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3520844	3520890	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3520891	3521106	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521107	3521129	0.39	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521107	3521129	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521130	3521246	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521247	3521302	0.77	+	2	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521247	3521302	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521303	3521475	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521476	3521622	1	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521476	3521622	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521623	3521712	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3521713	3521954	0.97	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3521713	3521954	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	intron	3521955	3522040	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	CDS	3522041	3522134	0.97	+	1	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	exon	3522041	3522134	.	+	.	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
Phchi.S1	AUGUSTUS	stop_codon	3522135	3522137	.	+	0	transcript_id "Phchi.S1G057900.t2"; gene_id "Phchi.S1G057900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg166.t1 is derived from g9948.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	946398	947861	.	+	.	Phchi.S6G012500
Phchi.S6	AUGUSTUS	transcript	946398	947861	.	+	.	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	start_codon	946398	946400	.	+	0	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	CDS	946398	946616	0.57	+	0	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	exon	946398	946616	.	+	.	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	intron	946617	946727	.	+	.	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	CDS	946728	947861	0.56	+	0	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	exon	946728	947861	.	+	.	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
Phchi.S6	AUGUSTUS	stop_codon	947862	947864	.	+	0	transcript_id "Phchi.S6G012500.t1"; gene_id "Phchi.S6G012500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1857.t1 is derived from g8777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3572089	3573493	.	+	.	Phchi.S5G046600
Phchi.S5	AUGUSTUS	transcript	3572089	3573493	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	start_codon	3572089	3572091	.	+	0	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	CDS	3572089	3572324	1	+	0	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	exon	3572089	3572324	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	intron	3572325	3572429	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	CDS	3572430	3572684	1	+	1	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	exon	3572430	3572684	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	intron	3572685	3572789	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	CDS	3572790	3572873	0.99	+	1	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	exon	3572790	3572873	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	intron	3572874	3572973	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	CDS	3572974	3573103	1	+	1	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	exon	3572974	3573103	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	intron	3573104	3573202	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	CDS	3573203	3573493	1	+	0	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	exon	3573203	3573493	.	+	.	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
Phchi.S5	AUGUSTUS	stop_codon	3573494	3573496	.	+	0	transcript_id "Phchi.S5G046600.t1"; gene_id "Phchi.S5G046600"
# This transcript jg2495.t2 is derived from g9415.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2495.t3 is derived from g9415.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2495.t4 is derived from g9415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2496.t1 is derived from g9416.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6974169	6975380	.	-	.	Phchi.S5G110500
Phchi.S5	AUGUSTUS	transcript	6974169	6975380	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	stop_codon	6974166	6974168	.	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	CDS	6974169	6974358	0.99	-	1	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	exon	6974169	6974358	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	intron	6974359	6974436	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	CDS	6974437	6974561	0.88	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	exon	6974437	6974561	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	intron	6974562	6974662	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	CDS	6974663	6974725	0.88	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	exon	6974663	6974725	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	intron	6974726	6974898	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	CDS	6974899	6975027	1	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	exon	6974899	6975027	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	intron	6975028	6975112	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	CDS	6975113	6975193	1	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	exon	6975113	6975193	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	intron	6975194	6975290	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	CDS	6975291	6975380	0.99	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	exon	6975291	6975380	.	-	.	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
Phchi.S5	AUGUSTUS	start_codon	6975378	6975380	.	-	0	transcript_id "Phchi.S5G110500.t1"; gene_id "Phchi.S5G110500"
# This transcript jg10317.t2 is derived from g7493.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10318.t1 is derived from g7494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47092657	47093820	.	+	.	Phchi.S1G747700
Phchi.S1	AUGUSTUS	transcript	47092657	47093820	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	start_codon	47092657	47092659	.	+	0	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	CDS	47092657	47092975	1	+	0	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	exon	47092657	47092975	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	intron	47092976	47093094	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	CDS	47093095	47093247	1	+	2	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	exon	47093095	47093247	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	intron	47093248	47093397	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	CDS	47093398	47093495	0.99	+	2	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	exon	47093398	47093495	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	intron	47093496	47093604	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	CDS	47093605	47093820	0.76	+	0	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	exon	47093605	47093820	.	+	.	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
Phchi.S1	AUGUSTUS	stop_codon	47093821	47093823	.	+	0	transcript_id "Phchi.S1G747700.t1"; gene_id "Phchi.S1G747700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6767.t1 is derived from g3939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24975915	24977557	.	+	.	Phchi.S1G392600
Phchi.S1	AUGUSTUS	transcript	24975915	24977557	.	+	.	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	start_codon	24975915	24975917	.	+	0	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	CDS	24975915	24977020	0.46	+	0	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	exon	24975915	24977020	.	+	.	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	intron	24977021	24977103	.	+	.	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	CDS	24977104	24977557	0.46	+	1	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	exon	24977104	24977557	.	+	.	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
Phchi.S1	AUGUSTUS	stop_codon	24977558	24977560	.	+	0	transcript_id "Phchi.S1G392600.t1"; gene_id "Phchi.S1G392600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg368.t1 is derived from g10150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2681307	2681848	.	+	.	Phchi.S6G032700
Phchi.S6	AUGUSTUS	transcript	2681307	2681848	.	+	.	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	start_codon	2681307	2681309	.	+	0	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	CDS	2681307	2681319	0.77	+	0	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	exon	2681307	2681319	.	+	.	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	intron	2681320	2681510	.	+	.	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	CDS	2681511	2681848	0.32	+	2	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	exon	2681511	2681848	.	+	.	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
Phchi.S6	AUGUSTUS	stop_codon	2681849	2681851	.	+	0	transcript_id "Phchi.S6G032700.t1"; gene_id "Phchi.S6G032700"
# This transcript jg8078.t2 is derived from g5253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8079.t1 is derived from g5254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32860757	32862312	.	+	.	Phchi.S1G523800
Phchi.S1	AUGUSTUS	transcript	32860757	32862312	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	start_codon	32860757	32860759	.	+	0	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	CDS	32860757	32861770	0.6	+	0	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	exon	32860757	32861770	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	intron	32861771	32861853	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	CDS	32861854	32861866	0.84	+	0	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	exon	32861854	32861866	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	intron	32861867	32862055	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	CDS	32862056	32862060	0.99	+	2	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	exon	32862056	32862060	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	intron	32862061	32862153	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	CDS	32862154	32862203	0.75	+	0	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	exon	32862154	32862203	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	intron	32862204	32862293	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	CDS	32862294	32862312	0.67	+	1	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	exon	32862294	32862312	.	+	.	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
Phchi.S1	AUGUSTUS	stop_codon	32862313	32862315	.	+	0	transcript_id "Phchi.S1G523800.t1"; gene_id "Phchi.S1G523800"
# This transcript jg4594.t2 is derived from g1764.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4594.t3 is derived from g1764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4595.t1 is derived from g1765.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11267188	11270987	.	-	.	Phchi.S1G175400
Phchi.S1	AUGUSTUS	transcript	11267188	11270987	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	stop_codon	11267185	11267187	.	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11267188	11267251	0.99	-	1	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11267188	11267251	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11267252	11267473	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11267474	11267552	0.99	-	2	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11267474	11267552	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11267553	11267647	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11267648	11267702	0.99	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11267648	11267702	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11267703	11267796	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11267797	11267926	1	-	1	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11267797	11267926	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11267927	11268051	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11268052	11268271	0.53	-	2	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11268052	11268271	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11268272	11268365	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11268366	11268486	1	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11268366	11268486	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11268487	11268630	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11268631	11268837	0.99	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11268631	11268837	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11268838	11269021	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11269022	11269255	1	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11269022	11269255	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11269256	11269335	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11269336	11269435	0.89	-	1	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11269336	11269435	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11269436	11269551	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11269552	11269955	0.79	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11269552	11269955	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11269956	11270065	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11270066	11270241	0.86	-	2	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11270066	11270241	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11270242	11270395	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11270396	11270441	1	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11270396	11270441	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11270442	11270571	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11270572	11270670	1	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11270572	11270670	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	intron	11270671	11270885	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	CDS	11270886	11270987	0.93	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	exon	11270886	11270987	.	-	.	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
Phchi.S1	AUGUSTUS	start_codon	11270985	11270987	.	-	0	transcript_id "Phchi.S1G175400.t1"; gene_id "Phchi.S1G175400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7975.t1 is derived from g5150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32195344	32197392	.	-	.	Phchi.S1G513400
Phchi.S1	AUGUSTUS	transcript	32195344	32197392	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	stop_codon	32195341	32195343	.	-	0	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	CDS	32195344	32195834	1	-	2	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	exon	32195344	32195834	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	intron	32195835	32195913	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	CDS	32195914	32196136	1	-	0	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	exon	32195914	32196136	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	intron	32196137	32196260	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	CDS	32196261	32196563	1	-	0	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	exon	32196261	32196563	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	intron	32196564	32196657	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	CDS	32196658	32196705	0.76	-	0	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	exon	32196658	32196705	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	intron	32196706	32196780	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	CDS	32196781	32196877	0.76	-	1	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	exon	32196781	32196877	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	intron	32196878	32196964	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	CDS	32196965	32197392	1	-	0	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	exon	32196965	32197392	.	-	.	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
Phchi.S1	AUGUSTUS	start_codon	32197390	32197392	.	-	0	transcript_id "Phchi.S1G513400.t1"; gene_id "Phchi.S1G513400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4709.t1 is derived from g1879.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12419220	12423306	.	-	.	Phchi.S1G186800
Phchi.S1	AUGUSTUS	transcript	12419220	12423306	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	stop_codon	12419217	12419219	.	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12419220	12419576	0.99	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12419220	12419576	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12419577	12419664	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12419665	12419800	1	-	1	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12419665	12419800	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12419801	12419906	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12419907	12420089	0.98	-	1	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12419907	12420089	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12420090	12420200	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12420201	12420358	0.98	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12420201	12420358	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12420359	12420504	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12420505	12420672	1	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12420505	12420672	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12420673	12420861	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12420862	12420945	1	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12420862	12420945	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12420946	12421021	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12421022	12421159	0.59	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12421022	12421159	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12421160	12421255	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12421256	12421309	0.83	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12421256	12421309	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12421310	12421412	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12421413	12421460	0.99	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12421413	12421460	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12421461	12421553	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12421554	12421689	1	-	1	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12421554	12421689	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12421690	12421773	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12421774	12421972	1	-	2	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12421774	12421972	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12421973	12422218	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12422219	12422403	1	-	1	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12422219	12422403	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12422404	12422531	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12422532	12422624	1	-	1	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12422532	12422624	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12422625	12422769	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12422770	12422915	1	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12422770	12422915	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12422916	12423007	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12423008	12423145	0.99	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12423008	12423145	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	intron	12423146	12423246	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	CDS	12423247	12423306	0.42	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	exon	12423247	12423306	.	-	.	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
Phchi.S1	AUGUSTUS	start_codon	12423304	12423306	.	-	0	transcript_id "Phchi.S1G186800.t1"; gene_id "Phchi.S1G186800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13609.t1 is derived from g12076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7681617	7683206	.	+	.	Phchi.S3G092800
Phchi.S3	AUGUSTUS	transcript	7681617	7683206	.	+	.	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	start_codon	7681617	7681619	.	+	0	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	CDS	7681617	7682216	0.5	+	0	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	exon	7681617	7682216	.	+	.	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	intron	7682217	7682347	.	+	.	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	CDS	7682348	7683017	0.27	+	0	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	exon	7682348	7683017	.	+	.	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	intron	7683018	7683165	.	+	.	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	CDS	7683166	7683206	0.79	+	2	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	exon	7683166	7683206	.	+	.	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
Phchi.S3	AUGUSTUS	stop_codon	7683207	7683209	.	+	0	transcript_id "Phchi.S3G092800.t1"; gene_id "Phchi.S3G092800"
# This transcript jg1581.t2 is derived from g8500.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1582.t1 is derived from g8501.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1870751	1872403	.	+	.	Phchi.S5G019100
Phchi.S5	AUGUSTUS	transcript	1870751	1872403	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	start_codon	1870751	1870753	.	+	0	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1870751	1870753	1	+	0	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1870751	1870753	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1870754	1870831	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1870832	1870881	1	+	0	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1870832	1870881	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1870882	1871264	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1871265	1871320	1	+	1	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1871265	1871320	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1871321	1871419	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1871420	1871497	1	+	2	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1871420	1871497	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1871498	1871590	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1871591	1871674	1	+	2	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1871591	1871674	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1871675	1871773	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1871774	1871955	1	+	2	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1871774	1871955	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1871956	1872110	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1872111	1872195	1	+	0	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1872111	1872195	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	intron	1872196	1872395	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	CDS	1872396	1872403	1	+	2	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	exon	1872396	1872403	.	+	.	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
Phchi.S5	AUGUSTUS	stop_codon	1872404	1872406	.	+	0	transcript_id "Phchi.S5G019100.t1"; gene_id "Phchi.S5G019100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7022.t1 is derived from g4194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26437375	26437683	.	-	.	Phchi.S1G418100
Phchi.S1	AUGUSTUS	transcript	26437375	26437683	.	-	.	transcript_id "Phchi.S1G418100.t1"; gene_id "Phchi.S1G418100"
Phchi.S1	AUGUSTUS	stop_codon	26437372	26437374	.	-	0	transcript_id "Phchi.S1G418100.t1"; gene_id "Phchi.S1G418100"
Phchi.S1	AUGUSTUS	CDS	26437375	26437683	0.61	-	0	transcript_id "Phchi.S1G418100.t1"; gene_id "Phchi.S1G418100"
Phchi.S1	AUGUSTUS	exon	26437375	26437683	.	-	.	transcript_id "Phchi.S1G418100.t1"; gene_id "Phchi.S1G418100"
Phchi.S1	AUGUSTUS	start_codon	26437681	26437683	.	-	0	transcript_id "Phchi.S1G418100.t1"; gene_id "Phchi.S1G418100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5372.t1 is derived from g2542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16536907	16539968	.	-	.	Phchi.S1G253100
Phchi.S1	AUGUSTUS	transcript	16536907	16539968	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	stop_codon	16536904	16536906	.	-	0	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	CDS	16536907	16537006	0.99	-	1	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	exon	16536907	16537006	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	intron	16537007	16537186	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	CDS	16537187	16537221	0.77	-	0	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	exon	16537187	16537221	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	intron	16537222	16537357	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	CDS	16537358	16537915	0.39	-	0	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	exon	16537358	16537915	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	intron	16537916	16538009	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	CDS	16538010	16538074	0.87	-	2	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	exon	16538010	16538074	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	intron	16538075	16538204	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	CDS	16538205	16538323	0.74	-	1	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	exon	16538205	16538323	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	intron	16538324	16538445	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	CDS	16538446	16539968	0.68	-	0	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	exon	16538446	16539968	.	-	.	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
Phchi.S1	AUGUSTUS	start_codon	16539966	16539968	.	-	0	transcript_id "Phchi.S1G253100.t1"; gene_id "Phchi.S1G253100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11360.t1 is derived from g15410.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5757632	5758318	.	+	.	Phchi.S4G094200
Phchi.S4	AUGUSTUS	transcript	5757632	5758318	.	+	.	transcript_id "Phchi.S4G094200.t1"; gene_id "Phchi.S4G094200"
Phchi.S4	AUGUSTUS	start_codon	5757632	5757634	.	+	0	transcript_id "Phchi.S4G094200.t1"; gene_id "Phchi.S4G094200"
Phchi.S4	AUGUSTUS	CDS	5757632	5758318	0.45	+	0	transcript_id "Phchi.S4G094200.t1"; gene_id "Phchi.S4G094200"
Phchi.S4	AUGUSTUS	exon	5757632	5758318	.	+	.	transcript_id "Phchi.S4G094200.t1"; gene_id "Phchi.S4G094200"
Phchi.S4	AUGUSTUS	stop_codon	5758319	5758321	.	+	0	transcript_id "Phchi.S4G094200.t1"; gene_id "Phchi.S4G094200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4602.t1 is derived from g1772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11310417	11311538	.	+	.	Phchi.S1G176100
Phchi.S1	AUGUSTUS	transcript	11310417	11311538	.	+	.	transcript_id "Phchi.S1G176100.t1"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	start_codon	11310417	11310419	.	+	0	transcript_id "Phchi.S1G176100.t1"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	CDS	11310417	11311538	0.94	+	0	transcript_id "Phchi.S1G176100.t1"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	exon	11310417	11311538	.	+	.	transcript_id "Phchi.S1G176100.t1"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	stop_codon	11311539	11311541	.	+	0	transcript_id "Phchi.S1G176100.t1"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	transcript	11310732	11311538	.	+	.	transcript_id "Phchi.S1G176100.t2"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	start_codon	11310732	11310734	.	+	0	transcript_id "Phchi.S1G176100.t2"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	CDS	11310732	11311538	0.9	+	0	transcript_id "Phchi.S1G176100.t2"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	exon	11310732	11311538	.	+	.	transcript_id "Phchi.S1G176100.t2"; gene_id "Phchi.S1G176100"
Phchi.S1	AUGUSTUS	stop_codon	11311539	11311541	.	+	0	transcript_id "Phchi.S1G176100.t2"; gene_id "Phchi.S1G176100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1387.t1 is derived from g16020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	12963	13178	.	-	.	Phchi.C243G000500
Phchi.C243	AUGUSTUS	transcript	12963	13178	.	-	.	transcript_id "Phchi.C243G000500.t1"; gene_id "Phchi.C243G000500"
Phchi.C243	AUGUSTUS	stop_codon	12960	12962	.	-	0	transcript_id "Phchi.C243G000500.t1"; gene_id "Phchi.C243G000500"
Phchi.C243	AUGUSTUS	CDS	12963	13178	0.62	-	0	transcript_id "Phchi.C243G000500.t1"; gene_id "Phchi.C243G000500"
Phchi.C243	AUGUSTUS	exon	12963	13178	.	-	.	transcript_id "Phchi.C243G000500.t1"; gene_id "Phchi.C243G000500"
Phchi.C243	AUGUSTUS	start_codon	13176	13178	.	-	0	transcript_id "Phchi.C243G000500.t1"; gene_id "Phchi.C243G000500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14956.t1 is derived from g13424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15711576	15717543	.	-	.	Phchi.S3G227500
Phchi.S3	AUGUSTUS	transcript	15711576	15717543	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	stop_codon	15711573	15711575	.	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15711576	15711902	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15711576	15711902	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15711903	15711982	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15711983	15712257	1	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15711983	15712257	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15712258	15712401	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15712402	15712630	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15712402	15712630	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15712631	15712726	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15712727	15712933	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15712727	15712933	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15712934	15713036	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15713037	15713255	0.99	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15713037	15713255	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15713256	15713341	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15713342	15713473	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15713342	15713473	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15713474	15713573	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15713574	15713671	1	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15713574	15713671	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15713672	15713764	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15713765	15714088	0.97	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15713765	15714088	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15714089	15714259	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15714260	15714283	0.98	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15714260	15714283	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15714284	15714419	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15714420	15714486	0.98	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15714420	15714486	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15714487	15714647	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15714648	15714755	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15714648	15714755	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15714756	15714835	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15714836	15714883	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15714836	15714883	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15714884	15714989	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15714990	15715174	1	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15714990	15715174	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15715175	15715326	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15715327	15715376	1	-	1	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15715327	15715376	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15715377	15715497	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15715498	15715542	1	-	1	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15715498	15715542	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15715543	15715629	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15715630	15715725	0.47	-	1	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15715630	15715725	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15715726	15715831	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15715832	15715884	0.98	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15715832	15715884	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15715885	15715975	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15715976	15716093	1	-	1	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15715976	15716093	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15716094	15716186	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15716187	15716288	1	-	1	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15716187	15716288	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15716289	15716450	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15716451	15716608	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15716451	15716608	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15716609	15716818	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15716819	15716896	1	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15716819	15716896	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15716897	15716986	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15716987	15717078	1	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15716987	15717078	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15717079	15717204	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15717205	15717255	1	-	2	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15717205	15717255	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	intron	15717256	15717359	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	CDS	15717360	15717543	0.99	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	exon	15717360	15717543	.	-	.	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
Phchi.S3	AUGUSTUS	start_codon	15717541	15717543	.	-	0	transcript_id "Phchi.S3G227500.t1"; gene_id "Phchi.S3G227500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9825.t1 is derived from g7001.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43967401	43967983	.	-	.	Phchi.S1G698400
Phchi.S1	AUGUSTUS	transcript	43967401	43967983	.	-	.	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	stop_codon	43967398	43967400	.	-	0	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	CDS	43967401	43967484	1	-	0	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	exon	43967401	43967484	.	-	.	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	intron	43967485	43967776	.	-	.	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	CDS	43967777	43967983	0.99	-	0	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	exon	43967777	43967983	.	-	.	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
Phchi.S1	AUGUSTUS	start_codon	43967981	43967983	.	-	0	transcript_id "Phchi.S1G698400.t1"; gene_id "Phchi.S1G698400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12733.t1 is derived from g11198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1439879	1443985	.	-	.	Phchi.S3G005200
Phchi.S3	AUGUSTUS	transcript	1439879	1443985	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	stop_codon	1439876	1439878	.	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1439879	1441246	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1439879	1441246	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1441247	1441329	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1441330	1441386	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1441330	1441386	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1441387	1441477	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1441478	1441591	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1441478	1441591	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1441592	1441692	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1441693	1441860	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1441693	1441860	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1441861	1442023	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1442024	1442134	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1442024	1442134	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1442135	1442280	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1442281	1442430	0.86	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1442281	1442430	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1442431	1442535	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1442536	1442596	0.95	-	1	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1442536	1442596	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1442597	1442733	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1442734	1442847	1	-	1	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1442734	1442847	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1442848	1442948	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1442949	1443046	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1442949	1443046	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1443047	1443155	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1443156	1443279	0.99	-	1	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1443156	1443279	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1443280	1443382	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1443383	1443570	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1443383	1443570	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1443571	1443694	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1443695	1443766	1	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1443695	1443766	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	intron	1443767	1443907	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	CDS	1443908	1443985	0.97	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	exon	1443908	1443985	.	-	.	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
Phchi.S3	AUGUSTUS	start_codon	1443983	1443985	.	-	0	transcript_id "Phchi.S3G005200.t1"; gene_id "Phchi.S3G005200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14032.t1 is derived from g12499.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10396822	10397247	.	-	.	Phchi.S3G135100
Phchi.S3	AUGUSTUS	transcript	10396822	10397247	.	-	.	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	stop_codon	10396819	10396821	.	-	0	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	CDS	10396822	10397018	1	-	2	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	exon	10396822	10397018	.	-	.	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	intron	10397019	10397186	.	-	.	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	CDS	10397187	10397247	1	-	0	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	exon	10397187	10397247	.	-	.	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	start_codon	10397245	10397247	.	-	0	transcript_id "Phchi.S3G135100.t1"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	transcript	10396822	10397247	.	-	.	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	stop_codon	10396819	10396821	.	-	0	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	CDS	10396822	10397069	0.32	-	2	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	exon	10396822	10397069	.	-	.	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	intron	10397070	10397186	.	-	.	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	CDS	10397187	10397247	0.37	-	0	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	exon	10397187	10397247	.	-	.	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
Phchi.S3	AUGUSTUS	start_codon	10397245	10397247	.	-	0	transcript_id "Phchi.S3G135100.t2"; gene_id "Phchi.S3G135100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8780.t1 is derived from g5955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37921960	37923018	.	+	.	Phchi.S1G593900
Phchi.S1	AUGUSTUS	transcript	37921960	37923018	.	+	.	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	start_codon	37921960	37921962	.	+	0	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	CDS	37921960	37922282	1	+	0	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	exon	37921960	37922282	.	+	.	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	intron	37922283	37922382	.	+	.	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	CDS	37922383	37922622	1	+	1	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	exon	37922383	37922622	.	+	.	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	intron	37922623	37922735	.	+	.	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	CDS	37922736	37923018	1	+	1	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	exon	37922736	37923018	.	+	.	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
Phchi.S1	AUGUSTUS	stop_codon	37923019	37923021	.	+	0	transcript_id "Phchi.S1G593900.t1"; gene_id "Phchi.S1G593900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6387.t1 is derived from g3559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22670689	22671666	.	-	.	Phchi.S1G354600
Phchi.S1	AUGUSTUS	transcript	22670689	22671666	.	-	.	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	stop_codon	22670686	22670688	.	-	0	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	CDS	22670689	22670767	0.96	-	1	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	exon	22670689	22670767	.	-	.	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	intron	22670768	22671199	.	-	.	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	CDS	22671200	22671666	0.72	-	0	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	exon	22671200	22671666	.	-	.	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
Phchi.S1	AUGUSTUS	start_codon	22671664	22671666	.	-	0	transcript_id "Phchi.S1G354600.t1"; gene_id "Phchi.S1G354600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1758.t1 is derived from g8678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2906383	2908020	.	+	.	Phchi.S5G036700
Phchi.S5	AUGUSTUS	transcript	2906383	2908020	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	start_codon	2906383	2906385	.	+	0	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2906383	2906525	0.38	+	0	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2906383	2906525	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	intron	2906526	2906644	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2906645	2906930	0.59	+	1	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2906645	2906930	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	intron	2906931	2907069	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2907070	2907402	0.97	+	0	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2907070	2907402	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	intron	2907403	2907490	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2907491	2907711	0.93	+	0	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2907491	2907711	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	intron	2907712	2907815	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2907816	2908020	1	+	1	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2907816	2908020	.	+	.	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	stop_codon	2908021	2908023	.	+	0	transcript_id "Phchi.S5G036700.t1"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	transcript	2906383	2907405	.	+	.	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	start_codon	2906383	2906385	.	+	0	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2906383	2906525	0.34	+	0	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2906383	2906525	.	+	.	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	intron	2906526	2906644	.	+	.	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2906645	2906930	0.58	+	1	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2906645	2906930	.	+	.	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	intron	2906931	2907069	.	+	.	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	CDS	2907070	2907405	1	+	0	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	exon	2907070	2907405	.	+	.	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
Phchi.S5	AUGUSTUS	stop_codon	2907406	2907408	.	+	0	transcript_id "Phchi.S5G036700.t2"; gene_id "Phchi.S5G036700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1767.t1 is derived from g8687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2931480	2932993	.	+	.	Phchi.S5G037600
Phchi.S5	AUGUSTUS	transcript	2931480	2932993	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	start_codon	2931480	2931482	.	+	0	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2931480	2931487	0.37	+	0	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2931480	2931487	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	intron	2931488	2931629	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2931630	2931659	0.38	+	1	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2931630	2931659	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	intron	2931660	2931764	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2931765	2931791	0.34	+	1	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2931765	2931791	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	intron	2931792	2931928	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2931929	2931996	0.46	+	1	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2931929	2931996	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	intron	2931997	2932130	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2932131	2932333	0.34	+	2	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2932131	2932333	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	intron	2932334	2932567	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2932568	2932717	0.58	+	0	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2932568	2932717	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	intron	2932718	2932897	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	CDS	2932898	2932993	0.95	+	0	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	exon	2932898	2932993	.	+	.	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
Phchi.S5	AUGUSTUS	stop_codon	2932994	2932996	.	+	0	transcript_id "Phchi.S5G037600.t1"; gene_id "Phchi.S5G037600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8373.t1 is derived from g5548.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35561352	35565226	.	-	.	Phchi.S1G553200
Phchi.S1	AUGUSTUS	transcript	35561352	35565226	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	stop_codon	35561349	35561351	.	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35561352	35561475	0.88	-	1	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35561352	35561475	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35561476	35561551	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35561552	35561622	1	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35561552	35561622	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35561623	35561746	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35561747	35561869	1	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35561747	35561869	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35561870	35561975	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35561976	35562115	0.99	-	2	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35561976	35562115	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35562116	35562206	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35562207	35562264	1	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35562207	35562264	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35562265	35562356	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35562357	35562438	1	-	1	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35562357	35562438	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35562439	35562621	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35562622	35562680	1	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35562622	35562680	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35562681	35562805	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35562806	35562980	1	-	1	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35562806	35562980	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35562981	35563079	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35563080	35563261	1	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35563080	35563261	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35563262	35563566	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35563567	35563747	0.98	-	1	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35563567	35563747	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35563748	35563861	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35563862	35563984	0.98	-	1	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35563862	35563984	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35563985	35564072	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35564073	35564360	0.46	-	1	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35564073	35564360	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35564361	35564484	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35564485	35564632	0.37	-	2	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35564485	35564632	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35564633	35564992	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35564993	35564999	0.68	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35564993	35564999	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	intron	35565000	35565154	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	CDS	35565155	35565226	0.86	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	exon	35565155	35565226	.	-	.	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
Phchi.S1	AUGUSTUS	start_codon	35565224	35565226	.	-	0	transcript_id "Phchi.S1G553200.t1"; gene_id "Phchi.S1G553200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7997.t1 is derived from g5172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32353856	32356633	.	+	.	Phchi.S1G515600
Phchi.S1	AUGUSTUS	transcript	32353856	32356633	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	start_codon	32353856	32353858	.	+	0	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	CDS	32353856	32353940	1	+	0	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	exon	32353856	32353940	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	intron	32353941	32354055	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	CDS	32354056	32354622	0.81	+	2	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	exon	32354056	32354622	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	intron	32354623	32354731	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	CDS	32354732	32355316	0.91	+	2	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	exon	32354732	32355316	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	intron	32355317	32355432	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	CDS	32355433	32355689	0.82	+	2	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	exon	32355433	32355689	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	intron	32355690	32355855	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	CDS	32355856	32356043	0.97	+	0	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	exon	32355856	32356043	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	intron	32356044	32356152	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	CDS	32356153	32356633	1	+	1	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	exon	32356153	32356633	.	+	.	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
Phchi.S1	AUGUSTUS	stop_codon	32356634	32356636	.	+	0	transcript_id "Phchi.S1G515600.t1"; gene_id "Phchi.S1G515600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10343.t1 is derived from g7519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47264999	47265800	.	-	.	Phchi.S1G750200
Phchi.S1	AUGUSTUS	transcript	47264999	47265800	.	-	.	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	stop_codon	47264996	47264998	.	-	0	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	CDS	47264999	47265057	0.85	-	2	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	exon	47264999	47265057	.	-	.	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	intron	47265058	47265226	.	-	.	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	CDS	47265227	47265326	0.84	-	0	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	exon	47265227	47265326	.	-	.	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	intron	47265327	47265695	.	-	.	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	CDS	47265696	47265800	0.72	-	0	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	exon	47265696	47265800	.	-	.	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
Phchi.S1	AUGUSTUS	start_codon	47265798	47265800	.	-	0	transcript_id "Phchi.S1G750200.t1"; gene_id "Phchi.S1G750200"
# This transcript jg10408.t2 is derived from g7584.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10408.t3 is derived from g7584.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10409.t1 is derived from g7585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47700067	47701661	.	+	.	Phchi.S1G756800
Phchi.S1	AUGUSTUS	transcript	47700067	47701661	.	+	.	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	start_codon	47700067	47700069	.	+	0	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	CDS	47700067	47700460	0.99	+	0	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	exon	47700067	47700460	.	+	.	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	intron	47700461	47700622	.	+	.	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	CDS	47700623	47700892	1	+	2	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	exon	47700623	47700892	.	+	.	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	intron	47700893	47700996	.	+	.	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	CDS	47700997	47701661	1	+	2	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	exon	47700997	47701661	.	+	.	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
Phchi.S1	AUGUSTUS	stop_codon	47701662	47701664	.	+	0	transcript_id "Phchi.S1G756800.t1"; gene_id "Phchi.S1G756800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6611.t1 is derived from g3783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23999038	23999660	.	+	.	Phchi.S1G377000
Phchi.S1	AUGUSTUS	transcript	23999038	23999660	.	+	.	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	start_codon	23999038	23999040	.	+	0	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	CDS	23999038	23999187	0.22	+	0	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	exon	23999038	23999187	.	+	.	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	intron	23999188	23999383	.	+	.	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	CDS	23999384	23999511	0.02	+	0	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	exon	23999384	23999511	.	+	.	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	intron	23999512	23999611	.	+	.	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	CDS	23999612	23999660	0.01	+	1	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	exon	23999612	23999660	.	+	.	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
Phchi.S1	AUGUSTUS	stop_codon	23999661	23999663	.	+	0	transcript_id "Phchi.S1G377000.t1"; gene_id "Phchi.S1G377000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10339.t1 is derived from g7515.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47248605	47251101	.	-	.	Phchi.S1G749800
Phchi.S1	AUGUSTUS	transcript	47248605	47251101	.	-	.	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	stop_codon	47248602	47248604	.	-	0	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	CDS	47248605	47248646	0.85	-	0	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	exon	47248605	47248646	.	-	.	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	intron	47248647	47248929	.	-	.	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	CDS	47248930	47250498	0.52	-	0	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	exon	47248930	47250498	.	-	.	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	intron	47250499	47250675	.	-	.	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	CDS	47250676	47251101	0.33	-	0	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	exon	47250676	47251101	.	-	.	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
Phchi.S1	AUGUSTUS	start_codon	47251099	47251101	.	-	0	transcript_id "Phchi.S1G749800.t1"; gene_id "Phchi.S1G749800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5611.t1 is derived from g2781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17888323	17889838	.	+	.	Phchi.S1G277000
Phchi.S1	AUGUSTUS	transcript	17888323	17889838	.	+	.	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	start_codon	17888323	17888325	.	+	0	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	CDS	17888323	17888862	0.86	+	0	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	exon	17888323	17888862	.	+	.	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	intron	17888863	17888963	.	+	.	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	CDS	17888964	17889505	0.75	+	0	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	exon	17888964	17889505	.	+	.	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	intron	17889506	17889582	.	+	.	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	CDS	17889583	17889838	0.82	+	1	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	exon	17889583	17889838	.	+	.	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
Phchi.S1	AUGUSTUS	stop_codon	17889839	17889841	.	+	0	transcript_id "Phchi.S1G277000.t1"; gene_id "Phchi.S1G277000"
# This transcript jg8677.t2 is derived from g5852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8677.t3 is derived from g5852.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8678.t1 is derived from g5853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37397145	37397994	.	+	.	Phchi.S1G583700
Phchi.S1	AUGUSTUS	transcript	37397145	37397994	.	+	.	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	start_codon	37397145	37397147	.	+	0	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	CDS	37397145	37397459	0.47	+	0	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	exon	37397145	37397459	.	+	.	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	intron	37397460	37397555	.	+	.	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	CDS	37397556	37397715	1	+	0	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	exon	37397556	37397715	.	+	.	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	intron	37397716	37397809	.	+	.	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	CDS	37397810	37397994	0.92	+	2	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	exon	37397810	37397994	.	+	.	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
Phchi.S1	AUGUSTUS	stop_codon	37397995	37397997	.	+	0	transcript_id "Phchi.S1G583700.t1"; gene_id "Phchi.S1G583700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2391.t1 is derived from g9311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6464394	6465058	.	-	.	Phchi.S5G100000
Phchi.S5	AUGUSTUS	transcript	6464394	6465058	.	-	.	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	stop_codon	6464391	6464393	.	-	0	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	CDS	6464394	6464547	1	-	1	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	exon	6464394	6464547	.	-	.	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	intron	6464548	6464639	.	-	.	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	CDS	6464640	6464757	1	-	2	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	exon	6464640	6464757	.	-	.	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	intron	6464758	6464985	.	-	.	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	CDS	6464986	6465058	1	-	0	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	exon	6464986	6465058	.	-	.	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
Phchi.S5	AUGUSTUS	start_codon	6465056	6465058	.	-	0	transcript_id "Phchi.S5G100000.t1"; gene_id "Phchi.S5G100000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15759.t1 is derived from g14229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21097213	21097966	.	-	.	Phchi.S3G307800
Phchi.S3	AUGUSTUS	transcript	21097213	21097966	.	-	.	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	stop_codon	21097210	21097212	.	-	0	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	CDS	21097213	21097436	1	-	2	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	exon	21097213	21097436	.	-	.	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	intron	21097437	21097806	.	-	.	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	CDS	21097807	21097966	1	-	0	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	exon	21097807	21097966	.	-	.	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
Phchi.S3	AUGUSTUS	start_codon	21097964	21097966	.	-	0	transcript_id "Phchi.S3G307800.t1"; gene_id "Phchi.S3G307800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7761.t1 is derived from g4935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31157437	31157919	.	+	.	Phchi.S1G492000
Phchi.S1	AUGUSTUS	transcript	31157437	31157919	.	+	.	transcript_id "Phchi.S1G492000.t1"; gene_id "Phchi.S1G492000"
Phchi.S1	AUGUSTUS	start_codon	31157437	31157439	.	+	0	transcript_id "Phchi.S1G492000.t1"; gene_id "Phchi.S1G492000"
Phchi.S1	AUGUSTUS	CDS	31157437	31157919	0.99	+	0	transcript_id "Phchi.S1G492000.t1"; gene_id "Phchi.S1G492000"
Phchi.S1	AUGUSTUS	exon	31157437	31157919	.	+	.	transcript_id "Phchi.S1G492000.t1"; gene_id "Phchi.S1G492000"
Phchi.S1	AUGUSTUS	stop_codon	31157920	31157922	.	+	0	transcript_id "Phchi.S1G492000.t1"; gene_id "Phchi.S1G492000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12208.t1 is derived from g7884.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6738570	6739251	.	+	.	Phchi.S2G028800
Phchi.S2	AUGUSTUS	transcript	6738570	6739251	.	+	.	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	start_codon	6738570	6738572	.	+	0	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	CDS	6738570	6738782	1	+	0	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	exon	6738570	6738782	.	+	.	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	intron	6738783	6738873	.	+	.	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	CDS	6738874	6739251	0.92	+	0	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	exon	6738874	6739251	.	+	.	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
Phchi.S2	AUGUSTUS	stop_codon	6739252	6739254	.	+	0	transcript_id "Phchi.S2G028800.t1"; gene_id "Phchi.S2G028800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12086.t1 is derived from g7761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2179853	2181834	.	-	.	Phchi.S2G016600
Phchi.S2	AUGUSTUS	transcript	2179853	2181834	.	-	.	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	stop_codon	2179850	2179852	.	-	0	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	CDS	2179853	2180643	0.72	-	2	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	exon	2179853	2180643	.	-	.	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	intron	2180644	2180711	.	-	.	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	CDS	2180712	2181834	0.77	-	0	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	exon	2180712	2181834	.	-	.	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
Phchi.S2	AUGUSTUS	start_codon	2181832	2181834	.	-	0	transcript_id "Phchi.S2G016600.t1"; gene_id "Phchi.S2G016600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3925.t1 is derived from g1094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6451425	6455015	.	+	.	Phchi.S1G108400
Phchi.S1	AUGUSTUS	transcript	6451425	6455015	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	start_codon	6451425	6451427	.	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6451425	6451649	0.98	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6451425	6451649	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6451650	6451774	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6451775	6452830	0.42	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6451775	6452830	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6452831	6453160	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6453161	6453259	0.97	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6453161	6453259	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6453260	6453351	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6453352	6453565	0.77	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6453352	6453565	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6453566	6453661	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6453662	6453736	0.81	+	2	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6453662	6453736	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6453737	6453823	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6453824	6454035	0.99	+	2	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6453824	6454035	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6454036	6454153	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6454154	6454336	1	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6454154	6454336	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6454337	6454438	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6454439	6454677	1	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6454439	6454677	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	intron	6454678	6454756	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	CDS	6454757	6455015	0.72	+	1	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	exon	6454757	6455015	.	+	.	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
Phchi.S1	AUGUSTUS	stop_codon	6455016	6455018	.	+	0	transcript_id "Phchi.S1G108400.t1"; gene_id "Phchi.S1G108400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4748.t1 is derived from g1918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12609390	12609825	.	-	.	Phchi.S1G190700
Phchi.S1	AUGUSTUS	transcript	12609390	12609825	.	-	.	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	stop_codon	12609387	12609389	.	-	0	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	CDS	12609390	12609410	0.98	-	0	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	exon	12609390	12609410	.	-	.	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	intron	12609411	12609503	.	-	.	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	CDS	12609504	12609609	0.89	-	1	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	exon	12609504	12609609	.	-	.	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	intron	12609610	12609733	.	-	.	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	CDS	12609734	12609825	0.9	-	0	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	exon	12609734	12609825	.	-	.	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
Phchi.S1	AUGUSTUS	start_codon	12609823	12609825	.	-	0	transcript_id "Phchi.S1G190700.t1"; gene_id "Phchi.S1G190700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4813.t1 is derived from g1983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12950226	12951062	.	+	.	Phchi.S1G197200
Phchi.S1	AUGUSTUS	transcript	12950757	12951062	.	+	.	transcript_id "Phchi.S1G197200.t1"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	start_codon	12950757	12950759	.	+	0	transcript_id "Phchi.S1G197200.t1"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	CDS	12950757	12951062	0.98	+	0	transcript_id "Phchi.S1G197200.t1"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	exon	12950757	12951062	.	+	.	transcript_id "Phchi.S1G197200.t1"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	stop_codon	12951063	12951065	.	+	0	transcript_id "Phchi.S1G197200.t1"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	transcript	12950226	12951062	.	+	.	transcript_id "Phchi.S1G197200.t2"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	start_codon	12950226	12950228	.	+	0	transcript_id "Phchi.S1G197200.t2"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	CDS	12950226	12951062	0.59	+	0	transcript_id "Phchi.S1G197200.t2"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	exon	12950226	12951062	.	+	.	transcript_id "Phchi.S1G197200.t2"; gene_id "Phchi.S1G197200"
Phchi.S1	AUGUSTUS	stop_codon	12951063	12951065	.	+	0	transcript_id "Phchi.S1G197200.t2"; gene_id "Phchi.S1G197200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14900.t1 is derived from g13368.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15439894	15442906	.	-	.	Phchi.S3G221900
Phchi.S3	AUGUSTUS	transcript	15439894	15442906	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	stop_codon	15439891	15439893	.	-	0	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	CDS	15439894	15440515	0.52	-	1	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	exon	15439894	15440515	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	intron	15440516	15440607	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	CDS	15440608	15442104	0.39	-	1	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	exon	15440608	15442104	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	intron	15442105	15442304	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	CDS	15442305	15442392	0.61	-	2	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	exon	15442305	15442392	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	intron	15442393	15442623	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	CDS	15442624	15442756	0.62	-	0	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	exon	15442624	15442756	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	intron	15442757	15442840	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	CDS	15442841	15442906	0.48	-	0	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	exon	15442841	15442906	.	-	.	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
Phchi.S3	AUGUSTUS	start_codon	15442904	15442906	.	-	0	transcript_id "Phchi.S3G221900.t1"; gene_id "Phchi.S3G221900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1983.t1 is derived from g8903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4243686	4244768	.	+	.	Phchi.S5G059200
Phchi.S5	AUGUSTUS	transcript	4243686	4244768	.	+	.	transcript_id "Phchi.S5G059200.t1"; gene_id "Phchi.S5G059200"
Phchi.S5	AUGUSTUS	start_codon	4243686	4243688	.	+	0	transcript_id "Phchi.S5G059200.t1"; gene_id "Phchi.S5G059200"
Phchi.S5	AUGUSTUS	CDS	4243686	4244768	1	+	0	transcript_id "Phchi.S5G059200.t1"; gene_id "Phchi.S5G059200"
Phchi.S5	AUGUSTUS	exon	4243686	4244768	.	+	.	transcript_id "Phchi.S5G059200.t1"; gene_id "Phchi.S5G059200"
Phchi.S5	AUGUSTUS	stop_codon	4244769	4244771	.	+	0	transcript_id "Phchi.S5G059200.t1"; gene_id "Phchi.S5G059200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14355.t1 is derived from g12822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12347643	12348667	.	+	.	Phchi.S3G167400
Phchi.S3	AUGUSTUS	transcript	12347643	12348667	.	+	.	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	start_codon	12347643	12347645	.	+	0	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	CDS	12347643	12347835	0.3	+	0	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	exon	12347643	12347835	.	+	.	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	intron	12347836	12348063	.	+	.	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	CDS	12348064	12348217	0.36	+	2	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	exon	12348064	12348217	.	+	.	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	intron	12348218	12348303	.	+	.	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	CDS	12348304	12348667	0.97	+	1	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	exon	12348304	12348667	.	+	.	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
Phchi.S3	AUGUSTUS	stop_codon	12348668	12348670	.	+	0	transcript_id "Phchi.S3G167400.t1"; gene_id "Phchi.S3G167400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11980.t1 is derived from g7655.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	325567	326877	.	+	.	Phchi.S2G006000
Phchi.S2	AUGUSTUS	transcript	325567	326877	.	+	.	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	start_codon	325567	325569	.	+	0	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	CDS	325567	325818	0.6	+	0	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	exon	325567	325818	.	+	.	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	intron	325819	325911	.	+	.	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	CDS	325912	326877	0.93	+	0	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	exon	325912	326877	.	+	.	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
Phchi.S2	AUGUSTUS	stop_codon	326878	326880	.	+	0	transcript_id "Phchi.S2G006000.t1"; gene_id "Phchi.S2G006000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3637.t1 is derived from g806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4873418	4875530	.	+	.	Phchi.S1G079600
Phchi.S1	AUGUSTUS	transcript	4873418	4875530	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	start_codon	4873418	4873420	.	+	0	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4873418	4873474	0.88	+	0	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4873418	4873474	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	intron	4873475	4873640	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4873641	4873965	1	+	0	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4873641	4873965	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	intron	4873966	4874049	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4874050	4874192	1	+	2	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4874050	4874192	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	intron	4874193	4874291	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4874292	4875530	0.99	+	0	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4874292	4875530	.	+	.	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	stop_codon	4875531	4875533	.	+	0	transcript_id "Phchi.S1G079600.t1"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	transcript	4873418	4875530	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	start_codon	4873418	4873420	.	+	0	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4873418	4873474	0.94	+	0	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4873418	4873474	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	intron	4873475	4873640	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4873641	4873914	0.58	+	0	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4873641	4873914	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	intron	4873915	4874049	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4874050	4874192	0.56	+	2	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4874050	4874192	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	intron	4874193	4874291	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	CDS	4874292	4875530	0.99	+	0	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	exon	4874292	4875530	.	+	.	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
Phchi.S1	AUGUSTUS	stop_codon	4875531	4875533	.	+	0	transcript_id "Phchi.S1G079600.t2"; gene_id "Phchi.S1G079600"
# This transcript jg12532.t2 is derived from g8209.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12533.t1 is derived from g8210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33572006	33576196	.	+	.	Phchi.S2G061300
Phchi.S2	AUGUSTUS	transcript	33572006	33576196	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	start_codon	33572006	33572008	.	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33572006	33572026	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33572006	33572026	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33572027	33572221	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33572222	33572374	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33572222	33572374	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33572375	33572525	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33572526	33572564	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33572526	33572564	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33572565	33572655	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33572656	33572747	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33572656	33572747	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33572748	33572858	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33572859	33573108	1	+	1	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33572859	33573108	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33573109	33573330	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33573331	33573450	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33573331	33573450	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33573451	33573536	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33573537	33573612	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33573537	33573612	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33573613	33574256	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33574257	33574465	1	+	2	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33574257	33574465	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33574466	33574767	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33574768	33574876	1	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33574768	33574876	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33574877	33575020	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33575021	33575113	1	+	2	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33575021	33575113	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33575114	33575395	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33575396	33575556	1	+	2	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33575396	33575556	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	intron	33575557	33575671	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	CDS	33575672	33576196	0.76	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	exon	33575672	33576196	.	+	.	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
Phchi.S2	AUGUSTUS	stop_codon	33576197	33576199	.	+	0	transcript_id "Phchi.S2G061300.t1"; gene_id "Phchi.S2G061300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9746.t1 is derived from g6922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43484383	43484896	.	+	.	Phchi.S1G690500
Phchi.S1	AUGUSTUS	transcript	43484383	43484896	.	+	.	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	start_codon	43484383	43484385	.	+	0	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	CDS	43484383	43484628	0.8	+	0	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	exon	43484383	43484628	.	+	.	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	intron	43484629	43484791	.	+	.	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	CDS	43484792	43484896	0.8	+	0	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	exon	43484792	43484896	.	+	.	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
Phchi.S1	AUGUSTUS	stop_codon	43484897	43484899	.	+	0	transcript_id "Phchi.S1G690500.t1"; gene_id "Phchi.S1G690500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6045.t1 is derived from g3216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20606331	20607218	.	+	.	Phchi.S1G320400
Phchi.S1	AUGUSTUS	transcript	20606331	20607218	.	+	.	transcript_id "Phchi.S1G320400.t1"; gene_id "Phchi.S1G320400"
Phchi.S1	AUGUSTUS	start_codon	20606331	20606333	.	+	0	transcript_id "Phchi.S1G320400.t1"; gene_id "Phchi.S1G320400"
Phchi.S1	AUGUSTUS	CDS	20606331	20607218	0.61	+	0	transcript_id "Phchi.S1G320400.t1"; gene_id "Phchi.S1G320400"
Phchi.S1	AUGUSTUS	exon	20606331	20607218	.	+	.	transcript_id "Phchi.S1G320400.t1"; gene_id "Phchi.S1G320400"
Phchi.S1	AUGUSTUS	stop_codon	20607219	20607221	.	+	0	transcript_id "Phchi.S1G320400.t1"; gene_id "Phchi.S1G320400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4122.t1 is derived from g1291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8361600	8363346	.	+	.	Phchi.S1G128100
Phchi.S1	AUGUSTUS	transcript	8361600	8363346	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	start_codon	8361600	8361602	.	+	0	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8361600	8361667	0.92	+	0	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8361600	8361667	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	intron	8361668	8361783	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8361784	8361929	0.98	+	1	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8361784	8361929	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	intron	8361930	8362004	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8362005	8362132	1	+	2	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8362005	8362132	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	intron	8362133	8362228	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8362229	8362488	1	+	0	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8362229	8362488	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	intron	8362489	8362575	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8362576	8362770	1	+	1	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8362576	8362770	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	intron	8362771	8362867	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8362868	8362948	1	+	1	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8362868	8362948	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	intron	8362949	8363024	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	CDS	8363025	8363346	0.6	+	1	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	exon	8363025	8363346	.	+	.	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
Phchi.S1	AUGUSTUS	stop_codon	8363347	8363349	.	+	0	transcript_id "Phchi.S1G128100.t1"; gene_id "Phchi.S1G128100"
# This transcript jg4183.t2 is derived from g1352.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4184.t1 is derived from g1353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8801619	8802710	.	+	.	Phchi.S1G134300
Phchi.S1	AUGUSTUS	transcript	8801619	8802710	.	+	.	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	start_codon	8801619	8801621	.	+	0	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	CDS	8801619	8801755	0.81	+	0	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	exon	8801619	8801755	.	+	.	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	intron	8801756	8802043	.	+	.	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	CDS	8802044	8802710	0.88	+	1	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	exon	8802044	8802710	.	+	.	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
Phchi.S1	AUGUSTUS	stop_codon	8802711	8802713	.	+	0	transcript_id "Phchi.S1G134300.t1"; gene_id "Phchi.S1G134300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5046.t1 is derived from g2216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14248557	14253780	.	+	.	Phchi.S1G220500
Phchi.S1	AUGUSTUS	transcript	14248557	14253780	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	start_codon	14248557	14248559	.	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14248557	14248569	0.77	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14248557	14248569	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14248570	14248658	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14248659	14248695	0.78	+	2	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14248659	14248695	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14248696	14248766	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14248767	14248825	0.83	+	1	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14248767	14248825	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14248826	14249149	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14249150	14249370	1	+	2	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14249150	14249370	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14249371	14249729	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14249730	14249865	1	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14249730	14249865	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14249866	14250027	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14250028	14250161	1	+	2	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14250028	14250161	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14250162	14251371	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14251372	14251477	1	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14251372	14251477	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14251478	14251945	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14251946	14252031	1	+	2	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14251946	14252031	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14252032	14252245	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14252246	14252434	1	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14252246	14252434	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14252435	14252600	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14252601	14252768	1	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14252601	14252768	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14252769	14252881	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14252882	14252995	1	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14252882	14252995	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	intron	14252996	14253534	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	CDS	14253535	14253780	1	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	exon	14253535	14253780	.	+	.	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
Phchi.S1	AUGUSTUS	stop_codon	14253781	14253783	.	+	0	transcript_id "Phchi.S1G220500.t1"; gene_id "Phchi.S1G220500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15446.t1 is derived from g13914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19211861	19212487	.	+	.	Phchi.S3G276500
Phchi.S3	AUGUSTUS	transcript	19211861	19212487	.	+	.	transcript_id "Phchi.S3G276500.t1"; gene_id "Phchi.S3G276500"
Phchi.S3	AUGUSTUS	start_codon	19211861	19211863	.	+	0	transcript_id "Phchi.S3G276500.t1"; gene_id "Phchi.S3G276500"
Phchi.S3	AUGUSTUS	CDS	19211861	19212487	0.74	+	0	transcript_id "Phchi.S3G276500.t1"; gene_id "Phchi.S3G276500"
Phchi.S3	AUGUSTUS	exon	19211861	19212487	.	+	.	transcript_id "Phchi.S3G276500.t1"; gene_id "Phchi.S3G276500"
Phchi.S3	AUGUSTUS	stop_codon	19212488	19212490	.	+	0	transcript_id "Phchi.S3G276500.t1"; gene_id "Phchi.S3G276500"
# This transcript jg15964.t2 is derived from g16003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15965.t1 is derived from g16004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	7496	8472	.	-	.	Phchi.C133G000400
Phchi.C133	AUGUSTUS	transcript	7496	8472	.	-	.	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	stop_codon	7493	7495	.	-	0	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	CDS	7496	8044	1	-	0	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	exon	7496	8044	.	-	.	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	intron	8045	8121	.	-	.	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	CDS	8122	8472	0.28	-	0	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	exon	8122	8472	.	-	.	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
Phchi.C133	AUGUSTUS	start_codon	8470	8472	.	-	0	transcript_id "Phchi.C133G000400.t1"; gene_id "Phchi.C133G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11445.t1 is derived from g15495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6395966	6396739	.	-	.	Phchi.S4G102700
Phchi.S4	AUGUSTUS	transcript	6395966	6396478	.	-	.	transcript_id "Phchi.S4G102700.t1"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	stop_codon	6395963	6395965	.	-	0	transcript_id "Phchi.S4G102700.t1"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	CDS	6395966	6396478	1	-	0	transcript_id "Phchi.S4G102700.t1"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	exon	6395966	6396478	.	-	.	transcript_id "Phchi.S4G102700.t1"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	start_codon	6396476	6396478	.	-	0	transcript_id "Phchi.S4G102700.t1"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	transcript	6395966	6396739	.	-	.	transcript_id "Phchi.S4G102700.t2"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	stop_codon	6395963	6395965	.	-	0	transcript_id "Phchi.S4G102700.t2"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	CDS	6395966	6396739	0.72	-	0	transcript_id "Phchi.S4G102700.t2"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	exon	6395966	6396739	.	-	.	transcript_id "Phchi.S4G102700.t2"; gene_id "Phchi.S4G102700"
Phchi.S4	AUGUSTUS	start_codon	6396737	6396739	.	-	0	transcript_id "Phchi.S4G102700.t2"; gene_id "Phchi.S4G102700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6293.t1 is derived from g3465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22129221	22130321	.	-	.	Phchi.S1G345200
Phchi.S1	AUGUSTUS	transcript	22129221	22130321	.	-	.	transcript_id "Phchi.S1G345200.t1"; gene_id "Phchi.S1G345200"
Phchi.S1	AUGUSTUS	stop_codon	22129218	22129220	.	-	0	transcript_id "Phchi.S1G345200.t1"; gene_id "Phchi.S1G345200"
Phchi.S1	AUGUSTUS	CDS	22129221	22130321	0.99	-	0	transcript_id "Phchi.S1G345200.t1"; gene_id "Phchi.S1G345200"
Phchi.S1	AUGUSTUS	exon	22129221	22130321	.	-	.	transcript_id "Phchi.S1G345200.t1"; gene_id "Phchi.S1G345200"
Phchi.S1	AUGUSTUS	start_codon	22130319	22130321	.	-	0	transcript_id "Phchi.S1G345200.t1"; gene_id "Phchi.S1G345200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10379.t1 is derived from g7555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47474245	47474957	.	-	.	Phchi.S1G753800
Phchi.S1	AUGUSTUS	transcript	47474245	47474957	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	stop_codon	47474242	47474244	.	-	0	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	CDS	47474245	47474288	1	-	2	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	exon	47474245	47474288	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	intron	47474289	47474473	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	CDS	47474474	47474536	1	-	2	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	exon	47474474	47474536	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	intron	47474537	47474632	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	CDS	47474633	47474793	1	-	1	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	exon	47474633	47474793	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	intron	47474794	47474916	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	CDS	47474917	47474957	1	-	0	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	exon	47474917	47474957	.	-	.	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
Phchi.S1	AUGUSTUS	start_codon	47474955	47474957	.	-	0	transcript_id "Phchi.S1G753800.t1"; gene_id "Phchi.S1G753800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14728.t1 is derived from g13196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14389155	14398680	.	-	.	Phchi.S3G204700
Phchi.S3	AUGUSTUS	transcript	14395244	14398680	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	stop_codon	14395241	14395243	.	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14395244	14395259	0.94	-	1	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14395244	14395259	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14395260	14395406	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14395407	14395997	0.82	-	1	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14395407	14395997	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14395998	14396095	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396096	14396169	1	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396096	14396169	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396170	14396319	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396320	14396442	1	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396320	14396442	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396443	14396535	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396536	14396666	1	-	2	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396536	14396666	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396667	14396799	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396800	14396948	1	-	1	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396800	14396948	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396949	14397227	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14397228	14397443	1	-	1	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14397228	14397443	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14397444	14397596	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14397597	14397679	1	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14397597	14397679	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14397680	14397786	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14397787	14397903	1	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14397787	14397903	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14397904	14398034	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14398035	14398413	0.83	-	1	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14398035	14398413	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14398414	14398564	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14398565	14398680	0.73	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14398565	14398680	.	-	.	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	start_codon	14398678	14398680	.	-	0	transcript_id "Phchi.S3G204700.t1"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	transcript	14389155	14398680	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	stop_codon	14389152	14389154	.	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14389155	14389538	0.68	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14389155	14389538	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14389539	14389683	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14389684	14390137	0.95	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14389684	14390137	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14390138	14390224	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14390225	14390469	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14390225	14390469	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14390470	14390672	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14390673	14390798	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14390673	14390798	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14390799	14390946	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14390947	14391012	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14390947	14391012	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14391013	14391154	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14391155	14392003	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14391155	14392003	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14392004	14392087	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14392088	14392119	1	-	2	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14392088	14392119	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14392120	14392199	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14392200	14392306	0.55	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14392200	14392306	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14392307	14392486	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14392487	14392608	0.54	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14392487	14392608	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14392609	14392712	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14392713	14394145	0.99	-	2	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14392713	14394145	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14394146	14394231	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14394232	14394529	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14394232	14394529	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14394530	14394620	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14394621	14394833	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14394621	14394833	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14394834	14394917	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14394918	14395055	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14394918	14395055	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14395056	14395164	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14395165	14395267	0.98	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14395165	14395267	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14395268	14395406	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14395407	14395997	0.82	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14395407	14395997	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14395998	14396095	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396096	14396169	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396096	14396169	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396170	14396319	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396320	14396442	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396320	14396442	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396443	14396535	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396536	14396666	1	-	2	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396536	14396666	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396667	14396799	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14396800	14396948	1	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14396800	14396948	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14396949	14397227	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14397228	14397443	1	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14397228	14397443	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14397444	14397596	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14397597	14397679	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14397597	14397679	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14397680	14397786	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14397787	14397903	1	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14397787	14397903	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14397904	14398034	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14398035	14398413	0.81	-	1	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14398035	14398413	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	intron	14398414	14398564	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	CDS	14398565	14398680	0.71	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	exon	14398565	14398680	.	-	.	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
Phchi.S3	AUGUSTUS	start_codon	14398678	14398680	.	-	0	transcript_id "Phchi.S3G204700.t2"; gene_id "Phchi.S3G204700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg782.t1 is derived from g10564.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5475235	5475765	.	+	.	Phchi.S6G074100
Phchi.S6	AUGUSTUS	transcript	5475235	5475765	.	+	.	transcript_id "Phchi.S6G074100.t1"; gene_id "Phchi.S6G074100"
Phchi.S6	AUGUSTUS	start_codon	5475235	5475237	.	+	0	transcript_id "Phchi.S6G074100.t1"; gene_id "Phchi.S6G074100"
Phchi.S6	AUGUSTUS	CDS	5475235	5475765	0.98	+	0	transcript_id "Phchi.S6G074100.t1"; gene_id "Phchi.S6G074100"
Phchi.S6	AUGUSTUS	exon	5475235	5475765	.	+	.	transcript_id "Phchi.S6G074100.t1"; gene_id "Phchi.S6G074100"
Phchi.S6	AUGUSTUS	stop_codon	5475766	5475768	.	+	0	transcript_id "Phchi.S6G074100.t1"; gene_id "Phchi.S6G074100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8966.t1 is derived from g6141.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38878180	38879060	.	-	.	Phchi.S1G612500
Phchi.S1	AUGUSTUS	transcript	38878180	38879060	.	-	.	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	stop_codon	38878177	38878179	.	-	0	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	CDS	38878180	38878429	0.8	-	1	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	exon	38878180	38878429	.	-	.	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	intron	38878430	38878520	.	-	.	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	CDS	38878521	38878942	0.98	-	0	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	exon	38878521	38878942	.	-	.	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	intron	38878943	38879033	.	-	.	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	CDS	38879034	38879060	0.81	-	0	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	exon	38879034	38879060	.	-	.	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
Phchi.S1	AUGUSTUS	start_codon	38879058	38879060	.	-	0	transcript_id "Phchi.S1G612500.t1"; gene_id "Phchi.S1G612500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9999.t1 is derived from g7175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44941674	44943500	.	+	.	Phchi.S1G715800
Phchi.S1	AUGUSTUS	transcript	44941674	44943500	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	start_codon	44941674	44941676	.	+	0	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	CDS	44941674	44941795	1	+	0	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	exon	44941674	44941795	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	intron	44941796	44942011	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	CDS	44942012	44942267	0.44	+	1	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	exon	44942012	44942267	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	intron	44942268	44942374	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	CDS	44942375	44942622	0.38	+	0	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	exon	44942375	44942622	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	intron	44942623	44942779	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	CDS	44942780	44943500	0.89	+	1	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	exon	44942780	44943500	.	+	.	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
Phchi.S1	AUGUSTUS	stop_codon	44943501	44943503	.	+	0	transcript_id "Phchi.S1G715800.t1"; gene_id "Phchi.S1G715800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4498.t1 is derived from g1668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10821249	10821940	.	-	.	Phchi.S1G165700
Phchi.S1	AUGUSTUS	transcript	10821249	10821940	.	-	.	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	stop_codon	10821246	10821248	.	-	0	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	CDS	10821249	10821335	1	-	0	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	exon	10821249	10821335	.	-	.	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	intron	10821336	10821415	.	-	.	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	CDS	10821416	10821541	1	-	0	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	exon	10821416	10821541	.	-	.	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	intron	10821542	10821667	.	-	.	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	CDS	10821668	10821940	1	-	0	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	exon	10821668	10821940	.	-	.	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
Phchi.S1	AUGUSTUS	start_codon	10821938	10821940	.	-	0	transcript_id "Phchi.S1G165700.t1"; gene_id "Phchi.S1G165700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11644.t1 is derived from g15695.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7440523	7441972	.	+	.	Phchi.S4G122600
Phchi.S4	AUGUSTUS	transcript	7440523	7441972	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	start_codon	7440523	7440525	.	+	0	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	CDS	7440523	7440594	0.96	+	0	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	exon	7440523	7440594	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	intron	7440595	7440857	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	CDS	7440858	7441033	0.99	+	0	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	exon	7440858	7441033	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	intron	7441034	7441142	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	CDS	7441143	7441544	0.93	+	1	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	exon	7441143	7441544	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	intron	7441545	7441767	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	CDS	7441768	7441972	0.98	+	1	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	exon	7441768	7441972	.	+	.	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
Phchi.S4	AUGUSTUS	stop_codon	7441973	7441975	.	+	0	transcript_id "Phchi.S4G122600.t1"; gene_id "Phchi.S4G122600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2620.t1 is derived from g9540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7802544	7803821	.	+	.	Phchi.S5G122900
Phchi.S5	AUGUSTUS	transcript	7802544	7803821	.	+	.	transcript_id "Phchi.S5G122900.t1"; gene_id "Phchi.S5G122900"
Phchi.S5	AUGUSTUS	start_codon	7802544	7802546	.	+	0	transcript_id "Phchi.S5G122900.t1"; gene_id "Phchi.S5G122900"
Phchi.S5	AUGUSTUS	CDS	7802544	7803821	0.61	+	0	transcript_id "Phchi.S5G122900.t1"; gene_id "Phchi.S5G122900"
Phchi.S5	AUGUSTUS	exon	7802544	7803821	.	+	.	transcript_id "Phchi.S5G122900.t1"; gene_id "Phchi.S5G122900"
Phchi.S5	AUGUSTUS	stop_codon	7803822	7803824	.	+	0	transcript_id "Phchi.S5G122900.t1"; gene_id "Phchi.S5G122900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9837.t1 is derived from g7013.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44012727	44014929	.	+	.	Phchi.S1G699600
Phchi.S1	AUGUSTUS	transcript	44012727	44014929	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	start_codon	44012727	44012729	.	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44012727	44012764	1	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44012727	44012764	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44012765	44013076	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013077	44013101	1	+	1	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013077	44013101	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013102	44013198	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013199	44013324	1	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013199	44013324	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013325	44013410	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013411	44013515	1	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013411	44013515	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013516	44013615	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013616	44013711	1	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013616	44013711	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013712	44013830	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013831	44013935	1	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013831	44013935	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013936	44014020	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44014021	44014929	1	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44014021	44014929	.	+	.	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	stop_codon	44014930	44014932	.	+	0	transcript_id "Phchi.S1G699600.t1"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	transcript	44012727	44014929	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	start_codon	44012727	44012729	.	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44012727	44012764	1	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44012727	44012764	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44012765	44013079	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013080	44013101	1	+	1	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013080	44013101	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013102	44013198	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013199	44013324	1	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013199	44013324	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013325	44013410	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013411	44013515	1	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013411	44013515	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013516	44013615	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013616	44013711	1	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013616	44013711	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013712	44013830	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44013831	44013935	0.99	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44013831	44013935	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	intron	44013936	44014020	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	CDS	44014021	44014929	0.99	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	exon	44014021	44014929	.	+	.	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
Phchi.S1	AUGUSTUS	stop_codon	44014930	44014932	.	+	0	transcript_id "Phchi.S1G699600.t2"; gene_id "Phchi.S1G699600"
# This transcript jg8032.t2 is derived from g5207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8033.t1 is derived from g5208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32565603	32567198	.	-	.	Phchi.S1G519200
Phchi.S1	AUGUSTUS	transcript	32565603	32567198	.	-	.	transcript_id "Phchi.S1G519200.t1"; gene_id "Phchi.S1G519200"
Phchi.S1	AUGUSTUS	stop_codon	32565600	32565602	.	-	0	transcript_id "Phchi.S1G519200.t1"; gene_id "Phchi.S1G519200"
Phchi.S1	AUGUSTUS	CDS	32565603	32567198	0.96	-	0	transcript_id "Phchi.S1G519200.t1"; gene_id "Phchi.S1G519200"
Phchi.S1	AUGUSTUS	exon	32565603	32567198	.	-	.	transcript_id "Phchi.S1G519200.t1"; gene_id "Phchi.S1G519200"
Phchi.S1	AUGUSTUS	start_codon	32567196	32567198	.	-	0	transcript_id "Phchi.S1G519200.t1"; gene_id "Phchi.S1G519200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15452.t1 is derived from g13920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19235617	19238446	.	-	.	Phchi.S3G277100
Phchi.S3	AUGUSTUS	transcript	19235617	19238446	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	stop_codon	19235614	19235616	.	-	0	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19235617	19235632	1	-	1	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19235617	19235632	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19235633	19235727	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19235728	19235770	0.98	-	2	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19235728	19235770	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19235771	19235876	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19235877	19235897	0.99	-	2	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19235877	19235897	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19235898	19236131	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19236132	19236163	0.98	-	1	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19236132	19236163	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19236164	19236350	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19236351	19236510	0.94	-	2	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19236351	19236510	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19236511	19236600	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19236601	19236666	0.79	-	2	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19236601	19236666	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19236667	19236838	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19236839	19237041	0.55	-	1	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19236839	19237041	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19237042	19237145	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19237146	19237475	0.99	-	1	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19237146	19237475	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19237476	19237575	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19237576	19237680	1	-	1	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19237576	19237680	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19237681	19237764	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19237765	19237925	1	-	0	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19237765	19237925	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19237926	19238083	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19238084	19238246	1	-	1	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19238084	19238246	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	intron	19238247	19238324	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	CDS	19238325	19238446	1	-	0	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	exon	19238325	19238446	.	-	.	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
Phchi.S3	AUGUSTUS	start_codon	19238444	19238446	.	-	0	transcript_id "Phchi.S3G277100.t1"; gene_id "Phchi.S3G277100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg941.t1 is derived from g10723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6565251	6565610	.	-	.	Phchi.S6G090000
Phchi.S6	AUGUSTUS	transcript	6565251	6565610	.	-	.	transcript_id "Phchi.S6G090000.t1"; gene_id "Phchi.S6G090000"
Phchi.S6	AUGUSTUS	stop_codon	6565248	6565250	.	-	0	transcript_id "Phchi.S6G090000.t1"; gene_id "Phchi.S6G090000"
Phchi.S6	AUGUSTUS	CDS	6565251	6565610	0.73	-	0	transcript_id "Phchi.S6G090000.t1"; gene_id "Phchi.S6G090000"
Phchi.S6	AUGUSTUS	exon	6565251	6565610	.	-	.	transcript_id "Phchi.S6G090000.t1"; gene_id "Phchi.S6G090000"
Phchi.S6	AUGUSTUS	start_codon	6565608	6565610	.	-	0	transcript_id "Phchi.S6G090000.t1"; gene_id "Phchi.S6G090000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8334.t1 is derived from g5509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35367618	35371084	.	+	.	Phchi.S1G549300
Phchi.S1	AUGUSTUS	transcript	35367618	35371084	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	start_codon	35367618	35367620	.	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35367618	35367764	0.43	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35367618	35367764	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35367765	35367877	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35367878	35367997	1	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35367878	35367997	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35367998	35368124	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35368125	35368247	1	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35368125	35368247	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35368248	35368341	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35368342	35368358	0.94	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35368342	35368358	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35368359	35368571	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35368572	35368588	0.95	+	1	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35368572	35368588	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35368589	35368874	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35368875	35368976	0.55	+	2	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35368875	35368976	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35368977	35369104	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35369105	35369168	0.47	+	2	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35369105	35369168	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35369169	35369364	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35369365	35369602	0.89	+	1	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35369365	35369602	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35369603	35369695	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35369696	35369739	0.46	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35369696	35369739	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35369740	35369932	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35369933	35370049	0.42	+	1	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35369933	35370049	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35370050	35370174	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35370175	35370181	0.8	+	1	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35370175	35370181	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35370182	35370283	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35370284	35370337	0.58	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35370284	35370337	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35370338	35370566	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35370567	35370632	1	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35370567	35370632	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35370633	35370718	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35370719	35370764	1	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35370719	35370764	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35370765	35370837	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35370838	35370884	1	+	2	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35370838	35370884	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	intron	35370885	35370958	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	CDS	35370959	35371084	0.91	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	exon	35370959	35371084	.	+	.	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
Phchi.S1	AUGUSTUS	stop_codon	35371085	35371087	.	+	0	transcript_id "Phchi.S1G549300.t1"; gene_id "Phchi.S1G549300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg179.t1 is derived from g9961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1029158	1030251	.	+	.	Phchi.S6G013800
Phchi.S6	AUGUSTUS	transcript	1029158	1030251	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	start_codon	1029158	1029160	.	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1029158	1029198	0.55	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1029158	1029198	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	intron	1029199	1029283	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1029284	1029425	0.54	+	1	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1029284	1029425	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	intron	1029426	1029524	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1029525	1029608	1	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1029525	1029608	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	intron	1029609	1029686	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1029687	1029736	1	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1029687	1029736	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	intron	1029737	1029823	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1029824	1029872	1	+	1	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1029824	1029872	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	intron	1029873	1029976	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1029977	1030051	1	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1029977	1030051	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	intron	1030052	1030131	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	CDS	1030132	1030251	1	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	exon	1030132	1030251	.	+	.	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
Phchi.S6	AUGUSTUS	stop_codon	1030252	1030254	.	+	0	transcript_id "Phchi.S6G013800.t1"; gene_id "Phchi.S6G013800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11924.t1 is derived from g7599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	48512	49099	.	+	.	Phchi.S2G000400
Phchi.S2	AUGUSTUS	transcript	48512	49099	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	start_codon	48512	48514	.	+	0	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	CDS	48512	48517	0.82	+	0	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	exon	48512	48517	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	intron	48518	48618	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	CDS	48619	48655	0.71	+	0	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	exon	48619	48655	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	intron	48656	48748	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	CDS	48749	48806	0.82	+	2	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	exon	48749	48806	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	intron	48807	48893	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	CDS	48894	48996	0.82	+	1	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	exon	48894	48996	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	intron	48997	49078	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	CDS	49079	49099	0.82	+	0	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	exon	49079	49099	.	+	.	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
Phchi.S2	AUGUSTUS	stop_codon	49100	49102	.	+	0	transcript_id "Phchi.S2G000400.t1"; gene_id "Phchi.S2G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg309.t1 is derived from g10091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2213758	2215175	.	+	.	Phchi.S6G026800
Phchi.S6	AUGUSTUS	transcript	2213758	2215175	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	start_codon	2213758	2213760	.	+	0	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	CDS	2213758	2213866	1	+	0	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	exon	2213758	2213866	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	intron	2213867	2214073	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	CDS	2214074	2214182	1	+	2	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	exon	2214074	2214182	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	intron	2214183	2214435	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	CDS	2214436	2214514	0.99	+	1	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	exon	2214436	2214514	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	intron	2214515	2214621	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	CDS	2214622	2214738	1	+	0	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	exon	2214622	2214738	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	intron	2214739	2215037	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	CDS	2215038	2215175	0.99	+	0	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	exon	2215038	2215175	.	+	.	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
Phchi.S6	AUGUSTUS	stop_codon	2215176	2215178	.	+	0	transcript_id "Phchi.S6G026800.t1"; gene_id "Phchi.S6G026800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12243.t1 is derived from g7919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6947805	6949463	.	+	.	Phchi.S2G032300
Phchi.S2	AUGUSTUS	transcript	6947805	6949463	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	start_codon	6947805	6947807	.	+	0	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6947805	6947871	0.8	+	0	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6947805	6947871	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6947872	6948090	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6948091	6948128	1	+	2	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6948091	6948128	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6948129	6948217	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6948218	6948292	1	+	0	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6948218	6948292	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6948293	6948478	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6948479	6948562	1	+	0	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6948479	6948562	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6948563	6948782	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6948783	6948817	1	+	0	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6948783	6948817	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6948818	6948986	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6948987	6949072	1	+	1	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6948987	6949072	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6949073	6949268	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6949269	6949334	1	+	2	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6949269	6949334	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	intron	6949335	6949431	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	CDS	6949432	6949463	1	+	2	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	exon	6949432	6949463	.	+	.	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
Phchi.S2	AUGUSTUS	stop_codon	6949464	6949466	.	+	0	transcript_id "Phchi.S2G032300.t1"; gene_id "Phchi.S2G032300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2094.t1 is derived from g9014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4841666	4842801	.	+	.	Phchi.S5G070300
Phchi.S5	AUGUSTUS	transcript	4841666	4842801	.	+	.	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	start_codon	4841666	4841668	.	+	0	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	CDS	4841666	4841825	0.73	+	0	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	exon	4841666	4841825	.	+	.	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	intron	4841826	4841932	.	+	.	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	CDS	4841933	4842195	0.93	+	2	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	exon	4841933	4842195	.	+	.	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	intron	4842196	4842279	.	+	.	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	CDS	4842280	4842801	0.94	+	0	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	exon	4842280	4842801	.	+	.	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
Phchi.S5	AUGUSTUS	stop_codon	4842802	4842804	.	+	0	transcript_id "Phchi.S5G070300.t1"; gene_id "Phchi.S5G070300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7987.t1 is derived from g5162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32265657	32266141	.	-	.	Phchi.S1G514600
Phchi.S1	AUGUSTUS	transcript	32265657	32266141	.	-	.	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	stop_codon	32265654	32265656	.	-	0	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	CDS	32265657	32265791	1	-	0	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	exon	32265657	32265791	.	-	.	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	intron	32265792	32266000	.	-	.	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	CDS	32266001	32266141	0.93	-	0	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	exon	32266001	32266141	.	-	.	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
Phchi.S1	AUGUSTUS	start_codon	32266139	32266141	.	-	0	transcript_id "Phchi.S1G514600.t1"; gene_id "Phchi.S1G514600"
# This transcript jg13067.t2 is derived from g11532.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13068.t1 is derived from g11533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3995535	3996431	.	+	.	Phchi.S3G038700
Phchi.S3	AUGUSTUS	transcript	3995535	3996431	.	+	.	transcript_id "Phchi.S3G038700.t1"; gene_id "Phchi.S3G038700"
Phchi.S3	AUGUSTUS	start_codon	3995535	3995537	.	+	0	transcript_id "Phchi.S3G038700.t1"; gene_id "Phchi.S3G038700"
Phchi.S3	AUGUSTUS	CDS	3995535	3996431	0.93	+	0	transcript_id "Phchi.S3G038700.t1"; gene_id "Phchi.S3G038700"
Phchi.S3	AUGUSTUS	exon	3995535	3996431	.	+	.	transcript_id "Phchi.S3G038700.t1"; gene_id "Phchi.S3G038700"
Phchi.S3	AUGUSTUS	stop_codon	3996432	3996434	.	+	0	transcript_id "Phchi.S3G038700.t1"; gene_id "Phchi.S3G038700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10011.t1 is derived from g7187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45043554	45044505	.	+	.	Phchi.S1G717000
Phchi.S1	AUGUSTUS	transcript	45043554	45044505	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	start_codon	45043554	45043556	.	+	0	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	CDS	45043554	45043652	0.78	+	0	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	exon	45043554	45043652	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	intron	45043653	45043740	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	CDS	45043741	45043869	1	+	0	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	exon	45043741	45043869	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	intron	45043870	45044091	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	CDS	45044092	45044147	0.6	+	0	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	exon	45044092	45044147	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	intron	45044148	45044291	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	CDS	45044292	45044505	0.87	+	1	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	exon	45044292	45044505	.	+	.	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
Phchi.S1	AUGUSTUS	stop_codon	45044506	45044508	.	+	0	transcript_id "Phchi.S1G717000.t1"; gene_id "Phchi.S1G717000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2992.t1 is derived from g161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1044486	1046015	.	+	.	Phchi.S1G015100
Phchi.S1	AUGUSTUS	transcript	1044486	1046015	.	+	.	transcript_id "Phchi.S1G015100.t1"; gene_id "Phchi.S1G015100"
Phchi.S1	AUGUSTUS	start_codon	1044486	1044488	.	+	0	transcript_id "Phchi.S1G015100.t1"; gene_id "Phchi.S1G015100"
Phchi.S1	AUGUSTUS	CDS	1044486	1046015	1	+	0	transcript_id "Phchi.S1G015100.t1"; gene_id "Phchi.S1G015100"
Phchi.S1	AUGUSTUS	exon	1044486	1046015	.	+	.	transcript_id "Phchi.S1G015100.t1"; gene_id "Phchi.S1G015100"
Phchi.S1	AUGUSTUS	stop_codon	1046016	1046018	.	+	0	transcript_id "Phchi.S1G015100.t1"; gene_id "Phchi.S1G015100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3180.t1 is derived from g349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2120413	2121286	.	+	.	Phchi.S1G033900
Phchi.S1	AUGUSTUS	transcript	2120413	2121286	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	start_codon	2120413	2120415	.	+	0	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	CDS	2120413	2120772	0.74	+	0	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	exon	2120413	2120772	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	intron	2120773	2120897	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	CDS	2120898	2120912	0.68	+	0	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	exon	2120898	2120912	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	intron	2120913	2120995	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	CDS	2120996	2121091	0.68	+	0	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	exon	2120996	2121091	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	intron	2121092	2121277	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	CDS	2121278	2121286	0.85	+	0	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	exon	2121278	2121286	.	+	.	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
Phchi.S1	AUGUSTUS	stop_codon	2121287	2121289	.	+	0	transcript_id "Phchi.S1G033900.t1"; gene_id "Phchi.S1G033900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9973.t1 is derived from g7149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44723102	44725146	.	+	.	Phchi.S1G713200
Phchi.S1	AUGUSTUS	transcript	44723102	44725146	.	+	.	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	start_codon	44723102	44723104	.	+	0	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	CDS	44723102	44723327	0.93	+	0	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	exon	44723102	44723327	.	+	.	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	intron	44723328	44723407	.	+	.	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	CDS	44723408	44725146	0.86	+	2	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	exon	44723408	44725146	.	+	.	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
Phchi.S1	AUGUSTUS	stop_codon	44725147	44725149	.	+	0	transcript_id "Phchi.S1G713200.t1"; gene_id "Phchi.S1G713200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15454.t1 is derived from g13922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19245695	19246794	.	+	.	Phchi.S3G277300
Phchi.S3	AUGUSTUS	transcript	19245695	19246794	.	+	.	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	start_codon	19245695	19245697	.	+	0	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	CDS	19245695	19246266	0.55	+	0	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	exon	19245695	19246266	.	+	.	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	intron	19246267	19246403	.	+	.	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	CDS	19246404	19246794	0.96	+	1	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	exon	19246404	19246794	.	+	.	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
Phchi.S3	AUGUSTUS	stop_codon	19246795	19246797	.	+	0	transcript_id "Phchi.S3G277300.t1"; gene_id "Phchi.S3G277300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4473.t1 is derived from g1643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10679169	10679546	.	+	.	Phchi.S1G163200
Phchi.S1	AUGUSTUS	transcript	10679169	10679546	.	+	.	transcript_id "Phchi.S1G163200.t1"; gene_id "Phchi.S1G163200"
Phchi.S1	AUGUSTUS	start_codon	10679169	10679171	.	+	0	transcript_id "Phchi.S1G163200.t1"; gene_id "Phchi.S1G163200"
Phchi.S1	AUGUSTUS	CDS	10679169	10679546	0.73	+	0	transcript_id "Phchi.S1G163200.t1"; gene_id "Phchi.S1G163200"
Phchi.S1	AUGUSTUS	exon	10679169	10679546	.	+	.	transcript_id "Phchi.S1G163200.t1"; gene_id "Phchi.S1G163200"
Phchi.S1	AUGUSTUS	stop_codon	10679547	10679549	.	+	0	transcript_id "Phchi.S1G163200.t1"; gene_id "Phchi.S1G163200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6835.t1 is derived from g4007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25475211	25475629	.	-	.	Phchi.S1G399400
Phchi.S1	AUGUSTUS	transcript	25475211	25475629	.	-	.	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	stop_codon	25475208	25475210	.	-	0	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	CDS	25475211	25475287	0.97	-	2	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	exon	25475211	25475287	.	-	.	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	intron	25475288	25475379	.	-	.	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	CDS	25475380	25475629	0.92	-	0	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	exon	25475380	25475629	.	-	.	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
Phchi.S1	AUGUSTUS	start_codon	25475627	25475629	.	-	0	transcript_id "Phchi.S1G399400.t1"; gene_id "Phchi.S1G399400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg268.t1 is derived from g10050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1916430	1917596	.	-	.	Phchi.S6G022700
Phchi.S6	AUGUSTUS	transcript	1916430	1917596	.	-	.	transcript_id "Phchi.S6G022700.t1"; gene_id "Phchi.S6G022700"
Phchi.S6	AUGUSTUS	stop_codon	1916427	1916429	.	-	0	transcript_id "Phchi.S6G022700.t1"; gene_id "Phchi.S6G022700"
Phchi.S6	AUGUSTUS	CDS	1916430	1917596	0.69	-	0	transcript_id "Phchi.S6G022700.t1"; gene_id "Phchi.S6G022700"
Phchi.S6	AUGUSTUS	exon	1916430	1917596	.	-	.	transcript_id "Phchi.S6G022700.t1"; gene_id "Phchi.S6G022700"
Phchi.S6	AUGUSTUS	start_codon	1917594	1917596	.	-	0	transcript_id "Phchi.S6G022700.t1"; gene_id "Phchi.S6G022700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4689.t1 is derived from g1859.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12155021	12155800	.	-	.	Phchi.S1G184800
Phchi.S1	AUGUSTUS	transcript	12155021	12155800	.	-	.	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	stop_codon	12155018	12155020	.	-	0	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	CDS	12155021	12155570	0.59	-	1	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	exon	12155021	12155570	.	-	.	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	intron	12155571	12155681	.	-	.	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	CDS	12155682	12155800	0.61	-	0	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	exon	12155682	12155800	.	-	.	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
Phchi.S1	AUGUSTUS	start_codon	12155798	12155800	.	-	0	transcript_id "Phchi.S1G184800.t1"; gene_id "Phchi.S1G184800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12720.t1 is derived from g11185.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1116501	1117454	.	+	.	Phchi.S3G003900
Phchi.S3	AUGUSTUS	transcript	1116501	1117454	.	+	.	transcript_id "Phchi.S3G003900.t1"; gene_id "Phchi.S3G003900"
Phchi.S3	AUGUSTUS	start_codon	1116501	1116503	.	+	0	transcript_id "Phchi.S3G003900.t1"; gene_id "Phchi.S3G003900"
Phchi.S3	AUGUSTUS	CDS	1116501	1117454	0.82	+	0	transcript_id "Phchi.S3G003900.t1"; gene_id "Phchi.S3G003900"
Phchi.S3	AUGUSTUS	exon	1116501	1117454	.	+	.	transcript_id "Phchi.S3G003900.t1"; gene_id "Phchi.S3G003900"
Phchi.S3	AUGUSTUS	stop_codon	1117455	1117457	.	+	0	transcript_id "Phchi.S3G003900.t1"; gene_id "Phchi.S3G003900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2408.t1 is derived from g9328.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6520499	6523204	.	+	.	Phchi.S5G101700
Phchi.S5	AUGUSTUS	transcript	6520499	6523204	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	start_codon	6520499	6520501	.	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6520499	6520675	0.99	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6520499	6520675	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6520676	6520804	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6520805	6521127	1	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6520805	6521127	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6521128	6521228	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6521229	6521799	0.56	+	1	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6521229	6521799	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6521800	6521936	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6521937	6522233	0.35	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6521937	6522233	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6522234	6522313	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6522314	6522535	0.37	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6522314	6522535	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6522536	6522620	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6522621	6522890	0.99	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6522621	6522890	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6522891	6522981	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6522982	6523088	0.97	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6522982	6523088	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	intron	6523089	6523182	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	CDS	6523183	6523204	0.57	+	1	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	exon	6523183	6523204	.	+	.	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
Phchi.S5	AUGUSTUS	stop_codon	6523205	6523207	.	+	0	transcript_id "Phchi.S5G101700.t1"; gene_id "Phchi.S5G101700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15755.t1 is derived from g14225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21078846	21081548	.	+	.	Phchi.S3G307400
Phchi.S3	AUGUSTUS	transcript	21078846	21081548	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	start_codon	21078846	21078848	.	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21078846	21078900	0.93	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21078846	21078900	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21078901	21079036	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21079037	21079065	1	+	2	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21079037	21079065	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21079066	21079152	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21079153	21079236	1	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21079153	21079236	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21079237	21079334	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21079335	21079388	0.95	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21079335	21079388	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21079389	21079505	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21079506	21079583	0.95	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21079506	21079583	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21079584	21079672	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21079673	21079726	1	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21079673	21079726	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21079727	21079809	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21079810	21079869	1	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21079810	21079869	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21079870	21080002	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21080003	21080098	1	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21080003	21080098	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21080099	21080194	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21080195	21080296	1	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21080195	21080296	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21080297	21080414	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21080415	21080495	1	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21080415	21080495	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21080496	21080578	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21080579	21080896	0.92	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21080579	21080896	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21080897	21081024	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21081025	21081076	0.98	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21081025	21081076	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	intron	21081077	21081351	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	CDS	21081352	21081548	0.49	+	2	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	exon	21081352	21081548	.	+	.	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
Phchi.S3	AUGUSTUS	stop_codon	21081549	21081551	.	+	0	transcript_id "Phchi.S3G307400.t1"; gene_id "Phchi.S3G307400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13510.t1 is derived from g11977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7240760	7241437	.	+	.	Phchi.S3G082900
Phchi.S3	AUGUSTUS	transcript	7240760	7241437	.	+	.	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	start_codon	7240760	7240762	.	+	0	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	CDS	7240760	7240840	0.83	+	0	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	exon	7240760	7240840	.	+	.	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	intron	7240841	7240936	.	+	.	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	CDS	7240937	7241068	0.95	+	0	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	exon	7240937	7241068	.	+	.	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	intron	7241069	7241209	.	+	.	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	CDS	7241210	7241437	1	+	0	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	exon	7241210	7241437	.	+	.	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
Phchi.S3	AUGUSTUS	stop_codon	7241438	7241440	.	+	0	transcript_id "Phchi.S3G082900.t1"; gene_id "Phchi.S3G082900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15273.t1 is derived from g13741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18054332	18055608	.	+	.	Phchi.S3G259200
Phchi.S3	AUGUSTUS	transcript	18054332	18055608	.	+	.	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	start_codon	18054332	18054334	.	+	0	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	CDS	18054332	18054499	0.96	+	0	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	exon	18054332	18054499	.	+	.	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	intron	18054500	18054576	.	+	.	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	CDS	18054577	18055608	0.99	+	0	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	exon	18054577	18055608	.	+	.	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
Phchi.S3	AUGUSTUS	stop_codon	18055609	18055611	.	+	0	transcript_id "Phchi.S3G259200.t1"; gene_id "Phchi.S3G259200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15130.t1 is derived from g13598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17200195	17202372	.	-	.	Phchi.S3G244900
Phchi.S3	AUGUSTUS	transcript	17200195	17202372	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	stop_codon	17200192	17200194	.	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17200195	17200914	0.99	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17200195	17200914	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	intron	17200915	17201052	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17201053	17201193	1	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17201053	17201193	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	intron	17201194	17201338	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17201339	17201389	1	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17201339	17201389	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	intron	17201390	17201497	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17201498	17201623	1	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17201498	17201623	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	intron	17201624	17201753	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17201754	17201810	1	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17201754	17201810	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	intron	17201811	17202122	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17202123	17202203	1	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17202123	17202203	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	intron	17202204	17202303	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	CDS	17202304	17202372	1	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	exon	17202304	17202372	.	-	.	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
Phchi.S3	AUGUSTUS	start_codon	17202370	17202372	.	-	0	transcript_id "Phchi.S3G244900.t1"; gene_id "Phchi.S3G244900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4475.t1 is derived from g1645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10686989	10687919	.	+	.	Phchi.S1G163400
Phchi.S1	AUGUSTUS	transcript	10686989	10687919	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	start_codon	10686989	10686991	.	+	0	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	CDS	10686989	10687016	0.96	+	0	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	exon	10686989	10687016	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	intron	10687017	10687150	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	CDS	10687151	10687192	0.45	+	2	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	exon	10687151	10687192	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	intron	10687193	10687270	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	CDS	10687271	10687403	0.56	+	2	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	exon	10687271	10687403	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	intron	10687404	10687717	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	CDS	10687718	10687919	0.93	+	1	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	exon	10687718	10687919	.	+	.	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
Phchi.S1	AUGUSTUS	stop_codon	10687920	10687922	.	+	0	transcript_id "Phchi.S1G163400.t1"; gene_id "Phchi.S1G163400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10665.t1 is derived from g14715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1503092	1504378	.	-	.	Phchi.S4G024700
Phchi.S4	AUGUSTUS	transcript	1503092	1504378	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	stop_codon	1503089	1503091	.	-	0	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1503092	1503548	1	-	1	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1503092	1503548	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1503549	1503628	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1503629	1503696	1	-	0	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1503629	1503696	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1503697	1503820	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1503821	1504089	0.5	-	2	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1503821	1504089	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1504090	1504197	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1504198	1504261	0.99	-	0	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1504198	1504261	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1504262	1504354	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1504355	1504378	0.69	-	0	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1504355	1504378	.	-	.	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	start_codon	1504376	1504378	.	-	0	transcript_id "Phchi.S4G024700.t1"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	transcript	1503092	1504378	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	stop_codon	1503089	1503091	.	-	0	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1503092	1503548	1	-	1	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1503092	1503548	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1503549	1503628	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1503629	1503696	1	-	0	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1503629	1503696	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1503697	1503820	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1503821	1503953	0.24	-	1	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1503821	1503953	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1503954	1504197	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1504198	1504261	0.37	-	2	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1504198	1504261	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	intron	1504262	1504356	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	CDS	1504357	1504378	0.27	-	0	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	exon	1504357	1504378	.	-	.	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
Phchi.S4	AUGUSTUS	start_codon	1504376	1504378	.	-	0	transcript_id "Phchi.S4G024700.t2"; gene_id "Phchi.S4G024700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3653.t1 is derived from g822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4980159	4980497	.	+	.	Phchi.S1G081200
Phchi.S1	AUGUSTUS	transcript	4980159	4980497	.	+	.	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	start_codon	4980159	4980161	.	+	0	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	CDS	4980159	4980274	0.95	+	0	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	exon	4980159	4980274	.	+	.	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	intron	4980275	4980382	.	+	.	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	CDS	4980383	4980497	0.84	+	1	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	exon	4980383	4980497	.	+	.	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
Phchi.S1	AUGUSTUS	stop_codon	4980498	4980500	.	+	0	transcript_id "Phchi.S1G081200.t1"; gene_id "Phchi.S1G081200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4676.t1 is derived from g1846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11778252	11779494	.	-	.	Phchi.S1G183500
Phchi.S1	AUGUSTUS	transcript	11778252	11779494	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	stop_codon	11778249	11778251	.	-	0	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	CDS	11778252	11778640	0.99	-	2	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	exon	11778252	11778640	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	intron	11778641	11778760	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	CDS	11778761	11778926	1	-	0	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	exon	11778761	11778926	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	intron	11778927	11779001	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	CDS	11779002	11779199	1	-	0	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	exon	11779002	11779199	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	intron	11779200	11779284	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	CDS	11779285	11779494	0.89	-	0	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	exon	11779285	11779494	.	-	.	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
Phchi.S1	AUGUSTUS	start_codon	11779492	11779494	.	-	0	transcript_id "Phchi.S1G183500.t1"; gene_id "Phchi.S1G183500"
# This transcript jg1718.t2 is derived from g8638.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1719.t1 is derived from g8639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2689247	2690372	.	+	.	Phchi.S5G032800
Phchi.S5	AUGUSTUS	transcript	2689247	2690372	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	start_codon	2689247	2689249	.	+	0	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	CDS	2689247	2689452	0.53	+	0	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	exon	2689247	2689452	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	intron	2689453	2689785	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	CDS	2689786	2689937	0.55	+	1	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	exon	2689786	2689937	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	intron	2689938	2690022	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	CDS	2690023	2690087	0.41	+	2	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	exon	2690023	2690087	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	intron	2690088	2690237	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	CDS	2690238	2690372	0.46	+	0	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	exon	2690238	2690372	.	+	.	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
Phchi.S5	AUGUSTUS	stop_codon	2690373	2690375	.	+	0	transcript_id "Phchi.S5G032800.t1"; gene_id "Phchi.S5G032800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3677.t1 is derived from g846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5146940	5147278	.	+	.	Phchi.S1G083600
Phchi.S1	AUGUSTUS	transcript	5146940	5147278	.	+	.	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	start_codon	5146940	5146942	.	+	0	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	CDS	5146940	5147055	0.89	+	0	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	exon	5146940	5147055	.	+	.	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	intron	5147056	5147163	.	+	.	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	CDS	5147164	5147278	0.8	+	1	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	exon	5147164	5147278	.	+	.	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
Phchi.S1	AUGUSTUS	stop_codon	5147279	5147281	.	+	0	transcript_id "Phchi.S1G083600.t1"; gene_id "Phchi.S1G083600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2038.t1 is derived from g8958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4552466	4553327	.	+	.	Phchi.S5G064700
Phchi.S5	AUGUSTUS	transcript	4552466	4553327	.	+	.	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	start_codon	4552466	4552468	.	+	0	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	CDS	4552466	4552473	1	+	0	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	exon	4552466	4552473	.	+	.	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	intron	4552474	4552842	.	+	.	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	CDS	4552843	4553020	0.9	+	1	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	exon	4552843	4553020	.	+	.	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	intron	4553021	4553300	.	+	.	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	CDS	4553301	4553327	0.85	+	0	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	exon	4553301	4553327	.	+	.	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
Phchi.S5	AUGUSTUS	stop_codon	4553328	4553330	.	+	0	transcript_id "Phchi.S5G064700.t1"; gene_id "Phchi.S5G064700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8096.t1 is derived from g5271.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32920913	32923972	.	-	.	Phchi.S1G525500
Phchi.S1	AUGUSTUS	transcript	32920913	32921696	.	-	.	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	stop_codon	32920910	32920912	.	-	0	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	CDS	32920913	32921420	0.54	-	1	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	exon	32920913	32921420	.	-	.	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	intron	32921421	32921472	.	-	.	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	CDS	32921473	32921696	0.32	-	0	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	exon	32921473	32921696	.	-	.	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	start_codon	32921694	32921696	.	-	0	transcript_id "Phchi.S1G525500.t1"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	transcript	32921403	32923972	.	-	.	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	stop_codon	32921400	32921402	.	-	0	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	CDS	32921403	32921777	0.26	-	0	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	exon	32921403	32921777	.	-	.	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	intron	32921778	32922130	.	-	.	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	CDS	32922131	32923972	0.19	-	0	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	exon	32922131	32923972	.	-	.	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	start_codon	32923970	32923972	.	-	0	transcript_id "Phchi.S1G525500.t2"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	transcript	32921849	32923972	.	-	.	transcript_id "Phchi.S1G525500.t3"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	stop_codon	32921846	32921848	.	-	0	transcript_id "Phchi.S1G525500.t3"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	CDS	32921849	32923972	0.41	-	0	transcript_id "Phchi.S1G525500.t3"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	exon	32921849	32923972	.	-	.	transcript_id "Phchi.S1G525500.t3"; gene_id "Phchi.S1G525500"
Phchi.S1	AUGUSTUS	start_codon	32923970	32923972	.	-	0	transcript_id "Phchi.S1G525500.t3"; gene_id "Phchi.S1G525500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11292.t1 is derived from g15342.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5256096	5256622	.	-	.	Phchi.S4G087400
Phchi.S4	AUGUSTUS	transcript	5256096	5256622	.	-	.	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	stop_codon	5256093	5256095	.	-	0	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	CDS	5256096	5256204	0.95	-	1	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	exon	5256096	5256204	.	-	.	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	intron	5256205	5256317	.	-	.	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	CDS	5256318	5256622	0.95	-	0	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	exon	5256318	5256622	.	-	.	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
Phchi.S4	AUGUSTUS	start_codon	5256620	5256622	.	-	0	transcript_id "Phchi.S4G087400.t1"; gene_id "Phchi.S4G087400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9826.t1 is derived from g7002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43968611	43985594	.	+	.	Phchi.S1G698500
Phchi.S1	AUGUSTUS	transcript	43968611	43985594	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	start_codon	43968611	43968613	.	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43968611	43968985	0.97	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43968611	43968985	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43968986	43969233	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43969234	43969578	0.99	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43969234	43969578	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43969579	43969663	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43969664	43969789	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43969664	43969789	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43969790	43970093	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43970094	43970179	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43970094	43970179	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43970180	43970265	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43970266	43970374	1	+	1	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43970266	43970374	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43970375	43970517	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43970518	43970613	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43970518	43970613	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43970614	43970813	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43970814	43970876	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43970814	43970876	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43970877	43970965	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43970966	43971025	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43970966	43971025	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43971026	43971232	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43971233	43971307	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43971233	43971307	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43971308	43971413	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43971414	43971495	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43971414	43971495	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43971496	43971718	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43971719	43971825	1	+	2	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43971719	43971825	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43971826	43972000	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43972001	43972889	0.47	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43972001	43972889	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43972890	43973035	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43973036	43973232	0.63	+	2	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43973036	43973232	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43973233	43973347	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43973348	43974352	0.98	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43973348	43974352	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43974353	43974445	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43974446	43974781	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43974446	43974781	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43974782	43975040	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43975041	43975302	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43975041	43975302	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43975303	43975442	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43975443	43975665	1	+	2	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43975443	43975665	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43975666	43975749	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43975750	43976149	1	+	1	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43975750	43976149	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43976150	43976244	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43976245	43976394	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43976245	43976394	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43976395	43976485	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43976486	43976710	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43976486	43976710	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43976711	43976856	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43976857	43977078	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43976857	43977078	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43977079	43977177	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43977178	43977843	0.66	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43977178	43977843	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43977844	43978017	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43978018	43978278	0.94	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43978018	43978278	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43978279	43978380	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43978381	43978740	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43978381	43978740	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43978741	43978846	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43978847	43979253	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43978847	43979253	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43979254	43979348	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43979349	43979775	0.91	+	1	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43979349	43979775	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43979776	43979853	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43979854	43981161	0.98	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43979854	43981161	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43981162	43981278	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43981279	43981542	0.98	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43981279	43981542	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43981543	43981672	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43981673	43981963	0.97	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43981673	43981963	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43981964	43982067	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43982068	43982559	0.99	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43982068	43982559	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43982560	43982703	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43982704	43983135	0.99	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43982704	43983135	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43983136	43983227	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43983228	43983506	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43983228	43983506	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43983507	43983589	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43983590	43983992	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43983590	43983992	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43983993	43984085	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43984086	43984234	1	+	2	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43984086	43984234	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43984235	43984331	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43984332	43984532	1	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43984332	43984532	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43984533	43984690	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43984691	43984772	0.47	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43984691	43984772	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43984773	43985021	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43985022	43985088	0.26	+	2	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43985022	43985088	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43985089	43985199	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43985200	43985222	0.74	+	1	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43985200	43985222	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43985223	43985319	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43985320	43985359	0.74	+	2	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43985320	43985359	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	intron	43985360	43985521	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	CDS	43985522	43985594	0.74	+	1	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	exon	43985522	43985594	.	+	.	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
Phchi.S1	AUGUSTUS	stop_codon	43985595	43985597	.	+	0	transcript_id "Phchi.S1G698500.t1"; gene_id "Phchi.S1G698500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9854.t1 is derived from g7031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44096658	44097317	.	-	.	Phchi.S1G701400
Phchi.S1	AUGUSTUS	transcript	44096658	44097317	.	-	.	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	stop_codon	44096655	44096657	.	-	0	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	CDS	44096658	44097089	0.94	-	0	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	exon	44096658	44097089	.	-	.	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	intron	44097090	44097197	.	-	.	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	CDS	44097198	44097317	0.95	-	0	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	exon	44097198	44097317	.	-	.	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
Phchi.S1	AUGUSTUS	start_codon	44097315	44097317	.	-	0	transcript_id "Phchi.S1G701400.t1"; gene_id "Phchi.S1G701400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12995.t1 is derived from g11460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3552665	3554729	.	-	.	Phchi.S3G031400
Phchi.S3	AUGUSTUS	transcript	3552665	3554729	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	stop_codon	3552662	3552664	.	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3552665	3552742	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3552665	3552742	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3552743	3552862	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3552863	3552928	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3552863	3552928	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3552929	3553019	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3553020	3553103	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3553020	3553103	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3553104	3553190	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3553191	3553286	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3553191	3553286	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3553287	3553377	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3553378	3553476	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3553378	3553476	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3553477	3553647	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3553648	3553779	0.97	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3553648	3553779	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3553780	3553884	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3553885	3554033	0.96	-	2	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3553885	3554033	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3554034	3554106	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3554107	3554205	1	-	2	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3554107	3554205	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3554206	3554327	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3554328	3554361	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3554328	3554361	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3554362	3554454	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3554455	3554510	1	-	2	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3554455	3554510	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	intron	3554511	3554647	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	CDS	3554648	3554729	1	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	exon	3554648	3554729	.	-	.	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
Phchi.S3	AUGUSTUS	start_codon	3554727	3554729	.	-	0	transcript_id "Phchi.S3G031400.t1"; gene_id "Phchi.S3G031400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6357.t1 is derived from g3529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22536099	22536863	.	+	.	Phchi.S1G351600
Phchi.S1	AUGUSTUS	transcript	22536099	22536863	.	+	.	transcript_id "Phchi.S1G351600.t1"; gene_id "Phchi.S1G351600"
Phchi.S1	AUGUSTUS	start_codon	22536099	22536101	.	+	0	transcript_id "Phchi.S1G351600.t1"; gene_id "Phchi.S1G351600"
Phchi.S1	AUGUSTUS	CDS	22536099	22536863	0.75	+	0	transcript_id "Phchi.S1G351600.t1"; gene_id "Phchi.S1G351600"
Phchi.S1	AUGUSTUS	exon	22536099	22536863	.	+	.	transcript_id "Phchi.S1G351600.t1"; gene_id "Phchi.S1G351600"
Phchi.S1	AUGUSTUS	stop_codon	22536864	22536866	.	+	0	transcript_id "Phchi.S1G351600.t1"; gene_id "Phchi.S1G351600"
# This transcript jg2753.t2 is derived from g9673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2753.t3 is derived from g9673.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2754.t1 is derived from g9674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8633116	8633650	.	+	.	Phchi.S5G136300
Phchi.S5	AUGUSTUS	transcript	8633116	8633650	.	+	.	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	start_codon	8633116	8633118	.	+	0	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	CDS	8633116	8633293	1	+	0	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	exon	8633116	8633293	.	+	.	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	intron	8633294	8633369	.	+	.	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	CDS	8633370	8633650	1	+	2	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	exon	8633370	8633650	.	+	.	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
Phchi.S5	AUGUSTUS	stop_codon	8633651	8633653	.	+	0	transcript_id "Phchi.S5G136300.t1"; gene_id "Phchi.S5G136300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9160.t1 is derived from g6335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40148666	40150138	.	-	.	Phchi.S1G631900
Phchi.S1	AUGUSTUS	transcript	40148666	40150138	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	stop_codon	40148663	40148665	.	-	0	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40148666	40148766	0.88	-	2	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40148666	40148766	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40148767	40148851	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40148852	40148930	1	-	0	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40148852	40148930	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40148931	40149026	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40149027	40149132	1	-	1	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40149027	40149132	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40149133	40149270	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40149271	40149391	0.95	-	2	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40149271	40149391	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40149392	40149492	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40149493	40149565	0.87	-	0	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40149493	40149565	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40149566	40149674	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40149675	40149766	0.78	-	2	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40149675	40149766	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40149767	40149874	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40149875	40149923	0.83	-	0	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40149875	40149923	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	intron	40149924	40149997	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	CDS	40149998	40150138	0.38	-	0	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	exon	40149998	40150138	.	-	.	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
Phchi.S1	AUGUSTUS	start_codon	40150136	40150138	.	-	0	transcript_id "Phchi.S1G631900.t1"; gene_id "Phchi.S1G631900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg21.t1 is derived from g9783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C19	AUGUSTUS	gene	84101	84346	.	-	.	Phchi.C19G000100
Phchi.C19	AUGUSTUS	transcript	84101	84346	.	-	.	transcript_id "Phchi.C19G000100.t1"; gene_id "Phchi.C19G000100"
Phchi.C19	AUGUSTUS	stop_codon	84098	84100	.	-	0	transcript_id "Phchi.C19G000100.t1"; gene_id "Phchi.C19G000100"
Phchi.C19	AUGUSTUS	CDS	84101	84346	0.93	-	0	transcript_id "Phchi.C19G000100.t1"; gene_id "Phchi.C19G000100"
Phchi.C19	AUGUSTUS	exon	84101	84346	.	-	.	transcript_id "Phchi.C19G000100.t1"; gene_id "Phchi.C19G000100"
Phchi.C19	AUGUSTUS	start_codon	84344	84346	.	-	0	transcript_id "Phchi.C19G000100.t1"; gene_id "Phchi.C19G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9348.t1 is derived from g6524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41074299	41074562	.	+	.	Phchi.S1G650700
Phchi.S1	AUGUSTUS	transcript	41074299	41074562	.	+	.	transcript_id "Phchi.S1G650700.t1"; gene_id "Phchi.S1G650700"
Phchi.S1	AUGUSTUS	start_codon	41074299	41074301	.	+	0	transcript_id "Phchi.S1G650700.t1"; gene_id "Phchi.S1G650700"
Phchi.S1	AUGUSTUS	CDS	41074299	41074562	0.99	+	0	transcript_id "Phchi.S1G650700.t1"; gene_id "Phchi.S1G650700"
Phchi.S1	AUGUSTUS	exon	41074299	41074562	.	+	.	transcript_id "Phchi.S1G650700.t1"; gene_id "Phchi.S1G650700"
Phchi.S1	AUGUSTUS	stop_codon	41074563	41074565	.	+	0	transcript_id "Phchi.S1G650700.t1"; gene_id "Phchi.S1G650700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13246.t1 is derived from g11711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4896926	4898686	.	+	.	Phchi.S3G056500
Phchi.S3	AUGUSTUS	transcript	4896926	4898686	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	start_codon	4896926	4896928	.	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4896926	4896979	0.98	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4896926	4896979	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4896980	4897058	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4897059	4897181	1	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4897059	4897181	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4897182	4897270	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4897271	4897468	0.96	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4897271	4897468	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4897469	4897553	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4897554	4897632	1	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4897554	4897632	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4897633	4897758	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4897759	4897907	0.99	+	2	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4897759	4897907	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4897908	4897989	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4897990	4898103	1	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4897990	4898103	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4898104	4898178	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4898179	4898310	1	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4898179	4898310	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4898311	4898392	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4898393	4898527	1	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4898393	4898527	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	intron	4898528	4898656	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	CDS	4898657	4898686	1	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	exon	4898657	4898686	.	+	.	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
Phchi.S3	AUGUSTUS	stop_codon	4898687	4898689	.	+	0	transcript_id "Phchi.S3G056500.t1"; gene_id "Phchi.S3G056500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13663.t1 is derived from g12130.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8055305	8055595	.	+	.	Phchi.S3G098200
Phchi.S3	AUGUSTUS	transcript	8055305	8055595	.	+	.	transcript_id "Phchi.S3G098200.t1"; gene_id "Phchi.S3G098200"
Phchi.S3	AUGUSTUS	start_codon	8055305	8055307	.	+	0	transcript_id "Phchi.S3G098200.t1"; gene_id "Phchi.S3G098200"
Phchi.S3	AUGUSTUS	CDS	8055305	8055595	0.61	+	0	transcript_id "Phchi.S3G098200.t1"; gene_id "Phchi.S3G098200"
Phchi.S3	AUGUSTUS	exon	8055305	8055595	.	+	.	transcript_id "Phchi.S3G098200.t1"; gene_id "Phchi.S3G098200"
Phchi.S3	AUGUSTUS	stop_codon	8055596	8055598	.	+	0	transcript_id "Phchi.S3G098200.t1"; gene_id "Phchi.S3G098200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10102.t1 is derived from g7278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45752430	45753238	.	+	.	Phchi.S1G726100
Phchi.S1	AUGUSTUS	transcript	45752430	45753238	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	start_codon	45752430	45752432	.	+	0	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	CDS	45752430	45752564	0.98	+	0	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	exon	45752430	45752564	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	intron	45752565	45752647	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	CDS	45752648	45752734	1	+	0	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	exon	45752648	45752734	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	intron	45752735	45752818	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	CDS	45752819	45752889	1	+	0	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	exon	45752819	45752889	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	intron	45752890	45753011	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	CDS	45753012	45753078	1	+	1	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	exon	45753012	45753078	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	intron	45753079	45753172	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	CDS	45753173	45753238	1	+	0	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	exon	45753173	45753238	.	+	.	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
Phchi.S1	AUGUSTUS	stop_codon	45753239	45753241	.	+	0	transcript_id "Phchi.S1G726100.t1"; gene_id "Phchi.S1G726100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4652.t1 is derived from g1822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11644367	11647888	.	-	.	Phchi.S1G181100
Phchi.S1	AUGUSTUS	transcript	11644367	11647888	.	-	.	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	stop_codon	11644364	11644366	.	-	0	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	CDS	11644367	11644428	0.45	-	2	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	exon	11644367	11644428	.	-	.	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	intron	11644429	11644501	.	-	.	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	CDS	11644502	11645143	0.42	-	2	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	exon	11644502	11645143	.	-	.	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	intron	11645144	11645289	.	-	.	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	CDS	11645290	11647888	0.37	-	0	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	exon	11645290	11647888	.	-	.	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
Phchi.S1	AUGUSTUS	start_codon	11647886	11647888	.	-	0	transcript_id "Phchi.S1G181100.t1"; gene_id "Phchi.S1G181100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2829.t1 is derived from g9749.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9083905	9086433	.	-	.	Phchi.S5G143800
Phchi.S5	AUGUSTUS	transcript	9083905	9086433	.	-	.	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	stop_codon	9083902	9083904	.	-	0	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	CDS	9083905	9084791	0.42	-	2	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	exon	9083905	9084791	.	-	.	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	intron	9084792	9084965	.	-	.	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	CDS	9084966	9085028	0.72	-	2	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	exon	9084966	9085028	.	-	.	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	intron	9085029	9085271	.	-	.	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	CDS	9085272	9086433	0.6	-	0	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	exon	9085272	9086433	.	-	.	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
Phchi.S5	AUGUSTUS	start_codon	9086431	9086433	.	-	0	transcript_id "Phchi.S5G143800.t1"; gene_id "Phchi.S5G143800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4366.t1 is derived from g1535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10073630	10074622	.	-	.	Phchi.S1G152500
Phchi.S1	AUGUSTUS	transcript	10073630	10074622	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	stop_codon	10073627	10073629	.	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	CDS	10073630	10073719	0.22	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	exon	10073630	10073719	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	intron	10073720	10073801	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	CDS	10073802	10073879	0.94	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	exon	10073802	10073879	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	intron	10073880	10073959	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	CDS	10073960	10074049	1	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	exon	10073960	10074049	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	intron	10074050	10074151	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	CDS	10074152	10074328	0.44	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	exon	10074152	10074328	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	intron	10074329	10074517	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	CDS	10074518	10074622	0.66	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	exon	10074518	10074622	.	-	.	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
Phchi.S1	AUGUSTUS	start_codon	10074620	10074622	.	-	0	transcript_id "Phchi.S1G152500.t1"; gene_id "Phchi.S1G152500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8931.t1 is derived from g6106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38720869	38723913	.	-	.	Phchi.S1G609000
Phchi.S1	AUGUSTUS	transcript	38720869	38723913	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	stop_codon	38720866	38720868	.	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38720869	38720912	1	-	2	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38720869	38720912	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38720913	38720998	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38720999	38721059	1	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38720999	38721059	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38721060	38721139	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38721140	38721225	1	-	2	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38721140	38721225	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38721226	38721313	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38721314	38721484	1	-	2	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38721314	38721484	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38721485	38721572	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38721573	38721747	1	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38721573	38721747	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38721748	38721869	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38721870	38721961	0.97	-	2	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38721870	38721961	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38721962	38722070	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38722071	38722173	0.76	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38722071	38722173	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38722174	38722382	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38722383	38723048	0.98	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38722383	38723048	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38723049	38723238	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38723239	38723316	1	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38723239	38723316	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	intron	38723317	38723403	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	CDS	38723404	38723913	0.86	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	exon	38723404	38723913	.	-	.	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
Phchi.S1	AUGUSTUS	start_codon	38723911	38723913	.	-	0	transcript_id "Phchi.S1G609000.t1"; gene_id "Phchi.S1G609000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6428.t1 is derived from g3600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22990261	22991564	.	-	.	Phchi.S1G358700
Phchi.S1	AUGUSTUS	transcript	22990261	22991564	.	-	.	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	stop_codon	22990258	22990260	.	-	0	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	CDS	22990261	22991389	0.56	-	1	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	exon	22990261	22991389	.	-	.	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	intron	22991390	22991469	.	-	.	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	CDS	22991470	22991564	0.35	-	0	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	exon	22991470	22991564	.	-	.	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
Phchi.S1	AUGUSTUS	start_codon	22991562	22991564	.	-	0	transcript_id "Phchi.S1G358700.t1"; gene_id "Phchi.S1G358700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3394.t1 is derived from g563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3327899	3330366	.	+	.	Phchi.S1G055300
Phchi.S1	AUGUSTUS	transcript	3327899	3328738	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	start_codon	3327899	3327901	.	+	0	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3327899	3327952	0.46	+	0	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3327899	3327952	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3327953	3328040	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3328041	3328173	1	+	0	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3328041	3328173	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3328174	3328354	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3328355	3328533	1	+	2	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3328355	3328533	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3328534	3328696	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3328697	3328738	1	+	0	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3328697	3328738	.	+	.	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	stop_codon	3328739	3328741	.	+	0	transcript_id "Phchi.S1G055300.t1"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	transcript	3327899	3330366	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	start_codon	3327899	3327901	.	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3327899	3327952	0.5	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3327899	3327952	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3327953	3328040	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3328041	3328173	1	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3328041	3328173	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3328174	3328354	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3328355	3328533	1	+	2	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3328355	3328533	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3328534	3328688	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3328689	3328878	0.79	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3328689	3328878	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3328879	3329067	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3329068	3329163	1	+	2	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3329068	3329163	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3329164	3329246	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3329247	3329392	0.94	+	2	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3329247	3329392	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3329393	3329496	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3329497	3329604	0.9	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3329497	3329604	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3329605	3329722	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3329723	3329811	0.9	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3329723	3329811	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	intron	3329812	3329921	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	CDS	3329922	3330366	0.68	+	1	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	exon	3329922	3330366	.	+	.	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
Phchi.S1	AUGUSTUS	stop_codon	3330367	3330369	.	+	0	transcript_id "Phchi.S1G055300.t2"; gene_id "Phchi.S1G055300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7365.t1 is derived from g4537.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28786765	28788425	.	+	.	Phchi.S1G452400
Phchi.S1	AUGUSTUS	transcript	28786765	28788425	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	start_codon	28786765	28786767	.	+	0	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	CDS	28786765	28787204	0.97	+	0	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	exon	28786765	28787204	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	intron	28787205	28787307	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	CDS	28787308	28787558	0.98	+	1	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	exon	28787308	28787558	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	intron	28787559	28787647	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	CDS	28787648	28787952	0.99	+	2	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	exon	28787648	28787952	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	intron	28787953	28788042	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	CDS	28788043	28788161	1	+	0	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	exon	28788043	28788161	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	intron	28788162	28788301	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	CDS	28788302	28788425	0.67	+	1	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	exon	28788302	28788425	.	+	.	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
Phchi.S1	AUGUSTUS	stop_codon	28788426	28788428	.	+	0	transcript_id "Phchi.S1G452400.t1"; gene_id "Phchi.S1G452400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12131.t1 is derived from g7807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4055894	4056455	.	+	.	Phchi.S2G021100
Phchi.S2	AUGUSTUS	transcript	4055894	4056455	.	+	.	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	start_codon	4055894	4055896	.	+	0	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	CDS	4055894	4056146	0.93	+	0	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	exon	4055894	4056146	.	+	.	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	intron	4056147	4056327	.	+	.	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	CDS	4056328	4056455	0.95	+	2	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	exon	4056328	4056455	.	+	.	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
Phchi.S2	AUGUSTUS	stop_codon	4056456	4056458	.	+	0	transcript_id "Phchi.S2G021100.t1"; gene_id "Phchi.S2G021100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8789.t1 is derived from g5964.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37960279	37962852	.	-	.	Phchi.S1G594800
Phchi.S1	AUGUSTUS	transcript	37960279	37962852	.	-	.	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	stop_codon	37960276	37960278	.	-	0	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	CDS	37960279	37960379	0.98	-	2	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	exon	37960279	37960379	.	-	.	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	intron	37960380	37960515	.	-	.	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	CDS	37960516	37962201	0.92	-	2	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	exon	37960516	37962201	.	-	.	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	intron	37962202	37962656	.	-	.	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	CDS	37962657	37962852	0.7	-	0	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	exon	37962657	37962852	.	-	.	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
Phchi.S1	AUGUSTUS	start_codon	37962850	37962852	.	-	0	transcript_id "Phchi.S1G594800.t1"; gene_id "Phchi.S1G594800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7584.t1 is derived from g4758.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30153683	30155581	.	-	.	Phchi.S1G474300
Phchi.S1	AUGUSTUS	transcript	30153683	30155581	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	stop_codon	30153680	30153682	.	-	0	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	CDS	30153683	30154026	0.99	-	2	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	exon	30153683	30154026	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	intron	30154027	30154173	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	CDS	30154174	30154341	1	-	2	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	exon	30154174	30154341	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	intron	30154342	30154498	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	CDS	30154499	30155106	1	-	1	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	exon	30154499	30155106	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	intron	30155107	30155246	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	CDS	30155247	30155581	0.7	-	0	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	exon	30155247	30155581	.	-	.	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
Phchi.S1	AUGUSTUS	start_codon	30155579	30155581	.	-	0	transcript_id "Phchi.S1G474300.t1"; gene_id "Phchi.S1G474300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12925.t1 is derived from g11390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3181561	3182562	.	+	.	Phchi.S3G024400
Phchi.S3	AUGUSTUS	transcript	3181561	3182562	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	start_codon	3181561	3181563	.	+	0	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	CDS	3181561	3181650	0.93	+	0	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	exon	3181561	3181650	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	intron	3181651	3181822	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	CDS	3181823	3182009	0.92	+	0	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	exon	3181823	3182009	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	intron	3182010	3182096	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	CDS	3182097	3182185	0.48	+	2	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	exon	3182097	3182185	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	intron	3182186	3182322	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	CDS	3182323	3182407	0.51	+	0	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	exon	3182323	3182407	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	intron	3182408	3182503	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	CDS	3182504	3182562	0.95	+	2	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	exon	3182504	3182562	.	+	.	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
Phchi.S3	AUGUSTUS	stop_codon	3182563	3182565	.	+	0	transcript_id "Phchi.S3G024400.t1"; gene_id "Phchi.S3G024400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2583.t1 is derived from g9503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7487216	7487813	.	+	.	Phchi.S5G119200
Phchi.S5	AUGUSTUS	transcript	7487216	7487813	.	+	.	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	start_codon	7487216	7487218	.	+	0	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	CDS	7487216	7487531	0.75	+	0	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	exon	7487216	7487531	.	+	.	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	intron	7487532	7487784	.	+	.	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	CDS	7487785	7487813	0.75	+	2	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	exon	7487785	7487813	.	+	.	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
Phchi.S5	AUGUSTUS	stop_codon	7487814	7487816	.	+	0	transcript_id "Phchi.S5G119200.t1"; gene_id "Phchi.S5G119200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13166.t1 is derived from g11631.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4457683	4461014	.	+	.	Phchi.S3G048500
Phchi.S3	AUGUSTUS	transcript	4457683	4461014	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	start_codon	4457683	4457685	.	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4457683	4457979	0.98	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4457683	4457979	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4457980	4458071	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4458072	4458230	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4458072	4458230	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4458231	4458315	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4458316	4458498	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4458316	4458498	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4458499	4458587	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4458588	4458720	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4458588	4458720	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4458721	4458841	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4458842	4458936	1	+	2	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4458842	4458936	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4458937	4459025	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4459026	4459187	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4459026	4459187	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4459188	4459273	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4459274	4459342	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4459274	4459342	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4459343	4459472	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4459473	4459608	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4459473	4459608	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4459609	4459703	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4459704	4459742	1	+	2	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4459704	4459742	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4459743	4459828	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4459829	4459935	1	+	2	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4459829	4459935	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4459936	4460031	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4460032	4460109	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4460032	4460109	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4460110	4460198	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4460199	4460264	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4460199	4460264	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4460265	4460350	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4460351	4460527	1	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4460351	4460527	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4460528	4460625	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4460626	4460781	0.87	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4460626	4460781	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	intron	4460782	4460924	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	CDS	4460925	4461014	0.38	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	exon	4460925	4461014	.	+	.	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
Phchi.S3	AUGUSTUS	stop_codon	4461015	4461017	.	+	0	transcript_id "Phchi.S3G048500.t1"; gene_id "Phchi.S3G048500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14311.t1 is derived from g12778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12053780	12056023	.	+	.	Phchi.S3G163000
Phchi.S3	AUGUSTUS	transcript	12053780	12056023	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	start_codon	12053780	12053782	.	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12053780	12053881	0.96	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12053780	12053881	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12053882	12053990	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12053991	12054077	0.96	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12053991	12054077	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12054078	12054235	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12054236	12054741	0.99	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12054236	12054741	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12054742	12054854	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12054855	12055086	1	+	1	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12054855	12055086	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12055087	12055167	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12055168	12055311	1	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12055168	12055311	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12055312	12055397	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12055398	12055498	0.92	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12055398	12055498	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12055499	12055601	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12055602	12055664	0.76	+	1	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12055602	12055664	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12055665	12055753	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12055754	12055797	0.76	+	1	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12055754	12055797	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	intron	12055798	12055883	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	CDS	12055884	12056023	0.76	+	2	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	exon	12055884	12056023	.	+	.	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
Phchi.S3	AUGUSTUS	stop_codon	12056024	12056026	.	+	0	transcript_id "Phchi.S3G163000.t1"; gene_id "Phchi.S3G163000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg183.t1 is derived from g9965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1058479	1059870	.	-	.	Phchi.S6G014200
Phchi.S6	AUGUSTUS	transcript	1058479	1059870	.	-	.	transcript_id "Phchi.S6G014200.t1"; gene_id "Phchi.S6G014200"
Phchi.S6	AUGUSTUS	stop_codon	1058476	1058478	.	-	0	transcript_id "Phchi.S6G014200.t1"; gene_id "Phchi.S6G014200"
Phchi.S6	AUGUSTUS	CDS	1058479	1059870	0.99	-	0	transcript_id "Phchi.S6G014200.t1"; gene_id "Phchi.S6G014200"
Phchi.S6	AUGUSTUS	exon	1058479	1059870	.	-	.	transcript_id "Phchi.S6G014200.t1"; gene_id "Phchi.S6G014200"
Phchi.S6	AUGUSTUS	start_codon	1059868	1059870	.	-	0	transcript_id "Phchi.S6G014200.t1"; gene_id "Phchi.S6G014200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3982.t1 is derived from g1151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6858207	6859058	.	-	.	Phchi.S1G114100
Phchi.S1	AUGUSTUS	transcript	6858207	6859058	.	-	.	transcript_id "Phchi.S1G114100.t1"; gene_id "Phchi.S1G114100"
Phchi.S1	AUGUSTUS	stop_codon	6858204	6858206	.	-	0	transcript_id "Phchi.S1G114100.t1"; gene_id "Phchi.S1G114100"
Phchi.S1	AUGUSTUS	CDS	6858207	6859058	0.53	-	0	transcript_id "Phchi.S1G114100.t1"; gene_id "Phchi.S1G114100"
Phchi.S1	AUGUSTUS	exon	6858207	6859058	.	-	.	transcript_id "Phchi.S1G114100.t1"; gene_id "Phchi.S1G114100"
Phchi.S1	AUGUSTUS	start_codon	6859056	6859058	.	-	0	transcript_id "Phchi.S1G114100.t1"; gene_id "Phchi.S1G114100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg693.t1 is derived from g10475.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4943258	4943662	.	+	.	Phchi.S6G065200
Phchi.S6	AUGUSTUS	transcript	4943258	4943662	.	+	.	transcript_id "Phchi.S6G065200.t1"; gene_id "Phchi.S6G065200"
Phchi.S6	AUGUSTUS	start_codon	4943258	4943260	.	+	0	transcript_id "Phchi.S6G065200.t1"; gene_id "Phchi.S6G065200"
Phchi.S6	AUGUSTUS	CDS	4943258	4943662	0.6	+	0	transcript_id "Phchi.S6G065200.t1"; gene_id "Phchi.S6G065200"
Phchi.S6	AUGUSTUS	exon	4943258	4943662	.	+	.	transcript_id "Phchi.S6G065200.t1"; gene_id "Phchi.S6G065200"
Phchi.S6	AUGUSTUS	stop_codon	4943663	4943665	.	+	0	transcript_id "Phchi.S6G065200.t1"; gene_id "Phchi.S6G065200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8908.t1 is derived from g6083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38587345	38587614	.	-	.	Phchi.S1G606700
Phchi.S1	AUGUSTUS	transcript	38587345	38587614	.	-	.	transcript_id "Phchi.S1G606700.t1"; gene_id "Phchi.S1G606700"
Phchi.S1	AUGUSTUS	stop_codon	38587342	38587344	.	-	0	transcript_id "Phchi.S1G606700.t1"; gene_id "Phchi.S1G606700"
Phchi.S1	AUGUSTUS	CDS	38587345	38587614	1	-	0	transcript_id "Phchi.S1G606700.t1"; gene_id "Phchi.S1G606700"
Phchi.S1	AUGUSTUS	exon	38587345	38587614	.	-	.	transcript_id "Phchi.S1G606700.t1"; gene_id "Phchi.S1G606700"
Phchi.S1	AUGUSTUS	start_codon	38587612	38587614	.	-	0	transcript_id "Phchi.S1G606700.t1"; gene_id "Phchi.S1G606700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15812.t1 is derived from g14282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21512986	21513354	.	-	.	Phchi.S3G313100
Phchi.S3	AUGUSTUS	transcript	21512986	21513354	.	-	.	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	stop_codon	21512983	21512985	.	-	0	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	CDS	21512986	21513151	1	-	1	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	exon	21512986	21513151	.	-	.	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	intron	21513152	21513292	.	-	.	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	CDS	21513293	21513354	1	-	0	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	exon	21513293	21513354	.	-	.	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
Phchi.S3	AUGUSTUS	start_codon	21513352	21513354	.	-	0	transcript_id "Phchi.S3G313100.t1"; gene_id "Phchi.S3G313100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14804.t1 is derived from g13272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14795689	14798036	.	+	.	Phchi.S3G212300
Phchi.S3	AUGUSTUS	transcript	14795689	14798036	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	start_codon	14795689	14795691	.	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14795689	14795827	1	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14795689	14795827	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14795828	14795909	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14795910	14796103	1	+	2	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14795910	14796103	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14796104	14796195	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14796196	14796333	1	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14796196	14796333	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14796334	14796476	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14796477	14796587	1	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14796477	14796587	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14796588	14796811	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14796812	14796891	1	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14796812	14796891	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14796892	14797070	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14797071	14797190	1	+	1	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14797071	14797190	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14797191	14797302	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14797303	14797425	1	+	1	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14797303	14797425	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14797426	14797595	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14797596	14797662	1	+	1	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14797596	14797662	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14797663	14797785	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14797786	14797862	1	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14797786	14797862	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	intron	14797863	14798017	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	CDS	14798018	14798036	1	+	1	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	exon	14798018	14798036	.	+	.	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
Phchi.S3	AUGUSTUS	stop_codon	14798037	14798039	.	+	0	transcript_id "Phchi.S3G212300.t1"; gene_id "Phchi.S3G212300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7616.t1 is derived from g4790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30284095	30286228	.	-	.	Phchi.S1G477500
Phchi.S1	AUGUSTUS	transcript	30284095	30286228	.	-	.	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	stop_codon	30284092	30284094	.	-	0	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	CDS	30284095	30284504	0.99	-	2	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	exon	30284095	30284504	.	-	.	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	intron	30284505	30284616	.	-	.	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	CDS	30284617	30286228	0.83	-	0	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	exon	30284617	30286228	.	-	.	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
Phchi.S1	AUGUSTUS	start_codon	30286226	30286228	.	-	0	transcript_id "Phchi.S1G477500.t1"; gene_id "Phchi.S1G477500"
# This transcript jg1720.t2 is derived from g8640.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1721.t1 is derived from g8641.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2702694	2704024	.	+	.	Phchi.S5G033000
Phchi.S5	AUGUSTUS	transcript	2702694	2704024	.	+	.	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	start_codon	2702694	2702696	.	+	0	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	CDS	2702694	2702852	1	+	0	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	exon	2702694	2702852	.	+	.	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	intron	2702853	2702948	.	+	.	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	CDS	2702949	2703164	1	+	0	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	exon	2702949	2703164	.	+	.	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	intron	2703165	2703256	.	+	.	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	CDS	2703257	2704024	1	+	0	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	exon	2703257	2704024	.	+	.	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	stop_codon	2704025	2704027	.	+	0	transcript_id "Phchi.S5G033000.t1"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	transcript	2702694	2704024	.	+	.	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	start_codon	2702694	2702696	.	+	0	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	CDS	2702694	2702852	0.99	+	0	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	exon	2702694	2702852	.	+	.	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	intron	2702853	2702951	.	+	.	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	CDS	2702952	2703164	1	+	0	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	exon	2702952	2703164	.	+	.	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	intron	2703165	2703256	.	+	.	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	CDS	2703257	2704024	0.98	+	0	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	exon	2703257	2704024	.	+	.	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
Phchi.S5	AUGUSTUS	stop_codon	2704025	2704027	.	+	0	transcript_id "Phchi.S5G033000.t2"; gene_id "Phchi.S5G033000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13753.t1 is derived from g12220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8708153	8709501	.	-	.	Phchi.S3G107200
Phchi.S3	AUGUSTUS	transcript	8708153	8709501	.	-	.	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	stop_codon	8708150	8708152	.	-	0	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	CDS	8708153	8708261	0.56	-	1	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	exon	8708153	8708261	.	-	.	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	intron	8708262	8708370	.	-	.	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	CDS	8708371	8708438	0.6	-	0	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	exon	8708371	8708438	.	-	.	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	intron	8708439	8708613	.	-	.	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	CDS	8708614	8709501	0.63	-	0	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	exon	8708614	8709501	.	-	.	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
Phchi.S3	AUGUSTUS	start_codon	8709499	8709501	.	-	0	transcript_id "Phchi.S3G107200.t1"; gene_id "Phchi.S3G107200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13458.t1 is derived from g11925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7005834	7006441	.	-	.	Phchi.S3G077700
Phchi.S3	AUGUSTUS	transcript	7005834	7006441	.	-	.	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	stop_codon	7005831	7005833	.	-	0	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	CDS	7005834	7005995	1	-	0	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	exon	7005834	7005995	.	-	.	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	intron	7005996	7006084	.	-	.	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	CDS	7006085	7006113	0.53	-	2	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	exon	7006085	7006113	.	-	.	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	intron	7006114	7006272	.	-	.	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	CDS	7006273	7006441	0.29	-	0	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	exon	7006273	7006441	.	-	.	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
Phchi.S3	AUGUSTUS	start_codon	7006439	7006441	.	-	0	transcript_id "Phchi.S3G077700.t1"; gene_id "Phchi.S3G077700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11213.t1 is derived from g15263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4804701	4807874	.	+	.	Phchi.S4G079500
Phchi.S4	AUGUSTUS	transcript	4804701	4807874	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	start_codon	4804701	4804703	.	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4804701	4805025	0.97	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4804701	4805025	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4805026	4805153	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4805154	4805247	1	+	2	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4805154	4805247	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4805248	4805343	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4805344	4805429	1	+	1	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4805344	4805429	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4805430	4805584	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4805585	4805700	1	+	2	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4805585	4805700	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4805701	4805778	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4805779	4805859	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4805779	4805859	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4805860	4805962	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4805963	4806088	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4805963	4806088	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4806089	4806182	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4806183	4806465	0.97	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4806183	4806465	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4806466	4806571	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4806572	4806668	1	+	2	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4806572	4806668	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4806669	4806743	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4806744	4806900	1	+	1	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4806744	4806900	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4806901	4806998	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4806999	4807142	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4806999	4807142	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4807143	4807231	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4807232	4807300	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4807232	4807300	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4807301	4807407	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4807408	4807551	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4807408	4807551	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4807552	4807648	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4807649	4807702	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4807649	4807702	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	intron	4807703	4807829	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	CDS	4807830	4807874	1	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	exon	4807830	4807874	.	+	.	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
Phchi.S4	AUGUSTUS	stop_codon	4807875	4807877	.	+	0	transcript_id "Phchi.S4G079500.t1"; gene_id "Phchi.S4G079500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10213.t1 is derived from g7389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46397536	46398766	.	-	.	Phchi.S1G737200
Phchi.S1	AUGUSTUS	transcript	46397536	46398766	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	stop_codon	46397533	46397535	.	-	0	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	CDS	46397536	46397871	0.99	-	0	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	exon	46397536	46397871	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	intron	46397872	46397959	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	CDS	46397960	46398304	0.97	-	0	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	exon	46397960	46398304	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	intron	46398305	46398388	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	CDS	46398389	46398605	0.75	-	1	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	exon	46398389	46398605	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	intron	46398606	46398689	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	CDS	46398690	46398766	0.65	-	0	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	exon	46398690	46398766	.	-	.	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
Phchi.S1	AUGUSTUS	start_codon	46398764	46398766	.	-	0	transcript_id "Phchi.S1G737200.t1"; gene_id "Phchi.S1G737200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6789.t1 is derived from g3961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25091018	25092462	.	-	.	Phchi.S1G394800
Phchi.S1	AUGUSTUS	transcript	25091018	25092462	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	stop_codon	25091015	25091017	.	-	0	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	CDS	25091018	25091318	1	-	1	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	exon	25091018	25091318	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	intron	25091319	25091446	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	CDS	25091447	25091670	0.99	-	0	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	exon	25091447	25091670	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	intron	25091671	25091851	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	CDS	25091852	25092123	0.98	-	2	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	exon	25091852	25092123	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	intron	25092124	25092308	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	CDS	25092309	25092462	0.97	-	0	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	exon	25092309	25092462	.	-	.	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
Phchi.S1	AUGUSTUS	start_codon	25092460	25092462	.	-	0	transcript_id "Phchi.S1G394800.t1"; gene_id "Phchi.S1G394800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11614.t1 is derived from g15665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7332177	7333049	.	-	.	Phchi.S4G119600
Phchi.S4	AUGUSTUS	transcript	7332177	7333049	.	-	.	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	stop_codon	7332174	7332176	.	-	0	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	CDS	7332177	7332267	0.93	-	1	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	exon	7332177	7332267	.	-	.	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	intron	7332268	7332454	.	-	.	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	CDS	7332455	7332635	1	-	2	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	exon	7332455	7332635	.	-	.	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	intron	7332636	7332913	.	-	.	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	CDS	7332914	7333049	0.98	-	0	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	exon	7332914	7333049	.	-	.	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
Phchi.S4	AUGUSTUS	start_codon	7333047	7333049	.	-	0	transcript_id "Phchi.S4G119600.t1"; gene_id "Phchi.S4G119600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10679.t1 is derived from g14729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1562662	1565080	.	+	.	Phchi.S4G026100
Phchi.S4	AUGUSTUS	transcript	1562662	1565080	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	start_codon	1562662	1562664	.	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1562662	1562706	1	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1562662	1562706	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1562707	1562781	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1562782	1562830	0.97	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1562782	1562830	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1562831	1562903	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1562904	1562908	0.78	+	2	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1562904	1562908	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1562909	1563005	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563006	1563125	0.97	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563006	1563125	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563126	1563230	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563231	1563339	0.99	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563231	1563339	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563340	1563460	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563461	1563712	1	+	2	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563461	1563712	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563713	1563805	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563806	1563924	0.68	+	2	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563806	1563924	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563925	1564037	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564038	1564102	1	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564038	1564102	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1564103	1564198	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564199	1564467	0.99	+	1	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564199	1564467	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1564468	1564650	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564651	1564875	0.97	+	2	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564651	1564875	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1564876	1564964	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564965	1565080	1	+	2	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564965	1565080	.	+	.	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	stop_codon	1565081	1565083	.	+	0	transcript_id "Phchi.S4G026100.t1"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	transcript	1562662	1565080	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	start_codon	1562662	1562664	.	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1562662	1562706	1	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1562662	1562706	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1562707	1562781	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1562782	1562830	0.97	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1562782	1562830	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1562831	1562903	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1562904	1562908	0.76	+	2	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1562904	1562908	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1562909	1563005	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563006	1563125	0.89	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563006	1563125	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563126	1563230	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563231	1563339	0.99	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563231	1563339	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563340	1563460	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563461	1563712	1	+	2	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563461	1563712	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563713	1563805	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1563806	1563924	0.67	+	2	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1563806	1563924	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1563925	1564037	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564038	1564102	1	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564038	1564102	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1564103	1564198	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564199	1564467	1	+	1	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564199	1564467	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1564468	1564641	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564642	1564875	1	+	2	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564642	1564875	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	intron	1564876	1564964	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	CDS	1564965	1565080	1	+	2	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	exon	1564965	1565080	.	+	.	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
Phchi.S4	AUGUSTUS	stop_codon	1565081	1565083	.	+	0	transcript_id "Phchi.S4G026100.t2"; gene_id "Phchi.S4G026100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7234.t1 is derived from g4406.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27755928	27760244	.	-	.	Phchi.S1G439300
Phchi.S1	AUGUSTUS	transcript	27755928	27760244	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	stop_codon	27755925	27755927	.	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27755928	27756095	0.61	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27755928	27756095	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756096	27756179	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756180	27756419	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756180	27756419	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756420	27756498	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756499	27756579	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756499	27756579	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756580	27756722	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756723	27756782	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756723	27756782	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756783	27756897	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756898	27757003	1	-	1	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756898	27757003	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27757004	27757943	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27757944	27758020	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27757944	27758020	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758021	27758108	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758109	27758233	0.91	-	2	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758109	27758233	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758234	27758354	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758355	27758472	0.99	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758355	27758472	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758473	27758560	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758561	27758621	1	-	1	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758561	27758621	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758622	27758714	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758715	27758779	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758715	27758779	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758780	27758900	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758901	27758972	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758901	27758972	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758973	27759063	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759064	27759191	1	-	2	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759064	27759191	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759192	27759282	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759283	27759382	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759283	27759382	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759383	27759482	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759483	27759623	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759483	27759623	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759624	27759699	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759700	27759816	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759700	27759816	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759817	27759913	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759914	27760018	1	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759914	27760018	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27760019	27760133	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27760134	27760244	0.91	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27760134	27760244	.	-	.	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	start_codon	27760242	27760244	.	-	0	transcript_id "Phchi.S1G439300.t1"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	transcript	27755928	27760244	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	stop_codon	27755925	27755927	.	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27755928	27756095	0.53	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27755928	27756095	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756096	27756299	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756300	27756419	0.79	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756300	27756419	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756420	27756498	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756499	27756579	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756499	27756579	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756580	27756722	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756723	27756782	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756723	27756782	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27756783	27756897	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27756898	27757003	1	-	1	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27756898	27757003	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27757004	27757943	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27757944	27758020	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27757944	27758020	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758021	27758108	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758109	27758233	0.92	-	2	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758109	27758233	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758234	27758354	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758355	27758472	0.99	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758355	27758472	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758473	27758560	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758561	27758621	1	-	1	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758561	27758621	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758622	27758714	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758715	27758779	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758715	27758779	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758780	27758900	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27758901	27758972	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27758901	27758972	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27758973	27759063	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759064	27759191	1	-	2	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759064	27759191	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759192	27759282	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759283	27759382	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759283	27759382	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759383	27759482	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759483	27759623	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759483	27759623	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759624	27759699	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759700	27759816	1	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759700	27759816	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27759817	27759913	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27759914	27760018	0.98	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27759914	27760018	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	intron	27760019	27760133	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	CDS	27760134	27760244	0.89	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	exon	27760134	27760244	.	-	.	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
Phchi.S1	AUGUSTUS	start_codon	27760242	27760244	.	-	0	transcript_id "Phchi.S1G439300.t2"; gene_id "Phchi.S1G439300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12585.t1 is derived from g8262.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36017174	36017539	.	-	.	Phchi.S2G066500
Phchi.S2	AUGUSTUS	transcript	36017174	36017539	.	-	.	transcript_id "Phchi.S2G066500.t1"; gene_id "Phchi.S2G066500"
Phchi.S2	AUGUSTUS	stop_codon	36017171	36017173	.	-	0	transcript_id "Phchi.S2G066500.t1"; gene_id "Phchi.S2G066500"
Phchi.S2	AUGUSTUS	CDS	36017174	36017539	0.27	-	0	transcript_id "Phchi.S2G066500.t1"; gene_id "Phchi.S2G066500"
Phchi.S2	AUGUSTUS	exon	36017174	36017539	.	-	.	transcript_id "Phchi.S2G066500.t1"; gene_id "Phchi.S2G066500"
Phchi.S2	AUGUSTUS	start_codon	36017537	36017539	.	-	0	transcript_id "Phchi.S2G066500.t1"; gene_id "Phchi.S2G066500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5882.t1 is derived from g3052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19573295	19574679	.	-	.	Phchi.S1G304100
Phchi.S1	AUGUSTUS	transcript	19573295	19574679	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	stop_codon	19573292	19573294	.	-	0	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	CDS	19573295	19573539	0.87	-	2	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	exon	19573295	19573539	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	intron	19573540	19573632	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	CDS	19573633	19573870	1	-	0	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	exon	19573633	19573870	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	intron	19573871	19573961	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	CDS	19573962	19574295	0.88	-	1	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	exon	19573962	19574295	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	intron	19574296	19574391	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	CDS	19574392	19574507	0.64	-	0	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	exon	19574392	19574507	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	intron	19574508	19574595	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	CDS	19574596	19574679	0.94	-	0	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	exon	19574596	19574679	.	-	.	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
Phchi.S1	AUGUSTUS	start_codon	19574677	19574679	.	-	0	transcript_id "Phchi.S1G304100.t1"; gene_id "Phchi.S1G304100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4114.t1 is derived from g1283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8034823	8036430	.	-	.	Phchi.S1G127300
Phchi.S1	AUGUSTUS	transcript	8034823	8036430	.	-	.	transcript_id "Phchi.S1G127300.t1"; gene_id "Phchi.S1G127300"
Phchi.S1	AUGUSTUS	stop_codon	8034820	8034822	.	-	0	transcript_id "Phchi.S1G127300.t1"; gene_id "Phchi.S1G127300"
Phchi.S1	AUGUSTUS	CDS	8034823	8036430	0.41	-	0	transcript_id "Phchi.S1G127300.t1"; gene_id "Phchi.S1G127300"
Phchi.S1	AUGUSTUS	exon	8034823	8036430	.	-	.	transcript_id "Phchi.S1G127300.t1"; gene_id "Phchi.S1G127300"
Phchi.S1	AUGUSTUS	start_codon	8036428	8036430	.	-	0	transcript_id "Phchi.S1G127300.t1"; gene_id "Phchi.S1G127300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12878.t1 is derived from g11343.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2896238	2896985	.	+	.	Phchi.S3G019700
Phchi.S3	AUGUSTUS	transcript	2896238	2896902	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	start_codon	2896238	2896240	.	+	0	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896238	2896319	0.92	+	0	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896238	2896319	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	intron	2896320	2896403	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896404	2896546	1	+	2	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896404	2896546	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	intron	2896547	2896627	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896628	2896795	1	+	0	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896628	2896795	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	intron	2896796	2896872	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896873	2896902	0.99	+	0	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896873	2896902	.	+	.	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	stop_codon	2896903	2896905	.	+	0	transcript_id "Phchi.S3G019700.t1"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	transcript	2896238	2896985	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	start_codon	2896238	2896240	.	+	0	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896238	2896319	0.91	+	0	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896238	2896319	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	intron	2896320	2896403	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896404	2896546	1	+	2	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896404	2896546	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	intron	2896547	2896627	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896628	2896795	1	+	0	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896628	2896795	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	intron	2896796	2896892	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	CDS	2896893	2896985	1	+	0	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	exon	2896893	2896985	.	+	.	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
Phchi.S3	AUGUSTUS	stop_codon	2896986	2896988	.	+	0	transcript_id "Phchi.S3G019700.t2"; gene_id "Phchi.S3G019700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2534.t1 is derived from g9454.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7190414	7195235	.	-	.	Phchi.S5G114300
Phchi.S5	AUGUSTUS	transcript	7190414	7195235	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	stop_codon	7190411	7190413	.	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7190414	7190694	0.73	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7190414	7190694	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7190695	7190814	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7190815	7191162	0.98	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7190815	7191162	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7191163	7191248	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7191249	7191408	0.79	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7191249	7191408	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7191409	7191517	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7191518	7191750	0.83	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7191518	7191750	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7191751	7191844	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7191845	7191943	0.49	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7191845	7191943	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7191944	7192075	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7192076	7192192	0.57	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7192076	7192192	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7192193	7192374	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7192375	7192525	0.89	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7192375	7192525	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7192526	7192633	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7192634	7192878	0.89	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7192634	7192878	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7192879	7192960	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7192961	7193302	0.99	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7192961	7193302	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7193303	7193440	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7193441	7193582	1	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7193441	7193582	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7193583	7193658	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7193659	7194189	1	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7193659	7194189	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7194190	7194372	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7194373	7194624	0.99	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7194373	7194624	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7194625	7194758	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7194759	7194928	1	-	2	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7194759	7194928	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	intron	7194929	7195027	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	CDS	7195028	7195235	1	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	exon	7195028	7195235	.	-	.	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
Phchi.S5	AUGUSTUS	start_codon	7195233	7195235	.	-	0	transcript_id "Phchi.S5G114300.t1"; gene_id "Phchi.S5G114300"
# This transcript jg11752.t2 is derived from g15804.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11753.t1 is derived from g15805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8009680	8010495	.	+	.	Phchi.S4G133500
Phchi.S4	AUGUSTUS	transcript	8009680	8010495	.	+	.	transcript_id "Phchi.S4G133500.t1"; gene_id "Phchi.S4G133500"
Phchi.S4	AUGUSTUS	start_codon	8009680	8009682	.	+	0	transcript_id "Phchi.S4G133500.t1"; gene_id "Phchi.S4G133500"
Phchi.S4	AUGUSTUS	CDS	8009680	8010495	0.8	+	0	transcript_id "Phchi.S4G133500.t1"; gene_id "Phchi.S4G133500"
Phchi.S4	AUGUSTUS	exon	8009680	8010495	.	+	.	transcript_id "Phchi.S4G133500.t1"; gene_id "Phchi.S4G133500"
Phchi.S4	AUGUSTUS	stop_codon	8010496	8010498	.	+	0	transcript_id "Phchi.S4G133500.t1"; gene_id "Phchi.S4G133500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4621.t1 is derived from g1791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11445502	11445774	.	+	.	Phchi.S1G178000
Phchi.S1	AUGUSTUS	transcript	11445502	11445774	.	+	.	transcript_id "Phchi.S1G178000.t1"; gene_id "Phchi.S1G178000"
Phchi.S1	AUGUSTUS	start_codon	11445502	11445504	.	+	0	transcript_id "Phchi.S1G178000.t1"; gene_id "Phchi.S1G178000"
Phchi.S1	AUGUSTUS	CDS	11445502	11445774	0.57	+	0	transcript_id "Phchi.S1G178000.t1"; gene_id "Phchi.S1G178000"
Phchi.S1	AUGUSTUS	exon	11445502	11445774	.	+	.	transcript_id "Phchi.S1G178000.t1"; gene_id "Phchi.S1G178000"
Phchi.S1	AUGUSTUS	stop_codon	11445775	11445777	.	+	0	transcript_id "Phchi.S1G178000.t1"; gene_id "Phchi.S1G178000"
# This transcript jg5081.t2 is derived from g2251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5082.t1 is derived from g2252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14600257	14600665	.	-	.	Phchi.S1G224100
Phchi.S1	AUGUSTUS	transcript	14600257	14600665	.	-	.	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	stop_codon	14600254	14600256	.	-	0	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	CDS	14600257	14600490	0.89	-	0	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	exon	14600257	14600490	.	-	.	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	intron	14600491	14600587	.	-	.	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	CDS	14600588	14600665	0.54	-	0	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	exon	14600588	14600665	.	-	.	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
Phchi.S1	AUGUSTUS	start_codon	14600663	14600665	.	-	0	transcript_id "Phchi.S1G224100.t1"; gene_id "Phchi.S1G224100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5798.t1 is derived from g2968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18997643	18998275	.	+	.	Phchi.S1G295700
Phchi.S1	AUGUSTUS	transcript	18997643	18998275	.	+	.	transcript_id "Phchi.S1G295700.t1"; gene_id "Phchi.S1G295700"
Phchi.S1	AUGUSTUS	start_codon	18997643	18997645	.	+	0	transcript_id "Phchi.S1G295700.t1"; gene_id "Phchi.S1G295700"
Phchi.S1	AUGUSTUS	CDS	18997643	18998275	0.97	+	0	transcript_id "Phchi.S1G295700.t1"; gene_id "Phchi.S1G295700"
Phchi.S1	AUGUSTUS	exon	18997643	18998275	.	+	.	transcript_id "Phchi.S1G295700.t1"; gene_id "Phchi.S1G295700"
Phchi.S1	AUGUSTUS	stop_codon	18998276	18998278	.	+	0	transcript_id "Phchi.S1G295700.t1"; gene_id "Phchi.S1G295700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13271.t1 is derived from g11736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5000669	5001256	.	+	.	Phchi.S3G059000
Phchi.S3	AUGUSTUS	transcript	5000669	5001256	.	+	.	transcript_id "Phchi.S3G059000.t1"; gene_id "Phchi.S3G059000"
Phchi.S3	AUGUSTUS	start_codon	5000669	5000671	.	+	0	transcript_id "Phchi.S3G059000.t1"; gene_id "Phchi.S3G059000"
Phchi.S3	AUGUSTUS	CDS	5000669	5001256	0.83	+	0	transcript_id "Phchi.S3G059000.t1"; gene_id "Phchi.S3G059000"
Phchi.S3	AUGUSTUS	exon	5000669	5001256	.	+	.	transcript_id "Phchi.S3G059000.t1"; gene_id "Phchi.S3G059000"
Phchi.S3	AUGUSTUS	stop_codon	5001257	5001259	.	+	0	transcript_id "Phchi.S3G059000.t1"; gene_id "Phchi.S3G059000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6622.t1 is derived from g3794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24098000	24098408	.	+	.	Phchi.S1G378100
Phchi.S1	AUGUSTUS	transcript	24098000	24098408	.	+	.	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	start_codon	24098000	24098002	.	+	0	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	CDS	24098000	24098045	1	+	0	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	exon	24098000	24098045	.	+	.	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	intron	24098046	24098128	.	+	.	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	CDS	24098129	24098276	1	+	2	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	exon	24098129	24098276	.	+	.	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	intron	24098277	24098374	.	+	.	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	CDS	24098375	24098408	1	+	1	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	exon	24098375	24098408	.	+	.	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
Phchi.S1	AUGUSTUS	stop_codon	24098409	24098411	.	+	0	transcript_id "Phchi.S1G378100.t1"; gene_id "Phchi.S1G378100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14307.t1 is derived from g12774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12034472	12035038	.	-	.	Phchi.S3G162600
Phchi.S3	AUGUSTUS	transcript	12034472	12035038	.	-	.	transcript_id "Phchi.S3G162600.t1"; gene_id "Phchi.S3G162600"
Phchi.S3	AUGUSTUS	stop_codon	12034469	12034471	.	-	0	transcript_id "Phchi.S3G162600.t1"; gene_id "Phchi.S3G162600"
Phchi.S3	AUGUSTUS	CDS	12034472	12035038	0.79	-	0	transcript_id "Phchi.S3G162600.t1"; gene_id "Phchi.S3G162600"
Phchi.S3	AUGUSTUS	exon	12034472	12035038	.	-	.	transcript_id "Phchi.S3G162600.t1"; gene_id "Phchi.S3G162600"
Phchi.S3	AUGUSTUS	start_codon	12035036	12035038	.	-	0	transcript_id "Phchi.S3G162600.t1"; gene_id "Phchi.S3G162600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4808.t1 is derived from g1978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12913439	12914246	.	-	.	Phchi.S1G196700
Phchi.S1	AUGUSTUS	transcript	12913439	12914246	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	stop_codon	12913436	12913438	.	-	0	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	CDS	12913439	12913645	0.99	-	0	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	exon	12913439	12913645	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	intron	12913646	12913737	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	CDS	12913738	12913816	1	-	1	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	exon	12913738	12913816	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	intron	12913817	12913920	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	CDS	12913921	12914017	0.96	-	2	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	exon	12913921	12914017	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	intron	12914018	12914101	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	CDS	12914102	12914246	1	-	0	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	exon	12914102	12914246	.	-	.	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
Phchi.S1	AUGUSTUS	start_codon	12914244	12914246	.	-	0	transcript_id "Phchi.S1G196700.t1"; gene_id "Phchi.S1G196700"
# This transcript jg2332.t2 is derived from g9252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2333.t1 is derived from g9253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6213882	6214810	.	+	.	Phchi.S5G094200
Phchi.S5	AUGUSTUS	transcript	6213882	6214810	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	start_codon	6213882	6213884	.	+	0	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	CDS	6213882	6214011	1	+	0	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	exon	6213882	6214011	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	intron	6214012	6214098	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	CDS	6214099	6214160	1	+	2	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	exon	6214099	6214160	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	intron	6214161	6214246	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	CDS	6214247	6214385	1	+	0	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	exon	6214247	6214385	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	intron	6214386	6214769	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	CDS	6214770	6214810	0.91	+	2	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	exon	6214770	6214810	.	+	.	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
Phchi.S5	AUGUSTUS	stop_codon	6214811	6214813	.	+	0	transcript_id "Phchi.S5G094200.t1"; gene_id "Phchi.S5G094200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11411.t1 is derived from g15461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6227867	6230023	.	+	.	Phchi.S4G099300
Phchi.S4	AUGUSTUS	transcript	6227867	6230023	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	start_codon	6227867	6227869	.	+	0	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6227867	6228137	0.98	+	0	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6227867	6228137	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	intron	6228138	6228244	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6228245	6228436	1	+	2	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6228245	6228436	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	intron	6228437	6228533	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6228534	6228870	1	+	2	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6228534	6228870	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	intron	6228871	6228962	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6228963	6229180	1	+	1	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6228963	6229180	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	intron	6229181	6229258	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6229259	6229449	1	+	2	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6229259	6229449	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	intron	6229450	6229523	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6229524	6229817	1	+	0	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6229524	6229817	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	intron	6229818	6229900	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	CDS	6229901	6230023	1	+	0	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	exon	6229901	6230023	.	+	.	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
Phchi.S4	AUGUSTUS	stop_codon	6230024	6230026	.	+	0	transcript_id "Phchi.S4G099300.t1"; gene_id "Phchi.S4G099300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4996.t1 is derived from g2166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13935342	13936624	.	+	.	Phchi.S1G215500
Phchi.S1	AUGUSTUS	transcript	13935342	13936624	.	+	.	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	start_codon	13935342	13935344	.	+	0	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	CDS	13935342	13935455	0.45	+	0	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	exon	13935342	13935455	.	+	.	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	intron	13935456	13935535	.	+	.	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	CDS	13935536	13936624	0.32	+	0	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	exon	13935536	13936624	.	+	.	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
Phchi.S1	AUGUSTUS	stop_codon	13936625	13936627	.	+	0	transcript_id "Phchi.S1G215500.t1"; gene_id "Phchi.S1G215500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11363.t1 is derived from g15413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5772005	5772634	.	-	.	Phchi.S4G094500
Phchi.S4	AUGUSTUS	transcript	5772005	5772634	.	-	.	transcript_id "Phchi.S4G094500.t1"; gene_id "Phchi.S4G094500"
Phchi.S4	AUGUSTUS	stop_codon	5772002	5772004	.	-	0	transcript_id "Phchi.S4G094500.t1"; gene_id "Phchi.S4G094500"
Phchi.S4	AUGUSTUS	CDS	5772005	5772634	0.48	-	0	transcript_id "Phchi.S4G094500.t1"; gene_id "Phchi.S4G094500"
Phchi.S4	AUGUSTUS	exon	5772005	5772634	.	-	.	transcript_id "Phchi.S4G094500.t1"; gene_id "Phchi.S4G094500"
Phchi.S4	AUGUSTUS	start_codon	5772632	5772634	.	-	0	transcript_id "Phchi.S4G094500.t1"; gene_id "Phchi.S4G094500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13749.t1 is derived from g12216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8685628	8688953	.	-	.	Phchi.S3G106800
Phchi.S3	AUGUSTUS	transcript	8685628	8688953	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	stop_codon	8685625	8685627	.	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8685628	8685924	0.98	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8685628	8685924	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8685925	8686070	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8686071	8686178	1	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8686071	8686178	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8686179	8686314	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8686315	8686587	1	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8686315	8686587	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8686588	8686695	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8686696	8686782	1	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8686696	8686782	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8686783	8686924	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8686925	8687119	1	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8686925	8687119	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8687120	8687237	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8687238	8687369	1	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8687238	8687369	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8687370	8687525	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8687526	8687651	1	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8687526	8687651	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8687652	8687747	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8687748	8687944	0.99	-	2	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8687748	8687944	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8687945	8688111	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8688112	8688313	0.99	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8688112	8688313	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8688314	8688430	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8688431	8688513	0.99	-	2	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8688431	8688513	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	intron	8688514	8688673	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	CDS	8688674	8688953	0.65	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	exon	8688674	8688953	.	-	.	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
Phchi.S3	AUGUSTUS	start_codon	8688951	8688953	.	-	0	transcript_id "Phchi.S3G106800.t1"; gene_id "Phchi.S3G106800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8224.t1 is derived from g5399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34540931	34541405	.	+	.	Phchi.S1G538300
Phchi.S1	AUGUSTUS	transcript	34540931	34541405	.	+	.	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	start_codon	34540931	34540933	.	+	0	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	CDS	34540931	34540975	0.72	+	0	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	exon	34540931	34540975	.	+	.	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	intron	34540976	34541160	.	+	.	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	CDS	34541161	34541270	0.73	+	0	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	exon	34541161	34541270	.	+	.	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	intron	34541271	34541362	.	+	.	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	CDS	34541363	34541405	0.99	+	1	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	exon	34541363	34541405	.	+	.	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
Phchi.S1	AUGUSTUS	stop_codon	34541406	34541408	.	+	0	transcript_id "Phchi.S1G538300.t1"; gene_id "Phchi.S1G538300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6069.t1 is derived from g3240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20728444	20730307	.	-	.	Phchi.S1G322800
Phchi.S1	AUGUSTUS	transcript	20728444	20730307	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	stop_codon	20728441	20728443	.	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20728444	20728545	0.98	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20728444	20728545	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20728546	20728639	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20728640	20728686	1	-	2	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20728640	20728686	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20728687	20728785	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20728786	20728870	1	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20728786	20728870	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20728871	20728975	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20728976	20729118	0.59	-	2	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20728976	20729118	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20729119	20729207	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20729208	20729357	1	-	2	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20729208	20729357	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20729358	20729477	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20729478	20729618	1	-	2	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20729478	20729618	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20729619	20729716	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20729717	20729804	0.69	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20729717	20729804	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20729805	20729896	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20729897	20730016	0.76	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20729897	20730016	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	intron	20730017	20730220	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	CDS	20730221	20730307	0.92	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	exon	20730221	20730307	.	-	.	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
Phchi.S1	AUGUSTUS	start_codon	20730305	20730307	.	-	0	transcript_id "Phchi.S1G322800.t1"; gene_id "Phchi.S1G322800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3116.t1 is derived from g285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1803396	1806284	.	+	.	Phchi.S1G027500
Phchi.S1	AUGUSTUS	transcript	1803396	1806284	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	start_codon	1803396	1803398	.	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1803396	1804631	0.76	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1803396	1804631	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	intron	1804632	1804719	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1804720	1804962	0.81	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1804720	1804962	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	intron	1804963	1805069	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1805070	1805135	1	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1805070	1805135	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	intron	1805136	1805255	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1805256	1805501	0.75	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1805256	1805501	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	intron	1805502	1805629	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1805630	1805908	1	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1805630	1805908	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	intron	1805909	1806063	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1806064	1806157	1	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1806064	1806157	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	intron	1806158	1806249	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	CDS	1806250	1806284	0.98	+	2	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	exon	1806250	1806284	.	+	.	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
Phchi.S1	AUGUSTUS	stop_codon	1806285	1806287	.	+	0	transcript_id "Phchi.S1G027500.t1"; gene_id "Phchi.S1G027500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6499.t1 is derived from g3671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23331552	23334063	.	-	.	Phchi.S1G365800
Phchi.S1	AUGUSTUS	transcript	23331552	23334063	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	stop_codon	23331549	23331551	.	-	0	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23331552	23331693	0.81	-	1	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23331552	23331693	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23331694	23331818	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23331819	23332270	0.98	-	0	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23331819	23332270	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23332271	23332364	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23332365	23332695	1	-	1	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23332365	23332695	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23332696	23332842	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23332843	23332920	1	-	1	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23332843	23332920	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23332921	23333028	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23333029	23333232	1	-	1	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23333029	23333232	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23333233	23333330	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23333331	23333490	1	-	2	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23333331	23333490	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23333491	23333578	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23333579	23333627	0.94	-	0	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23333579	23333627	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	intron	23333628	23334057	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	CDS	23334058	23334063	0.82	-	0	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	exon	23334058	23334063	.	-	.	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
Phchi.S1	AUGUSTUS	start_codon	23334061	23334063	.	-	0	transcript_id "Phchi.S1G365800.t1"; gene_id "Phchi.S1G365800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13151.t1 is derived from g11616.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4408075	4410048	.	-	.	Phchi.S3G047000
Phchi.S3	AUGUSTUS	transcript	4408075	4410048	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	stop_codon	4408072	4408074	.	-	0	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4408075	4408333	0.99	-	1	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4408075	4408333	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4408334	4408433	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4408434	4408727	0.98	-	1	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4408434	4408727	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4408728	4408836	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4408837	4408927	0.95	-	2	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4408837	4408927	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4408928	4409037	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409038	4409175	0.77	-	2	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409038	4409175	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4409176	4409261	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409262	4409394	1	-	0	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409262	4409394	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4409395	4409494	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409495	4409701	1	-	0	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409495	4409701	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4409702	4409820	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409821	4410048	0.38	-	0	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409821	4410048	.	-	.	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	start_codon	4410046	4410048	.	-	0	transcript_id "Phchi.S3G047000.t1"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	transcript	4408770	4410048	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	stop_codon	4408767	4408769	.	-	0	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4408770	4408927	0.96	-	2	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4408770	4408927	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4408928	4409037	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409038	4409175	0.8	-	2	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409038	4409175	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4409176	4409261	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409262	4409394	1	-	0	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409262	4409394	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4409395	4409494	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409495	4409701	0.99	-	0	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409495	4409701	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	intron	4409702	4409820	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	CDS	4409821	4410048	0.42	-	0	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	exon	4409821	4410048	.	-	.	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
Phchi.S3	AUGUSTUS	start_codon	4410046	4410048	.	-	0	transcript_id "Phchi.S3G047000.t2"; gene_id "Phchi.S3G047000"
# This transcript jg3140.t2 is derived from g309.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3141.t1 is derived from g310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1961121	1962614	.	+	.	Phchi.S1G030000
Phchi.S1	AUGUSTUS	transcript	1961121	1962614	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	start_codon	1961121	1961123	.	+	0	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	CDS	1961121	1961330	0.93	+	0	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	exon	1961121	1961330	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	intron	1961331	1961409	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	CDS	1961410	1961492	0.98	+	0	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	exon	1961410	1961492	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	intron	1961493	1961662	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	CDS	1961663	1961765	1	+	1	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	exon	1961663	1961765	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	intron	1961766	1961857	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	CDS	1961858	1962002	1	+	0	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	exon	1961858	1962002	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	intron	1962003	1962084	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	CDS	1962085	1962362	1	+	2	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	exon	1962085	1962362	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	intron	1962363	1962446	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	CDS	1962447	1962614	1	+	0	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	exon	1962447	1962614	.	+	.	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
Phchi.S1	AUGUSTUS	stop_codon	1962615	1962617	.	+	0	transcript_id "Phchi.S1G030000.t1"; gene_id "Phchi.S1G030000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11158.t1 is derived from g15208.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4422863	4425235	.	-	.	Phchi.S4G074000
Phchi.S4	AUGUSTUS	transcript	4422863	4425235	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	stop_codon	4422860	4422862	.	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4422863	4422973	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4422863	4422973	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4422974	4423050	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4423051	4423140	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4423051	4423140	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4423141	4423339	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4423340	4423465	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4423340	4423465	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4423466	4423544	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4423545	4423604	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4423545	4423604	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4423605	4423840	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4423841	4423903	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4423841	4423903	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4423904	4424021	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4424022	4424142	1	-	1	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4424022	4424142	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4424143	4424246	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4424247	4424320	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4424247	4424320	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4424321	4424416	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4424417	4424486	1	-	1	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4424417	4424486	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4424487	4424578	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4424579	4424695	1	-	1	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4424579	4424695	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4424696	4424789	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4424790	4424869	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4424790	4424869	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4424870	4424963	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4424964	4425042	1	-	1	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4424964	4425042	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	intron	4425043	4425191	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	CDS	4425192	4425235	1	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	exon	4425192	4425235	.	-	.	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
Phchi.S4	AUGUSTUS	start_codon	4425233	4425235	.	-	0	transcript_id "Phchi.S4G074000.t1"; gene_id "Phchi.S4G074000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9924.t1 is derived from g7100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44498461	44502852	.	+	.	Phchi.S1G708300
Phchi.S1	AUGUSTUS	transcript	44498461	44502852	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	start_codon	44498461	44498463	.	+	0	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	CDS	44498461	44500030	0.74	+	0	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	exon	44498461	44500030	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	intron	44500031	44500163	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	CDS	44500164	44501587	1	+	2	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	exon	44500164	44501587	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	intron	44501588	44501703	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	CDS	44501704	44501928	0.95	+	0	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	exon	44501704	44501928	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	intron	44501929	44502048	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	CDS	44502049	44502144	0.98	+	0	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	exon	44502049	44502144	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	intron	44502145	44502258	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	CDS	44502259	44502852	1	+	0	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	exon	44502259	44502852	.	+	.	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
Phchi.S1	AUGUSTUS	stop_codon	44502853	44502855	.	+	0	transcript_id "Phchi.S1G708300.t1"; gene_id "Phchi.S1G708300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg735.t1 is derived from g10517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5244094	5244706	.	+	.	Phchi.S6G069400
Phchi.S6	AUGUSTUS	transcript	5244094	5244706	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	start_codon	5244094	5244096	.	+	0	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	CDS	5244094	5244165	0.97	+	0	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	exon	5244094	5244165	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	intron	5244166	5244243	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	CDS	5244244	5244312	1	+	0	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	exon	5244244	5244312	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	intron	5244313	5244436	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	CDS	5244437	5244530	1	+	0	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	exon	5244437	5244530	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	intron	5244531	5244632	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	CDS	5244633	5244706	1	+	2	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	exon	5244633	5244706	.	+	.	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
Phchi.S6	AUGUSTUS	stop_codon	5244707	5244709	.	+	0	transcript_id "Phchi.S6G069400.t1"; gene_id "Phchi.S6G069400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10853.t1 is derived from g14903.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2514639	2515271	.	-	.	Phchi.S4G043500
Phchi.S4	AUGUSTUS	transcript	2514639	2515271	.	-	.	transcript_id "Phchi.S4G043500.t1"; gene_id "Phchi.S4G043500"
Phchi.S4	AUGUSTUS	stop_codon	2514636	2514638	.	-	0	transcript_id "Phchi.S4G043500.t1"; gene_id "Phchi.S4G043500"
Phchi.S4	AUGUSTUS	CDS	2514639	2515271	1	-	0	transcript_id "Phchi.S4G043500.t1"; gene_id "Phchi.S4G043500"
Phchi.S4	AUGUSTUS	exon	2514639	2515271	.	-	.	transcript_id "Phchi.S4G043500.t1"; gene_id "Phchi.S4G043500"
Phchi.S4	AUGUSTUS	start_codon	2515269	2515271	.	-	0	transcript_id "Phchi.S4G043500.t1"; gene_id "Phchi.S4G043500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3635.t1 is derived from g804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4870871	4871821	.	+	.	Phchi.S1G079400
Phchi.S1	AUGUSTUS	transcript	4870871	4871821	.	+	.	transcript_id "Phchi.S1G079400.t1"; gene_id "Phchi.S1G079400"
Phchi.S1	AUGUSTUS	start_codon	4870871	4870873	.	+	0	transcript_id "Phchi.S1G079400.t1"; gene_id "Phchi.S1G079400"
Phchi.S1	AUGUSTUS	CDS	4870871	4871821	1	+	0	transcript_id "Phchi.S1G079400.t1"; gene_id "Phchi.S1G079400"
Phchi.S1	AUGUSTUS	exon	4870871	4871821	.	+	.	transcript_id "Phchi.S1G079400.t1"; gene_id "Phchi.S1G079400"
Phchi.S1	AUGUSTUS	stop_codon	4871822	4871824	.	+	0	transcript_id "Phchi.S1G079400.t1"; gene_id "Phchi.S1G079400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2237.t1 is derived from g9157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5590491	5591152	.	-	.	Phchi.S5G084600
Phchi.S5	AUGUSTUS	transcript	5590491	5591152	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	stop_codon	5590488	5590490	.	-	0	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	CDS	5590491	5590500	0.53	-	1	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	exon	5590491	5590500	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	intron	5590501	5590578	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	CDS	5590579	5590670	0.5	-	0	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	exon	5590579	5590670	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	intron	5590671	5590759	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	CDS	5590760	5590855	0.41	-	0	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	exon	5590760	5590855	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	intron	5590856	5591071	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	CDS	5591072	5591152	0.4	-	0	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	exon	5591072	5591152	.	-	.	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
Phchi.S5	AUGUSTUS	start_codon	5591150	5591152	.	-	0	transcript_id "Phchi.S5G084600.t1"; gene_id "Phchi.S5G084600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2002.t1 is derived from g8922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4404662	4405812	.	+	.	Phchi.S5G061100
Phchi.S5	AUGUSTUS	transcript	4404662	4405812	.	+	.	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	start_codon	4404662	4404664	.	+	0	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	CDS	4404662	4405322	0.15	+	0	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	exon	4404662	4405322	.	+	.	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	intron	4405323	4405559	.	+	.	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	CDS	4405560	4405593	1	+	2	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	exon	4405560	4405593	.	+	.	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	intron	4405594	4405682	.	+	.	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	CDS	4405683	4405812	0.93	+	1	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	exon	4405683	4405812	.	+	.	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
Phchi.S5	AUGUSTUS	stop_codon	4405813	4405815	.	+	0	transcript_id "Phchi.S5G061100.t1"; gene_id "Phchi.S5G061100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1135.t1 is derived from g10918.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7882754	7883354	.	+	.	Phchi.S6G109400
Phchi.S6	AUGUSTUS	transcript	7882754	7883354	.	+	.	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	start_codon	7882754	7882756	.	+	0	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	CDS	7882754	7883004	0.93	+	0	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	exon	7882754	7883004	.	+	.	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	intron	7883005	7883146	.	+	.	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	CDS	7883147	7883354	1	+	1	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	exon	7883147	7883354	.	+	.	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
Phchi.S6	AUGUSTUS	stop_codon	7883355	7883357	.	+	0	transcript_id "Phchi.S6G109400.t1"; gene_id "Phchi.S6G109400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11898.t1 is derived from g15950.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9150199	9151035	.	-	.	Phchi.S4G148000
Phchi.S4	AUGUSTUS	transcript	9150199	9151035	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	stop_codon	9150108	9150110	.	-	0	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	CDS	9150199	9150280	1	-	1	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	exon	9150199	9150280	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	intron	9150281	9150354	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	CDS	9150355	9150382	0.95	-	2	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	exon	9150355	9150382	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	intron	9150383	9150461	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	CDS	9150462	9150662	0.93	-	2	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	exon	9150462	9150662	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	intron	9150663	9150743	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	CDS	9150744	9150813	0.95	-	0	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	exon	9150744	9150813	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	intron	9150814	9150912	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	CDS	9150913	9151035	0.75	-	0	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	exon	9150913	9151035	.	-	.	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
Phchi.S4	AUGUSTUS	start_codon	9151033	9151035	.	-	0	transcript_id "Phchi.S4G148000.t1"; gene_id "Phchi.S4G148000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13603.t1 is derived from g12070.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7657540	7658594	.	-	.	Phchi.S3G092200
Phchi.S3	AUGUSTUS	transcript	7657540	7658594	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	stop_codon	7657537	7657539	.	-	0	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	CDS	7657540	7657761	0.33	-	0	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	exon	7657540	7657761	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	intron	7657762	7657853	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	CDS	7657854	7657978	0.48	-	2	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	exon	7657854	7657978	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	intron	7657979	7658063	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	CDS	7658064	7658159	0.39	-	2	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	exon	7658064	7658159	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	intron	7658160	7658258	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	CDS	7658259	7658393	1	-	2	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	exon	7658259	7658393	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	intron	7658394	7658494	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	CDS	7658495	7658594	0.99	-	0	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	exon	7658495	7658594	.	-	.	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
Phchi.S3	AUGUSTUS	start_codon	7658592	7658594	.	-	0	transcript_id "Phchi.S3G092200.t1"; gene_id "Phchi.S3G092200"
# This transcript jg15702.t2 is derived from g14172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15703.t1 is derived from g14173.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20778736	20779692	.	+	.	Phchi.S3G302200
Phchi.S3	AUGUSTUS	transcript	20778736	20779692	.	+	.	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	start_codon	20778736	20778738	.	+	0	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	CDS	20778736	20779380	0.51	+	0	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	exon	20778736	20779380	.	+	.	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	intron	20779381	20779470	.	+	.	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	CDS	20779471	20779692	0.99	+	0	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	exon	20779471	20779692	.	+	.	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
Phchi.S3	AUGUSTUS	stop_codon	20779693	20779695	.	+	0	transcript_id "Phchi.S3G302200.t1"; gene_id "Phchi.S3G302200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12952.t1 is derived from g11417.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3288691	3289149	.	+	.	Phchi.S3G027100
Phchi.S3	AUGUSTUS	transcript	3288691	3289149	.	+	.	transcript_id "Phchi.S3G027100.t1"; gene_id "Phchi.S3G027100"
Phchi.S3	AUGUSTUS	start_codon	3288691	3288693	.	+	0	transcript_id "Phchi.S3G027100.t1"; gene_id "Phchi.S3G027100"
Phchi.S3	AUGUSTUS	CDS	3288691	3289149	1	+	0	transcript_id "Phchi.S3G027100.t1"; gene_id "Phchi.S3G027100"
Phchi.S3	AUGUSTUS	exon	3288691	3289149	.	+	.	transcript_id "Phchi.S3G027100.t1"; gene_id "Phchi.S3G027100"
Phchi.S3	AUGUSTUS	stop_codon	3289150	3289152	.	+	0	transcript_id "Phchi.S3G027100.t1"; gene_id "Phchi.S3G027100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15677.t1 is derived from g14146.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20623964	20625517	.	+	.	Phchi.S3G299600
Phchi.S3	AUGUSTUS	transcript	20623964	20625517	.	+	.	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	start_codon	20623964	20623966	.	+	0	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	CDS	20623964	20624110	0.92	+	0	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	exon	20623964	20624110	.	+	.	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	intron	20624111	20624385	.	+	.	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	CDS	20624386	20624782	1	+	0	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	exon	20624386	20624782	.	+	.	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	intron	20624783	20625200	.	+	.	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	CDS	20625201	20625517	1	+	2	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	exon	20625201	20625517	.	+	.	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	stop_codon	20625518	20625520	.	+	0	transcript_id "Phchi.S3G299600.t1"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	transcript	20623964	20625517	.	+	.	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	start_codon	20623964	20623966	.	+	0	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	CDS	20623964	20624110	0.9	+	0	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	exon	20623964	20624110	.	+	.	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	intron	20624111	20624385	.	+	.	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	CDS	20624386	20624782	1	+	0	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	exon	20624386	20624782	.	+	.	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	intron	20624783	20625194	.	+	.	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	CDS	20625195	20625517	1	+	2	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	exon	20625195	20625517	.	+	.	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
Phchi.S3	AUGUSTUS	stop_codon	20625518	20625520	.	+	0	transcript_id "Phchi.S3G299600.t2"; gene_id "Phchi.S3G299600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5119.t1 is derived from g2289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14817740	14819626	.	-	.	Phchi.S1G227800
Phchi.S1	AUGUSTUS	transcript	14817740	14819626	.	-	.	transcript_id "Phchi.S1G227800.t1"; gene_id "Phchi.S1G227800"
Phchi.S1	AUGUSTUS	stop_codon	14817737	14817739	.	-	0	transcript_id "Phchi.S1G227800.t1"; gene_id "Phchi.S1G227800"
Phchi.S1	AUGUSTUS	CDS	14817740	14819626	0.98	-	0	transcript_id "Phchi.S1G227800.t1"; gene_id "Phchi.S1G227800"
Phchi.S1	AUGUSTUS	exon	14817740	14819626	.	-	.	transcript_id "Phchi.S1G227800.t1"; gene_id "Phchi.S1G227800"
Phchi.S1	AUGUSTUS	start_codon	14819624	14819626	.	-	0	transcript_id "Phchi.S1G227800.t1"; gene_id "Phchi.S1G227800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12339.t1 is derived from g8015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11299160	11302872	.	-	.	Phchi.S2G041900
Phchi.S2	AUGUSTUS	transcript	11299160	11302872	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	stop_codon	11299157	11299159	.	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11299160	11299261	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11299160	11299261	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11299262	11299350	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11299351	11299572	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11299351	11299572	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11299573	11299649	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11299650	11299815	1	-	1	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11299650	11299815	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11299816	11299908	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11299909	11300109	1	-	1	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11299909	11300109	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11300110	11300241	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11300242	11300414	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11300242	11300414	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11300415	11300539	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11300540	11300731	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11300540	11300731	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11300732	11300973	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11300974	11301148	0.93	-	1	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11300974	11301148	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11301149	11301258	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11301259	11301401	0.85	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11301259	11301401	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11301402	11301538	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11301539	11301628	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11301539	11301628	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11301629	11301702	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11301703	11301825	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11301703	11301825	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11301826	11301911	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11301912	11302089	1	-	1	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11301912	11302089	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11302090	11302212	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11302213	11302424	0.83	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11302213	11302424	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11302425	11302511	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11302512	11302571	1	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11302512	11302571	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11302572	11302692	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11302693	11302760	1	-	2	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11302693	11302760	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	intron	11302761	11302841	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	CDS	11302842	11302872	0.98	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	exon	11302842	11302872	.	-	.	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
Phchi.S2	AUGUSTUS	start_codon	11302870	11302872	.	-	0	transcript_id "Phchi.S2G041900.t1"; gene_id "Phchi.S2G041900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14130.t1 is derived from g12597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11043152	11045551	.	+	.	Phchi.S3G144900
Phchi.S3	AUGUSTUS	transcript	11043152	11045551	.	+	.	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	start_codon	11043152	11043154	.	+	0	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	CDS	11043152	11044795	0.95	+	0	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	exon	11043152	11044795	.	+	.	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	intron	11044796	11044898	.	+	.	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	CDS	11044899	11045363	0.99	+	0	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	exon	11044899	11045363	.	+	.	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	intron	11045364	11045476	.	+	.	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	CDS	11045477	11045551	0.98	+	0	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	exon	11045477	11045551	.	+	.	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
Phchi.S3	AUGUSTUS	stop_codon	11045552	11045554	.	+	0	transcript_id "Phchi.S3G144900.t1"; gene_id "Phchi.S3G144900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14856.t1 is derived from g13324.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15075499	15077661	.	+	.	Phchi.S3G217500
Phchi.S3	AUGUSTUS	transcript	15075499	15077661	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	start_codon	15075499	15075501	.	+	0	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15075499	15075667	1	+	0	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15075499	15075667	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15075668	15075767	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15075768	15075883	1	+	2	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15075768	15075883	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15075884	15076074	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15076075	15076193	1	+	0	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15076075	15076193	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15076194	15076360	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15076361	15076514	1	+	1	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15076361	15076514	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15076515	15076769	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15076770	15077126	0.83	+	0	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15076770	15077126	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15077127	15077271	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15077272	15077390	1	+	0	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15077272	15077390	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15077391	15077531	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15077532	15077661	0.98	+	1	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15077532	15077661	.	+	.	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	stop_codon	15077662	15077664	.	+	0	transcript_id "Phchi.S3G217500.t1"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	transcript	15075499	15077661	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	start_codon	15075499	15075501	.	+	0	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15075499	15075670	0.99	+	0	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15075499	15075670	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15075671	15075767	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15075768	15075883	1	+	2	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15075768	15075883	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15075884	15076074	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15076075	15076193	1	+	0	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15076075	15076193	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15076194	15076360	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15076361	15076514	1	+	1	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15076361	15076514	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15076515	15076769	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15076770	15077126	0.8	+	0	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15076770	15077126	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15077127	15077271	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15077272	15077390	1	+	0	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15077272	15077390	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	intron	15077391	15077531	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	CDS	15077532	15077661	0.98	+	1	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	exon	15077532	15077661	.	+	.	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
Phchi.S3	AUGUSTUS	stop_codon	15077662	15077664	.	+	0	transcript_id "Phchi.S3G217500.t2"; gene_id "Phchi.S3G217500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8444.t1 is derived from g5619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35953853	35954774	.	-	.	Phchi.S1G560300
Phchi.S1	AUGUSTUS	transcript	35953853	35954774	.	-	.	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	stop_codon	35953850	35953852	.	-	0	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	CDS	35953853	35953954	0.93	-	0	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	exon	35953853	35953954	.	-	.	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	intron	35953955	35954102	.	-	.	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	CDS	35954103	35954774	1	-	0	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	exon	35954103	35954774	.	-	.	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
Phchi.S1	AUGUSTUS	start_codon	35954772	35954774	.	-	0	transcript_id "Phchi.S1G560300.t1"; gene_id "Phchi.S1G560300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10985.t1 is derived from g15035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3532832	3533392	.	-	.	Phchi.S4G056700
Phchi.S4	AUGUSTUS	transcript	3532832	3533392	.	-	.	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	stop_codon	3532829	3532831	.	-	0	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	CDS	3532832	3532929	1	-	2	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	exon	3532832	3532929	.	-	.	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	intron	3532930	3533019	.	-	.	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	CDS	3533020	3533122	0.86	-	0	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	exon	3533020	3533122	.	-	.	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	intron	3533123	3533362	.	-	.	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	CDS	3533363	3533392	0.51	-	0	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	exon	3533363	3533392	.	-	.	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
Phchi.S4	AUGUSTUS	start_codon	3533390	3533392	.	-	0	transcript_id "Phchi.S4G056700.t1"; gene_id "Phchi.S4G056700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7488.t1 is derived from g4661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29622153	29622660	.	+	.	Phchi.S1G464700
Phchi.S1	AUGUSTUS	transcript	29622153	29622660	.	+	.	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	start_codon	29622153	29622155	.	+	0	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	CDS	29622153	29622212	1	+	0	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	exon	29622153	29622212	.	+	.	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	intron	29622213	29622306	.	+	.	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	CDS	29622307	29622437	1	+	0	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	exon	29622307	29622437	.	+	.	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	intron	29622438	29622509	.	+	.	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	CDS	29622510	29622660	0.89	+	1	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	exon	29622510	29622660	.	+	.	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
Phchi.S1	AUGUSTUS	stop_codon	29622661	29622663	.	+	0	transcript_id "Phchi.S1G464700.t1"; gene_id "Phchi.S1G464700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg129.t1 is derived from g9911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	708148	710350	.	-	.	Phchi.S6G008800
Phchi.S6	AUGUSTUS	transcript	708148	710350	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	stop_codon	708145	708147	.	-	0	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	CDS	708148	708152	0.67	-	2	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	exon	708148	708152	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	intron	708153	708292	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	CDS	708293	709976	0.84	-	0	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	exon	708293	709976	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	intron	709977	710062	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	CDS	710063	710145	0.98	-	2	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	exon	710063	710145	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	intron	710146	710268	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	CDS	710269	710350	0.49	-	0	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	exon	710269	710350	.	-	.	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
Phchi.S6	AUGUSTUS	start_codon	710348	710350	.	-	0	transcript_id "Phchi.S6G008800.t1"; gene_id "Phchi.S6G008800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13304.t1 is derived from g11770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5604478	5607556	.	+	.	Phchi.S3G062300
Phchi.S3	AUGUSTUS	transcript	5604478	5607556	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	start_codon	5604478	5604480	.	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5604478	5604591	0.76	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5604478	5604591	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5604592	5604668	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5604669	5604761	0.53	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5604669	5604761	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5604762	5604856	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5604857	5605243	0.4	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5604857	5605243	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5605244	5605396	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5605397	5605597	0.52	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5605397	5605597	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5605598	5605738	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5605739	5605932	0.71	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5605739	5605932	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5605933	5606103	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5606104	5606192	0.84	+	1	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5606104	5606192	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5606193	5606309	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5606310	5606366	0.32	+	2	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5606310	5606366	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5606367	5606465	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5606466	5606538	0.64	+	2	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5606466	5606538	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5606539	5606687	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5606688	5606786	0.4	+	1	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5606688	5606786	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	intron	5606787	5606889	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	CDS	5606890	5607556	0.74	+	1	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	exon	5606890	5607556	.	+	.	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
Phchi.S3	AUGUSTUS	stop_codon	5607557	5607559	.	+	0	transcript_id "Phchi.S3G062300.t1"; gene_id "Phchi.S3G062300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7655.t1 is derived from g4829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30438177	30439074	.	+	.	Phchi.S1G481400
Phchi.S1	AUGUSTUS	transcript	30438177	30439074	.	+	.	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	start_codon	30438177	30438179	.	+	0	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	CDS	30438177	30438278	0.74	+	0	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	exon	30438177	30438278	.	+	.	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	intron	30438279	30438534	.	+	.	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	CDS	30438535	30438872	0.91	+	0	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	exon	30438535	30438872	.	+	.	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	intron	30438873	30439073	.	+	.	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	CDS	30439074	30439074	1	+	1	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	exon	30439074	30439074	.	+	.	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
Phchi.S1	AUGUSTUS	stop_codon	30439075	30439077	.	+	0	transcript_id "Phchi.S1G481400.t1"; gene_id "Phchi.S1G481400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10874.t1 is derived from g14924.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2709102	2709578	.	-	.	Phchi.S4G045600
Phchi.S4	AUGUSTUS	transcript	2709102	2709578	.	-	.	transcript_id "Phchi.S4G045600.t1"; gene_id "Phchi.S4G045600"
Phchi.S4	AUGUSTUS	stop_codon	2709099	2709101	.	-	0	transcript_id "Phchi.S4G045600.t1"; gene_id "Phchi.S4G045600"
Phchi.S4	AUGUSTUS	CDS	2709102	2709578	0.19	-	0	transcript_id "Phchi.S4G045600.t1"; gene_id "Phchi.S4G045600"
Phchi.S4	AUGUSTUS	exon	2709102	2709578	.	-	.	transcript_id "Phchi.S4G045600.t1"; gene_id "Phchi.S4G045600"
Phchi.S4	AUGUSTUS	start_codon	2709576	2709578	.	-	0	transcript_id "Phchi.S4G045600.t1"; gene_id "Phchi.S4G045600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2622.t1 is derived from g9542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7807129	7807848	.	+	.	Phchi.S5G123100
Phchi.S5	AUGUSTUS	transcript	7807129	7807848	.	+	.	transcript_id "Phchi.S5G123100.t1"; gene_id "Phchi.S5G123100"
Phchi.S5	AUGUSTUS	start_codon	7807129	7807131	.	+	0	transcript_id "Phchi.S5G123100.t1"; gene_id "Phchi.S5G123100"
Phchi.S5	AUGUSTUS	CDS	7807129	7807848	0.68	+	0	transcript_id "Phchi.S5G123100.t1"; gene_id "Phchi.S5G123100"
Phchi.S5	AUGUSTUS	exon	7807129	7807848	.	+	.	transcript_id "Phchi.S5G123100.t1"; gene_id "Phchi.S5G123100"
Phchi.S5	AUGUSTUS	stop_codon	7807849	7807851	.	+	0	transcript_id "Phchi.S5G123100.t1"; gene_id "Phchi.S5G123100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8762.t1 is derived from g5937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37857054	37857944	.	-	.	Phchi.S1G592100
Phchi.S1	AUGUSTUS	transcript	37857054	37857944	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	stop_codon	37857051	37857053	.	-	0	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	CDS	37857054	37857152	0.94	-	0	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	exon	37857054	37857152	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	intron	37857153	37857491	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	CDS	37857492	37857540	0.57	-	1	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	exon	37857492	37857540	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	intron	37857541	37857705	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	CDS	37857706	37857818	0.5	-	0	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	exon	37857706	37857818	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	intron	37857819	37857908	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	CDS	37857909	37857944	0.44	-	0	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	exon	37857909	37857944	.	-	.	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
Phchi.S1	AUGUSTUS	start_codon	37857942	37857944	.	-	0	transcript_id "Phchi.S1G592100.t1"; gene_id "Phchi.S1G592100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8012.t1 is derived from g5187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32474036	32476109	.	+	.	Phchi.S1G517100
Phchi.S1	AUGUSTUS	transcript	32474036	32476109	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	start_codon	32474036	32474038	.	+	0	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474036	32474040	1	+	0	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474036	32474040	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474041	32474411	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474412	32474479	1	+	1	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474412	32474479	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474480	32474560	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474561	32474832	1	+	2	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474561	32474832	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474833	32474922	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474923	32474965	1	+	0	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474923	32474965	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474966	32475061	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475062	32475368	1	+	2	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475062	32475368	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32475369	32475459	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475460	32475494	1	+	1	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475460	32475494	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32475495	32475602	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475603	32475710	0.97	+	2	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475603	32475710	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32475711	32475795	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475796	32476109	1	+	2	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475796	32476109	.	+	.	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	stop_codon	32476110	32476112	.	+	0	transcript_id "Phchi.S1G517100.t1"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	transcript	32474036	32476109	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	start_codon	32474036	32474038	.	+	0	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474036	32474040	1	+	0	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474036	32474040	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474041	32474411	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474412	32474479	1	+	1	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474412	32474479	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474480	32474560	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474561	32474832	1	+	2	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474561	32474832	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474833	32474922	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32474923	32474965	1	+	0	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32474923	32474965	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32474966	32475061	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475062	32475368	1	+	2	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475062	32475368	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32475369	32475459	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475460	32475494	1	+	1	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475460	32475494	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32475495	32475602	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475603	32475710	0.96	+	2	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475603	32475710	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	intron	32475711	32475786	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	CDS	32475787	32476109	1	+	2	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	exon	32475787	32476109	.	+	.	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
Phchi.S1	AUGUSTUS	stop_codon	32476110	32476112	.	+	0	transcript_id "Phchi.S1G517100.t2"; gene_id "Phchi.S1G517100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11092.t1 is derived from g15142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4083491	4084691	.	-	.	Phchi.S4G067400
Phchi.S4	AUGUSTUS	transcript	4083491	4084691	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	stop_codon	4083488	4083490	.	-	0	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	CDS	4083491	4083600	1	-	2	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	exon	4083491	4083600	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	intron	4083601	4083737	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	CDS	4083738	4083951	1	-	0	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	exon	4083738	4083951	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	intron	4083952	4084085	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	CDS	4084086	4084192	1	-	2	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	exon	4084086	4084192	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	intron	4084193	4084627	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	CDS	4084628	4084691	0.87	-	0	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	exon	4084628	4084691	.	-	.	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
Phchi.S4	AUGUSTUS	start_codon	4084689	4084691	.	-	0	transcript_id "Phchi.S4G067400.t1"; gene_id "Phchi.S4G067400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10753.t1 is derived from g14803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1936559	1938924	.	+	.	Phchi.S4G033500
Phchi.S4	AUGUSTUS	transcript	1936559	1938924	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	start_codon	1936559	1936561	.	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1936559	1936630	0.95	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1936559	1936630	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1936631	1936705	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1936706	1936804	1	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1936706	1936804	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1936805	1936900	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1936901	1937071	0.99	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1936901	1937071	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1937072	1937183	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1937184	1937249	0.68	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1937184	1937249	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1937250	1937360	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1937361	1937426	0.62	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1937361	1937426	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1937427	1937509	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1937510	1937659	1	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1937510	1937659	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1937660	1937730	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1937731	1937802	1	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1937731	1937802	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1937803	1937902	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1937903	1938039	1	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1937903	1938039	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1938040	1938157	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1938158	1938248	1	+	1	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1938158	1938248	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1938249	1938348	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1938349	1938417	1	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1938349	1938417	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1938418	1938493	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1938494	1938585	1	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1938494	1938585	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1938586	1938662	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1938663	1938726	1	+	1	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1938663	1938726	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	intron	1938727	1938822	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	CDS	1938823	1938924	0.98	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	exon	1938823	1938924	.	+	.	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
Phchi.S4	AUGUSTUS	stop_codon	1938925	1938927	.	+	0	transcript_id "Phchi.S4G033500.t1"; gene_id "Phchi.S4G033500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6259.t1 is derived from g3431.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21904676	21909479	.	-	.	Phchi.S1G341800
Phchi.S1	AUGUSTUS	transcript	21904676	21909479	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	stop_codon	21904673	21904675	.	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	CDS	21904676	21906697	0.63	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	exon	21904676	21906697	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	intron	21906698	21906807	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	CDS	21906808	21907077	0.99	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	exon	21906808	21907077	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	intron	21907078	21907299	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	CDS	21907300	21907428	1	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	exon	21907300	21907428	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	intron	21907429	21907558	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	CDS	21907559	21907762	1	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	exon	21907559	21907762	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	intron	21907763	21908056	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	CDS	21908057	21909120	1	-	2	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	exon	21908057	21909120	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	intron	21909121	21909463	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	CDS	21909464	21909479	1	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	exon	21909464	21909479	.	-	.	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
Phchi.S1	AUGUSTUS	start_codon	21909477	21909479	.	-	0	transcript_id "Phchi.S1G341800.t1"; gene_id "Phchi.S1G341800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13162.t1 is derived from g11627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4450907	4452057	.	-	.	Phchi.S3G048100
Phchi.S3	AUGUSTUS	transcript	4450907	4452057	.	-	.	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	stop_codon	4450904	4450906	.	-	0	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	CDS	4450907	4451587	0.3	-	0	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	exon	4450907	4451587	.	-	.	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	intron	4451588	4451709	.	-	.	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	CDS	4451710	4452057	0.34	-	0	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	exon	4451710	4452057	.	-	.	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
Phchi.S3	AUGUSTUS	start_codon	4452055	4452057	.	-	0	transcript_id "Phchi.S3G048100.t1"; gene_id "Phchi.S3G048100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12114.t1 is derived from g7790.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3579195	3579976	.	+	.	Phchi.S2G019400
Phchi.S2	AUGUSTUS	transcript	3579195	3579976	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	start_codon	3579195	3579197	.	+	0	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	CDS	3579195	3579327	0.96	+	0	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	exon	3579195	3579327	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	intron	3579328	3579397	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	CDS	3579398	3579491	1	+	2	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	exon	3579398	3579491	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	intron	3579492	3579576	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	CDS	3579577	3579588	0.51	+	1	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	exon	3579577	3579588	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	intron	3579589	3579665	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	CDS	3579666	3579729	0.71	+	1	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	exon	3579666	3579729	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	intron	3579730	3579813	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	CDS	3579814	3579858	0.82	+	0	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	exon	3579814	3579858	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	intron	3579859	3579925	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	CDS	3579926	3579976	0.82	+	0	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	exon	3579926	3579976	.	+	.	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
Phchi.S2	AUGUSTUS	stop_codon	3579977	3579979	.	+	0	transcript_id "Phchi.S2G019400.t1"; gene_id "Phchi.S2G019400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2830.t1 is derived from g9750.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9086758	9090051	.	-	.	Phchi.S5G143900
Phchi.S5	AUGUSTUS	transcript	9086758	9090051	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	stop_codon	9086755	9086757	.	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9086758	9086853	1	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9086758	9086853	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9086854	9086937	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9086938	9087062	1	-	2	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9086938	9087062	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087063	9087143	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087144	9087239	1	-	2	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087144	9087239	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087240	9087334	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087335	9087418	1	-	2	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087335	9087418	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087419	9087539	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087540	9087642	0.97	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087540	9087642	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087643	9087742	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087743	9087844	1	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087743	9087844	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087845	9088000	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088001	9088093	1	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088001	9088093	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088094	9088190	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088191	9088309	1	-	2	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088191	9088309	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088310	9088396	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088397	9088524	1	-	1	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088397	9088524	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088525	9088604	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088605	9088828	0.96	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088605	9088828	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088829	9088935	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088936	9089472	0.7	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088936	9089472	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9089473	9089565	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9089566	9089701	1	-	1	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9089566	9089701	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9089702	9089797	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9089798	9090051	1	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9089798	9090051	.	-	.	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	start_codon	9090049	9090051	.	-	0	transcript_id "Phchi.S5G143900.t1"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	transcript	9086758	9090051	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	stop_codon	9086755	9086757	.	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9086758	9086853	1	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9086758	9086853	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9086854	9086937	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9086938	9087062	1	-	2	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9086938	9087062	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087063	9087143	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087144	9087239	1	-	2	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087144	9087239	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087240	9087334	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087335	9087418	1	-	2	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087335	9087418	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087419	9087539	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087540	9087642	0.97	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087540	9087642	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087643	9087742	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9087743	9087844	1	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9087743	9087844	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9087845	9088000	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088001	9088093	1	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088001	9088093	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088094	9088190	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088191	9088309	1	-	2	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088191	9088309	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088310	9088396	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088397	9088524	1	-	1	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088397	9088524	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088525	9088604	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088605	9088828	0.98	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088605	9088828	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9088829	9088935	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9088936	9089478	0.67	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9088936	9089478	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9089479	9089565	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9089566	9089701	1	-	1	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9089566	9089701	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	intron	9089702	9089797	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	CDS	9089798	9090051	1	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	exon	9089798	9090051	.	-	.	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
Phchi.S5	AUGUSTUS	start_codon	9090049	9090051	.	-	0	transcript_id "Phchi.S5G143900.t2"; gene_id "Phchi.S5G143900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6485.t1 is derived from g3657.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23219440	23222423	.	-	.	Phchi.S1G364400
Phchi.S1	AUGUSTUS	transcript	23219440	23222423	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	stop_codon	23219437	23219439	.	-	0	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	CDS	23219440	23221174	1	-	1	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	exon	23219440	23221174	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	intron	23221175	23221272	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	CDS	23221273	23221357	1	-	2	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	exon	23221273	23221357	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	intron	23221358	23221441	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	CDS	23221442	23221748	1	-	0	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	exon	23221442	23221748	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	intron	23221749	23221830	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	CDS	23221831	23222079	0.33	-	0	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	exon	23221831	23222079	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	intron	23222080	23222186	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	CDS	23222187	23222423	0.33	-	0	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	exon	23222187	23222423	.	-	.	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
Phchi.S1	AUGUSTUS	start_codon	23222421	23222423	.	-	0	transcript_id "Phchi.S1G364400.t1"; gene_id "Phchi.S1G364400"
# This transcript jg13689.t2 is derived from g12156.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13690.t1 is derived from g12157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8222460	8223505	.	+	.	Phchi.S3G100900
Phchi.S3	AUGUSTUS	transcript	8222460	8223505	.	+	.	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	start_codon	8222460	8222462	.	+	0	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	CDS	8222460	8222619	0.82	+	0	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	exon	8222460	8222619	.	+	.	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	intron	8222620	8222705	.	+	.	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	CDS	8222706	8223505	0.9	+	2	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	exon	8222706	8223505	.	+	.	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
Phchi.S3	AUGUSTUS	stop_codon	8223506	8223508	.	+	0	transcript_id "Phchi.S3G100900.t1"; gene_id "Phchi.S3G100900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10429.t1 is derived from g14478.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	223075	223566	.	+	.	Phchi.S4G001100
Phchi.S4	AUGUSTUS	transcript	223075	223566	.	+	.	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	start_codon	223075	223077	.	+	0	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	CDS	223075	223344	0.81	+	0	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	exon	223075	223344	.	+	.	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	intron	223345	223431	.	+	.	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	CDS	223432	223566	0.93	+	0	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	exon	223432	223566	.	+	.	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
Phchi.S4	AUGUSTUS	stop_codon	223567	223569	.	+	0	transcript_id "Phchi.S4G001100.t1"; gene_id "Phchi.S4G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15794.t1 is derived from g14264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21368964	21370955	.	-	.	Phchi.S3G311300
Phchi.S3	AUGUSTUS	transcript	21368964	21370955	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	stop_codon	21368961	21368963	.	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21368964	21369248	0.99	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21368964	21369248	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21369249	21369534	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21369535	21369699	1	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21369535	21369699	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21369700	21369840	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21369841	21369975	1	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21369841	21369975	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21369976	21370121	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370122	21370244	0.68	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370122	21370244	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21370245	21370433	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370434	21370718	0.32	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370434	21370718	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21370719	21370814	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370815	21370955	0.99	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370815	21370955	.	-	.	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	start_codon	21370953	21370955	.	-	0	transcript_id "Phchi.S3G311300.t1"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	transcript	21368964	21370955	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	stop_codon	21368961	21368963	.	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21368964	21369248	0.99	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21368964	21369248	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21369249	21369534	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21369535	21369699	1	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21369535	21369699	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21369700	21369840	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21369841	21369947	0.6	-	2	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21369841	21369947	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21369948	21370018	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370019	21370061	0.43	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370019	21370061	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21370062	21370254	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370255	21370309	0.69	-	1	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370255	21370309	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21370310	21370433	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370434	21370505	0.36	-	1	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370434	21370505	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21370506	21370656	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370657	21370718	0.71	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370657	21370718	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	intron	21370719	21370814	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	CDS	21370815	21370955	1	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	exon	21370815	21370955	.	-	.	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
Phchi.S3	AUGUSTUS	start_codon	21370953	21370955	.	-	0	transcript_id "Phchi.S3G311300.t2"; gene_id "Phchi.S3G311300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6333.t1 is derived from g3505.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22319989	22321366	.	-	.	Phchi.S1G349200
Phchi.S1	AUGUSTUS	transcript	22319989	22321366	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	stop_codon	22319986	22319988	.	-	0	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22319989	22320041	1	-	2	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22319989	22320041	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22320042	22320220	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22320221	22320321	0.97	-	1	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22320221	22320321	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22320322	22320686	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22320687	22320885	0.78	-	2	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22320687	22320885	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22320886	22321082	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22321083	22321142	0.38	-	2	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22321083	22321142	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22321143	22321233	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22321234	22321366	0.1	-	0	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22321234	22321366	.	-	.	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	start_codon	22321364	22321366	.	-	0	transcript_id "Phchi.S1G349200.t1"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	transcript	22319989	22321366	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	stop_codon	22319986	22319988	.	-	0	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22319989	22320041	1	-	2	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22319989	22320041	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22320042	22320220	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22320221	22320321	0.98	-	1	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22320221	22320321	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22320322	22320686	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22320687	22320891	0.78	-	2	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22320687	22320891	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22320892	22321082	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22321083	22321142	0.36	-	2	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22321083	22321142	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	intron	22321143	22321233	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	CDS	22321234	22321366	0.12	-	0	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	exon	22321234	22321366	.	-	.	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
Phchi.S1	AUGUSTUS	start_codon	22321364	22321366	.	-	0	transcript_id "Phchi.S1G349200.t2"; gene_id "Phchi.S1G349200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13823.t1 is derived from g12290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9078167	9080671	.	-	.	Phchi.S3G114200
Phchi.S3	AUGUSTUS	transcript	9078167	9080671	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	stop_codon	9078164	9078166	.	-	0	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	CDS	9078167	9078406	0.9	-	0	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	exon	9078167	9078406	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	intron	9078407	9078530	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	CDS	9078531	9078591	0.97	-	1	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	exon	9078531	9078591	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	intron	9078592	9078776	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	CDS	9078777	9080149	0.69	-	0	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	exon	9078777	9080149	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	intron	9080150	9080332	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	CDS	9080333	9080671	0.69	-	0	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	exon	9080333	9080671	.	-	.	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
Phchi.S3	AUGUSTUS	start_codon	9080669	9080671	.	-	0	transcript_id "Phchi.S3G114200.t1"; gene_id "Phchi.S3G114200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg697.t1 is derived from g10479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4952883	4953287	.	+	.	Phchi.S6G065600
Phchi.S6	AUGUSTUS	transcript	4952883	4953287	.	+	.	transcript_id "Phchi.S6G065600.t1"; gene_id "Phchi.S6G065600"
Phchi.S6	AUGUSTUS	start_codon	4952883	4952885	.	+	0	transcript_id "Phchi.S6G065600.t1"; gene_id "Phchi.S6G065600"
Phchi.S6	AUGUSTUS	CDS	4952883	4953287	0.57	+	0	transcript_id "Phchi.S6G065600.t1"; gene_id "Phchi.S6G065600"
Phchi.S6	AUGUSTUS	exon	4952883	4953287	.	+	.	transcript_id "Phchi.S6G065600.t1"; gene_id "Phchi.S6G065600"
Phchi.S6	AUGUSTUS	stop_codon	4953288	4953290	.	+	0	transcript_id "Phchi.S6G065600.t1"; gene_id "Phchi.S6G065600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15921.t1 is derived from g14391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22222247	22224370	.	-	.	Phchi.S3G324000
Phchi.S3	AUGUSTUS	transcript	22222247	22224370	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	stop_codon	22222244	22222246	.	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22222247	22222345	1	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22222247	22222345	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	intron	22222346	22222437	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22222438	22222587	1	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22222438	22222587	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	intron	22222588	22222672	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22222673	22222765	0.47	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22222673	22222765	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	intron	22222766	22222867	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22222868	22222982	0.47	-	1	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22222868	22222982	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	intron	22222983	22223156	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22223157	22223407	1	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22223157	22223407	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	intron	22223408	22223524	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22223525	22223711	1	-	1	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22223525	22223711	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	intron	22223712	22223966	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	CDS	22223967	22224370	1	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	exon	22223967	22224370	.	-	.	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
Phchi.S3	AUGUSTUS	start_codon	22224368	22224370	.	-	0	transcript_id "Phchi.S3G324000.t1"; gene_id "Phchi.S3G324000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9002.t1 is derived from g6177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39114128	39115927	.	+	.	Phchi.S1G616100
Phchi.S1	AUGUSTUS	transcript	39114128	39115927	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	start_codon	39114128	39114130	.	+	0	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39114128	39114203	0.93	+	0	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39114128	39114203	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	intron	39114204	39114423	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39114424	39114509	1	+	2	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39114424	39114509	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	intron	39114510	39114652	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39114653	39114799	0.91	+	0	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39114653	39114799	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	intron	39114800	39114894	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39114895	39115003	1	+	0	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39114895	39115003	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	intron	39115004	39115207	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39115208	39115331	1	+	2	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39115208	39115331	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	intron	39115332	39115422	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39115423	39115696	1	+	1	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39115423	39115696	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	intron	39115697	39115822	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	CDS	39115823	39115927	0.99	+	0	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	exon	39115823	39115927	.	+	.	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
Phchi.S1	AUGUSTUS	stop_codon	39115928	39115930	.	+	0	transcript_id "Phchi.S1G616100.t1"; gene_id "Phchi.S1G616100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5226.t1 is derived from g2396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15634492	15635469	.	-	.	Phchi.S1G238500
Phchi.S1	AUGUSTUS	transcript	15634492	15635469	.	-	.	transcript_id "Phchi.S1G238500.t1"; gene_id "Phchi.S1G238500"
Phchi.S1	AUGUSTUS	stop_codon	15634489	15634491	.	-	0	transcript_id "Phchi.S1G238500.t1"; gene_id "Phchi.S1G238500"
Phchi.S1	AUGUSTUS	CDS	15634492	15635469	0.28	-	0	transcript_id "Phchi.S1G238500.t1"; gene_id "Phchi.S1G238500"
Phchi.S1	AUGUSTUS	exon	15634492	15635469	.	-	.	transcript_id "Phchi.S1G238500.t1"; gene_id "Phchi.S1G238500"
Phchi.S1	AUGUSTUS	start_codon	15635467	15635469	.	-	0	transcript_id "Phchi.S1G238500.t1"; gene_id "Phchi.S1G238500"
# This transcript jg7246.t2 is derived from g4418.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7247.t1 is derived from g4419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27832014	27832715	.	-	.	Phchi.S1G440600
Phchi.S1	AUGUSTUS	transcript	27832014	27832715	.	-	.	transcript_id "Phchi.S1G440600.t1"; gene_id "Phchi.S1G440600"
Phchi.S1	AUGUSTUS	stop_codon	27832011	27832013	.	-	0	transcript_id "Phchi.S1G440600.t1"; gene_id "Phchi.S1G440600"
Phchi.S1	AUGUSTUS	CDS	27832014	27832715	0.46	-	0	transcript_id "Phchi.S1G440600.t1"; gene_id "Phchi.S1G440600"
Phchi.S1	AUGUSTUS	exon	27832014	27832715	.	-	.	transcript_id "Phchi.S1G440600.t1"; gene_id "Phchi.S1G440600"
Phchi.S1	AUGUSTUS	start_codon	27832713	27832715	.	-	0	transcript_id "Phchi.S1G440600.t1"; gene_id "Phchi.S1G440600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15124.t1 is derived from g13592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17172652	17174385	.	-	.	Phchi.S3G244300
Phchi.S3	AUGUSTUS	transcript	17172652	17174385	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	stop_codon	17172649	17172651	.	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17172652	17172845	0.22	-	2	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17172652	17172845	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17172846	17172990	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17172991	17173169	0.7	-	1	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17172991	17173169	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17173170	17173270	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17173271	17173368	0.98	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17173271	17173368	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17173369	17173459	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17173460	17173654	1	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17173460	17173654	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17173655	17173726	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17173727	17173837	1	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17173727	17173837	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17173838	17173915	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17173916	17173957	1	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17173916	17173957	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17173958	17174039	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17174040	17174123	1	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17174040	17174123	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	intron	17174124	17174250	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	CDS	17174251	17174385	0.97	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	exon	17174251	17174385	.	-	.	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
Phchi.S3	AUGUSTUS	start_codon	17174383	17174385	.	-	0	transcript_id "Phchi.S3G244300.t1"; gene_id "Phchi.S3G244300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5476.t1 is derived from g2646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17028225	17037312	.	-	.	Phchi.S1G263500
Phchi.S1	AUGUSTUS	transcript	17028225	17037312	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	stop_codon	17028222	17028224	.	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028225	17028302	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028225	17028302	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028303	17028380	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028381	17028548	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028381	17028548	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028549	17028628	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028629	17028818	1	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028629	17028818	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028819	17028919	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028920	17029107	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028920	17029107	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029108	17029187	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029188	17029349	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029188	17029349	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029350	17029441	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029442	17029552	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029442	17029552	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029553	17029671	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029672	17029764	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029672	17029764	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029765	17029855	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029856	17029954	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029856	17029954	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029955	17030039	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030040	17030162	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030040	17030162	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030163	17030356	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030357	17030410	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030357	17030410	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030411	17030544	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030545	17030589	0.97	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030545	17030589	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030590	17030640	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030641	17030655	0.97	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030641	17030655	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030656	17030752	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030753	17030779	0.96	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030753	17030779	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030780	17031045	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031046	17031202	1	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031046	17031202	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031203	17031298	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031299	17031363	0.88	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031299	17031363	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031364	17031603	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031604	17031729	0.92	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031604	17031729	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031730	17031815	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031816	17031963	1	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031816	17031963	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031964	17032110	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032111	17032242	1	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032111	17032242	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032243	17032346	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032347	17032414	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032347	17032414	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032415	17032646	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032647	17032748	0.93	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032647	17032748	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032749	17032875	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032876	17033145	0.46	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032876	17033145	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033146	17033253	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033254	17033334	0.96	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033254	17033334	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033335	17033497	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033498	17033614	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033498	17033614	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033615	17033740	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033741	17033858	1	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033741	17033858	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033859	17033932	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033933	17033999	1	-	2	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033933	17033999	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034000	17034109	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034110	17034207	0.91	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034110	17034207	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034208	17034324	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034325	17034389	0.39	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034325	17034389	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034390	17034554	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034555	17034642	0.64	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034555	17034642	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034643	17034744	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034745	17034811	0.93	-	2	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034745	17034811	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034812	17034971	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034972	17035041	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034972	17035041	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035042	17035152	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035153	17035326	0.71	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035153	17035326	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035327	17035509	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035510	17035582	1	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035510	17035582	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035583	17035693	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035694	17035812	0.81	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035694	17035812	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035813	17035908	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035909	17036034	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035909	17036034	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036035	17036117	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036118	17036291	1	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036118	17036291	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036292	17036432	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036433	17036505	0.64	-	1	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036433	17036505	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036506	17036661	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036662	17036702	0.64	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036662	17036702	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036703	17037219	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17037220	17037312	0.89	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17037220	17037312	.	-	.	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	start_codon	17037310	17037312	.	-	0	transcript_id "Phchi.S1G263500.t1"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	transcript	17028225	17037312	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	stop_codon	17028222	17028224	.	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028225	17028302	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028225	17028302	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028303	17028380	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028381	17028548	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028381	17028548	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028549	17028628	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028629	17028818	1	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028629	17028818	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028819	17028919	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028920	17029107	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028920	17029107	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029108	17029187	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029188	17029349	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029188	17029349	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029350	17029441	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029442	17029552	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029442	17029552	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029553	17029671	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029672	17029764	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029672	17029764	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029765	17029855	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029856	17029954	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029856	17029954	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029955	17030039	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030040	17030162	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030040	17030162	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030163	17030356	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030357	17030410	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030357	17030410	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030411	17030544	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030545	17030589	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030545	17030589	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030590	17030640	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030641	17030655	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030641	17030655	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030656	17030752	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030753	17030779	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030753	17030779	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030780	17031045	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031046	17031202	0.99	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031046	17031202	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031203	17031298	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031299	17031363	0.92	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031299	17031363	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031364	17031603	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031604	17031729	0.95	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031604	17031729	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031730	17031815	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031816	17031963	1	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031816	17031963	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031964	17032110	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032111	17032242	1	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032111	17032242	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032243	17032346	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032347	17032414	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032347	17032414	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032415	17032646	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032647	17032748	0.93	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032647	17032748	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032749	17032875	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032876	17033145	0.4	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032876	17033145	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033146	17033253	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033254	17033334	0.95	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033254	17033334	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033335	17033497	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033498	17033614	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033498	17033614	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033615	17033740	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033741	17033858	1	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033741	17033858	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033859	17033932	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033933	17033999	0.99	-	2	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033933	17033999	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034000	17034109	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034110	17034207	0.91	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034110	17034207	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034208	17034324	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034325	17034389	0.26	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034325	17034389	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034390	17034554	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034555	17034642	0.57	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034555	17034642	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034643	17034744	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034745	17034811	0.97	-	2	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034745	17034811	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034812	17034971	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034972	17035041	1	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034972	17035041	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035042	17035152	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035153	17035326	0.73	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035153	17035326	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035327	17035509	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035510	17035582	0.96	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035510	17035582	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035583	17035693	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035694	17035812	0.83	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035694	17035812	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035813	17035963	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035964	17036034	0.96	-	2	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035964	17036034	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036035	17036117	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036118	17036131	0.96	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036118	17036131	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036132	17036271	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036272	17036291	0.57	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036272	17036291	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036292	17036432	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036433	17036505	0.62	-	1	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036433	17036505	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036506	17036661	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036662	17036702	0.62	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036662	17036702	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036703	17037219	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17037220	17037312	0.86	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17037220	17037312	.	-	.	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	start_codon	17037310	17037312	.	-	0	transcript_id "Phchi.S1G263500.t2"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	transcript	17028225	17037312	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	stop_codon	17028222	17028224	.	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028225	17028302	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028225	17028302	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028303	17028380	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028381	17028548	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028381	17028548	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028549	17028628	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028629	17028818	1	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028629	17028818	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17028819	17028919	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17028920	17029107	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17028920	17029107	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029108	17029187	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029188	17029349	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029188	17029349	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029350	17029441	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029442	17029552	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029442	17029552	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029553	17029671	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029672	17029764	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029672	17029764	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029765	17029855	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17029856	17029954	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17029856	17029954	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17029955	17030039	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030040	17030162	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030040	17030162	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030163	17030356	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030357	17030410	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030357	17030410	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030411	17030544	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030545	17030589	0.98	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030545	17030589	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030590	17030640	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030641	17030655	0.98	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030641	17030655	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030656	17030752	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17030753	17030779	0.98	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17030753	17030779	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17030780	17031045	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031046	17031202	0.99	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031046	17031202	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031203	17031298	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031299	17031363	0.89	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031299	17031363	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031364	17031603	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031604	17031729	0.95	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031604	17031729	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031730	17031815	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17031816	17031963	1	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17031816	17031963	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17031964	17032110	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032111	17032242	0.9	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032111	17032242	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032243	17032346	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032347	17032395	0.89	-	2	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032347	17032395	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032396	17032646	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032647	17032660	0.41	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032647	17032660	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17032661	17032948	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17032949	17033145	0.38	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17032949	17033145	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033146	17033253	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033254	17033334	0.98	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033254	17033334	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033335	17033497	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033498	17033614	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033498	17033614	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033615	17033740	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033741	17033858	1	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033741	17033858	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17033859	17033932	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17033933	17033999	1	-	2	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17033933	17033999	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034000	17034109	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034110	17034207	0.92	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034110	17034207	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034208	17034324	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034325	17034389	0.38	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034325	17034389	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034390	17034554	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034555	17034642	0.64	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034555	17034642	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034643	17034744	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034745	17034811	0.99	-	2	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034745	17034811	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17034812	17034971	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17034972	17035041	1	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17034972	17035041	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035042	17035152	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035153	17035326	0.76	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035153	17035326	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035327	17035509	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035510	17035582	0.97	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035510	17035582	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035583	17035693	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035694	17035812	0.84	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035694	17035812	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17035813	17035908	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17035909	17036034	0.85	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17035909	17036034	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036035	17036117	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036118	17036291	0.87	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036118	17036291	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036292	17036432	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036433	17036505	0.58	-	1	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036433	17036505	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036506	17036661	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17036662	17036702	0.58	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17036662	17036702	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	intron	17036703	17037219	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	CDS	17037220	17037312	0.79	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	exon	17037220	17037312	.	-	.	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
Phchi.S1	AUGUSTUS	start_codon	17037310	17037312	.	-	0	transcript_id "Phchi.S1G263500.t3"; gene_id "Phchi.S1G263500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13502.t1 is derived from g11969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7200103	7202485	.	-	.	Phchi.S3G082100
Phchi.S3	AUGUSTUS	transcript	7200103	7202485	.	-	.	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	stop_codon	7200100	7200102	.	-	0	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	CDS	7200103	7200401	0.59	-	2	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	exon	7200103	7200401	.	-	.	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	intron	7200402	7200490	.	-	.	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	CDS	7200491	7201832	0.32	-	0	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	exon	7200491	7201832	.	-	.	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	intron	7201833	7202161	.	-	.	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	CDS	7202162	7202485	0.44	-	0	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	exon	7202162	7202485	.	-	.	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
Phchi.S3	AUGUSTUS	start_codon	7202483	7202485	.	-	0	transcript_id "Phchi.S3G082100.t1"; gene_id "Phchi.S3G082100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4360.t1 is derived from g1529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10015295	10015925	.	-	.	Phchi.S1G151900
Phchi.S1	AUGUSTUS	transcript	10015295	10015925	.	-	.	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	stop_codon	10015292	10015294	.	-	0	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	CDS	10015295	10015563	1	-	2	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	exon	10015295	10015563	.	-	.	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	intron	10015564	10015714	.	-	.	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	CDS	10015715	10015925	0.96	-	0	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	exon	10015715	10015925	.	-	.	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
Phchi.S1	AUGUSTUS	start_codon	10015923	10015925	.	-	0	transcript_id "Phchi.S1G151900.t1"; gene_id "Phchi.S1G151900"
# This transcript jg3033.t2 is derived from g202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3034.t1 is derived from g203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1257447	1257896	.	-	.	Phchi.S1G019300
Phchi.S1	AUGUSTUS	transcript	1257447	1257896	.	-	.	transcript_id "Phchi.S1G019300.t1"; gene_id "Phchi.S1G019300"
Phchi.S1	AUGUSTUS	stop_codon	1257444	1257446	.	-	0	transcript_id "Phchi.S1G019300.t1"; gene_id "Phchi.S1G019300"
Phchi.S1	AUGUSTUS	CDS	1257447	1257896	0.93	-	0	transcript_id "Phchi.S1G019300.t1"; gene_id "Phchi.S1G019300"
Phchi.S1	AUGUSTUS	exon	1257447	1257896	.	-	.	transcript_id "Phchi.S1G019300.t1"; gene_id "Phchi.S1G019300"
Phchi.S1	AUGUSTUS	start_codon	1257894	1257896	.	-	0	transcript_id "Phchi.S1G019300.t1"; gene_id "Phchi.S1G019300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8475.t1 is derived from g5650.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36123055	36126364	.	-	.	Phchi.S1G563400
Phchi.S1	AUGUSTUS	transcript	36123055	36126364	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	stop_codon	36123052	36123054	.	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123055	36123247	0.91	-	1	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123055	36123247	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36123248	36123361	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123362	36123434	1	-	2	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123362	36123434	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36123435	36123606	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123607	36123766	1	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123607	36123766	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36123767	36123960	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123961	36124072	1	-	1	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123961	36124072	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36124073	36124161	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36124162	36124259	1	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36124162	36124259	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36124260	36124457	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36124458	36124878	0.98	-	1	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36124458	36124878	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36124879	36125041	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36125042	36125193	1	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36125042	36125193	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36125194	36125281	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36125282	36125490	1	-	2	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36125282	36125490	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36125491	36125813	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36125814	36125901	1	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36125814	36125901	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36125902	36126001	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36126002	36126364	1	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36126002	36126364	.	-	.	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	start_codon	36126362	36126364	.	-	0	transcript_id "Phchi.S1G563400.t1"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	transcript	36123055	36126364	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	stop_codon	36123052	36123054	.	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123055	36123247	0.88	-	1	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123055	36123247	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36123248	36123361	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123362	36123434	1	-	2	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123362	36123434	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36123435	36123606	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123607	36123766	1	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123607	36123766	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36123767	36123960	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36123961	36124072	1	-	1	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36123961	36124072	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36124073	36124161	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36124162	36124259	1	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36124162	36124259	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36124260	36124457	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36124458	36124881	1	-	1	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36124458	36124881	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36124882	36125041	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36125042	36125193	1	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36125042	36125193	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36125194	36125281	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36125282	36125490	1	-	2	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36125282	36125490	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36125491	36125813	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36125814	36125901	1	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36125814	36125901	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	intron	36125902	36126001	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	CDS	36126002	36126364	0.98	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	exon	36126002	36126364	.	-	.	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
Phchi.S1	AUGUSTUS	start_codon	36126362	36126364	.	-	0	transcript_id "Phchi.S1G563400.t2"; gene_id "Phchi.S1G563400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7701.t1 is derived from g4875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30704681	30706675	.	-	.	Phchi.S1G486000
Phchi.S1	AUGUSTUS	transcript	30704681	30706675	.	-	.	transcript_id "Phchi.S1G486000.t1"; gene_id "Phchi.S1G486000"
Phchi.S1	AUGUSTUS	stop_codon	30704678	30704680	.	-	0	transcript_id "Phchi.S1G486000.t1"; gene_id "Phchi.S1G486000"
Phchi.S1	AUGUSTUS	CDS	30704681	30706675	0.98	-	0	transcript_id "Phchi.S1G486000.t1"; gene_id "Phchi.S1G486000"
Phchi.S1	AUGUSTUS	exon	30704681	30706675	.	-	.	transcript_id "Phchi.S1G486000.t1"; gene_id "Phchi.S1G486000"
Phchi.S1	AUGUSTUS	start_codon	30706673	30706675	.	-	0	transcript_id "Phchi.S1G486000.t1"; gene_id "Phchi.S1G486000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13507.t1 is derived from g11974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7227437	7229810	.	-	.	Phchi.S3G082600
Phchi.S3	AUGUSTUS	transcript	7227437	7229810	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	stop_codon	7227434	7227436	.	-	0	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7227437	7227534	1	-	2	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7227437	7227534	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7227535	7227616	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7227617	7227650	1	-	0	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7227617	7227650	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7227651	7227747	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7227748	7227904	1	-	1	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7227748	7227904	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7227905	7228026	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228027	7228149	1	-	1	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228027	7228149	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7228150	7228288	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228289	7228306	1	-	1	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228289	7228306	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7228307	7228469	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228470	7228527	1	-	2	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228470	7228527	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7228528	7228664	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228665	7228803	1	-	0	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228665	7228803	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7228804	7228873	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228874	7228982	1	-	1	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228874	7228982	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7228983	7229071	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7229072	7229316	1	-	0	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7229072	7229316	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7229317	7229498	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7229499	7229810	1	-	0	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7229499	7229810	.	-	.	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	start_codon	7229808	7229810	.	-	0	transcript_id "Phchi.S3G082600.t1"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	transcript	7227437	7228249	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	stop_codon	7227434	7227436	.	-	0	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7227437	7227534	1	-	2	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7227437	7227534	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7227535	7227616	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7227617	7227650	1	-	0	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7227617	7227650	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7227651	7227747	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7227748	7227904	1	-	1	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7227748	7227904	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7227905	7228026	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228027	7228149	1	-	1	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228027	7228149	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	intron	7228150	7228244	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	CDS	7228245	7228249	0.51	-	0	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	exon	7228245	7228249	.	-	.	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
Phchi.S3	AUGUSTUS	start_codon	7228247	7228249	.	-	0	transcript_id "Phchi.S3G082600.t2"; gene_id "Phchi.S3G082600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5280.t1 is derived from g2450.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16013922	16014492	.	+	.	Phchi.S1G243900
Phchi.S1	AUGUSTUS	transcript	16013922	16014492	.	+	.	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	start_codon	16013922	16013924	.	+	0	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	CDS	16013922	16014022	0.92	+	0	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	exon	16013922	16014022	.	+	.	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	intron	16014023	16014110	.	+	.	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	CDS	16014111	16014492	0.83	+	1	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	exon	16014111	16014492	.	+	.	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
Phchi.S1	AUGUSTUS	stop_codon	16014493	16014495	.	+	0	transcript_id "Phchi.S1G243900.t1"; gene_id "Phchi.S1G243900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15018.t1 is derived from g13486.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16558587	16559309	.	-	.	Phchi.S3G233700
Phchi.S3	AUGUSTUS	transcript	16558587	16559309	.	-	.	transcript_id "Phchi.S3G233700.t1"; gene_id "Phchi.S3G233700"
Phchi.S3	AUGUSTUS	stop_codon	16558584	16558586	.	-	0	transcript_id "Phchi.S3G233700.t1"; gene_id "Phchi.S3G233700"
Phchi.S3	AUGUSTUS	CDS	16558587	16559309	0.23	-	0	transcript_id "Phchi.S3G233700.t1"; gene_id "Phchi.S3G233700"
Phchi.S3	AUGUSTUS	exon	16558587	16559309	.	-	.	transcript_id "Phchi.S3G233700.t1"; gene_id "Phchi.S3G233700"
Phchi.S3	AUGUSTUS	start_codon	16559307	16559309	.	-	0	transcript_id "Phchi.S3G233700.t1"; gene_id "Phchi.S3G233700"
# This transcript jg9784.t2 is derived from g6960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9785.t1 is derived from g6961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43678714	43679352	.	+	.	Phchi.S1G694400
Phchi.S1	AUGUSTUS	transcript	43678714	43679352	.	+	.	transcript_id "Phchi.S1G694400.t1"; gene_id "Phchi.S1G694400"
Phchi.S1	AUGUSTUS	start_codon	43678714	43678716	.	+	0	transcript_id "Phchi.S1G694400.t1"; gene_id "Phchi.S1G694400"
Phchi.S1	AUGUSTUS	CDS	43678714	43679352	1	+	0	transcript_id "Phchi.S1G694400.t1"; gene_id "Phchi.S1G694400"
Phchi.S1	AUGUSTUS	exon	43678714	43679352	.	+	.	transcript_id "Phchi.S1G694400.t1"; gene_id "Phchi.S1G694400"
Phchi.S1	AUGUSTUS	stop_codon	43679353	43679355	.	+	0	transcript_id "Phchi.S1G694400.t1"; gene_id "Phchi.S1G694400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8653.t1 is derived from g5828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37251770	37253403	.	+	.	Phchi.S1G581200
Phchi.S1	AUGUSTUS	transcript	37251770	37253403	.	+	.	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	start_codon	37251770	37251772	.	+	0	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	CDS	37251770	37251772	0.81	+	0	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	exon	37251770	37251772	.	+	.	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	intron	37251773	37251939	.	+	.	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	CDS	37251940	37253403	0.79	+	0	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	exon	37251940	37253403	.	+	.	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
Phchi.S1	AUGUSTUS	stop_codon	37253404	37253406	.	+	0	transcript_id "Phchi.S1G581200.t1"; gene_id "Phchi.S1G581200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5127.t1 is derived from g2297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15045796	15046574	.	+	.	Phchi.S1G228600
Phchi.S1	AUGUSTUS	transcript	15045796	15046574	.	+	.	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	start_codon	15045796	15045798	.	+	0	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	CDS	15045796	15045934	0.69	+	0	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	exon	15045796	15045934	.	+	.	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	intron	15045935	15046083	.	+	.	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	CDS	15046084	15046139	0.65	+	2	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	exon	15046084	15046139	.	+	.	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	intron	15046140	15046235	.	+	.	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	CDS	15046236	15046574	0.7	+	0	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	exon	15046236	15046574	.	+	.	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
Phchi.S1	AUGUSTUS	stop_codon	15046575	15046577	.	+	0	transcript_id "Phchi.S1G228600.t1"; gene_id "Phchi.S1G228600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1766.t1 is derived from g8686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2930451	2930864	.	-	.	Phchi.S5G037500
Phchi.S5	AUGUSTUS	transcript	2930451	2930864	.	-	.	transcript_id "Phchi.S5G037500.t1"; gene_id "Phchi.S5G037500"
Phchi.S5	AUGUSTUS	stop_codon	2930448	2930450	.	-	0	transcript_id "Phchi.S5G037500.t1"; gene_id "Phchi.S5G037500"
Phchi.S5	AUGUSTUS	CDS	2930451	2930864	0.75	-	0	transcript_id "Phchi.S5G037500.t1"; gene_id "Phchi.S5G037500"
Phchi.S5	AUGUSTUS	exon	2930451	2930864	.	-	.	transcript_id "Phchi.S5G037500.t1"; gene_id "Phchi.S5G037500"
Phchi.S5	AUGUSTUS	start_codon	2930862	2930864	.	-	0	transcript_id "Phchi.S5G037500.t1"; gene_id "Phchi.S5G037500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12295.t1 is derived from g7971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	9159866	9160646	.	+	.	Phchi.S2G037500
Phchi.S2	AUGUSTUS	transcript	9159866	9160646	.	+	.	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	start_codon	9159866	9159868	.	+	0	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	CDS	9159866	9160158	0.45	+	0	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	exon	9159866	9160158	.	+	.	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	intron	9160159	9160237	.	+	.	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	CDS	9160238	9160646	0.72	+	1	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	exon	9160238	9160646	.	+	.	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
Phchi.S2	AUGUSTUS	stop_codon	9160647	9160649	.	+	0	transcript_id "Phchi.S2G037500.t1"; gene_id "Phchi.S2G037500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5283.t1 is derived from g2453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16021000	16021570	.	+	.	Phchi.S1G244200
Phchi.S1	AUGUSTUS	transcript	16021000	16021570	.	+	.	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	start_codon	16021000	16021002	.	+	0	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	CDS	16021000	16021100	0.93	+	0	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	exon	16021000	16021100	.	+	.	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	intron	16021101	16021188	.	+	.	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	CDS	16021189	16021570	0.63	+	1	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	exon	16021189	16021570	.	+	.	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
Phchi.S1	AUGUSTUS	stop_codon	16021571	16021573	.	+	0	transcript_id "Phchi.S1G244200.t1"; gene_id "Phchi.S1G244200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10115.t1 is derived from g7291.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45798461	45802696	.	-	.	Phchi.S1G727400
Phchi.S1	AUGUSTUS	transcript	45798461	45802696	.	-	.	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	stop_codon	45798458	45798460	.	-	0	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	CDS	45798461	45799600	0.92	-	0	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	exon	45798461	45799600	.	-	.	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	intron	45799601	45799724	.	-	.	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	CDS	45799725	45801100	1	-	2	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	exon	45799725	45801100	.	-	.	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	intron	45801101	45801246	.	-	.	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	CDS	45801247	45802696	0.51	-	0	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	exon	45801247	45802696	.	-	.	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
Phchi.S1	AUGUSTUS	start_codon	45802694	45802696	.	-	0	transcript_id "Phchi.S1G727400.t1"; gene_id "Phchi.S1G727400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13446.t1 is derived from g11913.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6751215	6755777	.	+	.	Phchi.S3G076500
Phchi.S3	AUGUSTUS	transcript	6751215	6755777	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	start_codon	6751215	6751217	.	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6751215	6751308	0.77	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6751215	6751308	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6751309	6751409	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6751410	6751708	0.61	+	2	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6751410	6751708	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6751709	6751816	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6751817	6752094	1	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6751817	6752094	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6752095	6752174	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6752175	6752238	0.88	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6752175	6752238	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6752239	6752326	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6752327	6752445	0.99	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6752327	6752445	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6752446	6752522	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6752523	6752758	1	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6752523	6752758	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6752759	6752838	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6752839	6752956	1	+	2	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6752839	6752956	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6752957	6753043	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6753044	6753118	1	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6753044	6753118	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6753119	6753199	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6753200	6753268	1	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6753200	6753268	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6753269	6753460	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6753461	6753532	1	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6753461	6753532	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6753533	6753624	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6753625	6753693	0.82	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6753625	6753693	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6753694	6753805	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6753806	6754014	0.88	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6753806	6754014	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6754015	6754111	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6754112	6754359	0.99	+	2	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6754112	6754359	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6754360	6754438	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6754439	6754565	1	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6754439	6754565	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6754566	6754801	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6754802	6754870	1	+	2	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6754802	6754870	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6754871	6754949	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6754950	6755112	1	+	2	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6754950	6755112	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6755113	6755194	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6755195	6755336	1	+	1	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6755195	6755336	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	intron	6755337	6755429	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	CDS	6755430	6755777	0.99	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	exon	6755430	6755777	.	+	.	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
Phchi.S3	AUGUSTUS	stop_codon	6755778	6755780	.	+	0	transcript_id "Phchi.S3G076500.t1"; gene_id "Phchi.S3G076500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7707.t1 is derived from g4881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30718683	30720641	.	-	.	Phchi.S1G486600
Phchi.S1	AUGUSTUS	transcript	30718683	30720641	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	stop_codon	30718680	30718682	.	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30718683	30718790	0.98	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30718683	30718790	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30718791	30718883	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30718884	30718971	1	-	1	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30718884	30718971	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30718972	30719055	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30719056	30719126	1	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30719056	30719126	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30719127	30719204	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30719205	30719303	1	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30719205	30719303	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30719304	30719546	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30719547	30719623	1	-	2	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30719547	30719623	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30719624	30719743	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30719744	30719882	0.77	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30719744	30719882	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30719883	30719992	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30719993	30720040	0.96	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30719993	30720040	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30720041	30720116	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30720117	30720176	1	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30720117	30720176	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	intron	30720177	30720404	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	CDS	30720405	30720641	0.91	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	exon	30720405	30720641	.	-	.	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
Phchi.S1	AUGUSTUS	start_codon	30720639	30720641	.	-	0	transcript_id "Phchi.S1G486600.t1"; gene_id "Phchi.S1G486600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg549.t1 is derived from g10331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4011646	4015769	.	-	.	Phchi.S6G050800
Phchi.S6	AUGUSTUS	transcript	4011646	4015769	.	-	.	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	stop_codon	4011643	4011645	.	-	0	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	CDS	4011646	4015200	0.71	-	0	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	exon	4011646	4015200	.	-	.	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	intron	4015201	4015287	.	-	.	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	CDS	4015288	4015382	1	-	2	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	exon	4015288	4015382	.	-	.	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	intron	4015383	4015501	.	-	.	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	CDS	4015502	4015769	0.89	-	0	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	exon	4015502	4015769	.	-	.	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
Phchi.S6	AUGUSTUS	start_codon	4015767	4015769	.	-	0	transcript_id "Phchi.S6G050800.t1"; gene_id "Phchi.S6G050800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4599.t1 is derived from g1769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11284932	11286407	.	+	.	Phchi.S1G175800
Phchi.S1	AUGUSTUS	transcript	11284932	11286407	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	start_codon	11284932	11284934	.	+	0	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	CDS	11284932	11285163	0.63	+	0	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	exon	11284932	11285163	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	intron	11285164	11285323	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	CDS	11285324	11285427	0.79	+	2	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	exon	11285324	11285427	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	intron	11285428	11285767	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	CDS	11285768	11285837	0.94	+	0	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	exon	11285768	11285837	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	intron	11285838	11285937	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	CDS	11285938	11286407	0.76	+	2	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	exon	11285938	11286407	.	+	.	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
Phchi.S1	AUGUSTUS	stop_codon	11286408	11286410	.	+	0	transcript_id "Phchi.S1G175800.t1"; gene_id "Phchi.S1G175800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10926.t1 is derived from g14976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3012554	3013681	.	+	.	Phchi.S4G050800
Phchi.S4	AUGUSTUS	transcript	3012554	3013681	.	+	.	transcript_id "Phchi.S4G050800.t1"; gene_id "Phchi.S4G050800"
Phchi.S4	AUGUSTUS	start_codon	3012554	3012556	.	+	0	transcript_id "Phchi.S4G050800.t1"; gene_id "Phchi.S4G050800"
Phchi.S4	AUGUSTUS	CDS	3012554	3013681	0.99	+	0	transcript_id "Phchi.S4G050800.t1"; gene_id "Phchi.S4G050800"
Phchi.S4	AUGUSTUS	exon	3012554	3013681	.	+	.	transcript_id "Phchi.S4G050800.t1"; gene_id "Phchi.S4G050800"
Phchi.S4	AUGUSTUS	stop_codon	3013682	3013684	.	+	0	transcript_id "Phchi.S4G050800.t1"; gene_id "Phchi.S4G050800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4007.t1 is derived from g1176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6997349	6998911	.	+	.	Phchi.S1G116600
Phchi.S1	AUGUSTUS	transcript	6997349	6998911	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	start_codon	6997349	6997351	.	+	0	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	CDS	6997349	6998171	0.2	+	0	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	exon	6997349	6998171	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	intron	6998172	6998263	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	CDS	6998264	6998348	0.4	+	2	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	exon	6998264	6998348	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	intron	6998349	6998525	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	CDS	6998526	6998648	0.47	+	1	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	exon	6998526	6998648	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	intron	6998649	6998730	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	CDS	6998731	6998911	0.73	+	1	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	exon	6998731	6998911	.	+	.	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	stop_codon	6998912	6998914	.	+	0	transcript_id "Phchi.S1G116600.t1"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	transcript	6997349	6998239	.	+	.	transcript_id "Phchi.S1G116600.t2"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	start_codon	6997349	6997351	.	+	0	transcript_id "Phchi.S1G116600.t2"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	CDS	6997349	6998239	0.38	+	0	transcript_id "Phchi.S1G116600.t2"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	exon	6997349	6998239	.	+	.	transcript_id "Phchi.S1G116600.t2"; gene_id "Phchi.S1G116600"
Phchi.S1	AUGUSTUS	stop_codon	6998240	6998242	.	+	0	transcript_id "Phchi.S1G116600.t2"; gene_id "Phchi.S1G116600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15112.t1 is derived from g13580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17134003	17136269	.	+	.	Phchi.S3G243100
Phchi.S3	AUGUSTUS	transcript	17134003	17136269	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	start_codon	17134003	17134005	.	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17134003	17134177	0.63	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17134003	17134177	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17134178	17134274	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17134275	17134436	1	+	2	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17134275	17134436	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17134437	17134576	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17134577	17134752	1	+	2	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17134577	17134752	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17134753	17134842	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17134843	17134938	1	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17134843	17134938	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17134939	17135049	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17135050	17135095	1	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17135050	17135095	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17135096	17135182	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17135183	17135316	1	+	2	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17135183	17135316	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17135317	17135458	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17135459	17135563	1	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17135459	17135563	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	intron	17135564	17135756	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	CDS	17135757	17136269	0.94	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	exon	17135757	17136269	.	+	.	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
Phchi.S3	AUGUSTUS	stop_codon	17136270	17136272	.	+	0	transcript_id "Phchi.S3G243100.t1"; gene_id "Phchi.S3G243100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11814.t1 is derived from g15866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8368748	8369952	.	+	.	Phchi.S4G139600
Phchi.S4	AUGUSTUS	transcript	8368748	8369952	.	+	.	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	start_codon	8368748	8368750	.	+	0	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	CDS	8368748	8369314	0.57	+	0	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	exon	8368748	8369314	.	+	.	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	intron	8369315	8369400	.	+	.	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	CDS	8369401	8369952	1	+	0	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	exon	8369401	8369952	.	+	.	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
Phchi.S4	AUGUSTUS	stop_codon	8369953	8369955	.	+	0	transcript_id "Phchi.S4G139600.t1"; gene_id "Phchi.S4G139600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11553.t1 is derived from g15604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7012427	7013744	.	+	.	Phchi.S4G113500
Phchi.S4	AUGUSTUS	transcript	7012427	7013665	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	start_codon	7012427	7012429	.	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012427	7012447	0.99	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012427	7012447	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7012448	7012580	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012581	7012667	0.99	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012581	7012667	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7012668	7012763	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012764	7012848	1	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012764	7012848	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7012849	7012915	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012916	7013010	0.99	+	2	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012916	7013010	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013011	7013134	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013135	7013167	1	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013135	7013167	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013168	7013451	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013452	7013502	1	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013452	7013502	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013503	7013659	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013660	7013665	1	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013660	7013665	.	+	.	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	stop_codon	7013666	7013668	.	+	0	transcript_id "Phchi.S4G113500.t1"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	transcript	7012427	7013744	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	start_codon	7012427	7012429	.	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012427	7012447	1	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012427	7012447	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7012448	7012580	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012581	7012667	1	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012581	7012667	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7012668	7012763	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012764	7012848	1	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012764	7012848	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7012849	7012915	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7012916	7013010	0.99	+	2	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7012916	7013010	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013011	7013134	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013135	7013167	1	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013135	7013167	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013168	7013301	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013302	7013339	0.74	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013302	7013339	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013340	7013451	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013452	7013502	0.73	+	1	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013452	7013502	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	intron	7013503	7013659	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	CDS	7013660	7013744	0.73	+	1	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	exon	7013660	7013744	.	+	.	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
Phchi.S4	AUGUSTUS	stop_codon	7013745	7013747	.	+	0	transcript_id "Phchi.S4G113500.t2"; gene_id "Phchi.S4G113500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11527.t1 is derived from g15577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6911468	6912376	.	+	.	Phchi.S4G110900
Phchi.S4	AUGUSTUS	transcript	6911468	6912376	.	+	.	transcript_id "Phchi.S4G110900.t1"; gene_id "Phchi.S4G110900"
Phchi.S4	AUGUSTUS	start_codon	6911468	6911470	.	+	0	transcript_id "Phchi.S4G110900.t1"; gene_id "Phchi.S4G110900"
Phchi.S4	AUGUSTUS	CDS	6911468	6912376	0.93	+	0	transcript_id "Phchi.S4G110900.t1"; gene_id "Phchi.S4G110900"
Phchi.S4	AUGUSTUS	exon	6911468	6912376	.	+	.	transcript_id "Phchi.S4G110900.t1"; gene_id "Phchi.S4G110900"
Phchi.S4	AUGUSTUS	stop_codon	6912377	6912379	.	+	0	transcript_id "Phchi.S4G110900.t1"; gene_id "Phchi.S4G110900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2360.t1 is derived from g9280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6335572	6336917	.	-	.	Phchi.S5G096900
Phchi.S5	AUGUSTUS	transcript	6335572	6336917	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	stop_codon	6335569	6335571	.	-	0	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	CDS	6335572	6335886	0.9	-	0	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	exon	6335572	6335886	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	intron	6335887	6335963	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	CDS	6335964	6336028	1	-	2	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	exon	6335964	6336028	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	intron	6336029	6336107	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	CDS	6336108	6336655	1	-	1	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	exon	6336108	6336655	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	intron	6336656	6336729	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	CDS	6336730	6336917	0.55	-	0	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	exon	6336730	6336917	.	-	.	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
Phchi.S5	AUGUSTUS	start_codon	6336915	6336917	.	-	0	transcript_id "Phchi.S5G096900.t1"; gene_id "Phchi.S5G096900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3616.t1 is derived from g785.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4769025	4772591	.	-	.	Phchi.S1G077500
Phchi.S1	AUGUSTUS	transcript	4769025	4772591	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	stop_codon	4769022	4769024	.	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4769025	4769217	0.82	-	1	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4769025	4769217	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4769218	4769337	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4769338	4769380	1	-	2	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4769338	4769380	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4769381	4769527	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4769528	4769702	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4769528	4769702	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4769703	4769925	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4769926	4770012	0.97	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4769926	4770012	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4770013	4770120	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4770121	4770237	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4770121	4770237	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4770238	4770345	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4770346	4770456	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4770346	4770456	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4770457	4770543	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4770544	4771002	0.99	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4770544	4771002	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4771003	4771156	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4771157	4771678	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4771157	4771678	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4771679	4771764	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4771765	4771852	1	-	1	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4771765	4771852	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4771853	4771945	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4771946	4772007	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4771946	4772007	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4772008	4772142	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4772143	4772230	1	-	1	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4772143	4772230	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4772231	4772415	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4772416	4772477	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4772416	4772477	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	intron	4772478	4772588	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	CDS	4772589	4772591	1	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	exon	4772589	4772591	.	-	.	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
Phchi.S1	AUGUSTUS	start_codon	4772589	4772591	.	-	0	transcript_id "Phchi.S1G077500.t1"; gene_id "Phchi.S1G077500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg619.t1 is derived from g10401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4442370	4443993	.	-	.	Phchi.S6G057800
Phchi.S6	AUGUSTUS	transcript	4442370	4443993	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	stop_codon	4442367	4442369	.	-	0	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	CDS	4442370	4442510	0.92	-	0	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	exon	4442370	4442510	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	intron	4442511	4442600	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	CDS	4442601	4442768	1	-	0	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	exon	4442601	4442768	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	intron	4442769	4442872	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	CDS	4442873	4442989	0.92	-	0	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	exon	4442873	4442989	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	intron	4442990	4443387	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	CDS	4443388	4443993	0.86	-	0	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	exon	4443388	4443993	.	-	.	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
Phchi.S6	AUGUSTUS	start_codon	4443991	4443993	.	-	0	transcript_id "Phchi.S6G057800.t1"; gene_id "Phchi.S6G057800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11874.t1 is derived from g15926.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8943344	8945449	.	-	.	Phchi.S4G145600
Phchi.S4	AUGUSTUS	transcript	8943344	8945449	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	stop_codon	8943341	8943343	.	-	0	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	CDS	8943344	8944162	0.99	-	0	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	exon	8943344	8944162	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	intron	8944163	8944255	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	CDS	8944256	8944624	0.96	-	0	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	exon	8944256	8944624	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	intron	8944625	8944750	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	CDS	8944751	8944945	0.95	-	0	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	exon	8944751	8944945	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	intron	8944946	8945038	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	CDS	8945039	8945449	0.78	-	0	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	exon	8945039	8945449	.	-	.	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
Phchi.S4	AUGUSTUS	start_codon	8945447	8945449	.	-	0	transcript_id "Phchi.S4G145600.t1"; gene_id "Phchi.S4G145600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5903.t1 is derived from g3073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19676133	19679444	.	-	.	Phchi.S1G306200
Phchi.S1	AUGUSTUS	transcript	19676133	19679444	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	stop_codon	19676130	19676132	.	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19676133	19676219	1	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19676133	19676219	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19676220	19676317	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19676318	19676386	1	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19676318	19676386	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19676387	19676469	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19676470	19676643	1	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19676470	19676643	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19676644	19676714	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19676715	19678515	0.97	-	1	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19676715	19678515	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19678516	19678633	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19678634	19678891	0.97	-	1	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19678634	19678891	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19678892	19678981	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19678982	19679011	1	-	1	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19678982	19679011	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19679012	19679132	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19679133	19679197	0.99	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19679133	19679197	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	intron	19679198	19679366	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	CDS	19679367	19679444	0.96	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	exon	19679367	19679444	.	-	.	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
Phchi.S1	AUGUSTUS	start_codon	19679442	19679444	.	-	0	transcript_id "Phchi.S1G306200.t1"; gene_id "Phchi.S1G306200"
# This transcript jg12684.t2 is derived from g11149.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12684.t3 is derived from g11149.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12685.t1 is derived from g11150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	131402	132523	.	+	.	Phchi.S3G000400
Phchi.S3	AUGUSTUS	transcript	131402	132523	.	+	.	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	start_codon	131402	131404	.	+	0	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	CDS	131402	131744	0.33	+	0	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	exon	131402	131744	.	+	.	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	intron	131745	131969	.	+	.	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	CDS	131970	132071	0.18	+	2	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	exon	131970	132071	.	+	.	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	intron	132072	132182	.	+	.	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	CDS	132183	132523	0.51	+	2	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	exon	132183	132523	.	+	.	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
Phchi.S3	AUGUSTUS	stop_codon	132524	132526	.	+	0	transcript_id "Phchi.S3G000400.t1"; gene_id "Phchi.S3G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7583.t1 is derived from g4757.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30146920	30148960	.	+	.	Phchi.S1G474200
Phchi.S1	AUGUSTUS	transcript	30146920	30148960	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	start_codon	30146920	30146922	.	+	0	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	CDS	30146920	30147137	0.7	+	0	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	exon	30146920	30147137	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	intron	30147138	30147218	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	CDS	30147219	30147333	0.94	+	1	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	exon	30147219	30147333	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	intron	30147334	30147487	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	CDS	30147488	30147650	1	+	0	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	exon	30147488	30147650	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	intron	30147651	30147794	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	CDS	30147795	30148960	0.99	+	2	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	exon	30147795	30148960	.	+	.	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
Phchi.S1	AUGUSTUS	stop_codon	30148961	30148963	.	+	0	transcript_id "Phchi.S1G474200.t1"; gene_id "Phchi.S1G474200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6785.t1 is derived from g3957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25082451	25083251	.	-	.	Phchi.S1G394400
Phchi.S1	AUGUSTUS	transcript	25082451	25083251	.	-	.	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	stop_codon	25082448	25082450	.	-	0	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	CDS	25082451	25082559	0.37	-	1	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	exon	25082451	25082559	.	-	.	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	intron	25082560	25082642	.	-	.	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	CDS	25082643	25083026	0.51	-	1	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	exon	25082643	25083026	.	-	.	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	intron	25083027	25083192	.	-	.	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	CDS	25083193	25083251	0.93	-	0	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	exon	25083193	25083251	.	-	.	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
Phchi.S1	AUGUSTUS	start_codon	25083249	25083251	.	-	0	transcript_id "Phchi.S1G394400.t1"; gene_id "Phchi.S1G394400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5425.t1 is derived from g2595.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16810575	16811324	.	+	.	Phchi.S1G258400
Phchi.S1	AUGUSTUS	transcript	16810575	16811324	.	+	.	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	start_codon	16810575	16810577	.	+	0	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	CDS	16810575	16810705	0.67	+	0	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	exon	16810575	16810705	.	+	.	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	intron	16810706	16810798	.	+	.	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	CDS	16810799	16811324	0.75	+	1	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	exon	16810799	16811324	.	+	.	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
Phchi.S1	AUGUSTUS	stop_codon	16811325	16811327	.	+	0	transcript_id "Phchi.S1G258400.t1"; gene_id "Phchi.S1G258400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1136.t1 is derived from g10919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7883833	7884928	.	+	.	Phchi.S6G109500
Phchi.S6	AUGUSTUS	transcript	7883833	7884928	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	start_codon	7883833	7883835	.	+	0	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	CDS	7883833	7884182	0.64	+	0	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	exon	7883833	7884182	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	intron	7884183	7884299	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	CDS	7884300	7884387	1	+	1	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	exon	7884300	7884387	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	intron	7884388	7884473	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	CDS	7884474	7884601	1	+	0	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	exon	7884474	7884601	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	intron	7884602	7884731	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	CDS	7884732	7884790	0.67	+	1	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	exon	7884732	7884790	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	intron	7884791	7884887	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	CDS	7884888	7884928	0.41	+	2	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	exon	7884888	7884928	.	+	.	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
Phchi.S6	AUGUSTUS	stop_codon	7884929	7884931	.	+	0	transcript_id "Phchi.S6G109500.t1"; gene_id "Phchi.S6G109500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4372.t1 is derived from g1541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10112923	10113555	.	+	.	Phchi.S1G153100
Phchi.S1	AUGUSTUS	transcript	10112923	10113555	.	+	.	transcript_id "Phchi.S1G153100.t1"; gene_id "Phchi.S1G153100"
Phchi.S1	AUGUSTUS	start_codon	10112923	10112925	.	+	0	transcript_id "Phchi.S1G153100.t1"; gene_id "Phchi.S1G153100"
Phchi.S1	AUGUSTUS	CDS	10112923	10113555	0.4	+	0	transcript_id "Phchi.S1G153100.t1"; gene_id "Phchi.S1G153100"
Phchi.S1	AUGUSTUS	exon	10112923	10113555	.	+	.	transcript_id "Phchi.S1G153100.t1"; gene_id "Phchi.S1G153100"
Phchi.S1	AUGUSTUS	stop_codon	10113556	10113558	.	+	0	transcript_id "Phchi.S1G153100.t1"; gene_id "Phchi.S1G153100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13648.t1 is derived from g12115.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8003813	8005502	.	+	.	Phchi.S3G096700
Phchi.S3	AUGUSTUS	transcript	8003813	8005502	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	start_codon	8003813	8003815	.	+	0	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8003813	8003854	1	+	0	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8003813	8003854	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	intron	8003855	8004215	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8004216	8004303	1	+	0	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8004216	8004303	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	intron	8004304	8004516	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8004517	8004661	1	+	2	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8004517	8004661	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	intron	8004662	8004778	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8004779	8004889	1	+	1	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8004779	8004889	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	intron	8004890	8004993	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8004994	8005140	1	+	1	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8004994	8005140	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	intron	8005141	8005232	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8005233	8005355	1	+	1	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8005233	8005355	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	intron	8005356	8005444	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	CDS	8005445	8005502	1	+	1	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	exon	8005445	8005502	.	+	.	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
Phchi.S3	AUGUSTUS	stop_codon	8005503	8005505	.	+	0	transcript_id "Phchi.S3G096700.t1"; gene_id "Phchi.S3G096700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6324.t1 is derived from g3496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22287254	22288173	.	+	.	Phchi.S1G348300
Phchi.S1	AUGUSTUS	transcript	22287254	22288173	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	start_codon	22287254	22287256	.	+	0	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	CDS	22287254	22287499	0.7	+	0	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	exon	22287254	22287499	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	intron	22287500	22287587	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	CDS	22287588	22287736	0.88	+	0	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	exon	22287588	22287736	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	intron	22287737	22287858	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	CDS	22287859	22287991	0.99	+	1	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	exon	22287859	22287991	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	intron	22287992	22288077	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	CDS	22288078	22288173	0.99	+	0	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	exon	22288078	22288173	.	+	.	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
Phchi.S1	AUGUSTUS	stop_codon	22288174	22288176	.	+	0	transcript_id "Phchi.S1G348300.t1"; gene_id "Phchi.S1G348300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14869.t1 is derived from g13337.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15189409	15190601	.	-	.	Phchi.S3G218800
Phchi.S3	AUGUSTUS	transcript	15189409	15190601	.	-	.	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	stop_codon	15189406	15189408	.	-	0	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	CDS	15189409	15189969	1	-	0	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	exon	15189409	15189969	.	-	.	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	intron	15189970	15190066	.	-	.	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	CDS	15190067	15190258	1	-	0	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	exon	15190067	15190258	.	-	.	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	intron	15190259	15190367	.	-	.	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	CDS	15190368	15190601	0.95	-	0	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	exon	15190368	15190601	.	-	.	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
Phchi.S3	AUGUSTUS	start_codon	15190599	15190601	.	-	0	transcript_id "Phchi.S3G218800.t1"; gene_id "Phchi.S3G218800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11291.t1 is derived from g15341.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5254180	5254588	.	-	.	Phchi.S4G087300
Phchi.S4	AUGUSTUS	transcript	5254180	5254588	.	-	.	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	stop_codon	5254177	5254179	.	-	0	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	CDS	5254180	5254305	0.61	-	0	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	exon	5254180	5254305	.	-	.	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	intron	5254306	5254447	.	-	.	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	CDS	5254448	5254588	0.68	-	0	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	exon	5254448	5254588	.	-	.	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
Phchi.S4	AUGUSTUS	start_codon	5254586	5254588	.	-	0	transcript_id "Phchi.S4G087300.t1"; gene_id "Phchi.S4G087300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4035.t1 is derived from g1204.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7291151	7294324	.	+	.	Phchi.S1G119400
Phchi.S1	AUGUSTUS	transcript	7291151	7294324	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	start_codon	7291151	7291153	.	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7291151	7291708	0.31	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7291151	7291708	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	intron	7291709	7291847	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7291848	7292005	1	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7291848	7292005	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	intron	7292006	7292167	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7292168	7293179	1	+	1	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7292168	7293179	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	intron	7293180	7293290	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7293291	7293437	1	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7293291	7293437	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	intron	7293438	7293527	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7293528	7293845	1	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7293528	7293845	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	intron	7293846	7293956	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7293957	7294016	1	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7293957	7294016	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	intron	7294017	7294135	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	CDS	7294136	7294324	1	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	exon	7294136	7294324	.	+	.	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
Phchi.S1	AUGUSTUS	stop_codon	7294325	7294327	.	+	0	transcript_id "Phchi.S1G119400.t1"; gene_id "Phchi.S1G119400"
# This transcript jg9491.t2 is derived from g6667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9492.t1 is derived from g6668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42010475	42013918	.	-	.	Phchi.S1G665100
Phchi.S1	AUGUSTUS	transcript	42010475	42013918	.	-	.	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	stop_codon	42010472	42010474	.	-	0	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	CDS	42010475	42011484	0.99	-	2	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	exon	42010475	42011484	.	-	.	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	intron	42011485	42011595	.	-	.	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	CDS	42011596	42013918	1	-	0	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	exon	42011596	42013918	.	-	.	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	start_codon	42013916	42013918	.	-	0	transcript_id "Phchi.S1G665100.t1"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	transcript	42011641	42013918	.	-	.	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	stop_codon	42011638	42011640	.	-	0	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	CDS	42011641	42011644	0.41	-	1	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	exon	42011641	42011644	.	-	.	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	intron	42011645	42011708	.	-	.	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	CDS	42011709	42013918	0.57	-	0	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	exon	42011709	42013918	.	-	.	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
Phchi.S1	AUGUSTUS	start_codon	42013916	42013918	.	-	0	transcript_id "Phchi.S1G665100.t2"; gene_id "Phchi.S1G665100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1281.t1 is derived from g11064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8798665	8800142	.	+	.	Phchi.S6G124000
Phchi.S6	AUGUSTUS	transcript	8798665	8800142	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	start_codon	8798665	8798667	.	+	0	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	CDS	8798665	8798883	0.67	+	0	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	exon	8798665	8798883	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	intron	8798884	8798993	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	CDS	8798994	8799625	0.72	+	0	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	exon	8798994	8799625	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	intron	8799626	8799714	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	CDS	8799715	8799749	0.9	+	1	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	exon	8799715	8799749	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	intron	8799750	8799876	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	CDS	8799877	8800142	0.61	+	2	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	exon	8799877	8800142	.	+	.	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
Phchi.S6	AUGUSTUS	stop_codon	8800143	8800145	.	+	0	transcript_id "Phchi.S6G124000.t1"; gene_id "Phchi.S6G124000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11718.t1 is derived from g15770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7827433	7830931	.	-	.	Phchi.S4G130000
Phchi.S4	AUGUSTUS	transcript	7827433	7830931	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	stop_codon	7827430	7827432	.	-	0	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	CDS	7827433	7828010	1	-	2	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	exon	7827433	7828010	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	intron	7828011	7828096	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	CDS	7828097	7828125	1	-	1	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	exon	7828097	7828125	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	intron	7828126	7828249	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	CDS	7828250	7828378	1	-	1	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	exon	7828250	7828378	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	intron	7828379	7828477	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	CDS	7828478	7830375	0.93	-	0	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	exon	7828478	7830375	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	intron	7830376	7830454	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	CDS	7830455	7830600	1	-	2	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	exon	7830455	7830600	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	intron	7830601	7830693	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	CDS	7830694	7830931	1	-	0	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	exon	7830694	7830931	.	-	.	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
Phchi.S4	AUGUSTUS	start_codon	7830929	7830931	.	-	0	transcript_id "Phchi.S4G130000.t1"; gene_id "Phchi.S4G130000"
# This transcript jg13754.t2 is derived from g12221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13755.t1 is derived from g12222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8720646	8725260	.	+	.	Phchi.S3G107400
Phchi.S3	AUGUSTUS	transcript	8720646	8725260	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	start_codon	8720646	8720648	.	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8720646	8720699	1	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8720646	8720699	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8720700	8720794	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8720795	8720847	1	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8720795	8720847	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8720848	8720921	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8720922	8721000	1	+	1	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8720922	8721000	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8721001	8721152	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8721153	8721798	1	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8721153	8721798	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8721799	8721927	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8721928	8722185	1	+	2	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8721928	8722185	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8722186	8722280	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8722281	8722378	1	+	2	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8722281	8722378	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8722379	8722469	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8722470	8722725	1	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8722470	8722725	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8722726	8722801	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8722802	8722939	1	+	2	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8722802	8722939	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8722940	8723022	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8723023	8723347	1	+	2	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8723023	8723347	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8723348	8723436	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8723437	8723636	1	+	1	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8723437	8723636	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8723637	8723721	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8723722	8723867	1	+	2	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8723722	8723867	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8723868	8723957	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8723958	8724026	1	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8723958	8724026	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8724027	8724107	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8724108	8724755	0.86	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8724108	8724755	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	intron	8724756	8724849	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	CDS	8724850	8725260	0.8	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	exon	8724850	8725260	.	+	.	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
Phchi.S3	AUGUSTUS	stop_codon	8725261	8725263	.	+	0	transcript_id "Phchi.S3G107400.t1"; gene_id "Phchi.S3G107400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11758.t1 is derived from g15810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8024326	8025980	.	+	.	Phchi.S4G134000
Phchi.S4	AUGUSTUS	transcript	8024326	8025980	.	+	.	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	start_codon	8024326	8024328	.	+	0	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	CDS	8024326	8025620	0.49	+	0	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	exon	8024326	8025620	.	+	.	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	intron	8025621	8025712	.	+	.	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	CDS	8025713	8025980	1	+	1	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	exon	8025713	8025980	.	+	.	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
Phchi.S4	AUGUSTUS	stop_codon	8025981	8025983	.	+	0	transcript_id "Phchi.S4G134000.t1"; gene_id "Phchi.S4G134000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14742.t1 is derived from g13210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14489172	14492056	.	-	.	Phchi.S3G206100
Phchi.S3	AUGUSTUS	transcript	14489172	14492056	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	stop_codon	14489169	14489171	.	-	0	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14489172	14489196	0.93	-	1	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14489172	14489196	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14489197	14489312	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14489313	14489430	0.92	-	2	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14489313	14489430	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14489431	14489533	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14489534	14489615	0.99	-	0	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14489534	14489615	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14489616	14489809	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14489810	14489890	1	-	0	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14489810	14489890	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14489891	14490062	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14490063	14490309	0.97	-	1	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14490063	14490309	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14490310	14490414	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14490415	14490574	0.66	-	2	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14490415	14490574	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14490575	14490753	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14490754	14491085	0.98	-	1	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14490754	14491085	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14491086	14491172	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14491173	14491339	1	-	0	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14491173	14491339	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14491340	14491431	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14491432	14491523	1	-	2	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14491432	14491523	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	intron	14491524	14491704	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	CDS	14491705	14492056	0.59	-	0	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	exon	14491705	14492056	.	-	.	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
Phchi.S3	AUGUSTUS	start_codon	14492054	14492056	.	-	0	transcript_id "Phchi.S3G206100.t1"; gene_id "Phchi.S3G206100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4221.t1 is derived from g1390.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8992165	8993915	.	+	.	Phchi.S1G138000
Phchi.S1	AUGUSTUS	transcript	8992165	8993915	.	+	.	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	start_codon	8992165	8992167	.	+	0	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	CDS	8992165	8993546	0.82	+	0	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	exon	8992165	8993546	.	+	.	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	intron	8993547	8993866	.	+	.	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	CDS	8993867	8993915	0.96	+	1	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	exon	8993867	8993915	.	+	.	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
Phchi.S1	AUGUSTUS	stop_codon	8993916	8993918	.	+	0	transcript_id "Phchi.S1G138000.t1"; gene_id "Phchi.S1G138000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3868.t1 is derived from g1037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6134885	6136830	.	-	.	Phchi.S1G102700
Phchi.S1	AUGUSTUS	transcript	6135141	6136830	.	-	.	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	stop_codon	6135138	6135140	.	-	0	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	CDS	6135141	6135146	0.95	-	0	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	exon	6135141	6135146	.	-	.	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	intron	6135147	6135214	.	-	.	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	CDS	6135215	6136570	0.9	-	0	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	exon	6135215	6136570	.	-	.	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	intron	6136571	6136695	.	-	.	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	CDS	6136696	6136830	0.69	-	0	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	exon	6136696	6136830	.	-	.	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	start_codon	6136828	6136830	.	-	0	transcript_id "Phchi.S1G102700.t1"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	transcript	6134885	6136830	.	-	.	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	stop_codon	6134882	6134884	.	-	0	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	CDS	6134885	6136570	0.92	-	0	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	exon	6134885	6136570	.	-	.	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	intron	6136571	6136695	.	-	.	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	CDS	6136696	6136830	0.73	-	0	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	exon	6136696	6136830	.	-	.	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
Phchi.S1	AUGUSTUS	start_codon	6136828	6136830	.	-	0	transcript_id "Phchi.S1G102700.t2"; gene_id "Phchi.S1G102700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4586.t1 is derived from g1756.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11213344	11213643	.	+	.	Phchi.S1G174500
Phchi.S1	AUGUSTUS	transcript	11213344	11213643	.	+	.	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	start_codon	11213344	11213346	.	+	0	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	CDS	11213344	11213535	0.68	+	0	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	exon	11213344	11213535	.	+	.	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	intron	11213536	11213619	.	+	.	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	CDS	11213620	11213643	0.53	+	0	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	exon	11213620	11213643	.	+	.	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
Phchi.S1	AUGUSTUS	stop_codon	11213644	11213646	.	+	0	transcript_id "Phchi.S1G174500.t1"; gene_id "Phchi.S1G174500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15348.t1 is derived from g13816.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18511718	18514706	.	-	.	Phchi.S3G266700
Phchi.S3	AUGUSTUS	transcript	18511718	18514706	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	stop_codon	18511715	18511717	.	-	0	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	CDS	18511718	18512226	0.6	-	2	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	exon	18511718	18512226	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	intron	18512227	18512400	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	CDS	18512401	18512536	0.15	-	0	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	exon	18512401	18512536	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	intron	18512537	18512857	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	CDS	18512858	18514083	0.3	-	2	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	exon	18512858	18514083	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	intron	18514084	18514205	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	CDS	18514206	18514432	0.42	-	1	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	exon	18514206	18514432	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	intron	18514433	18514545	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	CDS	18514546	18514706	0.6	-	0	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	exon	18514546	18514706	.	-	.	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
Phchi.S3	AUGUSTUS	start_codon	18514704	18514706	.	-	0	transcript_id "Phchi.S3G266700.t1"; gene_id "Phchi.S3G266700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1707.t1 is derived from g8627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2639370	2642459	.	+	.	Phchi.S5G031600
Phchi.S5	AUGUSTUS	transcript	2639370	2642459	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	start_codon	2639370	2639372	.	+	0	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2639370	2639650	0.97	+	0	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2639370	2639650	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	intron	2639651	2639918	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2639919	2640014	1	+	1	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2639919	2640014	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	intron	2640015	2640100	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2640101	2640230	1	+	1	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2640101	2640230	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	intron	2640231	2640419	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2640420	2640961	0.99	+	0	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2640420	2640961	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	intron	2640962	2641126	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2641127	2641244	1	+	1	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2641127	2641244	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	intron	2641245	2641384	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2641385	2641669	1	+	0	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2641385	2641669	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	intron	2641670	2641772	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	CDS	2641773	2642459	1	+	0	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	exon	2641773	2642459	.	+	.	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
Phchi.S5	AUGUSTUS	stop_codon	2642460	2642462	.	+	0	transcript_id "Phchi.S5G031600.t1"; gene_id "Phchi.S5G031600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11180.t1 is derived from g15230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4520339	4523635	.	-	.	Phchi.S4G076200
Phchi.S4	AUGUSTUS	transcript	4520339	4523635	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	stop_codon	4520336	4520338	.	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4520339	4520422	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4520339	4520422	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4520423	4520511	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4520512	4520609	1	-	2	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4520512	4520609	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4520610	4520723	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4520724	4520838	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4520724	4520838	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4520839	4520932	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4520933	4520980	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4520933	4520980	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4520981	4521131	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4521132	4521266	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4521132	4521266	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4521267	4521363	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4521364	4521458	0.86	-	2	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4521364	4521458	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4521459	4521569	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4521570	4521695	0.86	-	2	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4521570	4521695	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4521696	4521771	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4521772	4521866	1	-	1	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4521772	4521866	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4521867	4521965	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4521966	4522039	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4521966	4522039	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4522040	4522140	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4522141	4522302	0.99	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4522141	4522302	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4522303	4522397	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4522398	4522469	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4522398	4522469	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4522470	4522590	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4522591	4522657	1	-	1	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4522591	4522657	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4522658	4522743	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4522744	4522838	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4522744	4522838	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4522839	4522954	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4522955	4523017	1	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4522955	4523017	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4523018	4523113	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4523114	4523222	1	-	1	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4523114	4523222	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4523223	4523388	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4523389	4523452	1	-	2	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4523389	4523452	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	intron	4523453	4523553	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	CDS	4523554	4523635	0.94	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	exon	4523554	4523635	.	-	.	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
Phchi.S4	AUGUSTUS	start_codon	4523633	4523635	.	-	0	transcript_id "Phchi.S4G076200.t1"; gene_id "Phchi.S4G076200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg541.t1 is derived from g10323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3981993	3982863	.	-	.	Phchi.S6G050000
Phchi.S6	AUGUSTUS	transcript	3981993	3982863	.	-	.	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	stop_codon	3981990	3981992	.	-	0	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	CDS	3981993	3982708	0.55	-	2	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	exon	3981993	3982708	.	-	.	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	intron	3982709	3982799	.	-	.	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	CDS	3982800	3982863	0.59	-	0	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	exon	3982800	3982863	.	-	.	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
Phchi.S6	AUGUSTUS	start_codon	3982861	3982863	.	-	0	transcript_id "Phchi.S6G050000.t1"; gene_id "Phchi.S6G050000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2825.t1 is derived from g9745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9062142	9062831	.	+	.	Phchi.S5G143400
Phchi.S5	AUGUSTUS	transcript	9062142	9062831	.	+	.	transcript_id "Phchi.S5G143400.t1"; gene_id "Phchi.S5G143400"
Phchi.S5	AUGUSTUS	start_codon	9062142	9062144	.	+	0	transcript_id "Phchi.S5G143400.t1"; gene_id "Phchi.S5G143400"
Phchi.S5	AUGUSTUS	CDS	9062142	9062831	0.91	+	0	transcript_id "Phchi.S5G143400.t1"; gene_id "Phchi.S5G143400"
Phchi.S5	AUGUSTUS	exon	9062142	9062831	.	+	.	transcript_id "Phchi.S5G143400.t1"; gene_id "Phchi.S5G143400"
Phchi.S5	AUGUSTUS	stop_codon	9062832	9062834	.	+	0	transcript_id "Phchi.S5G143400.t1"; gene_id "Phchi.S5G143400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2145.t1 is derived from g9065.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5049466	5052552	.	-	.	Phchi.S5G075400
Phchi.S5	AUGUSTUS	transcript	5049466	5052552	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	stop_codon	5049463	5049465	.	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049466	5049640	0.91	-	1	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049466	5049640	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5049641	5049746	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049747	5049814	0.94	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049747	5049814	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5049815	5049946	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049947	5050012	1	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049947	5050012	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050013	5050126	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050127	5050183	0.98	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050127	5050183	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050184	5050264	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050265	5050366	1	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050265	5050366	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050367	5050467	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050468	5050500	0.99	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050468	5050500	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050501	5050681	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050682	5050771	1	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050682	5050771	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050772	5050912	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050913	5051026	0.52	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050913	5051026	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051027	5051105	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051106	5051165	1	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051106	5051165	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051166	5051257	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051258	5051424	1	-	2	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051258	5051424	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051425	5051537	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051538	5051660	0.79	-	2	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051538	5051660	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051661	5051789	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051790	5051923	0.79	-	1	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051790	5051923	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051924	5052050	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052051	5052203	0.41	-	1	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052051	5052203	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5052204	5052305	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052306	5052367	0.67	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052306	5052367	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5052368	5052525	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052526	5052552	1	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052526	5052552	.	-	.	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	start_codon	5052550	5052552	.	-	0	transcript_id "Phchi.S5G075400.t1"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	transcript	5049542	5052552	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	stop_codon	5049539	5049541	.	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049542	5049575	0.44	-	1	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049542	5049575	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5049576	5049746	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049747	5049814	0.94	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049747	5049814	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5049815	5049946	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049947	5050012	1	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049947	5050012	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050013	5050126	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050127	5050183	0.98	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050127	5050183	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050184	5050264	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050265	5050366	0.99	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050265	5050366	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050367	5050467	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050468	5050500	0.97	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050468	5050500	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050501	5050681	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050682	5050771	1	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050682	5050771	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050772	5050912	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050913	5051026	0.65	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050913	5051026	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051027	5051105	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051106	5051165	1	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051106	5051165	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051166	5051257	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051258	5051424	1	-	2	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051258	5051424	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051425	5051537	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051538	5051660	0.88	-	2	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051538	5051660	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051661	5051789	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051790	5051923	0.73	-	1	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051790	5051923	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051924	5052050	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052051	5052203	0.35	-	1	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052051	5052203	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5052204	5052305	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052306	5052367	0.63	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052306	5052367	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5052368	5052525	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052526	5052552	0.98	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052526	5052552	.	-	.	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	start_codon	5052550	5052552	.	-	0	transcript_id "Phchi.S5G075400.t2"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	transcript	5049542	5052552	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	stop_codon	5049539	5049541	.	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049542	5049575	0.45	-	1	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049542	5049575	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5049576	5049746	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049747	5049814	0.97	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049747	5049814	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5049815	5049946	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5049947	5050012	1	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5049947	5050012	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050013	5050126	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050127	5050183	0.98	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050127	5050183	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050184	5050264	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050265	5050366	1	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050265	5050366	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050367	5050467	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050468	5050500	0.98	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050468	5050500	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050501	5050681	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050682	5050771	1	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050682	5050771	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5050772	5050912	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5050913	5051026	0.53	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5050913	5051026	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051027	5051105	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051106	5051168	1	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051106	5051168	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051169	5051257	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051258	5051424	1	-	2	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051258	5051424	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051425	5051537	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051538	5051660	0.89	-	2	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051538	5051660	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051661	5051789	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5051790	5051923	0.75	-	1	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5051790	5051923	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5051924	5052050	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052051	5052203	0.38	-	1	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052051	5052203	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5052204	5052305	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052306	5052367	0.6	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052306	5052367	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	intron	5052368	5052525	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	CDS	5052526	5052552	0.98	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	exon	5052526	5052552	.	-	.	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
Phchi.S5	AUGUSTUS	start_codon	5052550	5052552	.	-	0	transcript_id "Phchi.S5G075400.t3"; gene_id "Phchi.S5G075400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5742.t1 is derived from g2912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18684103	18686295	.	+	.	Phchi.S1G290100
Phchi.S1	AUGUSTUS	transcript	18684103	18686295	.	+	.	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	start_codon	18684103	18684105	.	+	0	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	CDS	18684103	18684547	0.7	+	0	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	exon	18684103	18684547	.	+	.	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	intron	18684548	18684634	.	+	.	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	CDS	18684635	18684710	0.83	+	2	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	exon	18684635	18684710	.	+	.	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	intron	18684711	18684920	.	+	.	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	CDS	18684921	18686295	0.78	+	1	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	exon	18684921	18686295	.	+	.	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
Phchi.S1	AUGUSTUS	stop_codon	18686296	18686298	.	+	0	transcript_id "Phchi.S1G290100.t1"; gene_id "Phchi.S1G290100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2328.t1 is derived from g9248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6195645	6197836	.	-	.	Phchi.S5G093700
Phchi.S5	AUGUSTUS	transcript	6195645	6197389	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	stop_codon	6195642	6195644	.	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6195645	6195728	0.97	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6195645	6195728	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6195729	6195922	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6195923	6196057	0.97	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6195923	6196057	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196058	6196159	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196160	6196291	0.8	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196160	6196291	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196292	6196421	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196422	6196577	1	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196422	6196577	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196578	6196662	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196663	6196773	1	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196663	6196773	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196774	6196896	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196897	6196955	1	-	2	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196897	6196955	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196956	6197048	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6197049	6197224	0.92	-	1	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6197049	6197224	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6197225	6197333	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6197334	6197389	0.67	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6197334	6197389	.	-	.	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	start_codon	6197387	6197389	.	-	0	transcript_id "Phchi.S5G093700.t1"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	transcript	6195645	6197836	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	stop_codon	6195642	6195644	.	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6195645	6195728	0.97	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6195645	6195728	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6195729	6195922	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6195923	6196057	0.96	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6195923	6196057	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196058	6196159	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196160	6196291	0.72	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196160	6196291	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196292	6196421	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196422	6196577	1	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196422	6196577	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196578	6196662	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196663	6196773	1	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196663	6196773	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196774	6196896	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6196897	6196955	1	-	2	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6196897	6196955	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6196956	6197048	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6197049	6197195	0.99	-	2	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6197049	6197195	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6197196	6197333	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6197334	6197395	0.66	-	1	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6197334	6197395	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6197396	6197578	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6197579	6197668	0.74	-	1	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6197579	6197668	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	intron	6197669	6197756	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	CDS	6197757	6197836	0.94	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	exon	6197757	6197836	.	-	.	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
Phchi.S5	AUGUSTUS	start_codon	6197834	6197836	.	-	0	transcript_id "Phchi.S5G093700.t2"; gene_id "Phchi.S5G093700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8708.t1 is derived from g5883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37560644	37561623	.	+	.	Phchi.S1G586700
Phchi.S1	AUGUSTUS	transcript	37560644	37561623	.	+	.	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	start_codon	37560644	37560646	.	+	0	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	CDS	37560644	37560730	0.64	+	0	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	exon	37560644	37560730	.	+	.	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	intron	37560731	37560810	.	+	.	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	CDS	37560811	37561623	0.79	+	0	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	exon	37560811	37561623	.	+	.	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
Phchi.S1	AUGUSTUS	stop_codon	37561624	37561626	.	+	0	transcript_id "Phchi.S1G586700.t1"; gene_id "Phchi.S1G586700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12991.t1 is derived from g11456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3497256	3501423	.	-	.	Phchi.S3G031000
Phchi.S3	AUGUSTUS	transcript	3497256	3501423	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	stop_codon	3497253	3497255	.	-	0	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3497256	3497408	0.67	-	0	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3497256	3497408	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3497409	3497509	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3497510	3497666	0.69	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3497510	3497666	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3497667	3497759	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3497760	3497863	0.46	-	0	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3497760	3497863	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3497864	3498020	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3498021	3498121	0.43	-	2	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3498021	3498121	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3498122	3498206	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3498207	3498477	0.97	-	0	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3498207	3498477	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3498478	3498568	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3498569	3498861	1	-	2	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3498569	3498861	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3498862	3498946	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3498947	3498991	1	-	2	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3498947	3498991	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3498992	3499079	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3499080	3499420	1	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3499080	3499420	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3499421	3499522	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3499523	3499594	0.9	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3499523	3499594	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3499595	3499717	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3499718	3499789	1	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3499718	3499789	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3499790	3499867	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3499868	3499939	1	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3499868	3499939	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3499940	3500049	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3500050	3500121	1	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3500050	3500121	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3500122	3500259	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3500260	3500331	0.99	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3500260	3500331	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3500332	3500442	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3500443	3500508	1	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3500443	3500508	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3500509	3500598	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3500599	3500679	1	-	1	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3500599	3500679	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3500680	3500760	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3500761	3500908	1	-	2	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3500761	3500908	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	intron	3500909	3501335	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	CDS	3501336	3501423	0.96	-	0	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	exon	3501336	3501423	.	-	.	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
Phchi.S3	AUGUSTUS	start_codon	3501421	3501423	.	-	0	transcript_id "Phchi.S3G031000.t1"; gene_id "Phchi.S3G031000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11844.t1 is derived from g15896.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8540399	8542293	.	+	.	Phchi.S4G142600
Phchi.S4	AUGUSTUS	transcript	8540399	8542293	.	+	.	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	start_codon	8540399	8540401	.	+	0	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	CDS	8540399	8541744	0.48	+	0	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	exon	8540399	8541744	.	+	.	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	intron	8541745	8541884	.	+	.	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	CDS	8541885	8542293	0.99	+	1	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	exon	8541885	8542293	.	+	.	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
Phchi.S4	AUGUSTUS	stop_codon	8542294	8542296	.	+	0	transcript_id "Phchi.S4G142600.t1"; gene_id "Phchi.S4G142600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1125.t1 is derived from g10908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7852143	7854383	.	-	.	Phchi.S6G108400
Phchi.S6	AUGUSTUS	transcript	7852143	7854383	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	stop_codon	7852140	7852142	.	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7852143	7852364	0.98	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7852143	7852364	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7852365	7852447	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7852448	7852750	1	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7852448	7852750	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7852751	7852898	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7852899	7853009	0.97	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7852899	7853009	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7853010	7853110	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7853111	7853271	0.84	-	2	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7853111	7853271	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7853272	7853406	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7853407	7853489	1	-	1	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7853407	7853489	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7853490	7853588	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7853589	7853728	1	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7853589	7853728	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7853729	7853836	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7853837	7853952	0.99	-	2	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7853837	7853952	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	intron	7853953	7854064	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	CDS	7854065	7854383	0.67	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	exon	7854065	7854383	.	-	.	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
Phchi.S6	AUGUSTUS	start_codon	7854381	7854383	.	-	0	transcript_id "Phchi.S6G108400.t1"; gene_id "Phchi.S6G108400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11570.t1 is derived from g15621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7104435	7107005	.	-	.	Phchi.S4G115200
Phchi.S4	AUGUSTUS	transcript	7104435	7107005	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	stop_codon	7104432	7104434	.	-	0	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7104435	7104587	0.99	-	0	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7104435	7104587	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7104588	7104689	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7104690	7104790	1	-	2	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7104690	7104790	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7104791	7104913	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7104914	7105058	1	-	0	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7104914	7105058	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7105059	7105145	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7105146	7105612	0.51	-	2	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7105146	7105612	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7105613	7105728	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7105729	7105824	0.3	-	2	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7105729	7105824	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7105825	7105923	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7105924	7105962	0.51	-	2	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7105924	7105962	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7105963	7106038	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7106039	7106122	0.96	-	2	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7106039	7106122	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7106123	7106289	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7106290	7106692	0.96	-	0	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7106290	7106692	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	intron	7106693	7106990	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	CDS	7106991	7107005	0.97	-	0	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	exon	7106991	7107005	.	-	.	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
Phchi.S4	AUGUSTUS	start_codon	7107003	7107005	.	-	0	transcript_id "Phchi.S4G115200.t1"; gene_id "Phchi.S4G115200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7868.t1 is derived from g5042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31626876	31629017	.	+	.	Phchi.S1G502700
Phchi.S1	AUGUSTUS	transcript	31626876	31629017	.	+	.	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	start_codon	31626876	31626878	.	+	0	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	CDS	31626876	31628295	0.75	+	0	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	exon	31626876	31628295	.	+	.	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	intron	31628296	31628502	.	+	.	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	CDS	31628503	31629017	1	+	2	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	exon	31628503	31629017	.	+	.	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
Phchi.S1	AUGUSTUS	stop_codon	31629018	31629020	.	+	0	transcript_id "Phchi.S1G502700.t1"; gene_id "Phchi.S1G502700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9373.t1 is derived from g6549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41217900	41220210	.	-	.	Phchi.S1G653200
Phchi.S1	AUGUSTUS	transcript	41217900	41220210	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	stop_codon	41217897	41217899	.	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41217900	41217936	0.96	-	1	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41217900	41217936	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41217937	41218153	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41218154	41218294	0.97	-	1	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41218154	41218294	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41218295	41218363	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41218364	41218428	0.88	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41218364	41218428	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41218429	41218538	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41218539	41218626	1	-	1	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41218539	41218626	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41218627	41218725	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41218726	41218835	1	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41218726	41218835	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41218836	41218911	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41218912	41219013	1	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41218912	41219013	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41219014	41219132	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41219133	41219207	1	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41219133	41219207	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41219208	41219313	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41219314	41219447	1	-	2	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41219314	41219447	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41219448	41219534	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41219535	41219775	1	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41219535	41219775	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	intron	41219776	41219907	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	CDS	41219908	41220210	0.99	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	exon	41219908	41220210	.	-	.	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
Phchi.S1	AUGUSTUS	start_codon	41220208	41220210	.	-	0	transcript_id "Phchi.S1G653200.t1"; gene_id "Phchi.S1G653200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3718.t1 is derived from g887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5355394	5355903	.	+	.	Phchi.S1G087700
Phchi.S1	AUGUSTUS	transcript	5355394	5355903	.	+	.	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	start_codon	5355394	5355396	.	+	0	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	CDS	5355394	5355598	1	+	0	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	exon	5355394	5355598	.	+	.	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	intron	5355599	5355679	.	+	.	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	CDS	5355680	5355903	1	+	2	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	exon	5355680	5355903	.	+	.	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
Phchi.S1	AUGUSTUS	stop_codon	5355904	5355906	.	+	0	transcript_id "Phchi.S1G087700.t1"; gene_id "Phchi.S1G087700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2670.t1 is derived from g9590.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8132958	8135686	.	-	.	Phchi.S5G127900
Phchi.S5	AUGUSTUS	transcript	8132958	8135686	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	stop_codon	8132955	8132957	.	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8132958	8132981	1	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8132958	8132981	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8132982	8133066	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8133067	8133282	0.99	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8133067	8133282	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8133283	8133404	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8133405	8133524	1	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8133405	8133524	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8133525	8133639	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8133640	8134257	1	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8133640	8134257	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8134258	8134461	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8134462	8134503	1	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8134462	8134503	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8134504	8134698	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8134699	8134819	1	-	1	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8134699	8134819	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8134820	8135073	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8135074	8135155	1	-	2	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8135074	8135155	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8135156	8135423	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8135424	8135482	1	-	1	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8135424	8135482	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	intron	8135483	8135651	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	CDS	8135652	8135686	0.88	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	exon	8135652	8135686	.	-	.	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
Phchi.S5	AUGUSTUS	start_codon	8135684	8135686	.	-	0	transcript_id "Phchi.S5G127900.t1"; gene_id "Phchi.S5G127900"
# This transcript jg13152.t2 is derived from g11617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13152.t3 is derived from g11617.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13153.t1 is derived from g11618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4415922	4417489	.	-	.	Phchi.S3G047200
Phchi.S3	AUGUSTUS	transcript	4415922	4417489	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	stop_codon	4415919	4415921	.	-	0	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	CDS	4415922	4416041	0.66	-	0	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	exon	4415922	4416041	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	intron	4416042	4416410	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	CDS	4416411	4416425	0.75	-	0	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	exon	4416411	4416425	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	intron	4416426	4416500	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	CDS	4416501	4416546	0.59	-	1	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	exon	4416501	4416546	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	intron	4416547	4417112	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	CDS	4417113	4417489	0.57	-	0	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	exon	4417113	4417489	.	-	.	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
Phchi.S3	AUGUSTUS	start_codon	4417487	4417489	.	-	0	transcript_id "Phchi.S3G047200.t1"; gene_id "Phchi.S3G047200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5807.t1 is derived from g2977.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19042754	19045609	.	-	.	Phchi.S1G296600
Phchi.S1	AUGUSTUS	transcript	19042754	19045609	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	stop_codon	19042751	19042753	.	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19042754	19042888	0.88	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19042754	19042888	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19042889	19042982	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19042983	19043075	1	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19042983	19043075	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19043076	19043180	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19043181	19043380	0.87	-	2	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19043181	19043380	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19043381	19043522	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19043523	19043664	1	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19043523	19043664	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19043665	19043782	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19043783	19043894	0.89	-	1	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19043783	19043894	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19043895	19044007	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19044008	19044297	0.71	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19044008	19044297	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19044298	19044425	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19044426	19044646	0.86	-	2	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19044426	19044646	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19044647	19044769	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19044770	19044929	1	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19044770	19044929	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19044930	19045055	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19045056	19045149	1	-	1	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19045056	19045149	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	intron	19045150	19045355	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	CDS	19045356	19045609	1	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	exon	19045356	19045609	.	-	.	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
Phchi.S1	AUGUSTUS	start_codon	19045607	19045609	.	-	0	transcript_id "Phchi.S1G296600.t1"; gene_id "Phchi.S1G296600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9103.t1 is derived from g6278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39840136	39841698	.	-	.	Phchi.S1G626200
Phchi.S1	AUGUSTUS	transcript	39840136	39841698	.	-	.	transcript_id "Phchi.S1G626200.t1"; gene_id "Phchi.S1G626200"
Phchi.S1	AUGUSTUS	stop_codon	39840133	39840135	.	-	0	transcript_id "Phchi.S1G626200.t1"; gene_id "Phchi.S1G626200"
Phchi.S1	AUGUSTUS	CDS	39840136	39841698	0.85	-	0	transcript_id "Phchi.S1G626200.t1"; gene_id "Phchi.S1G626200"
Phchi.S1	AUGUSTUS	exon	39840136	39841698	.	-	.	transcript_id "Phchi.S1G626200.t1"; gene_id "Phchi.S1G626200"
Phchi.S1	AUGUSTUS	start_codon	39841696	39841698	.	-	0	transcript_id "Phchi.S1G626200.t1"; gene_id "Phchi.S1G626200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11424.t1 is derived from g15474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6274362	6275256	.	-	.	Phchi.S4G100600
Phchi.S4	AUGUSTUS	transcript	6274362	6275256	.	-	.	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	stop_codon	6274359	6274361	.	-	0	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	CDS	6274362	6275026	0.47	-	2	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	exon	6274362	6275026	.	-	.	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	intron	6275027	6275165	.	-	.	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	CDS	6275166	6275256	0.35	-	0	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	exon	6275166	6275256	.	-	.	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
Phchi.S4	AUGUSTUS	start_codon	6275254	6275256	.	-	0	transcript_id "Phchi.S4G100600.t1"; gene_id "Phchi.S4G100600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11911.t1 is derived from g15963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9272798	9273257	.	+	.	Phchi.S4G149300
Phchi.S4	AUGUSTUS	transcript	9272798	9273257	.	+	.	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	start_codon	9272798	9272800	.	+	0	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	CDS	9272798	9272876	0.82	+	0	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	exon	9272798	9272876	.	+	.	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	intron	9272877	9273018	.	+	.	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	CDS	9273019	9273257	0.91	+	2	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	exon	9273019	9273257	.	+	.	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
Phchi.S4	AUGUSTUS	stop_codon	9273258	9273260	.	+	0	transcript_id "Phchi.S4G149300.t1"; gene_id "Phchi.S4G149300"
# This transcript jg14205.t2 is derived from g12672.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14206.t1 is derived from g12673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11500697	11501117	.	-	.	Phchi.S3G152500
Phchi.S3	AUGUSTUS	transcript	11500697	11501117	.	-	.	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	stop_codon	11500694	11500696	.	-	0	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	CDS	11500697	11500746	0.53	-	2	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	exon	11500697	11500746	.	-	.	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	intron	11500747	11500903	.	-	.	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	CDS	11500904	11501117	0.57	-	0	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	exon	11500904	11501117	.	-	.	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
Phchi.S3	AUGUSTUS	start_codon	11501115	11501117	.	-	0	transcript_id "Phchi.S3G152500.t1"; gene_id "Phchi.S3G152500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9186.t1 is derived from g6361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40257095	40257900	.	-	.	Phchi.S1G634500
Phchi.S1	AUGUSTUS	transcript	40257095	40257900	.	-	.	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	stop_codon	40257092	40257094	.	-	0	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	CDS	40257095	40257613	0.5	-	0	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	exon	40257095	40257613	.	-	.	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	intron	40257614	40257738	.	-	.	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	CDS	40257739	40257900	0.56	-	0	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	exon	40257739	40257900	.	-	.	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
Phchi.S1	AUGUSTUS	start_codon	40257898	40257900	.	-	0	transcript_id "Phchi.S1G634500.t1"; gene_id "Phchi.S1G634500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10197.t1 is derived from g7373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46336931	46337816	.	-	.	Phchi.S1G735600
Phchi.S1	AUGUSTUS	transcript	46336931	46337816	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	stop_codon	46336928	46336930	.	-	0	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	CDS	46336931	46337023	0.98	-	0	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	exon	46336931	46337023	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	intron	46337024	46337117	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	CDS	46337118	46337381	1	-	0	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	exon	46337118	46337381	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	intron	46337382	46337521	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	CDS	46337522	46337634	0.8	-	2	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	exon	46337522	46337634	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	intron	46337635	46337731	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	CDS	46337732	46337816	0.88	-	0	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	exon	46337732	46337816	.	-	.	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
Phchi.S1	AUGUSTUS	start_codon	46337814	46337816	.	-	0	transcript_id "Phchi.S1G735600.t1"; gene_id "Phchi.S1G735600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4917.t1 is derived from g2087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13549429	13551920	.	-	.	Phchi.S1G207600
Phchi.S1	AUGUSTUS	transcript	13549429	13551920	.	-	.	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	stop_codon	13549426	13549428	.	-	0	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	CDS	13549429	13550669	0.99	-	2	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	exon	13549429	13550669	.	-	.	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	intron	13550670	13550812	.	-	.	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	CDS	13550813	13551920	0.5	-	0	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	exon	13550813	13551920	.	-	.	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
Phchi.S1	AUGUSTUS	start_codon	13551918	13551920	.	-	0	transcript_id "Phchi.S1G207600.t1"; gene_id "Phchi.S1G207600"
# This transcript jg9054.t2 is derived from g6229.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9055.t1 is derived from g6230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39420277	39421367	.	+	.	Phchi.S1G621400
Phchi.S1	AUGUSTUS	transcript	39420277	39421367	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	start_codon	39420277	39420279	.	+	0	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	CDS	39420277	39420334	0.9	+	0	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	exon	39420277	39420334	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	intron	39420335	39420525	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	CDS	39420526	39420584	0.89	+	2	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	exon	39420526	39420584	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	intron	39420585	39420812	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	CDS	39420813	39420862	0.52	+	0	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	exon	39420813	39420862	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	intron	39420863	39420939	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	CDS	39420940	39420995	0.41	+	1	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	exon	39420940	39420995	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	intron	39420996	39421155	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	CDS	39421156	39421271	0.45	+	2	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	exon	39421156	39421271	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	intron	39421272	39421349	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	CDS	39421350	39421367	0.45	+	0	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	exon	39421350	39421367	.	+	.	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
Phchi.S1	AUGUSTUS	stop_codon	39421368	39421370	.	+	0	transcript_id "Phchi.S1G621400.t1"; gene_id "Phchi.S1G621400"
# This transcript jg5044.t2 is derived from g2214.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5045.t1 is derived from g2215.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14234388	14236501	.	+	.	Phchi.S1G220400
Phchi.S1	AUGUSTUS	transcript	14234388	14236501	.	+	.	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	start_codon	14234388	14234390	.	+	0	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	CDS	14234388	14234779	0.58	+	0	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	exon	14234388	14234779	.	+	.	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	intron	14234780	14234883	.	+	.	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	CDS	14234884	14235309	0.45	+	1	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	exon	14234884	14235309	.	+	.	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	intron	14235310	14235510	.	+	.	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	CDS	14235511	14236501	0.85	+	1	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	exon	14235511	14236501	.	+	.	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
Phchi.S1	AUGUSTUS	stop_codon	14236502	14236504	.	+	0	transcript_id "Phchi.S1G220400.t1"; gene_id "Phchi.S1G220400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7270.t1 is derived from g4442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27995419	27999028	.	-	.	Phchi.S1G442900
Phchi.S1	AUGUSTUS	transcript	27995419	27999028	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	stop_codon	27995416	27995418	.	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995419	27995492	0.94	-	2	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995419	27995492	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27995493	27995579	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995580	27995670	1	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995580	27995670	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27995671	27995774	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995775	27995885	0.96	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995775	27995885	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27995886	27995970	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995971	27996018	0.92	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995971	27996018	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996019	27996119	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996120	27996218	0.86	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996120	27996218	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996219	27996343	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996344	27996456	1	-	2	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996344	27996456	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996457	27996551	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996552	27996807	1	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996552	27996807	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996808	27996886	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996887	27996979	1	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996887	27996979	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996980	27997117	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997118	27997331	0.97	-	1	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997118	27997331	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997332	27997438	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997439	27997775	0.99	-	2	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997439	27997775	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997776	27997866	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997867	27997879	0.74	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997867	27997879	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997880	27997932	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997933	27997995	0.74	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997933	27997995	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997996	27998089	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998090	27998224	1	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998090	27998224	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27998225	27998406	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998407	27998540	1	-	2	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998407	27998540	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27998541	27998622	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998623	27999028	0.45	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998623	27999028	.	-	.	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	start_codon	27999026	27999028	.	-	0	transcript_id "Phchi.S1G442900.t1"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	transcript	27995419	27999028	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	stop_codon	27995416	27995418	.	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995419	27995492	0.95	-	2	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995419	27995492	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27995493	27995579	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995580	27995670	1	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995580	27995670	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27995671	27995774	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995775	27995885	0.94	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995775	27995885	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27995886	27995970	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27995971	27996018	0.89	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27995971	27996018	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996019	27996119	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996120	27996218	0.87	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996120	27996218	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996219	27996343	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996344	27996456	1	-	2	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996344	27996456	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996457	27996551	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996552	27996807	1	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996552	27996807	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996808	27996886	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27996887	27996979	1	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27996887	27996979	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27996980	27997117	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997118	27997331	0.98	-	1	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997118	27997331	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997332	27997438	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997439	27997775	0.99	-	2	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997439	27997775	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997776	27997866	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997867	27997879	0.74	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997867	27997879	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997880	27997932	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27997933	27997995	0.74	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27997933	27997995	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27997996	27998089	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998090	27998264	1	-	1	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998090	27998264	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27998265	27998406	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998407	27998432	0.66	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998407	27998432	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27998433	27998514	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998515	27998540	0.48	-	2	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998515	27998540	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	intron	27998541	27998622	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	CDS	27998623	27999028	0.43	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	exon	27998623	27999028	.	-	.	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
Phchi.S1	AUGUSTUS	start_codon	27999026	27999028	.	-	0	transcript_id "Phchi.S1G442900.t2"; gene_id "Phchi.S1G442900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9478.t1 is derived from g6654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41943915	41945153	.	+	.	Phchi.S1G663700
Phchi.S1	AUGUSTUS	transcript	41943915	41945153	.	+	.	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	start_codon	41943915	41943917	.	+	0	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	CDS	41943915	41944316	0.62	+	0	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	exon	41943915	41944316	.	+	.	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	intron	41944317	41944544	.	+	.	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	CDS	41944545	41945153	0.67	+	0	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	exon	41944545	41945153	.	+	.	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
Phchi.S1	AUGUSTUS	stop_codon	41945154	41945156	.	+	0	transcript_id "Phchi.S1G663700.t1"; gene_id "Phchi.S1G663700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9062.t1 is derived from g6237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39541359	39542657	.	-	.	Phchi.S1G622100
Phchi.S1	AUGUSTUS	transcript	39541359	39542657	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	stop_codon	39541356	39541358	.	-	0	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	CDS	39541359	39541926	0.95	-	1	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	exon	39541359	39541926	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	intron	39541927	39542017	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	CDS	39542018	39542349	0.56	-	0	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	exon	39542018	39542349	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	intron	39542350	39542461	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	CDS	39542462	39542488	0.9	-	0	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	exon	39542462	39542488	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	intron	39542489	39542636	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	CDS	39542637	39542657	1	-	0	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	exon	39542637	39542657	.	-	.	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
Phchi.S1	AUGUSTUS	start_codon	39542655	39542657	.	-	0	transcript_id "Phchi.S1G622100.t1"; gene_id "Phchi.S1G622100"
# This transcript jg15806.t2 is derived from g14276.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15807.t1 is derived from g14277.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21487787	21496590	.	-	.	Phchi.S3G312600
Phchi.S3	AUGUSTUS	transcript	21487787	21496590	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	stop_codon	21487784	21487786	.	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21487787	21488355	0.99	-	2	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21487787	21488355	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21488356	21488442	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21488443	21488778	1	-	2	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21488443	21488778	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21488779	21488863	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21488864	21489899	0.94	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21488864	21489899	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21489900	21489991	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21489992	21490269	1	-	2	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21489992	21490269	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490270	21490444	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21490445	21490523	1	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21490445	21490523	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490524	21490612	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21490613	21490700	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21490613	21490700	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490701	21490887	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21490888	21490983	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21490888	21490983	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490984	21491175	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21491176	21491282	1	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21491176	21491282	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21491283	21491406	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21491407	21491731	0.51	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21491407	21491731	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21491732	21491805	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21491806	21492869	0.44	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21491806	21492869	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21492870	21493097	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21493098	21493406	1	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21493098	21493406	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21493407	21493550	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21493551	21493878	0.99	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21493551	21493878	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21493879	21493991	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21493992	21494078	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21493992	21494078	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494079	21494168	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21494169	21494537	0.95	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21494169	21494537	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494538	21494825	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21494826	21494904	1	-	2	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21494826	21494904	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494905	21494999	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495000	21495088	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495000	21495088	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495089	21495201	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495202	21495279	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495202	21495279	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495280	21495376	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495377	21495463	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495377	21495463	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495464	21495560	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495561	21495648	1	-	2	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495561	21495648	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495649	21495793	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495794	21495880	1	-	2	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495794	21495880	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495881	21496016	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21496017	21496156	1	-	1	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21496017	21496156	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21496157	21496289	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21496290	21496357	1	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21496290	21496357	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21496358	21496566	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21496567	21496590	1	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21496567	21496590	.	-	.	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	start_codon	21496588	21496590	.	-	0	transcript_id "Phchi.S3G312600.t1"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	transcript	21487787	21496590	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	stop_codon	21487784	21487786	.	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21487787	21488355	0.94	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21487787	21488355	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21488356	21488442	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21488443	21488778	0.98	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21488443	21488778	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21488779	21488863	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21488864	21489899	0.97	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21488864	21489899	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21489900	21489991	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21489992	21490269	1	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21489992	21490269	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490270	21490444	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21490445	21490523	1	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21490445	21490523	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490524	21490612	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21490613	21490700	1	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21490613	21490700	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490701	21490887	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21490888	21490983	1	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21490888	21490983	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21490984	21491175	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21491176	21491282	1	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21491176	21491282	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21491283	21491406	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21491407	21491731	0.56	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21491407	21491731	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21491732	21491805	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21491806	21492869	0.5	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21491806	21492869	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21492870	21493097	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21493098	21493406	1	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21493098	21493406	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21493407	21493550	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21493551	21493878	0.99	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21493551	21493878	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21493879	21493991	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21493992	21494078	1	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21493992	21494078	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494079	21494168	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21494169	21494385	0.87	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21494169	21494385	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494386	21494524	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21494525	21494601	0.88	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21494525	21494601	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494602	21494825	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21494826	21494904	1	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21494826	21494904	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21494905	21494999	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495000	21495088	0.99	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495000	21495088	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495089	21495201	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495202	21495279	0.99	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495202	21495279	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495280	21495376	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495377	21495463	1	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495377	21495463	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495464	21495560	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495561	21495648	1	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495561	21495648	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495649	21495793	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21495794	21495880	1	-	2	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21495794	21495880	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21495881	21496016	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21496017	21496156	1	-	1	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21496017	21496156	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21496157	21496289	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21496290	21496357	1	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21496290	21496357	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	intron	21496358	21496566	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	CDS	21496567	21496590	1	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	exon	21496567	21496590	.	-	.	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
Phchi.S3	AUGUSTUS	start_codon	21496588	21496590	.	-	0	transcript_id "Phchi.S3G312600.t2"; gene_id "Phchi.S3G312600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13770.t1 is derived from g12237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8832288	8836522	.	-	.	Phchi.S3G108900
Phchi.S3	AUGUSTUS	transcript	8832288	8836522	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	stop_codon	8832285	8832287	.	-	0	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8832288	8832557	0.97	-	0	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8832288	8832557	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8832558	8832630	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8832631	8832772	1	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8832631	8832772	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8832773	8832849	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8832850	8833039	1	-	2	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8832850	8833039	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8833040	8833128	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8833129	8833194	1	-	2	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8833129	8833194	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8833195	8833280	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8833281	8833407	1	-	0	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8833281	8833407	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8833408	8833512	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8833513	8833766	0.95	-	2	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8833513	8833766	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8833767	8833875	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8833876	8834141	0.94	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8833876	8834141	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8834142	8834261	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8834262	8834333	1	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8834262	8834333	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8834334	8834410	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8834411	8834482	1	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8834411	8834482	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8834483	8834559	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8834560	8834628	1	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8834560	8834628	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8834629	8834746	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8834747	8834818	0.99	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8834747	8834818	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8834819	8834907	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8834908	8835037	1	-	2	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8834908	8835037	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8835038	8835174	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8835175	8835689	0.65	-	1	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8835175	8835689	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8835690	8835769	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8835770	8836343	0.95	-	2	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8835770	8836343	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	intron	8836344	8836446	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	CDS	8836447	8836522	0.71	-	0	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	exon	8836447	8836522	.	-	.	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
Phchi.S3	AUGUSTUS	start_codon	8836520	8836522	.	-	0	transcript_id "Phchi.S3G108900.t1"; gene_id "Phchi.S3G108900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15098.t1 is derived from g13566.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17060317	17061840	.	-	.	Phchi.S3G241700
Phchi.S3	AUGUSTUS	transcript	17060317	17061840	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	stop_codon	17060314	17060316	.	-	0	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17060317	17060594	1	-	2	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17060317	17060594	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17060595	17060713	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17060714	17060859	1	-	1	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17060714	17060859	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17060860	17060959	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17060960	17060964	0.99	-	0	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17060960	17060964	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17060965	17061058	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17061059	17061419	0.7	-	1	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17061059	17061419	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17061420	17061575	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17061576	17061669	0.98	-	2	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17061576	17061669	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17061670	17061806	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17061807	17061840	0.99	-	0	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17061807	17061840	.	-	.	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	start_codon	17061838	17061840	.	-	0	transcript_id "Phchi.S3G241700.t1"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	transcript	17060317	17061840	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	stop_codon	17060314	17060316	.	-	0	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17060317	17060594	1	-	2	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17060317	17060594	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17060595	17060713	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17060714	17060859	1	-	1	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17060714	17060859	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17060860	17061005	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17061006	17061419	0.72	-	1	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17061006	17061419	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17061420	17061575	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17061576	17061669	0.95	-	2	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17061576	17061669	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	intron	17061670	17061806	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	CDS	17061807	17061840	0.99	-	0	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	exon	17061807	17061840	.	-	.	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
Phchi.S3	AUGUSTUS	start_codon	17061838	17061840	.	-	0	transcript_id "Phchi.S3G241700.t2"; gene_id "Phchi.S3G241700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14626.t1 is derived from g13094.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13827747	13829944	.	+	.	Phchi.S3G194500
Phchi.S3	AUGUSTUS	transcript	13827747	13829944	.	+	.	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	start_codon	13827747	13827749	.	+	0	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	CDS	13827747	13827970	0.64	+	0	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	exon	13827747	13827970	.	+	.	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	intron	13827971	13828077	.	+	.	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	CDS	13828078	13829944	0.65	+	1	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	exon	13828078	13829944	.	+	.	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
Phchi.S3	AUGUSTUS	stop_codon	13829945	13829947	.	+	0	transcript_id "Phchi.S3G194500.t1"; gene_id "Phchi.S3G194500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3914.t1 is derived from g1083.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6414712	6416246	.	-	.	Phchi.S1G107300
Phchi.S1	AUGUSTUS	transcript	6414712	6416246	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	stop_codon	6414709	6414711	.	-	0	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	CDS	6414712	6414942	0.98	-	0	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	exon	6414712	6414942	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	intron	6414943	6415022	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	CDS	6415023	6415256	0.99	-	0	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	exon	6415023	6415256	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	intron	6415257	6415357	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	CDS	6415358	6415682	0.91	-	1	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	exon	6415358	6415682	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	intron	6415683	6415788	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	CDS	6415789	6416031	0.98	-	1	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	exon	6415789	6416031	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	intron	6416032	6416160	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	CDS	6416161	6416246	0.81	-	0	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	exon	6416161	6416246	.	-	.	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
Phchi.S1	AUGUSTUS	start_codon	6416244	6416246	.	-	0	transcript_id "Phchi.S1G107300.t1"; gene_id "Phchi.S1G107300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2719.t1 is derived from g9639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8396345	8398782	.	-	.	Phchi.S5G132800
Phchi.S5	AUGUSTUS	transcript	8396345	8398782	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	stop_codon	8396342	8396344	.	-	0	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8396345	8396472	0.99	-	2	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8396345	8396472	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8396473	8396581	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8396582	8396798	0.91	-	0	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8396582	8396798	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8396799	8396884	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8396885	8396944	0.87	-	0	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8396885	8396944	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8396945	8397045	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8397046	8397632	1	-	2	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8397046	8397632	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8397633	8397762	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8397763	8397891	1	-	2	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8397763	8397891	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8397892	8398011	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8398012	8398259	1	-	1	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8398012	8398259	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8398260	8398348	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8398349	8398468	0.48	-	1	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8398349	8398468	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	intron	8398469	8398561	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	CDS	8398562	8398782	0.47	-	0	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	exon	8398562	8398782	.	-	.	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
Phchi.S5	AUGUSTUS	start_codon	8398780	8398782	.	-	0	transcript_id "Phchi.S5G132800.t1"; gene_id "Phchi.S5G132800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1452.t1 is derived from g8371.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	957380	958590	.	+	.	Phchi.S5G006100
Phchi.S5	AUGUSTUS	transcript	957380	958590	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	start_codon	957380	957382	.	+	0	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	CDS	957380	957446	0.48	+	0	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	exon	957380	957446	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	intron	957447	957588	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	CDS	957589	957740	1	+	2	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	exon	957589	957740	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	intron	957741	957820	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	CDS	957821	957945	1	+	0	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	exon	957821	957945	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	intron	957946	958043	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	CDS	958044	958232	1	+	1	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	exon	958044	958232	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	intron	958233	958330	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	CDS	958331	958382	1	+	1	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	exon	958331	958382	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	intron	958383	958476	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	CDS	958477	958590	0.96	+	0	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	exon	958477	958590	.	+	.	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
Phchi.S5	AUGUSTUS	stop_codon	958591	958593	.	+	0	transcript_id "Phchi.S5G006100.t1"; gene_id "Phchi.S5G006100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8956.t1 is derived from g6131.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38842178	38844699	.	+	.	Phchi.S1G611500
Phchi.S1	AUGUSTUS	transcript	38842178	38844699	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	start_codon	38842178	38842180	.	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38842178	38842192	0.71	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38842178	38842192	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38842193	38842283	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38842284	38842458	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38842284	38842458	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38842459	38842559	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38842560	38842657	0.78	+	2	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38842560	38842657	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38842658	38842800	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38842801	38843112	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38842801	38843112	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38843113	38843254	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38843255	38843434	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38843255	38843434	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38843435	38843516	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38843517	38843611	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38843517	38843611	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38843612	38843749	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38843750	38843825	1	+	1	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38843750	38843825	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38843826	38843934	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38843935	38844012	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38843935	38844012	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38844013	38844103	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38844104	38844197	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38844104	38844197	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38844198	38844278	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38844279	38844328	1	+	2	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38844279	38844328	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38844329	38844415	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38844416	38844529	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38844416	38844529	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	intron	38844530	38844618	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	CDS	38844619	38844699	1	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	exon	38844619	38844699	.	+	.	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
Phchi.S1	AUGUSTUS	stop_codon	38844700	38844702	.	+	0	transcript_id "Phchi.S1G611500.t1"; gene_id "Phchi.S1G611500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5773.t1 is derived from g2943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18886013	18886759	.	-	.	Phchi.S1G293200
Phchi.S1	AUGUSTUS	transcript	18886013	18886759	.	-	.	transcript_id "Phchi.S1G293200.t1"; gene_id "Phchi.S1G293200"
Phchi.S1	AUGUSTUS	stop_codon	18886010	18886012	.	-	0	transcript_id "Phchi.S1G293200.t1"; gene_id "Phchi.S1G293200"
Phchi.S1	AUGUSTUS	CDS	18886013	18886759	0.71	-	0	transcript_id "Phchi.S1G293200.t1"; gene_id "Phchi.S1G293200"
Phchi.S1	AUGUSTUS	exon	18886013	18886759	.	-	.	transcript_id "Phchi.S1G293200.t1"; gene_id "Phchi.S1G293200"
Phchi.S1	AUGUSTUS	start_codon	18886757	18886759	.	-	0	transcript_id "Phchi.S1G293200.t1"; gene_id "Phchi.S1G293200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5979.t1 is derived from g3150.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20213720	20214697	.	-	.	Phchi.S1G313800
Phchi.S1	AUGUSTUS	transcript	20213720	20214697	.	-	.	transcript_id "Phchi.S1G313800.t1"; gene_id "Phchi.S1G313800"
Phchi.S1	AUGUSTUS	stop_codon	20213717	20213719	.	-	0	transcript_id "Phchi.S1G313800.t1"; gene_id "Phchi.S1G313800"
Phchi.S1	AUGUSTUS	CDS	20213720	20214697	0.99	-	0	transcript_id "Phchi.S1G313800.t1"; gene_id "Phchi.S1G313800"
Phchi.S1	AUGUSTUS	exon	20213720	20214697	.	-	.	transcript_id "Phchi.S1G313800.t1"; gene_id "Phchi.S1G313800"
Phchi.S1	AUGUSTUS	start_codon	20214695	20214697	.	-	0	transcript_id "Phchi.S1G313800.t1"; gene_id "Phchi.S1G313800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5163.t1 is derived from g2333.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15229531	15231388	.	+	.	Phchi.S1G232200
Phchi.S1	AUGUSTUS	transcript	15229531	15231388	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	start_codon	15229531	15229533	.	+	0	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	CDS	15229531	15230204	0.28	+	0	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	exon	15229531	15230204	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	intron	15230205	15230305	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	CDS	15230306	15230345	0.61	+	1	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	exon	15230306	15230345	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	intron	15230346	15230443	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	CDS	15230444	15230513	1	+	0	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	exon	15230444	15230513	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	intron	15230514	15230605	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	CDS	15230606	15230739	1	+	2	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	exon	15230606	15230739	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	intron	15230740	15230827	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	CDS	15230828	15231073	1	+	0	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	exon	15230828	15231073	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	intron	15231074	15231160	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	CDS	15231161	15231388	0.99	+	0	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	exon	15231161	15231388	.	+	.	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
Phchi.S1	AUGUSTUS	stop_codon	15231389	15231391	.	+	0	transcript_id "Phchi.S1G232200.t1"; gene_id "Phchi.S1G232200"
# This transcript jg5155.t2 is derived from g2325.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5156.t1 is derived from g2326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15183748	15184495	.	+	.	Phchi.S1G231500
Phchi.S1	AUGUSTUS	transcript	15183748	15184495	.	+	.	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	start_codon	15183748	15183750	.	+	0	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	CDS	15183748	15183864	0.99	+	0	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	exon	15183748	15183864	.	+	.	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	intron	15183865	15184035	.	+	.	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	CDS	15184036	15184123	0.95	+	0	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	exon	15184036	15184123	.	+	.	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	intron	15184124	15184250	.	+	.	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	CDS	15184251	15184495	0.75	+	2	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	exon	15184251	15184495	.	+	.	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
Phchi.S1	AUGUSTUS	stop_codon	15184496	15184498	.	+	0	transcript_id "Phchi.S1G231500.t1"; gene_id "Phchi.S1G231500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15206.t1 is derived from g13674.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17562205	17563296	.	+	.	Phchi.S3G252500
Phchi.S3	AUGUSTUS	transcript	17562205	17563296	.	+	.	transcript_id "Phchi.S3G252500.t1"; gene_id "Phchi.S3G252500"
Phchi.S3	AUGUSTUS	start_codon	17562205	17562207	.	+	0	transcript_id "Phchi.S3G252500.t1"; gene_id "Phchi.S3G252500"
Phchi.S3	AUGUSTUS	CDS	17562205	17563296	0.24	+	0	transcript_id "Phchi.S3G252500.t1"; gene_id "Phchi.S3G252500"
Phchi.S3	AUGUSTUS	exon	17562205	17563296	.	+	.	transcript_id "Phchi.S3G252500.t1"; gene_id "Phchi.S3G252500"
Phchi.S3	AUGUSTUS	stop_codon	17563297	17563299	.	+	0	transcript_id "Phchi.S3G252500.t1"; gene_id "Phchi.S3G252500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10112.t1 is derived from g7288.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45785134	45786195	.	-	.	Phchi.S1G727100
Phchi.S1	AUGUSTUS	transcript	45785134	45786195	.	-	.	transcript_id "Phchi.S1G727100.t1"; gene_id "Phchi.S1G727100"
Phchi.S1	AUGUSTUS	stop_codon	45785131	45785133	.	-	0	transcript_id "Phchi.S1G727100.t1"; gene_id "Phchi.S1G727100"
Phchi.S1	AUGUSTUS	CDS	45785134	45786195	1	-	0	transcript_id "Phchi.S1G727100.t1"; gene_id "Phchi.S1G727100"
Phchi.S1	AUGUSTUS	exon	45785134	45786195	.	-	.	transcript_id "Phchi.S1G727100.t1"; gene_id "Phchi.S1G727100"
Phchi.S1	AUGUSTUS	start_codon	45786193	45786195	.	-	0	transcript_id "Phchi.S1G727100.t1"; gene_id "Phchi.S1G727100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3675.t1 is derived from g844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5143127	5144443	.	+	.	Phchi.S1G083400
Phchi.S1	AUGUSTUS	transcript	5143127	5144443	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	start_codon	5143127	5143129	.	+	0	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	CDS	5143127	5143376	0.7	+	0	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	exon	5143127	5143376	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	intron	5143377	5143762	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	CDS	5143763	5143773	0.91	+	2	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	exon	5143763	5143773	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	intron	5143774	5144127	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	CDS	5144128	5144237	0.96	+	0	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	exon	5144128	5144237	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	intron	5144238	5144385	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	CDS	5144386	5144443	1	+	1	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	exon	5144386	5144443	.	+	.	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
Phchi.S1	AUGUSTUS	stop_codon	5144444	5144446	.	+	0	transcript_id "Phchi.S1G083400.t1"; gene_id "Phchi.S1G083400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10132.t1 is derived from g7308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45906651	45911211	.	-	.	Phchi.S1G729100
Phchi.S1	AUGUSTUS	transcript	45906651	45911211	.	-	.	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	stop_codon	45906648	45906650	.	-	0	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	CDS	45906651	45907784	0.93	-	0	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	exon	45906651	45907784	.	-	.	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	intron	45907785	45907897	.	-	.	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	CDS	45907898	45909357	0.92	-	2	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	exon	45907898	45909357	.	-	.	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	intron	45909358	45909512	.	-	.	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	CDS	45909513	45911211	0.81	-	0	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	exon	45909513	45911211	.	-	.	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
Phchi.S1	AUGUSTUS	start_codon	45911209	45911211	.	-	0	transcript_id "Phchi.S1G729100.t1"; gene_id "Phchi.S1G729100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2947.t1 is derived from g116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	712759	714271	.	+	.	Phchi.S1G010600
Phchi.S1	AUGUSTUS	transcript	712759	714271	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	start_codon	712759	712761	.	+	0	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	CDS	712759	713280	0.99	+	0	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	exon	712759	713280	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	intron	713281	713435	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	CDS	713436	713701	1	+	0	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	exon	713436	713701	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	intron	713702	713846	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	CDS	713847	713940	1	+	1	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	exon	713847	713940	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	intron	713941	714037	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	CDS	714038	714271	1	+	0	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	exon	714038	714271	.	+	.	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
Phchi.S1	AUGUSTUS	stop_codon	714272	714274	.	+	0	transcript_id "Phchi.S1G010600.t1"; gene_id "Phchi.S1G010600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11979.t1 is derived from g7654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	312718	313080	.	+	.	Phchi.S2G005900
Phchi.S2	AUGUSTUS	transcript	312718	313080	.	+	.	transcript_id "Phchi.S2G005900.t1"; gene_id "Phchi.S2G005900"
Phchi.S2	AUGUSTUS	start_codon	312718	312720	.	+	0	transcript_id "Phchi.S2G005900.t1"; gene_id "Phchi.S2G005900"
Phchi.S2	AUGUSTUS	CDS	312718	313080	0.01	+	0	transcript_id "Phchi.S2G005900.t1"; gene_id "Phchi.S2G005900"
Phchi.S2	AUGUSTUS	exon	312718	313080	.	+	.	transcript_id "Phchi.S2G005900.t1"; gene_id "Phchi.S2G005900"
Phchi.S2	AUGUSTUS	stop_codon	313081	313083	.	+	0	transcript_id "Phchi.S2G005900.t1"; gene_id "Phchi.S2G005900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4677.t1 is derived from g1847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11782748	11783511	.	+	.	Phchi.S1G183600
Phchi.S1	AUGUSTUS	transcript	11782748	11783511	.	+	.	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	start_codon	11782748	11782750	.	+	0	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	CDS	11782748	11782788	0.72	+	0	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	exon	11782748	11782788	.	+	.	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	intron	11782789	11782862	.	+	.	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	CDS	11782863	11783511	0.33	+	1	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	exon	11782863	11783511	.	+	.	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
Phchi.S1	AUGUSTUS	stop_codon	11783512	11783514	.	+	0	transcript_id "Phchi.S1G183600.t1"; gene_id "Phchi.S1G183600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14075.t1 is derived from g12542.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10669528	10669948	.	+	.	Phchi.S3G139400
Phchi.S3	AUGUSTUS	transcript	10669528	10669948	.	+	.	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	start_codon	10669528	10669530	.	+	0	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	CDS	10669528	10669741	0.94	+	0	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	exon	10669528	10669741	.	+	.	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	intron	10669742	10669940	.	+	.	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	CDS	10669941	10669948	1	+	2	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	exon	10669941	10669948	.	+	.	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
Phchi.S3	AUGUSTUS	stop_codon	10669949	10669951	.	+	0	transcript_id "Phchi.S3G139400.t1"; gene_id "Phchi.S3G139400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13618.t1 is derived from g12085.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7773858	7774499	.	+	.	Phchi.S3G093700
Phchi.S3	AUGUSTUS	transcript	7773858	7774499	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	start_codon	7773858	7773860	.	+	0	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7773858	7773892	0.83	+	0	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7773858	7773892	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	intron	7773893	7774074	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7774075	7774126	0.98	+	1	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7774075	7774126	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	intron	7774127	7774210	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7774211	7774216	0.98	+	0	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7774211	7774216	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	intron	7774217	7774295	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7774296	7774499	0.89	+	0	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7774296	7774499	.	+	.	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	stop_codon	7774500	7774502	.	+	0	transcript_id "Phchi.S3G093700.t1"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	transcript	7773865	7774499	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	start_codon	7773865	7773867	.	+	0	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7773865	7773896	0.83	+	0	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7773865	7773896	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	intron	7773897	7774074	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7774075	7774126	0.83	+	1	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7774075	7774126	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	intron	7774127	7774210	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7774211	7774216	0.8	+	0	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7774211	7774216	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	intron	7774217	7774295	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	CDS	7774296	7774499	0.8	+	0	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	exon	7774296	7774499	.	+	.	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
Phchi.S3	AUGUSTUS	stop_codon	7774500	7774502	.	+	0	transcript_id "Phchi.S3G093700.t2"; gene_id "Phchi.S3G093700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14854.t1 is derived from g13322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15073439	15073913	.	+	.	Phchi.S3G217300
Phchi.S3	AUGUSTUS	transcript	15073439	15073913	.	+	.	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	start_codon	15073439	15073441	.	+	0	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	CDS	15073439	15073615	1	+	0	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	exon	15073439	15073615	.	+	.	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	intron	15073616	15073697	.	+	.	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	CDS	15073698	15073913	1	+	0	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	exon	15073698	15073913	.	+	.	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
Phchi.S3	AUGUSTUS	stop_codon	15073914	15073916	.	+	0	transcript_id "Phchi.S3G217300.t1"; gene_id "Phchi.S3G217300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1598.t1 is derived from g8517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1945383	1949743	.	+	.	Phchi.S5G020700
Phchi.S5	AUGUSTUS	transcript	1945383	1949743	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	start_codon	1945383	1945385	.	+	0	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1945383	1946883	0.41	+	0	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1945383	1946883	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	intron	1946884	1946995	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1946996	1947242	0.66	+	2	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1946996	1947242	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	intron	1947243	1947358	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1947359	1948686	0.34	+	1	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1947359	1948686	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	intron	1948687	1948782	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1948783	1949039	1	+	2	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1948783	1949039	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	intron	1949040	1949128	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1949129	1949291	0.46	+	0	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1949129	1949291	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	intron	1949292	1949575	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1949576	1949611	0.52	+	2	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1949576	1949611	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	intron	1949612	1949708	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	CDS	1949709	1949743	0.99	+	2	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	exon	1949709	1949743	.	+	.	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
Phchi.S5	AUGUSTUS	stop_codon	1949744	1949746	.	+	0	transcript_id "Phchi.S5G020700.t1"; gene_id "Phchi.S5G020700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9011.t1 is derived from g6186.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39135240	39139197	.	+	.	Phchi.S1G617000
Phchi.S1	AUGUSTUS	transcript	39136594	39139197	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	start_codon	39136594	39136596	.	+	0	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39136594	39136755	0.9	+	0	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39136594	39136755	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	intron	39136756	39136973	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39136974	39136995	0.75	+	0	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39136974	39136995	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	intron	39136996	39137322	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39137323	39138879	0.36	+	2	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39137323	39138879	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	intron	39138880	39139057	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39139058	39139197	0.93	+	2	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39139058	39139197	.	+	.	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	stop_codon	39139198	39139200	.	+	0	transcript_id "Phchi.S1G617000.t1"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	transcript	39135240	39139197	.	+	.	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	start_codon	39135240	39135242	.	+	0	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39135240	39136755	0.84	+	0	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39135240	39136755	.	+	.	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	intron	39136756	39137322	.	+	.	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39137323	39138879	0.21	+	2	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39137323	39138879	.	+	.	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	intron	39138880	39139057	.	+	.	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39139058	39139197	0.98	+	2	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39139058	39139197	.	+	.	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	stop_codon	39139198	39139200	.	+	0	transcript_id "Phchi.S1G617000.t2"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	transcript	39135240	39136820	.	+	.	transcript_id "Phchi.S1G617000.t3"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	start_codon	39135240	39135242	.	+	0	transcript_id "Phchi.S1G617000.t3"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	CDS	39135240	39136820	0.97	+	0	transcript_id "Phchi.S1G617000.t3"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	exon	39135240	39136820	.	+	.	transcript_id "Phchi.S1G617000.t3"; gene_id "Phchi.S1G617000"
Phchi.S1	AUGUSTUS	stop_codon	39136821	39136823	.	+	0	transcript_id "Phchi.S1G617000.t3"; gene_id "Phchi.S1G617000"
# This transcript jg7122.t2 is derived from g4294.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7122.t3 is derived from g4294.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7123.t1 is derived from g4295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27071510	27071977	.	-	.	Phchi.S1G428200
Phchi.S1	AUGUSTUS	transcript	27071510	27071977	.	-	.	transcript_id "Phchi.S1G428200.t1"; gene_id "Phchi.S1G428200"
Phchi.S1	AUGUSTUS	stop_codon	27071507	27071509	.	-	0	transcript_id "Phchi.S1G428200.t1"; gene_id "Phchi.S1G428200"
Phchi.S1	AUGUSTUS	CDS	27071510	27071977	0.95	-	0	transcript_id "Phchi.S1G428200.t1"; gene_id "Phchi.S1G428200"
Phchi.S1	AUGUSTUS	exon	27071510	27071977	.	-	.	transcript_id "Phchi.S1G428200.t1"; gene_id "Phchi.S1G428200"
Phchi.S1	AUGUSTUS	start_codon	27071975	27071977	.	-	0	transcript_id "Phchi.S1G428200.t1"; gene_id "Phchi.S1G428200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6477.t1 is derived from g3649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23191550	23192710	.	-	.	Phchi.S1G363600
Phchi.S1	AUGUSTUS	transcript	23191550	23192710	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	stop_codon	23191547	23191549	.	-	0	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23191550	23191551	0.73	-	2	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23191550	23191551	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23191552	23191716	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23191717	23191805	0.73	-	1	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23191717	23191805	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23191806	23191914	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23191915	23191963	1	-	2	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23191915	23191963	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23191964	23192183	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23192184	23192289	0.99	-	0	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23192184	23192289	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23192290	23192420	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23192421	23192495	1	-	0	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23192421	23192495	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23192496	23192632	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23192633	23192710	0.79	-	0	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23192633	23192710	.	-	.	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	start_codon	23192708	23192710	.	-	0	transcript_id "Phchi.S1G363600.t1"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	transcript	23191550	23192523	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	stop_codon	23191547	23191549	.	-	0	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23191550	23191551	0.6	-	2	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23191550	23191551	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23191552	23191716	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23191717	23191805	0.6	-	1	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23191717	23191805	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23191806	23191914	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23191915	23191963	0.99	-	2	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23191915	23191963	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23191964	23192183	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23192184	23192289	1	-	0	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23192184	23192289	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	intron	23192290	23192517	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	CDS	23192518	23192523	0.83	-	0	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	exon	23192518	23192523	.	-	.	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
Phchi.S1	AUGUSTUS	start_codon	23192521	23192523	.	-	0	transcript_id "Phchi.S1G363600.t2"; gene_id "Phchi.S1G363600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7379.t1 is derived from g4551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28835196	28839413	.	+	.	Phchi.S1G453800
Phchi.S1	AUGUSTUS	transcript	28835196	28839413	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	start_codon	28835196	28835198	.	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28835196	28835327	0.64	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28835196	28835327	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28835328	28835422	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28835423	28835773	0.88	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28835423	28835773	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28835774	28835882	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28835883	28836014	0.99	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28835883	28836014	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28836015	28836122	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28836123	28836255	0.99	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28836123	28836255	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28836256	28836409	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28836410	28836523	1	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28836410	28836523	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28836524	28836614	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28836615	28836688	1	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28836615	28836688	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28836689	28836809	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28836810	28836884	1	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28836810	28836884	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28836885	28836994	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28836995	28837087	1	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28836995	28837087	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28837088	28837174	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28837175	28837235	1	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28837175	28837235	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28837236	28837339	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28837340	28837672	0.98	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28837340	28837672	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28837673	28837749	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28837750	28837876	1	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28837750	28837876	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28837877	28837983	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28837984	28838083	0.95	+	1	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28837984	28838083	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28838084	28838176	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28838177	28838246	1	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28838177	28838246	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28838247	28838378	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28838379	28838531	1	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28838379	28838531	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28838532	28838612	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28838613	28838708	1	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28838613	28838708	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28838709	28838925	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28838926	28839241	1	+	2	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28838926	28839241	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	intron	28839242	28839319	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	CDS	28839320	28839413	0.98	+	1	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	exon	28839320	28839413	.	+	.	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
Phchi.S1	AUGUSTUS	stop_codon	28839414	28839416	.	+	0	transcript_id "Phchi.S1G453800.t1"; gene_id "Phchi.S1G453800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5381.t1 is derived from g2551.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16591071	16595570	.	+	.	Phchi.S1G254000
Phchi.S1	AUGUSTUS	transcript	16591071	16595570	.	+	.	transcript_id "Phchi.S1G254000.t1"; gene_id "Phchi.S1G254000"
Phchi.S1	AUGUSTUS	start_codon	16591071	16591073	.	+	0	transcript_id "Phchi.S1G254000.t1"; gene_id "Phchi.S1G254000"
Phchi.S1	AUGUSTUS	CDS	16591071	16595570	0.95	+	0	transcript_id "Phchi.S1G254000.t1"; gene_id "Phchi.S1G254000"
Phchi.S1	AUGUSTUS	exon	16591071	16595570	.	+	.	transcript_id "Phchi.S1G254000.t1"; gene_id "Phchi.S1G254000"
Phchi.S1	AUGUSTUS	stop_codon	16595571	16595573	.	+	0	transcript_id "Phchi.S1G254000.t1"; gene_id "Phchi.S1G254000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1128.t1 is derived from g10911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7860282	7862983	.	-	.	Phchi.S6G108700
Phchi.S6	AUGUSTUS	transcript	7860282	7862983	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	stop_codon	7860279	7860281	.	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7860282	7860494	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7860282	7860494	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7860495	7860651	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7860652	7860753	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7860652	7860753	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7860754	7860866	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7860867	7861061	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7860867	7861061	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7861062	7861146	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7861147	7861272	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7861147	7861272	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7861273	7861369	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7861370	7861651	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7861370	7861651	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7861652	7861782	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7861783	7861956	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7861783	7861956	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7861957	7862091	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7862092	7862253	1	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7862092	7862253	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7862254	7862338	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7862339	7862402	1	-	1	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7862339	7862402	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	intron	7862403	7862561	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	CDS	7862562	7862983	0.58	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	exon	7862562	7862983	.	-	.	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
Phchi.S6	AUGUSTUS	start_codon	7862981	7862983	.	-	0	transcript_id "Phchi.S6G108700.t1"; gene_id "Phchi.S6G108700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4295.t1 is derived from g1464.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9489057	9490157	.	-	.	Phchi.S1G145400
Phchi.S1	AUGUSTUS	transcript	9489057	9490157	.	-	.	transcript_id "Phchi.S1G145400.t1"; gene_id "Phchi.S1G145400"
Phchi.S1	AUGUSTUS	stop_codon	9489054	9489056	.	-	0	transcript_id "Phchi.S1G145400.t1"; gene_id "Phchi.S1G145400"
Phchi.S1	AUGUSTUS	CDS	9489057	9490157	0.95	-	0	transcript_id "Phchi.S1G145400.t1"; gene_id "Phchi.S1G145400"
Phchi.S1	AUGUSTUS	exon	9489057	9490157	.	-	.	transcript_id "Phchi.S1G145400.t1"; gene_id "Phchi.S1G145400"
Phchi.S1	AUGUSTUS	start_codon	9490155	9490157	.	-	0	transcript_id "Phchi.S1G145400.t1"; gene_id "Phchi.S1G145400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8301.t1 is derived from g5476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35160193	35161825	.	-	.	Phchi.S1G546000
Phchi.S1	AUGUSTUS	transcript	35160193	35161825	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	stop_codon	35160190	35160192	.	-	0	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	CDS	35160193	35160240	1	-	0	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	exon	35160193	35160240	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	intron	35160241	35160334	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	CDS	35160335	35160401	1	-	1	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	exon	35160335	35160401	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	intron	35160402	35160523	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	CDS	35160524	35160708	1	-	0	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	exon	35160524	35160708	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	intron	35160709	35160841	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	CDS	35160842	35161825	1	-	0	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	exon	35160842	35161825	.	-	.	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
Phchi.S1	AUGUSTUS	start_codon	35161823	35161825	.	-	0	transcript_id "Phchi.S1G546000.t1"; gene_id "Phchi.S1G546000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4511.t1 is derived from g1681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10891044	10892188	.	+	.	Phchi.S1G167000
Phchi.S1	AUGUSTUS	transcript	10891044	10892188	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	start_codon	10891044	10891046	.	+	0	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	CDS	10891044	10891284	1	+	0	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	exon	10891044	10891284	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	intron	10891285	10891415	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	CDS	10891416	10891541	0.91	+	2	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	exon	10891416	10891541	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	intron	10891542	10891715	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	CDS	10891716	10891991	0.58	+	2	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	exon	10891716	10891991	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	intron	10891992	10892120	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	CDS	10892121	10892188	0.8	+	2	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	exon	10892121	10892188	.	+	.	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
Phchi.S1	AUGUSTUS	stop_codon	10892189	10892191	.	+	0	transcript_id "Phchi.S1G167000.t1"; gene_id "Phchi.S1G167000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg744.t1 is derived from g10526.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5290015	5291795	.	-	.	Phchi.S6G070300
Phchi.S6	AUGUSTUS	transcript	5290015	5291795	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	stop_codon	5290012	5290014	.	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5290015	5290072	1	-	1	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5290015	5290072	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5290073	5290156	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5290157	5290215	1	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5290157	5290215	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5290216	5290343	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5290344	5290446	1	-	1	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5290344	5290446	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5290447	5290558	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5290559	5290638	1	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5290559	5290638	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5290639	5290716	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5290717	5290799	1	-	2	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5290717	5290799	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5290800	5290887	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5290888	5290936	1	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5290888	5290936	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5290937	5291010	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5291011	5291076	0.82	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5291011	5291076	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5291077	5291398	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5291399	5291573	0.81	-	1	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5291399	5291573	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	intron	5291574	5291691	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	CDS	5291692	5291795	0.64	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	exon	5291692	5291795	.	-	.	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
Phchi.S6	AUGUSTUS	start_codon	5291793	5291795	.	-	0	transcript_id "Phchi.S6G070300.t1"; gene_id "Phchi.S6G070300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3408.t1 is derived from g577.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3375408	3375977	.	-	.	Phchi.S1G056700
Phchi.S1	AUGUSTUS	transcript	3375408	3375977	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	stop_codon	3375405	3375407	.	-	0	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	CDS	3375408	3375457	1	-	2	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	exon	3375408	3375457	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	intron	3375458	3375531	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	CDS	3375532	3375615	1	-	2	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	exon	3375532	3375615	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	intron	3375616	3375701	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	CDS	3375702	3375738	1	-	0	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	exon	3375702	3375738	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	intron	3375739	3375869	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	CDS	3375870	3375977	0.59	-	0	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	exon	3375870	3375977	.	-	.	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
Phchi.S1	AUGUSTUS	start_codon	3375975	3375977	.	-	0	transcript_id "Phchi.S1G056700.t1"; gene_id "Phchi.S1G056700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5891.t1 is derived from g3061.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19623335	19625709	.	+	.	Phchi.S1G305000
Phchi.S1	AUGUSTUS	transcript	19623335	19625709	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	start_codon	19623335	19623337	.	+	0	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623335	19623398	0.32	+	0	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623335	19623398	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19623399	19623560	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623561	19623688	0.74	+	2	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623561	19623688	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19623689	19623786	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623787	19623879	1	+	0	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623787	19623879	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19623880	19623967	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623968	19625517	0.24	+	0	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623968	19625517	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19625518	19625639	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19625640	19625709	0.72	+	1	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19625640	19625709	.	+	.	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	stop_codon	19625710	19625712	.	+	0	transcript_id "Phchi.S1G305000.t1"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	transcript	19623335	19625709	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	start_codon	19623335	19623337	.	+	0	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623335	19623398	0.21	+	0	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623335	19623398	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19623399	19623560	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623561	19623688	0.72	+	2	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623561	19623688	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19623689	19623786	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623787	19623879	1	+	0	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623787	19623879	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19623880	19623955	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19623956	19625517	0.19	+	0	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19623956	19625517	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	intron	19625518	19625639	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	CDS	19625640	19625709	0.67	+	1	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	exon	19625640	19625709	.	+	.	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
Phchi.S1	AUGUSTUS	stop_codon	19625710	19625712	.	+	0	transcript_id "Phchi.S1G305000.t2"; gene_id "Phchi.S1G305000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11685.t1 is derived from g15736.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7657707	7658462	.	+	.	Phchi.S4G126700
Phchi.S4	AUGUSTUS	transcript	7657707	7658462	.	+	.	transcript_id "Phchi.S4G126700.t1"; gene_id "Phchi.S4G126700"
Phchi.S4	AUGUSTUS	start_codon	7657707	7657709	.	+	0	transcript_id "Phchi.S4G126700.t1"; gene_id "Phchi.S4G126700"
Phchi.S4	AUGUSTUS	CDS	7657707	7658462	0.97	+	0	transcript_id "Phchi.S4G126700.t1"; gene_id "Phchi.S4G126700"
Phchi.S4	AUGUSTUS	exon	7657707	7658462	.	+	.	transcript_id "Phchi.S4G126700.t1"; gene_id "Phchi.S4G126700"
Phchi.S4	AUGUSTUS	stop_codon	7658463	7658465	.	+	0	transcript_id "Phchi.S4G126700.t1"; gene_id "Phchi.S4G126700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1176.t1 is derived from g10959.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8309581	8311478	.	+	.	Phchi.S6G113500
Phchi.S6	AUGUSTUS	transcript	8309581	8311478	.	+	.	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	start_codon	8309581	8309583	.	+	0	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	CDS	8309581	8310171	0.51	+	0	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	exon	8309581	8310171	.	+	.	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	intron	8310172	8310248	.	+	.	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	CDS	8310249	8311478	0.86	+	0	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	exon	8310249	8311478	.	+	.	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	stop_codon	8311479	8311481	.	+	0	transcript_id "Phchi.S6G113500.t1"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	transcript	8309704	8311478	.	+	.	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	start_codon	8309704	8309706	.	+	0	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	CDS	8309704	8310171	0.58	+	0	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	exon	8309704	8310171	.	+	.	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	intron	8310172	8310248	.	+	.	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	CDS	8310249	8311478	0.88	+	0	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	exon	8310249	8311478	.	+	.	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
Phchi.S6	AUGUSTUS	stop_codon	8311479	8311481	.	+	0	transcript_id "Phchi.S6G113500.t2"; gene_id "Phchi.S6G113500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7678.t1 is derived from g4852.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30587783	30588628	.	-	.	Phchi.S1G483700
Phchi.S1	AUGUSTUS	transcript	30587783	30588628	.	-	.	transcript_id "Phchi.S1G483700.t1"; gene_id "Phchi.S1G483700"
Phchi.S1	AUGUSTUS	stop_codon	30587780	30587782	.	-	0	transcript_id "Phchi.S1G483700.t1"; gene_id "Phchi.S1G483700"
Phchi.S1	AUGUSTUS	CDS	30587783	30588628	0.9	-	0	transcript_id "Phchi.S1G483700.t1"; gene_id "Phchi.S1G483700"
Phchi.S1	AUGUSTUS	exon	30587783	30588628	.	-	.	transcript_id "Phchi.S1G483700.t1"; gene_id "Phchi.S1G483700"
Phchi.S1	AUGUSTUS	start_codon	30588626	30588628	.	-	0	transcript_id "Phchi.S1G483700.t1"; gene_id "Phchi.S1G483700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1568.t1 is derived from g8487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1795299	1797562	.	-	.	Phchi.S5G017700
Phchi.S5	AUGUSTUS	transcript	1795299	1797562	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	stop_codon	1795296	1795298	.	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1795299	1795352	0.94	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1795299	1795352	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1795353	1795428	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1795429	1795486	0.97	-	1	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1795429	1795486	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1795487	1795587	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1795588	1795634	0.99	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1795588	1795634	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1795635	1795735	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1795736	1795786	0.99	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1795736	1795786	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1795787	1795871	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1795872	1795961	0.99	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1795872	1795961	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1795962	1796072	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1796073	1796162	0.93	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1796073	1796162	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1796163	1796274	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1796275	1796355	1	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1796275	1796355	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1796356	1796455	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1796456	1796544	1	-	2	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1796456	1796544	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1796545	1796849	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1796850	1796979	1	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1796850	1796979	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1796980	1797223	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1797224	1797325	1	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1797224	1797325	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	intron	1797326	1797406	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	CDS	1797407	1797562	0.53	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	exon	1797407	1797562	.	-	.	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
Phchi.S5	AUGUSTUS	start_codon	1797560	1797562	.	-	0	transcript_id "Phchi.S5G017700.t1"; gene_id "Phchi.S5G017700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3314.t1 is derived from g483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2803660	2804052	.	-	.	Phchi.S1G047300
Phchi.S1	AUGUSTUS	transcript	2803660	2804052	.	-	.	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	stop_codon	2803657	2803659	.	-	0	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	CDS	2803660	2803738	0.55	-	1	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	exon	2803660	2803738	.	-	.	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	intron	2803739	2803819	.	-	.	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	CDS	2803820	2803937	0.86	-	2	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	exon	2803820	2803937	.	-	.	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	intron	2803938	2804033	.	-	.	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	CDS	2804034	2804052	0.94	-	0	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	exon	2804034	2804052	.	-	.	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
Phchi.S1	AUGUSTUS	start_codon	2804050	2804052	.	-	0	transcript_id "Phchi.S1G047300.t1"; gene_id "Phchi.S1G047300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15593.t1 is derived from g14062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20164856	20168595	.	+	.	Phchi.S3G291200
Phchi.S3	AUGUSTUS	transcript	20164856	20168595	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	start_codon	20164856	20164858	.	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	CDS	20164856	20165104	1	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	exon	20164856	20165104	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	intron	20165105	20165560	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	CDS	20165561	20165647	1	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	exon	20165561	20165647	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	intron	20165648	20165750	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	CDS	20165751	20165975	1	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	exon	20165751	20165975	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	intron	20165976	20166090	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	CDS	20166091	20166177	0.98	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	exon	20166091	20166177	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	intron	20166178	20166309	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	CDS	20166310	20166381	1	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	exon	20166310	20166381	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	intron	20166382	20166561	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	CDS	20166562	20168595	0.91	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	exon	20166562	20168595	.	+	.	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
Phchi.S3	AUGUSTUS	stop_codon	20168596	20168598	.	+	0	transcript_id "Phchi.S3G291200.t1"; gene_id "Phchi.S3G291200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14409.t1 is derived from g12877.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12687842	12689659	.	-	.	Phchi.S3G172800
Phchi.S3	AUGUSTUS	transcript	12687842	12689659	.	-	.	transcript_id "Phchi.S3G172800.t1"; gene_id "Phchi.S3G172800"
Phchi.S3	AUGUSTUS	stop_codon	12687839	12687841	.	-	0	transcript_id "Phchi.S3G172800.t1"; gene_id "Phchi.S3G172800"
Phchi.S3	AUGUSTUS	CDS	12687842	12689659	1	-	0	transcript_id "Phchi.S3G172800.t1"; gene_id "Phchi.S3G172800"
Phchi.S3	AUGUSTUS	exon	12687842	12689659	.	-	.	transcript_id "Phchi.S3G172800.t1"; gene_id "Phchi.S3G172800"
Phchi.S3	AUGUSTUS	start_codon	12689657	12689659	.	-	0	transcript_id "Phchi.S3G172800.t1"; gene_id "Phchi.S3G172800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6925.t1 is derived from g4097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26016997	26020602	.	-	.	Phchi.S1G408400
Phchi.S1	AUGUSTUS	transcript	26016997	26020602	.	-	.	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	stop_codon	26016994	26016996	.	-	0	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	CDS	26016997	26019473	0.47	-	2	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	exon	26016997	26019473	.	-	.	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	intron	26019474	26019551	.	-	.	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	CDS	26019552	26019621	0.59	-	0	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	exon	26019552	26019621	.	-	.	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	intron	26019622	26019705	.	-	.	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	CDS	26019706	26020602	0.91	-	0	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	exon	26019706	26020602	.	-	.	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
Phchi.S1	AUGUSTUS	start_codon	26020600	26020602	.	-	0	transcript_id "Phchi.S1G408400.t1"; gene_id "Phchi.S1G408400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10760.t1 is derived from g14810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1987742	1988706	.	+	.	Phchi.S4G034200
Phchi.S4	AUGUSTUS	transcript	1987742	1988706	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	start_codon	1987742	1987744	.	+	0	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	CDS	1987742	1987799	0.81	+	0	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	exon	1987742	1987799	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	intron	1987800	1987917	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	CDS	1987918	1988026	1	+	2	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	exon	1987918	1988026	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	intron	1988027	1988147	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	CDS	1988148	1988225	1	+	1	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	exon	1988148	1988225	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	intron	1988226	1988315	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	CDS	1988316	1988349	0.99	+	1	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	exon	1988316	1988349	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	intron	1988350	1988452	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	CDS	1988453	1988521	1	+	0	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	exon	1988453	1988521	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	intron	1988522	1988634	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	CDS	1988635	1988706	1	+	0	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	exon	1988635	1988706	.	+	.	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
Phchi.S4	AUGUSTUS	stop_codon	1988707	1988709	.	+	0	transcript_id "Phchi.S4G034200.t1"; gene_id "Phchi.S4G034200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6178.t1 is derived from g3349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21327973	21329205	.	+	.	Phchi.S1G333700
Phchi.S1	AUGUSTUS	transcript	21327973	21329205	.	+	.	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	start_codon	21327973	21327975	.	+	0	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	CDS	21327973	21328348	0.42	+	0	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	exon	21327973	21328348	.	+	.	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	intron	21328349	21328436	.	+	.	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	CDS	21328437	21328591	1	+	2	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	exon	21328437	21328591	.	+	.	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	intron	21328592	21328689	.	+	.	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	CDS	21328690	21329205	1	+	0	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	exon	21328690	21329205	.	+	.	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
Phchi.S1	AUGUSTUS	stop_codon	21329206	21329208	.	+	0	transcript_id "Phchi.S1G333700.t1"; gene_id "Phchi.S1G333700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4872.t1 is derived from g2042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13179807	13181064	.	-	.	Phchi.S1G203100
Phchi.S1	AUGUSTUS	transcript	13179807	13181064	.	-	.	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	stop_codon	13179804	13179806	.	-	0	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	CDS	13179807	13180802	1	-	0	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	exon	13179807	13180802	.	-	.	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	intron	13180803	13181007	.	-	.	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	CDS	13181008	13181064	1	-	0	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	exon	13181008	13181064	.	-	.	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
Phchi.S1	AUGUSTUS	start_codon	13181062	13181064	.	-	0	transcript_id "Phchi.S1G203100.t1"; gene_id "Phchi.S1G203100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6773.t1 is derived from g3945.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25014225	25015586	.	-	.	Phchi.S1G393200
Phchi.S1	AUGUSTUS	transcript	25014225	25015586	.	-	.	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	stop_codon	25014222	25014224	.	-	0	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	CDS	25014225	25015139	0.58	-	0	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	exon	25014225	25015139	.	-	.	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	intron	25015140	25015238	.	-	.	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	CDS	25015239	25015586	0.78	-	0	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	exon	25015239	25015586	.	-	.	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
Phchi.S1	AUGUSTUS	start_codon	25015584	25015586	.	-	0	transcript_id "Phchi.S1G393200.t1"; gene_id "Phchi.S1G393200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7181.t1 is derived from g4353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27430631	27431476	.	-	.	Phchi.S1G434000
Phchi.S1	AUGUSTUS	transcript	27430631	27431476	.	-	.	transcript_id "Phchi.S1G434000.t1"; gene_id "Phchi.S1G434000"
Phchi.S1	AUGUSTUS	stop_codon	27430628	27430630	.	-	0	transcript_id "Phchi.S1G434000.t1"; gene_id "Phchi.S1G434000"
Phchi.S1	AUGUSTUS	CDS	27430631	27431476	0.52	-	0	transcript_id "Phchi.S1G434000.t1"; gene_id "Phchi.S1G434000"
Phchi.S1	AUGUSTUS	exon	27430631	27431476	.	-	.	transcript_id "Phchi.S1G434000.t1"; gene_id "Phchi.S1G434000"
Phchi.S1	AUGUSTUS	start_codon	27431474	27431476	.	-	0	transcript_id "Phchi.S1G434000.t1"; gene_id "Phchi.S1G434000"
# This transcript jg5054.t2 is derived from g2224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5054.t3 is derived from g2224.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5054.t4 is derived from g2224.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5055.t1 is derived from g2225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14417974	14422615	.	-	.	Phchi.S1G221400
Phchi.S1	AUGUSTUS	transcript	14417974	14422615	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	stop_codon	14417971	14417973	.	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14417974	14418216	0.99	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14417974	14418216	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14418217	14418377	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14418378	14419346	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14418378	14419346	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14419347	14419454	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14419455	14419580	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14419455	14419580	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14419581	14419674	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14419675	14419829	1	-	2	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14419675	14419829	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14419830	14419919	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14419920	14420136	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14419920	14420136	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14420137	14420261	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14420262	14420362	1	-	2	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14420262	14420362	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14420363	14420487	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14420488	14420615	1	-	1	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14420488	14420615	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14420616	14420749	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14420750	14420844	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14420750	14420844	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14420845	14420944	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14420945	14421009	1	-	2	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14420945	14421009	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14421010	14421107	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14421108	14421174	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14421108	14421174	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14421175	14421325	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14421326	14421424	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14421326	14421424	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14421425	14421573	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14421574	14421642	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14421574	14421642	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14421643	14421742	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14421743	14421866	1	-	1	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14421743	14421866	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14421867	14421976	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14421977	14422036	0.97	-	1	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14421977	14422036	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	intron	14422037	14422124	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	CDS	14422125	14422615	1	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	exon	14422125	14422615	.	-	.	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
Phchi.S1	AUGUSTUS	start_codon	14422613	14422615	.	-	0	transcript_id "Phchi.S1G221400.t1"; gene_id "Phchi.S1G221400"
# This transcript jg2926.t2 is derived from g95.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2927.t1 is derived from g96.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	590010	592451	.	+	.	Phchi.S1G008600
Phchi.S1	AUGUSTUS	transcript	590010	592451	.	+	.	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	start_codon	590010	590012	.	+	0	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	CDS	590010	591678	0.86	+	0	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	exon	590010	591678	.	+	.	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	intron	591679	591766	.	+	.	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	CDS	591767	591930	0.66	+	2	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	exon	591767	591930	.	+	.	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	intron	591931	592064	.	+	.	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	CDS	592065	592451	0.93	+	0	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	exon	592065	592451	.	+	.	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
Phchi.S1	AUGUSTUS	stop_codon	592452	592454	.	+	0	transcript_id "Phchi.S1G008600.t1"; gene_id "Phchi.S1G008600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4523.t1 is derived from g1693.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10941300	10943711	.	+	.	Phchi.S1G168200
Phchi.S1	AUGUSTUS	transcript	10941300	10943711	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	start_codon	10941300	10941302	.	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10941300	10941356	0.99	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10941300	10941356	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10941357	10941458	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10941459	10941677	0.91	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10941459	10941677	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10941678	10941761	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10941762	10941817	0.91	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10941762	10941817	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10941818	10941891	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10941892	10941957	0.96	+	1	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10941892	10941957	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10941958	10942043	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10942044	10942151	0.99	+	1	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10942044	10942151	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10942152	10942303	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10942304	10942370	0.98	+	1	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10942304	10942370	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10942371	10942487	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10942488	10942572	0.79	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10942488	10942572	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10942573	10942779	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10942780	10942940	0.99	+	2	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10942780	10942940	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10942941	10943056	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10943057	10943158	0.54	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10943057	10943158	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10943159	10943266	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10943267	10943480	0.97	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10943267	10943480	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	intron	10943481	10943583	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	CDS	10943584	10943711	0.98	+	2	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	exon	10943584	10943711	.	+	.	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
Phchi.S1	AUGUSTUS	stop_codon	10943712	10943714	.	+	0	transcript_id "Phchi.S1G168200.t1"; gene_id "Phchi.S1G168200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14805.t1 is derived from g13273.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14798358	14798975	.	-	.	Phchi.S3G212400
Phchi.S3	AUGUSTUS	transcript	14798358	14798975	.	-	.	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	stop_codon	14798355	14798357	.	-	0	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	CDS	14798358	14798463	0.99	-	1	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	exon	14798358	14798463	.	-	.	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	intron	14798464	14798542	.	-	.	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	CDS	14798543	14798802	1	-	0	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	exon	14798543	14798802	.	-	.	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	intron	14798803	14798882	.	-	.	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	CDS	14798883	14798975	0.96	-	0	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	exon	14798883	14798975	.	-	.	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
Phchi.S3	AUGUSTUS	start_codon	14798973	14798975	.	-	0	transcript_id "Phchi.S3G212400.t1"; gene_id "Phchi.S3G212400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9548.t1 is derived from g6724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42413829	42414731	.	-	.	Phchi.S1G670700
Phchi.S1	AUGUSTUS	transcript	42413829	42414731	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	stop_codon	42413826	42413828	.	-	0	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	CDS	42413829	42414047	0.96	-	0	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	exon	42413829	42414047	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	intron	42414048	42414138	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	CDS	42414139	42414292	1	-	1	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	exon	42414139	42414292	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	intron	42414293	42414367	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	CDS	42414368	42414439	0.85	-	1	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	exon	42414368	42414439	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	intron	42414440	42414537	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	CDS	42414538	42414731	0.72	-	0	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	exon	42414538	42414731	.	-	.	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
Phchi.S1	AUGUSTUS	start_codon	42414729	42414731	.	-	0	transcript_id "Phchi.S1G670700.t1"; gene_id "Phchi.S1G670700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13924.t1 is derived from g12391.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9687624	9692156	.	+	.	Phchi.S3G124300
Phchi.S3	AUGUSTUS	transcript	9687624	9692156	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	start_codon	9687624	9687626	.	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9687624	9687695	0.64	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9687624	9687695	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9687696	9687783	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9687784	9687850	0.97	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9687784	9687850	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9687851	9688055	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688056	9688103	1	+	2	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688056	9688103	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688104	9688191	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688192	9688357	1	+	2	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688192	9688357	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688358	9688498	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688499	9688590	1	+	1	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688499	9688590	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688591	9688666	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688667	9688754	1	+	2	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688667	9688754	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688755	9688846	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688847	9689003	1	+	1	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688847	9689003	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689004	9689121	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689122	9689338	0.85	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689122	9689338	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689339	9689445	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689446	9689617	0.99	+	2	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689446	9689617	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689618	9689692	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689693	9689876	1	+	1	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689693	9689876	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689877	9689997	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689998	9690099	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689998	9690099	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690100	9690250	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9690251	9690559	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9690251	9690559	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690560	9690669	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9690670	9690753	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9690670	9690753	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690754	9690830	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9690831	9690989	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9690831	9690989	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690990	9691165	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691166	9691249	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691166	9691249	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691250	9691371	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691372	9691506	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691372	9691506	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691507	9691599	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691600	9691712	1	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691600	9691712	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691713	9691787	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691788	9691924	1	+	1	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691788	9691924	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691925	9691995	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691996	9692156	1	+	2	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691996	9692156	.	+	.	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	stop_codon	9692157	9692159	.	+	0	transcript_id "Phchi.S3G124300.t1"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	transcript	9687673	9692156	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	start_codon	9687673	9687675	.	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9687673	9687695	0.36	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9687673	9687695	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9687696	9688055	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688056	9688103	0.42	+	1	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688056	9688103	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688104	9688191	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688192	9688300	0.41	+	1	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688192	9688300	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688301	9688412	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688413	9688590	0.42	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688413	9688590	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688591	9688666	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688667	9688754	1	+	2	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688667	9688754	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9688755	9688846	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9688847	9689003	1	+	1	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9688847	9689003	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689004	9689121	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689122	9689338	0.9	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689122	9689338	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689339	9689445	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689446	9689617	0.97	+	2	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689446	9689617	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689618	9689692	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689693	9689876	1	+	1	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689693	9689876	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9689877	9689997	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9689998	9690099	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9689998	9690099	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690100	9690250	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9690251	9690559	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9690251	9690559	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690560	9690669	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9690670	9690753	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9690670	9690753	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690754	9690830	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9690831	9690989	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9690831	9690989	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9690990	9691165	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691166	9691249	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691166	9691249	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691250	9691371	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691372	9691506	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691372	9691506	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691507	9691599	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691600	9691712	1	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691600	9691712	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691713	9691787	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691788	9691924	1	+	1	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691788	9691924	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	intron	9691925	9691995	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	CDS	9691996	9692156	1	+	2	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	exon	9691996	9692156	.	+	.	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
Phchi.S3	AUGUSTUS	stop_codon	9692157	9692159	.	+	0	transcript_id "Phchi.S3G124300.t2"; gene_id "Phchi.S3G124300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8112.t1 is derived from g5287.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33171623	33178431	.	+	.	Phchi.S1G527100
Phchi.S1	AUGUSTUS	transcript	33171623	33178431	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	start_codon	33171623	33171625	.	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33171623	33171685	0.63	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33171623	33171685	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33171686	33171854	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33171855	33172062	0.8	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33171855	33172062	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33172063	33172185	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33172186	33172274	0.91	+	2	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33172186	33172274	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33172275	33172343	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33172344	33172463	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33172344	33172463	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33172464	33172653	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33172654	33172730	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33172654	33172730	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33172731	33172813	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33172814	33172877	1	+	1	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33172814	33172877	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33172878	33172972	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33172973	33173043	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33172973	33173043	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33173044	33173128	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33173129	33173206	1	+	1	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33173129	33173206	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33173207	33173283	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33173284	33173329	1	+	1	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33173284	33173329	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33173330	33173453	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33173454	33173634	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33173454	33173634	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33173635	33173720	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33173721	33173773	1	+	2	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33173721	33173773	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33173774	33173859	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33173860	33173933	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33173860	33173933	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33173934	33174124	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33174125	33174242	1	+	1	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33174125	33174242	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33174243	33174365	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33174366	33174453	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33174366	33174453	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33174454	33174664	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33174665	33174777	0.98	+	2	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33174665	33174777	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33174778	33174881	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33174882	33175009	0.97	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33174882	33175009	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33175010	33175117	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33175118	33175197	1	+	1	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33175118	33175197	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33175198	33175361	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33175362	33175603	1	+	2	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33175362	33175603	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33175604	33175686	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33175687	33175851	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33175687	33175851	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33175852	33175929	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33175930	33176097	0.83	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33175930	33176097	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33176098	33176240	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33176241	33176315	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33176241	33176315	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33176316	33176535	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33176536	33176639	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33176536	33176639	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33176640	33176757	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33176758	33176833	1	+	1	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33176758	33176833	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33176834	33176949	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33176950	33177096	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33176950	33177096	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33177097	33177197	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33177198	33177341	0.99	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33177198	33177341	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33177342	33177435	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33177436	33177648	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33177436	33177648	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33177649	33177721	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33177722	33177976	1	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33177722	33177976	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	intron	33177977	33178047	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	CDS	33178048	33178431	0.91	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	exon	33178048	33178431	.	+	.	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
Phchi.S1	AUGUSTUS	stop_codon	33178432	33178434	.	+	0	transcript_id "Phchi.S1G527100.t1"; gene_id "Phchi.S1G527100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13605.t1 is derived from g12072.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7665401	7668652	.	-	.	Phchi.S3G092400
Phchi.S3	AUGUSTUS	transcript	7665401	7668652	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	stop_codon	7665398	7665400	.	-	0	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665401	7665452	0.99	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665401	7665452	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7665453	7665543	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665544	7665602	0.92	-	0	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665544	7665602	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7665603	7665718	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665719	7665787	1	-	0	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665719	7665787	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7665788	7665952	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665953	7666022	1	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665953	7666022	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666023	7666114	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666115	7666199	0.46	-	2	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666115	7666199	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666200	7666363	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666364	7666368	0.84	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666364	7666368	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666369	7666534	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666535	7666693	0.84	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666535	7666693	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666694	7666778	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666779	7666856	1	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666779	7666856	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666857	7666941	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666942	7667162	1	-	0	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666942	7667162	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667163	7667288	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7667289	7667538	1	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7667289	7667538	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667539	7667642	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7667643	7667780	1	-	1	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7667643	7667780	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667781	7668329	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7668330	7668652	0.64	-	0	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7668330	7668652	.	-	.	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	start_codon	7668650	7668652	.	-	0	transcript_id "Phchi.S3G092400.t1"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	transcript	7665401	7668652	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	stop_codon	7665398	7665400	.	-	0	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665401	7665452	0.98	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665401	7665452	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7665453	7665543	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665544	7665602	0.83	-	0	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665544	7665602	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7665603	7665718	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665719	7665787	1	-	0	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665719	7665787	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7665788	7665952	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7665953	7666022	1	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7665953	7666022	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666023	7666114	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666115	7666199	0.35	-	2	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666115	7666199	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666200	7666363	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666364	7666368	0.81	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666364	7666368	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666369	7666534	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666535	7666693	0.81	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666535	7666693	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666694	7666778	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666779	7666856	1	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666779	7666856	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7666857	7666941	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7666942	7667162	1	-	0	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7666942	7667162	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667163	7667288	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7667289	7667538	1	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7667289	7667538	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667539	7667642	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7667643	7667726	0.5	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7667643	7667726	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667727	7667909	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7667910	7667921	0.36	-	1	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7667910	7667921	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	intron	7667922	7668329	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	CDS	7668330	7668652	0.48	-	0	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	exon	7668330	7668652	.	-	.	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
Phchi.S3	AUGUSTUS	start_codon	7668650	7668652	.	-	0	transcript_id "Phchi.S3G092400.t2"; gene_id "Phchi.S3G092400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9905.t1 is derived from g7081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44382944	44383488	.	-	.	Phchi.S1G706400
Phchi.S1	AUGUSTUS	transcript	44382944	44383488	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	stop_codon	44382941	44382943	.	-	0	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	CDS	44382944	44383016	1	-	1	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	exon	44382944	44383016	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	intron	44383017	44383099	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	CDS	44383100	44383197	1	-	0	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	exon	44383100	44383197	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	intron	44383198	44383278	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	CDS	44383279	44383323	1	-	0	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	exon	44383279	44383323	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	intron	44383324	44383443	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	CDS	44383444	44383488	1	-	0	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	exon	44383444	44383488	.	-	.	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
Phchi.S1	AUGUSTUS	start_codon	44383486	44383488	.	-	0	transcript_id "Phchi.S1G706400.t1"; gene_id "Phchi.S1G706400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg791.t1 is derived from g10573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5600398	5601322	.	-	.	Phchi.S6G075000
Phchi.S6	AUGUSTUS	transcript	5600398	5601322	.	-	.	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	stop_codon	5600395	5600397	.	-	0	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	CDS	5600398	5600622	0.57	-	0	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	exon	5600398	5600622	.	-	.	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	intron	5600623	5600712	.	-	.	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	CDS	5600713	5600898	0.97	-	0	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	exon	5600713	5600898	.	-	.	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	intron	5600899	5600995	.	-	.	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	CDS	5600996	5601322	0.81	-	0	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	exon	5600996	5601322	.	-	.	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
Phchi.S6	AUGUSTUS	start_codon	5601320	5601322	.	-	0	transcript_id "Phchi.S6G075000.t1"; gene_id "Phchi.S6G075000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8713.t1 is derived from g5888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37597662	37601137	.	-	.	Phchi.S1G587200
Phchi.S1	AUGUSTUS	transcript	37597662	37601137	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	stop_codon	37597659	37597661	.	-	0	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37597662	37597825	0.75	-	2	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37597662	37597825	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37597826	37597926	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37597927	37599250	0.77	-	0	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37597927	37599250	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37599251	37599389	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37599390	37599627	1	-	1	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37599390	37599627	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37599628	37599903	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37599904	37600127	1	-	0	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37599904	37600127	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37600128	37600303	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37600304	37600308	0.81	-	2	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37600304	37600308	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37600309	37600518	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37600519	37600592	0.49	-	1	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37600519	37600592	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37600593	37600766	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37600767	37600782	0.46	-	2	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37600767	37600782	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	intron	37600783	37600989	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	CDS	37600990	37601137	0.49	-	0	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	exon	37600990	37601137	.	-	.	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
Phchi.S1	AUGUSTUS	start_codon	37601135	37601137	.	-	0	transcript_id "Phchi.S1G587200.t1"; gene_id "Phchi.S1G587200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg727.t1 is derived from g10509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5191264	5192796	.	-	.	Phchi.S6G068600
Phchi.S6	AUGUSTUS	transcript	5191264	5192796	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	stop_codon	5191261	5191263	.	-	0	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	CDS	5191264	5191411	0.92	-	1	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	exon	5191264	5191411	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	intron	5191412	5191494	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	CDS	5191495	5191730	0.8	-	0	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	exon	5191495	5191730	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	intron	5191731	5191818	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	CDS	5191819	5192025	0.79	-	0	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	exon	5191819	5192025	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	intron	5192026	5192107	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	CDS	5192108	5192279	0.98	-	1	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	exon	5192108	5192279	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	intron	5192280	5192392	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	CDS	5192393	5192796	0.77	-	0	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	exon	5192393	5192796	.	-	.	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
Phchi.S6	AUGUSTUS	start_codon	5192794	5192796	.	-	0	transcript_id "Phchi.S6G068600.t1"; gene_id "Phchi.S6G068600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4861.t1 is derived from g2031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13144180	13145943	.	-	.	Phchi.S1G202000
Phchi.S1	AUGUSTUS	transcript	13144180	13145943	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	stop_codon	13144177	13144179	.	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13144180	13144261	1	-	1	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13144180	13144261	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13144262	13144385	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13144386	13144457	1	-	1	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13144386	13144457	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13144458	13144541	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13144542	13144630	1	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13144542	13144630	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13144631	13144724	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13144725	13144814	1	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13144725	13144814	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13144815	13144920	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13144921	13144999	0.94	-	1	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13144921	13144999	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13145000	13145082	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13145083	13145160	1	-	1	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13145083	13145160	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13145161	13145258	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13145259	13145306	1	-	1	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13145259	13145306	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13145307	13145411	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13145412	13145509	0.95	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13145412	13145509	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13145510	13145611	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13145612	13145725	0.92	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13145612	13145725	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	intron	13145726	13145832	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	CDS	13145833	13145943	0.86	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	exon	13145833	13145943	.	-	.	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
Phchi.S1	AUGUSTUS	start_codon	13145941	13145943	.	-	0	transcript_id "Phchi.S1G202000.t1"; gene_id "Phchi.S1G202000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12441.t1 is derived from g8118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	20523819	20524217	.	-	.	Phchi.S2G052100
Phchi.S2	AUGUSTUS	transcript	20523819	20524217	.	-	.	transcript_id "Phchi.S2G052100.t1"; gene_id "Phchi.S2G052100"
Phchi.S2	AUGUSTUS	stop_codon	20523816	20523818	.	-	0	transcript_id "Phchi.S2G052100.t1"; gene_id "Phchi.S2G052100"
Phchi.S2	AUGUSTUS	CDS	20523819	20524217	0.69	-	0	transcript_id "Phchi.S2G052100.t1"; gene_id "Phchi.S2G052100"
Phchi.S2	AUGUSTUS	exon	20523819	20524217	.	-	.	transcript_id "Phchi.S2G052100.t1"; gene_id "Phchi.S2G052100"
Phchi.S2	AUGUSTUS	start_codon	20524215	20524217	.	-	0	transcript_id "Phchi.S2G052100.t1"; gene_id "Phchi.S2G052100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg440.t1 is derived from g10222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3091352	3092573	.	+	.	Phchi.S6G039900
Phchi.S6	AUGUSTUS	transcript	3092223	3092573	.	+	.	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	start_codon	3092223	3092225	.	+	0	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	CDS	3092223	3092283	0.83	+	0	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	exon	3092223	3092283	.	+	.	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	intron	3092284	3092376	.	+	.	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	CDS	3092377	3092573	0.94	+	2	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	exon	3092377	3092573	.	+	.	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	stop_codon	3092574	3092576	.	+	0	transcript_id "Phchi.S6G039900.t1"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	transcript	3091352	3092573	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	start_codon	3091352	3091354	.	+	0	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	CDS	3091352	3091498	0.46	+	0	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	exon	3091352	3091498	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	intron	3091499	3091653	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	CDS	3091654	3091680	0.4	+	0	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	exon	3091654	3091680	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	intron	3091681	3092044	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	CDS	3092045	3092283	0.45	+	0	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	exon	3092045	3092283	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	intron	3092284	3092350	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	CDS	3092351	3092573	0.8	+	1	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	exon	3092351	3092573	.	+	.	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
Phchi.S6	AUGUSTUS	stop_codon	3092574	3092576	.	+	0	transcript_id "Phchi.S6G039900.t2"; gene_id "Phchi.S6G039900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8090.t1 is derived from g5265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32896434	32897010	.	+	.	Phchi.S1G524900
Phchi.S1	AUGUSTUS	transcript	32896434	32897010	.	+	.	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	start_codon	32896434	32896436	.	+	0	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	CDS	32896434	32896439	0.72	+	0	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	exon	32896434	32896439	.	+	.	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	intron	32896440	32896520	.	+	.	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	CDS	32896521	32896702	0.72	+	0	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	exon	32896521	32896702	.	+	.	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	intron	32896703	32896967	.	+	.	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	CDS	32896968	32897010	0.71	+	1	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	exon	32896968	32897010	.	+	.	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
Phchi.S1	AUGUSTUS	stop_codon	32897011	32897013	.	+	0	transcript_id "Phchi.S1G524900.t1"; gene_id "Phchi.S1G524900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3429.t1 is derived from g598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3604349	3604874	.	-	.	Phchi.S1G058800
Phchi.S1	AUGUSTUS	transcript	3604349	3604874	.	-	.	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	stop_codon	3604346	3604348	.	-	0	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	CDS	3604349	3604461	0.74	-	2	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	exon	3604349	3604461	.	-	.	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	intron	3604462	3604618	.	-	.	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	CDS	3604619	3604689	0.82	-	1	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	exon	3604619	3604689	.	-	.	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	intron	3604690	3604794	.	-	.	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	CDS	3604795	3604874	0.49	-	0	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	exon	3604795	3604874	.	-	.	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
Phchi.S1	AUGUSTUS	start_codon	3604872	3604874	.	-	0	transcript_id "Phchi.S1G058800.t1"; gene_id "Phchi.S1G058800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11917.t1 is derived from g15969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9311255	9313401	.	+	.	Phchi.S4G149900
Phchi.S4	AUGUSTUS	transcript	9311255	9313401	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	start_codon	9311255	9311257	.	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9311255	9311269	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9311255	9311269	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9311270	9311719	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9311720	9311812	0.99	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9311720	9311812	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9311813	9311927	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9311928	9311996	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9311928	9311996	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9311997	9312083	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9312084	9312143	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9312084	9312143	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9312144	9312233	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9312234	9312374	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9312234	9312374	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9312375	9312473	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9312474	9312518	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9312474	9312518	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9312519	9312664	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9312665	9312739	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9312665	9312739	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9312740	9312878	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9312879	9312911	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9312879	9312911	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9312912	9313022	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9313023	9313065	1	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9313023	9313065	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9313066	9313195	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9313196	9313283	1	+	2	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9313196	9313283	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	intron	9313284	9313376	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	CDS	9313377	9313401	1	+	1	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	exon	9313377	9313401	.	+	.	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
Phchi.S4	AUGUSTUS	stop_codon	9313402	9313404	.	+	0	transcript_id "Phchi.S4G149900.t1"; gene_id "Phchi.S4G149900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10171.t1 is derived from g7347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46090098	46091443	.	-	.	Phchi.S1G733000
Phchi.S1	AUGUSTUS	transcript	46090098	46091443	.	-	.	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	stop_codon	46090095	46090097	.	-	0	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	CDS	46090098	46091198	0.99	-	0	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	exon	46090098	46091198	.	-	.	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	intron	46091199	46091320	.	-	.	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	CDS	46091321	46091443	0.7	-	0	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	exon	46091321	46091443	.	-	.	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
Phchi.S1	AUGUSTUS	start_codon	46091441	46091443	.	-	0	transcript_id "Phchi.S1G733000.t1"; gene_id "Phchi.S1G733000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10742.t1 is derived from g14792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1873850	1875438	.	+	.	Phchi.S4G032400
Phchi.S4	AUGUSTUS	transcript	1873850	1875438	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	start_codon	1873850	1873852	.	+	0	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	CDS	1873850	1874500	0.37	+	0	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	exon	1873850	1874500	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	intron	1874501	1874642	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	CDS	1874643	1874894	0.99	+	0	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	exon	1874643	1874894	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	intron	1874895	1874991	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	CDS	1874992	1875114	0.99	+	0	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	exon	1874992	1875114	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	intron	1875115	1875228	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	CDS	1875229	1875438	1	+	0	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	exon	1875229	1875438	.	+	.	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
Phchi.S4	AUGUSTUS	stop_codon	1875439	1875441	.	+	0	transcript_id "Phchi.S4G032400.t1"; gene_id "Phchi.S4G032400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11026.t1 is derived from g15076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3705113	3705725	.	-	.	Phchi.S4G060800
Phchi.S4	AUGUSTUS	transcript	3705113	3705725	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	stop_codon	3705110	3705112	.	-	0	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	CDS	3705113	3705166	0.96	-	0	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	exon	3705113	3705166	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	intron	3705167	3705299	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	CDS	3705300	3705340	0.66	-	2	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	exon	3705300	3705340	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	intron	3705341	3705410	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	CDS	3705411	3705479	0.67	-	2	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	exon	3705411	3705479	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	intron	3705480	3705577	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	CDS	3705578	3705725	0.33	-	0	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	exon	3705578	3705725	.	-	.	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
Phchi.S4	AUGUSTUS	start_codon	3705723	3705725	.	-	0	transcript_id "Phchi.S4G060800.t1"; gene_id "Phchi.S4G060800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13351.t1 is derived from g11817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6287158	6288667	.	-	.	Phchi.S3G067000
Phchi.S3	AUGUSTUS	transcript	6287158	6288667	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	stop_codon	6287155	6287157	.	-	0	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	CDS	6287158	6287382	1	-	0	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	exon	6287158	6287382	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	intron	6287383	6287467	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	CDS	6287468	6287758	1	-	0	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	exon	6287468	6287758	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	intron	6287759	6287925	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	CDS	6287926	6288048	1	-	0	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	exon	6287926	6288048	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	intron	6288049	6288394	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	CDS	6288395	6288667	0.89	-	0	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	exon	6288395	6288667	.	-	.	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
Phchi.S3	AUGUSTUS	start_codon	6288665	6288667	.	-	0	transcript_id "Phchi.S3G067000.t1"; gene_id "Phchi.S3G067000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6304.t1 is derived from g3476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22174185	22175873	.	-	.	Phchi.S1G346300
Phchi.S1	AUGUSTUS	transcript	22174185	22175873	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	stop_codon	22174182	22174184	.	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22174185	22174307	0.98	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22174185	22174307	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	intron	22174308	22174399	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22174400	22174465	1	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22174400	22174465	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	intron	22174466	22174633	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22174634	22174719	1	-	2	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22174634	22174719	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	intron	22174720	22174852	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22174853	22174979	1	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22174853	22174979	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	intron	22174980	22175106	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22175107	22175198	1	-	2	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22175107	22175198	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	intron	22175199	22175429	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22175430	22175682	1	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22175430	22175682	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	intron	22175683	22175843	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	CDS	22175844	22175873	0.64	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	exon	22175844	22175873	.	-	.	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
Phchi.S1	AUGUSTUS	start_codon	22175871	22175873	.	-	0	transcript_id "Phchi.S1G346300.t1"; gene_id "Phchi.S1G346300"
# This transcript jg1613.t2 is derived from g8532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1613.t3 is derived from g8532.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1614.t1 is derived from g8533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2028398	2031011	.	-	.	Phchi.S5G022300
Phchi.S5	AUGUSTUS	transcript	2028398	2031011	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	stop_codon	2028395	2028397	.	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2028398	2028508	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2028398	2028508	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2028509	2028619	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2028620	2028687	1	-	2	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2028620	2028687	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2028688	2028766	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2028767	2028830	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2028767	2028830	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2028831	2028916	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2028917	2028998	1	-	1	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2028917	2028998	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2028999	2029226	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2029227	2029285	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2029227	2029285	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2029286	2029423	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2029424	2029481	1	-	1	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2029424	2029481	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2029482	2029595	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2029596	2029766	1	-	1	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2029596	2029766	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2029767	2029876	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2029877	2030001	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2029877	2030001	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2030002	2030113	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2030114	2030176	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2030114	2030176	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2030177	2030271	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2030272	2030331	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2030272	2030331	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2030332	2030440	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2030441	2030674	1	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2030441	2030674	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	intron	2030675	2030846	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	CDS	2030847	2031011	0.93	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	exon	2030847	2031011	.	-	.	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
Phchi.S5	AUGUSTUS	start_codon	2031009	2031011	.	-	0	transcript_id "Phchi.S5G022300.t1"; gene_id "Phchi.S5G022300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2217.t1 is derived from g9137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5457850	5461727	.	+	.	Phchi.S5G082600
Phchi.S5	AUGUSTUS	transcript	5457850	5461727	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	start_codon	5457850	5457852	.	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5457850	5458042	0.99	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5457850	5458042	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5458043	5458119	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5458120	5458292	1	+	2	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5458120	5458292	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5458293	5458401	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5458402	5458530	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5458402	5458530	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5458531	5458675	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5458676	5458768	0.85	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5458676	5458768	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5458769	5458912	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5458913	5458961	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5458913	5458961	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5458962	5459113	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5459114	5459228	1	+	2	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5459114	5459228	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5459229	5459308	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5459309	5459382	1	+	1	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5459309	5459382	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5459383	5459473	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5459474	5459550	1	+	2	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5459474	5459550	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5459551	5459638	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5459639	5459722	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5459639	5459722	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5459723	5459853	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5459854	5459946	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5459854	5459946	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5459947	5460028	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5460029	5460136	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5460029	5460136	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5460137	5460215	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5460216	5460290	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5460216	5460290	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5460291	5460391	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5460392	5460831	0.49	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5460392	5460831	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5460832	5461002	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5461003	5461074	0.46	+	1	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5461003	5461074	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5461075	5461170	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5461171	5461192	0.31	+	1	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5461171	5461192	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5461193	5461343	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5461344	5461379	0.9	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5461344	5461379	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5461380	5461471	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5461472	5461571	1	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5461472	5461571	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	intron	5461572	5461719	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	CDS	5461720	5461727	1	+	2	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	exon	5461720	5461727	.	+	.	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
Phchi.S5	AUGUSTUS	stop_codon	5461728	5461730	.	+	0	transcript_id "Phchi.S5G082600.t1"; gene_id "Phchi.S5G082600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11777.t1 is derived from g15829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8119721	8121272	.	-	.	Phchi.S4G135900
Phchi.S4	AUGUSTUS	transcript	8119721	8121272	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	stop_codon	8119718	8119720	.	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8119721	8119856	1	-	1	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8119721	8119856	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8119857	8119945	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8119946	8120022	1	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8119946	8120022	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8120023	8120123	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8120124	8120180	1	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8120124	8120180	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8120181	8120379	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8120380	8120416	1	-	1	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8120380	8120416	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8120417	8120617	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8120618	8120649	1	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8120618	8120649	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8120650	8120795	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8120796	8120827	1	-	2	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8120796	8120827	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8120828	8120926	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8120927	8120967	1	-	1	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8120927	8120967	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8120968	8121054	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8121055	8121113	1	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8121055	8121113	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	intron	8121114	8121188	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	CDS	8121189	8121272	1	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	exon	8121189	8121272	.	-	.	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
Phchi.S4	AUGUSTUS	start_codon	8121270	8121272	.	-	0	transcript_id "Phchi.S4G135900.t1"; gene_id "Phchi.S4G135900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3902.t1 is derived from g1071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6318593	6318835	.	-	.	Phchi.S1G106100
Phchi.S1	AUGUSTUS	transcript	6318593	6318835	.	-	.	transcript_id "Phchi.S1G106100.t1"; gene_id "Phchi.S1G106100"
Phchi.S1	AUGUSTUS	stop_codon	6318590	6318592	.	-	0	transcript_id "Phchi.S1G106100.t1"; gene_id "Phchi.S1G106100"
Phchi.S1	AUGUSTUS	CDS	6318593	6318835	0.96	-	0	transcript_id "Phchi.S1G106100.t1"; gene_id "Phchi.S1G106100"
Phchi.S1	AUGUSTUS	exon	6318593	6318835	.	-	.	transcript_id "Phchi.S1G106100.t1"; gene_id "Phchi.S1G106100"
Phchi.S1	AUGUSTUS	start_codon	6318833	6318835	.	-	0	transcript_id "Phchi.S1G106100.t1"; gene_id "Phchi.S1G106100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg100.t1 is derived from g9882.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	506752	507596	.	-	.	Phchi.S6G005900
Phchi.S6	AUGUSTUS	transcript	506752	507596	.	-	.	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	stop_codon	506749	506751	.	-	0	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	CDS	506752	507264	0.99	-	0	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	exon	506752	507264	.	-	.	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	intron	507265	507401	.	-	.	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	CDS	507402	507596	0.99	-	0	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	exon	507402	507596	.	-	.	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
Phchi.S6	AUGUSTUS	start_codon	507594	507596	.	-	0	transcript_id "Phchi.S6G005900.t1"; gene_id "Phchi.S6G005900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13346.t1 is derived from g11812.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6204967	6219537	.	+	.	Phchi.S3G066500
Phchi.S3	AUGUSTUS	transcript	6204967	6219537	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	start_codon	6204967	6204969	.	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6204967	6206673	0.33	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6204967	6206673	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6206674	6206775	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6206776	6207130	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6206776	6207130	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6207131	6207256	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6207257	6207405	0.45	+	2	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6207257	6207405	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6207406	6207566	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6207567	6207936	0.47	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6207567	6207936	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6207937	6208231	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6208232	6208682	0.68	+	2	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6208232	6208682	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6208683	6208780	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6208781	6208798	0.68	+	1	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6208781	6208798	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6208799	6208892	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6208893	6209043	1	+	1	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6208893	6209043	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6209044	6209156	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6209157	6209939	0.98	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6209157	6209939	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6209940	6210022	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210023	6210157	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210023	6210157	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210158	6210246	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210247	6210351	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210247	6210351	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210352	6210531	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210532	6210648	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210532	6210648	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210649	6210789	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210790	6210866	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210790	6210866	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210867	6210959	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210960	6211041	1	+	1	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210960	6211041	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6211042	6211226	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6211227	6211595	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6211227	6211595	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6211596	6211814	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6211815	6212151	0.64	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6211815	6212151	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6212152	6212252	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6212253	6212457	0.73	+	2	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6212253	6212457	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6212458	6212729	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6212730	6212814	1	+	1	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6212730	6212814	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6212815	6212998	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6212999	6213193	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6212999	6213193	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6213194	6213330	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6213331	6213873	0.99	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6213331	6213873	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6213874	6213974	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6213975	6214115	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6213975	6214115	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6214116	6214242	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6214243	6214731	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6214243	6214731	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6214732	6214875	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6214876	6215069	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6214876	6215069	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215070	6215261	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215262	6215331	0.83	+	1	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215262	6215331	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215332	6215434	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215435	6215518	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215435	6215518	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215519	6215652	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215653	6215709	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215653	6215709	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215710	6215863	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215864	6215932	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215864	6215932	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215933	6216024	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216025	6216111	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216025	6216111	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216112	6216219	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216220	6216336	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216220	6216336	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216337	6216470	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216471	6216620	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216471	6216620	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216621	6216769	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216770	6216854	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216770	6216854	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216855	6217067	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217068	6217188	1	+	2	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217068	6217188	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6217189	6217286	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217287	6217383	1	+	1	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217287	6217383	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6217384	6217490	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217491	6217604	0.99	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217491	6217604	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6217605	6217690	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217691	6218063	0.98	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217691	6218063	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6218064	6218146	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6218147	6218943	0.82	+	2	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6218147	6218943	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6218944	6219025	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6219026	6219070	0.81	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6219026	6219070	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6219071	6219191	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6219192	6219314	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6219192	6219314	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6219315	6219468	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6219469	6219537	1	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6219469	6219537	.	+	.	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	stop_codon	6219538	6219540	.	+	0	transcript_id "Phchi.S3G066500.t1"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	transcript	6204967	6219537	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	start_codon	6204967	6204969	.	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6204967	6206673	0.38	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6204967	6206673	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6206674	6206775	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6206776	6207130	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6206776	6207130	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6207131	6207256	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6207257	6207405	0.41	+	2	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6207257	6207405	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6207406	6207566	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6207567	6207936	0.45	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6207567	6207936	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6207937	6208231	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6208232	6208682	0.6	+	2	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6208232	6208682	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6208683	6208780	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6208781	6208798	0.6	+	1	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6208781	6208798	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6208799	6208892	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6208893	6209043	1	+	1	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6208893	6209043	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6209044	6209156	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6209157	6209939	0.98	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6209157	6209939	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6209940	6210022	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210023	6210157	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210023	6210157	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210158	6210246	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210247	6210351	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210247	6210351	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210352	6210531	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210532	6210648	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210532	6210648	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210649	6210789	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210790	6210866	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210790	6210866	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6210867	6210950	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6210951	6211041	1	+	1	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6210951	6211041	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6211042	6211226	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6211227	6211595	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6211227	6211595	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6211596	6211814	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6211815	6212151	0.57	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6211815	6212151	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6212152	6212252	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6212253	6212457	0.76	+	2	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6212253	6212457	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6212458	6212729	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6212730	6212814	1	+	1	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6212730	6212814	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6212815	6212998	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6212999	6213193	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6212999	6213193	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6213194	6213330	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6213331	6213873	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6213331	6213873	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6213874	6213974	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6213975	6214115	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6213975	6214115	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6214116	6214242	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6214243	6214731	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6214243	6214731	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6214732	6214875	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6214876	6215069	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6214876	6215069	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215070	6215261	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215262	6215331	0.96	+	1	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215262	6215331	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215332	6215434	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215435	6215518	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215435	6215518	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215519	6215652	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215653	6215709	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215653	6215709	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215710	6215863	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6215864	6215932	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6215864	6215932	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6215933	6216024	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216025	6216111	0.98	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216025	6216111	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216112	6216219	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216220	6216336	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216220	6216336	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216337	6216470	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216471	6216620	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216471	6216620	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216621	6216769	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6216770	6216854	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6216770	6216854	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6216855	6217067	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217068	6217188	1	+	2	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217068	6217188	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6217189	6217286	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217287	6217383	1	+	1	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217287	6217383	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6217384	6217490	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217491	6217604	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217491	6217604	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6217605	6217690	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6217691	6218063	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6217691	6218063	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6218064	6218146	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6218147	6218943	0.68	+	2	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6218147	6218943	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6218944	6219025	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6219026	6219070	0.8	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6219026	6219070	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6219071	6219191	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6219192	6219314	1	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6219192	6219314	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	intron	6219315	6219468	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	CDS	6219469	6219537	0.98	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	exon	6219469	6219537	.	+	.	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
Phchi.S3	AUGUSTUS	stop_codon	6219538	6219540	.	+	0	transcript_id "Phchi.S3G066500.t2"; gene_id "Phchi.S3G066500"
# This transcript jg1163.t2 is derived from g10946.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1163.t3 is derived from g10946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1164.t1 is derived from g10947.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8112212	8114934	.	-	.	Phchi.S6G112300
Phchi.S6	AUGUSTUS	transcript	8112212	8114934	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	stop_codon	8112209	8112211	.	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8112212	8112310	1	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8112212	8112310	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8112311	8112398	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8112399	8112476	1	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8112399	8112476	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8112477	8112558	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8112559	8112613	1	-	1	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8112559	8112613	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8112614	8112696	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8112697	8112863	1	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8112697	8112863	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8112864	8112969	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8112970	8113050	0.97	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8112970	8113050	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8113051	8113219	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8113220	8113287	1	-	2	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8113220	8113287	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8113288	8113423	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8113424	8113552	1	-	2	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8113424	8113552	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8113553	8113643	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8113644	8113729	1	-	1	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8113644	8113729	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8113730	8113857	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8113858	8113955	1	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8113858	8113955	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8113956	8114038	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8114039	8114097	1	-	2	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8114039	8114097	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8114098	8114183	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8114184	8114463	0.71	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8114184	8114463	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8114464	8114613	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8114614	8114721	0.93	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8114614	8114721	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	intron	8114722	8114907	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	CDS	8114908	8114934	1	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	exon	8114908	8114934	.	-	.	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
Phchi.S6	AUGUSTUS	start_codon	8114932	8114934	.	-	0	transcript_id "Phchi.S6G112300.t1"; gene_id "Phchi.S6G112300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1406.t1 is derived from g8325.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	156060	165149	.	-	.	Phchi.S5G001500
Phchi.S5	AUGUSTUS	transcript	156060	165149	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	stop_codon	156057	156059	.	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	156060	156215	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	156060	156215	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	156216	156299	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	156300	156587	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	156300	156587	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	156588	156670	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	156671	156766	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	156671	156766	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	156767	156910	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	156911	157009	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	156911	157009	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	157010	157094	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	157095	157175	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	157095	157175	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	157176	157257	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	157258	157350	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	157258	157350	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	157351	157835	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	157836	157907	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	157836	157907	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	157908	158252	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	158253	158372	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	158253	158372	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	158373	158454	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	158455	158506	1	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	158455	158506	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	158507	158694	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	158695	158780	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	158695	158780	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	158781	158879	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	158880	158952	1	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	158880	158952	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	158953	159080	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	159081	159160	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	159081	159160	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	159161	159331	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	159332	159449	1	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	159332	159449	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	159450	159623	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	159624	159724	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	159624	159724	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	159725	159808	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	159809	159937	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	159809	159937	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	159938	160030	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	160031	160201	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	160031	160201	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	160202	160344	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	160345	160457	1	-	2	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	160345	160457	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	160458	160598	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	160599	160777	1	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	160599	160777	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	160778	160951	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	160952	161103	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	160952	161103	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	161104	161313	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	161314	161372	1	-	2	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	161314	161372	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	161373	161619	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	161620	161699	1	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	161620	161699	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	161700	161847	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	161848	161969	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	161848	161969	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	161970	162055	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	162056	162126	0.96	-	2	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	162056	162126	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	162127	162205	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	162206	162242	0.93	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	162206	162242	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	162243	162329	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	162330	162504	0.93	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	162330	162504	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	162505	162671	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	162672	162859	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	162672	162859	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	162860	162964	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	162965	163048	0.99	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	162965	163048	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	163049	163150	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	163151	163273	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	163151	163273	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	163274	163353	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	163354	163504	1	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	163354	163504	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	163505	163655	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	163656	163798	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	163656	163798	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	163799	163961	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	163962	164048	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	163962	164048	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	164049	164139	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	164140	164220	1	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	164140	164220	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	164221	164314	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	164315	164424	1	-	2	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	164315	164424	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	164425	164530	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	164531	164604	0.99	-	1	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	164531	164604	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	164605	164706	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	164707	164785	0.99	-	2	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	164707	164785	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	intron	164786	164980	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	CDS	164981	165149	0.66	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	exon	164981	165149	.	-	.	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
Phchi.S5	AUGUSTUS	start_codon	165147	165149	.	-	0	transcript_id "Phchi.S5G001500.t1"; gene_id "Phchi.S5G001500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2635.t1 is derived from g9555.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7898300	7900405	.	-	.	Phchi.S5G124400
Phchi.S5	AUGUSTUS	transcript	7898300	7900405	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	stop_codon	7898297	7898299	.	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	CDS	7898300	7898344	0.96	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	exon	7898300	7898344	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	intron	7898345	7898433	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	CDS	7898434	7898874	1	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	exon	7898434	7898874	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	intron	7898875	7898978	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	CDS	7898979	7899026	1	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	exon	7898979	7899026	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	intron	7899027	7899119	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	CDS	7899120	7900091	0.99	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	exon	7899120	7900091	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	intron	7900092	7900195	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	CDS	7900196	7900405	0.95	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	exon	7900196	7900405	.	-	.	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
Phchi.S5	AUGUSTUS	start_codon	7900403	7900405	.	-	0	transcript_id "Phchi.S5G124400.t1"; gene_id "Phchi.S5G124400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12094.t1 is derived from g7769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2563507	2563797	.	-	.	Phchi.S2G017400
Phchi.S2	AUGUSTUS	transcript	2563507	2563797	.	-	.	transcript_id "Phchi.S2G017400.t1"; gene_id "Phchi.S2G017400"
Phchi.S2	AUGUSTUS	stop_codon	2563504	2563506	.	-	0	transcript_id "Phchi.S2G017400.t1"; gene_id "Phchi.S2G017400"
Phchi.S2	AUGUSTUS	CDS	2563507	2563797	1	-	0	transcript_id "Phchi.S2G017400.t1"; gene_id "Phchi.S2G017400"
Phchi.S2	AUGUSTUS	exon	2563507	2563797	.	-	.	transcript_id "Phchi.S2G017400.t1"; gene_id "Phchi.S2G017400"
Phchi.S2	AUGUSTUS	start_codon	2563795	2563797	.	-	0	transcript_id "Phchi.S2G017400.t1"; gene_id "Phchi.S2G017400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7494.t1 is derived from g4667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29635675	29641560	.	-	.	Phchi.S1G465300
Phchi.S1	AUGUSTUS	transcript	29635675	29641560	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	stop_codon	29635672	29635674	.	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29635675	29635781	1	-	2	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29635675	29635781	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29635782	29635882	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29635883	29635951	0.91	-	2	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29635883	29635951	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29635952	29636033	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29636034	29636108	1	-	2	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29636034	29636108	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29636109	29636211	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29636212	29636419	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29636212	29636419	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29636420	29636488	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29636489	29636581	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29636489	29636581	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29636582	29636722	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29636723	29636795	1	-	1	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29636723	29636795	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29636796	29637017	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29637018	29637142	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29637018	29637142	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29637143	29637224	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29637225	29637264	1	-	1	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29637225	29637264	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29637265	29637447	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29637448	29637629	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29637448	29637629	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29637630	29637751	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29637752	29637842	1	-	1	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29637752	29637842	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29637843	29637929	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29637930	29638099	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29637930	29638099	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29638100	29638199	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29638200	29638253	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29638200	29638253	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29638254	29638338	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29638339	29638549	1	-	1	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29638339	29638549	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29638550	29638649	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29638650	29638774	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29638650	29638774	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29638775	29638873	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29638874	29639071	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29638874	29639071	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29639072	29639172	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29639173	29639324	0.97	-	2	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29639173	29639324	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29639325	29639434	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29639435	29639571	1	-	1	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29639435	29639571	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29639572	29639667	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29639668	29639729	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29639668	29639729	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29639730	29639821	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29639822	29639897	1	-	1	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29639822	29639897	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29639898	29639996	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29639997	29640064	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29639997	29640064	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29640065	29640172	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29640173	29640351	0.74	-	2	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29640173	29640351	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29640352	29640483	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29640484	29640685	0.76	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29640484	29640685	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29640686	29640769	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29640770	29640820	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29640770	29640820	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29640821	29640907	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29640908	29640973	1	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29640908	29640973	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29640974	29641285	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29641286	29641350	0.95	-	2	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29641286	29641350	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29641351	29641437	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29641438	29641471	0.62	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29641438	29641471	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	intron	29641472	29641557	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	CDS	29641558	29641560	0.79	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	exon	29641558	29641560	.	-	.	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
Phchi.S1	AUGUSTUS	start_codon	29641558	29641560	.	-	0	transcript_id "Phchi.S1G465300.t1"; gene_id "Phchi.S1G465300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7400.t1 is derived from g4572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28954056	28956500	.	-	.	Phchi.S1G455900
Phchi.S1	AUGUSTUS	transcript	28954056	28956500	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	stop_codon	28954053	28954055	.	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28954056	28954406	0.99	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28954056	28954406	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28954407	28954515	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28954516	28954679	0.99	-	2	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28954516	28954679	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28954680	28954807	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28954808	28954913	1	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28954808	28954913	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28954914	28955032	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28955033	28955197	0.88	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28955033	28955197	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28955198	28955313	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28955314	28955409	0.99	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28955314	28955409	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28955410	28955489	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28955490	28955690	1	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28955490	28955690	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28955691	28955787	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28955788	28956000	1	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28955788	28956000	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	intron	28956001	28956080	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	CDS	28956081	28956500	0.63	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	exon	28956081	28956500	.	-	.	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
Phchi.S1	AUGUSTUS	start_codon	28956498	28956500	.	-	0	transcript_id "Phchi.S1G455900.t1"; gene_id "Phchi.S1G455900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2687.t1 is derived from g9607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8216751	8217918	.	-	.	Phchi.S5G129600
Phchi.S5	AUGUSTUS	transcript	8216751	8217918	.	-	.	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	stop_codon	8216748	8216750	.	-	0	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	CDS	8216751	8216866	0.93	-	2	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	exon	8216751	8216866	.	-	.	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	intron	8216867	8216978	.	-	.	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	CDS	8216979	8217918	0.51	-	0	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	exon	8216979	8217918	.	-	.	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
Phchi.S5	AUGUSTUS	start_codon	8217916	8217918	.	-	0	transcript_id "Phchi.S5G129600.t1"; gene_id "Phchi.S5G129600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15028.t1 is derived from g13496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16597424	16598756	.	-	.	Phchi.S3G234700
Phchi.S3	AUGUSTUS	transcript	16597424	16598756	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	stop_codon	16597421	16597423	.	-	0	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16597424	16597525	1	-	0	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16597424	16597525	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	intron	16597526	16597625	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16597626	16597698	1	-	1	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16597626	16597698	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	intron	16597699	16597777	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16597778	16597902	1	-	0	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16597778	16597902	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	intron	16597903	16597994	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16597995	16598066	1	-	0	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16597995	16598066	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	intron	16598067	16598142	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16598143	16598240	1	-	2	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16598143	16598240	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	intron	16598241	16598350	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16598351	16598506	0.89	-	2	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16598351	16598506	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	intron	16598507	16598587	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	CDS	16598588	16598756	1	-	0	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	exon	16598588	16598756	.	-	.	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
Phchi.S3	AUGUSTUS	start_codon	16598754	16598756	.	-	0	transcript_id "Phchi.S3G234700.t1"; gene_id "Phchi.S3G234700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12569.t1 is derived from g8246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35547856	35548431	.	-	.	Phchi.S2G064900
Phchi.S2	AUGUSTUS	transcript	35547856	35548431	.	-	.	transcript_id "Phchi.S2G064900.t1"; gene_id "Phchi.S2G064900"
Phchi.S2	AUGUSTUS	stop_codon	35547853	35547855	.	-	0	transcript_id "Phchi.S2G064900.t1"; gene_id "Phchi.S2G064900"
Phchi.S2	AUGUSTUS	CDS	35547856	35548431	0.97	-	0	transcript_id "Phchi.S2G064900.t1"; gene_id "Phchi.S2G064900"
Phchi.S2	AUGUSTUS	exon	35547856	35548431	.	-	.	transcript_id "Phchi.S2G064900.t1"; gene_id "Phchi.S2G064900"
Phchi.S2	AUGUSTUS	start_codon	35548429	35548431	.	-	0	transcript_id "Phchi.S2G064900.t1"; gene_id "Phchi.S2G064900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11228.t1 is derived from g15278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4900357	4902117	.	+	.	Phchi.S4G081000
Phchi.S4	AUGUSTUS	transcript	4900357	4902117	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	start_codon	4900357	4900359	.	+	0	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4900357	4900465	0.81	+	0	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4900357	4900465	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4900466	4900707	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4900708	4900883	1	+	2	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4900708	4900883	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4900884	4901005	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4901006	4901120	0.98	+	0	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4901006	4901120	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4901121	4901191	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4901192	4901242	0.95	+	2	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4901192	4901242	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4901243	4901361	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4901362	4901498	1	+	2	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4901362	4901498	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4901499	4901648	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4901649	4901756	0.42	+	0	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4901649	4901756	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4901757	4901880	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4901881	4901954	0.68	+	0	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4901881	4901954	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	intron	4901955	4902035	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	CDS	4902036	4902117	0.72	+	1	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	exon	4902036	4902117	.	+	.	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
Phchi.S4	AUGUSTUS	stop_codon	4902118	4902120	.	+	0	transcript_id "Phchi.S4G081000.t1"; gene_id "Phchi.S4G081000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14835.t1 is derived from g13303.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14928392	14929968	.	-	.	Phchi.S3G215400
Phchi.S3	AUGUSTUS	transcript	14928392	14929968	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	stop_codon	14928389	14928391	.	-	0	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	CDS	14928392	14928519	0.96	-	2	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	exon	14928392	14928519	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	intron	14928520	14928654	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	CDS	14928655	14928784	0.9	-	0	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	exon	14928655	14928784	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	intron	14928785	14928938	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	CDS	14928939	14929010	0.66	-	0	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	exon	14928939	14929010	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	intron	14929011	14929183	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	CDS	14929184	14929427	0.72	-	1	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	exon	14929184	14929427	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	intron	14929428	14929549	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	CDS	14929550	14929968	0.45	-	0	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	exon	14929550	14929968	.	-	.	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
Phchi.S3	AUGUSTUS	start_codon	14929966	14929968	.	-	0	transcript_id "Phchi.S3G215400.t1"; gene_id "Phchi.S3G215400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11045.t1 is derived from g15095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3803352	3803947	.	-	.	Phchi.S4G062700
Phchi.S4	AUGUSTUS	transcript	3803352	3803947	.	-	.	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	stop_codon	3803349	3803351	.	-	0	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	CDS	3803352	3803607	0.99	-	1	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	exon	3803352	3803607	.	-	.	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	intron	3803608	3803694	.	-	.	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	CDS	3803695	3803809	1	-	2	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	exon	3803695	3803809	.	-	.	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	intron	3803810	3803925	.	-	.	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	CDS	3803926	3803947	0.97	-	0	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	exon	3803926	3803947	.	-	.	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
Phchi.S4	AUGUSTUS	start_codon	3803945	3803947	.	-	0	transcript_id "Phchi.S4G062700.t1"; gene_id "Phchi.S4G062700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg292.t1 is derived from g10074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2099789	2100218	.	-	.	Phchi.S6G025100
Phchi.S6	AUGUSTUS	transcript	2099789	2100218	.	-	.	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	stop_codon	2099786	2099788	.	-	0	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	CDS	2099789	2099810	1	-	1	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	exon	2099789	2099810	.	-	.	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	intron	2099811	2099907	.	-	.	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	CDS	2099908	2100218	0.44	-	0	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	exon	2099908	2100218	.	-	.	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
Phchi.S6	AUGUSTUS	start_codon	2100216	2100218	.	-	0	transcript_id "Phchi.S6G025100.t1"; gene_id "Phchi.S6G025100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4116.t1 is derived from g1285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8201506	8203001	.	-	.	Phchi.S1G127500
Phchi.S1	AUGUSTUS	transcript	8201506	8203001	.	-	.	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	stop_codon	8201503	8201505	.	-	0	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	CDS	8201506	8202262	0.82	-	1	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	exon	8201506	8202262	.	-	.	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	intron	8202263	8202387	.	-	.	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	CDS	8202388	8203001	0.75	-	0	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	exon	8202388	8203001	.	-	.	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
Phchi.S1	AUGUSTUS	start_codon	8202999	8203001	.	-	0	transcript_id "Phchi.S1G127500.t1"; gene_id "Phchi.S1G127500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12553.t1 is derived from g8230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34634256	34636820	.	-	.	Phchi.S2G063300
Phchi.S2	AUGUSTUS	transcript	34634256	34636820	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	stop_codon	34634253	34634255	.	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34634256	34634669	0.95	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34634256	34634669	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34634670	34634749	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34634750	34634854	1	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34634750	34634854	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34634855	34634995	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34634996	34635055	1	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34634996	34635055	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34635056	34635139	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34635140	34635249	1	-	2	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34635140	34635249	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34635250	34635363	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34635364	34635489	1	-	2	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34635364	34635489	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34635490	34635613	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34635614	34635796	1	-	2	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34635614	34635796	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34635797	34635878	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34635879	34635999	1	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34635879	34635999	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34636000	34636131	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34636132	34636189	1	-	1	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34636132	34636189	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	intron	34636190	34636656	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	CDS	34636657	34636820	0.52	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	exon	34636657	34636820	.	-	.	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
Phchi.S2	AUGUSTUS	start_codon	34636818	34636820	.	-	0	transcript_id "Phchi.S2G063300.t1"; gene_id "Phchi.S2G063300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10497.t1 is derived from g14546.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	708947	709675	.	-	.	Phchi.S4G007900
Phchi.S4	AUGUSTUS	transcript	708947	709675	.	-	.	transcript_id "Phchi.S4G007900.t1"; gene_id "Phchi.S4G007900"
Phchi.S4	AUGUSTUS	stop_codon	708944	708946	.	-	0	transcript_id "Phchi.S4G007900.t1"; gene_id "Phchi.S4G007900"
Phchi.S4	AUGUSTUS	CDS	708947	709675	0.97	-	0	transcript_id "Phchi.S4G007900.t1"; gene_id "Phchi.S4G007900"
Phchi.S4	AUGUSTUS	exon	708947	709675	.	-	.	transcript_id "Phchi.S4G007900.t1"; gene_id "Phchi.S4G007900"
Phchi.S4	AUGUSTUS	start_codon	709673	709675	.	-	0	transcript_id "Phchi.S4G007900.t1"; gene_id "Phchi.S4G007900"
# This transcript jg12412.t2 is derived from g8089.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12413.t1 is derived from g8090.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18511970	18522638	.	-	.	Phchi.S2G049300
Phchi.S2	AUGUSTUS	transcript	18511970	18522638	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	stop_codon	18511967	18511969	.	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18511970	18512161	0.57	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18511970	18512161	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512162	18512321	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512322	18512453	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512322	18512453	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512454	18512589	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512590	18512701	1	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512590	18512701	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512702	18512810	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512811	18512878	0.97	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512811	18512878	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512879	18513070	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513071	18513145	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513071	18513145	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513146	18513389	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513390	18513464	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513390	18513464	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513465	18513542	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513543	18513698	0.97	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513543	18513698	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513699	18513816	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513817	18513904	1	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513817	18513904	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513905	18514027	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514028	18514101	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514028	18514101	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18514102	18514724	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514725	18514827	1	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514725	18514827	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18514828	18514981	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514982	18515073	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514982	18515073	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515074	18515333	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515334	18515420	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515334	18515420	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515421	18515520	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515521	18515580	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515521	18515580	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515581	18515927	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515928	18515981	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515928	18515981	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515982	18516195	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516196	18516273	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516196	18516273	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516274	18516428	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516429	18516551	0.93	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516429	18516551	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516552	18516631	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516632	18516664	0.88	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516632	18516664	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516665	18516795	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516796	18516876	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516796	18516876	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516877	18517142	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517143	18517229	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517143	18517229	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517230	18517410	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517411	18517462	0.9	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517411	18517462	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517463	18517582	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517583	18517903	0.83	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517583	18517903	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517904	18518058	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518059	18518273	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518059	18518273	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518274	18518405	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518406	18518561	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518406	18518561	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518562	18518649	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518650	18518712	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518650	18518712	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518713	18519525	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18519526	18519636	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18519526	18519636	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18519637	18519720	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18519721	18519841	1	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18519721	18519841	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18519842	18520005	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520006	18520091	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520006	18520091	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520092	18520168	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520169	18520264	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520169	18520264	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520265	18520358	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520359	18520460	1	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520359	18520460	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520461	18520655	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520656	18520761	1	-	1	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520656	18520761	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520762	18521433	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18521434	18522638	0.99	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18521434	18522638	.	-	.	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	start_codon	18522636	18522638	.	-	0	transcript_id "Phchi.S2G049300.t1"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	transcript	18512463	18522638	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	stop_codon	18512460	18512462	.	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512463	18512498	0.74	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512463	18512498	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512499	18512589	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512590	18512701	0.79	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512590	18512701	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512702	18512810	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512811	18512878	0.97	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512811	18512878	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512879	18513070	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513071	18513145	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513071	18513145	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513146	18513389	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513390	18513464	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513390	18513464	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513465	18513542	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513543	18513698	0.95	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513543	18513698	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513699	18513816	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513817	18513904	1	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513817	18513904	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513905	18514027	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514028	18514101	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514028	18514101	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18514102	18514724	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514725	18514827	1	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514725	18514827	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18514828	18514981	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514982	18515073	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514982	18515073	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515074	18515333	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515334	18515420	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515334	18515420	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515421	18515520	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515521	18515580	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515521	18515580	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515581	18515927	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515928	18515981	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515928	18515981	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515982	18516195	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516196	18516273	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516196	18516273	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516274	18516428	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516429	18516551	0.93	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516429	18516551	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516552	18516631	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516632	18516664	0.89	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516632	18516664	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516665	18516795	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516796	18516876	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516796	18516876	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516877	18517142	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517143	18517229	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517143	18517229	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517230	18517410	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517411	18517462	0.85	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517411	18517462	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517463	18517582	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517583	18517903	0.77	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517583	18517903	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517904	18518058	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518059	18518273	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518059	18518273	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518274	18518405	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518406	18518561	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518406	18518561	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518562	18518649	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518650	18518712	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518650	18518712	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518713	18519525	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18519526	18519636	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18519526	18519636	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18519637	18519720	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18519721	18519841	1	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18519721	18519841	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18519842	18520005	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520006	18520091	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520006	18520091	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520092	18520168	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520169	18520264	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520169	18520264	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520265	18520358	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520359	18520460	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520359	18520460	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520461	18520655	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520656	18520761	1	-	1	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520656	18520761	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520762	18521433	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18521434	18522638	1	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18521434	18522638	.	-	.	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	start_codon	18522636	18522638	.	-	0	transcript_id "Phchi.S2G049300.t2"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	transcript	18511970	18522638	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	stop_codon	18511967	18511969	.	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18511970	18512161	0.53	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18511970	18512161	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512162	18512321	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512322	18512453	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512322	18512453	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512454	18512589	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512590	18512701	1	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512590	18512701	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512702	18512810	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18512811	18512878	0.97	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18512811	18512878	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18512879	18513070	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513071	18513145	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513071	18513145	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513146	18513389	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513390	18513464	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513390	18513464	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513465	18513542	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513543	18513698	0.98	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513543	18513698	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513699	18513816	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18513817	18513904	1	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18513817	18513904	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18513905	18514027	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514028	18514101	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514028	18514101	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18514102	18514724	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514725	18514827	1	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514725	18514827	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18514828	18514981	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18514982	18515073	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18514982	18515073	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515074	18515333	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515334	18515420	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515334	18515420	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515421	18515520	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515521	18515580	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515521	18515580	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515581	18515927	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18515928	18515981	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18515928	18515981	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18515982	18516195	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516196	18516273	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516196	18516273	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516274	18516428	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516429	18516551	0.89	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516429	18516551	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516552	18516631	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516632	18516664	0.85	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516632	18516664	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516665	18516795	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18516796	18516876	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18516796	18516876	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18516877	18517142	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517143	18517229	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517143	18517229	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517230	18517410	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517411	18517462	0.92	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517411	18517462	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517463	18517582	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18517583	18517903	0.85	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18517583	18517903	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18517904	18518058	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518059	18518273	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518059	18518273	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518274	18518405	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518406	18518561	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518406	18518561	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518562	18518649	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18518650	18518712	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18518650	18518712	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18518713	18519525	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18519526	18519636	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18519526	18519636	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18519637	18519720	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18519721	18519841	1	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18519721	18519841	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18519842	18520005	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520006	18520091	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520006	18520091	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520092	18520168	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520169	18520264	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520169	18520264	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520265	18520358	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520359	18520460	1	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520359	18520460	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520461	18520655	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18520656	18520755	0.73	-	1	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18520656	18520755	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	intron	18520756	18521433	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	CDS	18521434	18522638	0.81	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	exon	18521434	18522638	.	-	.	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
Phchi.S2	AUGUSTUS	start_codon	18522636	18522638	.	-	0	transcript_id "Phchi.S2G049300.t3"; gene_id "Phchi.S2G049300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12026.t1 is derived from g7701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	632354	632810	.	-	.	Phchi.S2G010600
Phchi.S2	AUGUSTUS	transcript	632354	632810	.	-	.	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	stop_codon	632351	632353	.	-	0	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	CDS	632354	632633	0.9	-	1	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	exon	632354	632633	.	-	.	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	intron	632634	632715	.	-	.	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	CDS	632716	632810	0.55	-	0	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	exon	632716	632810	.	-	.	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
Phchi.S2	AUGUSTUS	start_codon	632808	632810	.	-	0	transcript_id "Phchi.S2G010600.t1"; gene_id "Phchi.S2G010600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11788.t1 is derived from g15840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8155754	8156176	.	+	.	Phchi.S4G137000
Phchi.S4	AUGUSTUS	transcript	8155754	8156176	.	+	.	transcript_id "Phchi.S4G137000.t1"; gene_id "Phchi.S4G137000"
Phchi.S4	AUGUSTUS	start_codon	8155754	8155756	.	+	0	transcript_id "Phchi.S4G137000.t1"; gene_id "Phchi.S4G137000"
Phchi.S4	AUGUSTUS	CDS	8155754	8156176	1	+	0	transcript_id "Phchi.S4G137000.t1"; gene_id "Phchi.S4G137000"
Phchi.S4	AUGUSTUS	exon	8155754	8156176	.	+	.	transcript_id "Phchi.S4G137000.t1"; gene_id "Phchi.S4G137000"
Phchi.S4	AUGUSTUS	stop_codon	8156177	8156179	.	+	0	transcript_id "Phchi.S4G137000.t1"; gene_id "Phchi.S4G137000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14739.t1 is derived from g13207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14460282	14462899	.	+	.	Phchi.S3G205800
Phchi.S3	AUGUSTUS	transcript	14460282	14462899	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	start_codon	14460282	14460284	.	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14460282	14460605	0.99	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14460282	14460605	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14460606	14460719	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14460720	14460854	1	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14460720	14460854	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14460855	14460999	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14461000	14461099	1	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14461000	14461099	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14461100	14461187	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14461188	14461313	1	+	2	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14461188	14461313	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14461314	14461411	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14461412	14461725	0.99	+	2	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14461412	14461725	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14461726	14461852	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14461853	14461972	1	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14461853	14461972	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14461973	14462048	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14462049	14462303	0.99	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14462049	14462303	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14462304	14462403	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14462404	14462529	1	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14462404	14462529	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	intron	14462530	14462617	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	CDS	14462618	14462899	1	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	exon	14462618	14462899	.	+	.	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
Phchi.S3	AUGUSTUS	stop_codon	14462900	14462902	.	+	0	transcript_id "Phchi.S3G205800.t1"; gene_id "Phchi.S3G205800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12689.t1 is derived from g11154.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	246704	248488	.	+	.	Phchi.S3G000800
Phchi.S3	AUGUSTUS	transcript	246704	247164	.	+	.	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	start_codon	246704	246706	.	+	0	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	CDS	246704	246978	0.75	+	0	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	exon	246704	246978	.	+	.	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	intron	246979	247079	.	+	.	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	CDS	247080	247164	0.75	+	1	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	exon	247080	247164	.	+	.	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	stop_codon	247165	247167	.	+	0	transcript_id "Phchi.S3G000800.t1"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	transcript	246704	248055	.	+	.	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	start_codon	246704	246706	.	+	0	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	CDS	246704	247970	0.51	+	0	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	exon	246704	247970	.	+	.	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	intron	247971	248041	.	+	.	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	CDS	248042	248055	0.79	+	2	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	exon	248042	248055	.	+	.	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	stop_codon	248056	248058	.	+	0	transcript_id "Phchi.S3G000800.t2"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	transcript	246704	248488	.	+	.	transcript_id "Phchi.S3G000800.t3"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	start_codon	246704	246706	.	+	0	transcript_id "Phchi.S3G000800.t3"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	CDS	246704	248488	0.91	+	0	transcript_id "Phchi.S3G000800.t3"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	exon	246704	248488	.	+	.	transcript_id "Phchi.S3G000800.t3"; gene_id "Phchi.S3G000800"
Phchi.S3	AUGUSTUS	stop_codon	248489	248491	.	+	0	transcript_id "Phchi.S3G000800.t3"; gene_id "Phchi.S3G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2403.t1 is derived from g9323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6497026	6497542	.	-	.	Phchi.S5G101200
Phchi.S5	AUGUSTUS	transcript	6497026	6497542	.	-	.	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	stop_codon	6497023	6497025	.	-	0	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	CDS	6497026	6497137	0.78	-	1	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	exon	6497026	6497137	.	-	.	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	intron	6497138	6497240	.	-	.	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	CDS	6497241	6497542	0.78	-	0	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	exon	6497241	6497542	.	-	.	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
Phchi.S5	AUGUSTUS	start_codon	6497540	6497542	.	-	0	transcript_id "Phchi.S5G101200.t1"; gene_id "Phchi.S5G101200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7842.t1 is derived from g5016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31485761	31489249	.	-	.	Phchi.S1G500100
Phchi.S1	AUGUSTUS	transcript	31485761	31489249	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	stop_codon	31485758	31485760	.	-	0	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	CDS	31485761	31488055	1	-	0	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	exon	31485761	31488055	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	intron	31488056	31488146	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	CDS	31488147	31488314	0.97	-	0	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	exon	31488147	31488314	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	intron	31488315	31489072	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	CDS	31489073	31489127	0.81	-	1	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	exon	31489073	31489127	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	intron	31489128	31489244	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	CDS	31489245	31489249	0.4	-	0	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	exon	31489245	31489249	.	-	.	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
Phchi.S1	AUGUSTUS	start_codon	31489247	31489249	.	-	0	transcript_id "Phchi.S1G500100.t1"; gene_id "Phchi.S1G500100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10169.t1 is derived from g7345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46082869	46086671	.	-	.	Phchi.S1G732800
Phchi.S1	AUGUSTUS	transcript	46082869	46086671	.	-	.	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	stop_codon	46082866	46082868	.	-	0	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	CDS	46082869	46086081	0.92	-	0	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	exon	46082869	46086081	.	-	.	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	intron	46086082	46086278	.	-	.	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	CDS	46086279	46086671	0.99	-	0	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	exon	46086279	46086671	.	-	.	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
Phchi.S1	AUGUSTUS	start_codon	46086669	46086671	.	-	0	transcript_id "Phchi.S1G732800.t1"; gene_id "Phchi.S1G732800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15768.t1 is derived from g14238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21264649	21269405	.	-	.	Phchi.S3G308700
Phchi.S3	AUGUSTUS	transcript	21264649	21269405	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	stop_codon	21264646	21264648	.	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21264649	21265047	0.94	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21264649	21265047	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	intron	21265048	21265144	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21265145	21265493	0.98	-	1	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21265145	21265493	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	intron	21265494	21265659	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21265660	21268058	0.73	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21265660	21268058	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	intron	21268059	21268155	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21268156	21268266	1	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21268156	21268266	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	intron	21268267	21268356	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21268357	21268461	1	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21268357	21268461	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	intron	21268462	21268541	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21268542	21268697	0.99	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21268542	21268697	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	intron	21268698	21268823	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	CDS	21268824	21269405	1	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	exon	21268824	21269405	.	-	.	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
Phchi.S3	AUGUSTUS	start_codon	21269403	21269405	.	-	0	transcript_id "Phchi.S3G308700.t1"; gene_id "Phchi.S3G308700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4162.t1 is derived from g1331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8686795	8690837	.	+	.	Phchi.S1G132100
Phchi.S1	AUGUSTUS	transcript	8686795	8690837	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	start_codon	8686795	8686797	.	+	0	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	CDS	8686795	8687019	0.69	+	0	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	exon	8686795	8687019	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	intron	8687020	8687196	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	CDS	8687197	8687203	1	+	0	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	exon	8687197	8687203	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	intron	8687204	8687283	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	CDS	8687284	8687347	1	+	2	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	exon	8687284	8687347	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	intron	8687348	8687499	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	CDS	8687500	8689610	0.98	+	1	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	exon	8687500	8689610	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	intron	8689611	8689851	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	CDS	8689852	8690346	0.64	+	2	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	exon	8689852	8690346	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	intron	8690347	8690457	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	CDS	8690458	8690837	0.6	+	2	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	exon	8690458	8690837	.	+	.	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
Phchi.S1	AUGUSTUS	stop_codon	8690838	8690840	.	+	0	transcript_id "Phchi.S1G132100.t1"; gene_id "Phchi.S1G132100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2852.t1 is derived from g21.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24250	28398	.	-	.	Phchi.S1G001100
Phchi.S1	AUGUSTUS	transcript	24250	28398	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	stop_codon	24247	24249	.	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	24250	24322	0.99	-	1	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	24250	24322	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	24323	24427	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	24428	24501	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	24428	24501	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	24502	24594	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	24595	24675	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	24595	24675	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	24676	24974	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	24975	25066	1	-	2	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	24975	25066	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	25067	25155	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	25156	25313	1	-	1	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	25156	25313	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	25314	25414	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	25415	25505	1	-	2	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	25415	25505	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	25506	25612	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	25613	25698	1	-	1	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	25613	25698	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	25699	25853	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	25854	25909	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	25854	25909	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	25910	26012	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	26013	26084	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	26013	26084	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	26085	26220	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	26221	26307	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	26221	26307	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	26308	26429	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	26430	26489	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	26430	26489	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	26490	26569	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	26570	26656	1	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	26570	26656	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	26657	26821	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	26822	27023	0.99	-	1	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	26822	27023	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	27024	27208	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	27209	27338	1	-	2	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	27209	27338	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	27339	27472	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	27473	27568	1	-	2	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	27473	27568	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	intron	27569	27869	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	CDS	27870	28398	0.93	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	exon	27870	28398	.	-	.	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
Phchi.S1	AUGUSTUS	start_codon	28396	28398	.	-	0	transcript_id "Phchi.S1G001100.t1"; gene_id "Phchi.S1G001100"
# This transcript jg1788.t2 is derived from g8708.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1789.t1 is derived from g8709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3019103	3022470	.	+	.	Phchi.S5G039800
Phchi.S5	AUGUSTUS	transcript	3019103	3022470	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	start_codon	3019103	3019105	.	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3019103	3019158	0.5	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3019103	3019158	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3019159	3019247	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3019248	3019566	0.47	+	1	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3019248	3019566	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3019567	3019701	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3019702	3019750	1	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3019702	3019750	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3019751	3019863	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3019864	3020071	0.95	+	2	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3019864	3020071	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3020072	3020174	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3020175	3020349	1	+	1	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3020175	3020349	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3020350	3020441	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3020442	3020507	1	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3020442	3020507	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3020508	3020597	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3020598	3020711	1	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3020598	3020711	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3020712	3020832	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3020833	3020949	1	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3020833	3020949	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3020950	3021055	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3021056	3021182	1	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3021056	3021182	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3021183	3021299	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3021300	3021586	1	+	2	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3021300	3021586	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3021587	3021678	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3021679	3021869	0.99	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3021679	3021869	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3021870	3021944	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3021945	3022030	1	+	1	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3021945	3022030	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3022031	3022137	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3022138	3022214	1	+	2	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3022138	3022214	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	intron	3022215	3022311	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	CDS	3022312	3022470	0.96	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	exon	3022312	3022470	.	+	.	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
Phchi.S5	AUGUSTUS	stop_codon	3022471	3022473	.	+	0	transcript_id "Phchi.S5G039800.t1"; gene_id "Phchi.S5G039800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11201.t1 is derived from g15251.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4659884	4662087	.	+	.	Phchi.S4G078300
Phchi.S4	AUGUSTUS	transcript	4659884	4662080	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	start_codon	4659884	4659886	.	+	0	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4659884	4660178	0.98	+	0	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4659884	4660178	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660179	4660279	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4660280	4660429	0.99	+	2	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4660280	4660429	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660430	4660597	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4660598	4660812	1	+	2	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4660598	4660812	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660813	4660915	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4660916	4660986	0.78	+	0	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4660916	4660986	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660987	4661096	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661097	4661259	1	+	1	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661097	4661259	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661260	4661337	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661338	4661512	1	+	0	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661338	4661512	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661513	4661578	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661579	4661737	1	+	2	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661579	4661737	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661738	4661812	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661813	4661890	0.97	+	2	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661813	4661890	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661891	4661982	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661983	4662080	0.94	+	2	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661983	4662080	.	+	.	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	stop_codon	4662081	4662083	.	+	0	transcript_id "Phchi.S4G078300.t1"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	transcript	4659884	4662087	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	start_codon	4659884	4659886	.	+	0	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4659884	4660178	0.99	+	0	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4659884	4660178	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660179	4660279	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4660280	4660429	0.94	+	2	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4660280	4660429	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660430	4660597	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4660598	4660812	1	+	2	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4660598	4660812	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660813	4660915	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4660916	4660986	0.87	+	0	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4660916	4660986	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4660987	4661096	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661097	4661259	1	+	1	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661097	4661259	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661260	4661337	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661338	4661512	1	+	0	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661338	4661512	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661513	4661578	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661579	4661737	1	+	2	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661579	4661737	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661738	4661812	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661813	4661901	1	+	2	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661813	4661901	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	intron	4661902	4661982	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	CDS	4661983	4662087	0.67	+	0	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	exon	4661983	4662087	.	+	.	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
Phchi.S4	AUGUSTUS	stop_codon	4662088	4662090	.	+	0	transcript_id "Phchi.S4G078300.t2"; gene_id "Phchi.S4G078300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11222.t1 is derived from g15272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4862765	4863325	.	-	.	Phchi.S4G080400
Phchi.S4	AUGUSTUS	transcript	4862765	4863325	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	stop_codon	4862762	4862764	.	-	0	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	CDS	4862765	4862804	1	-	1	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	exon	4862765	4862804	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	intron	4862805	4862910	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	CDS	4862911	4862978	1	-	0	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	exon	4862911	4862978	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	intron	4862979	4863068	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	CDS	4863069	4863120	0.63	-	1	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	exon	4863069	4863120	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	intron	4863121	4863242	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	CDS	4863243	4863325	0.62	-	0	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	exon	4863243	4863325	.	-	.	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
Phchi.S4	AUGUSTUS	start_codon	4863323	4863325	.	-	0	transcript_id "Phchi.S4G080400.t1"; gene_id "Phchi.S4G080400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1534.t1 is derived from g8453.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1652906	1653816	.	-	.	Phchi.S5G014300
Phchi.S5	AUGUSTUS	transcript	1652906	1653816	.	-	.	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	stop_codon	1652903	1652905	.	-	0	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	CDS	1652906	1653106	0.99	-	0	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	exon	1652906	1653106	.	-	.	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	intron	1653107	1653200	.	-	.	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	CDS	1653201	1653282	1	-	1	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	exon	1653201	1653282	.	-	.	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	intron	1653283	1653391	.	-	.	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	CDS	1653392	1653816	0.43	-	0	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	exon	1653392	1653816	.	-	.	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
Phchi.S5	AUGUSTUS	start_codon	1653814	1653816	.	-	0	transcript_id "Phchi.S5G014300.t1"; gene_id "Phchi.S5G014300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg14771.t1 is derived from g13239.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14637183	14643175	.	-	.	Phchi.S3G209000
Phchi.S3	AUGUSTUS	transcript	14637183	14643110	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	stop_codon	14637180	14637182	.	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14637183	14637650	0.89	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14637183	14637650	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14637651	14637744	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14637745	14638010	1	-	2	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14637745	14638010	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638011	14638102	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638103	14638415	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638103	14638415	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638416	14638507	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638508	14638718	1	-	1	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638508	14638718	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638719	14638794	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638795	14638913	0.95	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638795	14638913	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638914	14639029	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639030	14639326	0.94	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639030	14639326	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639327	14639411	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639412	14639681	0.99	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639412	14639681	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639682	14639770	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639771	14639971	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639771	14639971	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639972	14640226	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640227	14640427	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640227	14640427	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640428	14640649	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640650	14640730	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640650	14640730	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640731	14640819	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640820	14641023	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640820	14641023	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641024	14641172	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641173	14641256	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641173	14641256	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641257	14641350	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641351	14641503	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641351	14641503	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641504	14641639	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641640	14641729	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641640	14641729	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641730	14641824	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641825	14641953	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641825	14641953	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641954	14642042	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642043	14642050	0.59	-	2	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642043	14642050	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642051	14642103	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642104	14642138	0.59	-	1	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642104	14642138	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642139	14642219	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642220	14642300	0.59	-	1	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642220	14642300	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642301	14642389	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642390	14642461	0.59	-	1	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642390	14642461	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642462	14642561	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642562	14642658	0.63	-	2	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642562	14642658	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642659	14642745	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642746	14642829	1	-	2	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642746	14642829	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642830	14642916	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642917	14642968	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642917	14642968	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642969	14643077	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14643078	14643110	1	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14643078	14643110	.	-	.	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	start_codon	14643108	14643110	.	-	0	transcript_id "Phchi.S3G209000.t1"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	transcript	14637183	14643175	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	stop_codon	14637180	14637182	.	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14637183	14637650	0.81	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14637183	14637650	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14637651	14637744	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14637745	14638010	1	-	2	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14637745	14638010	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638011	14638102	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638103	14638415	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638103	14638415	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638416	14638507	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638508	14638718	1	-	1	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638508	14638718	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638719	14638794	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638795	14638913	0.95	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638795	14638913	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638914	14639029	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639030	14639326	0.96	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639030	14639326	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639327	14639411	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639412	14639681	0.99	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639412	14639681	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639682	14639770	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639771	14639971	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639771	14639971	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639972	14640226	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640227	14640427	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640227	14640427	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640428	14640649	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640650	14640730	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640650	14640730	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640731	14640819	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640820	14641023	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640820	14641023	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641024	14641172	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641173	14641256	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641173	14641256	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641257	14641350	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641351	14641503	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641351	14641503	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641504	14641639	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641640	14641729	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641640	14641729	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641730	14641824	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641825	14641953	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641825	14641953	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641954	14642042	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642043	14642138	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642043	14642138	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642139	14642219	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642220	14642300	1	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642220	14642300	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642301	14642389	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642390	14642472	0.65	-	2	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642390	14642472	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642473	14642561	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642562	14642658	0.65	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642562	14642658	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642659	14642745	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642746	14642829	0.65	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642746	14642829	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642830	14642916	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642917	14642968	0.63	-	1	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642917	14642968	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642969	14643077	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14643078	14643175	0.32	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14643078	14643175	.	-	.	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	start_codon	14643173	14643175	.	-	0	transcript_id "Phchi.S3G209000.t2"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	transcript	14637183	14643110	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	stop_codon	14637180	14637182	.	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14637183	14637650	0.86	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14637183	14637650	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14637651	14637744	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14637745	14638010	1	-	2	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14637745	14638010	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638011	14638102	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638103	14638415	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638103	14638415	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638416	14638507	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638508	14638718	1	-	1	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638508	14638718	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638719	14638794	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14638795	14638913	0.94	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14638795	14638913	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14638914	14639029	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639030	14639326	0.98	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639030	14639326	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639327	14639411	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639412	14639681	0.98	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639412	14639681	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639682	14639770	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14639771	14639971	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14639771	14639971	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14639972	14640226	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640227	14640347	0.59	-	1	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640227	14640347	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640348	14640427	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640428	14640432	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640428	14640432	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640433	14640649	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640650	14640730	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640650	14640730	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14640731	14640819	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14640820	14641023	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14640820	14641023	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641024	14641172	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641173	14641256	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641173	14641256	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641257	14641350	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641351	14641503	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641351	14641503	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641504	14641639	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641640	14641729	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641640	14641729	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641730	14641824	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14641825	14641953	1	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14641825	14641953	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14641954	14642042	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642043	14642050	0.35	-	2	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642043	14642050	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642051	14642103	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642104	14642138	0.35	-	1	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642104	14642138	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642139	14642219	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642220	14642300	0.35	-	1	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642220	14642300	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642301	14642389	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642390	14642461	0.35	-	1	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642390	14642461	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642462	14642561	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642562	14642658	0.41	-	2	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642562	14642658	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642659	14642745	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642746	14642829	0.76	-	2	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642746	14642829	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642830	14642916	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14642917	14642968	0.76	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14642917	14642968	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	intron	14642969	14643077	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	CDS	14643078	14643110	0.76	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	exon	14643078	14643110	.	-	.	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
Phchi.S3	AUGUSTUS	start_codon	14643108	14643110	.	-	0	transcript_id "Phchi.S3G209000.t3"; gene_id "Phchi.S3G209000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13445.t1 is derived from g11912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6740384	6741701	.	-	.	Phchi.S3G076400
Phchi.S3	AUGUSTUS	transcript	6740384	6741701	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	stop_codon	6740381	6740383	.	-	0	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6740384	6740446	1	-	0	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6740384	6740446	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	intron	6740447	6740538	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6740539	6740615	1	-	2	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6740539	6740615	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	intron	6740616	6740732	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6740733	6740777	1	-	2	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6740733	6740777	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	intron	6740778	6740857	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6740858	6740980	1	-	2	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6740858	6740980	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	intron	6740981	6741076	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6741077	6741110	1	-	0	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6741077	6741110	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	intron	6741111	6741197	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6741198	6741336	0.95	-	1	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6741198	6741336	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	intron	6741337	6741438	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	CDS	6741439	6741701	0.99	-	0	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	exon	6741439	6741701	.	-	.	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
Phchi.S3	AUGUSTUS	start_codon	6741699	6741701	.	-	0	transcript_id "Phchi.S3G076400.t1"; gene_id "Phchi.S3G076400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3138.t1 is derived from g307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1945475	1947614	.	-	.	Phchi.S1G029700
Phchi.S1	AUGUSTUS	transcript	1945475	1947614	.	-	.	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	stop_codon	1945472	1945474	.	-	0	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	CDS	1945475	1947194	1	-	1	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	exon	1945475	1947194	.	-	.	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	intron	1947195	1947333	.	-	.	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	CDS	1947334	1947614	1	-	0	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	exon	1947334	1947614	.	-	.	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
Phchi.S1	AUGUSTUS	start_codon	1947612	1947614	.	-	0	transcript_id "Phchi.S1G029700.t1"; gene_id "Phchi.S1G029700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1478.t1 is derived from g8397.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1117045	1117644	.	+	.	Phchi.S5G008700
Phchi.S5	AUGUSTUS	transcript	1117045	1117644	.	+	.	transcript_id "Phchi.S5G008700.t1"; gene_id "Phchi.S5G008700"
Phchi.S5	AUGUSTUS	start_codon	1117045	1117047	.	+	0	transcript_id "Phchi.S5G008700.t1"; gene_id "Phchi.S5G008700"
Phchi.S5	AUGUSTUS	CDS	1117045	1117644	0.67	+	0	transcript_id "Phchi.S5G008700.t1"; gene_id "Phchi.S5G008700"
Phchi.S5	AUGUSTUS	exon	1117045	1117644	.	+	.	transcript_id "Phchi.S5G008700.t1"; gene_id "Phchi.S5G008700"
Phchi.S5	AUGUSTUS	stop_codon	1117645	1117647	.	+	0	transcript_id "Phchi.S5G008700.t1"; gene_id "Phchi.S5G008700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7029.t1 is derived from g4201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26489999	26490526	.	-	.	Phchi.S1G418800
Phchi.S1	AUGUSTUS	transcript	26489999	26490526	.	-	.	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	stop_codon	26489996	26489998	.	-	0	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	CDS	26489999	26490081	0.87	-	2	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	exon	26489999	26490081	.	-	.	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	intron	26490082	26490286	.	-	.	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	CDS	26490287	26490370	0.87	-	2	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	exon	26490287	26490370	.	-	.	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	intron	26490371	26490477	.	-	.	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	CDS	26490478	26490526	0.12	-	0	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	exon	26490478	26490526	.	-	.	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
Phchi.S1	AUGUSTUS	start_codon	26490524	26490526	.	-	0	transcript_id "Phchi.S1G418800.t1"; gene_id "Phchi.S1G418800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8849.t1 is derived from g6024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38268510	38270422	.	+	.	Phchi.S1G600800
Phchi.S1	AUGUSTUS	transcript	38268510	38270422	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	start_codon	38268510	38268512	.	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38268510	38268590	1	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38268510	38268590	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38268591	38268681	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38268682	38268756	1	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38268682	38268756	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38268757	38268867	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38268868	38268940	1	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38268868	38268940	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38268941	38269050	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38269051	38269095	1	+	2	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38269051	38269095	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38269096	38269269	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38269270	38269381	1	+	2	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38269270	38269381	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38269382	38269506	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38269507	38269573	1	+	1	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38269507	38269573	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38269574	38269673	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38269674	38269718	1	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38269674	38269718	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38269719	38269801	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38269802	38269857	1	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38269802	38269857	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38269858	38269976	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38269977	38270152	1	+	1	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38269977	38270152	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	intron	38270153	38270255	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	CDS	38270256	38270422	0.65	+	2	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	exon	38270256	38270422	.	+	.	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
Phchi.S1	AUGUSTUS	stop_codon	38270423	38270425	.	+	0	transcript_id "Phchi.S1G600800.t1"; gene_id "Phchi.S1G600800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10048.t1 is derived from g7224.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45277960	45279195	.	+	.	Phchi.S1G720700
Phchi.S1	AUGUSTUS	transcript	45277960	45279195	.	+	.	transcript_id "Phchi.S1G720700.t1"; gene_id "Phchi.S1G720700"
Phchi.S1	AUGUSTUS	start_codon	45277960	45277962	.	+	0	transcript_id "Phchi.S1G720700.t1"; gene_id "Phchi.S1G720700"
Phchi.S1	AUGUSTUS	CDS	45277960	45279195	0.49	+	0	transcript_id "Phchi.S1G720700.t1"; gene_id "Phchi.S1G720700"
Phchi.S1	AUGUSTUS	exon	45277960	45279195	.	+	.	transcript_id "Phchi.S1G720700.t1"; gene_id "Phchi.S1G720700"
Phchi.S1	AUGUSTUS	stop_codon	45279196	45279198	.	+	0	transcript_id "Phchi.S1G720700.t1"; gene_id "Phchi.S1G720700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6435.t1 is derived from g3607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23027011	23028695	.	-	.	Phchi.S1G359400
Phchi.S1	AUGUSTUS	transcript	23027011	23028695	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	stop_codon	23027008	23027010	.	-	0	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	CDS	23027011	23027087	1	-	2	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	exon	23027011	23027087	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	intron	23027088	23027179	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	CDS	23027180	23027293	1	-	2	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	exon	23027180	23027293	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	intron	23027294	23027549	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	CDS	23027550	23027574	0.99	-	0	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	exon	23027550	23027574	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	intron	23027575	23027780	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	CDS	23027781	23028695	0.63	-	0	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	exon	23027781	23028695	.	-	.	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
Phchi.S1	AUGUSTUS	start_codon	23028693	23028695	.	-	0	transcript_id "Phchi.S1G359400.t1"; gene_id "Phchi.S1G359400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12938.t1 is derived from g11403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3250928	3253252	.	+	.	Phchi.S3G025700
Phchi.S3	AUGUSTUS	transcript	3250928	3253252	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	start_codon	3250928	3250930	.	+	0	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	CDS	3250928	3251196	0.75	+	0	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	exon	3250928	3251196	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	intron	3251197	3251287	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	CDS	3251288	3251986	0.53	+	1	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	exon	3251288	3251986	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	intron	3251987	3252069	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	CDS	3252070	3252228	0.53	+	1	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	exon	3252070	3252228	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	intron	3252229	3252894	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	CDS	3252895	3253252	0.42	+	1	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	exon	3252895	3253252	.	+	.	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
Phchi.S3	AUGUSTUS	stop_codon	3253253	3253255	.	+	0	transcript_id "Phchi.S3G025700.t1"; gene_id "Phchi.S3G025700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14154.t1 is derived from g12621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11178199	11179865	.	+	.	Phchi.S3G147300
Phchi.S3	AUGUSTUS	transcript	11178199	11179865	.	+	.	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	start_codon	11178199	11178201	.	+	0	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	CDS	11178199	11179540	0.39	+	0	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	exon	11178199	11179540	.	+	.	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	intron	11179541	11179593	.	+	.	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	CDS	11179594	11179688	0.55	+	2	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	exon	11179594	11179688	.	+	.	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	intron	11179689	11179817	.	+	.	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	CDS	11179818	11179865	0.71	+	0	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	exon	11179818	11179865	.	+	.	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
Phchi.S3	AUGUSTUS	stop_codon	11179866	11179868	.	+	0	transcript_id "Phchi.S3G147300.t1"; gene_id "Phchi.S3G147300"
# This transcript jg7845.t2 is derived from g5019.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7846.t1 is derived from g5020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31510036	31510939	.	-	.	Phchi.S1G500500
Phchi.S1	AUGUSTUS	transcript	31510036	31510939	.	-	.	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	stop_codon	31510033	31510035	.	-	0	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	CDS	31510036	31510314	0.91	-	0	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	exon	31510036	31510314	.	-	.	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	intron	31510315	31510398	.	-	.	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	CDS	31510399	31510595	1	-	2	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	exon	31510399	31510595	.	-	.	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	intron	31510596	31510680	.	-	.	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	CDS	31510681	31510939	0.59	-	0	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	exon	31510681	31510939	.	-	.	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
Phchi.S1	AUGUSTUS	start_codon	31510937	31510939	.	-	0	transcript_id "Phchi.S1G500500.t1"; gene_id "Phchi.S1G500500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13101.t1 is derived from g11566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4137021	4137485	.	+	.	Phchi.S3G042000
Phchi.S3	AUGUSTUS	transcript	4137021	4137485	.	+	.	transcript_id "Phchi.S3G042000.t1"; gene_id "Phchi.S3G042000"
Phchi.S3	AUGUSTUS	start_codon	4137021	4137023	.	+	0	transcript_id "Phchi.S3G042000.t1"; gene_id "Phchi.S3G042000"
Phchi.S3	AUGUSTUS	CDS	4137021	4137485	0.57	+	0	transcript_id "Phchi.S3G042000.t1"; gene_id "Phchi.S3G042000"
Phchi.S3	AUGUSTUS	exon	4137021	4137485	.	+	.	transcript_id "Phchi.S3G042000.t1"; gene_id "Phchi.S3G042000"
Phchi.S3	AUGUSTUS	stop_codon	4137486	4137488	.	+	0	transcript_id "Phchi.S3G042000.t1"; gene_id "Phchi.S3G042000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3328.t1 is derived from g497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2935911	2939769	.	+	.	Phchi.S1G048700
Phchi.S1	AUGUSTUS	transcript	2935911	2939481	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	start_codon	2935911	2935913	.	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2935911	2936069	0.74	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2935911	2936069	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2936070	2936186	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2936187	2936488	1	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2936187	2936488	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2936489	2936612	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2936613	2936856	0.99	+	1	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2936613	2936856	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2936857	2937090	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2937091	2937376	1	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2937091	2937376	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2937377	2937465	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2937466	2937692	1	+	2	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2937466	2937692	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2937693	2937811	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2937812	2937919	1	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2937812	2937919	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2937920	2938034	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2938035	2938307	1	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2938035	2938307	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2938308	2938408	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2938409	2938511	1	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2938409	2938511	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2938512	2938640	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2938641	2939011	0.98	+	2	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2938641	2939011	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2939012	2939094	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2939095	2939331	1	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2939095	2939331	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2939332	2939406	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2939407	2939481	0.98	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2939407	2939481	.	+	.	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	stop_codon	2939482	2939484	.	+	0	transcript_id "Phchi.S1G048700.t1"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	transcript	2935911	2939769	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	start_codon	2935911	2935913	.	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2935911	2936069	0.75	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2935911	2936069	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2936070	2936186	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2936187	2936488	1	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2936187	2936488	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2936489	2936612	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2936613	2936856	1	+	1	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2936613	2936856	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2936857	2937090	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2937091	2937376	1	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2937091	2937376	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2937377	2937465	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2937466	2937692	1	+	2	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2937466	2937692	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2937693	2937811	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2937812	2937919	1	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2937812	2937919	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2937920	2938034	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2938035	2938307	0.99	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2938035	2938307	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2938308	2938408	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2938409	2938511	1	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2938409	2938511	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2938512	2938640	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2938641	2939011	1	+	2	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2938641	2939011	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2939012	2939094	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2939095	2939331	1	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2939095	2939331	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2939332	2939428	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2939429	2939532	0.35	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2939429	2939532	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	intron	2939533	2939633	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	CDS	2939634	2939769	0.4	+	1	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	exon	2939634	2939769	.	+	.	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
Phchi.S1	AUGUSTUS	stop_codon	2939770	2939772	.	+	0	transcript_id "Phchi.S1G048700.t2"; gene_id "Phchi.S1G048700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14047.t1 is derived from g12514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10467534	10468627	.	-	.	Phchi.S3G136600
Phchi.S3	AUGUSTUS	transcript	10467534	10468627	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	stop_codon	10467531	10467533	.	-	0	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	CDS	10467534	10467617	0.98	-	0	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	exon	10467534	10467617	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	intron	10467618	10467703	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	CDS	10467704	10467901	0.99	-	0	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	exon	10467704	10467901	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	intron	10467902	10468064	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	CDS	10468065	10468377	1	-	1	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	exon	10468065	10468377	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	intron	10468378	10468460	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	CDS	10468461	10468627	0.91	-	0	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	exon	10468461	10468627	.	-	.	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
Phchi.S3	AUGUSTUS	start_codon	10468625	10468627	.	-	0	transcript_id "Phchi.S3G136600.t1"; gene_id "Phchi.S3G136600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13789.t1 is derived from g12256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8897644	8900024	.	-	.	Phchi.S3G110800
Phchi.S3	AUGUSTUS	transcript	8897644	8900024	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	stop_codon	8897641	8897643	.	-	0	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8897644	8897997	0.86	-	0	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8897644	8897997	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	intron	8897998	8898144	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8898145	8898277	1	-	1	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8898145	8898277	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	intron	8898278	8898402	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8898403	8898595	1	-	2	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8898403	8898595	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	intron	8898596	8898690	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8898691	8898721	0.92	-	0	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8898691	8898721	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	intron	8898722	8898878	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8898879	8899004	0.92	-	0	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8898879	8899004	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	intron	8899005	8899094	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8899095	8899357	1	-	2	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8899095	8899357	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	intron	8899358	8899456	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	CDS	8899457	8900024	0.61	-	0	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	exon	8899457	8900024	.	-	.	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
Phchi.S3	AUGUSTUS	start_codon	8900022	8900024	.	-	0	transcript_id "Phchi.S3G110800.t1"; gene_id "Phchi.S3G110800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10440.t1 is derived from g14490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	349087	350351	.	+	.	Phchi.S4G002300
Phchi.S4	AUGUSTUS	transcript	349087	350351	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	start_codon	349087	349089	.	+	0	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	CDS	349087	349302	0.21	+	0	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	exon	349087	349302	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	intron	349303	349609	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	CDS	349610	349685	0.78	+	0	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	exon	349610	349685	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	intron	349686	349750	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	CDS	349751	349818	0.95	+	2	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	exon	349751	349818	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	intron	349819	349906	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	CDS	349907	349999	1	+	0	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	exon	349907	349999	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	intron	350000	350086	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	CDS	350087	350220	1	+	0	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	exon	350087	350220	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	intron	350221	350311	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	CDS	350312	350351	1	+	1	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	exon	350312	350351	.	+	.	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
Phchi.S4	AUGUSTUS	stop_codon	350352	350354	.	+	0	transcript_id "Phchi.S4G002300.t1"; gene_id "Phchi.S4G002300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg717.t1 is derived from g10499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5078615	5079670	.	-	.	Phchi.S6G067600
Phchi.S6	AUGUSTUS	transcript	5078615	5079670	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	stop_codon	5078612	5078614	.	-	0	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	CDS	5078615	5078802	0.99	-	2	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	exon	5078615	5078802	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	intron	5078803	5078907	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	CDS	5078908	5079087	1	-	2	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	exon	5078908	5079087	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	intron	5079088	5079163	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	CDS	5079164	5079287	1	-	0	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	exon	5079164	5079287	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	intron	5079288	5079382	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	CDS	5079383	5079470	0.99	-	1	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	exon	5079383	5079470	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	intron	5079471	5079554	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	CDS	5079555	5079670	0.98	-	0	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	exon	5079555	5079670	.	-	.	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
Phchi.S6	AUGUSTUS	start_codon	5079668	5079670	.	-	0	transcript_id "Phchi.S6G067600.t1"; gene_id "Phchi.S6G067600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8739.t1 is derived from g5914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37754199	37754603	.	-	.	Phchi.S1G589800
Phchi.S1	AUGUSTUS	transcript	37754199	37754603	.	-	.	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	stop_codon	37754196	37754198	.	-	0	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	CDS	37754199	37754266	0.44	-	2	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	exon	37754199	37754266	.	-	.	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	intron	37754267	37754352	.	-	.	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	CDS	37754353	37754397	0.39	-	2	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	exon	37754353	37754397	.	-	.	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	intron	37754398	37754515	.	-	.	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	CDS	37754516	37754603	0.31	-	0	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	exon	37754516	37754603	.	-	.	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
Phchi.S1	AUGUSTUS	start_codon	37754601	37754603	.	-	0	transcript_id "Phchi.S1G589800.t1"; gene_id "Phchi.S1G589800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4193.t1 is derived from g1362.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8859193	8861489	.	+	.	Phchi.S1G135200
Phchi.S1	AUGUSTUS	transcript	8859193	8861489	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	start_codon	8859193	8859195	.	+	0	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	CDS	8859193	8859330	0.66	+	0	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	exon	8859193	8859330	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	intron	8859331	8859429	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	CDS	8859430	8859742	0.62	+	0	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	exon	8859430	8859742	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	intron	8859743	8859901	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	CDS	8859902	8860099	0.87	+	2	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	exon	8859902	8860099	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	intron	8860100	8860341	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	CDS	8860342	8861489	0.88	+	2	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	exon	8860342	8861489	.	+	.	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
Phchi.S1	AUGUSTUS	stop_codon	8861490	8861492	.	+	0	transcript_id "Phchi.S1G135200.t1"; gene_id "Phchi.S1G135200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7195.t1 is derived from g4367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27565874	27567986	.	-	.	Phchi.S1G435400
Phchi.S1	AUGUSTUS	transcript	27565874	27567986	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	stop_codon	27565871	27565873	.	-	0	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	CDS	27565874	27566506	1	-	0	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	exon	27565874	27566506	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	intron	27566507	27566596	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	CDS	27566597	27566796	1	-	2	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	exon	27566597	27566796	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	intron	27566797	27566931	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	CDS	27566932	27567001	1	-	0	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	exon	27566932	27567001	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	intron	27567002	27567086	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	CDS	27567087	27567237	1	-	1	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	exon	27567087	27567237	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	intron	27567238	27567328	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	CDS	27567329	27567562	1	-	1	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	exon	27567329	27567562	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	intron	27567563	27567672	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	CDS	27567673	27567986	0.99	-	0	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	exon	27567673	27567986	.	-	.	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
Phchi.S1	AUGUSTUS	start_codon	27567984	27567986	.	-	0	transcript_id "Phchi.S1G435400.t1"; gene_id "Phchi.S1G435400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12482.t1 is derived from g8159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28558600	28559457	.	+	.	Phchi.S2G056200
Phchi.S2	AUGUSTUS	transcript	28558600	28559457	.	+	.	transcript_id "Phchi.S2G056200.t1"; gene_id "Phchi.S2G056200"
Phchi.S2	AUGUSTUS	start_codon	28558600	28558602	.	+	0	transcript_id "Phchi.S2G056200.t1"; gene_id "Phchi.S2G056200"
Phchi.S2	AUGUSTUS	CDS	28558600	28559457	0.95	+	0	transcript_id "Phchi.S2G056200.t1"; gene_id "Phchi.S2G056200"
Phchi.S2	AUGUSTUS	exon	28558600	28559457	.	+	.	transcript_id "Phchi.S2G056200.t1"; gene_id "Phchi.S2G056200"
Phchi.S2	AUGUSTUS	stop_codon	28559458	28559460	.	+	0	transcript_id "Phchi.S2G056200.t1"; gene_id "Phchi.S2G056200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8091.t1 is derived from g5266.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32897216	32900308	.	-	.	Phchi.S1G525000
Phchi.S1	AUGUSTUS	transcript	32897216	32900308	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	stop_codon	32897213	32897215	.	-	0	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32897216	32897278	0.61	-	0	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32897216	32897278	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	intron	32897279	32897419	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32897420	32897439	0.46	-	2	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32897420	32897439	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	intron	32897440	32897575	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32897576	32897731	1	-	2	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32897576	32897731	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	intron	32897732	32898004	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32898005	32898831	0.74	-	1	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32898005	32898831	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	intron	32898832	32899155	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32899156	32899425	0.3	-	1	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32899156	32899425	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	intron	32899426	32899764	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32899765	32900216	0.45	-	0	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32899765	32900216	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	intron	32900217	32900302	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	CDS	32900303	32900308	0.39	-	0	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	exon	32900303	32900308	.	-	.	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
Phchi.S1	AUGUSTUS	start_codon	32900306	32900308	.	-	0	transcript_id "Phchi.S1G525000.t1"; gene_id "Phchi.S1G525000"
# This transcript jg5730.t2 is derived from g2900.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5731.t1 is derived from g2901.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18590771	18592592	.	+	.	Phchi.S1G289000
Phchi.S1	AUGUSTUS	transcript	18590771	18592592	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	start_codon	18590771	18590773	.	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18590771	18590960	0.47	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18590771	18590960	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18590961	18591055	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18591056	18591315	1	+	2	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18591056	18591315	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18591316	18591424	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18591425	18591469	1	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18591425	18591469	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18591470	18591638	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18591639	18591746	1	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18591639	18591746	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18591747	18591867	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18591868	18591963	1	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18591868	18591963	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18591964	18592055	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18592056	18592154	1	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18592056	18592154	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18592155	18592233	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18592234	18592293	0.98	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18592234	18592293	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18592294	18592365	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18592366	18592505	0.98	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18592366	18592505	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	intron	18592506	18592591	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	CDS	18592592	18592592	1	+	1	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	exon	18592592	18592592	.	+	.	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
Phchi.S1	AUGUSTUS	stop_codon	18592593	18592595	.	+	0	transcript_id "Phchi.S1G289000.t1"; gene_id "Phchi.S1G289000"
# This transcript jg7421.t2 is derived from g4593.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7422.t1 is derived from g4594.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29069437	29070450	.	+	.	Phchi.S1G458100
Phchi.S1	AUGUSTUS	transcript	29069437	29070268	.	+	.	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	start_codon	29069437	29069439	.	+	0	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	CDS	29069437	29070173	0.48	+	0	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	exon	29069437	29070173	.	+	.	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	intron	29070174	29070258	.	+	.	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	CDS	29070259	29070268	0.73	+	1	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	exon	29070259	29070268	.	+	.	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	stop_codon	29070269	29070271	.	+	0	transcript_id "Phchi.S1G458100.t1"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	transcript	29069437	29070450	.	+	.	transcript_id "Phchi.S1G458100.t2"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	start_codon	29069437	29069439	.	+	0	transcript_id "Phchi.S1G458100.t2"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	CDS	29069437	29070450	0.7	+	0	transcript_id "Phchi.S1G458100.t2"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	exon	29069437	29070450	.	+	.	transcript_id "Phchi.S1G458100.t2"; gene_id "Phchi.S1G458100"
Phchi.S1	AUGUSTUS	stop_codon	29070451	29070453	.	+	0	transcript_id "Phchi.S1G458100.t2"; gene_id "Phchi.S1G458100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10939.t1 is derived from g14989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3189333	3191361	.	-	.	Phchi.S4G052100
Phchi.S4	AUGUSTUS	transcript	3189333	3191361	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	stop_codon	3189330	3189332	.	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3189333	3189374	0.76	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3189333	3189374	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3189375	3189466	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3189467	3189548	1	-	1	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3189467	3189548	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3189549	3189696	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3189697	3189782	1	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3189697	3189782	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3189783	3189878	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3189879	3189942	1	-	1	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3189879	3189942	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3189943	3190083	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3190084	3190236	1	-	1	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3190084	3190236	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3190237	3190367	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3190368	3190420	1	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3190368	3190420	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3190421	3190612	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3190613	3190765	1	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3190613	3190765	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3190766	3191046	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3191047	3191112	1	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3191047	3191112	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	intron	3191113	3191223	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	CDS	3191224	3191361	0.79	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	exon	3191224	3191361	.	-	.	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
Phchi.S4	AUGUSTUS	start_codon	3191359	3191361	.	-	0	transcript_id "Phchi.S4G052100.t1"; gene_id "Phchi.S4G052100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6436.t1 is derived from g3608.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23028835	23030080	.	-	.	Phchi.S1G359500
Phchi.S1	AUGUSTUS	transcript	23028835	23030080	.	-	.	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	stop_codon	23028832	23028834	.	-	0	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	CDS	23028835	23028862	0.66	-	1	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	exon	23028835	23028862	.	-	.	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	intron	23028863	23028954	.	-	.	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	CDS	23028955	23029380	0.47	-	1	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	exon	23028955	23029380	.	-	.	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	intron	23029381	23029634	.	-	.	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	CDS	23029635	23030080	0.38	-	0	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	exon	23029635	23030080	.	-	.	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
Phchi.S1	AUGUSTUS	start_codon	23030078	23030080	.	-	0	transcript_id "Phchi.S1G359500.t1"; gene_id "Phchi.S1G359500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14060.t1 is derived from g12527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10583912	10584828	.	-	.	Phchi.S3G137900
Phchi.S3	AUGUSTUS	transcript	10583912	10584828	.	-	.	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	stop_codon	10583909	10583911	.	-	0	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	CDS	10583912	10584471	1	-	2	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	exon	10583912	10584471	.	-	.	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	intron	10584472	10584578	.	-	.	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	CDS	10584579	10584828	0.62	-	0	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	exon	10584579	10584828	.	-	.	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
Phchi.S3	AUGUSTUS	start_codon	10584826	10584828	.	-	0	transcript_id "Phchi.S3G137900.t1"; gene_id "Phchi.S3G137900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13049.t1 is derived from g11514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3905413	3907830	.	+	.	Phchi.S3G036800
Phchi.S3	AUGUSTUS	transcript	3905413	3907830	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	start_codon	3905413	3905415	.	+	0	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3905413	3905680	0.94	+	0	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3905413	3905680	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	intron	3905681	3905773	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3905774	3906639	1	+	2	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3905774	3906639	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	intron	3906640	3906756	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3906757	3906979	0.77	+	0	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3906757	3906979	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	intron	3906980	3907057	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3907058	3907203	0.38	+	2	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3907058	3907203	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	intron	3907204	3907282	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3907283	3907325	0.54	+	0	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3907283	3907325	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	intron	3907326	3907478	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3907479	3907681	0.9	+	2	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3907479	3907681	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	intron	3907682	3907785	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	CDS	3907786	3907830	0.88	+	0	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	exon	3907786	3907830	.	+	.	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
Phchi.S3	AUGUSTUS	stop_codon	3907831	3907833	.	+	0	transcript_id "Phchi.S3G036800.t1"; gene_id "Phchi.S3G036800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1955.t1 is derived from g8875.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4007867	4010649	.	+	.	Phchi.S5G056400
Phchi.S5	AUGUSTUS	transcript	4007867	4010649	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	start_codon	4007867	4007869	.	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4007867	4007938	0.63	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4007867	4007938	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4007939	4008016	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008017	4008173	0.99	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008017	4008173	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4008174	4008256	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008257	4008375	0.75	+	2	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008257	4008375	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4008376	4008474	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008475	4008567	0.79	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008475	4008567	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4008568	4008650	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008651	4009263	0.3	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008651	4009263	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4009264	4009427	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4009428	4010152	0.17	+	2	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4009428	4010152	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4010153	4010523	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4010524	4010649	0.36	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4010524	4010649	.	+	.	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	stop_codon	4010650	4010652	.	+	0	transcript_id "Phchi.S5G056400.t1"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	transcript	4007867	4010649	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	start_codon	4007867	4007869	.	+	0	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4007867	4007938	0.65	+	0	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4007867	4007938	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4007939	4008016	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008017	4008173	1	+	0	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008017	4008173	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4008174	4008256	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008257	4008375	0.72	+	2	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008257	4008375	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4008376	4008455	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4008456	4009263	0.42	+	0	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4008456	4009263	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4009264	4009427	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4009428	4010152	0.18	+	2	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4009428	4010152	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	intron	4010153	4010523	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	CDS	4010524	4010649	0.36	+	0	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	exon	4010524	4010649	.	+	.	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
Phchi.S5	AUGUSTUS	stop_codon	4010650	4010652	.	+	0	transcript_id "Phchi.S5G056400.t2"; gene_id "Phchi.S5G056400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6756.t1 is derived from g3928.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24901357	24902166	.	-	.	Phchi.S1G391500
Phchi.S1	AUGUSTUS	transcript	24901357	24902166	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	stop_codon	24901354	24901356	.	-	0	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	CDS	24901357	24901417	0.38	-	1	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	exon	24901357	24901417	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	intron	24901418	24901624	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	CDS	24901625	24901713	0.38	-	0	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	exon	24901625	24901713	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	intron	24901714	24901810	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	CDS	24901811	24901902	0.98	-	2	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	exon	24901811	24901902	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	intron	24901903	24902084	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	CDS	24902085	24902166	1	-	0	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	exon	24902085	24902166	.	-	.	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
Phchi.S1	AUGUSTUS	start_codon	24902164	24902166	.	-	0	transcript_id "Phchi.S1G391500.t1"; gene_id "Phchi.S1G391500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2472.t1 is derived from g9392.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6828773	6830091	.	+	.	Phchi.S5G108100
Phchi.S5	AUGUSTUS	transcript	6828773	6830091	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	start_codon	6828773	6828775	.	+	0	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6828773	6828900	1	+	0	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6828773	6828900	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6828901	6829002	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829003	6829102	1	+	1	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829003	6829102	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829103	6829193	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829194	6829268	1	+	0	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829194	6829268	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829269	6829349	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829350	6829464	1	+	0	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829350	6829464	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829465	6829594	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829595	6829677	1	+	2	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829595	6829677	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829678	6829798	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829799	6829860	0.8	+	0	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829799	6829860	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829861	6829967	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829968	6830091	0.99	+	1	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829968	6830091	.	+	.	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	stop_codon	6830092	6830094	.	+	0	transcript_id "Phchi.S5G108100.t1"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	transcript	6828773	6830091	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	start_codon	6828773	6828775	.	+	0	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6828773	6828900	1	+	0	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6828773	6828900	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6828901	6829002	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829003	6829102	1	+	1	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829003	6829102	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829103	6829193	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829194	6829268	1	+	0	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829194	6829268	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829269	6829349	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829350	6829464	1	+	0	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829350	6829464	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829465	6829594	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829595	6829638	0.53	+	2	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829595	6829638	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829639	6829798	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829799	6829860	0.58	+	0	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829799	6829860	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	intron	6829861	6829967	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	CDS	6829968	6830091	1	+	1	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	exon	6829968	6830091	.	+	.	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
Phchi.S5	AUGUSTUS	stop_codon	6830092	6830094	.	+	0	transcript_id "Phchi.S5G108100.t2"; gene_id "Phchi.S5G108100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg6793.t1 is derived from g3965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25105787	25108408	.	+	.	Phchi.S1G395200
Phchi.S1	AUGUSTUS	transcript	25105787	25108408	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	start_codon	25105787	25105789	.	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25105787	25106113	0.43	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25105787	25106113	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106114	25106237	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106238	25106423	1	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106238	25106423	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106424	25106544	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106545	25106615	1	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106545	25106615	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106616	25106841	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106842	25106989	1	+	1	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106842	25106989	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106990	25107135	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107136	25107399	1	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107136	25107399	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107400	25107491	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107492	25107561	1	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107492	25107561	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107562	25107666	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107667	25107866	0.94	+	2	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107667	25107866	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107867	25108036	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25108037	25108147	0.93	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25108037	25108147	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25108148	25108249	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25108250	25108408	0.92	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25108250	25108408	.	+	.	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	stop_codon	25108409	25108411	.	+	0	transcript_id "Phchi.S1G395200.t1"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	transcript	25105787	25108408	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	start_codon	25105787	25105789	.	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25105787	25106113	0.52	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25105787	25106113	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106114	25106237	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106238	25106423	1	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106238	25106423	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106424	25106544	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106545	25106615	1	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106545	25106615	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106616	25106841	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106842	25106994	1	+	1	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106842	25106994	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106995	25107135	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107136	25107177	1	+	1	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107136	25107177	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107178	25107332	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107333	25107399	0.65	+	1	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107333	25107399	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107400	25107491	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107492	25107561	1	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107492	25107561	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107562	25107666	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107667	25107866	0.96	+	2	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107667	25107866	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107867	25108036	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25108037	25108147	0.97	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25108037	25108147	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25108148	25108249	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25108250	25108408	0.97	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25108250	25108408	.	+	.	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	stop_codon	25108409	25108411	.	+	0	transcript_id "Phchi.S1G395200.t2"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	transcript	25105787	25108408	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	start_codon	25105787	25105789	.	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25105787	25106113	0.46	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25105787	25106113	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106114	25106237	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106238	25106280	0.86	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106238	25106280	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106281	25106368	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106369	25106423	0.32	+	2	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106369	25106423	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106424	25106583	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106584	25106615	0.64	+	1	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106584	25106615	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106616	25106834	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25106835	25106994	0.9	+	2	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25106835	25106994	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25106995	25107135	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107136	25107177	0.99	+	1	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107136	25107177	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107178	25107332	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107333	25107399	0.65	+	1	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107333	25107399	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107400	25107491	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107492	25107561	1	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107492	25107561	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107562	25107666	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25107667	25107866	0.99	+	2	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25107667	25107866	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25107867	25108036	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25108037	25108147	0.98	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25108037	25108147	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	intron	25108148	25108249	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	CDS	25108250	25108408	0.98	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	exon	25108250	25108408	.	+	.	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
Phchi.S1	AUGUSTUS	stop_codon	25108409	25108411	.	+	0	transcript_id "Phchi.S1G395200.t3"; gene_id "Phchi.S1G395200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11533.t1 is derived from g15583.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6946589	6948662	.	+	.	Phchi.S4G111500
Phchi.S4	AUGUSTUS	transcript	6946614	6948662	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	start_codon	6946614	6946616	.	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6946614	6946706	0.99	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6946614	6946706	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6946707	6946856	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6946857	6946883	0.64	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6946857	6946883	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6946884	6947101	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947102	6947174	0.65	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947102	6947174	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947175	6947260	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947261	6947320	1	+	2	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947261	6947320	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947321	6947405	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947406	6947484	0.46	+	2	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947406	6947484	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947485	6947596	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947597	6947687	0.41	+	1	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947597	6947687	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947688	6947926	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947927	6947940	0.63	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947927	6947940	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947941	6948054	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6948055	6948307	0.62	+	1	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6948055	6948307	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6948308	6948388	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6948389	6948444	0.98	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6948389	6948444	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6948445	6948544	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6948545	6948662	0.92	+	1	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6948545	6948662	.	+	.	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	stop_codon	6948663	6948665	.	+	0	transcript_id "Phchi.S4G111500.t1"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	transcript	6946589	6948662	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	start_codon	6946589	6946591	.	+	0	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6946589	6946706	1	+	0	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6946589	6946706	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6946707	6946773	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6946774	6946832	0.74	+	2	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6946774	6946832	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6946833	6947101	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947102	6947174	0.74	+	0	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947102	6947174	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947175	6947260	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947261	6947320	1	+	2	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947261	6947320	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947321	6947405	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947406	6947484	0.45	+	2	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947406	6947484	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947485	6947596	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947597	6947687	0.4	+	1	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947597	6947687	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947688	6947926	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6947927	6947940	0.52	+	0	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6947927	6947940	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6947941	6948054	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6948055	6948307	0.49	+	1	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6948055	6948307	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6948308	6948388	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6948389	6948444	1	+	0	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6948389	6948444	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	intron	6948445	6948544	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	CDS	6948545	6948662	0.94	+	1	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	exon	6948545	6948662	.	+	.	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
Phchi.S4	AUGUSTUS	stop_codon	6948663	6948665	.	+	0	transcript_id "Phchi.S4G111500.t2"; gene_id "Phchi.S4G111500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7231.t1 is derived from g4403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27748459	27751029	.	+	.	Phchi.S1G439000
Phchi.S1	AUGUSTUS	transcript	27748459	27751029	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	start_codon	27748459	27748461	.	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27748459	27748513	0.98	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27748459	27748513	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27748514	27748757	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27748758	27749140	0.62	+	2	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27748758	27749140	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27749141	27749292	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27749293	27749532	1	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27749293	27749532	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27749533	27749635	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27749636	27749926	0.61	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27749636	27749926	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27749927	27750054	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27750055	27750144	0.81	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27750055	27750144	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27750145	27750227	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27750228	27750329	1	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27750228	27750329	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27750330	27750412	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27750413	27750531	1	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27750413	27750531	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27750532	27750623	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27750624	27750686	1	+	1	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27750624	27750686	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27750687	27750782	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27750783	27750844	1	+	1	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27750783	27750844	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	intron	27750845	27750928	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	CDS	27750929	27751029	1	+	2	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	exon	27750929	27751029	.	+	.	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
Phchi.S1	AUGUSTUS	stop_codon	27751030	27751032	.	+	0	transcript_id "Phchi.S1G439000.t1"; gene_id "Phchi.S1G439000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg622.t1 is derived from g10404.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4448167	4450405	.	+	.	Phchi.S6G058100
Phchi.S6	AUGUSTUS	transcript	4448167	4450405	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	start_codon	4448167	4448169	.	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4448167	4448283	0.85	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4448167	4448283	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4448284	4448374	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4448375	4448507	1	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4448375	4448507	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4448508	4448581	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4448582	4448662	1	+	2	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4448582	4448662	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4448663	4448759	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4448760	4448875	1	+	2	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4448760	4448875	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4448876	4448968	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4448969	4449022	1	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4448969	4449022	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4449023	4449107	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4449108	4449195	0.99	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4449108	4449195	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4449196	4449314	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4449315	4449407	1	+	2	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4449315	4449407	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4449408	4449521	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4449522	4449562	1	+	2	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4449522	4449562	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4449563	4449667	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4449668	4449721	0.94	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4449668	4449721	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4449722	4449831	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4449832	4449995	1	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4449832	4449995	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4449996	4450087	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4450088	4450157	1	+	1	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4450088	4450157	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	intron	4450158	4450237	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	CDS	4450238	4450405	0.97	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	exon	4450238	4450405	.	+	.	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
Phchi.S6	AUGUSTUS	stop_codon	4450406	4450408	.	+	0	transcript_id "Phchi.S6G058100.t1"; gene_id "Phchi.S6G058100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7419.t1 is derived from g4591.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29056414	29060821	.	-	.	Phchi.S1G457800
Phchi.S1	AUGUSTUS	transcript	29056414	29060821	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	stop_codon	29056411	29056413	.	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29056414	29056538	0.98	-	2	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29056414	29056538	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29056539	29056623	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29056624	29056690	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29056624	29056690	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29056691	29056847	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29056848	29056934	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29056848	29056934	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29056935	29057051	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29057052	29057145	1	-	1	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29057052	29057145	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29057146	29057323	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29057324	29057396	1	-	2	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29057324	29057396	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29057397	29057543	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29057544	29057652	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29057544	29057652	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29057653	29057797	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29057798	29057894	1	-	1	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29057798	29057894	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29057895	29058051	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29058052	29058150	1	-	1	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29058052	29058150	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29058151	29058239	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29058240	29058310	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29058240	29058310	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29058311	29058394	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29058395	29058472	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29058395	29058472	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29058473	29058560	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29058561	29058647	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29058561	29058647	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29058648	29058738	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29058739	29058845	1	-	2	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29058739	29058845	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29058846	29058928	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29058929	29059009	1	-	2	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29058929	29059009	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29059010	29059148	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29059149	29059182	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29059149	29059182	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29059183	29059270	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29059271	29059327	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29059271	29059327	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29059328	29059455	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29059456	29059513	1	-	1	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29059456	29059513	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29059514	29059599	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29059600	29059691	1	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29059600	29059691	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29059692	29059809	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29059810	29059937	0.97	-	2	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29059810	29059937	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29059938	29060092	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29060093	29060176	1	-	2	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29060093	29060176	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	intron	29060177	29060676	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	CDS	29060677	29060821	0.73	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	exon	29060677	29060821	.	-	.	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
Phchi.S1	AUGUSTUS	start_codon	29060819	29060821	.	-	0	transcript_id "Phchi.S1G457800.t1"; gene_id "Phchi.S1G457800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4420.t1 is derived from g1589.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10425240	10426771	.	+	.	Phchi.S1G157900
Phchi.S1	AUGUSTUS	transcript	10425240	10426771	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	start_codon	10425240	10425242	.	+	0	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425240	10425245	0.95	+	0	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425240	10425245	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425246	10425345	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425346	10425355	0.77	+	0	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425346	10425355	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425356	10425454	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425455	10425527	0.45	+	2	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425455	10425527	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425528	10425723	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425724	10425811	1	+	1	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425724	10425811	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425812	10425932	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425933	10426027	1	+	0	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425933	10426027	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10426028	10426506	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10426507	10426583	0.96	+	1	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10426507	10426583	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10426584	10426700	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10426701	10426771	0.96	+	2	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10426701	10426771	.	+	.	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	stop_codon	10426772	10426774	.	+	0	transcript_id "Phchi.S1G157900.t1"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	transcript	10425240	10426771	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	start_codon	10425240	10425242	.	+	0	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425240	10425245	0.94	+	0	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425240	10425245	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425246	10425345	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425346	10425355	0.73	+	0	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425346	10425355	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425356	10425454	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425455	10425527	0.45	+	2	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425455	10425527	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425528	10425726	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425727	10425811	1	+	1	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425727	10425811	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10425812	10425932	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10425933	10426027	1	+	0	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10425933	10426027	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10426028	10426506	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10426507	10426583	0.93	+	1	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10426507	10426583	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	intron	10426584	10426700	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	CDS	10426701	10426771	0.93	+	2	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	exon	10426701	10426771	.	+	.	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
Phchi.S1	AUGUSTUS	stop_codon	10426772	10426774	.	+	0	transcript_id "Phchi.S1G157900.t2"; gene_id "Phchi.S1G157900"
# This transcript jg2740.t2 is derived from g9660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2741.t1 is derived from g9661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8515564	8517506	.	+	.	Phchi.S5G135000
Phchi.S5	AUGUSTUS	transcript	8515564	8517506	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	start_codon	8515564	8515566	.	+	0	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	CDS	8515564	8515680	0.23	+	0	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	exon	8515564	8515680	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	intron	8515681	8515760	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	CDS	8515761	8515772	0.86	+	0	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	exon	8515761	8515772	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	intron	8515773	8515918	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	CDS	8515919	8516200	1	+	0	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	exon	8515919	8516200	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	intron	8516201	8516325	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	CDS	8516326	8517082	0.94	+	0	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	exon	8516326	8517082	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	intron	8517083	8517164	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	CDS	8517165	8517192	1	+	2	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	exon	8517165	8517192	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	intron	8517193	8517484	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	CDS	8517485	8517506	1	+	1	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	exon	8517485	8517506	.	+	.	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
Phchi.S5	AUGUSTUS	stop_codon	8517507	8517509	.	+	0	transcript_id "Phchi.S5G135000.t1"; gene_id "Phchi.S5G135000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14214.t1 is derived from g12681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11531283	11532950	.	-	.	Phchi.S3G153300
Phchi.S3	AUGUSTUS	transcript	11531283	11532950	.	-	.	transcript_id "Phchi.S3G153300.t1"; gene_id "Phchi.S3G153300"
Phchi.S3	AUGUSTUS	stop_codon	11531280	11531282	.	-	0	transcript_id "Phchi.S3G153300.t1"; gene_id "Phchi.S3G153300"
Phchi.S3	AUGUSTUS	CDS	11531283	11532950	0.87	-	0	transcript_id "Phchi.S3G153300.t1"; gene_id "Phchi.S3G153300"
Phchi.S3	AUGUSTUS	exon	11531283	11532950	.	-	.	transcript_id "Phchi.S3G153300.t1"; gene_id "Phchi.S3G153300"
Phchi.S3	AUGUSTUS	start_codon	11532948	11532950	.	-	0	transcript_id "Phchi.S3G153300.t1"; gene_id "Phchi.S3G153300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1160.t1 is derived from g10943.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8095121	8095780	.	+	.	Phchi.S6G111900
Phchi.S6	AUGUSTUS	transcript	8095121	8095780	.	+	.	transcript_id "Phchi.S6G111900.t1"; gene_id "Phchi.S6G111900"
Phchi.S6	AUGUSTUS	start_codon	8095121	8095123	.	+	0	transcript_id "Phchi.S6G111900.t1"; gene_id "Phchi.S6G111900"
Phchi.S6	AUGUSTUS	CDS	8095121	8095780	1	+	0	transcript_id "Phchi.S6G111900.t1"; gene_id "Phchi.S6G111900"
Phchi.S6	AUGUSTUS	exon	8095121	8095780	.	+	.	transcript_id "Phchi.S6G111900.t1"; gene_id "Phchi.S6G111900"
Phchi.S6	AUGUSTUS	stop_codon	8095781	8095783	.	+	0	transcript_id "Phchi.S6G111900.t1"; gene_id "Phchi.S6G111900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12199.t1 is derived from g7875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6700613	6714912	.	-	.	Phchi.S2G027900
Phchi.S2	AUGUSTUS	transcript	6700613	6714912	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	stop_codon	6700610	6700612	.	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6700613	6700691	0.63	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6700613	6700691	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6700692	6700965	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6700966	6701006	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6700966	6701006	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6701007	6701095	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6701096	6701156	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6701096	6701156	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6701157	6701251	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6701252	6701323	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6701252	6701323	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6701324	6701443	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6701444	6701493	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6701444	6701493	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6701494	6701597	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6701598	6701710	1	-	2	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6701598	6701710	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6701711	6701993	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6701994	6702096	0.79	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6701994	6702096	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6702097	6702346	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6702347	6702496	0.82	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6702347	6702496	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6702497	6702584	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6702585	6702777	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6702585	6702777	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6702778	6702883	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6702884	6702990	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6702884	6702990	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6702991	6703104	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6703105	6703317	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6703105	6703317	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6703318	6703459	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6703460	6703633	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6703460	6703633	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6703634	6703759	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6703760	6703891	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6703760	6703891	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6703892	6703984	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6703985	6704051	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6703985	6704051	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6704052	6704150	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6704151	6704311	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6704151	6704311	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6704312	6704480	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6704481	6704529	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6704481	6704529	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6704530	6704623	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6704624	6704886	0.98	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6704624	6704886	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6704887	6704986	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6704987	6705046	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6704987	6705046	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6705047	6705213	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6705214	6705288	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6705214	6705288	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6705289	6705372	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6705373	6705456	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6705373	6705456	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6705457	6705534	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6705535	6705636	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6705535	6705636	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6705637	6705769	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6705770	6705902	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6705770	6705902	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6705903	6706044	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6706045	6706109	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6706045	6706109	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6706110	6706188	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6706189	6706372	0.53	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6706189	6706372	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6706373	6706477	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6706478	6706668	0.55	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6706478	6706668	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6706669	6706843	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6706844	6706918	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6706844	6706918	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6706919	6707074	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6707075	6707272	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6707075	6707272	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6707273	6707359	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6707360	6707501	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6707360	6707501	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6707502	6707705	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6707706	6708121	0.96	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6707706	6708121	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6708122	6708222	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6708223	6708365	0.94	-	2	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6708223	6708365	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6708366	6708455	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6708456	6708510	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6708456	6708510	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6708511	6708648	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6708649	6708849	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6708649	6708849	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6708850	6708954	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6708955	6709050	0.99	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6708955	6709050	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6709051	6709190	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6709191	6709334	0.99	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6709191	6709334	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6709335	6709457	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6709458	6709538	0.97	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6709458	6709538	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6709539	6709647	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6709648	6709732	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6709648	6709732	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6709733	6709809	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6709810	6709986	0.99	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6709810	6709986	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6709987	6710092	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6710093	6710172	0.96	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6710093	6710172	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6710173	6710355	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6710356	6710461	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6710356	6710461	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6710462	6710613	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6710614	6710708	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6710614	6710708	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6710709	6710784	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6710785	6710926	0.98	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6710785	6710926	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6710927	6711042	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6711043	6711161	0.96	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6711043	6711161	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6711162	6711380	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6711381	6711485	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6711381	6711485	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6711486	6711573	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6711574	6711684	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6711574	6711684	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6711685	6711831	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6711832	6712008	0.96	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6711832	6712008	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6712009	6712112	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6712113	6712277	0.84	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6712113	6712277	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6712278	6712418	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6712419	6712502	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6712419	6712502	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6712503	6712616	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6712617	6712739	0.65	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6712617	6712739	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6712740	6712852	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6712853	6712987	0.8	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6712853	6712987	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6712988	6713072	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6713073	6713159	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6713073	6713159	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6713160	6713245	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6713246	6713463	1	-	2	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6713246	6713463	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6713464	6713617	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6713618	6713721	1	-	1	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6713618	6713721	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6713722	6713816	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6713817	6713977	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6713817	6713977	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6713978	6714113	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6714114	6714209	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6714114	6714209	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6714210	6714310	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6714311	6714370	0.99	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6714311	6714370	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6714371	6714448	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6714449	6714517	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6714449	6714517	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	intron	6714518	6714603	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	CDS	6714604	6714912	1	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	exon	6714604	6714912	.	-	.	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
Phchi.S2	AUGUSTUS	start_codon	6714910	6714912	.	-	0	transcript_id "Phchi.S2G027900.t1"; gene_id "Phchi.S2G027900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10177.t1 is derived from g7353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46142893	46147296	.	-	.	Phchi.S1G733600
Phchi.S1	AUGUSTUS	transcript	46142893	46147296	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	stop_codon	46142890	46142892	.	-	0	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	CDS	46142893	46144026	0.93	-	0	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	exon	46142893	46144026	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	intron	46144027	46144143	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	CDS	46144144	46145603	0.96	-	2	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	exon	46144144	46145603	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	intron	46145604	46145745	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	CDS	46145746	46146220	0.73	-	0	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	exon	46145746	46146220	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	intron	46146221	46146327	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	CDS	46146328	46147296	0.62	-	0	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	exon	46146328	46147296	.	-	.	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
Phchi.S1	AUGUSTUS	start_codon	46147294	46147296	.	-	0	transcript_id "Phchi.S1G733600.t1"; gene_id "Phchi.S1G733600"
# This transcript jg4410.t2 is derived from g1579.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4411.t1 is derived from g1580.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10269448	10272209	.	+	.	Phchi.S1G157000
Phchi.S1	AUGUSTUS	transcript	10269448	10272209	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	start_codon	10269448	10269450	.	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10269448	10269601	0.85	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10269448	10269601	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10269602	10269685	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10269686	10269861	1	+	2	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10269686	10269861	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10269862	10269999	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10270000	10270111	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10270000	10270111	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10270112	10270253	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10270254	10270318	1	+	2	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10270254	10270318	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10270319	10270407	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10270408	10270521	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10270408	10270521	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10270522	10270655	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10270656	10270730	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10270656	10270730	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10270731	10270849	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10270850	10270888	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10270850	10270888	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10270889	10271018	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10271019	10271090	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10271019	10271090	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10271091	10271183	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10271184	10271297	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10271184	10271297	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10271298	10271365	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10271366	10271437	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10271366	10271437	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10271438	10271516	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10271517	10271553	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10271517	10271553	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10271554	10271652	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10271653	10271765	1	+	2	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10271653	10271765	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10271766	10271850	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10271851	10272033	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10271851	10272033	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	intron	10272034	10272122	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	CDS	10272123	10272209	1	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	exon	10272123	10272209	.	+	.	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
Phchi.S1	AUGUSTUS	stop_codon	10272210	10272212	.	+	0	transcript_id "Phchi.S1G157000.t1"; gene_id "Phchi.S1G157000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9487.t1 is derived from g6663.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41990758	41991341	.	+	.	Phchi.S1G664600
Phchi.S1	AUGUSTUS	transcript	41990758	41991341	.	+	.	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	start_codon	41990758	41990760	.	+	0	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	CDS	41990758	41990854	1	+	0	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	exon	41990758	41990854	.	+	.	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	intron	41990855	41991034	.	+	.	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	CDS	41991035	41991107	1	+	2	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	exon	41991035	41991107	.	+	.	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	intron	41991108	41991187	.	+	.	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	CDS	41991188	41991341	1	+	1	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	exon	41991188	41991341	.	+	.	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
Phchi.S1	AUGUSTUS	stop_codon	41991342	41991344	.	+	0	transcript_id "Phchi.S1G664600.t1"; gene_id "Phchi.S1G664600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14336.t1 is derived from g12803.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12294219	12295827	.	+	.	Phchi.S3G165500
Phchi.S3	AUGUSTUS	transcript	12294219	12295827	.	+	.	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	start_codon	12294219	12294221	.	+	0	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	CDS	12294219	12294755	0.81	+	0	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	exon	12294219	12294755	.	+	.	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	intron	12294756	12294846	.	+	.	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	CDS	12294847	12295827	1	+	0	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	exon	12294847	12295827	.	+	.	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
Phchi.S3	AUGUSTUS	stop_codon	12295828	12295830	.	+	0	transcript_id "Phchi.S3G165500.t1"; gene_id "Phchi.S3G165500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6252.t1 is derived from g3424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21879951	21881671	.	-	.	Phchi.S1G341100
Phchi.S1	AUGUSTUS	transcript	21879951	21881671	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	stop_codon	21879948	21879950	.	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	CDS	21879951	21880175	0.99	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	exon	21879951	21880175	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	intron	21880176	21880309	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	CDS	21880310	21880535	1	-	1	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	exon	21880310	21880535	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	intron	21880536	21880621	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	CDS	21880622	21880767	1	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	exon	21880622	21880767	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	intron	21880768	21880908	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	CDS	21880909	21881004	1	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	exon	21880909	21881004	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	intron	21881005	21881112	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	CDS	21881113	21881325	1	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	exon	21881113	21881325	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	intron	21881326	21881452	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	CDS	21881453	21881671	0.74	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	exon	21881453	21881671	.	-	.	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
Phchi.S1	AUGUSTUS	start_codon	21881669	21881671	.	-	0	transcript_id "Phchi.S1G341100.t1"; gene_id "Phchi.S1G341100"
# This transcript jg7216.t2 is derived from g4388.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7216.t3 is derived from g4388.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg7216.t4 is derived from g4388.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7217.t1 is derived from g4389.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27678357	27680354	.	+	.	Phchi.S1G437600
Phchi.S1	AUGUSTUS	transcript	27678357	27680354	.	+	.	transcript_id "Phchi.S1G437600.t1"; gene_id "Phchi.S1G437600"
Phchi.S1	AUGUSTUS	start_codon	27678357	27678359	.	+	0	transcript_id "Phchi.S1G437600.t1"; gene_id "Phchi.S1G437600"
Phchi.S1	AUGUSTUS	CDS	27678357	27680354	1	+	0	transcript_id "Phchi.S1G437600.t1"; gene_id "Phchi.S1G437600"
Phchi.S1	AUGUSTUS	exon	27678357	27680354	.	+	.	transcript_id "Phchi.S1G437600.t1"; gene_id "Phchi.S1G437600"
Phchi.S1	AUGUSTUS	stop_codon	27680355	27680357	.	+	0	transcript_id "Phchi.S1G437600.t1"; gene_id "Phchi.S1G437600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11326.t1 is derived from g15376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5423488	5424374	.	+	.	Phchi.S4G090800
Phchi.S4	AUGUSTUS	transcript	5423488	5424374	.	+	.	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	start_codon	5423488	5423490	.	+	0	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	CDS	5423488	5423605	0.87	+	0	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	exon	5423488	5423605	.	+	.	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	intron	5423606	5423754	.	+	.	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	CDS	5423755	5424374	0.48	+	2	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	exon	5423755	5424374	.	+	.	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
Phchi.S4	AUGUSTUS	stop_codon	5424375	5424377	.	+	0	transcript_id "Phchi.S4G090800.t1"; gene_id "Phchi.S4G090800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15985.t1 is derived from g9774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C16	AUGUSTUS	gene	43995	44444	.	-	.	Phchi.C16G000300
Phchi.C16	AUGUSTUS	transcript	43995	44444	.	-	.	transcript_id "Phchi.C16G000300.t1"; gene_id "Phchi.C16G000300"
Phchi.C16	AUGUSTUS	stop_codon	43992	43994	.	-	0	transcript_id "Phchi.C16G000300.t1"; gene_id "Phchi.C16G000300"
Phchi.C16	AUGUSTUS	CDS	43995	44444	0.82	-	0	transcript_id "Phchi.C16G000300.t1"; gene_id "Phchi.C16G000300"
Phchi.C16	AUGUSTUS	exon	43995	44444	.	-	.	transcript_id "Phchi.C16G000300.t1"; gene_id "Phchi.C16G000300"
Phchi.C16	AUGUSTUS	start_codon	44442	44444	.	-	0	transcript_id "Phchi.C16G000300.t1"; gene_id "Phchi.C16G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9420.t1 is derived from g6596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41402852	41404467	.	+	.	Phchi.S1G657900
Phchi.S1	AUGUSTUS	transcript	41402852	41404467	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	start_codon	41402852	41402854	.	+	0	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	CDS	41402852	41403093	0.35	+	0	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	exon	41402852	41403093	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	intron	41403094	41403204	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	CDS	41403205	41403379	0.88	+	1	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	exon	41403205	41403379	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	intron	41403380	41403461	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	CDS	41403462	41404014	0.99	+	0	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	exon	41403462	41404014	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	intron	41404015	41404096	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	CDS	41404097	41404467	1	+	2	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	exon	41404097	41404467	.	+	.	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
Phchi.S1	AUGUSTUS	stop_codon	41404468	41404470	.	+	0	transcript_id "Phchi.S1G657900.t1"; gene_id "Phchi.S1G657900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12132.t1 is derived from g7808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4079640	4080547	.	+	.	Phchi.S2G021200
Phchi.S2	AUGUSTUS	transcript	4079640	4080547	.	+	.	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	start_codon	4079640	4079642	.	+	0	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	CDS	4079640	4079667	1	+	0	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	exon	4079640	4079667	.	+	.	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	intron	4079668	4080020	.	+	.	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	CDS	4080021	4080547	1	+	2	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	exon	4080021	4080547	.	+	.	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
Phchi.S2	AUGUSTUS	stop_codon	4080548	4080550	.	+	0	transcript_id "Phchi.S2G021200.t1"; gene_id "Phchi.S2G021200"
# This transcript jg3392.t2 is derived from g561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3393.t1 is derived from g562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3327042	3327577	.	+	.	Phchi.S1G055200
Phchi.S1	AUGUSTUS	transcript	3327042	3327577	.	+	.	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	start_codon	3327042	3327044	.	+	0	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	CDS	3327042	3327110	0.95	+	0	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	exon	3327042	3327110	.	+	.	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	intron	3327111	3327195	.	+	.	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	CDS	3327196	3327321	1	+	0	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	exon	3327196	3327321	.	+	.	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	intron	3327322	3327409	.	+	.	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	CDS	3327410	3327577	0.5	+	0	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	exon	3327410	3327577	.	+	.	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
Phchi.S1	AUGUSTUS	stop_codon	3327578	3327580	.	+	0	transcript_id "Phchi.S1G055200.t1"; gene_id "Phchi.S1G055200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg718.t1 is derived from g10500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5080096	5082717	.	-	.	Phchi.S6G067700
Phchi.S6	AUGUSTUS	transcript	5080096	5082717	.	-	.	transcript_id "Phchi.S6G067700.t1"; gene_id "Phchi.S6G067700"
Phchi.S6	AUGUSTUS	stop_codon	5080093	5080095	.	-	0	transcript_id "Phchi.S6G067700.t1"; gene_id "Phchi.S6G067700"
Phchi.S6	AUGUSTUS	CDS	5080096	5082717	0.86	-	0	transcript_id "Phchi.S6G067700.t1"; gene_id "Phchi.S6G067700"
Phchi.S6	AUGUSTUS	exon	5080096	5082717	.	-	.	transcript_id "Phchi.S6G067700.t1"; gene_id "Phchi.S6G067700"
Phchi.S6	AUGUSTUS	start_codon	5082715	5082717	.	-	0	transcript_id "Phchi.S6G067700.t1"; gene_id "Phchi.S6G067700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6933.t1 is derived from g4105.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26044950	26046971	.	+	.	Phchi.S1G409200
Phchi.S1	AUGUSTUS	transcript	26044950	26046971	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	start_codon	26044950	26044952	.	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	CDS	26044950	26045531	1	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	exon	26044950	26045531	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	intron	26045532	26045812	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	CDS	26045813	26046073	0.78	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	exon	26045813	26046073	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	intron	26046074	26046175	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	CDS	26046176	26046292	0.79	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	exon	26046176	26046292	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	intron	26046293	26046375	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	CDS	26046376	26046669	1	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	exon	26046376	26046669	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	intron	26046670	26046752	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	CDS	26046753	26046971	0.61	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	exon	26046753	26046971	.	+	.	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
Phchi.S1	AUGUSTUS	stop_codon	26046972	26046974	.	+	0	transcript_id "Phchi.S1G409200.t1"; gene_id "Phchi.S1G409200"
# This transcript jg7847.t2 is derived from g5021.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7848.t1 is derived from g5022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31512739	31515656	.	+	.	Phchi.S1G500700
Phchi.S1	AUGUSTUS	transcript	31512739	31515656	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	start_codon	31512739	31512741	.	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31512739	31512755	0.88	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31512739	31512755	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31512756	31512852	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31512853	31513103	0.88	+	1	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31512853	31513103	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513104	31513184	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513185	31513279	1	+	2	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513185	31513279	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513280	31513350	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513351	31513438	1	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513351	31513438	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513439	31513555	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513556	31513650	0.7	+	2	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513556	31513650	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513651	31513768	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513769	31513849	0.98	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513769	31513849	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513850	31513968	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513969	31514024	1	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513969	31514024	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514025	31514167	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514168	31514249	0.98	+	1	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514168	31514249	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514250	31514363	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514364	31514433	0.98	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514364	31514433	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514434	31514585	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514586	31514801	1	+	2	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514586	31514801	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514802	31514895	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514896	31514978	1	+	2	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514896	31514978	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514979	31515055	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515056	31515118	1	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515056	31515118	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31515119	31515203	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515204	31515302	1	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515204	31515302	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31515303	31515392	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515393	31515467	1	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515393	31515467	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31515468	31515566	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515567	31515656	1	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515567	31515656	.	+	.	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	stop_codon	31515657	31515659	.	+	0	transcript_id "Phchi.S1G500700.t1"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	transcript	31512739	31515656	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	start_codon	31512739	31512741	.	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31512739	31512755	0.88	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31512739	31512755	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31512756	31512852	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31512853	31513103	0.88	+	1	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31512853	31513103	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513104	31513184	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513185	31513279	1	+	2	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513185	31513279	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513280	31513350	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513351	31513438	0.96	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513351	31513438	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513439	31513555	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513556	31513650	0.2	+	2	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513556	31513650	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513651	31513768	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513769	31513849	0.3	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513769	31513849	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513850	31513973	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31513974	31513990	0.32	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31513974	31513990	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31513991	31514167	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514168	31514249	0.94	+	1	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514168	31514249	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514250	31514363	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514364	31514433	0.95	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514364	31514433	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514434	31514585	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514586	31514801	1	+	2	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514586	31514801	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514802	31514895	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31514896	31514978	1	+	2	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31514896	31514978	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31514979	31515055	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515056	31515118	1	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515056	31515118	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31515119	31515203	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515204	31515302	1	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515204	31515302	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31515303	31515392	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515393	31515467	1	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515393	31515467	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	intron	31515468	31515566	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	CDS	31515567	31515656	1	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	exon	31515567	31515656	.	+	.	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
Phchi.S1	AUGUSTUS	stop_codon	31515657	31515659	.	+	0	transcript_id "Phchi.S1G500700.t2"; gene_id "Phchi.S1G500700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1338.t1 is derived from g11121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9096942	9098769	.	-	.	Phchi.S6G129700
Phchi.S6	AUGUSTUS	transcript	9096942	9098769	.	-	.	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	stop_codon	9096939	9096941	.	-	0	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	CDS	9096942	9096994	1	-	2	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	exon	9096942	9096994	.	-	.	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	intron	9096995	9097163	.	-	.	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	CDS	9097164	9097226	1	-	2	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	exon	9097164	9097226	.	-	.	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	intron	9097227	9097514	.	-	.	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	CDS	9097515	9098769	0.94	-	0	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	exon	9097515	9098769	.	-	.	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
Phchi.S6	AUGUSTUS	start_codon	9098767	9098769	.	-	0	transcript_id "Phchi.S6G129700.t1"; gene_id "Phchi.S6G129700"
# This transcript jg2096.t2 is derived from g9016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2096.t3 is derived from g9016.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg2097.t1 is derived from g9017.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4851352	4854863	.	+	.	Phchi.S5G070600
Phchi.S5	AUGUSTUS	transcript	4851352	4854863	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	start_codon	4851352	4851354	.	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4851352	4851623	0.7	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4851352	4851623	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4851624	4851817	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4851818	4851938	1	+	1	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4851818	4851938	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4851939	4852133	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4852134	4852579	1	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4852134	4852579	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4852580	4852782	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4852783	4852939	1	+	1	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4852783	4852939	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4852940	4853108	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853109	4853197	1	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853109	4853197	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853198	4853314	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853315	4853411	0.99	+	1	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853315	4853411	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853412	4853510	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853511	4853583	1	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853511	4853583	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853584	4853675	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853676	4853801	1	+	2	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853676	4853801	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853802	4854020	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854021	4854187	1	+	2	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854021	4854187	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854188	4854307	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854308	4854409	1	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854308	4854409	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854410	4854494	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854495	4854592	1	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854495	4854592	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854593	4854682	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854683	4854863	0.71	+	1	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854683	4854863	.	+	.	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	stop_codon	4854864	4854866	.	+	0	transcript_id "Phchi.S5G070600.t1"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	transcript	4851352	4854863	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	start_codon	4851352	4851354	.	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4851352	4851623	0.54	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4851352	4851623	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4851624	4851817	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4851818	4851938	1	+	1	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4851818	4851938	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4851939	4852133	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4852134	4852579	1	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4852134	4852579	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4852580	4852782	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4852783	4852939	1	+	1	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4852783	4852939	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4852940	4853108	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853109	4853197	1	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853109	4853197	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853198	4853314	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853315	4853411	1	+	1	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853315	4853411	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853412	4853510	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853511	4853583	1	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853511	4853583	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853584	4853675	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853676	4853801	1	+	2	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853676	4853801	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853802	4854020	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854021	4854187	1	+	2	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854021	4854187	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854188	4854307	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854308	4854409	1	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854308	4854409	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854410	4854494	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854495	4854592	1	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854495	4854592	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854593	4854688	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854689	4854863	0.77	+	1	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854689	4854863	.	+	.	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	stop_codon	4854864	4854866	.	+	0	transcript_id "Phchi.S5G070600.t2"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	transcript	4851352	4854863	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	start_codon	4851352	4851354	.	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4851352	4851623	0.64	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4851352	4851623	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4851624	4851817	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4851818	4851938	1	+	1	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4851818	4851938	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4851939	4852133	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4852134	4852579	1	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4852134	4852579	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4852580	4852782	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4852783	4852939	1	+	1	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4852783	4852939	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4852940	4853108	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853109	4853197	1	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853109	4853197	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853198	4853314	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853315	4853411	1	+	1	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853315	4853411	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853412	4853510	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853511	4853583	1	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853511	4853583	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853584	4853675	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4853676	4853909	0.41	+	2	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4853676	4853909	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4853910	4854020	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854021	4854187	1	+	2	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854021	4854187	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854188	4854307	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854308	4854409	1	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854308	4854409	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854410	4854494	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854495	4854592	1	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854495	4854592	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	intron	4854593	4854682	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	CDS	4854683	4854863	0.7	+	1	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	exon	4854683	4854863	.	+	.	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
Phchi.S5	AUGUSTUS	stop_codon	4854864	4854866	.	+	0	transcript_id "Phchi.S5G070600.t3"; gene_id "Phchi.S5G070600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4069.t1 is derived from g1238.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7621789	7622536	.	-	.	Phchi.S1G122800
Phchi.S1	AUGUSTUS	transcript	7621789	7622536	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	stop_codon	7621786	7621788	.	-	0	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	CDS	7621789	7621916	1	-	2	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	exon	7621789	7621916	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	intron	7621917	7622065	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	CDS	7622066	7622108	1	-	0	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	exon	7622066	7622108	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	intron	7622109	7622208	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	CDS	7622209	7622232	1	-	0	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	exon	7622209	7622232	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	intron	7622233	7622338	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	CDS	7622339	7622407	1	-	0	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	exon	7622339	7622407	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	intron	7622408	7622533	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	CDS	7622534	7622536	1	-	0	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	exon	7622534	7622536	.	-	.	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
Phchi.S1	AUGUSTUS	start_codon	7622534	7622536	.	-	0	transcript_id "Phchi.S1G122800.t1"; gene_id "Phchi.S1G122800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11421.t1 is derived from g15471.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6259438	6262958	.	-	.	Phchi.S4G100300
Phchi.S4	AUGUSTUS	transcript	6261387	6262958	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	stop_codon	6261384	6261386	.	-	0	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261387	6261405	0.99	-	1	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261387	6261405	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261406	6261487	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261488	6261546	1	-	0	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261488	6261546	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261547	6261721	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261722	6261798	1	-	2	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261722	6261798	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261799	6261872	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261873	6261937	1	-	1	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261873	6261937	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261938	6262023	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262024	6262127	1	-	0	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262024	6262127	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262128	6262260	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262261	6262309	1	-	1	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262261	6262309	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262310	6262418	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262419	6262600	0.99	-	0	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262419	6262600	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262601	6262688	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262689	6262759	1	-	2	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262689	6262759	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262760	6262846	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262847	6262958	1	-	0	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262847	6262958	.	-	.	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	start_codon	6262956	6262958	.	-	0	transcript_id "Phchi.S4G100300.t1"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	transcript	6259438	6262958	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	stop_codon	6259435	6259437	.	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6259438	6259494	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6259438	6259494	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6259495	6259567	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6259568	6259617	1	-	2	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6259568	6259617	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6259618	6259732	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6259733	6259808	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6259733	6259808	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6259809	6259934	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6259935	6260012	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6259935	6260012	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6260013	6260157	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6260158	6260239	1	-	1	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6260158	6260239	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6260240	6260325	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6260326	6260418	1	-	1	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6260326	6260418	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6260419	6260507	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6260508	6260617	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6260508	6260617	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6260618	6260705	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6260706	6260768	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6260706	6260768	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6260769	6260877	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6260878	6260929	1	-	1	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6260878	6260929	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6260930	6261060	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261061	6261185	0.97	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261061	6261185	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261186	6261313	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261314	6261405	0.98	-	2	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261314	6261405	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261406	6261487	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261488	6261546	1	-	1	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261488	6261546	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261547	6261683	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261684	6261798	1	-	2	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261684	6261798	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261799	6261872	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6261873	6261937	1	-	1	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6261873	6261937	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6261938	6262023	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262024	6262127	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262024	6262127	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262128	6262260	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262261	6262309	1	-	1	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262261	6262309	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262310	6262418	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262419	6262600	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262419	6262600	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262601	6262688	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262689	6262759	1	-	2	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262689	6262759	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	intron	6262760	6262846	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	CDS	6262847	6262958	1	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	exon	6262847	6262958	.	-	.	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
Phchi.S4	AUGUSTUS	start_codon	6262956	6262958	.	-	0	transcript_id "Phchi.S4G100300.t2"; gene_id "Phchi.S4G100300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2407.t1 is derived from g9327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6508853	6512105	.	+	.	Phchi.S5G101600
Phchi.S5	AUGUSTUS	transcript	6508853	6512105	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	start_codon	6508853	6508855	.	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	CDS	6508853	6509029	0.96	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	exon	6508853	6509029	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	intron	6509030	6509172	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	CDS	6509173	6509409	0.16	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	exon	6509173	6509409	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	intron	6509410	6509605	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	CDS	6509606	6510166	0.19	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	exon	6509606	6510166	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	intron	6510167	6510303	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	CDS	6510304	6510903	0.8	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	exon	6510304	6510903	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	intron	6510904	6510988	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	CDS	6510989	6511258	0.99	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	exon	6510989	6511258	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	intron	6511259	6511349	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	CDS	6511350	6512105	0.7	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	exon	6511350	6512105	.	+	.	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
Phchi.S5	AUGUSTUS	stop_codon	6512106	6512108	.	+	0	transcript_id "Phchi.S5G101600.t1"; gene_id "Phchi.S5G101600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14443.t1 is derived from g12911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12853380	12855124	.	-	.	Phchi.S3G176200
Phchi.S3	AUGUSTUS	transcript	12853380	12855124	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	stop_codon	12853377	12853379	.	-	0	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12853380	12853587	0.98	-	1	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12853380	12853587	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	intron	12853588	12853684	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12853685	12853768	1	-	1	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12853685	12853768	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	intron	12853769	12853878	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12853879	12854017	1	-	2	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12853879	12854017	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	intron	12854018	12854102	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12854103	12854229	1	-	0	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12854103	12854229	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	intron	12854230	12854336	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12854337	12854429	0.99	-	0	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12854337	12854429	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	intron	12854430	12854524	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12854525	12854662	1	-	0	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12854525	12854662	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	intron	12854663	12854878	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	CDS	12854879	12855124	0.73	-	0	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	exon	12854879	12855124	.	-	.	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
Phchi.S3	AUGUSTUS	start_codon	12855122	12855124	.	-	0	transcript_id "Phchi.S3G176200.t1"; gene_id "Phchi.S3G176200"
# This transcript jg12831.t2 is derived from g11296.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12832.t1 is derived from g11297.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2601823	2602239	.	+	.	Phchi.S3G015100
Phchi.S3	AUGUSTUS	transcript	2601823	2602239	.	+	.	transcript_id "Phchi.S3G015100.t1"; gene_id "Phchi.S3G015100"
Phchi.S3	AUGUSTUS	start_codon	2601823	2601825	.	+	0	transcript_id "Phchi.S3G015100.t1"; gene_id "Phchi.S3G015100"
Phchi.S3	AUGUSTUS	CDS	2601823	2602239	0.81	+	0	transcript_id "Phchi.S3G015100.t1"; gene_id "Phchi.S3G015100"
Phchi.S3	AUGUSTUS	exon	2601823	2602239	.	+	.	transcript_id "Phchi.S3G015100.t1"; gene_id "Phchi.S3G015100"
Phchi.S3	AUGUSTUS	stop_codon	2602240	2602242	.	+	0	transcript_id "Phchi.S3G015100.t1"; gene_id "Phchi.S3G015100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11111.t1 is derived from g15161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4207719	4208644	.	-	.	Phchi.S4G069300
Phchi.S4	AUGUSTUS	transcript	4207719	4208644	.	-	.	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	stop_codon	4207716	4207718	.	-	0	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	CDS	4207719	4207886	1	-	0	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	exon	4207719	4207886	.	-	.	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	intron	4207887	4208242	.	-	.	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	CDS	4208243	4208644	1	-	0	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	exon	4208243	4208644	.	-	.	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
Phchi.S4	AUGUSTUS	start_codon	4208642	4208644	.	-	0	transcript_id "Phchi.S4G069300.t1"; gene_id "Phchi.S4G069300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6051.t1 is derived from g3222.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20635678	20637805	.	+	.	Phchi.S1G321000
Phchi.S1	AUGUSTUS	transcript	20635678	20637805	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	start_codon	20635678	20635680	.	+	0	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	CDS	20635678	20636431	0.51	+	0	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	exon	20635678	20636431	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	intron	20636432	20636536	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	CDS	20636537	20636727	0.68	+	2	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	exon	20636537	20636727	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	intron	20636728	20636790	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	CDS	20636791	20637228	0.8	+	0	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	exon	20636791	20637228	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	intron	20637229	20637315	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	CDS	20637316	20637533	0.94	+	0	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	exon	20637316	20637533	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	intron	20637534	20637621	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	CDS	20637622	20637805	1	+	1	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	exon	20637622	20637805	.	+	.	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
Phchi.S1	AUGUSTUS	stop_codon	20637806	20637808	.	+	0	transcript_id "Phchi.S1G321000.t1"; gene_id "Phchi.S1G321000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8048.t1 is derived from g5223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32712470	32713162	.	+	.	Phchi.S1G520700
Phchi.S1	AUGUSTUS	transcript	32712470	32713162	.	+	.	transcript_id "Phchi.S1G520700.t1"; gene_id "Phchi.S1G520700"
Phchi.S1	AUGUSTUS	start_codon	32712470	32712472	.	+	0	transcript_id "Phchi.S1G520700.t1"; gene_id "Phchi.S1G520700"
Phchi.S1	AUGUSTUS	CDS	32712470	32713162	0.75	+	0	transcript_id "Phchi.S1G520700.t1"; gene_id "Phchi.S1G520700"
Phchi.S1	AUGUSTUS	exon	32712470	32713162	.	+	.	transcript_id "Phchi.S1G520700.t1"; gene_id "Phchi.S1G520700"
Phchi.S1	AUGUSTUS	stop_codon	32713163	32713165	.	+	0	transcript_id "Phchi.S1G520700.t1"; gene_id "Phchi.S1G520700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7894.t1 is derived from g5068.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31785876	31787094	.	+	.	Phchi.S1G505300
Phchi.S1	AUGUSTUS	transcript	31785876	31787094	.	+	.	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	start_codon	31785876	31785878	.	+	0	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	CDS	31785876	31786883	0.38	+	0	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	exon	31785876	31786883	.	+	.	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	intron	31786884	31787025	.	+	.	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	CDS	31787026	31787094	0.88	+	0	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	exon	31787026	31787094	.	+	.	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
Phchi.S1	AUGUSTUS	stop_codon	31787095	31787097	.	+	0	transcript_id "Phchi.S1G505300.t1"; gene_id "Phchi.S1G505300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12487.t1 is derived from g8164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	28872704	28873021	.	+	.	Phchi.S2G056700
Phchi.S2	AUGUSTUS	transcript	28872704	28873021	.	+	.	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	start_codon	28872704	28872706	.	+	0	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	CDS	28872704	28872894	0.42	+	0	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	exon	28872704	28872894	.	+	.	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	intron	28872895	28872975	.	+	.	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	CDS	28872976	28873021	0.4	+	1	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	exon	28872976	28873021	.	+	.	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
Phchi.S2	AUGUSTUS	stop_codon	28873022	28873024	.	+	0	transcript_id "Phchi.S2G056700.t1"; gene_id "Phchi.S2G056700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9252.t1 is derived from g6427.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40599441	40601051	.	-	.	Phchi.S1G641100
Phchi.S1	AUGUSTUS	transcript	40599441	40601051	.	-	.	transcript_id "Phchi.S1G641100.t1"; gene_id "Phchi.S1G641100"
Phchi.S1	AUGUSTUS	stop_codon	40599438	40599440	.	-	0	transcript_id "Phchi.S1G641100.t1"; gene_id "Phchi.S1G641100"
Phchi.S1	AUGUSTUS	CDS	40599441	40601051	1	-	0	transcript_id "Phchi.S1G641100.t1"; gene_id "Phchi.S1G641100"
Phchi.S1	AUGUSTUS	exon	40599441	40601051	.	-	.	transcript_id "Phchi.S1G641100.t1"; gene_id "Phchi.S1G641100"
Phchi.S1	AUGUSTUS	start_codon	40601049	40601051	.	-	0	transcript_id "Phchi.S1G641100.t1"; gene_id "Phchi.S1G641100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4143.t1 is derived from g1312.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8621256	8627307	.	+	.	Phchi.S1G130200
Phchi.S1	AUGUSTUS	transcript	8621256	8627307	.	+	.	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	start_codon	8621256	8621258	.	+	0	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	CDS	8621256	8622137	0.52	+	0	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	exon	8621256	8622137	.	+	.	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	intron	8622138	8622435	.	+	.	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	CDS	8622436	8627307	1	+	0	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	exon	8622436	8627307	.	+	.	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
Phchi.S1	AUGUSTUS	stop_codon	8627308	8627310	.	+	0	transcript_id "Phchi.S1G130200.t1"; gene_id "Phchi.S1G130200"
# This transcript jg1637.t2 is derived from g8556.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1638.t1 is derived from g8557.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2141751	2147940	.	-	.	Phchi.S5G024700
Phchi.S5	AUGUSTUS	transcript	2141751	2147940	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	stop_codon	2141748	2141750	.	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2141751	2142101	0.48	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2141751	2142101	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2142102	2142193	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2142194	2142541	0.99	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2142194	2142541	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2142542	2142644	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2142645	2143292	0.75	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2142645	2143292	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2143293	2143369	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2143370	2143612	0.74	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2143370	2143612	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2143613	2143699	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2143700	2144335	0.96	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2143700	2144335	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2144336	2144503	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2144504	2144582	0.94	-	1	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2144504	2144582	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2144583	2144667	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2144668	2144715	0.98	-	1	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2144668	2144715	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2144716	2144852	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2144853	2144947	0.98	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2144853	2144947	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2144948	2145044	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2145045	2145314	1	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2145045	2145314	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2145315	2145400	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2145401	2145846	0.9	-	2	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2145401	2145846	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2145847	2145958	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2145959	2146283	0.98	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2145959	2146283	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2146284	2146379	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2146380	2146510	0.68	-	2	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2146380	2146510	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2146511	2146608	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2146609	2146876	1	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2146609	2146876	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2146877	2146955	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2146956	2147044	1	-	2	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2146956	2147044	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2147045	2147132	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2147133	2147328	1	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2147133	2147328	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2147329	2147409	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2147410	2147463	1	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2147410	2147463	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2147464	2147546	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2147547	2147717	1	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2147547	2147717	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	intron	2147718	2147799	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	CDS	2147800	2147940	1	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	exon	2147800	2147940	.	-	.	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
Phchi.S5	AUGUSTUS	start_codon	2147938	2147940	.	-	0	transcript_id "Phchi.S5G024700.t1"; gene_id "Phchi.S5G024700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7627.t1 is derived from g4801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30316223	30319130	.	+	.	Phchi.S1G478600
Phchi.S1	AUGUSTUS	transcript	30316223	30319130	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	start_codon	30316223	30316225	.	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30316223	30316475	0.98	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30316223	30316475	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30316476	30316613	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30316614	30316897	0.98	+	2	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30316614	30316897	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30316898	30317150	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30317151	30317198	1	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30317151	30317198	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30317199	30317297	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30317298	30317357	1	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30317298	30317357	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30317358	30317464	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30317465	30317551	1	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30317465	30317551	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30317552	30317637	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30317638	30317742	1	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30317638	30317742	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30317743	30317838	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30317839	30317952	1	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30317839	30317952	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30317953	30318077	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30318078	30318178	1	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30318078	30318178	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30318179	30318336	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30318337	30318448	1	+	1	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30318337	30318448	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30318449	30318530	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30318531	30318602	0.76	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30318531	30318602	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30318603	30318835	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30318836	30318951	0.48	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30318836	30318951	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	intron	30318952	30319099	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	CDS	30319100	30319130	0.99	+	1	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	exon	30319100	30319130	.	+	.	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
Phchi.S1	AUGUSTUS	stop_codon	30319131	30319133	.	+	0	transcript_id "Phchi.S1G478600.t1"; gene_id "Phchi.S1G478600"
# This transcript jg9011.t2 is derived from g6186.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9011.t3 is derived from g6186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9012.t1 is derived from g6187.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39139638	39144415	.	+	.	Phchi.S1G617100
Phchi.S1	AUGUSTUS	transcript	39139638	39144357	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	start_codon	39139638	39139640	.	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39139638	39139937	0.57	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39139638	39139937	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39139938	39140091	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140092	39140283	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140092	39140283	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39140284	39140373	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140374	39140478	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140374	39140478	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39140479	39140617	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140618	39140800	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140618	39140800	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39140801	39140885	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140886	39141029	0.99	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140886	39141029	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141030	39141180	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141181	39141241	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141181	39141241	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141242	39141430	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141431	39141537	1	+	2	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141431	39141537	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141538	39141677	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141678	39141801	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141678	39141801	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141802	39141974	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141975	39142381	0.88	+	2	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141975	39142381	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39142382	39142477	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39142478	39142621	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39142478	39142621	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39142622	39142707	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39142708	39142812	0.78	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39142708	39142812	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39142813	39142911	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39142912	39143220	0.99	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39142912	39143220	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143221	39143307	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143308	39143457	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143308	39143457	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143458	39143594	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143595	39143655	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143595	39143655	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143656	39143755	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143756	39143796	0.89	+	2	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143756	39143796	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143797	39143913	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143914	39143976	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143914	39143976	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143977	39144058	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39144059	39144120	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39144059	39144120	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39144121	39144229	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39144230	39144266	1	+	1	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39144230	39144266	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39144267	39144339	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39144340	39144357	1	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39144340	39144357	.	+	.	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	stop_codon	39144358	39144360	.	+	0	transcript_id "Phchi.S1G617100.t1"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	transcript	39139638	39144415	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	start_codon	39139638	39139640	.	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39139638	39139937	0.74	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39139638	39139937	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39139938	39140091	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140092	39140283	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140092	39140283	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39140284	39140373	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140374	39140478	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140374	39140478	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39140479	39140617	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140618	39140800	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140618	39140800	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39140801	39140885	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39140886	39141029	0.98	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39140886	39141029	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141030	39141180	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141181	39141241	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141181	39141241	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141242	39141430	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141431	39141537	1	+	2	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141431	39141537	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141538	39141677	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141678	39141801	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141678	39141801	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39141802	39141974	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39141975	39142381	0.85	+	2	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39141975	39142381	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39142382	39142477	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39142478	39142621	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39142478	39142621	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39142622	39142707	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39142708	39142812	0.7	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39142708	39142812	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39142813	39142911	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39142912	39143220	0.99	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39142912	39143220	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143221	39143307	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143308	39143457	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143308	39143457	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143458	39143594	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143595	39143655	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143595	39143655	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143656	39143755	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143756	39143796	0.85	+	2	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143756	39143796	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143797	39143913	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39143914	39143976	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39143914	39143976	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39143977	39144058	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39144059	39144120	0.99	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39144059	39144120	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39144121	39144229	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39144230	39144266	0.99	+	1	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39144230	39144266	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	intron	39144267	39144352	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	CDS	39144353	39144415	1	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	exon	39144353	39144415	.	+	.	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
Phchi.S1	AUGUSTUS	stop_codon	39144416	39144418	.	+	0	transcript_id "Phchi.S1G617100.t2"; gene_id "Phchi.S1G617100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9462.t1 is derived from g6638.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41573870	41576759	.	-	.	Phchi.S1G662100
Phchi.S1	AUGUSTUS	transcript	41573870	41576759	.	-	.	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	stop_codon	41573867	41573869	.	-	0	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	CDS	41573870	41576285	0.46	-	1	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	exon	41573870	41576285	.	-	.	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	intron	41576286	41576415	.	-	.	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	CDS	41576416	41576759	0.42	-	0	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	exon	41576416	41576759	.	-	.	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
Phchi.S1	AUGUSTUS	start_codon	41576757	41576759	.	-	0	transcript_id "Phchi.S1G662100.t1"; gene_id "Phchi.S1G662100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7003.t1 is derived from g4175.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26359145	26361152	.	-	.	Phchi.S1G416200
Phchi.S1	AUGUSTUS	transcript	26359145	26361152	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	stop_codon	26359142	26359144	.	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	CDS	26359145	26359225	0.98	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	exon	26359145	26359225	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	intron	26359226	26359451	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	CDS	26359452	26359592	1	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	exon	26359452	26359592	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	intron	26359593	26359688	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	CDS	26359689	26359905	1	-	1	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	exon	26359689	26359905	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	intron	26359906	26359997	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	CDS	26359998	26360167	1	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	exon	26359998	26360167	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	intron	26360168	26360250	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	CDS	26360251	26360496	1	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	exon	26360251	26360496	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	intron	26360497	26360672	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	CDS	26360673	26361152	0.7	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	exon	26360673	26361152	.	-	.	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
Phchi.S1	AUGUSTUS	start_codon	26361150	26361152	.	-	0	transcript_id "Phchi.S1G416200.t1"; gene_id "Phchi.S1G416200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8182.t1 is derived from g5357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34328657	34329382	.	-	.	Phchi.S1G534100
Phchi.S1	AUGUSTUS	transcript	34328657	34329382	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	stop_codon	34328654	34328656	.	-	0	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	CDS	34328657	34328731	0.99	-	0	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	exon	34328657	34328731	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	intron	34328732	34328821	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	CDS	34328822	34328878	1	-	0	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	exon	34328822	34328878	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	intron	34328879	34328965	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	CDS	34328966	34329067	1	-	0	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	exon	34328966	34329067	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	intron	34329068	34329146	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	CDS	34329147	34329187	1	-	2	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	exon	34329147	34329187	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	intron	34329188	34329261	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	CDS	34329262	34329382	0.98	-	0	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	exon	34329262	34329382	.	-	.	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
Phchi.S1	AUGUSTUS	start_codon	34329380	34329382	.	-	0	transcript_id "Phchi.S1G534100.t1"; gene_id "Phchi.S1G534100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg271.t1 is derived from g10053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1942511	1945575	.	+	.	Phchi.S6G023000
Phchi.S6	AUGUSTUS	transcript	1942511	1945575	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	start_codon	1942511	1942513	.	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1942511	1942858	1	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1942511	1942858	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1942859	1942994	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1942995	1943396	0.99	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1942995	1943396	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1943397	1943489	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1943490	1943807	1	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1943490	1943807	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1943808	1943905	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1943906	1943989	1	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1943906	1943989	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1943990	1944071	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1944072	1944248	0.99	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1944072	1944248	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1944249	1944354	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1944355	1944818	0.94	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1944355	1944818	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1944819	1944944	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1944945	1945205	0.35	+	1	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1944945	1945205	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	intron	1945206	1945391	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	CDS	1945392	1945575	0.34	+	1	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	exon	1945392	1945575	.	+	.	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
Phchi.S6	AUGUSTUS	stop_codon	1945576	1945578	.	+	0	transcript_id "Phchi.S6G023000.t1"; gene_id "Phchi.S6G023000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12232.t1 is derived from g7908.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6915778	6918276	.	-	.	Phchi.S2G031200
Phchi.S2	AUGUSTUS	transcript	6915778	6918276	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	stop_codon	6915775	6915777	.	-	0	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6915778	6915937	1	-	1	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6915778	6915937	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6915938	6916011	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916012	6916235	1	-	0	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916012	6916235	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6916236	6916319	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916320	6916396	1	-	2	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916320	6916396	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6916397	6916493	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916494	6916694	1	-	2	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916494	6916694	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6916695	6916805	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916806	6917043	0.99	-	0	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916806	6917043	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6917044	6917157	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6917158	6918276	0.92	-	0	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6917158	6918276	.	-	.	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	start_codon	6918274	6918276	.	-	0	transcript_id "Phchi.S2G031200.t1"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	transcript	6915778	6918276	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	stop_codon	6915775	6915777	.	-	0	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6915778	6915937	1	-	1	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6915778	6915937	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6915938	6916023	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916024	6916235	1	-	0	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916024	6916235	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6916236	6916319	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916320	6916396	1	-	2	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916320	6916396	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6916397	6916493	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916494	6916694	1	-	2	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916494	6916694	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6916695	6916805	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6916806	6917043	1	-	0	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6916806	6917043	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	intron	6917044	6917157	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	CDS	6917158	6918276	0.88	-	0	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	exon	6917158	6918276	.	-	.	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
Phchi.S2	AUGUSTUS	start_codon	6918274	6918276	.	-	0	transcript_id "Phchi.S2G031200.t2"; gene_id "Phchi.S2G031200"
# This transcript jg11754.t2 is derived from g15806.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11755.t1 is derived from g15807.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8013238	8016149	.	+	.	Phchi.S4G133700
Phchi.S4	AUGUSTUS	transcript	8013238	8016149	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	start_codon	8013238	8013240	.	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8013238	8013266	0.89	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8013238	8013266	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8013267	8013870	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8013871	8013909	1	+	1	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8013871	8013909	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8013910	8014066	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8014067	8014133	0.97	+	1	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8014067	8014133	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8014134	8014234	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8014235	8014308	1	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8014235	8014308	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8014309	8014543	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8014544	8014682	1	+	1	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8014544	8014682	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8014683	8014885	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8014886	8014978	1	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8014886	8014978	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8014979	8015099	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8015100	8015168	1	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8015100	8015168	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8015169	8015295	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8015296	8015433	1	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8015296	8015433	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8015434	8015553	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8015554	8015667	1	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8015554	8015667	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	intron	8015668	8015768	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	CDS	8015769	8016149	1	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	exon	8015769	8016149	.	+	.	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
Phchi.S4	AUGUSTUS	stop_codon	8016150	8016152	.	+	0	transcript_id "Phchi.S4G133700.t1"; gene_id "Phchi.S4G133700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14144.t1 is derived from g12611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11128578	11130215	.	-	.	Phchi.S3G146300
Phchi.S3	AUGUSTUS	transcript	11128578	11130215	.	-	.	transcript_id "Phchi.S3G146300.t1"; gene_id "Phchi.S3G146300"
Phchi.S3	AUGUSTUS	stop_codon	11128575	11128577	.	-	0	transcript_id "Phchi.S3G146300.t1"; gene_id "Phchi.S3G146300"
Phchi.S3	AUGUSTUS	CDS	11128578	11130215	0.89	-	0	transcript_id "Phchi.S3G146300.t1"; gene_id "Phchi.S3G146300"
Phchi.S3	AUGUSTUS	exon	11128578	11130215	.	-	.	transcript_id "Phchi.S3G146300.t1"; gene_id "Phchi.S3G146300"
Phchi.S3	AUGUSTUS	start_codon	11130213	11130215	.	-	0	transcript_id "Phchi.S3G146300.t1"; gene_id "Phchi.S3G146300"
# This transcript jg15896.t2 is derived from g14366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15897.t1 is derived from g14367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22058727	22060404	.	-	.	Phchi.S3G321600
Phchi.S3	AUGUSTUS	transcript	22058727	22060404	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	stop_codon	22058724	22058726	.	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22058727	22058747	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22058727	22058747	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22058748	22058972	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22058973	22059065	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22058973	22059065	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22059066	22059161	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22059162	22059356	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22059162	22059356	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22059357	22059446	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22059447	22059590	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22059447	22059590	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22059591	22059690	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22059691	22059753	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22059691	22059753	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22059754	22059844	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22059845	22059928	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22059845	22059928	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22059929	22060033	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22060034	22060185	1	-	2	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22060034	22060185	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	intron	22060186	22060337	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	CDS	22060338	22060404	1	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	exon	22060338	22060404	.	-	.	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
Phchi.S3	AUGUSTUS	start_codon	22060402	22060404	.	-	0	transcript_id "Phchi.S3G321600.t1"; gene_id "Phchi.S3G321600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg57.t1 is derived from g9839.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	275497	278366	.	-	.	Phchi.S6G001600
Phchi.S6	AUGUSTUS	transcript	275497	278366	.	-	.	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	stop_codon	275494	275496	.	-	0	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	CDS	275497	277243	0.78	-	1	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	exon	275497	277243	.	-	.	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	intron	277244	277491	.	-	.	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	CDS	277492	277832	0.85	-	0	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	exon	277492	277832	.	-	.	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	intron	277833	277994	.	-	.	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	CDS	277995	278366	0.63	-	0	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	exon	277995	278366	.	-	.	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
Phchi.S6	AUGUSTUS	start_codon	278364	278366	.	-	0	transcript_id "Phchi.S6G001600.t1"; gene_id "Phchi.S6G001600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8429.t1 is derived from g5604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35894765	35895976	.	-	.	Phchi.S1G558800
Phchi.S1	AUGUSTUS	transcript	35894765	35895976	.	-	.	transcript_id "Phchi.S1G558800.t1"; gene_id "Phchi.S1G558800"
Phchi.S1	AUGUSTUS	stop_codon	35894762	35894764	.	-	0	transcript_id "Phchi.S1G558800.t1"; gene_id "Phchi.S1G558800"
Phchi.S1	AUGUSTUS	CDS	35894765	35895976	0.32	-	0	transcript_id "Phchi.S1G558800.t1"; gene_id "Phchi.S1G558800"
Phchi.S1	AUGUSTUS	exon	35894765	35895976	.	-	.	transcript_id "Phchi.S1G558800.t1"; gene_id "Phchi.S1G558800"
Phchi.S1	AUGUSTUS	start_codon	35895974	35895976	.	-	0	transcript_id "Phchi.S1G558800.t1"; gene_id "Phchi.S1G558800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10930.t1 is derived from g14980.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3041385	3041978	.	+	.	Phchi.S4G051200
Phchi.S4	AUGUSTUS	transcript	3041385	3041978	.	+	.	transcript_id "Phchi.S4G051200.t1"; gene_id "Phchi.S4G051200"
Phchi.S4	AUGUSTUS	start_codon	3041385	3041387	.	+	0	transcript_id "Phchi.S4G051200.t1"; gene_id "Phchi.S4G051200"
Phchi.S4	AUGUSTUS	CDS	3041385	3041978	0.35	+	0	transcript_id "Phchi.S4G051200.t1"; gene_id "Phchi.S4G051200"
Phchi.S4	AUGUSTUS	exon	3041385	3041978	.	+	.	transcript_id "Phchi.S4G051200.t1"; gene_id "Phchi.S4G051200"
Phchi.S4	AUGUSTUS	stop_codon	3041979	3041981	.	+	0	transcript_id "Phchi.S4G051200.t1"; gene_id "Phchi.S4G051200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15582.t1 is derived from g14051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20123348	20126304	.	+	.	Phchi.S3G290100
Phchi.S3	AUGUSTUS	transcript	20123348	20126304	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	start_codon	20123348	20123350	.	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20123348	20123380	0.98	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20123348	20123380	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20123381	20123497	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20123498	20123584	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20123498	20123584	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20123585	20123676	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20123677	20123734	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20123677	20123734	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20123735	20123863	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20123864	20123927	1	+	2	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20123864	20123927	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20123928	20124061	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20124062	20124161	1	+	1	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20124062	20124161	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20124162	20124284	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20124285	20124385	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20124285	20124385	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20124386	20124470	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20124471	20124522	1	+	1	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20124471	20124522	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20124523	20124599	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20124600	20124662	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20124600	20124662	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20124663	20124760	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20124761	20124850	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20124761	20124850	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20124851	20124940	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20124941	20125013	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20124941	20125013	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20125014	20125107	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20125108	20125187	1	+	2	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20125108	20125187	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20125188	20125299	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20125300	20125404	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20125300	20125404	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20125405	20125574	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20125575	20125670	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20125575	20125670	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20125671	20125844	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20125845	20125906	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20125845	20125906	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20125907	20125988	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20125989	20126103	1	+	1	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20125989	20126103	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	intron	20126104	20126196	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	CDS	20126197	20126304	1	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	exon	20126197	20126304	.	+	.	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
Phchi.S3	AUGUSTUS	stop_codon	20126305	20126307	.	+	0	transcript_id "Phchi.S3G290100.t1"; gene_id "Phchi.S3G290100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4061.t1 is derived from g1230.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7586979	7587345	.	-	.	Phchi.S1G122000
Phchi.S1	AUGUSTUS	transcript	7586979	7587345	.	-	.	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	stop_codon	7586976	7586978	.	-	0	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	CDS	7586979	7587005	1	-	0	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	exon	7586979	7587005	.	-	.	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	intron	7587006	7587087	.	-	.	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	CDS	7587088	7587345	0.57	-	0	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	exon	7587088	7587345	.	-	.	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
Phchi.S1	AUGUSTUS	start_codon	7587343	7587345	.	-	0	transcript_id "Phchi.S1G122000.t1"; gene_id "Phchi.S1G122000"
# This transcript jg9865.t2 is derived from g7041.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9866.t1 is derived from g7042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44140311	44141753	.	+	.	Phchi.S1G702500
Phchi.S1	AUGUSTUS	transcript	44140311	44141753	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	start_codon	44140311	44140313	.	+	0	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	CDS	44140311	44140388	0.98	+	0	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	exon	44140311	44140388	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	intron	44140389	44140514	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	CDS	44140515	44140666	0.99	+	0	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	exon	44140515	44140666	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	intron	44140667	44140787	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	CDS	44140788	44140945	0.99	+	1	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	exon	44140788	44140945	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	intron	44140946	44141036	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	CDS	44141037	44141256	1	+	2	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	exon	44141037	44141256	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	intron	44141257	44141350	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	CDS	44141351	44141753	1	+	1	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	exon	44141351	44141753	.	+	.	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
Phchi.S1	AUGUSTUS	stop_codon	44141754	44141756	.	+	0	transcript_id "Phchi.S1G702500.t1"; gene_id "Phchi.S1G702500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1283.t1 is derived from g11066.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8803518	8805996	.	+	.	Phchi.S6G124200
Phchi.S6	AUGUSTUS	transcript	8803518	8805996	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	start_codon	8803518	8803520	.	+	0	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8803518	8804031	0.8	+	0	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8803518	8804031	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804032	8804134	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804135	8804348	0.59	+	2	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804135	8804348	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804349	8804584	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804585	8804668	0.73	+	1	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804585	8804668	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804669	8804814	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804815	8804861	0.73	+	1	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804815	8804861	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804862	8804942	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804943	8805043	0.76	+	2	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804943	8805043	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8805044	8805292	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8805293	8805400	1	+	0	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8805293	8805400	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8805401	8805592	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8805593	8805814	1	+	0	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8805593	8805814	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8805815	8805903	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8805904	8805996	1	+	0	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8805904	8805996	.	+	.	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	stop_codon	8805997	8805999	.	+	0	transcript_id "Phchi.S6G124200.t1"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	transcript	8803518	8805996	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	start_codon	8803518	8803520	.	+	0	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8803518	8804031	0.77	+	0	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8803518	8804031	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804032	8804134	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804135	8804348	0.54	+	2	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804135	8804348	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804349	8804584	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804585	8804668	0.34	+	1	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804585	8804668	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804669	8804814	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804815	8804861	0.34	+	1	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804815	8804861	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8804862	8804942	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8804943	8805043	0.34	+	2	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8804943	8805043	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8805044	8805283	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8805284	8805400	0.43	+	0	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8805284	8805400	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8805401	8805592	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8805593	8805814	1	+	0	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8805593	8805814	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	intron	8805815	8805903	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	CDS	8805904	8805996	1	+	0	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	exon	8805904	8805996	.	+	.	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
Phchi.S6	AUGUSTUS	stop_codon	8805997	8805999	.	+	0	transcript_id "Phchi.S6G124200.t2"; gene_id "Phchi.S6G124200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7516.t1 is derived from g4690.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29799257	29801945	.	+	.	Phchi.S1G467500
Phchi.S1	AUGUSTUS	transcript	29799257	29801945	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	start_codon	29799257	29799259	.	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29799257	29799422	0.62	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29799257	29799422	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29799423	29799676	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29799677	29799753	1	+	2	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29799677	29799753	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29799754	29799907	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29799908	29800066	1	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29799908	29800066	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29800067	29800175	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29800176	29800309	1	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29800176	29800309	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29800310	29800551	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29800552	29800682	1	+	1	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29800552	29800682	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29800683	29800917	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29800918	29800962	0.99	+	2	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29800918	29800962	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29800963	29801085	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29801086	29801183	0.99	+	2	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29801086	29801183	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29801184	29801441	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29801442	29801549	1	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29801442	29801549	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29801550	29801639	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29801640	29801696	1	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29801640	29801696	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	intron	29801697	29801873	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	CDS	29801874	29801945	1	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	exon	29801874	29801945	.	+	.	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
Phchi.S1	AUGUSTUS	stop_codon	29801946	29801948	.	+	0	transcript_id "Phchi.S1G467500.t1"; gene_id "Phchi.S1G467500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2320.t1 is derived from g9240.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6161915	6163859	.	-	.	Phchi.S5G092900
Phchi.S5	AUGUSTUS	transcript	6161915	6163859	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	stop_codon	6161912	6161914	.	-	0	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6161915	6161965	1	-	0	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6161915	6161965	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6161966	6162039	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6162040	6162111	1	-	0	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6162040	6162111	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6162112	6162201	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6162202	6162283	1	-	1	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6162202	6162283	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6162284	6162409	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6162410	6162523	1	-	1	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6162410	6162523	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6162524	6162684	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6162685	6162726	1	-	1	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6162685	6162726	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6162727	6162942	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6162943	6162992	1	-	0	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6162943	6162992	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6162993	6163079	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6163080	6163125	1	-	1	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6163080	6163125	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	intron	6163126	6163218	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	CDS	6163219	6163859	1	-	0	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	exon	6163219	6163859	.	-	.	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
Phchi.S5	AUGUSTUS	start_codon	6163857	6163859	.	-	0	transcript_id "Phchi.S5G092900.t1"; gene_id "Phchi.S5G092900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15226.t1 is derived from g13694.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17825737	17826744	.	+	.	Phchi.S3G254500
Phchi.S3	AUGUSTUS	transcript	17825737	17826744	.	+	.	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	start_codon	17825737	17825739	.	+	0	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	CDS	17825737	17826362	0.37	+	0	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	exon	17825737	17826362	.	+	.	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	intron	17826363	17826454	.	+	.	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	CDS	17826455	17826573	0.77	+	1	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	exon	17826455	17826573	.	+	.	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	intron	17826574	17826673	.	+	.	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	CDS	17826674	17826744	0.81	+	2	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	exon	17826674	17826744	.	+	.	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
Phchi.S3	AUGUSTUS	stop_codon	17826745	17826747	.	+	0	transcript_id "Phchi.S3G254500.t1"; gene_id "Phchi.S3G254500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3601.t1 is derived from g770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4676915	4678871	.	+	.	Phchi.S1G076000
Phchi.S1	AUGUSTUS	transcript	4676915	4678871	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	start_codon	4676915	4676917	.	+	0	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	CDS	4676915	4678045	0.51	+	0	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	exon	4676915	4678045	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	intron	4678046	4678139	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	CDS	4678140	4678208	0.66	+	0	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	exon	4678140	4678208	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	intron	4678209	4678449	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	CDS	4678450	4678549	1	+	0	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	exon	4678450	4678549	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	intron	4678550	4678842	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	CDS	4678843	4678871	1	+	2	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	exon	4678843	4678871	.	+	.	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
Phchi.S1	AUGUSTUS	stop_codon	4678872	4678874	.	+	0	transcript_id "Phchi.S1G076000.t1"; gene_id "Phchi.S1G076000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13282.t1 is derived from g11747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5174968	5176496	.	+	.	Phchi.S3G060100
Phchi.S3	AUGUSTUS	transcript	5174968	5176496	.	+	.	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	start_codon	5174968	5174970	.	+	0	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	CDS	5174968	5175069	0.49	+	0	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	exon	5174968	5175069	.	+	.	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	intron	5175070	5175236	.	+	.	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	CDS	5175237	5176496	1	+	0	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	exon	5175237	5176496	.	+	.	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
Phchi.S3	AUGUSTUS	stop_codon	5176497	5176499	.	+	0	transcript_id "Phchi.S3G060100.t1"; gene_id "Phchi.S3G060100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15805.t1 is derived from g14275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21479643	21482620	.	-	.	Phchi.S3G312400
Phchi.S3	AUGUSTUS	transcript	21479643	21482620	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	stop_codon	21479640	21479642	.	-	0	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	CDS	21479643	21479649	0.75	-	1	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	exon	21479643	21479649	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	intron	21479650	21479935	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	CDS	21479936	21480077	0.75	-	2	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	exon	21479936	21480077	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	intron	21480078	21480865	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	CDS	21480866	21480923	0.42	-	0	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	exon	21480866	21480923	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	intron	21480924	21482539	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	CDS	21482540	21482620	0.16	-	0	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	exon	21482540	21482620	.	-	.	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
Phchi.S3	AUGUSTUS	start_codon	21482618	21482620	.	-	0	transcript_id "Phchi.S3G312400.t1"; gene_id "Phchi.S3G312400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15369.t1 is derived from g13837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18667049	18668689	.	+	.	Phchi.S3G268800
Phchi.S3	AUGUSTUS	transcript	18667049	18668689	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	start_codon	18667049	18667051	.	+	0	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	CDS	18667049	18667334	0.73	+	0	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	exon	18667049	18667334	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	intron	18667335	18667792	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	CDS	18667793	18667920	1	+	2	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	exon	18667793	18667920	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	intron	18667921	18668017	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	CDS	18668018	18668062	1	+	0	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	exon	18668018	18668062	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	intron	18668063	18668261	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	CDS	18668262	18668335	1	+	0	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	exon	18668262	18668335	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	intron	18668336	18668442	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	CDS	18668443	18668492	1	+	1	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	exon	18668443	18668492	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	intron	18668493	18668579	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	CDS	18668580	18668689	1	+	2	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	exon	18668580	18668689	.	+	.	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
Phchi.S3	AUGUSTUS	stop_codon	18668690	18668692	.	+	0	transcript_id "Phchi.S3G268800.t1"; gene_id "Phchi.S3G268800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5572.t1 is derived from g2742.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17641788	17642834	.	+	.	Phchi.S1G273100
Phchi.S1	AUGUSTUS	transcript	17641788	17642834	.	+	.	transcript_id "Phchi.S1G273100.t1"; gene_id "Phchi.S1G273100"
Phchi.S1	AUGUSTUS	start_codon	17641788	17641790	.	+	0	transcript_id "Phchi.S1G273100.t1"; gene_id "Phchi.S1G273100"
Phchi.S1	AUGUSTUS	CDS	17641788	17642834	0.67	+	0	transcript_id "Phchi.S1G273100.t1"; gene_id "Phchi.S1G273100"
Phchi.S1	AUGUSTUS	exon	17641788	17642834	.	+	.	transcript_id "Phchi.S1G273100.t1"; gene_id "Phchi.S1G273100"
Phchi.S1	AUGUSTUS	stop_codon	17642835	17642837	.	+	0	transcript_id "Phchi.S1G273100.t1"; gene_id "Phchi.S1G273100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14692.t1 is derived from g13160.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14189542	14192539	.	-	.	Phchi.S3G201100
Phchi.S3	AUGUSTUS	transcript	14189542	14192539	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	stop_codon	14189539	14189541	.	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14189542	14189628	0.79	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14189542	14189628	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14189629	14189763	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14189764	14189970	0.83	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14189764	14189970	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14189971	14190049	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14190050	14190145	1	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14190050	14190145	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14190146	14190241	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14190242	14190360	1	-	2	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14190242	14190360	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14190361	14190452	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14190453	14190513	1	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14190453	14190513	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14190514	14190589	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14190590	14190700	1	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14190590	14190700	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14190701	14190772	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14190773	14190832	1	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14190773	14190832	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14190833	14190959	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14190960	14191049	1	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14190960	14191049	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14191050	14191148	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14191149	14191221	1	-	1	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14191149	14191221	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14191222	14191297	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14191298	14191376	1	-	2	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14191298	14191376	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14191377	14191469	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14191470	14191516	1	-	1	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14191470	14191516	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14191517	14191702	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14191703	14191758	1	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14191703	14191758	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14191759	14191853	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14191854	14191954	1	-	2	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14191854	14191954	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14191955	14192049	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14192050	14192204	1	-	1	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14192050	14192204	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14192205	14192282	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14192283	14192351	1	-	1	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14192283	14192351	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	intron	14192352	14192438	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	CDS	14192439	14192539	0.8	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	exon	14192439	14192539	.	-	.	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
Phchi.S3	AUGUSTUS	start_codon	14192537	14192539	.	-	0	transcript_id "Phchi.S3G201100.t1"; gene_id "Phchi.S3G201100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10520.t1 is derived from g14570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	812470	813831	.	+	.	Phchi.S4G010200
Phchi.S4	AUGUSTUS	transcript	812470	813831	.	+	.	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	start_codon	812470	812472	.	+	0	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	CDS	812470	812970	0.68	+	0	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	exon	812470	812970	.	+	.	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	intron	812971	813085	.	+	.	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	CDS	813086	813141	1	+	0	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	exon	813086	813141	.	+	.	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	intron	813142	813218	.	+	.	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	CDS	813219	813831	0.94	+	1	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	exon	813219	813831	.	+	.	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
Phchi.S4	AUGUSTUS	stop_codon	813832	813834	.	+	0	transcript_id "Phchi.S4G010200.t1"; gene_id "Phchi.S4G010200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10650.t1 is derived from g14700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1427096	1430972	.	-	.	Phchi.S4G023200
Phchi.S4	AUGUSTUS	transcript	1427096	1430972	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	stop_codon	1427093	1427095	.	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1427096	1427170	1	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1427096	1427170	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	intron	1427171	1427263	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1427264	1427326	1	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1427264	1427326	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	intron	1427327	1427403	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1427404	1427553	1	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1427404	1427553	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	intron	1427554	1427633	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1427634	1427747	1	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1427634	1427747	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	intron	1427748	1427834	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1427835	1427911	1	-	2	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1427835	1427911	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	intron	1427912	1427991	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1427992	1429830	0.78	-	2	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1427992	1429830	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	intron	1429831	1429930	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	CDS	1429931	1430972	0.52	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	exon	1429931	1430972	.	-	.	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
Phchi.S4	AUGUSTUS	start_codon	1430970	1430972	.	-	0	transcript_id "Phchi.S4G023200.t1"; gene_id "Phchi.S4G023200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14699.t1 is derived from g13167.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14241208	14241816	.	-	.	Phchi.S3G201800
Phchi.S3	AUGUSTUS	transcript	14241208	14241816	.	-	.	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	stop_codon	14241205	14241207	.	-	0	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	CDS	14241208	14241328	1	-	1	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	exon	14241208	14241328	.	-	.	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	intron	14241329	14241412	.	-	.	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	CDS	14241413	14241582	1	-	0	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	exon	14241413	14241582	.	-	.	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	intron	14241583	14241789	.	-	.	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	CDS	14241790	14241816	1	-	0	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	exon	14241790	14241816	.	-	.	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
Phchi.S3	AUGUSTUS	start_codon	14241814	14241816	.	-	0	transcript_id "Phchi.S3G201800.t1"; gene_id "Phchi.S3G201800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11379.t1 is derived from g15429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5979086	5979469	.	-	.	Phchi.S4G096100
Phchi.S4	AUGUSTUS	transcript	5979086	5979469	.	-	.	transcript_id "Phchi.S4G096100.t1"; gene_id "Phchi.S4G096100"
Phchi.S4	AUGUSTUS	stop_codon	5979083	5979085	.	-	0	transcript_id "Phchi.S4G096100.t1"; gene_id "Phchi.S4G096100"
Phchi.S4	AUGUSTUS	CDS	5979086	5979469	0.93	-	0	transcript_id "Phchi.S4G096100.t1"; gene_id "Phchi.S4G096100"
Phchi.S4	AUGUSTUS	exon	5979086	5979469	.	-	.	transcript_id "Phchi.S4G096100.t1"; gene_id "Phchi.S4G096100"
Phchi.S4	AUGUSTUS	start_codon	5979467	5979469	.	-	0	transcript_id "Phchi.S4G096100.t1"; gene_id "Phchi.S4G096100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg513.t1 is derived from g10295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3546454	3547215	.	+	.	Phchi.S6G047200
Phchi.S6	AUGUSTUS	transcript	3546454	3547215	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	start_codon	3546454	3546456	.	+	0	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	CDS	3546454	3546510	0.96	+	0	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	exon	3546454	3546510	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	intron	3546511	3546661	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	CDS	3546662	3546729	0.96	+	0	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	exon	3546662	3546729	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	intron	3546730	3546807	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	CDS	3546808	3546827	1	+	1	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	exon	3546808	3546827	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	intron	3546828	3546934	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	CDS	3546935	3546997	1	+	2	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	exon	3546935	3546997	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	intron	3546998	3547096	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	CDS	3547097	3547215	1	+	2	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	exon	3547097	3547215	.	+	.	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
Phchi.S6	AUGUSTUS	stop_codon	3547216	3547218	.	+	0	transcript_id "Phchi.S6G047200.t1"; gene_id "Phchi.S6G047200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11031.t1 is derived from g15081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3731048	3731538	.	+	.	Phchi.S4G061300
Phchi.S4	AUGUSTUS	transcript	3731048	3731538	.	+	.	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	start_codon	3731048	3731050	.	+	0	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	CDS	3731048	3731137	0.77	+	0	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	exon	3731048	3731137	.	+	.	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	intron	3731138	3731211	.	+	.	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	CDS	3731212	3731260	0.64	+	0	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	exon	3731212	3731260	.	+	.	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	intron	3731261	3731344	.	+	.	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	CDS	3731345	3731538	0.62	+	2	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	exon	3731345	3731538	.	+	.	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
Phchi.S4	AUGUSTUS	stop_codon	3731539	3731541	.	+	0	transcript_id "Phchi.S4G061300.t1"; gene_id "Phchi.S4G061300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg877.t1 is derived from g10659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6194356	6195846	.	+	.	Phchi.S6G083600
Phchi.S6	AUGUSTUS	transcript	6194356	6195846	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	start_codon	6194356	6194358	.	+	0	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	CDS	6194356	6194539	1	+	0	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	exon	6194356	6194539	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	intron	6194540	6194652	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	CDS	6194653	6194954	1	+	2	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	exon	6194653	6194954	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	intron	6194955	6195057	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	CDS	6195058	6195300	1	+	0	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	exon	6195058	6195300	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	intron	6195301	6195396	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	CDS	6195397	6195846	0.63	+	0	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	exon	6195397	6195846	.	+	.	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
Phchi.S6	AUGUSTUS	stop_codon	6195847	6195849	.	+	0	transcript_id "Phchi.S6G083600.t1"; gene_id "Phchi.S6G083600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12388.t1 is derived from g8065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	15429590	15430195	.	-	.	Phchi.S2G046800
Phchi.S2	AUGUSTUS	transcript	15429590	15430195	.	-	.	transcript_id "Phchi.S2G046800.t1"; gene_id "Phchi.S2G046800"
Phchi.S2	AUGUSTUS	stop_codon	15429587	15429589	.	-	0	transcript_id "Phchi.S2G046800.t1"; gene_id "Phchi.S2G046800"
Phchi.S2	AUGUSTUS	CDS	15429590	15430195	0.9	-	0	transcript_id "Phchi.S2G046800.t1"; gene_id "Phchi.S2G046800"
Phchi.S2	AUGUSTUS	exon	15429590	15430195	.	-	.	transcript_id "Phchi.S2G046800.t1"; gene_id "Phchi.S2G046800"
Phchi.S2	AUGUSTUS	start_codon	15430193	15430195	.	-	0	transcript_id "Phchi.S2G046800.t1"; gene_id "Phchi.S2G046800"
# This transcript jg13243.t2 is derived from g11708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13243.t3 is derived from g11708.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13244.t1 is derived from g11709.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4894170	4895796	.	-	.	Phchi.S3G056300
Phchi.S3	AUGUSTUS	transcript	4894170	4895796	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	stop_codon	4894167	4894169	.	-	0	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894170	4894212	0.96	-	1	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894170	4894212	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894213	4894333	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894334	4894410	1	-	0	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894334	4894410	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894411	4894489	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894490	4894561	1	-	0	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894490	4894561	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894562	4894652	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894653	4894702	1	-	2	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894653	4894702	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894703	4894800	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894801	4894845	1	-	2	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894801	4894845	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894846	4894946	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894947	4895042	0.86	-	2	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894947	4895042	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4895043	4895131	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4895132	4895210	1	-	0	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4895132	4895210	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4895211	4895394	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4895395	4895796	0.97	-	0	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4895395	4895796	.	-	.	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	start_codon	4895794	4895796	.	-	0	transcript_id "Phchi.S3G056300.t1"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	transcript	4894170	4895796	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	stop_codon	4894167	4894169	.	-	0	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894170	4894212	0.96	-	1	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894170	4894212	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894213	4894333	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894334	4894410	1	-	0	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894334	4894410	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894411	4894489	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894490	4894561	1	-	0	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894490	4894561	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894562	4894652	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894653	4894702	1	-	2	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894653	4894702	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894703	4894800	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894801	4894845	1	-	2	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894801	4894845	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4894846	4894946	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4894947	4895042	0.89	-	2	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4894947	4895042	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4895043	4895131	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4895132	4895238	0.9	-	1	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4895132	4895238	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4895239	4895394	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4895395	4895406	0.9	-	1	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4895395	4895406	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	intron	4895407	4895560	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	CDS	4895561	4895796	0.83	-	0	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	exon	4895561	4895796	.	-	.	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
Phchi.S3	AUGUSTUS	start_codon	4895794	4895796	.	-	0	transcript_id "Phchi.S3G056300.t2"; gene_id "Phchi.S3G056300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6868.t1 is derived from g4040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25695510	25696494	.	+	.	Phchi.S1G402700
Phchi.S1	AUGUSTUS	transcript	25695510	25696494	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	start_codon	25695510	25695512	.	+	0	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	CDS	25695510	25695580	1	+	0	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	exon	25695510	25695580	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	intron	25695581	25695668	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	CDS	25695669	25695897	1	+	1	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	exon	25695669	25695897	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	intron	25695898	25695973	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	CDS	25695974	25696051	0.65	+	0	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	exon	25695974	25696051	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	intron	25696052	25696212	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	CDS	25696213	25696272	0.87	+	0	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	exon	25696213	25696272	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	intron	25696273	25696488	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	CDS	25696489	25696494	0.9	+	0	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	exon	25696489	25696494	.	+	.	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
Phchi.S1	AUGUSTUS	stop_codon	25696495	25696497	.	+	0	transcript_id "Phchi.S1G402700.t1"; gene_id "Phchi.S1G402700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4154.t1 is derived from g1323.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8658503	8663586	.	-	.	Phchi.S1G131300
Phchi.S1	AUGUSTUS	transcript	8658503	8663586	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	stop_codon	8658500	8658502	.	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8658503	8659711	1	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8658503	8659711	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8659712	8659792	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8659793	8659867	0.99	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8659793	8659867	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8659868	8659944	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8659945	8660033	0.65	-	2	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8659945	8660033	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8660034	8660117	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8660118	8660357	0.63	-	2	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8660118	8660357	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8660358	8660525	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8660526	8660746	0.53	-	1	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8660526	8660746	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8660747	8660826	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8660827	8661173	0.98	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8660827	8661173	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8661174	8661259	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8661260	8661483	1	-	2	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8661260	8661483	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8661484	8661561	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8661562	8661878	1	-	1	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8661562	8661878	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8661879	8661982	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8661983	8662242	0.96	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8661983	8662242	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8662243	8662326	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8662327	8662527	1	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8662327	8662527	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8662528	8662618	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8662619	8662794	1	-	2	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8662619	8662794	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8662795	8662883	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8662884	8662938	1	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8662884	8662938	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	intron	8662939	8663037	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	CDS	8663038	8663586	0.83	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	exon	8663038	8663586	.	-	.	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
Phchi.S1	AUGUSTUS	start_codon	8663584	8663586	.	-	0	transcript_id "Phchi.S1G131300.t1"; gene_id "Phchi.S1G131300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4167.t1 is derived from g1336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8711660	8712493	.	-	.	Phchi.S1G132600
Phchi.S1	AUGUSTUS	transcript	8711660	8712493	.	-	.	transcript_id "Phchi.S1G132600.t1"; gene_id "Phchi.S1G132600"
Phchi.S1	AUGUSTUS	stop_codon	8711657	8711659	.	-	0	transcript_id "Phchi.S1G132600.t1"; gene_id "Phchi.S1G132600"
Phchi.S1	AUGUSTUS	CDS	8711660	8712493	0.6	-	0	transcript_id "Phchi.S1G132600.t1"; gene_id "Phchi.S1G132600"
Phchi.S1	AUGUSTUS	exon	8711660	8712493	.	-	.	transcript_id "Phchi.S1G132600.t1"; gene_id "Phchi.S1G132600"
Phchi.S1	AUGUSTUS	start_codon	8712491	8712493	.	-	0	transcript_id "Phchi.S1G132600.t1"; gene_id "Phchi.S1G132600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3996.t1 is derived from g1165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6902186	6904208	.	+	.	Phchi.S1G115500
Phchi.S1	AUGUSTUS	transcript	6902186	6904208	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	start_codon	6902186	6902188	.	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6902186	6902417	0.99	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6902186	6902417	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6902418	6902564	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6902565	6902686	1	+	2	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6902565	6902686	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6902687	6902765	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6902766	6902832	0.93	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6902766	6902832	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6902833	6902938	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6902939	6903180	0.93	+	2	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6902939	6903180	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6903181	6903265	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6903266	6903409	1	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6903266	6903409	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6903410	6903495	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6903496	6903678	1	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6903496	6903678	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6903679	6903762	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6903763	6903873	1	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6903763	6903873	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	intron	6903874	6903956	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	CDS	6903957	6904208	0.98	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	exon	6903957	6904208	.	+	.	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
Phchi.S1	AUGUSTUS	stop_codon	6904209	6904211	.	+	0	transcript_id "Phchi.S1G115500.t1"; gene_id "Phchi.S1G115500"
# This transcript jg9876.t2 is derived from g7052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9877.t1 is derived from g7053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44207681	44208688	.	-	.	Phchi.S1G703600
Phchi.S1	AUGUSTUS	transcript	44207681	44208688	.	-	.	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	stop_codon	44207678	44207680	.	-	0	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	CDS	44207681	44207708	1	-	1	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	exon	44207681	44207708	.	-	.	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	intron	44207709	44207832	.	-	.	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	CDS	44207833	44208031	0.85	-	2	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	exon	44207833	44208031	.	-	.	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	intron	44208032	44208669	.	-	.	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	CDS	44208670	44208688	0.1	-	0	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	exon	44208670	44208688	.	-	.	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
Phchi.S1	AUGUSTUS	start_codon	44208686	44208688	.	-	0	transcript_id "Phchi.S1G703600.t1"; gene_id "Phchi.S1G703600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15509.t1 is derived from g13978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19604381	19610103	.	+	.	Phchi.S3G282800
Phchi.S3	AUGUSTUS	transcript	19604381	19610103	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	start_codon	19604381	19604383	.	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19604381	19604500	0.94	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19604381	19604500	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19604501	19604599	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19604600	19604718	1	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19604600	19604718	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19604719	19604859	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19604860	19606020	0.74	+	1	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19604860	19606020	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19606021	19606396	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19606397	19606490	0.76	+	1	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19606397	19606490	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19606491	19606631	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19606632	19606745	0.53	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19606632	19606745	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19606746	19607064	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19607065	19607142	0.87	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19607065	19607142	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19607143	19607306	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19607307	19607561	0.23	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19607307	19607561	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19607562	19607689	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19607690	19609050	0.19	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19607690	19609050	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19609051	19609196	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19609197	19610103	0.98	+	1	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19609197	19610103	.	+	.	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	stop_codon	19610104	19610106	.	+	0	transcript_id "Phchi.S3G282800.t1"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	transcript	19604763	19610103	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	start_codon	19604763	19604765	.	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19604763	19604767	0.98	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19604763	19604767	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19604768	19604859	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19604860	19606020	0.75	+	1	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19604860	19606020	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19606021	19606396	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19606397	19606490	0.76	+	1	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19606397	19606490	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19606491	19606631	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19606632	19606745	0.63	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19606632	19606745	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19606746	19607064	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19607065	19607142	0.87	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19607065	19607142	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19607143	19607306	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19607307	19607561	0.3	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19607307	19607561	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19607562	19607689	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19607690	19609050	0.25	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19607690	19609050	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	intron	19609051	19609196	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	CDS	19609197	19610103	0.99	+	1	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	exon	19609197	19610103	.	+	.	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
Phchi.S3	AUGUSTUS	stop_codon	19610104	19610106	.	+	0	transcript_id "Phchi.S3G282800.t2"; gene_id "Phchi.S3G282800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5373.t1 is derived from g2543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16549845	16551233	.	-	.	Phchi.S1G253200
Phchi.S1	AUGUSTUS	transcript	16549845	16551233	.	-	.	transcript_id "Phchi.S1G253200.t1"; gene_id "Phchi.S1G253200"
Phchi.S1	AUGUSTUS	stop_codon	16549842	16549844	.	-	0	transcript_id "Phchi.S1G253200.t1"; gene_id "Phchi.S1G253200"
Phchi.S1	AUGUSTUS	CDS	16549845	16551233	0.33	-	0	transcript_id "Phchi.S1G253200.t1"; gene_id "Phchi.S1G253200"
Phchi.S1	AUGUSTUS	exon	16549845	16551233	.	-	.	transcript_id "Phchi.S1G253200.t1"; gene_id "Phchi.S1G253200"
Phchi.S1	AUGUSTUS	start_codon	16551231	16551233	.	-	0	transcript_id "Phchi.S1G253200.t1"; gene_id "Phchi.S1G253200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1434.t1 is derived from g8353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	822669	824835	.	+	.	Phchi.S5G004300
Phchi.S5	AUGUSTUS	transcript	822669	824835	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	start_codon	822669	822671	.	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	822669	822791	0.71	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	822669	822791	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	822792	822877	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	822878	823063	1	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	822878	823063	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	823064	823208	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	823209	823338	1	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	823209	823338	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	823339	823438	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	823439	823528	1	+	2	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	823439	823528	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	823529	823619	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	823620	823789	1	+	2	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	823620	823789	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	823790	824027	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	824028	824123	1	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	824028	824123	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	824124	824208	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	824209	824302	1	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	824209	824302	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	824303	824522	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	824523	824639	1	+	2	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	824523	824639	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	intron	824640	824734	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	CDS	824735	824835	1	+	2	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	exon	824735	824835	.	+	.	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
Phchi.S5	AUGUSTUS	stop_codon	824836	824838	.	+	0	transcript_id "Phchi.S5G004300.t1"; gene_id "Phchi.S5G004300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg229.t1 is derived from g10011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1557443	1559634	.	-	.	Phchi.S6G018800
Phchi.S6	AUGUSTUS	transcript	1557443	1559634	.	-	.	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	stop_codon	1557440	1557442	.	-	0	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	CDS	1557443	1558720	0.67	-	0	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	exon	1557443	1558720	.	-	.	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	intron	1558721	1558803	.	-	.	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	CDS	1558804	1559634	0.38	-	0	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	exon	1558804	1559634	.	-	.	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
Phchi.S6	AUGUSTUS	start_codon	1559632	1559634	.	-	0	transcript_id "Phchi.S6G018800.t1"; gene_id "Phchi.S6G018800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4157.t1 is derived from g1326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8675621	8677533	.	-	.	Phchi.S1G131600
Phchi.S1	AUGUSTUS	transcript	8675621	8677533	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	stop_codon	8675618	8675620	.	-	0	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	CDS	8675621	8675638	1	-	0	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	exon	8675621	8675638	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	intron	8675639	8675715	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	CDS	8675716	8675856	1	-	0	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	exon	8675716	8675856	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	intron	8675857	8675969	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	CDS	8675970	8676357	1	-	1	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	exon	8675970	8676357	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	intron	8676358	8676435	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	CDS	8676436	8676548	0.27	-	0	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	exon	8676436	8676548	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	intron	8676549	8676631	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	CDS	8676632	8676668	0.27	-	1	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	exon	8676632	8676668	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	intron	8676669	8676757	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	CDS	8676758	8677533	0.67	-	0	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	exon	8676758	8677533	.	-	.	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
Phchi.S1	AUGUSTUS	start_codon	8677531	8677533	.	-	0	transcript_id "Phchi.S1G131600.t1"; gene_id "Phchi.S1G131600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5530.t1 is derived from g2700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17429651	17430774	.	+	.	Phchi.S1G268900
Phchi.S1	AUGUSTUS	transcript	17429651	17430774	.	+	.	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	start_codon	17429651	17429653	.	+	0	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	CDS	17429651	17429942	0.7	+	0	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	exon	17429651	17429942	.	+	.	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	intron	17429943	17430125	.	+	.	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	CDS	17430126	17430456	0.99	+	2	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	exon	17430126	17430456	.	+	.	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	intron	17430457	17430599	.	+	.	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	CDS	17430600	17430774	1	+	1	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	exon	17430600	17430774	.	+	.	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
Phchi.S1	AUGUSTUS	stop_codon	17430775	17430777	.	+	0	transcript_id "Phchi.S1G268900.t1"; gene_id "Phchi.S1G268900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1288.t1 is derived from g11071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8856212	8857731	.	-	.	Phchi.S6G124700
Phchi.S6	AUGUSTUS	transcript	8856212	8857731	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	stop_codon	8856209	8856211	.	-	0	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	CDS	8856212	8856462	0.95	-	2	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	exon	8856212	8856462	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	intron	8856463	8856566	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	CDS	8856567	8856963	1	-	0	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	exon	8856567	8856963	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	intron	8856964	8857049	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	CDS	8857050	8857420	1	-	2	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	exon	8857050	8857420	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	intron	8857421	8857508	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	CDS	8857509	8857731	0.86	-	0	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	exon	8857509	8857731	.	-	.	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
Phchi.S6	AUGUSTUS	start_codon	8857729	8857731	.	-	0	transcript_id "Phchi.S6G124700.t1"; gene_id "Phchi.S6G124700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6774.t1 is derived from g3946.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25015667	25016376	.	-	.	Phchi.S1G393300
Phchi.S1	AUGUSTUS	transcript	25015667	25016376	.	-	.	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	stop_codon	25015664	25015666	.	-	0	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	CDS	25015667	25015746	0.93	-	2	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	exon	25015667	25015746	.	-	.	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	intron	25015747	25016105	.	-	.	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	CDS	25016106	25016232	0.72	-	0	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	exon	25016106	25016232	.	-	.	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	intron	25016233	25016316	.	-	.	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	CDS	25016317	25016376	0.66	-	0	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	exon	25016317	25016376	.	-	.	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
Phchi.S1	AUGUSTUS	start_codon	25016374	25016376	.	-	0	transcript_id "Phchi.S1G393300.t1"; gene_id "Phchi.S1G393300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9712.t1 is derived from g6888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43375386	43377322	.	+	.	Phchi.S1G687100
Phchi.S1	AUGUSTUS	transcript	43375386	43377322	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	start_codon	43375386	43375388	.	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43375386	43375391	0.76	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43375386	43375391	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43375392	43375491	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43375492	43375536	0.8	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43375492	43375536	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43375537	43375944	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43375945	43376009	0.76	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43375945	43376009	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43376010	43376152	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43376153	43376243	1	+	1	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43376153	43376243	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43376244	43376321	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43376322	43376413	1	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43376322	43376413	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43376414	43376510	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43376511	43376604	1	+	1	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43376511	43376604	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43376605	43376690	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43376691	43376770	1	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43376691	43376770	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43376771	43376858	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43376859	43376945	1	+	1	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43376859	43376945	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43376946	43377039	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43377040	43377139	1	+	1	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43377040	43377139	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	intron	43377140	43377232	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	CDS	43377233	43377322	1	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	exon	43377233	43377322	.	+	.	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
Phchi.S1	AUGUSTUS	stop_codon	43377323	43377325	.	+	0	transcript_id "Phchi.S1G687100.t1"; gene_id "Phchi.S1G687100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4121.t1 is derived from g1290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8359183	8360982	.	-	.	Phchi.S1G128000
Phchi.S1	AUGUSTUS	transcript	8359183	8360982	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	stop_codon	8359180	8359182	.	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8359183	8359216	1	-	1	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8359183	8359216	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8359217	8359368	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8359369	8359406	1	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8359369	8359406	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8359407	8359541	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8359542	8359598	1	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8359542	8359598	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8359599	8359974	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8359975	8360034	0.99	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8359975	8360034	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8360035	8360154	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8360155	8360198	1	-	2	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8360155	8360198	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8360199	8360286	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8360287	8360374	1	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8360287	8360374	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8360375	8360617	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8360618	8360665	1	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8360618	8360665	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	intron	8360666	8360901	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	CDS	8360902	8360982	0.99	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	exon	8360902	8360982	.	-	.	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
Phchi.S1	AUGUSTUS	start_codon	8360980	8360982	.	-	0	transcript_id "Phchi.S1G128000.t1"; gene_id "Phchi.S1G128000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13215.t1 is derived from g11680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4725961	4728806	.	-	.	Phchi.S3G053400
Phchi.S3	AUGUSTUS	transcript	4725961	4728806	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	stop_codon	4725958	4725960	.	-	0	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	CDS	4725961	4726472	1	-	2	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	exon	4725961	4726472	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	intron	4726473	4726612	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	CDS	4726613	4727602	0.79	-	2	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	exon	4726613	4727602	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	intron	4727603	4727792	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	CDS	4727793	4728574	0.45	-	1	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	exon	4727793	4728574	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	intron	4728575	4728675	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	CDS	4728676	4728806	0.54	-	0	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	exon	4728676	4728806	.	-	.	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
Phchi.S3	AUGUSTUS	start_codon	4728804	4728806	.	-	0	transcript_id "Phchi.S3G053400.t1"; gene_id "Phchi.S3G053400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10994.t1 is derived from g15044.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3567736	3568191	.	-	.	Phchi.S4G057600
Phchi.S4	AUGUSTUS	transcript	3567736	3568191	.	-	.	transcript_id "Phchi.S4G057600.t1"; gene_id "Phchi.S4G057600"
Phchi.S4	AUGUSTUS	stop_codon	3567733	3567735	.	-	0	transcript_id "Phchi.S4G057600.t1"; gene_id "Phchi.S4G057600"
Phchi.S4	AUGUSTUS	CDS	3567736	3568191	0.77	-	0	transcript_id "Phchi.S4G057600.t1"; gene_id "Phchi.S4G057600"
Phchi.S4	AUGUSTUS	exon	3567736	3568191	.	-	.	transcript_id "Phchi.S4G057600.t1"; gene_id "Phchi.S4G057600"
Phchi.S4	AUGUSTUS	start_codon	3568189	3568191	.	-	0	transcript_id "Phchi.S4G057600.t1"; gene_id "Phchi.S4G057600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8312.t1 is derived from g5487.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35243519	35248230	.	+	.	Phchi.S1G547100
Phchi.S1	AUGUSTUS	transcript	35243519	35248230	.	+	.	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	start_codon	35243519	35243521	.	+	0	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	CDS	35243519	35243711	0.37	+	0	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	exon	35243519	35243711	.	+	.	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	intron	35243712	35248138	.	+	.	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	CDS	35248139	35248230	0.98	+	2	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	exon	35248139	35248230	.	+	.	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
Phchi.S1	AUGUSTUS	stop_codon	35248231	35248233	.	+	0	transcript_id "Phchi.S1G547100.t1"; gene_id "Phchi.S1G547100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2847.t1 is derived from g16.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10951	13067	.	-	.	Phchi.S1G000600
Phchi.S1	AUGUSTUS	transcript	10951	13067	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	stop_codon	10948	10950	.	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	10951	11027	0.99	-	2	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	10951	11027	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	11028	11121	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	11122	11200	1	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	11122	11200	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	11201	11396	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	11397	11447	1	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	11397	11447	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	11448	11564	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	11565	11624	1	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	11565	11624	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	11625	11772	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	11773	11848	1	-	1	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	11773	11848	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	11849	12026	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	12027	12142	1	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	12027	12142	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	12143	12274	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	12275	12291	0.86	-	2	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	12275	12291	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	12292	12377	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	12378	12476	0.86	-	2	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	12378	12476	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	12477	12563	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	12564	12627	1	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	12564	12627	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	12628	12756	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	12757	12813	1	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	12757	12813	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	intron	12814	12977	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	CDS	12978	13067	0.96	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	exon	12978	13067	.	-	.	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
Phchi.S1	AUGUSTUS	start_codon	13065	13067	.	-	0	transcript_id "Phchi.S1G000600.t1"; gene_id "Phchi.S1G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8729.t1 is derived from g5904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37699928	37700893	.	+	.	Phchi.S1G588800
Phchi.S1	AUGUSTUS	transcript	37699928	37700893	.	+	.	transcript_id "Phchi.S1G588800.t1"; gene_id "Phchi.S1G588800"
Phchi.S1	AUGUSTUS	start_codon	37699928	37699930	.	+	0	transcript_id "Phchi.S1G588800.t1"; gene_id "Phchi.S1G588800"
Phchi.S1	AUGUSTUS	CDS	37699928	37700893	0.86	+	0	transcript_id "Phchi.S1G588800.t1"; gene_id "Phchi.S1G588800"
Phchi.S1	AUGUSTUS	exon	37699928	37700893	.	+	.	transcript_id "Phchi.S1G588800.t1"; gene_id "Phchi.S1G588800"
Phchi.S1	AUGUSTUS	stop_codon	37700894	37700896	.	+	0	transcript_id "Phchi.S1G588800.t1"; gene_id "Phchi.S1G588800"
# This transcript jg2179.t2 is derived from g9099.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2180.t1 is derived from g9100.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5250601	5251074	.	-	.	Phchi.S5G078900
Phchi.S5	AUGUSTUS	transcript	5250601	5251074	.	-	.	transcript_id "Phchi.S5G078900.t1"; gene_id "Phchi.S5G078900"
Phchi.S5	AUGUSTUS	stop_codon	5250598	5250600	.	-	0	transcript_id "Phchi.S5G078900.t1"; gene_id "Phchi.S5G078900"
Phchi.S5	AUGUSTUS	CDS	5250601	5251074	0.95	-	0	transcript_id "Phchi.S5G078900.t1"; gene_id "Phchi.S5G078900"
Phchi.S5	AUGUSTUS	exon	5250601	5251074	.	-	.	transcript_id "Phchi.S5G078900.t1"; gene_id "Phchi.S5G078900"
Phchi.S5	AUGUSTUS	start_codon	5251072	5251074	.	-	0	transcript_id "Phchi.S5G078900.t1"; gene_id "Phchi.S5G078900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14939.t1 is derived from g13407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15635925	15637864	.	-	.	Phchi.S3G225800
Phchi.S3	AUGUSTUS	transcript	15635925	15637864	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	stop_codon	15635922	15635924	.	-	0	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15635925	15635971	0.98	-	2	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15635925	15635971	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	intron	15635972	15636099	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15636100	15636241	1	-	0	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15636100	15636241	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	intron	15636242	15636387	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15636388	15636548	1	-	2	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15636388	15636548	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	intron	15636549	15636726	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15636727	15636814	1	-	0	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15636727	15636814	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	intron	15636815	15636909	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15636910	15637057	1	-	1	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15636910	15637057	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	intron	15637058	15637242	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15637243	15637379	1	-	0	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15637243	15637379	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	intron	15637380	15637474	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	CDS	15637475	15637864	0.23	-	0	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	exon	15637475	15637864	.	-	.	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
Phchi.S3	AUGUSTUS	start_codon	15637862	15637864	.	-	0	transcript_id "Phchi.S3G225800.t1"; gene_id "Phchi.S3G225800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5519.t1 is derived from g2689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17201244	17203640	.	+	.	Phchi.S1G267800
Phchi.S1	AUGUSTUS	transcript	17201244	17203640	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	start_codon	17201244	17201246	.	+	0	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	CDS	17201244	17201260	0.8	+	0	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	exon	17201244	17201260	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	intron	17201261	17201485	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	CDS	17201486	17201526	0.52	+	1	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	exon	17201486	17201526	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	intron	17201527	17201831	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	CDS	17201832	17201994	0.72	+	2	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	exon	17201832	17201994	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	intron	17201995	17202290	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	CDS	17202291	17202310	0.72	+	1	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	exon	17202291	17202310	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	intron	17202311	17202411	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	CDS	17202412	17203640	0.48	+	2	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	exon	17202412	17203640	.	+	.	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
Phchi.S1	AUGUSTUS	stop_codon	17203641	17203643	.	+	0	transcript_id "Phchi.S1G267800.t1"; gene_id "Phchi.S1G267800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14793.t1 is derived from g13261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14742702	14744525	.	-	.	Phchi.S3G211200
Phchi.S3	AUGUSTUS	transcript	14742702	14744525	.	-	.	transcript_id "Phchi.S3G211200.t1"; gene_id "Phchi.S3G211200"
Phchi.S3	AUGUSTUS	stop_codon	14742699	14742701	.	-	0	transcript_id "Phchi.S3G211200.t1"; gene_id "Phchi.S3G211200"
Phchi.S3	AUGUSTUS	CDS	14742702	14744525	0.68	-	0	transcript_id "Phchi.S3G211200.t1"; gene_id "Phchi.S3G211200"
Phchi.S3	AUGUSTUS	exon	14742702	14744525	.	-	.	transcript_id "Phchi.S3G211200.t1"; gene_id "Phchi.S3G211200"
Phchi.S3	AUGUSTUS	start_codon	14744523	14744525	.	-	0	transcript_id "Phchi.S3G211200.t1"; gene_id "Phchi.S3G211200"
# This transcript jg8616.t2 is derived from g5791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg8616.t3 is derived from g5791.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8617.t1 is derived from g5792.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36989533	36990027	.	+	.	Phchi.S1G577600
Phchi.S1	AUGUSTUS	transcript	36989533	36990027	.	+	.	transcript_id "Phchi.S1G577600.t1"; gene_id "Phchi.S1G577600"
Phchi.S1	AUGUSTUS	start_codon	36989533	36989535	.	+	0	transcript_id "Phchi.S1G577600.t1"; gene_id "Phchi.S1G577600"
Phchi.S1	AUGUSTUS	CDS	36989533	36990027	0.97	+	0	transcript_id "Phchi.S1G577600.t1"; gene_id "Phchi.S1G577600"
Phchi.S1	AUGUSTUS	exon	36989533	36990027	.	+	.	transcript_id "Phchi.S1G577600.t1"; gene_id "Phchi.S1G577600"
Phchi.S1	AUGUSTUS	stop_codon	36990028	36990030	.	+	0	transcript_id "Phchi.S1G577600.t1"; gene_id "Phchi.S1G577600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg221.t1 is derived from g10003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1463352	1464104	.	+	.	Phchi.S6G018000
Phchi.S6	AUGUSTUS	transcript	1463352	1464104	.	+	.	transcript_id "Phchi.S6G018000.t1"; gene_id "Phchi.S6G018000"
Phchi.S6	AUGUSTUS	start_codon	1463352	1463354	.	+	0	transcript_id "Phchi.S6G018000.t1"; gene_id "Phchi.S6G018000"
Phchi.S6	AUGUSTUS	CDS	1463352	1464104	0.55	+	0	transcript_id "Phchi.S6G018000.t1"; gene_id "Phchi.S6G018000"
Phchi.S6	AUGUSTUS	exon	1463352	1464104	.	+	.	transcript_id "Phchi.S6G018000.t1"; gene_id "Phchi.S6G018000"
Phchi.S6	AUGUSTUS	stop_codon	1464105	1464107	.	+	0	transcript_id "Phchi.S6G018000.t1"; gene_id "Phchi.S6G018000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9359.t1 is derived from g6535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41155472	41156489	.	+	.	Phchi.S1G651800
Phchi.S1	AUGUSTUS	transcript	41155472	41156489	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	start_codon	41155472	41155474	.	+	0	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	CDS	41155472	41155523	0.99	+	0	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	exon	41155472	41155523	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	intron	41155524	41155599	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	CDS	41155600	41155736	0.99	+	2	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	exon	41155600	41155736	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	intron	41155737	41155843	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	CDS	41155844	41155943	1	+	0	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	exon	41155844	41155943	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	intron	41155944	41156107	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	CDS	41156108	41156174	1	+	2	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	exon	41156108	41156174	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	intron	41156175	41156271	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	CDS	41156272	41156350	1	+	1	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	exon	41156272	41156350	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	intron	41156351	41156444	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	CDS	41156445	41156489	1	+	0	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	exon	41156445	41156489	.	+	.	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
Phchi.S1	AUGUSTUS	stop_codon	41156490	41156492	.	+	0	transcript_id "Phchi.S1G651800.t1"; gene_id "Phchi.S1G651800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5049.t1 is derived from g2219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14335262	14336770	.	-	.	Phchi.S1G220800
Phchi.S1	AUGUSTUS	transcript	14335262	14336770	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	stop_codon	14335259	14335261	.	-	0	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	CDS	14335262	14335361	0.72	-	1	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	exon	14335262	14335361	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	intron	14335362	14335646	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	CDS	14335647	14335727	0.55	-	1	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	exon	14335647	14335727	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	intron	14335728	14335816	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	CDS	14335817	14336032	0.46	-	1	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	exon	14335817	14336032	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	intron	14336033	14336126	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	CDS	14336127	14336770	0.16	-	0	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	exon	14336127	14336770	.	-	.	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
Phchi.S1	AUGUSTUS	start_codon	14336768	14336770	.	-	0	transcript_id "Phchi.S1G220800.t1"; gene_id "Phchi.S1G220800"
# This transcript jg71.t2 is derived from g9853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg72.t1 is derived from g9854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	358940	360621	.	-	.	Phchi.S6G003100
Phchi.S6	AUGUSTUS	transcript	358940	360621	.	-	.	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	stop_codon	358937	358939	.	-	0	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	CDS	358940	359170	0.35	-	0	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	exon	358940	359170	.	-	.	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	intron	359171	359301	.	-	.	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	CDS	359302	359594	0.67	-	2	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	exon	359302	359594	.	-	.	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	intron	359595	359825	.	-	.	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	CDS	359826	360621	0.59	-	0	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	exon	359826	360621	.	-	.	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
Phchi.S6	AUGUSTUS	start_codon	360619	360621	.	-	0	transcript_id "Phchi.S6G003100.t1"; gene_id "Phchi.S6G003100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2446.t1 is derived from g9366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6662305	6664344	.	-	.	Phchi.S5G105500
Phchi.S5	AUGUSTUS	transcript	6662305	6664344	.	-	.	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	stop_codon	6662302	6662304	.	-	0	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	CDS	6662305	6662490	1	-	0	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	exon	6662305	6662490	.	-	.	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	intron	6662491	6662655	.	-	.	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	CDS	6662656	6664344	0.96	-	0	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	exon	6662656	6664344	.	-	.	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
Phchi.S5	AUGUSTUS	start_codon	6664342	6664344	.	-	0	transcript_id "Phchi.S5G105500.t1"; gene_id "Phchi.S5G105500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3449.t1 is derived from g618.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3800663	3801265	.	+	.	Phchi.S1G060800
Phchi.S1	AUGUSTUS	transcript	3800663	3801265	.	+	.	transcript_id "Phchi.S1G060800.t1"; gene_id "Phchi.S1G060800"
Phchi.S1	AUGUSTUS	start_codon	3800663	3800665	.	+	0	transcript_id "Phchi.S1G060800.t1"; gene_id "Phchi.S1G060800"
Phchi.S1	AUGUSTUS	CDS	3800663	3801265	0.66	+	0	transcript_id "Phchi.S1G060800.t1"; gene_id "Phchi.S1G060800"
Phchi.S1	AUGUSTUS	exon	3800663	3801265	.	+	.	transcript_id "Phchi.S1G060800.t1"; gene_id "Phchi.S1G060800"
Phchi.S1	AUGUSTUS	stop_codon	3801266	3801268	.	+	0	transcript_id "Phchi.S1G060800.t1"; gene_id "Phchi.S1G060800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8421.t1 is derived from g5596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35875529	35878293	.	-	.	Phchi.S1G558000
Phchi.S1	AUGUSTUS	transcript	35875529	35878293	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	stop_codon	35875526	35875528	.	-	0	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	CDS	35875529	35877018	0.9	-	2	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	exon	35875529	35877018	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	intron	35877019	35877148	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	CDS	35877149	35877468	1	-	1	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	exon	35877149	35877468	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	intron	35877469	35877599	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	CDS	35877600	35877652	0.52	-	0	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	exon	35877600	35877652	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	intron	35877653	35877768	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	CDS	35877769	35878293	0.47	-	0	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	exon	35877769	35878293	.	-	.	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
Phchi.S1	AUGUSTUS	start_codon	35878291	35878293	.	-	0	transcript_id "Phchi.S1G558000.t1"; gene_id "Phchi.S1G558000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8681.t1 is derived from g5856.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37426818	37428464	.	-	.	Phchi.S1G584000
Phchi.S1	AUGUSTUS	transcript	37426818	37428216	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	stop_codon	37426815	37426817	.	-	0	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37426818	37426988	1	-	0	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37426818	37426988	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37426989	37427067	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427068	37427223	1	-	0	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427068	37427223	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37427224	37427322	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427323	37427502	1	-	0	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427323	37427502	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37427503	37427588	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427589	37427847	1	-	1	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427589	37427847	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37427848	37427944	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427945	37428020	0.97	-	2	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427945	37428020	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37428021	37428161	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37428162	37428216	0.53	-	0	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37428162	37428216	.	-	.	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	start_codon	37428214	37428216	.	-	0	transcript_id "Phchi.S1G584000.t1"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	transcript	37426818	37428464	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	stop_codon	37426815	37426817	.	-	0	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37426818	37426988	0.99	-	0	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37426818	37426988	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37426989	37427067	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427068	37427223	1	-	0	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427068	37427223	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37427224	37427322	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427323	37427502	1	-	0	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427323	37427502	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37427503	37427588	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427589	37427847	1	-	1	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427589	37427847	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37427848	37427944	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37427945	37428013	0.98	-	1	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37427945	37428013	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37428014	37428161	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37428162	37428218	0.67	-	1	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37428162	37428218	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	intron	37428219	37428393	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	CDS	37428394	37428464	0.42	-	0	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	exon	37428394	37428464	.	-	.	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
Phchi.S1	AUGUSTUS	start_codon	37428462	37428464	.	-	0	transcript_id "Phchi.S1G584000.t2"; gene_id "Phchi.S1G584000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10496.t1 is derived from g14545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	694995	695591	.	-	.	Phchi.S4G007800
Phchi.S4	AUGUSTUS	transcript	694995	695591	.	-	.	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	stop_codon	694992	694994	.	-	0	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	CDS	694995	695184	0.98	-	1	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	exon	694995	695184	.	-	.	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	intron	695185	695351	.	-	.	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	CDS	695352	695407	0.85	-	0	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	exon	695352	695407	.	-	.	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	intron	695408	695543	.	-	.	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	CDS	695544	695591	0.49	-	0	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	exon	695544	695591	.	-	.	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
Phchi.S4	AUGUSTUS	start_codon	695589	695591	.	-	0	transcript_id "Phchi.S4G007800.t1"; gene_id "Phchi.S4G007800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10204.t1 is derived from g7380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46368875	46375003	.	+	.	Phchi.S1G736300
Phchi.S1	AUGUSTUS	transcript	46368875	46375003	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	start_codon	46368875	46368877	.	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46368875	46368906	0.75	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46368875	46368906	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46368907	46369308	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46369309	46369412	1	+	1	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46369309	46369412	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46369413	46369659	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46369660	46369712	1	+	2	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46369660	46369712	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46369713	46369893	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46369894	46369949	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46369894	46369949	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46369950	46370106	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46370107	46370207	1	+	1	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46370107	46370207	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46370208	46370470	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46370471	46371046	0.6	+	2	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46370471	46371046	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46371047	46371266	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46371267	46372258	0.95	+	2	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46371267	46372258	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46372259	46372654	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46372655	46372846	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46372655	46372846	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46372847	46373101	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46373102	46373326	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46373102	46373326	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46373327	46373416	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46373417	46373620	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46373417	46373620	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46373621	46373732	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46373733	46373948	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46373733	46373948	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46373949	46374049	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46374050	46374244	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46374050	46374244	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46374245	46374358	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46374359	46374418	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46374359	46374418	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46374419	46374548	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46374549	46374671	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46374549	46374671	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	intron	46374672	46374901	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	CDS	46374902	46375003	1	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	exon	46374902	46375003	.	+	.	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
Phchi.S1	AUGUSTUS	stop_codon	46375004	46375006	.	+	0	transcript_id "Phchi.S1G736300.t1"; gene_id "Phchi.S1G736300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7221.t1 is derived from g4393.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27699952	27702041	.	-	.	Phchi.S1G438000
Phchi.S1	AUGUSTUS	transcript	27699952	27702041	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	stop_codon	27699949	27699951	.	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27699952	27700014	1	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27699952	27700014	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	intron	27700015	27700095	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27700096	27700146	1	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27700096	27700146	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	intron	27700147	27700219	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27700220	27700366	1	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27700220	27700366	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	intron	27700367	27700479	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27700480	27700797	1	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27700480	27700797	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	intron	27700798	27700881	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27700882	27701036	1	-	2	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27700882	27701036	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	intron	27701037	27701162	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27701163	27701470	1	-	1	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27701163	27701470	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	intron	27701471	27701589	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	CDS	27701590	27702041	1	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	exon	27701590	27702041	.	-	.	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
Phchi.S1	AUGUSTUS	start_codon	27702039	27702041	.	-	0	transcript_id "Phchi.S1G438000.t1"; gene_id "Phchi.S1G438000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9625.t1 is derived from g6801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42965178	42966422	.	+	.	Phchi.S1G678400
Phchi.S1	AUGUSTUS	transcript	42965178	42966422	.	+	.	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	start_codon	42965178	42965180	.	+	0	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	CDS	42965178	42965693	0.62	+	0	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	exon	42965178	42965693	.	+	.	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	intron	42965694	42965805	.	+	.	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	CDS	42965806	42965958	1	+	0	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	exon	42965806	42965958	.	+	.	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	intron	42965959	42966035	.	+	.	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	CDS	42966036	42966422	0.93	+	0	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	exon	42966036	42966422	.	+	.	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
Phchi.S1	AUGUSTUS	stop_codon	42966423	42966425	.	+	0	transcript_id "Phchi.S1G678400.t1"; gene_id "Phchi.S1G678400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12404.t1 is derived from g8081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18369141	18374514	.	-	.	Phchi.S2G048400
Phchi.S2	AUGUSTUS	transcript	18369141	18374514	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	stop_codon	18369138	18369140	.	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18369141	18369254	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18369141	18369254	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18369255	18369360	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18369361	18369447	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18369361	18369447	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18369448	18369532	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18369533	18369622	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18369533	18369622	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18369623	18369708	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18369709	18369794	1	-	2	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18369709	18369794	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18369795	18369882	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18369883	18369986	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18369883	18369986	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18369987	18370144	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18370145	18370231	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18370145	18370231	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18370232	18370311	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18370312	18370435	1	-	2	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18370312	18370435	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18370436	18370580	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18370581	18370699	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18370581	18370699	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18370700	18370870	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18370871	18371000	1	-	2	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18370871	18371000	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18371001	18371098	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18371099	18371187	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18371099	18371187	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18371188	18371365	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18371366	18371454	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18371366	18371454	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18371455	18371527	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18371528	18371621	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18371528	18371621	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18371622	18371702	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18371703	18371782	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18371703	18371782	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18371783	18371911	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18371912	18372001	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18371912	18372001	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18372002	18372277	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18372278	18372364	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18372278	18372364	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18372365	18372488	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18372489	18372533	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18372489	18372533	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18372534	18372757	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18372758	18372834	1	-	2	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18372758	18372834	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18372835	18372918	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18372919	18373024	1	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18372919	18373024	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18373025	18373111	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18373112	18373193	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18373112	18373193	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18373194	18373295	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18373296	18373367	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18373296	18373367	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18373368	18373465	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18373466	18373543	1	-	1	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18373466	18373543	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18373544	18373644	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18373645	18373705	1	-	2	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18373645	18373705	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18373706	18373953	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18373954	18374004	1	-	2	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18373954	18374004	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	intron	18374005	18374297	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	CDS	18374298	18374514	0.6	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	exon	18374298	18374514	.	-	.	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
Phchi.S2	AUGUSTUS	start_codon	18374512	18374514	.	-	0	transcript_id "Phchi.S2G048400.t1"; gene_id "Phchi.S2G048400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12119.t1 is derived from g7795.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3714814	3715438	.	+	.	Phchi.S2G019900
Phchi.S2	AUGUSTUS	transcript	3714814	3715438	.	+	.	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	start_codon	3714814	3714816	.	+	0	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	CDS	3714814	3715095	0.62	+	0	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	exon	3714814	3715095	.	+	.	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	intron	3715096	3715198	.	+	.	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	CDS	3715199	3715438	0.61	+	0	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	exon	3715199	3715438	.	+	.	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
Phchi.S2	AUGUSTUS	stop_codon	3715439	3715441	.	+	0	transcript_id "Phchi.S2G019900.t1"; gene_id "Phchi.S2G019900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15020.t1 is derived from g13488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16562913	16563767	.	+	.	Phchi.S3G233900
Phchi.S3	AUGUSTUS	transcript	16562913	16563767	.	+	.	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	start_codon	16562913	16562915	.	+	0	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	CDS	16562913	16563476	0.99	+	0	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	exon	16562913	16563476	.	+	.	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	intron	16563477	16563572	.	+	.	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	CDS	16563573	16563767	0.99	+	0	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	exon	16563573	16563767	.	+	.	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
Phchi.S3	AUGUSTUS	stop_codon	16563768	16563770	.	+	0	transcript_id "Phchi.S3G233900.t1"; gene_id "Phchi.S3G233900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6839.t1 is derived from g4011.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25498113	25499259	.	-	.	Phchi.S1G399800
Phchi.S1	AUGUSTUS	transcript	25498113	25499259	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	stop_codon	25498110	25498112	.	-	0	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	CDS	25498113	25498449	0.94	-	1	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	exon	25498113	25498449	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	intron	25498450	25498527	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	CDS	25498528	25498640	0.99	-	0	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	exon	25498528	25498640	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	intron	25498641	25498747	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	CDS	25498748	25498969	0.94	-	0	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	exon	25498748	25498969	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	intron	25498970	25499067	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	CDS	25499068	25499259	0.95	-	0	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	exon	25499068	25499259	.	-	.	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
Phchi.S1	AUGUSTUS	start_codon	25499257	25499259	.	-	0	transcript_id "Phchi.S1G399800.t1"; gene_id "Phchi.S1G399800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7927.t1 is derived from g5101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31934011	31937402	.	-	.	Phchi.S1G508600
Phchi.S1	AUGUSTUS	transcript	31934011	31937402	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	stop_codon	31934008	31934010	.	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31934011	31934219	1	-	2	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31934011	31934219	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31934220	31934312	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31934313	31934463	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31934313	31934463	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31934464	31934571	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31934572	31934697	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31934572	31934697	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31934698	31935180	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31935181	31935271	1	-	1	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31935181	31935271	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31935272	31935525	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31935526	31935720	1	-	1	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31935526	31935720	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31935721	31935919	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31935920	31936152	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31935920	31936152	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936153	31936238	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936239	31936319	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936239	31936319	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936320	31936480	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936481	31936577	1	-	1	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936481	31936577	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936578	31936692	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936693	31936784	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936693	31936784	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936785	31936874	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936875	31936990	1	-	2	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936875	31936990	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936991	31937118	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31937119	31937248	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31937119	31937248	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31937249	31937327	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31937328	31937402	1	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31937328	31937402	.	-	.	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	start_codon	31937400	31937402	.	-	0	transcript_id "Phchi.S1G508600.t1"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	transcript	31934011	31937402	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	stop_codon	31934008	31934010	.	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31934011	31934219	1	-	2	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31934011	31934219	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31934220	31934312	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31934313	31934463	1	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31934313	31934463	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31934464	31934571	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31934572	31934697	1	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31934572	31934697	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31934698	31935180	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31935181	31935271	1	-	1	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31935181	31935271	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31935272	31935525	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31935526	31935720	1	-	1	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31935526	31935720	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31935721	31935919	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31935920	31936152	1	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31935920	31936152	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936153	31936238	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936239	31936336	0.64	-	2	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936239	31936336	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936337	31936480	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936481	31936524	0.47	-	1	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936481	31936524	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936525	31936692	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936693	31936784	1	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936693	31936784	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936785	31936874	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31936875	31936990	1	-	2	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31936875	31936990	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31936991	31937118	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31937119	31937248	1	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31937119	31937248	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	intron	31937249	31937327	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	CDS	31937328	31937402	1	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	exon	31937328	31937402	.	-	.	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
Phchi.S1	AUGUSTUS	start_codon	31937400	31937402	.	-	0	transcript_id "Phchi.S1G508600.t2"; gene_id "Phchi.S1G508600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8375.t1 is derived from g5550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35578626	35580978	.	+	.	Phchi.S1G553400
Phchi.S1	AUGUSTUS	transcript	35578626	35580978	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	start_codon	35578626	35578628	.	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35578626	35578873	0.8	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35578626	35578873	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35578874	35578966	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35578967	35579007	0.27	+	1	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35578967	35579007	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35579008	35579093	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35579094	35579102	0.42	+	2	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35579094	35579102	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35579103	35579187	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35579188	35579573	0.42	+	2	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35579188	35579573	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35579574	35579684	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35579685	35579984	0.89	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35579685	35579984	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35579985	35580087	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35580088	35580174	1	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35580088	35580174	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35580175	35580275	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35580276	35580399	1	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35580276	35580399	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35580400	35580500	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35580501	35580664	1	+	2	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35580501	35580664	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	intron	35580665	35580759	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	CDS	35580760	35580978	0.99	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	exon	35580760	35580978	.	+	.	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
Phchi.S1	AUGUSTUS	stop_codon	35580979	35580981	.	+	0	transcript_id "Phchi.S1G553400.t1"; gene_id "Phchi.S1G553400"
# This transcript jg7111.t2 is derived from g4283.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7112.t1 is derived from g4284.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27036910	27038973	.	+	.	Phchi.S1G427100
Phchi.S1	AUGUSTUS	transcript	27036910	27038973	.	+	.	transcript_id "Phchi.S1G427100.t1"; gene_id "Phchi.S1G427100"
Phchi.S1	AUGUSTUS	start_codon	27036910	27036912	.	+	0	transcript_id "Phchi.S1G427100.t1"; gene_id "Phchi.S1G427100"
Phchi.S1	AUGUSTUS	CDS	27036910	27038973	0.98	+	0	transcript_id "Phchi.S1G427100.t1"; gene_id "Phchi.S1G427100"
Phchi.S1	AUGUSTUS	exon	27036910	27038973	.	+	.	transcript_id "Phchi.S1G427100.t1"; gene_id "Phchi.S1G427100"
Phchi.S1	AUGUSTUS	stop_codon	27038974	27038976	.	+	0	transcript_id "Phchi.S1G427100.t1"; gene_id "Phchi.S1G427100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4796.t1 is derived from g1966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12834610	12835250	.	-	.	Phchi.S1G195500
Phchi.S1	AUGUSTUS	transcript	12834610	12835250	.	-	.	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	stop_codon	12834607	12834609	.	-	0	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	CDS	12834610	12834696	1	-	0	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	exon	12834610	12834696	.	-	.	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	intron	12834697	12834928	.	-	.	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	CDS	12834929	12835105	0.99	-	0	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	exon	12834929	12835105	.	-	.	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	intron	12835106	12835184	.	-	.	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	CDS	12835185	12835250	0.47	-	0	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	exon	12835185	12835250	.	-	.	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
Phchi.S1	AUGUSTUS	start_codon	12835248	12835250	.	-	0	transcript_id "Phchi.S1G195500.t1"; gene_id "Phchi.S1G195500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14337.t1 is derived from g12804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12296165	12296776	.	+	.	Phchi.S3G165600
Phchi.S3	AUGUSTUS	transcript	12296165	12296776	.	+	.	transcript_id "Phchi.S3G165600.t1"; gene_id "Phchi.S3G165600"
Phchi.S3	AUGUSTUS	start_codon	12296165	12296167	.	+	0	transcript_id "Phchi.S3G165600.t1"; gene_id "Phchi.S3G165600"
Phchi.S3	AUGUSTUS	CDS	12296165	12296776	0.95	+	0	transcript_id "Phchi.S3G165600.t1"; gene_id "Phchi.S3G165600"
Phchi.S3	AUGUSTUS	exon	12296165	12296776	.	+	.	transcript_id "Phchi.S3G165600.t1"; gene_id "Phchi.S3G165600"
Phchi.S3	AUGUSTUS	stop_codon	12296777	12296779	.	+	0	transcript_id "Phchi.S3G165600.t1"; gene_id "Phchi.S3G165600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11834.t1 is derived from g15886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8482592	8484185	.	-	.	Phchi.S4G141600
Phchi.S4	AUGUSTUS	transcript	8482592	8484185	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	stop_codon	8482589	8482591	.	-	0	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	CDS	8482592	8482684	1	-	0	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	exon	8482592	8482684	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	intron	8482685	8482786	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	CDS	8482787	8482851	1	-	2	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	exon	8482787	8482851	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	intron	8482852	8482937	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	CDS	8482938	8483000	1	-	2	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	exon	8482938	8483000	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	intron	8483001	8483214	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	CDS	8483215	8483263	1	-	0	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	exon	8483215	8483263	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	intron	8483264	8483670	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	CDS	8483671	8483803	1	-	1	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	exon	8483671	8483803	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	intron	8483804	8484105	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	CDS	8484106	8484185	0.54	-	0	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	exon	8484106	8484185	.	-	.	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
Phchi.S4	AUGUSTUS	start_codon	8484183	8484185	.	-	0	transcript_id "Phchi.S4G141600.t1"; gene_id "Phchi.S4G141600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3206.t1 is derived from g375.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2235926	2237556	.	+	.	Phchi.S1G036500
Phchi.S1	AUGUSTUS	transcript	2235926	2237556	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	start_codon	2235926	2235928	.	+	0	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	CDS	2235926	2236258	1	+	0	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	exon	2235926	2236258	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	intron	2236259	2236409	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	CDS	2236410	2236544	1	+	0	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	exon	2236410	2236544	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	intron	2236545	2236638	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	CDS	2236639	2236888	0.89	+	0	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	exon	2236639	2236888	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	intron	2236889	2237056	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	CDS	2237057	2237260	0.98	+	2	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	exon	2237057	2237260	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	intron	2237261	2237359	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	CDS	2237360	2237556	1	+	2	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	exon	2237360	2237556	.	+	.	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
Phchi.S1	AUGUSTUS	stop_codon	2237557	2237559	.	+	0	transcript_id "Phchi.S1G036500.t1"; gene_id "Phchi.S1G036500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13186.t1 is derived from g11651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4588757	4590791	.	-	.	Phchi.S3G050500
Phchi.S3	AUGUSTUS	transcript	4588757	4590791	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	stop_codon	4588754	4588756	.	-	0	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4588757	4588823	1	-	1	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4588757	4588823	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4588824	4588900	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4588901	4588980	1	-	0	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4588901	4588980	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4588981	4589112	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4589113	4589158	1	-	1	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4589113	4589158	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4589159	4589253	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4589254	4589310	1	-	1	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4589254	4589310	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4589311	4589403	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4589404	4589462	1	-	0	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4589404	4589462	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4589463	4589541	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4589542	4589642	1	-	2	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4589542	4589642	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4589643	4589735	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4589736	4589857	1	-	1	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4589736	4589857	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4589858	4589944	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4589945	4590004	0.8	-	1	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4589945	4590004	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4590005	4590073	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4590074	4590125	0.99	-	2	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4590074	4590125	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4590126	4590207	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4590208	4590303	0.6	-	2	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4590208	4590303	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4590304	4590380	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4590381	4590576	1	-	0	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4590381	4590576	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	intron	4590577	4590701	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	CDS	4590702	4590791	0.99	-	0	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	exon	4590702	4590791	.	-	.	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
Phchi.S3	AUGUSTUS	start_codon	4590789	4590791	.	-	0	transcript_id "Phchi.S3G050500.t1"; gene_id "Phchi.S3G050500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11918.t1 is derived from g15970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9313437	9314139	.	+	.	Phchi.S4G150000
Phchi.S4	AUGUSTUS	transcript	9313437	9314139	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	start_codon	9313437	9313439	.	+	0	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	CDS	9313437	9313484	1	+	0	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	exon	9313437	9313484	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	intron	9313485	9313581	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	CDS	9313582	9313677	1	+	0	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	exon	9313582	9313677	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	intron	9313678	9313760	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	CDS	9313761	9313851	1	+	0	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	exon	9313761	9313851	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	intron	9313852	9313945	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	CDS	9313946	9314139	1	+	2	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	exon	9313946	9314139	.	+	.	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
Phchi.S4	AUGUSTUS	stop_codon	9314140	9314142	.	+	0	transcript_id "Phchi.S4G150000.t1"; gene_id "Phchi.S4G150000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10146.t1 is derived from g7322.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45980269	45981861	.	+	.	Phchi.S1G730500
Phchi.S1	AUGUSTUS	transcript	45980269	45981861	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	start_codon	45980269	45980271	.	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	CDS	45980269	45980556	0.81	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	exon	45980269	45980556	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	intron	45980557	45980651	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	CDS	45980652	45980843	0.78	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	exon	45980652	45980843	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	intron	45980844	45981081	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	CDS	45981082	45981390	0.97	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	exon	45981082	45981390	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	intron	45981391	45981471	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	CDS	45981472	45981678	0.76	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	exon	45981472	45981678	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	intron	45981679	45981777	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	CDS	45981778	45981861	0.77	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	exon	45981778	45981861	.	+	.	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
Phchi.S1	AUGUSTUS	stop_codon	45981862	45981864	.	+	0	transcript_id "Phchi.S1G730500.t1"; gene_id "Phchi.S1G730500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8497.t1 is derived from g5672.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36256234	36256941	.	-	.	Phchi.S1G565600
Phchi.S1	AUGUSTUS	transcript	36256234	36256941	.	-	.	transcript_id "Phchi.S1G565600.t1"; gene_id "Phchi.S1G565600"
Phchi.S1	AUGUSTUS	stop_codon	36256231	36256233	.	-	0	transcript_id "Phchi.S1G565600.t1"; gene_id "Phchi.S1G565600"
Phchi.S1	AUGUSTUS	CDS	36256234	36256941	0.94	-	0	transcript_id "Phchi.S1G565600.t1"; gene_id "Phchi.S1G565600"
Phchi.S1	AUGUSTUS	exon	36256234	36256941	.	-	.	transcript_id "Phchi.S1G565600.t1"; gene_id "Phchi.S1G565600"
Phchi.S1	AUGUSTUS	start_codon	36256939	36256941	.	-	0	transcript_id "Phchi.S1G565600.t1"; gene_id "Phchi.S1G565600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg759.t1 is derived from g10541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5364573	5365277	.	-	.	Phchi.S6G071800
Phchi.S6	AUGUSTUS	transcript	5364573	5365277	.	-	.	transcript_id "Phchi.S6G071800.t1"; gene_id "Phchi.S6G071800"
Phchi.S6	AUGUSTUS	stop_codon	5364570	5364572	.	-	0	transcript_id "Phchi.S6G071800.t1"; gene_id "Phchi.S6G071800"
Phchi.S6	AUGUSTUS	CDS	5364573	5365277	0.35	-	0	transcript_id "Phchi.S6G071800.t1"; gene_id "Phchi.S6G071800"
Phchi.S6	AUGUSTUS	exon	5364573	5365277	.	-	.	transcript_id "Phchi.S6G071800.t1"; gene_id "Phchi.S6G071800"
Phchi.S6	AUGUSTUS	start_codon	5365275	5365277	.	-	0	transcript_id "Phchi.S6G071800.t1"; gene_id "Phchi.S6G071800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14752.t1 is derived from g13220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14539161	14540669	.	+	.	Phchi.S3G207100
Phchi.S3	AUGUSTUS	transcript	14539161	14540669	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	start_codon	14539161	14539163	.	+	0	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14539161	14539385	0.36	+	0	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14539161	14539385	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	intron	14539386	14539480	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14539481	14539487	0.35	+	0	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14539481	14539487	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	intron	14539488	14539613	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14539614	14539698	1	+	2	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14539614	14539698	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	intron	14539699	14539799	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14539800	14539850	1	+	1	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14539800	14539850	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	intron	14539851	14539936	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14539937	14540057	1	+	1	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14539937	14540057	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	intron	14540058	14540170	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14540171	14540317	1	+	0	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14540171	14540317	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	intron	14540318	14540414	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	CDS	14540415	14540669	1	+	0	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	exon	14540415	14540669	.	+	.	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
Phchi.S3	AUGUSTUS	stop_codon	14540670	14540672	.	+	0	transcript_id "Phchi.S3G207100.t1"; gene_id "Phchi.S3G207100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7229.t1 is derived from g4401.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27727245	27730071	.	+	.	Phchi.S1G438800
Phchi.S1	AUGUSTUS	transcript	27727245	27730071	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	start_codon	27727245	27727247	.	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27727245	27727424	0.35	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27727245	27727424	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27727425	27727543	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27727544	27727655	1	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27727544	27727655	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27727656	27727754	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27727755	27727888	1	+	2	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27727755	27727888	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27727889	27728022	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27728023	27728218	1	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27728023	27728218	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27728219	27728347	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27728348	27728418	1	+	2	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27728348	27728418	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27728419	27728546	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27728547	27728632	1	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27728547	27728632	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27728633	27728786	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27728787	27729068	0.93	+	1	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27728787	27729068	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27729069	27729183	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27729184	27729245	0.99	+	1	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27729184	27729245	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27729246	27729394	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27729395	27729453	1	+	2	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27729395	27729453	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27729454	27729545	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27729546	27729755	1	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27729546	27729755	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	intron	27729756	27729846	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	CDS	27729847	27730071	0.97	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	exon	27729847	27730071	.	+	.	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
Phchi.S1	AUGUSTUS	stop_codon	27730072	27730074	.	+	0	transcript_id "Phchi.S1G438800.t1"; gene_id "Phchi.S1G438800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10458.t1 is derived from g14507.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	438406	439380	.	+	.	Phchi.S4G004000
Phchi.S4	AUGUSTUS	transcript	438406	439380	.	+	.	transcript_id "Phchi.S4G004000.t1"; gene_id "Phchi.S4G004000"
Phchi.S4	AUGUSTUS	start_codon	438406	438408	.	+	0	transcript_id "Phchi.S4G004000.t1"; gene_id "Phchi.S4G004000"
Phchi.S4	AUGUSTUS	CDS	438406	439380	0.66	+	0	transcript_id "Phchi.S4G004000.t1"; gene_id "Phchi.S4G004000"
Phchi.S4	AUGUSTUS	exon	438406	439380	.	+	.	transcript_id "Phchi.S4G004000.t1"; gene_id "Phchi.S4G004000"
Phchi.S4	AUGUSTUS	stop_codon	439381	439383	.	+	0	transcript_id "Phchi.S4G004000.t1"; gene_id "Phchi.S4G004000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1276.t1 is derived from g11059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8783426	8784339	.	-	.	Phchi.S6G123500
Phchi.S6	AUGUSTUS	transcript	8783426	8784339	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	stop_codon	8783423	8783425	.	-	0	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	CDS	8783426	8783587	0.96	-	0	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	exon	8783426	8783587	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	intron	8783588	8783694	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	CDS	8783695	8783855	0.44	-	2	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	exon	8783695	8783855	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	intron	8783856	8783994	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	CDS	8783995	8784022	0.33	-	0	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	exon	8783995	8784022	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	intron	8784023	8784114	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	CDS	8784115	8784146	1	-	2	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	exon	8784115	8784146	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	intron	8784147	8784230	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	CDS	8784231	8784339	0.88	-	0	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	exon	8784231	8784339	.	-	.	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
Phchi.S6	AUGUSTUS	start_codon	8784337	8784339	.	-	0	transcript_id "Phchi.S6G123500.t1"; gene_id "Phchi.S6G123500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13254.t1 is derived from g11719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4936161	4937592	.	-	.	Phchi.S3G057300
Phchi.S3	AUGUSTUS	transcript	4936161	4937592	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	stop_codon	4936158	4936160	.	-	0	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936161	4936204	0.99	-	2	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936161	4936204	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4936205	4936285	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936286	4936441	0.99	-	2	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936286	4936441	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4936442	4936524	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936525	4936653	1	-	2	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936525	4936653	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4936654	4936738	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936739	4937064	0.92	-	1	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936739	4937064	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4937065	4937164	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4937165	4937592	0.99	-	0	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4937165	4937592	.	-	.	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	start_codon	4937590	4937592	.	-	0	transcript_id "Phchi.S3G057300.t1"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	transcript	4936161	4937592	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	stop_codon	4936158	4936160	.	-	0	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936161	4936204	0.99	-	2	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936161	4936204	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4936205	4936285	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936286	4936441	0.99	-	2	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936286	4936441	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4936442	4936524	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936525	4936653	1	-	2	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936525	4936653	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4936654	4936738	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4936739	4937074	0.73	-	2	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4936739	4937074	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4937075	4937164	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4937165	4937219	0.82	-	0	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4937165	4937219	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	intron	4937220	4937346	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	CDS	4937347	4937592	0.79	-	0	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	exon	4937347	4937592	.	-	.	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
Phchi.S3	AUGUSTUS	start_codon	4937590	4937592	.	-	0	transcript_id "Phchi.S3G057300.t2"; gene_id "Phchi.S3G057300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9436.t1 is derived from g6612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41448849	41450894	.	+	.	Phchi.S1G659500
Phchi.S1	AUGUSTUS	transcript	41448849	41450894	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	start_codon	41448849	41448851	.	+	0	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	CDS	41448849	41449022	0.97	+	0	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	exon	41448849	41449022	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	intron	41449023	41449160	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	CDS	41449161	41449411	1	+	0	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	exon	41449161	41449411	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	intron	41449412	41449669	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	CDS	41449670	41449855	1	+	1	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	exon	41449670	41449855	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	intron	41449856	41449942	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	CDS	41449943	41450444	0.94	+	1	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	exon	41449943	41450444	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	intron	41450445	41450519	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	CDS	41450520	41450660	1	+	0	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	exon	41450520	41450660	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	intron	41450661	41450735	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	CDS	41450736	41450894	1	+	0	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	exon	41450736	41450894	.	+	.	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
Phchi.S1	AUGUSTUS	stop_codon	41450895	41450897	.	+	0	transcript_id "Phchi.S1G659500.t1"; gene_id "Phchi.S1G659500"
# This transcript jg6089.t2 is derived from g3260.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6089.t3 is derived from g3260.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6089.t4 is derived from g3260.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg6089.t5 is derived from g3260.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6090.t1 is derived from g3261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20913662	20917751	.	-	.	Phchi.S1G324900
Phchi.S1	AUGUSTUS	transcript	20913662	20917751	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	stop_codon	20913659	20913661	.	-	0	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	CDS	20913662	20913867	0.93	-	2	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	exon	20913662	20913867	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	intron	20913868	20914338	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	CDS	20914339	20915500	0.82	-	0	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	exon	20914339	20915500	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	intron	20915501	20915717	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	CDS	20915718	20915822	0.7	-	0	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	exon	20915718	20915822	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	intron	20915823	20916373	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	CDS	20916374	20917236	0.54	-	2	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	exon	20916374	20917236	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	intron	20917237	20917363	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	CDS	20917364	20917751	0.4	-	0	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	exon	20917364	20917751	.	-	.	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
Phchi.S1	AUGUSTUS	start_codon	20917749	20917751	.	-	0	transcript_id "Phchi.S1G324900.t1"; gene_id "Phchi.S1G324900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg745.t1 is derived from g10527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5307137	5307508	.	-	.	Phchi.S6G070400
Phchi.S6	AUGUSTUS	transcript	5307137	5307508	.	-	.	transcript_id "Phchi.S6G070400.t1"; gene_id "Phchi.S6G070400"
Phchi.S6	AUGUSTUS	stop_codon	5307134	5307136	.	-	0	transcript_id "Phchi.S6G070400.t1"; gene_id "Phchi.S6G070400"
Phchi.S6	AUGUSTUS	CDS	5307137	5307508	0.92	-	0	transcript_id "Phchi.S6G070400.t1"; gene_id "Phchi.S6G070400"
Phchi.S6	AUGUSTUS	exon	5307137	5307508	.	-	.	transcript_id "Phchi.S6G070400.t1"; gene_id "Phchi.S6G070400"
Phchi.S6	AUGUSTUS	start_codon	5307506	5307508	.	-	0	transcript_id "Phchi.S6G070400.t1"; gene_id "Phchi.S6G070400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15788.t1 is derived from g14258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21350200	21351944	.	-	.	Phchi.S3G310700
Phchi.S3	AUGUSTUS	transcript	21350200	21351944	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	stop_codon	21350197	21350199	.	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21350200	21350289	1	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21350200	21350289	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21350290	21350376	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21350377	21350473	1	-	1	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21350377	21350473	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21350474	21350555	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21350556	21350635	1	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21350556	21350635	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21350636	21350754	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21350755	21351075	0.99	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21350755	21351075	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21351076	21351157	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21351158	21351198	1	-	2	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21351158	21351198	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21351199	21351275	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21351276	21351336	1	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21351276	21351336	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21351337	21351423	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21351424	21351488	1	-	2	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21351424	21351488	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21351489	21351580	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21351581	21351659	1	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21351581	21351659	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	intron	21351660	21351779	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	CDS	21351780	21351944	0.91	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	exon	21351780	21351944	.	-	.	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
Phchi.S3	AUGUSTUS	start_codon	21351942	21351944	.	-	0	transcript_id "Phchi.S3G310700.t1"; gene_id "Phchi.S3G310700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2110.t1 is derived from g9030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4916409	4917446	.	-	.	Phchi.S5G071900
Phchi.S5	AUGUSTUS	transcript	4916409	4917446	.	-	.	transcript_id "Phchi.S5G071900.t1"; gene_id "Phchi.S5G071900"
Phchi.S5	AUGUSTUS	stop_codon	4916406	4916408	.	-	0	transcript_id "Phchi.S5G071900.t1"; gene_id "Phchi.S5G071900"
Phchi.S5	AUGUSTUS	CDS	4916409	4917446	0.62	-	0	transcript_id "Phchi.S5G071900.t1"; gene_id "Phchi.S5G071900"
Phchi.S5	AUGUSTUS	exon	4916409	4917446	.	-	.	transcript_id "Phchi.S5G071900.t1"; gene_id "Phchi.S5G071900"
Phchi.S5	AUGUSTUS	start_codon	4917444	4917446	.	-	0	transcript_id "Phchi.S5G071900.t1"; gene_id "Phchi.S5G071900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7157.t1 is derived from g4329.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27327575	27329985	.	+	.	Phchi.S1G431600
Phchi.S1	AUGUSTUS	transcript	27327575	27329985	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	start_codon	27327575	27327577	.	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27327575	27327761	0.97	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27327575	27327761	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27327762	27327970	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27327971	27328017	1	+	2	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27327971	27328017	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328018	27328100	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328101	27328217	1	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328101	27328217	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328218	27328356	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328357	27328413	1	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328357	27328413	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328414	27328498	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328499	27328703	1	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328499	27328703	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328704	27328838	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328839	27328901	1	+	2	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328839	27328901	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328902	27329004	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329005	27329009	1	+	2	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329005	27329009	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329010	27329133	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329134	27329199	1	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329134	27329199	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329200	27329309	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329310	27329394	1	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329310	27329394	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329395	27329591	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329592	27329672	1	+	2	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329592	27329672	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329673	27329812	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329813	27329985	1	+	2	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329813	27329985	.	+	.	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	stop_codon	27329986	27329988	.	+	0	transcript_id "Phchi.S1G431600.t1"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	transcript	27327575	27329985	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	start_codon	27327575	27327577	.	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27327575	27327761	0.94	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27327575	27327761	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27327762	27327970	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27327971	27328017	1	+	2	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27327971	27328017	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328018	27328097	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328098	27328217	1	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328098	27328217	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328218	27328356	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328357	27328413	1	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328357	27328413	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328414	27328498	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328499	27328703	0.99	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328499	27328703	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328704	27328838	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27328839	27328901	0.99	+	2	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27328839	27328901	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27328902	27329004	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329005	27329009	1	+	2	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329005	27329009	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329010	27329133	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329134	27329199	1	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329134	27329199	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329200	27329309	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329310	27329394	1	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329310	27329394	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329395	27329591	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329592	27329672	1	+	2	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329592	27329672	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	intron	27329673	27329812	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	CDS	27329813	27329985	1	+	2	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	exon	27329813	27329985	.	+	.	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
Phchi.S1	AUGUSTUS	stop_codon	27329986	27329988	.	+	0	transcript_id "Phchi.S1G431600.t2"; gene_id "Phchi.S1G431600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15055.t1 is derived from g13523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16767555	16768188	.	+	.	Phchi.S3G237400
Phchi.S3	AUGUSTUS	transcript	16767555	16768188	.	+	.	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	start_codon	16767555	16767557	.	+	0	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	CDS	16767555	16767641	1	+	0	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	exon	16767555	16767641	.	+	.	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	intron	16767642	16767879	.	+	.	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	CDS	16767880	16768188	1	+	0	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	exon	16767880	16768188	.	+	.	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
Phchi.S3	AUGUSTUS	stop_codon	16768189	16768191	.	+	0	transcript_id "Phchi.S3G237400.t1"; gene_id "Phchi.S3G237400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15831.t1 is derived from g14301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21647626	21651148	.	-	.	Phchi.S3G315000
Phchi.S3	AUGUSTUS	transcript	21647626	21651148	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	stop_codon	21647623	21647625	.	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21647626	21647666	1	-	2	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21647626	21647666	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21647667	21647762	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21647763	21647841	1	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21647763	21647841	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21647842	21648007	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21648008	21648235	1	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21648008	21648235	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21648236	21648318	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21648319	21648663	1	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21648319	21648663	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21648664	21648849	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21648850	21649221	0.97	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21648850	21649221	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21649222	21649388	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21649389	21649481	1	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21649389	21649481	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21649482	21649590	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21649591	21649842	1	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21649591	21649842	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	intron	21649843	21649957	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	CDS	21649958	21651148	0.91	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	exon	21649958	21651148	.	-	.	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
Phchi.S3	AUGUSTUS	start_codon	21651146	21651148	.	-	0	transcript_id "Phchi.S3G315000.t1"; gene_id "Phchi.S3G315000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6604.t1 is derived from g3776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23951820	23956519	.	-	.	Phchi.S1G376300
Phchi.S1	AUGUSTUS	transcript	23951820	23956519	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	stop_codon	23951817	23951819	.	-	0	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	CDS	23951820	23952988	0.88	-	2	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	exon	23951820	23952988	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	intron	23952989	23953071	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	CDS	23953072	23955296	0.28	-	1	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	exon	23953072	23955296	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	intron	23955297	23955424	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	CDS	23955425	23956056	0.65	-	0	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	exon	23955425	23956056	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	intron	23956057	23956261	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	CDS	23956262	23956519	0.87	-	0	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	exon	23956262	23956519	.	-	.	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
Phchi.S1	AUGUSTUS	start_codon	23956517	23956519	.	-	0	transcript_id "Phchi.S1G376300.t1"; gene_id "Phchi.S1G376300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3416.t1 is derived from g585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3397392	3398897	.	+	.	Phchi.S1G057500
Phchi.S1	AUGUSTUS	transcript	3397392	3398897	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	start_codon	3397392	3397394	.	+	0	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3397392	3397512	1	+	0	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3397392	3397512	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3397513	3397605	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3397606	3397725	1	+	2	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3397606	3397725	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3397726	3397816	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3397817	3397899	1	+	2	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3397817	3397899	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3397900	3397989	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3397990	3398073	1	+	0	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3397990	3398073	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3398074	3398151	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3398152	3398227	1	+	0	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3398152	3398227	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3398228	3398352	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3398353	3398425	1	+	2	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3398353	3398425	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3398426	3398500	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3398501	3398574	1	+	1	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3398501	3398574	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3398575	3398651	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3398652	3398745	1	+	2	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3398652	3398745	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	intron	3398746	3398830	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	CDS	3398831	3398897	1	+	1	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	exon	3398831	3398897	.	+	.	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
Phchi.S1	AUGUSTUS	stop_codon	3398898	3398900	.	+	0	transcript_id "Phchi.S1G057500.t1"; gene_id "Phchi.S1G057500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11119.t1 is derived from g15169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4239607	4240602	.	+	.	Phchi.S4G070100
Phchi.S4	AUGUSTUS	transcript	4239607	4240602	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	start_codon	4239607	4239609	.	+	0	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4239607	4239695	1	+	0	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4239607	4239695	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	intron	4239696	4239781	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4239782	4239810	1	+	1	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4239782	4239810	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	intron	4239811	4239883	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4239884	4239925	1	+	2	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4239884	4239925	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	intron	4239926	4240014	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4240015	4240082	1	+	2	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4240015	4240082	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	intron	4240083	4240297	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4240298	4240351	1	+	0	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4240298	4240351	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	intron	4240352	4240443	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4240444	4240502	0.86	+	0	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4240444	4240502	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	intron	4240503	4240577	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	CDS	4240578	4240602	0.5	+	1	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	exon	4240578	4240602	.	+	.	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
Phchi.S4	AUGUSTUS	stop_codon	4240603	4240605	.	+	0	transcript_id "Phchi.S4G070100.t1"; gene_id "Phchi.S4G070100"
# This transcript jg8936.t2 is derived from g6111.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8937.t1 is derived from g6112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38756124	38756723	.	+	.	Phchi.S1G609600
Phchi.S1	AUGUSTUS	transcript	38756124	38756723	.	+	.	transcript_id "Phchi.S1G609600.t1"; gene_id "Phchi.S1G609600"
Phchi.S1	AUGUSTUS	start_codon	38756124	38756126	.	+	0	transcript_id "Phchi.S1G609600.t1"; gene_id "Phchi.S1G609600"
Phchi.S1	AUGUSTUS	CDS	38756124	38756723	0.62	+	0	transcript_id "Phchi.S1G609600.t1"; gene_id "Phchi.S1G609600"
Phchi.S1	AUGUSTUS	exon	38756124	38756723	.	+	.	transcript_id "Phchi.S1G609600.t1"; gene_id "Phchi.S1G609600"
Phchi.S1	AUGUSTUS	stop_codon	38756724	38756726	.	+	0	transcript_id "Phchi.S1G609600.t1"; gene_id "Phchi.S1G609600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13033.t1 is derived from g11498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3801886	3803000	.	-	.	Phchi.S3G035200
Phchi.S3	AUGUSTUS	transcript	3801886	3803000	.	-	.	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	stop_codon	3801883	3801885	.	-	0	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	CDS	3801886	3802466	0.84	-	2	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	exon	3801886	3802466	.	-	.	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	intron	3802467	3802678	.	-	.	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	CDS	3802679	3803000	0.48	-	0	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	exon	3802679	3803000	.	-	.	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
Phchi.S3	AUGUSTUS	start_codon	3802998	3803000	.	-	0	transcript_id "Phchi.S3G035200.t1"; gene_id "Phchi.S3G035200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6216.t1 is derived from g3388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21497559	21498024	.	-	.	Phchi.S1G337500
Phchi.S1	AUGUSTUS	transcript	21497559	21498024	.	-	.	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	stop_codon	21497556	21497558	.	-	0	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	CDS	21497559	21497574	1	-	1	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	exon	21497559	21497574	.	-	.	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	intron	21497575	21497653	.	-	.	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	CDS	21497654	21497767	0.8	-	1	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	exon	21497654	21497767	.	-	.	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	intron	21497768	21497869	.	-	.	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	CDS	21497870	21498024	0.57	-	0	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	exon	21497870	21498024	.	-	.	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
Phchi.S1	AUGUSTUS	start_codon	21498022	21498024	.	-	0	transcript_id "Phchi.S1G337500.t1"; gene_id "Phchi.S1G337500"
# This transcript jg1967.t2 is derived from g8887.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1968.t1 is derived from g8888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4071259	4073371	.	-	.	Phchi.S5G057700
Phchi.S5	AUGUSTUS	transcript	4071259	4073371	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	stop_codon	4071256	4071258	.	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4071259	4071330	1	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4071259	4071330	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4071331	4071459	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4071460	4071515	1	-	2	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4071460	4071515	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4071516	4071622	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4071623	4071682	0.91	-	2	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4071623	4071682	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4071683	4071789	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4071790	4071894	1	-	2	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4071790	4071894	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4071895	4071975	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4071976	4072030	1	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4071976	4072030	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072031	4072101	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4072102	4072230	1	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4072102	4072230	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072231	4072311	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4072312	4072339	1	-	1	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4072312	4072339	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072340	4072418	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4072419	4072494	1	-	2	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4072419	4072494	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072495	4072594	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4072595	4072668	1	-	1	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4072595	4072668	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072669	4072781	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4072782	4072827	1	-	2	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4072782	4072827	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072828	4072922	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4072923	4072989	1	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4072923	4072989	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4072990	4073072	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4073073	4073183	1	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4073073	4073183	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	intron	4073184	4073254	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	CDS	4073255	4073371	0.96	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	exon	4073255	4073371	.	-	.	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
Phchi.S5	AUGUSTUS	start_codon	4073369	4073371	.	-	0	transcript_id "Phchi.S5G057700.t1"; gene_id "Phchi.S5G057700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15587.t1 is derived from g14056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20147335	20148590	.	-	.	Phchi.S3G290600
Phchi.S3	AUGUSTUS	transcript	20147335	20148590	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	stop_codon	20147332	20147334	.	-	0	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	CDS	20147335	20147382	1	-	0	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	exon	20147335	20147382	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	intron	20147383	20147475	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	CDS	20147476	20147519	1	-	2	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	exon	20147476	20147519	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	intron	20147520	20147603	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	CDS	20147604	20147666	1	-	2	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	exon	20147604	20147666	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	intron	20147667	20147760	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	CDS	20147761	20147878	1	-	0	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	exon	20147761	20147878	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	intron	20147879	20148578	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	CDS	20148579	20148590	1	-	0	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	exon	20148579	20148590	.	-	.	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
Phchi.S3	AUGUSTUS	start_codon	20148588	20148590	.	-	0	transcript_id "Phchi.S3G290600.t1"; gene_id "Phchi.S3G290600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12511.t1 is derived from g8188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32205451	32207147	.	-	.	Phchi.S2G059100
Phchi.S2	AUGUSTUS	transcript	32205451	32207147	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	stop_codon	32205448	32205450	.	-	0	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	CDS	32205451	32205618	0.89	-	0	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	exon	32205451	32205618	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	intron	32205619	32205766	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	CDS	32205767	32205883	0.68	-	0	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	exon	32205767	32205883	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	intron	32205884	32206394	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	CDS	32206395	32206477	0.36	-	2	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	exon	32206395	32206477	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	intron	32206478	32206631	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	CDS	32206632	32206885	0.17	-	1	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	exon	32206632	32206885	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	intron	32206886	32206956	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	CDS	32206957	32207147	0.45	-	0	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	exon	32206957	32207147	.	-	.	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
Phchi.S2	AUGUSTUS	start_codon	32207145	32207147	.	-	0	transcript_id "Phchi.S2G059100.t1"; gene_id "Phchi.S2G059100"
# This transcript jg6289.t2 is derived from g3461.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6290.t1 is derived from g3462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22100206	22101535	.	-	.	Phchi.S1G344900
Phchi.S1	AUGUSTUS	transcript	22100206	22101535	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	stop_codon	22100203	22100205	.	-	0	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	CDS	22100206	22100294	1	-	2	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	exon	22100206	22100294	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	intron	22100295	22100386	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	CDS	22100387	22100447	1	-	0	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	exon	22100387	22100447	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	intron	22100448	22100543	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	CDS	22100544	22100613	1	-	1	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	exon	22100544	22100613	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	intron	22100614	22100740	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	CDS	22100741	22100873	1	-	2	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	exon	22100741	22100873	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	intron	22100874	22101059	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	CDS	22101060	22101150	1	-	0	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	exon	22101060	22101150	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	intron	22101151	22101457	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	CDS	22101458	22101535	0.93	-	0	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	exon	22101458	22101535	.	-	.	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
Phchi.S1	AUGUSTUS	start_codon	22101533	22101535	.	-	0	transcript_id "Phchi.S1G344900.t1"; gene_id "Phchi.S1G344900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10149.t1 is derived from g7325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45990751	45992181	.	-	.	Phchi.S1G730800
Phchi.S1	AUGUSTUS	transcript	45990751	45992181	.	-	.	transcript_id "Phchi.S1G730800.t1"; gene_id "Phchi.S1G730800"
Phchi.S1	AUGUSTUS	stop_codon	45990748	45990750	.	-	0	transcript_id "Phchi.S1G730800.t1"; gene_id "Phchi.S1G730800"
Phchi.S1	AUGUSTUS	CDS	45990751	45992181	0.74	-	0	transcript_id "Phchi.S1G730800.t1"; gene_id "Phchi.S1G730800"
Phchi.S1	AUGUSTUS	exon	45990751	45992181	.	-	.	transcript_id "Phchi.S1G730800.t1"; gene_id "Phchi.S1G730800"
Phchi.S1	AUGUSTUS	start_codon	45992179	45992181	.	-	0	transcript_id "Phchi.S1G730800.t1"; gene_id "Phchi.S1G730800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5551.t1 is derived from g2721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17559369	17561528	.	-	.	Phchi.S1G271000
Phchi.S1	AUGUSTUS	transcript	17559369	17561528	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	stop_codon	17559249	17559251	.	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17559369	17559437	0.75	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17559369	17559437	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17559438	17559518	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17559519	17559610	1	-	2	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17559519	17559610	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17559611	17559710	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17559711	17559846	0.97	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17559711	17559846	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17559847	17559954	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17559955	17560146	1	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17559955	17560146	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17560147	17560231	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17560232	17560487	0.98	-	1	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17560232	17560487	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17560488	17560587	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17560588	17561001	0.81	-	1	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17560588	17561001	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17561002	17561126	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17561127	17561332	1	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17561127	17561332	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	intron	17561333	17561450	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	CDS	17561451	17561528	0.97	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	exon	17561451	17561528	.	-	.	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
Phchi.S1	AUGUSTUS	start_codon	17561526	17561528	.	-	0	transcript_id "Phchi.S1G271000.t1"; gene_id "Phchi.S1G271000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14743.t1 is derived from g13211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14492182	14492613	.	+	.	Phchi.S3G206200
Phchi.S3	AUGUSTUS	transcript	14492182	14492613	.	+	.	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	start_codon	14492182	14492184	.	+	0	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	CDS	14492182	14492264	1	+	0	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	exon	14492182	14492264	.	+	.	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	intron	14492265	14492348	.	+	.	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	CDS	14492349	14492613	1	+	1	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	exon	14492349	14492613	.	+	.	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
Phchi.S3	AUGUSTUS	stop_codon	14492614	14492616	.	+	0	transcript_id "Phchi.S3G206200.t1"; gene_id "Phchi.S3G206200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3517.t1 is derived from g686.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4166733	4167621	.	+	.	Phchi.S1G067600
Phchi.S1	AUGUSTUS	transcript	4166733	4167621	.	+	.	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	start_codon	4166733	4166735	.	+	0	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	CDS	4166733	4166897	1	+	0	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	exon	4166733	4166897	.	+	.	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	intron	4166898	4166991	.	+	.	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	CDS	4166992	4167621	0.76	+	0	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	exon	4166992	4167621	.	+	.	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
Phchi.S1	AUGUSTUS	stop_codon	4167622	4167624	.	+	0	transcript_id "Phchi.S1G067600.t1"; gene_id "Phchi.S1G067600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4444.t1 is derived from g1613.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10544968	10545921	.	+	.	Phchi.S1G160300
Phchi.S1	AUGUSTUS	transcript	10544968	10545921	.	+	.	transcript_id "Phchi.S1G160300.t1"; gene_id "Phchi.S1G160300"
Phchi.S1	AUGUSTUS	start_codon	10544968	10544970	.	+	0	transcript_id "Phchi.S1G160300.t1"; gene_id "Phchi.S1G160300"
Phchi.S1	AUGUSTUS	CDS	10544968	10545921	0.67	+	0	transcript_id "Phchi.S1G160300.t1"; gene_id "Phchi.S1G160300"
Phchi.S1	AUGUSTUS	exon	10544968	10545921	.	+	.	transcript_id "Phchi.S1G160300.t1"; gene_id "Phchi.S1G160300"
Phchi.S1	AUGUSTUS	stop_codon	10545922	10545924	.	+	0	transcript_id "Phchi.S1G160300.t1"; gene_id "Phchi.S1G160300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6375.t1 is derived from g3547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22637446	22640470	.	-	.	Phchi.S1G353400
Phchi.S1	AUGUSTUS	transcript	22637446	22640470	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	stop_codon	22637443	22637445	.	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22637446	22637695	0.95	-	1	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22637446	22637695	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22637696	22637775	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22637776	22637905	1	-	2	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22637776	22637905	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22637906	22637986	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22637987	22638090	1	-	1	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22637987	22638090	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22638091	22638184	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22638185	22638270	1	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22638185	22638270	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22638271	22638370	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22638371	22638437	1	-	1	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22638371	22638437	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22638438	22638524	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22638525	22638820	1	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22638525	22638820	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22638821	22638914	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22638915	22638998	1	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22638915	22638998	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22638999	22639089	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22639090	22639179	0.6	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22639090	22639179	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22639180	22639254	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22639255	22639419	1	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22639255	22639419	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22639420	22639541	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22639542	22639626	1	-	1	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22639542	22639626	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22639627	22639720	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22639721	22639766	1	-	2	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22639721	22639766	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22639767	22639907	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22639908	22639952	0.93	-	2	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22639908	22639952	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22639953	22640142	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22640143	22640275	0.93	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22640143	22640275	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	intron	22640276	22640395	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	CDS	22640396	22640470	0.96	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	exon	22640396	22640470	.	-	.	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
Phchi.S1	AUGUSTUS	start_codon	22640468	22640470	.	-	0	transcript_id "Phchi.S1G353400.t1"; gene_id "Phchi.S1G353400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9678.t1 is derived from g6854.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43248762	43250454	.	-	.	Phchi.S1G683700
Phchi.S1	AUGUSTUS	transcript	43248762	43250454	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	stop_codon	43248759	43248761	.	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43248762	43248893	0.95	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43248762	43248893	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	intron	43248894	43248982	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43248983	43249062	0.93	-	2	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43248983	43249062	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	intron	43249063	43249175	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43249176	43249256	0.96	-	2	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43249176	43249256	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	intron	43249257	43249517	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43249518	43249608	0.67	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43249518	43249608	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	intron	43249609	43249699	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43249700	43249795	1	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43249700	43249795	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	intron	43249796	43249919	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43249920	43250129	0.99	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43249920	43250129	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	intron	43250130	43250367	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	CDS	43250368	43250454	0.86	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	exon	43250368	43250454	.	-	.	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
Phchi.S1	AUGUSTUS	start_codon	43250452	43250454	.	-	0	transcript_id "Phchi.S1G683700.t1"; gene_id "Phchi.S1G683700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8676.t1 is derived from g5851.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37381121	37387294	.	+	.	Phchi.S1G583500
Phchi.S1	AUGUSTUS	transcript	37381121	37387294	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	start_codon	37381121	37381123	.	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37381121	37383121	0.53	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37381121	37383121	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37383122	37383251	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37383252	37383611	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37383252	37383611	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37383612	37383736	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37383737	37383865	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37383737	37383865	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37383866	37383946	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37383947	37384069	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37383947	37384069	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37384070	37384202	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37384203	37384391	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37384203	37384391	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37384392	37384482	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37384483	37384608	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37384483	37384608	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37384609	37384727	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37384728	37384862	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37384728	37384862	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37384863	37384938	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37384939	37385066	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37384939	37385066	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37385067	37385153	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37385154	37385265	0.76	+	1	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37385154	37385265	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37385266	37385366	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37385367	37385400	0.59	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37385367	37385400	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37385401	37385477	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37385478	37385710	0.18	+	2	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37385478	37385710	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37385711	37385798	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37385799	37385930	1	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37385799	37385930	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37385931	37386084	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37386085	37386174	0.92	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37386085	37386174	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37386175	37386316	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37386317	37386330	0.98	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37386317	37386330	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	intron	37386331	37386477	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	CDS	37386478	37387294	0.83	+	1	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	exon	37386478	37387294	.	+	.	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
Phchi.S1	AUGUSTUS	stop_codon	37387295	37387297	.	+	0	transcript_id "Phchi.S1G583500.t1"; gene_id "Phchi.S1G583500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2745.t1 is derived from g9665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8581010	8582553	.	+	.	Phchi.S5G135400
Phchi.S5	AUGUSTUS	transcript	8581010	8582553	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	start_codon	8581010	8581012	.	+	0	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8581010	8581200	0.95	+	0	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8581010	8581200	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	intron	8581201	8581342	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8581343	8581436	1	+	1	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8581343	8581436	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	intron	8581437	8581640	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8581641	8581780	1	+	0	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8581641	8581780	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	intron	8581781	8581889	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8581890	8581964	1	+	1	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8581890	8581964	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	intron	8581965	8582052	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8582053	8582210	1	+	1	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8582053	8582210	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	intron	8582211	8582295	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8582296	8582396	1	+	2	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8582296	8582396	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	intron	8582397	8582490	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	CDS	8582491	8582553	1	+	0	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	exon	8582491	8582553	.	+	.	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
Phchi.S5	AUGUSTUS	stop_codon	8582554	8582556	.	+	0	transcript_id "Phchi.S5G135400.t1"; gene_id "Phchi.S5G135400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10510.t1 is derived from g14559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	761278	764623	.	-	.	Phchi.S4G009200
Phchi.S4	AUGUSTUS	transcript	761278	764623	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	stop_codon	761275	761277	.	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	761278	761347	1	-	1	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	761278	761347	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	761348	761422	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	761423	761503	1	-	1	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	761423	761503	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	761504	761586	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	761587	761675	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	761587	761675	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	761676	761776	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	761777	761836	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	761777	761836	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	761837	761931	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	761932	762024	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	761932	762024	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	762025	762127	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	762128	762232	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	762128	762232	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	762233	762318	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	762319	762323	0.7	-	2	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	762319	762323	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	762324	762391	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	762392	762488	0.7	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	762392	762488	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	762489	762587	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	762588	762657	0.95	-	1	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	762588	762657	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	762658	762775	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	762776	762861	0.95	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	762776	762861	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	762862	762949	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	762950	763096	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	762950	763096	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	763097	763177	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	763178	763250	1	-	1	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	763178	763250	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	763251	763344	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	763345	763418	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	763345	763418	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	763419	763537	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	763538	763660	1	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	763538	763660	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	intron	763661	763744	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	CDS	763745	764623	0.54	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	exon	763745	764623	.	-	.	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
Phchi.S4	AUGUSTUS	start_codon	764621	764623	.	-	0	transcript_id "Phchi.S4G009200.t1"; gene_id "Phchi.S4G009200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8072.t1 is derived from g5247.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32802303	32806141	.	+	.	Phchi.S1G523100
Phchi.S1	AUGUSTUS	transcript	32802303	32806141	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	start_codon	32802303	32802305	.	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32802303	32802857	0.62	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32802303	32802857	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32802858	32802988	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32802989	32803102	1	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32802989	32803102	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32803103	32803206	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32803207	32803308	1	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32803207	32803308	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32803309	32803397	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32803398	32803549	0.39	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32803398	32803549	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32803550	32803681	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32803682	32803691	0.53	+	1	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32803682	32803691	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32803692	32803845	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32803846	32804442	0.99	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32803846	32804442	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32804443	32804540	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32804541	32804684	0.73	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32804541	32804684	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32804685	32804786	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32804787	32804951	0.77	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32804787	32804951	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32804952	32805047	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32805048	32805140	1	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32805048	32805140	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32805141	32805238	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32805239	32805479	0.88	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32805239	32805479	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32805480	32805921	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32805922	32805978	0.96	+	2	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32805922	32805978	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	intron	32805979	32806067	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	CDS	32806068	32806141	0.95	+	2	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	exon	32806068	32806141	.	+	.	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
Phchi.S1	AUGUSTUS	stop_codon	32806142	32806144	.	+	0	transcript_id "Phchi.S1G523100.t1"; gene_id "Phchi.S1G523100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15258.t1 is derived from g13726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17956864	17959243	.	-	.	Phchi.S3G257700
Phchi.S3	AUGUSTUS	transcript	17956864	17959243	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	stop_codon	17956861	17956863	.	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17956864	17957033	0.98	-	2	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17956864	17957033	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17957034	17957114	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17957115	17957211	1	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17957115	17957211	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17957212	17957301	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17957302	17957340	1	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17957302	17957340	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17957341	17957460	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17957461	17957514	1	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17957461	17957514	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17957515	17957654	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17957655	17957736	1	-	1	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17957655	17957736	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17957737	17957834	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17957835	17957955	1	-	2	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17957835	17957955	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17957956	17958043	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17958044	17958173	1	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17958044	17958173	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17958174	17958530	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17958531	17958659	1	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17958531	17958659	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17958660	17958745	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17958746	17958969	1	-	2	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17958746	17958969	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	intron	17958970	17959194	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	CDS	17959195	17959243	0.99	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	exon	17959195	17959243	.	-	.	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
Phchi.S3	AUGUSTUS	start_codon	17959241	17959243	.	-	0	transcript_id "Phchi.S3G257700.t1"; gene_id "Phchi.S3G257700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg216.t1 is derived from g9998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1368599	1370263	.	+	.	Phchi.S6G017500
Phchi.S6	AUGUSTUS	transcript	1368599	1370263	.	+	.	transcript_id "Phchi.S6G017500.t1"; gene_id "Phchi.S6G017500"
Phchi.S6	AUGUSTUS	start_codon	1368599	1368601	.	+	0	transcript_id "Phchi.S6G017500.t1"; gene_id "Phchi.S6G017500"
Phchi.S6	AUGUSTUS	CDS	1368599	1370263	0.34	+	0	transcript_id "Phchi.S6G017500.t1"; gene_id "Phchi.S6G017500"
Phchi.S6	AUGUSTUS	exon	1368599	1370263	.	+	.	transcript_id "Phchi.S6G017500.t1"; gene_id "Phchi.S6G017500"
Phchi.S6	AUGUSTUS	stop_codon	1370264	1370266	.	+	0	transcript_id "Phchi.S6G017500.t1"; gene_id "Phchi.S6G017500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4774.t1 is derived from g1944.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12771244	12771882	.	+	.	Phchi.S1G193300
Phchi.S1	AUGUSTUS	transcript	12771244	12771882	.	+	.	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	start_codon	12771244	12771246	.	+	0	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	CDS	12771244	12771439	0.78	+	0	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	exon	12771244	12771439	.	+	.	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	intron	12771440	12771607	.	+	.	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	CDS	12771608	12771882	1	+	2	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	exon	12771608	12771882	.	+	.	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
Phchi.S1	AUGUSTUS	stop_codon	12771883	12771885	.	+	0	transcript_id "Phchi.S1G193300.t1"; gene_id "Phchi.S1G193300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10733.t1 is derived from g14783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1805464	1805808	.	-	.	Phchi.S4G031500
Phchi.S4	AUGUSTUS	transcript	1805464	1805808	.	-	.	transcript_id "Phchi.S4G031500.t1"; gene_id "Phchi.S4G031500"
Phchi.S4	AUGUSTUS	stop_codon	1805461	1805463	.	-	0	transcript_id "Phchi.S4G031500.t1"; gene_id "Phchi.S4G031500"
Phchi.S4	AUGUSTUS	CDS	1805464	1805808	0.5	-	0	transcript_id "Phchi.S4G031500.t1"; gene_id "Phchi.S4G031500"
Phchi.S4	AUGUSTUS	exon	1805464	1805808	.	-	.	transcript_id "Phchi.S4G031500.t1"; gene_id "Phchi.S4G031500"
Phchi.S4	AUGUSTUS	start_codon	1805806	1805808	.	-	0	transcript_id "Phchi.S4G031500.t1"; gene_id "Phchi.S4G031500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11626.t1 is derived from g15677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7377486	7379236	.	-	.	Phchi.S4G120800
Phchi.S4	AUGUSTUS	transcript	7377486	7379236	.	-	.	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	stop_codon	7377483	7377485	.	-	0	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	CDS	7377486	7378362	0.99	-	1	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	exon	7377486	7378362	.	-	.	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	intron	7378363	7378468	.	-	.	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	CDS	7378469	7378977	0.95	-	0	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	exon	7378469	7378977	.	-	.	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	intron	7378978	7379227	.	-	.	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	CDS	7379228	7379236	0.53	-	0	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	exon	7379228	7379236	.	-	.	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
Phchi.S4	AUGUSTUS	start_codon	7379234	7379236	.	-	0	transcript_id "Phchi.S4G120800.t1"; gene_id "Phchi.S4G120800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8445.t1 is derived from g5620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35960159	35960791	.	-	.	Phchi.S1G560400
Phchi.S1	AUGUSTUS	transcript	35960159	35960791	.	-	.	transcript_id "Phchi.S1G560400.t1"; gene_id "Phchi.S1G560400"
Phchi.S1	AUGUSTUS	stop_codon	35960156	35960158	.	-	0	transcript_id "Phchi.S1G560400.t1"; gene_id "Phchi.S1G560400"
Phchi.S1	AUGUSTUS	CDS	35960159	35960791	1	-	0	transcript_id "Phchi.S1G560400.t1"; gene_id "Phchi.S1G560400"
Phchi.S1	AUGUSTUS	exon	35960159	35960791	.	-	.	transcript_id "Phchi.S1G560400.t1"; gene_id "Phchi.S1G560400"
Phchi.S1	AUGUSTUS	start_codon	35960789	35960791	.	-	0	transcript_id "Phchi.S1G560400.t1"; gene_id "Phchi.S1G560400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1111.t1 is derived from g10894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7673493	7674737	.	+	.	Phchi.S6G107000
Phchi.S6	AUGUSTUS	transcript	7673493	7674737	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	start_codon	7673493	7673495	.	+	0	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	CDS	7673493	7673654	0.4	+	0	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	exon	7673493	7673654	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	intron	7673655	7673870	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	CDS	7673871	7674093	0.61	+	0	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	exon	7673871	7674093	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	intron	7674094	7674377	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	CDS	7674378	7674544	0.84	+	2	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	exon	7674378	7674544	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	intron	7674545	7674722	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	CDS	7674723	7674737	0.84	+	0	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	exon	7674723	7674737	.	+	.	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
Phchi.S6	AUGUSTUS	stop_codon	7674738	7674740	.	+	0	transcript_id "Phchi.S6G107000.t1"; gene_id "Phchi.S6G107000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg138.t1 is derived from g9920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	764542	766545	.	-	.	Phchi.S6G009700
Phchi.S6	AUGUSTUS	transcript	764542	766545	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	stop_codon	764539	764541	.	-	0	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	764542	764692	0.7	-	1	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	764542	764692	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	764693	764846	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	764847	764882	0.52	-	1	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	764847	764882	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	764883	764962	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	764963	765317	0.41	-	2	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	764963	765317	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	765318	765531	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	765532	765622	0.47	-	0	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	765532	765622	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	765623	765699	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	765700	765758	0.38	-	2	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	765700	765758	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	765759	765907	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	765908	765958	0.79	-	2	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	765908	765958	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	765959	766052	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	766053	766260	0.69	-	0	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	766053	766260	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	intron	766261	766482	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	CDS	766483	766545	0.66	-	0	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	exon	766483	766545	.	-	.	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
Phchi.S6	AUGUSTUS	start_codon	766543	766545	.	-	0	transcript_id "Phchi.S6G009700.t1"; gene_id "Phchi.S6G009700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg525.t1 is derived from g10307.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3778393	3779706	.	+	.	Phchi.S6G048400
Phchi.S6	AUGUSTUS	transcript	3778393	3779706	.	+	.	transcript_id "Phchi.S6G048400.t1"; gene_id "Phchi.S6G048400"
Phchi.S6	AUGUSTUS	start_codon	3778393	3778395	.	+	0	transcript_id "Phchi.S6G048400.t1"; gene_id "Phchi.S6G048400"
Phchi.S6	AUGUSTUS	CDS	3778393	3779706	1	+	0	transcript_id "Phchi.S6G048400.t1"; gene_id "Phchi.S6G048400"
Phchi.S6	AUGUSTUS	exon	3778393	3779706	.	+	.	transcript_id "Phchi.S6G048400.t1"; gene_id "Phchi.S6G048400"
Phchi.S6	AUGUSTUS	stop_codon	3779707	3779709	.	+	0	transcript_id "Phchi.S6G048400.t1"; gene_id "Phchi.S6G048400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11160.t1 is derived from g15210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4426905	4427675	.	+	.	Phchi.S4G074200
Phchi.S4	AUGUSTUS	transcript	4426905	4427675	.	+	.	transcript_id "Phchi.S4G074200.t1"; gene_id "Phchi.S4G074200"
Phchi.S4	AUGUSTUS	start_codon	4426905	4426907	.	+	0	transcript_id "Phchi.S4G074200.t1"; gene_id "Phchi.S4G074200"
Phchi.S4	AUGUSTUS	CDS	4426905	4427675	0.98	+	0	transcript_id "Phchi.S4G074200.t1"; gene_id "Phchi.S4G074200"
Phchi.S4	AUGUSTUS	exon	4426905	4427675	.	+	.	transcript_id "Phchi.S4G074200.t1"; gene_id "Phchi.S4G074200"
Phchi.S4	AUGUSTUS	stop_codon	4427676	4427678	.	+	0	transcript_id "Phchi.S4G074200.t1"; gene_id "Phchi.S4G074200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7897.t1 is derived from g5071.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31797485	31797778	.	+	.	Phchi.S1G505600
Phchi.S1	AUGUSTUS	transcript	31797485	31797778	.	+	.	transcript_id "Phchi.S1G505600.t1"; gene_id "Phchi.S1G505600"
Phchi.S1	AUGUSTUS	start_codon	31797485	31797487	.	+	0	transcript_id "Phchi.S1G505600.t1"; gene_id "Phchi.S1G505600"
Phchi.S1	AUGUSTUS	CDS	31797485	31797778	1	+	0	transcript_id "Phchi.S1G505600.t1"; gene_id "Phchi.S1G505600"
Phchi.S1	AUGUSTUS	exon	31797485	31797778	.	+	.	transcript_id "Phchi.S1G505600.t1"; gene_id "Phchi.S1G505600"
Phchi.S1	AUGUSTUS	stop_codon	31797779	31797781	.	+	0	transcript_id "Phchi.S1G505600.t1"; gene_id "Phchi.S1G505600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6328.t1 is derived from g3500.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22298220	22302115	.	-	.	Phchi.S1G348700
Phchi.S1	AUGUSTUS	transcript	22298220	22302115	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	stop_codon	22298217	22298219	.	-	0	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22298220	22299150	0.85	-	1	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22298220	22299150	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	intron	22299151	22299272	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22299273	22299444	0.86	-	2	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22299273	22299444	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	intron	22299445	22299539	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22299540	22299606	1	-	0	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22299540	22299606	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	intron	22299607	22299728	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22299729	22299824	1	-	0	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22299729	22299824	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	intron	22299825	22299906	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22299907	22300084	1	-	1	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22299907	22300084	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	intron	22300085	22300224	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22300225	22300302	0.99	-	1	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22300225	22300302	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	intron	22300303	22300409	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	CDS	22300410	22302115	0.57	-	0	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	exon	22300410	22302115	.	-	.	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
Phchi.S1	AUGUSTUS	start_codon	22302113	22302115	.	-	0	transcript_id "Phchi.S1G348700.t1"; gene_id "Phchi.S1G348700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8932.t1 is derived from g6107.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38724707	38725226	.	-	.	Phchi.S1G609100
Phchi.S1	AUGUSTUS	transcript	38724707	38725226	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	stop_codon	38724704	38724706	.	-	0	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	CDS	38724707	38724735	0.99	-	2	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	exon	38724707	38724735	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	intron	38724736	38724826	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	CDS	38724827	38724921	0.92	-	1	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	exon	38724827	38724921	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	intron	38724922	38725023	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	CDS	38725024	38725082	0.74	-	0	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	exon	38725024	38725082	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	intron	38725083	38725190	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	CDS	38725191	38725226	0.86	-	0	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	exon	38725191	38725226	.	-	.	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
Phchi.S1	AUGUSTUS	start_codon	38725224	38725226	.	-	0	transcript_id "Phchi.S1G609100.t1"; gene_id "Phchi.S1G609100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12680.t1 is derived from g14414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C62	AUGUSTUS	gene	39073	41106	.	-	.	Phchi.C62G001100
Phchi.C62	AUGUSTUS	transcript	39073	41106	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	stop_codon	39070	39072	.	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	39073	39318	0.64	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	39073	39318	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	39319	39402	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	39403	39519	1	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	39403	39519	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	39520	39613	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	39614	39715	1	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	39614	39715	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	39716	39805	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	39806	39832	0.99	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	39806	39832	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	39833	39890	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	39891	39899	1	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	39891	39899	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	39900	40093	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	40094	40345	1	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	40094	40345	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	40346	40459	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	40460	40693	0.83	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	40460	40693	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	intron	40694	40797	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	CDS	40798	41106	0.8	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	exon	40798	41106	.	-	.	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
Phchi.C62	AUGUSTUS	start_codon	41104	41106	.	-	0	transcript_id "Phchi.C62G001100.t1"; gene_id "Phchi.C62G001100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7939.t1 is derived from g5113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32016617	32020540	.	+	.	Phchi.S1G509800
Phchi.S1	AUGUSTUS	transcript	32016617	32020540	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	start_codon	32016617	32016619	.	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32016617	32016737	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32016617	32016737	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32016738	32016824	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32016825	32016885	1	+	2	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32016825	32016885	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32016886	32016957	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32016958	32017075	1	+	1	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32016958	32017075	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32017076	32017222	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32017223	32017283	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32017223	32017283	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32017284	32017377	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32017378	32017472	1	+	2	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32017378	32017472	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32017473	32017548	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32017549	32017620	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32017549	32017620	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32017621	32017719	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32017720	32018268	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32017720	32018268	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32018269	32018358	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32018359	32018661	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32018359	32018661	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32018662	32018752	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32018753	32019082	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32018753	32019082	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32019083	32019187	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32019188	32019394	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32019188	32019394	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32019395	32019476	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32019477	32019566	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32019477	32019566	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32019567	32019704	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32019705	32019799	1	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32019705	32019799	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32019800	32019917	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32019918	32020040	1	+	1	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32019918	32020040	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	intron	32020041	32020128	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	CDS	32020129	32020540	0.99	+	1	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	exon	32020129	32020540	.	+	.	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
Phchi.S1	AUGUSTUS	stop_codon	32020541	32020543	.	+	0	transcript_id "Phchi.S1G509800.t1"; gene_id "Phchi.S1G509800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9588.t1 is derived from g6764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42805525	42805905	.	-	.	Phchi.S1G674700
Phchi.S1	AUGUSTUS	transcript	42805525	42805905	.	-	.	transcript_id "Phchi.S1G674700.t1"; gene_id "Phchi.S1G674700"
Phchi.S1	AUGUSTUS	stop_codon	42805522	42805524	.	-	0	transcript_id "Phchi.S1G674700.t1"; gene_id "Phchi.S1G674700"
Phchi.S1	AUGUSTUS	CDS	42805525	42805905	0.51	-	0	transcript_id "Phchi.S1G674700.t1"; gene_id "Phchi.S1G674700"
Phchi.S1	AUGUSTUS	exon	42805525	42805905	.	-	.	transcript_id "Phchi.S1G674700.t1"; gene_id "Phchi.S1G674700"
Phchi.S1	AUGUSTUS	start_codon	42805903	42805905	.	-	0	transcript_id "Phchi.S1G674700.t1"; gene_id "Phchi.S1G674700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg863.t1 is derived from g10645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5987526	5989078	.	+	.	Phchi.S6G082200
Phchi.S6	AUGUSTUS	transcript	5987526	5989078	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	start_codon	5987526	5987528	.	+	0	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	CDS	5987526	5987737	0.85	+	0	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	exon	5987526	5987737	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	intron	5987738	5988296	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	CDS	5988297	5988374	0.95	+	1	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	exon	5988297	5988374	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	intron	5988375	5988517	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	CDS	5988518	5988543	0.95	+	1	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	exon	5988518	5988543	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	intron	5988544	5988681	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	CDS	5988682	5988731	0.64	+	2	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	exon	5988682	5988731	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	intron	5988732	5988844	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	CDS	5988845	5989078	0.96	+	0	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	exon	5988845	5989078	.	+	.	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
Phchi.S6	AUGUSTUS	stop_codon	5989079	5989081	.	+	0	transcript_id "Phchi.S6G082200.t1"; gene_id "Phchi.S6G082200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4899.t1 is derived from g2069.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13319750	13321033	.	-	.	Phchi.S1G205800
Phchi.S1	AUGUSTUS	transcript	13319875	13321033	.	-	.	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	stop_codon	13319872	13319874	.	-	0	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	CDS	13319875	13319878	0.82	-	1	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	exon	13319875	13319878	.	-	.	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	intron	13319879	13319987	.	-	.	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	CDS	13319988	13321033	0.7	-	0	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	exon	13319988	13321033	.	-	.	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	start_codon	13321031	13321033	.	-	0	transcript_id "Phchi.S1G205800.t1"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	transcript	13319750	13321033	.	-	.	transcript_id "Phchi.S1G205800.t2"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	stop_codon	13319747	13319749	.	-	0	transcript_id "Phchi.S1G205800.t2"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	CDS	13319750	13321033	0.84	-	0	transcript_id "Phchi.S1G205800.t2"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	exon	13319750	13321033	.	-	.	transcript_id "Phchi.S1G205800.t2"; gene_id "Phchi.S1G205800"
Phchi.S1	AUGUSTUS	start_codon	13321031	13321033	.	-	0	transcript_id "Phchi.S1G205800.t2"; gene_id "Phchi.S1G205800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9662.t1 is derived from g6838.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43119853	43125744	.	-	.	Phchi.S1G682100
Phchi.S1	AUGUSTUS	transcript	43119853	43125744	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	stop_codon	43119850	43119852	.	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43119853	43120095	0.96	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43119853	43120095	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43120096	43120171	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43120172	43120237	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43120172	43120237	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43120238	43120423	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43120424	43120549	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43120424	43120549	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43120550	43120703	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43120704	43120832	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43120704	43120832	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43120833	43120949	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43120950	43121100	1	-	1	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43120950	43121100	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43121101	43121197	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43121198	43121267	1	-	2	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43121198	43121267	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43121268	43121378	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43121379	43121487	0.71	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43121379	43121487	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43121488	43121612	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43121613	43121792	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43121613	43121792	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43121793	43121936	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43121937	43122033	1	-	1	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43121937	43122033	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43122034	43122164	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43122165	43122202	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43122165	43122202	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43122203	43122298	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43122299	43122475	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43122299	43122475	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43122476	43122566	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43122567	43122619	1	-	2	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43122567	43122619	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43122620	43122711	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43122712	43122811	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43122712	43122811	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43122812	43122893	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43122894	43122981	1	-	1	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43122894	43122981	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43122982	43123074	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43123075	43123201	1	-	2	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43123075	43123201	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43123202	43123298	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43123299	43123393	1	-	1	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43123299	43123393	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43123394	43123516	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43123517	43123653	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43123517	43123653	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43123654	43123798	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43123799	43123897	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43123799	43123897	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43123898	43123985	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43123986	43124079	1	-	1	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43123986	43124079	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43124080	43124168	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43124169	43124302	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43124169	43124302	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43124303	43124398	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43124399	43124509	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43124399	43124509	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43124510	43124606	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43124607	43124780	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43124607	43124780	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43124781	43124867	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43124868	43124990	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43124868	43124990	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43124991	43125135	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43125136	43125310	1	-	1	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43125136	43125310	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43125311	43125405	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43125406	43125497	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43125406	43125497	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	intron	43125498	43125639	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	CDS	43125640	43125744	1	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	exon	43125640	43125744	.	-	.	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
Phchi.S1	AUGUSTUS	start_codon	43125742	43125744	.	-	0	transcript_id "Phchi.S1G682100.t1"; gene_id "Phchi.S1G682100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12820.t1 is derived from g11285.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2558876	2561630	.	-	.	Phchi.S3G013900
Phchi.S3	AUGUSTUS	transcript	2558876	2561630	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	stop_codon	2558873	2558875	.	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2558876	2559070	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2558876	2559070	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2559071	2559166	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2559167	2559316	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2559167	2559316	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2559317	2559423	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2559424	2559564	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2559424	2559564	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2559565	2559653	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2559654	2559741	1	-	1	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2559654	2559741	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2559742	2559828	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2559829	2559884	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2559829	2559884	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2559885	2559976	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2559977	2560052	1	-	1	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2559977	2560052	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2560053	2560149	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2560150	2560223	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2560150	2560223	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2560224	2560378	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2560379	2560537	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2560379	2560537	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2560538	2560645	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2560646	2560789	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2560646	2560789	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2560790	2560920	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2560921	2561053	1	-	1	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2560921	2561053	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2561054	2561146	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2561147	2561253	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2561147	2561253	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	intron	2561254	2561558	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	CDS	2561559	2561630	1	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	exon	2561559	2561630	.	-	.	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
Phchi.S3	AUGUSTUS	start_codon	2561628	2561630	.	-	0	transcript_id "Phchi.S3G013900.t1"; gene_id "Phchi.S3G013900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15935.t1 is derived from g9786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C18	AUGUSTUS	gene	100917	101869	.	-	.	Phchi.C18G000200
Phchi.C18	AUGUSTUS	transcript	100917	101869	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	stop_codon	100914	100916	.	-	0	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	CDS	100917	100959	0.97	-	1	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	exon	100917	100959	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	intron	100960	101129	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	CDS	101130	101171	0.92	-	1	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	exon	101130	101171	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	intron	101172	101328	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	CDS	101329	101436	0.95	-	1	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	exon	101329	101436	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	intron	101437	101635	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	CDS	101636	101745	0.82	-	0	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	exon	101636	101745	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	intron	101746	101845	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	CDS	101846	101869	0.42	-	0	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	exon	101846	101869	.	-	.	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
Phchi.C18	AUGUSTUS	start_codon	101867	101869	.	-	0	transcript_id "Phchi.C18G000200.t1"; gene_id "Phchi.C18G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7061.t1 is derived from g4233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26684312	26686327	.	-	.	Phchi.S1G422000
Phchi.S1	AUGUSTUS	transcript	26684312	26686327	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	stop_codon	26684309	26684311	.	-	0	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	CDS	26684312	26684517	0.99	-	2	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	exon	26684312	26684517	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	intron	26684518	26684710	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	CDS	26684711	26684878	1	-	2	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	exon	26684711	26684878	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	intron	26684879	26684998	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	CDS	26684999	26685093	1	-	1	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	exon	26684999	26685093	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	intron	26685094	26685212	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	CDS	26685213	26685297	1	-	2	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	exon	26685213	26685297	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	intron	26685298	26685534	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	CDS	26685535	26685669	1	-	2	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	exon	26685535	26685669	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	intron	26685670	26685993	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	CDS	26685994	26686327	0.95	-	0	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	exon	26685994	26686327	.	-	.	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
Phchi.S1	AUGUSTUS	start_codon	26686325	26686327	.	-	0	transcript_id "Phchi.S1G422000.t1"; gene_id "Phchi.S1G422000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5734.t1 is derived from g2904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18602187	18608072	.	+	.	Phchi.S1G289300
Phchi.S1	AUGUSTUS	transcript	18602187	18608072	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	start_codon	18602187	18602189	.	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18602187	18602313	0.9	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18602187	18602313	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18602314	18602767	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18602768	18602867	0.99	+	2	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18602768	18602867	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18602868	18602974	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18602975	18603083	0.97	+	1	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18602975	18603083	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18603084	18603169	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18603170	18604705	0.88	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18603170	18604705	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18604706	18604855	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18604856	18605098	1	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18604856	18605098	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18605099	18605188	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18605189	18605503	0.91	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18605189	18605503	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18605504	18605601	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18605602	18605841	1	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18605602	18605841	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18605842	18605983	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18605984	18606268	1	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18605984	18606268	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18606269	18606355	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18606356	18606577	0.87	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18606356	18606577	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18606578	18606683	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18606684	18606845	0.89	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18606684	18606845	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18606846	18606993	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18606994	18607128	1	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18606994	18607128	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18607129	18607224	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18607225	18607492	0.87	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18607225	18607492	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18607493	18607562	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18607563	18607735	0.91	+	2	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18607563	18607735	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	intron	18607736	18607832	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	CDS	18607833	18608072	0.98	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	exon	18607833	18608072	.	+	.	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
Phchi.S1	AUGUSTUS	stop_codon	18608073	18608075	.	+	0	transcript_id "Phchi.S1G289300.t1"; gene_id "Phchi.S1G289300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg14161.t1 is derived from g12629.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11224285	11224816	.	+	.	Phchi.S3G148100
Phchi.S3	AUGUSTUS	transcript	11224285	11224655	.	+	.	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	start_codon	11224285	11224287	.	+	0	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	CDS	11224285	11224311	1	+	0	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	exon	11224285	11224311	.	+	.	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	intron	11224312	11224383	.	+	.	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	CDS	11224384	11224526	1	+	0	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	exon	11224384	11224526	.	+	.	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	intron	11224527	11224621	.	+	.	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	CDS	11224622	11224655	1	+	1	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	exon	11224622	11224655	.	+	.	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	stop_codon	11224656	11224658	.	+	0	transcript_id "Phchi.S3G148100.t1"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	transcript	11224285	11224816	.	+	.	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	start_codon	11224285	11224287	.	+	0	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	CDS	11224285	11224311	0.88	+	0	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	exon	11224285	11224311	.	+	.	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	intron	11224312	11224466	.	+	.	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	CDS	11224467	11224526	0.88	+	0	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	exon	11224467	11224526	.	+	.	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	intron	11224527	11224621	.	+	.	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	CDS	11224622	11224816	0.88	+	0	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	exon	11224622	11224816	.	+	.	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
Phchi.S3	AUGUSTUS	stop_codon	11224817	11224819	.	+	0	transcript_id "Phchi.S3G148100.t2"; gene_id "Phchi.S3G148100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5302.t1 is derived from g2472.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16103050	16107564	.	+	.	Phchi.S1G246100
Phchi.S1	AUGUSTUS	transcript	16103050	16107564	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	start_codon	16103050	16103052	.	+	0	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16103050	16103128	0.8	+	0	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16103050	16103128	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16103129	16103226	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16103227	16103543	1	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16103227	16103543	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16103544	16103622	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16103623	16103718	0.64	+	0	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16103623	16103718	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16103719	16104024	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16104025	16104251	0.73	+	0	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16104025	16104251	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16104252	16104338	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16104339	16104562	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16104339	16104562	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16104563	16104671	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16104672	16104798	1	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16104672	16104798	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16104799	16104903	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16104904	16104978	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16104904	16104978	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16104979	16105070	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16105071	16105142	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16105071	16105142	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16105143	16105260	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16105261	16105323	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16105261	16105323	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16105324	16105473	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16105474	16105539	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16105474	16105539	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16105540	16105630	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16105631	16105860	0.96	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16105631	16105860	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16105861	16105997	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16105998	16106036	1	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16105998	16106036	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16106037	16106155	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16106156	16106224	0.73	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16106156	16106224	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16106225	16106319	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16106320	16106445	1	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16106320	16106445	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16106446	16106540	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16106541	16106606	1	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16106541	16106606	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16106607	16106686	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16106687	16106732	1	+	2	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16106687	16106732	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16106733	16106815	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16106816	16106962	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16106816	16106962	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16106963	16107047	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16107048	16107186	1	+	1	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16107048	16107186	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	intron	16107187	16107276	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	CDS	16107277	16107564	0.99	+	0	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	exon	16107277	16107564	.	+	.	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
Phchi.S1	AUGUSTUS	stop_codon	16107565	16107567	.	+	0	transcript_id "Phchi.S1G246100.t1"; gene_id "Phchi.S1G246100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16013.t1 is derived from g9769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C120	AUGUSTUS	gene	18552	18920	.	-	.	Phchi.C120G000200
Phchi.C120	AUGUSTUS	transcript	18552	18920	.	-	.	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	stop_codon	18549	18551	.	-	0	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	CDS	18552	18755	1	-	0	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	exon	18552	18755	.	-	.	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	intron	18756	18842	.	-	.	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	CDS	18843	18920	1	-	0	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	exon	18843	18920	.	-	.	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
Phchi.C120	AUGUSTUS	start_codon	18918	18920	.	-	0	transcript_id "Phchi.C120G000200.t1"; gene_id "Phchi.C120G000200"
# This transcript jg528.t2 is derived from g10310.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg529.t1 is derived from g10311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3802491	3804755	.	+	.	Phchi.S6G048800
Phchi.S6	AUGUSTUS	transcript	3802491	3804755	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	start_codon	3802491	3802493	.	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3802491	3802505	0.92	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3802491	3802505	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3802506	3802647	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3802648	3802710	1	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3802648	3802710	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3802711	3802897	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3802898	3802947	1	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3802898	3802947	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3802948	3803059	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3803060	3803135	1	+	1	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3803060	3803135	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3803136	3803222	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3803223	3803501	0.99	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3803223	3803501	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3803502	3803612	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3803613	3803700	0.99	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3803613	3803700	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3803701	3803818	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3803819	3803904	1	+	2	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3803819	3803904	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3803905	3804003	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3804004	3804111	0.98	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3804004	3804111	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3804112	3804231	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3804232	3804276	0.98	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3804232	3804276	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3804277	3804378	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3804379	3804467	1	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3804379	3804467	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3804468	3804560	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3804561	3804601	0.98	+	1	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3804561	3804601	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	intron	3804602	3804693	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	CDS	3804694	3804755	0.87	+	2	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	exon	3804694	3804755	.	+	.	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
Phchi.S6	AUGUSTUS	stop_codon	3804756	3804758	.	+	0	transcript_id "Phchi.S6G048800.t1"; gene_id "Phchi.S6G048800"
# This transcript jg4888.t2 is derived from g2058.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg4888.t3 is derived from g2058.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4889.t1 is derived from g2059.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13246439	13247923	.	-	.	Phchi.S1G204800
Phchi.S1	AUGUSTUS	transcript	13246439	13247923	.	-	.	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	stop_codon	13246436	13246438	.	-	0	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	CDS	13246439	13246653	0.91	-	2	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	exon	13246439	13246653	.	-	.	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	intron	13246654	13246740	.	-	.	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	CDS	13246741	13247923	0.97	-	0	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	exon	13246741	13247923	.	-	.	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
Phchi.S1	AUGUSTUS	start_codon	13247921	13247923	.	-	0	transcript_id "Phchi.S1G204800.t1"; gene_id "Phchi.S1G204800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7277.t1 is derived from g4449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28103691	28104595	.	+	.	Phchi.S1G443600
Phchi.S1	AUGUSTUS	transcript	28103691	28104595	.	+	.	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	start_codon	28103691	28103693	.	+	0	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	CDS	28103691	28103720	0.86	+	0	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	exon	28103691	28103720	.	+	.	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	intron	28103721	28103932	.	+	.	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	CDS	28103933	28104595	1	+	0	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	exon	28103933	28104595	.	+	.	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
Phchi.S1	AUGUSTUS	stop_codon	28104596	28104598	.	+	0	transcript_id "Phchi.S1G443600.t1"; gene_id "Phchi.S1G443600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3944.t1 is derived from g1113.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6584410	6586273	.	+	.	Phchi.S1G110300
Phchi.S1	AUGUSTUS	transcript	6584410	6586273	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	start_codon	6584410	6584412	.	+	0	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6584410	6584907	0.78	+	0	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6584410	6584907	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	intron	6584908	6584995	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6584996	6585114	0.98	+	0	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6584996	6585114	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	intron	6585115	6585227	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6585228	6585341	1	+	1	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6585228	6585341	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	intron	6585342	6585451	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6585452	6585547	1	+	1	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6585452	6585547	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	intron	6585548	6585637	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6585638	6585728	1	+	1	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6585638	6585728	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	intron	6585729	6585838	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6585839	6585907	1	+	0	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6585839	6585907	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	intron	6585908	6586030	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	CDS	6586031	6586273	1	+	0	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	exon	6586031	6586273	.	+	.	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
Phchi.S1	AUGUSTUS	stop_codon	6586274	6586276	.	+	0	transcript_id "Phchi.S1G110300.t1"; gene_id "Phchi.S1G110300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4438.t1 is derived from g1607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10502051	10506214	.	-	.	Phchi.S1G159700
Phchi.S1	AUGUSTUS	transcript	10502051	10506214	.	-	.	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	stop_codon	10502048	10502050	.	-	0	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	CDS	10502051	10502362	0.39	-	0	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	exon	10502051	10502362	.	-	.	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	intron	10502363	10502497	.	-	.	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	CDS	10502498	10506214	0.6	-	0	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	exon	10502498	10506214	.	-	.	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
Phchi.S1	AUGUSTUS	start_codon	10506212	10506214	.	-	0	transcript_id "Phchi.S1G159700.t1"; gene_id "Phchi.S1G159700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg366.t1 is derived from g10148.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2670491	2672784	.	+	.	Phchi.S6G032500
Phchi.S6	AUGUSTUS	transcript	2670491	2672784	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	start_codon	2670491	2670493	.	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2670491	2670638	0.49	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2670491	2670638	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2670639	2670729	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2670730	2670977	0.53	+	2	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2670730	2670977	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2670978	2671168	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2671169	2671345	1	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2671169	2671345	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2671346	2671510	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2671511	2671624	1	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2671511	2671624	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2671625	2671721	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2671722	2671901	1	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2671722	2671901	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2671902	2672042	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2672043	2672279	1	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2672043	2672279	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2672280	2672419	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2672420	2672518	1	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2672420	2672518	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	intron	2672519	2672622	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	CDS	2672623	2672784	0.99	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	exon	2672623	2672784	.	+	.	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
Phchi.S6	AUGUSTUS	stop_codon	2672785	2672787	.	+	0	transcript_id "Phchi.S6G032500.t1"; gene_id "Phchi.S6G032500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10746.t1 is derived from g14796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1901628	1902448	.	+	.	Phchi.S4G032800
Phchi.S4	AUGUSTUS	transcript	1901628	1902448	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	start_codon	1901628	1901630	.	+	0	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1901628	1901861	0.64	+	0	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1901628	1901861	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	intron	1901862	1902022	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1902023	1902097	1	+	0	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1902023	1902097	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	intron	1902098	1902296	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1902297	1902333	0.92	+	0	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1902297	1902333	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	intron	1902334	1902419	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1902420	1902448	0.77	+	2	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1902420	1902448	.	+	.	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	stop_codon	1902449	1902451	.	+	0	transcript_id "Phchi.S4G032800.t1"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	transcript	1901628	1902448	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	start_codon	1901628	1901630	.	+	0	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1901628	1901861	0.65	+	0	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1901628	1901861	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	intron	1901862	1902022	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1902023	1902061	1	+	0	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1902023	1902061	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	intron	1902062	1902296	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1902297	1902333	0.88	+	0	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1902297	1902333	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	intron	1902334	1902419	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	CDS	1902420	1902448	0.78	+	2	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	exon	1902420	1902448	.	+	.	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
Phchi.S4	AUGUSTUS	stop_codon	1902449	1902451	.	+	0	transcript_id "Phchi.S4G032800.t2"; gene_id "Phchi.S4G032800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10008.t1 is derived from g7184.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45022029	45023861	.	+	.	Phchi.S1G716700
Phchi.S1	AUGUSTUS	transcript	45022029	45023861	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	start_codon	45022029	45022031	.	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	CDS	45022029	45022346	0.59	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	exon	45022029	45022346	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	intron	45022347	45022599	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	CDS	45022600	45022773	0.91	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	exon	45022600	45022773	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	intron	45022774	45022859	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	CDS	45022860	45023003	0.93	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	exon	45022860	45023003	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	intron	45023004	45023091	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	CDS	45023092	45023220	1	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	exon	45023092	45023220	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	intron	45023221	45023314	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	CDS	45023315	45023584	0.5	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	exon	45023315	45023584	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	intron	45023585	45023699	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	CDS	45023700	45023861	0.98	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	exon	45023700	45023861	.	+	.	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
Phchi.S1	AUGUSTUS	stop_codon	45023862	45023864	.	+	0	transcript_id "Phchi.S1G716700.t1"; gene_id "Phchi.S1G716700"
# This transcript jg462.t2 is derived from g10244.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg463.t1 is derived from g10245.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3250958	3254896	.	-	.	Phchi.S6G042200
Phchi.S6	AUGUSTUS	transcript	3250958	3254896	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	stop_codon	3250955	3250957	.	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3250958	3251254	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3250958	3251254	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3251255	3251333	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3251334	3251410	0.94	-	2	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3251334	3251410	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3251411	3251512	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3251513	3251601	1	-	1	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3251513	3251601	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3251602	3251738	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3251739	3251793	0.98	-	2	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3251739	3251793	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3251794	3251846	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3251847	3251877	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3251847	3251877	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3251878	3251976	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3251977	3252027	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3251977	3252027	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3252028	3252117	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3252118	3252234	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3252118	3252234	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3252235	3252396	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3252397	3252438	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3252397	3252438	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3252439	3252563	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3252564	3252691	1	-	2	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3252564	3252691	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3252692	3252932	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3252933	3252993	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3252933	3252993	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3252994	3253128	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3253129	3253194	0.99	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3253129	3253194	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3253195	3253305	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3253306	3253413	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3253306	3253413	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3253414	3253516	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3253517	3253624	0.93	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3253517	3253624	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3253625	3253711	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3253712	3253777	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3253712	3253777	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3253778	3253868	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3253869	3254037	1	-	1	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3253869	3254037	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3254038	3254141	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3254142	3254364	1	-	2	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3254142	3254364	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3254365	3254461	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3254462	3254510	1	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3254462	3254510	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	intron	3254511	3254608	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	CDS	3254609	3254896	0.89	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	exon	3254609	3254896	.	-	.	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
Phchi.S6	AUGUSTUS	start_codon	3254894	3254896	.	-	0	transcript_id "Phchi.S6G042200.t1"; gene_id "Phchi.S6G042200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12965.t1 is derived from g11430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3358663	3359608	.	-	.	Phchi.S3G028400
Phchi.S3	AUGUSTUS	transcript	3358663	3359608	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	stop_codon	3358660	3358662	.	-	0	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	CDS	3358663	3358742	1	-	2	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	exon	3358663	3358742	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	intron	3358743	3358914	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	CDS	3358915	3358967	1	-	1	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	exon	3358915	3358967	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	intron	3358968	3359105	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	CDS	3359106	3359152	1	-	0	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	exon	3359106	3359152	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	intron	3359153	3359233	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	CDS	3359234	3359608	1	-	0	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	exon	3359234	3359608	.	-	.	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
Phchi.S3	AUGUSTUS	start_codon	3359606	3359608	.	-	0	transcript_id "Phchi.S3G028400.t1"; gene_id "Phchi.S3G028400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11508.t1 is derived from g15558.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6805269	6811875	.	-	.	Phchi.S4G109000
Phchi.S4	AUGUSTUS	transcript	6805269	6811875	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	stop_codon	6805266	6805268	.	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6805269	6805370	0.69	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6805269	6805370	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6805371	6805490	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6805491	6805536	1	-	1	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6805491	6805536	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6805537	6805709	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6805710	6805915	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6805710	6805915	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6805916	6806074	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6806075	6806257	0.98	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6806075	6806257	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6806258	6806367	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6806368	6806592	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6806368	6806592	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6806593	6806675	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6806676	6806798	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6806676	6806798	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6806799	6806891	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6806892	6806982	1	-	1	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6806892	6806982	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6806983	6807212	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6807213	6807299	0.77	-	1	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6807213	6807299	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6807300	6807448	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6807449	6807480	0.59	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6807449	6807480	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6807481	6807566	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6807567	6807661	0.81	-	2	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6807567	6807661	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6807662	6807785	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6807786	6807975	0.43	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6807786	6807975	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6807976	6808065	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6808066	6808302	0.42	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6808066	6808302	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6808303	6808423	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6808424	6808561	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6808424	6808561	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6808562	6808644	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6808645	6808743	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6808645	6808743	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6808744	6808835	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6808836	6808916	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6808836	6808916	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6808917	6809005	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6809006	6809107	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6809006	6809107	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6809108	6809187	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6809188	6809235	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6809188	6809235	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6809236	6809322	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6809323	6809682	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6809323	6809682	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6809683	6809773	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6809774	6809875	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6809774	6809875	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6809876	6809965	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6809966	6810090	1	-	2	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6809966	6810090	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6810091	6810239	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6810240	6810333	0.75	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6810240	6810333	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6810334	6810418	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6810419	6810478	0.99	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6810419	6810478	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6810479	6810644	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6810645	6810723	1	-	1	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6810645	6810723	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6810724	6810866	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6810867	6810982	1	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6810867	6810982	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6810983	6811095	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6811096	6811276	1	-	1	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6811096	6811276	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6811277	6811495	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6811496	6811566	0.98	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6811496	6811566	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6811567	6811649	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6811650	6811694	0.9	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6811650	6811694	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	intron	6811695	6811821	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	CDS	6811822	6811875	0.88	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	exon	6811822	6811875	.	-	.	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
Phchi.S4	AUGUSTUS	start_codon	6811873	6811875	.	-	0	transcript_id "Phchi.S4G109000.t1"; gene_id "Phchi.S4G109000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9915.t1 is derived from g7091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44425786	44428343	.	-	.	Phchi.S1G707400
Phchi.S1	AUGUSTUS	transcript	44425786	44428343	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	stop_codon	44425783	44425785	.	-	0	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44425786	44425876	0.99	-	1	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44425786	44425876	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44425877	44425954	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44425955	44426091	1	-	0	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44425955	44426091	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44426092	44426223	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44426224	44426302	0.5	-	1	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44426224	44426302	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44426303	44426491	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44426492	44426613	0.94	-	0	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44426492	44426613	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44426614	44426913	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44426914	44427055	1	-	1	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44426914	44427055	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44427056	44427196	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44427197	44427350	0.8	-	2	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44427197	44427350	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44427351	44427436	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44427437	44427557	1	-	0	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44427437	44427557	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	intron	44427558	44427650	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	CDS	44427651	44428343	0.59	-	0	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	exon	44427651	44428343	.	-	.	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
Phchi.S1	AUGUSTUS	start_codon	44428341	44428343	.	-	0	transcript_id "Phchi.S1G707400.t1"; gene_id "Phchi.S1G707400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15784.t1 is derived from g14254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21328750	21331062	.	+	.	Phchi.S3G310300
Phchi.S3	AUGUSTUS	transcript	21328750	21331062	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	start_codon	21328750	21328752	.	+	0	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21328750	21328941	1	+	0	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21328750	21328941	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21328942	21329279	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21329280	21329427	1	+	0	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21329280	21329427	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21329428	21329520	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21329521	21329564	0.97	+	2	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21329521	21329564	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21329565	21329775	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21329776	21329900	1	+	0	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21329776	21329900	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21329901	21329987	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21329988	21330068	1	+	1	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21329988	21330068	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21330069	21330161	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21330162	21330354	0.99	+	1	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21330162	21330354	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21330355	21330460	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21330461	21330731	0.62	+	0	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21330461	21330731	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	intron	21330732	21330838	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	CDS	21330839	21331062	0.99	+	2	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	exon	21330839	21331062	.	+	.	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
Phchi.S3	AUGUSTUS	stop_codon	21331063	21331065	.	+	0	transcript_id "Phchi.S3G310300.t1"; gene_id "Phchi.S3G310300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9526.t1 is derived from g6702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42318279	42319542	.	-	.	Phchi.S1G668500
Phchi.S1	AUGUSTUS	transcript	42318279	42319542	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	stop_codon	42318276	42318278	.	-	0	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	CDS	42318279	42318419	1	-	0	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	exon	42318279	42318419	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	intron	42318420	42318539	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	CDS	42318540	42318603	1	-	1	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	exon	42318540	42318603	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	intron	42318604	42318734	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	CDS	42318735	42318888	1	-	2	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	exon	42318735	42318888	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	intron	42318889	42318995	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	CDS	42318996	42319167	1	-	0	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	exon	42318996	42319167	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	intron	42319168	42319368	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	CDS	42319369	42319542	0.42	-	0	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	exon	42319369	42319542	.	-	.	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
Phchi.S1	AUGUSTUS	start_codon	42319540	42319542	.	-	0	transcript_id "Phchi.S1G668500.t1"; gene_id "Phchi.S1G668500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7957.t1 is derived from g5132.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32092957	32093525	.	+	.	Phchi.S1G511600
Phchi.S1	AUGUSTUS	transcript	32092957	32093525	.	+	.	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	start_codon	32092957	32092959	.	+	0	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	CDS	32092957	32093052	0.83	+	0	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	exon	32092957	32093052	.	+	.	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	intron	32093053	32093189	.	+	.	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	CDS	32093190	32093525	0.97	+	0	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	exon	32093190	32093525	.	+	.	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
Phchi.S1	AUGUSTUS	stop_codon	32093526	32093528	.	+	0	transcript_id "Phchi.S1G511600.t1"; gene_id "Phchi.S1G511600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15467.t1 is derived from g13935.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19339685	19340892	.	-	.	Phchi.S3G278600
Phchi.S3	AUGUSTUS	transcript	19339685	19340892	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	stop_codon	19339682	19339684	.	-	0	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19339685	19339843	1	-	0	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19339685	19339843	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	intron	19339844	19339958	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19339959	19340043	1	-	1	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19339959	19340043	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	intron	19340044	19340161	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19340162	19340410	1	-	1	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19340162	19340410	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	intron	19340411	19340500	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19340501	19340892	0.85	-	0	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19340501	19340892	.	-	.	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	start_codon	19340890	19340892	.	-	0	transcript_id "Phchi.S3G278600.t1"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	transcript	19339685	19340509	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	stop_codon	19339682	19339684	.	-	0	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19339685	19339843	1	-	0	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19339685	19339843	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	intron	19339844	19339958	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19339959	19340043	1	-	1	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19339959	19340043	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	intron	19340044	19340161	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19340162	19340415	0.81	-	0	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19340162	19340415	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	intron	19340416	19340500	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	CDS	19340501	19340509	0.72	-	0	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	exon	19340501	19340509	.	-	.	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
Phchi.S3	AUGUSTUS	start_codon	19340507	19340509	.	-	0	transcript_id "Phchi.S3G278600.t2"; gene_id "Phchi.S3G278600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14687.t1 is derived from g13155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14170271	14175179	.	-	.	Phchi.S3G200600
Phchi.S3	AUGUSTUS	transcript	14170271	14175179	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	stop_codon	14170268	14170270	.	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14170271	14170363	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14170271	14170363	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14170364	14170475	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14170476	14170577	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14170476	14170577	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14170578	14170698	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14170699	14170821	0.78	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14170699	14170821	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14170822	14170899	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14170900	14171043	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14170900	14171043	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14171044	14171129	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14171130	14171174	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14171130	14171174	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14171175	14171262	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14171263	14171373	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14171263	14171373	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14171374	14171522	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14171523	14171692	1	-	2	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14171523	14171692	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14171693	14171801	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14171802	14171871	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14171802	14171871	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14171872	14172012	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14172013	14172314	1	-	2	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14172013	14172314	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14172315	14172516	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14172517	14172660	1	-	2	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14172517	14172660	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14172661	14172942	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14172943	14173007	1	-	1	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14172943	14173007	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14173008	14173141	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14173142	14173237	1	-	1	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14173142	14173237	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14173238	14173385	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14173386	14173489	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14173386	14173489	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14173490	14173627	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14173628	14173674	1	-	2	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14173628	14173674	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14173675	14173795	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14173796	14173888	0.95	-	2	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14173796	14173888	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14173889	14173999	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14174000	14174046	0.89	-	1	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14174000	14174046	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14174047	14174121	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14174122	14174183	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14174122	14174183	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14174184	14174273	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14174274	14174339	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14174274	14174339	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14174340	14174421	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14174422	14174475	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14174422	14174475	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14174476	14174633	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14174634	14174708	1	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14174634	14174708	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	intron	14174709	14175032	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	CDS	14175033	14175179	0.95	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	exon	14175033	14175179	.	-	.	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
Phchi.S3	AUGUSTUS	start_codon	14175177	14175179	.	-	0	transcript_id "Phchi.S3G200600.t1"; gene_id "Phchi.S3G200600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11577.t1 is derived from g15628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7161524	7163134	.	-	.	Phchi.S4G115900
Phchi.S4	AUGUSTUS	transcript	7161524	7163134	.	-	.	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	stop_codon	7161521	7161523	.	-	0	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	CDS	7161524	7161755	1	-	1	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	exon	7161524	7161755	.	-	.	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	intron	7161756	7161902	.	-	.	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	CDS	7161903	7163134	0.35	-	0	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	exon	7161903	7163134	.	-	.	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
Phchi.S4	AUGUSTUS	start_codon	7163132	7163134	.	-	0	transcript_id "Phchi.S4G115900.t1"; gene_id "Phchi.S4G115900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13026.t1 is derived from g11491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3671666	3673960	.	+	.	Phchi.S3G034500
Phchi.S3	AUGUSTUS	transcript	3671666	3673960	.	+	.	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	start_codon	3671666	3671668	.	+	0	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	CDS	3671666	3672508	0.56	+	0	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	exon	3671666	3672508	.	+	.	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	intron	3672509	3672594	.	+	.	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	CDS	3672595	3672879	0.86	+	0	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	exon	3672595	3672879	.	+	.	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	intron	3672880	3673030	.	+	.	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	CDS	3673031	3673960	0.55	+	0	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	exon	3673031	3673960	.	+	.	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
Phchi.S3	AUGUSTUS	stop_codon	3673961	3673963	.	+	0	transcript_id "Phchi.S3G034500.t1"; gene_id "Phchi.S3G034500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12923.t1 is derived from g11388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3175799	3179402	.	+	.	Phchi.S3G024200
Phchi.S3	AUGUSTUS	transcript	3175799	3179402	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	start_codon	3175799	3175801	.	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3175799	3175945	0.99	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3175799	3175945	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3175946	3176099	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176100	3176147	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176100	3176147	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176148	3176245	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176246	3176394	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176246	3176394	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176395	3176475	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176476	3176524	1	+	1	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176476	3176524	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176525	3176786	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176787	3176843	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176787	3176843	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176844	3176916	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176917	3177093	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176917	3177093	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177094	3177196	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3177197	3177334	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3177197	3177334	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177335	3177513	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3177514	3177575	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3177514	3177575	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177576	3177774	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3177775	3177877	1	+	1	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3177775	3177877	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177878	3178050	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178051	3178162	0.97	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178051	3178162	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178163	3178265	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178266	3178342	0.93	+	2	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178266	3178342	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178343	3178451	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178452	3178589	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178452	3178589	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178590	3178672	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178673	3178837	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178673	3178837	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178838	3178915	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178916	3179029	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178916	3179029	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3179030	3179109	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3179110	3179203	1	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3179110	3179203	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3179204	3179283	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3179284	3179402	1	+	2	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3179284	3179402	.	+	.	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	stop_codon	3179403	3179405	.	+	0	transcript_id "Phchi.S3G024200.t1"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	transcript	3175799	3179402	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	start_codon	3175799	3175801	.	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3175799	3175933	0.55	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3175799	3175933	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3175934	3176099	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176100	3176147	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176100	3176147	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176148	3176245	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176246	3176394	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176246	3176394	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176395	3176475	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176476	3176524	0.99	+	1	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176476	3176524	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176525	3176655	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176656	3176697	0.98	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176656	3176697	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176698	3176786	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176787	3176843	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176787	3176843	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3176844	3176916	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3176917	3177093	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3176917	3177093	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177094	3177196	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3177197	3177334	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3177197	3177334	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177335	3177513	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3177514	3177575	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3177514	3177575	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177576	3177774	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3177775	3177877	1	+	1	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3177775	3177877	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3177878	3178050	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178051	3178162	0.97	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178051	3178162	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178163	3178265	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178266	3178342	0.85	+	2	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178266	3178342	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178343	3178451	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178452	3178589	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178452	3178589	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178590	3178672	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178673	3178837	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178673	3178837	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3178838	3178915	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3178916	3179029	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3178916	3179029	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3179030	3179109	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3179110	3179203	1	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3179110	3179203	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	intron	3179204	3179283	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	CDS	3179284	3179402	1	+	2	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	exon	3179284	3179402	.	+	.	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
Phchi.S3	AUGUSTUS	stop_codon	3179403	3179405	.	+	0	transcript_id "Phchi.S3G024200.t2"; gene_id "Phchi.S3G024200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7025.t1 is derived from g4197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26476396	26478024	.	-	.	Phchi.S1G418400
Phchi.S1	AUGUSTUS	transcript	26476396	26478024	.	-	.	transcript_id "Phchi.S1G418400.t1"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	stop_codon	26476393	26476395	.	-	0	transcript_id "Phchi.S1G418400.t1"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	CDS	26476396	26478024	1	-	0	transcript_id "Phchi.S1G418400.t1"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	exon	26476396	26478024	.	-	.	transcript_id "Phchi.S1G418400.t1"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	start_codon	26478022	26478024	.	-	0	transcript_id "Phchi.S1G418400.t1"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	transcript	26476396	26477844	.	-	.	transcript_id "Phchi.S1G418400.t2"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	stop_codon	26476393	26476395	.	-	0	transcript_id "Phchi.S1G418400.t2"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	CDS	26476396	26477844	0.53	-	0	transcript_id "Phchi.S1G418400.t2"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	exon	26476396	26477844	.	-	.	transcript_id "Phchi.S1G418400.t2"; gene_id "Phchi.S1G418400"
Phchi.S1	AUGUSTUS	start_codon	26477842	26477844	.	-	0	transcript_id "Phchi.S1G418400.t2"; gene_id "Phchi.S1G418400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12278.t1 is derived from g7954.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8080674	8081173	.	-	.	Phchi.S2G035800
Phchi.S2	AUGUSTUS	transcript	8080674	8081173	.	-	.	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	stop_codon	8080671	8080673	.	-	0	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	CDS	8080674	8080737	1	-	1	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	exon	8080674	8080737	.	-	.	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	intron	8080738	8080810	.	-	.	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	CDS	8080811	8080853	1	-	2	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	exon	8080811	8080853	.	-	.	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	intron	8080854	8080998	.	-	.	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	CDS	8080999	8081173	0.51	-	0	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	exon	8080999	8081173	.	-	.	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
Phchi.S2	AUGUSTUS	start_codon	8081171	8081173	.	-	0	transcript_id "Phchi.S2G035800.t1"; gene_id "Phchi.S2G035800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11640.t1 is derived from g15691.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7422303	7422854	.	-	.	Phchi.S4G122200
Phchi.S4	AUGUSTUS	transcript	7422303	7422854	.	-	.	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	stop_codon	7422300	7422302	.	-	0	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	CDS	7422303	7422382	0.8	-	2	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	exon	7422303	7422382	.	-	.	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	intron	7422383	7422658	.	-	.	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	CDS	7422659	7422854	0.8	-	0	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	exon	7422659	7422854	.	-	.	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
Phchi.S4	AUGUSTUS	start_codon	7422852	7422854	.	-	0	transcript_id "Phchi.S4G122200.t1"; gene_id "Phchi.S4G122200"
# This transcript jg6425.t2 is derived from g3597.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6426.t1 is derived from g3598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22986583	22987225	.	-	.	Phchi.S1G358500
Phchi.S1	AUGUSTUS	transcript	22986583	22987225	.	-	.	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	stop_codon	22986580	22986582	.	-	0	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	CDS	22986583	22986717	0.43	-	0	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	exon	22986583	22986717	.	-	.	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	intron	22986718	22986895	.	-	.	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	CDS	22986896	22987225	0.97	-	0	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	exon	22986896	22987225	.	-	.	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
Phchi.S1	AUGUSTUS	start_codon	22987223	22987225	.	-	0	transcript_id "Phchi.S1G358500.t1"; gene_id "Phchi.S1G358500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5311.t1 is derived from g2481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16230019	16230749	.	-	.	Phchi.S1G247000
Phchi.S1	AUGUSTUS	transcript	16230019	16230749	.	-	.	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	stop_codon	16230016	16230018	.	-	0	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	CDS	16230019	16230081	1	-	0	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	exon	16230019	16230081	.	-	.	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	intron	16230082	16230334	.	-	.	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	CDS	16230335	16230481	1	-	0	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	exon	16230335	16230481	.	-	.	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	intron	16230482	16230623	.	-	.	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	CDS	16230624	16230749	1	-	0	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	exon	16230624	16230749	.	-	.	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
Phchi.S1	AUGUSTUS	start_codon	16230747	16230749	.	-	0	transcript_id "Phchi.S1G247000.t1"; gene_id "Phchi.S1G247000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3326.t1 is derived from g495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2924034	2931923	.	-	.	Phchi.S1G048500
Phchi.S1	AUGUSTUS	transcript	2924034	2931923	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	stop_codon	2924031	2924033	.	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2924034	2924434	0.8	-	2	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2924034	2924434	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2924435	2924537	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2924538	2924655	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2924538	2924655	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2924656	2924722	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2924723	2924827	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2924723	2924827	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2924828	2924907	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2924908	2925070	1	-	1	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2924908	2925070	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2925071	2925194	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2925195	2925373	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2925195	2925373	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2925374	2925445	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2925446	2925514	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2925446	2925514	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2925515	2925622	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2925623	2925829	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2925623	2925829	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2925830	2925924	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2925925	2926017	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2925925	2926017	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2926018	2926103	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2926104	2926223	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2926104	2926223	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2926224	2926305	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2926306	2926387	1	-	1	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2926306	2926387	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2926388	2926474	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2926475	2926554	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2926475	2926554	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2926555	2926653	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2926654	2926744	1	-	1	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2926654	2926744	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2926745	2926873	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2926874	2926995	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2926874	2926995	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2926996	2927087	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2927088	2927291	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2927088	2927291	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2927292	2927379	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2927380	2927454	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2927380	2927454	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2927455	2927562	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2927563	2927653	0.99	-	1	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2927563	2927653	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2927654	2927785	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2927786	2927866	1	-	1	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2927786	2927866	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2927867	2927980	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2927981	2928066	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2927981	2928066	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2928067	2928152	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2928153	2928206	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2928153	2928206	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2928207	2928339	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2928340	2928518	1	-	2	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2928340	2928518	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2928519	2928628	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2928629	2928731	0.98	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2928629	2928731	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2928732	2928853	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2928854	2928933	1	-	2	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2928854	2928933	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2928934	2929033	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2929034	2929127	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2929034	2929127	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2929128	2929229	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2929230	2929364	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2929230	2929364	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2929365	2929471	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2929472	2929546	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2929472	2929546	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2929547	2929746	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2929747	2929848	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2929747	2929848	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2929849	2929918	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2929919	2929993	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2929919	2929993	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2929994	2930095	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2930096	2930184	0.99	-	2	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2930096	2930184	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2930185	2930285	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2930286	2930442	0.99	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2930286	2930442	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2930443	2930632	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2930633	2930707	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2930633	2930707	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2930708	2930782	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2930783	2930933	1	-	1	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2930783	2930933	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2930934	2931031	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2931032	2931111	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2931032	2931111	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2931112	2931240	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2931241	2931308	1	-	2	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2931241	2931308	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2931309	2931448	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2931449	2931515	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2931449	2931515	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2931516	2931595	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2931596	2931697	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2931596	2931697	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	intron	2931698	2931845	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	CDS	2931846	2931923	1	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	exon	2931846	2931923	.	-	.	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
Phchi.S1	AUGUSTUS	start_codon	2931921	2931923	.	-	0	transcript_id "Phchi.S1G048500.t1"; gene_id "Phchi.S1G048500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13828.t1 is derived from g12295.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9090081	9093332	.	+	.	Phchi.S3G114700
Phchi.S3	AUGUSTUS	transcript	9090081	9093332	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	start_codon	9090081	9090083	.	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9090081	9090247	0.96	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9090081	9090247	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9090248	9090335	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9090336	9090490	1	+	1	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9090336	9090490	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9090491	9090718	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9090719	9090801	1	+	2	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9090719	9090801	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9090802	9090884	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9090885	9090977	1	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9090885	9090977	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9090978	9091105	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9091106	9091267	1	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9091106	9091267	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9091268	9091439	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9091440	9091780	1	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9091440	9091780	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9091781	9091872	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9091873	9091985	1	+	1	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9091873	9091985	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9091986	9092079	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9092080	9092161	1	+	2	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9092080	9092161	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9092162	9092293	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9092294	9092525	1	+	1	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9092294	9092525	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9092526	9092620	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9092621	9092718	1	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9092621	9092718	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9092719	9092817	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9092818	9092935	1	+	1	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9092818	9092935	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9092936	9093007	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9093008	9093139	1	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9093008	9093139	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	intron	9093140	9093215	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	CDS	9093216	9093332	1	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	exon	9093216	9093332	.	+	.	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
Phchi.S3	AUGUSTUS	stop_codon	9093333	9093335	.	+	0	transcript_id "Phchi.S3G114700.t1"; gene_id "Phchi.S3G114700"
# This transcript jg11132.t2 is derived from g15182.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11133.t1 is derived from g15183.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4340318	4346185	.	+	.	Phchi.S4G071500
Phchi.S4	AUGUSTUS	transcript	4340318	4346185	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	start_codon	4340318	4340320	.	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4340318	4340704	0.51	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4340318	4340704	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4340705	4341522	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4341523	4341664	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4341523	4341664	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4341665	4341757	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4341758	4341813	1	+	2	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4341758	4341813	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4341814	4341927	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4341928	4342185	0.95	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4341928	4342185	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4342186	4342285	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4342286	4342482	0.98	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4342286	4342482	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4342483	4342583	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4342584	4342662	0.95	+	1	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4342584	4342662	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4342663	4342765	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4342766	4342804	0.88	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4342766	4342804	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4342805	4342911	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4342912	4343031	0.99	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4342912	4343031	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4343032	4343122	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4343123	4343224	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4343123	4343224	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4343225	4343312	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4343313	4343396	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4343313	4343396	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4343397	4343487	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4343488	4343730	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4343488	4343730	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4343731	4343982	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4343983	4344108	0.99	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4343983	4344108	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4344109	4344219	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4344220	4344294	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4344220	4344294	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4344295	4344422	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4344423	4344494	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4344423	4344494	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4344495	4344579	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4344580	4344702	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4344580	4344702	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4344703	4344883	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4344884	4344981	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4344884	4344981	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4344982	4345087	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4345088	4345247	1	+	1	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4345088	4345247	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4345248	4345341	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4345342	4345440	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4345342	4345440	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4345441	4345521	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4345522	4345719	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4345522	4345719	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4345720	4345822	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4345823	4345916	1	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4345823	4345916	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	intron	4345917	4346000	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	CDS	4346001	4346185	0.89	+	2	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	exon	4346001	4346185	.	+	.	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
Phchi.S4	AUGUSTUS	stop_codon	4346186	4346188	.	+	0	transcript_id "Phchi.S4G071500.t1"; gene_id "Phchi.S4G071500"
# This transcript jg5658.t2 is derived from g2828.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg5658.t3 is derived from g2828.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5659.t1 is derived from g2829.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18169732	18172463	.	-	.	Phchi.S1G281800
Phchi.S1	AUGUSTUS	transcript	18169732	18172463	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	stop_codon	18169729	18169731	.	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18169732	18169740	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18169732	18169740	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18169741	18169968	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18169969	18170028	0.98	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18169969	18170028	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18170029	18170125	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18170126	18170185	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18170126	18170185	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18170186	18170275	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18170276	18170425	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18170276	18170425	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18170426	18170514	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18170515	18170852	0.98	-	2	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18170515	18170852	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18170853	18171034	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18171035	18171137	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18171035	18171137	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18171138	18171227	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18171228	18171497	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18171228	18171497	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18171498	18171582	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18171583	18171771	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18171583	18171771	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18171772	18171894	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18171895	18172011	1	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18171895	18172011	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18172012	18172179	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18172180	18172303	0.79	-	1	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18172180	18172303	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	intron	18172304	18172443	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	CDS	18172444	18172463	0.76	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	exon	18172444	18172463	.	-	.	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
Phchi.S1	AUGUSTUS	start_codon	18172461	18172463	.	-	0	transcript_id "Phchi.S1G281800.t1"; gene_id "Phchi.S1G281800"
# This transcript jg10482.t2 is derived from g14531.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10483.t1 is derived from g14532.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	647841	648515	.	-	.	Phchi.S4G006500
Phchi.S4	AUGUSTUS	transcript	647841	648515	.	-	.	transcript_id "Phchi.S4G006500.t1"; gene_id "Phchi.S4G006500"
Phchi.S4	AUGUSTUS	stop_codon	647838	647840	.	-	0	transcript_id "Phchi.S4G006500.t1"; gene_id "Phchi.S4G006500"
Phchi.S4	AUGUSTUS	CDS	647841	648515	0.92	-	0	transcript_id "Phchi.S4G006500.t1"; gene_id "Phchi.S4G006500"
Phchi.S4	AUGUSTUS	exon	647841	648515	.	-	.	transcript_id "Phchi.S4G006500.t1"; gene_id "Phchi.S4G006500"
Phchi.S4	AUGUSTUS	start_codon	648513	648515	.	-	0	transcript_id "Phchi.S4G006500.t1"; gene_id "Phchi.S4G006500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3089.t1 is derived from g258.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1676727	1678859	.	-	.	Phchi.S1G024800
Phchi.S1	AUGUSTUS	transcript	1676727	1677683	.	-	.	transcript_id "Phchi.S1G024800.t1"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	stop_codon	1676724	1676726	.	-	0	transcript_id "Phchi.S1G024800.t1"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	CDS	1676727	1677683	0.77	-	0	transcript_id "Phchi.S1G024800.t1"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	exon	1676727	1677683	.	-	.	transcript_id "Phchi.S1G024800.t1"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	start_codon	1677681	1677683	.	-	0	transcript_id "Phchi.S1G024800.t1"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	transcript	1676727	1678052	.	-	.	transcript_id "Phchi.S1G024800.t2"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	stop_codon	1676724	1676726	.	-	0	transcript_id "Phchi.S1G024800.t2"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	CDS	1676727	1678052	0.75	-	0	transcript_id "Phchi.S1G024800.t2"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	exon	1676727	1678052	.	-	.	transcript_id "Phchi.S1G024800.t2"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	start_codon	1678050	1678052	.	-	0	transcript_id "Phchi.S1G024800.t2"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	transcript	1676727	1678859	.	-	.	transcript_id "Phchi.S1G024800.t3"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	stop_codon	1676724	1676726	.	-	0	transcript_id "Phchi.S1G024800.t3"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	CDS	1676727	1678859	0.7	-	0	transcript_id "Phchi.S1G024800.t3"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	exon	1676727	1678859	.	-	.	transcript_id "Phchi.S1G024800.t3"; gene_id "Phchi.S1G024800"
Phchi.S1	AUGUSTUS	start_codon	1678857	1678859	.	-	0	transcript_id "Phchi.S1G024800.t3"; gene_id "Phchi.S1G024800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9817.t1 is derived from g6993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43926632	43928523	.	-	.	Phchi.S1G697600
Phchi.S1	AUGUSTUS	transcript	43926632	43928523	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	stop_codon	43926629	43926631	.	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43926632	43926684	0.97	-	2	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43926632	43926684	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43926685	43926780	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43926781	43926795	0.97	-	2	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43926781	43926795	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43926796	43926897	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43926898	43927068	0.97	-	2	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43926898	43927068	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43927069	43927169	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43927170	43927206	1	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43927170	43927206	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43927207	43927300	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43927301	43927357	1	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43927301	43927357	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43927358	43927442	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43927443	43927601	1	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43927443	43927601	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43927602	43927682	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43927683	43927784	1	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43927683	43927784	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43927785	43927983	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43927984	43928105	1	-	2	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43927984	43928105	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43928106	43928213	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43928214	43928328	0.99	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43928214	43928328	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	intron	43928329	43928412	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	CDS	43928413	43928523	0.99	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	exon	43928413	43928523	.	-	.	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
Phchi.S1	AUGUSTUS	start_codon	43928521	43928523	.	-	0	transcript_id "Phchi.S1G697600.t1"; gene_id "Phchi.S1G697600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9527.t1 is derived from g6703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42320944	42322644	.	-	.	Phchi.S1G668600
Phchi.S1	AUGUSTUS	transcript	42320944	42322644	.	-	.	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	stop_codon	42320941	42320943	.	-	0	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	CDS	42320944	42322021	1	-	1	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	exon	42320944	42322021	.	-	.	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	intron	42322022	42322108	.	-	.	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	CDS	42322109	42322374	1	-	0	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	exon	42322109	42322374	.	-	.	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	intron	42322375	42322500	.	-	.	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	CDS	42322501	42322644	1	-	0	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	exon	42322501	42322644	.	-	.	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
Phchi.S1	AUGUSTUS	start_codon	42322642	42322644	.	-	0	transcript_id "Phchi.S1G668600.t1"; gene_id "Phchi.S1G668600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12066.t1 is derived from g7741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1778234	1779648	.	-	.	Phchi.S2G014600
Phchi.S2	AUGUSTUS	transcript	1778234	1779648	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	stop_codon	1778231	1778233	.	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1778234	1778302	0.95	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1778234	1778302	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	intron	1778303	1778450	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1778451	1778537	1	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1778451	1778537	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	intron	1778538	1778807	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1778808	1778843	1	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1778808	1778843	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	intron	1778844	1778965	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1778966	1779074	0.99	-	1	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1778966	1779074	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	intron	1779075	1779181	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1779182	1779273	1	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1779182	1779273	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	intron	1779274	1779370	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1779371	1779457	1	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1779371	1779457	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	intron	1779458	1779645	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	CDS	1779646	1779648	0.99	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	exon	1779646	1779648	.	-	.	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
Phchi.S2	AUGUSTUS	start_codon	1779646	1779648	.	-	0	transcript_id "Phchi.S2G014600.t1"; gene_id "Phchi.S2G014600"
# This transcript jg11509.t2 is derived from g15559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11509.t3 is derived from g15559.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11509.t4 is derived from g15559.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11510.t1 is derived from g15560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6819398	6826069	.	-	.	Phchi.S4G109200
Phchi.S4	AUGUSTUS	transcript	6819398	6826069	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	stop_codon	6819395	6819397	.	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819398	6819434	0.76	-	1	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819398	6819434	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819435	6819641	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819642	6819736	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819642	6819736	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819737	6819852	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819853	6819915	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819853	6819915	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819916	6820009	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820010	6820221	1	-	2	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820010	6820221	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820222	6820310	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820311	6820653	0.52	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820311	6820653	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820654	6820812	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820813	6820918	1	-	1	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820813	6820918	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820919	6821015	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821016	6821086	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821016	6821086	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821087	6821175	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821176	6821299	1	-	1	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821176	6821299	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821300	6821421	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821422	6821549	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821422	6821549	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821550	6821625	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821626	6821966	0.8	-	2	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821626	6821966	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821967	6822054	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822055	6822373	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822055	6822373	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822374	6822520	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822521	6822648	1	-	2	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822521	6822648	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822649	6822752	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822753	6822831	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822753	6822831	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822832	6822967	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822968	6823060	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822968	6823060	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823061	6823150	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823151	6823348	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823151	6823348	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823349	6823438	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823439	6823762	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823439	6823762	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823763	6823974	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823975	6823992	0.8	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823975	6823992	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823993	6824099	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824100	6824409	0.8	-	1	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824100	6824409	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824410	6824528	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824529	6824607	1	-	2	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824529	6824607	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824608	6824738	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824739	6824842	1	-	1	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824739	6824842	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824843	6825027	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825028	6825119	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825028	6825119	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825120	6825282	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825283	6825336	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825283	6825336	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825337	6825510	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825511	6825595	1	-	1	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825511	6825595	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825596	6825691	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825692	6825849	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825692	6825849	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825850	6826045	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6826046	6826069	1	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6826046	6826069	.	-	.	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	start_codon	6826067	6826069	.	-	0	transcript_id "Phchi.S4G109200.t1"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	transcript	6819398	6826069	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	stop_codon	6819395	6819397	.	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819398	6819437	0.99	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819398	6819437	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819438	6819641	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819642	6819736	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819642	6819736	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819737	6819852	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819853	6819915	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819853	6819915	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819916	6820009	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820010	6820221	1	-	2	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820010	6820221	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820222	6820310	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820311	6820653	0.57	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820311	6820653	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820654	6820812	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820813	6820918	1	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820813	6820918	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820919	6821015	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821016	6821086	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821016	6821086	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821087	6821175	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821176	6821299	1	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821176	6821299	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821300	6821421	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821422	6821549	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821422	6821549	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821550	6821625	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821626	6821966	0.79	-	2	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821626	6821966	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821967	6822054	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822055	6822373	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822055	6822373	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822374	6822520	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822521	6822648	1	-	2	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822521	6822648	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822649	6822752	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822753	6822831	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822753	6822831	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822832	6822967	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822968	6823060	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822968	6823060	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823061	6823150	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823151	6823348	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823151	6823348	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823349	6823438	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823439	6823623	0.29	-	2	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823439	6823623	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823624	6823703	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823704	6823762	0.38	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823704	6823762	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823763	6823966	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823967	6823992	0.88	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823967	6823992	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823993	6824099	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824100	6824409	0.94	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824100	6824409	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824410	6824528	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824529	6824607	1	-	2	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824529	6824607	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824608	6824738	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824739	6824842	1	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824739	6824842	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824843	6825027	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825028	6825119	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825028	6825119	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825120	6825282	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825283	6825336	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825283	6825336	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825337	6825510	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825511	6825595	1	-	1	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825511	6825595	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825596	6825691	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825692	6825849	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825692	6825849	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825850	6826045	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6826046	6826069	1	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6826046	6826069	.	-	.	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	start_codon	6826067	6826069	.	-	0	transcript_id "Phchi.S4G109200.t2"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	transcript	6819398	6826069	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	stop_codon	6819395	6819397	.	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819398	6819434	0.79	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819398	6819434	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819435	6819641	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819642	6819736	0.99	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819642	6819736	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819737	6819852	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6819853	6819915	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6819853	6819915	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6819916	6820009	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820010	6820221	1	-	2	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820010	6820221	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820222	6820310	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820311	6820653	0.55	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820311	6820653	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820654	6820812	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6820813	6820918	1	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6820813	6820918	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6820919	6821015	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821016	6821086	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821016	6821086	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821087	6821175	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821176	6821299	1	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821176	6821299	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821300	6821421	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821422	6821549	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821422	6821549	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821550	6821625	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6821626	6821966	0.76	-	2	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6821626	6821966	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6821967	6822054	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822055	6822373	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822055	6822373	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822374	6822520	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822521	6822648	1	-	2	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822521	6822648	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822649	6822752	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822753	6822831	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822753	6822831	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6822832	6822967	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6822968	6823060	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6822968	6823060	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823061	6823150	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823151	6823348	0.98	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823151	6823348	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823349	6823438	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823439	6823623	0.33	-	2	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823439	6823623	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823624	6823703	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823704	6823762	0.41	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823704	6823762	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823763	6823966	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6823967	6823992	0.89	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6823967	6823992	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6823993	6824099	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824100	6824409	0.95	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824100	6824409	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824410	6824528	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824529	6824607	1	-	2	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824529	6824607	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824608	6824738	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6824739	6824842	1	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6824739	6824842	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6824843	6825027	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825028	6825119	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825028	6825119	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825120	6825282	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825283	6825336	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825283	6825336	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825337	6825510	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825511	6825595	1	-	1	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825511	6825595	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825596	6825691	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6825692	6825849	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6825692	6825849	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	intron	6825850	6826045	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	CDS	6826046	6826069	1	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	exon	6826046	6826069	.	-	.	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
Phchi.S4	AUGUSTUS	start_codon	6826067	6826069	.	-	0	transcript_id "Phchi.S4G109200.t3"; gene_id "Phchi.S4G109200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10403.t1 is derived from g7579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47610514	47614633	.	-	.	Phchi.S1G756200
Phchi.S1	AUGUSTUS	transcript	47610514	47614633	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	stop_codon	47610511	47610513	.	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47610514	47610755	1	-	2	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47610514	47610755	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47610756	47610880	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47610881	47611004	1	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47610881	47611004	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47611005	47611112	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47611113	47611328	1	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47611113	47611328	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47611329	47611444	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47611445	47611573	1	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47611445	47611573	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47611574	47611710	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47611711	47611957	0.82	-	1	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47611711	47611957	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47611958	47612044	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47612045	47612377	0.99	-	1	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47612045	47612377	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47612378	47612463	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47612464	47612690	1	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47612464	47612690	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47612691	47612898	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47612899	47612953	1	-	1	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47612899	47612953	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	intron	47612954	47613077	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	CDS	47613078	47614633	0.98	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	exon	47613078	47614633	.	-	.	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
Phchi.S1	AUGUSTUS	start_codon	47614631	47614633	.	-	0	transcript_id "Phchi.S1G756200.t1"; gene_id "Phchi.S1G756200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3714.t1 is derived from g883.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5342855	5344626	.	-	.	Phchi.S1G087300
Phchi.S1	AUGUSTUS	transcript	5342855	5344626	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	stop_codon	5342704	5342706	.	-	0	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5342855	5342949	0.98	-	2	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5342855	5342949	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5342950	5343009	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343010	5343034	1	-	0	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343010	5343034	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343035	5343175	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343176	5343514	0.99	-	0	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343176	5343514	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343515	5343730	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343731	5343779	1	-	1	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343731	5343779	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343780	5343907	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343908	5343979	1	-	1	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343908	5343979	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343980	5344090	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5344091	5344214	1	-	2	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5344091	5344214	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5344215	5344324	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5344325	5344429	1	-	2	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5344325	5344429	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5344430	5344583	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5344584	5344626	0.72	-	0	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5344584	5344626	.	-	.	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	start_codon	5344624	5344626	.	-	0	transcript_id "Phchi.S1G087300.t1"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	transcript	5342855	5344626	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	stop_codon	5342704	5342706	.	-	0	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5342855	5342949	1	-	2	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5342855	5342949	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5342950	5343175	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343176	5343237	0.95	-	1	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343176	5343237	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343238	5343407	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343408	5343514	0.99	-	0	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343408	5343514	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343515	5343730	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343731	5343779	1	-	1	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343731	5343779	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343780	5343907	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5343908	5343979	1	-	1	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5343908	5343979	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5343980	5344090	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5344091	5344214	1	-	2	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5344091	5344214	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5344215	5344324	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5344325	5344429	1	-	2	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5344325	5344429	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	intron	5344430	5344583	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	CDS	5344584	5344626	0.66	-	0	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	exon	5344584	5344626	.	-	.	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
Phchi.S1	AUGUSTUS	start_codon	5344624	5344626	.	-	0	transcript_id "Phchi.S1G087300.t2"; gene_id "Phchi.S1G087300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg588.t1 is derived from g10370.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4315795	4320452	.	-	.	Phchi.S6G054700
Phchi.S6	AUGUSTUS	transcript	4315795	4320452	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	stop_codon	4315792	4315794	.	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4315795	4315859	0.53	-	2	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4315795	4315859	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4315860	4315959	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4315960	4316015	0.69	-	1	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4315960	4316015	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4316016	4316162	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4316163	4316278	0.96	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4316163	4316278	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4316279	4316382	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4316383	4316448	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4316383	4316448	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4316449	4316537	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4316538	4316652	1	-	1	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4316538	4316652	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4316653	4316722	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4316723	4316829	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4316723	4316829	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4316830	4316961	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4316962	4317051	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4316962	4317051	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4317052	4317227	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4317228	4317338	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4317228	4317338	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4317339	4317456	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4317457	4317522	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4317457	4317522	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4317523	4317653	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4317654	4317719	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4317654	4317719	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4317720	4317838	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4317839	4317988	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4317839	4317988	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4317989	4318368	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4318369	4318443	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4318369	4318443	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4318444	4318539	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4318540	4318622	0.61	-	2	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4318540	4318622	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4318623	4318734	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4318735	4318800	1	-	2	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4318735	4318800	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4318801	4319041	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4319042	4319141	0.82	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4319042	4319141	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4319142	4319436	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4319437	4319474	0.25	-	2	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4319437	4319474	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4319475	4319836	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4319837	4319924	0.96	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4319837	4319924	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4319925	4320093	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4320094	4320255	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4320094	4320255	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	intron	4320256	4320368	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	CDS	4320369	4320452	1	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	exon	4320369	4320452	.	-	.	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
Phchi.S6	AUGUSTUS	start_codon	4320450	4320452	.	-	0	transcript_id "Phchi.S6G054700.t1"; gene_id "Phchi.S6G054700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9274.t1 is derived from g6449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40722863	40724106	.	+	.	Phchi.S1G643300
Phchi.S1	AUGUSTUS	transcript	40722863	40724106	.	+	.	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	start_codon	40722863	40722865	.	+	0	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	CDS	40722863	40723538	0.57	+	0	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	exon	40722863	40723538	.	+	.	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	intron	40723539	40723609	.	+	.	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	CDS	40723610	40724106	0.92	+	2	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	exon	40723610	40724106	.	+	.	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
Phchi.S1	AUGUSTUS	stop_codon	40724107	40724109	.	+	0	transcript_id "Phchi.S1G643300.t1"; gene_id "Phchi.S1G643300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12344.t1 is derived from g8020.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12211879	12215609	.	-	.	Phchi.S2G042400
Phchi.S2	AUGUSTUS	transcript	12211879	12215609	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	stop_codon	12211876	12211878	.	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12211879	12211947	0.98	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12211879	12211947	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12211948	12212154	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12212155	12212313	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12212155	12212313	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12212314	12212448	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12212449	12212571	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12212449	12212571	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12212572	12212662	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12212663	12212725	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12212663	12212725	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12212726	12212975	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12212976	12213080	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12212976	12213080	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12213081	12213220	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12213221	12213320	1	-	1	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12213221	12213320	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12213321	12213395	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12213396	12213466	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12213396	12213466	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12213467	12213992	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12213993	12214049	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12213993	12214049	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12214050	12214541	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12214542	12214619	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12214542	12214619	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12214620	12214706	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12214707	12214781	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12214707	12214781	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12214782	12214898	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12214899	12214949	1	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12214899	12214949	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12214950	12215056	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12215057	12215136	1	-	2	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12215057	12215136	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	intron	12215137	12215590	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	CDS	12215591	12215609	0.82	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	exon	12215591	12215609	.	-	.	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
Phchi.S2	AUGUSTUS	start_codon	12215607	12215609	.	-	0	transcript_id "Phchi.S2G042400.t1"; gene_id "Phchi.S2G042400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8643.t1 is derived from g5818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37200222	37201629	.	+	.	Phchi.S1G580200
Phchi.S1	AUGUSTUS	transcript	37200222	37201629	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	start_codon	37200222	37200224	.	+	0	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	CDS	37200222	37200373	0.73	+	0	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	exon	37200222	37200373	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	intron	37200374	37200485	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	CDS	37200486	37201175	1	+	1	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	exon	37200486	37201175	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	intron	37201176	37201385	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	CDS	37201386	37201409	0.64	+	1	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	exon	37201386	37201409	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	intron	37201410	37201505	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	CDS	37201506	37201629	0.64	+	1	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	exon	37201506	37201629	.	+	.	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
Phchi.S1	AUGUSTUS	stop_codon	37201630	37201632	.	+	0	transcript_id "Phchi.S1G580200.t1"; gene_id "Phchi.S1G580200"
# This transcript jg10341.t2 is derived from g7517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10342.t1 is derived from g7518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47256500	47258980	.	-	.	Phchi.S1G750100
Phchi.S1	AUGUSTUS	transcript	47256500	47258980	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	stop_codon	47256497	47256499	.	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47256500	47256550	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47256500	47256550	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47256551	47256647	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47256648	47256716	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47256648	47256716	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47256717	47256813	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47256814	47256876	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47256814	47256876	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47256877	47257002	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47257003	47257104	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47257003	47257104	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47257105	47257190	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47257191	47257451	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47257191	47257451	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47257452	47257579	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47257580	47257759	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47257580	47257759	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47257760	47257866	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47257867	47257971	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47257867	47257971	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47257972	47258100	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47258101	47258223	1	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47258101	47258223	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47258224	47258360	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47258361	47258532	0.36	-	1	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47258361	47258532	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	intron	47258533	47258630	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	CDS	47258631	47258980	0.64	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	exon	47258631	47258980	.	-	.	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
Phchi.S1	AUGUSTUS	start_codon	47258978	47258980	.	-	0	transcript_id "Phchi.S1G750100.t1"; gene_id "Phchi.S1G750100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2699.t1 is derived from g9619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8247384	8250336	.	-	.	Phchi.S5G130800
Phchi.S5	AUGUSTUS	transcript	8247384	8250336	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	stop_codon	8247381	8247383	.	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8247384	8247452	1	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8247384	8247452	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8247453	8247534	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8247535	8247684	0.94	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8247535	8247684	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8247685	8247787	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8247788	8247922	0.86	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8247788	8247922	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8247923	8248015	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8248016	8248074	1	-	2	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8248016	8248074	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8248075	8248172	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8248173	8248292	1	-	2	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8248173	8248292	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8248293	8248387	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8248388	8248568	0.95	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8248388	8248568	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8248569	8248658	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8248659	8248742	1	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8248659	8248742	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8248743	8248823	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8248824	8248892	1	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8248824	8248892	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8248893	8248997	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8248998	8249129	1	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8248998	8249129	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8249130	8249214	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8249215	8249307	0.99	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8249215	8249307	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8249308	8249416	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8249417	8249545	1	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8249417	8249545	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8249546	8249665	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8249666	8249957	0.53	-	1	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8249666	8249957	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8249958	8250084	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8250085	8250122	0.54	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8250085	8250122	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	intron	8250123	8250252	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	CDS	8250253	8250336	1	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	exon	8250253	8250336	.	-	.	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
Phchi.S5	AUGUSTUS	start_codon	8250334	8250336	.	-	0	transcript_id "Phchi.S5G130800.t1"; gene_id "Phchi.S5G130800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1215.t1 is derived from g10998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8439189	8440700	.	+	.	Phchi.S6G117400
Phchi.S6	AUGUSTUS	transcript	8439189	8440700	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	start_codon	8439189	8439191	.	+	0	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8439189	8439244	1	+	0	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8439189	8439244	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8439245	8439325	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8439326	8439402	0.89	+	1	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8439326	8439402	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8439403	8439510	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8439511	8439558	0.89	+	2	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8439511	8439558	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8439559	8439661	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8439662	8439750	1	+	2	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8439662	8439750	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8439751	8439867	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8439868	8439921	1	+	0	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8439868	8439921	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8439922	8440059	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8440060	8440127	1	+	0	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8440060	8440127	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8440128	8440260	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8440261	8440307	1	+	1	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8440261	8440307	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8440308	8440405	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8440406	8440503	1	+	2	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8440406	8440503	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	intron	8440504	8440592	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	CDS	8440593	8440700	1	+	0	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	exon	8440593	8440700	.	+	.	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
Phchi.S6	AUGUSTUS	stop_codon	8440701	8440703	.	+	0	transcript_id "Phchi.S6G117400.t1"; gene_id "Phchi.S6G117400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9871.t1 is derived from g7047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44180819	44181598	.	-	.	Phchi.S1G703000
Phchi.S1	AUGUSTUS	transcript	44180819	44181598	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	stop_codon	44180816	44180818	.	-	0	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	CDS	44180819	44180938	0.99	-	0	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	exon	44180819	44180938	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	intron	44180939	44181027	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	CDS	44181028	44181108	0.87	-	0	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	exon	44181028	44181108	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	intron	44181109	44181242	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	CDS	44181243	44181279	0.87	-	1	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	exon	44181243	44181279	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	intron	44181280	44181575	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	CDS	44181576	44181598	0.44	-	0	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	exon	44181576	44181598	.	-	.	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
Phchi.S1	AUGUSTUS	start_codon	44181596	44181598	.	-	0	transcript_id "Phchi.S1G703000.t1"; gene_id "Phchi.S1G703000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg936.t1 is derived from g10718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6506190	6506630	.	-	.	Phchi.S6G089500
Phchi.S6	AUGUSTUS	transcript	6506190	6506630	.	-	.	transcript_id "Phchi.S6G089500.t1"; gene_id "Phchi.S6G089500"
Phchi.S6	AUGUSTUS	stop_codon	6506187	6506189	.	-	0	transcript_id "Phchi.S6G089500.t1"; gene_id "Phchi.S6G089500"
Phchi.S6	AUGUSTUS	CDS	6506190	6506630	0.93	-	0	transcript_id "Phchi.S6G089500.t1"; gene_id "Phchi.S6G089500"
Phchi.S6	AUGUSTUS	exon	6506190	6506630	.	-	.	transcript_id "Phchi.S6G089500.t1"; gene_id "Phchi.S6G089500"
Phchi.S6	AUGUSTUS	start_codon	6506628	6506630	.	-	0	transcript_id "Phchi.S6G089500.t1"; gene_id "Phchi.S6G089500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10691.t1 is derived from g14741.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1595868	1598434	.	-	.	Phchi.S4G027300
Phchi.S4	AUGUSTUS	transcript	1595868	1598434	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	stop_codon	1595865	1595867	.	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1595868	1595945	0.99	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1595868	1595945	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1595946	1596034	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1596035	1596133	1	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1596035	1596133	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1596134	1596213	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1596214	1596321	1	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1596214	1596321	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1596322	1596426	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1596427	1596537	0.88	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1596427	1596537	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1596538	1596638	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1596639	1596758	1	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1596639	1596758	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1596759	1597093	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1597094	1597186	1	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1597094	1597186	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1597187	1597304	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1597305	1597451	1	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1597305	1597451	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1597452	1597587	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1597588	1597812	1	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1597588	1597812	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1597813	1597928	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1597929	1598157	1	-	1	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1597929	1598157	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	intron	1598158	1598384	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	CDS	1598385	1598434	0.94	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	exon	1598385	1598434	.	-	.	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
Phchi.S4	AUGUSTUS	start_codon	1598432	1598434	.	-	0	transcript_id "Phchi.S4G027300.t1"; gene_id "Phchi.S4G027300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2973.t1 is derived from g142.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	906119	910847	.	-	.	Phchi.S1G013200
Phchi.S1	AUGUSTUS	transcript	906119	910847	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	stop_codon	906116	906118	.	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	906119	906412	0.98	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	906119	906412	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	906413	906491	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	906492	906604	1	-	2	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	906492	906604	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	906605	906680	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	906681	906886	1	-	1	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	906681	906886	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	906887	906977	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	906978	907092	1	-	2	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	906978	907092	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	907093	907179	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	907180	907312	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	907180	907312	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	907313	907427	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	907428	907499	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	907428	907499	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	907500	907588	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	907589	907715	1	-	1	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	907589	907715	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	907716	907796	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	907797	907930	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	907797	907930	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	907931	908002	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	908003	908181	0.93	-	2	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	908003	908181	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	908182	908295	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	908296	908400	1	-	2	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	908296	908400	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	908401	908543	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	908544	908622	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	908544	908622	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	908623	908739	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	908740	908886	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	908740	908886	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	908887	908976	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	908977	909234	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	908977	909234	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	909235	909308	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	909309	909504	1	-	1	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	909309	909504	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	909505	909598	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	909599	909780	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	909599	909780	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	909781	909868	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	909869	909982	1	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	909869	909982	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	909983	910068	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	910069	910177	1	-	1	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	910069	910177	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	intron	910178	910356	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	CDS	910357	910847	0.93	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	exon	910357	910847	.	-	.	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
Phchi.S1	AUGUSTUS	start_codon	910845	910847	.	-	0	transcript_id "Phchi.S1G013200.t1"; gene_id "Phchi.S1G013200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10478.t1 is derived from g14527.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	571675	572656	.	-	.	Phchi.S4G006000
Phchi.S4	AUGUSTUS	transcript	571675	572656	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	stop_codon	571672	571674	.	-	0	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	CDS	571675	571719	0.56	-	0	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	exon	571675	571719	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	intron	571720	571816	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	CDS	571817	571885	0.51	-	0	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	exon	571817	571885	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	intron	571886	571985	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	CDS	571986	572021	0.51	-	0	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	exon	571986	572021	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	intron	572022	572125	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	CDS	572126	572656	0.47	-	0	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	exon	572126	572656	.	-	.	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
Phchi.S4	AUGUSTUS	start_codon	572654	572656	.	-	0	transcript_id "Phchi.S4G006000.t1"; gene_id "Phchi.S4G006000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9469.t1 is derived from g6645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41605939	41606169	.	+	.	Phchi.S1G662800
Phchi.S1	AUGUSTUS	transcript	41605939	41606169	.	+	.	transcript_id "Phchi.S1G662800.t1"; gene_id "Phchi.S1G662800"
Phchi.S1	AUGUSTUS	start_codon	41605939	41605941	.	+	0	transcript_id "Phchi.S1G662800.t1"; gene_id "Phchi.S1G662800"
Phchi.S1	AUGUSTUS	CDS	41605939	41606169	0.6	+	0	transcript_id "Phchi.S1G662800.t1"; gene_id "Phchi.S1G662800"
Phchi.S1	AUGUSTUS	exon	41605939	41606169	.	+	.	transcript_id "Phchi.S1G662800.t1"; gene_id "Phchi.S1G662800"
Phchi.S1	AUGUSTUS	stop_codon	41606170	41606172	.	+	0	transcript_id "Phchi.S1G662800.t1"; gene_id "Phchi.S1G662800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg411.t1 is derived from g10193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2946984	2949511	.	+	.	Phchi.S6G037000
Phchi.S6	AUGUSTUS	transcript	2946984	2949511	.	+	.	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	start_codon	2946984	2946986	.	+	0	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	CDS	2946984	2947274	0.82	+	0	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	exon	2946984	2947274	.	+	.	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	intron	2947275	2947411	.	+	.	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	CDS	2947412	2947567	0.78	+	0	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	exon	2947412	2947567	.	+	.	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	intron	2947568	2947708	.	+	.	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	CDS	2947709	2949511	0.76	+	0	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	exon	2947709	2949511	.	+	.	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
Phchi.S6	AUGUSTUS	stop_codon	2949512	2949514	.	+	0	transcript_id "Phchi.S6G037000.t1"; gene_id "Phchi.S6G037000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9687.t1 is derived from g6863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43286779	43288392	.	+	.	Phchi.S1G684600
Phchi.S1	AUGUSTUS	transcript	43286779	43288392	.	+	.	transcript_id "Phchi.S1G684600.t1"; gene_id "Phchi.S1G684600"
Phchi.S1	AUGUSTUS	start_codon	43286779	43286781	.	+	0	transcript_id "Phchi.S1G684600.t1"; gene_id "Phchi.S1G684600"
Phchi.S1	AUGUSTUS	CDS	43286779	43288392	0.86	+	0	transcript_id "Phchi.S1G684600.t1"; gene_id "Phchi.S1G684600"
Phchi.S1	AUGUSTUS	exon	43286779	43288392	.	+	.	transcript_id "Phchi.S1G684600.t1"; gene_id "Phchi.S1G684600"
Phchi.S1	AUGUSTUS	stop_codon	43288393	43288395	.	+	0	transcript_id "Phchi.S1G684600.t1"; gene_id "Phchi.S1G684600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4398.t1 is derived from g1567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10234881	10236388	.	-	.	Phchi.S1G155700
Phchi.S1	AUGUSTUS	transcript	10234881	10236388	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	stop_codon	10234878	10234880	.	-	0	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	CDS	10234881	10234952	1	-	0	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	exon	10234881	10234952	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	intron	10234953	10235098	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	CDS	10235099	10235262	1	-	2	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	exon	10235099	10235262	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	intron	10235263	10235362	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	CDS	10235363	10235496	1	-	1	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	exon	10235363	10235496	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	intron	10235497	10235633	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	CDS	10235634	10235727	1	-	2	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	exon	10235634	10235727	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	intron	10235728	10236312	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	CDS	10236313	10236388	0.01	-	0	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	exon	10236313	10236388	.	-	.	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
Phchi.S1	AUGUSTUS	start_codon	10236386	10236388	.	-	0	transcript_id "Phchi.S1G155700.t1"; gene_id "Phchi.S1G155700"
# This transcript jg532.t2 is derived from g10314.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg533.t1 is derived from g10315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3835879	3837384	.	+	.	Phchi.S6G049200
Phchi.S6	AUGUSTUS	transcript	3835879	3837384	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	start_codon	3835879	3835881	.	+	0	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	CDS	3835879	3836279	0.92	+	0	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	exon	3835879	3836279	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	intron	3836280	3836387	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	CDS	3836388	3836622	0.99	+	1	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	exon	3836388	3836622	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	intron	3836623	3836766	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	CDS	3836767	3837069	0.85	+	0	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	exon	3836767	3837069	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	intron	3837070	3837240	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	CDS	3837241	3837384	1	+	0	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	exon	3837241	3837384	.	+	.	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
Phchi.S6	AUGUSTUS	stop_codon	3837385	3837387	.	+	0	transcript_id "Phchi.S6G049200.t1"; gene_id "Phchi.S6G049200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15751.t1 is derived from g14221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21065233	21068580	.	+	.	Phchi.S3G307000
Phchi.S3	AUGUSTUS	transcript	21065233	21068580	.	+	.	transcript_id "Phchi.S3G307000.t1"; gene_id "Phchi.S3G307000"
Phchi.S3	AUGUSTUS	start_codon	21065233	21065235	.	+	0	transcript_id "Phchi.S3G307000.t1"; gene_id "Phchi.S3G307000"
Phchi.S3	AUGUSTUS	CDS	21065233	21068580	0.61	+	0	transcript_id "Phchi.S3G307000.t1"; gene_id "Phchi.S3G307000"
Phchi.S3	AUGUSTUS	exon	21065233	21068580	.	+	.	transcript_id "Phchi.S3G307000.t1"; gene_id "Phchi.S3G307000"
Phchi.S3	AUGUSTUS	stop_codon	21068581	21068583	.	+	0	transcript_id "Phchi.S3G307000.t1"; gene_id "Phchi.S3G307000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8989.t1 is derived from g6164.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38991656	38992267	.	+	.	Phchi.S1G614800
Phchi.S1	AUGUSTUS	transcript	38991656	38992267	.	+	.	transcript_id "Phchi.S1G614800.t1"; gene_id "Phchi.S1G614800"
Phchi.S1	AUGUSTUS	start_codon	38991656	38991658	.	+	0	transcript_id "Phchi.S1G614800.t1"; gene_id "Phchi.S1G614800"
Phchi.S1	AUGUSTUS	CDS	38991656	38992267	0.47	+	0	transcript_id "Phchi.S1G614800.t1"; gene_id "Phchi.S1G614800"
Phchi.S1	AUGUSTUS	exon	38991656	38992267	.	+	.	transcript_id "Phchi.S1G614800.t1"; gene_id "Phchi.S1G614800"
Phchi.S1	AUGUSTUS	stop_codon	38992268	38992270	.	+	0	transcript_id "Phchi.S1G614800.t1"; gene_id "Phchi.S1G614800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15675.t1 is derived from g14144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20614306	20616377	.	+	.	Phchi.S3G299400
Phchi.S3	AUGUSTUS	transcript	20614306	20616377	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	start_codon	20614306	20614308	.	+	0	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	CDS	20614306	20614582	0.98	+	0	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	exon	20614306	20614582	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	intron	20614583	20614705	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	CDS	20614706	20614932	1	+	2	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	exon	20614706	20614932	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	intron	20614933	20615031	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	CDS	20615032	20615302	0.87	+	0	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	exon	20615032	20615302	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	intron	20615303	20615439	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	CDS	20615440	20615460	0.31	+	2	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	exon	20615440	20615460	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	intron	20615461	20615530	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	CDS	20615531	20615814	0.31	+	2	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	exon	20615531	20615814	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	intron	20615815	20615951	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	CDS	20615952	20616377	0.99	+	0	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	exon	20615952	20616377	.	+	.	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
Phchi.S3	AUGUSTUS	stop_codon	20616378	20616380	.	+	0	transcript_id "Phchi.S3G299400.t1"; gene_id "Phchi.S3G299400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1337.t1 is derived from g11120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9094078	9095286	.	+	.	Phchi.S6G129600
Phchi.S6	AUGUSTUS	transcript	9094078	9095286	.	+	.	transcript_id "Phchi.S6G129600.t1"; gene_id "Phchi.S6G129600"
Phchi.S6	AUGUSTUS	start_codon	9094078	9094080	.	+	0	transcript_id "Phchi.S6G129600.t1"; gene_id "Phchi.S6G129600"
Phchi.S6	AUGUSTUS	CDS	9094078	9095286	0.82	+	0	transcript_id "Phchi.S6G129600.t1"; gene_id "Phchi.S6G129600"
Phchi.S6	AUGUSTUS	exon	9094078	9095286	.	+	.	transcript_id "Phchi.S6G129600.t1"; gene_id "Phchi.S6G129600"
Phchi.S6	AUGUSTUS	stop_codon	9095287	9095289	.	+	0	transcript_id "Phchi.S6G129600.t1"; gene_id "Phchi.S6G129600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1199.t1 is derived from g10982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8383964	8384481	.	+	.	Phchi.S6G115800
Phchi.S6	AUGUSTUS	transcript	8383964	8384481	.	+	.	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	start_codon	8383964	8383966	.	+	0	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	CDS	8383964	8384125	0.38	+	0	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	exon	8383964	8384125	.	+	.	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	intron	8384126	8384250	.	+	.	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	CDS	8384251	8384481	0.66	+	0	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	exon	8384251	8384481	.	+	.	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
Phchi.S6	AUGUSTUS	stop_codon	8384482	8384484	.	+	0	transcript_id "Phchi.S6G115800.t1"; gene_id "Phchi.S6G115800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12101.t1 is derived from g7776.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	3117496	3120796	.	-	.	Phchi.S2G018100
Phchi.S2	AUGUSTUS	transcript	3117496	3118579	.	-	.	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	stop_codon	3117493	3117495	.	-	0	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3117496	3117648	1	-	0	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3117496	3117648	.	-	.	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3117649	3117769	.	-	.	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3117770	3118579	0.37	-	0	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3117770	3118579	.	-	.	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	start_codon	3118577	3118579	.	-	0	transcript_id "Phchi.S2G018100.t1"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	transcript	3117518	3118579	.	-	.	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	stop_codon	3117515	3117517	.	-	0	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3117518	3117565	0.96	-	0	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3117518	3117565	.	-	.	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3117566	3117769	.	-	.	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3117770	3118579	0.37	-	0	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3117770	3118579	.	-	.	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	start_codon	3118577	3118579	.	-	0	transcript_id "Phchi.S2G018100.t2"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	transcript	3117496	3120796	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	stop_codon	3117493	3117495	.	-	0	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3117496	3117648	0.96	-	0	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3117496	3117648	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3117649	3117769	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3117770	3118732	0.74	-	0	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3117770	3118732	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3118733	3118883	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3118884	3118979	0.71	-	0	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3118884	3118979	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3118980	3119148	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3119149	3119182	0.69	-	1	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3119149	3119182	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3119183	3119377	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3119378	3119471	0.41	-	2	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3119378	3119471	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3119472	3119749	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3119750	3120187	0.4	-	2	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3119750	3120187	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	intron	3120188	3120699	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	CDS	3120700	3120796	0.31	-	0	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	exon	3120700	3120796	.	-	.	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
Phchi.S2	AUGUSTUS	start_codon	3120794	3120796	.	-	0	transcript_id "Phchi.S2G018100.t3"; gene_id "Phchi.S2G018100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3072.t1 is derived from g241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1436532	1436951	.	+	.	Phchi.S1G023100
Phchi.S1	AUGUSTUS	transcript	1436532	1436951	.	+	.	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	start_codon	1436532	1436534	.	+	0	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	CDS	1436532	1436670	0.54	+	0	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	exon	1436532	1436670	.	+	.	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	intron	1436671	1436760	.	+	.	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	CDS	1436761	1436951	0.68	+	2	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	exon	1436761	1436951	.	+	.	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
Phchi.S1	AUGUSTUS	stop_codon	1436952	1436954	.	+	0	transcript_id "Phchi.S1G023100.t1"; gene_id "Phchi.S1G023100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3261.t1 is derived from g430.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2575492	2576400	.	-	.	Phchi.S1G042000
Phchi.S1	AUGUSTUS	transcript	2575492	2576400	.	-	.	transcript_id "Phchi.S1G042000.t1"; gene_id "Phchi.S1G042000"
Phchi.S1	AUGUSTUS	stop_codon	2575489	2575491	.	-	0	transcript_id "Phchi.S1G042000.t1"; gene_id "Phchi.S1G042000"
Phchi.S1	AUGUSTUS	CDS	2575492	2576400	1	-	0	transcript_id "Phchi.S1G042000.t1"; gene_id "Phchi.S1G042000"
Phchi.S1	AUGUSTUS	exon	2575492	2576400	.	-	.	transcript_id "Phchi.S1G042000.t1"; gene_id "Phchi.S1G042000"
Phchi.S1	AUGUSTUS	start_codon	2576398	2576400	.	-	0	transcript_id "Phchi.S1G042000.t1"; gene_id "Phchi.S1G042000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg694.t1 is derived from g10476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4945673	4945978	.	+	.	Phchi.S6G065300
Phchi.S6	AUGUSTUS	transcript	4945673	4945978	.	+	.	transcript_id "Phchi.S6G065300.t1"; gene_id "Phchi.S6G065300"
Phchi.S6	AUGUSTUS	start_codon	4945673	4945675	.	+	0	transcript_id "Phchi.S6G065300.t1"; gene_id "Phchi.S6G065300"
Phchi.S6	AUGUSTUS	CDS	4945673	4945978	0.95	+	0	transcript_id "Phchi.S6G065300.t1"; gene_id "Phchi.S6G065300"
Phchi.S6	AUGUSTUS	exon	4945673	4945978	.	+	.	transcript_id "Phchi.S6G065300.t1"; gene_id "Phchi.S6G065300"
Phchi.S6	AUGUSTUS	stop_codon	4945979	4945981	.	+	0	transcript_id "Phchi.S6G065300.t1"; gene_id "Phchi.S6G065300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9039.t1 is derived from g6214.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39244467	39245607	.	-	.	Phchi.S1G619800
Phchi.S1	AUGUSTUS	transcript	39244467	39245607	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	stop_codon	39244464	39244466	.	-	0	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244467	39244503	1	-	1	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244467	39244503	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39244504	39244599	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244600	39244745	1	-	0	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244600	39244745	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39244746	39244828	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244829	39244906	1	-	0	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244829	39244906	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39244907	39244982	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244983	39245049	1	-	1	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244983	39245049	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39245050	39245128	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39245129	39245271	1	-	0	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39245129	39245271	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39245272	39245341	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39245342	39245391	1	-	2	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39245342	39245391	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39245392	39245483	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39245484	39245607	0.5	-	0	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39245484	39245607	.	-	.	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	start_codon	39245605	39245607	.	-	0	transcript_id "Phchi.S1G619800.t1"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	transcript	39244467	39245607	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	stop_codon	39244464	39244466	.	-	0	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244467	39244503	0.99	-	1	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244467	39244503	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39244504	39244599	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244600	39244745	0.99	-	0	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244600	39244745	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39244746	39244828	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244829	39244906	1	-	0	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244829	39244906	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39244907	39244982	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39244983	39245049	1	-	1	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39244983	39245049	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39245050	39245128	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39245129	39245271	1	-	0	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39245129	39245271	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39245272	39245341	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39245342	39245394	1	-	2	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39245342	39245394	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	intron	39245395	39245483	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	CDS	39245484	39245607	0.44	-	0	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	exon	39245484	39245607	.	-	.	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
Phchi.S1	AUGUSTUS	start_codon	39245605	39245607	.	-	0	transcript_id "Phchi.S1G619800.t2"; gene_id "Phchi.S1G619800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8993.t1 is derived from g6168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39025609	39027749	.	-	.	Phchi.S1G615200
Phchi.S1	AUGUSTUS	transcript	39025609	39027749	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	stop_codon	39025606	39025608	.	-	0	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39025609	39026056	0.98	-	1	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39025609	39026056	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39026057	39026200	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39026201	39026356	0.96	-	1	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39026201	39026356	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39026357	39026444	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39026445	39026509	0.92	-	0	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39026445	39026509	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39026510	39026621	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39026622	39026728	1	-	2	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39026622	39026728	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39026729	39026850	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39026851	39027076	0.99	-	0	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39026851	39027076	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39027077	39027183	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39027184	39027263	0.97	-	2	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39027184	39027263	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39027264	39027370	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39027371	39027421	1	-	2	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39027371	39027421	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	intron	39027422	39027583	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	CDS	39027584	39027749	0.81	-	0	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	exon	39027584	39027749	.	-	.	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
Phchi.S1	AUGUSTUS	start_codon	39027747	39027749	.	-	0	transcript_id "Phchi.S1G615200.t1"; gene_id "Phchi.S1G615200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8324.t1 is derived from g5499.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35295911	35297035	.	+	.	Phchi.S1G548300
Phchi.S1	AUGUSTUS	transcript	35295911	35297035	.	+	.	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	start_codon	35295911	35295913	.	+	0	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	CDS	35295911	35296268	0.92	+	0	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	exon	35295911	35296268	.	+	.	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	intron	35296269	35296670	.	+	.	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	CDS	35296671	35297035	0.94	+	2	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	exon	35296671	35297035	.	+	.	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
Phchi.S1	AUGUSTUS	stop_codon	35297036	35297038	.	+	0	transcript_id "Phchi.S1G548300.t1"; gene_id "Phchi.S1G548300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11067.t1 is derived from g15117.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3954267	3958717	.	-	.	Phchi.S4G064900
Phchi.S4	AUGUSTUS	transcript	3954267	3958717	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	stop_codon	3954264	3954266	.	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954267	3954350	1	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954267	3954350	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3954351	3954431	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954432	3954555	1	-	1	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954432	3954555	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3954556	3954651	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954652	3954872	1	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954652	3954872	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3954873	3954992	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954993	3955375	1	-	2	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954993	3955375	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3955376	3955524	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3955525	3956149	1	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3955525	3956149	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956150	3956301	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956302	3956361	1	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956302	3956361	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956362	3956510	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956511	3956577	1	-	1	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956511	3956577	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956578	3956732	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956733	3956829	1	-	2	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956733	3956829	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956830	3956923	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956924	3957037	0.98	-	2	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956924	3957037	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957038	3957153	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957154	3957226	0.99	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957154	3957226	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957227	3957357	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957358	3957520	1	-	1	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957358	3957520	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957521	3957911	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957912	3958717	0.73	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957912	3958717	.	-	.	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	start_codon	3958715	3958717	.	-	0	transcript_id "Phchi.S4G064900.t1"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	transcript	3954267	3958717	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	stop_codon	3954264	3954266	.	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954267	3954350	1	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954267	3954350	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3954351	3954431	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954432	3954555	1	-	1	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954432	3954555	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3954556	3954651	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954652	3954872	1	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954652	3954872	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3954873	3954992	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3954993	3955375	1	-	2	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3954993	3955375	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3955376	3955524	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3955525	3956149	1	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3955525	3956149	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956150	3956301	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956302	3956361	1	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956302	3956361	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956362	3956510	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956511	3956577	1	-	1	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956511	3956577	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956578	3956732	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956733	3956829	1	-	2	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956733	3956829	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3956830	3956923	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3956924	3957037	0.99	-	2	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3956924	3957037	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957038	3957153	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957154	3957226	1	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957154	3957226	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957227	3957357	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957358	3957472	1	-	1	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957358	3957472	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957473	3957554	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957555	3957593	0.88	-	1	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957555	3957593	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	intron	3957594	3957911	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	CDS	3957912	3958717	0.65	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	exon	3957912	3958717	.	-	.	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
Phchi.S4	AUGUSTUS	start_codon	3958715	3958717	.	-	0	transcript_id "Phchi.S4G064900.t2"; gene_id "Phchi.S4G064900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2750.t1 is derived from g9670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8615425	8618356	.	-	.	Phchi.S5G135900
Phchi.S5	AUGUSTUS	transcript	8615425	8618356	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	stop_codon	8615422	8615424	.	-	0	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	CDS	8615425	8615468	0.01	-	2	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	exon	8615425	8615468	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	intron	8615469	8615559	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	CDS	8615560	8615914	0.01	-	0	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	exon	8615560	8615914	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	intron	8615915	8616058	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	CDS	8616059	8616187	0.11	-	0	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	exon	8616059	8616187	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	intron	8616188	8616715	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	CDS	8616716	8618356	0.01	-	0	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	exon	8616716	8618356	.	-	.	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
Phchi.S5	AUGUSTUS	start_codon	8618354	8618356	.	-	0	transcript_id "Phchi.S5G135900.t1"; gene_id "Phchi.S5G135900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12631.t1 is derived from g8308.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	37662770	37665655	.	+	.	Phchi.S2G071100
Phchi.S2	AUGUSTUS	transcript	37662770	37665655	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	start_codon	37662770	37662772	.	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37662770	37662812	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37662770	37662812	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37662813	37662908	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37662909	37662920	1	+	2	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37662909	37662920	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37662921	37662994	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37662995	37663021	1	+	2	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37662995	37663021	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37663022	37663102	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37663103	37663245	1	+	2	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37663103	37663245	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37663246	37663337	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37663338	37663491	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37663338	37663491	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37663492	37663583	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37663584	37663813	0.63	+	2	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37663584	37663813	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37663814	37663918	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37663919	37664008	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37663919	37664008	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37664009	37664114	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37664115	37664288	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37664115	37664288	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37664289	37664377	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37664378	37664383	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37664378	37664383	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37664384	37664507	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37664508	37664516	0.96	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37664508	37664516	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37664517	37664593	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37664594	37664731	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37664594	37664731	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37664732	37664844	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37664845	37664906	1	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37664845	37664906	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37664907	37665031	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37665032	37665301	0.8	+	1	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37665032	37665301	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37665302	37665439	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37665440	37665463	1	+	1	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37665440	37665463	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	intron	37665464	37665609	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	CDS	37665610	37665655	1	+	1	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	exon	37665610	37665655	.	+	.	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
Phchi.S2	AUGUSTUS	stop_codon	37665656	37665658	.	+	0	transcript_id "Phchi.S2G071100.t1"; gene_id "Phchi.S2G071100"
# This transcript jg7670.t2 is derived from g4844.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7671.t1 is derived from g4845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30563488	30564576	.	-	.	Phchi.S1G483000
Phchi.S1	AUGUSTUS	transcript	30563488	30564576	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	stop_codon	30563485	30563487	.	-	0	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	CDS	30563488	30563706	0.42	-	0	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	exon	30563488	30563706	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	intron	30563707	30563877	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	CDS	30563878	30564012	0.75	-	0	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	exon	30563878	30564012	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	intron	30564013	30564115	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	CDS	30564116	30564328	0.88	-	0	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	exon	30564116	30564328	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	intron	30564329	30564471	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	CDS	30564472	30564576	0.95	-	0	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	exon	30564472	30564576	.	-	.	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
Phchi.S1	AUGUSTUS	start_codon	30564574	30564576	.	-	0	transcript_id "Phchi.S1G483000.t1"; gene_id "Phchi.S1G483000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13853.t1 is derived from g12320.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9246604	9247496	.	+	.	Phchi.S3G117200
Phchi.S3	AUGUSTUS	transcript	9246604	9247496	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	start_codon	9246604	9246606	.	+	0	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	CDS	9246604	9246864	0.31	+	0	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	exon	9246604	9246864	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	intron	9246865	9247008	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	CDS	9247009	9247131	1	+	0	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	exon	9247009	9247131	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	intron	9247132	9247222	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	CDS	9247223	9247303	1	+	0	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	exon	9247223	9247303	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	intron	9247304	9247382	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	CDS	9247383	9247496	0.99	+	0	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	exon	9247383	9247496	.	+	.	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
Phchi.S3	AUGUSTUS	stop_codon	9247497	9247499	.	+	0	transcript_id "Phchi.S3G117200.t1"; gene_id "Phchi.S3G117200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9286.t1 is derived from g6461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40763482	40767410	.	-	.	Phchi.S1G644500
Phchi.S1	AUGUSTUS	transcript	40763482	40767410	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	stop_codon	40763479	40763481	.	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40763482	40763715	0.75	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40763482	40763715	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	intron	40763716	40763858	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40763859	40764011	1	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40763859	40764011	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	intron	40764012	40764082	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40764083	40764206	1	-	1	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40764083	40764206	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	intron	40764207	40764328	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40764329	40764417	0.73	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40764329	40764417	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	intron	40764418	40764491	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40764492	40764787	0.97	-	2	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40764492	40764787	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	intron	40764788	40764980	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40764981	40766250	0.38	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40764981	40766250	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	intron	40766251	40766480	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	CDS	40766481	40767410	0.97	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	exon	40766481	40767410	.	-	.	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
Phchi.S1	AUGUSTUS	start_codon	40767408	40767410	.	-	0	transcript_id "Phchi.S1G644500.t1"; gene_id "Phchi.S1G644500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13593.t1 is derived from g12060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7621654	7622724	.	-	.	Phchi.S3G091200
Phchi.S3	AUGUSTUS	transcript	7621654	7622724	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	stop_codon	7621651	7621653	.	-	0	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	CDS	7621654	7621785	0.96	-	0	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	exon	7621654	7621785	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	intron	7621786	7621871	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	CDS	7621872	7622034	1	-	1	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	exon	7621872	7622034	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	intron	7622035	7622138	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	CDS	7622139	7622208	0.74	-	2	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	exon	7622139	7622208	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	intron	7622209	7622312	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	CDS	7622313	7622724	1	-	0	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	exon	7622313	7622724	.	-	.	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
Phchi.S3	AUGUSTUS	start_codon	7622722	7622724	.	-	0	transcript_id "Phchi.S3G091200.t1"; gene_id "Phchi.S3G091200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10223.t1 is derived from g7399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46465647	46467614	.	-	.	Phchi.S1G738200
Phchi.S1	AUGUSTUS	transcript	46465647	46467614	.	-	.	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	stop_codon	46465644	46465646	.	-	0	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	CDS	46465647	46465767	1	-	1	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	exon	46465647	46465767	.	-	.	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	intron	46465768	46465936	.	-	.	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	CDS	46465937	46466524	0.79	-	1	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	exon	46465937	46466524	.	-	.	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	intron	46466525	46466637	.	-	.	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	CDS	46466638	46467614	0.55	-	0	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	exon	46466638	46467614	.	-	.	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
Phchi.S1	AUGUSTUS	start_codon	46467612	46467614	.	-	0	transcript_id "Phchi.S1G738200.t1"; gene_id "Phchi.S1G738200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8474.t1 is derived from g5649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36118547	36118822	.	+	.	Phchi.S1G563300
Phchi.S1	AUGUSTUS	transcript	36118547	36118822	.	+	.	transcript_id "Phchi.S1G563300.t1"; gene_id "Phchi.S1G563300"
Phchi.S1	AUGUSTUS	start_codon	36118547	36118549	.	+	0	transcript_id "Phchi.S1G563300.t1"; gene_id "Phchi.S1G563300"
Phchi.S1	AUGUSTUS	CDS	36118547	36118822	0.89	+	0	transcript_id "Phchi.S1G563300.t1"; gene_id "Phchi.S1G563300"
Phchi.S1	AUGUSTUS	exon	36118547	36118822	.	+	.	transcript_id "Phchi.S1G563300.t1"; gene_id "Phchi.S1G563300"
Phchi.S1	AUGUSTUS	stop_codon	36118823	36118825	.	+	0	transcript_id "Phchi.S1G563300.t1"; gene_id "Phchi.S1G563300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7646.t1 is derived from g4820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30387350	30388436	.	-	.	Phchi.S1G480500
Phchi.S1	AUGUSTUS	transcript	30387350	30388436	.	-	.	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	stop_codon	30387347	30387349	.	-	0	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	CDS	30387350	30387466	0.86	-	0	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	exon	30387350	30387466	.	-	.	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	intron	30387467	30387581	.	-	.	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	CDS	30387582	30387803	0.71	-	0	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	exon	30387582	30387803	.	-	.	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	intron	30387804	30387980	.	-	.	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	CDS	30387981	30388436	0.8	-	0	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	exon	30387981	30388436	.	-	.	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
Phchi.S1	AUGUSTUS	start_codon	30388434	30388436	.	-	0	transcript_id "Phchi.S1G480500.t1"; gene_id "Phchi.S1G480500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2977.t1 is derived from g146.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	935707	940392	.	+	.	Phchi.S1G013600
Phchi.S1	AUGUSTUS	transcript	935707	940392	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	start_codon	935707	935709	.	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	935707	935753	0.46	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	935707	935753	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	935754	935901	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	935902	935953	1	+	1	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	935902	935953	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	935954	936029	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	936030	936106	0.98	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	936030	936106	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	936107	936207	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	936208	936344	0.93	+	1	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	936208	936344	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	936345	936454	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	936455	936551	1	+	2	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	936455	936551	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	936552	936716	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	936717	936774	0.98	+	1	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	936717	936774	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	936775	936876	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	936877	936985	0.98	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	936877	936985	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	936986	937209	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	937210	937333	1	+	2	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	937210	937333	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	937334	937487	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	937488	937692	1	+	1	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	937488	937692	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	937693	937780	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	937781	938055	1	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	937781	938055	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	938056	938139	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	938140	938249	0.93	+	1	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	938140	938249	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	938250	938367	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	938368	938438	0.97	+	2	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	938368	938438	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	938439	938543	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	938544	938660	0.97	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	938544	938660	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	938661	938812	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	938813	938953	0.99	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	938813	938953	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	938954	939049	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	939050	939155	1	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	939050	939155	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	939156	939239	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	939240	939314	1	+	2	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	939240	939314	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	939315	939423	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	939424	939473	1	+	2	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	939424	939473	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	939474	939554	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	939555	939714	1	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	939555	939714	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	939715	939838	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	939839	940011	1	+	2	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	939839	940011	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	intron	940012	940107	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	CDS	940108	940392	0.99	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	exon	940108	940392	.	+	.	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
Phchi.S1	AUGUSTUS	stop_codon	940393	940395	.	+	0	transcript_id "Phchi.S1G013600.t1"; gene_id "Phchi.S1G013600"
# This transcript jg9168.t2 is derived from g6343.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9169.t1 is derived from g6344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40194447	40196456	.	-	.	Phchi.S1G632800
Phchi.S1	AUGUSTUS	transcript	40194447	40196456	.	-	.	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	stop_codon	40194444	40194446	.	-	0	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	CDS	40194447	40194719	1	-	0	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	exon	40194447	40194719	.	-	.	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	intron	40194720	40194803	.	-	.	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	CDS	40194804	40196057	1	-	0	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	exon	40194804	40196057	.	-	.	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	intron	40196058	40196312	.	-	.	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	CDS	40196313	40196456	0.52	-	0	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	exon	40196313	40196456	.	-	.	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
Phchi.S1	AUGUSTUS	start_codon	40196454	40196456	.	-	0	transcript_id "Phchi.S1G632800.t1"; gene_id "Phchi.S1G632800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15782.t1 is derived from g14252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21317572	21318826	.	-	.	Phchi.S3G310100
Phchi.S3	AUGUSTUS	transcript	21317572	21318826	.	-	.	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	stop_codon	21317569	21317571	.	-	0	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	CDS	21317572	21317777	1	-	2	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	exon	21317572	21317777	.	-	.	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	intron	21317778	21317865	.	-	.	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	CDS	21317866	21317925	1	-	2	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	exon	21317866	21317925	.	-	.	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	intron	21317926	21318006	.	-	.	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	CDS	21318007	21318826	0.94	-	0	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	exon	21318007	21318826	.	-	.	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
Phchi.S3	AUGUSTUS	start_codon	21318824	21318826	.	-	0	transcript_id "Phchi.S3G310100.t1"; gene_id "Phchi.S3G310100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12935.t1 is derived from g11400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3239119	3240188	.	-	.	Phchi.S3G025400
Phchi.S3	AUGUSTUS	transcript	3239119	3240188	.	-	.	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	stop_codon	3239116	3239118	.	-	0	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	CDS	3239119	3239129	0.92	-	2	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	exon	3239119	3239129	.	-	.	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	intron	3239130	3239329	.	-	.	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	CDS	3239330	3240188	0.67	-	0	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	exon	3239330	3240188	.	-	.	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
Phchi.S3	AUGUSTUS	start_codon	3240186	3240188	.	-	0	transcript_id "Phchi.S3G025400.t1"; gene_id "Phchi.S3G025400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11937.t1 is derived from g7612.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	101232	104738	.	+	.	Phchi.S2G001700
Phchi.S2	AUGUSTUS	transcript	101232	104738	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	start_codon	101232	101234	.	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	101232	101738	0.45	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	101232	101738	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	101739	101833	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	101834	101919	0.37	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	101834	101919	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	101920	101998	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	101999	102041	0.76	+	1	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	101999	102041	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	102042	102133	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	102134	102374	1	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	102134	102374	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	102375	102519	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	102520	103152	0.76	+	2	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	102520	103152	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	103153	103236	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	103237	103437	0.64	+	2	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	103237	103437	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	103438	103594	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	103595	103830	0.79	+	2	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	103595	103830	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	103831	103912	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	103913	104119	1	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	103913	104119	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	104120	104220	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	104221	104479	1	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	104221	104479	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	intron	104480	104562	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	CDS	104563	104738	0.95	+	2	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	exon	104563	104738	.	+	.	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
Phchi.S2	AUGUSTUS	stop_codon	104739	104741	.	+	0	transcript_id "Phchi.S2G001700.t1"; gene_id "Phchi.S2G001700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12025.t1 is derived from g7700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	621860	625444	.	-	.	Phchi.S2G010500
Phchi.S2	AUGUSTUS	transcript	621860	625444	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	stop_codon	621857	621859	.	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	621860	621998	0.86	-	1	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	621860	621998	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	621999	622103	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	622104	622192	0.93	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	622104	622192	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	622193	622316	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	622317	622472	1	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	622317	622472	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	622473	622631	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	622632	622842	1	-	1	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	622632	622842	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	622843	622926	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	622927	623438	1	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	622927	623438	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	623439	623573	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	623574	623926	1	-	2	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	623574	623926	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	623927	624105	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	624106	624175	1	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	624106	624175	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	624176	624282	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	624283	624716	1	-	2	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	624283	624716	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	624717	624897	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	624898	625070	1	-	1	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	624898	625070	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	intron	625071	625331	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	CDS	625332	625444	1	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	exon	625332	625444	.	-	.	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
Phchi.S2	AUGUSTUS	start_codon	625442	625444	.	-	0	transcript_id "Phchi.S2G010500.t1"; gene_id "Phchi.S2G010500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13547.t1 is derived from g12014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7442209	7442762	.	-	.	Phchi.S3G086600
Phchi.S3	AUGUSTUS	transcript	7442209	7442762	.	-	.	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	stop_codon	7442206	7442208	.	-	0	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	CDS	7442209	7442470	1	-	1	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	exon	7442209	7442470	.	-	.	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	intron	7442471	7442676	.	-	.	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	CDS	7442677	7442762	0.98	-	0	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	exon	7442677	7442762	.	-	.	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
Phchi.S3	AUGUSTUS	start_codon	7442760	7442762	.	-	0	transcript_id "Phchi.S3G086600.t1"; gene_id "Phchi.S3G086600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3900.t1 is derived from g1069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6313477	6315246	.	+	.	Phchi.S1G105900
Phchi.S1	AUGUSTUS	transcript	6313477	6315246	.	+	.	transcript_id "Phchi.S1G105900.t1"; gene_id "Phchi.S1G105900"
Phchi.S1	AUGUSTUS	start_codon	6313477	6313479	.	+	0	transcript_id "Phchi.S1G105900.t1"; gene_id "Phchi.S1G105900"
Phchi.S1	AUGUSTUS	CDS	6313477	6315246	1	+	0	transcript_id "Phchi.S1G105900.t1"; gene_id "Phchi.S1G105900"
Phchi.S1	AUGUSTUS	exon	6313477	6315246	.	+	.	transcript_id "Phchi.S1G105900.t1"; gene_id "Phchi.S1G105900"
Phchi.S1	AUGUSTUS	stop_codon	6315247	6315249	.	+	0	transcript_id "Phchi.S1G105900.t1"; gene_id "Phchi.S1G105900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6525.t1 is derived from g3697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23481315	23484617	.	+	.	Phchi.S1G368400
Phchi.S1	AUGUSTUS	transcript	23481315	23484617	.	+	.	transcript_id "Phchi.S1G368400.t1"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	start_codon	23481315	23481317	.	+	0	transcript_id "Phchi.S1G368400.t1"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	CDS	23481315	23484617	1	+	0	transcript_id "Phchi.S1G368400.t1"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	exon	23481315	23484617	.	+	.	transcript_id "Phchi.S1G368400.t1"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	stop_codon	23484618	23484620	.	+	0	transcript_id "Phchi.S1G368400.t1"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	transcript	23482194	23484617	.	+	.	transcript_id "Phchi.S1G368400.t2"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	start_codon	23482194	23482196	.	+	0	transcript_id "Phchi.S1G368400.t2"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	CDS	23482194	23484617	0.93	+	0	transcript_id "Phchi.S1G368400.t2"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	exon	23482194	23484617	.	+	.	transcript_id "Phchi.S1G368400.t2"; gene_id "Phchi.S1G368400"
Phchi.S1	AUGUSTUS	stop_codon	23484618	23484620	.	+	0	transcript_id "Phchi.S1G368400.t2"; gene_id "Phchi.S1G368400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14957.t1 is derived from g13425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15720697	15721257	.	-	.	Phchi.S3G227600
Phchi.S3	AUGUSTUS	transcript	15720697	15721257	.	-	.	transcript_id "Phchi.S3G227600.t1"; gene_id "Phchi.S3G227600"
Phchi.S3	AUGUSTUS	stop_codon	15720694	15720696	.	-	0	transcript_id "Phchi.S3G227600.t1"; gene_id "Phchi.S3G227600"
Phchi.S3	AUGUSTUS	CDS	15720697	15721257	1	-	0	transcript_id "Phchi.S3G227600.t1"; gene_id "Phchi.S3G227600"
Phchi.S3	AUGUSTUS	exon	15720697	15721257	.	-	.	transcript_id "Phchi.S3G227600.t1"; gene_id "Phchi.S3G227600"
Phchi.S3	AUGUSTUS	start_codon	15721255	15721257	.	-	0	transcript_id "Phchi.S3G227600.t1"; gene_id "Phchi.S3G227600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11660.t1 is derived from g15711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7556881	7561320	.	-	.	Phchi.S4G124200
Phchi.S4	AUGUSTUS	transcript	7556881	7561320	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	stop_codon	7556878	7556880	.	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7556881	7556918	0.95	-	2	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7556881	7556918	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7556919	7556998	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7556999	7557064	1	-	2	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7556999	7557064	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7557065	7557265	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7557266	7557297	1	-	1	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7557266	7557297	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7557298	7557384	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7557385	7557395	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7557385	7557395	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7557396	7557495	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7557496	7557573	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7557496	7557573	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7557574	7557661	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7557662	7557739	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7557662	7557739	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7557740	7557887	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7557888	7557944	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7557888	7557944	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7557945	7558079	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7558080	7558153	1	-	2	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7558080	7558153	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7558154	7558288	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7558289	7558360	1	-	2	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7558289	7558360	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7558361	7558491	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7558492	7558553	1	-	1	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7558492	7558553	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7558554	7558631	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7558632	7558733	1	-	1	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7558632	7558733	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7558734	7558842	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7558843	7558955	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7558843	7558955	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7558956	7559073	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7559074	7559205	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7559074	7559205	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7559206	7559298	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7559299	7559386	1	-	1	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7559299	7559386	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7559387	7559492	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7559493	7559587	0.97	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7559493	7559587	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7559588	7559748	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7559749	7559979	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7559749	7559979	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7559980	7560160	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7560161	7560277	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7560161	7560277	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7560278	7560365	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7560366	7560467	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7560366	7560467	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7560468	7560627	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7560628	7560744	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7560628	7560744	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7560745	7560867	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7560868	7561097	1	-	2	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7560868	7561097	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	intron	7561098	7561175	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	CDS	7561176	7561320	1	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	exon	7561176	7561320	.	-	.	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
Phchi.S4	AUGUSTUS	start_codon	7561318	7561320	.	-	0	transcript_id "Phchi.S4G124200.t1"; gene_id "Phchi.S4G124200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3456.t1 is derived from g625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3865654	3866613	.	+	.	Phchi.S1G061500
Phchi.S1	AUGUSTUS	transcript	3865654	3866613	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	start_codon	3865654	3865656	.	+	0	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	CDS	3865654	3865735	0.56	+	0	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	exon	3865654	3865735	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	intron	3865736	3865925	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	CDS	3865926	3866095	1	+	2	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	exon	3865926	3866095	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	intron	3866096	3866227	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	CDS	3866228	3866302	1	+	0	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	exon	3866228	3866302	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	intron	3866303	3866379	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	CDS	3866380	3866455	0.99	+	0	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	exon	3866380	3866455	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	intron	3866456	3866560	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	CDS	3866561	3866613	0.98	+	2	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	exon	3866561	3866613	.	+	.	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
Phchi.S1	AUGUSTUS	stop_codon	3866614	3866616	.	+	0	transcript_id "Phchi.S1G061500.t1"; gene_id "Phchi.S1G061500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11843.t1 is derived from g15895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8538710	8539719	.	+	.	Phchi.S4G142500
Phchi.S4	AUGUSTUS	transcript	8538710	8539719	.	+	.	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	start_codon	8538710	8538712	.	+	0	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	CDS	8538710	8538882	0.99	+	0	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	exon	8538710	8538882	.	+	.	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	intron	8538883	8539005	.	+	.	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	CDS	8539006	8539141	1	+	1	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	exon	8539006	8539141	.	+	.	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	intron	8539142	8539260	.	+	.	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	CDS	8539261	8539719	1	+	0	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	exon	8539261	8539719	.	+	.	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
Phchi.S4	AUGUSTUS	stop_codon	8539720	8539722	.	+	0	transcript_id "Phchi.S4G142500.t1"; gene_id "Phchi.S4G142500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6636.t1 is derived from g3808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24189465	24190876	.	-	.	Phchi.S1G379500
Phchi.S1	AUGUSTUS	transcript	24189465	24190876	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	stop_codon	24189462	24189464	.	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24189465	24189537	1	-	1	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24189465	24189537	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24189538	24189635	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24189636	24189721	1	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24189636	24189721	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24189722	24189797	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24189798	24189878	1	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24189798	24189878	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24189879	24190010	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24190011	24190045	1	-	2	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24190011	24190045	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24190046	24190127	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24190128	24190194	1	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24190128	24190194	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24190195	24190296	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24190297	24190377	1	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24190297	24190377	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24190378	24190502	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24190503	24190706	1	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24190503	24190706	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	intron	24190707	24190780	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	CDS	24190781	24190876	1	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	exon	24190781	24190876	.	-	.	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
Phchi.S1	AUGUSTUS	start_codon	24190874	24190876	.	-	0	transcript_id "Phchi.S1G379500.t1"; gene_id "Phchi.S1G379500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10.t1 is derived from g9777.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C265	AUGUSTUS	gene	290	798	.	+	.	Phchi.C265G000100
Phchi.C265	AUGUSTUS	transcript	290	798	.	+	.	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	start_codon	290	292	.	+	0	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	CDS	290	574	0.4	+	0	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	exon	290	574	.	+	.	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	intron	575	768	.	+	.	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	CDS	769	798	0.47	+	0	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	exon	769	798	.	+	.	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
Phchi.C265	AUGUSTUS	stop_codon	799	801	.	+	0	transcript_id "Phchi.C265G000100.t1"; gene_id "Phchi.C265G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6854.t1 is derived from g4026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25583896	25588328	.	+	.	Phchi.S1G401300
Phchi.S1	AUGUSTUS	transcript	25583896	25588328	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	start_codon	25583896	25583898	.	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25583896	25584383	0.86	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25583896	25584383	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25584384	25584607	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25584608	25584671	1	+	1	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25584608	25584671	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25584672	25584786	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25584787	25584931	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25584787	25584931	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25584932	25585043	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25585044	25585159	0.99	+	2	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25585044	25585159	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25585160	25585275	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25585276	25585404	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25585276	25585404	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25585405	25585488	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25585489	25585659	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25585489	25585659	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25585660	25585759	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25585760	25585811	0.93	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25585760	25585811	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25585812	25585882	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25585883	25585923	0.81	+	2	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25585883	25585923	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25585924	25586073	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25586074	25586214	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25586074	25586214	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25586215	25586301	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25586302	25586401	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25586302	25586401	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25586402	25586505	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25586506	25586614	1	+	2	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25586506	25586614	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25586615	25586688	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25586689	25586780	1	+	1	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25586689	25586780	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25586781	25586870	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25586871	25586976	1	+	2	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25586871	25586976	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25586977	25587073	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25587074	25587308	1	+	1	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25587074	25587308	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25587309	25587389	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25587390	25587482	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25587390	25587482	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25587483	25587659	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25587660	25587708	1	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25587660	25587708	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25587709	25587789	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25587790	25587886	1	+	2	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25587790	25587886	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	intron	25587887	25588009	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	CDS	25588010	25588328	0.82	+	1	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	exon	25588010	25588328	.	+	.	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
Phchi.S1	AUGUSTUS	stop_codon	25588329	25588331	.	+	0	transcript_id "Phchi.S1G401300.t1"; gene_id "Phchi.S1G401300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4176.t1 is derived from g1345.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8768624	8770927	.	+	.	Phchi.S1G133500
Phchi.S1	AUGUSTUS	transcript	8768624	8770927	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	start_codon	8768624	8768626	.	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8768624	8768825	1	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8768624	8768825	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	intron	8768826	8768922	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8768923	8769083	1	+	2	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8768923	8769083	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	intron	8769084	8769197	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8769198	8769359	0.99	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8769198	8769359	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	intron	8769360	8769487	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8769488	8769892	1	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8769488	8769892	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	intron	8769893	8769988	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8769989	8770156	0.99	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8769989	8770156	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	intron	8770157	8770283	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8770284	8770478	1	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8770284	8770478	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	intron	8770479	8770579	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	CDS	8770580	8770927	0.92	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	exon	8770580	8770927	.	+	.	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
Phchi.S1	AUGUSTUS	stop_codon	8770928	8770930	.	+	0	transcript_id "Phchi.S1G133500.t1"; gene_id "Phchi.S1G133500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15761.t1 is derived from g14231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21107107	21110048	.	+	.	Phchi.S3G308000
Phchi.S3	AUGUSTUS	transcript	21107107	21110048	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	start_codon	21107107	21107109	.	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21107107	21107172	0.77	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21107107	21107172	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21107173	21107251	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21107252	21107368	1	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21107252	21107368	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21107369	21107442	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21107443	21107728	1	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21107443	21107728	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21107729	21107827	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21107828	21107946	1	+	2	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21107828	21107946	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21107947	21108023	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21108024	21108153	1	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21108024	21108153	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21108154	21108248	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21108249	21108325	1	+	2	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21108249	21108325	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21108326	21108412	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21108413	21108610	1	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21108413	21108610	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21108611	21108751	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21108752	21108938	1	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21108752	21108938	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21108939	21109017	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21109018	21109211	1	+	2	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21109018	21109211	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21109212	21109299	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21109300	21109385	0.99	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21109300	21109385	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21109386	21109552	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21109553	21109801	0.38	+	1	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21109553	21109801	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	intron	21109802	21109990	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	CDS	21109991	21110048	0.51	+	1	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	exon	21109991	21110048	.	+	.	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
Phchi.S3	AUGUSTUS	stop_codon	21110049	21110051	.	+	0	transcript_id "Phchi.S3G308000.t1"; gene_id "Phchi.S3G308000"
# This transcript jg14659.t2 is derived from g13127.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14659.t3 is derived from g13127.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14660.t1 is derived from g13128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14001736	14002101	.	-	.	Phchi.S3G197900
Phchi.S3	AUGUSTUS	transcript	14001736	14002101	.	-	.	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	stop_codon	14001733	14001735	.	-	0	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	CDS	14001736	14001813	0.64	-	0	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	exon	14001736	14001813	.	-	.	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	intron	14001814	14001921	.	-	.	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	CDS	14001922	14002101	0.62	-	0	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	exon	14001922	14002101	.	-	.	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
Phchi.S3	AUGUSTUS	start_codon	14002099	14002101	.	-	0	transcript_id "Phchi.S3G197900.t1"; gene_id "Phchi.S3G197900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4954.t1 is derived from g2124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13722028	13723574	.	+	.	Phchi.S1G211300
Phchi.S1	AUGUSTUS	transcript	13722028	13723574	.	+	.	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	start_codon	13722028	13722030	.	+	0	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	CDS	13722028	13722494	0.37	+	0	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	exon	13722028	13722494	.	+	.	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	intron	13722495	13722630	.	+	.	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	CDS	13722631	13723180	1	+	1	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	exon	13722631	13723180	.	+	.	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	intron	13723181	13723313	.	+	.	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	CDS	13723314	13723574	0.98	+	0	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	exon	13723314	13723574	.	+	.	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
Phchi.S1	AUGUSTUS	stop_codon	13723575	13723577	.	+	0	transcript_id "Phchi.S1G211300.t1"; gene_id "Phchi.S1G211300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15659.t1 is derived from g14128.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20526066	20529347	.	+	.	Phchi.S3G297800
Phchi.S3	AUGUSTUS	transcript	20526066	20529347	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	start_codon	20526066	20526068	.	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20526066	20526202	1	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20526066	20526202	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20526203	20526397	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20526398	20526632	1	+	1	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20526398	20526632	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20526633	20526737	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20526738	20526884	0.98	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20526738	20526884	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20526885	20526976	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20526977	20527105	1	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20526977	20527105	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20527106	20527209	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20527210	20527338	0.98	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20527210	20527338	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20527339	20527429	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20527430	20527513	1	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20527430	20527513	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20527514	20527659	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20527660	20527784	1	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20527660	20527784	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20527785	20527879	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20527880	20528078	1	+	1	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20527880	20528078	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20528079	20528172	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20528173	20528705	1	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20528173	20528705	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20528706	20528796	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20528797	20528905	1	+	1	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20528797	20528905	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	intron	20528906	20529002	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	CDS	20529003	20529347	1	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	exon	20529003	20529347	.	+	.	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
Phchi.S3	AUGUSTUS	stop_codon	20529348	20529350	.	+	0	transcript_id "Phchi.S3G297800.t1"; gene_id "Phchi.S3G297800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10135.t1 is derived from g7311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45930165	45934604	.	-	.	Phchi.S1G729400
Phchi.S1	AUGUSTUS	transcript	45930165	45934604	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	stop_codon	45930162	45930164	.	-	0	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	CDS	45930165	45931298	0.86	-	0	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	exon	45930165	45931298	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	intron	45931299	45931422	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	CDS	45931423	45931703	0.69	-	2	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	exon	45931423	45931703	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	intron	45931704	45931829	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	CDS	45931830	45932876	0.53	-	2	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	exon	45931830	45932876	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	intron	45932877	45933031	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	CDS	45933032	45934604	0.89	-	0	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	exon	45933032	45934604	.	-	.	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
Phchi.S1	AUGUSTUS	start_codon	45934602	45934604	.	-	0	transcript_id "Phchi.S1G729400.t1"; gene_id "Phchi.S1G729400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9870.t1 is derived from g7046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44180137	44180742	.	+	.	Phchi.S1G702900
Phchi.S1	AUGUSTUS	transcript	44180137	44180742	.	+	.	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	start_codon	44180137	44180139	.	+	0	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	CDS	44180137	44180141	0.99	+	0	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	exon	44180137	44180141	.	+	.	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	intron	44180142	44180435	.	+	.	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	CDS	44180436	44180742	0.38	+	1	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	exon	44180436	44180742	.	+	.	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
Phchi.S1	AUGUSTUS	stop_codon	44180743	44180745	.	+	0	transcript_id "Phchi.S1G702900.t1"; gene_id "Phchi.S1G702900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7699.t1 is derived from g4873.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30697018	30697557	.	-	.	Phchi.S1G485800
Phchi.S1	AUGUSTUS	transcript	30697018	30697557	.	-	.	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	stop_codon	30697015	30697017	.	-	0	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	CDS	30697018	30697175	0.82	-	2	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	exon	30697018	30697175	.	-	.	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	intron	30697176	30697346	.	-	.	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	CDS	30697347	30697557	1	-	0	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	exon	30697347	30697557	.	-	.	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
Phchi.S1	AUGUSTUS	start_codon	30697555	30697557	.	-	0	transcript_id "Phchi.S1G485800.t1"; gene_id "Phchi.S1G485800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3563.t1 is derived from g732.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4497587	4499519	.	+	.	Phchi.S1G072200
Phchi.S1	AUGUSTUS	transcript	4497587	4499519	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	start_codon	4497587	4497589	.	+	0	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	CDS	4497587	4497855	0.24	+	0	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	exon	4497587	4497855	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	intron	4497856	4498064	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	CDS	4498065	4498083	0.47	+	1	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	exon	4498065	4498083	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	intron	4498084	4498233	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	CDS	4498234	4499305	0.84	+	0	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	exon	4498234	4499305	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	intron	4499306	4499430	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	CDS	4499431	4499519	0.75	+	2	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	exon	4499431	4499519	.	+	.	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
Phchi.S1	AUGUSTUS	stop_codon	4499520	4499522	.	+	0	transcript_id "Phchi.S1G072200.t1"; gene_id "Phchi.S1G072200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3910.t1 is derived from g1079.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6409655	6410227	.	+	.	Phchi.S1G106900
Phchi.S1	AUGUSTUS	transcript	6409655	6410227	.	+	.	transcript_id "Phchi.S1G106900.t1"; gene_id "Phchi.S1G106900"
Phchi.S1	AUGUSTUS	start_codon	6409655	6409657	.	+	0	transcript_id "Phchi.S1G106900.t1"; gene_id "Phchi.S1G106900"
Phchi.S1	AUGUSTUS	CDS	6409655	6410227	0.74	+	0	transcript_id "Phchi.S1G106900.t1"; gene_id "Phchi.S1G106900"
Phchi.S1	AUGUSTUS	exon	6409655	6410227	.	+	.	transcript_id "Phchi.S1G106900.t1"; gene_id "Phchi.S1G106900"
Phchi.S1	AUGUSTUS	stop_codon	6410228	6410230	.	+	0	transcript_id "Phchi.S1G106900.t1"; gene_id "Phchi.S1G106900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5060.t1 is derived from g2230.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14477542	14481743	.	+	.	Phchi.S1G221900
Phchi.S1	AUGUSTUS	transcript	14477542	14481743	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	start_codon	14477542	14477544	.	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14477542	14477688	1	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14477542	14477688	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14477689	14478253	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478254	14478306	1	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478254	14478306	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478307	14478442	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478443	14478611	1	+	1	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478443	14478611	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478612	14478696	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478697	14478760	0.96	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478697	14478760	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478761	14478854	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478855	14478955	0.54	+	2	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478855	14478955	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478956	14479061	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479062	14479224	1	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479062	14479224	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479225	14479372	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479373	14479434	1	+	2	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479373	14479434	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479435	14479595	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479596	14479658	1	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479596	14479658	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479659	14479918	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479919	14479977	1	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479919	14479977	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479978	14480064	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480065	14480146	1	+	1	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480065	14480146	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14480147	14480294	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480295	14480341	1	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480295	14480341	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14480342	14480462	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480463	14480726	0.95	+	1	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480463	14480726	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14480727	14480985	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480986	14481044	0.99	+	1	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480986	14481044	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14481045	14481130	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14481131	14481232	0.99	+	2	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14481131	14481232	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14481233	14481496	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14481497	14481538	0.87	+	2	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14481497	14481538	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14481539	14481714	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14481715	14481743	0.93	+	2	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14481715	14481743	.	+	.	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	stop_codon	14481744	14481746	.	+	0	transcript_id "Phchi.S1G221900.t1"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	transcript	14477542	14481743	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	start_codon	14477542	14477544	.	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14477542	14477688	1	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14477542	14477688	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14477689	14478253	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478254	14478306	1	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478254	14478306	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478307	14478442	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478443	14478611	1	+	1	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478443	14478611	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478612	14478696	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478697	14478760	0.98	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478697	14478760	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478761	14478854	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14478855	14478955	0.5	+	2	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14478855	14478955	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14478956	14479061	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479062	14479224	0.96	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479062	14479224	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479225	14479372	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479373	14479434	1	+	2	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479373	14479434	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479435	14479595	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479596	14479658	1	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479596	14479658	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479659	14479912	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14479913	14479977	1	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14479913	14479977	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14479978	14480064	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480065	14480146	1	+	1	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480065	14480146	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14480147	14480294	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480295	14480341	1	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480295	14480341	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14480342	14480462	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480463	14480726	0.98	+	1	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480463	14480726	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14480727	14480985	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14480986	14481044	1	+	1	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14480986	14481044	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14481045	14481130	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14481131	14481232	1	+	2	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14481131	14481232	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14481233	14481496	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14481497	14481538	0.85	+	2	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14481497	14481538	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	intron	14481539	14481714	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	CDS	14481715	14481743	0.96	+	2	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	exon	14481715	14481743	.	+	.	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
Phchi.S1	AUGUSTUS	stop_codon	14481744	14481746	.	+	0	transcript_id "Phchi.S1G221900.t2"; gene_id "Phchi.S1G221900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13639.t1 is derived from g12106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7965174	7965605	.	-	.	Phchi.S3G095800
Phchi.S3	AUGUSTUS	transcript	7965174	7965605	.	-	.	transcript_id "Phchi.S3G095800.t1"; gene_id "Phchi.S3G095800"
Phchi.S3	AUGUSTUS	stop_codon	7965171	7965173	.	-	0	transcript_id "Phchi.S3G095800.t1"; gene_id "Phchi.S3G095800"
Phchi.S3	AUGUSTUS	CDS	7965174	7965605	0.98	-	0	transcript_id "Phchi.S3G095800.t1"; gene_id "Phchi.S3G095800"
Phchi.S3	AUGUSTUS	exon	7965174	7965605	.	-	.	transcript_id "Phchi.S3G095800.t1"; gene_id "Phchi.S3G095800"
Phchi.S3	AUGUSTUS	start_codon	7965603	7965605	.	-	0	transcript_id "Phchi.S3G095800.t1"; gene_id "Phchi.S3G095800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8597.t1 is derived from g5772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36828785	36831595	.	+	.	Phchi.S1G575600
Phchi.S1	AUGUSTUS	transcript	36828785	36831595	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	start_codon	36828785	36828787	.	+	0	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36828785	36828908	0.64	+	0	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36828785	36828908	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36828909	36828992	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36828993	36829104	0.92	+	2	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36828993	36829104	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36829105	36829191	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36829192	36829534	0.93	+	1	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36829192	36829534	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36829535	36829624	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36829625	36829974	1	+	0	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36829625	36829974	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36829975	36830080	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36830081	36830329	0.98	+	1	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36830081	36830329	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36830330	36830452	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36830453	36830576	0.56	+	1	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36830453	36830576	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36830577	36830708	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36830709	36830807	0.87	+	0	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36830709	36830807	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	intron	36830808	36830932	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	CDS	36830933	36831595	0.83	+	0	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	exon	36830933	36831595	.	+	.	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
Phchi.S1	AUGUSTUS	stop_codon	36831596	36831598	.	+	0	transcript_id "Phchi.S1G575600.t1"; gene_id "Phchi.S1G575600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14802.t1 is derived from g13270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14783835	14785571	.	+	.	Phchi.S3G212100
Phchi.S3	AUGUSTUS	transcript	14783835	14785571	.	+	.	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	start_codon	14783835	14783837	.	+	0	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	CDS	14783835	14784281	1	+	0	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	exon	14783835	14784281	.	+	.	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	intron	14784282	14784378	.	+	.	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	CDS	14784379	14784644	0.99	+	0	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	exon	14784379	14784644	.	+	.	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	intron	14784645	14784802	.	+	.	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	CDS	14784803	14785571	0.97	+	1	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	exon	14784803	14785571	.	+	.	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
Phchi.S3	AUGUSTUS	stop_codon	14785572	14785574	.	+	0	transcript_id "Phchi.S3G212100.t1"; gene_id "Phchi.S3G212100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3109.t1 is derived from g278.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1768306	1769730	.	+	.	Phchi.S1G026800
Phchi.S1	AUGUSTUS	transcript	1768306	1769730	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	start_codon	1768306	1768308	.	+	0	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768306	1768432	0.93	+	0	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768306	1768432	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	intron	1768433	1768515	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768516	1768601	0.98	+	2	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768516	1768601	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	intron	1768602	1768711	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768712	1768786	0.97	+	0	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768712	1768786	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	intron	1768787	1768902	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768903	1769730	0.94	+	0	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768903	1769730	.	+	.	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	stop_codon	1769731	1769733	.	+	0	transcript_id "Phchi.S1G026800.t1"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	transcript	1768306	1769730	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	start_codon	1768306	1768308	.	+	0	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768306	1768441	0.79	+	0	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768306	1768441	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	intron	1768442	1768515	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768516	1768601	1	+	2	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768516	1768601	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	intron	1768602	1768711	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768712	1768786	0.94	+	0	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768712	1768786	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	intron	1768787	1768902	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	CDS	1768903	1769730	1	+	0	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	exon	1768903	1769730	.	+	.	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
Phchi.S1	AUGUSTUS	stop_codon	1769731	1769733	.	+	0	transcript_id "Phchi.S1G026800.t2"; gene_id "Phchi.S1G026800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15459.t1 is derived from g13927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19288178	19288929	.	+	.	Phchi.S3G277800
Phchi.S3	AUGUSTUS	transcript	19288178	19288929	.	+	.	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	start_codon	19288178	19288180	.	+	0	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	CDS	19288178	19288287	0.65	+	0	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	exon	19288178	19288287	.	+	.	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	intron	19288288	19288736	.	+	.	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	CDS	19288737	19288929	0.81	+	1	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	exon	19288737	19288929	.	+	.	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
Phchi.S3	AUGUSTUS	stop_codon	19288930	19288932	.	+	0	transcript_id "Phchi.S3G277800.t1"; gene_id "Phchi.S3G277800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13777.t1 is derived from g12244.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8857583	8858812	.	-	.	Phchi.S3G109600
Phchi.S3	AUGUSTUS	transcript	8857583	8858812	.	-	.	transcript_id "Phchi.S3G109600.t1"; gene_id "Phchi.S3G109600"
Phchi.S3	AUGUSTUS	stop_codon	8857580	8857582	.	-	0	transcript_id "Phchi.S3G109600.t1"; gene_id "Phchi.S3G109600"
Phchi.S3	AUGUSTUS	CDS	8857583	8858812	0.98	-	0	transcript_id "Phchi.S3G109600.t1"; gene_id "Phchi.S3G109600"
Phchi.S3	AUGUSTUS	exon	8857583	8858812	.	-	.	transcript_id "Phchi.S3G109600.t1"; gene_id "Phchi.S3G109600"
Phchi.S3	AUGUSTUS	start_codon	8858810	8858812	.	-	0	transcript_id "Phchi.S3G109600.t1"; gene_id "Phchi.S3G109600"
# This transcript jg12250.t2 is derived from g7926.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12250.t3 is derived from g7926.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12251.t1 is derived from g7927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7014155	7015008	.	-	.	Phchi.S2G033100
Phchi.S2	AUGUSTUS	transcript	7014155	7015008	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	stop_codon	7014152	7014154	.	-	0	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	CDS	7014155	7014235	0.98	-	0	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	exon	7014155	7014235	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	intron	7014236	7014328	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	CDS	7014329	7014496	1	-	0	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	exon	7014329	7014496	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	intron	7014497	7014592	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	CDS	7014593	7014798	1	-	2	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	exon	7014593	7014798	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	intron	7014799	7014893	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	CDS	7014894	7015008	1	-	0	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	exon	7014894	7015008	.	-	.	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
Phchi.S2	AUGUSTUS	start_codon	7015006	7015008	.	-	0	transcript_id "Phchi.S2G033100.t1"; gene_id "Phchi.S2G033100"
# This transcript jg1960.t2 is derived from g8880.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1961.t1 is derived from g8881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4053688	4055137	.	-	.	Phchi.S5G057000
Phchi.S5	AUGUSTUS	transcript	4053688	4055137	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	stop_codon	4053685	4053687	.	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	CDS	4053688	4053831	0.94	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	exon	4053688	4053831	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	intron	4053832	4054042	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	CDS	4054043	4054174	1	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	exon	4054043	4054174	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	intron	4054175	4054316	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	CDS	4054317	4054445	0.79	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	exon	4054317	4054445	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	intron	4054446	4054529	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	CDS	4054530	4054622	0.78	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	exon	4054530	4054622	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	intron	4054623	4054675	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	CDS	4054676	4054746	0.79	-	2	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	exon	4054676	4054746	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	intron	4054747	4054830	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	CDS	4054831	4055137	0.71	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	exon	4054831	4055137	.	-	.	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
Phchi.S5	AUGUSTUS	start_codon	4055135	4055137	.	-	0	transcript_id "Phchi.S5G057000.t1"; gene_id "Phchi.S5G057000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6415.t1 is derived from g3587.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22859370	22859748	.	+	.	Phchi.S1G357400
Phchi.S1	AUGUSTUS	transcript	22859370	22859748	.	+	.	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	start_codon	22859370	22859372	.	+	0	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	CDS	22859370	22859523	0.65	+	0	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	exon	22859370	22859523	.	+	.	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	intron	22859524	22859623	.	+	.	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	CDS	22859624	22859748	0.93	+	2	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	exon	22859624	22859748	.	+	.	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
Phchi.S1	AUGUSTUS	stop_codon	22859749	22859751	.	+	0	transcript_id "Phchi.S1G357400.t1"; gene_id "Phchi.S1G357400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6380.t1 is derived from g3552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22649157	22652482	.	-	.	Phchi.S1G353900
Phchi.S1	AUGUSTUS	transcript	22649157	22652482	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	stop_codon	22649154	22649156	.	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22649157	22649406	0.94	-	1	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22649157	22649406	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22649407	22649499	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22649500	22649629	1	-	2	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22649500	22649629	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22649630	22649722	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22649723	22649826	1	-	1	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22649723	22649826	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22649827	22649912	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22649913	22649998	1	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22649913	22649998	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22649999	22650113	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22650114	22650180	1	-	1	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22650114	22650180	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22650181	22650268	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22650269	22650624	0.59	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22650269	22650624	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22650625	22650744	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22650745	22650828	0.58	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22650745	22650828	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22650829	22650943	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22650944	22650994	1	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22650944	22650994	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22650995	22651197	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22651198	22651266	0.61	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22651198	22651266	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22651267	22651477	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22651478	22651630	0.76	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22651478	22651630	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22651631	22651845	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22651846	22651890	1	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22651846	22651890	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22651891	22652084	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22652085	22652294	1	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22652085	22652294	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	intron	22652295	22652437	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	CDS	22652438	22652482	0.96	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	exon	22652438	22652482	.	-	.	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
Phchi.S1	AUGUSTUS	start_codon	22652480	22652482	.	-	0	transcript_id "Phchi.S1G353900.t1"; gene_id "Phchi.S1G353900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2249.t1 is derived from g9169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5687329	5689034	.	+	.	Phchi.S5G085800
Phchi.S5	AUGUSTUS	transcript	5687329	5689034	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	start_codon	5687329	5687331	.	+	0	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	CDS	5687329	5688498	0.79	+	0	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	exon	5687329	5688498	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	intron	5688499	5688703	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	CDS	5688704	5688747	1	+	0	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	exon	5688704	5688747	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	intron	5688748	5688837	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	CDS	5688838	5688911	1	+	1	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	exon	5688838	5688911	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	intron	5688912	5689005	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	CDS	5689006	5689034	1	+	2	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	exon	5689006	5689034	.	+	.	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
Phchi.S5	AUGUSTUS	stop_codon	5689035	5689037	.	+	0	transcript_id "Phchi.S5G085800.t1"; gene_id "Phchi.S5G085800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13501.t1 is derived from g11968.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7198784	7199716	.	-	.	Phchi.S3G082000
Phchi.S3	AUGUSTUS	transcript	7198784	7199716	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	stop_codon	7198781	7198783	.	-	0	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	CDS	7198784	7198904	0.91	-	1	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	exon	7198784	7198904	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	intron	7198905	7199003	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	CDS	7199004	7199187	1	-	2	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	exon	7199004	7199187	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	intron	7199188	7199276	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	CDS	7199277	7199517	1	-	0	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	exon	7199277	7199517	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	intron	7199518	7199644	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	CDS	7199645	7199716	1	-	0	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	exon	7199645	7199716	.	-	.	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
Phchi.S3	AUGUSTUS	start_codon	7199714	7199716	.	-	0	transcript_id "Phchi.S3G082000.t1"; gene_id "Phchi.S3G082000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg828.t1 is derived from g10610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5769427	5769903	.	+	.	Phchi.S6G078700
Phchi.S6	AUGUSTUS	transcript	5769427	5769903	.	+	.	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	start_codon	5769427	5769429	.	+	0	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	CDS	5769427	5769465	0.34	+	0	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	exon	5769427	5769465	.	+	.	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	intron	5769466	5769543	.	+	.	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	CDS	5769544	5769645	0.5	+	0	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	exon	5769544	5769645	.	+	.	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	intron	5769646	5769777	.	+	.	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	CDS	5769778	5769903	0.42	+	0	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	exon	5769778	5769903	.	+	.	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
Phchi.S6	AUGUSTUS	stop_codon	5769904	5769906	.	+	0	transcript_id "Phchi.S6G078700.t1"; gene_id "Phchi.S6G078700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15866.t1 is derived from g14336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21937566	21939625	.	+	.	Phchi.S3G318500
Phchi.S3	AUGUSTUS	transcript	21937566	21939625	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	start_codon	21937566	21937568	.	+	0	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21937566	21937971	0.99	+	0	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21937566	21937971	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21937972	21938165	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21938166	21938313	1	+	2	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21938166	21938313	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21938314	21938503	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21938504	21938695	1	+	1	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21938504	21938695	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21938696	21938814	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21938815	21938943	1	+	1	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21938815	21938943	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21938944	21939033	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939034	21939095	0.62	+	1	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939034	21939095	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21939096	21939181	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939182	21939203	1	+	2	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939182	21939203	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21939204	21939335	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939336	21939465	1	+	1	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939336	21939465	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21939466	21939553	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939554	21939625	1	+	0	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939554	21939625	.	+	.	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	stop_codon	21939626	21939628	.	+	0	transcript_id "Phchi.S3G318500.t1"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	transcript	21937566	21939625	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	start_codon	21937566	21937568	.	+	0	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21937566	21937971	0.98	+	0	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21937566	21937971	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21937972	21938165	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21938166	21938313	1	+	2	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21938166	21938313	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21938314	21938503	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21938504	21938695	1	+	1	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21938504	21938695	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21938696	21938814	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21938815	21938943	1	+	1	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21938815	21938943	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21938944	21939047	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939048	21939064	0.44	+	1	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939048	21939064	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21939065	21939181	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939182	21939203	0.87	+	2	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939182	21939203	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21939204	21939335	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939336	21939465	1	+	1	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939336	21939465	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	intron	21939466	21939553	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	CDS	21939554	21939625	1	+	0	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	exon	21939554	21939625	.	+	.	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
Phchi.S3	AUGUSTUS	stop_codon	21939626	21939628	.	+	0	transcript_id "Phchi.S3G318500.t2"; gene_id "Phchi.S3G318500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg787.t1 is derived from g10569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5586555	5590058	.	+	.	Phchi.S6G074600
Phchi.S6	AUGUSTUS	transcript	5586555	5590058	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	start_codon	5586555	5586557	.	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5586555	5586657	0.45	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5586555	5586657	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5586658	5586781	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5586782	5586841	1	+	2	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5586782	5586841	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5586842	5587283	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5587284	5587321	1	+	2	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5587284	5587321	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5587322	5587456	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5587457	5588391	1	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5587457	5588391	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5588392	5588496	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5588497	5588938	0.79	+	1	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5588497	5588938	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5588939	5589029	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5589030	5589179	1	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5589030	5589179	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5589180	5589270	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5589271	5589570	0.64	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5589271	5589570	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5589571	5589652	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5589653	5589664	0.64	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5589653	5589664	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5589665	5589735	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5589736	5589849	0.66	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5589736	5589849	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	intron	5589850	5589935	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	CDS	5589936	5590058	1	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	exon	5589936	5590058	.	+	.	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
Phchi.S6	AUGUSTUS	stop_codon	5590059	5590061	.	+	0	transcript_id "Phchi.S6G074600.t1"; gene_id "Phchi.S6G074600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3719.t1 is derived from g888.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5359190	5360802	.	+	.	Phchi.S1G087800
Phchi.S1	AUGUSTUS	transcript	5359190	5360802	.	+	.	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	start_codon	5359190	5359192	.	+	0	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	CDS	5359190	5359287	0.38	+	0	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	exon	5359190	5359287	.	+	.	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	intron	5359288	5359383	.	+	.	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	CDS	5359384	5359599	0.36	+	1	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	exon	5359384	5359599	.	+	.	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	intron	5359600	5359694	.	+	.	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	CDS	5359695	5360802	0.57	+	1	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	exon	5359695	5360802	.	+	.	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
Phchi.S1	AUGUSTUS	stop_codon	5360803	5360805	.	+	0	transcript_id "Phchi.S1G087800.t1"; gene_id "Phchi.S1G087800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg363.t1 is derived from g10145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2654969	2656764	.	+	.	Phchi.S6G032200
Phchi.S6	AUGUSTUS	transcript	2654969	2656764	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	start_codon	2654969	2654971	.	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2654969	2655209	0.88	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2654969	2655209	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	intron	2655210	2655315	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2655316	2655533	0.97	+	2	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2655316	2655533	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	intron	2655534	2655634	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2655635	2655742	1	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2655635	2655742	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	intron	2655743	2655842	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2655843	2656007	1	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2655843	2656007	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	intron	2656008	2656235	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2656236	2656407	1	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2656236	2656407	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	intron	2656408	2656521	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2656522	2656595	1	+	2	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2656522	2656595	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	intron	2656596	2656680	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	CDS	2656681	2656764	0.99	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	exon	2656681	2656764	.	+	.	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
Phchi.S6	AUGUSTUS	stop_codon	2656765	2656767	.	+	0	transcript_id "Phchi.S6G032200.t1"; gene_id "Phchi.S6G032200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3501.t1 is derived from g670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4111682	4112836	.	+	.	Phchi.S1G066000
Phchi.S1	AUGUSTUS	transcript	4111682	4112836	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	start_codon	4111682	4111684	.	+	0	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	CDS	4111682	4111786	0.72	+	0	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	exon	4111682	4111786	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	intron	4111787	4111949	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	CDS	4111950	4111972	0.5	+	0	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	exon	4111950	4111972	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	intron	4111973	4112211	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	CDS	4112212	4112320	0.43	+	1	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	exon	4112212	4112320	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	intron	4112321	4112416	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	CDS	4112417	4112836	0.51	+	0	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	exon	4112417	4112836	.	+	.	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
Phchi.S1	AUGUSTUS	stop_codon	4112837	4112839	.	+	0	transcript_id "Phchi.S1G066000.t1"; gene_id "Phchi.S1G066000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4967.t1 is derived from g2137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13798455	13800770	.	+	.	Phchi.S1G212600
Phchi.S1	AUGUSTUS	transcript	13798455	13800770	.	+	.	transcript_id "Phchi.S1G212600.t1"; gene_id "Phchi.S1G212600"
Phchi.S1	AUGUSTUS	start_codon	13798455	13798457	.	+	0	transcript_id "Phchi.S1G212600.t1"; gene_id "Phchi.S1G212600"
Phchi.S1	AUGUSTUS	CDS	13798455	13800770	0.9	+	0	transcript_id "Phchi.S1G212600.t1"; gene_id "Phchi.S1G212600"
Phchi.S1	AUGUSTUS	exon	13798455	13800770	.	+	.	transcript_id "Phchi.S1G212600.t1"; gene_id "Phchi.S1G212600"
Phchi.S1	AUGUSTUS	stop_codon	13800771	13800773	.	+	0	transcript_id "Phchi.S1G212600.t1"; gene_id "Phchi.S1G212600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15523.t1 is derived from g13992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19712182	19714262	.	+	.	Phchi.S3G284200
Phchi.S3	AUGUSTUS	transcript	19712182	19714262	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	start_codon	19712182	19712184	.	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19712182	19712457	0.67	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19712182	19712457	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	intron	19712458	19712546	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19712547	19712753	0.3	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19712547	19712753	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	intron	19712754	19712968	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19712969	19713019	1	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19712969	19713019	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	intron	19713020	19713156	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19713157	19713214	0.44	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19713157	19713214	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	intron	19713215	19713327	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19713328	19713626	0.65	+	2	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19713328	19713626	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	intron	19713627	19713706	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19713707	19713884	0.75	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19713707	19713884	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	intron	19713885	19714026	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	CDS	19714027	19714262	0.88	+	2	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	exon	19714027	19714262	.	+	.	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
Phchi.S3	AUGUSTUS	stop_codon	19714263	19714265	.	+	0	transcript_id "Phchi.S3G284200.t1"; gene_id "Phchi.S3G284200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6456.t1 is derived from g3628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23114134	23116808	.	-	.	Phchi.S1G361500
Phchi.S1	AUGUSTUS	transcript	23114134	23116808	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	stop_codon	23114131	23114133	.	-	0	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	CDS	23114134	23114152	0.82	-	1	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	exon	23114134	23114152	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	intron	23114153	23114256	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	CDS	23114257	23114464	0.87	-	2	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	exon	23114257	23114464	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	intron	23114465	23114827	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	CDS	23114828	23116223	0.64	-	0	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	exon	23114828	23116223	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	intron	23116224	23116306	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	CDS	23116307	23116395	1	-	2	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	exon	23116307	23116395	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	intron	23116396	23116558	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	CDS	23116559	23116808	1	-	0	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	exon	23116559	23116808	.	-	.	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
Phchi.S1	AUGUSTUS	start_codon	23116806	23116808	.	-	0	transcript_id "Phchi.S1G361500.t1"; gene_id "Phchi.S1G361500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4211.t1 is derived from g1380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8920684	8922360	.	+	.	Phchi.S1G137000
Phchi.S1	AUGUSTUS	transcript	8920684	8922360	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	start_codon	8920684	8920686	.	+	0	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	CDS	8920684	8921016	0.97	+	0	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	exon	8920684	8921016	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	intron	8921017	8921126	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	CDS	8921127	8921923	1	+	0	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	exon	8921127	8921923	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	intron	8921924	8922006	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	CDS	8922007	8922101	1	+	1	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	exon	8922007	8922101	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	intron	8922102	8922184	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	CDS	8922185	8922360	1	+	2	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	exon	8922185	8922360	.	+	.	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
Phchi.S1	AUGUSTUS	stop_codon	8922361	8922363	.	+	0	transcript_id "Phchi.S1G137000.t1"; gene_id "Phchi.S1G137000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg587.t1 is derived from g10369.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4313721	4315354	.	-	.	Phchi.S6G054600
Phchi.S6	AUGUSTUS	transcript	4313721	4315354	.	-	.	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	stop_codon	4313718	4313720	.	-	0	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	CDS	4313721	4313826	0.29	-	1	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	exon	4313721	4313826	.	-	.	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	intron	4313827	4313896	.	-	.	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	CDS	4313897	4314754	0.33	-	1	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	exon	4313897	4314754	.	-	.	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	intron	4314755	4314857	.	-	.	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	CDS	4314858	4315354	0.5	-	0	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	exon	4314858	4315354	.	-	.	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
Phchi.S6	AUGUSTUS	start_codon	4315352	4315354	.	-	0	transcript_id "Phchi.S6G054600.t1"; gene_id "Phchi.S6G054600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10291.t1 is derived from g7467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46842679	46843304	.	+	.	Phchi.S1G745000
Phchi.S1	AUGUSTUS	transcript	46842679	46843304	.	+	.	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	start_codon	46842679	46842681	.	+	0	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	CDS	46842679	46842844	0.96	+	0	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	exon	46842679	46842844	.	+	.	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	intron	46842845	46843015	.	+	.	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	CDS	46843016	46843109	1	+	2	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	exon	46843016	46843109	.	+	.	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	intron	46843110	46843252	.	+	.	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	CDS	46843253	46843304	0.71	+	1	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	exon	46843253	46843304	.	+	.	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
Phchi.S1	AUGUSTUS	stop_codon	46843305	46843307	.	+	0	transcript_id "Phchi.S1G745000.t1"; gene_id "Phchi.S1G745000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg602.t1 is derived from g10384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4360919	4362937	.	-	.	Phchi.S6G056100
Phchi.S6	AUGUSTUS	transcript	4360919	4362937	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	stop_codon	4360916	4360918	.	-	0	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	CDS	4360919	4361077	0.97	-	0	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	exon	4360919	4361077	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	intron	4361078	4361165	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	CDS	4361166	4361286	0.84	-	1	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	exon	4361166	4361286	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	intron	4361287	4361436	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	CDS	4361437	4361493	0.19	-	1	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	exon	4361437	4361493	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	intron	4361494	4361655	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	CDS	4361656	4362495	0.3	-	1	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	exon	4361656	4362495	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	intron	4362496	4362581	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	CDS	4362582	4362937	0.47	-	0	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	exon	4362582	4362937	.	-	.	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
Phchi.S6	AUGUSTUS	start_codon	4362935	4362937	.	-	0	transcript_id "Phchi.S6G056100.t1"; gene_id "Phchi.S6G056100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1031.t1 is derived from g10814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7214965	7218588	.	-	.	Phchi.S6G099000
Phchi.S6	AUGUSTUS	transcript	7214965	7218588	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	stop_codon	7214962	7214964	.	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7214965	7215032	0.98	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7214965	7215032	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7215033	7215121	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7215122	7215208	1	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7215122	7215208	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7215209	7215298	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7215299	7215463	0.61	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7215299	7215463	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7215464	7215610	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7215611	7215627	0.61	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7215611	7215627	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7215628	7215724	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7215725	7215778	1	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7215725	7215778	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7215779	7215859	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7215860	7216153	1	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7215860	7216153	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7216154	7216304	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7216305	7216335	1	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7216305	7216335	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7216336	7216479	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7216480	7216496	0.88	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7216480	7216496	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7216497	7216552	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7216553	7216590	0.98	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7216553	7216590	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7216591	7216679	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7216680	7216737	1	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7216680	7216737	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7216738	7216814	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7216815	7216882	1	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7216815	7216882	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7216883	7216959	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7216960	7217019	1	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7216960	7217019	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217020	7217116	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7217117	7217158	1	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7217117	7217158	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217159	7217253	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7217254	7217297	1	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7217254	7217297	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217298	7217403	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7217404	7217473	1	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7217404	7217473	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217474	7217573	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7217574	7217693	1	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7217574	7217693	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217694	7217795	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7217796	7217814	1	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7217796	7217814	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217815	7217925	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7217926	7217998	1	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7217926	7217998	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7217999	7218083	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7218084	7218151	1	-	1	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7218084	7218151	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7218152	7218265	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7218266	7218338	1	-	2	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7218266	7218338	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	intron	7218339	7218413	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	CDS	7218414	7218588	0.96	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	exon	7218414	7218588	.	-	.	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
Phchi.S6	AUGUSTUS	start_codon	7218586	7218588	.	-	0	transcript_id "Phchi.S6G099000.t1"; gene_id "Phchi.S6G099000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14066.t1 is derived from g12533.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10632994	10634374	.	+	.	Phchi.S3G138500
Phchi.S3	AUGUSTUS	transcript	10632994	10634374	.	+	.	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	start_codon	10632994	10632996	.	+	0	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	CDS	10632994	10633555	1	+	0	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	exon	10632994	10633555	.	+	.	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	intron	10633556	10634054	.	+	.	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	CDS	10634055	10634374	1	+	2	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	exon	10634055	10634374	.	+	.	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
Phchi.S3	AUGUSTUS	stop_codon	10634375	10634377	.	+	0	transcript_id "Phchi.S3G138500.t1"; gene_id "Phchi.S3G138500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8905.t1 is derived from g6080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38581870	38583259	.	+	.	Phchi.S1G606400
Phchi.S1	AUGUSTUS	transcript	38581870	38583259	.	+	.	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	start_codon	38581870	38581872	.	+	0	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	CDS	38581870	38582731	1	+	0	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	exon	38581870	38582731	.	+	.	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	intron	38582732	38583251	.	+	.	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	CDS	38583252	38583259	1	+	2	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	exon	38583252	38583259	.	+	.	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
Phchi.S1	AUGUSTUS	stop_codon	38583260	38583262	.	+	0	transcript_id "Phchi.S1G606400.t1"; gene_id "Phchi.S1G606400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1374.t1 is derived from g11133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C13	AUGUSTUS	gene	48494	49102	.	-	.	Phchi.C13G000100
Phchi.C13	AUGUSTUS	transcript	48494	49102	.	-	.	transcript_id "Phchi.C13G000100.t1"; gene_id "Phchi.C13G000100"
Phchi.C13	AUGUSTUS	stop_codon	48491	48493	.	-	0	transcript_id "Phchi.C13G000100.t1"; gene_id "Phchi.C13G000100"
Phchi.C13	AUGUSTUS	CDS	48494	49102	0.65	-	0	transcript_id "Phchi.C13G000100.t1"; gene_id "Phchi.C13G000100"
Phchi.C13	AUGUSTUS	exon	48494	49102	.	-	.	transcript_id "Phchi.C13G000100.t1"; gene_id "Phchi.C13G000100"
Phchi.C13	AUGUSTUS	start_codon	49100	49102	.	-	0	transcript_id "Phchi.C13G000100.t1"; gene_id "Phchi.C13G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11137.t1 is derived from g15187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4357769	4359079	.	+	.	Phchi.S4G071900
Phchi.S4	AUGUSTUS	transcript	4357769	4359079	.	+	.	transcript_id "Phchi.S4G071900.t1"; gene_id "Phchi.S4G071900"
Phchi.S4	AUGUSTUS	start_codon	4357769	4357771	.	+	0	transcript_id "Phchi.S4G071900.t1"; gene_id "Phchi.S4G071900"
Phchi.S4	AUGUSTUS	CDS	4357769	4359079	0.85	+	0	transcript_id "Phchi.S4G071900.t1"; gene_id "Phchi.S4G071900"
Phchi.S4	AUGUSTUS	exon	4357769	4359079	.	+	.	transcript_id "Phchi.S4G071900.t1"; gene_id "Phchi.S4G071900"
Phchi.S4	AUGUSTUS	stop_codon	4359080	4359082	.	+	0	transcript_id "Phchi.S4G071900.t1"; gene_id "Phchi.S4G071900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5403.t1 is derived from g2573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16699054	16703631	.	-	.	Phchi.S1G256200
Phchi.S1	AUGUSTUS	transcript	16699054	16703631	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	stop_codon	16699051	16699053	.	-	0	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	CDS	16699054	16701608	1	-	2	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	exon	16699054	16701608	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	intron	16701609	16701682	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	CDS	16701683	16701719	1	-	0	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	exon	16701683	16701719	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	intron	16701720	16701863	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	CDS	16701864	16702024	1	-	2	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	exon	16701864	16702024	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	intron	16702025	16702142	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	CDS	16702143	16703631	0.97	-	0	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	exon	16702143	16703631	.	-	.	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
Phchi.S1	AUGUSTUS	start_codon	16703629	16703631	.	-	0	transcript_id "Phchi.S1G256200.t1"; gene_id "Phchi.S1G256200"
# This transcript jg7848.t2 is derived from g5022.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7849.t1 is derived from g5023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31517164	31517868	.	-	.	Phchi.S1G500800
Phchi.S1	AUGUSTUS	transcript	31517164	31517868	.	-	.	transcript_id "Phchi.S1G500800.t1"; gene_id "Phchi.S1G500800"
Phchi.S1	AUGUSTUS	stop_codon	31517161	31517163	.	-	0	transcript_id "Phchi.S1G500800.t1"; gene_id "Phchi.S1G500800"
Phchi.S1	AUGUSTUS	CDS	31517164	31517868	0.93	-	0	transcript_id "Phchi.S1G500800.t1"; gene_id "Phchi.S1G500800"
Phchi.S1	AUGUSTUS	exon	31517164	31517868	.	-	.	transcript_id "Phchi.S1G500800.t1"; gene_id "Phchi.S1G500800"
Phchi.S1	AUGUSTUS	start_codon	31517866	31517868	.	-	0	transcript_id "Phchi.S1G500800.t1"; gene_id "Phchi.S1G500800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13685.t1 is derived from g12152.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8194990	8198202	.	-	.	Phchi.S3G100400
Phchi.S3	AUGUSTUS	transcript	8194990	8198202	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	stop_codon	8194987	8194989	.	-	0	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8194990	8195027	0.9	-	2	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8194990	8195027	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	intron	8195028	8195251	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8195252	8195314	0.93	-	2	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8195252	8195314	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	intron	8195315	8195404	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8195405	8195415	0.94	-	1	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8195405	8195415	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	intron	8195416	8195501	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8195502	8195513	0.77	-	1	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8195502	8195513	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	intron	8195514	8195600	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8195601	8195620	0.53	-	0	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8195601	8195620	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	intron	8195621	8196129	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8196130	8197908	0.36	-	0	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8196130	8197908	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	intron	8197909	8197989	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	CDS	8197990	8198202	0.96	-	0	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	exon	8197990	8198202	.	-	.	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
Phchi.S3	AUGUSTUS	start_codon	8198200	8198202	.	-	0	transcript_id "Phchi.S3G100400.t1"; gene_id "Phchi.S3G100400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7529.t1 is derived from g4703.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29901327	29904489	.	+	.	Phchi.S1G468800
Phchi.S1	AUGUSTUS	transcript	29901327	29904489	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	start_codon	29901327	29901329	.	+	0	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	CDS	29901327	29902450	0.59	+	0	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	exon	29901327	29902450	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	intron	29902451	29902625	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	CDS	29902626	29902924	0.88	+	1	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	exon	29902626	29902924	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	intron	29902925	29903118	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	CDS	29903119	29903720	0.69	+	2	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	exon	29903119	29903720	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	intron	29903721	29903973	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	CDS	29903974	29903984	0.75	+	0	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	exon	29903974	29903984	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	intron	29903985	29904173	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	CDS	29904174	29904489	0.43	+	1	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	exon	29904174	29904489	.	+	.	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
Phchi.S1	AUGUSTUS	stop_codon	29904490	29904492	.	+	0	transcript_id "Phchi.S1G468800.t1"; gene_id "Phchi.S1G468800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10489.t1 is derived from g14538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	672770	674451	.	+	.	Phchi.S4G007100
Phchi.S4	AUGUSTUS	transcript	672770	674451	.	+	.	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	start_codon	672770	672772	.	+	0	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	CDS	672770	674103	0.86	+	0	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	exon	672770	674103	.	+	.	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	intron	674104	674265	.	+	.	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	CDS	674266	674292	0.98	+	1	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	exon	674266	674292	.	+	.	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	intron	674293	674381	.	+	.	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	CDS	674382	674451	1	+	1	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	exon	674382	674451	.	+	.	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
Phchi.S4	AUGUSTUS	stop_codon	674452	674454	.	+	0	transcript_id "Phchi.S4G007100.t1"; gene_id "Phchi.S4G007100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7302.t1 is derived from g4474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28394159	28396378	.	+	.	Phchi.S1G446100
Phchi.S1	AUGUSTUS	transcript	28394159	28396378	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	start_codon	28394159	28394161	.	+	0	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28394159	28394509	0.61	+	0	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28394159	28394509	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	intron	28394510	28394811	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28394812	28395484	0.93	+	0	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28394812	28395484	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	intron	28395485	28395572	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28395573	28395990	0.77	+	2	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28395573	28395990	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	intron	28395991	28396071	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28396072	28396378	0.98	+	1	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28396072	28396378	.	+	.	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	stop_codon	28396379	28396381	.	+	0	transcript_id "Phchi.S1G446100.t1"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	transcript	28395236	28396378	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	start_codon	28395236	28395238	.	+	0	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28395236	28395323	0.29	+	0	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28395236	28395323	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	intron	28395324	28395403	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28395404	28395484	0.38	+	2	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28395404	28395484	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	intron	28395485	28395572	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28395573	28395990	0.84	+	2	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28395573	28395990	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	intron	28395991	28396071	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	CDS	28396072	28396378	0.99	+	1	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	exon	28396072	28396378	.	+	.	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
Phchi.S1	AUGUSTUS	stop_codon	28396379	28396381	.	+	0	transcript_id "Phchi.S1G446100.t2"; gene_id "Phchi.S1G446100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4986.t1 is derived from g2156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13889198	13895032	.	+	.	Phchi.S1G214500
Phchi.S1	AUGUSTUS	transcript	13889198	13895032	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	start_codon	13889198	13889200	.	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13889198	13889618	0.84	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13889198	13889618	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13889619	13889932	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13889933	13889979	1	+	2	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13889933	13889979	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13889980	13890122	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13890123	13890226	1	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13890123	13890226	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13890227	13890344	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13890345	13890600	1	+	1	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13890345	13890600	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13890601	13890754	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13890755	13891054	0.61	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13890755	13891054	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13891055	13891155	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13891156	13891227	1	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13891156	13891227	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13891228	13891391	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13891392	13892192	1	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13891392	13892192	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13892193	13892417	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13892418	13892498	0.98	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13892418	13892498	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13892499	13892596	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13892597	13892601	0.98	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13892597	13892601	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13892602	13892699	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13892700	13892930	0.98	+	1	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13892700	13892930	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13892931	13893123	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13893124	13893344	1	+	1	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13893124	13893344	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13893345	13893521	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13893522	13893680	0.45	+	2	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13893522	13893680	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13893681	13893773	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13893774	13893902	0.55	+	2	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13893774	13893902	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	intron	13893903	13894247	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	CDS	13894248	13895032	0.3	+	2	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	exon	13894248	13895032	.	+	.	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
Phchi.S1	AUGUSTUS	stop_codon	13895033	13895035	.	+	0	transcript_id "Phchi.S1G214500.t1"; gene_id "Phchi.S1G214500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2604.t1 is derived from g9524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7738188	7738862	.	-	.	Phchi.S5G121300
Phchi.S5	AUGUSTUS	transcript	7738188	7738862	.	-	.	transcript_id "Phchi.S5G121300.t1"; gene_id "Phchi.S5G121300"
Phchi.S5	AUGUSTUS	stop_codon	7738185	7738187	.	-	0	transcript_id "Phchi.S5G121300.t1"; gene_id "Phchi.S5G121300"
Phchi.S5	AUGUSTUS	CDS	7738188	7738862	0.73	-	0	transcript_id "Phchi.S5G121300.t1"; gene_id "Phchi.S5G121300"
Phchi.S5	AUGUSTUS	exon	7738188	7738862	.	-	.	transcript_id "Phchi.S5G121300.t1"; gene_id "Phchi.S5G121300"
Phchi.S5	AUGUSTUS	start_codon	7738860	7738862	.	-	0	transcript_id "Phchi.S5G121300.t1"; gene_id "Phchi.S5G121300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8043.t1 is derived from g5218.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32649069	32650053	.	+	.	Phchi.S1G520200
Phchi.S1	AUGUSTUS	transcript	32649069	32650053	.	+	.	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	start_codon	32649069	32649071	.	+	0	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	CDS	32649069	32649525	1	+	0	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	exon	32649069	32649525	.	+	.	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	intron	32649526	32649612	.	+	.	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	CDS	32649613	32649764	1	+	2	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	exon	32649613	32649764	.	+	.	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	intron	32649765	32649849	.	+	.	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	CDS	32649850	32650053	1	+	0	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	exon	32649850	32650053	.	+	.	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
Phchi.S1	AUGUSTUS	stop_codon	32650054	32650056	.	+	0	transcript_id "Phchi.S1G520200.t1"; gene_id "Phchi.S1G520200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12957.t1 is derived from g11422.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3303051	3305495	.	-	.	Phchi.S3G027600
Phchi.S3	AUGUSTUS	transcript	3303051	3305495	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	stop_codon	3303048	3303050	.	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3303051	3303401	1	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3303051	3303401	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3303402	3303502	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3303503	3303604	1	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3303503	3303604	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3303605	3303712	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3303713	3304333	1	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3303713	3304333	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3304334	3304445	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3304446	3304513	1	-	2	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3304446	3304513	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3304514	3304616	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3304617	3304731	1	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3304617	3304731	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3304732	3304826	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3304827	3304872	1	-	1	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3304827	3304872	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3304873	3304979	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3304980	3305052	1	-	2	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3304980	3305052	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	intron	3305053	3305476	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	CDS	3305477	3305495	1	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	exon	3305477	3305495	.	-	.	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
Phchi.S3	AUGUSTUS	start_codon	3305493	3305495	.	-	0	transcript_id "Phchi.S3G027600.t1"; gene_id "Phchi.S3G027600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6191.t1 is derived from g3362.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21397946	21402536	.	-	.	Phchi.S1G335000
Phchi.S1	AUGUSTUS	transcript	21397946	21402536	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	stop_codon	21397943	21397945	.	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21397946	21398183	0.99	-	1	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21397946	21398183	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21398184	21398264	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21398265	21398353	1	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21398265	21398353	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21398354	21398519	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21398520	21398699	1	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21398520	21398699	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21398700	21398803	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21398804	21399124	1	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21398804	21399124	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21399125	21399361	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21399362	21400822	1	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21399362	21400822	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21400823	21400930	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21400931	21401005	1	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21400931	21401005	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21401006	21401103	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21401104	21401174	1	-	2	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21401104	21401174	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21401175	21401262	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21401263	21402081	0.95	-	2	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21401263	21402081	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21402082	21402186	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21402187	21402295	0.97	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21402187	21402295	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21402296	21402425	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21402426	21402536	0.95	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21402426	21402536	.	-	.	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	start_codon	21402534	21402536	.	-	0	transcript_id "Phchi.S1G335000.t1"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	transcript	21397946	21402536	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	stop_codon	21397943	21397945	.	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21397946	21398183	1	-	1	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21397946	21398183	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21398184	21398264	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21398265	21398353	1	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21398265	21398353	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21398354	21398435	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21398436	21398699	0.99	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21398436	21398699	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21398700	21398803	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21398804	21399124	1	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21398804	21399124	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21399125	21399361	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21399362	21400822	0.97	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21399362	21400822	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21400823	21400930	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21400931	21401005	1	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21400931	21401005	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21401006	21401103	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21401104	21401174	1	-	2	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21401104	21401174	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21401175	21401262	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21401263	21402081	0.93	-	2	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21401263	21402081	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21402082	21402186	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21402187	21402295	0.97	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21402187	21402295	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	intron	21402296	21402425	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	CDS	21402426	21402536	0.86	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	exon	21402426	21402536	.	-	.	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
Phchi.S1	AUGUSTUS	start_codon	21402534	21402536	.	-	0	transcript_id "Phchi.S1G335000.t2"; gene_id "Phchi.S1G335000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7067.t1 is derived from g4239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26705145	26706583	.	-	.	Phchi.S1G422600
Phchi.S1	AUGUSTUS	transcript	26705145	26706583	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	stop_codon	26705142	26705144	.	-	0	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	CDS	26705145	26705221	0.66	-	2	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	exon	26705145	26705221	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	intron	26705222	26705303	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	CDS	26705304	26705343	0.59	-	0	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	exon	26705304	26705343	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	intron	26705344	26705703	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	CDS	26705704	26705799	0.64	-	0	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	exon	26705704	26705799	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	intron	26705800	26706015	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	CDS	26706016	26706301	0.73	-	1	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	exon	26706016	26706301	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	intron	26706302	26706401	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	CDS	26706402	26706583	0.99	-	0	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	exon	26706402	26706583	.	-	.	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
Phchi.S1	AUGUSTUS	start_codon	26706581	26706583	.	-	0	transcript_id "Phchi.S1G422600.t1"; gene_id "Phchi.S1G422600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2369.t1 is derived from g9289.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6377541	6378427	.	-	.	Phchi.S5G097800
Phchi.S5	AUGUSTUS	transcript	6377541	6378427	.	-	.	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	stop_codon	6377538	6377540	.	-	0	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	CDS	6377541	6378107	0.98	-	0	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	exon	6377541	6378107	.	-	.	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	intron	6378108	6378217	.	-	.	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	CDS	6378218	6378427	1	-	0	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	exon	6378218	6378427	.	-	.	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
Phchi.S5	AUGUSTUS	start_codon	6378425	6378427	.	-	0	transcript_id "Phchi.S5G097800.t1"; gene_id "Phchi.S5G097800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg215.t1 is derived from g9997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1347248	1348606	.	-	.	Phchi.S6G017400
Phchi.S6	AUGUSTUS	transcript	1347248	1348606	.	-	.	transcript_id "Phchi.S6G017400.t1"; gene_id "Phchi.S6G017400"
Phchi.S6	AUGUSTUS	stop_codon	1347245	1347247	.	-	0	transcript_id "Phchi.S6G017400.t1"; gene_id "Phchi.S6G017400"
Phchi.S6	AUGUSTUS	CDS	1347248	1348606	0.54	-	0	transcript_id "Phchi.S6G017400.t1"; gene_id "Phchi.S6G017400"
Phchi.S6	AUGUSTUS	exon	1347248	1348606	.	-	.	transcript_id "Phchi.S6G017400.t1"; gene_id "Phchi.S6G017400"
Phchi.S6	AUGUSTUS	start_codon	1348604	1348606	.	-	0	transcript_id "Phchi.S6G017400.t1"; gene_id "Phchi.S6G017400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10173.t1 is derived from g7349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46115541	46116645	.	-	.	Phchi.S1G733200
Phchi.S1	AUGUSTUS	transcript	46115541	46116645	.	-	.	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	stop_codon	46115538	46115540	.	-	0	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	CDS	46115541	46115903	0.87	-	0	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	exon	46115541	46115903	.	-	.	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	intron	46115904	46115980	.	-	.	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	CDS	46115981	46116310	0.75	-	0	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	exon	46115981	46116310	.	-	.	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	intron	46116311	46116423	.	-	.	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	CDS	46116424	46116645	0.3	-	0	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	exon	46116424	46116645	.	-	.	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
Phchi.S1	AUGUSTUS	start_codon	46116643	46116645	.	-	0	transcript_id "Phchi.S1G733200.t1"; gene_id "Phchi.S1G733200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3428.t1 is derived from g597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3600897	3601988	.	+	.	Phchi.S1G058700
Phchi.S1	AUGUSTUS	transcript	3600897	3601988	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	start_codon	3600897	3600899	.	+	0	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	CDS	3600897	3600952	0.74	+	0	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	exon	3600897	3600952	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	intron	3600953	3601027	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	CDS	3601028	3601335	0.66	+	1	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	exon	3601028	3601335	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	intron	3601336	3601683	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	CDS	3601684	3601864	0.71	+	2	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	exon	3601684	3601864	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	intron	3601865	3601948	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	CDS	3601949	3601988	0.69	+	1	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	exon	3601949	3601988	.	+	.	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
Phchi.S1	AUGUSTUS	stop_codon	3601989	3601991	.	+	0	transcript_id "Phchi.S1G058700.t1"; gene_id "Phchi.S1G058700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11813.t1 is derived from g15865.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8364660	8365970	.	+	.	Phchi.S4G139500
Phchi.S4	AUGUSTUS	transcript	8364660	8365970	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	start_codon	8364660	8364662	.	+	0	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	CDS	8364660	8364732	1	+	0	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	exon	8364660	8364732	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	intron	8364733	8364942	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	CDS	8364943	8365033	1	+	2	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	exon	8364943	8365033	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	intron	8365034	8365200	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	CDS	8365201	8365344	1	+	1	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	exon	8365201	8365344	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	intron	8365345	8365428	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	CDS	8365429	8365546	1	+	1	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	exon	8365429	8365546	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	intron	8365547	8365630	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	CDS	8365631	8365771	1	+	0	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	exon	8365631	8365771	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	intron	8365772	8365889	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	CDS	8365890	8365970	1	+	0	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	exon	8365890	8365970	.	+	.	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
Phchi.S4	AUGUSTUS	stop_codon	8365971	8365973	.	+	0	transcript_id "Phchi.S4G139500.t1"; gene_id "Phchi.S4G139500"
# This transcript jg10020.t2 is derived from g7196.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10020.t3 is derived from g7196.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10020.t4 is derived from g7196.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10021.t1 is derived from g7197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45108618	45109418	.	-	.	Phchi.S1G718000
Phchi.S1	AUGUSTUS	transcript	45108618	45109418	.	-	.	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	stop_codon	45108615	45108617	.	-	0	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	CDS	45108618	45108674	0.58	-	0	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	exon	45108618	45108674	.	-	.	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	intron	45108675	45108817	.	-	.	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	CDS	45108818	45108839	0.95	-	1	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	exon	45108818	45108839	.	-	.	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	intron	45108840	45109035	.	-	.	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	CDS	45109036	45109418	0.73	-	0	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	exon	45109036	45109418	.	-	.	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
Phchi.S1	AUGUSTUS	start_codon	45109416	45109418	.	-	0	transcript_id "Phchi.S1G718000.t1"; gene_id "Phchi.S1G718000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2347.t1 is derived from g9267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6284563	6285822	.	-	.	Phchi.S5G095600
Phchi.S5	AUGUSTUS	transcript	6284563	6285822	.	-	.	transcript_id "Phchi.S5G095600.t1"; gene_id "Phchi.S5G095600"
Phchi.S5	AUGUSTUS	stop_codon	6284560	6284562	.	-	0	transcript_id "Phchi.S5G095600.t1"; gene_id "Phchi.S5G095600"
Phchi.S5	AUGUSTUS	CDS	6284563	6285822	0.92	-	0	transcript_id "Phchi.S5G095600.t1"; gene_id "Phchi.S5G095600"
Phchi.S5	AUGUSTUS	exon	6284563	6285822	.	-	.	transcript_id "Phchi.S5G095600.t1"; gene_id "Phchi.S5G095600"
Phchi.S5	AUGUSTUS	start_codon	6285820	6285822	.	-	0	transcript_id "Phchi.S5G095600.t1"; gene_id "Phchi.S5G095600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14913.t1 is derived from g13381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15479012	15479872	.	+	.	Phchi.S3G223200
Phchi.S3	AUGUSTUS	transcript	15479012	15479872	.	+	.	transcript_id "Phchi.S3G223200.t1"; gene_id "Phchi.S3G223200"
Phchi.S3	AUGUSTUS	start_codon	15479012	15479014	.	+	0	transcript_id "Phchi.S3G223200.t1"; gene_id "Phchi.S3G223200"
Phchi.S3	AUGUSTUS	CDS	15479012	15479872	0.66	+	0	transcript_id "Phchi.S3G223200.t1"; gene_id "Phchi.S3G223200"
Phchi.S3	AUGUSTUS	exon	15479012	15479872	.	+	.	transcript_id "Phchi.S3G223200.t1"; gene_id "Phchi.S3G223200"
Phchi.S3	AUGUSTUS	stop_codon	15479873	15479875	.	+	0	transcript_id "Phchi.S3G223200.t1"; gene_id "Phchi.S3G223200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3430.t1 is derived from g599.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3605000	3605494	.	+	.	Phchi.S1G058900
Phchi.S1	AUGUSTUS	transcript	3605000	3605494	.	+	.	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	start_codon	3605000	3605002	.	+	0	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	CDS	3605000	3605148	0.52	+	0	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	exon	3605000	3605148	.	+	.	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	intron	3605149	3605229	.	+	.	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	CDS	3605230	3605267	0.52	+	1	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	exon	3605230	3605267	.	+	.	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	intron	3605268	3605429	.	+	.	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	CDS	3605430	3605494	0.52	+	2	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	exon	3605430	3605494	.	+	.	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
Phchi.S1	AUGUSTUS	stop_codon	3605495	3605497	.	+	0	transcript_id "Phchi.S1G058900.t1"; gene_id "Phchi.S1G058900"
# This transcript jg234.t2 is derived from g10016.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg235.t1 is derived from g10017.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1597652	1598648	.	+	.	Phchi.S6G019400
Phchi.S6	AUGUSTUS	transcript	1597652	1598648	.	+	.	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	start_codon	1597652	1597654	.	+	0	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	CDS	1597652	1598359	0.41	+	0	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	exon	1597652	1598359	.	+	.	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	intron	1598360	1598642	.	+	.	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	CDS	1598643	1598648	0.58	+	0	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	exon	1598643	1598648	.	+	.	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
Phchi.S6	AUGUSTUS	stop_codon	1598649	1598651	.	+	0	transcript_id "Phchi.S6G019400.t1"; gene_id "Phchi.S6G019400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3459.t1 is derived from g628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3870736	3871026	.	-	.	Phchi.S1G061800
Phchi.S1	AUGUSTUS	transcript	3870736	3871026	.	-	.	transcript_id "Phchi.S1G061800.t1"; gene_id "Phchi.S1G061800"
Phchi.S1	AUGUSTUS	stop_codon	3870733	3870735	.	-	0	transcript_id "Phchi.S1G061800.t1"; gene_id "Phchi.S1G061800"
Phchi.S1	AUGUSTUS	CDS	3870736	3871026	0.94	-	0	transcript_id "Phchi.S1G061800.t1"; gene_id "Phchi.S1G061800"
Phchi.S1	AUGUSTUS	exon	3870736	3871026	.	-	.	transcript_id "Phchi.S1G061800.t1"; gene_id "Phchi.S1G061800"
Phchi.S1	AUGUSTUS	start_codon	3871024	3871026	.	-	0	transcript_id "Phchi.S1G061800.t1"; gene_id "Phchi.S1G061800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5455.t1 is derived from g2625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16933112	16935519	.	+	.	Phchi.S1G261400
Phchi.S1	AUGUSTUS	transcript	16933112	16935519	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	start_codon	16933112	16933114	.	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16933112	16933145	0.86	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16933112	16933145	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16933146	16933240	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16933241	16933459	0.95	+	2	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16933241	16933459	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16933460	16933543	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16933544	16933968	0.65	+	2	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16933544	16933968	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16933969	16934050	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16934051	16934183	0.67	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16934051	16934183	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16934184	16934342	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16934343	16934509	0.71	+	2	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16934343	16934509	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16934510	16934591	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16934592	16934819	0.93	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16934592	16934819	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16934820	16934899	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16934900	16935154	0.99	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16934900	16935154	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	intron	16935155	16935240	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	CDS	16935241	16935519	0.76	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	exon	16935241	16935519	.	+	.	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
Phchi.S1	AUGUSTUS	stop_codon	16935520	16935522	.	+	0	transcript_id "Phchi.S1G261400.t1"; gene_id "Phchi.S1G261400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3234.t1 is derived from g403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2379441	2380895	.	+	.	Phchi.S1G039300
Phchi.S1	AUGUSTUS	transcript	2379441	2380895	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	start_codon	2379441	2379443	.	+	0	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2379441	2379514	0.99	+	0	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2379441	2379514	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	intron	2379515	2379643	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2379644	2379809	0.89	+	1	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2379644	2379809	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	intron	2379810	2379899	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2379900	2379951	0.45	+	0	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2379900	2379951	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	intron	2379952	2380056	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2380057	2380141	0.3	+	2	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2380057	2380141	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	intron	2380142	2380266	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2380267	2380393	0.71	+	1	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2380267	2380393	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	intron	2380394	2380491	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2380492	2380536	0.39	+	0	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2380492	2380536	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	intron	2380537	2380664	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	CDS	2380665	2380895	0.23	+	0	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	exon	2380665	2380895	.	+	.	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
Phchi.S1	AUGUSTUS	stop_codon	2380896	2380898	.	+	0	transcript_id "Phchi.S1G039300.t1"; gene_id "Phchi.S1G039300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13515.t1 is derived from g11982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7267496	7268026	.	+	.	Phchi.S3G083400
Phchi.S3	AUGUSTUS	transcript	7267496	7268026	.	+	.	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	start_codon	7267496	7267498	.	+	0	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	CDS	7267496	7267636	0.49	+	0	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	exon	7267496	7267636	.	+	.	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	intron	7267637	7267706	.	+	.	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	CDS	7267707	7267868	0.86	+	0	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	exon	7267707	7267868	.	+	.	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	intron	7267869	7267951	.	+	.	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	CDS	7267952	7268026	1	+	0	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	exon	7267952	7268026	.	+	.	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
Phchi.S3	AUGUSTUS	stop_codon	7268027	7268029	.	+	0	transcript_id "Phchi.S3G083400.t1"; gene_id "Phchi.S3G083400"
# This transcript jg9012.t2 is derived from g6187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9013.t1 is derived from g6188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39145102	39146855	.	-	.	Phchi.S1G617200
Phchi.S1	AUGUSTUS	transcript	39145102	39146855	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	stop_codon	39145099	39145101	.	-	0	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	CDS	39145102	39145270	1	-	1	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	exon	39145102	39145270	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	intron	39145271	39145463	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	CDS	39145464	39145551	0.58	-	2	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	exon	39145464	39145551	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	intron	39145552	39145655	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	CDS	39145656	39145935	0.37	-	0	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	exon	39145656	39145935	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	intron	39145936	39146037	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	CDS	39146038	39146184	0.97	-	0	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	exon	39146038	39146184	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	intron	39146185	39146372	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	CDS	39146373	39146855	0.87	-	0	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	exon	39146373	39146855	.	-	.	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
Phchi.S1	AUGUSTUS	start_codon	39146853	39146855	.	-	0	transcript_id "Phchi.S1G617200.t1"; gene_id "Phchi.S1G617200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg514.t1 is derived from g10296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3646767	3647289	.	+	.	Phchi.S6G047300
Phchi.S6	AUGUSTUS	transcript	3646767	3647289	.	+	.	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	start_codon	3646767	3646769	.	+	0	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	CDS	3646767	3646964	0.76	+	0	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	exon	3646767	3646964	.	+	.	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	intron	3646965	3647103	.	+	.	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	CDS	3647104	3647289	0.98	+	0	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	exon	3647104	3647289	.	+	.	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
Phchi.S6	AUGUSTUS	stop_codon	3647290	3647292	.	+	0	transcript_id "Phchi.S6G047300.t1"; gene_id "Phchi.S6G047300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1704.t1 is derived from g8623.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2627401	2628956	.	-	.	Phchi.S5G031300
Phchi.S5	AUGUSTUS	transcript	2627401	2628956	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	stop_codon	2627398	2627400	.	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2627401	2627472	1	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2627401	2627472	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	intron	2627473	2627599	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2627600	2627654	1	-	1	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2627600	2627654	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	intron	2627655	2627732	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2627733	2628036	0.95	-	2	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2627733	2628036	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	intron	2628037	2628178	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2628179	2628305	1	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2628179	2628305	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	intron	2628306	2628389	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2628390	2628491	1	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2628390	2628491	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	intron	2628492	2628628	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2628629	2628667	1	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2628629	2628667	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	intron	2628668	2628830	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	CDS	2628831	2628956	0.56	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	exon	2628831	2628956	.	-	.	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
Phchi.S5	AUGUSTUS	start_codon	2628954	2628956	.	-	0	transcript_id "Phchi.S5G031300.t1"; gene_id "Phchi.S5G031300"
# This transcript jg6746.t1 is derived from g3917.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24829671	24832700	.	+	.	Phchi.S1G390500
Phchi.S1	AUGUSTUS	transcript	24829671	24832700	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	start_codon	24829671	24829673	.	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24829671	24829975	0.32	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24829671	24829975	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24829976	24830067	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24830068	24830088	0.94	+	1	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24830068	24830088	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24830089	24830185	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24830186	24830273	0.87	+	1	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24830186	24830273	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24830274	24830373	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24830374	24830394	0.98	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24830374	24830394	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24830395	24830507	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24830508	24830960	0.48	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24830508	24830960	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24830961	24831034	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24831035	24831048	1	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24831035	24831048	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24831049	24831283	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24831284	24831755	0.44	+	1	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24831284	24831755	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24831756	24831901	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24831902	24831968	0.79	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24831902	24831968	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24831969	24832415	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24832416	24832473	0.6	+	2	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24832416	24832473	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24832474	24832547	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24832548	24832606	0.64	+	1	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24832548	24832606	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	intron	24832607	24832686	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	CDS	24832687	24832700	1	+	2	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	exon	24832687	24832700	.	+	.	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
Phchi.S1	AUGUSTUS	stop_codon	24832701	24832703	.	+	0	transcript_id "Phchi.S1G390500.t1"; gene_id "Phchi.S1G390500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg418.t1 is derived from g10200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2963064	2963996	.	-	.	Phchi.S6G037700
Phchi.S6	AUGUSTUS	transcript	2963064	2963996	.	-	.	transcript_id "Phchi.S6G037700.t1"; gene_id "Phchi.S6G037700"
Phchi.S6	AUGUSTUS	stop_codon	2963061	2963063	.	-	0	transcript_id "Phchi.S6G037700.t1"; gene_id "Phchi.S6G037700"
Phchi.S6	AUGUSTUS	CDS	2963064	2963996	0.39	-	0	transcript_id "Phchi.S6G037700.t1"; gene_id "Phchi.S6G037700"
Phchi.S6	AUGUSTUS	exon	2963064	2963996	.	-	.	transcript_id "Phchi.S6G037700.t1"; gene_id "Phchi.S6G037700"
Phchi.S6	AUGUSTUS	start_codon	2963994	2963996	.	-	0	transcript_id "Phchi.S6G037700.t1"; gene_id "Phchi.S6G037700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2322.t1 is derived from g9242.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6167670	6171493	.	-	.	Phchi.S5G093100
Phchi.S5	AUGUSTUS	transcript	6167670	6171493	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	stop_codon	6167667	6167669	.	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6167670	6167861	0.96	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6167670	6167861	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6167862	6167967	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6167968	6168060	1	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6167968	6168060	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6168061	6168141	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6168142	6168235	1	-	1	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6168142	6168235	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6168236	6168320	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6168321	6168406	1	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6168321	6168406	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6168407	6168495	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6168496	6168705	1	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6168496	6168705	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6168706	6168835	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6168836	6169057	1	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6168836	6169057	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6169058	6169154	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6169155	6169255	1	-	2	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6169155	6169255	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	intron	6169256	6169347	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	CDS	6169348	6171493	0.67	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	exon	6169348	6171493	.	-	.	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
Phchi.S5	AUGUSTUS	start_codon	6171491	6171493	.	-	0	transcript_id "Phchi.S5G093100.t1"; gene_id "Phchi.S5G093100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5675.t1 is derived from g2845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18248263	18252982	.	-	.	Phchi.S1G283400
Phchi.S1	AUGUSTUS	transcript	18248263	18252982	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	stop_codon	18248260	18248262	.	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18248263	18248384	1	-	2	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18248263	18248384	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18248385	18248472	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18248473	18248564	1	-	1	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18248473	18248564	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18248565	18248706	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18248707	18248786	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18248707	18248786	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18248787	18248868	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18248869	18248964	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18248869	18248964	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18248965	18249085	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18249086	18249229	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18249086	18249229	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18249230	18249383	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18249384	18249491	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18249384	18249491	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18249492	18249656	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18249657	18249737	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18249657	18249737	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18249738	18249866	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18249867	18249986	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18249867	18249986	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18249987	18250138	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18250139	18250270	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18250139	18250270	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18250271	18250472	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18250473	18250565	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18250473	18250565	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18250566	18250689	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18250690	18250855	1	-	1	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18250690	18250855	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18250856	18250971	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18250972	18251030	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18250972	18251030	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18251031	18251127	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18251128	18251222	1	-	2	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18251128	18251222	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18251223	18251342	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18251343	18251452	1	-	1	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18251343	18251452	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18251453	18251600	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18251601	18251689	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18251601	18251689	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18251690	18251798	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18251799	18251948	1	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18251799	18251948	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18251949	18252079	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18252080	18252189	1	-	2	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18252080	18252189	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18252190	18252290	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18252291	18252395	1	-	2	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18252291	18252395	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18252396	18252534	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18252535	18252839	0.43	-	1	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18252535	18252839	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	intron	18252840	18252938	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	CDS	18252939	18252982	0.71	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	exon	18252939	18252982	.	-	.	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
Phchi.S1	AUGUSTUS	start_codon	18252980	18252982	.	-	0	transcript_id "Phchi.S1G283400.t1"; gene_id "Phchi.S1G283400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11232.t1 is derived from g15282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4917870	4925889	.	+	.	Phchi.S4G081400
Phchi.S4	AUGUSTUS	transcript	4917870	4925889	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	start_codon	4917870	4917872	.	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4917870	4917906	0.76	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4917870	4917906	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4917907	4918003	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4918004	4918071	0.73	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4918004	4918071	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4918072	4918158	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4918159	4918523	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4918159	4918523	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4918524	4918662	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4918663	4919119	0.99	+	1	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4918663	4919119	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4919120	4919216	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4919217	4919474	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4919217	4919474	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4919475	4919647	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4919648	4919860	0.99	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4919648	4919860	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4919861	4919957	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4919958	4920089	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4919958	4920089	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4920090	4920194	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4920195	4920324	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4920195	4920324	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4920325	4920422	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4920423	4920469	1	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4920423	4920469	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4920470	4920559	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4920560	4920661	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4920560	4920661	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4920662	4920733	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4920734	4920832	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4920734	4920832	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4920833	4920975	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4920976	4921118	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4920976	4921118	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4921119	4921317	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4921318	4921415	0.84	+	1	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4921318	4921415	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4921416	4921531	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4921532	4921613	0.87	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4921532	4921613	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4921614	4921742	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4921743	4921812	0.87	+	1	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4921743	4921812	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4921813	4921914	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4921915	4922193	0.83	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4921915	4922193	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4922194	4922278	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4922279	4922382	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4922279	4922382	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4922383	4922515	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4922516	4922981	0.78	+	1	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4922516	4922981	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4922982	4923069	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4923070	4923108	0.99	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4923070	4923108	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4923109	4923213	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4923214	4923436	0.66	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4923214	4923436	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4923437	4923519	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4923520	4923668	1	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4923520	4923668	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4923669	4923757	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4923758	4923944	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4923758	4923944	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4923945	4924025	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4924026	4924258	1	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4924026	4924258	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4924259	4924336	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4924337	4924432	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4924337	4924432	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4924433	4924535	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4924536	4924616	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4924536	4924616	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4924617	4924733	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4924734	4924766	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4924734	4924766	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4924767	4924860	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4924861	4924945	0.96	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4924861	4924945	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4924946	4925128	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4925129	4925188	0.99	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4925129	4925188	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4925189	4925270	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4925271	4925326	1	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4925271	4925326	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4925327	4925407	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4925408	4925464	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4925408	4925464	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4925465	4925544	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4925545	4925665	1	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4925545	4925665	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	intron	4925666	4925743	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	CDS	4925744	4925889	1	+	2	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	exon	4925744	4925889	.	+	.	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
Phchi.S4	AUGUSTUS	stop_codon	4925890	4925892	.	+	0	transcript_id "Phchi.S4G081400.t1"; gene_id "Phchi.S4G081400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7464.t1 is derived from g4637.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29404285	29405769	.	-	.	Phchi.S1G462300
Phchi.S1	AUGUSTUS	transcript	29404285	29405769	.	-	.	transcript_id "Phchi.S1G462300.t1"; gene_id "Phchi.S1G462300"
Phchi.S1	AUGUSTUS	stop_codon	29404282	29404284	.	-	0	transcript_id "Phchi.S1G462300.t1"; gene_id "Phchi.S1G462300"
Phchi.S1	AUGUSTUS	CDS	29404285	29405769	1	-	0	transcript_id "Phchi.S1G462300.t1"; gene_id "Phchi.S1G462300"
Phchi.S1	AUGUSTUS	exon	29404285	29405769	.	-	.	transcript_id "Phchi.S1G462300.t1"; gene_id "Phchi.S1G462300"
Phchi.S1	AUGUSTUS	start_codon	29405767	29405769	.	-	0	transcript_id "Phchi.S1G462300.t1"; gene_id "Phchi.S1G462300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1705.t1 is derived from g8625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2630938	2632758	.	-	.	Phchi.S5G031400
Phchi.S5	AUGUSTUS	transcript	2630938	2632758	.	-	.	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	stop_codon	2630935	2630937	.	-	0	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	CDS	2630938	2631701	0.8	-	2	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	exon	2630938	2631701	.	-	.	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	intron	2631702	2631776	.	-	.	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	CDS	2631777	2631878	1	-	2	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	exon	2631777	2631878	.	-	.	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	intron	2631879	2631959	.	-	.	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	CDS	2631960	2632758	0.99	-	0	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	exon	2631960	2632758	.	-	.	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
Phchi.S5	AUGUSTUS	start_codon	2632756	2632758	.	-	0	transcript_id "Phchi.S5G031400.t1"; gene_id "Phchi.S5G031400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14584.t1 is derived from g13052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13579451	13582215	.	+	.	Phchi.S3G190300
Phchi.S3	AUGUSTUS	transcript	13579451	13582215	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	start_codon	13579451	13579453	.	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	CDS	13579451	13581016	0.89	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	exon	13579451	13581016	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	intron	13581017	13581177	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	CDS	13581178	13581417	0.78	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	exon	13581178	13581417	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	intron	13581418	13581541	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	CDS	13581542	13581640	0.6	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	exon	13581542	13581640	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	intron	13581641	13581759	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	CDS	13581760	13581918	0.98	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	exon	13581760	13581918	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	intron	13581919	13581993	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	CDS	13581994	13582215	0.67	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	exon	13581994	13582215	.	+	.	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
Phchi.S3	AUGUSTUS	stop_codon	13582216	13582218	.	+	0	transcript_id "Phchi.S3G190300.t1"; gene_id "Phchi.S3G190300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11679.t1 is derived from g15730.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7641937	7644342	.	+	.	Phchi.S4G126100
Phchi.S4	AUGUSTUS	transcript	7641937	7644342	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	start_codon	7641937	7641939	.	+	0	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7641937	7642184	0.45	+	0	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7641937	7642184	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7642185	7642254	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7642255	7642471	0.7	+	1	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7642255	7642471	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7642472	7642595	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7642596	7643042	0.77	+	0	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7642596	7643042	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7643043	7643142	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7643143	7643267	1	+	0	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7643143	7643267	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7643268	7643375	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7643376	7644046	1	+	1	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7643376	7644046	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7644047	7644154	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7644155	7644342	1	+	2	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7644155	7644342	.	+	.	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	stop_codon	7644343	7644345	.	+	0	transcript_id "Phchi.S4G126100.t1"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	transcript	7641937	7643081	.	+	.	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	start_codon	7641937	7641939	.	+	0	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7641937	7642184	0.52	+	0	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7641937	7642184	.	+	.	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7642185	7642254	.	+	.	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7642255	7642471	0.75	+	1	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7642255	7642471	.	+	.	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	intron	7642472	7642595	.	+	.	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	CDS	7642596	7643081	0.9	+	0	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	exon	7642596	7643081	.	+	.	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
Phchi.S4	AUGUSTUS	stop_codon	7643082	7643084	.	+	0	transcript_id "Phchi.S4G126100.t2"; gene_id "Phchi.S4G126100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9914.t1 is derived from g7090.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44424365	44425569	.	+	.	Phchi.S1G707300
Phchi.S1	AUGUSTUS	transcript	44424365	44425569	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	start_codon	44424365	44424367	.	+	0	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	CDS	44424365	44424581	0.84	+	0	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	exon	44424365	44424581	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	intron	44424582	44424685	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	CDS	44424686	44424789	0.83	+	2	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	exon	44424686	44424789	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	intron	44424790	44424880	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	CDS	44424881	44424994	1	+	0	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	exon	44424881	44424994	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	intron	44424995	44425100	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	CDS	44425101	44425357	1	+	0	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	exon	44425101	44425357	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	intron	44425358	44425433	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	CDS	44425434	44425569	1	+	1	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	exon	44425434	44425569	.	+	.	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
Phchi.S1	AUGUSTUS	stop_codon	44425570	44425572	.	+	0	transcript_id "Phchi.S1G707300.t1"; gene_id "Phchi.S1G707300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2813.t1 is derived from g9733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8987981	8991269	.	+	.	Phchi.S5G142200
Phchi.S5	AUGUSTUS	transcript	8987981	8991269	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	start_codon	8987981	8987983	.	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8987981	8988461	0.42	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8987981	8988461	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8988462	8988538	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8988539	8988965	0.54	+	2	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8988539	8988965	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8988966	8989049	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8989050	8989188	0.97	+	1	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8989050	8989188	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8989189	8989299	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8989300	8989466	1	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8989300	8989466	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8989467	8989581	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8989582	8989803	1	+	1	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8989582	8989803	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8989804	8989952	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8989953	8990127	0.94	+	1	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8989953	8990127	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8990128	8990228	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8990229	8990462	0.92	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8990229	8990462	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8990463	8990556	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8990557	8990691	0.84	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8990557	8990691	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8990692	8990784	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8990785	8990914	1	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8990785	8990914	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	intron	8990915	8991012	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	CDS	8991013	8991269	0.99	+	2	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	exon	8991013	8991269	.	+	.	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
Phchi.S5	AUGUSTUS	stop_codon	8991270	8991272	.	+	0	transcript_id "Phchi.S5G142200.t1"; gene_id "Phchi.S5G142200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12079.t1 is derived from g7754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2147823	2149459	.	-	.	Phchi.S2G015900
Phchi.S2	AUGUSTUS	transcript	2147823	2149459	.	-	.	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	stop_codon	2147820	2147822	.	-	0	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	CDS	2147823	2147857	0.99	-	2	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	exon	2147823	2147857	.	-	.	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	intron	2147858	2147953	.	-	.	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	CDS	2147954	2148461	0.97	-	0	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	exon	2147954	2148461	.	-	.	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	intron	2148462	2148538	.	-	.	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	CDS	2148539	2149459	0.76	-	0	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	exon	2148539	2149459	.	-	.	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
Phchi.S2	AUGUSTUS	start_codon	2149457	2149459	.	-	0	transcript_id "Phchi.S2G015900.t1"; gene_id "Phchi.S2G015900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9266.t1 is derived from g6441.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40668933	40669703	.	-	.	Phchi.S1G642500
Phchi.S1	AUGUSTUS	transcript	40668933	40669703	.	-	.	transcript_id "Phchi.S1G642500.t1"; gene_id "Phchi.S1G642500"
Phchi.S1	AUGUSTUS	stop_codon	40668930	40668932	.	-	0	transcript_id "Phchi.S1G642500.t1"; gene_id "Phchi.S1G642500"
Phchi.S1	AUGUSTUS	CDS	40668933	40669703	0.48	-	0	transcript_id "Phchi.S1G642500.t1"; gene_id "Phchi.S1G642500"
Phchi.S1	AUGUSTUS	exon	40668933	40669703	.	-	.	transcript_id "Phchi.S1G642500.t1"; gene_id "Phchi.S1G642500"
Phchi.S1	AUGUSTUS	start_codon	40669701	40669703	.	-	0	transcript_id "Phchi.S1G642500.t1"; gene_id "Phchi.S1G642500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1386.t1 is derived from g16019.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C243	AUGUSTUS	gene	12082	12837	.	+	.	Phchi.C243G000400
Phchi.C243	AUGUSTUS	transcript	12082	12837	.	+	.	transcript_id "Phchi.C243G000400.t1"; gene_id "Phchi.C243G000400"
Phchi.C243	AUGUSTUS	start_codon	12082	12084	.	+	0	transcript_id "Phchi.C243G000400.t1"; gene_id "Phchi.C243G000400"
Phchi.C243	AUGUSTUS	CDS	12082	12837	0.97	+	0	transcript_id "Phchi.C243G000400.t1"; gene_id "Phchi.C243G000400"
Phchi.C243	AUGUSTUS	exon	12082	12837	.	+	.	transcript_id "Phchi.C243G000400.t1"; gene_id "Phchi.C243G000400"
Phchi.C243	AUGUSTUS	stop_codon	12838	12840	.	+	0	transcript_id "Phchi.C243G000400.t1"; gene_id "Phchi.C243G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9743.t1 is derived from g6919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43477824	43478198	.	-	.	Phchi.S1G690200
Phchi.S1	AUGUSTUS	transcript	43477824	43478198	.	-	.	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	stop_codon	43477821	43477823	.	-	0	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	CDS	43477824	43477893	0.85	-	1	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	exon	43477824	43477893	.	-	.	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	intron	43477894	43477971	.	-	.	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	CDS	43477972	43478198	0.49	-	0	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	exon	43477972	43478198	.	-	.	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
Phchi.S1	AUGUSTUS	start_codon	43478196	43478198	.	-	0	transcript_id "Phchi.S1G690200.t1"; gene_id "Phchi.S1G690200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2032.t1 is derived from g8952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4534677	4536177	.	+	.	Phchi.S5G064100
Phchi.S5	AUGUSTUS	transcript	4534677	4536177	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	start_codon	4534677	4534679	.	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4534677	4534733	0.7	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4534677	4534733	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4534734	4534832	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4534833	4534867	0.67	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4534833	4534867	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4534868	4534943	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4534944	4535008	0.67	+	1	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4534944	4535008	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4535009	4535163	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4535164	4535222	1	+	2	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4535164	4535222	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4535223	4535308	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4535309	4535491	1	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4535309	4535491	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4535492	4535578	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4535579	4535749	0.96	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4535579	4535749	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4535750	4536013	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4536014	4536035	0.78	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4536014	4536035	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	intron	4536036	4536121	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	CDS	4536122	4536177	0.78	+	2	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	exon	4536122	4536177	.	+	.	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
Phchi.S5	AUGUSTUS	stop_codon	4536178	4536180	.	+	0	transcript_id "Phchi.S5G064100.t1"; gene_id "Phchi.S5G064100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1142.t1 is derived from g10925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7951796	7952251	.	-	.	Phchi.S6G110100
Phchi.S6	AUGUSTUS	transcript	7951796	7952251	.	-	.	transcript_id "Phchi.S6G110100.t1"; gene_id "Phchi.S6G110100"
Phchi.S6	AUGUSTUS	stop_codon	7951793	7951795	.	-	0	transcript_id "Phchi.S6G110100.t1"; gene_id "Phchi.S6G110100"
Phchi.S6	AUGUSTUS	CDS	7951796	7952251	0.69	-	0	transcript_id "Phchi.S6G110100.t1"; gene_id "Phchi.S6G110100"
Phchi.S6	AUGUSTUS	exon	7951796	7952251	.	-	.	transcript_id "Phchi.S6G110100.t1"; gene_id "Phchi.S6G110100"
Phchi.S6	AUGUSTUS	start_codon	7952249	7952251	.	-	0	transcript_id "Phchi.S6G110100.t1"; gene_id "Phchi.S6G110100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7819.t1 is derived from g4993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31353974	31355135	.	-	.	Phchi.S1G497800
Phchi.S1	AUGUSTUS	transcript	31353974	31355135	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	stop_codon	31353971	31353973	.	-	0	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	CDS	31353974	31354111	1	-	0	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	exon	31353974	31354111	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	intron	31354112	31354209	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	CDS	31354210	31354468	0.99	-	1	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	exon	31354210	31354468	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	intron	31354469	31354587	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	CDS	31354588	31354710	1	-	1	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	exon	31354588	31354710	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	intron	31354711	31354840	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	CDS	31354841	31354867	1	-	1	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	exon	31354841	31354867	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	intron	31354868	31355088	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	CDS	31355089	31355135	1	-	0	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	exon	31355089	31355135	.	-	.	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
Phchi.S1	AUGUSTUS	start_codon	31355133	31355135	.	-	0	transcript_id "Phchi.S1G497800.t1"; gene_id "Phchi.S1G497800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1734.t1 is derived from g8654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2775977	2777019	.	+	.	Phchi.S5G034300
Phchi.S5	AUGUSTUS	transcript	2775977	2777019	.	+	.	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	start_codon	2775977	2775979	.	+	0	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	CDS	2775977	2776265	0.53	+	0	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	exon	2775977	2776265	.	+	.	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	intron	2776266	2776543	.	+	.	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	CDS	2776544	2776839	1	+	2	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	exon	2776544	2776839	.	+	.	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	intron	2776840	2776926	.	+	.	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	CDS	2776927	2777019	0.93	+	0	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	exon	2776927	2777019	.	+	.	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
Phchi.S5	AUGUSTUS	stop_codon	2777020	2777022	.	+	0	transcript_id "Phchi.S5G034300.t1"; gene_id "Phchi.S5G034300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15105.t1 is derived from g13573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17100692	17102429	.	-	.	Phchi.S3G242400
Phchi.S3	AUGUSTUS	transcript	17100692	17102429	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	stop_codon	17100689	17100691	.	-	0	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	CDS	17100692	17100719	1	-	1	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	exon	17100692	17100719	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	intron	17100720	17100953	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	CDS	17100954	17101204	1	-	0	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	exon	17100954	17101204	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	intron	17101205	17101470	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	CDS	17101471	17101795	0.51	-	1	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	exon	17101471	17101795	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	intron	17101796	17101903	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	CDS	17101904	17102067	0.72	-	0	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	exon	17101904	17102067	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	intron	17102068	17102195	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	CDS	17102196	17102429	0.78	-	0	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	exon	17102196	17102429	.	-	.	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
Phchi.S3	AUGUSTUS	start_codon	17102427	17102429	.	-	0	transcript_id "Phchi.S3G242400.t1"; gene_id "Phchi.S3G242400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4455.t1 is derived from g1625.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10582211	10582720	.	+	.	Phchi.S1G161400
Phchi.S1	AUGUSTUS	transcript	10582211	10582720	.	+	.	transcript_id "Phchi.S1G161400.t1"; gene_id "Phchi.S1G161400"
Phchi.S1	AUGUSTUS	start_codon	10582211	10582213	.	+	0	transcript_id "Phchi.S1G161400.t1"; gene_id "Phchi.S1G161400"
Phchi.S1	AUGUSTUS	CDS	10582211	10582720	1	+	0	transcript_id "Phchi.S1G161400.t1"; gene_id "Phchi.S1G161400"
Phchi.S1	AUGUSTUS	exon	10582211	10582720	.	+	.	transcript_id "Phchi.S1G161400.t1"; gene_id "Phchi.S1G161400"
Phchi.S1	AUGUSTUS	stop_codon	10582721	10582723	.	+	0	transcript_id "Phchi.S1G161400.t1"; gene_id "Phchi.S1G161400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7751.t1 is derived from g4925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30956208	30957072	.	-	.	Phchi.S1G491000
Phchi.S1	AUGUSTUS	transcript	30956208	30957072	.	-	.	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	stop_codon	30956205	30956207	.	-	0	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	CDS	30956208	30956949	1	-	1	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	exon	30956208	30956949	.	-	.	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	intron	30956950	30957034	.	-	.	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	CDS	30957035	30957072	0.53	-	0	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	exon	30957035	30957072	.	-	.	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
Phchi.S1	AUGUSTUS	start_codon	30957070	30957072	.	-	0	transcript_id "Phchi.S1G491000.t1"; gene_id "Phchi.S1G491000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2113.t1 is derived from g9033.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4921684	4923573	.	+	.	Phchi.S5G072200
Phchi.S5	AUGUSTUS	transcript	4921684	4923573	.	+	.	transcript_id "Phchi.S5G072200.t1"; gene_id "Phchi.S5G072200"
Phchi.S5	AUGUSTUS	start_codon	4921684	4921686	.	+	0	transcript_id "Phchi.S5G072200.t1"; gene_id "Phchi.S5G072200"
Phchi.S5	AUGUSTUS	CDS	4921684	4923573	0.22	+	0	transcript_id "Phchi.S5G072200.t1"; gene_id "Phchi.S5G072200"
Phchi.S5	AUGUSTUS	exon	4921684	4923573	.	+	.	transcript_id "Phchi.S5G072200.t1"; gene_id "Phchi.S5G072200"
Phchi.S5	AUGUSTUS	stop_codon	4923574	4923576	.	+	0	transcript_id "Phchi.S5G072200.t1"; gene_id "Phchi.S5G072200"
# This transcript jg11510.t2 is derived from g15560.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg11510.t3 is derived from g15560.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11511.t1 is derived from g15561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6844107	6845579	.	-	.	Phchi.S4G109300
Phchi.S4	AUGUSTUS	transcript	6844107	6845579	.	-	.	transcript_id "Phchi.S4G109300.t1"; gene_id "Phchi.S4G109300"
Phchi.S4	AUGUSTUS	stop_codon	6844104	6844106	.	-	0	transcript_id "Phchi.S4G109300.t1"; gene_id "Phchi.S4G109300"
Phchi.S4	AUGUSTUS	CDS	6844107	6845579	0.64	-	0	transcript_id "Phchi.S4G109300.t1"; gene_id "Phchi.S4G109300"
Phchi.S4	AUGUSTUS	exon	6844107	6845579	.	-	.	transcript_id "Phchi.S4G109300.t1"; gene_id "Phchi.S4G109300"
Phchi.S4	AUGUSTUS	start_codon	6845577	6845579	.	-	0	transcript_id "Phchi.S4G109300.t1"; gene_id "Phchi.S4G109300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9397.t1 is derived from g6573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41327335	41333171	.	+	.	Phchi.S1G655600
Phchi.S1	AUGUSTUS	transcript	41327335	41333171	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	start_codon	41327335	41327337	.	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41327335	41327400	0.7	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41327335	41327400	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41327401	41327524	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41327525	41327600	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41327525	41327600	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41327601	41327717	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41327718	41327794	1	+	2	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41327718	41327794	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41327795	41327877	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41327878	41327890	0.93	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41327878	41327890	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41327891	41327958	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41327959	41327990	0.93	+	2	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41327959	41327990	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41327991	41328086	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41328087	41328161	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41328087	41328161	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41328162	41328329	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41328330	41328437	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41328330	41328437	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41328438	41328537	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41328538	41328750	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41328538	41328750	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41328751	41328827	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41328828	41328889	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41328828	41328889	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41328890	41329034	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41329035	41329062	1	+	1	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41329035	41329062	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41329063	41329209	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41329210	41329296	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41329210	41329296	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41329297	41329408	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41329409	41329434	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41329409	41329434	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41329435	41329533	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41329534	41329597	1	+	1	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41329534	41329597	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41329598	41329731	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41329732	41329812	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41329732	41329812	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41329813	41329963	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41329964	41330011	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41329964	41330011	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41330012	41330180	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41330181	41330204	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41330181	41330204	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41330205	41330363	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41330364	41330375	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41330364	41330375	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41330376	41330477	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41330478	41330534	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41330478	41330534	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41330535	41330633	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41330634	41330743	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41330634	41330743	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41330744	41330847	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41330848	41330928	1	+	1	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41330848	41330928	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41330929	41331050	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41331051	41331237	1	+	1	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41331051	41331237	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41331238	41331329	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41331330	41331478	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41331330	41331478	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41331479	41331602	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41331603	41331741	1	+	1	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41331603	41331741	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41331742	41331825	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41331826	41331972	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41331826	41331972	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41331973	41332068	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41332069	41332150	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41332069	41332150	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41332151	41332236	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41332237	41332412	1	+	2	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41332237	41332412	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41332413	41332501	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41332502	41332612	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41332502	41332612	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41332613	41332696	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41332697	41332813	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41332697	41332813	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41332814	41332940	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41332941	41333012	1	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41332941	41333012	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	intron	41333013	41333093	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	CDS	41333094	41333171	0.99	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	exon	41333094	41333171	.	+	.	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
Phchi.S1	AUGUSTUS	stop_codon	41333172	41333174	.	+	0	transcript_id "Phchi.S1G655600.t1"; gene_id "Phchi.S1G655600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5204.t1 is derived from g2374.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15446817	15450556	.	-	.	Phchi.S1G236300
Phchi.S1	AUGUSTUS	transcript	15446817	15450556	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	stop_codon	15446814	15446816	.	-	0	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15446817	15447047	0.96	-	0	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15446817	15447047	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	intron	15447048	15447258	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15447259	15447602	0.25	-	2	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15447259	15447602	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	intron	15447603	15447812	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15447813	15448704	0.25	-	0	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15447813	15448704	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	intron	15448705	15448811	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15448812	15449052	0.99	-	1	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15448812	15449052	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	intron	15449053	15449154	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15449155	15449270	0.99	-	0	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15449155	15449270	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	intron	15449271	15449867	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15449868	15450177	0.27	-	1	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15449868	15450177	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	intron	15450178	15450320	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	CDS	15450321	15450556	0.27	-	0	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	exon	15450321	15450556	.	-	.	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
Phchi.S1	AUGUSTUS	start_codon	15450554	15450556	.	-	0	transcript_id "Phchi.S1G236300.t1"; gene_id "Phchi.S1G236300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6262.t1 is derived from g3434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21922598	21923084	.	-	.	Phchi.S1G342100
Phchi.S1	AUGUSTUS	transcript	21922598	21923084	.	-	.	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	stop_codon	21922595	21922597	.	-	0	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	CDS	21922598	21922680	0.22	-	2	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	exon	21922598	21922680	.	-	.	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	intron	21922681	21922751	.	-	.	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	CDS	21922752	21922864	0.26	-	1	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	exon	21922752	21922864	.	-	.	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	intron	21922865	21922956	.	-	.	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	CDS	21922957	21923084	0.26	-	0	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	exon	21922957	21923084	.	-	.	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
Phchi.S1	AUGUSTUS	start_codon	21923082	21923084	.	-	0	transcript_id "Phchi.S1G342100.t1"; gene_id "Phchi.S1G342100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12917.t1 is derived from g11382.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3126833	3128308	.	-	.	Phchi.S3G023600
Phchi.S3	AUGUSTUS	transcript	3126833	3128308	.	-	.	transcript_id "Phchi.S3G023600.t1"; gene_id "Phchi.S3G023600"
Phchi.S3	AUGUSTUS	stop_codon	3126830	3126832	.	-	0	transcript_id "Phchi.S3G023600.t1"; gene_id "Phchi.S3G023600"
Phchi.S3	AUGUSTUS	CDS	3126833	3128308	0.66	-	0	transcript_id "Phchi.S3G023600.t1"; gene_id "Phchi.S3G023600"
Phchi.S3	AUGUSTUS	exon	3126833	3128308	.	-	.	transcript_id "Phchi.S3G023600.t1"; gene_id "Phchi.S3G023600"
Phchi.S3	AUGUSTUS	start_codon	3128306	3128308	.	-	0	transcript_id "Phchi.S3G023600.t1"; gene_id "Phchi.S3G023600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10022.t1 is derived from g7198.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45114637	45115959	.	-	.	Phchi.S1G718100
Phchi.S1	AUGUSTUS	transcript	45114637	45115959	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	stop_codon	45114634	45114636	.	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	CDS	45114637	45114669	0.43	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	exon	45114637	45114669	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	intron	45114670	45114836	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	CDS	45114837	45114851	0.45	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	exon	45114837	45114851	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	intron	45114852	45114942	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	CDS	45114943	45115029	0.42	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	exon	45114943	45115029	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	intron	45115030	45115200	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	CDS	45115201	45115215	0.37	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	exon	45115201	45115215	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	intron	45115216	45115358	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	CDS	45115359	45115380	0.45	-	1	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	exon	45115359	45115380	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	intron	45115381	45115576	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	CDS	45115577	45115959	0.42	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	exon	45115577	45115959	.	-	.	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
Phchi.S1	AUGUSTUS	start_codon	45115957	45115959	.	-	0	transcript_id "Phchi.S1G718100.t1"; gene_id "Phchi.S1G718100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7696.t1 is derived from g4870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30692538	30693572	.	+	.	Phchi.S1G485500
Phchi.S1	AUGUSTUS	transcript	30692538	30693572	.	+	.	transcript_id "Phchi.S1G485500.t1"; gene_id "Phchi.S1G485500"
Phchi.S1	AUGUSTUS	start_codon	30692538	30692540	.	+	0	transcript_id "Phchi.S1G485500.t1"; gene_id "Phchi.S1G485500"
Phchi.S1	AUGUSTUS	CDS	30692538	30693572	0.26	+	0	transcript_id "Phchi.S1G485500.t1"; gene_id "Phchi.S1G485500"
Phchi.S1	AUGUSTUS	exon	30692538	30693572	.	+	.	transcript_id "Phchi.S1G485500.t1"; gene_id "Phchi.S1G485500"
Phchi.S1	AUGUSTUS	stop_codon	30693573	30693575	.	+	0	transcript_id "Phchi.S1G485500.t1"; gene_id "Phchi.S1G485500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6054.t1 is derived from g3225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20653098	20654150	.	+	.	Phchi.S1G321300
Phchi.S1	AUGUSTUS	transcript	20653098	20654150	.	+	.	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	start_codon	20653098	20653100	.	+	0	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	CDS	20653098	20653851	0.38	+	0	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	exon	20653098	20653851	.	+	.	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	intron	20653852	20653956	.	+	.	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	CDS	20653957	20654150	0.39	+	2	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	exon	20653957	20654150	.	+	.	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
Phchi.S1	AUGUSTUS	stop_codon	20654151	20654153	.	+	0	transcript_id "Phchi.S1G321300.t1"; gene_id "Phchi.S1G321300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10397.t1 is derived from g7573.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47537316	47539765	.	+	.	Phchi.S1G755600
Phchi.S1	AUGUSTUS	transcript	47537316	47539765	.	+	.	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	start_codon	47537316	47537318	.	+	0	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	CDS	47537316	47537408	0.89	+	0	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	exon	47537316	47537408	.	+	.	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	intron	47537409	47537491	.	+	.	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	CDS	47537492	47539765	0.99	+	0	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	exon	47537492	47539765	.	+	.	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
Phchi.S1	AUGUSTUS	stop_codon	47539766	47539768	.	+	0	transcript_id "Phchi.S1G755600.t1"; gene_id "Phchi.S1G755600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9756.t1 is derived from g6932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43527594	43530200	.	-	.	Phchi.S1G691500
Phchi.S1	AUGUSTUS	transcript	43527594	43530200	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	stop_codon	43527591	43527593	.	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43527594	43527661	0.99	-	2	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43527594	43527661	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43527662	43527767	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43527768	43527870	0.99	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43527768	43527870	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43527871	43527960	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43527961	43528005	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43527961	43528005	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43528006	43528102	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43528103	43528201	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43528103	43528201	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43528202	43528306	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43528307	43528375	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43528307	43528375	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43528376	43528452	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43528453	43528512	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43528453	43528512	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43528513	43528932	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43528933	43529026	1	-	1	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43528933	43529026	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43529027	43529284	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43529285	43529359	1	-	1	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43529285	43529359	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43529360	43529623	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43529624	43529742	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43529624	43529742	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43529743	43529825	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43529826	43529987	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43529826	43529987	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	intron	43529988	43530080	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	CDS	43530081	43530200	1	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	exon	43530081	43530200	.	-	.	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
Phchi.S1	AUGUSTUS	start_codon	43530198	43530200	.	-	0	transcript_id "Phchi.S1G691500.t1"; gene_id "Phchi.S1G691500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2504.t1 is derived from g9424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7003273	7005164	.	+	.	Phchi.S5G111300
Phchi.S5	AUGUSTUS	transcript	7003273	7005164	.	+	.	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	start_codon	7003273	7003275	.	+	0	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	CDS	7003273	7004288	0.55	+	0	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	exon	7003273	7004288	.	+	.	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	intron	7004289	7004399	.	+	.	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	CDS	7004400	7004614	0.7	+	1	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	exon	7004400	7004614	.	+	.	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	intron	7004615	7004706	.	+	.	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	CDS	7004707	7005164	0.72	+	2	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	exon	7004707	7005164	.	+	.	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
Phchi.S5	AUGUSTUS	stop_codon	7005165	7005167	.	+	0	transcript_id "Phchi.S5G111300.t1"; gene_id "Phchi.S5G111300"
# This transcript jg7055.t2 is derived from g4227.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7056.t1 is derived from g4228.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26650512	26651296	.	-	.	Phchi.S1G421500
Phchi.S1	AUGUSTUS	transcript	26650512	26651296	.	-	.	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	stop_codon	26650509	26650511	.	-	0	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	CDS	26650512	26650837	0.35	-	2	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	exon	26650512	26650837	.	-	.	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	intron	26650838	26651106	.	-	.	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	CDS	26651107	26651296	0.99	-	0	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	exon	26651107	26651296	.	-	.	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
Phchi.S1	AUGUSTUS	start_codon	26651294	26651296	.	-	0	transcript_id "Phchi.S1G421500.t1"; gene_id "Phchi.S1G421500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3639.t1 is derived from g808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4903320	4904990	.	+	.	Phchi.S1G079800
Phchi.S1	AUGUSTUS	transcript	4903320	4904990	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	start_codon	4903320	4903322	.	+	0	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	CDS	4903320	4903816	0.57	+	0	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	exon	4903320	4903816	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	intron	4903817	4903909	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	CDS	4903910	4904151	0.88	+	1	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	exon	4903910	4904151	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	intron	4904152	4904266	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	CDS	4904267	4904769	0.7	+	2	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	exon	4904267	4904769	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	intron	4904770	4904909	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	CDS	4904910	4904990	0.63	+	0	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	exon	4904910	4904990	.	+	.	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
Phchi.S1	AUGUSTUS	stop_codon	4904991	4904993	.	+	0	transcript_id "Phchi.S1G079800.t1"; gene_id "Phchi.S1G079800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13370.t1 is derived from g11836.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6374425	6374741	.	+	.	Phchi.S3G068900
Phchi.S3	AUGUSTUS	transcript	6374425	6374741	.	+	.	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	start_codon	6374425	6374427	.	+	0	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	CDS	6374425	6374622	0.76	+	0	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	exon	6374425	6374622	.	+	.	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	intron	6374623	6374714	.	+	.	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	CDS	6374715	6374741	0.89	+	0	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	exon	6374715	6374741	.	+	.	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
Phchi.S3	AUGUSTUS	stop_codon	6374742	6374744	.	+	0	transcript_id "Phchi.S3G068900.t1"; gene_id "Phchi.S3G068900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4728.t1 is derived from g1898.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12503290	12504382	.	-	.	Phchi.S1G188700
Phchi.S1	AUGUSTUS	transcript	12503290	12504382	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	stop_codon	12503287	12503289	.	-	0	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	CDS	12503290	12503391	0.8	-	0	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	exon	12503290	12503391	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	intron	12503392	12503535	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	CDS	12503536	12503540	0.85	-	2	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	exon	12503536	12503540	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	intron	12503541	12503635	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	CDS	12503636	12503690	0.63	-	0	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	exon	12503636	12503690	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	intron	12503691	12504115	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	CDS	12504116	12504154	0.87	-	0	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	exon	12504116	12504154	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	intron	12504155	12504307	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	CDS	12504308	12504382	0.88	-	0	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	exon	12504308	12504382	.	-	.	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
Phchi.S1	AUGUSTUS	start_codon	12504380	12504382	.	-	0	transcript_id "Phchi.S1G188700.t1"; gene_id "Phchi.S1G188700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3740.t1 is derived from g909.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5460043	5463363	.	+	.	Phchi.S1G089900
Phchi.S1	AUGUSTUS	transcript	5460043	5463363	.	+	.	transcript_id "Phchi.S1G089900.t1"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	start_codon	5460043	5460045	.	+	0	transcript_id "Phchi.S1G089900.t1"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	CDS	5460043	5463363	0.79	+	0	transcript_id "Phchi.S1G089900.t1"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	exon	5460043	5463363	.	+	.	transcript_id "Phchi.S1G089900.t1"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	stop_codon	5463364	5463366	.	+	0	transcript_id "Phchi.S1G089900.t1"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	transcript	5460262	5463363	.	+	.	transcript_id "Phchi.S1G089900.t2"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	start_codon	5460262	5460264	.	+	0	transcript_id "Phchi.S1G089900.t2"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	CDS	5460262	5463363	0.66	+	0	transcript_id "Phchi.S1G089900.t2"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	exon	5460262	5463363	.	+	.	transcript_id "Phchi.S1G089900.t2"; gene_id "Phchi.S1G089900"
Phchi.S1	AUGUSTUS	stop_codon	5463364	5463366	.	+	0	transcript_id "Phchi.S1G089900.t2"; gene_id "Phchi.S1G089900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2835.t1 is derived from g9755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9099583	9104009	.	-	.	Phchi.S5G144400
Phchi.S5	AUGUSTUS	transcript	9099583	9104009	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	stop_codon	9099580	9099582	.	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9099583	9099882	0.83	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9099583	9099882	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9099883	9099972	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9099973	9099986	0.64	-	2	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9099973	9099986	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9099987	9100126	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9100127	9100202	0.87	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9100127	9100202	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9100203	9100295	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9100296	9100346	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9100296	9100346	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9100347	9100437	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9100438	9100560	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9100438	9100560	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9100561	9100643	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9100644	9100712	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9100644	9100712	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9100713	9100823	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9100824	9100952	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9100824	9100952	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9100953	9101045	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9101046	9101249	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9101046	9101249	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9101250	9101376	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9101377	9101608	1	-	1	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9101377	9101608	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9101609	9101698	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9101699	9101880	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9101699	9101880	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9101881	9101972	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9101973	9102098	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9101973	9102098	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9102099	9102225	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9102226	9103344	0.86	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9102226	9103344	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9103345	9103458	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9103459	9103674	1	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9103459	9103674	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	intron	9103675	9103766	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	CDS	9103767	9104009	0.99	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	exon	9103767	9104009	.	-	.	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
Phchi.S5	AUGUSTUS	start_codon	9104007	9104009	.	-	0	transcript_id "Phchi.S5G144400.t1"; gene_id "Phchi.S5G144400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3359.t1 is derived from g528.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3139408	3142495	.	-	.	Phchi.S1G051800
Phchi.S1	AUGUSTUS	transcript	3139408	3142495	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	stop_codon	3139405	3139407	.	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3139408	3139610	0.99	-	2	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3139408	3139610	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3139611	3139697	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3139698	3139869	1	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3139698	3139869	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3139870	3139974	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3139975	3140090	1	-	2	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3139975	3140090	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140091	3140169	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140170	3140257	1	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140170	3140257	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140258	3140419	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140420	3140562	1	-	2	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140420	3140562	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140563	3140682	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140683	3140746	1	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140683	3140746	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140747	3140862	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140863	3141018	1	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140863	3141018	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141019	3141181	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3141182	3141192	1	-	2	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3141182	3141192	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141193	3141321	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3141322	3141631	1	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3141322	3141631	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141632	3141710	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3141711	3141749	0.99	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3141711	3141749	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141750	3142006	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3142007	3142050	0.68	-	2	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3142007	3142050	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3142051	3142240	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3142241	3142319	0.59	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3142241	3142319	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3142320	3142471	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3142472	3142495	0.9	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3142472	3142495	.	-	.	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	start_codon	3142493	3142495	.	-	0	transcript_id "Phchi.S1G051800.t1"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	transcript	3139408	3142495	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	stop_codon	3139405	3139407	.	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3139408	3139610	0.98	-	2	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3139408	3139610	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3139611	3139718	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3139719	3139869	0.7	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3139719	3139869	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3139870	3139974	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3139975	3140090	1	-	2	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3139975	3140090	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140091	3140169	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140170	3140257	1	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140170	3140257	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140258	3140419	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140420	3140562	1	-	2	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140420	3140562	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140563	3140682	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140683	3140746	1	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140683	3140746	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3140747	3140862	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3140863	3141018	1	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3140863	3141018	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141019	3141181	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3141182	3141192	1	-	2	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3141182	3141192	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141193	3141321	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3141322	3141631	1	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3141322	3141631	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141632	3141710	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3141711	3141749	1	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3141711	3141749	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3141750	3142006	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3142007	3142050	0.53	-	2	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3142007	3142050	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3142051	3142240	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3142241	3142319	0.45	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3142241	3142319	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	intron	3142320	3142471	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	CDS	3142472	3142495	0.97	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	exon	3142472	3142495	.	-	.	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
Phchi.S1	AUGUSTUS	start_codon	3142493	3142495	.	-	0	transcript_id "Phchi.S1G051800.t2"; gene_id "Phchi.S1G051800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg871.t1 is derived from g10653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6023201	6025640	.	+	.	Phchi.S6G083000
Phchi.S6	AUGUSTUS	transcript	6023201	6025640	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	start_codon	6023201	6023203	.	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6023201	6023305	0.51	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6023201	6023305	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6023306	6023404	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6023405	6023497	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6023405	6023497	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6023498	6023637	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6023638	6023697	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6023638	6023697	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6023698	6023790	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6023791	6024063	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6023791	6024063	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6024064	6024157	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6024158	6024232	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6024158	6024232	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6024233	6024358	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6024359	6024415	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6024359	6024415	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6024416	6024513	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6024514	6024654	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6024514	6024654	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6024655	6024775	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6024776	6024826	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6024776	6024826	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6024827	6024903	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6024904	6024999	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6024904	6024999	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6025000	6025106	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6025107	6025190	0.99	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6025107	6025190	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6025191	6025378	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6025379	6025481	1	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6025379	6025481	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	intron	6025482	6025560	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	CDS	6025561	6025640	1	+	2	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	exon	6025561	6025640	.	+	.	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
Phchi.S6	AUGUSTUS	stop_codon	6025641	6025643	.	+	0	transcript_id "Phchi.S6G083000.t1"; gene_id "Phchi.S6G083000"
# This transcript jg1291.t2 is derived from g11074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1292.t1 is derived from g11075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8870216	8870941	.	+	.	Phchi.S6G125100
Phchi.S6	AUGUSTUS	transcript	8870216	8870941	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	start_codon	8870216	8870218	.	+	0	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	CDS	8870216	8870220	0.82	+	0	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	exon	8870216	8870220	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	intron	8870221	8870297	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	CDS	8870298	8870396	0.82	+	1	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	exon	8870298	8870396	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	intron	8870397	8870502	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	CDS	8870503	8870575	0.96	+	1	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	exon	8870503	8870575	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	intron	8870576	8870655	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	CDS	8870656	8870741	1	+	0	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	exon	8870656	8870741	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	intron	8870742	8870826	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	CDS	8870827	8870941	1	+	1	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	exon	8870827	8870941	.	+	.	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
Phchi.S6	AUGUSTUS	stop_codon	8870942	8870944	.	+	0	transcript_id "Phchi.S6G125100.t1"; gene_id "Phchi.S6G125100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7085.t1 is derived from g4257.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26808766	26809982	.	-	.	Phchi.S1G424400
Phchi.S1	AUGUSTUS	transcript	26808766	26809982	.	-	.	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	stop_codon	26808763	26808765	.	-	0	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	CDS	26808766	26808955	0.53	-	1	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	exon	26808766	26808955	.	-	.	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	intron	26808956	26809045	.	-	.	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	CDS	26809046	26809221	1	-	0	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	exon	26809046	26809221	.	-	.	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	intron	26809222	26809301	.	-	.	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	CDS	26809302	26809982	1	-	0	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	exon	26809302	26809982	.	-	.	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
Phchi.S1	AUGUSTUS	start_codon	26809980	26809982	.	-	0	transcript_id "Phchi.S1G424400.t1"; gene_id "Phchi.S1G424400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5558.t1 is derived from g2728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17592130	17592635	.	-	.	Phchi.S1G271700
Phchi.S1	AUGUSTUS	transcript	17592130	17592635	.	-	.	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	stop_codon	17592127	17592129	.	-	0	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	CDS	17592130	17592358	0.7	-	1	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	exon	17592130	17592358	.	-	.	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	intron	17592359	17592471	.	-	.	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	CDS	17592472	17592635	0.69	-	0	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	exon	17592472	17592635	.	-	.	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
Phchi.S1	AUGUSTUS	start_codon	17592633	17592635	.	-	0	transcript_id "Phchi.S1G271700.t1"; gene_id "Phchi.S1G271700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15219.t1 is derived from g13687.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17778118	17782144	.	+	.	Phchi.S3G253800
Phchi.S3	AUGUSTUS	transcript	17778118	17782144	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	start_codon	17778118	17778120	.	+	0	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778118	17778255	0.86	+	0	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778118	17778255	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778256	17778374	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778375	17778477	1	+	0	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778375	17778477	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778478	17778562	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778563	17778666	1	+	2	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778563	17778666	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778667	17778798	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778799	17778995	0.99	+	0	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778799	17778995	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778996	17779185	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17779186	17779583	0.95	+	1	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17779186	17779583	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17779584	17779823	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17779824	17780442	0.64	+	2	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17779824	17780442	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17780443	17780525	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17780526	17780546	0.76	+	1	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17780526	17780546	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17780547	17780684	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17780685	17780713	0.75	+	1	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17780685	17780713	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17780714	17780876	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17780877	17782144	0.65	+	2	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17780877	17782144	.	+	.	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	stop_codon	17782145	17782147	.	+	0	transcript_id "Phchi.S3G253800.t1"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	transcript	17778118	17782144	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	start_codon	17778118	17778120	.	+	0	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778118	17778255	0.79	+	0	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778118	17778255	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778256	17778374	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778375	17778477	1	+	0	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778375	17778477	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778478	17778562	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778563	17778666	1	+	2	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778563	17778666	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778667	17778798	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17778799	17778995	0.94	+	0	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17778799	17778995	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17778996	17779185	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17779186	17779583	0.93	+	1	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17779186	17779583	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17779584	17779823	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17779824	17780356	0.55	+	2	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17779824	17780356	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17780357	17780525	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17780526	17780575	0.43	+	0	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17780526	17780575	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17780576	17780684	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17780685	17780713	0.43	+	1	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17780685	17780713	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	intron	17780714	17780876	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	CDS	17780877	17782144	0.37	+	2	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	exon	17780877	17782144	.	+	.	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
Phchi.S3	AUGUSTUS	stop_codon	17782145	17782147	.	+	0	transcript_id "Phchi.S3G253800.t2"; gene_id "Phchi.S3G253800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg104.t1 is derived from g9886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	532010	533321	.	-	.	Phchi.S6G006300
Phchi.S6	AUGUSTUS	transcript	532010	533321	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	stop_codon	532007	532009	.	-	0	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	532010	532400	0.33	-	1	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	532010	532400	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	intron	532401	532519	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	532520	532858	0.25	-	1	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	532520	532858	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	intron	532859	533028	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	533029	533175	1	-	1	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	533029	533175	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	intron	533176	533316	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	533317	533321	0.88	-	0	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	533317	533321	.	-	.	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	start_codon	533319	533321	.	-	0	transcript_id "Phchi.S6G006300.t1"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	transcript	532010	533289	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	stop_codon	532007	532009	.	-	0	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	532010	532400	0.34	-	1	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	532010	532400	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	intron	532401	532519	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	532520	532858	0.31	-	1	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	532520	532858	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	intron	532859	533028	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	533029	533175	1	-	1	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	533029	533175	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	intron	533176	533275	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	CDS	533276	533289	0.75	-	0	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	exon	533276	533289	.	-	.	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
Phchi.S6	AUGUSTUS	start_codon	533287	533289	.	-	0	transcript_id "Phchi.S6G006300.t2"; gene_id "Phchi.S6G006300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg244.t1 is derived from g10026.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1682540	1688597	.	-	.	Phchi.S6G020300
Phchi.S6	AUGUSTUS	transcript	1682540	1688597	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	stop_codon	1682537	1682539	.	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1682540	1682630	1	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1682540	1682630	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1682631	1682725	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1682726	1682775	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1682726	1682775	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1682776	1682876	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1682877	1682972	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1682877	1682972	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1682973	1683061	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1683062	1683136	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1683062	1683136	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1683137	1683226	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1683227	1683328	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1683227	1683328	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1683329	1683516	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1683517	1683594	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1683517	1683594	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1683595	1683674	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1683675	1683876	1	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1683675	1683876	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1683877	1683968	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1683969	1684054	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1683969	1684054	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1684055	1684190	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1684191	1684400	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1684191	1684400	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1684401	1684487	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1684488	1684595	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1684488	1684595	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1684596	1684729	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1684730	1684842	1	-	2	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1684730	1684842	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1684843	1684940	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1684941	1685041	1	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1684941	1685041	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1685042	1685212	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1685213	1685262	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1685213	1685262	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1685263	1685413	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1685414	1685574	1	-	2	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1685414	1685574	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1685575	1685668	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1685669	1685736	1	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1685669	1685736	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1685737	1685888	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1685889	1686004	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1685889	1686004	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1686005	1686093	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1686094	1686260	1	-	2	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1686094	1686260	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1686261	1686352	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1686353	1686681	0.99	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1686353	1686681	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1686682	1686816	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1686817	1686923	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1686817	1686923	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1686924	1687030	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1687031	1687220	1	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1687031	1687220	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1687221	1687297	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1687298	1687462	1	-	1	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1687298	1687462	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1687463	1687566	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1687567	1687676	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1687567	1687676	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1687677	1687840	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1687841	1687945	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1687841	1687945	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1687946	1688105	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1688106	1688279	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1688106	1688279	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	intron	1688280	1688369	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	CDS	1688370	1688597	1	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	exon	1688370	1688597	.	-	.	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
Phchi.S6	AUGUSTUS	start_codon	1688595	1688597	.	-	0	transcript_id "Phchi.S6G020300.t1"; gene_id "Phchi.S6G020300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4329.t1 is derived from g1498.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9809910	9811420	.	+	.	Phchi.S1G148800
Phchi.S1	AUGUSTUS	transcript	9809910	9811420	.	+	.	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	start_codon	9809910	9809912	.	+	0	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	CDS	9809910	9810632	0.39	+	0	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	exon	9809910	9810632	.	+	.	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	intron	9810633	9810726	.	+	.	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	CDS	9810727	9810901	0.49	+	0	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	exon	9810727	9810901	.	+	.	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	intron	9810902	9811379	.	+	.	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	CDS	9811380	9811420	1	+	2	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	exon	9811380	9811420	.	+	.	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
Phchi.S1	AUGUSTUS	stop_codon	9811421	9811423	.	+	0	transcript_id "Phchi.S1G148800.t1"; gene_id "Phchi.S1G148800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4877.t1 is derived from g2047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13188359	13189447	.	-	.	Phchi.S1G203600
Phchi.S1	AUGUSTUS	transcript	13188359	13189447	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	stop_codon	13188356	13188358	.	-	0	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	CDS	13188359	13188368	1	-	1	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	exon	13188359	13188368	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	intron	13188369	13188585	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	CDS	13188586	13188656	1	-	0	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	exon	13188586	13188656	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	intron	13188657	13188791	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	CDS	13188792	13188837	0.46	-	1	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	exon	13188792	13188837	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	intron	13188838	13188974	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	CDS	13188975	13189447	0.32	-	0	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	exon	13188975	13189447	.	-	.	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
Phchi.S1	AUGUSTUS	start_codon	13189445	13189447	.	-	0	transcript_id "Phchi.S1G203600.t1"; gene_id "Phchi.S1G203600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg247.t1 is derived from g10029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1701903	1702229	.	+	.	Phchi.S6G020600
Phchi.S6	AUGUSTUS	transcript	1701903	1702229	.	+	.	transcript_id "Phchi.S6G020600.t1"; gene_id "Phchi.S6G020600"
Phchi.S6	AUGUSTUS	start_codon	1701903	1701905	.	+	0	transcript_id "Phchi.S6G020600.t1"; gene_id "Phchi.S6G020600"
Phchi.S6	AUGUSTUS	CDS	1701903	1702229	0.97	+	0	transcript_id "Phchi.S6G020600.t1"; gene_id "Phchi.S6G020600"
Phchi.S6	AUGUSTUS	exon	1701903	1702229	.	+	.	transcript_id "Phchi.S6G020600.t1"; gene_id "Phchi.S6G020600"
Phchi.S6	AUGUSTUS	stop_codon	1702230	1702232	.	+	0	transcript_id "Phchi.S6G020600.t1"; gene_id "Phchi.S6G020600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4496.t1 is derived from g1666.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10811600	10813360	.	+	.	Phchi.S1G165500
Phchi.S1	AUGUSTUS	transcript	10811600	10813360	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	start_codon	10811600	10811602	.	+	0	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	CDS	10811600	10812022	0.45	+	0	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	exon	10811600	10812022	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	intron	10812023	10812119	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	CDS	10812120	10812197	0.97	+	0	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	exon	10812120	10812197	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	intron	10812198	10812320	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	CDS	10812321	10812401	0.99	+	0	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	exon	10812321	10812401	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	intron	10812402	10812489	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	CDS	10812490	10812644	1	+	0	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	exon	10812490	10812644	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	intron	10812645	10812750	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	CDS	10812751	10813360	0.95	+	1	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	exon	10812751	10813360	.	+	.	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
Phchi.S1	AUGUSTUS	stop_codon	10813361	10813363	.	+	0	transcript_id "Phchi.S1G165500.t1"; gene_id "Phchi.S1G165500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6986.t1 is derived from g4158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26277247	26280517	.	-	.	Phchi.S1G414500
Phchi.S1	AUGUSTUS	transcript	26277247	26280517	.	-	.	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	stop_codon	26277244	26277246	.	-	0	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	CDS	26277247	26278715	0.93	-	2	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	exon	26277247	26278715	.	-	.	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	intron	26278716	26278811	.	-	.	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	CDS	26278812	26279127	1	-	0	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	exon	26278812	26279127	.	-	.	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	intron	26279128	26279278	.	-	.	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	CDS	26279279	26280517	0.72	-	0	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	exon	26279279	26280517	.	-	.	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
Phchi.S1	AUGUSTUS	start_codon	26280515	26280517	.	-	0	transcript_id "Phchi.S1G414500.t1"; gene_id "Phchi.S1G414500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg117.t1 is derived from g9899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	611874	615837	.	-	.	Phchi.S6G007600
Phchi.S6	AUGUSTUS	transcript	611874	615837	.	-	.	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	stop_codon	611871	611873	.	-	0	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	CDS	611874	615562	0.91	-	2	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	exon	611874	615562	.	-	.	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	intron	615563	615746	.	-	.	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	CDS	615747	615837	0.9	-	0	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	exon	615747	615837	.	-	.	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
Phchi.S6	AUGUSTUS	start_codon	615835	615837	.	-	0	transcript_id "Phchi.S6G007600.t1"; gene_id "Phchi.S6G007600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg910.t1 is derived from g10692.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6384067	6385191	.	+	.	Phchi.S6G086900
Phchi.S6	AUGUSTUS	transcript	6384067	6385191	.	+	.	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	start_codon	6384067	6384069	.	+	0	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	CDS	6384067	6384974	0.32	+	0	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	exon	6384067	6384974	.	+	.	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	intron	6384975	6385058	.	+	.	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	CDS	6385059	6385191	0.56	+	1	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	exon	6385059	6385191	.	+	.	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
Phchi.S6	AUGUSTUS	stop_codon	6385192	6385194	.	+	0	transcript_id "Phchi.S6G086900.t1"; gene_id "Phchi.S6G086900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1601.t1 is derived from g8520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1969097	1973059	.	+	.	Phchi.S5G021000
Phchi.S5	AUGUSTUS	transcript	1969097	1973059	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	start_codon	1969097	1969099	.	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1969097	1969190	0.84	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1969097	1969190	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1969191	1969350	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1969351	1969422	0.95	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1969351	1969422	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1969423	1969532	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1969533	1969595	0.82	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1969533	1969595	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1969596	1969741	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1969742	1969798	1	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1969742	1969798	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1969799	1969878	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1969879	1969946	1	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1969879	1969946	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1969947	1970026	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1970027	1970108	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1970027	1970108	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1970109	1970231	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1970232	1970287	1	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1970232	1970287	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1970288	1970397	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1970398	1970700	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1970398	1970700	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1970701	1970808	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1970809	1970895	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1970809	1970895	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1970896	1970964	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1970965	1971139	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1970965	1971139	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1971140	1971216	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1971217	1971245	0.99	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1971217	1971245	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1971246	1971316	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1971317	1971337	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1971317	1971337	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1971338	1971427	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1971428	1971591	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1971428	1971591	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1971592	1971695	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1971696	1971953	1	+	1	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1971696	1971953	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1971954	1972047	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1972048	1972169	0.97	+	1	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1972048	1972169	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1972170	1972292	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1972293	1972408	1	+	2	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1972293	1972408	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1972409	1972551	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1972552	1972700	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1972552	1972700	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1972701	1972792	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1972793	1972931	1	+	1	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1972793	1972931	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	intron	1972932	1973026	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	CDS	1973027	1973059	1	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	exon	1973027	1973059	.	+	.	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
Phchi.S5	AUGUSTUS	stop_codon	1973060	1973062	.	+	0	transcript_id "Phchi.S5G021000.t1"; gene_id "Phchi.S5G021000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11066.t1 is derived from g15116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3951290	3953805	.	+	.	Phchi.S4G064800
Phchi.S4	AUGUSTUS	transcript	3951290	3953805	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	start_codon	3951290	3951292	.	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3951290	3951518	0.8	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3951290	3951518	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3951519	3951641	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3951642	3952097	0.9	+	2	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3951642	3952097	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3952098	3952208	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3952209	3952303	0.96	+	2	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3952209	3952303	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3952304	3952394	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3952395	3952478	1	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3952395	3952478	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3952479	3952575	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3952576	3952653	1	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3952576	3952653	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3952654	3952741	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3952742	3952942	1	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3952742	3952942	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3952943	3953031	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3953032	3953139	1	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3953032	3953139	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3953140	3953218	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3953219	3953293	1	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3953219	3953293	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3953294	3953382	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3953383	3953478	1	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3953383	3953478	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3953479	3953542	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3953543	3953595	0.95	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3953543	3953595	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	intron	3953596	3953678	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	CDS	3953679	3953805	0.95	+	1	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	exon	3953679	3953805	.	+	.	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
Phchi.S4	AUGUSTUS	stop_codon	3953806	3953808	.	+	0	transcript_id "Phchi.S4G064800.t1"; gene_id "Phchi.S4G064800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13959.t1 is derived from g12426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9934620	9936327	.	-	.	Phchi.S3G127800
Phchi.S3	AUGUSTUS	transcript	9934620	9936327	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	stop_codon	9934617	9934619	.	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9934620	9934697	0.41	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9934620	9934697	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9934698	9934818	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9934819	9934911	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9934819	9934911	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9934912	9934993	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9934994	9935089	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9934994	9935089	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9935090	9935188	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9935189	9935288	1	-	1	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9935189	9935288	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9935289	9935442	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9935443	9935498	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9935443	9935498	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9935499	9935621	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9935622	9935657	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9935622	9935657	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9935658	9935740	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9935741	9935817	1	-	2	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9935741	9935817	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9935818	9935908	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9935909	9935975	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9935909	9935975	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9935976	9936062	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9936063	9936107	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9936063	9936107	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	intron	9936108	9936255	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	CDS	9936256	9936327	1	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	exon	9936256	9936327	.	-	.	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
Phchi.S3	AUGUSTUS	start_codon	9936325	9936327	.	-	0	transcript_id "Phchi.S3G127800.t1"; gene_id "Phchi.S3G127800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4056.t1 is derived from g1225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7565842	7568997	.	+	.	Phchi.S1G121500
Phchi.S1	AUGUSTUS	transcript	7565842	7568997	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	start_codon	7565842	7565844	.	+	0	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7565842	7565858	0.78	+	0	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7565842	7565858	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7565859	7565974	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7565975	7566055	0.89	+	1	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7565975	7566055	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7566056	7566390	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7566391	7566482	0.99	+	1	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7566391	7566482	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7566483	7566600	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7566601	7566848	1	+	2	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7566601	7566848	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7566849	7566937	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7566938	7566962	0.94	+	0	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7566938	7566962	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7566963	7567198	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7567199	7567342	0.94	+	2	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7567199	7567342	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7567343	7567439	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7567440	7567579	1	+	2	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7567440	7567579	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7567580	7567723	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7567724	7567759	1	+	0	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7567724	7567759	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	intron	7567760	7567977	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	CDS	7567978	7568997	1	+	0	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	exon	7567978	7568997	.	+	.	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
Phchi.S1	AUGUSTUS	stop_codon	7568998	7569000	.	+	0	transcript_id "Phchi.S1G121500.t1"; gene_id "Phchi.S1G121500"
# This transcript jg7982.t2 is derived from g5157.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7983.t1 is derived from g5158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32233012	32234782	.	+	.	Phchi.S1G514200
Phchi.S1	AUGUSTUS	transcript	32233012	32234782	.	+	.	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	start_codon	32233012	32233014	.	+	0	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	CDS	32233012	32233274	0.91	+	0	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	exon	32233012	32233274	.	+	.	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	intron	32233275	32233455	.	+	.	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	CDS	32233456	32234782	0.79	+	1	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	exon	32233456	32234782	.	+	.	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
Phchi.S1	AUGUSTUS	stop_codon	32234783	32234785	.	+	0	transcript_id "Phchi.S1G514200.t1"; gene_id "Phchi.S1G514200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12409.t1 is derived from g8086.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	18425260	18427001	.	-	.	Phchi.S2G048900
Phchi.S2	AUGUSTUS	transcript	18425260	18427001	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	stop_codon	18425257	18425259	.	-	0	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	CDS	18425260	18425343	0.75	-	0	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	exon	18425260	18425343	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	intron	18425344	18425495	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	CDS	18425496	18425566	0.76	-	2	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	exon	18425496	18425566	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	intron	18425567	18426040	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	CDS	18426041	18426118	1	-	2	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	exon	18426041	18426118	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	intron	18426119	18426382	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	CDS	18426383	18426670	0.98	-	2	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	exon	18426383	18426670	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	intron	18426671	18426862	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	CDS	18426863	18427001	1	-	0	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	exon	18426863	18427001	.	-	.	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
Phchi.S2	AUGUSTUS	start_codon	18426999	18427001	.	-	0	transcript_id "Phchi.S2G048900.t1"; gene_id "Phchi.S2G048900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1677.t1 is derived from g8596.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2464563	2466936	.	+	.	Phchi.S5G028600
Phchi.S5	AUGUSTUS	transcript	2464563	2466936	.	+	.	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	start_codon	2464563	2464565	.	+	0	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	CDS	2464563	2465996	1	+	0	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	exon	2464563	2465996	.	+	.	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	intron	2465997	2466084	.	+	.	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	CDS	2466085	2466936	0.99	+	0	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	exon	2466085	2466936	.	+	.	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
Phchi.S5	AUGUSTUS	stop_codon	2466937	2466939	.	+	0	transcript_id "Phchi.S5G028600.t1"; gene_id "Phchi.S5G028600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1591.t1 is derived from g8510.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1910315	1919325	.	+	.	Phchi.S5G020000
Phchi.S5	AUGUSTUS	transcript	1910315	1919325	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	start_codon	1910315	1910317	.	+	0	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1910315	1918327	0.99	+	0	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1910315	1918327	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1918328	1918493	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918494	1918626	1	+	0	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918494	1918626	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1918627	1918777	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918778	1918830	1	+	2	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918778	1918830	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1918831	1918924	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918925	1919032	0.98	+	0	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918925	1919032	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1919033	1919139	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1919140	1919325	1	+	0	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1919140	1919325	.	+	.	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	stop_codon	1919326	1919328	.	+	0	transcript_id "Phchi.S5G020000.t1"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	transcript	1910315	1918510	.	+	.	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	start_codon	1910315	1910317	.	+	0	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1910315	1918226	0.99	+	0	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1910315	1918226	.	+	.	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1918227	1918493	.	+	.	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918494	1918510	0.98	+	2	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918494	1918510	.	+	.	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	stop_codon	1918511	1918513	.	+	0	transcript_id "Phchi.S5G020000.t2"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	transcript	1918578	1919325	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	start_codon	1918578	1918580	.	+	0	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918578	1918626	0.8	+	0	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918578	1918626	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1918627	1918777	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918778	1918830	1	+	2	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918778	1918830	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1918831	1918924	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1918925	1919032	0.98	+	0	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1918925	1919032	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	intron	1919033	1919139	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	CDS	1919140	1919325	1	+	0	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	exon	1919140	1919325	.	+	.	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
Phchi.S5	AUGUSTUS	stop_codon	1919326	1919328	.	+	0	transcript_id "Phchi.S5G020000.t3"; gene_id "Phchi.S5G020000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg12368.t1 is derived from g8045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	13085030	13090883	.	-	.	Phchi.S2G044900
Phchi.S2	AUGUSTUS	transcript	13085364	13090883	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	stop_codon	13085361	13085363	.	-	0	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085364	13085368	0.98	-	2	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085364	13085368	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085369	13085585	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085586	13085772	0.98	-	0	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085586	13085772	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085773	13085934	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085935	13086537	1	-	0	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085935	13086537	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13086538	13086693	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13086694	13088214	0.93	-	0	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13086694	13088214	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13088215	13088333	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13088334	13088535	0.58	-	1	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13088334	13088535	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13088536	13088744	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13088745	13089851	0.71	-	1	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13088745	13089851	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13089852	13090192	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090193	13090259	1	-	2	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090193	13090259	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13090260	13090706	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090707	13090793	1	-	2	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090707	13090793	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13090794	13090873	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090874	13090883	1	-	0	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090874	13090883	.	-	.	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	start_codon	13090881	13090883	.	-	0	transcript_id "Phchi.S2G044900.t1"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	transcript	13085351	13090883	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	stop_codon	13085348	13085350	.	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085351	13085368	0.88	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085351	13085368	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085369	13085589	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085590	13085772	0.88	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085590	13085772	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085773	13085934	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085935	13086537	1	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085935	13086537	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13086538	13086693	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13086694	13088214	0.67	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13086694	13088214	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13088215	13088333	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13088334	13088535	0.41	-	1	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13088334	13088535	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13088536	13088744	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13088745	13089851	0.57	-	1	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13088745	13089851	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13089852	13090192	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090193	13090259	1	-	2	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090193	13090259	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13090260	13090706	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090707	13090793	1	-	2	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090707	13090793	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13090794	13090873	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090874	13090883	1	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090874	13090883	.	-	.	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	start_codon	13090881	13090883	.	-	0	transcript_id "Phchi.S2G044900.t2"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	transcript	13085030	13090883	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	stop_codon	13085027	13085029	.	-	0	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085030	13085154	0.44	-	2	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085030	13085154	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085155	13085297	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085298	13085368	0.46	-	1	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085298	13085368	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085369	13085473	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085474	13085772	0.77	-	0	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085474	13085772	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13085773	13085934	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13085935	13086537	1	-	0	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13085935	13086537	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13086538	13086693	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13086694	13088214	0.65	-	0	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13086694	13088214	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13088215	13088333	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13088334	13088535	0.48	-	1	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13088334	13088535	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13088536	13088744	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13088745	13089851	0.51	-	1	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13088745	13089851	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13089852	13090192	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090193	13090259	1	-	2	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090193	13090259	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13090260	13090706	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090707	13090793	1	-	2	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090707	13090793	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	intron	13090794	13090873	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	CDS	13090874	13090883	1	-	0	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	exon	13090874	13090883	.	-	.	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
Phchi.S2	AUGUSTUS	start_codon	13090881	13090883	.	-	0	transcript_id "Phchi.S2G044900.t3"; gene_id "Phchi.S2G044900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4928.t1 is derived from g2098.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13606719	13609720	.	-	.	Phchi.S1G208700
Phchi.S1	AUGUSTUS	transcript	13606719	13609720	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	stop_codon	13606716	13606718	.	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13606719	13606901	1	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13606719	13606901	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13606902	13606981	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13606982	13607092	1	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13606982	13607092	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13607093	13607166	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13607167	13607271	1	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13607167	13607271	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13607272	13607351	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13607352	13607477	1	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13607352	13607477	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13607478	13607560	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13607561	13607945	1	-	1	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13607561	13607945	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13607946	13608086	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13608087	13608364	1	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13608087	13608364	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13608365	13608491	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13608492	13608565	1	-	2	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13608492	13608565	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13608566	13608771	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13608772	13608843	1	-	2	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13608772	13608843	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13608844	13608942	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13608943	13609011	1	-	2	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13608943	13609011	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13609012	13609132	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13609133	13609202	1	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13609133	13609202	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13609203	13609300	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13609301	13609368	1	-	2	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13609301	13609368	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13609369	13609461	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13609462	13609596	1	-	2	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13609462	13609596	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	intron	13609597	13609695	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	CDS	13609696	13609720	0.66	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	exon	13609696	13609720	.	-	.	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
Phchi.S1	AUGUSTUS	start_codon	13609718	13609720	.	-	0	transcript_id "Phchi.S1G208700.t1"; gene_id "Phchi.S1G208700"
# This transcript jg3705.t2 is derived from g874.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3706.t1 is derived from g875.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5252516	5254659	.	+	.	Phchi.S1G086500
Phchi.S1	AUGUSTUS	transcript	5252516	5254659	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	start_codon	5252516	5252518	.	+	0	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5252516	5252759	0.65	+	0	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5252516	5252759	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5252760	5252975	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5252976	5253063	0.71	+	2	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5252976	5253063	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5253064	5253224	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5253225	5253258	0.57	+	1	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5253225	5253258	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5253259	5253403	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5253404	5253456	0.63	+	0	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5253404	5253456	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5253457	5253583	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5253584	5253705	0.54	+	1	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5253584	5253705	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5253706	5253880	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5253881	5254104	0.61	+	2	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5253881	5254104	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5254105	5254388	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5254389	5254461	0.87	+	0	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5254389	5254461	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	intron	5254462	5254600	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	CDS	5254601	5254659	0.96	+	2	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	exon	5254601	5254659	.	+	.	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
Phchi.S1	AUGUSTUS	stop_codon	5254660	5254662	.	+	0	transcript_id "Phchi.S1G086500.t1"; gene_id "Phchi.S1G086500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14506.t1 is derived from g12974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13224512	13225743	.	-	.	Phchi.S3G182500
Phchi.S3	AUGUSTUS	transcript	13224512	13225743	.	-	.	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	stop_codon	13224509	13224511	.	-	0	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	CDS	13224512	13225468	1	-	0	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	exon	13224512	13225468	.	-	.	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	intron	13225469	13225560	.	-	.	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	CDS	13225561	13225743	1	-	0	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	exon	13225561	13225743	.	-	.	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
Phchi.S3	AUGUSTUS	start_codon	13225741	13225743	.	-	0	transcript_id "Phchi.S3G182500.t1"; gene_id "Phchi.S3G182500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6212.t1 is derived from g3384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21489956	21490922	.	+	.	Phchi.S1G337100
Phchi.S1	AUGUSTUS	transcript	21489956	21490922	.	+	.	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	start_codon	21489956	21489958	.	+	0	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	CDS	21489956	21490280	0.28	+	0	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	exon	21489956	21490280	.	+	.	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	intron	21490281	21490518	.	+	.	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	CDS	21490519	21490613	0.92	+	2	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	exon	21490519	21490613	.	+	.	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	intron	21490614	21490808	.	+	.	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	CDS	21490809	21490922	1	+	0	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	exon	21490809	21490922	.	+	.	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
Phchi.S1	AUGUSTUS	stop_codon	21490923	21490925	.	+	0	transcript_id "Phchi.S1G337100.t1"; gene_id "Phchi.S1G337100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10976.t1 is derived from g15026.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3465286	3468633	.	-	.	Phchi.S4G055800
Phchi.S4	AUGUSTUS	transcript	3465286	3468633	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	stop_codon	3465283	3465285	.	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465286	3465304	1	-	1	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465286	3465304	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3465305	3465384	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465385	3465423	0.58	-	1	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465385	3465423	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3465424	3465501	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465502	3465612	0.77	-	1	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465502	3465612	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3465613	3465694	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465695	3466658	0.88	-	2	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465695	3466658	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3466659	3466916	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3466917	3466968	1	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3466917	3466968	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3466969	3467055	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467056	3467146	1	-	1	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467056	3467146	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467147	3467235	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467236	3467427	1	-	1	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467236	3467427	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467428	3467529	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467530	3467648	1	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467530	3467648	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467649	3467727	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467728	3467886	0.75	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467728	3467886	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467887	3467988	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467989	3468114	0.92	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467989	3468114	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3468115	3468201	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3468202	3468328	1	-	1	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3468202	3468328	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3468329	3468418	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3468419	3468633	0.63	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3468419	3468633	.	-	.	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	start_codon	3468631	3468633	.	-	0	transcript_id "Phchi.S4G055800.t1"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	transcript	3465286	3468633	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	stop_codon	3465283	3465285	.	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465286	3465304	1	-	1	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465286	3465304	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3465305	3465384	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465385	3465423	0.61	-	1	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465385	3465423	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3465424	3465501	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465502	3465612	0.79	-	1	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465502	3465612	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3465613	3465694	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3465695	3466658	0.88	-	2	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3465695	3466658	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3466659	3466916	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3466917	3466968	1	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3466917	3466968	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3466969	3467055	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467056	3467146	1	-	1	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467056	3467146	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467147	3467235	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467236	3467427	1	-	1	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467236	3467427	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467428	3467529	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467530	3467648	1	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467530	3467648	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467649	3467727	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467728	3467886	0.68	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467728	3467886	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3467887	3467988	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3467989	3468114	0.94	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3467989	3468114	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3468115	3468201	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3468202	3468334	1	-	1	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3468202	3468334	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	intron	3468335	3468418	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	CDS	3468419	3468633	0.59	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	exon	3468419	3468633	.	-	.	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
Phchi.S4	AUGUSTUS	start_codon	3468631	3468633	.	-	0	transcript_id "Phchi.S4G055800.t2"; gene_id "Phchi.S4G055800"
# This transcript jg1446.t2 is derived from g8365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1447.t1 is derived from g8366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	949169	949740	.	+	.	Phchi.S5G005600
Phchi.S5	AUGUSTUS	transcript	949169	949740	.	+	.	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	start_codon	949169	949171	.	+	0	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	CDS	949169	949402	0.69	+	0	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	exon	949169	949402	.	+	.	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	intron	949403	949515	.	+	.	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	CDS	949516	949740	0.99	+	0	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	exon	949516	949740	.	+	.	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
Phchi.S5	AUGUSTUS	stop_codon	949741	949743	.	+	0	transcript_id "Phchi.S5G005600.t1"; gene_id "Phchi.S5G005600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3649.t1 is derived from g818.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4963511	4967079	.	-	.	Phchi.S1G080800
Phchi.S1	AUGUSTUS	transcript	4963511	4967079	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	stop_codon	4963508	4963510	.	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4963511	4963651	0.96	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4963511	4963651	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4963652	4963743	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4963744	4963950	0.99	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4963744	4963950	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4963951	4964110	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4964111	4964179	0.49	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4964111	4964179	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4964180	4964347	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4964348	4964503	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4964348	4964503	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4964504	4964640	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4964641	4964790	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4964641	4964790	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4964791	4964942	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4964943	4965052	1	-	2	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4964943	4965052	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4965053	4965270	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4965271	4965415	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4965271	4965415	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4965416	4965522	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4965523	4965771	0.99	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4965523	4965771	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4965772	4965916	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4965917	4966159	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4965917	4966159	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4966160	4966249	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4966250	4966576	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4966250	4966576	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4966577	4966734	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4966735	4966775	1	-	2	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4966735	4966775	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4966776	4966863	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4966864	4966972	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4966864	4966972	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	intron	4966973	4967061	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	CDS	4967062	4967079	1	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	exon	4967062	4967079	.	-	.	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
Phchi.S1	AUGUSTUS	start_codon	4967077	4967079	.	-	0	transcript_id "Phchi.S1G080800.t1"; gene_id "Phchi.S1G080800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10625.t1 is derived from g14675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1287262	1287671	.	+	.	Phchi.S4G020700
Phchi.S4	AUGUSTUS	transcript	1287262	1287671	.	+	.	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	start_codon	1287262	1287264	.	+	0	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	CDS	1287262	1287416	0.85	+	0	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	exon	1287262	1287416	.	+	.	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	intron	1287417	1287562	.	+	.	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	CDS	1287563	1287671	0.95	+	1	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	exon	1287563	1287671	.	+	.	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
Phchi.S4	AUGUSTUS	stop_codon	1287672	1287674	.	+	0	transcript_id "Phchi.S4G020700.t1"; gene_id "Phchi.S4G020700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10714.t1 is derived from g14764.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1734584	1736479	.	-	.	Phchi.S4G029600
Phchi.S4	AUGUSTUS	transcript	1734584	1736479	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	stop_codon	1734581	1734583	.	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1734584	1734718	0.82	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1734584	1734718	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1734719	1734840	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1734841	1734900	1	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1734841	1734900	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1734901	1734967	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1734968	1735021	1	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1734968	1735021	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735022	1735135	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735136	1735250	0.95	-	1	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735136	1735250	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735251	1735365	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735366	1735430	0.95	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735366	1735430	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735431	1735562	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735563	1735648	0.97	-	2	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735563	1735648	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735649	1735749	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735750	1735831	0.53	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735750	1735831	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735832	1735941	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735942	1735973	0.97	-	2	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735942	1735973	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735974	1736078	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1736079	1736228	1	-	2	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1736079	1736228	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1736229	1736385	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1736386	1736479	1	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1736386	1736479	.	-	.	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	start_codon	1736477	1736479	.	-	0	transcript_id "Phchi.S4G029600.t1"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	transcript	1734584	1736479	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	stop_codon	1734581	1734583	.	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1734584	1734718	0.76	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1734584	1734718	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1734719	1734840	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1734841	1734900	1	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1734841	1734900	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1734901	1734967	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1734968	1735021	1	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1734968	1735021	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735022	1735135	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735136	1735250	1	-	1	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735136	1735250	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735251	1735327	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735328	1735430	0.8	-	2	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735328	1735430	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735431	1735562	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735563	1735580	0.8	-	2	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735563	1735580	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735581	1735749	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735750	1735831	0.59	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735750	1735831	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735832	1735941	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1735942	1735973	0.94	-	2	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1735942	1735973	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1735974	1736078	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1736079	1736228	1	-	2	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1736079	1736228	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	intron	1736229	1736385	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	CDS	1736386	1736479	0.99	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	exon	1736386	1736479	.	-	.	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
Phchi.S4	AUGUSTUS	start_codon	1736477	1736479	.	-	0	transcript_id "Phchi.S4G029600.t2"; gene_id "Phchi.S4G029600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7435.t1 is derived from g4607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29103069	29103602	.	+	.	Phchi.S1G459400
Phchi.S1	AUGUSTUS	transcript	29103069	29103602	.	+	.	transcript_id "Phchi.S1G459400.t1"; gene_id "Phchi.S1G459400"
Phchi.S1	AUGUSTUS	start_codon	29103069	29103071	.	+	0	transcript_id "Phchi.S1G459400.t1"; gene_id "Phchi.S1G459400"
Phchi.S1	AUGUSTUS	CDS	29103069	29103602	0.5	+	0	transcript_id "Phchi.S1G459400.t1"; gene_id "Phchi.S1G459400"
Phchi.S1	AUGUSTUS	exon	29103069	29103602	.	+	.	transcript_id "Phchi.S1G459400.t1"; gene_id "Phchi.S1G459400"
Phchi.S1	AUGUSTUS	stop_codon	29103603	29103605	.	+	0	transcript_id "Phchi.S1G459400.t1"; gene_id "Phchi.S1G459400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10047.t1 is derived from g7223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45274229	45276010	.	+	.	Phchi.S1G720600
Phchi.S1	AUGUSTUS	transcript	45274229	45276010	.	+	.	transcript_id "Phchi.S1G720600.t1"; gene_id "Phchi.S1G720600"
Phchi.S1	AUGUSTUS	start_codon	45274229	45274231	.	+	0	transcript_id "Phchi.S1G720600.t1"; gene_id "Phchi.S1G720600"
Phchi.S1	AUGUSTUS	CDS	45274229	45276010	0.9	+	0	transcript_id "Phchi.S1G720600.t1"; gene_id "Phchi.S1G720600"
Phchi.S1	AUGUSTUS	exon	45274229	45276010	.	+	.	transcript_id "Phchi.S1G720600.t1"; gene_id "Phchi.S1G720600"
Phchi.S1	AUGUSTUS	stop_codon	45276011	45276013	.	+	0	transcript_id "Phchi.S1G720600.t1"; gene_id "Phchi.S1G720600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3743.t1 is derived from g912.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5467649	5468482	.	+	.	Phchi.S1G090200
Phchi.S1	AUGUSTUS	transcript	5467649	5468482	.	+	.	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	start_codon	5467649	5467651	.	+	0	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	CDS	5467649	5467988	0.9	+	0	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	exon	5467649	5467988	.	+	.	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	intron	5467989	5468124	.	+	.	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	CDS	5468125	5468289	0.6	+	2	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	exon	5468125	5468289	.	+	.	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	intron	5468290	5468441	.	+	.	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	CDS	5468442	5468482	0.43	+	2	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	exon	5468442	5468482	.	+	.	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
Phchi.S1	AUGUSTUS	stop_codon	5468483	5468485	.	+	0	transcript_id "Phchi.S1G090200.t1"; gene_id "Phchi.S1G090200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7725.t1 is derived from g4899.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30829048	30830845	.	-	.	Phchi.S1G488400
Phchi.S1	AUGUSTUS	transcript	30829048	30830845	.	-	.	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	stop_codon	30829045	30829047	.	-	0	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	CDS	30829048	30830409	0.79	-	0	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	exon	30829048	30830409	.	-	.	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	intron	30830410	30830842	.	-	.	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	CDS	30830843	30830845	0.03	-	0	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	exon	30830843	30830845	.	-	.	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
Phchi.S1	AUGUSTUS	start_codon	30830843	30830845	.	-	0	transcript_id "Phchi.S1G488400.t1"; gene_id "Phchi.S1G488400"
# This transcript jg12397.t2 is derived from g8074.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12398.t1 is derived from g8075.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	17446417	17452126	.	+	.	Phchi.S2G047800
Phchi.S2	AUGUSTUS	transcript	17446417	17452126	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	start_codon	17446417	17446419	.	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17446417	17446587	0.71	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17446417	17446587	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17446588	17447010	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17447011	17447073	0.58	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17447011	17447073	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17447074	17447209	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17447210	17447253	0.62	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17447210	17447253	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17447254	17447400	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17447401	17447493	0.58	+	1	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17447401	17447493	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17447494	17447668	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17447669	17447767	1	+	1	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17447669	17447767	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17447768	17448010	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17448011	17448097	1	+	1	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17448011	17448097	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17448098	17448183	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17448184	17448506	1	+	1	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17448184	17448506	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17448507	17448746	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17448747	17448848	0.88	+	2	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17448747	17448848	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17448849	17448928	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17448929	17448945	0.75	+	2	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17448929	17448945	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17448946	17449085	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17449086	17449194	1	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17449086	17449194	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17449195	17449329	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17449330	17449673	0.89	+	2	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17449330	17449673	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17449674	17449992	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17449993	17450373	0.62	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17449993	17450373	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17450374	17450495	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17450496	17450574	1	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17450496	17450574	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	intron	17450575	17450744	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	CDS	17450745	17452126	0.98	+	2	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	exon	17450745	17452126	.	+	.	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
Phchi.S2	AUGUSTUS	stop_codon	17452127	17452129	.	+	0	transcript_id "Phchi.S2G047800.t1"; gene_id "Phchi.S2G047800"
# This transcript jg10941.t2 is derived from g14991.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10941.t3 is derived from g14991.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10942.t1 is derived from g14992.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3213687	3214137	.	-	.	Phchi.S4G052400
Phchi.S4	AUGUSTUS	transcript	3213687	3214137	.	-	.	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	stop_codon	3213684	3213686	.	-	0	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	CDS	3213687	3213699	0.77	-	1	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	exon	3213687	3213699	.	-	.	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	intron	3213700	3213838	.	-	.	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	CDS	3213839	3213918	0.77	-	0	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	exon	3213839	3213918	.	-	.	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	intron	3213919	3214011	.	-	.	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	CDS	3214012	3214137	0.68	-	0	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	exon	3214012	3214137	.	-	.	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
Phchi.S4	AUGUSTUS	start_codon	3214135	3214137	.	-	0	transcript_id "Phchi.S4G052400.t1"; gene_id "Phchi.S4G052400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5833.t1 is derived from g3003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19168798	19170064	.	-	.	Phchi.S1G299200
Phchi.S1	AUGUSTUS	transcript	19168798	19170064	.	-	.	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	stop_codon	19168795	19168797	.	-	0	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	CDS	19168798	19169601	0.72	-	0	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	exon	19168798	19169601	.	-	.	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	intron	19169602	19169758	.	-	.	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	CDS	19169759	19170064	0.88	-	0	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	exon	19169759	19170064	.	-	.	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
Phchi.S1	AUGUSTUS	start_codon	19170062	19170064	.	-	0	transcript_id "Phchi.S1G299200.t1"; gene_id "Phchi.S1G299200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7625.t1 is derived from g4799.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30305644	30306851	.	+	.	Phchi.S1G478400
Phchi.S1	AUGUSTUS	transcript	30305644	30306851	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	start_codon	30305644	30305646	.	+	0	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	CDS	30305644	30305694	1	+	0	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	exon	30305644	30305694	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	intron	30305695	30305795	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	CDS	30305796	30305880	1	+	0	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	exon	30305796	30305880	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	intron	30305881	30305970	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	CDS	30305971	30306176	1	+	2	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	exon	30305971	30306176	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	intron	30306177	30306261	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	CDS	30306262	30306369	1	+	0	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	exon	30306262	30306369	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	intron	30306370	30306489	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	CDS	30306490	30306604	1	+	0	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	exon	30306490	30306604	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	intron	30306605	30306687	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	CDS	30306688	30306851	1	+	2	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	exon	30306688	30306851	.	+	.	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
Phchi.S1	AUGUSTUS	stop_codon	30306852	30306854	.	+	0	transcript_id "Phchi.S1G478400.t1"; gene_id "Phchi.S1G478400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14073.t1 is derived from g12540.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10661880	10664197	.	+	.	Phchi.S3G139200
Phchi.S3	AUGUSTUS	transcript	10661880	10664197	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	start_codon	10661880	10661882	.	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10661880	10662040	0.3	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10661880	10662040	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10662041	10662127	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10662128	10662343	1	+	1	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10662128	10662343	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10662344	10662444	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10662445	10662535	0.51	+	1	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10662445	10662535	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10662536	10662606	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10662607	10662798	0.44	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10662607	10662798	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10662799	10662910	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10662911	10663000	1	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10662911	10663000	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10663001	10663145	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10663146	10663253	0.98	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10663146	10663253	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10663254	10663371	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10663372	10663425	1	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10663372	10663425	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10663426	10663542	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10663543	10663657	0.95	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10663543	10663657	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10663658	10663732	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10663733	10663893	1	+	2	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10663733	10663893	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10663894	10663978	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10663979	10664074	0.57	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10663979	10664074	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	intron	10664075	10664155	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	CDS	10664156	10664197	0.41	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	exon	10664156	10664197	.	+	.	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
Phchi.S3	AUGUSTUS	stop_codon	10664198	10664200	.	+	0	transcript_id "Phchi.S3G139200.t1"; gene_id "Phchi.S3G139200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12238.t1 is derived from g7914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	6931926	6933644	.	-	.	Phchi.S2G031800
Phchi.S2	AUGUSTUS	transcript	6931926	6933644	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	stop_codon	6931923	6931925	.	-	0	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	CDS	6931926	6932180	0.66	-	0	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	exon	6931926	6932180	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	intron	6932181	6932295	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	CDS	6932296	6932556	0.89	-	0	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	exon	6932296	6932556	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	intron	6932557	6932654	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	CDS	6932655	6932819	1	-	0	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	exon	6932655	6932819	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	intron	6932820	6932934	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	CDS	6932935	6933038	1	-	2	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	exon	6932935	6933038	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	intron	6933039	6933130	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	CDS	6933131	6933427	1	-	2	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	exon	6933131	6933427	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	intron	6933428	6933523	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	CDS	6933524	6933644	0.94	-	0	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	exon	6933524	6933644	.	-	.	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
Phchi.S2	AUGUSTUS	start_codon	6933642	6933644	.	-	0	transcript_id "Phchi.S2G031800.t1"; gene_id "Phchi.S2G031800"
# This transcript jg14379.t2 is derived from g12846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14380.t1 is derived from g12848.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12465282	12466641	.	+	.	Phchi.S3G169900
Phchi.S3	AUGUSTUS	transcript	12466134	12466641	.	+	.	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	start_codon	12466134	12466136	.	+	0	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12466134	12466136	0.99	+	0	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12466134	12466136	.	+	.	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	intron	12466137	12466273	.	+	.	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12466274	12466498	0.98	+	0	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12466274	12466498	.	+	.	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	intron	12466499	12466620	.	+	.	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12466621	12466641	1	+	0	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12466621	12466641	.	+	.	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	stop_codon	12466642	12466644	.	+	0	transcript_id "Phchi.S3G169900.t1"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	transcript	12465282	12466641	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	start_codon	12465282	12465284	.	+	0	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12465282	12465521	0.48	+	0	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12465282	12465521	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	intron	12465522	12465912	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12465913	12465967	0.89	+	0	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12465913	12465967	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	intron	12465968	12466043	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12466044	12466141	1	+	2	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12466044	12466141	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	intron	12466142	12466273	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12466274	12466498	1	+	0	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12466274	12466498	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	intron	12466499	12466620	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	CDS	12466621	12466641	1	+	0	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	exon	12466621	12466641	.	+	.	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
Phchi.S3	AUGUSTUS	stop_codon	12466642	12466644	.	+	0	transcript_id "Phchi.S3G169900.t2"; gene_id "Phchi.S3G169900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9693.t1 is derived from g6869.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43308921	43309580	.	+	.	Phchi.S1G685200
Phchi.S1	AUGUSTUS	transcript	43308921	43309580	.	+	.	transcript_id "Phchi.S1G685200.t1"; gene_id "Phchi.S1G685200"
Phchi.S1	AUGUSTUS	start_codon	43308921	43308923	.	+	0	transcript_id "Phchi.S1G685200.t1"; gene_id "Phchi.S1G685200"
Phchi.S1	AUGUSTUS	CDS	43308921	43309580	1	+	0	transcript_id "Phchi.S1G685200.t1"; gene_id "Phchi.S1G685200"
Phchi.S1	AUGUSTUS	exon	43308921	43309580	.	+	.	transcript_id "Phchi.S1G685200.t1"; gene_id "Phchi.S1G685200"
Phchi.S1	AUGUSTUS	stop_codon	43309581	43309583	.	+	0	transcript_id "Phchi.S1G685200.t1"; gene_id "Phchi.S1G685200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14965.t1 is derived from g13433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15779910	15782403	.	+	.	Phchi.S3G228400
Phchi.S3	AUGUSTUS	transcript	15779910	15782403	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	start_codon	15779910	15779912	.	+	0	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15779910	15780305	0.97	+	0	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15779910	15780305	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15780306	15780388	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15780389	15780553	1	+	0	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15780389	15780553	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15780554	15780752	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15780753	15780845	1	+	0	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15780753	15780845	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15780846	15780927	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15780928	15781043	0.98	+	0	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15780928	15781043	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15781044	15781145	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15781146	15781244	1	+	1	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15781146	15781244	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15781245	15781359	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15781360	15781671	1	+	1	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15781360	15781671	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15781672	15781829	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15781830	15781994	1	+	1	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15781830	15781994	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	intron	15781995	15782111	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	CDS	15782112	15782403	0.95	+	1	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	exon	15782112	15782403	.	+	.	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
Phchi.S3	AUGUSTUS	stop_codon	15782404	15782406	.	+	0	transcript_id "Phchi.S3G228400.t1"; gene_id "Phchi.S3G228400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14270.t1 is derived from g12737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11869074	11873990	.	+	.	Phchi.S3G158900
Phchi.S3	AUGUSTUS	transcript	11869074	11873990	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	start_codon	11869074	11869076	.	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11869074	11870189	0.65	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11869074	11870189	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	intron	11870190	11870329	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11870330	11870470	0.99	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11870330	11870470	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	intron	11870471	11870600	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11870601	11870865	0.53	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11870601	11870865	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	intron	11870866	11871016	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11871017	11871929	0.46	+	2	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11871017	11871929	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	intron	11871930	11872149	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11872150	11872498	0.53	+	1	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11872150	11872498	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	intron	11872499	11872612	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11872613	11872789	1	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11872613	11872789	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	intron	11872790	11872901	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	CDS	11872902	11873990	0.99	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	exon	11872902	11873990	.	+	.	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
Phchi.S3	AUGUSTUS	stop_codon	11873991	11873993	.	+	0	transcript_id "Phchi.S3G158900.t1"; gene_id "Phchi.S3G158900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3057.t1 is derived from g226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1380468	1381280	.	+	.	Phchi.S1G021600
Phchi.S1	AUGUSTUS	transcript	1380468	1381280	.	+	.	transcript_id "Phchi.S1G021600.t1"; gene_id "Phchi.S1G021600"
Phchi.S1	AUGUSTUS	start_codon	1380468	1380470	.	+	0	transcript_id "Phchi.S1G021600.t1"; gene_id "Phchi.S1G021600"
Phchi.S1	AUGUSTUS	CDS	1380468	1381280	0.46	+	0	transcript_id "Phchi.S1G021600.t1"; gene_id "Phchi.S1G021600"
Phchi.S1	AUGUSTUS	exon	1380468	1381280	.	+	.	transcript_id "Phchi.S1G021600.t1"; gene_id "Phchi.S1G021600"
Phchi.S1	AUGUSTUS	stop_codon	1381281	1381283	.	+	0	transcript_id "Phchi.S1G021600.t1"; gene_id "Phchi.S1G021600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1078.t1 is derived from g10861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7482361	7482996	.	-	.	Phchi.S6G103700
Phchi.S6	AUGUSTUS	transcript	7482361	7482996	.	-	.	transcript_id "Phchi.S6G103700.t1"; gene_id "Phchi.S6G103700"
Phchi.S6	AUGUSTUS	stop_codon	7482358	7482360	.	-	0	transcript_id "Phchi.S6G103700.t1"; gene_id "Phchi.S6G103700"
Phchi.S6	AUGUSTUS	CDS	7482361	7482996	0.55	-	0	transcript_id "Phchi.S6G103700.t1"; gene_id "Phchi.S6G103700"
Phchi.S6	AUGUSTUS	exon	7482361	7482996	.	-	.	transcript_id "Phchi.S6G103700.t1"; gene_id "Phchi.S6G103700"
Phchi.S6	AUGUSTUS	start_codon	7482994	7482996	.	-	0	transcript_id "Phchi.S6G103700.t1"; gene_id "Phchi.S6G103700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13269.t1 is derived from g11734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4995679	4997016	.	+	.	Phchi.S3G058800
Phchi.S3	AUGUSTUS	transcript	4995679	4997016	.	+	.	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	start_codon	4995679	4995681	.	+	0	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	CDS	4995679	4996587	0.33	+	0	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	exon	4995679	4996587	.	+	.	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	intron	4996588	4996740	.	+	.	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	CDS	4996741	4997016	0.88	+	0	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	exon	4996741	4997016	.	+	.	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
Phchi.S3	AUGUSTUS	stop_codon	4997017	4997019	.	+	0	transcript_id "Phchi.S3G058800.t1"; gene_id "Phchi.S3G058800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13842.t1 is derived from g12309.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9158662	9162155	.	+	.	Phchi.S3G116100
Phchi.S3	AUGUSTUS	transcript	9158662	9162155	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	start_codon	9158662	9158664	.	+	0	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9158662	9158890	0.69	+	0	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9158662	9158890	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9158891	9159304	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9159305	9159407	1	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9159305	9159407	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9159408	9159748	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9159749	9159830	1	+	1	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9159749	9159830	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9159831	9159921	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9159922	9160105	0.99	+	0	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9159922	9160105	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9160106	9160172	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9160173	9160252	0.99	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9160173	9160252	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9160253	9160340	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9160341	9160443	0.99	+	0	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9160341	9160443	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9160444	9160541	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9160542	9160698	1	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9160542	9160698	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9160699	9160813	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9160814	9160965	0.93	+	1	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9160814	9160965	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9160966	9161094	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9161095	9161277	0.97	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9161095	9161277	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9161278	9161376	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9161377	9161676	1	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9161377	9161676	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9161677	9161754	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9161755	9161826	1	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9161755	9161826	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9161827	9161911	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9161912	9161964	1	+	2	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9161912	9161964	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	intron	9161965	9162032	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	CDS	9162033	9162155	0.96	+	0	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	exon	9162033	9162155	.	+	.	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
Phchi.S3	AUGUSTUS	stop_codon	9162156	9162158	.	+	0	transcript_id "Phchi.S3G116100.t1"; gene_id "Phchi.S3G116100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4023.t1 is derived from g1192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7209336	7212584	.	+	.	Phchi.S1G118200
Phchi.S1	AUGUSTUS	transcript	7209336	7212584	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	start_codon	7209336	7209338	.	+	0	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	CDS	7209336	7210179	1	+	0	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	exon	7209336	7210179	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	intron	7210180	7210316	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	CDS	7210317	7211242	0.97	+	2	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	exon	7210317	7211242	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	intron	7211243	7211359	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	CDS	7211360	7211556	1	+	0	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	exon	7211360	7211556	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	intron	7211557	7211674	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	CDS	7211675	7211788	0.98	+	1	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	exon	7211675	7211788	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	intron	7211789	7211986	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	CDS	7211987	7212014	0.98	+	1	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	exon	7211987	7212014	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	intron	7212015	7212107	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	CDS	7212108	7212584	1	+	0	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	exon	7212108	7212584	.	+	.	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
Phchi.S1	AUGUSTUS	stop_codon	7212585	7212587	.	+	0	transcript_id "Phchi.S1G118200.t1"; gene_id "Phchi.S1G118200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1358.t1 is derived from g9782.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C9	AUGUSTUS	gene	135106	135591	.	-	.	Phchi.C9G000100
Phchi.C9	AUGUSTUS	transcript	135106	135591	.	-	.	transcript_id "Phchi.C9G000100.t1"; gene_id "Phchi.C9G000100"
Phchi.C9	AUGUSTUS	stop_codon	135103	135105	.	-	0	transcript_id "Phchi.C9G000100.t1"; gene_id "Phchi.C9G000100"
Phchi.C9	AUGUSTUS	CDS	135106	135591	0.54	-	0	transcript_id "Phchi.C9G000100.t1"; gene_id "Phchi.C9G000100"
Phchi.C9	AUGUSTUS	exon	135106	135591	.	-	.	transcript_id "Phchi.C9G000100.t1"; gene_id "Phchi.C9G000100"
Phchi.C9	AUGUSTUS	start_codon	135589	135591	.	-	0	transcript_id "Phchi.C9G000100.t1"; gene_id "Phchi.C9G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10962.t1 is derived from g15012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3315629	3316476	.	+	.	Phchi.S4G054400
Phchi.S4	AUGUSTUS	transcript	3315629	3316476	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	start_codon	3315629	3315631	.	+	0	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	CDS	3315629	3315670	1	+	0	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	exon	3315629	3315670	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	intron	3315671	3315852	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	CDS	3315853	3315957	0.99	+	0	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	exon	3315853	3315957	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	intron	3315958	3316062	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	CDS	3316063	3316185	0.98	+	0	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	exon	3316063	3316185	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	intron	3316186	3316350	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	CDS	3316351	3316476	1	+	0	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	exon	3316351	3316476	.	+	.	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
Phchi.S4	AUGUSTUS	stop_codon	3316477	3316479	.	+	0	transcript_id "Phchi.S4G054400.t1"; gene_id "Phchi.S4G054400"
# This transcript jg2850.t2 is derived from g19.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2851.t1 is derived from g20.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20422	23685	.	+	.	Phchi.S1G001000
Phchi.S1	AUGUSTUS	transcript	20422	23685	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	start_codon	20422	20424	.	+	0	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	CDS	20422	22624	0.28	+	0	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	exon	20422	22624	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	intron	22625	22939	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	CDS	22940	22993	0.34	+	2	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	exon	22940	22993	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	intron	22994	23303	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	CDS	23304	23381	0.91	+	2	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	exon	23304	23381	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	intron	23382	23469	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	CDS	23470	23544	0.66	+	2	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	exon	23470	23544	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	intron	23545	23674	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	CDS	23675	23685	0.99	+	2	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	exon	23675	23685	.	+	.	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
Phchi.S1	AUGUSTUS	stop_codon	23686	23688	.	+	0	transcript_id "Phchi.S1G001000.t1"; gene_id "Phchi.S1G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7472.t1 is derived from g4645.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29538624	29539950	.	-	.	Phchi.S1G463100
Phchi.S1	AUGUSTUS	transcript	29538624	29539950	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	stop_codon	29538621	29538623	.	-	0	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29538624	29538637	1	-	2	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29538624	29538637	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	intron	29538638	29538714	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29538715	29538772	1	-	0	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29538715	29538772	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	intron	29538773	29538915	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29538916	29539029	1	-	0	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29538916	29539029	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	intron	29539030	29539151	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29539152	29539210	1	-	2	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29539152	29539210	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	intron	29539211	29539291	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29539292	29539372	1	-	2	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29539292	29539372	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	intron	29539373	29539468	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29539469	29539724	1	-	0	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29539469	29539724	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	intron	29539725	29539809	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	CDS	29539810	29539950	0.8	-	0	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	exon	29539810	29539950	.	-	.	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
Phchi.S1	AUGUSTUS	start_codon	29539948	29539950	.	-	0	transcript_id "Phchi.S1G463100.t1"; gene_id "Phchi.S1G463100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4103.t1 is derived from g1272.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7825978	7829127	.	+	.	Phchi.S1G126200
Phchi.S1	AUGUSTUS	transcript	7825978	7829127	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	start_codon	7825978	7825980	.	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7825978	7826143	0.98	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7825978	7826143	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7826144	7826239	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7826240	7826685	0.95	+	2	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7826240	7826685	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7826686	7826884	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7826885	7826975	1	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7826885	7826975	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7826976	7827124	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7827125	7827282	1	+	2	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7827125	7827282	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7827283	7827374	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7827375	7827399	0.92	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7827375	7827399	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7827400	7827535	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7827536	7827621	1	+	2	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7827536	7827621	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7827622	7827832	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7827833	7827926	1	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7827833	7827926	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7827927	7828078	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7828079	7828257	0.97	+	2	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7828079	7828257	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7828258	7828355	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7828356	7828694	0.97	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7828356	7828694	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	intron	7828695	7829121	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	CDS	7829122	7829127	1	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	exon	7829122	7829127	.	+	.	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
Phchi.S1	AUGUSTUS	stop_codon	7829128	7829130	.	+	0	transcript_id "Phchi.S1G126200.t1"; gene_id "Phchi.S1G126200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2781.t1 is derived from g9701.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8846171	8846617	.	-	.	Phchi.S5G139000
Phchi.S5	AUGUSTUS	transcript	8846171	8846617	.	-	.	transcript_id "Phchi.S5G139000.t1"; gene_id "Phchi.S5G139000"
Phchi.S5	AUGUSTUS	stop_codon	8846168	8846170	.	-	0	transcript_id "Phchi.S5G139000.t1"; gene_id "Phchi.S5G139000"
Phchi.S5	AUGUSTUS	CDS	8846171	8846617	1	-	0	transcript_id "Phchi.S5G139000.t1"; gene_id "Phchi.S5G139000"
Phchi.S5	AUGUSTUS	exon	8846171	8846617	.	-	.	transcript_id "Phchi.S5G139000.t1"; gene_id "Phchi.S5G139000"
Phchi.S5	AUGUSTUS	start_codon	8846615	8846617	.	-	0	transcript_id "Phchi.S5G139000.t1"; gene_id "Phchi.S5G139000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6707.t1 is derived from g3879.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24641722	24643793	.	-	.	Phchi.S1G386600
Phchi.S1	AUGUSTUS	transcript	24641722	24643793	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	stop_codon	24641719	24641721	.	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24641722	24641793	1	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24641722	24641793	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24641794	24641877	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24641878	24641952	1	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24641878	24641952	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24641953	24642051	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642052	24642120	1	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642052	24642120	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642121	24642297	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642298	24642411	1	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642298	24642411	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642412	24642540	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642541	24642636	1	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642541	24642636	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642637	24642906	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642907	24642981	0.99	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642907	24642981	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642982	24643101	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24643102	24643260	0.95	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24643102	24643260	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24643261	24643361	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24643362	24643793	0.62	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24643362	24643793	.	-	.	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	start_codon	24643791	24643793	.	-	0	transcript_id "Phchi.S1G386600.t1"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	transcript	24641757	24643793	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	stop_codon	24641754	24641756	.	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24641757	24641793	0.49	-	1	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24641757	24641793	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24641794	24641877	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24641878	24641952	0.49	-	1	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24641878	24641952	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24641953	24642051	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642052	24642098	0.49	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642052	24642098	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642099	24642297	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642298	24642411	1	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642298	24642411	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642412	24642540	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642541	24642636	1	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642541	24642636	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642637	24642906	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24642907	24642981	1	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24642907	24642981	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24642982	24643101	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24643102	24643260	0.91	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24643102	24643260	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	intron	24643261	24643361	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	CDS	24643362	24643793	0.63	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	exon	24643362	24643793	.	-	.	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
Phchi.S1	AUGUSTUS	start_codon	24643791	24643793	.	-	0	transcript_id "Phchi.S1G386600.t2"; gene_id "Phchi.S1G386600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg865.t1 is derived from g10647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5991496	5992548	.	+	.	Phchi.S6G082400
Phchi.S6	AUGUSTUS	transcript	5991496	5992548	.	+	.	transcript_id "Phchi.S6G082400.t1"; gene_id "Phchi.S6G082400"
Phchi.S6	AUGUSTUS	start_codon	5991496	5991498	.	+	0	transcript_id "Phchi.S6G082400.t1"; gene_id "Phchi.S6G082400"
Phchi.S6	AUGUSTUS	CDS	5991496	5992548	0.83	+	0	transcript_id "Phchi.S6G082400.t1"; gene_id "Phchi.S6G082400"
Phchi.S6	AUGUSTUS	exon	5991496	5992548	.	+	.	transcript_id "Phchi.S6G082400.t1"; gene_id "Phchi.S6G082400"
Phchi.S6	AUGUSTUS	stop_codon	5992549	5992551	.	+	0	transcript_id "Phchi.S6G082400.t1"; gene_id "Phchi.S6G082400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11841.t1 is derived from g15893.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8530786	8533475	.	+	.	Phchi.S4G142300
Phchi.S4	AUGUSTUS	transcript	8530786	8533299	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	start_codon	8530786	8530788	.	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8530786	8531066	0.64	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8530786	8531066	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531067	8531183	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531184	8531252	1	+	1	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531184	8531252	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531253	8531336	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531337	8531430	1	+	1	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531337	8531430	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531431	8531594	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531595	8531704	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531595	8531704	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531705	8531828	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531829	8531874	1	+	1	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531829	8531874	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531875	8532031	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532032	8532091	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532032	8532091	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532092	8532213	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532214	8532282	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532214	8532282	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532283	8532389	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532390	8532473	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532390	8532473	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532474	8532558	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532559	8532648	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532559	8532648	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532649	8532753	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532754	8532839	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532754	8532839	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532840	8532921	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532922	8533012	1	+	1	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532922	8533012	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8533013	8533090	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8533091	8533176	1	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8533091	8533176	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8533177	8533262	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8533263	8533299	1	+	1	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8533263	8533299	.	+	.	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	stop_codon	8533300	8533302	.	+	0	transcript_id "Phchi.S4G142300.t1"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	transcript	8530786	8533475	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	start_codon	8530786	8530788	.	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8530786	8531066	0.61	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8530786	8531066	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531067	8531183	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531184	8531252	1	+	1	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531184	8531252	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531253	8531336	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531337	8531430	1	+	1	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531337	8531430	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531431	8531594	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531595	8531704	0.99	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531595	8531704	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531705	8531828	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8531829	8531874	0.99	+	1	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8531829	8531874	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8531875	8532031	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532032	8532091	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532032	8532091	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532092	8532213	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532214	8532282	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532214	8532282	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532283	8532389	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532390	8532473	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532390	8532473	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532474	8532558	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532559	8532648	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532559	8532648	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532649	8532753	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532754	8532839	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532754	8532839	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8532840	8532921	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8532922	8533012	1	+	1	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8532922	8533012	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8533013	8533090	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8533091	8533171	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8533091	8533171	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	intron	8533172	8533262	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	CDS	8533263	8533475	1	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	exon	8533263	8533475	.	+	.	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
Phchi.S4	AUGUSTUS	stop_codon	8533476	8533478	.	+	0	transcript_id "Phchi.S4G142300.t2"; gene_id "Phchi.S4G142300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11793.t1 is derived from g15845.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8184169	8184851	.	+	.	Phchi.S4G137500
Phchi.S4	AUGUSTUS	transcript	8184169	8184851	.	+	.	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	start_codon	8184169	8184171	.	+	0	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	CDS	8184169	8184234	0.43	+	0	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	exon	8184169	8184234	.	+	.	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	intron	8184235	8184587	.	+	.	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	CDS	8184588	8184683	0.71	+	0	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	exon	8184588	8184683	.	+	.	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	intron	8184684	8184770	.	+	.	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	CDS	8184771	8184851	0.99	+	0	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	exon	8184771	8184851	.	+	.	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
Phchi.S4	AUGUSTUS	stop_codon	8184852	8184854	.	+	0	transcript_id "Phchi.S4G137500.t1"; gene_id "Phchi.S4G137500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2311.t1 is derived from g9231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6009846	6010596	.	-	.	Phchi.S5G092000
Phchi.S5	AUGUSTUS	transcript	6009846	6010596	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	stop_codon	6009843	6009845	.	-	0	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	CDS	6009846	6009937	0.39	-	2	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	exon	6009846	6009937	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	intron	6009938	6010034	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	CDS	6010035	6010077	0.99	-	0	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	exon	6010035	6010077	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	intron	6010078	6010159	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	CDS	6010160	6010234	1	-	0	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	exon	6010160	6010234	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	intron	6010235	6010314	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	CDS	6010315	6010404	0.99	-	0	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	exon	6010315	6010404	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	intron	6010405	6010506	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	CDS	6010507	6010596	0.64	-	0	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	exon	6010507	6010596	.	-	.	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
Phchi.S5	AUGUSTUS	start_codon	6010594	6010596	.	-	0	transcript_id "Phchi.S5G092000.t1"; gene_id "Phchi.S5G092000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9264.t1 is derived from g6439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40651874	40658020	.	+	.	Phchi.S1G642300
Phchi.S1	AUGUSTUS	transcript	40651874	40658020	.	+	.	transcript_id "Phchi.S1G642300.t1"; gene_id "Phchi.S1G642300"
Phchi.S1	AUGUSTUS	start_codon	40651874	40651876	.	+	0	transcript_id "Phchi.S1G642300.t1"; gene_id "Phchi.S1G642300"
Phchi.S1	AUGUSTUS	CDS	40651874	40658020	0.93	+	0	transcript_id "Phchi.S1G642300.t1"; gene_id "Phchi.S1G642300"
Phchi.S1	AUGUSTUS	exon	40651874	40658020	.	+	.	transcript_id "Phchi.S1G642300.t1"; gene_id "Phchi.S1G642300"
Phchi.S1	AUGUSTUS	stop_codon	40658021	40658023	.	+	0	transcript_id "Phchi.S1G642300.t1"; gene_id "Phchi.S1G642300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6049.t1 is derived from g3220.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20627315	20629080	.	-	.	Phchi.S1G320800
Phchi.S1	AUGUSTUS	transcript	20627315	20629080	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	stop_codon	20627312	20627314	.	-	0	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	CDS	20627315	20627564	1	-	1	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	exon	20627315	20627564	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	intron	20627565	20627665	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	CDS	20627666	20627883	1	-	0	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	exon	20627666	20627883	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	intron	20627884	20627967	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	CDS	20627968	20628459	0.99	-	0	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	exon	20627968	20628459	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	intron	20628460	20628576	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	CDS	20628577	20629080	0.98	-	0	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	exon	20628577	20629080	.	-	.	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
Phchi.S1	AUGUSTUS	start_codon	20629078	20629080	.	-	0	transcript_id "Phchi.S1G320800.t1"; gene_id "Phchi.S1G320800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3711.t1 is derived from g880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5278087	5279488	.	+	.	Phchi.S1G087000
Phchi.S1	AUGUSTUS	transcript	5278087	5279488	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	start_codon	5278087	5278089	.	+	0	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278087	5278155	0.39	+	0	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278087	5278155	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5278156	5278272	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278273	5278309	1	+	0	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278273	5278309	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5278310	5278389	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278390	5278876	0.98	+	2	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278390	5278876	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5278877	5278959	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278960	5279193	1	+	1	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278960	5279193	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5279194	5279271	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5279272	5279488	0.98	+	1	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5279272	5279488	.	+	.	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	stop_codon	5279489	5279491	.	+	0	transcript_id "Phchi.S1G087000.t1"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	transcript	5278087	5279324	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	start_codon	5278087	5278089	.	+	0	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278087	5278155	0.42	+	0	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278087	5278155	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5278156	5278272	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278273	5278309	0.99	+	0	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278273	5278309	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5278310	5278389	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278390	5278876	0.97	+	2	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278390	5278876	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5278877	5278959	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5278960	5279090	0.77	+	1	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5278960	5279090	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	intron	5279091	5279271	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	CDS	5279272	5279324	0.77	+	2	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	exon	5279272	5279324	.	+	.	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
Phchi.S1	AUGUSTUS	stop_codon	5279325	5279327	.	+	0	transcript_id "Phchi.S1G087000.t2"; gene_id "Phchi.S1G087000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4124.t1 is derived from g1293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8370261	8375472	.	-	.	Phchi.S1G128300
Phchi.S1	AUGUSTUS	transcript	8370261	8375472	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	stop_codon	8370258	8370260	.	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8370261	8370564	0.79	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8370261	8370564	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8370565	8370652	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8370653	8370995	0.99	-	2	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8370653	8370995	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8370996	8371072	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8371073	8371688	0.97	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8371073	8371688	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8371689	8371805	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8371806	8372051	1	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8371806	8372051	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8372052	8372138	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8372139	8372319	1	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8372139	8372319	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8372320	8372435	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8372436	8372626	1	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8372436	8372626	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8372627	8372711	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8372712	8372853	1	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8372712	8372853	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8372854	8372987	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8372988	8373039	1	-	2	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8372988	8373039	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8373040	8373121	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8373122	8373249	1	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8373122	8373249	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8373250	8373327	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8373328	8373461	1	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8373328	8373461	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8373462	8373565	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8373566	8373696	1	-	2	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8373566	8373696	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8373697	8373770	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8373771	8373859	1	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8373771	8373859	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8373860	8373940	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8373941	8374000	1	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8373941	8374000	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8374001	8374089	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8374090	8374173	0.88	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8374090	8374173	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8374174	8374279	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8374280	8374369	0.76	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8374280	8374369	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8374370	8374453	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8374454	8374503	0.76	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8374454	8374503	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8374504	8374647	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8374648	8374689	0.3	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8374648	8374689	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8374690	8374777	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8374778	8375141	0.3	-	1	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8374778	8375141	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8375142	8375235	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8375236	8375363	0.82	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8375236	8375363	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	intron	8375364	8375460	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	CDS	8375461	8375472	0.57	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	exon	8375461	8375472	.	-	.	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
Phchi.S1	AUGUSTUS	start_codon	8375470	8375472	.	-	0	transcript_id "Phchi.S1G128300.t1"; gene_id "Phchi.S1G128300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15704.t1 is derived from g14174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20780602	20783497	.	-	.	Phchi.S3G302300
Phchi.S3	AUGUSTUS	transcript	20780602	20783497	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	stop_codon	20780599	20780601	.	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20780602	20781006	1	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20780602	20781006	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	intron	20781007	20781088	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20781089	20781168	1	-	2	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20781089	20781168	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	intron	20781169	20781256	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20781257	20781303	1	-	1	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20781257	20781303	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	intron	20781304	20781392	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20781393	20781493	1	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20781393	20781493	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	intron	20781494	20781602	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20781603	20781716	1	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20781603	20781716	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	intron	20781717	20782014	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20782015	20782869	0.97	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20782015	20782869	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	intron	20782870	20783011	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	CDS	20783012	20783497	0.32	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	exon	20783012	20783497	.	-	.	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
Phchi.S3	AUGUSTUS	start_codon	20783495	20783497	.	-	0	transcript_id "Phchi.S3G302300.t1"; gene_id "Phchi.S3G302300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1038.t1 is derived from g10821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7246109	7248024	.	-	.	Phchi.S6G099700
Phchi.S6	AUGUSTUS	transcript	7246109	7248024	.	-	.	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	stop_codon	7246106	7246108	.	-	0	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	CDS	7246109	7247638	0.7	-	0	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	exon	7246109	7247638	.	-	.	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	intron	7247639	7247751	.	-	.	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	CDS	7247752	7248024	0.62	-	0	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	exon	7247752	7248024	.	-	.	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
Phchi.S6	AUGUSTUS	start_codon	7248022	7248024	.	-	0	transcript_id "Phchi.S6G099700.t1"; gene_id "Phchi.S6G099700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9612.t1 is derived from g6788.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42929440	42934131	.	-	.	Phchi.S1G677100
Phchi.S1	AUGUSTUS	transcript	42929440	42934131	.	-	.	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	stop_codon	42929437	42929439	.	-	0	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	CDS	42929440	42929467	1	-	1	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	exon	42929440	42929467	.	-	.	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	intron	42929468	42929565	.	-	.	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	CDS	42929566	42929597	0.97	-	0	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	exon	42929566	42929597	.	-	.	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	intron	42929598	42929787	.	-	.	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	CDS	42929788	42934131	0.75	-	0	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	exon	42929788	42934131	.	-	.	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
Phchi.S1	AUGUSTUS	start_codon	42934129	42934131	.	-	0	transcript_id "Phchi.S1G677100.t1"; gene_id "Phchi.S1G677100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3121.t1 is derived from g290.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1837576	1840056	.	+	.	Phchi.S1G028000
Phchi.S1	AUGUSTUS	transcript	1837576	1840056	.	+	.	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	start_codon	1837576	1837578	.	+	0	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	CDS	1837576	1837829	0.78	+	0	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	exon	1837576	1837829	.	+	.	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	intron	1837830	1838007	.	+	.	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	CDS	1838008	1838939	0.89	+	1	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	exon	1838008	1838939	.	+	.	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	intron	1838940	1839028	.	+	.	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	CDS	1839029	1840056	0.89	+	2	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	exon	1839029	1840056	.	+	.	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	stop_codon	1840057	1840059	.	+	0	transcript_id "Phchi.S1G028000.t1"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	transcript	1837985	1840056	.	+	.	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	start_codon	1837985	1837987	.	+	0	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	CDS	1837985	1838939	0.49	+	0	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	exon	1837985	1838939	.	+	.	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	intron	1838940	1839028	.	+	.	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	CDS	1839029	1840056	0.78	+	2	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	exon	1839029	1840056	.	+	.	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
Phchi.S1	AUGUSTUS	stop_codon	1840057	1840059	.	+	0	transcript_id "Phchi.S1G028000.t2"; gene_id "Phchi.S1G028000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3862.t1 is derived from g1031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6082868	6086506	.	+	.	Phchi.S1G102100
Phchi.S1	AUGUSTUS	transcript	6082868	6086506	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	start_codon	6082868	6082870	.	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6082868	6082945	0.99	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6082868	6082945	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6082946	6083076	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6083077	6083148	1	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6083077	6083148	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6083149	6083229	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6083230	6083309	1	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6083230	6083309	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6083310	6083443	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6083444	6083669	1	+	1	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6083444	6083669	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6083670	6083829	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6083830	6083862	1	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6083830	6083862	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6083863	6083958	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6083959	6084041	1	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6083959	6084041	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6084042	6084186	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6084187	6084259	1	+	1	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6084187	6084259	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6084260	6084379	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6084380	6084731	0.74	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6084380	6084731	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6084732	6084942	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6084943	6085274	0.81	+	2	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6084943	6085274	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6085275	6085379	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6085380	6085714	0.87	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6085380	6085714	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6085715	6085807	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6085808	6086240	1	+	1	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6085808	6086240	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	intron	6086241	6086311	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	CDS	6086312	6086506	0.99	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	exon	6086312	6086506	.	+	.	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
Phchi.S1	AUGUSTUS	stop_codon	6086507	6086509	.	+	0	transcript_id "Phchi.S1G102100.t1"; gene_id "Phchi.S1G102100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12969.t1 is derived from g11434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3388406	3388884	.	-	.	Phchi.S3G028800
Phchi.S3	AUGUSTUS	transcript	3388406	3388884	.	-	.	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	stop_codon	3388403	3388405	.	-	0	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	CDS	3388406	3388417	0.98	-	0	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	exon	3388406	3388417	.	-	.	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	intron	3388418	3388503	.	-	.	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	CDS	3388504	3388884	0.28	-	0	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	exon	3388504	3388884	.	-	.	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
Phchi.S3	AUGUSTUS	start_codon	3388882	3388884	.	-	0	transcript_id "Phchi.S3G028800.t1"; gene_id "Phchi.S3G028800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2908.t1 is derived from g77.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	420094	421578	.	+	.	Phchi.S1G006700
Phchi.S1	AUGUSTUS	transcript	420094	421578	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	start_codon	420094	420096	.	+	0	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	CDS	420094	421161	0.98	+	0	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	exon	420094	421161	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	intron	421162	421234	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	CDS	421235	421379	0.49	+	0	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	exon	421235	421379	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	intron	421380	421453	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	CDS	421454	421464	0.54	+	2	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	exon	421454	421464	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	intron	421465	421560	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	CDS	421561	421578	0.54	+	0	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	exon	421561	421578	.	+	.	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
Phchi.S1	AUGUSTUS	stop_codon	421579	421581	.	+	0	transcript_id "Phchi.S1G006700.t1"; gene_id "Phchi.S1G006700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15011.t1 is derived from g13479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16479976	16480625	.	-	.	Phchi.S3G233000
Phchi.S3	AUGUSTUS	transcript	16479976	16480625	.	-	.	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	stop_codon	16479973	16479975	.	-	0	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	CDS	16479976	16480350	0.84	-	0	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	exon	16479976	16480350	.	-	.	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	intron	16480351	16480493	.	-	.	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	CDS	16480494	16480625	0.5	-	0	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	exon	16480494	16480625	.	-	.	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
Phchi.S3	AUGUSTUS	start_codon	16480623	16480625	.	-	0	transcript_id "Phchi.S3G233000.t1"; gene_id "Phchi.S3G233000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14137.t1 is derived from g12604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11083742	11086237	.	-	.	Phchi.S3G145600
Phchi.S3	AUGUSTUS	transcript	11083742	11086237	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	stop_codon	11083739	11083741	.	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11083742	11083822	0.99	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11083742	11083822	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11083823	11083956	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11083957	11084084	1	-	2	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11083957	11084084	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084085	11084173	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084174	11084226	1	-	1	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084174	11084226	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084227	11084318	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084319	11084414	1	-	1	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084319	11084414	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084415	11084716	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084717	11084743	0.94	-	1	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084717	11084743	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084744	11084808	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084809	11084818	0.94	-	2	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084809	11084818	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084819	11084940	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084941	11085001	1	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084941	11085001	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085002	11085102	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085103	11085174	1	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085103	11085174	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085175	11085267	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085268	11085348	1	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085268	11085348	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085349	11085447	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085448	11085516	1	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085448	11085516	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085517	11085700	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085701	11085787	1	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085701	11085787	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085788	11085910	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085911	11086035	1	-	2	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085911	11086035	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11086036	11086212	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11086213	11086237	1	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11086213	11086237	.	-	.	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	start_codon	11086235	11086237	.	-	0	transcript_id "Phchi.S3G145600.t1"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	transcript	11083742	11086237	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	stop_codon	11083739	11083741	.	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11083742	11083822	0.99	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11083742	11083822	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11083823	11083956	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11083957	11084075	1	-	2	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11083957	11084075	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084076	11084173	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084174	11084226	1	-	1	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084174	11084226	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084227	11084318	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084319	11084414	1	-	1	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084319	11084414	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084415	11084716	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084717	11084743	0.92	-	1	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084717	11084743	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084744	11084808	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084809	11084818	0.92	-	2	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084809	11084818	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11084819	11084940	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11084941	11085001	1	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11084941	11085001	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085002	11085102	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085103	11085174	1	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085103	11085174	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085175	11085267	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085268	11085348	1	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085268	11085348	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085349	11085447	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085448	11085516	1	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085448	11085516	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085517	11085700	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085701	11085787	1	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085701	11085787	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11085788	11085910	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11085911	11086035	1	-	2	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11085911	11086035	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	intron	11086036	11086212	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	CDS	11086213	11086237	1	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	exon	11086213	11086237	.	-	.	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
Phchi.S3	AUGUSTUS	start_codon	11086235	11086237	.	-	0	transcript_id "Phchi.S3G145600.t2"; gene_id "Phchi.S3G145600"
# This transcript jg14765.t2 is derived from g13233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14766.t1 is derived from g13234.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14592848	14593816	.	+	.	Phchi.S3G208500
Phchi.S3	AUGUSTUS	transcript	14592848	14593816	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	start_codon	14592848	14592850	.	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	CDS	14592848	14592963	0.99	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	exon	14592848	14592963	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	intron	14592964	14593043	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	CDS	14593044	14593209	1	+	1	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	exon	14593044	14593209	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	intron	14593210	14593294	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	CDS	14593295	14593345	1	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	exon	14593295	14593345	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	intron	14593346	14593453	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	CDS	14593454	14593519	1	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	exon	14593454	14593519	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	intron	14593520	14593598	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	CDS	14593599	14593667	1	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	exon	14593599	14593667	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	intron	14593668	14593750	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	CDS	14593751	14593816	0.93	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	exon	14593751	14593816	.	+	.	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
Phchi.S3	AUGUSTUS	stop_codon	14593817	14593819	.	+	0	transcript_id "Phchi.S3G208500.t1"; gene_id "Phchi.S3G208500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5823.t1 is derived from g2993.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19128764	19130317	.	+	.	Phchi.S1G298200
Phchi.S1	AUGUSTUS	transcript	19128764	19130317	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	start_codon	19128764	19128766	.	+	0	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	CDS	19128764	19128771	0.85	+	0	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	exon	19128764	19128771	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	intron	19128772	19128871	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	CDS	19128872	19128958	0.71	+	1	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	exon	19128872	19128958	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	intron	19128959	19129223	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	CDS	19129224	19129311	0.44	+	1	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	exon	19129224	19129311	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	intron	19129312	19129406	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	CDS	19129407	19129938	0.1	+	0	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	exon	19129407	19129938	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	intron	19129939	19130018	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	CDS	19130019	19130317	0.09	+	2	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	exon	19130019	19130317	.	+	.	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
Phchi.S1	AUGUSTUS	stop_codon	19130318	19130320	.	+	0	transcript_id "Phchi.S1G298200.t1"; gene_id "Phchi.S1G298200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10091.t1 is derived from g7267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45705639	45707488	.	-	.	Phchi.S1G725000
Phchi.S1	AUGUSTUS	transcript	45705639	45707488	.	-	.	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	stop_codon	45705636	45705638	.	-	0	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	CDS	45705639	45707140	0.39	-	2	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	exon	45705639	45707140	.	-	.	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	intron	45707141	45707247	.	-	.	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	CDS	45707248	45707488	0.17	-	0	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	exon	45707248	45707488	.	-	.	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
Phchi.S1	AUGUSTUS	start_codon	45707486	45707488	.	-	0	transcript_id "Phchi.S1G725000.t1"; gene_id "Phchi.S1G725000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6363.t1 is derived from g3535.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22571427	22573017	.	+	.	Phchi.S1G352200
Phchi.S1	AUGUSTUS	transcript	22571427	22573017	.	+	.	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	start_codon	22571427	22571429	.	+	0	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	CDS	22571427	22571945	0.6	+	0	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	exon	22571427	22571945	.	+	.	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	intron	22571946	22572060	.	+	.	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	CDS	22572061	22573017	1	+	0	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	exon	22572061	22573017	.	+	.	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
Phchi.S1	AUGUSTUS	stop_codon	22573018	22573020	.	+	0	transcript_id "Phchi.S1G352200.t1"; gene_id "Phchi.S1G352200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2987.t1 is derived from g156.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1019742	1021860	.	-	.	Phchi.S1G014600
Phchi.S1	AUGUSTUS	transcript	1019742	1021860	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	stop_codon	1019739	1019741	.	-	0	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1019742	1019814	0.62	-	1	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1019742	1019814	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1019815	1019923	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1019924	1020111	0.89	-	0	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1019924	1020111	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1020112	1020200	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1020201	1020326	1	-	0	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1020201	1020326	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1020327	1020441	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1020442	1020544	1	-	1	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1020442	1020544	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1020545	1020662	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1020663	1020767	1	-	1	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1020663	1020767	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1020768	1020907	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1020908	1021037	1	-	2	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1020908	1021037	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1021038	1021171	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1021172	1021456	1	-	2	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1021172	1021456	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1021457	1021537	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1021538	1021692	1	-	1	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1021538	1021692	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	intron	1021693	1021795	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	CDS	1021796	1021860	1	-	0	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	exon	1021796	1021860	.	-	.	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
Phchi.S1	AUGUSTUS	start_codon	1021858	1021860	.	-	0	transcript_id "Phchi.S1G014600.t1"; gene_id "Phchi.S1G014600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10615.t1 is derived from g14665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1242017	1243607	.	+	.	Phchi.S4G019700
Phchi.S4	AUGUSTUS	transcript	1242017	1243607	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	start_codon	1242017	1242019	.	+	0	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1242017	1242113	0.92	+	0	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1242017	1242113	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1242114	1242225	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1242226	1242247	1	+	2	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1242226	1242247	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1242248	1242337	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1242338	1242394	1	+	1	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1242338	1242394	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1242395	1242518	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1242519	1242600	1	+	1	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1242519	1242600	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1242601	1242674	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1242675	1242797	0.68	+	0	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1242675	1242797	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1242798	1242872	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1242873	1242997	0.84	+	0	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1242873	1242997	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1242998	1243117	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1243118	1243136	1	+	1	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1243118	1243136	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1243137	1243252	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1243253	1243476	0.98	+	0	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1243253	1243476	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	intron	1243477	1243603	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	CDS	1243604	1243607	0.97	+	1	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	exon	1243604	1243607	.	+	.	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
Phchi.S4	AUGUSTUS	stop_codon	1243608	1243610	.	+	0	transcript_id "Phchi.S4G019700.t1"; gene_id "Phchi.S4G019700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5565.t1 is derived from g2735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17607131	17608591	.	-	.	Phchi.S1G272400
Phchi.S1	AUGUSTUS	transcript	17607131	17608591	.	-	.	transcript_id "Phchi.S1G272400.t1"; gene_id "Phchi.S1G272400"
Phchi.S1	AUGUSTUS	stop_codon	17607128	17607130	.	-	0	transcript_id "Phchi.S1G272400.t1"; gene_id "Phchi.S1G272400"
Phchi.S1	AUGUSTUS	CDS	17607131	17608591	0.98	-	0	transcript_id "Phchi.S1G272400.t1"; gene_id "Phchi.S1G272400"
Phchi.S1	AUGUSTUS	exon	17607131	17608591	.	-	.	transcript_id "Phchi.S1G272400.t1"; gene_id "Phchi.S1G272400"
Phchi.S1	AUGUSTUS	start_codon	17608589	17608591	.	-	0	transcript_id "Phchi.S1G272400.t1"; gene_id "Phchi.S1G272400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12080.t1 is derived from g7755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2163416	2165675	.	-	.	Phchi.S2G016000
Phchi.S2	AUGUSTUS	transcript	2163416	2165675	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	stop_codon	2163413	2163415	.	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2163416	2163424	1	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2163416	2163424	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2163425	2163556	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2163557	2163785	1	-	1	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2163557	2163785	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2163786	2163876	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2163877	2164146	1	-	1	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2163877	2164146	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2164147	2164239	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2164240	2164555	0.75	-	2	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2164240	2164555	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2164556	2164652	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2164653	2164824	0.32	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2164653	2164824	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2164825	2164936	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2164937	2165080	0.27	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2164937	2165080	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2165081	2165226	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2165227	2165280	0.71	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2165227	2165280	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	intron	2165281	2165396	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	CDS	2165397	2165675	0.16	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	exon	2165397	2165675	.	-	.	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
Phchi.S2	AUGUSTUS	start_codon	2165673	2165675	.	-	0	transcript_id "Phchi.S2G016000.t1"; gene_id "Phchi.S2G016000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4094.t1 is derived from g1263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7792931	7794091	.	+	.	Phchi.S1G125300
Phchi.S1	AUGUSTUS	transcript	7792931	7794091	.	+	.	transcript_id "Phchi.S1G125300.t1"; gene_id "Phchi.S1G125300"
Phchi.S1	AUGUSTUS	start_codon	7792931	7792933	.	+	0	transcript_id "Phchi.S1G125300.t1"; gene_id "Phchi.S1G125300"
Phchi.S1	AUGUSTUS	CDS	7792931	7794091	0.78	+	0	transcript_id "Phchi.S1G125300.t1"; gene_id "Phchi.S1G125300"
Phchi.S1	AUGUSTUS	exon	7792931	7794091	.	+	.	transcript_id "Phchi.S1G125300.t1"; gene_id "Phchi.S1G125300"
Phchi.S1	AUGUSTUS	stop_codon	7794092	7794094	.	+	0	transcript_id "Phchi.S1G125300.t1"; gene_id "Phchi.S1G125300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1602.t1 is derived from g8521.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1976372	1978456	.	+	.	Phchi.S5G021100
Phchi.S5	AUGUSTUS	transcript	1976372	1977722	.	+	.	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	start_codon	1976372	1976374	.	+	0	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	CDS	1976372	1977619	0.87	+	0	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	exon	1976372	1977619	.	+	.	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	intron	1977620	1977710	.	+	.	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	CDS	1977711	1977722	0.99	+	0	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	exon	1977711	1977722	.	+	.	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	stop_codon	1977723	1977725	.	+	0	transcript_id "Phchi.S5G021100.t1"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	transcript	1977500	1978456	.	+	.	transcript_id "Phchi.S5G021100.t2"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	start_codon	1977500	1977502	.	+	0	transcript_id "Phchi.S5G021100.t2"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	CDS	1977500	1978456	0.96	+	0	transcript_id "Phchi.S5G021100.t2"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	exon	1977500	1978456	.	+	.	transcript_id "Phchi.S5G021100.t2"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	stop_codon	1978457	1978459	.	+	0	transcript_id "Phchi.S5G021100.t2"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	transcript	1976372	1978456	.	+	.	transcript_id "Phchi.S5G021100.t3"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	start_codon	1976372	1976374	.	+	0	transcript_id "Phchi.S5G021100.t3"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	CDS	1976372	1978456	0.94	+	0	transcript_id "Phchi.S5G021100.t3"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	exon	1976372	1978456	.	+	.	transcript_id "Phchi.S5G021100.t3"; gene_id "Phchi.S5G021100"
Phchi.S5	AUGUSTUS	stop_codon	1978457	1978459	.	+	0	transcript_id "Phchi.S5G021100.t3"; gene_id "Phchi.S5G021100"
# This transcript jg824.t2 is derived from g10606.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg825.t1 is derived from g10607.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5734561	5739762	.	-	.	Phchi.S6G078400
Phchi.S6	AUGUSTUS	transcript	5734561	5739762	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	stop_codon	5734558	5734560	.	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5734561	5734755	1	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5734561	5734755	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5734756	5734840	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5734841	5734987	1	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5734841	5734987	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5734988	5735074	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5735075	5735216	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5735075	5735216	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5735217	5735339	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5735340	5735485	1	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5735340	5735485	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5735486	5735606	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5735607	5735698	1	-	2	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5735607	5735698	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5735699	5735810	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5735811	5735862	1	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5735811	5735862	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5735863	5735976	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5735977	5736266	1	-	2	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5735977	5736266	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5736267	5736366	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5736367	5736510	1	-	2	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5736367	5736510	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5736511	5736604	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5736605	5736688	0.74	-	2	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5736605	5736688	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5736689	5736794	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5736795	5736895	0.98	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5736795	5736895	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5736896	5737009	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5737010	5737072	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5737010	5737072	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5737073	5737165	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5737166	5737234	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5737166	5737234	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5737235	5737354	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5737355	5737426	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5737355	5737426	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5737427	5737557	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5737558	5737629	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5737558	5737629	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5737630	5737750	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5737751	5737822	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5737751	5737822	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5737823	5737926	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5737927	5737998	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5737927	5737998	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5737999	5738129	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5738130	5738201	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5738130	5738201	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5738202	5738427	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5738428	5738499	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5738428	5738499	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5738500	5738579	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5738580	5738651	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5738580	5738651	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5738652	5738853	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5738854	5738997	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5738854	5738997	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5738998	5739097	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5739098	5739227	1	-	2	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5739098	5739227	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5739228	5739429	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5739430	5739512	1	-	1	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5739430	5739512	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	intron	5739513	5739697	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	CDS	5739698	5739762	0.42	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	exon	5739698	5739762	.	-	.	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
Phchi.S6	AUGUSTUS	start_codon	5739760	5739762	.	-	0	transcript_id "Phchi.S6G078400.t1"; gene_id "Phchi.S6G078400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14354.t1 is derived from g12821.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12340179	12341115	.	+	.	Phchi.S3G167300
Phchi.S3	AUGUSTUS	transcript	12340179	12341115	.	+	.	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	start_codon	12340179	12340181	.	+	0	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	CDS	12340179	12340554	0.54	+	0	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	exon	12340179	12340554	.	+	.	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	intron	12340555	12340650	.	+	.	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	CDS	12340651	12340798	0.84	+	2	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	exon	12340651	12340798	.	+	.	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	intron	12340799	12340886	.	+	.	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	CDS	12340887	12341115	0.96	+	1	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	exon	12340887	12341115	.	+	.	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
Phchi.S3	AUGUSTUS	stop_codon	12341116	12341118	.	+	0	transcript_id "Phchi.S3G167300.t1"; gene_id "Phchi.S3G167300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10446.t1 is derived from g14495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	367956	369291	.	+	.	Phchi.S4G002800
Phchi.S4	AUGUSTUS	transcript	367956	369291	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	start_codon	367956	367958	.	+	0	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	CDS	367956	368207	0.81	+	0	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	exon	367956	368207	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	intron	368208	368337	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	CDS	368338	368470	0.65	+	0	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	exon	368338	368470	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	intron	368471	368592	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	CDS	368593	368663	0.99	+	2	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	exon	368593	368663	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	intron	368664	368765	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	CDS	368766	368840	0.98	+	0	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	exon	368766	368840	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	intron	368841	369144	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	CDS	369145	369291	0.98	+	0	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	exon	369145	369291	.	+	.	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
Phchi.S4	AUGUSTUS	stop_codon	369292	369294	.	+	0	transcript_id "Phchi.S4G002800.t1"; gene_id "Phchi.S4G002800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10748.t1 is derived from g14798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1905983	1907943	.	+	.	Phchi.S4G033000
Phchi.S4	AUGUSTUS	transcript	1905983	1907943	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	start_codon	1905983	1905985	.	+	0	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1905983	1906213	0.93	+	0	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1905983	1906213	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	intron	1906214	1906301	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1906302	1906409	1	+	0	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1906302	1906409	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	intron	1906410	1906502	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1906503	1906659	1	+	0	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1906503	1906659	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	intron	1906660	1906743	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1906744	1907365	0.9	+	2	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1906744	1907365	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	intron	1907366	1907459	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1907460	1907618	1	+	1	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1907460	1907618	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	intron	1907619	1907712	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1907713	1907791	1	+	1	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1907713	1907791	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	intron	1907792	1907877	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	CDS	1907878	1907943	1	+	0	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	exon	1907878	1907943	.	+	.	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
Phchi.S4	AUGUSTUS	stop_codon	1907944	1907946	.	+	0	transcript_id "Phchi.S4G033000.t1"; gene_id "Phchi.S4G033000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg377.t1 is derived from g10159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2715470	2718420	.	-	.	Phchi.S6G033600
Phchi.S6	AUGUSTUS	transcript	2715470	2718420	.	-	.	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	stop_codon	2715467	2715469	.	-	0	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	CDS	2715470	2715490	0.54	-	0	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	exon	2715470	2715490	.	-	.	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	intron	2715491	2715591	.	-	.	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	CDS	2715592	2717954	0.41	-	2	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	exon	2715592	2717954	.	-	.	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	intron	2717955	2718047	.	-	.	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	CDS	2718048	2718420	0.3	-	0	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	exon	2718048	2718420	.	-	.	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
Phchi.S6	AUGUSTUS	start_codon	2718418	2718420	.	-	0	transcript_id "Phchi.S6G033600.t1"; gene_id "Phchi.S6G033600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6552.t1 is derived from g3724.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23677714	23677932	.	-	.	Phchi.S1G371100
Phchi.S1	AUGUSTUS	transcript	23677714	23677932	.	-	.	transcript_id "Phchi.S1G371100.t1"; gene_id "Phchi.S1G371100"
Phchi.S1	AUGUSTUS	stop_codon	23677711	23677713	.	-	0	transcript_id "Phchi.S1G371100.t1"; gene_id "Phchi.S1G371100"
Phchi.S1	AUGUSTUS	CDS	23677714	23677932	0.63	-	0	transcript_id "Phchi.S1G371100.t1"; gene_id "Phchi.S1G371100"
Phchi.S1	AUGUSTUS	exon	23677714	23677932	.	-	.	transcript_id "Phchi.S1G371100.t1"; gene_id "Phchi.S1G371100"
Phchi.S1	AUGUSTUS	start_codon	23677930	23677932	.	-	0	transcript_id "Phchi.S1G371100.t1"; gene_id "Phchi.S1G371100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7653.t1 is derived from g4827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30425070	30426678	.	+	.	Phchi.S1G481200
Phchi.S1	AUGUSTUS	transcript	30425070	30426678	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	start_codon	30425070	30425072	.	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30425070	30425265	0.65	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30425070	30425265	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	intron	30425266	30425443	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30425444	30425532	1	+	2	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30425444	30425532	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	intron	30425533	30425626	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30425627	30425683	1	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30425627	30425683	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	intron	30425684	30425777	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30425778	30425948	1	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30425778	30425948	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	intron	30425949	30426031	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30426032	30426223	1	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30426032	30426223	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	intron	30426224	30426321	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30426322	30426399	1	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30426322	30426399	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	intron	30426400	30426501	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	CDS	30426502	30426678	1	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	exon	30426502	30426678	.	+	.	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
Phchi.S1	AUGUSTUS	stop_codon	30426679	30426681	.	+	0	transcript_id "Phchi.S1G481200.t1"; gene_id "Phchi.S1G481200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8668.t1 is derived from g5843.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37357868	37358935	.	+	.	Phchi.S1G582700
Phchi.S1	AUGUSTUS	transcript	37357868	37358935	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	start_codon	37357868	37357870	.	+	0	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	CDS	37357868	37358091	1	+	0	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	exon	37357868	37358091	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	intron	37358092	37358270	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	CDS	37358271	37358380	0.58	+	1	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	exon	37358271	37358380	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	intron	37358381	37358579	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	CDS	37358580	37358638	0.97	+	2	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	exon	37358580	37358638	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	intron	37358639	37358890	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	CDS	37358891	37358935	0.94	+	0	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	exon	37358891	37358935	.	+	.	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
Phchi.S1	AUGUSTUS	stop_codon	37358936	37358938	.	+	0	transcript_id "Phchi.S1G582700.t1"; gene_id "Phchi.S1G582700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13831.t1 is derived from g12298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9100292	9102600	.	-	.	Phchi.S3G115000
Phchi.S3	AUGUSTUS	transcript	9100292	9102600	.	-	.	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	stop_codon	9100289	9100291	.	-	0	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	CDS	9100292	9100361	0.98	-	1	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	exon	9100292	9100361	.	-	.	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	intron	9100362	9100498	.	-	.	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	CDS	9100499	9102600	0.97	-	0	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	exon	9100499	9102600	.	-	.	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
Phchi.S3	AUGUSTUS	start_codon	9102598	9102600	.	-	0	transcript_id "Phchi.S3G115000.t1"; gene_id "Phchi.S3G115000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15440.t1 is derived from g13908.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19168665	19170666	.	-	.	Phchi.S3G275900
Phchi.S3	AUGUSTUS	transcript	19168665	19170666	.	-	.	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	stop_codon	19168662	19168664	.	-	0	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	CDS	19168665	19169565	0.97	-	1	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	exon	19168665	19169565	.	-	.	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	intron	19169566	19169929	.	-	.	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	CDS	19169930	19170666	1	-	0	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	exon	19169930	19170666	.	-	.	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
Phchi.S3	AUGUSTUS	start_codon	19170664	19170666	.	-	0	transcript_id "Phchi.S3G275900.t1"; gene_id "Phchi.S3G275900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13854.t1 is derived from g12321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9248129	9249039	.	-	.	Phchi.S3G117300
Phchi.S3	AUGUSTUS	transcript	9248129	9249039	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	stop_codon	9248126	9248128	.	-	0	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	CDS	9248129	9248269	1	-	0	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	exon	9248129	9248269	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	intron	9248270	9248365	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	CDS	9248366	9248446	1	-	0	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	exon	9248366	9248446	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	intron	9248447	9248567	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	CDS	9248568	9248702	0.81	-	0	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	exon	9248568	9248702	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	intron	9248703	9248793	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	CDS	9248794	9249039	0.99	-	0	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	exon	9248794	9249039	.	-	.	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
Phchi.S3	AUGUSTUS	start_codon	9249037	9249039	.	-	0	transcript_id "Phchi.S3G117300.t1"; gene_id "Phchi.S3G117300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10934.t1 is derived from g14984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3172036	3174832	.	-	.	Phchi.S4G051600
Phchi.S4	AUGUSTUS	transcript	3172036	3174832	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	stop_codon	3172033	3172035	.	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3172036	3172056	0.98	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3172036	3172056	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3172057	3172266	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3172267	3172350	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3172267	3172350	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3172351	3172456	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3172457	3172629	1	-	2	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3172457	3172629	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3172630	3172748	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3172749	3172788	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3172749	3172788	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3172789	3172953	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3172954	3173139	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3172954	3173139	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3173140	3173258	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3173259	3173393	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3173259	3173393	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3173394	3173583	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3173584	3173648	1	-	2	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3173584	3173648	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3173649	3173813	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3173814	3173868	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3173814	3173868	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3173869	3174032	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3174033	3174152	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3174033	3174152	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3174153	3174367	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3174368	3174556	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3174368	3174556	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	intron	3174557	3174715	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	CDS	3174716	3174832	1	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	exon	3174716	3174832	.	-	.	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
Phchi.S4	AUGUSTUS	start_codon	3174830	3174832	.	-	0	transcript_id "Phchi.S4G051600.t1"; gene_id "Phchi.S4G051600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11077.t1 is derived from g15127.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3981737	3983148	.	+	.	Phchi.S4G065900
Phchi.S4	AUGUSTUS	transcript	3981737	3983148	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	start_codon	3981737	3981739	.	+	0	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3981737	3981840	1	+	0	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3981737	3981840	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	intron	3981841	3981928	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3981929	3982060	1	+	1	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3981929	3982060	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	intron	3982061	3982148	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3982149	3982193	1	+	1	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3982149	3982193	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	intron	3982194	3982301	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3982302	3982471	1	+	1	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3982302	3982471	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	intron	3982472	3982644	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3982645	3982730	1	+	2	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3982645	3982730	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	intron	3982731	3982824	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3982825	3982929	1	+	0	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3982825	3982929	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	intron	3982930	3983019	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	CDS	3983020	3983148	0.99	+	0	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	exon	3983020	3983148	.	+	.	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
Phchi.S4	AUGUSTUS	stop_codon	3983149	3983151	.	+	0	transcript_id "Phchi.S4G065900.t1"; gene_id "Phchi.S4G065900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14691.t1 is derived from g13159.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14188474	14189334	.	+	.	Phchi.S3G201000
Phchi.S3	AUGUSTUS	transcript	14188474	14189334	.	+	.	transcript_id "Phchi.S3G201000.t1"; gene_id "Phchi.S3G201000"
Phchi.S3	AUGUSTUS	start_codon	14188474	14188476	.	+	0	transcript_id "Phchi.S3G201000.t1"; gene_id "Phchi.S3G201000"
Phchi.S3	AUGUSTUS	CDS	14188474	14189334	1	+	0	transcript_id "Phchi.S3G201000.t1"; gene_id "Phchi.S3G201000"
Phchi.S3	AUGUSTUS	exon	14188474	14189334	.	+	.	transcript_id "Phchi.S3G201000.t1"; gene_id "Phchi.S3G201000"
Phchi.S3	AUGUSTUS	stop_codon	14189335	14189337	.	+	0	transcript_id "Phchi.S3G201000.t1"; gene_id "Phchi.S3G201000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3520.t1 is derived from g689.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4186873	4187761	.	+	.	Phchi.S1G067900
Phchi.S1	AUGUSTUS	transcript	4186873	4187761	.	+	.	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	start_codon	4186873	4186875	.	+	0	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	CDS	4186873	4187037	1	+	0	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	exon	4186873	4187037	.	+	.	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	intron	4187038	4187131	.	+	.	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	CDS	4187132	4187761	0.82	+	0	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	exon	4187132	4187761	.	+	.	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
Phchi.S1	AUGUSTUS	stop_codon	4187762	4187764	.	+	0	transcript_id "Phchi.S1G067900.t1"; gene_id "Phchi.S1G067900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11752.t1 is derived from g15804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8006820	8009279	.	-	.	Phchi.S4G133400
Phchi.S4	AUGUSTUS	transcript	8006976	8009279	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	stop_codon	8006973	8006975	.	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8006976	8006995	1	-	2	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8006976	8006995	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8006996	8007201	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007202	8007258	0.98	-	2	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007202	8007258	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007259	8007376	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007377	8007485	1	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007377	8007485	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007486	8007634	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007635	8007691	1	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007635	8007691	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007692	8007773	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007774	8007915	1	-	1	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007774	8007915	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007916	8008004	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008005	8008053	1	-	2	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008005	8008053	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008054	8008158	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008159	8008252	1	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008159	8008252	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008253	8008330	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008331	8008403	1	-	1	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008331	8008403	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008404	8008558	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008559	8008659	1	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008559	8008659	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008660	8008793	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008794	8008873	1	-	2	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008794	8008873	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008874	8008951	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008952	8009279	0.95	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008952	8009279	.	-	.	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	start_codon	8009277	8009279	.	-	0	transcript_id "Phchi.S4G133400.t1"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	transcript	8006820	8009279	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	stop_codon	8006817	8006819	.	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8006820	8006932	0.53	-	2	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8006820	8006932	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8006933	8007201	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007202	8007258	0.77	-	2	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007202	8007258	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007259	8007376	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007377	8007485	0.9	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007377	8007485	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007486	8007634	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007635	8007691	1	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007635	8007691	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007692	8007773	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8007774	8007915	1	-	1	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8007774	8007915	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8007916	8008004	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008005	8008053	1	-	2	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008005	8008053	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008054	8008158	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008159	8008252	1	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008159	8008252	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008253	8008330	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008331	8008403	1	-	1	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008331	8008403	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008404	8008558	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008559	8008659	1	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008559	8008659	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008660	8008793	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008794	8008873	1	-	2	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008794	8008873	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	intron	8008874	8008951	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	CDS	8008952	8009279	0.99	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	exon	8008952	8009279	.	-	.	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
Phchi.S4	AUGUSTUS	start_codon	8009277	8009279	.	-	0	transcript_id "Phchi.S4G133400.t2"; gene_id "Phchi.S4G133400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10751.t1 is derived from g14801.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1931071	1931742	.	-	.	Phchi.S4G033300
Phchi.S4	AUGUSTUS	transcript	1931071	1931742	.	-	.	transcript_id "Phchi.S4G033300.t1"; gene_id "Phchi.S4G033300"
Phchi.S4	AUGUSTUS	stop_codon	1931068	1931070	.	-	0	transcript_id "Phchi.S4G033300.t1"; gene_id "Phchi.S4G033300"
Phchi.S4	AUGUSTUS	CDS	1931071	1931742	0.89	-	0	transcript_id "Phchi.S4G033300.t1"; gene_id "Phchi.S4G033300"
Phchi.S4	AUGUSTUS	exon	1931071	1931742	.	-	.	transcript_id "Phchi.S4G033300.t1"; gene_id "Phchi.S4G033300"
Phchi.S4	AUGUSTUS	start_codon	1931740	1931742	.	-	0	transcript_id "Phchi.S4G033300.t1"; gene_id "Phchi.S4G033300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg4888.t1 is derived from g2058.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13241036	13243590	.	-	.	Phchi.S1G204700
Phchi.S1	AUGUSTUS	transcript	13242611	13243590	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	stop_codon	13242608	13242610	.	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242611	13242616	1	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242611	13242616	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242617	13242715	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242716	13242814	1	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242716	13242814	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242815	13243027	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243028	13243104	1	-	2	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243028	13243104	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13243105	13243196	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243197	13243287	1	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243197	13243287	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13243288	13243372	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243373	13243429	1	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243373	13243429	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13243430	13243509	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243510	13243590	0.94	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243510	13243590	.	-	.	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	start_codon	13243588	13243590	.	-	0	transcript_id "Phchi.S1G204700.t1"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	transcript	13241036	13242406	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	stop_codon	13241033	13241035	.	-	0	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13241036	13241392	0.98	-	0	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13241036	13241392	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13241393	13241478	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13241479	13241670	1	-	0	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13241479	13241670	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13241671	13241761	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13241762	13241885	1	-	1	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13241762	13241885	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13241886	13242012	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242013	13242156	0.91	-	1	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242013	13242156	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242157	13242269	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242270	13242406	0.82	-	0	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242270	13242406	.	-	.	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	start_codon	13242404	13242406	.	-	0	transcript_id "Phchi.S1G204700.t2"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	transcript	13241036	13243590	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	stop_codon	13241033	13241035	.	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13241036	13241392	0.94	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13241036	13241392	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13241393	13241478	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13241479	13241670	1	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13241479	13241670	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13241671	13241761	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13241762	13241885	1	-	1	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13241762	13241885	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13241886	13242012	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242013	13242156	0.98	-	1	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242013	13242156	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242157	13242269	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242270	13242442	0.49	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242270	13242442	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242443	13242543	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242544	13242616	0.37	-	1	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242544	13242616	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242617	13242725	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13242726	13242814	0.98	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13242726	13242814	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13242815	13243027	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243028	13243104	1	-	2	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243028	13243104	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13243105	13243196	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243197	13243287	1	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243197	13243287	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13243288	13243372	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243373	13243429	1	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243373	13243429	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	intron	13243430	13243509	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	CDS	13243510	13243590	0.91	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	exon	13243510	13243590	.	-	.	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
Phchi.S1	AUGUSTUS	start_codon	13243588	13243590	.	-	0	transcript_id "Phchi.S1G204700.t3"; gene_id "Phchi.S1G204700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12143.t1 is derived from g7819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4839119	4840657	.	+	.	Phchi.S2G022300
Phchi.S2	AUGUSTUS	transcript	4839119	4840657	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	start_codon	4839119	4839121	.	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839119	4839149	0.95	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839119	4839149	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839150	4839299	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839300	4839382	0.95	+	2	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839300	4839382	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839383	4839496	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839497	4839570	0.97	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839497	4839570	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839571	4839672	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839673	4839763	0.97	+	1	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839673	4839763	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839764	4839867	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839868	4840028	0.96	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839868	4840028	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840029	4840132	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840133	4840175	1	+	1	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840133	4840175	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840176	4840271	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840272	4840337	1	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840272	4840337	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840338	4840409	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840410	4840499	1	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840410	4840499	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840500	4840579	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840580	4840657	1	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840580	4840657	.	+	.	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	stop_codon	4840658	4840660	.	+	0	transcript_id "Phchi.S2G022300.t1"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	transcript	4839119	4840657	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	start_codon	4839119	4839121	.	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839119	4839149	0.38	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839119	4839149	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839150	4839308	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839309	4839382	0.38	+	2	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839309	4839382	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839383	4839496	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839497	4839570	0.53	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839497	4839570	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839571	4839672	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839673	4839763	0.55	+	1	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839673	4839763	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4839764	4839867	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4839868	4840028	0.84	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4839868	4840028	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840029	4840132	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840133	4840175	0.99	+	1	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840133	4840175	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840176	4840271	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840272	4840337	1	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840272	4840337	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840338	4840409	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840410	4840499	1	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840410	4840499	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	intron	4840500	4840579	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	CDS	4840580	4840657	1	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	exon	4840580	4840657	.	+	.	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
Phchi.S2	AUGUSTUS	stop_codon	4840658	4840660	.	+	0	transcript_id "Phchi.S2G022300.t2"; gene_id "Phchi.S2G022300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3024.t1 is derived from g193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1189210	1191159	.	+	.	Phchi.S1G018300
Phchi.S1	AUGUSTUS	transcript	1189210	1191159	.	+	.	transcript_id "Phchi.S1G018300.t1"; gene_id "Phchi.S1G018300"
Phchi.S1	AUGUSTUS	start_codon	1189210	1189212	.	+	0	transcript_id "Phchi.S1G018300.t1"; gene_id "Phchi.S1G018300"
Phchi.S1	AUGUSTUS	CDS	1189210	1191159	1	+	0	transcript_id "Phchi.S1G018300.t1"; gene_id "Phchi.S1G018300"
Phchi.S1	AUGUSTUS	exon	1189210	1191159	.	+	.	transcript_id "Phchi.S1G018300.t1"; gene_id "Phchi.S1G018300"
Phchi.S1	AUGUSTUS	stop_codon	1191160	1191162	.	+	0	transcript_id "Phchi.S1G018300.t1"; gene_id "Phchi.S1G018300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4486.t1 is derived from g1656.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10767646	10768047	.	-	.	Phchi.S1G164500
Phchi.S1	AUGUSTUS	transcript	10767646	10768047	.	-	.	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	stop_codon	10767643	10767645	.	-	0	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	CDS	10767646	10767736	0.97	-	1	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	exon	10767646	10767736	.	-	.	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	intron	10767737	10767826	.	-	.	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	CDS	10767827	10768047	1	-	0	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	exon	10767827	10768047	.	-	.	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
Phchi.S1	AUGUSTUS	start_codon	10768045	10768047	.	-	0	transcript_id "Phchi.S1G164500.t1"; gene_id "Phchi.S1G164500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg740.t1 is derived from g10522.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5279317	5281296	.	+	.	Phchi.S6G069900
Phchi.S6	AUGUSTUS	transcript	5279317	5281296	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	start_codon	5279317	5279319	.	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	CDS	5279317	5279397	0.74	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	exon	5279317	5279397	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	intron	5279398	5279593	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	CDS	5279594	5279698	0.68	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	exon	5279594	5279698	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	intron	5279699	5279882	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	CDS	5279883	5280599	0.49	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	exon	5279883	5280599	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	intron	5280600	5280772	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	CDS	5280773	5280979	0.79	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	exon	5280773	5280979	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	intron	5280980	5281065	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	CDS	5281066	5281296	0.66	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	exon	5281066	5281296	.	+	.	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
Phchi.S6	AUGUSTUS	stop_codon	5281297	5281299	.	+	0	transcript_id "Phchi.S6G069900.t1"; gene_id "Phchi.S6G069900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7290.t1 is derived from g4462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28334986	28337688	.	+	.	Phchi.S1G444900
Phchi.S1	AUGUSTUS	transcript	28334986	28337688	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	start_codon	28334986	28334988	.	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28334986	28335129	0.71	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28334986	28335129	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28335130	28335546	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28335547	28335823	0.9	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28335547	28335823	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28335824	28335905	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28335906	28336045	0.95	+	2	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28335906	28336045	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28336046	28336404	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28336405	28336597	0.96	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28336405	28336597	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28336598	28336679	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28336680	28336765	1	+	2	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28336680	28336765	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28336766	28336850	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28336851	28336892	1	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28336851	28336892	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28336893	28336994	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28336995	28337036	1	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28336995	28337036	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28337037	28337129	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28337130	28337213	1	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28337130	28337213	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28337214	28337287	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28337288	28337375	1	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28337288	28337375	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28337376	28337459	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28337460	28337557	1	+	2	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28337460	28337557	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	intron	28337558	28337649	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	CDS	28337650	28337688	1	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	exon	28337650	28337688	.	+	.	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
Phchi.S1	AUGUSTUS	stop_codon	28337689	28337691	.	+	0	transcript_id "Phchi.S1G444900.t1"; gene_id "Phchi.S1G444900"
# This transcript jg1480.t1 is derived from g8399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1132871	1133500	.	-	.	Phchi.S5G008900
Phchi.S5	AUGUSTUS	transcript	1132871	1133500	.	-	.	transcript_id "Phchi.S5G008900.t1"; gene_id "Phchi.S5G008900"
Phchi.S5	AUGUSTUS	stop_codon	1132868	1132870	.	-	0	transcript_id "Phchi.S5G008900.t1"; gene_id "Phchi.S5G008900"
Phchi.S5	AUGUSTUS	CDS	1132871	1133500	0.43	-	0	transcript_id "Phchi.S5G008900.t1"; gene_id "Phchi.S5G008900"
Phchi.S5	AUGUSTUS	exon	1132871	1133500	.	-	.	transcript_id "Phchi.S5G008900.t1"; gene_id "Phchi.S5G008900"
Phchi.S5	AUGUSTUS	start_codon	1133498	1133500	.	-	0	transcript_id "Phchi.S5G008900.t1"; gene_id "Phchi.S5G008900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6698.t1 is derived from g3870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24582281	24584426	.	-	.	Phchi.S1G385700
Phchi.S1	AUGUSTUS	transcript	24582281	24584426	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	stop_codon	24582278	24582280	.	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24582281	24582851	0.44	-	1	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24582281	24582851	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24582852	24582949	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24582950	24583034	1	-	2	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24582950	24583034	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24583035	24583115	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24583116	24583191	0.99	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24583116	24583191	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24583192	24583294	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24583295	24583354	1	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24583295	24583354	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24583355	24583514	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24583515	24583583	1	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24583515	24583583	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24583584	24583681	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24583682	24583705	1	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24583682	24583705	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24583706	24583782	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24583783	24583903	0.99	-	1	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24583783	24583903	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24583904	24584026	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24584027	24584064	0.99	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24584027	24584064	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	intron	24584065	24584339	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	CDS	24584340	24584426	1	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	exon	24584340	24584426	.	-	.	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
Phchi.S1	AUGUSTUS	start_codon	24584424	24584426	.	-	0	transcript_id "Phchi.S1G385700.t1"; gene_id "Phchi.S1G385700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1706.t1 is derived from g8626.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2634168	2637418	.	-	.	Phchi.S5G031500
Phchi.S5	AUGUSTUS	transcript	2634168	2637418	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	stop_codon	2634165	2634167	.	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2634168	2634246	0.93	-	1	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2634168	2634246	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2634247	2634337	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2634338	2634570	1	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2634338	2634570	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2634571	2634648	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2634649	2634861	1	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2634649	2634861	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2634862	2634984	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2634985	2635263	1	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2634985	2635263	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2635264	2635410	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2635411	2635515	1	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2635411	2635515	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2635516	2635644	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2635645	2636093	0.95	-	2	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2635645	2636093	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2636094	2636234	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2636235	2636429	1	-	2	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2636235	2636429	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2636430	2636572	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2636573	2636981	0.77	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2636573	2636981	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	intron	2636982	2637100	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	CDS	2637101	2637418	0.99	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	exon	2637101	2637418	.	-	.	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
Phchi.S5	AUGUSTUS	start_codon	2637416	2637418	.	-	0	transcript_id "Phchi.S5G031500.t1"; gene_id "Phchi.S5G031500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9829.t1 is derived from g7005.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43993276	43994480	.	+	.	Phchi.S1G698800
Phchi.S1	AUGUSTUS	transcript	43993276	43994480	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	start_codon	43993276	43993278	.	+	0	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	CDS	43993276	43993350	0.63	+	0	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	exon	43993276	43993350	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	intron	43993351	43993489	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	CDS	43993490	43993557	1	+	0	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	exon	43993490	43993557	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	intron	43993558	43993696	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	CDS	43993697	43993810	1	+	1	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	exon	43993697	43993810	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	intron	43993811	43993966	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	CDS	43993967	43994129	1	+	1	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	exon	43993967	43994129	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	intron	43994130	43994205	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	CDS	43994206	43994352	0.71	+	0	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	exon	43994206	43994352	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	intron	43994353	43994456	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	CDS	43994457	43994480	0.91	+	0	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	exon	43994457	43994480	.	+	.	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
Phchi.S1	AUGUSTUS	stop_codon	43994481	43994483	.	+	0	transcript_id "Phchi.S1G698800.t1"; gene_id "Phchi.S1G698800"
# This transcript jg5313.t2 is derived from g2483.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5314.t1 is derived from g2484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16252797	16253723	.	+	.	Phchi.S1G247300
Phchi.S1	AUGUSTUS	transcript	16252797	16253723	.	+	.	transcript_id "Phchi.S1G247300.t1"; gene_id "Phchi.S1G247300"
Phchi.S1	AUGUSTUS	start_codon	16252797	16252799	.	+	0	transcript_id "Phchi.S1G247300.t1"; gene_id "Phchi.S1G247300"
Phchi.S1	AUGUSTUS	CDS	16252797	16253723	0.62	+	0	transcript_id "Phchi.S1G247300.t1"; gene_id "Phchi.S1G247300"
Phchi.S1	AUGUSTUS	exon	16252797	16253723	.	+	.	transcript_id "Phchi.S1G247300.t1"; gene_id "Phchi.S1G247300"
Phchi.S1	AUGUSTUS	stop_codon	16253724	16253726	.	+	0	transcript_id "Phchi.S1G247300.t1"; gene_id "Phchi.S1G247300"
# This transcript jg14796.t2 is derived from g13264.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14797.t1 is derived from g13265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14757440	14759081	.	+	.	Phchi.S3G211600
Phchi.S3	AUGUSTUS	transcript	14757440	14759081	.	+	.	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	start_codon	14757440	14757442	.	+	0	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	CDS	14757440	14757988	1	+	0	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	exon	14757440	14757988	.	+	.	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	intron	14757989	14758157	.	+	.	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	CDS	14758158	14759081	1	+	0	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	exon	14758158	14759081	.	+	.	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
Phchi.S3	AUGUSTUS	stop_codon	14759082	14759084	.	+	0	transcript_id "Phchi.S3G211600.t1"; gene_id "Phchi.S3G211600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11828.t1 is derived from g15880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8462678	8465458	.	+	.	Phchi.S4G141000
Phchi.S4	AUGUSTUS	transcript	8462678	8465458	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	start_codon	8462678	8462680	.	+	0	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8462678	8463157	0.21	+	0	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8462678	8463157	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	intron	8463158	8463325	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8463326	8463628	0.18	+	0	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8463326	8463628	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	intron	8463629	8463841	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8463842	8464850	0.25	+	0	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8463842	8464850	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	intron	8464851	8464937	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8464938	8464985	0.93	+	2	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8464938	8464985	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	intron	8464986	8465085	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8465086	8465138	0.85	+	2	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8465086	8465138	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	intron	8465139	8465226	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8465227	8465254	0.85	+	0	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8465227	8465254	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	intron	8465255	8465408	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	CDS	8465409	8465458	0.87	+	2	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	exon	8465409	8465458	.	+	.	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
Phchi.S4	AUGUSTUS	stop_codon	8465459	8465461	.	+	0	transcript_id "Phchi.S4G141000.t1"; gene_id "Phchi.S4G141000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3493.t1 is derived from g662.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4040609	4040960	.	+	.	Phchi.S1G065200
Phchi.S1	AUGUSTUS	transcript	4040609	4040960	.	+	.	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	start_codon	4040609	4040611	.	+	0	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	CDS	4040609	4040787	1	+	0	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	exon	4040609	4040787	.	+	.	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	intron	4040788	4040938	.	+	.	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	CDS	4040939	4040960	1	+	1	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	exon	4040939	4040960	.	+	.	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
Phchi.S1	AUGUSTUS	stop_codon	4040961	4040963	.	+	0	transcript_id "Phchi.S1G065200.t1"; gene_id "Phchi.S1G065200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12591.t1 is derived from g8268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36304493	36304720	.	-	.	Phchi.S2G067100
Phchi.S2	AUGUSTUS	transcript	36304493	36304720	.	-	.	transcript_id "Phchi.S2G067100.t1"; gene_id "Phchi.S2G067100"
Phchi.S2	AUGUSTUS	stop_codon	36304490	36304492	.	-	0	transcript_id "Phchi.S2G067100.t1"; gene_id "Phchi.S2G067100"
Phchi.S2	AUGUSTUS	CDS	36304493	36304720	0.89	-	0	transcript_id "Phchi.S2G067100.t1"; gene_id "Phchi.S2G067100"
Phchi.S2	AUGUSTUS	exon	36304493	36304720	.	-	.	transcript_id "Phchi.S2G067100.t1"; gene_id "Phchi.S2G067100"
Phchi.S2	AUGUSTUS	start_codon	36304718	36304720	.	-	0	transcript_id "Phchi.S2G067100.t1"; gene_id "Phchi.S2G067100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10392.t1 is derived from g7568.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47519901	47520340	.	-	.	Phchi.S1G755100
Phchi.S1	AUGUSTUS	transcript	47519901	47520340	.	-	.	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	stop_codon	47519898	47519900	.	-	0	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	CDS	47519901	47519996	0.97	-	0	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	exon	47519901	47519996	.	-	.	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	intron	47519997	47520229	.	-	.	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	CDS	47520230	47520340	0.97	-	0	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	exon	47520230	47520340	.	-	.	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
Phchi.S1	AUGUSTUS	start_codon	47520338	47520340	.	-	0	transcript_id "Phchi.S1G755100.t1"; gene_id "Phchi.S1G755100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2046.t1 is derived from g8966.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4574359	4575774	.	+	.	Phchi.S5G065500
Phchi.S5	AUGUSTUS	transcript	4574359	4575774	.	+	.	transcript_id "Phchi.S5G065500.t1"; gene_id "Phchi.S5G065500"
Phchi.S5	AUGUSTUS	start_codon	4574359	4574361	.	+	0	transcript_id "Phchi.S5G065500.t1"; gene_id "Phchi.S5G065500"
Phchi.S5	AUGUSTUS	CDS	4574359	4575774	1	+	0	transcript_id "Phchi.S5G065500.t1"; gene_id "Phchi.S5G065500"
Phchi.S5	AUGUSTUS	exon	4574359	4575774	.	+	.	transcript_id "Phchi.S5G065500.t1"; gene_id "Phchi.S5G065500"
Phchi.S5	AUGUSTUS	stop_codon	4575775	4575777	.	+	0	transcript_id "Phchi.S5G065500.t1"; gene_id "Phchi.S5G065500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13848.t1 is derived from g12315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9213838	9215026	.	+	.	Phchi.S3G116700
Phchi.S3	AUGUSTUS	transcript	9213838	9215026	.	+	.	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	start_codon	9213838	9213840	.	+	0	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	CDS	9213838	9213842	0.58	+	0	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	exon	9213838	9213842	.	+	.	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	intron	9213843	9213936	.	+	.	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	CDS	9213937	9214071	1	+	1	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	exon	9213937	9214071	.	+	.	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	intron	9214072	9214176	.	+	.	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	CDS	9214177	9215026	0.96	+	1	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	exon	9214177	9215026	.	+	.	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
Phchi.S3	AUGUSTUS	stop_codon	9215027	9215029	.	+	0	transcript_id "Phchi.S3G116700.t1"; gene_id "Phchi.S3G116700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12828.t1 is derived from g11293.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2587284	2588135	.	+	.	Phchi.S3G014700
Phchi.S3	AUGUSTUS	transcript	2587284	2588135	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	start_codon	2587284	2587286	.	+	0	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587284	2587316	1	+	0	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587284	2587316	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	intron	2587317	2587399	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587400	2587495	1	+	0	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587400	2587495	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	intron	2587496	2587612	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587613	2587789	1	+	0	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587613	2587789	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	intron	2587790	2587862	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587863	2588135	0.9	+	0	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587863	2588135	.	+	.	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	stop_codon	2588136	2588138	.	+	0	transcript_id "Phchi.S3G014700.t1"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	transcript	2587284	2588135	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	start_codon	2587284	2587286	.	+	0	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587284	2587316	1	+	0	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587284	2587316	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	intron	2587317	2587399	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587400	2587495	1	+	0	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587400	2587495	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	intron	2587496	2587612	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587613	2587789	1	+	0	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587613	2587789	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	intron	2587790	2587865	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	CDS	2587866	2588135	0.88	+	0	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	exon	2587866	2588135	.	+	.	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
Phchi.S3	AUGUSTUS	stop_codon	2588136	2588138	.	+	0	transcript_id "Phchi.S3G014700.t2"; gene_id "Phchi.S3G014700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4670.t1 is derived from g1840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11736710	11738096	.	-	.	Phchi.S1G182900
Phchi.S1	AUGUSTUS	transcript	11736710	11738096	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	stop_codon	11736707	11736709	.	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11736710	11736737	0.99	-	1	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11736710	11736737	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11736738	11736843	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11736844	11736923	1	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11736844	11736923	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11736924	11737028	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11737029	11737076	0.99	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11737029	11737076	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11737077	11737216	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11737217	11737265	1	-	1	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11737217	11737265	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11737266	11737354	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11737355	11737407	1	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11737355	11737407	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11737408	11737491	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11737492	11737587	1	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11737492	11737587	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11737588	11737659	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11737660	11737759	1	-	1	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11737660	11737759	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	intron	11737760	11737851	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	CDS	11737852	11738096	0.73	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	exon	11737852	11738096	.	-	.	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
Phchi.S1	AUGUSTUS	start_codon	11738094	11738096	.	-	0	transcript_id "Phchi.S1G182900.t1"; gene_id "Phchi.S1G182900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2019.t1 is derived from g8939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4474587	4477054	.	+	.	Phchi.S5G062800
Phchi.S5	AUGUSTUS	transcript	4474587	4477054	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	start_codon	4474587	4474589	.	+	0	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4474587	4474630	0.92	+	0	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4474587	4474630	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4474631	4474862	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4474863	4474972	1	+	1	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4474863	4474972	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4474973	4475543	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4475544	4475668	1	+	2	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4475544	4475668	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4475669	4476014	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476015	4476447	0.94	+	0	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476015	4476447	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476448	4476539	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476540	4476703	0.98	+	2	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476540	4476703	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476704	4476814	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476815	4476868	0.98	+	0	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476815	4476868	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476869	4476976	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476977	4477054	0.82	+	0	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476977	4477054	.	+	.	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	stop_codon	4477055	4477057	.	+	0	transcript_id "Phchi.S5G062800.t1"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	transcript	4474587	4477054	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	start_codon	4474587	4474589	.	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4474587	4474630	0.9	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4474587	4474630	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4474631	4474862	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4474863	4474972	1	+	1	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4474863	4474972	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4474973	4475543	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4475544	4475629	0.56	+	2	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4475544	4475629	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4475630	4475716	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4475717	4475730	0.47	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4475717	4475730	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4475731	4476014	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476015	4476099	0.34	+	1	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476015	4476099	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476100	4476209	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476210	4476447	0.34	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476210	4476447	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476448	4476539	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476540	4476703	0.95	+	2	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476540	4476703	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476704	4476814	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476815	4476868	0.97	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476815	4476868	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	intron	4476869	4476976	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	CDS	4476977	4477054	0.72	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	exon	4476977	4477054	.	+	.	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
Phchi.S5	AUGUSTUS	stop_codon	4477055	4477057	.	+	0	transcript_id "Phchi.S5G062800.t2"; gene_id "Phchi.S5G062800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10202.t1 is derived from g7378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46357135	46357575	.	-	.	Phchi.S1G736100
Phchi.S1	AUGUSTUS	transcript	46357135	46357575	.	-	.	transcript_id "Phchi.S1G736100.t1"; gene_id "Phchi.S1G736100"
Phchi.S1	AUGUSTUS	stop_codon	46357132	46357134	.	-	0	transcript_id "Phchi.S1G736100.t1"; gene_id "Phchi.S1G736100"
Phchi.S1	AUGUSTUS	CDS	46357135	46357575	0.47	-	0	transcript_id "Phchi.S1G736100.t1"; gene_id "Phchi.S1G736100"
Phchi.S1	AUGUSTUS	exon	46357135	46357575	.	-	.	transcript_id "Phchi.S1G736100.t1"; gene_id "Phchi.S1G736100"
Phchi.S1	AUGUSTUS	start_codon	46357573	46357575	.	-	0	transcript_id "Phchi.S1G736100.t1"; gene_id "Phchi.S1G736100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9435.t1 is derived from g6611.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41447586	41447921	.	-	.	Phchi.S1G659400
Phchi.S1	AUGUSTUS	transcript	41447586	41447921	.	-	.	transcript_id "Phchi.S1G659400.t1"; gene_id "Phchi.S1G659400"
Phchi.S1	AUGUSTUS	stop_codon	41447583	41447585	.	-	0	transcript_id "Phchi.S1G659400.t1"; gene_id "Phchi.S1G659400"
Phchi.S1	AUGUSTUS	CDS	41447586	41447921	1	-	0	transcript_id "Phchi.S1G659400.t1"; gene_id "Phchi.S1G659400"
Phchi.S1	AUGUSTUS	exon	41447586	41447921	.	-	.	transcript_id "Phchi.S1G659400.t1"; gene_id "Phchi.S1G659400"
Phchi.S1	AUGUSTUS	start_codon	41447919	41447921	.	-	0	transcript_id "Phchi.S1G659400.t1"; gene_id "Phchi.S1G659400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8385.t1 is derived from g5560.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35610973	35616784	.	+	.	Phchi.S1G554400
Phchi.S1	AUGUSTUS	transcript	35610973	35616784	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	start_codon	35610973	35610975	.	+	0	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	CDS	35610973	35614660	0.46	+	0	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	exon	35610973	35614660	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	intron	35614661	35614738	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	CDS	35614739	35616015	0.96	+	2	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	exon	35614739	35616015	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	intron	35616016	35616101	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	CDS	35616102	35616251	1	+	0	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	exon	35616102	35616251	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	intron	35616252	35616435	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	CDS	35616436	35616621	1	+	0	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	exon	35616436	35616621	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	intron	35616622	35616712	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	CDS	35616713	35616784	1	+	0	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	exon	35616713	35616784	.	+	.	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
Phchi.S1	AUGUSTUS	stop_codon	35616785	35616787	.	+	0	transcript_id "Phchi.S1G554400.t1"; gene_id "Phchi.S1G554400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4189.t1 is derived from g1358.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8824121	8825173	.	-	.	Phchi.S1G134800
Phchi.S1	AUGUSTUS	transcript	8824121	8825173	.	-	.	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	stop_codon	8824118	8824120	.	-	0	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	CDS	8824121	8824319	0.92	-	1	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	exon	8824121	8824319	.	-	.	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	intron	8824320	8824667	.	-	.	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	CDS	8824668	8825173	0.84	-	0	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	exon	8824668	8825173	.	-	.	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
Phchi.S1	AUGUSTUS	start_codon	8825171	8825173	.	-	0	transcript_id "Phchi.S1G134800.t1"; gene_id "Phchi.S1G134800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8635.t1 is derived from g5810.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37172903	37173327	.	+	.	Phchi.S1G579400
Phchi.S1	AUGUSTUS	transcript	37172903	37173327	.	+	.	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	start_codon	37172903	37172905	.	+	0	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	CDS	37172903	37172952	1	+	0	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	exon	37172903	37172952	.	+	.	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	intron	37172953	37173025	.	+	.	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	CDS	37173026	37173158	0.96	+	1	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	exon	37173026	37173158	.	+	.	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	intron	37173159	37173267	.	+	.	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	CDS	37173268	37173327	1	+	0	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	exon	37173268	37173327	.	+	.	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
Phchi.S1	AUGUSTUS	stop_codon	37173328	37173330	.	+	0	transcript_id "Phchi.S1G579400.t1"; gene_id "Phchi.S1G579400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3566.t1 is derived from g735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4529327	4537478	.	-	.	Phchi.S1G072500
Phchi.S1	AUGUSTUS	transcript	4529327	4537478	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	stop_codon	4529324	4529326	.	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4529327	4531992	1	-	2	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4529327	4531992	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4531993	4532094	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4532095	4532329	0.97	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4532095	4532329	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4532330	4532425	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4532426	4532773	0.87	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4532426	4532773	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4532774	4532881	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4532882	4534226	0.99	-	1	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4532882	4534226	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4534227	4534314	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4534315	4534824	0.99	-	1	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4534315	4534824	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4534825	4534921	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4534922	4535277	0.98	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4534922	4535277	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4535278	4535372	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4535373	4535580	1	-	1	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4535373	4535580	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4535581	4535670	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4535671	4535926	0.69	-	2	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4535671	4535926	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4535927	4536047	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4536048	4536375	1	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4536048	4536375	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	intron	4536376	4536485	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	CDS	4536486	4537478	0.57	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	exon	4536486	4537478	.	-	.	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
Phchi.S1	AUGUSTUS	start_codon	4537476	4537478	.	-	0	transcript_id "Phchi.S1G072500.t1"; gene_id "Phchi.S1G072500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 4 different transcripts
# This transcript jg1755.t1 is derived from g8675.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2890892	2894191	.	-	.	Phchi.S5G036400
Phchi.S5	AUGUSTUS	transcript	2892772	2894191	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	stop_codon	2892769	2892771	.	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892772	2892777	0.97	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892772	2892777	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892778	2892868	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892869	2892955	0.99	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892869	2892955	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892956	2893119	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893120	2893203	1	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893120	2893203	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893204	2893291	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893292	2893357	1	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893292	2893357	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893358	2893440	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893441	2893557	1	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893441	2893557	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893558	2893648	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893649	2893803	1	-	2	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893649	2893803	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893804	2893884	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893885	2894191	0.81	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893885	2894191	.	-	.	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	start_codon	2894189	2894191	.	-	0	transcript_id "Phchi.S5G036400.t1"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	transcript	2890892	2894191	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	stop_codon	2890889	2890891	.	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2890892	2891023	0.57	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2890892	2891023	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891024	2891117	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891118	2891214	1	-	1	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891118	2891214	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891215	2891296	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891297	2891382	1	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891297	2891382	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891383	2891463	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891464	2891535	1	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891464	2891535	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891536	2891617	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891618	2891736	1	-	2	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891618	2891736	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891737	2891835	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891836	2891943	1	-	2	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891836	2891943	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891944	2892027	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892028	2892088	0.96	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892028	2892088	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892089	2892209	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892210	2892269	0.96	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892210	2892269	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892270	2892512	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892513	2892573	1	-	1	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892513	2892573	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892574	2892659	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892660	2892751	0.89	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892660	2892751	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892752	2892868	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892869	2892955	0.94	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892869	2892955	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892956	2893119	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893120	2893203	1	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893120	2893203	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893204	2893291	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893292	2893357	1	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893292	2893357	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893358	2893440	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893441	2893557	1	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893441	2893557	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893558	2893648	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893649	2893803	1	-	2	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893649	2893803	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893804	2893884	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893885	2894191	0.75	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893885	2894191	.	-	.	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	start_codon	2894189	2894191	.	-	0	transcript_id "Phchi.S5G036400.t2"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	transcript	2890892	2892723	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	stop_codon	2890889	2890891	.	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2890892	2891023	0.35	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2890892	2891023	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891024	2891117	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891118	2891214	1	-	1	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891118	2891214	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891215	2891296	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891297	2891382	1	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891297	2891382	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891383	2891463	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891464	2891535	1	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891464	2891535	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891536	2891617	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891618	2891736	1	-	2	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891618	2891736	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891737	2891835	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891836	2891943	1	-	2	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891836	2891943	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891944	2892027	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892028	2892088	1	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892028	2892088	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892089	2892217	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892218	2892269	0.99	-	1	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892218	2892269	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892270	2892512	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892513	2892573	0.99	-	2	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892513	2892573	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892574	2892659	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892660	2892723	0.75	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892660	2892723	.	-	.	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	start_codon	2892721	2892723	.	-	0	transcript_id "Phchi.S5G036400.t3"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	transcript	2890892	2894191	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	stop_codon	2890889	2890891	.	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2890892	2891023	0.45	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2890892	2891023	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891024	2891117	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891118	2891214	1	-	1	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891118	2891214	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891215	2891296	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891297	2891382	1	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891297	2891382	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891383	2891463	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891464	2891535	1	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891464	2891535	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891536	2891617	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891618	2891736	1	-	2	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891618	2891736	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891737	2891835	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2891836	2891943	1	-	2	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2891836	2891943	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2891944	2892027	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892028	2892088	1	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892028	2892088	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892089	2892217	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892218	2892269	0.99	-	1	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892218	2892269	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892270	2892512	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892513	2892573	0.99	-	2	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892513	2892573	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892574	2892659	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892660	2892691	0.27	-	1	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892660	2892691	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2892692	2892868	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2892869	2893038	0.61	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2892869	2893038	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893039	2893119	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893120	2893203	1	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893120	2893203	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893204	2893291	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893292	2893357	1	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893292	2893357	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893358	2893440	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893441	2893557	1	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893441	2893557	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893558	2893648	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893649	2893803	1	-	2	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893649	2893803	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	intron	2893804	2893884	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	CDS	2893885	2894191	0.82	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	exon	2893885	2894191	.	-	.	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
Phchi.S5	AUGUSTUS	start_codon	2894189	2894191	.	-	0	transcript_id "Phchi.S5G036400.t4"; gene_id "Phchi.S5G036400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14980.t1 is derived from g13448.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15859051	15859407	.	-	.	Phchi.S3G229900
Phchi.S3	AUGUSTUS	transcript	15859051	15859407	.	-	.	transcript_id "Phchi.S3G229900.t1"; gene_id "Phchi.S3G229900"
Phchi.S3	AUGUSTUS	stop_codon	15859048	15859050	.	-	0	transcript_id "Phchi.S3G229900.t1"; gene_id "Phchi.S3G229900"
Phchi.S3	AUGUSTUS	CDS	15859051	15859407	0.77	-	0	transcript_id "Phchi.S3G229900.t1"; gene_id "Phchi.S3G229900"
Phchi.S3	AUGUSTUS	exon	15859051	15859407	.	-	.	transcript_id "Phchi.S3G229900.t1"; gene_id "Phchi.S3G229900"
Phchi.S3	AUGUSTUS	start_codon	15859405	15859407	.	-	0	transcript_id "Phchi.S3G229900.t1"; gene_id "Phchi.S3G229900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3243.t1 is derived from g412.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2417257	2417910	.	+	.	Phchi.S1G040200
Phchi.S1	AUGUSTUS	transcript	2417257	2417910	.	+	.	transcript_id "Phchi.S1G040200.t1"; gene_id "Phchi.S1G040200"
Phchi.S1	AUGUSTUS	start_codon	2417257	2417259	.	+	0	transcript_id "Phchi.S1G040200.t1"; gene_id "Phchi.S1G040200"
Phchi.S1	AUGUSTUS	CDS	2417257	2417910	0.67	+	0	transcript_id "Phchi.S1G040200.t1"; gene_id "Phchi.S1G040200"
Phchi.S1	AUGUSTUS	exon	2417257	2417910	.	+	.	transcript_id "Phchi.S1G040200.t1"; gene_id "Phchi.S1G040200"
Phchi.S1	AUGUSTUS	stop_codon	2417911	2417913	.	+	0	transcript_id "Phchi.S1G040200.t1"; gene_id "Phchi.S1G040200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4697.t1 is derived from g1867.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12343007	12345001	.	+	.	Phchi.S1G185600
Phchi.S1	AUGUSTUS	transcript	12343007	12345001	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	start_codon	12343007	12343009	.	+	0	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	CDS	12343007	12343015	0.98	+	0	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	exon	12343007	12343015	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	intron	12343016	12343094	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	CDS	12343095	12343435	1	+	0	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	exon	12343095	12343435	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	intron	12343436	12343531	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	CDS	12343532	12344309	1	+	1	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	exon	12343532	12344309	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	intron	12344310	12344431	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	CDS	12344432	12344638	1	+	0	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	exon	12344432	12344638	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	intron	12344639	12344773	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	CDS	12344774	12345001	1	+	0	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	exon	12344774	12345001	.	+	.	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
Phchi.S1	AUGUSTUS	stop_codon	12345002	12345004	.	+	0	transcript_id "Phchi.S1G185600.t1"; gene_id "Phchi.S1G185600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13712.t1 is derived from g12179.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8316721	8319350	.	+	.	Phchi.S3G103100
Phchi.S3	AUGUSTUS	transcript	8316721	8319350	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	start_codon	8316721	8316723	.	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8316721	8317116	0.94	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8316721	8317116	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8317117	8317228	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8317229	8317304	0.98	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8317229	8317304	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8317305	8317408	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8317409	8317617	1	+	2	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8317409	8317617	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8317618	8317709	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8317710	8317796	1	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8317710	8317796	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8317797	8317884	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8317885	8317977	1	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8317885	8317977	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8317978	8318060	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8318061	8318215	1	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8318061	8318215	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8318216	8318384	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8318385	8318469	1	+	1	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8318385	8318469	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8318470	8318558	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8318559	8318645	1	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8318559	8318645	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8318646	8318732	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8318733	8318852	1	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8318733	8318852	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8318853	8318968	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8318969	8319070	1	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8318969	8319070	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	intron	8319071	8319185	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	CDS	8319186	8319350	0.57	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	exon	8319186	8319350	.	+	.	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
Phchi.S3	AUGUSTUS	stop_codon	8319351	8319353	.	+	0	transcript_id "Phchi.S3G103100.t1"; gene_id "Phchi.S3G103100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9203.t1 is derived from g6378.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40360448	40362426	.	-	.	Phchi.S1G636200
Phchi.S1	AUGUSTUS	transcript	40360448	40362426	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	stop_codon	40360445	40360447	.	-	0	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	CDS	40360448	40360783	0.88	-	0	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	exon	40360448	40360783	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	intron	40360784	40360857	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	CDS	40360858	40361145	1	-	0	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	exon	40360858	40361145	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	intron	40361146	40361240	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	CDS	40361241	40361270	1	-	0	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	exon	40361241	40361270	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	intron	40361271	40361376	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	CDS	40361377	40361572	1	-	1	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	exon	40361377	40361572	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	intron	40361573	40361686	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	CDS	40361687	40362426	0.37	-	0	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	exon	40361687	40362426	.	-	.	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
Phchi.S1	AUGUSTUS	start_codon	40362424	40362426	.	-	0	transcript_id "Phchi.S1G636200.t1"; gene_id "Phchi.S1G636200"
# This transcript jg6312.t2 is derived from g3484.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6313.t1 is derived from g3485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22222677	22224647	.	+	.	Phchi.S1G347200
Phchi.S1	AUGUSTUS	transcript	22222677	22224647	.	+	.	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	start_codon	22222677	22222679	.	+	0	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	CDS	22222677	22223600	0.48	+	0	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	exon	22222677	22223600	.	+	.	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	intron	22223601	22223726	.	+	.	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	CDS	22223727	22224647	0.95	+	0	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	exon	22223727	22224647	.	+	.	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
Phchi.S1	AUGUSTUS	stop_codon	22224648	22224650	.	+	0	transcript_id "Phchi.S1G347200.t1"; gene_id "Phchi.S1G347200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6598.t1 is derived from g3770.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23929741	23931133	.	-	.	Phchi.S1G375700
Phchi.S1	AUGUSTUS	transcript	23929741	23931133	.	-	.	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	stop_codon	23929738	23929740	.	-	0	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	CDS	23929741	23930538	0.41	-	0	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	exon	23929741	23930538	.	-	.	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	intron	23930539	23930641	.	-	.	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	CDS	23930642	23931133	0.84	-	0	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	exon	23930642	23931133	.	-	.	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
Phchi.S1	AUGUSTUS	start_codon	23931131	23931133	.	-	0	transcript_id "Phchi.S1G375700.t1"; gene_id "Phchi.S1G375700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14041.t1 is derived from g12508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10424266	10426927	.	+	.	Phchi.S3G136000
Phchi.S3	AUGUSTUS	transcript	10424266	10426927	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	start_codon	10424266	10424268	.	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10424266	10424277	0.96	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10424266	10424277	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10424278	10424404	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10424405	10424466	1	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10424405	10424466	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10424467	10424552	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10424553	10424689	1	+	1	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10424553	10424689	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10424690	10424815	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10424816	10424874	1	+	2	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10424816	10424874	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10424875	10424960	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10424961	10424984	1	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10424961	10424984	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10424985	10425140	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10425141	10425223	1	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10425141	10425223	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10425224	10425353	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10425354	10425418	1	+	1	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10425354	10425418	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10425419	10425639	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10425640	10425689	1	+	2	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10425640	10425689	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10425690	10425877	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10425878	10425979	1	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10425878	10425979	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10425980	10426106	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10426107	10426166	1	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10426107	10426166	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10426167	10426264	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10426265	10426369	0.87	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10426265	10426369	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10426370	10426599	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10426600	10426721	0.23	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10426600	10426721	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	intron	10426722	10426809	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	CDS	10426810	10426927	0.23	+	1	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	exon	10426810	10426927	.	+	.	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
Phchi.S3	AUGUSTUS	stop_codon	10426928	10426930	.	+	0	transcript_id "Phchi.S3G136000.t1"; gene_id "Phchi.S3G136000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6563.t1 is derived from g3735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23735746	23736399	.	-	.	Phchi.S1G372200
Phchi.S1	AUGUSTUS	transcript	23735746	23736399	.	-	.	transcript_id "Phchi.S1G372200.t1"; gene_id "Phchi.S1G372200"
Phchi.S1	AUGUSTUS	stop_codon	23735743	23735745	.	-	0	transcript_id "Phchi.S1G372200.t1"; gene_id "Phchi.S1G372200"
Phchi.S1	AUGUSTUS	CDS	23735746	23736399	1	-	0	transcript_id "Phchi.S1G372200.t1"; gene_id "Phchi.S1G372200"
Phchi.S1	AUGUSTUS	exon	23735746	23736399	.	-	.	transcript_id "Phchi.S1G372200.t1"; gene_id "Phchi.S1G372200"
Phchi.S1	AUGUSTUS	start_codon	23736397	23736399	.	-	0	transcript_id "Phchi.S1G372200.t1"; gene_id "Phchi.S1G372200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8901.t1 is derived from g6076.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38558400	38560118	.	-	.	Phchi.S1G606000
Phchi.S1	AUGUSTUS	transcript	38558400	38560118	.	-	.	transcript_id "Phchi.S1G606000.t1"; gene_id "Phchi.S1G606000"
Phchi.S1	AUGUSTUS	stop_codon	38558397	38558399	.	-	0	transcript_id "Phchi.S1G606000.t1"; gene_id "Phchi.S1G606000"
Phchi.S1	AUGUSTUS	CDS	38558400	38560118	0.93	-	0	transcript_id "Phchi.S1G606000.t1"; gene_id "Phchi.S1G606000"
Phchi.S1	AUGUSTUS	exon	38558400	38560118	.	-	.	transcript_id "Phchi.S1G606000.t1"; gene_id "Phchi.S1G606000"
Phchi.S1	AUGUSTUS	start_codon	38560116	38560118	.	-	0	transcript_id "Phchi.S1G606000.t1"; gene_id "Phchi.S1G606000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4512.t1 is derived from g1682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10896224	10897633	.	-	.	Phchi.S1G167100
Phchi.S1	AUGUSTUS	transcript	10896224	10897633	.	-	.	transcript_id "Phchi.S1G167100.t1"; gene_id "Phchi.S1G167100"
Phchi.S1	AUGUSTUS	stop_codon	10896221	10896223	.	-	0	transcript_id "Phchi.S1G167100.t1"; gene_id "Phchi.S1G167100"
Phchi.S1	AUGUSTUS	CDS	10896224	10897633	0.83	-	0	transcript_id "Phchi.S1G167100.t1"; gene_id "Phchi.S1G167100"
Phchi.S1	AUGUSTUS	exon	10896224	10897633	.	-	.	transcript_id "Phchi.S1G167100.t1"; gene_id "Phchi.S1G167100"
Phchi.S1	AUGUSTUS	start_codon	10897631	10897633	.	-	0	transcript_id "Phchi.S1G167100.t1"; gene_id "Phchi.S1G167100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6759.t1 is derived from g3931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24910284	24913538	.	-	.	Phchi.S1G391800
Phchi.S1	AUGUSTUS	transcript	24910284	24913538	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	stop_codon	24910281	24910283	.	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24910284	24910348	0.95	-	2	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24910284	24910348	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24910349	24910451	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24910452	24910503	0.86	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24910452	24910503	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24910504	24910588	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24910589	24910810	1	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24910589	24910810	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24910811	24910912	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24910913	24910990	0.7	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24910913	24910990	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24910991	24911066	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24911067	24911965	1	-	2	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24911067	24911965	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24911966	24912113	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24912114	24912144	0.87	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24912114	24912144	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24912145	24912252	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24912253	24912389	0.5	-	2	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24912253	24912389	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24912390	24912481	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24912482	24912600	1	-	1	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24912482	24912600	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24912601	24912793	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24912794	24913037	0.94	-	2	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24912794	24913037	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24913038	24913153	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24913154	24913253	1	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24913154	24913253	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	intron	24913254	24913379	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	CDS	24913380	24913538	0.97	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	exon	24913380	24913538	.	-	.	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
Phchi.S1	AUGUSTUS	start_codon	24913536	24913538	.	-	0	transcript_id "Phchi.S1G391800.t1"; gene_id "Phchi.S1G391800"
# This transcript jg15022.t2 is derived from g13490.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15022.t3 is derived from g13490.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15023.t1 is derived from g13491.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16582892	16584667	.	+	.	Phchi.S3G234200
Phchi.S3	AUGUSTUS	transcript	16582892	16584667	.	+	.	transcript_id "Phchi.S3G234200.t1"; gene_id "Phchi.S3G234200"
Phchi.S3	AUGUSTUS	start_codon	16582892	16582894	.	+	0	transcript_id "Phchi.S3G234200.t1"; gene_id "Phchi.S3G234200"
Phchi.S3	AUGUSTUS	CDS	16582892	16584667	0.86	+	0	transcript_id "Phchi.S3G234200.t1"; gene_id "Phchi.S3G234200"
Phchi.S3	AUGUSTUS	exon	16582892	16584667	.	+	.	transcript_id "Phchi.S3G234200.t1"; gene_id "Phchi.S3G234200"
Phchi.S3	AUGUSTUS	stop_codon	16584668	16584670	.	+	0	transcript_id "Phchi.S3G234200.t1"; gene_id "Phchi.S3G234200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7398.t1 is derived from g4570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28942758	28945133	.	-	.	Phchi.S1G455700
Phchi.S1	AUGUSTUS	transcript	28942758	28945133	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	stop_codon	28942755	28942757	.	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28942758	28943075	1	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28942758	28943075	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28943076	28943212	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28943213	28943376	1	-	2	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28943213	28943376	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28943377	28943482	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28943483	28943588	1	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28943483	28943588	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28943589	28943681	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28943682	28943846	1	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28943682	28943846	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28943847	28943964	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28943965	28944060	0.99	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28943965	28944060	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28944061	28944185	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28944186	28944383	1	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28944186	28944383	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28944384	28944583	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28944584	28944796	1	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28944584	28944796	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	intron	28944797	28944896	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	CDS	28944897	28945133	0.74	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	exon	28944897	28945133	.	-	.	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
Phchi.S1	AUGUSTUS	start_codon	28945131	28945133	.	-	0	transcript_id "Phchi.S1G455700.t1"; gene_id "Phchi.S1G455700"
# This transcript jg9798.t2 is derived from g6974.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9799.t1 is derived from g6975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43742624	43743853	.	-	.	Phchi.S1G695800
Phchi.S1	AUGUSTUS	transcript	43742624	43743853	.	-	.	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	stop_codon	43742621	43742623	.	-	0	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	CDS	43742624	43743148	0.99	-	0	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	exon	43742624	43743148	.	-	.	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	intron	43743149	43743270	.	-	.	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	CDS	43743271	43743506	0.95	-	2	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	exon	43743271	43743506	.	-	.	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	intron	43743507	43743645	.	-	.	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	CDS	43743646	43743853	1	-	0	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	exon	43743646	43743853	.	-	.	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
Phchi.S1	AUGUSTUS	start_codon	43743851	43743853	.	-	0	transcript_id "Phchi.S1G695800.t1"; gene_id "Phchi.S1G695800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4355.t1 is derived from g1524.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9977650	9979325	.	-	.	Phchi.S1G151400
Phchi.S1	AUGUSTUS	transcript	9977650	9979325	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	stop_codon	9977647	9977649	.	-	0	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9977650	9977752	0.52	-	1	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9977650	9977752	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9977753	9977894	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9977895	9977988	0.58	-	2	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9977895	9977988	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9977989	9978177	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9978178	9978303	0.98	-	2	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9978178	9978303	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9978304	9978394	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9978395	9978440	0.67	-	0	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9978395	9978440	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9978441	9978522	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9978523	9978600	0.99	-	0	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9978523	9978600	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9978601	9978680	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9978681	9978770	0.99	-	0	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9978681	9978770	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9978771	9978856	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9978857	9979049	0.73	-	1	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9978857	9979049	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	intron	9979050	9979221	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	CDS	9979222	9979325	0.91	-	0	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	exon	9979222	9979325	.	-	.	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
Phchi.S1	AUGUSTUS	start_codon	9979323	9979325	.	-	0	transcript_id "Phchi.S1G151400.t1"; gene_id "Phchi.S1G151400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4270.t1 is derived from g1439.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9330033	9334020	.	+	.	Phchi.S1G142900
Phchi.S1	AUGUSTUS	transcript	9330033	9334020	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	start_codon	9330033	9330035	.	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9330033	9330347	0.52	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9330033	9330347	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	intron	9330348	9330435	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9330436	9330621	1	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9330436	9330621	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	intron	9330622	9330708	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9330709	9330975	0.86	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9330709	9330975	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	intron	9330976	9331056	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9331057	9331151	0.34	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9331057	9331151	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	intron	9331152	9331232	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9331233	9331716	0.56	+	1	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9331233	9331716	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	intron	9331717	9331835	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9331836	9332397	0.98	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9331836	9332397	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	intron	9332398	9332485	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	CDS	9332486	9334020	0.99	+	2	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	exon	9332486	9334020	.	+	.	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
Phchi.S1	AUGUSTUS	stop_codon	9334021	9334023	.	+	0	transcript_id "Phchi.S1G142900.t1"; gene_id "Phchi.S1G142900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7923.t1 is derived from g5097.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31921768	31924003	.	-	.	Phchi.S1G508200
Phchi.S1	AUGUSTUS	transcript	31921768	31924003	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	stop_codon	31921765	31921767	.	-	0	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31921768	31921971	1	-	0	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31921768	31921971	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31921972	31922063	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31922064	31922227	1	-	2	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31922064	31922227	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31922228	31922327	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31922328	31922478	1	-	0	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31922328	31922478	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31922479	31922580	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31922581	31922924	0.98	-	2	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31922581	31922924	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31922925	31923016	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31923017	31923110	1	-	0	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31923017	31923110	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31923111	31923216	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31923217	31923502	0.7	-	1	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31923217	31923502	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31923503	31923630	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31923631	31923735	0.28	-	1	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31923631	31923735	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31923736	31923840	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31923841	31923913	0.17	-	2	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31923841	31923913	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	intron	31923914	31923981	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	CDS	31923982	31924003	0.22	-	0	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	exon	31923982	31924003	.	-	.	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
Phchi.S1	AUGUSTUS	start_codon	31924001	31924003	.	-	0	transcript_id "Phchi.S1G508200.t1"; gene_id "Phchi.S1G508200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14319.t1 is derived from g12786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12079869	12081559	.	+	.	Phchi.S3G163800
Phchi.S3	AUGUSTUS	transcript	12079869	12081559	.	+	.	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	start_codon	12079869	12079871	.	+	0	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	CDS	12079869	12080030	1	+	0	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	exon	12079869	12080030	.	+	.	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	intron	12080031	12080152	.	+	.	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	CDS	12080153	12081559	0.59	+	0	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	exon	12080153	12081559	.	+	.	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
Phchi.S3	AUGUSTUS	stop_codon	12081560	12081562	.	+	0	transcript_id "Phchi.S3G163800.t1"; gene_id "Phchi.S3G163800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5016.t1 is derived from g2186.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14079724	14081346	.	-	.	Phchi.S1G217500
Phchi.S1	AUGUSTUS	transcript	14079724	14081346	.	-	.	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	stop_codon	14079721	14079723	.	-	0	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	CDS	14079724	14079906	1	-	0	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	exon	14079724	14079906	.	-	.	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	intron	14079907	14080105	.	-	.	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	CDS	14080106	14081071	0.35	-	0	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	exon	14080106	14081071	.	-	.	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	intron	14081072	14081214	.	-	.	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	CDS	14081215	14081346	0.65	-	0	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	exon	14081215	14081346	.	-	.	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
Phchi.S1	AUGUSTUS	start_codon	14081344	14081346	.	-	0	transcript_id "Phchi.S1G217500.t1"; gene_id "Phchi.S1G217500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15496.t1 is derived from g13965.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19513676	19514289	.	+	.	Phchi.S3G281500
Phchi.S3	AUGUSTUS	transcript	19513676	19514289	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	start_codon	19513676	19513678	.	+	0	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	CDS	19513676	19513802	0.72	+	0	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	exon	19513676	19513802	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	intron	19513803	19513947	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	CDS	19513948	19513955	0.71	+	2	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	exon	19513948	19513955	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	intron	19513956	19514076	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	CDS	19514077	19514107	0.75	+	0	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	exon	19514077	19514107	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	intron	19514108	19514257	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	CDS	19514258	19514289	0.85	+	2	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	exon	19514258	19514289	.	+	.	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
Phchi.S3	AUGUSTUS	stop_codon	19514290	19514292	.	+	0	transcript_id "Phchi.S3G281500.t1"; gene_id "Phchi.S3G281500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10761.t1 is derived from g14811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1989307	1990766	.	-	.	Phchi.S4G034300
Phchi.S4	AUGUSTUS	transcript	1989307	1990766	.	-	.	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	stop_codon	1989304	1989306	.	-	0	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	CDS	1989307	1990224	0.9	-	0	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	exon	1989307	1990224	.	-	.	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	intron	1990225	1990330	.	-	.	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	CDS	1990331	1990370	0.48	-	1	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	exon	1990331	1990370	.	-	.	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	intron	1990371	1990449	.	-	.	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	CDS	1990450	1990766	0.39	-	0	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	exon	1990450	1990766	.	-	.	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
Phchi.S4	AUGUSTUS	start_codon	1990764	1990766	.	-	0	transcript_id "Phchi.S4G034300.t1"; gene_id "Phchi.S4G034300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10736.t1 is derived from g14786.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1843605	1844641	.	+	.	Phchi.S4G031800
Phchi.S4	AUGUSTUS	transcript	1843605	1844641	.	+	.	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	start_codon	1843605	1843607	.	+	0	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	CDS	1843605	1843733	1	+	0	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	exon	1843605	1843733	.	+	.	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	intron	1843734	1844004	.	+	.	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	CDS	1844005	1844136	1	+	0	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	exon	1844005	1844136	.	+	.	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	intron	1844137	1844323	.	+	.	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	CDS	1844324	1844641	1	+	0	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	exon	1844324	1844641	.	+	.	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
Phchi.S4	AUGUSTUS	stop_codon	1844642	1844644	.	+	0	transcript_id "Phchi.S4G031800.t1"; gene_id "Phchi.S4G031800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1201.t1 is derived from g10984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8388625	8389743	.	+	.	Phchi.S6G116000
Phchi.S6	AUGUSTUS	transcript	8388625	8389743	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	start_codon	8388625	8388627	.	+	0	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	CDS	8388625	8388682	0.77	+	0	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	exon	8388625	8388682	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	intron	8388683	8388780	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	CDS	8388781	8388831	1	+	2	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	exon	8388781	8388831	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	intron	8388832	8389012	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	CDS	8389013	8389183	1	+	2	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	exon	8389013	8389183	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	intron	8389184	8389267	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	CDS	8389268	8389743	0.95	+	2	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	exon	8389268	8389743	.	+	.	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
Phchi.S6	AUGUSTUS	stop_codon	8389744	8389746	.	+	0	transcript_id "Phchi.S6G116000.t1"; gene_id "Phchi.S6G116000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9751.t1 is derived from g6927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43500313	43506381	.	-	.	Phchi.S1G691000
Phchi.S1	AUGUSTUS	transcript	43500313	43506381	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	stop_codon	43500310	43500312	.	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43500313	43500416	1	-	2	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43500313	43500416	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43500417	43500509	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43500510	43500749	0.99	-	2	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43500510	43500749	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43500750	43500851	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43500852	43500915	0.99	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43500852	43500915	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43500916	43501002	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43501003	43501308	1	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43501003	43501308	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43501309	43501400	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43501401	43501615	1	-	2	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43501401	43501615	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43501616	43501715	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43501716	43502010	0.98	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43501716	43502010	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43502011	43502123	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43502124	43502288	0.99	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43502124	43502288	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43502289	43502392	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43502393	43502854	0.58	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43502393	43502854	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43502855	43502982	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43502983	43503120	0.88	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43502983	43503120	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43503121	43503224	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43503225	43503311	0.96	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43503225	43503311	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43503312	43503404	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43503405	43503656	1	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43503405	43503656	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43503657	43503818	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43503819	43503887	1	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43503819	43503887	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43503888	43504135	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43504136	43506276	0.98	-	2	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43504136	43506276	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	intron	43506277	43506374	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	CDS	43506375	43506381	1	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	exon	43506375	43506381	.	-	.	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
Phchi.S1	AUGUSTUS	start_codon	43506379	43506381	.	-	0	transcript_id "Phchi.S1G691000.t1"; gene_id "Phchi.S1G691000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6055.t1 is derived from g3226.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20654191	20655223	.	+	.	Phchi.S1G321400
Phchi.S1	AUGUSTUS	transcript	20654191	20655223	.	+	.	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	start_codon	20654191	20654193	.	+	0	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	CDS	20654191	20654646	0.67	+	0	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	exon	20654191	20654646	.	+	.	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	intron	20654647	20654733	.	+	.	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	CDS	20654734	20654951	0.95	+	0	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	exon	20654734	20654951	.	+	.	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	intron	20654952	20655039	.	+	.	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	CDS	20655040	20655223	1	+	1	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	exon	20655040	20655223	.	+	.	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
Phchi.S1	AUGUSTUS	stop_codon	20655224	20655226	.	+	0	transcript_id "Phchi.S1G321400.t1"; gene_id "Phchi.S1G321400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2242.t1 is derived from g9162.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5614267	5618052	.	-	.	Phchi.S5G085100
Phchi.S5	AUGUSTUS	transcript	5614267	5618052	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	stop_codon	5614264	5614266	.	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5614267	5614548	0.93	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5614267	5614548	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5614549	5614646	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5614647	5614700	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5614647	5614700	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5614701	5614878	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5614879	5615025	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5614879	5615025	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5615026	5615102	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5615103	5615171	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5615103	5615171	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5615172	5615264	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5615265	5615452	1	-	2	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5615265	5615452	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5615453	5615533	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5615534	5615656	1	-	2	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5615534	5615656	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5615657	5615748	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5615749	5615809	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5615749	5615809	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5615810	5615890	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5615891	5616004	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5615891	5616004	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5616005	5616087	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5616088	5616195	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5616088	5616195	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5616196	5616281	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5616282	5616432	1	-	1	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5616282	5616432	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5616433	5616560	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5616561	5616709	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5616561	5616709	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5616710	5616853	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5616854	5616935	1	-	1	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5616854	5616935	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5616936	5617023	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5617024	5617046	1	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5617024	5617046	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5617047	5617168	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5617169	5617248	0.98	-	2	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5617169	5617248	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5617249	5617349	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5617350	5617461	0.98	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5617350	5617461	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	intron	5617462	5617572	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	CDS	5617573	5618052	0.98	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	exon	5617573	5618052	.	-	.	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
Phchi.S5	AUGUSTUS	start_codon	5618050	5618052	.	-	0	transcript_id "Phchi.S5G085100.t1"; gene_id "Phchi.S5G085100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11206.t1 is derived from g15256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4724442	4725524	.	-	.	Phchi.S4G078800
Phchi.S4	AUGUSTUS	transcript	4724442	4725524	.	-	.	transcript_id "Phchi.S4G078800.t1"; gene_id "Phchi.S4G078800"
Phchi.S4	AUGUSTUS	stop_codon	4724439	4724441	.	-	0	transcript_id "Phchi.S4G078800.t1"; gene_id "Phchi.S4G078800"
Phchi.S4	AUGUSTUS	CDS	4724442	4725524	0.33	-	0	transcript_id "Phchi.S4G078800.t1"; gene_id "Phchi.S4G078800"
Phchi.S4	AUGUSTUS	exon	4724442	4725524	.	-	.	transcript_id "Phchi.S4G078800.t1"; gene_id "Phchi.S4G078800"
Phchi.S4	AUGUSTUS	start_codon	4725522	4725524	.	-	0	transcript_id "Phchi.S4G078800.t1"; gene_id "Phchi.S4G078800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8328.t1 is derived from g5503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35334335	35336036	.	+	.	Phchi.S1G548700
Phchi.S1	AUGUSTUS	transcript	35334335	35336036	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	start_codon	35334335	35334337	.	+	0	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35334335	35334482	0.83	+	0	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35334335	35334482	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35334483	35334579	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35334580	35334664	1	+	2	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35334580	35334664	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35334665	35334818	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35334819	35334887	1	+	1	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35334819	35334887	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35334888	35334970	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35334971	35335083	1	+	1	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35334971	35335083	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35335084	35335198	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35335199	35335310	1	+	2	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35335199	35335310	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35335311	35335401	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35335402	35335545	1	+	1	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35335402	35335545	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35335546	35335633	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35335634	35335808	0.85	+	1	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35335634	35335808	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	intron	35335809	35335913	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	CDS	35335914	35336036	0.95	+	0	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	exon	35335914	35336036	.	+	.	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
Phchi.S1	AUGUSTUS	stop_codon	35336037	35336039	.	+	0	transcript_id "Phchi.S1G548700.t1"; gene_id "Phchi.S1G548700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6549.t1 is derived from g3721.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23583881	23588044	.	+	.	Phchi.S1G370800
Phchi.S1	AUGUSTUS	transcript	23583881	23588044	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	start_codon	23583881	23583883	.	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23583881	23583954	0.58	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23583881	23583954	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23583955	23584045	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23584046	23584222	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23584046	23584222	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23584223	23584316	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23584317	23584388	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23584317	23584388	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23584389	23584478	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23584479	23584550	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23584479	23584550	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23584551	23584631	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23584632	23584700	0.97	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23584632	23584700	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23584701	23584812	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23584813	23584884	0.94	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23584813	23584884	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23584885	23585038	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23585039	23585059	0.94	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23585039	23585059	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23585060	23585151	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23585152	23585223	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23585152	23585223	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23585224	23585319	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23585320	23585391	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23585320	23585391	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23585392	23585485	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23585486	23585554	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23585486	23585554	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23585555	23585667	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23585668	23585718	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23585668	23585718	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23585719	23585831	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23585832	23585911	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23585832	23585911	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23585912	23586051	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23586052	23586061	0.97	+	2	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23586052	23586061	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23586062	23586245	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23586246	23586325	0.94	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23586246	23586325	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23586326	23586422	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23586423	23586706	1	+	2	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23586423	23586706	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23586707	23586788	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23586789	23586840	1	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23586789	23586840	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23586841	23586935	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23586936	23587027	1	+	2	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23586936	23587027	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23587028	23587114	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23587115	23587260	1	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23587115	23587260	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23587261	23587351	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23587352	23587496	1	+	1	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23587352	23587496	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23587497	23587576	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23587577	23587723	0.94	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23587577	23587723	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	intron	23587724	23587828	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	CDS	23587829	23588044	0.92	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	exon	23587829	23588044	.	+	.	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
Phchi.S1	AUGUSTUS	stop_codon	23588045	23588047	.	+	0	transcript_id "Phchi.S1G370800.t1"; gene_id "Phchi.S1G370800"
# This transcript jg14162.t2 is derived from g12628.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14163.t1 is derived from g12630.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11229723	11231149	.	+	.	Phchi.S3G148200
Phchi.S3	AUGUSTUS	transcript	11229723	11231149	.	+	.	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	start_codon	11229723	11229725	.	+	0	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	CDS	11229723	11230136	0.47	+	0	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	exon	11229723	11230136	.	+	.	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	intron	11230137	11230207	.	+	.	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	CDS	11230208	11230902	0.28	+	0	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	exon	11230208	11230902	.	+	.	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	intron	11230903	11231052	.	+	.	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	CDS	11231053	11231149	0.53	+	1	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	exon	11231053	11231149	.	+	.	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
Phchi.S3	AUGUSTUS	stop_codon	11231150	11231152	.	+	0	transcript_id "Phchi.S3G148200.t1"; gene_id "Phchi.S3G148200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1714.t1 is derived from g8634.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2666385	2669297	.	-	.	Phchi.S5G032300
Phchi.S5	AUGUSTUS	transcript	2666385	2669297	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	stop_codon	2666382	2666384	.	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2666385	2667074	1	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2666385	2667074	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667075	2667149	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667150	2667281	1	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667150	2667281	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667282	2667380	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667381	2667482	1	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667381	2667482	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667483	2667566	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667567	2667712	1	-	2	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667567	2667712	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667713	2667925	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667926	2668255	1	-	2	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667926	2668255	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2668256	2668351	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2668352	2668835	0.99	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2668352	2668835	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2668836	2668918	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2668919	2669009	1	-	1	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2668919	2669009	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2669010	2669103	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2669104	2669297	0.91	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2669104	2669297	.	-	.	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	start_codon	2669295	2669297	.	-	0	transcript_id "Phchi.S5G032300.t1"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	transcript	2666385	2669297	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	stop_codon	2666382	2666384	.	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2666385	2667074	1	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2666385	2667074	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667075	2667149	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667150	2667281	1	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667150	2667281	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667282	2667380	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667381	2667482	1	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667381	2667482	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667483	2667566	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667567	2667744	1	-	1	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667567	2667744	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2667745	2667925	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2667926	2668001	1	-	2	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2667926	2668001	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2668002	2668075	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2668076	2668255	0.88	-	2	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2668076	2668255	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2668256	2668351	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2668352	2668835	1	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2668352	2668835	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2668836	2668918	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2668919	2669009	1	-	1	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2668919	2669009	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	intron	2669010	2669103	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	CDS	2669104	2669297	0.94	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	exon	2669104	2669297	.	-	.	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
Phchi.S5	AUGUSTUS	start_codon	2669295	2669297	.	-	0	transcript_id "Phchi.S5G032300.t2"; gene_id "Phchi.S5G032300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12491.t1 is derived from g8168.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	29293467	29294330	.	+	.	Phchi.S2G057100
Phchi.S2	AUGUSTUS	transcript	29293467	29294330	.	+	.	transcript_id "Phchi.S2G057100.t1"; gene_id "Phchi.S2G057100"
Phchi.S2	AUGUSTUS	start_codon	29293467	29293469	.	+	0	transcript_id "Phchi.S2G057100.t1"; gene_id "Phchi.S2G057100"
Phchi.S2	AUGUSTUS	CDS	29293467	29294330	0.47	+	0	transcript_id "Phchi.S2G057100.t1"; gene_id "Phchi.S2G057100"
Phchi.S2	AUGUSTUS	exon	29293467	29294330	.	+	.	transcript_id "Phchi.S2G057100.t1"; gene_id "Phchi.S2G057100"
Phchi.S2	AUGUSTUS	stop_codon	29294331	29294333	.	+	0	transcript_id "Phchi.S2G057100.t1"; gene_id "Phchi.S2G057100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1227.t1 is derived from g11010.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8499375	8503807	.	+	.	Phchi.S6G118600
Phchi.S6	AUGUSTUS	transcript	8499375	8503807	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	start_codon	8499375	8499377	.	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8499375	8499444	0.92	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8499375	8499444	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8499445	8499541	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8499542	8499678	0.87	+	2	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8499542	8499678	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8499679	8499784	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8499785	8499929	0.93	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8499785	8499929	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8499930	8500079	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500080	8500290	1	+	2	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500080	8500290	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500291	8500450	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500451	8500529	1	+	1	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500451	8500529	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500530	8500623	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500624	8500709	1	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500624	8500709	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500710	8500833	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500834	8500957	1	+	1	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500834	8500957	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500958	8501035	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8501036	8501068	1	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8501036	8501068	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8501069	8501187	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8501188	8501460	1	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8501188	8501460	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8501461	8501730	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8501731	8501999	1	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8501731	8501999	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502000	8502098	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502099	8502158	1	+	1	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502099	8502158	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502159	8502268	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502269	8502336	1	+	1	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502269	8502336	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502337	8502459	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502460	8502565	1	+	2	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502460	8502565	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502566	8502674	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502675	8502816	0.96	+	1	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502675	8502816	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502817	8502904	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502905	8503003	0.99	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502905	8503003	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8503004	8503112	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8503113	8503377	0.99	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8503113	8503377	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8503378	8503461	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8503462	8503529	1	+	2	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8503462	8503529	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8503530	8503636	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8503637	8503807	0.93	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8503637	8503807	.	+	.	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	stop_codon	8503808	8503810	.	+	0	transcript_id "Phchi.S6G118600.t1"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	transcript	8499375	8503807	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	start_codon	8499375	8499377	.	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8499375	8499444	0.92	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8499375	8499444	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8499445	8499541	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8499542	8499678	0.83	+	2	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8499542	8499678	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8499679	8499784	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8499785	8499968	0.54	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8499785	8499968	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8499969	8500079	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500080	8500290	0.91	+	2	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500080	8500290	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500291	8500450	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500451	8500529	1	+	1	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500451	8500529	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500530	8500623	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500624	8500709	1	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500624	8500709	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500710	8500833	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8500834	8500957	1	+	1	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8500834	8500957	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8500958	8501035	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8501036	8501068	1	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8501036	8501068	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8501069	8501187	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8501188	8501460	1	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8501188	8501460	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8501461	8501730	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8501731	8501999	1	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8501731	8501999	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502000	8502098	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502099	8502158	1	+	1	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502099	8502158	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502159	8502268	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502269	8502336	1	+	1	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502269	8502336	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502337	8502459	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502460	8502565	1	+	2	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502460	8502565	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502566	8502674	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502675	8502816	0.98	+	1	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502675	8502816	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8502817	8502904	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8502905	8503003	0.99	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8502905	8503003	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8503004	8503112	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8503113	8503377	0.99	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8503113	8503377	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8503378	8503461	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8503462	8503529	0.98	+	2	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8503462	8503529	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	intron	8503530	8503636	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	CDS	8503637	8503807	0.94	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	exon	8503637	8503807	.	+	.	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
Phchi.S6	AUGUSTUS	stop_codon	8503808	8503810	.	+	0	transcript_id "Phchi.S6G118600.t2"; gene_id "Phchi.S6G118600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1302.t1 is derived from g11085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8915112	8915402	.	+	.	Phchi.S6G126100
Phchi.S6	AUGUSTUS	transcript	8915112	8915402	.	+	.	transcript_id "Phchi.S6G126100.t1"; gene_id "Phchi.S6G126100"
Phchi.S6	AUGUSTUS	start_codon	8915112	8915114	.	+	0	transcript_id "Phchi.S6G126100.t1"; gene_id "Phchi.S6G126100"
Phchi.S6	AUGUSTUS	CDS	8915112	8915402	0.5	+	0	transcript_id "Phchi.S6G126100.t1"; gene_id "Phchi.S6G126100"
Phchi.S6	AUGUSTUS	exon	8915112	8915402	.	+	.	transcript_id "Phchi.S6G126100.t1"; gene_id "Phchi.S6G126100"
Phchi.S6	AUGUSTUS	stop_codon	8915403	8915405	.	+	0	transcript_id "Phchi.S6G126100.t1"; gene_id "Phchi.S6G126100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1198.t1 is derived from g10981.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8380749	8381809	.	-	.	Phchi.S6G115700
Phchi.S6	AUGUSTUS	transcript	8380749	8381809	.	-	.	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	stop_codon	8380746	8380748	.	-	0	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	CDS	8380749	8380898	0.76	-	0	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	exon	8380749	8380898	.	-	.	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	intron	8380899	8381057	.	-	.	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	CDS	8381058	8381176	0.77	-	2	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	exon	8381058	8381176	.	-	.	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	intron	8381177	8381256	.	-	.	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	CDS	8381257	8381809	0.94	-	0	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	exon	8381257	8381809	.	-	.	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
Phchi.S6	AUGUSTUS	start_codon	8381807	8381809	.	-	0	transcript_id "Phchi.S6G115700.t1"; gene_id "Phchi.S6G115700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10335.t1 is derived from g7511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47228463	47231993	.	+	.	Phchi.S1G749400
Phchi.S1	AUGUSTUS	transcript	47228463	47231993	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	start_codon	47228463	47228465	.	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47228463	47228768	0.99	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47228463	47228768	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47228769	47228841	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47228842	47228854	0.99	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47228842	47228854	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47228855	47229010	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47229011	47229096	0.93	+	2	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47229011	47229096	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47229097	47229225	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47229226	47229375	1	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47229226	47229375	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47229376	47229462	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47229463	47229521	0.5	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47229463	47229521	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47229522	47229824	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47229825	47229849	0.51	+	1	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47229825	47229849	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47229850	47229934	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47229935	47230015	1	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47229935	47230015	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47230016	47230099	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47230100	47230130	0.9	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47230100	47230130	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47230131	47230671	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47230672	47230759	0.48	+	2	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47230672	47230759	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47230760	47231129	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47231130	47231228	1	+	1	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47231130	47231228	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47231229	47231351	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47231352	47231460	1	+	1	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47231352	47231460	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47231461	47231581	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47231582	47231653	1	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47231582	47231653	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47231654	47231780	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47231781	47231786	1	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47231781	47231786	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	intron	47231787	47231879	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	CDS	47231880	47231993	1	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	exon	47231880	47231993	.	+	.	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
Phchi.S1	AUGUSTUS	stop_codon	47231994	47231996	.	+	0	transcript_id "Phchi.S1G749400.t1"; gene_id "Phchi.S1G749400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8656.t1 is derived from g5831.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37290631	37292883	.	-	.	Phchi.S1G581500
Phchi.S1	AUGUSTUS	transcript	37290631	37292883	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	stop_codon	37290628	37290630	.	-	0	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37290631	37290697	0.98	-	1	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37290631	37290697	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37290698	37290777	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37290778	37290834	0.94	-	1	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37290778	37290834	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37290835	37290922	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37290923	37291057	0.54	-	1	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37290923	37291057	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37291058	37291153	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37291154	37291521	1	-	0	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37291154	37291521	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37291522	37291682	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37291683	37291970	1	-	0	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37291683	37291970	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37291971	37292111	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37292112	37292370	1	-	1	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37292112	37292370	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37292371	37292494	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37292495	37292883	1	-	0	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37292495	37292883	.	-	.	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	start_codon	37292881	37292883	.	-	0	transcript_id "Phchi.S1G581500.t1"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	transcript	37290631	37292883	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	stop_codon	37290628	37290630	.	-	0	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37290631	37290697	0.97	-	1	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37290631	37290697	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37290698	37290777	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37290778	37290834	0.93	-	1	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37290778	37290834	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37290835	37290922	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37290923	37291057	0.51	-	1	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37290923	37291057	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37291058	37291153	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37291154	37291521	1	-	0	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37291154	37291521	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37291522	37291682	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37291683	37291976	1	-	0	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37291683	37291976	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37291977	37292111	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37292112	37292370	1	-	1	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37292112	37292370	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	intron	37292371	37292494	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	CDS	37292495	37292883	1	-	0	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	exon	37292495	37292883	.	-	.	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
Phchi.S1	AUGUSTUS	start_codon	37292881	37292883	.	-	0	transcript_id "Phchi.S1G581500.t2"; gene_id "Phchi.S1G581500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10774.t1 is derived from g14824.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2052073	2054670	.	+	.	Phchi.S4G035600
Phchi.S4	AUGUSTUS	transcript	2052073	2054670	.	+	.	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	start_codon	2052073	2052075	.	+	0	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	CDS	2052073	2053921	0.36	+	0	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	exon	2052073	2053921	.	+	.	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	intron	2053922	2054266	.	+	.	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	CDS	2054267	2054670	0.8	+	2	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	exon	2054267	2054670	.	+	.	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
Phchi.S4	AUGUSTUS	stop_codon	2054671	2054673	.	+	0	transcript_id "Phchi.S4G035600.t1"; gene_id "Phchi.S4G035600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3433.t1 is derived from g602.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3617810	3619367	.	+	.	Phchi.S1G059200
Phchi.S1	AUGUSTUS	transcript	3617810	3619367	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	start_codon	3617810	3617812	.	+	0	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3617810	3617901	0.84	+	0	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3617810	3617901	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	intron	3617902	3617998	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3617999	3618016	1	+	1	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3617999	3618016	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	intron	3618017	3618145	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3618146	3618376	0.71	+	1	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3618146	3618376	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	intron	3618377	3618590	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3618591	3618680	0.81	+	1	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3618591	3618680	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	intron	3618681	3618774	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3618775	3619024	0.78	+	1	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3618775	3619024	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	intron	3619025	3619114	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3619115	3619165	0.59	+	0	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3619115	3619165	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	intron	3619166	3619277	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	CDS	3619278	3619367	0.39	+	0	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	exon	3619278	3619367	.	+	.	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
Phchi.S1	AUGUSTUS	stop_codon	3619368	3619370	.	+	0	transcript_id "Phchi.S1G059200.t1"; gene_id "Phchi.S1G059200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4376.t1 is derived from g1545.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10125015	10125549	.	+	.	Phchi.S1G153500
Phchi.S1	AUGUSTUS	transcript	10125015	10125549	.	+	.	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	start_codon	10125015	10125017	.	+	0	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	CDS	10125015	10125093	0.25	+	0	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	exon	10125015	10125093	.	+	.	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	intron	10125094	10125193	.	+	.	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	CDS	10125194	10125549	0.27	+	2	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	exon	10125194	10125549	.	+	.	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
Phchi.S1	AUGUSTUS	stop_codon	10125550	10125552	.	+	0	transcript_id "Phchi.S1G153500.t1"; gene_id "Phchi.S1G153500"
# This transcript jg9892.t2 is derived from g7068.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9893.t1 is derived from g7069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44312210	44314660	.	+	.	Phchi.S1G705200
Phchi.S1	AUGUSTUS	transcript	44312210	44314660	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	start_codon	44312210	44312212	.	+	0	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	CDS	44312210	44313619	0.59	+	0	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	exon	44312210	44313619	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	intron	44313620	44313726	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	CDS	44313727	44313957	0.94	+	0	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	exon	44313727	44313957	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	intron	44313958	44314049	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	CDS	44314050	44314487	1	+	0	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	exon	44314050	44314487	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	intron	44314488	44314573	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	CDS	44314574	44314660	1	+	0	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	exon	44314574	44314660	.	+	.	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
Phchi.S1	AUGUSTUS	stop_codon	44314661	44314663	.	+	0	transcript_id "Phchi.S1G705200.t1"; gene_id "Phchi.S1G705200"
# This transcript jg6506.t2 is derived from g3678.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6507.t1 is derived from g3679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23363594	23367131	.	-	.	Phchi.S1G366600
Phchi.S1	AUGUSTUS	transcript	23363594	23367131	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	stop_codon	23363591	23363593	.	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23363594	23363697	0.63	-	2	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23363594	23363697	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23363698	23363800	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23363801	23364071	0.64	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23363801	23364071	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23364072	23364181	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23364182	23364691	0.99	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23364182	23364691	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23364692	23364788	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23364789	23364935	1	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23364789	23364935	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23364936	23365021	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23365022	23365307	1	-	1	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23365022	23365307	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23365308	23365399	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23365400	23365681	0.74	-	1	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23365400	23365681	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23365682	23365755	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23365756	23365793	0.83	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23365756	23365793	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23365794	23365886	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23365887	23366296	0.79	-	2	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23365887	23366296	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23366297	23366556	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23366557	23366758	0.92	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23366557	23366758	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23366759	23366862	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23366863	23366952	0.68	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23366863	23366952	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	intron	23366953	23367107	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	CDS	23367108	23367131	1	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	exon	23367108	23367131	.	-	.	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
Phchi.S1	AUGUSTUS	start_codon	23367129	23367131	.	-	0	transcript_id "Phchi.S1G366600.t1"; gene_id "Phchi.S1G366600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12656.t1 is derived from g14455.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	20492	21244	.	+	.	Phchi.C12G000600
Phchi.C12	AUGUSTUS	transcript	20492	21244	.	+	.	transcript_id "Phchi.C12G000600.t1"; gene_id "Phchi.C12G000600"
Phchi.C12	AUGUSTUS	start_codon	20492	20494	.	+	0	transcript_id "Phchi.C12G000600.t1"; gene_id "Phchi.C12G000600"
Phchi.C12	AUGUSTUS	CDS	20492	21244	0.78	+	0	transcript_id "Phchi.C12G000600.t1"; gene_id "Phchi.C12G000600"
Phchi.C12	AUGUSTUS	exon	20492	21244	.	+	.	transcript_id "Phchi.C12G000600.t1"; gene_id "Phchi.C12G000600"
Phchi.C12	AUGUSTUS	stop_codon	21245	21247	.	+	0	transcript_id "Phchi.C12G000600.t1"; gene_id "Phchi.C12G000600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg16010.t1 is derived from g14434.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C10	AUGUSTUS	gene	143498	144864	.	+	.	Phchi.C10G000800
Phchi.C10	AUGUSTUS	transcript	143498	144864	.	+	.	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	start_codon	143498	143500	.	+	0	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	CDS	143498	143588	0.62	+	0	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	exon	143498	143588	.	+	.	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	intron	143589	143668	.	+	.	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	CDS	143669	144864	0.75	+	2	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	exon	143669	144864	.	+	.	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
Phchi.C10	AUGUSTUS	stop_codon	144865	144867	.	+	0	transcript_id "Phchi.C10G000800.t1"; gene_id "Phchi.C10G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2122.t1 is derived from g9042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4950400	4951200	.	+	.	Phchi.S5G073100
Phchi.S5	AUGUSTUS	transcript	4950400	4951200	.	+	.	transcript_id "Phchi.S5G073100.t1"; gene_id "Phchi.S5G073100"
Phchi.S5	AUGUSTUS	start_codon	4950400	4950402	.	+	0	transcript_id "Phchi.S5G073100.t1"; gene_id "Phchi.S5G073100"
Phchi.S5	AUGUSTUS	CDS	4950400	4951200	0.9	+	0	transcript_id "Phchi.S5G073100.t1"; gene_id "Phchi.S5G073100"
Phchi.S5	AUGUSTUS	exon	4950400	4951200	.	+	.	transcript_id "Phchi.S5G073100.t1"; gene_id "Phchi.S5G073100"
Phchi.S5	AUGUSTUS	stop_codon	4951201	4951203	.	+	0	transcript_id "Phchi.S5G073100.t1"; gene_id "Phchi.S5G073100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2751.t1 is derived from g9671.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8618772	8620260	.	+	.	Phchi.S5G136000
Phchi.S5	AUGUSTUS	transcript	8618772	8620260	.	+	.	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	start_codon	8618772	8618774	.	+	0	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	CDS	8618772	8619871	0.59	+	0	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	exon	8618772	8619871	.	+	.	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	intron	8619872	8619947	.	+	.	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	CDS	8619948	8620008	0.22	+	1	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	exon	8619948	8620008	.	+	.	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	intron	8620009	8620176	.	+	.	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	CDS	8620177	8620260	0.41	+	0	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	exon	8620177	8620260	.	+	.	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
Phchi.S5	AUGUSTUS	stop_codon	8620261	8620263	.	+	0	transcript_id "Phchi.S5G136000.t1"; gene_id "Phchi.S5G136000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6982.t1 is derived from g4154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26263559	26265024	.	+	.	Phchi.S1G414100
Phchi.S1	AUGUSTUS	transcript	26263559	26265024	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	start_codon	26263559	26263561	.	+	0	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	CDS	26263559	26263720	0.56	+	0	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	exon	26263559	26263720	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	intron	26263721	26263845	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	CDS	26263846	26264119	1	+	0	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	exon	26263846	26264119	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	intron	26264120	26264246	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	CDS	26264247	26264380	1	+	2	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	exon	26264247	26264380	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	intron	26264381	26264475	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	CDS	26264476	26264623	1	+	0	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	exon	26264476	26264623	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	intron	26264624	26264764	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	CDS	26264765	26265024	0.52	+	2	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	exon	26264765	26265024	.	+	.	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
Phchi.S1	AUGUSTUS	stop_codon	26265025	26265027	.	+	0	transcript_id "Phchi.S1G414100.t1"; gene_id "Phchi.S1G414100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12319.t1 is derived from g7995.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	10426251	10426610	.	-	.	Phchi.S2G039900
Phchi.S2	AUGUSTUS	transcript	10426251	10426610	.	-	.	transcript_id "Phchi.S2G039900.t1"; gene_id "Phchi.S2G039900"
Phchi.S2	AUGUSTUS	stop_codon	10426248	10426250	.	-	0	transcript_id "Phchi.S2G039900.t1"; gene_id "Phchi.S2G039900"
Phchi.S2	AUGUSTUS	CDS	10426251	10426610	0.99	-	0	transcript_id "Phchi.S2G039900.t1"; gene_id "Phchi.S2G039900"
Phchi.S2	AUGUSTUS	exon	10426251	10426610	.	-	.	transcript_id "Phchi.S2G039900.t1"; gene_id "Phchi.S2G039900"
Phchi.S2	AUGUSTUS	start_codon	10426608	10426610	.	-	0	transcript_id "Phchi.S2G039900.t1"; gene_id "Phchi.S2G039900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5347.t1 is derived from g2517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16416592	16416876	.	-	.	Phchi.S1G250600
Phchi.S1	AUGUSTUS	transcript	16416592	16416876	.	-	.	transcript_id "Phchi.S1G250600.t1"; gene_id "Phchi.S1G250600"
Phchi.S1	AUGUSTUS	stop_codon	16416589	16416591	.	-	0	transcript_id "Phchi.S1G250600.t1"; gene_id "Phchi.S1G250600"
Phchi.S1	AUGUSTUS	CDS	16416592	16416876	0.82	-	0	transcript_id "Phchi.S1G250600.t1"; gene_id "Phchi.S1G250600"
Phchi.S1	AUGUSTUS	exon	16416592	16416876	.	-	.	transcript_id "Phchi.S1G250600.t1"; gene_id "Phchi.S1G250600"
Phchi.S1	AUGUSTUS	start_codon	16416874	16416876	.	-	0	transcript_id "Phchi.S1G250600.t1"; gene_id "Phchi.S1G250600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2834.t1 is derived from g9754.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	9098368	9099041	.	-	.	Phchi.S5G144300
Phchi.S5	AUGUSTUS	transcript	9098368	9099041	.	-	.	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	stop_codon	9098365	9098367	.	-	0	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	CDS	9098368	9098470	1	-	1	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	exon	9098368	9098470	.	-	.	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	intron	9098471	9098568	.	-	.	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	CDS	9098569	9098630	1	-	0	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	exon	9098569	9098630	.	-	.	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	intron	9098631	9098813	.	-	.	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	CDS	9098814	9099041	0.68	-	0	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	exon	9098814	9099041	.	-	.	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
Phchi.S5	AUGUSTUS	start_codon	9099039	9099041	.	-	0	transcript_id "Phchi.S5G144300.t1"; gene_id "Phchi.S5G144300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14631.t1 is derived from g13099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13841025	13841510	.	-	.	Phchi.S3G195000
Phchi.S3	AUGUSTUS	transcript	13841025	13841510	.	-	.	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	stop_codon	13841022	13841024	.	-	0	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	CDS	13841025	13841077	1	-	2	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	exon	13841025	13841077	.	-	.	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	intron	13841078	13841161	.	-	.	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	CDS	13841162	13841369	1	-	0	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	exon	13841162	13841369	.	-	.	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	intron	13841370	13841447	.	-	.	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	CDS	13841448	13841510	1	-	0	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	exon	13841448	13841510	.	-	.	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
Phchi.S3	AUGUSTUS	start_codon	13841508	13841510	.	-	0	transcript_id "Phchi.S3G195000.t1"; gene_id "Phchi.S3G195000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4557.t1 is derived from g1727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11106312	11107843	.	-	.	Phchi.S1G171600
Phchi.S1	AUGUSTUS	transcript	11106312	11107843	.	-	.	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	stop_codon	11106309	11106311	.	-	0	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	CDS	11106312	11106475	0.5	-	2	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	exon	11106312	11106475	.	-	.	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	intron	11106476	11106666	.	-	.	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	CDS	11106667	11106890	0.55	-	1	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	exon	11106667	11106890	.	-	.	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	intron	11106891	11107058	.	-	.	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	CDS	11107059	11107843	0.61	-	0	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	exon	11107059	11107843	.	-	.	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
Phchi.S1	AUGUSTUS	start_codon	11107841	11107843	.	-	0	transcript_id "Phchi.S1G171600.t1"; gene_id "Phchi.S1G171600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1727.t1 is derived from g8647.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2733946	2735683	.	+	.	Phchi.S5G033600
Phchi.S5	AUGUSTUS	transcript	2733946	2735683	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	start_codon	2733946	2733948	.	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2733946	2734182	0.99	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2733946	2734182	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	intron	2734183	2734283	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2734284	2734422	1	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2734284	2734422	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	intron	2734423	2734506	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2734507	2734678	1	+	2	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2734507	2734678	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	intron	2734679	2734761	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2734762	2734924	1	+	1	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2734762	2734924	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	intron	2734925	2735039	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2735040	2735258	0.78	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2735040	2735258	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	intron	2735259	2735365	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2735366	2735413	0.86	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2735366	2735413	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	intron	2735414	2735527	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	CDS	2735528	2735683	0.96	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	exon	2735528	2735683	.	+	.	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
Phchi.S5	AUGUSTUS	stop_codon	2735684	2735686	.	+	0	transcript_id "Phchi.S5G033600.t1"; gene_id "Phchi.S5G033600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14243.t1 is derived from g12710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11709617	11712038	.	+	.	Phchi.S3G156200
Phchi.S3	AUGUSTUS	transcript	11709617	11712038	.	+	.	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	start_codon	11709617	11709619	.	+	0	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	CDS	11709617	11710030	0.21	+	0	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	exon	11709617	11710030	.	+	.	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	intron	11710031	11711177	.	+	.	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	CDS	11711178	11711232	0.02	+	0	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	exon	11711178	11711232	.	+	.	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	intron	11711233	11712009	.	+	.	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	CDS	11712010	11712038	0.01	+	2	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	exon	11712010	11712038	.	+	.	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
Phchi.S3	AUGUSTUS	stop_codon	11712039	11712041	.	+	0	transcript_id "Phchi.S3G156200.t1"; gene_id "Phchi.S3G156200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10946.t1 is derived from g14996.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3223971	3224300	.	-	.	Phchi.S4G052800
Phchi.S4	AUGUSTUS	transcript	3223971	3224300	.	-	.	transcript_id "Phchi.S4G052800.t1"; gene_id "Phchi.S4G052800"
Phchi.S4	AUGUSTUS	stop_codon	3223968	3223970	.	-	0	transcript_id "Phchi.S4G052800.t1"; gene_id "Phchi.S4G052800"
Phchi.S4	AUGUSTUS	CDS	3223971	3224300	0.63	-	0	transcript_id "Phchi.S4G052800.t1"; gene_id "Phchi.S4G052800"
Phchi.S4	AUGUSTUS	exon	3223971	3224300	.	-	.	transcript_id "Phchi.S4G052800.t1"; gene_id "Phchi.S4G052800"
Phchi.S4	AUGUSTUS	start_codon	3224298	3224300	.	-	0	transcript_id "Phchi.S4G052800.t1"; gene_id "Phchi.S4G052800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15181.t1 is derived from g13649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17431938	17432803	.	+	.	Phchi.S3G250000
Phchi.S3	AUGUSTUS	transcript	17431938	17432803	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	start_codon	17431938	17431940	.	+	0	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	CDS	17431938	17431953	0.65	+	0	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	exon	17431938	17431953	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	intron	17431954	17432193	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	CDS	17432194	17432306	1	+	2	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	exon	17432194	17432306	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	intron	17432307	17432401	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	CDS	17432402	17432543	1	+	0	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	exon	17432402	17432543	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	intron	17432544	17432633	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	CDS	17432634	17432803	1	+	2	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	exon	17432634	17432803	.	+	.	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
Phchi.S3	AUGUSTUS	stop_codon	17432804	17432806	.	+	0	transcript_id "Phchi.S3G250000.t1"; gene_id "Phchi.S3G250000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4111.t1 is derived from g1280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7926053	7927334	.	+	.	Phchi.S1G127000
Phchi.S1	AUGUSTUS	transcript	7926053	7927334	.	+	.	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	start_codon	7926053	7926055	.	+	0	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	CDS	7926053	7927120	0.51	+	0	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	exon	7926053	7927120	.	+	.	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	intron	7927121	7927211	.	+	.	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	CDS	7927212	7927334	0.51	+	0	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	exon	7927212	7927334	.	+	.	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
Phchi.S1	AUGUSTUS	stop_codon	7927335	7927337	.	+	0	transcript_id "Phchi.S1G127000.t1"; gene_id "Phchi.S1G127000"
# This transcript jg2361.t2 is derived from g9281.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2362.t1 is derived from g9282.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6351164	6352409	.	-	.	Phchi.S5G097100
Phchi.S5	AUGUSTUS	transcript	6351164	6352409	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	stop_codon	6351161	6351163	.	-	0	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	CDS	6351164	6351478	1	-	0	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	exon	6351164	6351478	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	intron	6351479	6351555	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	CDS	6351556	6351620	1	-	2	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	exon	6351556	6351620	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	intron	6351621	6351699	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	CDS	6351700	6352247	1	-	1	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	exon	6351700	6352247	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	intron	6352248	6352320	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	CDS	6352321	6352409	0.76	-	0	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	exon	6352321	6352409	.	-	.	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
Phchi.S5	AUGUSTUS	start_codon	6352407	6352409	.	-	0	transcript_id "Phchi.S5G097100.t1"; gene_id "Phchi.S5G097100"
# This transcript jg7447.t2 is derived from g4619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7448.t1 is derived from g4620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29252960	29262468	.	+	.	Phchi.S1G460700
Phchi.S1	AUGUSTUS	transcript	29252960	29262468	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	start_codon	29252960	29252962	.	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29252960	29253121	0.35	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29252960	29253121	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29253122	29253610	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29253611	29253662	0.25	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29253611	29253662	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29253663	29253929	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29253930	29254160	0.6	+	2	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29253930	29254160	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29254161	29254316	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29254317	29254390	1	+	2	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29254317	29254390	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29254391	29254461	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29254462	29254530	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29254462	29254530	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29254531	29254608	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29254609	29254785	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29254609	29254785	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29254786	29254899	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29254900	29254966	0.4	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29254900	29254966	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29254967	29255187	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29255188	29255984	0.38	+	2	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29255188	29255984	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29255985	29256179	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29256180	29260459	0.97	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29256180	29260459	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29260460	29260549	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29260550	29260735	1	+	1	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29260550	29260735	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29260736	29260863	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29260864	29261221	1	+	1	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29260864	29261221	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29261222	29261313	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29261314	29261391	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29261314	29261391	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29261392	29261574	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29261575	29261676	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29261575	29261676	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29261677	29261755	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29261756	29261846	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29261756	29261846	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29261847	29261948	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29261949	29262037	0.98	+	2	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29261949	29262037	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29262038	29262224	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29262225	29262293	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29262225	29262293	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	intron	29262294	29262402	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	CDS	29262403	29262468	1	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	exon	29262403	29262468	.	+	.	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
Phchi.S1	AUGUSTUS	stop_codon	29262469	29262471	.	+	0	transcript_id "Phchi.S1G460700.t1"; gene_id "Phchi.S1G460700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg23.t1 is derived from g15992.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C64	AUGUSTUS	gene	49139	53111	.	-	.	Phchi.C64G000100
Phchi.C64	AUGUSTUS	transcript	49139	53111	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	stop_codon	49136	49138	.	-	0	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	49139	50065	0.92	-	0	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	49139	50065	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	50066	50176	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	50177	51846	1	-	2	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	50177	51846	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	51847	52013	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52014	52096	1	-	1	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52014	52096	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	52097	52203	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52204	52299	1	-	1	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52204	52299	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	52300	52541	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52542	52603	1	-	0	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52542	52603	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	52604	52826	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52827	53111	0.58	-	0	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52827	53111	.	-	.	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	start_codon	53109	53111	.	-	0	transcript_id "Phchi.C64G000100.t1"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	transcript	49139	53000	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	stop_codon	49136	49138	.	-	0	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	49139	50065	0.92	-	0	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	49139	50065	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	50066	50176	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	50177	51846	0.98	-	2	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	50177	51846	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	51847	52013	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52014	52096	1	-	1	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52014	52096	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	52097	52203	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52204	52299	1	-	1	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52204	52299	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	52300	52541	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52542	52603	1	-	0	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52542	52603	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	intron	52604	52775	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	CDS	52776	53000	0.53	-	0	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	exon	52776	53000	.	-	.	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
Phchi.C64	AUGUSTUS	start_codon	52998	53000	.	-	0	transcript_id "Phchi.C64G000100.t2"; gene_id "Phchi.C64G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4558.t1 is derived from g1728.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11111544	11112913	.	-	.	Phchi.S1G171700
Phchi.S1	AUGUSTUS	transcript	11111544	11112913	.	-	.	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	stop_codon	11111541	11111543	.	-	0	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	CDS	11111544	11111611	0.47	-	2	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	exon	11111544	11111611	.	-	.	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	intron	11111612	11111740	.	-	.	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	CDS	11111741	11112544	0.66	-	2	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	exon	11111741	11112544	.	-	.	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	intron	11112545	11112672	.	-	.	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	CDS	11112673	11112913	0.96	-	0	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	exon	11112673	11112913	.	-	.	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
Phchi.S1	AUGUSTUS	start_codon	11112911	11112913	.	-	0	transcript_id "Phchi.S1G171700.t1"; gene_id "Phchi.S1G171700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5273.t1 is derived from g2443.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15994195	15994833	.	+	.	Phchi.S1G243200
Phchi.S1	AUGUSTUS	transcript	15994195	15994833	.	+	.	transcript_id "Phchi.S1G243200.t1"; gene_id "Phchi.S1G243200"
Phchi.S1	AUGUSTUS	start_codon	15994195	15994197	.	+	0	transcript_id "Phchi.S1G243200.t1"; gene_id "Phchi.S1G243200"
Phchi.S1	AUGUSTUS	CDS	15994195	15994833	1	+	0	transcript_id "Phchi.S1G243200.t1"; gene_id "Phchi.S1G243200"
Phchi.S1	AUGUSTUS	exon	15994195	15994833	.	+	.	transcript_id "Phchi.S1G243200.t1"; gene_id "Phchi.S1G243200"
Phchi.S1	AUGUSTUS	stop_codon	15994834	15994836	.	+	0	transcript_id "Phchi.S1G243200.t1"; gene_id "Phchi.S1G243200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3882.t1 is derived from g1051.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6197260	6199193	.	+	.	Phchi.S1G104100
Phchi.S1	AUGUSTUS	transcript	6197260	6199193	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	start_codon	6197260	6197262	.	+	0	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	CDS	6197260	6197328	0.95	+	0	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	exon	6197260	6197328	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	intron	6197329	6197469	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	CDS	6197470	6197512	1	+	0	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	exon	6197470	6197512	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	intron	6197513	6197598	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	CDS	6197599	6197660	1	+	2	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	exon	6197599	6197660	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	intron	6197661	6197780	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	CDS	6197781	6197877	1	+	0	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	exon	6197781	6197877	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	intron	6197878	6197995	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	CDS	6197996	6198066	0.83	+	2	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	exon	6197996	6198066	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	intron	6198067	6198404	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	CDS	6198405	6199193	0.74	+	0	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	exon	6198405	6199193	.	+	.	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
Phchi.S1	AUGUSTUS	stop_codon	6199194	6199196	.	+	0	transcript_id "Phchi.S1G104100.t1"; gene_id "Phchi.S1G104100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1321.t1 is derived from g11104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	9012291	9016866	.	+	.	Phchi.S6G128000
Phchi.S6	AUGUSTUS	transcript	9012291	9016866	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	start_codon	9012291	9012293	.	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9012291	9012364	0.99	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9012291	9012364	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9012365	9012824	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9012825	9012966	1	+	1	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9012825	9012966	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9012967	9013056	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9013057	9013157	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9013057	9013157	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9013158	9013293	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9013294	9013342	1	+	1	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9013294	9013342	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9013343	9013472	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9013473	9013515	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9013473	9013515	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9013516	9013577	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9013578	9013583	1	+	2	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9013578	9013583	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9013584	9013770	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9013771	9013868	1	+	2	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9013771	9013868	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9013869	9014041	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9014042	9014118	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9014042	9014118	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9014119	9014232	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9014233	9014381	1	+	1	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9014233	9014381	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9014382	9014825	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9014826	9014885	1	+	2	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9014826	9014885	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9014886	9014999	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9015000	9015070	1	+	2	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9015000	9015070	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9015071	9015241	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9015242	9015334	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9015242	9015334	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9015335	9015582	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9015583	9015708	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9015583	9015708	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9015709	9015812	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9015813	9015868	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9015813	9015868	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9015869	9015958	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9015959	9016058	1	+	1	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9015959	9016058	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9016059	9016159	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9016160	9016268	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9016160	9016268	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9016269	9016349	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9016350	9016498	1	+	2	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9016350	9016498	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	intron	9016499	9016593	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	CDS	9016594	9016866	1	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	exon	9016594	9016866	.	+	.	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
Phchi.S6	AUGUSTUS	stop_codon	9016867	9016869	.	+	0	transcript_id "Phchi.S6G128000.t1"; gene_id "Phchi.S6G128000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10030.t1 is derived from g7206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45168153	45170963	.	-	.	Phchi.S1G718900
Phchi.S1	AUGUSTUS	transcript	45168153	45170963	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	stop_codon	45168150	45168152	.	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45168153	45168461	0.89	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45168153	45168461	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45168462	45168548	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45168549	45168725	1	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45168549	45168725	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45168726	45168812	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45168813	45168923	1	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45168813	45168923	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45168924	45169036	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45169037	45169106	0.95	-	1	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45169037	45169106	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45169107	45169256	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45169257	45169285	0.96	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45169257	45169285	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45169286	45169405	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45169406	45169465	1	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45169406	45169465	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45169466	45169562	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45169563	45169868	1	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45169563	45169868	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45169869	45169961	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45169962	45170105	1	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45169962	45170105	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45170106	45170193	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45170194	45170445	0.78	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45170194	45170445	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	intron	45170446	45170570	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	CDS	45170571	45170963	0.79	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	exon	45170571	45170963	.	-	.	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
Phchi.S1	AUGUSTUS	start_codon	45170961	45170963	.	-	0	transcript_id "Phchi.S1G718900.t1"; gene_id "Phchi.S1G718900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11880.t1 is derived from g15932.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8958345	8960012	.	+	.	Phchi.S4G146200
Phchi.S4	AUGUSTUS	transcript	8958345	8960012	.	+	.	transcript_id "Phchi.S4G146200.t1"; gene_id "Phchi.S4G146200"
Phchi.S4	AUGUSTUS	start_codon	8958345	8958347	.	+	0	transcript_id "Phchi.S4G146200.t1"; gene_id "Phchi.S4G146200"
Phchi.S4	AUGUSTUS	CDS	8958345	8960012	0.65	+	0	transcript_id "Phchi.S4G146200.t1"; gene_id "Phchi.S4G146200"
Phchi.S4	AUGUSTUS	exon	8958345	8960012	.	+	.	transcript_id "Phchi.S4G146200.t1"; gene_id "Phchi.S4G146200"
Phchi.S4	AUGUSTUS	stop_codon	8960013	8960015	.	+	0	transcript_id "Phchi.S4G146200.t1"; gene_id "Phchi.S4G146200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13509.t1 is derived from g11976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7237934	7238359	.	-	.	Phchi.S3G082800
Phchi.S3	AUGUSTUS	transcript	7237934	7238359	.	-	.	transcript_id "Phchi.S3G082800.t1"; gene_id "Phchi.S3G082800"
Phchi.S3	AUGUSTUS	stop_codon	7237931	7237933	.	-	0	transcript_id "Phchi.S3G082800.t1"; gene_id "Phchi.S3G082800"
Phchi.S3	AUGUSTUS	CDS	7237934	7238359	0.88	-	0	transcript_id "Phchi.S3G082800.t1"; gene_id "Phchi.S3G082800"
Phchi.S3	AUGUSTUS	exon	7237934	7238359	.	-	.	transcript_id "Phchi.S3G082800.t1"; gene_id "Phchi.S3G082800"
Phchi.S3	AUGUSTUS	start_codon	7238357	7238359	.	-	0	transcript_id "Phchi.S3G082800.t1"; gene_id "Phchi.S3G082800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2182.t1 is derived from g9102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5256610	5257723	.	-	.	Phchi.S5G079100
Phchi.S5	AUGUSTUS	transcript	5256610	5257723	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	stop_codon	5256607	5256609	.	-	0	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	CDS	5256610	5256726	0.53	-	0	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	exon	5256610	5256726	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	intron	5256727	5256913	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	CDS	5256914	5257017	0.27	-	2	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	exon	5256914	5257017	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	intron	5257018	5257161	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	CDS	5257162	5257250	0.42	-	1	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	exon	5257162	5257250	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	intron	5257251	5257324	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	CDS	5257325	5257412	0.99	-	2	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	exon	5257325	5257412	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	intron	5257413	5257608	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	CDS	5257609	5257723	0.34	-	0	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	exon	5257609	5257723	.	-	.	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
Phchi.S5	AUGUSTUS	start_codon	5257721	5257723	.	-	0	transcript_id "Phchi.S5G079100.t1"; gene_id "Phchi.S5G079100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14635.t1 is derived from g13103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13859062	13859511	.	+	.	Phchi.S3G195400
Phchi.S3	AUGUSTUS	transcript	13859062	13859511	.	+	.	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	start_codon	13859062	13859064	.	+	0	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	CDS	13859062	13859174	0.52	+	0	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	exon	13859062	13859174	.	+	.	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	intron	13859175	13859273	.	+	.	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	CDS	13859274	13859400	0.87	+	1	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	exon	13859274	13859400	.	+	.	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	intron	13859401	13859490	.	+	.	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	CDS	13859491	13859511	0.89	+	0	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	exon	13859491	13859511	.	+	.	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
Phchi.S3	AUGUSTUS	stop_codon	13859512	13859514	.	+	0	transcript_id "Phchi.S3G195400.t1"; gene_id "Phchi.S3G195400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9979.t1 is derived from g7155.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44765018	44767271	.	-	.	Phchi.S1G713800
Phchi.S1	AUGUSTUS	transcript	44765018	44767271	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	stop_codon	44765015	44765017	.	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44765018	44765764	0.99	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44765018	44765764	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	intron	44765765	44765847	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44765848	44766054	1	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44765848	44766054	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	intron	44766055	44766145	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44766146	44766308	1	-	1	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44766146	44766308	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	intron	44766309	44766590	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44766591	44766628	1	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44766591	44766628	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	intron	44766629	44766723	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44766724	44766792	1	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44766724	44766792	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	intron	44766793	44766984	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44766985	44767047	1	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44766985	44767047	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	intron	44767048	44767136	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	CDS	44767137	44767271	0.62	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	exon	44767137	44767271	.	-	.	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
Phchi.S1	AUGUSTUS	start_codon	44767269	44767271	.	-	0	transcript_id "Phchi.S1G713800.t1"; gene_id "Phchi.S1G713800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg60.t1 is derived from g9842.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	298963	301345	.	-	.	Phchi.S6G001900
Phchi.S6	AUGUSTUS	transcript	298963	301345	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	stop_codon	298960	298962	.	-	0	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	CDS	298963	299043	0.77	-	0	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	exon	298963	299043	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	intron	299044	299203	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	CDS	299204	299264	0.76	-	1	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	exon	299204	299264	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	intron	299265	299424	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	CDS	299425	299509	0.8	-	2	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	exon	299425	299509	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	intron	299510	299713	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	CDS	299714	300352	0.83	-	2	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	exon	299714	300352	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	intron	300353	300583	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	CDS	300584	300972	0.57	-	1	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	exon	300584	300972	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	intron	300973	301073	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	CDS	301074	301345	0.72	-	0	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	exon	301074	301345	.	-	.	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
Phchi.S6	AUGUSTUS	start_codon	301343	301345	.	-	0	transcript_id "Phchi.S6G001900.t1"; gene_id "Phchi.S6G001900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5083.t1 is derived from g2253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14602067	14602895	.	+	.	Phchi.S1G224200
Phchi.S1	AUGUSTUS	transcript	14602067	14602895	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	start_codon	14602067	14602069	.	+	0	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	CDS	14602067	14602383	0.71	+	0	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	exon	14602067	14602383	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	intron	14602384	14602513	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	CDS	14602514	14602548	0.9	+	1	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	exon	14602514	14602548	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	intron	14602549	14602682	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	CDS	14602683	14602750	0.88	+	2	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	exon	14602683	14602750	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	intron	14602751	14602886	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	CDS	14602887	14602895	0.89	+	0	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	exon	14602887	14602895	.	+	.	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
Phchi.S1	AUGUSTUS	stop_codon	14602896	14602898	.	+	0	transcript_id "Phchi.S1G224200.t1"; gene_id "Phchi.S1G224200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9172.t1 is derived from g6347.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40207076	40209112	.	-	.	Phchi.S1G633100
Phchi.S1	AUGUSTUS	transcript	40207076	40209112	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	stop_codon	40207073	40207075	.	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40207076	40207204	1	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40207076	40207204	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40207205	40207291	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40207292	40207397	1	-	1	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40207292	40207397	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40207398	40207503	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40207504	40207559	1	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40207504	40207559	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40207560	40207683	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40207684	40207743	1	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40207684	40207743	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40207744	40207861	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40207862	40207946	1	-	1	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40207862	40207946	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40207947	40208256	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40208257	40208351	1	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40208257	40208351	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40208352	40208504	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40208505	40208633	1	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40208505	40208633	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40208634	40208716	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40208717	40208771	1	-	1	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40208717	40208771	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	intron	40208772	40208951	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	CDS	40208952	40209112	0.7	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	exon	40208952	40209112	.	-	.	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
Phchi.S1	AUGUSTUS	start_codon	40209110	40209112	.	-	0	transcript_id "Phchi.S1G633100.t1"; gene_id "Phchi.S1G633100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13844.t1 is derived from g12311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9163823	9165055	.	-	.	Phchi.S3G116300
Phchi.S3	AUGUSTUS	transcript	9163823	9165055	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	stop_codon	9163820	9163822	.	-	0	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	CDS	9163823	9163910	1	-	1	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	exon	9163823	9163910	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	intron	9163911	9164070	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	CDS	9164071	9164167	1	-	2	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	exon	9164071	9164167	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	intron	9164168	9164279	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	CDS	9164280	9164442	0.93	-	0	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	exon	9164280	9164442	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	intron	9164443	9164556	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	CDS	9164557	9164648	1	-	2	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	exon	9164557	9164648	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	intron	9164649	9164796	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	CDS	9164797	9165055	1	-	0	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	exon	9164797	9165055	.	-	.	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
Phchi.S3	AUGUSTUS	start_codon	9165053	9165055	.	-	0	transcript_id "Phchi.S3G116300.t1"; gene_id "Phchi.S3G116300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2790.t1 is derived from g9710.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8888070	8889349	.	+	.	Phchi.S5G139900
Phchi.S5	AUGUSTUS	transcript	8888070	8889349	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	start_codon	8888070	8888072	.	+	0	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	CDS	8888070	8888089	0.98	+	0	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	exon	8888070	8888089	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	intron	8888090	8888191	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	CDS	8888192	8888381	0.92	+	1	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	exon	8888192	8888381	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	intron	8888382	8888603	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	CDS	8888604	8888780	0.96	+	0	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	exon	8888604	8888780	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	intron	8888781	8888920	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	CDS	8888921	8889349	0.99	+	0	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	exon	8888921	8889349	.	+	.	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
Phchi.S5	AUGUSTUS	stop_codon	8889350	8889352	.	+	0	transcript_id "Phchi.S5G139900.t1"; gene_id "Phchi.S5G139900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6645.t1 is derived from g3817.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24251296	24252229	.	-	.	Phchi.S1G380400
Phchi.S1	AUGUSTUS	transcript	24251296	24252229	.	-	.	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	stop_codon	24251293	24251295	.	-	0	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	CDS	24251296	24251925	0.9	-	0	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	exon	24251296	24251925	.	-	.	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	intron	24251926	24252010	.	-	.	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	CDS	24252011	24252229	0.78	-	0	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	exon	24252011	24252229	.	-	.	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
Phchi.S1	AUGUSTUS	start_codon	24252227	24252229	.	-	0	transcript_id "Phchi.S1G380400.t1"; gene_id "Phchi.S1G380400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5950.t1 is derived from g3121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20009974	20010540	.	-	.	Phchi.S1G310900
Phchi.S1	AUGUSTUS	transcript	20009974	20010540	.	-	.	transcript_id "Phchi.S1G310900.t1"; gene_id "Phchi.S1G310900"
Phchi.S1	AUGUSTUS	stop_codon	20009971	20009973	.	-	0	transcript_id "Phchi.S1G310900.t1"; gene_id "Phchi.S1G310900"
Phchi.S1	AUGUSTUS	CDS	20009974	20010540	1	-	0	transcript_id "Phchi.S1G310900.t1"; gene_id "Phchi.S1G310900"
Phchi.S1	AUGUSTUS	exon	20009974	20010540	.	-	.	transcript_id "Phchi.S1G310900.t1"; gene_id "Phchi.S1G310900"
Phchi.S1	AUGUSTUS	start_codon	20010538	20010540	.	-	0	transcript_id "Phchi.S1G310900.t1"; gene_id "Phchi.S1G310900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10935.t1 is derived from g14985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3175764	3178891	.	+	.	Phchi.S4G051700
Phchi.S4	AUGUSTUS	transcript	3175764	3178891	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	start_codon	3175764	3175766	.	+	0	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3175764	3175938	0.93	+	0	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3175764	3175938	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3175939	3176070	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3176071	3176223	1	+	2	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3176071	3176223	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3176224	3176411	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3176412	3176756	1	+	2	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3176412	3176756	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3176757	3176952	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3176953	3177029	1	+	2	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3176953	3177029	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3177030	3177272	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3177273	3178131	1	+	0	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3177273	3178131	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3178132	3178223	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3178224	3178333	0.72	+	2	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3178224	3178333	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3178334	3178499	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3178500	3178543	0.77	+	0	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3178500	3178543	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	intron	3178544	3178827	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	CDS	3178828	3178891	0.95	+	1	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	exon	3178828	3178891	.	+	.	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
Phchi.S4	AUGUSTUS	stop_codon	3178892	3178894	.	+	0	transcript_id "Phchi.S4G051700.t1"; gene_id "Phchi.S4G051700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11629.t1 is derived from g15680.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7384411	7384934	.	+	.	Phchi.S4G121100
Phchi.S4	AUGUSTUS	transcript	7384411	7384934	.	+	.	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	start_codon	7384411	7384413	.	+	0	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	CDS	7384411	7384638	0.81	+	0	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	exon	7384411	7384638	.	+	.	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	intron	7384639	7384760	.	+	.	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	CDS	7384761	7384934	0.89	+	0	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	exon	7384761	7384934	.	+	.	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
Phchi.S4	AUGUSTUS	stop_codon	7384935	7384937	.	+	0	transcript_id "Phchi.S4G121100.t1"; gene_id "Phchi.S4G121100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5862.t1 is derived from g3032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19469540	19471941	.	+	.	Phchi.S1G302100
Phchi.S1	AUGUSTUS	transcript	19469540	19471941	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	start_codon	19469540	19469542	.	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19469540	19469751	0.94	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19469540	19469751	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19469752	19469930	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19469931	19470249	0.88	+	1	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19469931	19470249	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19470250	19470341	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19470342	19470494	1	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19470342	19470494	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19470495	19470583	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19470584	19470835	1	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19470584	19470835	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19470836	19470963	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19470964	19471053	1	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19470964	19471053	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19471054	19471175	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19471176	19471254	1	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19471176	19471254	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19471255	19471417	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19471418	19471524	1	+	2	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19471418	19471524	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19471525	19471630	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19471631	19471749	1	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19471631	19471749	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	intron	19471750	19471838	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	CDS	19471839	19471941	0.99	+	1	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	exon	19471839	19471941	.	+	.	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
Phchi.S1	AUGUSTUS	stop_codon	19471942	19471944	.	+	0	transcript_id "Phchi.S1G302100.t1"; gene_id "Phchi.S1G302100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1052.t1 is derived from g10835.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7288798	7289411	.	+	.	Phchi.S6G101100
Phchi.S6	AUGUSTUS	transcript	7288798	7289411	.	+	.	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	start_codon	7288798	7288800	.	+	0	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	CDS	7288798	7288827	0.69	+	0	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	exon	7288798	7288827	.	+	.	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	intron	7288828	7288916	.	+	.	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	CDS	7288917	7289090	0.72	+	0	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	exon	7288917	7289090	.	+	.	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	intron	7289091	7289183	.	+	.	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	CDS	7289184	7289411	0.9	+	0	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	exon	7289184	7289411	.	+	.	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
Phchi.S6	AUGUSTUS	stop_codon	7289412	7289414	.	+	0	transcript_id "Phchi.S6G101100.t1"; gene_id "Phchi.S6G101100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6208.t1 is derived from g3379.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21473686	21475407	.	-	.	Phchi.S1G336700
Phchi.S1	AUGUSTUS	transcript	21473686	21475407	.	-	.	transcript_id "Phchi.S1G336700.t1"; gene_id "Phchi.S1G336700"
Phchi.S1	AUGUSTUS	stop_codon	21473683	21473685	.	-	0	transcript_id "Phchi.S1G336700.t1"; gene_id "Phchi.S1G336700"
Phchi.S1	AUGUSTUS	CDS	21473686	21475407	1	-	0	transcript_id "Phchi.S1G336700.t1"; gene_id "Phchi.S1G336700"
Phchi.S1	AUGUSTUS	exon	21473686	21475407	.	-	.	transcript_id "Phchi.S1G336700.t1"; gene_id "Phchi.S1G336700"
Phchi.S1	AUGUSTUS	start_codon	21475405	21475407	.	-	0	transcript_id "Phchi.S1G336700.t1"; gene_id "Phchi.S1G336700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9198.t1 is derived from g6373.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40321936	40322977	.	+	.	Phchi.S1G635700
Phchi.S1	AUGUSTUS	transcript	40321936	40322977	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	start_codon	40321936	40321938	.	+	0	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	CDS	40321936	40322314	0.14	+	0	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	exon	40321936	40322314	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	intron	40322315	40322419	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	CDS	40322420	40322499	0.31	+	2	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	exon	40322420	40322499	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	intron	40322500	40322585	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	CDS	40322586	40322713	0.94	+	0	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	exon	40322586	40322713	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	intron	40322714	40322841	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	CDS	40322842	40322977	0.45	+	1	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	exon	40322842	40322977	.	+	.	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
Phchi.S1	AUGUSTUS	stop_codon	40322978	40322980	.	+	0	transcript_id "Phchi.S1G635700.t1"; gene_id "Phchi.S1G635700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2126.t1 is derived from g9046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4978862	4979143	.	+	.	Phchi.S5G073500
Phchi.S5	AUGUSTUS	transcript	4978862	4979143	.	+	.	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	start_codon	4978862	4978864	.	+	0	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	CDS	4978862	4978995	1	+	0	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	exon	4978862	4978995	.	+	.	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	intron	4978996	4979070	.	+	.	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	CDS	4979071	4979143	1	+	1	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	exon	4979071	4979143	.	+	.	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
Phchi.S5	AUGUSTUS	stop_codon	4979144	4979146	.	+	0	transcript_id "Phchi.S5G073500.t1"; gene_id "Phchi.S5G073500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4106.t1 is derived from g1275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7858867	7860806	.	-	.	Phchi.S1G126500
Phchi.S1	AUGUSTUS	transcript	7858867	7860806	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	stop_codon	7858864	7858866	.	-	0	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7858867	7858888	0.89	-	1	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7858867	7858888	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7858889	7858971	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7858972	7859076	0.88	-	1	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7858972	7859076	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7859077	7859187	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7859188	7859365	0.61	-	2	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7859188	7859365	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7859366	7859528	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7859529	7859581	0.47	-	1	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7859529	7859581	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7859582	7860261	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7860262	7860313	0.46	-	2	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7860262	7860313	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7860314	7860386	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7860387	7860477	0.46	-	0	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7860387	7860477	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7860478	7860770	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7860771	7860806	0.56	-	0	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7860771	7860806	.	-	.	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	start_codon	7860804	7860806	.	-	0	transcript_id "Phchi.S1G126500.t1"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	transcript	7858884	7860806	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	stop_codon	7858881	7858883	.	-	0	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7858884	7858893	0.62	-	1	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7858884	7858893	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7858894	7858971	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7858972	7859076	0.62	-	1	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7858972	7859076	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7859077	7859187	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7859188	7859365	0.49	-	2	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7859188	7859365	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7859366	7859528	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7859529	7859581	0.41	-	1	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7859529	7859581	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7859582	7860261	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7860262	7860313	0.41	-	2	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7860262	7860313	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7860314	7860386	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7860387	7860477	0.41	-	0	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7860387	7860477	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	intron	7860478	7860770	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	CDS	7860771	7860806	0.59	-	0	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	exon	7860771	7860806	.	-	.	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
Phchi.S1	AUGUSTUS	start_codon	7860804	7860806	.	-	0	transcript_id "Phchi.S1G126500.t2"; gene_id "Phchi.S1G126500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1093.t1 is derived from g10876.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7570431	7572337	.	+	.	Phchi.S6G105200
Phchi.S6	AUGUSTUS	transcript	7570431	7572337	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	start_codon	7570431	7570433	.	+	0	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7570431	7570730	1	+	0	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7570431	7570730	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7570731	7570815	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7570816	7571078	1	+	0	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7570816	7571078	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571079	7571177	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7571178	7571499	1	+	1	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7571178	7571499	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571500	7571604	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7571605	7571750	0.81	+	0	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7571605	7571750	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571751	7571844	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7571845	7571902	1	+	1	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7571845	7571902	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571903	7572172	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7572173	7572337	0.96	+	0	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7572173	7572337	.	+	.	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	stop_codon	7572338	7572340	.	+	0	transcript_id "Phchi.S6G105200.t1"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	transcript	7570431	7572094	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	start_codon	7570431	7570433	.	+	0	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7570431	7570730	1	+	0	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7570431	7570730	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7570731	7570815	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7570816	7571078	1	+	0	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7570816	7571078	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571079	7571177	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7571178	7571499	1	+	1	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7571178	7571499	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571500	7571604	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7571605	7571750	0.77	+	0	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7571605	7571750	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571751	7571844	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7571845	7571902	0.91	+	1	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7571845	7571902	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	intron	7571903	7572049	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	CDS	7572050	7572094	0.91	+	0	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	exon	7572050	7572094	.	+	.	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
Phchi.S6	AUGUSTUS	stop_codon	7572095	7572097	.	+	0	transcript_id "Phchi.S6G105200.t2"; gene_id "Phchi.S6G105200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13602.t1 is derived from g12069.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7653926	7654513	.	+	.	Phchi.S3G092100
Phchi.S3	AUGUSTUS	transcript	7653926	7654513	.	+	.	transcript_id "Phchi.S3G092100.t1"; gene_id "Phchi.S3G092100"
Phchi.S3	AUGUSTUS	start_codon	7653926	7653928	.	+	0	transcript_id "Phchi.S3G092100.t1"; gene_id "Phchi.S3G092100"
Phchi.S3	AUGUSTUS	CDS	7653926	7654513	0.35	+	0	transcript_id "Phchi.S3G092100.t1"; gene_id "Phchi.S3G092100"
Phchi.S3	AUGUSTUS	exon	7653926	7654513	.	+	.	transcript_id "Phchi.S3G092100.t1"; gene_id "Phchi.S3G092100"
Phchi.S3	AUGUSTUS	stop_codon	7654514	7654516	.	+	0	transcript_id "Phchi.S3G092100.t1"; gene_id "Phchi.S3G092100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11667.t1 is derived from g15718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7587731	7590142	.	-	.	Phchi.S4G124900
Phchi.S4	AUGUSTUS	transcript	7587731	7590142	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	stop_codon	7587728	7587730	.	-	0	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	CDS	7587731	7588184	0.99	-	1	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	exon	7587731	7588184	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	intron	7588185	7588282	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	CDS	7588283	7588552	0.98	-	1	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	exon	7588283	7588552	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	intron	7588553	7588671	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	CDS	7588672	7589463	0.57	-	1	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	exon	7588672	7589463	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	intron	7589464	7589558	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	CDS	7589559	7590142	0.56	-	0	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	exon	7589559	7590142	.	-	.	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
Phchi.S4	AUGUSTUS	start_codon	7590140	7590142	.	-	0	transcript_id "Phchi.S4G124900.t1"; gene_id "Phchi.S4G124900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2070.t1 is derived from g8990.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4709600	4712988	.	+	.	Phchi.S5G067900
Phchi.S5	AUGUSTUS	transcript	4709600	4712988	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	start_codon	4709600	4709602	.	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4709600	4709608	0.97	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4709600	4709608	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4709609	4709694	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4709695	4709895	1	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4709695	4709895	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4709896	4710284	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4710285	4710420	1	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4710285	4710420	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4710421	4710590	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4710591	4710686	1	+	2	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4710591	4710686	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4710687	4710791	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4710792	4711148	0.84	+	2	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4710792	4711148	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4711149	4711259	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4711260	4711275	0.34	+	2	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4711260	4711275	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4711276	4711346	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4711347	4711537	0.65	+	1	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4711347	4711537	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4711538	4711608	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4711609	4711778	1	+	2	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4711609	4711778	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4711779	4711873	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4711874	4712062	0.96	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4711874	4712062	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4712063	4712298	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4712299	4712461	1	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4712299	4712461	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4712462	4712561	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4712562	4712754	0.97	+	2	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4712562	4712754	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	intron	4712755	4712855	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	CDS	4712856	4712988	1	+	1	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	exon	4712856	4712988	.	+	.	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
Phchi.S5	AUGUSTUS	stop_codon	4712989	4712991	.	+	0	transcript_id "Phchi.S5G067900.t1"; gene_id "Phchi.S5G067900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14131.t1 is derived from g12598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11059243	11061701	.	-	.	Phchi.S3G145000
Phchi.S3	AUGUSTUS	transcript	11059243	11061701	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	stop_codon	11059240	11059242	.	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11059243	11059261	1	-	1	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11059243	11059261	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11059262	11059342	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11059343	11059444	1	-	1	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11059343	11059444	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11059445	11059609	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11059610	11059681	0.86	-	1	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11059610	11059681	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11059682	11059866	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11059867	11060282	1	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11059867	11060282	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11060283	11060413	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11060414	11060534	1	-	1	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11060414	11060534	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11060535	11060617	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11060618	11060719	1	-	1	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11060618	11060719	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11060720	11060909	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11060910	11061046	1	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11060910	11061046	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11061047	11061138	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11061139	11061276	1	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11061139	11061276	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11061277	11061405	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11061406	11061444	1	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11061406	11061444	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	intron	11061445	11061560	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	CDS	11061561	11061701	0.98	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	exon	11061561	11061701	.	-	.	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
Phchi.S3	AUGUSTUS	start_codon	11061699	11061701	.	-	0	transcript_id "Phchi.S3G145000.t1"; gene_id "Phchi.S3G145000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2932.t1 is derived from g101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	606344	607904	.	-	.	Phchi.S1G009100
Phchi.S1	AUGUSTUS	transcript	606344	607904	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	stop_codon	606341	606343	.	-	0	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	CDS	606344	606448	1	-	0	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	exon	606344	606448	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	intron	606449	606531	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	CDS	606532	606675	0.99	-	0	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	exon	606532	606675	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	intron	606676	606782	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	CDS	606783	607041	0.99	-	1	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	exon	606783	607041	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	intron	607042	607162	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	CDS	607163	607229	0.72	-	2	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	exon	607163	607229	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	intron	607230	607327	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	CDS	607328	607467	0.62	-	1	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	exon	607328	607467	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	intron	607468	607551	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	CDS	607552	607904	0.93	-	0	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	exon	607552	607904	.	-	.	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
Phchi.S1	AUGUSTUS	start_codon	607902	607904	.	-	0	transcript_id "Phchi.S1G009100.t1"; gene_id "Phchi.S1G009100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7288.t1 is derived from g4460.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28330720	28333922	.	-	.	Phchi.S1G444700
Phchi.S1	AUGUSTUS	transcript	28330720	28333922	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	stop_codon	28330717	28330719	.	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28330720	28330911	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28330720	28330911	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28330912	28331002	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28331003	28331071	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28331003	28331071	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28331072	28331161	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28331162	28331263	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28331162	28331263	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28331264	28331359	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28331360	28331503	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28331360	28331503	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28331504	28331584	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28331585	28331701	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28331585	28331701	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28331702	28331900	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28331901	28332122	0.97	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28331901	28332122	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28332123	28332230	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28332231	28332413	0.75	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28332231	28332413	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28332414	28332603	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28332604	28332819	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28332604	28332819	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28332820	28333006	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28333007	28333171	1	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28333007	28333171	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	intron	28333172	28333235	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	CDS	28333236	28333922	0.27	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	exon	28333236	28333922	.	-	.	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
Phchi.S1	AUGUSTUS	start_codon	28333920	28333922	.	-	0	transcript_id "Phchi.S1G444700.t1"; gene_id "Phchi.S1G444700"
# This transcript jg3166.t2 is derived from g335.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3167.t1 is derived from g336.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2044347	2047297	.	+	.	Phchi.S1G032600
Phchi.S1	AUGUSTUS	transcript	2044347	2045685	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	start_codon	2044347	2044349	.	+	0	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2044347	2044405	1	+	0	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2044347	2044405	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2044406	2044548	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2044549	2044686	0.97	+	1	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2044549	2044686	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2044687	2044776	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2044777	2045012	0.99	+	1	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2044777	2045012	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2045013	2045296	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2045297	2045547	1	+	2	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2045297	2045547	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2045548	2045640	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2045641	2045685	0.85	+	0	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2045641	2045685	.	+	.	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	stop_codon	2045686	2045688	.	+	0	transcript_id "Phchi.S1G032600.t1"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	transcript	2044347	2047297	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	start_codon	2044347	2044349	.	+	0	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2044347	2044405	1	+	0	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2044347	2044405	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2044406	2044548	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2044549	2044686	0.97	+	1	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2044549	2044686	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2044687	2044776	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2044777	2045012	0.99	+	1	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2044777	2045012	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2045013	2045296	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2045297	2045547	1	+	2	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2045297	2045547	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2045548	2045715	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2045716	2046603	0.91	+	0	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2045716	2046603	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2046604	2046673	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2046674	2046764	0.69	+	0	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2046674	2046764	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2046765	2046904	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2046905	2046939	1	+	2	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2046905	2046939	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2046940	2047082	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2047083	2047155	1	+	0	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2047083	2047155	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	intron	2047156	2047238	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	CDS	2047239	2047297	1	+	2	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	exon	2047239	2047297	.	+	.	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
Phchi.S1	AUGUSTUS	stop_codon	2047298	2047300	.	+	0	transcript_id "Phchi.S1G032600.t2"; gene_id "Phchi.S1G032600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7166.t1 is derived from g4338.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27356612	27358931	.	+	.	Phchi.S1G432500
Phchi.S1	AUGUSTUS	transcript	27356612	27358931	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	start_codon	27356612	27356614	.	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27356612	27356899	0.99	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27356612	27356899	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27356900	27357145	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27357146	27357196	1	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27357146	27357196	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27357197	27357286	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27357287	27357454	1	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27357287	27357454	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27357455	27357557	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27357558	27357628	1	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27357558	27357628	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27357629	27357753	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27357754	27357811	1	+	1	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27357754	27357811	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27357812	27357985	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27357986	27358165	1	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27357986	27358165	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27358166	27358258	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27358259	27358343	1	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27358259	27358343	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27358344	27358435	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27358436	27358495	1	+	2	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27358436	27358495	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27358496	27358630	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27358631	27358704	1	+	2	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27358631	27358704	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	intron	27358705	27358817	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	CDS	27358818	27358931	1	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	exon	27358818	27358931	.	+	.	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
Phchi.S1	AUGUSTUS	stop_codon	27358932	27358934	.	+	0	transcript_id "Phchi.S1G432500.t1"; gene_id "Phchi.S1G432500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4631.t1 is derived from g1801.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11478975	11482649	.	+	.	Phchi.S1G179000
Phchi.S1	AUGUSTUS	transcript	11478975	11482649	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	start_codon	11478975	11478977	.	+	0	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11478975	11479622	0.88	+	0	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11478975	11479622	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11479623	11479818	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11479819	11480031	1	+	0	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11479819	11480031	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11480032	11480152	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11480153	11480309	1	+	0	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11480153	11480309	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11480310	11481429	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11481430	11481773	1	+	2	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11481430	11481773	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11481774	11481856	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11481857	11481938	1	+	0	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11481857	11481938	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11481939	11482062	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11482063	11482080	0.6	+	2	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11482063	11482080	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11482081	11482133	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11482134	11482205	0.59	+	2	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11482134	11482205	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11482206	11482346	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11482347	11482476	1	+	2	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11482347	11482476	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	intron	11482477	11482561	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	CDS	11482562	11482649	1	+	1	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	exon	11482562	11482649	.	+	.	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
Phchi.S1	AUGUSTUS	stop_codon	11482650	11482652	.	+	0	transcript_id "Phchi.S1G179000.t1"; gene_id "Phchi.S1G179000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3791.t1 is derived from g960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5764750	5765185	.	-	.	Phchi.S1G095000
Phchi.S1	AUGUSTUS	transcript	5764750	5765185	.	-	.	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	stop_codon	5764747	5764749	.	-	0	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	CDS	5764750	5764933	0.7	-	1	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	exon	5764750	5764933	.	-	.	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	intron	5764934	5765081	.	-	.	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	CDS	5765082	5765185	0.99	-	0	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	exon	5765082	5765185	.	-	.	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
Phchi.S1	AUGUSTUS	start_codon	5765183	5765185	.	-	0	transcript_id "Phchi.S1G095000.t1"; gene_id "Phchi.S1G095000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13314.t1 is derived from g11780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5950980	5953912	.	-	.	Phchi.S3G063300
Phchi.S3	AUGUSTUS	transcript	5950980	5953912	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	stop_codon	5950977	5950979	.	-	0	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	CDS	5950980	5951291	0.97	-	0	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	exon	5950980	5951291	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	intron	5951292	5951405	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	CDS	5951406	5951544	0.99	-	1	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	exon	5951406	5951544	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	intron	5951545	5951633	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	CDS	5951634	5951861	1	-	1	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	exon	5951634	5951861	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	intron	5951862	5951961	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	CDS	5951962	5952060	1	-	1	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	exon	5951962	5952060	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	intron	5952061	5952190	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	CDS	5952191	5952539	1	-	2	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	exon	5952191	5952539	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	intron	5952540	5952648	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	CDS	5952649	5953912	0.86	-	0	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	exon	5952649	5953912	.	-	.	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
Phchi.S3	AUGUSTUS	start_codon	5953910	5953912	.	-	0	transcript_id "Phchi.S3G063300.t1"; gene_id "Phchi.S3G063300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5949.t1 is derived from g3120.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19986396	19987803	.	+	.	Phchi.S1G310800
Phchi.S1	AUGUSTUS	transcript	19986396	19987803	.	+	.	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	start_codon	19986396	19986398	.	+	0	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	CDS	19986396	19987591	0.98	+	0	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	exon	19986396	19987591	.	+	.	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	intron	19987592	19987688	.	+	.	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	CDS	19987689	19987803	1	+	1	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	exon	19987689	19987803	.	+	.	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
Phchi.S1	AUGUSTUS	stop_codon	19987804	19987806	.	+	0	transcript_id "Phchi.S1G310800.t1"; gene_id "Phchi.S1G310800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg815.t1 is derived from g10597.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5703645	5704731	.	-	.	Phchi.S6G077400
Phchi.S6	AUGUSTUS	transcript	5703645	5704731	.	-	.	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	stop_codon	5703642	5703644	.	-	0	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	CDS	5703645	5704509	1	-	1	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	exon	5703645	5704509	.	-	.	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	intron	5704510	5704645	.	-	.	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	CDS	5704646	5704731	0.91	-	0	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	exon	5704646	5704731	.	-	.	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
Phchi.S6	AUGUSTUS	start_codon	5704729	5704731	.	-	0	transcript_id "Phchi.S6G077400.t1"; gene_id "Phchi.S6G077400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5806.t1 is derived from g2976.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19040612	19041772	.	+	.	Phchi.S1G296500
Phchi.S1	AUGUSTUS	transcript	19040612	19041772	.	+	.	transcript_id "Phchi.S1G296500.t1"; gene_id "Phchi.S1G296500"
Phchi.S1	AUGUSTUS	start_codon	19040612	19040614	.	+	0	transcript_id "Phchi.S1G296500.t1"; gene_id "Phchi.S1G296500"
Phchi.S1	AUGUSTUS	CDS	19040612	19041772	1	+	0	transcript_id "Phchi.S1G296500.t1"; gene_id "Phchi.S1G296500"
Phchi.S1	AUGUSTUS	exon	19040612	19041772	.	+	.	transcript_id "Phchi.S1G296500.t1"; gene_id "Phchi.S1G296500"
Phchi.S1	AUGUSTUS	stop_codon	19041773	19041775	.	+	0	transcript_id "Phchi.S1G296500.t1"; gene_id "Phchi.S1G296500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10231.t1 is derived from g7407.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46496021	46498165	.	-	.	Phchi.S1G739000
Phchi.S1	AUGUSTUS	transcript	46496021	46498165	.	-	.	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	stop_codon	46496018	46496020	.	-	0	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	CDS	46496021	46496470	0.97	-	0	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	exon	46496021	46496470	.	-	.	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	intron	46496471	46496650	.	-	.	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	CDS	46496651	46498165	0.27	-	0	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	exon	46496651	46498165	.	-	.	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
Phchi.S1	AUGUSTUS	start_codon	46498163	46498165	.	-	0	transcript_id "Phchi.S1G739000.t1"; gene_id "Phchi.S1G739000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1518.t1 is derived from g8437.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1507869	1509713	.	+	.	Phchi.S5G012700
Phchi.S5	AUGUSTUS	transcript	1507869	1509713	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	start_codon	1507869	1507871	.	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1507869	1507904	0.73	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1507869	1507904	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1507905	1508016	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1508017	1508120	1	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1508017	1508120	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1508121	1508193	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1508194	1508296	0.97	+	1	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1508194	1508296	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1508297	1508555	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1508556	1508635	0.41	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1508556	1508635	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1508636	1508791	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1508792	1508810	0.91	+	1	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1508792	1508810	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1508811	1508908	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1508909	1508972	0.94	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1508909	1508972	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1508973	1509079	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1509080	1509168	0.66	+	2	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1509080	1509168	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1509169	1509413	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1509414	1509459	0.48	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1509414	1509459	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1509460	1509509	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1509510	1509534	0.68	+	2	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1509510	1509534	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	intron	1509535	1509631	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	CDS	1509632	1509713	0.65	+	1	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	exon	1509632	1509713	.	+	.	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
Phchi.S5	AUGUSTUS	stop_codon	1509714	1509716	.	+	0	transcript_id "Phchi.S5G012700.t1"; gene_id "Phchi.S5G012700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14250.t1 is derived from g12717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11755579	11755904	.	-	.	Phchi.S3G156900
Phchi.S3	AUGUSTUS	transcript	11755579	11755904	.	-	.	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	stop_codon	11755576	11755578	.	-	0	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	CDS	11755579	11755776	1	-	0	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	exon	11755579	11755776	.	-	.	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	intron	11755777	11755898	.	-	.	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	CDS	11755899	11755904	0.99	-	0	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	exon	11755899	11755904	.	-	.	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
Phchi.S3	AUGUSTUS	start_codon	11755902	11755904	.	-	0	transcript_id "Phchi.S3G156900.t1"; gene_id "Phchi.S3G156900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4390.t1 is derived from g1559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10195170	10196908	.	-	.	Phchi.S1G154900
Phchi.S1	AUGUSTUS	transcript	10195170	10196908	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	stop_codon	10195167	10195169	.	-	0	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10195170	10195286	0.99	-	0	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10195170	10195286	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	intron	10195287	10195372	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10195373	10195454	0.93	-	1	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10195373	10195454	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	intron	10195455	10195644	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10195645	10195720	0.5	-	2	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10195645	10195720	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	intron	10195721	10195902	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10195903	10196195	0.5	-	1	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10195903	10196195	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	intron	10196196	10196296	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10196297	10196481	0.98	-	0	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10196297	10196481	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	intron	10196482	10196568	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10196569	10196697	1	-	0	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10196569	10196697	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	intron	10196698	10196830	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	CDS	10196831	10196908	0.99	-	0	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	exon	10196831	10196908	.	-	.	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
Phchi.S1	AUGUSTUS	start_codon	10196906	10196908	.	-	0	transcript_id "Phchi.S1G154900.t1"; gene_id "Phchi.S1G154900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11500.t1 is derived from g15550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6678022	6678515	.	+	.	Phchi.S4G108200
Phchi.S4	AUGUSTUS	transcript	6678022	6678515	.	+	.	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	start_codon	6678022	6678024	.	+	0	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	CDS	6678022	6678283	0.99	+	0	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	exon	6678022	6678283	.	+	.	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	intron	6678284	6678414	.	+	.	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	CDS	6678415	6678515	1	+	2	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	exon	6678415	6678515	.	+	.	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
Phchi.S4	AUGUSTUS	stop_codon	6678516	6678518	.	+	0	transcript_id "Phchi.S4G108200.t1"; gene_id "Phchi.S4G108200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8213.t1 is derived from g5388.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34446212	34448867	.	+	.	Phchi.S1G537200
Phchi.S1	AUGUSTUS	transcript	34446212	34448867	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	start_codon	34446212	34446214	.	+	0	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34446212	34446410	0.99	+	0	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34446212	34446410	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34446411	34446530	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34446531	34446575	1	+	2	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34446531	34446575	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34446576	34446764	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34446765	34446773	1	+	2	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34446765	34446773	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34446774	34446931	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34446932	34447782	1	+	2	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34446932	34447782	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34447783	34447864	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34447865	34448026	1	+	0	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34447865	34448026	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34448027	34448108	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34448109	34448338	1	+	0	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34448109	34448338	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34448339	34448432	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34448433	34448523	1	+	1	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34448433	34448523	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	intron	34448524	34448690	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	CDS	34448691	34448867	1	+	0	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	exon	34448691	34448867	.	+	.	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
Phchi.S1	AUGUSTUS	stop_codon	34448868	34448870	.	+	0	transcript_id "Phchi.S1G537200.t1"; gene_id "Phchi.S1G537200"
# This transcript jg1153.t2 is derived from g10936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1154.t1 is derived from g10937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8044003	8045423	.	-	.	Phchi.S6G111300
Phchi.S6	AUGUSTUS	transcript	8044003	8045423	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	stop_codon	8044000	8044002	.	-	0	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	CDS	8044003	8044308	1	-	0	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	exon	8044003	8044308	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	intron	8044309	8044408	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	CDS	8044409	8044491	1	-	2	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	exon	8044409	8044491	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	intron	8044492	8044600	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	CDS	8044601	8044722	1	-	1	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	exon	8044601	8044722	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	intron	8044723	8044815	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	CDS	8044816	8045069	1	-	0	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	exon	8044816	8045069	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	intron	8045070	8045189	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	CDS	8045190	8045423	1	-	0	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	exon	8045190	8045423	.	-	.	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
Phchi.S6	AUGUSTUS	start_codon	8045421	8045423	.	-	0	transcript_id "Phchi.S6G111300.t1"; gene_id "Phchi.S6G111300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8523.t1 is derived from g5698.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36427906	36432251	.	-	.	Phchi.S1G568200
Phchi.S1	AUGUSTUS	transcript	36427906	36432251	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	stop_codon	36427903	36427905	.	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36427906	36428446	0.99	-	1	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36427906	36428446	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36428447	36428522	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36428523	36428636	0.99	-	1	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36428523	36428636	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36428637	36428788	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36428789	36428934	1	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36428789	36428934	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36428935	36429085	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429086	36429164	0.89	-	1	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429086	36429164	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429165	36429338	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429339	36429421	0.99	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429339	36429421	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429422	36429520	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429521	36429617	1	-	1	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429521	36429617	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429618	36429764	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429765	36429844	1	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429765	36429844	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429845	36429924	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429925	36430236	0.99	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429925	36430236	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36430237	36430340	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36430341	36430448	0.96	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36430341	36430448	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36430449	36430527	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36430528	36430977	0.98	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36430528	36430977	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36430978	36431076	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431077	36431143	0.99	-	1	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431077	36431143	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431144	36431260	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431261	36431325	0.78	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431261	36431325	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431326	36431437	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431438	36431505	0.85	-	2	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431438	36431505	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431506	36431614	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431615	36431746	0.91	-	2	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431615	36431746	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431747	36431893	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431894	36432251	0.82	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431894	36432251	.	-	.	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	start_codon	36432249	36432251	.	-	0	transcript_id "Phchi.S1G568200.t1"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	transcript	36427906	36432251	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	stop_codon	36427903	36427905	.	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36427906	36428446	0.98	-	1	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36427906	36428446	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36428447	36428522	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36428523	36428636	1	-	1	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36428523	36428636	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36428637	36428788	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36428789	36428934	1	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36428789	36428934	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36428935	36429085	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429086	36429164	0.97	-	1	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429086	36429164	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429165	36429338	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429339	36429421	0.99	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429339	36429421	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429422	36429520	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429521	36429611	1	-	1	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429521	36429611	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429612	36429764	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429765	36429844	1	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429765	36429844	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36429845	36429924	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36429925	36430236	0.96	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36429925	36430236	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36430237	36430340	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36430341	36430448	0.96	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36430341	36430448	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36430449	36430527	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36430528	36430977	0.99	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36430528	36430977	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36430978	36431076	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431077	36431143	0.98	-	1	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431077	36431143	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431144	36431260	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431261	36431325	0.74	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431261	36431325	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431326	36431437	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431438	36431505	0.79	-	2	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431438	36431505	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431506	36431614	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431615	36431746	0.87	-	2	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431615	36431746	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	intron	36431747	36431893	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	CDS	36431894	36432251	0.82	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	exon	36431894	36432251	.	-	.	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
Phchi.S1	AUGUSTUS	start_codon	36432249	36432251	.	-	0	transcript_id "Phchi.S1G568200.t2"; gene_id "Phchi.S1G568200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12788.t1 is derived from g11253.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2377125	2377981	.	-	.	Phchi.S3G010700
Phchi.S3	AUGUSTUS	transcript	2377125	2377981	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	stop_codon	2377122	2377124	.	-	0	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	CDS	2377125	2377196	1	-	0	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	exon	2377125	2377196	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	intron	2377197	2377295	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	CDS	2377296	2377358	1	-	0	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	exon	2377296	2377358	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	intron	2377359	2377450	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	CDS	2377451	2377467	1	-	2	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	exon	2377451	2377467	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	intron	2377468	2377567	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	CDS	2377568	2377685	1	-	0	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	exon	2377568	2377685	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	intron	2377686	2377782	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	CDS	2377783	2377877	1	-	2	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	exon	2377783	2377877	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	intron	2377878	2377968	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	CDS	2377969	2377981	0.35	-	0	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	exon	2377969	2377981	.	-	.	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
Phchi.S3	AUGUSTUS	start_codon	2377979	2377981	.	-	0	transcript_id "Phchi.S3G010700.t1"; gene_id "Phchi.S3G010700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10430.t1 is derived from g14479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	239436	239681	.	+	.	Phchi.S4G001200
Phchi.S4	AUGUSTUS	transcript	239436	239681	.	+	.	transcript_id "Phchi.S4G001200.t1"; gene_id "Phchi.S4G001200"
Phchi.S4	AUGUSTUS	start_codon	239436	239438	.	+	0	transcript_id "Phchi.S4G001200.t1"; gene_id "Phchi.S4G001200"
Phchi.S4	AUGUSTUS	CDS	239436	239681	0.42	+	0	transcript_id "Phchi.S4G001200.t1"; gene_id "Phchi.S4G001200"
Phchi.S4	AUGUSTUS	exon	239436	239681	.	+	.	transcript_id "Phchi.S4G001200.t1"; gene_id "Phchi.S4G001200"
Phchi.S4	AUGUSTUS	stop_codon	239682	239684	.	+	0	transcript_id "Phchi.S4G001200.t1"; gene_id "Phchi.S4G001200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2345.t1 is derived from g9265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6265785	6266003	.	-	.	Phchi.S5G095400
Phchi.S5	AUGUSTUS	transcript	6265785	6266003	.	-	.	transcript_id "Phchi.S5G095400.t1"; gene_id "Phchi.S5G095400"
Phchi.S5	AUGUSTUS	stop_codon	6265782	6265784	.	-	0	transcript_id "Phchi.S5G095400.t1"; gene_id "Phchi.S5G095400"
Phchi.S5	AUGUSTUS	CDS	6265785	6266003	0.36	-	0	transcript_id "Phchi.S5G095400.t1"; gene_id "Phchi.S5G095400"
Phchi.S5	AUGUSTUS	exon	6265785	6266003	.	-	.	transcript_id "Phchi.S5G095400.t1"; gene_id "Phchi.S5G095400"
Phchi.S5	AUGUSTUS	start_codon	6266001	6266003	.	-	0	transcript_id "Phchi.S5G095400.t1"; gene_id "Phchi.S5G095400"
# This transcript jg11490.t2 is derived from g15540.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11491.t1 is derived from g15541.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6632675	6633027	.	+	.	Phchi.S4G107300
Phchi.S4	AUGUSTUS	transcript	6632675	6633027	.	+	.	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	start_codon	6632675	6632677	.	+	0	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	CDS	6632675	6632849	1	+	0	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	exon	6632675	6632849	.	+	.	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	intron	6632850	6632920	.	+	.	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	CDS	6632921	6633027	1	+	2	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	exon	6632921	6633027	.	+	.	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
Phchi.S4	AUGUSTUS	stop_codon	6633028	6633030	.	+	0	transcript_id "Phchi.S4G107300.t1"; gene_id "Phchi.S4G107300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7316.t1 is derived from g4488.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28469597	28471770	.	-	.	Phchi.S1G447500
Phchi.S1	AUGUSTUS	transcript	28469597	28471770	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	stop_codon	28469594	28469596	.	-	0	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	CDS	28469597	28470515	1	-	1	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	exon	28469597	28470515	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	intron	28470516	28470638	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	CDS	28470639	28470787	0.94	-	0	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	exon	28470639	28470787	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	intron	28470788	28470891	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	CDS	28470892	28471051	0.8	-	1	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	exon	28470892	28471051	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	intron	28471052	28471160	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	CDS	28471161	28471276	0.4	-	0	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	exon	28471161	28471276	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	intron	28471277	28471545	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	CDS	28471546	28471770	0.81	-	0	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	exon	28471546	28471770	.	-	.	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	start_codon	28471768	28471770	.	-	0	transcript_id "Phchi.S1G447500.t1"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	transcript	28469597	28470334	.	-	.	transcript_id "Phchi.S1G447500.t2"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	stop_codon	28469594	28469596	.	-	0	transcript_id "Phchi.S1G447500.t2"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	CDS	28469597	28470334	0.84	-	0	transcript_id "Phchi.S1G447500.t2"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	exon	28469597	28470334	.	-	.	transcript_id "Phchi.S1G447500.t2"; gene_id "Phchi.S1G447500"
Phchi.S1	AUGUSTUS	start_codon	28470332	28470334	.	-	0	transcript_id "Phchi.S1G447500.t2"; gene_id "Phchi.S1G447500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4634.t1 is derived from g1804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11488195	11490363	.	+	.	Phchi.S1G179300
Phchi.S1	AUGUSTUS	transcript	11488195	11490363	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	start_codon	11488195	11488197	.	+	0	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	CDS	11488195	11488505	0.61	+	0	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	exon	11488195	11488505	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	intron	11488506	11488605	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	CDS	11488606	11488707	1	+	1	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	exon	11488606	11488707	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	intron	11488708	11488804	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	CDS	11488805	11489254	1	+	1	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	exon	11488805	11489254	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	intron	11489255	11489330	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	CDS	11489331	11489692	1	+	1	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	exon	11489331	11489692	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	intron	11489693	11489803	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	CDS	11489804	11490363	1	+	2	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	exon	11489804	11490363	.	+	.	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
Phchi.S1	AUGUSTUS	stop_codon	11490364	11490366	.	+	0	transcript_id "Phchi.S1G179300.t1"; gene_id "Phchi.S1G179300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4591.t1 is derived from g1761.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11235827	11239060	.	-	.	Phchi.S1G175000
Phchi.S1	AUGUSTUS	transcript	11235827	11239060	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	stop_codon	11235824	11235826	.	-	0	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	CDS	11235827	11236369	1	-	0	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	exon	11235827	11236369	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	intron	11236370	11236459	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	CDS	11236460	11237154	1	-	2	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	exon	11236460	11237154	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	intron	11237155	11237272	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	CDS	11237273	11237584	1	-	2	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	exon	11237273	11237584	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	intron	11237585	11237696	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	CDS	11237697	11237943	1	-	0	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	exon	11237697	11237943	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	intron	11237944	11238067	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	CDS	11238068	11239060	1	-	0	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	exon	11238068	11239060	.	-	.	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
Phchi.S1	AUGUSTUS	start_codon	11239058	11239060	.	-	0	transcript_id "Phchi.S1G175000.t1"; gene_id "Phchi.S1G175000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13177.t1 is derived from g11642.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4534203	4537600	.	+	.	Phchi.S3G049600
Phchi.S3	AUGUSTUS	transcript	4534203	4537600	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	start_codon	4534203	4534205	.	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4534203	4534439	0.68	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4534203	4534439	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4534440	4534530	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4534531	4534941	1	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4534531	4534941	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4534942	4535037	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4535038	4535253	1	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4535038	4535253	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4535254	4535342	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4535343	4535998	1	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4535343	4535998	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4535999	4536087	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536088	4536184	1	+	1	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536088	4536184	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536185	4536290	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536291	4536347	0.88	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536291	4536347	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536348	4536472	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536473	4536594	0.99	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536473	4536594	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536595	4536712	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536713	4536903	1	+	1	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536713	4536903	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536904	4536986	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536987	4537600	0.99	+	2	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536987	4537600	.	+	.	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	stop_codon	4537601	4537603	.	+	0	transcript_id "Phchi.S3G049600.t1"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	transcript	4534203	4537600	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	start_codon	4534203	4534205	.	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4534203	4534439	0.65	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4534203	4534439	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4534440	4534530	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4534531	4534941	1	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4534531	4534941	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4534942	4535037	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4535038	4535253	1	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4535038	4535253	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4535254	4535342	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4535343	4535998	0.98	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4535343	4535998	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4535999	4536087	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536088	4536184	1	+	1	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536088	4536184	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536185	4536290	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536291	4536347	0.85	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536291	4536347	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536348	4536472	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536473	4536594	0.97	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536473	4536594	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536595	4536712	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536713	4536887	0.96	+	1	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536713	4536887	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4536888	4536986	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4536987	4537039	0.96	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4536987	4537039	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	intron	4537040	4537194	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	CDS	4537195	4537600	0.78	+	1	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	exon	4537195	4537600	.	+	.	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
Phchi.S3	AUGUSTUS	stop_codon	4537601	4537603	.	+	0	transcript_id "Phchi.S3G049600.t2"; gene_id "Phchi.S3G049600"
# This transcript jg9493.t2 is derived from g6669.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9494.t1 is derived from g6670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42018933	42020819	.	+	.	Phchi.S1G665300
Phchi.S1	AUGUSTUS	transcript	42018933	42020819	.	+	.	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	start_codon	42018933	42018935	.	+	0	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	CDS	42018933	42019359	0.7	+	0	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	exon	42018933	42019359	.	+	.	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	intron	42019360	42019464	.	+	.	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	CDS	42019465	42019633	0.9	+	2	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	exon	42019465	42019633	.	+	.	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	intron	42019634	42019711	.	+	.	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	CDS	42019712	42020819	0.56	+	1	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	exon	42019712	42020819	.	+	.	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
Phchi.S1	AUGUSTUS	stop_codon	42020820	42020822	.	+	0	transcript_id "Phchi.S1G665300.t1"; gene_id "Phchi.S1G665300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5039.t1 is derived from g2209.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14202323	14207973	.	+	.	Phchi.S1G219800
Phchi.S1	AUGUSTUS	transcript	14202323	14207973	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	start_codon	14202323	14202325	.	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14202323	14202355	0.94	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14202323	14202355	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14202356	14202447	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14202448	14202751	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14202448	14202751	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14202752	14202851	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14202852	14202912	1	+	2	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14202852	14202912	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14202913	14203000	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14203001	14203079	1	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14203001	14203079	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14203080	14203172	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14203173	14203252	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14203173	14203252	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14203253	14203350	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14203351	14203445	1	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14203351	14203445	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14203446	14203535	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14203536	14203635	1	+	2	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14203536	14203635	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14203636	14203810	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14203811	14203880	1	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14203811	14203880	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14203881	14204384	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14204385	14204486	0.96	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14204385	14204486	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14204487	14204593	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14204594	14204675	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14204594	14204675	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14204676	14204793	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14204794	14204973	1	+	2	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14204794	14204973	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14204974	14205065	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14205066	14205102	0.96	+	2	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14205066	14205102	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14205103	14205170	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14205171	14205320	0.96	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14205171	14205320	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14205321	14205422	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14205423	14205693	1	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14205423	14205693	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14205694	14205810	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14205811	14205981	0.96	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14205811	14205981	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14205982	14206085	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14206086	14206211	0.78	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14206086	14206211	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14206212	14206291	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14206292	14206323	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14206292	14206323	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14206324	14206490	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14206491	14206575	1	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14206491	14206575	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14206576	14206671	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14206672	14206770	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14206672	14206770	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14206771	14206950	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14206951	14207150	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14206951	14207150	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14207151	14207244	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14207245	14207320	0.99	+	1	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14207245	14207320	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14207321	14207433	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14207434	14207569	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14207434	14207569	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14207570	14207666	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14207667	14207806	1	+	2	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14207667	14207806	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	intron	14207807	14207892	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	CDS	14207893	14207973	1	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	exon	14207893	14207973	.	+	.	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
Phchi.S1	AUGUSTUS	stop_codon	14207974	14207976	.	+	0	transcript_id "Phchi.S1G219800.t1"; gene_id "Phchi.S1G219800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3603.t1 is derived from g772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4682498	4683721	.	-	.	Phchi.S1G076200
Phchi.S1	AUGUSTUS	transcript	4682498	4683721	.	-	.	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	stop_codon	4682495	4682497	.	-	0	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	CDS	4682498	4683089	0.85	-	1	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	exon	4682498	4683089	.	-	.	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	intron	4683090	4683208	.	-	.	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	CDS	4683209	4683559	0.5	-	1	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	exon	4683209	4683559	.	-	.	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	intron	4683560	4683635	.	-	.	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	CDS	4683636	4683721	0.98	-	0	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	exon	4683636	4683721	.	-	.	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
Phchi.S1	AUGUSTUS	start_codon	4683719	4683721	.	-	0	transcript_id "Phchi.S1G076200.t1"; gene_id "Phchi.S1G076200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6863.t1 is derived from g4035.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25647142	25652666	.	-	.	Phchi.S1G402200
Phchi.S1	AUGUSTUS	transcript	25647142	25652666	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	stop_codon	25647139	25647141	.	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25647142	25647317	0.99	-	2	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25647142	25647317	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25647318	25647401	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25647402	25647519	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25647402	25647519	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25647520	25647641	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25647642	25647741	1	-	1	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25647642	25647741	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25647742	25647832	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25647833	25647918	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25647833	25647918	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25647919	25648005	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25648006	25648164	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25648006	25648164	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25648165	25648293	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25648294	25648355	1	-	2	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25648294	25648355	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25648356	25648441	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25648442	25648476	1	-	1	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25648442	25648476	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25648477	25648682	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25648683	25648732	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25648683	25648732	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25648733	25648835	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25648836	25648943	0.97	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25648836	25648943	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25648944	25649028	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25649029	25649188	0.93	-	1	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25649029	25649188	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25649189	25649306	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25649307	25649372	0.91	-	1	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25649307	25649372	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25649373	25649539	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25649540	25649634	0.92	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25649540	25649634	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25649635	25649741	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25649742	25649789	0.91	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25649742	25649789	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25649790	25649888	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25649889	25650023	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25649889	25650023	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25650024	25650195	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25650196	25650298	1	-	1	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25650196	25650298	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25650299	25650518	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25650519	25650615	1	-	2	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25650519	25650615	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25650616	25650706	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25650707	25650809	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25650707	25650809	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25650810	25650921	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25650922	25651003	0.92	-	1	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25650922	25651003	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25651004	25651138	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25651139	25651256	1	-	2	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25651139	25651256	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	intron	25651257	25651402	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	CDS	25651403	25652666	1	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	exon	25651403	25652666	.	-	.	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
Phchi.S1	AUGUSTUS	start_codon	25652664	25652666	.	-	0	transcript_id "Phchi.S1G402200.t1"; gene_id "Phchi.S1G402200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7346.t1 is derived from g4518.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28635193	28636110	.	-	.	Phchi.S1G450500
Phchi.S1	AUGUSTUS	transcript	28635193	28636110	.	-	.	transcript_id "Phchi.S1G450500.t1"; gene_id "Phchi.S1G450500"
Phchi.S1	AUGUSTUS	stop_codon	28635190	28635192	.	-	0	transcript_id "Phchi.S1G450500.t1"; gene_id "Phchi.S1G450500"
Phchi.S1	AUGUSTUS	CDS	28635193	28636110	1	-	0	transcript_id "Phchi.S1G450500.t1"; gene_id "Phchi.S1G450500"
Phchi.S1	AUGUSTUS	exon	28635193	28636110	.	-	.	transcript_id "Phchi.S1G450500.t1"; gene_id "Phchi.S1G450500"
Phchi.S1	AUGUSTUS	start_codon	28636108	28636110	.	-	0	transcript_id "Phchi.S1G450500.t1"; gene_id "Phchi.S1G450500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5930.t1 is derived from g3101.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19898775	19903841	.	-	.	Phchi.S1G308900
Phchi.S1	AUGUSTUS	transcript	19898775	19900390	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	stop_codon	19898772	19898774	.	-	0	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19898775	19898906	1	-	0	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19898775	19898906	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19898907	19899024	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899025	19899106	1	-	1	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899025	19899106	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899107	19899194	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899195	19899304	1	-	0	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899195	19899304	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899305	19899442	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899443	19899579	1	-	2	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899443	19899579	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899580	19899673	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899674	19899780	1	-	1	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899674	19899780	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899781	19899875	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899876	19899921	0.88	-	2	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899876	19899921	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899922	19900050	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19900051	19900390	0.82	-	0	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19900051	19900390	.	-	.	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	start_codon	19900388	19900390	.	-	0	transcript_id "Phchi.S1G308900.t1"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	transcript	19898775	19903841	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	stop_codon	19898772	19898774	.	-	0	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19898775	19898906	1	-	0	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19898775	19898906	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19898907	19899024	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899025	19899106	1	-	1	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899025	19899106	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899107	19899194	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899195	19899304	1	-	0	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899195	19899304	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899305	19899442	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899443	19899579	1	-	2	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899443	19899579	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899580	19899673	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899674	19899780	1	-	1	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899674	19899780	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899781	19899875	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19899876	19899921	0.99	-	2	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19899876	19899921	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19899922	19900977	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19900978	19901026	0.41	-	0	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19900978	19901026	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	intron	19901027	19901156	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	CDS	19901157	19903841	0.16	-	0	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	exon	19901157	19903841	.	-	.	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
Phchi.S1	AUGUSTUS	start_codon	19903839	19903841	.	-	0	transcript_id "Phchi.S1G308900.t2"; gene_id "Phchi.S1G308900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13859.t1 is derived from g12326.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9270793	9275099	.	-	.	Phchi.S3G117800
Phchi.S3	AUGUSTUS	transcript	9270793	9275099	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	stop_codon	9270790	9270792	.	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9270793	9271391	0.83	-	2	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9270793	9271391	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9271392	9271579	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9271580	9271740	1	-	1	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9271580	9271740	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9271741	9271830	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9271831	9272125	1	-	2	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9271831	9272125	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9272126	9272216	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9272217	9272292	1	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9272217	9272292	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9272293	9272389	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9272390	9272578	1	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9272390	9272578	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9272579	9272676	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9272677	9272898	1	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9272677	9272898	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9272899	9272997	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9272998	9273096	1	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9272998	9273096	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9273097	9273178	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9273179	9273259	1	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9273179	9273259	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9273260	9273424	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9273425	9273720	0.92	-	2	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9273425	9273720	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9273721	9273872	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9273873	9274212	0.96	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9273873	9274212	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9274213	9274359	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9274360	9274423	1	-	1	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9274360	9274423	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9274424	9274544	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9274545	9274769	1	-	1	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9274545	9274769	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	intron	9274770	9274899	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	CDS	9274900	9275099	0.94	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	exon	9274900	9275099	.	-	.	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
Phchi.S3	AUGUSTUS	start_codon	9275097	9275099	.	-	0	transcript_id "Phchi.S3G117800.t1"; gene_id "Phchi.S3G117800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9108.t1 is derived from g6283.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39859422	39860009	.	-	.	Phchi.S1G626700
Phchi.S1	AUGUSTUS	transcript	39859422	39860009	.	-	.	transcript_id "Phchi.S1G626700.t1"; gene_id "Phchi.S1G626700"
Phchi.S1	AUGUSTUS	stop_codon	39859419	39859421	.	-	0	transcript_id "Phchi.S1G626700.t1"; gene_id "Phchi.S1G626700"
Phchi.S1	AUGUSTUS	CDS	39859422	39860009	0.91	-	0	transcript_id "Phchi.S1G626700.t1"; gene_id "Phchi.S1G626700"
Phchi.S1	AUGUSTUS	exon	39859422	39860009	.	-	.	transcript_id "Phchi.S1G626700.t1"; gene_id "Phchi.S1G626700"
Phchi.S1	AUGUSTUS	start_codon	39860007	39860009	.	-	0	transcript_id "Phchi.S1G626700.t1"; gene_id "Phchi.S1G626700"
# This transcript jg10870.t1 is derived from g14919.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2670842	2680151	.	+	.	Phchi.S4G045100
Phchi.S4	AUGUSTUS	transcript	2670842	2680151	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	start_codon	2670842	2670844	.	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2670842	2670974	0.99	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2670842	2670974	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2670975	2671050	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671051	2671140	1	+	2	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671051	2671140	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671141	2671216	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671217	2671335	1	+	2	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671217	2671335	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671336	2671411	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671412	2671525	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671412	2671525	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671526	2671625	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671626	2671707	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671626	2671707	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671708	2671845	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671846	2671913	1	+	2	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671846	2671913	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671914	2672073	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672074	2672145	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672074	2672145	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672146	2672314	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672315	2672460	0.77	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672315	2672460	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672461	2672589	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672590	2672692	0.99	+	1	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672590	2672692	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672693	2672775	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672776	2672856	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672776	2672856	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672857	2673007	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673008	2673076	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673008	2673076	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673077	2673173	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673174	2673233	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673174	2673233	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673234	2673306	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673307	2673465	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673307	2673465	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673466	2673567	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673568	2673633	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673568	2673633	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673634	2673721	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673722	2673940	0.5	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673722	2673940	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673941	2674100	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674101	2674166	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674101	2674166	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674167	2674264	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674265	2674452	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674265	2674452	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674453	2674539	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674540	2674636	1	+	1	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674540	2674636	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674637	2674708	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674709	2674777	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674709	2674777	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674778	2674860	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674861	2674932	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674861	2674932	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674933	2675025	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2675026	2675844	0.99	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2675026	2675844	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2675845	2676045	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2676046	2676246	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2676046	2676246	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2676247	2676360	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2676361	2676579	0.98	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2676361	2676579	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2676580	2676786	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2676787	2677014	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2676787	2677014	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677015	2677111	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677112	2677192	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677112	2677192	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677193	2677275	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677276	2677428	0.95	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677276	2677428	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677429	2677549	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677550	2677669	0.92	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677550	2677669	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677670	2677842	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677843	2677949	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677843	2677949	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677950	2678052	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678053	2678152	1	+	1	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678053	2678152	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2678153	2678282	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678283	2678492	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678283	2678492	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2678493	2678702	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678703	2678822	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678703	2678822	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2678823	2678918	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678919	2679089	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678919	2679089	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679090	2679184	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679185	2679264	1	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679185	2679264	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679265	2679330	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679331	2679457	1	+	1	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679331	2679457	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679458	2679548	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679549	2679614	0.98	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679549	2679614	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679615	2679717	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679718	2679894	0.97	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679718	2679894	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679895	2679971	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679972	2680151	0.97	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679972	2680151	.	+	.	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	stop_codon	2680152	2680154	.	+	0	transcript_id "Phchi.S4G045100.t1"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	transcript	2670842	2680151	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	start_codon	2670842	2670844	.	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2670842	2670974	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2670842	2670974	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2670975	2671050	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671051	2671140	1	+	2	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671051	2671140	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671141	2671216	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671217	2671335	1	+	2	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671217	2671335	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671336	2671411	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671412	2671525	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671412	2671525	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671526	2671625	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671626	2671707	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671626	2671707	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671708	2671845	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2671846	2671913	1	+	2	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2671846	2671913	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2671914	2672073	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672074	2672145	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672074	2672145	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672146	2672314	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672315	2672460	0.76	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672315	2672460	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672461	2672589	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672590	2672692	0.97	+	1	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672590	2672692	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672693	2672775	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2672776	2672856	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2672776	2672856	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2672857	2673007	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673008	2673076	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673008	2673076	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673077	2673173	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673174	2673233	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673174	2673233	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673234	2673306	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673307	2673465	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673307	2673465	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673466	2673567	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673568	2673633	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673568	2673633	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673634	2673721	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2673722	2673940	0.48	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2673722	2673940	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2673941	2674100	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674101	2674166	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674101	2674166	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674167	2674264	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674265	2674333	0.98	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674265	2674333	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674334	2674419	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674420	2674452	0.77	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674420	2674452	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674453	2674531	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674532	2674636	0.98	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674532	2674636	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674637	2674708	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674709	2674777	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674709	2674777	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674778	2674860	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2674861	2674932	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2674861	2674932	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2674933	2675025	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2675026	2675844	0.98	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2675026	2675844	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2675845	2676045	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2676046	2676246	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2676046	2676246	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2676247	2676360	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2676361	2676579	0.96	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2676361	2676579	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2676580	2676786	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2676787	2677014	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2676787	2677014	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677015	2677111	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677112	2677192	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677112	2677192	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677193	2677275	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677276	2677428	0.93	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677276	2677428	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677429	2677549	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677550	2677669	0.94	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677550	2677669	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677670	2677842	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2677843	2677949	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2677843	2677949	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2677950	2678052	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678053	2678152	1	+	1	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678053	2678152	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2678153	2678282	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678283	2678492	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678283	2678492	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2678493	2678702	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678703	2678822	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678703	2678822	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2678823	2678918	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2678919	2679089	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2678919	2679089	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679090	2679184	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679185	2679264	1	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679185	2679264	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679265	2679330	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679331	2679457	1	+	1	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679331	2679457	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679458	2679548	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679549	2679614	0.99	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679549	2679614	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679615	2679717	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679718	2679894	0.97	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679718	2679894	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	intron	2679895	2679971	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	CDS	2679972	2680151	0.97	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	exon	2679972	2680151	.	+	.	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
Phchi.S4	AUGUSTUS	stop_codon	2680152	2680154	.	+	0	transcript_id "Phchi.S4G045100.t2"; gene_id "Phchi.S4G045100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13205.t1 is derived from g11670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4658847	4660080	.	-	.	Phchi.S3G052400
Phchi.S3	AUGUSTUS	transcript	4658847	4660080	.	-	.	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	stop_codon	4658844	4658846	.	-	0	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	CDS	4658847	4659008	1	-	0	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	exon	4658847	4659008	.	-	.	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	intron	4659009	4659303	.	-	.	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	CDS	4659304	4660080	0.79	-	0	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	exon	4659304	4660080	.	-	.	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
Phchi.S3	AUGUSTUS	start_codon	4660078	4660080	.	-	0	transcript_id "Phchi.S3G052400.t1"; gene_id "Phchi.S3G052400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8350.t1 is derived from g5525.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35443655	35448529	.	-	.	Phchi.S1G550900
Phchi.S1	AUGUSTUS	transcript	35443655	35448529	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	stop_codon	35443652	35443654	.	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35443655	35444254	0.99	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35443655	35444254	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35444255	35444324	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35444325	35444406	1	-	1	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35444325	35444406	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35444407	35444494	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35444495	35444580	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35444495	35444580	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35444581	35444680	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35444681	35444761	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35444681	35444761	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35444762	35444850	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35444851	35444970	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35444851	35444970	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35444971	35445054	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35445055	35445132	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35445055	35445132	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35445133	35445233	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35445234	35445437	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35445234	35445437	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35445438	35445518	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35445519	35445584	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35445519	35445584	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35445585	35445695	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35445696	35445758	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35445696	35445758	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35445759	35445866	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35445867	35446022	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35445867	35446022	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35446023	35446141	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35446142	35446235	1	-	1	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35446142	35446235	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35446236	35446330	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35446331	35446434	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35446331	35446434	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35446435	35446558	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35446559	35446661	1	-	1	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35446559	35446661	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35446662	35446736	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35446737	35446827	1	-	2	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35446737	35446827	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35446828	35446917	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35446918	35447050	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35446918	35447050	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35447051	35447146	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35447147	35447449	0.98	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35447147	35447449	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35447450	35447565	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35447566	35447745	0.99	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35447566	35447745	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35447746	35447828	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35447829	35448098	1	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35447829	35448098	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	intron	35448099	35448184	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	CDS	35448185	35448529	0.47	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	exon	35448185	35448529	.	-	.	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
Phchi.S1	AUGUSTUS	start_codon	35448527	35448529	.	-	0	transcript_id "Phchi.S1G550900.t1"; gene_id "Phchi.S1G550900"
# This transcript jg2974.t2 is derived from g143.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2975.t1 is derived from g144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	917883	918248	.	-	.	Phchi.S1G013400
Phchi.S1	AUGUSTUS	transcript	917883	918248	.	-	.	transcript_id "Phchi.S1G013400.t1"; gene_id "Phchi.S1G013400"
Phchi.S1	AUGUSTUS	stop_codon	917880	917882	.	-	0	transcript_id "Phchi.S1G013400.t1"; gene_id "Phchi.S1G013400"
Phchi.S1	AUGUSTUS	CDS	917883	918248	0.99	-	0	transcript_id "Phchi.S1G013400.t1"; gene_id "Phchi.S1G013400"
Phchi.S1	AUGUSTUS	exon	917883	918248	.	-	.	transcript_id "Phchi.S1G013400.t1"; gene_id "Phchi.S1G013400"
Phchi.S1	AUGUSTUS	start_codon	918246	918248	.	-	0	transcript_id "Phchi.S1G013400.t1"; gene_id "Phchi.S1G013400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7375.t1 is derived from g4547.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28823670	28824686	.	+	.	Phchi.S1G453400
Phchi.S1	AUGUSTUS	transcript	28823670	28824686	.	+	.	transcript_id "Phchi.S1G453400.t1"; gene_id "Phchi.S1G453400"
Phchi.S1	AUGUSTUS	start_codon	28823670	28823672	.	+	0	transcript_id "Phchi.S1G453400.t1"; gene_id "Phchi.S1G453400"
Phchi.S1	AUGUSTUS	CDS	28823670	28824686	0.79	+	0	transcript_id "Phchi.S1G453400.t1"; gene_id "Phchi.S1G453400"
Phchi.S1	AUGUSTUS	exon	28823670	28824686	.	+	.	transcript_id "Phchi.S1G453400.t1"; gene_id "Phchi.S1G453400"
Phchi.S1	AUGUSTUS	stop_codon	28824687	28824689	.	+	0	transcript_id "Phchi.S1G453400.t1"; gene_id "Phchi.S1G453400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg993.t1 is derived from g10776.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6951649	6952474	.	-	.	Phchi.S6G095200
Phchi.S6	AUGUSTUS	transcript	6951649	6952474	.	-	.	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	stop_codon	6951646	6951648	.	-	0	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	CDS	6951649	6951913	1	-	1	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	exon	6951649	6951913	.	-	.	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	intron	6951914	6952091	.	-	.	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	CDS	6952092	6952474	0.98	-	0	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	exon	6952092	6952474	.	-	.	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
Phchi.S6	AUGUSTUS	start_codon	6952472	6952474	.	-	0	transcript_id "Phchi.S6G095200.t1"; gene_id "Phchi.S6G095200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13342.t1 is derived from g11808.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6181766	6183683	.	+	.	Phchi.S3G066100
Phchi.S3	AUGUSTUS	transcript	6181766	6183683	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	start_codon	6181766	6181768	.	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6181766	6181899	0.79	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6181766	6181899	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6181900	6182041	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6182042	6182107	1	+	1	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6182042	6182107	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6182108	6182228	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6182229	6182274	1	+	1	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6182229	6182274	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6182275	6182418	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6182419	6182579	1	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6182419	6182579	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6182580	6182674	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6182675	6182804	1	+	1	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6182675	6182804	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6182805	6182898	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6182899	6183066	1	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6182899	6183066	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6183067	6183219	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6183220	6183347	1	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6183220	6183347	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6183348	6183435	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6183436	6183535	1	+	1	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6183436	6183535	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	intron	6183536	6183632	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	CDS	6183633	6183683	1	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	exon	6183633	6183683	.	+	.	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
Phchi.S3	AUGUSTUS	stop_codon	6183684	6183686	.	+	0	transcript_id "Phchi.S3G066100.t1"; gene_id "Phchi.S3G066100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg811.t1 is derived from g10593.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5695608	5697390	.	-	.	Phchi.S6G077000
Phchi.S6	AUGUSTUS	transcript	5695608	5697390	.	-	.	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	stop_codon	5695605	5695607	.	-	0	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	CDS	5695608	5697012	0.55	-	1	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	exon	5695608	5697012	.	-	.	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	intron	5697013	5697086	.	-	.	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	CDS	5697087	5697211	0.55	-	0	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	exon	5697087	5697211	.	-	.	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	intron	5697212	5697312	.	-	.	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	CDS	5697313	5697390	0.72	-	0	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	exon	5697313	5697390	.	-	.	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
Phchi.S6	AUGUSTUS	start_codon	5697388	5697390	.	-	0	transcript_id "Phchi.S6G077000.t1"; gene_id "Phchi.S6G077000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1274.t1 is derived from g11057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8772786	8777017	.	-	.	Phchi.S6G123300
Phchi.S6	AUGUSTUS	transcript	8772786	8777017	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	stop_codon	8772783	8772785	.	-	0	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8772786	8774914	0.92	-	2	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8772786	8774914	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	intron	8774915	8775002	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8775003	8775192	0.97	-	0	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8775003	8775192	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	intron	8775193	8775328	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8775329	8775913	0.44	-	0	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8775329	8775913	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	intron	8775914	8775996	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8775997	8776203	0.85	-	0	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8775997	8776203	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	intron	8776204	8776321	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8776322	8776403	0.66	-	1	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8776322	8776403	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	intron	8776404	8776500	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8776501	8776515	0.77	-	1	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8776501	8776515	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	intron	8776516	8776685	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	CDS	8776686	8777017	0.62	-	0	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	exon	8776686	8777017	.	-	.	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
Phchi.S6	AUGUSTUS	start_codon	8777015	8777017	.	-	0	transcript_id "Phchi.S6G123300.t1"; gene_id "Phchi.S6G123300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6210.t1 is derived from g3381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21478378	21479276	.	+	.	Phchi.S1G336900
Phchi.S1	AUGUSTUS	transcript	21478378	21479276	.	+	.	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	start_codon	21478378	21478380	.	+	0	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	CDS	21478378	21478637	0.95	+	0	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	exon	21478378	21478637	.	+	.	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	intron	21478638	21478768	.	+	.	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	CDS	21478769	21479276	0.72	+	1	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	exon	21478769	21479276	.	+	.	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
Phchi.S1	AUGUSTUS	stop_codon	21479277	21479279	.	+	0	transcript_id "Phchi.S1G336900.t1"; gene_id "Phchi.S1G336900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6769.t1 is derived from g3941.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24996246	24998078	.	-	.	Phchi.S1G392800
Phchi.S1	AUGUSTUS	transcript	24996246	24998078	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	stop_codon	24996243	24996245	.	-	0	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24996246	24996299	1	-	0	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24996246	24996299	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24996300	24996395	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24996396	24996489	0.94	-	1	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24996396	24996489	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24996490	24996587	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24996588	24996680	0.41	-	1	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24996588	24996680	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24996681	24996757	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24996758	24996838	0.99	-	1	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24996758	24996838	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24996839	24996972	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24996973	24997082	0.95	-	0	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24996973	24997082	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24997083	24997275	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24997276	24997615	0.35	-	1	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24997276	24997615	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24997616	24997713	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24997714	24997817	0.36	-	0	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24997714	24997817	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	intron	24997818	24997940	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	CDS	24997941	24998078	0.88	-	0	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	exon	24997941	24998078	.	-	.	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
Phchi.S1	AUGUSTUS	start_codon	24998076	24998078	.	-	0	transcript_id "Phchi.S1G392800.t1"; gene_id "Phchi.S1G392800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11167.t1 is derived from g15217.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4444067	4446164	.	-	.	Phchi.S4G074900
Phchi.S4	AUGUSTUS	transcript	4444067	4446164	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	stop_codon	4444064	4444066	.	-	0	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444067	4444091	1	-	1	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444067	4444091	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444092	4444210	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444211	4444342	1	-	1	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444211	4444342	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444343	4444426	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444427	4444504	1	-	1	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444427	4444504	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444505	4444649	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444650	4444716	1	-	2	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444650	4444716	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444717	4444838	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444839	4444897	1	-	1	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444839	4444897	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444898	4444981	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444982	4445154	1	-	0	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444982	4445154	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445155	4445309	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445310	4445372	0.98	-	0	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445310	4445372	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445373	4445478	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445479	4445602	0.95	-	1	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445479	4445602	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445603	4445694	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445695	4445801	1	-	0	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445695	4445801	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445802	4445876	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445877	4445953	1	-	2	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445877	4445953	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445954	4446037	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4446038	4446164	0.97	-	0	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4446038	4446164	.	-	.	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	start_codon	4446162	4446164	.	-	0	transcript_id "Phchi.S4G074900.t1"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	transcript	4444067	4446164	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	stop_codon	4444064	4444066	.	-	0	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444067	4444091	1	-	1	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444067	4444091	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444092	4444210	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444211	4444342	1	-	1	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444211	4444342	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444343	4444426	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444427	4444504	1	-	1	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444427	4444504	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444505	4444649	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444650	4444716	1	-	2	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444650	4444716	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444717	4444838	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444839	4444897	1	-	1	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444839	4444897	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4444898	4444981	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4444982	4445181	0.48	-	0	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4444982	4445181	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445182	4445309	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445310	4445372	0.99	-	0	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445310	4445372	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445373	4445478	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445479	4445602	0.94	-	1	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445479	4445602	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445603	4445694	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445695	4445801	1	-	0	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445695	4445801	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445802	4445876	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4445877	4445953	1	-	2	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4445877	4445953	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	intron	4445954	4446037	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	CDS	4446038	4446164	0.96	-	0	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	exon	4446038	4446164	.	-	.	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
Phchi.S4	AUGUSTUS	start_codon	4446162	4446164	.	-	0	transcript_id "Phchi.S4G074900.t2"; gene_id "Phchi.S4G074900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10224.t1 is derived from g7400.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46470041	46472517	.	-	.	Phchi.S1G738300
Phchi.S1	AUGUSTUS	transcript	46470041	46472517	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	stop_codon	46470038	46470040	.	-	0	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	CDS	46470041	46470747	0.58	-	2	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	exon	46470041	46470747	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	intron	46470748	46471005	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	CDS	46471006	46471165	0.24	-	0	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	exon	46471006	46471165	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	intron	46471166	46471276	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	CDS	46471277	46472213	0.25	-	1	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	exon	46471277	46472213	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	intron	46472214	46472305	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	CDS	46472306	46472517	0.49	-	0	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	exon	46472306	46472517	.	-	.	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
Phchi.S1	AUGUSTUS	start_codon	46472515	46472517	.	-	0	transcript_id "Phchi.S1G738300.t1"; gene_id "Phchi.S1G738300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10661.t1 is derived from g14711.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1485692	1486754	.	+	.	Phchi.S4G024300
Phchi.S4	AUGUSTUS	transcript	1485692	1486754	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	start_codon	1485692	1485694	.	+	0	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	CDS	1485692	1485926	0.98	+	0	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	exon	1485692	1485926	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	intron	1485927	1486006	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	CDS	1486007	1486053	1	+	2	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	exon	1486007	1486053	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	intron	1486054	1486143	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	CDS	1486144	1486236	1	+	0	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	exon	1486144	1486236	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	intron	1486237	1486315	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	CDS	1486316	1486453	1	+	0	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	exon	1486316	1486453	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	intron	1486454	1486739	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	CDS	1486740	1486754	0.93	+	0	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	exon	1486740	1486754	.	+	.	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
Phchi.S4	AUGUSTUS	stop_codon	1486755	1486757	.	+	0	transcript_id "Phchi.S4G024300.t1"; gene_id "Phchi.S4G024300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11162.t1 is derived from g15212.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4429036	4432676	.	-	.	Phchi.S4G074400
Phchi.S4	AUGUSTUS	transcript	4429036	4432676	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	stop_codon	4429033	4429035	.	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4429036	4429182	1	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4429036	4429182	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4429183	4429259	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4429260	4429364	1	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4429260	4429364	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4429365	4429466	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4429467	4429598	1	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4429467	4429598	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4429599	4429691	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4429692	4430339	1	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4429692	4430339	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4430340	4430430	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4430431	4430525	1	-	2	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4430431	4430525	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4430526	4430609	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4430610	4430663	0.86	-	2	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4430610	4430663	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4430664	4430791	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4430792	4430858	0.86	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4430792	4430858	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4430859	4430954	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4430955	4431014	1	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4430955	4431014	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4431015	4431096	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4431097	4431192	1	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4431097	4431192	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4431193	4431310	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4431311	4431364	0.92	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4431311	4431364	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4431365	4431442	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4431443	4431592	0.76	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4431443	4431592	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4431593	4431779	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4431780	4431801	0.53	-	1	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4431780	4431801	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4431802	4431953	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4431954	4432135	0.45	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4431954	4432135	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4432136	4432327	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4432328	4432381	0.75	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4432328	4432381	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4432382	4432479	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4432480	4432557	0.44	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4432480	4432557	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	intron	4432558	4432655	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	CDS	4432656	4432676	0.52	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	exon	4432656	4432676	.	-	.	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
Phchi.S4	AUGUSTUS	start_codon	4432674	4432676	.	-	0	transcript_id "Phchi.S4G074400.t1"; gene_id "Phchi.S4G074400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4797.t1 is derived from g1967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12835706	12836326	.	-	.	Phchi.S1G195600
Phchi.S1	AUGUSTUS	transcript	12835706	12836326	.	-	.	transcript_id "Phchi.S1G195600.t1"; gene_id "Phchi.S1G195600"
Phchi.S1	AUGUSTUS	stop_codon	12835703	12835705	.	-	0	transcript_id "Phchi.S1G195600.t1"; gene_id "Phchi.S1G195600"
Phchi.S1	AUGUSTUS	CDS	12835706	12836326	1	-	0	transcript_id "Phchi.S1G195600.t1"; gene_id "Phchi.S1G195600"
Phchi.S1	AUGUSTUS	exon	12835706	12836326	.	-	.	transcript_id "Phchi.S1G195600.t1"; gene_id "Phchi.S1G195600"
Phchi.S1	AUGUSTUS	start_codon	12836324	12836326	.	-	0	transcript_id "Phchi.S1G195600.t1"; gene_id "Phchi.S1G195600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14165.t1 is derived from g12632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11232980	11234848	.	+	.	Phchi.S3G148400
Phchi.S3	AUGUSTUS	transcript	11232980	11234848	.	+	.	transcript_id "Phchi.S3G148400.t1"; gene_id "Phchi.S3G148400"
Phchi.S3	AUGUSTUS	start_codon	11232980	11232982	.	+	0	transcript_id "Phchi.S3G148400.t1"; gene_id "Phchi.S3G148400"
Phchi.S3	AUGUSTUS	CDS	11232980	11234848	1	+	0	transcript_id "Phchi.S3G148400.t1"; gene_id "Phchi.S3G148400"
Phchi.S3	AUGUSTUS	exon	11232980	11234848	.	+	.	transcript_id "Phchi.S3G148400.t1"; gene_id "Phchi.S3G148400"
Phchi.S3	AUGUSTUS	stop_codon	11234849	11234851	.	+	0	transcript_id "Phchi.S3G148400.t1"; gene_id "Phchi.S3G148400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8414.t1 is derived from g5589.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35838417	35840596	.	+	.	Phchi.S1G557300
Phchi.S1	AUGUSTUS	transcript	35838417	35840596	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	start_codon	35838417	35838419	.	+	0	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35838417	35838552	0.98	+	0	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35838417	35838552	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35838553	35838646	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35838647	35838802	0.98	+	2	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35838647	35838802	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35838803	35838895	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35838896	35839034	1	+	2	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35838896	35839034	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839035	35839195	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839196	35839317	1	+	1	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839196	35839317	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839318	35839407	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839408	35839478	1	+	2	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839408	35839478	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839479	35839614	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839615	35839657	1	+	0	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839615	35839657	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839658	35839744	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839745	35839841	1	+	2	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839745	35839841	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839842	35839944	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839945	35840028	1	+	1	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839945	35840028	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35840029	35840140	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35840141	35840253	1	+	1	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35840141	35840253	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35840254	35840339	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35840340	35840400	1	+	2	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35840340	35840400	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35840401	35840499	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35840500	35840596	0.99	+	1	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35840500	35840596	.	+	.	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	stop_codon	35840597	35840599	.	+	0	transcript_id "Phchi.S1G557300.t1"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	transcript	35838958	35840596	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	start_codon	35838958	35838960	.	+	0	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35838958	35839034	0.84	+	0	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35838958	35839034	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839035	35839195	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839196	35839317	1	+	1	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839196	35839317	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839318	35839407	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839408	35839478	1	+	2	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839408	35839478	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839479	35839614	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839615	35839657	1	+	0	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839615	35839657	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839658	35839744	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839745	35839841	1	+	2	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839745	35839841	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35839842	35839944	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35839945	35840028	1	+	1	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35839945	35840028	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35840029	35840140	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35840141	35840253	1	+	1	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35840141	35840253	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35840254	35840339	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35840340	35840400	1	+	2	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35840340	35840400	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	intron	35840401	35840499	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	CDS	35840500	35840596	1	+	1	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	exon	35840500	35840596	.	+	.	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
Phchi.S1	AUGUSTUS	stop_codon	35840597	35840599	.	+	0	transcript_id "Phchi.S1G557300.t2"; gene_id "Phchi.S1G557300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12456.t1 is derived from g8133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	23734458	23734758	.	+	.	Phchi.S2G053600
Phchi.S2	AUGUSTUS	transcript	23734458	23734758	.	+	.	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	start_codon	23734458	23734460	.	+	0	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	CDS	23734458	23734465	0.56	+	0	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	exon	23734458	23734465	.	+	.	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	intron	23734466	23734565	.	+	.	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	CDS	23734566	23734758	0.56	+	1	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	exon	23734566	23734758	.	+	.	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
Phchi.S2	AUGUSTUS	stop_codon	23734759	23734761	.	+	0	transcript_id "Phchi.S2G053600.t1"; gene_id "Phchi.S2G053600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7866.t1 is derived from g5040.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31602298	31603097	.	+	.	Phchi.S1G502500
Phchi.S1	AUGUSTUS	transcript	31602298	31603097	.	+	.	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	start_codon	31602298	31602300	.	+	0	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	CDS	31602298	31602575	0.27	+	0	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	exon	31602298	31602575	.	+	.	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	intron	31602576	31602661	.	+	.	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	CDS	31602662	31603097	0.35	+	1	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	exon	31602662	31603097	.	+	.	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	stop_codon	31603098	31603100	.	+	0	transcript_id "Phchi.S1G502500.t1"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	transcript	31602298	31602642	.	+	.	transcript_id "Phchi.S1G502500.t2"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	start_codon	31602298	31602300	.	+	0	transcript_id "Phchi.S1G502500.t2"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	CDS	31602298	31602642	0.47	+	0	transcript_id "Phchi.S1G502500.t2"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	exon	31602298	31602642	.	+	.	transcript_id "Phchi.S1G502500.t2"; gene_id "Phchi.S1G502500"
Phchi.S1	AUGUSTUS	stop_codon	31602643	31602645	.	+	0	transcript_id "Phchi.S1G502500.t2"; gene_id "Phchi.S1G502500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15161.t1 is derived from g13629.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17324689	17325594	.	+	.	Phchi.S3G248000
Phchi.S3	AUGUSTUS	transcript	17324689	17325594	.	+	.	transcript_id "Phchi.S3G248000.t1"; gene_id "Phchi.S3G248000"
Phchi.S3	AUGUSTUS	start_codon	17324689	17324691	.	+	0	transcript_id "Phchi.S3G248000.t1"; gene_id "Phchi.S3G248000"
Phchi.S3	AUGUSTUS	CDS	17324689	17325594	0.45	+	0	transcript_id "Phchi.S3G248000.t1"; gene_id "Phchi.S3G248000"
Phchi.S3	AUGUSTUS	exon	17324689	17325594	.	+	.	transcript_id "Phchi.S3G248000.t1"; gene_id "Phchi.S3G248000"
Phchi.S3	AUGUSTUS	stop_codon	17325595	17325597	.	+	0	transcript_id "Phchi.S3G248000.t1"; gene_id "Phchi.S3G248000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14627.t1 is derived from g13095.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13830516	13835046	.	-	.	Phchi.S3G194600
Phchi.S3	AUGUSTUS	transcript	13830516	13835046	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	stop_codon	13830513	13830515	.	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13830516	13830595	0.96	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13830516	13830595	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13830596	13830677	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13830678	13830790	0.96	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13830678	13830790	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13830791	13830882	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13830883	13830964	0.98	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13830883	13830964	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13830965	13831063	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13831064	13831191	0.78	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13831064	13831191	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13831192	13831278	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13831279	13831387	0.84	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13831279	13831387	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13831388	13831477	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13831478	13831600	0.91	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13831478	13831600	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13831601	13831889	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13831890	13832259	0.86	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13831890	13832259	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13832260	13832381	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13832382	13832549	0.98	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13832382	13832549	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13832550	13832642	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13832643	13832869	0.98	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13832643	13832869	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13832870	13832956	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13832957	13833018	0.99	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13832957	13833018	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13833019	13833119	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13833120	13833180	0.88	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13833120	13833180	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13833181	13833289	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13833290	13833395	0.98	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13833290	13833395	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13833396	13833517	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13833518	13833620	0.98	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13833518	13833620	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13833621	13833695	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13833696	13833769	0.77	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13833696	13833769	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13833770	13833936	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13833937	13834033	0.35	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13833937	13834033	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13834034	13834200	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13834201	13834330	0.85	-	2	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13834201	13834330	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13834331	13834476	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13834477	13834535	0.54	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13834477	13834535	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13834536	13834684	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13834685	13834753	0.55	-	1	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13834685	13834753	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	intron	13834754	13834993	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	CDS	13834994	13835046	0.7	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	exon	13834994	13835046	.	-	.	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
Phchi.S3	AUGUSTUS	start_codon	13835044	13835046	.	-	0	transcript_id "Phchi.S3G194600.t1"; gene_id "Phchi.S3G194600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2430.t1 is derived from g9350.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6616580	6617497	.	-	.	Phchi.S5G103900
Phchi.S5	AUGUSTUS	transcript	6616580	6617497	.	-	.	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	stop_codon	6616577	6616579	.	-	0	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	CDS	6616580	6616786	1	-	0	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	exon	6616580	6616786	.	-	.	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	intron	6616787	6616895	.	-	.	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	CDS	6616896	6617031	0.92	-	1	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	exon	6616896	6617031	.	-	.	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	intron	6617032	6617186	.	-	.	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	CDS	6617187	6617497	0.99	-	0	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	exon	6617187	6617497	.	-	.	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
Phchi.S5	AUGUSTUS	start_codon	6617495	6617497	.	-	0	transcript_id "Phchi.S5G103900.t1"; gene_id "Phchi.S5G103900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1813.t1 is derived from g8733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3230330	3230920	.	-	.	Phchi.S5G042200
Phchi.S5	AUGUSTUS	transcript	3230330	3230920	.	-	.	transcript_id "Phchi.S5G042200.t1"; gene_id "Phchi.S5G042200"
Phchi.S5	AUGUSTUS	stop_codon	3230327	3230329	.	-	0	transcript_id "Phchi.S5G042200.t1"; gene_id "Phchi.S5G042200"
Phchi.S5	AUGUSTUS	CDS	3230330	3230920	0.55	-	0	transcript_id "Phchi.S5G042200.t1"; gene_id "Phchi.S5G042200"
Phchi.S5	AUGUSTUS	exon	3230330	3230920	.	-	.	transcript_id "Phchi.S5G042200.t1"; gene_id "Phchi.S5G042200"
Phchi.S5	AUGUSTUS	start_codon	3230918	3230920	.	-	0	transcript_id "Phchi.S5G042200.t1"; gene_id "Phchi.S5G042200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1067.t1 is derived from g10850.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7408942	7410558	.	+	.	Phchi.S6G102600
Phchi.S6	AUGUSTUS	transcript	7408942	7410558	.	+	.	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	start_codon	7408942	7408944	.	+	0	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	CDS	7408942	7409343	0.77	+	0	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	exon	7408942	7409343	.	+	.	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	intron	7409344	7409841	.	+	.	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	CDS	7409842	7410558	0.7	+	0	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	exon	7409842	7410558	.	+	.	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
Phchi.S6	AUGUSTUS	stop_codon	7410559	7410561	.	+	0	transcript_id "Phchi.S6G102600.t1"; gene_id "Phchi.S6G102600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15504.t1 is derived from g13973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19588104	19589030	.	-	.	Phchi.S3G282300
Phchi.S3	AUGUSTUS	transcript	19588104	19589030	.	-	.	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	stop_codon	19588101	19588103	.	-	0	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	CDS	19588104	19588330	1	-	2	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	exon	19588104	19588330	.	-	.	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	intron	19588331	19588458	.	-	.	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	CDS	19588459	19588565	1	-	1	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	exon	19588459	19588565	.	-	.	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	intron	19588566	19588653	.	-	.	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	CDS	19588654	19589030	0.51	-	0	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	exon	19588654	19589030	.	-	.	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
Phchi.S3	AUGUSTUS	start_codon	19589028	19589030	.	-	0	transcript_id "Phchi.S3G282300.t1"; gene_id "Phchi.S3G282300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9571.t1 is derived from g6747.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42722005	42723505	.	-	.	Phchi.S1G673000
Phchi.S1	AUGUSTUS	transcript	42722005	42723505	.	-	.	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	stop_codon	42722002	42722004	.	-	0	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	CDS	42722005	42722843	0.02	-	2	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	exon	42722005	42722843	.	-	.	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	intron	42722844	42722872	.	-	.	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	CDS	42722873	42723395	0.04	-	0	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	exon	42722873	42723395	.	-	.	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	intron	42723396	42723493	.	-	.	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	CDS	42723494	42723505	0.04	-	0	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	exon	42723494	42723505	.	-	.	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
Phchi.S1	AUGUSTUS	start_codon	42723503	42723505	.	-	0	transcript_id "Phchi.S1G673000.t1"; gene_id "Phchi.S1G673000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7467.t1 is derived from g4640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29523035	29524455	.	+	.	Phchi.S1G462600
Phchi.S1	AUGUSTUS	transcript	29523035	29524455	.	+	.	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	start_codon	29523035	29523037	.	+	0	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	CDS	29523035	29524243	0.48	+	0	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	exon	29523035	29524243	.	+	.	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	intron	29524244	29524329	.	+	.	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	CDS	29524330	29524455	0.74	+	0	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	exon	29524330	29524455	.	+	.	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
Phchi.S1	AUGUSTUS	stop_codon	29524456	29524458	.	+	0	transcript_id "Phchi.S1G462600.t1"; gene_id "Phchi.S1G462600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2051.t1 is derived from g8971.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4601058	4603928	.	-	.	Phchi.S5G066000
Phchi.S5	AUGUSTUS	transcript	4601058	4603928	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	stop_codon	4601055	4601057	.	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601058	4601113	0.98	-	2	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601058	4601113	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601114	4601199	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601200	4601257	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601200	4601257	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601258	4601334	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601335	4601390	1	-	2	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601335	4601390	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601391	4601467	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601468	4601510	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601468	4601510	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601511	4601590	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601591	4601656	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601591	4601656	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601657	4601738	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601739	4601784	1	-	1	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601739	4601784	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601785	4601868	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4601869	4601933	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4601869	4601933	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4601934	4602041	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4602042	4602145	1	-	2	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4602042	4602145	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4602146	4602268	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4602269	4602339	1	-	1	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4602269	4602339	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4602340	4602426	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4602427	4602504	1	-	1	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4602427	4602504	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4602505	4602710	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4602711	4602832	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4602711	4602832	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4602833	4602980	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4602981	4603031	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4602981	4603031	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4603032	4603120	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4603121	4603216	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4603121	4603216	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4603217	4603290	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4603291	4603396	1	-	1	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4603291	4603396	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4603397	4603477	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4603478	4603569	1	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4603478	4603569	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	intron	4603570	4603649	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	CDS	4603650	4603928	0.97	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	exon	4603650	4603928	.	-	.	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
Phchi.S5	AUGUSTUS	start_codon	4603926	4603928	.	-	0	transcript_id "Phchi.S5G066000.t1"; gene_id "Phchi.S5G066000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1097.t1 is derived from g10880.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7594806	7596218	.	-	.	Phchi.S6G105600
Phchi.S6	AUGUSTUS	transcript	7594806	7596218	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	stop_codon	7594803	7594805	.	-	0	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	CDS	7594806	7595015	0.96	-	0	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	exon	7594806	7595015	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	intron	7595016	7595108	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	CDS	7595109	7595253	1	-	1	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	exon	7595109	7595253	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	intron	7595254	7595331	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	CDS	7595332	7595509	1	-	2	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	exon	7595332	7595509	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	intron	7595510	7595582	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	CDS	7595583	7595651	1	-	2	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	exon	7595583	7595651	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	intron	7595652	7595750	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	CDS	7595751	7595877	1	-	0	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	exon	7595751	7595877	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	intron	7595878	7595975	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	CDS	7595976	7596218	1	-	0	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	exon	7595976	7596218	.	-	.	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
Phchi.S6	AUGUSTUS	start_codon	7596216	7596218	.	-	0	transcript_id "Phchi.S6G105600.t1"; gene_id "Phchi.S6G105600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9444.t1 is derived from g6620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41493854	41494687	.	-	.	Phchi.S1G660300
Phchi.S1	AUGUSTUS	transcript	41493854	41494687	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	stop_codon	41493851	41493853	.	-	0	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	CDS	41493854	41494053	1	-	2	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	exon	41493854	41494053	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	intron	41494054	41494148	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	CDS	41494149	41494272	0.39	-	0	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	exon	41494149	41494272	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	intron	41494273	41494418	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	CDS	41494419	41494478	0.75	-	0	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	exon	41494419	41494478	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	intron	41494479	41494666	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	CDS	41494667	41494687	0.58	-	0	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	exon	41494667	41494687	.	-	.	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
Phchi.S1	AUGUSTUS	start_codon	41494685	41494687	.	-	0	transcript_id "Phchi.S1G660300.t1"; gene_id "Phchi.S1G660300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3335.t1 is derived from g504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2973604	2974175	.	+	.	Phchi.S1G049400
Phchi.S1	AUGUSTUS	transcript	2973604	2974175	.	+	.	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	start_codon	2973604	2973606	.	+	0	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	CDS	2973604	2973750	0.54	+	0	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	exon	2973604	2973750	.	+	.	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	intron	2973751	2973848	.	+	.	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	CDS	2973849	2974175	0.87	+	0	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	exon	2973849	2974175	.	+	.	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
Phchi.S1	AUGUSTUS	stop_codon	2974176	2974178	.	+	0	transcript_id "Phchi.S1G049400.t1"; gene_id "Phchi.S1G049400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14069.t1 is derived from g12536.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10643481	10644516	.	-	.	Phchi.S3G138800
Phchi.S3	AUGUSTUS	transcript	10643481	10644516	.	-	.	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	stop_codon	10643478	10643480	.	-	0	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	CDS	10643481	10643987	0.93	-	0	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	exon	10643481	10643987	.	-	.	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	intron	10643988	10644145	.	-	.	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	CDS	10644146	10644237	0.54	-	2	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	exon	10644146	10644237	.	-	.	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	intron	10644238	10644440	.	-	.	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	CDS	10644441	10644516	0.96	-	0	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	exon	10644441	10644516	.	-	.	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
Phchi.S3	AUGUSTUS	start_codon	10644514	10644516	.	-	0	transcript_id "Phchi.S3G138800.t1"; gene_id "Phchi.S3G138800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg342.t1 is derived from g10124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2485622	2486161	.	-	.	Phchi.S6G030100
Phchi.S6	AUGUSTUS	transcript	2485622	2486161	.	-	.	transcript_id "Phchi.S6G030100.t1"; gene_id "Phchi.S6G030100"
Phchi.S6	AUGUSTUS	stop_codon	2485619	2485621	.	-	0	transcript_id "Phchi.S6G030100.t1"; gene_id "Phchi.S6G030100"
Phchi.S6	AUGUSTUS	CDS	2485622	2486161	0.53	-	0	transcript_id "Phchi.S6G030100.t1"; gene_id "Phchi.S6G030100"
Phchi.S6	AUGUSTUS	exon	2485622	2486161	.	-	.	transcript_id "Phchi.S6G030100.t1"; gene_id "Phchi.S6G030100"
Phchi.S6	AUGUSTUS	start_codon	2486159	2486161	.	-	0	transcript_id "Phchi.S6G030100.t1"; gene_id "Phchi.S6G030100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14413.t1 is derived from g12881.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12698859	12701025	.	-	.	Phchi.S3G173200
Phchi.S3	AUGUSTUS	transcript	12698859	12701025	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	stop_codon	12698856	12698858	.	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12698859	12698897	1	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12698859	12698897	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12698898	12698973	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12698974	12699114	1	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12698974	12699114	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12699115	12699212	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12699213	12699320	1	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12699213	12699320	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12699321	12699449	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12699450	12699497	1	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12699450	12699497	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12699498	12699590	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12699591	12699806	1	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12699591	12699806	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12699807	12699901	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12699902	12699966	1	-	2	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12699902	12699966	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12699967	12700080	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12700081	12700205	1	-	1	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12700081	12700205	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12700206	12700338	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12700339	12700525	1	-	2	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12700339	12700525	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	intron	12700526	12700868	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	CDS	12700869	12701025	1	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	exon	12700869	12701025	.	-	.	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
Phchi.S3	AUGUSTUS	start_codon	12701023	12701025	.	-	0	transcript_id "Phchi.S3G173200.t1"; gene_id "Phchi.S3G173200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1681.t1 is derived from g8600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2481166	2482369	.	+	.	Phchi.S5G029000
Phchi.S5	AUGUSTUS	transcript	2481166	2482369	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	start_codon	2481166	2481168	.	+	0	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	CDS	2481166	2481741	0.84	+	0	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	exon	2481166	2481741	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	intron	2481742	2481860	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	CDS	2481861	2481966	1	+	0	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	exon	2481861	2481966	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	intron	2481967	2482085	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	CDS	2482086	2482172	1	+	2	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	exon	2482086	2482172	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	intron	2482173	2482268	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	CDS	2482269	2482369	0.99	+	2	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	exon	2482269	2482369	.	+	.	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
Phchi.S5	AUGUSTUS	stop_codon	2482370	2482372	.	+	0	transcript_id "Phchi.S5G029000.t1"; gene_id "Phchi.S5G029000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6487.t1 is derived from g3659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23233174	23234280	.	+	.	Phchi.S1G364600
Phchi.S1	AUGUSTUS	transcript	23233174	23234280	.	+	.	transcript_id "Phchi.S1G364600.t1"; gene_id "Phchi.S1G364600"
Phchi.S1	AUGUSTUS	start_codon	23233174	23233176	.	+	0	transcript_id "Phchi.S1G364600.t1"; gene_id "Phchi.S1G364600"
Phchi.S1	AUGUSTUS	CDS	23233174	23234280	0.37	+	0	transcript_id "Phchi.S1G364600.t1"; gene_id "Phchi.S1G364600"
Phchi.S1	AUGUSTUS	exon	23233174	23234280	.	+	.	transcript_id "Phchi.S1G364600.t1"; gene_id "Phchi.S1G364600"
Phchi.S1	AUGUSTUS	stop_codon	23234281	23234283	.	+	0	transcript_id "Phchi.S1G364600.t1"; gene_id "Phchi.S1G364600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9975.t1 is derived from g7151.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44727248	44728699	.	-	.	Phchi.S1G713400
Phchi.S1	AUGUSTUS	transcript	44727248	44728699	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	stop_codon	44727245	44727247	.	-	0	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	CDS	44727248	44727500	1	-	1	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	exon	44727248	44727500	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	intron	44727501	44727671	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	CDS	44727672	44727913	1	-	0	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	exon	44727672	44727913	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	intron	44727914	44727995	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	CDS	44727996	44728178	1	-	0	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	exon	44727996	44728178	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	intron	44728179	44728302	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	CDS	44728303	44728514	0.99	-	2	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	exon	44728303	44728514	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	intron	44728515	44728629	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	CDS	44728630	44728699	0.75	-	0	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	exon	44728630	44728699	.	-	.	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
Phchi.S1	AUGUSTUS	start_codon	44728697	44728699	.	-	0	transcript_id "Phchi.S1G713400.t1"; gene_id "Phchi.S1G713400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15325.t1 is derived from g13793.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18390940	18393645	.	-	.	Phchi.S3G264400
Phchi.S3	AUGUSTUS	transcript	18390940	18393645	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	stop_codon	18390937	18390939	.	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	CDS	18390940	18391110	1	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	exon	18390940	18391110	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	intron	18391111	18391194	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	CDS	18391195	18391381	1	-	1	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	exon	18391195	18391381	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	intron	18391382	18391467	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	CDS	18391468	18391607	1	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	exon	18391468	18391607	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	intron	18391608	18391755	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	CDS	18391756	18391851	0.99	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	exon	18391756	18391851	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	intron	18391852	18391954	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	CDS	18391955	18392860	0.99	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	exon	18391955	18392860	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	intron	18392861	18392973	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	CDS	18392974	18393645	0.62	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	exon	18392974	18393645	.	-	.	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
Phchi.S3	AUGUSTUS	start_codon	18393643	18393645	.	-	0	transcript_id "Phchi.S3G264400.t1"; gene_id "Phchi.S3G264400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7876.t1 is derived from g5050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31674165	31675964	.	-	.	Phchi.S1G503500
Phchi.S1	AUGUSTUS	transcript	31674165	31675964	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	stop_codon	31674162	31674164	.	-	0	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31674165	31674245	1	-	0	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31674165	31674245	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	intron	31674246	31674387	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31674388	31674581	0.99	-	2	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31674388	31674581	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	intron	31674582	31674690	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31674691	31674849	0.99	-	2	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31674691	31674849	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	intron	31674850	31674932	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31674933	31675096	1	-	1	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31674933	31675096	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	intron	31675097	31675289	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31675290	31675501	1	-	0	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31675290	31675501	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	intron	31675502	31675587	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31675588	31675767	1	-	0	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31675588	31675767	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	intron	31675768	31675853	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	CDS	31675854	31675964	0.62	-	0	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	exon	31675854	31675964	.	-	.	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
Phchi.S1	AUGUSTUS	start_codon	31675962	31675964	.	-	0	transcript_id "Phchi.S1G503500.t1"; gene_id "Phchi.S1G503500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15583.t1 is derived from g14052.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20129768	20130364	.	-	.	Phchi.S3G290200
Phchi.S3	AUGUSTUS	transcript	20129768	20130364	.	-	.	transcript_id "Phchi.S3G290200.t1"; gene_id "Phchi.S3G290200"
Phchi.S3	AUGUSTUS	stop_codon	20129765	20129767	.	-	0	transcript_id "Phchi.S3G290200.t1"; gene_id "Phchi.S3G290200"
Phchi.S3	AUGUSTUS	CDS	20129768	20130364	0.52	-	0	transcript_id "Phchi.S3G290200.t1"; gene_id "Phchi.S3G290200"
Phchi.S3	AUGUSTUS	exon	20129768	20130364	.	-	.	transcript_id "Phchi.S3G290200.t1"; gene_id "Phchi.S3G290200"
Phchi.S3	AUGUSTUS	start_codon	20130362	20130364	.	-	0	transcript_id "Phchi.S3G290200.t1"; gene_id "Phchi.S3G290200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11453.t1 is derived from g15503.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6442855	6443345	.	+	.	Phchi.S4G103500
Phchi.S4	AUGUSTUS	transcript	6442855	6443345	.	+	.	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	start_codon	6442855	6442857	.	+	0	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	CDS	6442855	6443025	0.44	+	0	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	exon	6442855	6443025	.	+	.	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	intron	6443026	6443132	.	+	.	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	CDS	6443133	6443345	0.58	+	0	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	exon	6443133	6443345	.	+	.	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
Phchi.S4	AUGUSTUS	stop_codon	6443346	6443348	.	+	0	transcript_id "Phchi.S4G103500.t1"; gene_id "Phchi.S4G103500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15804.t1 is derived from g14274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21475980	21479349	.	+	.	Phchi.S3G312300
Phchi.S3	AUGUSTUS	transcript	21475980	21479349	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	start_codon	21475980	21475982	.	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21475980	21476528	1	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21475980	21476528	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21476529	21476818	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21476819	21476945	0.75	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21476819	21476945	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21476946	21477401	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21477402	21477468	0.76	+	2	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21477402	21477468	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21477469	21477610	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21477611	21477693	1	+	1	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21477611	21477693	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21477694	21477840	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21477841	21477879	0.62	+	2	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21477841	21477879	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21477880	21478046	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21478047	21478174	0.62	+	2	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21478047	21478174	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21478175	21478253	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21478254	21478433	0.52	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21478254	21478433	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21478434	21478541	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21478542	21478700	0.33	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21478542	21478700	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21478701	21478798	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21478799	21478920	0.37	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21478799	21478920	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21478921	21478996	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21478997	21479086	0.51	+	1	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21478997	21479086	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	intron	21479087	21479189	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	CDS	21479190	21479349	0.55	+	1	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	exon	21479190	21479349	.	+	.	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
Phchi.S3	AUGUSTUS	stop_codon	21479350	21479352	.	+	0	transcript_id "Phchi.S3G312300.t1"; gene_id "Phchi.S3G312300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6972.t1 is derived from g4144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26235483	26237904	.	+	.	Phchi.S1G413100
Phchi.S1	AUGUSTUS	transcript	26235483	26237904	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	start_codon	26235483	26235485	.	+	0	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26235483	26235485	1	+	0	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26235483	26235485	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	intron	26235486	26235560	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26235561	26235693	1	+	0	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26235561	26235693	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	intron	26235694	26235792	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26235793	26236010	1	+	2	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26235793	26236010	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	intron	26236011	26236180	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26236181	26236474	1	+	0	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26236181	26236474	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	intron	26236475	26236587	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26236588	26236847	1	+	0	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26236588	26236847	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	intron	26236848	26236945	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26236946	26237274	1	+	1	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26236946	26237274	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	intron	26237275	26237386	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	CDS	26237387	26237904	1	+	2	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	exon	26237387	26237904	.	+	.	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
Phchi.S1	AUGUSTUS	stop_codon	26237905	26237907	.	+	0	transcript_id "Phchi.S1G413100.t1"; gene_id "Phchi.S1G413100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9647.t1 is derived from g6823.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43049636	43050343	.	+	.	Phchi.S1G680600
Phchi.S1	AUGUSTUS	transcript	43049636	43050343	.	+	.	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	start_codon	43049636	43049638	.	+	0	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	CDS	43049636	43049922	1	+	0	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	exon	43049636	43049922	.	+	.	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	intron	43049923	43050159	.	+	.	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	CDS	43050160	43050343	1	+	1	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	exon	43050160	43050343	.	+	.	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	stop_codon	43050344	43050346	.	+	0	transcript_id "Phchi.S1G680600.t1"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	transcript	43049636	43050343	.	+	.	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	start_codon	43049636	43049638	.	+	0	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	CDS	43049636	43049821	0.97	+	0	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	exon	43049636	43049821	.	+	.	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	intron	43049822	43049922	.	+	.	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	CDS	43049923	43050068	1	+	0	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	exon	43049923	43050068	.	+	.	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	intron	43050069	43050159	.	+	.	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	CDS	43050160	43050343	0.99	+	1	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	exon	43050160	43050343	.	+	.	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
Phchi.S1	AUGUSTUS	stop_codon	43050344	43050346	.	+	0	transcript_id "Phchi.S1G680600.t2"; gene_id "Phchi.S1G680600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12729.t1 is derived from g11194.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1421645	1422339	.	-	.	Phchi.S3G004800
Phchi.S3	AUGUSTUS	transcript	1421645	1422339	.	-	.	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	stop_codon	1421642	1421644	.	-	0	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	CDS	1421645	1421683	1	-	0	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	exon	1421645	1421683	.	-	.	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	intron	1421684	1421778	.	-	.	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	CDS	1421779	1421853	1	-	0	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	exon	1421779	1421853	.	-	.	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	intron	1421854	1422180	.	-	.	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	CDS	1422181	1422339	1	-	0	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	exon	1422181	1422339	.	-	.	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	start_codon	1422337	1422339	.	-	0	transcript_id "Phchi.S3G004800.t1"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	transcript	1421645	1422339	.	-	.	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	stop_codon	1421642	1421644	.	-	0	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	CDS	1421645	1421680	0.99	-	0	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	exon	1421645	1421680	.	-	.	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	intron	1421681	1421778	.	-	.	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	CDS	1421779	1421853	1	-	0	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	exon	1421779	1421853	.	-	.	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	intron	1421854	1422180	.	-	.	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	CDS	1422181	1422339	1	-	0	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	exon	1422181	1422339	.	-	.	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
Phchi.S3	AUGUSTUS	start_codon	1422337	1422339	.	-	0	transcript_id "Phchi.S3G004800.t2"; gene_id "Phchi.S3G004800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9812.t1 is derived from g6988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43859773	43863343	.	+	.	Phchi.S1G697100
Phchi.S1	AUGUSTUS	transcript	43859773	43863343	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	start_codon	43859773	43859775	.	+	0	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43859773	43859832	0.98	+	0	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43859773	43859832	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43859833	43860007	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43860008	43860095	0.98	+	0	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43860008	43860095	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43860096	43860199	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43860200	43860332	0.52	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43860200	43860332	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43860333	43860425	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43860426	43860529	1	+	1	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43860426	43860529	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43860530	43860672	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43860673	43860741	1	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43860673	43860741	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43860742	43860850	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43860851	43860911	1	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43860851	43860911	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43860912	43860989	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43860990	43861129	1	+	1	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43860990	43861129	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43861130	43861437	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43861438	43861624	1	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43861438	43861624	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43861625	43861726	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43861727	43861788	1	+	1	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43861727	43861788	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43861789	43861956	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43861957	43861998	1	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43861957	43861998	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43861999	43862335	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43862336	43862478	1	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43862336	43862478	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43862479	43862631	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43862632	43862709	1	+	0	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43862632	43862709	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43862710	43862838	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43862839	43862878	0.45	+	0	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43862839	43862878	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43862879	43863024	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43863025	43863103	0.98	+	2	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43863025	43863103	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	intron	43863104	43863234	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	CDS	43863235	43863343	1	+	1	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	exon	43863235	43863343	.	+	.	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
Phchi.S1	AUGUSTUS	stop_codon	43863344	43863346	.	+	0	transcript_id "Phchi.S1G697100.t1"; gene_id "Phchi.S1G697100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6005.t1 is derived from g3176.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20353194	20353996	.	-	.	Phchi.S1G316400
Phchi.S1	AUGUSTUS	transcript	20353194	20353996	.	-	.	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	stop_codon	20353191	20353193	.	-	0	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	CDS	20353194	20353203	0.92	-	1	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	exon	20353194	20353203	.	-	.	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	intron	20353204	20353292	.	-	.	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	CDS	20353293	20353996	0.5	-	0	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	exon	20353293	20353996	.	-	.	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
Phchi.S1	AUGUSTUS	start_codon	20353994	20353996	.	-	0	transcript_id "Phchi.S1G316400.t1"; gene_id "Phchi.S1G316400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15205.t1 is derived from g13673.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17545942	17547424	.	-	.	Phchi.S3G252400
Phchi.S3	AUGUSTUS	transcript	17545942	17547424	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	stop_codon	17545939	17545941	.	-	0	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	CDS	17545942	17546391	0.97	-	0	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	exon	17545942	17546391	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	intron	17546392	17546498	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	CDS	17546499	17546566	1	-	2	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	exon	17546499	17546566	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	intron	17546567	17546661	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	CDS	17546662	17546712	1	-	2	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	exon	17546662	17546712	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	intron	17546713	17546809	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	CDS	17546810	17546960	1	-	0	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	exon	17546810	17546960	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	intron	17546961	17547039	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	CDS	17547040	17547103	1	-	1	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	exon	17547040	17547103	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	intron	17547104	17547203	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	CDS	17547204	17547424	0.94	-	0	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	exon	17547204	17547424	.	-	.	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
Phchi.S3	AUGUSTUS	start_codon	17547422	17547424	.	-	0	transcript_id "Phchi.S3G252400.t1"; gene_id "Phchi.S3G252400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3044.t1 is derived from g213.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1316891	1318144	.	-	.	Phchi.S1G020300
Phchi.S1	AUGUSTUS	transcript	1316891	1318144	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	stop_codon	1316888	1316890	.	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1316891	1316970	0.47	-	2	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1316891	1316970	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	intron	1316971	1317067	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1317068	1317150	1	-	1	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1317068	1317150	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	intron	1317151	1317278	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1317279	1317385	1	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1317279	1317385	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	intron	1317386	1317472	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1317473	1317532	1	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1317473	1317532	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	intron	1317533	1317703	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1317704	1317805	1	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1317704	1317805	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	intron	1317806	1317880	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1317881	1317979	1	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1317881	1317979	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	intron	1317980	1318072	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	CDS	1318073	1318144	0.93	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	exon	1318073	1318144	.	-	.	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
Phchi.S1	AUGUSTUS	start_codon	1318142	1318144	.	-	0	transcript_id "Phchi.S1G020300.t1"; gene_id "Phchi.S1G020300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3589.t1 is derived from g758.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4640858	4644033	.	-	.	Phchi.S1G074800
Phchi.S1	AUGUSTUS	transcript	4640877	4644033	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	stop_codon	4640874	4640876	.	-	0	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4640877	4640908	1	-	2	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4640877	4640908	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	intron	4640909	4641045	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4641046	4641380	0.95	-	1	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4641046	4641380	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	intron	4641381	4641522	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4641523	4641699	1	-	1	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4641523	4641699	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	intron	4641700	4641790	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4641791	4644033	0.43	-	0	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4641791	4644033	.	-	.	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	start_codon	4644031	4644033	.	-	0	transcript_id "Phchi.S1G074800.t1"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	transcript	4640858	4644033	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	stop_codon	4640855	4640857	.	-	0	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4640858	4640908	0.7	-	0	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4640858	4640908	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	intron	4640909	4641127	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4641128	4641380	0.66	-	1	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4641128	4641380	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	intron	4641381	4641522	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4641523	4641699	1	-	1	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4641523	4641699	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	intron	4641700	4641790	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	CDS	4641791	4644033	0.56	-	0	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	exon	4641791	4644033	.	-	.	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
Phchi.S1	AUGUSTUS	start_codon	4644031	4644033	.	-	0	transcript_id "Phchi.S1G074800.t2"; gene_id "Phchi.S1G074800"
# This transcript jg13427.t2 is derived from g11894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13427.t3 is derived from g11894.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13428.t1 is derived from g11895.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6648010	6649752	.	+	.	Phchi.S3G074700
Phchi.S3	AUGUSTUS	transcript	6648010	6649752	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	start_codon	6648010	6648012	.	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6648010	6648327	0.99	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6648010	6648327	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6648328	6648423	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6648424	6648486	1	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6648424	6648486	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6648487	6648598	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6648599	6648691	0.96	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6648599	6648691	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6648692	6648826	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6648827	6648874	1	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6648827	6648874	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6648875	6649068	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6649069	6649140	1	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6649069	6649140	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6649141	6649273	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6649274	6649332	1	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6649274	6649332	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6649333	6649422	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6649423	6649519	1	+	1	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6649423	6649519	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	intron	6649520	6649620	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	CDS	6649621	6649752	0.82	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	exon	6649621	6649752	.	+	.	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
Phchi.S3	AUGUSTUS	stop_codon	6649753	6649755	.	+	0	transcript_id "Phchi.S3G074700.t1"; gene_id "Phchi.S3G074700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3474.t1 is derived from g643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3967886	3969130	.	+	.	Phchi.S1G063300
Phchi.S1	AUGUSTUS	transcript	3967886	3969130	.	+	.	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	start_codon	3967886	3967888	.	+	0	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	CDS	3967886	3968010	0.35	+	0	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	exon	3967886	3968010	.	+	.	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	intron	3968011	3968123	.	+	.	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	CDS	3968124	3968513	0.19	+	1	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	exon	3968124	3968513	.	+	.	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	intron	3968514	3968580	.	+	.	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	CDS	3968581	3969130	0.43	+	1	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	exon	3968581	3969130	.	+	.	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
Phchi.S1	AUGUSTUS	stop_codon	3969131	3969133	.	+	0	transcript_id "Phchi.S1G063300.t1"; gene_id "Phchi.S1G063300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6285.t1 is derived from g3457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22085170	22088162	.	+	.	Phchi.S1G344400
Phchi.S1	AUGUSTUS	transcript	22085170	22088162	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	start_codon	22085170	22085172	.	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22085170	22085791	0.77	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22085170	22085791	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22085792	22085994	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22085995	22086021	1	+	2	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22085995	22086021	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22086022	22086121	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22086122	22086442	1	+	2	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22086122	22086442	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22086443	22086518	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22086519	22086661	1	+	2	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22086519	22086661	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22086662	22086750	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22086751	22086840	0.7	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22086751	22086840	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22086841	22086941	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22086942	22087047	1	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22086942	22087047	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22087048	22087140	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22087141	22087292	1	+	2	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22087141	22087292	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22087293	22087381	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22087382	22087482	1	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22087382	22087482	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22087483	22087586	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22087587	22087737	1	+	1	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22087587	22087737	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22087738	22087812	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22087813	22087911	1	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22087813	22087911	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	intron	22087912	22088000	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	CDS	22088001	22088162	0.94	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	exon	22088001	22088162	.	+	.	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
Phchi.S1	AUGUSTUS	stop_codon	22088163	22088165	.	+	0	transcript_id "Phchi.S1G344400.t1"; gene_id "Phchi.S1G344400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11517.t1 is derived from g15567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6872526	6873500	.	-	.	Phchi.S4G109900
Phchi.S4	AUGUSTUS	transcript	6872526	6873500	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	stop_codon	6872523	6872525	.	-	0	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	CDS	6872526	6872604	1	-	1	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	exon	6872526	6872604	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	intron	6872605	6872700	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	CDS	6872701	6872800	1	-	2	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	exon	6872701	6872800	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	intron	6872801	6872918	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	CDS	6872919	6872979	1	-	0	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	exon	6872919	6872979	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	intron	6872980	6873362	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	CDS	6873363	6873500	0.99	-	0	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	exon	6873363	6873500	.	-	.	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
Phchi.S4	AUGUSTUS	start_codon	6873498	6873500	.	-	0	transcript_id "Phchi.S4G109900.t1"; gene_id "Phchi.S4G109900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7129.t1 is derived from g4301.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27095057	27095872	.	-	.	Phchi.S1G428800
Phchi.S1	AUGUSTUS	transcript	27095057	27095872	.	-	.	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	stop_codon	27095054	27095056	.	-	0	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	CDS	27095057	27095074	0.99	-	0	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	exon	27095057	27095074	.	-	.	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	intron	27095075	27095362	.	-	.	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	CDS	27095363	27095392	0.99	-	0	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	exon	27095363	27095392	.	-	.	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	intron	27095393	27095491	.	-	.	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	CDS	27095492	27095872	0.91	-	0	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	exon	27095492	27095872	.	-	.	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	start_codon	27095870	27095872	.	-	0	transcript_id "Phchi.S1G428800.t1"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	transcript	27095376	27095872	.	-	.	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	stop_codon	27095373	27095375	.	-	0	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	CDS	27095376	27095392	0.92	-	2	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	exon	27095376	27095392	.	-	.	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	intron	27095393	27095562	.	-	.	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	CDS	27095563	27095872	0.89	-	0	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	exon	27095563	27095872	.	-	.	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
Phchi.S1	AUGUSTUS	start_codon	27095870	27095872	.	-	0	transcript_id "Phchi.S1G428800.t2"; gene_id "Phchi.S1G428800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1087.t1 is derived from g10870.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7525858	7526841	.	+	.	Phchi.S6G104600
Phchi.S6	AUGUSTUS	transcript	7525858	7526841	.	+	.	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	start_codon	7525858	7525860	.	+	0	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	CDS	7525858	7526489	0.73	+	0	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	exon	7525858	7526489	.	+	.	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	intron	7526490	7526592	.	+	.	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	CDS	7526593	7526717	0.77	+	1	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	exon	7526593	7526717	.	+	.	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	intron	7526718	7526806	.	+	.	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	CDS	7526807	7526841	0.66	+	2	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	exon	7526807	7526841	.	+	.	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
Phchi.S6	AUGUSTUS	stop_codon	7526842	7526844	.	+	0	transcript_id "Phchi.S6G104600.t1"; gene_id "Phchi.S6G104600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12745.t1 is derived from g11210.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1692360	1694138	.	-	.	Phchi.S3G006400
Phchi.S3	AUGUSTUS	transcript	1692360	1694138	.	-	.	transcript_id "Phchi.S3G006400.t1"; gene_id "Phchi.S3G006400"
Phchi.S3	AUGUSTUS	stop_codon	1692357	1692359	.	-	0	transcript_id "Phchi.S3G006400.t1"; gene_id "Phchi.S3G006400"
Phchi.S3	AUGUSTUS	CDS	1692360	1694138	1	-	0	transcript_id "Phchi.S3G006400.t1"; gene_id "Phchi.S3G006400"
Phchi.S3	AUGUSTUS	exon	1692360	1694138	.	-	.	transcript_id "Phchi.S3G006400.t1"; gene_id "Phchi.S3G006400"
Phchi.S3	AUGUSTUS	start_codon	1694136	1694138	.	-	0	transcript_id "Phchi.S3G006400.t1"; gene_id "Phchi.S3G006400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15052.t1 is derived from g13520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16756492	16757520	.	-	.	Phchi.S3G237100
Phchi.S3	AUGUSTUS	transcript	16756492	16757520	.	-	.	transcript_id "Phchi.S3G237100.t1"; gene_id "Phchi.S3G237100"
Phchi.S3	AUGUSTUS	stop_codon	16756489	16756491	.	-	0	transcript_id "Phchi.S3G237100.t1"; gene_id "Phchi.S3G237100"
Phchi.S3	AUGUSTUS	CDS	16756492	16757520	0.8	-	0	transcript_id "Phchi.S3G237100.t1"; gene_id "Phchi.S3G237100"
Phchi.S3	AUGUSTUS	exon	16756492	16757520	.	-	.	transcript_id "Phchi.S3G237100.t1"; gene_id "Phchi.S3G237100"
Phchi.S3	AUGUSTUS	start_codon	16757518	16757520	.	-	0	transcript_id "Phchi.S3G237100.t1"; gene_id "Phchi.S3G237100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7800.t1 is derived from g4974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31251004	31252844	.	+	.	Phchi.S1G495900
Phchi.S1	AUGUSTUS	transcript	31251004	31252844	.	+	.	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	start_codon	31251004	31251006	.	+	0	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	CDS	31251004	31251159	0.59	+	0	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	exon	31251004	31251159	.	+	.	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	intron	31251160	31251282	.	+	.	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	CDS	31251283	31252104	0.67	+	0	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	exon	31251283	31252104	.	+	.	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	intron	31252105	31252301	.	+	.	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	CDS	31252302	31252844	0.8	+	0	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	exon	31252302	31252844	.	+	.	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
Phchi.S1	AUGUSTUS	stop_codon	31252845	31252847	.	+	0	transcript_id "Phchi.S1G495900.t1"; gene_id "Phchi.S1G495900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11438.t1 is derived from g15488.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6379571	6380482	.	+	.	Phchi.S4G102000
Phchi.S4	AUGUSTUS	transcript	6379571	6380482	.	+	.	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	start_codon	6379571	6379573	.	+	0	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	CDS	6379571	6379817	0.55	+	0	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	exon	6379571	6379817	.	+	.	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	intron	6379818	6379993	.	+	.	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	CDS	6379994	6380191	0.9	+	2	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	exon	6379994	6380191	.	+	.	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	intron	6380192	6380438	.	+	.	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	CDS	6380439	6380482	1	+	2	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	exon	6380439	6380482	.	+	.	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
Phchi.S4	AUGUSTUS	stop_codon	6380483	6380485	.	+	0	transcript_id "Phchi.S4G102000.t1"; gene_id "Phchi.S4G102000"
# This transcript jg2083.t2 is derived from g9003.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2083.t3 is derived from g9003.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2084.t1 is derived from g9004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4774070	4775620	.	-	.	Phchi.S5G069300
Phchi.S5	AUGUSTUS	transcript	4774070	4775620	.	-	.	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	stop_codon	4774067	4774069	.	-	0	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	CDS	4774070	4774097	0.83	-	1	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	exon	4774070	4774097	.	-	.	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	intron	4774098	4774185	.	-	.	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	CDS	4774186	4774222	0.8	-	2	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	exon	4774186	4774222	.	-	.	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	intron	4774223	4774410	.	-	.	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	CDS	4774411	4775620	0.25	-	0	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	exon	4774411	4775620	.	-	.	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
Phchi.S5	AUGUSTUS	start_codon	4775618	4775620	.	-	0	transcript_id "Phchi.S5G069300.t1"; gene_id "Phchi.S5G069300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5817.t1 is derived from g2987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19093159	19095125	.	-	.	Phchi.S1G297600
Phchi.S1	AUGUSTUS	transcript	19093159	19095125	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	stop_codon	19093156	19093158	.	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19093159	19093318	0.99	-	1	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19093159	19093318	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19093319	19093443	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19093444	19093535	1	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19093444	19093535	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19093536	19093631	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19093632	19093714	1	-	2	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19093632	19093714	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19093715	19093829	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19093830	19093911	1	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19093830	19093911	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19093912	19094002	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19094003	19094230	1	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19094003	19094230	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19094231	19094316	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19094317	19094418	1	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19094317	19094418	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19094419	19094511	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19094512	19094647	1	-	1	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19094512	19094647	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19094648	19094732	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19094733	19094782	1	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19094733	19094782	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	intron	19094783	19094909	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	CDS	19094910	19095125	0.84	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	exon	19094910	19095125	.	-	.	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
Phchi.S1	AUGUSTUS	start_codon	19095123	19095125	.	-	0	transcript_id "Phchi.S1G297600.t1"; gene_id "Phchi.S1G297600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15947.t1 is derived from g14440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C116	AUGUSTUS	gene	12434	13117	.	-	.	Phchi.C116G000300
Phchi.C116	AUGUSTUS	transcript	12434	13117	.	-	.	transcript_id "Phchi.C116G000300.t1"; gene_id "Phchi.C116G000300"
Phchi.C116	AUGUSTUS	stop_codon	12431	12433	.	-	0	transcript_id "Phchi.C116G000300.t1"; gene_id "Phchi.C116G000300"
Phchi.C116	AUGUSTUS	CDS	12434	13117	0.99	-	0	transcript_id "Phchi.C116G000300.t1"; gene_id "Phchi.C116G000300"
Phchi.C116	AUGUSTUS	exon	12434	13117	.	-	.	transcript_id "Phchi.C116G000300.t1"; gene_id "Phchi.C116G000300"
Phchi.C116	AUGUSTUS	start_codon	13115	13117	.	-	0	transcript_id "Phchi.C116G000300.t1"; gene_id "Phchi.C116G000300"
# This transcript jg3815.t2 is derived from g984.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3816.t1 is derived from g985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5878118	5878508	.	+	.	Phchi.S1G097500
Phchi.S1	AUGUSTUS	transcript	5878118	5878508	.	+	.	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	start_codon	5878118	5878120	.	+	0	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	CDS	5878118	5878376	0.88	+	0	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	exon	5878118	5878376	.	+	.	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	intron	5878377	5878470	.	+	.	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	CDS	5878471	5878508	0.92	+	2	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	exon	5878471	5878508	.	+	.	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
Phchi.S1	AUGUSTUS	stop_codon	5878509	5878511	.	+	0	transcript_id "Phchi.S1G097500.t1"; gene_id "Phchi.S1G097500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11397.t1 is derived from g15447.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6136992	6140016	.	-	.	Phchi.S4G097900
Phchi.S4	AUGUSTUS	transcript	6136992	6140016	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	stop_codon	6136989	6136991	.	-	0	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6136992	6137129	1	-	0	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6136992	6137129	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6137130	6137239	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6137240	6137408	1	-	1	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6137240	6137408	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6137409	6137503	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6137504	6137673	1	-	0	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6137504	6137673	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6137674	6137777	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6137778	6137956	1	-	2	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6137778	6137956	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6137957	6138049	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6138050	6138115	1	-	2	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6138050	6138115	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6138116	6138271	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6138272	6138445	1	-	2	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6138272	6138445	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6138446	6138534	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6138535	6138833	1	-	1	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6138535	6138833	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6138834	6138915	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6138916	6139016	1	-	0	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6138916	6139016	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6139017	6139117	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6139118	6139202	1	-	1	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6139118	6139202	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6139203	6139298	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6139299	6139452	1	-	2	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6139299	6139452	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6139453	6139553	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6139554	6139714	1	-	1	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6139554	6139714	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	intron	6139715	6139840	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	CDS	6139841	6140016	0.98	-	0	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	exon	6139841	6140016	.	-	.	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
Phchi.S4	AUGUSTUS	start_codon	6140014	6140016	.	-	0	transcript_id "Phchi.S4G097900.t1"; gene_id "Phchi.S4G097900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6270.t1 is derived from g3442.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21945467	21946282	.	+	.	Phchi.S1G342900
Phchi.S1	AUGUSTUS	transcript	21945467	21946282	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	start_codon	21945467	21945469	.	+	0	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	CDS	21945467	21945471	1	+	0	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	exon	21945467	21945471	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	intron	21945472	21945647	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	CDS	21945648	21945803	1	+	1	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	exon	21945648	21945803	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	intron	21945804	21945928	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	CDS	21945929	21946055	1	+	1	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	exon	21945929	21946055	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	intron	21946056	21946144	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	CDS	21946145	21946282	1	+	0	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	exon	21946145	21946282	.	+	.	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
Phchi.S1	AUGUSTUS	stop_codon	21946283	21946285	.	+	0	transcript_id "Phchi.S1G342900.t1"; gene_id "Phchi.S1G342900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11775.t1 is derived from g15827.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8117048	8118151	.	-	.	Phchi.S4G135700
Phchi.S4	AUGUSTUS	transcript	8117048	8118151	.	-	.	transcript_id "Phchi.S4G135700.t1"; gene_id "Phchi.S4G135700"
Phchi.S4	AUGUSTUS	stop_codon	8117045	8117047	.	-	0	transcript_id "Phchi.S4G135700.t1"; gene_id "Phchi.S4G135700"
Phchi.S4	AUGUSTUS	CDS	8117048	8118151	1	-	0	transcript_id "Phchi.S4G135700.t1"; gene_id "Phchi.S4G135700"
Phchi.S4	AUGUSTUS	exon	8117048	8118151	.	-	.	transcript_id "Phchi.S4G135700.t1"; gene_id "Phchi.S4G135700"
Phchi.S4	AUGUSTUS	start_codon	8118149	8118151	.	-	0	transcript_id "Phchi.S4G135700.t1"; gene_id "Phchi.S4G135700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8873.t1 is derived from g6048.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38397428	38401985	.	+	.	Phchi.S1G603200
Phchi.S1	AUGUSTUS	transcript	38397428	38401985	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	start_codon	38397428	38397430	.	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38397428	38397467	0.55	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38397428	38397467	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38397468	38397630	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38397631	38397908	0.98	+	2	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38397631	38397908	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38397909	38398009	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398010	38398166	0.97	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398010	38398166	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398167	38398267	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398268	38398412	0.97	+	2	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398268	38398412	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398413	38398520	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398521	38398683	1	+	1	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398521	38398683	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398684	38398766	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398767	38398974	0.98	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398767	38398974	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398975	38399067	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399068	38399118	1	+	2	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399068	38399118	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38399119	38399205	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399206	38399349	1	+	2	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399206	38399349	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38399350	38399508	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399509	38399697	1	+	2	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399509	38399697	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38399698	38399826	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399827	38400125	0.98	+	2	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399827	38400125	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400126	38400288	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400289	38400383	1	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400289	38400383	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400384	38400540	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400541	38400607	1	+	1	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400541	38400607	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400608	38400706	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400707	38400805	0.68	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400707	38400805	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400806	38400909	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400910	38400969	0.99	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400910	38400969	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400970	38401056	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401057	38401113	1	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401057	38401113	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401114	38401203	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401204	38401287	1	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401204	38401287	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401288	38401423	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401424	38401507	1	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401424	38401507	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401508	38401595	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401596	38401679	1	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401596	38401679	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401680	38401763	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401764	38401810	1	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401764	38401810	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401811	38401885	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401886	38401985	1	+	1	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401886	38401985	.	+	.	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	stop_codon	38401986	38401988	.	+	0	transcript_id "Phchi.S1G603200.t1"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	transcript	38397428	38401985	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	start_codon	38397428	38397430	.	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38397428	38397467	0.53	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38397428	38397467	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38397468	38397630	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38397631	38397908	0.99	+	2	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38397631	38397908	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38397909	38398009	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398010	38398166	0.92	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398010	38398166	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398167	38398267	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398268	38398412	0.98	+	2	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398268	38398412	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398413	38398520	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398521	38398683	1	+	1	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398521	38398683	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398684	38398766	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38398767	38398974	0.99	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38398767	38398974	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38398975	38399067	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399068	38399118	1	+	2	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399068	38399118	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38399119	38399211	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399212	38399349	0.96	+	2	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399212	38399349	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38399350	38399508	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399509	38399697	1	+	2	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399509	38399697	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38399698	38399826	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38399827	38400125	0.98	+	2	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38399827	38400125	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400126	38400288	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400289	38400383	1	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400289	38400383	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400384	38400540	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400541	38400607	1	+	1	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400541	38400607	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400608	38400706	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400707	38400805	0.63	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400707	38400805	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400806	38400909	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38400910	38400969	0.99	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38400910	38400969	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38400970	38401056	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401057	38401113	1	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401057	38401113	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401114	38401203	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401204	38401287	1	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401204	38401287	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401288	38401423	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401424	38401507	1	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401424	38401507	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401508	38401595	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401596	38401679	1	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401596	38401679	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401680	38401763	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401764	38401810	1	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401764	38401810	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	intron	38401811	38401885	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	CDS	38401886	38401985	1	+	1	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	exon	38401886	38401985	.	+	.	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
Phchi.S1	AUGUSTUS	stop_codon	38401986	38401988	.	+	0	transcript_id "Phchi.S1G603200.t2"; gene_id "Phchi.S1G603200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15940.t1 is derived from g7.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C143	AUGUSTUS	gene	18964	20124	.	-	.	Phchi.C143G000200
Phchi.C143	AUGUSTUS	transcript	18964	20124	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	stop_codon	18961	18963	.	-	0	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	CDS	18964	19071	0.98	-	0	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	exon	18964	19071	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	intron	19072	19220	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	CDS	19221	19320	0.87	-	1	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	exon	19221	19320	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	intron	19321	19394	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	CDS	19395	19716	0.77	-	2	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	exon	19395	19716	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	intron	19717	19803	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	CDS	19804	19852	1	-	0	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	exon	19804	19852	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	intron	19853	19977	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	CDS	19978	20124	0.98	-	0	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	exon	19978	20124	.	-	.	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
Phchi.C143	AUGUSTUS	start_codon	20122	20124	.	-	0	transcript_id "Phchi.C143G000200.t1"; gene_id "Phchi.C143G000200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10336.t1 is derived from g7512.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47234445	47236813	.	-	.	Phchi.S1G749500
Phchi.S1	AUGUSTUS	transcript	47234445	47236813	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	stop_codon	47234442	47234444	.	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47234445	47234587	0.98	-	2	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47234445	47234587	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47234588	47234706	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47234707	47234754	0.99	-	2	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47234707	47234754	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47234755	47234856	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47234857	47234954	0.94	-	1	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47234857	47234954	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47234955	47235052	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47235053	47235132	1	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47235053	47235132	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47235133	47235263	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47235264	47235335	1	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47235264	47235335	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47235336	47235504	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47235505	47235546	1	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47235505	47235546	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47235547	47235667	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47235668	47235829	1	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47235668	47235829	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47235830	47235971	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47235972	47236052	0.51	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47235972	47236052	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47236053	47236180	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47236181	47236211	0.46	-	1	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47236181	47236211	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47236212	47236458	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47236459	47236549	0.98	-	2	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47236459	47236549	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	intron	47236550	47236695	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	CDS	47236696	47236813	0.86	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	exon	47236696	47236813	.	-	.	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
Phchi.S1	AUGUSTUS	start_codon	47236811	47236813	.	-	0	transcript_id "Phchi.S1G749500.t1"; gene_id "Phchi.S1G749500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15731.t1 is derived from g14201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20922282	20928135	.	-	.	Phchi.S3G305000
Phchi.S3	AUGUSTUS	transcript	20922282	20928135	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	stop_codon	20922279	20922281	.	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20922282	20922556	0.8	-	2	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20922282	20922556	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20922557	20922720	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20922721	20922808	1	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20922721	20922808	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20922809	20922910	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20922911	20923033	0.99	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20922911	20923033	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20923034	20923124	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20923125	20923272	1	-	1	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20923125	20923272	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20923273	20923394	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20923395	20923558	1	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20923395	20923558	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20923559	20923649	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20923650	20923802	1	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20923650	20923802	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20923803	20923890	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20923891	20923992	1	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20923891	20923992	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20923993	20924093	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20924094	20926351	0.48	-	2	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20924094	20926351	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20926352	20926455	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20926456	20926578	0.38	-	2	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20926456	20926578	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20926579	20926802	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20926803	20927405	0.62	-	2	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20926803	20927405	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	intron	20927406	20927702	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	CDS	20927703	20928135	0.82	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	exon	20927703	20928135	.	-	.	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
Phchi.S3	AUGUSTUS	start_codon	20928133	20928135	.	-	0	transcript_id "Phchi.S3G305000.t1"; gene_id "Phchi.S3G305000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6246.t1 is derived from g3418.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21848959	21851082	.	-	.	Phchi.S1G340500
Phchi.S1	AUGUSTUS	transcript	21848959	21851082	.	-	.	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	stop_codon	21848956	21848958	.	-	0	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	CDS	21848959	21849348	0.8	-	0	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	exon	21848959	21849348	.	-	.	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	intron	21849349	21849629	.	-	.	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	CDS	21849630	21850907	0.99	-	0	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	exon	21849630	21850907	.	-	.	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	intron	21850908	21851001	.	-	.	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	CDS	21851002	21851082	0.73	-	0	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	exon	21851002	21851082	.	-	.	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
Phchi.S1	AUGUSTUS	start_codon	21851080	21851082	.	-	0	transcript_id "Phchi.S1G340500.t1"; gene_id "Phchi.S1G340500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10599.t1 is derived from g14649.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1137965	1138977	.	+	.	Phchi.S4G018100
Phchi.S4	AUGUSTUS	transcript	1137965	1138977	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	start_codon	1137965	1137967	.	+	0	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	CDS	1137965	1138001	1	+	0	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	exon	1137965	1138001	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	intron	1138002	1138190	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	CDS	1138191	1138231	1	+	2	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	exon	1138191	1138231	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	intron	1138232	1138340	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	CDS	1138341	1138415	1	+	0	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	exon	1138341	1138415	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	intron	1138416	1138493	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	CDS	1138494	1138546	1	+	0	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	exon	1138494	1138546	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	intron	1138547	1138750	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	CDS	1138751	1138759	0.68	+	1	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	exon	1138751	1138759	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	intron	1138760	1138928	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	CDS	1138929	1138977	0.67	+	1	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	exon	1138929	1138977	.	+	.	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
Phchi.S4	AUGUSTUS	stop_codon	1138978	1138980	.	+	0	transcript_id "Phchi.S4G018100.t1"; gene_id "Phchi.S4G018100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12649.t1 is derived from g2.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C212	AUGUSTUS	gene	1766	2209	.	+	.	Phchi.C212G000100
Phchi.C212	AUGUSTUS	transcript	1766	2209	.	+	.	transcript_id "Phchi.C212G000100.t1"; gene_id "Phchi.C212G000100"
Phchi.C212	AUGUSTUS	start_codon	1766	1768	.	+	0	transcript_id "Phchi.C212G000100.t1"; gene_id "Phchi.C212G000100"
Phchi.C212	AUGUSTUS	CDS	1766	2209	0.55	+	0	transcript_id "Phchi.C212G000100.t1"; gene_id "Phchi.C212G000100"
Phchi.C212	AUGUSTUS	exon	1766	2209	.	+	.	transcript_id "Phchi.C212G000100.t1"; gene_id "Phchi.C212G000100"
Phchi.C212	AUGUSTUS	stop_codon	2210	2212	.	+	0	transcript_id "Phchi.C212G000100.t1"; gene_id "Phchi.C212G000100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg55.t1 is derived from g9837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	147684	148346	.	+	.	Phchi.S6G001400
Phchi.S6	AUGUSTUS	transcript	147684	148346	.	+	.	transcript_id "Phchi.S6G001400.t1"; gene_id "Phchi.S6G001400"
Phchi.S6	AUGUSTUS	start_codon	147684	147686	.	+	0	transcript_id "Phchi.S6G001400.t1"; gene_id "Phchi.S6G001400"
Phchi.S6	AUGUSTUS	CDS	147684	148346	0.74	+	0	transcript_id "Phchi.S6G001400.t1"; gene_id "Phchi.S6G001400"
Phchi.S6	AUGUSTUS	exon	147684	148346	.	+	.	transcript_id "Phchi.S6G001400.t1"; gene_id "Phchi.S6G001400"
Phchi.S6	AUGUSTUS	stop_codon	148347	148349	.	+	0	transcript_id "Phchi.S6G001400.t1"; gene_id "Phchi.S6G001400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7159.t1 is derived from g4331.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27336804	27340113	.	-	.	Phchi.S1G431800
Phchi.S1	AUGUSTUS	transcript	27336804	27340113	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	stop_codon	27336801	27336803	.	-	0	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27336804	27336825	0.5	-	1	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27336804	27336825	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27336826	27336988	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27336989	27337034	0.5	-	2	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27336989	27337034	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27337035	27337386	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27337387	27337430	0.7	-	1	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27337387	27337430	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27337431	27337622	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27337623	27337858	0.44	-	0	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27337623	27337858	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27337859	27337947	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27337948	27338037	0.48	-	0	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27337948	27338037	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27338038	27338142	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27338143	27338290	0.89	-	1	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27338143	27338290	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27338291	27338375	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27338376	27338622	1	-	2	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27338376	27338622	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27338623	27338699	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27338700	27339083	1	-	2	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27338700	27339083	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27339084	27339206	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27339207	27339395	1	-	2	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27339207	27339395	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27339396	27339479	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27339480	27339902	0.37	-	2	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27339480	27339902	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	intron	27339903	27339983	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	CDS	27339984	27340113	0.72	-	0	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	exon	27339984	27340113	.	-	.	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
Phchi.S1	AUGUSTUS	start_codon	27340111	27340113	.	-	0	transcript_id "Phchi.S1G431800.t1"; gene_id "Phchi.S1G431800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8848.t1 is derived from g6023.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38266599	38268180	.	-	.	Phchi.S1G600700
Phchi.S1	AUGUSTUS	transcript	38266599	38268180	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	stop_codon	38266596	38266598	.	-	0	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	CDS	38266599	38267173	0.46	-	2	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	exon	38266599	38267173	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	intron	38267174	38267298	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	CDS	38267299	38267425	0.95	-	0	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	exon	38267299	38267425	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	intron	38267426	38267505	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	CDS	38267506	38267705	1	-	2	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	exon	38267506	38267705	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	intron	38267706	38267804	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	CDS	38267805	38268180	0.64	-	0	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	exon	38267805	38268180	.	-	.	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
Phchi.S1	AUGUSTUS	start_codon	38268178	38268180	.	-	0	transcript_id "Phchi.S1G600700.t1"; gene_id "Phchi.S1G600700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4789.t1 is derived from g1959.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12818960	12820408	.	-	.	Phchi.S1G194800
Phchi.S1	AUGUSTUS	transcript	12818960	12820408	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	stop_codon	12818957	12818959	.	-	0	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12818960	12819026	1	-	1	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12818960	12819026	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12819027	12819126	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12819127	12819204	1	-	1	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12819127	12819204	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12819205	12819313	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12819314	12819493	1	-	1	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12819314	12819493	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12819494	12819580	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12819581	12819670	1	-	1	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12819581	12819670	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12819671	12819829	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12819830	12819947	1	-	2	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12819830	12819947	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12819948	12820019	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12820020	12820076	1	-	2	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12820020	12820076	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12820077	12820159	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12820160	12820232	1	-	0	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12820160	12820232	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	intron	12820233	12820405	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	CDS	12820406	12820408	1	-	0	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	exon	12820406	12820408	.	-	.	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
Phchi.S1	AUGUSTUS	start_codon	12820406	12820408	.	-	0	transcript_id "Phchi.S1G194800.t1"; gene_id "Phchi.S1G194800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2461.t1 is derived from g9381.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6770540	6770749	.	-	.	Phchi.S5G107000
Phchi.S5	AUGUSTUS	transcript	6770540	6770749	.	-	.	transcript_id "Phchi.S5G107000.t1"; gene_id "Phchi.S5G107000"
Phchi.S5	AUGUSTUS	stop_codon	6770537	6770539	.	-	0	transcript_id "Phchi.S5G107000.t1"; gene_id "Phchi.S5G107000"
Phchi.S5	AUGUSTUS	CDS	6770540	6770749	0.45	-	0	transcript_id "Phchi.S5G107000.t1"; gene_id "Phchi.S5G107000"
Phchi.S5	AUGUSTUS	exon	6770540	6770749	.	-	.	transcript_id "Phchi.S5G107000.t1"; gene_id "Phchi.S5G107000"
Phchi.S5	AUGUSTUS	start_codon	6770747	6770749	.	-	0	transcript_id "Phchi.S5G107000.t1"; gene_id "Phchi.S5G107000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg903.t1 is derived from g10685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6360874	6363543	.	-	.	Phchi.S6G086200
Phchi.S6	AUGUSTUS	transcript	6360874	6363543	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	stop_codon	6360871	6360873	.	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6360874	6361305	1	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6360874	6361305	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6361306	6361535	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6361536	6361862	1	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6361536	6361862	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6361863	6361965	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6361966	6362050	1	-	1	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6361966	6362050	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6362051	6362173	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6362174	6362310	1	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6362174	6362310	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6362311	6362454	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6362455	6362716	1	-	1	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6362455	6362716	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6362717	6362955	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6362956	6363065	0.35	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6362956	6363065	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6363066	6363154	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6363155	6363349	0.99	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6363155	6363349	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	intron	6363350	6363441	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	CDS	6363442	6363543	0.27	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	exon	6363442	6363543	.	-	.	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
Phchi.S6	AUGUSTUS	start_codon	6363541	6363543	.	-	0	transcript_id "Phchi.S6G086200.t1"; gene_id "Phchi.S6G086200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2444.t1 is derived from g9364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6655824	6657751	.	-	.	Phchi.S5G105300
Phchi.S5	AUGUSTUS	transcript	6655824	6657751	.	-	.	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	stop_codon	6655821	6655823	.	-	0	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	CDS	6655824	6656015	0.98	-	0	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	exon	6655824	6656015	.	-	.	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	intron	6656016	6656095	.	-	.	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	CDS	6656096	6657751	0.91	-	0	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	exon	6656096	6657751	.	-	.	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
Phchi.S5	AUGUSTUS	start_codon	6657749	6657751	.	-	0	transcript_id "Phchi.S5G105300.t1"; gene_id "Phchi.S5G105300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11699.t1 is derived from g15750.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7759826	7760384	.	-	.	Phchi.S4G128100
Phchi.S4	AUGUSTUS	transcript	7759826	7760384	.	-	.	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	stop_codon	7759823	7759825	.	-	0	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	CDS	7759826	7759967	1	-	1	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	exon	7759826	7759967	.	-	.	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	intron	7759968	7760136	.	-	.	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	CDS	7760137	7760384	1	-	0	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	exon	7760137	7760384	.	-	.	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
Phchi.S4	AUGUSTUS	start_codon	7760382	7760384	.	-	0	transcript_id "Phchi.S4G128100.t1"; gene_id "Phchi.S4G128100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8186.t1 is derived from g5361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34335954	34338144	.	-	.	Phchi.S1G534500
Phchi.S1	AUGUSTUS	transcript	34335954	34338144	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	stop_codon	34335951	34335953	.	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34335954	34336023	0.95	-	1	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34335954	34336023	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34336024	34336131	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34336132	34336313	0.96	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34336132	34336313	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34336314	34336421	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34336422	34336587	0.93	-	1	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34336422	34336587	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34336588	34336702	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34336703	34336784	0.95	-	2	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34336703	34336784	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34336785	34336864	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34336865	34336970	1	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34336865	34336970	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34336971	34337065	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34337066	34337167	1	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34337066	34337167	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34337168	34337373	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34337374	34337383	1	-	1	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34337374	34337383	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34337384	34337501	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34337502	34337507	1	-	1	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34337502	34337507	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34337508	34337690	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34337691	34337779	1	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34337691	34337779	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	intron	34337780	34337859	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	CDS	34337860	34338144	1	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	exon	34337860	34338144	.	-	.	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
Phchi.S1	AUGUSTUS	start_codon	34338142	34338144	.	-	0	transcript_id "Phchi.S1G534500.t1"; gene_id "Phchi.S1G534500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4909.t1 is derived from g2079.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13352452	13353576	.	-	.	Phchi.S1G206800
Phchi.S1	AUGUSTUS	transcript	13352452	13353485	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	stop_codon	13352449	13352451	.	-	0	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13352452	13352516	0.45	-	2	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13352452	13352516	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13352517	13352786	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13352787	13352850	0.45	-	0	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13352787	13352850	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13352851	13352986	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13352987	13353002	0.43	-	1	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13352987	13353002	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13353003	13353093	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13353094	13353341	0.25	-	0	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13353094	13353341	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13353342	13353434	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13353435	13353485	0.38	-	0	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13353435	13353485	.	-	.	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	start_codon	13353483	13353485	.	-	0	transcript_id "Phchi.S1G206800.t1"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	transcript	13352452	13353576	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	stop_codon	13352449	13352451	.	-	0	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13352452	13352516	0.49	-	2	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13352452	13352516	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13352517	13352786	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13352787	13352850	0.49	-	0	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13352787	13352850	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13352851	13352986	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13352987	13353002	0.47	-	1	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13352987	13353002	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13353003	13353220	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13353221	13353344	0.19	-	2	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13353221	13353344	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	intron	13353345	13353434	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	CDS	13353435	13353576	0.13	-	0	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	exon	13353435	13353576	.	-	.	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
Phchi.S1	AUGUSTUS	start_codon	13353574	13353576	.	-	0	transcript_id "Phchi.S1G206800.t2"; gene_id "Phchi.S1G206800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 6 different transcripts
# This transcript jg1295.t1 is derived from g11078.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8890396	8893386	.	+	.	Phchi.S6G125400
Phchi.S6	AUGUSTUS	transcript	8891766	8893386	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	start_codon	8891766	8891768	.	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891766	8891795	0.61	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891766	8891795	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891796	8891891	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891892	8891960	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891892	8891960	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891961	8892040	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892041	8892136	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892041	8892136	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892137	8892291	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892292	8892336	0.97	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892292	8892336	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892337	8892454	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892455	8892525	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892455	8892525	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892526	8892605	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892606	8892672	1	+	1	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892606	8892672	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892673	8892747	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892748	8892798	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892748	8892798	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892799	8892897	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892898	8893008	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892898	8893008	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893009	8893103	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893104	8893151	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893104	8893151	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893152	8893236	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893237	8893276	1	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893237	8893276	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893277	8893348	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893349	8893386	1	+	2	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893349	8893386	.	+	.	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	stop_codon	8893387	8893389	.	+	0	transcript_id "Phchi.S6G125400.t1"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	transcript	8892509	8893386	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	start_codon	8892509	8892511	.	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892509	8892525	0.56	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892509	8892525	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892526	8892605	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892606	8892672	1	+	1	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892606	8892672	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892673	8892747	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892748	8892798	1	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892748	8892798	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892799	8892897	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892898	8893008	1	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892898	8893008	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893009	8893103	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893104	8893151	1	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893104	8893151	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893152	8893236	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893237	8893276	1	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893237	8893276	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893277	8893348	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893349	8893386	1	+	2	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893349	8893386	.	+	.	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	stop_codon	8893387	8893389	.	+	0	transcript_id "Phchi.S6G125400.t2"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	transcript	8890396	8892479	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	start_codon	8890396	8890398	.	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8890396	8890868	1	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8890396	8890868	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8890869	8891000	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891001	8891181	1	+	1	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891001	8891181	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891182	8891290	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891291	8891350	0.98	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891291	8891350	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891351	8891464	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891465	8891628	1	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891465	8891628	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891629	8891731	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891732	8891795	1	+	1	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891732	8891795	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891796	8891891	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891892	8891960	1	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891892	8891960	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891961	8892040	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892041	8892136	1	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892041	8892136	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892137	8892291	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892292	8892336	0.99	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892292	8892336	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892337	8892413	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892414	8892479	0.58	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892414	8892479	.	+	.	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	stop_codon	8892480	8892482	.	+	0	transcript_id "Phchi.S6G125400.t3"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	transcript	8891766	8893386	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	start_codon	8891766	8891768	.	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891766	8891795	0.79	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891766	8891795	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891796	8891891	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891892	8891960	1	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891892	8891960	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891961	8892040	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892041	8892141	0.9	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892041	8892141	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892142	8892291	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892292	8892336	0.9	+	1	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892292	8892336	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892337	8892474	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892475	8892525	0.65	+	1	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892475	8892525	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892526	8892605	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892606	8892672	1	+	1	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892606	8892672	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892673	8892747	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892748	8892798	1	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892748	8892798	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892799	8892897	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892898	8893008	1	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892898	8893008	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893009	8893103	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893104	8893151	1	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893104	8893151	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893152	8893236	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893237	8893276	1	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893237	8893276	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8893277	8893348	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8893349	8893386	1	+	2	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8893349	8893386	.	+	.	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	stop_codon	8893387	8893389	.	+	0	transcript_id "Phchi.S6G125400.t4"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	transcript	8891766	8892479	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	start_codon	8891766	8891768	.	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891766	8891795	0.73	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891766	8891795	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891796	8891891	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891892	8891960	1	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891892	8891960	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891961	8892040	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892041	8892136	1	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892041	8892136	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892137	8892291	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892292	8892336	1	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892292	8892336	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8892337	8892413	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8892414	8892479	0.73	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8892414	8892479	.	+	.	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	stop_codon	8892480	8892482	.	+	0	transcript_id "Phchi.S6G125400.t5"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	transcript	8890396	8891734	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	start_codon	8890396	8890398	.	+	0	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8890396	8890868	1	+	0	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8890396	8890868	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8890869	8891000	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891001	8891181	1	+	1	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891001	8891181	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891182	8891290	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891291	8891350	1	+	0	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891291	8891350	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891351	8891464	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891465	8891635	0.72	+	0	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891465	8891635	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	intron	8891636	8891731	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	CDS	8891732	8891734	0.72	+	0	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	exon	8891732	8891734	.	+	.	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
Phchi.S6	AUGUSTUS	stop_codon	8891735	8891737	.	+	0	transcript_id "Phchi.S6G125400.t6"; gene_id "Phchi.S6G125400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5765.t1 is derived from g2935.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18863996	18864911	.	-	.	Phchi.S1G292400
Phchi.S1	AUGUSTUS	transcript	18863996	18864911	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	stop_codon	18863993	18863995	.	-	0	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	CDS	18863996	18864047	1	-	1	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	exon	18863996	18864047	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	intron	18864048	18864120	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	CDS	18864121	18864241	1	-	2	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	exon	18864121	18864241	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	intron	18864242	18864366	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	CDS	18864367	18864411	1	-	2	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	exon	18864367	18864411	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	intron	18864412	18864487	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	CDS	18864488	18864518	1	-	0	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	exon	18864488	18864518	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	intron	18864519	18864621	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	CDS	18864622	18864714	1	-	0	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	exon	18864622	18864714	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	intron	18864715	18864851	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	CDS	18864852	18864911	1	-	0	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	exon	18864852	18864911	.	-	.	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
Phchi.S1	AUGUSTUS	start_codon	18864909	18864911	.	-	0	transcript_id "Phchi.S1G292400.t1"; gene_id "Phchi.S1G292400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6871.t1 is derived from g4043.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25701018	25702590	.	-	.	Phchi.S1G403000
Phchi.S1	AUGUSTUS	transcript	25701018	25702590	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	stop_codon	25701015	25701017	.	-	0	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25701018	25701225	1	-	1	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25701018	25701225	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25701226	25701331	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25701332	25701390	1	-	0	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25701332	25701390	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25701391	25701492	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25701493	25701569	1	-	2	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25701493	25701569	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25701570	25701686	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25701687	25701732	1	-	0	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25701687	25701732	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25701733	25701817	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25701818	25701926	1	-	1	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25701818	25701926	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25701927	25702005	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25702006	25702227	1	-	1	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25702006	25702227	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25702228	25702326	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25702327	25702421	1	-	0	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25702327	25702421	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	intron	25702422	25702512	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	CDS	25702513	25702590	0.91	-	0	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	exon	25702513	25702590	.	-	.	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
Phchi.S1	AUGUSTUS	start_codon	25702588	25702590	.	-	0	transcript_id "Phchi.S1G403000.t1"; gene_id "Phchi.S1G403000"
# This transcript jg11661.t2 is derived from g15712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11662.t1 is derived from g15713.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7565432	7566978	.	-	.	Phchi.S4G124400
Phchi.S4	AUGUSTUS	transcript	7565432	7566978	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	stop_codon	7565429	7565431	.	-	0	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	CDS	7565432	7565580	0.99	-	2	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	exon	7565432	7565580	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	intron	7565581	7565713	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	CDS	7565714	7566138	1	-	1	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	exon	7565714	7566138	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	intron	7566139	7566253	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	CDS	7566254	7566447	1	-	0	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	exon	7566254	7566447	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	intron	7566448	7566726	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	CDS	7566727	7566978	0.97	-	0	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	exon	7566727	7566978	.	-	.	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
Phchi.S4	AUGUSTUS	start_codon	7566976	7566978	.	-	0	transcript_id "Phchi.S4G124400.t1"; gene_id "Phchi.S4G124400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7185.t1 is derived from g4357.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27448480	27450714	.	-	.	Phchi.S1G434400
Phchi.S1	AUGUSTUS	transcript	27448480	27450714	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	stop_codon	27448477	27448479	.	-	0	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	CDS	27448480	27448669	1	-	1	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	exon	27448480	27448669	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	intron	27448670	27448749	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	CDS	27448750	27448840	1	-	2	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	exon	27448750	27448840	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	intron	27448841	27448921	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	CDS	27448922	27449710	0.98	-	2	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	exon	27448922	27449710	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	intron	27449711	27450230	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	CDS	27450231	27450714	0.99	-	0	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	exon	27450231	27450714	.	-	.	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
Phchi.S1	AUGUSTUS	start_codon	27450712	27450714	.	-	0	transcript_id "Phchi.S1G434400.t1"; gene_id "Phchi.S1G434400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12010.t1 is derived from g7685.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	514589	515764	.	+	.	Phchi.S2G009000
Phchi.S2	AUGUSTUS	transcript	514589	515764	.	+	.	transcript_id "Phchi.S2G009000.t1"; gene_id "Phchi.S2G009000"
Phchi.S2	AUGUSTUS	start_codon	514589	514591	.	+	0	transcript_id "Phchi.S2G009000.t1"; gene_id "Phchi.S2G009000"
Phchi.S2	AUGUSTUS	CDS	514589	515764	1	+	0	transcript_id "Phchi.S2G009000.t1"; gene_id "Phchi.S2G009000"
Phchi.S2	AUGUSTUS	exon	514589	515764	.	+	.	transcript_id "Phchi.S2G009000.t1"; gene_id "Phchi.S2G009000"
Phchi.S2	AUGUSTUS	stop_codon	515765	515767	.	+	0	transcript_id "Phchi.S2G009000.t1"; gene_id "Phchi.S2G009000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14693.t1 is derived from g13161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14194067	14197261	.	+	.	Phchi.S3G201200
Phchi.S3	AUGUSTUS	transcript	14194112	14197261	.	+	.	transcript_id "Phchi.S3G201200.t1"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	start_codon	14194112	14194114	.	+	0	transcript_id "Phchi.S3G201200.t1"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	CDS	14194112	14197261	0.96	+	0	transcript_id "Phchi.S3G201200.t1"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	exon	14194112	14197261	.	+	.	transcript_id "Phchi.S3G201200.t1"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	stop_codon	14197262	14197264	.	+	0	transcript_id "Phchi.S3G201200.t1"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	transcript	14194067	14197261	.	+	.	transcript_id "Phchi.S3G201200.t2"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	start_codon	14194067	14194069	.	+	0	transcript_id "Phchi.S3G201200.t2"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	CDS	14194067	14197261	0.46	+	0	transcript_id "Phchi.S3G201200.t2"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	exon	14194067	14197261	.	+	.	transcript_id "Phchi.S3G201200.t2"; gene_id "Phchi.S3G201200"
Phchi.S3	AUGUSTUS	stop_codon	14197262	14197264	.	+	0	transcript_id "Phchi.S3G201200.t2"; gene_id "Phchi.S3G201200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1248.t1 is derived from g11031.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8631537	8634704	.	+	.	Phchi.S6G120700
Phchi.S6	AUGUSTUS	transcript	8631537	8634704	.	+	.	transcript_id "Phchi.S6G120700.t1"; gene_id "Phchi.S6G120700"
Phchi.S6	AUGUSTUS	start_codon	8631537	8631539	.	+	0	transcript_id "Phchi.S6G120700.t1"; gene_id "Phchi.S6G120700"
Phchi.S6	AUGUSTUS	CDS	8631537	8634704	0.95	+	0	transcript_id "Phchi.S6G120700.t1"; gene_id "Phchi.S6G120700"
Phchi.S6	AUGUSTUS	exon	8631537	8634704	.	+	.	transcript_id "Phchi.S6G120700.t1"; gene_id "Phchi.S6G120700"
Phchi.S6	AUGUSTUS	stop_codon	8634705	8634707	.	+	0	transcript_id "Phchi.S6G120700.t1"; gene_id "Phchi.S6G120700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9427.t1 is derived from g6603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41418740	41427748	.	+	.	Phchi.S1G658600
Phchi.S1	AUGUSTUS	transcript	41418740	41427748	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	start_codon	41418740	41418742	.	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41418740	41418755	0.43	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41418740	41418755	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41418756	41418843	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41418844	41418899	0.43	+	2	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41418844	41418899	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41418900	41419157	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41419158	41419217	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41419158	41419217	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41419218	41419295	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41419296	41419381	0.86	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41419296	41419381	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41419382	41419488	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41419489	41419584	0.89	+	1	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41419489	41419584	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41419585	41419802	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41419803	41419911	1	+	1	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41419803	41419911	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41419912	41420030	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41420031	41420123	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41420031	41420123	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41420124	41420265	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41420266	41420331	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41420266	41420331	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41420332	41420438	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41420439	41420701	0.97	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41420439	41420701	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41420702	41420790	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41420791	41420917	1	+	1	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41420791	41420917	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41420918	41421003	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41421004	41421075	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41421004	41421075	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41421076	41421321	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41421322	41421390	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41421322	41421390	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41421391	41421465	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41421466	41421594	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41421466	41421594	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41421595	41421685	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41421686	41421781	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41421686	41421781	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41421782	41421853	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41421854	41421955	0.88	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41421854	41421955	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41421956	41422097	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41422098	41422168	0.58	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41422098	41422168	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41422169	41422321	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41422322	41422418	0.98	+	1	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41422322	41422418	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41422419	41422488	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41422489	41422614	0.68	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41422489	41422614	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41422615	41422702	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41422703	41422759	0.69	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41422703	41422759	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41422760	41422859	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41422860	41423024	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41422860	41423024	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41423025	41423120	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41423121	41423240	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41423121	41423240	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41423241	41423376	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41423377	41423526	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41423377	41423526	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41423527	41423616	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41423617	41423814	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41423617	41423814	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41423815	41423896	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41423897	41423948	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41423897	41423948	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41423949	41424029	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41424030	41424091	0.82	+	2	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41424030	41424091	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41424092	41424188	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41424189	41424266	0.97	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41424189	41424266	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41424267	41424354	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41424355	41424516	0.99	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41424355	41424516	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41424517	41424608	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41424609	41424788	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41424609	41424788	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41424789	41424878	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41424879	41424944	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41424879	41424944	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41424945	41425018	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41425019	41425152	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41425019	41425152	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41425153	41425285	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41425286	41425427	1	+	1	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41425286	41425427	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41425428	41425514	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41425515	41425661	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41425515	41425661	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41425662	41425741	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41425742	41425822	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41425742	41425822	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41425823	41425946	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41425947	41426066	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41425947	41426066	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41426067	41426141	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41426142	41426228	0.99	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41426142	41426228	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41426229	41426336	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41426337	41426471	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41426337	41426471	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41426472	41426545	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41426546	41426612	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41426546	41426612	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41426613	41426687	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41426688	41426758	1	+	2	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41426688	41426758	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41426759	41426848	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41426849	41426953	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41426849	41426953	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41426954	41427037	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41427038	41427197	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41427038	41427197	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41427198	41427278	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41427279	41427334	1	+	2	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41427279	41427334	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41427335	41427411	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41427412	41427495	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41427412	41427495	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	intron	41427496	41427586	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	CDS	41427587	41427748	1	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	exon	41427587	41427748	.	+	.	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
Phchi.S1	AUGUSTUS	stop_codon	41427749	41427751	.	+	0	transcript_id "Phchi.S1G658600.t1"; gene_id "Phchi.S1G658600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6060.t1 is derived from g3231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20687654	20689114	.	-	.	Phchi.S1G321900
Phchi.S1	AUGUSTUS	transcript	20687654	20689114	.	-	.	transcript_id "Phchi.S1G321900.t1"; gene_id "Phchi.S1G321900"
Phchi.S1	AUGUSTUS	stop_codon	20687651	20687653	.	-	0	transcript_id "Phchi.S1G321900.t1"; gene_id "Phchi.S1G321900"
Phchi.S1	AUGUSTUS	CDS	20687654	20689114	1	-	0	transcript_id "Phchi.S1G321900.t1"; gene_id "Phchi.S1G321900"
Phchi.S1	AUGUSTUS	exon	20687654	20689114	.	-	.	transcript_id "Phchi.S1G321900.t1"; gene_id "Phchi.S1G321900"
Phchi.S1	AUGUSTUS	start_codon	20689112	20689114	.	-	0	transcript_id "Phchi.S1G321900.t1"; gene_id "Phchi.S1G321900"
# This transcript jg15670.t2 is derived from g14139.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15670.t3 is derived from g14139.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg15670.t4 is derived from g14139.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15671.t1 is derived from g14140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20597818	20600838	.	+	.	Phchi.S3G299000
Phchi.S3	AUGUSTUS	transcript	20597818	20600838	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	start_codon	20597818	20597820	.	+	0	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20597818	20598189	0.71	+	0	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20597818	20598189	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20598190	20598267	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20598268	20598645	0.96	+	0	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20598268	20598645	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20598646	20598752	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20598753	20598922	0.9	+	0	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20598753	20598922	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20598923	20599014	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20599015	20599045	1	+	1	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20599015	20599045	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20599046	20599143	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20599144	20599165	1	+	0	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20599144	20599165	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20599166	20599260	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20599261	20599611	1	+	2	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20599261	20599611	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20599612	20599701	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20599702	20600121	0.96	+	2	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20599702	20600121	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	intron	20600122	20600230	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	CDS	20600231	20600838	0.89	+	2	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	exon	20600231	20600838	.	+	.	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
Phchi.S3	AUGUSTUS	stop_codon	20600839	20600841	.	+	0	transcript_id "Phchi.S3G299000.t1"; gene_id "Phchi.S3G299000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4829.t1 is derived from g1999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13030736	13033804	.	-	.	Phchi.S1G198800
Phchi.S1	AUGUSTUS	transcript	13030736	13033804	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	stop_codon	13030733	13030735	.	-	0	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	CDS	13030736	13031154	0.98	-	2	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	exon	13030736	13031154	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	intron	13031155	13031469	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	CDS	13031470	13033249	0.98	-	0	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	exon	13031470	13033249	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	intron	13033250	13033326	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	CDS	13033327	13033421	1	-	2	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	exon	13033327	13033421	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	intron	13033422	13033510	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	CDS	13033511	13033640	1	-	0	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	exon	13033511	13033640	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	intron	13033641	13033711	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	CDS	13033712	13033804	1	-	0	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	exon	13033712	13033804	.	-	.	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
Phchi.S1	AUGUSTUS	start_codon	13033802	13033804	.	-	0	transcript_id "Phchi.S1G198800.t1"; gene_id "Phchi.S1G198800"
# This transcript jg14725.t2 is derived from g13193.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg14725.t3 is derived from g13193.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14726.t1 is derived from g13194.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14379503	14381092	.	-	.	Phchi.S3G204500
Phchi.S3	AUGUSTUS	transcript	14379503	14381092	.	-	.	transcript_id "Phchi.S3G204500.t1"; gene_id "Phchi.S3G204500"
Phchi.S3	AUGUSTUS	stop_codon	14379500	14379502	.	-	0	transcript_id "Phchi.S3G204500.t1"; gene_id "Phchi.S3G204500"
Phchi.S3	AUGUSTUS	CDS	14379503	14381092	0.42	-	0	transcript_id "Phchi.S3G204500.t1"; gene_id "Phchi.S3G204500"
Phchi.S3	AUGUSTUS	exon	14379503	14381092	.	-	.	transcript_id "Phchi.S3G204500.t1"; gene_id "Phchi.S3G204500"
Phchi.S3	AUGUSTUS	start_codon	14381090	14381092	.	-	0	transcript_id "Phchi.S3G204500.t1"; gene_id "Phchi.S3G204500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12088.t1 is derived from g7763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	2184621	2185825	.	+	.	Phchi.S2G016800
Phchi.S2	AUGUSTUS	transcript	2184621	2185825	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	start_codon	2184621	2184623	.	+	0	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	CDS	2184621	2184877	0.75	+	0	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	exon	2184621	2184877	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	intron	2184878	2184948	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	CDS	2184949	2185205	1	+	1	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	exon	2184949	2185205	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	intron	2185206	2185295	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	CDS	2185296	2185363	1	+	2	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	exon	2185296	2185363	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	intron	2185364	2185448	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	CDS	2185449	2185625	1	+	0	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	exon	2185449	2185625	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	intron	2185626	2185717	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	CDS	2185718	2185825	1	+	0	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	exon	2185718	2185825	.	+	.	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
Phchi.S2	AUGUSTUS	stop_codon	2185826	2185828	.	+	0	transcript_id "Phchi.S2G016800.t1"; gene_id "Phchi.S2G016800"
# This transcript jg6567.t2 is derived from g3739.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6568.t1 is derived from g3740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23745382	23747616	.	+	.	Phchi.S1G372700
Phchi.S1	AUGUSTUS	transcript	23745382	23747616	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	start_codon	23745382	23745384	.	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23745382	23745732	1	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23745382	23745732	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23745733	23746190	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23746191	23746240	1	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23746191	23746240	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23746241	23746376	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23746377	23746512	1	+	1	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23746377	23746512	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23746513	23746613	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23746614	23746715	1	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23746614	23746715	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23746716	23746800	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23746801	23747028	1	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23746801	23747028	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23747029	23747166	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23747167	23747248	1	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23747167	23747248	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23747249	23747409	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23747410	23747492	1	+	2	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23747410	23747492	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	intron	23747493	23747583	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	CDS	23747584	23747616	0.86	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	exon	23747584	23747616	.	+	.	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
Phchi.S1	AUGUSTUS	stop_codon	23747617	23747619	.	+	0	transcript_id "Phchi.S1G372700.t1"; gene_id "Phchi.S1G372700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3684.t1 is derived from g853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5164095	5164535	.	+	.	Phchi.S1G084300
Phchi.S1	AUGUSTUS	transcript	5164095	5164535	.	+	.	transcript_id "Phchi.S1G084300.t1"; gene_id "Phchi.S1G084300"
Phchi.S1	AUGUSTUS	start_codon	5164095	5164097	.	+	0	transcript_id "Phchi.S1G084300.t1"; gene_id "Phchi.S1G084300"
Phchi.S1	AUGUSTUS	CDS	5164095	5164535	0.38	+	0	transcript_id "Phchi.S1G084300.t1"; gene_id "Phchi.S1G084300"
Phchi.S1	AUGUSTUS	exon	5164095	5164535	.	+	.	transcript_id "Phchi.S1G084300.t1"; gene_id "Phchi.S1G084300"
Phchi.S1	AUGUSTUS	stop_codon	5164536	5164538	.	+	0	transcript_id "Phchi.S1G084300.t1"; gene_id "Phchi.S1G084300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4832.t1 is derived from g2002.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13041462	13041725	.	-	.	Phchi.S1G199100
Phchi.S1	AUGUSTUS	transcript	13041462	13041725	.	-	.	transcript_id "Phchi.S1G199100.t1"; gene_id "Phchi.S1G199100"
Phchi.S1	AUGUSTUS	stop_codon	13041459	13041461	.	-	0	transcript_id "Phchi.S1G199100.t1"; gene_id "Phchi.S1G199100"
Phchi.S1	AUGUSTUS	CDS	13041462	13041725	0.39	-	0	transcript_id "Phchi.S1G199100.t1"; gene_id "Phchi.S1G199100"
Phchi.S1	AUGUSTUS	exon	13041462	13041725	.	-	.	transcript_id "Phchi.S1G199100.t1"; gene_id "Phchi.S1G199100"
Phchi.S1	AUGUSTUS	start_codon	13041723	13041725	.	-	0	transcript_id "Phchi.S1G199100.t1"; gene_id "Phchi.S1G199100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8317.t1 is derived from g5492.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35257942	35260769	.	+	.	Phchi.S1G547600
Phchi.S1	AUGUSTUS	transcript	35257942	35260769	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	start_codon	35257942	35257944	.	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35257942	35258097	0.85	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35257942	35258097	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35258098	35258175	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35258176	35258317	1	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35258176	35258317	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35258318	35258427	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35258428	35258549	0.56	+	2	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35258428	35258549	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35258550	35258644	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35258645	35258715	1	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35258645	35258715	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35258716	35258852	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35258853	35258944	1	+	1	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35258853	35258944	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35258945	35259029	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35259030	35259117	1	+	2	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35259030	35259117	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35259118	35259240	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35259241	35259352	1	+	1	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35259241	35259352	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35259353	35259446	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35259447	35259543	1	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35259447	35259543	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35259544	35259711	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35259712	35259793	1	+	2	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35259712	35259793	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35259794	35259885	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35259886	35260003	1	+	1	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35259886	35260003	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35260004	35260076	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35260077	35260184	1	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35260077	35260184	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35260185	35260266	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35260267	35260369	1	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35260267	35260369	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35260370	35260461	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35260462	35260568	1	+	2	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35260462	35260568	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	intron	35260569	35260703	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	CDS	35260704	35260769	0.95	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	exon	35260704	35260769	.	+	.	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
Phchi.S1	AUGUSTUS	stop_codon	35260770	35260772	.	+	0	transcript_id "Phchi.S1G547600.t1"; gene_id "Phchi.S1G547600"
# This transcript jg6215.t1 is derived from g3387.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21494641	21495033	.	+	.	Phchi.S1G337400
Phchi.S1	AUGUSTUS	transcript	21494641	21495033	.	+	.	transcript_id "Phchi.S1G337400.t1"; gene_id "Phchi.S1G337400"
Phchi.S1	AUGUSTUS	start_codon	21494641	21494643	.	+	0	transcript_id "Phchi.S1G337400.t1"; gene_id "Phchi.S1G337400"
Phchi.S1	AUGUSTUS	CDS	21494641	21495033	0.35	+	0	transcript_id "Phchi.S1G337400.t1"; gene_id "Phchi.S1G337400"
Phchi.S1	AUGUSTUS	exon	21494641	21495033	.	+	.	transcript_id "Phchi.S1G337400.t1"; gene_id "Phchi.S1G337400"
Phchi.S1	AUGUSTUS	stop_codon	21495034	21495036	.	+	0	transcript_id "Phchi.S1G337400.t1"; gene_id "Phchi.S1G337400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13636.t1 is derived from g12103.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7919983	7920752	.	-	.	Phchi.S3G095500
Phchi.S3	AUGUSTUS	transcript	7919983	7920752	.	-	.	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	stop_codon	7919980	7919982	.	-	0	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	CDS	7919983	7920173	0.64	-	2	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	exon	7919983	7920173	.	-	.	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	intron	7920174	7920307	.	-	.	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	CDS	7920308	7920752	0.63	-	0	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	exon	7920308	7920752	.	-	.	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
Phchi.S3	AUGUSTUS	start_codon	7920750	7920752	.	-	0	transcript_id "Phchi.S3G095500.t1"; gene_id "Phchi.S3G095500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg351.t1 is derived from g10133.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2539129	2542243	.	+	.	Phchi.S6G031000
Phchi.S6	AUGUSTUS	transcript	2539129	2542243	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	start_codon	2539129	2539131	.	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2539129	2539566	0.69	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2539129	2539566	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2539567	2539660	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2539661	2539806	1	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2539661	2539806	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2539807	2539895	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2539896	2539995	1	+	1	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2539896	2539995	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2539996	2540092	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2540093	2540145	0.99	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2540093	2540145	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2540146	2540258	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2540259	2540333	0.99	+	1	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2540259	2540333	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2540334	2540437	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2540438	2540518	1	+	1	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2540438	2540518	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2540519	2540603	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2540604	2540680	1	+	1	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2540604	2540680	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2540681	2540827	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2540828	2540919	1	+	2	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2540828	2540919	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2540920	2541005	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2541006	2541121	1	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2541006	2541121	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2541122	2541209	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2541210	2541246	1	+	1	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2541210	2541246	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2541247	2541351	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2541352	2541447	1	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2541352	2541447	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2541448	2541536	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2541537	2541678	1	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2541537	2541678	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2541679	2541759	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2541760	2541812	1	+	2	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2541760	2541812	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2541813	2541941	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2541942	2542028	1	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2541942	2542028	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	intron	2542029	2542123	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	CDS	2542124	2542243	0.74	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	exon	2542124	2542243	.	+	.	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
Phchi.S6	AUGUSTUS	stop_codon	2542244	2542246	.	+	0	transcript_id "Phchi.S6G031000.t1"; gene_id "Phchi.S6G031000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg322.t1 is derived from g10104.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2264164	2265516	.	+	.	Phchi.S6G028100
Phchi.S6	AUGUSTUS	transcript	2264164	2265516	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	start_codon	2264164	2264166	.	+	0	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	CDS	2264164	2264379	1	+	0	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	exon	2264164	2264379	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	intron	2264380	2264471	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	CDS	2264472	2264727	0.97	+	0	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	exon	2264472	2264727	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	intron	2264728	2264825	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	CDS	2264826	2264832	0.85	+	2	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	exon	2264826	2264832	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	intron	2264833	2264975	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	CDS	2264976	2265147	0.85	+	1	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	exon	2264976	2265147	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	intron	2265148	2265264	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	CDS	2265265	2265516	0.68	+	0	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	exon	2265265	2265516	.	+	.	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
Phchi.S6	AUGUSTUS	stop_codon	2265517	2265519	.	+	0	transcript_id "Phchi.S6G028100.t1"; gene_id "Phchi.S6G028100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11346.t1 is derived from g15396.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5667889	5669919	.	-	.	Phchi.S4G092800
Phchi.S4	AUGUSTUS	transcript	5667889	5669919	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	stop_codon	5667886	5667888	.	-	0	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	CDS	5667889	5668404	1	-	0	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	exon	5667889	5668404	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	intron	5668405	5668573	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	CDS	5668574	5668934	1	-	1	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	exon	5668574	5668934	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	intron	5668935	5669058	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	CDS	5669059	5669240	1	-	0	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	exon	5669059	5669240	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	intron	5669241	5669367	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	CDS	5669368	5669445	1	-	0	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	exon	5669368	5669445	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	intron	5669446	5669781	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	CDS	5669782	5669919	1	-	0	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	exon	5669782	5669919	.	-	.	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
Phchi.S4	AUGUSTUS	start_codon	5669917	5669919	.	-	0	transcript_id "Phchi.S4G092800.t1"; gene_id "Phchi.S4G092800"
# This transcript jg2282.t2 is derived from g9202.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2283.t1 is derived from g9203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5863548	5867001	.	+	.	Phchi.S5G089200
Phchi.S5	AUGUSTUS	transcript	5863548	5867001	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	start_codon	5863548	5863550	.	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5863548	5864348	0.71	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5863548	5864348	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5864349	5864440	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5864441	5864503	1	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5864441	5864503	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5864504	5864695	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5864696	5864725	1	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5864696	5864725	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5864726	5864860	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5864861	5864934	0.84	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5864861	5864934	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5864935	5865094	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5865095	5865120	0.84	+	1	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5865095	5865120	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5865121	5865206	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5865207	5865279	1	+	2	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5865207	5865279	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5865280	5865378	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5865379	5865445	1	+	1	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5865379	5865445	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5865446	5865544	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5865545	5865637	1	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5865545	5865637	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5865638	5865719	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5865720	5865965	1	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5865720	5865965	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5865966	5866042	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5866043	5866093	1	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5866043	5866093	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5866094	5866197	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5866198	5866340	1	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5866198	5866340	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5866341	5866472	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5866473	5866854	0.89	+	1	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5866473	5866854	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	intron	5866855	5866944	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	CDS	5866945	5867001	0.69	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	exon	5866945	5867001	.	+	.	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
Phchi.S5	AUGUSTUS	stop_codon	5867002	5867004	.	+	0	transcript_id "Phchi.S5G089200.t1"; gene_id "Phchi.S5G089200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9140.t1 is derived from g6315.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40057144	40058882	.	-	.	Phchi.S1G629900
Phchi.S1	AUGUSTUS	transcript	40057144	40058882	.	-	.	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	stop_codon	40057141	40057143	.	-	0	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	CDS	40057144	40058607	0.59	-	0	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	exon	40057144	40058607	.	-	.	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	intron	40058608	40058705	.	-	.	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	CDS	40058706	40058882	0.96	-	0	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	exon	40058706	40058882	.	-	.	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
Phchi.S1	AUGUSTUS	start_codon	40058880	40058882	.	-	0	transcript_id "Phchi.S1G629900.t1"; gene_id "Phchi.S1G629900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7069.t1 is derived from g4241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26711309	26712807	.	-	.	Phchi.S1G422800
Phchi.S1	AUGUSTUS	transcript	26711309	26712807	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	stop_codon	26711306	26711308	.	-	0	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26711309	26711410	1	-	0	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26711309	26711410	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26711411	26711502	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26711503	26711650	1	-	1	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26711503	26711650	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26711651	26711784	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26711785	26711829	1	-	1	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26711785	26711829	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26711830	26711920	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26711921	26712041	1	-	2	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26711921	26712041	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26712042	26712139	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26712140	26712258	1	-	1	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26712140	26712258	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26712259	26712368	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26712369	26712413	0.99	-	1	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26712369	26712413	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26712414	26712497	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26712498	26712537	1	-	2	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26712498	26712537	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	intron	26712538	26712665	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	CDS	26712666	26712807	0.46	-	0	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	exon	26712666	26712807	.	-	.	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
Phchi.S1	AUGUSTUS	start_codon	26712805	26712807	.	-	0	transcript_id "Phchi.S1G422800.t1"; gene_id "Phchi.S1G422800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6989.t1 is derived from g4161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26295104	26296890	.	+	.	Phchi.S1G414800
Phchi.S1	AUGUSTUS	transcript	26295104	26296890	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	start_codon	26295104	26295106	.	+	0	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26295104	26295373	0.64	+	0	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26295104	26295373	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	intron	26295374	26295446	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26295447	26295515	0.83	+	0	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26295447	26295515	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	intron	26295516	26295712	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26295713	26295803	0.99	+	0	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26295713	26295803	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	intron	26295804	26295903	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26295904	26296113	1	+	2	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26295904	26296113	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	intron	26296114	26296195	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26296196	26296285	1	+	2	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26296196	26296285	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	intron	26296286	26296421	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26296422	26296554	1	+	2	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26296422	26296554	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	intron	26296555	26296655	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	CDS	26296656	26296890	0.93	+	1	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	exon	26296656	26296890	.	+	.	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
Phchi.S1	AUGUSTUS	stop_codon	26296891	26296893	.	+	0	transcript_id "Phchi.S1G414800.t1"; gene_id "Phchi.S1G414800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9511.t1 is derived from g6687.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42132318	42133389	.	+	.	Phchi.S1G667000
Phchi.S1	AUGUSTUS	transcript	42132318	42133389	.	+	.	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	start_codon	42132318	42132320	.	+	0	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	CDS	42132318	42132662	0.57	+	0	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	exon	42132318	42132662	.	+	.	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	intron	42132663	42132756	.	+	.	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	CDS	42132757	42133389	0.44	+	0	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	exon	42132757	42133389	.	+	.	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
Phchi.S1	AUGUSTUS	stop_codon	42133390	42133392	.	+	0	transcript_id "Phchi.S1G667000.t1"; gene_id "Phchi.S1G667000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12276.t1 is derived from g7952.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	8000974	8005952	.	+	.	Phchi.S2G035600
Phchi.S2	AUGUSTUS	transcript	8000974	8005952	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	start_codon	8000974	8000976	.	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8000974	8000991	0.79	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8000974	8000991	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8000992	8001344	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8001345	8001524	0.79	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8001345	8001524	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8001525	8002032	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8002033	8002157	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8002033	8002157	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8002158	8002654	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8002655	8002763	1	+	1	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8002655	8002763	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8002764	8002854	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8002855	8002945	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8002855	8002945	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8002946	8003126	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8003127	8003299	1	+	2	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8003127	8003299	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8003300	8003435	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8003436	8003540	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8003436	8003540	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8003541	8003701	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8003702	8003790	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8003702	8003790	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8003791	8003901	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8003902	8004009	1	+	1	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8003902	8004009	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8004010	8004172	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8004173	8004263	1	+	1	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8004173	8004263	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8004264	8004356	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8004357	8004446	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8004357	8004446	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8004447	8004554	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8004555	8004602	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8004555	8004602	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8004603	8004728	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8004729	8004800	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8004729	8004800	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8004801	8005028	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8005029	8005128	1	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8005029	8005128	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8005129	8005446	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8005447	8005573	1	+	2	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8005447	8005573	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	intron	8005574	8005672	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	CDS	8005673	8005952	0.96	+	1	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	exon	8005673	8005952	.	+	.	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
Phchi.S2	AUGUSTUS	stop_codon	8005953	8005955	.	+	0	transcript_id "Phchi.S2G035600.t1"; gene_id "Phchi.S2G035600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14623.t1 is derived from g13091.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13820658	13821341	.	-	.	Phchi.S3G194200
Phchi.S3	AUGUSTUS	transcript	13820658	13821341	.	-	.	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	stop_codon	13820655	13820657	.	-	0	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	CDS	13820658	13821053	1	-	0	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	exon	13820658	13821053	.	-	.	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	intron	13821054	13821146	.	-	.	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	CDS	13821147	13821341	0.58	-	0	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	exon	13821147	13821341	.	-	.	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
Phchi.S3	AUGUSTUS	start_codon	13821339	13821341	.	-	0	transcript_id "Phchi.S3G194200.t1"; gene_id "Phchi.S3G194200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg101.t1 is derived from g9883.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	507775	508056	.	+	.	Phchi.S6G006000
Phchi.S6	AUGUSTUS	transcript	507775	508056	.	+	.	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	start_codon	507775	507777	.	+	0	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	CDS	507775	507968	0.36	+	0	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	exon	507775	507968	.	+	.	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	intron	507969	508037	.	+	.	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	CDS	508038	508056	0.57	+	1	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	exon	508038	508056	.	+	.	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
Phchi.S6	AUGUSTUS	stop_codon	508057	508059	.	+	0	transcript_id "Phchi.S6G006000.t1"; gene_id "Phchi.S6G006000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg59.t1 is derived from g9841.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	296524	298080	.	-	.	Phchi.S6G001800
Phchi.S6	AUGUSTUS	transcript	296524	298080	.	-	.	transcript_id "Phchi.S6G001800.t1"; gene_id "Phchi.S6G001800"
Phchi.S6	AUGUSTUS	stop_codon	296521	296523	.	-	0	transcript_id "Phchi.S6G001800.t1"; gene_id "Phchi.S6G001800"
Phchi.S6	AUGUSTUS	CDS	296524	298080	0.49	-	0	transcript_id "Phchi.S6G001800.t1"; gene_id "Phchi.S6G001800"
Phchi.S6	AUGUSTUS	exon	296524	298080	.	-	.	transcript_id "Phchi.S6G001800.t1"; gene_id "Phchi.S6G001800"
Phchi.S6	AUGUSTUS	start_codon	298078	298080	.	-	0	transcript_id "Phchi.S6G001800.t1"; gene_id "Phchi.S6G001800"
# This transcript jg900.t2 is derived from g10682.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg901.t1 is derived from g10683.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6359407	6360010	.	-	.	Phchi.S6G086000
Phchi.S6	AUGUSTUS	transcript	6359407	6360010	.	-	.	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	stop_codon	6359404	6359406	.	-	0	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	CDS	6359407	6359838	0.99	-	0	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	exon	6359407	6359838	.	-	.	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	intron	6359839	6359923	.	-	.	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	CDS	6359924	6360010	0.74	-	0	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	exon	6359924	6360010	.	-	.	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
Phchi.S6	AUGUSTUS	start_codon	6360008	6360010	.	-	0	transcript_id "Phchi.S6G086000.t1"; gene_id "Phchi.S6G086000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10783.t1 is derived from g14833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2089054	2090160	.	-	.	Phchi.S4G036500
Phchi.S4	AUGUSTUS	transcript	2089054	2090160	.	-	.	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	stop_codon	2089051	2089053	.	-	0	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	CDS	2089054	2089104	1	-	0	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	exon	2089054	2089104	.	-	.	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	intron	2089105	2089204	.	-	.	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	CDS	2089205	2089414	1	-	0	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	exon	2089205	2089414	.	-	.	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	intron	2089415	2089512	.	-	.	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	CDS	2089513	2090160	0.96	-	0	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	exon	2089513	2090160	.	-	.	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
Phchi.S4	AUGUSTUS	start_codon	2090158	2090160	.	-	0	transcript_id "Phchi.S4G036500.t1"; gene_id "Phchi.S4G036500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg206.t1 is derived from g9988.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1140356	1141438	.	-	.	Phchi.S6G016500
Phchi.S6	AUGUSTUS	transcript	1140356	1141438	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	stop_codon	1140353	1140355	.	-	0	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1140356	1140492	0.95	-	2	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1140356	1140492	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	intron	1140493	1140820	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1140821	1140953	0.99	-	0	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1140821	1140953	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	intron	1140954	1141133	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1141134	1141220	0.9	-	0	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1141134	1141220	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	intron	1141221	1141333	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1141334	1141438	0.57	-	0	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1141334	1141438	.	-	.	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	start_codon	1141436	1141438	.	-	0	transcript_id "Phchi.S6G016500.t1"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	transcript	1140356	1141329	.	-	.	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	stop_codon	1140353	1140355	.	-	0	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1140356	1140492	0.39	-	2	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1140356	1140492	.	-	.	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	intron	1140493	1140800	.	-	.	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1140801	1140953	0.35	-	2	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1140801	1140953	.	-	.	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	intron	1140954	1141259	.	-	.	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	CDS	1141260	1141329	0.24	-	0	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	exon	1141260	1141329	.	-	.	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
Phchi.S6	AUGUSTUS	start_codon	1141327	1141329	.	-	0	transcript_id "Phchi.S6G016500.t2"; gene_id "Phchi.S6G016500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9146.t1 is derived from g6321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40087358	40087921	.	-	.	Phchi.S1G630500
Phchi.S1	AUGUSTUS	transcript	40087358	40087921	.	-	.	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	stop_codon	40087355	40087357	.	-	0	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	CDS	40087358	40087415	0.76	-	1	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	exon	40087358	40087415	.	-	.	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	intron	40087416	40087501	.	-	.	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	CDS	40087502	40087577	0.73	-	2	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	exon	40087502	40087577	.	-	.	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	intron	40087578	40087707	.	-	.	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	CDS	40087708	40087921	0.14	-	0	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	exon	40087708	40087921	.	-	.	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
Phchi.S1	AUGUSTUS	start_codon	40087919	40087921	.	-	0	transcript_id "Phchi.S1G630500.t1"; gene_id "Phchi.S1G630500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6190.t1 is derived from g3361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21386513	21388538	.	-	.	Phchi.S1G334900
Phchi.S1	AUGUSTUS	transcript	21386513	21388538	.	-	.	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	stop_codon	21386510	21386512	.	-	0	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	CDS	21386513	21387639	0.33	-	2	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	exon	21386513	21387639	.	-	.	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	intron	21387640	21387811	.	-	.	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	CDS	21387812	21388538	0.87	-	0	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	exon	21387812	21388538	.	-	.	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
Phchi.S1	AUGUSTUS	start_codon	21388536	21388538	.	-	0	transcript_id "Phchi.S1G334900.t1"; gene_id "Phchi.S1G334900"
# This transcript jg13331.t2 is derived from g11797.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg13331.t3 is derived from g11797.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13332.t1 is derived from g11798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6136331	6137452	.	-	.	Phchi.S3G065100
Phchi.S3	AUGUSTUS	transcript	6136331	6137452	.	-	.	transcript_id "Phchi.S3G065100.t1"; gene_id "Phchi.S3G065100"
Phchi.S3	AUGUSTUS	stop_codon	6136328	6136330	.	-	0	transcript_id "Phchi.S3G065100.t1"; gene_id "Phchi.S3G065100"
Phchi.S3	AUGUSTUS	CDS	6136331	6137452	0.45	-	0	transcript_id "Phchi.S3G065100.t1"; gene_id "Phchi.S3G065100"
Phchi.S3	AUGUSTUS	exon	6136331	6137452	.	-	.	transcript_id "Phchi.S3G065100.t1"; gene_id "Phchi.S3G065100"
Phchi.S3	AUGUSTUS	start_codon	6137450	6137452	.	-	0	transcript_id "Phchi.S3G065100.t1"; gene_id "Phchi.S3G065100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10075.t1 is derived from g7251.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45633124	45634031	.	+	.	Phchi.S1G723400
Phchi.S1	AUGUSTUS	transcript	45633124	45634031	.	+	.	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	start_codon	45633124	45633126	.	+	0	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	CDS	45633124	45633441	0.93	+	0	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	exon	45633124	45633441	.	+	.	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	intron	45633442	45633641	.	+	.	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	CDS	45633642	45634031	1	+	0	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	exon	45633642	45634031	.	+	.	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
Phchi.S1	AUGUSTUS	stop_codon	45634032	45634034	.	+	0	transcript_id "Phchi.S1G723400.t1"; gene_id "Phchi.S1G723400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11576.t1 is derived from g15627.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7145822	7150043	.	+	.	Phchi.S4G115800
Phchi.S4	AUGUSTUS	transcript	7145822	7150043	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	start_codon	7145822	7145824	.	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7145822	7146157	0.98	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7145822	7146157	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7146158	7146238	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7146239	7146474	1	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7146239	7146474	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7146475	7146567	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7146568	7146724	1	+	1	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7146568	7146724	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7146725	7146843	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7146844	7146921	1	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7146844	7146921	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7146922	7147059	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7147060	7147131	1	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7147060	7147131	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7147132	7147348	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7147349	7147468	1	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7147349	7147468	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7147469	7147607	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7147608	7147781	1	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7147608	7147781	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7147782	7147907	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7147908	7148095	0.4	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7147908	7148095	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7148096	7148358	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7148359	7148412	0.43	+	1	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7148359	7148412	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7148413	7148510	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7148511	7148666	0.85	+	1	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7148511	7148666	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7148667	7148775	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7148776	7148885	0.88	+	1	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7148776	7148885	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7148886	7149045	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7149046	7149158	1	+	2	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7149046	7149158	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7149159	7149261	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7149262	7149622	0.69	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7149262	7149622	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	intron	7149623	7149732	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	CDS	7149733	7150043	0.37	+	2	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	exon	7149733	7150043	.	+	.	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
Phchi.S4	AUGUSTUS	stop_codon	7150044	7150046	.	+	0	transcript_id "Phchi.S4G115800.t1"; gene_id "Phchi.S4G115800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7591.t1 is derived from g4765.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30181840	30184822	.	+	.	Phchi.S1G475000
Phchi.S1	AUGUSTUS	transcript	30181840	30184822	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	start_codon	30181840	30181842	.	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30181840	30181904	0.82	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30181840	30181904	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30181905	30182033	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30182034	30182121	1	+	1	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30182034	30182121	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30182122	30182668	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30182669	30182765	1	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30182669	30182765	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30182766	30182944	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30182945	30183030	1	+	2	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30182945	30183030	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183031	30183233	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30183234	30183364	0.5	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30183234	30183364	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183365	30183530	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30183531	30183547	0.85	+	1	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30183531	30183547	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183548	30183642	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30183643	30183815	0.85	+	2	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30183643	30183815	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183816	30184047	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30184048	30184189	1	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30184048	30184189	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30184190	30184390	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30184391	30184581	0.68	+	2	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30184391	30184581	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30184582	30184765	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30184766	30184822	0.7	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30184766	30184822	.	+	.	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	stop_codon	30184823	30184825	.	+	0	transcript_id "Phchi.S1G475000.t1"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	transcript	30182412	30184822	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	start_codon	30182412	30182414	.	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30182412	30182495	0.46	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30182412	30182495	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30182496	30182668	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30182669	30182765	0.96	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30182669	30182765	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30182766	30182944	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30182945	30183030	1	+	2	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30182945	30183030	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183031	30183233	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30183234	30183364	0.46	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30183234	30183364	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183365	30183530	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30183531	30183547	0.91	+	1	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30183531	30183547	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183548	30183642	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30183643	30183815	0.91	+	2	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30183643	30183815	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30183816	30184047	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30184048	30184189	1	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30184048	30184189	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30184190	30184390	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30184391	30184581	0.66	+	2	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30184391	30184581	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	intron	30184582	30184765	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	CDS	30184766	30184822	0.7	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	exon	30184766	30184822	.	+	.	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
Phchi.S1	AUGUSTUS	stop_codon	30184823	30184825	.	+	0	transcript_id "Phchi.S1G475000.t2"; gene_id "Phchi.S1G475000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10960.t1 is derived from g15010.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3309161	3309706	.	+	.	Phchi.S4G054200
Phchi.S4	AUGUSTUS	transcript	3309161	3309706	.	+	.	transcript_id "Phchi.S4G054200.t1"; gene_id "Phchi.S4G054200"
Phchi.S4	AUGUSTUS	start_codon	3309161	3309163	.	+	0	transcript_id "Phchi.S4G054200.t1"; gene_id "Phchi.S4G054200"
Phchi.S4	AUGUSTUS	CDS	3309161	3309706	0.33	+	0	transcript_id "Phchi.S4G054200.t1"; gene_id "Phchi.S4G054200"
Phchi.S4	AUGUSTUS	exon	3309161	3309706	.	+	.	transcript_id "Phchi.S4G054200.t1"; gene_id "Phchi.S4G054200"
Phchi.S4	AUGUSTUS	stop_codon	3309707	3309709	.	+	0	transcript_id "Phchi.S4G054200.t1"; gene_id "Phchi.S4G054200"
# This transcript jg7248.t2 is derived from g4420.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7249.t1 is derived from g4421.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27837151	27837947	.	-	.	Phchi.S1G440800
Phchi.S1	AUGUSTUS	transcript	27837151	27837947	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	stop_codon	27837148	27837150	.	-	0	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	CDS	27837151	27837198	0.6	-	0	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	exon	27837151	27837198	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	intron	27837199	27837307	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	CDS	27837308	27837365	0.9	-	1	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	exon	27837308	27837365	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	intron	27837366	27837457	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	CDS	27837458	27837760	1	-	1	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	exon	27837458	27837760	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	intron	27837761	27837855	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	CDS	27837856	27837947	0.8	-	0	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	exon	27837856	27837947	.	-	.	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
Phchi.S1	AUGUSTUS	start_codon	27837945	27837947	.	-	0	transcript_id "Phchi.S1G440800.t1"; gene_id "Phchi.S1G440800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1809.t1 is derived from g8729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3154362	3155840	.	+	.	Phchi.S5G041800
Phchi.S5	AUGUSTUS	transcript	3154362	3155840	.	+	.	transcript_id "Phchi.S5G041800.t1"; gene_id "Phchi.S5G041800"
Phchi.S5	AUGUSTUS	start_codon	3154362	3154364	.	+	0	transcript_id "Phchi.S5G041800.t1"; gene_id "Phchi.S5G041800"
Phchi.S5	AUGUSTUS	CDS	3154362	3155840	0.82	+	0	transcript_id "Phchi.S5G041800.t1"; gene_id "Phchi.S5G041800"
Phchi.S5	AUGUSTUS	exon	3154362	3155840	.	+	.	transcript_id "Phchi.S5G041800.t1"; gene_id "Phchi.S5G041800"
Phchi.S5	AUGUSTUS	stop_codon	3155841	3155843	.	+	0	transcript_id "Phchi.S5G041800.t1"; gene_id "Phchi.S5G041800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4419.t1 is derived from g1588.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10421471	10424443	.	-	.	Phchi.S1G157800
Phchi.S1	AUGUSTUS	transcript	10421471	10424443	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	stop_codon	10421468	10421470	.	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10421471	10421530	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10421471	10421530	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10421531	10421649	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10421650	10421820	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10421650	10421820	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10421821	10421888	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10421889	10422102	1	-	1	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10421889	10422102	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10422103	10422174	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10422175	10422227	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10422175	10422227	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10422228	10422370	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10422371	10422421	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10422371	10422421	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10422422	10422540	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10422541	10422607	1	-	1	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10422541	10422607	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10422608	10422702	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10422703	10422824	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10422703	10422824	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10422825	10422915	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10422916	10423114	1	-	1	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10422916	10423114	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10423115	10423259	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10423260	10423342	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10423260	10423342	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10423343	10423562	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10423563	10423757	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10423563	10423757	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10423758	10423941	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10423942	10424085	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10423942	10424085	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	intron	10424086	10424320	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	CDS	10424321	10424443	1	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	exon	10424321	10424443	.	-	.	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
Phchi.S1	AUGUSTUS	start_codon	10424441	10424443	.	-	0	transcript_id "Phchi.S1G157800.t1"; gene_id "Phchi.S1G157800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6873.t1 is derived from g4045.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25753814	25754533	.	-	.	Phchi.S1G403200
Phchi.S1	AUGUSTUS	transcript	25753814	25754533	.	-	.	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	stop_codon	25753811	25753813	.	-	0	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	CDS	25753814	25754364	1	-	2	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	exon	25753814	25754364	.	-	.	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	intron	25754365	25754460	.	-	.	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	CDS	25754461	25754533	0.99	-	0	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	exon	25754461	25754533	.	-	.	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
Phchi.S1	AUGUSTUS	start_codon	25754531	25754533	.	-	0	transcript_id "Phchi.S1G403200.t1"; gene_id "Phchi.S1G403200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1538.t1 is derived from g8457.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1671290	1673006	.	+	.	Phchi.S5G014700
Phchi.S5	AUGUSTUS	transcript	1671290	1673006	.	+	.	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	start_codon	1671290	1671292	.	+	0	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	CDS	1671290	1671991	0.47	+	0	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	exon	1671290	1671991	.	+	.	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	intron	1671992	1672331	.	+	.	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	CDS	1672332	1673006	1	+	0	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	exon	1672332	1673006	.	+	.	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
Phchi.S5	AUGUSTUS	stop_codon	1673007	1673009	.	+	0	transcript_id "Phchi.S5G014700.t1"; gene_id "Phchi.S5G014700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4018.t1 is derived from g1187.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7192567	7193526	.	-	.	Phchi.S1G117700
Phchi.S1	AUGUSTUS	transcript	7192567	7193526	.	-	.	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	stop_codon	7192564	7192566	.	-	0	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	CDS	7192567	7192789	0.99	-	1	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	exon	7192567	7192789	.	-	.	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	intron	7192790	7192873	.	-	.	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	CDS	7192874	7193526	0.84	-	0	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	exon	7192874	7193526	.	-	.	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
Phchi.S1	AUGUSTUS	start_codon	7193524	7193526	.	-	0	transcript_id "Phchi.S1G117700.t1"; gene_id "Phchi.S1G117700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13247.t1 is derived from g11712.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4914858	4916933	.	+	.	Phchi.S3G056600
Phchi.S3	AUGUSTUS	transcript	4914858	4916933	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	start_codon	4914858	4914860	.	+	0	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	CDS	4914858	4915141	1	+	0	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	exon	4914858	4915141	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	intron	4915142	4915226	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	CDS	4915227	4915328	1	+	1	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	exon	4915227	4915328	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	intron	4915329	4915449	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	CDS	4915450	4916249	0.99	+	1	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	exon	4915450	4916249	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	intron	4916250	4916349	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	CDS	4916350	4916933	1	+	2	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	exon	4916350	4916933	.	+	.	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
Phchi.S3	AUGUSTUS	stop_codon	4916934	4916936	.	+	0	transcript_id "Phchi.S3G056600.t1"; gene_id "Phchi.S3G056600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10669.t1 is derived from g14719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1514292	1516841	.	+	.	Phchi.S4G025100
Phchi.S4	AUGUSTUS	transcript	1514292	1516841	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	start_codon	1514292	1514294	.	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1514292	1514394	1	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1514292	1514394	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1514395	1514492	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1514493	1514578	1	+	2	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1514493	1514578	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1514579	1514704	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1514705	1514802	1	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1514705	1514802	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1514803	1514879	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1514880	1514997	1	+	1	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1514880	1514997	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1514998	1515083	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1515084	1515173	1	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1515084	1515173	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1515174	1515266	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1515267	1515571	0.94	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1515267	1515571	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1515572	1515676	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1515677	1515872	1	+	1	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1515677	1515872	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1515873	1515953	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1515954	1516139	1	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1515954	1516139	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1516140	1516226	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1516227	1516496	1	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1516227	1516496	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	intron	1516497	1516595	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	CDS	1516596	1516841	0.34	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	exon	1516596	1516841	.	+	.	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
Phchi.S4	AUGUSTUS	stop_codon	1516842	1516844	.	+	0	transcript_id "Phchi.S4G025100.t1"; gene_id "Phchi.S4G025100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3490.t1 is derived from g659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4028804	4029199	.	-	.	Phchi.S1G064900
Phchi.S1	AUGUSTUS	transcript	4028804	4029199	.	-	.	transcript_id "Phchi.S1G064900.t1"; gene_id "Phchi.S1G064900"
Phchi.S1	AUGUSTUS	stop_codon	4028801	4028803	.	-	0	transcript_id "Phchi.S1G064900.t1"; gene_id "Phchi.S1G064900"
Phchi.S1	AUGUSTUS	CDS	4028804	4029199	0.72	-	0	transcript_id "Phchi.S1G064900.t1"; gene_id "Phchi.S1G064900"
Phchi.S1	AUGUSTUS	exon	4028804	4029199	.	-	.	transcript_id "Phchi.S1G064900.t1"; gene_id "Phchi.S1G064900"
Phchi.S1	AUGUSTUS	start_codon	4029197	4029199	.	-	0	transcript_id "Phchi.S1G064900.t1"; gene_id "Phchi.S1G064900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14143.t1 is derived from g12610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11118106	11121194	.	+	.	Phchi.S3G146200
Phchi.S3	AUGUSTUS	transcript	11118106	11121194	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	start_codon	11118106	11118108	.	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11118106	11118266	1	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11118106	11118266	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11118267	11119009	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11119010	11119223	1	+	1	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11119010	11119223	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11119224	11119321	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11119322	11119534	1	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11119322	11119534	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11119535	11119673	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11119674	11119850	1	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11119674	11119850	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11119851	11119987	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11119988	11120054	1	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11119988	11120054	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11120055	11120152	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11120153	11120241	1	+	2	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11120153	11120241	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11120242	11120366	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11120367	11120492	0.69	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11120367	11120492	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11120493	11120601	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11120602	11120739	0.98	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11120602	11120739	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11120740	11120845	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11120846	11121004	0.95	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11120846	11121004	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	intron	11121005	11121089	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	CDS	11121090	11121194	1	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	exon	11121090	11121194	.	+	.	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
Phchi.S3	AUGUSTUS	stop_codon	11121195	11121197	.	+	0	transcript_id "Phchi.S3G146200.t1"; gene_id "Phchi.S3G146200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2597.t1 is derived from g9517.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7646698	7647015	.	+	.	Phchi.S5G120600
Phchi.S5	AUGUSTUS	transcript	7646698	7647015	.	+	.	transcript_id "Phchi.S5G120600.t1"; gene_id "Phchi.S5G120600"
Phchi.S5	AUGUSTUS	start_codon	7646698	7646700	.	+	0	transcript_id "Phchi.S5G120600.t1"; gene_id "Phchi.S5G120600"
Phchi.S5	AUGUSTUS	CDS	7646698	7647015	0.65	+	0	transcript_id "Phchi.S5G120600.t1"; gene_id "Phchi.S5G120600"
Phchi.S5	AUGUSTUS	exon	7646698	7647015	.	+	.	transcript_id "Phchi.S5G120600.t1"; gene_id "Phchi.S5G120600"
Phchi.S5	AUGUSTUS	stop_codon	7647016	7647018	.	+	0	transcript_id "Phchi.S5G120600.t1"; gene_id "Phchi.S5G120600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2282.t1 is derived from g9202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5861660	5863189	.	+	.	Phchi.S5G089100
Phchi.S5	AUGUSTUS	transcript	5861660	5863189	.	+	.	transcript_id "Phchi.S5G089100.t1"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	start_codon	5861660	5861662	.	+	0	transcript_id "Phchi.S5G089100.t1"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	CDS	5861660	5863189	0.99	+	0	transcript_id "Phchi.S5G089100.t1"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	exon	5861660	5863189	.	+	.	transcript_id "Phchi.S5G089100.t1"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	stop_codon	5863190	5863192	.	+	0	transcript_id "Phchi.S5G089100.t1"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	transcript	5862554	5863189	.	+	.	transcript_id "Phchi.S5G089100.t2"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	start_codon	5862554	5862556	.	+	0	transcript_id "Phchi.S5G089100.t2"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	CDS	5862554	5863189	0.94	+	0	transcript_id "Phchi.S5G089100.t2"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	exon	5862554	5863189	.	+	.	transcript_id "Phchi.S5G089100.t2"; gene_id "Phchi.S5G089100"
Phchi.S5	AUGUSTUS	stop_codon	5863190	5863192	.	+	0	transcript_id "Phchi.S5G089100.t2"; gene_id "Phchi.S5G089100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7060.t1 is derived from g4232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26661397	26664095	.	+	.	Phchi.S1G421900
Phchi.S1	AUGUSTUS	transcript	26661397	26664095	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	start_codon	26661397	26661399	.	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	CDS	26661397	26662080	0.97	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	exon	26661397	26662080	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	intron	26662081	26662190	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	CDS	26662191	26662394	1	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	exon	26662191	26662394	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	intron	26662395	26662527	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	CDS	26662528	26662713	0.97	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	exon	26662528	26662713	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	intron	26662714	26662821	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	CDS	26662822	26663112	0.99	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	exon	26662822	26663112	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	intron	26663113	26663195	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	CDS	26663196	26664095	1	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	exon	26663196	26664095	.	+	.	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
Phchi.S1	AUGUSTUS	stop_codon	26664096	26664098	.	+	0	transcript_id "Phchi.S1G421900.t1"; gene_id "Phchi.S1G421900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15828.t1 is derived from g14298.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21641906	21642124	.	+	.	Phchi.S3G314700
Phchi.S3	AUGUSTUS	transcript	21641906	21642124	.	+	.	transcript_id "Phchi.S3G314700.t1"; gene_id "Phchi.S3G314700"
Phchi.S3	AUGUSTUS	start_codon	21641906	21641908	.	+	0	transcript_id "Phchi.S3G314700.t1"; gene_id "Phchi.S3G314700"
Phchi.S3	AUGUSTUS	CDS	21641906	21642124	0.52	+	0	transcript_id "Phchi.S3G314700.t1"; gene_id "Phchi.S3G314700"
Phchi.S3	AUGUSTUS	exon	21641906	21642124	.	+	.	transcript_id "Phchi.S3G314700.t1"; gene_id "Phchi.S3G314700"
Phchi.S3	AUGUSTUS	stop_codon	21642125	21642127	.	+	0	transcript_id "Phchi.S3G314700.t1"; gene_id "Phchi.S3G314700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg303.t1 is derived from g10085.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2145937	2147392	.	+	.	Phchi.S6G026200
Phchi.S6	AUGUSTUS	transcript	2145937	2147392	.	+	.	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	start_codon	2145937	2145939	.	+	0	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	CDS	2145937	2146538	1	+	0	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	exon	2145937	2146538	.	+	.	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	intron	2146539	2146675	.	+	.	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	CDS	2146676	2146680	0.99	+	1	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	exon	2146676	2146680	.	+	.	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	intron	2146681	2146808	.	+	.	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	CDS	2146809	2147392	0.99	+	2	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	exon	2146809	2147392	.	+	.	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
Phchi.S6	AUGUSTUS	stop_codon	2147393	2147395	.	+	0	transcript_id "Phchi.S6G026200.t1"; gene_id "Phchi.S6G026200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7336.t1 is derived from g4508.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28565808	28568458	.	-	.	Phchi.S1G449500
Phchi.S1	AUGUSTUS	transcript	28565808	28568458	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	stop_codon	28565805	28565807	.	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28565808	28566029	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28565808	28566029	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28566030	28566158	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28566159	28566294	0.99	-	1	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28566159	28566294	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28566295	28566405	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28566406	28566461	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28566406	28566461	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28566462	28566607	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28566608	28566661	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28566608	28566661	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28566662	28566749	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28566750	28566827	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28566750	28566827	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28566828	28566913	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28566914	28567000	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28566914	28567000	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28567001	28567095	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28567096	28567156	1	-	1	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28567096	28567156	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28567157	28567321	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28567322	28567410	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28567322	28567410	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28567411	28567543	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28567544	28567641	1	-	2	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28567544	28567641	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28567642	28567758	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28567759	28567858	1	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28567759	28567858	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	intron	28567859	28568392	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	CDS	28568393	28568458	0.95	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	exon	28568393	28568458	.	-	.	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
Phchi.S1	AUGUSTUS	start_codon	28568456	28568458	.	-	0	transcript_id "Phchi.S1G449500.t1"; gene_id "Phchi.S1G449500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3756.t1 is derived from g925.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5546702	5548319	.	+	.	Phchi.S1G091500
Phchi.S1	AUGUSTUS	transcript	5546702	5548319	.	+	.	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	start_codon	5546702	5546704	.	+	0	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	CDS	5546702	5547880	0.49	+	0	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	exon	5546702	5547880	.	+	.	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	intron	5547881	5548002	.	+	.	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	CDS	5548003	5548016	0.51	+	0	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	exon	5548003	5548016	.	+	.	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	intron	5548017	5548273	.	+	.	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	CDS	5548274	5548319	0.51	+	1	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	exon	5548274	5548319	.	+	.	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
Phchi.S1	AUGUSTUS	stop_codon	5548320	5548322	.	+	0	transcript_id "Phchi.S1G091500.t1"; gene_id "Phchi.S1G091500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3878.t1 is derived from g1047.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6183370	6185090	.	-	.	Phchi.S1G103700
Phchi.S1	AUGUSTUS	transcript	6183370	6185090	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	stop_codon	6183367	6183369	.	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6183370	6183447	0.98	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6183370	6183447	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6183448	6183545	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6183546	6183640	1	-	2	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6183546	6183640	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6183641	6183749	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6183750	6183906	0.8	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6183750	6183906	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6183907	6184006	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6184007	6184069	0.99	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6184007	6184069	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6184070	6184195	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6184196	6184258	0.78	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6184196	6184258	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6184259	6184334	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6184335	6184430	1	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6184335	6184430	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6184431	6184546	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6184547	6184620	1	-	2	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6184547	6184620	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6184621	6184695	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6184696	6184785	1	-	2	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6184696	6184785	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	intron	6184786	6184870	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	CDS	6184871	6185090	0.7	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	exon	6184871	6185090	.	-	.	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
Phchi.S1	AUGUSTUS	start_codon	6185088	6185090	.	-	0	transcript_id "Phchi.S1G103700.t1"; gene_id "Phchi.S1G103700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10040.t1 is derived from g7216.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45210876	45211250	.	-	.	Phchi.S1G719900
Phchi.S1	AUGUSTUS	transcript	45210876	45211250	.	-	.	transcript_id "Phchi.S1G719900.t1"; gene_id "Phchi.S1G719900"
Phchi.S1	AUGUSTUS	stop_codon	45210873	45210875	.	-	0	transcript_id "Phchi.S1G719900.t1"; gene_id "Phchi.S1G719900"
Phchi.S1	AUGUSTUS	CDS	45210876	45211250	0.52	-	0	transcript_id "Phchi.S1G719900.t1"; gene_id "Phchi.S1G719900"
Phchi.S1	AUGUSTUS	exon	45210876	45211250	.	-	.	transcript_id "Phchi.S1G719900.t1"; gene_id "Phchi.S1G719900"
Phchi.S1	AUGUSTUS	start_codon	45211248	45211250	.	-	0	transcript_id "Phchi.S1G719900.t1"; gene_id "Phchi.S1G719900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3686.t1 is derived from g855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5182165	5182839	.	+	.	Phchi.S1G084500
Phchi.S1	AUGUSTUS	transcript	5182165	5182839	.	+	.	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	start_codon	5182165	5182167	.	+	0	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	CDS	5182165	5182401	0.86	+	0	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	exon	5182165	5182401	.	+	.	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	intron	5182402	5182491	.	+	.	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	CDS	5182492	5182839	0.66	+	0	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	exon	5182492	5182839	.	+	.	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
Phchi.S1	AUGUSTUS	stop_codon	5182840	5182842	.	+	0	transcript_id "Phchi.S1G084500.t1"; gene_id "Phchi.S1G084500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5391.t1 is derived from g2561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16646900	16647429	.	-	.	Phchi.S1G255000
Phchi.S1	AUGUSTUS	transcript	16646900	16647429	.	-	.	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	stop_codon	16646897	16646899	.	-	0	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	CDS	16646900	16647032	0.98	-	1	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	exon	16646900	16647032	.	-	.	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	intron	16647033	16647128	.	-	.	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	CDS	16647129	16647242	1	-	1	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	exon	16647129	16647242	.	-	.	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	intron	16647243	16647373	.	-	.	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	CDS	16647374	16647429	0.52	-	0	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	exon	16647374	16647429	.	-	.	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
Phchi.S1	AUGUSTUS	start_codon	16647427	16647429	.	-	0	transcript_id "Phchi.S1G255000.t1"; gene_id "Phchi.S1G255000"
# This transcript jg2166.t2 is derived from g9086.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg2166.t3 is derived from g9086.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2167.t1 is derived from g9087.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5148246	5148876	.	+	.	Phchi.S5G077600
Phchi.S5	AUGUSTUS	transcript	5148246	5148876	.	+	.	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	start_codon	5148246	5148248	.	+	0	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	CDS	5148246	5148333	0.98	+	0	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	exon	5148246	5148333	.	+	.	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	intron	5148334	5148418	.	+	.	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	CDS	5148419	5148876	1	+	2	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	exon	5148419	5148876	.	+	.	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
Phchi.S5	AUGUSTUS	stop_codon	5148877	5148879	.	+	0	transcript_id "Phchi.S5G077600.t1"; gene_id "Phchi.S5G077600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15418.t1 is derived from g13886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18990385	18992791	.	-	.	Phchi.S3G273700
Phchi.S3	AUGUSTUS	transcript	18990385	18992791	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	stop_codon	18990382	18990384	.	-	0	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	CDS	18990385	18990750	0.6	-	0	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	exon	18990385	18990750	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	intron	18990751	18990845	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	CDS	18990846	18990971	1	-	0	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	exon	18990846	18990971	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	intron	18990972	18991208	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	CDS	18991209	18991284	1	-	1	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	exon	18991209	18991284	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	intron	18991285	18991380	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	CDS	18991381	18991579	1	-	2	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	exon	18991381	18991579	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	intron	18991580	18991712	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	CDS	18991713	18991827	1	-	0	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	exon	18991713	18991827	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	intron	18991828	18992116	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	CDS	18992117	18992791	1	-	0	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	exon	18992117	18992791	.	-	.	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
Phchi.S3	AUGUSTUS	start_codon	18992789	18992791	.	-	0	transcript_id "Phchi.S3G273700.t1"; gene_id "Phchi.S3G273700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1861.t1 is derived from g8781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3578923	3580404	.	+	.	Phchi.S5G047000
Phchi.S5	AUGUSTUS	transcript	3578923	3580404	.	+	.	transcript_id "Phchi.S5G047000.t1"; gene_id "Phchi.S5G047000"
Phchi.S5	AUGUSTUS	start_codon	3578923	3578925	.	+	0	transcript_id "Phchi.S5G047000.t1"; gene_id "Phchi.S5G047000"
Phchi.S5	AUGUSTUS	CDS	3578923	3580404	0.68	+	0	transcript_id "Phchi.S5G047000.t1"; gene_id "Phchi.S5G047000"
Phchi.S5	AUGUSTUS	exon	3578923	3580404	.	+	.	transcript_id "Phchi.S5G047000.t1"; gene_id "Phchi.S5G047000"
Phchi.S5	AUGUSTUS	stop_codon	3580405	3580407	.	+	0	transcript_id "Phchi.S5G047000.t1"; gene_id "Phchi.S5G047000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg885.t1 is derived from g10667.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6273887	6275455	.	+	.	Phchi.S6G084400
Phchi.S6	AUGUSTUS	transcript	6273887	6275455	.	+	.	transcript_id "Phchi.S6G084400.t1"; gene_id "Phchi.S6G084400"
Phchi.S6	AUGUSTUS	start_codon	6273887	6273889	.	+	0	transcript_id "Phchi.S6G084400.t1"; gene_id "Phchi.S6G084400"
Phchi.S6	AUGUSTUS	CDS	6273887	6275455	0.33	+	0	transcript_id "Phchi.S6G084400.t1"; gene_id "Phchi.S6G084400"
Phchi.S6	AUGUSTUS	exon	6273887	6275455	.	+	.	transcript_id "Phchi.S6G084400.t1"; gene_id "Phchi.S6G084400"
Phchi.S6	AUGUSTUS	stop_codon	6275456	6275458	.	+	0	transcript_id "Phchi.S6G084400.t1"; gene_id "Phchi.S6G084400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg677.t1 is derived from g10459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4660916	4661510	.	+	.	Phchi.S6G063600
Phchi.S6	AUGUSTUS	transcript	4660916	4661510	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	start_codon	4660916	4660918	.	+	0	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	CDS	4660916	4661045	0.81	+	0	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	exon	4660916	4661045	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	intron	4661046	4661172	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	CDS	4661173	4661203	0.83	+	2	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	exon	4661173	4661203	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	intron	4661204	4661290	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	CDS	4661291	4661360	0.52	+	1	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	exon	4661291	4661360	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	intron	4661361	4661447	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	CDS	4661448	4661510	0.48	+	0	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	exon	4661448	4661510	.	+	.	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
Phchi.S6	AUGUSTUS	stop_codon	4661511	4661513	.	+	0	transcript_id "Phchi.S6G063600.t1"; gene_id "Phchi.S6G063600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10248.t1 is derived from g7424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46594014	46594754	.	+	.	Phchi.S1G740700
Phchi.S1	AUGUSTUS	transcript	46594014	46594754	.	+	.	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	start_codon	46594014	46594016	.	+	0	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	CDS	46594014	46594192	0.99	+	0	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	exon	46594014	46594192	.	+	.	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	intron	46594193	46594436	.	+	.	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	CDS	46594437	46594445	0.98	+	1	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	exon	46594437	46594445	.	+	.	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	intron	46594446	46594525	.	+	.	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	CDS	46594526	46594754	0.98	+	1	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	exon	46594526	46594754	.	+	.	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
Phchi.S1	AUGUSTUS	stop_codon	46594755	46594757	.	+	0	transcript_id "Phchi.S1G740700.t1"; gene_id "Phchi.S1G740700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9288.t1 is derived from g6463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40771215	40772702	.	+	.	Phchi.S1G644700
Phchi.S1	AUGUSTUS	transcript	40771215	40772702	.	+	.	transcript_id "Phchi.S1G644700.t1"; gene_id "Phchi.S1G644700"
Phchi.S1	AUGUSTUS	start_codon	40771215	40771217	.	+	0	transcript_id "Phchi.S1G644700.t1"; gene_id "Phchi.S1G644700"
Phchi.S1	AUGUSTUS	CDS	40771215	40772702	0.79	+	0	transcript_id "Phchi.S1G644700.t1"; gene_id "Phchi.S1G644700"
Phchi.S1	AUGUSTUS	exon	40771215	40772702	.	+	.	transcript_id "Phchi.S1G644700.t1"; gene_id "Phchi.S1G644700"
Phchi.S1	AUGUSTUS	stop_codon	40772703	40772705	.	+	0	transcript_id "Phchi.S1G644700.t1"; gene_id "Phchi.S1G644700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11655.t1 is derived from g15706.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7524855	7528220	.	-	.	Phchi.S4G123700
Phchi.S4	AUGUSTUS	transcript	7524855	7528220	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	stop_codon	7524852	7524854	.	-	0	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	CDS	7524855	7527372	0.55	-	1	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	exon	7524855	7527372	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	intron	7527373	7527498	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	CDS	7527499	7527644	0.51	-	0	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	exon	7527499	7527644	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	intron	7527645	7527727	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	CDS	7527728	7527874	1	-	0	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	exon	7527728	7527874	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	intron	7527875	7527965	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	CDS	7527966	7528220	0.75	-	0	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	exon	7527966	7528220	.	-	.	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
Phchi.S4	AUGUSTUS	start_codon	7528218	7528220	.	-	0	transcript_id "Phchi.S4G123700.t1"; gene_id "Phchi.S4G123700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9502.t1 is derived from g6678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42078446	42081017	.	-	.	Phchi.S1G666100
Phchi.S1	AUGUSTUS	transcript	42078446	42081017	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	stop_codon	42078443	42078445	.	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42078446	42078595	0.9	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42078446	42078595	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42078596	42078682	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42078683	42078774	1	-	2	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42078683	42078774	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42078775	42078960	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42078961	42079087	0.98	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42078961	42079087	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42079088	42079190	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42079191	42079362	1	-	1	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42079191	42079362	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42079363	42079464	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42079465	42079514	0.99	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42079465	42079514	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42079515	42079618	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42079619	42079799	0.99	-	1	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42079619	42079799	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42079800	42079943	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42079944	42080070	1	-	2	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42079944	42080070	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42080071	42080216	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42080217	42080394	1	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42080217	42080394	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42080395	42080482	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42080483	42080639	0.99	-	1	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42080483	42080639	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42080640	42080741	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42080742	42080842	0.99	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42080742	42080842	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	intron	42080843	42080906	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	CDS	42080907	42081017	1	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	exon	42080907	42081017	.	-	.	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
Phchi.S1	AUGUSTUS	start_codon	42081015	42081017	.	-	0	transcript_id "Phchi.S1G666100.t1"; gene_id "Phchi.S1G666100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6378.t1 is derived from g3550.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22644542	22646335	.	-	.	Phchi.S1G353700
Phchi.S1	AUGUSTUS	transcript	22644542	22646335	.	-	.	transcript_id "Phchi.S1G353700.t1"; gene_id "Phchi.S1G353700"
Phchi.S1	AUGUSTUS	stop_codon	22644539	22644541	.	-	0	transcript_id "Phchi.S1G353700.t1"; gene_id "Phchi.S1G353700"
Phchi.S1	AUGUSTUS	CDS	22644542	22646335	1	-	0	transcript_id "Phchi.S1G353700.t1"; gene_id "Phchi.S1G353700"
Phchi.S1	AUGUSTUS	exon	22644542	22646335	.	-	.	transcript_id "Phchi.S1G353700.t1"; gene_id "Phchi.S1G353700"
Phchi.S1	AUGUSTUS	start_codon	22646333	22646335	.	-	0	transcript_id "Phchi.S1G353700.t1"; gene_id "Phchi.S1G353700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14096.t1 is derived from g12563.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10831668	10832588	.	+	.	Phchi.S3G141500
Phchi.S3	AUGUSTUS	transcript	10831668	10832588	.	+	.	transcript_id "Phchi.S3G141500.t1"; gene_id "Phchi.S3G141500"
Phchi.S3	AUGUSTUS	start_codon	10831668	10831670	.	+	0	transcript_id "Phchi.S3G141500.t1"; gene_id "Phchi.S3G141500"
Phchi.S3	AUGUSTUS	CDS	10831668	10832588	0.97	+	0	transcript_id "Phchi.S3G141500.t1"; gene_id "Phchi.S3G141500"
Phchi.S3	AUGUSTUS	exon	10831668	10832588	.	+	.	transcript_id "Phchi.S3G141500.t1"; gene_id "Phchi.S3G141500"
Phchi.S3	AUGUSTUS	stop_codon	10832589	10832591	.	+	0	transcript_id "Phchi.S3G141500.t1"; gene_id "Phchi.S3G141500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15046.t1 is derived from g13514.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16738640	16739293	.	-	.	Phchi.S3G236500
Phchi.S3	AUGUSTUS	transcript	16738640	16739293	.	-	.	transcript_id "Phchi.S3G236500.t1"; gene_id "Phchi.S3G236500"
Phchi.S3	AUGUSTUS	stop_codon	16738637	16738639	.	-	0	transcript_id "Phchi.S3G236500.t1"; gene_id "Phchi.S3G236500"
Phchi.S3	AUGUSTUS	CDS	16738640	16739293	1	-	0	transcript_id "Phchi.S3G236500.t1"; gene_id "Phchi.S3G236500"
Phchi.S3	AUGUSTUS	exon	16738640	16739293	.	-	.	transcript_id "Phchi.S3G236500.t1"; gene_id "Phchi.S3G236500"
Phchi.S3	AUGUSTUS	start_codon	16739291	16739293	.	-	0	transcript_id "Phchi.S3G236500.t1"; gene_id "Phchi.S3G236500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8219.t1 is derived from g5394.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34466318	34468210	.	-	.	Phchi.S1G537800
Phchi.S1	AUGUSTUS	transcript	34466318	34468210	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	stop_codon	34466315	34466317	.	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34466318	34466359	0.9	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34466318	34466359	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34466360	34466438	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34466439	34466493	0.99	-	1	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34466439	34466493	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34466494	34466587	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34466588	34466673	0.98	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34466588	34466673	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34466674	34466765	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34466766	34466876	0.96	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34466766	34466876	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34466877	34466973	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34466974	34467054	1	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34466974	34467054	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34467055	34467214	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34467215	34467322	1	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34467215	34467322	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34467323	34467444	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34467445	34467522	1	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34467445	34467522	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34467523	34467612	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34467613	34467714	0.99	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34467613	34467714	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34467715	34467837	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34467838	34467906	0.99	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34467838	34467906	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	intron	34467907	34468093	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	CDS	34468094	34468210	0.81	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	exon	34468094	34468210	.	-	.	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
Phchi.S1	AUGUSTUS	start_codon	34468208	34468210	.	-	0	transcript_id "Phchi.S1G537800.t1"; gene_id "Phchi.S1G537800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4570.t1 is derived from g1740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11161124	11162205	.	+	.	Phchi.S1G172900
Phchi.S1	AUGUSTUS	transcript	11161124	11162205	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	start_codon	11161124	11161126	.	+	0	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	CDS	11161124	11161328	0.57	+	0	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	exon	11161124	11161328	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	intron	11161329	11161418	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	CDS	11161419	11161540	1	+	2	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	exon	11161419	11161540	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	intron	11161541	11161679	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	CDS	11161680	11161720	1	+	0	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	exon	11161680	11161720	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	intron	11161721	11161839	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	CDS	11161840	11161938	1	+	1	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	exon	11161840	11161938	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	intron	11161939	11162039	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	CDS	11162040	11162205	1	+	1	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	exon	11162040	11162205	.	+	.	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
Phchi.S1	AUGUSTUS	stop_codon	11162206	11162208	.	+	0	transcript_id "Phchi.S1G172900.t1"; gene_id "Phchi.S1G172900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3042.t1 is derived from g211.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1307295	1309534	.	-	.	Phchi.S1G020100
Phchi.S1	AUGUSTUS	transcript	1307295	1309534	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	stop_codon	1307292	1307294	.	-	0	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1307295	1308268	0.93	-	2	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1307295	1308268	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	intron	1308269	1308417	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1308418	1309035	0.82	-	2	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1308418	1309035	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	intron	1309036	1309204	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1309205	1309432	0.99	-	2	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1309205	1309432	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	intron	1309433	1309524	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1309525	1309534	0.97	-	0	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1309525	1309534	.	-	.	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	start_codon	1309532	1309534	.	-	0	transcript_id "Phchi.S1G020100.t1"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	transcript	1307295	1309534	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	stop_codon	1307292	1307294	.	-	0	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1307295	1308268	0.91	-	2	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1307295	1308268	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	intron	1308269	1308417	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1308418	1309035	0.81	-	2	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1308418	1309035	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	intron	1309036	1309204	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1309205	1309429	0.98	-	2	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1309205	1309429	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	intron	1309430	1309524	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	CDS	1309525	1309534	0.98	-	0	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	exon	1309525	1309534	.	-	.	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
Phchi.S1	AUGUSTUS	start_codon	1309532	1309534	.	-	0	transcript_id "Phchi.S1G020100.t2"; gene_id "Phchi.S1G020100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3618.t1 is derived from g787.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4777205	4779484	.	+	.	Phchi.S1G077700
Phchi.S1	AUGUSTUS	transcript	4777205	4779484	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	start_codon	4777205	4777207	.	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4777205	4777633	0.99	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4777205	4777633	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4777634	4777756	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4777757	4777843	1	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4777757	4777843	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4777844	4778032	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4778033	4778089	1	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4778033	4778089	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4778090	4778236	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4778237	4778377	0.94	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4778237	4778377	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4778378	4778478	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4778479	4778544	1	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4778479	4778544	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4778545	4778714	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4778715	4778882	1	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4778715	4778882	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4778883	4778963	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4778964	4779296	0.99	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4778964	4779296	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	intron	4779297	4779373	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	CDS	4779374	4779484	0.84	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	exon	4779374	4779484	.	+	.	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
Phchi.S1	AUGUSTUS	stop_codon	4779485	4779487	.	+	0	transcript_id "Phchi.S1G077700.t1"; gene_id "Phchi.S1G077700"
# This transcript jg7854.t2 is derived from g5028.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7855.t1 is derived from g5029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31541172	31541952	.	+	.	Phchi.S1G501400
Phchi.S1	AUGUSTUS	transcript	31541172	31541952	.	+	.	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	start_codon	31541172	31541174	.	+	0	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	CDS	31541172	31541498	0.53	+	0	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	exon	31541172	31541498	.	+	.	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	intron	31541499	31541579	.	+	.	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	CDS	31541580	31541775	1	+	0	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	exon	31541580	31541775	.	+	.	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	intron	31541776	31541860	.	+	.	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	CDS	31541861	31541952	1	+	2	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	exon	31541861	31541952	.	+	.	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
Phchi.S1	AUGUSTUS	stop_codon	31541953	31541955	.	+	0	transcript_id "Phchi.S1G501400.t1"; gene_id "Phchi.S1G501400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11773.t1 is derived from g15825.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8113544	8114461	.	+	.	Phchi.S4G135500
Phchi.S4	AUGUSTUS	transcript	8113544	8114461	.	+	.	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	start_codon	8113544	8113546	.	+	0	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	CDS	8113544	8113981	1	+	0	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	exon	8113544	8113981	.	+	.	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	intron	8113982	8114079	.	+	.	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	CDS	8114080	8114269	0.84	+	0	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	exon	8114080	8114269	.	+	.	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	intron	8114270	8114429	.	+	.	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	CDS	8114430	8114461	0.51	+	2	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	exon	8114430	8114461	.	+	.	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
Phchi.S4	AUGUSTUS	stop_codon	8114462	8114464	.	+	0	transcript_id "Phchi.S4G135500.t1"; gene_id "Phchi.S4G135500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg4030.t1 is derived from g1199.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	7256177	7259870	.	+	.	Phchi.S1G118900
Phchi.S1	AUGUSTUS	transcript	7256177	7259870	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	start_codon	7256177	7256179	.	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256177	7256189	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256177	7256189	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256190	7256373	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256374	7256465	1	+	2	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256374	7256465	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256466	7256623	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256624	7256788	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256624	7256788	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256789	7256885	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256886	7256959	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256886	7256959	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256960	7257121	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257122	7257202	1	+	1	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257122	7257202	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257203	7257288	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257289	7257349	1	+	1	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257289	7257349	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257350	7257482	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257483	7257523	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257483	7257523	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257524	7257678	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257679	7257733	1	+	1	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257679	7257733	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257734	7257814	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257815	7257892	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257815	7257892	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257893	7257974	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257975	7258028	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257975	7258028	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258029	7258119	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258120	7258173	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258120	7258173	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258174	7258369	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258370	7258430	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258370	7258430	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258431	7258580	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258581	7258632	1	+	2	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258581	7258632	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258633	7258784	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258785	7258813	1	+	1	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258785	7258813	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258814	7258945	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258946	7259010	1	+	2	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258946	7259010	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259011	7259149	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259150	7259212	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259150	7259212	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259213	7259303	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259304	7259366	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259304	7259366	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259367	7259456	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259457	7259521	1	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259457	7259521	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259522	7259675	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259676	7259744	1	+	1	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259676	7259744	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259745	7259827	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259828	7259870	1	+	1	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259828	7259870	.	+	.	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	stop_codon	7259871	7259873	.	+	0	transcript_id "Phchi.S1G118900.t1"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	transcript	7256177	7259870	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	start_codon	7256177	7256179	.	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256177	7256189	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256177	7256189	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256190	7256373	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256374	7256465	1	+	2	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256374	7256465	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256466	7256623	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256624	7256788	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256624	7256788	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256789	7256885	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7256886	7256959	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7256886	7256959	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7256960	7257121	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257122	7257202	1	+	1	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257122	7257202	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257203	7257288	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257289	7257349	1	+	1	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257289	7257349	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257350	7257456	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257457	7257506	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257457	7257506	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257507	7257678	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257679	7257733	1	+	1	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257679	7257733	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257734	7257814	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257815	7257892	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257815	7257892	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7257893	7257974	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7257975	7258028	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7257975	7258028	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258029	7258119	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258120	7258173	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258120	7258173	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258174	7258369	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258370	7258430	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258370	7258430	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258431	7258580	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258581	7258632	1	+	2	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258581	7258632	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258633	7258784	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258785	7258813	1	+	1	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258785	7258813	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7258814	7258945	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7258946	7259010	1	+	2	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7258946	7259010	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259011	7259149	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259150	7259212	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259150	7259212	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259213	7259303	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259304	7259366	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259304	7259366	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259367	7259456	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259457	7259521	1	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259457	7259521	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259522	7259675	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259676	7259744	1	+	1	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259676	7259744	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	intron	7259745	7259827	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	CDS	7259828	7259870	1	+	1	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	exon	7259828	7259870	.	+	.	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
Phchi.S1	AUGUSTUS	stop_codon	7259871	7259873	.	+	0	transcript_id "Phchi.S1G118900.t2"; gene_id "Phchi.S1G118900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6318.t1 is derived from g3490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22238829	22242845	.	-	.	Phchi.S1G347700
Phchi.S1	AUGUSTUS	transcript	22238829	22242845	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	stop_codon	22238826	22238828	.	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22238829	22239390	0.88	-	1	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22238829	22239390	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22239391	22239478	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22239479	22239586	1	-	1	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22239479	22239586	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22239587	22239675	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22239676	22239833	1	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22239676	22239833	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22239834	22239917	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22239918	22240220	1	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22239918	22240220	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22240221	22240346	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22240347	22240615	0.65	-	2	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22240347	22240615	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22240616	22240818	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22240819	22240840	0.52	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22240819	22240840	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22240841	22240950	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22240951	22241085	0.64	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22240951	22241085	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22241086	22241193	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22241194	22241361	1	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22241194	22241361	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22241362	22241473	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22241474	22241731	0.45	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22241474	22241731	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22241732	22241856	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22241857	22242015	0.51	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22241857	22242015	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22242016	22242103	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22242104	22242155	0.51	-	1	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22242104	22242155	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22242156	22242338	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22242339	22242449	1	-	1	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22242339	22242449	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22242450	22242530	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22242531	22242656	1	-	1	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22242531	22242656	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	intron	22242657	22242747	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	CDS	22242748	22242845	1	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	exon	22242748	22242845	.	-	.	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
Phchi.S1	AUGUSTUS	start_codon	22242843	22242845	.	-	0	transcript_id "Phchi.S1G347700.t1"; gene_id "Phchi.S1G347700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2645.t1 is derived from g9565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7947438	7947788	.	-	.	Phchi.S5G125400
Phchi.S5	AUGUSTUS	transcript	7947438	7947788	.	-	.	transcript_id "Phchi.S5G125400.t1"; gene_id "Phchi.S5G125400"
Phchi.S5	AUGUSTUS	stop_codon	7947435	7947437	.	-	0	transcript_id "Phchi.S5G125400.t1"; gene_id "Phchi.S5G125400"
Phchi.S5	AUGUSTUS	CDS	7947438	7947788	0.74	-	0	transcript_id "Phchi.S5G125400.t1"; gene_id "Phchi.S5G125400"
Phchi.S5	AUGUSTUS	exon	7947438	7947788	.	-	.	transcript_id "Phchi.S5G125400.t1"; gene_id "Phchi.S5G125400"
Phchi.S5	AUGUSTUS	start_codon	7947786	7947788	.	-	0	transcript_id "Phchi.S5G125400.t1"; gene_id "Phchi.S5G125400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13058.t1 is derived from g11523.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3948919	3951217	.	+	.	Phchi.S3G037700
Phchi.S3	AUGUSTUS	transcript	3948919	3951217	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	start_codon	3948919	3948921	.	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3948919	3949127	0.52	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3948919	3949127	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3949128	3949211	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3949212	3949539	0.77	+	1	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3949212	3949539	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3949540	3949634	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3949635	3949784	0.99	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3949635	3949784	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3949785	3949891	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3949892	3950155	0.84	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3949892	3950155	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3950156	3950239	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3950240	3950326	0.96	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3950240	3950326	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3950327	3950442	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3950443	3950521	0.83	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3950443	3950521	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3950522	3950607	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3950608	3950714	0.9	+	2	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3950608	3950714	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3950715	3950838	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3950839	3950960	1	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3950839	3950960	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	intron	3950961	3951114	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	CDS	3951115	3951217	0.98	+	1	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	exon	3951115	3951217	.	+	.	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
Phchi.S3	AUGUSTUS	stop_codon	3951218	3951220	.	+	0	transcript_id "Phchi.S3G037700.t1"; gene_id "Phchi.S3G037700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg633.t1 is derived from g10415.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4485543	4485980	.	+	.	Phchi.S6G059200
Phchi.S6	AUGUSTUS	transcript	4485543	4485980	.	+	.	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	start_codon	4485543	4485545	.	+	0	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	CDS	4485543	4485673	0.65	+	0	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	exon	4485543	4485673	.	+	.	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	intron	4485674	4485764	.	+	.	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	CDS	4485765	4485802	0.83	+	1	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	exon	4485765	4485802	.	+	.	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	intron	4485803	4485942	.	+	.	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	CDS	4485943	4485980	0.99	+	2	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	exon	4485943	4485980	.	+	.	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
Phchi.S6	AUGUSTUS	stop_codon	4485981	4485983	.	+	0	transcript_id "Phchi.S6G059200.t1"; gene_id "Phchi.S6G059200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7781.t1 is derived from g4955.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31185470	31187277	.	+	.	Phchi.S1G494000
Phchi.S1	AUGUSTUS	transcript	31185470	31187277	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	start_codon	31185470	31185472	.	+	0	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	CDS	31185470	31185579	0.46	+	0	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	exon	31185470	31185579	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	intron	31185580	31185665	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	CDS	31185666	31185960	0.21	+	1	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	exon	31185666	31185960	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	intron	31185961	31186255	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	CDS	31186256	31186724	0.41	+	0	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	exon	31186256	31186724	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	intron	31186725	31186921	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	CDS	31186922	31187277	0.83	+	2	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	exon	31186922	31187277	.	+	.	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
Phchi.S1	AUGUSTUS	stop_codon	31187278	31187280	.	+	0	transcript_id "Phchi.S1G494000.t1"; gene_id "Phchi.S1G494000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3374.t1 is derived from g543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3233644	3234477	.	+	.	Phchi.S1G053300
Phchi.S1	AUGUSTUS	transcript	3233644	3234477	.	+	.	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	start_codon	3233644	3233646	.	+	0	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	CDS	3233644	3233874	0.97	+	0	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	exon	3233644	3233874	.	+	.	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	intron	3233875	3233972	.	+	.	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	CDS	3233973	3234048	1	+	0	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	exon	3233973	3234048	.	+	.	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	intron	3234049	3234229	.	+	.	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	CDS	3234230	3234477	1	+	2	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	exon	3234230	3234477	.	+	.	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
Phchi.S1	AUGUSTUS	stop_codon	3234478	3234480	.	+	0	transcript_id "Phchi.S1G053300.t1"; gene_id "Phchi.S1G053300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg951.t1 is derived from g10733.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	6626511	6627392	.	+	.	Phchi.S6G091000
Phchi.S6	AUGUSTUS	transcript	6626511	6627392	.	+	.	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	start_codon	6626511	6626513	.	+	0	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	CDS	6626511	6626983	0.22	+	0	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	exon	6626511	6626983	.	+	.	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	intron	6626984	6627144	.	+	.	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	CDS	6627145	6627261	0.3	+	1	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	exon	6627145	6627261	.	+	.	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	intron	6627262	6627343	.	+	.	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	CDS	6627344	6627392	0.53	+	1	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	exon	6627344	6627392	.	+	.	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
Phchi.S6	AUGUSTUS	stop_codon	6627393	6627395	.	+	0	transcript_id "Phchi.S6G091000.t1"; gene_id "Phchi.S6G091000"
# This transcript jg1755.t2 is derived from g8675.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1755.t3 is derived from g8675.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1755.t4 is derived from g8675.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1756.t1 is derived from g8676.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2894358	2898843	.	+	.	Phchi.S5G036500
Phchi.S5	AUGUSTUS	transcript	2894358	2898843	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	start_codon	2894358	2894360	.	+	0	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	CDS	2894358	2894421	0.73	+	0	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	exon	2894358	2894421	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	intron	2894422	2894581	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	CDS	2894582	2894631	0.9	+	2	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	exon	2894582	2894631	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	intron	2894632	2894807	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	CDS	2894808	2895189	0.6	+	0	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	exon	2894808	2895189	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	intron	2895190	2895289	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	CDS	2895290	2896791	0.59	+	2	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	exon	2895290	2896791	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	intron	2896792	2896898	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	CDS	2896899	2898250	0.45	+	0	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	exon	2896899	2898250	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	intron	2898251	2898374	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	CDS	2898375	2898843	0.76	+	1	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	exon	2898375	2898843	.	+	.	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
Phchi.S5	AUGUSTUS	stop_codon	2898844	2898846	.	+	0	transcript_id "Phchi.S5G036500.t1"; gene_id "Phchi.S5G036500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7779.t1 is derived from g4953.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31183044	31183441	.	+	.	Phchi.S1G493800
Phchi.S1	AUGUSTUS	transcript	31183044	31183441	.	+	.	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	start_codon	31183044	31183046	.	+	0	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	CDS	31183044	31183148	0.35	+	0	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	exon	31183044	31183148	.	+	.	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	intron	31183149	31183273	.	+	.	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	CDS	31183274	31183441	0.61	+	0	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	exon	31183274	31183441	.	+	.	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
Phchi.S1	AUGUSTUS	stop_codon	31183442	31183444	.	+	0	transcript_id "Phchi.S1G493800.t1"; gene_id "Phchi.S1G493800"
# This transcript jg5891.t2 is derived from g3061.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5892.t1 is derived from g3062.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19626996	19628714	.	-	.	Phchi.S1G305100
Phchi.S1	AUGUSTUS	transcript	19626996	19628714	.	-	.	transcript_id "Phchi.S1G305100.t1"; gene_id "Phchi.S1G305100"
Phchi.S1	AUGUSTUS	stop_codon	19626993	19626995	.	-	0	transcript_id "Phchi.S1G305100.t1"; gene_id "Phchi.S1G305100"
Phchi.S1	AUGUSTUS	CDS	19626996	19628714	0.58	-	0	transcript_id "Phchi.S1G305100.t1"; gene_id "Phchi.S1G305100"
Phchi.S1	AUGUSTUS	exon	19626996	19628714	.	-	.	transcript_id "Phchi.S1G305100.t1"; gene_id "Phchi.S1G305100"
Phchi.S1	AUGUSTUS	start_codon	19628712	19628714	.	-	0	transcript_id "Phchi.S1G305100.t1"; gene_id "Phchi.S1G305100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11768.t1 is derived from g15820.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8084962	8086105	.	-	.	Phchi.S4G135000
Phchi.S4	AUGUSTUS	transcript	8084962	8086105	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	stop_codon	8084959	8084961	.	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8084962	8084988	0.99	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8084962	8084988	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	intron	8084989	8085079	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8085080	8085103	0.83	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8085080	8085103	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	intron	8085104	8085322	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8085323	8085379	0.99	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8085323	8085379	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	intron	8085380	8085560	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8085561	8085620	1	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8085561	8085620	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	intron	8085621	8085723	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8085724	8085839	1	-	2	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8085724	8085839	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	intron	8085840	8085946	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8085947	8086019	1	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8085947	8086019	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	intron	8086020	8086102	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	CDS	8086103	8086105	1	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	exon	8086103	8086105	.	-	.	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
Phchi.S4	AUGUSTUS	start_codon	8086103	8086105	.	-	0	transcript_id "Phchi.S4G135000.t1"; gene_id "Phchi.S4G135000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7397.t1 is derived from g4569.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28939892	28942356	.	+	.	Phchi.S1G455600
Phchi.S1	AUGUSTUS	transcript	28939892	28942356	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	start_codon	28939892	28939894	.	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28939892	28939992	0.69	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28939892	28939992	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28939993	28940116	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28940117	28940145	0.98	+	1	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28940117	28940145	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28940146	28940291	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28940292	28940434	1	+	2	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28940292	28940434	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28940435	28940570	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28940571	28940783	1	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28940571	28940783	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28940784	28940850	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28940851	28941051	1	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28940851	28941051	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28941052	28941134	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28941135	28941227	1	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28941135	28941227	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28941228	28941355	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28941356	28941520	1	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28941356	28941520	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28941521	28941648	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28941649	28941763	1	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28941649	28941763	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	intron	28941764	28941856	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	CDS	28941857	28942356	1	+	2	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	exon	28941857	28942356	.	+	.	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
Phchi.S1	AUGUSTUS	stop_codon	28942357	28942359	.	+	0	transcript_id "Phchi.S1G455600.t1"; gene_id "Phchi.S1G455600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10031.t1 is derived from g7207.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	45171095	45172607	.	+	.	Phchi.S1G719000
Phchi.S1	AUGUSTUS	transcript	45171095	45172607	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	start_codon	45171095	45171097	.	+	0	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	CDS	45171095	45171256	1	+	0	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	exon	45171095	45171256	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	intron	45171257	45171398	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	CDS	45171399	45171584	1	+	0	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	exon	45171399	45171584	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	intron	45171585	45171702	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	CDS	45171703	45171892	1	+	0	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	exon	45171703	45171892	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	intron	45171893	45172074	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	CDS	45172075	45172107	1	+	2	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	exon	45172075	45172107	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	intron	45172108	45172187	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	CDS	45172188	45172273	1	+	2	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	exon	45172188	45172273	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	intron	45172274	45172376	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	CDS	45172377	45172607	0.99	+	0	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	exon	45172377	45172607	.	+	.	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
Phchi.S1	AUGUSTUS	stop_codon	45172608	45172610	.	+	0	transcript_id "Phchi.S1G719000.t1"; gene_id "Phchi.S1G719000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2355.t1 is derived from g9275.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6325007	6326765	.	-	.	Phchi.S5G096400
Phchi.S5	AUGUSTUS	transcript	6325007	6326765	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	stop_codon	6325004	6325006	.	-	0	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	CDS	6325007	6325051	0.93	-	0	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	exon	6325007	6325051	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	intron	6325052	6325221	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	CDS	6325222	6325264	0.76	-	1	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	exon	6325222	6325264	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	intron	6325265	6325675	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	CDS	6325676	6325796	0.75	-	2	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	exon	6325676	6325796	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	intron	6325797	6325976	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	CDS	6325977	6326047	0.53	-	1	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	exon	6325977	6326047	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	intron	6326048	6326403	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	CDS	6326404	6326765	0.4	-	0	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	exon	6326404	6326765	.	-	.	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
Phchi.S5	AUGUSTUS	start_codon	6326763	6326765	.	-	0	transcript_id "Phchi.S5G096400.t1"; gene_id "Phchi.S5G096400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10655.t1 is derived from g14705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1446655	1448385	.	+	.	Phchi.S4G023700
Phchi.S4	AUGUSTUS	transcript	1446655	1448385	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	start_codon	1446655	1446657	.	+	0	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	CDS	1446655	1446873	0.72	+	0	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	exon	1446655	1446873	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	intron	1446874	1446982	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	CDS	1446983	1447115	1	+	0	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	exon	1446983	1447115	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	intron	1447116	1447210	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	CDS	1447211	1448013	0.98	+	2	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	exon	1447211	1448013	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	intron	1448014	1448115	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	CDS	1448116	1448385	0.95	+	0	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	exon	1448116	1448385	.	+	.	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
Phchi.S4	AUGUSTUS	stop_codon	1448386	1448388	.	+	0	transcript_id "Phchi.S4G023700.t1"; gene_id "Phchi.S4G023700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2536.t1 is derived from g9456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7210917	7213331	.	+	.	Phchi.S5G114500
Phchi.S5	AUGUSTUS	transcript	7210917	7213331	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	start_codon	7210917	7210919	.	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7210917	7211087	1	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7210917	7211087	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7211088	7211176	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7211177	7211296	1	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7211177	7211296	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7211297	7211390	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7211391	7211518	1	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7211391	7211518	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7211519	7211662	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7211663	7211741	0.94	+	1	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7211663	7211741	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7211742	7211865	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7211866	7211946	0.94	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7211866	7211946	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7211947	7212047	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7212048	7212227	0.99	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7212048	7212227	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7212228	7212336	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7212337	7212486	1	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7212337	7212486	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7212487	7212571	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7212572	7212676	1	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7212572	7212676	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7212677	7212766	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7212767	7212898	1	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7212767	7212898	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7212899	7212992	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7212993	7213124	0.97	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7212993	7213124	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	intron	7213125	7213229	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	CDS	7213230	7213331	0.99	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	exon	7213230	7213331	.	+	.	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
Phchi.S5	AUGUSTUS	stop_codon	7213332	7213334	.	+	0	transcript_id "Phchi.S5G114500.t1"; gene_id "Phchi.S5G114500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6690.t1 is derived from g3862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	24525942	24527943	.	+	.	Phchi.S1G384900
Phchi.S1	AUGUSTUS	transcript	24525942	24527943	.	+	.	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	start_codon	24525942	24525944	.	+	0	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	CDS	24525942	24525972	0.43	+	0	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	exon	24525942	24525972	.	+	.	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	intron	24525973	24526084	.	+	.	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	CDS	24526085	24527943	0.42	+	2	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	exon	24526085	24527943	.	+	.	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
Phchi.S1	AUGUSTUS	stop_codon	24527944	24527946	.	+	0	transcript_id "Phchi.S1G384900.t1"; gene_id "Phchi.S1G384900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2776.t1 is derived from g9696.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8779546	8783853	.	-	.	Phchi.S5G138500
Phchi.S5	AUGUSTUS	transcript	8779546	8783853	.	-	.	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	stop_codon	8779543	8779545	.	-	0	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	CDS	8779546	8780488	0.44	-	1	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	exon	8779546	8780488	.	-	.	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	intron	8780489	8781116	.	-	.	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	CDS	8781117	8781232	1	-	0	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	exon	8781117	8781232	.	-	.	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	intron	8781233	8783775	.	-	.	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	CDS	8783776	8783853	0.49	-	0	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	exon	8783776	8783853	.	-	.	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
Phchi.S5	AUGUSTUS	start_codon	8783851	8783853	.	-	0	transcript_id "Phchi.S5G138500.t1"; gene_id "Phchi.S5G138500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10879.t1 is derived from g14929.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2729130	2733354	.	-	.	Phchi.S4G046100
Phchi.S4	AUGUSTUS	transcript	2729130	2733354	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	stop_codon	2729127	2729129	.	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2729130	2729226	1	-	1	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2729130	2729226	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2729227	2729360	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2729361	2729503	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2729361	2729503	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2729504	2729584	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2729585	2729668	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2729585	2729668	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2729669	2729767	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2729768	2729827	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2729768	2729827	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2729828	2729949	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2729950	2730030	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2729950	2730030	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2730031	2730116	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2730117	2730230	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2730117	2730230	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2730231	2730319	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2730320	2730392	1	-	1	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2730320	2730392	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2730393	2730507	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2730508	2730671	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2730508	2730671	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2730672	2730801	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2730802	2730995	1	-	2	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2730802	2730995	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2730996	2731094	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2731095	2731170	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2731095	2731170	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2731171	2731270	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2731271	2731608	1	-	2	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2731271	2731608	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2731609	2731811	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2731812	2731899	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2731812	2731899	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2731900	2731994	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2731995	2732075	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2731995	2732075	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2732076	2732156	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2732157	2732309	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2732157	2732309	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2732310	2732403	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2732404	2732460	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2732404	2732460	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2732461	2732580	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2732581	2732803	1	-	1	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2732581	2732803	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2732804	2732906	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2732907	2733078	1	-	2	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2732907	2733078	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2733079	2733160	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2733161	2733239	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2733161	2733239	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	intron	2733240	2733315	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	CDS	2733316	2733354	1	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	exon	2733316	2733354	.	-	.	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
Phchi.S4	AUGUSTUS	start_codon	2733352	2733354	.	-	0	transcript_id "Phchi.S4G046100.t1"; gene_id "Phchi.S4G046100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2297.t1 is derived from g9217.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5922571	5923423	.	+	.	Phchi.S5G090600
Phchi.S5	AUGUSTUS	transcript	5922571	5923423	.	+	.	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	start_codon	5922571	5922573	.	+	0	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	CDS	5922571	5923301	0.51	+	0	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	exon	5922571	5923301	.	+	.	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	intron	5923302	5923401	.	+	.	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	CDS	5923402	5923423	0.6	+	1	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	exon	5923402	5923423	.	+	.	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
Phchi.S5	AUGUSTUS	stop_codon	5923424	5923426	.	+	0	transcript_id "Phchi.S5G090600.t1"; gene_id "Phchi.S5G090600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10383.t1 is derived from g7559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47486843	47487694	.	+	.	Phchi.S1G754200
Phchi.S1	AUGUSTUS	transcript	47486843	47487694	.	+	.	transcript_id "Phchi.S1G754200.t1"; gene_id "Phchi.S1G754200"
Phchi.S1	AUGUSTUS	start_codon	47486843	47486845	.	+	0	transcript_id "Phchi.S1G754200.t1"; gene_id "Phchi.S1G754200"
Phchi.S1	AUGUSTUS	CDS	47486843	47487694	1	+	0	transcript_id "Phchi.S1G754200.t1"; gene_id "Phchi.S1G754200"
Phchi.S1	AUGUSTUS	exon	47486843	47487694	.	+	.	transcript_id "Phchi.S1G754200.t1"; gene_id "Phchi.S1G754200"
Phchi.S1	AUGUSTUS	stop_codon	47487695	47487697	.	+	0	transcript_id "Phchi.S1G754200.t1"; gene_id "Phchi.S1G754200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15142.t1 is derived from g13610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17249200	17250308	.	-	.	Phchi.S3G246100
Phchi.S3	AUGUSTUS	transcript	17249200	17250308	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	stop_codon	17249197	17249199	.	-	0	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	CDS	17249200	17249322	0.98	-	0	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	exon	17249200	17249322	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	intron	17249323	17249411	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	CDS	17249412	17249642	0.37	-	0	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	exon	17249412	17249642	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	intron	17249643	17249743	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	CDS	17249744	17249824	0.47	-	0	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	exon	17249744	17249824	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	intron	17249825	17250089	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	CDS	17250090	17250308	0.99	-	0	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	exon	17250090	17250308	.	-	.	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
Phchi.S3	AUGUSTUS	start_codon	17250306	17250308	.	-	0	transcript_id "Phchi.S3G246100.t1"; gene_id "Phchi.S3G246100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5694.t1 is derived from g2864.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18370912	18371762	.	+	.	Phchi.S1G285300
Phchi.S1	AUGUSTUS	transcript	18370912	18371762	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	start_codon	18370912	18370914	.	+	0	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	CDS	18370912	18370963	1	+	0	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	exon	18370912	18370963	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	intron	18370964	18371147	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	CDS	18371148	18371246	1	+	2	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	exon	18371148	18371246	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	intron	18371247	18371347	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	CDS	18371348	18371400	1	+	2	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	exon	18371348	18371400	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	intron	18371401	18371500	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	CDS	18371501	18371574	1	+	0	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	exon	18371501	18371574	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	intron	18371575	18371713	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	CDS	18371714	18371762	1	+	1	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	exon	18371714	18371762	.	+	.	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
Phchi.S1	AUGUSTUS	stop_codon	18371763	18371765	.	+	0	transcript_id "Phchi.S1G285300.t1"; gene_id "Phchi.S1G285300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2133.t1 is derived from g9053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5001749	5004032	.	-	.	Phchi.S5G074200
Phchi.S5	AUGUSTUS	transcript	5001749	5004032	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	stop_codon	5001746	5001748	.	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5001749	5001797	1	-	1	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5001749	5001797	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5001798	5001954	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5001955	5002085	1	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5001955	5002085	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5002086	5002191	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5002192	5002349	1	-	2	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5002192	5002349	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5002350	5002500	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5002501	5002615	1	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5002501	5002615	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5002616	5002840	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5002841	5002904	1	-	1	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5002841	5002904	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5002905	5003019	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5003020	5003102	1	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5003020	5003102	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5003103	5003197	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5003198	5003303	1	-	1	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5003198	5003303	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5003304	5003396	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5003397	5003521	1	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5003397	5003521	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5003522	5003607	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5003608	5003720	1	-	2	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5003608	5003720	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	intron	5003721	5003812	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	CDS	5003813	5004032	1	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	exon	5003813	5004032	.	-	.	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
Phchi.S5	AUGUSTUS	start_codon	5004030	5004032	.	-	0	transcript_id "Phchi.S5G074200.t1"; gene_id "Phchi.S5G074200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9018.t1 is derived from g6193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39165923	39167760	.	+	.	Phchi.S1G617700
Phchi.S1	AUGUSTUS	transcript	39165923	39167760	.	+	.	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	start_codon	39165923	39165925	.	+	0	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	CDS	39165923	39167588	0.49	+	0	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	exon	39165923	39167588	.	+	.	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	intron	39167589	39167677	.	+	.	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	CDS	39167678	39167760	1	+	2	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	exon	39167678	39167760	.	+	.	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
Phchi.S1	AUGUSTUS	stop_codon	39167761	39167763	.	+	0	transcript_id "Phchi.S1G617700.t1"; gene_id "Phchi.S1G617700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5182.t1 is derived from g2352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15370086	15371906	.	-	.	Phchi.S1G234100
Phchi.S1	AUGUSTUS	transcript	15370086	15371906	.	-	.	transcript_id "Phchi.S1G234100.t1"; gene_id "Phchi.S1G234100"
Phchi.S1	AUGUSTUS	stop_codon	15370083	15370085	.	-	0	transcript_id "Phchi.S1G234100.t1"; gene_id "Phchi.S1G234100"
Phchi.S1	AUGUSTUS	CDS	15370086	15371906	0.4	-	0	transcript_id "Phchi.S1G234100.t1"; gene_id "Phchi.S1G234100"
Phchi.S1	AUGUSTUS	exon	15370086	15371906	.	-	.	transcript_id "Phchi.S1G234100.t1"; gene_id "Phchi.S1G234100"
Phchi.S1	AUGUSTUS	start_codon	15371904	15371906	.	-	0	transcript_id "Phchi.S1G234100.t1"; gene_id "Phchi.S1G234100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14373.t1 is derived from g12840.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12417447	12419343	.	-	.	Phchi.S3G169200
Phchi.S3	AUGUSTUS	transcript	12417447	12419343	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	stop_codon	12417444	12417446	.	-	0	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12417447	12417460	1	-	2	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12417447	12417460	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12417461	12417727	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12417728	12417840	0.99	-	1	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12417728	12417840	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12417841	12418507	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12418508	12418585	0.99	-	1	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12418508	12418585	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12418586	12418795	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12418796	12418895	0.9	-	2	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12418796	12418895	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12418896	12419129	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12419130	12419343	0.75	-	0	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12419130	12419343	.	-	.	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	start_codon	12419341	12419343	.	-	0	transcript_id "Phchi.S3G169200.t1"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	transcript	12417447	12419343	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	stop_codon	12417444	12417446	.	-	0	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12417447	12417460	1	-	2	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12417447	12417460	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12417461	12417727	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12417728	12417847	1	-	2	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12417728	12417847	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12417848	12418507	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12418508	12418585	1	-	2	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12418508	12418585	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12418586	12418795	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12418796	12419035	0.39	-	2	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12418796	12419035	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	intron	12419036	12419129	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	CDS	12419130	12419343	0.81	-	0	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	exon	12419130	12419343	.	-	.	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
Phchi.S3	AUGUSTUS	start_codon	12419341	12419343	.	-	0	transcript_id "Phchi.S3G169200.t2"; gene_id "Phchi.S3G169200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5259.t1 is derived from g2429.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15902045	15904461	.	-	.	Phchi.S1G241800
Phchi.S1	AUGUSTUS	transcript	15902045	15904461	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	stop_codon	15902042	15902044	.	-	0	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	CDS	15902045	15902060	0.72	-	1	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	exon	15902045	15902060	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	intron	15902061	15902175	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	CDS	15902176	15903597	0.56	-	1	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	exon	15902176	15903597	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	intron	15903598	15903690	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	CDS	15903691	15903784	1	-	2	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	exon	15903691	15903784	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	intron	15903785	15903873	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	CDS	15903874	15904036	1	-	0	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	exon	15903874	15904036	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	intron	15904037	15904122	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	CDS	15904123	15904190	1	-	2	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	exon	15904123	15904190	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	intron	15904191	15904271	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	CDS	15904272	15904461	0.79	-	0	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	exon	15904272	15904461	.	-	.	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
Phchi.S1	AUGUSTUS	start_codon	15904459	15904461	.	-	0	transcript_id "Phchi.S1G241800.t1"; gene_id "Phchi.S1G241800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14426.t1 is derived from g12894.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12757388	12758278	.	-	.	Phchi.S3G174500
Phchi.S3	AUGUSTUS	transcript	12757388	12758278	.	-	.	transcript_id "Phchi.S3G174500.t1"; gene_id "Phchi.S3G174500"
Phchi.S3	AUGUSTUS	stop_codon	12757385	12757387	.	-	0	transcript_id "Phchi.S3G174500.t1"; gene_id "Phchi.S3G174500"
Phchi.S3	AUGUSTUS	CDS	12757388	12758278	0.83	-	0	transcript_id "Phchi.S3G174500.t1"; gene_id "Phchi.S3G174500"
Phchi.S3	AUGUSTUS	exon	12757388	12758278	.	-	.	transcript_id "Phchi.S3G174500.t1"; gene_id "Phchi.S3G174500"
Phchi.S3	AUGUSTUS	start_codon	12758276	12758278	.	-	0	transcript_id "Phchi.S3G174500.t1"; gene_id "Phchi.S3G174500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11412.t1 is derived from g15462.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6230836	6231372	.	-	.	Phchi.S4G099400
Phchi.S4	AUGUSTUS	transcript	6230836	6231372	.	-	.	transcript_id "Phchi.S4G099400.t1"; gene_id "Phchi.S4G099400"
Phchi.S4	AUGUSTUS	stop_codon	6230833	6230835	.	-	0	transcript_id "Phchi.S4G099400.t1"; gene_id "Phchi.S4G099400"
Phchi.S4	AUGUSTUS	CDS	6230836	6231372	0.69	-	0	transcript_id "Phchi.S4G099400.t1"; gene_id "Phchi.S4G099400"
Phchi.S4	AUGUSTUS	exon	6230836	6231372	.	-	.	transcript_id "Phchi.S4G099400.t1"; gene_id "Phchi.S4G099400"
Phchi.S4	AUGUSTUS	start_codon	6231370	6231372	.	-	0	transcript_id "Phchi.S4G099400.t1"; gene_id "Phchi.S4G099400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12054.t1 is derived from g7729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	1043076	1045344	.	-	.	Phchi.S2G013400
Phchi.S2	AUGUSTUS	transcript	1043076	1045344	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	stop_codon	1043073	1043075	.	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1043076	1043117	1	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1043076	1043117	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	intron	1043118	1043192	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1043193	1043264	1	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1043193	1043264	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	intron	1043265	1043356	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1043357	1043450	1	-	1	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1043357	1043450	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	intron	1043451	1043548	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1043549	1043697	1	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1043549	1043697	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	intron	1043698	1043830	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1043831	1044161	1	-	1	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1043831	1044161	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	intron	1044162	1044308	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1044309	1044640	1	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1044309	1044640	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	intron	1044641	1044762	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	CDS	1044763	1045344	1	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	exon	1044763	1045344	.	-	.	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
Phchi.S2	AUGUSTUS	start_codon	1045342	1045344	.	-	0	transcript_id "Phchi.S2G013400.t1"; gene_id "Phchi.S2G013400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7486.t1 is derived from g4659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29616967	29620304	.	-	.	Phchi.S1G464500
Phchi.S1	AUGUSTUS	transcript	29616967	29620304	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	stop_codon	29616964	29616966	.	-	0	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	CDS	29616967	29617280	0.54	-	2	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	exon	29616967	29617280	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	intron	29617281	29617509	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	CDS	29617510	29618072	0.95	-	1	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	exon	29617510	29618072	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	intron	29618073	29618146	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	CDS	29618147	29618618	1	-	2	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	exon	29618147	29618618	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	intron	29618619	29618743	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	CDS	29618744	29618864	0.96	-	0	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	exon	29618744	29618864	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	intron	29618865	29619020	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	CDS	29619021	29620304	0.97	-	0	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	exon	29619021	29620304	.	-	.	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
Phchi.S1	AUGUSTUS	start_codon	29620302	29620304	.	-	0	transcript_id "Phchi.S1G464500.t1"; gene_id "Phchi.S1G464500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2007.t1 is derived from g8927.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4416954	4420044	.	+	.	Phchi.S5G061600
Phchi.S5	AUGUSTUS	transcript	4416954	4420044	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	start_codon	4416954	4416956	.	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4416954	4417302	0.99	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4416954	4417302	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4417303	4417392	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4417393	4417563	1	+	2	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4417393	4417563	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4417564	4417652	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4417653	4417699	1	+	2	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4417653	4417699	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4417700	4417855	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4417856	4418002	1	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4417856	4418002	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4418003	4418101	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4418102	4418176	1	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4418102	4418176	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4418177	4418307	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4418308	4418420	1	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4418308	4418420	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4418421	4418523	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4418524	4418651	0.99	+	1	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4418524	4418651	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4418652	4418741	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4418742	4418803	1	+	2	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4418742	4418803	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4418804	4418934	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4418935	4419039	1	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4418935	4419039	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4419040	4419134	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4419135	4419169	1	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4419135	4419169	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4419170	4419259	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4419260	4419328	1	+	1	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4419260	4419328	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4419329	4419409	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4419410	4419504	1	+	1	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4419410	4419504	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4419505	4419596	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4419597	4419673	1	+	2	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4419597	4419673	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4419674	4419775	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4419776	4419853	0.97	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4419776	4419853	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	intron	4419854	4419939	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	CDS	4419940	4420044	1	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	exon	4419940	4420044	.	+	.	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
Phchi.S5	AUGUSTUS	stop_codon	4420045	4420047	.	+	0	transcript_id "Phchi.S5G061600.t1"; gene_id "Phchi.S5G061600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg459.t1 is derived from g10241.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3235339	3236954	.	-	.	Phchi.S6G041800
Phchi.S6	AUGUSTUS	transcript	3235339	3236954	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	stop_codon	3235336	3235338	.	-	0	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	CDS	3235339	3235600	0.98	-	1	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	exon	3235339	3235600	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	intron	3235601	3235830	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	CDS	3235831	3235951	1	-	2	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	exon	3235831	3235951	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	intron	3235952	3236304	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	CDS	3236305	3236403	1	-	2	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	exon	3236305	3236403	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	intron	3236404	3236497	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	CDS	3236498	3236954	0.97	-	0	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	exon	3236498	3236954	.	-	.	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
Phchi.S6	AUGUSTUS	start_codon	3236952	3236954	.	-	0	transcript_id "Phchi.S6G041800.t1"; gene_id "Phchi.S6G041800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11671.t1 is derived from g15722.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7596720	7599422	.	+	.	Phchi.S4G125300
Phchi.S4	AUGUSTUS	transcript	7596720	7599422	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	start_codon	7596720	7596722	.	+	0	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7596720	7596894	1	+	0	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7596720	7596894	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	intron	7596895	7597013	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7597014	7597150	1	+	2	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7597014	7597150	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	intron	7597151	7597243	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7597244	7597608	1	+	0	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7597244	7597608	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	intron	7597609	7597697	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7597698	7597794	1	+	1	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7597698	7597794	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	intron	7597795	7597980	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7597981	7598271	1	+	0	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7597981	7598271	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	intron	7598272	7598370	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7598371	7598602	0.93	+	0	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7598371	7598602	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	intron	7598603	7598697	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	CDS	7598698	7599422	0.78	+	2	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	exon	7598698	7599422	.	+	.	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
Phchi.S4	AUGUSTUS	stop_codon	7599423	7599425	.	+	0	transcript_id "Phchi.S4G125300.t1"; gene_id "Phchi.S4G125300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2420.t1 is derived from g9340.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6560552	6561626	.	+	.	Phchi.S5G102900
Phchi.S5	AUGUSTUS	transcript	6560552	6561626	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	start_codon	6560552	6560554	.	+	0	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	CDS	6560552	6560562	0.85	+	0	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	exon	6560552	6560562	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	intron	6560563	6560655	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	CDS	6560656	6560900	0.42	+	1	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	exon	6560656	6560900	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	intron	6560901	6560982	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	CDS	6560983	6561105	0.43	+	2	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	exon	6560983	6561105	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	intron	6561106	6561243	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	CDS	6561244	6561626	0.5	+	2	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	exon	6561244	6561626	.	+	.	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
Phchi.S5	AUGUSTUS	stop_codon	6561627	6561629	.	+	0	transcript_id "Phchi.S5G102900.t1"; gene_id "Phchi.S5G102900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1889.t1 is derived from g8809.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3714888	3716595	.	-	.	Phchi.S5G049800
Phchi.S5	AUGUSTUS	transcript	3714888	3716595	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	stop_codon	3714885	3714887	.	-	0	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3714888	3714888	1	-	1	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3714888	3714888	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3714889	3715016	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3715017	3715106	0.83	-	1	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3715017	3715106	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3715107	3715237	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3715238	3715532	1	-	2	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3715238	3715532	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3715533	3715670	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3715671	3715753	0.66	-	1	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3715671	3715753	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3715754	3715839	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3715840	3715886	0.63	-	0	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3715840	3715886	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3715887	3716079	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3716080	3716240	0.64	-	2	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3716080	3716240	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3716241	3716386	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3716387	3716407	0.64	-	2	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3716387	3716407	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	intron	3716408	3716498	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	CDS	3716499	3716595	1	-	0	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	exon	3716499	3716595	.	-	.	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
Phchi.S5	AUGUSTUS	start_codon	3716593	3716595	.	-	0	transcript_id "Phchi.S5G049800.t1"; gene_id "Phchi.S5G049800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10001.t1 is derived from g7177.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44992548	44993741	.	+	.	Phchi.S1G716000
Phchi.S1	AUGUSTUS	transcript	44992548	44993741	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	start_codon	44992548	44992550	.	+	0	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	CDS	44992548	44992832	0.5	+	0	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	exon	44992548	44992832	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	intron	44992833	44993117	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	CDS	44993118	44993291	0.9	+	0	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	exon	44993118	44993291	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	intron	44993292	44993377	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	CDS	44993378	44993521	0.87	+	0	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	exon	44993378	44993521	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	intron	44993522	44993609	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	CDS	44993610	44993741	0.87	+	0	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	exon	44993610	44993741	.	+	.	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
Phchi.S1	AUGUSTUS	stop_codon	44993742	44993744	.	+	0	transcript_id "Phchi.S1G716000.t1"; gene_id "Phchi.S1G716000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1774.t1 is derived from g8694.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2964720	2965553	.	-	.	Phchi.S5G038300
Phchi.S5	AUGUSTUS	transcript	2964720	2965553	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	stop_codon	2964717	2964719	.	-	0	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2964720	2964765	0.93	-	1	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2964720	2964765	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2964766	2964876	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2964877	2964961	0.96	-	2	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2964877	2964961	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2964962	2965074	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2965075	2965183	0.98	-	0	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2965075	2965183	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2965184	2965278	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2965279	2965376	0.99	-	2	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2965279	2965376	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2965377	2965474	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2965475	2965553	0.99	-	0	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2965475	2965553	.	-	.	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	start_codon	2965551	2965553	.	-	0	transcript_id "Phchi.S5G038300.t1"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	transcript	2964720	2965553	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	stop_codon	2964717	2964719	.	-	0	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2964720	2964765	0.94	-	1	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2964720	2964765	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2964766	2964876	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2964877	2964961	0.95	-	2	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2964877	2964961	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2964962	2965074	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2965075	2965108	0.7	-	0	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2965075	2965108	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2965109	2965278	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2965279	2965376	0.99	-	2	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2965279	2965376	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	intron	2965377	2965474	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	CDS	2965475	2965553	0.99	-	0	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	exon	2965475	2965553	.	-	.	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
Phchi.S5	AUGUSTUS	start_codon	2965551	2965553	.	-	0	transcript_id "Phchi.S5G038300.t2"; gene_id "Phchi.S5G038300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12246.t1 is derived from g7922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7001875	7003363	.	+	.	Phchi.S2G032600
Phchi.S2	AUGUSTUS	transcript	7001875	7003363	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	start_codon	7001875	7001877	.	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7001875	7001888	0.99	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7001875	7001888	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7001889	7001959	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7001960	7002041	1	+	1	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7001960	7002041	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7002042	7002175	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7002176	7002256	1	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7002176	7002256	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7002257	7002343	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7002344	7002457	1	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7002344	7002457	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7002458	7002553	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7002554	7002655	1	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7002554	7002655	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7002656	7002755	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7002756	7002814	1	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7002756	7002814	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7002815	7002915	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7002916	7003018	1	+	1	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7002916	7003018	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7003019	7003098	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7003099	7003164	0.87	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7003099	7003164	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	intron	7003165	7003273	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	CDS	7003274	7003363	0.87	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	exon	7003274	7003363	.	+	.	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
Phchi.S2	AUGUSTUS	stop_codon	7003364	7003366	.	+	0	transcript_id "Phchi.S2G032600.t1"; gene_id "Phchi.S2G032600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13444.t1 is derived from g11911.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	6737843	6738548	.	+	.	Phchi.S3G076300
Phchi.S3	AUGUSTUS	transcript	6737843	6738548	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	start_codon	6737843	6737845	.	+	0	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	CDS	6737843	6737845	0.56	+	0	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	exon	6737843	6737845	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	intron	6737846	6738024	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	CDS	6738025	6738126	1	+	0	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	exon	6738025	6738126	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	intron	6738127	6738299	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	CDS	6738300	6738328	1	+	0	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	exon	6738300	6738328	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	intron	6738329	6738424	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	CDS	6738425	6738548	1	+	1	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	exon	6738425	6738548	.	+	.	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
Phchi.S3	AUGUSTUS	stop_codon	6738549	6738551	.	+	0	transcript_id "Phchi.S3G076300.t1"; gene_id "Phchi.S3G076300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10460.t1 is derived from g14509.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	445117	445694	.	+	.	Phchi.S4G004200
Phchi.S4	AUGUSTUS	transcript	445117	445694	.	+	.	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	start_codon	445117	445119	.	+	0	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	CDS	445117	445588	0.29	+	0	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	exon	445117	445588	.	+	.	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	intron	445589	445665	.	+	.	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	CDS	445666	445694	0.41	+	2	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	exon	445666	445694	.	+	.	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
Phchi.S4	AUGUSTUS	stop_codon	445695	445697	.	+	0	transcript_id "Phchi.S4G004200.t1"; gene_id "Phchi.S4G004200"
# This transcript jg2689.t2 is derived from g9609.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2690.t1 is derived from g9610.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8226120	8227791	.	-	.	Phchi.S5G129900
Phchi.S5	AUGUSTUS	transcript	8226120	8227791	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	stop_codon	8226117	8226119	.	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8226120	8226281	0.61	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8226120	8226281	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8226282	8226384	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8226385	8226456	0.9	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8226385	8226456	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8226457	8226547	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8226548	8226616	1	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8226548	8226616	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8226617	8226785	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8226786	8226839	1	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8226786	8226839	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8226840	8227004	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8227005	8227103	0.99	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8227005	8227103	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8227104	8227217	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8227218	8227291	0.98	-	2	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8227218	8227291	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8227292	8227393	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8227394	8227514	0.96	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8227394	8227514	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	intron	8227515	8227611	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	CDS	8227612	8227791	1	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	exon	8227612	8227791	.	-	.	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
Phchi.S5	AUGUSTUS	start_codon	8227789	8227791	.	-	0	transcript_id "Phchi.S5G129900.t1"; gene_id "Phchi.S5G129900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9990.t1 is derived from g7166.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44837223	44841581	.	+	.	Phchi.S1G714900
Phchi.S1	AUGUSTUS	transcript	44837223	44841581	.	+	.	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	start_codon	44837223	44837225	.	+	0	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	CDS	44837223	44838753	0.53	+	0	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	exon	44837223	44838753	.	+	.	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	intron	44838754	44838865	.	+	.	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	CDS	44838866	44840319	1	+	2	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	exon	44838866	44840319	.	+	.	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	intron	44840320	44840441	.	+	.	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	CDS	44840442	44841581	0.97	+	0	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	exon	44840442	44841581	.	+	.	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
Phchi.S1	AUGUSTUS	stop_codon	44841582	44841584	.	+	0	transcript_id "Phchi.S1G714900.t1"; gene_id "Phchi.S1G714900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1147.t1 is derived from g10930.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8004089	8004583	.	-	.	Phchi.S6G110600
Phchi.S6	AUGUSTUS	transcript	8004089	8004583	.	-	.	transcript_id "Phchi.S6G110600.t1"; gene_id "Phchi.S6G110600"
Phchi.S6	AUGUSTUS	stop_codon	8004086	8004088	.	-	0	transcript_id "Phchi.S6G110600.t1"; gene_id "Phchi.S6G110600"
Phchi.S6	AUGUSTUS	CDS	8004089	8004583	0.82	-	0	transcript_id "Phchi.S6G110600.t1"; gene_id "Phchi.S6G110600"
Phchi.S6	AUGUSTUS	exon	8004089	8004583	.	-	.	transcript_id "Phchi.S6G110600.t1"; gene_id "Phchi.S6G110600"
Phchi.S6	AUGUSTUS	start_codon	8004581	8004583	.	-	0	transcript_id "Phchi.S6G110600.t1"; gene_id "Phchi.S6G110600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5621.t1 is derived from g2791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17919701	17921823	.	+	.	Phchi.S1G278000
Phchi.S1	AUGUSTUS	transcript	17919701	17921823	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	start_codon	17919701	17919703	.	+	0	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	CDS	17919701	17920034	0.67	+	0	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	exon	17919701	17920034	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	intron	17920035	17920160	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	CDS	17920161	17920416	1	+	2	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	exon	17920161	17920416	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	intron	17920417	17920537	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	CDS	17920538	17920715	1	+	1	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	exon	17920538	17920715	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	intron	17920716	17920914	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	CDS	17920915	17921823	0.98	+	0	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	exon	17920915	17921823	.	+	.	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
Phchi.S1	AUGUSTUS	stop_codon	17921824	17921826	.	+	0	transcript_id "Phchi.S1G278000.t1"; gene_id "Phchi.S1G278000"
# This transcript jg11725.t2 is derived from g15777.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11726.t1 is derived from g15778.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7856647	7859238	.	+	.	Phchi.S4G130800
Phchi.S4	AUGUSTUS	transcript	7856647	7859238	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	start_codon	7856647	7856649	.	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7856647	7856883	0.99	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7856647	7856883	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7856884	7856960	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7856961	7857026	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7856961	7857026	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7857027	7857156	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7857157	7857279	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7857157	7857279	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7857280	7857366	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7857367	7857447	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7857367	7857447	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7857448	7857526	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7857527	7857619	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7857527	7857619	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7857620	7857864	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7857865	7857940	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7857865	7857940	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7857941	7858095	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7858096	7858175	1	+	2	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7858096	7858175	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7858176	7858316	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7858317	7858388	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7858317	7858388	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7858389	7858476	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7858477	7858539	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7858477	7858539	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7858540	7858654	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7858655	7858751	1	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7858655	7858751	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7858752	7858878	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7858879	7858942	1	+	2	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7858879	7858942	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7858943	7859031	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7859032	7859091	1	+	1	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7859032	7859091	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	intron	7859092	7859162	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	CDS	7859163	7859238	0.94	+	1	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	exon	7859163	7859238	.	+	.	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
Phchi.S4	AUGUSTUS	stop_codon	7859239	7859241	.	+	0	transcript_id "Phchi.S4G130800.t1"; gene_id "Phchi.S4G130800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13698.t1 is derived from g12165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8252718	8253682	.	+	.	Phchi.S3G101700
Phchi.S3	AUGUSTUS	transcript	8252718	8253682	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	start_codon	8252718	8252720	.	+	0	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	CDS	8252718	8252732	0.91	+	0	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	exon	8252718	8252732	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	intron	8252733	8252810	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	CDS	8252811	8252912	0.99	+	0	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	exon	8252811	8252912	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	intron	8252913	8253057	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	CDS	8253058	8253165	0.99	+	0	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	exon	8253058	8253165	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	intron	8253166	8253313	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	CDS	8253314	8253381	1	+	0	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	exon	8253314	8253381	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	intron	8253382	8253471	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	CDS	8253472	8253682	0.37	+	1	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	exon	8253472	8253682	.	+	.	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
Phchi.S3	AUGUSTUS	stop_codon	8253683	8253685	.	+	0	transcript_id "Phchi.S3G101700.t1"; gene_id "Phchi.S3G101700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10628.t1 is derived from g14678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1324213	1327523	.	-	.	Phchi.S4G021000
Phchi.S4	AUGUSTUS	transcript	1324213	1327523	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	stop_codon	1324210	1324212	.	-	0	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	CDS	1324213	1324849	1	-	1	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	exon	1324213	1324849	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	intron	1324850	1324938	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	CDS	1324939	1325214	1	-	1	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	exon	1324939	1325214	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	intron	1325215	1325434	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	CDS	1325435	1325492	1	-	2	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	exon	1325435	1325492	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	intron	1325493	1325645	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	CDS	1325646	1325863	0.65	-	1	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	exon	1325646	1325863	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	intron	1325864	1325953	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	CDS	1325954	1327010	0.65	-	2	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	exon	1325954	1327010	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	intron	1327011	1327114	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	CDS	1327115	1327523	0.59	-	0	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	exon	1327115	1327523	.	-	.	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
Phchi.S4	AUGUSTUS	start_codon	1327521	1327523	.	-	0	transcript_id "Phchi.S4G021000.t1"; gene_id "Phchi.S4G021000"
# This transcript jg9793.t2 is derived from g6969.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9794.t1 is derived from g6970.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43721641	43722976	.	-	.	Phchi.S1G695300
Phchi.S1	AUGUSTUS	transcript	43721802	43722976	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	stop_codon	43721799	43721801	.	-	0	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43721802	43721848	1	-	2	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43721802	43721848	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43721849	43721992	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43721993	43722136	1	-	2	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43721993	43722136	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722137	43722360	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722361	43722371	1	-	1	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722361	43722371	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722372	43722443	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722444	43722506	0.97	-	1	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722444	43722506	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722507	43722633	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722634	43722667	0.64	-	2	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722634	43722667	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722668	43722879	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722880	43722976	0.51	-	0	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722880	43722976	.	-	.	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	start_codon	43722974	43722976	.	-	0	transcript_id "Phchi.S1G695300.t1"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	transcript	43721641	43722976	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	stop_codon	43721638	43721640	.	-	0	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43721641	43721848	0.99	-	1	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43721641	43721848	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43721849	43721967	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43721968	43722136	0.99	-	2	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43721968	43722136	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722137	43722360	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722361	43722371	1	-	1	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722361	43722371	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722372	43722443	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722444	43722506	1	-	1	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722444	43722506	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722507	43722633	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722634	43722667	0.56	-	2	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722634	43722667	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	intron	43722668	43722879	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	CDS	43722880	43722976	0.45	-	0	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	exon	43722880	43722976	.	-	.	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
Phchi.S1	AUGUSTUS	start_codon	43722974	43722976	.	-	0	transcript_id "Phchi.S1G695300.t2"; gene_id "Phchi.S1G695300"
# This transcript jg8391.t2 is derived from g5566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8392.t1 is derived from g5567.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35678809	35681565	.	-	.	Phchi.S1G555100
Phchi.S1	AUGUSTUS	transcript	35678809	35681565	.	-	.	transcript_id "Phchi.S1G555100.t1"; gene_id "Phchi.S1G555100"
Phchi.S1	AUGUSTUS	stop_codon	35678806	35678808	.	-	0	transcript_id "Phchi.S1G555100.t1"; gene_id "Phchi.S1G555100"
Phchi.S1	AUGUSTUS	CDS	35678809	35681565	0.77	-	0	transcript_id "Phchi.S1G555100.t1"; gene_id "Phchi.S1G555100"
Phchi.S1	AUGUSTUS	exon	35678809	35681565	.	-	.	transcript_id "Phchi.S1G555100.t1"; gene_id "Phchi.S1G555100"
Phchi.S1	AUGUSTUS	start_codon	35681563	35681565	.	-	0	transcript_id "Phchi.S1G555100.t1"; gene_id "Phchi.S1G555100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12027.t1 is derived from g7702.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	634322	641746	.	+	.	Phchi.S2G010700
Phchi.S2	AUGUSTUS	transcript	634322	641746	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	start_codon	634322	634324	.	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	634322	635034	0.9	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	634322	635034	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	635035	635602	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	635603	635974	1	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	635603	635974	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	635975	636068	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	636069	636299	0.97	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	636069	636299	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	636300	636447	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	636448	636591	1	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	636448	636591	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	636592	636679	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	636680	637016	0.96	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	636680	637016	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	637017	637134	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	637135	637292	1	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	637135	637292	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	637293	637417	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	637418	637575	1	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	637418	637575	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	637576	637680	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	637681	637802	0.63	+	2	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	637681	637802	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	637803	638004	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	638005	638028	0.94	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	638005	638028	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	638029	638117	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	638118	638138	0.99	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	638118	638138	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	638139	638558	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	638559	638683	1	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	638559	638683	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	638684	638822	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	638823	638927	1	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	638823	638927	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	638928	639053	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	639054	639287	0.99	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	639054	639287	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	639288	639473	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	639474	639807	1	+	1	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	639474	639807	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	639808	639897	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	639898	640086	0.99	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	639898	640086	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	640087	640190	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	640191	640496	0.72	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	640191	640496	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	intron	640497	640618	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	CDS	640619	641746	0.95	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	exon	640619	641746	.	+	.	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
Phchi.S2	AUGUSTUS	stop_codon	641747	641749	.	+	0	transcript_id "Phchi.S2G010700.t1"; gene_id "Phchi.S2G010700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8680.t1 is derived from g5855.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37423295	37426578	.	+	.	Phchi.S1G583900
Phchi.S1	AUGUSTUS	transcript	37423295	37426578	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	start_codon	37423295	37423297	.	+	0	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37423295	37423462	0.49	+	0	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37423295	37423462	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37423463	37423556	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37423557	37423782	0.93	+	0	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37423557	37423782	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37423783	37423926	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37423927	37424175	0.84	+	2	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37423927	37424175	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37424176	37424300	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37424301	37424351	0.94	+	2	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37424301	37424351	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37424352	37424430	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37424431	37424737	0.91	+	2	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37424431	37424737	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37424738	37424816	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37424817	37424871	0.35	+	1	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37424817	37424871	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37424872	37424964	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37424965	37425079	0.43	+	0	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37424965	37425079	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37425080	37425180	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37425181	37425435	1	+	2	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37425181	37425435	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	intron	37425436	37425523	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	CDS	37425524	37426578	1	+	2	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	exon	37425524	37426578	.	+	.	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
Phchi.S1	AUGUSTUS	stop_codon	37426579	37426581	.	+	0	transcript_id "Phchi.S1G583900.t1"; gene_id "Phchi.S1G583900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1079.t1 is derived from g10862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7485303	7488292	.	-	.	Phchi.S6G103800
Phchi.S6	AUGUSTUS	transcript	7485303	7488292	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	stop_codon	7485300	7485302	.	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7485303	7485461	0.94	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7485303	7485461	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7485462	7485555	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7485556	7485606	1	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7485556	7485606	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7485607	7485702	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7485703	7485771	1	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7485703	7485771	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7485772	7485851	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7485852	7485921	1	-	1	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7485852	7485921	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7485922	7486021	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7486022	7486072	1	-	1	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7486022	7486072	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7486073	7486156	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7486157	7486368	1	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7486157	7486368	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7486369	7486468	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7486469	7486570	1	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7486469	7486570	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7486571	7486717	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7486718	7486858	1	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7486718	7486858	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7486859	7487051	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7487052	7487489	1	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7487052	7487489	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7487490	7487689	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7487690	7487854	0.48	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7487690	7487854	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7487855	7487945	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7487946	7488034	0.5	-	2	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7487946	7488034	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	intron	7488035	7488279	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	CDS	7488280	7488292	0.65	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	exon	7488280	7488292	.	-	.	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
Phchi.S6	AUGUSTUS	start_codon	7488290	7488292	.	-	0	transcript_id "Phchi.S6G103800.t1"; gene_id "Phchi.S6G103800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6850.t1 is derived from g4022.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25545985	25547406	.	-	.	Phchi.S1G400900
Phchi.S1	AUGUSTUS	transcript	25545985	25547406	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	stop_codon	25545982	25545984	.	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25545985	25546053	1	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25545985	25546053	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	intron	25546054	25546243	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25546244	25546354	1	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25546244	25546354	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	intron	25546355	25546454	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25546455	25546541	1	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25546455	25546541	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	intron	25546542	25546625	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25546626	25546699	1	-	2	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25546626	25546699	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	intron	25546700	25546782	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25546783	25546876	1	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25546783	25546876	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	intron	25546877	25547020	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25547021	25547066	1	-	1	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25547021	25547066	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	intron	25547067	25547287	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	CDS	25547288	25547406	1	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	exon	25547288	25547406	.	-	.	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
Phchi.S1	AUGUSTUS	start_codon	25547404	25547406	.	-	0	transcript_id "Phchi.S1G400900.t1"; gene_id "Phchi.S1G400900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6194.t1 is derived from g3365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21431010	21432680	.	-	.	Phchi.S1G335300
Phchi.S1	AUGUSTUS	transcript	21431010	21432680	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	stop_codon	21431007	21431009	.	-	0	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	CDS	21431010	21431929	0.96	-	2	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	exon	21431010	21431929	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	intron	21431930	21432027	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	CDS	21432028	21432124	1	-	0	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	exon	21432028	21432124	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	intron	21432125	21432254	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	CDS	21432255	21432366	0.87	-	1	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	exon	21432255	21432366	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	intron	21432367	21432603	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	CDS	21432604	21432680	0.81	-	0	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	exon	21432604	21432680	.	-	.	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
Phchi.S1	AUGUSTUS	start_codon	21432678	21432680	.	-	0	transcript_id "Phchi.S1G335300.t1"; gene_id "Phchi.S1G335300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg762.t1 is derived from g10544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5384721	5387343	.	-	.	Phchi.S6G072100
Phchi.S6	AUGUSTUS	transcript	5384721	5387343	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	stop_codon	5384718	5384720	.	-	0	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	CDS	5384721	5385205	1	-	2	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	exon	5384721	5385205	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	intron	5385206	5385298	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	CDS	5385299	5385652	0.63	-	2	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	exon	5385299	5385652	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	intron	5385653	5385771	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	CDS	5385772	5385887	0.99	-	1	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	exon	5385772	5385887	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	intron	5385888	5386093	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	CDS	5386094	5386263	0.94	-	0	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	exon	5386094	5386263	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	intron	5386264	5386384	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	CDS	5386385	5386759	0.63	-	0	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	exon	5386385	5386759	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	intron	5386760	5386896	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	CDS	5386897	5387343	0.94	-	0	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	exon	5386897	5387343	.	-	.	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
Phchi.S6	AUGUSTUS	start_codon	5387341	5387343	.	-	0	transcript_id "Phchi.S6G072100.t1"; gene_id "Phchi.S6G072100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6358.t1 is derived from g3530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22545337	22545897	.	-	.	Phchi.S1G351700
Phchi.S1	AUGUSTUS	transcript	22545337	22545897	.	-	.	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	stop_codon	22545334	22545336	.	-	0	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	CDS	22545337	22545363	0.58	-	0	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	exon	22545337	22545363	.	-	.	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	intron	22545364	22545442	.	-	.	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	CDS	22545443	22545712	0.58	-	0	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	exon	22545443	22545712	.	-	.	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	intron	22545713	22545795	.	-	.	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	CDS	22545796	22545897	0.95	-	0	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	exon	22545796	22545897	.	-	.	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
Phchi.S1	AUGUSTUS	start_codon	22545895	22545897	.	-	0	transcript_id "Phchi.S1G351700.t1"; gene_id "Phchi.S1G351700"
# This transcript jg11005.t2 is derived from g15055.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11006.t1 is derived from g15056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3607330	3610468	.	+	.	Phchi.S4G058800
Phchi.S4	AUGUSTUS	transcript	3607330	3610468	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	start_codon	3607330	3607332	.	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3607330	3607371	0.97	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3607330	3607371	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3607372	3607500	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3607501	3607638	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3607501	3607638	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3607639	3607722	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3607723	3607830	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3607723	3607830	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3607831	3607916	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3607917	3608009	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3607917	3608009	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3608010	3608087	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3608088	3608227	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3608088	3608227	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3608228	3608314	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3608315	3608390	0.99	+	1	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3608315	3608390	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3608391	3608501	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3608502	3608570	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3608502	3608570	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3608571	3608648	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3608649	3608729	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3608649	3608729	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3608730	3608856	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3608857	3608992	1	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3608857	3608992	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3608993	3609093	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3609094	3609169	1	+	2	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3609094	3609169	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3609170	3609310	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3609311	3609516	1	+	1	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3609311	3609516	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3609517	3609602	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3609603	3609853	1	+	2	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3609603	3609853	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	intron	3609854	3609940	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	CDS	3609941	3610468	0.95	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	exon	3609941	3610468	.	+	.	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
Phchi.S4	AUGUSTUS	stop_codon	3610469	3610471	.	+	0	transcript_id "Phchi.S4G058800.t1"; gene_id "Phchi.S4G058800"
# This transcript jg1410.t2 is derived from g8329.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1410.t3 is derived from g8329.t4 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg1410.t4 is derived from g8329.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg1411.t1 is derived from g8330.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	497591	500728	.	+	.	Phchi.S5G002000
Phchi.S5	AUGUSTUS	transcript	497591	500728	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	start_codon	497591	497593	.	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	497591	497996	0.97	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	497591	497996	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	497997	498524	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	498525	499063	0.37	+	2	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	498525	499063	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	499064	499160	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	499161	499214	0.42	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	499161	499214	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	499215	499306	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	499307	499442	0.86	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	499307	499442	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	499443	499584	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	499585	500076	0.98	+	2	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	499585	500076	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500077	500245	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500246	500374	1	+	2	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500246	500374	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500375	500501	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500502	500512	1	+	2	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500502	500512	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500513	500576	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500577	500582	1	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500577	500582	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500583	500719	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500720	500728	1	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500720	500728	.	+	.	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	stop_codon	500729	500731	.	+	0	transcript_id "Phchi.S5G002000.t1"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	transcript	497591	500728	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	start_codon	497591	497593	.	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	497591	497996	0.95	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	497591	497996	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	497997	498524	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	498525	499063	0.38	+	2	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	498525	499063	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	499064	499160	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	499161	499214	0.45	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	499161	499214	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	499215	499306	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	499307	499442	0.84	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	499307	499442	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	499443	499596	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	499597	500076	0.93	+	2	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	499597	500076	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500077	500245	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500246	500374	1	+	2	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500246	500374	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500375	500501	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500502	500512	1	+	2	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500502	500512	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500513	500576	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500577	500582	1	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500577	500582	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	intron	500583	500719	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	CDS	500720	500728	1	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	exon	500720	500728	.	+	.	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
Phchi.S5	AUGUSTUS	stop_codon	500729	500731	.	+	0	transcript_id "Phchi.S5G002000.t2"; gene_id "Phchi.S5G002000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg2432.t1 is derived from g9352.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6619943	6622605	.	+	.	Phchi.S5G104100
Phchi.S5	AUGUSTUS	transcript	6619943	6622605	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	start_codon	6619943	6619945	.	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6619943	6619969	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6619943	6619969	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6619970	6620091	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620092	6620173	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620092	6620173	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620174	6620265	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620266	6620355	0.98	+	2	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620266	6620355	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620356	6620471	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620472	6620597	1	+	2	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620472	6620597	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620598	6620737	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620738	6620865	1	+	2	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620738	6620865	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620866	6620988	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620989	6621188	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620989	6621188	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621189	6621379	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621380	6621443	1	+	1	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621380	6621443	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621444	6621532	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621533	6621643	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621533	6621643	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621644	6621741	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621742	6621879	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621742	6621879	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621880	6621979	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621980	6622122	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621980	6622122	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6622123	6622200	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6622201	6622255	1	+	1	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6622201	6622255	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6622256	6622386	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6622387	6622443	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6622387	6622443	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6622444	6622524	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6622525	6622605	1	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6622525	6622605	.	+	.	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	stop_codon	6622606	6622608	.	+	0	transcript_id "Phchi.S5G104100.t1"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	transcript	6619943	6622605	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	start_codon	6619943	6619945	.	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6619943	6619969	0.96	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6619943	6619969	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6619970	6620091	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620092	6620173	0.96	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620092	6620173	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620174	6620265	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620266	6620355	0.98	+	2	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620266	6620355	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620356	6620471	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620472	6620597	1	+	2	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620472	6620597	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620598	6620737	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620738	6620865	1	+	2	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620738	6620865	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6620866	6620988	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6620989	6621053	0.69	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6620989	6621053	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621054	6621142	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621143	6621188	0.69	+	1	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621143	6621188	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621189	6621386	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621387	6621443	0.91	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621387	6621443	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621444	6621532	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621533	6621643	1	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621533	6621643	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621644	6621741	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621742	6621879	1	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621742	6621879	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6621880	6621979	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6621980	6622122	1	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6621980	6622122	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6622123	6622200	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6622201	6622255	1	+	1	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6622201	6622255	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6622256	6622386	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6622387	6622443	1	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6622387	6622443	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	intron	6622444	6622524	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	CDS	6622525	6622605	1	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	exon	6622525	6622605	.	+	.	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
Phchi.S5	AUGUSTUS	stop_codon	6622606	6622608	.	+	0	transcript_id "Phchi.S5G104100.t2"; gene_id "Phchi.S5G104100"
# This transcript jg3869.t2 is derived from g1038.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3870.t1 is derived from g1039.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6140080	6147913	.	+	.	Phchi.S1G102900
Phchi.S1	AUGUSTUS	transcript	6140080	6147913	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	start_codon	6140080	6140082	.	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6140080	6140107	0.97	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6140080	6140107	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6140108	6140259	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6140260	6140814	0.65	+	2	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6140260	6140814	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6140815	6140921	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6140922	6141345	0.69	+	2	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6140922	6141345	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6141346	6141441	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6141442	6142675	1	+	1	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6141442	6142675	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6142676	6142813	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6142814	6143170	1	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6142814	6143170	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6143171	6143269	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6143270	6144575	1	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6143270	6144575	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6144576	6144750	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6144751	6145010	0.99	+	2	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6144751	6145010	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6145011	6145121	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6145122	6146300	0.93	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6145122	6146300	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	intron	6146301	6146437	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	CDS	6146438	6147913	0.97	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	exon	6146438	6147913	.	+	.	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
Phchi.S1	AUGUSTUS	stop_codon	6147914	6147916	.	+	0	transcript_id "Phchi.S1G102900.t1"; gene_id "Phchi.S1G102900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15577.t1 is derived from g14046.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20103078	20104375	.	+	.	Phchi.S3G289600
Phchi.S3	AUGUSTUS	transcript	20103078	20104375	.	+	.	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	start_codon	20103078	20103080	.	+	0	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	CDS	20103078	20103308	1	+	0	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	exon	20103078	20103308	.	+	.	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	intron	20103309	20103539	.	+	.	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	CDS	20103540	20103926	0.97	+	0	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	exon	20103540	20103926	.	+	.	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	intron	20103927	20104057	.	+	.	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	CDS	20104058	20104375	0.99	+	0	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	exon	20104058	20104375	.	+	.	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
Phchi.S3	AUGUSTUS	stop_codon	20104376	20104378	.	+	0	transcript_id "Phchi.S3G289600.t1"; gene_id "Phchi.S3G289600"
# This transcript jg7106.t2 is derived from g4278.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7107.t1 is derived from g4279.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27026209	27028027	.	+	.	Phchi.S1G426600
Phchi.S1	AUGUSTUS	transcript	27026209	27028027	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	start_codon	27026209	27026211	.	+	0	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	CDS	27026209	27026545	0.57	+	0	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	exon	27026209	27026545	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	intron	27026546	27026648	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	CDS	27026649	27027429	0.24	+	2	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	exon	27026649	27027429	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	intron	27027430	27027511	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	CDS	27027512	27027740	0.99	+	1	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	exon	27027512	27027740	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	intron	27027741	27027837	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	CDS	27027838	27027900	1	+	0	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	exon	27027838	27027900	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	intron	27027901	27027973	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	CDS	27027974	27028027	1	+	0	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	exon	27027974	27028027	.	+	.	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
Phchi.S1	AUGUSTUS	stop_codon	27028028	27028030	.	+	0	transcript_id "Phchi.S1G426600.t1"; gene_id "Phchi.S1G426600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8712.t1 is derived from g5887.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37593549	37596757	.	-	.	Phchi.S1G587100
Phchi.S1	AUGUSTUS	transcript	37593549	37596757	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	stop_codon	37593546	37593548	.	-	0	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37593549	37593712	0.96	-	2	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37593549	37593712	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37593713	37593825	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37593826	37594538	1	-	1	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37593826	37594538	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37594539	37594697	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37594698	37594902	0.46	-	2	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37594698	37594902	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37594903	37595079	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37595080	37595407	0.98	-	0	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37595080	37595407	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37595408	37595545	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37595546	37595783	1	-	1	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37595546	37595783	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37595784	37595913	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37595914	37596132	0.93	-	1	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37595914	37596132	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37596133	37596242	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37596243	37596339	1	-	2	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37596243	37596339	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	intron	37596340	37596570	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	CDS	37596571	37596757	0.99	-	0	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	exon	37596571	37596757	.	-	.	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
Phchi.S1	AUGUSTUS	start_codon	37596755	37596757	.	-	0	transcript_id "Phchi.S1G587100.t1"; gene_id "Phchi.S1G587100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14052.t1 is derived from g12519.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	10503065	10503457	.	+	.	Phchi.S3G137100
Phchi.S3	AUGUSTUS	transcript	10503065	10503457	.	+	.	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	start_codon	10503065	10503067	.	+	0	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	CDS	10503065	10503225	0.51	+	0	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	exon	10503065	10503225	.	+	.	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	intron	10503226	10503321	.	+	.	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	CDS	10503322	10503457	0.39	+	1	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	exon	10503322	10503457	.	+	.	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
Phchi.S3	AUGUSTUS	stop_codon	10503458	10503460	.	+	0	transcript_id "Phchi.S3G137100.t1"; gene_id "Phchi.S3G137100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14179.t1 is derived from g12646.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11308311	11309975	.	-	.	Phchi.S3G149800
Phchi.S3	AUGUSTUS	transcript	11308311	11309975	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	stop_codon	11308308	11308310	.	-	0	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	CDS	11308311	11308745	0.96	-	0	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	exon	11308311	11308745	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	intron	11308746	11308836	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	CDS	11308837	11309004	1	-	0	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	exon	11308837	11309004	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	intron	11309005	11309128	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	CDS	11309129	11309206	1	-	0	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	exon	11309129	11309206	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	intron	11309207	11309365	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	CDS	11309366	11309490	1	-	2	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	exon	11309366	11309490	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	intron	11309491	11309686	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	CDS	11309687	11309975	0.62	-	0	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	exon	11309687	11309975	.	-	.	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
Phchi.S3	AUGUSTUS	start_codon	11309973	11309975	.	-	0	transcript_id "Phchi.S3G149800.t1"; gene_id "Phchi.S3G149800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13677.t1 is derived from g12144.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8109788	8110770	.	+	.	Phchi.S3G099600
Phchi.S3	AUGUSTUS	transcript	8109788	8110770	.	+	.	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	start_codon	8109788	8109790	.	+	0	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	CDS	8109788	8109988	0.49	+	0	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	exon	8109788	8109988	.	+	.	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	intron	8109989	8110329	.	+	.	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	CDS	8110330	8110770	1	+	0	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	exon	8110330	8110770	.	+	.	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
Phchi.S3	AUGUSTUS	stop_codon	8110771	8110773	.	+	0	transcript_id "Phchi.S3G099600.t1"; gene_id "Phchi.S3G099600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7155.t1 is derived from g4327.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27316748	27318295	.	-	.	Phchi.S1G431400
Phchi.S1	AUGUSTUS	transcript	27316748	27318295	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	stop_codon	27316745	27316747	.	-	0	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27316748	27316888	0.88	-	0	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27316748	27316888	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27316889	27316981	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27316982	27317052	1	-	2	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27316982	27317052	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27317053	27317169	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27317170	27317237	1	-	1	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27317170	27317237	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27317238	27317315	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27317316	27317460	0.61	-	2	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27317316	27317460	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27317461	27318009	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27318010	27318295	0.59	-	0	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27318010	27318295	.	-	.	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	start_codon	27318293	27318295	.	-	0	transcript_id "Phchi.S1G431400.t1"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	transcript	27316748	27318089	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	stop_codon	27316745	27316747	.	-	0	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27316748	27316888	0.88	-	0	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27316748	27316888	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27316889	27316981	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27316982	27317052	1	-	2	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27316982	27317052	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27317053	27317169	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27317170	27317237	1	-	1	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27317170	27317237	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27317238	27317315	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27317316	27317450	0.84	-	1	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27317316	27317450	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	intron	27317451	27318009	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	CDS	27318010	27318089	0.22	-	0	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	exon	27318010	27318089	.	-	.	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
Phchi.S1	AUGUSTUS	start_codon	27318087	27318089	.	-	0	transcript_id "Phchi.S1G431400.t2"; gene_id "Phchi.S1G431400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4597.t1 is derived from g1767.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11275267	11277148	.	+	.	Phchi.S1G175600
Phchi.S1	AUGUSTUS	transcript	11275267	11277148	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	start_codon	11275267	11275269	.	+	0	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	CDS	11275267	11275474	0.5	+	0	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	exon	11275267	11275474	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	intron	11275475	11275640	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	CDS	11275641	11275740	0.63	+	2	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	exon	11275641	11275740	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	intron	11275741	11276005	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	CDS	11276006	11276162	0.46	+	1	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	exon	11276006	11276162	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	intron	11276163	11276296	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	CDS	11276297	11276388	0.39	+	0	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	exon	11276297	11276388	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	intron	11276389	11276538	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	CDS	11276539	11277148	0.57	+	1	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	exon	11276539	11277148	.	+	.	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
Phchi.S1	AUGUSTUS	stop_codon	11277149	11277151	.	+	0	transcript_id "Phchi.S1G175600.t1"; gene_id "Phchi.S1G175600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6291.t1 is derived from g3463.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22102972	22107834	.	+	.	Phchi.S1G345000
Phchi.S1	AUGUSTUS	transcript	22102972	22107834	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	start_codon	22102972	22102974	.	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22102972	22103059	0.81	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22102972	22103059	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22103060	22103444	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22103445	22103649	1	+	2	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22103445	22103649	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22103650	22103797	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22103798	22103908	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22103798	22103908	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22103909	22104044	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22104045	22104093	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22104045	22104093	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22104094	22104190	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22104191	22104300	1	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22104191	22104300	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22104301	22104512	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22104513	22105016	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22104513	22105016	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22105017	22105262	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22105263	22105382	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22105263	22105382	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22105383	22105577	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22105578	22105874	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22105578	22105874	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22105875	22106033	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22106034	22106090	0.75	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22106034	22106090	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22106091	22106161	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22106162	22106491	0.86	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22106162	22106491	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22106492	22106588	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22106589	22106654	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22106589	22106654	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22106655	22106741	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22106742	22106802	1	+	1	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22106742	22106802	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22106803	22106922	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22106923	22107072	1	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22106923	22107072	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22107073	22107201	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22107202	22107339	1	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22107202	22107339	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22107340	22107482	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22107483	22107659	0.93	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22107483	22107659	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	intron	22107660	22107732	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	CDS	22107733	22107834	0.67	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	exon	22107733	22107834	.	+	.	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
Phchi.S1	AUGUSTUS	stop_codon	22107835	22107837	.	+	0	transcript_id "Phchi.S1G345000.t1"; gene_id "Phchi.S1G345000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4626.t1 is derived from g1796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	11452594	11457114	.	+	.	Phchi.S1G178500
Phchi.S1	AUGUSTUS	transcript	11452594	11457114	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	start_codon	11452594	11452596	.	+	0	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11452594	11452759	0.98	+	0	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11452594	11452759	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11452760	11453158	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11453159	11453261	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11453159	11453261	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11453262	11453588	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11453589	11453670	1	+	1	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11453589	11453670	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11453671	11453760	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11453761	11453909	1	+	0	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11453761	11453909	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11453910	11454030	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11454031	11454137	0.98	+	1	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11454031	11454137	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11454138	11454258	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11454259	11454324	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11454259	11454324	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11454325	11454420	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11454421	11454577	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11454421	11454577	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11454578	11454700	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11454701	11454852	1	+	1	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11454701	11454852	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11454853	11454945	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11454946	11455128	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11454946	11455128	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11455129	11455225	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11455226	11455549	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11455226	11455549	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11455550	11455643	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11455644	11455715	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11455644	11455715	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11455716	11455813	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11455814	11455866	1	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11455814	11455866	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11455867	11456100	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11456101	11456215	0.99	+	0	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11456101	11456215	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11456216	11456322	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11456323	11456497	0.96	+	2	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11456323	11456497	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11456498	11456592	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11456593	11456715	1	+	1	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11456593	11456715	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11456716	11456798	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11456799	11456853	1	+	1	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11456799	11456853	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	intron	11456854	11456946	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	CDS	11456947	11457114	0.93	+	0	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	exon	11456947	11457114	.	+	.	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
Phchi.S1	AUGUSTUS	stop_codon	11457115	11457117	.	+	0	transcript_id "Phchi.S1G178500.t1"; gene_id "Phchi.S1G178500"
# This transcript jg11415.t2 is derived from g15465.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11416.t1 is derived from g15466.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6252776	6254285	.	+	.	Phchi.S4G099800
Phchi.S4	AUGUSTUS	transcript	6252776	6254285	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	start_codon	6252776	6252778	.	+	0	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	CDS	6252776	6252890	0.98	+	0	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	exon	6252776	6252890	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	intron	6252891	6252970	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	CDS	6252971	6253227	0.8	+	2	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	exon	6252971	6253227	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	intron	6253228	6253310	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	CDS	6253311	6253920	0.63	+	0	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	exon	6253311	6253920	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	intron	6253921	6254013	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	CDS	6254014	6254285	0.9	+	2	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	exon	6254014	6254285	.	+	.	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
Phchi.S4	AUGUSTUS	stop_codon	6254286	6254288	.	+	0	transcript_id "Phchi.S4G099800.t1"; gene_id "Phchi.S4G099800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8619.t1 is derived from g5794.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37022095	37022493	.	+	.	Phchi.S1G577800
Phchi.S1	AUGUSTUS	transcript	37022095	37022493	.	+	.	transcript_id "Phchi.S1G577800.t1"; gene_id "Phchi.S1G577800"
Phchi.S1	AUGUSTUS	start_codon	37022095	37022097	.	+	0	transcript_id "Phchi.S1G577800.t1"; gene_id "Phchi.S1G577800"
Phchi.S1	AUGUSTUS	CDS	37022095	37022493	1	+	0	transcript_id "Phchi.S1G577800.t1"; gene_id "Phchi.S1G577800"
Phchi.S1	AUGUSTUS	exon	37022095	37022493	.	+	.	transcript_id "Phchi.S1G577800.t1"; gene_id "Phchi.S1G577800"
Phchi.S1	AUGUSTUS	stop_codon	37022494	37022496	.	+	0	transcript_id "Phchi.S1G577800.t1"; gene_id "Phchi.S1G577800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8056.t1 is derived from g5231.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32733305	32733760	.	-	.	Phchi.S1G521500
Phchi.S1	AUGUSTUS	transcript	32733305	32733760	.	-	.	transcript_id "Phchi.S1G521500.t1"; gene_id "Phchi.S1G521500"
Phchi.S1	AUGUSTUS	stop_codon	32733302	32733304	.	-	0	transcript_id "Phchi.S1G521500.t1"; gene_id "Phchi.S1G521500"
Phchi.S1	AUGUSTUS	CDS	32733305	32733760	0.68	-	0	transcript_id "Phchi.S1G521500.t1"; gene_id "Phchi.S1G521500"
Phchi.S1	AUGUSTUS	exon	32733305	32733760	.	-	.	transcript_id "Phchi.S1G521500.t1"; gene_id "Phchi.S1G521500"
Phchi.S1	AUGUSTUS	start_codon	32733758	32733760	.	-	0	transcript_id "Phchi.S1G521500.t1"; gene_id "Phchi.S1G521500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8005.t1 is derived from g5180.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32414925	32416494	.	-	.	Phchi.S1G516400
Phchi.S1	AUGUSTUS	transcript	32414925	32416494	.	-	.	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	stop_codon	32414922	32414924	.	-	0	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	CDS	32414925	32414988	0.78	-	1	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	exon	32414925	32414988	.	-	.	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	intron	32414989	32415280	.	-	.	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	CDS	32415281	32415815	0.72	-	2	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	exon	32415281	32415815	.	-	.	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	intron	32415816	32415902	.	-	.	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	CDS	32415903	32416494	0.68	-	0	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	exon	32415903	32416494	.	-	.	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
Phchi.S1	AUGUSTUS	start_codon	32416492	32416494	.	-	0	transcript_id "Phchi.S1G516400.t1"; gene_id "Phchi.S1G516400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5309.t1 is derived from g2479.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16220331	16221660	.	-	.	Phchi.S1G246800
Phchi.S1	AUGUSTUS	transcript	16220331	16221660	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	stop_codon	16220328	16220330	.	-	0	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	CDS	16220331	16220389	1	-	2	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	exon	16220331	16220389	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	intron	16220390	16220469	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	CDS	16220470	16220535	1	-	2	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	exon	16220470	16220535	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	intron	16220536	16220696	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	CDS	16220697	16220894	1	-	2	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	exon	16220697	16220894	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	intron	16220895	16220986	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	CDS	16220987	16221382	0.8	-	2	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	exon	16220987	16221382	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	intron	16221383	16221482	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	CDS	16221483	16221660	0.39	-	0	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	exon	16221483	16221660	.	-	.	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
Phchi.S1	AUGUSTUS	start_codon	16221658	16221660	.	-	0	transcript_id "Phchi.S1G246800.t1"; gene_id "Phchi.S1G246800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12361.t1 is derived from g8037.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	12732059	12735836	.	-	.	Phchi.S2G044100
Phchi.S2	AUGUSTUS	transcript	12732059	12735836	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	stop_codon	12732056	12732058	.	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12732059	12732190	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12732059	12732190	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12732191	12732389	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12732390	12732770	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12732390	12732770	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12732771	12733446	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12733447	12733552	1	-	1	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12733447	12733552	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12733553	12733717	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12733718	12733782	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12733718	12733782	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12733783	12733884	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12733885	12733992	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12733885	12733992	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12733993	12734477	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12734478	12734570	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12734478	12734570	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12734571	12734787	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12734788	12734835	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12734788	12734835	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12734836	12735064	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12735065	12735163	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12735065	12735163	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12735164	12735250	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12735251	12735367	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12735251	12735367	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12735368	12735618	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12735619	12735672	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12735619	12735672	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	intron	12735673	12735803	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	CDS	12735804	12735836	1	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	exon	12735804	12735836	.	-	.	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
Phchi.S2	AUGUSTUS	start_codon	12735834	12735836	.	-	0	transcript_id "Phchi.S2G044100.t1"; gene_id "Phchi.S2G044100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2815.t1 is derived from g9735.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8993445	8995800	.	+	.	Phchi.S5G142400
Phchi.S5	AUGUSTUS	transcript	8993445	8995800	.	+	.	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	start_codon	8993445	8993447	.	+	0	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	CDS	8993445	8994184	0.23	+	0	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	exon	8993445	8994184	.	+	.	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	intron	8994185	8994449	.	+	.	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	CDS	8994450	8995800	0.64	+	1	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	exon	8994450	8995800	.	+	.	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
Phchi.S5	AUGUSTUS	stop_codon	8995801	8995803	.	+	0	transcript_id "Phchi.S5G142400.t1"; gene_id "Phchi.S5G142400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8711.t1 is derived from g5886.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37590731	37592705	.	+	.	Phchi.S1G587000
Phchi.S1	AUGUSTUS	transcript	37590731	37592705	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	start_codon	37590731	37590733	.	+	0	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	CDS	37590731	37590935	0.89	+	0	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	exon	37590731	37590935	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	intron	37590936	37591065	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	CDS	37591066	37591281	1	+	2	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	exon	37591066	37591281	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	intron	37591282	37591365	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	CDS	37591366	37591471	1	+	2	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	exon	37591366	37591471	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	intron	37591472	37591564	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	CDS	37591565	37591982	0.91	+	1	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	exon	37591565	37591982	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	intron	37591983	37592197	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	CDS	37592198	37592482	1	+	0	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	exon	37592198	37592482	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	intron	37592483	37592600	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	CDS	37592601	37592705	1	+	0	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	exon	37592601	37592705	.	+	.	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
Phchi.S1	AUGUSTUS	stop_codon	37592706	37592708	.	+	0	transcript_id "Phchi.S1G587000.t1"; gene_id "Phchi.S1G587000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg518.t1 is derived from g10300.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3730278	3731141	.	+	.	Phchi.S6G047700
Phchi.S6	AUGUSTUS	transcript	3730278	3731141	.	+	.	transcript_id "Phchi.S6G047700.t1"; gene_id "Phchi.S6G047700"
Phchi.S6	AUGUSTUS	start_codon	3730278	3730280	.	+	0	transcript_id "Phchi.S6G047700.t1"; gene_id "Phchi.S6G047700"
Phchi.S6	AUGUSTUS	CDS	3730278	3731141	0.95	+	0	transcript_id "Phchi.S6G047700.t1"; gene_id "Phchi.S6G047700"
Phchi.S6	AUGUSTUS	exon	3730278	3731141	.	+	.	transcript_id "Phchi.S6G047700.t1"; gene_id "Phchi.S6G047700"
Phchi.S6	AUGUSTUS	stop_codon	3731142	3731144	.	+	0	transcript_id "Phchi.S6G047700.t1"; gene_id "Phchi.S6G047700"
# This transcript jg134.t2 is derived from g9916.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg135.t1 is derived from g9917.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	758112	759567	.	+	.	Phchi.S6G009400
Phchi.S6	AUGUSTUS	transcript	758112	759567	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	start_codon	758112	758114	.	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	CDS	758112	758492	0.42	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	exon	758112	758492	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	intron	758493	758596	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	CDS	758597	758695	0.96	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	exon	758597	758695	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	intron	758696	758771	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	CDS	758772	758816	1	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	exon	758772	758816	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	intron	758817	759099	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	CDS	759100	759237	0.93	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	exon	759100	759237	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	intron	759238	759354	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	CDS	759355	759567	0.93	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	exon	759355	759567	.	+	.	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
Phchi.S6	AUGUSTUS	stop_codon	759568	759570	.	+	0	transcript_id "Phchi.S6G009400.t1"; gene_id "Phchi.S6G009400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3105.t1 is derived from g274.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1763031	1764192	.	-	.	Phchi.S1G026400
Phchi.S1	AUGUSTUS	transcript	1763031	1764192	.	-	.	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	stop_codon	1763028	1763030	.	-	0	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	CDS	1763031	1763693	1	-	0	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	exon	1763031	1763693	.	-	.	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	intron	1763694	1763943	.	-	.	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	CDS	1763944	1764192	0.42	-	0	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	exon	1763944	1764192	.	-	.	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
Phchi.S1	AUGUSTUS	start_codon	1764190	1764192	.	-	0	transcript_id "Phchi.S1G026400.t1"; gene_id "Phchi.S1G026400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5430.t1 is derived from g2600.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16836287	16839082	.	-	.	Phchi.S1G258900
Phchi.S1	AUGUSTUS	transcript	16836287	16839082	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	stop_codon	16836284	16836286	.	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16836287	16836382	0.79	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16836287	16836382	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16836383	16836522	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16836523	16836579	0.8	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16836523	16836579	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16836580	16836711	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16836712	16836820	1	-	1	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16836712	16836820	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16836821	16836958	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16836959	16837052	0.96	-	2	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16836959	16837052	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16837053	16837154	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16837155	16837218	1	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16837155	16837218	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16837219	16837314	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16837315	16837427	0.98	-	2	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16837315	16837427	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16837428	16837537	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16837538	16837664	0.95	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16837538	16837664	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16837665	16837751	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16837752	16837901	1	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16837752	16837901	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16837902	16838035	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16838036	16838132	1	-	1	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16838036	16838132	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16838133	16838280	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16838281	16838531	0.97	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16838281	16838531	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	intron	16838532	16838899	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	CDS	16838900	16839082	0.99	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	exon	16838900	16839082	.	-	.	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
Phchi.S1	AUGUSTUS	start_codon	16839080	16839082	.	-	0	transcript_id "Phchi.S1G258900.t1"; gene_id "Phchi.S1G258900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5602.t1 is derived from g2772.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17835231	17836901	.	-	.	Phchi.S1G276100
Phchi.S1	AUGUSTUS	transcript	17835231	17836901	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	stop_codon	17835228	17835230	.	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17835231	17835309	1	-	1	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17835231	17835309	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17835310	17835399	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17835400	17835494	1	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17835400	17835494	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17835495	17835579	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17835580	17835669	1	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17835580	17835669	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17835670	17835764	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17835765	17835800	1	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17835765	17835800	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17835801	17835904	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17835905	17835988	1	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17835905	17835988	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17835989	17836081	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17836082	17836171	0.88	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17836082	17836171	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17836172	17836288	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17836289	17836302	0.32	-	2	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17836289	17836302	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17836303	17836460	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17836461	17836605	0.44	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17836461	17836605	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	intron	17836606	17836709	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	CDS	17836710	17836901	0.85	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	exon	17836710	17836901	.	-	.	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
Phchi.S1	AUGUSTUS	start_codon	17836899	17836901	.	-	0	transcript_id "Phchi.S1G276100.t1"; gene_id "Phchi.S1G276100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11759.t1 is derived from g15811.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8034601	8038783	.	+	.	Phchi.S4G134100
Phchi.S4	AUGUSTUS	transcript	8034601	8038783	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	start_codon	8034601	8034603	.	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8034601	8035541	0.8	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8034601	8035541	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8035542	8036227	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8036228	8036393	1	+	1	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8036228	8036393	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8036394	8036536	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8036537	8036660	1	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8036537	8036660	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8036661	8036875	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8036876	8036988	1	+	2	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8036876	8036988	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8036989	8037176	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8037177	8037545	0.99	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8037177	8037545	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8037546	8037792	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8037793	8037912	0.96	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8037793	8037912	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8037913	8038007	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8038008	8038055	0.96	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8038008	8038055	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8038056	8038233	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8038234	8038323	1	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8038234	8038323	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	intron	8038324	8038408	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	CDS	8038409	8038783	0.98	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	exon	8038409	8038783	.	+	.	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
Phchi.S4	AUGUSTUS	stop_codon	8038784	8038786	.	+	0	transcript_id "Phchi.S4G134100.t1"; gene_id "Phchi.S4G134100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8503.t1 is derived from g5678.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36357798	36359276	.	-	.	Phchi.S1G566200
Phchi.S1	AUGUSTUS	transcript	36357798	36359276	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	stop_codon	36357795	36357797	.	-	0	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	CDS	36357798	36357858	0.98	-	1	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	exon	36357798	36357858	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	intron	36357859	36358041	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	CDS	36358042	36358161	0.99	-	1	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	exon	36358042	36358161	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	intron	36358162	36358364	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	CDS	36358365	36358393	0.99	-	0	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	exon	36358365	36358393	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	intron	36358394	36358646	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	CDS	36358647	36358706	1	-	0	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	exon	36358647	36358706	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	intron	36358707	36358928	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	CDS	36358929	36359032	0.9	-	2	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	exon	36358929	36359032	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	intron	36359033	36359203	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	CDS	36359204	36359276	0.84	-	0	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	exon	36359204	36359276	.	-	.	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
Phchi.S1	AUGUSTUS	start_codon	36359274	36359276	.	-	0	transcript_id "Phchi.S1G566200.t1"; gene_id "Phchi.S1G566200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4215.t1 is derived from g1384.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	8959521	8960797	.	-	.	Phchi.S1G137400
Phchi.S1	AUGUSTUS	transcript	8959521	8960797	.	-	.	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	stop_codon	8959518	8959520	.	-	0	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	CDS	8959521	8959984	0.94	-	2	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	exon	8959521	8959984	.	-	.	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	intron	8959985	8960073	.	-	.	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	CDS	8960074	8960797	0.49	-	0	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	exon	8960074	8960797	.	-	.	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
Phchi.S1	AUGUSTUS	start_codon	8960795	8960797	.	-	0	transcript_id "Phchi.S1G137400.t1"; gene_id "Phchi.S1G137400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8961.t1 is derived from g6136.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38858645	38861929	.	+	.	Phchi.S1G612000
Phchi.S1	AUGUSTUS	transcript	38858645	38861929	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	start_codon	38858645	38858647	.	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38858645	38858694	0.49	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38858645	38858694	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38858695	38858773	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38858774	38858891	1	+	1	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38858774	38858891	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38858892	38859094	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38859095	38859304	1	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38859095	38859304	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38859305	38859519	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38859520	38859619	0.75	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38859520	38859619	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38859620	38859695	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38859696	38859771	0.7	+	2	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38859696	38859771	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38859772	38859868	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38859869	38860139	1	+	1	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38859869	38860139	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38860140	38860226	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38860227	38860310	1	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38860227	38860310	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38860311	38860439	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38860440	38860571	1	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38860440	38860571	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	intron	38860572	38860714	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	CDS	38860715	38861929	0.53	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	exon	38860715	38861929	.	+	.	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
Phchi.S1	AUGUSTUS	stop_codon	38861930	38861932	.	+	0	transcript_id "Phchi.S1G612000.t1"; gene_id "Phchi.S1G612000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3142.t1 is derived from g311.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1963014	1965646	.	+	.	Phchi.S1G030100
Phchi.S1	AUGUSTUS	transcript	1963014	1965646	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	start_codon	1963014	1963016	.	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963014	1963138	0.43	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963014	1963138	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963139	1963217	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963218	1963410	1	+	1	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963218	1963410	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963411	1963534	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963535	1963648	1	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963535	1963648	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963649	1963830	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963831	1963933	1	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963831	1963933	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963934	1964107	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964108	1964309	0.76	+	2	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964108	1964309	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964310	1964421	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964422	1964518	1	+	1	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964422	1964518	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964519	1964612	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964613	1964679	0.62	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964613	1964679	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964680	1964771	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964772	1964914	1	+	2	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964772	1964914	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964915	1964992	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964993	1965082	1	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964993	1965082	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965083	1965161	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965162	1965209	1	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965162	1965209	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965210	1965286	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965287	1965325	1	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965287	1965325	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965326	1965396	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965397	1965437	1	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965397	1965437	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965438	1965522	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965523	1965646	1	+	1	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965523	1965646	.	+	.	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	stop_codon	1965647	1965649	.	+	0	transcript_id "Phchi.S1G030100.t1"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	transcript	1963014	1965646	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	start_codon	1963014	1963016	.	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963014	1963138	0.4	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963014	1963138	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963139	1963217	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963218	1963410	1	+	1	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963218	1963410	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963411	1963534	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963535	1963648	1	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963535	1963648	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963649	1963830	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1963831	1963933	0.91	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1963831	1963933	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1963934	1964115	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964116	1964203	0.35	+	2	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964116	1964203	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964204	1964421	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964422	1964518	0.68	+	1	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964422	1964518	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964519	1964612	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964613	1964679	0.65	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964613	1964679	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964680	1964771	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964772	1964914	1	+	2	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964772	1964914	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1964915	1964992	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1964993	1965082	1	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1964993	1965082	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965083	1965161	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965162	1965209	1	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965162	1965209	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965210	1965286	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965287	1965325	0.99	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965287	1965325	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965326	1965396	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965397	1965437	0.99	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965397	1965437	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	intron	1965438	1965522	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	CDS	1965523	1965646	0.99	+	1	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	exon	1965523	1965646	.	+	.	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
Phchi.S1	AUGUSTUS	stop_codon	1965647	1965649	.	+	0	transcript_id "Phchi.S1G030100.t2"; gene_id "Phchi.S1G030100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11093.t1 is derived from g15143.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4085832	4087641	.	+	.	Phchi.S4G067500
Phchi.S4	AUGUSTUS	transcript	4085832	4087641	.	+	.	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	start_codon	4085832	4085834	.	+	0	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	CDS	4085832	4086294	0.61	+	0	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	exon	4085832	4086294	.	+	.	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	intron	4086295	4086391	.	+	.	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	CDS	4086392	4087641	1	+	2	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	exon	4086392	4087641	.	+	.	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
Phchi.S4	AUGUSTUS	stop_codon	4087642	4087644	.	+	0	transcript_id "Phchi.S4G067500.t1"; gene_id "Phchi.S4G067500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3451.t1 is derived from g620.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3817149	3817817	.	+	.	Phchi.S1G061000
Phchi.S1	AUGUSTUS	transcript	3817149	3817817	.	+	.	transcript_id "Phchi.S1G061000.t1"; gene_id "Phchi.S1G061000"
Phchi.S1	AUGUSTUS	start_codon	3817149	3817151	.	+	0	transcript_id "Phchi.S1G061000.t1"; gene_id "Phchi.S1G061000"
Phchi.S1	AUGUSTUS	CDS	3817149	3817817	0.62	+	0	transcript_id "Phchi.S1G061000.t1"; gene_id "Phchi.S1G061000"
Phchi.S1	AUGUSTUS	exon	3817149	3817817	.	+	.	transcript_id "Phchi.S1G061000.t1"; gene_id "Phchi.S1G061000"
Phchi.S1	AUGUSTUS	stop_codon	3817818	3817820	.	+	0	transcript_id "Phchi.S1G061000.t1"; gene_id "Phchi.S1G061000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8146.t1 is derived from g5321.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34067601	34068494	.	-	.	Phchi.S1G530500
Phchi.S1	AUGUSTUS	transcript	34067601	34068494	.	-	.	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	stop_codon	34067598	34067600	.	-	0	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	CDS	34067601	34067888	0.68	-	0	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	exon	34067601	34067888	.	-	.	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	intron	34067889	34068029	.	-	.	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	CDS	34068030	34068494	0.52	-	0	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	exon	34068030	34068494	.	-	.	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
Phchi.S1	AUGUSTUS	start_codon	34068492	34068494	.	-	0	transcript_id "Phchi.S1G530500.t1"; gene_id "Phchi.S1G530500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9028.t1 is derived from g6203.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39212323	39216157	.	+	.	Phchi.S1G618700
Phchi.S1	AUGUSTUS	transcript	39215389	39216157	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	start_codon	39215389	39215391	.	+	0	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215389	39215450	0.89	+	0	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215389	39215450	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215451	39215542	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215543	39215628	1	+	1	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215543	39215628	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215629	39215718	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215719	39215831	0.96	+	2	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215719	39215831	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215832	39215935	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215936	39215968	0.9	+	0	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215936	39215968	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215969	39216061	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39216062	39216157	0.93	+	0	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39216062	39216157	.	+	.	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	stop_codon	39216158	39216160	.	+	0	transcript_id "Phchi.S1G618700.t1"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	transcript	39212323	39216157	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	start_codon	39212323	39212325	.	+	0	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39212323	39212759	0.53	+	0	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39212323	39212759	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39212760	39212851	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39212852	39212857	0.67	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39212852	39212857	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39212858	39213025	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39213026	39213073	0.67	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39213026	39213073	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39213074	39213227	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39213228	39213775	0.38	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39213228	39213775	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39213776	39213921	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39213922	39214177	0.22	+	2	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39213922	39214177	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39214178	39214281	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39214282	39214344	0.35	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39214282	39214344	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39214345	39214427	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39214428	39214540	1	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39214428	39214540	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39214541	39214636	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39214637	39215039	1	+	2	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39214637	39215039	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215040	39215130	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215131	39215247	1	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215131	39215247	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215248	39215337	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215338	39215439	0.98	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215338	39215439	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215440	39215542	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215543	39215628	0.98	+	1	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215543	39215628	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215629	39215718	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215719	39215831	0.99	+	2	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215719	39215831	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215832	39215935	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215936	39215968	0.98	+	0	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215936	39215968	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215969	39216061	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39216062	39216157	0.98	+	0	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39216062	39216157	.	+	.	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	stop_codon	39216158	39216160	.	+	0	transcript_id "Phchi.S1G618700.t2"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	transcript	39212323	39215351	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	start_codon	39212323	39212325	.	+	0	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39212323	39212759	0.32	+	0	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39212323	39212759	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39212760	39212851	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39212852	39212857	0.74	+	1	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39212852	39212857	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39212858	39213025	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39213026	39213073	0.73	+	1	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39213026	39213073	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39213074	39213227	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39213228	39213775	0.42	+	1	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39213228	39213775	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39213776	39213921	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39213922	39214177	0.24	+	2	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39213922	39214177	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39214178	39214281	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39214282	39214344	0.3	+	1	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39214282	39214344	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39214345	39214427	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39214428	39214540	1	+	1	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39214428	39214540	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39214541	39214636	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39214637	39215039	1	+	2	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39214637	39215039	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215040	39215130	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215131	39215255	0.89	+	1	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215131	39215255	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	intron	39215256	39215337	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	CDS	39215338	39215351	0.89	+	2	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	exon	39215338	39215351	.	+	.	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
Phchi.S1	AUGUSTUS	stop_codon	39215352	39215354	.	+	0	transcript_id "Phchi.S1G618700.t3"; gene_id "Phchi.S1G618700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3137.t1 is derived from g306.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	1934167	1935144	.	+	.	Phchi.S1G029600
Phchi.S1	AUGUSTUS	transcript	1934167	1935144	.	+	.	transcript_id "Phchi.S1G029600.t1"; gene_id "Phchi.S1G029600"
Phchi.S1	AUGUSTUS	start_codon	1934167	1934169	.	+	0	transcript_id "Phchi.S1G029600.t1"; gene_id "Phchi.S1G029600"
Phchi.S1	AUGUSTUS	CDS	1934167	1935144	0.71	+	0	transcript_id "Phchi.S1G029600.t1"; gene_id "Phchi.S1G029600"
Phchi.S1	AUGUSTUS	exon	1934167	1935144	.	+	.	transcript_id "Phchi.S1G029600.t1"; gene_id "Phchi.S1G029600"
Phchi.S1	AUGUSTUS	stop_codon	1935145	1935147	.	+	0	transcript_id "Phchi.S1G029600.t1"; gene_id "Phchi.S1G029600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9205.t1 is derived from g6380.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40381640	40383930	.	+	.	Phchi.S1G636400
Phchi.S1	AUGUSTUS	transcript	40381640	40383930	.	+	.	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	start_codon	40381640	40381642	.	+	0	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	CDS	40381640	40383474	0.85	+	0	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	exon	40381640	40383474	.	+	.	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	intron	40383475	40383578	.	+	.	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	CDS	40383579	40383930	1	+	1	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	exon	40383579	40383930	.	+	.	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
Phchi.S1	AUGUSTUS	stop_codon	40383931	40383933	.	+	0	transcript_id "Phchi.S1G636400.t1"; gene_id "Phchi.S1G636400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12137.t1 is derived from g7813.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4635802	4636871	.	+	.	Phchi.S2G021700
Phchi.S2	AUGUSTUS	transcript	4635802	4636871	.	+	.	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	start_codon	4635802	4635804	.	+	0	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	CDS	4635802	4635895	0.77	+	0	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	exon	4635802	4635895	.	+	.	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	intron	4635896	4636278	.	+	.	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	CDS	4636279	4636871	0.82	+	2	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	exon	4636279	4636871	.	+	.	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
Phchi.S2	AUGUSTUS	stop_codon	4636872	4636874	.	+	0	transcript_id "Phchi.S2G021700.t1"; gene_id "Phchi.S2G021700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1620.t1 is derived from g8539.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2052607	2054386	.	-	.	Phchi.S5G022900
Phchi.S5	AUGUSTUS	transcript	2052607	2054386	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	stop_codon	2052604	2052606	.	-	0	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	CDS	2052607	2052718	0.98	-	1	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	exon	2052607	2052718	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	intron	2052719	2052832	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	CDS	2052833	2052900	1	-	0	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	exon	2052833	2052900	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	intron	2052901	2052996	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	CDS	2052997	2053094	1	-	2	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	exon	2052997	2053094	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	intron	2053095	2053178	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	CDS	2053179	2053356	1	-	0	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	exon	2053179	2053356	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	intron	2053357	2053472	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	CDS	2053473	2053571	1	-	0	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	exon	2053473	2053571	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	intron	2053572	2053762	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	CDS	2053763	2054386	0.54	-	0	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	exon	2053763	2054386	.	-	.	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
Phchi.S5	AUGUSTUS	start_codon	2054384	2054386	.	-	0	transcript_id "Phchi.S5G022900.t1"; gene_id "Phchi.S5G022900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg447.t1 is derived from g10229.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3128603	3131107	.	-	.	Phchi.S6G040600
Phchi.S6	AUGUSTUS	transcript	3128603	3131107	.	-	.	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	stop_codon	3128600	3128602	.	-	0	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	CDS	3128603	3129980	0.97	-	1	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	exon	3128603	3129980	.	-	.	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	intron	3129981	3130190	.	-	.	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	CDS	3130191	3131107	0.66	-	0	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	exon	3130191	3131107	.	-	.	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
Phchi.S6	AUGUSTUS	start_codon	3131105	3131107	.	-	0	transcript_id "Phchi.S6G040600.t1"; gene_id "Phchi.S6G040600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4465.t1 is derived from g1635.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10634471	10634973	.	+	.	Phchi.S1G162400
Phchi.S1	AUGUSTUS	transcript	10634471	10634973	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	start_codon	10634471	10634473	.	+	0	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	CDS	10634471	10634501	0.79	+	0	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	exon	10634471	10634501	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	intron	10634502	10634625	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	CDS	10634626	10634771	0.61	+	2	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	exon	10634626	10634771	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	intron	10634772	10634841	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	CDS	10634842	10634865	0.49	+	0	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	exon	10634842	10634865	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	intron	10634866	10634955	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	CDS	10634956	10634973	0.49	+	0	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	exon	10634956	10634973	.	+	.	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
Phchi.S1	AUGUSTUS	stop_codon	10634974	10634976	.	+	0	transcript_id "Phchi.S1G162400.t1"; gene_id "Phchi.S1G162400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4766.t1 is derived from g1936.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12730101	12730911	.	-	.	Phchi.S1G192500
Phchi.S1	AUGUSTUS	transcript	12730101	12730911	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	stop_codon	12730098	12730100	.	-	0	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	CDS	12730101	12730198	0.62	-	2	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	exon	12730101	12730198	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	intron	12730199	12730296	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	CDS	12730297	12730342	1	-	0	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	exon	12730297	12730342	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	intron	12730343	12730423	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	CDS	12730424	12730523	1	-	1	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	exon	12730424	12730523	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	intron	12730524	12730605	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	CDS	12730606	12730709	0.8	-	0	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	exon	12730606	12730709	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	intron	12730710	12730800	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	CDS	12730801	12730911	1	-	0	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	exon	12730801	12730911	.	-	.	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
Phchi.S1	AUGUSTUS	start_codon	12730909	12730911	.	-	0	transcript_id "Phchi.S1G192500.t1"; gene_id "Phchi.S1G192500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5279.t1 is derived from g2449.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16009203	16009544	.	+	.	Phchi.S1G243800
Phchi.S1	AUGUSTUS	transcript	16009203	16009544	.	+	.	transcript_id "Phchi.S1G243800.t1"; gene_id "Phchi.S1G243800"
Phchi.S1	AUGUSTUS	start_codon	16009203	16009205	.	+	0	transcript_id "Phchi.S1G243800.t1"; gene_id "Phchi.S1G243800"
Phchi.S1	AUGUSTUS	CDS	16009203	16009544	0.88	+	0	transcript_id "Phchi.S1G243800.t1"; gene_id "Phchi.S1G243800"
Phchi.S1	AUGUSTUS	exon	16009203	16009544	.	+	.	transcript_id "Phchi.S1G243800.t1"; gene_id "Phchi.S1G243800"
Phchi.S1	AUGUSTUS	stop_codon	16009545	16009547	.	+	0	transcript_id "Phchi.S1G243800.t1"; gene_id "Phchi.S1G243800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15026.t1 is derived from g13494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16593083	16594238	.	-	.	Phchi.S3G234500
Phchi.S3	AUGUSTUS	transcript	16593083	16594238	.	-	.	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	stop_codon	16593080	16593082	.	-	0	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	CDS	16593083	16593813	1	-	2	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	exon	16593083	16593813	.	-	.	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	intron	16593814	16593914	.	-	.	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	CDS	16593915	16593930	0.97	-	0	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	exon	16593915	16593930	.	-	.	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	intron	16593931	16594229	.	-	.	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	CDS	16594230	16594238	0.97	-	0	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	exon	16594230	16594238	.	-	.	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
Phchi.S3	AUGUSTUS	start_codon	16594236	16594238	.	-	0	transcript_id "Phchi.S3G234500.t1"; gene_id "Phchi.S3G234500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7856.t1 is derived from g5030.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31542397	31545507	.	-	.	Phchi.S1G501500
Phchi.S1	AUGUSTUS	transcript	31542397	31545507	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	stop_codon	31542394	31542396	.	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31542397	31542440	1	-	2	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31542397	31542440	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31542441	31542534	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31542535	31542647	1	-	1	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31542535	31542647	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31542648	31542735	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31542736	31542785	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31542736	31542785	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31542786	31542872	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31542873	31542943	1	-	2	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31542873	31542943	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31542944	31543054	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31543055	31543127	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31543055	31543127	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31543128	31543372	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31543373	31543470	1	-	2	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31543373	31543470	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31543471	31543637	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31543638	31543704	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31543638	31543704	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31543705	31543823	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31543824	31543904	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31543824	31543904	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31543905	31544046	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31544047	31544214	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31544047	31544214	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31544215	31544342	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31544343	31544510	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31544343	31544510	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31544511	31544650	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31544651	31544947	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31544651	31544947	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31544948	31545077	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31545078	31545335	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31545078	31545335	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	intron	31545336	31545468	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	CDS	31545469	31545507	1	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	exon	31545469	31545507	.	-	.	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
Phchi.S1	AUGUSTUS	start_codon	31545505	31545507	.	-	0	transcript_id "Phchi.S1G501500.t1"; gene_id "Phchi.S1G501500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15091.t1 is derived from g13559.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16972023	16977407	.	-	.	Phchi.S3G241000
Phchi.S3	AUGUSTUS	transcript	16972023	16977407	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	stop_codon	16972020	16972022	.	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16972023	16972078	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16972023	16972078	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16972079	16972332	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16972333	16972396	0.93	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16972333	16972396	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16972397	16972498	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16972499	16972567	0.93	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16972499	16972567	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16972568	16972658	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16972659	16972703	1	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16972659	16972703	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16972704	16972795	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16972796	16972879	1	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16972796	16972879	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16972880	16972983	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16972984	16973039	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16972984	16973039	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16973040	16973122	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16973123	16973378	1	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16973123	16973378	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16973379	16973478	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16973479	16973829	0.98	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16973479	16973829	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16973830	16973922	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16973923	16974068	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16973923	16974068	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16974069	16974226	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16974227	16974448	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16974227	16974448	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16974449	16974619	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16974620	16975169	0.59	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16974620	16975169	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16975170	16975299	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16975300	16975469	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16975300	16975469	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16975470	16975588	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16975589	16975625	0.97	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16975589	16975625	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16975626	16975747	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16975748	16975862	0.96	-	1	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16975748	16975862	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16975863	16975980	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16975981	16976069	0.99	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16975981	16976069	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976070	16976248	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16976249	16976298	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16976249	16976298	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976299	16976446	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16976447	16976587	1	-	2	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16976447	16976587	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976588	16976679	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16976680	16976702	1	-	1	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16976680	16976702	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976703	16976837	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16976838	16976861	0.85	-	1	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16976838	16976861	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976862	16977011	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16977012	16977062	0.98	-	1	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16977012	16977062	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16977063	16977138	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16977139	16977407	0.98	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16977139	16977407	.	-	.	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	start_codon	16977405	16977407	.	-	0	transcript_id "Phchi.S3G241000.t1"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	transcript	16976558	16977407	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	stop_codon	16976555	16976557	.	-	0	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16976558	16976587	0.49	-	0	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16976558	16976587	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976588	16976679	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16976680	16976800	0.48	-	1	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16976680	16976800	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16976801	16977011	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16977012	16977062	1	-	1	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16977012	16977062	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	intron	16977063	16977138	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	CDS	16977139	16977407	1	-	0	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	exon	16977139	16977407	.	-	.	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
Phchi.S3	AUGUSTUS	start_codon	16977405	16977407	.	-	0	transcript_id "Phchi.S3G241000.t2"; gene_id "Phchi.S3G241000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7820.t1 is derived from g4994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31358192	31359350	.	-	.	Phchi.S1G497900
Phchi.S1	AUGUSTUS	transcript	31358192	31359350	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	stop_codon	31358189	31358191	.	-	0	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	CDS	31358192	31358386	1	-	0	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	exon	31358192	31358386	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	intron	31358387	31358472	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	CDS	31358473	31358554	1	-	1	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	exon	31358473	31358554	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	intron	31358555	31358647	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	CDS	31358648	31358858	0.55	-	2	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	exon	31358648	31358858	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	intron	31358859	31358943	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	CDS	31358944	31359010	0.91	-	0	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	exon	31358944	31359010	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	intron	31359011	31359272	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	CDS	31359273	31359350	0.52	-	0	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	exon	31359273	31359350	.	-	.	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
Phchi.S1	AUGUSTUS	start_codon	31359348	31359350	.	-	0	transcript_id "Phchi.S1G497900.t1"; gene_id "Phchi.S1G497900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9802.t1 is derived from g6978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43780256	43781485	.	-	.	Phchi.S1G696100
Phchi.S1	AUGUSTUS	transcript	43780256	43781485	.	-	.	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	stop_codon	43780253	43780255	.	-	0	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	CDS	43780256	43780780	1	-	0	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	exon	43780256	43780780	.	-	.	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	intron	43780781	43780902	.	-	.	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	CDS	43780903	43781138	1	-	2	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	exon	43780903	43781138	.	-	.	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	intron	43781139	43781277	.	-	.	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	CDS	43781278	43781485	1	-	0	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	exon	43781278	43781485	.	-	.	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
Phchi.S1	AUGUSTUS	start_codon	43781483	43781485	.	-	0	transcript_id "Phchi.S1G696100.t1"; gene_id "Phchi.S1G696100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3361.t1 is derived from g530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	3146574	3146912	.	-	.	Phchi.S1G052000
Phchi.S1	AUGUSTUS	transcript	3146574	3146912	.	-	.	transcript_id "Phchi.S1G052000.t1"; gene_id "Phchi.S1G052000"
Phchi.S1	AUGUSTUS	stop_codon	3146571	3146573	.	-	0	transcript_id "Phchi.S1G052000.t1"; gene_id "Phchi.S1G052000"
Phchi.S1	AUGUSTUS	CDS	3146574	3146912	0.59	-	0	transcript_id "Phchi.S1G052000.t1"; gene_id "Phchi.S1G052000"
Phchi.S1	AUGUSTUS	exon	3146574	3146912	.	-	.	transcript_id "Phchi.S1G052000.t1"; gene_id "Phchi.S1G052000"
Phchi.S1	AUGUSTUS	start_codon	3146910	3146912	.	-	0	transcript_id "Phchi.S1G052000.t1"; gene_id "Phchi.S1G052000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12758.t1 is derived from g11223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	1932008	1935135	.	-	.	Phchi.S3G007700
Phchi.S3	AUGUSTUS	transcript	1932008	1935135	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	stop_codon	1932005	1932007	.	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1932008	1932379	0.95	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1932008	1932379	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1932380	1932576	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1932577	1932918	0.99	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1932577	1932918	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1932919	1933004	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933005	1933039	1	-	2	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933005	1933039	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933040	1933158	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933159	1933261	0.98	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933159	1933261	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933262	1933522	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933523	1933600	1	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933523	1933600	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933601	1933699	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933700	1933750	1	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933700	1933750	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933751	1933853	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933854	1933979	1	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933854	1933979	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933980	1934145	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934146	1934214	1	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934146	1934214	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1934215	1934324	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934325	1934379	0.98	-	1	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934325	1934379	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1934380	1934679	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934680	1934731	1	-	2	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934680	1934731	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1934732	1934906	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934907	1935135	0.8	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934907	1935135	.	-	.	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	start_codon	1935133	1935135	.	-	0	transcript_id "Phchi.S3G007700.t1"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	transcript	1932008	1935135	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	stop_codon	1932005	1932007	.	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1932008	1932379	0.92	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1932008	1932379	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1932380	1932576	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1932577	1932918	1	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1932577	1932918	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1932919	1933004	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933005	1933039	1	-	2	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933005	1933039	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933040	1933158	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933159	1933236	0.48	-	2	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933159	1933236	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933237	1933331	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933332	1933431	0.96	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933332	1933431	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933432	1933522	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933523	1933600	1	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933523	1933600	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933601	1933699	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933700	1933750	1	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933700	1933750	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933751	1933853	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1933854	1933979	1	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1933854	1933979	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1933980	1934145	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934146	1934214	0.99	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934146	1934214	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1934215	1934324	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934325	1934379	0.99	-	1	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934325	1934379	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1934380	1934679	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934680	1934731	1	-	2	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934680	1934731	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	intron	1934732	1934906	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	CDS	1934907	1935135	0.91	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	exon	1934907	1935135	.	-	.	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
Phchi.S3	AUGUSTUS	start_codon	1935133	1935135	.	-	0	transcript_id "Phchi.S3G007700.t2"; gene_id "Phchi.S3G007700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12128.t1 is derived from g7804.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	4041033	4041308	.	+	.	Phchi.S2G020800
Phchi.S2	AUGUSTUS	transcript	4041033	4041308	.	+	.	transcript_id "Phchi.S2G020800.t1"; gene_id "Phchi.S2G020800"
Phchi.S2	AUGUSTUS	start_codon	4041033	4041035	.	+	0	transcript_id "Phchi.S2G020800.t1"; gene_id "Phchi.S2G020800"
Phchi.S2	AUGUSTUS	CDS	4041033	4041308	0.33	+	0	transcript_id "Phchi.S2G020800.t1"; gene_id "Phchi.S2G020800"
Phchi.S2	AUGUSTUS	exon	4041033	4041308	.	+	.	transcript_id "Phchi.S2G020800.t1"; gene_id "Phchi.S2G020800"
Phchi.S2	AUGUSTUS	stop_codon	4041309	4041311	.	+	0	transcript_id "Phchi.S2G020800.t1"; gene_id "Phchi.S2G020800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9398.t1 is derived from g6574.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41337675	41337944	.	+	.	Phchi.S1G655700
Phchi.S1	AUGUSTUS	transcript	41337675	41337944	.	+	.	transcript_id "Phchi.S1G655700.t1"; gene_id "Phchi.S1G655700"
Phchi.S1	AUGUSTUS	start_codon	41337675	41337677	.	+	0	transcript_id "Phchi.S1G655700.t1"; gene_id "Phchi.S1G655700"
Phchi.S1	AUGUSTUS	CDS	41337675	41337944	0.89	+	0	transcript_id "Phchi.S1G655700.t1"; gene_id "Phchi.S1G655700"
Phchi.S1	AUGUSTUS	exon	41337675	41337944	.	+	.	transcript_id "Phchi.S1G655700.t1"; gene_id "Phchi.S1G655700"
Phchi.S1	AUGUSTUS	stop_codon	41337945	41337947	.	+	0	transcript_id "Phchi.S1G655700.t1"; gene_id "Phchi.S1G655700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2503.t1 is derived from g9423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7000863	7002353	.	-	.	Phchi.S5G111200
Phchi.S5	AUGUSTUS	transcript	7000863	7002353	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	stop_codon	7000860	7000862	.	-	0	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	CDS	7000863	7001528	0.79	-	0	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	exon	7000863	7001528	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	intron	7001529	7001784	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	CDS	7001785	7001867	0.43	-	2	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	exon	7001785	7001867	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	intron	7001868	7002093	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	CDS	7002094	7002155	0.85	-	1	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	exon	7002094	7002155	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	intron	7002156	7002282	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	CDS	7002283	7002353	0.69	-	0	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	exon	7002283	7002353	.	-	.	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
Phchi.S5	AUGUSTUS	start_codon	7002351	7002353	.	-	0	transcript_id "Phchi.S5G111200.t1"; gene_id "Phchi.S5G111200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7253.t1 is derived from g4425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27871698	27874246	.	-	.	Phchi.S1G441200
Phchi.S1	AUGUSTUS	transcript	27871698	27874246	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	stop_codon	27871695	27871697	.	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27871698	27871899	0.5	-	1	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27871698	27871899	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27871900	27871973	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27871974	27872104	0.97	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27871974	27872104	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27872105	27872211	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27872212	27872286	1	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27872212	27872286	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27872287	27872383	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27872384	27872627	1	-	1	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27872384	27872627	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27872628	27872761	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27872762	27872823	1	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27872762	27872823	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27872824	27872908	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27872909	27873131	1	-	1	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27872909	27873131	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27873132	27873225	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27873226	27873293	1	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27873226	27873293	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27873294	27873419	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27873420	27873527	1	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27873420	27873527	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27873528	27873686	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27873687	27873767	1	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27873687	27873767	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	intron	27873768	27873859	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	CDS	27873860	27874246	0.69	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	exon	27873860	27874246	.	-	.	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
Phchi.S1	AUGUSTUS	start_codon	27874244	27874246	.	-	0	transcript_id "Phchi.S1G441200.t1"; gene_id "Phchi.S1G441200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15261.t1 is derived from g13729.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17968399	17971269	.	-	.	Phchi.S3G258000
Phchi.S3	AUGUSTUS	transcript	17968399	17971269	.	-	.	transcript_id "Phchi.S3G258000.t1"; gene_id "Phchi.S3G258000"
Phchi.S3	AUGUSTUS	stop_codon	17968396	17968398	.	-	0	transcript_id "Phchi.S3G258000.t1"; gene_id "Phchi.S3G258000"
Phchi.S3	AUGUSTUS	CDS	17968399	17971269	0.99	-	0	transcript_id "Phchi.S3G258000.t1"; gene_id "Phchi.S3G258000"
Phchi.S3	AUGUSTUS	exon	17968399	17971269	.	-	.	transcript_id "Phchi.S3G258000.t1"; gene_id "Phchi.S3G258000"
Phchi.S3	AUGUSTUS	start_codon	17971267	17971269	.	-	0	transcript_id "Phchi.S3G258000.t1"; gene_id "Phchi.S3G258000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg5155.t1 is derived from g2325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15177533	15178361	.	+	.	Phchi.S1G231400
Phchi.S1	AUGUSTUS	transcript	15177533	15178361	.	+	.	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	start_codon	15177533	15177535	.	+	0	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	CDS	15177533	15177612	0.79	+	0	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	exon	15177533	15177612	.	+	.	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	intron	15177613	15177876	.	+	.	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	CDS	15177877	15178030	1	+	1	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	exon	15177877	15178030	.	+	.	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	intron	15178031	15178193	.	+	.	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	CDS	15178194	15178361	1	+	0	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	exon	15178194	15178361	.	+	.	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	stop_codon	15178362	15178364	.	+	0	transcript_id "Phchi.S1G231400.t1"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	transcript	15177533	15178361	.	+	.	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	start_codon	15177533	15177535	.	+	0	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	CDS	15177533	15177612	0.73	+	0	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	exon	15177533	15177612	.	+	.	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	intron	15177613	15177873	.	+	.	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	CDS	15177874	15178030	1	+	1	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	exon	15177874	15178030	.	+	.	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	intron	15178031	15178193	.	+	.	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	CDS	15178194	15178361	1	+	0	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	exon	15178194	15178361	.	+	.	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
Phchi.S1	AUGUSTUS	stop_codon	15178362	15178364	.	+	0	transcript_id "Phchi.S1G231400.t2"; gene_id "Phchi.S1G231400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6163.t1 is derived from g3334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21261146	21262045	.	-	.	Phchi.S1G332200
Phchi.S1	AUGUSTUS	transcript	21261146	21262045	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	stop_codon	21261143	21261145	.	-	0	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	CDS	21261146	21261308	0.78	-	1	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	exon	21261146	21261308	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	intron	21261309	21261451	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	CDS	21261452	21261531	1	-	0	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	exon	21261452	21261531	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	intron	21261532	21261614	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	CDS	21261615	21261710	1	-	0	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	exon	21261615	21261710	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	intron	21261711	21261852	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	CDS	21261853	21261897	1	-	0	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	exon	21261853	21261897	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	intron	21261898	21261982	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	CDS	21261983	21262045	0.32	-	0	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	exon	21261983	21262045	.	-	.	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
Phchi.S1	AUGUSTUS	start_codon	21262043	21262045	.	-	0	transcript_id "Phchi.S1G332200.t1"; gene_id "Phchi.S1G332200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15160.t1 is derived from g13628.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17316700	17318360	.	+	.	Phchi.S3G247900
Phchi.S3	AUGUSTUS	transcript	17316700	17318360	.	+	.	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	start_codon	17316700	17316702	.	+	0	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	CDS	17316700	17317872	0.67	+	0	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	exon	17316700	17317872	.	+	.	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	intron	17317873	17317976	.	+	.	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	CDS	17317977	17318360	0.42	+	0	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	exon	17317977	17318360	.	+	.	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
Phchi.S3	AUGUSTUS	stop_codon	17318361	17318363	.	+	0	transcript_id "Phchi.S3G247900.t1"; gene_id "Phchi.S3G247900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1885.t1 is derived from g8805.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3705121	3705721	.	-	.	Phchi.S5G049400
Phchi.S5	AUGUSTUS	transcript	3705121	3705721	.	-	.	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	stop_codon	3705118	3705120	.	-	0	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	CDS	3705121	3705184	0.96	-	1	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	exon	3705121	3705184	.	-	.	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	intron	3705185	3705388	.	-	.	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	CDS	3705389	3705559	0.96	-	1	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	exon	3705389	3705559	.	-	.	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	intron	3705560	3705668	.	-	.	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	CDS	3705669	3705721	0.34	-	0	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	exon	3705669	3705721	.	-	.	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
Phchi.S5	AUGUSTUS	start_codon	3705719	3705721	.	-	0	transcript_id "Phchi.S5G049400.t1"; gene_id "Phchi.S5G049400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1871.t1 is derived from g8791.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3632480	3634383	.	-	.	Phchi.S5G048000
Phchi.S5	AUGUSTUS	transcript	3632480	3634383	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	stop_codon	3632477	3632479	.	-	0	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3632480	3632491	0.96	-	0	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3632480	3632491	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3632492	3632588	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3632589	3632745	0.85	-	1	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3632589	3632745	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3632746	3632842	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3632843	3632900	0.76	-	2	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3632843	3632900	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3632901	3632950	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3632951	3632993	0.73	-	0	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3632951	3632993	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3632994	3633100	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3633101	3633259	0.88	-	0	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3633101	3633259	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3633260	3633352	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3633353	3633647	1	-	1	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3633353	3633647	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3633648	3633741	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3633742	3633858	1	-	1	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3633742	3633858	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3633859	3633996	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3633997	3634059	1	-	1	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3633997	3634059	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	intron	3634060	3634150	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	CDS	3634151	3634383	1	-	0	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	exon	3634151	3634383	.	-	.	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
Phchi.S5	AUGUSTUS	start_codon	3634381	3634383	.	-	0	transcript_id "Phchi.S5G048000.t1"; gene_id "Phchi.S5G048000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14828.t1 is derived from g13296.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14910588	14911547	.	-	.	Phchi.S3G214700
Phchi.S3	AUGUSTUS	transcript	14910588	14911547	.	-	.	transcript_id "Phchi.S3G214700.t1"; gene_id "Phchi.S3G214700"
Phchi.S3	AUGUSTUS	stop_codon	14910585	14910587	.	-	0	transcript_id "Phchi.S3G214700.t1"; gene_id "Phchi.S3G214700"
Phchi.S3	AUGUSTUS	CDS	14910588	14911547	0.57	-	0	transcript_id "Phchi.S3G214700.t1"; gene_id "Phchi.S3G214700"
Phchi.S3	AUGUSTUS	exon	14910588	14911547	.	-	.	transcript_id "Phchi.S3G214700.t1"; gene_id "Phchi.S3G214700"
Phchi.S3	AUGUSTUS	start_codon	14911545	14911547	.	-	0	transcript_id "Phchi.S3G214700.t1"; gene_id "Phchi.S3G214700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3207.t1 is derived from g376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2237877	2239405	.	-	.	Phchi.S1G036600
Phchi.S1	AUGUSTUS	transcript	2237877	2239405	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	stop_codon	2237874	2237876	.	-	0	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2237877	2237974	0.99	-	2	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2237877	2237974	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2237975	2238077	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2238078	2238154	1	-	1	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2238078	2238154	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2238155	2238259	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2238260	2238322	1	-	1	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2238260	2238322	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2238323	2238429	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2238430	2238509	1	-	0	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2238430	2238509	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2238510	2238593	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2238594	2238663	1	-	1	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2238594	2238663	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2238664	2238745	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2238746	2238912	1	-	0	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2238746	2238912	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2238913	2238988	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2238989	2239078	1	-	0	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2238989	2239078	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2239079	2239155	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2239156	2239165	0.92	-	1	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2239156	2239165	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2239166	2239227	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2239228	2239236	0.92	-	1	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2239228	2239236	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	intron	2239237	2239328	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	CDS	2239329	2239405	0.92	-	0	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	exon	2239329	2239405	.	-	.	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
Phchi.S1	AUGUSTUS	start_codon	2239403	2239405	.	-	0	transcript_id "Phchi.S1G036600.t1"; gene_id "Phchi.S1G036600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8819.t1 is derived from g5994.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38127259	38131026	.	-	.	Phchi.S1G597800
Phchi.S1	AUGUSTUS	transcript	38127259	38131026	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	stop_codon	38127256	38127258	.	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38127259	38127336	0.96	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38127259	38127336	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38127337	38127439	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38127440	38127553	0.97	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38127440	38127553	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38127554	38127657	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38127658	38127780	0.99	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38127658	38127780	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38127781	38127866	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38127867	38127944	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38127867	38127944	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38127945	38128056	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38128057	38128215	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38128057	38128215	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38128216	38128299	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38128300	38128396	1	-	1	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38128300	38128396	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38128397	38128488	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38128489	38128640	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38128489	38128640	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38128641	38128736	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38128737	38128820	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38128737	38128820	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38128821	38128948	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38128949	38128971	1	-	2	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38128949	38128971	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38128972	38129036	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38129037	38129182	1	-	1	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38129037	38129182	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38129183	38129271	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38129272	38129364	0.99	-	1	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38129272	38129364	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38129365	38129472	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38129473	38129670	0.98	-	1	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38129473	38129670	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38129671	38129787	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38129788	38129857	1	-	2	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38129788	38129857	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38129858	38129968	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38129969	38130005	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38129969	38130005	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38130006	38130105	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38130106	38130186	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38130106	38130186	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38130187	38130277	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38130278	38130344	1	-	1	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38130278	38130344	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38130345	38130431	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38130432	38130508	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38130432	38130508	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38130509	38130608	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38130609	38130671	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38130609	38130671	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	intron	38130672	38130774	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	CDS	38130775	38131026	1	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	exon	38130775	38131026	.	-	.	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
Phchi.S1	AUGUSTUS	start_codon	38131024	38131026	.	-	0	transcript_id "Phchi.S1G597800.t1"; gene_id "Phchi.S1G597800"
# This transcript jg14786.t2 is derived from g13254.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14787.t1 is derived from g13255.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14707843	14709053	.	+	.	Phchi.S3G210600
Phchi.S3	AUGUSTUS	transcript	14707843	14709053	.	+	.	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	start_codon	14707843	14707845	.	+	0	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	CDS	14707843	14708472	0.8	+	0	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	exon	14707843	14708472	.	+	.	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	intron	14708473	14708558	.	+	.	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	CDS	14708559	14709053	0.98	+	0	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	exon	14708559	14709053	.	+	.	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	stop_codon	14709054	14709056	.	+	0	transcript_id "Phchi.S3G210600.t1"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	transcript	14708478	14709053	.	+	.	transcript_id "Phchi.S3G210600.t2"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	start_codon	14708478	14708480	.	+	0	transcript_id "Phchi.S3G210600.t2"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	CDS	14708478	14709053	1	+	0	transcript_id "Phchi.S3G210600.t2"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	exon	14708478	14709053	.	+	.	transcript_id "Phchi.S3G210600.t2"; gene_id "Phchi.S3G210600"
Phchi.S3	AUGUSTUS	stop_codon	14709054	14709056	.	+	0	transcript_id "Phchi.S3G210600.t2"; gene_id "Phchi.S3G210600"
# This transcript jg4480.t2 is derived from g1650.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4481.t1 is derived from g1651.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10713551	10714034	.	+	.	Phchi.S1G164000
Phchi.S1	AUGUSTUS	transcript	10713551	10714034	.	+	.	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	start_codon	10713551	10713553	.	+	0	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	CDS	10713551	10713673	1	+	0	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	exon	10713551	10713673	.	+	.	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	intron	10713674	10713764	.	+	.	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	CDS	10713765	10713913	1	+	0	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	exon	10713765	10713913	.	+	.	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	intron	10713914	10713994	.	+	.	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	CDS	10713995	10714034	1	+	1	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	exon	10713995	10714034	.	+	.	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
Phchi.S1	AUGUSTUS	stop_codon	10714035	10714037	.	+	0	transcript_id "Phchi.S1G164000.t1"; gene_id "Phchi.S1G164000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9150.t1 is derived from g6325.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40107156	40108725	.	-	.	Phchi.S1G630900
Phchi.S1	AUGUSTUS	transcript	40107156	40108725	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	stop_codon	40107153	40107155	.	-	0	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	CDS	40107156	40107347	0.99	-	0	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	exon	40107156	40107347	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	intron	40107348	40107428	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	CDS	40107429	40107629	1	-	0	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	exon	40107429	40107629	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	intron	40107630	40107800	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	CDS	40107801	40107893	1	-	0	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	exon	40107801	40107893	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	intron	40107894	40107997	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	CDS	40107998	40108103	1	-	1	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	exon	40107998	40108103	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	intron	40108104	40108207	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	CDS	40108208	40108725	0.42	-	0	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	exon	40108208	40108725	.	-	.	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
Phchi.S1	AUGUSTUS	start_codon	40108723	40108725	.	-	0	transcript_id "Phchi.S1G630900.t1"; gene_id "Phchi.S1G630900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8369.t1 is derived from g5544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35541318	35543039	.	+	.	Phchi.S1G552800
Phchi.S1	AUGUSTUS	transcript	35541318	35543039	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	start_codon	35541318	35541320	.	+	0	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	CDS	35541318	35541619	0.5	+	0	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	exon	35541318	35541619	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	intron	35541620	35541730	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	CDS	35541731	35541875	0.6	+	1	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	exon	35541731	35541875	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	intron	35541876	35541976	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	CDS	35541977	35542239	0.59	+	0	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	exon	35541977	35542239	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	intron	35542240	35542366	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	CDS	35542367	35543039	0.99	+	1	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	exon	35542367	35543039	.	+	.	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
Phchi.S1	AUGUSTUS	stop_codon	35543040	35543042	.	+	0	transcript_id "Phchi.S1G552800.t1"; gene_id "Phchi.S1G552800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14778.t1 is derived from g13246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14655299	14655806	.	-	.	Phchi.S3G209700
Phchi.S3	AUGUSTUS	transcript	14655299	14655806	.	-	.	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	stop_codon	14655296	14655298	.	-	0	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	CDS	14655299	14655694	0.89	-	0	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	exon	14655299	14655694	.	-	.	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	intron	14655695	14655788	.	-	.	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	CDS	14655789	14655806	1	-	0	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	exon	14655789	14655806	.	-	.	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
Phchi.S3	AUGUSTUS	start_codon	14655804	14655806	.	-	0	transcript_id "Phchi.S3G209700.t1"; gene_id "Phchi.S3G209700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10191.t1 is derived from g7367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46246489	46248050	.	-	.	Phchi.S1G735000
Phchi.S1	AUGUSTUS	transcript	46246489	46248050	.	-	.	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	stop_codon	46246486	46246488	.	-	0	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	CDS	46246489	46247511	0.83	-	0	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	exon	46246489	46247511	.	-	.	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	intron	46247512	46247597	.	-	.	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	CDS	46247598	46248050	0.77	-	0	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	exon	46247598	46248050	.	-	.	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
Phchi.S1	AUGUSTUS	start_codon	46248048	46248050	.	-	0	transcript_id "Phchi.S1G735000.t1"; gene_id "Phchi.S1G735000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15968.t1 is derived from g16007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C133	AUGUSTUS	gene	28710	30449	.	+	.	Phchi.C133G000700
Phchi.C133	AUGUSTUS	transcript	28710	30449	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	start_codon	28710	28712	.	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	28710	28799	0.6	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	28710	28799	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	28800	28905	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	28906	29028	0.86	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	28906	29028	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	29029	29202	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	29203	29394	1	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	29203	29394	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	29395	29488	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	29489	29572	1	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	29489	29572	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	29573	29669	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	29670	29756	1	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	29670	29756	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	29757	29839	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	29840	29893	1	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	29840	29893	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	29894	30019	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	30020	30102	1	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	30020	30102	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	30103	30196	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	30197	30306	1	+	1	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	30197	30306	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	intron	30307	30387	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	CDS	30388	30449	0.98	+	2	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	exon	30388	30449	.	+	.	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
Phchi.C133	AUGUSTUS	stop_codon	30450	30452	.	+	0	transcript_id "Phchi.C133G000700.t1"; gene_id "Phchi.C133G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5018.t1 is derived from g2188.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14083482	14086650	.	-	.	Phchi.S1G217700
Phchi.S1	AUGUSTUS	transcript	14083482	14086650	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	stop_codon	14083479	14083481	.	-	0	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	CDS	14083482	14084542	1	-	2	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	exon	14083482	14084542	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	intron	14084543	14084686	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	CDS	14084687	14084930	1	-	0	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	exon	14084687	14084930	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	intron	14084931	14085120	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	CDS	14085121	14085633	1	-	0	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	exon	14085121	14085633	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	intron	14085634	14085714	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	CDS	14085715	14086650	1	-	0	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	exon	14085715	14086650	.	-	.	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
Phchi.S1	AUGUSTUS	start_codon	14086648	14086650	.	-	0	transcript_id "Phchi.S1G217700.t1"; gene_id "Phchi.S1G217700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg15022.t1 is derived from g13490.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16571813	16580810	.	+	.	Phchi.S3G234100
Phchi.S3	AUGUSTUS	transcript	16571813	16580810	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	start_codon	16571813	16571815	.	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16571813	16571836	0.48	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16571813	16571836	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16571837	16571934	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16571935	16572022	0.48	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16571935	16572022	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16572023	16572224	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16572225	16572710	0.61	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16572225	16572710	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16572711	16572794	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16572795	16573136	0.99	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16572795	16573136	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573137	16573325	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573326	16573535	0.46	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573326	16573535	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573536	16573612	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573613	16573654	0.46	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573613	16573654	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573655	16573780	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573781	16574082	0.44	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573781	16574082	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574083	16574222	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574223	16574443	0.48	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574223	16574443	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574444	16574526	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574527	16574687	0.83	+	1	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574527	16574687	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574688	16574786	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574787	16575137	0.96	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574787	16575137	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16575138	16575244	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16575245	16575559	1	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16575245	16575559	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16575560	16575675	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16575676	16575999	0.9	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16575676	16575999	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576000	16576100	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576101	16576436	0.95	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576101	16576436	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576437	16576519	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576520	16576762	0.99	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576520	16576762	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576763	16576886	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576887	16576974	1	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576887	16576974	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576975	16577146	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577147	16577322	1	+	1	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577147	16577322	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577323	16577409	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577410	16577718	0.92	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577410	16577718	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577719	16577882	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577883	16577973	1	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577883	16577973	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577974	16578063	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578064	16578282	1	+	1	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578064	16578282	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16578283	16578547	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578548	16578750	1	+	1	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578548	16578750	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16578751	16578905	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578906	16579183	1	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578906	16579183	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579184	16579266	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579267	16579417	0.99	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579267	16579417	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579418	16579519	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579520	16579674	0.91	+	2	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579520	16579674	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579675	16579822	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579823	16579983	0.98	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579823	16579983	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579984	16580111	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580112	16580247	0.97	+	1	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580112	16580247	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16580248	16580332	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580333	16580512	1	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580333	16580512	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16580513	16580612	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580613	16580810	1	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580613	16580810	.	+	.	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	stop_codon	16580811	16580813	.	+	0	transcript_id "Phchi.S3G234100.t1"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	transcript	16571813	16580810	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	start_codon	16571813	16571815	.	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16571813	16571836	0.47	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16571813	16571836	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16571837	16571934	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16571935	16572022	0.47	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16571935	16572022	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16572023	16572224	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16572225	16572710	0.62	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16572225	16572710	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16572711	16572794	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16572795	16573136	0.97	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16572795	16573136	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573137	16573325	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573326	16573535	0.46	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573326	16573535	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573536	16573612	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573613	16573654	0.48	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573613	16573654	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573655	16573780	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573781	16574082	0.43	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573781	16574082	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574083	16574222	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574223	16574443	0.48	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574223	16574443	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574444	16574526	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574527	16574687	0.79	+	1	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574527	16574687	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574688	16574786	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574787	16575137	0.92	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574787	16575137	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16575138	16575244	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16575245	16575559	0.99	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16575245	16575559	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16575560	16575675	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16575676	16575999	0.92	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16575676	16575999	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576000	16576100	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576101	16576436	0.94	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576101	16576436	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576437	16576519	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576520	16576762	1	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576520	16576762	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576763	16576886	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576887	16576974	0.98	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576887	16576974	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576975	16577146	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577147	16577322	1	+	1	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577147	16577322	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577323	16577409	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577410	16577607	0.99	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577410	16577607	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577608	16577882	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577883	16577973	1	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577883	16577973	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577974	16578063	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578064	16578282	1	+	1	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578064	16578282	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16578283	16578547	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578548	16578750	1	+	1	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578548	16578750	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16578751	16578905	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578906	16579183	1	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578906	16579183	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579184	16579266	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579267	16579417	0.99	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579267	16579417	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579418	16579519	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579520	16579674	0.86	+	2	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579520	16579674	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579675	16579822	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579823	16579983	0.99	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579823	16579983	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579984	16580111	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580112	16580247	0.98	+	1	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580112	16580247	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16580248	16580332	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580333	16580512	1	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580333	16580512	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16580513	16580612	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580613	16580810	0.99	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580613	16580810	.	+	.	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	stop_codon	16580811	16580813	.	+	0	transcript_id "Phchi.S3G234100.t2"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	transcript	16571813	16580810	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	start_codon	16571813	16571815	.	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16571813	16571836	0.39	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16571813	16571836	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16571837	16571934	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16571935	16572022	0.39	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16571935	16572022	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16572023	16572224	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16572225	16572710	0.64	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16572225	16572710	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16572711	16572794	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16572795	16573136	1	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16572795	16573136	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573137	16573325	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573326	16573535	0.5	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573326	16573535	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573536	16573612	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573613	16573654	0.51	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573613	16573654	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16573655	16573780	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16573781	16574082	0.42	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16573781	16574082	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574083	16574222	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574223	16574443	0.41	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574223	16574443	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574444	16574526	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574527	16574687	0.81	+	1	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574527	16574687	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16574688	16574786	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16574787	16575137	0.86	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16574787	16575137	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16575138	16575244	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16575245	16575559	0.97	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16575245	16575559	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16575560	16575675	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16575676	16575999	0.91	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16575676	16575999	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576000	16576100	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576101	16576436	0.95	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576101	16576436	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576437	16576519	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16576520	16576837	0.95	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16576520	16576837	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16576838	16576999	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577000	16577054	0.52	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577000	16577054	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577055	16577146	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577147	16577322	0.82	+	1	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577147	16577322	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577323	16577409	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577410	16577718	0.97	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577410	16577718	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577719	16577882	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16577883	16577973	1	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16577883	16577973	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16577974	16578063	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578064	16578282	1	+	1	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578064	16578282	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16578283	16578547	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578548	16578750	1	+	1	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578548	16578750	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16578751	16578905	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16578906	16579183	1	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16578906	16579183	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579184	16579266	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579267	16579417	0.99	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579267	16579417	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579418	16579519	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579520	16579674	0.9	+	2	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579520	16579674	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579675	16579822	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16579823	16579983	0.97	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16579823	16579983	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16579984	16580111	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580112	16580247	0.93	+	1	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580112	16580247	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16580248	16580332	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580333	16580512	1	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580333	16580512	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	intron	16580513	16580612	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	CDS	16580613	16580810	1	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	exon	16580613	16580810	.	+	.	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
Phchi.S3	AUGUSTUS	stop_codon	16580811	16580813	.	+	0	transcript_id "Phchi.S3G234100.t3"; gene_id "Phchi.S3G234100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12447.t1 is derived from g8124.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	22443724	22444029	.	-	.	Phchi.S2G052700
Phchi.S2	AUGUSTUS	transcript	22443724	22444029	.	-	.	transcript_id "Phchi.S2G052700.t1"; gene_id "Phchi.S2G052700"
Phchi.S2	AUGUSTUS	stop_codon	22443721	22443723	.	-	0	transcript_id "Phchi.S2G052700.t1"; gene_id "Phchi.S2G052700"
Phchi.S2	AUGUSTUS	CDS	22443724	22444029	0.65	-	0	transcript_id "Phchi.S2G052700.t1"; gene_id "Phchi.S2G052700"
Phchi.S2	AUGUSTUS	exon	22443724	22444029	.	-	.	transcript_id "Phchi.S2G052700.t1"; gene_id "Phchi.S2G052700"
Phchi.S2	AUGUSTUS	start_codon	22444027	22444029	.	-	0	transcript_id "Phchi.S2G052700.t1"; gene_id "Phchi.S2G052700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9781.t1 is derived from g6957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43652428	43653737	.	-	.	Phchi.S1G694000
Phchi.S1	AUGUSTUS	transcript	43652428	43653737	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	stop_codon	43652425	43652427	.	-	0	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	CDS	43652428	43652640	1	-	0	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	exon	43652428	43652640	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	intron	43652641	43652732	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	CDS	43652733	43652835	1	-	1	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	exon	43652733	43652835	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	intron	43652836	43652943	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	CDS	43652944	43653023	1	-	0	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	exon	43652944	43653023	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	intron	43653024	43653149	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	CDS	43653150	43653207	1	-	1	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	exon	43653150	43653207	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	intron	43653208	43653298	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	CDS	43653299	43653396	1	-	0	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	exon	43653299	43653396	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	intron	43653397	43653545	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	CDS	43653546	43653737	1	-	0	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	exon	43653546	43653737	.	-	.	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
Phchi.S1	AUGUSTUS	start_codon	43653735	43653737	.	-	0	transcript_id "Phchi.S1G694000.t1"; gene_id "Phchi.S1G694000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9529.t1 is derived from g6705.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42324467	42325519	.	-	.	Phchi.S1G668800
Phchi.S1	AUGUSTUS	transcript	42324467	42325519	.	-	.	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	stop_codon	42324464	42324466	.	-	0	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	CDS	42324467	42324927	1	-	2	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	exon	42324467	42324927	.	-	.	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	intron	42324928	42325152	.	-	.	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	CDS	42325153	42325519	1	-	0	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	exon	42325153	42325519	.	-	.	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
Phchi.S1	AUGUSTUS	start_codon	42325517	42325519	.	-	0	transcript_id "Phchi.S1G668800.t1"; gene_id "Phchi.S1G668800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7084.t1 is derived from g4256.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26806650	26807831	.	+	.	Phchi.S1G424300
Phchi.S1	AUGUSTUS	transcript	26806650	26807831	.	+	.	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	start_codon	26806650	26806652	.	+	0	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	CDS	26806650	26807245	0.34	+	0	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	exon	26806650	26807245	.	+	.	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	intron	26807246	26807334	.	+	.	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	CDS	26807335	26807561	1	+	1	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	exon	26807335	26807561	.	+	.	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	intron	26807562	26807646	.	+	.	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	CDS	26807647	26807831	0.49	+	2	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	exon	26807647	26807831	.	+	.	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
Phchi.S1	AUGUSTUS	stop_codon	26807832	26807834	.	+	0	transcript_id "Phchi.S1G424300.t1"; gene_id "Phchi.S1G424300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7534.t1 is derived from g4708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29939529	29940243	.	+	.	Phchi.S1G469300
Phchi.S1	AUGUSTUS	transcript	29939529	29940243	.	+	.	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	start_codon	29939529	29939531	.	+	0	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	CDS	29939529	29939706	1	+	0	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	exon	29939529	29939706	.	+	.	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	intron	29939707	29939801	.	+	.	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	CDS	29939802	29939928	1	+	2	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	exon	29939802	29939928	.	+	.	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	intron	29939929	29940185	.	+	.	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	CDS	29940186	29940243	1	+	1	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	exon	29940186	29940243	.	+	.	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
Phchi.S1	AUGUSTUS	stop_codon	29940244	29940246	.	+	0	transcript_id "Phchi.S1G469300.t1"; gene_id "Phchi.S1G469300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9831.t1 is derived from g7007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43997109	43997818	.	-	.	Phchi.S1G699000
Phchi.S1	AUGUSTUS	transcript	43997109	43997818	.	-	.	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	stop_codon	43997106	43997108	.	-	0	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	CDS	43997109	43997504	0.76	-	0	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	exon	43997109	43997504	.	-	.	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	intron	43997505	43997601	.	-	.	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	CDS	43997602	43997650	0.76	-	1	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	exon	43997602	43997650	.	-	.	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	intron	43997651	43997813	.	-	.	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	CDS	43997814	43997818	0.73	-	0	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	exon	43997814	43997818	.	-	.	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
Phchi.S1	AUGUSTUS	start_codon	43997816	43997818	.	-	0	transcript_id "Phchi.S1G699000.t1"; gene_id "Phchi.S1G699000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5857.t1 is derived from g3027.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19385004	19385290	.	-	.	Phchi.S1G301600
Phchi.S1	AUGUSTUS	transcript	19385004	19385290	.	-	.	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	stop_codon	19385001	19385003	.	-	0	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	CDS	19385004	19385053	0.55	-	2	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	exon	19385004	19385053	.	-	.	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	intron	19385054	19385139	.	-	.	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	CDS	19385140	19385290	0.85	-	0	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	exon	19385140	19385290	.	-	.	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
Phchi.S1	AUGUSTUS	start_codon	19385288	19385290	.	-	0	transcript_id "Phchi.S1G301600.t1"; gene_id "Phchi.S1G301600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3192.t1 is derived from g361.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2156264	2156728	.	-	.	Phchi.S1G035100
Phchi.S1	AUGUSTUS	transcript	2156264	2156728	.	-	.	transcript_id "Phchi.S1G035100.t1"; gene_id "Phchi.S1G035100"
Phchi.S1	AUGUSTUS	stop_codon	2156261	2156263	.	-	0	transcript_id "Phchi.S1G035100.t1"; gene_id "Phchi.S1G035100"
Phchi.S1	AUGUSTUS	CDS	2156264	2156728	0.94	-	0	transcript_id "Phchi.S1G035100.t1"; gene_id "Phchi.S1G035100"
Phchi.S1	AUGUSTUS	exon	2156264	2156728	.	-	.	transcript_id "Phchi.S1G035100.t1"; gene_id "Phchi.S1G035100"
Phchi.S1	AUGUSTUS	start_codon	2156726	2156728	.	-	0	transcript_id "Phchi.S1G035100.t1"; gene_id "Phchi.S1G035100"
# This transcript jg10187.t2 is derived from g7363.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg10187.t3 is derived from g7363.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10188.t1 is derived from g7364.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46225429	46226007	.	+	.	Phchi.S1G734700
Phchi.S1	AUGUSTUS	transcript	46225429	46226007	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	start_codon	46225429	46225431	.	+	0	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	CDS	46225429	46225575	0.36	+	0	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	exon	46225429	46225575	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	intron	46225576	46225671	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	CDS	46225672	46225688	0.99	+	0	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	exon	46225672	46225688	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	intron	46225689	46225780	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	CDS	46225781	46225853	0.99	+	1	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	exon	46225781	46225853	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	intron	46225854	46225986	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	CDS	46225987	46226007	0.99	+	0	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	exon	46225987	46226007	.	+	.	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
Phchi.S1	AUGUSTUS	stop_codon	46226008	46226010	.	+	0	transcript_id "Phchi.S1G734700.t1"; gene_id "Phchi.S1G734700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8174.t1 is derived from g5349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34280962	34282549	.	-	.	Phchi.S1G533300
Phchi.S1	AUGUSTUS	transcript	34280962	34282549	.	-	.	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	stop_codon	34280959	34280961	.	-	0	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	CDS	34280962	34281744	1	-	0	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	exon	34280962	34281744	.	-	.	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	intron	34281745	34281874	.	-	.	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	CDS	34281875	34282549	0.96	-	0	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	exon	34281875	34282549	.	-	.	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
Phchi.S1	AUGUSTUS	start_codon	34282547	34282549	.	-	0	transcript_id "Phchi.S1G533300.t1"; gene_id "Phchi.S1G533300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1277.t1 is derived from g11060.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8784845	8788468	.	-	.	Phchi.S6G123600
Phchi.S6	AUGUSTUS	transcript	8784845	8788468	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	stop_codon	8784842	8784844	.	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8784845	8784937	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8784845	8784937	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8784938	8785017	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8785018	8785224	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8785018	8785224	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8785225	8785307	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8785308	8785418	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8785308	8785418	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8785419	8785507	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8785508	8785706	1	-	1	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8785508	8785706	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8785707	8785794	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8785795	8785880	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8785795	8785880	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8785881	8785976	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8785977	8786135	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8785977	8786135	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8786136	8786262	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8786263	8786361	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8786263	8786361	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8786362	8786465	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8786466	8786656	0.97	-	2	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8786466	8786656	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8786657	8786803	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8786804	8787659	0.97	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8786804	8787659	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8787660	8787749	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8787750	8787818	1	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8787750	8787818	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	intron	8787819	8787904	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	CDS	8787905	8788468	0.99	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	exon	8787905	8788468	.	-	.	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
Phchi.S6	AUGUSTUS	start_codon	8788466	8788468	.	-	0	transcript_id "Phchi.S6G123600.t1"; gene_id "Phchi.S6G123600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10889.t1 is derived from g14939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2769234	2772808	.	-	.	Phchi.S4G047100
Phchi.S4	AUGUSTUS	transcript	2769234	2772808	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	stop_codon	2769231	2769233	.	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2769234	2769527	0.65	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2769234	2769527	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2769528	2769646	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2769647	2769886	1	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2769647	2769886	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2769887	2769966	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2769967	2770074	1	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2769967	2770074	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2770075	2770350	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2770351	2770436	0.81	-	2	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2770351	2770436	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2770437	2770522	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2770523	2770607	0.98	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2770523	2770607	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2770608	2770696	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2770697	2770882	0.71	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2770697	2770882	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2770883	2770980	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2770981	2771079	1	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2770981	2771079	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2771080	2771157	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2771158	2771296	0.54	-	1	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2771158	2771296	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2771297	2771400	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2771401	2771484	0.54	-	1	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2771401	2771484	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2771485	2771600	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2771601	2771695	1	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2771601	2771695	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2771696	2771847	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2771848	2771974	1	-	1	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2771848	2771974	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2771975	2772064	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2772065	2772168	1	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2772065	2772168	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2772169	2772249	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2772250	2772331	1	-	1	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2772250	2772331	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	intron	2772332	2772767	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	CDS	2772768	2772808	1	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	exon	2772768	2772808	.	-	.	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
Phchi.S4	AUGUSTUS	start_codon	2772806	2772808	.	-	0	transcript_id "Phchi.S4G047100.t1"; gene_id "Phchi.S4G047100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2196.t1 is derived from g9116.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5358963	5364248	.	-	.	Phchi.S5G080500
Phchi.S5	AUGUSTUS	transcript	5358963	5364248	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	stop_codon	5358960	5358962	.	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5358963	5359979	0.66	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5358963	5359979	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5359980	5360067	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5360068	5360334	1	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5360068	5360334	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5360335	5360468	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5360469	5360697	1	-	1	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5360469	5360697	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5360698	5360865	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5360866	5361285	0.81	-	1	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5360866	5361285	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5361286	5361431	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5361432	5361627	1	-	2	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5361432	5361627	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5361628	5361714	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5361715	5361988	1	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5361715	5361988	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5361989	5362068	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5362069	5362594	0.99	-	1	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5362069	5362594	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5362595	5362692	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5362693	5362931	1	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5362693	5362931	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5362932	5363065	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5363066	5363287	0.99	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5363066	5363287	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5363288	5363385	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5363386	5363561	0.86	-	2	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5363386	5363561	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5363562	5363679	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5363680	5363734	0.96	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5363680	5363734	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	intron	5363735	5363861	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	CDS	5363862	5364248	0.82	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	exon	5363862	5364248	.	-	.	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
Phchi.S5	AUGUSTUS	start_codon	5364246	5364248	.	-	0	transcript_id "Phchi.S5G080500.t1"; gene_id "Phchi.S5G080500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14176.t1 is derived from g12643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11280091	11284981	.	-	.	Phchi.S3G149500
Phchi.S3	AUGUSTUS	transcript	11280091	11284981	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	stop_codon	11280088	11280090	.	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11280091	11280237	0.99	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11280091	11280237	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11280238	11280375	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11280376	11280525	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11280376	11280525	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11280526	11280623	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11280624	11280729	1	-	1	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11280624	11280729	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11280730	11280822	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11280823	11281148	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11280823	11281148	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11281149	11281263	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11281264	11281401	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11281264	11281401	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11281402	11281490	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11281491	11281571	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11281491	11281571	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11281572	11281666	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11281667	11281849	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11281667	11281849	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11281850	11281949	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11281950	11282145	1	-	1	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11281950	11282145	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11282146	11282231	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11282232	11282338	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11282232	11282338	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11282339	11282422	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11282423	11282497	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11282423	11282497	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11282498	11282591	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11282592	11282747	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11282592	11282747	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11282748	11282887	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11282888	11282971	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11282888	11282971	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11282972	11283097	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11283098	11283211	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11283098	11283211	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11283212	11283307	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11283308	11283403	1	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11283308	11283403	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11283404	11283500	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11283501	11283591	1	-	1	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11283501	11283591	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11283592	11283697	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11283698	11283798	0.97	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11283698	11283798	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11283799	11283911	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11283912	11284122	1	-	1	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11283912	11284122	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	intron	11284123	11284766	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	CDS	11284767	11284981	0.76	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	exon	11284767	11284981	.	-	.	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
Phchi.S3	AUGUSTUS	start_codon	11284979	11284981	.	-	0	transcript_id "Phchi.S3G149500.t1"; gene_id "Phchi.S3G149500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8322.t1 is derived from g5497.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35285534	35287075	.	+	.	Phchi.S1G548100
Phchi.S1	AUGUSTUS	transcript	35285534	35287075	.	+	.	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	start_codon	35285534	35285536	.	+	0	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	CDS	35285534	35286106	0.79	+	0	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	exon	35285534	35286106	.	+	.	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	intron	35286107	35286248	.	+	.	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	CDS	35286249	35286669	0.65	+	0	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	exon	35286249	35286669	.	+	.	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	intron	35286670	35286758	.	+	.	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	CDS	35286759	35287075	0.74	+	2	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	exon	35286759	35287075	.	+	.	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
Phchi.S1	AUGUSTUS	stop_codon	35287076	35287078	.	+	0	transcript_id "Phchi.S1G548100.t1"; gene_id "Phchi.S1G548100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3884.t1 is derived from g1053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6201229	6204275	.	-	.	Phchi.S1G104300
Phchi.S1	AUGUSTUS	transcript	6201229	6204275	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	stop_codon	6201226	6201228	.	-	0	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	CDS	6201229	6202029	0.95	-	0	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	exon	6201229	6202029	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	intron	6202030	6202150	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	CDS	6202151	6202570	0.57	-	0	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	exon	6202151	6202570	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	intron	6202571	6202677	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	CDS	6202678	6203586	0.12	-	0	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	exon	6202678	6203586	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	intron	6203587	6203738	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	CDS	6203739	6204275	0.54	-	0	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	exon	6203739	6204275	.	-	.	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
Phchi.S1	AUGUSTUS	start_codon	6204273	6204275	.	-	0	transcript_id "Phchi.S1G104300.t1"; gene_id "Phchi.S1G104300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2426.t1 is derived from g9346.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6593672	6594908	.	-	.	Phchi.S5G103500
Phchi.S5	AUGUSTUS	transcript	6593672	6594908	.	-	.	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	stop_codon	6593669	6593671	.	-	0	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	CDS	6593672	6594179	0.79	-	1	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	exon	6593672	6594179	.	-	.	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	intron	6594180	6594368	.	-	.	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	CDS	6594369	6594523	0.23	-	0	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	exon	6594369	6594523	.	-	.	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	intron	6594524	6594650	.	-	.	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	CDS	6594651	6594908	0.29	-	0	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	exon	6594651	6594908	.	-	.	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
Phchi.S5	AUGUSTUS	start_codon	6594906	6594908	.	-	0	transcript_id "Phchi.S5G103500.t1"; gene_id "Phchi.S5G103500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2919.t1 is derived from g88.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	566296	567792	.	-	.	Phchi.S1G007800
Phchi.S1	AUGUSTUS	transcript	566296	567792	.	-	.	transcript_id "Phchi.S1G007800.t1"; gene_id "Phchi.S1G007800"
Phchi.S1	AUGUSTUS	stop_codon	566293	566295	.	-	0	transcript_id "Phchi.S1G007800.t1"; gene_id "Phchi.S1G007800"
Phchi.S1	AUGUSTUS	CDS	566296	567792	0.93	-	0	transcript_id "Phchi.S1G007800.t1"; gene_id "Phchi.S1G007800"
Phchi.S1	AUGUSTUS	exon	566296	567792	.	-	.	transcript_id "Phchi.S1G007800.t1"; gene_id "Phchi.S1G007800"
Phchi.S1	AUGUSTUS	start_codon	567790	567792	.	-	0	transcript_id "Phchi.S1G007800.t1"; gene_id "Phchi.S1G007800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9345.t1 is derived from g6520.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41065845	41066681	.	+	.	Phchi.S1G650400
Phchi.S1	AUGUSTUS	transcript	41065845	41066681	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	start_codon	41065845	41065847	.	+	0	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	CDS	41065845	41065879	1	+	0	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	exon	41065845	41065879	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	intron	41065880	41066058	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	CDS	41066059	41066233	0.99	+	1	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	exon	41066059	41066233	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	intron	41066234	41066364	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	CDS	41066365	41066426	0.56	+	0	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	exon	41066365	41066426	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	intron	41066427	41066521	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	CDS	41066522	41066569	0.56	+	1	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	exon	41066522	41066569	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	intron	41066570	41066659	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	CDS	41066660	41066681	1	+	1	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	exon	41066660	41066681	.	+	.	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
Phchi.S1	AUGUSTUS	stop_codon	41066682	41066684	.	+	0	transcript_id "Phchi.S1G650400.t1"; gene_id "Phchi.S1G650400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5994.t1 is derived from g3165.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20288378	20290679	.	-	.	Phchi.S1G315300
Phchi.S1	AUGUSTUS	transcript	20288378	20290679	.	-	.	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	stop_codon	20288375	20288377	.	-	0	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	CDS	20288378	20289346	0.37	-	0	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	exon	20288378	20289346	.	-	.	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	intron	20289347	20289471	.	-	.	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	CDS	20289472	20289771	0.88	-	0	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	exon	20289472	20289771	.	-	.	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	intron	20289772	20289866	.	-	.	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	CDS	20289867	20290679	0.92	-	0	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	exon	20289867	20290679	.	-	.	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
Phchi.S1	AUGUSTUS	start_codon	20290677	20290679	.	-	0	transcript_id "Phchi.S1G315300.t1"; gene_id "Phchi.S1G315300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5529.t1 is derived from g2699.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17425051	17429466	.	-	.	Phchi.S1G268800
Phchi.S1	AUGUSTUS	transcript	17425051	17429466	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	stop_codon	17425048	17425050	.	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17425051	17425122	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17425051	17425122	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17425123	17425220	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17425221	17425292	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17425221	17425292	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17425293	17425375	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17425376	17425438	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17425376	17425438	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17425439	17425517	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17425518	17425623	1	-	1	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17425518	17425623	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17425624	17425717	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17425718	17425812	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17425718	17425812	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17425813	17425912	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17425913	17425942	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17425913	17425942	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17425943	17426037	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17426038	17426109	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17426038	17426109	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17426110	17426199	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17426200	17426259	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17426200	17426259	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17426260	17426394	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17426395	17426441	1	-	2	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17426395	17426441	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17426442	17426525	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17426526	17426590	1	-	1	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17426526	17426590	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17426591	17426682	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17426683	17426771	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17426683	17426771	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17426772	17426895	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17426896	17426934	0.99	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17426896	17426934	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17426935	17427058	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17427059	17427118	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17427059	17427118	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17427119	17427205	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17427206	17427278	1	-	1	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17427206	17427278	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17427279	17427449	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17427450	17427619	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17427450	17427619	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17427620	17427696	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17427697	17427777	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17427697	17427777	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17427778	17427903	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17427904	17428035	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17427904	17428035	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17428036	17428129	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17428130	17428224	1	-	2	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17428130	17428224	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17428225	17428320	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17428321	17428444	1	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17428321	17428444	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17428445	17428553	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17428554	17428698	0.98	-	1	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17428554	17428698	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17428699	17428778	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17428779	17428920	1	-	2	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17428779	17428920	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17428921	17429007	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17429008	17429111	1	-	1	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17429008	17429111	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	intron	17429112	17429197	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	CDS	17429198	17429466	0.7	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	exon	17429198	17429466	.	-	.	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
Phchi.S1	AUGUSTUS	start_codon	17429464	17429466	.	-	0	transcript_id "Phchi.S1G268800.t1"; gene_id "Phchi.S1G268800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg5240.t1 is derived from g2410.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15806322	15809808	.	-	.	Phchi.S1G239900
Phchi.S1	AUGUSTUS	transcript	15808871	15809808	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	stop_codon	15808868	15808870	.	-	0	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808871	15808894	1	-	0	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808871	15808894	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808895	15809058	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809059	15809103	1	-	0	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809059	15809103	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15809104	15809273	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809274	15809398	1	-	2	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809274	15809398	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15809399	15809529	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809530	15809600	1	-	1	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809530	15809600	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15809601	15809698	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809699	15809808	1	-	0	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809699	15809808	.	-	.	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	start_codon	15809806	15809808	.	-	0	transcript_id "Phchi.S1G239900.t1"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	transcript	15806322	15809808	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	stop_codon	15806319	15806321	.	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15806322	15806819	0.82	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15806322	15806819	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15806820	15806893	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15806894	15807224	1	-	1	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15806894	15807224	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15807225	15807310	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15807311	15807438	1	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15807311	15807438	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15807439	15807519	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15807520	15807963	1	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15807520	15807963	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15807964	15808112	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808113	15808203	0.98	-	1	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808113	15808203	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808204	15808334	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808335	15808444	1	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808335	15808444	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808445	15808540	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808541	15808650	1	-	2	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808541	15808650	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808651	15808786	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808787	15808889	1	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808787	15808889	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808890	15809058	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809059	15809103	1	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809059	15809103	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15809104	15809273	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809274	15809398	1	-	2	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809274	15809398	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15809399	15809529	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809530	15809600	1	-	1	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809530	15809600	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15809601	15809698	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15809699	15809808	1	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15809699	15809808	.	-	.	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	start_codon	15809806	15809808	.	-	0	transcript_id "Phchi.S1G239900.t2"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	transcript	15806322	15808829	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	stop_codon	15806319	15806321	.	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15806322	15806819	0.95	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15806322	15806819	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15806820	15806893	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15806894	15807224	1	-	1	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15806894	15807224	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15807225	15807310	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15807311	15807438	1	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15807311	15807438	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15807439	15807519	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15807520	15807963	1	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15807520	15807963	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15807964	15808112	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808113	15808203	0.99	-	1	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808113	15808203	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808204	15808334	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808335	15808444	1	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808335	15808444	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808445	15808540	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808541	15808650	1	-	2	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808541	15808650	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	intron	15808651	15808786	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	CDS	15808787	15808829	0.52	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	exon	15808787	15808829	.	-	.	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
Phchi.S1	AUGUSTUS	start_codon	15808827	15808829	.	-	0	transcript_id "Phchi.S1G239900.t3"; gene_id "Phchi.S1G239900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10725.t1 is derived from g14775.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1770223	1773361	.	+	.	Phchi.S4G030700
Phchi.S4	AUGUSTUS	transcript	1770223	1773361	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	start_codon	1770223	1770225	.	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1770223	1770341	0.79	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1770223	1770341	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1770342	1770564	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1770565	1770657	0.81	+	1	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1770565	1770657	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1770658	1770896	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1770897	1770954	1	+	1	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1770897	1770954	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1770955	1771161	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1771162	1771270	1	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1771162	1771270	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1771271	1771396	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1771397	1771608	1	+	2	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1771397	1771608	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1771609	1771708	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1771709	1771960	1	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1771709	1771960	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1771961	1772044	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1772045	1772121	1	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1772045	1772121	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1772122	1772215	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1772216	1772363	0.45	+	1	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1772216	1772363	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1772364	1772476	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1772477	1772626	0.45	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1772477	1772626	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1772627	1772779	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1772780	1772839	1	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1772780	1772839	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1772840	1772918	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1772919	1772998	1	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1772919	1772998	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	intron	1772999	1773117	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	CDS	1773118	1773361	0.51	+	1	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	exon	1773118	1773361	.	+	.	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
Phchi.S4	AUGUSTUS	stop_codon	1773362	1773364	.	+	0	transcript_id "Phchi.S4G030700.t1"; gene_id "Phchi.S4G030700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15643.t1 is derived from g14112.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20455837	20462513	.	+	.	Phchi.S3G296200
Phchi.S3	AUGUSTUS	transcript	20455837	20462513	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	start_codon	20455837	20455839	.	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20455837	20455898	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20455837	20455898	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20455899	20455992	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20455993	20456236	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20455993	20456236	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20456237	20456364	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20456365	20456589	0.9	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20456365	20456589	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20456590	20456704	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20456705	20456902	0.94	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20456705	20456902	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20456903	20457003	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20457004	20457458	0.92	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20457004	20457458	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20457459	20457572	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20457573	20457711	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20457573	20457711	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20457712	20457796	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20457797	20457875	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20457797	20457875	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20457876	20457965	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20457966	20458204	1	+	2	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20457966	20458204	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20458205	20458365	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20458366	20458670	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20458366	20458670	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20458671	20458759	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20458760	20458868	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20458760	20458868	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20458869	20458948	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20458949	20459110	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20458949	20459110	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20459111	20459189	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20459190	20459289	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20459190	20459289	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20459290	20459367	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20459368	20459476	1	+	2	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20459368	20459476	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20459477	20459568	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20459569	20459659	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20459569	20459659	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20459660	20459763	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20459764	20459888	0.99	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20459764	20459888	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20459889	20460085	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20460086	20460235	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20460086	20460235	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20460236	20460391	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20460392	20460464	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20460392	20460464	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20460465	20460550	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20460551	20460731	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20460551	20460731	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20460732	20460816	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20460817	20460975	1	+	2	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20460817	20460975	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20460976	20461074	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20461075	20461251	1	+	2	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20461075	20461251	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20461252	20461373	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20461374	20461604	1	+	2	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20461374	20461604	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20461605	20461694	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20461695	20461891	0.99	+	2	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20461695	20461891	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20461892	20461999	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20462000	20462052	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20462000	20462052	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20462053	20462171	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20462172	20462250	1	+	1	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20462172	20462250	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	intron	20462251	20462375	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	CDS	20462376	20462513	1	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	exon	20462376	20462513	.	+	.	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
Phchi.S3	AUGUSTUS	stop_codon	20462514	20462516	.	+	0	transcript_id "Phchi.S3G296200.t1"; gene_id "Phchi.S3G296200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10396.t1 is derived from g7572.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	47536698	47537268	.	+	.	Phchi.S1G755500
Phchi.S1	AUGUSTUS	transcript	47536698	47537268	.	+	.	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	start_codon	47536698	47536700	.	+	0	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	CDS	47536698	47536851	0.99	+	0	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	exon	47536698	47536851	.	+	.	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	intron	47536852	47536948	.	+	.	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	CDS	47536949	47537016	0.99	+	2	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	exon	47536949	47537016	.	+	.	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	intron	47537017	47537082	.	+	.	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	CDS	47537083	47537268	0.47	+	0	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	exon	47537083	47537268	.	+	.	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
Phchi.S1	AUGUSTUS	stop_codon	47537269	47537271	.	+	0	transcript_id "Phchi.S1G755500.t1"; gene_id "Phchi.S1G755500"
# This transcript jg14509.t2 is derived from g12977.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14510.t1 is derived from g12978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13234639	13238571	.	+	.	Phchi.S3G182900
Phchi.S3	AUGUSTUS	transcript	13234639	13238571	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	start_codon	13234639	13234641	.	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13234639	13234800	1	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13234639	13234800	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13234801	13235682	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13235683	13235946	1	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13235683	13235946	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13235947	13236162	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13236163	13236268	1	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13236163	13236268	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13236269	13236409	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13236410	13236509	1	+	2	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13236410	13236509	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13236510	13236669	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13236670	13236775	1	+	1	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13236670	13236775	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13236776	13236975	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13236976	13237066	1	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13236976	13237066	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13237067	13237201	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13237202	13237343	1	+	2	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13237202	13237343	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13237344	13237444	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13237445	13237592	1	+	1	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13237445	13237592	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13237593	13237683	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13237684	13237793	1	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13237684	13237793	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13237794	13237944	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13237945	13238101	1	+	1	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13237945	13238101	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13238102	13238191	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13238192	13238317	1	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13238192	13238317	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	intron	13238318	13238433	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	CDS	13238434	13238571	0.98	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	exon	13238434	13238571	.	+	.	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
Phchi.S3	AUGUSTUS	stop_codon	13238572	13238574	.	+	0	transcript_id "Phchi.S3G182900.t1"; gene_id "Phchi.S3G182900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2104.t1 is derived from g9024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4888115	4892392	.	+	.	Phchi.S5G071300
Phchi.S5	AUGUSTUS	transcript	4888115	4892392	.	+	.	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	start_codon	4888115	4888117	.	+	0	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	CDS	4888115	4888659	0.57	+	0	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	exon	4888115	4888659	.	+	.	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	intron	4888660	4888749	.	+	.	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	CDS	4888750	4892392	0.42	+	1	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	exon	4888750	4892392	.	+	.	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
Phchi.S5	AUGUSTUS	stop_codon	4892393	4892395	.	+	0	transcript_id "Phchi.S5G071300.t1"; gene_id "Phchi.S5G071300"
# This transcript jg7823.t2 is derived from g4997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7824.t1 is derived from g4998.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31381383	31382114	.	+	.	Phchi.S1G498300
Phchi.S1	AUGUSTUS	transcript	31381383	31382114	.	+	.	transcript_id "Phchi.S1G498300.t1"; gene_id "Phchi.S1G498300"
Phchi.S1	AUGUSTUS	start_codon	31381383	31381385	.	+	0	transcript_id "Phchi.S1G498300.t1"; gene_id "Phchi.S1G498300"
Phchi.S1	AUGUSTUS	CDS	31381383	31382114	1	+	0	transcript_id "Phchi.S1G498300.t1"; gene_id "Phchi.S1G498300"
Phchi.S1	AUGUSTUS	exon	31381383	31382114	.	+	.	transcript_id "Phchi.S1G498300.t1"; gene_id "Phchi.S1G498300"
Phchi.S1	AUGUSTUS	stop_codon	31382115	31382117	.	+	0	transcript_id "Phchi.S1G498300.t1"; gene_id "Phchi.S1G498300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg810.t1 is derived from g10592.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5694629	5695282	.	+	.	Phchi.S6G076900
Phchi.S6	AUGUSTUS	transcript	5694629	5695282	.	+	.	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	start_codon	5694629	5694631	.	+	0	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	CDS	5694629	5694865	1	+	0	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	exon	5694629	5694865	.	+	.	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	intron	5694866	5695027	.	+	.	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	CDS	5695028	5695282	1	+	0	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	exon	5695028	5695282	.	+	.	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
Phchi.S6	AUGUSTUS	stop_codon	5695283	5695285	.	+	0	transcript_id "Phchi.S6G076900.t1"; gene_id "Phchi.S6G076900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4230.t1 is derived from g1399.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9024855	9026278	.	+	.	Phchi.S1G138900
Phchi.S1	AUGUSTUS	transcript	9024855	9026278	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	start_codon	9024855	9024857	.	+	0	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9024855	9024893	0.95	+	0	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9024855	9024893	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	intron	9024894	9025029	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9025030	9025132	0.97	+	0	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9025030	9025132	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	intron	9025133	9025275	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9025276	9025370	0.51	+	2	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9025276	9025370	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	intron	9025371	9025459	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9025460	9025553	0.51	+	0	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9025460	9025553	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	intron	9025554	9025663	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9025664	9025788	1	+	2	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9025664	9025788	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	intron	9025789	9025910	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9025911	9026029	0.91	+	0	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9025911	9026029	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	intron	9026030	9026151	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	CDS	9026152	9026278	1	+	1	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	exon	9026152	9026278	.	+	.	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
Phchi.S1	AUGUSTUS	stop_codon	9026279	9026281	.	+	0	transcript_id "Phchi.S1G138900.t1"; gene_id "Phchi.S1G138900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1061.t1 is derived from g10844.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7366135	7368494	.	-	.	Phchi.S6G102000
Phchi.S6	AUGUSTUS	transcript	7366135	7368494	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	stop_codon	7366132	7366134	.	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7366135	7366225	1	-	1	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7366135	7366225	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7366226	7366339	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7366340	7366423	1	-	1	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7366340	7366423	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7366424	7366521	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7366522	7366571	1	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7366522	7366571	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7366572	7366662	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7366663	7366769	1	-	2	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7366663	7366769	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7366770	7366870	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7366871	7366949	0.99	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7366871	7366949	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7366950	7367029	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7367030	7367119	0.99	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7367030	7367119	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7367120	7367227	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7367228	7367479	1	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7367228	7367479	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7367480	7367584	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7367585	7367737	1	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7367585	7367737	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7367738	7367825	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7367826	7368150	0.84	-	1	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7367826	7368150	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	intron	7368151	7368255	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	CDS	7368256	7368494	0.47	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	exon	7368256	7368494	.	-	.	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
Phchi.S6	AUGUSTUS	start_codon	7368492	7368494	.	-	0	transcript_id "Phchi.S6G102000.t1"; gene_id "Phchi.S6G102000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1316.t1 is derived from g11099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8987053	8990359	.	+	.	Phchi.S6G127500
Phchi.S6	AUGUSTUS	transcript	8987053	8990359	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	start_codon	8987053	8987055	.	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8987053	8987100	0.82	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8987053	8987100	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8987101	8987306	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8987307	8987706	0.96	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8987307	8987706	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8987707	8987837	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8987838	8988202	1	+	2	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8987838	8988202	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8988203	8988454	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8988455	8988565	1	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8988455	8988565	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8988566	8988690	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8988691	8989086	0.96	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8988691	8989086	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8989087	8989208	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8989209	8989388	1	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8989209	8989388	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8989389	8989508	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8989509	8989555	1	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8989509	8989555	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8989556	8989665	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8989666	8990000	1	+	1	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8989666	8990000	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	intron	8990001	8990087	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	CDS	8990088	8990359	0.99	+	2	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	exon	8990088	8990359	.	+	.	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
Phchi.S6	AUGUSTUS	stop_codon	8990360	8990362	.	+	0	transcript_id "Phchi.S6G127500.t1"; gene_id "Phchi.S6G127500"
# This transcript jg7832.t2 is derived from g5006.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7833.t1 is derived from g5007.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31428472	31430542	.	-	.	Phchi.S1G499200
Phchi.S1	AUGUSTUS	transcript	31428472	31430542	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	stop_codon	31428469	31428471	.	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31428472	31428645	0.97	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31428472	31428645	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31428646	31428734	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31428735	31428875	1	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31428735	31428875	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31428876	31428947	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31428948	31429043	1	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31428948	31429043	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31429044	31429131	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31429132	31429224	1	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31429132	31429224	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31429225	31429381	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31429382	31429576	1	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31429382	31429576	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31429577	31429695	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31429696	31429794	1	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31429696	31429794	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31429795	31429887	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31429888	31430120	1	-	2	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31429888	31430120	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	intron	31430121	31430235	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	CDS	31430236	31430542	0.99	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	exon	31430236	31430542	.	-	.	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
Phchi.S1	AUGUSTUS	start_codon	31430540	31430542	.	-	0	transcript_id "Phchi.S1G499200.t1"; gene_id "Phchi.S1G499200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7874.t1 is derived from g5048.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31654248	31661753	.	-	.	Phchi.S1G503300
Phchi.S1	AUGUSTUS	transcript	31661236	31661753	.	-	.	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	stop_codon	31661233	31661235	.	-	0	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31661236	31661262	0.72	-	0	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31661236	31661262	.	-	.	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31661263	31661420	.	-	.	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31661421	31661616	1	-	1	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31661421	31661616	.	-	.	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31661617	31661748	.	-	.	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31661749	31661753	0.95	-	0	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31661749	31661753	.	-	.	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	start_codon	31661751	31661753	.	-	0	transcript_id "Phchi.S1G503300.t1"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	transcript	31654248	31661753	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	stop_codon	31654245	31654247	.	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31654248	31654362	0.98	-	1	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31654248	31654362	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31654363	31654460	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31654461	31654510	0.98	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31654461	31654510	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31654511	31654666	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31654667	31654715	0.52	-	1	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31654667	31654715	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31654716	31655025	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31655026	31655783	0.32	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31655026	31655783	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31655784	31655932	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31655933	31656043	1	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31655933	31656043	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31656044	31656213	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31656214	31656303	1	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31656214	31656303	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31656304	31656379	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31656380	31656484	1	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31656380	31656484	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31656485	31656568	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31656569	31657729	0.65	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31656569	31657729	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31657730	31657847	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31657848	31659683	1	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31657848	31659683	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31659684	31659875	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31659876	31660546	0.89	-	2	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31659876	31660546	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31660547	31660632	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31660633	31660684	0.81	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31660633	31660684	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31660685	31660759	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31660760	31661056	0.72	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31660760	31661056	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31661057	31661420	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31661421	31661616	1	-	1	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31661421	31661616	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	intron	31661617	31661748	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	CDS	31661749	31661753	0.94	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	exon	31661749	31661753	.	-	.	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
Phchi.S1	AUGUSTUS	start_codon	31661751	31661753	.	-	0	transcript_id "Phchi.S1G503300.t2"; gene_id "Phchi.S1G503300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4380.t1 is derived from g1549.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10168271	10168699	.	+	.	Phchi.S1G153900
Phchi.S1	AUGUSTUS	transcript	10168271	10168699	.	+	.	transcript_id "Phchi.S1G153900.t1"; gene_id "Phchi.S1G153900"
Phchi.S1	AUGUSTUS	start_codon	10168271	10168273	.	+	0	transcript_id "Phchi.S1G153900.t1"; gene_id "Phchi.S1G153900"
Phchi.S1	AUGUSTUS	CDS	10168271	10168699	0.4	+	0	transcript_id "Phchi.S1G153900.t1"; gene_id "Phchi.S1G153900"
Phchi.S1	AUGUSTUS	exon	10168271	10168699	.	+	.	transcript_id "Phchi.S1G153900.t1"; gene_id "Phchi.S1G153900"
Phchi.S1	AUGUSTUS	stop_codon	10168700	10168702	.	+	0	transcript_id "Phchi.S1G153900.t1"; gene_id "Phchi.S1G153900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9086.t1 is derived from g6261.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39789035	39793912	.	-	.	Phchi.S1G624500
Phchi.S1	AUGUSTUS	transcript	39790261	39793912	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	stop_codon	39790258	39790260	.	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39790261	39790299	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39790261	39790299	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39790300	39790453	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39790454	39790530	0.99	-	2	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39790454	39790530	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39790531	39790852	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39790853	39790925	0.97	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39790853	39790925	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39790926	39791011	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791012	39791176	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791012	39791176	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791177	39791262	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791263	39791330	1	-	2	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791263	39791330	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791331	39791410	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791411	39791546	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791411	39791546	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791547	39791701	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791702	39791807	1	-	1	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791702	39791807	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791808	39791943	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791944	39792094	1	-	2	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791944	39792094	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792095	39792190	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792191	39792255	1	-	1	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792191	39792255	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792256	39792357	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792358	39792512	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792358	39792512	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792513	39792631	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792632	39792694	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792632	39792694	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792695	39792812	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792813	39792884	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792813	39792884	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792885	39793000	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793001	39793046	1	-	1	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793001	39793046	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39793047	39793151	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793152	39793263	0.99	-	2	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793152	39793263	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39793264	39793382	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793383	39793517	1	-	2	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793383	39793517	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39793518	39793728	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793729	39793912	1	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793729	39793912	.	-	.	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	start_codon	39793910	39793912	.	-	0	transcript_id "Phchi.S1G624500.t1"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	transcript	39789035	39793912	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	stop_codon	39789032	39789034	.	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39789035	39789248	1	-	1	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39789035	39789248	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39789249	39789484	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39789485	39789901	0.75	-	1	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39789485	39789901	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39789902	39790250	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39790251	39790299	0.79	-	2	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39790251	39790299	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39790300	39790437	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39790438	39790530	0.98	-	2	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39790438	39790530	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39790531	39790852	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39790853	39790925	1	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39790853	39790925	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39790926	39791011	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791012	39791176	1	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791012	39791176	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791177	39791262	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791263	39791330	1	-	2	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791263	39791330	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791331	39791410	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791411	39791546	1	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791411	39791546	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791547	39791701	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791702	39791807	1	-	1	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791702	39791807	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39791808	39791943	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39791944	39792094	1	-	2	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39791944	39792094	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792095	39792190	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792191	39792255	1	-	1	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792191	39792255	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792256	39792357	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792358	39792512	1	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792358	39792512	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792513	39792631	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792632	39792694	1	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792632	39792694	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792695	39792812	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39792813	39792884	1	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39792813	39792884	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39792885	39793000	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793001	39793046	1	-	1	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793001	39793046	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39793047	39793151	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793152	39793263	0.98	-	2	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793152	39793263	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39793264	39793382	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793383	39793517	1	-	2	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793383	39793517	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39793518	39793728	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39793729	39793912	0.99	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39793729	39793912	.	-	.	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	start_codon	39793910	39793912	.	-	0	transcript_id "Phchi.S1G624500.t2"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	transcript	39789035	39789627	.	-	.	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	stop_codon	39789032	39789034	.	-	0	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39789035	39789248	1	-	1	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39789035	39789248	.	-	.	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	intron	39789249	39789484	.	-	.	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	CDS	39789485	39789627	0.85	-	0	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	exon	39789485	39789627	.	-	.	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
Phchi.S1	AUGUSTUS	start_codon	39789625	39789627	.	-	0	transcript_id "Phchi.S1G624500.t3"; gene_id "Phchi.S1G624500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5409.t1 is derived from g2579.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16731265	16732814	.	-	.	Phchi.S1G256800
Phchi.S1	AUGUSTUS	transcript	16731265	16732814	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	stop_codon	16731262	16731264	.	-	0	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	CDS	16731265	16731364	0.78	-	1	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	exon	16731265	16731364	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	intron	16731365	16731464	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	CDS	16731465	16731567	0.65	-	2	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	exon	16731465	16731567	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	intron	16731568	16731666	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	CDS	16731667	16731925	0.77	-	0	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	exon	16731667	16731925	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	intron	16731926	16732012	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	CDS	16732013	16732252	0.89	-	0	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	exon	16732013	16732252	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	intron	16732253	16732340	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	CDS	16732341	16732465	0.84	-	2	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	exon	16732341	16732465	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	intron	16732466	16732543	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	CDS	16732544	16732814	0.88	-	0	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	exon	16732544	16732814	.	-	.	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
Phchi.S1	AUGUSTUS	start_codon	16732812	16732814	.	-	0	transcript_id "Phchi.S1G256800.t1"; gene_id "Phchi.S1G256800"
# This transcript jg4931.t2 is derived from g2101.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4932.t1 is derived from g2102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13622521	13624683	.	+	.	Phchi.S1G209100
Phchi.S1	AUGUSTUS	transcript	13622521	13624683	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	start_codon	13622521	13622523	.	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13622521	13622732	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13622521	13622732	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13622733	13622817	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13622818	13622937	1	+	1	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13622818	13622937	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13622938	13623046	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13623047	13623232	1	+	1	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13623047	13623232	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13623233	13623309	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13623310	13623361	1	+	1	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13623310	13623361	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13623362	13623453	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13623454	13623519	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13623454	13623519	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13623520	13623620	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13623621	13623707	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13623621	13623707	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13623708	13623793	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13623794	13623886	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13623794	13623886	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13623887	13623975	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13623976	13624056	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13623976	13624056	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13624057	13624129	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13624130	13624201	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13624130	13624201	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13624202	13624284	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13624285	13624353	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13624285	13624353	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13624354	13624435	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13624436	13624546	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13624436	13624546	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	intron	13624547	13624635	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	CDS	13624636	13624683	1	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	exon	13624636	13624683	.	+	.	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
Phchi.S1	AUGUSTUS	stop_codon	13624684	13624686	.	+	0	transcript_id "Phchi.S1G209100.t1"; gene_id "Phchi.S1G209100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12538.t1 is derived from g8215.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	33718093	33722690	.	-	.	Phchi.S2G061800
Phchi.S2	AUGUSTUS	transcript	33718093	33722690	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	stop_codon	33718090	33718092	.	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33718093	33718243	1	-	1	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33718093	33718243	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33718244	33718343	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33718344	33718459	1	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33718344	33718459	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33718460	33718538	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33718539	33718642	1	-	2	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33718539	33718642	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33718643	33718838	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33718839	33719090	0.99	-	2	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33718839	33719090	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33719091	33719158	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33719159	33719257	0.67	-	2	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33719159	33719257	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33719258	33719329	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33719330	33719416	1	-	2	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33719330	33719416	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33719417	33719645	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33719646	33719676	1	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33719646	33719676	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33719677	33719852	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33719853	33719931	0.68	-	1	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33719853	33719931	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33719932	33720154	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33720155	33720171	0.61	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33720155	33720171	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33720172	33720400	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33720401	33720438	0.59	-	2	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33720401	33720438	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33720439	33720617	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33720618	33720764	0.76	-	2	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33720618	33720764	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33720765	33720889	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33720890	33721088	0.82	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33720890	33721088	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33721089	33721174	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33721175	33721198	0.53	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33721175	33721198	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	intron	33721199	33721307	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	CDS	33721308	33722690	0.29	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	exon	33721308	33722690	.	-	.	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
Phchi.S2	AUGUSTUS	start_codon	33722688	33722690	.	-	0	transcript_id "Phchi.S2G061800.t1"; gene_id "Phchi.S2G061800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg535.t1 is derived from g10317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3894083	3896205	.	-	.	Phchi.S6G049400
Phchi.S6	AUGUSTUS	transcript	3894083	3896205	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	stop_codon	3894080	3894082	.	-	0	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	CDS	3894083	3894338	1	-	1	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	exon	3894083	3894338	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	intron	3894339	3894472	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	CDS	3894473	3894843	1	-	0	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	exon	3894473	3894843	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	intron	3894844	3895014	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	CDS	3895015	3895317	0.79	-	0	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	exon	3895015	3895317	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	intron	3895318	3895461	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	CDS	3895462	3895696	1	-	1	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	exon	3895462	3895696	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	intron	3895697	3895804	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	CDS	3895805	3896205	0.98	-	0	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	exon	3895805	3896205	.	-	.	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
Phchi.S6	AUGUSTUS	start_codon	3896203	3896205	.	-	0	transcript_id "Phchi.S6G049400.t1"; gene_id "Phchi.S6G049400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5022.t1 is derived from g2192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14092137	14094789	.	-	.	Phchi.S1G218100
Phchi.S1	AUGUSTUS	transcript	14092137	14094789	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	stop_codon	14092134	14092136	.	-	0	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	CDS	14092137	14093197	1	-	2	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	exon	14092137	14093197	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	intron	14093198	14093341	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	CDS	14093342	14093585	0.9	-	0	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	exon	14093342	14093585	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	intron	14093586	14093775	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	CDS	14093776	14094288	0.92	-	0	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	exon	14093776	14094288	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	intron	14094289	14094374	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	CDS	14094375	14094395	0.99	-	0	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	exon	14094375	14094395	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	intron	14094396	14094744	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	CDS	14094745	14094789	0.35	-	0	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	exon	14094745	14094789	.	-	.	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
Phchi.S1	AUGUSTUS	start_codon	14094787	14094789	.	-	0	transcript_id "Phchi.S1G218100.t1"; gene_id "Phchi.S1G218100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5100.t1 is derived from g2270.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14739897	14744511	.	-	.	Phchi.S1G225900
Phchi.S1	AUGUSTUS	transcript	14739897	14744511	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	stop_codon	14739894	14739896	.	-	0	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14739897	14740006	0.65	-	2	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14739897	14740006	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14740007	14740258	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14740259	14740461	0.24	-	1	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14740259	14740461	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14740462	14740652	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14740653	14740878	0.87	-	2	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14740653	14740878	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14740879	14741006	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14741007	14741130	1	-	0	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14741007	14741130	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14741131	14741204	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14741205	14741317	0.82	-	2	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14741205	14741317	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14741318	14741606	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14741607	14741655	0.92	-	0	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14741607	14741655	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14741656	14741739	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14741740	14741986	0.82	-	1	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14741740	14741986	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14741987	14742078	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14742079	14742411	0.81	-	1	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14742079	14742411	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14742412	14742578	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14742579	14742805	1	-	0	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14742579	14742805	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14742806	14742906	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14742907	14742961	1	-	1	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14742907	14742961	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	intron	14742962	14743102	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	CDS	14743103	14744511	1	-	0	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	exon	14743103	14744511	.	-	.	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
Phchi.S1	AUGUSTUS	start_codon	14744509	14744511	.	-	0	transcript_id "Phchi.S1G225900.t1"; gene_id "Phchi.S1G225900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2505.t1 is derived from g9425.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7008256	7010175	.	+	.	Phchi.S5G111400
Phchi.S5	AUGUSTUS	transcript	7008256	7010175	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	start_codon	7008256	7008258	.	+	0	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	CDS	7008256	7008657	0.79	+	0	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	exon	7008256	7008657	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	intron	7008658	7008770	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	CDS	7008771	7009073	1	+	0	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	exon	7008771	7009073	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	intron	7009074	7009184	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	CDS	7009185	7009355	1	+	0	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	exon	7009185	7009355	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	intron	7009356	7009810	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	CDS	7009811	7009913	0.94	+	0	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	exon	7009811	7009913	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	intron	7009914	7010044	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	CDS	7010045	7010175	0.86	+	2	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	exon	7010045	7010175	.	+	.	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
Phchi.S5	AUGUSTUS	stop_codon	7010176	7010178	.	+	0	transcript_id "Phchi.S5G111400.t1"; gene_id "Phchi.S5G111400"
# This transcript jg9837.t2 is derived from g7013.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg9838.t1 is derived from g7014.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44015406	44017205	.	-	.	Phchi.S1G699700
Phchi.S1	AUGUSTUS	transcript	44015406	44016251	.	-	.	transcript_id "Phchi.S1G699700.t1"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	stop_codon	44015403	44015405	.	-	0	transcript_id "Phchi.S1G699700.t1"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	CDS	44015406	44016251	1	-	0	transcript_id "Phchi.S1G699700.t1"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	exon	44015406	44016251	.	-	.	transcript_id "Phchi.S1G699700.t1"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	start_codon	44016249	44016251	.	-	0	transcript_id "Phchi.S1G699700.t1"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	transcript	44015406	44017205	.	-	.	transcript_id "Phchi.S1G699700.t2"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	stop_codon	44015403	44015405	.	-	0	transcript_id "Phchi.S1G699700.t2"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	CDS	44015406	44017205	1	-	0	transcript_id "Phchi.S1G699700.t2"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	exon	44015406	44017205	.	-	.	transcript_id "Phchi.S1G699700.t2"; gene_id "Phchi.S1G699700"
Phchi.S1	AUGUSTUS	start_codon	44017203	44017205	.	-	0	transcript_id "Phchi.S1G699700.t2"; gene_id "Phchi.S1G699700"
# This transcript jg5803.t2 is derived from g2973.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5804.t1 is derived from g2974.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19028746	19030488	.	+	.	Phchi.S1G296300
Phchi.S1	AUGUSTUS	transcript	19028746	19030488	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	start_codon	19028746	19028748	.	+	0	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19028746	19028912	0.95	+	0	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19028746	19028912	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	intron	19028913	19029119	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19029120	19029292	1	+	1	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19029120	19029292	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	intron	19029293	19029384	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19029385	19029494	1	+	2	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19029385	19029494	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	intron	19029495	19029654	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19029655	19029773	1	+	0	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19029655	19029773	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	intron	19029774	19029970	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19029971	19029986	0.3	+	1	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19029971	19029986	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	intron	19029987	19030092	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19030093	19030111	1	+	0	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19030093	19030111	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	intron	19030112	19030339	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	CDS	19030340	19030488	0.93	+	2	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	exon	19030340	19030488	.	+	.	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
Phchi.S1	AUGUSTUS	stop_codon	19030489	19030491	.	+	0	transcript_id "Phchi.S1G296300.t1"; gene_id "Phchi.S1G296300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14866.t1 is derived from g13334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15101212	15101874	.	-	.	Phchi.S3G218500
Phchi.S3	AUGUSTUS	transcript	15101212	15101874	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	stop_codon	15101209	15101211	.	-	0	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	CDS	15101212	15101233	0.93	-	1	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	exon	15101212	15101233	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	intron	15101234	15101325	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	CDS	15101326	15101356	0.87	-	2	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	exon	15101326	15101356	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	intron	15101357	15101499	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	CDS	15101500	15101594	0.55	-	1	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	exon	15101500	15101594	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	intron	15101595	15101671	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	CDS	15101672	15101874	0.95	-	0	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	exon	15101672	15101874	.	-	.	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
Phchi.S3	AUGUSTUS	start_codon	15101872	15101874	.	-	0	transcript_id "Phchi.S3G218500.t1"; gene_id "Phchi.S3G218500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10803.t1 is derived from g14853.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2176848	2179557	.	+	.	Phchi.S4G038500
Phchi.S4	AUGUSTUS	transcript	2176848	2179557	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	start_codon	2176848	2176850	.	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2176848	2176934	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2176848	2176934	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2176935	2177047	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2177048	2177110	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2177048	2177110	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2177111	2177198	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2177199	2177282	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2177199	2177282	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2177283	2177491	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2177492	2177599	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2177492	2177599	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2177600	2177749	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2177750	2177922	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2177750	2177922	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2177923	2178080	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2178081	2178192	1	+	1	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2178081	2178192	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2178193	2178278	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2178279	2178359	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2178279	2178359	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2178360	2178459	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2178460	2178522	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2178460	2178522	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2178523	2178605	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2178606	2178707	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2178606	2178707	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2178708	2178788	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2178789	2178913	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2178789	2178913	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2178914	2179015	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2179016	2179226	1	+	1	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2179016	2179226	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2179227	2179317	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2179318	2179392	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2179318	2179392	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	intron	2179393	2179509	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	CDS	2179510	2179557	1	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	exon	2179510	2179557	.	+	.	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
Phchi.S4	AUGUSTUS	stop_codon	2179558	2179560	.	+	0	transcript_id "Phchi.S4G038500.t1"; gene_id "Phchi.S4G038500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8644.t1 is derived from g5819.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	37203363	37204142	.	-	.	Phchi.S1G580300
Phchi.S1	AUGUSTUS	transcript	37203363	37204142	.	-	.	transcript_id "Phchi.S1G580300.t1"; gene_id "Phchi.S1G580300"
Phchi.S1	AUGUSTUS	stop_codon	37203360	37203362	.	-	0	transcript_id "Phchi.S1G580300.t1"; gene_id "Phchi.S1G580300"
Phchi.S1	AUGUSTUS	CDS	37203363	37204142	0.98	-	0	transcript_id "Phchi.S1G580300.t1"; gene_id "Phchi.S1G580300"
Phchi.S1	AUGUSTUS	exon	37203363	37204142	.	-	.	transcript_id "Phchi.S1G580300.t1"; gene_id "Phchi.S1G580300"
Phchi.S1	AUGUSTUS	start_codon	37204140	37204142	.	-	0	transcript_id "Phchi.S1G580300.t1"; gene_id "Phchi.S1G580300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3606.t1 is derived from g775.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4712750	4714013	.	+	.	Phchi.S1G076500
Phchi.S1	AUGUSTUS	transcript	4712750	4714013	.	+	.	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	start_codon	4712750	4712752	.	+	0	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	CDS	4712750	4712970	0.94	+	0	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	exon	4712750	4712970	.	+	.	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	intron	4712971	4713070	.	+	.	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	CDS	4713071	4714013	0.95	+	1	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	exon	4713071	4714013	.	+	.	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	stop_codon	4714014	4714016	.	+	0	transcript_id "Phchi.S1G076500.t1"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	transcript	4713327	4714013	.	+	.	transcript_id "Phchi.S1G076500.t2"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	start_codon	4713327	4713329	.	+	0	transcript_id "Phchi.S1G076500.t2"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	CDS	4713327	4714013	0.93	+	0	transcript_id "Phchi.S1G076500.t2"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	exon	4713327	4714013	.	+	.	transcript_id "Phchi.S1G076500.t2"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	stop_codon	4714014	4714016	.	+	0	transcript_id "Phchi.S1G076500.t2"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	transcript	4713321	4714013	.	+	.	transcript_id "Phchi.S1G076500.t3"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	start_codon	4713321	4713323	.	+	0	transcript_id "Phchi.S1G076500.t3"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	CDS	4713321	4714013	0.57	+	0	transcript_id "Phchi.S1G076500.t3"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	exon	4713321	4714013	.	+	.	transcript_id "Phchi.S1G076500.t3"; gene_id "Phchi.S1G076500"
Phchi.S1	AUGUSTUS	stop_codon	4714014	4714016	.	+	0	transcript_id "Phchi.S1G076500.t3"; gene_id "Phchi.S1G076500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15749.t1 is derived from g14219.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21051140	21052894	.	+	.	Phchi.S3G306800
Phchi.S3	AUGUSTUS	transcript	21051140	21052894	.	+	.	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	start_codon	21051140	21051142	.	+	0	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	CDS	21051140	21051526	0.89	+	0	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	exon	21051140	21051526	.	+	.	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	intron	21051527	21051636	.	+	.	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	CDS	21051637	21051816	1	+	0	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	exon	21051637	21051816	.	+	.	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	intron	21051817	21051910	.	+	.	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	CDS	21051911	21052894	1	+	0	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	exon	21051911	21052894	.	+	.	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
Phchi.S3	AUGUSTUS	stop_codon	21052895	21052897	.	+	0	transcript_id "Phchi.S3G306800.t1"; gene_id "Phchi.S3G306800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg687.t1 is derived from g10469.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4901390	4902188	.	+	.	Phchi.S6G064600
Phchi.S6	AUGUSTUS	transcript	4901390	4902188	.	+	.	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	start_codon	4901390	4901392	.	+	0	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	CDS	4901390	4901794	1	+	0	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	exon	4901390	4901794	.	+	.	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	intron	4901795	4902035	.	+	.	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	CDS	4902036	4902188	0.99	+	0	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	exon	4902036	4902188	.	+	.	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
Phchi.S6	AUGUSTUS	stop_codon	4902189	4902191	.	+	0	transcript_id "Phchi.S6G064600.t1"; gene_id "Phchi.S6G064600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15003.t1 is derived from g13471.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16257816	16258647	.	+	.	Phchi.S3G232200
Phchi.S3	AUGUSTUS	transcript	16257816	16258647	.	+	.	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	start_codon	16257816	16257818	.	+	0	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	CDS	16257816	16258067	0.74	+	0	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	exon	16257816	16258067	.	+	.	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	intron	16258068	16258164	.	+	.	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	CDS	16258165	16258301	0.54	+	0	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	exon	16258165	16258301	.	+	.	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	intron	16258302	16258442	.	+	.	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	CDS	16258443	16258647	0.74	+	1	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	exon	16258443	16258647	.	+	.	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
Phchi.S3	AUGUSTUS	stop_codon	16258648	16258650	.	+	0	transcript_id "Phchi.S3G232200.t1"; gene_id "Phchi.S3G232200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5297.t1 is derived from g2467.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16078002	16078652	.	-	.	Phchi.S1G245600
Phchi.S1	AUGUSTUS	transcript	16078002	16078652	.	-	.	transcript_id "Phchi.S1G245600.t1"; gene_id "Phchi.S1G245600"
Phchi.S1	AUGUSTUS	stop_codon	16077999	16078001	.	-	0	transcript_id "Phchi.S1G245600.t1"; gene_id "Phchi.S1G245600"
Phchi.S1	AUGUSTUS	CDS	16078002	16078652	0.67	-	0	transcript_id "Phchi.S1G245600.t1"; gene_id "Phchi.S1G245600"
Phchi.S1	AUGUSTUS	exon	16078002	16078652	.	-	.	transcript_id "Phchi.S1G245600.t1"; gene_id "Phchi.S1G245600"
Phchi.S1	AUGUSTUS	start_codon	16078650	16078652	.	-	0	transcript_id "Phchi.S1G245600.t1"; gene_id "Phchi.S1G245600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11603.t1 is derived from g15654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7289423	7293204	.	-	.	Phchi.S4G118500
Phchi.S4	AUGUSTUS	transcript	7289423	7293204	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	stop_codon	7289420	7289422	.	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7289423	7289567	0.89	-	1	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7289423	7289567	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7289568	7289757	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7289758	7290326	0.25	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7289758	7290326	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7290327	7290429	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7290430	7290516	0.93	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7290430	7290516	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7290517	7290609	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7290610	7290738	1	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7290610	7290738	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7290739	7290818	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7290819	7290905	1	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7290819	7290905	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7290906	7290999	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7291000	7291119	0.98	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7291000	7291119	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7291120	7291200	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7291201	7291554	0.98	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7291201	7291554	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7291555	7291651	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7291652	7291809	0.87	-	2	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7291652	7291809	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7291810	7291897	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7291898	7291964	0.63	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7291898	7291964	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7291965	7292042	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7292043	7292114	1	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7292043	7292114	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7292115	7292447	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7292448	7292819	0.79	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7292448	7292819	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	intron	7292820	7292901	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	CDS	7292902	7293204	0.93	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	exon	7292902	7293204	.	-	.	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
Phchi.S4	AUGUSTUS	start_codon	7293202	7293204	.	-	0	transcript_id "Phchi.S4G118500.t1"; gene_id "Phchi.S4G118500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5507.t1 is derived from g2677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17161129	17161568	.	-	.	Phchi.S1G266600
Phchi.S1	AUGUSTUS	transcript	17161129	17161568	.	-	.	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	stop_codon	17161126	17161128	.	-	0	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	CDS	17161129	17161205	1	-	2	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	exon	17161129	17161205	.	-	.	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	intron	17161206	17161291	.	-	.	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	CDS	17161292	17161568	0.99	-	0	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	exon	17161292	17161568	.	-	.	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
Phchi.S1	AUGUSTUS	start_codon	17161566	17161568	.	-	0	transcript_id "Phchi.S1G266600.t1"; gene_id "Phchi.S1G266600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8248.t1 is derived from g5423.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34682960	34685010	.	-	.	Phchi.S1G540700
Phchi.S1	AUGUSTUS	transcript	34682960	34685010	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	stop_codon	34682957	34682959	.	-	0	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34682960	34682981	1	-	1	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34682960	34682981	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34682982	34683111	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34683112	34683360	1	-	1	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34683112	34683360	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34683361	34683444	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34683445	34683596	1	-	0	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34683445	34683596	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34683597	34683711	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34683712	34683870	1	-	0	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34683712	34683870	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34683871	34683946	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34683947	34684229	1	-	1	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34683947	34684229	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34684230	34684331	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34684332	34684448	0.62	-	1	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34684332	34684448	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34684449	34684587	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34684588	34684649	1	-	0	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34684588	34684649	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34684650	34684825	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34684826	34684875	0.73	-	2	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34684826	34684875	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	intron	34684876	34684976	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	CDS	34684977	34685010	0.74	-	0	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	exon	34684977	34685010	.	-	.	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
Phchi.S1	AUGUSTUS	start_codon	34685008	34685010	.	-	0	transcript_id "Phchi.S1G540700.t1"; gene_id "Phchi.S1G540700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1741.t1 is derived from g8661.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2798114	2800653	.	-	.	Phchi.S5G035000
Phchi.S5	AUGUSTUS	transcript	2798114	2800653	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	stop_codon	2798111	2798113	.	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2798114	2798194	0.82	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2798114	2798194	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2798195	2798296	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2798297	2798522	0.93	-	1	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2798297	2798522	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2798523	2798607	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2798608	2798684	1	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2798608	2798684	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2798685	2798891	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2798892	2798957	1	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2798892	2798957	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2798958	2799061	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2799062	2799093	0.72	-	2	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2799062	2799093	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2799094	2799205	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2799206	2799267	0.74	-	1	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2799206	2799267	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2799268	2799398	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2799399	2799451	1	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2799399	2799451	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2799452	2799627	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2799628	2799682	1	-	1	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2799628	2799682	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2799683	2799787	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2799788	2799876	1	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2799788	2799876	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2799877	2800062	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2800063	2800148	1	-	2	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2800063	2800148	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2800149	2800281	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2800282	2800341	1	-	2	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2800282	2800341	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	intron	2800342	2800622	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	CDS	2800623	2800653	0.92	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	exon	2800623	2800653	.	-	.	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
Phchi.S5	AUGUSTUS	start_codon	2800651	2800653	.	-	0	transcript_id "Phchi.S5G035000.t1"; gene_id "Phchi.S5G035000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11727.t1 is derived from g15779.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7859645	7861376	.	-	.	Phchi.S4G130900
Phchi.S4	AUGUSTUS	transcript	7859645	7861376	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	stop_codon	7859642	7859644	.	-	0	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7859645	7860202	1	-	0	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7859645	7860202	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7860203	7860290	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7860291	7860461	1	-	0	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7860291	7860461	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7860462	7860578	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7860579	7860773	0.99	-	0	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7860579	7860773	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7860774	7860862	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7860863	7861185	0.59	-	2	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7860863	7861185	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7861186	7861270	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7861271	7861376	0.59	-	0	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7861271	7861376	.	-	.	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	start_codon	7861374	7861376	.	-	0	transcript_id "Phchi.S4G130900.t1"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	transcript	7859645	7860930	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	stop_codon	7859642	7859644	.	-	0	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7859645	7860202	1	-	0	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7859645	7860202	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7860203	7860290	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7860291	7860461	0.99	-	0	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7860291	7860461	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7860462	7860578	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7860579	7860777	0.68	-	1	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7860579	7860777	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	intron	7860778	7860862	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	CDS	7860863	7860930	0.49	-	0	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	exon	7860863	7860930	.	-	.	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
Phchi.S4	AUGUSTUS	start_codon	7860928	7860930	.	-	0	transcript_id "Phchi.S4G130900.t2"; gene_id "Phchi.S4G130900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14605.t1 is derived from g13073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13728421	13729215	.	-	.	Phchi.S3G192400
Phchi.S3	AUGUSTUS	transcript	13728421	13729215	.	-	.	transcript_id "Phchi.S3G192400.t1"; gene_id "Phchi.S3G192400"
Phchi.S3	AUGUSTUS	stop_codon	13728418	13728420	.	-	0	transcript_id "Phchi.S3G192400.t1"; gene_id "Phchi.S3G192400"
Phchi.S3	AUGUSTUS	CDS	13728421	13729215	0.57	-	0	transcript_id "Phchi.S3G192400.t1"; gene_id "Phchi.S3G192400"
Phchi.S3	AUGUSTUS	exon	13728421	13729215	.	-	.	transcript_id "Phchi.S3G192400.t1"; gene_id "Phchi.S3G192400"
Phchi.S3	AUGUSTUS	start_codon	13729213	13729215	.	-	0	transcript_id "Phchi.S3G192400.t1"; gene_id "Phchi.S3G192400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg585.t1 is derived from g10367.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	4300502	4302342	.	+	.	Phchi.S6G054400
Phchi.S6	AUGUSTUS	transcript	4300502	4302342	.	+	.	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	start_codon	4300502	4300504	.	+	0	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	CDS	4300502	4301143	0.81	+	0	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	exon	4300502	4301143	.	+	.	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	intron	4301144	4301277	.	+	.	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	CDS	4301278	4302342	0.8	+	0	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	exon	4301278	4302342	.	+	.	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
Phchi.S6	AUGUSTUS	stop_codon	4302343	4302345	.	+	0	transcript_id "Phchi.S6G054400.t1"; gene_id "Phchi.S6G054400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3937.t1 is derived from g1106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6566787	6569076	.	+	.	Phchi.S1G109600
Phchi.S1	AUGUSTUS	transcript	6566787	6569076	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	start_codon	6566787	6566789	.	+	0	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	CDS	6566787	6568430	0.79	+	0	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	exon	6566787	6568430	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	intron	6568431	6568541	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	CDS	6568542	6568673	0.47	+	0	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	exon	6568542	6568673	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	intron	6568674	6568769	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	CDS	6568770	6568949	0.45	+	0	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	exon	6568770	6568949	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	intron	6568950	6569037	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	CDS	6569038	6569076	0.9	+	0	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	exon	6569038	6569076	.	+	.	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
Phchi.S1	AUGUSTUS	stop_codon	6569077	6569079	.	+	0	transcript_id "Phchi.S1G109600.t1"; gene_id "Phchi.S1G109600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9864.t1 is derived from g7040.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44132123	44135926	.	-	.	Phchi.S1G702300
Phchi.S1	AUGUSTUS	transcript	44132123	44135926	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	stop_codon	44132120	44132122	.	-	0	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44132123	44132151	1	-	2	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44132123	44132151	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44132152	44132480	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44132481	44132579	0.51	-	2	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44132481	44132579	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44132580	44132691	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44132692	44133751	0.95	-	0	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44132692	44133751	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44133752	44133845	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44133846	44133973	1	-	2	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44133846	44133973	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44133974	44134061	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44134062	44134099	1	-	1	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44134062	44134099	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44134100	44134215	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44134216	44134428	1	-	1	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44134216	44134428	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44134429	44134514	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44134515	44134676	1	-	1	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44134515	44134676	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44134677	44134759	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44134760	44134941	1	-	0	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44134760	44134941	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44134942	44135038	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44135039	44135145	1	-	2	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44135039	44135145	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44135146	44135248	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44135249	44135413	0.99	-	2	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44135249	44135413	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44135414	44135512	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44135513	44135596	1	-	2	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44135513	44135596	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	intron	44135597	44135682	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	CDS	44135683	44135926	0.64	-	0	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	exon	44135683	44135926	.	-	.	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
Phchi.S1	AUGUSTUS	start_codon	44135924	44135926	.	-	0	transcript_id "Phchi.S1G702300.t1"; gene_id "Phchi.S1G702300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5693.t1 is derived from g2863.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18346394	18348868	.	-	.	Phchi.S1G285200
Phchi.S1	AUGUSTUS	transcript	18346394	18348868	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	stop_codon	18346391	18346393	.	-	0	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18346394	18346469	0.68	-	1	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18346394	18346469	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18346470	18346612	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18346613	18346646	0.67	-	2	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18346613	18346646	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18346647	18346786	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18346787	18346835	0.54	-	0	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18346787	18346835	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18346836	18346919	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18346920	18346998	1	-	1	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18346920	18346998	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18346999	18347090	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18347091	18347456	1	-	1	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18347091	18347456	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18347457	18347544	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18347545	18347893	1	-	2	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18347545	18347893	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18347894	18347974	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18347975	18348089	1	-	0	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18347975	18348089	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18348090	18348176	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18348177	18348447	1	-	1	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18348177	18348447	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18348448	18348538	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18348539	18348648	1	-	0	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18348539	18348648	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	intron	18348649	18348730	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	CDS	18348731	18348868	0.58	-	0	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	exon	18348731	18348868	.	-	.	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
Phchi.S1	AUGUSTUS	start_codon	18348866	18348868	.	-	0	transcript_id "Phchi.S1G285200.t1"; gene_id "Phchi.S1G285200"
# This transcript jg5574.t2 is derived from g2744.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5575.t1 is derived from g2745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17676045	17678124	.	+	.	Phchi.S1G273400
Phchi.S1	AUGUSTUS	transcript	17676045	17678124	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	start_codon	17676045	17676047	.	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17676045	17676077	0.96	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17676045	17676077	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17676078	17676270	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17676271	17676412	0.65	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17676271	17676412	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17676413	17676514	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17676515	17676655	0.91	+	2	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17676515	17676655	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17676656	17676757	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17676758	17676843	0.73	+	2	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17676758	17676843	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17676844	17676945	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17676946	17677136	0.79	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17676946	17677136	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17677137	17677234	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17677235	17677399	1	+	1	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17677235	17677399	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17677400	17677493	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17677494	17677581	1	+	1	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17677494	17677581	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17677582	17677752	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17677753	17677932	1	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17677753	17677932	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	intron	17677933	17678016	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	CDS	17678017	17678124	1	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	exon	17678017	17678124	.	+	.	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
Phchi.S1	AUGUSTUS	stop_codon	17678125	17678127	.	+	0	transcript_id "Phchi.S1G273400.t1"; gene_id "Phchi.S1G273400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15763.t1 is derived from g14233.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21115193	21118185	.	+	.	Phchi.S3G308200
Phchi.S3	AUGUSTUS	transcript	21115193	21118185	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	start_codon	21115193	21115195	.	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21115193	21115448	0.67	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21115193	21115448	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21115449	21115526	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21115527	21115681	1	+	2	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21115527	21115681	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21115682	21115771	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21115772	21115897	0.77	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21115772	21115897	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21115898	21115999	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21116000	21116095	0.77	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21116000	21116095	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21116096	21116184	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21116185	21116285	1	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21116185	21116285	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21116286	21116392	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21116393	21116429	1	+	1	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21116393	21116429	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21116430	21116678	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21116679	21116897	0.87	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21116679	21116897	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21116898	21117006	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21117007	21117118	1	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21117007	21117118	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21117119	21117304	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21117305	21117399	1	+	2	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21117305	21117399	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21117400	21117488	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21117489	21117668	1	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21117489	21117668	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21117669	21117771	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21117772	21117885	1	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21117772	21117885	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	intron	21117886	21117978	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	CDS	21117979	21118185	0.51	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	exon	21117979	21118185	.	+	.	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
Phchi.S3	AUGUSTUS	stop_codon	21118186	21118188	.	+	0	transcript_id "Phchi.S3G308200.t1"; gene_id "Phchi.S3G308200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12634.t1 is derived from g15983.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C86	AUGUSTUS	gene	21850	25222	.	-	.	Phchi.C86G000300
Phchi.C86	AUGUSTUS	transcript	21850	25222	.	-	.	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	stop_codon	21847	21849	.	-	0	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	CDS	21850	22950	1	-	0	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	exon	21850	22950	.	-	.	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	intron	22951	23057	.	-	.	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	CDS	23058	24451	0.99	-	2	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	exon	23058	24451	.	-	.	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	intron	24452	24600	.	-	.	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	CDS	24601	25222	0.97	-	0	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	exon	24601	25222	.	-	.	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
Phchi.C86	AUGUSTUS	start_codon	25220	25222	.	-	0	transcript_id "Phchi.C86G000300.t1"; gene_id "Phchi.C86G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7095.t1 is derived from g4267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26884803	26885934	.	+	.	Phchi.S1G425400
Phchi.S1	AUGUSTUS	transcript	26884803	26885934	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	start_codon	26884803	26884805	.	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	CDS	26884803	26884826	1	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	exon	26884803	26884826	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	intron	26884827	26884910	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	CDS	26884911	26884995	1	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	exon	26884911	26884995	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	intron	26884996	26885196	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	CDS	26885197	26885351	1	+	2	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	exon	26885197	26885351	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	intron	26885352	26885467	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	CDS	26885468	26885548	1	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	exon	26885468	26885548	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	intron	26885549	26885660	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	CDS	26885661	26885717	1	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	exon	26885661	26885717	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	intron	26885718	26885805	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	CDS	26885806	26885934	1	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	exon	26885806	26885934	.	+	.	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
Phchi.S1	AUGUSTUS	stop_codon	26885935	26885937	.	+	0	transcript_id "Phchi.S1G425400.t1"; gene_id "Phchi.S1G425400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14173.t1 is derived from g12640.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11271150	11276185	.	+	.	Phchi.S3G149200
Phchi.S3	AUGUSTUS	transcript	11271150	11276185	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	start_codon	11271150	11271152	.	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11271150	11271221	0.99	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11271150	11271221	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11271222	11271467	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11271468	11271587	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11271468	11271587	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11271588	11271728	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11271729	11271827	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11271729	11271827	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11271828	11271954	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11271955	11272092	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11271955	11272092	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11272093	11272174	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11272175	11272309	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11272175	11272309	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11272310	11272403	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11272404	11272583	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11272404	11272583	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11272584	11272700	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11272701	11272907	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11272701	11272907	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11272908	11273001	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11273002	11273121	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11273002	11273121	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11273122	11273201	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11273202	11273321	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11273202	11273321	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11273322	11273411	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11273412	11273534	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11273412	11273534	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11273535	11273629	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11273630	11273734	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11273630	11273734	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11273735	11273819	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11273820	11273964	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11273820	11273964	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11273965	11274068	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11274069	11274233	0.99	+	2	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11274069	11274233	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11274234	11274334	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11274335	11274573	0.99	+	2	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11274335	11274573	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11274574	11274682	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11274683	11274715	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11274683	11274715	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11274716	11274815	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11274816	11274897	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11274816	11274897	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11274898	11275012	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11275013	11275173	1	+	2	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11275013	11275173	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11275174	11275265	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11275266	11275439	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11275266	11275439	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11275440	11275534	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11275535	11275717	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11275535	11275717	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11275718	11275819	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11275820	11276001	1	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11275820	11276001	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	intron	11276002	11276091	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	CDS	11276092	11276185	0.94	+	1	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	exon	11276092	11276185	.	+	.	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
Phchi.S3	AUGUSTUS	stop_codon	11276186	11276188	.	+	0	transcript_id "Phchi.S3G149200.t1"; gene_id "Phchi.S3G149200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3602.t1 is derived from g771.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4679221	4681514	.	-	.	Phchi.S1G076100
Phchi.S1	AUGUSTUS	transcript	4679221	4681514	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	stop_codon	4679218	4679220	.	-	0	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	CDS	4679221	4679306	1	-	2	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	exon	4679221	4679306	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	intron	4679307	4679454	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	CDS	4679455	4679478	0.93	-	2	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	exon	4679455	4679478	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	intron	4679479	4680116	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	CDS	4680117	4680569	0.27	-	2	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	exon	4680117	4680569	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	intron	4680570	4680724	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	CDS	4680725	4681514	0.53	-	0	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	exon	4680725	4681514	.	-	.	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
Phchi.S1	AUGUSTUS	start_codon	4681512	4681514	.	-	0	transcript_id "Phchi.S1G076100.t1"; gene_id "Phchi.S1G076100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12437.t1 is derived from g8114.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	19842166	19844032	.	+	.	Phchi.S2G051700
Phchi.S2	AUGUSTUS	transcript	19842166	19844032	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	start_codon	19842166	19842168	.	+	0	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19842166	19842477	0.4	+	0	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19842166	19842477	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19842478	19842566	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19842567	19842610	1	+	0	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19842567	19842610	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19842611	19842790	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19842791	19842838	1	+	1	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19842791	19842838	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19842839	19842987	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19842988	19843037	0.88	+	1	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19842988	19843037	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19843038	19843143	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19843144	19843203	0.89	+	2	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19843144	19843203	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19843204	19843299	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19843300	19843441	1	+	2	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19843300	19843441	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19843442	19843584	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19843585	19843690	1	+	1	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19843585	19843690	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19843691	19843775	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19843776	19843858	0.89	+	0	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19843776	19843858	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	intron	19843859	19844007	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	CDS	19844008	19844032	0.73	+	1	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	exon	19844008	19844032	.	+	.	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
Phchi.S2	AUGUSTUS	stop_codon	19844033	19844035	.	+	0	transcript_id "Phchi.S2G051700.t1"; gene_id "Phchi.S2G051700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13187.t1 is derived from g11652.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4592838	4594609	.	+	.	Phchi.S3G050600
Phchi.S3	AUGUSTUS	transcript	4592838	4594609	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	start_codon	4592838	4592840	.	+	0	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4592838	4592918	0.9	+	0	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4592838	4592918	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4592919	4593037	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4593038	4593236	0.94	+	0	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4593038	4593236	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4593237	4593354	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4593355	4593453	0.86	+	2	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4593355	4593453	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4593454	4593575	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4593576	4593627	0.99	+	2	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4593576	4593627	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4593628	4593773	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4593774	4593895	1	+	1	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4593774	4593895	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4593896	4594004	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4594005	4594105	0.96	+	2	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4594005	4594105	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4594106	4594218	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4594219	4594277	1	+	0	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4594219	4594277	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4594278	4594377	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4594378	4594434	0.97	+	1	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4594378	4594434	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	intron	4594435	4594542	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	CDS	4594543	4594609	0.52	+	1	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	exon	4594543	4594609	.	+	.	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
Phchi.S3	AUGUSTUS	stop_codon	4594610	4594612	.	+	0	transcript_id "Phchi.S3G050600.t1"; gene_id "Phchi.S3G050600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11909.t1 is derived from g15961.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	9266065	9267915	.	+	.	Phchi.S4G149100
Phchi.S4	AUGUSTUS	transcript	9266065	9267915	.	+	.	transcript_id "Phchi.S4G149100.t1"; gene_id "Phchi.S4G149100"
Phchi.S4	AUGUSTUS	start_codon	9266065	9266067	.	+	0	transcript_id "Phchi.S4G149100.t1"; gene_id "Phchi.S4G149100"
Phchi.S4	AUGUSTUS	CDS	9266065	9267915	0.47	+	0	transcript_id "Phchi.S4G149100.t1"; gene_id "Phchi.S4G149100"
Phchi.S4	AUGUSTUS	exon	9266065	9267915	.	+	.	transcript_id "Phchi.S4G149100.t1"; gene_id "Phchi.S4G149100"
Phchi.S4	AUGUSTUS	stop_codon	9267916	9267918	.	+	0	transcript_id "Phchi.S4G149100.t1"; gene_id "Phchi.S4G149100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6583.t1 is derived from g3755.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23853122	23853775	.	+	.	Phchi.S1G374200
Phchi.S1	AUGUSTUS	transcript	23853122	23853775	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	start_codon	23853122	23853124	.	+	0	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	CDS	23853122	23853124	0.89	+	0	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	exon	23853122	23853124	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	intron	23853125	23853246	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	CDS	23853247	23853348	1	+	0	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	exon	23853247	23853348	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	intron	23853349	23853499	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	CDS	23853500	23853528	1	+	0	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	exon	23853500	23853528	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	intron	23853529	23853651	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	CDS	23853652	23853775	1	+	1	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	exon	23853652	23853775	.	+	.	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
Phchi.S1	AUGUSTUS	stop_codon	23853776	23853778	.	+	0	transcript_id "Phchi.S1G374200.t1"; gene_id "Phchi.S1G374200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14546.t1 is derived from g13014.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13417726	13420196	.	+	.	Phchi.S3G186500
Phchi.S3	AUGUSTUS	transcript	13417726	13420196	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	start_codon	13417726	13417728	.	+	0	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	CDS	13417726	13418271	0.56	+	0	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	exon	13417726	13418271	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	intron	13418272	13418342	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	CDS	13418343	13418435	0.76	+	0	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	exon	13418343	13418435	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	intron	13418436	13418593	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	CDS	13418594	13419438	0.8	+	0	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	exon	13418594	13419438	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	intron	13419439	13419528	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	CDS	13419529	13419809	1	+	1	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	exon	13419529	13419809	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	intron	13419810	13419939	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	CDS	13419940	13420196	0.77	+	2	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	exon	13419940	13420196	.	+	.	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
Phchi.S3	AUGUSTUS	stop_codon	13420197	13420199	.	+	0	transcript_id "Phchi.S3G186500.t1"; gene_id "Phchi.S3G186500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4977.t1 is derived from g2147.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13840311	13841754	.	+	.	Phchi.S1G213600
Phchi.S1	AUGUSTUS	transcript	13840311	13841754	.	+	.	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	start_codon	13840311	13840313	.	+	0	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	CDS	13840311	13840421	0.01	+	0	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	exon	13840311	13840421	.	+	.	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	intron	13840422	13840497	.	+	.	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	CDS	13840498	13840586	0.02	+	0	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	exon	13840498	13840586	.	+	.	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	intron	13840587	13841705	.	+	.	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	CDS	13841706	13841754	1	+	1	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	exon	13841706	13841754	.	+	.	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
Phchi.S1	AUGUSTUS	stop_codon	13841755	13841757	.	+	0	transcript_id "Phchi.S1G213600.t1"; gene_id "Phchi.S1G213600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg532.t1 is derived from g10314.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3834057	3835052	.	+	.	Phchi.S6G049100
Phchi.S6	AUGUSTUS	transcript	3834100	3835052	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	start_codon	3834100	3834102	.	+	0	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834100	3834201	1	+	0	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834100	3834201	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834202	3834300	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834301	3834408	1	+	0	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834301	3834408	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834409	3834528	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834529	3834573	0.99	+	0	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834529	3834573	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834574	3834675	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834676	3834764	1	+	0	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834676	3834764	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834765	3834857	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834858	3834898	0.98	+	1	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834858	3834898	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834899	3834990	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834991	3835052	0.91	+	2	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834991	3835052	.	+	.	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	stop_codon	3835053	3835055	.	+	0	transcript_id "Phchi.S6G049100.t1"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	transcript	3834057	3835052	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	start_codon	3834057	3834059	.	+	0	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834057	3834206	0.83	+	0	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834057	3834206	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834207	3834300	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834301	3834408	1	+	0	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834301	3834408	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834409	3834528	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834529	3834573	1	+	0	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834529	3834573	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834574	3834675	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834676	3834764	1	+	0	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834676	3834764	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834765	3834857	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834858	3834898	0.98	+	1	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834858	3834898	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	intron	3834899	3834990	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	CDS	3834991	3835052	0.91	+	2	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	exon	3834991	3835052	.	+	.	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
Phchi.S6	AUGUSTUS	stop_codon	3835053	3835055	.	+	0	transcript_id "Phchi.S6G049100.t2"; gene_id "Phchi.S6G049100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13262.t1 is derived from g11727.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4969723	4972463	.	+	.	Phchi.S3G058100
Phchi.S3	AUGUSTUS	transcript	4969723	4972463	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	start_codon	4969723	4969725	.	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4969723	4969800	0.47	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4969723	4969800	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4969801	4969889	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4969890	4969958	0.42	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4969890	4969958	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4969959	4970044	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4970045	4970300	0.16	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4970045	4970300	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4970301	4970526	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4970527	4970674	0.34	+	2	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4970527	4970674	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4970675	4970789	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4970790	4970919	1	+	1	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4970790	4970919	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4970920	4971303	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4971304	4971504	1	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4971304	4971504	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4971505	4971694	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4971695	4971862	0.99	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4971695	4971862	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	intron	4971863	4971971	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	CDS	4971972	4972463	1	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	exon	4971972	4972463	.	+	.	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
Phchi.S3	AUGUSTUS	stop_codon	4972464	4972466	.	+	0	transcript_id "Phchi.S3G058100.t1"; gene_id "Phchi.S3G058100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4692.t1 is derived from g1862.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12176772	12177967	.	-	.	Phchi.S1G185100
Phchi.S1	AUGUSTUS	transcript	12176772	12177967	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	stop_codon	12176769	12176771	.	-	0	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	CDS	12176772	12176851	1	-	2	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	exon	12176772	12176851	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	intron	12176852	12177006	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	CDS	12177007	12177217	0.53	-	0	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	exon	12177007	12177217	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	intron	12177218	12177550	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	CDS	12177551	12177651	0.59	-	2	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	exon	12177551	12177651	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	intron	12177652	12177723	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	CDS	12177724	12177967	0.37	-	0	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	exon	12177724	12177967	.	-	.	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
Phchi.S1	AUGUSTUS	start_codon	12177965	12177967	.	-	0	transcript_id "Phchi.S1G185100.t1"; gene_id "Phchi.S1G185100"
# This transcript jg14650.t2 is derived from g13118.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14651.t1 is derived from g13119.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13951093	13952606	.	+	.	Phchi.S3G197000
Phchi.S3	AUGUSTUS	transcript	13951093	13952606	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	start_codon	13951093	13951095	.	+	0	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	CDS	13951093	13951444	1	+	0	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	exon	13951093	13951444	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	intron	13951445	13951634	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	CDS	13951635	13951715	1	+	2	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	exon	13951635	13951715	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	intron	13951716	13951841	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	CDS	13951842	13952116	0.93	+	2	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	exon	13951842	13952116	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	intron	13952117	13952201	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	CDS	13952202	13952606	0.97	+	0	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	exon	13952202	13952606	.	+	.	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
Phchi.S3	AUGUSTUS	stop_codon	13952607	13952609	.	+	0	transcript_id "Phchi.S3G197000.t1"; gene_id "Phchi.S3G197000"
# This transcript jg7906.t2 is derived from g5080.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7907.t1 is derived from g5081.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31836778	31838788	.	-	.	Phchi.S1G506600
Phchi.S1	AUGUSTUS	transcript	31836778	31838788	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	stop_codon	31836775	31836777	.	-	0	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	CDS	31836778	31837351	1	-	1	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	exon	31836778	31837351	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	intron	31837352	31837529	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	CDS	31837530	31837608	0.41	-	2	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	exon	31837530	31837608	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	intron	31837609	31837721	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	CDS	31837722	31837923	1	-	0	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	exon	31837722	31837923	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	intron	31837924	31838028	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	CDS	31838029	31838284	1	-	1	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	exon	31838029	31838284	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	intron	31838285	31838645	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	CDS	31838646	31838788	0.81	-	0	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	exon	31838646	31838788	.	-	.	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
Phchi.S1	AUGUSTUS	start_codon	31838786	31838788	.	-	0	transcript_id "Phchi.S1G506600.t1"; gene_id "Phchi.S1G506600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7944.t1 is derived from g5118.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32042208	32043306	.	+	.	Phchi.S1G510300
Phchi.S1	AUGUSTUS	transcript	32042208	32043306	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	start_codon	32042208	32042210	.	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042208	32042282	0.73	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042208	32042282	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042283	32042372	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042373	32042459	0.99	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042373	32042459	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042460	32042569	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042570	32042632	1	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042570	32042632	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042633	32042724	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042725	32042826	1	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042725	32042826	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042827	32042919	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042920	32043041	0.87	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042920	32043041	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32043042	32043118	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32043119	32043166	0.5	+	1	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32043119	32043166	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32043167	32043260	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32043261	32043306	0.97	+	1	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32043261	32043306	.	+	.	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	stop_codon	32043307	32043309	.	+	0	transcript_id "Phchi.S1G510300.t1"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	transcript	32042208	32043306	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	start_codon	32042208	32042210	.	+	0	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042208	32042282	0.85	+	0	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042208	32042282	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042283	32042372	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042373	32042436	0.73	+	0	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042373	32042436	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042437	32042569	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042570	32042632	0.99	+	2	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042570	32042632	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042633	32042719	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042720	32042826	1	+	2	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042720	32042826	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32042827	32042919	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32042920	32043041	0.83	+	0	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32042920	32043041	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32043042	32043118	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32043119	32043166	0.57	+	1	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32043119	32043166	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	intron	32043167	32043260	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	CDS	32043261	32043306	0.98	+	1	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	exon	32043261	32043306	.	+	.	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
Phchi.S1	AUGUSTUS	stop_codon	32043307	32043309	.	+	0	transcript_id "Phchi.S1G510300.t2"; gene_id "Phchi.S1G510300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg772.t1 is derived from g10554.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	5446058	5449393	.	-	.	Phchi.S6G073100
Phchi.S6	AUGUSTUS	transcript	5446058	5449393	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	stop_codon	5446055	5446057	.	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5446058	5446163	1	-	1	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5446058	5446163	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5446164	5446251	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5446252	5446364	1	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5446252	5446364	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5446365	5446438	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5446439	5446620	1	-	2	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5446439	5446620	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5446621	5446804	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5446805	5446937	1	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5446805	5446937	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5446938	5447035	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5447036	5447156	0.87	-	1	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5447036	5447156	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5447157	5447248	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5447249	5447275	0.87	-	1	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5447249	5447275	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5447276	5447363	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5447364	5447386	0.38	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5447364	5447386	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5447387	5447456	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5447457	5447535	0.85	-	1	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5447457	5447535	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5447536	5447664	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5447665	5447937	0.96	-	1	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5447665	5447937	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5447938	5448088	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5448089	5448224	1	-	2	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5448089	5448224	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5448225	5448314	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5448315	5448408	1	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5448315	5448408	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5448409	5448503	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5448504	5448773	0.89	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5448504	5448773	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5448774	5448898	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5448899	5449151	0.84	-	1	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5448899	5449151	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	intron	5449152	5449298	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	CDS	5449299	5449393	0.53	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	exon	5449299	5449393	.	-	.	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
Phchi.S6	AUGUSTUS	start_codon	5449391	5449393	.	-	0	transcript_id "Phchi.S6G073100.t1"; gene_id "Phchi.S6G073100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7783.t1 is derived from g4957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31188670	31189068	.	+	.	Phchi.S1G494200
Phchi.S1	AUGUSTUS	transcript	31188670	31189068	.	+	.	transcript_id "Phchi.S1G494200.t1"; gene_id "Phchi.S1G494200"
Phchi.S1	AUGUSTUS	start_codon	31188670	31188672	.	+	0	transcript_id "Phchi.S1G494200.t1"; gene_id "Phchi.S1G494200"
Phchi.S1	AUGUSTUS	CDS	31188670	31189068	1	+	0	transcript_id "Phchi.S1G494200.t1"; gene_id "Phchi.S1G494200"
Phchi.S1	AUGUSTUS	exon	31188670	31189068	.	+	.	transcript_id "Phchi.S1G494200.t1"; gene_id "Phchi.S1G494200"
Phchi.S1	AUGUSTUS	stop_codon	31189069	31189071	.	+	0	transcript_id "Phchi.S1G494200.t1"; gene_id "Phchi.S1G494200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2739.t1 is derived from g9659.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8507381	8511709	.	+	.	Phchi.S5G134800
Phchi.S5	AUGUSTUS	transcript	8507381	8511709	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	start_codon	8507381	8507383	.	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8507381	8507461	0.92	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8507381	8507461	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8507462	8507842	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8507843	8507993	1	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8507843	8507993	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8507994	8508339	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8508340	8508527	1	+	2	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8508340	8508527	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8508528	8508688	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8508689	8508835	1	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8508689	8508835	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8508836	8508920	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8508921	8509116	1	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8508921	8509116	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8509117	8509216	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8509217	8509329	1	+	2	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8509217	8509329	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8509330	8509609	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8509610	8509854	0.76	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8509610	8509854	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8509855	8509950	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8509951	8510056	1	+	1	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8509951	8510056	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8510057	8510248	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8510249	8510395	1	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8510249	8510395	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8510396	8510528	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8510529	8510736	1	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8510529	8510736	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8510737	8510920	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8510921	8511120	1	+	2	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8510921	8511120	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8511121	8511217	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8511218	8511304	1	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8511218	8511304	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	intron	8511305	8511514	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	CDS	8511515	8511709	0.96	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	exon	8511515	8511709	.	+	.	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
Phchi.S5	AUGUSTUS	stop_codon	8511710	8511712	.	+	0	transcript_id "Phchi.S5G134800.t1"; gene_id "Phchi.S5G134800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1458.t1 is derived from g8377.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1001667	1006073	.	+	.	Phchi.S5G006700
Phchi.S5	AUGUSTUS	transcript	1001667	1006073	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	start_codon	1001667	1001669	.	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1001667	1002269	0.72	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1001667	1002269	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1002270	1002643	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1002644	1002829	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1002644	1002829	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1002830	1002956	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1002957	1003172	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1002957	1003172	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1003173	1003258	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1003259	1003369	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1003259	1003369	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1003370	1003455	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1003456	1003653	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1003456	1003653	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1003654	1003761	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1003762	1003893	0.97	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1003762	1003893	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1003894	1004067	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1004068	1004124	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1004068	1004124	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1004125	1004252	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1004253	1004369	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1004253	1004369	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1004370	1004459	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1004460	1004537	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1004460	1004537	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1004538	1004624	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1004625	1004768	1	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1004625	1004768	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1004769	1004885	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1004886	1005504	0.78	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1004886	1005504	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	intron	1005505	1005681	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	CDS	1005682	1006073	0.75	+	2	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	exon	1005682	1006073	.	+	.	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
Phchi.S5	AUGUSTUS	stop_codon	1006074	1006076	.	+	0	transcript_id "Phchi.S5G006700.t1"; gene_id "Phchi.S5G006700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4315.t1 is derived from g1484.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9585511	9586305	.	-	.	Phchi.S1G147400
Phchi.S1	AUGUSTUS	transcript	9585511	9586305	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	stop_codon	9585508	9585510	.	-	0	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	CDS	9585511	9585558	0.72	-	0	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	exon	9585511	9585558	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	intron	9585559	9585698	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	CDS	9585699	9585924	0.43	-	1	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	exon	9585699	9585924	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	intron	9585925	9586061	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	CDS	9586062	9586108	0.52	-	0	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	exon	9586062	9586108	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	intron	9586109	9586272	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	CDS	9586273	9586305	0.94	-	0	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	exon	9586273	9586305	.	-	.	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
Phchi.S1	AUGUSTUS	start_codon	9586303	9586305	.	-	0	transcript_id "Phchi.S1G147400.t1"; gene_id "Phchi.S1G147400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13100.t1 is derived from g11565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4135800	4136543	.	+	.	Phchi.S3G041900
Phchi.S3	AUGUSTUS	transcript	4135800	4136543	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	start_codon	4135800	4135802	.	+	0	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	CDS	4135800	4135802	0.68	+	0	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	exon	4135800	4135802	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	intron	4135803	4136042	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	CDS	4136043	4136178	1	+	0	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	exon	4136043	4136178	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	intron	4136179	4136266	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	CDS	4136267	4136368	1	+	2	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	exon	4136267	4136368	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	intron	4136369	4136496	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	CDS	4136497	4136543	0.98	+	2	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	exon	4136497	4136543	.	+	.	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
Phchi.S3	AUGUSTUS	stop_codon	4136544	4136546	.	+	0	transcript_id "Phchi.S3G041900.t1"; gene_id "Phchi.S3G041900"
# This transcript jg10249.t2 is derived from g7425.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10250.t1 is derived from g7426.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46597036	46598629	.	+	.	Phchi.S1G740900
Phchi.S1	AUGUSTUS	transcript	46597036	46598629	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	start_codon	46597036	46597038	.	+	0	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	CDS	46597036	46597092	0.41	+	0	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	exon	46597036	46597092	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	intron	46597093	46597230	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	CDS	46597231	46597349	0.56	+	0	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	exon	46597231	46597349	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	intron	46597350	46597444	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	CDS	46597445	46597701	1	+	1	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	exon	46597445	46597701	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	intron	46597702	46597794	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	CDS	46597795	46598243	1	+	2	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	exon	46597795	46598243	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	intron	46598244	46598374	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	CDS	46598375	46598629	1	+	0	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	exon	46598375	46598629	.	+	.	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
Phchi.S1	AUGUSTUS	stop_codon	46598630	46598632	.	+	0	transcript_id "Phchi.S1G740900.t1"; gene_id "Phchi.S1G740900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg9135.t1 is derived from g6310.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	40029014	40031737	.	+	.	Phchi.S1G629400
Phchi.S1	AUGUSTUS	transcript	40029014	40031737	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	start_codon	40029014	40029016	.	+	0	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40029014	40029316	0.66	+	0	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40029014	40029316	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40029317	40029433	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40029434	40030010	0.96	+	0	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40029434	40030010	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40030011	40030142	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40030143	40030259	0.78	+	2	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40030143	40030259	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40030260	40030757	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40030758	40031737	0.94	+	2	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40030758	40031737	.	+	.	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	stop_codon	40031738	40031740	.	+	0	transcript_id "Phchi.S1G629400.t1"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	transcript	40029128	40031737	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	start_codon	40029128	40029130	.	+	0	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40029128	40029316	0.65	+	0	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40029128	40029316	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40029317	40029433	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40029434	40030010	0.95	+	0	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40029434	40030010	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40030011	40030142	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40030143	40030259	0.78	+	2	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40030143	40030259	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40030260	40030757	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40030758	40031737	0.92	+	2	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40030758	40031737	.	+	.	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	stop_codon	40031738	40031740	.	+	0	transcript_id "Phchi.S1G629400.t2"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	transcript	40029014	40030166	.	+	.	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	start_codon	40029014	40029016	.	+	0	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40029014	40029316	0.71	+	0	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40029014	40029316	.	+	.	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40029317	40029433	.	+	.	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40029434	40030024	0.46	+	0	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40029434	40030024	.	+	.	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	intron	40030025	40030142	.	+	.	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	CDS	40030143	40030166	0.62	+	0	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	exon	40030143	40030166	.	+	.	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
Phchi.S1	AUGUSTUS	stop_codon	40030167	40030169	.	+	0	transcript_id "Phchi.S1G629400.t3"; gene_id "Phchi.S1G629400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12578.t1 is derived from g8255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	35819547	35820211	.	-	.	Phchi.S2G065800
Phchi.S2	AUGUSTUS	transcript	35819547	35820211	.	-	.	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	stop_codon	35819544	35819546	.	-	0	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	CDS	35819547	35819792	0.27	-	0	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	exon	35819547	35819792	.	-	.	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	intron	35819793	35819998	.	-	.	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	CDS	35819999	35820211	0.57	-	0	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	exon	35819999	35820211	.	-	.	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
Phchi.S2	AUGUSTUS	start_codon	35820209	35820211	.	-	0	transcript_id "Phchi.S2G065800.t1"; gene_id "Phchi.S2G065800"
# This transcript jg8584.t2 is derived from g5759.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8585.t1 is derived from g5760.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36741888	36744141	.	-	.	Phchi.S1G574400
Phchi.S1	AUGUSTUS	transcript	36741888	36744141	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	stop_codon	36741885	36741887	.	-	0	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36741888	36741989	1	-	0	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36741888	36741989	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36741990	36742066	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36742067	36742156	1	-	0	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36742067	36742156	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36742157	36742248	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36742249	36742399	1	-	1	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36742249	36742399	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36742400	36742480	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36742481	36742519	1	-	1	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36742481	36742519	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36742520	36742605	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36742606	36742675	1	-	2	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36742606	36742675	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36742676	36742801	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36742802	36742890	1	-	1	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36742802	36742890	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36742891	36742971	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36742972	36743048	1	-	0	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36742972	36743048	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36743049	36743155	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36743156	36743195	1	-	1	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36743156	36743195	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36743196	36743276	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36743277	36743385	0.99	-	2	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36743277	36743385	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	intron	36743386	36743495	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	CDS	36743496	36744141	0.53	-	0	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	exon	36743496	36744141	.	-	.	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
Phchi.S1	AUGUSTUS	start_codon	36744139	36744141	.	-	0	transcript_id "Phchi.S1G574400.t1"; gene_id "Phchi.S1G574400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7813.t1 is derived from g4987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31313482	31318386	.	+	.	Phchi.S1G497200
Phchi.S1	AUGUSTUS	transcript	31313482	31318386	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	start_codon	31313482	31313484	.	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31313482	31313532	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31313482	31313532	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31313533	31314100	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31314101	31314172	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31314101	31314172	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31314173	31314262	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31314263	31314366	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31314263	31314366	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31314367	31314478	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31314479	31314581	1	+	1	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31314479	31314581	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31314582	31314695	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31314696	31314857	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31314696	31314857	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31314858	31315016	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31315017	31315294	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31315017	31315294	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31315295	31315424	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31315425	31315575	1	+	1	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31315425	31315575	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31315576	31315729	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31315730	31315894	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31315730	31315894	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31315895	31316002	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31316003	31316080	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31316003	31316080	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31316081	31316188	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31316189	31316278	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31316189	31316278	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31316279	31316467	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31316468	31316554	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31316468	31316554	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31316555	31316690	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31316691	31316777	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31316691	31316777	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31316778	31316862	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31316863	31316959	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31316863	31316959	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31316960	31317046	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31317047	31317150	1	+	2	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31317047	31317150	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31317151	31317240	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31317241	31317316	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31317241	31317316	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31317317	31317436	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31317437	31317587	1	+	2	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31317437	31317587	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31317588	31317689	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31317690	31317758	1	+	1	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31317690	31317758	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31317759	31317848	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31317849	31317915	1	+	1	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31317849	31317915	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31317916	31318009	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31318010	31318080	1	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31318010	31318080	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	intron	31318081	31318181	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	CDS	31318182	31318386	0.94	+	1	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	exon	31318182	31318386	.	+	.	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
Phchi.S1	AUGUSTUS	stop_codon	31318387	31318389	.	+	0	transcript_id "Phchi.S1G497200.t1"; gene_id "Phchi.S1G497200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15417.t1 is derived from g13885.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18973498	18974637	.	-	.	Phchi.S3G273600
Phchi.S3	AUGUSTUS	transcript	18973498	18974637	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	stop_codon	18973495	18973497	.	-	0	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18973498	18973504	1	-	1	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18973498	18973504	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	intron	18973505	18973687	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18973688	18973749	0.99	-	0	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18973688	18973749	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	intron	18973750	18973912	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18973913	18973997	0.61	-	1	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18973913	18973997	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	intron	18973998	18974089	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18974090	18974209	0.51	-	1	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18974090	18974209	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	intron	18974210	18974279	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18974280	18974364	1	-	2	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18974280	18974364	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	intron	18974365	18974452	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18974453	18974504	0.88	-	0	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18974453	18974504	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	intron	18974505	18974580	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	CDS	18974581	18974637	0.27	-	0	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	exon	18974581	18974637	.	-	.	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
Phchi.S3	AUGUSTUS	start_codon	18974635	18974637	.	-	0	transcript_id "Phchi.S3G273600.t1"; gene_id "Phchi.S3G273600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg8129.t1 is derived from g5304.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	33630317	33634050	.	+	.	Phchi.S1G528800
Phchi.S1	AUGUSTUS	transcript	33630317	33634050	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	start_codon	33630317	33630319	.	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630317	33630450	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630317	33630450	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630451	33630597	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630598	33630670	0.96	+	1	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630598	33630670	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630671	33630771	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630772	33630837	0.88	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630772	33630837	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630838	33631015	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631016	33631081	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631016	33631081	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631082	33631171	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631172	33631278	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631172	33631278	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631279	33631451	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631452	33631503	1	+	1	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631452	33631503	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631504	33631617	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631618	33631683	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631618	33631683	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631684	33631825	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631826	33631890	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631826	33631890	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631891	33632077	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632078	33632126	1	+	1	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632078	33632126	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632127	33632217	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632218	33632302	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632218	33632302	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632303	33632387	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632388	33632486	1	+	2	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632388	33632486	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632487	33632566	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632567	33632648	1	+	2	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632567	33632648	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632649	33632815	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632816	33632867	1	+	1	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632816	33632867	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632868	33632973	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632974	33633090	1	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632974	33633090	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633091	33633178	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633179	33633540	0.92	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633179	33633540	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633541	33633614	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633615	33633739	0.99	+	1	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633615	33633739	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633740	33633895	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633896	33634050	0.62	+	2	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633896	33634050	.	+	.	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	stop_codon	33634051	33634053	.	+	0	transcript_id "Phchi.S1G528800.t1"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	transcript	33630317	33634050	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	start_codon	33630317	33630319	.	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630317	33630450	0.94	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630317	33630450	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630451	33630614	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630615	33630837	0.71	+	1	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630615	33630837	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630838	33631015	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631016	33631081	1	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631016	33631081	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631082	33631171	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631172	33631278	1	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631172	33631278	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631279	33631451	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631452	33631503	1	+	1	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631452	33631503	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631504	33631617	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631618	33631683	1	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631618	33631683	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631684	33631825	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631826	33631890	1	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631826	33631890	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631891	33632077	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632078	33632126	1	+	1	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632078	33632126	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632127	33632217	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632218	33632302	1	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632218	33632302	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632303	33632387	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632388	33632486	1	+	2	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632388	33632486	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632487	33632566	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632567	33632648	1	+	2	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632567	33632648	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632649	33632815	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632816	33632867	1	+	1	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632816	33632867	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632868	33632973	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632974	33633090	1	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632974	33633090	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633091	33633178	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633179	33633540	0.92	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633179	33633540	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633541	33633614	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633615	33633739	0.98	+	1	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633615	33633739	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633740	33633895	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633896	33634050	0.48	+	2	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633896	33634050	.	+	.	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	stop_codon	33634051	33634053	.	+	0	transcript_id "Phchi.S1G528800.t2"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	transcript	33630317	33633902	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	start_codon	33630317	33630319	.	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630317	33630450	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630317	33630450	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630451	33630597	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630598	33630670	0.97	+	1	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630598	33630670	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630671	33630771	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33630772	33630837	0.88	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33630772	33630837	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33630838	33631015	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631016	33631081	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631016	33631081	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631082	33631171	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631172	33631278	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631172	33631278	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631279	33631451	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631452	33631503	1	+	1	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631452	33631503	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631504	33631617	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631618	33631683	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631618	33631683	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631684	33631825	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33631826	33631890	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33631826	33631890	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33631891	33632077	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632078	33632126	1	+	1	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632078	33632126	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632127	33632217	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632218	33632302	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632218	33632302	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632303	33632387	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632388	33632486	1	+	2	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632388	33632486	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632487	33632566	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632567	33632648	1	+	2	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632567	33632648	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632649	33632815	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632816	33632867	1	+	1	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632816	33632867	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33632868	33632973	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33632974	33633090	1	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33632974	33633090	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633091	33633178	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633179	33633732	0.53	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633179	33633732	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	intron	33633733	33633895	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	CDS	33633896	33633902	0.52	+	1	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	exon	33633896	33633902	.	+	.	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
Phchi.S1	AUGUSTUS	stop_codon	33633903	33633905	.	+	0	transcript_id "Phchi.S1G528800.t3"; gene_id "Phchi.S1G528800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14589.t1 is derived from g13057.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13608437	13608793	.	+	.	Phchi.S3G190800
Phchi.S3	AUGUSTUS	transcript	13608437	13608793	.	+	.	transcript_id "Phchi.S3G190800.t1"; gene_id "Phchi.S3G190800"
Phchi.S3	AUGUSTUS	start_codon	13608437	13608439	.	+	0	transcript_id "Phchi.S3G190800.t1"; gene_id "Phchi.S3G190800"
Phchi.S3	AUGUSTUS	CDS	13608437	13608793	0.81	+	0	transcript_id "Phchi.S3G190800.t1"; gene_id "Phchi.S3G190800"
Phchi.S3	AUGUSTUS	exon	13608437	13608793	.	+	.	transcript_id "Phchi.S3G190800.t1"; gene_id "Phchi.S3G190800"
Phchi.S3	AUGUSTUS	stop_codon	13608794	13608796	.	+	0	transcript_id "Phchi.S3G190800.t1"; gene_id "Phchi.S3G190800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7193.t1 is derived from g4365.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	27498510	27500515	.	-	.	Phchi.S1G435200
Phchi.S1	AUGUSTUS	transcript	27498510	27500515	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	stop_codon	27498507	27498509	.	-	0	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	CDS	27498510	27499100	1	-	0	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	exon	27498510	27499100	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	intron	27499101	27499190	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	CDS	27499191	27499390	0.98	-	2	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	exon	27499191	27499390	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	intron	27499391	27499518	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	CDS	27499519	27499534	0.9	-	0	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	exon	27499519	27499534	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	intron	27499535	27499664	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	CDS	27499665	27499815	0.91	-	1	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	exon	27499665	27499815	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	intron	27499816	27499906	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	CDS	27499907	27500140	1	-	1	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	exon	27499907	27500140	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	intron	27500141	27500243	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	CDS	27500244	27500515	0.82	-	0	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	exon	27500244	27500515	.	-	.	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
Phchi.S1	AUGUSTUS	start_codon	27500513	27500515	.	-	0	transcript_id "Phchi.S1G435200.t1"; gene_id "Phchi.S1G435200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13079.t1 is derived from g11544.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4060121	4060850	.	+	.	Phchi.S3G039800
Phchi.S3	AUGUSTUS	transcript	4060121	4060850	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	start_codon	4060121	4060123	.	+	0	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	CDS	4060121	4060274	0.54	+	0	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	exon	4060121	4060274	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	intron	4060275	4060371	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	CDS	4060372	4060471	0.55	+	2	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	exon	4060372	4060471	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	intron	4060472	4060568	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	CDS	4060569	4060601	0.93	+	1	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	exon	4060569	4060601	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	intron	4060602	4060750	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	CDS	4060751	4060850	0.81	+	1	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	exon	4060751	4060850	.	+	.	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
Phchi.S3	AUGUSTUS	stop_codon	4060851	4060853	.	+	0	transcript_id "Phchi.S3G039800.t1"; gene_id "Phchi.S3G039800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1106.t1 is derived from g10889.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7653764	7654923	.	+	.	Phchi.S6G106500
Phchi.S6	AUGUSTUS	transcript	7653764	7654923	.	+	.	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	start_codon	7653764	7653766	.	+	0	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	CDS	7653764	7654049	0.66	+	0	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	exon	7653764	7654049	.	+	.	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	intron	7654050	7654141	.	+	.	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	CDS	7654142	7654923	0.62	+	2	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	exon	7654142	7654923	.	+	.	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
Phchi.S6	AUGUSTUS	stop_codon	7654924	7654926	.	+	0	transcript_id "Phchi.S6G106500.t1"; gene_id "Phchi.S6G106500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6084.t1 is derived from g3255.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20873283	20873731	.	+	.	Phchi.S1G324300
Phchi.S1	AUGUSTUS	transcript	20873283	20873731	.	+	.	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	start_codon	20873283	20873285	.	+	0	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	CDS	20873283	20873301	0.9	+	0	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	exon	20873283	20873301	.	+	.	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	intron	20873302	20873396	.	+	.	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	CDS	20873397	20873526	0.91	+	2	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	exon	20873397	20873526	.	+	.	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	intron	20873527	20873682	.	+	.	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	CDS	20873683	20873731	0.73	+	1	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	exon	20873683	20873731	.	+	.	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
Phchi.S1	AUGUSTUS	stop_codon	20873732	20873734	.	+	0	transcript_id "Phchi.S1G324300.t1"; gene_id "Phchi.S1G324300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15365.t1 is derived from g13833.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18624159	18625299	.	-	.	Phchi.S3G268400
Phchi.S3	AUGUSTUS	transcript	18624159	18625299	.	-	.	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	stop_codon	18624156	18624158	.	-	0	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	CDS	18624159	18624939	0.86	-	1	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	exon	18624159	18624939	.	-	.	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	intron	18624940	18625087	.	-	.	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	CDS	18625088	18625152	1	-	0	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	exon	18625088	18625152	.	-	.	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	intron	18625153	18625296	.	-	.	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	CDS	18625297	18625299	1	-	0	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	exon	18625297	18625299	.	-	.	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
Phchi.S3	AUGUSTUS	start_codon	18625297	18625299	.	-	0	transcript_id "Phchi.S3G268400.t1"; gene_id "Phchi.S3G268400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg273.t1 is derived from g10055.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1948271	1949353	.	-	.	Phchi.S6G023200
Phchi.S6	AUGUSTUS	transcript	1948271	1949353	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	stop_codon	1948268	1948270	.	-	0	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	CDS	1948271	1948545	1	-	2	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	exon	1948271	1948545	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	intron	1948546	1948646	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	CDS	1948647	1948842	0.73	-	0	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	exon	1948647	1948842	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	intron	1948843	1949010	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	CDS	1949011	1949040	0.34	-	0	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	exon	1949011	1949040	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	intron	1949041	1949230	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	CDS	1949231	1949353	0.65	-	0	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	exon	1949231	1949353	.	-	.	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
Phchi.S6	AUGUSTUS	start_codon	1949351	1949353	.	-	0	transcript_id "Phchi.S6G023200.t1"; gene_id "Phchi.S6G023200"
# This transcript jg380.t2 is derived from g10162.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg381.t1 is derived from g10163.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2735026	2737106	.	+	.	Phchi.S6G034000
Phchi.S6	AUGUSTUS	transcript	2735026	2737106	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	start_codon	2735026	2735028	.	+	0	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2735026	2735307	0.58	+	0	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2735026	2735307	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2735308	2735398	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2735399	2735474	0.99	+	0	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2735399	2735474	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2735475	2735576	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2735577	2735662	0.62	+	2	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2735577	2735662	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2735663	2735760	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2735761	2735854	1	+	0	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2735761	2735854	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2735855	2735996	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2735997	2736073	1	+	2	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2735997	2736073	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2736074	2736148	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2736149	2736276	1	+	0	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2736149	2736276	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2736277	2736346	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2736347	2736418	1	+	1	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2736347	2736418	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2736419	2736511	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2736512	2736582	1	+	1	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2736512	2736582	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2736583	2736674	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2736675	2736747	1	+	2	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2736675	2736747	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2736748	2736831	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2736832	2736975	1	+	1	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2736832	2736975	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	intron	2736976	2737069	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	CDS	2737070	2737106	1	+	1	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	exon	2737070	2737106	.	+	.	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
Phchi.S6	AUGUSTUS	stop_codon	2737107	2737109	.	+	0	transcript_id "Phchi.S6G034000.t1"; gene_id "Phchi.S6G034000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13308.t1 is derived from g11774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5690992	5694288	.	-	.	Phchi.S3G062700
Phchi.S3	AUGUSTUS	transcript	5690992	5694288	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	stop_codon	5690989	5690991	.	-	0	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5690992	5691273	1	-	0	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5690992	5691273	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	intron	5691274	5691393	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5691394	5691639	1	-	0	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5691394	5691639	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	intron	5691640	5691753	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5691754	5691892	1	-	1	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5691754	5691892	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	intron	5691893	5691981	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5691982	5692209	1	-	1	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5691982	5692209	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	intron	5692210	5692310	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5692311	5692409	1	-	1	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5692311	5692409	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	intron	5692410	5692546	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5692547	5692895	1	-	2	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5692547	5692895	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	intron	5692896	5692994	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	CDS	5692995	5694288	0.87	-	0	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	exon	5692995	5694288	.	-	.	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
Phchi.S3	AUGUSTUS	start_codon	5694286	5694288	.	-	0	transcript_id "Phchi.S3G062700.t1"; gene_id "Phchi.S3G062700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15624.t1 is derived from g14093.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20349940	20353629	.	+	.	Phchi.S3G294300
Phchi.S3	AUGUSTUS	transcript	20349940	20353629	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	start_codon	20349940	20349942	.	+	0	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	CDS	20349940	20350540	0.7	+	0	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	exon	20349940	20350540	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	intron	20350541	20350681	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	CDS	20350682	20350806	1	+	2	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	exon	20350682	20350806	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	intron	20350807	20350906	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	CDS	20350907	20351186	0.68	+	0	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	exon	20350907	20351186	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	intron	20351187	20351392	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	CDS	20351393	20352873	0.86	+	2	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	exon	20351393	20352873	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	intron	20352874	20352966	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	CDS	20352967	20353629	1	+	0	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	exon	20352967	20353629	.	+	.	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
Phchi.S3	AUGUSTUS	stop_codon	20353630	20353632	.	+	0	transcript_id "Phchi.S3G294300.t1"; gene_id "Phchi.S3G294300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4879.t1 is derived from g2049.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	13190739	13191474	.	+	.	Phchi.S1G203800
Phchi.S1	AUGUSTUS	transcript	13190739	13191474	.	+	.	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	start_codon	13190739	13190741	.	+	0	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	CDS	13190739	13190939	0.83	+	0	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	exon	13190739	13190939	.	+	.	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	intron	13190940	13191033	.	+	.	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	CDS	13191034	13191474	0.89	+	0	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	exon	13191034	13191474	.	+	.	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
Phchi.S1	AUGUSTUS	stop_codon	13191475	13191477	.	+	0	transcript_id "Phchi.S1G203800.t1"; gene_id "Phchi.S1G203800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4276.t1 is derived from g1445.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	9344213	9344872	.	+	.	Phchi.S1G143500
Phchi.S1	AUGUSTUS	transcript	9344213	9344872	.	+	.	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	start_codon	9344213	9344215	.	+	0	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	CDS	9344213	9344652	0.84	+	0	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	exon	9344213	9344652	.	+	.	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	intron	9344653	9344723	.	+	.	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	CDS	9344724	9344774	0.55	+	1	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	exon	9344724	9344774	.	+	.	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	intron	9344775	9344868	.	+	.	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	CDS	9344869	9344872	0.97	+	1	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	exon	9344869	9344872	.	+	.	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
Phchi.S1	AUGUSTUS	stop_codon	9344873	9344875	.	+	0	transcript_id "Phchi.S1G143500.t1"; gene_id "Phchi.S1G143500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8410.t1 is derived from g5585.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35834026	35834495	.	+	.	Phchi.S1G556900
Phchi.S1	AUGUSTUS	transcript	35834026	35834495	.	+	.	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	start_codon	35834026	35834028	.	+	0	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	CDS	35834026	35834176	0.54	+	0	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	exon	35834026	35834176	.	+	.	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	intron	35834177	35834340	.	+	.	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	CDS	35834341	35834495	0.43	+	2	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	exon	35834341	35834495	.	+	.	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
Phchi.S1	AUGUSTUS	stop_codon	35834496	35834498	.	+	0	transcript_id "Phchi.S1G556900.t1"; gene_id "Phchi.S1G556900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15957.t1 is derived from g11140.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C91	AUGUSTUS	gene	23737	25904	.	-	.	Phchi.C91G000400
Phchi.C91	AUGUSTUS	transcript	23737	25904	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	stop_codon	23734	23736	.	-	0	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	23737	23795	1	-	2	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	23737	23795	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	23796	23872	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	23873	23950	1	-	2	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	23873	23950	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	23951	24078	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	24079	24165	1	-	2	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	24079	24165	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	24166	24299	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	24300	24640	1	-	1	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	24300	24640	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	24641	24765	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	24766	24934	1	-	2	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	24766	24934	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	24935	25147	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	25148	25345	1	-	2	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	25148	25345	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	25346	25443	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	25444	25549	1	-	0	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	25444	25549	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	intron	25550	25631	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	CDS	25632	25904	0.72	-	0	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	exon	25632	25904	.	-	.	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
Phchi.C91	AUGUSTUS	start_codon	25902	25904	.	-	0	transcript_id "Phchi.C91G000400.t1"; gene_id "Phchi.C91G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13589.t1 is derived from g12056.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7607026	7607937	.	+	.	Phchi.S3G090800
Phchi.S3	AUGUSTUS	transcript	7607026	7607937	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	start_codon	7607026	7607028	.	+	0	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	CDS	7607026	7607079	0.96	+	0	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	exon	7607026	7607079	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	intron	7607080	7607365	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	CDS	7607366	7607414	1	+	0	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	exon	7607366	7607414	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	intron	7607415	7607493	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	CDS	7607494	7607725	1	+	2	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	exon	7607494	7607725	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	intron	7607726	7607825	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	CDS	7607826	7607937	1	+	1	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	exon	7607826	7607937	.	+	.	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
Phchi.S3	AUGUSTUS	stop_codon	7607938	7607940	.	+	0	transcript_id "Phchi.S3G090800.t1"; gene_id "Phchi.S3G090800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14582.t1 is derived from g13050.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13567137	13568074	.	+	.	Phchi.S3G190100
Phchi.S3	AUGUSTUS	transcript	13567137	13568074	.	+	.	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	start_codon	13567137	13567139	.	+	0	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	CDS	13567137	13567667	0.96	+	0	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	exon	13567137	13567667	.	+	.	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	intron	13567668	13567799	.	+	.	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	CDS	13567800	13567917	0.66	+	0	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	exon	13567800	13567917	.	+	.	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	intron	13567918	13568045	.	+	.	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	CDS	13568046	13568074	0.53	+	2	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	exon	13568046	13568074	.	+	.	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
Phchi.S3	AUGUSTUS	stop_codon	13568075	13568077	.	+	0	transcript_id "Phchi.S3G190100.t1"; gene_id "Phchi.S3G190100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10589.t1 is derived from g14639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1081434	1083727	.	-	.	Phchi.S4G017100
Phchi.S4	AUGUSTUS	transcript	1081434	1083727	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	stop_codon	1081431	1081433	.	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1081434	1082006	0.71	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1081434	1082006	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1082007	1082129	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1082130	1082186	1	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1082130	1082186	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1082187	1082270	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1082271	1082367	1	-	1	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1082271	1082367	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1082368	1082450	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1082451	1082542	1	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1082451	1082542	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1082543	1082625	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1082626	1082671	0.61	-	1	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1082626	1082671	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1082672	1082778	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1082779	1082933	0.85	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1082779	1082933	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1082934	1083024	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1083025	1083277	0.81	-	1	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1083025	1083277	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1083278	1083368	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1083369	1083445	0.89	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1083369	1083445	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	intron	1083446	1083562	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	CDS	1083563	1083727	0.74	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	exon	1083563	1083727	.	-	.	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
Phchi.S4	AUGUSTUS	start_codon	1083725	1083727	.	-	0	transcript_id "Phchi.S4G017100.t1"; gene_id "Phchi.S4G017100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10716.t1 is derived from g14766.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1738406	1741456	.	-	.	Phchi.S4G029800
Phchi.S4	AUGUSTUS	transcript	1738406	1741456	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	stop_codon	1738403	1738405	.	-	0	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	CDS	1738406	1739440	0.82	-	0	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	exon	1738406	1739440	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	intron	1739441	1739926	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	CDS	1739927	1740049	0.52	-	0	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	exon	1739927	1740049	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	intron	1740050	1740232	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	CDS	1740233	1740584	0.51	-	1	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	exon	1740233	1740584	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	intron	1740585	1740848	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	CDS	1740849	1741456	0.63	-	0	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	exon	1740849	1741456	.	-	.	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	start_codon	1741454	1741456	.	-	0	transcript_id "Phchi.S4G029800.t1"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	transcript	1738406	1738963	.	-	.	transcript_id "Phchi.S4G029800.t2"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	stop_codon	1738403	1738405	.	-	0	transcript_id "Phchi.S4G029800.t2"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	CDS	1738406	1738963	0.97	-	0	transcript_id "Phchi.S4G029800.t2"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	exon	1738406	1738963	.	-	.	transcript_id "Phchi.S4G029800.t2"; gene_id "Phchi.S4G029800"
Phchi.S4	AUGUSTUS	start_codon	1738961	1738963	.	-	0	transcript_id "Phchi.S4G029800.t2"; gene_id "Phchi.S4G029800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8142.t1 is derived from g5317.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	34049801	34055451	.	+	.	Phchi.S1G530100
Phchi.S1	AUGUSTUS	transcript	34049801	34055451	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	start_codon	34049801	34049803	.	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34049801	34050006	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34049801	34050006	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34050007	34050095	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34050096	34050348	1	+	1	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34050096	34050348	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34050349	34050608	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34050609	34050693	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34050609	34050693	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34050694	34050837	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34050838	34051591	0.73	+	2	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34050838	34051591	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34051592	34051752	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34051753	34051902	0.9	+	1	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34051753	34051902	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34051903	34052038	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34052039	34052090	1	+	1	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34052039	34052090	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34052091	34052218	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34052219	34052341	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34052219	34052341	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34052342	34052474	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34052475	34052550	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34052475	34052550	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34052551	34053166	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34053167	34053351	0.98	+	2	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34053167	34053351	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34053352	34053627	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34053628	34053822	0.99	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34053628	34053822	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34053823	34053984	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34053985	34054056	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34053985	34054056	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34054057	34054151	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34054152	34054358	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34054152	34054358	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34054359	34054438	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34054439	34054564	0.97	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34054439	34054564	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34054565	34054666	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34054667	34054816	0.92	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34054667	34054816	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34054817	34054918	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34054919	34054980	0.94	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34054919	34054980	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34054981	34055109	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34055110	34055185	1	+	1	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34055110	34055185	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	intron	34055186	34055265	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	CDS	34055266	34055451	1	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	exon	34055266	34055451	.	+	.	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
Phchi.S1	AUGUSTUS	stop_codon	34055452	34055454	.	+	0	transcript_id "Phchi.S1G530100.t1"; gene_id "Phchi.S1G530100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15298.t1 is derived from g13766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18275253	18278502	.	-	.	Phchi.S3G261700
Phchi.S3	AUGUSTUS	transcript	18275253	18278502	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	stop_codon	18275250	18275252	.	-	0	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	CDS	18275253	18275795	1	-	0	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	exon	18275253	18275795	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	intron	18275796	18275902	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	CDS	18275903	18276615	1	-	2	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	exon	18275903	18276615	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	intron	18276616	18276729	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	CDS	18276730	18277023	0.99	-	2	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	exon	18276730	18277023	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	intron	18277024	18277129	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	CDS	18277130	18277339	0.51	-	2	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	exon	18277130	18277339	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	intron	18277340	18277595	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	CDS	18277596	18278502	0.49	-	0	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	exon	18277596	18278502	.	-	.	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
Phchi.S3	AUGUSTUS	start_codon	18278500	18278502	.	-	0	transcript_id "Phchi.S3G261700.t1"; gene_id "Phchi.S3G261700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2618.t1 is derived from g9538.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7798311	7800059	.	+	.	Phchi.S5G122700
Phchi.S5	AUGUSTUS	transcript	7798311	7800059	.	+	.	transcript_id "Phchi.S5G122700.t1"; gene_id "Phchi.S5G122700"
Phchi.S5	AUGUSTUS	start_codon	7798311	7798313	.	+	0	transcript_id "Phchi.S5G122700.t1"; gene_id "Phchi.S5G122700"
Phchi.S5	AUGUSTUS	CDS	7798311	7800059	0.96	+	0	transcript_id "Phchi.S5G122700.t1"; gene_id "Phchi.S5G122700"
Phchi.S5	AUGUSTUS	exon	7798311	7800059	.	+	.	transcript_id "Phchi.S5G122700.t1"; gene_id "Phchi.S5G122700"
Phchi.S5	AUGUSTUS	stop_codon	7800060	7800062	.	+	0	transcript_id "Phchi.S5G122700.t1"; gene_id "Phchi.S5G122700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9484.t1 is derived from g6660.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41970188	41971389	.	+	.	Phchi.S1G664300
Phchi.S1	AUGUSTUS	transcript	41970188	41971389	.	+	.	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	start_codon	41970188	41970190	.	+	0	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	CDS	41970188	41970662	0.59	+	0	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	exon	41970188	41970662	.	+	.	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	intron	41970663	41970772	.	+	.	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	CDS	41970773	41971389	0.6	+	2	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	exon	41970773	41971389	.	+	.	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
Phchi.S1	AUGUSTUS	stop_codon	41971390	41971392	.	+	0	transcript_id "Phchi.S1G664300.t1"; gene_id "Phchi.S1G664300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9821.t1 is derived from g6997.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43949643	43950621	.	-	.	Phchi.S1G698000
Phchi.S1	AUGUSTUS	transcript	43949643	43950621	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	stop_codon	43949640	43949642	.	-	0	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	CDS	43949643	43949858	1	-	0	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	exon	43949643	43949858	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	intron	43949859	43949957	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	CDS	43949958	43950047	1	-	0	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	exon	43949958	43950047	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	intron	43950048	43950127	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	CDS	43950128	43950265	1	-	0	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	exon	43950128	43950265	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	intron	43950266	43950414	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	CDS	43950415	43950621	1	-	0	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	exon	43950415	43950621	.	-	.	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
Phchi.S1	AUGUSTUS	start_codon	43950619	43950621	.	-	0	transcript_id "Phchi.S1G698000.t1"; gene_id "Phchi.S1G698000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10553.t1 is derived from g14603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	963571	964741	.	+	.	Phchi.S4G013500
Phchi.S4	AUGUSTUS	transcript	963571	964741	.	+	.	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	start_codon	963571	963573	.	+	0	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	CDS	963571	964403	1	+	0	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	exon	963571	964403	.	+	.	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	intron	964404	964509	.	+	.	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	CDS	964510	964741	1	+	1	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	exon	964510	964741	.	+	.	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
Phchi.S4	AUGUSTUS	stop_codon	964742	964744	.	+	0	transcript_id "Phchi.S4G013500.t1"; gene_id "Phchi.S4G013500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7065.t1 is derived from g4237.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26699874	26703173	.	+	.	Phchi.S1G422400
Phchi.S1	AUGUSTUS	transcript	26699874	26703173	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	start_codon	26699874	26699876	.	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26699874	26700026	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26699874	26700026	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26700027	26700253	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26700254	26700389	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26700254	26700389	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26700390	26700488	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26700489	26700591	1	+	2	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26700489	26700591	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26700592	26700732	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26700733	26700856	1	+	1	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26700733	26700856	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26700857	26701058	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26701059	26701124	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26701059	26701124	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26701125	26701341	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26701342	26701380	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26701342	26701380	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26701381	26701630	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26701631	26701711	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26701631	26701711	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26701712	26701854	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26701855	26701902	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26701855	26701902	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26701903	26702052	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26702053	26702103	1	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26702053	26702103	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26702104	26702284	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26702285	26702353	0.99	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26702285	26702353	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26702354	26702470	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26702471	26702741	0.97	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26702471	26702741	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	intron	26702742	26702829	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	CDS	26702830	26703173	0.72	+	2	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	exon	26702830	26703173	.	+	.	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
Phchi.S1	AUGUSTUS	stop_codon	26703174	26703176	.	+	0	transcript_id "Phchi.S1G422400.t1"; gene_id "Phchi.S1G422400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8094.t1 is derived from g5269.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32918246	32919298	.	+	.	Phchi.S1G525300
Phchi.S1	AUGUSTUS	transcript	32918246	32919298	.	+	.	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	start_codon	32918246	32918248	.	+	0	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	CDS	32918246	32919148	0.84	+	0	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	exon	32918246	32919148	.	+	.	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	intron	32919149	32919286	.	+	.	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	CDS	32919287	32919298	0.74	+	0	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	exon	32919287	32919298	.	+	.	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
Phchi.S1	AUGUSTUS	stop_codon	32919299	32919301	.	+	0	transcript_id "Phchi.S1G525300.t1"; gene_id "Phchi.S1G525300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3930.t1 is derived from g1099.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6485201	6487060	.	+	.	Phchi.S1G108900
Phchi.S1	AUGUSTUS	transcript	6485201	6487060	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	start_codon	6485201	6485203	.	+	0	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	CDS	6485201	6485297	1	+	0	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	exon	6485201	6485297	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	intron	6485298	6485439	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	CDS	6485440	6485809	0.55	+	2	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	exon	6485440	6485809	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	intron	6485810	6485983	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	CDS	6485984	6486599	0.35	+	1	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	exon	6485984	6486599	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	intron	6486600	6486777	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	CDS	6486778	6486916	0.99	+	0	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	exon	6486778	6486916	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	intron	6486917	6487031	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	CDS	6487032	6487060	1	+	2	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	exon	6487032	6487060	.	+	.	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
Phchi.S1	AUGUSTUS	stop_codon	6487061	6487063	.	+	0	transcript_id "Phchi.S1G108900.t1"; gene_id "Phchi.S1G108900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14331.t1 is derived from g12798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12125119	12127128	.	+	.	Phchi.S3G165000
Phchi.S3	AUGUSTUS	transcript	12125119	12127128	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	start_codon	12125119	12125121	.	+	0	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	CDS	12125119	12125973	0.4	+	0	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	exon	12125119	12125973	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	intron	12125974	12126056	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	CDS	12126057	12126391	1	+	0	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	exon	12126057	12126391	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	intron	12126392	12126487	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	CDS	12126488	12126654	1	+	1	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	exon	12126488	12126654	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	intron	12126655	12126757	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	CDS	12126758	12126842	1	+	2	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	exon	12126758	12126842	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	intron	12126843	12126950	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	CDS	12126951	12127128	0.97	+	1	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	exon	12126951	12127128	.	+	.	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
Phchi.S3	AUGUSTUS	stop_codon	12127129	12127131	.	+	0	transcript_id "Phchi.S3G165000.t1"; gene_id "Phchi.S3G165000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6029.t1 is derived from g3200.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20509416	20510555	.	+	.	Phchi.S1G318800
Phchi.S1	AUGUSTUS	transcript	20509416	20510555	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	start_codon	20509416	20509418	.	+	0	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	CDS	20509416	20509662	0.92	+	0	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	exon	20509416	20509662	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	intron	20509663	20509775	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	CDS	20509776	20509815	0.99	+	2	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	exon	20509776	20509815	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	intron	20509816	20509893	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	CDS	20509894	20509966	1	+	1	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	exon	20509894	20509966	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	intron	20509967	20510063	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	CDS	20510064	20510168	1	+	0	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	exon	20510064	20510168	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	intron	20510169	20510248	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	CDS	20510249	20510329	1	+	0	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	exon	20510249	20510329	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	intron	20510330	20510426	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	CDS	20510427	20510555	0.99	+	0	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	exon	20510427	20510555	.	+	.	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
Phchi.S1	AUGUSTUS	stop_codon	20510556	20510558	.	+	0	transcript_id "Phchi.S1G318800.t1"; gene_id "Phchi.S1G318800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15494.t1 is derived from g13963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19488266	19490903	.	-	.	Phchi.S3G281300
Phchi.S3	AUGUSTUS	transcript	19488266	19490903	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	stop_codon	19488263	19488265	.	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19488266	19488661	1	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19488266	19488661	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	intron	19488662	19488829	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19488830	19488883	0.59	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19488830	19488883	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	intron	19488884	19488976	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19488977	19489190	0.54	-	1	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19488977	19489190	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	intron	19489191	19489386	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19489387	19489545	0.99	-	1	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19489387	19489545	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	intron	19489546	19489654	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19489655	19490115	1	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19489655	19490115	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	intron	19490116	19490243	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19490244	19490429	1	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19490244	19490429	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	intron	19490430	19490534	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	CDS	19490535	19490903	0.87	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	exon	19490535	19490903	.	-	.	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
Phchi.S3	AUGUSTUS	start_codon	19490901	19490903	.	-	0	transcript_id "Phchi.S3G281300.t1"; gene_id "Phchi.S3G281300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15432.t1 is derived from g13900.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19067327	19067635	.	+	.	Phchi.S3G275100
Phchi.S3	AUGUSTUS	transcript	19067327	19067635	.	+	.	transcript_id "Phchi.S3G275100.t1"; gene_id "Phchi.S3G275100"
Phchi.S3	AUGUSTUS	start_codon	19067327	19067329	.	+	0	transcript_id "Phchi.S3G275100.t1"; gene_id "Phchi.S3G275100"
Phchi.S3	AUGUSTUS	CDS	19067327	19067635	0.61	+	0	transcript_id "Phchi.S3G275100.t1"; gene_id "Phchi.S3G275100"
Phchi.S3	AUGUSTUS	exon	19067327	19067635	.	+	.	transcript_id "Phchi.S3G275100.t1"; gene_id "Phchi.S3G275100"
Phchi.S3	AUGUSTUS	stop_codon	19067636	19067638	.	+	0	transcript_id "Phchi.S3G275100.t1"; gene_id "Phchi.S3G275100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14553.t1 is derived from g13021.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13449197	13450169	.	-	.	Phchi.S3G187200
Phchi.S3	AUGUSTUS	transcript	13449197	13450169	.	-	.	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	stop_codon	13449194	13449196	.	-	0	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	CDS	13449197	13449471	0.29	-	2	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	exon	13449197	13449471	.	-	.	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	intron	13449472	13449602	.	-	.	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	CDS	13449603	13449698	0.92	-	2	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	exon	13449603	13449698	.	-	.	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	intron	13449699	13449934	.	-	.	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	CDS	13449935	13450169	0.95	-	0	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	exon	13449935	13450169	.	-	.	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
Phchi.S3	AUGUSTUS	start_codon	13450167	13450169	.	-	0	transcript_id "Phchi.S3G187200.t1"; gene_id "Phchi.S3G187200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2799.t1 is derived from g9719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8938908	8939777	.	+	.	Phchi.S5G140800
Phchi.S5	AUGUSTUS	transcript	8938908	8939777	.	+	.	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	start_codon	8938908	8938910	.	+	0	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	CDS	8938908	8938926	0.99	+	0	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	exon	8938908	8938926	.	+	.	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	intron	8938927	8938996	.	+	.	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	CDS	8938997	8939292	1	+	2	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	exon	8938997	8939292	.	+	.	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	intron	8939293	8939378	.	+	.	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	CDS	8939379	8939777	1	+	0	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	exon	8939379	8939777	.	+	.	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
Phchi.S5	AUGUSTUS	stop_codon	8939778	8939780	.	+	0	transcript_id "Phchi.S5G140800.t1"; gene_id "Phchi.S5G140800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1780.t1 is derived from g8700.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2974632	2976537	.	+	.	Phchi.S5G038900
Phchi.S5	AUGUSTUS	transcript	2974632	2976537	.	+	.	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	start_codon	2974632	2974634	.	+	0	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	CDS	2974632	2975170	0.03	+	0	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	exon	2974632	2975170	.	+	.	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	intron	2975171	2976530	.	+	.	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	CDS	2976531	2976537	0.01	+	1	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	exon	2976531	2976537	.	+	.	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
Phchi.S5	AUGUSTUS	stop_codon	2976538	2976540	.	+	0	transcript_id "Phchi.S5G038900.t1"; gene_id "Phchi.S5G038900"
# This transcript jg14186.t2 is derived from g12653.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14187.t1 is derived from g12654.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	11390903	11393106	.	-	.	Phchi.S3G150600
Phchi.S3	AUGUSTUS	transcript	11390903	11393106	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	stop_codon	11390900	11390902	.	-	0	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	CDS	11390903	11391172	0.86	-	0	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	exon	11390903	11391172	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	intron	11391173	11391342	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	CDS	11391343	11391579	1	-	0	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	exon	11391343	11391579	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	intron	11391580	11391686	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	CDS	11391687	11392054	0.93	-	2	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	exon	11391687	11392054	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	intron	11392055	11392151	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	CDS	11392152	11392193	0.62	-	2	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	exon	11392152	11392193	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	intron	11392194	11392814	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	CDS	11392815	11393106	0.88	-	0	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	exon	11392815	11393106	.	-	.	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
Phchi.S3	AUGUSTUS	start_codon	11393104	11393106	.	-	0	transcript_id "Phchi.S3G150600.t1"; gene_id "Phchi.S3G150600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12590.t1 is derived from g8267.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	36302674	36303631	.	-	.	Phchi.S2G067000
Phchi.S2	AUGUSTUS	transcript	36302674	36303631	.	-	.	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	stop_codon	36302671	36302673	.	-	0	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	CDS	36302674	36302854	0.25	-	1	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	exon	36302674	36302854	.	-	.	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	intron	36302855	36303128	.	-	.	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	CDS	36303129	36303188	0.4	-	1	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	exon	36303129	36303188	.	-	.	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	intron	36303189	36303314	.	-	.	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	CDS	36303315	36303631	0.35	-	0	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	exon	36303315	36303631	.	-	.	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
Phchi.S2	AUGUSTUS	start_codon	36303629	36303631	.	-	0	transcript_id "Phchi.S2G067000.t1"; gene_id "Phchi.S2G067000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14885.t1 is derived from g13353.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15275452	15278494	.	-	.	Phchi.S3G220400
Phchi.S3	AUGUSTUS	transcript	15275452	15278494	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	stop_codon	15275449	15275451	.	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15275452	15275558	1	-	2	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15275452	15275558	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15275559	15275649	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15275650	15275713	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15275650	15275713	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15275714	15275805	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15275806	15275890	1	-	1	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15275806	15275890	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15275891	15275966	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15275967	15276013	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15275967	15276013	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15276014	15276129	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15276130	15276183	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15276130	15276183	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15276184	15276288	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15276289	15276523	1	-	1	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15276289	15276523	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15276524	15276634	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15276635	15276756	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15276635	15276756	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15276757	15276894	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15276895	15276918	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15276895	15276918	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15276919	15277030	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15277031	15277110	0.99	-	2	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15277031	15277110	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15277111	15277224	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15277225	15277321	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15277225	15277321	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15277322	15277406	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15277407	15277472	1	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15277407	15277472	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15277473	15277608	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15277609	15277928	1	-	2	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15277609	15277928	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	intron	15277929	15278085	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	CDS	15278086	15278494	0.89	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	exon	15278086	15278494	.	-	.	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
Phchi.S3	AUGUSTUS	start_codon	15278492	15278494	.	-	0	transcript_id "Phchi.S3G220400.t1"; gene_id "Phchi.S3G220400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11071.t1 is derived from g15121.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3965648	3967045	.	+	.	Phchi.S4G065300
Phchi.S4	AUGUSTUS	transcript	3965648	3967045	.	+	.	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	start_codon	3965648	3965650	.	+	0	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	CDS	3965648	3966628	0.99	+	0	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	exon	3965648	3966628	.	+	.	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	intron	3966629	3966735	.	+	.	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	CDS	3966736	3966856	0.98	+	0	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	exon	3966736	3966856	.	+	.	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	intron	3966857	3966947	.	+	.	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	CDS	3966948	3967045	0.5	+	2	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	exon	3966948	3967045	.	+	.	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
Phchi.S4	AUGUSTUS	stop_codon	3967046	3967048	.	+	0	transcript_id "Phchi.S4G065300.t1"; gene_id "Phchi.S4G065300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8409.t1 is derived from g5584.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35819889	35820577	.	-	.	Phchi.S1G556800
Phchi.S1	AUGUSTUS	transcript	35819889	35820577	.	-	.	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	stop_codon	35819886	35819888	.	-	0	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	CDS	35819889	35820075	0.63	-	1	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	exon	35819889	35820075	.	-	.	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	intron	35820076	35820518	.	-	.	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	CDS	35820519	35820577	0.63	-	0	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	exon	35820519	35820577	.	-	.	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
Phchi.S1	AUGUSTUS	start_codon	35820575	35820577	.	-	0	transcript_id "Phchi.S1G556800.t1"; gene_id "Phchi.S1G556800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12660.t1 is derived from g14459.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C12	AUGUSTUS	gene	37509	38602	.	-	.	Phchi.C12G001000
Phchi.C12	AUGUSTUS	transcript	37509	38602	.	-	.	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	stop_codon	37506	37508	.	-	0	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	CDS	37509	37994	0.74	-	0	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	exon	37509	37994	.	-	.	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	intron	37995	38077	.	-	.	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	CDS	38078	38284	0.95	-	0	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	exon	38078	38284	.	-	.	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	intron	38285	38419	.	-	.	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	CDS	38420	38602	0.6	-	0	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	exon	38420	38602	.	-	.	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
Phchi.C12	AUGUSTUS	start_codon	38600	38602	.	-	0	transcript_id "Phchi.C12G001000.t1"; gene_id "Phchi.C12G001000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1066.t1 is derived from g10849.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7407735	7408226	.	+	.	Phchi.S6G102500
Phchi.S6	AUGUSTUS	transcript	7407735	7408226	.	+	.	transcript_id "Phchi.S6G102500.t1"; gene_id "Phchi.S6G102500"
Phchi.S6	AUGUSTUS	start_codon	7407735	7407737	.	+	0	transcript_id "Phchi.S6G102500.t1"; gene_id "Phchi.S6G102500"
Phchi.S6	AUGUSTUS	CDS	7407735	7408226	0.99	+	0	transcript_id "Phchi.S6G102500.t1"; gene_id "Phchi.S6G102500"
Phchi.S6	AUGUSTUS	exon	7407735	7408226	.	+	.	transcript_id "Phchi.S6G102500.t1"; gene_id "Phchi.S6G102500"
Phchi.S6	AUGUSTUS	stop_codon	7408227	7408229	.	+	0	transcript_id "Phchi.S6G102500.t1"; gene_id "Phchi.S6G102500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7823.t1 is derived from g4997.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31379052	31381253	.	-	.	Phchi.S1G498200
Phchi.S1	AUGUSTUS	transcript	31379052	31381253	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	stop_codon	31379049	31379051	.	-	0	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31379052	31379100	0.87	-	1	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31379052	31379100	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31379101	31379203	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31379204	31379298	0.92	-	0	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31379204	31379298	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31379299	31379392	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31379393	31379424	1	-	2	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31379393	31379424	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31379425	31380384	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380385	31380447	1	-	2	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380385	31380447	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31380448	31380542	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380543	31380637	0.98	-	1	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380543	31380637	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31380638	31380713	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380714	31380770	0.98	-	1	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380714	31380770	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31380771	31380912	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380913	31381007	0.99	-	0	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380913	31381007	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31381008	31381157	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31381158	31381253	0.98	-	0	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31381158	31381253	.	-	.	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	start_codon	31381251	31381253	.	-	0	transcript_id "Phchi.S1G498200.t1"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	transcript	31379052	31381253	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	stop_codon	31379049	31379051	.	-	0	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31379052	31379100	0.85	-	1	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31379052	31379100	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31379101	31379203	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31379204	31379298	0.87	-	0	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31379204	31379298	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31379299	31379392	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31379393	31379424	1	-	2	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31379393	31379424	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31379425	31380384	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380385	31380447	1	-	2	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380385	31380447	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31380448	31380542	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380543	31380673	1	-	1	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380543	31380673	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31380674	31380912	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31380913	31381007	1	-	0	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31380913	31381007	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	intron	31381008	31381157	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	CDS	31381158	31381253	0.99	-	0	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	exon	31381158	31381253	.	-	.	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
Phchi.S1	AUGUSTUS	start_codon	31381251	31381253	.	-	0	transcript_id "Phchi.S1G498200.t2"; gene_id "Phchi.S1G498200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10515.t1 is derived from g14565.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	793488	794029	.	-	.	Phchi.S4G009700
Phchi.S4	AUGUSTUS	transcript	793488	794029	.	-	.	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	stop_codon	793485	793487	.	-	0	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	CDS	793488	793760	0.84	-	0	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	exon	793488	793760	.	-	.	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	intron	793761	793870	.	-	.	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	CDS	793871	794029	0.84	-	0	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	exon	793871	794029	.	-	.	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
Phchi.S4	AUGUSTUS	start_codon	794027	794029	.	-	0	transcript_id "Phchi.S4G009700.t1"; gene_id "Phchi.S4G009700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5808.t1 is derived from g2978.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19046227	19046700	.	+	.	Phchi.S1G296700
Phchi.S1	AUGUSTUS	transcript	19046227	19046700	.	+	.	transcript_id "Phchi.S1G296700.t1"; gene_id "Phchi.S1G296700"
Phchi.S1	AUGUSTUS	start_codon	19046227	19046229	.	+	0	transcript_id "Phchi.S1G296700.t1"; gene_id "Phchi.S1G296700"
Phchi.S1	AUGUSTUS	CDS	19046227	19046700	0.98	+	0	transcript_id "Phchi.S1G296700.t1"; gene_id "Phchi.S1G296700"
Phchi.S1	AUGUSTUS	exon	19046227	19046700	.	+	.	transcript_id "Phchi.S1G296700.t1"; gene_id "Phchi.S1G296700"
Phchi.S1	AUGUSTUS	stop_codon	19046701	19046703	.	+	0	transcript_id "Phchi.S1G296700.t1"; gene_id "Phchi.S1G296700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3614.t1 is derived from g783.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4752084	4752516	.	+	.	Phchi.S1G077300
Phchi.S1	AUGUSTUS	transcript	4752084	4752516	.	+	.	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	start_codon	4752084	4752086	.	+	0	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	CDS	4752084	4752182	0.75	+	0	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	exon	4752084	4752182	.	+	.	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	intron	4752183	4752318	.	+	.	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	CDS	4752319	4752516	0.95	+	0	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	exon	4752319	4752516	.	+	.	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
Phchi.S1	AUGUSTUS	stop_codon	4752517	4752519	.	+	0	transcript_id "Phchi.S1G077300.t1"; gene_id "Phchi.S1G077300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5788.t1 is derived from g2958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18960781	18964363	.	+	.	Phchi.S1G294700
Phchi.S1	AUGUSTUS	transcript	18960781	18964363	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	start_codon	18960781	18960783	.	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18960781	18960932	0.67	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18960781	18960932	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18960933	18961145	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18961146	18961238	1	+	1	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18961146	18961238	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18961239	18961360	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18961361	18961514	1	+	1	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18961361	18961514	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18961515	18961643	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18961644	18961827	1	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18961644	18961827	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18961828	18961952	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18961953	18962022	1	+	2	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18961953	18962022	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18962023	18962199	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18962200	18962273	1	+	1	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18962200	18962273	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18962274	18962368	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18962369	18962436	1	+	2	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18962369	18962436	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18962437	18962558	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18962559	18962650	1	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18962559	18962650	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18962651	18962819	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18962820	18962964	1	+	1	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18962820	18962964	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18962965	18963099	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18963100	18963228	0.58	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18963100	18963228	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18963229	18963337	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18963338	18963409	0.59	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18963338	18963409	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18963410	18963935	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18963936	18964046	0.74	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18963936	18964046	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18964047	18964221	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18964222	18964264	1	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18964222	18964264	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	intron	18964265	18964349	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	CDS	18964350	18964363	1	+	2	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	exon	18964350	18964363	.	+	.	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
Phchi.S1	AUGUSTUS	stop_codon	18964364	18964366	.	+	0	transcript_id "Phchi.S1G294700.t1"; gene_id "Phchi.S1G294700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5511.t1 is derived from g2681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17167354	17171175	.	-	.	Phchi.S1G267000
Phchi.S1	AUGUSTUS	transcript	17167354	17171175	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	stop_codon	17167351	17167353	.	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17167354	17167530	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17167354	17167530	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17167531	17167627	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17167628	17167693	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17167628	17167693	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17167694	17167765	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17167766	17167828	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17167766	17167828	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17167829	17167982	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17167983	17168112	1	-	1	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17167983	17168112	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17168113	17168197	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17168198	17168337	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17168198	17168337	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17168338	17168447	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17168448	17168493	1	-	1	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17168448	17168493	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17168494	17168622	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17168623	17168720	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17168623	17168720	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17168721	17168915	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17168916	17168993	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17168916	17168993	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17168994	17169185	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17169186	17169242	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17169186	17169242	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17169243	17169344	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17169345	17169413	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17169345	17169413	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17169414	17169502	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17169503	17169568	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17169503	17169568	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17169569	17169667	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17169668	17169679	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17169668	17169679	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17169680	17169915	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17169916	17169994	1	-	1	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17169916	17169994	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17169995	17170116	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17170117	17170217	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17170117	17170217	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17170218	17170402	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17170403	17170507	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17170403	17170507	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17170508	17170589	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17170590	17170792	1	-	2	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17170590	17170792	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17170793	17170886	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17170887	17170970	1	-	2	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17170887	17170970	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	intron	17170971	17171063	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	CDS	17171064	17171175	1	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	exon	17171064	17171175	.	-	.	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
Phchi.S1	AUGUSTUS	start_codon	17171173	17171175	.	-	0	transcript_id "Phchi.S1G267000.t1"; gene_id "Phchi.S1G267000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10526.t1 is derived from g14576.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	835741	838395	.	-	.	Phchi.S4G010800
Phchi.S4	AUGUSTUS	transcript	835741	838395	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	stop_codon	835738	835740	.	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	835741	835794	0.93	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	835741	835794	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	835795	835894	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	835895	835977	1	-	2	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	835895	835977	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	835978	836071	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	836072	836245	0.97	-	2	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	836072	836245	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	836246	836346	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	836347	836479	1	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	836347	836479	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	836480	836600	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	836601	836685	1	-	1	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	836601	836685	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	836686	836893	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	836894	837017	1	-	2	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	836894	837017	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	837018	837090	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	837091	837160	1	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	837091	837160	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	837161	837309	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	837310	837336	1	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	837310	837336	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	837337	837537	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	837538	837740	0.62	-	2	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	837538	837740	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	837741	838114	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	838115	838245	0.89	-	1	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	838115	838245	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	intron	838246	838339	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	CDS	838340	838395	0.92	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	exon	838340	838395	.	-	.	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
Phchi.S4	AUGUSTUS	start_codon	838393	838395	.	-	0	transcript_id "Phchi.S4G010800.t1"; gene_id "Phchi.S4G010800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1703.t1 is derived from g8622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2610632	2611132	.	+	.	Phchi.S5G031200
Phchi.S5	AUGUSTUS	transcript	2610632	2611132	.	+	.	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	start_codon	2610632	2610634	.	+	0	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	CDS	2610632	2610806	0.92	+	0	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	exon	2610632	2610806	.	+	.	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	intron	2610807	2610926	.	+	.	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	CDS	2610927	2611132	0.95	+	2	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	exon	2610927	2611132	.	+	.	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
Phchi.S5	AUGUSTUS	stop_codon	2611133	2611135	.	+	0	transcript_id "Phchi.S5G031200.t1"; gene_id "Phchi.S5G031200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13154.t1 is derived from g11619.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4425100	4427083	.	-	.	Phchi.S3G047300
Phchi.S3	AUGUSTUS	transcript	4425100	4427083	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	stop_codon	4425097	4425099	.	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4425100	4425195	0.98	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4425100	4425195	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4425196	4425285	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4425286	4425370	1	-	1	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4425286	4425370	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4425371	4425463	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4425464	4425552	0.65	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4425464	4425552	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4425553	4425661	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4425662	4425736	0.95	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4425662	4425736	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4425737	4425841	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4425842	4425907	1	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4425842	4425907	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4425908	4426002	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4426003	4426068	1	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4426003	4426068	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4426069	4426151	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4426152	4426266	1	-	1	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4426152	4426266	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4426267	4426390	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4426391	4426419	1	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4426391	4426419	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	intron	4426420	4426543	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	CDS	4426544	4427083	0.96	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	exon	4426544	4427083	.	-	.	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
Phchi.S3	AUGUSTUS	start_codon	4427081	4427083	.	-	0	transcript_id "Phchi.S3G047300.t1"; gene_id "Phchi.S3G047300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14706.t1 is derived from g13174.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14265062	14266763	.	-	.	Phchi.S3G202500
Phchi.S3	AUGUSTUS	transcript	14265062	14266763	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	stop_codon	14265059	14265061	.	-	0	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	CDS	14265062	14265223	1	-	0	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	exon	14265062	14265223	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	intron	14265224	14265368	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	CDS	14265369	14265576	1	-	1	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	exon	14265369	14265576	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	intron	14265577	14265663	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	CDS	14265664	14265796	1	-	2	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	exon	14265664	14265796	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	intron	14265797	14265882	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	CDS	14265883	14266012	1	-	0	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	exon	14265883	14266012	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	intron	14266013	14266099	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	CDS	14266100	14266193	1	-	1	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	exon	14266100	14266193	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	intron	14266194	14266347	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	CDS	14266348	14266763	0.59	-	0	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	exon	14266348	14266763	.	-	.	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
Phchi.S3	AUGUSTUS	start_codon	14266761	14266763	.	-	0	transcript_id "Phchi.S3G202500.t1"; gene_id "Phchi.S3G202500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2499.t1 is derived from g9419.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6981117	6985926	.	+	.	Phchi.S5G110800
Phchi.S5	AUGUSTUS	transcript	6981117	6985926	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	start_codon	6981117	6981119	.	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6981117	6981182	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6981117	6981182	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6981183	6981271	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6981272	6981344	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6981272	6981344	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6981345	6981458	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6981459	6981581	0.98	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6981459	6981581	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6981582	6981695	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6981696	6981865	1	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6981696	6981865	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6981866	6981949	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6981950	6982102	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6981950	6982102	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6982103	6982238	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6982239	6982276	0.55	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6982239	6982276	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6982277	6982386	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6982387	6982429	0.55	+	1	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6982387	6982429	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6982430	6982516	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6982517	6982577	0.42	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6982517	6982577	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6982578	6982804	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6982805	6982995	0.7	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6982805	6982995	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6982996	6983077	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6983078	6983221	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6983078	6983221	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6983222	6983304	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6983305	6983439	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6983305	6983439	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6983440	6983536	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6983537	6983623	0.79	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6983537	6983623	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6983624	6983732	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6983733	6983861	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6983733	6983861	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6983862	6983951	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6983952	6984084	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6983952	6984084	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6984085	6984215	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6984216	6984341	1	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6984216	6984341	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6984342	6984536	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6984537	6984674	1	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6984537	6984674	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6984675	6984817	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6984818	6984864	0.96	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6984818	6984864	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6984865	6985092	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6985093	6985236	0.99	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6985093	6985236	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6985237	6985331	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6985332	6985464	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6985332	6985464	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6985465	6985556	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6985557	6985693	1	+	2	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6985557	6985693	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	intron	6985694	6985827	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	CDS	6985828	6985926	1	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	exon	6985828	6985926	.	+	.	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
Phchi.S5	AUGUSTUS	stop_codon	6985927	6985929	.	+	0	transcript_id "Phchi.S5G110800.t1"; gene_id "Phchi.S5G110800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10764.t1 is derived from g14814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1997350	2000824	.	-	.	Phchi.S4G034600
Phchi.S4	AUGUSTUS	transcript	1997350	2000824	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	stop_codon	1997347	1997349	.	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997350	1997425	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997350	1997425	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1997426	1997502	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997503	1997633	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997503	1997633	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1997634	1997751	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997752	1997853	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997752	1997853	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1997854	1997938	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997939	1998027	1	-	2	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997939	1998027	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998028	1998112	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998113	1998189	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998113	1998189	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998190	1998280	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998281	1998423	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998281	1998423	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998424	1998497	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998498	1998593	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998498	1998593	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998594	1998680	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998681	1998840	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998681	1998840	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998841	1998962	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998963	1999013	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998963	1999013	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999014	1999120	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999121	1999198	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999121	1999198	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999199	1999400	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999401	1999512	1	-	2	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999401	1999512	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999513	1999590	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999591	1999649	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999591	1999649	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999650	1999771	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999772	1999914	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999772	1999914	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999915	1999996	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999997	2000121	1	-	2	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999997	2000121	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	2000122	2000245	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	2000246	2000390	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	2000246	2000390	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	2000391	2000489	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	2000490	2000613	1	-	1	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	2000490	2000613	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	2000614	2000759	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	2000760	2000824	1	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	2000760	2000824	.	-	.	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	start_codon	2000822	2000824	.	-	0	transcript_id "Phchi.S4G034600.t1"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	transcript	1997350	2000824	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	stop_codon	1997347	1997349	.	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997350	1997425	1	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997350	1997425	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1997426	1997502	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997503	1997633	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997503	1997633	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1997634	1997751	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997752	1997853	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997752	1997853	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1997854	1997938	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1997939	1998027	1	-	2	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1997939	1998027	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998028	1998112	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998113	1998189	1	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998113	1998189	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998190	1998280	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998281	1998423	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998281	1998423	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998424	1998497	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998498	1998593	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998498	1998593	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998594	1998680	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998681	1998840	1	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998681	1998840	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1998841	1998962	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1998963	1999013	0.92	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1998963	1999013	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999014	1999125	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999126	1999254	0.82	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999126	1999254	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999255	1999400	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999401	1999512	1	-	2	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999401	1999512	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999513	1999590	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999591	1999649	1	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999591	1999649	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999650	1999771	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999772	1999914	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999772	1999914	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	1999915	1999996	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	1999997	2000121	1	-	2	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	1999997	2000121	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	2000122	2000245	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	2000246	2000390	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	2000246	2000390	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	2000391	2000489	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	2000490	2000613	1	-	1	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	2000490	2000613	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	intron	2000614	2000759	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	CDS	2000760	2000824	1	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	exon	2000760	2000824	.	-	.	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
Phchi.S4	AUGUSTUS	start_codon	2000822	2000824	.	-	0	transcript_id "Phchi.S4G034600.t2"; gene_id "Phchi.S4G034600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14329.t1 is derived from g12796.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12117692	12119014	.	+	.	Phchi.S3G164800
Phchi.S3	AUGUSTUS	transcript	12117692	12119014	.	+	.	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	start_codon	12117692	12117694	.	+	0	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	CDS	12117692	12118274	0.53	+	0	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	exon	12117692	12118274	.	+	.	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	intron	12118275	12118350	.	+	.	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	CDS	12118351	12118425	0.56	+	2	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	exon	12118351	12118425	.	+	.	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	intron	12118426	12118619	.	+	.	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	CDS	12118620	12119014	0.55	+	2	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	exon	12118620	12119014	.	+	.	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
Phchi.S3	AUGUSTUS	stop_codon	12119015	12119017	.	+	0	transcript_id "Phchi.S3G164800.t1"; gene_id "Phchi.S3G164800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14370.t1 is derived from g12837.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12401309	12403147	.	-	.	Phchi.S3G168900
Phchi.S3	AUGUSTUS	transcript	12401309	12403147	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	stop_codon	12401306	12401308	.	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	CDS	12401309	12401432	0.8	-	1	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	exon	12401309	12401432	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	intron	12401433	12401547	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	CDS	12401548	12401615	1	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	exon	12401548	12401615	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	intron	12401616	12401693	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	CDS	12401694	12401780	1	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	exon	12401694	12401780	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	intron	12401781	12401872	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	CDS	12401873	12401941	1	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	exon	12401873	12401941	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	intron	12401942	12402046	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	CDS	12402047	12402115	0.99	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	exon	12402047	12402115	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	intron	12402116	12402205	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	CDS	12402206	12403147	0.76	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	exon	12402206	12403147	.	-	.	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
Phchi.S3	AUGUSTUS	start_codon	12403145	12403147	.	-	0	transcript_id "Phchi.S3G168900.t1"; gene_id "Phchi.S3G168900"
# This transcript jg12376.t2 is derived from g8052.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12377.t1 is derived from g8053.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	14077006	14078481	.	+	.	Phchi.S2G045700
Phchi.S2	AUGUSTUS	transcript	14077006	14078481	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	start_codon	14077006	14077008	.	+	0	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14077006	14077043	0.81	+	0	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14077006	14077043	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	intron	14077044	14077333	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14077334	14077389	1	+	1	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14077334	14077389	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	intron	14077390	14077587	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14077588	14077603	1	+	2	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14077588	14077603	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	intron	14077604	14077934	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14077935	14077944	0.79	+	1	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14077935	14077944	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	intron	14077945	14078089	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14078090	14078105	0.85	+	0	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14078090	14078105	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	intron	14078106	14078274	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14078275	14078291	0.84	+	2	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14078275	14078291	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	intron	14078292	14078433	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	CDS	14078434	14078481	0.84	+	0	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	exon	14078434	14078481	.	+	.	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
Phchi.S2	AUGUSTUS	stop_codon	14078482	14078484	.	+	0	transcript_id "Phchi.S2G045700.t1"; gene_id "Phchi.S2G045700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2424.t1 is derived from g9344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6580223	6582790	.	-	.	Phchi.S5G103300
Phchi.S5	AUGUSTUS	transcript	6580223	6582790	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	stop_codon	6580220	6580222	.	-	0	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	CDS	6580223	6580554	0.71	-	2	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	exon	6580223	6580554	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	intron	6580555	6580699	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	CDS	6580700	6580847	1	-	0	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	exon	6580700	6580847	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	intron	6580848	6580944	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	CDS	6580945	6582155	0.98	-	2	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	exon	6580945	6582155	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	intron	6582156	6582301	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	CDS	6582302	6582551	1	-	0	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	exon	6582302	6582551	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	intron	6582552	6582643	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	CDS	6582644	6582790	0.58	-	0	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	exon	6582644	6582790	.	-	.	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
Phchi.S5	AUGUSTUS	start_codon	6582788	6582790	.	-	0	transcript_id "Phchi.S5G103300.t1"; gene_id "Phchi.S5G103300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8423.t1 is derived from g5598.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35880446	35882593	.	-	.	Phchi.S1G558200
Phchi.S1	AUGUSTUS	transcript	35880446	35882593	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	stop_codon	35880443	35880445	.	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35880446	35880462	1	-	2	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35880446	35880462	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35880463	35880540	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35880541	35880605	1	-	1	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35880541	35880605	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35880606	35880696	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35880697	35880764	1	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35880697	35880764	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35880765	35880842	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35880843	35880938	1	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35880843	35880938	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35880939	35881028	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35881029	35881106	1	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35881029	35881106	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35881107	35881183	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35881184	35881283	1	-	1	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35881184	35881283	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35881284	35881380	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35881381	35881433	1	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35881381	35881433	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35881434	35881589	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35881590	35881724	0.89	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35881590	35881724	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35881725	35881808	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35881809	35881920	1	-	1	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35881809	35881920	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	intron	35881921	35882000	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	CDS	35882001	35882593	0.43	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	exon	35882001	35882593	.	-	.	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
Phchi.S1	AUGUSTUS	start_codon	35882591	35882593	.	-	0	transcript_id "Phchi.S1G558200.t1"; gene_id "Phchi.S1G558200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3485.t1 is derived from g654.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4012079	4013323	.	+	.	Phchi.S1G064400
Phchi.S1	AUGUSTUS	transcript	4012079	4013323	.	+	.	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	start_codon	4012079	4012081	.	+	0	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	CDS	4012079	4012203	0.19	+	0	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	exon	4012079	4012203	.	+	.	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	intron	4012204	4012316	.	+	.	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	CDS	4012317	4012706	0.07	+	1	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	exon	4012317	4012706	.	+	.	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	intron	4012707	4012773	.	+	.	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	CDS	4012774	4013323	0.44	+	1	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	exon	4012774	4013323	.	+	.	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
Phchi.S1	AUGUSTUS	stop_codon	4013324	4013326	.	+	0	transcript_id "Phchi.S1G064400.t1"; gene_id "Phchi.S1G064400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2203.t1 is derived from g9123.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5408876	5409943	.	+	.	Phchi.S5G081200
Phchi.S5	AUGUSTUS	transcript	5408876	5409943	.	+	.	transcript_id "Phchi.S5G081200.t1"; gene_id "Phchi.S5G081200"
Phchi.S5	AUGUSTUS	start_codon	5408876	5408878	.	+	0	transcript_id "Phchi.S5G081200.t1"; gene_id "Phchi.S5G081200"
Phchi.S5	AUGUSTUS	CDS	5408876	5409943	0.55	+	0	transcript_id "Phchi.S5G081200.t1"; gene_id "Phchi.S5G081200"
Phchi.S5	AUGUSTUS	exon	5408876	5409943	.	+	.	transcript_id "Phchi.S5G081200.t1"; gene_id "Phchi.S5G081200"
Phchi.S5	AUGUSTUS	stop_codon	5409944	5409946	.	+	0	transcript_id "Phchi.S5G081200.t1"; gene_id "Phchi.S5G081200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6553.t1 is derived from g3725.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23683887	23684502	.	+	.	Phchi.S1G371200
Phchi.S1	AUGUSTUS	transcript	23683887	23684502	.	+	.	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	start_codon	23683887	23683889	.	+	0	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	CDS	23683887	23684255	0.65	+	0	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	exon	23683887	23684255	.	+	.	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	intron	23684256	23684433	.	+	.	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	CDS	23684434	23684502	0.75	+	0	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	exon	23684434	23684502	.	+	.	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
Phchi.S1	AUGUSTUS	stop_codon	23684503	23684505	.	+	0	transcript_id "Phchi.S1G371200.t1"; gene_id "Phchi.S1G371200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15466.t1 is derived from g13934.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	19334651	19335349	.	-	.	Phchi.S3G278500
Phchi.S3	AUGUSTUS	transcript	19334651	19335349	.	-	.	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	stop_codon	19334648	19334650	.	-	0	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	CDS	19334651	19334676	0.71	-	2	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	exon	19334651	19334676	.	-	.	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	intron	19334677	19335066	.	-	.	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	CDS	19335067	19335349	0.33	-	0	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	exon	19335067	19335349	.	-	.	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
Phchi.S3	AUGUSTUS	start_codon	19335347	19335349	.	-	0	transcript_id "Phchi.S3G278500.t1"; gene_id "Phchi.S3G278500"
# This transcript jg12878.t2 is derived from g11343.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12879.t1 is derived from g11344.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2897484	2901298	.	+	.	Phchi.S3G019800
Phchi.S3	AUGUSTUS	transcript	2897484	2901298	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	start_codon	2897484	2897486	.	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2897484	2897687	1	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2897484	2897687	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2897688	2897807	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2897808	2898027	1	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2897808	2898027	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2898028	2898106	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2898107	2898183	1	+	2	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2898107	2898183	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2898184	2898291	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2898292	2898504	1	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2898292	2898504	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2898505	2898595	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2898596	2898661	0.99	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2898596	2898661	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2898662	2898771	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2898772	2898822	0.98	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2898772	2898822	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2898823	2898909	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2898910	2898992	0.99	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2898910	2898992	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2898993	2899100	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2899101	2899201	1	+	1	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2899101	2899201	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2899202	2899300	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2899301	2899424	1	+	2	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2899301	2899424	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2899425	2899521	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2899522	2899676	1	+	1	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2899522	2899676	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2899677	2899755	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2899756	2899892	1	+	2	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2899756	2899892	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2899893	2899985	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2899986	2900156	1	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2899986	2900156	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2900157	2900280	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2900281	2900505	1	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2900281	2900505	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2900506	2900611	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2900612	2900963	0.98	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2900612	2900963	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2900964	2901127	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2901128	2901186	0.95	+	2	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2901128	2901186	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	intron	2901187	2901265	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	CDS	2901266	2901298	0.97	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	exon	2901266	2901298	.	+	.	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
Phchi.S3	AUGUSTUS	stop_codon	2901299	2901301	.	+	0	transcript_id "Phchi.S3G019800.t1"; gene_id "Phchi.S3G019800"
# This transcript jg1450.t2 is derived from g8369.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1451.t1 is derived from g8370.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	955515	956989	.	-	.	Phchi.S5G006000
Phchi.S5	AUGUSTUS	transcript	955515	956989	.	-	.	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	stop_codon	955512	955514	.	-	0	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	CDS	955515	955663	0.32	-	2	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	exon	955515	955663	.	-	.	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	intron	955664	955806	.	-	.	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	CDS	955807	956898	0.31	-	2	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	exon	955807	956898	.	-	.	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	intron	956899	956979	.	-	.	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	CDS	956980	956989	1	-	0	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	exon	956980	956989	.	-	.	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
Phchi.S5	AUGUSTUS	start_codon	956987	956989	.	-	0	transcript_id "Phchi.S5G006000.t1"; gene_id "Phchi.S5G006000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2584.t1 is derived from g9504.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7490311	7491489	.	+	.	Phchi.S5G119300
Phchi.S5	AUGUSTUS	transcript	7490311	7491489	.	+	.	transcript_id "Phchi.S5G119300.t1"; gene_id "Phchi.S5G119300"
Phchi.S5	AUGUSTUS	start_codon	7490311	7490313	.	+	0	transcript_id "Phchi.S5G119300.t1"; gene_id "Phchi.S5G119300"
Phchi.S5	AUGUSTUS	CDS	7490311	7491489	0.61	+	0	transcript_id "Phchi.S5G119300.t1"; gene_id "Phchi.S5G119300"
Phchi.S5	AUGUSTUS	exon	7490311	7491489	.	+	.	transcript_id "Phchi.S5G119300.t1"; gene_id "Phchi.S5G119300"
Phchi.S5	AUGUSTUS	stop_codon	7491490	7491492	.	+	0	transcript_id "Phchi.S5G119300.t1"; gene_id "Phchi.S5G119300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10864.t1 is derived from g14914.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2659412	2660575	.	+	.	Phchi.S4G044600
Phchi.S4	AUGUSTUS	transcript	2659412	2660575	.	+	.	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	start_codon	2659412	2659414	.	+	0	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	CDS	2659412	2659560	1	+	0	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	exon	2659412	2659560	.	+	.	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	intron	2659561	2659926	.	+	.	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	CDS	2659927	2660575	1	+	1	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	exon	2659927	2660575	.	+	.	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
Phchi.S4	AUGUSTUS	stop_codon	2660576	2660578	.	+	0	transcript_id "Phchi.S4G044600.t1"; gene_id "Phchi.S4G044600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15255.t1 is derived from g13723.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17929593	17930668	.	+	.	Phchi.S3G257400
Phchi.S3	AUGUSTUS	transcript	17929593	17930668	.	+	.	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	start_codon	17929593	17929595	.	+	0	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	CDS	17929593	17930493	1	+	0	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	exon	17929593	17930493	.	+	.	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	intron	17930494	17930591	.	+	.	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	CDS	17930592	17930668	1	+	2	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	exon	17930592	17930668	.	+	.	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
Phchi.S3	AUGUSTUS	stop_codon	17930669	17930671	.	+	0	transcript_id "Phchi.S3G257400.t1"; gene_id "Phchi.S3G257400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14406.t1 is derived from g12874.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12681159	12682357	.	-	.	Phchi.S3G172500
Phchi.S3	AUGUSTUS	transcript	12681159	12682357	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	stop_codon	12681156	12681158	.	-	0	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	CDS	12681159	12681269	0.94	-	0	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	exon	12681159	12681269	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	intron	12681270	12681354	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	CDS	12681355	12681480	1	-	0	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	exon	12681355	12681480	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	intron	12681481	12681608	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	CDS	12681609	12682115	0.64	-	0	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	exon	12681609	12682115	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	intron	12682116	12682297	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	CDS	12682298	12682357	0.66	-	0	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	exon	12682298	12682357	.	-	.	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
Phchi.S3	AUGUSTUS	start_codon	12682355	12682357	.	-	0	transcript_id "Phchi.S3G172500.t1"; gene_id "Phchi.S3G172500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9761.t1 is derived from g6937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43553706	43557144	.	+	.	Phchi.S1G692000
Phchi.S1	AUGUSTUS	transcript	43553706	43557144	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	start_codon	43553706	43553708	.	+	0	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	CDS	43553706	43553900	0.96	+	0	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	exon	43553706	43553900	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	intron	43553901	43553980	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	CDS	43553981	43554166	0.98	+	0	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	exon	43553981	43554166	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	intron	43554167	43554322	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	CDS	43554323	43556327	0.31	+	0	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	exon	43554323	43556327	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	intron	43556328	43556661	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	CDS	43556662	43556753	0.7	+	2	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	exon	43556662	43556753	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	intron	43556754	43556945	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	CDS	43556946	43557022	0.92	+	0	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	exon	43556946	43557022	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	intron	43557023	43557113	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	CDS	43557114	43557144	0.77	+	1	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	exon	43557114	43557144	.	+	.	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
Phchi.S1	AUGUSTUS	stop_codon	43557145	43557147	.	+	0	transcript_id "Phchi.S1G692000.t1"; gene_id "Phchi.S1G692000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7080.t1 is derived from g4252.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	26797502	26798042	.	+	.	Phchi.S1G423900
Phchi.S1	AUGUSTUS	transcript	26797502	26798042	.	+	.	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	start_codon	26797502	26797504	.	+	0	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	CDS	26797502	26797714	0.93	+	0	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	exon	26797502	26797714	.	+	.	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	intron	26797715	26797943	.	+	.	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	CDS	26797944	26798042	1	+	0	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	exon	26797944	26798042	.	+	.	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
Phchi.S1	AUGUSTUS	stop_codon	26798043	26798045	.	+	0	transcript_id "Phchi.S1G423900.t1"; gene_id "Phchi.S1G423900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7503.t1 is derived from g4677.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29697512	29701891	.	+	.	Phchi.S1G466200
Phchi.S1	AUGUSTUS	transcript	29697512	29701891	.	+	.	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	start_codon	29697512	29697514	.	+	0	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	CDS	29697512	29698151	0.9	+	0	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	exon	29697512	29698151	.	+	.	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	intron	29698152	29698275	.	+	.	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	CDS	29698276	29698584	0.75	+	2	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	exon	29698276	29698584	.	+	.	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	intron	29698585	29698670	.	+	.	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	CDS	29698671	29701891	1	+	2	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	exon	29698671	29701891	.	+	.	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
Phchi.S1	AUGUSTUS	stop_codon	29701892	29701894	.	+	0	transcript_id "Phchi.S1G466200.t1"; gene_id "Phchi.S1G466200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4433.t1 is derived from g1602.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	10479533	10481331	.	-	.	Phchi.S1G159200
Phchi.S1	AUGUSTUS	transcript	10479533	10481331	.	-	.	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	stop_codon	10479530	10479532	.	-	0	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	CDS	10479533	10480146	1	-	2	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	exon	10479533	10480146	.	-	.	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	intron	10480147	10480241	.	-	.	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	CDS	10480242	10481331	0.52	-	0	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	exon	10480242	10481331	.	-	.	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
Phchi.S1	AUGUSTUS	start_codon	10481329	10481331	.	-	0	transcript_id "Phchi.S1G159200.t1"; gene_id "Phchi.S1G159200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg10427.t1 is derived from g14476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	206874	210218	.	+	.	Phchi.S4G000900
Phchi.S4	AUGUSTUS	transcript	206874	210218	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	start_codon	206874	206876	.	+	0	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	206874	206930	0.52	+	0	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	206874	206930	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	206931	207123	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	207124	207947	0.36	+	0	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	207124	207947	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	207948	208135	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	208136	208377	1	+	1	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	208136	208377	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	208378	208612	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	208613	208631	1	+	2	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	208613	208631	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	208632	208758	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	208759	208964	1	+	1	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	208759	208964	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	208965	209058	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	209059	209168	1	+	2	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	209059	209168	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	209169	209306	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	209307	209405	1	+	0	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	209307	209405	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	209406	209559	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	209560	210046	1	+	0	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	209560	210046	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	210047	210132	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	210133	210218	1	+	2	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	210133	210218	.	+	.	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	stop_codon	210219	210221	.	+	0	transcript_id "Phchi.S4G000900.t1"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	transcript	206874	210218	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	start_codon	206874	206876	.	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	206874	206930	0.5	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	206874	206930	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	206931	207123	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	207124	207947	0.41	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	207124	207947	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	207948	208135	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	208136	208277	0.39	+	1	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	208136	208277	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	208278	208360	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	208361	208377	0.68	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	208361	208377	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	208378	208758	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	208759	208964	0.99	+	1	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	208759	208964	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	208965	209058	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	209059	209168	1	+	2	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	209059	209168	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	209169	209306	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	209307	209405	1	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	209307	209405	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	209406	209559	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	209560	210046	1	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	209560	210046	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	intron	210047	210132	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	CDS	210133	210218	1	+	2	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	exon	210133	210218	.	+	.	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
Phchi.S4	AUGUSTUS	stop_codon	210219	210221	.	+	0	transcript_id "Phchi.S4G000900.t2"; gene_id "Phchi.S4G000900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14517.t1 is derived from g12985.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13273489	13275648	.	+	.	Phchi.S3G183600
Phchi.S3	AUGUSTUS	transcript	13273489	13275648	.	+	.	transcript_id "Phchi.S3G183600.t1"; gene_id "Phchi.S3G183600"
Phchi.S3	AUGUSTUS	start_codon	13273489	13273491	.	+	0	transcript_id "Phchi.S3G183600.t1"; gene_id "Phchi.S3G183600"
Phchi.S3	AUGUSTUS	CDS	13273489	13275648	0.99	+	0	transcript_id "Phchi.S3G183600.t1"; gene_id "Phchi.S3G183600"
Phchi.S3	AUGUSTUS	exon	13273489	13275648	.	+	.	transcript_id "Phchi.S3G183600.t1"; gene_id "Phchi.S3G183600"
Phchi.S3	AUGUSTUS	stop_codon	13275649	13275651	.	+	0	transcript_id "Phchi.S3G183600.t1"; gene_id "Phchi.S3G183600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1429.t1 is derived from g8348.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	800960	802595	.	-	.	Phchi.S5G003800
Phchi.S5	AUGUSTUS	transcript	800960	802595	.	-	.	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	stop_codon	800957	800959	.	-	0	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	CDS	800960	802027	0.99	-	0	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	exon	800960	802027	.	-	.	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	intron	802028	802148	.	-	.	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	CDS	802149	802595	0.65	-	0	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	exon	802149	802595	.	-	.	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
Phchi.S5	AUGUSTUS	start_codon	802593	802595	.	-	0	transcript_id "Phchi.S5G003800.t1"; gene_id "Phchi.S5G003800"
# This transcript jg3527.t2 is derived from g696.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3528.t1 is derived from g697.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4236606	4237061	.	+	.	Phchi.S1G068700
Phchi.S1	AUGUSTUS	transcript	4236606	4237061	.	+	.	transcript_id "Phchi.S1G068700.t1"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	start_codon	4236606	4236608	.	+	0	transcript_id "Phchi.S1G068700.t1"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	CDS	4236606	4237061	0.91	+	0	transcript_id "Phchi.S1G068700.t1"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	exon	4236606	4237061	.	+	.	transcript_id "Phchi.S1G068700.t1"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	stop_codon	4237062	4237064	.	+	0	transcript_id "Phchi.S1G068700.t1"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	transcript	4236741	4237061	.	+	.	transcript_id "Phchi.S1G068700.t2"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	start_codon	4236741	4236743	.	+	0	transcript_id "Phchi.S1G068700.t2"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	CDS	4236741	4237061	0.7	+	0	transcript_id "Phchi.S1G068700.t2"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	exon	4236741	4237061	.	+	.	transcript_id "Phchi.S1G068700.t2"; gene_id "Phchi.S1G068700"
Phchi.S1	AUGUSTUS	stop_codon	4237062	4237064	.	+	0	transcript_id "Phchi.S1G068700.t2"; gene_id "Phchi.S1G068700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14988.t1 is derived from g13456.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15948702	15950518	.	-	.	Phchi.S3G230700
Phchi.S3	AUGUSTUS	transcript	15948702	15950518	.	-	.	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	stop_codon	15948699	15948701	.	-	0	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	CDS	15948702	15948878	1	-	0	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	exon	15948702	15948878	.	-	.	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	intron	15948879	15949054	.	-	.	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	CDS	15949055	15950518	0.96	-	0	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	exon	15949055	15950518	.	-	.	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
Phchi.S3	AUGUSTUS	start_codon	15950516	15950518	.	-	0	transcript_id "Phchi.S3G230700.t1"; gene_id "Phchi.S3G230700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6857.t1 is derived from g4029.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25605310	25606215	.	-	.	Phchi.S1G401600
Phchi.S1	AUGUSTUS	transcript	25605310	25606215	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	stop_codon	25605307	25605309	.	-	0	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	CDS	25605310	25605341	0.97	-	2	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	exon	25605310	25605341	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	intron	25605342	25605441	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	CDS	25605442	25605538	0.97	-	0	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	exon	25605442	25605538	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	intron	25605539	25605629	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	CDS	25605630	25605721	1	-	2	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	exon	25605630	25605721	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	intron	25605722	25605833	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	CDS	25605834	25606215	1	-	0	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	exon	25605834	25606215	.	-	.	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
Phchi.S1	AUGUSTUS	start_codon	25606213	25606215	.	-	0	transcript_id "Phchi.S1G401600.t1"; gene_id "Phchi.S1G401600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9604.t1 is derived from g6780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42905011	42906554	.	+	.	Phchi.S1G676300
Phchi.S1	AUGUSTUS	transcript	42905011	42906554	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	start_codon	42905011	42905013	.	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	CDS	42905011	42905277	1	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	exon	42905011	42905277	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	intron	42905278	42905381	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	CDS	42905382	42905414	1	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	exon	42905382	42905414	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	intron	42905415	42905488	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	CDS	42905489	42905686	1	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	exon	42905489	42905686	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	intron	42905687	42905909	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	CDS	42905910	42905972	1	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	exon	42905910	42905972	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	intron	42905973	42906132	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	CDS	42906133	42906330	1	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	exon	42906133	42906330	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	intron	42906331	42906422	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	CDS	42906423	42906554	0.99	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	exon	42906423	42906554	.	+	.	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
Phchi.S1	AUGUSTUS	stop_codon	42906555	42906557	.	+	0	transcript_id "Phchi.S1G676300.t1"; gene_id "Phchi.S1G676300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2018.t1 is derived from g8938.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4472866	4474131	.	-	.	Phchi.S5G062700
Phchi.S5	AUGUSTUS	transcript	4472866	4474131	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	stop_codon	4472863	4472865	.	-	0	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	CDS	4472866	4473025	1	-	1	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	exon	4472866	4473025	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	intron	4473026	4473109	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	CDS	4473110	4473241	1	-	1	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	exon	4473110	4473241	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	intron	4473242	4473329	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	CDS	4473330	4473427	1	-	0	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	exon	4473330	4473427	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	intron	4473428	4473514	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	CDS	4473515	4473627	1	-	2	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	exon	4473515	4473627	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	intron	4473628	4473716	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	CDS	4473717	4473871	0.67	-	1	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	exon	4473717	4473871	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	intron	4473872	4473976	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	CDS	4473977	4474131	0.99	-	0	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	exon	4473977	4474131	.	-	.	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
Phchi.S5	AUGUSTUS	start_codon	4474129	4474131	.	-	0	transcript_id "Phchi.S5G062700.t1"; gene_id "Phchi.S5G062700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11374.t1 is derived from g15424.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	5943793	5944080	.	-	.	Phchi.S4G095600
Phchi.S4	AUGUSTUS	transcript	5943793	5944080	.	-	.	transcript_id "Phchi.S4G095600.t1"; gene_id "Phchi.S4G095600"
Phchi.S4	AUGUSTUS	stop_codon	5943790	5943792	.	-	0	transcript_id "Phchi.S4G095600.t1"; gene_id "Phchi.S4G095600"
Phchi.S4	AUGUSTUS	CDS	5943793	5944080	0.97	-	0	transcript_id "Phchi.S4G095600.t1"; gene_id "Phchi.S4G095600"
Phchi.S4	AUGUSTUS	exon	5943793	5944080	.	-	.	transcript_id "Phchi.S4G095600.t1"; gene_id "Phchi.S4G095600"
Phchi.S4	AUGUSTUS	start_codon	5944078	5944080	.	-	0	transcript_id "Phchi.S4G095600.t1"; gene_id "Phchi.S4G095600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15879.t1 is derived from g14349.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22011416	22012058	.	-	.	Phchi.S3G319800
Phchi.S3	AUGUSTUS	transcript	22011416	22012058	.	-	.	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	stop_codon	22011413	22011415	.	-	0	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	CDS	22011416	22011612	0.37	-	2	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	exon	22011416	22011612	.	-	.	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	intron	22011613	22011752	.	-	.	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	CDS	22011753	22011849	0.53	-	0	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	exon	22011753	22011849	.	-	.	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	intron	22011850	22011971	.	-	.	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	CDS	22011972	22012058	0.78	-	0	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	exon	22011972	22012058	.	-	.	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
Phchi.S3	AUGUSTUS	start_codon	22012056	22012058	.	-	0	transcript_id "Phchi.S3G319800.t1"; gene_id "Phchi.S3G319800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11108.t1 is derived from g15158.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4173475	4176006	.	-	.	Phchi.S4G069000
Phchi.S4	AUGUSTUS	transcript	4173475	4176006	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	stop_codon	4173472	4173474	.	-	0	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	CDS	4173475	4173513	0.44	-	0	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	exon	4173475	4173513	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	intron	4173514	4173613	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	CDS	4173614	4173628	0.38	-	0	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	exon	4173614	4173628	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	intron	4173629	4173726	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	CDS	4173727	4174345	0.38	-	1	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	exon	4173727	4174345	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	intron	4174346	4174428	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	CDS	4174429	4174527	1	-	1	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	exon	4174429	4174527	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	intron	4174528	4174629	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	CDS	4174630	4175051	1	-	0	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	exon	4174630	4175051	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	intron	4175052	4175340	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	CDS	4175341	4176006	0.5	-	0	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	exon	4175341	4176006	.	-	.	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
Phchi.S4	AUGUSTUS	start_codon	4176004	4176006	.	-	0	transcript_id "Phchi.S4G069000.t1"; gene_id "Phchi.S4G069000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1926.t1 is derived from g8846.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3875731	3876290	.	-	.	Phchi.S5G053500
Phchi.S5	AUGUSTUS	transcript	3875731	3876290	.	-	.	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	stop_codon	3875728	3875730	.	-	0	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	CDS	3875731	3875778	1	-	0	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	exon	3875731	3875778	.	-	.	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	intron	3875779	3875924	.	-	.	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	CDS	3875925	3876081	0.68	-	1	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	exon	3875925	3876081	.	-	.	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	intron	3876082	3876213	.	-	.	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	CDS	3876214	3876290	0.69	-	0	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	exon	3876214	3876290	.	-	.	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
Phchi.S5	AUGUSTUS	start_codon	3876288	3876290	.	-	0	transcript_id "Phchi.S5G053500.t1"; gene_id "Phchi.S5G053500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4805.t1 is derived from g1975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12902742	12903050	.	+	.	Phchi.S1G196400
Phchi.S1	AUGUSTUS	transcript	12902742	12903050	.	+	.	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	start_codon	12902742	12902744	.	+	0	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	CDS	12902742	12902789	0.64	+	0	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	exon	12902742	12902789	.	+	.	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	intron	12902790	12902876	.	+	.	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	CDS	12902877	12903050	1	+	0	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	exon	12902877	12903050	.	+	.	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
Phchi.S1	AUGUSTUS	stop_codon	12903051	12903053	.	+	0	transcript_id "Phchi.S1G196400.t1"; gene_id "Phchi.S1G196400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15251.t1 is derived from g13719.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17903324	17906623	.	+	.	Phchi.S3G257000
Phchi.S3	AUGUSTUS	transcript	17903324	17906623	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	start_codon	17903324	17903326	.	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17903324	17903399	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17903324	17903399	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17903400	17903495	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17903496	17903990	0.91	+	2	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17903496	17903990	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17903991	17904127	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904128	17904377	1	+	2	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904128	17904377	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904378	17904473	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904474	17904558	1	+	1	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904474	17904558	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904559	17904687	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904688	17904777	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904688	17904777	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904778	17904858	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904859	17904932	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904859	17904932	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904933	17905073	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905074	17905155	1	+	1	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905074	17905155	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905156	17905292	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905293	17905382	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905293	17905382	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905383	17905473	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905474	17905601	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905474	17905601	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905602	17905696	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905697	17905778	1	+	1	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905697	17905778	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905779	17905865	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905866	17905913	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905866	17905913	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905914	17906020	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17906021	17906093	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17906021	17906093	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17906094	17906292	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17906293	17906396	1	+	2	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17906293	17906396	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17906397	17906524	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17906525	17906623	1	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17906525	17906623	.	+	.	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	stop_codon	17906624	17906626	.	+	0	transcript_id "Phchi.S3G257000.t1"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	transcript	17903324	17906623	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	start_codon	17903324	17903326	.	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17903324	17903399	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17903324	17903399	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17903400	17903495	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17903496	17903990	0.91	+	2	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17903496	17903990	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17903991	17904130	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904131	17904377	1	+	2	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904131	17904377	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904378	17904473	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904474	17904558	1	+	1	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904474	17904558	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904559	17904687	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904688	17904777	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904688	17904777	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904778	17904858	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17904859	17904932	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17904859	17904932	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17904933	17905073	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905074	17905155	1	+	1	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905074	17905155	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905156	17905292	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905293	17905382	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905293	17905382	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905383	17905473	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905474	17905601	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905474	17905601	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905602	17905696	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905697	17905778	1	+	1	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905697	17905778	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905779	17905865	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17905866	17905913	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17905866	17905913	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17905914	17906020	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17906021	17906093	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17906021	17906093	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17906094	17906292	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17906293	17906396	1	+	2	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17906293	17906396	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	intron	17906397	17906524	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	CDS	17906525	17906623	1	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	exon	17906525	17906623	.	+	.	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
Phchi.S3	AUGUSTUS	stop_codon	17906624	17906626	.	+	0	transcript_id "Phchi.S3G257000.t2"; gene_id "Phchi.S3G257000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7541.t1 is derived from g4715.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29966116	29967185	.	+	.	Phchi.S1G470000
Phchi.S1	AUGUSTUS	transcript	29966116	29967185	.	+	.	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	start_codon	29966116	29966118	.	+	0	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	CDS	29966116	29966805	0.62	+	0	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	exon	29966116	29966805	.	+	.	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	intron	29966806	29966909	.	+	.	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	CDS	29966910	29967059	0.85	+	0	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	exon	29966910	29967059	.	+	.	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	intron	29967060	29967134	.	+	.	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	CDS	29967135	29967185	0.72	+	0	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	exon	29967135	29967185	.	+	.	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
Phchi.S1	AUGUSTUS	stop_codon	29967186	29967188	.	+	0	transcript_id "Phchi.S1G470000.t1"; gene_id "Phchi.S1G470000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10731.t1 is derived from g14781.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1794352	1794942	.	+	.	Phchi.S4G031300
Phchi.S4	AUGUSTUS	transcript	1794352	1794942	.	+	.	transcript_id "Phchi.S4G031300.t1"; gene_id "Phchi.S4G031300"
Phchi.S4	AUGUSTUS	start_codon	1794352	1794354	.	+	0	transcript_id "Phchi.S4G031300.t1"; gene_id "Phchi.S4G031300"
Phchi.S4	AUGUSTUS	CDS	1794352	1794942	0.6	+	0	transcript_id "Phchi.S4G031300.t1"; gene_id "Phchi.S4G031300"
Phchi.S4	AUGUSTUS	exon	1794352	1794942	.	+	.	transcript_id "Phchi.S4G031300.t1"; gene_id "Phchi.S4G031300"
Phchi.S4	AUGUSTUS	stop_codon	1794943	1794945	.	+	0	transcript_id "Phchi.S4G031300.t1"; gene_id "Phchi.S4G031300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1814.t1 is derived from g8734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	3244458	3246603	.	-	.	Phchi.S5G042300
Phchi.S5	AUGUSTUS	transcript	3244458	3246603	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	stop_codon	3244455	3244457	.	-	0	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	CDS	3244458	3244783	0.99	-	2	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	exon	3244458	3244783	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	intron	3244784	3244890	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	CDS	3244891	3245059	1	-	0	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	exon	3244891	3245059	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	intron	3245060	3245144	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	CDS	3245145	3245459	1	-	0	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	exon	3245145	3245459	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	intron	3245460	3245572	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	CDS	3245573	3245870	1	-	1	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	exon	3245573	3245870	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	intron	3245871	3245937	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	CDS	3245938	3246395	1	-	0	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	exon	3245938	3246395	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	intron	3246396	3246513	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	CDS	3246514	3246603	0.96	-	0	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	exon	3246514	3246603	.	-	.	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
Phchi.S5	AUGUSTUS	start_codon	3246601	3246603	.	-	0	transcript_id "Phchi.S5G042300.t1"; gene_id "Phchi.S5G042300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5547.t1 is derived from g2717.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17483167	17484249	.	-	.	Phchi.S1G270600
Phchi.S1	AUGUSTUS	transcript	17483167	17484249	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	stop_codon	17483164	17483166	.	-	0	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	CDS	17483167	17483180	0.89	-	2	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	exon	17483167	17483180	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	intron	17483181	17483483	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	CDS	17483484	17483627	0.9	-	2	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	exon	17483484	17483627	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	intron	17483628	17483796	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	CDS	17483797	17483835	1	-	2	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	exon	17483797	17483835	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	intron	17483836	17484209	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	CDS	17484210	17484249	0.9	-	0	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	exon	17484210	17484249	.	-	.	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
Phchi.S1	AUGUSTUS	start_codon	17484247	17484249	.	-	0	transcript_id "Phchi.S1G270600.t1"; gene_id "Phchi.S1G270600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg8064.t1 is derived from g5239.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32759189	32760897	.	+	.	Phchi.S1G522300
Phchi.S1	AUGUSTUS	transcript	32759189	32760897	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	start_codon	32759189	32759191	.	+	0	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759189	32759401	1	+	0	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759189	32759401	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32759402	32759490	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759491	32759594	1	+	0	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759491	32759594	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32759595	32759684	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759685	32760055	0.97	+	1	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759685	32760055	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32760056	32760159	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32760160	32760467	1	+	2	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32760160	32760467	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32760468	32760543	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32760544	32760897	1	+	0	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32760544	32760897	.	+	.	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	stop_codon	32760898	32760900	.	+	0	transcript_id "Phchi.S1G522300.t1"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	transcript	32759189	32760897	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	start_codon	32759189	32759191	.	+	0	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759189	32759401	0.99	+	0	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759189	32759401	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32759402	32759490	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759491	32759594	1	+	0	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759491	32759594	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32759595	32759736	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759737	32759752	0.85	+	1	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759737	32759752	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32759753	32759838	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32759839	32760055	0.76	+	0	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32759839	32760055	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32760056	32760159	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32760160	32760467	1	+	2	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32760160	32760467	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	intron	32760468	32760543	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	CDS	32760544	32760897	0.99	+	0	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	exon	32760544	32760897	.	+	.	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
Phchi.S1	AUGUSTUS	stop_codon	32760898	32760900	.	+	0	transcript_id "Phchi.S1G522300.t2"; gene_id "Phchi.S1G522300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5076.t1 is derived from g2246.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14560880	14568699	.	-	.	Phchi.S1G223500
Phchi.S1	AUGUSTUS	transcript	14560880	14568699	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	stop_codon	14560877	14560879	.	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14560880	14560962	1	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14560880	14560962	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14560963	14561045	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14561046	14561115	1	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14561046	14561115	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14561116	14561255	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14561256	14561311	0.52	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14561256	14561311	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14561312	14561391	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14561392	14561503	1	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14561392	14561503	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14561504	14561636	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14561637	14561785	1	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14561637	14561785	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14561786	14561871	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14561872	14561963	1	-	1	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14561872	14561963	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14561964	14562061	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14562062	14562140	0.99	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14562062	14562140	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14562141	14562220	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14562221	14562274	0.53	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14562221	14562274	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14562275	14562352	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14562353	14562448	1	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14562353	14562448	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14562449	14562616	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14562617	14562694	1	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14562617	14562694	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14562695	14562790	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14562791	14563106	1	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14562791	14563106	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14563107	14563186	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14563187	14563396	0.98	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14563187	14563396	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14563397	14563499	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14563500	14563679	0.93	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14563500	14563679	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14563680	14563768	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14563769	14563887	0.43	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14563769	14563887	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14563888	14564039	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14564040	14564083	0.5	-	1	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14564040	14564083	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14564084	14564174	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14564175	14564443	0.99	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14564175	14564443	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14564444	14564527	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14564528	14564847	0.99	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14564528	14564847	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14564848	14565012	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14565013	14567562	0.99	-	2	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14565013	14567562	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14567563	14567780	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14567781	14567920	1	-	1	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14567781	14567920	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14567921	14567994	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14567995	14568179	0.72	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14567995	14568179	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14568180	14568263	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14568264	14568416	0.72	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14568264	14568416	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	intron	14568417	14568492	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	CDS	14568493	14568699	0.87	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	exon	14568493	14568699	.	-	.	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
Phchi.S1	AUGUSTUS	start_codon	14568697	14568699	.	-	0	transcript_id "Phchi.S1G223500.t1"; gene_id "Phchi.S1G223500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12907.t1 is derived from g11372.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3089533	3090720	.	+	.	Phchi.S3G022600
Phchi.S3	AUGUSTUS	transcript	3089533	3090720	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	start_codon	3089533	3089535	.	+	0	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3089533	3089607	0.97	+	0	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3089533	3089607	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	intron	3089608	3089739	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3089740	3089805	1	+	0	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3089740	3089805	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	intron	3089806	3089900	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3089901	3089940	1	+	0	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3089901	3089940	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	intron	3089941	3090033	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3090034	3090153	1	+	2	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3090034	3090153	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	intron	3090154	3090251	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3090252	3090332	1	+	2	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3090252	3090332	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	intron	3090333	3090453	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3090454	3090609	1	+	2	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3090454	3090609	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	intron	3090610	3090682	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	CDS	3090683	3090720	0.83	+	2	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	exon	3090683	3090720	.	+	.	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
Phchi.S3	AUGUSTUS	stop_codon	3090721	3090723	.	+	0	transcript_id "Phchi.S3G022600.t1"; gene_id "Phchi.S3G022600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8562.t1 is derived from g5737.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36626648	36627979	.	+	.	Phchi.S1G572100
Phchi.S1	AUGUSTUS	transcript	36626648	36627979	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	start_codon	36626648	36626650	.	+	0	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	CDS	36626648	36626777	1	+	0	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	exon	36626648	36626777	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	intron	36626778	36626852	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	CDS	36626853	36626992	1	+	2	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	exon	36626853	36626992	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	intron	36626993	36627125	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	CDS	36627126	36627257	1	+	0	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	exon	36627126	36627257	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	intron	36627258	36627343	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	CDS	36627344	36627466	1	+	0	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	exon	36627344	36627466	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	intron	36627467	36627538	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	CDS	36627539	36627979	1	+	0	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	exon	36627539	36627979	.	+	.	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
Phchi.S1	AUGUSTUS	stop_codon	36627980	36627982	.	+	0	transcript_id "Phchi.S1G572100.t1"; gene_id "Phchi.S1G572100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8308.t1 is derived from g5483.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35211127	35222629	.	-	.	Phchi.S1G546700
Phchi.S1	AUGUSTUS	transcript	35211127	35222629	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	stop_codon	35211124	35211126	.	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35211127	35213357	0.96	-	2	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35211127	35213357	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35213358	35213440	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35213441	35214407	0.98	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35213441	35214407	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35214408	35214521	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35214522	35214725	0.94	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35214522	35214725	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35214726	35214815	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35214816	35214873	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35214816	35214873	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35214874	35214956	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35214957	35215064	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35214957	35215064	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35215065	35215244	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35215245	35215342	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35215245	35215342	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35215343	35215424	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35215425	35215499	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35215425	35215499	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35215500	35215610	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35215611	35215689	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35215611	35215689	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35215690	35215807	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35215808	35215977	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35215808	35215977	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35215978	35216138	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35216139	35216246	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35216139	35216246	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35216247	35216316	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35216317	35216397	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35216317	35216397	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35216398	35216549	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35216550	35216666	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35216550	35216666	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35216667	35216762	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35216763	35216852	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35216763	35216852	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35216853	35216949	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35216950	35217075	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35216950	35217075	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35217076	35217184	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35217185	35217398	0.99	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35217185	35217398	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35217399	35217499	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35217500	35217672	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35217500	35217672	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35217673	35217776	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35217777	35217873	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35217777	35217873	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35217874	35217976	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35217977	35218033	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35217977	35218033	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35218034	35218127	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35218128	35218171	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35218128	35218171	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35218172	35218260	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35218261	35218425	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35218261	35218425	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35218426	35218529	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35218530	35218713	0.75	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35218530	35218713	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35218714	35218799	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35218800	35218985	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35218800	35218985	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35218986	35219117	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35219118	35219215	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35219118	35219215	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35219216	35219295	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35219296	35220455	1	-	2	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35219296	35220455	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35220456	35220552	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35220553	35220614	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35220553	35220614	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35220615	35220761	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35220762	35221078	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35220762	35221078	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35221079	35221246	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35221247	35221465	0.23	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35221247	35221465	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35221466	35221542	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35221543	35221716	0.33	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35221543	35221716	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35221717	35221865	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35221866	35222310	1	-	1	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35221866	35222310	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35222311	35222384	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35222385	35222446	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35222385	35222446	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	intron	35222447	35222524	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	CDS	35222525	35222629	1	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	exon	35222525	35222629	.	-	.	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
Phchi.S1	AUGUSTUS	start_codon	35222627	35222629	.	-	0	transcript_id "Phchi.S1G546700.t1"; gene_id "Phchi.S1G546700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg443.t1 is derived from g10225.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3105986	3109824	.	-	.	Phchi.S6G040200
Phchi.S6	AUGUSTUS	transcript	3105986	3109824	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	stop_codon	3105983	3105985	.	-	0	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	CDS	3105986	3106174	1	-	0	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	exon	3105986	3106174	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	intron	3106175	3106240	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	CDS	3106241	3106403	1	-	1	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	exon	3106241	3106403	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	intron	3106404	3108566	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	CDS	3108567	3108634	0.91	-	0	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	exon	3108567	3108634	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	intron	3108635	3109545	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	CDS	3109546	3109824	0.94	-	0	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	exon	3109546	3109824	.	-	.	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
Phchi.S6	AUGUSTUS	start_codon	3109822	3109824	.	-	0	transcript_id "Phchi.S6G040200.t1"; gene_id "Phchi.S6G040200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5084.t1 is derived from g2254.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	14603604	14603918	.	+	.	Phchi.S1G224300
Phchi.S1	AUGUSTUS	transcript	14603604	14603918	.	+	.	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	start_codon	14603604	14603606	.	+	0	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	CDS	14603604	14603771	0.6	+	0	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	exon	14603604	14603771	.	+	.	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	intron	14603772	14603852	.	+	.	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	CDS	14603853	14603918	0.97	+	0	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	exon	14603853	14603918	.	+	.	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
Phchi.S1	AUGUSTUS	stop_codon	14603919	14603921	.	+	0	transcript_id "Phchi.S1G224300.t1"; gene_id "Phchi.S1G224300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg1613.t1 is derived from g8532.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2026189	2027543	.	+	.	Phchi.S5G022200
Phchi.S5	AUGUSTUS	transcript	2026189	2027543	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	start_codon	2026189	2026191	.	+	0	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026189	2026224	0.67	+	0	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026189	2026224	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026225	2026346	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026347	2026414	0.96	+	0	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026347	2026414	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026415	2026577	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026578	2026646	1	+	1	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026578	2026646	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026647	2026754	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026755	2026837	1	+	1	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026755	2026837	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026838	2026935	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026936	2027035	1	+	2	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026936	2027035	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027036	2027131	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027132	2027194	1	+	1	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027132	2027194	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027195	2027290	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027291	2027384	1	+	1	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027291	2027384	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027385	2027468	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027469	2027543	1	+	0	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027469	2027543	.	+	.	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	stop_codon	2027544	2027546	.	+	0	transcript_id "Phchi.S5G022200.t1"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	transcript	2026189	2027543	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	start_codon	2026189	2026191	.	+	0	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026189	2026224	0.57	+	0	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026189	2026224	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026225	2026346	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026347	2026414	0.97	+	0	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026347	2026414	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026415	2026577	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026578	2026646	1	+	1	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026578	2026646	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026647	2026754	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026755	2026837	1	+	1	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026755	2026837	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026838	2026935	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026936	2027035	1	+	2	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026936	2027035	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027036	2027131	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027132	2027194	1	+	1	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027132	2027194	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027195	2027275	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027276	2027384	0.97	+	1	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027276	2027384	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027385	2027468	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027469	2027543	0.99	+	0	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027469	2027543	.	+	.	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	stop_codon	2027544	2027546	.	+	0	transcript_id "Phchi.S5G022200.t2"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	transcript	2026189	2027543	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	start_codon	2026189	2026191	.	+	0	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026189	2026224	0.61	+	0	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026189	2026224	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026225	2026346	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026347	2026422	0.8	+	0	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026347	2026422	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026423	2026577	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026578	2026620	0.76	+	2	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026578	2026620	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026621	2026754	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026755	2026837	0.86	+	1	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026755	2026837	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2026838	2026935	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2026936	2027035	1	+	2	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2026936	2027035	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027036	2027131	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027132	2027194	1	+	1	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027132	2027194	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027195	2027290	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027291	2027384	1	+	1	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027291	2027384	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	intron	2027385	2027468	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	CDS	2027469	2027543	1	+	0	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	exon	2027469	2027543	.	+	.	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
Phchi.S5	AUGUSTUS	stop_codon	2027544	2027546	.	+	0	transcript_id "Phchi.S5G022200.t3"; gene_id "Phchi.S5G022200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1259.t1 is derived from g11042.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8692349	8693958	.	-	.	Phchi.S6G121800
Phchi.S6	AUGUSTUS	transcript	8692349	8693958	.	-	.	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	stop_codon	8692346	8692348	.	-	0	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	CDS	8692349	8693069	0.43	-	1	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	exon	8692349	8693069	.	-	.	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	intron	8693070	8693149	.	-	.	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	CDS	8693150	8693376	0.6	-	0	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	exon	8693150	8693376	.	-	.	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	intron	8693377	8693505	.	-	.	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	CDS	8693506	8693958	0.91	-	0	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	exon	8693506	8693958	.	-	.	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
Phchi.S6	AUGUSTUS	start_codon	8693956	8693958	.	-	0	transcript_id "Phchi.S6G121800.t1"; gene_id "Phchi.S6G121800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10982.t1 is derived from g15032.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	3519148	3520772	.	+	.	Phchi.S4G056400
Phchi.S4	AUGUSTUS	transcript	3519148	3520772	.	+	.	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	start_codon	3519148	3519150	.	+	0	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	CDS	3519148	3519916	0.33	+	0	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	exon	3519148	3519916	.	+	.	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	intron	3519917	3520056	.	+	.	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	CDS	3520057	3520772	0.79	+	2	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	exon	3520057	3520772	.	+	.	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
Phchi.S4	AUGUSTUS	stop_codon	3520773	3520775	.	+	0	transcript_id "Phchi.S4G056400.t1"; gene_id "Phchi.S4G056400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7746.t1 is derived from g4920.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30934822	30935115	.	+	.	Phchi.S1G490500
Phchi.S1	AUGUSTUS	transcript	30934822	30935115	.	+	.	transcript_id "Phchi.S1G490500.t1"; gene_id "Phchi.S1G490500"
Phchi.S1	AUGUSTUS	start_codon	30934822	30934824	.	+	0	transcript_id "Phchi.S1G490500.t1"; gene_id "Phchi.S1G490500"
Phchi.S1	AUGUSTUS	CDS	30934822	30935115	0.64	+	0	transcript_id "Phchi.S1G490500.t1"; gene_id "Phchi.S1G490500"
Phchi.S1	AUGUSTUS	exon	30934822	30935115	.	+	.	transcript_id "Phchi.S1G490500.t1"; gene_id "Phchi.S1G490500"
Phchi.S1	AUGUSTUS	stop_codon	30935116	30935118	.	+	0	transcript_id "Phchi.S1G490500.t1"; gene_id "Phchi.S1G490500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg536.t1 is derived from g10318.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3896977	3898298	.	-	.	Phchi.S6G049500
Phchi.S6	AUGUSTUS	transcript	3896977	3898298	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	stop_codon	3896974	3896976	.	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3896977	3897093	0.59	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3896977	3897093	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3897094	3897185	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3897186	3897226	0.94	-	2	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3897186	3897226	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3897227	3897319	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3897320	3897407	0.96	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3897320	3897407	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3897408	3897509	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3897510	3897554	0.98	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3897510	3897554	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3897555	3897674	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3897675	3897782	1	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3897675	3897782	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3897783	3897881	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3897882	3897967	1	-	2	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3897882	3897967	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3897968	3898085	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3898086	3898173	0.69	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3898086	3898173	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	intron	3898174	3898283	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	CDS	3898284	3898298	0.33	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	exon	3898284	3898298	.	-	.	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
Phchi.S6	AUGUSTUS	start_codon	3898296	3898298	.	-	0	transcript_id "Phchi.S6G049500.t1"; gene_id "Phchi.S6G049500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11236.t1 is derived from g15286.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4933232	4934026	.	-	.	Phchi.S4G081800
Phchi.S4	AUGUSTUS	transcript	4933232	4934026	.	-	.	transcript_id "Phchi.S4G081800.t1"; gene_id "Phchi.S4G081800"
Phchi.S4	AUGUSTUS	stop_codon	4933229	4933231	.	-	0	transcript_id "Phchi.S4G081800.t1"; gene_id "Phchi.S4G081800"
Phchi.S4	AUGUSTUS	CDS	4933232	4934026	0.69	-	0	transcript_id "Phchi.S4G081800.t1"; gene_id "Phchi.S4G081800"
Phchi.S4	AUGUSTUS	exon	4933232	4934026	.	-	.	transcript_id "Phchi.S4G081800.t1"; gene_id "Phchi.S4G081800"
Phchi.S4	AUGUSTUS	start_codon	4934024	4934026	.	-	0	transcript_id "Phchi.S4G081800.t1"; gene_id "Phchi.S4G081800"
# This transcript jg8432.t2 is derived from g5607.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8433.t1 is derived from g5608.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	35918609	35922978	.	+	.	Phchi.S1G559200
Phchi.S1	AUGUSTUS	transcript	35918609	35922978	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	start_codon	35918609	35918611	.	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35918609	35918825	0.6	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35918609	35918825	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35918826	35918916	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35918917	35918997	0.47	+	2	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35918917	35918997	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35918998	35919074	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35919075	35919112	0.47	+	2	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35919075	35919112	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35919113	35919211	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35919212	35919305	0.91	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35919212	35919305	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35919306	35919602	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35919603	35919762	1	+	2	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35919603	35919762	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35919763	35919854	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35919855	35919991	0.29	+	1	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35919855	35919991	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35919992	35920074	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35920075	35920717	0.26	+	2	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35920075	35920717	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35920718	35920809	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35920810	35922002	0.99	+	1	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35920810	35922002	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35922003	35922100	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35922101	35922186	1	+	2	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35922101	35922186	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35922187	35922278	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35922279	35922383	1	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35922279	35922383	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35922384	35922477	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35922478	35922554	1	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35922478	35922554	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35922555	35922641	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35922642	35922795	1	+	1	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35922642	35922795	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	intron	35922796	35922900	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	CDS	35922901	35922978	0.99	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	exon	35922901	35922978	.	+	.	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
Phchi.S1	AUGUSTUS	stop_codon	35922979	35922981	.	+	0	transcript_id "Phchi.S1G559200.t1"; gene_id "Phchi.S1G559200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7508.t1 is derived from g4682.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29737235	29745891	.	-	.	Phchi.S1G466700
Phchi.S1	AUGUSTUS	transcript	29737235	29745891	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	stop_codon	29737232	29737234	.	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29737235	29737243	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29737235	29737243	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29737244	29737330	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29737331	29737436	0.56	-	1	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29737331	29737436	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29737437	29737829	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29737830	29738135	0.52	-	1	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29737830	29738135	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29738136	29738304	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29738305	29738312	0.99	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29738305	29738312	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29738313	29738412	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29738413	29738433	0.99	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29738413	29738433	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29738434	29738562	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29738563	29738662	1	-	1	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29738563	29738662	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29738663	29738756	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29738757	29739216	1	-	2	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29738757	29739216	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29739217	29739308	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29739309	29739412	1	-	1	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29739309	29739412	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29739413	29739505	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29739506	29739744	0.82	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29739506	29739744	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29739745	29739849	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29739850	29740007	0.94	-	2	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29739850	29740007	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29740008	29740104	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29740105	29740200	1	-	2	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29740105	29740200	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29740201	29740348	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29740349	29741129	0.97	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29740349	29741129	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29741130	29741228	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29741229	29741378	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29741229	29741378	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29741379	29741496	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29741497	29741742	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29741497	29741742	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29741743	29741825	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29741826	29742002	0.99	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29741826	29742002	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29742003	29742108	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29742109	29742319	0.98	-	1	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29742109	29742319	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29742320	29742508	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29742509	29742690	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29742509	29742690	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29742691	29742831	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29742832	29743560	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29742832	29743560	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29743561	29743650	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29743651	29743794	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29743651	29743794	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29743795	29743915	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29743916	29744023	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29743916	29744023	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29744024	29744115	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29744116	29744214	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29744116	29744214	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29744215	29744290	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29744291	29744527	0.96	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29744291	29744527	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29744528	29744689	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29744690	29744860	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29744690	29744860	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29744861	29745038	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29745039	29745067	0.78	-	2	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29745039	29745067	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29745068	29745156	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29745157	29745329	0.75	-	1	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29745157	29745329	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29745330	29745453	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29745454	29745701	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29745454	29745701	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	intron	29745702	29745795	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	CDS	29745796	29745891	1	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	exon	29745796	29745891	.	-	.	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
Phchi.S1	AUGUSTUS	start_codon	29745889	29745891	.	-	0	transcript_id "Phchi.S1G466700.t1"; gene_id "Phchi.S1G466700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5722.t1 is derived from g2892.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18548424	18549863	.	+	.	Phchi.S1G288100
Phchi.S1	AUGUSTUS	transcript	18548424	18549863	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	start_codon	18548424	18548426	.	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18548424	18548495	0.84	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18548424	18548495	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18548496	18548581	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18548582	18548676	1	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18548582	18548676	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18548677	18548768	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18548769	18548836	1	+	1	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18548769	18548836	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18548837	18548919	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18548920	18548951	0.87	+	2	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18548920	18548951	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18548952	18549134	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18549135	18549275	0.76	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18549135	18549275	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18549276	18549335	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18549336	18549533	0.91	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18549336	18549533	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18549534	18549614	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18549615	18549706	1	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18549615	18549706	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	intron	18549707	18549784	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	CDS	18549785	18549863	1	+	1	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	exon	18549785	18549863	.	+	.	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
Phchi.S1	AUGUSTUS	stop_codon	18549864	18549866	.	+	0	transcript_id "Phchi.S1G288100.t1"; gene_id "Phchi.S1G288100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2315.t1 is derived from g9235.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	6038721	6039098	.	-	.	Phchi.S5G092400
Phchi.S5	AUGUSTUS	transcript	6038721	6039098	.	-	.	transcript_id "Phchi.S5G092400.t1"; gene_id "Phchi.S5G092400"
Phchi.S5	AUGUSTUS	stop_codon	6038718	6038720	.	-	0	transcript_id "Phchi.S5G092400.t1"; gene_id "Phchi.S5G092400"
Phchi.S5	AUGUSTUS	CDS	6038721	6039098	0.94	-	0	transcript_id "Phchi.S5G092400.t1"; gene_id "Phchi.S5G092400"
Phchi.S5	AUGUSTUS	exon	6038721	6039098	.	-	.	transcript_id "Phchi.S5G092400.t1"; gene_id "Phchi.S5G092400"
Phchi.S5	AUGUSTUS	start_codon	6039096	6039098	.	-	0	transcript_id "Phchi.S5G092400.t1"; gene_id "Phchi.S5G092400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11122.t1 is derived from g15172.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4263715	4265980	.	+	.	Phchi.S4G070400
Phchi.S4	AUGUSTUS	transcript	4263957	4265980	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	start_codon	4263957	4263959	.	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4263957	4264040	0.92	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4263957	4264040	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264041	4264366	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264367	4264420	1	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264367	4264420	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264421	4264573	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264574	4264686	1	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264574	4264686	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264687	4264784	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264785	4264866	1	+	1	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264785	4264866	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264867	4264939	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264940	4265032	1	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264940	4265032	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265033	4265169	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265170	4265234	1	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265170	4265234	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265235	4265330	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265331	4265343	0.89	+	1	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265331	4265343	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265344	4265459	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265460	4265540	0.97	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265460	4265540	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265541	4265614	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265615	4265723	1	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265615	4265723	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265724	4265873	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265874	4265980	0.99	+	2	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265874	4265980	.	+	.	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	stop_codon	4265981	4265983	.	+	0	transcript_id "Phchi.S4G070400.t1"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	transcript	4263715	4265980	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	start_codon	4263715	4263717	.	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4263715	4263734	0.9	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4263715	4263734	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4263735	4263861	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4263862	4263974	0.83	+	1	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4263862	4263974	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4263975	4264205	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264206	4264261	0.8	+	2	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264206	4264261	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264262	4264366	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264367	4264420	1	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264367	4264420	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264421	4264573	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264574	4264686	1	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264574	4264686	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264687	4264784	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264785	4264866	1	+	1	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264785	4264866	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4264867	4264939	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4264940	4265032	1	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4264940	4265032	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265033	4265169	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265170	4265234	1	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265170	4265234	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265235	4265330	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265331	4265343	0.78	+	1	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265331	4265343	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265344	4265459	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265460	4265540	0.96	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265460	4265540	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265541	4265614	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265615	4265723	1	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265615	4265723	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	intron	4265724	4265873	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	CDS	4265874	4265980	0.99	+	2	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	exon	4265874	4265980	.	+	.	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
Phchi.S4	AUGUSTUS	stop_codon	4265981	4265983	.	+	0	transcript_id "Phchi.S4G070400.t2"; gene_id "Phchi.S4G070400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5793.t1 is derived from g2963.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18976574	18977605	.	-	.	Phchi.S1G295200
Phchi.S1	AUGUSTUS	transcript	18976574	18977605	.	-	.	transcript_id "Phchi.S1G295200.t1"; gene_id "Phchi.S1G295200"
Phchi.S1	AUGUSTUS	stop_codon	18976571	18976573	.	-	0	transcript_id "Phchi.S1G295200.t1"; gene_id "Phchi.S1G295200"
Phchi.S1	AUGUSTUS	CDS	18976574	18977605	0.81	-	0	transcript_id "Phchi.S1G295200.t1"; gene_id "Phchi.S1G295200"
Phchi.S1	AUGUSTUS	exon	18976574	18977605	.	-	.	transcript_id "Phchi.S1G295200.t1"; gene_id "Phchi.S1G295200"
Phchi.S1	AUGUSTUS	start_codon	18977603	18977605	.	-	0	transcript_id "Phchi.S1G295200.t1"; gene_id "Phchi.S1G295200"
# This transcript jg15615.t2 is derived from g14084.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg15616.t1 is derived from g14085.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20303500	20306804	.	-	.	Phchi.S3G293500
Phchi.S3	AUGUSTUS	transcript	20303500	20306804	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	stop_codon	20303497	20303499	.	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20303500	20303554	1	-	1	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20303500	20303554	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20303555	20303670	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20303671	20303820	1	-	1	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20303671	20303820	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20303821	20303899	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20303900	20303997	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20303900	20303997	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20303998	20304079	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304080	20304220	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304080	20304220	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20304221	20304293	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304294	20304458	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304294	20304458	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20304459	20304702	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304703	20304879	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304703	20304879	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20304880	20304948	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304949	20305129	1	-	1	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304949	20305129	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305130	20305254	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305255	20305300	1	-	2	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305255	20305300	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305301	20305484	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305485	20305548	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305485	20305548	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305549	20305679	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305680	20305702	1	-	2	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305680	20305702	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305703	20305799	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305800	20305872	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305800	20305872	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305873	20305949	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305950	20306081	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305950	20306081	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20306082	20306157	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20306158	20306244	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20306158	20306244	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20306245	20306663	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20306664	20306804	1	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20306664	20306804	.	-	.	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	start_codon	20306802	20306804	.	-	0	transcript_id "Phchi.S3G293500.t1"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	transcript	20303500	20306474	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	stop_codon	20303497	20303499	.	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20303500	20303554	1	-	1	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20303500	20303554	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20303555	20303670	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20303671	20303820	1	-	1	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20303671	20303820	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20303821	20303899	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20303900	20303997	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20303900	20303997	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20303998	20304079	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304080	20304220	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304080	20304220	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20304221	20304293	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304294	20304458	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304294	20304458	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20304459	20304702	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304703	20304879	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304703	20304879	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20304880	20304948	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20304949	20305129	1	-	1	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20304949	20305129	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305130	20305254	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305255	20305300	1	-	2	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305255	20305300	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305301	20305484	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305485	20305548	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305485	20305548	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305549	20305679	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305680	20305702	1	-	2	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305680	20305702	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305703	20305799	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305800	20305872	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305800	20305872	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20305873	20305949	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20305950	20306081	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20305950	20306081	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20306082	20306157	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20306158	20306244	1	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20306158	20306244	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	intron	20306245	20306459	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	CDS	20306460	20306474	0.47	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	exon	20306460	20306474	.	-	.	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
Phchi.S3	AUGUSTUS	start_codon	20306472	20306474	.	-	0	transcript_id "Phchi.S3G293500.t2"; gene_id "Phchi.S3G293500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7808.t1 is derived from g4982.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31277166	31280792	.	+	.	Phchi.S1G496700
Phchi.S1	AUGUSTUS	transcript	31277166	31280792	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	start_codon	31277166	31277168	.	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31277166	31277476	0.91	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31277166	31277476	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31277477	31277625	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31277626	31277692	0.99	+	1	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31277626	31277692	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31277693	31277823	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31277824	31277925	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31277824	31277925	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31277926	31278023	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31278024	31278080	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31278024	31278080	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31278081	31278182	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31278183	31278248	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31278183	31278248	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31278249	31278368	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31278369	31278545	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31278369	31278545	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31278546	31278647	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31278648	31278734	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31278648	31278734	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31278735	31278852	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31278853	31278917	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31278853	31278917	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31278918	31279056	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31279057	31279133	1	+	1	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31279057	31279133	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31279134	31279260	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31279261	31279307	1	+	2	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31279261	31279307	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31279308	31279457	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31279458	31279588	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31279458	31279588	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31279589	31279706	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31279707	31279776	1	+	1	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31279707	31279776	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	intron	31279777	31279964	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	CDS	31279965	31280792	1	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	exon	31279965	31280792	.	+	.	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
Phchi.S1	AUGUSTUS	stop_codon	31280793	31280795	.	+	0	transcript_id "Phchi.S1G496700.t1"; gene_id "Phchi.S1G496700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3316.t1 is derived from g485.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2835215	2836200	.	-	.	Phchi.S1G047500
Phchi.S1	AUGUSTUS	transcript	2835215	2836200	.	-	.	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	stop_codon	2835212	2835214	.	-	0	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	CDS	2835215	2835687	1	-	2	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	exon	2835215	2835687	.	-	.	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	intron	2835688	2835790	.	-	.	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	CDS	2835791	2835839	1	-	0	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	exon	2835791	2835839	.	-	.	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	intron	2835840	2836053	.	-	.	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	CDS	2836054	2836200	0.94	-	0	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	exon	2836054	2836200	.	-	.	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
Phchi.S1	AUGUSTUS	start_codon	2836198	2836200	.	-	0	transcript_id "Phchi.S1G047500.t1"; gene_id "Phchi.S1G047500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3245.t1 is derived from g414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2420944	2422681	.	+	.	Phchi.S1G040400
Phchi.S1	AUGUSTUS	transcript	2420944	2422681	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	start_codon	2420944	2420946	.	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2420944	2421006	1	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2420944	2421006	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	intron	2421007	2421190	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2421191	2421358	1	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2421191	2421358	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	intron	2421359	2421453	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2421454	2421654	1	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2421454	2421654	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	intron	2421655	2421809	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2421810	2421982	1	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2421810	2421982	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	intron	2421983	2422068	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2422069	2422156	1	+	1	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2422069	2422156	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	intron	2422157	2422240	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2422241	2422394	0.76	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2422241	2422394	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	intron	2422395	2422505	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	CDS	2422506	2422681	0.74	+	2	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	exon	2422506	2422681	.	+	.	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
Phchi.S1	AUGUSTUS	stop_codon	2422682	2422684	.	+	0	transcript_id "Phchi.S1G040400.t1"; gene_id "Phchi.S1G040400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12263.t1 is derived from g7939.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	7227785	7230414	.	-	.	Phchi.S2G034300
Phchi.S2	AUGUSTUS	transcript	7227785	7230414	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	stop_codon	7227782	7227784	.	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7227785	7227898	1	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7227785	7227898	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7227899	7228009	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7228010	7228129	1	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7228010	7228129	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7228130	7228338	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7228339	7228437	1	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7228339	7228437	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7228438	7228615	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7228616	7228727	1	-	1	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7228616	7228727	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7228728	7228907	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7228908	7229011	1	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7228908	7229011	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7229012	7229120	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7229121	7229300	0.9	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7229121	7229300	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7229301	7229381	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7229382	7229651	1	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7229382	7229651	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7229652	7229745	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7229746	7230042	1	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7229746	7230042	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	intron	7230043	7230165	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	CDS	7230166	7230414	0.98	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	exon	7230166	7230414	.	-	.	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
Phchi.S2	AUGUSTUS	start_codon	7230412	7230414	.	-	0	transcript_id "Phchi.S2G034300.t1"; gene_id "Phchi.S2G034300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11619.t1 is derived from g15670.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	7351255	7352796	.	-	.	Phchi.S4G120100
Phchi.S4	AUGUSTUS	transcript	7351255	7352796	.	-	.	transcript_id "Phchi.S4G120100.t1"; gene_id "Phchi.S4G120100"
Phchi.S4	AUGUSTUS	stop_codon	7351252	7351254	.	-	0	transcript_id "Phchi.S4G120100.t1"; gene_id "Phchi.S4G120100"
Phchi.S4	AUGUSTUS	CDS	7351255	7352796	0.86	-	0	transcript_id "Phchi.S4G120100.t1"; gene_id "Phchi.S4G120100"
Phchi.S4	AUGUSTUS	exon	7351255	7352796	.	-	.	transcript_id "Phchi.S4G120100.t1"; gene_id "Phchi.S4G120100"
Phchi.S4	AUGUSTUS	start_codon	7352794	7352796	.	-	0	transcript_id "Phchi.S4G120100.t1"; gene_id "Phchi.S4G120100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15906.t1 is derived from g14376.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	22091328	22092142	.	+	.	Phchi.S3G322500
Phchi.S3	AUGUSTUS	transcript	22091328	22092142	.	+	.	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	start_codon	22091328	22091330	.	+	0	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	CDS	22091328	22091557	0.62	+	0	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	exon	22091328	22091557	.	+	.	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	intron	22091558	22091634	.	+	.	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	CDS	22091635	22092142	0.85	+	1	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	exon	22091635	22092142	.	+	.	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
Phchi.S3	AUGUSTUS	stop_codon	22092143	22092145	.	+	0	transcript_id "Phchi.S3G322500.t1"; gene_id "Phchi.S3G322500"
# This transcript jg1575.t2 is derived from g8494.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1576.t1 is derived from g8495.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1849342	1850783	.	-	.	Phchi.S5G018500
Phchi.S5	AUGUSTUS	transcript	1849342	1850783	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	stop_codon	1849339	1849341	.	-	0	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	CDS	1849342	1849457	0.38	-	2	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	exon	1849342	1849457	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	intron	1849458	1849606	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	CDS	1849607	1849700	0.38	-	0	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	exon	1849607	1849700	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	intron	1849701	1849813	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	CDS	1849814	1850098	0.99	-	0	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	exon	1849814	1850098	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	intron	1850099	1850244	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	CDS	1850245	1850293	0.77	-	1	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	exon	1850245	1850293	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	intron	1850294	1850466	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	CDS	1850467	1850783	0.98	-	0	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	exon	1850467	1850783	.	-	.	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
Phchi.S5	AUGUSTUS	start_codon	1850781	1850783	.	-	0	transcript_id "Phchi.S5G018500.t1"; gene_id "Phchi.S5G018500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15240.t1 is derived from g13708.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17875772	17876554	.	-	.	Phchi.S3G255900
Phchi.S3	AUGUSTUS	transcript	17875772	17876554	.	-	.	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	stop_codon	17875769	17875771	.	-	0	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	CDS	17875772	17875852	0.86	-	0	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	exon	17875772	17875852	.	-	.	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	intron	17875853	17875986	.	-	.	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	CDS	17875987	17876060	0.56	-	2	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	exon	17875987	17876060	.	-	.	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	intron	17876061	17876136	.	-	.	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	CDS	17876137	17876554	0.57	-	0	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	exon	17876137	17876554	.	-	.	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
Phchi.S3	AUGUSTUS	start_codon	17876552	17876554	.	-	0	transcript_id "Phchi.S3G255900.t1"; gene_id "Phchi.S3G255900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11151.t1 is derived from g15201.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4394590	4395465	.	+	.	Phchi.S4G073300
Phchi.S4	AUGUSTUS	transcript	4394590	4395465	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	start_codon	4394590	4394592	.	+	0	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	CDS	4394590	4394608	1	+	0	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	exon	4394590	4394608	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	intron	4394609	4394744	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	CDS	4394745	4394885	1	+	2	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	exon	4394745	4394885	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	intron	4394886	4394994	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	CDS	4394995	4395155	1	+	2	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	exon	4394995	4395155	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	intron	4395156	4395369	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	CDS	4395370	4395465	0.7	+	0	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	exon	4395370	4395465	.	+	.	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
Phchi.S4	AUGUSTUS	stop_codon	4395466	4395468	.	+	0	transcript_id "Phchi.S4G073300.t1"; gene_id "Phchi.S4G073300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7841.t1 is derived from g5015.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31474881	31482630	.	-	.	Phchi.S1G500000
Phchi.S1	AUGUSTUS	transcript	31474881	31482630	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	stop_codon	31474878	31474880	.	-	0	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	CDS	31474881	31477648	0.71	-	2	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	exon	31474881	31477648	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	intron	31477649	31477752	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	CDS	31477753	31479300	0.93	-	2	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	exon	31477753	31479300	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	intron	31479301	31479518	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	CDS	31479519	31479945	0.8	-	0	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	exon	31479519	31479945	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	intron	31479946	31480052	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	CDS	31480053	31480810	0.84	-	2	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	exon	31480053	31480810	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	intron	31480811	31480962	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	CDS	31480963	31482000	1	-	2	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	exon	31480963	31482000	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	intron	31482001	31482359	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	CDS	31482360	31482630	0.97	-	0	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	exon	31482360	31482630	.	-	.	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
Phchi.S1	AUGUSTUS	start_codon	31482628	31482630	.	-	0	transcript_id "Phchi.S1G500000.t1"; gene_id "Phchi.S1G500000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6432.t1 is derived from g3604.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23014836	23016650	.	-	.	Phchi.S1G359100
Phchi.S1	AUGUSTUS	transcript	23014836	23016650	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	stop_codon	23014833	23014835	.	-	0	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	CDS	23014836	23014966	1	-	2	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	exon	23014836	23014966	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	intron	23014967	23015127	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	CDS	23015128	23015263	1	-	0	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	exon	23015128	23015263	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	intron	23015264	23015350	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	CDS	23015351	23015459	1	-	1	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	exon	23015351	23015459	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	intron	23015460	23015634	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	CDS	23015635	23016650	0.39	-	0	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	exon	23015635	23016650	.	-	.	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
Phchi.S1	AUGUSTUS	start_codon	23016648	23016650	.	-	0	transcript_id "Phchi.S1G359100.t1"; gene_id "Phchi.S1G359100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10908.t1 is derived from g14958.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2875506	2876068	.	-	.	Phchi.S4G049000
Phchi.S4	AUGUSTUS	transcript	2875506	2876068	.	-	.	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	stop_codon	2875503	2875505	.	-	0	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	CDS	2875506	2875791	0.71	-	1	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	exon	2875506	2875791	.	-	.	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	intron	2875792	2876030	.	-	.	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	CDS	2876031	2876068	0.57	-	0	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	exon	2876031	2876068	.	-	.	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
Phchi.S4	AUGUSTUS	start_codon	2876066	2876068	.	-	0	transcript_id "Phchi.S4G049000.t1"; gene_id "Phchi.S4G049000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10215.t1 is derived from g7391.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	46413364	46416390	.	-	.	Phchi.S1G737400
Phchi.S1	AUGUSTUS	transcript	46413364	46416390	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	stop_codon	46413361	46413363	.	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46413364	46413672	0.98	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46413364	46413672	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46413673	46413836	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46413837	46414015	1	-	2	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46413837	46414015	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46414016	46414256	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46414257	46414593	1	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46414257	46414593	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46414594	46414697	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46414698	46414877	1	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46414698	46414877	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46414878	46415060	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46415061	46415318	1	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46415061	46415318	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46415319	46415446	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46415447	46415642	1	-	1	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46415447	46415642	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46415643	46415807	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46415808	46415979	1	-	2	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46415808	46415979	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	intron	46415980	46416158	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	CDS	46416159	46416390	0.75	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	exon	46416159	46416390	.	-	.	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
Phchi.S1	AUGUSTUS	start_codon	46416388	46416390	.	-	0	transcript_id "Phchi.S1G737400.t1"; gene_id "Phchi.S1G737400"
# This transcript jg3922.t2 is derived from g1091.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3923.t1 is derived from g1092.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6439154	6440393	.	-	.	Phchi.S1G108200
Phchi.S1	AUGUSTUS	transcript	6439154	6440393	.	-	.	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	stop_codon	6439151	6439153	.	-	0	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	CDS	6439154	6439682	0.86	-	1	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	exon	6439154	6439682	.	-	.	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	intron	6439683	6439777	.	-	.	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	CDS	6439778	6439917	0.99	-	0	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	exon	6439778	6439917	.	-	.	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	intron	6439918	6440030	.	-	.	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	CDS	6440031	6440393	0.99	-	0	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	exon	6440031	6440393	.	-	.	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	start_codon	6440391	6440393	.	-	0	transcript_id "Phchi.S1G108200.t1"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	transcript	6439154	6440105	.	-	.	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	stop_codon	6439151	6439153	.	-	0	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	CDS	6439154	6439682	0.75	-	1	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	exon	6439154	6439682	.	-	.	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	intron	6439683	6439777	.	-	.	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	CDS	6439778	6439917	1	-	0	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	exon	6439778	6439917	.	-	.	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	intron	6439918	6440030	.	-	.	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	CDS	6440031	6440105	0.96	-	0	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	exon	6440031	6440105	.	-	.	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
Phchi.S1	AUGUSTUS	start_codon	6440103	6440105	.	-	0	transcript_id "Phchi.S1G108200.t2"; gene_id "Phchi.S1G108200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14753.t1 is derived from g13221.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14551467	14551979	.	-	.	Phchi.S3G207200
Phchi.S3	AUGUSTUS	transcript	14551467	14551979	.	-	.	transcript_id "Phchi.S3G207200.t1"; gene_id "Phchi.S3G207200"
Phchi.S3	AUGUSTUS	stop_codon	14551464	14551466	.	-	0	transcript_id "Phchi.S3G207200.t1"; gene_id "Phchi.S3G207200"
Phchi.S3	AUGUSTUS	CDS	14551467	14551979	0.78	-	0	transcript_id "Phchi.S3G207200.t1"; gene_id "Phchi.S3G207200"
Phchi.S3	AUGUSTUS	exon	14551467	14551979	.	-	.	transcript_id "Phchi.S3G207200.t1"; gene_id "Phchi.S3G207200"
Phchi.S3	AUGUSTUS	start_codon	14551977	14551979	.	-	0	transcript_id "Phchi.S3G207200.t1"; gene_id "Phchi.S3G207200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14946.t1 is derived from g13414.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	15655680	15656091	.	-	.	Phchi.S3G226500
Phchi.S3	AUGUSTUS	transcript	15655680	15656091	.	-	.	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	stop_codon	15655677	15655679	.	-	0	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	CDS	15655680	15655741	0.98	-	2	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	exon	15655680	15655741	.	-	.	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	intron	15655742	15655826	.	-	.	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	CDS	15655827	15656091	1	-	0	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	exon	15655827	15656091	.	-	.	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
Phchi.S3	AUGUSTUS	start_codon	15656089	15656091	.	-	0	transcript_id "Phchi.S3G226500.t1"; gene_id "Phchi.S3G226500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3788.t1 is derived from g957.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5734757	5737234	.	-	.	Phchi.S1G094700
Phchi.S1	AUGUSTUS	transcript	5734757	5737234	.	-	.	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	stop_codon	5734754	5734756	.	-	0	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	CDS	5734757	5735253	1	-	2	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	exon	5734757	5735253	.	-	.	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	intron	5735254	5735334	.	-	.	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	CDS	5735335	5737234	1	-	0	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	exon	5735335	5737234	.	-	.	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
Phchi.S1	AUGUSTUS	start_codon	5737232	5737234	.	-	0	transcript_id "Phchi.S1G094700.t1"; gene_id "Phchi.S1G094700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7544.t1 is derived from g4718.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29975647	29977187	.	-	.	Phchi.S1G470300
Phchi.S1	AUGUSTUS	transcript	29975647	29977187	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	stop_codon	29975644	29975646	.	-	0	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	CDS	29975647	29975742	0.98	-	0	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	exon	29975647	29975742	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	intron	29975743	29975952	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	CDS	29975953	29976063	1	-	0	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	exon	29975953	29976063	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	intron	29976064	29976259	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	CDS	29976260	29976380	0.81	-	1	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	exon	29976260	29976380	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	intron	29976381	29976606	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	CDS	29976607	29977187	0.38	-	0	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	exon	29976607	29977187	.	-	.	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
Phchi.S1	AUGUSTUS	start_codon	29977185	29977187	.	-	0	transcript_id "Phchi.S1G470300.t1"; gene_id "Phchi.S1G470300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11152.t1 is derived from g15202.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4396055	4397292	.	+	.	Phchi.S4G073400
Phchi.S4	AUGUSTUS	transcript	4396055	4397292	.	+	.	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	start_codon	4396055	4396057	.	+	0	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	CDS	4396055	4396148	0.74	+	0	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	exon	4396055	4396148	.	+	.	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	intron	4396149	4396597	.	+	.	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	CDS	4396598	4397292	0.68	+	2	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	exon	4396598	4397292	.	+	.	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
Phchi.S4	AUGUSTUS	stop_codon	4397293	4397295	.	+	0	transcript_id "Phchi.S4G073400.t1"; gene_id "Phchi.S4G073400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3735.t1 is derived from g904.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5449181	5449849	.	-	.	Phchi.S1G089400
Phchi.S1	AUGUSTUS	transcript	5449181	5449849	.	-	.	transcript_id "Phchi.S1G089400.t1"; gene_id "Phchi.S1G089400"
Phchi.S1	AUGUSTUS	stop_codon	5449178	5449180	.	-	0	transcript_id "Phchi.S1G089400.t1"; gene_id "Phchi.S1G089400"
Phchi.S1	AUGUSTUS	CDS	5449181	5449849	0.74	-	0	transcript_id "Phchi.S1G089400.t1"; gene_id "Phchi.S1G089400"
Phchi.S1	AUGUSTUS	exon	5449181	5449849	.	-	.	transcript_id "Phchi.S1G089400.t1"; gene_id "Phchi.S1G089400"
Phchi.S1	AUGUSTUS	start_codon	5449847	5449849	.	-	0	transcript_id "Phchi.S1G089400.t1"; gene_id "Phchi.S1G089400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12492.t1 is derived from g8169.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	29318787	29319164	.	-	.	Phchi.S2G057200
Phchi.S2	AUGUSTUS	transcript	29318787	29319164	.	-	.	transcript_id "Phchi.S2G057200.t1"; gene_id "Phchi.S2G057200"
Phchi.S2	AUGUSTUS	stop_codon	29318784	29318786	.	-	0	transcript_id "Phchi.S2G057200.t1"; gene_id "Phchi.S2G057200"
Phchi.S2	AUGUSTUS	CDS	29318787	29319164	0.74	-	0	transcript_id "Phchi.S2G057200.t1"; gene_id "Phchi.S2G057200"
Phchi.S2	AUGUSTUS	exon	29318787	29319164	.	-	.	transcript_id "Phchi.S2G057200.t1"; gene_id "Phchi.S2G057200"
Phchi.S2	AUGUSTUS	start_codon	29319162	29319164	.	-	0	transcript_id "Phchi.S2G057200.t1"; gene_id "Phchi.S2G057200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10724.t1 is derived from g14774.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1767464	1769080	.	-	.	Phchi.S4G030600
Phchi.S4	AUGUSTUS	transcript	1767464	1769080	.	-	.	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	stop_codon	1767461	1767463	.	-	0	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	CDS	1767464	1767951	1	-	2	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	exon	1767464	1767951	.	-	.	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	intron	1767952	1768074	.	-	.	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	CDS	1768075	1769080	0.97	-	0	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	exon	1768075	1769080	.	-	.	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
Phchi.S4	AUGUSTUS	start_codon	1769078	1769080	.	-	0	transcript_id "Phchi.S4G030600.t1"; gene_id "Phchi.S4G030600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2759.t1 is derived from g9679.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8702831	8703139	.	-	.	Phchi.S5G136800
Phchi.S5	AUGUSTUS	transcript	8702831	8703139	.	-	.	transcript_id "Phchi.S5G136800.t1"; gene_id "Phchi.S5G136800"
Phchi.S5	AUGUSTUS	stop_codon	8702828	8702830	.	-	0	transcript_id "Phchi.S5G136800.t1"; gene_id "Phchi.S5G136800"
Phchi.S5	AUGUSTUS	CDS	8702831	8703139	1	-	0	transcript_id "Phchi.S5G136800.t1"; gene_id "Phchi.S5G136800"
Phchi.S5	AUGUSTUS	exon	8702831	8703139	.	-	.	transcript_id "Phchi.S5G136800.t1"; gene_id "Phchi.S5G136800"
Phchi.S5	AUGUSTUS	start_codon	8703137	8703139	.	-	0	transcript_id "Phchi.S5G136800.t1"; gene_id "Phchi.S5G136800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13899.t1 is derived from g12366.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9539646	9540723	.	-	.	Phchi.S3G121800
Phchi.S3	AUGUSTUS	transcript	9539646	9540723	.	-	.	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	stop_codon	9539643	9539645	.	-	0	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	CDS	9539646	9540605	0.99	-	0	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	exon	9539646	9540605	.	-	.	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	intron	9540606	9540696	.	-	.	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	CDS	9540697	9540723	0.52	-	0	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	exon	9540697	9540723	.	-	.	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
Phchi.S3	AUGUSTUS	start_codon	9540721	9540723	.	-	0	transcript_id "Phchi.S3G121800.t1"; gene_id "Phchi.S3G121800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9390.t1 is derived from g6566.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41308453	41308758	.	-	.	Phchi.S1G654900
Phchi.S1	AUGUSTUS	transcript	41308453	41308758	.	-	.	transcript_id "Phchi.S1G654900.t1"; gene_id "Phchi.S1G654900"
Phchi.S1	AUGUSTUS	stop_codon	41308450	41308452	.	-	0	transcript_id "Phchi.S1G654900.t1"; gene_id "Phchi.S1G654900"
Phchi.S1	AUGUSTUS	CDS	41308453	41308758	0.72	-	0	transcript_id "Phchi.S1G654900.t1"; gene_id "Phchi.S1G654900"
Phchi.S1	AUGUSTUS	exon	41308453	41308758	.	-	.	transcript_id "Phchi.S1G654900.t1"; gene_id "Phchi.S1G654900"
Phchi.S1	AUGUSTUS	start_codon	41308756	41308758	.	-	0	transcript_id "Phchi.S1G654900.t1"; gene_id "Phchi.S1G654900"
# This transcript jg12555.t2 is derived from g8232.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12556.t1 is derived from g8233.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	34745178	34747318	.	+	.	Phchi.S2G063600
Phchi.S2	AUGUSTUS	transcript	34745178	34747318	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	start_codon	34745178	34745180	.	+	0	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34745178	34745241	0.85	+	0	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34745178	34745241	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34745242	34745328	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34745329	34745350	0.86	+	2	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34745329	34745350	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34745351	34745451	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34745452	34745478	0.52	+	1	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34745452	34745478	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34745479	34745605	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34745606	34745812	0.98	+	1	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34745606	34745812	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34745813	34746046	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34746047	34746198	0.98	+	1	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34746047	34746198	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34746199	34746303	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34746304	34746395	0.54	+	2	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34746304	34746395	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34746396	34746510	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34746511	34746572	0.14	+	0	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34746511	34746572	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34746573	34746952	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34746953	34747054	0.79	+	1	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34746953	34747054	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	intron	34747055	34747230	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	CDS	34747231	34747318	1	+	1	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	exon	34747231	34747318	.	+	.	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
Phchi.S2	AUGUSTUS	stop_codon	34747319	34747321	.	+	0	transcript_id "Phchi.S2G063600.t1"; gene_id "Phchi.S2G063600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10772.t1 is derived from g14822.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2047683	2049232	.	+	.	Phchi.S4G035400
Phchi.S4	AUGUSTUS	transcript	2047683	2049232	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	start_codon	2047683	2047685	.	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	CDS	2047683	2047920	0.55	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	exon	2047683	2047920	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	intron	2047921	2048037	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	CDS	2048038	2048105	0.55	+	2	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	exon	2048038	2048105	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	intron	2048106	2048200	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	CDS	2048201	2048356	0.94	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	exon	2048201	2048356	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	intron	2048357	2048458	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	CDS	2048459	2048701	0.98	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	exon	2048459	2048701	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	intron	2048702	2048785	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	CDS	2048786	2048971	0.98	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	exon	2048786	2048971	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	intron	2048972	2049082	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	CDS	2049083	2049232	0.99	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	exon	2049083	2049232	.	+	.	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
Phchi.S4	AUGUSTUS	stop_codon	2049233	2049235	.	+	0	transcript_id "Phchi.S4G035400.t1"; gene_id "Phchi.S4G035400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7560.t1 is derived from g4734.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30035097	30035656	.	+	.	Phchi.S1G471900
Phchi.S1	AUGUSTUS	transcript	30035097	30035656	.	+	.	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	start_codon	30035097	30035099	.	+	0	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	CDS	30035097	30035100	0.55	+	0	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	exon	30035097	30035100	.	+	.	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	intron	30035101	30035273	.	+	.	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	CDS	30035274	30035656	1	+	2	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	exon	30035274	30035656	.	+	.	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
Phchi.S1	AUGUSTUS	stop_codon	30035657	30035659	.	+	0	transcript_id "Phchi.S1G471900.t1"; gene_id "Phchi.S1G471900"
# This transcript jg12696.t2 is derived from g11161.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg12696.t3 is derived from g11161.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12697.t1 is derived from g11162.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	612147	614612	.	+	.	Phchi.S3G001600
Phchi.S3	AUGUSTUS	transcript	612147	614418	.	+	.	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	start_codon	612147	612149	.	+	0	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	CDS	612147	614248	0.67	+	0	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	exon	612147	614248	.	+	.	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	intron	614249	614387	.	+	.	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	CDS	614388	614418	0.61	+	1	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	exon	614388	614418	.	+	.	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	stop_codon	614419	614421	.	+	0	transcript_id "Phchi.S3G001600.t1"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	transcript	612147	614612	.	+	.	transcript_id "Phchi.S3G001600.t2"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	start_codon	612147	612149	.	+	0	transcript_id "Phchi.S3G001600.t2"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	CDS	612147	614612	0.99	+	0	transcript_id "Phchi.S3G001600.t2"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	exon	612147	614612	.	+	.	transcript_id "Phchi.S3G001600.t2"; gene_id "Phchi.S3G001600"
Phchi.S3	AUGUSTUS	stop_codon	614613	614615	.	+	0	transcript_id "Phchi.S3G001600.t2"; gene_id "Phchi.S3G001600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9811.t1 is derived from g6987.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	43855318	43857584	.	-	.	Phchi.S1G697000
Phchi.S1	AUGUSTUS	transcript	43855318	43857584	.	-	.	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	stop_codon	43855315	43855317	.	-	0	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	CDS	43855318	43856339	1	-	2	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	exon	43855318	43856339	.	-	.	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	intron	43856340	43856452	.	-	.	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	CDS	43856453	43856537	0.99	-	0	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	exon	43856453	43856537	.	-	.	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	intron	43856538	43856654	.	-	.	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	CDS	43856655	43857584	0.99	-	0	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	exon	43856655	43857584	.	-	.	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
Phchi.S1	AUGUSTUS	start_codon	43857582	43857584	.	-	0	transcript_id "Phchi.S1G697000.t1"; gene_id "Phchi.S1G697000"
# This transcript jg6021.t2 is derived from g3192.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6022.t1 is derived from g3193.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	20486632	20487176	.	-	.	Phchi.S1G318100
Phchi.S1	AUGUSTUS	transcript	20486632	20487176	.	-	.	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	stop_codon	20486629	20486631	.	-	0	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	CDS	20486632	20486790	1	-	0	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	exon	20486632	20486790	.	-	.	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	intron	20486791	20487032	.	-	.	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	CDS	20487033	20487084	1	-	1	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	exon	20487033	20487084	.	-	.	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	intron	20487085	20487168	.	-	.	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	CDS	20487169	20487176	1	-	0	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	exon	20487169	20487176	.	-	.	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
Phchi.S1	AUGUSTUS	start_codon	20487174	20487176	.	-	0	transcript_id "Phchi.S1G318100.t1"; gene_id "Phchi.S1G318100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1651.t1 is derived from g8570.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	2224976	2228008	.	+	.	Phchi.S5G026000
Phchi.S5	AUGUSTUS	transcript	2224976	2228008	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	start_codon	2224976	2224978	.	+	0	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	CDS	2224976	2225682	0.47	+	0	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	exon	2224976	2225682	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	intron	2225683	2225777	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	CDS	2225778	2226037	0.99	+	1	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	exon	2225778	2226037	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	intron	2226038	2226139	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	CDS	2226140	2226280	0.99	+	2	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	exon	2226140	2226280	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	intron	2226281	2226379	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	CDS	2226380	2226612	1	+	2	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	exon	2226380	2226612	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	intron	2226613	2226701	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	CDS	2226702	2227222	0.65	+	0	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	exon	2226702	2227222	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	intron	2227223	2227365	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	CDS	2227366	2228008	0.65	+	1	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	exon	2227366	2228008	.	+	.	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
Phchi.S5	AUGUSTUS	stop_codon	2228009	2228011	.	+	0	transcript_id "Phchi.S5G026000.t1"; gene_id "Phchi.S5G026000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2782.t1 is derived from g9702.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8848546	8851652	.	+	.	Phchi.S5G139100
Phchi.S5	AUGUSTUS	transcript	8848546	8851652	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	start_codon	8848546	8848548	.	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8848546	8849052	1	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8848546	8849052	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8849053	8849513	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8849514	8849582	1	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8849514	8849582	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8849583	8849634	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8849635	8849664	1	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8849635	8849664	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8849665	8849908	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8849909	8849991	1	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8849909	8849991	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8849992	8850078	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8850079	8850152	0.51	+	1	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8850079	8850152	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8850153	8850239	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8850240	8850334	1	+	2	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8850240	8850334	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8850335	8850459	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8850460	8850487	1	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8850460	8850487	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8850488	8850599	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8850600	8851144	1	+	2	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8850600	8851144	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8851145	8851238	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8851239	8851326	1	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8851239	8851326	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	intron	8851327	8851524	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	CDS	8851525	8851652	0.99	+	2	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	exon	8851525	8851652	.	+	.	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
Phchi.S5	AUGUSTUS	stop_codon	8851653	8851655	.	+	0	transcript_id "Phchi.S5G139100.t1"; gene_id "Phchi.S5G139100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg38.t1 is derived from g9798.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C67	AUGUSTUS	gene	22717	23502	.	+	.	Phchi.C67G000400
Phchi.C67	AUGUSTUS	transcript	22717	23502	.	+	.	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	start_codon	22717	22719	.	+	0	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	CDS	22717	22901	0.36	+	0	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	exon	22717	22901	.	+	.	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	intron	22902	23004	.	+	.	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	CDS	23005	23114	0.51	+	1	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	exon	23005	23114	.	+	.	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	intron	23115	23206	.	+	.	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	CDS	23207	23502	0.92	+	2	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	exon	23207	23502	.	+	.	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
Phchi.C67	AUGUSTUS	stop_codon	23503	23505	.	+	0	transcript_id "Phchi.C67G000400.t1"; gene_id "Phchi.C67G000400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14359.t1 is derived from g12826.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12357708	12359342	.	+	.	Phchi.S3G167800
Phchi.S3	AUGUSTUS	transcript	12357708	12359342	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	start_codon	12357708	12357710	.	+	0	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	CDS	12357708	12358352	1	+	0	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	exon	12357708	12358352	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	intron	12358353	12358523	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	CDS	12358524	12358574	0.93	+	0	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	exon	12358524	12358574	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	intron	12358575	12358657	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	CDS	12358658	12358761	0.83	+	0	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	exon	12358658	12358761	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	intron	12358762	12358994	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	CDS	12358995	12359172	0.93	+	1	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	exon	12358995	12359172	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	intron	12359173	12359300	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	CDS	12359301	12359342	0.93	+	0	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	exon	12359301	12359342	.	+	.	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
Phchi.S3	AUGUSTUS	stop_codon	12359343	12359345	.	+	0	transcript_id "Phchi.S3G167800.t1"; gene_id "Phchi.S3G167800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11493.t1 is derived from g15543.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6639049	6640075	.	+	.	Phchi.S4G107500
Phchi.S4	AUGUSTUS	transcript	6639049	6640075	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	start_codon	6639049	6639051	.	+	0	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	CDS	6639049	6639080	0.47	+	0	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	exon	6639049	6639080	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	intron	6639081	6639175	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	CDS	6639176	6639241	0.93	+	1	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	exon	6639176	6639241	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	intron	6639242	6639336	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	CDS	6639337	6639427	1	+	1	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	exon	6639337	6639427	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	intron	6639428	6639721	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	CDS	6639722	6639727	1	+	0	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	exon	6639722	6639727	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	intron	6639728	6639812	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	CDS	6639813	6639923	1	+	0	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	exon	6639813	6639923	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	intron	6639924	6640006	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	CDS	6640007	6640075	1	+	0	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	exon	6640007	6640075	.	+	.	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
Phchi.S4	AUGUSTUS	stop_codon	6640076	6640078	.	+	0	transcript_id "Phchi.S4G107500.t1"; gene_id "Phchi.S4G107500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5797.t1 is derived from g2967.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	18991697	18994350	.	-	.	Phchi.S1G295600
Phchi.S1	AUGUSTUS	transcript	18991697	18994350	.	-	.	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	stop_codon	18991694	18991696	.	-	0	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	CDS	18991697	18992688	0.97	-	2	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	exon	18991697	18992688	.	-	.	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	intron	18992689	18992993	.	-	.	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	CDS	18992994	18994350	0.63	-	0	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	exon	18992994	18994350	.	-	.	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
Phchi.S1	AUGUSTUS	start_codon	18994348	18994350	.	-	0	transcript_id "Phchi.S1G295600.t1"; gene_id "Phchi.S1G295600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5599.t1 is derived from g2769.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17825272	17826182	.	+	.	Phchi.S1G275800
Phchi.S1	AUGUSTUS	transcript	17825272	17826182	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	start_codon	17825272	17825274	.	+	0	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	CDS	17825272	17825342	0.54	+	0	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	exon	17825272	17825342	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	intron	17825343	17825459	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	CDS	17825460	17825721	1	+	1	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	exon	17825460	17825721	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	intron	17825722	17825809	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	CDS	17825810	17826018	1	+	0	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	exon	17825810	17826018	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	intron	17826019	17826118	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	CDS	17826119	17826182	1	+	1	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	exon	17826119	17826182	.	+	.	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
Phchi.S1	AUGUSTUS	stop_codon	17826183	17826185	.	+	0	transcript_id "Phchi.S1G275800.t1"; gene_id "Phchi.S1G275800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3611.t1 is derived from g780.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4740518	4744972	.	+	.	Phchi.S1G077000
Phchi.S1	AUGUSTUS	transcript	4740518	4744972	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	start_codon	4740518	4740520	.	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4740518	4740563	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4740518	4740563	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4740564	4740648	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4740649	4740713	1	+	2	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4740649	4740713	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4740714	4740795	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4740796	4740873	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4740796	4740873	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4740874	4740967	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4740968	4741044	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4740968	4741044	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4741045	4741145	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4741146	4741227	1	+	1	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4741146	4741227	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4741228	4741307	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4741308	4741355	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4741308	4741355	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4741356	4741475	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4741476	4741631	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4741476	4741631	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4741632	4741715	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4741716	4741812	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4741716	4741812	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4741813	4741953	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4741954	4741996	1	+	2	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4741954	4741996	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4741997	4742113	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4742114	4742181	1	+	1	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4742114	4742181	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4742182	4742284	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4742285	4742369	1	+	2	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4742285	4742369	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4742370	4742484	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4742485	4742533	1	+	1	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4742485	4742533	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4742534	4742633	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4742634	4742706	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4742634	4742706	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4742707	4742791	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4742792	4742852	1	+	2	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4742792	4742852	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4742853	4742964	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4742965	4743031	1	+	1	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4742965	4743031	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4743032	4743130	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4743131	4743187	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4743131	4743187	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4743188	4743277	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4743278	4743331	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4743278	4743331	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4743332	4743516	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4743517	4743645	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4743517	4743645	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4743646	4743742	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4743743	4743806	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4743743	4743806	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4743807	4743897	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4743898	4743971	1	+	2	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4743898	4743971	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4743972	4744117	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4744118	4744171	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4744118	4744171	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4744172	4744261	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4744262	4744330	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4744262	4744330	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4744331	4744431	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4744432	4744521	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4744432	4744521	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4744522	4744621	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4744622	4744729	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4744622	4744729	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	intron	4744730	4744825	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	CDS	4744826	4744972	1	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	exon	4744826	4744972	.	+	.	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
Phchi.S1	AUGUSTUS	stop_codon	4744973	4744975	.	+	0	transcript_id "Phchi.S1G077000.t1"; gene_id "Phchi.S1G077000"
# This transcript jg13945.t2 is derived from g12412.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13946.t1 is derived from g12413.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	9854290	9858652	.	+	.	Phchi.S3G126500
Phchi.S3	AUGUSTUS	transcript	9854290	9858652	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	start_codon	9854290	9854292	.	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9854290	9854457	0.52	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9854290	9854457	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9854458	9854762	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9854763	9854915	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9854763	9854915	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9854916	9855044	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9855045	9855200	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9855045	9855200	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9855201	9855360	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9855361	9855483	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9855361	9855483	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9855484	9855564	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9855565	9855733	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9855565	9855733	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9855734	9855909	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9855910	9855992	1	+	2	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9855910	9855992	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9855993	9856085	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9856086	9856187	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9856086	9856187	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9856188	9856285	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9856286	9856374	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9856286	9856374	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9856375	9856533	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9856534	9856624	0.98	+	1	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9856534	9856624	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9856625	9856734	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9856735	9856848	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9856735	9856848	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9856849	9856950	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9856951	9857027	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9856951	9857027	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857028	9857114	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9857115	9857193	1	+	1	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9857115	9857193	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857194	9857278	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9857279	9857347	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9857279	9857347	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857348	9857465	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9857466	9857522	0.4	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9857466	9857522	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857523	9857608	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9857609	9857640	0.47	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9857609	9857640	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857641	9857755	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9857756	9857812	0.77	+	1	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9857756	9857812	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857813	9857904	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9857905	9857995	1	+	1	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9857905	9857995	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9857996	9858075	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9858076	9858174	1	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9858076	9858174	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9858175	9858260	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9858261	9858442	0.97	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9858261	9858442	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	intron	9858443	9858648	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	CDS	9858649	9858652	0.97	+	1	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	exon	9858649	9858652	.	+	.	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
Phchi.S3	AUGUSTUS	stop_codon	9858653	9858655	.	+	0	transcript_id "Phchi.S3G126500.t1"; gene_id "Phchi.S3G126500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7574.t1 is derived from g4748.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30099472	30100008	.	-	.	Phchi.S1G473300
Phchi.S1	AUGUSTUS	transcript	30099472	30100008	.	-	.	transcript_id "Phchi.S1G473300.t1"; gene_id "Phchi.S1G473300"
Phchi.S1	AUGUSTUS	stop_codon	30099469	30099471	.	-	0	transcript_id "Phchi.S1G473300.t1"; gene_id "Phchi.S1G473300"
Phchi.S1	AUGUSTUS	CDS	30099472	30100008	0.35	-	0	transcript_id "Phchi.S1G473300.t1"; gene_id "Phchi.S1G473300"
Phchi.S1	AUGUSTUS	exon	30099472	30100008	.	-	.	transcript_id "Phchi.S1G473300.t1"; gene_id "Phchi.S1G473300"
Phchi.S1	AUGUSTUS	start_codon	30100006	30100008	.	-	0	transcript_id "Phchi.S1G473300.t1"; gene_id "Phchi.S1G473300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8588.t1 is derived from g5763.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	36777118	36777687	.	+	.	Phchi.S1G574700
Phchi.S1	AUGUSTUS	transcript	36777118	36777687	.	+	.	transcript_id "Phchi.S1G574700.t1"; gene_id "Phchi.S1G574700"
Phchi.S1	AUGUSTUS	start_codon	36777118	36777120	.	+	0	transcript_id "Phchi.S1G574700.t1"; gene_id "Phchi.S1G574700"
Phchi.S1	AUGUSTUS	CDS	36777118	36777687	1	+	0	transcript_id "Phchi.S1G574700.t1"; gene_id "Phchi.S1G574700"
Phchi.S1	AUGUSTUS	exon	36777118	36777687	.	+	.	transcript_id "Phchi.S1G574700.t1"; gene_id "Phchi.S1G574700"
Phchi.S1	AUGUSTUS	stop_codon	36777688	36777690	.	+	0	transcript_id "Phchi.S1G574700.t1"; gene_id "Phchi.S1G574700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg13174.t1 is derived from g11639.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4500416	4502449	.	-	.	Phchi.S3G049300
Phchi.S3	AUGUSTUS	transcript	4500416	4502278	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	stop_codon	4500413	4500415	.	-	0	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4500416	4500549	0.48	-	2	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4500416	4500549	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4500550	4500636	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4500637	4500704	0.47	-	1	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4500637	4500704	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4500705	4500901	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4500902	4501109	0.36	-	2	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4500902	4501109	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4501110	4501277	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4501278	4501383	0.52	-	0	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4501278	4501383	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4501384	4501479	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4501480	4501727	0.48	-	2	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4501480	4501727	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4501728	4501848	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4501849	4502278	0.98	-	0	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4501849	4502278	.	-	.	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	start_codon	4502276	4502278	.	-	0	transcript_id "Phchi.S3G049300.t1"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	transcript	4500416	4502449	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	stop_codon	4500413	4500415	.	-	0	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4500416	4500549	0.43	-	2	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4500416	4500549	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4500550	4500636	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4500637	4500704	0.44	-	1	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4500637	4500704	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4500705	4500901	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4500902	4501109	0.33	-	2	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4500902	4501109	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4501110	4501277	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4501278	4501383	0.51	-	0	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4501278	4501383	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4501384	4501479	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4501480	4501727	0.43	-	2	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4501480	4501727	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	intron	4501728	4501848	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	CDS	4501849	4502449	0.78	-	0	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	exon	4501849	4502449	.	-	.	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
Phchi.S3	AUGUSTUS	start_codon	4502447	4502449	.	-	0	transcript_id "Phchi.S3G049300.t2"; gene_id "Phchi.S3G049300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5473.t1 is derived from g2643.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	17001344	17002043	.	-	.	Phchi.S1G263200
Phchi.S1	AUGUSTUS	transcript	17001344	17002043	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	stop_codon	17001341	17001343	.	-	0	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	CDS	17001344	17001508	0.93	-	0	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	exon	17001344	17001508	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	intron	17001509	17001593	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	CDS	17001594	17001639	1	-	1	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	exon	17001594	17001639	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	intron	17001640	17001726	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	CDS	17001727	17001895	1	-	2	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	exon	17001727	17001895	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	intron	17001896	17002009	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	CDS	17002010	17002043	0.7	-	0	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	exon	17002010	17002043	.	-	.	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
Phchi.S1	AUGUSTUS	start_codon	17002041	17002043	.	-	0	transcript_id "Phchi.S1G263200.t1"; gene_id "Phchi.S1G263200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3985.t1 is derived from g1154.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6873349	6875233	.	+	.	Phchi.S1G114400
Phchi.S1	AUGUSTUS	transcript	6873349	6875233	.	+	.	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	start_codon	6873349	6873351	.	+	0	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	CDS	6873349	6873458	0.69	+	0	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	exon	6873349	6873458	.	+	.	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	intron	6873459	6873535	.	+	.	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	CDS	6873536	6874789	0.85	+	1	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	exon	6873536	6874789	.	+	.	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	intron	6874790	6875109	.	+	.	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	CDS	6875110	6875233	0.88	+	1	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	exon	6875110	6875233	.	+	.	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
Phchi.S1	AUGUSTUS	stop_codon	6875234	6875236	.	+	0	transcript_id "Phchi.S1G114400.t1"; gene_id "Phchi.S1G114400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2702.t1 is derived from g9622.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	8253351	8255167	.	+	.	Phchi.S5G131100
Phchi.S5	AUGUSTUS	transcript	8253351	8255167	.	+	.	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	start_codon	8253351	8253353	.	+	0	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	CDS	8253351	8254308	0.36	+	0	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	exon	8253351	8254308	.	+	.	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	intron	8254309	8254548	.	+	.	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	CDS	8254549	8255003	0.26	+	2	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	exon	8254549	8255003	.	+	.	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	intron	8255004	8255092	.	+	.	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	CDS	8255093	8255167	0.58	+	0	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	exon	8255093	8255167	.	+	.	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
Phchi.S5	AUGUSTUS	stop_codon	8255168	8255170	.	+	0	transcript_id "Phchi.S5G131100.t1"; gene_id "Phchi.S5G131100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13300.t1 is derived from g11766.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	5550176	5551466	.	-	.	Phchi.S3G061900
Phchi.S3	AUGUSTUS	transcript	5550176	5551466	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	stop_codon	5550173	5550175	.	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	CDS	5550176	5550295	1	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	exon	5550176	5550295	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	intron	5550296	5550405	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	CDS	5550406	5550576	0.99	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	exon	5550406	5550576	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	intron	5550577	5550766	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	CDS	5550767	5550855	1	-	2	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	exon	5550767	5550855	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	intron	5550856	5551007	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	CDS	5551008	5551068	0.95	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	exon	5551008	5551068	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	intron	5551069	5551142	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	CDS	5551143	5551172	0.95	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	exon	5551143	5551172	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	intron	5551173	5551253	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	CDS	5551254	5551466	0.93	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	exon	5551254	5551466	.	-	.	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
Phchi.S3	AUGUSTUS	start_codon	5551464	5551466	.	-	0	transcript_id "Phchi.S3G061900.t1"; gene_id "Phchi.S3G061900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg12005.t1 is derived from g7680.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	501547	503986	.	+	.	Phchi.S2G008500
Phchi.S2	AUGUSTUS	transcript	501713	503986	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	start_codon	501713	501715	.	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	501713	501753	0.76	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	501713	501753	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	501754	501835	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	501836	501984	0.84	+	1	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	501836	501984	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	501985	502069	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502070	502262	1	+	2	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502070	502262	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502263	502403	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502404	502542	1	+	1	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502404	502542	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502543	502639	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502640	502771	0.73	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502640	502771	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502772	502882	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502883	502987	0.73	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502883	502987	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502988	503137	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503138	503198	1	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503138	503198	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503199	503328	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503329	503465	1	+	2	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503329	503465	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503466	503552	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503553	503663	1	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503553	503663	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503664	503759	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503760	503808	1	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503760	503808	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503809	503903	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503904	503986	1	+	2	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503904	503986	.	+	.	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	stop_codon	503987	503989	.	+	0	transcript_id "Phchi.S2G008500.t1"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	transcript	501713	503986	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	start_codon	501713	501715	.	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	501713	501753	0.78	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	501713	501753	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	501754	501835	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	501836	501984	0.85	+	1	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	501836	501984	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	501985	502069	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502070	502262	1	+	2	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502070	502262	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502263	502403	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502404	502542	1	+	1	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502404	502542	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502543	502639	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502640	502771	0.72	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502640	502771	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502772	502882	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502883	502987	0.72	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502883	502987	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502988	503137	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503138	503198	1	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503138	503198	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503199	503331	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503332	503465	1	+	2	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503332	503465	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503466	503552	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503553	503663	1	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503553	503663	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503664	503759	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503760	503808	1	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503760	503808	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503809	503903	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503904	503986	0.98	+	2	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503904	503986	.	+	.	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	stop_codon	503987	503989	.	+	0	transcript_id "Phchi.S2G008500.t2"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	transcript	501547	503986	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	start_codon	501547	501549	.	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	501547	501753	0.56	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	501547	501753	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	501754	501845	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	501846	501984	1	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	501846	501984	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	501985	502069	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502070	502262	1	+	2	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502070	502262	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502263	502403	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502404	502542	1	+	1	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502404	502542	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502543	502639	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502640	502771	0.76	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502640	502771	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502772	502882	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	502883	502987	0.76	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	502883	502987	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	502988	503137	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503138	503198	1	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503138	503198	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503199	503328	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503329	503465	0.57	+	2	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503329	503465	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503466	503552	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503553	503663	1	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503553	503663	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503664	503759	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503760	503808	1	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503760	503808	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	intron	503809	503903	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	CDS	503904	503986	0.99	+	2	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	exon	503904	503986	.	+	.	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
Phchi.S2	AUGUSTUS	stop_codon	503987	503989	.	+	0	transcript_id "Phchi.S2G008500.t3"; gene_id "Phchi.S2G008500"
# This transcript jg206.t2 is derived from g9988.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg207.t1 is derived from g9989.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1161850	1163693	.	-	.	Phchi.S6G016600
Phchi.S6	AUGUSTUS	transcript	1161850	1163693	.	-	.	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	stop_codon	1161847	1161849	.	-	0	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	CDS	1161850	1161996	0.99	-	0	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	exon	1161850	1161996	.	-	.	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	intron	1161997	1162155	.	-	.	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	CDS	1162156	1163514	0.5	-	0	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	exon	1162156	1163514	.	-	.	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	intron	1163515	1163609	.	-	.	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	CDS	1163610	1163693	0.15	-	0	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	exon	1163610	1163693	.	-	.	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
Phchi.S6	AUGUSTUS	start_codon	1163691	1163693	.	-	0	transcript_id "Phchi.S6G016600.t1"; gene_id "Phchi.S6G016600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7389.t1 is derived from g4561.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28891503	28892591	.	-	.	Phchi.S1G454800
Phchi.S1	AUGUSTUS	transcript	28891503	28892591	.	-	.	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	stop_codon	28891500	28891502	.	-	0	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	CDS	28891503	28892380	0.59	-	2	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	exon	28891503	28892380	.	-	.	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	intron	28892381	28892494	.	-	.	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	CDS	28892495	28892591	0.7	-	0	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	exon	28892495	28892591	.	-	.	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
Phchi.S1	AUGUSTUS	start_codon	28892589	28892591	.	-	0	transcript_id "Phchi.S1G454800.t1"; gene_id "Phchi.S1G454800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg3801.t1 is derived from g970.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	5806367	5807572	.	-	.	Phchi.S1G096000
Phchi.S1	AUGUSTUS	transcript	5806367	5807572	.	-	.	transcript_id "Phchi.S1G096000.t1"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	stop_codon	5806364	5806366	.	-	0	transcript_id "Phchi.S1G096000.t1"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	CDS	5806367	5807572	0.77	-	0	transcript_id "Phchi.S1G096000.t1"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	exon	5806367	5807572	.	-	.	transcript_id "Phchi.S1G096000.t1"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	start_codon	5807570	5807572	.	-	0	transcript_id "Phchi.S1G096000.t1"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	transcript	5806449	5807572	.	-	.	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	stop_codon	5806446	5806448	.	-	0	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	CDS	5806449	5806477	0.26	-	2	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	exon	5806449	5806477	.	-	.	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	intron	5806478	5806560	.	-	.	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	CDS	5806561	5807572	0.24	-	0	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	exon	5806561	5807572	.	-	.	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
Phchi.S1	AUGUSTUS	start_codon	5807570	5807572	.	-	0	transcript_id "Phchi.S1G096000.t2"; gene_id "Phchi.S1G096000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12800.t1 is derived from g11265.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2442312	2442947	.	-	.	Phchi.S3G011900
Phchi.S3	AUGUSTUS	transcript	2442312	2442947	.	-	.	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	stop_codon	2442309	2442311	.	-	0	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	CDS	2442312	2442851	1	-	0	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	exon	2442312	2442851	.	-	.	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	intron	2442852	2442935	.	-	.	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	CDS	2442936	2442947	0.33	-	0	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	exon	2442936	2442947	.	-	.	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
Phchi.S3	AUGUSTUS	start_codon	2442945	2442947	.	-	0	transcript_id "Phchi.S3G011900.t1"; gene_id "Phchi.S3G011900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg7673.t1 is derived from g4847.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30567313	30568805	.	-	.	Phchi.S1G483200
Phchi.S1	AUGUSTUS	transcript	30567313	30568590	.	-	.	transcript_id "Phchi.S1G483200.t1"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	stop_codon	30567310	30567312	.	-	0	transcript_id "Phchi.S1G483200.t1"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	CDS	30567313	30568590	0.81	-	0	transcript_id "Phchi.S1G483200.t1"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	exon	30567313	30568590	.	-	.	transcript_id "Phchi.S1G483200.t1"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	start_codon	30568588	30568590	.	-	0	transcript_id "Phchi.S1G483200.t1"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	transcript	30567313	30568805	.	-	.	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	stop_codon	30567310	30567312	.	-	0	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	CDS	30567313	30568519	0.43	-	1	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	exon	30567313	30568519	.	-	.	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	intron	30568520	30568683	.	-	.	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	CDS	30568684	30568805	0.32	-	0	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	exon	30568684	30568805	.	-	.	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
Phchi.S1	AUGUSTUS	start_codon	30568803	30568805	.	-	0	transcript_id "Phchi.S1G483200.t2"; gene_id "Phchi.S1G483200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1557.t1 is derived from g8476.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1758127	1759725	.	+	.	Phchi.S5G016600
Phchi.S5	AUGUSTUS	transcript	1758127	1759725	.	+	.	transcript_id "Phchi.S5G016600.t1"; gene_id "Phchi.S5G016600"
Phchi.S5	AUGUSTUS	start_codon	1758127	1758129	.	+	0	transcript_id "Phchi.S5G016600.t1"; gene_id "Phchi.S5G016600"
Phchi.S5	AUGUSTUS	CDS	1758127	1759725	0.55	+	0	transcript_id "Phchi.S5G016600.t1"; gene_id "Phchi.S5G016600"
Phchi.S5	AUGUSTUS	exon	1758127	1759725	.	+	.	transcript_id "Phchi.S5G016600.t1"; gene_id "Phchi.S5G016600"
Phchi.S5	AUGUSTUS	stop_codon	1759726	1759728	.	+	0	transcript_id "Phchi.S5G016600.t1"; gene_id "Phchi.S5G016600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7380.t1 is derived from g4552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	28839967	28841873	.	-	.	Phchi.S1G453900
Phchi.S1	AUGUSTUS	transcript	28839967	28841873	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	stop_codon	28839964	28839966	.	-	0	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	CDS	28839967	28840464	1	-	0	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	exon	28839967	28840464	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	intron	28840465	28840564	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	CDS	28840565	28841191	0.99	-	0	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	exon	28840565	28841191	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	intron	28841192	28841313	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	CDS	28841314	28841633	1	-	2	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	exon	28841314	28841633	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	intron	28841634	28841743	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	CDS	28841744	28841873	0.93	-	0	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	exon	28841744	28841873	.	-	.	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
Phchi.S1	AUGUSTUS	start_codon	28841871	28841873	.	-	0	transcript_id "Phchi.S1G453900.t1"; gene_id "Phchi.S1G453900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7786.t1 is derived from g4960.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	31191786	31192267	.	+	.	Phchi.S1G494500
Phchi.S1	AUGUSTUS	transcript	31191786	31192267	.	+	.	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	start_codon	31191786	31191788	.	+	0	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	CDS	31191786	31192001	0.46	+	0	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	exon	31191786	31192001	.	+	.	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	intron	31192002	31192081	.	+	.	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	CDS	31192082	31192267	0.52	+	0	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	exon	31192082	31192267	.	+	.	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
Phchi.S1	AUGUSTUS	stop_codon	31192268	31192270	.	+	0	transcript_id "Phchi.S1G494500.t1"; gene_id "Phchi.S1G494500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3292.t1 is derived from g461.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2701298	2701792	.	+	.	Phchi.S1G045100
Phchi.S1	AUGUSTUS	transcript	2701298	2701792	.	+	.	transcript_id "Phchi.S1G045100.t1"; gene_id "Phchi.S1G045100"
Phchi.S1	AUGUSTUS	start_codon	2701298	2701300	.	+	0	transcript_id "Phchi.S1G045100.t1"; gene_id "Phchi.S1G045100"
Phchi.S1	AUGUSTUS	CDS	2701298	2701792	0.61	+	0	transcript_id "Phchi.S1G045100.t1"; gene_id "Phchi.S1G045100"
Phchi.S1	AUGUSTUS	exon	2701298	2701792	.	+	.	transcript_id "Phchi.S1G045100.t1"; gene_id "Phchi.S1G045100"
Phchi.S1	AUGUSTUS	stop_codon	2701793	2701795	.	+	0	transcript_id "Phchi.S1G045100.t1"; gene_id "Phchi.S1G045100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15094.t1 is derived from g13562.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16989567	16992404	.	+	.	Phchi.S3G241300
Phchi.S3	AUGUSTUS	transcript	16989567	16992404	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	start_codon	16989567	16989569	.	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16989567	16989772	0.67	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16989567	16989772	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16989773	16989948	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16989949	16990046	0.95	+	1	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16989949	16990046	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16990047	16990152	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16990153	16990236	0.98	+	2	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16990153	16990236	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16990237	16990377	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16990378	16990490	1	+	2	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16990378	16990490	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16990491	16990592	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16990593	16990658	1	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16990593	16990658	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16990659	16990774	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16990775	16990876	0.95	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16990775	16990876	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16990877	16991042	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16991043	16991577	0.96	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16991043	16991577	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16991578	16991672	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16991673	16991878	1	+	2	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16991673	16991878	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16991879	16991955	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16991956	16992119	1	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16991956	16992119	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	intron	16992120	16992253	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	CDS	16992254	16992404	1	+	1	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	exon	16992254	16992404	.	+	.	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
Phchi.S3	AUGUSTUS	stop_codon	16992405	16992407	.	+	0	transcript_id "Phchi.S3G241300.t1"; gene_id "Phchi.S3G241300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6827.t1 is derived from g3999.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25234456	25236301	.	-	.	Phchi.S1G398600
Phchi.S1	AUGUSTUS	transcript	25234456	25236301	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	stop_codon	25234453	25234455	.	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25234456	25234503	1	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25234456	25234503	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25234504	25234593	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25234594	25234672	1	-	1	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25234594	25234672	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25234673	25234775	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25234776	25234813	0.84	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25234776	25234813	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25234814	25234947	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25234948	25235040	0.85	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25234948	25235040	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25235041	25235176	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25235177	25235252	1	-	1	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25235177	25235252	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25235253	25235382	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25235383	25235468	1	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25235383	25235468	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25235469	25235693	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25235694	25235756	1	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25235694	25235756	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25235757	25235844	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25235845	25235997	1	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25235845	25235997	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	intron	25235998	25236160	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	CDS	25236161	25236301	1	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	exon	25236161	25236301	.	-	.	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
Phchi.S1	AUGUSTUS	start_codon	25236299	25236301	.	-	0	transcript_id "Phchi.S1G398600.t1"; gene_id "Phchi.S1G398600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11993.t1 is derived from g7668.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	427716	430411	.	+	.	Phchi.S2G007300
Phchi.S2	AUGUSTUS	transcript	427716	430411	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	start_codon	427716	427718	.	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	427716	427878	0.87	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	427716	427878	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	427879	427965	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	427966	428006	1	+	2	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	427966	428006	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	428007	428109	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	428110	428202	1	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	428110	428202	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	428203	428325	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	428326	428400	1	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	428326	428400	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	428401	428519	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	428520	428569	1	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	428520	428569	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	428570	428716	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	428717	428806	1	+	1	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	428717	428806	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	428807	428897	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	428898	428954	1	+	1	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	428898	428954	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	428955	429085	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	429086	429155	1	+	1	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	429086	429155	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	429156	429280	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	429281	429382	1	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	429281	429382	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	429383	429471	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	429472	429524	1	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	429472	429524	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	429525	429615	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	429616	429754	1	+	1	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	429616	429754	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	429755	429840	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	429841	429925	1	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	429841	429925	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	429926	430007	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	430008	430142	1	+	2	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	430008	430142	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	intron	430143	430235	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	CDS	430236	430411	0.98	+	2	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	exon	430236	430411	.	+	.	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
Phchi.S2	AUGUSTUS	stop_codon	430412	430414	.	+	0	transcript_id "Phchi.S2G007300.t1"; gene_id "Phchi.S2G007300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg227.t1 is derived from g10009.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	1543743	1545422	.	+	.	Phchi.S6G018600
Phchi.S6	AUGUSTUS	transcript	1543743	1545422	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	start_codon	1543743	1543745	.	+	0	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	CDS	1543743	1543821	0.92	+	0	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	exon	1543743	1543821	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	intron	1543822	1543971	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	CDS	1543972	1544114	0.49	+	2	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	exon	1543972	1544114	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	intron	1544115	1544310	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	CDS	1544311	1544351	0.99	+	0	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	exon	1544311	1544351	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	intron	1544352	1544506	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	CDS	1544507	1544605	0.96	+	1	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	exon	1544507	1544605	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	intron	1544606	1544767	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	CDS	1544768	1545422	0.96	+	1	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	exon	1544768	1545422	.	+	.	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
Phchi.S6	AUGUSTUS	stop_codon	1545423	1545425	.	+	0	transcript_id "Phchi.S6G018600.t1"; gene_id "Phchi.S6G018600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2088.t1 is derived from g9008.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	4808398	4809598	.	+	.	Phchi.S5G069700
Phchi.S5	AUGUSTUS	transcript	4808398	4809598	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	start_codon	4808398	4808400	.	+	0	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	CDS	4808398	4808485	1	+	0	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	exon	4808398	4808485	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	intron	4808486	4808613	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	CDS	4808614	4808804	1	+	2	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	exon	4808614	4808804	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	intron	4808805	4808904	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	CDS	4808905	4808977	0.93	+	0	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	exon	4808905	4808977	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	intron	4808978	4809080	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	CDS	4809081	4809145	0.87	+	2	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	exon	4809081	4809145	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	intron	4809146	4809245	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	CDS	4809246	4809259	0.9	+	0	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	exon	4809246	4809259	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	intron	4809260	4809456	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	CDS	4809457	4809598	0.71	+	1	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	exon	4809457	4809598	.	+	.	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
Phchi.S5	AUGUSTUS	stop_codon	4809599	4809601	.	+	0	transcript_id "Phchi.S5G069700.t1"; gene_id "Phchi.S5G069700"
# This transcript jg14728.t2 is derived from g13196.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg14729.t1 is derived from g13197.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	14400023	14403554	.	-	.	Phchi.S3G204800
Phchi.S3	AUGUSTUS	transcript	14400023	14403554	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	stop_codon	14400020	14400022	.	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400023	14400135	1	-	2	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400023	14400135	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400136	14400226	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400227	14400320	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400227	14400320	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400321	14400395	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400396	14400509	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400396	14400509	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400510	14400680	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400681	14400842	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400681	14400842	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400843	14400934	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400935	14401072	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400935	14401072	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401073	14401176	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401177	14401253	1	-	2	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401177	14401253	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401254	14401343	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401344	14401455	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401344	14401455	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401456	14401543	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401544	14401634	1	-	1	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401544	14401634	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401635	14401885	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401886	14401947	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401886	14401947	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401948	14402162	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402163	14402303	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402163	14402303	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402304	14402396	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402397	14402579	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402397	14402579	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402580	14402677	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402678	14402734	1	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402678	14402734	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402735	14402871	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402872	14402920	1	-	1	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402872	14402920	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402921	14403020	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14403021	14403169	0.96	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14403021	14403169	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14403170	14403274	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14403275	14403322	0.96	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14403275	14403322	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14403323	14403416	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14403417	14403554	0.93	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14403417	14403554	.	-	.	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	start_codon	14403552	14403554	.	-	0	transcript_id "Phchi.S3G204800.t1"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	transcript	14400023	14403554	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	stop_codon	14400020	14400022	.	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400023	14400135	1	-	2	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400023	14400135	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400136	14400226	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400227	14400320	1	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400227	14400320	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400321	14400395	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400396	14400509	1	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400396	14400509	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400510	14400680	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400681	14400842	1	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400681	14400842	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14400843	14400934	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14400935	14401072	1	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14400935	14401072	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401073	14401176	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401177	14401253	1	-	2	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401177	14401253	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401254	14401343	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401344	14401455	1	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401344	14401455	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401456	14401543	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401544	14401634	1	-	1	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401544	14401634	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14401635	14401885	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14401886	14402017	0.56	-	1	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14401886	14402017	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402018	14402162	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402163	14402180	0.52	-	1	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402163	14402180	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402181	14402265	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402266	14402303	0.53	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402266	14402303	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402304	14402396	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402397	14402579	0.99	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402397	14402579	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402580	14402677	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402678	14402734	1	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402678	14402734	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402735	14402871	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14402872	14402920	1	-	1	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14402872	14402920	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14402921	14403020	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14403021	14403169	0.94	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14403021	14403169	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14403170	14403274	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14403275	14403322	0.94	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14403275	14403322	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	intron	14403323	14403416	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	CDS	14403417	14403554	0.93	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	exon	14403417	14403554	.	-	.	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
Phchi.S3	AUGUSTUS	start_codon	14403552	14403554	.	-	0	transcript_id "Phchi.S3G204800.t2"; gene_id "Phchi.S3G204800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11431.t1 is derived from g15481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6335740	6336411	.	-	.	Phchi.S4G101300
Phchi.S4	AUGUSTUS	transcript	6335740	6336411	.	-	.	transcript_id "Phchi.S4G101300.t1"; gene_id "Phchi.S4G101300"
Phchi.S4	AUGUSTUS	stop_codon	6335737	6335739	.	-	0	transcript_id "Phchi.S4G101300.t1"; gene_id "Phchi.S4G101300"
Phchi.S4	AUGUSTUS	CDS	6335740	6336411	0.93	-	0	transcript_id "Phchi.S4G101300.t1"; gene_id "Phchi.S4G101300"
Phchi.S4	AUGUSTUS	exon	6335740	6336411	.	-	.	transcript_id "Phchi.S4G101300.t1"; gene_id "Phchi.S4G101300"
Phchi.S4	AUGUSTUS	start_codon	6336409	6336411	.	-	0	transcript_id "Phchi.S4G101300.t1"; gene_id "Phchi.S4G101300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg4770.t1 is derived from g1940.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	12746216	12747702	.	+	.	Phchi.S1G192900
Phchi.S1	AUGUSTUS	transcript	12746216	12747702	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	start_codon	12746216	12746218	.	+	0	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12746216	12746453	0.86	+	0	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12746216	12746453	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	intron	12746454	12746613	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12746614	12746792	1	+	2	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12746614	12746792	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	intron	12746793	12746879	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12746880	12746985	1	+	0	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12746880	12746985	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	intron	12746986	12747072	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12747073	12747145	1	+	2	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12747073	12747145	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	intron	12747146	12747234	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12747235	12747275	0.63	+	1	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12747235	12747275	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	intron	12747276	12747352	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12747353	12747405	0.46	+	2	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12747353	12747405	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	intron	12747406	12747636	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	CDS	12747637	12747702	0.68	+	0	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	exon	12747637	12747702	.	+	.	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
Phchi.S1	AUGUSTUS	stop_codon	12747703	12747705	.	+	0	transcript_id "Phchi.S1G192900.t1"; gene_id "Phchi.S1G192900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15014.t1 is derived from g13482.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	16532637	16534020	.	-	.	Phchi.S3G233300
Phchi.S3	AUGUSTUS	transcript	16532637	16534020	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	stop_codon	16532634	16532636	.	-	0	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	CDS	16532637	16532708	1	-	0	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	exon	16532637	16532708	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	intron	16532709	16532882	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	CDS	16532883	16533266	1	-	0	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	exon	16532883	16533266	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	intron	16533267	16533355	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	CDS	16533356	16533504	0.96	-	2	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	exon	16533356	16533504	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	intron	16533505	16533662	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	CDS	16533663	16533766	0.54	-	1	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	exon	16533663	16533766	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	intron	16533767	16533874	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	CDS	16533875	16534020	0.26	-	0	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	exon	16533875	16534020	.	-	.	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
Phchi.S3	AUGUSTUS	start_codon	16534018	16534020	.	-	0	transcript_id "Phchi.S3G233300.t1"; gene_id "Phchi.S3G233300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9564.t1 is derived from g6740.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42683522	42687432	.	+	.	Phchi.S1G672300
Phchi.S1	AUGUSTUS	transcript	42683522	42687432	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	start_codon	42683522	42683524	.	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42683522	42683544	0.62	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42683522	42683544	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42683545	42683671	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42683672	42683827	0.33	+	1	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42683672	42683827	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42683828	42683925	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42683926	42683979	0.62	+	1	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42683926	42683979	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42683980	42684064	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42684065	42684152	0.97	+	1	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42684065	42684152	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42684153	42684239	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42684240	42684298	0.99	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42684240	42684298	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42684299	42684386	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42684387	42684435	0.99	+	1	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42684387	42684435	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42684436	42684512	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42684513	42684743	0.99	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42684513	42684743	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42684744	42684818	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42684819	42684988	1	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42684819	42684988	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42684989	42685167	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42685168	42685372	1	+	1	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42685168	42685372	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42685373	42685442	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42685443	42685711	1	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42685443	42685711	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42685712	42685835	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42685836	42686247	0.98	+	1	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42685836	42686247	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42686248	42686339	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42686340	42686451	1	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42686340	42686451	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42686452	42686536	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42686537	42686652	1	+	2	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42686537	42686652	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	intron	42686653	42686733	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	CDS	42686734	42687432	0.91	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	exon	42686734	42687432	.	+	.	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
Phchi.S1	AUGUSTUS	stop_codon	42687433	42687435	.	+	0	transcript_id "Phchi.S1G672300.t1"; gene_id "Phchi.S1G672300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12862.t1 is derived from g11327.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	2809144	2810276	.	+	.	Phchi.S3G018100
Phchi.S3	AUGUSTUS	transcript	2809144	2810276	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	start_codon	2809144	2809146	.	+	0	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809144	2809299	1	+	0	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809144	2809299	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2809300	2809416	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809417	2809477	1	+	0	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809417	2809477	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2809478	2809565	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809566	2809676	1	+	2	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809566	2809676	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2809677	2809751	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809752	2810142	1	+	2	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809752	2810142	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2810143	2810257	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2810258	2810276	1	+	1	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2810258	2810276	.	+	.	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	stop_codon	2810277	2810279	.	+	0	transcript_id "Phchi.S3G018100.t1"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	transcript	2809144	2810276	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	start_codon	2809144	2809146	.	+	0	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809144	2809299	1	+	0	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809144	2809299	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2809300	2809416	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809417	2809477	1	+	0	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809417	2809477	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2809478	2809565	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809566	2809676	1	+	2	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809566	2809676	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2809677	2809796	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2809797	2810142	0.57	+	2	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2809797	2810142	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	intron	2810143	2810257	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	CDS	2810258	2810276	0.99	+	1	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	exon	2810258	2810276	.	+	.	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
Phchi.S3	AUGUSTUS	stop_codon	2810277	2810279	.	+	0	transcript_id "Phchi.S3G018100.t2"; gene_id "Phchi.S3G018100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10887.t1 is derived from g14937.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2763191	2763570	.	-	.	Phchi.S4G046900
Phchi.S4	AUGUSTUS	transcript	2763191	2763570	.	-	.	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	stop_codon	2763188	2763190	.	-	0	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	CDS	2763191	2763192	1	-	2	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	exon	2763191	2763192	.	-	.	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	intron	2763193	2763350	.	-	.	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	CDS	2763351	2763570	0.98	-	0	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	exon	2763351	2763570	.	-	.	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
Phchi.S4	AUGUSTUS	start_codon	2763568	2763570	.	-	0	transcript_id "Phchi.S4G046900.t1"; gene_id "Phchi.S4G046900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10872.t1 is derived from g14922.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2687512	2690687	.	+	.	Phchi.S4G045400
Phchi.S4	AUGUSTUS	transcript	2687512	2690687	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	start_codon	2687512	2687514	.	+	0	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	CDS	2687512	2688501	0.97	+	0	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	exon	2687512	2688501	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	intron	2688502	2688586	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	CDS	2688587	2688833	0.96	+	0	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	exon	2688587	2688833	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	intron	2688834	2688940	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	CDS	2688941	2689237	1	+	2	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	exon	2688941	2689237	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	intron	2689238	2689327	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	CDS	2689328	2690022	0.99	+	2	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	exon	2689328	2690022	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	intron	2690023	2690144	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	CDS	2690145	2690687	1	+	0	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	exon	2690145	2690687	.	+	.	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
Phchi.S4	AUGUSTUS	stop_codon	2690688	2690690	.	+	0	transcript_id "Phchi.S4G045400.t1"; gene_id "Phchi.S4G045400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8829.t1 is derived from g6004.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	38159565	38162701	.	-	.	Phchi.S1G598800
Phchi.S1	AUGUSTUS	transcript	38159565	38162701	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	stop_codon	38159562	38159564	.	-	0	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	CDS	38159565	38159615	0.46	-	0	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	exon	38159565	38159615	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	intron	38159616	38159724	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	CDS	38159725	38159802	0.88	-	0	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	exon	38159725	38159802	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	intron	38159803	38159908	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	CDS	38159909	38160299	0.56	-	1	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	exon	38159909	38160299	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	intron	38160300	38160393	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	CDS	38160394	38160915	1	-	1	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	exon	38160394	38160915	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	intron	38160916	38162093	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	CDS	38162094	38162392	0.58	-	0	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	exon	38162094	38162392	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	intron	38162393	38162587	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	CDS	38162588	38162701	0.43	-	0	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	exon	38162588	38162701	.	-	.	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
Phchi.S1	AUGUSTUS	start_codon	38162699	38162701	.	-	0	transcript_id "Phchi.S1G598800.t1"; gene_id "Phchi.S1G598800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg11928.t1 is derived from g7603.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	68324	70936	.	-	.	Phchi.S2G000800
Phchi.S2	AUGUSTUS	transcript	68601	69706	.	-	.	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	stop_codon	68598	68600	.	-	0	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	CDS	68601	68714	0.69	-	0	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	exon	68601	68714	.	-	.	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	intron	68715	68848	.	-	.	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	CDS	68849	69706	0.8	-	0	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	exon	68849	69706	.	-	.	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	start_codon	69704	69706	.	-	0	transcript_id "Phchi.S2G000800.t1"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	transcript	68324	70936	.	-	.	transcript_id "Phchi.S2G000800.t2"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	stop_codon	68321	68323	.	-	0	transcript_id "Phchi.S2G000800.t2"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	CDS	68324	70936	0.5	-	0	transcript_id "Phchi.S2G000800.t2"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	exon	68324	70936	.	-	.	transcript_id "Phchi.S2G000800.t2"; gene_id "Phchi.S2G000800"
Phchi.S2	AUGUSTUS	start_codon	70934	70936	.	-	0	transcript_id "Phchi.S2G000800.t2"; gene_id "Phchi.S2G000800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9445.t1 is derived from g6621.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41495798	41502436	.	-	.	Phchi.S1G660400
Phchi.S1	AUGUSTUS	transcript	41495798	41502436	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	stop_codon	41495795	41495797	.	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41495798	41495902	0.99	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41495798	41495902	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41495903	41495977	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41495978	41496181	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41495978	41496181	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41496182	41496266	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41496267	41496332	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41496267	41496332	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41496333	41496467	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41496468	41496506	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41496468	41496506	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41496507	41496589	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41496590	41496601	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41496590	41496601	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41496602	41496675	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41496676	41496743	1	-	2	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41496676	41496743	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41496744	41496838	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41496839	41496902	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41496839	41496902	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41496903	41496996	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41496997	41497138	1	-	1	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41496997	41497138	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41497139	41497303	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41497304	41497392	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41497304	41497392	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41497393	41497524	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41497525	41497588	1	-	1	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41497525	41497588	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41497589	41497668	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41497669	41497772	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41497669	41497772	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41497773	41497869	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41497870	41498010	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41497870	41498010	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41498011	41498133	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41498134	41498259	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41498134	41498259	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41498260	41498367	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41498368	41498580	0.94	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41498368	41498580	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41498581	41498681	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41498682	41498765	0.99	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41498682	41498765	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41498766	41498911	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41498912	41499071	1	-	1	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41498912	41499071	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41499072	41499211	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41499212	41499345	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41499212	41499345	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41499346	41499466	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41499467	41499556	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41499467	41499556	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41499557	41499659	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41499660	41499818	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41499660	41499818	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41499819	41499900	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41499901	41499979	1	-	1	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41499901	41499979	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41499980	41500093	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41500094	41500191	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41500094	41500191	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41500192	41500289	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41500290	41500403	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41500290	41500403	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41500404	41500499	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41500500	41500665	1	-	1	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41500500	41500665	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41500666	41500747	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41500748	41500977	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41500748	41500977	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41500978	41501062	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41501063	41501206	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41501063	41501206	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41501207	41501299	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41501300	41501365	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41501300	41501365	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41501366	41501450	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41501451	41501660	0.99	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41501451	41501660	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41501661	41501748	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41501749	41502118	1	-	1	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41501749	41502118	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41502119	41502202	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41502203	41502230	1	-	2	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41502203	41502230	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41502231	41502306	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41502307	41502322	1	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41502307	41502322	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	intron	41502323	41502406	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	CDS	41502407	41502436	0.92	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	exon	41502407	41502436	.	-	.	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
Phchi.S1	AUGUSTUS	start_codon	41502434	41502436	.	-	0	transcript_id "Phchi.S1G660400.t1"; gene_id "Phchi.S1G660400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3855.t1 is derived from g1024.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6046745	6048751	.	-	.	Phchi.S1G101400
Phchi.S1	AUGUSTUS	transcript	6046745	6048751	.	-	.	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	stop_codon	6046742	6046744	.	-	0	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	CDS	6046745	6048543	0.84	-	2	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	exon	6046745	6048543	.	-	.	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	intron	6048544	6048642	.	-	.	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	CDS	6048643	6048751	0.99	-	0	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	exon	6048643	6048751	.	-	.	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
Phchi.S1	AUGUSTUS	start_codon	6048749	6048751	.	-	0	transcript_id "Phchi.S1G101400.t1"; gene_id "Phchi.S1G101400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6339.t1 is derived from g3511.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	22395576	22396751	.	+	.	Phchi.S1G349800
Phchi.S1	AUGUSTUS	transcript	22395576	22396751	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	start_codon	22395576	22395578	.	+	0	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	CDS	22395576	22395584	0.99	+	0	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	exon	22395576	22395584	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	intron	22395585	22395866	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	CDS	22395867	22395949	0.99	+	0	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	exon	22395867	22395949	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	intron	22395950	22396040	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	CDS	22396041	22396120	0.99	+	1	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	exon	22396041	22396120	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	intron	22396121	22396197	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	CDS	22396198	22396285	1	+	2	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	exon	22396198	22396285	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	intron	22396286	22396543	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	CDS	22396544	22396610	1	+	1	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	exon	22396544	22396610	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	intron	22396611	22396700	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	CDS	22396701	22396751	1	+	0	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	exon	22396701	22396751	.	+	.	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
Phchi.S1	AUGUSTUS	stop_codon	22396752	22396754	.	+	0	transcript_id "Phchi.S1G349800.t1"; gene_id "Phchi.S1G349800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5164.t1 is derived from g2334.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	15232095	15234080	.	-	.	Phchi.S1G232300
Phchi.S1	AUGUSTUS	transcript	15232095	15234080	.	-	.	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	stop_codon	15232092	15232094	.	-	0	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	CDS	15232095	15232509	0.97	-	1	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	exon	15232095	15232509	.	-	.	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	intron	15232510	15232623	.	-	.	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	CDS	15232624	15234080	0.99	-	0	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	exon	15232624	15234080	.	-	.	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
Phchi.S1	AUGUSTUS	start_codon	15234078	15234080	.	-	0	transcript_id "Phchi.S1G232300.t1"; gene_id "Phchi.S1G232300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2250.t1 is derived from g9170.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	5689295	5691650	.	-	.	Phchi.S5G085900
Phchi.S5	AUGUSTUS	transcript	5689295	5691650	.	-	.	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	stop_codon	5689292	5689294	.	-	0	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	CDS	5689295	5690849	0.47	-	1	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	exon	5689295	5690849	.	-	.	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	intron	5690850	5690953	.	-	.	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	CDS	5690954	5691472	0.44	-	1	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	exon	5690954	5691472	.	-	.	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	intron	5691473	5691555	.	-	.	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	CDS	5691556	5691650	0.85	-	0	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	exon	5691556	5691650	.	-	.	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
Phchi.S5	AUGUSTUS	start_codon	5691648	5691650	.	-	0	transcript_id "Phchi.S5G085900.t1"; gene_id "Phchi.S5G085900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13087.t1 is derived from g11552.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	4093986	4096104	.	-	.	Phchi.S3G040600
Phchi.S3	AUGUSTUS	transcript	4093986	4096104	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	stop_codon	4093983	4093985	.	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4093986	4094389	1	-	2	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4093986	4094389	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4094390	4094567	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4094568	4094733	0.58	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4094568	4094733	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4094734	4094849	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4094850	4095038	1	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4094850	4095038	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4095039	4095161	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4095162	4095378	0.71	-	1	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4095162	4095378	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4095379	4095486	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4095487	4095587	0.92	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4095487	4095587	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4095588	4095734	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4095735	4095795	0.84	-	1	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4095735	4095795	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4095796	4095935	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4095936	4095994	0.85	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4095936	4095994	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	intron	4095995	4096071	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	CDS	4096072	4096104	0.61	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	exon	4096072	4096104	.	-	.	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
Phchi.S3	AUGUSTUS	start_codon	4096102	4096104	.	-	0	transcript_id "Phchi.S3G040600.t1"; gene_id "Phchi.S3G040600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9441.t1 is derived from g6617.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41488223	41489344	.	-	.	Phchi.S1G660000
Phchi.S1	AUGUSTUS	transcript	41488223	41489344	.	-	.	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	stop_codon	41488220	41488222	.	-	0	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	CDS	41488223	41489050	1	-	0	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	exon	41488223	41489050	.	-	.	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	intron	41489051	41489206	.	-	.	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	CDS	41489207	41489344	1	-	0	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	exon	41489207	41489344	.	-	.	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
Phchi.S1	AUGUSTUS	start_codon	41489342	41489344	.	-	0	transcript_id "Phchi.S1G660000.t1"; gene_id "Phchi.S1G660000"
# This transcript jg497.t2 is derived from g10279.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg498.t1 is derived from g10280.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3451895	3454109	.	+	.	Phchi.S6G045700
Phchi.S6	AUGUSTUS	transcript	3451895	3454109	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	start_codon	3451895	3451897	.	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3451895	3452218	1	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3451895	3452218	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3452219	3452295	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3452296	3452510	1	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3452296	3452510	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3452511	3452598	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3452599	3452710	1	+	1	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3452599	3452710	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3452711	3452918	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3452919	3452969	1	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3452919	3452969	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3452970	3453061	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3453062	3453133	1	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3453062	3453133	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3453134	3453234	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3453235	3453367	0.99	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3453235	3453367	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3453368	3453502	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3453503	3453561	1	+	2	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3453503	3453561	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3453562	3453707	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3453708	3453808	1	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3453708	3453808	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3453809	3453906	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3453907	3453973	1	+	1	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3453907	3453973	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	intron	3453974	3454070	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	CDS	3454071	3454109	1	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	exon	3454071	3454109	.	+	.	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
Phchi.S6	AUGUSTUS	stop_codon	3454110	3454112	.	+	0	transcript_id "Phchi.S6G045700.t1"; gene_id "Phchi.S6G045700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6121.t1 is derived from g3292.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	21027966	21029318	.	+	.	Phchi.S1G328000
Phchi.S1	AUGUSTUS	transcript	21027966	21029318	.	+	.	transcript_id "Phchi.S1G328000.t1"; gene_id "Phchi.S1G328000"
Phchi.S1	AUGUSTUS	start_codon	21027966	21027968	.	+	0	transcript_id "Phchi.S1G328000.t1"; gene_id "Phchi.S1G328000"
Phchi.S1	AUGUSTUS	CDS	21027966	21029318	0.67	+	0	transcript_id "Phchi.S1G328000.t1"; gene_id "Phchi.S1G328000"
Phchi.S1	AUGUSTUS	exon	21027966	21029318	.	+	.	transcript_id "Phchi.S1G328000.t1"; gene_id "Phchi.S1G328000"
Phchi.S1	AUGUSTUS	stop_codon	21029319	21029321	.	+	0	transcript_id "Phchi.S1G328000.t1"; gene_id "Phchi.S1G328000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12529.t1 is derived from g8206.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	32998195	32999135	.	+	.	Phchi.S2G060900
Phchi.S2	AUGUSTUS	transcript	32998195	32999135	.	+	.	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	start_codon	32998195	32998197	.	+	0	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	CDS	32998195	32998600	0.5	+	0	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	exon	32998195	32998600	.	+	.	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	intron	32998601	32998683	.	+	.	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	CDS	32998684	32999135	1	+	2	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	exon	32998684	32999135	.	+	.	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
Phchi.S2	AUGUSTUS	stop_codon	32999136	32999138	.	+	0	transcript_id "Phchi.S2G060900.t1"; gene_id "Phchi.S2G060900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11087.t1 is derived from g15137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4027809	4031103	.	-	.	Phchi.S4G066900
Phchi.S4	AUGUSTUS	transcript	4027809	4031103	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	stop_codon	4027806	4027808	.	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4027809	4027866	1	-	1	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4027809	4027866	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4027867	4027956	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4027957	4028087	1	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4027957	4028087	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4028088	4028176	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4028177	4028281	1	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4028177	4028281	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4028282	4028403	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4028404	4028493	1	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4028404	4028493	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4028494	4028625	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4028626	4028733	1	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4028626	4028733	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4028734	4028822	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4028823	4029102	0.99	-	1	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4028823	4029102	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4029103	4029354	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4029355	4029620	1	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4029355	4029620	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4029621	4029727	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4029728	4029833	1	-	1	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4029728	4029833	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4029834	4030030	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4030031	4030244	1	-	2	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4030031	4030244	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	intron	4030245	4030778	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	CDS	4030779	4031103	1	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	exon	4030779	4031103	.	-	.	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
Phchi.S4	AUGUSTUS	start_codon	4031101	4031103	.	-	0	transcript_id "Phchi.S4G066900.t1"; gene_id "Phchi.S4G066900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1083.t1 is derived from g10866.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	7511322	7513438	.	-	.	Phchi.S6G104200
Phchi.S6	AUGUSTUS	transcript	7511322	7513438	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	stop_codon	7511319	7511321	.	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7511322	7511348	0.26	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7511322	7511348	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7511349	7511524	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7511525	7511687	0.48	-	1	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7511525	7511687	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7511688	7511866	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7511867	7512015	0.71	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7511867	7512015	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7512016	7512118	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7512119	7512442	0.98	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7512119	7512442	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7512443	7512564	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7512565	7512705	1	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7512565	7512705	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7512706	7512796	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7512797	7512928	0.98	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7512797	7512928	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7512929	7513047	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7513048	7513195	0.98	-	1	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7513048	7513195	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	intron	7513196	7513280	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	CDS	7513281	7513438	1	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	exon	7513281	7513438	.	-	.	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
Phchi.S6	AUGUSTUS	start_codon	7513436	7513438	.	-	0	transcript_id "Phchi.S6G104200.t1"; gene_id "Phchi.S6G104200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg6901.t1 is derived from g4073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25899888	25902347	.	+	.	Phchi.S1G406000
Phchi.S1	AUGUSTUS	transcript	25899888	25902347	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	start_codon	25899888	25899890	.	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25899888	25899899	0.88	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25899888	25899899	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25899900	25900123	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900124	25900241	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900124	25900241	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900242	25900337	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900338	25900411	1	+	2	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900338	25900411	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900412	25900503	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900504	25900575	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900504	25900575	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900576	25900664	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900665	25900731	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900665	25900731	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900732	25900831	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900832	25900950	1	+	2	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900832	25900950	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900951	25901069	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901070	25901180	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901070	25901180	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901181	25901306	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901307	25901430	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901307	25901430	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901431	25901525	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901526	25901593	1	+	2	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901526	25901593	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901594	25901671	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901672	25901715	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901672	25901715	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901716	25901810	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901811	25901874	0.75	+	1	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901811	25901874	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901875	25901976	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901977	25902039	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901977	25902039	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25902040	25902116	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25902117	25902347	1	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25902117	25902347	.	+	.	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	stop_codon	25902348	25902350	.	+	0	transcript_id "Phchi.S1G406000.t1"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	transcript	25899888	25902347	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	start_codon	25899888	25899890	.	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25899888	25899899	0.93	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25899888	25899899	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25899900	25900123	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900124	25900241	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900124	25900241	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900242	25900337	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900338	25900411	1	+	2	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900338	25900411	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900412	25900503	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900504	25900575	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900504	25900575	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900576	25900658	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900659	25900731	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900659	25900731	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900732	25900831	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25900832	25900950	1	+	2	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25900832	25900950	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25900951	25901069	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901070	25901180	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901070	25901180	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901181	25901306	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901307	25901430	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901307	25901430	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901431	25901525	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901526	25901593	1	+	2	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901526	25901593	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901594	25901671	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901672	25901715	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901672	25901715	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901716	25901810	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901811	25901874	0.61	+	1	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901811	25901874	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25901875	25901976	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25901977	25902039	1	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25901977	25902039	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	intron	25902040	25902116	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	CDS	25902117	25902347	0.98	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	exon	25902117	25902347	.	+	.	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
Phchi.S1	AUGUSTUS	stop_codon	25902348	25902350	.	+	0	transcript_id "Phchi.S1G406000.t2"; gene_id "Phchi.S1G406000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10432.t1 is derived from g14481.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	304019	304525	.	-	.	Phchi.S4G001400
Phchi.S4	AUGUSTUS	transcript	304019	304525	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	stop_codon	304016	304018	.	-	0	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	CDS	304019	304046	1	-	1	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	exon	304019	304046	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	intron	304047	304133	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	CDS	304134	304224	1	-	2	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	exon	304134	304224	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	intron	304225	304318	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	CDS	304319	304395	1	-	1	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	exon	304319	304395	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	intron	304396	304484	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	CDS	304485	304525	1	-	0	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	exon	304485	304525	.	-	.	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
Phchi.S4	AUGUSTUS	start_codon	304523	304525	.	-	0	transcript_id "Phchi.S4G001400.t1"; gene_id "Phchi.S4G001400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1369.t1 is derived from g9814.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.C217	AUGUSTUS	gene	19592	22540	.	-	.	Phchi.C217G000300
Phchi.C217	AUGUSTUS	transcript	19592	22540	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	stop_codon	19589	19591	.	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	19592	19948	1	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	19592	19948	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	intron	19949	20087	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	20088	20425	0.56	-	2	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	20088	20425	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	intron	20426	20525	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	20526	20600	0.73	-	2	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	20526	20600	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	intron	20601	20744	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	20745	20988	0.97	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	20745	20988	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	intron	20989	21282	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	21283	21528	0.7	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	21283	21528	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	intron	21529	21661	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	21662	21691	0.86	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	21662	21691	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	intron	21692	21772	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	CDS	21773	22540	1	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	exon	21773	22540	.	-	.	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
Phchi.C217	AUGUSTUS	start_codon	22538	22540	.	-	0	transcript_id "Phchi.C217G000300.t1"; gene_id "Phchi.C217G000300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9961.t1 is derived from g7137.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	44679223	44679666	.	-	.	Phchi.S1G712000
Phchi.S1	AUGUSTUS	transcript	44679223	44679666	.	-	.	transcript_id "Phchi.S1G712000.t1"; gene_id "Phchi.S1G712000"
Phchi.S1	AUGUSTUS	stop_codon	44679220	44679222	.	-	0	transcript_id "Phchi.S1G712000.t1"; gene_id "Phchi.S1G712000"
Phchi.S1	AUGUSTUS	CDS	44679223	44679666	0.88	-	0	transcript_id "Phchi.S1G712000.t1"; gene_id "Phchi.S1G712000"
Phchi.S1	AUGUSTUS	exon	44679223	44679666	.	-	.	transcript_id "Phchi.S1G712000.t1"; gene_id "Phchi.S1G712000"
Phchi.S1	AUGUSTUS	start_codon	44679664	44679666	.	-	0	transcript_id "Phchi.S1G712000.t1"; gene_id "Phchi.S1G712000"
# This transcript jg13573.t2 is derived from g12040.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13574.t1 is derived from g12041.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	7551428	7552585	.	+	.	Phchi.S3G089300
Phchi.S3	AUGUSTUS	transcript	7551428	7552585	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	start_codon	7551428	7551430	.	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7551428	7551514	0.85	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7551428	7551514	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	intron	7551515	7551586	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7551587	7551627	1	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7551587	7551627	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	intron	7551628	7551713	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7551714	7551765	1	+	1	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7551714	7551765	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	intron	7551766	7551901	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7551902	7552018	1	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7551902	7552018	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	intron	7552019	7552093	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7552094	7552192	1	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7552094	7552192	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	intron	7552193	7552273	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7552274	7552409	1	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7552274	7552409	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	intron	7552410	7552499	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	CDS	7552500	7552585	1	+	2	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	exon	7552500	7552585	.	+	.	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
Phchi.S3	AUGUSTUS	stop_codon	7552586	7552588	.	+	0	transcript_id "Phchi.S3G089300.t1"; gene_id "Phchi.S3G089300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7698.t1 is derived from g4872.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30695582	30696332	.	-	.	Phchi.S1G485700
Phchi.S1	AUGUSTUS	transcript	30695582	30696332	.	-	.	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	stop_codon	30695579	30695581	.	-	0	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	CDS	30695582	30695830	0.99	-	0	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	exon	30695582	30695830	.	-	.	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	intron	30695831	30695954	.	-	.	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	CDS	30695955	30696332	0.53	-	0	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	exon	30695955	30696332	.	-	.	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
Phchi.S1	AUGUSTUS	start_codon	30696330	30696332	.	-	0	transcript_id "Phchi.S1G485700.t1"; gene_id "Phchi.S1G485700"
# This transcript jg5930.t2 is derived from g3101.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5931.t1 is derived from g3102.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19904292	19912066	.	-	.	Phchi.S1G309000
Phchi.S1	AUGUSTUS	transcript	19904292	19912066	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	stop_codon	19904289	19904291	.	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19904292	19904419	0.24	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19904292	19904419	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19904420	19904560	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19904561	19904688	0.51	-	1	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19904561	19904688	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19904689	19904778	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19904779	19904963	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19904779	19904963	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19904964	19905060	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19905061	19905159	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19905061	19905159	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19905160	19905239	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19905240	19905346	1	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19905240	19905346	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19905347	19905441	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19905442	19905637	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19905442	19905637	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19905638	19905715	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19905716	19905832	0.98	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19905716	19905832	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19905833	19905933	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19905934	19906102	0.98	-	1	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19905934	19906102	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19906103	19906199	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19906200	19906328	0.99	-	1	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19906200	19906328	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19906329	19906429	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19906430	19906538	0.31	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19906430	19906538	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19906539	19906636	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19906637	19906697	0.29	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19906637	19906697	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19906698	19906801	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19906802	19906978	0.63	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19906802	19906978	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19906979	19907111	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19907112	19907297	0.98	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19907112	19907297	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19907298	19907379	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19907380	19907461	0.98	-	1	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19907380	19907461	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19907462	19907550	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19907551	19907557	0.98	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19907551	19907557	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19907558	19907833	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19907834	19907888	0.6	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19907834	19907888	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19907889	19907973	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19907974	19908026	0.98	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19907974	19908026	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19908027	19908101	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19908102	19908267	0.86	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19908102	19908267	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19908268	19908349	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19908350	19908413	1	-	1	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19908350	19908413	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19908414	19908521	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19908522	19908601	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19908522	19908601	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19908602	19908712	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19908713	19908793	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19908713	19908793	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19908794	19908907	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19908908	19909009	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19908908	19909009	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19909010	19909144	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19909145	19909255	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19909145	19909255	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19909256	19909478	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19909479	19909603	1	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19909479	19909603	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19909604	19909695	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19909696	19909765	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19909696	19909765	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19909766	19909895	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19909896	19910003	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19909896	19910003	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19910004	19910095	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19910096	19910318	1	-	1	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19910096	19910318	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19910319	19910415	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19910416	19910552	1	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19910416	19910552	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19910553	19910646	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19910647	19910730	0.89	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19910647	19910730	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19910731	19910851	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19910852	19911010	0.84	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19910852	19911010	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19911011	19911116	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19911117	19911241	0.8	-	2	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19911117	19911241	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	intron	19911242	19911747	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	CDS	19911748	19912066	0.64	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	exon	19911748	19912066	.	-	.	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
Phchi.S1	AUGUSTUS	start_codon	19912064	19912066	.	-	0	transcript_id "Phchi.S1G309000.t1"; gene_id "Phchi.S1G309000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg466.t1 is derived from g10248.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	3270622	3272735	.	+	.	Phchi.S6G042500
Phchi.S6	AUGUSTUS	transcript	3270622	3272735	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	start_codon	3270622	3270624	.	+	0	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3270622	3270644	0.57	+	0	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3270622	3270644	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	intron	3270645	3270888	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3270889	3270948	0.7	+	1	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3270889	3270948	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	intron	3270949	3271066	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3271067	3271143	0.49	+	1	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3271067	3271143	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	intron	3271144	3271238	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3271239	3271481	0.49	+	2	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3271239	3271481	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	intron	3271482	3271917	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3271918	3272174	1	+	2	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3271918	3272174	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	intron	3272175	3272300	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3272301	3272447	1	+	0	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3272301	3272447	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	intron	3272448	3272537	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	CDS	3272538	3272735	0.77	+	0	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	exon	3272538	3272735	.	+	.	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
Phchi.S6	AUGUSTUS	stop_codon	3272736	3272738	.	+	0	transcript_id "Phchi.S6G042500.t1"; gene_id "Phchi.S6G042500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3496.t1 is derived from g665.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	4051539	4052928	.	-	.	Phchi.S1G065500
Phchi.S1	AUGUSTUS	transcript	4051539	4052928	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	stop_codon	4051536	4051538	.	-	0	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	CDS	4051539	4051789	0.58	-	2	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	exon	4051539	4051789	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	intron	4051790	4051976	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	CDS	4051977	4052112	0.35	-	0	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	exon	4051977	4052112	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	intron	4052113	4052213	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	CDS	4052214	4052525	0.78	-	0	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	exon	4052214	4052525	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	intron	4052526	4052667	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	CDS	4052668	4052928	0.48	-	0	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	exon	4052668	4052928	.	-	.	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
Phchi.S1	AUGUSTUS	start_codon	4052926	4052928	.	-	0	transcript_id "Phchi.S1G065500.t1"; gene_id "Phchi.S1G065500"
# This transcript jg2936.t2 is derived from g105.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2937.t1 is derived from g106.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	660134	667111	.	+	.	Phchi.S1G009600
Phchi.S1	AUGUSTUS	transcript	660134	667111	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	start_codon	660134	660136	.	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	660134	660153	0.52	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	660134	660153	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	660154	660318	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	660319	660557	0.44	+	1	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	660319	660557	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	660558	660853	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	660854	660935	1	+	2	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	660854	660935	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	660936	661022	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	661023	661278	1	+	1	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	661023	661278	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	661279	661367	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	661368	661525	0.98	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	661368	661525	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	661526	661628	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	661629	661691	0.51	+	1	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	661629	661691	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	661692	661772	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	661773	662877	0.57	+	1	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	661773	662877	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	662878	663018	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	663019	663210	0.92	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	663019	663210	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	663211	663331	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	663332	664000	0.49	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	663332	664000	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	664001	664079	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	664080	664256	1	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	664080	664256	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	664257	664475	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	664476	664543	1	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	664476	664543	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	664544	664664	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	664665	664887	0.87	+	1	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	664665	664887	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	664888	665006	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	665007	665106	0.98	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	665007	665106	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	665107	665215	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	665216	665331	0.99	+	2	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	665216	665331	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	665332	665429	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	665430	665487	1	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	665430	665487	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	665488	665621	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	665622	665773	1	+	2	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	665622	665773	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	665774	665866	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	665867	666101	1	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	665867	666101	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	666102	666196	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	666197	667001	1	+	2	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	666197	667001	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	intron	667002	667077	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	CDS	667078	667111	1	+	1	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	exon	667078	667111	.	+	.	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
Phchi.S1	AUGUSTUS	stop_codon	667112	667114	.	+	0	transcript_id "Phchi.S1G009600.t1"; gene_id "Phchi.S1G009600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11383.t1 is derived from g15433.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	6022289	6023577	.	+	.	Phchi.S4G096500
Phchi.S4	AUGUSTUS	transcript	6022289	6023577	.	+	.	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	start_codon	6022289	6022291	.	+	0	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	CDS	6022289	6022385	1	+	0	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	exon	6022289	6022385	.	+	.	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	intron	6022386	6022531	.	+	.	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	CDS	6022532	6022901	1	+	2	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	exon	6022532	6022901	.	+	.	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	intron	6022902	6023018	.	+	.	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	CDS	6023019	6023577	1	+	1	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	exon	6023019	6023577	.	+	.	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
Phchi.S4	AUGUSTUS	stop_codon	6023578	6023580	.	+	0	transcript_id "Phchi.S4G096500.t1"; gene_id "Phchi.S4G096500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10445.t1 is derived from g14494.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	366292	366948	.	+	.	Phchi.S4G002700
Phchi.S4	AUGUSTUS	transcript	366292	366948	.	+	.	transcript_id "Phchi.S4G002700.t1"; gene_id "Phchi.S4G002700"
Phchi.S4	AUGUSTUS	start_codon	366292	366294	.	+	0	transcript_id "Phchi.S4G002700.t1"; gene_id "Phchi.S4G002700"
Phchi.S4	AUGUSTUS	CDS	366292	366948	0.65	+	0	transcript_id "Phchi.S4G002700.t1"; gene_id "Phchi.S4G002700"
Phchi.S4	AUGUSTUS	exon	366292	366948	.	+	.	transcript_id "Phchi.S4G002700.t1"; gene_id "Phchi.S4G002700"
Phchi.S4	AUGUSTUS	stop_codon	366949	366951	.	+	0	transcript_id "Phchi.S4G002700.t1"; gene_id "Phchi.S4G002700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15843.t1 is derived from g14313.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	21741002	21744853	.	-	.	Phchi.S3G316200
Phchi.S3	AUGUSTUS	transcript	21741002	21744853	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	stop_codon	21740999	21741001	.	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21741002	21741499	0.91	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21741002	21741499	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21741500	21741700	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21741701	21741934	1	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21741701	21741934	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21741935	21742029	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21742030	21742354	0.99	-	1	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21742030	21742354	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21742355	21742430	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21742431	21742673	1	-	1	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21742431	21742673	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21742674	21742767	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21742768	21743108	0.98	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21742768	21743108	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21743109	21743327	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21743328	21743408	1	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21743328	21743408	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21743409	21743517	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21743518	21743637	1	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21743518	21743637	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21743638	21743717	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21743718	21743819	1	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21743718	21743819	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21743820	21744004	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21744005	21744140	1	-	1	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21744005	21744140	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21744141	21744259	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21744260	21744430	0.98	-	1	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21744260	21744430	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	intron	21744431	21744536	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	CDS	21744537	21744853	0.96	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	exon	21744537	21744853	.	-	.	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
Phchi.S3	AUGUSTUS	start_codon	21744851	21744853	.	-	0	transcript_id "Phchi.S3G316200.t1"; gene_id "Phchi.S3G316200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7442.t1 is derived from g4614.t2 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 1 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	29129351	29131921	.	+	.	Phchi.S1G460100
Phchi.S1	AUGUSTUS	transcript	29129351	29131921	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	start_codon	29129351	29129353	.	+	0	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	CDS	29129351	29129564	0.31	+	0	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	exon	29129351	29129564	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	intron	29129565	29129658	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	CDS	29129659	29129779	0.68	+	2	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	exon	29129659	29129779	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	intron	29129780	29129855	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	CDS	29129856	29129861	0.52	+	1	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	exon	29129856	29129861	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	intron	29129862	29129961	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	CDS	29129962	29130193	0.98	+	1	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	exon	29129962	29130193	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	intron	29130194	29130338	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	CDS	29130339	29130358	0.93	+	0	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	exon	29130339	29130358	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	intron	29130359	29130456	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	CDS	29130457	29131921	0.28	+	1	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	exon	29130457	29131921	.	+	.	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
Phchi.S1	AUGUSTUS	stop_codon	29131922	29131924	.	+	0	transcript_id "Phchi.S1G460100.t1"; gene_id "Phchi.S1G460100"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg291.t1 is derived from g10073.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	2093257	2095470	.	+	.	Phchi.S6G025000
Phchi.S6	AUGUSTUS	transcript	2093257	2095470	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	start_codon	2093257	2093259	.	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2093257	2093378	0.28	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2093257	2093378	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2093379	2093489	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2093490	2093808	0.99	+	1	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2093490	2093808	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2093809	2093909	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2093910	2094065	1	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2093910	2094065	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2094066	2094214	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2094215	2094469	1	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2094215	2094469	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2094470	2094564	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2094565	2094654	1	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2094565	2094654	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2094655	2094759	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2094760	2094838	1	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2094760	2094838	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2094839	2094934	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2094935	2095041	1	+	2	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2094935	2095041	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2095042	2095154	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2095155	2095273	1	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2095155	2095273	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	intron	2095274	2095355	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	CDS	2095356	2095470	0.99	+	1	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	exon	2095356	2095470	.	+	.	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
Phchi.S6	AUGUSTUS	stop_codon	2095471	2095473	.	+	0	transcript_id "Phchi.S6G025000.t1"; gene_id "Phchi.S6G025000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1148.t1 is derived from g10931.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S6	AUGUSTUS	gene	8020456	8020857	.	-	.	Phchi.S6G110700
Phchi.S6	AUGUSTUS	transcript	8020456	8020857	.	-	.	transcript_id "Phchi.S6G110700.t1"; gene_id "Phchi.S6G110700"
Phchi.S6	AUGUSTUS	stop_codon	8020453	8020455	.	-	0	transcript_id "Phchi.S6G110700.t1"; gene_id "Phchi.S6G110700"
Phchi.S6	AUGUSTUS	CDS	8020456	8020857	0.78	-	0	transcript_id "Phchi.S6G110700.t1"; gene_id "Phchi.S6G110700"
Phchi.S6	AUGUSTUS	exon	8020456	8020857	.	-	.	transcript_id "Phchi.S6G110700.t1"; gene_id "Phchi.S6G110700"
Phchi.S6	AUGUSTUS	start_codon	8020855	8020857	.	-	0	transcript_id "Phchi.S6G110700.t1"; gene_id "Phchi.S6G110700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6509.t1 is derived from g3681.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	23371229	23374152	.	-	.	Phchi.S1G366800
Phchi.S1	AUGUSTUS	transcript	23371229	23374152	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	stop_codon	23371226	23371228	.	-	0	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23371229	23371372	1	-	0	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23371229	23371372	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	intron	23371373	23371623	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23371624	23371634	1	-	2	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23371624	23371634	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	intron	23371635	23371733	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23371734	23372101	0.27	-	1	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23371734	23372101	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	intron	23372102	23372228	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23372229	23372304	0.23	-	2	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23372229	23372304	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	intron	23372305	23372428	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23372429	23372852	0.24	-	0	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23372429	23372852	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	intron	23372853	23372956	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23372957	23373558	0.72	-	2	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23372957	23373558	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	intron	23373559	23373686	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	CDS	23373687	23374152	0.72	-	0	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	exon	23373687	23374152	.	-	.	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
Phchi.S1	AUGUSTUS	start_codon	23374150	23374152	.	-	0	transcript_id "Phchi.S1G366800.t1"; gene_id "Phchi.S1G366800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15720.t1 is derived from g14190.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	20882168	20883524	.	+	.	Phchi.S3G303900
Phchi.S3	AUGUSTUS	transcript	20882168	20883524	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	start_codon	20882168	20882170	.	+	0	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	CDS	20882168	20882395	1	+	0	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	exon	20882168	20882395	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	intron	20882396	20882476	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	CDS	20882477	20882742	1	+	0	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	exon	20882477	20882742	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	intron	20882743	20882826	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	CDS	20882827	20882945	1	+	1	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	exon	20882827	20882945	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	intron	20882946	20883020	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	CDS	20883021	20883103	1	+	2	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	exon	20883021	20883103	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	intron	20883104	20883212	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	CDS	20883213	20883524	1	+	0	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	exon	20883213	20883524	.	+	.	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
Phchi.S3	AUGUSTUS	stop_codon	20883525	20883527	.	+	0	transcript_id "Phchi.S3G303900.t1"; gene_id "Phchi.S3G303900"
# This transcript jg9353.t2 is derived from g6529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# This transcript jg9354.t1 is derived from g6530.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	41102362	41102640	.	-	.	Phchi.S1G651300
Phchi.S1	AUGUSTUS	transcript	41102362	41102640	.	-	.	transcript_id "Phchi.S1G651300.t1"; gene_id "Phchi.S1G651300"
Phchi.S1	AUGUSTUS	stop_codon	41102359	41102361	.	-	0	transcript_id "Phchi.S1G651300.t1"; gene_id "Phchi.S1G651300"
Phchi.S1	AUGUSTUS	CDS	41102362	41102640	0.41	-	0	transcript_id "Phchi.S1G651300.t1"; gene_id "Phchi.S1G651300"
Phchi.S1	AUGUSTUS	exon	41102362	41102640	.	-	.	transcript_id "Phchi.S1G651300.t1"; gene_id "Phchi.S1G651300"
Phchi.S1	AUGUSTUS	start_codon	41102638	41102640	.	-	0	transcript_id "Phchi.S1G651300.t1"; gene_id "Phchi.S1G651300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9088.t1 is derived from g6263.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	39796696	39797433	.	-	.	Phchi.S1G624700
Phchi.S1	AUGUSTUS	transcript	39796696	39797433	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	stop_codon	39796693	39796695	.	-	0	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	CDS	39796696	39796841	1	-	2	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	exon	39796696	39796841	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	intron	39796842	39796919	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	CDS	39796920	39797038	1	-	1	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	exon	39796920	39797038	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	intron	39797039	39797124	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	CDS	39797125	39797328	0.37	-	1	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	exon	39797125	39797328	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	intron	39797329	39797413	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	CDS	39797414	39797433	0.58	-	0	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	exon	39797414	39797433	.	-	.	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
Phchi.S1	AUGUSTUS	start_codon	39797431	39797433	.	-	0	transcript_id "Phchi.S1G624700.t1"; gene_id "Phchi.S1G624700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5383.t1 is derived from g2553.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	16615689	16617431	.	+	.	Phchi.S1G254200
Phchi.S1	AUGUSTUS	transcript	16615689	16617431	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	start_codon	16615689	16615691	.	+	0	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	CDS	16615689	16615985	1	+	0	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	exon	16615689	16615985	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	intron	16615986	16616302	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	CDS	16616303	16616455	1	+	0	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	exon	16616303	16616455	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	intron	16616456	16616583	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	CDS	16616584	16616725	0.97	+	0	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	exon	16616584	16616725	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	intron	16616726	16616838	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	CDS	16616839	16617080	0.98	+	2	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	exon	16616839	16617080	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	intron	16617081	16617227	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	CDS	16617228	16617431	1	+	0	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	exon	16617228	16617431	.	+	.	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
Phchi.S1	AUGUSTUS	stop_codon	16617432	16617434	.	+	0	transcript_id "Phchi.S1G254200.t1"; gene_id "Phchi.S1G254200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13704.t1 is derived from g12171.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	8287816	8288229	.	-	.	Phchi.S3G102300
Phchi.S3	AUGUSTUS	transcript	8287816	8288229	.	-	.	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	stop_codon	8287813	8287815	.	-	0	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	CDS	8287816	8287962	1	-	0	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	exon	8287816	8287962	.	-	.	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	intron	8287963	8288046	.	-	.	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	CDS	8288047	8288229	0.97	-	0	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	exon	8288047	8288229	.	-	.	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
Phchi.S3	AUGUSTUS	start_codon	8288227	8288229	.	-	0	transcript_id "Phchi.S3G102300.t1"; gene_id "Phchi.S3G102300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 2 different transcripts
# This transcript jg12336.t1 is derived from g8012.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	11050595	11057731	.	+	.	Phchi.S2G041600
Phchi.S2	AUGUSTUS	transcript	11050595	11057731	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	start_codon	11050595	11050597	.	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11050595	11050753	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11050595	11050753	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11050754	11051217	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11051218	11051315	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11051218	11051315	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11051316	11051634	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11051635	11051762	1	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11051635	11051762	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11051763	11051849	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11051850	11051961	1	+	2	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11051850	11051961	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11051962	11052105	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11052106	11052292	1	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11052106	11052292	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11052293	11052391	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11052392	11052580	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11052392	11052580	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11052581	11052824	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11052825	11053007	0.96	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11052825	11053007	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053008	11053142	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11053143	11053230	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11053143	11053230	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053231	11053325	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11053326	11053438	0.98	+	2	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11053326	11053438	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053439	11053549	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11053550	11053878	0.99	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11053550	11053878	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053879	11054009	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054010	11054106	1	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054010	11054106	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054107	11054268	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054269	11054421	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054269	11054421	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054422	11054506	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054507	11054593	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054507	11054593	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054594	11054679	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054680	11054766	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054680	11054766	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054767	11054949	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054950	11055090	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054950	11055090	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055091	11055197	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11055198	11055252	0.96	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11055198	11055252	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055253	11055504	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11055505	11055528	1	+	2	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11055505	11055528	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055529	11055607	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11055608	11055674	1	+	2	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11055608	11055674	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055675	11056287	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056288	11056354	1	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056288	11056354	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056355	11056453	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056454	11056624	0.88	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056454	11056624	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056625	11056726	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056727	11056816	0.82	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056727	11056816	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056817	11056904	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056905	11056985	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056905	11056985	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056986	11057099	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057100	11057173	1	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057100	11057173	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11057174	11057330	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057331	11057402	1	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057331	11057402	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11057403	11057489	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057490	11057582	1	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057490	11057582	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11057583	11057667	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057668	11057731	0.98	+	1	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057668	11057731	.	+	.	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	stop_codon	11057732	11057734	.	+	0	transcript_id "Phchi.S2G041600.t1"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	transcript	11050595	11057731	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	start_codon	11050595	11050597	.	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11050595	11050753	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11050595	11050753	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11050754	11051217	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11051218	11051315	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11051218	11051315	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11051316	11051634	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11051635	11051762	1	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11051635	11051762	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11051763	11051849	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11051850	11051961	1	+	2	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11051850	11051961	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11051962	11052105	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11052106	11052292	1	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11052106	11052292	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11052293	11052394	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11052395	11052580	0.52	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11052395	11052580	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11052581	11052824	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11052825	11053007	0.96	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11052825	11053007	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053008	11053142	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11053143	11053230	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11053143	11053230	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053231	11053325	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11053326	11053438	0.99	+	2	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11053326	11053438	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053439	11053549	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11053550	11053878	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11053550	11053878	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11053879	11054009	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054010	11054106	1	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054010	11054106	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054107	11054268	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054269	11054421	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054269	11054421	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054422	11054506	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054507	11054593	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054507	11054593	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054594	11054679	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054680	11054766	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054680	11054766	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11054767	11054949	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11054950	11055090	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11054950	11055090	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055091	11055197	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11055198	11055252	0.96	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11055198	11055252	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055253	11055504	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11055505	11055528	1	+	2	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11055505	11055528	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055529	11055607	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11055608	11055674	1	+	2	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11055608	11055674	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11055675	11056287	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056288	11056354	1	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056288	11056354	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056355	11056453	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056454	11056624	0.91	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056454	11056624	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056625	11056726	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056727	11056816	0.82	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056727	11056816	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056817	11056904	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11056905	11056985	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11056905	11056985	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11056986	11057099	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057100	11057173	1	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057100	11057173	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11057174	11057330	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057331	11057402	1	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057331	11057402	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11057403	11057489	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057490	11057582	1	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057490	11057582	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	intron	11057583	11057667	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	CDS	11057668	11057731	0.98	+	1	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	exon	11057668	11057731	.	+	.	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
Phchi.S2	AUGUSTUS	stop_codon	11057732	11057734	.	+	0	transcript_id "Phchi.S2G041600.t2"; gene_id "Phchi.S2G041600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg11173.t1 is derived from g15223.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	4489946	4492387	.	-	.	Phchi.S4G075500
Phchi.S4	AUGUSTUS	transcript	4489946	4492387	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	stop_codon	4489943	4489945	.	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4489946	4490029	0.97	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4489946	4490029	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4490030	4490148	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4490149	4490214	1	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4490149	4490214	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4490215	4490329	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4490330	4490378	1	-	1	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4490330	4490378	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4490379	4490505	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4490506	4490573	1	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4490506	4490573	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4490574	4490674	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4490675	4490720	1	-	1	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4490675	4490720	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4490721	4490852	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4490853	4490946	1	-	2	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4490853	4490946	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4490947	4491044	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4491045	4491113	1	-	2	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4491045	4491113	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4491114	4491386	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4491387	4491509	1	-	2	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4491387	4491509	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4491510	4491604	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4491605	4491638	1	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4491605	4491638	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4491639	4491838	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4491839	4491907	1	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4491839	4491907	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4491908	4491987	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4491988	4492068	0.59	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4491988	4492068	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4492069	4492168	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4492169	4492231	1	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4492169	4492231	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	intron	4492232	4492330	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	CDS	4492331	4492387	1	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	exon	4492331	4492387	.	-	.	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
Phchi.S4	AUGUSTUS	start_codon	4492385	4492387	.	-	0	transcript_id "Phchi.S4G075500.t1"; gene_id "Phchi.S4G075500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14597.t1 is derived from g13065.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	13656448	13658106	.	-	.	Phchi.S3G191600
Phchi.S3	AUGUSTUS	transcript	13656448	13658106	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	stop_codon	13656445	13656447	.	-	0	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	CDS	13656448	13656570	0.68	-	0	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	exon	13656448	13656570	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	intron	13656571	13656682	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	CDS	13656683	13656761	0.48	-	1	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	exon	13656683	13656761	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	intron	13656762	13656896	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	CDS	13656897	13657090	0.19	-	0	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	exon	13656897	13657090	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	intron	13657091	13657285	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	CDS	13657286	13657443	0.64	-	2	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	exon	13657286	13657443	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	intron	13657444	13657526	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	CDS	13657527	13658106	0.42	-	0	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	exon	13657527	13658106	.	-	.	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
Phchi.S3	AUGUSTUS	start_codon	13658104	13658106	.	-	0	transcript_id "Phchi.S3G191600.t1"; gene_id "Phchi.S3G191600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10582.t1 is derived from g14632.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	1057702	1059269	.	+	.	Phchi.S4G016400
Phchi.S4	AUGUSTUS	transcript	1057702	1059269	.	+	.	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	start_codon	1057702	1057704	.	+	0	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	CDS	1057702	1057897	0.99	+	0	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	exon	1057702	1057897	.	+	.	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	intron	1057898	1057990	.	+	.	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	CDS	1057991	1058533	1	+	2	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	exon	1057991	1058533	.	+	.	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	intron	1058534	1058604	.	+	.	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	CDS	1058605	1059269	0.97	+	2	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	exon	1058605	1059269	.	+	.	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
Phchi.S4	AUGUSTUS	stop_codon	1059270	1059272	.	+	0	transcript_id "Phchi.S4G016400.t1"; gene_id "Phchi.S4G016400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1521.t1 is derived from g8440.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1534201	1534647	.	+	.	Phchi.S5G013000
Phchi.S5	AUGUSTUS	transcript	1534201	1534647	.	+	.	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	start_codon	1534201	1534203	.	+	0	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	CDS	1534201	1534338	1	+	0	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	exon	1534201	1534338	.	+	.	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	intron	1534339	1534427	.	+	.	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	CDS	1534428	1534473	1	+	0	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	exon	1534428	1534473	.	+	.	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	intron	1534474	1534570	.	+	.	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	CDS	1534571	1534647	1	+	2	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	exon	1534571	1534647	.	+	.	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
Phchi.S5	AUGUSTUS	stop_codon	1534648	1534650	.	+	0	transcript_id "Phchi.S5G013000.t1"; gene_id "Phchi.S5G013000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10925.t1 is derived from g14975.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	2987702	2994069	.	-	.	Phchi.S4G050700
Phchi.S4	AUGUSTUS	transcript	2987702	2994069	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	stop_codon	2987699	2987701	.	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2987702	2988268	0.83	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2987702	2988268	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2988269	2988426	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2988427	2988550	0.9	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2988427	2988550	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2988551	2988774	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2988775	2988839	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2988775	2988839	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2988840	2988996	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2988997	2989023	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2988997	2989023	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2989024	2989175	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2989176	2989323	1	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2989176	2989323	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2989324	2989461	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2989462	2989544	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2989462	2989544	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2989545	2989808	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2989809	2989922	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2989809	2989922	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2989923	2990144	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2990145	2990310	1	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2990145	2990310	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2990311	2990442	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2990443	2990546	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2990443	2990546	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2990547	2990657	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2990658	2990755	1	-	2	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2990658	2990755	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2990756	2990944	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2990945	2991150	1	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2990945	2991150	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2991151	2991321	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2991322	2991416	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2991322	2991416	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2991417	2991568	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2991569	2991685	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2991569	2991685	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2991686	2991904	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2991905	2991964	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2991905	2991964	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2991965	2992131	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2992132	2992185	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2992132	2992185	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2992186	2992283	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2992284	2992358	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2992284	2992358	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2992359	2992545	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2992546	2992621	1	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2992546	2992621	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2992622	2992719	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2992720	2992806	1	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2992720	2992806	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2992807	2992913	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2992914	2993017	1	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2992914	2993017	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2993018	2993303	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2993304	2993400	1	-	1	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2993304	2993400	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	intron	2993401	2993512	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	CDS	2993513	2994069	0.97	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	exon	2993513	2994069	.	-	.	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
Phchi.S4	AUGUSTUS	start_codon	2994067	2994069	.	-	0	transcript_id "Phchi.S4G050700.t1"; gene_id "Phchi.S4G050700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg9550.t1 is derived from g6726.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	42420647	42421121	.	+	.	Phchi.S1G670900
Phchi.S1	AUGUSTUS	transcript	42420647	42421121	.	+	.	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	start_codon	42420647	42420649	.	+	0	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	CDS	42420647	42420715	0.82	+	0	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	exon	42420647	42420715	.	+	.	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	intron	42420716	42420806	.	+	.	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	CDS	42420807	42420947	1	+	0	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	exon	42420807	42420947	.	+	.	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	intron	42420948	42421082	.	+	.	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	CDS	42421083	42421121	1	+	0	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	exon	42421083	42421121	.	+	.	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
Phchi.S1	AUGUSTUS	stop_codon	42421122	42421124	.	+	0	transcript_id "Phchi.S1G670900.t1"; gene_id "Phchi.S1G670900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2545.t1 is derived from g9465.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7262302	7265380	.	-	.	Phchi.S5G115400
Phchi.S5	AUGUSTUS	transcript	7262302	7265380	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	stop_codon	7262299	7262301	.	-	0	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7262302	7262448	0.91	-	0	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7262302	7262448	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	intron	7262449	7262534	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7262535	7262621	0.94	-	0	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7262535	7262621	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	intron	7262622	7262722	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7262723	7262902	0.69	-	0	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7262723	7262902	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	intron	7262903	7263410	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7263411	7263436	0.38	-	2	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7263411	7263436	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	intron	7263437	7263661	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7263662	7263954	0.43	-	1	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7263662	7263954	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	intron	7263955	7264038	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7264039	7265082	1	-	1	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7264039	7265082	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	intron	7265083	7265171	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	CDS	7265172	7265380	0.61	-	0	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	exon	7265172	7265380	.	-	.	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
Phchi.S5	AUGUSTUS	start_codon	7265378	7265380	.	-	0	transcript_id "Phchi.S5G115400.t1"; gene_id "Phchi.S5G115400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg10425.t1 is derived from g14474.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	199872	200528	.	+	.	Phchi.S4G000700
Phchi.S4	AUGUSTUS	transcript	199872	200528	.	+	.	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	start_codon	199872	199874	.	+	0	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	CDS	199872	200367	0.87	+	0	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	exon	199872	200367	.	+	.	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	intron	200368	200463	.	+	.	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	CDS	200464	200528	1	+	2	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	exon	200464	200528	.	+	.	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
Phchi.S4	AUGUSTUS	stop_codon	200529	200531	.	+	0	transcript_id "Phchi.S4G000700.t1"; gene_id "Phchi.S4G000700"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg14333.t1 is derived from g12800.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	12170343	12173288	.	-	.	Phchi.S3G165200
Phchi.S3	AUGUSTUS	transcript	12170343	12173288	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	stop_codon	12170340	12170342	.	-	0	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12170343	12170481	1	-	1	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12170343	12170481	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12170482	12170649	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12170650	12170702	0.69	-	0	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12170650	12170702	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12170703	12171112	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12171113	12171193	0.78	-	0	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12171113	12171193	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12171194	12171275	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12171276	12171357	1	-	1	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12171276	12171357	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12171358	12171445	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12171446	12171607	1	-	1	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12171446	12171607	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12171608	12171723	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12171724	12171934	1	-	2	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12171724	12171934	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12171935	12172128	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12172129	12172229	1	-	1	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12172129	12172229	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12172230	12172323	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12172324	12172523	1	-	0	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12172324	12172523	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12172524	12172666	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12172667	12172770	1	-	2	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12172667	12172770	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	intron	12172771	12172870	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	CDS	12172871	12173288	1	-	0	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	exon	12172871	12173288	.	-	.	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
Phchi.S3	AUGUSTUS	start_codon	12173286	12173288	.	-	0	transcript_id "Phchi.S3G165200.t1"; gene_id "Phchi.S3G165200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg3955.t1 is derived from g1124.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	6682755	6683655	.	+	.	Phchi.S1G111400
Phchi.S1	AUGUSTUS	transcript	6682755	6683421	.	+	.	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	start_codon	6682755	6682757	.	+	0	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6682755	6682928	0.69	+	0	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6682755	6682928	.	+	.	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	intron	6682929	6683118	.	+	.	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6683119	6683242	1	+	0	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6683119	6683242	.	+	.	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	intron	6683243	6683416	.	+	.	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6683417	6683421	0.99	+	2	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6683417	6683421	.	+	.	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	stop_codon	6683422	6683424	.	+	0	transcript_id "Phchi.S1G111400.t1"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	transcript	6682755	6683421	.	+	.	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	start_codon	6682755	6682757	.	+	0	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6682755	6682955	0.63	+	0	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6682755	6682955	.	+	.	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	intron	6682956	6683118	.	+	.	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6683119	6683242	1	+	0	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6683119	6683242	.	+	.	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	intron	6683243	6683416	.	+	.	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6683417	6683421	0.99	+	2	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6683417	6683421	.	+	.	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	stop_codon	6683422	6683424	.	+	0	transcript_id "Phchi.S1G111400.t2"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	transcript	6682755	6683655	.	+	.	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	start_codon	6682755	6682757	.	+	0	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6682755	6682928	0.59	+	0	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6682755	6682928	.	+	.	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	intron	6682929	6683118	.	+	.	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6683119	6683242	0.87	+	0	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6683119	6683242	.	+	.	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	intron	6683243	6683629	.	+	.	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	CDS	6683630	6683655	0.79	+	2	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	exon	6683630	6683655	.	+	.	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
Phchi.S1	AUGUSTUS	stop_codon	6683656	6683658	.	+	0	transcript_id "Phchi.S1G111400.t3"; gene_id "Phchi.S1G111400"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg7571.t1 is derived from g4745.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	30087999	30088517	.	-	.	Phchi.S1G473000
Phchi.S1	AUGUSTUS	transcript	30087999	30088517	.	-	.	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	stop_codon	30087996	30087998	.	-	0	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	CDS	30087999	30088056	0.88	-	1	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	exon	30087999	30088056	.	-	.	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	intron	30088057	30088305	.	-	.	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	CDS	30088306	30088517	0.89	-	0	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	exon	30088306	30088517	.	-	.	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
Phchi.S1	AUGUSTUS	start_codon	30088515	30088517	.	-	0	transcript_id "Phchi.S1G473000.t1"; gene_id "Phchi.S1G473000"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15190.t1 is derived from g13658.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	17482610	17483243	.	-	.	Phchi.S3G250900
Phchi.S3	AUGUSTUS	transcript	17482610	17483243	.	-	.	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	stop_codon	17482607	17482609	.	-	0	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	CDS	17482610	17482612	1	-	0	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	exon	17482610	17482612	.	-	.	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	intron	17482613	17482949	.	-	.	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	CDS	17482950	17483071	1	-	2	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	exon	17482950	17483071	.	-	.	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	intron	17483072	17483170	.	-	.	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	CDS	17483171	17483243	1	-	0	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	exon	17483171	17483243	.	-	.	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
Phchi.S3	AUGUSTUS	start_codon	17483241	17483243	.	-	0	transcript_id "Phchi.S3G250900.t1"; gene_id "Phchi.S3G250900"
# overlap start --------------------------------------------------------------------------------
# this overlap has 3 different transcripts
# This transcript jg11765.t1 is derived from g15817.t3 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S4	AUGUSTUS	gene	8049685	8051061	.	+	.	Phchi.S4G134700
Phchi.S4	AUGUSTUS	transcript	8049685	8051008	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	start_codon	8049685	8049687	.	+	0	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8049685	8049806	1	+	0	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8049685	8049806	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8049807	8050111	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050112	8050163	1	+	1	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050112	8050163	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050164	8050396	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050397	8050470	1	+	0	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050397	8050470	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050471	8050560	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050561	8050653	1	+	1	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050561	8050653	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050654	8050998	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050999	8051008	1	+	1	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050999	8051008	.	+	.	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	stop_codon	8051009	8051011	.	+	0	transcript_id "Phchi.S4G134700.t1"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	transcript	8049685	8051061	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	start_codon	8049685	8049687	.	+	0	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8049685	8049806	1	+	0	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8049685	8049806	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8049807	8050111	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050112	8050163	1	+	1	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050112	8050163	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050164	8050396	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050397	8050470	1	+	0	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050397	8050470	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050471	8050560	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050561	8050653	1	+	1	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050561	8050653	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050654	8051003	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8051004	8051061	0.97	+	1	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8051004	8051061	.	+	.	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	stop_codon	8051062	8051064	.	+	0	transcript_id "Phchi.S4G134700.t2"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	transcript	8049685	8050803	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	start_codon	8049685	8049687	.	+	0	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8049685	8049806	1	+	0	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8049685	8049806	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8049807	8050111	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050112	8050163	1	+	1	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050112	8050163	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050164	8050396	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050397	8050470	1	+	0	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050397	8050470	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050471	8050560	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050561	8050653	1	+	1	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050561	8050653	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	intron	8050654	8050736	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	CDS	8050737	8050803	0.71	+	1	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	exon	8050737	8050803	.	+	.	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
Phchi.S4	AUGUSTUS	stop_codon	8050804	8050806	.	+	0	transcript_id "Phchi.S4G134700.t3"; gene_id "Phchi.S4G134700"
# This transcript jg1483.t2 is derived from g8402.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg1484.t1 is derived from g8403.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	1146044	1147146	.	-	.	Phchi.S5G009300
Phchi.S5	AUGUSTUS	transcript	1146044	1147146	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	stop_codon	1146041	1146043	.	-	0	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	CDS	1146044	1146238	1	-	0	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	exon	1146044	1146238	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	intron	1146239	1146340	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	CDS	1146341	1146427	0.99	-	0	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	exon	1146341	1146427	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	intron	1146428	1146539	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	CDS	1146540	1146694	1	-	2	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	exon	1146540	1146694	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	intron	1146695	1147040	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	CDS	1147041	1147146	1	-	0	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	exon	1147041	1147146	.	-	.	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
Phchi.S5	AUGUSTUS	start_codon	1147144	1147146	.	-	0	transcript_id "Phchi.S5G009300.t1"; gene_id "Phchi.S5G009300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg8093.t1 is derived from g5268.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	32904940	32906085	.	+	.	Phchi.S1G525200
Phchi.S1	AUGUSTUS	transcript	32904940	32906085	.	+	.	transcript_id "Phchi.S1G525200.t1"; gene_id "Phchi.S1G525200"
Phchi.S1	AUGUSTUS	start_codon	32904940	32904942	.	+	0	transcript_id "Phchi.S1G525200.t1"; gene_id "Phchi.S1G525200"
Phchi.S1	AUGUSTUS	CDS	32904940	32906085	0.99	+	0	transcript_id "Phchi.S1G525200.t1"; gene_id "Phchi.S1G525200"
Phchi.S1	AUGUSTUS	exon	32904940	32906085	.	+	.	transcript_id "Phchi.S1G525200.t1"; gene_id "Phchi.S1G525200"
Phchi.S1	AUGUSTUS	stop_codon	32906086	32906088	.	+	0	transcript_id "Phchi.S1G525200.t1"; gene_id "Phchi.S1G525200"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg12468.t1 is derived from g8145.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S2	AUGUSTUS	gene	25812055	25812678	.	+	.	Phchi.S2G054800
Phchi.S2	AUGUSTUS	transcript	25812055	25812678	.	+	.	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	start_codon	25812055	25812057	.	+	0	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	CDS	25812055	25812430	0.55	+	0	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	exon	25812055	25812430	.	+	.	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	intron	25812431	25812643	.	+	.	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	CDS	25812644	25812678	0.69	+	2	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	exon	25812644	25812678	.	+	.	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
Phchi.S2	AUGUSTUS	stop_codon	25812679	25812681	.	+	0	transcript_id "Phchi.S2G054800.t1"; gene_id "Phchi.S2G054800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg2576.t1 is derived from g9496.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S5	AUGUSTUS	gene	7442604	7445598	.	+	.	Phchi.S5G118500
Phchi.S5	AUGUSTUS	transcript	7442604	7445598	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	start_codon	7442604	7442606	.	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7442604	7442606	0.94	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7442604	7442606	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7442607	7442690	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7442691	7444184	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7442691	7444184	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7444185	7444335	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7444336	7444416	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7444336	7444416	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7444417	7444558	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7444559	7444633	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7444559	7444633	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7444634	7444767	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7444768	7444812	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7444768	7444812	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7444813	7444906	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7444907	7444996	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7444907	7444996	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7444997	7445081	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7445082	7445183	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7445082	7445183	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	intron	7445184	7445271	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	CDS	7445272	7445598	1	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	exon	7445272	7445598	.	+	.	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
Phchi.S5	AUGUSTUS	stop_codon	7445599	7445601	.	+	0	transcript_id "Phchi.S5G118500.t1"; gene_id "Phchi.S5G118500"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg13064.t1 is derived from g11529.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	3971435	3974187	.	-	.	Phchi.S3G038300
Phchi.S3	AUGUSTUS	transcript	3971435	3974187	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	stop_codon	3971432	3971434	.	-	0	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3971435	3971776	0.95	-	0	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3971435	3971776	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3971777	3971860	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3971861	3972159	1	-	2	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3971861	3972159	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3972160	3972242	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3972243	3972332	1	-	2	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3972243	3972332	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3972333	3972428	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3972429	3972597	1	-	0	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3972429	3972597	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3972598	3972692	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3972693	3972928	1	-	2	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3972693	3972928	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3972929	3973035	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3973036	3973335	0.98	-	2	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3973036	3973335	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3973336	3973434	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3973435	3973606	0.86	-	0	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3973435	3973606	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	intron	3973607	3974151	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	CDS	3974152	3974187	0.64	-	0	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	exon	3974152	3974187	.	-	.	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
Phchi.S3	AUGUSTUS	start_codon	3974185	3974187	.	-	0	transcript_id "Phchi.S3G038300.t1"; gene_id "Phchi.S3G038300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg5894.t1 is derived from g3064.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	19635140	19637277	.	+	.	Phchi.S1G305300
Phchi.S1	AUGUSTUS	transcript	19635140	19637277	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	start_codon	19635140	19635142	.	+	0	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	CDS	19635140	19635506	0.41	+	0	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	exon	19635140	19635506	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	intron	19635507	19635599	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	CDS	19635600	19635926	1	+	2	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	exon	19635600	19635926	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	intron	19635927	19636017	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	CDS	19636018	19636297	1	+	2	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	exon	19636018	19636297	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	intron	19636298	19636445	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	CDS	19636446	19637277	1	+	1	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	exon	19636446	19637277	.	+	.	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
Phchi.S1	AUGUSTUS	stop_codon	19637278	19637280	.	+	0	transcript_id "Phchi.S1G305300.t1"; gene_id "Phchi.S1G305300"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg3187.t1 is derived from g356.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	2139881	2142750	.	-	.	Phchi.S1G034600
Phchi.S1	AUGUSTUS	transcript	2139881	2142750	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	stop_codon	2139878	2139880	.	-	0	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2139881	2140129	0.84	-	0	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2139881	2140129	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2140130	2140243	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2140244	2140613	1	-	1	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2140244	2140613	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2140614	2140736	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2140737	2140896	1	-	2	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2140737	2140896	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2140897	2141046	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2141047	2141255	1	-	1	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2141047	2141255	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2141256	2141387	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2141388	2141537	1	-	1	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2141388	2141537	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2141538	2141729	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2141730	2141906	1	-	1	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2141730	2141906	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2141907	2141993	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2141994	2142562	0.92	-	0	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2141994	2142562	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	intron	2142563	2142660	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	CDS	2142661	2142750	0.52	-	0	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	exon	2142661	2142750	.	-	.	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
Phchi.S1	AUGUSTUS	start_codon	2142748	2142750	.	-	0	transcript_id "Phchi.S1G034600.t1"; gene_id "Phchi.S1G034600"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg6779.t1 is derived from g3951.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S1	AUGUSTUS	gene	25057091	25058735	.	+	.	Phchi.S1G393800
Phchi.S1	AUGUSTUS	transcript	25057091	25058735	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	start_codon	25057091	25057093	.	+	0	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25057091	25057131	1	+	0	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25057091	25057131	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25057132	25057251	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25057252	25057328	1	+	1	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25057252	25057328	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25057329	25057411	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25057412	25057476	1	+	2	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25057412	25057476	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25057477	25057564	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25057565	25057611	1	+	0	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25057565	25057611	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25057612	25057695	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25057696	25057771	1	+	1	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25057696	25057771	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25057772	25057865	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25057866	25057933	1	+	0	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25057866	25057933	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25057934	25058024	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25058025	25058094	1	+	1	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25058025	25058094	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25058095	25058193	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25058194	25058279	1	+	0	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25058194	25058279	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25058280	25058371	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25058372	25058434	1	+	1	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25058372	25058434	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25058435	25058540	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25058541	25058606	1	+	1	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25058541	25058606	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	intron	25058607	25058689	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	CDS	25058690	25058735	1	+	1	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	exon	25058690	25058735	.	+	.	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
Phchi.S1	AUGUSTUS	stop_codon	25058736	25058738	.	+	0	transcript_id "Phchi.S1G393800.t1"; gene_id "Phchi.S1G393800"
# overlap start --------------------------------------------------------------------------------
# this overlap has 1 different transcripts
# This transcript jg15393.t1 is derived from g13861.t1 from the input file /mnt/data/ps997/projects/hornwort_genomes/analysis/Phaeomegaceros_fimbriatus/reannotation/genes/braker/braker/augustus.E.gtf
# It is supported by 0 other predicted genes
# the core of this joined transcript has priority 2
Phchi.S3	AUGUSTUS	gene	18814017	18814370	.	+	.	Phchi.S3G271200
Phchi.S3	AUGUSTUS	transcript	18814017	18814370	.	+	.	transcript_id "Phchi.S3G271200.t1"; gene_id "Phchi.S3G271200"
Phchi.S3	AUGUSTUS	start_codon	18814017	18814019	.	+	0	transcript_id "Phchi.S3G271200.t1"; gene_id "Phchi.S3G271200"
Phchi.S3	AUGUSTUS	CDS	18814017	18814370	0.99	+	0	transcript_id "Phchi.S3G271200.t1"; gene_id "Phchi.S3G271200"
Phchi.S3	AUGUSTUS	exon	18814017	18814370	.	+	.	transcript_id "Phchi.S3G271200.t1"; gene_id "Phchi.S3G271200"
Phchi.S3	AUGUSTUS	stop_codon	18814371	18814373	.	+	0	transcript_id "Phchi.S3G271200.t1"; gene_id "Phchi.S3G271200"